# STOCKHOLM 1.0

#=GF AC   RF00001
#=GF ID   5S_rRNA
#=GF DE   5S ribosomal RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Mifsud W; 0000-0002-9805-6461
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Szymanski et al, 5S ribosomal database, PMID:11752286
#=GF SS   Published; PMID:11283358
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.90
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.99 -Z 549862.597050 CM SEQDB
#=GF CL   CL00113
#=GF DR   URL; http://rose.man.poznan.pl/5SData/;
#=GF DR   SO; 0000652; rRNA_5S;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   11752286
#=GF RT   5S Ribosomal RNA Database.
#=GF RA   Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J
#=GF RL   Nucleic Acids Res 2002;30:176-178.
#=GF RN   [2]
#=GF RM   11283358
#=GF RT   Crystal structure of the ribosome at 5.5 A resolution.
#=GF RA   Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH,
#=GF RA   Noller HF
#=GF RL   Science 2001;292:883-896.
#=GF RN   [3]
#=GF RM   10926492
#=GF RT   The role of the central zinc fingers of transcription factor IIIA in
#=GF RT   binding to 5 S RNA.
#=GF RA   Searles MA, Lu D, Klug A
#=GF RL   J Mol Biol 2000;301:47-60.
#=GF RN   [4]
#=GF RM   23838690
#=GF RT   Systematic analysis and evolution of 5S ribosomal DNA in metazoans.
#=GF RA   Vierna J, Wehner S, Honer zu Siederdissen C, Martinez-Lage A, Marz M
#=GF RL   Heredity (Edinb). 2013;111:410-421.
#=GF CC   5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit
#=GF CC   in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by
#=GF CC   RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S
#=GF CC   precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has
#=GF CC   been shown that fingers 4-7 of the nine-zinc finger transcription factor
#=GF CC   TFIIIA can bind to the central region of 5S RNA. Thus, in addition to
#=GF CC   positively regulating 5S rRNA transcription, TFIIIA also stabilises 5S
#=GF CC   rRNA until it is required for transcription.
#=GF WK   5S_ribosomal_RNA
#=GF SQ   712



X01556.1/3-118           --CUUGAC-GA-U-C-AU-AGA----GC-G-U-U-G---GA----------A-CC-A----------C--CUG----A-UC----CCUUCC------CGA-ACUCA-GA-AGUGAA-A-----------------CGACGCA-U-C--G---CC--GAUG----GUAGUGUG----GGGUUUC-C-CCAUG-UGA---G---AGUA----GG-U-CA-UC--G-UCAAGC
X55260.1/3-119           --UACGGC-GG-C-C-AU-AGC----GA-A-G-G-G---GA----------A-AU-A----------C--CCG----G-UC----CCAUCC------CGA-ACCCG-GA-AGUCAA-G-----------------CCCUUCA-G-C--G---CC--GAUG----GUACUGCAA---CCGAGAG-G-CUGUG-GGA---G---AGUA----GG-A-CG-CC--G-CCGGAC
M16174.1/3-119           --UACGGC-GG-C-C-AU-AGC----GG-C-G-G-G---GA----------A-AC-A----------C--CCG----G-UC----CCAUGC------CGA-ACCCG-GA-AGUUAA-G-----------------CCUGCCA-G-C--G---CC--GAUG----GUACUGCAA---CCGAGAG-G-CUGUG-GGA---G---AGUA----GG-A-CG-CC--G-CCGGAC
X55267.1/3-119           --UACGGC-GG-C-C-AU-AGC----GG-A-G-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCUCCA-G-C--G---CC--GAUG----GUACUGCAC---CCGAGAG-A-GUGUG-GGA---G---AGUA----GG-A-CG-CC--G-CCGGAC
M16172.1/3-119           --UACGGC-GG-U-C-AU-AGC----GA-A-G-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCUUCA-G-C--G---CC--GAUG----GUACUGCAC---UCGCCAG-G-GUGUG-GGA---G---AGUA----GG-A-CG-CC--G-CCGGAC
AF001265.1/6033-6149     --UACGGC-GG-U-C-AU-AGC----GA-A-G-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCUUCA-G-C--G---CC--GAUG----GUACUGCAC---UCGACGG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGAAC
X05057.1/3-119           --UACGGC-GG-U-C-AU-AGC----GA-A-G-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCUUCA-G-C--G---CC--GAUG----GUACUGCAC---UCGACAG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGGAC
X15126.1/3-120           --UACGGC-GG-C-C-AU-AGC----GG-A-G-G-G---GA----------A-ACCG----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCUCCA-G-C--G---CC--GAUG----GUACUGCAC---UCGACAG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGAAC
Z50737.1/3-119           --AACGGC-GG-U-C-AU-AGC----GG-U-G-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUCC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCACCA-G-C--G---CC--GAUG----GUACUGCAC---UCGUGAG-G-GUGUG-GGA---G---AGUA----GG-A-CG-CC--G-CCGGAC
X55261.1/3-119           --UACGGC-GG-U-U-AU-AGC----GG-U-G-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------GCCACCU-G-C--G---CC--GAUG----GUACUGCAC---UCGACAG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGGAA
Z50059.1/3-119           --UUCGGU-GG-U-U-UU-AGC----GU-C-A-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGACA-G-C--G---CC--GAUG----GUACUGCAA---CCGAAGG-G-UUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGAAC
Z50061.1/3-119           --UUCGGU-GG-U-C-AU-AGC----GU-C-A-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGACA-G-C--G---CC--GAUG----GUACUGCAA---CCGAAGG-G-UUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGGAC
Z50060.1/3-119           --UUCGGU-GG-U-U-AU-GGC----GG-U-A-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGCCA-G-C--G---CC--GAUG----GUACUGCAC---CCCCGCG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGAAC
Z50075.1/3-119           --UUCGGU-GG-U-G-AU-AGC----GG-U-A-G-G---GG----------U-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGCCA-G-C--G---CC--GAUG----GUACUGCAC---UCGUAGG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGAAC
Z50066.1/3-119           --UUCGGU-GG-U-A-AU-AGC----GG-U-G-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCACCA-G-C--G---CC--GAUG----GUACUGCAC---CCGCCGG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGAAC
Z50062.1/3-119           --UUCGGU-GG-U-U-AU-AGC----GG-U-G-G-G---GA----------C-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCACCA-G-C--G---CC--GAUG----GUACUGCAC---UCGAAGG-A-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGAAC
Z50065.1/3-120           --UUCGGU-GG-U-C-AC-AGC----GG-UAG-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCACCA-G-C--G---CC--GAUG----GUACUGCAC---CCGAAGG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGAAC
M33888.1/3-119           --UACGGC-GG-C-C-AU-AGC----GG-C-A-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGCCA-G-C--G---CC--GAUG----GUACUGCAC---UCGUGAG-G-GUGUG-GGA---G---AGUA----GG-U-CA-CC--G-CCGAAC
X05526.1/2-115           --UACGGC-GG-C-C-AU-AGC----GG-C-A-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUGC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGCCA-G-C--G---CC--GAUGA----UACUGCC----CCUCCGG-G-GU----GGA---A--AAGUA----GG-G-CA-CC--G-CCGAAC
X75601.1/91-203          --UACGGC-GG-C-C-AC-AGC----GG-C-A-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGCCA-G-C--G---CC--GAUGA----UACUGCC----CCUCCGG-G-U-----GGA---A--AAGUA----GG-A-CA-CC--G-CCGAAC
X55251.1/3-116           --UACGGC-GG-UCC-AU-AGC----GG-C-A-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUCC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGCCA-G-C--G---CC--GAUGA----UACUACCC---AUCCGGG-U-------GGA---A--AAGUA----GG-A-CA-CC--G-CCGAAC
X55259.1/3-117           --UACGGC-GG-U-CAAU-AGC----GG-C-A-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUCC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGCCA-G-C--G---CC--AAUGA----UACUGCCC--U----CAC-C-GGGUG-GAA---A---AGUA----GG-A-CA-CC--G-CCGAAC
X55254.1/3-119           --UACGGC-GG-C-C-AU-AGC----GA-C-A-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGUCU-G-C--G---CC--GAUG----GUACUGCAC---UCGACAG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGAAC
X00991.1/1-118           --GCCUAC-GA-C-C-AU-ACC----AC-C-A-U-G---AA----------U-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------NAUGGUA-G-G--G---CC--GGGUCA--GUACCUGGA--UGGGUGAC-C-GCCUG-GGA---A--CACCC----GG-U--G-UU--G-UAGGC-
K02348.1/1-119           --GCCUAC-GA-C-C-AU-ACC----AC-C-A-U-G---AG----------U-AU-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GG-AGUCAA-G-----------------CAUGGUC-G-G--G---CC--GGGUCA--GUACCUGGA--UGGGUGAC-C-GCCUG-GGA---A--CACCU----GG-U--G-UU--G-UAGGCC
K02350.1/1-119           --GUCUAC-GA-C-C-AU-ACC----AC-A-A-U-G---AA----------C-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAUUGUC-G-G--G---CC--AGGAUA--GUACCUGGA--UGGGGGAC-C-GCCUG-GGA---A--CGCCU----GG-U--G-UC--G-UAGACU
K02349.1/1-119           --GUCUAC-GG-C-C-AU-ACC----AC-G-A-U-G---AA----------U-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAUUGUC-G-G--G---CC--AGGAUA--GUACUUGGA--UGGGGGAC-C-GCCUG-GGA---A--CUCCU----GG-U--G-CC--G-UAGACU
X05233.1/1-119           --GUCUAC-GG-C-C-AU-ACC----AC-C-G-G-G---AA----------A-AU-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CCCGGUA-G-G--G---CC--AGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCU----GG-U--G-CU--G-UAGACU
X06837.1/1-119           --GUCUAC-GG-C-C-AU-ACC----AC-C-G-G-G---AA----------A-AA-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CCCGGUA-G-G--G---CC--AGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCU----GG-U--G-CU--G-UAGACU
X01534.1/1-119           --GCCUAC-GG-C-C-AU-ACC----AC-G-U-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCU-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUA-G-G--G---CC--UGCCCA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--CAGCA----GG-U--G-UU--G-UAGGCU
X01535.1/1-119           --GUCUAC-GA-C-C-AU-ACC----AC-G-U-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUA-G-G--G---CC--UGCCCA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--CAGCA----GG-U--G-UU--G-UAGACU
AJ243001.2/1-116         --GUCAAC-GG-C-C-AU-ACC----AC-G-U-U-G---AA----------A-GC-A----------C--CAC----U-UC----UCGUCC-------GA-UCAGC-GA-AGUUAA-G-----------------CAACGUU-G-G--G---UC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--CACCA----GA-U--G-CU--G-UUG---
X04305.1/1-118           --GGCUAC-GG-C-C-AU-ACC----AC-G-U-U-G---AA----------C-CU-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CAACGUC-G-G--G---CG--UGGUUA--GUACUUAGA--UGGGUGAC-C-GCUUG-GGA---A--CACCA----CG-U--G-CU--G-UAGGC-
J01888.1/1-119           --GUCUAC-GG-C-C-AU-ACC----AC-G-U-U-G---AA----------A-AU-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CAACGUC-G-G--G---CG--UGGUUA--GUACUUAGA--UGGGUGAC-C-GCUUG-GGA---A--CACCA----CG-U--G-UU--G-UAGACA
J01889.1/1-119           --GUCUAC-GG-C-C-AU-ACC----AC-G-U-U-G---AA----------A-AU-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CAACGUC-G-G--G---CG--UGGUUA--GUACUUAGA--UGGGUGAC-C-GCUUG-GGA---A--CACCA----CG-U--G-UU--G-UAGAUA
X01003.1/1-119           --GUUUAC-GA-C-C-AU-ACU----AC-G-U-U-G---AA----------U-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUC-G-G--G---CU--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-UC--G-UAGGCU
X00996.1/1-119           --GCCUAC-GG-C-C-AU-ACU----AC-G-U-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCU-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUC-G-G--G---CC--UGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-CU--G-UAGGUU
AJ132198.1/1-116         --GUCUAC-GG-C-C-AU-AUC----AC-G-U-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUC-G-A--G---CC--CGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCG----GG-U--G-CU--G-UAG---
AJ312082.1/1-119         --GUCUAC-GA-C-C-AU-AUC----AC-G-U-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUC-G-A--G---CC--CGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCG----GG-U--G-UU--G-UAGACA
X00020.1/1-119           --GUCUAC-GA-C-C-AU-AUC----AC-G-U-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUC-G-A--G---CG--UGGUUA--GUACGUGGA--UGGGUGAC-C-GCCUC-GGA---A--UACCA----CG-U--G-UU--G-UAGGCU
X03911.1/1-119           --GUCUAC-GG-C-C-AU-ACC----AC-G-U-U-G---AA----------A-GC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUC-G-G--G---CC--CGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCG----GG-U--G-CU--G-UAGACU
X00998.1/1-119           --GUCUAC-GG-C-C-AU-ACC----AC-G-U-U-G---AA----------A-AC-A----------C--CAG----U-UC----UCGUCC-------GA-UCACU-GA-AGUUAA-G-----------------CAACGUC-G-G--G---CC--CGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCG----GG-U--G-CU--G-UAGACU
M35395.1/1-119           --GUCUAC-GA-C-C-AU-ACC----AC-G-U-U-G---AA----------A-GC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUC-G-G--G---CC--AGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCU----GG-U--G-CC--G-UAGACA
X00994.1/1-119           --GCCUAC-GA-C-C-AU-ACC----AC-G-U-U-G---AA----------A-AC-A----------C--CAG----U-UC----UCGUCC-------GA-UCACU-GA-AGUUAA-G-----------------CAACGUC-G-G--G---CC--AGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCU----GG-U--G-UU--G-UAGGCU
X06836.1/1-119           --GCCUAC-GG-C-C-AU-ACC----AC-G-U-A-G---AA----------U-GC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CUGCGUC-G-G--G---CG--UGGUUA--GUACUUGCA--UGGGAGAC-C-GGCUG-GGA---A--UACCA----CG-U--G-CU--G-UAGGCU
M16074.1/307-425         --GCCAAC-GU-C-C-AU-ACC----AC-G-U-U-G---AA----------A-GC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAGCGUC-G-G--G---CG--CGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--CCCCG----CG-U--G-AC--G-UUGGCA
X13035.1/1-119           --GACAAC-GU-C-C-AU-ACC----AC-G-U-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUC-G-G--G---CG--CGGUCA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--CACCG----CG-U--G-AC--G-UUGGCU
K02354.1/1-118           --GCCAAC-GU-C-C-AU-ACC----AC-G-U-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUC-G-G--G---CG--CGGUCA--GUACUUGGA--UGGGUGAC-C-ACCUG-GGA---A--CACCG----CG-U--G-CC--G-UUGGC-
M25201.1/1-119           --GCCAAC-GU-C-C-AU-ACC----AU-G-U-U-G---AA----------U-AC-A----------C--UGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CAACAUC-G-G--G---CG--UGGUCA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--CACCA----CG-U--G-AU--G-UUGGCU
M35394.1/1-119           --GCCAAC-GU-C-C-AU-ACC----AU-G-U-U-G---AA----------U-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CAACAUC-G-G--G---CG--UGGUCA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--CACCA----CG-U--G-AU--G-UUGGCU
X13037.1/1-119           --GCCAAC-GU-C-C-AU-ACC----AU-G-U-U-G---AA----------U-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CAACAUC-G-G--G---CG--UAGUCA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--CACUA----CG-U--G-AU--G-UUGGCU
X01518.1/1-119           --GGCAAC-GA-C-C-AU-ACC----AC-G-U-U-G---AA----------U-AC-A----------C--CAG----U-UC----UCGUCC-------GA-UCACU-GA-AGUUAA-G-----------------CAACGUC-G-G--G---CG--UAGUUA--GUACUUGGA--UGGGUGAC-C-GCUUG-GGA---A--CACUA----CG-U--G-CC--G-UUGGCA
X83208.1/1-119           --GUCAAC-GG-C-C-AU-AGC----AC-G-C-U-G---UA----------A-AU-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CAGCGUU-G-C--G---CG--CGGUUA--GUACCUGGA--UGGGUGAC-C-GCUUG-GGA---A--CACCG----CG-U--G-CC--G-UUGACA
X00992.1/1-119           --GUCUAC-AG-C-C-AU-ACU----AC-G-C-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCU-------GA-UCACC-GA-AGUUAA-G-----------------CAGCAUC-A-G--G---CC--CAGUCA--GUACUUGGA--UGGGAGAC-C-UCCUG-GGA---A--UACUG----GG-U--G-CC--G-UAGACU
X00022.1/1-119           --GGCAAC-GA-C-C-AU-ACC----AU-G-C-U-G---AA----------A-AU-A----------C--CAG----U-UC----CCGUCC-------GA-UCACU-GA-AGUCAA-G-----------------CAGCAUC-G-G--G---CC--CGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--CACCG----GG-U--G-UC--G-UUGUCA
X01004.1/1-119           --GUUUAC-GA-C-C-AU-ACC----AU-G-C-U-G---AA----------U-AU-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CAGCAUA-G-G--G---CC--CGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCG----GG-U--G-UU--G-UAGGCA
AJ417699.1/1-119         --GCCUAC-GA-C-C-AU-ACC----AU-G-C-U-G---AA----------U-AU-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CAGCAUA-G-G--G---CC--CGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCG----GG-U--G-UU--G-UAGGCU
X00997.1/1-119           --GCCUAC-GG-C-C-AU-ACC----AU-G-C-U-G---AA----------U-AC-A----------C--CCG----U-UC----UCGUCC-------GA-UCACG-GA-AGUUAA-G-----------------CAGCAUC-G-G--G---CA--CGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCG----UG-U--G-CA--G-UAGGCU
X06834.1/1-119           --GUUUAC-GG-C-C-AU-AUC----AC-G-U-U-G---AA----------A-AC-G----------C--CAG----U-UC----UCGUCC-------GA-UCACU-GA-AGCUAA-G-----------------CAACGUC-G-A--G---CC--UGGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-CU--G-UAGACU
X01002.1/1-119           --GUUUAC-GA-C-C-AU-AUC----AC-G-U-U-G---AA----------U-AU-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUCAA-G-----------------CAGCGUC-G-A--G---CC--UAGUNA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACUA----GG-U--G-CC--G-UAGACU
X00993.1/1-119           --GCUUAC-GG-C-C-AU-AUC----AC-G-C-U-G---AA----------U-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACGUA-G-A--G---CC--UAGUCA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACUA----GG-U--G-CU--G-UAAGCA
X05234.1/1-119           --GCUUAC-GG-C-C-AU-AUC----AC-G-C-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCC-------GA-ACACC-GA-AGUUAA-G-----------------CAACGUA-G-A--G---CC--UGGUGA--GUACUUGGA--UGGGUGAC-C-GCUUG-GGA---A--UACCA----GG-U--G-CU--G-UAAGCA
X06835.1/1-119           --GCUUAC-GG-C-C-AU-AUG----AC-G-U-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AGUUAA-G-----------------CAACAUC-G-A--G---CC--UAGUUA--GUACUUAGA--UGGGUGAC-C-GCUUG-GGA---A--CCCUA----GG-U--G-CU--G-UAAGCA
X57691.1/1-116           ----CUAC-GA-C-U-AU-AUG----AC-G-U-U-G---AA----------U-AU-A----------C--CCG----U-UC----UCGUCU-------GA-UUACG-GA-AGUUAA-G-----------------UAACGUC-G-A--G---UG--GGGUUA--GUACUUAGA--UGGGUGAC-C-GCUUG-GGA---A--UACCU----CA-U--G-CC--G-UAGGC-
AB015590.1/1-119         --GCUUAC-GG-C-C-AU-ACC----AC-C-C-U-G---AG----------C-AC-G----------C--CCG----A-UC----UCGUCU-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGGUC-G-G--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-CU--G-UAAGCU
V00647.1/1-119           --GCUUAC-GG-C-C-AU-ACC----AC-C-C-U-G---AG----------C-AC-G----------C--CCG----A-UC----UCGUCC-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGGUC-G-G--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-U-GCCUG-GGA---A--UACCA----GG-U--G-UU--G-UAAGCU
V00648.1/1-119           --GCUUAC-GG-C-C-AC-ACC----AA-C-C-U-G---AG----------C-AA-G----------C--CCG----A-UC----UCGUCU-------GA-UCUCG-GA-AGCCAA-G-----------------CAGGGUU-G-G--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-U-GCCUG-GGA---A--UACCA----GG-U--G-UU--G-UAAGCU
D00076.1/1-119           --GCCUAC-GA-C-C-AU-AUC----AC-C-C-U-G---AA----------U-AC-G----------C--CCG----A-UC----UCGUCC-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGGUC-G-A--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-UU--G-UAGGCU
X04309.1/2-120           --GCCUAC-GA-C-C-AU-AUC----AC-C-C-U-G---AA----------U-GC-G----------C--CCG----A-UC----UCGUCC-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGGUC-G-A--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-UU--G-UAGGCU
M10817.1/1-119           --GCCUAC-GG-C-C-AU-ACC----AC-C-C-U-G---AA----------C-AC-G----------C--CCG----A-UC----UCGUCU-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGGUC-G-G--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCG----GG-U--G-CU--G-UAGGCU
X71804.1/109-227         --GUCUAC-GG-C-C-AU-ACC----AC-C-C-U-G---AA----------C-GC-G----------C--CCG----A-UC----UCGUCU-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGGUC-G-G--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCG----GG-U--G-CU--G-UAGGCU
X12624.1/61-178          --GCCUAC-GG-C-C-AU-ACC----AC-C-C-U-G---AA----------A-GC-G----------C--CCG----A-UC----UCGUCU-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGGAC-G-G--G---CU--UGGUUA--GUACCUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-UU--G-UAGGC-
X12622.1/1-118           --GCCUAC-GG-C-C-AU-ACC----AC-C-C-U-G---AA----------A-GC-G----------C--CCG----A-UC----UCGUCU-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGGAC-G-G--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCU----GG-U--G-CU--G-UAGGC-
X16851.1/1-119           --GCCUAC-GG-C-C-AU-ACC----AC-C-C-U-G---AA----------U-GC-G----------C--CCG----A-UC----UCGUCC-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGGUC-G-G--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-CU--G-UAGGCA
M10850.1/361-479         --GCCUAC-GG-C-C-AC-ACC----AC-C-C-U-G---AA----------A-GU-G----------C--CUG----A-UC----UCGUCU-------GA-UCUCA-GA-AGCGAU-A-----------------CAGGGUC-G-G--G---CC--UGGUUA--GUACCUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-UC--G-UAGGCU
J01012.1/1-119           --GCCUAC-GG-C-C-AC-ACC----AC-C-C-U-G---AA----------A-GU-G----------C--CCG----A-UC----UCGUCU-------GA-UCUCG-GA-AGCGAU-C-----------------CAGGGCC-G-G--G---CC--UGGUUA--GUACCUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCG----GG-U--G-UC--G-UAGGCU
K01537.1/51-169          --GCCUAC-GG-C-C-AU-ACC----AC-C-C-U-G---AA----------A-GU-G----------C--CCG----A-UA----UCGUCU-------GA-UCUCG-GA-AGCCAA-G-----------------CAGGGUC-G-G--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-UC--G-UAGGCU
J01009.1/607-725         --GCCUAC-GG-C-C-AC-ACC----AC-C-C-U-G---AA----------A-GU-G----------C--CCG----A-UC----UCGUCU-------GA-UCUCG-GA-AGCCAA-G-----------------CAGGGUC-G-G--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-UC--G-UAGGCU
X00190.1/1-118           --GCCUAC-GG-C-C-AU-ACC----AC-C-C-U-G---GA----------A-AC-G----------C--CCG----A-UC----UCGUCU-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGGUC-G-G--G---CU--CGGUUA--GUACUUGGA--UGGGAGAC-U-GCCUG-GGA---A--UACCG----AG-U--G-UC--G-UAGGC-
M24954.1/1-119           --GCCUAC-GG-C-C-AU-ACU----AG-U-C-U-G---AA----------A-AC-G----------C--CCG----A-UC----UCGUCU-------GA-UCUCG-GA-AGCUAA-G-----------------CAGAUUC-A-G--G---CC--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UACCA----GG-U--G-CA--G-UAGGCU
X13034.1/1-119           --GCCUAC-GG-C-C-AU-AUC----AC-G-U-U-G---AG----------U-AC-A----------C--CCG----A-UC----UCGUUC-------GA-UCUCG-GA-AGUUAA-G-----------------CAACGUC-G-A--G---UC--CGGUCA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--CACCG----GG-A--G-UU--G-UAGGCA
V00476.1/1-119           --AUCUAC-GG-C-C-AU-ACC----AC-A-U-U-G---AG----------A-GC-A----------C--CCG----A-UC----UCGUUC-------GA-UCUCG-GA-AGUUAA-G-----------------CAAUGUA-G-G--G---AU--CAGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACUG----GU-U--G-CU--G-UAGAAA
M27961.1/79-196          --GCUUAC-GG-C-C-AA-ACC----AC-G-U-U-G---AA----------A-GC-A----------C--GAC----A-UC----CCGUCC-------GA-UCUGU-CA-AGUUAA-G-----------------CAACGUU-G-G--G---CC--UGGUUA--GUACUUGGA--UCGGAGAC-G-GCUUG-GGA---A--UCCCA----GG-U--G-CU--G-UAAGC-
X16225.1/825-943         --GCUUAC-GA-C-C-AU-AUC----AC-G-U-U-G---AA----------U-GC-A----------C--GCC----A-UC----CCGUCC-------GA-UCUGG-CA-AGUUAA-G-----------------CAACGUU-G-A--G---UC--CAGUUA--GUACUUGGA--UCGGAGAC-G-GCCUG-GGA---A--UCCUG----GA-U--G-UU--G-UAAGCU
X01536.1/1-119           --GCCUGC-GG-C-C-AU-ACC----AC-G-U-U-G---AA----------U-GC-A----------C--CGG----U-UC----CCAUCU-------GA-ACACC-GA-AGUUAA-G-----------------CAACGUC-G-G--G---CC--AGCUUA--GUACCUGGA--UGGGUGAC-C-GCCUG-GGA---A--UCGCU----GG-U--G-CU--G-CAGGCU
X01550.1/1-119           --GAUAGC-GU-C-C-AU-ACC----AC-A-C-U-G---AA----------A-AC-A----------C--CGG----U-UC----UCGUCC-------GA-UCACC-GC-AGUUAA-G-----------------CAGUGUC-G-G--G---CC--CAGUUA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--UACUG----GG-U--G-UC--G-CUACCU
M34003.1/489-607         --GGAUAC-GG-C-C-AU-ACU----GC-G-C-A-G---AA----------A-GC-A----------C--CGC----U-UC----CCAUCC-------GA-ACAGC-GA-AGUUAA-G-----------------CUGCGCC-A-G--G---CG--GUGUUA--GUACUGGGG--UGGGCGAC-C-ACCCG-GGA---A--UCCAC----CG-U--G-CC--G-UAUCCU
M28984.1/1-119           --GGAUAC-GG-C-C-AU-ACU----GC-G-C-A-G---AA----------A-GC-A----------C--CGC----U-UC----CCAUCC-------GA-ACAGC-GA-AGUUAA-G-----------------CUGCGCG-A-G--G---CG--GUGUUA--GUACUGGGG--UGGGCGAC-C-ACCCG-GGA---A--UCCAC----CG-U--G-CC--G-UAUCCU
M36306.1/1-119           --GGUUAC-GG-C-C-AU-ACC----UA-G-C-A-G---AA----------A-GC-A----------C--CCC----A-UC----UCGUCC-------GA-UCUGG-GA-AGUUAA-A-----------------CUGCUAU-G-G--G---CG--UGGUUA--GUACUGCGG--UGGGGGAC-C-ACGCG-GGA---A--UACCA----CG-U--G-CU--G-UAAUCU
X02036.1/1-119           --GGAUGC-GG-C-C-AU-ACU----AA-G-G-A-G---AA----------A-GC-A----------C--CUC----A-UC----CCGUCC-------GA-UCUGA-GA-AGUUAA-G-----------------CUCCUUC-A-G--G---CG--UGGUUA--GUACUGGGG--UGGGGGAC-C-ACCUG-GGA---A--UCCCA----CG-U--G-CU--G-CAUUCU
X06833.1/1-115           ----GUAC-GA-U-C-AU-ACU----UG-G-C-C-G---UA----------A-GC-A----------C--CCG----U-UC----UCAGCC-------GA-CCACG-GA-AGUUAA-G-----------------CGGUUAU-A-G--G---CU--GUGUUA--GUACUUGGC--UGGGUGAC-C-GCCUG-GGA---A--CUCAC----AG-U--G-UC--G-UACU--
AF072692.1/240-358       --AGGUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----UG-U--G-UU--G-CACCUC
X15199.1/158-276         --AGGUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CACCUC
X06844.1/1-119           --AGGUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CACUUU
AF331021.1/183-301       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCU----CG-U--G-UU--G-CAUCCC
X65710.1/35-152          --GGGUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCU----CG-U--G-UU--G-CACCC-
X05059.1/1-119           --GGGUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CACCCC
X56490.1/1-119           --GGGUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-CCCUG-GGA---A--GUCCU----UG-U--G-UU--G-CACCCC
X06843.1/1-119           --GGUUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-CCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAACCC
AF101250.1/1-119         --GGGUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CACCCC
X06840.1/1-119           --GGGUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AG----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGCA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CACCCU
AF237335.1/140-258       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAUUCC
M18171.1/1-119           --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----UG-U--G-UU--G-CAUCCC
X55697.1/1-119           --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------C-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-CCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAUCCC
X13040.1/1-118           ---GGUUC-AA-U-C-AU-ACC----GA-C-A-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGCA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-AACCCU
M18170.1/1-119           --GGAUGC-GA-U-C-AU-ACG----AG-G-A-C-G---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----UG-U--G-UU--G-CAUCCC
X01620.1/1-118           ---GGUGC-GG-U-C-AU-ACC----AG-G-G-C-U---AC----------U-AC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GU-AGUUAA-G-----------------CGCCCUU-G-G--G---CC--GGAUCA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCC----GG-U--G-CU--G-CACCCU
X00378.1/2-120           --UGGUGC-GG-U-C-AU-ACC----AG-C-G-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGCGCUU-G-G--G---CC--AGAACA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCU----GG-U--G-CU--G-CACCCU
X00377.1/2-120           --UGGUGC-GG-U-C-AU-ACC----AG-C-G-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGCGCUU-G-G--G---CC--AGAACA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCU----GG-U--G-CC--G-CACCCC
M10435.1/2-120           --UGGUGC-GG-U-C-AU-ACC----AG-C-A-C-U---AC----------U-AG-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CC--UGAAUA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A---GUCC----GG-G-UG-CC--G-CACCCU
M10434.1/1-119           --GGGUGC-GA-U-C-AU-ACC----AG-C-G-U-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGCGCUU-G-G--G---UU--GGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----AA-U--A-UU--G-CACCCU
M10433.1/1-119           --GGGUGC-GA-U-C-AU-ACC----AG-C-G-U-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CACGCUU-G-G--G---CU--GGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCC----AG-U--G-UU--G-CACCCU
X06996.1/1-118           --GGGUGC-GA-U-C-AU-ACC----AG-C-G-U-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGCGCUU-G-G--G---CU--AGAGUA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCU----AG-U--G-UU--G-CACCC-
X06995.1/1-119           --GGGUGC-GA-U-A-AU-ACC----AC-C-G-C-U---AA----------C-GU-A----------U--CGG----A-UC----CGAUCA-------GA-ACUCC-GU-AAUUAA-G-----------------CGCGCUU-G-G--G---CU--AGAGUA--GUACUGGGA--UGGGUGAC-C-UCUCG-GGA---A--GUCCU----AG-U--G-UU--G-CACCCA
M10432.1/1-119           --GGGUGC-GA-U-C-AU-ACC----AG-C-G-U-U---AG----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CGCGCUU-G-G--G---CC--GGAGUA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCC----GG-U--A-UU--G-CACCCU
M10436.1/2-120           --UGGUGC-GG-U-C-AU-ACC----AC-C-G-U-U---AA----------U-GC-A----------C--CGG----A-UC----CCGUCG-------GA-ACUCC-GU-AGUUAA-G-----------------CGCGCUU-G-G--G---CC--GGAAUA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCC----GG-U--G-CC--G-CGCCCA
X01618.1/1-119           --GGAUGC-GG-U-C-AU-ACC----AA-G-G-C-U---AC----------U-AC-A----------C--CAG----A-UC----CCAUCA-------GA-ACUCU-GC-AGUUAA-G-----------------CGCCUUU-G-G--G---CC--GGAAUA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCC----GG-U--G-CU--G-CAUCCA
X01619.1/1-119           --GGAUGC-GG-U-C-AU-ACC----AA-G-G-C-U---AC----------U-AC-A----------C--CAG----A-UC----CCAUCA-------GA-ACUCU-GA-AGUUAA-G-----------------CGCCUUU-G-G--G---CC--GGAAUA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCC----GG-U--G-CU--G-CAUCCA
X01617.1/1-119           --GGAUGC-GG-U-C-AU-ACC----AG-G-G-C-U---AC----------U-AC-A----------C--CAG----A-UC----CCAUCA-------GA-ACUCU-GC-AGUUAA-G-----------------CGCCCUU-G-G--G---CC--GGAAUA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCC----GG-U--G-CU--G-CAUCCA
M10437.1/2-120           --UGGUAC-GG-U-C-AU-ACC----AC-G-G-C-U---AA----------U-GC-G----------C--CCG----A-UC----CCAUCC-------GA-ACUCG-GA-AGCCAA-G-----------------CGCCGUU-G-G--G---CC--GGAAUA--GUACUGGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCC----GG-U--G-CU--G-UACCUA
X52052.1/4-118           --GUU--C-CA-U-C-AU-ACC----AU-G-C-C-U---AC----------U-AC-G----------C--CGC----A-UC----CCAUCA-------GA-ACUGC-GA-AGCUAA-G-----------------CGGCAUU-G-G--G---CC--AGAAUA--GUACUGGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCU----GG-U--G-UG--G---AACC
X52049.1/2-120           --UGGUUC-GU-U-C-AU-ACC----UA-G-G-C-U---AU----------U-GC-G----------C--CGG----A-UC----CCAUCA-------GA-CCUCC-GA-AGCUAA-A-----------------GGCCUGU-G-G--G---CG--AGAAUA--GUACUGGAA--UGGGUGAC-C-UUCCG-GGA---A--GUCCU----CG-U--G-AC--G-AACCCA
X52050.1/1-119           --AGGUAC-GA-U-C-AU-ACC----CG-G-G-U-U---AC----------U-AC-G----------C--CGG----A-UC----CCAUCC-------GA-ACUCC-GC-AGCUAA-G-----------------UCCCCGU-G-G--G---CU--CGAAUA--GUACUGGCU--AGGGUGAC-C-CGCCG-GGA---A--GUCCG----AG-U--G-UC--G-UACCUU
M10358.1/2-120           --UGCUAC-GU-U-C-AU-ACC----AC-C-A-C-G---AA----------A-GC-A----------C--CCG----A-UC----CCAUCA-------GA-ACUCG-GA-AGUUAA-A-----------------CGUGGUU-G-G--G---CU--CGACUA--GUACUGGGU--UGAGGGAU-U-ACCUG-GGA---A--CCCCG----AG-U--G-AC--G-UAGUGU
M10202.1/3-117           ---GCUAC-GU-U-C-AU-ACC----AC-C-A-C-G---AA----------A-GC-A----------C--CCG----A-UC----CCAUCA-------GA-ACUCG-GA-AGUUAA-A-----------------CGUGGUU-G-G--G---CU--UGAUUA--GUACUGGGU--UGAGGGAU-C-ACCUG-GGA---A--CCCCG----AG-U--G-AC--G-UAG---
M10438.1/2-120           --UGCUAC-GG-U-C-AU-ACC----AC-C-A-C-G---AA----------A-GC-A----------C--CCG----A-UC----CCAUCA-------GA-ACUCG-GA-AGUUAG-A-----------------CGUGGUU-G-G--G---CC--AGAUUA--GUACUGGGU--UGAGGGAU-C-ACUUG-GGA---A--CCCCU----GG-U--G-CU--G-UAGUGU
X52047.1/2-120           --UGCUAC-GU-U-C-AU-ACC----AC-U-C-A-G---AA----------A-AC-G----------C--CGG----G-UC----CCAUCA-------GA-UCCCC-GA-AGCUAA-G-----------------CUGAGUU-G-G--G---CU--GGAUUA--GUACUGGAU--UCAGGAAU-G-AUCUG-GGA---A--UCCCC----AG-U--G-AC--G-UAGUGU
X52048.1/2-120           --UGCUAC-GA-U-C-AU-ACC----AC-U-U-A-G---AA----------A-GC-A----------C--CCG----G-UC----CCAUCA-------GA-CCCCG-GA-AGUUAA-G-----------------CUGAGUU-G-G--G---CU--GGACUA--GUACUGGAU--UCAGGAAU-G-AUCUG-GGA---A--UCCCC----AG-U--G-UC--G-UAGUGU
V01420.1/2-120           --UGAUAC-GG-U-C-AU-ACC----AC-C-A-G-G---AA----------A-AC-A----------G--GCG----A-UC----CCAUCU-------GA-ACUCG-CA-ACUUAA-G-----------------CCUGGUU-G-G--G---CA--GGAUUA--GUACUGGGC--UGAGUGAU-C-UCCUG-GGA---A--UCCCC----UG-U--G-CU--G-UAUCGC
X52051.1/2-120           --UGAUGC-GU-U-C-AU-ACU----AC-U-U-C-G---AA----------A-GC-A----------C--CCG----A-UC----CCAUCA-------GA-ACUCG-GA-AGUUAA-G-----------------CGGAGUU-A-G--G---CC--GGUCUA--GUACUGAGU--UGAGUGAU-C-ACUCG-GGA---A--UCACC----GG-U--G-AC--G-CAUUGC
J01851.1/1-119           --GUUGUC-GG-C-C-AU-ACU----AU-G-C-C-U---AA----------C-GC-A----------C--CAG----A-UC----CCAUCC-------GA-ACUCU-GA-AGUUAA-G-----------------CGGCAUA-A-G--G---CG--AGGUUA--GUACUUGGG--UGGGGGAC-C-GCCAG-GGA---A--GCCCU----CG-U--G-CU--G-ACAGCU
K02343.1/1-119           --GUUAUC-GG-C-C-AU-ACU----AA-G-C-C-A---AA----------A-GC-A----------C--CGG----A-UC----CCAUUC-------GA-ACUCC-GA-AGUUAA-G-----------------CGGCUUA-A-G--G---CA--UGGUUA--GUACUAAGG--UGGGGGAC-C-GCUUG-GGA---A--GCCCA----UG-U--G-CU--G-AUAGCU
J01872.1/1-119           --GUUGGU-GG-C-C-AU-ACU----AA-G-C-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUUC-------GA-ACUCC-GA-AGUUAA-G-----------------CGGCUUA-A-G--G---CG--AGGUUA--GUACUAAGG--UGGGGGAC-C-GCUUG-GGA---A--GUCCU----CG-U--G-UU--G-ACAACC
AJ419791.1/210-328       --GCUAUC-GG-C-C-AU-ACU----AA-G-C-C-A---AA----------U-GC-A----------C--CGG----A-UC----CCAUCC-------GA-ACUCC-GA-AGUUAA-G-----------------CGGUUUA-A-G--G---CC--UGUUAA--GUACUGAGG--UGGGGGAC-C-ACUCG-GGA---A--CUUCA----GG-U--G-CU--G-AUAGCU
J01893.1/5-114           ------UC-GG-C-C-AU-ACU----AA-G-G-U-G---AA----------A-AC-A----------C--CGG----A-UC----CCAUUC-------GA-ACUCC-GA-AGUUAA-G-----------------CGCCUUA-A-G--G---CU--GGGUUA--GUACUAAGG--UGGGGGAC-C-GCUUG-GGA---A--GUCCC----AG-U--G-UC--G-A-----
X00475.1/121-239         --GCUGUC-GG-C-C-AU-ACU----AA-G-G-U-G---AA----------A-AC-A----------C--CGG----A-UC----CCAUUC-------GA-ACUCC-GA-AGUUAA-G-----------------CGCCUUA-A-G--G---CU--GGGUUA--GUACUAAGG--UGGGGGAC-C-GCUUG-GGA---A--GUCCC----AG-U--G-UC--G-ACAGCC
M25115.1/1-122           --GCUGAC-GG-C-C-AU-ACC----GU-G-U-C-G---AA----------U-GC-A----------C--CGG----A-UC----UCUUCU-------GA-CCUCC-GA-AGUUAA-G-----------------CGGCACA-G-G--G---CC--CGGAUA--GUACUGGGG--UGGGGGAC-C-GCCCG-GGA---A--GUCCUU--AGG-G-UG-CU--G-UCAGCU
M19136.1/148-266         --UGACUC-GU-U-C-AU-ACU----AC-A-G-U-G---GC----------C-AC-A----------C--CAG----A-UC----CCAUCA-------GA-ACUCU-GA-AGUUAA-G-----------------CACUGUA-A-G--G---CU--UGGCUA--GUACUGAGG--UGGGAGAC-C-GCUCG-GGA---A--CACCA----GG-U--G-AU--G-AGUCAU
X01551.1/1-119           --GUCGAC-GC-U-C-AU-ACU----AG-G-U-U-G---GG----------U-CC-A----------C--CCG----A-UC----UCGUUC-------GA-UCUCG-GC-AGUUAA-A-----------------CAACCUU-A-G--G---CC--UCGUUA--GUACUUGAA--UGCGUGAG-C-GUCUG-GGA---A--UACGA----GG-U--G-GU--G-UCGACU
K03160.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-GC-A----------C--UGC----A-UC----CCGUCC-------GA-UCUGC-AA-AGUUAA-C-----------------CAGAGUA-C-C--G---CC--CAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
M58368.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-GC-A----------C--UGC----A-GC----CCGUCC-------GA-UCUGC-AA-AGUUAA-C-----------------CAGAGUA-C-C--G---CU--CAGUUA--GUACCAUGG--UGGGGGAC-C-AUGCG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
X00073.1/1-117           --AUCCAC-GG-C-C-AU-AGG----AC-A-C-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-G--AGUUAA-C-----------------CAGUGUG-C-C--G---CC--CGGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A---UCCU----GG-G-UG-CU--G-UGGUU-
X00074.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUUAA-C-----------------CAGAGUG-C-C--G---CC--UAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
M58384.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUUAA-C-----------------CAGAGUG-C-C--G---CC--UAGUUA--GUACCACGG--AGGGGGAC-C-ACGCG-GGA---A---UCUU----GG-G-UG-CU--G-UGGUU-
K02344.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUUAA-C-----------------CAGAGUG-C-C--G---CU--CAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
K03168.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCU-------GA-UCUGC-GC-AGUUAA-C-----------------CAGAGUG-C-C--G---CU--CAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
X01570.1/1-119           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUUC-------GA-UCUGC-GC-AGUUAA-C-----------------CAGAGUG-C-C--G---CC--CAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUUU
Z49275.1/645-762         --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUUAA-C-----------------CAGAGUG-C-C--G---CC--CAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
X06851.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-AC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUUAA-C-----------------CAGAGUG-C-C--G---CC--UAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUA----GG-U--G-CU--G-UGGUU-
X73890.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-AC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GA-AGUUAA-C-----------------CAGAGUG-C-C--G---CC--UAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
X73589.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-C-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GA-AGUUAA-C-----------------CGGAGUG-C-C--G---CC--CAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
M35578.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-U-C-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUUAA-C-----------------CGGAGUG-C-C--G---CC--UAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
X00574.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-C-C-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUUAA-C-----------------CAGGGUG-C-C--G---CC--UAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUA----GG-U--G-CU--G-UGGUU-
K03169.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-C-U-U-G---AA----------A-AC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUUAA-C-----------------CAGGGUG-C-C--G---CC--UAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUA----GG-U--G-CU--G-UGGUU-
X06854.1/5-111           ------AC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GA-AGUUAA-C-----------------CAGAGUG-C-C--G---CC--UAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUA----GG-U--G-C-----------
M58383.1/4-115           -----CAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUUAA-C-----------------CAGAGUG-C-C--G---CC--UAGUUA--GUACCACGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUA----GG-U--G-CU--G-UG----
K03161.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-G-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCU-------GA-UCUGC-GC-AGUUAA-A-----------------CACAGUG-C-C--G---CC--UAGUUA--GUACCAUGG--UGGGGGAC-C-ACAUG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
X06852.1/1-118           --AUCCAC-GG-C-C-AU-AGG----AC-U-C-U-G---AA----------A-AU-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GA-AGUCAA-G-----------------CCGAGUA-C-C--G---CU--CAGUUA--GUACCACGG--UGGGGGAC-C-ACGUG-GGA---A--UCCUG----GG-U--G-CU--G-UGGUU-
X00575.1/1-121           --AUCCAC-GG-C-C-AU-AGG----AC-A-C-A-G---AA----------A-AC-A----------U--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AAUCAA-G-----------------CUGUGUA-C-C--G---CC--CAGUCA--GUACCGGAG--UGGGGGAC-C-AUCCG-GGA---A--UCCUGC-CAGG-U--G-CU--G-UGGUU-
M35576.1/1-118           --AUCUUC-GG-C-C-AU-AGG----AC-A-G-A-G---AA----------A-AU-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUCAA-G-----------------CUCUGUA-C-C--G---CU--UAGUUA--GUACCAUAG--UGGGGGAC-C-AUAUG-GGA---A--UCCUG----AG-U--G-CU--G-AAGUU-
X00069.1/1-118           --AUCUGC-GG-C-C-AU-AGA----AC-C-G-U-G---AA----------A-AU-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GA-AGUCAA-G-----------------CACGGUA-U-C--G---CC--UAGUCA--GUACUGCGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----GG-U--G-CU--G-CAGUU-
X00071.1/1-118           --AUCUGC-GG-C-C-AU-AGA----AC-C-U-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GA-AGUUAA-C-----------------CAAGGUA-U-C--G---CU--CAGUUA--GUACUGCGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUG----AG-U--G-CU--G-CAGUU-
X00070.1/1-118           --AUCUGC-GG-C-C-AU-AGA----AC-C-U-U-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GA-AGUUAA-G-----------------CAAGGUA-U-C--G---CC--UAGUCA--GUACUGCGG--UGGGGGAC-C-ACGCG-GGA---A--UCCUA----GG-U--G-CU--G-CAGUU-
X00072.1/1-118           --AUCCGC-GG-C-C-AU-AGG----AU-C-A-G-G---AA----------A-GC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GA-AGUUAA-G-----------------CCUGAUA-C-C--G---CC--GAGUUA--GUACUAAGG--UAGGGGAC-U-ACUUG-GGA---A--UCCUG----GG-U--G-CU--G-CGGUU-
M58387.1/5-112           ------AC-GG-C-C-AC-AGU----CA-G-C-U-G---AA----------A-AC-U----------G--GGC----A-UC----CCGUCC-------GC-UCUGC-CAUACAUAA-G-----------------CAGUUGA-A-C--G---GC--AGAUUA--GUACCACGG--UGGGUGAC-C-ACCUG-GGA---A--UCCCU----GC-U--G-C-----------
X67494.1/1-118           --AUCCUC-GG-C-C-AU-AGA----AU-G-A-C-G---AA----------A-AC-G----------A--CGC----G-UC----CCGUCC-------GA-UCUGC-GA-AUCUAA-G-----------------CGUCGUA-U-C--G---CU--AGGUUA--GUACCAAGG--UGGGGGAC-C-ACUUG-GGA---A--UCCCU----AG-U--G-CC--G-AGGUU-
X05535.1/1-118           --AGGAAC-GG-C-C-AU-ACC----AC-G-U-C-G---AU----------C-GC-A----------C--CAC----A-UC----CCGUCC-------GC-UCUGU-GA-AGUUAA-G-----------------CGACGUC-G-G--G---CC--AGGCUA--GUACUACGG--UGGGGGAC-C-ACGUG-GGA---A--GCCCU----GG-U--G-CU--G-UUCCU-
X05534.1/1-118           --AGGAAC-GG-C-C-AU-ACC----AC-G-C-C-G---AU----------C-GC-A----------C--CAU----A-UC----CCGUCC-------GC-UCUGU-GA-AGUUAA-G-----------------CGGCGUC-G-G--G---CC--AGGCUA--GUACUACGG--UGGGGGAC-C-ACGUG-GGA---A--GCCCU----GG-U--G-CU--G-UUCCU-
D16558.1/6715-6832       --AGGAAC-GG-C-C-AU-ACC----AC-G-C-C-G---AU----------C-GC-A----------C--CAC----A-UC----CCGUCC-------GC-UCUGU-GA-AGUUAA-G-----------------CGGCGUC-G-G--G---CC--AGGCUA--GUACUACGG--UGGGGGAC-C-ACGUG-GGA---A--GCCCU----GG-U--G-CU--G-UUCCU-
X05532.1/1-118           --AGGAAC-GG-C-C-AU-ACC----AC-G-U-C-G---AU----------C-GC-A----------C--CAC----A-UC----CCGUCC-------GC-UCUGU-GA-AGUUAA-G-----------------CGGCGUC-G-G--G---CC--AGGCUA--GUACUACGG--UGGGGGAC-C-ACGUG-GGG---G--ACCCU----GG-U--G-CU--G-UUCCU-
X05533.1/1-118           --AGGAAC-GG-C-C-AU-ACC----AC-G-U-C-G---AU----------C-GC-A----------C--CAC----A-UC----CCGUCC-------GC-UCUGU-GA-AGUUAA-G-----------------CGGCGUC-G-G--G---CC--GGGCUA--GUACUACGG--UGGGGGAC-C-ACGUG-GGA---A--GCCCC----GG-U--G-CU--G-UUCCU-
D00058.1/1-118           --AGGAAC-GA-C-C-AU-ACC----AC-G-A-U-G---CC----------A-AU-A----------C--CGC----U-UC----CCGUCU-------GC-UCAGC-GA-AGUCAA-G-----------------CAUCGUC-G-G--G---CC--CGGUUA--GUACUACGG--UGGGGGAC-C-ACGUU-GGA---A---UCCC----GG-G-UG-UU--G-UUCUU-
M58385.1/5-116           ------GC-GG-C-C-AU-ACC----UC-C-A-U-G---AA----------A-AU-A----------C--UGC----U-UC----CCGUCC-------GA-UCAGC-AA-AGUCAA-G-----------------CAUGGAA-G-G--G---AU--UGGGUU-AGUACUAUCG--UGGGAGAC-C-AGAUG-GGA---A---UCCG----GG-U-UG-CU--G-CA----
M36310.1/2-120           --AGUUAC-GG-C-C-AC-AUC----AU-C-G-U-G---AA----------A-AG-A----------C--CAA----A-UC----CCGUCC-------GA-UCUUU-GC-AGUCAA-A-----------------CACGAUC-G-A--G---CU--UCGUCA--GUACUAUGG--UGAGAGAU-C-ACAUG-GGA---A--UACGA----AG-U--G-CU--G-UAAUUU
M36307.1/1-119           --AGUUAC-GA-C-C-AU-AUC----AA-C-U-U-G---AA----------A-GC-A----------C--CAC----A-CC----CCGUCA-------GA-UCUGU-GA-AGUUAA-G-----------------CAAGUUA-G-A--G---CU--UCGUUA--GUAGUUUGG--UGGGGGAC-C-ACAAG-CGA---A--UACGA----AG-U--G-CC--G-UAGCUU
M36308.1/1-119           --AGUAAC-GG-C-C-AU-AUC----AG-C-U-U-G---AA----------A-GC-A----------C--CGC----A-AC----CCGUCA-------GA-UCUGC-GA-AGUUAA-G-----------------CAAGCUA-G-A--G---CU--AGGUUA--GUACUAUGG--UGGGGGAC-C-ACAUG-GGA---A--UACUU----AG-U--G-UC--G-UUAUUU
M36309.1/1-120           --AGCUGG-GG-C-C-AU-AUG----AA-C-C-U-A---UA----------A-GU-A----------C--CGC----A-UC----CCGUCC------CGA-UCUGC-GA-AGUCAA-G-----------------CAGGUUA-C-A--G---CU--CGGUUA--GUACUAUGA--UGGGAGAC-C-ACAUG-GGA---A--UACCG----GG-U--G-UC--C-CAGCUU
M36313.1/2-120           --AGCAUC-GG-C-C-AU-ACA----UA-C-C-A-G---AA----------A-AU-A----------C--CGG----A-UC----CCGUCC-------GA-UCUCC-GA-AGUCAA-A-----------------CUGGUAA-U-G--G---CC--UAGUCA--GUACUACGG--UGGGGGAC-C-ACGUG-GGA---A--UACUA----GG-U--G-CU--G-AUGUUU
X01543.1/1-118           --AGCUAC-GG-C-C-AU-ACA----CA-C-C-A-G---AA----------A-GC-U----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GA-AGAUAA-U-----------------CUGGUGC-U-G--G---CG--CGGUCA--GUACUGUCG--UGGGAGAC-C-AGAUG-GGA---A--UACCG----CG-U--G-CU--G-UAGUU-
M36312.1/2-120           --AAUUAC-GG-C-C-AU-ACA----CA-G-G-A-G---AA----------A-GC-U----------C--CGC----A-UC----CCGUUC-------GA-UCUGC-GC-AGAUAA-C-----------------CUCCUGA-U-G--G---CA--GGGUCA--GUACUAUGG--UGGGGGAC-C-ACAUG-GGA---A--UACCC----UG-U--G-CU--G-UAAUUU
M36316.1/2-120           --UCUUAC-GG-C-C-AU-UCA----CA-C-C-A-G---AA----------A-GC-A----------C--CAA----A-UC----CCGUCC-------GA-UCUUU-GA-AGUUAA-G-----------------CUGGUGA-U-G--G---CG--UCGUCA--GUACUGUGG--UGGGGGAC-C-ACACG-GGA---A--UACGG----CG-U--G-CC--G-UAGGUC
M36315.1/3-121           --UCUUAC-GG-C-C-AU-UCA----CA-C-C-A-G---AA----------A-GC-A----------C--CAA----A-UC----CCGUCC-------GA-UCUUU-GA-AGUUAA-G-----------------CUGGUGA-U-G--G---CG--UCGUCA--GUACUGUGG--UGGGGGAC-C-ACACG-GGA---A--UACGG----CG-U--G-CC--G-UAAGUC
M36314.1/2-120           --UCCUAC-GG-C-C-AU-ACA----CA-C-C-A-G---AA----------A-GC-A----------C--CAA----A-UC----CCGUCC-------GA-UCUUU-GA-AGUUAA-G-----------------CUGGUGA-U-G--G---CG--UCGUCA--GUACUGUGG--UGGGGGAC-C-ACACG-GGA---A--UACGA----UG-U--G-CC--G-UAAGUU
X01544.1/1-118           --AGCUAC-GG-C-C-AU-ACA----UA-G-A-U-G---AA----------A-AU-A----------C--CGG----A-UC----CCGUCC-------GA-UCUCC-GA-AGUCAA-G-----------------CAUCUAA-U-G--G---CG--ACGUCA--GUACUGUGA--UGGGGGAC-C-GCACG-GGA---A--UACGU----CG-U--G-CU--G-UAGUU-
M28193.1/1-119           --AGUUAC-GG-C-C-AU-ACC----UC-A-G-A-G---AA----------U-AU-A----------C--CGU----A-UC----CCGUUC-------GA-UCUGC-GA-AGUUAA-G-----------------CUCUGAA-G-G--G---CG--UCGUCA--GUACUAUAG--UGGGUGAC-C-AUAUG-GGA---A--UACGA----CG-U--G-CU--G-UAGCUU
M36311.1/2-120           --AGCUAC-GG-C-C-AU-AUA----AU-A-C-C-G---AA----------A-GC-A----------C--CGG----A-UC----CCGUCC-------GA-UCUCC-GC-AGUUAA-A-----------------CGGUAUA-U-A--G---AU--CAGUCA--GUACUAUGG--UGGGGGAC-C-ACAUG-GGA---A--UACUG----GU-U--G-CU--G-UAGUUU
X58912.1/148-266         --AGCUAC-GG-C-C-AU-ACA----AU-G-U-U-G---AA----------A-AC-A----------C--CGG----A-UC----CCGUCC-------GA-UCUCC-GC-AGUUAAAG-----------------CAACAUC-U-G--G---AC--CAGUCA--GUACUAUGG--UGGGGGAC-C-ACAUG-GGA---A--UACUG----GU-U--G-CU--G-UAGUU-
V01120.1/2-120           --AUCUAC-GG-C-C-AU-ACA----GA-U-A-G-U---AA----------C-AC-A----------C--CGG----A-UC----CCGUCU-------GA-UCUCC-GC-AGUUAA-G-----------------UCUCUCC-U-G--G---UA--GCGUCA--GUACUAUGG--UGGGGGAC-C-ACAUG-GGA---A--UACGC----UA-U--G-UC--G-UAGGUU
X00867.1/1-119           --ACAUAC-GA-C-C-AU-ACC----UA-G-U-G-G---AA----------A-AU-A----------C--GGG----A-UC----CCGUCC-------GC-UCUCC-CAUAGUCAA-G-----------------CCGCUAA-G-G--G---GC--UGAUUA--GUAGUUGGG--UCGGUGAC-G-ACCAG-CGA---A--UACCG----GC-U--G-UU--G-UAUGU-
X00865.1/1-119           --ACAUAC-GA-C-C-AU-AGA----CG-C-U-A-G---AA----------A-AU-A----------C--GGG----A-UC----CCGUCC-------GC-UCUCC-CAUAGUCAA-G-----------------CUGGCGA-U-C--G---GC--GGAUUA--GUAGUUGGG--UCGGUGAC-G-ACCAG-CGA---A--UACCU----GC-U--G-UU--G-UAUGU-
X00866.1/1-119           --ACAUAC-GA-C-C-AU-AGG----CG-C-U-A-G---AA----------A-AU-A----------C--GGG----A-UC----CCGUCC-------GC-UCUCC-CAUAGUCAA-G-----------------CUGGCGA-C-C--G---GC--UGAUUA--GUAGUUGGG--UCGGUGAC-G-ACCAG-CGA---A--UACCG----GC-U--G-UU--G-UAUGU-
X00864.1/1-119           --ACAUAC-GA-C-C-AU-AGC----UC-U-C-A-G---AG----------A-AC-U----------C--GGG----A-UC----CCGUCU-------GC-UCUCC-UGUAGAUAA-G-----------------CUGACAA-G-C--G---GC--CGAUUA--GUAGUUGGG--UCGGUGAC-G-ACCAG-CGA---A--UACCG----GC-U--G-UU--G-UAUGU-
X00687.1/1-119           --ACAUAC-GA-C-C-AU-AGG----GU-G-U-G-G---AG----------A-AC-A----------G--GGC----U-UC----CCGUCC-------GC-UCAGC-CGUACUUAA-G-----------------CCACACG-C-C--G---GU--AGGUUA--GUAGUAUGG--UGGGUGAC-C-ACAUG-CGA---A--UCCCU----AC-U--G-UU--G-UAUGU-
X00689.1/1-119           --ACAUAC-GA-C-C-AU-AGG----GU-G-U-G-G---AG----------A-AC-A----------G--GGC----U-UC----CCGUCC-------GC-UCAGC-CGUACUUAA-G-----------------CCACACG-C-C--G---GC--UGGUUA--GUAGUAUGG--UGGGUGAC-C-ACAUG-CGA---A--UCCCA----GC-U--G-UU--G-UAUGU-
X03567.1/108-226         --ACAUAC-GA-C-C-AU-AGG----GU-G-U-G-G---AA----------A-AC-A----------G--GGC----U-UC----CCGUCC-------GC-UCAGC-CGUACUUAA-G-----------------CCACACG-C-C--G---GC--UGGUUA--GUAGUAUGG--UGGGUGAC-C-ACAUG-CGA---A--UCCCA----GC-U--G-UU--G-UAUGU-
X00691.1/1-119           --ACAUAC-GA-C-C-AC-AGG----GU-G-U-G-G---AA----------A-AC-A----------G--GGC----U-UC----CCGUCC-------GC-UCAGC-CGUACUUAA-G-----------------CCACACG-C-C--G---GG--AGGUUA--GUAGUUGGG--UGGGUGAC-C-ACCAG-CGA---A---UCCC----UU-C-UG-UU--G-UAUGU-
X00692.1/1-119           --ACAUAC-GA-C-C-AU-AGG----GU-G-U-G-G---AA----------A-AC-A----------G--GGC----U-UC----CCGUCC-------GC-UCAGC-CGUACUUAA-G-----------------CCACACG-C-C--G---GU--GAGUUA--GUAGUUGGG--UGGGUGAC-C-ACCAG-CGA---A--UCCUC----AC-U--G-UU--G-UAUGU-
X16688.1/41-159          --ACAUGC-GA-C-C-AU-AGG----GU-G-U-G-G---AA----------A-AC-A----------G--GGC----U-UC----CCGUCC-------GC-UCAGC-CGUACUUAA-G-----------------CCACACG-C-C--G---GC--UGGUUA--GUAGUUGGG--UGGGUGAC-C-ACCAG-CGA---A--UCCCA----GC-U--G-UU--G-CAUGU-
X06849.1/1-119           --AUCUGC-GG-C-C-AU-ACC----GC-G-A-U-G---AA----------C-CC-U----------C--CGC----G-UC----UCGUCC-------GA-UCCGC-GC-AGAUAA-G-----------------CAUCGCA-G-G--G---GC--CAGAGA--GUAUUGACG--UGGGUGAC-C-AGUCG-AGA---A--CACUG---UGC-U--G-CC--G-CAGGU-
X06847.1/1-119           --AUCUGC-GG-C-C-AU-ACC----GC-G-C-U-G---AA----------C-GU-U----------C--CGC----G-UC----UCGUCC-------GA-UCCGC-GC-AGACAA-G-----------------CAUCGCA-G-G--G---GC--CAGAGA--GUAUUGACG--UGGGUGAC-C-AGUCG-AGA---A--CACUG---UGC-U--G-CC--G-CAGGU-
M35571.1/1-119           --AUCUGC-GG-C-C-AU-ACC----GU-G-A-U-G---AA----------C-AU-U----------C--CGC----G-UC----CCGUCC-------GA-UCCGC-GC-AGACAA-G-----------------CAUCACA-G-G--G---GC--CAGAGA--GUAUUGACG--UGGGUGAC-C-AGUCG-AGA---A--CACUG---UGC-U--G-CC--G-CAGGU-
X06848.1/1-119           --AUCUGC-GG-C-C-AU-ACC----GC-G-A-U-G---AA----------C-AC-A----------C--CGC----G-UC----UCGUCC-------GA-UCCGC-GA-AGUUAA-G-----------------CAUCGCA-G-G--G---GC--CAGAGA--GUAUUGCCG--UGGGUGAC-C-AGGCG-AGA---A--CACUG---UGC-U--G-CC--G-CAGGU-
M35573.1/1-119           --AGGUGC-GA-C-C-AU-ACC----GU-G-U-U-G---AA----------A-AU-U----------C--UGC----A-UC----CCGUCC-------GA-UCUGC-AA-AGACAA-G-----------------CAACACA-G-G--G---CC--CAGUCA--GUAGUGCGG--UGGGUGAC-C-ACGUG-CGA---A--UACUG---UGG-U--G-UU--G-CACUU-
M35574.1/1-119           --AUGUGC-GA-C-C-AU-ACC----AA-G-C-U-G---AA----------A-AU-A----------C--UGC----A-UC----CCGUCU-------GA-UCUGC-AC-AGUCAA-G-----------------CAGCUUA-G-G--G---CC--CAGUCA--GUAGUGCGG--UGGGGGAC-C-AUGCG-CGA---A--CAUUG---UGG-U--G-UU--G-CACUU-
X00067.1/1-119           --AUCUGG-GG-C-C-AU-ACC----AC-A-G-C-C---GA----------A-UC-A----------C--CGC----A-UC----CCGUUC-------GA-UCUGC-GC-AGUUAA-A-----------------UGCUGUA-G-G--G---CC--GAGUCA--GUAGUGCGG--UGGGGGAC-C-ACGCG-CGA---A--UACUC---UGG-U--G-CC--C-CAGGU-
X00068.1/1-119           --AUCUGG-GG-C-C-AU-ACC----AC-A-G-U-U---AA----------A-UC-A----------C--CGC----A-UC----CCGUCU-------GA-UCUGC-GA-AGUUAA-G-----------------CACUGUA-G-G--G---CC--GAGUCA--GUAGUGCGG--UGGGGGAC-C-ACGCG-CGA---A--UACUC---UGG-U--G-CC--C-CAGGU-
M35572.1/1-119           --AUCUGG-GG-C-C-AU-ACC----AC-A-G-U-G---AA----------C-AC-A----------C--CGC----A-UC----CCGUCC-------GA-UCUGC-GC-AGUUAA-C-----------------CACUGUA-G-G--G---CC--GAGUCA--GUAGUGCGG--UGGGGGAC-C-ACGCG-CGA---A--UACUC---UGG-U--G-CC--C-CAGGU-
D10525.1/1-120           --GCCUAC-GG-U-C-AU-AUC----AA-U-G-C-G---AA----------U-AU-A----------C--GAU----U-UC----CCGUCU-------GA-UCAAU-CAUAGUCAA-A-----------------CGCGUUA-G-A--G---CC--ACAUUC-AGUAUUACGG--UGGGAGAC-C-ACGUG-AGA---A--CGGGU----GG-U--A-CU--G-AAGGU-
D10532.1/1-120           --AGCUGC-GG-C-C-AA-ACC----CA-G-G-U-G---AA----------U-AC-A----------A--GAC----U-UC----CCGUCC-------GA-UCAGU-CCUAUUUAA-A-----------------CACCUGA-G-G--G---CC--UUACCA-AGUAUUGUAG--UGGGAGAC-C-AUACG-AGA---A--CAGAA----GG-U--G-CU--G-CAGUU-
D10530.1/1-120           --AGCUAC-GG-C-C-AU-AUC----CA-G-A-U-G---AA----------A-AU-A----------A--GAC----U-UC----CCGUCC-------GA-UCAGU-CCUAUUCAA-G-----------------CAUCUGA-G-A--G---CC--UUACUA-AGUACUAUAG--UGGGUGAC-C-AUAUG-GGA---A--CUGAA----GG-U--G-CU--G-UAGUU-
X16634.1/937-1057        --GGUUGC-GG-C-C-AU-AUC----UA-G-C-A-G---AA----------A-GC-A----------C--CGU----U-CC----CCGUUC-------GA-UCAACCGU-AGUUAA-G-----------------CUGCUAA-G-A--G---CA--AUACCG-AGUAGUGUAG--UGGGAGAC-C-AUACG-CGA---A--ACUAU----UG-U--G-CU--G-CAAUCU
D10535.1/1-121           --GGUUGC-GG-C-C-AU-AUC----UA-G-C-A-G---AA----------A-GC-A----------C--CGU----U-UC----CCGUCC-------GA-UCAACAGU-AGUUAA-G-----------------CUGCUAA-G-A--G---CG--AGACCG-AGUAGUGUAG--UGGGAGAC-C-AUACG-CGA---A--ACUCU----CG-U--G-CU--G-CAAUCU
D10529.1/1-121           --GGUUGC-GG-C-C-AU-AUC----UA-G-C-A-G---AA----------A-GC-A----------C--CGU----U-UC----CCGUCC-------GA-UCAACUGU-AGUUAA-G-----------------CUGCUAA-G-A--G---CG--AGACCG-AGUAGUGUAG--UGGGAGAC-C-AUACG-CGA---A--ACUCU----CG-U--G-CU--G-CAAUCU
K01050.1/1-121           --GGUUGC-GG-C-C-AU-AUC----UA-G-C-A-G---AA----------A-GC-A----------C--CGU----U-CU----CCGUCC-------GA-UCAACUGU-AGUUAA-G-----------------CUGCUAA-G-A--G---CC--UGAUCG-AGUAGUGUAG--UGGGUGAC-C-AUACG-CGA---A--ACUCA----GG-U--G-CU--G-CAAUCU
M19950.1/1-120           --GGUUGC-GG-C-C-AU-AUC----UA-G-C-A-G---AA----------A-GC-A----------C--CGU----U-UC----CCGUCC-------GA-UCAACUGU-AGUUAA-G-----------------CUGCUAA-G-A--G---CC--UGACCG-AGUAGUGUAG--AGGGCGAC-C-AUACG-CGA---A--ACUCA----GG-U--G-CU--G-CAAUC-
D10533.1/1-120           --GGUUGC-GG-C-C-AU-AUC----UA-G-C-A-G---AA----------A-GC-A----------C--CGU----U-UC----CCGUCC-------GA-UCAACUGC-AGUUAA-G-----------------CUGCUAA-G-A--G---CC--UGACCG-AGUAGUGUAG--UGGGAGAC-C-AUACG-CGA---A--ACUCA----GG-U--G-CU--G-CAAUC-
D10527.1/1-120           --GGUUGC-GG-C-C-AU-AUC----UA-G-C-G-G---AA----------A-GC-A----------C--CGU----U-UC----CCGUCC-------GA-UCAACUGC-AGUUAA-G-----------------CCGCUGA-G-A--G---CC--UGACCG-AGUAGUGUAG--UGGGAGAC-C-AUACG-CGA---A--ACUCA----GG-U--G-CU--G-CAAUC-
D10534.1/1-121           --AGCUAC-GG-C-C-AU-AUC----UA-G-C-A-G---UC----------A-GC-A----------C--CGU----U-UC----CCGUCC-------GA-UCAACAGU-AGUGAA-U-----------------CUGCUAA-G-A--G---CC--UGACCG-AGUAGUGUAG--UGGGAGAC-C-AUACG-CGA---A--ACUCA----GG-U--G-CU--G-UAGUUU
D10528.1/1-121           --GGUUGC-GG-C-C-AU-ACC----UA-G-U-A-G---AA----------A-GC-A----------C--CAU----U-UC----CCGUCC-------GA-UCAAUUGC-AGUUAA-G-----------------CUACUAA-G-G--G---UC--UGAUUG-AGUAGUGUAG--UGGGAGAC-C-AUACG-CGA---A--AUUCA----GA-U--G-CU--G-CAAUCU
D10526.1/1-121           --GGUUGC-GG-C-C-AU-ACC----AA-G-U-G-G---AA----------A-AU-A----------C--UGU----U-UC----CCGUCC-------GA-UCAAC-GUUAGUCAA-G-----------------CCACUUA-G-G--G---CC--ACAGUG-AGUAAUACAG--UGGGAGAC-C-AUGUG-UGA---A--AUUGU----GG-U--G-CU--G-CAAUCU
D00063.1/1-121           --ACAUAC-GA-C-C-AU-AGU----AC-GAG-G-A---CA----------U-GC-G----------C--AGG----A-GC----CCAUCU------CGA-ACUCC-UC-AGCUAA-A-----------------UCCCGUC-A-C--G---CA--CGCUUA--GUACUCCGG--AGGGGGAC-C-ACGGU-GGA---A--UCGCG----UG-U--G-UC--G-UAUGUU
X05541.1/1-121           --ACAUGC-GG-C-C-AU-AGU----GCAG-G-A-A---CA----------U-GC-G----------C--CGA----A-AC----CCAUCC------CGA-AUUUC-GA-AGCUAA-G-----------------CUCCGCC-A-C--G---CA--CGAUUA--GUACUCUGG--AGGGGGAC-C-ACAGU-GGA---A--UCUCG----UG-U--G-CC--G-CAUGUU
X13222.1/1-121           --ACGUGC-GG-C-C-AU-AGU----GCAG-G-A-A---CA----------U-GC-G----------C--CGA----A-AC----CCAUCC------CGA-AUUUC-GA-AGCUAA-G-----------------CUCCGCC-A-C--G---CA--CGAUUA--GUACUCUGG--AGGGGGAC-C-UCAGU-GGA---A--UCUCG----UG-U--G-CC--G-CAUGUU
X68666.1/1-122           --ACGUUC-GG-U-C-AU-ACU----AG-U-GAC-A---CA----------U-GC-G----------C--CUG----A-AC----CCAUUU------CGA-AUUCA-GA-AGCUAA-G-----------------CGCCCUC-A-G--G---CU--UGGUUA--GUACUGAGG--UGAGGGAU-CCACUCG-GGA---A--CCCCA----AG-U--G-CC--G-UACGUU
K02362.1/1-121           --ACGUAC-GG-C-C-AU-AUC----CGAG-A-C-A---CG----------C-GU-A----------C--CGG----A-AC----CCAUUC------CGA-AUUCC-GA-AGUCAA-G-----------------CGUCCGC-G-A--G---UU--GGGUUA--GUAAUCUGG--UGAAAGAU-C-ACAGG-CGA---A--CCCCC----AA-U--G-CU--G-UACGUC
X01000.1/1-121           --ACGUAC-GG-C-C-AU-AUC----CGAG-A-C-A---CG----------C-GU-A----------C--CGG----A-AC----CCAUUC------CGA-AUUCC-GA-AGUCAA-G-----------------CGUCCGC-G-A--G---UU--GGGUUA--GUAGUCUGG--UGAGGGAU-C-ACAGG-CGA---A--CCCCC----AA-U--G-CU--G-UACGUC
D00062.1/1-121           --ACAUUC-GG-C-C-AU-ACC----AG-G-ACG-A---CA----------A-AU-A----------C--CCC----A-UC----CCAUCU------CGA-ACUGG-GC-AGUUAA-G-----------------UCUCCUC-G-G--G---CG--CGCUUA--GUACUGAGG--UCAGGGAU-G-ACUCG-GGA---A--UCGCG----CG-U--G-CU--G-AAUGUU
X05527.1/1-120           --ACAUUC-GG-C-C-AU-ACU----AA-GUC-G-A---CA----------U-GU-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GA-AGUCAA-G-----------------UCGCUUC-A-G--G---CC--GGGUUA--GUACUGAGG--UGAGGGAU-C-ACUCG-GGA---A--UCCCC----GG-U--G-CC--G-AAUGU-
D00061.1/1-120           --ACAUGC-GG-C-C-AU-ACU----AA-A-U-GAU---GA----------U-GU-A----------C--CGG----A-UC----CCAUCU------CGA-ACUCC-GA-AGUCAA-G-----------------GCAUUUC-A-G--G---CA--GGGCUA--GUACUGACG--AUAGAGAU-G-AGUCC-GGA---A--CCCCC----UG-U--G-CC--G-CAUGU-
X00999.1/1-121           --ACAUUC-GG-C-C-AU-AUC----AA-GUU-G-A---CA----------A-AC-G----------C--CGU----A-UC----CCAUCC------CGA-ACUAC-GA-AGCUAA-G-----------------UCACUUU-G-A--G---CU--GGGCUA--GUACUGAGA--UGAGGGAU-C-GGUCU-GGA---A--UCCCC----AG-U--G-CU--G-AAUGUU
X05528.1/1-121           --ACAUUC-GG-C-C-AU-ACU----UG-GUA-G-A---UA----------U-GC-G----------C--CUU----A-UC----CCAUCC------CGA-ACUGA-GA-AGCUAA-G-----------------UCUCCAU-A-G--G---CC--CAGGGA--GUACUGCGG--UCAGGGAU-G-ACGCU-GGA---A--AUCUG----GG-U--G-CU--G-AAUGUU
M28975.1/65-183          --GAGUAC-GA-C-C-AU-ACU----UG-A-G-U-G---AA----------A-AC-A----------C--CAU----A-UC----CCGUCC-------GA-UUUGU-GA-AGUUAA-G-----------------CACCCAC-A-G--G---CU--UAGUUA--GUACUGAGG--UCAGUGAU-G-ACUCG-GGA---A--CCCUG----AG-U--G-CC--G-UACUCC
X54477.1/2-120           --GAGUAC-GA-C-C-AU-ACU----UG-A-G-U-G---AA----------U-AC-A----------C--CAU----A-UC----CCGUCC-------GA-UUUGU-GA-AGUUAA-G-----------------CGCCCAC-A-G--G---CU--UCGUCA--GUACGGCGA--UCAGUGAU-G-GCGCU-GGA---A--CCCGG----GG-U--G-CC--G-UACUCC
M25202.1/1-119           --GUAUAC-GG-C-C-AU-ACU----AG-G-U-U-G---GA----------A-AC-A----------C--AUC----A-UC----CCGUUC-------GA-UCUGA-UA-AGUAAA-U-----------------CGACCUC-A-G--G---CC--UUCCAA--GUACUCUGG--UUGGAGAC-A-ACAGG-GGA---A--CAUAG----GG-U--G-CU--G-UAUACU
M32450.1/1-119           --GUGUAC-GG-C-U-AU-ACU----AC-C-G-G-A---AA----------A-GC-G----------C--CCG----U-UC----CCGUCC-------GA-UUACG-AG-AGCCUA-G-----------------CCCGGUC-A-G--G---CC--CGACUA--GUACUAGGG--UGGGGGAC-C-ACCUG-GGA---A--CAUCG----GG-U--G-CU--G-UACACU
X02031.1/1-118           --GAGUAC-GG-C-C-AU-ACU----AC-C-G-G-G---AA----------U-AC-A----------C--CUG----A-AC----CCGUUC-------GA-UUUCA-GA-AGUUAA-G-----------------CCGGGUU-A-G--G---CC--CAGUUA--GUACUGAG---UGGGCGAC-C-ACUUG-GGA---A--CACUG----GG-U--G-CU--G-UACGCU
X01484.1/2-120           --GCGUAC-GG-C-C-AU-ACU----AC-C-G-G-G---AA----------U-AC-A----------C--CUG----A-AC----CCGUUC-------GA-UUUCA-GA-AGUUAA-G-----------------CCUGGUC-A-G--G---CC--CAGUUA--GUACUGAGG--UGGGCGAC-C-ACUUG-GGA---A--CACUG----GG-U--G-CU--G-UACGCU
X06839.1/3-124           --CUGUAC-GG-U-C-AU-ACC----UG-G-U-U-G---GA----------A-AC-G----------G--CGG----A-UC----CCGUCC-------GA-UCUCC-GA-AGCUAA-G-----------------CAACCAU-G-G--G---CG--UGUCUA--GUACUCAGG--UGGGGGAC-C-ACUGG-GGA---A--GCGCNN-NACG-U--A-CU--G-UACAGC
M38645.1/2-120           --CGCUAC-GG-C-C-AU-ACC----AG-C-G-A-G---AA----------A-GC-U----------U--CAG----A-UC----CCAUCA-------GA-ACUCU-GC-AAAUAA-G-----------------CUCGUUU-G-G--G---CG--CCACUA--GUAACAGGG--UUAGUAAU-A-ACCUG-UGA---A--CCUGG----UG-U--G-CU--G-UAGUGC
X02706.1/2-120           --UGGAUC-GU-U-C-AA-ACC----UU-C-A-A-G---GC----------C-CC-U----------C--CCC----A-UC----CCAUCA-------GC-ACUGG-GA-AGAUAA-G-----------------CCUGAAU-G-G--G---CU--GAACUA--GUAGUACGG--UGGGGGAC-C-ACGUG-CGA---A--UCCUC----AG-U--G-AC--G-ACCUGG
X02707.1/2-120           --UGGAUU-GC-U-U-AU-ACC----UU-U-A-U-G---AA----------A-AC-U----------C--CCC----A-UC----CCAUUA-------GC-ACUGG-GA-AGAUAA-G-----------------UAUGAAU-G-G--G---CU--GAAUCA--GUAGUACGG--UGGGGGAC-C-ACGUG-CGA---A--CCCUC----AG-U--G-AC--G-ACCUGU
K02345.1/1-118           --AUGGUC-GU-U-C-AU-ACU----AG-C-A-C-U---AC----------U-GC-A----------C--CCU----A-AC----CCGUCA-------GA-UCUAG-GA-AGUUAA-G-----------------CGUGCUC-A-G--G---CG--AGGCCA--GUAGUACGG--UGGGUGAC-C-ACGUG-CGA---A--GCCCU----CG-U--G-AC--G-AUCGU-
D00059.1/1-118           --AUGAAC-GG-U-C-AU-AUC----AC-G-U-A-A---AC----------U-GC-A----------C--CCG----G-UC----UCGUCC-------GA-UCCCG-GA-AGUUAA-G-----------------CUGCGUC-G-A--G---UC--CAGCCA--GUAGUACGG--UGCGUGAG-C-ACGUG-CGA---A--GCCUG----GG-U--A-CU--G-UUCGU-
X06104.1/1-119           --ACAGCC-GU-U-C-AU-ACC----AC-A-C-G-G---AG----------A-AU-A----------C--CGG----A-UC----UCGUUC-------GA-ACUCC-GC-AGUCAA-G-----------------CCGUGUC-G-G--G---CG--UGCUCA--GUACUACCA--UAGGGGAC-U-GGGUG-GGA---A--GCGUG----CG-U--G-AC--G-GCUGUU
X06103.1/1-119           --AUGAGC-CC-U-C-AU-AUC----AU-G-U-G-G---AG----------U-GC-A----------C--CGG----A-UC----UCAUCC-------GA-ACUCC-GU-AGUUAA-G-----------------CCACAUA-G-A--G---CG--CGUCUA--GUACUGCCG--UAGGGGAC-U-AGGUG-GGA---A--GCACG----CG-U--G-GG--G-CUCAUU
AL445066.1/280290-280410 --GGCAAC-GG-U-C-AU-AGC----AG-C-A-G-G---GA----------A-AC-A----------C--CAG----A-UC----CCAUUC------CGA-ACUCG-AC-GGUUAA-G-----------------CCUGCUG-C-G--U---AU--UGCGUU--GUACUGUAU--GCCGCGAG-G-GUACG-GGA---A--GCGCA----AU-A-UG-CU--G-UUACCA
X07545.1/505-619         --A--CCC-GG-C-C-AU-AGU----GG-C-C-G-G---GC----------A-AC-A----------C--CCG----G-UC----UCGUUU------CGA-ACCCG-GA-AGUUAA-G-----------------CCGGCCACG-U--C---AG--AACG----GCCGUGAGG--UCCGAGAG-G--CCUC-GCA---G--CCGUU----CU-G-AG-CU--G-GGAU--
U05019.1/544-658         --A--CCC-GG-U-C-AU-AGU----GA-G-C-G-G---GU----------A-AC-A----------C--CCG----G-AC----UCGUUU------CGA-ACCCG-GA-AGUUAA-G-----------------CCGCUCA-C-G--U---CA--GAGGG---GCCGUGGGA--UCCGAGAG-G-GCCC--GCA---G-CCUCUC----UG-A--G-CU--G-GGAU--
M21086.1/8-123           --A--CCC-GG-C-C-AU-AGC----GG-C-C-G-G---GC----------A-AC-A----------C--CCG----G-AC----UCAUGU------CGA-ACCCG-GA-AGUUAA-G-----------------CCGGCCGCG-U--U---GG--GGGAU---GCUGUGGGG--UCCGCGAG-G-CCCC--GCA---G--CGCCC----CC-A-AG-CC--G-GGAU--
X05870.1/304-418         --A--CCC-GG-C-C-AC-AGU----GA-G-C-G-G---GC----------A-AC-A----------C--CCG----G-AC----UCAUUU------CGA-ACCCG-GA-AGUUAA-G-----------------CCGCUCACG-U--U---GG--UGGG----GCCGUGGAU--ACCGUGAG-G-AUCC--GCA---G--CCCCA----CU-A-AG-CU--G-GGAU--
X01588.1/5-119           --A--CCC-GG-U-C-AC-AGU----GA-G-C-G-G---GC----------A-AC-A----------C--CCG----G-AC----UCAUUU------CGA-ACCCG-GA-AGUUAA-G-----------------CCGCUCACG-U--U---AG--UGGG----GCCGUGGAU--ACCGUGAG-G-AUCC--GCA---G--CCCCA----CU-A-AG-CU--G-GGAU--
M16530.1/8-123           ----ACCC-GG-C-A-AU-AGG---CGC-C-G-G-U---GC----------U-AC-G----------C--CCG----G-UC----UCUUCA-------GA-ACCCG-GA-AGCUAA-G-----------------GCCGGCG-C-C--G---CGGACGGGA---GUACUGGGG--UCCGCGAG-G-CCCCG-GGA---A---ACCG---CCG-U--G-CU--G-GGA---
AF034619.1/5584-5700     -----GGC-GG-C-C-AC-AGC----GG-U-G-G-G---GU----------U-GCCU----------C--CCG----U-AC----CCAUCC------CGA-ACACG-GA-AGAUAA-G-----------------CCCACCA-G-C--GU-UCC--AGGGA---GUACUGGAG--UGCGCGAG-C-CUCUG-GGA---A---AUCC----GGUU-CG-CC--G-CCA---
L27163.1/1-119           ---GUAGC-GG-C-C-AC-AGC----GG-U-G-G-G---GU----------U-CC-U----------C--CCG----U-AC----CCAUCC------CGA-ACACG-GA-AGAUAA-G-----------------CCCACCA-G-C--GU-UCC--GGGGA---GUACUGGAG--UGCGCGAC-C-CUCUG-GGA---A---ACCG----GGUU-CG-CC--G-CUAC--
X03407.1/5927-6048       --UAAGGC-GG-C-C-AU-AGC----GG-U-G-G-G---GU----------U-AC-U----------C--CCG----U-AC----CCAUCC------CGA-ACACG-GA-AGAUAA-G-----------------CCCGCCU-G-C--GU-UCC--GGUCA---GUACUGGAG--UGCGCGAG-C-CUCUG-GGA---A---AUCC----GGUU-CG-CC--G-CCUACU
L27170.1/1-120           --AGUGGU-GG-C-C-AU-AUC----GG-C-G-G-G---GU----------U-CC-U----------C-CCCG----U-AC----CCAUCC------UGA-ACACG-GA-AGAUAA-G-----------------CCCGCCA-G-C--G---UC--CGGCAA--GUACUGGAG--UGCGCGAG-C-CUCUG-GGA---A--AUCCG----GU-U-CG-CC--G-CCAC--
L27168.1/1-120           ---UUGGC-GA-C-C-AU-AGC----GG-C-G-A-G---UG----------A-CC-U----------C--CCG----U-AC----CCAUCC------CGA-ACACG-GA-AGAUAA-G-----------------CUCGCCU-G-C--GU-UUC--GGUCA---GUACUGGAU--UGGGCGAC-C-CUCUG-GGA---A---AUCU----GAUU-CG-CC--G-CCACC-
X72495.1/5075-5190       ----AGGC-GG-C-C-AU-CGC----GG-C-G-G-G---GU----------U-CC-U----------C--CCG----U-AC----CCAUCC------CGA-ACACG-GA-AGAUAA-G-----------------CCUGCCU-G-C--GU-AUU--GGUGA---GUACUGGAG--UGGGAGAC-C-CUCUG-GGA---G---AGCC----GAUU-CG-CC--G-CC----
X14441.1/5-123           ----GGGC-GG-C-C-AG-AGC----GG-U-G-A-G---GU----------U-CC-A----------C--CCG----U-AC----CCAUCC------CGA-ACACG-GA-AGUUAA-G-----------------CUCGCCU-G-C--G--UUC--UGGUCA--GUACUGGAG--UGAGCGAU-C-CUCUG-GGA---A--AUCCA----GU-U-CG-CC--G-CCCCU-
X02128.1/24-139          -----GGC-GG-C-C-AG-AGC----GG-U-G-A-G---GU----------U-CC-A----------C--CCG----U-AC----CCAUCC------CGA-ACACG-GA-AGUUAA-G-----------------CUCACCU-G-C--G--UUC--UGGUCA--GUACUGGAG--UGAGCGAU-C-CUCUG-GGA---A--AUCCA----GU-U-CG-CC--G-CCC---
L27236.1/1-122           --GUAGGC-GG-C-C-AG-AGC----GG-U-A-G-G---GA----------A-AC-A----------C--CCG----U-AC----CCAUUC------CGA-ACACG-GA-AGUUAA-G-----------------CCUACCA-G-C--G--UAU--CGUGAA--GUACUGGAG--UGAGCGAU-C-CUCUG-GGA---A--CCGCG----GU-U-CG-CC--G-CCUGCC
L27166.1/1-122           --GUAGGC-GG-C-C-AG-AGC----GG-U-A-G-G---GA----------A-AC-A----------C--CCG----U-AC----CCAUUC------CGA-ACACG-GA-AGUUAA-G-----------------CCUACCA-G-C--GU-AUC--GUGAA---GUACUGGAG--UGAGCGAU-C-CUCAG-GGA---A---CCAC----GAGU-CG-CC--G-CCUACC
L27169.1/1-121           --GUAGGC-GG-C-C-AG-AGC----GG-U-A-G-G---GA----------A-AC-A----------C--CCG----U-AC----CCAUUC------CGA-ACACG-GA-AGUUAA-G-----------------CCUACCA-G-C--GU-AUC--GUGAA---GUACUGGAG--UGAGCGAU-C-CUCUG-GGA---A---CCAC----GAGU-CG-CC--G-CCUAC-
L27167.1/1-122           --GAAGGC-GG-C-C-AG-AGC----GG-U-G-G-G---GA----------A-AC-A----------C--CCG----U-AC----CCAUUC------CGA-ACACG-GA-AGUUAA-G-----------------CCCACCA-G-C--GU-ACC--GUGAA---GUACUGGAG--UGAGCGAU-C-CUCUG-GGA---A---CCAC----GAGU-CG-CC--G-CCUGCC
L27162.1/2-122           --GCA-GC-GG-C-C-AU-AGC----GG-U-G-G-G---GC----------G-AC-A----------C--CCG----U-AC----CCAUUC------CGA-ACACG-GA-AGUUAA-G-----------------CCCACCA-G-C--GU-ACC--GGGAA---GUACUGGAG--UGAGCGAU-C-CUCUG-GGA---A---GCGG----GGUU-CG-CC--G-CCUGCC
L27343.1/3-116           ------GC-GG-C-C-AG-GGC----GG-A-G-G-G---GA----------A-AC-A----------C--CCG----U-AC----CCAUUC------CGA-ACACG-GA-AGUGAA-G-----------------CCCUCCA-G-C--GA-ACC--AGCUA---GUACUAGAG--UGGGAGAC-C-CUCUG-GGA---G---CGCU----GGUU-CG-CC--G-CC----
X72588.1/6990-7093       ------GC-GG-C-C-AC-AGC----GG-C-G-G-G---GC----------G-AC-U----------C--CCG----U-AC----CCAUCC------CGA-ACACG-GC-AGAUAA-G-----------------CCCGCCA-G-C--G---UUCCAGCGA---GUACUGGAG--UGUGCGAA-C-CUCUG-GGA---A---AACU----------G-------------
X62865.1/3-123           ---UUGGC-GG-U-C-AU-GAC----GG-C-A-G-G---GU----------A-AC-U----------C--CUG----U-AC----CCAUUC------CGA-ACACA-GC-AGAUAA-G-----------------CCUGCCC-G-U--GU-UCC--UUACU---GUACUGAAG--UGUGCGAG-C-CUUCG-GGA---A---CUCU----GGAU-CG-CU--G-CCAACU
M36188.1/5-125           --UUUGGC--G-C-C-AU-AGC----GG-C-A-G-U---GU----------A-AC-U----------C--CUG----U-AC----CCAUCC------CGA-ACACA-GU-AGAUAA-G-----------------CCUGCCC-G-C--GU-UCC--UUACU---GUACUGAAG--UGUGCGAG-C-CUUCG-GGA---A---CUCU----GGAU-CG-CU--G-CCAUAC
X62864.1/3-123           --UCUGGC-AG-C-C-AU-AGC----GG-C-A-G-G---UG----------U-AA-U----------C--CUG----U-AC----CCAUCC------CGA-ACACA-GU-AGAUAA-G-----------------CCUGCCC-G-C--GUUCCU--UGCCU---GUACUGAAG--UGUGCGAG-C--UUCG-GGA---A---CUCU----GGAU-CG--U--G-CCAUAU
X62860.1/3-123           ---UUGGC-GG-C-C-AU-GGC----GG-C-G-G-G---GU----------A-AC-U----------C--CUG----U-AC----CCAUCC------CGA-ACACA-GC-AGAUAA-A-----------------CCCGCCC-G-C--G--UUC--CGUACG--GUACUAAAG--UGCGCGAG-C-CUUUG-GGA---A--CUGCG----GA-U-AG-CU--G-CCAGCU
X62862.1/2-123           --GGUGGC-GG-C-C-AU-AGC----GG-C-G-G-G---GC----------A-AU-U----------C--CUG----U-AC----CCAUCC------CGA-ACACA-GA-AGAUAA-G-----------------CCCGCCU-G-C-GU---UC--UAUACU--GUACUAAAG--UAUGAGAG-U-CUUUG-GGA---A--AUAUG----GA-A-CG-CU--G-CCACCA
M34910.1/5-126           --UUUGGC-GG-C-C-AU-AGC----GG-C-G-G-G---GC----------A-AU-U----------C--CUG----U-AC----CCAUCC------CGA-ACACA-GA-AGAUAA-G-----------------CCCGCCU-G-C-GU---UC--UAUACU--GUACUAAAG--UAUGAGAG-U-CUUUG-GGA---A--AUAUG----GA-A-CG-CU--G-CCAUCU
X62861.1/3-124           ---UUAGC-GG-C-C-AU-GGC----GG-C-A-G-G---GU---------UA-AC-U----------C--CUG----U-AC----CCAUCC------CGA-ACACA-GA-AGAUAA-G-----------------CCUGCCA-G-C--GU-UGU--AUACG---GUACUAAAG--UGCGAGAG-C-CUUUG-GGA---A---CUAU----ACUC-CG-CU--G-CUGAUC
X62863.1/2-121           --GCUAGU-GG-C-C-AU-AGU----GG-C-A-G-G---GA----------C-CC-U----------C--CUG----U-UC----ACCUUC------CGA-ACACA-GA-AGAUAA-G-----------------CCUGCCC-A-C--GU-UGC--UUACU---GUACUGAGG--UAC-AGAG-U-CCUCG-GGA---A---AUCU----GCGU-CG-CU--G-CUAGC-
D90253.1/251-366         --GCUGGC-GC-C-A-AU-AGA----GA-G-G-G-U---GA----------U-AC-A----------C--CUG----U-UC----CCAUCC------CGA-ACACA-GA-AGUUAA-G-----------------CCCCUCA-U-C--G---CC--GAUG----GUACUGCAG---AGUUCGC-U-CUGUG-GGA---G---AGCA----GG-A-CG-GU--G-CCA-CA
X62859.1/3-124           --GUUGGC-GG-C-C-AU-AGC----GG-A-G-G-G---GC----------C-AU-A----------C--CUG----G-UC----UCGUUU------CGA-UCCCA-GA-AGUGAA-G-----------------UCCUCCU-G-C--G---UU--UUGUUGUUGUACUGUGG---ACGAGAG-U-CUAUG-GGA---A-GCUCAU----AA-C--G-CU--G-CCGGCC
X62858.1/1-121           --GUUGGC-GG-U-C-AU-GGC----GU-G-G-G-G---UU----------A-AU-A----------C--CUG----A-UC----UCGUUU------CGA-UCUCA-GU-AGUUAA-G-----------------UCCUGCU-G-C--GU-UGU--GGGUGU--GUACUGCGG--UUUUUUG----CUGUG-GGA---A---GCCC----ACUU-CA-CU--G-CCAGCA
X62857.1/1-121           --GUUGGC-GG-U-C-AU-GGC----GU-G-G-G-G---UU----------U-AU-A----------C--CUG----A-UC----UCGUUU------CGA-UCUCA-GU-AGUUAA-G-----------------UCCUGCU-G-C--GU-UGU--GGGUGU--GUACUGCGG--UUUUUUG----CUGUG-GGA---A---GCCC----ACUU-CA-CU--G-CCAGAC
M36187.1/5-126           --UUUGGC-GG-U-C-AU-GGC----GU-G-G-G-G---GU---------UU-AU-A----------C--CUG----A-UC----UCGUUU------CGA-UCUCA-GU-AGUUAA-G-----------------UCCUGCU-G-C--GU-UGU--GGGUGU--GUACUGCGG--UUUUUUG----CUGUG-GGA---A---GCCC----ACUU-CA-CU--G-CCAGAC
M36186.1/5-125           --CAUGGC-GG-U-C-AU-GGC----GC-A-G-G-G---GU----------U-AU-A----------C--CUG----A-UC----UCGUUU------CGA-UCUCA-GU-AGUUAA-G-----------------UCCUGCU-G-C--GU-UGU--GGGUGU--GUACUGCGG--UUUUUUG----CUGUG-GGA---A---GCCC----ACUU-CA-CU--G-CCAGCC
X15364.1/6601-6721       --UUUGGC-GG-U-C-AU-GGC----GU-G-G-G-G---GU----------U-AU-A----------C--CUG----A-UC----UCGUUU------CGA-UCUCA-GU-AGUUAA-G-----------------UCCUGCU-G-C--GU-UGU--GGGUGU--GUACUGCGG--U--GUUUU-G-CUGUG-GGA---A---GCCC----AUUU-CA-CU--G-CCAGCC
M26976.1/105-223         --UACGGC-GA-C-C-AU-AGC----GG-G-G-G-G---GC----------C-AC-A----------C--CUG----A-AC----CCGUUC------CGA-UCUCA-GA-AGUUAA-G-----------------CCCCCCU-G-C-GU---UG--GAGGUG--GUACUGCA----ACGUUAG-U-UGCGG-GAA---G---CCUC----CA-A-CG-UC--G-CCGGCC
X15329.1/3-123           --UACGGC-GG-U-C-AU-AGC----GG-G-G-G-G---GC----------C-AC-A----------C--CCG----G-UC----UCAUUU------CGA-ACCCG-GA-AGUUAA-G-----------------CCCCCCA-G-CGAU---CC--CGGCU---GUACUGCCC--UCCGAGAG-G-GGGCG-GGA---A---CCGG----GG-A-CG-CC--G-CCGGCC
X07692.1/700-821         --UACGGC-GG-U-C-AU-AGC----GG-C-G-G-G---GU----------C-AC-A----------C--CCG----G-UC----UCGUUU------CGA-CCCCG-GA-AGUUAA-G-----------------CCCGCCA-G-C--GA-UCC--CGGUU---GUACUGCCC--UCCGGGAG-G-GGGCG-GGA---A---GCCG----GGGA-CG-CC--G-CCGGCC
M34911.1/4-118           --UAUAAC-GG-U-C-AU-AGC----GG-A-G-G-A---GC----------C-AC-A----------U--CCG----A-UC----CCGUCC------CGA-UCUCG-GA-AAUUAA-G-----------------CCCUCCA-G-C--G---AU--ACCCUA-AGUACUGCCA--U---UUG------GUG-GGA---A--CAGGG----UG-A-CG-CU--G-UUGAUC
X02729.1/3021-3135       --CAUAAC-GG-U-C-AA-AGC----GG-A-G-G-U---GU----------A-AC-A----------U--CCG----A-UC----CCAUCC------CGA-UCUCG-GA-AAUUAA-G-----------------CCCUCCA-G-C--G---AU--UCUUUA-AGUACUGCUA--U---CUA------GUG-GGA---A-CAAAGU----GA-C--G-CC--G-UUAGUC
X00916.1/1218-1332       --UACGGC-GG-U-C-AU-AGC----GG-G-G-G-U---GU----------A-AC-A----------U--CCG----A-UC----CCAUCC------CGA-UCUCG-GA-AAUUAA-G-----------------CCCUCCA-G-C--G---AU--UCCUUA-AGUACUGCUA--U---CUA------GUG-GGA---A-CAAGGU----GA-C--G-CU--G-CCGAUC
AB035926.1/5989-6104     --CCUGGC-GG-C-C-UU-AGC----GC-G-G-U-G---GU----------C-CC-A----------C--CUG----A-CC----CCAUGC------CGA-ACUCA-GA-AGUGAA-A-----------------CGCCGUA-G-C--G---CC--GAUG----GUAGUGUG----GGGUCUC-C-CCAUG-CGA---G---AGUA----GG-G-AA-CU--G-CCAGGC
AF170176.1/1092-1207     --CCUGGC-GG-C-A-CU-AGC----GC-G-G-U-G---GU----------C-CC-A----------C--CUG----A-CC----CCAUGC------CGA-ACUCA-GA-AGUGAA-A-----------------CGCCGUA-G-C--G---CC--GAUG----GUAGUGUG----GGGUCUC-C-CCAUG-CGA---G---AGUA----GG-G-AA-CU--G-CCAGGC
X00501.1/7-121           ---CUGGC-GG-C-C-GU-AGC----GC-G-G-U-G---GU----------C-CC-A----------C--CUG----A-CC----CCAUGC------CGA-ACUCA-GA-AGUGAA-A-----------------CGCCGUA-G-C--G---CC--GAUG----GUAGUGUG----GGGUCUC-C-CCAUG-CGA---G---AGUA----GG-G-AA-CU--G-CCAGAC
X02264.1/3-118           --CCUGGC-GG-C-C-AU-AGU----GC-G-G-U-G---GU----------C-CC-A----------C--CUG----A-CC----CCAUGC------CGA-ACUCA-GA-AGUGAA-A-----------------CGCUGUA-G-C--G---CC--GAUG----GUAGUGUG----GGGUCUC-C-CCAUG-UGA---G---AGUA----GG-G-AA-CU--G-CCAGGC
X02039.1/3-118           --UCUGGC-GG-C-C-AU-AGC----GC-A-G-U-G---GU----------C-CC-A----------C--CUG----A-UC----CCAUGC------CGA-ACUCA-GA-AGUGAA-A-----------------CGUUGUA-G-C--G---CC--GAUGA----UGGUGUG----GGGUCUC-C-CCAUG-UGA---G---AGUA----GG-G-AA-CU--G-CCAGGC
X05519.1/1-116           --UCUGGC-GG-C-G-AU-AGU----GC-G-G-U-G---GA----------C-CC-A----------C--CUG----A-GA----CCAUAC------CGA-ACUCA-GA-AGUGAA-A-----------------CGCUGUA-A-U--G---CC--GAUG----GUAGUGUG----GGGUUUC-C-CCAUG-UGA---G---AGUA----GG-G-CA-CC--G-CCAGGU
X00931.1/3-117           --CCUGGC-GG-C-C-AU-AGC----GC-C-G-U-G---GA----------A-CC-A----------C--CUG----A-UC----CCAUGC------CGA-ACUCA-GA-AGUGAA-A-----------------CGCGGUA-G-C--G---CC--GAUG----GUAGUGUG----GCAUUUG-C--CAUG-CGA---G---AGUA----GG-A-CA-CU--G-CCAGGC
X02259.1/3-117           --CCUGGC-GG-C-C-AU-AGC----GC-C-G-U-G---GA----------A-CC-A----------C--CUG----A-UC----CCAUGC------CGA-ACUCA-GA-AGUGAA-A-----------------CGCGGUA-G-C--G---CC--GAUG----GUAGUGUG----GCAUUUG-C--CAUG-UGA---G---AGUA----GG-A-CA-CU--G-CCAGGC
X02258.1/3-117           --CCUGGC-GG-C-C-AU-AGC----GC-C-G-U-G---GA----------A-CC-A----------C--CUG----A-UU----CCAUGC------CGA-ACUCA-GA-AGUGAA-A-----------------CGCGGUA-G-C--G---CC--GAUG----GUAGUGUG----GCAUUUG-C--CAUG-UGA---G---AGUA----GG-A-CA-CU--G-CCAGGC
X15180.1/3-118           --UCUGGA-AA-C-C-AU-AGC----AU-U-G-U-G---GC----------A-CC-A----------C--CUG----A-UC----CCAUCC------CGA-ACUCA-GA-AGUGAA-A-----------------CGCAAUU-G-C--G---CC--GAUG----GUAGUGUG----GGGUCUC-C-CCAUG-UGA---G---AGUA----GG-U-CA-UU--U-CCAGGC
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X52297.1/1-116           ---CCGGU-GG-C-A-AU-GUC----GG-A-G-G-G---GU----------C-CC-A----------C--CCG----U-UC----CCAUCC------CGA-ACACG-GA-AGUUAA-G-----------------CCCUCCA-G-A--G---CC--GAUG----GUACUCCGC---GGGAAAC-C-GCGCG-GGA---G---AGUA----GG-U-CG-CU--G-CCGGAU
M35310.1/1-117           --UCCGGU-GG-C-A-AU-GUC----GG-A-G-G-G---GU----------C-CC-A----------C--CCG----U-UC----CCAUCC------CGA-ACACG-GA-AGUUAA-G-----------------CCCUCCA-G-A--G---CC--GAUG----GUACUCCGC---GGGGAAC-C-GCGCG-GGA---G---AGUA----GG-U-CG-CU--G-CCGGAU
X52301.1/1-117           --UCGGGU-GG-C-A-AU-GUC----GG-A-G-G-G---GU----------C-AC-A----------C--CCG----U-UC----CCAUCC------CGA-ACACG-GA-AGUUAA-G-----------------CCCUCCA-G-A--G---CC--GAUG----GUACUCCGC---GGGAAAC-C-GCGUG-GGA---G---AGUA----GG-U-CG-CU--G-CCGGAU
M32519.1/4-118           --CCUGGC-GU-C-C-AU-GGA----GG-A-G-G-G---GG----------C-AC-A----------C--CUG----A-UC----CCAUUC------CGA-ACUCG-GA-AGUUAA-G-----------------CCCUCCA-U-C--G---CC--GAUGA----UACUGCGG--GGU---AG-C-UCGUG-GGA---A---AGUA----GG-C-CG-AC--G-CCAGGA
X52302.1/2-117           --GCUGGU-GG-C-U-AU-GGC----GG-A-A-G-G---GC----------C-AC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GU-CGUUAA-G-----------------ACUUCCA-G-C--G---CC--GAUG----GUACUGCAG---GGGCGAC-C-CUGUG-GGA---G---AGUA----GG-A-CG-CC--G-CCAGC-
M35570.1/5-120           --GUUGGU-GA-U-U-AC-AGA----GA-A-A-A-G---GU----------C-AC-A----------C--UCA----G-CU----CCAUUU------CGA-ACCUG-AA-AGUUAA-G-----------------CUUUUCU-U-C--G---UC--GAUAA----UACUGCC----CCCUACG-G-GGGUG-GGA---C---GGUA----GA-U-CG-UU--G-CCAACC
M76573.1/4-118           --CCUGGU-GG-C-U-AU-GGC----GG-G-A-G-A---GA----------U-CC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------ACCCCCA-G-C--G---CC--UAUGA----UACUGCG----GCUUAAG-C--CGUG-GGA---A---AGUC----GG-U-CG-CC--G-CCAGGU
M76569.1/4-118           --CCUGGU-GG-C-C-AU-GGC----GG-G-A-G-A---GA----------U-CC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------ACCCCCA-G-C--G---CC--UAUGA----UACGUUG----GCUUAAG-C--CACG-GGA---A---AGUC----GG-U-CG-CC--G-CCAGGU
M76572.1/4-118           --CCUGGU-GG-C-A-AU-GGC----GG-G-G-A-A---UA----------U-CC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------UGCCCCA-G-C--G---CC--CAUGA----UACUGUG----CCUUAAG-G--CACG-GGA---A---AGUC----GG-U-CG-CC--G-CCAGGU
M11545.1/4-118           --CCUGGU-GG-C-C-AU-UGC----GG-G-G-A-G---CC----------U-GC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------AUCCCCA-G-C--G---CC--CAUG----GUACUGUG----CCUCAAG-G--CACG-GGA---G---AGUA----GG-U-CG-CC--G-CCAGGU
M11546.1/4-118           --CCUGGU-GG-C-C-AU-UGC----GG-G-G-G-G---CC----------C-GC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------ACCCCCA-G-C--G---CC--CAUG----GUACUGUG----CCUCAAG-G--CACG-GGA---G---AGUA----GG-U-CG-CC--G-CCAGGU
M76577.1/4-118           --CCUGGU-GG-C-C-AU-UGC----GA-G-G-G-C---CC----------U-AC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------UCCCUCA-G-C--G---CC--UAUGA----UACCGUA----CCUUAAG-G-UGC---GGA---A--AAGUC----GG-U-CG-CC--G-CCAGGU
M76579.1/4-118           --CCUGGU-GG-C-C-AU-UGC----GA-G-G-G-C---CC----------U-AC-A----------C--CCG----A-UC----CCUUCC------CGA-ACUCG-GC-CGUGAA-A-----------------UCCCUCA-G-C--G---CC--UAUGA----UACUGCA----CCUCAAG-G-UGC---GGA---A--AAGUC----GG-U-CG-CC--G-CCAGGU
M76571.1/4-117           --UCUGGU-GG-C-C-AU-GGC----GG-G-A-G-C---AA----------A-UC-A----------G--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUCAA-A-----------------UGCCCCA-G-C--G---CC--CAUGA----UACUCUG----CCUCAAG-G-CAC---GGA---A--AAGUC----GG-U-CG-CC--G-CCAGA-
M76576.1/4-118           --UCUGAU-GA-C-C-AU-GGC----GG-G-A-G-C---AA----------A-UC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUCAA-A-----------------UGCCCCA-G-C--G---CC--CAUGA----UACUCUG----CCUCAAG-G-CAC---GGA---A--AAGUC----GG-U-CG-CC--G-CCAGAU
M76580.1/4-118           --UCUGAU-GG-C-C-AU-GGC----GG-G-A-G-C---AA----------A-UC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUCAA-A-----------------UGCCCCA-G-C--G---CC--CAUGA----UACUCUG----CCUCAAG-G-CAC---GGA---A--AAGUC----GG-U-CG-CC--G-CCAGAU
M76574.1/4-118           --UCUGGU-GG-C-C-AU-GGC----GG-C-A-G-C---AA----------A-UC-A----------C--CCG----A-UC----CCAUGC------CGA-ACUCG-GC-CGUCAA-A-----------------UGCCCCA-G-C--G---CC--CAUGA----UACUCUG----CCUCAAG-G-CAC---GGA---A--AAGUC----GG-U-CG-CC--G-CCAGAU
M76575.1/4-118           --UCUGGU-GG-U-C-AU-AGC----GG-G-A-G-U---AA----------A-UC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUCAA-A-----------------UGCCUCA-G-C--G---CC--CAUGA----UACUCUG----CCUCAAG-G-CAC---GGA---A--AAGUC----GG-U-CG-CC--G-CCAGAC
X06577.1/4-117           --CCUGGU-GG-C-C-CA-AGU----GA-G-G-G-G---GC----------U-GC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------ACCCUCA-G-C--G---CC--GAUG----GUACUGCG----UCUUAAG-G-CGC---GGA---A--GAGUA----GG-U-CG-CC--G-CCAGG-
M34775.1/1-115           --CCUGGU-GG-C-C-AU-UGC----GA-G-G-A-G---CC----------C-CA-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUUAA-A-----------------CUCCUCA-G-C--G---CC--GAUG----GUACUAUG---UCU--CAA-G-ACCUG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGGC
M34773.1/1-114           ---CUGGU-GG-C-C-AU-UGC----GA-G-G-A-G---CC----------C-CA-A----------U--UCG----A-UC----UCACUC------CGA-ACUCG-GC-CGUUAA-A-----------------CUCCUCA-G-C--G---CC--GAUG----GUACUAUG---UCU--CAA-G-ACCUG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGGC
M34772.1/1-114           ---CUGGU-GG-C-C-AU-UGC----GA-G-G-A-G---CC----------U-GA-A----------C--CCG----A-CU----CCACUC------CGA-ACUCG-GC-CGUUAA-A-----------------CUCCUCA-G-C--G---CC--GAUG----GUACUAUG---UCU--CAA-G-ACCUG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGGU
M11544.1/4-118           --CCUGGU-GG-C-C-AU-UGC----GA-G-G-A-G---CC----------U-GA-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUUAA-A-----------------CUCCUCA-G-C--G---CC--GAUG----GUACUAUG---UCU--UAA-G-ACCUG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGGC
Z35330.1/6121-6235       --CCUGGU-GG-U-U-UU-AGC----GA-A-G-A-G---CC----------U-CA-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUUAA-A-----------------CUCUUCA-G-C--G---CC--AAUG----GUACUAUG----GCUUAAG-C--CCUG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGGC
X06575.1/4-117           --CCUGGU-GG-U-U-CU-AGC----GA-G-G-A-G---CU----------U-GA-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUUAA-A-----------------CUCCUCA-G-C--G---CC--AAUG----GUACCAUG----GCUUAAG-C--CCUG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGG-
M34776.1/2-116           --CCUGGU-GG-C-U-AU-GGC----GA-G-G-A-G---GC----------C-UA-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUUAA-A-----------------CUCCUCA-G-U--G---CC--GAUG----GUACUAUG---UCU--UAA-G-ACCUG-GGA---G---AGUA----GG-U-CG-UC--G-CCAGGC
M34774.1/2-116           --CCUGGU-GG-C-U-AU-GGC----GA-G-G-A-G---UC----------C-GA-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUUAA-A-----------------CUCCUCA-G-C--G---CC--AAUG----GUACUUCG---UCU--CAA-G-ACGCG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGGC
X03903.1/4-117           --CCUGGU-GG-U-U-CU-AGC----GA-G-G-A-G---CC----------U-GA-A----------C--CCG----U-UC----CCAUCC------CGA-ACACG-GC-CGUUAA-A-----------------CUCCUCA-G-C--G---CC--AAUG----GUACUCCG---UCU--CAA-G-ACGCG-GGA---G---AGUA----GG-U--G-CC--G-CCAGGC
S39188.1/3-117           --CCUGGU-GG-C-U-UU-AGC----GA-A-G-C-G---AU----------C-AG-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUCAA-A-----------------CGCUCCA-G-C--G---CC--AAUG----GUACUAUG---UCU--CAA-G-ACCUG-GGA---G---AGUA----GG-U-CG-UC--G-CCAGGC
AF454951.1/1084-1198     --CCUGGU-GG-U-U-AU-GGC----GG-A-G-C-G---GC----------U-GC-A----------C--CCG----A-UC----CCAUUC------CGA-ACUCG-GC-CGUGAA-A-----------------CGCUCCA-G-C--G---CC--AAUG----GUACUUCG---UCU--CAA-G-ACGCG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGGU
L12402.1/3-117           --CCUGGU-GG-U-U-AU-GGC----GG-A-G-C-G---GC----------U-GC-A----------C--CCG----A-UC----CCAUUC------CGA-ACUCG-GC-CGUGAA-A-----------------CGCUCCA-G-C--G---CC--AAUG----GUACUUCG----UCUCAAG-A-GGA---GGC---A--GAGUA----GG-U-CG-AU--G-CCAGGU
X16192.1/3-117           --CCUGGU-GG-U-U-AU-GGC----GG-A-G-C-G---GC----------U-GC-A----------C--CCG----A-UC----CCAUUC------CGA-ACUCG-GC-CGUGAA-A-----------------CGCUCCA-G-C--G---CU--GAUG----GUACUUCG---UCU--CAA-G-ACGCG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGGU
X02627.1/4-118           --CCUGGU-GG-U-C-AU-CGC----GG-G-G-C-G---GC----------U-GC-A----------C--CCG----U-UC----CCUUUC------CGA-ACACG-GC-CGUGAA-A-----------------CGCCCCA-G-C--G---CC--AAUG----GUACUUCG---UCU--CAA-G-ACGCG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGGU
U28505.1/6807-6921       --CCUGGU-GG-U-C-AU-GGC----GG-G-G-C-G---GC----------C-GC-A----------C--CCG----U-UC----CCAUUC------CGA-ACACG-GC-CGUGAA-A-----------------CGCCCCU-G-C--G---CC--AAUG----GUACUUCG---UCU--UAA-G-ACGCG-GGA---G---AGUA----GG-U-CG-CU--G-CCAGGU
M34769.1/10-105          ----------A-U-U-AU-GGC----GG-G-G-U-G---GC----------U-GC-A----------C--CCG----A-UC----CCAUUC------CGA-ACUCG-GC-CGUGAA-A-----------------CGCCCCU-G-C--G---CC--GAUG----GUACUUCG---UCU--UAA-G-ACGCG-GGA---G---AGUA----GG------------------
M34768.1/3-117           --CCUGGU-GA-U-U-AU-GGC----GG-G-U-G-G---UC----------U-GC-A----------C--CCG----A-UC----UCAUUC------CGA-ACUCG-GC-CGUGAA-A-----------------CCGCCCA-G-C--G---CC--AAUG----GUACUUCG---UCU--UAA-G-ACGCG-GGA---G---AGUA----GG-U-CG-UC--G-CCAGGU
L08503.1/3-117           --CUUGGU-GG-U-U-AU-GGC----GG-A-A-C-G---CC----------U-GC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------CGUUCCA-G-C--G---CU--GAUG----GUACUUUG---UCU--UAA-G-GCACG-GGA---G---AGUA----AG-U-CG-CU--G-CCAGGU
L24488.1/3-117           --CUUGGU-GG-U-U-AU-GGC----GG-A-G-U-G---AA----------U-GC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------CGCUCCA-G-C--G---CU--GAUG----GUACUUCG----CCUCAAG-G--CACG-GGA---G---AGUA----AG-U-CG-CU--G-CCAGGU
L12403.1/3-117           --CUUGGU-GG-U-U-AU-GGC----GG-A-G-U-G---AA----------C-GC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------CGCUCCA-G-C--G---CU--GAUG----GUACUUUG----CCUCAAG-G-CAC---GGC---A--GAGUA----AG-U-CG-UU--G-CCAGGU
L12404.1/3-117           --CUUGGU-GG-U-U-AU-GGC----GG-A-G-C-G---AA----------C-GC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------CGUUCCA-G-C--G---CU--GAUG----GUACUUUG----CCUCAAG-G-CAC---GGC---A--GAGUA----AG-U-CG-UU--G-CCAGGU
M34771.1/2-116           --CCUGGC-GG-C-C-UG-AGC----GG-U-G-U-G---GA----------A-GA-A----------C--CCG----A-UC----CCAUCU------CGA-ACUCG-GC-CGUUAA-A-----------------CACACCA-G-C--G---CC--GAUG----GUACUGUG---UCU--CAA-G-ACACG-GGA---G---AGUC----GG-U-CG-CC--G-CCAGGC
M34770.1/1-114           --CC-GGC-GG-C-C-UG-AGC----GG-U-G-U-G---CC----------A-GA-A----------C--CCG----A-UC----CCAUCU------CGA-ACUCG-GC-CGUUAA-A-----------------CACACCA-G-C--G---CC--CAUG----GUACUGUG----CU-CCAA-G-ACACG-GGA---G---AGUC----GG-U-CG-CC--G-CCAGGC
X03902.1/1-114           ---CUGGU-GG-C-C-UG-AGC----GG-U-G-U-G---CC----------C-AGAA----------C--CCG----A-UC----CCAUCU------CGA-ACUCG-GC-CGUUAA-A-----------------CACACCA-G-C--G---CC--CAUG----GUACUGUG---UCU--CAA-G-ACACG-GGA---G---AGUC----GG-U--G-CC--G-CCAGGC
L37449.1/4-118           --GCUUGC-GC-U-C-GG-UGU----GU-A-G-U-G---UA----------C-AU-A----------C--CCG----A-UC----CCAUCC------CGA-GCUCG-GC-CGUGAA-A-----------------CACUCCA-G-C--G---CC--UAUU----GUACCGAG----GCUUAAG-C-GGCG--GGA---G---AGUC----GG-U-CA-GC--G-CCAGGG
X02044.1/4-118           --CCUGGU-GG-U-C-AU-UGC----GG-G-C-U-C---GA----------A-AC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUGAA-A-----------------GAGCCCU-G-C--G---CC--AAUG----GUACUGCG---UCU--UAA-G-GCGUG-GGA---G---AGUA----GG-U-CG-CC--G-CCAGGC
X06576.1/4-117           --CCUGGU-GG-C-U-AU-GCC----GG-G-G-G-U---UA----------C-CC-A----------C--CCG----A-UC----CCAUUC------CGA-ACUCG-GU-CGUUAA-G-----------------UCCCCCU-G-G--G---CC--AAUG----GUACUUCG---UCU--CAA-G-GCGCG-GGA---G---AGUA----GG-U-CG-CC--G-CCAGG-
X01501.1/2-116           --UCUGGU-GG-C-C-AA-AGC----AC-G-A-G-C---AA----------A-AC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUUAA-G-----------------UGCCGUA-G-C--G---CC--AAUG----GUACUGCG----UCAAAAG-A--CGUG-GGA---G---AGUA----GG-U-CA-CC--G-CCAGAC
M11543.1/1-115           --UCUGGU-GG-C-U-UU-AGC----AC-G-A-G-C---AA----------A-AC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUUAA-G-----------------UGCCGUC-G-C--G---CC--AAUG----GUACUGCG----UCAAAAG-A--CGUG-GGA---G---AGUA----GG-U-CA-CC--G-CCAGAC
X05520.1/1-114           ---UUGGU-GG-C-C-AU-AGU----AC-G-A-G-U---AA----------A-AU-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-AGUUAA-G-----------------UGCCGUC-G-C--G---CC--AAUG----GUACUGCG---UCU--GAA-G-ACGUG-GGA---G---AGUA----GG-U-CG-CC--G-CCAGAC
X53853.1/5621-5735       --UCUGGU-GG-C-C-AU-AGC----AC-G-A-G-C---AA----------A-AC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-AGUUAA-G-----------------UGCCGUC-G-C--G---CC--AAUG----GUACUGCG---UCU--CAA-G-ACGUG-GGA---G---AGUA----GG-U-CG-CC--G-CCAGAC
X04585.1/3-117           --UUUGGU-GG-U-C-AU-AGC----GU-U-G-G-C---UA----------A-AC-A----------C--CCG----A-UC----CCAUCC------CGA-ACUCG-GC-CGUUAA-G-----------------GGCCAAC-A-C--G---CC--GAUG----GUACUGCG---UCU--CAA-G-ACGUG-GGA---G---AGUA----GG-U-CA-CC--G-CCAAAC
X03904.1/2-116           --UUUGGU-GG-U-C-AU-AGC---GAC-G-G-C-U---AA----------A--C-U----------C--CCG----A-UC----CCUUCC------CGA-ACUCG-GC-CGAUAA-G-----------------GGCCGUC-A-C--G---CC--AAUG----GUACUGCG---UCU--CAA-G-ACGUG-GGA---G---AGUA----GG-U-CA-CC--G-CCAAAC
X55255.1/4-120           --GUUGGU-GG-U-U-AU-UGU----GU-C-G-G-G---GG----------U-AC-G----------C--CCG----G-UC----CCUUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCGAUU-G-C--G---CU--GAUG----GUACUGCAC---CUGGGAG-G-GUGUG-GGA---G---AGUA----GG-U-CG-CU--G-CCAACC
D13617.1/2-117           --UGUGGU-GG-U-U-AU-UGC----UG-G-A-G-G---GU----------C-AC-A----------C--CCG----G-UC----UCUUUC------CGA-ACCCG-GU-CGUUAA-G-----------------UCUCUUU-G-C--G---CU--GAUG----GUACUGCC----CUGUGGU-G-GGGUG-GGA---G---AGUA----GG-U-CG-CU--G-CCACGG
X55264.1/4-122           --UGCGGU-GG-U-G-AU-AGU----GG-U-G-G-G---GA----------A-AC-G----------C--CCG----G-UUA--ACCGUUC------CGA-UCCCG-GU-AGCUAA-G-----------------CCCAUGU-A-U--G---CU--GAUG----GUACUGCAA---CUUGGUG-G-UUGUG-GGA---G---AGUA----AG-U-GA-CU--G-CCGCAA
M16205.1/4-122           --UGCGGU-GG-U-G-AU-AGU----GG-U-G-G-G---GA----------A-AC-G----------C--CCG----G-UUA--ACCGUUC------CGA-UCCCG-GU-AGCUAA-G-----------------CCCAUUC-G-C--G---CU--GAUG----GUACUGCAA---CUUGGUG-G-UUGUG-GGA---G---AGUA----AG-U-GA-CU--G-CCGCAA
M33890.1/5-120           ---UCGGU-GG-C-CUAU-AGC----AG-C-A-G-G---GA----------A--C-G----------C--CCG----G-AC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGCUA-A-C--G---CU--GAUG----GUACUGCAA---CCGGGAG-G-UUGUG-GGA---G---AGUA----AG-A-AA-CC--G-CCGACA
Z50058.1/3-119           --GUCGGU-GG-U-U-AU-GGC----GG-A-G-G-G---GG----------A-AC-G----------C--CCG----G-UC----CCAUCC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCUCCA-G-C--G---CC--GAUG----GUACUGCAC---CUGUCAG-G-GUGUG-GGA---G---AGUA----GG-U-CG-CC--G-CCGACA
Z50056.1/3-119           --GUCGGU-GG-U-C-AU-GGC----GG-A-G-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCAUCC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCUCCA-G-C--G---CC--GAUG----GUACUGCAC---UCGUCAG-G-GUGUG-GGA---G---AGUA----GG-U-CG-CC--G-CCGACA
Z50057.1/2-118           --GUCGGU-GG-U-C-AU-UGC----GG-A-G-G-G---GG----------A-AC-G----------C--CCG----G-UC----CCAUCC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCUCCA-G-C--G---CC--GAUG----GUACUGCAC---UCGCCAG-G-GUGUG-GGA---G---AGUA----GG-U-CG-CC--G-CCGACA
Z50073.1/3-119           --GUCGGU-GG-U-U-AU-GGC----GG-A-G-U-G---GG----------A-AC-G----------C--CCG----G-UC----CCAUCC------CGA-ACCCG-GA-AGCUAA-G-----------------CACUCCA-G-C--G---CC--GAUG----GUACUGCAC---UCGCUAG-G-GUGUG-GGA---G---AGUA----GG-U-CG-CC--G-CCGACA
Z50077.1/4-121           --GUCGGU-GG-U-U-UU-AGC----GG-A-GCG-G---GG----------A-AC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCCUCCA-G-C--G---CC--GAUG----GUACUGCAC---UCGAUAG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGACA
Z50054.1/4-120           --GUCGGU-GG-C-G-AU-AGC----GG-U-G-G-G---GA----------A-AC-G----------C--CCG----G-UC----CCUUUC------CGA-ACCCG-GA-AGCUAA-G-----------------CCUGCCA-G-C--G---CC--GAUG----GUACUGUAC---UCGAUAG-G-GUGUG-GGA---G---AGUA----GG-A-CA-CC--G-CCGACA
Z50067.1/4-120           --GUCGGU-GG-C-G-AU-AGC----GG-G-G-A-G---GG----------U-CC-G----------C--CCG----G-UC----CCAUUC------CGA-ACCCG-GU-AGCUAA-G-----------------CUCCCCA-G-C--G---CU--GAUG----GUACUGCAC---UCGGUAG-G-GUGUG-GGA---G---AGUA----AG-A-CA-CC--G-CCGACA
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AY924945.1/1-119         --ACAUAC-GA-C-C-AU-AGG----CA-C-U-U-G---AA----------A-AC-U----------C--GGG----A-UC----CCGUCC-------GC-UCUCC-GAUCGAUAA-G-----------------CCAGUGA-C-C--G---CC--AGGCCA--GUAGUCGGU--UCGGUGAC-G-GCCGG-CGA---A--UACCU----GG-U--G-UU--G-UAUGU-
AY544491.1/372-484       --AUGC---GA-U-C-AU-ACC----AG-C-A-C-U---GA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AAUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAG-----GAUUGAU-C-CCAUC-AGA---A---CUC-----CG-A-AG-UU--A-AGCGUG
AY544260.1/513-620       --AGUGCU-GG-U-A-UG-AUC----GG-C-A-U-G---AU----------C-CC-A----------U--CAG----A-----------------------ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU----GCAUUC
X99089.1/298-417         --ACAUAC-GG-C-C-AU-AGA----UU-G-A-A-G---AA----------U-AU-A----------C--GGG----A-UC----CCGUCC-------GC-UCUCC-CAUAGUCAA-G-----------------CUUCUAA-U-C--G---CC--UCGUUA--GUACUGCGG--UGGGUGAC-C-ACACG-GGA---A--UCCGA----GG-U--G-CU--G-UAUGCU
AB045287.1/5831-5948     --UCUGGU-GA-U-G-AU-GUU---CUU-U-A-G-G---GU----------A-AC-A----------C--CCG----U-UC----CCAUUC------CGA-ACACG-AC-GGUUAA-G-----------------CCUUUAG-A-A--G---CC--GAUG----GUACUGCAC---GGGAGAC-U-GUGUG-GGA---G---AGUA----GG-U-GG-UC--G-CCAGGU
DQ178956.1/683-802       --ACGAAC-GA-C-C-AC-AGA----UA-C-G-U-G---AA----------A-GC-U----------A--GGC----A-UC----CCGUCC-------GC-UCUGC-CAUAUAUAA-G-----------------CACGUAA-U-C--G---CU--GGAUUA--GUACUACGG--UGGGUGAC-C-ACGUG-GGA---A--UCCCC----AG-U--G-UU--G-UUCGUU
AY544550.1/370-493       --GAUGCC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-ACCG----GAUC--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CAUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGGC-C-UCCUG-GGA---A--GUCCU----CG-U-GG-U-----GCAUUC
AY034724.1/369-476       --GGAUGC-GA-U-C-AU-ACC----CG-C-A-C-U---AA----------A-GC-A----------C--UGG----------------AU------C------CC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UAGGUGAU-C-UCCUG-GGA---A--GUCCU----CG-U--A-UU--G-CAUUCC
AJ628165.1/1-119         --GCUUAG-CG-U-C-AU-ACC----GC-G-U-A-G---AA----------U-AA-A----------C--CAG----U-UC----UCGUCC-------GA-UCACU-GA-AGUCAA-A-----------------CUACGAC-G-G--G---CG--GGGUUA--GUACUUACA--UGGGUGAC-C-GGUUG-GGA---A--UACCU----CG-U--G-CG--C-UAAGCA
AY245251.1/371-487       --UUUGGC-GA-C-U-AU-GGC----GG-A-G-G-G---GU----------U-CC-A----------C--GCG----U-UC----CCAUCU------CGA-ACACG-AC-CGUUAA-G-----------------CCCUCCA-G-C--G---CC--GAUG----GUACUUGGA---CCGCAGG-G-UCCUG-GGA---G---AGCA----GG-A-CG-UU--G-CCAAGC
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AF083351.1/469-590       --GGGUAC-GAGC-C-AU-ACU---UAG-G-C-C-G---AA----------C-GC-A----------C--CAC----A-UC----CCGUCC------AGUCUCUGU-GA-AGUUAA-------------------CGCGCAC-A-G--G---CC--UCGUUA--GUACGGCGA--UGCGUGAU-G-GCGCU-GGA---A--CCCGG----GG-U--G-UC--G-UACUCU
AY007786.1/359-476       --GGAUAC-GA-C-C-AU-ACU----CU-G-G-U-G---AA----------A-GC-A----------C--CCC----A-UC----CCGCCU-------GA-UUUGG-GA-AGUUAA-G-----------------CACCAGC-A-G--G---CU--GACUA---GUACUGCGG--UGAGUGAU-C-ACGUG-GGA---A---CCCC----AG-G-UG-UU--G-UAUUCU
AF150533.1/320-444       --UAAAGC-AC-C-G-AU-CCC---CGG-U-A-C-C---GAGC-----UCGA-AU-U----------C--AGA----A-UC----CCAUUA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAUUCC
AF416766.1/2880-2994     --GCUGGU-GG-U-A-AU-GGC----AG-G-A-G-U---GA----------A-AC-A----------C--CCG----G-UA----ACAUUC------CGA-ACCCG-GA-AGUUAA-G-----------------CCUCCUA-G-C--G---CC--UGUG----GUACUUUG---UCU--UAA-G-ACAUG-GGA---G---AGAG----GG-U-CG-CU--G-CCAGCC
AJ872266.1/17328-17444   --CCGGGU-GC-C-G-AU-ACU---GGG-G-C-G-G---GA----------A-AC-A----------C--CCG----G-UU----CCAUUC------CGA-ACCCG-GC-CGUUAA-G-----------------CCGCCCU-G-G--G---CC--GAUG----GUAGUAUGG---GGGCAGC-C-CCAUG-CGA---G---AGUA----GG-U--A-GC--G-CCCGGG
DQ776911.1/373-483       --UGCGA-----U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-------CGU---G---CUUG----GG-C-GA-GA--G-UAGUAC
AY544288.1/150-264       --GCUUG--GG-C-G-AG-AGU----AG-U-A-C-U---AG----------G-A----------------UGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUGCUAGGA--UAGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAUUCC
AY547485.1/1-119         --AGGUAC-GU-U-C-AU-ACU----UU-G-C-U-G---AA----------U-AC-A----------C--CAU----A-UC----CCGUCC-------GA-UUUGU-GA-AGUUAA-G-----------------CAGCUAU-A-G--G---CC--ACGUUA--GUACUAAGG--UUAGUGAU-A-ACUUG-GGA---A--CCCGC----GG-U--G-AU--G-UACCUC
L20049.1/222-341         --GCAAUC-GG-C-C-AU-ACU----AC-A-U-C-G---AA----------U-AU-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUCAA-G-----------------CGGUGUA-A-G--G---UU--CGGUUA--GUACUAGGG--UGGGGGAC-C-ACCUG-GGA---A--GACCA----GA-A-UG-UC--G-AUCGCC
AY544262.1/351-457       ----AUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-G----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAG-----GAUUGAU-C-C-----GGU---G---UUUU----AG-U-GC-UG--G-UAU---
X06056.1/924-806         --GUCUAG-GG-C-C-AU-AUC----AU-G-U-U-G---AA----------A-AC-A----------C--CAG----U-UC----UCGUCC-------GA-UCACU-GA-AGUUAA-G-----------------CAACAUU-G-A--G---UU--GUGUUA--GUACUUGGA--UGGGUGAC-C-GCUUG-GGA---A--UACAC----AA-U--G-UC--C-UAGACA
AJ745020.1/1-119         --ACCUGC-AG-C-C-AC-ACC----AC-C-U-U-G---AA----------U-AA-G----------C--CUG----A-UC----UCAUCU-------GA-UCUCA-GA-AGCUAA-G-----------------CAACGUU-G-G--G---UU--UGGUUA--GUACUUGGA--UGGGAUUC-C-ACCUG-GGA---A--UAUCA----AG-U--G-CU--G-UAGGCA
EF064607.1/193-298       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-CG-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--U--------------G-GGU---G---ACCU----CG-U--G-UU--G-CAUCCC
DQ776912.1/370-490       --GGAUGC-GA-U-C-AU-ACU----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCU-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGGG-C-GAGAGUAGU---A-CUAGGA----UG-G--G-UG--A-CCUCCU
AY544566.1/361-487       --GGCAGC-GU-C-G-A---CC----UG-C-A-G-C---CA----------A-GC-UUUUCACUGGCC--GGG----A-UC----CCAUAA-------GA-ACUCC-GA-AGUUAA-G-----------------CCUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UAGGUGAC-C-UCCUA-GGA---A--GUCCU----UG-U--G-UU--G-CAUUCC
AJ390167.1/190-313       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-G----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG-AGAGUA---GUACUAGGA--UGGGUGAC-CUCCGAG-AGU---A-GUACUAG-GAUG-G--G-UG--A-CCUCCC
AF096716.1/373-495       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------G--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCAU-UGC---C---ACCAUUGCCA-C-UA-UU--G-CCAUCU
AY924923.1/1-119         --ACAUAC-GG-C-C-AU-AAC----UA-U-C-A-G---AU----------A-AC-U----------C--GGG----A-UC----CCGUCC-------GC-UCUCC-GUUCGAUAA-A-----------------CUGAUAA-G-U--G---CU--GAAUUA--GUAGUUAGG--UCAGUAAC-G-ACCAG-CGA---A--UCCUC----AG-U--G-UU--A-UAUGU-
X14817.1/224-341         --ACCAAC-GG-C-C-AU-ACC----AU-G-U-U-G---AA----------A-GU-A----------C--CCA----G-UC----UCGUCA-------GA-UCCUG-G--AGUCCC-A-----------------CAACGUC-G-G--G---CC--CGGUCA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--CACCG----GG-U--G-UU--G-UUGGCA
AB109769.1/5352-5468     --UAUGGU-GA-U-A-AA-AGC----AA-G-A-G-G---GA----------U-AC-A----------C--CUG----U-AC----CCAUGC------CGA-ACACA-GA-AGUUAA-G-----------------CCUCUUA-A-C--G---CC--GAUG----GUACUACGA---UGGAAAC-G-UCGUG-GGA---G---AGUA----GG-U-AG-UC--G-CCAAAC
AY704408.1/197-314       --UCUGGU-GC-C-G-AU-GCG---CUU-A-G-G-G---GA----------G-AC-A----------C--CCG----U-UC----CCAUCC------CGA-ACACG-AU-GGUUAA-G-----------------ACUUAAG-C-G--G---CC--GAUG----GUACUAUGC---UGGAGAC-G-GCAUG-GGA---G---AGCA----GG-U-GG-GU--G-CCAGAU
Z18289.1/4653-4769       --CUUGAU-AC-U-U-AU-AGC----GC-A-G-U-G---GA----------C-CC-A----------C-AUCG----A-UC-----CAUCC------CGA-ACUCG-AU-UGUUAA-A-----------------CACUACA-G-C--G---GC--AAUGA----UACUGAAG---GGGAAGC-C-UUUUG-GGA---A---AGUA----GC-U-CA-GU--G-CCAAGG
AY544266.1/386-501       --CAUGCC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAG-----GAUCGAU-C-CCAU--CAA---A---ACUC----CG-A-AG-UU--AAGCGUGC
M11398.1/1543-1662       --AUAUAC-GG-C-U-AU-AGA----UG-G-U-A-G---AA----------A-AU-U----------C--AGG----A-UC----CCGUCC-------GC-UCUCC-UAUAGAUAA-G-----------------CUACUAA-U-C--G---CU--UAAUUA--AUAGUUAGG--UCAGUAAC-G-ACCAG-CGA---A--UCCUA----GG-U--G-CU--G-UAUGUU
M74438.1/534-648         --GUCUACUGG-C-C-CC-ACCCCCAAC-C-C-U-G---GG----------U-AC-U----------C--CCG----A-----------------------UCUCG-GA-AGCAAA-G-----------------CAGGGUCGG-G--C---UC--AGGCAA--CUACUUGGA--UGGGAGAC-C-UCCUG-GGA---A---CACC----GA-G-UG-CU--G-UAGACU
AY130476.1/307-424       --GGAUGC-GA-U-C-AU-ACC----AA-C-A-A-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-C-----------------A-UGCUU-G-G--A---CA--UGAGGA--GUACUACGA--UGAGUGAA-C-UCCCG-GGA---A---GUCC----UC-C-AA-UU--G-CAUCCC
AY544351.1/286-392       --UUCAA----------A-ACU----AA-A-A-U-G-----------------GC-C----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U-G--------UUGCAU
AF516403.1/371-484       --UGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UC----CGA---A---GUUA----AG-C-G---U--G-CUUGGG
AY305327.1/3653-3773     --GCCAGC-GG-C-C-AU-ACU----GC-A-U-C-G---AA----------U-AC-G----------C--CGG----A-UC----CCAUCC-------GA-ACUCC-GA-AGUUAA-G-----------------CGGUGCA-A-G--G---CC--CGGAUA--GUACUGGGG--UGGGGGAC-C-GCCCG-GGA---A--GUCCUU--AGG-G-UG-CU--G-CUGGC-
DQ867108.1/1-118         --GCUUAC-GG-C-C-AU-ACC----AG-C-C-U-G---------------U-AC-G----------C--CCG----A-UC----UCGUCC-------GA-UCGCG-GA-AGAUAA-A----------------ACGCGUUU-G-G--U---CU--UGGCCA--GUACUUGGA--UGGGAGAC-C-ACAUA-GGA---A--CCCCG----AG-U--G-CU--G-ACAGCU
AF516427.1/370-470       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--C--------------------------C---------GA-AGUUAA-G-----------------CGUGCUU-G-G--U---UG--AGAGUA--GUACUAGGA--UGGGUGAC-U--CUUG-GGA---A---GUCC----UC-G-UG-UU--G-CAUUCC
EF175854.1/1-112         --GGGUGC-GA-U-C-GU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--C-G----A-UC----CCAUCA-------GA-ACUCU-GC-AGUUAA-G-----------------CGUGCUC-G-G--G---CG--AGAGUA--GUACUGGCU--UGGGUGAC-C-------CGC---A---AUUU----CU-U--U-UC--C-UUCUUA
U89919.1/939-1056        --CUUUAC-GG-C-C-AC-ACC----AC-C-C-U-G---AA----------C-GC-A----------C--CGG----A-UC----UCGACU-------GA-CCUUG-AA-AGCUAA-G-----------------CAGGAUC-G-G--G---CC--UGGUUA--GUAUUGGGA--UGGCAGAC-C-CCCUG-GAA---A---UACA----GG-G-UG-CU--G--AAGGU
AY313646.1/296-411       --GGAUGC-UA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCC-------GA-ACUCC-AA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AAGUA---GUAUUAGAU--AAG--UAC-C-UCCUG-GAA---A--GUCCU----CG-U--G-UU--G-CAUUCC
AL096764.11/46123-46004  --GUCUAU-GG-C-C-AU-ACC----AC-C-C-U-G---AA----------U-GU-G----------C--UUG----A-UC----UCAUCU-------GA-UCUCGUGA-AGCCAA-G-----------------CAGGGUG-G-G--G---CC--UAGUUA--GUACUUGGA--UGGGAGAC-U-UCCUG-GGA---A---UAUA----AG-C-UG-CU--G-UUGGCU
AY544489.1/356-472       --GGGGGU-AA-C-A-UG-G------UG-G-A-U-G---UU----------A-UU-A----------U--AGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A---GUCC----UC-A-AG-UU--G-CAUUCC
AJ005582.1/157-275       --GAUUAC-GG-C-C-AU-AUC----CA-C-G-G-A---AA----------A-GC-A----------C--CGG----A-AC----UCGUCA-------GA-UCUCC-GA-AGUUAA-G-----------------CCCGUGC-G-A--G---CC--UGGGUA--GUACUGAGA--AGGGAGAC-C-GCUCG-GGA---A--UACCG----GG-U--G-CC--G-UAAUCU
DQ340386.1/10887-11006   --AGAUAC-GG-C-C-AU-ACC----AU-G-U-A-A---GA----------A-AA-A---------UC--CUC----A-UC----UCGUUC-------GA-UCUGA-GA-AGAUAA-G-----------------UUGCAUC-G-G--G---CC--UUCCUA--GUACUCAAG--UUGGAGAC-A-AUUGG-GGA---A--AAUAA----GG-U--G-CU--G-UAUCUU
L07260.1/753-869         --UUUGGU-GC-C-A-AU-AGC----AC-A-G-U-G---GA----------A-CC-A----------C-ACCG----A--C----CCAUCU------CGA-ACUCG-GU-UGUUAA-A-----------------CGCUGUA-G-C--G---GC--AAGAA----UACUUAAG---GGGCAGC-U-CUUUG-GGA---A---AGUA----GC-U-CA-GU--G-CCAAAG
DQ020568.1/1-118         --GCCUAC-GG-C-C-AU-ACU----AG-C-C-U-G---AA----------C-AC-G----------C--CCG----A-UC----CCGUCU-------GA-UCUCG-GA-AGCUAA-G-----------------CAGGUCA-G-G--C---CU--GGUUA---GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A---UACC----AG-G-UG-CC--G-UAGGCU
M25016.1/1-119           --GCCAAC-GA-C-C-AU-ACC----AC-G-C-U-G---AA----------U-AC-A----------U--CGG----U-UC----UCGUCC-------GA-UCACC-GA-AAUUAA-G-----------------CAGCGUC-GCG--G---GC--GGUUA---GUACUUAGA--UGGGGGAC-C-GCUUG-GGA---A---CACC----GC-G-UG-UU--G-UUGGCC
AY924903.1/1-119         --ACAUAC-GG-C-C-AA-AGC----UC-G-U-A-G---AG----------A-AU-A----------C--GGG----G-UC----CCGUCC-------GC-UCCCC-CAUCGUCAA-G-----------------CUGCGAA-G-C--G---CU--GGAUUA--GUAGUUGGG--UCGGUGAC-G-ACCAG-CGA---A--UCCCC----AG-U--G-UU--G-UAUGU-
AF416765.1/2878-2993     --GUUGGU-GG-U-A-AU-AGC----GG-A-A-G-U---GG----------U-AC-A----------C--CCA----GCUU----ACAUUU------CGA-ACCUG-GA-AGUUAA-G-----------------CCUUCUA-G-C--G---CU--GAUG----GUACUUUG---UCU--UAA-G-ACAUG-GGA---G---AGUA----AG-U-CA-CU--G-CCACCC
AF095839.1/346-228       --GCGUAC-GG-C-C-AU-ACU----AU-G-G-G-G---AA----------U-AC-A----------C--CUG----A-UC----CCGUCC-------GA-UUUCA-GA-AGUUAA-G-----------------CCUCAUC-A-G--G---CA--UCCUAA--GUACUAGGG--UGGGCGAC-C-ACCUG-GGA---A--CCGGA----UG-U--G-CU--G-UACGCU
AJ272600.1/602-724       --GGGUAC-GA-C-C-AU-ACU----UG-G-C-C-A---AA----------U-GC-A----------C--CAC----A-UC----CCGUCC-------GA-UUUGU-GA-AGUUAA-G----------------CCGGUCAC-A-G--G---CC--UCGUUA--GUACGGCGNNAWCAGUGAUNG-GCGUU-GGA---A--CCCGG----GG-U--G-CC--G-UACCCU
AJ744982.1/1-129         --ACCUUC-GG-C-C-AC-ACC----AC-U-U-U-G---AAUAAGCCUGAUC-UC-G----------C--CUG----A-UC----UCGUCU-------GA-UCUCA-GA-AGUGAA-A-----------------CAAUGUU-G-G--G---CU--UGGUUA--GUACUUGGA--UGGGAGAC-C-GCCUG-GGA---A--UAUCA----AG-U--G-CU--G-UAGGCA
AF237320.1/326-425       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------UGUGCUU-G-G--G---CG--AGAGUA--GUACU------------A----------GGA---A---CAUG----CG-U--A--C--G-UGUGCG
AY934066.1/157-271       --CCUGGU-UG-U-U-AU-AGC----AA-A-G-G-G---UU----------A-AA-A----------C--CGG----A-UC----CCAUCU------CGA-ACUCA-UU-GGAGAA-U-----------------UCCUUUA-G-C--G---CC--GAUG----GUACUUAG---UCU--UAA-G-GCUUG-GGA---G---AGUA----GG-A-CG-UA--G-CCAGGC
AF516460.1/348-446       --GGAUGC-GA-U-C-AU-ACC----AG-C-G-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUAC-GAGAGU----------------------AGUACUA-G-G--A---UG--GGUGA----CCUCCUGG-------------------GAA---G---UCCU----CG-U--G-UU--G-CAUUCC
X75364.1/777-892         --UUUGGU-AU-U-U-AU-UGC----AU-A-G-G-A---GA----------U-AU-A----------C--CUG----U-UC----CCAUGU------CGA-ACACA-GA-AGUCAA-G-----------------UCCUUUU-G-C--G---CU--GGAA----GUACUUGG----GGGUUGC-C-CCCUG-GGA---G---AUAA----AG-A-CG-AU--G-CCAAGU
M29278.1/713-832         --ACAUAC-GG-C-C-AU-AGA----UG-G-U-G-G---AA----------A-AC-U----------C--GGG----A-UC----CCGUCC-------GC-UCUCC-CAUAGAUAA-G-----------------CCACCAA-U-C--G---CU--UGACUA--GUAGUUGGG--UCGGUGAC-G-ACCAG-CGA---A---UCCC----AG-G-UG-CU--G-UAUGUU
AF516424.1/400-520       --CUUGCC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UAGGUGCU-U-GGGCG-AGA---GUAGUACU----AG-G--A-UA--G-GUGACC
V01425.1/590-708         --CCCUGC-GG-C-U-AC-ACC----CC-C-C-U-G---AA----------A-GA-G----------C--CUG----A-UC----UUGUCU-------GA-UCUCA-GA-AGCCAU-G-----------------CGGGGCC-G-A--C---CC--UGGUUA--GUACCUGGA--UGGGAGAC-C-ACCUG-GGA---A---UACA----AG-G-UG-UU--G-UAGUCU
AY599019.1/4972-5080     --CCUGGU-GA-U-C-AU-AGC----GA-A-G-A-G---GU----------C-CC-A----------C--CCG----U-UC----CCAUCC------CGA-ACACG-GA-AGUUAA-G-----------------CUCUUCA-G-C--G---CC--GAUG----GUACUGCUA--U-----------UGCG-GGA---G---AGUA----GG-U-CG-UC--G-CCAGGC
AY544461.1/401-518       --CGAUGC-UU-U-A-GU-GCU----GG-U-A-U-G---AU----------CGGC-A----------U----G----A-UC----CCAUCA-------GA-ACUCC-AA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAUUA--GUUCUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAUUAC
AY544517.1/371-474       --GGACGC-GA-U-C-AU-AUC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUG--ACCUCCUGG-------------------GAA---G---UCCU----CG-U--G-UU--G-CAUUCC
DQ867109.1/1-117         --GCUUAC-GG-C-C-AU-ACC----AG-C-C-U-G---UA----------C----G----------C--CCG----A-UC----UCGUCC-------GA-UCCUG-AA-AAAUAA-A-----------------CAUGCUU-G-G--G---CU--UGGCCA--GUACUUGGA--UGGGUGAC-C-GCCUG-GGA---A--CACCG----AG-U--G-CU--G-UAAGCU
AY034723.1/387-496       --UAGUGC-UG-U-U-AUGAUC----GG-C-A-U-G---AU----------C-CU-A----------U--CAG----G-----------------------ACUCC-GA-AGUUAA-G-----------------CAUGUUU-G-G--G---CG--AGAGUA--GUACUAGGA--UAGGUGAC-C-UCCUG-GGA---A--GUUCU----CG-U--G-UU--G-CAUUCC
M32451.1/1-117           --CCUGGU-GC-U-U-AU-UGC----GU-G-G-U-G---GA----------A-CC-A----------C-ACCG----A-UC-----CAUAC------CGA-ACUCG-GU-UGUGAA-A-----------------CAUUACU-G-C--G---GC--GACAA----UACUUGAA---GGGUAAC-U-UUCUG-GAA---A---GAUA----GC-U-UA-GU--G-CCAGGA
M86547.1/142-262         --GCCGUC-GU-U-C-AU-ACU----GC-G-U-C-U---AA----------U-GC-A----------C--CGG----A-UC----CCAUCU-------GA-ACUCC-GA-AGUUAA-U-----------------CGGCGCA-A-G--G---CC--CGGUUA--GUACUGCGG--UAGGGGAC-U-CCGCG-GGA---A---UCCUU--UGG-G-UG-AU--G-ACGGCC
AJ510153.1/1-116         --UGUCGU-GU-U-A-AU-UCC----GA-U-G-A-G---GU----------C-AC-A----------C--CUG----U-UC----CCAUUC------CGA-ACACA-GA-AGUUAA-G-----------------CUUGUCA-G-G--G---CC--CAAA----GUAGUUACA---GGAACGC-C-UGUUG-CAA---G---GUUA----GG-A-CG-AC--G-CGAUG-
AF516401.1/456-574       --GAUGCC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UAGGUGAC-C-UCCGA-AGU---U--AAGCG----UG-C--U-UG--G-GCGAGA
AF330837.1/213-340       --GUAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---RA----------U-AC-A----------CAGUAG----A-UC----CCRWUYCCCAUCAGA-ACUCC-GC-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AAUAUU--GUACUAGGA--UGGGUGAC-C-UCCCG-GGA---A--GUCCU----CG-U--G-UU--G-CAUCCC
AB205145.1/27903-27784   --ACAUAC-GA-C-C-AC-AGC----CG-C-C-A-G---CC----------A-AA-U----------C--CGG----A-UC----CCGUCC-------GA-UCUCC-GCUAGAUAA-U-----------------CUGGCGA-G-C--G---CU--AGAUUA--GUAGUUGAG--UCGGUGAC-G-AUCAG-CGA---A--UACCU----AG-U--G-UU--G-UAUGUU
AY034752.1/354-454       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--C------------------------------------GG-AUCCCA-U-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAUUUC
AY544430.1/375-465       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGGAA-------------------GU---------------------CCU----CG-U--G-UU--G-CAUUCC
AF516416.1/267-382       --CGGUGC-GG-U------AUC----CG-U-U-A-U---UA----------G-GA-G----------C--GGG----A-UC----CCAUCA-------AA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UAGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAUUCC
M24957.1/152-36          --GGUUGC-GG-C-C-AU-AUC----UA-C-C-A-G---AA----------A-GC-A----------C--CGU----U-UC----CCGUCC-------GA-UCAACUGU-AGUUAA-G-----------------CUGGUAA-G-A--G---CC--UGACCG-AGUAGUGUA----GUGGGUA-C-UGA---ACA---U---GUCU----GG-A-CC-CU--G-CCCUCA
AF135389.2/2013-1896     --CCUGGU-GU-C-U-AU-UGC----GC-U-G-U-G---GA----------A-CC-A----------C-ACUG----A-CU----CCAUCC------CGA-ACUCA-GA-GGUGAA-A-----------------CGCUGCU-G-C--G---GC--CACGA----UAGUCUAG---GGGUUGC-C-CUACG-CCA---C---AAUA----GC-U-CG-AU--G-CCAGGU
L79956.1/1-118           --AUCCUC-GG-C-C-AU-AGCC--UUU-G-C-A-U---GA----------A-AU-A----------C--CAC----G-UC----CCGUCC-------GA-UCCGU-GA-AGUCAA-G-----------------UUGCAUA-U-C--G---CU--CGGUUA--GUACCAAGG--UGGGGGAC-C-ACUUG-GGA---A---UCCC----GG-G-UG-CC--G-AGG---
X01545.1/1-118           --GGAAUC-GG-C-C-AU-AUU----AG-C-C-U-G---AC----------U-AG-A----------C--UGC----A-UC----CCGUCC-------GC-UCUGC-AA-AGUUAA-C-----------------CAGGCUC-A-A--G---CG--UGGGUA--GUACUCAGG--UGGGUGAC-C-ACUGG-GGA---A--GUCCA----CG-U--G-CU--G-AUUCU-
DQ867109.1/245-353       --GCUUAC-GG-C-C-AC-ACC----AG-U-G-U-G---AA----------A-GC-A----------U--CUG----A-----------------------UCUCA-GA-AGCUAA-A-----------------CACACUU-G-G--G---CU--CGAUCA--GUACUUGGA--UGGGAGAC-C-GCCUG-GAA---A--CACCG----AG-U--G-CU--G-UAAGCU
DQ776902.1/368-481       --GGAUGC-GA-U-C-AU-ACU----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUGA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAG-----GAUCGAU-C-CCAUC-AGA---A---CUC-----CG-A--A-GC--G-AAGCGU
AY544260.1/501-381       --UCUGCC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UU----CCAUCA-------GA-AAUCC-GA-AGUUAA-G-----------------CGUGCAU-G-G--G---UG--AGAGUA--CUACUAGGA--UGCGUGA--C-AUGUC-CGAUGCG---AUCA----UA-C-CA-GC--A-CUAAAG
AY034715.1/370-504       --GCAUGG-AC-U-C-AU-ACC----AG-C-A-C-U----A----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-AA-AGUUAA-GCGUGCUUGGGCGAGAGUAGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAUUCC
AJ390158.1/188-305       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGG--C-G-AGAGU-AGU---A-CUAGGA----UG-G--G-UG--A-CCUCCU
AF516423.1/138-256       --GGUGGC-AA-U-G-GU-ACC----GC-G-U-U-G---UG----------A-AA-G----------G--GGG----A-UC----CCAUCA-------GA-ACUUC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---UG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCUUG-GGA---A--GUUCU----CG-U--G-UU--G-CAUUCC
AF330846.1/196-319       --NGUAGG-GA-U-C-AU-ACC----AG-C-A-N-U---NA----------U-AC-A----------C--GAG----A-UC----CCAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------NGUGCUU-G-G--G---CG--AAUAUU--GUAAUAGGA--UGGGUGAC-C-UCCCG-GGA---A-GUCCUNGUGUUG-C--A-UC--C-CUCUUU
AF516438.1/428-540       --CCGAUC--------AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UAGGUGCU-U-GGGCG-AGA---G--UAGUA----CU-A-G------G-AUAGGU
AF237322.1/124-242       --AGGGGC-GU-C-G-UU--GC----GG-U-G-G-A---AA----------A-GU-G----------G-UCGG----A-UC----CCAUCA-------GA-ACUCC-AA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAUUCC
AJ508600.1/161-58        --GUCUAC-AG-C-C-AU-ACC----AU-C-C-U-G---AA----------C-AU-G----------C--CAG----A-UC----UUGUCU-------GA-CCUCU-GA-AGCUAA-G-----------------CAGGGUC-A-A--G---CC--UGGUUA--GUACUUGGG-------------------AGA---A----GCU----GG-U--G-UG--GCUAGACC
M11398.1/749-868         --AUAUAC-GG-C-U-AU-AGA----UG-G-U-A-G---AA----------A-AU-U----------C--GGG----A-UC----CUAUCC-------AU-UUUCC-UAUAAAUAA-G-----------------CUACUAA-U-U--A---CU--UAACUA--GUAGUUAGG--UUGGUGAC-G-AUUAG-CGA---A--UCCUA----AG-U--G-UU--G-UAUAUU
DQ840051.1/217-335       --GGGUGC-GA-U-C-AU-ACU----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CUAUCA-------GA-ACUCC-GC-AGUUAA-G-----------------CAUGCUU-G-G--G---CC--AGAGUA--GUACUAGGA--UGGGGGAU-C-UCCUA-GUA---A--GUCCU----UG-U-UA--G--G-UGGUCA
U62086.1/19-126          --GAAAGUUAA-G-C-GU-GCU----UG-G-G-C-G---AG----------A-GU-A----------G--UAC----U-------------------------AGG-AU-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---A--GUCCU----CG-U--G-UU--G-CAUUCC
DQ776904.1/441-560       --GAAGGU-AA-G-C-GU-GCU----UG-G-G-C-GAGAGU----------A-GU-A----------C--UAG----G-AU----GGGU---------GA-CCUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUA-GGA---A--GUCCU----CG-U--G-UU--G-CAUUCC
AY034776.1/370-483       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------UGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA---GG----U-C-UUAAG-UGU---G---CUUG----GG-C-GA-GA--G-UAGUAC
AF096755.1/373-488       --GGAUGCCGA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-UC----CCAUCA-------AC-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA-UGUACUAGG----GA----U-C-CCAUC-UGA---A---CUC-----CG-A-AG-UUAAG-CGUGCU
AJ318074.1/3315-3429     --UCUGGU-GU-C-C-UA-GGC----GU-A-G-A-G---GA----------A-GC-A----------C--ACC----A-AU----CCAUCC-------AU-CCUGG-U--GGUUAA-A-----------------CUCUACU-G-C--G---GU--GACGA----UACUGUAG---GGGAGGU-C-CUGCG-GAA---A---AAUA----GC-U-CG-AC--G-CCAGGA
AY544572.1/31-151        --ACAUGC-G-------U-ACG----UG-C-G-C-G---GAAUAU--AUUAA-GC-A-------------CGG----A-UC----CCAUCA-------GA-ACUCC-GA-AGUUAA-G-----------------CGUGCUU-G-G--G---CA--AGAGUA--GUACUAGGA--UGGGUGAC-C-UCCUG-GGA---G---ACCU----CG-U--A-UU--G-CAUUCC
EF175853.1/1-105         --GGGUGC-GA-U-C-GU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C---CG----A-UC----CCAUCA-------GA-ACUCU-UU-AGUUAA-A-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUGGCU--U--------------G-GGU---G---AAC-----CG-C-AA-UU--U-CUUUUC
DQ867109.1/483-591       --GCUUAC-GG-C-C-AC-AUC----AG-U-G-U-G---AA----------A-GU-G----------U--CUG----A-----------------------UCUUC-GA-AGUUAA-A-----------------CACGCCU-G-U--G---CU--CGGCUA--GUACGUGGA--UGGGAAAU-C-GCCUG-AGA---A---CCCC----AG-G-UG-CU--A-UAAGCU
AF516462.1/347-450       --GGAUGC-GA-U-C-AU-ACC----AG-C-A-C-U---AA----------A-GC-A----------C--CGG----A-------------------------UCC-CA-U---CA-G-----------------CGUGCUU-G-G--G---CG--AGAGUA--GUACUAGGA--UAGGUGAC-C-UCCUG-GGA---A---GUCG---UCG-U--G-UU--G-CAUUCC
#=GC SS_cons             ..((((((.((.(.,.,,.,<<....-<.<.<.<.<...--..........-.<<.-..........-..<<<....<.<<....______.......>>.-->>>.>-.->>---.-.................>>>>>--.>.>..<...<<..-<<---..-<-<<----..-<<____>.>.-----.>>-...>..-->>-....>>.>..).))..).))))):
#=GC RF                  ..gccuGc.gg.c.C.AU.Acc....ag.c.g.c.g...aA..........a.gc.A..........C..cgG....a.uC....CCAUCc.......Ga.ACuCc.gA.AguUAA.G.................cgcgcUu.g.g..g...Cc..agggUA..GUAcuagGa..UGgGuGAc.C.uCcUG.ggA...A..gacca....gG.u..g.cc..g.Caggcc
//
# STOCKHOLM 1.0

#=GF AC   RF00002
#=GF ID   5_8S_rRNA
#=GF DE   5.8S ribosomal RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Mifsud W; 0000-0002-9805-6461
#=GF SE   Wuyts et al, European LSU rRNA database, PMID:11125083
#=GF SS   Published; PMID:11125083
#=GF GA   42.00
#=GF TC   42.00
#=GF NC   41.90
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00112
#=GF DR   URL; http://rrna.uia.ac.be/lsu/index.html;
#=GF DR   SO; 0000375; rRNA_5_8S;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   11125083
#=GF RT   The European Large Subunit Ribosomal RNA Database.
#=GF RA   Wuyts J, De Rijk P, Van de Peer Y, Winkelmans T, De Wachter R
#=GF RL   Nucleic Acids Res 2001;29:175-177.
#=GF RN   [2]
#=GF RM   9108162
#=GF RT   Role of the 5.8S rRNA in ribosome translocation.
#=GF RA   Abou Elela S, Nazar RN
#=GF RL   Nucleic Acids Res 1997;25:1788-1794.
#=GF RN   [3]
#=GF RM   9154813
#=GF RT   Cytoplasmic p53 polypeptide is associated with ribosomes.
#=GF RA   Fontoura BM, Atienza CA, Sorokina EA, Morimoto T, Carroll RB
#=GF RL   Mol Cell Biol 1997;17:3146-3154.
#=GF CC   5.8S ribosomal RNA (5.8S rRNA) is a component of the large subunit of the
#=GF CC   eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the
#=GF CC   45S precursor that also contains 18S and 28S rRNA. Functionally, it is
#=GF CC   thought that 5.8S rRNA may be involved in ribosome translocation [2]. It
#=GF CC   is also known to form covalent linkage to the p53 tumour suppressor
#=GF CC   protein [3]. 5.8S rRNA is also found in archaea.
#=GF WK   5.8S_ribosomal_RNA
#=GF SQ   61


L78065.1/3758-3910     AACCCUAGGCAGGGGAUCACUCGGC-UCAUGGAUCGAUGAAGACCGCAGC-UAAA-UG-CGCGUCAGAAUGU-----GAACUG--CAG-GAC---------ACAU-GAACACCGACA--------CGUUGAACG-AUAUUGC-GCAUUGCAC--------GACUC------AGUGCG--AUGUACACA---UUU---UUGAGUGCCC
AB011808.1/289-442     AACUUUCAACAACGGAUCUCUUGGU-UCUCGCAUCGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUAAUGU-----GAAUUG--CAG-AAUU--------CCGUGAAUCAUCGAAU--------CUUUGAACGCACAUUGC-GCCCCUUGG--------UAUU--------CCAGG--GGGCAUGCC---UGU---UUGAGCGUCA
AB021684.1/14108-14260 GACUCUCAGCAACGGAUAUCUUGGC-UCCCGCAACGAUGAAGAACGCAGC-GAAA-UG-CGAUAUCUAGUGU-----GAAUUG--CAG-AAUU--------CCGCGAAUCAUCGAGU--------UUUUGAACGCAUGUUGC-GCCCGAGGC--------UU-U--------GCCGA--GGGCAUGUC---UGC---CUGAGCGUCA
AF026388.1/2852-3006   AACUUUCAGCAAUGGAUGUCUUGGC-UCACGCAUCGAUGAAGGACGCAGC-GAAA-UG-CGAUACGCAUUGU-----GAAUUG--CAG-AUUU--------CAGUGAACCAUCAGAU--------UUCUGAACGCACAUGGC-GCUGCUGGUA-------UUUU--------GCCCG--CAGCACGUC---UGU---UUCAGUGUCU
AF093014.1/662-809     CACUUUAAGUAAUGGAUGUCUUGGU-UCUCAUAACGAUGAAGGACGCAGC-AAAG-UG-CGAUAAGCAAUGU-----GAACUG--CAU-AAUU--------CUAUGAACAAUCAGAU--------CUCUCAACGCAAAUAGC-AGUAAU-----------UUAC-----------AU--UACUAUAUU---UAU---AUCAGUGUCU
AF158724.1/274-427     GACUCUUAACGGUGGAUCACUCGGC-UCGCGAGUCGAUGAAGGACGCAGC-CAAG-UG-CGAGAAGUAAUGU-----GAAUUG--CAG-AAC---------ACAUUGAACGUCGACC--------UUCUGAACGCGAAUUGC-GGUCUCGGG--------UCAA-------UCCCGG--GACCGCGUC---UGC---CUCAGGGUCG
AF158725.1/345-497     AUCUCUUAGCGGUGGAUCACUCGGC-UCGAGCGUCGAUGAAGGACGGAGC-UAGC-UC-CGAGAAGUAAUGU-----GAAUUG--CAG-GAC---------ACAUUGAGCAUCGAUA--------UUCUGAACGCGUAUUGC-GGCCUCGGG--------UAAU--------CCUGG--GGCCACGUC---CGU---CUCAGGGUCU
AF169230.1/225-380     GACUCUCGGCAACGGAUAUCUCGGC-UCUCGCAUCGAUGAAGAACGUAGC-GAAA-UG-CGAUACCUGGUGU-----GAAUUG--CAG-AAUC--------CCGUGAACCAUCGAGU--------CUUUGAACGCAAGUUGC-GCCCGAGGCC-------AUCC-------GGCCGA--GGGCACGCC---UGC---CUGGGCGUCA
AF196778.1/2-154       AACUUUAAGCAAUGGAUCACUUGGU-UCUCGCAUCGAUGAAGAACGUAGC-AAAU-UG-CGAAAAGUAAUGC-----GAUCUG--CA--ACCU--------UUGCGAAUCAUCGAAU--------UCUCGAACGCAUCUUGC-ACCCUUUGG--------UCAU--------CCAAU--GGGUACGUC---UAG---UUCAGUAUCU
AF223066.1/5881-6030   GACUCUCGGCAACGGAUAUCUCGGC-UCUCGCAUCGAUGAAGAACGUAGC-GAAA-UG-CGAUACUUGGUGU-----GAAUUG--CAG-AAUC--------CCGUGAACCAUCGAGU--------CUUUGAACGCAAGUUGC-GCCCGAA----------GCCA----------CUA--GGGCACGUC---UGC---CUGGGCGUCA
AF223570.1/244-389     AAUUUUCAACGAUGGAUGUCUUGGC-UCCCAUAUCGAUGAAGAACGCAGCUAGAA-UG-CGAUAUGCAGUGU-----GAAUUG--CAG-AA----------CCACGAAUCAUCGGAU--------CUUUGAACGCAACUGGC-GCUGAU-----------AAAC------------U--CAGCAUACU---UGC---UUCAGUGUGC
AF223571.1/210-358     AACCUUCAACGGUGGAUGUCUUGGC-UCUCAUAUCGAUGAAGAACGCAGC-AAAG-UG-CGAUAAGCAAUGC-----GAAUUG--CAG--A----------CCGUGAGUCAUUAGAA--------UUUCGAAAGCAAUCUGC-ACCUCCGCC--------UA----------GCGAG--AGGUAUGUC---UGC---UUCAGUGUUC
AF306774.1/466-634     AACGUGUCGCGAUGGAUGACUUGGCUUCCUAUUUCGUUGAAGAACGCAGC-AAAG-UG-CGAUAAGUGGUAU-----CAAUUG--CAG-AAU---------CAUUUCAUUGCCCAAU--------CUUUGAACGCAAACGGC-GCAUGGGAGAAGCUC--UCUCGAGCC--AUCCCC--GUGCAUGCCACAUUU---CUCAGUGUCG
AF307619.1/287-442     GACUCUCGGCAACGGAUAUCUCGGC-UCUCGCAUCGAUGAAGAACGUAGC-GAAA-UG-CGAUACUUGGUGU-----GAAUUG--CAG-AAUC--------CCGUGAACCAUCGAGU--------CUUUGAACGCAAGUUGC-GCCCCAAGCC-------UUCU-------GGCCGA--GGGCACGUC---UGC---CUGGGUGUCA
AF319429.1/172-325     AACUUUCAACAACGGAUCUCUUGGC-UCUCGCAUCGAUGAAGAACGCAGC-GAAA-UG-CGAUAAGUAAUGU-----GAAUUG--CAG-AAUU--------CAGUGAAUCAUCGAAU--------CUUUGAACGCACCUUGC-GCUCCUUGG--------UAUU--------CCGAG--GAGCAUGCC---UGU---UUGAGUGUCA
AF403508.1/235-389     AACUUUCAGCAGUGGAUGUCUAGGC-UCGCACAUCGAUGAAGAACGCUGC-GAAC-UG-CGAUACGUAAUGC-----GAAUUG--CAG-GAUU--------CAGUGAGUCAUCGAAA--------UUUUGAACGCAUAUUGC-ACUUCCGGG--------UUAG-------UCCUGG--GAGUAUGCC---UGU---AUCAGUGUCC
AF422961.1/176-329     AACUUUCAACAACGGAUCUCUUGGU-UCUGGCAUCGAUGAAGAACGCAGC-GAAA-UG-CGAUAAGUAAUGU-----GAAUUG--CAG-AAUU--------CAGUGAAUCAUCGAAU--------CUUUGAACGCACAUUGC-GCCCGCCGG--------UAUU--------CCGGC--GGGCAUGCC---UGU---UCGAGCGUCA
AF444327.1/152-305     AACUUUCAACAACGGAUCUCUUGGC-UUCCACAUCGAUGAAGAACGCAGC-GAAA-UG-CGAUAAGUAAUGU-----GAAUUG--CAG-AAUU--------CAGUGAAUCAUCGAGU--------CUUUGAACGCAACUUGC-GCCCUUUGG--------UAUU--------CCGAA--GGGCAUGCC---UGU---UUGAGAGUCA
AF468917.1/611-763     AACUCGUAACGGUGGAUGUCUCGGC-UCCUACAUCGAUGAAGAACGUAGC-AAAC-UG-CGAAACGUAAUGC-----GAAUUG--CAG-AAC---------UCGUGAAUCAUCAAAU--------UUUUGAACGCAAGUGGC-GCUCGCGGG--------UAAC--------CCUGC--GAGCAUGUC---UGU---UUGAGUGUCC
U09322.1/209-362       AACUUUCAACAACGGAUCUCUUGGU-UCUCGCAUCGAUGAAGAACGCAGC-GAAU-UG-CGAUAAGUAUUGU-----GAAUUG--CAG-AUUU--------UCGUGAAUCAUCGAAU--------CUUUGAACGCACAUUGC-GUCCUCUGG--------UAUU--------CCAGG--GGGCAUGCC---UGU---UUGAGCGUCA
AY029385.1/986-1138    AACUCGUGACGGAGGAUAUCUUGGC-UCCCACAUCGAUGAAGAACGCAGC-AAAA-UG-CGAUACGUAGUGU-----GAAUUG--CAG-AAC---------AUGUGAAUCAUCGAAU--------UUUUGAACGCAAGUGGC-GCUCGCGGG--------CAAU--------CCUGC--GAGCAUGUC---UGU---UUGAGUGUCC
X90410.1/15-165        AACUUUCAGCAAUGGAUCUCUUGGC-UCUUGCAUCGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUAAUGU-----GAAUUG--CAG--A----------ACGCGAGUCAUCGAAA--------UUUUGAACGCACAUUGC-ACUUGGUGG--------CAUU--------CCGCC--AAGUAUGUU---UGU---UUGAGUGUCU
L07796.1/2-156         AACUUUCAACAACGGAUCUCUUGGU-UCUCGCAUCGAUGAAGAACGCAGC-GAAA-UGCCGAUACGUAAUAU-----GAAUUG--CAG-AUAU--------CCGUGAAUCAUCGAAU--------CUUUGAACGCACAUUGC-GCCCUCUGG--------UAUU--------CCGGA--GGGCAUGCC---UGU---UUGAGCGUCG
X03680.1/3159-3308     UAGCUUCAGCGAUGGAUCGGUUGCA-UCGAGUAUCGAUGAAGAACGCAGC-UUGC-UG-CGUUACUUACCAC-----GAAUUG--CAG--AC---------GCUUAGAGUGGUGAAA--------UUUCGAACGCAUA--GC-ACCAACUGG--------GCCU--------CCAGU--UGGUACGUC---UGG---UUCAGGGUUG
Y00055.1/4327-4494     AACGUGUCGCGAUGGAUGACUUGGCUUCCUAUCUCGUUGAAGAACGCAGU-AAAG-UG-CGAUAAGUGGUAU-----CAAUUG--CAG-AAU---------CAUUCAAUUACCGAAU--------CUUUGAACGCAAACGGC-GCAUGGGAGAAGCUC--UUUUGAGUC--AUCCCC--GUGCAUGCC---AUAUU-CUCAGUGUCG
X99212.1/685-824       AACCCUAGACAGGGGAUCACUUGGC-UCAUGGGUCGAUGAAGACCGCAGC-AAAC-UG-CGCGUCGCCAUGU-----GAACUG--CAG-GAC---------ACAU-GAUCAUUGACA--------UGUUGAACGCAUAUUGC-GCCUUA-----------UACA-----------UU--UGGU-UCUC---UUU---AUAA-----U
D10840.1/200-355       GACUCUCGGCAACGGAUAUCUCGGC-UCUCACAUCGAUGAAGAACGUAGC-GAAA-UG-CGAUACUUGGUGU-----GAAUUG--CAG-AAUC--------CCGUGAACCAUCGAGU--------CUUUGAACGCAAGUUGC-GCCCCAAGCC-------UUCU-------GGCCGA--GGGCACGUC---UGC---CUGGGUGUCA
X00601.1/3997-4154     AAGCAUAAACGGUGAAUACCUCGAC-UCCUAAAUCGAUGAAGACCGUAGC-AAAC-UG-CGAUAAUUCACUU-----GAAUUG--CAG-CCU---------ACUGGGAUAGUUGAAA--------UGUUGAACGCACAUGAU-GACAUCGGUCC------UUUCGG-----AUUAGG--UGUUAUACU---UGG---GUGAGAGUGG
X60210.1/1-148         ACCGUUAGGCGAUGGAUUGCUGGGU-ACCCGCUUCGACGAAGAGCGCAGU-GAAA-CG-CGAUAACGCUUGU-----GAUUCG--CA--CUCU--------CUGU-GAUCAACGUCA--------CCUCGAACAUCGA-UGC-GGCCUUGCC--------UUCG-------GGCACU--GGCC-CCCC---UGG---UU---UGCCU
M21017.1/2722-2844     AACUCUAAGCGGUGGAUCACUCGGC-UCAUGGGUCGAUGAAGAACGCAGC-AAAC-UG-UGCGUCAUCGUGU-----GAACUG--CAG-GAC---------ACAUGAA-CAUCGACA--------UUUUGAACGCAUAUCGC--A---------------GUCC-------------------AUG-----------CUG-------
U35394.1/2008-2158     AACUUUUGACGAUGGAUCUCUCGGC-UCUCUCAUCGAUGAAGAACGUAGU-AGAA-UG-CGAUACAUAAUGU-----GAAUUG--CA--AAUC--------CUGUGAAUCAUUGAGU--------UUUUGAACGCACAUUGC-ACCGACAG---------UUUA---------CUGU--UGGUUUGUU---UGU---UUGAAUUGCU
X53361.2/1206-1368     ACCUGUU-GUGGUGGAUGUCUUGGC-CCAGGUUCUGAGGAAGGACACAGC-AGCCUUG-CGAUACGUUCGGU-----GAUACG--CAG-AGU---------CUUGUGAUCUGGACAAAGGAACAGCUUCGAACGCAACUGGCCAGCAAGGGG--------UUCC-------CCCCCG--AGCUGCCUG---UGC---GCCAGUGUUG
X15589.1/256-410       GACUCUCGGCAACGGAUAUCUCGGC-UCUCGCAUCGAUGAAGAACGUAGC-GAAA-UG-CGAUACUUGGUGU-----GAAUUG--CAG-AAUC--------CCGUGAACCAUCGAGU--------CUUUGAACGCAAGUUGC-GCCCGAAGCCG------UUAC--------GC-GA--GGGCACGUC---UGC---CUGGGCGUCA
X80212.2/2104-2256     AACUCUCAGCAACGGAUAUCUUGGC-UCUUGCAACGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUAGUGU-----GAAUUG--CAG-AAUU--------CCGCGAAUCAUCGAGU--------UUUUGAACGCAAGUUGC-GCCCGAGG---------CUCG--------UCCGA--GGGCAUUCC---UGC---CAGAGCGUCA
X58290.1/119-234       GACCCAGACCGGCGGAUGCCUGGGC-UCGGGCCUCGAGGAAGGACGCGGC-GGAC-AG-CGAGAUGCGGUGC--------------AG-CCCG--------GCACGAAGCACCGG-U--------UUCCGAACGCUCG--GC-CUCC-------------CCCG---------------GGAG------------------------
M73682.1/109-223       GACGCGACCCGGUGGAUGCCUUGGC-UCGGGGGACGAUGAAGGACGUGGC-UGAC-GA-CGAUACUCGAUGU----GG---UC--CAA-GC----------ACGUGA--CAUCGA-U--------CUUCGAAUG--------------------------GAUC-------------------A---------U---CGGGGUGGUG
X80346.1/67-220        AACUUUCAGCGAUGGAUAUCUUGGC-UCUCGCAACGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUAAUGC-----GAAUUG--CAG-AAUU--------CAGUGAAUCAUCAAAA--------CUUUGAACGCAAAUUGC-GCUUCCGGG--------UAUC--------CCUGG--GAGCAUGCC---UGU---AUGAGUGUCU
X53538.1/2090-2241     GACUCUCAACGGUGGAUCACUCGGC-UCGCGAGUCGAUGAAGGACGCAGC-UAAG-UG-CGAGAAGUGGUGU-----GAAUUG--CAG-AAC---------ACAUUGAACGUCGAC---------CUUCGAACGCGAAUGGC-GGUCUCGGG--------UUAA--------UCCGG--GACCACGUC---UGC---CUCAGGGUUG
U13369.1/6624-6776     GACUCUUAGCGGUGGAUCACUCGGC-UCGUGCGUCGAUGAAGAACGCAGC-UAGC-UG-CGAGAAUUAAUGU-----GAAUUG--CAG-GAC---------ACAUUGAUCAUCGACA--------CUUCGAACGCACU-UGC-GGCCCCGGG--------UUCC-------UCCCGG--GGCUACGCC---UGU---CUGAGCGUCG
Y07974.1/75-229        AACUUUCAGCAACGGAUGUCUUGGC-UCCCACAACGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUAAUGC-----GAAUUG--CAG-AAUU--------CCGCGAGUCAUCAAAC--------CUUUGAACGCACCUUGC-GCUUUCGGGA-------UAUG--------CCCGU--UAGCAUGUU---UGU---UGGAGUGUCU
Y07976.1/124-271       CACUUUCAGCAACGGAUGUCUCGGU-UCCCAUAACGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUAAUGC-----GAAACG--CAU-CAG---------UAGUGAGUCAUCGAAA--------CUUUGAACGCAACUUGC-ACUUCCC----------UUUG-----------GG--GAGUAUAUC---UAU---UGGAGUGUCU
M86760.1/218-371       AACUUUCAGCAAUGGAUCUCUUGGU-UCCCGCGUCGAUGAAGAACGUGGC-AAAA-UG-CGAUAAGUAGUGU-----GAAUUG--CAG-AAUU--------CAGUGACUCAUCGAAU--------UUUUGAACGCAUAUUGC-GCUCCUCAG--------UAUU--------CUGUG--GAGCAUGCC---UGU---UUGAGCGUCA
U21939.1/68-218        CAGUCUUAACGAUGGAUGUCUUGGU-UCCUACAGCGAUGAAGGCCGCAGC-AAAA-UG-CGAUACGCAAUGA-----AAAUUG--CAGUGA----------CUGUGAAUCAUCAGAA--------UGCUGAAUGUAAACUAC-ACCAAUUCC--------UUCG-------GGGAAUAGUGGUACUCC---UAC---AGAA-----A
U48228.1/7-166         CAAUCUUAACGAUGGAUGUCUUGGU-UCCUAUAGCGAUGAAGGCCGCAGC-AAAG-UG-CGAUAUGCAAUGA-----AAAAUG--CA--AUUA--------CUGUGAAUCAUCAGAA--------UGCUGAAUGUAAACUAU-ACCAUAUUUACCC----UUAUGGGCAAAUUAACG--UGGUAUUCC---UAC---AGAA-----A
M14649.1/2015-2169     AACUUUCAGCGACGGAUGUCUCGGC-UCGAACAACGAUGAAGGGCGCAGC-GAAA-UG-UGAUAAGCAAUGU-----GAAUUG--CAG-AAUU--------CCGUGAACCAAUAGGG--------ACUUGAACGUAUACUGC-GCUUUCGGGA-------UAUC--------CCUGA--AGGCAUGCC---UGC---UUCAGUGUCU
U58510.1/2022-2198     AACCCU-AGUGAUGGAUGUCUAGGC-UCCCGUAUCGAUGAAGAACGUAGC-AGAA-AG-CGACAUGCGAUGAUACGCGCAUAGACCAG-GAUUCCGCGGACUCGUGAAUCAUUGAAU--------CUUCGAACGCAUCUGGC-GCUCAGCAGUGGAGCCGUAGC--------AGGCU--GAGCAUGCCC--UGG---AGUAGUGACA
V01159.1/185-331       ACCGUUGGGCGAUGGAUUGCUUGGU-GCCUGCUUCGACGAAGAGCGCAGU-GAAA-CG-CGAUAACUUUUGU-----GACUCG--CA--CUCU--------CUGUGA-UCAACGUCU--------CCUUGAACAUUAG-UGC-GGCCUUGCC--------UUCG-------GGCACU--GGCCCC--------C---UUGGGAUGCC
X66325.1/2369-2523     GACUCUCGGCAACGGAUAUCUU-GC-UCUCGCAUCGAUGAAGAACGUAGC-GAAA-UG-CGAUACUUGGUGU-----GAAUUG--CAA-GAUC--------CCGUGAACCAUCGAGU--------CUUUGAACGCAAGUUGC-GCCCCAAGCC-------UUCU-------GGCCGA--GGGCACGUC---UGC---CUGGGUGUCA
U10409.1/2025-2178     AACUUUCAGCAACGGAUCUCUUGGU-UCUCGCAUCGAUGAAGAACGCAGC-GAAU-UG-CGAUAAGUAAUGU-----GAAUUG--CAG-AUUU--------UCGUGAAUCAUCGAAU--------CUUUGAACGCAUAUUGC-GCUCUAUAG--------UAUU--------CUAUA--GAGCAUGCC---UGU---UUGAGCGUCA
Z32848.1/2558-2712     AACUUUCAGCAACGGAUCUCUUGGC-UCUCGCAUCGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUAAUGU-----GAAUUG--CAG-AAUU--------CCGUGAAUCAUCGAAU--------CUUUGAACGCACAUUGC-GCCUUUGGG--------UUAU-------UCCCAA--AGGCAUGCC---UGU---UUGAGUGUCA
D16558.1/2710-2862     AACUUUCAGCGACGGAUGUCUUGGC-UCCCACAACGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUCUUGC-----GACUUG--CAG-AAUC--------CAGUGAAUCAUCAAAA--------CUUUGAACGCAUC-UGC-G-UUCCGGGA-------UAUG--------CCUGG--GAGCAUGCU---UGU---CGGAGUGUCU
Y11511.1/115-268       AACUUUUAGCAAUGGAUGUCUUGGG-UCACACAACGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUAAUGC-----GAAUUG--CAG-AACU--------UCGUGAAUCAUCAAAA--------UUUUGAACGCACAUUGC-GCUACUGAG--------UAAU--------CUCAG--UAGCAUGCU---UAU---CUGAGUGUCU
AJ229062.1/241-389     AACUUUCAACAACGGAUCUCUUGGU-UCUCGCAUCGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUAAUGU-----GAAUUG--CAG-AAUU--------CCGUGAAUCAUCGAAU--------CUUUGAACGCACAUUGC-GCCCCUUGG--------UAUU--------CCAGG--GGGCAUGCC---UGU---UUGAG-----
Y07978.1/48-201        AACUUUCAGCGACGGAUAUCUAGGC-UCCCACAACGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUCUUGC-----GACUUG--CAG-AACC--------CAGUGAAUCAUCAAAC--------CUUCGAACGCACCUUGC-GCUCUCGGG--------CAUU--------CCCGG--GAGCAUGCU---UGU---CGGAGUGUCC
M63701.1/247-415       AACGUGUCGCGAUGGAUGACUUGGCUUCCUAUUUCGUUGAAGAACGCAGC-AAAG-UG-CGAUAAGUGGUAU-----CAAUUG--CAG-AAU---------CAUUCAAUUACCGAAU--------CUUUGAACGCAAACGGC-GCAUGGGAGAAGC----UCCUCAGAGUCAUCCCC--GUGCAUGCC---AUAUUUCUCAGUGUCG
X75430.1/2186-2339     AAUUUUCAGCAAUGGAUGUCUUGGC-UCGCGCAACGAUGAAGGACGCAGC-GAAC-UG-C-AAACGCAAUGU-----GAAUUG--CAG-AAUU--------CAGUGAAUCAUCAGAU--------UUCUGAACGCAAAUGGC-ACCUUGGGGA-------UAUU--------CUCCU--UGGUACGUC---UGU---UUCAGUGUCU
L25635.1/211-360       AAUUUUCAGCAAUGGAUGUCUUGGC-UCGCGCAACGAUGAAGGACGCAGC-GAAC-UG-CGAAACGCAAUGU----GGAAUUG--CAG-AAUU--------CAGUGAAUCAUCAGAU--------UUCUGAACGCAA--UGC-ACCUGGG--A-------UAUC----------UCC--UGGUACGUC---UGU---UUCAGUGUCU
X01533.1/5-152         AACUUUCAACGGUGGAUAUCUUGGU-UCCCGUGACGAUGAAGAACGCAGC-GAAA-UG-CGAUACGUAAUGC-----GAAUUG--CAG-AA----------CCGCGAGUCAACAGAU--------CUUUGAAAGCAAGUGGU-GGAGGUG----------UAAA----------AAC--CUUCAUGUU---UGU---AUUAGUGUGG
X54512.1/4422-4569     AACUUUCAACGGUGGAUAUCUAGGU-UCCCGUGACGAUGAAGAACGCAGC-GAAA-UG-CGAUACGCAAUGC-----GAAUUG--CAG-AA----------CCGCGAGUCAUCAGAU--------CUUUGAACGCAAGUGGU-GGAGGUG----------UAAA----------AAC--CUUCAUGUU---UGU---UUCAGUGUGG
X60705.1/112-265       AACUUUUAACAACGGAUCUCUUGGC-UCUAGCAUCGAUGAAGAACGCAGC-GAAA-CG-CGAUAUGUAGUGU-----GAAUUG--CAG-AAUU--------CAGUGAAUCAUCGAAU--------CUUUGAACGCACAUGGC-GCCUUCCAG--------UAUC--------CUGGG--AGGCAUGCC---UGU---CCGAGCGUCG
M36008.1/959-1112      GACUCUUAGCGGUGGAUCACUCGGC-UCGUGCGUCGAUGAAGAACGCAGC-UAGC-UG-CGAGAAUUAGUGU-----GAAUUG--CAG-GAC---------ACAUUGAUCAUCGACA--------CUUCGAACGCACCUUGC-GGCCCCGGG--------UUCC-------UCCCGG--GGCUACGCC---UGU---CUGAGGGUCG
#=GC SS_cons           :::::::::::::::::::::::::.::::::::::::::((((<<<<__.____.>>.>>,,,,,,,<<<-.....---<<_..___.>>--........-------->>>,,,,,........,)))),,,<<<___>>>.<<<<<<<<<........____........>>>>>..>>>>:::::...:::...::::::::::
#=GC RF                AACuuUuAgCGAUGGAUguCUuGGC.UCccGuaUCGAUGAAgaaCGCaGC.aAAa.uG.CGAUAcGUaguGU.....GAAuuG..CAG.aaUu........ccgUgAAUCacCGAAu........cuucGAACGCaaaUuGC.Gcccccggg........Uuuu........cccgg..gggCAUgcc...UGu...uugAGUGUCa
//
# STOCKHOLM 1.0

#=GF AC   RF00003
#=GF ID   U1
#=GF DE   U1 spliceosomal RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Mifsud W; 0000-0002-9805-6461
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Zwieb C, The uRNA database, PMID:9016512
#=GF SS   Published; PMID:2405391
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00005
#=GF DR   SO; 0000391; U1_snRNA;
#=GF DR   GO; 0000395; mRNA 5'-splice site recognition;
#=GF DR   GO; 0030627; pre-mRNA 5'-splice site binding;
#=GF DR   GO; 0005685; U1 snRNP;
#=GF RN   [1]
#=GF RM   9016512
#=GF RT   The uRNA database.
#=GF RA   Zwieb C
#=GF RL   Nucleic Acids Res 1997;25:102-103.
#=GF RN   [2]
#=GF RM   2405391
#=GF RT   Saccharomyces cerevisiae U1 small nuclear RNA secondary structure contains
#=GF RT   both universal and yeast-specific domains.
#=GF RA   Kretzner L, Krol A, Rosbash M
#=GF RL   Proc Natl Acad Sci U S A 1990;87:851-855.
#=GF RN   [3]
#=GF RM   7984237
#=GF RT   Crystal structure at 1.92 A resolution of the RNA-binding domain of the
#=GF RT   U1A spliceosomal protein complexed with an RNA hairpin.
#=GF RA   Oubridge C, Ito N, Evans PR, Teo CH, Nagai K
#=GF RL   Nature 1994;372:432-438.
#=GF RN   [4]
#=GF RM   11297556
#=GF RT   Two functionally distinct steps mediate high affinity binding of U1A
#=GF RT   protein to U1 hairpin II RNA.
#=GF RA   Katsamba PS, Myszka DG, Laird-Offringa IA
#=GF RL   J Biol Chem 2001;276:21476-21481.
#=GF CC   U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved
#=GF CC   in pre-mRNA splicing). Its 5' end forms complementary base pairs with the
#=GF CC   5' splice junction, thus defining the 5' donor site of an intron. There
#=GF CC   are significant differences in sequence and secondary structure between
#=GF CC   metazoan and yeast U1 snRNAs, the latter being much longer (568
#=GF CC   nucleotides as compared to 164 nucleotides in human). Nevertheless,
#=GF CC   secondary structure predictions suggest that all U1 snRNAs share a 'common
#=GF CC   core' consisting of helices I, II, the proximal region of III, and IV [1].
#=GF CC   This family does not contain the larger yeast sequences.
#=GF WK   U1_spliceosomal_RNA
#=GF SQ   100


X06810.1/261-421     AUACUUACCUGGACGG-GGUCA-AUGG---AUGAUCAA-UAAG-GUCCA-UGGCCU---AGG-GAAGUAACCUCCAUU-----GCACUU-AGGAGG-GGUGCUUU---------CCUA-AGGUCUGCCCAA---GUGG--CAG-AGCCU-ACGUCAUAAUUUGUGGUAG--UGGGGG--CUUGCGUU--CGCGCAGCCCCUUC
X14417.1/177-340     AUACUUACCUGGACGG-GGUCA-AUGG---GUAAUCAA-GAAG-UUCCA-UGGCCU---AGG-UUGGUGACCUCCAUU-----GCACUA-AGGAGG-GGUGCUUG---------CCUA-AGGUCGACCCAA---GUGG--UUG-AGCCU-ACGUCAUAAUUUGUUGUUGCAGAGGGGG-CCUGUGUU--CGCGCAGCCCCUAC
Z11883.1/3441-3603   UUACUG--GUGGGUGGCGGAGA-AGAGAUCGUGACAUC-GUAG-ACCUA-UGGCUU---AGA-UUGAUGACCUCCAUU-----GCACUU-UGGAGG-GGUGCCUG---------CCUAAAGUCUG-CCCAA---GUGG--UCG-AGCCU-ACACUAUAAUUUGUGAUAG---UGGGGG-CUUGCGUU--CGCGCAGCCCCUAG
X14419.1/178-338     AUACUUACCUGGACGG-GGUCA-AUGG---GCGAUCAU-GAAC-ACCCA-UGGCCU---AGG-UUGGUGACCAUCAUU-----GCACUU-UGAAGG-GGUGCCCG---------CCUA-AGGUCGGCCCAA---GUGG--UCG-AGCCU-ACGUCAUAAUUUGUUGCUG---AGGGGG-CCUGCGUU--CGCGCGGCCCCUGC
X14416.1/171-331     AUACUUACCUGGACGG-GGUCU-AUGG---GCGAUCAU-GUAG-GUCCA-UGGCCU---AGG-UUGGUGACUUUCAUU-----GCACUU-UGGAGG-GGUGCCCG---------CCUA-AGAUCAGCCCAA---GAGG--UUG-AGUCU-ACAUCAUAAUUUGUUGCUG---AGGGGG-CAUGCGUU--CGCGCAGCCCCUGC
X14415.1/175-335     UUACUUACCUGGACGG-GGUCA-AUUG---GCGAUCAU-GAAG-GUCCA-UGGCCU---AGG-UUGGUAACCUCCAUU-----GCACUU-AGGAGA-GGUGCCUA---------CCUA-AGAUCGGCCCAA---GUGG--CCG-AAUCU-ACGUCAUAAUUUGUUGCUG---AGGGGG-CCUGCGUU--CGCGCGGCCCCUGC
X14414.1/152-312     AUACUUACCUGGACGG-GGUCA-AUAG---GCGAUCAA-UAAG-ACCCA-UGGCCU---AGG-UUGGUGACCUCCAUU-----GCACUU-UGGAGG-GGUGCCAA---------UCUA-AGGUCGGCCCAA---GUGG--UCG-AGCCU-ACGUCAUAAUUUGUUGCUG--UGAGGG--CCUGUGUU--CGCGCGGCCCCUGC
Z11883.1/2839-2998   AUACUUACCUGGACGG-GGUUA-AUGG---GCGAUCAA-UAAG-ACCCA-UGGGCCU--AGG-UUGGUGACCUCCAUU-----GCACUU-UGGAGG-GGUGCCUA---------CCUA-AGGUCGGCUCAA---GUAG--UCG-AGCCU-ACGUCAUAAUUUGUUGCAG----UGGG--CCUGCGUU--CGCGCGGCCCCUAC
Z11883.1/1496-1656   UUACUUACCUGGACGG-GGUCA-AUGG---GCAAUCAA-UAAG-ACCCA-UGGCCU---AGG-UUGGUGACCUCCAUU-----GCACUU-UGGAGG-GGUGCCUU---------CCUA-AGGUCGACCCAA---GUGG--UCG-AGCCU-AUGUCAUAAUUUGUUGCAG---UGGGGG-CCAGCGUU--CGCGCGGCCCCUAC
Z11883.1/361-521     AUACUUACCUGGACGG-GGUCA-AUGG---ACGAUCAA-UAAG-ACCCA-UGGCCU---AGG-UUGGUGACCUCCAUU-----GCACUU-UGGAGG-GGUGCCUG---------CCUA-AGGUCGGCCCAA---GUGG--UCG-AGCCU-ACGUCAUAAUUUGUUGCAG---UGGGGG-CCUGCGUU--CGCGCGGCCCCUAU
Z11882.1/353-512     AUACUUACCUGGACGG-GGUCA-AUGG---GCGAUCAA-UAAG-ACCCA-UGGCCU---AGG-CUUGUGACCUCCAUU-----GCACUU-UGGAGG-GGUGCCUG---------CCUA-AGGUCGACCUAA---GUGG--UCG-GGCCU-AUGUCAUAAUUUGUUGCUG--UGGGGG--CCUGCGUU--C-UGCGCGCCCCUG
Z11881.1/1515-1675   AUACUUACCUGGACGG-GGUCA-AUGG---GCGAUCAA-UAAG-ACCUA-UGGCCU---AGG-CUUGUGACCUCCAUU-----GCACUU-UGGAGG-GGUGCCUG---------CCUA-AGGUCGGCCCAA---GUGG--UCG-AGCCU-ACGUCAUAAUUUGUUACAG--CGGGGG--CCUGCGUU--CGCGCGGCCCUACC
Z11881.1/315-475     AUACUUACCUGGACGG-GGUCA-AUGG---GCGAUCAA-UAAG-ACCUA-UGGCCU---AGG-CUUGUGACCUCCAUU-----GCACUU-UGGAGG-GGUGCCUG---------CCUA-AGGUCGACCCAA---GUGG--UCG-AGCCU-ACGUCAUAAUUUGUUGCUG--UGGGGG--CCUGCGUU--CGCGCGGCCCUGCC
Z11881.1/2581-2742   AUACUUACCUGGACGG-GGUCA-AUGG---GUGAUCAA-UAAG-ACCCAAUGACCC---AGG-CUUGUGACCUACAUU-----GCACUU-UGGAGG-GGUGCCUG---------CCUA-AGGUCAGCCCAA---GUGG--UUG-AGCCU-AUGUCAUAAUUUGUUGCAG---UGGGUG-CCUGUGUU--UGCGCACGCCCUAC
K02430.1/690-853     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCCCUG
X12936.1/575-738     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCCCUG
V00590.1/1-162       --ACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
M28012.1/108-271     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
M28013.1/108-271     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
V00591.1/394-557     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
M38483.1/1-164       AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
M14387.1/399-562     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
K00788.1/2-165       AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
J00318.1/433-596     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
K00529.1/225-388     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUC--CGCGCUUUCCCCUG
J00645.1/51-213      AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGUGUAUCCAUU-----GCA-UC-CGG-AU-GUGCUGAC---------CACUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--UGUGCUCUCCCCUU
M14585.1/106-268     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGCC---------CCUG-CGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
M14586.1/106-268     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGCC---------CCUG-CGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
M14587.1/106-268     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGCC---------CCUG-CGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
M14385.1/106-268     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGCC---------CCUG-CGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
M14386.1/106-268     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUUAUCCAUU-----GCACUC-CGG-AU-GUGCUGCC---------CCUG-CGAUUUCCCCAAAU-GUGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
M32270.1/371-535     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAU-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUCACCCAUU-----GCACUU-UGGGGU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCCCUG
K03128.1/241-77      AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAU-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUCACCCAUU-----GCACUU-UGGGGU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCCCUG
Y00131.1/944-1108    AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAU-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUCACCCAUUU----GCACUGUUGGGGU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-A-UGCA-AAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCCCUG
V00444.1/1-162       --ACUUACCUGGCAGG-GGAGA-CACC---AUGAUCAG-GCAG-GUGGU-UUUCCCA--GGG-CGAGGCUCAUCCCCU-----GCACUC-CGG-GU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCCCUG
X01093.1/329-492     AUACUUACCUGGCAGG-GGAGA-CACC---AUGAUCAG-GCAG-GUGGU-UUUCCCA--GGG-CGAGGCUCAUCCCCU-----GCACUC-CGG-GU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCCCUG
J00914.1/146-309     AUACUUACCUGGCAGG-GGAGA-CACC---AUGAUCAG-GCAG-GUGGU-UUUCCCA--GGG-CGAGGCUCAUCCCCU-----GCACUC-CGG-GU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCCCUG
X01091.1/442-605     AUACUUACCUGGCAGG-GGAGA-CACC---AUGAUCAG-GCAG-GUGGU-UUUCCCA--GGG-CGAGGCUCAUCCCCU-----GCACUC-CGG-GU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCCCUG
X01092.1/374-537     AUACUUACCUGGCAGG-GGAGA-CACC---AUGAUCAG-GCAG-GUGGU-UUUCCCA--GGG-CGAGGCUCAUCCCCU-----GCACUC-CGG-GU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGG--ACUGCGUU--CGCGCUCUCCCCUG
X00549.1/150-313     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAU-GAAG-GUGGU-UCUCCCA--GGG-CGAGGCUCAGCCAUU-----GCACUC-CGG-UU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUCUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
X02585.1/923-1086    AUACUUACCUGGCAGG-CGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UCUCCCA--GGG-CGAGGCUCAGCCAUU-----GCACUC-CGG-CU-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAACUCG-ACUGCAUAAUUUCUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
X02585.1/1513-1676   AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UCUCCCA--GGG-CGAGGCUCAGCCAUU-----GCACUC-CGG-CC-GUGCUGAC---------CCCUGCGAUUUCCCCAAAU-GCGG---GAAAGUCG-ACUGCAUAAUUUCUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
M32271.1/288-452     AUACUUACCUGGCAGG-GGAGA-UACC---AUGAUCAC-GAAG-GUGGU-UUUCCCA--GGG-CGAGGCUCACCCAUU-----GCACUU-UGGGGU-GUGCUGAC---------CCCUGCGAUUUCCCAAAU--GCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGGGGGA-GCUGCGUU--CGCGCGCCCCCCUG
M59827.1/771-934     AUACUUACCUGGCAGG-GGAGC-AUCU---GUGAUCAG-CAAG-GCAGA-GCUCCCA--GGG-UGAGGCUCAUCCAUU-----GCACAU-CGGAUU--UGCUGAC---------CCCUGCGAUGUCCCCAAAU-GCGG---GAUUCUCG-ACUGUAUUAUUUCUGGUAG--UGGGGG--ACUGCGUU--CGCGCUUUCCCCUG
V01266.1/1-168       --ACUUACCUGGCAGG-GAGAU--ACC---AUGAUCAC-GAAG-GUGUU-UUCUCUCCAGGG-CGUGGUCUAUCCAUUGAGGCGCACUC-CGU-GG-AUGCUGAC---------CCCUGCGAUUUCCUCCAAAUGCGG---GAAACUCG-ACUGCAUAAUUUGUGGUAG--UGCGGGG--GACUGUU--CGCGCUC-CUCUCG
DQ058357.1/1-164     AUACUUAACUGGCAAG-GGAAA-UAAC---AUGAUCAUUAAAG-GUGGA-UUUUUCA--GGG-UGAGGUUUGUCUCUU-----GCAUUG-UGG-AU-GUGCUGAC---------CCCUGUGGUUUUCUACAAAUGUGG---GAAACUUA-AUUGCAUAAUUUGUGGUAG--UGGGGAC-U---AUGU--UGGUUCUCUCCCCU
M27880.1/1-161       AUACUUACCUGGCGCA-GGGGU-CGCA---UUGAUCAA-GAAG-GAUGC-ACCCCC---AGG-GCGAGGCUUGCCAUU-----GCACUC-CGG-CU--UGCUGAA---------CCUUGCGAUUCCCCCAAAC-GUGG---GGAACUCG-GGCGUAUUAUUUAUGGUAG--CGGAGAU--CUGCGUU--CGCGCUA-UCUCCU
X04994.1/620-781     AUACUUACCUGGCGCA-GGGGU-CGCA---UUGAUCAA-GAAG-GAUGC-ACCCCC---AGG-GCGAGGCUUGCCAUU-----GCACUC-CGG-CU--UGCUGAA---------CCUUGCGAUUCCCCCAAAC-GUGG---GGAACUCG-GGCGUACAAUUUAUGAUAG---CGGAGA-UCUGCGUU--CGCGCUAUCUCCUA
X01749.1/448-609     AUACUUACCUGGCGCA-GGGGU-CGCA---UUGAUCAA-GAAG-GAUGC-ACCCCC---AGG-GCGAGGCUUGCCAUU-----GCACUC-CGG-CU--UGCUGAA---------CCUUGCGAUUCCCCCAAAC-GUGG---GGAACUCG-GGCGUACAAUUUAUGGUAG---CGGAGA-UCUGCGUU--CGCGCUAUCUCCUA
X04993.1/647-808     AUACUUACCUGGCGCA-GGGGU-CGCA---UUGAUCAA-GAAG-GAUGC-ACCCCC---AGG-GCGAGGCUUGCCAUU-----GCACUC-CGG-CU--UGCUGAA---------CCUUGCGAUUCCCCCAAAC-GUGG---GGAACUCG-GGCGUACAAUUUAUGGUAG---CGGAGA-UCUGCGUU--CGCGCUAUCUCCUA
X56629.1/421-582     AUACUUACCUGGCGCA-GGGGU-CGCA---UUGAUCAA-GAAG-GAUGC-ACCCCC---AGG-GCGAGGCUUGCCAUU-----GCACUC-CGG-CU--UGCUGAA---------CCUUGCGAUUCCCCCAAAC-GUGG---GGAACUCG-GGCGUAUUAUUUAUGGUAG---CGGAGA-UCUGCGUU--CGCGCUAUCUCCUA
X75936.1/1034-1195   AUACUUACCUGGCGCA-GGGGU-AGCA---UUGAUCAA-GAAG-GAUGC-ACCCCC---AGG-ACGAGGCUUGCUAUU-----GCACAC-CGG-CU--CGCUGAA---------GCUUGCGAUUCCCUCAAAC-GUAG---GGAACUCG-GGCGUAUUAUUUAUGGUAG---CGGGGA-UCUGCGUU--CGCGCUAUCCCCUU
X53544.1/117-281     AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAGUUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-UGCGCGUAAUUUUUGGUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCCGAC
X53543.1/383-547     AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAGUUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-UGCGUGUAAUUUUUGGUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCCGAC
X53544.1/1653-1817   AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAGUUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-UGCGUGUAAUUUUUGGUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCCGAC
X01725.1/69-233      AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAGUUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-UGCGUGUAAUUUUUGUUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCCGAC
X53541.1/1195-1359   AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAGUUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-UGCGUGUAAUUUUUGUUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCCGAC
X53542.1/2592-2756   AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAGUUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-UGCGUGUAAUUUUUGUUAG---CCGGGA-AUGGCGUU--CGCGCCGUCCCGAC
J01156.1/9-172       AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAGUUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-UGCGUGUAAUUUUUGGUAG--CCGGGAA--UGGCGUU--CGCGCCG-UCCCGA
X04257.1/1-164       AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAGUUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-UGCGUGUAAUUUUUGGUAG--CCGGGAA--UGGCGUU--CGCGCCG-UCCCGA
K00787.1/2-165       AUACUUACCUGGCGUA-GAGGUUAACC---GUGAUCAC-GAAG-GCGGU-UCCUCCG--GAG-UGAGGCUUGGCCAUU-----GCACCU-CGG-CU-GAGUUGAC---------CUCUGCGAUUAUUCCUAAU-GUGA--AUA-ACUCG-UGCGUGUAAUUUUUGGUAG--CCGGGAA--UGGCGUU--CGCGCCG-UCCCGA
AJ243001.2/347-509   AUACUUACCUGGCACA-GGGGA-UACC---ACGAUCAC-CAAG-GUGGU-UCCCCC---AAG-ACGAGGCUCACCAUU-----GCACUC-CGG-UG-GCGCUGACC--------CUUG-CAAUGACCCCAAAU-GUGG--GUU-ACUCG-GGUGUGUAAUUUCUGUUAG--CUGGGG--ACUGCGUU--CGCGCUUUCCCCUU
AY198212.1/1-163     AUACUUACCUGGCACA-GGGGA-UACC---ACGAUCAC-CAAG-GUGGU-UCCCCC---AAG-ACGAGGCUCACCAUU-----GCACUC-CGG-UG-GCGCUGACC--------CUUG-CGAUGACCCCAAAU-GUGG--GUU-ACUCG-GGUGUGUAAUUUCUGUUAG--CUGGGG--ACUGCGUU--CGCGCUUUCCCCUU
AY198211.1/1-163     AUACUUACCUGGCACA-GGGGA-UACC---ACGAUCAC-CAAG-GUGGU-UCCCCC---AAG-ACGAGGCUCACCAUU-----GCACUC-CGG-UG-GCGCUGACC--------CUUG-CGAGGACCCCAAAU-GUGG--GUU-ACUCG-GGUGUGUAAUUUCUGUUAG--CUGGGG--ACUGCGUU--CGCGCUUUCCCCUU
AY198213.1/1-163     AUACUUACCUGGCACA-GGGAA-UACC---ACGAUCAC-UAAG-GUGGU-UCCCCCA--AGG-CGAGGCUCA-CCAUU-----GCACCU-CGG--UGGCGCUGAC---------CCUUGCGAUGACCCCAAAU-GUGG--GUU-ACUCG-GGUGUGUAAUUUCUGUUAG--CUGGGG--ACUGCGUU--CGCGCUUUCCCCUU
AY198214.1/1-163     AUACUUACCUGGCACA-GGGGA-UACC---ACGAUCAC-UAAG-GUGGU-UCCCCCA--AGG-CGAGGCCCC-CCAUU-----GCACUU-CGG-UG-GUGUUGAC---------CCUUGCGAUGAUCCCAAAU-GUGG--AUU-ACUCG-GGUGUGUAAUUUUUGGUAG--CUGGGG--ACUGCGUU--CGCGCUAUCCCCUU
M73768.1/361-517     AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-CAAG-GCUCC-GACCCCA--GGU-GGAGGCUCA-GCAUU-----GCACUC-CGC--U-GUGUUGAA---------GCCUGCGACGGACUCUAA--UCGG--GUUCGCUCG-GGUGCAUAGUUUUUGCCAG--UGGGGA-----GCCUU--CGGGC--GUCCCUU
L25919.1/1-159       AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-GAAU-GCUCU-GACCCCG--GGU-GGAGGCUCA-CCAUU-----GCACUU-CGG--U-GGGUUGAA---------ACUUGCGACGAACCCUAA--UUGG--GUGCGCUCG-GACGCGUAGUUUUUGUCAG--UGGGGA----GGUCUU--CGGAUCA-UCCCUU
L25914.1/1-159       AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-GAAU-GCUCU-GACCCCG--GGU-GGAGGCUCA-CCAUU-----GCACUU-CGG--U-GGGUUGAA---------ACUCGCGACGAACCCUAA--UUGG--GCUCGCUCG-GACGCGUAGUUUUUGUCAG--UGGGGA----GGUCUU--CGGAUCA-UCCCUU
L25921.1/1-159       AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-GAAU-GCUCU-GACCCCG--GGU-GGAGGCUCA-CCAUU-----GCACUU-CGG--U-GGGUUGAA---------ACUCGCGACGAACCCUAA--UUGG--GUGCGCUCG-GGCGUGUAGUUUUUGUCAG--UGGGGA----GGUCUU--CGGAUCA-UCCCUU
L25916.1/1-159       AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-GAAU-GCUCU-GACCCCG--GGU-GGAGGCUCA-CCAUU-----GCACUU-CGG--U-GGGUUGAA---------ACUCGCGACGAACCCUAA--UUGG--GUGCGCUCG-GGCGUGUAGUUUUUGUCAG--UGGGGA---GGUCUCA--C-AGUCA-UCCCUU
L25915.1/1-159       AAACUUACCUGGCGCC-GGGUU-CAGG---GUGAUCAG-GAAU-GCUCU-GACCCCG--GGU-GGAGGCUCA-CCAUU-----GCACUU-CGG--U-GGGUUGAA---------ACUCGCGACGAACCCUAA--UUGG--GUGCGCUCG-GGCGUGUAGUUUUUGUCAG--UGGGGA---GGUCUCA--C-AGUCC-UCCCUU
L25917.1/1-158       AAACUUACUUGGCGCC-GGGAC-CAGG---GUGAUCAC-GAAU-GCCCU-GGCCCCA--GGU-GGAGGCUCG-CCAUU-----GCACUC-CGG--C-GUGUUGAA---------GCCUGCGACGAUCCCUAA--UUGG--GUGCGCUCG-GACGCGUAGUUUUUGUCAG--UGGGGA----GGUCUU--CGGAUCA-UCCUU-
DQ092354.1/1778-1949 AUACUUACCUGACGGU-GAAGC-AAAC---CUGGUCAA-CAUG-GGGCU-UCUUCC---AGGGUGAGGCUUUUGCAUU-----GCACUU-CGCCUG-G-GCUGACUCUGGGUUGACUG-CGAUUACCGCUAAC-GUCG--GUA-ACUCG-ACCGUACACUUUCUGGCUG--UGGGGG--CCUGCGUU--GGCGCUCGCCCCUU
DQ058356.1/1-168     AUGUCUUCGUGGCGGG-GGAGA-GACGCUGUUGGUCCU-GAUAAAGUGU-UUUUCUUG-GGG-GAGGGUUUUUACUUU-----GUGUUU-GGGAUG-UGUUUGCU---------CCCG-CGAUUUCCCCGA---AUGA--GAAAACUCG-GCUGCAUAACUUGUGGUAG--UGGGGG--ACUGCUUU--UGCGCUUUUCUGUC
L22246.1/3195-3356   AGACUUAUUUGGUUGG-GAGGA-UUUC---GUAAUCAG--AAG-GCGGG-ACCUCCA--UGG-CGAGGCUUGGUCAUU-----GCACUUUCGA-CC-AGGCUGAC---------CAGUGUGGCAGACCCGAG--UUGGGAUUGG--CCA-ACAGCAUAAUUUUUGCGUU---UGGGGA--CAGCGUU--CGCGCUU-CCCCGC
L22246.1/2071-2235   AAACUAACCUGGCUGG-GGGGCAUCUC---GCGAUCAU-GAAG-GCGGG-ACCUCCA--UGG-UGAGGUCUGGUCAUU-----GCACUUCCGA-CC-AGGCUGAC---------CUGUGUGGCAGUCCCGAG--UUGGGAUUGG--CCA-ACAGCAUAAUUUUUGCGUU----UGGGG-ACAGCGUU--CGCGCUUCCCCGCC
L22246.1/5535-5699   AAACUAACCUGGCUGG-GAGGCAUCUC---GCGAUCAU-GAAG-GCGGG-ACCUCCA--UGG-CGAGGUUUGGCCAUU-----GCACUUUCGG-CC-AGGCUGAC---------CCGUGUGGCAGUCCCGAG--UUGGGAUUGG--CCA-ACAGCAUAAUUUUUGCGUU----UGGGG-ACAGCGUU--CGCGCUUCCCCGCC
L22246.1/4551-4714   AAACUUACCUGGCUGG-GAGGC-UUUC---GUGAUCAU-GAAG-GCGGA-ACCUCCA--UGG-UGAGGCUUGGUCAUU-----GCACUUUCGA-CC-AGGCUGAC---------CCGUGUGGCAGUCCCGAG--UUGGGAUUGG--CCA-ACAGCAUAAUUUUUGCGUU----UGGGG-ACAGCGUU--CGCGCUUCCCCGCC
X51371.1/181-345     AAACUUACCUGGCUGG-GGGUUAUUUC---GCGAUCAC-AAAG-GCGGA-AUCCCCA--UGG-UUAGGCCUACCCAUU-----GCACUUUUGGUGC-GGGCUGAC---------CUGUGUGGCAGUCUCGAGU-UGAG--AUU-CGCCA-ACAGCUUAAUUUUUGCGUA--UCGGGG---CUGCGUG--CGCGCGG-CCCUGA
X70869.1/1-161       AUACUUACCUGGCCCG-CUUCU-CGAG---GUGGUCAC-CAUG-GCCUC-GGUUGU---GUG-GUCGGUCUUCACCUU-----GCACUU-UGU-GA-GGGCCUUC---------CGCA-GUCGGCCCUUCG-----GG--UGU-CCGGC-AGGGCUAAAUUUUUGUUAG--GCUGAGGACCCGCGCUA-UGCGCGGCCUCGGC
X06880.1/1-162       AUACUUACCUGUCCGG-CCUGC-GACC---UCGAGCAA-GAAG-GGGGU-CUAGGUA--GUG-CUUGUACCUCGCCUU-----GUACUA-UGCUUG-GGGUA--G---------CGCUGUGUGCGGGGCAA---GUCC---UCGUUACA-ACGGAAUAAUUUCUGGCAG--GCCGUUG-CACGCGCU--UGCGCGUCCUCGGC
M29062.1/238-387     UUACUUACCUGGCAUG-AGUUU--CUG---CAGCACAA-GAAU-UGUGG-AGACUCA--GUU-AUUUGUCUUGGCAUU-----GCACUG-AGCCCU-G-ACGAAU---------AACUGUGGACUGGCUAA----GGU--CAG-CUCCG-GAUGCAUCAUUUUUGAGUU--CGU-----CCCUCAUU----UGGGGC-----A
X63783.1/596-756     UAAAUUACAAUGUUGU-AGUUA-GCUA---UAUAUCAA-AAAA-UAUAG-CAACUA---AGG--UGGAGCAAGUCAUU-----GUACUAAAGAUGU-UUGUAAUA---------CCUUG--AUGUUCCCGC----UGG--GAGCAAUA--ACAACAAAAUUUCUGAUUG--GAAAUAG--UCAUUAAACUAACUGGCUAUUUC
X63783.1/2024-2186   UUACUUACCUGGCUGG-AGUUU-GCUA---UCGAUCAU-GAAG-GGUAG-CGGCUU---AGG-GUGGAGCAGGUCAUU-----GCACAAAAGAUGU-CUGUAAUA---------CCUUAUUGUUC-CCCGU---GCGG---GGAACCGAAACAGCACAAUUUCUGCUAG--GGGAGAC-GUGCACUU--A-GUGCUGUCUCCG
X58845.1/1-161       --ACUUACCUGGCUGG-AGUUU-GCUA---UCGAUCAU-GAAG-GGUAG-CGGCUU---AGG-GUGGAGCAGGUCAUU-----GCACAAAAGAUGU-CUGUAAUA---------CCUUAUUGUUC-CCCGU---GCGG---GGAACCGAAACAGCACAAUUUCUGCUAG--GGGAGAC-GUGCACUU--A-GUGCUGUCUCCG
X63783.1/1394-1556   UUACUUACCUGGCUGG-AGUUA-GCUA---UCGAUCAU-GAAG-GGUAG-CGGCUU---AGG-GUGGAGCAGGUCAUU-----GCACAAAAGAUGU-CUGUAAUA---------CCUUAUUGUUC-CCCGU---GCGG---GGAACCGAAACAGCACAAUUUCUGCUAG--GGGAGAC-GUGCACUU--A-GUGCUGUCUCCG
X13842.1/1-150       ------ACCUGGCCGG-GGGAA-GUCG---GUGAUCAA-GACG-GCCGA-GUCCCU---AGU-UGGGGAACCUCUCCU-----GCACUU-GAGAGG-G-GCUCCU---------UCUA-UGAUUG-CCUUC-----GG--GUA-ACUCA-ACGGCAUAAUUUGUGAUAG--CGUGGG---GUGCGCUU-GUCGCGC-CCUGCA
X13841.1/396-551     AUACAUACCUGGCCGG-GGGAA-GUCG---GUGAUCAA-GACG-GCCGA-GUCCCU---AGU-UGGGGUACCUCUCCU-----GCACUU-GAGAGG-G-GCCCCU---------UCUA-UGAUUG-CCUUC-----GG--GUA-ACUCA-ACGGCAUAAUUUGUGAUAG--CGUGGG---GUGCGCUU-GUCGCGC-CCUGCA
X69329.1/1-160       AUACUUACCUGGACGG-GGUCG-ACGG---GCGAUCAA-GAAG-GCCCG-UGGCU----GGG-UCAAUGGCUCACAUU-----GCACUU-GGUGGGUG-CGUUGG---------CCCA-CCAUCUCCCCAA---GUGG---GAGAGUGG-ACGUCAUAAUUUGUGCUAG---AGGGGG-UACGCGUU--CGCGCGGCCCCUGC
S72336.1/2-161       AUACUUACCUGGACGG-GGUCG-ACGG---GCGAUCAA-GAAG-GCCCG-UGGCU----GGG-UCAAUGGCUCACAUU-----GCACUU-GGUGGGUG-CGUUGG---------CCCA-CCAUCUCCCCAA---GUGG---GAGAGUGG-ACGUCAUAAUUUGUGCUAG---AGGGGG-UACGCGUU--CGCGCGGCCCCUGC
X69334.1/1-160       AUACUUACCUGGACGG-GGUCG-ACGA---GCGAUCAA-GAAG-GCUCG-UGGCCU---GGG-UCAGUGGUCCACAUU-----GCACUU-GGU-GG-AUGCCUGG---------CCCA-CCAUCUCCCCAA---GUGG---GAGAGUGG-AUGUCAUAAUUUGUGGUAG---AGGGGG-UACGCGUU--CGCGCGGCCCCUGC
X69333.1/1-157       ----UUACCUGGACGG-GGUCG-ACGA---GCGAUCAA-GAAG-GCUCG-UGGCCU---AGG-UUAGUGGCCCACAUU-----GCACUU-GGUGGGUG-CGCUGG---------CCUA-UCAUCUCCCCAA---GUGG---GAGAGUGA-ACGUCAUAAUUUGUGGUAG---AGGGGG-UACGCGUU--CGCGCGGCCCCUGC
X69328.1/1-158       --ACUUACCUGGACGG-GGUCG-ACGG---CCGAUCAA-GAAG-GGUCG-UGGCCU---AGA--UCAAUGGUCACAUU-----GCACCU-GGUGAG-CGCGUUGG---------CCUA-CCAUCUCCCCAA---GUGG---GAGAGUGG-ACGUCGUAAUUUGUGGUAG---AGGGGG-UACGCGUU--CGCGCGGCCCCUAC
AY222070.1/1-157     AUACUUACCUGGACGG-GGUCG-UUGG---GUGAUCAU-GAAG-AUCCG-UGGCCUA--GCG-UGGUGGC---UUCCU-----GCACUU-GAGGU----GGCUAA---------CGCAAAGGU-CACCCCAA--GUGG---GAGAUCCU-GCGUCAUUAUUUGUUGCCU---UGGGGG-CCUGCGUU--CGCGCAGCCCCCAC
X15928.1/1-160       AUACUUACCUGGAUGG-GGUCA-AUGG---GUGAUCAU-GAAG-GCCCA-UGGCU----AGG-CAAGUGACUUCCAUU-----GCACUU-AGGAGG-GGUGCUUG---------CCUA-AGGUCUACCCAA---GUGG--UGG-AACCU-ACAUCAUAAUUUGUUGCUG--UGGGGG--CCUGCGUU--CGCGCGGCCCUCUU
X15927.1/1-160       AUACUUACCUGGAUGG-GGUCA-AUGG---GUGAUCAA-GAAG-GCCCA-UGGCU----AGG-CAAGUGACCUCCAUU-----GCACUU-AGGAGG-GGUGCUAG---------CCUA-AGGUCUACCCAA---GUGG--UGG-AGCCU-ACAUCAUAAUUUGUUGCUG--UGGGGG--CCUGUGUU--CGCGCGGCCCCCUC
X15926.1/1-161       AUACUUACCUGGAUGG-GGUCG-AUGG---GUGAUCAU-GAAG-GCCCA-UGGCU----AGG-AUUGUGACCUCCAUU-----GCACUU-AGGAGG-GGUGCUUU---------CCUA-AGGUCUACCCAA---GUGG--UGG-AGCCU-ACAUCAUAAUUUGUUGCCU--GAGGGGG-CCUGCGUU--CGCGCGGCCCCCAC
X06809.1/232-392     AUACUUACCUGGACGG-GGUCA-AUGG---AUGAUCAA-GAAG-GUCCA-UGGCCU---AGG-GAAGUAACCUCCAUU-----GCACUG-AGGAGG-GGUGCCUU---------UCUA-AGGUCUGUCCAA---GUGA--CAG-AGCCU-ACGUCAUAAUUUGUGGUAG--UGGGGG--CCUGCGUU--CGCGCGGCCCCUUU
J03563.1/352-512     AUACUUACCUGGACGG-GGUCA-AUGG---AUGAUCUA-UAAG-GUCCA-UGGCCU---AGG-GAAGUGACCUUCAUU-----GCACUC-AGAAGG-GGUGCUAC---------UCUA-AGGUCUGUCCAA---GUGA--UGG-AGCCU-ACGUCAUAAUUUGUGGUAG--UGGGGG--CCUGCGUU--CGCGCGGCCCCUUA
#=GC SS_cons         :::::::::::((((<.<<<<<.-<<<...<<______.____.>>>>>.>>>>>>,..<<<.------<<<-<<___.....______._>>-->.>->-----.........>>>,,<<<-<<-<<____..__>>..->>--->>>.,))))--------------..-<<<<<-.-<<<<<__..__>>>>>->>>>>:
#=GC RF              AUACUUACCUGGccgg.GGgga.aacg...gcGAUCAa.GAAG.gccgu.uccCCca..gGg.ugaGGucccucCAUU.....GCACUu.cGgagg.gugcugac.........cCcuGcGgUuccCCCaAA..GUGG..ugaaAccCg.AcggCAUAAUUUgUGgUAG..ucgGGGg.accGcgUU..cGcgCggcCCCcgc
//
# STOCKHOLM 1.0

#=GF AC   RF00004
#=GF ID   U2
#=GF DE   U2 spliceosomal RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Mifsud W; 0000-0002-9805-6461
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   The uRNA database, PMID:9016512; Griffiths-Jones SR; PMID:18390578
#=GF SS   Published; PMID:2339054; Griffiths-Jones SR
#=GF GA   46.00
#=GF TC   46.00
#=GF NC   45.90
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00006
#=GF DR   SO; 0000392; U2_snRNA;
#=GF DR   GO; 0000348; mRNA branch site recognition;
#=GF DR   GO; 0045131; pre-mRNA branch point binding;
#=GF DR   GO; 0005686; U2 snRNP;
#=GF RN   [1]
#=GF RM   9016512
#=GF RT   The uRNA database.
#=GF RA   Zwieb C
#=GF RL   Nucleic Acids Res 1997;25:102-103.
#=GF RN   [2]
#=GF RM   11424937
#=GF RT   A conserved pseudouridine modification in eukaryotic U2 snRNA induces a
#=GF RT   change in branch-site architecture.
#=GF RA   Newby MI, Greenbaum NL
#=GF RL   RNA 2001;7:833-845.
#=GF RN   [3]
#=GF RM   11350032
#=GF RT   Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged
#=GF RT   adenosines.
#=GF RA   Berglund JA, Rosbash M, Schultz SC
#=GF RL   RNA 2001;7:682-691.
#=GF RN   [4]
#=GF RM   2339054
#=GF RT   The spliceosomal snRNAs of Caenorhabditis elegans.
#=GF RA   Thomas J, Lea K, Zucker-Aprison E, Blumenthal T
#=GF RL   Nucleic Acids Res 1990;18:2633-2642.
#=GF CC   U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved
#=GF CC   in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area
#=GF CC   lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence
#=GF CC   (BPS) of the intron results the bulging out of an unpaired adenosine, on
#=GF CC   the BPS, which initiates a nucleophilic attack at the intronic 5' splice
#=GF CC   site, thus starting the first of two transesterification reactions that
#=GF CC   mediate splicing.
#=GF WK   U2_spliceosomal_RNA
#=GF SQ   208


AALT01209640.1/567-377         AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAU--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCAGAGGACAA------------UAUAUUAAA------UGGAUUUUUGGAAUUA------GGAG-UUGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------UUCCAGG--AA--------CGGUGCACCCCCU
AAFR03033875.1/20528-20718     AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA------------UAUAUUAAA------UGGAUUUUUGAAACAG------GGAG-UCGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------UUCCAGG--AA--------CGGUGCACUUCCC
AAIY01044029.1/787-597         AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAGAUCUGAUA--UGUCCUCU-AUCUGAGGACAA------------CAUAUUAAA------CGUAUUUUUGGAAAUA------GGAG-UUGGACCA-------GGAGC---U-----U----G-CUCCA-------UCCA-CUCCAC-GCAUCAG---CCUGGUAUUGCAGUAU------UUCCAGG--AA--------UGGUGCAGCCCCU
AAZO01007389.1/15370-15178     AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAAUAUCUGAUA--CGACCCUC-AUUGAGGGUCCAG-----------AAUAUUAAA------CUGAUUUUUGGAAACG------GAUG-GAGUGUUA-------GGGGC---U-----U----G-CUCCA-------CCUC-CGUCAC-GGGUUGG---CUCGGCAUUGCAGUAC------AGCCGAG--AU--------CGGCCCACCCUUA
AAYZ01695118.1/310-500         AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA------------UAUAUUAAA------UGGAUUUUUGGACGCU------GGAG-UUGGACUA-------GGAGC---U-----U----G-CUCCA-------UCCA-CUCCGC-GCAUCGA---CCUGGUAUUGCAGUAC------UUCCAGG--AC--------CGGUGCACCCCGU
AAHX01044404.1/26102-26292     AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUAUUAUCAGUUUAAUAUCUGAUA--UGUCCUCU-AUCUGAGGACAA------------UAUAUUAAA------UGAAUUUUUGGUACUA------GGAG-UUGGAAUA-------GGAGC---U-----U----G-CUCCA-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAU------UUCCAGG--AA--------UGGUGCACUCCUC
AACN010750078.1/657-848        AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA------------UAUAUUAAA------UGGAUUUUUGGAGCAG------GGAGAUGGAAUAG-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCGC-GCAUCGA---CCUGGUAUUGCAGUAC------CUCCAGG--AA--------CGGUGCACCCCCU
ABAV01019481.1/5988-6180       AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGCUUAAUAUCUGAUA--CGCUGCUC-AUUGAGUAGCUCA-----------UAUAUUAAA------CUGAUUUUUGGAAACU------GGCU-GUGGAAUAA------GCGGC---U-----U----G-CUGCG-------UCCC-AGCCAC-GGGUUGU---CUCGGUAUUGCACUAC------CUCCGAG--UA--------CGGCCCCCUUCCC
AAZX01018356.1/721-913         AUCGCU-UCU----CGGCC--UAU-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUGAUAUCUGAUA--CGCUCCUC-AUUGAGGAGCCAG-----------AAUAUCGAA------CUGAUUUUUGGAAUAU------GGCG-GAGUGUCU-------GGGGC---U-----U----G-CUCCG-------ACUC-CGCCAC-GGGUCGA---CCUUGCAUUGCAGUAC------CGCAAGG--AA--------CGGCCCACACAAU
AY765362.1/650-458             AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAAUAUCUGAUA--CGUUCCCU-ACAUGGGAACUAC-----------GAUAUUAAA------CUGAUUUUUGGUCAGA------GGUG-AGAUGUCA-------GGGGC---U-----U----G-CUCCG-------CUCU-CGCCAC-GGGUUGG---CCUGGUAUUGCAGUAC------CUCCAGG--AA--------CGGCCCACCUUAU
BX927129.10/97355-97165        AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUGCCCU-ACCCGGGCACCA------------UAUAUUAAA------UUGAUUUUUGGAACAG------GGAG-AUGGAAUA-------GGGGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCCGGUAUUGCAGUAC------CUCCGGG--AA--------CGGUGCACCCCCU
AAFC03011281.1/26348-26158     AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-GUCCGAGGACAG------------UAUAUUAAA------UGGAUUUUUGGAGCAG------GGAG-UUGGAAUG-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------UUCCAGG--AA--------CGGUGCACCAAAA
AAVX01416582.1/429-619         AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCCCU-AUCUGGGGACCA------------UAUAUUAAA------UUGAUUUUUGGAGCAG------GGAG-AUGGAAUA-------GGGGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAU------CUCCAGG--CA--------CGGUGCACCUCCC
X00093.1/360-550               AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCCCU-AUCUGGGGACCA------------UAUAUUAAA------UGGAUUUUUGGAACAG------GGAG-AUGGAAGA-------AGAGC---U-----U----G-CUCUG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------CUCCAGG--AC--------CGGUGCACUUCUC
CAAE01009132.1/1078-888        AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUCCCCG-AAAAGGGGACUU------------CAUAUUAAA------CCCAUUUUUGCACUCU------GGAG-UUGUAAUG-------GGAGC---U-----U----G-CUCCA-------UUGA-CUCCAC-GCAUUAG---CCCAGUAUUGCAGUGC------CUCUGGG--AG--------UAGUGCACCUCCU
AF095839.1/1586-1389           AUACCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGCUUAAUUUCUGAUA--UAUCGGAC-ACUGUCCGAUUGA-----------GAAAUUAAA------CUAAUUUUUUGAUGGG------GGCA-AGGGGUUCCCCU---CGUGC---U-----U----G-CGCGA-----GUCCCU-UGCCAC-GGGUUGC---CCUGCUAUUGCACUAC------CGGCAGG--CG--------CGGCCCAACCCAC
AANH01015084.1/457-647         AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUCCUCU-AUAAGAGGACUA------------CAUAUUAAG------CCGAUUUUUAGCUCUG------GGAG-AUGAAAAA-------GGGGC---U-----U----G-CUCCG-------UUCA-CUCCAA-GCAUCGA---CCCGGUAUUGCAGCAC------CUCCGGG--AA--------CGGUGCACCCUUC
AC004138.3/33098-33293         AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUCGGCCCACAC------------GAUAUUAAC------UCUAUUUUUUAAGGGA------GAAA-GCCCGUUAAG-----AUAGC---U-----U----G-CUAUC------UGGGC-UUUCAC-GAGUCGC---CCAUGCGUUGCACUAC------UGCAUGG-GCC--------UGGCUCAACCCGC
AAJJ01003841.1/8097-7907       AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAAUAUCUGAUA--CGCUCCGC-AU-GCGGAGCCAG-----------UAUAUUAAA------CUGAUUUUUGGAACAU------GAUG-AAGG-CUA-------GGAGC---U-----U----G-CUCCA-------CCUU-CGUCAC-GGGUUGG---CCCGGCAUUGCAGUAC------AGUCGGG--AU--------CGGCCCACCUAAU
AACY020405974.1/944-1135       AUCGCU-UCU----CGGCC--UAA-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGGUA--CGCCGGGC-AUAGCCUGGCUCA-----------UAUAUUAAU------CUGAUUUUUAGCAUUC------GAUC-AAGGGAGC-------GAGGU---U-----U----A-CCUCA-------CCCU-GAUCAC-GGGUUGC---CUCGGCAUUGCACUAC------AGCCGAG--UG--------CGGCCCACUUUUA
AM465080.2/15550-15355         AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUGGGAC-AUCGUCCCACAU------------GAUAUUAAA------UUAAUUUUUUAAGGGG------GAGG-GUCCACCACA-----AUAGC---U-----U----G-CUAUU------GGGAU-CCUCGA-GCGUCGC---CCUAGCGUUGCACUAC------UGCUUGG-GCC--------UGGCGCACCCCUC
M72891.1/1-196                 AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUGAACC-AUCGGUUCACAC------------GAUAUUAAC------UCAAUUUUUUAAGGGG------GAAG-ACCCAUCAAA-----GUAGC---U-----U----G-CUACU------UGGGU-CUUCAC-GCGUCGC---CUGGGCGUUGCACUAC------AGCCCAG-GCC--------UGGCACACCCCAC
BAAB01070452.1/1509-1701       AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUUUCAGCUUAAUAUCUGAAA--GUUCCCUC-AUUGAGGGACCAG-----------UAUAUUAAA------CUGAUUUUUGUAAAAC------GACG-AGAUGUUC-------GGGGC---U-----C----G-CUCCA-------CUCU-CGUCAC-GGGUCGG---CCCGGCAUUGCAGUGC------CGCCGGG--AU--------CGGCCCUCAGAUU
X04243.1/69-264                AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--AGUCCUCC-AUUGGAGGACAACA----------AAUGUUAAA------CUGAUUUUUGGAAUCA------GACG-GAGUGCUA-------GGAGC---U-----U----G-CUCCG-------CCUC-UGUCGC-GGGUUGG---CCCGGUAUUGCAGUAC------CCCCGGGAUUU--------CGGCCCAACUUAA
AAPY01817437.1/27757-27567     AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUCCUCU-AUCUGAGGAUAA------------UGUAUUAAA------UGGAUUUUUGGAGUUU------GGAG-AUGGAGUA-------GGAGC---U-----U----G-CUCUG-------UCCA-CUCCAC-GCAUUGA---CCUGGUAUUGCAGUAU------UUCCAGG--AA--------CGGUGCACCCCUU
AANG01476605.1/2311-2501       AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCUUCU-AUCGGAGGACAA------------UAUAUUAAA------UGGAUUUUUAGAGCUA------GGAG-AUGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------UUCCGGG--AA--------CGGUGUCUUCCUC
AANN01265286.1/964-773         AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAU------------UAUAUUAAA------UGGAUUUUUGGAGCAG------GGAG-UCGGAAUA-------GGGGC---U-----U----G-CUCCG-------UCCG-CUCCAC-GCAUCGA---CCUGGUAUUGCACGGGG-----UUCCAGG--AA--------CGGUGCACCCCCA
AASG02001826.1/33924-33729     AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUGAGCU-AUUAGCUCACAU------------GAUAUUAAA------UUAAUUUUUUUUGGGA------GAGA-GCUCGUAACA-----GUAGC---U-----U----G-CUACU------GGAGU-UCUCGA-GCGUCGC---CUGUGCGUUGCACUAC------UGCACUG-GCU--------AGGCGCAUCCCAC
AAEU02000279.1/6988-6794       AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GUUCCUCC-AUUGGAGGACAACA----------AAUGUUAAA------CUGAUUUUUGGGAUCA------GACG-GAGUGCUA-------GGGGC---U-----U----G-CUCCA-------CCUC-UGUCGC-GGGUUGC---CCCGGUAUUGCAGUAC------CGCCGGGAUUU--------CGGCCCAACUGAA
AC189506.1/7126-6931           AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUGGUCC-AUCGGACCACAC------------GAUAUUAAC------UCUAUUUUUCAAGGGU------GAAA-GCCCAAUAAG-----AUAGC---U-----U----G-CUAUC------UGGGC-UUUCGC-GAGUUGU---CCAAGCGUUGCACUAC------UGCAUGG-ACC--------UGGCUCAACCCAC
X69327.1/1-196                 AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUGUGCCCACAAC-----------GAUAUUAAA------UUUAUUUUUUAUGGGG------GAGG-GCCCACCACA-----GUAGC---U-----U----G-CUGCU------GGGGC-CCUUGC-GUGUCGC---CCAGGCGUUGCACUGC------UGCCUGG--GC--------CGGCGCACCCCAC
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AAPU01010615.1/193731-193537   AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GUUUCUCC-AUUGGAGAACAACA----------AAUGUUAAA------CUGAUUUUUGGAAAUA------GACG-GAGUGUUA-------GGGGC---U-----U----G-CUCCA-------CCUC-UGUCGC-GGGUUGG---CCCGGUAUUGCAGUAC------CGCCGGG-AUU--------CGGCCCAACUAAG
AADA01287270.1/15999-15809     AUCACU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUCAUCAGUUUAGUAUCUGAUA--UGUCCUCU-AUCUGAGGACAA------------UAUAUUAAA------UAGAUUUUUGGAGCAG------GGAG-AUGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCAU-GCAUCGA---CCUGGUAUUGCAGUAC------CUCCAGG--AA--------CGGUGCACUCGCU
AAPT01020503.1/50330-50135     AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GAUCCUCC-AUCGGAGGACAACA----------AAUGUUAAA------CUGAUUUUUGGAAAUA------GACG-GAGUGCUA-------GGAGC---U-----U----G-CUCCA-------CCUC-UGUCGC-GGGUUGG---CCUGGCAUUGCAGUAC------CGCCAGGAUUU--------CGGCCCAACUAAU
AAAB01008933.1/737524-737331   AUCGCU-UCU----CGGCC--UAA-A-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GCUCUCCC-AUUGGGAGACGACA----------AAUGUUAAA------CUGAUUUUUGGAAAGA------GGCG-GAUCGUAC-------GGGGC---U-----U----G-CUCCA-------CAUC-CGCCAC-GGGUUGG---CCCGGUAUUGCAGUAC------CGCCGGG--AU--------CGGCCCAACUAAU
ABDC01189504.1/6312-6122       AUUGCC-UCU----CGGCU--GUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA------------UAUAUUAAA------UGGAUUUUUGGAGCAG------GGAG-AUGGAAUA-------GGAGC---U-----U----G-CUCCA-------CCCA-CUCCAU-GCAUCGA---CCUGGUAUUGCAGUAC------UUUCAGG--GA--------CGGUGCACCCCUC
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AANI01016115.1/56636-56831     AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GUUUCUCC-AUUGGAGAACAACA----------AAUGUUAAA------CUGAUUUUUGGAAUCA------GACG-GAGUGCUA-------GGGGC---U-----U----G-CUCCA-------CCUC-UGUCAC-GGGUUGG---CCCGGCAUUGCAGUAU------CGCCGGGACUU--------CGGCCCAAUUCAA
AC157776.1/115175-114979       AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUGGACC-AUGUGUUCACUUU-----------GAUAUUAAA------UUUAUUUUUUGUGGGG------GAGG-GCUCACUACA-----GUAGC---U-----U----G-CUACU------GGGGU-CCUCAC-GUGUCGC---UUGGGCGUUGCACUAU------AGUCCAA-GCC--------UGGCGCACCCCAA
AAPP01015704.1/576899-577092   AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GUUCCUCC-AAUGGAGGACAAGC----------AAUGUUAAA------CAGAUUUUUGAUAUCA------GACG-GAGG-GUA-------GGGGC---U-----U----G-CUCCA-------CCUC-AGUCAC-GGGUCGU---CCCGGUAUUGCACUAC------CGCCGGG-AUU--------CGGCCCACAAAAU
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AAGE02006086.1/44202-44008     AUCGCU-UCU----CGGCC--UAA-A-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GCUCUCCC-AUAGGGAGACAACA----------AAUGUUAAA------CUGAUUUUUGGAAAAG------GGCG-GAACGGUCA------GGGGC---U-----U----G-CUCCA-------CUUC-CGCCAC-GGGUUGA---CCCGGUAUUGCAGUAC------CGCCGGG--AU--------CGGCCCACGUUAA
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AAQB01006449.1/663346-663151   AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GUUUCUCC-AUUGGAGAACAACA----------AAUGUUAAA------CUGAUUUUUGGAAUCA------GACG-AAGUGCUA-------GGGGC---U-----U----G-CUCCA-------CCUU-UGUCGC-GGGUUGG---CCCGGUUUUGCAGUAC------CUCCGGGAUUU--------CGGCCCACUUUAU
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AACT01003467.1/10053-10247     AUCGCU-UCU----CGGCUC-UUU-UGAGCUAAGAUCAA--GUGUAGUAUCUGUUCUUCUCAGUUUAAUACCUGGGA--CGGAAACG-AUUCGUUUCCUCUA----------UGUAUUAAU------CGGAUUUUUGAACAUG------GAGU-AUGGUGCU-------GGAGC---U-----U----G-CUCCA-------CCCU-GCUCAC-GGGUUGU---CCUGGUAUUGCAGUAC------CUCCAGG--CU--------CGGCCCACACCCC
AF106845.1/1870-2065           AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUGUGUCUACUUU-----------GAUAUUAAA------UUUAUUUUUCGUGGGG------GAGA-GUCCACCAUA-----GUGGC---U-----U----G-CCACU------AGGGC-CCUCAU-GUGUCGC---CUAGGCGUUGCACUAC------AGCCUUG--GC--------UGGUGCACCCCAU
ABBA01028418.1/3128-3319       AUCUCU-UCU----CGUCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCAGAGAACAAU-----------UAUAUUAGA------UAGAUUUUUGGAGCAG------GGAG-AUGAAAUA-------GGAGC---U-----U----G-CUCUG-------UCCA-CUCCAC-GCGUCGA---CCUGGUAUUGCAGUAC------CUCCAGG--AA--------UGGGGCUCCCUCU
X15930.1/1-195                 AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUUGGUCCACAC------------GAUAUUAAA------UUUAUUUCUUGAGGGG------AAGA-GUCCACCACA-----AUAGC---U-----U----G-CUAUU------CGGUC-UCUUGU-GUGUCGC---UUUUGCGUUGCACUAU------AGCAAUU--GC--------UGGCGCACCCCAC
AASR01035668.1/1184-988        AUCGCU-UCU----CGGCC--UUA-U-GGCUAUGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GUUCCUCC-AUUGGAGGACAACAA---------AUGUUAAAA------CUGAUUUUUGGAAUCA------GACG-GAGUGCUA-------GGAGC---U-----U----G-CUCCA-------CCUC-UGUCGC-GGGUUGG---CCCGGUAUUGCAGUAC------CGCCGGGAUUU--------CGGCCCAACUGAA
D25323.1/7242-7047             AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUGGGCU-AUGUGCCUACUUC-----------GAUAUUAAA------UUUAUUUUUUGUGGGG------AAGG-GUCCACCAUA-----GUGGC---U-----A----G-CCACU------GGGGC-CCUUGA-GCGUUGC---UCAGCCGUUGCACUGC------UGGCAGG--GC--------UGGCGCACCCCAA
AADE01000447.1/58660-58464     AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GUUUCUCC-AUUGGGAGAACAACA---------AAUGUUAAA------CUGAUUUUUGGAAUCA------GACG-GAGUGCUA-------GGGGC---U-----U----G-CUCCA-------CCUC-UGUCGC-GGGUUGG---CCCGGUAUUGCAGUAC------CGCCGGGAUUU--------CGGCCCAACUGAU
X55772.1/223-413               AUUCUC-UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCGCUGAAA---UCACCUC-ACUGAGGUGUUU------------CCGAUUAAU------CUUGUUUUUGGUUUGA------GUUG-GAAAGCCU-------CUGGC---U-----U----G-CUAUG------CUUUC-CGACAC-UGGUGUU---CUUGCUAUUGCACUAC------UGGCAAG--CG--------ACGCCGAAUCUUC
AP007151.1/1974779-1974972     CCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCC-AUAGGAACACAACA----------UUGAUUAAU------CUUAUUUUUGGUCUCC------GUGG-CAGGGCCCC------UGUGC---U-----U----G-CGCAU-----GCCUUG-CCACAC-AGUGUCA---UCGGGC-UUACACUAU-------CCCCGA--UA--------GACGCGAACUCCU
X54113.1/230-419               AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAU--GUGUAGUAUCUGUUCUUUUCAGAAUAAUAUCUGAAA--UGCUGCUC-AUCGAGCAGCAAG-----------UAUAUUAAU------CUGAUUUUUGGAUGAUC-----GGCC-AUGGAAUA-------GGGGC---U-----U----G-CC--G-------UCCU-GGCCAC-GGGUUGG---CCCGGU-UUGCACUAC------UGCCGGG--AU--------CGGCCACACUCCC
AATM01000136.1/58626-58436     AUUCUC-UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCGCUGAAA---UCACCCC-AUCGGGGUGUUU------------CCGAUUAUU------CUUGUUUUUGGGAAUC------GCCG-AGAGACCU-------AUGGC---U-----U----G-CUAUG------UCUCU-UGGCAC-CGGUGUC---CUUGCCGUUGCACUCC------UGGCAUG--CG--------ACGCCGAAAACUC
AAHF01000004.1/976953-976761   UCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCU-AA-GGAACACAACA----------UUGAUUAAU------CUCAUUUUUGGAUCUC------GUGG-CAAGGCCUC------UGUGC---U-----U----G-CGCAU-----GCCUUG-CCACAC-AGUGUCA---UUGGGC-UUACACUAC-------CCCCAA--UU--------GACGCGACCCUUU
CAAA01181619.1/3682-3492       AUUGCU-CGU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAAUUUAAUAUCUGAUA--CUUCCUCU-AUCUGAGGACAA------------UGUAUUAAA------UGGAUUUUUGGAAGUA------GGAG-UUGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-UUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------CUCCAGG--AA--------CGGUGCACCCCCU
X05084.1/1-193                 AUACCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUUAGUUUAAUAUCUGAUA--UGUGGGCC-AAUGGCCCACAC------------GAUAUUAAA------UUUAUUUCUUGAGGGG------AAGA-GGCCACCACA-----GUAGC---U-----U----G-CUAUU------GGGUC-UCUUAC-GUGUCGC---UCUUGCGUUGCACUAU------AGCAAUU--GC--------UGGCGCACCCCA-
ABAR01000024.1/421358-421550   UUAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCU-AA-GGAACACAACA----------UUGAUUAUU------CUCAUUUUUGGAUCGC------GCAC-UGAAGUCUC------UGUGC---U-----U----G-CACAU-----GCUUCG-GUGCAC-UGUGUC----CUUGGUCUUACACUAC------CACCAAG---U--------GACGCGAAUACUU
AAQA01000616.1/21523-21715     AUCGCU-UCU----CGGCC--UAU-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAAUCUCUGAUA--UGUGGUCA-AU-CGAUCACUUC-----------GAGAUUAUC------CUAUUUUUGAGACCAU------GGUG-GGUUUGAA-------GGGGC---U-----U----G-CUCCU-------CACC-UACCGC-GGGUCGA---CCCGGUAUUGCACCUAC-----CUCCGGG--AA--------CGGCCCAUUCACC
AY661656.1/2159-2358           AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUGGAUC-AUGUGUCCAUUUUGAU--------AUUAUAAAA------UUAAUUUUUAAUGGGG------GAAG-GCUCAUAAUA-----GUAGC---U-----U----G-CUACU------AAGGU-CUUCAA-GUGUCGC---UUGGGUAUUGCACUAU------UGCCUUA-GUC--------UGGCGCACCCCAA
ABAS01000032.1/96356-96164     UCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCU-AA-GGAACACAACA----------UUGAUUAUU------CUCAUUUUUGGAUCUC------GCAU-UGAGGUCUC------UGUGC---U-----U----G-CACAU-----GCCUCG-AUGCAU-UGUGUC----CUUGGUCUUACACUAC------CACCAAG---U--------GACGCGAACUACU
AAJN01000116.1/21716-21908     CCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCU-AA-GGAACACAACA----------UUGAUUAAU------CUCAUUUUUGGAUCUC------GUGG-CGGGUCCUC------UGUGC---U-----U----G-CGCAU-----GUCCUG-CCACAC-AGUGUCA---UCGGGC-UUACACUAC-------CCCCGA--UC--------GACGCGAACUCUU
ABDB01000030.1/249236-249428   CCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCU-AA-GGAACACAACA----------UUGAUUAAU------CUCAUUUUUGGAUCCC------GUGG-UGAGGCCUC------UGUGC---U-----U----G-CGCAU-----GCCUCG-CCACAC-AGUGUCA---UCGGGC-UUACACUAC-------CCCCGA--UU--------GACGCGAACCACC
CAAL01000198.1/59590-59777     AUACCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGAGUGAUAUCUGAUA--U--CUCCU-ACGAGGAG--AAU-----------GAUAUCACU------GCAAUUUUUAAAUGGG------GCUG-GGUUUACUU------GGGGC---U-----U----G-CCCCG-------GUCC-CAGCA--UAGUCGA---CCCUGACUUACACGAC------CUCGGGG--AA--------CGGCUAACCCGCU
AACD01000084.1/492354-492546   CCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCU-AA-GGAACACAACA----------UUGAUUAAU------CUUAUUUUUGGUCUGA------GCGG-CAGGACCUC------UGUGC---U-----U----G-CGCAU-----GUCCUG-CUGCAC-AGUGUCA---UCGGGC-UUACACUAC-------CCCCGA--UC--------GACGCGAACGCAA
AACM02000140.1/27654-27846     UUAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GGUCUCC-AA-GGAGACCAACA----------UUGAUUAUU------CCUAUUUUUGGAUUCC------GGGC-AAUUUCCUC------UGUGC---U-----U----G-CACAU-----GAUUUU-GCCCAC-UGUGUC----CCUAGUAUUACACUGC------CUCUAGG---U--------GACGCGAACGCGC
AAKD03000004.1/610702-610510   UCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCU-AA-GGAACACAACA----------UUGAUUAAU------CUCAUUUUUGGAUUCU------GUGGAGAGGCCUC-------UGUGC---U-----U----G-CGCAU------GCCUCACCACAC-AGUGUCA---UCGGGC-UUACACUAC-------UCCCGA--UU--------GACGCGAACCACC
AANU01167734.1/2229-2419       AUCACU-UCU----CGGCC--UUU-U-GGCUAAUAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGGUA--UGUCCUCU-AUCCGAGGACAA------------UAUAUUAAA------UGGAUUUUUGGAAAUA------AGAG-AUGGAAUA-------GGGGC---U-----U----G-CUCCG-------UCCA-CUCCAC-UCAUUGA---CCUGGUAUUGCAGUAC------UUCCAGA--AA--------CGGUGCACAAAAA
AAEE01000010.1/89978-89784     AUACCU-UCU----CGGCC--UUU-U-GGCUAUGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUGUGACAACUGAUA--UGGGUCCU-AC-GGGACCUAUUA----------AUAGUCACA------GAAAUUUUUUUCUGGG------UGAA-UGCGAUCUC------UGAGC---U-----U----G-CUCAU-----GUCUCG-UUCAAA-UUGUUGC---CUCGUCCUUACACUAC------CGACUUG--UG--------CAGCAUACCCUCU
AARE01006627.1/693-886         CCAGCUCUCU----UUGCC--GUA-A-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUAUUCC-ACUGGAAUACAACA----------UUGAUUAAU------CUCAUUUUUGGUCCCC------GUGG-GAAUUCCUC------UGUGC---U-----U----G-CACAU-----GUAUUC-CCGCAC-UGUGUCA---CUGGUC-UUACACUGU-------CACCAG--UA--------GACGCGAACUCAU
AACW02000228.1/581455-581260   UUAUCC-UCUC---AGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUUAUAGUUUAACAACUAUAA--UGAGGGAC-AUUGUCCCUCUC------------GUUGUUAAU------CUAAUUUUUUCCACCA------GGAA-ACUAAGGCU------CUGGC---U-----U----G-CUAUC-----UUUGGU-UUCCAC-AGGUGUC---CCUUGCCUUACACUAUC-----AGCGAGG--UG--------ACGCCGACCUUUU
AM270020.1/5920-6112           CCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCU-AA-GGAACACAACA----------UUGAUUAAU------CUUAUUUUUGCAUCCC------GUGG-CGAGACCUC------UGUGC---U-----U----G-CGCAU-----GUCUUG-CUGCAC-AGUGUCA---UCGGGC-UUACACUAC-------CCCCGA--UC--------GACGCGAACACCC
AAIM02000113.1/450420-450612   UUAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GAUGUCU-AA-GGACAUCAAUC----------GUGAUUAUU------CCUAUUUUUGGCCAGG------GGAC-GGCUUCCUC------UAUGC---U-----U----G-CAUAU-----GAUCCC-GUCCAC-AGUGUC----CCUAGUAUUACACUGC------CUCUAGG---U--------GACGCGAACGCGC
ABBB01000093.1/1472-1279       CCAGCUCUCU----UUGCC--AUUAU-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUAUUCU-AA-GGAAUACAACA----------UUGAUUAAU------CUUAUUUUUGGACCUC------GCGG-AGAGACCUC------UGUGC---U-----U----G-CGCAU-----GUCUUU-CCGCAC-CGUGUCA---UCGGUC-UUACACUAC-------CACCGA--UC--------GACGCGAAACCCA
AAFU01000671.1/40760-40955     UUAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---CUGCUCU-AC-GGAGUAGAUUUAU--------UUGAUUAAA------UUAAUUUUUGUCCCUC------GGGA-CUCAGUCCAC-----UCGGC---U-----U----G-CCGAG-----CCUGAA-UCCCAC-CGUGUC----UCCAGUAUUACACUGC------CUCUGGA---C--------GACGCAAACCUUU
CR382129.1/446178-446370       ACAAAUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA---CGGCCCA-AUUUGGGUCUUUU-----------AAUGUUACA------ACUAUUUUUGCAGCUA------GUGG-GUCUCUCUC------UGGGC---U-----U----G-CUCAU-----GGAGAC-CCGCAC-UGUGUC----GUUGCCCUUACACUAC------CGGCUUC---U--------GACGCUAUCUAUG
AAPN01113121.1/7070-7251       AUUGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGCAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGU-------CC-----UCUAUC----------CAUAUUAAA------UGGAUUUUUGGAGCAA------GGAG-AUGGAAUA-------GGGGC---U-----U----G-CUCCG-------CCCA-CUCCAU-GCAUUGA---CCUGGUAUUGCACUAC------UUCCAGG--AA--------CGGUGCGCUCCCC
AAQQ01759780.1/669-855         AUCACU-UUU----UGGCC--UUU-U-GGCUAAAAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUUCUC----U-GAGGACAA------------UAUAUUAAA------UGGAUUUUUGGAGCAG------GGAA-AUGGAAUA-------GGAGC---U-----U----G-CUCCA-------UCCA-CUCCAC-ACAUUGA---CCUGGUAUCGCAGUAC------CUUUAGG--AA--------GAGUGCACUCUCC
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ABBC01002283.1/5942-6135       CCAGCUCUCU----UUGCC--AUUAU-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUAUUCU-AA-GGAAUACAACA----------UUGAUUAAU------CUUAUUUUUGGAUCCC------GCAG-GAAAAUCUC------UGUGC---U-----U----G-CGCAU-----GUUUUC-CGGCAC-CGUGUCA---UCAGUC-UUACACUAC-------CGCUGA--UU--------GACGCGAAUUUUC
AASM01001106.1/7439-7242       CACCCU-UCU----CGGCC--UCU-U-GGCUAAGAUCAAU-UUGUAGUACCUGUUCUUAUCAGCGUGAUAGCUGAUA--UGGUCUCA-AU-AGAGGCCUUAUC---------AAUUUCACA------AAAAUUUUUGAUAGGG------GAAA-GGAUAAUUU------GAAGC---U-----U----G-CUUCU----UAUAACC-UUUCGC-GCGUUGC---CUUACCCUUGCACUAA------AGGUUUG--UA--------CAGUGCACCCUUA
AAWC01001022.1/39371-39181     AUCCAU-UCU-----GGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUGUAAUUACUGGUA---UUGGUUC-AUCGAACCAAUCAA----------UUAAUUACU------CUUAUCUUUGCAAUGCC-----CUCA-AUCAUAAC-------CUAGC---U-----U----G-CUAGA------CUGAU-UGGGAU-GAUGGC----CUUGGGCUCACACUAC------UCCCUUG---U--------GCUGUCAGGCAAA
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AAKM01000005.1/1407395-1407197 ACCCCU-UCU----CGGCC--UCU-U-GGCUAAGAUCAAU-UUGUAGUACCUGUUCUUAUCAGCGUGAUAGCUGAUA--UGGUCUCA-AU-CGAGACCUUAUCA--------AUUUUCACA------GUAAUUUUUGAUGGGG------GAAA-GGAUAAUUU------GAAGC---U-----U----G-CUUCA----UGUAACC-UUUCGC-GCGUUGC---CUUACCCUAGCACCAU------AGGUUUG--UA--------CAGUGCACCCUUU
AAXT01000001.1/1056302-1056495 AUACCU-UCU----CGGCC--UCU-U-GGCUAAGAUCAAU-UUGUAGUACCUGUUCUUAUCAGCGUGAUAGCUGAUA--CGAGUCCA-AU-UGGACUCUAU-----------CUCAUCACG------GGUAUUUUUCUUUGGG------GAAGAAACAUACC-------UGGGC---U-----U----G-CCCGG------UAGUU-CUUCAG-GCGUCGC---CUCCCCCUUACACUCU------CGGGUUG--UG--------CGGUGCACCCAUC
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AABS01001062.1/345-536         AUCGCU-UCA----AGGCUA-UUU-U-AGCUGUGAUCAA--GUGUAGUACCUGUUCUUCUCAGGUUGAAAUCUGAGA--CGGAAACG-AUUCGUUUCCUCUA----------UAUUUCAUU------CGGAUUUUUGAACACAC-----GGAA-GGUAAU---------GAAGC---U-----U----G-CUUC--------UACU-UGCUCC-GGGUUGU---CCUGGUUUUGCAUUAU------CGCCAGG--UU--------CGGCCCACGUUCC
X71483.1/1-192                 AUACCUUUCU----CGGCC--UUU-U-GGCUCAGAUCAU--GUGUAGUAUCUGUUCUUAUAAGCUUAAUCGCUUAUA--UGGUUCUC-AUUGAGAACCUG------------CGAUUAACU------UUAAUAUUUUAGGGGG------UCAA-GGCAAUGGG------GGCGC---U-----U----G-CGUCC-------CGCC-GCGACA-GCUUGGC---AGGAGGCUUACACUAC------CUCUCUU---G--------CCGAGCACCCCAG
AAXJ01017415.1/259-455         AUACCU-UCU----CGGCC--UUU-U-GGCUAUGAUCAA--GUGUAGUAUCUGUUCUUAUAAGUGUGACAACUUAUA--UGUUAGCU-AC-UGCUAACUUGA----------ACUGUCACA------ACAAUUUUUCACUGGG------GAGU-CGGUGGCUU------UGGUC---UC----U----G-ACCAU-----GCUCCG-ACUCGA-CUGUCGC---CUCAGCCCUGCACGACU-----UGCUGAG--UG--------CGGCGGACCCGAG
X51375.1/389-580               AUCGCU-UCUU---CGGCU--UAU-U-AGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAUA----------AAGGUUAUA------UGAUUUUUGGAACCUA------GGGA-AGACUC---------GGGGC---U-----U----G-CUCUC-------GANU-UCCCAA-GGGUCGU---CCUGGCGUUGCACUGC------UGCCGGN--NU--------CGGCCCANNCCCC
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AAFT01000058.1/3256-3060       CUAAAUCUCU----UUGCC--AUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAGCUGAAA---CGUCAUC-AUUGAUGACAUUUA----------CAUUUUUAC------CCUAUUUUUGGAUCUCAG----GUGG-UAAAGCUUGA-----UGGGC---U-----U----G-CUCAC-----ACUUUA-CCACAC-AGUGUC----GUUACCAUUGCACCUU------CGGUUUC---U--------GACGCGAACUUCA
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AAID01003241.1/2743-2932       AGACUU-UCU----CU--C--UAU-A-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GAUCGUC-ACUGACGGUCACA-----------UUGAUUAUA------CUUAUUUUUGUCCCUC------GGGA-UUGGUCCGC------UGUGC---U-----U----G-CGCAU-----GAUCAU-UCCCAC-AGUUUC----CCUGGUAUUACACUGC------CUCCAGG---U--------GAAGCGAACAUCU
AATT01000021.1/233305-233109   GCAUCC-UCUC---AGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUGACAACUGAAA--CUCGGAGU-UC-GCUCCGAUU------------GUUGUCAAA------CUUAUUUUUGAUGGUUCGCAGAGCUU-GGUUA----------GUUGC---U-----U----G-CAACG----CCUCGCC-GAGCAC-AGGUGUC---CCUCCUAUUGCACUAU------CUGGAGG--UG--------ACGCCGAGUGCUC
CP000498.1/1665432-1665627     AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAGCUGAAA---CGUCAUC-AUUGAUGACUUUACUA--------AUUGUUACC------UUUAUUUUUGGACUACCA----GCUG-GCAGGCUUGA-----UGGGC---U-----U----G-CUCAC-----ACCUAC-CAGCAC-AGUGUCG---AUGCCA-UUGCACACC------CCGGUUU--CU--------GACGCAAAUCUUU
AAFM01000022.1/42807-42996     AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGCGUAACAGCUGAAA--CGUCGUC--AUU-GACGACAU------------CAAUAUAUA------CAUAUUUUUGGACAAUU-----GCUU-GUGGGAUCGA-----UGGGC---U-----U----G-CUCAC-----ACCCAC-UAGCGC-AGUGUCG---UUGCCA-UUGCACAUC------UCGGCUU--CU--------GACGCAACCCCUC
AY007785.1/849-1044            AUACCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GNGUAGUAUCUGUUCUUAUCAGCUUAAUAUCUGAUA--CAGCACAC-UU-GUGUGUCGAU-----------GAGUUGAUG------UGAAUUUUUCACGGGG------GUGG-CGGGUAGC-------UCUGA---GGCAAAC----U-CAGAG-------UCCG-CCACAC-GUGUUGC---CCUGGAGCUGCACUAC-------AUCAGG-AGU--------UGGCACACCCGAU
AAGT01000476.1/108951-108760   ACAGUG-UUU----UCACG--UAC-A-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GAUCGUC-ACAGACGGUCACA-----------UUGAUUAUA------CUUAUUUUUGUCCUUC------GGGG-AUGGUCCGC------UGUGC---U-----U----G-CGCAU-----GAUCAU-UCCCAU-AGUUUC----CCUGGUAUUACACUGC------CUCCAGG---U--------GAAGCGAACAACU
DQ235686.1/7795-7608           AUCCUC-UCU-----GGCC--UUU-U-GGCUUAGAUCAU--GUGUAGUAUCUGUUCUUAUAAGUUUAACCACUUAUA---UGGGUCC-ACCGGACCCAUC------------UGGUUUACU------UCUUUUUGCCUUGCCC------GUCC-GGCCAUCC-------UCUGC---U-----U----G-CACGA------CGGCC-GGACAC-GAUGAC----CUUGCCACUGCACUGC------CGGCUUG---U--------GUUGUCAGGGACC
AATU01001299.1/7335-7151       AUACCU-UCU----CGGCC--UCA-A-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUAAUCAGUGUGAAAACUGGUU--UUCGCCU---UU-UGGCGGAC------------UUUUUCACU------CGCAUUUUUGGGCAAU------CGUC-UGCGG----------CUAGC---U-----U----G-CUAGC-------GGCG-GACGAG-CGGUCUC---CGGGGGCGUUCACCUU------UCCCCCG--CG--------AGGCCAACUACAC
AAGI01000215.1/38061-38253     UCUCCU-UCUCAGUUUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUCUAGUUUAAUCGCUAGAA--C--UUUCC-UACGGGAA--UUC-----------ACGAUUAUU------CUUAUUUUUGCAACUG------GUCA-AUGGCUCAC------UGGGC---U-----U----G-CCCAU-----AGUCAC-UGGCAC-UGUGUCG---UUCCUC-UCACACUAC-------CUGGAA--UG--------UACGCGACCCUUU
AAGD02001363.1/26266-26450     AUCGCU-UCUU---CGGCU--UAU-U-AGCUAAGAUCAAA-GUGUAGUAUCUGCUCUUAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAU-----------AAAGGUUAU------AUGAUUUUUGGAACCU------AGGA-A--------------AGGGC---U-----U----U-CUCC--------GACU-UUCUAA-GGGUCGU---CCCGGCGUUGCACUGC------UGCCGGG--CU--------CGGCCCAGUCCCC
AADS01000047.1/234093-233905   UUACCACUCU-----GGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUAAUAGUUUAACCACUAUUA---UGAGGGC-ACCGCCCUCAUU------------AUUGGUUAU------CAAAUUUUUGCCGCCCUUGU--CCCC-CGAGCU----------CUGC---U-----U----G-CAA---------CUCG-GGGGCG-UGAUGAC---CUUGCCACUGCAGUAC------CGGCUUG--CG--------UCGUCGGGGGAUA
AANW02001910.1/4438-4250       AACCCU-UCU----CGGCC--UUUAU-GGCUUUGAUCAA--GUGUAGUAUCUGUUCUAGCAAGCUUAAUAUCUUGCU---CACCUCU-AC-GGAGGUGCA------------AAUAUUAAA------CAAUUUUUGCGAUGGG------GUCU-AGUCGUGUU------GAGGC---U-----U----G-CCAAA--GACACGAUU-AGACAA-GAAUGUG---CUUGGU-------UAC------GGCCAUG--UC--------GCAUUUACCCUCU
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CP000599.1/149439-149632       AACUUU-UCU----CGAGC--UUU-C-GCUC-AGAUCAA--GUGUAGUAUCUGUUCUAUUAUGUUUAAACACAUAAU--GAGGCUUU-CU-UAAGCCUUCAU----------UAGUUUAAC------CGAAUUUCUUCAGAGG------GCGUUAUUCAAACAGG----CUUGU---U-----U----A-CAAGU------CGAAU-ACGCGA-GCAUGUU---CUUGGCCUUGCACUUU-------GCCUCG---A--------ACGUGUACCUCGA
AAWT01070971.1/3028-3217       AGUGCU-UCU-----AGCU--UCA-U-AGCUAUGAUCAAAAGUGUAAGAACUGUUCUUCUCAGUUUAAUCGCUGGGA--CAAAGUUC-AUUGAUCUUAAUUC----------GAGAUUAAA------UUGAUUUUUGUAACUU------UACA-GACACUCC-------AAGGC---U-----U----G-CC--A------AGCUC-UGUCGU-AGUGGA----CCUUACAUUGCAUUAC------AGUUUGG------------UCUGCUUGUUUAA
AACP01000091.1/4899-4707       CUCACC-UCU----CACAG--GGC-U-----UAGAUCAU--GUGUAGUAUCUGUUCUAAAUAGAUUGACAUCUAUUU--UUCCUUGCUCCGGCGAGGAUAUA----------AUUGUCAUA------CACUUUUUCCUUGCGG------GAGA-UCACCGUUCU-----GGUGC---U-----U----G-CACCU------CGGGA-UCUCAU-GGAUGUC---CUUGGCCCUACACUUC------CGCCUUG--AG--------ACGUCCGCCGUCC
AAFP01000557.1/11449-11264     AUCCUC-UCU-----GGCCUCUUU-U-GGCUAAGAUCAU--GUGUAGUAUCUGUUCUUAACGCUGUGAGAAGCGUUA--CAACCCU---AC-GGGGUUUA------------CUUCUCGCG------AAGUUUUUCUGCGCCC------GCGU-UGCC-UCU-------UCAGC---U-----U----G-CUGAA-------UGUA-ACGCAC-GAUGUC----GCUGGCACCGCACUAC------CGCCUUC---U--------GAUGUCAGGGUUC
AAFI02000140.1/17830-17618     AUUCUUCUUG----AAGCG--UAA-U-AGCUUUAAUCAA--GUGUAGUAUCUGUUCUAGAACGUUUAAAAUCGUUCU--UGCUUUCU-AAGUGAAAGCAUUC----------GAAUUUAAA------AUAAUUUUUUAUUCGAGG----UUUA-GAUGUUAUGAUA---UCGGC---A-----U----G-CCUUU---AUUACAUC-UAAAAUAGCAUUCG---CUCUGUAUUGCACAAU------UUCAGAG--UUUAUAAAAAGAGUGCUACCUCU
AAFB02000004.1/138313-138494   UCACCU-UCU----CGGCC--UUUAU-GGCUUUGAUCAA--GUGUAGUAUCUGUUCUAGCAAGCUUAACAUCUUGCU---UGCCCUU-AC-GGGGGUAAA---------------AGAAAA------AUAAUUUUUAGAGGGAG-----GUUA-AGGGAAUUG------AAGGC---A-----A----G-CCUUU---UAUGAACU-UAACGA-GGAUGUG---CAUGGA-----------------AACAUG--AU--------GCGUCUACCCUAA
AAPO01000010.1/72363-72562     AUC----UCU----UUGCC--AUU-U-GGCUUAGAUCCA--GUGUAGUAUCUGUUCUUUUCAGUGUAAUAGCUGAAA---UGUCAUC-AUUGAUGGCAAAUACAAAUAUAA-UUUUUUACA------UUUAUUUUUGGAACAAAUGGU-GGGA-UUGGUUUCAAA----UGGGC---U-----U----G-CUCAU-----AAUCAU-UCCCAC-ACAGUGU---CGU----UGCCAUUAC----------ACG--UU--------CAUCGAGGCUCCU
AAFX01115267.1/519-717         UUUGUU-CCC----CAGCU--UUU---GGCUUUGAUCAA--GUGUAGUAUCUGUUCUUUUGAUUUUGAUAAAUCAAA---CGUGGCU-UC-GGUCACGCUU-----------UAUAUCAAA------UCAUUCUUUGGCUUGGG-----GAGG-CGGCGUGU-------GCAGC---U-----U----G-CUGUG----CUCGCCG-UCUCGC-GUGCUGC---GCGUCCUUUGCACUAACUGGGACGAAUGC--UG--------CGGCGCACCUACU
AANV02000585.1/5693-5873       ACACCU-UCU----CGGCC--UUUAU-GGCUUUGAUCAA--GUGUAGUAUCUGUUCUAGCAAGCUUAACAUCUUGCU---UGCCCUU-AC-GGGGGUAAA----------------AGAAA------AGAAUUUUUAGAGGGAA-----GUUA-AGGAAAUGG------AAGGC---A-----A----G-CUUUU---CAAGAACU-UAACAA-GGAUGUG---CAUGGA-----------------AACAUG--AU--------GCGUCUACCCUAA
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AAFO01000053.1/189105-188894   AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCCA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA---UGUCAUC-AUUGAUGACUUUACAUU-------UAUGUUACAAAUUUAUUUAUUUUUGGAUAUUGG----GUAG-AUUGAUUUAUUAAAGUGGGC---U-----U----G-CUCAC----AGUCUUU-CUACAUAGUGUCGU---UGCCACUGUACUUUUAU-----UUUGGCU--UC--------UGACGCAAAUUUU
AABY01000227.1/3654-3483       AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA--UGA-CCUC-AAUGAGGCUCAUU-----------ACCUUUUAA------UUUGUUACAAUACACA------UUUU-UUGGCAC-----------------------------------------CCAA-AUAAUA-AAAUGGA---CGG--GAAGGGACUUU------CCAAGCG--GG--------CUGUUUUCCGCUA
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AC167922.2/17996-18182         ACAUUC-AGA----C--GC--AUU-U-GCUGACCUUCAACCUUCUA------GUUCUUUUCAGUUUAAUCUCUGAAA---CGUCACU-AC-GGUGACAUUCU----------AUGAUUAUA------CUUAUUUUUGGACCUCC-----GUCG-GUGGCCGC-------UGGGC---U-----U----G-CUCAU------GUCAC-UGACGA-CCGUGUC---GCCAGUAUUGCACUGC------CUCUGGC--UG--------ACGCGAACUACUU
AAZN01000309.1/86876-87072     AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAGCUGAAA--UGA-CCUC-AAUGAGGCUCAU------------UACCUUACG------UUUUGUUACAACACAUUUU---UUGG-AAACUUUU-------AUUUCGGGU-----UUAGAG-AGAUU-------GUUA-CUUAUU-UGAUUUUC--UGAGAUUAUGCACUUC-------AUUGGG--UA--------UAGUCUUCUCCCU
AADM01000307.1/26094-25895     AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA---UGUCCUC-AAUGAGGAUGUUUAUUAA------GUUACAAAU------CAUAUUUUUGGAAAUGA-----CUUA-GGGAGGAGAGAGAUGUAAGG---G-----U----C-CCUGG-------UAUC-CAGGGG-AAGGGGU---CUUAUAUGUGGCUGGG------CUGUAAG---U--------UUUGUUACGGAGA
AL590446.1/168546-168725       CCACCUCUCA-----AGCC--AAU-C-GGCUUUGAUCAA--GUGUAGUAUCUGUUCUUGCCAGUGUAAGAACUGGCA---UUAUCCG-UC-AGGAUAAACUC----------ACGAAUUUU------UGGGCGGCGAGAUGAG------GCAG-CGGAGCUUG------AGCGC---U-----U----G-CGUU--------UCGG-UUGCUC-UGCCAGA---GGCUCG-----------------CGGGCU--CC--------CGGGCUGUAGAUC
AF053589.1/90-279              CCACCUCUCA----AAGCU--CAU---AGCUUUGAUCAA--GUGUAGUAUCUGUUCUUGUCAGUGUGACAGCUGACAAACUAGCUCC-UU-GGAGCUAGA-----------------------------AUAUGCUGGUGUGU------GUGU-GGAUGCUUUGA----CAGGC---U-----U----G-CUUGUAGGGGCCAUGC-ACACACCAGGCAGACUCCCGGAAGUUG---UUC------CGUCCGG--AG--------CUGC--ACUUUUU
Z50072.1/229-412               CUCACUCUCA----AAGUU--AUC---GGCUUUGAUCAA--GUGUAGUAUCUGUUCUAGUCGGCUUAACAACUGACU---UAUCCGC-AAGGAGUAUAAU------------------ACU------UAGAAAAGUGGAGAUG------UAAA-AUGAGAGA-------UGUGC---U-----U----G-CAUAA----UCAUCAU-UUUUUA-UAGAUCU---CUGGCA---UCUUAAG------AUGCUUU--UU--------UAUUUAAUUUUUU
AAHC01001365.1/13705-13888     UUUGCACUCA----GGGCG--AUU---CGCUCUGAAUAA--GUGUAGUAUCUGUUCUGAAUCGCUUGACAGCGGUUC--GCCUGGUA-UG-UGCCAGGCGCCU---------CUGUUCAUA------CUAAUUUAUUAACUCA------UUG--------UC-------CUAGC---A-----U----GUCUAGG-------------CGAUG-GAUUUAG---GCGGUGUCUUCACUAUC-----UCACCUA-ACC--------UAAAUCACCCAAU
AF287991.1/4898-5088           AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA------------UAUAUUAAA------UGGAUUUUUGGAGCAG------GGAG-AUGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------CUCCAGG--AA--------CGGUGCACCCCCU
M33777.1/191-381               AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA------------UAUAUUAAA------UGGAUUUUUGGAGCAG------GGAG-AUGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------CUCCAGG--AA--------CGGUGCACCCCCU
S64581.1/735-926               AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAU--GUGUAGUAUCUGUUCUUUUCAGCUUAAUAUCUGAAA--CGCGACUC-ACCGAGUCGCUUG-----------UAUAUUAAA------CUGAUUUUUGAACUUA------GGCC-AUGGAAUA-------GGGGC---U-----U----G-CUCCG-------UCCU-GGCCAC-GGGUUGG---CCCGGUAUUGCAGUAC------CUCCGGG--AU--------CGGCCCACCCCUC
AAKO01002676.1/16743-16938     AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GUUCCUCC-AUUGGAGGACAACA----------AAUGUUAAA------CUGAUUUUUGGAAUCA------GACG-GAGUGCUA-------GGAGC---U-----U----G-CUCCA-------CCUC-UGUCGC-GGGUUGG---CCCGGUAUUGCAGUAC------CGCCGGGAUUU--------CGGCCCAACUGAA
AAPQ01007349.1/370124-370319   AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GUUCCUCC-AUUGGAGGACAACA----------AAUGUUAAA------CUGAUUUUUGGAAUCA------GACG-GAGUGCUA-------GGAGC---U-----U----G-CUCCA-------CCUC-UGUCGC-GGGUUGG---CCCGGUAUUGCAGUAC------CGCCGGGAUUU--------CGGCCCAACUGAA
AAIZ01004041.1/16829-17024     AUCGCU-UCU----CGGCC--UUA-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUA--GUUUCUCC-AUUGGAGAACAACA----------AAUGUUAAA------CUGAUUUUUGGAAUCA------GACG-GAGUGCUA-------GGGGC---U-----U----G-CUCCA-------CCUC-UGUCGC-GGGUUGG---CCCGGUAUUGCAGUAC------CGCCGGGAUUU--------CGGCCCAACUUAA
AAYL01000061.1/287788-287596   AUACCU-UCU----CGGCC--UUU-U-GGCUAUGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUGUGACAACUGAUA--UGGGUCCA-AC-UGGACCCAAU-----------UAUGUCACA------UCAAUUUUUGUUUGGG------GAGGCUAGGUUUC-------UGAGC---U-----U----G-CUCAG------GCCUU-CCUCAA-GCGUCGC---CUUCCUCCUGCACUCC------CGGGAAG--AG--------CGGUGCACCCUUU
AL683874.1/16263-16071         UCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCU-AA-GGAACACAACA----------UUGAUUAAU------CUCAUUUUUGGAUCUC------GUGG-CAAGGCCUC------UGUGC---U-----U----G-CGCAU-----GCCUUG-CCACAC-AGUGUCA---UUGGGC-UUACACUAC-------CCCCAA--UU--------GACGCGACCCUUU
AAIH02000488.1/9382-9189       CCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCC-AUAGGAACACAACA----------UUGAUUAAU------CUUAUUUUUGGUCUCC------GUGG-CAGGGCCCC------UGUGC---U-----U----G-CGCAU-----GCCUUG-CCACAC-AGUGUCA---UCGGGC-UUACACUAU-------CCCCGA--UA--------GACGCGAACUCCU
AAKE03000002.1/1730972-1731164 UCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUGUUCU-AA-GGAACACAACA----------UUGAUUAAU------CUCAUUUUUGGACCCC------GUGG-CGAGGCCUC------UGUGC---U-----U----G-CGCAU-----GCCUUG-CCACAC-AGUGUCA---UUGGGC-UUACACUAC-------CCCCAA--UA--------GACGCGACCCUUU
AAEL01000160.1/10170-10364     AUACCU-UCU----CGGCC--UUU-U-GGCUAUGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUGUGACAACUGAUA--UGGGUCCU-AC-GGGACCUAUUA----------AUAGUCACA------GAAAUUUUUUUCUGGG------UGAA-UGCGAUCUC------UGAGC---U-----U----G-CUCAU-----GUCUCG-UUCAAA-UUGUUGC---CUCGUCCUUACACUAC------CGACUUG--UG--------CGGCAUACCCUCU
AATX01000107.1/79359-79166     CCAGCUCUCU----UUGCC--AUUAU-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUAUUCU-AA-GGAAUACAACA----------UUGAUUAAU------CUUAUUUUUGGACCUC------GCGG-AGAGACCUC------UGUGC---U-----U----G-CGCAU-----AUCUUU-CCGCAC-CGUGUC----AUCGGUCUUACACUAC------CACCGAU---C--------GACGCGAAACCCA
AANS01001054.1/6664-6467       CACCCU-UCU----CGGCC--UCU-U-GGCUAAGAUCAAU-UUGUAGUACCUGUUCUUAUCAGCGUGAUAGCUGAUA--UGGUCUCA-AU-AGAGGCCUUAUC---------AAUUUCACA------AAAAUUUUUGAUAGGG------GAAA-GGAUAAUUU------GAAGC---U-----U----G-CUUCU----UAUAACC-UUUCGC-GCGUUGC---CUUACCCUUGCACUAA------AGGUUUG--UA--------CAGUGCACCCUUA
AABL01000318.1/11806-12005     ACCCCU-UCU----CGGCC--UCU-U-GGCUAAGAUCAAU-UUGUAGUACCUGUUCUUAUCAGCGUGAUAGCUGAUA--UGGUCUCA-AU-UGAGACCUUAUCA--------AUUUUCACA------UAAAUUUUUAAUAGGG------GAAA-GGAUCAUUU------GAAGC---U-----U----G-CUUCU----UAUAGCC-UUUCGC-GCGUUGC---CUUACCCUAGCACUAAU-----AGGUUUG--UA--------CAGUGCACCCUUA
CAAJ01003844.1/3754-3953       ACCCCU-UCU----CGGCC--UCU-U-GGCUAAGAUCAAU-UUGUAGUACCUGUUCUUAUCAGCGUGAUAGCUGAUA--UGGUCUCA-AU-UGAGACCUUAUCA--------AUUUUCACA------UAAAUUUUUAAUAGGG------GAAA-GGAUCAUUU------GAAGC---U-----U----G-CUUCU----UAUAGCC-UUUCGC-GCGUUGC---CUUACCCUAGCACUAAU-----AGGUUUG--UA--------CAGUGCACCCUUA
EF140768.1/2-192               CCU----UCU----CGGCC--UCU-U-GGCUAAGAUCAAU-UUGUAGUACCUGUUCUUAUCAGCGUGAUAGCUGAUA--UGGUCUCA-AU-AGAGGCCUUAUC---------AAUUUCACA------AAAAUUUUUGAUAGGG------GAAA-GGAUAAUUU------GAAGC---U-----U----G-CUUCU----UAUAACC-UUUCGC-GCGUUGC---CUUACCCUUGCACUAA------AGGUUUG--UA--------CAGUGCACC----
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AC198944.2/184805-184614       AUUGCU-UCU----CGGCC--UUU-U-GGCUAACAUCAA--GUGUAAUGUUUGUCCUUAUCAAUUUAAUAUCUGAUA--UGUCCUGU-AUCCAAGGAACAA-----------UAUAUUAAG------UGGACUUUUGGAAGUA------GGAG-GUAGAAUA-------ACAAC---U-----U----C-CUCUG-------UCCA-CUCCAC-ACAUCAU---CUUGGUAUUGCAGUAC------UUCCAUA--AA--------UGAUGCAUCCUCC
AACQ01000018.1/49571-49783     AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCCA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA---UGUCAUC-AUUGAUGACUUUACAUU-------UAUGUUACAAAUUUAUUUAUUUUUGGAUAUUGG----GUAG-AUUGAUUUAUUAAAGUGGGC---U-----U----G-CUCAC----AGUCUUU-CUACAU-AGUGUCG---UUGCCA-CUGUACUUUUAUU--UUGGCUU--CU--------GACGCAAAUUUUU
AE017345.1/926592-926777       AUCCUC-UCU-----GGCCUCUUU-U-GGCUAAGAUCAU--GUGUAGUAUCUGUUCUUAACGCUGUGAGAAGCGUUA--CAACCCU---AC-GGGGUUUA------------CUUCUCGCG------AAGUUUUUCUGCGCCC------GCGU-UGCC-UCU-------UCAGC---U-----U----G-CUGAA-------UGUA-ACGCAC-GAUGUC----GCUGGCACCGCACUAC------CGCCUUC---U--------GAUGUCAGGGUUC
AAEY01000026.1/44265-44450     AUCCUC-UCU-----GGCCUCUUU-U-GGCUAAGAUCAU--GUGUAGUAUCUGUUCUUAACGCUGUGAGAAGCGUUA--CAACCCU---AC-GGGGUUUA------------CUUCUCGCG------AAGUUUUUCUGCGCCC------GCGU-UGCC-UCU-------UCAGC---U-----U----G-CUGAA-------UGUA-ACGCAC-GAUGUC----GCUGGCACCGCACUAC------CGCCUUC---U--------GAUGUCAGGGUUC
AACO02000044.1/38107-37922     AUCCUC-UCU-----GGCCUCUUU-U-GGCUAAGAUCAU--GUGUAGUAUCUGUUCUUAACGCUGUGAGAAGCGUUA--CAACCCU---AC-GGGGUUUA------------CUUCUCGCG------AAGUUUUUCUGCGCCC------GCGU-UGCC-UCU-------UCAGC---U-----U----G-CUGAA-------UGUA-ACGCAC-GAUGUC----GCUGGCACCGCACUAC------CGCCUUC---U--------GAUGUCAGGGUUC
AACI02000565.1/65-236          AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA--UGA-CCUC-AAUGAGGCUCAUU-----------ACCUUUUAA------UUUGUUACAAUACACA------UUUU-UUGGCAC-----------------------------------------UCAA-AAUAAU-AAAUGGA---UGG--GAAGAGACUUU------CCAAGCG--GG--------CUAUUUCCCGCUA
AACF01000175.1/12372-12544     AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA--UGA-CCUC-AAUGAGGCUCAU-----------------UACC------UUUAUUAUUUGUUACA-------------AUACUC-------AUUUU---U-----U----G-GAAGC------ACUUA-A---AU-GGGCGGG---AAGAAACUGAGAGGAU------CCUUCCU---A--------UUGUCUAUUCAAU
AAFW02000011.1/661534-661345   AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA--UGA-CCUC-AAUGAGGCUCAUUA----------CCUUUUAAU------UUGUUACAAUACACAU------UUUU-UGGCACCCAAA----AUAAU---A-----A----A---AUG-------GACG-GGAAGA-GACUUUU---UAAGCAAGUUGUUUUC-------CGCUAA-UGU--------CAGGUCUCACUAC
AAEG01000106.1/129944-130133   AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA--UGA-CCUC-AAUGAGGCUCAUUA----------CCUUUUAAU------UUGUUACAAUACACAU------UUUU-UGGCACCCAAA----AUAAU---A-----A----A---AUG-------GACG-GGAAGA-GACUUUU---UAAGCAAGUUGUUUUC-------CGCUAA-UGU--------CAGGUCUCACUAC
AY007788.1/537-683             AUAUCU-UCU----CGGCU--AUU-U-AGCUAAGAUCAU--GUUUAUAAACUGUUCUUAUCAGAGUAACUCCUGAUA--CUGCCU----UC--GGGCAAA----------------GGAAU------AGAAAUUAUAACUCAA--------------------------------------------------------------------GG-UUGUUUC---CCUGGAGUUCCACGUU-------UCCAGG---G--------GAGCAACUCUUUU
M58665.1/571-739               AUAUCU-UCU----CGGCU--AUU-U-AGCUAAGAUCAU--GUUUAUAAACUGUUCUUAUCAGAGUAACUCCUGAUA--CUGCCU----UC--GGGCAAA----------------GGAAU------AGAAAUUAUAUCUCAA------GG--------UUG-------UUUCC---C-----U----G-GAGUU--------------CCAC-GUUUCCA---GGGAGCAACUCUUUUU------UUCUCCU--AG--------GAGCAGAACAUCU
U23406.1/206-352               AUAUCU-UCU----CGGCU--AUU-U-AGCUAAGAUCAU--GUUUAUAAACUGUUCUUAUCAGAGUAACUCCUGAUA---UUGCCU---UC-GGGCAAAG-----------------GAAU------AGAAAUCAUGGUACUA--------------------------------------------------------------------GG-UUGUUUC---UCUGGAGUUCCACCUU-------UCCAGG---G--------GAGCAGCUACCUU
EF052257.1/89-253              AUUCAG---U----CAGCC--UUU-G-AGUUAAAAUCAA--GUGUAGUAUAGGU---UACCAGUUUAACAUCUGAUG------------AC-------AA------------GAUCUUAAA------UGCAUUUUUGGAGCUG------GGAG-ACAAAA---------GAAGC---U-----U----G-CU---------GUUCA-CUCCAC-GCAUCAA---CCUGGUAUUGCAGUAC------CUCCAGG--AA--------UGA-GCCCCCGAC
AACA01000784.1/509-337         AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA--UGA-CCUC-AAUGAGGCUCAUU-----------ACCUUUUAC------UUUGUUACAAUACUCA------UUUU-UUGGCACU----------------------------------------CAAA-AUAAUA-AAAUGGA---CGG--GGAGAGAUUUU------CCAAGCG--GG--------CUGUUGCCGCUAA
AABZ01000169.1/11839-11668     AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA--UGA-CCUC-AAUGAGGCUCAU------------UACCUUUAA------UUUGUUACAAUACACA------UUUU-UUGGCACA----------------------------------------CUCA-AAUAAU-AAAUGAA---UGG--AAAGAGAUUUU------UUAAGCG--AG--------CUGUUUCCUGCUA
X56454.1/125-277               AUAUCU-UCU----CGGCU--UUU-U-AGCUAAGAUCAU--GUUUUUAAAAUGUUCUUAUCAGAGUAACUCCUGAUA---UUUGCCU-UC-GGGCAAUUA---------------GGAAUA------CGAAAUCUUUGAUCAC--------------------------------------------------------------------GC-GAGUUUU---CCUGGAGUUCCACUCU------UUCCAGG--CG--------AAGCUCGCCCUUU
AC008368.21/83891-84039        AUAUCU-UCU----CGGCU--AUU-U-AGCUAAGAUCAA--GUUAUUAAACUGUUCUUAUCAGAGUAACUCCUGAUA--CGGGCC---UUU--GGCCCAA----------------GGAUC------AAAACUGUUGGCUGUC--------------------------------------------------------------------CC-GCGUUCU---UCCGGGGUUCCACUUG-------UCCGGA--UG--------GAGCGCGACGGUC
M58666.1/571-718               AUAUCU-UCU----CGGCU--AUU-U-AGCUAAGAUCAA--GUUAUUAAACUGUUCUUAUCAGAGUAACUCCUGAUA--UGGGCC----UC--GGCCCAA----------------GGAUA------GUAACUGUUGAGGCGC--------------------------------------------------------------------CG-GCGUCCU---CCCGGAGUUCCACGUG-------UCCGGU--UG--------GGGCGCCGCCUCC
AAHK01000589.1/17217-17069     AUAUCU-UCU----CGGCU--AUU-U-AGCUAAGAUCAA--GUUUUUAAACUGUUCUUAUCAGAGUAAUUCCUGAUA--UGGGCU----UC--GUCCCAG-----------------GAAU------AGAAACCGCUGAUCUC----------------------------------U-----C---------------------------AA-GCGUUCU---UCCGGAGUUCCACGUG-------UCCGGA--UG--------GAGCGCUUCCUUU
AF326335.1/1-142               AUAUCU-UCU----CGGCU--UUU-U-AGCUAAGAUCAU--GUUUAUAAACUGUUCUUAUCAGAGUAACUCCUGAUA--UUGCCU----UC--GGGCAAA-----------------------------------GGAAUACA------AAUG-AUCGCACU----------------------------------------AGGU-UGUUUC-----------CCUGGAGUUCCACCUU-------UCCAGG--GG--------------AGCAACU
CAAC02000548.1/434719-434909   AUCGCU-UCUU---CGGCU--UAU-U-AGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCGUAUUAACCUACGGUA--UACGCUCG-AA-UGAGUGUAAU-----------AAAGGUUAU------GUGAUUUUUGGAACCUA-----GGAA-AGACUC---------GGGGC---U-----U----G-CUCC--------GACU-UUCCAA-GGGUCGU---CCCGGCGUUGCACUGC------UGCCGGG--CU--------CGGCCCAGUCCCC
AACE03000009.1/583940-584128   AUAAAUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGGAA---UGUCCUC-AACGAGGGCGUUACGC--------UAAGUUACA------GCCCACUUUUUGGAAC------CUUA-GGGAGAAG-------AAGGC---U-----C----G-GAAUC------GUCGC-UGGGUG-GCGCAUC------GGCAAUACGGAGC------UACC------U--------GGAUGCAGGCCUG
AABX02000002.1/241678-241484   UUAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---CUGCUCU-AC-GGAGUAGAAUC----------GUGAUUAUU------CUAAUUUUUGCAACUC------GGUC-GGCAUCCCUC-----UGGGC---U-----U----G-CCUAU----GGUUGCC-GACCAC-UGUGUC----CCUGGUAUUACACUGC------CUCCAGG---C--------GACGCGAACUCAA
AASC02023314.1/7214-7405       AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAAUAUCUGAUA--CGUGGCUU-CC-UAGCGACUAC-----------GAUAUUAAA------CUGAUUUUUGGACACA------GGCG-AGAUGCCC-------GGGGC---U-----U----G-CUCCG-------CUCU-CGCCAC-GGGUCGG---CCCGGUAUUGCAGUCC------CUCCGGG--AA--------UGGCCCAAUAUAA
AAFD02000010.1/1244775-1244583 ACAUCUCUCU----UCGCC--UAU-U-GGCUUUGAUCUU--GUGUAGUAACUGUUCUAAAACUUUUAACAAAGUUUU---GAGGGCC-ACUGGUCCUCAC------------ACUGUUAAA------CUACUUUUUGCACUCU------AGGA-GCAUCACU-------UCUGC---U-----U----G-CAGAA------CAUGC-CUCCGC-GGAUGGU---CGAAGCAUUUCACUAGC-----CGCUACG--AU--------CCGUCCACCCCCC
AAZY02000001.1/986053-985858   AUACCU-UCU----CGGCC--UUU-U-GGCUAUGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUGUGACAACUGAUA--UGGAUCCU-AC-GGGAUCCAAACU---------CUAGUCACA------GAAAUUUUUAUACGGGA-----GAUA-UAGAUCAC-------UGAGC---U-----U----G-CUCAU------AUCAA-UGUCGAAAUGUCGC---CUCGUCCUUACACUAC------CGAUGAG--AG--------UGGCAUGCCCUAC
ABFM01000169.1/24531-24724     CCAGCUCUCU----UUGCC--AUUAU-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GUAUUCU-AA-GGAAUACAACA----------UUGAUUAAU------CUUAUUUUUGGACCUC------GCGG-AGAGACCUC------UGUGC---U-----U----G-CGCAU-----GUCUUU-CCGCAC-CGUGUC----AUCGGUCUUACACUAC------CACCGAU---C--------GACGCGAAACCCA
AAQM02000124.1/160019-159827   AUACCU-UCU----CGGCC--UUU-U-GGCUAUGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUGUGACAACUGAUA--UGGGUCCA-AC-UGGACCCAAU-----------UAUGUCACA------UCAAUUUUUGUUUGGG------GAGGUUAGGUUUC-------UGAGC---U-----U----G-CUCAG------GCCUU-CCUCAA-GCGUCGC---CUUCCUCUUGCACUCC------CGGGAAG--AG--------CGGUGCACCCUUU
CR382136.2/900319-900516       AUC----UCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAA---CGUCAUC-AUUGAUGACUUUUAUAA-------AAUGUUACC------UUUAUUUUUGGAUUAUUC----GUUC-GAAGGAUUGA-----UAAGC---U-----U----G-CUUAC-----ACCUUU-GGACAC-AGUGUCG---UUGCUA-UUGCACCAUA-----UUGGCUU--CU--------GACGCAAUUUUUU
AAGV020390824.1/478-668        AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUCCUCC-AUUUGAGGACAG------------CAUAUUAAA------UUGAUUUUUGGAACAG------GGAU-GUGGAAAA-------GGAGC---U-----U----G-CUCUA-------UCCA-CUCCAC-GCAUCAG---CCUGGUAUUGCAGUAC------UUCCAGG--AA--------UGGUGCACUUCCC
X58842.1/1-191                 AUACCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUGUGAAAACUGAUA--CUGUCCCU-ACUAGGGACAUGU-----------GGUUUCACA------UUAAUUUUUCACAGGG------GUCG-GAUUUACUA------GUGGC---U-----U----G-CCCUA-------GUCC-CGACGC-GGUUGCC---CUUGGC-AUGCACGCU-------ACUAAG--GA--------GCGGCUACCCCUG
AAKN02019678.1/9356-9546       AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA------------UAUAUUAAA------UGGAUUUUUGGAGCUG------GGAG-AUGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------CUCCAGG--AA--------CGGUGCACCCCUC
AAWR02015112.1/62289-62483     ACCGCU-UCU----AGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CAUCCUCU-AUCCAAGGACAA------------UAUAUUAAA------UGGAUUUUUGGAACAA------GGAG-AUGGAAUA-------GGAGC---U-----UGCUUG-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------UUCCAGG--AA--------CGGUGCACCAAAA
ABDF02000003.1/1932068-1932260 UUAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GGUCUCU-AA-GGAGACCAAUC----------GUGAUUAUU------CUUAUUUUUGUCCUCG------GAGC-AGUUUCCUC------UGUGC---U-----U----G-CGCAU-----GAUUCU-GCUCAC-AGUGUC----CCUGGUAUUACACUGC------CUCCAGG---C--------GACGCGACCUUGA
M12856.1/361-551               AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCG-AUGAGAGGACUU------------UAUAUUAAA------CGGAUUUUUGGGCGCG------GGAG-UUGGACCC-------GGAGC---U-----U----G-CUCCC-------UCCG-CUCCGC-GCAUCGU---CCCGGUAUGGCAGUAC------CUCCGGG--CA--------CGGUGCACCUCCC
AACS02000012.1/1565410-1565598 UUACCACUCU-----GGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUAAUAGUUUAACCACUAUUA---UGAGGGC-ACCGCCCUCAUU------------UUUGGUUAU------CUAAUUUUUGCCGCCCCAGU--UCCU-CGAGCU----------CUGC---U-----U----G-CAA---------CUCG-AGGACG-CGAUGAC---CUUGCUAUUGCAGUAC------CGGCUUG--UG--------UCGUCGGGGGAUC
ABEG02004067.1/53561-53371     AUCGCU-UCUU---CGGCU--UAU-U-AGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCGUAUUAACCUACGGUA--UACACUCG-AA-UGAGUGUAAUA----------AAGGUUAUA------UGAUUUUUGGAAUCUA------GGAA-AGACUC---------GGGGC---U-----U----G-CUCC--------GACU-UUCCAA-GGGUCGU---CCUGGCGUUGCACUAC------UGCCAGG--CU--------CGGCCCAGUCCCC
AAIL02000026.1/644385-644193   UUAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GGUCCCC-AA-GGGGACCAAUC----------GUGAUUAUU------CUUAUUUUUGCACCUC------GAGC-AGUUUCCUC------UGCGC---U-----U----G-CGCAU-----GAUCCU-GCUCAC-UGUGUC----CCUGGUAUUACACUGC------CUCCAGG---C--------GACGCGACCCUUU
AAQY02000293.1/11238-11050     AUACCU-UCU----CGGCC--UUU---GGCUAAGAUCAA--GUGUAGUAUCUGUUCUAAUCAGUGUGAAAACUGGUU--UCCCUGCU-UUUGGUGGGGUC------------UUUUUCACA------UUUAUUUUUGGAACUG------CUGC---UUUCGG-------UUAGC---U-----U----G-CUAGC------CAAUC-GCGGUA-CGGUCUC---CGGGGGCUUUCACCUA------UCCCUCG--UG--------AGGCCAACUACUA
AADG06003467.1/1334-1527       AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAAA-GUGUAGUAUCUGUUCUUAUCAGCUUAAUAUCUGAUA--UACUCUCU-AG-UGAGAGUUAAA----------AAUAUUAUA------CUGAUUUUUGAAACGU------GGUG-GAAGUUUU-------AGAGC---U-----U----G-CUCUA-------CUUC-UACCGU-GAGUCGG---CAUGACAUUGCAGAUU------UGUCGUG-UUU--------CGGCUCAAUAUUA
AAGJ04020931.1/13670-13861     AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAU--GUGUAGUAUCUGUUCUUUUCAGCUUAAUAUCUGAAA--CGCGACUC-ACCGAGUCGCUUG-----------UAUAUUAAA------CUGAUUUUUGAAUCUA------GACC-AUGGAAUA-------GGGGC---U-----U----G-CUCCA-------UCCU-GGUCAC-GGGUUGG---CCCGGUAUUGCAGUAC------CUCCGGG--AU--------CGGCCCACCCCUC
AAGU03035529.1/35295-35485     AUUGCU-UCU----UGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--AGUCCGCU-AUCUGAGGACAA------------UAUAUUAAA------CAGAUUUUCGGAGCUG------GGAG-AUGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-CUUCUC-UCAUCGA---CUUGGUAUUGCACUAC------CUCCAGG--AA--------GGGUGCAUGCCUC
AFQF01002518.1/111488-111680   UUAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GAUGUCU-AA-GGACAUCAAUC----------GUGAUUAUU------CCUAUUUUUGGCUUUC------GGGC-AGUUUCCUC------UGUGC---U-----U----G-CACAU-----GAUUCU-GCCCAC-AGUGUC----CCUGGUAUUACACUGC------CUCCAGG---U--------GACGCGAACACUA
AAGW02065159.1/39337-39527     AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA------------CAUAUUAAA------UGGAUUUUUGGAGCCG------GGAG-UUGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCUC-GCAUCGA---CCCGGUAUUGCAGUAC------CUCCGGG--CA--------CGGUGCAAAAAAA
AAWZ02022241.1/1219-1409       AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUCCUCU-AUCUGAGGACUA------------UAUAUUAAA------UGGAUUUUUGGACUUG------GGAG-AUGGAAUA-------GGGGC---U-----U----G-CUCCA-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUGC------UUCCAGG--AA--------CGGUGCACCUCCC
CAAB02025078.1/1453-1643       AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCCCU-ACCCGGGGACCA------------UAUAUUAAA------UUGAUUUUUGGAACAG------GGAG-AUGGAAUA-------GGGGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAU------CUCCAGG--AA--------CGGUGCACCCCCC
AAQR03042593.1/1155-1347       AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA------------CGUAUUAAA------UGGAUUUUUGGAGUAG------GGAGUUGGAACUA-------GGAGC---U-----U----G-CUCUG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAUC-----UUCCGGG--AA--------CGGUGCACCCUUC
AACU03000093.1/631552-631747   CCAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---CUGGUCU-AUUUGACCAGAAUCAA--------AUGAUUAUA------CUUAUUUUUGUCACUA------GGAG-GGUUUCCGC------UGGGC---U-----U----G-CCCAU-----GAUUCC-CUCCAC-UGUGUC----CCUCCUAUCACACUGC------CUGGAGG---C--------GACGCGAACCUUU
AE014186.2/1461495-1461298     CACCCU-UCU----CGGCC--UCU-U-GGCUAAGAUCAAU-UUGUAGUACCUGUUCUUAUCAGCGUGAUAGCUGAUA--UGGUCUCA-AU-AGAGGCCUUAUC---------AAUUUCACA------AAAAUUUUUGAUAGGG------GAAA-GGAUAAUUU------GAAGC---U-----U----G-CUUCU----UAUAACC-UUUCGC-GCGUUGC---CUUACCCUUGCACUAA------AGGUUUG--UA--------CAGUGCACCCUUA
FR799006.1/251703-251558       AUAUCU-UCU----CGGCU--AUU-U-AGCUAAGAUCAU--GUUUAUAAACUGUUCUUAUCAGAGUAACUCCUGAUA--CUGCCU----UC--GGGCAAA---------------GGAAUA------GAAAUUAUAAGUCGAG--------------------------------------------------------------------GU-UGUUUC----CCUGGAGCUCCACCUU-------UCCAGG------------GGAGCAACUUCUU
AAFN02000024.1/475809-475596   AUC----UCU----UUGCC--AUU-U-GGCUUAGAUCCA--GUGUAGUAUCUGUUCUUUUCAGUGUAACAGCUGAAA---UGUCAUC-AUUGAUGACUUUACAUUAUGUUACAAAUUUAUA------CUUAUUUUUGGAUAUUGG----GUAG-AUUGAUGUAUUAAAGUGGGC---U-----U----G-CUCAC----AGUCUUU-CUACAU-AGUGUCG---UUGCCA-CUGUACUUUUAUU--UUGGCUU--CU--------GACGCAAAUUCUU
K00034.1/420-610               AUCGCU-UCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--CGUCCUCU-AUCCGAGGACAA------------UAUAUUAAA------UGGAUUUUUGGAACUA------GGAG-UUGGAAUA-------GGAGC---U-----U----G-CUCCG-------UCCA-CUCCAC-GCAUCGA---CCUGGUAUUGCAGUAC------CUCCAGG--AA--------CGGUGCACCCCCU
ABDG02000029.1/618164-617972   UUAGCUCUCU----UUGCC--UUU-U-GGCUUAGAUCAA--GUGUAGUAUCUGUUCUUUUCAGUUUAAUCUCUGAAA---GGUCUCU-AA-GGAGACCAAUC----------GUGAUUAUU------CUUAUUUUUGUCCUCA------GGGC-GGUCUCCUC------UGUGC---U-----U----G-CACAU-----GAUUCC-GCCCAC-AGUGUC----CCUGGUAUUACACUGC------CUCCAGG---C--------GACGCGAACACUU
AP004871.3/124344-124540       AUACCUUUCU----CGGCC--UUU-U-GGCUAAGAUCAA--GUGUAGUAUCUGUUCUUAUCAGUUUAAUAUCUGAUA--UGUGGGCC-AUGUGCCCACUUC-----------GAUAUUAAA------UUUAUUUUUUGUGGGG------GAGG-GCCCACUACA-----GUGGC---U-----U----G-CCACU------GGGGU-CCUCGC-GUGUCGC---CCAGGCGUUGCACUAC------AGCCUGG-GCC--------UGGCGCACCCCAA
#=GC SS_cons                   ::::::.<<<....-<<<<..___._.>>>>->>>,,,,..,,,,,,,,,,,,,,,,<<<<<<________>>>>>>..,<<<<<<<.___>>>>>>>,,,...........,,,,,,,,,......,,,,,,,,,,,,,,,,......<<<<.<<<<----.......<<<<<..._....._....>.>>>>-......->>>>.>>>>,,.<<<<<<-...<<<<<<__________......_>>>>>>..--........>>>>>>:::::::
#=GC RF                        AUacCU.UCu....cgGCc..UUU.U.gGCuaaGAUCAA..GUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauA..uggccccc.Auugggggccaau...........uauaUUAaa......uuaAUUUUUggaacua......Gugg.gggcauuu.......uggGC...U.....U....G.Cccau......ugccc.ccaCac.ggguuga...ccuggcaUUGCAcUac......cgccagg..uu........cagcccAcccuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00005
#=GF ID   tRNA
#=GF DE   tRNA
#=GF AU   Eddy SR; 0000-0001-6676-4706
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Mifsud W; 0000-0002-9805-6461
#=GF SE   Eddy SR
#=GF SS   Published; PMID:8256282
#=GF GA   29.00
#=GF TC   29.00
#=GF NC   28.90
#=GF TP   Gene; tRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00001
#=GF DR   SO; 0000253; tRNA;
#=GF DR   GO; 0030533; triplet codon-amino acid adaptor activity;
#=GF RN   [1]
#=GF RM   8256282
#=GF RT   The tertiary structure of tRNA and the development of the genetic code.
#=GF RA   Hou YM
#=GF RL   Trends Biochem Sci 1993;18:362-364.
#=GF RN   [2]
#=GF RM   9023104
#=GF RT   tRNAscan-SE: a program for improved detection of transfer RNA genes in
#=GF RT   genomic sequence.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Nucleic Acids Res 1997;25:955-964.
#=GF CC   Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length.
#=GF CC   Their secondary structure includes four short double-helical elements and
#=GF CC   three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate
#=GF CC   the characteristic L-shaped molecular structure. tRNAs have two regions of
#=GF CC   fundamental functional importance: the anti-codon, which is responsible
#=GF CC   for specific mRNA codon recognition, and the 3' end, to which the tRNAs
#=GF CC   corresponding amino acid is attached (by aminoacyl-tRNA synthetases).
#=GF CC   tRNAs cope with the degeneracy of the genetic code in two manners: having
#=GF CC   more than one tRNA (with a specific anti-codon) for a particular amino
#=GF CC   acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing
#=GF CC   at the 3rd anti-codon position.
#=GF WK   Transfer_RNA
#=GF SQ   954


AB003409.1/96-167          GGGCCCAU-A-GCUCAGU---GGU---AGAGUG-C-CUCCU-UUGCAAGGAG-GAU------------------------GC--CCUG-GGU-UCG-AA--UCCCA-G-UGGGUCC-A
AB009835.1/1-71            CAUUAGAU-G-ACUGAA----AG----CAAGUA-C-UGGUC-UCUUAAACCA-UUU------------------------AA--UAGUAAAU-UAG-CA--CUUAC-U-UCUAAUG-A
AB013372.1/8-81            GCGCCCGU-A-GCUCAAUU--GGAU--AGAGCG-U-UUGAC-UACGGAUCAA-AAG------------------------GU--UAGG-GGU-UCG-AC--UCCUC-U-CGGGCGC-G
AB013373.1/3754-3825       GCGGAAGU-A-GUUCAGU---GGU---AGAACA-C-CACCU-UGCCAAGGUG-GGG------------------------GU--CGCG-GGU-UCG-AA--UCCCG-U-CUUCCGC-U
AB017063.1/58819-58900     GUGGACGU-G-CCGGAGU---GGUU--AUCGGG-C-AUGAC-UAGAAAUCAU-GU--GGG-C---UUU--------GCCCG---CGCA-GGU-UCG-AA--UCCUG-C-CGUUCAC-G
AB027572.1/4261-4342       GGGUCGAU-G-CCCGAGU---GGUUA-AUGGGG-A-CGGAC-UGUAAAUUCG-UU--GAC-----AAU---------GUCUA--CGCU-GGU-UCA-AA--UCCAG-C-UCGGCCC-A
AB031211.1/7799-7884       GCCGGGGU-G-GUGGAAUU--GGCA--GACACA-C-AGGAC-UUAAAAUCCU-GC--GGU-AG--GUG---A---CUACCG---UGCC-GGU-UCA-AG--UCCGG-C-CCUCGGC-A
AB031211.1/8065-8137       GGGGCCUU-A-GCUCAGCU--GGG---AGAGCG-C-CUGCU-UUGCACGCAG-GAG------------------------GU--CAGC-GGU-UCG-AU--CCCGC-U-AGGCUCC-A
AB031213.1/2203-2276       GGUCCGGU-A-GUUCAGUU--GGUU--AGAAUG-C-CUGCC-UGUCACGCAG-GAG------------------------GU--CGCG-GGU-UCG-AG--UCCCG-U-CCGGACC-G
AB031213.1/2678-2748       GCGGGUGU-A-GUUUAGU---GGU---AAAACC-U-CAGCC-UUCCAAGCUG-AUG------------------------U---CGUG-GGU-UCG-AU--UCCCA-U-CACCCGC-U
AB031214.1/4204-4277       GGGCCUGU-A-GCUCAGCU--GGUU--AGAGCG-C-ACGCC-UGAUAAGCGU-GAG------------------------GU--CGGU-GGU-UCG-AG--UCCAC-U-CAGGCCC-A
AB031215.1/9125-9195       AGGGGCAU-A-GUUUAAC---GGU---AGAACA-G-AGGUC-UCCAAAACCU-CCG------------------------G---UGUG-GGU-UCG-AU--UCCUA-C-UGCCCCU-G
AB035922.1/6128-6200       AGGGGCGU-A-GUUCAAUU--GGU---AGAGCA-C-CGGUC-UCCAAAACCG-GGU------------------------GU--UGGG-AGU-UCG-AG--UCUCU-C-CGCCCCU-G
AB035923.1/6106-6178       GCUGAUAU-G-GCUCAGUU--GGU---AGAGCG-C-ACCCU-UGGUAAGGGU-GAG------------------------GU--CCCC-AGU-UCG-AC--UCUGG-G-UAUCAGC-A
AB042240.3/6758-6687       UGGGGCGU-G-GCCAAGU---GGU---AAGGCA-G-CGGGU-UUUGGUCCCG-UUA------------------------CU--CGGA-GGU-UCG-AA--UCCUU-C-CGUCCCA-G
AB042240.3/15036-15107     GCCCUUUU-A-ACUCAGU---GGU---AGAGUA-A-UGCCA-UGGUAAGGCA-UAA------------------------GU--CAUC-GGU-UCA-AA--UCCGA-U-AAAGGGC-U
AB042240.3/36390-36319     GCGUCCAU-U-GUCUAAU---GGAU--AGGACA-G-AGGUC-UUCUAAACCU-UUG------------------------G---UAUA-GGU-UCA-AA--UCCUA-U-UGGACGC-A
AB042240.3/82974-82901     GCAUCCAU-G-GCUGAAU---GGUU--AAAGCG-C-CCAAC-UCAUAAUUGG-UAA------------------------AUU-UGCG-GGU-UCA-AU--UCCUG-C-UGGAUGC-A
AB042240.3/84552-84472     GCCUUGAU-G-GUGAAAU---GGU-A-GACACG-C-GAGAC-UCAAAAUCUC-GU--GCU-----AAA---G-----AGCG---UGGA-GGU-UCG-AG--UCCUC-U-UCAAGGC-A
AB042432.1/3845-3913       AGUAAGGU-C-AGCUAA----UU----AAGCUA-U-CGGGC-CCAUACCCCG-AAA------------------------A---CGUU-GGU-UUA-AA--UCCUU-C-CCGUACU-A
AB042432.1/6942-7011       AAGAUAUU-A-GUAAAAU---CA----AUUACA-U-AACUU-UGUCAAAGUU-AAA------------------------U---UAUA-GAU-CAA-UA--AUCUA-U-AUAUCUU-A
AB042432.1/14140-14072     GUUUCUGU-A-GUUGAA----UU----ACAACG-A-UGAUU-UUUCAUGUCA-UUG------------------------G---UCGC-AGU-UGA-AU--GCUGU-G-UAGAAAU-A
AB042524.1/5257-5192       GGUCUUAA-G-GUGAUA----------UUCAUG-U-CGAAU-UGCAAAUUCG-AAG------------------------G---UGUA-GAG-AAA-U---CUCUA-C-UAAGACU-U
AB042524.1/9391-9458       ACUCCCUU-A-GUAUAA----UU----AAUAUA-A-CUGAC-UUCCAAUUAG-UAG------------------------A---UUCU-GAA-UAA-AC---CCAG-A-AGAGAGU-A
AB042809.1/5159-5089       UAGAUUGA-A-GCCAGUA---AU----AGGGUA-U-UUAGC-UGUUAACUAA-AUU------------------------UU--CGUA-GGU-UUA-AU--UCCUG-C-CAAUCUA-G
AB042809.1/7700-7764       CACUAUGA-A-GCUA------------AGAGCG-U-UAACC-UUUUAAGUUA-AAG------------------------UU--AGAG-ACC-UUA-AA---AUCU-C-CAUAGUG-A
AB049357.1/1-68            GUUAAUGU-A-GCUUAAUA--AC----AAAGCA-A-AGCAC-UGAAAAUGCU-UAG------------------------A---UGGA-U-A-AUU-GU----AUC-C-CAUAAAC-A
AB049357.1/11673-11743     ACUUUUAU-A-GGAUAAU---AGU---AAUCCA-U-UGGUC-UUAGGAACCA-AAA------------------------A---CCUU-GGU-GCA-AA--UCCAA-A-UAAAAGU-A
AB066098.1/1687-1760       GGGCCUAU-A-GCUCAGCU--GGUU--AGAGUG-C-ACCCC-UGAUAAGGGU-GAG------------------------GU--CACA-AGU-UCA-AG--UCUUG-U-UAGGCCC-A
AB067577.1/1615-1688       GGGCUAUU-A-GCUCAGGU--GGUU--AGAGCG-C-ACCCC-UGAUAAGGGU-GAG------------------------GU--CCCU-GGU-UCA-AG--UCCAG-G-AUGGCCC-A
AC002512.1/77401-77473     GCCCGGAU-A-GCUCAGUC--GGU---AGAGCA-U-UGGAC-UUUUAAUCCA-AGG------------------------GU--CCAG-GGU-UCA-AG--UCCCU-G-UUCGGGC-G
AC004941.2/32735-32806     GGGGGUAU-A-GCUCAGGG--GUA----GAGCA-U-UUGAC-UGCAGAUCAA-GAG------------------------GU--CCCU-GGU-UCA-AA--UCCAG-G-UGCCCCC-U
AC005329.1/7043-6971       GCCGAAAU-A-GCUCAGUU--GGG---AGAGCG-U-UAGAC-UGAAGAUCUA-AAG------------------------GU--CCCU-GGU-UCG-AU--CCCGG-G-UUUCGGC-A
AC005783.1/27398-27326     GUUUCCGU-A-GUGUAGC---GGUU--AUCACA-U-UCGCC-UCACACGCGA-AAG------------------------GU--CCCC-GGU-UCG-AU--CCCGG-G-CGGAAAC-A
AC006449.19/196857-196784  GUCUCUGU-G-GCGCAAUC--GGUU--AGCGCG-U-UCGGC-UGUUAACCGA-AAG------------------------GU--UGGU-GGU-UCG-AG--CCCAC-C-CAGGGAC-G
AC007298.17/145366-145295  UCCUCGUU-A-GUAUAGU---GGUG--AGUAUC-C-CCGCC-UGUCACGCGG-GAG------------------------A---CCGG-GGU-UCG-AU--UCCCC-G-ACGGGGA-G
AC008345.4/147881-147810   AGCAGAGU-G-GCGCAGU---GGA---AGCGUG-C-UGGGC-CCAUAACCCA-GAG------------------------GU--CCGA-GGA-UCG-AA--ACCUU-G-CUCUGCU-A
AC008443.10/8240-8321      GGUAGCGU-G-GCCGAGC---GGUCU-AAGGCG-C-UGGAU-UAAGGCUCCA-GU--CUC-----UUC---G-----GGGG---CGUG-GGU-UCG-AA--UCCCA-C-CGCUGCC-A
AC008443.10/9027-8955      GUUUCCGU-A-GUGUAGU---GGUC--AUCACG-U-UCGCC-UAACACGCGA-AAG------------------------GU--CCCC-GGU-UCG-AA--ACCGG-G-CGGAAAC-A
AC008443.10/42590-42518    GCCCGGCU-A-GCUCAGUC--GGU---AGAGCA-U-GAGAC-UCUUAAUCUC-AGG------------------------GU--CGUG-GGU-UCG-AG--CCCCA-C-GUUGGGC-G
AC008443.10/43006-42934    GUUUCCGU-A-GUGUAGU---GGUU--AUCACG-U-UCGCC-UCACACGCGA-AAG------------------------GU--CCCC-GGU-UCG-AA--ACCGG-G-CGGAAAC-A
AC008670.6/83597-83665     GUAAAUAU-A-GUUUAA----CC----AAAACA-U-CAGAU-UGUGAAUCUG-ACA------------------------A---CAGA-GGC-UCA-CG--ACCCC-U-UAUUUAC-C
AC008670.6/83725-83795     ACUUUUAA-A-GGAUAAC---AGC---CAUCCG-U-UGGUC-UUAGGCCCCA-AAA------------------------A---UUUU-GGU-GCA-AC--UCCAA-A-UAAAAGU-A
AC009323.4/12825-12742     GUGGACAU-G-CCGGAGU---GGUGUUAUCGGG-C-AUAAC-UAGAAAUCAU--GU-GGG-C---UUU--------GCCCG---CGCA-GGU-UCG-AA--UCAUG-C-CGUUUAC-G
AC009323.4/14362-14281     GUGGACGU-G-CCGGAGU---GGUU--AUCGGG-A-AUGAC-UAGAAAUCAU-GGA-GGC-----UUU---------GCCCG--CGCA-CGU-UUG-AA--UCUUG-C-CGUUUAC-G
AC009395.7/99012-98941     GGCUCAAU-G-GUCUAGG---GGU---AUGAUU-C-UCGCU-UUGGGUGCGA-GAG------------------------GU--CCCG-GGU-UCA-AA--UCCCG-G-UUGAGCC-C
AC009461.5/128651-128579   GUUUCCGU-G-GUGUAGU---GGUU--AUCACA-U-CCGCC-UAACACGCGG-AAG------------------------GC--CCCC-GGU-UCA-AU--CCCGG-G-CGGAAAC-A
AC009742.4/51767-51839     GUUUUCGU-A-GUGUAGU---GGUU--AUCACG-U-GUGCU-UCACACGCAC-AAG------------------------GU--CCCC-GGU-UCG-AA--CCCGG-G-CGAAAAC-A
AC018638.5/4694-4623       GGCUCGUU-G-GUCUAGG---GGU---AUGAUU-C-UCGCU-UAGGGUGCGA-GAG------------------------GU--CCCG-GGU-UCA-AA--UCCCG-G-ACGAGCC-C
AC018907.5/9587-9517       GCACCAGU-G-GUCUAGU---GGU---AGAAUA-G-UACCC-UGCCACGGUA-CAG------------------------A---CCCG-GGU-UCG-AU--UCCCG-G-CUGGUGC-A
AC021639.5/181586-181505   GCAGUCGU-G-GCCGAGU---GGUU--AAGGCG-U-CUGAC-UCGAAAUCAG-AU--UCC-C---UCU--------GGGAG---CGUA-GGU-UCG-AA--UCCUA-C-CGGCUGC-G
AC024995.8/165717-165798   GUAGUCGU-G-GCCGAGU---GGUU--AAGGCG-A-UGGAC-UAGAAAUCCA-UU--GGG-G---UCU--------CCCCG---CGCA-GGU-UCG-AA--UCCUG-C-CGACUAC-G
AC067849.6/4771-4840       CACUGUAA-A-GCUAAC----------UUAGCA-U-UAACC-UUUUAAGUUA-AAG------------------------AU--UAAG-AGA-ACC-AACACCUCU-U-UACAGUG-A
AC068900.3/7333-7404       GUCGUUGU-A-GUAUAGU---GGUA--AGUAUU-C-CCGCC-UGUCACGCGG-GUG------------------------A---CCCG-GGU-UCG-AU--CCCCG-G-CAACGGC-G
AC084429.5/20418-20485     GUGAAUAU-A-GUUUAC----AA----AAAACA-U-UAGAC-UGUGAAUCUG-ACA------------------------A---CAGG-AAA-UAA-AC---CUCC-U-UAUUCAC-C
AC084571.1/17976-18047     GGCCGAAU-G-GUCUAGU---GGU---AUGAUU-C-UCGCU-UUGGGUGCGA-GAG------------------------GU--CCCG-GGU-UCA-AU--CCCCG-G-UUCGGCC-C
AC084609.1/20256-20184     GCCCGGUU-A-GCUCAGUC--GGU---AGAGCA-C-CAGAC-UCUUAAUCUG-GUU------------------------GU--CGCG-GGU-UCG-AG--CCCCG-C-AUUGGGC-U
AC092686.3/29631-29561     GCAUUGGU-G-GUUCAGU---GGU---AGAAUU-C-UCGCC-UGCCACGCGG-GAG------------------------G---CCCG-GGU-UCG-AU--UCCCG-G-CCAAUGC-A
AC093311.2/140036-139968   GUUCUUGU-A-GUUGAA----AU----ACAACG-A-UGGUU-UUUCAUAUCA-UUG------------------------G---UCGU-GGU-UGU-AG--UCCGU-G-CGAGAAU-A
AC099014.1/146549-146620   GCCGUGAU-C-GUCUAGU---GGUU--AGGACC-C-CACGU-UGUGGCCGUG-GUA------------------------A---CCCA-GGU-UCG-AA--UCCUG-G-UCACGGC-A
AC108081.2/59868-59786     GUCAGGAU-G-GCCGAGC---GGUCU-AAGGCG-C-UGCGU-UCAGGUCGCA-GU--CUC-C---CCU--------GGAGG---CGUG-GGU-UCG-AA--UCCCA-C-UUCUGAC-A
AC122544.1/63069-62986     GUCAGGAU-G-GCCGAGU---GGUCU-AAGGCG-C-CAGAC-UCAAGUUCUG-GU--CCU-CGU----------GAGAGGG---CGUG-GGU-UCA-AA--UCCCA-C-UUCUGAC-A
AF004309.1/87-160          CGGGGUGU-G-GCGCAGCU-UGGU---AGCGCG-C-UUCGU-UCGGGACGAA-GAG------------------------GU--CGUG-GGU-UCA-AA--UCCCG-C-CACCCCG-A
AF008220.1/5322-5394       GGAGGAUU-A-GCUCAGCU--GGG---AGAGCA-U-CUGCC-UUACAAGCAG-AGG------------------------GU--CGGC-GGU-UCG-AG--CCCGU-C-AUCCUCC-A
AF008220.1/5430-5502       GCCGGUGU-A-GCUCAAUU--GGU---AGAGCA-A-CUGAC-UUGUAAUCAG-UAG------------------------GU--UGGG-GGU-UCA-AG--UCCUC-U-UGCCGGC-A
AF008220.1/5629-5712       GCGGAUGU-G-GCGGAAUU--GGCA--GACGCG-C-UAGAA-UCAGGCUCUA-GU--GUC-U---UUA---C----AGACG---UGGG-GGU-UCA-AG--UCCCU-U-CAUCCGC-A
AF008220.1/5997-6070       CGGGAAGU-A-GCUCAGCU-UGGU---AGAGCA-C-AUGGU-UUGGGACCAU-GGG------------------------GU--CGCA-GGU-UCG-AA--UCCUG-U-CUUCCCG-A
AF008220.1/6172-6245       GGCGGUGU-A-GCUCAGCU--GGCU--AGAGCG-U-ACGGU-UCAUACCCGU-GAG------------------------GU--CGGG-GGU-UCG-AU--CCCCU-C-CGCCGCU-A
AF008220.1/6251-6324       GGACCUUU-A-GCUCAGUU--GGUU--AGAGCA-G-ACGGC-UCAUAACCGU-CCG------------------------GU--CGUA-GGU-UCG-AG--UCCUA-C-AAGGUCC-A
AF008220.1/6334-6422       GGAGGAAU-A-CCCAAGUC-UGGCUG-AAGGGA-U-CGGUC-UUGAAAACCG-AC--AGG-GUG-UCA---A--AGCCCG----CGGG-GGU-UCG-AA--UCCCU-C-UUCCUCC-G
AF008220.1/6443-6516       CGCGGGGU-G-GAGCAGUU-CGGU---AGCUCG-U-CGGGC-UCAUAACCCG-AAG------------------------GU--CGCA-GGU-UCA-AA--UCCUG-C-CCCCGCA-A
AF008220.1/6620-6692       GGCUCGGU-A-GCUCAGUU--GGU---AGAGCA-A-CGGAC-UGAAAAUCCG-UGU------------------------GU--CGGC-GGU-UCG-AU--UCCGU-C-CCGAGCC-A
AF008220.1/6713-6785       GCGGUUGU-G-GCGAAGU---GGUU--AACGCA-C-CAGAU-UGUGGCUCUG-GCA------------------------UU--CGUG-GGU-UCG-AU--UCCCA-U-CAAUCGC-C
AF008220.1/6888-6961       GGGCCUGU-A-GCUCAGCU--GGUU--AGAGCG-C-ACGCC-UGAUAAGCGU-GAG------------------------GU--CGAU-GGU-UCG-AG--UCCAU-U-CAGGCCC-A
AF008220.1/6975-7046       UCCACAGU-A-GCUCAGU---GGU---AGAGCU-A-UCGGC-UGUUAACCGA-UCG------------------------GU--CGCA-GGU-UCG-AA--UCCUG-C-CUGUGGA-G
AF008220.1/7053-7140       GGAGAAGU-A-CUCAAGU---GGCUG-AAGAGG-C-GCCCC-UGCUAAGGGU-GUA-GGU-CGU-GUA---A--GCGGCG----CGAG-GGU-UCA-AA--UCCCU-C-CUUCUCC-G
AF008220.1/7169-7240       GGCCCGUU-G-GUCAAGC---GGUU--AAGACA-C-CGCCC-UUUCACGGCG-GUA------------------------A---CACG-GGU-UCG-AA--UCCCG-U-ACGGGUC-A
AF034440.1/1115-1181       GUUGAUGU-A-GCUUAAC---CC----AAAGCA-A-GGCAC-UGAAAAUGCC-UAG------------------------A---UGAG-U-C-UCC-CA----ACU-C-CAUAAAC-A
AF037042.2/2935-2864       UCCUCAUU-G-GUGUAGUC--GGU---AACACU-C-UAGUC-UUUCACACUG-GUA------------------------C---CUCG-GGU-UCG-AU--UCCCG-A-AUGGGGA-G
AF041468.1/40566-40494     GGGGGUAU-A-GCUCAGUU--GGU---AGAGCG-C-UGCCU-UUGCACGGCA-GAU------------------------GU--CAGG-GGU-UCG-AG--UCCCC-U-UACCUCC-A
AF041468.1/43811-43739     GGGCUCAU-C-GUCUAAU---GGAUC-AGGACA-G-GGACC-UUCUAAGUCU-CUA------------------------A---UGUA-GGU-UCG-AA--UCCUA-C-UGAGCCU-A
AF047723.1/4036-4107       GUCCGUGU-G-GCUCAAU---GGA---AGAGCA-U-CUGAC-UACGGAUCAG-AGG------------------------GU--UGCA-GGU-UCG-AA--UCCUG-U-CACGGAU-G
AF047724.1/439-367         GCCCUUCU-A-GCUCAGUC--GGU---AGAGCG-C-ACGGC-UCUUAACCGU-GUG------------------------GU--CGUG-GGU-UCG-AG--CCCCA-C-GGGGGGU-G
AF047724.1/711-640         GGUCCUAU-A-GUGUAGU---GGUU--AUCACU-U-CGGAC-UUUGAAUCCG-AAA------------------------A---CCCA-GGU-UCG-AA--UCCUG-G-UAGGACC-A
AF052653.1/130-203         AGCGGGGU-A-GAGUAAUU--GGUC--AACUCA-U-CAGGC-UCAUGACCUG-AAG------------------------AU--UGCA-GGU-UCG-AA--UCCUG-U-CCCCGCC-U
AF067200.1/16-89           GUUCGGAU-G-GUGUAGUC--GGUU--AUCACG-A-AUCCU-UAACACGGAU-UAG------------------------GU--CGUG-GGU-UCG-AU--UCCCG-C-UCUGAAU-A
AF069749.1/1422-1494       UCCUCUGU-A-GUUCAGUC--GGU---AGAACG-G-CGGAC-UGUUAAUCCG-UAU------------------------GU--CACU-GGU-UCG-AG--UCCAG-U-CAGAGGA-G
AF074839.1/52-124          GGGGAAUU-A-GCUCAGCU--GGG---AGAGCG-C-CUGCU-UUGCACGCAG-GAG------------------------GU--CAGC-GGU-UCG-AU--CCCGC-U-AUUCUCC-A
AF076356.1/60-128          GCUCUUCU-A-GUAUAC----UC----AUUACA-A-CUGAC-UUCCAAUCUU-UAA------------------------A---AUCU-GGU-AUC-AA--CCCAG-A-GAAGAGC-A
AF083212.1/212-284         GGGGCCAU-A-GCUCAGCU--GGG---AGAGCG-C-CUGCU-UUGCACGCAG-GAG------------------------GU--CAGG-AGU-UCG-AU--CCUCC-U-UGGCUCC-A
AF105125.1/104-176         GGGGGUUU-A-GCUCAGUU--GGU---AGAGCG-C-CUGCU-UUGCAAGCAG-GAU------------------------GU--CAGC-GGU-UCG-AG--UCCGC-U-AACCUCC-A
AF108356.1/1-74            GGGCCCGU-A-GCUUAGUCU-GGU---AGAGCG-C-CUGAC-UUUUAAUCAG-GCG------------------------GU--CGAG-GGU-UCG-AA--UCCCU-U-CGGGCCC-G
AF125213.1/1282-1213       CAGAGGGU-A-GUUUAAU---UU----AGAAUC-U-UAGCU-UUGGGAGUUA-AGG------------------------G---UGGG-AGU-UAA-AA--UCUCC-U-CUCUCUG-A
AF127584.1/98-171          GGGUCUGU-A-GCUCAGUU--GGUU--AGAGCG-C-ACCCC-UGAUAAGGGU-GAG------------------------GU--CGGC-AGU-UCG-AA--UCUGC-C-CAGACCC-A
AF134583.1/1599-1666       AGAAAUUU-A-GGUUAAAU--AC----AGACCA-A-GAGCC-UUCAAAGCCC-UCA------------------------G---UAAG-U-U-GCA-AU----ACU-U-AAUUUCU-G
AF134583.1/1816-1744       UAGAUUGA-A-GCCAGUU---GAUU--AGGGUG-C-UUAGC-UGUUAACUAA-GUG------------------------UU--UGUG-GGU-UUA-AG--UCCCA-U-UGGUCUA-G
AF155162.1/115-49          CAAGGAAU-A-GUUUAU----GU----AGAAUU-C-CAGCU-UUGGGUGUUG-GUG------------------------G---UGAG-GU--UUA-AU---GUCU-C-UUCCUUG-A
AF158101.6/72033-71960     GGCCCUGU-A-GCUCAAU---GGUUA-GCAGCA-G-UCCCC-UCAUAAGGGA-AAG------------------------GU--UACC-AGU-UCA-AA--UCUGG-U-CUGGGUC-A
AF158101.6/72364-72294     GCGGAUAU-C-GUAUAAU---GGU---AUUACC-U-CAGAC-UUCCAAUCUG-AUG------------------------A---UGUG-AGU-UCG-AU--UCUCA-U-UAUCCGC-U
AF158101.6/72456-72373     GCGAGAAU-G-GUCAAAUU--GGUA--AAGGCA-C-AGCAC-UUAAAAUGCU-GC--GGA-A---UGA---U----UUCCU---UGUG-GGU-UCG-AG--UCCCA-C-UUCUCGC-A
AF158101.6/72530-72458     UGGGAAUU-A-GCCAAGUU--GGU---AAGGCA-U-AGCAC-UUUGACUGCU-AGA------------------------UG--CAAA-GGU-UCG-AG--UCCUU-U-AUUCCCA-G
AF160864.1/14524-14453     GCUUAAGU-A-GCUCAGU---GGU---AGAGCG-U-CAGGC-UGAAAACCUG-AAG------------------------GU--CAUU-GGU-CCG-AU--UCCAU-U-CUUAGGC-A
AF160864.1/20552-20480     GUGGAUAU-A-GCUCAAUC--GGU---AGAGCG-U-UAGAU-UGUGGAUCUA-AAG------------------------GU--CGCG-GGU-UCG-AU--UCCUG-C-UAUUUAC-C
AF164586.1/93-158          AGUUAAUG-A-GCUUG-----AA----CAAGCG-U-AUGUU-UUGAAAACAU-AAG------------------------A---UAGA-A-U-UUA-AU--U-UUC-U-AUUAACU-U
AF166114.1/53704-53775     GGGUCGCU-A-ACUCAAU---GGU---AGAGUA-C-UCGGC-UUUUAACCGA-CUA------------------------GU--UCCG-GGU-UCG-AA--UCCCG-G-GCGACCC-A
AF185056.1/845-774         CAAUUUAA-A-GCUUAUUA--AGU---AAAGCA-U-UUCAU-UUACAUUGAA-AAG------------------------A---UUUU-UGU-GCA-AA--UCAAU-A-UAAAUUG-A
AF186372.1/596-669         CGCGGGGU-G-GAGCAGCUC-GGU---AGCUCG-C-UGGGC-UCAUAACCCA-GAG------------------------GU--CGCA-GGU-UCA-AA--UCCUG-U-CCCCGCU-A
AF200830.1/9887-9951       GUUUUAAU-A-GUUUAA----UA----AAAACA-U-UGGUC-UUGUAAAUCA-AAA------------------------A---UAAG-A---UUA-UU----UCU-U-UUAAAAC-U
AF200831.1/165-97          UAUAUUUU-G-GUGUAU----GA----UGCACA-A-AAGUU-UUUGAUACUU-UUA------------------------G---AAAU-AGU-UUA-AU--UCUAU-U-AAAUAUA-A
AF200837.1/6039-6103       AGGGUUGU-A-GUUAAUU---------AUAACA-U-UUGAU-UUGCAUUCAA-AAA------------------------G---UAUU-G-A-AU--AU--U-CAA-U-CUACCUU-A
AF200843.1/1266-1331       AAGGCUUU-A-AGUUAA----UA----AAACUA-A-UAACC-UUCAAAGCUA-UAA------------------------A---UAAA-G-A-AAU-UU----CUU-U-AAGCCUU-A
AF217350.1/193-122         GCUUGAGU-A-GCAAAGC---GGUU--AAUGCU-U-GAGAU-UUAGGUUCUC-ACA------------------------U---CAAA-GGU-UCA-AG--CCCUU-U-CUCUAGU-U
AF217350.1/265-194         UGAGUUGU-A-GCCUAGU---GGA---AAGGCG-U-UUGGC-CGUUAACUAA-AAG------------------------AC--AGCA-AGA-UCA-AU--ACUUG-C-CAGCUCA-G
AF233324.1/37223-37296     CGGCGAGU-A-GCGCAGCU-UGGU---AGCGCA-A-CUGGU-UUGGGACCAG-UGG------------------------GU--CGGA-GGU-UCG-AA--UCCUC-U-CUCGCCG-A
AF234285.1/261-333         GGGGCUAU-A-GCUCAGCU--GGG---AGAGCG-C-CUGCU-UUGCACGCAG-GAG------------------------GU--CUGC-GGU-UCG-AU--CCCGC-A-UAGCUCC-A
AF269787.1/2464-2393       UCCGCAGU-A-GCUCAGU---GGU---AGAGCU-A-UCGGC-UGUUAACCGA-UCG------------------------GU--CGUA-GGU-UCG-AA--UCCUA-C-CUGCGGA-G
AF276832.1/1449-1514       UCUAAUAU-G-GCAGAUU---------AGUGCA-A-UGGAU-UUAAGCUCCA-UAU------------------------A---UAAA-GU--AUU-UU---ACUU-U-UAUUAGA-A
AF314016.1/365-435         GGAAGCGU-G-CCUGAA----AGU---UAAGGA-C-CUCCU-UGAUAGGGAG-GCU------------------------UA--UAGG-GGU-UCA-AA--CCCCC-U-CACUUCC-U
AF314016.1/506-436         UAAGGAGU-A-GUAUAAA---GGA---AGUACA-A-AGGGU-UUUGAUCUCU-UAA------------------------G---UAUA-GGU-UCA-AU--UCCUA-U-CUCUUUA-G
AF314018.1/1820-1748       UAGAAUGA-A-GCUCGCU---GGAU--AGAGUG-U-UUAGC-UGUUAACUAA-AAU------------------------AU--UACG-GGA-UCG-AG--GCCCG-U-CAUUCUA-G
AF340025.1/630-698         GCAAACAU-A-GUUUAA----CC----CAAACA-U-UAGAU-UGUGAUUCUA-AAA------------------------A---UAGG-AGU-UUA-AC--CCUCC-U-UGUUCGC-C
AF346992.1/15890-15955     GUCCUUGU-A-GUAUAA----ACU---AAUACA-C-CAGUC-UUGUAAACCG-GAG------------------------A---UGAA-A---ACC-UU----UUU-C-CAAGGAC-A
AF346999.1/4402-4331       UAGGAUGG-G-GUGUGAUA--GGU---GGCACG-G-AGAAU-UUUGGAUUCU-CAG------------------------G---GAUG-GGU-UCG-AU--UCUCA-U-AGUCCUA-G
AF347001.1/16015-15948     CAGAGAAU-A-GUUUAAA---UU----AGAAUC-U-UAGCU-UUGGGUGCUA-AUG------------------------G---UGGA-G-U-UAA-AG--A-CUU-U-UUCUCUG-A
AF347005.1/12268-12338     ACUUUUAA-A-GGAUAAC---AGC---UAUCCA-U-UGGUC-UUAGGCCCCA-AAA------------------------A---UUUU-GGU-GCA-AC--UCCAA-A-UAAAAGU-A
AF347015.1/1604-1672       CAGAGUGU-A-GCUUAAC---AC----AAAGCA-C-CCAAC-UUACACUUAG-GAG------------------------A---UUUC-AAC-UUA-AC---UUGA-C-CGCUCUG-A
AF347015.1/5827-5762       AGCUCCGA-G-GUGAUU----------UUCAUA-U-UGAAU-UGCAAAUUCG-AAG------------------------A---AGCA-GCU-UCA-AA---CCUG-C-CGGGGCU-U
AF347015.1/5892-5827       GGUAAAAU-G-GCUGAGU---------GAAGCA-U-UGGAC-UGUAAAUCUA-AAG------------------------A---CAGG-GG--UUA-GG---CCUC-U-UUUUACC-A
AF349769.2/1315-1395       CCCCGUGU-G-GCGAAAU---GGUA--GACGCG-C-UUGAC-UCAAAAUCAA-GU--AGU-----GAA---G-----ACUG---UGCU-GGU-UCG-AG--UCCGG-U-CACGGGG-A
AF381996.2/4265-4333       AGAAAUAU-G-UCUGAUA---------AAAGAG-U-UACUU-UGAUAGAGUA-AAU------------------------AA--UAGG-AGC-UUA-AA--CCCCC-U-UAUUUCU-A
AF382005.1/581-651         GUUUAUGU-A-GCUUACCU-CCUC---AAAGCA-A-UACAC-UGAAAAUGUU-UAG------------------------A---CGGG-C-U-CAC-AU--C-ACC-C-CAUAAAC-A
AF382013.1/10403-10467     UGGUAUAU-A-GUUUAA----AC----AAAACG-A-AUGAU-UUCGACUCAU-UAA------------------------A---UUAU-G---AUA-AU----CAU-A-UUUACCA-A
AF396436.1/528-448         ACUUAUGU-G-GCGGAAUA--GGUA--GACGCG-U-GGGAC-UUAAAAUCUC-AU--UCC-----UAC---------GGAG---UGCC-GGU-UCG-AC--CCCGG-U-CAUAAGU-A
AF396436.1/47447-47513     GCCGCUUG-G-AUGGU-----------UCCGGU-G-UGGGC-UCAUUUCCCA-UAA------------------------CU--AUAA-AGU-UCG-AU--UCUUU-A-AAGUGGC-U
AF401668.1/481-552         GCGGAAGU-A-GUUCAGU---GGU---AGAACA-U-CACCU-UGCCAUGGUG-GGG------------------------GU--CGCG-GGU-UCG-AA--UCCCG-U-CUUCCGC-U
AF449163.1/604-532         GCCCCUAU-C-GUCUAGU---GGUUC-AGGACA-U-CUCUC-UUUCAAGGAG-GCA------------------------G---CGGG-GAU-UCG-AC--UUCCC-C-UGGGGGU-A
AF467991.1/42-125          GCCCGAGU-G-GUGGAAUC--GGUA--GACACA-A-GGGAU-UUAAAAUCCC-UC--GCC-UUU----------CGAGGCG---UGCC-AGU-UCA-AG--UCUGG-C-UUCGGGC-A
AF487242.1/558-475         GGGUCGAU-G-CCCGAGC---GGUUA-AUGGGG-A-CGGAC-UGUAAAUUCG-UU--GGC-A---AUA--------UGUCUA--CGCU-GGU-UCA-AA--UCCAG-C-UCGGCCC-A
AF490528.1/1519-1448       UAGAAUUU-G-GUGUAAUU--GGG---AGCACG-A-AGAGU-UUUGGAUUCU-UAG------------------------G---AGUA-GGU-UCG-AU--UCCUA-U-AGUUCUA-G
AF490528.1/4630-4697       GAGGUGUU-A-GUAAA-----AC----AUUAUA-U-AAUUU-UGUCAAAGUU-AAG------------------------U---UACA-AGU-GAA-AG--UCCUG-U-ACACCUC-A
AF490529.1/2769-2701       GAGGAUUU-A-GCUUAA----UU----AAAGUG-G-UUGAU-UUGCAUUCAA-UUG------------------------A---UGUA-AGG-UGU-AG--UCUUG-C-AAUCCUU-A
AF490529.1/3010-2943       GGUAAAAU-G-GCUGAGC---------AAAGCA-U-UAGAC-UGUAAAUCUA-AAG------------------------A---UAGA-GGU-UUG-AC--UCCUC-U-UUUUACC-A
AF490529.1/11834-11766     GUUCUUGU-A-GUUGAA----UG----ACAACG-A-UGGUU-UUUCAUAUCA-UUA------------------------G---UCAU-GGU-UAG-AU--UCCAU-G-UAAGAAU-A
AF491005.1/5436-5355       GACAUCGU-A-GCGAAGU---GGUCU-AACGCG-U-UUGAC-UUGAAAUCAA-AU--CUC-C---UA---------GGAGG---CGCA-GGU-UCG-AA--CCCUG-C-CGAUGUC-G
AF493541.1/2418-2346       UAGAUUGA-A-GCCAGUU---AGCU--AGGGUG-U-UUAGC-UGUUAACUAA-AGU------------------------UU--CGUG-GGG-GUG-GA--GCCCA-C-CAGUCUA-G
AF493542.1/2517-2451       AGCCCUGU-G-GUGAAUU---------UACACG-U-UGAAU-UGCAAAUUCA-GAG------------------------A---AGCA-GCU-UCA-AU---UCUG-C-CGGGGCU-U
AF493542.1/6654-6722       AUUCUUUU-A-GUAUUAA---CU----AGUACA-G-CUGAC-UUCCAAUCAG-CUA------------------------G---UUUC-GGU-CUA-GU---CCGA-A-AAAGAAU-A
X12977.1/94-167            GCGCCCGU-A-GCUCAGCU--GGAU--AGAGCG-C-UGCCC-UCCGGAGGCA-GAG------------------------GU--CACA-GGU-UCG-AA--UCCUG-U-CGGGCGC-A
X12977.1/221-293           GUGGCUGU-A-GCUCAGUU--GGU---AGAGUC-C-CGGAU-UGUGAUUCCG-GUU------------------------GU--CGUG-GGU-UCG-AG--CCCCA-U-CAGCCAC-C
X12977.1/317-399           GCGAAGGU-G-GCGGAAUU--GGUA--GACGCG-C-UAGCU-UCAGGUGUUA-GU--GCC-C---CCC--------GGGUG---UGAG-GGU-UCG-AG--UCCCU-C-UCUUCGC-A
X12977.1/475-548           CGGUGAUU-A-GCGCAGCC-CGGU---AGCGCA-U-CUGGU-UUGGGACCAG-AGG------------------------GU--CAAA-GGU-UCG-AA--UCCUU-U-AUCACCG-A
AL133551.13/12355-12436    GCAGCGAU-G-GCCGAGU---GGUU--AAGGCG-U-UGGAC-UUGAAAUCCA-AU--GGG-G---UCU--------CCCCG---CGCA-GGU-UCG-AA--CCCUG-C-UCGCUGC-G
AL355149.13/15278-15208    GCAUUGGU-G-GUUCAGU---GGU---AGAAUU-C-UCGCC-UCCCACGCGG-GAG------------------------A---CCCG-GGU-UCA-AU--UCCCG-G-CCAAUGC-A
AL356957.27/121645-121572  GUCUCUGU-G-GCGCAAUG--GGUU--AGCGCG-U-UCGGC-UGUUAACCGA-AAG------------------------GU--UGGU-GGU-UCG-AG--CCCAU-C-CAGGGAC-G
AL589879.21/171955-172027  GCCUGGAU-A-GCUCAAUU--GGU---AGAGCA-U-CAGAC-UUUUAAUCUG-AGG------------------------GU--UCAG-GGU-UCA-AG--UCCCU-G-UUCAGGC-G
AL590385.23/26487-26416    GCGUUGGU-G-GUAUAGU---GGUG--AGCAUA-G-CUGCC-UUCCAAGCAG-UUG------------------------A---CCCG-GGU-UCG-AU--UCCCG-G-CCAACGC-A
AL590385.23/26129-26058    UCCCUGGU-G-GUCUAGU---GGUU--AGGAUU-C-GGCGC-UCUCACCGCC-GCG------------------------G---CCCG-GGU-UCG-AU--UCCCG-G-UCAGGGA-A
AL662865.4/12206-12135     GGUUCCAU-G-GUGUAAU---GGUU--AGCACU-C-UGGAC-UCUGAAUCCA-GCG------------------------A---UCCG-AGU-UCA-AA--UCUCG-G-UGGAACC-U
AL671879.2/100356-100285   GGGGAUGU-A-GCUCAGU---GGU---AGAGCG-C-AUGCU-UCGCAUGUAU-GAG------------------------GC--CCCG-GGU-UCG-AU--CCCCG-G-CAUCUCC-A
X61068.1/393-465           GGAGGAUU-A-GCUCAGUU--GGG---AGAGCA-C-CUGCC-UUACAAGCAG-GGG------------------------GU--CGGC-GGU-UCA-AG--CCCGU-C-AUCCUCC-A
X61068.1/477-549           GCCGAAAU-A-GCUCAAUC--GGU---AGAGCA-A-CUGAU-UUGUAAUCAG-UAG------------------------GU--UGCG-GGU-UCA-AU--UCCUG-U-UUUCGGC-A
X61068.1/560-632           GUCCCGUU-A-GCUCAGGU--GGU---AGAGCA-C-UUGAC-UUUUAAUCAA-GGU------------------------GU--CGAU-GGU-UCG-AG--UCCAU-C-ACGGGAC-A
X61068.1/651-734           GCCCGGGU-G-GUGAAAUC--GGUA--GACACG-C-AGGAC-UUAAAAUCCU-GU--GGC-A---UAA---A----AGCCA---UGUC-GGU-UCA-AG--UCCGA-C-CCCGGGC-A
X61068.1/760-831           GGGGCUUU-A-GCUCAGCU--GGG---AGAGCG-C-CUGCC-UUGCACGCAG-GAG------------------------GU--CAGC-GGU-UCG-AU---CCGC-U-AAGCUCC-A
X61068.1/880-953           GGCGGUGU-A-GCUCAGCU--GGCU--AGAGCG-U-GCGGU-UCAUACCCGC-AAG------------------------GU--CGAG-GGU-UCA-AG--UCCCC-C-CGCCGCU-A
X61068.1/961-1034          GGACCCGU-A-GCUCAGUU--GGUU--AGAGCU-A-CCGGC-UCAUAACCGG-UCG------------------------GU--CGUU-GGU-UCG-AG--UCCAA-C-CGGGUCC-A
X61068.1/1060-1145         GGAGGAAU-A-CCCAAGA---GGCUG-AAGGGA-U-CGGUC-UUGAAAACCG-ACA-GGG-U---GUA---AA---AGCCG---CGGG-GGU-UCA-AA--UCCCU-C-UUCCUCC-G
X61068.1/1189-1262         CGCGGGAU-A-GAGCAGUC-UGGU---AGCUCG-U-CGGGC-UCAUAACCCG-AAG------------------------GU--CGAU-GGU-UCA-AA--UCCAU-C-UCCCGCA-A
X61068.1/1281-1353         GGUCCGGU-G-GUGUAGG---GGUU--AACAUG-C-CUGCC-UGUCACGCAG-GAG------------------------AU--CGCG-GGU-UCA-AA--UCCCG-U-CCGGACC-G
X61068.1/1364-1437         GGCUCUGU-A-GCUCAGUC--GGU---AGAGCA-G-UGGCC-UGAAGAGCCU-CGU------------------------GU--CAGCCGGU-UCG-AU--UCCGC-U-UGGAGCC-A
X61061.1/74-147            GUCCGAAU-A-GCUCAGCU--GGAU--AGAGCA-A-UAGCC-UUCUAAGCUA-UCG------------------------GU--CGGG-GGU-UCG-AA--UCCCU-C-UUCGGAC-G
X61066.1/339-412           GCCUACUU-A-GCUCAGUU--GGUU--AGAGCA-C-CUGAC-UGUUAAUCAG-GGG------------------------GU--CGCU-GGU-UCG-AG--UCCAG-C-AGUGGGC-G
X61063.1/119-188           GUCGGUGU-C-GUAUAU----GGU-U-AUUAC--A-GGCCU-UGCCAAGGCU-UAG------------------------A---CGGC-AGU-UCG-AU--CCUGC-U-CACCGGC-U
X61067.1/133-205           GCGGUUGU-G-GCGAAGU---GGUU--AACGCA-U-CGGCU-UGUGGCGCCG-ACA------------------------CU--CGGG-GGU-UCA-AU--UCCCC-U-CGGCCGC-C
X61067.1/232-303           AGGCCCAU-A-GCCAAGC---GGU---AAGGCA-A-CGGAC-UUUGACUCCG-UCA------------------------CU--CGUA-GGU-UCA-AA--UCCUG-C-UGGGCCU-G
X61067.1/334-415           GCGGGUGU-G-GCGAAAUU--GGCA--GACGCA-C-UAGAC-UUAGGAUCUA-GC--GCU-----UUA---C-----GGCA---UGCA-GGU-UCA-AG--UCCUG-U-CACCCGC-A
X61064.1/63-135            GCAUCCAU-A-GCUCAGUU--GGU---AGAGCA-A-CAGAC-UCUUAAUCUG-UGG------------------------GU--CCAC-GGU-UCG-AG--CCCGU-G-UGGGUGU-A
X61065.1/77-164            GGAGCGAU-A-CUCAAGA---GGCCG-AAGAGG-G-CGCAC-UGCUAACGCG-UUAGACG-GU--UAA---C---CCCGUG---CGAG-GGU-UCA-AA--UCCCU-C-UCGCUCC-G
X61065.1/170-242           GGCCCGUU-G-GAGAAAC---GGUU--AACUCA-C-AUGCC-UUUCACGCAU-GCA------------------------UU--CACG-GGU-UCG-AA--UCCCG-U-ACGGGUC-A
X15508.1/140-211           GGGGGCAU-G-GUGUCAAC--GGU---AGCACA-C-AGGUC-UCCAAAACCU-UUA------------------------G---UGUG-GGU-UCG-AA--UCCUG-C-UGCCCUC-G
AJ270287.1/567-495         GCCCCCAU-C-GUCUAGUG--GUUC--AGGACA-U-CUCUC-UUUCAAGGAG-GCA------------------------G---CGGG-GAU-UCG-AC--UUCCC-C-UGGGGGU-A
AP000423.1/76-4            GCGGAUGU-A-GCCAAGU---GGAUU-AAGGCA-G-UGGAU-UGUGAAUUCA-CCA------------------------U---CGCG-GGU-UCA-AU--UCCCG-U-CGUUCGC-C
AP000442.6/2022-1950       GCCCGGAU-A-GCUCAGUC--GGU---AGAGCA-U-CAGAC-UUUUAAUCUG-AGG------------------------GU--CCAG-GGU-UCA-AG--UCCCU-G-UUCGGGC-G
AP002983.1/121-48          GCGGAUGU-A-GCCAAGU---GGAUC-AAGGCA-G-UGGAU-UGUGAAUCCA-CCA------------------------UG--CGCG-GGU-UCA-AU--UCCCG-U-CGUUCGC-C
AP002983.1/63669-63596     GCGCUCUU-A-GUUCAGUU-CGGU---AGAACG-C-GGGUC-UCCAAAACCC-GAU------------------------GU--CGUA-GGU-UCA-AA--UCCUA-C-AGAGCGU-G
AJ011900.1/63-136          AGCGGGGU-A-GAGGAAUU--GGUC--AACUCA-U-CAGGC-UCAUGACCUG-AAG------------------------AC--UGCA-GGU-UCG-AA--UCCUG-U-CCCCGCC-U
AJ012132.1/54-126          GUCAGGAU-A-GCUCAGUU--GGU---AGAGCA-G-AGGAC-UGAAAAUCCU-CGU------------------------GU--CACC-AGU-UCA-AA--UCUGG-U-UCCUGGC-A
AC002341.3/6810-6881       GGGCAUUU-G-GUCUAGU---GGU---AUGAUU-C-UCGCU-UAGGGUGCGA-GAG------------------------GU--CCCG-AGU-UCA-AU--UCUCG-G-AAUGCCC-C
AL161496.2/172002-171930   GCGGGGAU-A-GCUCAGUU--GGG---AGAGCG-U-CAGAC-UGAAGAUCUG-AAG------------------------GU--CGCG-UGU-UCG-AU--CCACG-C-UCACCGC-A
M58320.1/108-194           GGAUGGAU-G-UCUGAGC---GGUUG-AAAGAG-U-CGGUC-UUGAAAACCG-AA--GUA-UUU-CUA---G--GAAUAC----CGGG-GGU-UCG-AA--UCCCU-C-UCCAUCC-G
X67736.1/4837-4923         GGAGAGAU-G-GCCGAGU---GGUUU-AAGGCG-U-AGCAU-UGGAACUGCU-AU--GUA-GGC-UUU---U--GUUUAC----CGAG-GGU-UCG-AA--UCCCU-C-UCUUUCC-G
AL138651.1/64525-64597     GGGGAUGU-A-GCUCAUAU--GGU---AGAGCG-C-UCGCU-UUGCAUGCGA-GAG------------------------GC--ACAG-GGU-UCG-AU--UCCCU-G-CAUCUCC-A
AL162971.1/11752-11825     GGUUUCGU-G-GUGUAGUU--GGUU--AUCACG-U-CAGUC-UAACACACUG-AAG------------------------GU--CUCC-GGU-UCG-AA--CCCGG-G-CGAAGCC-A
L35909.1/103-174           GGAUCCGU-G-GCGCAAU---GGU---AGCGCG-U-CUGAC-UCCAGAUCAG-AAG------------------------GU--UGCG-UGU-UCG-AU--UCACG-U-CGGGUUC-A
X66414.1/9-82              GCAUCCAU-G-GCUGAAU---GGUU--AAAGCG-C-CCAAC-UCAUAAUUGGCGAA------------------------UU--CGUA-GGU-UCA-AU--UCCUA-C-UGGAUGC-A
X66520.1/7-88              GUGGAAGU-G-GCGGAGU---GGUU--AUCGGG-C-AUGAC-UAGAAAUCAU-GU--GGG-C---UUU--------GCCCG---CGCA-GGU-UCG-AA--UCCUG-C-CGUUCAC-G
AY012114.1/954-1022        CAUAGUGU-A-GCUUAAUA--UU----AAAGCA-U-CUGGC-CUACACCCAG-AAG------------------------A---UUUC-A-U-GAC-CA--A-UGA-A-CACUCUG-A
AY017179.1/1528-1601       GGGCCGGU-A-GCUCAGCC-UGGG---AGAGCG-U-CGGCU-UUGCAAGCCG-AAG------------------------GC--CCCG-GGU-UCG-AA--UCCCG-G-CCGGUCC-A
X55523.1/17-90             CGGGGUAU-G-GCGCAGUC-UGGU---AGCGCG-C-ACCCU-UGGGGUGGGU-GAG------------------------GC--CGUG-GGU-UCA-AA--UCCCG-C-UACUCCG-A
U24159.1/431-359           GGGUCGUU-A-GCUCAGUC--GGU---AGAGCA-G-CGGAC-UUUUAAUCCG-UUG------------------------GU--CGAA-GGU-UCG-AA--UCCUU-C-ACGACCC-A
K03317.1/4-76              GGGGGCGU-A-GCUCAGAU--GGU---AGAGCG-C-UCGCU-UAGCAUGCGA-GAG------------------------GU--ACCG-GGA-UCG-AU--ACCCG-G-CGCCUCC-A
X03602.1/660-731           UCCCGUAU-G-GUCUAGU---GGUU--AGGAUA-C-CUGGC-UUUCACCCAG-GAG------------------------G---CUCG-GGU-UCG-AU--UCCCG-G-UACGGGA-A
AB001488.1/62222-62293     UGGGCUAU-A-GCCAAGC---GGU---AAGGCA-A-CGGAC-UUUGACUCCG-UCA------------------------UG--CGUU-GGU-UCG-AA--UCCAG-C-UAGCCCA-G
K01389.1/345-433           GGAGAGCU-G-UCCGAGU---GGUCG-AAGGAG-C-ACGAU-UGGAAAUCGU-GU--AGG-CGGUCAA---C-UCCGUCU----CAAG-GGU-UCG-AA--UCCCU-U-GCUCUCC-G
X60981.1/3182-3253         UCCGCAGU-A-GCUCAGU---GGU---AGAGCA-A-UCGGC-UGUUAACCGA-UUG------------------------GU--CGCA-GGU-UCG-AA--UCCUG-C-CUGCGGA-G
X60981.1/3261-3348         GGAGAGCU-G-UCCGAGU---GGUCG-AAGGAG-C-ACGAU-UGGAAAUCGU-GU--AGG-CGU-GAA---UA-GCGCCU----CAAG-GGU-UCG-AA--UCCCU-U-GCUCUCC-G
X60981.1/3446-3518         GGAGGAUU-A-GCUCAGCU--GGG---AGAGCA-C-UUGCC-UUACAAGCAA-GGG------------------------GU--CGGC-GGU-UCG-AU--CCCGU-C-AUCCUCC-A
X60981.1/3898-3969         GGUCCCGU-A-GUGUAGU---GGUU--AACAUG-C-CUGCC-UGUCACGCAG-GAG------------------------AU--CGCG-GGU-UCG-AU---GCCG-U-CGGGACC-G
Z82044.1/15843-15924       GGAGGGGU-A-GCGAAGU---GGCUA-AACGCG-G-CGGAC-UGUAAAUCCG-CU--CCC-----UCA---------GGGUU--CGGC-AGU-UCG-AA--UCUGC-C-CCCCUCC-A
Z82044.1/16317-16387       GGCGGCAU-A-GCCAAGU---GGU---AAGGCA-G-AGGUC-UGCAAAACCU-UU-------------------------AU--CCCC-GGU-UCG-AA--UCCGG-G-UGUCGCC-U
AJ235316.1/1023-1090       GUUAAUGU-A-GCUUAAA---GUCC--AAAGCA-A-GGCAC-UGAAAAUGCC-UAG------------------------A---UGAG-U-A-CAC-CA----ACU-C-CAUAAAC--
M25659.1/553-621           GUCUACGU-A-GCUUAACC--CCC---AAAGCA-A-GACAC-UGAAAAUGCC-UAG------------------------A---UGGA-U-U-CAC-AC----AUC-C-CAUAGAC-A
M19493.1/263-336           GGGCUAUU-A-GCUCAGUU--GGUU--AGAGCG-C-ACCCC-UGAUAAGGGU-GAG------------------------GC--CCCU-GGU-UCG-AA--UCCAG-G-AUGGCCC-A
M19493.1/340-412           GGGGGUAU-A-GCUCAGUU--GGU---AGAGCG-C-UGCCU-UUGCAAGGCA-GAU------------------------GU--CAGC-GGU-UCG-AG--UCCGC-U-UACCUCC-A
M22563.1/69-141            GCCCCCAU-C-GUCUAGA---GGCCU-AGGACA-C-CUCCC-UUUCACGGAG-GCG------------------------A---CGGG-GAU-UCG-AA--UUCCC-C-UGGGGGU-A
L00194.1/554-627           AGGCCUGU-A-GCUCAGGU--GGUU--AGAGCG-U-ACGCC-UGAUAAGCGU-AAG------------------------GU--CGGC-AGU-UCG-AG--UCUGC-C-UAGGCCU-A
L00194.1/685-756           GGGGCCAU-A-GCUCAGUU--GGU---AGAGCG-C-CUGCU-UUGCAAGCAG-GUG------------------------U---CGUC-GGU-UCG-AA--UCCGU-C-UGGCUCC-A
D17791.1/52-123            GGGUUGCU-A-ACUCAAU---GGU---AGAGUA-C-UCGGC-UUUUAACCGA-UUA------------------------GU--UCCG-GGU-UCG-AG--UCCCG-G-GCAACCC-A
M34508.1/318-404           GCCCGGAUGAACCAUGGC---GGUC--UGUGGU-G-CAGAC-UUCAAAUCUG-UA--GGC-G---GUU---AG---CGCCG---CAGU-GGU-UCG-AC--UCCACCU-UUCGGGU-G
X54299.1/1793-1866         GGGCUAUU-A-GCUCAGUU--GGUU--AGAGCG-C-ACCCC-UGAUAAGGGU-GAG------------------------GU--CCCU-GGU-UCA-AA--UCCAG-G-AUGGCCC-A
X12889.1/644-572           ACCUACUU-A-ACUCAGU---GGUU--AGAGUA-U-UGCUU-UCAUACGGCA-GGA------------------------GU--CAUU-GGU-UCA-AA--UCCAA-U-AGUAGGU-A
X54300.1/29-102            GGGUUAUU-A-GCUCAGUU--GGUU--AGAGCA-C-ACCCC-UGAUAAGGGU-GAG------------------------GU--CCCU-GGU-UCA-AA--UCCAG-G-AUAACCC-A
X54300.1/105-177           GGGGGUAU-A-GCUUAGUU--GGU---AGAGCG-C-UGCUU-UUGCAAGGCA-GAU------------------------GU--CAGC-GGU-UCG-AA--UCCGC-U-UACCUCC-A
X62800.1/3583-3669         GGAGUGAU-G-UCUGAGU---GGCCG-AAAGAG-C-UCGAU-UGCUAAUCGA-GUA-UAC-AG--CUC---C---CUGUAC---CGAG-GGU-UCG-AA--UCCCU-C-UCACUCC-G
X05693.1/1054-1126         GGGAGUAU-A-GCUCAGUU--GGU---AGAGCG-C-UGCCU-UUGCAAGGCA-GAU------------------------GU--CAGC-GGU-UCG-AG--UCCGC-U-UACUUCC-A
X03848.1/3091-3164         GGGCUAUU-A-GCUCAGUU--GGUU--AGAGCG-C-ACCCC-UGAUAAGGGU-GAG------------------------GU--CGCU-GAU-UCG-AA--UUCAG-C-AUAGCCC-A
X15090.1/41-114            GGGUGUGU-A-GCUCAGU---GGACU-AGAGCA-C-GUGGC-UACGAACCAC-GGU------------------------GU--CGGG-GGU-UCG-AA--UCCCU-C-CUCGCCC-G
X51398.1/2-75              GCUUGCUU-A-GCUCAAUU-CGGU---AGAGCU-U-UGGUU-UUGUAAACCA-AAG------------------------GU--UAUC-GGU-UCA-AG--UCCGA-U-AGCAAGC-U
X61698.1/1470-1542         ACCUACUU-A-ACUCAGU---GGUU--AGAGUA-C-UGCUU-UCAUACGGCG-GGA------------------------GG--CAUU-GGU-UCA-AA--UCCAA-U-AGUAGGU-A
L13782.1/442-515           GAGCUUGU-A-GCUCAGU---GGACU-AGAGCA-C-AUGGC-UACGAACCAU-GGG------------------------GU--CGGG-GGU-UCG-AA--ACCCU-C-CUGGCUC-G
J01399.1/2867-2939         GCGGAUGU-A-ACUCAAUC--GGU---AGAGUG-C-GAUCC-UUCCAAGUUC-GAG------------------------GU--UGUG-GGU-UCG-AG--UCCCA-U-CAUCCGC-U
X54408.1/1-73              GCCCCCAU-C-GUCUAGA---GGCCU-AGGACA-C-CUCCC-UUUCACGGAG-AAA------------------------A---CGCG-GAU-UCG-AA--UUCCG-C-UGGGGGU-A
X62566.1/248-320           ACGUCCUU-A-GUUCAGUC--GGU---AGAACG-C-AGGUU-UCCAAAACCU-GAU------------------------GU--CGUG-GGU-UCA-AU--UCCUA-C-AGGGCGU-G
V00158.1/276-361           GGAGAAGU-G-UCUGAGU---GGUCG-AAAGAG-C-UCGAU-UGCUAAUCGA-GU--GUG-UCU-AAU------AAACAC----CGAG-GGU-UCA-AA--UCCCU-U-CUUCUCC-U
V00158.1/694-623           GCAGAUGU-A-GCUCAGU---GGU---AGAGCG-C-AACCU-UGCCAAGGUU-GAU------------------------GC--CAUG-GGU-UCG-AG--UCCCA-U-UAUCUGC-U
M22010.1/2624-2705         GAGUUGUU-G-CCCGAGU---GGUUA-AUGGGG-G-CGGAU-UGUAAAUCCG-CU--AGU-----UCA---------UCUUU--CGCU-GGU-UCG-AA--UCCAG-C-ACGACUC-A
M22010.1/2934-3006         GCGCUUUU-A-GUUCAAUU--GGU---AGAACG-U-AGGUC-UCCAAAACCU-GAU------------------------GU--AGUA-GGU-UCG-AA--UCCUA-C-AGAGCGC-G
M22010.1/3034-3106         GCCCCCAU-C-GUCUAGA---GGCCU-AGGACA-U-CUCCC-UUUCACGGAG-GCA------------------------A---CGGG-GAU-UCG-AA--UUCCC-C-UGGGGGU-A
M22010.1/3113-3185         GCGGGUAU-A-GCUCAGUU--GGU---AGAGCG-U-GGUCC-UUCCAAGUCC-AAU------------------------GU--UGCG-UGU-UCG-AA--UCACG-U-UACCCGC-U
X12890.1/1972-2045         GGGCUAUU-A-GCUCAGUU--GGUU--AGAGCA-U-ACCCU-UGAUAAGGGU-AAG------------------------GU--CGCU-AGU-UCA-AG--UCUAG-C-AUGGCCC-U
M18672.1/347-431           GGAGAGGU-G-UCUGAGU---GGUUU-AAAGUA-C-UGGUC-UUGAAAACCA-GC--GUA-GU--UUU---U---GCUAC----CGAG-GGU-UCG-AA--UCCCU-C-CUUCUCC-G
M17309.1/99-171            GGGAUUGU-A-GUUUAAU---GGUU--AGAGCA-C-CGCCC-UGUCACGGCG-GAA------------------------GU--UGCG-GGU-UCG-AG--UCCCG-U-CAGUCCC-G
M17309.1/774-846           GAGUUGGU-A-GCUCAGUU--GGU---AGAGCA-C-UCGGC-UUUUAACCGA-UCG------------------------GU--CCUG-GGU-UCG-AA--UCCCA-G-CCAACUC-A
V00160.1/1137-1054         GCAGGCAU-G-GCGGAAUU-UGGUA--GACGCG-C-AGGAU-UUAGGUUCCU-GU--GUC-----UUU---AU----GAUG---UGAG-AGU-UCG-AG--UCUCU-C-UGCCUGU-A
X15240.1/604-676           GCUGGGAU-A-GCUCAGUU--GGU---AGAGCG-G-AGGAC-UGAAAAUCCU-UGU------------------------GU--CACC-AGU-UCA-AA--UCUGG-U-UCCUAGC-A
Z11874.1/40212-40285       CGGGAUGU-A-GCGCAGUU-UGGU---AGCGCA-U-UGCAU-UUGGGAUGCA-AGG------------------------GU--CGCA-GGU-UCG-AA--UCCUG-U-CAUCCCG-A
M81884.1/41401-41330       UCCUCAGU-A-GCUCAGU---GGUA---GAGUG-G-UCGGC-UGUUAACCGA-UUG------------------------GC--CGUA-GGU-UCG-AC--UCCUA-C-UUGAGGA-G
M81884.1/42594-42515       GCCGCUAU-G-GUGAAAUU--GGUA--GACACG-U-UGCUC-UUAGGAAGCA-GU--GCU-----AU----------AGCA---UCUU-GGU-UCG-AG--UCCGA-G-UGGCGGC-A
X61368.1/228-301           GGGCCUGU-A-GAUCAGA---GGAUU-AGAGCA-C-GUGGC-UACGAACCAC-GGU------------------------GU--CGUG-GGU-UCG-AA--UCCCU-C-CUCGCCC-A
X00476.1/1-85              GGGGAUAU-G-GCGAAAUU--GGUA--GACGCU-A-CGGAC-UUAAAAUCCG-UC--GAC-U---UAA---GA---AAUCA---UGAG-GGU-UCA-AG--UCCCU-C-UAUCCCC-A
X06428.1/229-300           AGGGAUAU-A-ACUCAGC---GGU---AGAGUG-U-CACCU-UGACGUGGUG-GAA------------------------GU--UAUC-AGU-UCG-AG--CCUGA-U-UAUCCCU-A
M20942.1/1-73              GGGGAUAU-A-GCUCAGUU--GGU---AGAGCG-C-CGCCC-UUGCAAGGCG-GAU------------------------GU--CAGC-GGU-UCG-AG--UCCGC-U-UAUCUCC-A
M20948.1/1-71              GGCGACAU-G-GCCAAGU---GGU---AAGGCA-G-AGGAC-UGCAAAUCCU-UUA------------------------U---CCCC-AGU-UCA-AA--UCUGG-G-UGUCGCU-U
M20947.1/1-74              GGGAUUGU-A-GUUCAAUU--GGUU--AGAGUA-C-CGCCC-UGUCAAGACG-GAA------------------------GU--UGCG-GGU-UCG-AG--CCCCG-U-CAAUCCC-G
M20951.1/1-71              GCGGGUAU-A-GUUUAAU---GGU---AAAAUU-C-CUCCU-UGCCAAGGAG-AAU------------------------A---UGCG-GGU-UCG-AU--UCCCG-C-UACCCGC-C
M20952.1/1-71              GCGGGUAU-A-GUUUAGU---GGU---AAAACC-U-UAGCC-UUCCAAGCUA-ACG------------------------A---UGCG-GGU-UCG-AU--UCCCG-C-UACCCGC-U
M20954.1/1-74              GCAUCCAU-G-GCUGAAU---GGUU--AAAGCA-C-CCAAC-UCAUAAUUGG-CGA------------------------AU-UCACA-GGU-UCA-AU--UCCUG-U-UGGAUGC-A
M20959.1/1-72              GGGUUGCU-A-ACUCAAU---GGU---AGAGUA-C-UCGGC-UUUUAACCGA-CGA------------------------GU--UCCG-GGU-UCG-AG--CCCCG-G-GCAACCC-A
M20957.1/1-85              GGGGGUAU-G-GCGAAAUU--GGUA--GACGCU-G-CGGAC-UUAAAAUCCG-UU--GGC-UU--UAA-------AGACCG---UGAG-GGU-UCA-AG--UCCCU-C-UACCCCC-A
M20958.1/1-80              GCCGCUAU-G-GUGAAAUU--GGUA--GACACG-C-UGCUC-UUAGGAAGCA-GU--GC------UAA---G------GCU---UCUC-GGU-UCG-AA--UCCGA-G-UAGCGGC-A
M20960.1/1-74              ACCUACUU-A-ACUCAGU---GGUUU-AGAGUA-U-CGCUU-UCAUACGGCG-AGA------------------------GU--CAUU-GGU-UCA-AA--UCCAA-U-AGUAGGU-A
X01647.1/2451-2378         CGCGGAGU-A-GAGCAGUC-UGGU---AGCUCG-C-AAGGC-UCAUAACCUU-GAG------------------------GU--CAUA-GGU-UCA-AA--UCCUG-U-CUCCGCC-A
M20949.1/1-72              UGGGGCGU-C-GCCAAGU---GGU---AAGGCU-G-CAGGU-UUUGGUCCUG-UUA------------------------UU--CGGA-GGU-UCG-AA--UCCUU-C-CGUCCCA-G
M20945.1/1-72              GCGUCCAU-C-GUCUAAA---GGAU--AGGACA-G-AGGUU-UUCUAAACCU-CCA------------------------G---UAUA-GGU-UCG-AA--UCCUA-U-UGGACGU-A
M20964.1/1-88              GGAGAGAU-G-GCCGAGU---GGACG-AAAGCG-G-CGGAU-UGCUAAUCCG-UU--GUA-CAAGCUU-----UUUGUAC----CGAG-GGU-UCG-AA--UCCCU-C-UCUCUCC-G
M20966.1/1-88              GGAGAGAU-G-GCCGAGU---GGUUU-AUGGCG-U-CGGUC-UUGAAAACCG-AU--AUA-GUUUUUA-----AGAUUAU----CGAG-GGU-UCA-AA--UCCCU-C-UCUCUCC-U
M20968.1/1-73              GCCUGUUU-A-GCUCAGA---GGUC--AGAGCG-U-CGCAC-UUGUAAUGCG-AUG------------------------GU--CAUC-GGU-UCG-AC--UCCGA-U-AGCGGGC-U
M20972.1/1-72              AGGGCUAU-A-GCUCAGC---GGU---AGAGCG-C-CUCGU-UUACACCGAG-AAU------------------------GU--CUAC-GGU-UCA-AA--UCCGU-A-UAGCCCU-A
M20969.1/1-74              GCGCUUUU-A-GUUCAGUU-CGGU---AGAACG-U-AGGUC-UCCAAAACCU-AAU------------------------GU--CGUA-GGU-UCA-AA--UCCUA-C-AGAGCGU-G
X04465.1/3679-3758         GCCUUGAU-G-GUGAAAU---GGUA--GACACG-C-GAGAU-UCAAAAUUUC-GU--GCU-----UAA---------AGCA---UGGA-GGU-UCG-AG--UCCUC-U-UCAAGGC-A
X04465.1/29596-29669       GCGGACGU-A-GCCAAGU---GGAUU-AAGGCA-G-UGGAU-UGUGGAUCCU-CUA------------------------CG--CGCG-GGU-UCA-AU--UCCCG-U-CGUUCGC-C
X04465.1/36643-36562       GGGUCGAU-G-CUCGAGU---GGUUA-AUGGGG-A-CGGAC-UGUAAAUCCG-CU--GGC-----AAU---------GCCUA--CGCU-GGU-UCA-AA--UCCAG-C-UCGACCC-A
X04465.1/36787-36715       GCCCCCAU-C-GUCUAGU---GGCCU-AGGACA-C-CUCUC-UUUCAAGGAG-GCG------------------------A---CGGG-GAU-UCG-AA--UUCCC-C-UGGGGGU-A
X04465.1/38367-38438       GCCCUUUU-A-ACUCAGU---GGU---AGAGUA-A-CGCCA-UGGUAGGGCG-UAA------------------------GU--CAUC-GGU-UCA-AA--UCUGA-U-AAAGGGC-U
X04465.1/48845-48932       GGAAAGAU-G-GUUGAGU---GGUUU-AAGGCG-U-AGCAU-UGGAAAUGCU-AU--GUA-GGCUUUU-----GGUCUAU----CGAG-GGU-UCG-AA--UCCCU-C-UCUUUCC-G
X04465.1/50998-51070       GCCGGGAU-A-GCUCAGUU--GGU---AGAGCA-G-AGGAC-UGAAAAUCCU-CGU------------------------GU--CACC-AGU-UCA-AA--UCUGG-U-UUCUGGC-A
X04465.1/57877-57950       GGGUUUGU-A-GCUCAGU---GGAUU-AGAGCU-C-AUGGU-UCCGAAUCAU-GAA------------------------GU--CAAG-GGU-UCG-AA--UCCCU-U-CUAACCC-U
X04465.1/64788-64715       AGGGAUGU-A-GCGCAGUU-UGGU---AGCGCG-U-UUGUU-UUGGGUACAA-AAU------------------------GU--CGCA-GGU-UCG-AA--UCCUG-U-CAUCCCU-A
X04465.1/90332-90261       UCCUUAGU-A-GCUCAGU---GGU---AGAGCG-G-UCGGC-UGUUAACCGA-UUG------------------------GU--CGUA-GGU-UCA-AA--UCCUA-C-CUGAGGA-G
X04465.1/112638-112565     GGGUUUGU-A-GCUCAGA---GGAUU-AGAGCA-C-GUGGC-UACGAACCAC-GGU------------------------GU--CGGG-GGU-UCG-AA--UCCCU-C-CUUGCCC-A
X04465.1/120306-120235     AGGGAUAU-A-ACUCAGC---GGU---AGAGUA-U-CACCU-UGACGUGGUG-GAA------------------------GU--CAUC-AGU-UCG-AA--CCUGA-U-UAUCCCU-A
X72895.1/1-72              GGCGACAU-G-GCCGAGU---GGU---AAGGCA-G-AGGAC-UGCAAAUCCU-UUU------------------------UU--CCCC-AGU-UCA-AA--UCCGG-G-UGUCGCC-U
X00181.1/495-582           GGAGAGAU-G-GCUGAGU---GGACU-AAAGCG-G-CGGAU-UGCUAAUCCG-UU--GUA-CGA-GUU---AA-UCGUAC----CGAG-GGU-UCG-AA--UCCCU-C-UCUUUCC-G
X01016.1/450-523           AGGGAUGU-G-GCGCAGCU-UGGU---AGCGCG-U-UUGUU-UUGGGUACAA-AAU------------------------GU--CACA-GGU-UCA-AA--UCCUG-U-CAUCCCU-A
X01017.1/116-189           CGCGGGGU-A-GAGCAGUU-UGGU---AGCUCG-C-AAGGC-UCAUAACCUU-GAG------------------------GU--CACG-GGU-UCA-AA--UCCUG-U-CUCCGCA-A
X01017.1/487-417           GCGGAUAU-G-GUCGAAU---GGU---AAAAUU-U-CUCUU-UGCCAAGGAG-AAG------------------------A---UGCG-GGU-UCG-AU--UCCCG-C-UAUCCGC-C
M16909.1/81-161            GCCUUGGU-G-GUGAAAU---GGUA--GACACG-C-GAGAC-UCAAAAUCUC-GU--GCU-A---AA---------UAGCG---UGGA-GGU-UCG-AG--UCCUC-U-UCAAGGC-A
M23767.1/162-241           GCCGCUAU-G-GUGAAAUU--GGUA--GACACG-C-UGCUC-UUAGGAAGCA-GU--GC------UAA---U------GCA---UCUC-GGU-UCG-AG--UCCGA-G-UGGCGGC-A
X02217.1/416-488           GCCCCCAU-C-GUCUAGU---GGUUU-AGGACA-U-CUCUC-UUUCAAGGAG-GCA------------------------G---CGGG-GAU-UCG-AA--UUCCC-C-UGGGGGU-A
M16912.1/86-157            GCCCUUUU-A-ACUCAGU---GGU---AGAGUA-A-CGCCA-UGGUAAGGCG-UAA------------------------GU--CAUC-GGU-UCA-AA--UCCGA-U-AAGGGGC-U
M16897.1/160-88            GCCCGCUU-A-GCUCAGA---GGUU--AGAGCA-U-CGCAU-UUGUAAUGCG-AUG------------------------GU--CAUC-GGU-UCG-AU--UCCGA-U-AGCCGGC-U
X07922.1/12-85             AGGGAUGU-A-GCGCAGCU-UGGU---AGCGCG-U-UUGUU-UUGGGUACAA-AAU------------------------GU--CACG-GGU-UCA-AA--UCCUG-U-CAUCCCU-A
X15768.1/134-207           GGGCUAUU-A-GCUCAGUU--GGUU--AGAGCG-C-ACCCC-UGAUAAGGGU-GAG------------------------GU--CUCU-GGU-UCA-AA--UCCAG-A-AUGGCCC-A
X15768.1/211-283           GGGGGUAU-A-GCUCAGUU--GGU---AGAGCG-C-UGCCU-UUGCAAGGCA-GUG------------------------GU--CAGC-GGU-UCG-AG--UCCGC-U-UACCUCC-A
X15901.1/44438-44524       GGAGAGAU-G-GCCGAGC---GGUUC-AAGGCG-U-AGCAU-UGGAACUGCU-AU--GUA-GAC-UUU---U--GUUUAC----CGAG-GGU-UCG-AA--UCCCU-C-UCUUUCC-G
X15901.1/99287-99217       UCCUCAGU-A-GCUCAGU---GGU---AGAGCG-G-UCGGC-UGUUAACUGA-CUG------------------------GU--CGUA-GGU-UCG-AA--UCCUA-C-UUGGGGA--
X15901.1/105074-105153     GCCGCCAU-G-GUGAAAUU--GGUA--GACACG-C-UGCUC-UUAGGAAGCA-GU--GCU-----CA----------AGCA---UCUC-GGU-UCG-AG--UCCGA-G-UGGCGGC-A
M21373.1/208-280           GGGGGUAU-A-GCUCAGUU--GGU---AGAGCG-U-UGCUU-UUGCAUAGCA-GAC------------------------GU--CAGC-AGU-UCG-AG--UCUGC-U-UAUCUCC-A
X05394.1/580-653           CGCGGAGU-A-GAGCAACU-UGGU---AGCUCG-C-AAGGC-UCAUAACCUU-GAG------------------------GU--UACG-GGU-UCA-AA--UCCCG-U-CUCCGCA-C
X05394.1/803-733           GCGGAUAU-A-GUUGAAU---GGU---AUAAUU-U-CUCUU-UGCCAAGGAG-AAG------------------------A---CGCG-GGU-UCA-AU--UCCCG-C-UAUCCGC-C
X55033.1/412-483           AGGGGUAU-A-ACUCAGC---GGU---AGAGUG-U-CACCU-UGACGUGGUG-GAA------------------------GU--CAUC-AGU-UCG-AA--CCUGA-U-UAUCCCU-A
M16864.1/642-714           GCCCCCAU-C-GUCUAGC---GGUUU-AGGACA-U-CUCUC-UUUCAAGGAG-GCA------------------------A---CGGG-GAU-UCG-AC--UUCCC-C-UGGGGGU-A
M16863.1/21-94             GGGCUCGU-A-GCUCAGA---GGAUU-AGAGCA-C-GCGGC-UACGAACCAC-GGU------------------------GU--CGGG-GGU-UCG-AA--UCCCU-C-CUCGCCC-A
M16863.1/456-385           UCCCCAGU-A-GCUCAGU---GGU---AGAGCG-G-UCGGC-UGUUAACCGA-UUG------------------------GU--CGUA-GGU-UCA-AA--UCCUA-U-UUGGGGA-G
M16863.1/577-660           GCCUUGGU-G-GUGAAAUGGUGGUA--GACACG-C-GAGAC-UCAAAAUCUC-GU--GCU-----AAA---C-----AGCG---AGGA-GGU-UCG-AG--UCCUC-U-UCAAGGC-A
X04761.1/963-892           GCCCUUUU-A-ACUCAGU---GGU---AGAGUA-A-CGCCA-UGGUAAGGCG-UAA------------------------GU--CGUC-GGU-UCA-AA--UCCGA-U-AAAGGGC-U
X05395.1/122-195           AGGGAUGU-A-GCGCAGCU-UUGU---AGCGCG-U-UUGUU-UUGGGUACAA-AAU------------------------GU--CACA-GGU-UCA-AA--UCCUG-U-CAUCCCU-A
D11467.1/1-72              UGGGGCGU-G-GCCAAGC---GGU---AAGGCA-G-CAGGU-UUUGAUCCUG-UUA------------------------UU--CGGA-GGU-UCG-AA--UCCUU-C-CGUCCCA-G
D11467.1/6989-6916         GCAUCCAU-G-GCUGAAU---GGUU--AAAGCG-C-CCAAC-UCAUAAUUGGCGAA------------------------CU--CGCG-GGU-UCA-AU--UCCUG-C-UGGAUGC-A
D17510.1/119065-118992     GCGGACGU-A-GCCAAGU---GGACC-AAGGCA-G-UGGAU-UGUGAAUCCA-CCA------------------------CG--CGCG-GGU-UCA-AU--UCCCG-U-CGUUCGC-C
K00235.1/1-85              GGGGAUAU-G-GCGAAAUU--GGUA--GACGCU-A-CGGAC-UUAAAAUCCG-UC--GAC-UU--AAU-------AAAUCA---UGAG-GGU-UCA-AG--UCCCU-C-UAUCCCC-A
X01120.1/76-149            GGGCCUGU-A-GCUCAGA---GGAUU-AGAGCA-C-GUGGC-UACGAACCAC-GAU------------------------GU--CGGG-GGU-UCG-AA--UCCCU-C-CUAGCCC-A
X13558.1/186-115           UGGGGCGU-A-GCCAAGC---GGU---AAGGCA-A-CGGGU-UUUGGUCCCG-CUA------------------------UU--CGGA-GGU-UCG-AA--UCCUU-C-CGUCCCA-G
X52739.1/1-72              GGGCUAUU-A-GCUCAGU---GGU---AGAGCG-C-GCCCC-UGAUAAGGGC-GAG------------------------GU--CUCU-GGU-UCA-AG--UCCAG-G-AUAGCCC-A
M31489.1/112-183           GCGUCCAU-A-GUCUAAU---GGAU--AGGACA-U-AGGUC-UUCUAAACCU-UUG------------------------G---UAUA-GGU-UCA-AA--UCCUA-U-UGGACGC-A
Y00125.1/116-196           GCCUUGGU-G-GUGAAAU---GGUA--GACACG-C-GAGAC-UCAAAAUCUC-GU--GCU-----AAA---A-----AGCG---UGGA-GGU-UCG-AG--UCCUC-U-UCAAGGC-A
M16843.1/2824-2752         GCCUACUU-A-ACUCAGU---GGUU--AGAGUA-U-UGCUU-UCAUACGGCG-GGA------------------------GU--CAUU-GGU-UCA-AA--UCCAA-U-AGUAGGU-A
M16839.1/41-111            GCGAGCGU-A-GUUCAAU---GGU---AAAAUA-U-CUCCU-UGCCAAGGAG-AAG------------------------A---UACG-GGU-UCG-AU--UCCCG-C-CGCUCGC-C
X07379.1/305-375           GGCGGCAU-G-GCCAAGC---GGU---AAGGCA-G-GGGAC-UGCAAAUCCU-UUA------------------------U---CCCC-AGU-UCA-AA--UCUGG-G-UGCCGCC-U
X62453.1/1-74              GGGAUUGU-A-GUUCAAUU--GGUC--AGAGCA-C-CGCCC-UGUCAAGGCG-GAA------------------------GC--UGCG-GGU-UCG-AG--CCCCG-U-CAGUCCC-G
L02941.1/716-643           AGCGGAGU-A-GAGCAGUU-UGGU---AGCUCA-C-GAGGC-UCAUAACCUU-GAG------------------------GU--CACG-GGU-UCG-AU--UCCCG-U-CUCCGCA-C
X05295.1/313-226           GGAGAGAU-G-GCUGAGU---GGUUG-AUAGCU-C-CGGUC-UUGAAAACCG-GU--AUA-GUUCUAG-----GAACUAU----CGAG-GGU-UCG-AA--UCCCU-C-UCUCUCC-U
X70810.2/2089-2011         UCCUUCGU-G-GUGAAAU---GGUA--AACACG-U-GUGAU-UCAAAAUCAC-AU--GC------AUA---A------GCU---UGCC-GGU-UCG-AG--UCCGG-U-CGAAGGU-A
X70810.2/30807-30878       GCCUUUUU-A-GCUCAGU---GGU---AGAGCA-U-UGUAU-UUGUAAUGCG-GUG------------------------GU--CGUC-GGU-UCG-AA--UCCGA-C-AAAAGGC-U
X70810.2/30968-31041       GGCGGAGU-A-GAGCAGUC-AGGU---AGCUCG-C-AGGGC-UCAUAAUCCU-GAA------------------------GU--CAGA-GGU-UCA-AA--UCCUU-U-CUCCGCU-A
X70810.2/31388-31317       UGAGGCGU-A-GCCAAGU---GGU---AAGGCA-A-CGGGU-UUUGGCCCUG-UCA------------------------UU--CGGA-GGU-UCG-AA--UCCUC-C-CGCCUCA-G
X70810.2/60996-61067       GGCGGCAU-G-GCCAAGC---GGU---AAGGCA-G-AAGAU-UGCAAAUCUU-UUA------------------------UU--CCCC-AGU-UCG-AU--UCUGG-G-UGUCGUC-U
X70810.2/100844-100773     GUGGGUGU-A-GCCAAGU---GGU---AAGGCA-A-AGGAC-UGUGACUCCU-UCA------------------------UU--CGCG-GGU-UCG-AU--CCCCG-U-CAUUCAC-C
X70810.2/102679-102606     GGGCUUGU-A-GCUCAGU---GGACU-AGAGCA-C-GUGGC-UACGAACUAC-GGA------------------------GU--CAGG-GGU-UCG-AA--UCCCU-U-CUUGCCC-G
X70810.2/102754-102683     UCCUUAAU-A-GCUCAGU---GGU---AGAGCA-A-UCGGC-UGUUAACCGA-UCG------------------------GU--CGUA-GGU-UCG-AA--UCCUA-C-UUAAGGA-G
X70810.2/102843-102771     GGGGGUAU-A-GCUCAGUU--GGU---AGAGCG-U-CUGCC-UUACAAGCAG-AAU------------------------GU--CAGC-GGU-UCG-AA--UCCGU-U-UGCCCUC-A
X17318.1/109-39            GGCGGCAU-G-GCCAAGU---GGU---AAGGCA-G-GGGAC-UGCAAAUCCU-UUA------------------------C---CCCC-AGU-UCA-AA--UCUGG-G-UGCCGCC-U
AL132988.4/95773-95841     AAGGGCUU-A-GCUUAA----UU----AAAGUG-G-CUGAU-UUGCGUUCAG-UUG------------------------A---UGCA-GAG-UGG-GG--UUUUG-C-AGUCCUU-A
AL163195.5/3702-3774       GGCUCCAU-A-GCUCAGG---GGUU--AGAGCA-C-UGGUC-UUGUAAACCA-GGG------------------------GU--CGCG-AGU-UCA-AA--UCUCG-C-UGGGGCC-U
AL352978.6/119697-119770   GGCCGGUU-A-GCUCAGUU--GGUU--AGAGCG-U-GGUGC-UAAUAACGCC-AAG------------------------GU--CGCG-GGU-UCG-AU--CCCCG-U-ACGGGCC-A
X07925.1/53-125            GCGGGUGU-A-GCUCAGCU--GGU---AGAGCG-C-AACCU-UGCCAAGGUU-GAU------------------------GU--CGCG-CGU-UCG-AA--UCGCG-U-CACCCGC-U
X07924.1/110-197           GGAGAGAU-G-GCCGAGU---GGUUG-AAGGCG-C-AGCAC-UGGAAAUGCU-GU--UUA-AGG-UUU---UC-CCUUAA----CGAG-GGU-UCG-AA--UCCCU-C-UCUCUCC-G
J01395.1/2878-2951         GGGCUAUU-A-GCUCAGUU--GGUU--AGAGCG-U-UGCUU-UGAUAAGGCA-AAA------------------------GU--CGAA-AGU-UCA-AA--UCUUU-C-AUAGCCC-A
J01395.1/3006-3078         GGGGAUAU-A-GCUCAGUU--GGU---AGAGCG-C-UGCCU-UUGCAAGGCA-GAU------------------------GU--CAGC-GGU-UCG-AA--UCCGC-U-UAUCUCC-A
X55320.1/1-72              UGGGGCAU-A-GCCAAGU---GGU---AAGGCA-U-UGGAC-UUUGACUCCA-AGA------------------------UG--CAUG-GGU-UCG-AA--UCCUA-U-UGCCCCA-G
X55321.1/1-72              AGACACGU-A-GCUUAGU---GGU---AAAGCA-C-UGGUC-UCAUAAGCCA-GCU------------------------AU--CGCA-AGU-UCG-AA--UCUCG-C-CGUGUCU-A
X55319.1/1-74              AGAGGUGU-A-GCUUAGUU--GGUU--AAAGCG-C-AAGAU-UCCAAAUCUU-GAA------------------------AU--CGAG-GGU-UCG-AG--UCCUU-U-CAUCUCU-G
X17616.1/380-293           GGAGAGAU-G-GCUGAGU---GGACU-AAAGCG-U-UGGAU-UGCUAAUCCA-UU--GUA-CGA-GUU---AA-UCGUAC----CGAG-GGU-UCG-AA--UCCCU-C-UCUUUCC-C
D89936.1/1231-1150         GCCGGUGU-G-GCGGAAUU--GGCA--GACGCG-C-ACGAC-UCAAAAUCGU-GU--UCC-----UUC---U-----GGAG---UGUC-GGU-UCG-AC--CCCGA-C-CACCGGU-A
U25144.1/1062-991          GGCUCCUU-A-GCAUAGU---GGU---AUUGCG-C-UUCCC-UAGUAAGGAA-GAG------------------------GU--CAUG-AGU-UCG-AU--CCUCA-U-AGGAGCC-U
X59563.1/1377-1449         GCCCGUUU-A-GCAAAGUU--GGA---AUUGCG-G-CAGCC-UUCUAAGCUG-CAG------------------------GU--CGUG-GGA-UCG-AG--ACCCA-C-AAUGGGU-G
X59562.1/71-144            GGGACUAU-A-GUUUAGUU--GGAU--AUAACG-A-CCGGC-UACGAACCGG-UAG------------------------GU--CUCA-GGU-UCG-AC--CCCUG-A-UGGUCUC-G
K02322.1/59-130            AGCUUCUU-A-ACUCAGG---GGU---AGAGUG-C-GAGGC-CCAUAACCUC-GAG------------------------GU--CCUA-GGA-UCG-AA--ACCUA-G-AGAAGCU-A
M24578.1/1373-1445         GCCCGGCU-A-GCUCAGUC--GGU---AGAGCG-C-CAGAC-UCUUAAUCUG-GUG------------------------GU--CGGG-GGU-UCG-AG--CCCCC-C-GUUGGGC-G
X53443.1/135-206           GCCUGGAU-G-GCUAAAU---GGC---AGAGCG-A-GCGGC-UGUUAACCGC-UAG------------------------GU--CCAU-GGU-UCG-AU--CCCAU-G-UCUAGGC-A
X53444.1/72-144            GGGGAAGU-A-GCUCAGAU--GGU---AGAGCG-C-UCGCU-UAGCAUGCGA-GAG------------------------GU--AAAG-GGU-UCG-AU--ACCCU-U-CUUCCUC-A
X59566.1/318-390           GGUUUUAU-A-GUGUAAUU--GGUU--AGCACC-C-AGGAC-UUUGAAUCCU-GUA------------------------A---UCUG-AGU-UCG-AG--UCUCA-G-UAGAACC-A
X59571.1/319-390           GCCGUGAU-A-GUAUAGU---GGU---AGUACA-U-CAGAU-UGUGGCUCUG-UUG------------------------AC--CCUU-GGU-UCG-AU--UCCAG-G-UCGCGGC-A
X59573.1/314-396           GCAAGGGU-A-GGAAAGUC-UGGUUA-AAUCCG-U-GUGAC-UUAAGAUCUC-AU--CC------AUU---C------GGUU--CGCG-AGU-UCG-AA--UCUCG-C-CUCUUGC-A
X59582.1/477-558           GACAUCGU-A-GCAAAGU---GGUCU-AAUGCG-U-CUGAC-UAGAAAUCAG-AU--CCC-U---UC---------GGGGG---CGCA-GGU-UCG-AA--CCCUG-C-CGAUGUC-G
X59583.1/330-410           GACACCUU-A-GCAAAGU---GGUU--AAUGCG-G-CGCCC-UGCUAAGGCG-UU--CUC-U---UC---------GGAGG---CGCA-GGU-UCG-AA--CCCUG-C-AGGUGUC-G
X69660.1/114-186           GCCCAGAU-A-GCUCAGUC--GGU---AGAGCG-C-AAGGC-UUUUAACCUU-GUG------------------------GU--CGGG-GGU-UCG-AG--CCCCC-C-UUUGGGC-G
X03499.1/37-110            GGUCGGAU-G-GUGUAGUC--GGUU--AUCACG-G-UUGCU-UUACACGCAA-CAG------------------------GU--CUCG-AGU-UCG-AU--CCUCG-G-UCGGAUC-A
V00238.1/262-333           UCCUAUAU-U-GUCUAGU---GGUU--AGGAUA-U-CCGGC-UCUCACCCGG-AAG------------------------G---CCCG-GGU-UCA-AU--UCCCG-G-UAUGGGA-A
X07778.1/115-45            GCAUCGGU-G-GUUCAGU---GGU---AGAAUG-C-UCGCC-UGCCACGCGG-GCG------------------------G---CCCG-GGU-UCG-AU--UCCCG-A-CCGAUGC-A
V00334.1/358-430           GCUGAUAU-G-GCUCAGUU--GGU---AGAGCG-C-ACCCU-UGGUAGGGGU-GGG------------------------GU--CCCC-AGU-UCG-AC--UCUGG-G-UAUCAGC-A
K01941.1/217-303           GCCCGGAUGACCCUCAGU---GGUC--UGGGGU-G-CAGGC-UUCAAACCUG-UA--GCU-GU--CUA-------GCGACA---GAGU-GGU-UCA-AU--UCCACCU-UUCGGGC-G
X16401.1/1-69              GAGACGUU-A-GUAAAC----CA----AUUACA-U-AGACC-UGUCAAGACU-AAA------------------------U---CACA-GGU-GCA-AA--CCCUG-U-ACAUCUC-A
X99772.1/5062-5131         AGGGGCUU-A-GGAUAA----ACU---AGACCA-A-GGGCC-UUCAAAGCCC-UCA------------------------G---CGGA-GGU-GAA-AA--UCCUC-C-AGCCCCU-G
X99772.1/5276-5204         UAGAUAGA-U-GCUCGCU---GGUU--UGAGUG-C-UUAGC-UGUUAACUAA-GAG------------------------UU--UAAA-GGA-UCG-AG--GCCUU-U-CUGUCUA-G
X99772.1/5441-5375         GGUAGGAU-G-GCUGAG----------UAAGCG-G-UGGAU-UGUAACCCCA-CAU------------------------A---CAGA-GGU-UUG-AG--CCCUC-U-UCUUGCC-A
X99772.1/7842-7915         CACUAAGA-A-GCUAAUAU--GGGU--UAAGCA-C-CAGCC-UUUUAAGCUG-GAA------------------------GC--AGGU-GAC-UCC-CA--ACCAC-C-CUUAAUG-A
X99772.1/9544-9611         -UCUUUCU-A-GUACUAA---GG----AGUAUA-A-GUGGC-UUCCAACCAC-ACG------------------------G---UCUU-GGU-UAG-AG--UCCAA-G-GAAAGAU--
X99772.1/11702-11770       GUAGAUUU-A-GUUUAA----CC----AAGACA-U-UAGAU-UGUGAUUCUA-AAA------------------------A---UAGA-GGU-UAA-AC--CCCUC-U-AAUCCAC-C
X99772.1/11841-11913       GCUCCUAA-A-GGAUAAU---AGCU--CAUCCG-U-UGGUC-UUAGGAACCA-AAA------------------------AC--UCUU-GGU-GCA-AC--UCCAA-G-UAGCAGC-U
M17129.1/151-222           AUCAGAGU-G-GCGCAGC---GGAA---GCGUG-G-UGGGC-CCAUAACCCA-CAG------------------------GU--CCCA-GGA-UCG-AA--ACCUG-G-CUCUGAU-A
X87209.2/181-268           GAAGGUAU-G-GCUGAGU---GGCUU-AAGGCA-U-UGGUU-UGCUAAAUCG-AC--AUA-CAA-GAA---GA-UUGUAU----CAUG-GGU-UCA-AA--UCCCA-U-UUCCUCC-G
X99256.1/11558-11626       GUAAACAU-A-GUUUAA----UC----AAAACA-U-UAGAU-UGUGAAUCUA-ACA------------------------A---UAGA-GGC-UCG-AA--ACCUC-U-UGCUUAC-C
M87833.1/353-437           GUCGUGGU-A-GCCAAGCC-UGGCCC-AAGGCG-C-AGGGU-UGCUAACUCU-GU--GGC-----GUA---CA----GCC-U--CCGG-GGU-UCG-AA--UCCCC-G-CCACGAC-G
M87833.1/2781-2865         GCAGGGAU-A-GCCAAGUU-UGGCCA-ACGGCG-C-AGCGU-UCAGGGCGCU-GU--CCC-----GUA---G-----GGGUC--CGCA-GGU-UCA-AA--UCCUG-C-UCCCUGC-A
Z54587.1/126-45            GGUAGCGU-G-GCCGAGC---GGUCU-AAGGCG-C-UGGAU-UUAGGCUCCA-GU--CUC-----UUC---G-----GAGG---CGUG-GGU-UCG-AA--UCCCA-C-CGCUGCC-A
AL031229.2/40502-40430     GUUUCCGU-A-GUGUAGU---GGUU--AUCACG-U-UCGCC-UAACACGCGA-AAG------------------------GU--CCCU-GGA-UCA-AA--ACCAG-G-CGGAAAC-A
Z98744.2/66305-66234       AGCAGAGU-G-GCGCAGC---GGA---AGCGUG-C-UGGGC-CCAUAACCCA-GAG------------------------GU--CGAU-GGA-UCG-AA--ACCAU-C-CUCUGCU-A
AL021808.2/65570-65498     GCUUCUGU-A-GUGUAGU---GGUU--AUCACG-U-UCGCC-UCACACGCGA-AAG------------------------GU--CCCC-GGU-UCG-AA--ACCGG-G-CAGAAGC-A
AL021918.1/54817-54736     GUAGUCGU-G-GCCGAGU---GGUU--AAGGCG-A-UGGAC-UUGAAAUCCA-UU--GGG-G---UUU--------CCCCG---CGCA-GGU-UCG-AA--UCCUG-U-CGGCUAC-G
AL021918.1/81116-81197     GUAGUCGU-G-GCCGAGU---GGUU--AAGGCG-A-UGGAC-UAGAAAUCCA-UU--GGG-G---UUU--------CCCCA---CGCA-GGU-UCG-AA--UCCUG-C-CGACUAC-G
AL021918.1/94597-94678     GUAGUCGU-G-GCCGAGU---GGUU--AAGGCG-A-UGGAC-UUGAAAUCCA-UU--GGG-G---UUU--------CCCCG---CGCA-GGU-UCG-AA--UCCUG-C-CGACUAC-G
X93334.1/6942-7009         AAGGUAUU-A-GAAAAA----CC----AUUUCA-U-AACUU-UGUCAAAGUU-AAA------------------------U---UAUA-GGC-UAA-AU---CCUA-U-AUAUCUU-A
L23320.1/77-10             ACUCUUUU-A-GUAUAA----AU----AGUACC-G-UUAAC-UUCCAAUUAA-CUA------------------------G---UUUU-GAC-AAC-AU---UCAA-A-AAAGAGU-A
J00309.1/356-427           UCCCUGGU-G-GUCUAGU---GGCU--AGGAUU-C-GGCGC-UUUCACCGCC-GCG------------------------C---CCCG-GGU-UCG-AU--UCCCG-G-CCAGGAA-U
M15347.1/1040-968          GGCUCCAU-A-GCUCAGG---GGUU--AGAGCA-C-UGGUC-UUGUAAACCA-GGG------------------------GU--CGCG-AGU-UCA-AU--UCUCG-C-UGGGGCU-U
M16479.1/42-123            GGUGGGGU-U-CCCGAGC---GGCCA-AAGGGA-G-CAGAC-UCUAAAUCUG-CC--GUC-----AUC---------GACUU--CGAA-GGU-UCG-AA--UCCUU-C-CCCCACC-A
X58792.1/174-245           GGUCCCAU-G-GUGUAAU---GGUU--AGCACU-C-UGGAC-UUUGAAUCCA-GCG------------------------A---UCCG-AGU-UCA-AA--UCUCG-G-UGGGACC-U
X04779.1/1-73              CCUUCGAU-A-GCUCAGCU--GGU---AGAGCG-G-AGGAC-UGUAGAUCCU-UAG------------------------GU--CGCU-GGU-UCG-AU--UCCGG-C-UCGAAGG-A
X02584.1/1-77              GCCAAGGU-G-GCAGAGUU-CGGCCC-AACGCA-U-CCGCC-UGCAGAGCGG-AAC------------------------CC-CCGCC-GGU-UCA-AA--UCCGG-C-CCUUGGC-U
K02528.1/1-74              GGGGCUGU-G-GCCAAUCCC-GGC---AUGGCG-A-CUGAC-UCCAGAUCAG-UCG------------------------AU--CGGG-GGU-UCG-AA--UCCCU-C-CGGCCCC-A
L76657.1/1-67              UUAAUUGA-A-ACCAAA----AA----GAGGUA-U-AUCAC-UGUUAAUGAU-AUA------------------------AU--UGAA-UA--UUA-U----UAUU-C-CAAUUAA-G
M18744.1/76-164            GGAGAGUU-G-GCAGAGC---GGU---AAUGCA-G-CGGAC-UCGAAAUCCG-CCG-AAC-CAAUGUU---GAAUUGGUG----CGCA-GGU-UCA-AA--UCCUG-U-ACUCUCC-U
X15245.1/160-231           UCCGCCUU-A-GCUCAGUU--GGU---AGAGCG-C-UUGAC-UGUUAAUCAG-GAU------------------------GU--CGUC-AGU-UCG-AG--UCUGA-C-AGGCGGA--
X15245.1/236-309           CGGGAAGU-G-GCUCAGUU-UGGU---AGAGCA-C-CUGGU-UUGGGACCAG-GGG------------------------GU--CGCA-GGU-UCA-AA--UCCUG-U-CUUCCCG-A
X15245.1/512-584           GGAGGAUU-A-GCUCAGCU--GGG---AGAGCA-U-CUGCC-UUACAAGCAG-AGG------------------------GU--CACA-GGU-UCG-AG--CCCUG-U-AUCCUCC-A
X15245.1/588-660           GGUCCAUU-G-GAGCAGU---GGUCU-AUCUCG-C-CUCCC-UGUCACGGAG-GAG------------------------AU--CGCG-GGU-UCA-AA--UCCCG-C-AUGGACC--
X15246.1/271-344           GCACCCAU-A-GCGCAACU--GGAU--AGAGUG-U-CUGAC-UACGAAUCAG-AAG------------------------GU--UGUA-GGU-UCA-AG--UCCUA-C-UGGGUGC-A
X15246.1/423-494           GGCCCGUU-G-GUCAAGU---GGUU--AAGACA-C-CGCCC-UUUCACGGCG-GUA------------------------A---CAUG-GGU-UCA-AA--UCCCG-U-ACGGGUC-A
D00550.1/152-232           GGGGGAUU-G-GCGGAAUU--GGCA--GACGCA-C-UAGAC-UUAGGAUCUA-GC--GUC-----UUU---------GACG---UAAG-GGU-UCA-AG--UCCCU-U-AUCCCCC-A
D00548.1/191-271           GGAGGGGU-A-GCGAAGU---GGCUA-AACGCG-G-GUGGC-UGUAACCCAC-UU--CC------UUA---C------GGUU--CGGG-GGU-UCG-AA--UCCCU-C-CCCCUCC-A
D00547.1/242-315           CGGGAAGU-G-GCUCAGUU-UGGU---AGAGCA-U-UCGGU-UUGGGACCGA-AGG------------------------GU--CGCA-GGU-UCA-AA--UCCUG-U-CUUCCCG-A
D00547.1/329-401           GGGCCCUU-A-GCUCAGCU--GGG---AGAGCA-C-CUGCC-UUGCACGCAG-GGG------------------------GU--CGAC-GGU-UCG-AU--CCCGU-U-AGGGUCC-A
D00552.1/73-146            GCCCAUGU-A-GCUCAGUA--GGAU--AGAGCA-C-GCGCC-UUCUAAGCGU-GAG------------------------GU--CGGA-AGU-UCG-AG--CCUUC-U-CGUGGGC-A
K00202.1/1-71              GCAGGUGU-A-GUUUAAU---GGC---AGAACU-U-CAGCC-UUCCAAGCUG-AUU------------------------G---UGAG-GGU-UCG-AU--UCCCU-U-CACCUGC-U
D00558.1/58-130            GUCUGAUU-A-GCGCAACU--GGC---AGAGCA-A-CUGAC-UCUUAAUCAG-UGG------------------------GU--UGUG-GGU-UCG-AU--UCCCA-C-AUCAGGC-A
D00559.1/56-142            GGGUUAAU-A-CUCAAGUU--GGUG--AAGAGG-A-CACCC-UGCUAAGGUG-UUA-GGU-CGG-UCU------CCGGCG----CGAG-GGU-UCG-AG--UCCCU-C-UUAACCC-G
M18050.1/100-172           GCUGACUU-A-GCUCAGUU--GGU---AGAGCA-A-UUGAC-UAGUAAUCAA-UAG------------------------GU--CGAA-GGU-UCA-AA--UCCUU-U-AGUCAGC-A
M18050.1/273-344           UGGGCUAU-A-GCCAAGC---GGU---AAGGCA-A-GGGAC-UUUGACUCCC-UCA------------------------UG--CGCC-GGU-UCG-AA--UCCUG-C-UAGCCCA-A
M18050.1/352-424           GACUCGUU-A-GCUCAGCC--GGU---AGAGCA-A-CUGGC-UUUUAACCAG-UGG------------------------GU--CCGG-GGU-UCG-AA--UCCCC-G-ACGAGUC-A
X16745.1/1-74              GGCCCCAU-A-GCGAAGUU--GGUU--AUCGCG-C-CUCCC-UGUCACGGAG-GAG------------------------AU--CACG-GGU-UCG-AG--UCCCG-U-UGGGGUC-G
X16746.1/1-72              GGCAACAU-G-GCCAAGC---GGCU--AAGGCA-U-GGGUC-UGCAACACCC-UGA------------------------U---CAUC-GGU-UCG-AA--UCCGA-U-UGUUGCC-U
X16748.1/1-73              GGCCUGUU-G-GUGAAGC---GGUU--AACACA-C-ACGGU-UUUCAUCCGU-GGA------------------------CA--CACG-GGU-UCG-AA--CCCCG-U-ACAGGCU-A
X16760.1/1-73              GGUCGUGU-A-GCUCAGUC--GGU---AGAGCA-G-CAGAC-UGAAGCUCUG-CGU------------------------GU--CGGC-GGU-UCA-AU--UCCGU-C-CACGACC-A
X16759.1/1-73              CGCGGGGU-A-GAGCAGUU--GGU---AGCUCG-C-CGGGC-UCAUAACCCG-GAG------------------------GU--CGCA-GGU-UCG-AG--UCCUG-C-CCCCGCA-A
X16750.1/2-74              GCGUAGGU-G-GUGAAGU---GGUU--AACACA-U-CAGGU-UGUGGCUCUG-ACA------------------------UA--CGCG-GGU-UCG-AU--CCCCG-U-UCUACGC-C
X16752.1/1-74              CGGAAUAU-A-GCUCAGCU--GGUU--AGAGCA-U-UCCGC-UGAUAACGGA-GAG------------------------GU--CGUU-GGU-UCA-AG--UCCAA-U-UAUUCCG-A
X16754.1/1-86              CCCCAAGU-G-GCGGAAUA--GGUA--GACGCA-U-UGGAC-UUAAAAUCCA-AC--GGG-C---UUA---AU---AUCCUG--UGCC-GGU-UCA-AG--UCCGG-C-CUUGGGG-A
X16758.1/1-74              GGCGGGGU-A-GCUCAGUU--GGUU--AGAGCG-U-UCGGU-UCAUACCCGA-AAG------------------------GU--CGAG-AGU-UCA-AA--UCUCU-C-CCCCGCU-A
K02974.1/529-600           AGGAGAGU-A-GUUCAAU---GGU---AGAACG-U-CGGUC-UCCAAAACCG-AGC------------------------GU--UGAG-GGU-UCG-AU--UCCUU-U-CUCUCCU-G
X16763.1/1-89              GGAAGAUU-A-CCCAAGUC-CGGCUG-AAGGGA-U-CGGUC-UUGAAAACCG-AGA-GUC-GG--GGA---AA--CCGAG----CGGG-GGU-UCG-AA--UCCCU-C-AUCUUCC-G
X16765.1/1-73              GCUGACUU-A-GCUCAGCA--GGC---AGAGCA-A-CUGAC-UUGUAAUCAG-UAG------------------------GU--CGUA-GGU-UCG-AU--UCCUA-U-AGUCAGC-A
X16767.1/1-73              AGGGGCAU-A-GUUCAGUA--GGU---AGAACA-U-CGGUC-UUCAAAACCG-AGU------------------------GU--CACG-AGU-UCG-AG--UCUUG-U-UGCCCCU-G
M32222.1/1277-1363         GCCGGGGU-G-GCCCAGCC-UGGU---AGGGCG-U-CGGCC-UGCUAAGCCG-AU--GAU-CC--GUU---AA--GGAUCG---CGCG-GGU-UCA-AA--UCCCG-U-CCCCGGC-G
M32222.1/3110-3183         GGGCCCAU-A-GCUCAGCC-UGGG---AGAGCG-C-CGCCC-UUGCAAGGCG-GAG------------------------GC--CCCG-GGU-UCA-AA--UCCCG-G-UGGGUCC-A
M26977.1/276-348           GCCUCGGU-A-GCUCAGCU--GGU---AGAGCG-C-GAGAC-UUGUAAUCUC-GUG------------------------GU--CGCG-GGU-UCA-AA--UCCCG-C-CCGAGGC-U
M26977.1/379-453           GGGGCCAU-A-GGGUAGCC-UGGUCU-AUCCUU-U-GGGCU-UUGGGAGCCU-GAG------------------------A---CCCC-GGU-UCA-AA--UCCGG-G-UGGCCCC-A
M26977.1/557-628           GCCCUGGU-G-GUGUAGU---GGCU--AUCAUG-C-GGGCC-UGUCGAGCCC-GCG------------------------A---CUCG-GGU-UCA-AU--UCCCG-G-CCAGGGC-G
M26977.1/635-708           GGGCCCGU-A-GCUCAGUC-UGGU---AGAGCG-C-UUGGC-UUUUAACCAA-GUA------------------------GU--CGCG-GGU-UCA-AA--UCCCG-U-CGGGCCC-G
M26978.1/826-899           GCCGCCGU-A-GCUCAGUA--GGUA--GGAGCG-C-UCGGC-UGUUAACCGA-GUG------------------------GU--CGCA-GGU-UCG-AG--UCCUG-C-CGGCGGC-G
M26978.1/907-980           GGGCCCAU-A-GCUUAGCC-AGGU---AGAGCG-C-CCGGC-UCAUAACCGG-GCG------------------------GU--CAUG-GGU-UCG-AA--UCCCA-U-UGGGCCC-A
M26978.1/994-1068          GCUCCGGU-G-GUGUAGCC-CGGCCA-AUCAUU-U-CGGCC-UUUCGAGCCG-AAG------------------------A---CUCG-GGU-UCA-AA--UCCCG-A-CCGGAGC-A
M26978.1/1092-1174         GCGGGGGU-G-CCCGAGU---GGUCA-AAGGGG-A-CAGGC-UUAGGACCUG-UU--GGC-----GUU---AG----GCUU---CCAG-GGU-UCG-AA--UCCCU-G-CCCCCGC-A
M26978.1/1192-1264         GCCGGGGU-G-GGGUAGUU--GGCC--AUCCUU-C-GGGAC-UGUGGAUCCC-GCG------------------------A---CUCG-GGU-UCA-AA--UCCCG-G-CCCUGGC-C
M19342.1/69-141            GGGCUCGU-A-GCUCAGCU--GGA---AGAGCG-C-GGCGU-UUGCAACGCC-GAG------------------------GC--CUGG-GGU-UCA-AA--UCCCC-A-CGGGUCC-A
X01078.1/1396-1463         ACUAUUUU-G-GCAGAUU---------AGUGCA-G-UAAAU-UUAGAAUUUA-UUU------------------------A---UAUA-AUU-UAA-UU--AAUUA-U-AAAUAGU-A
X03924.1/17-83             AUUUAUAU-A-GUAUAUA---AU----UGUAUA-U-GUGAC-UUCCAAUCAC-AAG------------------------G---ACUA-AA--UAA-U----UUUA-G-UAUAAAU-A
X03924.1/500-567           AGGGUAAU-A-GUUAAUU---------AUAACA-U-UUAAU-UUGCACUUAA-AAA------------------------G---UAUU-GAA-UUU-AA--UUCAA-U-UUACCUU-A
X03924.1/848-782           AUUUAAAU-A-GCUUAU----AAUU--AGAGCA-U-AACAU-UGAAGAUGUU-GGG------------------------G---AAAU-U---AUU-UU----AAU-U-UUUAAAU-A
X03925.1/1-72              CAAUUUAA-A-GCUUAAUU--AGU---AAAGUA-U-UUCAU-UUACAUUGAA-AAG------------------------A---AAUU-UGU-GCA-AA--UCAAU-U-UAAAUUG-A
U32309.1/158-89            CAGAGAAU-A-GUUUAAU---GU----AGAAUC-U-UAGCU-UUGGGAGUUA-AGG------------------------G---UGAG-AGU-UGA-AU--UCUCU-U-UUCUCUG-A
X16885.1/460-388           GUUGCAGU-A-GCAAAGC---GGUU--AAUGCG-A-GAAUC-CUAAAAUUUC-UUU------------------------AU--CAGA-GGU-UCA-AA--UCCUC-U-CUCCAAC-U
X16885.1/631-561           GGCAGGGU-G-GCAGAAA---GUC---AAUGCG-C-UAAAU-UGUAAAUUUA-UAA------------------------A---AAAA-GGU-UUA-AU--UCCUU-U-CUUUGCC-A
X16885.1/635-704           AAGGAACU-A-GUUAAG----UU----AUAACA-C-UGGAU-UGUCAGACCG-GAG------------------------U---AACU-GGU-AAACAA--CCCAG-U-GUUCCUU-A
X16885.1/779-708           GGUAAAGU-A-AGCUAAAU--GUU---AAGCUU-U-UGGGU-UCAUACCUCA-AAA------------------------A---UAGAAGGA-UAA-AA--ACCUC-U-CUUUAUC--
X16885.1/811-882           CCUCGCAG-A-GCUUGUCA--ACC---UAAGCA-U-CUCUU-UUACACGGAG-AAG------------------------A---AGUU-UGU-GAA-AU--UCGAA-C-UGUUUGG-A
X16885.1/950-882           GGUUUUGU-A-GUGUAA----UU----AACAUA-U-UAGAU-UGCAAAUCUA-UAG------------------------A---UGCG-GCC-AGU-UU--AUCCG-C-CAAAACU-U
X16885.1/1019-953          AGAGAUUU-A-AGUUAA----------UAACUA-A-AA-CC-UUCAAAGUUU-UCA------------------------AU--AGAG-AGU-GAA-AC--CCUCU-U-AAUCUUU-A
X16885.1/1030-1101         GUGAAUUU-A-GUUUAAUA--GAA---AAAACA-U-UUGCU-UUGCAAGCAG-ACU------------------------U---UGAA-AGU-UUA-AC--UCCUU-C-AAUACAC-A
M86496.1/1-68              GUUAAUGU-A-GCUUAAA---AUU---AAAGCA-A-GGCAC-UGAAAAUGCC-UAG------------------------A---UGAG-U-A-UAU-UA----ACU-C-CAUAAAC-A
M86496.1/1024-1089         CAAGAUAU-A-GCUUAA----AC----AAAGUA-U-CUAGU-UUACACCUAG-AAG------------------------A---UUUC-AU--ACA-C----AUGA-A-UAUCUUG-A
X04161.1/733-803           UUCUUAUU-A-GCUCAAU---GGU---AGAGCA-A-AAUAC-UUCUAAUAUU-UUG------------------------A---UCUA-AGU-UCG-AG--UCUUA-G-AUAAGAA-G
X07795.1/26-96             GCCAAAGU-A-GUUUAAU---GGU---AGAACA-A-UAAUU-UCAUGAAUUA-AGA------------------------A---UGAG-AAU-UCG-AU--UUUCU-C-CUUUGGC-U
J01390.1/5955-6026         GAGACUUU-A-GUUUAAU---GGU---AAAACA-U-AUGAC-UUUUAAUCAU-UCU------------------------AC--UAUA-GGU-UCG-AG--UCCUA-U-AAGUCUU-A
J01390.1/6035-6106         AUGACUAU-A-AGUUAAUA--GGU---AGACUG-U-UCGUC-UUCCAAACGA-AGU------------------------G---UGUC-GAU-UCG-AA--UUCGA-C-UAGUCAU-A
J01390.1/6161-6231         ACGGCUAU-A-AGUUAAU---GGU---AGACUA-C-UUAGC-UACCACCUAA-GAU------------------------G---UGUC-GAU-UCG-AA--UUCGA-C-UAGCCGU-A
J01390.1/6234-6306         GGGUUAGU-A-GUUUAAUA--GGU---AAAGCG-C-UUUUU-UGUCAAGGAA-GUU------------------------UA--UGCC-GGU-UCA-AG--UCCGG-C-CUAACCC-G
J01390.1/6367-6447         GGGAAAGU---UUCCAUG---GGUA--GGGUAA-G-AUAUU-UGCUAAAUAU-UG--UGC-G---UUU---G----CACA----UAGA-UGU-UCG-AA--UCAUC-U-CUUUCCC-G
J01390.1/6449-6519         AAGAGUAU-A-GUUUAAU---GGU---AAAACU-G-UAAGC-UUCAACCUUA-UAU------------------------U---UCUU-AGU-UCA-AA--UCUAA-G-UACUCUU-G
J01390.1/6669-6740         GGUUCUUU-A-ACUUAACC--GGU---AAAGUG-U-GUUCU-UGAUAAGGAU-AUG------------------------U---UCAG-UGU-UCG-AG--UCACU-G-AAGAAUC-A
J01390.1/6761-6842         AGAGAGUU-G-GCUGAGU---GGU---AAGGCG-A-CUAGC-UUGAGUCUAG-UU--AAG-UU--AAA-------ACUUU----CAUA-UGU-UCG-AA--UCAUA-U-ACUCUCU-G
J01390.1/6861-6932         CAGGUUAG-A-GCCAGGU---GGU---UAGGCG-U-CUUGU-UUGGGUCAAG-AAA------------------------UU--GUUA-UGU-UCG-AA--UCAUA-A-UAACCUG-A
J01390.1/11761-11831       GCCCGGUU-A-GCAUAAA---AGU---AAUGUA-U-CCGUU-UUGUAAUCGG-AAU------------------------A---AACA-AGU-GCG-AU--ACUUG-U-ACUGGGC-U
J01390.1/11859-11931       GACCCAAU-G-GUCAAGAU--GGUU--AAGACA-U-AACAU-UUUCACUGUU-AGU------------------------G---GGGG-AGU-UCA-AU--CCUCC-C-UUGGGUU-G
J01390.1/11933-12004       AAGAAAUU-A-GCUCAGUU--GGU---AGAGCG-U-UCGUU-UUACACACGA-AGG------------------------U---CAGG-UGU-UCA-AA--UCACC-U-AUUUCUU-A
J01390.1/12028-12098       AGCGGGUU-G-AUGUAAU---AGU---AACAUA-U-AUGGC-UCAUGCCCAU-AAU------------------------A---UUUA-GGU-GCA-AC--UCCUA-A-AUCCGCU-A
J01390.1/12100-12172       AAGACUAU-A-GCUUAAUC--GGU---AAAGCG-A-ACCAC-UCAUGAUGGU-UUG------------------------AG--UAAA-UGU-UCA-AG--UCAUU-U-UAGUCUU-A
J01390.1/12177-12258       AUCCGAGU-G-CUGGAAUU--GGUA--GACAGU-C-UUAGC-UUAAGUUUAA-GU--GAC-----GCA---A-----GUCG---UAAA-CGU-UCG-AA--UCGUU-U-CUCGGAU-A
J01390.1/12259-12330       GGGGCUAU-A-GUUUAACU--GGU---AAAACG-G-CGAUU-UUGCAUAUCG-UUA------------------------U---UUCA-GGA-UCG-AG--UCCUG-A-UAACUCC-A
J01390.1/12336-12408       GCUUGAGA-A-GCUCAAUU--GGU---AGAGCG-G-GUCAG-UGAAGUUGAU-UAG------------------------GU--UGUA-AGU-UCA-AG--UCUUA-U-CUCGAGC-A
J01390.1/12417-12498       AUGGGUAU-G-CUGAAAUA-AGGUA--AACAGG-U-UCCGC-UUAGGACGGA-AU--AGU-----CAA---------ACUU---UGCA-AGU-UCA-AG--UCUUG-U-UACCCGU-A
J01390.1/12505-12576       UAUGUUGU-C-GACUAAUC--GGU---AAGUCA-U-AAAUU-UUUGGUAUUU-AUA------------------------U---UGGG-UGU-UCG-AG--UCGCC-C-CAACAUA-A
J01390.1/13362-13432       GUGGGUGU-A-GUUCAAA---GGU---AGAACA-G-CUGUA-UGUGGCAUAG-UAU------------------------A---UCCU-AGU-UCA-AU--UCUAG-G-UAUCCAC-C
J01391.1/18-88             GCCUUUAU-A-GCUCAAC---GGU---AGAGCG-G-AAUAC-UGUUAAUAUU-UUG------------------------A---UAGA-UGU-UCA-AU--UCAUC-U-UAAGGGC-U
D16387.1/276-206           GGAGAAAU-G-GCAGACA---GG----GAUGCA-U-UUAGC-UUGAAACUAA-AUA------------------------GA--GGAA-GGU-UCG-AA--UCCUU-U-UUUCUCU-U
D16387.1/11325-11257       GUUUCAUG-A-GUAUAGC---------AGUACA-U-UCGGC-UUCCAACCGA-AAG------------------------GU--UUUU-GUA-AAC-AA--CCAAA-A-AUGAAAU-A
D16387.1/11397-11328       GAUUGGGU-G-GCAGAUA---GG----GAUGCG-A-UAGAU-UGUAAAUCUA-GGU------------------------A---GGAA-GGU-UCA-AG--UCCUU-U-CCUGGUC-A
D16387.1/11403-11471       AAAGAGCU-A-GUUAAA----AA----AUAACC-C-CAGAU-UGUCAGACUG-GAA------------------------U---UAUC-UGU-AACCAC--CCUGA-U-GCUCUUU--
D16387.1/11555-11625       CCUGGCGG-A-GCUUGAU---AGU---UAAGCA-U-CUCUU-UUACACAGAG-CUG------------------------A---UAUU-UGU-GCA-AA--UCAAA-U-UGCCUUG-A
D16387.1/11909-11838       GCUGGGGU-A-GCAAAGU---GGUU--ACUGCA-G-UAGAU-UUAGGAUCUA-CGA------------------------U---CAAG-GGU-UCA-AA--UCCUU-U-UCCUAGU-U
X16886.1/458-387           GCUGAAAU-A-GCAAAGU---GGU---AAUGCG-A-GAAGC-CUAAGAUUUC-UUU------------------------AU--CGAA-GGU-UCA-AA--UCCUU-C-UUUCAGU-U
X16886.1/781-711           AGUAAAGU-A-AGCUAAU---AAA---AAGCUU-U-UGGGU-UCAUACCUCA-AAA------------------------A---UGGAAGGA-UAA-AU--ACCUC-C-CUUUAUU--
X16886.1/923-857           GGUUUUGU-A-GUGUAA----UU----AACAUU-U-UAGAU-UGCAAAUCUA-UAG------------------------A---UGCG-G-G-UAA-UC--U-CCG-U-CAAAACU-U
X16886.1/993-924           AGGGGUUU-A-AGUUAA----UCU---AAACUA-A-AAGCC-UUCAAAGCUU-UAA------------------------A---UAAG-AAU-GGG-AA--UUUUU-U-AACCUCU-G
X16886.1/999-1070          GUGGACUU-A-GUUUAAAA--GAU---AAAACA-A-UUGAU-UUGCAAUCAG-UAA------------------------C---UCCA-AGU-UUA-AC--UCUCG-G-AGUCCAC-A
X16886.1/1215-1285         UAGAAAGU-A-GUAUAAC---GGU---AAAACC-A-AGAAU-UUUGAUUUCU-UAA------------------------A---UAUA-AGU-UCA-AC--UCUUA-U-CUUUCUA-A
X16886.1/1355-1286         CAGAAAAU-A-GUUUAG----UG----AGAAUG-A-UAGCU-UUGGGAGCUG-UUG------------------------G---UGUA-AGU-AUA-AA-GUCUUG-C-UUUUCUG-A
X14110.1/261-348           GGAGGGAU-G-GCUGAGU---GGCUU-AAGGCA-U-UGGUU-UGCUAAAUCG-AC--AUA-CAA-GAA---GA-UUGUAU----CAUG-GGU-UCG-AA--UCCCA-U-UUCCUCC-G
X13485.1/5-77              GCCCUAGU-A-GCUUAGAC--AUC---AAAGCA-C-CGGUC-UUGUAAACCG-AAG------------------------AU--CGAA-GGU-UAA-AA--UCCUU-C-CUAGCGC-C
K00242.1/1-75              GUUAAGGU-G-GCAGAGCC-CGGUA--AUUGCA-U-AAAAC-UUAAACUUUU-AUA------------------------UC--CAGA-GAU-UCA-AA--UCCUC-U-CCUUAAC-A
M86494.1/1026-1092         CAAGAUAU-A-GCUUAAAC--------AAAGCA-U-CUAGU-UUACACCUAG-AAG------------------------A---UUUC-ACA-U---AC--UAUGA-A-UGUCUUG-A
V00654.1/4197-4265         AGUAAGGU-C-AGCUAA----UU----AAGCUA-U-CGGGC-CCAUACCCCG-AAA------------------------A---UGUU-GGU-UUA-UA--UCCUU-C-CCGUACU-A
V00654.1/11907-11976       GUAAAUAU-A-GUUUAA----CA----AAAACA-U-UAGAU-UGUGAAUCUA-ACA------------------------A---UAGA-AAC-UCA-UUA-CCUUC-U-UAUUUAC-C
V00654.1/12038-12108       ACUUUUAA-A-GGAUAGU---AGUU--UAUCCG-U-UGGUC-UUAGGAACCA-AAA----------------------------AAUU-GGU-GCA-AC--UCCAA-A-UAAAAGU-A
V00654.1/15791-15726       CAGGGAAU-A-GUUUAA----AU----AGAACU-U-CAGCU-UUGGGGGUUG-AUG------------------------G---UGAG-AC--UGC-A----GUUU-C-UUCCUUG-A
M86498.1/1-69              GUUAAUGU-A-GCUUUAA---AAUU--AAAGCA-A-GGCAC-UGAAAAUGCC-UAG------------------------A---UGAG-U-G-CUC-CA----ACU-C-CAUAAAC-A
M86498.1/1026-1092         CAAGACAU-A-GCUUAA----AU----AAAGCA-U-CUAGU-UUACACCUAG-AAG------------------------A---UUUC-ACC-CAC-C----AUGA-A-UGCCUUG-A
M86499.1/1-68              GUUAAUGU-A-GCUUAAA---CUA---AAGGCA-A-GGCAC-UGAAAAUGCC-AAG------------------------A---UGAG-UG--UAC-G----CACU-C-CAUGAAC-A
M86499.1/1022-1088         CGAGAUAU-A-GCUUAA----AC----AAAGCA-U-CUAGU-UUACACCUAG-AAG------------------------A---UUUC-ACA-CAU-C----AUGA-A-UAUCUUG-A
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M57910.1/1028-963          GAUUAAGU-G-GCUGAA----GUU---UAGGCG-A-UAGAU-UGUAAAUCUA-UAU------------------------A---UAAG-A---UUU-AU----UCU-U-CUUAAUC-A
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X05914.1/400-337           AAUGAAUU-G-CCUGAUA---------AAAGGG-U-UAUCU-UGAUAGGGUA-AAU------------------------UA--UGUA-G---GAU-U-----CUA-C-AUUCAUU-G
X03240.1/1-65              AAUGAAUU-G-CCUGAU----AA----AAAGGG-U-UACCU-UGAUAGGGUA-AAU------------------------UA--UGCA-G---UUU-U-----CUG-C-AUUCAUU-G
X03240.1/1267-1333         AAGGCUUU-A-AGUUAA----CU----AAACUA-A-UAGCC-UUCAAAGCUG-UAA------------------------A---UAAA-GG--GUA-UU---CCUU-U-AAGUCUU-A
X03240.1/1388-1326         GGUCUUAU-A-GUCAAUA---------AUGAUA-U-CAAAC-UGCAAUUUUG-AAG------------------------G---AGUA-A-A-UUU-------UUA-C-UAAGACU-U
X00432.1/532-596           UUAAUUGA-A-GCCAAA----AA----GAGGCG-U-AUCAC-UGUUAAUGAU-AUA------------------------AU--UGAG-U---AUA-A-----ACU-C-CAAUUAA-G
X05915.1/238-170           AAAAAGAU-A-AGCUAA----UU----AAGCUA-C-UGGGU-UCAUACCCCA-UUU------------------------A---UAAA-GGU-UAU-AA--UCCUU-U-UCUUUUU-A
M93388.1/1318-1384         CUGGGGGU-A-GCUUAA----GAUU--AAAGUU-U-GGAAU-UCUUACUUCU-AAG------------------------A---UAUC-UG--GUU------UGGA-U-UCUUCAG-G
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X52392.1/2273-2345         CAAGGCGU-A-GCUAUAAC--UUC---AAAGCA-U-UCAGC-UUACACCUGA-AAG------------------------A---UACC-CUC-AAC-AG-ACAAGG-U-CGCCUUG-A
X52392.1/3967-4040         GCUAGCGU-G-GCAGAGCU-CGGCA--AAUGCA-A-AAGGC-UUAAGCCCUU-UAU------------------------C---CAGA-GGU-UCA-AA--UCCUC-U-CCCUAGC-U
X52392.1/5025-5096         GGAAGCGU-G-CCUGAAC---AA----AAAGGA-U-CACUA-UGAUAAAGUG-AAC------------------------A---UAGA-GGU-AUA-ACAACCCUC-U-CACUUCC-U
X52392.1/5172-5102         UAGAAAAU-A-AUAUAGA---GGG---AGUAUG-A-AGAGU-UUUGAUCUCU-UCU------------------------G---UGUA-GGU-UCG-AU--UCCUA-C-UUUUCUA-G
X52392.1/5172-5240         AGUAAGGU-C-AGCUAA----CU----AAGCUA-U-CGGGC-CCAUACCCCG-AAA------------------------A---UGAU-GGU-UUA-AC--CCCUU-C-CCCUACU-A
X52392.1/6280-6355         AGAAACUU-A-GGAUUAAC-UGUCACCAAACCA-A-AGGCC-UUCAAAGCCU-UAA------------------------A---UAAG-AGU-UAA-AC--UCUCU-U-AGUUUCU-G
X52392.1/6430-6362         GAGGCCUU-A-GCUUAA----UU----AAAGCG-U-CUGAU-UUGCAUUCAG-GAG------------------------A---UACA-GGU-UAA-UG--UCCUG-U-UGGUCUU-A
X52392.1/6506-6434         UAGGCAGA-A-GCCAAUU---GGUG--UUGGCA-U-UUAGC-UGUUAACUAA-AAU------------------------UG--UAUG-GGA-UCG-AA--GCCCA-U-CUGUCUA-G
X52392.1/6573-6508         GACUCUGU-A-GUGAAGU----------UCAUA-A-UGAGU-UGCAAACUCG-UUG------------------------A---UGUA-CAC-UAA-AG---UGUG-C-CGGGGUC-U
X52392.1/8258-8184         AAGAAAGA-A-GCAUUAAG-UGGUUU-GAUGCG-G-UUGGC-UUGAAACCAA-CAU------------------------G---UGAG-GGU-UCG-AU--UCCUU-C-CUUUCUU-G
X52392.1/9016-9083         CAUUAAGA-A-GCUAUG----CA----CCAGCA-C-UAGCC-UUUUAAGCUA-GAG------------------------AG--AGGG-G-A-CAC-CC--U-CCC-C-CUUAAUG-A
X52392.1/11128-11195       AGAAAGUU-A-GUCUAA----CU----AAGACA-G-CUGGU-UUCGACCCAG-CAA------------------------A---UUAU-AGA-CCC-AC---CUAU-A-ACUUUCU-U
X52392.1/13000-13070       ACUUUUAA-A-GGAUAAG---AGC---AAUCCG-U-UGGUC-UUAGGAACCA-CCU------------------------A---UCUU-GGU-GCA-AA--UCCAA-G-UAAAAGU-A
X52392.1/16039-16107       ACUCUAAU-A-GUUUAU----GA----AAAACA-U-UGGUC-UUGUAAACCA-AAA------------------------AC--UGAA-GAC-UCC-AC---CCUU-C-UUAGAGU-A
X52392.1/16177-16108       CAGAGAGU-A-GUUUAUU---UG----AAAAUA-C-CAGCU-UUGGGAGCUG-GAG------------------------A---UGGA-GGU-UUG-AG--CCCUC-C-UUUUCUG-A
X52392.1/16775-16708       GUUCCCGU-A-GUUGAGAA---------CAACA-A-UGGCU-UUUCAAGCCG-UAG------------------------U---CCUU-GGG-GUC-UA--ACCAA-G-CGGGAAU-A
X07375.1/305-376           GUCCCUUU-C-GUCCAGU---GGUU--AGGACA-U-CGUCU-UUUCAUGUCG-AAG------------------------A---CACG-GGU-UCG-AU--UCCCG-U-AAGGGAU-G
M86501.1/1-68              GUUAAUGU-A-GCUUAA----AUCC--AAAGCA-A-GGUAC-UGAAAAUGCC-UAG------------------------A---UGAG-U---GUA-UU--A-ACU-C-CAUAAAC-A
M86501.1/1024-1090         CAAGACAU-A-GCUUAA----AC----AAAGCA-U-CUAGU-UUACACCUAG-AAG------------------------A---UUCC-AUA-CAC-U----AUGA-A-UGUCUUG-A
X15613.1/59-121            GACGGUAU-A-GUUUAA----GUU---GAGAUG-U-GUGCU-CUGCGAGCAU-UCG------------------------G---UAGA---G-GUU--------UC-U-UGCCGUU-G
X15613.1/1106-1175         GUGCGUGU-A-GAUUAUAUUUGGU-A-AAAUCG-U-AAGGC-UGUUAACUUU-GAG------------------------A---UGGU-G---UGU-U-----UGC-C-CGCGGAC-G
X15613.1/1813-1875         AGUGAUCU-A-GGUUAUU---UU----GGACUG-U-CUGUU-UUCAAAACAG-GAG------------------------G---UGGC-----UUU-G------GU-C-GGUUGCU-G
D31785.1/714-785           GAUCUUAU-A-GUUAAAU---GGUU--AUAACA-C-CAUCC-CUUCACGAUG-GGA------------------------G---UACC-AGU-UCG-AU--UCUGG-U-UGAGAUU-A
D31785.1/832-903           AGAGAGGA-G-UGAAUAA---GGUU--GUUCAU-A-UAAAU-UGCAAAUUUA-UAC------------------------AUU-UAGG-G-U-UCG-AU--U-CCC-U-CUUCUCU-C
D31785.1/12211-12283       AAGGGUAU-A-GUUUAAUU--GGU---AAAACA-G-UUGAC-UUCAAAUCAA-UAU------------------------AG--UGAU-AGU-UCA-AU--UCUGU-C-UGCCCUU-G
D31785.1/14571-14644       AAGGGAUU-U-GCUUAAUU--GGU---AUAGCA-U-UUGUU-UUACACACAA-AA----------UUA------------G---UAUA-GGU-UCG-AG--UCCUA-U-AUUCCUU-A
D10743.1/4-76              GUUGCAUU-A-GCUCAAUU--GGU---AGAGCG-U-UUGUU-UUGUAAUCAA-AAG------------------------GU--UUAG-AGU-UCA-AC--UCUCU-A-AUGCANU-N
D10744.1/201-272           AUGAGUAU-A-AGUUAAU---GGUU--AAACUA-A-AUGUC-UUCCACACAU-UCC------------------------A---UGUG-AGU-UCG-AU--UCUCA-C-UACUCAU-A
D10744.1/389-471           GGAAAAUU-G-AUCAUC----GGC---AAGAUAAG-UUAUU-UACUAAAUAA-UA--GGAUU---UAA---U----AACCU---GGUG-AGU-UCG-AA--UCUCA-C-AUUUUCC-G
D10745.1/410-483           UGAAUUGU-A-GACUAAUA--GGU---AAGUCC-C-CAAAA-UUUGAGUUUG-GCU-U----------------------AU--GGUG-UGU-UCG-AA--UCACC-C-CAAUUCA-A
M86497.1/1-66              GUUAAUGU-A-GCUUAAA---CU----AAAGCA-A-GGCAC-UGAAAAUGCC-UAG------------------------A---UGGG-U-A-UUU-A-----ACU-C-CAUAAAC-A
M86497.1/1020-1086         CAAGAUAU-A-GCUUAA----AU----AAAGCA-C-CUAGU-UUACACCUAG-AAG------------------------A---UUUC-ACA-CGC-C----ACGA-A-UAUCUUG-A
X13823.1/142-214           GGAAAUGU-U-GUUUAAA---GGUU--AAACUG-U-UAGAU-UGCAAAUCUA-CAC------------------------AU--UUAG-AGU-UCG-AU--UCUCU-U-CAUUUCU-U
X13824.1/2-83              GCUACUUU-G-GUGGAAAU--GGUA--GACACG-A-CACUC-UUAAGAUGUG-UU--AUC-----GCA---A-----GAUA---UGAA-GGU-UCA-AA--UCCUU-U-AAGUAGU-A
X14821.1/1-72              GAGAAUAU-U-GUUUAAU---GGU---AAAACA-G-UUGCC-UUUUAAGCAU-CCC------------------------AU--GUUU-GGU-UCG-AU--UCCAA-C-UAUUCUU-A
X14822.1/1-73              UGAAUCGU-A-GACUAAUA--GGU---AAGUCA-C-CAAAA-UUUGAGUUUG-GAA------------------------UU--UGUU-UGU-UCG-AA--UCAAA-C-CGGUUCA-A
X03676.1/445-516           GCGGAAAU-A-GCUUAAU---GGU---AGAGCA-U-AGCCU-UGCCAAGGCU-GAG------------------------GU--UGAG-GGU-UCA-AG--UCCCU-C-CUUCCGC-U
X04377.1/307-380           AGCGGGGU-A-GAGUAGUU--GGUU--AACUCG-U-CAGGC-UCAUGACCUG-AAG------------------------AU--UGCA-GGU-UCG-AA--UCCUG-C-CCCCGCC-A
M22657.1/587-656           ACUUUUAA-A-GGAUAGA---AGU---AAUCCA-U-UGGCC-UUAGGAGCCA-AAA----------------------------AAUU-GGU-GCA-AC--UCCAA-A-UAAAAGU-A
X13975.1/39-104            UCUAAUAU-G-GCAGAUU---------AAUGCA-U-UAGAU-UUAAGCUCUA-AAA------------------------A---UAAA-GUU-UUG-A----CCUU-U-UAUUAGA-A
X13975.1/791-854           AAGGAGUU-A-GUUAAA----AU----AUAACA-U-UAGAA-UGUCAAUCUA-AAA------------------------U---AACU-A---AAA-A-----UAG-U-ACACCUU-G
X13975.1/858-928           CAUCAGAU-G-ACUGAA----AG----UAAGUA-A-UGGUC-UCUUAAACCA-AAA------------------------AA--UAGU-AAA-UUA-AC-GUUUAC-U-UCUGAUG-A
X13975.1/2575-2637         AUUUUUCU-A-GUAUAA----UU----AGUACA-U-UUGAC-UUCCAAUCAA-AAG------------------------A----UUG-A---AAU-A-----UCA-A-GAAAAAU-A
L07095.1/2676-2750         AUUAGGGU-G-GCAGAGCC-AGGAA--AUUGCG-U-AAGAC-UUAAAACCUU-GUU------------------------CC--CAGA-GGU-UCA-AA--UCCUC-U-CCCUAAU-A
L07095.1/5086-5018         GAGGUCUU-A-GCUUAA----UU----AAAGCA-A-UUGAU-UUGCAUUCAA-UAG------------------------A---UGUA-GGA-UGA-AG--UCUUA-C-AGUCCUU-A
L07095.1/5327-5261         GGUAAAAU-G-GCUGAG----------UAAGCA-U-UAGAC-UGUAAAUCUA-AAC------------------------A---CAGA-GGU-UUA-AA--UCCUC-U-UUUUACC-A
L07095.1/15292-15358       GUCUUGAU-A-GUAUAA----AC----AUUACU-C-UGGUC-UUGUAAACCU-GAA------------------------A---UGAA-G-A-UCU-UC--U-CUU-C-UCAAGAC-A
D85268.1/459-527           GUAGAUAU-A-GUUUAACU--------AAAACA-C-UAGAU-UGUGAAUCUA-ACC------------------------A---UAGA-GAC-UCA-CC--ACCUC-U-UAUUUAC-C
D85275.1/459-527           GUAAAUAU-A-GUUUAA----CU----AAAACA-U-UAGAU-UGUGAAUCUA-ACU------------------------A---UAGA-GGC-CUA-CC--ACUUC-U-UAUUUAC-C
M86495.1/1-68              GUUAAUGU-A-GCUUAAA---UCU---AAAGCA-A-GGCAC-UGAAAAUGCC-UAG------------------------A---UGAG-U-G-CAC-UA----ACU-C-CAUAAAC-A
M86495.1/1026-1092         CAAGAUAU-A-GCUUAA----AC----AAAGCA-C-CUAGU-UUACACCUAG-AAG------------------------A---UUUC-ACA-CAC-UA----UGA-A-UAUCUUG-A
U47458.1/87-21             CAAGAAGU-A-GUUUAA----UU----AGAAUA-C-CAGCU-UUGGGUGCUG-GUG------------------------G---UGGG-GA--GUA-GC---UCCU-U-CUUCUUG-A
D85271.1/587-657           ACUUUUAA-A-GGAUAAC---AGC---UAUCCA-U-UGACC-UUAGGAGUCA-AAA------------------------A---UAUU-GGU-GCA-AC--UCCAA-A-UAAAAGU-A
M22650.1/459-527           GUAGAUAU-A-GUUUAA----CU----AAAACA-U-UAGAU-UGUGAAUCUA-ACC------------------------A---UAGA-GAC-UUA-CC--ACCUC-U-UAUUUAC-C
M68929.1/1540-1461         GCGCAUUU-G-GUGAAAAA--GGUA--AACACG-A-CGGAU-UUAAAAUCCG-UU--CC------UAU---U------GGU---UAUU-GGU-UCA-AG--UCCAA-U-AAUGCGC-A
M68929.1/15170-15243       GCAUUCUU-A-GCUCAGUU--GGAU--AGAGCA-A-CAACC-UUCUAAGUUG-AAG------------------------GU--CACA-GGU-UCA-AA--UCCUG-U-AGAAUGC-G
M68929.1/17407-17480       GUGCUUGU-A-GCUCAAUU--GGAU--AGAGCA-C-CAAAC-UACGGAUUUG-GGG------------------------GU--UGAG-AGU-UCA-AA--UCUUU-C-CAAGCAU-G
M68929.1/18311-18382       GCGGAAAU-A-GCUUAAU---GGU---AGAGUA-U-AGCCU-UGCCAAGGCU-AAG------------------------GU--UGAG-GGU-UCA-AG--UCCCU-U-UUUCCGC-U
M68929.1/20078-20150       GUCCCUUU-C-GUCUAGG---GGUAU-AGGACA-U-CGUCU-UUUCAUGUCG-AAA------------------------A---CACG-GGU-UCA-AA--UCCCG-U-AAGGGAU-A
M68929.1/32684-32756       UCUUUAGU-A-GCUCAGC---GGUU--AGAGCA-A-AUGGC-UGUUAACUAU-UGG------------------------GU--CGUU-GGU-UCG-AA--UCCAA-C-CUAGAGA-G
M68929.1/36559-36632       CAAGGUGU-A-GCGCAAUC-UGGU---AGCGCG-U-CUGCC-UUGGGCGCAG-AAA------------------------GU--UACA-GGU-UCA-AA--UCCUG-U-CACCUUG-A
M68929.1/39446-39374       AGGAGAAU-A-GUUCCAAU--GGU---AGAACA-A-UGGUC-UCCAAAACCA-AAG------------------------GU--UAAG-GGU-UCG-AA--UCCCU-U-UUCUCCU-G
M68929.1/41917-41989       GGGUAAUU-A-GCUCAGUU--GGU---AGAGUG-C-CUCGU-UUACACCGAG-AGA------------------------GU--CAGC-GGU-UCA-AG--UCCGU-U-AUUACCC-A
M68929.1/48611-48684       GGGGAAAU-A-GCUUAGU---GGUUU-AUAGCG-C-UGGUC-UGUCAAGCCA-GAA------------------------GU--CGCG-GGU-UCA-AA--UCCCG-U-UUUUCCC-G
M68929.1/49940-50012       GGGGACGU-A-GCUCAAUU--GGU---AGAGCG-U-AUGUU-UUGCAAGCAU-AAA------------------------GC--UGUC-GGU-UCA-AA--UCCGA-U-CGUCUCC-A
M68929.1/50694-50622       GCCCGCGU-A-GCUCAGAU--GGU---AGAGCA-U-UCCCA-UGGUAAGGGA-AAG------------------------GC--CUCC-GGU-UCA-AG--UCCGG-U-CGUAGGC-U
M68929.1/79397-79315       GGGAGAGU-G-GCCGAGU---GGUUA-AAAGCG-A-CAGAC-UGUAAAUCUG-CU--GAA-----GGU---U-----UUCUA--CGUA-GGU-UCG-AA--UCCUG-C-CUCUCCC-A
M68929.1/79613-79540       GCAUUCUU-A-GCUCAGUU--GGAU--AGAGCA-A-CAACC-UUCGAAGUUG-AUG------------------------GU--CACA-GGU-UCA-AA--UCCUG-U-AGGAUGC-G
M68929.1/151018-150946     CGCGGGAU-A-GAGUAAUU--GGU---AACUCG-U-CAGGC-UCAUAAUCUG-AAU------------------------GU--UGUG-GGU-UCG-AA--UCCGA-C-UCCCGCC-A
M68929.1/152677-152605     GUCGGAAU-A-GUUUAGUA--GGGU--AGAACA-G-CGGGA-UCAUAAUUCG-CAC------------------------A---CGGG-GGU-UCA-AA--UCCCU-C-UUCCGAU-A
M68929.1/163972-163902     GCGGAUAU-A-GAUUAAA---GGU---AAAUUA-U-CUGCC-UUCCAAGCAG-AGG------------------------A---UAUG-GGU-UCG-AU--UCCCG-U-UAUCCGC-A
M68929.1/164824-164907     GGAUGGAU-G-UCUGAGC---GGUUG-AAAGAG-U-CGGUC-UUGAAAACCG-AA--GUA-UU--GAG-------AAUAC----CGGG-GGU-UCG-AA--UCCCU-C-UCCAUCC-G
M68929.1/165481-165397     GCGGAUAU-G-AUGGAAUU--GGUA--GACAUG-C-CAGGU-UUAGGUUCUG-GU--GAC-CA--UAA-------UGUUCG---UGGG-GGU-UCG-AG--UCCCU-C-UAUCCGU-A
M68929.1/166107-166035     GGGUGUAU-A-GCUCAGUU--GGU---AGAGCA-A-UAGGC-UUUUAACUUA-AAG------------------------GU--CGCA-GGU-UCA-AG--UCCUG-C-UAUACCC-A
M68929.1/166929-166856     GGGCUUAU-A-GUUUAAUU--GGUU--CAAACG-C-ACCGC-UCAUAACGGU-GAU------------------------AU--UGUA-GGU-UCG-AG--UCCUA-C-UAAGCCU-A
M68929.1/172005-172075     GGCUAAGU-A-ACAUAAG---GGU---AAUGUA-U-UGGAU-UGCAAAUCCU-AUA------------------------A---AGAU-GGU-UCG-AA--UCCGU-C-CUUAGCC-U
M68929.1/174348-174275     GUUUAGAU-A-GCUCAGGU--GGUU--AGAGCA-A-AGGAC-UGAAAAUCCU-UGU------------------------GU--CAGU-GGU-UCG-AA--UCCAC-U-UCUAAAC-A
M68929.1/182805-182734     UGGAGUAU-A-GCCAAGU---GGU---AAGGCA-U-CGGCC-UUUGAUGCCG-AGA------------------------AA--CAAA-GGU-UCG-AA--UCCUU-U-UACUCCA-G
M68929.1/186481-186410     GCGGAUAU-A-ACUUAGG---GGUU--AAAGUU-G-CAGAU-UGUGGCUCUG-AAA------------------------A---CACG-GGU-UCG-AA--UCCCG-U-UAUUCGC-C
M68929.1/186579-186500     ACUCGCUU-G-GUGGAAC---GGCA--AACACG-G-CAGAC-UCAAAAUCUG-UU--UCU-----AAU---------GGAA---UAUC-GGU-UCG-AA--UCCGA-U-AGCGAGU-A
D85289.1/459-527           GUAAAUAU-A-GUUUAA----UU----AAAACA-U-UAGAC-UGUGAAUCUA-ACU------------------------A---UAGA-AGC-UUA-CC--ACUUC-U-UAUUUAC-C
K00144.1/1-72              GGGGGUAU-A-GUAUAAUU--GGU---AGUACA-G-CAAUC-UUGCUCAUUG-CUU------------------------G---UCAA-GGU-UCA-AA--UCCUU-G-UAUCUCC-A
X04512.1/2563-2632         UUCUCAUU-A-GCUCAAA---GGA---AGAGCA-G-GAUAC-UUCUAAUAUU-CCG------------------------A---UUUU-AGU-UCG-AA--UCUAA-A-AUGAGAA--
X01738.1/122-190           GAUUACGA-U-GUAAAU----GGU---UUACCC-U-UUGAC-UGCAAAUCUU-AAG------------------------GA--UUAG-G-U-UCG-AU--U-CCU-A-CGUAAUC-C
M58319.1/196-282           GGAUGGAU-G-UCUGAGC---GGUUG-AAAGAG-U-CGGUC-UUGAAAACCG-AA--GUA-UUG-AUA---A--GGAUAC----CGGG-GGU-UCG-AA--UCCCU-C-UCCAUCC-G
M86500.1/1-68              GUUCAUGU-A-GCUUAAA---ACC---AAAGCA-A-GGCAU-UGAAAAUGCC-UAG------------------------A---UGAG-U-A-UAU-UA----ACU-C-CAUAAAC-A
L29771.1/1004-1071         GCUGACGU-A-GCUUAA----CU----AAAGCA-U-AACAC-UGAAGCUGUU-AAG------------------------A---CGGA-CCC-UAG-AA---AGUC-C-CGCUAGC-A
M81755.1/6-77              GCCCUAGU-A-GCUCAGC---GC--C-AGAGCG-C-CGGUC-UUGUAAUCCG-GAA------------------------GU--CGGA-GGU-UAA-AA--CCCUC-C-CUAGUGC-U
D13102.1/342-269           GCGCUCUU-A-GUUCAGUU-CGGU---AGAACG-U-GGGUC-UCCAAAACCC-AAU------------------------GU--CGUA-GGU-UCA-AA--UCCUA-C-AGAGCGU-G
X07125.1/118-191           AGCGGGGU-A-GAGGAUUU--GGUA--AACUCA-U-CAGGC-UCAUGACCUG-AAG------------------------AC--AGCA-GGU-UCG-AA--UCCUG-U-CCCCGCC-U
X15602.1/102-172           GCCCCUAU-A-GCUCAAU---GGU---AGAGCA-U-AAUAC-UGUUAAUAUU-AUG------------------------A---UAGA-UGU-UCG-AU--UCAUC-U-UGGGGGC-U
X15917.1/6364-6435         GCUUAAGU-A-GCUCAGU---GGU---AGAGCG-U-UAGAC-UGAAAAUCUA-AAG------------------------GU--CGUU-GGU-UCA-AU--UCCAA-U-CUUGAGC-A
X14485.1/2-72              GCCCGGGU-A-GUUUAAA---GGU---AAAACC-U-UAAUU-UCAUACGUUA-AAG------------------------A---UGAG-AAU-UCG-AU--UUUCU-C-CCCAGGU-U
X03126.1/162-234           GAAUUAGU-A-ACUUAAUU--GGU---AGAGGG-U-UUCCU-UGUCACGGAA-GCA------------------------GA--UGCC-GGU-UCG-AU--GCCGG-U-CUAGUUC-G
X03126.1/244-324           GGAAAAGU---UGCCAUA---GGU-A-AGGUAA-G-AUAUU-UGCUAAAUAU-UG--UGU-U---UAA---G----CACC----UAGG-UGU-UCG-AG--UCACC-U-CUUUUCC-G
X03126.1/364-434           AAGAGUAU-A-GUUUAAA---GGU---AAAACA-G-AAAGC-UUCAACCUUU-AAU------------------------U---UCUU-AGU-UCG-AG--UCUAA-G-UGCUCUU-G
J04815.1/1-73              GCAAAGGU-A-GCUUAACA--GAUU--AAAGCA-U-AGCAC-UGAAAAUGCU-UCA------------------------A---AGAG-AGU-UAA-AG--UCCCU-C-CCUUAGC-A
J04815.1/952-1020          GCUCCUAU-A-GUUGAA----CU----ACAACA-A-GAGCU-UUUCACGCUC-UAA------------------------G---UUUG-AGU-UAA-AA--UCUCA-A-UAGAAGC-U
J04815.1/1026-1098         ACCUUGAA-G-GCUCAAU---AGUU--AGAGCGCC-AAGUC-UUGUAAACUU-GGA------------------------G---AGAG-GGU-UAA-AG--UCCCU-C-UCAAGGC-U
J04815.1/1231-1299         CAAAGAAU-A-GUUUAA----GA----AAAACA-A-CAGCU-UUGGGAGUUG-UAG------------------------A---CGUA-AGU-GAA-AA--CCUUA-C-UUCUUUG-A
J04815.1/1371-1301         UAAGGAGU-A-GUUUAAU---GGA---AAAACG-A-GGAAC-UUUGACUUCC-UUG------------------------U---UGUG-GGU-UCA-AU--UCCCA-U-CUCCUUA-A
J04815.1/1380-1451         UGGGUUGU-A-GCUAAAU---GUA---AAGGCG-C-UUGGC-CGUUAACCAA-GAA------------------------AU--AGUA-GGA-UAA-AA--ACCUA-U-CUUCCCA-G
J04815.1/1592-1523         GUGGUUCU-A-GUUUAGU---GA----AAAACG-U-UUGCU-UUGCAAGCAG-AAA------------------------U---CCUA-AGU-UAA-AU--UCUUA-G-GAACUAC-A
J04815.1/1662-1729         GGCUUUGU-A-GUGUAA----AU----AACAUU-U-UGGAU-UGCAAAUCCU-UAG------------------------A---UGCA-AUU-AGU-UC---AUUG-C-CAAAGCU-U
J04815.1/1812-1884         AGCAGAGU-A-AGCUAAGU--GCU---AAGCUU-U-UGGGC-UCAUACCCCA-AGA------------------------A---UGGAAGGA-UAG-AA--ACCUC-C-CUCUGCU-U
J04815.1/1953-1885         AGAGGUCU-A-GUUAAA----AU----AUAACU-U-UGGGU-UGUCAGGCCA-AAA------------------------U---UGCU-GGU-UAA-AU--UCCAG-C-GGCUUCU-G
J04815.1/1966-2036         AAUAAGAU-G-GCUGAGA---GAA---CAAGCG-G-UGGAU-UGUAAAUCCA-UAC------------------------A---CAAA-GGU-UAA-AU--CCCUU-U-UCUUAUU-A
J04815.1/2041-2109         ACUCUAUG-A-GUACAAC---------AGUACC-U-UUGAC-UUCCAAUCAA-AUA------------------------GC--UCUU-AGC-GAA-AA--UCUAA-G-AUAGAGU-A
J04815.1/3159-3231         AGAGCUUG-C-UCCCAAA---GCU---UGGGUG-U-CUAGC-UGAUAAUUAG-ACU------------------------AU--CAAG-GGU-UAA-AU--UCCCU-UCAAGCUCU-A
J04815.1/7401-7469         UGAGAGUU-A-GUUUAA----GA----AGAACC-C-CUGAU-UUCGGCUCAG-AAG------------------------G---CUUU-GGU-UAA-AG--UCCAA-A-ACUCUUU-A
J04815.1/10228-10159       GGAGAAGU-G-GCAGAU----AGA---AAUGCA-U-GCGGC-UUGAAACCGU-UGG------------------------A---UAGA-GGU-UCA-AU--UCCUC-U-CUUCUCU-U
J04815.1/11997-12064       ACUAAAGU-A-GUUUAUA---------AAAACA-C-CAGCC-UGUGGAACUG-GAG------------------------U---AACU-GGU-UAA-AA--CCCGG-U-CUUAAGU-C
M28270.1/1-73              GCUAAAAU-A-GCAAAGU---GGUU--AAUGCA-G-AAGGC-CUAAGACCUU-CCU------------------------AU--CAAA-GGU-UCA-AC--UCCCU-U-UUUUAGC-U
M37162.1/1211-1282         GCUGAAAU-A-GCAAAGU---GGUU--AAUGCA-A-AAGAC-UUAGGAUUUU-UC-------------------------AU--CGAA-GGU-UCA-AC--UCCUU-C-UUUCAGC-U
M37162.1/1352-1420         AAGAGCUU-A-AGUUAA----AU----AAACUG-A-AAGCC-UUCAAAGCUU-UUU------------------------A---UAAG-AAU-GGA-AA--CUUCU-U-AGCUCUU-G
M37162.1/1557-1488         CAAGACAU-A-GCUAGUU---AG----UAAGUU-C-CUCUU-UUACACGGAG-GUC------------------------A---CACU-CGU-GCA-AU--UCGGG-U-UGUCUUG-A
X55514.2/3696-3624         GUUGAAGU-A-GCAAAGA---GGUA--AAUGCG-A-GAAUC-CUAAGAUUUC-UUU------------------------AU--CAAG-GGU-UCA-AU--UCCCU-U-CUUCAAU-U
X55514.2/3882-3954         AAGAAAUU-A-GUUAAAC---CUA---AUAACA-U-UGGGAUUGUCAGACCA-AAG------------------------U---UACU-GGU-AAUCAA--CCCAG-U-AUUUCUU-A
X55514.2/4047-4119         CCUCGCAG-A-GCUUGUCA--AUCC--UAAGCA-U-CUCUU-UUACACAGAG-AAG------------------------A---AGUU-UGU-GAA-AU--UCGAA-C-UGCCUGG-A
X55514.2/4187-4119         GGUUUUGU-A-GUGUAA----UA----AACAUA-U-UAGAU-UGCAAAUCUA-CAG------------------------A---UGCG-GUU-AUA-AU--UGUCG-C-CAAAACU-U
X55514.2/4257-4189         AGAGAUUU-A-AGUUAA----UA----AAACUG-A-AAACC-UUCAAAGUUU-UAA------------------------A---UAAG-AGU-GGA-AC--UCUCU-U-AGUCUUU-A
X55514.2/4416-4343         GCUUGAGU-A-GCAAAGAG--GGUUU-AAUGCU-U-GAGAU-UUAGGUUCUU-ACA------------------------U---CAAG-GGU-UCA-AU--UCCCU-U-CUCUAGU-U
X16887.1/483-416           CCUUAAAA-C-UACAAA----------AAGCAG-A-CAAUC-UUGUAAAUUG-UAA---------GAU------------A---AAAG-G-U-UUA-AG--U-CCU-U-UUUAAGG-U
X16887.1/553-487           AUUCCUGU-A-GUUGAA----------ACAACA-A-UAACU-UUUCAUGUUA-UAG------------------------G---UUUA-GGU-UGA-AC--CCCUA-A-CAGGAAU-C
M25321.1/113-184           GUGAAUUU-A-GUUUAAUA--GAU---AAAACA-U-UUGCU-UUGCAAGCAA-AAC------------------------U---UGAA-AGU-UUA-AA--UCCUU-C-AAUCCAC-A
M25321.1/478-410           CAGGAGAU-A-GUUUAU----UA----AAAAUA-G-UAGCU-UUGGGAGUUG-UAG------------------------A---UGCA-AGU-UUA-AU--UCUUG-U-UUUCCUG-A
X16888.1/178-111           -CUUUAUU-AGUAUAAU----UA----GUAUA--U-UUGAU-UUCCAAUCAA-AAG------------------------G---GCUU-UGU-UAAGAA--UCAAA-G-AUGGAGU--
X16888.1/255-184           GGCAAGGU-G-GCAGAU----GGUUU-AAUGCG-C-UAAAU-UGUAAAUUUA-UUU------------------------A---UAAA-GGU-UUA-AG--UCCUU-U-CUUUGUC-A
X16888.1/864-793           UGAGUUGU-A-GCCUAAU---GGA---AAGGCG-U-UUGGC-CGUUAACUAA-AAG------------------------AG--AGCA-AGA-UCA-AU--ACUUG-U-CGACUCA-G
X16888.1/869-940           UAGAAAAU-A-GUUUAACC--AGU---AAAACU-A-AGAAA-UUUGAAUUCU-UUA------------------------A---UACA-AGU-GCA-AC--CCUUG-U-UUUUCUA-A
D38115.1/11583-11651       GUAAAUAU-A-GUUUAA----CC----AAAACA-U-UAGAU-UGUGAAUCUA-AUA------------------------A---UAGG-GCC-CCA-CA--ACCCC-U-UAUUUAC-C
K00634.1/531-596           GCAGCAAG-G-GUGGU-----------CUCAAC-C-UGGGU-UCAUUCCCCA-GCU------------------------A---AUAA-AGU-UCG-AU--UCUUU-G-UAGCGGC-U
K01749.1/2878-2958         GAAGUAAU-G-GCUGAGU---GGUU--AAAGCG-G-CAGAC-UGUAAAUCUG-UU--GGU-----AGU---------ACCGU--CGUU-GGU-UCG-AA--UCCAA-C-UUACUUC-A
U50045.1/216-145           UGGGUUGU-A-GCCUAAU---GGA---AAGGCA-A-UUGGC-CGUUAACCAG-GAG------------------------AU--AACA-AGA-UCA-AU--ACUUG-U-CAACUCA-G
X04175.1/1-71              AGGGGAGU-A-GUUCAAC---GGA---AAAACU-U-UAGUC-UUCAAAACUG-AC-------------------------AU--CGUG-GGU-UCG-AC--UCCCG-C-CUCCCUU-G
X15059.1/507-589           GGGAGAGU-G-GCCGAGU---GGUCA-AAAGCG-A-CAGAC-UGUAAAUCUG-UU--GAA-----GUU---U-----UUCUA--CGUA-GGU-UCG-AA--UCCUG-C-CUCUCCC-A
V00675.1/586-656           GCUUUUAA-A-GGAUAAC---AGC---UAUCCC-U-UGGUC-UUAGGAUCCA-AAA------------------------A---UUUU-GGU-GCA-AC--UCCAA-A-UAAAAGU-A
D12694.1/2533-2604         GCUUUUAA-A-GGAAAAG---AGC---CCUCCA-C-UGGUC-UUAGGCGCCA-GCA------------------------UC--UCUU-GGU-GCA-AG--UCCAA-G-UAAAAGC-U
D12694.1/2607-2676         GCCUUGAU-A-GCUUAAA---CU----AAAGCA-C-CGGUC-UUGUAAGCCG-GAG------------------------AC--UGUA-GCC-UAA-CC---CCUA-C-UCAAGGC-U
D12694.1/2745-2677         CAGGAUAU-A-GUUUAG----GU----AGAAUG-C-CGGUU-UUGGGGACCG-GUG------------------------G---UAAA-GGU-UAA-AG--UCCUU-U-UAUCCUG-A
D12695.1/203-134           AGGGCUUU-A-UCUUAAU---UU----AAAGGG-C-CUGAG-UUGCAUUCAG-GAG------------------------A---UGUA-GGU-UAA-UA--UCCUG-C-AAGUCCU-A
D12695.1/368-304           GGCCUUGG-G-GUGUC-----------AACACG-U-GGGGU-UGCAAACCCC-AAG------------------------A---UGCA-GUA-UAA-UA---CCUG-C-CGGGGCU-U
D12695.1/435-369           GGUAAAGU-G-GCCGAG----------CAGGCG-G-CGAAU-UGUAGCUUCG-AAG------------------------A---CAGA-GGU-UUG-AG--UCCCC-U-CUUUACC-A
M57527.1/1-70              ACUCUUAU-A-GCUUAAU---AUU---AAAGUA-U-AGCGC-UGAAAACGCU-AAG------------------------A---UGAA-CCC-UAA-AA---AGUU-C-UAGGGGU-A
V00676.1/23-88             GGUAAAAU-G-GCUGAG----------UAAGCA-U-UAGAC-UGUAAAUCUA-AAG------------------------A---CAGG-GGU-UGA-GC---CCCC-U-UUUUACC-A
V00676.1/400-335           AGAAGUUU-A-GGAUAU----AC----AGUCCA-A-GAGCC-UUCAAAGCCC-UUA------------------------G---AAAA-C-A-AAC-AA----GUU-U-AACUUCU-G
V00677.1/264-332           GAGGAUUU-A-GCUUAA----UU----AAAGCA-G-UUGAU-UUGCAUUUAA-CAG------------------------A---UGUA-AGA-UAU-AG--UCUUA-C-AGUCCUU-A
V00678.1/193-264           UAGAUUGA-A-GCCAGUA---AGU---AGGGUA-U-UUAGC-UGUUAACUAA-AUU------------------------UU--CGUA-GGU-UUG-AA--UCCUU-C-CAAUCUA-G
V01556.1/306-238           GUUUCUAU-A-GUUGAA----UU----ACAACG-A-UGAUU-UUUCAUGUCA-UUA------------------------G---UCAC-AGU-UAA-AU--GCCGU-G-UAGAAAU-A
V01556.1/1456-1523         GUCCCGAU-A-GUAUAA----AA----AUUACU-C-UGGUC-UUGUAAACCA-AAA------------------------A---UGAA-GAG-UCA-GC---UCUU-C-UCGGGAC-A
J01436.1/1456-1522         GUCCCGAU-A-GUAUAA----AA----AUUACU-C-UGGUC-UUGUAAACCA-AAA------------------------A---UGAA-GA--GUC-AG---UCUU-C-UCAGGAC-A
J01435.1/4494-4561         ACUCCCUU-A-GUAUAA----AC----AAUACA-A-CUGAC-UUCCAAUCAG-UUA------------------------A---UUCU-GAA-AAA-AC---UCAG-A-AGAGAGU-A
J01435.1/6776-6846         ACUUUUAU-A-GGAUAGA---AGU---AAUCCA-U-UGGUC-UUAGGAACCA-AAA------------------------A---CCUU-GGU-GCA-AC--UCCAA-A-UAAAAGU-A
K00174.1/1-68              GAGAUAUU-A-GUAAAA----UA----AUUACA-U-AACCU-UGUCAAGGUU-AAG------------------------U---UAUA-GAC-UUA-AA---UCUA-U-AUAUCUU-A
V00680.1/447-380           CACAGUGU-A-GCUUAAUC--AC----AAAGCA-U-CUGGC-CUACACCCAG-AAG------------------------A---AUUC-A-U-AAA-AA----UGA-A-CACUUUG-A
K00434.1/154-84            UAGGAUAG-G-GUGUAUU---GGU---AGCACG-G-AAAAU-UUUGAAUUCU-UAG------------------------G---UGUA-GGU-UCA-AU--UCCUA-U-UGUCCUA-G
X14848.1/1-67              GUUAAUGU-A-GCUUAUA---AU----AAAGCA-A-AGCAC-UGAAAAUGCU-UAG------------------------A---UGGA-U-U-CAA-AA----AUC-C-CAUAAAC-A
X14848.1/2654-2728         AUUAGGGU-G-GCAGAGCC-AAGUA--AUUGCG-U-AAGAC-UUAAAACCUU-GUU------------------------CC--CAGA-GGU-UCA-AA--UCCUC-U-CCCUAAU-A
X14848.1/3684-3752         AGAAAUAU-G-UCUGACA---------AAAGAG-U-UACUU-UGAUAGAGUA-AAU------------------------AA--UAGA-GGU-UUA-AA--UCCUC-U-UAUUUCU-A
X14848.1/3820-3750         UAGGAUAG-G-GUGUAUU---GGU---GGCACG-G-AGAAU-UUUGAAUUCU-UAG------------------------G---UGUA-GGU-UCA-AU--UCCUA-U-UGUCCUA-G
X14848.1/5139-5066         UAGAUUGA-A-GCCAGUA---AGU---AGGGUA-U-UUAGC-UGUUAACUAA-AUU------------------------UU--CGUA-GGAAUUU-GA-UUCCUU-C-CAAUCUA-G
V00695.1/3453-3525         GGGGUUAU-A-GUUAAAUU-UGGU---GAAACG-A-CUGCG-UUGCAUGCAU-UUA------------------------A---UAUG-AGU-UCA-AG--UCUCA-U-UAACUCC-A
X00892.1/1-74              GCUUGUAU-A-GUUUAAUU--GGUU--AAAACA-U-UUGUC-UCAUAAAUAA-AUA------------------------AU--GUAA-GGU-UCA-AU--UCCUU-C-UACAAGU-A
L36887.1/535-616           GCUAUUUU-G-GUGGAAUU--GGUA--GACACG-A-UACUC-UUAAGAUGUA-UU--ACU-----UUA---C-----AGUA---UGAA-GGU-UCA-AG--UCCUU-U-AAAUAGC-A
L36887.1/650-721           UGAGUCGU-A-GACAAUA---GGU---AAGUUA-C-CAAAA-UUUGAGUUUG-GAG------------------------UU--UGUU-UGU-UCG-AA--UCAAA-C-CGAUUCA-A
L36887.1/1748-1820         GCUCUCUU-A-GCUUAAU---GGUU--AAAGCA-U-AAUAC-UUCUAAUAUU-AAU------------------------AU--UCCA-UGU-UCA-AA--UCAUG-G-AGAGAGU-A
L36887.1/3769-3839         AUAUCUUU-A-AUUUAAU---GGU---AAAAUA-U-UAGAA-UACGAAUCUA-AUU------------------------A---UAUA-GGU-UCA-AA--UCCUA-U-AAGAUAU-U
L36887.1/4319-4391         GGGGUUAU-A-GUUAAAUU-UGGU---AGAACG-A-CUGCG-UUGCAUGCAU-UUA------------------------A---UAUG-AGU-UCA-AG--UCUCA-U-UAACUCC-A
L36887.1/4635-4707         GAAACUAU-A-AUUCAAUU--GGUU--AGAAUA-G-UAUUU-UGAUAAGGUA-CAA------------------------A---UAUA-GGU-UCA-AU--CCCUG-U-UAGUUUC-A
L36889.1/130-201           GCUUUUAU-A-GCUUAGU---GGU---AAAGCG-A-UAAAU-UGAAGAUUUA-UUU------------------------A---CAUGUAGU-UCG-AU--UCUCA-U-UAAGGGC-A
L36895.1/3467-3537         AAGGAUAU-A-GUUUAAU---GGU---AAAACA-G-UUGAU-UUCAAAUCAA-UCA------------------------U---UAGG-AGU-UCG-AA--UCUCU-U-UAUCCUU-G
J01478.1/118-188           AGGAGAUU-A-GCUUAAUU--GGU---AUAGCA-U-UCGUU-UUACACACGA-AAG------------------------AU--UAUA-GGU-UCG-A----CCUA-U-AUUUCCU-A
U46121.1/66-138            UGCAAUAU-G-AUGUAAUU--GGUU--AACAUU-U-UAGGG-UCAUGACCUA-AUU------------------------A---UAUA-CGU-UCA-AA--UCGUA-U-UAUUGCU-A
J01470.1/315-386           GACCUUAU-C-GUCUAAU---GGUU--ACGACA-U-CACCU-CUUCAUGUUG-AUA------------------------A---UAUC-GGU-UCG-AU--UCCGA-U-UAAGGUU-A
K02232.1/1-72              GGAUCUGU-A-GCUUAAU---AGU---AAAGUA-C-CAUUU-UGUCAUAAUG-GAG------------------------GA--UGUC-AGU-GCA-AA--UCUGA-U-UAGAUUC-G
K01981.1/82-168            GGAUGGUU-G-ACUGAGU---GGUUU-AAAGUG-U-GAUAU-UUGAGCUAUC-AU--UAG-UCU-UUA---U--UGGCUA----CGUA-GGU-UCA-AA--UCCUA-C-AUCAUCC-G
J01533.1/143-72            GUAAAUAU-A-AUUUAAU---GGU---AAAAUG-U-AUGUUUUUAGGUGCAU-AUU------------------------A---UCUA-AGU-UCA-AA--UCUUA-G-UAUUUAC-A
X04163.1/59-131            GGAGAUGU-U-GUUUUAA---GGU---UAAACU-AUUAGAU-UGCAAAUCUA-CUU------------------------AU--UAAG-AGU-UCG-AU--UCUCU-U-CAUCUCU-U
X04163.1/219-289           GUGAAUAU-A-UUUCAAU---GGU---AGAAAA-U-ACGCU-UGUGGUGCGU-UAA------------------------A---UCUG-AGU-UCG-AU--UCUCA-G-UAUUCAC-C
K00205.1/1-72              AUAGAUAU-A-AGUUAAUU--GGU---AAACUG-G-AUGUC-UUCCAAACAU-UGA------------------------A---UGCG-AGU-UCG-AU--UCUCG-C-UAUCUAU-A
X04561.1/1-72              GAGAAUAU-U-GUUUAAU---GGU---AAAACA-G-UUGUC-UUUUAAGCAA-CCC------------------------A---UGCUUGGU-UCA-AC--UCCAG-C-UAUUCUC-A
K02229.1/1-83              GGAAAAUU-A-ACUAUA----GGU---AAAGUGGA-UUAUU-UGCUAAGUAA-UU--GAA-UU--GUA-------AAUUCU---UAUG-AGU-UCG-AA--UCUCA-U-AUUUUCC-G
X56005.1/1-73              AGUAAUAU-G-AUGUAAUU--GGUU--AACAUA-U-UAGGC-UCAUGACUUA-AUU------------------------A---UAUA-CGU-UCA-AA--UCGUG-U-UAUUGCU-A
X56006.1/1-72              CAGAUAGA-A-GCCAAAA---GGU---CAGGCG-C-UUUCU-UUGGGUGAAA-GAU------------------------CU--AGUU-AGU-UCG-AG--UCUAU-C-CUAUCUG-A
X54421.1/14314-14385       GCAGAUAU-A-AGUCAAUU--GGC---AGACCU-U-CUGAU-UUCCACUUAG-AUU------------------------A---UGUU-CGU-UCG-AA--UCGGA-C-UAUCUGC-A
X54421.1/14394-14476       GCCUAAAU-G-CUGGAAUU-UGGUA--GACAGA-A-CAAAC-UUAAGAUUUG-UC--GCU-----UUC---G-----AGCG---UGUU-GGU-UCG-AG--UCCAA-C-UUUAGGU-A
X54421.1/15747-15819       UGGGUUGU-U-GACUAAUA--GGU---AAGUCC-C-UGAAA-UUUGACUUCA-GUC------------------------UA--UGUA-AGU-UCG-AA--UCUUA-C-CAUCCCA-U
X54552.1/66-137            GUGAUUGU-A-AUUCAAU---GGU---AGAAUG-C-UUAUU-UGUGGCAUAA-GAA------------------------GU--UCUU-GGU-UCG-AU--UCCAA-G-UAAUCAC-C
X54552.1/167-241           ACGAUAGA-A-ACAUGUAU-UGGUU--CAUGUA-C-UUGCU-UUGGGUGUGA-GAG------------------------UU--UGUU-AGU-UCG-AA--UCUAA-C-CUAUCCG-A
X12631.1/1-73              GCAAAGGU-A-GCUUAAC---GGAUU-AAAGCA-C-AGCAC-UGAAAAUGCU-UCA------------------------A---AGGG-AGU-UAA-AG--UCCCU-C-CCUUAGC-A
X12631.1/939-1009          GCCCCUAU-A-GUUGAAA---CA----CAACCA-A-GAGCU-UUUCACGCUC-UUA------------------------AG--UUUG-AGU-UAA-AA--UCUCA-A-UAGGAGC-U
X12631.1/1014-1084         GCCUUGAA-A-GCUCAAC---AACU--AGAGCU-U-UGGUC-UUGUAAACCA-GGA------------------------G---AGAG-GGU-AAA-CU---CCCU-C-UCAAGGC-U
X12631.1/1207-1274         CAGGAGAA-A-GUUUAAU---AA----AAAACC-G-CAGCU-UUGGGAGUUG-CA-------------------------A---UGUA-AG--GUA-AG--CCUUA-U-UCUCUUG-A
X12631.1/1347-1277         UAAGGAUU-A-GUUUAAUU--GGA---AAAACG-A-AGAGC-UUUGACUUCU-UCU------------------------G---CUUG-GGU-CCA-UU--CCCCA-C--UCCUUA-A
X12631.1/1426-1497         GCUGAAGU-A-GCAAAAGU--GGU---UAUGCA-A-AAGAC-UUAGGAUCUU-UUA------------------------A---CGAG-GGU-UCA-AC--UCCUU-C-UUUCAGC-U
X12631.1/1567-1497         GUGGUUUU-A-GUUUAAUU--GA----AAAACG-U-UUGCU-UUGCAAGCAA-AAG------------------------U---UCUA-AGU-UAA-AG--UCUUA-G-AAGCUAC-A
X12631.1/1570-1639         AAGGACUU-A-AGUUAAAU--------AAACUG-A-AAGCC-UUCAAAGCUU-UAA------------------------A---CAAG-AAU-UGG-AAA-CUUCU-U-AGUCCUU-G
X12631.1/1775-1706         CAAGGCAU-A-GCUAGUU---AG----UAAGUU-U-CUCCU-UUACACGGAG-ACC------------------------A---CACU-CGU-GCA-AU--UCGAG-U-UGUUUUG-A
X12631.1/1795-1866         AGUAGAGU-A-AGCUAAGU--GCU---AAGCUU-U-UGGGC-UCAUACCCCA-GGA------------------------A---UGAA-GGA-UAA-AA--ACCUC-C-CUCUACU-U
X12631.1/1937-1868         AGAGGCCU-A-GUUAAA----CUU---AUAACU-U-UGGGU-UGUCAGGCCA-AA-------------------------AU--UGCU-GGU-UAA-AC--UCCAG-C-GGCUUCU-G
X12631.1/1944-2014         AGUAAGGU-G-GCUGAG----GGAA--UAAGCG-G-UGGAU-UGUAAAUCCA-UAU------------------------A---CAAG-GGU-UAG-AC--UCCUU-U-UCUUACU-A
X12631.1/2020-2087         GCUUUAUG-A-AUACAAC---------AGUAUU-U-UUGAC-UUCCAAUCAG-ACA------------------------G---UCUU-GGU-GAA-AA--UUUAA-G-AUAAAGC-A
X12631.1/2088-2158         CUAAAGUA---GCAAAGU---GGUU--AAUGCA-G-AAGGC-CUAAAACUUU-CCU------------------------AU--CAAG-GGU-UCA-AC---UCCU-U-UCUUUAG-C
X12631.1/3132-3200         GAGCUUGC---CCCUAAA---GUU---AAGGUG-U-CUAGC-UGAUAAUUAG-AUU----------------------------UAAG-GGU-UAA-AU--UCCCU-U-CAAGCUC-U
X12631.1/7348-7416         AAAGAGUU-A-GUUUAA----GG----AGAACC-U-CUGAU-UUCGGCUCAG-AUG------------------------G---UUUU-GGU-UCA-AC--CCCAA-A-ACUCUUG-A
X12631.1/8405-8475         CCUUAAUU-A-GCUUAUUUU-------AAAGCU-U-UAGAC-UCUUAAUUUA-AAA------------------------GA--AAUU-AGC-UAA-UA--CCUAU-U-AUUAAGG-A
X12631.1/10184-10115       GGAGAAGU-G-GCACGAUA--GG----AAUGCA-U-GCGGC-UUGAAACCGU-UUG------------------------A---UAGA-GGU-UUC-UU---CCUC-U-CUUCUCU-U
X12631.1/11945-12013       GAUUAAAGUA-GUUUAA----GA----AAAGCA-U-CAGCC-UGUGGAGCUG-AAG------------------------A---CGCC-AGU-AAA-CU---CUGG-C-UUAAAUC-C
M22655.1/587-657           ACUUUUAA-A-GGAUAGU---AGU---UAUCCA-U-UGGUC-UUAGGAGCCA-AAA------------------------A---CAUU-GGU-GCA-AC--UCCAA-A-UAAAAGU-A
X53392.1/97-170            GGGCUUAU-A-GUUUAAUU--GGUU--GAAACG-U-ACCGC-UCAUAACGGU-GAU------------------------AU--UGUA-GGU-UCG-AG--CCCUA-C-UAAGCCU-A
X15379.1/71-144            GGGGAAAU-A-GCUCAGUU--GGUU--AGAGUG-C-UGGUC-UGUCACGCCA-GAA------------------------GU--CGCG-GGU-UCG-AA--CCCCG-U-UUUCCCC-G
X13247.1/151-237           GGAUGGAU-G-UCUGAGC---GGUUG-AAAGAG-U-CGGUC-UUGAAAACCG-AA--GUA-UUG-AUA---G--GAAUAC----CGGG-GGU-UCG-AA--UCCCU-C-UCCAUCC-G
X13246.1/151-233           GGGAGAGU-G-GCCGAGC---GGUCA-AAAGCG-A-CAGAC-UGUAAAUCUG-UU--GAA-----GGU---U-----UUCUA--CGUA-GGU-UCG-AA--UCCUG-C-CUCUCCC-A
M55314.1/21-92             UGGAGUAU-A-GCCAAGU---GGU---AAGGCA-U-CGGUU-UUUGGUAUCG-GCA------------------------UG--CAAA-GGU-UCG-AA--UCCUU-U-UACUCCA-G
X14698.1/250-321           GUCCCUUU-C-GUCCAGA---GGUU--AGGACA-U-CGUCU-UUUCAUGUCG-AAG------------------------A---CACG-GGU-UCG-AU--UCCCG-U-AAGGGAU-A
X02167.1/179-251           GUUAUAUU-A-GCUCAAUU--GGU---AGAGCA-U-UCGUU-UUGUAAUCGA-AAG------------------------GU--UUGG-GGU-UCA-AA--UCCCU-A-AUAUAAC-A
X02167.1/268-340           CUAAAUAU-A-UUUCAAU---GGUUA-GCAAAA-U-ACGCU-UGUGGUGCGU-UAA------------------------A---UCUA-AGU-UCG-AU--UCUUA-G-UAUUUAC-C
X02167.1/345-416           GAUCUUAU-C-GUCUAAU---GGUU--ACGACA-U-CAACU-UUUCAUGUUG-AAA------------------------A---UGUU-GGU-UCA-AU--CCCAA-C-UAAGAUU-A
X02168.1/63-135            UGUAAUAU-G-AUGUAAUU--GGUU--AACAUA-U-UAGGU-UCAUGACCUA-AUU------------------------A---UAUA-CGU-UCA-AA--UCGUA-U-UAUUGCU-A
X02172.1/74-145            GCCUUUAU-A-GCUUAGU---GGU---AAAGCG-A-UAAAC-UGAAGAUUUA-UUU------------------------A---CAUGUAGU-UCG-AU--UCUCA-U-UAAGGGC-A
X02172.1/155-228           GUAGAUAU-A-AUUUAAUC--GGU---AAAAUGUA-UGUUU-UUAGGGUACA-UAU------------------------UA--UCUA-AGU-UCA-AA--UCUUA-G-UAUUUAC-A
X02172.1/247-319           GGAGGUGU-U-GUUUAAA---GGUU--AAGCUA-U-UAGAU-UGCAGAUCUA-CUU------------------------AU--UAAG-AGU-UCG-AU--UCUCU-U-CAUCUCU-U
X02173.1/54-135            GCUAUUUU-G-GUGGAAUU--GGUA--GACACG-A-UACUC-UUAAGAUGUA-UU--ACU-----UUA---U-----AGUA---UGAA-GGU-UCA-AA--UCCUU-C-AAAUAGC-A
X02173.1/152-223           UGAGUCGU-A-GACUAAUA--GGU---AAGUUA-C-CAAAA-UUUGAGUUUG-GAG------------------------U---UGUU-UGU-UCG-AA--UCAAA-C-CGAUUCA-A
X02173.1/256-326           GAGAGUAU-U-GUUUAAA---GGU---AAAACA-G-UUGUC-UUUUAAGCAA-CCC------------------------A---UGCU-GGU-UCG-AA--UCCAG-C-UAUUCUC-A
X02173.1/441-512           AUAGAUAU-A-AGUUAAGU--GGU---AAACUG-A-AUGUC-UUCCACACAU-UGA------------------------U---UGUG-AGU-UCG-AU--UCUCA-C-UAUCUAG-A
X02173.1/522-593           GGAUCCAU-A-GCUUAAU---AGU---AAAGUC-C-UAUUU-UGUCAUAAUA-GAG------------------------GA--UGUC-AGU-GCA-AA--UCUGA-U-UGGAUUC-G
X02173.1/617-699           GGAAAAUU-C-ACCAUA----GGUA---AGGUAAA-UUAUU-UGCUAUGUAA-UU--GAA-U---UUA---UU---AUUCU---UAUG-AGU-UCG-AA--UCUCA-U-AUUUUCC-G
X02173.1/718-802           GGAUGGUU-G-ACUGAGU---GGUUU-AAGGUG-U-GAUAU-UUGAGCUAUC-AU--UAG-UU--UAA---U---AACUA----CGUA-GGU-UCA-AA--UCCUA-C-AUCAUCC-G
X02205.1/368-453           GGAGGGAU-U-UCCAAUGU-UGGUAA-UUGGAG-U-UGAGC-UGUAAACUCA-AU--GAU-----UAU---AU----AUCUU--CAUA-GGU-UCA-AU--UCCUA-U-UCCCUUC-A
X02205.1/471-542           GUCUUUAU-G-GCUUAGU---GGUU--AAAGCA-U-CUCAC-UGUUAAUGAG-AAU------------------------A---CAUA-GGU-UCA-AU--UCCUA-U-UGAAGAC-G
X02205.1/562-633           GGGGUUAU-A-GUUAAAUU--GGU---AGAACA-A-UUGUG-UUGCAUGCAA-UAG------------------------A---UAUG-AGU-UCA-AU--UCUCA-U-UAACUCC-A
X02205.1/668-740           GAAACUAU-A-AUUCAAUU--GGUU--AGAAUA-G-UAUUU-UGAUAAGGUA-CCA------------------------A---UAUA-GGU-UCG-AU--UCCUG-U-UAGUUUC-A
X02205.1/746-816           AAGGAUAU-A-GUUUAAU---GGU---AAAACU-A-UUGAU-UUCAAAUCAA-UCA------------------------U---UAAG-AGU-UCG-AA--UCUUU-U-UAUCCUU-G
X02893.1/57-130            ACUUGUAU-A-GUUUAAAU--GGUU--AAAACA-U-UUGUC-UCAUAAACAA-AUA------------------------AU--GUAA-GGU-UCA-AA--UCCUU-C-UACAAGU-A
M86493.1/1-68              GUUGAUGU-A-GCUUAAA---ACC---AAAGCA-A-GGCGC-UGAAAAUGCC-UAG------------------------A---UGAG-U-A-UAU-GA----ACU-C-CAUAAAC-A
M86493.1/1025-1091         CAAGAUAU-A-GCUUAA----AC----AAAGCA-U-CUAGU-UUACACCUAG-AAG------------------------A---UUUC-ACA-CAC-C----AUGA-A-UAUCUUG-A
V00711.1/3842-3772         UAGGAUAAGG-UGUUUA----GGU---GCACGG-A-GAAAU-UUUGAAUUCU-UAA------------------------G---UGUA-GGU-UCA-AU--UCCUA-U-UGUCCUA-G
L28677.1/8809-8880         ACUCUUAU-C-GUCUAAC---GGUG--AGGACA-A-CGGGU-UUUCACCCCG-UAA------------------------A---UUUG-GGU-UCG-AU--UCCCA-A-UAAGAGU-A
X04815.1/1-81              ACUUAUGU-G-GCGGAACA--GGUA--GACGCG-U-GGGAC-UUAAAAUCUC-AU--UCC-----AUA---------GGAG---UGCC-GGU-UCG-AU--UCCGG-U-CAUAAGU-A
X02437.1/274-344           GGGGGAAU-A-GUUUAAC---GGU---AGAACA-A-CGGUC-UUCAAAAUCG-UUA------------------------G---CGUG-GGU-UCG-AA--UCCUG-C-UUCCCUC-G
M22656.1/459-528           GUAAAUAU-A-GUUUAAAC--------AAAACA-U-UAGAU-UGUGAGUCUA-AUA------------------------A---UAGA-AGC-CCA-AAG-AUUUC-U-UAUUUAC-C
M22656.1/587-656           ACUUUUAA-A-GGAUAGA---AGU---AAUCCA-U-CGGUC-UUAGGAACCG-AAA----------------------------AAUU-GGU-GCA-AC--UCCAA-A-UAAAAGU-A
M10217.1/2136-2204         GCUUACGU-A-GCUUAA----GU----AAAGCA-C-AGCAC-UGAAGAUGCU-GAG------------------------A---UGAGCCCU-ACG-AA--A-GCU-C-CGUAAGC-A
M10217.1/4724-4798         GCUAGCGU-G-GCAGAGCC-UGGCU--AAUGCG-A-AAGAC-CUAAGCUCUU-UUU------------------------AU--CAGG-GGU-UCA-AA--UCCCC-U-CGCUAAC-U
M10217.1/5770-5840         GGAAAUGU-G-CCCGAA----AGU---CAGGGA-U-CACUU-UGAUAGAGUG-AAA------------------------UA--UAUG-GGU-UCA-AA--CCCCA-U-CAUCUCC-U
M10217.1/5909-5841         -AGGAAGU-G-GUAUAGU---GGG---AGUACG-G-AGGGU-UUUGAUCUCU-CAG------------------------G---UGCA-GGU-UCA-AU--UCCUG-U-CUUUCUA--
M10217.1/5910-5978         AGUAAAGU-C-AGCUAA----AA----AAGCUU-U-UGGGC-CCAUACCCCA-AAC------------------------A---UGUU-GGU-UAA-AC--CCCUU-C-CUUUACU-A
M10217.1/7015-7083         AGAGAUUU-A-AGUUAACA--------AGACUA-A-GAGCC-UUCAAAGCCC-UAA------------------------G---CAGG-AGU-UAG-AA--UCUCC-U-AAUCUCU-G
M10217.1/7154-7086         AAGGCUUU-ACGUUAAUU---------AAAGUG-U-UUGAG-UUGCAUUCAA-UUG------------------------A---UGUU-GGA-UAA-AA--UCCUG-C-AAGCCUU-A
M10217.1/7325-7260         AAGCCUGC-G-GUGUUU----------GACAUG-C-CAGAU-UGCAAAUCUC-GAG------------------------A---AGCA-A---ACG-AAGGU-UUG-C-CGGGCUU-C
M10217.1/7394-7325         GGUAAGGU-G-GCCGAGU---AA----UAGGCG-G-CGGAU-UGUAGCUCCG-UGU------------------------A---CAGA-GGU-UCA-AG--UCCUC-U-UCUUAUC-A
M10217.1/9038-9106         GAGAUGUU-A-GUAAAA----CA----AUUAGC-A-CGCCU-UGUCAAGGCG-AAA------------------------U---AGCU-GGU-UAG-AC--UCCGG-C-ACAUCUC-A
M10217.1/9797-9871         CACUAAGA-A-GCUAAAUA--GGGCA-UUAGCG-A-CAGCC-UUUUAAGCUG-UAG------------------------AU--UGGU-GAC-UCC-CA--ACCAC-C-CUUAAUG-A
M10217.1/11492-11561       ACUUUCUU-A-GUAUUA----ACC---AGUACA-C-GUGAC-UUCCAAUCAC-AAA------------------------G---UCUU-AGU-UAG-AA--UCUAA-G-AGAAAGU-A
M10217.1/11905-11973       GAGUUGUU-A-GUCUAAAC--------AAGACA-G-UUGAU-UUCGGCUCAA-CAA------------------------A---UUAU-GGU-UAA-AC--CCCAU-A-AUAACUC-U
M10217.1/13648-13715       GUAGAUAU-A-GUUUAAU---------AAAACA-C-UAGAU-UGUGAUUCUA-GAG------------------------U---CAGA-GGU-UAA-AC--CCCUC-U-UAUCAAC-C
M10217.1/13781-13853       GCUUUUAA-A-GGAAAAC---AGUC--UAUCCG-C-UGGUC-UUAGGAACCA-GAA------------------------AC--UCUU-GGU-GCA-AA--UCCAA-G-UGAAAAG-C
M10217.1/16246-16178       GUUCCUAU-A-GUUGAA----UA----ACAACG-G-UGGUU-UUUCAGAUCA-CAA------------------------G---UUCU-GGU-UAG-AG--UCCUG-G-UGGGAAU-U
M10217.1/17388-17457       GUCCUGAU-A-GCUUAAU---UU----AAAGCA-U-CGGUC-UUGUAAGCCG-AAG------------------------A---UUGA-GGC-UAA-AA--CCCUC-C-UCAAGAC-U
U15659.1/246-176           AAGAAAAU-G-GCAGAGU---GGU---GAUGCA-A-CUGAC-UUGAAAUCAG-AGU------------------------A---UGGG-GGU-UCG-AU--UCCCU-C-UUUUCUC-G
M13046.1/2222-2289         GCUUACGU-A-GCUUAA----GU----AAAGCA-C-AGCAC-UGAAGAUGCU-GAG------------------------A---UGAG-CCC-UAG-AA---AGCU-C-CGAAAGC-A
Y10943.1/948-1016          CAAAGUAU-A-GCUUAACC--------AAAGCC-U-UUCGC-UUACACCGAA-ACA------------------------A---UAUC-UGU-UAA-AC--CCGGA-U-UACUUUG-A
J00642.1/462-533           GCCGUGAU-C-GUAUAGG---GGUU--AGUACU-C-UGCGU-UGUGGCCGCA-GCA------------------------A---CCUC-GGU-UCG-AA--UCCGA-G-UCACGGC-A
M16450.1/142-214           GGCUUUUU-A-GCUCAGCA--GGU---AGAGCA-A-CCGGC-UGUUAACCGG-UUU------------------------GU--CACA-GGU-UCG-AG--CCCUG-U-AAAAGCC-G
M16450.1/308-380           GGAGUGUU-A-GCUCAGCU--GGG---AGAGCU-C-CUGCC-UUACAAGCAG-GCG------------------------GU--CAUA-GGU-UCA-AG--UCCUA-U-ACACUCC-A
X03154.1/110-183           GCGCCCGU-A-GAUCAAUU--GGAU--AGAUCG-C-UUGAC-UACGGAUCAA-AAG------------------------GU--UGGG-GGU-UCG-AG--UCCCU-C-CGGGCGC-A
X03154.1/489-562           GGACCUUU-A-GCUCAGUU--GGUU--AGAGCA-U-CCGGC-UCAUAACCGG-ACG------------------------GU--CAUU-GGU-UCA-AG--UCCAA-U-AAGGUCC-A
X03154.1/608-697           GGAAGAUU-A-CCCAAGUC-CGGCUG-AAGGGA-U-CGGUC-UUGAAAACCG-AGA-GUC-GGG-GAA---A--CCCGAG----CGGG-GGU-UCG-AA--UCCCU-C-AUCUUCC-G
X03154.1/801-875           GGCCCCAU-A-GCGAACGU-UGGUU--AUCGCG-C-CUCCC-UGUCACGGAG-GAG------------------------AU--CACG-GGU-UCG-AG--UCCCG-U-UGGGGUC-G
AJ296990.1/141-209         AGAAAUAU-G-UCUGAUA---------AAAGAA-U-UACUU-UGAUAGAGUA-AAU------------------------UA--UAGA-GGU-UCA-AG--CCCUC-U-UAUUUCU-A
X17113.1/351-433           GCCCAAGU-G-GCGGAAU---GGUA--GACGCA-U-GGGAU-UUAAGAUCCC-AC--GCU-A---GCA---A----UAGCG---UGCC-GGU-UCA-AG--UCCGG-C-UUUGGGC-A
X51423.1/1802-1874         GGGCUUGU-A-GCUCAGCU--GGU---AGAGCG-C-CGCCU-UUGCAAGGCG-GAG------------------------GC--CCUG-GGU-CCG-AA--UCCCA-G-CAAGUCC-A
X69067.1/6022-6086         AUUUAUAU-A-GUAUAUUU--------AAUACA-A-UGCAU-UUUCAAUGCA-UAA------------------------A---UGGA-U----AA-AA--U-AUC-C-UUUAAAU-A
X63088.1/299-371           GGGUGUAU-A-GCUCAGUU--GGU---AGAGCA-U-UGGGC-UUUUAACCUA-AUG------------------------GU--CGCA-GGU-UCA-AG--UCCUG-C-UAUACCC-A
X58913.1/1046-981          GAUUAAGU-G-GCUGAA----GUU---UAGGCG-A-UAGAU-UGUAAAUCUA-UUU------------------------A---UAAG-A---AUU-AU----UCU-U-CUUAAUC-A
X17658.1/140-72            AAGGUCUU-A-GCUUAA----UU----AAAGUA-U-UUGUU-UUGCAUACAG-AAG------------------------A---UGUG-GGG-UAG-UG--UCCUG-C-AGAUCUU-A
X17660.1/1002-1069         GCUAUCGU-A-GCUUAA----UU----AAAGUU-U-AAUAC-UGAAGAUAUU-AGG------------------------A---UGGA-CCC-UAG-AA---AGUC-C-CGAAAGC-A
X17661.1/419-487           AGGUGAUU-A-GUCUAA----GU----AAAAUA-C-UUGAU-UUCGGCUCAA-GAG------------------------U---CUGU-GGU-UAA-AG--UCCAC-A-AUUGCCU-A
X80245.1/11535-11604       AGUUAAUU-A-GCUUAACA--------AAAGCA-A-AUGUU-UUGAAAACAU-AAG------------------------AA--AAGA-AGU-UCA-AU--UCUUC-U-AUUAACU-U
X55026.1/20537-20608       AAGAAAUU-A-GCUCAAC---GGU---AGAGCA-A-CCGUU-UUACACACGG-AAG------------------------GC--UAUG-AGU-UCG-AA--UCUCC-U-AUUUCUU-A
AJ223323.1/613-684         GUCCUUAU-A-GCUUAUC---GGUU--AAAGCA-U-CUCAC-UGUUAAUGAG-AAU------------------------A---GAUG-GGU-UCA-AU--UCCUA-U-UAAGGAC-G
X66594.1/101-182           GGAAAAUU---GAUCAUC---GGCA--AGAUAA-G-UUAUU-UACUAAAUAA-UA--GAA-U---AUU---A----UUUCU---GAGG-AGU-UCG-AA--UCUCC-U-AUUUUCC-G
X66594.1/1984-2065         GCUACUUU-G-GUGGAAUC--GGUA--GACACG-A-CGCAC-UUAAAAUGCG-UU--ACU-U---AU---------AAGUA---UAAA-AGU-UCA-AG--UCUUU-U-AAGUAGC-A
X00083.1/99-171            GGGCCCGU-A-GCUCAGUU--GGG---AGAGCG-C-UGCCC-UUGCAAGGCA-GAG------------------------GC--CGUG-GGU-UCA-AA--UCCCG-C-CGGGUCC-A
X00916.1/823-896           GCCUCGGU-G-GCUCAGCCU-GGU---AGAGCG-C-CUGAC-UUGUAAUCAG-GUG------------------------GU--CGGG-GGU-UCG-AA--UCCCC-C-CCGAGGC-U
X00916.1/933-1007          GGGCCUGU-G-GGGUAGCC-UGGUCC-AUCCUU-U-GGGAU-UUGGGAUCCU-GAG------------------------A---CCCC-AGU-UCA-AA--UCUGG-G-CAGGCCC-A
X00916.1/1018-1091         CCCGCGAU-A-GUUCAGAU-UGGU---AGAACG-G-CGGAC-UGUAGAUCCG-CAU------------------------GU--CGCU-GGU-UCA-AA--UCCGG-C-UCGCGGG-A
X00916.1/1570-1644         GCCCUGGU-G-GUGUAGCU-CGGCCU-AUCAUA-C-AGGAC-UGUCACUCCU-GUG------------------------A---CUCG-GGU-UCA-AA--UCCCG-G-CCAGGGC-G
K00354.1/1-74              CUCCGUGU-A-GCUCAGUU-UGGU---AGAGCG-C-CUGAU-UUGGGAUCAG-GAG------------------------GU--CCAA-GGU-UCA-AA--UCCUU-G-UAUGGAG-A
K00277.1/1-73              GCUGAUUU-A-GCUCAGUA--GGU---AGAGCA-C-CUCAC-UUGUAAUGAG-GAU------------------------GU--CGGC-GGU-UCG-AU--UCCGU-C-AAUCAGC-A
X03016.1/3583-3669         GGAGGCGU-G-GCAGAGU---GGUUU-AAUGCA-C-CGGUC-UUGAAAACCG-GC--AGU-CGCUCC------GGCGACU----CAUA-GGU-UCA-AA--UCCUA-U-CGCCUCC-G
X03016.1/4539-4610         GUCCCGCU-G-GUGUAAU---GGAU--AGCAUA-C-GAUCC-UUCUAAGUUU-GCG------------------------G---UCCU-GGU-UCG-AU--CCCAG-G-GCGGGAU-A
X02710.1/1-73              GCGGGUUU-A-GCUCAGUU--GGG---AGAGCG-U-CAGAC-UGAAGAUCUG-AAG------------------------GU--CGUG-UGU-UCG-AU--CCACA-C-AAACCGC-A
X00360.1/1-73              CCGACCUU-A-GCUCAGUU--GGU---AGAGCG-G-AGGAC-UGUAGAUCCU-UAG------------------------GU--CACU-GGU-UCG-AA--UCCGG-U-AGGUCGG-A
X05226.1/35-116            GGCGCGAU-G-GCAGAGU---GGUCU-AAUGCG-U-GAGAC-UUCAAAUCUC-AU--UUC-UU------------CGGAAG---CGUC-GGU-UCA-AA--UCCGG-C-UCGCGUC-G
X07950.1/1-81              GGAGGGAU-C-CCUUAGU---GGCC--AAAGGA-U-CAGAC-UGUAAAUCUG-AC--GUC-----AUA---------GACUU--CGAA-GGU-UCG-AA--UCCUU-C-UCCCUCC-A
X52969.1/525-607           GCGGAAGU-G-GCGGAAUU--GGUA--GACGCA-C-UAGAU-UUAGGUUCAU-GC--GCC-U---GUA--------AGGUG---UGAG-AGU-UCA-AG--UCUCU-C-CUUCCGC-A
X66438.1/1-72              UGCAUUAU-G-AUGUAAUU--GGU---AACAUA-C-AAGGC-UCAUGUCCUU-UUU------------------------A---UAUA-CGU-UCA-AA--UCGUG-U-UGAUGCA-U
X66437.1/1-83              AUGACUAU-G-GCGGAAUU--GGUA--GACGCG-A-UUAGU-UUAGGUCUAA-UU--UAU-U---UUU--------AAUAA---UAUG-GGU-UCA-AA--UCCCA-U-UAGUCAU-A
X66439.1/1-73              AGAAUUAU-A-GCUUAAUC-UGGU---AAAGCA-G-UCCAC-UCAUAAUGGA-CCU------------------------A---UCAA-AGU-UCA-AU--UCUUU-G-UUAUUCU-A
X12975.1/234-306           GUGGCUAU-A-GCUCAGUU--GGU---AGAGUC-C-CGGAU-UGUGAUUCCG-GUU------------------------GU--CGCG-AGU-UCA-AG--CCUCG-U-UAGCCAC-C
M21542.1/51-134            GUCAGGAU-G-GCCGAGU---GGUCU-AAGGCG-C-CAGAC-UCAAGUUCUG-GU--CUU-C---GAG---A----GAGGG---CGUG-GGU-UCA-AA--UCCCA-C-UUCUGAC-A
M10671.1/1-72              GACCUCGU-G-GCGCAAC---GGU---AGCGCG-U-CUGAC-UCCAGAUCAG-AAG------------------------GC--UGCG-UGU-UCG-AA--UCACG-U-CGGGGUC-A
AJ428514.1/11535-11602     GUAGAUAU-A-GUUUAC----AA----AAAACA-U-UAGAC-UGUGAAUCUA-ACA------------------------A---CAGG-AAA-UCA-AA---UUCC-U-UAUUUAC-C
M22764.1/167-240           GCCGAAAU-A-GCUCAGUU--GGG---AGAGCG-U-UAGAC-UGAAGAUCUA-AAA------------------------GG-UCCCU-GGU-UCG-AU--CCCGG-G-UUUCGGC-A
U18917.1/50408-50336       UUCCUCGU-G-GCCCAAU---GGUC--ACGGCG-U-CUGGC-UACGAACCAG-AAG------------------------AU--UCCA-GGU-UCA-AG--UCCUG-G-CGGGGAA-G
Z49705.1/23030-22957       GGUUUCGU-G-GUCUAGUC--GGUU--AUGGCA-U-CUGCU-UAACACGCAG-AAC------------------------GU--CCCC-AGU-UCG-AU--CCUGG-G-CGAAAUC-A
U33007.1/60769-60697       GCCUUGUU-G-GCGCAAUC--GGU---AGCGCG-U-AUGAC-UCUUAAUCAU-AAG------------------------GU--UAGG-GGU-UCG-AG--CCCCC-U-ACAGGGC-U
U18916.2/60498-60427       GCCAUCUU-A-GUAUAGU---GGUU--AGUACA-C-AUCGU-UGUGGCCGAU-GAA------------------------A---CCCU-GGU-UCG-AU--UCUAG-G-AGAUGGC-A
X61674.1/1095-1008         GGAGAGAU-G-GCUGAGU---GGACU-AAAGCG-G-CGGAU-UGCUAAUCCG-UU--GUA-CAA-UUU---UU-UUGUAC----CGAG-GGU-UCG-AA--UCCCU-C-UCUUUCC-G
U51030.1/22201-22130       UCCGAUGU-A-GUGUAAC---GGCU--AUCACA-U-CACGU-UCUCACCGUG-GAG------------------------A---CCGG-GGU-UCG-AC--UCCCC-G-CUUCGGA-G
AJ011856.1/70824-70908     GGAGGGAU-U-UUCAAUGU-UGGUAG-UUGGAG-U-UGAGC-UGUAAACUCA-AU--GAC-U---UA---------GGUCUU--CAUA-GGU-UCA-AU--UCCUA-U-UCCCUUC-A
K01553.1/1-73              GCGGAUUU-A-GCUCAGUU--GGG---AGAGCG-C-CAGAC-UGAAGAUCUG-GAG------------------------GU--CCUG-UGU-UCG-AU--CCACA-G-AAUUCGC-A
K00287.1/1-73              UCCUUGUU-A-GCUCAGUU--GGU---AGAGCG-U-UCGGC-UUUUAACCGA-AAU------------------------GU--CAGG-GGU-UCG-AG--CCCCC-U-AUGAGGA-G
K00228.1/1-82              GGUUGUUU-G-GCCGAGC---GGUCU-AAGGCG-C-CUGAU-UCAAGCUCAG-GU--AUC-----GUA---A-----GAUG---CAAG-AGU-UCG-AA--UCUCU-U-AGCAACC-A
U22383.1/8197-8124         GGUCUCUU-G-GCCCAGUU--GGUU--AAGGCA-C-CGUGC-UAAUAACGCG-GGG------------------------AU--CAGC-GGU-UCG-AU--CCCGC-U-AGAGACC-A
X56506.1/61-144            GGAGGGUU-G-GCCGAGC---GGUCU-AAGGCG-G-CAGAC-UUAAGAUCUG-UU--GGA-C---GGU---U----GUCCG---CGCG-AGU-UCG-AA--CCUCG-C-AUCCUUC-A
J01373.1/73-144            GGCGCCGU-G-GCGCAGU---GGA---AGCGCG-C-AGGGC-UCAUAACCCU-GAU------------------------GU--CCUC-GGA-UCG-AA--ACCGA-G-CGGCGCU-A
M26928.1/1266-1194         GGGCACAU-G-GCGCAGUU--GGU---AGCGCG-C-UUCCC-UUGCAAGGAA-GAG------------------------GU--CAUC-GGU-UCG-AU--UCCGG-U-UGCGUCC-A
K00368.1/1-82              GGCACUAU-G-GCCGAGU---GGUU--AAGGCG-A-CAGAC-UUGAAAUCUG-UU--GGG-C---UCU--------GCCCG---CGCU-GGU-UCA-AA--UCCUG-C-UGGUGUC-G
K00367.1/1-82              GGCACUAU-G-GCCGAGU---GGUU--AAGGCG-A-GAGAC-UCGAAAUCUC-UU--GGG-C---UCU--------GCCCG---CGCU-GGU-UCA-AA--UCCUG-C-UGGUGUC-G
X55342.1/30-101            GUUCCGUU-G-GCGUAAU---GGU---AACGCG-U-CUCCC-UCCUAAGGAG-AAG------------------------AC--UGCG-GGU-UCG-AG--UCCCG-U-ACGGAAC-G
X51551.1/101-172           GCUCGCGU-G-GCGUAAU---GGC---AACGCG-U-CUGAC-UUCUAAUCAG-AAG------------------------AU--UAUG-GGU-UCG-AC--CCCCA-U-CGUGAGU-G
X69098.1/1-73              GCUCGUGU-A-GCUCAGU---GGUU--AGAGCU-U-CGUGC-UUAUAACGCG-ACC------------------------GU--CGUG-GGU-UCA-AU--CCCCA-C-CUCGAGC-A
M26096.1/1-72              GGGCGUGU-G-GUCUAGU---GGU---AUGAUU-C-UCGCU-UUGGGUGCGA-GAG------------------------GC--CCUG-GGU-UCA-AU--UCCCA-G-CUCGCCC-C
M91385.1/1046-1118         AGGGGUAU-A-GUUCAAUC--GGU---AGAACA-C-CGGAC-UUCAAAUCCG-GGU------------------------GU--UGUG-GGU-UCA-AG--UCCUG-C-UACCCCU-G
M91385.1/1205-1276         AGGGGUGU-A-GUUUAAU---GGU---AGAACA-G-CGGUC-UCCAACACCG-UAC------------------------GU--UGUG-GGU-UCA-AG--UCCUG-U-CACCCCU-G
M91385.1/1291-1381         GGAAGUAU-A-CCCAAGUCUCGGUUG-AAGGGG-G-CGGUC-UCGAAAACCG-UUAGAUG-GA--GUA---A---UCCAUG---CAAG-AGU-UCG-AA--UCUCU-U-UACUUCC-G
M35060.1/1-72              GAAGCGGU-G-GCUCAAU---GGU---AGAGCU-U-UCGAC-UCCAAAUCGA-AGG------------------------GU--UGCA-GGU-UCA-AU--UCCUG-U-CCGUUUC-A
X55339.1/30-104            CUCUCGGU-A-GCCAAGUU--GGUUU-AAGGCG-C-AAGAC-UGUAAAUCUU-GAG------------------------AU--CGGG-CGU-UCG-AC--UCGCC-C-CCGGGAG-A
X66375.1/99-169            GGUCCUAU-A-GUGUAGU---GGUU--AUCACU-U-UCGGU-UCUGAUCCGA-ACA------------------------A---CCCC-AGU-UCG-AA--UCCGG-G-UGGGACC--
Z35950.1/5070-5141         UCCGUGAU-A-GUUUAAU---GGUC--AGAAUG-G-GCGCU-UGUCGCGUGC-CAG------------------------A---UCGG-GGU-UCA-AU--UCCCC-G-UCGCGGA-G
Z36079.1/181-110           GCUCGUAU-G-GCGCAGU---GGU---AGCGCA-G-CAGAU-UGCAAAUCUG-UUG------------------------GU--CCUU-AGU-UCG-AU--CCUGA-G-UGCGAGC-U
Z74072.1/3173-3245         GGGCGUGU-G-GCGUAGUC--GGU---AGCGCG-C-UCCCU-UAGCAUGGGA-GAG------------------------GU--CUCC-GGU-UCG-AU--UCCGG-A-CUCGUCC-A
Z74387.1/1846-1765         GGCAACUU-G-GCCGAGU---GGUU--AAGGCG-A-AAGAU-UAGAAAUCUU-UU--GGG-C---UUU--------GCCCG---CGCA-GGU-UCG-AG--UCCUG-C-AGUUGUC-G
Z28209.1/4569-4498         GCCCUUUU-G-GCCAAGU---GGU---AAGGCA-U-CGCAC-UCGUAAUGCG-GGG------------------------AU--CGUG-GGU-UCA-AU--UCCCA-C-AGAGGGC-A
Z73326.1/1146-1075         GGUCCUAU-A-GUGUAGU---GGUU--AUCACU-U-UCGGU-UUUGAUCCGG-ACA------------------------A---CCCC-GGU-UCG-AA--UCCGG-G-UAGGACC-U
Z71311.1/286-214           GCUUCUAU-G-GCCAAGUU--GGU---AAGGCG-C-CACAC-UAGUAAUGUG-GAG------------------------AU--CAUC-GGU-UCA-AA--UCCGA-U-UGGAAGC-A
Z71616.1/3983-4056         GACUCCAU-G-GCCAAGUU--GGUU--AAGGCG-U-GCGAC-UGUUAAUCGC-AAG------------------------AU--CGUG-AGU-UCA-AC--CCUCA-C-UGGGGUC-G
Z74797.1/2502-2432         GCGCAAGU-G-GUUUAGU---GGU---AAAAUC-C-AACGU-UGCCAUCGUU-GGG------------------------C---CCCC-GGU-UCG-AU--UCCGG-G-CUUGCGC-A
X81069.1/365-436           UCCGAUAU-A-GUGUAAC---GGCU--AUCACA-U-CACGC-UUUCACCGUG-GAG------------------------A---CCGG-GGU-UCG-AC--UCCCC-G-UAUCGGA-G
X65556.1/351-423           GCGGACGU-A-GCUCAGUU--GGU---AGAGCG-C-AACCU-UGCCAAGGUU-GAG------------------------GU--CGCG-AGU-UCG-AG--CCUCG-U-CGUCCGC-U
X52070.1/699-771           UCCUCGGU-A-GCUCAAUU--GGC---AGAGCA-G-CCGGC-UGUUAACCGG-CAG------------------------GU--UACU-GGU-UCG-AG--UCCAG-U-CCGGGGA-G
X52070.1/777-849           UCCUCCGU-A-GCUCAAUU--GGC---AGAGCA-G-CCGGC-UGUUAACCGG-CAG------------------------GU--UACU-GGU-UCG-AG--UCCAG-U-CGGGGGA-G
X03715.1/171-243           GGCACUAU-A-GCCAAGGU--GGCU--AAGGCA-U-GGGAC-UGCAACUCCC-CGA------------------------U---CGUC-GGU-UCG-AA--UCCGA-C-UAGUGCC-U
X03715.1/288-361           GCGCCCAU-A-GAUCAAUU--GGAU--AGAUCG-U-UUGAC-UACGGAUCAA-AAG------------------------GU--UGAG-GGU-UCG-AU--UCCUU-C-UGGGCGC-G
X03715.1/388-461           CGGAAAGU-A-GCUUAGCU-UGGU---AGAGCA-C-UCGGU-UUGGGACCGA-GGG------------------------GU--CGCA-GGU-UCG-AA--UCCUG-U-CUUUCCG-A
X03715.1/481-553           GGGCCCGU-A-GCUCAGCU--GGG---AGAGCA-C-CUGCC-UUGCACGCAG-GGG------------------------GU--CGAC-GGU-UCG-AU--CCCGU-U-CGGGUCC-A
X03715.1/589-662           GGCGGGAU-A-GCUCAGCU--GGUU--AGAGCG-C-UCGGC-UCAUACCCGG-GAG------------------------GU--CAAG-AGU-UCA-AG--UCUCU-U-UCUCGCU-A
X03715.1/667-740           GGACCCUU-A-GCUCAGUU--GGUU--AGAGCA-U-CCGGC-UCAUAACCGG-AUG------------------------GU--CACU-GGU-UCA-AG--UCCAG-U-AGGGUCC-A
X03715.1/779-868           GGAAGAUU-A-CCCAAGUC-UGGUUG-AAGGGA-U-CGGUC-UUGAAAAUUG-ACA-GGC-GGU-GAA---A--GCCGCG----CGGG-GGU-UCG-AA--UCCCU-C-AUCUUCC-G
X03715.1/926-998           CGUGGGGU-G-GAGCAGUU--GGU---AGCUCG-U-UGGGC-UCAUAACCCA-AAG------------------------GU--CGCA-GGU-UCA-AG--UCCUG-C-CCCCGCA-A
X03715.1/1004-1077         GGUCUUGU-A-GUGAAGUU--GGUU--AUCAUG-C-CUCUC-UGUCACAGAG-GAG------------------------AU--CGCG-GGU-UCA-AG--UCCCG-U-CAAGACC-G
X03715.1/1086-1158         GGUUCAGU-A-GCUCAGUU--GGU---AGAGCA-U-UUGAU-UGAAGCUCAA-AGU------------------------GU--CGGC-AGU-UCA-AU--UCUGU-C-CUGAACC-A
AJ400848.1/26718-26788     GGCGGCAU-G-GCCGAGU---GGU---AAGGCG-G-AGGAC-UGCAAAUCCU-UGU------------------------U---CCCC-AGU-UCA-AA--UCCGG-G-UGUCGCC-U
AJ400848.1/29803-29731     GCCCCCAU-C-GUCUAGC---GGUUC-AGGACA-U-CUCUC-UUUCAAGGAG-ACA------------------------A---CGGG-GAU-UCG-AC--UUCCC-C-UGGGGGU-A
AJ400848.1/34280-34188     GGAGAGAU-G-GCUGAGU---GGUUG-AUAGCU-C-CGGUC-UUGAAAACCG-GC--AUA-GUUCUUUAUUCAGAACUAU----CGAG-GGU-UCG-AA--UCCCU-C-UCUCUCC-U
AJ400848.1/44024-44110     GGAGAGAU-G-GCCGAGU---GGUUG-AAGGUG-U-AGCAU-UGGAACUGCU-AU--GUA-GGC-UUU---U--GUUUAC----CGAG-GGU-UCG-AA--UCCCU-C-UCUUUCC-G
AJ400848.1/50859-50931     ACCUACUU-A-ACUCAGC---GGUU--AGAGUA-U-UGCUU-UCAUACGGCG-GGA------------------------GU--CAUU-GGU-UCA-AA--UCCAA-U-AGUAGGU-A
K00344.1/1-73              GUCGCAAU-G-GUGUAGUU--GGG---AGCAUG-A-CAGAC-UGAAGAUCUG-UUG------------------------GU--CAUC-GGU-UCG-AU--CCCGG-U-UUGUGAC-A
K00570.1/851-921           UCUCCUUU-A-GUAUAGG---GGU---AGUACA-C-AAGCC-UGUCACGCUU-GCA------------------------G---CCCG-GGU-UCG-AA--UCCCG-G-AGGGAGA-G
X00239.1/111-183           GGUCUCGU-G-GCCCAAU---GGUU--AAGGCG-C-UUGAC-UACGAAUCAA-GAG------------------------AU--UCCA-GGU-UCG-AC--UCUUG-G-CGGGAUC-G
K00369.1/1-82              GUCACUAU-G-UCCGAGU---GGUU--AAGGAG-U-UAGAC-UUCAAAUCUA-AU--GGG-C---UUU--------GCCCG---CGCA-GGU-UCA-AA--UCCUG-C-UGGUGAC-G
M57698.1/294-367           GGUCGCAU-G-AUGUAGUC--GGUU--AUCAUG-U-CGAUC-UAAUAAGUCG-AAU------------------------GU--CGCC-GGU-UCG-AA--CCCGG-C-UGUGACC-A
K03079.1/135-206           UGCGCGGU-A-GGAGAGU---GGA---ACUCCG-A-CGGGC-UCAUAACCCG-UAG------------------------GU--CCCA-GGA-UCG-AA--ACCUG-G-CCGCGCA-A
M32254.1/51-124            CGCGGGGU-G-GAGCAGCU-CGGU---AGCUCG-C-UGGGC-UCAUAACUCA-GAG------------------------GU--CGCA-GGU-UCA-AA--UCCUG-U-CCCCGCU-A
X53649.1/160-231           UGGGCUAU-G-GUGUAAUU--GGC---AGCACG-A-CUGAU-UCUGGUUCAG-UUA------------------------G---UCUA-GGU-UCG-AG--UCCUG-G-UAGCCCA-G
X53649.1/604-676           GCCCCCGU-U-GUGUAGC---GGCCU-AGCACG-C-CGCCC-UCUCAAGGCG-GUA------------------------G---CGCC-GGU-UCG-AA--UCCGG-U-CGGGGGU-A
X53649.1/495-566           UGGGCUAU-G-GUGUAAUU--GGC---AGCACG-A-GUGAU-UCUGGUUCAU-UUA------------------------G---UCUA-GGU-UCG-AG--UCCUG-G-UAGCCCA-G
X06054.1/711-637           GGGCCCGU-C-GUCUAGCC-UGGUU--AGGACG-C-UGCCC-UGACGCGGCA-GAA------------------------AU--CCUG-GGU-UCA-AG--UCCCA-G-CGGGCCC-A
AJ243756.1/1-71            GGCUAGGU-A-ACAUAAU---GGA---AAUGUA-U-CGGAC-UGCAAAUCCU-GGA------------------------A---UGAC-GGU-UCG-AC--CCCGU-C-CUUGGCC-U
K02003.1/1-74              GGGGUGGU-G-GCGCAGUU--GGCU--AGCGCG-U-AGGUC-UCAUAAUCCU-GAG------------------------GU--CGAG-AGU-UCG-AG--CCUCU-C-UCACCCC-A
X68198.1/9818-9745         AGCGGGGU-G-GGGUAGUC-AGGA---AAUCCG-A-UGGGC-UCAUAACCCG-UAG------------------------AU--CGAU-GGU-UCA-AA--UCCAU-C-CCCCGCU-A
X57045.1/288-359           UCCUCCCU-G-GCGCAGUC--GGC---AGCGCG-U-UAGGC-UGUUAACCAU-CAG------------------------G---UGUU-GGU-UCG-AA--UCCAA-C-GGGAGGA-G
X57045.1/503-432           GGGCGUGU-A-GCUCAGU---GGU---AGAGCG-C-CCUGU-UUUGCAUACG-GAG------------------------GC--CUAG-GGU-UCA-AA--CCCCU-A-CUCGUCC-A
X57045.1/606-678           GCUCCAGU-G-GCCUAAU---GGAU--AUGGCU-U-UGGAC-UUCUAAUCCA-AAG------------------------GU--UGCG-GGU-UCG-AG--UCCCG-U-CUGGAGU-A
X57046.1/121-203           CCUUCUGU-A-GCUCAAUU--GGU---AGAGCA-U-GUGAC-UGUAGAGUAU-GC--GGG-UAUCACA---GGGU---------CGCU-GGU-UCG-AU--UCCGG-C-CGGAAGG--
X57046.1/341-271           GGCCGCUU-A-GCACAU----GGC---AGUGCA-C-CACUC-UCGUAAAGUG-GGG------------------------GU--CGCG-AGU-UCG-AU--UCUCG-C-AGUGGCC-U
Z11884.1/254-326           UCCUCCCU-G-GCGCAGUC--GGC---AGCGCG-U-UAGGC-UGUUAACCUA-CAG------------------------GU--CGUU-GGU-UCG-AA--UCCAA-C-GGGAGGA-G
Z11880.1/124-195           GCCUUCCU-A-GCUCAGU---GGU---AGAGCG-C-ACGGC-UUUUAACCGU-GUG------------------------GU--CGUG-GGU-UCG-AU--CCCCA-C-GGAAGGC-G
Z11880.1/281-353           GCCCCCGU-A-GCCCAAU---GGAU--AAGGCG-U-UCGCU-UCCUAAGCGA-AAG------------------------AU--UGCG-GGU-UCG-AG--UCCCG-C-CGGAGGU-A
U18089.1/221-293           GGGGCUGU-A-GCUCAGUU--GGG---AGAGCA-C-CUGCU-UUGCAAGCAG-GGG------------------------GU--CAUC-GGU-UCG-AG--ACCGG-U-CAGCUCC-A
X07395.1/103-176           GGGCCUAU-A-GCUCAGCU--GGCU--AGAGCA-C-ACGCC-UGAUAAGCGU-GAG------------------------GU--CAGU-GGU-UCG-AG--UCCAC-U-UGGGCCC-A
X14835.1/6927-7002         GCCGGGGU-C-GCCUAGCC-UGGUCA-AGGGCG-C-CGGAC-UCAUAAUCCG-GUC------------------------UU--CCCG-GGU-UCG-AA--UCCCG-G-CCCCGGC-A
X16643.1/820-900           GACAAUUU-G-UCCGAGU---GGUU--AAGGAG-G-AAGAC-UAGAAAUCUU-UU--GGG-U---UU---------ACCCG---CGCA-GGU-UCG-AA--UCCUG-C-AGUUGUC-G
X16643.1/1078-1151         GCUCGAUU-A-GCUCAGCU--GGUU--AGAGCA-U-GCGGC-UGUUAACCGC-AAG------------------------GU--CGUA-GGU-UCG-AU--CCCUA-C-AUCGAGC-G
D17540.1/1-73              GCGGGAGU-A-GCUCAGUU--GGU---AGAGCA-U-CGGCU-UCCCAAGCCG-AGG------------------------GU--CGCG-GGU-UCG-AG--UCCCG-U-CUCCCGC-U
X51824.1/190-272           GGGCAGGU-G-CCCGAGC---GGCCA-AAGGGG-A-CGGUC-UGUAAAACCG-UU--GGC-----GUA---U-----GCCUU--CGCU-GGU-UCG-AA--UCCAG-C-CCUGCCC-A
X51824.1/381-453           GCUCGCGU-A-GCUCAGCA--GGU---AGAGCA-C-ACCCU-UGGUAAGGGU-GAG------------------------GU--CGCC-GGU-UCG-AG--CCCGG-C-CGCGAGC-U
X05071.1/204-288           GCGGGGGU-G-CCCGAGCCA-GGUCA-AAGGGG-C-AGGGC-UCAAGACCCU-GU--GGC-----GUA---G-----GCCUG--CGUG-GGU-UCG-AA--UCCCA-C-CCCCCGC-A
M11464.1/1-72              GGUUCCAU-A-GUAUAGU---GGUU--AGUACU-G-GGGAC-UUUAAAUCCC-UUG------------------------A---CCUG-GGU-UCG-AA--UCCCA-G-UGGGACC-U
Y14522.1/1-81              GAGGUGGU-G-GCUGAAU---GGUU--AAAGCG-G-UAGAC-UGUAAAUCUA-UU--GGG-----AUU---------CCCGU--CGCC-GGU-UCG-AU--UCCGG-U-CCACCUC-A
X66443.1/1-72              CAGAUAAA-A-GCCAACC---GGUG---AGGCG-C-UUUCU-UUGGGAGAAA-GAG------------------------UU--AGUU-AGU-UCG-AU--UCUAG-C-UUAUCUG-A
Y00430.1/2429-2358         GGGGGUGU-A-GCUCAGU---GGU---AGAGCG-C-AUGCU-UUGCAUGUAU-GAG------------------------GU--CUUG-GGU-UCA-AU--CCCCA-G-CAUCUCC-A
X04821.1/1-73              GUUUCUGU-A-GUGUAGC---GGUU--AUCACG-U-UCGCC-UCACAUGCGA-AAG------------------------GU--CCCC-GGU-UCG-AA--ACCGG-G-CAGAAAC-A
X86563.2/48153-48081       GCCCACUU-A-GCUCAGA---GGUU--AGAGCA-U-CGCAU-UUGUAAUGCG-AGG------------------------GU--CAUC-GGU-UCA-AA--UCCGA-U-AGUCGGC-U
X86563.2/119998-119925     GGGCCUGU-A-GCUCAGA---GGAUU-AGAGCA-C-GUGGC-UACGAACCAC-GGU------------------------GU--CGGG-GGU-UCG-AA--UCCCU-C-CUCGCCC-A
X13704.1/1807-1880         AGGGAUGU-A-GCGCAGCU-UGGU---AGCGCG-U-UUGUU-UUGGGUACAA-AAU------------------------GU--AACG-GGU-UCA-AA--UCCAG-U-CAUCCCU-A
X52797.1/114-203           GGUGAGGU-G-GCCGAGA---GGCUG-AAGGCG-C-UCCCC-UGCUAAGGGA-GU--AUG-CGGUCAA---AAGCUGCAU----CCGG-GGU-UCG-AA--UCCCC-G-CCUCACC-G
CP000660.1/1877584-1877500 GCGGGGGU-G-CCCGAGCCA-GGUCA-AAGGGG-C-AGGGU-UCAGGUCCCU-GU--GGC-----GUA---G-----GCCUG--CGUG-GGU-UCA-AA--UCCCA-C-CCCCCGC-A
EF108342.1/4950-5016       AGAAGUUU-A-GGAUAUA---CU----AGUCCG-C-GAGCC-UUCAAAGCUC-UAA------------------------G---AAAA-C-A-CAC-AA----GUU-U-AACUUCU-G
D26185.1/159248-159330     GCGGGUGU-G-GCGGAAUU--GGCA--GACGCG-C-UAGAC-UUAGGAUCUA-GU--GUC-----UUU---AU----GACG---UGGG-GGU-UCA-AG--UCCCU-U-CACCCGC-A
K01667.1/50-136            GGAGAGAU-G-CCGGAGC---GGCUG-AACGGA-C-CGGUC-UCGAAAACCG-GA--GUA-GGG-GCA---A--CUCUAC----CGGG-GGU-UCA-AA--UCCCC-C-UCUCUCC-G
EU349704.1/1154-1217       CAUUGCGA-A-GCUU------------AGAGCG-U-UAACC-UUUUAAGUUA-AAG------------------------UU--AGAG-A-U-CAC-AA--A-UCU-C-CACAAUG-A
CP001399.1/1433538-1433611 GCCGCCGU-A-GCUCAGCC-CGGG---AGAGCG-C-CCGGC-UGAAGACCGG-GUU------------------------GU--CCGG-GGU-UCA-AG--UCCCC-G-CGGCGGC-A
X02434.1/248-321           CGGUGAUU-G-GCGCAGCC-UGGU---AGCGCA-C-UUCGU-UCGGGACGAA-GGG------------------------GU--CGGA-GGU-UCG-AA--UCCUC-U-AUCACCG-A
X00547.1/128-212           GGAAGUGU-G-GCCGAGC---GGUUG-AAGGCA-C-CGGUC-UUGAAAACCG-GC--GAC-CC--GAA---A---GGGUU----CCAG-AGU-UCG-AA--UCUCU-G-CGCUUCC-G
K01986.1/320-392           GCUUCCAU-A-GCUCAGCA--GGU---AGAGCA-C-UUCCA-UGGUAAGGAA-GAG------------------------GU--CAGC-GGU-UCG-AG--CCCGC-U-UGGAAGC-U
M29107.1/8-80              GCCGACUU-A-GCUCAGUA--GGU---AGAGCA-A-CUGAC-UUGUAAUCAG-UAG------------------------GU--CACC-AGU-UCG-AU--UCCGG-U-AGUCGGC-A
AJ391519.1/189-125         ACUAUUUU-G-GCAGAUU---------AGUGCA-A-UAAAU-UUAGAAUUUA-UGG------------------------A---UGUA-AU--UUU-U----AUUA-C-AAAUAGU-A
M17116.1/122-205           GCCCAGAU-G-GCGGAAUU--GGUA--GACGCG-C-CAGCU-UCAGGUGCUG-GU--ACU-C---GAA---A----GGGUG---UGGA-GGU-UCG-AG--UCCUC-U-UCUGGGC-A
FJ479743.1/1541-1606       UCUAAUAU-G-GCAGAUU---------AGUGCA-A-UGGAU-UUAAGCUCCA-UAU------------------------A---UAAA-GU--AUU-UU---ACUU-U-UAUUAGA-A
DQ023210.1/1-73            GCCGAUAU-A-GCUCAGUU--GGU---AGAGCA-G-CGCAU-UCGUAAUGCG-AAG------------------------GU--CGUA-GGU-UCG-AC--UCCUA-U-UAUCGGC-A
EU273712.1/9790-9857       UGGUAAUU-A-GUUUAA----GU----AAAAUU-A-AUGAU-UUCGACUCAU-UAG------------------------A---UUAU-GAU-AAU-AG---UCAU-A-AUUACCA-A
K00763.1/69-142            AGGCUUGU-A-GCUCAGGU--GGUU--AGAGCG-C-ACCCC-UGAUAAGGGU-GAG------------------------GU--CGGU-GGU-UCA-AG--UCCAC-U-CAGGCCU-A
EU623091.1/86-157          GUCCCCUU-C-GUCUAGA---GGCCC-AG-ACA-C-CGCCC-UUUCACGGCG-GUA------------------------A---CAGG-GGU-UCG-AA--UCCCC-U-AGGGGAC-G
CP001399.1/1388329-1388256 GGGCCCGU-A-GCUUAGCUC-GGU---AGAGCG-C-UCGGC-UCAUAACCGA-GUG------------------------GU--CAGG-GGU-UCA-AA--UCCCC-U-CGGGCCC-A
AAEU02004214.1/433-498     AUUCAAAU-A-GCUUAUA---UUU---AGAGUA-U-GACAC-UGAAGAUGUC-AUG------------------------G---AGAU-U---AAU-U-----AAU-C-UUUGAAU-A
X00066.1/307-380           GCGCCCGU-A-GCUCAGCU--GGAU--AGAGCG-C-UGCCC-UCCGGAGGCA-GAG------------------------GU--CUCA-GGU-UCG-AA--UCCUG-U-CGGGCGU-A
J01713.1/270-351           GCGGGAGU-G-GCGAAAUU--GGUA--GACGCA-C-CAGAU-UUAGGUUCUG-GC--GCC-----GCA---A-----GGUG---UGCG-AGU-UCA-AG--UCUCG-C-CUCCCGC-A
X52800.1/82-154            GGCCCCUU-A-GCUCAGU---GGUU--AGAGCA-G-GCGAC-UCAUAAUCGC-UUG------------------------GU--CGCU-GGU-UCA-AG--UCCAG-C-AGGGGCC-A
K00282.1/1-73              GGGUCGUU-A-GCUCAGUU--GGU---AGAGCA-G-UUGAC-UUUUAAUCAA-UUG------------------------GU--CGCA-GGU-UCG-AA--UCCUG-C-ACGACCC-A
X93579.1/201-272           UCCUCAGU-A-GCUCAGU---GGU---AGAGCG-G-UCGGC-UGUUAACCGA-UUG------------------------GU--CGUA-GGU-UCG-AA--UCCUA-C-UUGGGGA-G
CP000660.1/704452-704523   GGGCCGGU-A-GUCUAGC---GGA---AGGAUG-C-CCGCC-UCGCGCGCGG-GAG------------------------AU--CCCG-GGU-UCG-AA--UCCCG-G-CCGGUCC-A
X63776.1/648-721           CGGCACGU-A-GCGCAGCC-UGGU---AGCGCA-C-CGUCA-UGGGGUGUCG-GGG------------------------GU--CGGA-GGU-UCA-AA--UCCUC-U-CGUGCCG-A
DQ927305.1/46859-46925     GCUGCUUG-A-AUGGU-----------UUCAGU-G-UGGGC-UCAUUUCCCA-UUA------------------------CU--CAAA-AGU-UCG-AU--UCUUU-U-AAGCGGC-C
K01561.1/1-74              GCGUUCAU-A-GCUCAGUU--GGUU--AGAGCA-C-CACCU-UGACAUGGUG-GGG------------------------GU--CGUU-GGU-UCG-AG--UCCAA-U-UGAACGC-A
X17321.1/66-138            GGGUGAUU-A-GCUCAGCU--GGG---AGAGCA-C-CUCCC-UUACAAGGAG-GGG------------------------GU--CGGC-GGU-UCG-AU--CCCGU-C-AUCACCC-A
AY632242.1/10-80           CAUUAGAU-G-ACUGAA----AG----CAAGUA-C-UGGUC-UCUUAAACCA-UUU------------------------UA--UAGU-AAA-UUA-GC-AUUUAC-U-UCUAAUG-A
J01404.1/5140-5204         AUCUAUAU-A-GUAUAAA---------AGUAUA-U-UUGAC-UUCCAAUCAU-AAG------------------------G---UCUA-UU--AAU-U----AAUA-G-UAUAGAU-A
EU273712.1/5242-5176       AGCCUUAA-A-GUGUUU----------AUCAUG-U-CGAAU-UGCAAAUUCG-AAG------------------------G---UGUA-GAG-AAU-C-C-CUCUA-C-UAAGGCU-U
EU255777.1/1590-1519       UGGGGCGU-G-GCCAAGU---GGU---AAGGCA-A-CGGGU-UUUGGUCCCG-CUA------------------------UU--CGGA-GGU-UCG-AA--UCCUU-C-CGUCCCA-G
X13994.1/40-129            GAAGAUCG-U-CGUCUCC---GGUG--AGGCGG-C-UGGAC-UUCAAAUCCA-GU--UGG-GGCCGCCA--GCGGUCCCG----GGCA-GGU-UCG-AC--UCCUG-U-GAUCUUCC-
M21681.1/156-228           CGCGGGGU-G-GAGCAGCC-UGGU---AGCUCG-U-CGG-C-UCAUAACCCG-AAG------------------------GU--CGUC-GGU-UCA-AA--UCCGG-C-CCCCGCA-A
K00197.1/1-71              GCGGGCGU-A-GUUCAAU---GGU---AGAACG-A-GAGCU-UCCCAAGCUC-UAU------------------------A---CGAG-GGU-UCG-AU--UCCCU-U-CGCCCGC-U
X51770.1/245-317           GGCCGCGU-G-GCGCAAU---GGAU--AACGCG-U-CUGCC-UACGGAGCAG-AAG------------------------AU--UGCA-GGU-UCG-AA--UCCUG-C-CGUGGUC-G
K01856.1/1-82              GGAGAGAU-G-GCCGAGC---GGUCU-AAGGCG-C-UGGUU-UAAGGCACCA-GU--CCC-----UUC---G-----GGGG---CGUG-GGU-UCG-AA--UCCCA-C-UCUCUUC-A
Z83129.1/22044-21973       UCCUCGGU-A-GUAUAGU---GGUG--AGUAUC-C-GCGUC-UGUCACAUGC-GAG------------------------A---CCCG-GGU-UCA-AU--UCCCG-G-CCGGGGA-G
M25476.1/51-122            AGCAGCGU-G-GCGCAGU---GGA---AGCGUG-C-UGGGC-CCAUAACCCA-GAG------------------------GU--CGGU-GGA-UCG-AA--ACCAC-U-CGCUGCU-A
X54124.1/910-981           GACUGCUU-G-GCGCAAU---GGU---AGCGCG-U-UCGAC-UCCAGAUCGA-AAG------------------------GU--UGGG-CGU-UCG-AU--CCGCU-C-AGUGGUC-A
K01390.1/442-514           GAGCCAUU-A-GCUCAGUU--GGU---AGAGCA-U-CUGAC-UUUUAAUCAG-AGG------------------------GU--CGAA-GGU-UCG-AG--UCCUU-C-AUGGCUC-A
#=GC SS_cons               (((((((,.,.<<<<___...___..._>>>>,.<.<<<<_.______>>>>.>,,........................,...,<<<.<<_.___.__.._>>>>.>.))))))).:
#=GC RF                    GgagauaU.A.GCucAgU...GGU...AgaGCg.u.cgGaC.UuaaAAuCcg.aag........................g...cgcg.GGU.UCg.Aa..UCCcg.c.uaucucC.a
//
# STOCKHOLM 1.0

#=GF AC   RF00006
#=GF ID   Vault
#=GF DE   Vault RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19491402
#=GF SS   Published; PMID:19491402
#=GF GA   34.00
#=GF TC   34.10
#=GF NC   33.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://vaults.arc.ucla.edu/sci/sci_home.htm;
#=GF DR   SO; 0000404; vault_RNA;
#=GF RN   [1]
#=GF RM   19491402
#=GF RT   Evolution of Vault RNAs.
#=GF RA   Stadler PF, Chen JJ, Hackermueller J, Hoffmann S, Horn F, Khaitovich P,
#=GF RA   Kretzschmar AK, Mosig A, Prohaska SJ, Qi X, Schutt K, Ullmann K
#=GF RL   Mol Biol Evol. 2009;27:1-17.
#=GF CC   This family of RNAs are found as part of the enigmatic vault
#=GF CC   ribonucleoprotein complex. The complex consists of a major vault protein
#=GF CC   (MVP), two minor vault proteins (VPARP and TEP1), and several small
#=GF CC   untranslated RNA molecules. It has been suggested that the vault complex
#=GF CC   is involved in drug resistance. We have identified a putative novel vault
#=GF CC   RNA on chromosome 5 EMBL:AC005219.
#=GF WK   Vault_RNA
#=GF SQ   73


AF045145.1/1-88              -GGCUGGC-UUUAGCUC-AGCGGUUACUUCGCGUGUCAUCAAACCACCUCUCU-------------------------------------------------------GGGUUGUUCGAGAC-----------------CCGCGGGCGCUCUCCAGCCCUCUU
AADA01028285.1/4499-4587     GGGCUGGC-UUUAGCUC-AGCGGUUACUUCGCGUGUCAUCAAACCACCUCUCU-------------------------------------------------------GGGUGGUUCGAGAC-----------------CCGUGGGCGCUCUCCAUCUCUCUU
AANU01185798.1/9761-9673     GGGCUGGC-UUUAGCUC-AGCGGUUACUUCGCAGUUCAGCAAACCACCUCUCU-------------------------------------------------------GGGUUGUUCGAGAC-----------------CCGCGGGCACUCUCCAGCCCUUUU
AADA01117796.1/4260-4348     GGGCUGGC-UUUAGCUC-AGCGGUUACUUCGAGUACAUUGUAACCACCUCUCU-------------------------------------------------------GGGUGGUUCGAGAC-----------------CCGCGGGUGCUUUCCAGCUCUUUU
AF045144.1/1-88              -GGCUGGC-UUUAGCUC-AGCGGUUACUUCGAGUACAUUGUAACCACCUCUCU-------------------------------------------------------GGGUGGUUCGAGAC-----------------CCGCGGGUGCUUUCCAGCUCUUUU
AANN01510211.1/1211-1299     GGGCUGGC-UUUAGCUC-AGCGGUUACUUCGUGCUUAACAAUCACACUUACGA-------------------------------------------------------GUGAGGUUCGAUAC-----------------CCGCGGGCGCUCUCCAGCUCUUUU
ABDC01204167.1/4653-4552     GGGCUGGC-CUUAGCUC-AGCGGUUCCUUCGAUCGCAUGUCAACAACUUCUCUGUGUAGUCA----------------------------------------------GAGCGGUUCGAUACCC-------------ACCCGCGGGCGCUCUCCAGCCCUUUU
AAYZ01312112.1/750-847       GGGCUGGC-UUUAGCUC-AGCGGUUCCUUCGUGUAGUUUGACACUUGGUUACAACUGUAGAU----------------------------------------------GAACAGUUCGCGAC-----------------CCGCGGGCGCUCUCCAGUCCUUUU
AAFR03032607.1/51488-51600   GGGCUGGC-UUUAGCCC-AGCGGUUCCUUCCCUCAUUUAAACAUUUCUUACAAUUUCCCUUGGUGGUUCG-------------------------------AAUCCCAGGACCAUCAGAGAC-----------------CCGCGGGCGCUUCCCGGUCCUUUU
AAYZ01312112.1/5102-5200     GGGCUGGC-UCUAGCUC-AGCGGUUCCUUCGUCUACAUGCAUCAGACCUAACCACCAACUCGU---------------------------------------------UGGUGGUUCGCGAC-----------------CCGCGGGCGCUCUCCAGUCCUUUU
AAQQ01588127.1/1805-1892     GGGCUGGC-UUUAGCUC-AGCGGUUCCUUCGCCAGAAAACUUGCAAUCAUCU--------------------------------------------------------CGGUGGUUCGAGAC-----------------CCGCGGGCGCUCACCAGUCCUUUU
AF045143.1/1-98              -GGCUGGC-UUUAGCUC-AGCGGUUACUUCGACAGUUCUUUAAUUGAAACAAGCAACCUGUCU---------------------------------------------GGGUUGUUCGAGAC-----------------CCGCGGGCGCUCUCCAGUCCUUUU
AADA01319887.1/7078-7176     GGGCUGGC-UUUAGCUC-AGCGGUUACUUCGACAAUUCUUUAAUUGAAACAAGCAACCUGUCU---------------------------------------------GGGUUGUUCGAGAC-----------------CCGCGGGCGCUCUCCAGUCCUUUU
AANU01185800.1/1378-1280     GGGCUGGC-UUUAGCUC-AGCGGUUACUUCGGCGACACCUCCUAGGAUUACACCAACCUCUCU---------------------------------------------GGGUUGUUCGAGAC-----------------CCGCGGGCGCUCUCCAGUCCUUUU
AAPY01617272.1/690-825       GGACUGGC-UUUAGCUC-AGCGGUUCCUUCGGCGACUUCAGCUGCGAAUUCCACCCUCUCUGGGCGGAUGGCUGGCUGCAAA--------UCCACCCCUCCCCUGGGCGGGUGGCUCGAGUC-----------------CCGCGGGCGCUCUCCAGUCCUUUU
AAFC03082657.1/5139-5043     GGGCUGGC-CGUAGCUC-AGCGGUUCCUUCGACUACACAGUGUUUAAAUUACUCUCUCUGA-----------------------------------------------GGGUGGUUCGAGAC-----------------CCGCGGGCGCUCUCCAGUCCUUUU
AALT01490920.1/880-979       GGGCUGGC-UUUAGCUC-AGCGGUUACUUCGUCAGUCUACGGAGCUUUGCUUUGUAACUAUCCU--------------------------------------------UGAUGGUUCGAGAC-----------------CCGCGGGCGCUCUCCAGUCCUUUU
CAAA01055262.1/2914-2772     GGGCCAGC-UUUAGCUC-AGCGGUUACUUCGACAGUGGUUCAGUUCAUUACCAGCUAUUCGUAGCAGGUUCGAACAACACAACCA-ACCACUUACCUAACCCGUGAGUGUUUGGUUCGAGAC-----------------CCGCGGGCGCUCCCUGGCCCUUUU
AAPY01035584.1/271-170       GGGUCGGC-UUUAGCUCAAGCGGUUACUUCCUCAGUCUGGAUGUUCUAUCCACAUAAUCCCUGU-------------------------------------------GCUGGGGUUCGAGAC-----------------CCGCGGGUGCUUUCUGACCCUUUU
AANU01297565.1/11257-11357   GGGUCGGA-GUUAGCUCAAGCGGUUACCUCCUCAUGCCGCACUUUCUAACUGUCCAUCUCUGUG--------------------------------------------CUGGGGUUCGAGAC-----------------CCGCGGGUGCUUACUGACCCUUUU
AADA01053495.1/13035-13135   GGGUCGGA-GUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUG--------------------------------------------CUGGGGUUCGAGAC-----------------CCGCGGGUGCUUACUGACCCUUUU
AC005219.1/49914-50014       GGGUCGGA-GUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUG--------------------------------------------CUGGGGUUCGAGAC-----------------CCGCGGGUGCUUACUGACCCUUUU
AAFC03124581.1/19885-19976   -GGUCAGA-UUCAGCGCAAGCAGUUACUCCGAUCCAUUGGACUUCAGAUACCUAUA----------------------------------------------------UUGAGGUUUGAGAC-----------------CUGAGGGUGCUUUCUGAUCCUUUU
AAIY01676155.1/2446-2346     GGGUCAGC-UUUAGCUC-AGCGGCUACUUCGUCAUUUCAUUUCAUGAUUCAGAUCAUCUAACCU-------------------------------------------UUUGGGGUUCGAGGC-----------------CUGCGGGCGCUUUCUGACCCUUUU
AANG01340911.1/391-293       GGGUCGGC-UUUAGCUCAAGCGGUUACUUCGCAUGUGGUUACUAAACCUUCCAACCCUCUCG----------------------------------------------UUAGGGUUCGAGAC-----------------CCGCGGGUGCUUUCUGACCCUUUU
AAIY01523309.1/3001-2891     GGGUCAGC-UUUAGCUC-AGCGGUUACUUCGUCAAGCUUGAAUUAAUCAUUCCAUGAUUCAGUUCAUCC---------------------------------AACCCCUUAGGGUUCGAGGC-----------------CCGCGGGCGAUUUCUGACCCUUUU
Z11765.1/2-89                --GUCAGC-AACAGCUC-AGCGGUUACUUCUCGACACGGAAUUGUAAUUCUGAAAACCUU------------------------------------------------UCGGGGUUCGAAAC-----------------CCGCGGGCGCCACCUGAC------
Z11770.1/2-94                --GUCAGC-AACAGCUC-AGCGGUUACUUCUCGAAAUACCACGGAAUUGUAAUUCUGAAAACCU-------------------------------------------UUCGGGGUUCGAAAC-----------------CCGCGGGCGCCACCUGAC------
AAFR03013168.1/17587-17486   GGGCCGGCUUUUAGCCC-AGCGGUUCCUUCGGCAUUUCAGAACAUUUCCUGCUCUGACUAACGU-------------------------------------------UAAGGCGUUCGAGCC-----------------CCGCGGGCGCUUCCUGGCCCUUUU
AABS01000020.1/180914-180809 GCGUCGGC--UUAGCCU-AGUGGUUACUUCACUUCACAACCUUUGUCUGACACAAAGUU-------------------------------------------------CGUGGGCUCGAAGCCCACCC-----CUACCACCACGGGCGCAGCCCGGUGCCACU
AABS01000153.1/65061-65164   GAGUCAGC--UUAGCCU-AGUGGUUACUUCACUUGAAACAAUUCAUCAAUUGU-------------------------------------------------------UGUGGGUUCGAAUCCGUCCCCACCCCUUCCACCACGGGCGCCGUCUGACCAUUU-
AACT01010020.1/5401-5301     AUACCGGC--UUAGCCU-AGUGGUUACUUCUAAAUGAAUACACUCUGUCCAGUGAU----------------------------------------------------UCUGGGUUCACCACCCACC-------CCACACCACGGGCGCCGUCCGGUAUCUUU
CAAE01015120.1/740254-740351 GCGCUGG--UUUAGCUC-AGUGGUUACUUCACCACAAAUCCUUUGGAUUUCGCGGUCUCCUCCC-------------------------------------------AACUGGGAUCCAA-------------------CCACGGGCGCUGCUCAGCGUUUUU
BAAF04090272.1/3579-3481     GCACUGG--UUUAGCUC-AGCGGUUACUUCAACUCAACUCUUUUGAAGAUUACACUUUUACCCU-------------------------------------------UUCUGGGUUUGAAA------------------CCACGGCCGCUGUUCAGUGCAUUU
BX663520.9/47050-47141       ACGCUGG---UUAGCUC-AGUGGUUACUUCCGAAAAUCUUACUGUUGAUUUCUCUCCCGU------------------------------------------------CAUGGGAUCGAA-------------------CCACGGGCACCGUCCAGCGUUUUC
DQ986918.1/68217-68269       GCGCCGG--UUUAGCUC-AGUGCUA-----------------------------------------------------------------------------------GGUUCGA------------------------CCACGAGCGCUGUCUGGCGUUUUG
CAAE01009081.1/10241-10331   GCGCCGG--UUUAGCUC-AGUGGUUACUUCUUGAAGUUCCCGCUUGCGGCUCGCGCGGGC------------------------------------------------UGCGGGUUCG---------------------CCACGGGCGCUGCCCGGCGUUUUG
AANH01005876.1/66236-66335   GCGUCGG--UUUAGCUC-AGUGGUUACUUCUACAAUCCACGUAUCUUUCUCUGACGGGCUGCUGUC----------------------------------------CGUCGGAGAUCGA--------------------CCACGGGCGCUGUCCGAUGCUUUU
BAAF04125921.1/125-27        GCAUCGG--UUUAGCUC-AGUGGUUACUUCCAACAAUCGACAGUUGUCCUUUGACGAUCCGCGGG-----------------------------------------UUGUCAAGUUCGA--------------------CCACGGGCGCUGUCCGAUGUUUUU
AANH01005876.1/65973-65874   GCGUCGG--UUUAGCUC-AGUGGUUACUUCUGGUCAUGUGUUUGCCUUCCCUCGGGCUCUUCUGGG----------------------------------------GCCCUGAGUUCGA--------------------CCACGGGCGCUGUCCGAUGCAUUU
AANH01005876.1/66956-66857   GCAUCGG--UUUAGCUC-AGUGGUUACUUCCAAACAUGAGUUUCUUUCUUCACGGGCUCUUCUGGG----------------------------------------GCCCAUCGAUCGA--------------------CCACGGGCGCUGUCCGAUGCUUUU
AAVX01043580.1/1126-1028     GCGUCAGC-UAUAGCUC-AGUGGAUACUUCGUUUAUUGCAAAACACUUAACAGCCCCGAGUAAC-------------------------------------------AUCGGGACUCGUG-------------------CCACGGGCGCUGUCUGACGUUUUU
BAAF04125918.1/845-746       GCAUCGG--UUUAGCUC-AGCGGUUACUUCAUCGUUUGUGUACGAAAAACUUUGUCUGUCCUCGCA----------------------------------------UAGACGGGUUCGA--------------------CCGCGGGUGCCGUCCGAUGUUUUU
AC150310.1/65487-65586       GUGUUGGCAUUUAGCUC-AGUGGAUACUUCAGCUGUCACAGACUCUUCUUGUAAUACAGU------------------------------------------------AACAUGUUCAAAUCC--------------UACCACAGGCGCUGCCCAACACUUUA
BAAF04097857.1/315-413       ACAUUGG--UUUGGCUC-AGUGGUUUUUUCUACCGGUGAUUUGUCACAUCUGACGGU---------------------------------------------------CAGCGGUUCGAAACAGU----------UUGACUACAGGGACUGCCCGAUGUUUUU
AANG01341798.1/2156-2244     -GAUUGGC-CGUAGCUG-AGUGGUUUCUUCAAGUAAAGCAUCUCCUAGCUACUC------------------------------------------------------AAGUGGUUCAGGAC-----------------CUGCUGGUACUUUCUAGCCCUUUU
AAPN01235812.1/520-620       GGGCCGGC-CGUAGCUC-AGCGGUUACUUCUGUCAACGAAAGGCUUCUUUCGGUUAAAUCUCUU--------------------------------------------CGGAGGUUCGAGCC----------------CCCGCGGGCGCUUUCCGGUCCUUUU
AAHX01094554.1/16303-16446   GGGCCAGC-UUUAGCUC-AGCGGUUACUUCGACGUGCUCCAGUUUGAGCAGGCUAUGUAACGUGGUCGGUUCGAGCAACACAACCAGCCGCUUGCCUAUCUGGUGAGUGGUUGGUUCGAGAC-----------------CCGCGGGCGCUCUCUGGCCCUUUU
CU855896.20/66057-65953      GCGCCGG--GUUAGCUC-AGUGGUUACUUCUCAGCCAAAAGACAACUCUCAUGGCCGCCGGGUCUCCG------------------------------------GAAGCCAGAGAUCGAA-------------------CCACGGGCACUGUCCAGCGUUUUA
AAKN02022956.1/147590-147489 GGGUCGGC-UUUAGCUCAAGCGGUUACUUCCUCACGCUGGACUUAUCAUCUGUCUACAUCCUGC-------------------------------------------GCUGGGGUUCGAGAC-----------------CCGCGGGUGCUUUCUGACCCUUUU
CU855896.20/65648-65545      GCGUUGG--UUUAGCUC-AGUGGUUACUUCUGUGACCUUCACAAAAUCAACCUCUCAUGGUUGC-------------------------------------------GUUGCGGCCAGAGAUCG-------------AACUACGGGCACUGUCCAACGUUUUA
CU855896.20/65265-65162      GCGUUGG--UUUAGCUC-AGUGGUUACUUCUGUGAUCCCUGAAAAAUCAACCUUUCAUGGUCAC-------------------------------------------CUCGGUGCCAGAGAUCG-------------AACCACGGGCGCUGUCCAACGUUUUA
AAKN02009897.1/69401-69496   GGGCUGGC-UUUAUCUC-AGCGGUUCCUUCGACUGUUCUUAGUUGACUUCUUGGGCUGGU------------------------------------------------CUGGUGUUUGAGAC-----------------CCGCGGGCGCUCUCUGGUCCUUUU
AAWR02002461.1/13655-13752   GGGUCGGC-UGUAGCUCAAGCGGUUACUUCGCAACUUCAGAAUGCUUCUGGACAACCCCUU-----------------------------------------------CCAGGGUUCGAGAC-----------------CCGCGGGCGCCCUCUGACCCUUUU
AAWR02002381.1/633-543       UUCCCGGA-UGUAGCUC-AGCGGUUCUUUCGACUAAGGCAUCAGCUUCUAACCACGCG--------------------------------------------------AGGUGGUUCGAGAC-----------------CCGGGGGCGUUCUCCAG---UUUU
AAKN02009897.1/76911-77020   GGGCUGGC-UUUAGCUC-AGCGGUUCCUUCGAUCAAUCAAGCUUAGUCACUUGGGCCGGUGGCUUCCAU----------------------------------CGGUCCGGUGGUUCGAGAC-----------------CCGCGGGCGCUCUCCAGUCCUUUU
AAQR03019327.1/46254-46153   GGGCUGGC-UUUAGCUC-AGCGGUUCCUUCGACGGUGCAUUGCUUUCGAUCCUCUGCAUCUGGCA------------------------------------------GAGCCGGUUCGAGAC-----------------CCGCGGGCGCUCUCCAGCCCUUUU
AAWZ02017265.1/11968-11880   GGGCCAGC--UUAGCCU-AGCGGUUCCUUCGCAGUUUGAGCAAGUAACUACCAC------------------------------------------------------ACCUGGUUCAAGUC-----------------CCGCGGGCGCUGCCUGGCCUUUUG
CAAB02006781.1/1623-1725     GCACUGGC--UUGGCUC-AGCGGUUACUUCACCUCAAAUCAAAUCUGUUUGAUUACGUGGUCUCCUC--------------------------------------CCAACCGGGAUCGAA-------------------CCGCGGGCGCCGUCCAGUGUUUUC
AAEX03007799.1/48369-48272   GGGUCAGC-UUUAGCUCGAGCGGUUACUUCGCGACUUGUCUUCGGACUAACAACCCCCUUG-----------------------------------------------CGGGGGUUCGAGAC-----------------CCGCGGGCGCUCCCUGACCCUUUU
AAPE02012895.1/9444-9339     GGGCUGGC-UUUAGCUC-AGCGGUUCCUUCGCAUACAGAACUUCCUACUCGCAGUUGCUCACUUGAG--------------------------------------CGACAGCGGUUCGAGAC-----------------CCGCGGGCGCUCUCCAGCCCUUUU
AAWZ02017265.1/33588-33681   GGGCCAGC--UUAGCCU-AGCGGUUCCUUCGCUUUCUCUGCAAGAAACCACUUCGAUGU-------------------------------------------------UCGAUGUUCAGGUC-----------------CCGCGGGCGCUGCCUGGUCUUUUG
AADN03006686.1/3019-2926     GGGCCGGC-UUUAGCCC-AGCGGUUCCUUCGGCAAACAGUUUCUGAGUUGCGGGCCCCGA------------------------------------------------CUGGGGUUCGAU-C-----------------CCGCGGGCAC-CCCUGGCCCAUUU
AAGW02013702.1/28641-28535   GGGCUGGC-UAUAGCUC-AGCGGUUCCUUCGAACUACCAGCUACAUUUAAGCUACUAAGUCAGCACG-------------------------------------UCAGUGUUGGUUCGAGUC-----------------CCGCGGGCGCUCCCCAGCCUUUUU
AAPE02012974.1/61822-61921   GGGUCAGC-UUUAGCUCAAGCGGUUACUUCGGUUUCUGCUCGUUGCGGACACAUAACCCUACC---------------------------------------------UUAGGGUUCGAGAC-----------------CCGCGGGCGCUCUCUGACCCUUUU
CAAB02016770.1/2532-2438     GCGGAGG--UUUAGCUC-AGGGGUUACUUCACAGCUUGUUACCACCUAAAUGAUCCGCGGGU----------------------------------------------CACAGGUUCCAA-------------------CCCCGGGCGCCGCCCUCCGUUUUG
AAGU03004543.1/85259-85169   GGGUCAGC-UUUAGCUCUAGCGGUUACUUCGAUCAAAGUCAGAACAACUCUGUC------------------------------------------------------GUGGAGUUCGAGAC-----------------CCGCGGGCGCUCUCUGACCCUUUU
AAGW02008962.1/166-64        GGGCUGGC-UAUAGCUC-AGCGGUUCCUUCGACGCAGAAGCUACUUGAAGCUAAGUCAGCAUGCA-----------------------------------------AGUGCUGGUUCGAGUC-----------------CCGCGGGCGCUCCCCAGCCUUUUU
AAGJ04060735.1/3776-3896     UGGCUGGC--UAAGCAG-UGUGGAUACUUCGUAUAGCAUAAUGGCAUUGCAAUUAACCUUCAUUUAA-------------------------------------UGAUAGUGGGUUCGAUCCCCACUGC--GUUUAUUUCUACACGCGCGAUCCAGCCUUUUU
AAGJ04060731.1/512-632       UGGCUGGC--UAAGCAG-UGUGGAUACUUCGUAAAGCAAAAUGGUAUUGCAAUUAACUGUCACUUAA-------------------------------------UGUUUGUGGGUUCGAUCCCCACUGC--GUUUCUUUCUACACGCGCGAUCCAGCUUUUUU
AAGJ04060733.1/971-1090      UGGCUGGC--UAGGCAG-UGUGGAUACUUCGUAUAGCAAAACGGUAUUGCAAUUAAUUGUGGCUUAA--------------------------------------UGUUGUGGGUUCGAUCCCCACUGC--GUUUCUUUCUACACGCGCGAUCCAGCUCUUUU
AAGJ04020426.1/4514-4635     UGGCUGGC--UAAGCAG-UGUGGAUACUUCGUAUAGCUAAAUGGUAAAGCCCUUAUUAAUCACAUGAG------------------------------------UAUUUGUGGGUUCGAUCCCCACUAC--GUCUCUUUCUACACGCGCGAUCCAGCUUUUUU
AAGJ04060733.1/252-131       UGGCUGGC--UAAGCAG-UGUGGAUACUUCGUAUAGCUAAAUGGAAUAGCACUUACUAAUCACAUGAG------------------------------------UAUUUGUGGGUUCGAUCCCCACUAC--GUCUCUUUCUACAUGUGCGUUCCAGCUUUUUU
#=GC SS_cons                 :<<<<<<-.----<<<<.-<<<<----<<<<<________________________________...........................................________>>>>>--.................>>>>>>>>----->>>>>>:::::
#=GC RF                      GgGccGGC.UUUAGCuc.AGcGGUUACuUCgacuauuuuaauuuuauuuaucuuauuuuuuuuu...........................................uuguuGGUucGAgaC.................CCgCggGCGCUcUCCggCccUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00007
#=GF ID   U12
#=GF DE   U12 minor spliceosomal RNA
#=GF AU   Griffiths-Jones S; 0000-0001-6043-807X
#=GF AU   Mifsud W; 0000-0002-9805-6461
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Shukla GC and Padgett RA, PMID:10199569; PMID:18390578
#=GF SS   Predicted; Griffiths-Jones S
#=GF GA   53.00
#=GF TC   53.00
#=GF NC   52.90
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00006
#=GF DR   SO; 0000399; U12_snRNA;
#=GF DR   GO; 0000348; mRNA branch site recognition;
#=GF DR   GO; 0045131; pre-mRNA branch point binding;
#=GF DR   GO; 0005693; U12 snRNP;
#=GF RN   [1]
#=GF RM   10199569
#=GF RT   Conservation of functional features of U6atac and U12 snRNAs between
#=GF RT   vertebrates and higher plants.
#=GF RA   Shukla GC, Padgett RA
#=GF RL   RNA 1999;5:525-538.
#=GF RN   [2]
#=GF RM   9149533
#=GF RT   Pre-mRNA splicing: the discovery of a new spliceosome doubles the
#=GF RT   challenge.
#=GF RA   Tarn WY, Steitz JA
#=GF RL   Trends Biochem Sci 1997;22:132-137.
#=GF RN   [3]
#=GF RM   11864616
#=GF RT   The divergent U12-type spliceosome is required for pre-mRNA splicing and
#=GF RT   is essential for development in Drosophila.
#=GF RA   Otake LR, Scamborova P, Hashimoto C, Steitz JA
#=GF RL   Mol Cell 2002;9:439-446.
#=GF CC   The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11
#=GF CC   snRNAs and associated proteins, forms a spliceosome that cleaves a
#=GF CC   divergent class of low-abundance pre-mRNA introns. Although the U12
#=GF CC   sequence is very divergent from that of U2 (Rfam:RF00004), the two are
#=GF CC   functionally analogous [2]. The predicted secondary structure of U12 RNA
#=GF CC   is published (see for example, PMID:10199569), but the alternative single
#=GF CC   hairpin in the 3' end shown here seems to better match the alignment of
#=GF CC   divergent Drosophila and Arabidopsis sequences.
#=GF WK   U12_minor_spliceosomal_RNA
#=GF SQ   62


AANN01056468.1/521-372         AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUC--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGUU---GCG-AUCU----GCCCG
AADA01322814.1/1127-978        AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUC--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGUU---GCG-AUCU----GCCCG
AANU01293824.1/906-757         AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUC--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGUU---GCG-AUCU----GCCCG
ABBA01017933.1/18965-18816     AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUC--GC-C-CUC--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGUU---GCG-AUCU----GCCCG
ABDC01356688.1/591-740         AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUC--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGCU---GCG-AUCU----GCCCG
AAFC03093377.1/31487-31636     AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUU--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGUU---GCG-AUCU----GCCCG
AAQQ01306058.1/1332-1183       AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCAAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUU--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGUC---GCG-AUCU----GCCCG
AANG01542153.1/730-879         AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUU--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGUC---GCG-AUCU----GCCCG
AAIY01326656.1/671-820         AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-CCGGGGUGA-CGCCCGGAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUU--GC-C-CCU--ACGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGUGUU---GCG-AUCU----GCCCG
AAPN01231707.1/282-431         AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUAA-CGCCCGAAUC------CUCACUACGCAU-----------------------------------GUGAG------AAGAAUUUUUG----------------------------------------AGCGGGU-AC--AGGUU--GU-C-CCU--AAGGUG---ACCCGCUUACUUC-GCGGG---A--UGCCUG--GGUGUC---GCG-AUCU----GCCCG
AAHX01055169.1/34088-34238     AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAGUC------CUCACUGCUUAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUU--GC-U-AUCU-AAGGCG---ACCCGCCUACUUU-GCGGG---A--UGCCUA--GGUAAC---GCG-AUCU----GCCCG
AALT01414211.1/1221-1073       AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUC--GA-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGCGAG----CG-AUCU----GCCCG
AAHY01168842.1/1247-1097       AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAGUC------CUCACUGCUUAU-----------------------------------GUGAG------AAGAAUUUUUG----------------------------------------AGCGGGU-AU--AGGUU--GC-A-AUCU-GAGGCG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGUGAC---GCG-AUCU----GCCCG
AAPY01023785.1/1285-1135       AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGGAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUU--GU-C-CCCU-AAGGUG---ACCUGCCUACUUU-GCGGG---A--UGCCUG--GGAGGU---GCG-AUCU----GCCCG
AAVX01293999.1/160-11          AUGCCUUAAACU-AAUGAGUAAGGAAAA-UAACGGU-CCGGGGUGA-CGCCCGGGUC------CCCGCCCCACAG----------------------------------UGCGGG------AGGAAUUUUUG----------------------------------------UGCGGGU-AC--AGGUC--CC-C-CUC--GCGGUG---ACCCGUCUACUUU-GCGGG---A--UGCC-A--GAGAGC---GUG-AACU----GCCCG
CAAE01014653.1/353935-353782   AUGCCUUAAACU-GAUGAGUAAGGAAAA-UAACGAU-GCGGGGUGA-CGCCCGUGUC------CUCGUUGAACUU-----------------------------------ACGAG------AUCAAUUUUUG----------------------------------------AAAGGGU-AC--AGGUC--UG-C-CCGCUCUGGUG---ACUCGCCUACUUU-GCGAG---A--UGCCUU-GCGGGAC---UAGGACCU----ACCCC
BAAE01110703.1/791-944         AUGCCUUAAACU-GAUGAGUAAGGAAAA-UAACGAU-GCGGGGUGA-CGCCCGUAUC------CUCGUUCACAAU-----------------------------------ACGAG------AGGAAUUUUUG----------------------------------------ACGGGGC-AC--AGGCCUGCC-U-GCU--GAGGUG---ACUUGCUUACUUC-GCGAG---A--UGCCUCGUGGGACU---GGG-GUCU----GCCCU
AANH01004214.1/17675-17828     AUGCCUUAAACU-GAUGAGUAAGGAAAA-UAACGAC-GCGGGGUGA-CGCCCGUGUC------CUCGUAAACAUA-----------------------------------ACGAG------AAGAAUUUUUG----------------------------------------AAAGGGC-AC--AGGUC--UG-U-CUG--CUGAGGUG-ACUCGCCUACUUU-GUGAG---AUGCCUCGU--GGAGCC---AGG-ACCU----UCCCC
ABAV01000136.1/26200-26351     UUGCCUUAAACU-AAUGAGUAAGGAAAA-UAAC-GA-UCUGGGUGA-CGCCAGAUCC------CACGAUCAGUUU-----------------------------------UCGUG------AAGAAUUUUUG----------------------------------------ACGGGACCAG--AGGCU--AC-C--CG--UAGGUG---ACCCGCUUACUUUUGCGGG---A--CGCCUG--CGUUGC---GAA-UCCU--CCGUCCA
AAZO01006159.1/30950-30796     GUGCCUUAAACU-AAUGAGUAAGGAAAA-UAUUGAG-CCCUGGUAA-CGCUUGGCUC------GGCUAUAAUAUA------------------------------AUUAAUAGCU------UUGAAUUUUUG----------------------------------------AAGGGGU-CG--AGGUC--GUCC-UCU--GGAGUG----UCUGCCUACUUUAGCAGA------UAUUCG--AGUGAA---GCG-AUUU----ACCCC
AAAB01008960.1/5726267-5726086 GUGCCUUAAACU-AAUGAGUAAGGAAAA-UUACGGG-CCUUGGUGA-CGCUUGGCUCUG----CCUACGAACUAG--------CGGGUGCGGCUCAAUGGGUCGUGCUCGGUAGG------CUGUAUUUUUG----------------------------------------AAGAGGC-AC--AGGUC--GU-C--CU--CGAGCUUG-UCCUGCCUACUUU-GCAGG---A--UGCUCGAGAGUGUU---GCG-AUCU----GCCUC
AAJJ01000520.1/29099-28948     GUGCCUUAAACU-AAUGAGUAAGGAAAAUAAACGAG-CCUUGGUAA-CGCUUGGCUUACA---UGCUAGGCUUCC-----------------------------------UAGCC------UCGAAUUUUUG----------------------------------------UAAGGGC-AA--AGGUC--GU-C--CC--GUGGAC---AG-UGCCUACUUUUGCAAC---G--GUCC-U--GGUGAA---GCG-AUCU----GCCCU
AAZX01007808.1/26508-26658     GUGCCUUAAACU-AAUGAGUAAGGAAAA-UAUGAGG-CUUUGGUGA-CGCUUAGCAA------UGCUCGAAUUGU-----------------------------------AAGCGA-----ACCUAUUUUUG----------------------------------------AAGGGGU-AC--AGGUC--GU-C-CUG--UGGCUG---CCUGAACUACUUU-UUUAG---G--CGGUCU--AGUGAA---GCG-AUCU----ACCUC
AABS01000019.1/293615-293466   GUGCCGUAAACU-AAUGAGUAAGGAAAAUAAACGAU-CCCCGGUGA-CGCGGGGUUC------AGAGGGUUUUUC-----------------------------------CCUUCC-----UCCGAUUUUUG----------------------------------------AGGGGGU-AA--AGGUC--AC-C-UUG---CUGUG---AA-AGCUUACUUU-GCUAU---U--CGCAGU--CAUUGA---GGG-AUCU----CCCCU
AAYZ01032557.1/2146-2294       AUGCCUUCAACU-UAUGAGUAAGGAAAA-UAACGAU-UCAGGAUCA-CGCCCGAAUU------CUCACUGCUACU-----------------------------------GGGAG------ACAAAUUUUUG----------------------------------------GCUGGUA-A---AGGUC--AU-C-CCU--AAGGUG---ACCUGCAUACUUU-GUGGG---A--UGCCUC--GAAGCU---GUA-AUCU----GCCCA
AACT01038531.1/95659-95808     GUGCCGUAAACU-AAUGAGUAAGGAAAAUAAACGAA-CCCUGGUGA-CGCGGGGUUU------AAAGGGUAUUUC-----------------------------------CCUUG------CGUGAUUUUUG----------------------------------------A-GGGGC-AC--AGGUC--GC-UAUUG--GCUGUG----GAAGCUUACUUU-GCUUU---C--CGCAGU--UGAAGU---GGG-AUCU----UCCCC
AASG02002046.1/26669-26822     CUGCCUUAAACU-AAUGAGUAAGGAAAA-CAAAGCG-AGCGGUGGG-AGCCGCUCGC------CGCGCUUCUAAG----------------------------UAAUCAUGCGCA------AUAAUUUGUGG----------------------------------------AGGGGUA-AU--AGGCU--GG-C--CG--AGCGCUGA-CGCUGCUUACUUU-GCAGA---A--CUCGCU--CGUG-----CGG-GCCU------CCC
AADK01040274.1/1841-1691       GUGCCUCAAUCU-AAUGAGUAAGGAAAU-UAUUGGG-CCUUGGUAA-CACUUGGCAA------UUGUCCUUAUUA----------------------------------GGGCGA------ACUUAUUUUUG----------------------------------------UU-GGGU-AC--AGGUC--GU-C-CCCU-UGAGCC---GCUCGCCUACUUU-GCAAG---C--GGCUCG--GGUGAA---GCG-AUUU----GCCCU
AC198009.4/84558-84712         UUGCCUUAAACU-AAUGAGUAAGGAAAA-CAAAGCGAACUGGUGGG-AGCCGGUCGC------AGCAUCUAACAA-------------------------------CAUGAUGCA------AUGAUUUUUGG----------------------------------------AGGGGUG-AU--AGGCU--GG-U--CG--UGUGUAGA-CGCUGCUUACUUUUGCAGA---A--CUCACA--CGUG-----CGG-GCCU----CCCUU
AAGE02014219.1/46421-46245     GUGCCUUAAACU-AAUGAGUAAGGAAAA-UUACGAG-CCCUGUUAA-CGCUUGGCUC------AGCUUCCUCAUU-------------GCAGUCGGUUAUCCGGCUGCGUAAGCG------CUAAUUUUUCA----------------------------------------UAGAGGU-AC--AGGUC--GU-C-CCC--UCGUAGUUACCCUGCCUACUUU-GCGGG---GUGCUCGGG--CGUGCU---GCG-AUUU----GCCUC
AARH01003540.1/648176-648022   UUGCCUUAAACU-AAUGAGUAAGGAAAA-CAAAGCG-AGAGGUGGG-AGCCGCUCGC------CGCGCCGACACA-------------------------------GUUUGUGCGC-----AUUAAUUUGUG----------------------------------------GAGGGGU-UAU-AGGCU--GG-C--CG--AGCGUUGA-CGCUGCUUACUUU-GCAGA---A--CUCGCU--UGCG-----CGG-GCCU----CCCUA
AC004255.1/89334-89170         UUGCCUUAAACU-AAUGAGUAAGGAAAA-CAAAGCG-UCCGGUGAG-AACCGGUCGCG-----GCGCUAAUCGUA-----------------------AAACACAAAAUUGGCGC------AAUAAUUUAUG----------------------------------------GAGGGGU-UAUAGGCUG--GC-C--GA--UGUGUUGA-CGCUGCUUACUUUUGCAGA---A--CUCACC--UCGU-----GCG-GGCC----UCCCU
AP005874.3/27602-27759         UUGCCUUAAACU-AAUGAGUAAGGAAAA-CAAAGCGUUGCGGUGAG-AGCCGCUCGCG-----GUGCGGGACUCA------------------------------AACCCUGCAC------GGCAAUUUUUG----------------------------------------CGAGGGG-AAGAGGCUC--GC-G--CG--GGUAUUGA-CACUGCUUACUUUUGCAGG---A--CUUGCC--UGU------GUG-GGCC----UCCCU
AAAA02006813.1/31506-31663     UUGCCUUAAACU-AAUGAGUAAGGAAAA-CAAAGCGUUGCGGUGAG-AGCCGCUCGCG-----GUGCGGGACUCA------------------------------AACCCUGCAC------GGCAAUUUUUG----------------------------------------CGAGGGG-AAGAGGCUC--GC-G--CG--GGUAUUGA-CACUGCUUACUUUUGCAGG---A--CUUGCC--UGU------GUG-GGCC----UCCCU
AAWT01090545.1/3123-3274       AUGCCUAAAUCU-AAAGAGUAAGGAAAA-UAAUGGC-UGAGGAGAAAUACCGAGGCCG-----CCAAGAAUAACU-----------------------------------CUUGG------GAAAAUUUUU-----------------------------------------AUAGGCC-AA--AGGUC--GU-C-CCU---GAGUG----UCAGCUUACUUU-GUUGG---C--CUCUU---GGUGUU---AUG-AUCUUAAAGGCUU
AAWU01013761.1/27501-27308     GUGCCUUAAACU-AAUGAGUAAGGAAAA-UUAAGAG-CACUGUUAG-CGCUUUGCUC------AGCUUCCGCACAUUGGGCCGAACUUCCCGAAUGGGAUUCGGUUUCGUAAGCA------GAAAUUUUUCC----------------------------------------UAGAGGU-AC--AGGUC--GU-C-CCCUCGCAGUCGU-CGCCGCCUACUUUUGCGGC---G-AUACUCG--GGCGUGCCAGCG-AUCU----GCCUC
AATU01009112.1/74318-74156     UUGGCUUAAACUCAAUGAGUAAGGAAAC-UAACGCC-CUAC-CUGA-CAAGUAGGGCU-----GCCUAUUGGGUC-------------------------AAGUGAUCCAUAGGU------CUGAAUUUAUGACGG------------------------------------AAAUGGA-AU--GGCCG--UC----UG--UUUAGU---AGCCCGCUACUUU-AGGGU---G--ACUAAU--UAGGGG---GCC-GGUC----CCCGC
AAQX01001042.1/31224-31386     CCGGCUUAAACUCAAUGAGUAAGGAAAC-UAAUGCC-CUAC-CUGA-CAAGUAGGGC------CGCCCAUUGGGU-----------------------CCAGCGAUCCAUGGGUU------UCCAAUUUAUGACG-------------------------------------GAGGUGG-AA--UGGCC--GU-C-GCU--U--AGG---AACCCGCUACUUU-AGGGU---G--ACUGAC--AGGGGG---CCG-GUCC----CCGCC
DQ888370.1/1-162               --GCCUUAAACU-AAUGAGUAAGGAAAA-UACC-GC-ACCGGUUGA-CACCGGUGUUAUGG--CGUGAACCGCGU-----------------------------------UCACGUCGGCUUCCAAUUUCUGGCGGGCU---------------------------------ACAGGCC-UC--GGCCC--UC-U--UGU-AGUGAC---CUGCGCCUACUUUCGCGCG---G--GAUGCU--CGA------GUU-GGCU----GGCCU
AAEU02001091.1/68476-68268     GUGCCUCAAACU-AAUGAGUAAGGAAAACCAAGAUG-CCUUGCUAAUCGCUUGGCAG------UAUUGGCUUCUA-----------GGCAGGGGGGCGUCCUGCGUCCCCUGAAG------CUCAAUUUUUGCAAGGGCACAGGUCGUCCCCUCCUCCGCCG----------AGUGGGU-----GGCGU--CC-G-GCC--AAGCAAAC-CGGCGCCUACUUU-GCGUCCGGC--UUGCGA--GGCUCA---GGG-UGCC----ACUCC
AAPQ01006579.1/170624-170417   GUGCCUCAAACU-AAUGAGUAAGGAAAACCAAGAAG-CCUUGCUAAUCGCUUGGCAG------UUUGGCUUCUAG-------------GCAGGGGGGCGUCCUGCGUCCCCUGAAG-----CUAAAUUUUUGCAAGGGCACAGGUCGUCCCCUCCUUCCCCG----------AGUGGGA-----GGCGU--CC-G-GCC--GAGCGAAC-CGGCGCCUACUUU-GCGUCCGGC--UAGCGA--GGCUCA---GGG-UGCC----ACCCA
AF459090.1/1-212               GUGCCUCAAACU-AAUGAGUAAGGAAAACCAAUCAG-CCUUGCUAAUCGCUUGGCAGUAUUG-GCUUCUAGGCAG-------------GGGGGCGUGUCCCGCGCCCCUUGAAGC------UCAAAUUUUUGCAAGGGCACAGGUCGUCCCCUCCUCCUCCGCG--------UGGGUGG-----CGUUC--GG----CC--GAGCGAAC-CGGCGCCUACUUU-GCGUCCGGC--UAGCGA--GGAUCU---CUG-GGUG----CCACC
AAKO01000167.1/274946-275154   GUGCCUCAAACU-AAUGAGUAAGGAUAACCAAGAUG-CCUUGCUAAUCGCUUGGCAG------UAUUGGCUUCUA-----------GGCAGGGGGGCGUCCUGCGCCCCUUGAAG------CUCAAUUUUUGCAAGGGCACAGGUCGUCCCCUCCUCCCCCG----------CGUGGGU-----GGCGU--UC-C-ACC--GAGCGAAC-CGGCGCCUACUUU-GCGUCCGGC--UAGCGA--GGAUCU---GGG-UGCC----AUCCC
AASV01051056.1/691-484         GUGCCUCAAACU-AAUGAGUAAGGAUAACCAAGAUG-CCUUGCUAAUCGCUUGGCAG------UAUUGGCUUCUA------------GGCAGAGGGGCGUCUGCGCCCCUUGAAG------CUCAAUUUUUGCAAGGGCACAGGUCGUCCCCUCCUCCCCCG----------CGUGGGU-----GGCGU--UC-G-ACC--GAGCGAAC-CGGCGCCUACUUU-GCGUCCGGC--UAGCGA--GGAUCU---GGG-UGCC----AUCCC
AAQB01007708.1/1369-1503       GUGCCUCAAACU-AAUGAGUAAGGAAAACCAAUUCG-CCUUGCUAAUCGCUCGGCAG------UUUGG----CUU-----------------------------------CUAAA------AG--------G----------------------------------------CAAUGGA-----AUGCC--GU-U-GGA--UGUUGG---GAGGGGAGACUCU-CCCUU---C--CCCUCG--UC---C---ACG-GCAU----UUCUU
AAIZ01008995.1/21704-21918     GUGCCUGAAAUU-AAUGAGUAAGGAAAACCAAUCCG-CCUUGCUAAUCGCUUGGUAGUAUUUGGCUUCUAGGCAA-------AGGGGCGGCCCUCAGAAGCCGCUCCCUUGAGGC------CUAAAUUUUUGCACGGGCACAGGUCGCCCCCUGCUUUGCCGGCACGGCCCCUCCCAUU-UGG-CGGCA--GG-A-ACC------------GGCACCUACUUUUGUGUC---G----------GGGAGC---GCU-GCUG----GAUGG
AAFS01000475.1/55736-55522     GUGCCUGAAAUU-AAUGAGUAAGGAAAACCAAUCCG-CCUUGCUAAUCGCUUGGUAGUAUUUGGCUUCUAGGCAA-------AGGGGCGGCCCUCAGAAGCCGCUCCCUUGAGGC------CUGAAUUUUUGCACGGGCACAGGUCGCCCCCUGCUUUGCCGGCACGGCCCCUCCCAUU-UGG-CGGCA--GG-A-ACC------------GGCACCUACUUUUGUGUC---G----------GGGAGC---GCU-GCUG----GAUGG
AAPU01011411.1/133226-133037   GUGCCAAAACAU-AAUGAGUAAGGAAAACCAAUAGG-CCUUGCUAAUCGCUUGGCAG------CUUGGCUUCUCG-----------GCAGAAGGGACUGCAAGGUCCCUUUGAAG------CUCAAUUUUUGAUAGGGCACAGGUCGUCCCCGUGUUC--------------AGAUGCG-C---AGUGC--GG-C-------GGGCC----GGCGCCUACUUU-GUGUC---C--GGUUUG-----------CUG-UGCU----CGCAU
AM487500.2/4877-4718           CUGCCUUAAACU-AAUGAGUAAGGAAAA-CAAAGCA-AGCGGUGAG-AGCUGCUUGC------CGCGCCUAUCUC-----------------------------UAUGAUGCGCA------AGAAUUUAUGG----------------------------------------AGGGGUU-AA--GGGCU--GG-C--CG--AGCGUUGA-CGCUGCUUACUUUUGCAGA---A--CUCGCU--UGUG-----CGG-GCCUCCCAAACCC
AASC02028416.1/49450-49599     AUGCCUUAAACU-AAUGAGUAAGGAAAA-UAACGAG-CCCGGGUAA-CGACGGGCUC------CCAGACUACCGU-----------------------------------UCUGG------AAGAAUUUCUA----------------------------------------CAGGGGC-AC--AGGUC--GC-C-CCC--AUGGUG---ACCCACCUACUUC-GUGGG---A--UGCCUG--GGUUGA---GUG-AUCU----GCCCU
AAGV020551495.1/1052-903       AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCGAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------CGCGGGU-AA--AGGUU--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGUC---GCG-AUCU----GCCCG
AAWR02025158.1/532-681         AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAGUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUC--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGUC---GCG-GUCU----GCCCG
AAWZ02031009.1/19848-19997     AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-CCGGGGUGA-CGCCCGGGUC------CUCACUGCAAAU-----------------------------------GUGAG------AGGAAUUUUUG----------------------------------------AACGGGU-AC--AGGUC--GU-C-CCC--GGAGUG---ACCCGCCUACUUA-GCGGG---A--UGCUCG--GGUGCC---AUG-AUCU----GCCCG
EU240273.1/1-149               AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAC-UCGGGGUGA-CGCCCGAGUC------CUCACUACUGAU-----------------------------------GUGAG------AGGAAUUUUUG----------------------------------------UGCGGGU-AC--AGGUC--GU-C-CCC---GGGUG---ACCCGCUUACUUC-GCGGG---A--UGCCCA--GGUGCA---AUG-AUCU----GCCCG
AAEX03007273.1/32318-32169     AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUC--GC-C-CCU--GAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGCC---GCG-AUCU----GCCCG
AAGJ04047220.1/14069-13916     AUGCCUUAAACU-AAUGAGUAAGGAAAA-UAACGAG-CCUAGGUAG-CCCUAGGUUC------CACAGCUUAUUA---------------------------------GUCUGUG------AGGAAUUUCUC----------------------------------------UAAGGGG-AC--AGGUU--GC-C-CUU--GGUGUGG--CCCAUCUUACUUU-GGUGG---G-AUGCCCA--UGACUG---GUG-AUCU----UCCCU
AADG06004603.1/1703-1555       GUGCCUUAAACU-AAUGAGUAAGGAAAA-UAUAGAG-CUUUGGUAA-CGCUUAGCUA------UGCUAAUUAUCA------------------------------------AGCGA-----CCAUAUUUUUG----------------------------------------AAGGGGC-AA--AGGUC--GU-C--CC--ACGGUA---ACGCGACUACUUUUUCGCG---U--GGCCG---GGUGAA---GCG-AUCU----ACCUC
AAGW02065961.1/10800-10651     AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-UCGGGGUGA-CGCCCGAAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUC--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGUGCC---GCG-AUCU----GCCCG
AAQY02000248.1/644530-644694   UUGGCUUAAACUCAAUGAGUAAGGAAAC-UAACGCC-CUAC-CUGA-CAAGUAGGGC------UGCCUGUUGGAU-----------------------CGAGUGAUCCAUGGGUU------UCUAAUAUUUGACGG------------------------------------AGGUGGA-AU--GGCCG--UC-A--UU---UUAGG---AACCCGCUACUUUUAGGGU---G--ACUAAA--AAGGGG---GCC-GGUC----CCCGC
AAQR03135034.1/15819-15671     AUACCUUAAAUU-UAUGAGUAGGGAAAA-UAACAAU-UUGGGAUGA-CGCCCAAAUU------CUCACUGCUUAU-----------------------------------GUGAG------ACAAAUUUUUG----------------------------------------AGCUGGU-AA--AGGUU--GU-C--CA--AAGGUG---ACCCAUCUACUUU-GUGGA---A--UGCCUG--GGUAUC---AUG-AUCU----GCCCG
AAGU03077213.1/2720-2571       AUGCCUUAAACU-UAUGAGUAAGGAAAA-UAACGAU-CCGGGGUGA-CGCCCGGAUC------CUCACUGCUAAU-----------------------------------GUGAG------ACGAAUUUUUG----------------------------------------AGCGGGU-AA--AGGUU--GC-C-CCU--AAGGUG---ACCCGCCUACUUU-GCGGG---A--UGCCUG--GGAGUU---GCG-AUCU----GCCCG
CAAB02002948.1/53519-53671     AUGCCUUAAACU-GAUGAGUAAGGAAAA-UAACGAU-GCGGGGUGA-CGCCCGUGUC------CUCGUUGCACUU-----------------------------------ACGAG------AUCAAUUUUUG----------------------------------------AAAGGGC-AC--AGGUC--UGCU-UGC--UGGGUG---ACUCGCCUACUUU-GCGAG---A--UGCCUU--GCGGGG-CUAGG-ACCU----GCCCC
#=GC SS_cons                   :::<<<<<____.______>>>>>,,,,.,,,,<<<.<<<<<____.__>>>>>>>>......<<<<<_______.............................._____>>>>>......-----------........................................--<<<<<.--..<<<<<..<<.-.-<<..-<<<<<...-<<<<<_______.>>>>>...-..>>>>>-..>>----...>>>.>>>>....>>>>>
#=GC RF                        gUGCCUuAAACU.AAUGAGUaAGGAAAA.uAAcgcg.cccgGuUaA.CGCcgggcgc......cccgcuuuuuau..............................uccuugcggg......auaAAUUUUUG........................................aaggGgc.Aa..gGgcc..gc.c.ccc..agggcc...acccGcCUACUUU.gCggg...a..ggcccu..gguguu...gcg.gcCc....gcCcc
//
# STOCKHOLM 1.0

#=GF AC   RF00008
#=GF ID   Hammerhead_3
#=GF PI   Hammerhead
#=GF DE   Hammerhead ribozyme (type III)
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:7969422
#=GF GA   29.00
#=GF TC   29.00
#=GF NC   28.90
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.75 -Z 549862.597050 CM SEQDB
#=GF CL   CL00010
#=GF DR   SO; 0000380; hammerhead_ribozyme;
#=GF RN   [1]
#=GF RM   7969422
#=GF RT   Three-dimensional structure of a hammerhead ribozyme.
#=GF RA   Pley HW, Flaherty KM, McKay DB
#=GF RL   Nature 1994;372:68-74.
#=GF RN   [2]
#=GF RM   9506521
#=GF RT   The structural basis of hammerhead ribozyme self-cleavage.
#=GF RA   Murray JB, Terwey DP, Maloney L, Karpeisky A, Usman N, Beigelman L, Scott
#=GF RA   WG
#=GF RL   Cell 1998;92:665-673.
#=GF RN   [3]
#=GF RM   10899150
#=GF RT   Distribution of hammerhead and hammerhead-like RNA motifs through the
#=GF RT   GenBank.
#=GF RA   Ferbeyre G, Bourdeau V, Pageau M, Miramontes P, Cedergren R
#=GF RL   Genome Res 2000;10:1011-1019.
#=GF CC   The hammerhead ribozyme is one of the smallest catalytic RNAs. These RNAs
#=GF CC   have an endonuclease function, and most often are autocatalytic.
#=GF CC   Structurally it is composed of three base paired helices, separated by
#=GF CC   short linkers of conserved sequence. These helices are called I, II and
#=GF CC   III. We have classified hammerhead ribozymes into three types based on
#=GF CC   which helix the 5' and 3' ends of the sequence join. This family are the
#=GF CC   type III hammerheads. The conserved uridine-turn links helix I to helix II
#=GF CC   and usually has the sequence CUGA. Helix II and III are linked by a
#=GF CC   sequence CGAAA. The cleavage reaction occurs between helix III and I, and
#=GF CC   is usually a C. Hammerhead ribozymes are found in plant viroids and other
#=GF CC   small replicating satellite RNA species. Hammerhead ribozymes have been
#=GF CC   found in animals as well as plants. This family includes a couple of false
#=GF CC   matches currently these are EMBL:AC078923 and EMBL:BC050488. These animal
#=GF CC   sequences are not expected to be hammerhead ribozymes.
#=GF WK   Hammerhead_ribozyme
#=GF SQ   82


D00685.1/1-46      ---------GCCAGACGU-GGACCCGGCCUGAUGAGUCCGAAA----------------------------GGACGAAACAGUA-
AJ247116.1/133-53  -UCCAGUC-GAGACCUGAAGUGGGUUUACUGAUGAGGCUGUGGAGAGAGCGAAAGCUUUACUCCCA-CACAAGCCGAAACUGGA-
Y14700.1/133-53    -UCCAGUC-GAGACCUGAAGUGGGUUUCCUGAUGAGGCUGUGGAGAGAGCGAAAGCUUUACUCCCA-CACAAGCCGAAACUGGA-
AJ247123.1/132-52  -UCCAGUC-GAGACCUGAAGUGGGUUUCCUGAUGAGGCUGUGGAGAGAGCGAAAGCUUUACUCCCG-CACAAGCCGAAACUGGA-
AJ247121.1/133-53  -UCCAGUC-GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGCUUUCGCUUUACUCCCG-CACAAGCCGAAACUGGA-
AJ247122.1/132-52  -UCCAGUC-GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGCUAUUGCUUUACUCCCG-CACAAGCCGAAACUGGA-
AJ247113.1/134-53  -UCCAGUC-GAGACCUGAAGUGGGUUUCCUGACGAGGCUGUGGAGAGAGCAAAUUGCUUUACUCCCGCACAAGCCGAAACUGGA-
AJ536620.1/1-40    ---------GGGUGGUGUGUG-CCACCCCUGAUGAGUCCGA----------------------------AAGGACGAA-------
AJ536617.1/1-40    ---------GGGUGGUGUGUA-CCACCCCUGAUGAGUCCGA----------------------------AAGGACGAA-------
Y12833.1/339-285   CCGCUAUA-UGGGGAUGUGUG-UCCCUACUGACGAGUUCAA----------------------------AAGAACGAAAUAGUUA
J02386.1/42-95     UGUCCGUA--GUGGAUGUGUA-UCCACUCUGAUGAGUCCAA----------------------------AAGGACGAAACGGAUG
J02439.1/42-95     UGUCCGUA--GUGGAUGUGUA-UCCACUCUGAUGAGUCCGA----------------------------AAGGACGAAACGGAUG
M63666.1/246-192   CCGGUGUC-UCAAGGUGCGUA-CCUUGACUGAUGAGUCCGA----------------------------AAGGACGAAACACCAG
M33000.1/55-110    ACGCUGUC-UGUACUUGUAUC-AGUACACUGACGAGUCCCU---------------------------AAAGGACGAAACAGCGC
M33001.1/56-111    ACGCUGUC-UGUACUUAUAUC-AGUACACUGACGAGUCCCU---------------------------AAAGGACGAAACAGCGC
AJ550909.1/282-333 GAAGAGUC--GCGCUU------AGCGCACUGAUGAGUCUCUGA-------------------------AUGAGACGAAACUCUUC
AJ550907.1/281-333 AAAGAGUC--GCGCUU------AGCGCACUGAUGAGUCUCUGA------------------------GAUGAGACGAAACUCUUC
AJ550908.1/281-334 GAAGAGUC-UGCGCUU------AGCGCACUCAUGAGUCUCUGA------------------------GAUGAGACGAAACUCUUC
AJ550910.1/282-336 GAAGAGUCCUGCGCUU------AGCGCACUGACGAGUCUCUGA------------------------GAUGAGACGAAACUCUUC
AJ550901.1/282-334 GAAGAGUC--GCGCUA------AGCGCACUGAUGAGUCUUUGA------------------------GAUAAGACGAAACUCUUC
AJ550898.1/282-335 GAAGAGUC-UGCGCUA------AGCGCACUGAUGAGUCUUUGA------------------------AAUAAGACGAAACUCUUC
AJ241850.1/282-334 UAAGAGUC--GUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AAAGAGACGAAACUCUUU
AJ005294.1/282-334 UAAGAGUC--GUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCUUG
AJ005321.1/281-333 GAAGAGUC--GUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCUUG
AJ241830.1/282-334 AAAGAGUC--GUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCUUG
AJ005320.1/281-333 GAAGAGUC--GUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCUUU
AJ241833.1/282-334 AAAGAGUC--GUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCUUU
AJ550903.1/281-333 GAAGAGUC--GUGCUU------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCUUU
AF170516.1/283-335 GAAGAGUC--GUGCUU------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCUUC
AJ550906.1/282-334 GAAGAGUC--GUGCUU------AGCACACUGAUGAGUCUCUGA------------------------GAUGAGACGAAACUCUUC
AJ005299.1/282-335 UAAGAGUC-UGUGCUA------AGCACACUGAUGAAUCUCUGA------------------------AAUGAGACGAAACUCUUG
AJ005300.1/282-335 UAAGAGUC-UGUGGUA------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCUUG
AJ241847.1/281-334 GAAGAGUC-UGUGCUA------AGCACACUGAUGAGUUUCUGA------------------------AAUGAGACGAAACUCUUG
AJ241831.1/281-334 GAAGAGUC-UGUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCUUA
AJ005302.1/281-334 AAAGAGUC-UGUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AUUGAGACGAAACUCUUG
AJ241823.1/282-335 AAAGAGUC-UGUGCUA------AGCACACUGAUGAGUCUCUAA------------------------AAUGAGACGAAACUCUUU
AJ005322.1/281-334 GAAGAGUC-UGUGCUA------AGCACACUGACGAGUCUCUGA------------------------AAUGAGACGAAACUCUUU
AJ005314.1/281-334 AAAGAGUC-UGUGCUA------AGCACACUGACGAGUCUCUGA------------------------AAUGAGACGAAACUCUUU
M83545.1/282-335   GAAGAGUC-UGUGCUA------AGCACACUGACGAGUCUCUGA------------------------GAUGAGACGAAACUCUUC
AJ550911.1/282-335 GAAGAGUC-UGUGCUA------AGCACACUGACGAGUCUCUGA------------------------AAUGAGACGAAACUCUUC
AJ241839.1/282-334 GAUGAGUC--GUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCAUA
AJ005312.1/282-335 GAUGAGUC-UGUGCUA------AGCACACUGAUGAGUCUAUGA------------------------AAUGAGACGAAACUCAUA
AJ241845.1/282-335 GAUGAGUC-UGUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUCAUG
AF170504.1/284-337 GAUAAGUC-UGUGCUA------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUUAUC
AF170520.1/282-335 GAUAAGUC-UGUGCUU------AGCACACUGAUGAGUCUCUGA------------------------AAUGAGACGAAACUUAUC
AF170503.1/280-333 GAAAGGUC-UGUGCUU------AGCACACUGACGAGUUCCUGA------------------------AAUGGAACGAAACCUUUU
AF170503.1/55-3    CAUAAGUC-UGGGCUU------AG-CCACUGACGAGUCGCUGG------------------------GAUACGGCGAAACUUAUG
AJ005305.1/56-3    CAAAAGUC-UGGGCUA------AGCCCACUGACGAGCCGCUGG------------------------GAUACGGCGAAACUUUUG
AF170519.1/55-3    CAUAAGUC-UGGGCUU------AG-CCACUGAUGAGCCGUUGA------------------------GAUACGGCGAAACUUAUG
AF170523.1/55-3    CAAAAGUC-UGGGCUU------AG-CCACUGAUGAGCCGUUGA------------------------GAUACGGCGAAACUUUUG
AF339740.1/56-3    CAUAAGUC-UGGGCUU------AGCCCACUGAUGAGCCGUUGA------------------------GAUACGGCGGAACUUAUG
AF170509.1/56-3    CAUAAGUC-UAGGCUU------AGCCCACUGAUGAGCCGUUGA------------------------GAUACGGCGAAACUUAUG
AF339739.1/56-3    CAUAAGUC-UGGGCUU------AGCCCACUGAUGAGGCGUUGA------------------------GAUACGGCGAAACUUAUG
AJ005318.1/56-3    CAUAAGUC-UGGGCUA------AGCCCACUGAUGAGCCGUUGA------------------------GAUACGGUGAAACUUAUG
AJ005319.1/56-3    CAUAAGUC-UGGGCUA------AGCCCACUGAUGAGCCGUUGA------------------------GAUACGGCGAAACUUAUG
AJ241828.1/56-3    CAUAAGUC-UGGGUUA------AGCCCACUGAUGAGCCGUUGA------------------------GAUACGGCGAAACUUAUG
AJ005322.1/56-3    CAUAAGUC-UGGGCUA------AGCCCACUGACGAGCCGUUGA------------------------GAUACGGCGAAACUUAUG
AJ241831.1/56-3    CAUAAGUC-UGGGCUA------AGCCCACUGAUGAGCCGUUGA------------------------GAUACGGCGAAACUUCUG
AJ005298.1/56-3    CAUAAGUC-UGGGCUA------AGCCCACUGAUGAGCCGUUGA------------------------GAUACGGCGAAACUUUUG
AJ241819.1/56-3    CAUAAGUC-UGGGCUA------AGCCCACUGAUGAGCCGUUGA------------------------AAUACGGCGAAACUUUUG
AJ005303.1/56-3    CAAAAGUC-UGGGCUA------AGCCCACUGAUGAGCCGUUGA------------------------GAUACGGCGAAACUUUUG
AJ550900.1/56-3    CAUAAGUC-UGGGCUA------AGCCCACUGAUGAGCCUUUGC------------------------GACAAGGCGAAACUUAUG
AJ550899.1/56-3    CAUAAGUC-UGGGCUA------AGCCCACUGAUGAGCCUUUGC------------------------GAUAAGGCGAAACUUAUG
AJ241838.1/56-3    CAAAAGUC-UGGGCUA------AGCCCACUGAUGAGCUGCUGA------------------------AAUGCGGCAAAACUUUUG
AJ005312.1/56-3    CAAAAGUC-UGGGCUA------AGCCCACUGAUGAGCCGCUGA------------------------AAUGCGGCUAAACUUUUG
AF170499.1/56-3    CAAAAGUC-UGGGCUA------AGCCCACUGAUGAGCCGCUGA------------------------AAUGCGGCGAAACUUUUG
AJ005310.1/56-3    CAUAAGUC-UGGGCUA------AGCCCACUGAUGAGCCGCUGA------------------------AAUGCGGCGAAACUUUUG
AJ241840.1/56-3    CAGAAGUC-UGGGCUA------AGCCCACUGAUGAGCCGCUGA------------------------AAUGCGGCGAAACUUUUG
AJ241841.1/57-3    CAAAAGUU-UGGGCUAA-----AGCCCACUGAUGAGCCGCUGA------------------------AAUGCGGCGAAACUUUUG
AJ241843.1/56-3    CAUAAGUC-UGGGCUU------AGCCCACUGAUGAGCCACUGA------------------------AAUGCGGCGAAACUUUUG
AJ550912.1/56-3    CAAAAGUC-UGGGCUA------AGCCCACUGAUGAGUUGCUGA------------------------GAUGCGACGAAACUUUUG
AJ550911.1/56-3    CAAAAGUC-UGGGCUA------AGCCCACUGAUGAGUUGCUGA------------------------AACGCAACGAAACUUUUG
AJ550907.1/56-3    CAUAAGUC-UGGGCUU------AGCCUACUGAUGAGUCGCUGC------------------------GAUGCGACGAAACUUAUG
AJ550906.1/56-3    CAUAAGUC-UGGGCUU------AGCCCACUGAUGAGUCGCUGC------------------------GAUGCGACGAAACUUAUG
AJ550909.1/56-3    CAUAAGUC-UGGGCUU------AGCCCACUGAUGAGUUGCUGC------------------------GAUGCAACGAAACUUAUG
M83545.1/56-3      CAUAAGUC-UGGGCUA------AGCCCACUGAUGAGUCGCUGA------------------------AAUGCGACGAAACUUAUG
AJ536615.1/1-44    ---------GGGUGGUG-UGUACCAUCCCUGAUGAGUCCAA----------------------------AAGGACGAAAUGG---
M17439.1/1-48      ---------ACCGGAUGUGCUUUCCGGUCUGAUGAGUCCGU----------------------------GAGGACGAAACAGGAC
AJ536614.1/206-152 UCACCGUC-GGAAAGUG-UGCGCUUUCCCUGAUGAGCCCAA----------------------------AAGGGCGAAACGGUAC
AJ536612.1/206-152 UCACCGUC-GGAAAGUG-UGCGCUUUCCCUGAUGAGCCCGA----------------------------AAGGGCGAAACGGUAC
AJ536620.1/206-152 CCACCGUC-GGAAAGUG-UGCGCUUUCCCUGAUGAGCCCAA----------------------------AAGGGCGAAACGGUAC
AJ536619.1/206-152 CCACCGUC-GGAAAGUG-UGUACUUUCCCUGAUGAGUCCGA----------------------------AAGGACGAAACGGUAC
#=GC SS_cons       :((((((,.<<<<<___.___._>>>>>,,,,,,,<<<<____........................____>>>>,,,)))))):
#=GC RF            caccAGUC.gGggCuUG.aGu.aGccCcCUGAUGAGuCugUGA........................aAuAaGaCGAAACUggug
//
# STOCKHOLM 1.0

#=GF AC   RF00009
#=GF ID   RNaseP_nuc
#=GF DE   Nuclear RNase P
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Mifsud W; 0000-0002-9805-6461
#=GF SE   Brown JW, The Ribonuclease P Database, PMID:9847214
#=GF SS   Published; PMID:9847214
#=GF GA   28.00
#=GF TC   28.00
#=GF NC   27.90
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 16.14 -Z 549862.597050 CM SEQDB
#=GF CL   CL00002
#=GF DR   URL; http://jwbrown.mbio.ncsu.edu/RNaseP/home.html;
#=GF DR   SO; 0000386; RNase_P_RNA;
#=GF DR   GO; 0008033; tRNA processing;
#=GF DR   GO; 0004526; ribonuclease P activity;
#=GF DR   GO; 0030677; ribonuclease P complex;
#=GF RN   [1]
#=GF RM   9759486
#=GF RT   Ribonuclease P: unity and diversity in a tRNA processing ribozyme.
#=GF RA   Frank DN, Pace NR
#=GF RL   Annu Rev Biochem 1998;67:153-180.
#=GF RN   [2]
#=GF RM   9847214
#=GF RT   The Ribonuclease P Database.
#=GF RA   Brown JW
#=GF RL   Nucleic Acids Res 1999;27:314.
#=GF RN   [3]
#=GF RM   11142387
#=GF RT   Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA.
#=GF RA   Frank DN, Adamidi C, Ehringer MA, Pitulle C, Pace NR
#=GF RL   RNA 2000;6:1895-1904.
#=GF RN   [4]
#=GF RM   12045094
#=GF RT   Eukaryotic Ribonuclease P: A Plurality of Ribonucleoprotein Enzymes.
#=GF RA   Xiao S, Scott F, Fierke CA, Engelke DR
#=GF RL   Annu Rev Biochem 2002;71:165-189.
#=GF RN   [5]
#=GF RM   15811915
#=GF RT   Structural implications of novel diversity in eucaryal RNase P RNA.
#=GF RA   Marquez SM, Harris JK, Kelley ST, Brown JW, Dawson SC, Roberts EC, Pace NR
#=GF RL   RNA. 2005;11:739-751.
#=GF CC   Ribonuclease P (RNase P) is a ubiquitous endoribonuclease, found in
#=GF CC   archaea, bacteria and eukarya as well as chloroplasts and mitochondria.
#=GF CC   Its best characterised activity is the generation of mature 5'-ends of
#=GF CC   tRNAs by cleaving the 5'-leader elements of precursor-tRNAs. Cellular
#=GF CC   RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its
#=GF CC   catalytic activity in the absence of the protein subunit, i.e. it is a
#=GF CC   ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown
#=GF CC   to retain its catalytic function, but is still essential for the catalytic
#=GF CC   activity of the holoenzyme. Although the archaeal and eukaryotic
#=GF CC   holoenzyme s have a much greater protein content than the bacterial ones,
#=GF CC   the RNA cores from all the three lineages are homologous -- helices
#=GF CC   corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular
#=GF CC   RNase P RNAs. Yet, there is considerable sequence variation, particularly
#=GF CC   among the eukaryotic RNAs.
#=GF WK   Nuclear_RNase_P
#=GF SQ   116


AF440361.1/5-337             UCAGGG----UGAAGCUUGUGUU--------------AGGUG-CAAACAUACG----------------CCCACCGUCC-------UCUUCAAGAG---CGGC-GG--UGGUACCUCAUUC------------AGUGCACUUGGG-AAGGUCUGAGGA--------------------AGCCGACA---------------------------------------------------------------------------------------------------AU-CUCUAAGCGGGAG-----------------------U-CCCUCUCAA----GAGGG-A---------------------------------GCUCGGGG-ACCAGAAAC-------GACA-CUCGCGCG----CUUUAGGGACCGGAGAGCUGGCACACGACCGCAGGGCGACCUGCGCGAUGCCCACACCACACACUC-------------------------------------------------------CGCCCCGCGCC-UGGUGAACC---GACCCGGG----UGGCU---AGCAACUAU----------------------------------------------------------------------------------------------------------------------------------------CAGUUCAAUACA-CAAAGCCGU---------------------------------------CAUC-G--A-CAGGC--AACUCAAUUCAGACUAC-----UCUCA-CC--CUGA
AY627759.1/1-246             AGGAAU---UAGGAGGGGCGCCA--------------CCGAC-----------------------------------------------CGCG--------------------------------------------GUCGGGGG-AAGGUCUGAG-----------------------GUCAU-----------------------------------------------------------------------------------------------------UU-UCCGUGA-GGGAG-----------------------G-CGCGCCAAC----GCGUG-C---------------------------------AGCAGUCGCACCAGAAAC-------CAAGAGCCUCUGU----GCUUAUGCCAGGAGGAGGGCCUUGCCCGACUGAGAGUG---------------------------------------------------------------------------------------------CUCGCUGAAAG----AGGCUGC-----GAC-G-CGGGUUAUUC-----------------------------------------------------------------------------------------------------------------------------------------AGUUCGAUGCG-CCCAGGCUG-AC------------------------------------GGUA-GGAC-G-CCU--AACCCGAUUCAGACUAC-----UCCUUGGU--UCCU
AF186214.1/1-364             ------------------------------------------------------------------------------------------------------------------------------------------------------------AAACGCA------------GAGGACCAGAACUUUGGGACGGGAGGCGGGGGUUUUGUUCGCAGGCUCCUUCUUCCCGCUCCUGGUUCUACGCGGCGUGCGCUGUACCACCAUCGGUGGUUAUGGCGCUUAC-CCCGUGA-GGGGG-----------------------G-CUUGGGGAA----CCGAG-UCU------------------------------AGCGUUGUU-AUAAGAAAU------CAAU--CUUUUGGA----UCCAGCCAGGGUCCUCUAGCAGAAAAGGGGGAUGGGGCUCUCUUGGGCUCUCCCCUCCACGCCUG----------------------------------------------------------CGGGAUUCU--GAUGGGAA---UGACAACGG--UCGGUCC-AUUUGACUUUAUCAUUACGAUGGUUCUAGUC----------------------------------------------------------------------------------------------GUGUUAUGGUAAAGGUCUGUUGAGUGCAAUUGU-AGAGCAAAU-UG------------------------------------AUU---CAA-U-UUG--AA----------------------------------
AF186218.1/1-219             -----------------------------------------------------------------------------------------GAAC---------------------------------------------------------------ACAGC----------------GAGACAACAAUCGCCAGGGGC----------------------------------------------------------------------------UUCGGCCCUGAUU-CUCGUGA-GAGAA-----------------------G-CCGCUGGAA----AGCGG-UUGU----------------------------GGGCGCUGUC-AUCAGAAAU------ACACAUGUUGGCCG----GCGCUAUCGCCGCACCAAU-----------------------------------------------------------------------------------------------------------------GUGAUGGGAA---AGGCAGCGG--AUGUCUC-GUUUGACUUUGCCUUAGGGUA-------------------------------------------------------------------------------------------------------------------AAGGUCUGUUGAGUGCAAUGGU-AGGAGGCCG-CU------------------------------------UUAU--GGU-G-GCC--AA----------------------------------
L12750.1/272-598             AACAGU----GGCAUUCCUACUAC-----------AAACCUG-UUUGCACAAG-----------------GAGCGGUCG-------GCGUCAG---------U-CG--CACCCUGCUCAGA------------AAUACAGGUGGG-AAAUUCGGUGAAACGCGG-----------CGGAGCAACUAUUUCCGAGGGCCGU-------------------------------------------------------------------------UCUCGGUCCUGAUU-UCCGUGA-GGAAA-----------------------G-CGUUUGGAAU-UUAAACG-CUU-----------------------------GGACGUUGUC-AUCAGAAAU------ACACCAGUCUCUUG----GC----------------------------------------------------------------------------------------------------------------------------------UGGAUGGGAA----GGCAGCGG---AUGCUC-CGUUUGACUGUGUUUAGCUUCGGC------------------------------------------------------------------------------------------------------------GACACAGGUCUGUUGAGUGCAAUCGU-AGGACACUU-C-------------------------------------UUAU---GA-G-GUG--AACCCGAUACCGAUUAU-----U-GCC-GG--UGUU
AF186221.1/4-232             -------------------------------------ACCUG-CCCACAAAAG-----------------GAGC--U------------CCGU------------G--CUCAGAAUUAC-----------------GCAGGUGGG-AAAUUCGGUGGUU-CAC------------GCUGUCCAACAUUAC--------------------------------------------------------------------------------------------CCUUU-CUCUUGA-GAGAUC---------------------CU-GGCGAGGAA----UCGCU-GG--------------------------------GUGCGGCC-AUAAGAAAU-------CAGCCCCCUAAAA----AG----------------------------------------------------------------------------------------------------------------------------------GGCAUGGGA-----GGCUGCA----CGGAC---AGUUGGUCCUUGGAAAGA-----------------------------------------------------------------------------------------------------------------------GGGCUAUUGAGUGCAAUAUA-CAGACUGGG-GG-----------------------------------CUUUG-GCCC-C-UGG--AA----------------------------------
AF186222.1/1-314             UUCUCA----UCAAAGUCUGUAUU------------UACCUG-CCUACACAAG-----------------GGGCCCUCUUC----CCCCAGAG---------G-GA--CCCAGCAGGAG------------------CAGGUGGG-AAAUUCGGUGGUA-CAC------------GCCGCCCAUUAAUU-----------------------------------------------------------------------------------------------UCU-CUCUUGA-GAGAGU---------------------CCAGGCGAGGAA----UCGCUAGG--------------------------------GUGUUGCC-AUAAGAAAU------UCAGUCCGCCUAGC----G-----------------------------------------------------------------------------------------------------------------------------------GGCAUGGGA-----GGCUUCA----CGGGC---GGUUGGUCCCUAGUGCAAAACUUUC--------------------------------------------------------------------------------------------------------GCGCUAGGAGGCUUUUGAGUGCAAUAUA-CAGACCGCC-UAGUGGUUC----------------------CUUGGGAUCAU-CUGG-G-CGG--AACGCGAUACCGAUUAU-----UUUGG-UG--AGAA
AF186220.1/1-189             ------------------------------------------------------------------------------------------------------------------------------------------------------------GUU-CUC------------UCCGUCCACGGAGGCAGGUUUCUGC-------------------------------------------------------------------------CUUCGCACAAAAUG-CUCCUGA-GAGCGU--------------------CCU-GGCGCGAAA----GCGCC-GG--------------------------------GCAGGGCC-AUCAGAAAU-------CAGUCGAGUUUAC----UU----------------------------------------------------------------------------------------------------------------------------------GGCAUGGGA-----GGCUCUG----CGGACG-GUUGGUCAUGUGUAUGAAC----------------------------------------------------------------------------------------------------------------------AUGGCUAUUGAGUGCAAUAUG-CGAACCUU----------------------------------------GAAA------A-AGG--CA----------------------------------
AF186219.1/1-333             ---------------UUCCCUCCAAAGUCUGUAUUUUACCUG-CCUACAAAAG-----------------GAGGAGUCCC------CGGCGGA---------CUUC--CUCAGUAUUCG------------------CAGGUGGG-AAAUUCGGUGAAAUCGC------------UCUGCCCACCAGGGAAAAGGUAAAACUCUCCCUGGU--------------------------------------------------CCUUGGAAGGACUUGUCCUUCUGAGU-CUCGUGA-GAGAUG---------------------CCAAGCGUGGAG----ACGCUAGG-------------------------------GUGGUCGCC-AUAAGAAAC------UUCAACAGGUCACA----CU----------------------------------------------------------------------------------------------------------------------------------GUUAUGGGA-----GGCGCCA----CGGGC---AGUUGGUCCCUUUGCAUCCAGAAGG--------------------------------------------------------------------------------------------------------AAGCUUUGGGGCUGUUGAGUGCAAUAUA-CAGAGCGCU-AGAAGGA--------------------------GUCCUUCCU-UCUACG-CGU--AA----------------------------------
L12748.1/280-607             GCAGUA----GCAACUCCUACGAUU---------UUAACCUG-CUUACGAAC------------------UAUUAGU-----------CUGAU---------C-UA--AUAAUACAUG-------------------CAGGUGGG-AAAUUCGGUGAAA-CACAACAAAUGAGGUUUCAGUUAUUUG--------------------------------------------------------------------------------------------------GG-CUCGUGA-GAGCA-----------------------G-CCUGGGGAA----CCUGG-UUAUA--------------------------AUAGCGGCGCU-AUCAGAAAU-------UCAACGCUAUCAA----AUUUUGAUG---------------------------------------------------------------------------------------------------------------------------GUGAUGGGAA---CGGCGCUAG---CAACA---AACAUAUUUUAUGUACCUCACGUGUUUGACUUA----------------------------------------------------------------------------------------AUCAUUUACUGGUUAAAGUCUGUUCAGUGCAAUCGU-AGGACUUCU-AA------------------------------------GCAA--UUA-G-UUG--CACCCGAUACCGAUCAA-------UGG-UA--CUGU
U18530.1/28436-28079         ACAGUG----GUAAUUCCUACGAUUA-------AGAAACCUG-UUUACAGAAG-----------------GAUCCCC------------ACCUAUG---GGCG-GGUUAUCAGAUAUUA-----------------UCAGGUGGG-AAAUUCGGUG----------------------GAACACAGUGGAGCCUUGUCCUCCGGGUUAA------------------------------------------------------UGUCGCUUUUGGCAUUGGCCCCUG-CUCCUGA-GAGAAGAA-----------------AUAU-ACUGGGGAA----CCAGU-CUUUA-------------------------CCGACCGUUGUU-AUCAGAAAU------UCACGGAGUUCGGC----CUAGGUCGGACU------------------------------------------------------------------------------------------------------------------------CCGAUGGGAA---CGGCAACGG--UUGUUCC-GUUUGACUUGUCGCCCGCUACGGCGUG-------------------------------------------------------------------------------------------------------AGCGUCAAGGUCUGUUGAGUGCAAUCGU-AGGACGUCA---------------------------------------UUAG----U-G-GCG--AACCCGAUACCGAUUAC-------UGC-UG--CUGU
AF186227.1/8-344             ACAGCG----ACGACUCCUACGACUU-------AGAGACCUG-UUUACACAAG-----------------GAGGGU--------------------------A-CC--CUCCCUCAACC----------------AACAGGUGGG-AAAUUCGGUGAA--------------------ACACAGUGGAAUCAUUCCUUCCAGCCUGGGCUCGC----------------------------------------------UUCCUUCGGGAAGCUAGGCUCAGGUCUU-UCCGUGA-GGACAGC-------------------CUA-GCCGGGGA-----CCGGU-CUGCC--------------------------UGGACGUUGUU-AUCAGAAAU------UCACACGGGUAACC----------------------------------------------------------------------------------------------------------------------------------------GUGAUGGGAA----AGCAACG----AGUGU---UUUAUUUGACGGGCUUCUGUUUACAC-------------------------------------------------------------------------------------------------------AGUGGUCCAGUCUGUUGAGUGCAAUCGU-AGGACAUGC-C-------------------------------------CUAG---GG-C-UUG--AACCCGAUACCGAUUAC-------CGU-CC--UUGU
AF186224.1/13-452            -----------UGAUUCCUACGUUUU-------AAGAACCUG-UUUACAGAAG-----------------GAGGAUA------------ACACUUUAGUGCUU-UU--CUCAUAUAAGU-----------------UCAGGUGGG-AAAUUCGGUGAAA-CACA-----------GCGGAACCAACAACAUCUACCAAGGUGUCGUUGCCCUCCCCAAGCCUAGA-----------------------CGGUGUCUUCUUCUAGGAGGAGCUUAAGUCCAGGUCCUU-CCCGUGA-GGGCAGUUUUCUUUGCAAUUUUAAAUUUU-ACUGGGGAA----CCGGU-CUGCCUAAAAAUUGCCAUUGAAGAAUUUAUUGGGACGUCGUU-AGCAGAAAU------UCACAGAGACCUCU----UUCAAAGAAAUUGGUCC-------------------------------------------------------------------------------------------------------------------CUGAUGGGAA---CAGCGACGG--UAGUUCC-AUUUGACUUGUGGUGUGAAAUAAUAUC-------------------------------------------------------------------------------------------------------GACCAUAAGGUCUGUUGAGUGCAAUCGU-AGGACAGAU-UUG----------------------------------AUUUG-AAAA-U-CUG--AACCCGAUCCCGACCAC-------UG----------
L12746.1/287-642             UGGAACAGUGGUGAUUCCUACGAUUA-------AGAAACCUG-UUUGCAAAAG-----------------GGCCUGC------------CCAC--------GC-GG--GUCAUCUUAUUU---------------AUCAGGUGGG-AAAUUCGGUG----------------------GAACACAGUGGAGCCUUGCCUUCCGGGCCA---------------------------------------------------------UUGUCUCUGGCAGUGGCCCCUG-CUCGUGA-GAGAAGAA-----------------ACUU-GCUGGGGAA----CCAGU-CUUUA-------------------------CCGACCGUUGCU-AUCAGAAAUU-----GAACGGGGCCCGGU----CCCGCCGGGCC-------------------------------------------------------------------------------------------------------------------------UCGAUGGGAA---CGGCAACGG--UUGUUCC-GUUUGACUUGUCGCCCGCCACGGCGC---------------------------------------------------------------------------------------------------------GCUGCAAGGUCUGUUGAGUGCAAUCGU-AGGACGCCA---------------------------------------UUCG----U-G-GCG--AACCCGAUACCGAUUAC----UGCUGCUGC--UCCA
AF186229.1/1-295             ---------------UCCUACGAUUU-------AGAAACCUG-UUUGCUAACG-----------------GAGUC--------------UCAG-----------GG--CUCACACUAAU----------------AGCAGGUGGG-AAAUUCGGUGAAU-CACU-----------GCGGAACCCGACAGAGCCUAACAAGCUUUGUC----------------------------------------------------------GACCGGUUGCCUUGGCGACUUU-UCCGUGA-GGAGG-----------------------G-CCUGGGGAA----CCAGG-CUCAU-------------------------AUGGUCAUUGUC-ACAAGAAAU-------CAACUCGGUAGUC----CUGUACUAUCG-------------------------------------------------------------------------------------------------------------------------AGGAUGGGAA----GGCAAUGG--ACGUUCC-GUUUAACUUGAUCUCAUCA----------------------------------------------------------------------------------------------------------------------AGGUUUGUUGAGUGCAAUCGU-AGGAC-GGU---------------------------------------CUUA-G--A-C-CUG--AA----------------------------------
AF186233.1/1-295             ---------------UCCUACGCAAU--------UUUACCUG-CCUUCAUAAG-----------------GAACUC--------------AAA---------G-GG--UUCAGUUAGUACUUAACUUACUAUAUAAGCAGGUGGG-AAAUUCGGUGGAA-CUCU-----------AAGAGACAAUCAGCCGGAUCUUUAGCUU------------------------------------------------------------------AAUUGUUAAAGAACUGUU-UCCGUGA-GGAAA-----------------------G-UCUGGGGAA----CUGGA-CUUG---------------------------CAGCUGCUGUC-ACAAGAAAU-------CAACGCCCUUUGU----UGG---------------------------------------------------------------------------------------------------------------------------------UGGAUGGGAA----GGCAGUAG--AGGUCUC-UUUUGGCUUGGAUGCAAAUUUGGAC-----------------------------------------------------------------------------------------------------------GUCCAAGGCUUGCUGAGUGCAAUCGU-GGGA--------------------------------------------CAAA-G-----------AA----------------------------------
AF186230.1/1-232             --------------GUUCUCUCCA-----------UCCAGAC--UUAUAGAUU-----------------GAAACUUUC--------CUUGAA---------A-GU--UUC--------------------------GGCUU--------------AUG-------------------AGUUACAAAC-------------------------------------------------------------------------------------------------UG-CUCUUGA-GAGCGUC-------------------CUU-AGCGUGCAA----ACGCU-GG--------------------------------GCGGUGCU-AUCAGAAAU------UUACCAGUCCUUAC----UUCGUAUUGGGAC-----------------------------------------------------------------------------------------------------------------------UGGAUGGGAA---UGGCACUGCGGAUGGUU---GGCCCUCUGAAUGAGAGAG---------------------------------------------------------------------------------------------------------------------AGGGCUUUUGAGUGCAAUAUG-CGAACUUGG---------------------------------------AUAU-U--C-C-AAG--AA----------------------------------
X52531.1/47-305              UACGGA----CAAACGCCGCACU--------------UCCUCAAAUUCAGACG-----------------CACUU--------------UUAC-----------AA--GUGUUACGCGCA---------------UUGAGGGGGU-AAGGUCGGAGGAA-CU---------------UCUUCGUUGCA-------------------------------------------------------------------------------------------------UG-CUCGUGAGGAGCG-----------------------G-AGGACGAAA----GUCCU-G----------------------------------CCGGGUGUACCAGAAAU-------UCGAUCUCUUGGU----UCGUCCUUUGAG------------------------------------------------------------------------------------------------------------------------AUCUUGAAAC---GCACCCGA-----GAAG---AUGUCUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCAAUGUG-CGGCACCUG-UG------------------------------------AAAA--GUC-A-GGC--AACUCGAUUCCGACUAA-----UCUUG-UC--UGUA
AL590447.1/87172-86932       GGCU------GGAAGCUUUCGAU-------------UAGGGG-----------------------------------------------CCUG--------------------------------------------CCCCUGGG-AAGGUCUGAGAUG-A-----------------GACGUC-----------------------------------------------------------------------------------------------------UA-GCCGAAA-GGGCA-----------------------C-UUGGUUAAU----GCCAA-GG--------------------------------GUCGUCCACAACAGAAACA-----CUCACUUCCCCCAU----GACCGGAACGGGAUGACUGGGGGG------------------------------------------------------------------------------------------------------------AGUUUGGAAA---UUGGACGA-----UGUC---UUAGACUCGA--------------------------------------------------------------------------------------------------------------------------------------AUAGUCCAACUCG-AAAGGCAGCCGU------------------------------------GUUC-CAUG-C-UGU--AACCAGAUUCAGACUAC-----UCUCCAGC--AGCC
AF440363.1/1-244             --------------------------------------------UUACACACG-----------------GAGACAG------------CCUUUG----GUUU-GU--CUCAGCAGAG-------------------CGCUUGGG-AAGGUC-GAGAA--------------------GGCCGAU----------------------------------------------------------------------------------------------------UU-CCCUCGGUGGGAA-----------------------U-GUCACGAAA----GUAAU-G----------------------------------CUUGGGG-ACCAGCAAU------GAGCCUGUUGAAGG----UCAGCACAAGAUCCCUUGAGCCAGGUGGUGAAGGGUGAUGCAGUAACCCCUCAGCU----------------------------------------------------------------------------AGGUUGGAAA----CCUCAAG----AGGCC---CAAAUCAUCG---------------------------------------------------------------------------------------------------------------------------------------AAGUUCAAUACA-CAAGGUGGC---------------------------------------AACA----G-C-CAU--A-----------------------------------
AF440364.1/1-258             --------------------------------------------UUACACACG-----------------GAGAUGGUCAGCACGCCUGAAUU---------C-AU-GCUCAGAGAAAG------------------CGCUUGGG-AAGGUCUGAGAA--------------------GGCCGAU----------------------------------------------------------------------------------------------------UU-CCCUUGGUGGGAA-----------------------U-GUCACGAAA----GUACU-A----------------------------------CUUGGGG-ACCAGCAAUG-----AUACCUGCUGAGGG----UAAGCACAAGAUCUCAGUGCCGGGUGGUGCUGGGUGAUGCGUUAUCAGCCCUUAGC---------------------------------------------------------------------------UUGGUUGGAAC---AACCCGAG----AGGCC---CAAAUCAUCA---------------------------------------------------------------------------------------------------------------------------------------AAGUUCAAUACA-CAAGGUGGC---------------------------------------UUCA-A--G-C-CAU--A-----------------------------------
AY726782.1/1-248             --------------------------------------------UUACACACG-----------------GAGACAG------------CCUUUG----GUUU-GU--CUCAGCAGAG-------------------CGCUUGGG-AAGGUCUGAGAA--------------------GGCCGAU----------------------------------------------------------------------------------------------------UU-CCCUCGGUGGGAA-----------------------U-GCCACGAAA----GUUAC-U---------------------------------GCUUGAGG-ACCAGCAAU------GUGCCUCUUGAGGG----CAAGCAGAAGAUCUCAGGACCAGGUGGUACUGGGUGAUGCGUUACAGCCCUCAGGU----------------------------------------------------------------------------UGGUUGGAAC---AACUCAAG----AGGCC---CAAAUCAUCG---------------------------------------------------------------------------------------------------------------------------------------AAGUUCAAUACA-CAAGGUGGC---------------------------------------UACC-A--G-C-CAU--A-----------------------------------
AF440362.1/1-328             ---------------AUCAAAAAAAAAA---AACUUUUGGCG----------------------------GGAAACUGU--------GCAAAA---------A-UU--UCCUCUGCCUG------------------CGCUUGGG-AAGGUCUGAGGU--------------------GUCGACUUUU-------------------------------------------------------------------------------------------------AU-CUCUUGGCGGGAAU---------------------CC-UCUCUCACG----AGGGA-G----------------------------------CUCAGGG-ACCAGAAAU-------GACC-CUUUCUCC----UUGGGUUGUCGCAGGCAAUGACUUGUGACCUGCCUAGGAUCGCUCUCUCUCUCUCUCUCUCCCUGGGGGAGGGAGGAGAGAG-----------------------AGGAGGAGGCAGGUUCCGAGGAGACAC-GGCUGGAACCAUACCUUGGG-----UGACA-CGAUGAACCAAUG-----------------------------------------------------------------------------------------------------------------------------------UUAAGUUCAAUACA-CAAGGCCAC-AC------------------------------------AUGA--CUG-U-GGU--A-----------------------------------
AC008221.5/55056-54762       UCAGUU----GCAAACUAGCAUC-------------UGGGGC--CCACACAAC-----------------GAGUAU-------------CUGA---------U-UA--CUCCACAAACCA---------------UUGCCCCGGG-AAGGUCUGAGAAU-C-----------------GGCCGAGCCAGCUGUUUGU------------------------------------------------------------------------------UGCGGCUUCAUU-UCCCAGCAGGAAA-----------------------C-CUGUGUGAU----UGCAG-G----------------------------------GCGAAAGUACCAGAAAU-------CCUGCUACCAGGU----GUUGCCGUUGCCCCCGGUGACCGCCGCCUGGUUG--------------------------------------------------------------------------------------------------GCAUUGAAAC----CUUUCGU-----GGCC---AGCGUUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-CUUGCUGCC---------------------------------------UCUA-A--G-G-CAG--AACUCAAUUCAGACUAA-----UCUGU-GA--CUGA
AF044331.1/5-307             GGAG------GGAAGCUCAUCAG--------------UGGGG--UCACAUGCA-----------------GGGUG-C------------UUGU-----------CA--CUCAACCAAUC-----------------ACCUUGGGG-AAGGUCUGAGACAAG-----------------AGCCAAUCAC-------------------------------------------------------------------------------------------------UU-CCCUAGCAGGGUA-----------------------U-CACCUG-------AUGUG-A----------------------------------GUGAGUG-CACAGAGAAU----AUGAGCCAUUGUGAG----CUGUCUUUACAGGAGAAACCAGCCAGUGCAGCUCUCCAGCACUACUGGUGGAUGUGACCU--------------------------------------------------------------------CACUGGCUUGGAAA----CACUCAU-----GGCU---GGCAUAUG------------------------------------------------------------------------------------------------------------------------------------------AGUGCAAUGUG-UGAGUUGGA-G-------------------------------------UACA-C-CU-C-CAG--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF004377.1/5-311             GGAG------GGAAGCUCAUCAG--------------UGGGG--UCACAUGUA-----------------GGGUG-C------------UUGU-----------CA--CUCAACCAAUC-----------------ACCUUGGGG-AAGGUCUGAGACAAG-----------------AGCCAAUCAC-------------------------------------------------------------------------------------------------UU-CCCUAGCAGGGUA-----------------------U-CACCUGAUC---UGGGUG-A----------------------------------GUGAGUG-CACAGAGAAU----AUGAGCCAUUGUGAG----UUGUCUUUACGGAAGAAACCAGCCAGUACAGCUCUCCAGCACUACUGGUGGAUGUGACCU--------------------------------------------------------------------CACUGGCUUGGAAA----CACUCAU-----GGCU---GGCAUAUG------------------------------------------------------------------------------------------------------------------------------------------AGUUUAAUGUG-UGAGUUGGA-G-------------------------------------UACA-C-CU-C-CAG--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
U50408.1/4-306               AGCGGA---AGGAAGCUCACUGU--------------AGAGG--UCACCCACU-----------------GAGUG-C------------UCGU-----------CA--CUCGCCAACA-------------------CCUCGGGG-AAGGUCUGAGACAGG-----------------AGCCACUCGC-------------------------------------------------------------------------------------------------UG-UCCUAGCAGGACA-----------------------U-CAUCUGAAU-----GAUG-A----------------------------------GCGAGUG-CACAGAAAAU-----CGGGUCACGCGCGC----GAUUCUCGCAGCAGACGUUGAUGCUCGCACACAUUCAGCGGAUCAACUGAUGCGACGCG---------------------------------------------------------------------CGCAGACUUGGAAA----CACUCGC-----GGCU---GGCGAAUG------------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-UGAGCUAGC-AU------------------------------------AAC---AUG-C-UAG--AACCCAAUUCAGACUAC-----UCUCCCUC--CGCU
AF004373.1/3-319             GGAA------GGAAGCUCACUGU--------------AGAGG--CUACUUGCU-----------------GGGUGC-------------UGUU---------GUUA--CUCUAUCAACC----------------AGCCUUGGGG-AAGGUCUGAGAUAAG-----------------AGCCACUUGU-------------------------------------------------------------------------------------------------UG-CCUUCACAAGGCA-----------------------U-UGCUUGGUG---UAAGCA-A----------------------------------GUGAGUU-CCCAUCAAAG-----AUGGCUCAGUUGCA----AGCUUAAUGCAAGAGACAUAGCAAAGAAGCCCAAUAUACUUCUGAUAUGGAUGCAAUGCC--------------------------------------------------------------------CAACAGACUGGAAA---UGACUCAC-----GGCU---GGCAUGUUC----------------------------------------------------------------------------------------------------------------------------------------AAGCUCAAUGAC-UGAGGGGAA-GCA---------------------------------AGUGAU-GGCU-U-CCU--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF004374.1/2-403             GGAA------GGAAGCUCACUGU--------------AGAGG--UCAUGUACG-----------------GAGUGCG------------UCACAACUGUGAUGUCA--CUCCAUUAAUU------------------CCUCCGGG-AAGGUCUGAGACAGG-----------------AGCCAUUAGC-------------------------------------------------------------------------------------------------UG-CCCUCACAGGGCG-----------------------U-CACCUGAGU----GGGUG-A----------------------------------GUGAGUC-CCCAGCAACC-----CCACGCUGGAGUGG----ACCGGCUCGACACGUGGAGUGGGCUCUGCAGGAGAGGCGGGGUGGACUGCAGUGAGAGGGUGGAGUUACAGAUUGACACUCCCACCCAACUCA--GUGAGGCUCCGCCCAGCUGAUGCCGCCCCCUCCCCGGGCCUUGGAAG---UGGCUCAC-----GGCU---GGCUGUGUU-----------------------------------------------------------------------------------------------------------------------------------------AGUCCAAUGGC-UGAGGUGGA-GCAGCUGCAC--------------------GGGAUGUGUGCG-CGCC-C-CAU--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF004372.1/3-405             GGAA------GGAAGCUCACUGU--------------AGAGG--UUACAUACU-----------------GAGUGCG------------UCAAUUCUGUGAUGUCA--CUUCAUUAUUC------------------CCUCCGGG-AAGGUCUGAGACAAG-----------------AGCCAAUAGC-------------------------------------------------------------------------------------------------CG-CCCUUACAGGGCG-----------------------U-CACUUGAGC----GGGUG-A----------------------------------GUGAGUC-CCCAGCAACC----CCACGGUGGAGUGGA----CCGGCCCGCUGUGUGGAGGAGGCUCUGCAGGAGAGGCGGGGUGGGCUUGUGGUGAGAGGGAGUGGUCGCAGAUUGAGGCUGCUCCCACCUUAC--ACACGGCUCCACCCGGCUGAUGCUGCCUCCUCCCCGGGCCUUGGAAG---UGGCUCUC-----GGCU---GGCUGUAUG-----------------------------------------------------------------------------------------------------------------------------------------AGUCCAAUGGC-UGAGGUGGG-GCAGCUGCAC--------------------GGGAUGUGUGCG-CGCC-C-CAU--AACCCAAUUCAGACCAC-----UGUCCGGA-AUUCC
AF004371.1/7-309             GGAG------GGAAGCUCAGUGC--------------UGAGG--CUACAACCU-----------------GAGUGC-------------AUUU---------GUCA--CUCUCAUACAU-----------------UCCUCAGGG-AAGGUCUGAGAUUAG-----------------AGCCAUCUAU-------------------------------------------------------------------------------------------------UG-UCUUAACAAGGCA-----------------------U-UGCUUGGUU---UGAGCA-A----------------------------------AUGAGUU-ACCAUCAAAC-----CUUGUUCUGUUGUC----GCUAGACUGCACAAGUAAUAGAAGUGGUUUUCCUCUAUGGAUGCUGAGGCAAC------------------------------------------------------------------------------UGAUUUGGAAA--GUGACUCAU-----GACU---AGCAAAUUC----------------------------------------------------------------------------------------------------------------------------------------AAGUUCAAUUGC-UGAGAGGAA-GU------------------------------------CAUU--ACU-U-CCU--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF044330.1/1-316             AGAUGUGGAGGGAAGCUCAGUGC--------------UGAGG--CUACAGACA-----------------GAGUGCU------------GGGG---------GUCA--CUCAGUGAGUG----------------UGACUCAGGG-AAGGUCUGAGAUUAG-----------------AGCCCCUUGC-------------------------------------------------------------------------------------------------UG-CUCUCACAGGGCA-----------------------U-CACUUGGAU---GAAGUG-A----------------------------------GUGGGUA-CUCAGAAAGC-----UUGGCUCUGAUUGG----CCAGUGAGUGCAAAAGAUGCAGUGAGUGCUCCUGGGUUGAGCUCCUGUAGAUGCAAAGGC--------------------------------------------------------------------AUCAGGCUUGGCAC----UGCCCAC-----AGCU---GGCACAUUC----------------------------------------------------------------------------------------------------------------------------------------AAGCUCAAUGGC-UGAGAGGG----------------------------------------AACU-G----C-CNC--AACCCAAUUCAGACUACUU-UUUUUCC-AC--AUUU
AF044737.1/3-396             GGAA------GGAAGCUCACUGU--------------AGAGG--UCACGUGCU-----------------GAGUGCG------------UCACGCUUGUGAUGUCA-UCUCUAUCCCA-------------------CCUCCGGG-AAGGUCUGAGACAGG-----------------AGCCCCUCGC-------------------------------------------------------------------------------------------------CG-CCCUCACAGGGCG-----------------------U-CACCUGAUAU-UCGGGUG-A----------------------------------GUGAGCC-CCCAGCAACC-----CACGUUGGAGUGGA----CCGGUCCGUUAUGUGGGAGAGGCUAUGCAAAAGACGCCGAGCAGGGAUGUGGUGAGAUGGGCGGGUCACUGAUUUGAGGCCCGCCUACUCUUCAUCUGCGCCUCUGCCUGGUGGAUGCCGCCUCCUCCCCGGACCUUGGAAG---UGACUCAC-----GGCU---GGCUUACUG-----------------------------------------------------------------------------------------------------------------------------------------AGUCCAAUGGC-UGAGGCGAG-GCA---------------------------------GCUGUG-CGCC-U-CGU--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF077370.1/3-396             GGAA------GGAAGCUCACUGU--------------AGAGG--UCACGUGCU-----------------GAGUGCGUCAC---UCUUGUGAU---------GUCA-UCUCUAUCCCA-------------------CCUCCGGG-AAGGUCUGAGACAGG-----------------AGCCCCUCGC-------------------------------------------------------------------------------------------------CG-CCCUCACAGGGCG-----------------------U-CACCUGAUGU--CGGGUG-A----------------------------------GUGAGCC-CCCAGCAACC----CCACGUUGGAGUGGA----CCGGUCCGUUAUGUGGGAGUGGCUAUGCAAAAGACACCGGGUAGGGGUGUGGUGAGAUGGGCGGGUCACUGAUUUGAGGUCCGCCCACUCUUCAUCUGCACCUCUGCCUAGUGGAUGCCGCCACCUCCCCGGACCUUGGAAG---CGACUCAC-----GGCU---GGCUUGCUG-----------------------------------------------------------------------------------------------------------------------------------------AGUCCAAUGGC-UGAGGCGAG-GCA---------------------------------GCUGUG-CGCC-U-CGU--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF044328.1/3-325             GGAA------GGAAGCUCACUGU--------------AGAGG--UCAUGUGCC-----------------GAGUAC-------------AUUU---------GUUA--CUCUCUCA---------------------CCUUGGGG-AAGGUCUGAGACAAG-----------------AGCCGUUUC--------------------------------------------------------------------------------------------------UG-UCCUUGCAGGACA-----------------------U-CUUCCGAGC---CGGGAG-A----------------------------------GCGAGCU-CCCAGACACU-----CGGUGCAUGGAGGG----GUUUGCACAAGAUGCUAGUUAGUAGUUGGUGGCUUGAUACUGCCUUCCCUGGACUAGUUGAUGCCU--------------------------------------------------------AUUCAUCUGGGCAUUGGAAG---UGGCUUGU-----GGCUAGCAUGGCACUG-----------------------------------------------------------------------------------------------------------------------------------------AGUCCAAUGGA-UGAGGUGAG-GC-----------------------------------AACUG-UGCC-U-CAU--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF004375.1/3-306             GGAA------GGAAGCUCACUGU--------------AGAGG--CUACAUGCA-----------------GAGUGC-------------AUAU---------GUCA--CUCAAGUA---------------------CCUUGGGG-AAGGUCUGAGACAGG-----------------AGCCGGUAAU-------------------------------------------------------------------------------------------------UG-CCCCAGCAGGGCA-----------------------U-CCCCUGAAA----AGGGG-A----------------------------------GCGAGCU-CCCAGAGACC-----CGGGGCCCAAAGGG----GGUGGCAUGAGACGCGUGACCGUGUAUCUGGUACUCGCUGAUGCUUACUCCUUCCG---------------------------------------------------------------------------GGCAUUGGAAG---UGGCUCGC-----GGCU---GGCACUCCCC--------------------------------------------------------------------------------------------------------------------------------------UGAGUGCAAUGGC-UGAGGUGAG-GU------------------------------------AAUGGCGCC-U-CAU--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF044327.1/3-330             GGAA------GGAAGCUCACUGU--------------AGAGG--UCACGCGCU-----------------GGGUGUA------------UCGA---------U-CA--CCCUCCUUGCU-----------------ACCUUUGGG-AAGGUCUGAGAGAAG-----------------GGCCAAGUGU-------------------------------------------------------------------------------------------------CG-CCUUAGCAGGGCG-----------------------C-CAUCUUAGG---AAGGUG-G----------------------------------GUGAGUU-CCCAGCAAUA-----GGGGUCUCCUGUAA----UGCCCCAGUUUGAGGCAGGAGAAGCGGGGCUGGAGGGGCUACUCCCUCCUUCCUGCGGAUGCCUCCG-----------------------------------------------------UGGCUUACGCGGGGCUUGGGAA---UGACUCAC-----GGCC---GGCAACGUU----------------------------------------------------------------------------------------------------------------------------------------GAGUACAAUGGGCAGAGGUGAA-GC------------------------------------GGCC--GCU-U-CAU--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF044325.1/3-327             GGAA------GGAAGCUCACUGU--------------AGAGG--UCACUCGCU-----------------GGGUGUC------------UUGA---------U-CA--CCCCCGUUGCU-----------------ACCUUGGGG-AAGGUCUGAGAGAAG-----------------GGCCAAGUGU-------------------------------------------------------------------------------------------------CG-UCCUAGCAGGGCG-----------------------C-CAUCUUAGG---AAGGUG-G----------------------------------GUGAGUU-CCCAGCAAUA-----UGGAUCUCCAGUAA----AGCCCUACUUUGAGGCAGGAGAAGCAGGGCUGGGGGGGUUCCCUCCUCCCUGCGGAUGCCUCCGUG--------------------------------------------------------GCUUACUCGGGGUUUGGGAA---UGACUCAC-----GGCC---GGCAACGUU----------------------------------------------------------------------------------------------------------------------------------------GAGUACAAUGGGCAGAGGUGGA-GC------------------------------------ACCC--GCU-U-CAU--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF044326.1/3-348             GGAA------GGAAGCUCACUGU--------------AGAGG--CCACUAGCU----------------UGGGUG-U------------CUAU-----------CA--CCCUACUUCCG------------------CCUGUGGG-AAGGUCUGAGGGAAG-----------------GGCCAAAUUG------------------------------------------------------------------------------------------------CCG-CCCUAGCAGGGUG-----------------------C-CACCUUCUG---AAGGUG-G---------------------------------AGUGAGUU-CCCACCAAUG-----UGGGUCUCCGAUGA----AGCCCUAGAAUUGAGGCAGGAGAAGCGGAGAGGGGUCGUGGGUCGUGGGUCGUAGGCAUCCUCCCCGCGGAUGC----------------------------------------CUCUGUGGCUCCGUUCGGGAUUUGAGAA---UGACUUAC-----GGCU---GACAGCUUU----------------------------------------------------------------------------------------------------------------------------------------GAGUACAAUGGGAAGAGGUGAA-GCA----------------------------------CCGCC-AGCU-U-CAUAUAACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF004376.1/3-330             GGAA------GGAAGCUCACUGU--------------AGAGG--CCACUAGCU----------------UGGGUG-U------------CUAU-----------CA--CCCUACUUCCG------------------CCUCUGGG-AAGGUCUGAGGGAAG-----------------GGCCAAAUUG------------------------------------------------------------------------------------------------CCG-CCCUAGCAGGGUG-----------------------C-CACCUUCUG---AAGGUG-G---------------------------------GGUGAGUU-CCCACCAAUG-----UGGGUCUCCGAUGA----AGCCCUAGAAUUGAGGCAGGAGAAGUGGAGAGGGGUCGUAGGCUCCUCCCCGCGGAUGCCUCUGUG-------------------------------------------------------GCUCCGUUCGGGAUUUGGGAA---UGACUCAC-----GGCU---GGCAGCUUU----------------------------------------------------------------------------------------------------------------------------------------GAGUACAAUGGGAAGAGGUGAA-GC-----------------------------------CCGCC-AGCU-U-CAU--AACCCAAUUCAGACCAC-----UCUCCGGA-AUUCC
AF191547.1/2290-1993         GGCGGA----GGAAGCUCAUCAG--------------CGGGG--CCACGUGCU-----------------GAGUG-C------------UCGU-----------CA--CUCUUCGG---------------------CCCCUGGG-AAGGUCUGAGACUGG-----------------GGCCUCCCGC-------------------------------------------------------------------------------------------------GG-CCCUAACCGGGCU-----------------------C-UCCCCGAGC----GGGGA-G----------------------------------GUGAGUU-CCCAGAGAGC-----AGGGCUCUACGCUU----GGGCAGACUGGGCAGGAGAAGCCCCGAGUCGGGGCGGAUGCCUCCCUCGCCGG-------------------------------------------------------------------------------AGCUUGGAAC---AGACUCAC-----GGCC---AGCAGUGCG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GCAC--------------------------------CUCCCG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UCUCC-CC--CGCC
L08800.1/29-285              --------------------------------------------CCACGCGCU-----------------GAGUG-C------------UCGU-----------CA--CUCUCUCGGCCC---------------CU-----GGG-AAGGUCUGAGACUGG-----------------GGCCUCCCGC-------------------------------------------------------------------------------------------------CG-CCCUAACCGGGCU-----------------------C-UCCCCGAGU----GGGGA-G----------------------------------GUGAGUU-CCCAGAGAGC-----AGGGCUCCACGCGU----GGGCAGACUGGGCAGGAGAAGCCCCCGGGUGGGCGGAUGCCUCCCUCGCCGG--------------------------------------------------------------------------------GGCUUGGAAC---AGACUCAC-----GGCC---AGCAAUUCG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GCAC--------------------------------CUCGCG-GGCC-U-CAU--AACCCAAUUCA-------------------------
L08687.1/15-320              -------------AGCUCAUCAG--------------UGGGG--CCACGAGCU-----------------GAGUGCG------------UCCU---------GUCA--CUCCACUCCCAU---------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAGAGGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCU-----------------------C-UCCCUGAUCU-UCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAU-----GGGGCUCCGCGCGA----GGUCAGACUGGGCAGGAGAUGCCGUGGACCCCGCCCUUCGGGGAGGGGCCCGNCGGAUGCCUCC------------------------------------------------------------UUUGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUACC-----------------------------CCGGAGGG-GACC-U-CAU--AACCCAAUUCA-------------------------
L08685.1/15-320              -------------AGCUCAUCAG--------------UGGGG--CCACGAGCU-----------------GAGUGCG------------UCCU---------GUCA--CUCCACUCCCAU---------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAGAAGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCU-----------------------C-UCCCUGAGCU-UCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGGCUCCGCGCGA----GGUCAGACUGGGCAGGAGAUGCCGUGGACCCCGCCCUUCGGGGAGGGGCCCGGCGGAUGCCUCC------------------------------------------------------------UUUGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUACC-----------------------------CCGUAGGG-GACC-U-CAU--AACCCAAUUCA-------------------------
X15624.1/4-336               GGCGGA---GGGAAGCUCAUCAG--------------UGGGG--CCACGAGCU-----------------GAGUGCG------------UCCU---------GUCA--CUCCACUCCCAU---------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAGAGGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCU-----------------------C-UCCCUGAGCU-UCAGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGGCUCCGCGCGA----GGUCAGACUGGGCAGGAGAUGCCGUGGACCCCGCCCUUCGGGGAGGGGCCCGGCGGAUGCCUCC------------------------------------------------------------UUUGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUACC-----------------------------CCGCAGGG-GACC-U-CAU--AACCCAAUUCAGACCAC-----UCUCC-UC--CGCC
L08686.1/15-320              -------------AGCUCAUCAG--------------UGGGG--CCACGAGCU-----------------GAGUGCG------------UCCU---------GUCA--CUCCACUCCCAU---------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAAAGGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCU-----------------------C-UCCCUGAGCU-UCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGGCUCCACGCGA----GGUCAGACUGGGCAGGAGAUGCCGUGGACCCCGCCCUUCGGGGAGGGGCCCGGCGGAUGCCUCC------------------------------------------------------------UUUGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUACC-----------------------------CCGCAGGG-GACC-U-CAU--AACCCAAUUCA-------------------------
L08688.1/15-320              -------------AGCUCAUCAG--------------UGGGG--CCACGUGCU-----------------GAGUGCG------------UCCU---------GUCA--CUCCACUCCCAU---------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAGAGGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCU-----------------------C-UCCCUGAGCU-UCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGGCUCCGCGCGA----GGUCAGACUGGGCAGGAGAUGCCGUGGACCCCGCCCUUCGGGGAGGGGCCCGGCGGAUGCCUCC------------------------------------------------------------UUUGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUACC-----------------------------CCGCAGGG-GACC-U-CAU--AACCCAAUUCA-------------------------
AF434764.1/4-250             GUUGGC---CGGAAGAAGACGGU-------------UGGGAG--AGACACAA------------------AGGCCUG------------AAAC---------AUGG--CCUACACAA--------------------CUCCCGGG-AAGGUCUGAGAGU-A-----------------GGCCUUUGAU------------------------------------------------------------------------------------------------GAG-AUCUAGGAGAUCU-----------------------U-CCAUUAUCCUUAUAGAGG-A----------------------------------GAGGCUGUAGAAGAAGAC-----GUUUCCCCUGCGAG----------------------------------------------------------------------------------------------------------------------------------------GGUUUGGAAA----CGGCCUC-----GGCC---AGCAAUUCUCGUGUA----------------------------------------------------------------------------------------------------------------------------AAUGCUGAGUGCGAUCGU-CAUA----------------------------------------------CC-------------AACACAAUUCAGACUAG-----UCUUCGGC--CAAC
AY627761.1/2-369             GUAUUGG--UUUGAAACCAAUGU-------------AAUAUU--CAACAAAUGGCAAUCAUUAAAAAAAGGAAUCUC------------UCAC---------A-AA--UUUUUAAAAUCAUAAAG-----AGAGAAUAAUAUGGG-AAGGUCUGAGUA--------------------CGCGAAA----------------------------------------------------------------------------------------------------AU-CUCUAGGGGGGAA-----------------------A-UUACAAACA---AUGUAA-U---------------------------------GGUCAGGU-AACAGAAAU-------AGUCUAAGCUCAU----ACUAAAAAACGACAAAGAAACCAAUUCAUCAACUUGCCGAAAGGUCGGAAAAUGUAAAGGUCGAGU-------------------------------------------------------CAGUAUGACAAAGGUUGGGAA---AACUUGGC-----UGCG---UAUAAAAUCAA------------------------------------------------------------------------------------------------------------------------------------UGAAGUUAGAUACA-UCGGAUAGU-UGAAAUU--------------------------UAAAAAAAA-UCAA-C-UAC--AACUCAAUUCAGAUUAAU---CUCUAACUG--AUAC
AY627758.1/6-264             UCACGA----UGGAGGAUGUGUA--------------ACAGC--CACCAUACU-----------------GAUAGAC------------UUGC---------U-CU--GUCUUACG---------------------GCUGU-GG-AAAGUCUGAG----------------------AGCGCUAAUU-------------------------------------------------------------------------------------------------GUUUUCUUGGCGGAAC-----------------------A-UGCGGUGAA-----CGCA-U---------------------------------UGCUUGGA-ACCAGUAAC------GAGCCCAUAUAAUG----GCAAGCCCUGCGAAGACCCAUUU-------------------------------------------------------------------------------------------------------------GGGAUGGAAC---GGCUAAGC----ACGCU---GCGUUUGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUGAGAUACA-UGUCGCCGG-A-------------------------------------UUCG---UC-C-GGA--AACUCGAUUCAGAUUAC-----UCCUGUUC--GUGA
AY609138.1/103-415           GGCG------GGAAGCUCAGCGG--------------UGGGG--CCACGCGCG-----------------GAGUG-C------------GCGU-----------CA--CUCUCCCGG--------------------CCCCUGGG-AAGGUCUGAGACUCG-----------------GGCCAGCAGC-------------------------------------------------------------------------------------------------GG-CCCUAGCAGGGCC-----------------------C-UCCCCGCGCG--CGGGGG-G----------------------------------GUGAGUU-CCCAGAGAG------CGGGCCCCGGCGAG----GGCCUUCGGGCAGGAGAGGCCGCGUGCGCGGCGGAUGCCCCCUCCCCGG-----------------------------------------------------------------------------------GGCUUGGAAU---AGACUCAC-----GGCC---GGCACGGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGGGCCGGG-GCACCCGAGCUGG-------------CCGCACCCGGCCGCGG-GGCU-C-CGG--AACCCAAUUCAGACUAC-----UCUCC-CC--CGCC
AANH01002636.1/64511-64819   GUGGGC----GGAAGCUCAUUGU--------------AGAGG--UCACAUGCU-----------------GAGUG-C------------UCGU-----------CA--CUCCACCAAUC-----------------ACCUCGGGG-AAGGUCUGAGACAAG-----------------AGCCAAUAGU-------------------------------------------------------------------------------------------------UA-CCCUUGCAGGGUG-----------------------U-CACCUGAUU---CGGGUG-A----------------------------------GCGAGUG-AACAGAAAAC-----AUGG--GUCUGUGA----GAGCAGCUGUCGCAGGAGAAGCUGUGUGGCGCAGUUUGUCAGCGCCAUUCAGUGGAUGUGGCG-------------------------------------------------------------CUCUCCGG--CUUGGAAU----CGCUUGC-----GGCU---GGCGUAUG------------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUA-UGAGGUGGG-GC------------------------------------ACA---GCU-C-CAG--AACCCAAUUCAGACUAC-----UCUCC-UC--CCAC
X04013.1/204-463             UACGGG----CGAACGCCGCACU--------------UCCUCAAAUUCAAAC------------------GCGUU--------------GAAA-----------AG--CGCACAGCUCG----------------UUGAGGGGGU-AAGGUCGGAGAAA-CA---------------UCUUCGUUGCG-------------------------------------------------------------------------------------------------UG-CUCGUGAGGAGCG-----------------------A-AGAACGAAC----GUUCU-G---------------------------------CCGAAUGU-ACCAGAAAU------UCAAUCAGUAUGGC----CUCGUUUGUCGUACCU--------------------------------------------------------------------------------------------------------------------GAUUUUGAAA---CGCAUUCG----AGAAG---AUUUAUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCAAUGUG-UGGCACCUG---------------------------------------UUUG-U--C-A-GGU--AACUCGAUUCCGACUAA-----UCUUG-UC--UGUA
AAGH01008041.1/2662-2957     UCAGUU----GCAAACUAGCAUC-------------UGGGGC--CCACACAAC-----------------GAGUAU-------------CUGA---------U-UA--CUCCACAAACCA---------------UUGCCCCGGG-AAGGUCUGAGAAU-C-----------------GGCCGAGCCAGCUGUUUGU------------------------------------------------------------------------------UGCGGCUUCAUU-UCCCAGCAGGAAA-----------------------C-CUGUGUGAU----UGCAG-G----------------------------------GCGAAAGUACCAGAAAU-------CCUGCUACCAGGC----GUUGCCGUUGCCCACCAGUGACCGCCGCCUGGUUG-------------------------------------------------------------------------------------------------GCAUUGAAAC----CUUUCGU-----GGCC---AGCGUUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-CUUGCUGCC---------------------------------------UCCC-A--G-G-CAG--AACUCAAUUCAGACUAA-----UCUGU-GA--CUGA
AAPQ01006786.1/48246-48539   UCAGUU----GCAAACUAGCAUC-------------UGGGGC--UCACACAAC-----------------GAGUAU-------------CUGA---------U-UA--CUCCACGAACCA---------------UUGCCCCGGG-AAGGUCUGAGAAU-U-----------------GGCCGAGCAUGCUGUUUGU------------------------------------------------------------------------------UGCGGCUCCAUU-UCCCAGCAGGAAA-----------------------C-CUGUGUGAU----UGCAG-G----------------------------------GCGAAAGUACCAGAAAU------CCUGCUACCAGGCG----UUGCCGUUCCCUCGGGGACCGCCGCCUGGUU-----------------------------------------------------------------------------------------------------GGCAUUGAAA---CCUUUCGU-----GGCC---AGCGUUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-CUUGCUGCC---------------------------------------UUCC-A--G-G-CAG--AACUCAAUUCAGACUAA-----UCUGU-GA--CUGA
BX294109.5/48751-48454       GUGGUA----GGAAGUUCACUGU--------------AGAGG--UUACAAACU-----------------GAGUG-U------------UCAU-----------CA--CUAUGCAUUCA------------------CCUCGGGG-AAGGUCUGAGACAUG-----------------AGCCAAUCGC-------------------------------------------------------------------------------------------------UG-CUCUAGCAGGGCA-----------------------U-CAUCUGAAU-----GAUG-A----------------------------------GCGAGUG-CACAGACACG-----UGGGUCACACUGUG----GUGUUUCGCACGAGACGUUGAUUUGCAAAAUAGCUAAUCAAUCGAUGCGAUCCCAGU--------------------------------------------------------------------------UGAUUUGGAAA----CACUCGC-----GGCU---GGCGGAUUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCGAUGUG-UGAACCAGC-GC------------------------------------UAC---GGG-C-UGG--AACCCAAUUCAGACUAC-----UCUCC-UA--CCAC
AAHY01756065.1/299-617       GGCGGA----GGAAGCUCAUCAG--------------CGGGG--CCACGUGCU-----------------GAGUG-C------------GUGU-----------CA--CUCUUCGG---------------------CCCCUGGG-AAGGUCUGAGACUUG-----------------GGCCUCCCGC-------------------------------------------------------------------------------------------------GG-CCCUAACCGGGCU-----------------------C-UCCCCGAGC----GGGGA-G----------------------------------GUGAGUU-CCCAGAGAGC-----AGGGCUCUACGCUU----GGGCAGACUGGGCAGGAGAAGCCCCGAGUCGGGGCGGAUGCCUCCCUCGCCGGAGCGGAUGCCUC----------------------------------------------------------CCUCGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCAGUGCG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GCAC--------------------------------CUCCCG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UCUCC-CC--CGCC
AAPY01506299.1/591-266       GGCGGA---GGGAAGCUCAUCGG--------------UGGGG--CUACGAGCU-----------------GAGUGCG------------UCAC---------GUCA--CUCCACCCCAU----------------GUCCCCUGGG-AAGGUCUGAGACUAG-----------------GGCCAGCAGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCU-----------------------C-UCCCUGAGUG--CGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAU-----GGGGCUCCGCGCGA----GGGCAGACUGGGCAGGAGAUGCCGUGGACCCGCUCCCGGACGGGCCCGGCGGAUGCCUCCUU----------------------------------------------------------------AAGCGGAGCUUGGAAC---AGACUCAC-----GGCC---GGCGCAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GCAC-------------------------------CCCGCGG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UCUCCCCG--CGCC
AAHX01082883.1/46075-45778   GGCGGG----GGAAGCUCAUCAG--------------CGGGG--CCACGCGCU-----------------GAGUG-C------------UCGU-----------CA--CUCUCUCGG--------------------CCCCUGGG-AAGGUCUGAGACUGG-----------------GGCCUCCCGC-------------------------------------------------------------------------------------------------GG-CCCUAACCGGGCU-----------------------C-UCCCCGAGU----GGGGA-G----------------------------------GUGAGUU-CCCAGAGAGC-----AGGGCUCCACGCGU----GGGCAGACUGGGCAGGAGAAGCCCCCGGGUGGGCGGAUGCCUCCCUCGCCGG--------------------------------------------------------------------------------GGCUUGGAAC---AGACUCAC-----GGCC---AGCAAUUCG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GCAC--------------------------------CUCGCG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UCUCC-CC--CGCC
AAFS01000235.1/74943-74603   UCAGUU----ACAAACUAGCAUC-------------UGGGGC--ACACACAAC-----------------GAGUAU-------------CUGA---------U-UA--CUCUUACUUU-------------------GCCCCGGG-AAGGUCUGAGAUU-U-----------------GGCCAAGCCUCCUUGUGUUGUUACAACAUGCAGUGCAU----------------------------------------CGAGAGGUGCCUGUGUGUCGGAGGCUUAAUU-UCCUAGCAGGAAA-----------------------C-CUGUGUGAU----UGCAG-G----------------------------------ACGAAAGUACCAGAAAU------ACUGCGGCUUGGCG----UUGCCAUCGGCGCUCGCGUCUGACUGCCGCCUUGU-------------------------------------------------------------------------------------------------UGCAUUGAAA---ACUUUCGU-----GGCC---GGCUGUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCAAUGUG-CUUGCUGCA-GAAC-------------------------------CUCCGGG-CAAC-G-CAG--AACUCAAUUCAGACUAA-----UCUGU-GA--CUGA
AAPP01019576.1/193412-193118 UCAGUU----ACAAUCCAGCAUC-------------UGGGGC--ACACACAAC-----------------GAGUAU-------------CUGA---------U-UA--CUCUCUUAUUU-----------------UGCCCCGGG-AAGGUCUGAGAAU-C-----------------GGCCAAGCCAUGUUGUUUCGCUU----------------------------------------------------------------------CGUGCGAGGCUCUAUU-UUCUAGCAGGAAA-----------------------C-CUGUAUGAU----UACAG-G----------------------------------GCGAGAGUACCAGAAAU---------CCUGCCCAGGU----GUUGCCGUUGCCCAGCAACCGCCGCCUGAU------------------------------------------------------------------------------------------------------GGCAUUGAAA---ACUCUCGU-----GGCC---AGCCUUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-CUUGCUGCC---------------------------------------UUCG----G-G-UAG--AACUCAAUUCAGACUAA-----UCUGU-GA--CUGA
CAAE01014991.1/324501-324806 GUGAGU----GGAAGCUCAUUGU--------------AGAGA--UCACGUGCU-----------------GAGUG-U------------UCAU-----------CA--CUCCACCAAUC-----------------AUCUCGGGG-AAGGUCUGAGACAAG-----------------AGCCAAUAGU-------------------------------------------------------------------------------------------------UG-UCCUUGCAGGACA-----------------------U-CACCUGACU---CGGGUG-A----------------------------------GCGAGUG-AACAGAGAA------UGGGUCAAGCGGUG----CAGUUCUAGCAGGAGAAGCUAGCAGGCGCAGUUUCCCGGCUCUGCUGGCGGAUGUGACGC-------------------------------------------------------------------ACGCUGACUUGGAAU----CGCUCGC-----GGCU---GGCGCAUG------------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUA-UGAGGUGGA-GC------------------------------------ACC---GCU-C-CAG--AACCCAAUUCAGACUAC-----UCUCC-AC--UCAC
AADA01028820.1/18592-18913   AGAG------UGAAACUCUUUAGAGA-------GUCAUGGGG--CCAUGAGCU-----------------GAGUGCU------------UCAU---------GUCA--CUCCAGCCCCAU---------------GUCCCUUGGG-AAGAUCAGAGACUAGGG-------------UC----AGAAGC-------------------------------------------------------------------------------------------------AG-CCUUAACAAGGCU-----------------------C-UCUUUGAGUU-GCAAGGA-G----------------------------------GUGAAUU-CCCAGAAAAC-----AGAGCUGCUUGAGG----UCAGACAGGGCAGGAGAUGCUGUAGACCCCACCCCUAGGGAGGAAUUCAGGGGAAGUCUCCU---------------------------------------------------------------AAGUGAGAGCUUGGAAC---GGAUUC--------------AGUGAAAUG-----------------------------------------------------------------------------------------------------------------------------------------AGCUCAACAGC-UAAGGUUAG-GUACCC----------------------------CACAUGGG-GUCC-U-CAU--AAC----UGCUG---------UCCUCCAUC--CUCU
AANH01002636.1/66726-67032   GUGGGU----GGAAGCUCAUUGU--------------AGAGG--UCACAAGCU-----------------GAGUG-C------------UCGU-----------CA--CUCCACCAAUC-----------------ACCUCGGGG-AAGGUCUGAGACAAG-----------------AGCCAAUAGU-------------------------------------------------------------------------------------------------UA-CCCUUGCAGGGUG-----------------------U-CACCUGAUA---CAGGUG-A----------------------------------GCAAGUG-AACAGAAAAU-----AUGGCCCUGUGAGA----GCAGCUGUCACAGGAGAAGCUGCAUGGUGCUGUUGGUCAGCGCCAUUCAGUGGAUGUGGC-------------------------------------------------------------------UCUCUGGCUUGGAAC----CGCUUGC-----GGCU---GGCGUAUG------------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUA-UGAGGUGGG-GC------------------------------------AUU---GCU-C-CAG--AACCCAAUUCAGACUAC-----UCUCC-UC--CCAC
AAFC03039865.1/140694-141025 GUAG------AGAAGCUCAUCAG--------------UGGGG--CUAGGAGCU-----------------GAGUGCA------------CUUA---------GUCA--CUCUGUCCCAU----------------GUCCCUUGGG-AAGGUCUGGGACUAG-----------------GGCCAUAGCG------------------------------------------------------------------------------------------------CGG-CCCUAAAAGGGCC-----------------------U-UCCCUGAGCU-UUGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGGCUCCACGCACACAAGGGCAGACUGGGCAGGAGGUGCUAUGGACCCCGCCUUUGCAGAGGGUCCUGGCGGAUGCCUCC--------------------------------------------------------------UUAGCAGAGUUUGGAAC---AGACUCAC-----UGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUAUCC----------------------------UGCGUGGG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UC-CC-GC--CCAU
AL954692.9/82863-82562       AGCGAA---AGGAAGCUCACUGU--------------AGAGG--UCACUUACU-----------------GAGUG-C------------UCGU-----------CA--CUCGCCAACA-------------------CCUCGGGG-AAGGUCUGAGACAGG-----------------AGCUCCUCGC-------------------------------------------------------------------------------------------------UG-ACCUAGCAGGACA-----------------------U-CAUCUGAAU-----GAUG-A----------------------------------GCGAGUG-CACAGAAAAU-----CGGGUCACGCGCGC----GACUCUCGCAGCAGACGUUGAUGCUCGCACACAUUCAGCGGAUCAACUGAAUGACGCGC----------------------------------------------------------------------GCAGACUUGGAAA----CACUCGC-----GGCU---GGCGAAUG------------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-UGAGCUAGC-AU------------------------------------AAC---AUG-C-UAG--AACCCAAUUCAGACUAC-----UCUCCCUC--CGCU
AACI02000962.1/1963-2317     GGAACAG-UGGUAACUCCUACGAUUA-------AGAAACCUG-UUUGCAAAAG-----------------GGCCCGC------------AUCUC-------GC-AG--GUCACUAAUUA-----------------UCAGGUGGG-AAAUUCGGUG----------------------GAACAUAAUGGAGCCUUGUCCUCCGGGUCA---------------------------------------------------------GCGUCUUUGACAAUGGCCCCUG-CUCCUGA-GAGAAGAA-----------------UCUU-ACUGGGGAA----CCAGU-CUUUA-------------------------UCGACCGUUGUU-AUCAGAAAUU-----AAACGGAGUCUGGC----CUAGUCGGGCU-------------------------------------------------------------------------------------------------------------------------CCGAUGGGAA---CGGCAACGG--UUGUUCC-GUUUGACUUGUCGCCCGCUACGGCGUG-------------------------------------------------------------------------------------------------------UGUGUCAAGGUCUGUUGAGUGCAAUCGU-AGGACGCCA---------------------------------------UUCG----U-G-GCG--AACCCGAUACCGAUUAC----UGCUGC-UG--UUCC
AY609135.1/99-412            GGCG------GGAAGCUCAGCGG--------------UGGGG--CCACGCGCG-----------------GAGUG-C------------GCGU-----------CA--CUCUCCCGG--------------------CCCCUGGG-AAGGUCUGAGACUCG-----------------GGCCAGCAGC-------------------------------------------------------------------------------------------------GG-CCCUAGCAGGGCC-----------------------C-UCCCCGCGCG--CGGGGG-G----------------------------------GUGAGUU-CCCAGAGAG------CGGG--CCCCGGCG----AGGGCCUUCGGGCAGGAGAGGCCGCGCGCGCGGCGGAUGCCCCCUCCCCGGAG---------------------------------------------------------------------------------CUUGGAAU---AGACUCAC-----GGCC---GGCACGGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGGGCCGGG-GCACCCGAGCUGGC------------CGGCACCGGGCCGCGG-GGCU-C-UGG--AACCCAAUUCAGACUAC-----UCUCC-CC--CGCC
AASU01035577.1/1717-1416     GUUG------CAAACUAGCAUCU--------------GGGGC--CCACACAAC-----------------GAGUAU-------------CUGA---------U-UA--CUCCACAAACCA---------------UUGCCCCGGG-AAGGUCUGAGAAU-C-----------------GGCCGAGCCAGCUGUUUGU------------------------------------------------------------------------------UGCGGCUUCAUU-UCCCAGCAGGAAA-----------------------C-CUGUGUGAU----UGCAG-G----------------------------------GCGAAAGUACCAGAAAU-------CCUGCUACCAGGC----GUUGCCGUUGCCCACCAGUGACCGCCGCCUGGUUG-------------------------------------------------------------------------------------------------GCAUUGAAAC----CUUUCGU-----GGCC---AGCGUUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-CUUGCUACU-AAGAAAAG------------------------GUUGGUUAUA-GAUA-U-UAG--AA----A-----ACUAA-----AUUUA-AAAACAAU
AAGD02004958.1/19351-19594   UUGGCC----GGAAGAAGACGGU-------------UGGGAG--AAACUCAA------------------AGGCCUA------------UUUA---------U-GG--CCUACAAAA--------------------CUCCCGGG-AAGGUCUGAGAGA-A-----------------GGCCCUUUCGU-----------------------------------------------------------------------------------------------GAG-AUCUAGGAGAUCU-----------------------U-CUAGUGUCCUUAUAGAAG-A----------------------------------GAGGCUGUAGAAGAAGGU-----GUUUCCCCCGAGUG----------------------------------------------------------------------------------------------------------------------------------------GGUUUGGAAA----CGGCCUC-----GGCC---AGCAAUCACCUAUAC-----------------------------------------------------------------------------------------------------------------------------AAGCUAAGUGCGAUCGU-CAUA----------------------------------------------CC-------------AACACAAUUCAGACUAG-----UCUUC-GG--CCAA
AAYZ01125348.1/5678-5374     GCGGA-----GGCAGCUCAUCAG--------------UGGGG--CUAUGAGCU-----------------GAGUGUG------------UCAC---------AUCA--CUCCCUUGU--------------------CCCUUGGG-AAGGUCUGAGACU-A----------------GGGCCAGCAGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCU-----------------------C-UCCCUGAGUC-UCGGGGA-G----------------------------------GUGAGUU-CCAAGAGAAC-----GGGGCUCCGUGCGA----GGGCAGACUGGGCAGGAGAUGCCGCGGCCCCUCUCCCCGGAGGGACCCGGCGGAUGCCUCCU---------------------------------------------------------------UAGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCGAAGUGA---------------------------------------------------------------------------------------------------------------------------------------GAUUACCAUGCC-ACCUAUUU----------------------------------------UGCU-U----A-UUU--A------UUUA-UCUAU-----ACCUA-UU--UUGC
AAFC03071173.1/67816-67484   GCGGAG----GGAAGCUCAUCAG--------------UGGGG--CUACGAGCU-----------------GAGUGCG------------CUUA---------GUCA--CUCUGUCCAUU----------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAUAGGG------------------------------------------------------------------------------------------------CGG-CCCUAACAGGGCC-----------------------C-UCCCUGAGCU-UCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGGCUCCGCGCGA----GGGCAGACUGGGCAGGAGAUGCUAUGGACCCCGCCCUCGCGGAGGGGCCUGGCGGAUGCCUCC-------------------------------------------------------------UUAGCCGGAGCUUGGAAU---AGACUCAC-----GGCC---GGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUACCC----------------------------CGCCUGGG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UCUCCCGC--CCGU
AANG01621100.1/3337-3671     GGCGGA---GGGAAGCUCAUCGG--------------UGGGG--CUACGCGCU-----------------GAGUGCC------------UUAA---------GUCA--CUCUACCCCAU----------------GUCCCCUGGG-AAGGUCUGAGACUAG-----------------GGCCAAAAGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGUC-----------------------C-UCCCUGAGUU-GCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGGCUCCGCGCGA----GGGCAGACUGGGCAGGAGAUGCCAUGGACCCCGCCCUCGAGGAGGGGCCUGGCGGAUGCCUCC-------------------------------------------------------------UUAGCCGGAGCUUGGAAA---AGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUACCCC-------------------------CCAACGGGGG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UCUCC-CC--CGUC
ABDC01377112.1/1708-1368     GGAG------GGGAGGUCAUCAG--------------UGUGG--CCACGAGCC-----------------GAGUGCG------------UCAU---------GUCA--CUCCACCCCCCA--------------UGUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAGAAGC-------------------------------------------------------------------------------------------------AC-CCCUAAACAGGGC----------------------UC-UCCCUGAGUU-UCGGGGA-G----------------------------------UUGAGUU-GGCAGAGACC-----CGGGCUCCGCGCGA----GGUCAGACUGGGCAGGAGAUGCCGUGGACCCCGCCCCCCAGGACGGGCGCGGCGGACGCC-------------------------------------------------------------------UCCUCAGCCUG--------AAC--AA-----GGUG---CUUUUUUUGCGAAACACCG--------------------------------------------------------------------------------------------------------------------CCAGCGAAGUGAGUUCAAUGGC-UGAGGUGAG-GUACCC----------------------------CGCAUGGG-GGCU-U-CAU--AACCCAAUUCAGACUAC-----UCUCCCCC--GUCC
AACA01000088.1/21374-21028   AGCG------GUGAUUCCUACGAUUA-------AGAAACCUG-UUUGCAAAAG-----------------GGCCCGC------------UCAC--------GC-GG--GUCAUCCUAUUU---------------AUCAGGUGGG-AAAUUCGGUG----------------------GAACACAGUGGAGCCUUGCCUUCCGGGUCA---------------------------------------------------------UUGUCUCUGGCAGUGGCCCCUG-CUCGUGA-GAGAAGAA-----------------ACUU-GCUGGGGAA----CCAGU-CUUUA-------------------------CCGACCGUUGCU-AUCAGAAAUU-----GAACGGGGUCCGGU----CCCGCCGGGCC-------------------------------------------------------------------------------------------------------------------------CCGAUGGGAA---CGGCAACGG--UUGUUCC-GUUUGACUUGUCGCCUGCCACGGCGC---------------------------------------------------------------------------------------------------------GCUACAAGGUCUGUUGAGUGCAAUCGU-AGGACGCCA---------------------------------------UUCG----U-G-GCG--AACCCGAUACCGAUUAC-------UGCUGC--UGCU
AAYZ01187716.1/7604-7282     GGCGGA----GGAAGCUCAUCAG--------------UGGGG--CUACGAGCU-----------------GAGUGCA------------UCAC---------GUCA--CUCCCUUGU--------------------CCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAGCAGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCU-----------------------C-UCCCUGAGUC-UCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGGCUCCGUGCGA----GGGCAGACUGGGCAGGAGAUGCCGCGGCCCCUCUCCCGGAGGGACCCGGCGGAUGCCUCCUU----------------------------------------------------------------AGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GCACC-----------------------------UGCCUGGG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UCUCC-CC--CGCC
AAQQ01078467.1/2582-2247     GGCGGA---GGGAAGCUCAUCAG--------------UGGGG--CUACGAACU-----------------GAGUGCG------------UUGC---------GUCA--CUCUACCCCAU----------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAAAUAG------------------------------------------------------------------------------------------------CGG-CCCUAACAGGGCC-----------------------C-UCCCUGAACC-GCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGGCUCCGCGCGA----GGGCAGACUGGGCAGGAGAUGCCGAGGACCUCACCCUCGGGGUGGGGCCCGGCGGAUGCCUCC-------------------------------------------------------------UUAGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCCAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUACCCC-------------------------CGCAAACGGG-GACC-U-CAU--AACCUAAUUCAGACUAC-----UCUCC-CC--CGUC
AABY01000076.1/21420-21783   GGAACAG-UGGUAAUUCCUACGAUUA-------AGAAACCUG-UUUGCAAAAG-----------------GAUCCGCCU--------UCCGGG---------G-GG--GUCAUCAAAAUUU-------------UAUCAGGUGGG-AAAUUCGGUG----------------------GAACACAGUGGAGCCUCGUCCUCCGGGCCAA------------------------------------------------------UGUCAUUUUAGGCAUUGUCCCCUG-CUCCUGA-GAGAAGAAC---------------UAUC---CUGGGGAA----CCAG---UCUUU-----------------------ACCGACCGUUGUU-AUCAGAAAU------UUACGGAGUCUGGC----UUAGGUCGGACC------------------------------------------------------------------------------------------------------------------------CCGAUGGGAA---CGGCAACGG--UUGUUCC-GUUUGACUUGUCGCCCGCCACGGCGUG-------------------------------------------------------------------------------------------------------CGUGUCAAGGUCUGUUGAGUGCAAUCGU-AGGACGUCA---------------------------------------UUCG----U-G-GCG--AACCCGAUACCGAUUAC----UGCUGC-UG--UUCC
BAAF04017480.1/6237-5930     GUGAGU----GGAAGCUCAUUGU--------------AGAGG--UCACGUGCU-----------------GAGUG-U------------UCGU-----------CA--CUCCUCCAAUC-----------------ACCUCGGGG-AAGGUCUGAGUCAAG-----------------AGCCAAUCGU-------------------------------------------------------------------------------------------------UA-CCCUUGCAGGGUA-----------------------U-CACCUGAUU---CGGGUG-A----------------------------------GCGAGUG-AACAGAAAAA----UUGGGCCACCGCACG----CAGUUUCAGCAGGAGAAGCUAGGUGGUGCUGGUUCACGCGCCUCCCAGUGGAUGUGCUGC-------------------------------------------------------------------GUGCUGGCUUGGAAU----CACUCGC-----GGCU---GGCGAAUG------------------------------------------------------------------------------------------------------------------------------------------AGUCCGAUGUA-UGAGGUGGA-GC------------------------------------AAU---GCU-C-CAG--AACCCAAUUCAGACUAC-----UCUCC-AC--UCAC
X56558.1/7-319               GGAG------GGAAGCUCAGUGC--------------UGAGG--CUACAGACA-----------------GAGUGCU------------GGGG---------GUCA--CUCAGUGAGUG----------------UGACUCAGGG-AAGGUCUGAGAUUUA----------------GAGCCCCUUGC-------------------------------------------------------------------------------------------------UG-CUCUCACAGGGCA-----------------------U-CACUUGGAN---NAAGUG-A----------------------------------GUG-GUA-CUCAGGAAAG----CUUGGCUCUGAUUGG----CCAGUGAGUGCAAAAGAUGCAGUGAGUGCUCCUGGGUUGAGCUCCUGUAGGAUGCAAAGG-------------------------------------------------------------------CAUCAGGCUUGGCAC----UGCCCAC-----AGCU---GGCACAUUC----------------------------------------------------------------------------------------------------------------------------------------AAGCUCAAUGGC-UGAGAGGG----------------------------------------AACU-G----C-CNC--AACCCAAUUCAGACUACUU-UUUUUCC-AC-AUUUC
AY609130.1/103-418           GGCG------GGAAGCUCAGCGG--------------UGGGG--CCACGCGCG-----------------GAGUG-C------------GCGU-----------CA--CUCUCCCGG--------------------CCCCUGGG-AAGGUCUGAGACUCG-----------------GGCCAGCAGC-------------------------------------------------------------------------------------------------GG-CCCUAGCAGGGCC-----------------------C-UCCCCGCGCG--CGGGGG-G----------------------------------GUGAGUU-CCCAGAGAG------CGGGCCCCGGCGAG----GGCCUUCGGGCAGGAGAGGCCGCGCGCGCGCGGCGGAUGCCCCCUCCCCGG---------------------------------------------------------------------------------GGCUUGGAAU---AGACUCAC-----GGCC---GGCACGGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGGGCCGGG-GCACCCGAGCUGGC------------CGGCAUCGGGCCGCGG-GGCU-C-CGG--AACCCAAUUCAGACUAC-----UCUCC-CC--CGCC
AACH01000030.1/12761-12402   GGAACAG-UGGUAAUUCCUACGAUUA-------AGAAACCUG-UUUGCAGAAG-----------------GACUCGC------------ACUAC-------GC-CA--GUCAUUAAAAUUU-------------UAUCAGGUGGG-AAAUUCGGUG----------------------GAACACAGUGGAGCCUCGUCCUCCGGGUCA---------------------------------------------------------AUGUCUUAGACAAUGGCCCCUA-CUCCUGA-GAGAAGAA-----------------AUAU-ACUGGGGAA----CCAGU-CUUUA-------------------------CCGACCGUUGUU-AUCAGAAAUA-----GUACGGAGCCUGGC----CUAGGUCAGACU------------------------------------------------------------------------------------------------------------------------UCGAUGGGAA---CGGCAACGG--UUGUUCC-GUUUGACUUGUCGCCUGCUACGGCGUG-------------------------------------------------------------------------------------------------------CGUGUCAAGGUCUGUUGAGUGCAAUCGU-AGGACGCCA---------------------------------------UACC----G-G-GCG--AACCCGAUACCGAUUAC----UGCUGC-UG--UUCC
AAPN01395706.1/4386-4039     AGUG------GGAAGCUCAGCGG--------------AGGGG--CCACGGGCG-----------------GAGUGCG-----------CAUGC---------GUCA--CUCUCUGGCCA-----------------GCCCUUGGG-AAGGUCUGAGACGAG-----------------GGCCAGCGGC-------------------------------------------------------------------------------------------------GG-CCCUAGCAGGGCC-----------------------C-CCCCCGAGCC-GCGGGGG-G----------------------------------GUGAGUU-CCCAGAGAAG-----GGGGCCUCGCGCGG----GGGCCGACCGGGCAGGAGAAGCCGCGCCGCGCUGGCGCCCCCUAGCGUCCGCCCGGCCCGCGGCGGAUG--------------------------------------------------CCCCUCCCGCCGGGGCUUGGAAA---CGACUCAC-----GGCC---GGCGGGCUG-----------------------------------------------------------------------------------------------------------------------------------------AGUGCAAUGGC-UGAGGGGGG-GCACGGUU-----------------------GCUUUGCCGCC-GGCU-C-CCU--AACCCAAUUCAGACUAC----UCUUCCCUG-CCACU
AALT01519858.1/2181-1847     GGCGGA---GGGAAGCUCAUCAG--------------UGGGG--CCACGCGCG-----------------GAGUGCG------------UCUC---------GUCA--CUCUAUCCAAU----------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAUUAGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCC-----------------------C-UCCCCGACCU--CGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAU-----GGGUCUCCGGCGAG----GGCAGACUGGGCAGGAGAUGCUACGGGUCCCCUCUCCCUCGCGGAAGGGGUCCUAGCGGAUGCCU---------------------------------------------------------CCUUAGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GCACC-----------------------------CCGGAGGG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UCUCCCGC--CGUC
AATM01000019.1/108951-109207 UACGGG---CGAACGCUGCACUU--------------CCCCG-AUCUCAUAC------------------GCGCA--------------GAAA-----------UG--UGCUUUUCAUUC---------------CUCGGGGGGGUAAGGUCGGAGGAA-CA---------------UCUUCGUUGCG-------------------------------------------------------------------------------------------------UG-CUCGUGAGGAGCG-----------------------G-UGAAUGAUU---AAUUCA-G---------------------------------CCAGAUGU-ACCAGAAAU-------UCGACAAAAGCAC----ACAAGUGUGGAU------------------------------------------------------------------------------------------------------------------------GUCUUGGAAC----GCAUCUG----AGAAG---AUUUCUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCAAUGUG-CGGCACCUG---------------------------------------CUUU-G--C-G-GGA--AACUCAAUUCCGACUAA-----UCUUG-CA--CGUA
AAFR03022275.1/195137-194802 GGCGGA---GGGAAGCUCAUCGU--------------UGGGG--CUACAAGCU-----------------GAGUGCG------------UCAC---------GUCA--CUCCCCAGCCC----------------AGCCCUUGGG-AAGGUCUGAGACGAG-----------------GGCCAAUAGC-------------------------------------------------------------------------------------------------GG-CCCUAGCAGGGCU-----------------------C-CUCCCGCGAUUGUGGGGG-G----------------------------------GUGAGUU-CCCAGAAAAU-----GGGGCCCGGUUUGG----GGGUAAGACUGGGCAGGAGAAGCCCAUGCGUACCACACCCCCGGGUGUGGCCUGGGCGGAUGCCU---------------------------------------------------------CCCUCGACCGGGCUUGGAAA---CGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUGCAAUGGC-UGAGGUGGG-UUACC-----------------------------UCCUCGAG-GAUC-C-CAU--AACCCAAUUCAGACUAC-----UCUCC-CC--CGCC
AACN010174136.1/601-933      GUACUC---UGAAAGCUUAUAGU--------------UUUAU----------------------------AAGUUU-------------UUAU---------A-AG--UUUAUAGCACUGAUCA-------AAGUAACUGAAGAU-GAAGUCUGAGACUAG-----------------GGCCAUAAGG------------------------------------------------------------------------------------------------UGG-CCCUAACAGAAUC-----------------------C-UCCCUGAGUU-UUGGAGA-G----------------------------------GUGAAUU-UCCAGAAAAU-----GGGGCUUCACAGAA----AGGCAGACUGGGCAGAUAUCAUGGACACCACCCUUGCAGAGUGGCCUGGUGGAUGCCUCCUU----------------------------------------------------------------AGCCAGAGCUUGGAAC---AGGCUCAU-----GGCC---AGUGAGUGA-----------------------------------------------------------------------------------------------------------------------------------------AGUG-AAUUUA-AAGGCUGAG-GCGAAGUA-----------------------CCCUGCGCGGG-AGCC-U-CAC--AACUCAAUUCAGACUAC-----UCUCCCUU--GUCC
AAHY01054080.1/31215-30889   GGCGGA----AGAAGUUUAUCAG--------------UGGGG--CCACGUGCU-----------------GAGUG-A------------UCGU-----------CA--CUCUUCGG---------------------UCCCUGGC-AAGGUCUGAGACUGG-----------------GGCCUCCCGC-------------------------------------------------------------------------------------------------AG-CCCUAACCGGGCU-----------------------C-UCCCCGAGC----GAGGA-G----------------------------------AUGAGUU-CCCAGAGAGC-----AGGGCUCUACGAGU----GGGCAGACUGGGCAGGAGAAGCCCUGAGUCUGGGCAGAUGCCUCCCUCGCCAG-------------------------------------------------------------------------------AGCUUGGAAC---AGACUCAC-----AGCC---AGCAGAGCG-----------------------------------------------------------------------------------------------------------------------------------------AGUUUUAACCA-UUUAUAUUU-UUUAACAUGAACCACAGAACAAUAAUCAUUCAAACAACAAAA-CAAA-A-ACA--AACACGA-----AUUAAC---AGAUUU-AU--GGAC
AAPT01018385.1/57001-57367   UCAGUU----ACAAUCUAGCAUC-------------UGGGGC--ACACACAAC-----------------GAGUAU-------------CUGA---------U-UA--CUCUAUAAAA-------------------GCCCCGGG-AAGGUCUGAGAAU-U-----------------GGUCAAAGCUCCCUUGUUUGUGUGCACAACAAGCGAUUUGC----------------------------------UGUUAAAGGUGAUCGUUUGUCGCGGAGUUUCAUU-UCCCAGCAGGAAA-----------------------C-CUGUGUGAU----CGCAG-G----------------------------------GCGAAAGUACCAGAAAUC-----CUGCCUCGCUGCUG----UUAUUGUUAUUGUUGUUGUUGCCAACGACGAUGACGACGACGCGCGU-------------------------------------------------------------------------------------UGCAUUGAAA---UCUUUCGU-----GACC---AGCAAUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-CUUGCUGCA-AAUCCCUC------------------------CUCGGAGGUG-GUGC-G-CAG--AACUCAAUUCAGACUAA-----UCUGU-GA--CUGA
AY609136.1/75-392            GGCGGC---GGGAAGCUCAGCGG--------------UGGGG--CCACGCGCG-----------------GAGUG-C------------GCGU-----------CA--CUCUCCCGG--------------------CCCCUGGG-AAGGUCUGAGACUUG-----------------GGCCAGCUGC-------------------------------------------------------------------------------------------------GG-CCCUAGCAGGGCC-----------------------C-UCCCCGCGCG--CGGGGG-G----------------------------------GUGAGUU-CCCAGAGAG------CGGGCCCCGGCGAG------GGCCUUCGGGCAGGAGAGGCCGCGGGCGCGGCGGAUGCCCCCUCCCCGG---------------------------------------------------------------------------------GGCUUGGAAU---AGACUCAC-----GGCC---GGCACGGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGGGCCGGG-GCACCCGUGCUGGC-----------CGGGCAUCGGGCCGCGG-GGCU-C-CGG--AACCCAAUUCAGACUAC-----UCUCC-CC--CGCC
AANI01014597.1/56085-56433   UCAGUU----ACAAUCUAGCAUC-------------UGGGGC--ACACACAAC-----------------GAGUAU-------------CUGA---------U-UA--CUCUUUUUACA----------------ACGCCCCGGG-AAGGUCUGAGAUA-U-----------------GGUCAAAGCUCCCUUGUUGCUGUAACAACAUACAAAAGC--------------------------------------CGAGAGGUGAUUGUGUGUCGCGGAGCUUCAUU-UUCUAGCCGGAAA-----------------------C-UUGUGUAAU----CACAA-G----------------------------------GCGAAAGUACCAGAAAU------GCUGCAGUAUGGCU----GUUGCCGCACCGCUUGCCGUUUGCCGCCGGCCAUGU------------------------------------------------------------------------------------------------UGCAUUGAAA---ACUUUCGU-----GACC---AGCAAUUUA-----------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-CUUGCUGCA-AACCU-----------------------------UGCCUGAG-GUGC-G-CAG--AACUCAAUUCAGACUAA-----UCUGU-GA--CUGA
AANG01442536.1/145-454       ACAG---------------------------------AGGGG--CUAUGAGCU-----------------GAGUGCU------------UUGU---------GUCA--CUCUACCCCGU----------------GUCCCCUGGG-AAGGUCUGAGACUAG-----------------GGCCAAAAGU-------------------------------------------------------------------------------------------------GG-CCCCAACAGGGUC-----------------------C-UCCCUGAGUU-UCAGGGA-G----------------------------------GUGAGUU-CCCAGAGAUU-----GGGUCUUUGCUUGA----GGUCAGACUGGGCAGGAGAUGCUCUGGACCCCACCCUUGGGGAGGAGGCAGAUGCCUCCUU-----------------------------------------------------------------AGCUGGAGGUUGGAAC---AGAUUUGC-----GGCC---AGCAAGUG------------------------------------------------------------------------------------------------------------------------------------------AGUUUAGUGGC-UGAGCUGAG-GUACCC----------------------------UGCCCAGG-GACC-U-CAU--AACCCAAUUCACACUAC-----UC---UCC-CCUGU
CR392032.9/77428-77725       GUGGUA----GGAAGUUCACUGU--------------AGAGG--UUACAAACU-----------------GAGUG-U------------UCAU-----------CA--CUAUUCAUUCA------------------CCUCGGGG-AAGGUCUGAGACGUG-----------------AGCCAAUCGC-------------------------------------------------------------------------------------------------UG-CUCUAGCAGGGCA-----------------------U-CAUCUGAAU-----GAUG-A----------------------------------GCGAGUG-CACAGACACG-----UGGGUCACUCUGUG----GUGUUUCGCACGAGACGUUGAUUUGCAAAAUAGCUAAUCAAUCGAUGCGAUCCCAGU--------------------------------------------------------------------------UGACUUGGAAA----CACUCGC-----GGCU---GGCGGAUUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUUGAUGUG-UGAACCAGC-GC------------------------------------UAC---GGG-C-UGG--AACCCAAUUCAGACUAC-----UCUCC-UA--CCAC
AAQB01008954.1/214928-214576 UCAGUU----GCAAUCUAGCAUC-------------UGGGGC--ACACAUAAC-----------------GAGUAU-------------CUGA---------U-UA--CUCUCUUU---------------------GCCCCGGG-AAGGUCUGAGAAU-U-----------------GGUCGAAGCUUGUGUGUUUUGUACAACAUGCCAAUUCA-----------------------------------------UCCGAAAGGGGUUUGGCGUGUAGCUUCAUU-UCCUAGCAGGAAA-----------------------C-CUGUGUGAU----UACAG-G----------------------------------GCGAAGGUACCAGAAAU------ACUGUACUGUUUGG----CU----------------------UGUUGCGGUCCCCUCGACCGCCGCCUUACGGA----------------------------------------------------------------------------UGCAUUGAAA---UCUUUCGU-----GACC---AGCCGUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-CUUGCUGCU-AUAAGCUACCCU---------------CCUUUGGAGGCAGUG-GAAA-G-CAG--AACUCAAUUCAGACUAA-----UCUGC-AA--CUGA
AAPU01011135.1/119858-120199 UCAGUU----ACAAUCUAGCAUC-------------UGGGGC--ACACACAAC-----------------GAGUAU-------------CUGA---------U-UA--CUCUUAUGAUU------------------GCCCCGGG-AAGGUCUGAGAUU-U-----------------GGUCAAAGCUCCCUUGUUGCCGUAACAACGCUCAAAAGC--------------------------------------UGAAAGGUGAUUGUGUGUCGUGGAGCUUCAUU-UCCUAGCAGGAAA-----------------------C-UUGUGUAAU----CACAA-G----------------------------------GCGAAAGUACCAGAAAU------GCUGCAGCAUGGCU----GU---------------------------------------------UGCCGCAUAACCUGCCGC----------------------------------------------------------CGGCCAUGUUGCAUUGAAA---GCUUUCGU-----GGCC---AGCAAUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-CUUGCUGCA-AACCUC---------------------------AACUCUGAG-GUGC-G-UAG--AACUCAAUUCAGACUAA-----UCUGU-GA--CUGA
AC154132.2/16832-17109       UAUGGC----AUAAUCUCGCAUU-------------UGGGGC--UCACAUACA-----------------GUGUA-U------------UAGU-----------UA--CACAACUAACA------------------GCCUCGGG-AAGGUCUGAGAAA-------------------ACCCGAUAA--------------------------------------------------------------------------------------------------CG-UUCUAGCAGGAUG-----------------------C-UUGUAUUUG-----GCAA-G----------------------------------GCGAGAACACCAGAAAU------ACGC-----GAAAA----AGUUUUUUAGCCAAGGAUUGACUUUGCGCAUAGGCGAUGGAACUUUUCC-------------------------------------------------------------------------------------GUUGGAAU----UUUUUGU-----GGGU---AGCGAUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUUUAAUUUG-CGAGCUAGA---------------------------------------GCGU-U--A-C-UAG--AACUCAAUUCAGACUAA-----UCUGU-GC--CAUA
AAIY01285770.1/2149-2419     GGAG------GGAAGCUCAUCGG--------------UGGAG--CUCUGAGCU-----------------GAGUGC--------------UGU---------GUCA--UGCUGUACCCU----------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGC-AGCAGC-------------------------------------------------------------------------------------------------AG-CCCUUACAGGUCC-----------------------U-CCCUGAGCU----CGGGC-G----------------------------------CUGAG-C-GCCUGAGAA--------GGCUCCGCCGGG------GCAGACUGGGCAGGAGAAGCAGUGG---------------------------------------------------------------------------------------------------------AGCUUGGAAC---AGACUCCC-----AGCC---GGCAAAUG------------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGAC-UGAGAUGGG-GCAUC------------------------------UUUUUGG-GGCU-U-CAU--AACCCAAUUCAGCUUGU-----UCUCC-CC-GGUCC
AC154132.2/16458-16734       UCUGUG----ACAAUCUUGCAUU-------------UGGGGC--UUACUUACU-----------------GUGUA-C------------UUGU-----------UA--CACUUGUAAA-------------------GCCCCGGG-AAGGUCUGAGAU--G-----------------UGUCUUUAA--------------------------------------------------------------------------------------------------UG-CUCCAGAAGGGCG-----------------------C-UUGCAUUUU-----GCAA-G----------------------------------GCGAGAACACCAGAAAU------CUGC-----GAUGA----GGUUUCAAAGCCAAGGAUUCGCUCUGGCGAUAGGUGGUGGAGCUUUAUC-------------------------------------------------------------------------------------GUUGGAAU----UUCUCGU-----GACC---GGCUGUUUU-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUUUG-CGGGCUAGU---------------------------------------GUUU-U--A-C-UAG--AACUCAAUUCAGACUAA-----UCUGU-UA--CAGA
AAHX01100535.1/4678-4411     AAAAAU----GUAAACUUGGGG---------------CGGGG--CCACGCGCU-----------------GAGUG-C------------UCGU-----------CA--CUCCAUCGG--------------------CCUCUGAG-AAGGUCUGAGACU-G----------------GGGCCUCCCGA-------------------------------------------------------------------------------------------------GG-CCCUAACCGGGCU-----------------------C-UCCCCGAGA----GGGGA-G----------------------------------GUGAGUU-CCCAGAGAGC-----AGGGCUCCACGCGU----GGGCAAAAAAAGAGAAAAAAAUGUAAACCUGAAGAG-----------------------------------------------------------------------------------------------GAGCUUCAUA-----GCUUCAU-----AGCUU-CAGCUAUGAC-----------------------------------------------------------------------------------------------------------------------------------------AGCGUGUUUCA-UUUCUUCCC-AGC----------------------------------GUGCU-CCUG-G-GUU--A------UACAG------------UACUUC--UUGU
AAGV020371666.1/2304-1973    GGCCGA---GGGAGGCUUAUCGG--------------CGGGG--CCACAAGCU-----------------GAGUGCG------------CCAU---------GUCA--CUCUAUGCCUU----------------GUCCCUUGGG-AAGGUCUGAGACUGG-----------------GGUCAAAAGC-------------------------------------------------------------------------------------------------GG-CCCUGACAGGGCU-----------------------U-UCCCAGUUC----UGGGG-A---------------------------------GGUGAGUA-CCCUGAAAC------AGGGCCCCGUGUGA----GGAUAGACUGGGCAGGAAGUGCUGUGGAUCCCGUACCUGUGGUGGGACCUGGUGGAUGUCUCC-------------------------------------------------------------UUAGGAGGAACUUGAAAG---AGACUCAU-----GGCC---AGCCAUCCAG--------------------------------------------------------------------------------------------------------------------------------------AGAGUUCAAUGGC-UGAGGUGAG-GAGCC-----------------------------CUGCAUGG-GGCC-U-CAG--AACCCAACUCAGACUGC-----UCUUCCAA--GACC
AAWR02001627.1/344857-344522 GGCGGA---GGGAAGCUCAUCGG--------------UGGGG--CCACGAGCU-----------------GAGUGCG-----------UUUAC---------GUCA--CUCUACCCCCCU---------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAUAAAG------------------------------------------------------------------------------------------------CGG-CCCUAACAGGGCC-----------------------C-UCCCUGACCU-UCAGGGA-G----------------------------------GUGGGUU-CCCAGAGAAC-----GGGGCUCCGCGCGA----GGGCAGACUGGGCAGGAGAUGCUGUGGACCCCGCCCUUGGGGAGGGGCCCGGCGGAUGCCUCC-------------------------------------------------------------UUAGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUACCC---------------------------GCCUACUGG-GGCC-U-CAU--AACCUAAUUCAGACUAC-----UCUCC-CC--CGUC
CAAC02000476.1/587558-587800 UUGGCC----GGAAGAAGACGGU-------------UGGGAG--AGACACAA------------------AGGCCUU------------AAAC--------UAUGG--CCUAAACA---------------------CUCCCGGG-AAGGUCUGAGAGA-A-----------------GGCUUGAAAUA----------------------------------------------------------------------------------------------AGAG-AUCUAGGAGAUCUUU------------------CAGU-UUCCUUAUA----GAGAA-G----------------------------------AGGCUGU-AGAAGAAGA------GUUUCCCCUGUUCG----------------------------------------------------------------------------------------------------------------------------------------GGUUUGGAA-----ACGGCCU----CAGCC---AGCAAUCCAAUAAG-------------------------------------------------------------------------------------------------------------------------------UACUGAGUGCGAUCGU-CAUA----------------------------------------------CC-------------AACACAAUUCAGACUAG-----UCUUC-GG--CCAA
AAHX01078853.1/4403-4730     UGGGCGG--GGGAAGCUCAUCAG--------------CGGGG--CCACGCGCU-----------------GAGUG-C------------UCGU-----------CA--CUCCAUCGG--------------------CCCCUGGG-AAGGUCUGAGACU-G----------------GGGCCUCCCGC-------------------------------------------------------------------------------------------------GG-CCCUAACCGGGCC-----------------------C-UCCCCGAGU----GGGGA-G----------------------------------GUGAGUU-CCCAGAGAGC-----AGGGCUCCACGCGU----GGGCAGACUGGGCAGAAAAUACCCUGAGUGAGGUAAGCCAGACACAAAAGAACACAC-------------------------------------------------------------------------AUGGUUUG--------UACUCACUGAUAAGUC---GAUAUUAGCCCGAAAGCUCAAAAUGCCCACU---------------------------------------------------------------------------------------------UUACAACUUACAGACUAUAUGAAGCUUAA--GA-AGAAGGAAG-AU------------------------------------UGUG-GAUG-U-UUC--AA----------------------UCC-UA--CUUA
AAKN02000179.1/26921-27216   GGCGGA---GGGAAGCUCAUCGG-------------U--GGG--CUACGAGCU-----------------GAGUGCG------------UGAU---------GUCA--CUCUGCAGCAC----------------GUCCCUUGGG-AAGGUCUGAGACCAG-----------------GGCCAGCGGC-------------------------------------------------------------------------------------------------GG-CCCUAAC-AGGCC-----------------------C-UCCCUGAACC-UCAGGGA-A----------------------------------GUGAGUU-CCCAGAGAGC-----AGGGCUGUGCGCGA----GGGCAGACCGGGCAGGAGAUGCCAGCCCACCCUCUGGAGGGGCUCGGCAGAUGCCUCCUUA------------------------------------------------------------------GCCGGAGCUUGGAAA--AAUGCUUUUU--AAGGCA---ACUAAAUU---------------------------------------------------------------------------------------------------------------------------------------------------GU-CACACAAGG-CU------------------------------------AAG---AAC-U-UUU-----CCAAUU---------------UUC-AU--CGUC
AAHX01021842.1/3344-3037     GGUGGG---AGGAUGCUCAUCAG--------------CAGGG--CCACGAGCU-----------------GAGAG-U------------UCAU-----------CU--CUCCAUGGA--------------------CCGUG-GG-AAGGUCUGAGACUGG-----------------AGCCUUCCCC-------------------------------------------------------------------------------------------------UG-CCCUAACCAGGCU-----------------------C-UCCUCGAGC----AGGGA-G----------------------------------GUGAGUU-CCCAGAGAGCAGGGAGGGGCUCCACGCAU----GGGCAGACUGGACAGGAGAAGCGAGGUAUCCGAGUGGGUGGAUACCUCCCUUACCA---------------------------------------------------------------------------GAGCUUGGAAC---AGACUCAC-----UGCC---UGCAGUGCG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-AGAGGUGAG-GCAC--------------------------------CUCUCG-GGUC-C-CAU--AACCCAAUUCAGACUAC-----UCUCC-CC--CGCC
AAKN02019215.1/6561-6232     GGCGGA---GGGAAGCUCAUCGG--------------UGGGG--CUACGAGCU-----------------GAGUGCG------------UGAU---------GUCA--CUCUGUAGCAC----------------GUCCCUUGGG-AAGGUCUGAGACUGG-----------------GGCCAGUGGC-------------------------------------------------------------------------------------------------GG-UCCUAACAGGGCC-----------------------C-UCCCUGAACC-GCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAGC-----GGGGCUCCGCGCAA----GGGCAGACUGGGCAGGAGAUGCCGAGUAUCUCGCCCUCGGGAGGGGCUCGGCGGAUGCCUCCU--------------------------------------------------------------UAGCCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCAAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GCACC-----------------------------CGGCCCGG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UCUCC-CC--CGUC
AAHX01110597.1/24771-24443   GGCGGG----GGAAGCUCAUCAGC------------U--GGG--CCACGCGCU-----------------GAGUG-C------------UCUU-----------CA--CUCCAUCAGCA------------------CCU--GGG-AAGGUCUGAGACUGGG--------------GCCUCCUGCGGCCCU-------------------------------------------------------------------------------------------AACCG-UUCUCUCUGGUCU-----------------------C-UCCCAGAGU----GGGGA-G----------------------------------GUGAGUU-CCCAGAGAGC-----AGGGCUCCACGCAU----GGGCAGACUGGGCAGGAGAAGCCCCUCCCCCCAAAAAG----------------------------------------------------------------------------------------------AGU-----------GGCUUCU-----GGAG---UGAACGAACAAUAAUUGUUCA----------------------------------------------------------------------------------------------------------------CUAUAGUUGUCAGAGUCAGAAAAA-UGAGGCUAG-GAAAGAAAUGGAAAUGAGU-GAAAACAAACAGGAAAUUUUUC-UUUC-U-UGU---------UUCA-ACU---------UUC-CC--UUCC
CAAB02015991.1/11289-11596   GUGAGU----GGAAGCUCAUUGU--------------AGAGA--UCACGUGCU-----------------GAGUG-U------------UCAU-----------CA--CUCUACCAAUC-----------------AUCUCGGGG-AAGGUCUGAGACAAG-----------------AGCCAAUAGU-------------------------------------------------------------------------------------------------UG-UCCUUGCAGGACA-----------------------U-CACCUGAUU---CGGGUG-A----------------------------------GCGAGUG-AACAGAAAAU----AUGGGUCAACUCGUG----CAGUUCUAACAGGAGAAGUCGGUGGGGGCAGUUUCUCAGCCCCGCCGGCGGAUGUGACGC-------------------------------------------------------------------ACGCUGACUUGGAAU----CGCUCGC-----GGCU---GGCAAAUG------------------------------------------------------------------------------------------------------------------------------------------AGUGCGAUGUG-UGAGGUGGA-GC------------------------------------ACU---GCU-C-UAG--AACCCAAUUCAGACUAC-----UCUCC-AC--UCAC
AAPE02015123.1/7133-7464     GGCGGA---GGGAAGCUCAUUGG--------------UGGGG--CUACGCGCU-----------------GAGUGCA------------CCUC---------GUCA--CUCUACCCCAU----------------GUCCCCUGGG-AAGGUCUGAGACUGG-----------------GGCCAAGAGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCC-----------------------C-UCCCUGAGCA-GCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGUCUCCGCGCGA----GGGCAGACUGGGCAGGAGAUGCCACGGACCCCGCCCUCGGGAGGGGCCUGGCGGAUGCCUCCU--------------------------------------------------------------CAAGCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCAAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GCACUC----------------------------CGCAAGGG-GGCC-U-CAU--AACCCAAUUCAGACUAC-----UCUCCCGC--CGUC
AAGW02024246.1/74397-74722   GGCGGA----GGAAGCUCAUCAG--------------UGGGG--CCACGAGCU-----------------GAGUGCG------------UCAC---------GUCA--CUCUACCCCAU----------------GUCCCUUGGG-AAGGUCUGAGACUAG-----------------GGCCAGUAGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCU-----------------------C-UCCCUGAGUC-UCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGGCUCCGCGCGA----GGGCAGACUGGGCAGGAGAUGCCGCGGGCCCGCCCCGGGUCCCGGCGGAUGCCUCCUUAG--------------------------------------------------------------------CCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCGAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GUACCCC--------------------------GCUGGUGGG-AGCC-U-CAU--AACCUAAUUCAGACUAC-----UCUCC-CC--CGCC
AAWZ02020194.1/10090-9770    -CUGGG---AGGAAGCUCUCCGA--------------AGAGG--CCACGUGCU-----------------GAGUG-U------------CCGU-----------CA--CUCUCGUUGCU------------------CCUCUGGG-AAGGUCUGAGAGAAG-----------------GGCCGCUAUUU-----------------------------------------------------------------------------------------------CCG-CCUUAGCAGGGCG-----------------------C-CACCUUCGG---AAGGUG-G----------------------------------GUGAGUU-CCCAGCGAUA-----CGGGCCUCCGGCAA----CGCCCCAGAUUGAGGCAGGAGAAGCGGGCACGGGAUUCACUCCUUCCCGCGGAUGCCUCCGCGG-----------------------------------------------------------CCUGCUUGGGGUUUGGGAA---CGACUCAC-----GGCC---GGCAAAUAU----------------------------------------------------------------------------------------------------------------------------------------GAGUACAAUGGGCAGAGGUGAA-GC------------------------------------CAUG--GCU-U-CAU--AACCCAAUUCAGACUAG-----UCUCCACC--CAG-
AADN03005512.1/31262-31583   UCCGGA----GGAAGCUCACCGU--------------CGAGG--CCACGCACU-----------------GGGUG-U------------CCGU-----------CA--CCCGCGCUUCUC---------------CGCCUCGGGG-AAGGUCUGAGGGAAG-----------------GGCCAUGAGG------------------------------------------------------------------------------------------------CGG-CUCCAGCAGAGCC-----------------------C-CGCCCGCGU----GGGUG-G----------------------------------GUGAGCC-ACCAGCAAGG-----GGGGGCGCCGCGCG----GGCCGGCCUGGGCAGGAGAAGCCCGAACGGCUGCGGAGCUGAUCUGAGCCGGGGCGGAUGCUCGUG--------------------------------------------------------GCCCCGCGGUGCUUUGAGAC---AGACUCAC-----GGCC---GGCGUGCUG-----------------------------------------------------------------------------------------------------------------------------------------AGUCCAAUGGG-UGAGGUGGG-GC------------------------------------AGC---GCC-C-CAC--AACCUAAUUCAGACUAC-----UCUCC-GC--CGGA
AAHX01000007.1/30875-31302   GGCGGG----GGAAGCUCAUCAG--------------CGGGG--CCACGCGCU-----------------GAGUG-C------------UUGU-----------CA--CUCCAUCGG--------------------CCCCUGGG-AAGGUCUGAGACUGG-----------------GGCCUCCCGC-------------------------------------------------------------------------------------------------GG-CCCUAACCGGGCU-----------------------C-UCCCCGAGU----GGGGA-G----------------------------------GUGAGUU-CCCAGAGAGC-----AGGGCUCCACGCGU----GGGCAGACUGGGCAGGAGAAGCCCCCGGGUGGGCGGAUGCCUCCCUCGCCGG--------------------------------------------------------------------------------GGCUUGGAAC---AGACUCAC-----GGCC---AGCAGUUCGAGAACUUAGGCAUCCAAAAGUGUAGCUCCUAGUUUCAGGUGUAGCUGUACCCAGGACUCAAAACCAUCCAGGGACACGGCUGGACCUGUUCUUUCCUUACUCACCCGGGCAUCUGAAUUCCUGUGUCGUUUUCGGUGAGCACAAGGUU-UCCCUGGUU-AU------------------------------------CAAG--CUA-U-CCC--AAC---AUUCAG-----UGCUUUCUUUUCC--UGCU
AAPE02023527.1/19019-19348   GUGGAG----GGAAGCUCAUUGG--------------UGGGG--CUAUGCACU-----------------GAGUGCA------------CCUU---------GUCA--CUGUACCCCAU----------------GUCCCCUGGG-AAGGUCUGAGACUAG-----------------GGCCAAGAGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCC-----------------------C-UCCCUGAGCA-GCGGGGA-G----------------------------------GUGAGUU-CCCAGAGAAC-----GGGUCUCCCCGUGA----GGGCAGACUAGGCAGGAGAUGCCACGGACCCCGCCCUUGGGAGGGGCCUGGCGGAUGCCUCCU--------------------------------------------------------------CAAGCGGAGCUUGGAAC---AGACUCAC-----GGCC---AGCAAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUCAAUGGC-UGAGGUGAG-GCACUC----------------------------CGCAAGGG-GGCC-U-CAU--AACUCAAUUCAGACUAC-----UCUCC-CC--CCCC
ABEG02000622.1/50836-51080   GUUGGC---CGGAAGAAGACGGU-------------UGGGAG--AGACACAA------------------AGGCUU-------------CUAA---------U-AG--CCUCAUCAUAA------------------CUCCCGGG-AAGGUCUGAGAGA-A-----------------GGUCCCUGUG-------------------------------------------------------------------------------------------------AG-AUCUAGGAGAUCU-----------------------U-CCACUAUCCUUAUAGAGG-A----------------------------------GAGGCUGUAGAAGAAGA------GUUUCCCCCGCGCG----------------------------------------------------------------------------------------------------------------------------------------GGUUUGGAAA----CGGCCUC-----GACC---AGCAACUCCAUCGAA----------------------------------------------------------------------------------------------------------------------------UUAGCUGAGUGCGAUCGU-CACA----------------------------------------------CC-------------AACACAAUUCAGACUAG-----UCUUCGGC--CAAC
AAPE02010827.1/4555-4226     GCGGAG----GGAAGCUCAUUGG--------------UGGGG--CUACGCACU-----------------GAGUGCA------------CCUC---------GUCA--CUCUACCCCAU----------------GUCCCCUGGG-AAGGUUUGAGACUAG-----------------GGCCAAGAGC-------------------------------------------------------------------------------------------------GG-CCCUAACAGGGCC-----------------------C-UCCCUGAGCU-GCAGGGA-G----------------------------------GUGAGUU-CCCAGAGAAU-----GGGUCUCCGCGCGA----GGGCAGACUGGGCAGGAGAUGCCACGGUCCCCGCCCUUGGGAGGGGCCUGGCAGAUGCCUCCU--------------------------------------------------------------CAAGCAGAGCUUGGAAU---AGACUCAC-----AGCC---AGCAAAGUG-----------------------------------------------------------------------------------------------------------------------------------------AGUUUAAUGGC-UGAGGUGAG-GCACUC----------------------------CGCAAAGG-GGCC-U-CAU--AACCUAAUUCAGACUAC-----UUUCC-CC--CCGC
#=GC SS_cons                 {{{{--....{{{,,AAAAAAA,..............<<<<<..---------.................<<<<<<_............____.........>.>>..>>>--------..................>>>>>,,,.,,,,,[[[[[,,,,,.................((((,,,,,,.................................................................................................<<.<<<_____>>>>>.......................<.<<<<<____....>>>>>.>..................................<<<<<<<.----------.....---<<<________....____________________________________________________................................................................................>>>-------...->>>>>>>.....))))...,,,,,,,,,,,....................................................................................................................................,,,,,,,,,,,aaa.aaaa<<<<<.<<....................................____._>>>.>.>>>..,,,,,,,]]]]],,,,,.....,,}}}.--..}}}}
#=GC RF                      ggaggg....ggAAGCUCaucgu..............aggGG..ccACacACu.................GAGugcc............ucau.........g.ca..CUCuaucaauu..................CCccuGGG.AAGGUCUGaGAcagG.................GGCCaauagc.................................................................................................ug.CCCUaGcaGGGca.......................c.cccccGaaa....ggggg.g..................................guGaGuu.ACCAGAAAuC.....agggccccacugGu....gggcagacugggcaGgagaaGcccugGgccgggcggaugcguuccugcccgg................................................................................ggcUUGGAAa...agaCuCac.....GGCC...aGCaauUUgag....................................................................................................................................UUGAGUgCAAUggu.uGagguGau.gc....................................uuag.ggca.u.Cau..AACCCAAUuCAGACUAC.....UCUcc.gc..cucc
//
# STOCKHOLM 1.0

#=GF AC   RF00010
#=GF ID   RNaseP_bact_a
#=GF DE   Bacterial RNase P class A
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Mifsud W; 0000-0002-9805-6461
#=GF SE   Brown JW, The Ribonuclease P Database, PMID:9847214
#=GF SS   Published; PMID:9847214
#=GF GA   100.00
#=GF TC   100.50
#=GF NC   99.60
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00002
#=GF DR   URL; http://jwbrown.mbio.ncsu.edu/RNaseP/home.html;
#=GF DR   SO; 0000386; RNase_P_RNA;
#=GF DR   GO; 0008033; tRNA processing;
#=GF DR   GO; 0004526; ribonuclease P activity;
#=GF DR   GO; 0030680; dimeric ribonuclease P complex;
#=GF RN   [1]
#=GF RM   9759486
#=GF RT   Ribonuclease P: unity and diversity in a tRNA processing ribozyme.
#=GF RA   Frank DN, Pace NR
#=GF RL   Annu Rev Biochem 1998;67:153-180.
#=GF RN   [2]
#=GF RM   9847214
#=GF RT   The Ribonuclease P Database.
#=GF RA   Brown JW
#=GF RL   Nucleic Acids Res 1999;27:314.
#=GF RN   [3]
#=GF RM   23324607
#=GF RT   Identification and characterization of small RNAs in Yersinia pestis.
#=GF RA   Beauregard A, Smith EA, Petrone BL, Singh N, Karch C, McDonough KA, Wade
#=GF RA   JT
#=GF RL   RNA Biol. 2013;10:397-405.
#=GF CC   Ribonuclease P (RNase P) is a ubiquitous endoribonuclease, found in
#=GF CC   archaea, bacteria and eukarya as well as chloroplasts and mitochondria.
#=GF CC   Its best characterised activity is the generation of mature 5'-ends of
#=GF CC   tRNAs by cleaving the 5'-leader elements of precursor-tRNAs. Cellular
#=GF CC   RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its
#=GF CC   catalytic activity in the absence of the protein subunit, i.e. it is a
#=GF CC   ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown
#=GF CC   to retain its catalytic function, but is still essential for the catalytic
#=GF CC   activity of the holoenzyme. Although the archaeal and eukaryotic
#=GF CC   holoenzyme s have a much greater protein content than the bacterial ones,
#=GF CC   the RNA cores from all the three lineages are homologous -- helices
#=GF CC   corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular
#=GF CC   RNase P RNAs. Yet, there is considerable sequence variation, particularly
#=GF CC   among the eukaryotic RNAs. Identified in Yersinia as Ysr151/RnpB. 
#=GF WK   Ribonuclease_P
#=GF SQ   458


AF012801.1/1-340               -------------------G------------------------------------------------------------------------------------------------------------------------------------AGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------GUUGC------------UAACG----------------GCAACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----CG---G--CCG-------------------------------------------------------------------------------------------------------------------------ACAGCGG-C----C--G---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGC-C-U-C-GG-GUGA--CC-G-G-G-GCGG-C-UC----------------GGUAAAC-CCCACCC-GGAGCAAGGCC-AAGAGGAAGCCCU------------CGGGCUUCUGCGCA--G-GCGUUC----------------------------------------------------GAGGGCGGCCC----GUCCG-------AUGCC---CG-C-----GGGU---A-----G---G-CCGC---------------------U--AGA-GCCU-G-U-CGGCGACGG-C--A-G-G-C-C--CAGAUGGAU-GGUCGCCC-----------------AUCGUCCGCCGCGAGGCGG----------------------------------GCGUGGAUAGAACCCGGCGUA--G-----------------
AF110048.1/1-309               -------------------------------------------------------------------------------------------------------------------------------------------------------------------------C---ACA--GAGCAAC-GG-UG----------------GUGGC------------UAACG----------------GCCACCCACG-----------------------GCGA------CGUGCGGG-AC---AGU-GCCACAGAAA--UCAG-ACC-GCC----AG---C--GGCCGCCGCU----------------------------------------------------------------------------------------------------------CCUCGGAGCAGCGGU-G----C--G---GGUAAGGGUGAAAC----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCGC-U-C-C-GG-GUGA--CC-G-G-G-GCGG-C-UA----------------GGUAAAC-CCCACCG-GGAGCAAGACC-AAGAGAGUCGCGUGGCG----CUUCGGCGGUGCACGGCU--U-GCGCUG----------------------------------------------------ACGGGCUGCUC----GUCCG-------AUGUC---AG-C-----GGGU---A-----G---G-UUGC---------------------A--CGA-GGCG-U-C-CAGCAAUGG-G--C-G-U-C-C--CAGAUGGAU------------------------------------------------------------------------------------GGUCGCCCACG-------------------------
AF110049.1/1-307               -------------------------------------------------------------------------------------------------------------------------------------------------------------------------C---ACA--GGGCA-G-GG-UG----------------GUGGC------------CAACA----------------GCCACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAGA--ACAG-ACC-GCC----GG---C--UGC-------------------------------------------------------------------------------------------------------------------------UCG-GCA-G----C--C---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGC-U-C-C-AG-GUGA--CU-G-G-A-GCGG-C-UC----------------GGUAAAC-CCCACCC-GGAGCAAGUCC-AGAC------------------------------A-GCG--U-GUGCACGGCGCCUUC---------------------------------GGGCGUCGAGGAGACCGGCCC----GGUCG--------AGCG---CG-C-----GGGU---A-----G---G-ACGC---------------------U--AGA-GCCG-G-C-CAGCAAUGG-U--C-G-G-C-C--CAGAUGGAU-GGCCGUCG-----------------CCGCGCCACCGGUA--------------------------------------------ACGGGGGCGCGGA-----------------------
AF110036.1/1-281               -------------------------------------------------------------------------------------------------------------------------------------------------------------------------C---ACA--GGACA-G-GG-UG----------------GUGGC------------UAACG----------------GCCACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAGA--ACAG-ACC-GCC----GC---U--ACC------------------------------------------------------------------------------------------------------------------------CUCCAGGU-A----G--C---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC-AGUCC-U-C-G-UG-GUGA--CA-C-G-A-GGAG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGACC-AGAC------------------------------A-GCG--U-ACGACGGUGUUAG-------------------------------------UUCACUGGGAGGGCGGUCC----GCCCG--------AGUG---CG-C-----GGGU---A-----G---G-UUGC---------------------U--AGA-GGCC-A-U-CGGCAACGA-U--G-G-U-C-C--GAGAUG---------------------------------------------------------------------------------------GAUGGUCGCCGACU----------------------
L25705.1/1-330                 --------------------------G-----------------------------------------------------------------------------------------------------------------------------AGGAAAGUCCGGACAA-C---ACA--GAGCA-A-CU-CA----------------CUUCC------------UAACG----------------GGAAGGCUCC----------------------GUUCAG---GCGGAGACAG-CA---AGU-GCCACAGAAA--AUAU-ACC-GCC----UU---G--UC---------------------------------------------------------------------------------------------------------------------------UUU-GA-U----G--A---GGUAAGGGUGAAAA----CGU---GA-G--G--U----------------------AAGAG-CUCACG-GUAUU-G-C-A-UG-GCGA--CA-U-G-G-AUU----AC----------------GGUAAAC-CUUGAGU-GUUGAAAGACC-AAAU------------------------------AGGUU--A-CGAAACUCGAAGGCUGC------------------------------UCGUCUUCUUUUACUUCGGUAA----GA--U--------UCGU---AA-U-----GGGU---A-----G---G-UUGA---------------------U--GGA-GUCU-G-U-CAGCAAUGG-C--A-G-A-U-C--UAGAUAAAU-GAUAGAAA-----------------ACCGAUUUUUCGGU-------------------------------------------GUACAGAACCCGGCUUA--------------------
X97391.1/1-342                 -------------------GGGG---------------------------------------------------------------------------------------------------------------------------------AGGAAAGUCCGGGCUC-CC-CAAU--GGCCA-G-GCUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAC--ACC-GCCG--AUG---G--CUCCGCUUCCG--------------------------------------------------------------------------------------------------------CUGCGGUGGAGACGAG-C---AC--A---GGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGCCGGGAGCAAGGCC-CA----------------------------------GGG--A-CCAACGG--------------------------------------------------UUGGCCAUGACA---CCGGUC--------CCGC---CC-C-----AAGU---G-----C---G-CCGC---------------------U--CGA-GGCC-G-C-CGGAGACGG-C--G-G-U-C-C--CAGACAGAU-GAUCACCCCGGG--------CAGGGUCCGCCCCACCCGG--------------------------------------------AACAGAACCCGGCUUA--------------------
AJ272219.1/1-333               ----------------G---------------------------------------------------------------------------------------------------------------------------------------AGGAAAGUCCGGGCUC-CU-AUUU--GGCCA-G-GCUUG----------------CUGGG------------UAAUU----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AU---AGU-GCCACAGAAA--CAC--ACC-GCCU--AAU---G--CUUAAUGGG------------------------------------------------------------------------------------------------------------GAAAUCCCAACAAG-C----G--C---GGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UA----------------GGUAAAC-CCCGGCCAGGAGCAAGGC-------------------------------------GAGG--G-GCACUG----------------------------------------------------GAUGGCCAUAG----ACCUU---------GUC---CC-U-----GUAG---A-----G--AG-CCGC---------------------U--UGA-GGCU-A-C-CGGUAACGU-U--A-G-U-C-C--CAGAUAGAU-GAUUACCCAUUCUC-----UUUCUAAAGAAAGAGGAAAG--------------------------------------------AACAGAACCCGGCUUA--C-----------------
U64880.1/1-331                 --------------------------G-----------------------------------------------------------------------------------------------------------------------------AGGAAAGUCCGGGCUC-C---GCA--GGGCA-G-GA-UG----------------CUGGG------------UAAUA----------------CCCAGUGGGG-----------------------GCGA------CCCUAAGG-AU---AGU-GCAACAGAAA--UAU--ACC-GCC----UG---A--CACUUAAUAUAUGUAGCUA-----------------------------------------------------------------------------------------UAGAUGUUACCAUAUAUUAAGUG-C----C--G---GGUAAGGGUGGGAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCAG-C-U-A-G--GCGA---C-U-A-G-CUGG-C-UC----------------UGUAAAC-CCCAUCU-GGAGCAAGACC-AAGU------------------------------UA-GG--G-ACAUAAA-------------------------------------------------AAGGUGGUGGCCC----GUCAC--------CGUC---CC-GG---UUGGU---A-----G---G-UCGC---------------------U--AGA-GCCU-A-U-UGGCGACAA-U--A-G-G-C-G--UAGAUAGAU--------G-----------------GCUGUCUAA-------------------------------------------------CACAGAACCCGGCUUA--------------------
M59354.1/1-402                 CCAG-UU-G-G-C-C-G--GGCAGCCGCGCC-UU--A-CCAAUGU---------------------------------------------------------------------------------CGAAAGAC-----GG-U-A-A-GGUGAGGAAAGUCCGGGCUC-C---ACG-GAAAUA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAGA--GCAA-ACC-GCC----AU---G--C----------------------------------------------------------------------------------------------------------------------------CUU--G-C----A--U---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGC-C-G-C-UG-GUGA--CA-G-U-G-GUGG-C-AA----------------GGUAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGA--U-GACACGGGGCGGGCGAAA----------------------------GCCUGUUCACAGCCGGUUUCCGG----GCCCG---------UCA---UC-C-----GGGU---G-----G---G-UUGC---------------------G--AGA-GGCG-G-C-AUGCAAAUG-C--C-G-U-C-C--CAGAUGAAU-GGCUGCCACG-------------UUCCGGGUCAAACCGGGG---------------------------------------CCAUACAGAACCCGGCUUA--C-AGGCCAA-CUGGCGAA
M59355.1/163-591               CCAG-UC-G-G-C-C-G--GAUGGCCGCUCU-CC--G-UCAUCGUCCCCGGGC------------------------------------------------------------------CACCCCCGAUGGACC-----GU-C-G-G-GGGGAGGAAAGUCCGGGCUC-C---ACG-GGAACA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCGGGG-----------------------GCGA------CCCUAGGG-AA---AGU-GCCACAGAGA--GCAA-ACC-GCC----GG---C--CU---------------------------------------------------------------------------------------------------------------------------AUA-CG-G----C--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCCU-G-C-C-CG-GCAA--CG-G-G-G-AGGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAGAUC-GAAU------------------------------AGGGA--C-GGCACGCCCCGGUUU---------------------------------UCCGGGGCAAGCGGCGUUUCC---GCGCCG---------CCG---UC-C-----GGGU---A-----G--UA-UCGC---------------------G--CGA-GGCG-U-C-CGGUAACGG-G--C-G-U-C-C--CAGAUGAAU-GGCCAUCC-----------------CCGUCGUCGCGUCCCUUGCGGGAUA----------------------CGGCCGGCGUGGACAGAACCCGGCUUA--C-AGGCCGU-CUGGCGGU
AJ235272.1/10905-10521         CUAA-AU-G-G-U-C-G--UGCAGUUGCGUG-AU------------------------------------------------------------------------------------------------GAUA----------A-U-CACGAGGAAAGUCCGGACUC-U---AUA-GAGGUA-U-GG-UG----------------CCGGU------------UAACA----------------UCCGGCAGAGUA-------------------UUAUUA------CUUUAGGG-CU---AGU-ACCACAGAAA--AUAU-ACC-GCC----GA---G-------------------------------------------------------------------------------------------------------------------------------UAU----U----U--C---GGUAAGGGUGAAAA----GGU---GU-G--G--U----------------------AAGAG-CACACC--GGUA-A-G-U-UG-GCAA--CA-A-G-U-UACG-C-AU----------------GGUUAAC-CCCACCA-AGAGCAAGAUC-AAAU------------------------------AGGCA--U-UACAGAAUUUAAAUAUUUAU------------------------UUAAGUUCCUGGGUUACCUCUAAUC----GGAUU--------GUAA---UG-C-----GGGU---A-----G---A-UCGC---------------------U--UGA-GGUA-A-A-CGGUAACGU-U--U-A-U-C-C--UAGAUAAAU-AACUGCAA-----------------UGAAUUAAUAUUCA--------------------------------------------UACAGAAUCCGGCUUA--U-AGACCAG-AUGAGCAG
M59353.1/255-595               AAAG-CA-G-G-C-C-A--GGCAACCGCUGC-CU--G-CACC----------------------------------------------------------------------------------------GCAAG---GUG-C-A-G-GGGGAGGAAAGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------UUGGC------------UAACA----------------GCCAUCCACG-----------------------GCAA------CGUGCGGA-AU---AGG-GCCACAGAGA--CGAG-UCUUGCC----GC---C--GGG-------------------------------------------------------------------------------------------------------------------------UUCGCCC-G----G--C---GGGAAGGGUGAAAC--------------------------------------------------------------------------------------------GC----------------GGUAACC-UCCACCU-GGAGCAAUCCC-AAAU------------------------------AGGCA--G-GCGAUG----------------------------------------------------A--AGCGGCCC----GCUGA---------GUC---UG-C-----GGGU---A-----G---G-GAGC---------------------U--GGA-GCCG-G-C-UGGUAACAG-C--C-G-G-C-C--UAGAGGAAU-GGUUGUCACGCA---------CCGUUUGCCGCAAGGCGGGCGG------------------------------------GGCGCACAGAAUCCGGCUUA--U-CGGCCUG-CUUUGCUU
BX640434.1/240958-240545       AGGG-CA-G-A-U-C-G--GGCAAUCGCGGG-GG--A-U-------------------------------------------------------------------------------------------GCAA------A-U-C-C-UUCGAGGAAGGUCCGGACUC-C---ACA--GGGCG-G-GA-UA----------------GCGGC------------UAACG----------------GCCGUCCGGCGACGCUGGCGGGCUUGCCCGCCGGAAA-----AGCCGAGGA-AC---AGG-GCCACAGAGA--CGAG-UCU-GUC----AU---G--AG--------------------------------------------------------------------------------------------------------------------------GGCG-CG-C----C--U---GGC----GCGCACC----GGC---AC-G--G--C----------------------CAUCUCCGUGCC--GCGC-C-GUC-CG-GAAA--CG-GGC-G-GCGG-C-AUGACAGGG-UGAAACGCGGCAACC-UCUAUCC-GGAGCAACAUC-AAAU------------------------------AGGCA--U-GCGUACGGCCGUA-------------------------------------AGGCCGGGAAGGGCGGCUC---CGUCCA--------AGCA---UG-C-----GGGU---A-----G---G-UGGC---------------------U--GGA-GCGG-U-C-CAGCAAUGG-U--U-C-G-C-C--AAGAGGAAU-GAUUGCCC-----------------GCCGGGGAAACCCGG-----------------------------------------CGUACAGAAUCCGGCCUA--U-AGAUCUG-CUCU----
M59356.1/53-421                GGAG-UC-G-G-C-C-A--GACAGUCGCUUC-CG--U-CCUG----------------------------------------------------------------------------------------G--------UG-A-C-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GAGA------GUCCACGG-AA---AGU-GCCGCAGAAA--AGAU-ACC-GCCG-ACCC---C--GUC-------------------------------------------------------------------------------------------------------------------------CUCGGAC-G----G--G--AGGUAAGGGUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-U-G-G-UG-GCAA--CA-U-C-A-GUGG-C-AG----------------GGUAAAC-CCCACCC-GGAGCAAGACC-AAAU------------------------------AGGGG--A-ACUCGCGGCUUC---------------------------------------GACCGCAGCGCGCGGCCC----GCGCG--------UGUU---CC-C-----GGGU---A-----G---G-UCGC---------------------U--AGA-GGCG-U-G-CGGCGACGC-A--C-G-U-C-C--CAGAUGAAU-GACUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGCCGA-CUCCCUUC
AF211853.1/1-377               GAAG-CU-G-A-C-C-A--GACAGUCGCCGC-UU--C-GUCGUCGUCCUCU----------------------------------------------------------------------UCGGGGGAGACGG-----GC-G-G-A-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGA------------UAACG----------------CCUGGG-GGG-----------------------GAAA------CCCA-CGA-CC---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CCCGC--------------------------------------------------------------------------------------------------------------------GCAAGCGGGA-U----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-C-UG-GUAA--CA-GUC-C-GUGG-C-AC----------------GGUAAAC-UCCACCC-GGAGCAAGGCC-AAAU------------------------------AGGGG--U-UCAUAA-----------------------------------------------------GGUACGGCCC----GUACU---------GAA---CC-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GCCA-G-U-GAGCGAUUG-C--U-G-G-C-C--UAGAUGAAU-GACUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGUCAG-UUUCACCU
M33657.1/1-383                 GAAG-CU-G-A-C-C-A--GACAGUCGCCGC-UU--C-GUCGUCGUCCUCCU--------------------------------------------------------------------UCGGGGGGAGACGG-----GC-G-G-A-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-A-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGU-----------------------GUCAC----GACCCACGA-CC---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CCCGC--------------------------------------------------------------------------------------------------------------------GCAAGCGGGA-U----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-C-UG-GUAA--CA-GUC-C-GCGG-C-AC----------------GGUAAAC-UCCACCC-GGAGCAAGGCC-AAAU------------------------------AGGGG--U-UCAUAA-----------------------------------------------------GGUACGGCCC----GUACU---------GAA---CC-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GCCA-G-U-GAGCGAUUG-C--U-G-G-C-C--UAGAUGAAU-GACUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGUCAG-UUUCACCU
M19024.1/1-354                 AGAG-UC-G-A-U-U-G--GACAGUCGCUGC-CC--U-CUAU----------------------------------------------------------------------------------------GAAAA--UUAG-G-G-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCG-A-AG-UG----------------CCAGG------------UAAUG----------------CCUGGGGGGC-----------------------GUGA------GCCUACGG-AA---AGU-GCCACAGAAA--AUA--ACC-GCC---UAA---G--CAC-------------------------------------------------------------------------------------------------------------------------UUCGGUG-C----C------GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-G-A-C-UG-GCAA--CA-GUU-C-GUGG-C-UA----------------GGUAAAC-CCCACUU-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCAA-------------------------------------------------------GGCGUGGCCC----GCGCU---------GGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--AAA-GAUG-U-C-CAGUGAUGG-C--C-A-U-C-G--UAGACGAAU-GACUGUUC------------------------AA-------------------------------------------------GACAGAACCCGGCUUA--U-AGAUCGA-CUCUCCAC
M59357.1/212-571               GGAG-UC-G-G-A-C-G--GAUCGUCGCCGC-GG--G-G-------------------------------------------------------------------------------------------GCAA------C-U-C-C-GGGGAGGAAAGUCCGGGCUC-C---AAA--GGGCA-G-AA-CG----------------CUGGA------------UAACA----------------UCCAGGGAGG-----------------------GCAA------CCUC-CGG-AC---AGC-GCCACAGAAA--GCAA-ACC-GCC----CG---G--CCU-----------------------------------------------------------------------------------------------------------------------------CGG-C----C--G---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGAUG-C-C-G-UG-GUGA--CA-C-G-G-CAUG-C-UC----------------GGCAUAC-CCCGUUC-GGAGCAAGACC-AAAU------------------------------AGGGA--A-GG---------------------------------------------------------CGGCCGGCCC----GGCCGA------AGCCU---UC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGGU-G-U-GGGCAACCG-C--A-C-U-C-C--UAGAGGAAU-GACGGUCAC---------------ACGCGGGCAACCGUGU------------------------------------------GGACAGAACCCGGCUUA--C-AGUCCGA-CUCCCGCA
AF181879.1/575-891             CGCA-UU-A-G-A-A----GAUGGUCGCUAU-U-------------------------------------------------------------------------------------------------UUAG------------A-AUAGAGGAAAGUCCGGGCUA-C---AUU--AGACA-A-AA-UU----------------CCAUC------------UAACG----------------GAUGGCUAGC-----------------------GCAA------GCUAAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----UU-----------------------------------------------------------------------------------------------------------------------------------UUU---------A--A---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--AGAG-C-U-A-AA-GCAA--UU-U-A-G-CUUG-UUUG----------------GGCAAAC-CCAAUUU-GUAGCAAGAAG-UGCA------------------------------UGGUA--A-GUCUAA---------------------------------------------------------------------------------AUU---GA-U-----ACGC---G-----C---U-UCGC---------------------U--UGA-GGAA-U-A-UUGCAAAAU-A--U-U-U-C-C--CAGAUAAAU-GGCCAUCC-----------------AUU-------------------------------------------------------GACAGAACCCGGCUUA-----UUCUAA-UGCUCAA-
BX248358.1/328133-327709       UGAG-CC-G-G-C-U-G--GGCGAUCGCGAC-UU--U-GCGUACCACAUGCG--------------------------------------------------------------------AUGAACAUGGUGGC-----GC-A-A-G-GACGAGGAAAGUCCGGACUC-C---ACA--GAGCA-C-GG-UG----------------AUUGU------------UAACA----------------ACAACCCGGG-----------------------GUGA------CCCGCGGG-CA---AGU-GCAACAGAAA--GUAA-ACC-GCC----UA---G--AA---------------------------------------------------------------------------------------------------------------------------UUU-UU-C----U--A---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGA-G-G-U-AG-GUGA--CU-A-C-C-UCGG-C-UA----------------GGUAAAC-CCCACUG-GGAGCAAGGC--AUUA------------------------------GGGCG--U-ACCGUCGUUUCAGACGGUAUG----------------------UCUGCACGAACGCUUGAAGGCUGCUC----GCCUG--------AGUU---CG-U-----GGGU---A---------G-CUGC---------------------U--UGA-GGCG-G-C-CAGUGAUGG-UUUC-G-U-C----CAGAUGGAU-GAUCGCCG-----------------CUGAUCUCCGCUUGUCGGG---------------------------------GGUGAGUACAGAAUCCGGCUUA--U-AUGCUGG-CUCAUUCG
X65648.1/164-611               GAGA-GU-A-G-G-C-GUUGGCGGUUGCAGA-CC--A-GUUA----------------------------------------------------------------------------------------GCUU----AAC-U-G-A-UUUGAGGAAAGUCCGGACUC-CC-GAAA--GACCA-G-ACUUG----------------CUGGA------------UAACG----------------UCCAGUGCGA-----------------------GCGA------UCGUGAGG-AU---AGU-GCCACAGAAA--AAU--ACC-GCC----AA---G--AUUGGGGACUGGGGACUAGGGGUUGGGGACUGGGGAA----------------------------------------------------GAAACUUCCCAAUCCCUAAUCCCCCAUACCCAAUACCCAACU-C----U--U---GGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-A-U-C--GAGA---G-G-U-A-CUGG-C-UC----------------GGUAAAC-CCCGGUUGGGAGCAAGGCC-GAAG------------------------------AACUA--U-GG---------------------------------------------------------UUGGUCUUUU----ACCAG-------UUCCG--CUA-U-----CAGA---G-----A---G-CCGC---------------------U--AGA-GGCG-U-U-UGGUAACAA-A--C-G-U-C-C--CAGAUAGAU-AAUCGCCC-----------------UCGUGUAAAGCAAUUUACA----------------------------------CAGAGAACAGAACCCGGCUUA--C-CACCAAC-UCUCUCCU
X65649.1/123-579               GAGA-GU-A-G-G-C-GUAGGCGGUUGCAGA-UC--A-GUCA----------------------------------------------------------------------------------------CAAA----AAC-U-GAA-UUUGAGGAAAGUCCGGGCUC-CC-GAAA--GACCA-A-ACUUG----------------CUGGA------------UAACG----------------UCCAGUGCGA-----------------------GCGA------UCGUGAGG-AU---AGU-GCCACAGAAA--GAU--ACC-GCC----AA---U--UAGUCAUUAGUCAUUUGUCAUUAGUCAUUUGGA------------------------------------------------------------AAAACACAAAGGACAAAGGACAAAGAACAAAUGACCAA-A----U--U---GGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-G-U-C--GAGA---G-G-C-G-UUGG-C-UC----------------GGUAAAC-CCCGGUUGGGAGCAAGGCG-AAA---------------------------------GGA--A-CUAU-------------------------------------------------------GGUUGGUCUU----UUACC---------AGU---UC-C-----GCUA---AAACAGA---G-CCGC---------------------U--AGA-GGCG-U-U-UGGUAACAA-A--C-G-U-C-C--CAGAUAGAU-AACCGCCC-----------------UCAUGUAGAGAAGUUACUUGUAACAU-------------------UUCUACAUUCGAGAACAGAACCCGGCUUA--C-UACCAAC-UCUUUCCC
Y16812.1/9-481                 AGAA-GU-A-G-G-C-G-AGGCGGCUGCGGA-UU--C-GGCGGCG----------------------------------------------------------------------------------AUGCUGA-----CU-G-A-A-UUCGAGGAAAGUCCGGGCUU-CC-GAAA--GACCA-C-ACUUG----------------CUGGG------------UAACG----------------CCCAGUGCGC-----------------------GUGA------GCGUGAGG-AU---AGU-GCCACAGAAA--AAU--ACC-GCC----CU---G--GCCCUUCGGGGUUUCGGUGUGGUGGGUCAGGCUCCU-------------------------------------------------------GGAGCCGAACCGCUGUCCCUGGAAUCUGUGAGUGAAGGGC-U----G--G---GGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGUGGGACGCAAGG--------------------------------------UCGG--A-GGAACUAGGGUUGGUCUUUUU---------------------CCCGUUCCGUACAGGGUCAAUCUUCGG----GUUGG--------CGCU---GC-G-----GUGU---A-----------CCGC---------------------U--AGA-GGUG-U-C-UGGUAACAG-G--C-A-U-U-C--GAGAUAGAU-AGCUGCCC-----------------CUAAGUCUGGAGACAGAU-----------------------------------GAGGGAACAGAACCCGGCUUA--U-GUCCAAC-UUCUUCGU
X73135.1/43-490                AAGA-GU-A-A-G-C-G--AGCAGUUGCGAA-AU--U-AGUCUUAAAGUAUAAUG--------------------------------------------------------------AAAAUUUGCUUUAAGUA-----CG-G-A-U-UUUGAGGAAAGUCCGGGCUU-CCAAGAA--GAUCA-G-GC-UG----------------CUGGA------------UAACG----------------CCCAGUGCGA-----------------------GCAA------UCGUGAGG-AU---AGU-GCCACAGAAA--GAU--ACC-GCC----UA---A--C---------------------------------------------------------------------------------------------------------------------------UUCG--G-U----U--A---GGUAAGGGUGCAAA----GGU---GU-G--U--U----------------------AAGAG-CGCACC-AGCAG-G-G-U-C--GUGA---G-G-C-U-CUGG-C-UC----------------GGUAAAC-CCCAGUCGGAAGCAAGGCG-AGAG------------------------------GAAAU--A-AGCGUUGCGAUCUUCAAUAGACCUUAUUUCC-GUGACUUAACUGCGUUUAGUGCGCGAAAGCGUGGCAA----GCGUA--------GUUA---A--------GUGU---G-----U---G-CCGC---------------------A--AGA-GGUA-U-U-UGGUAACAA-A--U-A-U-C-C--CAGAUAGAU-AACCGCUAGGGC--------AGUUGUUAUCAACUCCCAA--------------------------------------------AACAGAACCCGGCUUA--U-GUCUUAC-UCUUUCU-
AJ310737.1/2-388               CGGA-AG-A-G-U-A-A--GGCAACCGCUUC-UU--G-UACCUUA----------------------------------------------------------------------------------ACUAAGG-----UA-G-A-U-UAAGAGGAAAGUCUGGACUU-C---AUA--AGAAA-A-GA-UA----------------CUGGA------------GAAAC----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAU-UCC-GCU----AU---A--AAAG-----------------------------------------------------------------------------------------------------------------------GGUCUUUU-U----A--U---AGACAGGCUGAAAA---UUCC---UA-U--U--U----------------------UAAGA-AUAGGA--GCUA-U-U-A-AG-GUGA--CU-U-A-G-UAGA-C--A----------------UGCAAAC-CCUAUCU-GAAGCAAGA--------------------------------------GAAA--A-AGUUUUUGUUUCU--------------------------------------GCAUAAUGAGGGAGGGUA----UCCCUCA---UGAACUU---UU-U-----CAUA---A-----------UCGC---------------------U--UGA-GGGA-U-A-UAGUAAUAU-A--U-C-C-C-C--UAGAUGAAU-GGUUGCCC-----------------UCAAGAUGAGUUUUCUCAU---------------------------------CUUGUAGACAGAAYCCGGCUUA--C-UCGCUC----------
L25703.1/209-594               AAAC-CGCA-A-G-U-G--UGCAGUCGCUGU-AU--G-GCUU----------------------------------------------------------------------------------------GAC------GC-U-G-U-GCAGAGGAAAGUCCGAACUU-C---ACA--GGGCA-G-GG-UGCCGGUC----GAGAACCUGGU------------UCAAG----------------GCCGGGGGCAGC------------------GGUGCAAACCGUCUGUCACAG-AG---AGU-GCAACAGAAA--GCAA-ACC-GCC----CC---G--GC--------------------------------------------------------------------------------------------------------------------------UCCG-GC-C----G--G---AGUAAGGGUGAAAA----GGC---GG-U--G--U----------------------AAGAG-ACCACC-AGGUG-C-G-U-CA-GCAA--UG-C-C-G-UACG-C-UA----------------UGAAAAC-CUC-CCC-GAAGCAAGGCC-AAAU------------------------------AUGGA--A-GCUUUUUCCGCA---------------------------------------AGGAAAGAAGGGUUGCCC----GCCCA-------ACGUU---UC-C-----GGGU---A-----G---G-CCGC---------------------A------------------------------------U--CAGAUAAAU-GACUGCAGCUU----------CAUCACUCGAUGAUGAUU--------------------------------------------CACAGAAUUCGGCUUA--C-AGCUUCG-GUUUCAGC
L25704.1/3-383                 AAAC-CGCA-A-G-U-G--UGCAGUCGCUGU-AU--G-GU-------------------------------------------------------------------------------------------AUA-----AC-C-A-U-GCAGAGGAAAGUCCGAACUU-C---ACA--GGGCA-G-GG-UG----------------CCGGUC---------GAGAACGUUUGU------UCAAGACCGGGGGCAGC------------------GGCGCAAGCUGUCUGUCACAG-AG---AGU-GCAACAGAAA--GCAA-ACC-GCU----CC---G--GCU-------------------------------------------------------------------------------------------------------------------------UA--AAC-C----G--G---AGUAAGGGUGAAAA----GGG---GG-U--G--U----------------------AAGAG-ACCACC-AGGCA-G-G-U-CA-GCAA--UG-C-C-C-UGCG-C-UA----------------UGAAAAC-CUC-CCC-GAAGCAAGGCC-AAAU------------------------------AAGGA--A-GCAUUUCCUGCA---------------------------------------AGGGAAGAAGGGUUGCCC----GCCCA-------AUGUU---UC-C-----GGGU---A-----G---G-CCGC---------------------A------------------------------------U--CAGAUAAAU-GGCUGCAA-----------------CAUCACUACUUGAUGGU-------------------------------------GAUGGACAGAAUUCGGCUUA--C-AGCUUCG-GUUU----
Z15006.1/122-490               CAGG-AU-A-G-G-G-G--UGCGGUCGCGCC-CG--G-GGGAC--------------------------------------------------------------------------------------UUCCC-----CC-C-U-G-GGUGAGGAAAGUCCGGGCAC-C---AUA--GGGCA-G-GG-UG----------------CCAGC------------UAACG----------------GCUGGGCGGG-----------------------GCAA------CCCGACGG-AA---AGU-GCCACAGAGA--AGAG-ACC-GCC----AG---C--GGCCGGG-----------------------------------------------------------------------------------------------------------------GCUUCCCCGGU-G----C--G---GGCAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC-GCCUG-G-C-C-UG-GCAA--CA-G-G-C-UGGG-GCAC----------------GGCAAAC-CCCACCC-GGUGCAAGGCC-CGAU------------------------------AGGCA--G-GAA--------------------------------------------------------GGGCUUGCCC----GGCCCGU---UAGAACC---UG-C----GGGAU---G-----G---G-CCGC---------------------U--UGA-GGCC-G-G-UGGCGACAC-C--G-G-U-C-C--CAGAGAGAU-GACCGCGU------------------------AA-------------------------------------------------AACAGAACCCGGCUUA--C-GCCCUAU-CCUGGGGA
X60463.1/380-748               CGGG-AC-G-A-G-G-G--CGCGGUCGCGCC-GA--G-GGCC----------------------------------------------------------------------------------------GAAC-----CC-C-U-CGGGUGAGGAAAGUCCGGGCAC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGG-----------------------GUAA------CCCGACGG-AA---AGU-GCCACAGAGA--AGAG-ACC-GCC----AG---C--GGCCGGG----------------------------------------------------------------------------------------------------------------GCUUCCCCCGGU-G----C--G---GGCAAGGGUGAAAC----GGC---GG-G--G--U----------------------AAGAG-CCCACC-GCCUG-G-C-C-UG-GCAA--CA-G-G-C-CGGG-GCAC----------------GGCAAAC-CCCACCC-GGUGCAAGGCC-CGGU------------------------------AGGCA--G-GGA--------------------------------------------------------GGGCUUGCCC----GGCCCGA---GAGAACC---UG-C----GGGAU---G-----G---G-CCGC---------------------U--UGA-GGCC-G-G-UGGCGACAC-C--G-G-U-C-C--CAGAGAGAU-GACCGCGG------------------------AA-------------------------------------------------AACAGAACCCGGCUUA--C-GCCUCGU-CCCGGAGG
M64709.1/421-758               GGAG-AG-G-A-G-C-A--GGCGGUCGCGGG-GG--C-GCAC----------------------------------------------------------------------------------------ACCU-----GC-G-CUU-CCCGAGGAAAGUCCGGACUC-U-----G--GAGCG-G-GG-UG----------------CCGGG------------UAACG----------------CCCGGGAGGG-----------------------GUGA------CCCU-CGG-AC---AGG-GCCAUAGAGA--AGAAGACC-GCC----CG-----------------------------------------------------------------------------------------------------------------------------------UUG---------A--G---GGCAAGGGUGGAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC-AGCGU-C-G-G-G--GCAA---C-C-C-G-GCGG-C-UU----------------GGCAACC-CCCACCU-GGAGCAAGGCC-AAGC------------------------------AGGGG--G-----------------------------------------------------------UUGGGUCGCUC----CCCCU-------AUUCC---CC-C-----GGGU---U-----G---G-CCGC---------------------U--UGA-GGUG-U-G-CGGUAACGC-A--C-A-C-C-C--CAGAUUGAU-GACCGCCC------------------------AC-------------------------------------------------GACAGAAUCCGGCUUA--U--GCUCCU-CUCCCGUG
CP000388.1/820654-821039       GGAG-UU-G-G-U-C-A--GGCAAUCGCCGC-UU--G-UUAGAUAUUUCAUUAGGGCU--------------------------------------------------------AGUCCCUAGAGUAAUGUGUU-----AA-U-A-A-GGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGC-----------------------GCAA------GCCGACGA-CA---AGU-GCAGCAGAGA--GGAA-ACC-GCC---UAA---G--CGC-------------------------------------------------------------------------------------------------------------------------GCAAGCG-C----C------GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-C-A-C-UG-GUAA--CA-G-U-GUGUGG-C-AA----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGAU--C-UCUUAU-----------------------------------------------------GGCGUGGCCC----ACGUU---------GAG---AU-C-----GGGU---G-----U---G-UUGC---------------------U--UGA-GCCA-G-C-GAGUGAUUG-C--U-G-G-C-C--UAGAUGAAU-GGUUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGACCAA-CUCCACCU
CR522870.1/276762-277121       UGAA-GU-G-G-G-C-U--CAUGAUCGCCCC-GA--C-UUUC----------------------------------------------------------------------------------------G--------CA-G-U-C-GGAGAGGAAAGUCCGAACUC-C---GCA--GGGCA-A-GA-UG----------------GUUCG------------UAACA----------------CGAACACUGG-----------------------GUGA------CCGG-UGG-AA---AGU-GCCACAGAAA--AUAG-ACC-GCC----UG---G------------------------------------------------------------------------------------------------------------------------------UUCG----C----C--A---GGUAAGGGUGAAAC----GGC---GA-G--G--U----------------------AAGAG-CUCACC--GCUU-U-C-A-CG-GUGA--CG-U-G-G-AAGG-C-AG----------------GGCAAAC-CCCAUCU-GGAGCAAGACC-AAAU------------------------------AGAGA--G-AUGUUU----------------------------------------------------GAGGGCGGCUC---CGUCCG-------AGAUC---UC-C-----GGGU---A-----G---G-UUGC---------------------A--AGA-GGCG-U-C-GGGCAACCG-A--C-G-U-C-C--CAGUGAAAU-GAUCAUGG----------------CUCCCUUCGGGGAGA--------------------------------------------GACAGAAUUCGGCUUA--U-AGCCCAC-UUCGCACA
CP000527.1/1924800-1925156     GGAG-UC-G-G-A-C-A--GGUCGUCGUCGC-GG--G-UC------------------------------------------------------------------------------------------GCAA-----GA-C-C-C-GGGGAGGAAAGUCCGGGCUU-C---ACA--GGGCA-G-GA-CG----------------CUGGG------------UAACG----------------CCCAGGGGGA-----------------------GCGA------UCUC-CGG-AG---AGU-GCCACAGAGA--GCAG-ACC-GCC----CG---C--G---------------------------------------------------------------------------------------------------------------------------UUCG--C-G----C--G---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC-AGUUG-C-G-G-UG-GUGA--CA-U-C-G-CAAG-C-UA----------------GGAAAAC-CCCGUCC-GAAGCAAGACC-AAAU------------------------------AGGGG--A-GCGCCA----------------------------------------------------A-GGUCGGCCC----GACCG-------AUGCU---CC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGGU-G-C-AGGUAACUG-C--A-C-U-C-C--UAGAGGAAU-GACGACCC-----------------CCC----GCGAGGG--------------------------------------------GACAGAACCCGGCUUA--U-CGUCCGA-CUCCCACU
ABCE01000008.1/123447-123070   GGAG-UC-G-G-C-U-G--AGUGGUCGCUGC-GG--A-UUCU----------------------------------------------------------------------------------------UCGG-----AA-U-C-C-GUGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-C-GG-UG----------------GUGGG------------UAACG----------------CCCACCGUCC-----------------------GCGA------GGACAGGG-AA---AGU-GCAACAGAAA--GUAA-ACC-GCC---GGG---C--CAG-------------------------------------------------------------------------------------------------------------------------UUCGCUG-G----C--C--AGGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-A-C-C-GG-GUGA--CC-G-G-U-CUGG-C-UA----------------GGUAAAC-CCCACCG-GGUGCAAGACC-AAGC------------------------------AGGGA--G-CAGUUCUGGUUCG-------------------------------------CCAGAACACGGAUCGGCCC----GAUCCGU---UACGACU---UC-C-----GGGU---C-----G---G-UCGC---------------------G--CGA-GGCU-G-C-AGGCAACUG-C--G-G-U-C-C--CAGAUAAAU-GGCCACUC-----------------UC--------------------------------------------------------GACAUAACCCGGCUUA--C-AGGCUUG-CUCCCGCU
CR543861.1/2832237-2831882     GAAG-UG-G-A-C-U-G--GACGGUCGCUGC-UG--U-GGAGGUCU-------------------------------------------------------------------------------UCGUGACUG-----AA-A-C-A-GGGGAGGAAAGUCCGGGCUU-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GAAA------GCCGACGG-AA---AGU-GCAGCAGAGA--GUAG-ACC-GCC----UC---A------------------------------------------------------------------------------------------------------------------------------UUCG----U----G--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-G-U-C-UG-GUAA--CA-GUU-C-ACGG-C-AU----------------GGUAAAC-CCCACCA-GAAGCAAGACC-AAAU------------------------------AGGAA--U-CCUGA------------------------------------------------------GGUACGGCCC----GUACU---------GGA---UU-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCGU-A-U-GAGUGAUUG-U--A-C-G-C-C--UAGAGGAAU-GAUCGUCC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--C-AGGUCCA-CUUCACCA
AAKL01000009.1/106867-107210   GAAG-CG-G-A-C-C-A--GGCAACCGCUGC-UU--C-CACGUGU---------------------------------------------------------------------------------UCGCACGA-----CG-G-A-A-GGGGAGGAAAGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------AUGGC------------UAACG----------------ACCAUCCACG-----------------------GUGA------CGUGCGGA-AU---AGG-GCCACAGAGA--CGAG-UCUUCGC----CC--GC--GGC-------------------------------------------------------------------------------------------------------------------------UUCGGCC-G----G--G---GCGAAGGGUGAAAC--------------------------------------------------------------------------------------------GC----------------GGUAACC-UCCACCC-GGAGCAAUCCC-AAGU------------------------------AAGCA--G-GCGAUG----------------------------------------------------A--AGCGGCCC----GCCGA---------GCC---UG-C-----GGGU---A-----G---G-GAGC---------------------U--UGA-GCUG-G-U-CGGCAACGG-C--C-G-G-U-C--UAGAGGAAU-GGUUGUCACGC----------CGCGCGGUGUCAUGCCGCGCG--------------------------------------GCGCACAGAAUCCGGCUUA--U-CGGUUCG-CUUCGCGU
CP000608.1/759203-759541       AAAG-UC-A-G-U-C-G--GACAGUCGCGCU-UA-------------------------------------------------------------------------------------------------UAA----------U-G-AGUGAGGAAAGUCCGGGCUU-U---ACA--GAGCA-A-GA-UG----------------CCAGA------------UAACG----------------UCUGGGAGGC-----------------------GUGA------GCCUACGG-AA---AGU-GCAACAGAAA--AUAU-ACC-GCC----UU---A--U----------------------------------------------------------------------------------------------------------------------------UUU--U-U----A--A---GGUAAGGGUGAAAA----GGU---GU-G--G--U----------------------AAGAG-CGCACC--GCAU-U-G-G-UG-GUAA--CA-CUC-A-AUGG-C-AU----------------UGUAAAC-CCCAUCU-AAAGCAAGACC-AAAU------------------------------AGUGC--C-ACUAU------------------------------------------------------GAUGUUGCUC----GCAUC---------GUG---GC-A-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCUU-A-U-UGGUGACAA-U--A-G-G-C-C--UAGAUAAAU-GACUGUCU------------------------AU-------------------------------------------------UACAGAACCCGGCUUA--U-AGACUGG-CUUUGUAU
CP000738.1/2151542-2151145     CCAG-UU-G-G-C-C-G--GGCAGCCGCGCC-CC--G-CAAGUGC---------------------------------------------------------------------------------CGAAAGGC-----CG-C-G-G-GGCGAGGAAAGUCCGGGCUC-C---ACG-GAAACA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAAA--GCAG-ACC-GCU----CC---G--C-----------------------------------------------------------------------------------------------------------------------------UU--G-C----G--G---AGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-A-C-A-UG-GCGA--CA-U-G-G-ACGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGA--C-GACACGGGCGCGCA------------------------------------AGCGUCCAGCCGGUUUCCA----GGCGC--------GUCG---UC-C-----GGGU---G-----G---G-UUGC---------------------A--CGA-GGCU-G-C-GCGCAAGCG-C--A-G-U-C-C--CAGAUGAAU-GGCUGCCACGUUUC----GUCUCCUCGGAGGCGGAGCCA--------------------------------------------UACAGAACCCGGCUUA--C-AGGCCAA-CUGGCUUU
AP007255.1/4237307-4237707     UCAG-AC-G-G-C-C-G--GACGGCCGCCCU-CG--G-AU------------------------------------------------------------------------------------------UCAC-----CU-C-C-G-GGGGAGGAAAGUCCGGGCUC-C---ACGGAAUACA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCUAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----CG---C--UCCCAGGCC-------------------------------------------------------------------------------------------------------------UUCGGGUUUGGCA-G----C--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-A-C-CG-GCAA--CG-G-A-A-GCGG-C-AC----------------GGUAAAC-CCCACCG-GGAGCAAGACC-AAAU------------------------------AGGGA--C-GGCACUGUUCUUCUU---------------------------------CGGAAGGACGAAACGCGUUUC---CGCGUC--------GCCG---UC-C-----GGGU---C-----G---G-UCGC---------------------G--AGA-GGCG-U-C-CGGUAACGG-A--C-G-U-C-C--CAGAUGAAU-GGCCGUCA-----------------CCCGCUUUCGGGCGG------------------------------------------GGACAGAACCCGGCUUA--C-AGGCCGU-CUGACGCA
BA000008.3/606614-607013       CGGA-AG-A-G-A-A-A--GGCAACCGCUGU-UU--A-UAUUUCU----------------------------------------------------------------------------------CAAAAAA-----UA-U-A-A-AGAGAGGAAAGUCUGGACUU-C---AUA--AGAGA-A-GA-UA----------------CUGGA------------GAAAU----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAC-UCC-GCU----AU---A--AAA-------------------------------------------------------------------------------------------------------------------------UUUAUUU-U----A--U---AGACAGGCUGAAAA---UUCC---UA-C--U--U----------------------UAGGA-GUAGGA--GCCA-U-U-A-AG-GUGA--CU-U-A-A-UAGG-C--A----------------UGCAAAC-CCUAUCU-GAAGCAAGAG------------------------------------AAAAA--A-GCUUUUUGUGUCUG------------------------------------CAAAUGUGAGAGGAAUUCC----UCCCAU------AGGCU---UU-U-----UCGA---A---------A-UCGC---------------------U--UGA-GGGA-U-C-UAGUAAUAG-C--U-C-C-C-C--UAGAUGAAU-GGUUGCCC-----------------UUAGGAUAGUUCGCAAGAGCU-----------------------------AUCUUAUAGACAGAAUCCAGCUUA--C-CCUCUCU-UCCGAUAU
AF056379.1/1-407               UCGG-AG-A-G-U-A-A--GGCAACCGCUGA-AA--C-CAGCUUUU-------------------------------------------------------------------------------UAAAAAAGA-----UGAG-U-A-CCAGAGGAAAGUCCGGACUU-U---AUA--AGAAA-A-GA-UG----------------CUGGA------------GAAAU----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAC-UCC-GCU----AU---A--AAUU-----------------------------------------------------------------------------------------------------------------------GUAUAAUU-U----A--U---AGACAGGCUGAAAA---AUCU---UA-C--U--U----------------------UAGGA-GUAAGA--GCUG-C-U-A-GG-GAAA--CC-U-A-G-CAGA-C--U----------------UGUAAAC-CCCAUCU-GAAGCAAGA--------------------------------------GAAA--A-AGUUAUUUGUUUC-------------------------------------UGCAAACAACCUUUCUAAC---GAAAGGCA---CAGGCUU---UU-U-----CAUA---A-----------UCGC---------------------U--UGA-GGAG-U-A-CAGUAAUGU-G--C-U-C-C-C--UAGAUGAAU-GGUUGCCC-----------------GCAAGCAAGAACUUCCGUUCG-----------------------------UGCUUGUCGACAGAAUCCGGCUUA--C-UCGCUCUUCCGAGCUU
AE017180.1/3388229-3387862     CGAA-GC-A-G-AAC-A--GAUGGCCGCCCU-UC--G-CG---------------------------------------------------------------------------------------------------UG-C-G-G-GGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-U-GG-UG----------------CUGGA------------UAACG----------------UCCAGCGGGG-----------------------GCGA------CCCCAGGG-AU---AGU-GCCACAGAGA--GAAG-UCC-GCC----CG---C------------------------------------------------------------------------------------------------------------------------------UCAG----G----C--G---GGUAAGGGUGAAAG----GGU---GA-G--G--U----------------------AAGAG-CUCACC-GGGUU-C-G-G-CG-GUGA--CG-U-C-G-GAUG-C-CA----------------GGUAAAC-CCCACCA-GGAGCAAGGCC-GAAU------------------------------AGGGA--A-GCGUC-----------------------------------------------------AAGGAUGGCCC----GUCCG--------UGCU---UC-C-----GGGU---U-----G---G-CUGC---------------------U--UGA-GGCC-G-U-CGGUAACGG-C--G-G-U-C-C--CAGAGGAAU-GGUCAUCGCCC-----------GCCAAGGGGUAACCCGCGGC--------------------------------------GGGAACAGAACCCGGCUUA--U-GGGCUGC-UUCGACCA
AAVS01000005.1/163696-164059   CGAG-UC-A-G-C-C-A-AGAUAAUCGCUGC-CU--G-UGAC----------------------------------------------------------------------------------------GAAAA--UGAU-C-A-G-GGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-AG-UG----------------CCAGC------------UAACG----------------GCUGGGGGGC-----------------------GUGA------GCCCACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCC----AA---C------------------------------------------------------------------------------------------------------------------------------UUCG----G----U--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGGC-C-G-C-UA-GUAA--UA-GUC-G-GUUG-C-AA----------------GGUAAAC-UCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCUUAU-----------------------------------------------------GGCGUGGCCC----ACGUU---------GGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCA-U-A-GAGCGAUUU-A--U-G-G-C-C--UAGACGAAU-GAUUAUCA-----------------CUUUCUUCGGAAAG--------------------------------------------GACAAAACCCGGCUUA--U-AGGCUGA-CUCACUCA
CP000316.1/1076869-1077209     GAAG-CC-U-G-C-C-A--GACCGCCGCUGG-UG--C-AAUCUG-----------------------------------------------------------------------------------GGAAACC-----AG-G-C-A-CUGGAGGAACGUCCGGACUG-C---ACA--GGACA-G-CG-UA----------------GGAGG------------UAAUA----------------CCUCUCCACC-----------------------GUGA------GGUGAGGA-UC---AGA-GCAACAGAGA--CGAG--UC-GCU----UU---U--GGG-------------------------------------------------------------------------------------------------------------------------UAA-CUC-A----A--A---AGC--GGGUGAAAC----------------------------------------------G---------------------------------------------------------------GGCAAUC-UCUACGC-GCAGCAAUACC-AAGU------------------------------AGGCC--A-GCGUUG----------------------------------------------------A--UGUAGCUC---CGCAGA---------GCU---GG-C-----GGGU---A-----G---G-UAGC--------------------AC--CGA-GCCG-G-GUGGGCGACCC-C--C-G-G-C-C--CAGAUUAAU-GGCGGUCACACC---------GGGUUUGCCGCAAGGCACAUCC------------------------------------GGCGCACAGAAUCCGGCUUA--U-CGGCGGG-CUUCACAC
CP000323.1/441081-441444       UUGG-UA-G-A-C-U-A--GGCAAUCGCCGC-UG--C-ACACUGG---------------------------------------------------------------------------------CAACAGAC-----AU-G-C-A-GGGGAGGAAAGUCCGGGCUA-C---AUA--GGGCA-G-CG-UG----------------CCAGC------------UAACG----------------GCUGGGCAGG-----------------------GUAA------CUUGACGA-CC---AGU-GCAGCAGAGA--GUAG-ACC-GCC----UU---U--AGUG----------------------------------------------------------------------------------------------------------------------UCUGACACU-A----U--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-G-G-C-UG-GCAA--CA-GUU-C-ACGG-C-AU----------------GGUAAAC-UCCACGC-GUAGCAAGACC-AAAU------------------------------AGGCA--U-CGGCAU-----------------------------------------------------GGCGCGGCCC----GCGUU---------CGA---UG-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCGU-A-U-UAGCGAUGA-U--A-C-G-C-C--UAGAGGAAU-GAUUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGUUUA-CCAACCUU
AAUA01000001.1/1382814-1382421 GAAA-GC-A-G-G-C-G-AGGUGAUCGCGAU-CA--G-GGCAUCGGUGGCU----------------------------------------------------------------------UCGGCCCCGAGGC-----GC-U-U-G-GUUGAGGAAAGUCCGGGCUC-CC-CGAU--GGCCA-G-GCUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAC--ACC-GCCG-AUGG---C--CGG-------------------------------------------------------------------------------------------------------------------------CUUGCCG-G----C--AC-AGGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGCUGGGAGCAAGGCC-GA----------------------------------GGA--A-CGA-------------------------------------------------------CGGUUGGCCAU----CAACC--------CCGU---UC-CGC-UGAUGU---G-----C---G-CCGC---------------------U--CGA-GGUC-G-C-CGGUAACGG-C--G-A-U-C-C--CAGAUAGAU-GAUCACCCCC-------------CUUCUUUGGAAGGGAG--------------------------------------------AACAGAACCCGGCUUA--U-GUCCUGC-UUUCACCC
AACK01000018.1/26603-26989     UGAG-UU-G-G-U-U-A--GACAAUCGCUGG-UU--U-AUUGAAGCCCUUAAUUGUUCG-----------------------------------------------------CAAGAACGACCUAGCGGGACAA-----GU-A-A-A-CGAGAGGAAAGUCCGAGCUA-C---ACA--GGGCA-G-AG-UG----------------CCAGA------------UAACG----------------UCUGGGCGGU-----------------------GUGA------ACCGACGA-CC---AGU-GCAACAGAGA--GCAA-ACC-GCC---GAU---G--UGC-------------------------------------------------------------------------------------------------------------------------AUUAGCG-C----A------GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-G-G-G-UG-GCAA--CA-UUC-C-ACGG-C-AC----------------GGUAAAC-UCCACUC-GUAGCAAGACC-AAAU------------------------------AGGAA--C-UCAA-------------------------------------------------------UGGAUGGCCC----GUCCA---------GAG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCUU-G-U-GUGUGAAUG-C--A-A-G-C-C--UAGAGGAAU-GAUUGUCC-----------------GC--------------------------------------------------------GACAGAACUCGGCUUA--U-CGACCAA-CUCACUUU
CP000510.1/1469372-1469738     GGAG-UU-G-G-C-C-A--GAUCGUCGCCGC-UU--U-UAUUGC------------------------------------------------------------------------------------UUGCAA-----UA-A-G-A-GGGGAGGAAAGUCCGGGCUU-C--AACA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGUAGC-----------------------GUGA------GCUAACGA-CA---AGU-GCAGCAGAGA--GGAA-ACC-GCCG--AUG---U--GUUUAU-------------------------------------------------------------------------------------------------------------------GUAAAUAAAU-G----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGCC-A-U-C-UA-GUAA--UA-GUU-U-GGUG-C-AA----------------GGUAAAC-UCCACCC-GAAGCAAGACC-AAAU------------------------------AGGCU--U-CCUGA------------------------------------------------------GGUAUGGCCC----AUACU---------GGA---AG-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCU-G-U-GAGUGAUUG-C--A-G-G-C-C--UAGACGAAU-GACGAUUC-----------------AAC-------------------------------------------------------GACAAAACCCGGCUUA--U-AGGCUGA-CUCUAUUA
CP000514.1/2749725-2749375     CGAG-CU-C-G-C-C-A--GACAGUCGCCGC-CG--G-UUG--------------------------------------------------------------------------------------------------AU-C-C-G-GGGGAGGAAAGUCCGGGCUC-C---GCA--GGGCA-A-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGC-----------------------GUGA------GCCGACGG-AA---AGU-GCAACAGAAA--GUAU-ACC-GCCU--AAG---C--GCU-------------------------------------------------------------------------------------------------------------------------UUCGGGC-G----C--C---GGUAAGGUUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-G-G-C-UG-GCAA--CA-GUC-C-ACGG-CGAU----------------GGUAAAC-CCCACCU-GGAGCAAGACC-AAAU------------------------------AGGAA--U-CCAAU------------------------------------------------------GGCGUGGCCC----GCGCU---------GGA---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGCC-U-G-UGGUGACGC-A--G-G-C-C-C--UAGAUGAAU-GACUGUCC------------------------AA-------------------------------------------------GACAGAACCCGGCUUA--U-CGGCGAG-CUCGCCUC
BA000040.2/7288564-7288990     UCAG-UC-G-G-C-C-G--GACGGCCGCUCC-GG--C-AACGGU-----------------------------------------------------------------------------------CGAAAGG-----CC-G-C-C-GGGGAGGAAAGUCCGGGCUC-C---CUU-GACAUA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCAA------CCCCAGGG-AA---AGU-GCCACAGAGA--ACGA-ACC-GCC----CU---G--CUUCGCC-----------------------------------------------------------------------------------------------------------------UUCGGGCUUCG-C----U--G---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-C-U-G-CG-GCAA--CG-G-A-G-CCGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-GGCGUAGCGGGCUGUUCGCGC----------------------AAGCGAUAACGCCGCGGGGCGAUGUC---AGGCCC--------GCCG---UC-C-----GGGU---A-----G---G-UUGC---------------------U--CGA-GGCC-A-U-GUGCAAACA-U--G-G-C-C-C--CAGAGGAAU-GGCCGUCACGU----------AUCGUGCGCGCAAGCGAACGGU------------------------------------GCCCUACAGAACCCGGCUUA--C-AGGCCGG-CUGAUGUC
AP008229.1/4089958-4089609     GGAG-UC-G-G-C-C-A--GACAGUCGCGUC-AC--U-C-------------------------------------------------------------------------------------------GCAA------G-A-G-U-GCCGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-A-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGC-----------------------GCAA------GCCGACGG-AC---AGU-GCAACAGAAA--GAU--ACC-GCCU-ACGU---U--CCU-------------------------------------------------------------------------------------------------------------------------UUCGGGG-A----G--C--CGGUAAGGGUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGA-G-U-C-CG-GUAA--CG-G-A-C--CGG-C-AC----------------GGCAAAC-CCCACCU-GGAGCAAGACC-AAAU------------------------------AGGGA--U-CCAUU------------------------------------------------------GGCGUGGCCC----GCGCU---------GGA---UC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCGC-U-G-CGGUGACGU-G--G-C-G-C-C--UAGACGAAU-GACUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGCCGG-CUCCGCCG
AAEW02000009.1/28314-28685     CGAA-GA-A-G-GAC-A--GACGGUCGCCGG-UU--U-C-------------------------------------------------------------------------------------------GCAA------G-A-A-A-CGGGAGGAAAGUCCGGGCUC-C---GCA--GAGCA-G-GA-UG----------------GUUCC------------UAACG----------------GGAACCGGGG-----------------------GUGA------CCCCAGGG-AC---AGU-GCCACAGAGA--GAAG-ACC-GCC----UG---C------------------------------------------------------------------------------------------------------------------------------UUUG----G----C--A---GGUAAGGGUGAAAG----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCUC-U-G-G-UG-GUGA--CA-U-C-A-GAGG-C-UC----------------GGUAAAC-CCCAUCU-GGAGCAAGGCC-AAAU------------------------------AGGGA--A-GCGUUU----------------------------------------------------GAGAGCGGCUC----GCUCG-------AAGCU---UU-C-----GGGU---U-----G---G-CUGC---------------------U--UGA-GGCC-G-U-CGGCAACGG-C--G-G-U-C-C--UAGAGGAAU-GAUCGUUGCCC-----------GUCUCCGGGUAACCGGAUUC--------------------------------------GGGUACAGAACCCGGCUUA--C-GGCCUUC-UUCGACCA
CP000444.1/286633-286986       CGAG-UU-G-G-C-C-A--GACAGUCGCUGC-GC--U-C-------------------------------------------------------------------------------------------GCAA------G-A-G-C-GGGGAGGAAAGUCCGGGCUU-C---AAA--GAGCG-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GCGA------ACCGACGA-CA---AGU-GCAACAGAGA--GGAG-ACC-GCC----AU---C--AUAGC---------------------------------------------------------------------------------------------------------------------CUCGGCUAA-G----G--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-G-G-C-UA-GCAA--UA-GUC-C-GUAG-C-AA----------------GGUAAAC-UCCACCC-GAAGCAAGACC-AAAU------------------------------AGGGU--U-CCGUAU-----------------------------------------------------GGCGUGGCUC----GCGUU---------GGA---AC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCCU-G-C-GAGCGAUUG-C--A-G-G-C-C--UAGAUGAAU-GACUGUCC------------------------AA-------------------------------------------------GACAGGACCCGGCUUA--U-CGGCCAA-CUCAUUAA
CP000758.1/1818931-1819358     UCAG-UC-G-G-U-C-G--GGCAGCCGCGCU-UG--U-CAUAUGC----------------------------------------------------------------------------------CGAAAGG-----CG-G-C-A-GGUGAGGAAAGUCCGGGCUC-C---AUG-GAAACA-C-GA-UG----------------CCGGG------------UAACG----------------CCCGGCGGGG-----------------------GUGA------CCCCAGGG-AA---AGU-GCCACAGAAA--GCAG-ACC-GCC----CC---G--UCUUCCGUACCGUUGC----------------------------------------------------------------------------------------------GCAACGAAACGGCAGGGAUGA-C----G--G---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGU-C-U-G-CA-GCAA--UG-C-A-G-ACGG-C-AC----------------GGUAAAC-CCCAUCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-GGCGCGCUGGCUCGC----------------------------------AAGGGCCGGCAAUCGGUUUC----CGGAUC------AGCCG---UC-C-----GGGU---G-----G---G-UUGC---------------------A--CGA-GGCG-G-G-UGGCGACAU-C--C-G-U-C-C--CAGAUGAAU-GGCUGCCAC--------------GUCGGGCGAAAGCCCGGC----------------------------------------CAUACAGAACCCGGCUUA--C-AGACCGA-CUGACAAU
L42023.1/1746806-1746430       CGAG-UU-G-G-U-U-A--GACAAUCGCUGG-UU--U-AUUGAAGCCCUUAACCGUAU-------------------------------------------------------UUAUACGACCUAGUGGGACAA-----GU-A-A-A-CGAGAGGAAAGUCCGAGCUA-C---ACA--GGGCA-G-AG-UG----------------CCGGA------------UAACG----------------UCCGGGCGGC-----------------------GUGA------GCCGACGA-CC---AGU-GCAACAGAGA--GCAG-ACC-GCC----GU----------------------------------------------------------------------------------------------------------------------------------GUAA---------A--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-C-G-U-UG-GUAA--CA-A-C-GUGCAG-C-AG----------------GGUAAAC-UCCACUC-GUAGCAAGACC-AAAU------------------------------AGGAA--C-UCAA-------------------------------------------------------UGGGUGGCCC----GUCCA---------GAG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCGG-C-A-GAGUAAUUU-G--U-C-G-C-C--UAGAGGAAU-GAUUGUCC------------------------AC-------------------------------------------------GACAGAACUCGGCUUA--U-CGACCAA-CUCAAAAC
AAWG01000068.1/5641-6042       GGAG-UU-G-A-C-U-G--GGUAGUCGCUGC-CU--U-AUUGACGUCCCUUGGCC--------------------------------------------------------------UAUCGCCAGGGAGACUG-----AU-A-A-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCAA------GCCUACGA-CA---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CCUCUCC----------------------------------------------------------------------------------------------------------------UUCGGGAUGGGA-U----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-G-A-C-UG-GCAA--CA-GUU-C-GUAG-C-AG----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGCC--U-CCACA-----------------------------------------------------UAGCGUUGCUC----GCGUU--------AGGA---GG-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCA-G-U-GAGUGAUUG-C--U-G-G-C-C--UAGAGGAAU-GGCUACUA-----------------CCGCGCAAGCGG----------------------------------------------AACAGAACCCGGCUUA--U-ACGUCGA-CUCCACCU
AAKW01000074.1/145450-145799   AGAG-UG-G-A-U-U-G--GACAGUCGCUGU-CG--C-GC------------------------------------------------------------------------------------------AAUA-----GC-G-C-G-GUGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-AG-UG----------------CCAGG------------UAACG----------------CCUGGGAGGC-----------------------GCGA------GCCUACGG-AA---AGU-GCCACAGAAA--AUA--ACC-GCC---UAA---G--CGC-------------------------------------------------------------------------------------------------------------------------AACAGCG-C----C------GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-G-G-C-UG-GCAA--CA-GUG-C-GUGG-C-UA----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGAA--U-CCAUU------------------------------------------------------GGCGCGGCCC----GCGUU---------GGA---UU-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GGCG-U-A-CAGUGAUGU-G--C-G-U-C-C--CAGAGGAAU-GGCUGUCC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--U-AGAUCGA-CUCUCCCA
CP000356.1/1827933-1827551     CCAG-AG-G-G-U-C-G--GGCGAUCGCCGC-UU--U-C-------------------------------------------------------------------------------------------GCAA------G-A-A-A-GGGGAGGAAAGUCCGGGCUC-C---ACGGAAACCA-C-GG-UG----------------CCGGA------------UAACA----------------UCCGGCGGCCU--------------------CCGCAAG---GAGGUCAGGG-AA---AGU-GCCACAGAGA--GCAG-ACC-GCC----CA---C--GGC-------------------------------------------------------------------------------------------------------------------------UUCGGCC-C----G--G---CGAAAGG-UGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-A-CG-GUAA--CG-G-A-C-GCGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAGGUC-GAAU------------------------------AGGGA--U-GGCACGGGA---------------------------------------------AACCAGGGCUGGUUC---CGGCCC-------CGCCG---UC-C-----GGGU---U-----G---A-CUGC---------------------U--UGA-GCGU-U-C-GGGUAACCG-U--C-C-G-C-C--UAGAGGAAU-GAUCGCCCAU-------------CCCCGGCAACGGGGUG--------------------------------------------GACAGAACCCGGCUUA--C-AGACCCU-CUGGCAUC
AAQF01000433.1/856-1224        CGGG-GC-G-G-G-C-G--CGUGGUCGCCGU-CG--A-CGGCGGGCC-----------------------------------------------------------------------------GCAGGUCCGU-----CG-C-C-G-GCGGAGGAAAGUCCGAACUC-C---ACC--GGGCA-G-GG-AG----------------GUUCG------------UAACG----------------CGAACCGGGG-----------------------GCAA------CCCCAGGG-AA---AGU-GCCACAGAAA--AGAU-ACC-GCC----GG---C-------------------------------------------------------------------------------------------------------------------------------AUU----G----C--C---GGUAAGGGUGAAAU----GGU---GA-G--G--U----------------------AAGAG-CUCACC--GCUU-G-C-C-UG-GUGA--CA-G-G-C-AAGG-C-AG----------------GGUAAAC-CCCUCCC-GGAGCAAGAUC-AAAU------------------------------AGGGA--A-ACGCUU----------------------------------------------------GAGGGCGGCCC----GUCCG-------AAGUU---UC-C-----GGGU---A-----G---A-UCGC---------------------A--AGA-GACG-C-C-GGGCAACCG-G--C-G-C-CCC--CAGAUAAAU-GACCACGG-----------------CCC----GCAAGGG--------------------------------------------UACAGAAUUCGGCUUA--U-AGCCCGC-CCCGCUUC
CP000095.2/1668077-1668480     GAAA-GC-A-G-G-G-G-AGGUGAUCGCAAU-UG--A-ACUUCAGCAA---------------------------------------------------------------------------AAAGCUGAAGA-----AU-U-C-U-AUUGAGGAAAGUCCGGGCUC-CU-AUUU--GGCCA-G-GCUUG----------------CUGGG------------UAAUU----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AU---AGU-GCCACAGAAA--CAC--ACC-GCCU--AAC---G--CUUAAUGGG------------------------------------------------------------------------------------------------------------GAUAUCCCAACAAG-C----G--C---GGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UA----------------GGUAAAC-CCCGGCCAGGAGCAAGGC-------------------------------------GAGG--G-GCACUG----------------------------------------------------GAUGGCCAUAG----ACCUU---------GUC---CC-U-----GUAG---A-----G--AG-CCGC---------------------U--UGA-GGCU-A-G-CGGUAACGU-U--A-G-U-C-C--CAGAUAGAU-GAUUACCCAUUCGC-----UUUCUAAAGAAAGAGGAAUG--------------------------------------------AACAGAACCCGGCUUA--U-GACCUGC-UUUCACUU
CP000524.1/988732-988347       UCAG-UC-G-G-C-U-G--GGCAGCCGCGCU-UG--U-CUCA---------------------------------------------------------------------------------------UGUUA-----AG-A-U-A-GGUGAGGAAAGUCCGGGCUC-C---AUG-GAAAAA-C-GG-UG----------------CCGGG------------UAACA----------------CCCGGCGGGG-----------------------GUGA------CCCUAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----UA---U------------------------------------------------------------------------------------------------------------------------------UUUU----A----U--A---GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC--GCGC-A-C-G-CA-GUAA--UG-G-G-U-GUGG-C-AA----------------GGUAAAC-CCCACCG-GGAGCAAGACC-AAAU------------------------------AGAAA--U-GACGUGCAAGGUUU------------------------------------GGCUUGCAGCCAGUUUCCA----GGUGA--------GUCA---UU-U-----GGGU---A-----G---G-UUGC---------------------A--CGA-GGCG-G-A-UGGUAACAU-C--C-G-U-C-C--UAGAUGAAU-GGUUGCCA-----------------UGUAAAGUAUAAGCUUU-------------------------------------ACCAUACAGAACCCGGCUUA--U-AGGCCGA-CUGAUAUU
AAOH01000003.1/223452-223841   CGAG-UU-G-G-C-C-G-AGAUAAUCGCUGC-CU--G-UGAC----------------------------------------------------------------------------------------GAAAA--UGAU-C-A-G-GGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------CCAGU------------UAACG----------------ACUGGGGGGC-----------------------GCGA------GCCUACGA-CA---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CCUUC---------------------------------------------------------------------------------------------------------------------UUGUAAGGA-U----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-C-UG-GUAA--CA-GUC-C-GUGG-C-AC----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CUAUCAUUUUAA---------------------------------------AUAAUGAACGCGUGGCCC----ACGUG---------AGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCU-A-A-GAGCGAUUU-U--A-G-G-C-C--UAGACGAAU-GAUUAUCA-----------------CUUUCUUCGGAAAG--------------------------------------------CACAGAACCCGGCUUA--U-UGGCCGA-CUCACCAA
AB047584.1/531-872             GGAGACU-G-A-C-A-A-----AGGGG-----------------------------------------------------------------------------------------------------------------------------AGGAAAGUCCGGGCUU-C---AUA--GAGCA-A-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCAA------GCCUACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCCG--AUG---G--CCC-------------------------------------------------------------------------------------------------------------------------GCAAGGG-A---AC--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGAC-G-A-C-UA-GUAA--UA-GUU-C-GUAG-C-AG----------------GGUAAAC-UCCACCU-GAAGCAAGACC-AAAU------------------------------AGGCC--U-CCACA-----------------------------------------------------UUGCGUUGCUC----GCGUA--------AGGA---GG-C-----GGGU---A-----G---G-UUGC---------------------U--CGA-GCCA-G-U-GAGUGAUUG-C--U-G-G-C-C--UAGACGAAU-GGCUACCG-----------------CCGCGCAAGCGG----------------------------------------------AACAGAACCCGGCUUA--U-GUGUCGG-CUCCACCU
CP000453.1/2510108-2509745     GGAG-UC-G-G-C-C-G--GGCAGCCGCUGC-GG--C-CCGGGUCG--------------------------------------------------------------------------------CGAGACCC-----GG-U-G-C-GCGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GUGA------GCCCACGG-AA---AGU-GCCACAGAAA--ACAA-ACC-GCCG--AUG---G--CCC-------------------------------------------------------------------------------------------------------------------------UUCGGGG-C---AC--A---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-A-C-UG-GUAA--CA-GUU-C-GCGG-C-AC----------------GGUAAAC-CCCACCC-GGAGCAAGACC-AAAU------------------------------AGGGG--A-GCAAU------------------------------------------------------GGCGUGGCCC----GCGCU---------GCU---CC-C-----GGGU---A-----G---G-UUGC---------------------U--AGA-GGCA-G-G-UGGUGACAC-C--U-G-U-C-C--CAGAGGAAU-GGCUGUCC-----------------CC--------------------------------------------------------GACAGAACCCGGCUUA--C-AGGCCGA-CUCCACCU
CP000544.1/2306477-2306833     UGAG-UC-G-G-C-C-G--GAUGGCCGCUGU-GU--C-GCAA----------------------------------------------------------------------------------------G--------GC-G-A-C-ACGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GUGA------GCCCACGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCCGAUGGC---C--GCC-------------------------------------------------------------------------------------------------------------------------GCUAGGC-G----G--CACAGGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-A-C-CG-GCAA--CG-GUU-C-GCGG-C-AC----------------GGUAAAC-CCCACCC-GGAGCAAGGCC-AAAU------------------------------AGGGG--A-GCGAU------------------------------------------------------GGCGUGGCCC----GCGCC---------GCU---CC-C-----GGGU---A-----G---G-CCGC---------------------U--AGA-GGCG-U-G-CGGAGACGC-A--C-G-U-C-C--CAGAGGAAU-GGCCAUCC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--C-AGGCCGA-CUCACCCU
CP000606.1/242457-242816       CGAG-UU-G-G-C-C-A--GACAGUUGCCGC-GC--U-C-------------------------------------------------------------------------------------------AAUA------G-A-G-C-GGGGAGGAAAGUCCGGGCUU-C---AUA--GAGCA-G-GG-UA----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GUGA------ACCGACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCC----AG---U--C---------------------------------------------------------------------------------------------------------------------------UUCG--G-A----U--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-G-G-C-UG-GUAA--CA-GUC-C-GUAG-C-AA----------------GGUAAAC-UCUACCC-GAAGCAAGACC-AAAU------------------------------AGGGU--U-CCACUAUUCUUA----------------------------------------GGAAUUAAUGCGUGGCU----CGCGU--------UGGA---AC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCCU-G-U-GAGCGAUUG-C--A-G-G-C-C--UAGAUGAAU-AACUGUCC------------------------AC-------------------------------------------------GACAGGACCCGGCUUA--U-CGGCCAA-CUCAACAC
CP000096.1/1526478-1526882     AAAC-CGCA-A-G-U-G--UGCAGCCGCUCU-GC--G-CC------------------------------------------------------------------------------------------UUUG-----GG-C-G-C-AGGGAGGAAAGUCCGAACUU-C---ACA--GGGCA-G-GG-UG----------------CCGGUC---------GAGAUCCCCGAAAGGGAAUCAAGCCCGGGUAUGGC------------------GGUGCAAACCGUCCAUAACAG-AG---AGC-GCAGCAGAAA--GCAG-ACC-GCU----CC---G--G---------------------------------------------------------------------------------------------------------------------------GAAA--C-C----G--G---AGUAAGGGUGAAAC----GGC---GG-U--G--U----------------------AAGAG-ACCACC-AGGCA-U-U-C-CG-GCAA--CG-G-A-A-UGCG-C-UA----------------UGCAAAC-CUC-CCC-GAAGCAAGGCU-GAAU------------------------------AGGAA--A-GCUUUUCCCGUAAGGGAAAG-----------------------AGGGCGGCCCGCCCGAUUCC--GCAA-----GGAG--------AGUU---UU-C-----GGGU---A-----G---G-CCGC---------------------A------------------------------------U--CAGAUAAAU-GGCUGCAG-----------------UUUUAUCCGGCACGCCGGA----------------------------------UAAUUCACAGAAUUCGGCUUA--U-AUCUUCG-GUUUCGGC
CP000155.1/6015382-6015017     AGAG-CU-U-G-U-U-A--GGCAGUCGCUGU-UU--C-GCAUCCUU--------------------------------------------------------------------------------UAUUGGGC-----GC-G-A-G-AUGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-A-AG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGC-----------------------GCGA------GUCGACGG-AA---AGU-GCAACAGAAA--GUAU-ACC-GCCU-AAGU---C--UGC-------------------------------------------------------------------------------------------------------------------------UUCGGCA-G----A--C--CGGUAAGGUUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAU-G-G-C-UG-GUAA--CA-GUC-C-AUGG-CGAU----------------GGAAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGA--C-CCAAU------------------------------------------------------GGCGUGGCCC----ACGCU---------GGG---UC-C-----GGGU---A-----G---G-UCGC---------------------U--AGA-GGUG-C-A-UGGCGACAU-G--C-A-U-C-C--CAGAUGAAU-GACUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--C-AGACAAG-CUCUUCUU
CP000285.1/2476039-2475686     GGAG-CC-G-G-C-C-G--GACAGUCGCCGC-CG--U-GC-------------------------------------------------------------------------------------------CAU-----GC-A-C-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAAUG----------------CCUGGGCGGC-----------------------GCGA------GCCGACGG-AA---AGU-GCAGCAGAGA--GUAG-ACC-GCCU-AAGC---G--GGC-------------------------------------------------------------------------------------------------------------------------GUCAGCC-C----G--C--CGGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-C-C-UG-GUAA--CA-GUG-C-GUGG-C-AA----------------GGUAAAC-CCCACCC-GGAGCAAGACC-AAAU------------------------------AGGAA--C-CCAAA------------------------------------------------------GGCGUGGCCC----GCGCU---------GGG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGGU-C-G-CGGUGACGC-G--G-C-C-C-C--UAGAGGAAU-GGCUGUCC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--C-AGGCUGG-CUCCCAUU
AATS01000016.1/15472-15831     GGAG-UG-G-C-U-C-G--GAUGGUCGCGGC-AG--G-UUU--------------------------------------------------------------------------------------------------AA-C-C-U-GUCGAGGAAAGUCCGGGCUG-C---ACA--GGGCA-G-AG-CG----------------CCGGA------------UAACG----------------UCCGGUGGGG-----------------------GUGA------CCCC-GGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----GC---G--GCA-----------------------------------------------------------------------------------------------------------------------------UGC-C----G--C---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCCC-G-G-UGCG-GUAA--CGGA-C-C-GGGG-C-AC----------------GGUAAAC-CCCGCUC-GCAGCAAGGCC-AAAU------------------------------AGGGA--A-GCGCC-----------------------------------------------------AAACGUGGCCC----GCGUU--------UGCU---UC-C-----GGGU---A-----G---G-CUGC---------------------U--CGA-GCCU-G-U-CAGUAAUGG-C--A-G-G-C-C--CAGAUGAAU-GACCAUCU-----------------CCCCGCUCCGGCGGG------------------------------------------AGACAGAACCCGGCUUA--C-AGAGCCA-CUCCGCAU
ABCQ01000029.1/38223-38598     GGAG-UU-G-G-U-C-A--GACAAUCGCCGC-UU--U-AUGACUCGGUAU-----------------------------------------------------------------------UUAUAUCGAGGUU-----AU-A-G-A-GGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGAGGC-----------------------GCAA------GCCUACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCCG--AUG---G--CUUU-----------------------------------------------------------------------------------------------------------------------UUCGGAAG-C---AC--A---GGUAAGGCUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGAC-G-A-C-UA-GUAA--UA-GUU-C-GUUG-C-AG----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGCU--U-UCUAUA-----------------------------------------------------GGCGUGGCCC----ACGCU---------GAA---AG-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GUCU-G-U-GAGUGAUUG-C--A-G-A-C-C--UAGAGGAAU-GAUUGUCC------------------------AC-------------------------------------------------GACAAAACCCGGCUUA--U-CGACCAA-CUCCAAGA
AAMR01000081.1/12435-12061     GAAA-CU-G-A-C-G-U--UGAA---GUCCU-UC--G-GGAG----------------------------------------------------------------------------------------ACUG-----GU-A-G-A-GGGGAGGAACGUCCGGGCUC-C---AUA--GAGCA-G-GG-UG----------------CCAGA------------UAACG----------------UCUGGGGGGC-----------------------GCGA------GCCCACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCC----GA---U--GGCCUCAUU------------------------------------------------------------------------------------------------------------UCUUCGGAAGGGGC-A----C--A---GGUAAGGCUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-G-A-C-UG-GCAA--CA-GUU-C-GUAG-C-AA----------------GGUAAAC-UCCACCC-GGAGCAAGAUC-AAAU------------------------------AGGCC--C-UCGCA-----------------------------------------------------UUGCGCUGCUC----GCGUA--------UGGG---GG-C-----GGGU---A-----G---A-UUGC---------------------U--UGA-GCCU-G-U-GAGCGAUUG-C--A-G-G-C-C--UAGACGAAU-GGUUACCG-----------------CCGCGCAAGCGG----------------------------------------------AACAGAACCCGGCGUA--U-GUGUCAA-CUCCACCU
CP000249.1/1735135-1734723     CGAG-UU-G-G-C-C-G--GGCGGCCGCGUC-GG--C-GCCGGC-----------------------------------------------------------------------------------CGGUCCG-----GC-G-U-C-GCCGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-CG----------------GUGGG------------UAACA----------------CCCACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----GG---U--GCCG-----------------------------------------------------------------------------------------------------------------------GUCCCGGC-G----C--C---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGC-C-C-A-GG-GUGA--CC-U-G-G-GCGG-C-UC----------------GGUAAAC-CCCGCCC-GGAGCAAGGUC-AGAAGGCCCGUGGCCGUC--ACAGGUCGCGGACCGCGCA--G-GCGUUC----------------------------------------------------GAGGGCUGCCC----GCCCG--------AGCC---UG-C-----GGGU---G-----G---A-CCGC---------------------U--GGA-GGCU-G-C-CGGCAACGG-C--A-G-C-C-C--GAGAGAGAU-GGUCGCCG-----------------CCGGCGAGCCGUGAGGCGA----------------------------------GCCGGUACAGGACCCGGCUUA--U-AGGCCAC-CUCGUCCG
BA000035.2/2267229-2266802     UGAG-UC-G-G-U-C-A-AGGUGAUCGCGUC-UG--A-UGAACCAAGGUGA---------------------------------------------------------------------CUGGAUCACCCAGG-----CA-U-C-A-GCCGAGGAAAGUCUGGACUC-C---ACA--GAGCA-C-GG-UG----------------GUUGU------------UAACG----------------GCAACCCGGA-----------------------GUGA------UCCGCGGG-AA---AGU-GCAACAGAAA--GUAG-ACC-GCC----AC---C--GGU-------------------------------------------------------------------------------------------------------------------------UUUGGCC-G----G--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-GGCAG-G-C-C-AG-GUGA--CU-G-G-U-CUGG-C-CA----------------GGUAAAC-CCCACCG-GGAGCAAGGC------------------------------------AUGAG--G-ACGCACUCCAAUGGGUGUGU-----------------------CUGUGCAGGCGUUUUAAAGGCUGCUC----GCCGA---------GUC---UG-C-----AGGU---A---------G-CUGC---------------------U--GGA-GGCA-G-U-CAGCAAUGG-C--U-G-U-C-C--GAGAUGGAU-GUUCACCG-----------------CCCGCGGGUAGGGUUUCGGCCCG--------------------------GCCCGCGGGAACAGAAUCCGGCUUA--U-GCACCGG-CUCAUUCG
AAMN01000002.1/922597-922223   CGAG-UC-A-G-U-C-C--GACGGUCGCGGC-GU--G-G-------------------------------------------------------------------------------------------GCAA------C-C-A-U-GUCGAGGAAAGUCCGGGCUC-C---ACA--GGGCG-C-GG-UG----------------GUGGC------------CAACA----------------GCCACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC---UCC---C--GAC-------------------------------------------------------------------------------------------------------------------------UCCGGUC-G----G--G--CGGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGG-U-U-C-CG-GUGA--CG-G-A-G-UCGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGCUC-AGAC------------------------------A-GUG--U-GCGUUC----------------------------------------------------GAGGGCGGCCC----GCCCG--------AGUA---CA-C-----GGGU---A-----G---A-GCGC---------------------U--GGA-GGCC-A-C-UGGCAACAG-U--G-G-U-C-C--GAGAUGGAU-GACCGUCA-----------------GCGUGACCCGGGCAACCGG---------------------------------CCACGCGACAGAACCCGGCUUA--U--GACUGA-CUCGUCCG
AAVW01000028.1/42861-43300     GGGA-GU-A-G-G-C-GCAGGCGGUUGCAGA-UC--A-GUCA----------------------------------------------------------------------------------------GAGU----GAC-U-G-G-UUUGAGGAAAGUCCGGACUC-CC-GAAA--GACCA-A-ACUUG----------------CUGGG------------UAACG----------------CCCAGUGCGA-----------------------GCGA------UCGUGAGG-AU---AGU-GCCACAGAAA--GAU--ACC-GCC----AU---C--UUCAGUGAACAGUGAACAGUGAACAGUGAAC-----------------------------------------------------------------AGUCAAAACCUGAUAACUGAUAACUGAUAACUGAA-A----A--U---GGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-G-U-C--GAGA---G-G-C-G-CUGG-C-UC----------------GGUAAAC-CCCGGUAGGGAGCAAGGCC-AGA---------------------------------GGA--A-ACUAC------------------------------------------------------GGUUGGUCUU----UUACC--------AGUU---UC-C-----GUGCAUUA-----G--AG-CCGC---------------------U--AGA-GGCG-U-U-UGGUAACAA-G--C-G-U-C-C--CAGAUAGAU-AACUGCCCUCAAAG----GUGUUUUUAAACAUUGGCGAG--------------------------------------------AACAGAACCCGGCUUA--U-GUCCGAC-UCUCUCCC
CP000384.1/3537274-3536871     CGAG-UU-G-G-C-C-G--GGCGGCCGCGGA-CC--G---------------------------------------------------------------------------------------------GAAA--------C-G-G-UUCGAGGAAAGUCCGGACUU-C---ACA--GAGCA-G-GG-UG----------------AUUGC------------UAACG----------------GCAAUCCGAG-----------------------GUGA------CUCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----AC---C--CCUGACGC--------------------------------------------------------------------------------------------------------------CUUCGGGCAAAGG-G----G--C---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAC-C-C-C-GG-GUGA--CC-G-G-G-GUGG-C-UC----------------GGUAAAC-CCCACCC-GAAGCAAGGCC-AAGAGGCCGCACC-----------CGGUGCGGCUGCGCA--G-GCGCUC----------------------------------------------------GAGGGUUGCUC----GCCCG--------AGCC---UG-C-----GGGU---A-----G---G-CCGC---------------------U--CGA-GGCA-C-C-CGGCGACGGAG--U-G-C-C----CAGAUGGAU-GGUCGCCGC---------------CGCGCCGUCAGCAAUGACGG----------------------------------CGCGGAACAGAAUCCGGCUUA--C-AGGCCAG-CUCGUCCG
M64552.3/1392-1795             CGAG-CC-G-G-G-C-G--GGCGGCCGCGUG-GA--G-UCCC----------------------------------------------------------------------------------------UCACG---GGA-C-U-U-CCCGAGGAACGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------AUGGC------------UAACG----------------GCCACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAAA--GCAG-ACC-GCC----GG---A--GGC-------------------------------------------------------------------------------------------------------------------------UUCGGCC-C----C--C---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGUGC-C-C-A-GG-GCGA--CC-U-G-G-GCAG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGGUC-AAGAAGGAAGCGCC---------CCGGUGCUUCUGCGCG--G-ACGUUC----------------------------------------------------GAGGGCUGCCC----GCCCG--------AGUC---CG-C-----GGGU---A-----G---A-CCGC---------------------U--GGA-GGCC-G-G-UGGCAACGC-C--G-G-U-C-C--UAGAUGGAU-GGCCGUCG-----------------CCGACGGGACCCGCGAGGCC-------------------------------CCGUCGGAACAGAACCCGGCGUA--C-AGCCCGA-CUCGUCUG
CP000436.1/1012669-1012282     CGAG-UU-A-G-U-C-A--GGCAAUCGCUGG-UU--U-GUUGAAAUCUUUAACCGUUU-------------------------------------------------------UUAAACGACUUAGAGGCAUAA-----GU-A-A-A-CGAGAGGAAAGUCCGGGCUA-C---AUA--GGGCA-G-AG-UG----------------CCGGA------------UAACG----------------UCCGGGAGGC-----------------------GUGA------GUCUACGA-CC---AGU-GCAACAGAGA--GCAG-ACC-GCCA--AUG---G--CUC-------------------------------------------------------------------------------------------------------------------------GUAAGAGAU----C--A---GGUAAGGGUGAAAG----GGU---GU-G--G--U----------------------AAGAG-CACACC--GCAU-G-A-A-UG-GUAA--CA-UUU-U-AUGG-C-AU----------------GGUAAAC-UCCACUC-GUAGCAAGACC-AAAU------------------------------AGGAA--C-UCAA-------------------------------------------------------UGAGUUGCCC----GCUCA---------GAG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCGU-A-U-GUGUAAAUG-U--A-C-G-C-C--UAGAUGAAU-GAUUGUCC------------------------AA-------------------------------------------------GACAGAACCCGGCUUA--U-CGACUAA-CUCAACAU
AAOU01000016.1/100989-100601   GGAG-UA-G-G-U-C-A--GGUAAUCGCUGC-UU--C-AUUGAUGUCCU--------------------------------------------------------------------------UUGGGAGACUG-----AU-G-A-A-GGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------CCAGA------------UAACG----------------UCUGGGGGGC-----------------------GCAA------GCCCACGA-CA---AGU-GCAGCAGAGA--GCAA-ACC-GCC----GA---U--GGCCUAUUG-------------------------------------------------------------------------------------------------------------CUUGCAAUAGUGC-A----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-A-G-C-UA-GUAA--UA-GUU-U-GUGG-C-AG----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGUC--C-CUAAU------------------------------------------------------GGCGCGGCCC----GCGUU---------GGG---GA-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GUCU-G-U-GAGCGAUUG-C--A-G-A-C-C--UAGACGAAU-GAUUGCCG-----------------CCGCGUAAGCGG----------------------------------------------AACAAAACCCGGCUUA--U-CGACCGA-CUCCCUAC
AAOA01000002.1/350631-351049   GAAG-UU-G-G-C-C-A--GACGAUCGCGGU-AU--U-CCCUG-------------------------------------------------------------------------------------UUUCAG-----GG-G-G-U-ACGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGU-----------------------GUGA------GCCCACGG-AA---AGU-GCAGCAGAAA--GGAA-ACC-GCC----UU---U--CUCCAAGACCGCUCAGGGCUGUUAAUGCAAUGGC-----------------------------------------------------------UCGGACGUCUUGGCAGGACCUCUCAACGAUGUCCUGUG-A----A--G---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-C-UG-GUAA--CA-G-G-C-GCGG-CGAU----------------GGUAAAC-CCCACCU-GGAGCAAGACC-AAAU------------------------------AGGAA--U-CCACCA-----------------------------------------------------GCUGCGGCCC----GCAGU---------GGA---UU-C-----GGGU---A-----G---G-UCGC---------------------U--AGA-GGCG-G-G-CGGCGACGC-U--C-G-U-C-C--CAGAUGAAU-GAUCGUUC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGCCAA-CUUCUUUA
CP000716.1/1281435-1281114     UGAG-UG-G-A-G-C-G--AGGAGGCGCGGC-U---------------------------------------------------------------------------------------------------AA------------A-GCCGAGGAAAGUCCGGACUC-C----AG--GGGCA-A-GG-UA----------------CCGGA------------UAACG----------------UCCGGAGGGA-----------------------GUGA------UCCC-UGG-AU---AGG-GCCAUAGAAA--AGAAAACC-ACC----U------------------------------------------------------------------------------------------------------------------------------------UAA------------U---GGUAAGGGUGGAAC----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGGUA-U-G-G-A--GUAA---U-C-C-A-UACG-C-UU----------------GGUAACC-CCUACCU-GGAGCAAGGUC-AAGC------------------------------A-GAG--C-U----------------------------------------------------------UGGGUGGCCC----GCCCU--------AUAG---CU-C-----GGGU---A-----G---A-CCGC---------------------U--UGA-GGAA-U-U-UGGUAACAA-A--U-U-C-C-C--CAGAUAGAU-GCCUCCA-------------------------AA-------------------------------------------------AACAGAAUCCGGCUUA--C-UGCUCCA-CUCGAUUA
CP000109.2/627864-628230       CAAG-AA-G-G-U-U-G--GGCAGUCGCGAG-A--------U----------------------------------------------------------------------------------------UUUU------------U-CUCGAGGAAAGUCCGGGCAC-U---AUA--GAGCA-G-AA-UG----------------CCAGC------------UAACG----------------GCUGGGCGGU-----------------------GAAA------GCCGACGG-AA---AGU-GCAGCAGAGA--GUAG-ACC-GCC----AA---U-------------------------------------------------------------------------------------------------------------------------------UUG----A----U--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-A-A-C-GG-GUAA--CC-GUU-U-GUGG-C-AA----------------GGUAAAC-CCCAUUC-AGUGCAAGACC-AAAU------------------------------AGGGA--A-ACGCGUUCAAGCUUU----------------------------------GCUUGGGCAAGGUGCGGCUC----GUACC-------UGGUU---UC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGGA-A-G-UAGUGAUGC-U--U-C-U-C-C--UAGAUGAAU-GAUUGUCA-----------------CCAGCAAUGG------------------------------------------------UACAGAACCCGGCUUA--U-AGAUCUU-CUUGCAUU
AM412317.1/3122781-3122425     CGAG-UA-A-G-C-C-A--GACAAUCGCUGC-CG--U-ACAU----------------------------------------------------------------------------------------U--------GU-A-C-G-GGAGAGGAAAGUCCGAGCUC-C---AUA--GGGCA-G-GG-UG----------------CUGGG------------UAAUA----------------CCCAGUGGAG-----------------------GCGA------CUCUAAGG-AA---AGU-GCAACAGAGA--UAU--ACC-GCC----AG---G------------------------------------------------------------------------------------------------------------------------------UUUA----U----C--U---GGUAAGGGUGGAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC-AGCGU-A-U-A-G--GUGA---C-U-A-U-ACGG-C-UA----------------UGUAAAC-CCCAUCU-GGAGCAAGAUC-GAAU------------------------------AGGAG--A-GCAGGAAAUUUU---------------------------------------GGUUUCCAGGGGUGGCCC----GUCCC---------GCU---CU-C-----GGGU---A-----G--UA-UCGC---------------------U--GGA-GCCU-A-U-UGGUAACAA-U--A-G-G-C-C--UAGAUAGAU-GAUUGUCU------------------------AA-------------------------------------------------CACAGAACUCGGCUUA--U-AGGCUUG-GUCGUGCC
CP000607.1/801943-801538       AAAC-CGCA-A-G-U-G--UGCAGUCGCUGC-AG--G-GCCA----------------------------------------------------------------------------------------AUG------GC-C-C-U-GCAGAGGAAAGUCCGAACUU-C---ACA--GGGCA-G-GG-UG----------------CCGGUC---------GAGAGCGCCGAAAGGUUCUCAAGCCCGGGCAGGUC------------------GGCGCAAGCCGGUCCUGACAG-AG---AGC-GCAGCAGAAA--GCAG-ACC-GCU----CC---G--G---------------------------------------------------------------------------------------------------------------------------GAAA--C-C----G--G---AGUAAGGGUGAAAC----GGC---GG-U--G--U----------------------AAGAG-ACCACC-AGGCA-U-U-C-CG-GUAA--CG-G-A-G-UGCG-C-UA----------------UGCAAAC-CUC-CCC-GAAGCAAGGCC-GAAU------------------------------AGGAA--A-GCUUUUCCCCAAAGGGAAAG-----------------------AGGGCGGCCCGCCCGAUUCC--GCAA-----GGAG--------AGUU---UU-C-----GGGU---A-----G---G-CCGC---------------------A------------------------------------U--CAGAUAAAU-GACUGCAG-----------------UUUCUUCCGGCACGCCGGU----------------------------------UGAUUCACAGAAUUCGGCUUA--C-AUCUUCG-GUUUCGGC
CU207211.1/2797087-2796765     GAAG-CA-G-G-C-C-A-AGACAACCGCUGG-CU--G-UCAU----------------------------------------------------------------------------------------UUCGG---UGA-U-G-G-CGGGAGGAAGGUCCGGACUC-C---AUA--GAGCA-G-GG-UG----------------ACGGU------------UAACG----------------GCCGUCCGCC-----------------------GCGA------GGCGAGGA-AU---AGG-GCCACAGAGA--CGAG--CG----------------UAU-------------------------------------------------------------------------------------------------------------------------UAAGUUA------------------CGGUGAAAC--------------------------------------------------------G---------------------------------C-------------------GGUAACC-UCCACCU-GGAGCAAUUUC-AAAU------------------------------AGGCA--C-GCGUUG----------------------------------------------------A--CGUUGCUC----GCGGA---------GCG---UG-C-----GGGU---A-----G---A-AAGC---------------------U--UGA-GCCG-U-G-GAGUAAUUC-A--C-G-G-C-C--UAGAGGAAU-GGUUGUCA-----------------UAGCAAAUGGGCUUGCUCAU-------------------------------UUGCCGUAACAGAAUCCGGCCUA--U-CGGCUUG-CUUCAACU
CP000301.1/2380838-2380410     UCAG-UC-G-G-C-C-G--GACGGCCGCUCU-CG--C-UACGGU-----------------------------------------------------------------------------------CGAAAGG-----CU-G-C-G-AGGGAGGAAAGUCCGGGCUC-C---AUC-GACAUA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAGA--ACGA-ACC-GCU----CG---G--CGAAGUCC---------------------------------------------------------------------------------------------------------------GCAAGGACGAAG-C----G--G---AGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-U-U-C-CG-GCAA--CG-G-A-A-ACGG-C-AG----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGG--C-GGCAACGCAGAGCGUUCGCGC----------------------AAGCGAUAACACUGCAGGGCGAUGUC---AAGCUC--------GCCG---UC-C-----GGGU---A-----G---G-UUGC---------------------U--AGA-GGCA-G-C-GUGCAAACG-U--U-G-U-C-C--CAGAGGAAU-GGCCGUCGCGU----------AUCGCUCGUGCAAGCGGGCGGU------------------------------------GCCCUCCAGAACCCGGCUUA--C-AGGCCGG-CUGAUAUU
AAVT01000007.1/10464-10087     CGAG-UC-A-G-C-U-A--GGCAGUCGCCGU-UC--A-UUCUUAU----------------------------------------------------------------------------------UCGUAAG-----CG-U-G-A-AGGGAGGAAAGUCCGGGCUC-C---AUA--GGGUA-G-GA-CG----------------CCAGG------------UAACU----------------CCUGGGGGGC-----------------------GCAA------GCCUACGG-AU---AGU-GCAGCAGAGA--GUAG-ACC-GCCG--AUG---G--CUUCCUCUAU-----------------------------------------------------------------------------------------------------------UUCGGUAGAAGAAG-C---AC--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-G-A-C-UG-GUAA--CA-GCU-C-GUGG-C-AU----------------GGUAAAC-CCCGUUC-GGAGCAAGACC-AAAU------------------------------AGGAA--C-UCUAUA----------------------------------------------------GGCGUGUACC-----CGCGC--------UGAG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--AAA-GUGU-U-G-CGGUGACGU-A--A-C-G-C-G--UAGAUGAAU-GACUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGUUGG-CUCAAAUA
AAWL01000004.1/135246-134887   AUGA-GU-ACG-A-A-A--GAUGGUCGCGAA-UG--C-C-------------------------------------------------------------------------------------------GGAG------G-G-C-A-UUCGAGGAAAGUCCGAGCUC-C---GCA--GGGCA-G-GG-UG----------------CUGGA------------UAACG----------------UCCAGCGAGG-----------------------GCGA------CCUCAGGG-AA---AGU-GCCACAGAAA-UGUAG-ACC-GCC----GG---G--CGC-------------------------------------------------------------------------------------------------------------------------UUUCGCG-U----U--C---GGUAAGGAUGGAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-C-A-G--GCGA---C-U-G-G-CUGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGACC-GAAU------------------------------AGGGA--A-GGAAUG----------------------------------------------------A--GGCGGCCC----GCUGA---------CCU---UC-C-----GGGU---U-----G--UG-UCGC---------------------U--UGA-GCCG-U-C-AGGCAACUG-G--C-G-G-C-C--UAGAUAGAU-GACCAUCA-----------------CCGCGUGAGCGG----------------------------------------------AACAGAACUCGGCUUA--U-UGACUAC-UCAUAGCU
AAOW01000035.1/17820-17459     GGAG-UU-U-G-C-C-A--GGCAGUCGCUGC-CC--U-UU---------------------------------------------------------------------------------------------------CG-G-G-G-GUGGAGGAAAGUCCGGGCUC-C---AAA--GGGUA-G-AG-UG----------------CCAGA------------UAACG----------------UCUGGGCGGC-----------------------GCGA------GUCGACGG-AA---AGU-GCAGCAGAAA--AUAU-ACC-GCCU--ACG---U--AUCUCGAUU-------------------------------------------------------------------------------------------------------------UUCGGAUCGGGAU-G----C--C---GGUAAGGUUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-G-G-G-UG-GCAA--CA-UUC-C-ACGG-C-AU----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCUAUA-----------------------------------------------------GGCGUGACCC----GCGCU---------GGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGCC-U-G-UAGCGAUGC-A--G-G-U-C-C--UAGAUGAAU-GACUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--C-CGGCAAA-CUCCUCAU
AE017143.1/1340084-1339700     UGAG-UU-A-G-U-U-A--GGCAAUCACUGG-UU--U-AUUGAAGCCUAAAGUGUUCUU------------------------------------------------------UAGAACAAACUAGUGGGACAA-----AU-A-G-A-CGAGAGGAAAGUCCGAGCUA-C---AAA--GGGCA-G-AG-UG----------------CCAGA------------UAACG----------------UCUGGGAGGC-----------------------GUGA------GCCUACGA-CU---AGU-GCAACAGAGA--GCAG-ACC-GCC----UG---U--GAU-------------------------------------------------------------------------------------------------------------------------UAA-AAC-A----C--A---GGUAAGGGUGAAAG----GGU---GU-G--G--U----------------------AAGAG-CACACC--GCGU-G-A-A-UG-GUAA--CA-UUU-C-ACGG-C-AC----------------GGUAAAC-UCCACUC-GUAGCAAGACC-AAAU------------------------------AGGAA--U-CCAA-------------------------------------------------------UGAGUCGCCC----GUUCA---------GGA---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCUU-G-U-GUGUGAAUA-C--A-A-G-C-C--UAGAGGAAU-GAUUGUCC------------------------AC-------------------------------------------------GACAGAACUCGGCUUA--U-CGACUAA-CUCAGUUC
AAUW01000011.1/86086-85664     UCAG-UC-G-G-C-C-G--GACAGCCGCUGC-CG--C-AAGUGC-----------------------------------------------------------------------------------CGAAAGG-----CC-G-C-G-GGGGAGGAAAGUCCGGGCUC-C---AUG-GAAACA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCGAGG-----------------------GCGA------CCUUAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----CC---G--GCCAGAUC---------------------------------------------------------------------------------------------------------------GAGAGAUUUUCC-C----G--G---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGC-A-A-C-UG-GCAA--CA-G-C-G-GCGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-AGCGCGGACCGGAGC----------------------------------AAUCCGGUCCAGGCCGGUUUC-CAGGCCA--------GUUG---UC-C-----GGGU---U-----G---G-UUGC---------------------G--AUA-GGCG-U-C-UGGCAACAG-G--C-G-U-C-A--CAGAUGAAU-GGCUGUCA-----------------CGUCCGCGUCAGGUCUCGUAUCU-------------------------GGCCGGGCCAUACAGAACCCGGCUUA--C-AGGCCGG-CUGGCUCU
AE004969.1/1924437-1924796     CGGG-AC-G-G-G-C-A--GACAGUCGCCGC-GU--A-UCGC----------------------------------------------------------------------------------------GUAAG---GCA-U-A-C-GGGGAGGAAAGUCCGGGCUC-C---GCA--GGGUA-G-AA-UG----------------CCGGU------------UAACG----------------GCCGGGCGCG-----------------------GUAA------CGCGACGG-AA---AGU-GGAACAGAAA--GCAAAACC-GCCG-AUGG---C--UGC-------------------------------------------------------------------------------------------------------------------------UUUGGCA-G----C--AC-AGGCAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGGG-CGCACC--GCGC-A-U-U-UG-GUAA--CA-AUA-U-GCGG-C-AG----------------GCCAAAC-CCCAUUC-GGAGCAAGACC-AAAC------------------------------A-GAA--C-GCA-------------------------------------------------------AUGACGCUGCC----CGCCG--------AGCG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCAU-A-C-CGGCAACGG-U--A-U-G-C-C--UAGAGGAAU-GACUGUCC------------------------GA-------------------------------------------------GACAGAACCCGGCUUA--C-CGCCUGU-CCGGUGUG
CP000302.1/312051-312435       CGAG-UU-G-G-C-C-A--GACAGUCGCCGC-GU--U-CUUC-------------------------------------------------------------------------------------------------GG-A-A-C-GGGGAGGAAAGUCCGGGCUC-C---ACA--GAGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GCGA------ACCGACGA-CA---AGU-GCAGCAGAGA--GGAG-ACC-GCC----AU---U--UUAAGC-------------------------------------------------------------------------------------------------------------------UUCGGCUAUA-A----A--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-G-G-C-UA-GUAA--UA-GUC-C-GUAG-C-AA----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCAGUGCUUACUUA------------------------------------GGUAAGCUGAUGCGUGGCU----CGCGU--------UGGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCU-G-U-GAGCGAUUG-C--A-G-G-C-C--UAGAUGAAU-GACUGUCG------------------CUCCUCACGGAGA--------------------------------------------GACAAGACCCGGCUUA--U-AGGCCAA-CUCACCUC
AE002160.2/810850-811252       CGGA-AG-G-G-U-A-A--GGCAACCGCUGA-GC--C-AGUUUU-----------------------------------------------------------------------------------AGAAAAA-----CU-GCG-UAUCAGAGGAAAGUCCGGACUU-C---GUA--AGAAA-A-GA-UG----------------CUGGA------------GAAAU----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAU-UCC-GCU----AU---A--AAUG-----------------------------------------------------------------------------------------------------------------------AUAUCAUU-U----A--U---AGACAGGCUGAAAA---AUCC---UA-C--U--U----------------------UAGGA-GUAGGA--GCUG-C-U-A-GG-GAGA--CC-U-G-G-UAGA-C--U----------------UGUAAAC-CCCAUCU-GAAGCAAGA--------------------------------------GAAA--A-AGUUAUUUGUCUCUGC--------------------------------AAAAUCCUUUCUAAUGAAAGG----CAUAA--------ACUU---UU-U-----CAUA---A-----------UCGC---------------------U--UGA-GGAG-U-A-CAGUAAUGU-G--C-U-C-C-C--UAGAUGAAU-GGUUGCCC-----------------ACAAGUAAGAAUUUCUUAUUCG----------------------------UACUUGUUGACAGAAUCCGGCUUA--C-UCGCUCU-UCCGAGCU
AAPG01000076.1/1039-1399       GGAG-UU-G-G-C-U-A--GAUCGUCGCCGC-UU--U-AUUGCUAU-------------------------------------------------------------------------------UUAUAGUUU-----AU-A-G-A-GGGGAGGAAAGUCCGGGCUU-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGUAGC-----------------------GCAA------GCUAACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCC----UG---C--AAA-------------------------------------------------------------------------------------------------------------------------UUUAUUU-G----U--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGCU-A-A-U-GG-GUGA--UC-A-U-U-AGUG-C-AG----------------GGUAAAC-UCCACCU-GAAGCAAAACC-AAAU------------------------------AGGCU--U-CCUGA------------------------------------------------------GGUAUGGCCC----AUACU---------GGA---AG-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCG-U-C-GAGUGAUUG-G--C-G-G-C-C--UAGAGGAAU-GACGAUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGCCGA-CUCCAACC
CP000644.1/358018-358404       GGAG-UC-G-G-C-U-G--GGCAAUCGCUGC-UU--C-GUCGUUGUGUCCC----------------------------------------------------------------------UCGGGACAGACGG-----GC-G-G-A-GGGGAGGAAAGUCCGGGCUU-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GUGA------GCCCACGA-CC---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CCC-------------------------------------------------------------------------------------------------------------------------GCAAGGGAU----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-U-C-UG-GUAA--CA-GUU-C-GUGG-C-AC----------------GGUAAAC-UCCACCC-GAAGCAAGACC-AAAU------------------------------AGGCC--C-CUAUU------------------------------------------------------GGCGCGGCCC----GCGUU---------GGG---GG-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCA-G-C-GAGCGAUUG-C--U-G-G-C-C--UAGAGGAAU-GAUUGCUA----------------CCCGGGGCAACCCGG--------------------------------------------UACAGAACCCGGCUUA--C-AGGCCGA-CUCCGACC
CP000480.1/4393032-4392645     CGAG-UU-G-G-C-C-G--GGCGGCCGCGGC-AU--C-AGC--------------------------------------------------------------------------------------------------CU-G-A-U-GUCGAGGAAAGUCCGGACUU-C---ACA--GAGCA-G-GG-UG----------------AUUGC------------UAACG----------------GCAAUCCGAG-----------------------GUGA------CUCGCGGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----A-----------------------------------------------------------------------------------------------------------------------------------GAAA------------U---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAC-C-C-C-GG-GUGA--CC-G-G-G-GUGG-C-UA----------------GGCAAAC-CCCACCC-GAAGCAAGGCC-AAGAAGGCCGCAACU-------GCGGUUGCGGCCGCGCA--G-GCGCCC----------------------------------------------------GAGGGUUGCUC----GCCCG--------AGCC---UG-C-----GGGU---A-----G---G-CCGC---------------------U--UGA-GGUA-C-C-CGGCGACGG-G--C-U-A-C-C--CAGAUGGAU-GGUCGCCG-----------------CCCCACCGCCAGAGAUGGCG--------------------------------GCGGGGAACAGAAUCCGGCUUA--C-AGGCCAA-CUCGUUCG
CP000667.1/3848228-3847813     CGAG-UC-G-A-C-C-G--GGCGGUCGCGUC-GG--C-GGGU----------------------------------------------------------------------------------------UCCAG---CCC-G-C-C-GUCGAGGAACGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------GUUGC------------UAACG----------------GCAACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----GU---U--CCC-------------------------------------------------------------------------------------------------------------------------UAACGGG-G----A--C---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC-AGCAC-C-C-C-GG-GUGA--CC-G-G-G-GUGG-C-UC----------------GGUAAAC-CCCACCC-GGAGCAAGGCC-AAGAAGGGGCCGUCAUCCGCAGAGACGACGACCCGCGCA--G-GCGAUC----------------------------------------------------GAGGGCUGCCC----GCCCG-------AUGUC---UG-C-----GGGU---A-----G---G-CCGC---------------------U--GGA-GCCU-G-U-CGGUGACGG-C--A-G-G-C-C--GAGAUGGAU-GACCGCCG-----------------CCGGCGCGAGCCCUCGGGCCC-----------------------------GCGCCGCGCACAGAAUCCGGCGUA--C-AGGUCGA-CUCGUCCG
AASF01002160.1/1477-1126       GGAG-UC-G-G-C-C-G--GACAGUCGCUGC-CU--C-G-------------------------------------------------------------------------------------------GCAA------C-G-A-G-GUGGAGGAAAGUCCGGGCUC-C---ACA-GGGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGAC-----------------------GCAA------GUCUACGG-AA---AGU-GCCGCAGAAA--AGAU-ACC-GCCU--AAG---C--GCC-------------------------------------------------------------------------------------------------------------------------UUUAGGC-G----C--C---GGUAAGGGUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-U-G-A-CG-GUAA--CG-C-C-A-GUGG-C-AG----------------GGUAAAC-CCCACCC-GGAGCAAGACC-AAAU------------------------------AGGGG--A-GCAUU------------------------------------------------------GGUGUGGCCC----GCAUC---------GCU---CC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGUG-C-A-CGGUGACGU-G--C-A-U-C-C--CAGAUGAAUGGGCUGUCC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--C-AGGCCGG-CUCCCCCU
AE013218.1/93701-93332         GAAG-UU-G-A-C-U-A--AACAGUCGCUGU-UU--A-GUUU----------------------------------------------------------------------------------------UAAA-----AC-U-A-A-AGAGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-G-GG-UG----------------CCAGG------------UAACA----------------CCUGGAAAGC-----------------------GCAA------GCUUAUGA-CA---AGU-GCAACAGAAA--AAAA-ACC-ACC----UU---A--UUUUCUUUUU-----------------------------------------------------------------------------------------------------------UUAACUGCAGAUAA-U----A--G---GGAAAGGGUGAAAA----GGU---GU-G--G--U----------------------AAGAG-CACACC--GCAU-A-A-U-UG-GCAA--CA-AUU-U-AUGG-C-AA----------------UGUAAAC-UCCACCU-GGAGCAAAGCC-AAAU------------------------------AUAGG--U-UAU-------------------------------------------------------UAAUAUUGCUC----GUAUUUU----AAAAAA---CC-U-----GGGU---G-----G---G-CUGC---------------------U--UGA-AUUA-G-U-AAGUAAUUA-C--U-A-A-U-C--UAGAUGAAU-GACUGUU-------------------------AA-------------------------------------------------AACAGAACCCGGCUUA--U-AGGUCAA-CUUCUUAA
CP000110.1/152159-151769       GAAA-GC-A-G-G-C-G-AGGUGGUUGCGGC-CG--A-UCUCU--------------------------------------------------------------------------------------UUGAG-----UG-U-C-G-GCUGAGGAAAGUCCGGGCUC-CC-UGAU--GGCCA-G-GCUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAC--ACC-GCCG-AUGG---C--CGG-------------------------------------------------------------------------------------------------------------------------UUCGCCG-G----C--AC-AGGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGCUGGGAGCAAGGCC-AA----------------------------------GGA--A-CGA-------------------------------------------------------CGGCUGGCCAU----UGGCC--------CCGU---UC-CGC-UUGAAC---G-----C---G-CCGC---------------------U--UGA-GGCC-G-U-CGGUAACGG-C--G-G-U-C-C--CAGAUAGAU-AACCACCCACCCUCUGCAGACCAAACUCUGUGAGGCGUG--------------------------------------------AACAGAACCCGGCUUA--U-GUCCUGC-UUUCACCA
AM180355.1/3148245-3147911     UAAG-UA-A-G-C-C-A--GAUAAUCGCAUG-UA--A-U-----------------------------------------------------------------------------------------------------C-U-U-A-CAUGAGGAAAGUCGGAGCUC-C---AUA--GAGCA-G-GG-UG----------------CUAGG------------UAACG----------------CCUAGUGGGA-----------------------GCGA------UCCUAAGG-AU---AGU-GCAACAGAAA--UAA--ACC-GCC----AC----------------------------------------------------------------------------------------------------------------------------------UAUU---------G--U---GGUAAGGAUGGAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC-AGCAG-C-U-A-G--GCGA---C-U-A-G-UUGG-C-UA----------------UGUAAAC-CCCACCU-GGAGCAAGACC-AA---------------------------------GAUA--G-GAAUAA---------------------------------------------------AGAGUGCUGCUC----GUACU--------CUCC---GG-U-----AGGU---A-----G---G-UCGC---------------------U--UGA-GCCU-A-U-UGGUGACAA-U--A-G-G-C-C--UAGAAAGAU-GAUUAUCU------------------------AA-------------------------------------------------UACAGAACUCCGCUUA--U-AGACUUG-CUUAAUUA
CP000133.1/2984940-2984543     CCAG-UU-G-G-C-C-G--GGCAGCCGCGCU-UU--A-CCAAUGC---------------------------------------------------------------------------------CGAAAGGC-----GG-U-A-A-GGUGAGGAAAGUCCGGGCUC-C---ACG-GAAACA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGAGG-----------------------GCGA------CCUCAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----UG---U--CA-------------------------------------------------------------------------------------------------------------------------------UG-A----C--A---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCAU-C-U-C-CG-GCAA--CG-G-A-U-AUGG-C-AC----------------GGUAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGA--U-GACGCGGCGGGCUG-----------------------------------AAAGGUUCUCCGGCCGGUUUC-CAGGCCA--------GUCA---UC-C-----GGGU---G-----G---G-UUGC---------------------G--UGA-GGCA-G-C-GUGCGAGCG-C--U-G-U-C-C--CAGAGGAAU-GGCUGCCACG-------------UUCCGGUUCACGCCGGAG---------------------------------------CCAUACAGAACCCGGCUUA--C-AGGCCAA-CUGGCAAU
CP000319.1/3179466-3179883     UCAG-UC-G-G-C-C-G--GACGGCCGCUCC-CG--C-UGCGGC-----------------------------------------------------------------------------------CGAAAGG-----CU-G-C-G-GGAGAGGAAAGUCCGGGCUC-C---AUC-GACAUA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AC---AGU-GCCACAGAGA--ACGA-ACC-GCC----UC---C--UCC-------------------------------------------------------------------------------------------------------------------------CC--GGA-G----C--A---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-C-U-C-CG-GCAA--CG-G-A-G-ACGG-C-AU----------------GGCAAAC-CACACCG-GGAGCAAAACC-GAAU------------------------------AGGGG--C-GGCAUCGCGAGAGGUUCGCCU---------------------UCGGCGAUAACAUCGCAGGGCCAUGUC---GGGCCC--------GCUG---UC-C-----GGGU---A-----G---G-UUGC---------------------A--UGA-GGCA-A-C-GUGCAAACG-U--U-G-C-C-C--CAGAGGAAU-GGCCGUCAC--------------GUAUCGCGUGCGCAAGCGCGCG--------------------------------GUGCCCUACAGAACCCGGCUUA--C-AGGCCGG-CUGAUAUG
BA000030.3/7093666-7094071     CGAG-CC-G-G-G-C-G--GACGGCCGCGUG-GG--G-GUCC----------------------------------------------------------------------------------------UUGAG---GAC-C-U-C-CCCGAGGAACGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------GUGGC------------UAACG----------------GCCACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----CG---G--CGC-------------------------------------------------------------------------------------------------------------------------UUCGGCG-C----C--G---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGC-C-U-G-AG-GUGA--CU-C-A-G-GCGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGGUC-AAAAGGAGCCGCUGUG------AAAGGCGGCUCUGCGCG--G-ACGUUC----------------------------------------------------GAGGGCUGCCC----GCCCG--------AGUC---CG-C-----GGGU---A-----G---A-CCGC---------------------A--CGA-GACC-G-G-UGGCAACGC-C--G-G-U-C-C--UAGAUGGAU-GGCCGUCU-----------------CCCCGGCCGCCGCGAGGCGA--------------------------------CCGGGCGACAGAACCCGGCGUA--C-AGCCCGA-CUCGUCUG
CP000492.1/1954779-1955183     AAAC-CGCA-A-G-U-G--UGCAGUCGCUGU-GU--A-ACU-----------------------------------------------------------------------------------------ACAG-----GU-U-A-U-ACAGAGGAAAGUCCGAACUU-C---CCA--GGGCA-G-GG-UGCCGGUCGAGAGCCCUUGUGGC------------UCAAG----------------CCCGGGGGCAGC------------------GGUGCAAACCGUUUGUCACAG-AG---AGU-GCAACAGAAA--AAAA-ACC-GCU----CC---G--G---------------------------------------------------------------------------------------------------------------------------GAAA--C-C----G--G---AGUAAGGGUGAAAA----GGC---GG-U--G--U----------------------AAGAG-ACCACC-AGACA-U-U-U-CA-GAAA--UG-G-G-A-UGUG-C-UU----------------GGCAAAC-CUC-CCC-GAAGCAAGGCU-AAAU------------------------------AGGAA--U-GCUUUUCCUUUACGGAAAGA------------------------GAGUUGCCCGCUCAAUUCUUCUUCG---GAAGAG--------AGUU---UU-C-----GGGU---A-----A---G-CCGC---------------------A------------------------------------U--CAGAUAAAU-GGCUGCAG-----------------UUUUAUCCGGAUUCCGGA-----------------------------------UAAUUCACAGAAUUCGGCUUA--C-AGCUUCG-GUUUUGGC
CP000112.1/1785521-1785161     GGAG-CA-G-G-A-C-G--AGCUGCCGCUGC-GU--G-UCAU----------------------------------------------------------------------------------------UUG------UA-C-A-C-GGAGAGGAAAGUCCGGGCUC-C---GCA--GGGCA-A-GA-CG----------------CUGGG------------UAACC----------------CCCAGGUGAA-----------------------GUGA------UUCA-CGG-AC---AGU-GCCACAGAAA--ACAA-ACC-GCC----UG---C-------------------------------------------------------------------------------------------------------------------------------CAU----G----C--A---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC-AGAGG-U-G-A-CG-GUGA--CG-G-C-A-CCUG-C-UA----------------GGUAAAC-CCCGUCU-GGAGCAAGACC-AAAU------------------------------AGGAA--G-GCGCCA----------------------------------------------------A-GGCCGGCCC----GGCCG-------AUGCC---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGCU-G-C-AGGUAACUG-C--A-G-C-C-C--UAGAGGAAU-GGCAGCUGC---------------UUCCCUUUAUGGAAG--------------------------------------------AACAGAACCCGGCUUA--U-AGUCCGG-CUCCCGUC
AE017340.1/438671-439020       AGAG-CU-G-G-C-C-A--GACAAUCGCCGC-CU--G-UU---------------------------------------------------------------------------------------------------UA-C-A-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GUAA------GCCGACGA-CU---AGU-GCAGCAGAGA--GUAA-ACC-GCCG--AUG---G--CUG-------------------------------------------------------------------------------------------------------------------------CUUGCAG-C---AC--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-A-A-C-UG-GUAA--CA-GUU-U-GUGG-C-AC----------------GGUAAAC-UCCACCC-GGAGCAAGGUC-AAAU------------------------------AGGGG--U-UCUUU------------------------------------------------------GGCGCGGCCC----GCGUU---------GAA---CC-C-----GGGU---A-----G---A-CUGC---------------------U--UGA-GGGU-C-A-GGGCAACCU-G--A-U-C-A-C--UAGAUGAAU-GAUUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGCCGG-CUCUCCAC
CP000746.1/1834262-1833866     CGAG-UU-G-G-U-C-A--GACAAUCGCUGG-UU--U-AUUGAAGCCCUUAAUACCGAAAGGUUA------------------------------------------GCCUGAAACAGGUGAUAAGCGGGACAA-----GU-A-G-A-CGAGAGGAAAGUCCGGGCUA-C---AUA--GGGCA-G-AG-UG----------------CCGGA------------UAACG----------------UCCGGGGGGC-----------------------GCGA------GCCUACGA-CA---AGU-GCAGCAGAGA--GCAG-ACC-GCC----GU---U--UU--------------------------------------------------------------------------------------------------------------------------UAAU-AA-A----A--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-G-UG-GUAA--CA-UUC-C-GCGG-C-AA----------------GGUAAAC-UCCACUC-GUAGCAAGACC-AAAU------------------------------AGGAA--C-UCAAU------------------------------------------------------GAGUGUGCC-----CGCUC--------AGAG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCGA-C-G-GAGCAAUUC-G--U-C-G-C-C--UAGAGGAAU-GAUUGUCC-----------------GC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGACCGA-CUCAUUCA
AM420293.1/1744463-1744869     UGAG-UC-G-G-C-C-G--GGCGGCCGCGUC-GG--G-GUGC----------------------------------------------------------------------------------------G--------UC-C-C-C-GUCGAGGAAAGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------GUUGC------------UAACG----------------GCAACCCGGG-----------------------GUGA------CCCGCGGG-AA---AGU-GCCACAGAAA--GCAG-ACC-GCC----CG---G--CGGAGUGC--------------------------------------------------------------------------------------------------------------CCAGGCACUCCGG-C----C--G---AGCAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGC-C-C-C-GG-GUGA--CC-G-G-G-GCGG-C-UC----------------GGUAAAC-CCCACCC-GGAGCAAGGCC-AAGAGGACACCGC------------CAGGUGUCUGCGCA--G-GCGUUC----------------------------------------------------GAGGGUUGCCC----GCCCG-------AUGCC---UG-C-----GGGU---A-----G---G-CCGC---------------------U--GGA-GCCU-G-C-CGGCGACGG-C--A-G-G-C-C--GAGAUGGAU-GGCCGCCG-----------------ACUGGGAGCGCCGCAAGGCC--------------------------------CCCACGAACAGGAUCCGGCUUA--C-AGGCCGA-CUCGUCCG
AASE01000025.1/1252-1652       AAAC-CGCA-A-G-U-G--UGCAGUCGCUGU-GG--A-GCA-----------------------------------------------------------------------------------------UCAC-----GC-U-U-C-ACAGAGGAAAGUCCGAACUU-C---ACA--GGGCA-G-GG-UG----------------CCGGUCGAG----AGCCGAAAGGCU---------CAAGCCCGGGGAUAAC------------------GGCGCAAGCCGGUUAUCACAG-AG---AGU-GCAACAGAAA--ACAG-ACC-GCU----CC---G--GAC-----------------------------------------------------------------------------------------------------------------------------GGC-C----G--G---AGUAAGGGUGAAAC----GGC---GG-U--G--U----------------------AAGAG-ACCACC-AGGCA-G-U-G-CA-GUAA--UG-C-A-C-UGCG-C-UU----------------GGCAAAC-CUC-CCC-GAAGCAAGGCU-AAAU------------------------------AGGAA--A-ACUUUUCCCUCCGGGGAAAG-----------------------AGAGCGGCCCGUUCAAUUCCG---AA----AGGAG--------AGUU---UU-C-----GGGU---A-----A---G-CCGC---------------------A------------------------------------U--CAGAUAAAU-GGCUGCAG-----------------UUUUAUCCGGACUCCGGA-----------------------------------UAAUCCACAGAAUUCGGCUUA--C-AGCUUCG-GUUUCAGC
AE017282.2/2358615-2358258     GGAG-UC-G-G-C-C-A--GACAGCCGCUGU-CC--U-U--------------------------------------------------------------------------------------------GAA------G-G-G-G-AUGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCGA------GCCCACGG-AA---AGU-GCCACAGAAA--AUAU-ACC-GCC----CC---G--GU---------------------------------------------------------------------------------------------------------------------------GCG-UC-C----G--G---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-U-G-G-CG-GUAA--CG-C-C-AAGCGG-C-AG----------------GGUAAAC-CCCAUCC-GGAGCAAGACC-AAAU------------------------------AGGGG--A-GCAUUGGGUUC-----------------------------------------GCCCAGACGUGCGGCCC----GCACG---------GCU---CC-C-----GGGU---A-----G---G-UCGC---------------------U--CGA-GACG-U-A-CGGUGACGU-A--U-G-U-C-C--CAGAUGAAU-GGCUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--C-CGGCCGA-CUCUUCUU
AM167904.1/3141205-3140801     AAGG-CA-G-A-U-U-G--GGCAGUCGCGAU-GG--U-U----------------------------------------------------------------------------------------------A------G-A-C-C-AUCGAGGAAGGUCCGGACUC-C---AUA--GGGCA-G-GA-UA----------------GCGGC------------UAACG----------------GCCGUCCGGUAAGAUGC---------GCAAGCAUCGA------GCCGAGGA-AC---AGG-GCCACAGAGA--CGAG-UCU-G------CG---G--GGC-------------------------------------------------------------------------------------------------------------------------GGGCGCC-U----U--------CAGGGGCGCACC----GGC---AC-G--G--C----------------------CAUCUCCGUGCU-GCGGC-A-A-C-UG-GUGA--CA-G-U-U-GCCG-G-CAUCGCAGGGUGAAACGCGGCAACC-UCUAUCC-GGAGCAACAUC-AAAU------------------------------AGGCA--U-GCGCACAGCCUUC-------------------------------------GGGCUGGAAAGGGCGGCUC----GUUCG--------AGCA---UG-C-----GGGU---A-----G---G-UGGC---------------------U--AGA-GCGU-G-U-CAGCAAUGG-C--U-C-G-C-G--UAGAGGAAU-GAUUGCCA-----------------GUCGGGGAAACCCGG-----------------------------------------CGUACAGAAUCCGGCCUA--U-AGAUCUG-CUUUGCAC
CP000507.1/3981200-3980843     CGAG-UC-G-A-C-U-G--GGCAGUCGCUGC-GC--U-C-------------------------------------------------------------------------------------------GCAA------G-A-G-C-GGGGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-G-GG-UG----------------CCAGA------------UAACG----------------UCUGGGCGGC-----------------------GUAA------GCCGACGA-CA---AGU-GCAACAGAGA--ACAG-ACC-GCC----UG---C--C---------------------------------------------------------------------------------------------------------------------------UUCG--G-G----C--C---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-A-C-UG-GCAA--CA-GUU-C-GUGG-C-AA----------------GGUAAAC-UCCACCC-GGAGCAAGAUC-AAAU------------------------------AGGGU--U-CCUUAU-----------------------------------------------------GGCGUGGCUC----GCGUU---------GGA---AC-C-----GGGU---A-----G---A-UUGC---------------------U--UGA-GCCU-G-C-GAGCGAUUG-C--A-G-G-C-C--UAGAGGAAU-GGCUGCCA-----------------CUCCUUUCGGGGAG--------------------------------------------AACAGAACCCGGCUUA--C-AGGUCGG-CUCACCAC
AANE01000023.1/29684-29331     CAAG-UU-G-G-U-C-A--GGCAGUCGCUGU-AA--U-GCUG----------------------------------------------------------------------------------------UUUC----AGU-G-U-U-AUGGAGGAAAGUCCGGGCUU-C---GCA--GGGUA-A-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCGA------GUCUACGG-AA---AGU-GCAGCAGAAA--AAAU-ACC-GCC---UAA---G--CAG-------------------------------------------------------------------------------------------------------------------------UUUACUG-C----C------GGUAAGGUUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-A-U-C-UG-GUAA--CA-GUA-U-GUGG-C-AA----------------GGUAAAC-CCCACCU-GAAGCAAGACC-AAAU------------------------------AGGAA--U-CCAUU------------------------------------------------------GGCGUGACCC----GCGCU---------GGA---UU-C-----GGGU---A-----G---G-UCGC---------------------U--AGA-GGCA-U-G-UAGCGAUAC-A--U-G-U-U-C--GAGAGGAAU-GACUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGACCAA-CUUGCAAU
AAOE01000014.1/15829-15485     GGAG-UC-A-G-C-C-A--GACAGUCGCUGC-CU--G-CAU--------------------------------------------------------------------------------------------------UG-C-A-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGUA-A-GG-UG----------------CCAGA------------UAACG----------------UCUGGGCGGC-----------------------GCGA------GCCGACGG-CC---AGU-GCAGCAGAGA--GUAG-ACC-GCC----AG---G--CU---------------------------------------------------------------------------------------------------------------------------UCU-GG-C----C--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGA-C-A-C-UG-GUAA--CA-G-U-G-UUGG-C-AU----------------GGUAAAC-CCCACCU-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCUUAA-----------------------------------------------------GGCGUGACCC----GCGCC---------GGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-CCUC-A-G-GAGCAAUCC-U--G-C-G-G-C--UAGAUGAAU-GACUGUCC------------------------AU-------------------------------------------------GACAGAACCCGGCUUA--U-CGGCUGG-CUCCCAUU
AANO01000003.1/308359-307949   GAAA-GC-A-G-G-U-G-AGGUGGUCGCGAU-CG--A-AGGGAUGACGCCGGCU---------------------------------------------------------------UCGGCUGGUGGCUCCGG-----CU-U-C-G-GUUGAGGAAAGUCCGGGCUC-CC-CAAU--GGCCA-G-GCUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAC--ACC-GCCG--AUG---G--CCGGGGC----------------------------------------------------------------------------------------------------------------CUGGCCCCGCGC-A----C--A---GGCAAGGGUGCAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGCUAGGAGCAAGGCC-CAGGGA--------------------------CAACGGU--U-GGCCAU----------------------------------------------------GAC----ACCC-------GU--------CCCG---ACAC-----AAGU---G-----A---G-CCGC---------------------U--CGA-GGCC-G-C-CGGUAACGG-C--G-G-U-C-C--CAGACAGAU-GCCCACCCCGG----------UCCGCCCCGGCGGGCCGG--------------------------------------------AACAGAACCCGGCUUA--U-GUCCUGC-UUUCACCC
CP000699.1/68791-69173         CCAG-AG-G-G-C-C-G--GGCGGUCGCCGC-GC--A-GC---------------------------------------------------------------------------------------------------GA-U-G-C-GGGGAGGAAAGUCCGGGCUC-C---AAG-GAGUGA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCGGGG-----------------------GCGA------CCCCAGGG-AC---AGU-GCCACAGAAA--GCAG-ACC-GCC----CG---G--CGGACCGCCAA--------------------------------------------------------------------------------------------------------GCUCGCUUGGUAUGUU-C----C--G---GGCAAGGUCGAAAG----GGU---GC-G--G--C----------------------AAGAG-CGCACC--GCGG-U-C-C-CG-GCAA--CG-G-G-A-ACGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAGAUC-GAAU------------------------------AGGGA--C-GGCGC-----------------------------------------------------AUGGGCUACUC---CGCCCG--------GUCG---UC-C-----GGGU---U-----G---A-UUGC---------------------U--GGA-GGCC-G-G-GCGCGAGCC-C--G-G-U-C-C--UAGAGGAAU-GAUCGCCC-----------------AUCCGGCUUCGGCCGG----------------------------------------UGGACAGAACCCGGCUUA--C-AGGCCCU-CUGGUUCU
CP000774.1/2603043-2603414     UCAG-AU-G-G-C-C-G--GAUGGCCGCUGC-GU------------------------------------------------------------------------------------------------GCAA----------G-C-GCAGAGGAAAGUCCGGGCUC-C---ACG-GAAACA-C-GG-UG----------------CCGGU------------UAAUG----------------GCCGGCGGGG-----------------------GCGA------CCUCAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----GG---U--CC--------------------------------------------------------------------------------------------------------------------------UUCG-GG-G----C--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-A-CG-GUAA--CG-G-A-C-GCGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAAACC-AAAU------------------------------AGGGG--C-GGCAUUUCAGGCAU-----------------------------------UUAGCCUGACAACCCGUUUC---CGGGCC--------GCCG---CC-C-----GGGU---U-----G---G-UUGC---------------------U--CGA-GGCG-U-C-CGGCAACGG-G--C-G-U-C-C--CAGAUGAAU-GGCCAUCG-----------------CCC----GCAAGGG--------------------------------------------CACAGAACCCGGCUUA--C-AGGCCAU-CUGACACC
CP000282.1/1090695-1091052     CGAG-CC-A-G-C-U-A--GACAAUCGCUUC-AU--C-CUU--------------------------------------------------------------------------------------------------GU-G-G-U-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-AA-CG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCGA------GCCUACGG-AA---AGU-GCAGCAGAGA--GUAG-ACC-GCC----UG---U--GUUCUUG-----------------------------------------------------------------------------------------------------------------GCAACAAGAGC-A----U--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-A-G-C-UG-GUAA--CA-GUC-U-GUGG-CGAU----------------GGUAAAC-CCCGUUC-GGAGCAAGACC-AAAU------------------------------AGGAA--U-CCUACA-----------------------------------------------------GGUGCGGCCC----GCACU---------GGA---UU-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GGCG-U-A-UGGUGACAU-A--C-G-U-C-C--CAGAUGAAU-GAUUGUCC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGCUGG-CUCAUCAU
CP000158.1/471158-470783       CCAG-AU-G-G-C-C-G--GGCAGCCGCUGG-UA--U-GCGG----------------------------------------------------------------------------------------GUAAC---UGC-A-U-A-CUGGAGGAAAGUCCGGGCUC-C---AGG-UGGACA-G-GG-CG----------------ACGGC------------UAACG----------------GCCGCCCGGC-----------------------GUGA------GCCGAGGG-AA---AGU-GCCACAGAAA--GGAA-ACC-GCC----CG---A-AGGC-------------------------------------------------------------------------------------------------------------------------UUCGGCCAG----A--G---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCAG-C-G-C-UG-GCAA--CA-G-G-G-CUGG-C-AU----------------GGUAAAC-CCCGCCC-GGAGCAAGACC-AAGU------------------------------AGGGG--G-CACAUA----------------------------------------------------UGGGCUGUCCG---CCGCCC--------GUGC---CC-C-----GGGU---G-----C---G-UCGC--------------------GC--CGA-GGCG-U-U-CAGCAAUGA-A--C-G-C-C-C--CAGAGGAAU-GGCUGCCA----------------GAUCCCGCAAGGGAC-------------------------------------------GAACAGAACCCGGCUUA--U-UGGCCAU-CUGGUCUA
CP000238.1/37827-37463         AAAG-UU-G-A-C-U-A--GACAGUCGCUGC-UU--C-GCUUUUA----------------------------------------------------------------------------------UCAAAUA-----GC-G-U-A-GGAGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-A-GG-UG----------------CCAGG------------UAACA----------------CCUGGGGAGU-----------------------GUAA------GCUCACGA-CA---AGU-GCAACAGAAA--GCAA-ACC-GCC---AAU---A--ACCAA--------------------------------------------------------------------------------------------------------------------UUUUUUGGGA-U----A--A---GGUAAGGGUGAAAA----GGU---GU-G--G--U----------------------AAAAG-CGCACC--ACGU-A-G-C-UG-GUAA--CA-GUG-U-ACGG-U-AU----------------GGUAAAC-UCCACCU-GGAGCAAGGCC-AAAA------------------------------AGAGG--U-UAA-------------------------------------------------------AAGUGUAGCCC----GCAUU--------UAAA---CC-A-----GGGU---A-----G---G-CUGC---------------------U--GGA-ACUA-G-U-AUGUGAGUA-C--U-A-G-U-C--UAGAUAAAU-GACUGUCC------------------------AA-------------------------------------------------GACAGAACCCGGCUUA--A-CGGUCAA-CUUCACUC
AAVN02000001.1/251696-251335   UGAG-UG-G-A-C-C-A--GACGGUCGCGCGAUG--U-GCUGU--------------------------------------------------------------------------------------UUGCA-----GU-A-C-G-CGUGAGGAAAGUCCGGGCUC-C---AGA--GGGCG-G-GA-UG----------------CCGGC------------UAACG----------------GCCGGGCGGA-----------------------GUGA------UCCGACGG-AA---AGC-GCCGCAGAAA--AGAAGACU-CCCA-CCUG---C--GCC-------------------------------------------------------------------------------------------------------------------------GCAAGGC-G----U--AAAGGGAAAAGCUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGU-C-G-U-G--GCAA---C-A-C-G-GCGG-C-UU----------------GGCAAGC-CCCAUCC-GGAGCAAGCGC-GAAU------------------------------AGGAA--C-GCUAU------------------------------------------------------GGGCCGGCCC----GGUCC---------GCG---UU-C-----GGGU---A-----G---C-GUGC--------------------GU--GGA-GCUG-C-A-CGGUAACGU-G--C-A-G-A-C--AAGAUAAAU-GACCGUUC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-AGGCCCA-CUCAGCAC
CT978603.1/132775-132410       GAAA-GC-A-G-G-C-G-AGGUGAUCGCAGU-UG--C-CGCUGC------------------------------------------------------------------------------------UUGCAG-----UG-G-U-G-GCUGAGGAAAGUCCGGGCUC-CC-GAAU--GGCCA-G-GCUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAC--ACC-GCCG-AUGG---C--CGG-------------------------------------------------------------------------------------------------------------------------CUUGCCG-G----C--AC-AGGCAAGGGUGCAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGCCGGGAGCAAGGCC------------------------------------CAGG--G-ACGAU------------------------------------------------------GGUUGGCCAU----UGACC--------GGUC---CC-GAC-AACAGC---G-----C---G-CCGC---------------------U--CGA-GGCC-A-C-CGGUAACGG-U--G-G-U-C-C--CAGACAGAU-GAUCAUCC-----------------AGCG------------------------------------------------------AACAGAACCCGGCUUA--C-GUCCUGC-UUUCCGCC
CP000097.1/185956-185566       GAAA-GC-A-G-G-C-G-AGGUGGUUGCAAU-UG--A-AUCG----------------------------------------------------------------------------------------UUCGC---GAU-U-C-A-AUUGAGGAAAGUCCGGGCUC-CC-CGAU--GGCCA-G-GCUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAC--ACC-GCCG-AUGG---C--CGG-------------------------------------------------------------------------------------------------------------------------UUCGCCG-G----C--AC-AGGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGCUGGGAGCAAGGCC-AA----------------------------------GGA--A-CGA-------------------------------------------------------UGGCUGGCCAU----CUGCC--------CCGU---UC-C-----GCUUU-AU-----G--CG-CCGC---------------------U--CGA-GGCC-G-U-CGGCAACGG-C--G-G-U-C-C--CAGAUAGAU-AACCACCCACC----------CUCUGCAGACCAACCUCUGUGGU---------------------------------GGUGUGAACAGAACCCGGCUUA--U-GUCCUGC-UUUCACCC
AAPI01000003.1/215670-216054   CGAG-UU-G-A-C-C-A--GGCAGUCGCUGU-GU--U-GAUUUCUCUGAUGUUCG-------------------------------------------------------------CUUGCGAUCAUUAAGGGU-----GC-A-A-C-GCGGAGGAAAGUCCGGGCUC-C---ACA--GGGUA-G-AG-UG----------------CCAGG------------UAACA----------------CCUGGGAGGC-----------------------GAAA------GCCUACGG-CC---AGU-GCAGCAGAGA--GAAG-ACC-GCCG-AUGG---U--UCG-------------------------------------------------------------------------------------------------------------------------UUCGCGA-A----C--AC-AGGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-U-G-C-UG-GUAA--CA-G-U-A-GUGG-C-AA----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGUU--U-CCAUAU-----------------------------------------------------GGCGCGUCCC----GCGUU---------GGG---AA-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGCA-A-A-CGGCGACGU-U--U-G-U-C-C--CAGAUGAAU-GACUGUCC------------------------AA-------------------------------------------------GACAGAACCCGGCUUA--U-CGGUCAA-CUCACCUA
CP000089.1/575353-575735       AAAG-UC-G-G-C-C-A--GGCAAUCGCUGG-GC--A-C-------------------------------------------------------------------------------------------GUAA------G-U-G-C-CGGGAGGAAAGUCCGGGCUC-C---AUU--GGGCG-G-GA-UG----------------CCAGU------------UAACG----------------GCUGGGUGCUAUACGGU--------CGCAAGACCUAA------GGCAACGG-AA---AGU-GCAACAGAGA--AUAG-ACC-GCCG--AUG---G--CGUU-----------------------------------------------------------------------------------------------------------------------GUAAGACG-C---AC--A---GGUAAGGGUGAAAC----GGC---GA-G--G--U----------------------AAGAG-CUCACC--GCGU-C-C-A-CG-GUAA--CG-GCG-G-ACGG-C-AC----------------GGUAAAC-CCCAUCC-GGAGCAAGACC-AAAU------------------------------AGGGA--A-GCUGA------------------------------------------------------GGCGUGGCCC----GCGCU---------GCU---UC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCU-G-U-CGGUGACGG-C--A-G-G-C-C--UAGAGGAAU-GAUUGCCG----------------AACCUCGCAAGAGGG-------------------------------------------GAACAAAACCCGGCUUA--U-CGGCCGG-CUUUCCAA
CP000283.1/3783877-3784306     UCAG-UC-G-G-C-C-G--GACGGCCGCUCC-GG--C-AAGCGC-----------------------------------------------------------------------------------CGAAAGG-----CC-G-C-C-GGGGAGGAAAGUCCGGGCUC-C---AUC-GACAUA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAGA--ACGA-ACC-GCU----UC---C--CCCUCCC----------------------------------------------------------------------------------------------------------------CUCGGGGUGGGG-G----C--G---AGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-C-G-C-CG-GCAA--CG-G-A-G-ACGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-GGCAUCGCGGACAGUUCGCUUU--------------------CGGGCGAUAACUCCGCAGGGCGAUGUC---AGGCUC--------GCCG---UC-C-----GGGU---A-----G---G-UUGC---------------------U--CGA-GGCC-A-U-GUGCAAACA-U--G-G-U-C-C--CAGAGGAAU-GGCCGUCACGU----------AUCGGCUGCGCAAGCAGCCGGU------------------------------------GCCCUCCAGAACCCGGCUUA--C-AGGCCGA-CUGAUACU
X16580.1/131-474               GGAG-UG-G-G-C-C-A--GGCGACCGCCGC-GG--A---------------------------------------------------------------------------------------------GCAA--------U-C-C-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-A-GG-CG----------------CCGGU------------UAACG----------------GCCGGGGGGC-----------------------GUGA------GCGUACGG-AA---AGU-GCCACAGAAA--AUAU-ACC-GCC----AA---G--CGC-------------------------------------------------------------------------------------------------------------------------GUAAGCG-C-----------GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAU-U-U-C-CG-GUAA--CG-G-A-A-AUGG-C-AG----------------GGAAAAC-CCCGCCU-GGAGCAAGACC-AAAU------------------------------AGGCG--U-GCGAU------------------------------------------------------ACCGUGGCCC----GCGGU---------GCA---CG-C-----GGGU---A-----G---G-UUGC---------------------U--GGA-GCCU-G-U-GCGUAAGUG-C--A-G-G-C-C--UAGAGGAAU-GGUCGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGCCCA-CUCCAAUU
ABCH01000023.1/63801-64207     GAAG-UU-G-A-C-U-G--GAUAGUCGCUGC-UU--C-GUUGACGUCCCCUUGAGC------------------------------------------------------------UUGUCUUGGGGGAGACUG-----AC-G-G-A-GGGGAGGAACGUCCGGGCUC-C---ACA--GAGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GUGA------GCCCACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCCG--AUG---G--CUCCAUUU---------------------------------------------------------------------------------------------------------------CUUCGGAAGGAG-C---AC--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGAC-G-A-C-UG-GUAA--CA-GUU-C-GUUG-C-AA----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGCU--U-CCACA-----------------------------------------------------UUGCGUUGCUC----GCGUA--------UGGA---GG-C-----GGGU---A-----G---G-UUGC---------------------U--CGA-GCCA-G-U-GAGCGAUUG-C--U-G-G-C-C--UAGACGAAU-GGCUAUCA------------------CCGCUUCGGCGGA--------------------------------------------UACAGAACCCGGCGUA--C-AGGUCAA-CUUCACCU
AAQH01000027.1/16807-16441     GGAG-UU-G-G-C-C-G--CACGAUCGCUGC-UU--G-AA------------------------------------------------------------------------------------------UUUG-----UU-C-A-A-GGAGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGA------------UAACG----------------UCUGGGGGGC-----------------------GUGA------GCCCACGG-CC---AGU-GCAGCAGAGA--GUAU-ACC-GCCG-AUGG---C--UAU-------------------------------------------------------------------------------------------------------------------------UUAGGUA-G----C--AC-AGGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-U-C-CG-GUAA--CG-GUA-C-GCGG-C-AU----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGUU--C-CCUGA------------------------------------------------------GGUGCGGCCC----GCACU---------GGG---AA-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCUU-U-G-GAGCGAUCC-A--A-A-G-C-C--UAGAUGAAU-GAUCGUGA-----------------CCUUGUUCGCAAGG--------------------------------------------GACAGAACCCGGCUUA--U--GGCCAA-CUCCACUU
ABBZ01003066.1/465-96          AGAG-UU-A-G-U-C-G--GGUAGUCGCUAU-AU--C-UUGA----------------------------------------------------------------------------------------AAAU-----CA-G-A-U-AUGGAGGAAAGUCCGGGCUU-C---ACA--GGACA-A-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GUGA------GCCUAUGG-AA---AGU-GCCACAGAAA--AUAU-ACC-GCCU--AAG---U--CCA-------------------------------------------------------------------------------------------------------------------------UUAA-GG-A----C--C---GGUAAGGGUGAAAU----GGU---GC-G--G--UUGGUGAGUUAUCGGCUUAAUGUAAGAG-CGCACC--GCAU-U-G-A-UG-GUAA--CA-U-C-A-AUGG-C-AG----------------GGUAAAC-CCCACCU-GAAGCAAGAC--AAAU------------------------------AGGGG--A-AUUAU------------------------------------------------------AAUGUGGUCC----GCAUU---------GUU---CC-C-----GGGU---A-----A---G-UUGC---------------------U--AGA-GGUG-U-U-UGGUGACAA-G--C-A-U-C-C--CAGAUGAAU-GACUGCCA-----------------UACGGAUGAUUUUU--------------------------------------------------------------C-AAGCCGG-CUUUUGAU
AM286690.1/644585-644964       CGGA-CC-G-G-U-U-A--GACAGUCGCUGG-CG--G-UGGUUCUU-------------------------------------------------------------------------------UUAAAGAAU-----GG-C-C-G-CUGGAGGAAAGUCCGGGCUC-C---AAA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGCCACACUG-----------GGAACGGUGU------GGUUACGG-CU---AGU-GCCACAGAGA--AGAU-ACC-GCC----UU---U--UCCUUC------------------------------------------------------------------------------------------------------------------CUCGCGUUGGA-A----U--C---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-U-G-C-UG-GUAA--CA-G-U-G-GUGG-C-AG----------------GGUAAAC-CCCACCC-GGAGCAAAACC-AAAU------------------------------AGGGA--U-CCGUU------------------------------------------------------GGCGUGGCCC----GCGCU---------GGA---UC-C-----GGGU---A-----G---G-UUGC---------------------U--AGA-GGUU-U-G-UGGCGACGC-A--A-A-C-C-C--AAGAUGAAU-GACUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGACCGG-UCCACCUU
CT971583.1/222102-221705       GAAA-GC-A-G-G-C-G-AGGUGAUCGCGAC-CA--A-CCCUGGGCU-----------------------------------------------------------------------------UCGUGCACAG-----GC-G-A-G-GUUGAGGAAAGUCCGGGCUC-CC-CGAU--GGCCA-G-GCUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAC--ACC-GCC----GA---U--GGCCCCAUGGG---------------------------------------------------------------------------------------------------------AGCAAUCCCUUUGGC-A----C--A---GGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGCCGGGAGCAAGGCC-CA----------------------------------GGA--A-CAA-------------------------------------------------------CGGGUGGCCAU----CAUCC--------CCGU---UC-CGC-CUUUGU---G-----A---G-CCGC---------------------U--CGA-GGUC-G-U-CGGUAACGG-C--G-A-U-C-C--CAGAUAGAU-GAUCACCCCC-------------CUUCCGCGGAAGGGAG--------------------------------------------AACAGAACCCGGCUUA--U-GUCCUGC-UUUCACCC
CP000509.1/2179161-2178773     UGGG-CU-G-G-C-C-G--GGCGACCGCGUG-GA--G---------------------------------------------------------------------------------------------GAGA--------C-U-C-CCCGAGGAAGGUCCGGGCUC-C---ACA--GGGCA-G-AG-UG----------------GUGGG------------UAACA----------------CCCACCCGGG-----------------------GCAA------CCCGCGGG-AC---AGU-GCCACAGAGA--ACAG-ACC-GCC----CC---G--CCCCGC-------------------------------------------------------------------------------------------------------------------UCCGGCGAGG-A----G--G---GGUAAGGGUGAAAC----GGC---GG-U--G--U----------------------AAGAG-ACCACC-AGCGA-C-C-G-GG-GCGA--CC-C-G-G-CCGG-C-UC----------------GGCAAAC-CCCACUU-GGAGCAAGGUC-AAGAAGUCCCGUGC---------UUGCACGGGACGCGCG--C-ACGUUC----------------------------------------------------GAGGGCGGCCC----GCCCG--------AGUG---CG-C-----GGGU---A-----G---A-CCGC---------------------U--GGA-GGGU-G-U-CGGCAACGG-C--A-C-C-C-G--UAGAUGGAU-GGUCGCCC-----------------CCCGGCUCGCCGGG--------------------------------------------GACAGAACCCGGCCUA--C-AGGCCAG-CCCAUCCG
AAVV01000010.1/123053-122711   AGAG-CU-G-A-U-U-A--GACGAUCGCUGU-CG--C-CUU--------------------------------------------------------------------------------------------------AG-G-U-G-AUGGAGGAAAGUCCGGGCUC-C---UGA--GGUCA-G-AG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGU-----------------------GUGA------GCCCACGG-AA---AGU-GCAGCAGAAA--GGAA-ACC-GCC----UG---G--C-----------------------------------------------------------------------------------------------------------------------------UU--G-C----C--A---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-C-UG-GUAA--CA-G-G-C-GUGG-CGAU----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGA--U-CCAUUA-----------------------------------------------------GCCGUGACCU----CCGGC---------GGA---UC-C-----GGGU---A-----G---G-UCGC---------------------U--ACA-GGCG-A-A-CGGUGACGU-U--C-G-U-C-G--CAGAUGAAU-GAUCGUCC------------------------AA-------------------------------------------------GACAGAACCCGGCUUA--U-CGAUCGG-CUCAUUCU
CP000117.1/977743-978184       GAGA-GU-A-G-G-C-GUUGGCGGUUGCAGA-CC--A-GUUA----------------------------------------------------------------------------------------GUUU----AAC-U-G-A-UUUGAGGAAAGUCCGGACUC-CC-GAAA--GACCA-G-ACUUG----------------CUGGA------------UAACU----------------UCCAGUGCGA-----------------------GCGA------UCGUGAGG-AU---AGU-GCCACAGAAA--AAU--ACC-GCC----AA---A--ACAAUUCAAAAUUCAAAAUUCAAAAUUCAAAAUG-----------------------------------------------------------AAUAAUUUUGGAUUUUGAGUCUUAGUUAUGAAUUCAAU-U----U--U---GGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-A-U-C--GAGA---G-G-U-A-CUGG-C-UC----------------GGUAAAC-CCCGGUUGGGAGCAAGGCC-GAAG------------------------------GAACU--A-UGG--------------------------------------------------------UUGGUCUUUU----ACCAGU------UCCGU---UA-U-----CAGA---G-----A---G-CCGC---------------------U--AGA-GGCG-U-U-UGGUAACAA-A--C-G-U-C-C--CAGAUAGAU-AAUCGCCC-----------------UCGUGUAAAGCAAUUUACA----------------------------------CAGAGAACAGAACCCGGCUUA--C-UACCAAC-UCUCUCCU
AAPJ01000001.1/686700-686262   CCAG-CC-G-G-C-U-G--GACGGCCGCUCC-CG--U-CACAUGU----------------------------------------------------------------------------------CGAAAGA-----CG-G-C-G-GGGGAGGAAAGUCCGGGCUC-C---ACG-GAGAAA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGA-----------------------GUGA------UCCCAGGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----CC---G--CCUGCAGUGCGGCUCGCGCGAC-----------------------------------------------------------------------------------GAAGCGCGACGGAGCCGCAGUGCUGG-C----G--G---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGU-C-U-C-UG-GCAA--CA-G-C-G-ACGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGAA--C-GACGCGGUCGGUCCGUCG---------------------------CAAGACGGGUCGCCAGCCCUCUCC----GGGCC-------GGUCG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--AGA-GGCG-G-C-CCGCAAGGG-U--C-G-U-C-C--CAGAGGAAU-GGUCGUCC-----------------GGCGGUCAAUCCGC-------------------------------------------UGACAGAACCCGGCUUA--C-AGGCCGG-CUGGCACU
AP006861.1/929836-930219       CGGA-AG-A-G-A-A-A--GGCAACCGCUUC-CU--G-UAUCUC-----------------------------------------------------------------------------------UAGUAGA-----UA-U-G-G-UAAGAGGAAAGUCUGGACUU-C---AUA--AGAAG-A-GA-UA----------------CUGGA------------GAAAC----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAC-UCC-GCU----AU---A---------------------------------------------------------------------------------------------------------------------------------A----U----A--U---AGACAGGCUGAAAA---UUCC---UA-C--U--U----------------------UAAGA-GUAGGA--GCUA-U-U-A-AG-GUGA--CU-U-A-A-UAGA-C--G----------------UGCAAAC-CCUAUCU-GAAGCAAGA--------------------------------------GAAA--A-AGUUUUUGUUUCU--------------------------------------GCAUAAUGAGGAGCUCUG----UUCCUCA---UAAACUU---UU-U-----CACA---A-----------UCGC---------------------U--UGA-GGGA-U-A-UAGUAAUAU-A--U-C-C-C-C--UAGAUGAAU-GGUUGCCC-----------------UCAAGAUGGUCUUUGCCAU---------------------------------CUUGUAGACAGAAUCCGGCUUA--C-UCUCUCU-UCCGAUAU
CP000088.1/2284408-2284025     GGAG-UC-G-G-C-C-A--GACGGCCGCGGC-AC--C-GC------------------------------------------------------------------------------------------GCAC-----GC-G-G-U-GUCGAGGAAAGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------GUCGG------------UAACA----------------CCGACCCGGG-----------------------GUGA------CCCGCGGG-AU---AGU-GCCACAGAAA--ACAG-ACC-GCC----GU---C--CC---------------------------------------------------------------------------------------------------------------------------CGU-GG-G----A--C---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGG-C-C-G-GA-GUGA--UC-C-G-G-UCGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGGUC-AAGAGGGAGACUU------------CGGUCUCCUGCACG--G-ACGCUU----------------------------------------------------GAGGGCGGCCC----GUCCG-------AUGUC---CG-U-----GGGU---A-----G---A-CCGC---------------------A--UGA-GGCC-G-C-UGGCAACAG-C--G-G-U-C-C--UAGAUGGAU-GGCCGUCAC---------------AACCCGUUCAGGGUU--------------------------------------------GACAGAAUCCGGCUUA--C-CGGCCGA-CUCCCUGU
CP000781.1/1989320-1989711     CCAG-CC-G-G-C-C-G--GGCGGCCGCGGU-GU--G-GGAC----------------------------------------------------------------------------------------CUUGC---GUC-C-G-C-AUCGAGGAAAGUCCGGGCUC-C---ACU-CAGACA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GUGA------CCCUAGGG-AA---AGU-GCCACAGAAA--ACAA-ACC-ACC----CG---C--GAAGGAC----------------------------------------------------------------------------------------------------------------UUUCGGGUCCGC-G----U--G---GGCCAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGC-G-A-C-CG-GCAA--CG-G-G-A-GCGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAAGUC-GAAU------------------------------AGGGA--C-GGCACGGGA---------------------------------------------AACCACCCCUGUCUG----CGGGG-------CGCCG---UC-C-----GGGU---U-----G---A-CUGC---------------------U--AGA-GGCG-C-C-GGGCAACCG-G--C-G-U-C-C--CAGAGGAAU-GGUCGCCA-----------------CGCGGGUGCAAGCCCG---------------------------------------CCGUACAGAACCCGGCUUA--C-AGGCCGG-CUGGUGCA
BA000012.4/1306844-1306445     CCAG-CU-G-G-C-U-G--GGCGGCCGCACU-CG--C-AAACGC-----------------------------------------------------------------------------------CGAAAGG-----CC-G-C-A-AGUGAGGAAAGUCCGGGCUC-C---AUG-GAGACA-C-GG-UG----------------CCGGU------------UAAUG----------------GCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----AC---G--AC---------------------------------------------------------------------------------------------------------------------------UUU-GU-C----G--G---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGC-G-A-C-UG-GCAA--CA-G-G-A-GCGG-C-AC----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGG--C-GGUGCGAGGGGAA--------------------------------------ACCCUCGAGGGCUGUUUC---CGGCUC--------ACCG---UC-C-----GGGU---A-----G---G-UUGC---------------------G--UGA-GGCG-C-A-UGGCAACAU-G--C-G-C-C-C--AAGAUGAAU-GGCCGCCA-----------------CGUUCUCGUCCCGCGAGGGGC-----------------------------GAGGGCCAUACAGAACCCGGCUUA--C-AGGCCAG-CUGGCAGU
AAYI02000004.1/1757034-1756671 UCUG-CC-G-G-C-C-G--GGCGGCCGCGCG-CG------------------------------------------------------------------------------------------------GAAA----------C-G-CUCGAGGAACGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------GUGGC------------UAACA----------------GCCACCCGGG-----------------------GUAA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAA-ACC-ACC----GA---C--GC--------------------------------------------------------------------------------------------------------------------------GUAU-GC-G----G--C---GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCGG-C-G-C-AG-GUGA--CU-G-C-G-UCGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGACC-GAGC------------------------------A-GCA--G-GC---------------------------------------------------------AGGGCGGCCC----GUCCA-------AUGCC---UG-C-----GGGU---A-----G---G-UCGC---------------------U--GGA-GGCC-G-U-CGGUAACGA-C--G-G-U-C-C--UAGAUAGAU-GGUCGCCA-----------------CCGCACGACCGGUAACGGC---------------------------------GUGCGCGACAGAACCCGGCGUA--C-AGGCCGA-CAGAUGCC
CP000713.1/444808-445211       UUGG-UA-A-A-C-C-A--GACGAUCGCCGU-UU--U-AAGUUAAAUAUUGAUGCG-----------------------------------------------------------UUAAGUGUGAUUAUUUAAG-----AC-A-A-A-AGGGAGGAAAGUCCGGGCUA-C---AUA--AGGCA-G-CG-UG----------------CCAGC------------UAACG----------------GCUGGGCGGG-----------------------GUAA------CCCGACGA-CA---AGU-GCAACAGAGA--GCAG-ACC-GCC----UC---A--AUUUAAGCUCUAC----------------------------------------------------------------------------------------------------AGCCUAGCUGUAAAGUGG-U----G--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-G-G-C-UG-GCAA--CA-GUU-C-AUGG-C-AA----------------GGUAAAC-UCCACGC-GUAGCAAGACC-AAAU------------------------------AGGUG--U-CCAUUA-----------------------------------------------------CUUGUCGCCU----GCAGG---------GGA---CA-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCGU-A-C-UGGCAACGG-U--G-C-G-C-C--UAGAUGAAU-GAUCGUUC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGUUUA-CCAAAAUA
AAOF01000005.1/51333-50979     GAAG-UU-G-G-C-U-G--GGCAGUCGCUGU-GU--C-GUUA-------------------------------------------------------------------------------------------------AC-G-G-U-GCAGAGGAAAGUCCGGGCUC-C---GUA--GGGCG-A-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGC-----------------------GUGA------GCCGACGG-AA---AGU-GCCGCAGAAA--ACAG-ACC-GCCG--AUG---G--CCCGA---------------------------------------------------------------------------------------------------------------------CCAACGGGC-U----C--A---GGCAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-G-UG-GCAA--CA-CUC-C-GUGG-C-AC----------------GGUAAAC-CCCACCU-GGAGCAAGACC-AAAU------------------------------AGGGA--A-GCGAG------------------------------------------------------CGUGUGGCCC----GCACG---------GCU---UU-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GGUG-C-G-CGGUGACGC-G--U-A-C-U-C--CAGAGGAAU-GGCUGCCU-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--U-AGGCCGG-CUUCCCGU
AM180252.1/544020-543659       GGAG-UC-A-A-G-U-G--GACUGUCGCUGC-AU--A-UCCUUU------------------------------------------------------------------------------------UAUGGA-----UU-U-A-U-GGAGAGGAAAGUCCGGGCUU-C---AUA--GGGUA-A-AA-CG----------------CUGGG------------UAACA----------------CCCAGGAAGA-----------------------GUGA------UCUU-CGG-CA---AGC-GCAACAGAAA--GUAA-ACC-GCC----AU---U--AUU-------------------------------------------------------------------------------------------------------------------------AAU-AAU-A----G--U---GGUAAGGGUGAAAC----GGU---GG-A--G--U----------------------AAGAG-UCUACC-AGUCG-U-U-A-UA-GUGA--UA-U-A-G-CGAG-C-UA----------------GGCAAGC-CCCGUUU-GAAGCAAGACC-AAAU------------------------------AGGGG--A-AC---------------------------------------------------------AGGCUGACCC----GGCCA-------AUGUU---CC-U-----GGGU---A-----G---G-UUGC---------------------U--UGA-GAAU-A-U-AGGUAACUA-U--A-U-U-C-C--UAGAUGAAU-GACAGUCG-----------------CCC----AUUAGGG--------------------------------------------UACAGAACCCGGCUUA--U-AGCUUGA-CUCCUUUA
CP000513.1/836438-836105       UGAG-UU-U-G-C-C-A--GACAAUCGCUGA-C-------------------------------------------------------------------------------------------------GAAA------------G-UUGGAGGAAAGUCCGGGCUU-U---AUA--GGGCA-A-AG-CG----------------CUGGG------------UAACG----------------CCCAGGCAGC-----------------------GUGA------GCUGACGG-AA---AGU-GCCACAGAAA--AGAU-ACC-GCC----UC---G--A---------------------------------------------------------------------------------------------------------------------------------U-U----G--A---GGUAAGGGUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAU-U-U-G-CG-GCAA--CG-U-A-A-AUGG-C-AG----------------GGAAAAC-CCCGCUU-AAAGCAAGACC-AAAU------------------------------AGAGA--A-UCAAU------------------------------------------------------GCGGCGGCCC----GUCGU---------GAU---UC-U-----GGGU---A-----G---G-UCGC---------------------U--AGA-GGCU-G-G-CAGUAAUGU-U--A-G-U-C-G--CAGAGGAAU-GAUUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGUGAA-CUCAUCUU
CP000697.1/3151296-3151687     CCAG-AC-G-G-U-U-G--GACGGCCGCCGU-GC--C-GCUC-------------------------------------------------------------------------------------------------GC-G-G-C-GCGGAGGAAAGUCCGGGCUC-C---AUG-GAAUGA-C-GG-UG----------------CCGGC------------UAACG----------------GCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAAA--ACAU-ACC-GCC----GG---U--ACGC-----------------------------------------------------------------------------------------------------------------------CUCGGCCU-G----C--C---GGCAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-C-G-C-CG-GCAA--CG-G-G-G-GCGG-C-AG----------------GGAAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGG--C-GACCGGCGGCAUGAGCG------------------------------AUCAUGGCCGCGGAGGGAUUCC----GCCUC--------GUCG---CC-C-----GGGU---U-----G---G-UCGC---------------------G--CGA-GGCA-C-G-CAGCGAUGC-G--U-G-U-C-C--CAGAUGAAU-GGCCGUCC-----------------AGCAUCCGCGAGGGUG----------------------------------------UGGACAGAACCCGGCUUA--C-AGACCGU-CUGGCAUU
CP000473.1/5196142-5195786     GCUG-CC-G-G-A-C-G--GGUAGUCGCUCC-CA------------------------------------------------------------------------------------------------UUUU----------U-G-GGAGAGGAAAGUCCGGUCUC-C---AUA--GGGCA-G-CG-UG----------------CCGGC------------UAACG----------------GCCGGGCGGAU---------------------CGUAAG----GUCCGACGG-AU---AGU-GCCACAGAAA--AUAU-ACC-GCC----UC---G--CC--------------------------------------------------------------------------------------------------------------------------UUCG-GG-C----G--C---GGUAAGGGUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-C-A-G-GA-GUAA--UU-C-U-G-CCGG-C-AG----------------GGAAAAC-CCCACGC-GGAGCAAGACC-AAAU------------------------------AGGGG--A-GGAGGG----------------------------------------------------GCGGCCCGUCC----CGCUU--------GACU---UC-C-----GGGU---A-----G---G-UCGC---------------------U--AGA-ACCG-G-U-CAGUAAUGG-C--C-G-G-U-C--CAGAGGAAU-GACUACCG-----------------CCC----GCAAGGG--------------------------------------------UACAGGAACCGGCUUA--C-AGUCCGG-CAGCUAAU
CP000232.1/651737-652153       UGAG-UA-A-A-C-C-G--GAUGGUCGCAGG-CG--C-UUGC-------------------------------------------------------------------------------------------------AA-G-C-G-CCUGAGGAAAGUCCGAGCUC-C---GCA--GGGCA-G-GG-UG----------------CUGGA------------UAACG----------------UCCAGUGGAG-----------------------GCGA------CUCCAAGG-AU---AGU-GCCACAGAAA--CAG--ACC-GCC----CA---G--CACUCAAUUCGACAGUUGAACCCGGCCUGCUAUAAGU----------------------------------------------------AUCCUUAAUUUCAGGUUCGGGCCUCACCUGUCGAGUUGAGUG-C----U--G---GGUAAGGGUGGAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCGG-U-U-A-G--GCGA---C-U-A-A-CCGG-C-UC----------------GGUAAAC-CCCACCU-GGAGCAAGACC-GAAU------------------------------AGGGG--G-ACAAAA-----------------------------------------------------GGGGUGGCCC----GCCCC---------GUC---CC-C-----GGGU---A----AG---G-UCGC---------------------U--UGA-GGCG-C-C-AGGCAACUG-G--C-G-U-C-C--UAGAUAGAU-GACCAUCC-----------------AC--------------------------------------------------------GACAGAACUCGGCUUA--C-AGGUUUG-CUCAAAAG
AE017126.1/1616782-1617172     GAAA-GC-A-G-G-A-G-AGGUGAUCGCAAU-CG--A-GAUUUAUCGCGU-----------------------------------------------------------------------UUCCGCAAUAAAC-----UC-U-C-G-GUUGAGGAAAGUCCGGGCUC-CCAGAUG--GUCCA-A-CU-UG----------------CUGGG------------UAACU----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AU---AGU-GCCACAGAAA--CAC--ACC-GCCG--AUG---U--CUC-------------------------------------------------------------------------------------------------------------------------AUAGAGC-A----C--A---GGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-A-U-C--GAGA---G-G-U-A-CUGG-C-UU----------------GGUAAAC-CCCGGUUGGGUGCAAGGCA-AAGG------------------------------UUUUA--G-GAUGAC----------------------------------------------------CAUUUUGCCUA--------U--------UUCC---UA-U-----UUAA---A---------G-CCGC---------------------U--CGA-GGCU-G-U-UGGAGACAA-C--A-G-U-C-C--CAGAUAGAU-GAUCACCC-----------------ACUAACCAAUUUUGGAU-------------------------------------AGUGAACAGAACCCGGCUUA--C-UUCCUGC-UUUCUUUC
CP000478.1/2009941-2009564     UGGA-GU-A-G-CAC-A--AAUGAUCGCCGG-UU--C-CGUA-------------------------------------------------------------------------------------------------CG-G-G-A-UCGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------CUGGG------------UAACG----------------CCCAGUCCCG-----------------------GUGA------CGGGGAGG-AU---AGC-GCCACAGAAA--GCAA-ACC-GCC----CU---G--CA---------------------------------------------------------------------------------------------------------------------------UUG-CG-C----A--G---GGUAAGGGUGAAAC----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGUCC-C-G-A-UG-GUGA--CA-U-C-G-GGAG-C-UA----------------GGCAAGC-CCCACCC-GGAGCAAGACC-GAAU------------------------------AGGAG--A-GCGUUU----------------------------------------------------GAGGGCUGCCC----GUCCG-------AGGCU---CU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-UCCC-G-C-CGGCAACGG-C--G-G-G-A-C--UAGAGGAAU-GAUCAUUG-----------------CCUUUCGUCGCCUGCGGGCGU-----------------------------UCGAGGGGAACAGAACCCGGCUUA--U-GGGCUGC-UCCAAAUU
AE017283.1/718289-718669       CGAG-CC-A-U-C-C-G--GGUGAUCGCGGC-AG--C----G----------------------------------------------------------------------------------------GUGA--------G-U-U-GUCGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-G-GG-UG----------------GUGGG------------UAACG----------------CCCACCCGGG-----------------------GUGA------CCCGCGGG-AA---AGU-GCCACAGAGA--ACAG-ACU-GCC----GG---U--U----------------------------------------------------------------------------------------------------------------------------UCG--A-G----C--C---GGUGAGGGUGAAAC----GGU---GG-A--G--U----------------------AAGUG-CCCACC--GCGU-C-A-U-CG-GUGA--CG-G-U-G-ACGG-C-AU----------------GGCAAAC-CCCACCU-GGAGCAAGGCC-AAGAAGACCG-----------------UGAGGUCGCGGA--C-GCGUUU----------------------------------------------------GAGGGUUGCUC----GCUUG--------AGUG---UU-C-----GGGU---A-----G---G-CUGCGCAGCC--------GAAAGGCU--GGA-GGAC-A-C-CAGCAAUGG-U--G-U-U-C-A--CAGAUGGAU-GAUCACCG-----------------GCCCGGCGGGGC----------------------------------------------UACAGAACCCGGCUUA--U-AGGAUGG-CUCGUCCC
L78818.1/7603-8020             CGAG-UU-G-G-C-U-G--GGCGGCCGCGGC-UC--G-UGUCGGUCUG---------------------------------------------------------------------------AAAGGCCCGGU-----AA-C-G-A-GUCGAGGAAAGUCCGGACUU-C---ACA--GAGCA-G-GG-UG----------------AUUGC------------UAACA----------------GCAAUCCGAG-----------------------GUGA------CUCGCGGG-AU---AGU-GCCACAGAAA--ACAA-ACC-GCC----AU---C--C----------------------------------------------------------------------------------------------------------------------------UCG--C-G----G--U---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAU-C-C-C-GG-GUGA--CC-G-G-G-AUGG-C-UU----------------GGUAAAC-CCCACCC-GAAGCAAGGUC-AAGAAGGCUGCACUA--------CAAGUGCGGCCGCGCA--G-GCGUUC----------------------------------------------------GAGAGCUGCUC----GCCCG--------AGCC---UG-C-----GGGU---A-----G---G-CCGC---------------------U--UGA-GGCA-C-C-CGGCAACGGUG--U-G-U-C----CAGAUGGAU-GGUCGCCG-----------------CCGCGCCACCGUAGGCAAUGCCGC------------------------GUUGGCGGGGAACAGAAUCCGGCUUA--U-AGGCCAA-CUCGCCCG
CP000494.1/6425339-6425766     UCAG-UC-G-G-C-C-G--GACGGCCGCUCC-GG--C-AGGUGC-----------------------------------------------------------------------------------CGAAAGG-----CC-G-C-C-GGGGAGGAAAGUCCGGGCUC-C---AUC-GACAUG-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AC---AGU-GCCACAGAGA--ACGA-ACC-GCU---UCC---U--CCC-------------------------------------------------------------------------------------------------------------------------GAAAGGG-A----G--GC-GAGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-G-G-C-CG-GCAA--CG-G-A-A-CCGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-GGCCACGCGGAGACAAUCGCCUU------------------UGGCGAUGACGUCCGCGGGAGCGAUGUC---AGGCUC--------GCCG---UC-C-----GGGU---A-----G---G-UUGC---------------------C--CGA-GGUC-U-C-GCGCAAGCG-C--G-A-U-C-C--CAGAGGAAU-GGCCGUCA-----------------CGUAUCGUCAUGCGCAAGCAUC---------------------------ACGGUGCCCUACAGAACCCGGCUUA--C-AGGCCGG-CUGAUAUG
CP000431.1/1253711-1253273     CGAG-UU-G-G-C-C-G--GGCGACCGCGGC-AC--A-GGGAACCAGCACU----------------------------------------------------------------------UCAGUGCACAGGC-----CC-U-G-A-GUCGAGGAAAGUCCGGACUC-C---ACA--GAGCA-G-GG-CG----------------GUUGU------------UAACG----------------GCAACCCGAG-----------------------GUGA------CUCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----GA---U--GCCACAUCC-------------------------------------------------------------------------------------------------------------UCCGGGGUGUGGC-G----U--C---GGUCAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAC-C-C-C-GG-GUGA--CC-G-G-G-GUGG-C-UA----------------GGUAAAC-CCCGCCC-GGAGCAAGGUU-------------------------------------GAA--G-GCCGCACCGGUUCCUCCGGGAUCCCG------------GUGCGGCUGCGCAGGUGUUCGAGGGCUGCUC----GCCCG--------AGCC---UG-C-----GGGU---G-----A---A-CCGC---------------------U--CGA-GGUA-C-C-CGGCGACGGUG--U-G-C-C----CAGAUGGAU-GGUCGCCA-----------------CCCGGCGCUUCGGCGCC-------------------------------------CGGGGACAGGAUCCGGCUUA--C-ACGCCAA-CUCGUUCG
AAMS01000003.1/69108-69502     GCGG-AU-G-G-C-U-G--GAUGGCUGCGGG-CC--U-GUC--------------------------------------------------------------------------------------------------AU-G-G-G-UUCGAGGAAAGUCCGGACUC-C---ACA--AAGCA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCGGGG-----------------------GUAA------CCCCAGGG-AA---AGC-GCCACAGAGA--ACAG-ACU-ACC----UC---G--U----------------------------------------------------------------------------------------------------------------------------AUA--G-C----G--G---GGAAAAGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-G-A-C-GG-GCAA--CC-G-G-A-CCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGA--C-CGCGCGCGGUGUUGAUCCUGC----------------------AAAGGAUAUCAGCCGCAGGGAGGCUUG--AGCCCG-------AGCGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--AGAGAGCG-U-C-UGGCAACAG-G--C-G-U-U-C--CAGAUGAAU-GGUCAUCC-----------------AGGGUGGUUCGCCACC----------------------------------------UGGACAGAAUCCGGCUUA--C-AGGCCAU-CCGCGCAA
CP000115.1/2681927-2682376     UCAG-UC-G-G-C-U-G--GACGGCCGCUCC-CG--C-UCGGGCC----------------------------------------------------------------------------------GAAAGGC-----UU-G-C-G-GGAGAGGAAAGUCCGGGCUC-C---AUC-GACAUA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AC---AGU-GCCACAGAGA--ACGA-ACC-GCC----GC---G--UCCACUUCUAUUCUCCGC-------------------------------------------------------------------------------------------UUGCCGGGGAGAGAACAGUGUG-A----G--C---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-C-U-C-CG-GCAA--CG-G-A-G-GCGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-AGCAUAGCGAGGGGUUCGCCU----------------------UGGCGAUAACACCGCGGAGCCAUGUC---GGGCUC--------GCUG---UC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGCA-A-C-GUGCAAACG-U--U-G-U-C-C--CAGAGGAAU-GGCCGUCA-----------------CGCACCGCGUGCGCAAGUGCG-----------------------------CGGUGCCCUACAGAACCCGGCUUA--C-AGGCCGG-CUGAUAUC
CP000555.1/489173-489511       GAAG-UG-G-G-C-C-A--GACCGCCGCUGG-CA--C-ACCGGC-----------------------------------------------------------------------------------CGAAAGG-----CC-G-U-G-CUGGAGGAAGGUCCGGACUG-C---ACA--GGGCA-G-CG-CA----------------GCAGC------------CAACG----------------GCUGUCCACC-----------------------GCAA------GGUGAGGA-UC---AGA-GCAACAGAGA--CGAG-----UCC----GG---G--CGG------------------------------------------------------------------------------------------------------------------------CGUAGCCG-U----C--C---GGG----GUGAAAC----------------------------------------------G---------------------------------------------------------------GGCAAUC-UCUGCGC-GCAGCAACACC-AAAU------------------------------AGGCC--A-GCGUCG----------------------------------------------------AUGUGG---CU----CCGCG-------GAGCU---GG-C-----GGGU---A-----G---G-UGGC--------------------AC--CGA-GCCGUU-C-CCGCGAGGG-G--C-G-G-C-C--CAGAGGAAU-GGCGGUCA-----------------CGGCCGCGACGCCGCAAGGCGC----------------------------CGCGGCCGCACAGAAUCCGGCCUA--U-CGGCCCG-CUUCACAC
AP009044.1/2333762-2333355     UGAG-GC-A-A-C-C-G--GGUGAUUGCGUU-CG--A-CGAACUGGGGG-------------------------------------------------------------------------AUUGCUCCCAAG-----CG-U-C-G-GCCGAGGAAAGUCCGGACUC-C---ACA--GAGCA-C-GG-UG----------------GUUGU------------UAACA----------------ACAACCCGGA-----------------------GCGA------UCCGCGGG-AA---AGU-GCAACAGAGA--GUAA-ACC-GCC----AU---C--AAC-------------------------------------------------------------------------------------------------------------------------UUAGGUU-G----G--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-GGCAG-G-U-C-AG-GUGA--CU-G-A-U-UUGG-C-CA----------------GGUAAAC-CCCACCG-GGAGCAAGGCA-UGAGGACGUAUCCA---------AUGGUAUGUCUGUGCA--G-GUGUUG-----------------------------------------------------AAGGCUGCUC----GCCAA---------GCC---UG-C-----AGGU---A---------G-CUGC---------------------U--AGA-GGCA-G-U-CAGCAAUGG-C--U-G-C-GAC--GAGAUGGAU-GAUCGCCG-----------------CCGGUUGCUUUUGCAAC--------------------------------------UGGUACAGAAUCCGGCUUA--U-AGGUUGG-CUCAUUCG
AARG01000014.1/795122-794788   UUGG-GU-A-U-U-C-A-GGUUAGUCGCUGU-C--------U----------------------------------------------------------------------------------------UUAU------------G-AUAGAGGAAAGUCCGAGCUC-C---ACA--GAGCA-A-AA-GG----------------GUAGC------------UAACG----------------GCUACUAAAA-----------------------GUAA------UUUUAAGG-AA---AGU-GCCACAGAAA--AUAG-ACC-GCC---A------------------------------------------------------------------------------------------------------------------------------------UUAA----------------GGUAAGGGUGAAAA----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGUUU-U-U-U-AG-GAAA--CU-A-A-A-AAAG-C-UU----------------GGUAAAC-CCCCUUU-GGAGCAAGACU-AAAU------------------------------AG-GA--A-AGAUUA----------------------------------------------------AGGGGUUGCUC----GCUCU---------CUU---UC-A-----GGGU---A-----A---G-UCGC---------------------U--AGA-GAUU-A-U-AAGUGAUUA-U--A-A-U-U-C--GAGAAAAAU-GAUUAACA-----------------AA--------------------------------------------------------UACAAAACUCGGCUUA--U-UGAAUGC-CUAAAAAU
AP008231.1/2604107-2603736     GAAA-GG-A-G-G-C-G-AGGCAGUUGCGGC-UC--A-GGCU----------------------------------------------------------------------------------------UCGG----UUA-U-G-G-GCUGAGGAAAGUCCGGGCUC-CC-AAAA--GACCA-G-ACUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAU--ACC-GCCG-AUGG---C--CUG-------------------------------------------------------------------------------------------------------------------------CUUGCAG-G----C--AC-AGGUAAGGGUGCAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-A-U-C--GAGA---G-G-U-G-UUGG-C-UC----------------GGUAAAC-CCCGGUUGGGAGCAAGGUG-GA----------------------------------GGG--A-CAAC-------------------------------------------------------GGUUGGUCUU----UUACC---------UGU---UC-C-----GUUU---A-----UG-GA-CCGC---------------------U--AGA-GGUG-G-C-UAGUAAUAG-C--C-A-U-C-C--CAGAGAGAU-AACUGCCC-----------------UCUGUCUUCGACAGA------------------------------------------GAACAGAACCCGGCUUA--U-GUCCUGC-UUUCCCUA
AY728386.1/651-1008            AAGA-GU-U-G-G-C-G-CGAGAGUUGCGGA-UG--G-GUCA----------------------------------------------------------------------------------------AAUC----AAC-C-C-A-UUCGAGGAAAGUCCGGACUC-CC-GAAA--GACCA-G-ACUUG----------------CUGGG------------UAACG----------------CCCAGUGCGC-----------------------GCGA------GCGUGAGG-AU---AGU-GCCACAGAAA--AAU--ACC-GCC----UC---U--AAU-----------------------------------------------------------------------------------------------------------------------------UUU-A----G--A---GGUAAGGGUGCAAA----GGUUUUGC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-A-U-C--GUGA---G-G-U-A-CUGG-C-UC----------------GGUAAAC-CCCGGUUGGGAGCAAGGUC-GAAG------------------------------GGGCA--A-AGGUU------------------------------------------------------GGUCUUUUCC---CUGUCC---------CGU---UU-U-----AGGU---G-----U---A-CCGC---------------------A--UGA-GGCG-U-U-UGGUAACAA-A--C-G-U-C-C--UAGAUAGAU-AACUCUCC-----------------ACUG------------------------------------------------------AACAGAAUCCGGCUUA--U-GUCCAAC-UCUUUUCU
CP000554.1/2293497-2293898     GAAA-GC-A-G-G-U-G-AGGUGUUCGCGAU-CA--A-GUCGUCAUUGCC-----------------------------------------------------------------------CUUGGCAAGACGC-----GC-U-U-G-GUUGAGGAAAGUCCGGGCUC-CC-CGAU--GGCCA-G-ACUUG----------------CUGGG------------UAAUG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--AAC--ACC-GCC----GA---U--GGCCUCAUGG----------------------------------------------------------------------------------------------------------GGUUCUACUCCAGGC-A----C--A---GGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGUUGGGAGCAAGGCC-AA----------------------------------GGG--G-CGAU-------------------------------------------------------GGCUGGCCAU----CUGCC--------ACGU---UC-C-----ACAU---AAA-UGC---G-CCGC---------------------U--UGA-GGCC-G-U-CGGUAACGG-C--G-G-U-C-C--UAGAUAGAU-GAGCACCC-----------------ACUGCUCUUGAGCAG-----------------------------------------UGAACAGAACCCGGCUUA--C-GACCUGC-UUUCACCC
DQ366728.1/25651-25272         GAAA-GC-A-G-G-A-G-AGGCAAUCGCAAG-AA--A-GUUUUAUUUUGG------------------------------------------------------------------------AAACAAAAUAAA-----AC-U-U-U-CUUGAGGAAAGUCCGGGCUC-CC-AAAU--GGUCA-G-GCUUG----------------CUGGG------------UAAUU----------------CCCAGUGCGG-----------------------GCAA------CCGUGAGG-AU---AGU-GCCACAGAAA--CAU--ACC-GCC----UA---A--UAC------------------------------------------------------------------------------------------------------------------------UGUAUGUA-U-----------GGCAAGGGUGCAAG----GGU---GU-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-A-U-U--GAGA---A-G-U-G-UUGG-C-UA----------------GGUAAAC-CCCGGCUGGGAGCAAGGCU-UAGU------------------------------AGAUU--U-AUGACC----------------------------------------------------AUU----ACAC-------AA--------UCUA---CU-U-----AGAA---G-----C---G-CCGC---------------------U--UGA-GACU-GUG-AAGUAAUUC-C--A-G-U-C-C--UAGAUAGAU-GAUUGCCC-----------------AUCUUAAUUUAGAU-------------------------------------------GAACAGAACCCGGCUUA--U-GACCUGC-UUUCUAAU
CP000362.1/1906740-1906341     GCGG-AG-G-G-C-C-G--GAUGGCCGCGGC-AC--U-G-------------------------------------------------------------------------------------------GCAA------C-A-G-G-GUCGAGGAAAGUCCGGACUC-C---AAA-AAGCAA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGGCAAA-----------------------GCAA------UUUGACGG-AA---AGC-GCCACAGAAA--ACAG-ACC-ACC----UG---U--CGUGCAGGUCGG-------------------------------------------------------------------------------------------------------GCAACCGAAACCGCCG-A----C--G---GGCAAGGGUGAAAA----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGC-G-G-C-UG-GCAA--CA-G-C-G-GCGG-C-AU----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGA--C-CGCGCGUCGC-------------------------------------------AAGACGGGGCCGCUUU----GGCUCA------GCAGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--AGAGCCUU-G-C-GGGCAACCG-C--C-G-G-G-C--AAGAGGAAU-GGUCAUCG-----------------AACCGGGGGCAACUUCG--------------------------------------GGGAACAGAAUCCGGCUUA--C-AGGCCCU-CCGCGCAC
AE016822.1/1018030-1018399     UGGG-UC-G-G-C-A-A--GACGGUCGCGUC-GG--U-CUGCG--------------------------------------------------------------------------------------UCAGC-----GG-G-C-C-GCCGAGGAACGUCCGGGCUC-C---GCA--GAGCA-G-GG-CG----------------GUGGG------------UAACA----------------CCCACCCGGG-----------------------GCAA------CCCGCGAG-AA---AGU-GCAACAGAGA--GCAG-ACC-GCC----AC---G--GGC-------------------------------------------------------------------------------------------------------------------------UCCGGCC-C----G--C---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGG-C-C-G-GG-GCGA--CC-C-G-G-CCGG-C-UG----------------GGUAAAC-CUCGCCC-GGAGCAAGGUC-AGAC------------------------------A-GGG--A-ACGAU------------------------------------------------------GGGGUGGCUC----GCUCC---------GUU---CC-C-----GGGU---A-----G---A-CCGC---------------------U--AGA-GGGC-G-G-CGGCGACGU-C--G-U-C-C-C--GAGAGAGAU-GGCCGUCC-----------------ACGGCGCGCAAGCGCC----------------------------------------GUGACAGAACCCGGCGUA--U-CAGCCGG-CCCAUUCC
AP009247.1/754501-754160       GAAG-UU-G-G-U-C-G--GAUGGUCGCUGG-AG--A-UU---------------------------------------------------------------------------------------------------GA-U-C-U-UCAGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-A-AG-UG----------------UUAGU------------UAACG----------------GCUAGGUAUG-----------------------GCGA------CAUAACGG-AA---AGU-GAUGCAGAGA-UUUAG-ACC-GCC----UA---U--U----------------------------------------------------------------------------------------------------------------------------UUU--A-A----U--A---GGUAAGGGUGAGAA----GGU---GU-G--G--U----------------------AAGAG-CGCACC--GCGG-G-A-U-UG-GUGA--CA-A-U-C-GUGG-C-AA----------------GGAAAAC-CCCACUU-GGAGUAAGCUC-AAAU------------------------------AGACU--A-ACGAUA----------------------------------------------------A--CGUUGCUC----GCGAA---------GUU---UG-U-----GGGU---A-----G---A-GCGC---------------------U--AAA-GCGU-U-U-UGGUAACAA-A--A-C-A-C-G--UAGAUGAAU-GACCAUUU-----------------AU--------------------------------------------------------UACAGAACCCGGCUUA--U-AGACCGA-CUUCUUUU
AJ965256.1/262911-263265       CAAG-UA-G-A-C-C-G--GGUGGCCGCCCG-CC--U-U----------------------------------------------------------------------------------------------U------A-A-A-G-CGGGAGGAAAGUCCGAGCUC-C---UCC--AGACA-G-GA-UG----------------CUGGG------------UAACA----------------CCCAGGGGGG-----------------------GCGA------CCCUACGG-AA---AGU-GCAACAGAAA--CAU--ACC-GCC----UG---U------------------------------------------------------------------------------------------------------------------------------GAAA----A----U--A---GGUAAGGGCGAAAU----GGU---GA-G--G--U----------------------AAGAG-CUCACC-GGCAG-U-C-C-GG-GUGA--CC-G-G---CUGG-C-CG----------------GGUAAAC-CCCGUCC-GGAGCAAGGCC-AAAU------------------------------AGGGG--A-ACGCA------------------------------------------------------AGGACGUCUG----G-CCU---------GUU---CC-C-----GGGU---U-----G---G-CCGC---------------------A--UGA-ACCA-G-A-CGGUAACGU-C--U-G-G-U-C--UAGAUAGAU-GGUCAUCA-----------------CCUUUGCCUUCGGGCAA--------------------------------------GGGUACAGAACUCGGCUUA--C-AGGUCUG-CUUGGCUU
AE001437.1/1448287-1448628     CGAG-UA-A-G-C-C-A--GACAAUCGCUGC-UG--C-AAU--------------------------------------------------------------------------------------------------UU-G-C-A-GGAGAGGAAAGUCCGAGCUC-C---AUA--GGGCA-G-GG-UG----------------CCGGG------------UAACU----------------CCCGGUCAAG-----------------------GCGA------CUUGAAGG-AA---AGU-GCAACAGAGA--UAU--ACC-GCC----AU---U------------------------------------------------------------------------------------------------------------------------------UUAU----A----A--U---GGUAAGGGUGGAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC-AGCGC-A-U-U-G--GCGA---C-U-U-U-GCGG-C-UA----------------UGUAAAC-CCCAUCU-GGAGCAAGAUC-AAAU------------------------------AGGGA--A-GCGUUU----------------------------------------------------UGGAGUGGCCC----GCUCU---------GCU---UC-C-----GGGU---A-----G--CA-UCGC---------------------U--UGA-AUCU-U-A-UGGUAACAU-A--A-G-G-U-C--UAGAUAGAU-GAUUGUCG-----------------AA--------------------------------------------------------UACAGAACUCGGCUUA--C-AGGUUUA-GUCGUCCA
CP000009.1/162636-163054       CCAG-AC-G-G-C-U-G--GACGAUCGCUGU-GU--G-UGCGAUG----------------------------------------------------------------------------------AGGAUCG-----CA-U-A-C-AGGGAGGAAAGUCCGGGCUC-C---AUG-GGAAGA-C-GG-UA----------------CCGGC------------UAAUU----------------GCCGGCGGGG-----------------------GCGA------CCCCAGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----CG---C--CGGACUGUGCCUCAUGCG-------------------------------------------------------------------------------------------UUCAUUCGCGGGGGAACAUGUU-G----C--G---GGUAAGGGCGAAAC----GGU---GC-G--G--C----------------------AAGAG-CGCACC--GCAU-C-U-C-CG-GCAA--CG-G-C-G-AUGGUC-AU----------------GGUAAAC-CCUACCG-GGAGCAAGACC-GAAU------------------------------AGGAA--C-GGCAGGUUUCCGCA------------------------------------AGGAAACCGGGGGUUUCUC----GCCCC--------GUCG---UU-C-----GGGU---U-----G---G-UUGC---------------------G--UGA-GGCC-U-G-CAGCAAUGC-A--G-G-U-C-C--CAGAGGAAU-GAUCGUCC-----------------CGCUUUCGGGCG----------------------------------------------GACAGAACCCGGCUUA--C-AGGCCGU-CUGGCACC
BA000037.2/589369-589746       GGAG-AC-----U-G-A--CGUUGACGUCCU-UC--G-GGAG----------------------------------------------------------------------------------------ACUG-----AC-A-A-A-GGGGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCAA------GCCUACGA-CA---AGU-GCAACAGAGA--GAAG-ACC-GCCG--AUG---G--CCUUGAUUC------------------------------------------------------------------------------------------------------------GCAAGAUGAGAGGA-U----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGAC-G-A-C-UG-GCAA--CA-GUU-C-GUAG-C-AG----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGCC--U-CCACAU-----------------------------------------------------AGCGUUGCUC----GCGUU--------AGGA---GG-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCA-G-U-GAGCGAUUG-C--U-G-G-C-C--UAGAGGAAU-GGCUACCG-----------------CCGCGCAAGCGG----------------------------------------------AACAGAACCCGGCUUA--U-AUGUCGG-CUCCACCC
CP000474.1/2649291-2648900     UGGG-UC-G-A-C-C-A--GGCGGUCGCGCG-UC--A-C-------------------------------------------------------------------------------------------GGAA------G-U-G-G-CUCGAGGAACGUCCGGGCUC-C---GAA--GAGCA-G-GG-UG----------------GUGGG------------UAACG----------------CCCACUCGGG-----------------------GUAA------CCCGCAGG-CC---AGU-GCCACAGAGA--ACAG-ACC-GCC----UG---C---GCGUCGUGAUG-------------------------------------------------------------------------------------------------------UUUGCAUCGCGGGGCA-G----C--A---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCUC-C-C-C-GG-GUGA--CC-G-G-G-GAGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGGCC-AGAC------------------------------A-GGA--C-ACGUUU----------------------------------------------------GAGGGCUGCUC----GCCCG--------AGUG---UC-C-----GGGU---A-----G---G-CUGC---------------------U--GGA-GGGC-G-U-CGGCAACGG-C--G-U-U-C-G--UAGAUGGAU-GGCCGCUA-----------------CUCCCUUGCUGGUAACGGCA--------------------------------GGGGAUGACAGAACCCGGCGUA--U-CGGUCGA-CCCAUCCA
AY757776.1/311-1               UAAG-CC-G-G-G-U-U----------CU-----------------------------------------------------------------------------------------------------GUGG----------------GGAGGAAAGUCCGGGCUA-C---ACA--GGGCA-G-AG-UG----------------CCGGA------------UAACG----------------UCCGGGGGGC-----------------------GUGA------GCCUACGA-CC---AGU-GCAACAGAGA--GCAG-ACC-GCC----GU---U--UUC-------------------------------------------------------------------------------------------------------------------------UUCGGAA-A----A--A---GGUAAGGGUGAAAG----GGU---GU-G--G--U----------------------AAGAG-CACACC--GUGC-C-G-G-UG-GUAA--CA-UUC-G-GCAG-C-AA----------------GGUAAAC-UCCACUC-GUAGCAAGACC-AAAU------------------------------AGGAA--C-UCAA-------------------------------------------------------UCGGUGGCCC----GCCGA---------GAG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCAU-A-C-AAGUAAUUG-U--G-U---C-C--UAGAGGAAU------------------------------------------------------------------------------------GAUUGUCCACGACA----G-AACCGGG-CUUA----
AJ131089.2/7-399               ------G-A-G-U-A-A--GGCAACCGCUGU-UU--A-UGCUUUUUCA---------------------------------------------------------------------------CAAUGAAAAAG-----CA-U-A-A-AGAGAGGAAAGUCUGGACUU-C---AUA--AGAAA-A-GA-UA----------------CUGGA------------GAAAC----------------UCCAGGGGCC-----------------------GUGA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAU-UCC-GCU----AU---A--AAAU-----------------------------------------------------------------------------------------------------------------------GAAAGUUU-U----A--U---AGACAGGCUGAAAA---UUCC---UA-C--U--U----------------------UAGGA-GUAGGA--GCUA-U-U-A-AG-GUGA--CU-U-A-A-UAGA-C--A----------------UGCAAAC-CCUAUCU-GAAGCAAGA---GAAA------------------------------AAAGC--U-UUUUUGUUUCUG----------------------------------------CAAAAUUGAGAAGUUUU---CUUCUC--------AUAA---GU-U-----UUUU---CA---UA---A-UCGC---------------------U--UGA-GGGA-U-U-UAGAGAUAG-A--U-C-C-C-C--UAGAUGAAU-GGUUGCCC-----------------UCAGGGAGACGUUUGUCCAU--------------------------------CCUGCAGACAGAAYCCGGCUUA--C-UCGCUC----------
CP000771.1/981758-981428       CAAG-AG-G-G-G-C-G--AGCAAGCGCAGG-CA--G-CCGC----------------------------------------------------------------------------------------ACAA-----GG-C-U-GUCCUGAGGAAAGUCCGGACUC-C----GU--GGGCA-G-GA-UG----------------CUAGC------------UAACG----------------GCUAGGUGGC-----------------------GUGA------GCCA-CGG-AU---AGG-GCCAUAGAAA-CGGAA-ACC-GCC----UG---A--AAGGU---------------------------------------------------------------------------------------------------------------------UAUUCCGAG-U----A--A---GGCAAGGGUGGAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCAG-U-G-C-A--GUAA---U-G-C-A-CUGG-C-UU----------------GGCAACC-CACAUCC-GGAGCAAGGUC-AAAC------------------------------AGGGG--G-UUGGGC----------------------------------------------------G---GCCCCAC----UCUAA--------AUCC---CC-C-----GGGU---A-----G---A-CCGC----------------------------------------------------------U--UAGACAGAU-GCUUGCUC-----------------AA--------------------------------------------------------GACAGAAUCCGGCUUA--C-AGCCCCU-CUUGAGCU
CP000116.1/116696-116988       AAAG-CG-G-A-C-C-A--GGCAACCGCUGC-CA--U-GC------------------------------------------------------------------------------------------GUAC-----GC-G-U-G-GGAGAGGAAAGUCCGGGCUC-C---ACA--GAGCA-G-GA-UG----------------CCGGC------------UAACG----------------GCCGGACGCC-----------------------GCGA------GGCGAGGA-AC---AGG-GCCACAGAGA--CGAG--CG----------------UAU-------------------------------------------------------------------------------------------------------------------------UCAGUUA------------------CGGUGAAAC--------------------------------------------------------G---------------------------------C-------------------GGUAACC-UCCAUCC-GGAGCAACACC-AAAU------------------------------AGGCA--G-ACG-------------------------------------------------------AUGACGCGGCU----CGCCG--------AGUC---UG-C-----GGGU---A-----G---G-UGGC---------------------U--UGA-GCGG-G-U-CAGCAAUGG-C--C-C-G-C-C--UAGAGGAAU-GGUUGCCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGCCCG-CUUUCCCA
BA000039.2/2191681-2192047     AUGA-GU-U-A-G-C-G-UGGUGGUUGCGGG-AG--U-CUG--------------------------------------------------------------------------------------------------CC-A-C-U-CCUGAGGAAAGUCCGGGCUU-CC-GAAA--GACCA-A-GCUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGCGAGG-AA---AGU-GCCACAGAAA--UAA--ACC-GCCG--AUG---G--AGG-------------------------------------------------------------------------------------------------------------------------GAAACCU-C---AC--A---GGCAAGGGUGCAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-A-U-C--GAGA---G-A-U-G-UUGG-C-UC----------------GGUAAAC-CCCGGCUGGAAGCAAGGUG-UGCU------------------------------AGCGC--U-AAGGAACCAG--------------------------------------------GGUUGGUCUUUUCCC----CAGUU--------CUUU---GC-U-----AGCC---A-----G--AG-CCGC---------------------U--AGA-GGCA-C-U-UGGUAACAA-G--U-G-U-C-C--CAGAUAGAU-AACCACCC-----------------UUUG------------------------------------------------------AACAGAACCCGGCUUA--C-GUCUAAC-UCAUUCAU
CP000490.1/1471213-1470846     GCGG-AU-G-G-C-C-G--GAUGACCGCGGC-G-------------------------------------------------------------------------------------------------GCAA------------C-GUCGAGGAAAGUCCGGACUC-C---AUG-AAGGCA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCGGGG-----------------------GCAA------CCCCAGGG-AA---AGC-GCCACAGAGA--AGAG-ACC-GCC----CA---U--GCA-----------------------------------------------------------------------------------------------------------------------------UGC-A----U--G---GGCAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-G-G-C-UG-GUAA--CA-G-U-C-CCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-GAAU------------------------------AGGGA--C-CGCGCGUCGC-------------------------------------------AAGACAGGGCCGCCUU----UGCCCC-----AGCAGG---UC-C-----GGGU---U-----G---G-CAGC---------------------C--AGA-UCCC-G-C-CGGCAACGG-C--G-G-G-G-C--CAGAGGAAU-GGUCAUCG-----------------AAGGGGGCGACCCCG------------------------------------------GAACAAAAUCCGGCUUA--C-AGGCCAU-CCGCGCAA
BA000045.2/3542115-3542486     AGGA-GU-U-G-G-U-G-CGGUGGUCGCGGG-CC--G-G-------------------------------------------------------------------------------------------GCAA------C-C-G-G-CCUGAGGAAAGUCCGGGCUC-C---CCA-ACGAGC-G-GAUUG----------------CUGGG------------UAACG----------------CCCAGUGCGC-----------------------GCGA------GCGUGAGG-AU---AGU-GCCACAGAAA--CAU--ACC-GCCGAUGGG---G--GCG-------------------------------------------------------------------------------------------------------------------------CUUGCGC-C----C--CGCAGGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGG-C-A-U-C--GAGA---G-G-U-G-CCGG-C-UC----------------GGUAAAC-CCCGUCC-UGAGCAAGGCG-------------------------------------GGG--G-ACACGU----------------------------------------------------GGGUUGCUCGU----UGACC---------GUC---CC-C-----CAAC---A-----C---G-CCGC---------------------U--UGA-GGCG-C-C-GGGCAACCG-G--C-G-U-C-C--CAGAUAGAU-GACCGCCC-----------------CGCCGCGGCUCUGCUGCG------------------------------------GUGGAACAGAACCCGGCUUA--C-GUCCGGC-UCCUCCAC
CP000394.1/500310-499859       CCAG-AC-G-G-U-C-G--GACGGCCGCUGA-CC--C-UCCCGCUU--------------------------------------------------------------------------------UCGGGCAG-----AG-G-G-G-UUGGAGGAAAGUCCGGGCUC-C---ACG-GGAAUA-C-GG-UG----------------CCGGC------------UAACG----------------GCCGGCGGGG-----------------------GCGA------CCCCAGGG-AU---AGU-GCCACAGAAA--ACAA-ACC-GCC----CU---U--CCACCAUGC------------------------------------------------------------------------------------------------------------UUCGGCAUGAUCCG-A----A--G---GGCAUGGGUGAAAC----GGU---GC-G--G--U----------------------AAAAG-CGCACC--GCGC-C-C-C-CG-GCAA--CG-G-G-G-GUGG-C-AG----------------GGCAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGG--C-GGCCAGCGAGGCCCGUGUGCUCAGGACCGCAAGGUCAUGGGAUUUCAUGGGCCGGCGCAGGAGCAUUCC---CGCUCC--------GCUG---CC-C-----GGGU---U-----G---G-UCGC---------------------G--UGA-GGCG-U-G-CAGCGAUGU-A--C-G-U-C-C--CAGAGGAAU-GGCCGUCU-----------------CAUCCGCUUCUUUGGAAAC----------------------------------GGGUGGACAGAACCCGGCUUA--C-AGGCCGU-CUGGCGCU
CP000252.1/753012-753385       GGAG-UG-G-A-U-C-A--GAUGAUCGCCGG-CC--U-GCA-----------------------------------------------------------------------------------------GCAA-----GC-A-G-A-CGGGAGGAAAGUCCGAGCUC-C---AGA--GGGCA-G-GA-UG----------------GUCGC------------UAAUG----------------ACGACUGGAG-----------------------GCGA------CUCUAAGG-AA---AGU-GCCACAGAAA--AUAU-ACC-GCC----CG---A--C----------------------------------------------------------------------------------------------------------------------------UCC--G-U----U--G---GGUAAGGGUGAAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC--GUUU-U-C-C-GG-GUGA--CC-G-G-A-AAAG-C-AU----------------GGUAAAC-CCCAUCC-GGAGCAAGACC-AAAU------------------------------AGGAG--A-ACAUUU----------------------------------------------------GAGAGUGGCCC----GCUCG-------ACGUU---CU-C-----GGGU---A-----G--CG-UCGC---------------------U--UGA-GGCA-G-C-AGGCAACUG-C--U-G-U-C-C--UAGAGGAAU-GAUCAUCG-----------------CCAUACUCCGGGAGAUUGGA--------------------------------AUAUGGAACAGAACUCGGCUUA--U--GAUCUG-CUCCGACU
DQ645411.1/1-316               GCAU-UA-G-A-----A--GAUGGCCGCUAU-UU--U---------------------------------------------------------------------------------------------------------A-G-A-AUAGAGGAAAGUCCGGGCUA-C---AUU--AGACA-A-AA-UU----------------CCAUC------------UAACG----------------GAUGGCUAGC-----------------------GCAA------GCUAAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----UU-----------------------------------------------------------------------------------------------------------------------------------UUU---------A--A---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--AGAG-C-U-A-AA-GCAA--UU-U-A-G-CUUG-UUUG----------------GGCAAAC-CCAAUUU-GUAGCAAG----------------------------------------AAG--C-GCAUGG----------------------------------------------------UAAGUCUAAAU----CGAUA--------CACG---CU-U-------------------------CGC---------------------U--UGA-GGAA-U-A-UUGCAAAAU-A--U-U-U-C-C--CAGAUAAAU-GGCCAUCC-----------------AUU-------------------------------------------------------GACAGAACCCGGCUUA--U----UCUA-AUGCUCAA
CP000016.1/65801-66203         GGAG-UU-A-A-C-U-A--GACAAUCGCUGC-UU--U-UUUGUGUUUACAAGUGAUUA--------------------------------------------------------UAUAGUUGUUGUAAUUACAA-----AU-G-A-A-GGGGAGGAAAGUCCGGGCUC-C---AAA--GGGCA-G-AG-UG----------------CCAGG------------UAACA----------------CCUGGGGGAU-----------------------AUUA------AUCUACGA-CA---AGU-GCAACAGAAA--GAAA-ACC-GCC----GA---U--AAUUAUUUAUAA-------------------------------------------------------------------------------------------------------UAUGUUAUAGAAUAAU-A----U--G---GGUAAGGGUGAAAA----GGC---GU-G--G--U----------------------AAGAG-CACACC-AUCCG-A-A-U-UG-GUAA--CA-A-U-U-CGCG-U-UA----------------UGUAAAC-UCCACUC-GGAGCAAGGCU-AAAU------------------------------AGAAG--U-UCAAC------------------------------------------------------AGUAUGGUCC----GUACU---------GAA---CU-U-----GGGU---A-----A---G-CUGC---------------------U--GAA-ACUA-G-U-GUGUGAAUG-C--U-A-G-U-U--UAGAUGAAU-GAUUGUCC-----------------GA--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGUUAA-CUCCUUUU
BA000003.2/93359-92987         GAAG-UU-G-A-C-U-AAAAACAGUCGCUGU-UU--A-GUUUU--------------------------------------------------------------------------------------UAAAA-----AU-U-A-A-AAAGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-G-GG-UG----------------CCAGA------------UAACA----------------UCUGGAAAGC-----------------------GUGA------GCUUAUGA-CU---AGU-GCAACAGAAA--AUAA-ACC-ACC----UA---U--UUUGUA-------------------------------------------------------------------------------------------------------------------AUAUAUAAAA-A----U--A--UGGCCAGGGUGAAAA----GGC---GU-G--G--U----------------------AAGAG-CACACC--GCAU-A-A-U-UG-GUAA--CA-A-U-UCAUGG-C-AU----------------GGUAAAC-UCCACCC-GGAGCAAAGCC-AAAU------------------------------AUAGGAUA-AAUUUU----------------------------------------------------UUGUACUGCUC----GUACU--------UCUUAAACC-U-----GGGU---A-----G---G-CUGC---------------------U--UGA-AUUA-G-U-AAGUGAUUG-C--U-A-A-U-C--UAGAUGAAU-GACUGUUA-----------------A---------------------------------------------------------AACAGAACCCGGCUUACAC-GAGUCAA-CUUCAAUA
AE016826.1/92349-91999         GAAG-CU-G-A-C-C-G--GGCAGUCGCUGC-UA--U-UAUG----------------------------------------------------------------------------------------AAAAA---UAC-A-U-A-GAAGAGGAAAGUCCGGACUC-C--AAGA--GGCAA-A-GG-UA----------------CCAGA------------UAACA----------------UCUGGGGAAC-----------------------GUAA------GUUCACGA-CU---AGU-GCAACAGAAA--AUAA-ACC-GCU----AA---A--AAU-------------------------------------------------------------------------------------------------------------------------UAGAAUU-------------AGCAAGGGUGAAAA----GGU---GU-G--G--U----------------------AAAAG-CACACC--GAAU-A-C-U-UG-GUAA--CA-A-G-U-AUUGAC-UA----------------GGUAAACUUCUACCUUGGAGCAAGGCC-AAAU------------------------------AAGAG--U-AUUCGC----------------------------------------------------CCAA-----UU------UUU--------AAUA---CU-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-ACUA-A-U-GAGUAAUUA-U--U-A-G-U-C--UAGAUAAAU-GACUGUCA-----------------AA--------------------------------------------------------UACUGAACCCGGCUUA--U-AGGUCAG-CUUCAUUA
CP000390.1/2166038-2165598     CCAG-CC-G-G-U-C-G--GACGGCCGCACG-CG--C-AAGCGC-----------------------------------------------------------------------------------CGAAAGG-----CC-G-C-G-CGUGAGGAAAGUCCGGGCUC-C---ACG-GAAAUA-C-GG-UG----------------CCGGG------------UAACA----------------CCCGGCGGGG-----------------------GUAA------CCCUAGGG-AA---AGU-GCCACAGAAA--GCAG-ACC-GCC----CC---G--CCGGUAAAUCAGCCUUUGAAGCC--------------------------------------------------------------------------------GGCCUCGGUUCGAAGGCCGAUUUACAGG-C----G--G---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGGG-CCCACC--GCGU-U-U-C-UG-GCAA--CA-G-G-A-ACGG-C-AC----------------GGUAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGAA--C-GGCGCGAAGGGC---------------------------------------AACCUUCAGGGCAUUUCC----GGCCC-------GGCCG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGCC-G-G-CGGCGACGC-C--G-G-U-C-C--CAGAGGAAU-GGCCGUCA-----------------CGUCGCGCCGUCUCGGCGGC-------------------------------GCGGCCAUACAGAACCCGGCUUA--C-AGACCGG-CUGGUAUU
CP000673.1/950093-950451       UAAG-UA-A-G-C-C-A--GACAAUCGCUGC-UG--U-A-------------------------------------------------------------------------------------------UAAU------U-A-C-A-GGAGAGGAAAGUCCGAGCUU-C---AUA--GGGCA-G-GG-UG----------------CUGGG------------UAAUA----------------CCCAGUCAGG-----------------------GUGA------CCUGAAGG-AA---AGU-GCAACAGAAA--UAU--ACC-GCU----GA---A--GCAACAA-----------------------------------------------------------------------------------------------------------------GAAAUUAUUGC-U----U--C---AGUAAGGAUGGAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC-AGCGC-A-U-U-G--GUGA---C-U-U-U-GCGG-C-UA----------------UGUAAAC-CCCACCU-GAAGCAAGAUC-GAAU------------------------------AGGAA--A-GCAUAUU--------------------------------------------------AAAAAGUGGCCC----GCUUU---------GCU---UU-C-----GGGU---A-----G--UA-UCGC---------------------U--GGA-GCCU-A-U-UGGUAACAA-U--A-G-G-C-C--UAGAUAGAU-GAUUGUCU-----------------AA--------------------------------------------------------UACAGAACUCGGCUUA--U-AGACUUA-CUUACCCA
CP000053.1/799414-799765       CAAA-AA-G-A-G-C-A--AGGAGUUC--------------------------------------------------------------------------------------------------------ACA------------------AG-------------------ACG--AGGAA-C-GG-AG----------------CGUAU------------ACUUA----------------AUACGUGAGUA--------------------CCGUAG-----UACUUGUAG-AACGACGUAGCCAAUUUUU--GAAG-UUC-AUC----GA---G--UA-------------------------------------------------------------------------------------------------------------------------------UA-U----U--C---GGUAAGGGUGAAAA----GGU---AC-G--G--U----------------------AAGAG-CGUACC--GGUA-A-G-U-UG-GUAA--CA-A-A-U-UACG-C-AU----------------GGUAAAC-CCCACCA-AGAGCAAGAUC-AAAU------------------------------AGGCG--U-UACAGAACUUAUCAAGUU----------------------------CCCGGGUUAUCUCUAGCC---------GGCUU--------GUAA---UG-C-----GGGU---A-----G---A-UCGC---------------------U--UGA-GGUA-A-A-CGGUAACGU-U--U-A-U-C-C--UAGAUAAAU-AACUGCAA-----------------UGAAUUUAUAUUCA--------------------------------------------UACAGAAUCCGGCUUA--U-AGACCUU-AUUGUUAU
AAGP01000051.1/20859-21226     ACAG-GU-C-A-C-C-A--GACGGUCGCGGC-UC--U-C-------------------------------------------------------------------------------------------UCAC------G-A-G-G-GCUGAGGAACGUCCGGGCUC-C---GCA--GAGCAGG-GA-UG----------------GUGGG------------UAACA----------------CCCACCCGGG-----------------------GCAA------CCCGCGGG-CC---AGU-GCAACAGAAA--GCAG-ACC-GCC----CA---G--U---------------------------------------------------------------------------------------------------------------------------UUCG--A-C----U--G---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGGGU-G-U-C-GG-GUGA--CC-G-G-C-GCCG-C-UG----------------GGUAAAC-CCCAUCC-GGAGCAAGAUC-AGAC------------------------------A-GAC--G-ACGUUC-----------------------------------------------------GAGGCUGCUC----GCCGA---------GUC---GU-C-----GGGU---G-----G---A-UUGC---------------------U--UGA-GGCC-G-G-UGGCAACAU-C--G-G-U-C-C--CAGAUAGAU-GACCGUCC-----------------GUCGAGAAGGGUAACCGAC----------------------------------UCGAUGACAGAACCCGGCGUA--U-CGGUGGC-CUGUCCUC
CP000721.1/1039561-1039908     CGAG-UG-A-G-A-C-G--UGCAAUCGCUGC-UA--G-AC------------------------------------------------------------------------------------------UUAG-----AU-C-U-A-GGAGAGGAAAGUCCGAGCUC-C---AUA--GGGCA-G-GG-UG----------------CUGGA------------UAACG----------------UCCAGUCAAG-----------------------GCGA------CUUGAAGG-AA---AGU-GCAACAGAGA--UAU--ACC-GCC----UA---A--G---------------------------------------------------------------------------------------------------------------------------UUUA--C-U----U--A---GGUAAGGGUGGAAA----GGU---GAUG--G--U----------------------AAGAG-CUCACC-AGCGU-G-A-U-G--GAGA---C-U-U-C-ACGG-C-UA----------------UGUAAAC-CCCACUU-GGAGCAAGACC-GAAU------------------------------AGGGA--G-GCAAUU---------------------------------------------------AAGGGGCUGCCC----GUCCC---------GCC---UC-C-----GGGU---G-----C---G-UCGC---------------------U--UGA-GCUU-A-C-UGGCAACAG-U--A-G-G-C-C--UAGAUAGAU-GAUUGCUU-----------------AA--------------------------------------------------------UACAGAACUCGGCUUA--U-GGCUUAU-CUCGCAUA
CP000724.1/3019118-3018723     CGAG-UA-A-G-U-C-A--GAUGAUCGCGGC-CA--C-AGAC----------------------------------------------------------------------------------------UUGU----UCU-G-U-G-GACGAGGAAAGUCCGAGCUC-C---GUA--GGGCAAG-GG-UG----------------CUGGG------------UAAUU----------------CCCAGUGGAG-----------------------GUGA------CUCUAAGG-AU---AGU-GCAACAGAGA--UAU--ACC-GCC----AG---A--ACCCCUACUCAGUAGCAAUACU----------------------------------------------------------------------------------GGGUAUGUGGUGAGACAGCCUUAGGGC-UG--UC--U---GGUAAGGCUGGAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-U-A-G--GCGA---C-U-A-A-CUGG-C-UA----------------UGUAAAC-CCCAUCC-GGAGCAAGACC-AAGU------------------------------AG--G--G-ACUAGAA-------------------------------------------------AACGCGGCUGCCC----GUCGC---------GUC---CC-G-----UGGU---A-----G---G-UCGC---------------------U--UGA-GCUA-A-C-UGGUAACAG-U--U-A-G-C-C--UAGACAGAU-GAUCGUCA-----------------AA--------------------------------------------------------UACAGAACUCGGCUUA--U-AGACUUA-CUCGCUUA
AAOB01000003.1/8301-7930       UGGG-UC-G-G-C-A-A--GACGGUCGCGUU-AU--C-C-------------------------------------------------------------------------------------------GCAA------G-G-G-U-ACCGAGGAACGUCCGGGCUC-C---GCA--GAGCA-G-GA-UG----------------GUGGG------------UAACA----------------CCCACCCGGG-----------------------GCAA------CCCGCGAGAAC---AGU-GCAACAGAAA--GUAG-ACC-GCC----AC---A--GAC-------------------------------------------------------------------------------------------------------------------------UUCGGUC-U----G--G---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGG-C-C-G-GG-GUGA--CU-C-G-G-UCGG-C-UA----------------GGUAAAC-CUCGUCC-GGAGCAAGAUC-AGAC------------------------------A-GAA--G-ACGCUA----------------------------------------------------A--GGCUGCUC----GCCAA---------GUC---UU-C-----GGGU---A-----G---A-UCGC---------------------U--AGA-GGUG-U-G-CGGCAACGU-A--C-A-U-C-G--UAGAUAGAU-GACCGUCC-----------------AGCACGAAGGUUUCGGCCU---------------------------------CGUGUGAACAGAACCCGGCGUA--C-UAGCCGG-CCCAUUCC
AAVP02000015.1/14993-14640     UAAG-UA-A-G-A-C-A--GACAAUCGCGGA-UG--U-AAGUGC-----------------------------------------------------------------------------------CGAAAGG-----CA-G-C-A-GACGAGGAAAGUCCGGGCUU-C---AUA--GGGCA-G-GA-UG----------------CCGGA------------UAACG----------------UCCGGUGGAG-----------------------GUGA------CUCCCAGG-CC---AGU-GCAACAGAAA--UAA--ACC-GCG----UC---G--GAU-------------------------------------------------------------------------------------------------------------------------UCCAUAU-C----G--G---CGUAAGGGUGGAAA----GGC---AG-U--G--U----------------------AAGAG-ACUACC--GCCU-C-U-G-CG-GUAA--CG-G-A-G-AGGG-CACA----------------UGUAAAC-CCCAUUC-GAAGCAAGACC-GGAU------------------------------AG--A--A-GCAAU------------------------------------------------------GUGGCGGCCC----GUCAC---------GCU---UC-A------GGU---A-----G---G-UCGC---------------------U--UGA-GCAC-G-G-CGGCAACGU-C--G-U-G-C-C--UAGAUAGAU-GAUUGUCC-----------------AC--------------------------------------------------------GACAUAACCCGGCUUA--U-CGUUUUG-CUUAACAC
CP000542.1/2120942-2120613     GAAG-CG-C-G-C-C-A--GACCGCCGCUGG-UG--C-AAUCUG-----------------------------------------------------------------------------------GGAAACC-----AG-G-C-A-CUGGAGGAACGUCCGGACUG-C---ACA--GGACA-G-CG-UA----------------GCAGC------------UAACG----------------GCUGCCCACC-----------------------GCGA------GGUGAGGA-UC---AGA-GCAACAGAGA--CGAG--UC---------------------------------------------------------------------------------------------------------------------------------------------------------------------GG-----------GGG---GC-G--G--C----------------------AAC-G-CGCCCC--G--------G-GU-GAAA----------------C-G-----------------GGCAAUC-UCUACGC-GCAGCAAUACC-AAGU------------------------------AGGCC--A-GCGUCG----------------------------------------------------AUGUGG---UU----CCGCA-------GAGCU---GG-C-----GGGU---A-----G---G-UAGC--------------------AC--CGA-GCCGUG-G-UGGCGACAC-C--C-G-G-C-C--CAGAUCGAU-GGCGGUCA-----------------CGCUGCGGGUCACCGCA--------------------------------------GCGCACAGAAUCCGGCUUA--U-CGGCGCG-CUUCACAC
CP000284.1/2433638-2433334     GAAG-CU-G-G-C-C-A--GGCAGCCGCCGC-UC--G-C-------------------------------------------------------------------------------------------GCAA------G-C-G-A-GGGGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-G-GA-UG----------------ACGGC------------UAACG----------------GCCGUACGCC-----------------------GUGA------GGCGAGGA-AC---AGG-GCCACAGAGA--CGA---GU-AAG----CC---G--C----------------------------------------------------------------------------------------------------------------------------AAG--G-U----G--G--------ACGUGAAAC--------------------------------------------------------G---------------------------------C-------------------GGUAACC-UCCAUCC-GGAGCAAGGCC-AAAU------------------------------AGGGU--A-GCGAU------------------------------------------------------GGCGUGGCUC----GCGCC---------GCU---AC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCCU-G-G-UGGCAACGC-C--A-G-G-C-C--UAGAUGAAU-GGCUGCCA-----------------CCCGCUUUGCGGG---------------------------------------------GACAGAACCCGGCUUA--C-CGGCCAG-CUUCAUUC
AM711867.1/1842831-1843212     UGGG-UC-G-G-C-A-A--GACGGUCGCGCC-GC--G-GAGGAUCCCG----------------------------------------------------------------------------AGAGGGGGAG-----AC-C-G-C-GUCGAGGAACGUCCGGGCUC-C---GCA--GAGCA-G-GG-CG----------------GUGGG------------UAACA----------------CCCACCCGGG-----------------------GCGA------CCCGCGAG-AC---AGU-GCAACAGAGA--GCAG-ACC-GCC----CG---U--CGC-------------------------------------------------------------------------------------------------------------------------GCGAGCG-G----C--G---GGUGAGGGUGAAAC----GGC---GG-U--G--U----------------------AAGAG-ACCACC-AGCGG-C-C-C-GA-GUGA--UC-G-G-G-UCGG-C-UA----------------UGCAAAC-CUCGCCC-GGAGCAAGGUC-GAAC------------------------------A-GGG--G-ACGCA------------------------------------------------------CAGGCUGCUC----GUCCA---------GUC---CC-C-----GGGU---A-----G---A-CCGC---------------------U--GGA-GGGC-U-G-CGGUGACGC-A--G-C-U-C-C--GAGAUAGAU-GGCCGUCC-----------------AUGGUGCCGCGAGGCAC--------------------------------------CGGGACAGAACCCGGCGUA--U-CAGCCGG-CCCAUCCG
AAVU01000017.1/76609-76170     AGAG-UC-A-G-C-GAA--GGCAAUUGCGGA-CU--C-AA-------------------------------------------------------------------------------------------UAC-----CU-G-A-G-UCUGAGGAAAGUCCGGACUC-CCAAAAG--ACUAA-A-CC-UG----------------CUGGA------------UAACG----------------CCCAGUGCGA-----------------------GUGA------UCGUGAGG-AU---AGU-GCCACAGAAA--AAU--ACC-GCC----AA---G--AAUAGGGAACAGGGGACAGGUUACAGGUUACAGGGA-------------------------------------------------------AGACCCCUGAGAGCUGAUCACCUAGAACUAAUCAUCUGUU-G----U--U---GGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-G-U-C--GAGA---G-G-C-G-UUGG-C-UC----------------GGUAAAC-CCCAGGUGGGAGCAAGGUC---GG------------------------------AGGAA--C-UAAGGU----------------------------------------------------UGGUCUUUUCC----CCGUU--------CCGG---UU-U-----AAGA---G-----G--UA-CCGC---------------------U--UGA-GGUG-U-U-UGGUAACAA-A--C-A-U-C-C--CAGAUAGAU-AAUUGCCC-----------------UCUUGACUGUAUACAGUU-----------------------------------GAGAAAACAGAAUCCGGCUUA--U-G-UCUGG-CUCUCUCU
ABDQ01000018.1/32843-32491     CGAG-UA-A-G-C-C-A--GAUGAUCGCUGC-UA--C-ACUA----------------------------------------------------------------------------------------UUAU-----GU-G-U-A-GGAGAGGAAAGUCCGAGCUC-C---AUA--GGGCA-G-GG-UG----------------CUGGG------------UAACU----------------CCCAGUGGAG-----------------------GCGA------CUCUAAGG-AA---AGU-GCAACAGAGA--UAU--ACC-GCC----AU---A--AAC-------------------------------------------------------------------------------------------------------------------------UUU-GUU-U----A--U---GGUAAGGGUGGAAA----GGU---GA-G--G--U----------------------AAGAG-CUUACC-AGCGC-A-A-U-G--GCGA---C-U-U-U-GCGG-C-UA----------------UGUAAAC-CCCAUCU-GGAGCAAGAUU-GAAU------------------------------AGAGG--G-ACAUUA----------------------------------------------------AGGAGCGGCCC----GUUCC---------GUC---CC-C-----GGGU---A----AA---A-UCGC---------------------U--UGA-GUCU-A-A-UGGUAACAU-U--A-G-G-C-C--UAGAUAGAU-GAUCAUCA-----------------AA--------------------------------------------------------UACAGAACUCGGCUUA--U-AGACUUAUCUCGUAUA
CP000568.1/1068190-1067816     UGAG-UA-A-G-C-C-G--GAUAGUCGCGGG-UA--C-AGUGCC------------------------------------------------------------------------------------GAAAGG-----CC-G-U-A-CACGAGGAAAGUCCGGGCUC-C---GCA--GGGCA-G-GG-UG----------------CCGGG------------UAACU----------------CCCGGUGAAG-----------------------GCGA------CUUCAAGG-AA---AGU-GCAACAGAAA--UAU--ACC-GCC----UG---C--UGAAGAUUGAGGUC---------------------------------------------------------------------------------------------------GAGUGCUUUCGGUUUUCA-G----C--A--UGGUAAGGGUGGAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCGG-U-A-U-G--GCGA---C-U-U-A-CCGG-C-UA----------------UGUAAAC-CCCACCC-GGAGCAACACC-GCAU------------------------------AGAGG--G-ACGUUA----------------------------------------------------AGGUGG----C----CCGCC--------AGUC---CC-------GGGU---A-----G---G-UGGC---------------------U--UGA-GCUA-U-A-UAGAAAUAU-A--U-A-G-C-C--UAGAUAGAU-GACUAUCC-----------------AA--------------------------------------------------------GACAGAACCCGGCUUA--C-AGGCUUA-CUCAAUAU
CP000656.1/3066080-3066491     UGAG-CU-G-G-C-C-G--GGCGGCCGCGGC-AC--C-CAGA----------------------------------------------------------------------------------------UUCC-----UG-G-G-G-GUCGAGGAAAGUCCGGACUU-C---ACA--GAGCA-G-GG-UG----------------AUUGC------------UAACG----------------GCAAUCCGAG-----------------------GUGA------CUCGCGGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----UG---C--GUCGAGUC---------------------------------------------------------------------------------------------------------------UUCGGACGAGGC-G----C--A---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAC-U-C-C-GG-GUGA--CC-G-G-G-GUGG-C-UU----------------GGUAAAC-CCCACCC-GAAGCAAGGCC-AAGAAGGCCGCAACC--------UGGUUGCGGUCGCGCA--G-GCGUUC----------------------------------------------------GAGGGCUGCUC----GCCCG--------AGCC---UG-C-----GGGU---A-----G---G-CCGC---------------------U--CGA-GGUA-C-C-CGGCGACGGUG--U-G-C-C----CAGAUGGAU-GGUCGCCG-----------------CCUCCUCGUCAGAGAUGGCG--------------------------------UCGAGGAACAGAAUCCGGCUUA--C-AGGCCGG-CUCAUCCG
CP000031.1/3164292-3163898     GCGG-AG-G-G-C-C-G--GAUGGCCGCGUG-GG--G-G-------------------------------------------------------------------------------------------GCAA------C-C-C-C-CGCGAGGAAAGUCCGGACUC-C---AUG--AAGCAGC-GG-UG----------------CCGGG------------UAACG----------------CCCGGGCGGG-----------------------GAAA------CCCGACGG-AA---AGC-GCCACAGAGA--ACAG-UCC-GCC----GC---G--C----------------------------------------------------------------------------------------------------------------------------AGG--U-C----G--C---GGCAAGGGUGAAAC----GGU---GG-A--G--U----------------------AAGAG-CCCACC--GCGC-C-C-C-UG-GCAA--CA-G-G-G-GCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGAC--C-CCCGCGCGGGACGCGUCGGUUU--------------------CGGCCGAUACCUCCGCUAGGCCGCUUC----AGCCGA------GAGGG---GU-C-----GGGU---U-----G---G-CAGC---------------------U--AGA-GGCG-C-C-UGGCAACAG-G--C-G-C-A-C--CAGAGGAAU-GGUCAUCG-----------------AAGGGGGCAACCCUG------------------------------------------GAACAGAAUCCGGCUUA--C-AGGCCCU-CCGCGCGC
BA000021.3/523133-522804       AAAG-UU-A-G-C-U-A--GACAAUCGCUGU----------U----------------------------------------------------------------------------------------UAAU--------------ACAGAGGAAAGUCCGGGCCC-U---AAA--GAGCA-A-GA-UG----------------CCAGG------------UAAUU----------------CCUGGGAGGA-----------------------GUGA------UCCUACGA-CU---AGU-GCAACAGAAA--AAAA-ACC-GCC----AC---U-------------------------------------------------------------------------------------------------------------------------------UUU----G----U--U---GGUAAGGGUGAAAA----GGU---GC-G--A--U----------------------AAGAG-CGUACC--GCAA-U-UUA-UG-GUAA--CA-U-A-A-UUGG-C-AG----------------UGUAAAC-UCCAUCU-AGGGCAAGGCC-AAAU------------------------------AAAAG--C------------------------------------------------------------UUGAUUGCUC----GUCUU--------UAAG---CU-U-----UGGU---A-----G---G-CUGC---------------------A--AGA-AUAA-A-U-AUGUGAAUG-U--U-U-A-U-C--UAGAUAAAU-GAUUGUCC-----------------AA--------------------------------------------------------GACAGAACCCGGCUUA--C--AGCUAA-CUUUAUUU
CP000769.1/4353920-4353531     GGAG-CC-G-C-U-C-G--GGCGAACGCGUC-GG--U-CUGCAG------------------------------------------------------------------------------------GAACGG-----GG-G-C-C-GCCGAGGAAAGUCCGAGCAC-C---ACA--GGGCA-G-GG-UG----------------CCGGU------------UAACG----------------ACCGGUCGGG-----------------------GCGA------CCCGCAGG-AC---AGU-GCCACAGAGA--ACAG-ACC-GCC----GA---A--CGGCGUCCUGAG-------------------------------------------------------------------------------------------------------CUUGUCGAAGGACGCG-C----G--U---GGCAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-C-C-GG-GUGA--CC-G-G-C-GCGG-C-AC----------------GGAAAAC-CCCACCC-GGUGCAAGGGC-AAAU------------------------------AGGGA--G-GC----------------------------------------------------------GACCGGCCC----GGUCA-------UUGCC---UC-C-----GGGU---AU---GG---C-CCGC---------------------U--CGA-GACG-C-G-CGGCAACGC-G--C-G-U-C-C--UAGAGGAAU-GUUCGCCG-----------------CCGCGGGGAAACCCGC----------------------------------------GGGACAGAACUCGGCUUA--C-AGAGCGG-CUCCGGCA
AAVL02000025.1/21850-22196     UGAG-UA-G-A-G-C-A--GAUGAUCGCAGC-UG--C-UAUUGC-----------------------------------------------------------------------------------CGAAAGG-----AC-G-C-A-GGUGAGGAAAGUCCGGGCUU-C---AUA--GGGCA-G-GG-UG----------------CCGGC------------UAACG----------------GCCGGUGGAG-----------------------GUGA------CUCCCAGG-AA---AGU-GCAACAGAAA--UAAA-ACC-GCC----AG---C--------------------------------------------------------------------------------------------------------------------------------UU----G----C--U---GGUAAGGAUGAAAU----GGU---AG-U--G--U----------------------AAGAG-ACUACC--GCUU-C-G-G-UG-GUAA--CA-U-C-G-AGGGUC-AG----------------UGUAAAC-CCCACUU-GAAGCAAGACC-GAGC------------------------------A-GAA--A-GCAUA-------------------------------------------------------UGGUUGCCC----GCCA----------GCU---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-ACAU-A-U-UGGUAACGA-U--A-U-G-U-C--UAGAUAGAU-GAUCAUCC-----------------AC--------------------------------------------------------GACAUAACCCGGCUUA--C-AGCUUUA-CUCAUUCA
CP000450.1/2649362-2649650     GAAG-UC-G-G-U-C-A--GACAGUCGCUGC-CU--G-GU---------------------------------------------------------------------------------------------------AA-C-A-G-GGAGAGGAAAGUCCGGGCUC-C---ACA--GAGCA-G-GA-UG----------------CCGGU------------UAACG----------------GCCGGCCGCC-----------------------GUGA------GGUGAGGA-AC---AGG-GCCACAGAGA--CGAG--CG----------------UAU-------------------------------------------------------------------------------------------------------------------------UAAGUUA------------------CGGUGAAAC--------------------------------------------------------G---------------------------------C-------------------GGUAACC-UCCAUCC-GGAGCAAGAUC-AAAU------------------------------AGGCA--G-AUGAUG----------------------------------------------------ACGCUG---CU----CGCCG--------AGUC---UG-U-----GGGU---A-----G---A-UCGC---------------------U--UGA-GCAU-A-C-GGGUAACGG-U--A-U-G-C-C--UAGAGGAAU-GACUGUCC-----------------AU--------------------------------------------------------GACAGAACCCGGCUUA--U-CGACCGG-CUUCCCCC
AE005673.1/2774739-2774346     CCAG-AU-G-A-U-C-G--GGCGGUCGCGUC-GU--C-UU---------------------------------------------------------------------------------------------------CG-G-A-C-GCCGAGGAAAGUCCGGGCUC-C---ACG-GUGACA-A-GG-CG----------------GUGGG------------UAACG----------------CCCACCGGGA-----------------------GCGA------UCCCAGGG-AU---AGC-GCCACAGAAA--GCAA-ACC-UCC----UC---C--C---------------------------------------------------------------------------------------------------------------------------UACG--G-G----G--C---GGGAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-A-C-C-UG-GUGA--CA-G-G-G-ACGG-C-AU----------------GGCAAGC-CCCGCCU-GGAGCAAGACC-GAAU------------------------------AGGGA--U-CCCGCGUCGGCCUC------------------------------------GCGCCGACUAGGCCGUCAC---UGGCUGA------GAGGA---UC-C-----GGGU---A-----G---G-UCGC---------------------G--AGA-GCCG-U-C-CAGCAAUGG-C--C-G-G-C-C--UAGAGGAAU-GAUCGUCG-----------------CCGUCUCCCUGUCUUCGGAUGG---------------------------GCGGGGCGGAACAGAACCCGGCUUA--C-AGAUCAU-CUGGUCCG
AAMD01000020.1/46527-46921     GGAG-CG-G-C-C-C-G--GGUGAACGCUGG-CC--A-CCGCA-------------------------------------------------------------------------------------GGAACG-----GG-U-G-G-CGGGAGGAAAGUCCGAGCUC-C---ACA--GGGCA-G-GG-UG----------------CUGGC------------UAACG----------------GCCAGUCGAG-----------------------GUGA------CUCGCAGG-AC---AGU-GCCACAGAAA--ACAA-ACC-GCC----CG---U--UCC-------------------------------------------------------------------------------------------------------------------------GAAAGGG-G----C--G---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-C-C-G-GG-GUGA--CC-C-G-G-GCGG-C-AC----------------GGUAAAC-CCCACCU-GGAGCAAGAGC-CAAU------------------------------AGGAG--C-GCGUCCUCGCGGU-------------------------------------UGGGGGACAAGGAUGGCCC----GUCCG-------CUGCG---CU-C-----GGGU---U-----G---C-UCGC---------------------UGAUGA-GGCCCC-U-GGGCAACCA-G--G-G-C-C-C--UAGACGAAU-GUUCGCCG-----------------CCCACCUCGAAAGGGGU--------------------------------------GGGGACAAAACUCGGCUUA--C-AGGGCCG-CUCCGGCU
AAMT01000009.1/94327-93924     GCGG-AU-G-G-C-C-G--GACGGUCGCCGG-UG--G-CGGGGG------------------------------------------------------------------------------------CAACUC-----CG-C-U-G-CGGGAGGAAAGUCCGGACUC-C---ACA-AGGCAA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCCGGG-----------------------GCAA------CCCGAGGG-AA---AGC-GCCACAGAGA--ACAA-ACC-GCC----CG---G--GUCAAUCGC------------------------------------------------------------------------------------------------------------UGACGCGAUGAACC-C----C--G---GGUAAGGCUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-G-A-C-GG-GCAA--CC-G-G-A-CCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-GAAU------------------------------AGGGA--C-CUCGCGCCCCGC----------------------------------------GAGGGCAGGGCCGCCUU----GGCCC-------GGAGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--CGA-GCGG-U-U-CGGUAACGG-A--U-C-G-C-C--UAGAGGAAU-GAUCGUCG-----------------GCACCGGGGCGACCCGG--------------------------------------CGUCACAGAAUCCGGCUUA--C-AGGCCGU-CCGCGCAU
AAYB01000002.1/573345-573716   GCGG-AU-G-G-C-U-G--GAUGACUGCGGC-A-------------------------------------------------------------------------------------------------GCAA------------U-GUCGAGGAAAGUCCGGACUC-C---AAA--AAGCA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCGGGG-----------------------GUAA------CCCCAGGG-AA---AGC-GCCACAGAGA--ACAG-ACU-ACC----UG---A--U---------------------------------------------------------------------------------------------------------------------------UUCG--A-U----C--A---GGAAAAGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGC-A-A-G-CG-GCAA--CG-C-A-A-GCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGA--C-CUCGCGUCGCAA----------------------------------------GACGGGGAUGCUUGAAC----CCCAG--------AUGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--AGAGGGCG-U-C-UGGCAACAG-G--C-G-C-C-C--CAGAUGAAU-GGUCAUCC-----------------AUUUGUGGGCAACCACA--------------------------------------AAGGACAGAAUCCGGCUUA--U-AGGCCAU-CCGCGCAU
ABCB02000018.1/378881-379228   UGAG-CA-G-G-C-U-G--AACAGCCGCGGG-CGAUA-GCCG----------------------------------------------------------------------------------------AAAG-----GC-UCC-G-CCUGAGGAAAGUCCGAGCUC-C---ACA--GGGCAGG-AA-UA----------------GCGGU------------UAACG----------------GCCGCCGGGG-----------------------GCGA------CCCUAGGG-AU---AGU-GCAACAGAAA--GUU--ACC-GCC----GG---C-------------------------------------------------------------------------------------------------------------------------------UUU----G----C--C---GGUAAGGGUGGAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC-AGCGC-G-C-A-G--GAGA---C-U-G-C-GCGG-C-UG----------------UGUAAAC-CCUAUUC-GGAGCAACACC-GCAG------------------------------A-GGA--A-CGUAUC-----------------------------------------------------GCGCCGGCCC----GGCG----------UGU---UC-C-----GAGA---A-----G---G-UGGC--------------------GU--CGA-GCCGUG-A-UGGCAACAU-C--C-G-G-C-C--AAGAUAGAU-GGCUGUUC-----------------AC--------------------------------------------------------GACAGAACUCGGCUUA--U-AGGCCUG-GUCAUAAC
X65707.1/109-543               GAGA-GU-U-A-G-G-G-AGGGAGUUGCGGA-UU--C-CUGU----------------------------------------------------------------------------------------CACA-----GG-G-A-A-UCUGAGGAAAGUCCGGGCUU-CC-CAAA--GGCCA-A-ACUUG----------------CUGGG------------UAACG----------------CCCAGUGCGC-----------------------GCGA------GCGUGAGG-AC---AGU-GCCACAGAAA--AAU--ACC-GCC----CU---U--UUUAGAAAACAGCAACCAGUAAACAGUUAACAG-------------------------------------------------------------GGUUUUUCUGCUGACUAACUGGUAACUGACCACUGAA-A----A--G---GGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-A-U-C--GAGA---G-G-U-A-CUGG-C-UC----------------GGUAAAC-CCCGGUUGGAAGCAAGGUC-GGAG------------------------------GGGCA--A-AGGUU------------------------------------------------------GGUCUUUUUC----CUGCC--------CCAU---GA-U-----UGGU---G-----G--AA-CCGC---------------------U--UGA-GGAA-U-U-UGGUAACAA-A--U-U-U-C-C--CAGAUAGAU-AACUCCCC-----------------AAGGGUGCCUCGCAUCC--------------------------------------UGGAACAGAACCCGGCUUA--C-GACUAAC-UCUCUUUU
AAXG02000012.1/129014-129362   CAAG-UA-A-G-C-U-G--GACAGCCGCGGA-UC--G-AGGCC-------------------------------------------------------------------------------------GAAAGG-----CC-C-G-A-UAUGAGGAAAGUCCGGGCUC-C---ACA--GGGCAAG-GA-UA----------------ACGGG------------UAACA----------------CCCGCCGGGG-----------------------GCGA------CCCUAGGA-AA---AGG-GCAACAGAGA--UAUA--CC-GCC----AC---G--U----------------------------------------------------------------------------------------------------------------------------UCU--G-C----G--U---GGUAAGGGUGGAAA----GGC---GGAG--G--U----------------------AAGAG-CCCGCC--CGAC-G-A-C-UG-GGAA--CU-GCU-C-GUCG-C-------------------UGUAACC-UCUAUCC-GGAGCAACGCC-GUGG--------------------------------GAG--A-ACAUA------------------------------------------------------UGGCCGGCCC----GGCC----------GUU---CU-C-----AGGA---------G---G-CGGC---------------------U--UGA-UCGU-A-C-CGGCAACGG-U--A-C-G-G-C--UAGAUAGAU-GGCUGUCU-----------------UAAAA-----------------------------------------------------GACAGAACCCGGCUUA--C-AGGCUUA-CUUGCCGC
CP000263.1/59969-59622         AAAG-UU-A-G-U-U-G--AACAGUCGCUAU-UU--A-AUAUU--------------------------------------------------------------------------------------UCUAU-----AU-U-A-A-AUAGAGGAAAGUCCGGGCUC-C---GUA--AGGCA-A-GA-CG----------------CCAGA------------UAACG----------------UCUGGGAAGA-----------------------GAAA------UCUUACGA-CU---AGU-GCCACAGAAA--AUAA-ACU-AUC----UA---U----A-------------------------------------------------------------------------------------------------------------------------UAAUUUA-A----U--A---GAUACAGGUGAAAA----GGU---UC-G--G--U----------------------AAAAG-CGUACC--GCAG-A-A-U-UG-GUAA--CA-A-U-U-UUGG-C-UA----------------GGUAAACAUCCGUCU-GGAGCAAGGCU-AAAU------------------------------AAGAA--G------------------------------------------------------------AGUAUAGCCU----GUACU--------UAUC---UU-C-----GGGU---A-----A---G-CUGC---------------------U--UGA-AUUA-A-U-AAGUGAUUA-U--U-A-A-U-C--UGGAUAAAU-GACUGUGU-----------------A---------------------------------------------------------AACAGAACCCGGCUUA--U-AAAUUAA-CUUAUCUU
AJ012176.2/7-394               ------G-A-G-U-A-A--GGCAGCCGCUGG-AG--C-AGUUUG-----------------------------------------------------------------------------------UUUAAAG-----CU-G-A-UGUCAGAGGAAAGUCCGGACUU-Y---AUA--AGAAA-A-GA-UG----------------CUGGA------------GAAAU----------------UCCAGGGGCC-----------------------GAGA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAC-UCC-GCU----AU---A--AAUU-----------------------------------------------------------------------------------------------------------------------GCAAAAUU-U----A--U---AGACAGGCUGAAAA---AUCC---UA-C--U--U----------------------UAAGA-GUAGGA--GCUG-C-U-G-GG-GAGA--CC-C-G-G-UAGA-C--C----------------UGUAAAC-CCCAUCU-GAAGCAAGA--------------------------------------GAAA--A-AGUCUUUUGUCUCUGC--------------------------------AAAGAACCUCUCUAAGGGAAG---GUUCAG--------ACUU---UU-U-----CAUA---A-----------UCGC---------------------U--UGA-GAAG-U-A-UAGUAAUGU-G--C-U-U-C-C--UAGAUGAAU-GGCUGCCC-----------------GCAGGCAAGAAUUUUUAUUCG-----------------------------CGCUUGUUGACAGAAYCCGGCUUA--C-UCGCUC----------
CP000449.1/2272218-2271830     UCAG-GU-G-G-C-U-G--GGCGGUCGCGGC-AA--C-UGGGCC-----------------------------------------------------------------------------------GGAAACG-----GU-G-U-U-GUCGAGGAAAGUCCGGGCUC-C---ACG-GAGGCA-A-GG-UG----------------CCGGA------------UAGCG----------------UCCGGCGGGG-----------------------GUGA------CCCCAGGG-AA---AGC-GCAGCAGAGA--ACAG-ACC-GCC----GG---G--CC--------------------------------------------------------------------------------------------------------------------------UUCG-GG-C----C--A---GGCAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCCC-C-G-A-CC-GCAA--GG-A-A-G-GGGG-C-UA----------------GGCAAGC-CCCACCU-GGAGCAAGACC-GAAU------------------------------AGGGA--C-AGACCGCAGCCU---------------------------------------CGGCUGCACGUGCGCCUC---CGCAUG---------CUG---UC-C-----GGGU---A-----G---G-UCGC---------------------A--CCA-GGUC-G-U-GCGCAAGCA-C--G-A-U-C-G--CAGAUGAAU-GACCGUCG-----------------CCCCGGAUCUGAUCCG---------------------------------------GGGGACAAGACCCGGCUUA--C-AGGCCGC-CUGAUCAC
CP000237.1/23797-23440         CGAG-GU-G-C-C-U-G-AGGUAGUUGCUGC-UC--U-UUUGAUG---------------------------------------------------------------------------------AUUCAAAA-----AU-U-G-A-GGAGAGGAAAGUCCGGGCUC-C---ACG-GGAGAA-U-GG-UA----------------GCGGA------------UAACU----------------UCCGCCGGGC------------------------UUA------GCCCAGGA-CA---AGU-GCCACAGAAA--AUA--ACC-GCC----UG---U--U----------------------------------------------------------------------------------------------------------------------------UUU--U-U----C--A---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-U-C-G-CG-GCAA--CG-U-G-G-AUGG-CAUA----------------GGUAAAC-UCUACCA-GGAGCAAGACC-AAAC------------------------------A-GAA--G-AAGAGUG--------------------------------------------------UGCUCUC-GCGC----GAUAG--------AUUU---UU-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-AGUG-C-A-UAGUAAUGU-G--U-A-C-C-C--UAGAUGAAU-GACUACCG-----------------UA--------------------------------------------------------UACAGAACCCGGCUUA--U-GGGGCAC-CUCGUUUU
CP000142.2/3127195-3126800     GGAG-AG-C-G-C-C-A--GAUGAUCGUCGG-CU--C-GUUCCGUU-------------------------------------------------------------------------------UCGGCGGUA-----GC-G-G-G-CGGGAGGAAAGUCCGGGCUC-C---GCA--GGGCG-G-GA-UG----------------GUUCU------------UAACG----------------GGAACCGGGG-----------------------GUGA------CCCCAGGG-AC---AGU-GCCACAGAAA--GCAA-ACC-GCC----UG---U--CGAAGU-------------------------------------------------------------------------------------------------------------------CGAGGCUUGG-G----C--A---GGUAAGGGUGAAAC----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGUUC-C-G-A-CG-GCGA--CG-C-C-G-GAAG-C-UA----------------GGUAAAC-CCCAUCC-GGAGCAAGGCC-AAAU------------------------------AGGGA--A-GUGUUU----------------------------------------------------GAGGGCGGCCC----GUCCG-------AGACU---UC-C-----GGGU---U-----G---G-UUGC---------------------U--UGA-GGCC-G-U-CGGCAACGG-C--G-G-U-C-C--UAGAGGAAU-GAUCAUCG-----------------CCCUCCGUGCGGGUAACCGG-------------------------------CGGGGGGAACAGGACCCGGCUUA--C--GGUUCU-CUCCGGCC
AAMO01000002.1/442801-442402   ACGG-AG-G-G-C-C-G--GAUGGCCGCGGG-CC------------------------------------------------------------------------------------------------GGAA----------G-G-UCCGAGGAAAGUCCGGACUC-C---ACA-AGGCAA-A-GG-UG----------------CCGGG------------UAACG----------------CCCGGCGGGG-----------------------GCAA------CCCCAGGG-AA---AGC-GCCACAGAAA--ACAG-UCC-GCC----CC---G--CGGACCGGAGGUU-----------------------------------------------------------------------------------------------------CGCCGAAGGAUCAUCCG-C---CG--G---GGUCAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-G-A-C-GG-GCAA--CC-G-G-A-CCGG-C-AC----------------GGCAAGC-CCCACCU-GGAGCAAUGCC-GAAU------------------------------AGGGA--C-CUCGCGCGGGC-----------------------------------------GACCGCAGGGCCGUCUU----GGCCC-------GGAGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--UGAGGCGC-C-G-GGGCGAUCC-G--G-C-G-U-C--CAGAGGAAU-GGUCAUCG-----------------AACCGGGGGCGACCCCG--------------------------------------GGGAACAGAAUCCGGCUUA--C-AGGCCCU-CCGUGCGA
CP000512.1/850110-850447       GAAG-CG-C-G-C-C-A--GACCGCCGCUGG-UG--C-ACGUGC-----------------------------------------------------------------------------------CGAAAGG-----CC-G-C-A-CUGGAGGAACGUCCGGACUG-C---ACA--GGACG-G-CG-UA----------------GCAGC------------UAACG----------------GCUGUCCACC-----------------------GCGA------GGUGAGGA-UC---AGA-GCAACAGAGA--CGAG-UCC-G-------G---A--AGG-------------------------------------------------------------------------------------------------------------------------AGUGCCG---------------CAAGGCAGACCA----GCC--------------------------------------GG----GGU----------------GAAA------------------CG----------------GGCAAUC-UCUACGC-GCAGCAAUACC-AAGU------------------------------AGGCC--A-GCGUUG----------------------------------------------------ACGUGG---UU----CCGCG-------GAGCU---GG-C-----GGGU---A-----G---G-UAGC--------------------AU--CGA-GCCG-G-GUGGGCGACCC-C--C-G-G-C-C--CAGAGUAAU-GGCGGUCA-----------------CGUGCGGGCAACCGCA----------------------------------------UGCACAGAAUCCGGCUUA--U-CGGCGCG-CUUCACAC
AATP01000001.1/639443-638994   UCAG-CU-G-G-C-U-G--GGCGGCCGCUCC-CG--U-CAUGAGC----------------------------------------------------------------------------------CGAAAGG-----CG-G-C-G-GGAGAGGAAAGUCCGGGCUC-C---ACG-GAGAAA-C-GG-UG----------------CCGGA------------UAACC----------------UCCGGCGAGG-----------------------GAAA------CCUCAGGG-AA---AGC-GCCACAGAAA--ACAG-ACC-GCC----CC---G--CCUUCAGUUCGGCCGAGAGCCAUGGGA-------------------------------------------------------------------------ACGCAUGGGCGAUAGCCGGCCGCACUGAUGG-C----G--G---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGU-C-U-U-CG-GUAA--CG-A-A-G-GCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGA--C-GGCGCGGAUGGCGCAA--------------------------------GCCUUCCAUCAGCUCCG--------GGACA--------GCCG---UC-C-----GGGU---G-----G---G-UUGC---------------------U--CGA-GGCG-U-U-CCGCAAGGA-A--C-G-U-C-C--CAGAGGAAU-GGUCGCCG-----------------CGCAUGCGCCUUGACGGGUU--------------------------------CAUGCGUACAGAACCCGGCUUA--C-AGGCCGG-CUGACGCU
CP000251.1/4138335-4137926     GGAG-CC-G-C-C-C-G--GGCGAACGCGUC-GG--U-CCUGCA-----------------------------------------------------------------------------------GGGAAGG-----GG-G-C-C-GCCGAGGAAAGUCCGGGCAC-C---ACA--GGGCA-G-CG-UG----------------CCGGC------------CAACG----------------GCCGGUCGGG-----------------------GCGA------CCCGCAGG-AA---AGU-GCCACAGAGA--ACAG-ACC-GCCG-AACG---G--CGCCGG-------------------------------------------------------------------------------------------------------------------GCGACCGGCG-U---GC--G--UGGCAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-C-C-GG-GUGA--CC-G-G-C-GCGG-C-AC----------------GGCAAAC-CCCACGC-GGUGCAAGAGC-GAAU------------------------------AGGGA--G-GCGUCCCACCCGCGCG-------------------------------AGCGGGAGGGCAAGACCGGCCC----GGUCC-------AGGCC---UC-C-----GGGU---A----UG---C-UCGC---------------------U--GGA-GACG-C-G-CGGCAACGC-G--C-G-U-C-C--GAGAUGAAU-GUUCGUCG-----------------CCGCGGGGUUUCCCGC----------------------------------------GGAACAGAACCCGGCUUA--C-AGGGCGG-CUCCGGUC
CP000127.1/3251638-3251285     UGAG-AC-G-A-C-C-A--GACAGCCGCGUU-AC--C-UUGA----------------------------------------------------------------------------------------AUU------CA-G-G-U-AAUGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GUGA------GCUUACGG-AA---AGU-GCCGCAGAAA--AUAU-ACC-GCCU--AAG---C--GUC-------------------------------------------------------------------------------------------------------------------------UGCGGGC-G----C--C---GGUAAGGGUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-G-UG-GCAA--CA-CAC-C-GUGG-C-AA----------------GGUAAAC-CCCACUC-GGAGCAAGGCC-AAAU------------------------------AGAGG--A-ACAAA------------------------------------------------------GAUGUGGCCC----GCAUC---------GUU---CC-U-----GGGU---A-----G---G-CUGC---------------------U--UGA-GGUG-C-A-UGGUGACAU-G--U-A-U-C-C--CAGAUGAAU-GGCUGUCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGUCGU-CUCAAUCC
BX569689.1/147782-147396       GAAA-GC-A-G-G-C-G-AGGUGGUUGCGGU-CG--A-UCUCU--------------------------------------------------------------------------------------UUGAG-----UG-U-C-G-GCUGAGGAAAGUCCGGGCUC-CC-UGAU--GGCCA-G-GCUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAC--ACC-GCC----GA---U--GGCCCCGUGG-----------------------------------------------------------------------------------------------------------GGCUUCCCCCAGGC-A----C--A---GGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGCUGGGAGCAAGGCC-AAGG------------------------------AACGA--C-GGCUG------------------------------------------------------GCCAUUGGCC----CCGUU---------CCG---UC-U-----AAAC---G-----C---G-CCGC---------------------U--CGA-GGCC-G-U-CGGUAACGG-C--G-G-U-C-C--CAGAUAGAU-AGCCACCC-----------------ACCCUCUUCGGAGGCG----------------------------------------UGAACAGAACCCGGCUUA--U-GUCCUGC-UUUCACCC
CP000083.1/4670434-4669999     CGAG-UU-G-A-C-C-A--GACAAUCGCUGC-UU--U-AUCGUUGUAGUUUAAAUU------------------------------------------------------------UCGAUUUGAACUAAACAG-----AU-A-G-A-GGGGAGGAAAGUCCGGGCUC-C---AAU--GAGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGC-----------------------GUGA------GCCGACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCCG--AUG---G--CCG-------------------------------------------------------------------------------------------------------------------------CUUGCGG-A---AC--A---GGUAAGGCUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGAU-U-G-C-UG-GUAA--CA-G-U-A-AUUG-C-AG----------------GGUAAAC-UCCACCU-GGAGCAAGACC-AAAU------------------------------AGGGU--U-UCAUGAUUAUUAAAACGCA--------------------------AGUUUUGAUAAUAUAAGCGUGGCU----CGCGU--------GGAA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCUA-U-A-GAGCGAUUU-A--U-A-G-C-C--UAGACGAAU-GAUUGUCAUCUCU------UUUGCUUUUAGUAAAGGAGC--------------------------------------------UACAAAACCCGGCUUA--UGUGGUCAA-CUCAACUA
AAVO02000041.1/1066-715        CAAG-CA-G-G-U-C-A--GGUGAUCGCGGC-UG--U-ACAGAC------------------------------------------------------------------------------------GAAAGG-----GU-G-C-A-GACGAGGAAAGUCCGGGCUU-C---AAA--GGGCA-G-GA-UG----------------CCGGA------------UAACG----------------UCCGGUGGAG-----------------------GUGA------CUCCCAGA-CC---AGU-GCAACAGAAA--UAA--ACC-GCC----UU---C--U---------------------------------------------------------------------------------------------------------------------------UUAU--G-G----A--A---GGUAAGGGUGGAAA----GGC---AG-U--G--U----------------------AAGAG-ACUACC--GCCG-U-U-G-UG-GUAA--CA-G-A-A-CGGG-CACA----------------UGUAAAC-UCCAUUC-GAAGCAAGACC-GAAA------------------------------C-GAA--A-GCAAU------------------------------------------------------ACGGCUGCCC----GUCGU---------GCU---UU-C-----AGGU---G-----G---G-UCGC---------------------U--UGA-GCCA-U-C-UGGCAACGG-A--U-G-G-C-C--UAGACAGAU-GAUCACUC-----------------AAC-------------------------------------------------------GACAUAACCCGGCUUA--U-CGGUCUG-CUUGCAUA
AAQG01000002.1/124283-124671   CCAG-AG-G-G-C-C-G--GGCGGCCGCGGC-GU--G-GCGGG--------------------------------------------------------------------------------------UAACU-----UC-C-A-C-GGCGAGGAAAGUCCGGGCUU-C---ACG-AAAUGA-C-GG-UG----------------CCGGC------------UAACG----------------GCCGGCUGGA-----------------------GCGA------UCCAAGGG-AC---AGU-GCAACAGAAA--GCAG-GUC-GCU---AAG---G--CCU-----------------------------------------------------------------------------------------------------------------------------AGG-C----C--C---AGCGAAAUUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-C-U-G-CG-GCAA--CG-CAA-G-ACGG-C-AC----------------GGUAAAC-CCCACCG-GAAGCAAGACC-GAAU------------------------------AGGGG--C-GGCGCGCAGCGUCAUGC------------------------------UGCUAGGCAGAUUUCGG---------CCGAG--------ACCG---CC-C-----GGGU---U-----G---G-UUGC---------------------U--GGA-GGAA-C-G-GAGCAAUCC-G--U-U-C-C-C--UAGAGGAAU-GGUCGCCC-----------------AUCCUUCGCAAGAAGG----------------------------------------UGGACAGAACCCGGCUUA--C-AGGCCCU-CUGGCAUU
AAXB02000002.1/257265-256914   CAAG-UA-A-G-A-C-A--GGUAAUCGCAGC-UG--C-AGAUGC-----------------------------------------------------------------------------------CGAAAGG-----CA-G-C-A-GGUGAGGAAAGUCCGGGCUU-C---ACA--GGGCA-G-GA-UG----------------CCGGA------------UAACG----------------UCCGGUGGAG-----------------------GCGA------CUCCAAGG-AU---AGU-GCAACAGAAA--UAU--ACC-GCC----AG---G--AU---------------------------------------------------------------------------------------------------------------------------AUA-AU-U----C--U---GGUAAGGGUGGAAG----GGC---AG-U--G--U----------------------AAGAG-ACUACC--GCCU-U-G-C-UG-GUAA--CA-G-C-A-GGGG-CAUA----------------UGUAAAC-CCCAUUC-GAAGCAAGACC-GGAU------------------------------AA--A--G-ACAAU------------------------------------------------------GUGGCGGCCC----GUCAC---------GUC---UU-A------GGU---A-----G---G-UUGC---------------------U--UGA-ACCC-A-U-UGGUAACGA-U--G-G-G-U-C--UAGAAAGAU-GAUUACCC-----------------AAC-------------------------------------------------------GACAUAACCCGGCUUA--U-CGUUUUG-CUUGCAAU
AE015927.1/2135036-2134672     CGAG-UA-A-G-C-C-A--GACAGUCGCUGC-UG--U-AU-------------------------------------------------------------------------------------------AAU-----UU-A-C-A-GGAGAGGAAAGUCGGAGCUC-C---AUA--GAGCA-G-GG-UG----------------CUGGG------------UAACC----------------CCCAGUGGAG-----------------------GCGA------CUCUAAGG-AU---AGU-GCAACAGAGA--GAU--ACC-GCC----AA---A--GGUC----------------------------------------------------------------------------------------------------------------------UUGUAGACU-U----U--U---GGUAAGGGUGGAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCAC-A-C-U-G--GUGA---C-A-G-U-GUGG-C-UA----------------UGUAAAC-CCCACUU-GGAGCAAGAUC-AAAU------------------------------AGAGA--A-GCAGGGAGAUUA----------------------------------------ACUUCCAGGGGCUGCUC----GUCCC---------GCU---UC-C-----GGGU---A-----G--UA-UCGC---------------------U--AAA-GCCU-A-U-UGGCGACAA-U--A-G-G-C-U--UAGAUAGAU-GACUGUUU-----------------AA--------------------------------------------------------UACAGGACUCCGCUUA--U-AGACUUA-GUCGCUUA
AAOT01000013.1/60145-60517     GCGG-AU-G-G-C-U-G--GAUGACCGCGGG-C-------------------------------------------------------------------------------------------------UUCG------------G-CCCGAGGAAAGUCCGGACUC-C---GGC--AGGCA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCGGGG-----------------------GCGA------CCCCAGGG-AC---AGC-GCCACAGAGA--ACAG-ACC-GCC----CC---G--CA-------------------------------------------------------------------------------------------------------------------------------UG-C----G--G---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GGGG-A-C-C-GG-GCAA--CC-G-G-G-CCCG-C-AU----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-GAAU------------------------------AGGGG--C-CUCGCGCGGGGA---------------------------------------AACCCGCAGGGACGCCUG----CACCCG------AGAGG---CC-C-----GGGU---U-----G---G-CAGC---------------------U--GGAGGCGC-G-U-CGGCAACGG-C--G-C-G-U-C--GAGAGGAAU-GGUCAUCC-----------------AUCCGGGGGCGACCCCG--------------------------------------GGGGACAGAAUCCGGCUUA--C-AGGCCGU-CCGCGCAC
CP000248.1/3267249-3267659     CCAG-GG-G-G-C-C-G--GGCAGCCGCGUC-AU--C---------------------------------------------------------------------------------------------UCAC--------G-A-U-GCCGAGGAAAGUCCGGGCUC-C---ACG-AAACAA-G-GG-UG----------------GCGGG------------UAACG----------------CCCGCCGGGUC--------------------GGGCAAC---CGAUCAAGGG-AA---AGU-GCCACAGAGA--GCAG-ACC-GCC----GC---U--CCGGUC-------------------------------------------------------------------------------------------------------------------UUCGGACCCA-G----G--C---GGCAAGGGUGAAAG----GGU---GC-G--G--C----------------------AAGAG-CGCACC--GCGC-G-A-C-CG-GCAA--CG-G-A-A-GCGG-C-AC----------------GGCAAAC-CCCACCC-GGAGCAAGAUC-GAAU------------------------------AGGGA--C-UGCGCGCCCAGC---------------------------------------AAUGGGCAGGCCGGUUUC----GGGCC-------AGCAG---UC-C-----GGGU---U-----G---A-UUGC---------------------U--UGA-GCGU-U-C-CGGCAACGG-U--C-C-G-C-C--UAGAGGAAU-GGCUGCCA-----------------GCGGCGAUACGGUCCACUCGUGGGA---------------------UACCGUCGGCGCUACAGAACCCGGCUUA--C-AGGCCCC-CUGGCACU
ABCG01000012.1/35715-35319     CCAG-GG-G-G-C-C-G--GGCAGCCGCGUG-AU------------------------------------------------------------------------------------------------UUCG----------A-U-UGCGAGGAAAGUCCGGGCUC-C---ACG-AAACAA-G-GG-UG----------------GCGGG------------UAACG----------------CCCGCCGUGG-----------------------GCAA------CCACAGGG-AA---AGU-GCCACAGAGA--GCAU-ACC-GCCG-AUGG---C--CCG-------------------------------------------------------------------------------------------------------------------------UUCACGG-G---AU--C--AGGCAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGGG-C-U-U-CG-GUAA--CG-C-G-G-UCCG-C-AU----------------GGCAAAC-CCCACCC-GGAGCAAGGCC-GAAU------------------------------AGGGG--C-GGCGCGCUGGC-----------------------------------------AACAGCAGGUGCGUUUC----GCAUC-------GACCG---CC-C-----GGGU---U-----G---G-CUGC---------------------U--CGA-GCCC-U-G-GAGCAAUCC-A--G-G-G-C-C--CAGACGAAU-GGCUGCCG-----------------CCGCGCGGCUGGUGUGGAAGCAUA------------------------CCGCGUGCGGAACAGAACCCGGCUUA--C-AGGCCCC-CUGGCACU
CP000157.1/276357-276760       CCAG-GG-G-G-C-C-G--GGCAGCCGCUCC-UU--C-GACAAGCUCAG--------------------------------------------------------------------------GAUGAGCGGGU-----UG-U-U-A-GGAGAGGAAAGUCCGGGCUC-C---ACG-AAGCAA-G-GG-UG----------------GCGGG------------UAACA----------------CCCGCCCGGUGACCCCGGA----UUACGUCCGGGGGA------GCCGAGGG-AC---AGU-GCCACAGAGA--GCAG-ACC-GCC----UG---A------------------------------------------------------------------------------------------------------------------------------UCCG----U----C--A---GGCAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGGG-G-G-C-UG-GCGA--CA-G-U-C-UCCG-C-AU----------------GGCAAAC-CCCACCC-GGAGCAAGGCC-AAAU------------------------------AGGGA--C-CUCGCGCCGA-------------------------------------------AAGGCAGGAACGCUUC----GUUCCG------AGAGG---UC-C-----GGGU---U-----G---G-CUGC---------------------U--UGA-GCGC-G-C-GAGCAAUCG-C--U-C-G-C-C--CAGAUGAAU-GGCUGCCC-----------------CUGCAUCAGCAG----------------------------------------------GACAGAACCCGGCUUA--C-AGGCCCC-CUGGCACU
AAYW02000004.1/35153-34803     UGAG-CU-G-G-A-C-A--AGUGAUCGCGGC-UG--U-CAUA-------------------------------------------------------------------------------------------------UG-A-C-A-GGUGAGGAAAGUCCGGGCUU-C---GCA--GGGCA-G-GG-UG----------------CCGGA------------UAACG----------------UCCGGUGGAG-----------------------GAAA------CUCCCAGG-CU---AGU-GCAACAGAAA--UAA--ACC-GCC----AU---G--U---------------------------------------------------------------------------------------------------------------------------------A-C----A--U---GGUAAGGGUGGAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC--GCUGCU-U-C-UG-GUAA--CA-G-A-A-CAGG-C-UC----------------UGUAAAC-CCCACUC-GAAGCAAGACC-AAAAAAGCA--------------------GCUUCGGCUG--U-GAGACG----------------------------------------------------AAUGGCUGCCC----GUCAA--------GUCU---CA-G-------GU---A-----G---G-UCGC---------------------U--UGA-GCUU-U-A-UGGUAACAU-A--A-A-G-C-C--UAGAUAGAU-GAUCACUC-----------------UC--------------------------------------------------------GACAUAACCCGGCUUA--U-CGUCCAG-CUUUUAUA
CP000529.1/3654859-3654532     GAAG-CC-U-G-C-C-A--GACCGCCGCUGG-UG--C-AAUUUC-----------------------------------------------------------------------------------CGAAAGG-----AA-G-C-A-CUGGAGGAACGUCCGGACUG-C---ACA--GGACA-G-CG-UA----------------GGAGG------------UAAUA----------------CCUCUCCACC-----------------------GUGA------GGUGAGGA-UC---AGA-GCAACAGAGA--CGAG--CC----------------GAU-------------------------------------------------------------------------------------------------------------------------UCAGUUC------------------GGGUGAAAC----------------------------------------------G---------------------------------------------------------------GGCAAUC-UCUACGC-GCAGCAACACC-AAAU------------------------------AGGCC--A-GCGUUG----------------------------------------------------ACGUGG---UU----CCGCG-------GAGCU---GG-C-----GGGU---A-----G---G-UGGC--------------------AC--CGA-GCCG-G-GCAGGCGACUC-C--C-G-G-C-C--CAGAUUAAU-GGCGGUCA-----------------CACCGGGCAACCGAAAGGAAG------------------------------CCAGGCGCACAAAAUCCGGCUUA--U-CGGCGGG-CUUCACAC
AAMQ01000001.1/822672-822270   UCAG-AG-G-G-C-C-G--GGCGGCCGCUGC-UG--C-GAGAGG-----------------------------------------------------------------------------------GGAAACC-----CU-G-C-A-GGAGAGGAAAGUCCGGGCUC-C---AUG-GAGGCA-A-GG-CG----------------CCGGG------------GAAAU----------------CCCGGCGGGCCGG-----------------UUCGCCG------GUUCAGGG-AC---AGC-GCCGCAGAAA--UCAG-ACC-GCC----GC---A--C---------------------------------------------------------------------------------------------------------------------------UCAG--G-U----G--C---GGCAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCCC-C-G-A-CC-GCAA--GG-A-A-G-GGGG-C-AC----------------GGCAAGC-CCCGCCU-GGAGCAAGACC-GAAU------------------------------AGGGA--C-CCGCGCUGUGCUUC------------------------------------GGCGCAGCAGACGCGCCUC---CGCGUC--------GAGG---UC-C-----GGGU---A-----G---G-UUGC---------------------U--GGA-GGCG-U-C-GUGCAAGCG-G--C-G-U-C-C--UAGAGGAAU-GGUCGCCC-----------------CCGGUCAUCACAUGGGAUG---------------------------------ACAUGGGACAGAACCCGGCUUA--C-AGGCCCU-CUGAUCCU
CP000481.1/999499-999917       CGAG-CC-G-G-C-C-G--GGCGGCCGCGUC-GG--G-CCACGGU---------------------------------------------------------------------------------GCGCCGUG-----GA-C-C-C-GCCGAGGAAGGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------GUGGG------------UAACA----------------CCCACCCGGG-----------------------GCGA------CCCGCGGG-AU---AGU-GCCACAGAAA--ACAG-ACC-GCC----GC---G--CAGCCGG----------------------------------------------------------------------------------------------------------------CGCCUGCCGCUG-C----G--C---GGUAAGGGUGAAAC----GGC---GG-U--G--U----------------------AAGAG-ACCACC-AGCGC-C-C-G-GG-GUGA--CC-C-G-G-GCGG-C-UC----------------GGCAAAC-CCCACCC-GGAGCAAGGUC-AAGAGGCGGCGGACGCCGAUGGGCGGCCGCCGCUGCGCA--G-GCGCUC----------------------------------------------------GAGGACGGCCC----GUCCG-------AUGCC---UG-C-----GGGU---G-----G---A-CCGC---------------------U--GGA-GGUU-G-C-CGGCAACGG-C--A-G-C-C-C--AAGAGAGAU-GGCCGCCC-----------------GUCGCGGAUGACCGCG----------------------------------------ACGACAGAACCCGGCCUA--C-AGGCCGA-CUCGCCCG
EU020111.1/1-345               UC--------------G--GG-AUCCG--------------------------------------------------------------------------------------------------------GGG------------------AGGAAAGUCCGGGCUC-C---AUG-GAAAAA-C-GG-UG----------------CCGGG------------UAACA----------------CCCGGCGGGG-----------------------GUGA------CCCUAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----UA---U-------------------------------------------------------------------------------------------------------------------------------UUC----A----U--A---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGC-A-C-U-CA-GUAA--UG-A-G-U-GUGG-C-AA----------------GGUAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGAAA--U-GACGUGCAAGAUUU------------------------------------UACUUGCAGCCAGUUUCCA----GGUGA--------GUCA---UU-U-----GGGU---A-----G---G-UUGC---------------------A--CGA-GGCG-G-A-UGGUAACAU-C--C-G-U-C-C--CAGAUGAAU-GGUUGCCA-----------------UGUAGAGUGUAAACUUU-------------------------------------ACCAUACAGAACCCGGCUUA--C-----------GAAUUC
AAUX01000001.1/371828-372118   CAAG-UU-G-A-C-U-A--GACAGUCGCUAU-AU--A-U-------------------------------------------------------------------------------------------GCAA------A-U-A-U-AUAGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-A-AG-UG----------------AUGGC------------UAACA----------------GCCAUACGCC-----------------------GUGA------GGCGAGGA-AU---AGG-GCCACAGAGA--CGAG--CG----------------UAU-------------------------------------------------------------------------------------------------------------------------UAAGUUA------------------CGGUGAAAC--------------------------------------------------------G---------------------------------C-------------------GGUAACC-UCCACUU-GGAGCAAGGCC-AAAU------------------------------AGGGU--A-GCAUU------------------------------------------------------GGCACGGCUC----GUGUC---------GCU---AC-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GUGC-A-U-AAGUAAUUG-U--G-C-A-A-C--UAGAUGAAU-GACUGUCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGUCAA-CUUAACCU
AP006618.1/1794140-1794557     CGAG-UU-G-G-U-C-G--GGCGGCCGCGGC-GA--C-GGGAACGGGCACG----------------------------------------------------------------------CUGGUGUCGCAGC-----CC-G-G-C-GCCGAGGAAAGUCCGGACUC-C---ACA--GAGCA-G-GG-CG----------------GUUGC------------UAACG----------------GCAACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCCC--ACG---G--CCC-------------------------------------------------------------------------------------------------------------------------UGCGGGG-C----C--GUGCGGUGAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGC-C-C-C-GG-GUGA--CC-G-G-G-GCGG-C-UC----------------GGUAAAC-CCCGCCC-GGAGCAAGGUC-GAAGGUCGCAUUCGUU-----CGCGAGUGCGGCUGCGCA--G-GCGCUC----------------------------------------------------GAGGGCUGCUC----GCCCG--------AGCC---UG-C-----GGGU---G-----G---A-CCGC---------------------U--CGA-GGCA-C-C-CGGCGACGGUG--U-G-C-C----CAGAUGGAU-GGCCGCCA-----------------CCCGGUGCGAACCGG------------------------------------------GGACAGGAUCCGGCUUA--C-AGACCAA-CUCGUCCG
CP000471.1/942511-942148       GAAG-CG-G-G-U-U-G--GGUGAUCGCCGG-UG--U-UC------------------------------------------------------------------------------------------CUUG-----GA-A-C-A-CGGGAGGAAAGUCCGGGCUC-C----GU--UAAAA-G-GG-UG----------------CCGGG------------UAAUC----------------CCCGGCGGGG-----------------------GAAA------CCCCAGGG-AA---AGU-GCCACAGAGA--GCAG-ACC-GCC----GG---CCAGGA-------------------------------------------------------------------------------------------------------------------------GCAAUCC-G----C--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-GCA-C-CG-GUAA--CG-G-U-C-ACGG-C-AU----------------GGUAAAC-CCCACCU-GGAGCAAGGCC-AAAU------------------------------AGGGG--G-CGCUUG----------------------------------------------------A----------------------------CGC---CC-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GACC-U-A-CGGUAACGU-A--G-G-U-C-C--UAGAUGAAU-GAUCACCG-----------------CUGCGCCCUCCUGGGAACAG-------------------------------GGCGCAACACAGAACCCGGCUUA--C-AGACCCG-CUUCGGCC
AAYC01000006.1/234663-234257   GCAG-AA-G-G-C-U-G--GACGGCCGCUUU-CA--G-AGGG----------------------------------------------------------------------------------------UCAC----CCU-U-U-G-CGAGAGGAAAGUCCGGACUC-C---AUA-AAGCAA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGGCGGG-----------------------GGAA------CCCGACGG-AA---AGC-GCCACAGAAA--UGAA-ACC-GCC----UG---C------------------------------------------------------------------------------------------------------------------------------UUUU----G----C--A---GGUAAGGGUGAAAC----GGU---GG-A--G--U----------------------AAGAG-ACCACC--GCGC-C-C-C-UG-GCAA--CA-G-G-G-GUGG-C-AA----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGU--C-CCCGCGCGGGCAGGUCGGAGCAA------------------UCCGAAACCGCCGCUAGGCGCGCUUUAG----CCGAG--------AGGG---AC-C-----GGGU---U-----G---G-CAGC---------------------U--AGA-GGUG-C-A-UAGCAAUGU-G--C-A-U-C-G--CAGAUGAAU-GGUCGUCG-----------------AUCCCGGAGCCAUGGCUCC----------------------------------GGGGGGACAAAAUCCGGCUUA--C-AGGCCUU-CUGCGCAG
CP000679.1/2264216-2263857     CGAG-CA-G-G-U-C-G--AACGGCUGCGCA-AG--G-UGAAA-------------------------------------------------------------------------------------GUUUUU-----CA-C-C-U-UGUGAGGAAAGUCCGAGCUC-C---GCA--GGGCA-G-GG-UG----------------CCGGG------------UAACA----------------CCCGGUGGAG-----------------------GCGA------CUCCAAGG-AA---AGU-GCAACAGAAA--AGA--ACC-GCC----AU---C--CACA----------------------------------------------------------------------------------------------------------------------UUUUUGGUG-G----G--U---GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCAG-U-U-A-G--GCGA---C-U-A-A-CUGG-C-UG----------------UGCAAAC-CCCACCU-GGAGCAAGACC-AAAU------------------------------AGGGG--A-ACAAU------------------------------------------------------GCAGUGGCCC----GCUGC---------GUU---CC-C-----GGGU---U-----G---G-UCGC---------------------UUAUGA-GUCU-G-A-UGGUAACAU-C--A-G-A-C-CAAAAGAGAAAU-AGCCGUUC-----------------UC--------------------------------------------------------GACAGAACUCGGCUUA--C-AGACCUG-GUCGCACU
AANB01000016.1/41201-41624     GCAG-AA-G-G-C-U-G--GACGACCGCGCU-AA--G-GG------------------------------------------------------------------------------------------CUUG-----CC-C-C-U-UGCGAGGAAAGUCCGGACUC-C---CUA-AAGCAA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGGCGGG-----------------------GUAA------CUCGACGG-AU---AGC-GCCACAGAAA--CAA--ACC-GCC----AU---G--CCGCGGGGGCCUU-----------------------------------------------------------------------------------------------------CGGGCAACCGUAUCCGG-U----U--U---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGC-C-G-C-UG-GCAA--CA-G-G-G-GUGG-C-AA----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGU--C-CCCGUGUGGGAGAGAGCGGCGUU-----------------GGCCGAUCUCGCCACUAGGCUUGCUUUAG----CCGAG--------AGGG---AC-C-----GGGU---U-----G---G-CAGC---------------------U--AGA-GGUG-C-A-UAGCAAUAU-G--U-A-C-C-G--CAGAGGAAU-GGUCGUCU-----------------AAGGAGCGAAAGCUCU----------------------------------------GGGACAAAAUCCGGCUUA--C-AGGCCUU-CUGCGCAU
AE014295.3/328247-327873       UGAG-AC-C-U-C-U-U--GAUGGCCGCGGC-CG--U-GAUCUU------------------------------------------------------------------------------------CAUUGG-----GA-U-C-G-GCUGAGGAACUUCCGGGCUC-C---AUA--GAGCA-C-GA-UG----------------GCGGA------------UAACG----------------UCCGCCCAGG-----------------------GUGA------CCUGAGAG-AU---AGC-GCAACAGAGA--ACAG-ACC-GCC----CG---U--C----------------------------------------------------------------------------------------------------------------------------CUC--G-A----C--G---GGUAAGGGUGAAAC----GGC---GG-U--G--U----------------------AAGAG-ACCACC--GGGC-C-U-C-UG-GUAA--CA-GUA-G-GUCG-C-AU----------------GGCAAGC-CUCAUCG-GGAGCAAGGCC-AAGC------------------------------A-GAU--G-GCGGU-----------------------------------------------------AAGGGCUGCUC----GCCCG--------UGUC---AU-C-----GGGU---A-----G---G-CUGC---------------------U--AGA-GCCU-G-G-CGGUAACGU-C--A-G-G-U-C--GAGAUGGAU-GGCCAUCC-----------------GUGCCGUGCGUUCGCGCAC----------------------------------GGCACGACAGAACCCGGGGUA--U-AAGAGGU-CUCAUUUU
CP000325.1/1422068-1422493     CGAG-UU-G-G-C-U-G--GGCGGCCGCGGC-UC--G-GGUUGGGCUCGUGU-------------------------------------------------------------------UGUCACGAGUUCAGC-----GC-C-G-A-AUCGAGGAAAGUCCGGACUU-C---ACA--GAGCU-G-GG-UG----------------AUUGC------------UAACA----------------GCAAUCCGAG-----------------------GUGA------CUCGCGGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----AC---C--C----------------------------------------------------------------------------------------------------------------------------UCG--C-G----G--U---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAC-C-C-C-GG-GUGA--CC-G-G-G-GUGG-C-UA----------------GGCAAAC-CCCACCC-GAAGCAAGGUC-AAGA------------------------------AGGCC--GUACCGUAGGUGCGGCUG-------------------------------CGCAGGCGUUUGAGGGCUGCUC----GCCCG--------AGUC---UG-C-----GGGU---A-----G---G-CCGC---------------------U--CGA-GGUA-C-C-CGGCAACGGUG--U-G-C-C----CAGAUGGAU-GGUCGCCG-----------------CCGCGCCGCCGCUGGUUCAGCCGC------------------------GGCGGUGUGGAACAGAAUCCGGCUUA--C-AGGCCAA-CUCGUCCG
AP009256.1/1270382-1270746     UGAG-AC-C-U-C-U-U--GAUGGCCGCGAC-CG--A-UUU--------------------------------------------------------------------------------------------------UG-U-C-G-GUUGAGGAACUUCCGGGCUC-C---AUA--GAGCA-C-GA-UG----------------GCGGA------------UAACG----------------UCCGCCCAGG-----------------------GCGA------CCUGAGAG-AU---AGC-GCAGCAGAGA--AUAG-ACC-GCCU--UAC---C--GGU-------------------------------------------------------------------------------------------------------------------------UUCGGCC-G----G--U--GGGUAAGGGUGAAAC----GGC---GG-U--G--U----------------------AAGAG-ACCACC--GGGC-C-G-C-UG-GUGA--CA-GUU-G-GCCG-C-AU----------------GGCAAGC-CUCAUCG-GGAGCAAGGCC-AAGC------------------------------A-GAA--G-GCGUUC----------------------------------------------------GAGGACUGCUC----GUCCG-------AAGCC---UU-C-----GGGU---A-----G---G-CUGC---------------------U--AGA-GCCU-G-A-CGGCAACGC-C--A-G-G-U-C--GAGAUGGAU-GGCCAUCC-----------------GUGCCGUUGGCAC---------------------------------------------GACAGAACCCGGGGUA--U-AAGAGGU-CUCACUCU
AE017125.1/560403-560066       UAGG-CA-U-A-G-U-A--GGUGGUUGCUUU-UG------------------------------------------------------------------------------------------------AUUA----------C-A-AAAGAGGAAAGUCCGAGCUA-C----AA--AGACA-G-GA-UU----------------CCAUU------------UAACG----------------AAUGGCUAGG-----------------------GUAA------CCUAAGGG-AA---AGU-GCAACAGAAA--AUU--ACC-GCC----UU---A--UAGAAU-------------------------------------------------------------------------------------------------------------------CUUAAGAUCU-U----A--A---GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC--GGUC-U-U-U-CA-GCAA--UG-U-U-A-GGCGUC-UA----------------UGCAAAC-CCAAUUC-GUAGCAAGAAG-AAUA------------------------------UGGU--------UAA----------------------------------------------------AGUCUU---------AAGAU--------A-------A-U-----AAAU---U-----C---U-UCGC---------------------U--UGA-GAUA-U-G-UUGUGAAAC-A--U-A-U-C-C--UAGAUAAAU-AGCCACCC-----------------AC--------------------------------------------------------GACAGAACUCGGCUUA--U-CGCUAUG-CCUAUUUU
CP000143.1/890735-891132       GCGG-GU-G-G-C-C-G--GAUGACCGCGAG-CC------------------------------------------------------------------------------------------------UUCG----------G-G-CGCGAGGAAAGUCCGGACUC-C---AUG--GGACAAG-GG-UG----------------CCGGG------------UAACG----------------CCCGGCCGGG-----------------------GCAA------CCCGAGGG-AA---AGC-GCCACAGAGA--ACAG-ACC-GCCC-CACC---G--GCC-------------------------------------------------------------------------------------------------------------------------UUCGGGC-C----C--G--GGGCAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-G-A-C-UG-GCAA--CA-G-G-A-CCGG-C-AU----------------GGCAAGC-CCCACCC-GGAGCAAUGCC-GAAU------------------------------AGGGG--U-UCCGCGCGGGCCUGAUCCUUC----------------------CGGGGAUAUCGCCGCAGGGACGUCUC----AGCCCG------AGGAA---CC-C-----GGGU---U-----G---G-CAGC---------------------U--CGA-UCCC-G-U-CGGCAACGG-C--G-G-G-G-C--CAGAGGAAU-GGUCAUCG-----------------AAGGGGGCAACCCCG------------------------------------------GAACAGAAUCCGGCUUA--C-AGGCUGC-CCGCACAA
AE014184.1/342276-342626       GAGG-GC-U-U-G-C-G--GGCGGUCGCGGU-GU--C-UA---------------------------------------------------------------------------------------------------UU-G-G-U-ACCGAGGAACGUCCGGGCUC-C---GUA--GAGCA-A-GG-CG----------------GUGGG------------UAACG----------------CCCACCCGGG-----------------------GUGA------CCCGAGAG-CU--GAGU-GCCACAGAAA--AUA--ACC-GCC----G------------------------------------------------------------------------------------------------------------------------------------UUA------------C---GGUAAGGGUGAAAA----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGGGA-U-U-G-GG-GUGA--CC-C-A-A-UCUG-C-UG----------------GGUAAAC-CUCGCCU-GGAGCAAGAUC-AAGC------------------------------A-GGG--A-ACU--------------------------------------------------------UAGGCUGCUC----GUUUA---------GUU---CC-C-----GGGU---A-----G---A-UCGC---------------------U--AGA-GCCU-G-U-UGGCAACAA-C--A-G-G-U-C--AAGAUGGAU-GGCCGCCU-----------------CGUUGGUUUUUAAUCCA--------------------------------------ACGAACAGAACCCGGCGUA--U-AGCAAGC-CCUCGUUC
BX572604.1/165137-165616       C-AG-UC-G-G-C-C-G--GACGGCCGCUCC-GG--C-AAGUGC-----------------------------------------------------------------------------------CGAAAGG-----CC-G-C-C-GGGGAGGAAAGUCCGGGCUC-C---AUC-GACAUA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAGA--ACGA-ACC-GCC----CG---C--CUUCGCAGCUUCGCUGCUUCGGCGCGGCAAGC--------------------------------------------------------------CCUCGGGCUCGCUGCGCCAUAACCCGCAAGGGUGAAG-G----C--G---AGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-C-G-C-CG-GCAA--CG-G-G-G-ACGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-GGCAUCGCGGAUAGUUCGCUGCU------------------CGCAGCGAUAACUCCGCAGGGCGAUGUC---AGGCUC--------GCCG---UC-C-----GGGU---A-----G---G-UUGC---------------------U--CGA-GGCG-C-U-GUGCAAACA-G--U-G-U-C-C--CAGAGGAAU-GGCCGUCG-----------------CGCAUCGCCUCCGCAAGGAAG-----------------------------CGGUGCCCUCCAGAACCCGGCUUA--C-AGGCCGG-CU-GAUAC
CP000551.1/1546351-1546728     AAAG-CA-G-G-A-G-A--GGCAAUCGCAAG-AA--A-GUUUUAUUUUGU------------------------------------------------------------------------UUCCAAAAUAAA-----AC-U-U-U-CUUGAGGAAAGUCCGGGCUC-C--CACA-UGGUCA-G-GCUUG----------------CUGGG------------UAAUU----------------CCCAGUGCGG-----------------------GCAA------CCGUGAGG-AU---AGU-GCCACAGAAA--CAU--ACC-GCC----UA---A--UAC------------------------------------------------------------------------------------------------------------------------UUUAUGUA-U-----------GGCAAGGGUGCAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-A-U-U--GAGA---A-G-U-G-UUGG-C-UA----------------GGUAAAC-CCCGGCUGGGAGCAAGGCU-UA----------------------------------GUA--G-AU---------------------------------------------------------UUAUGACCAU----UACAA--------AAUC---UA-C-----UUUU---A-----AG-CG-CCGC---------------------U--UGA-GACU-GUG-AAGUAAUUC-C--A-G-U-C-C--UAGAUAGAU-GAUUGCCC-----------------AUCUUUAUUAAGAU-------------------------------------------GAACAGAACCCGGCUUA--U--GACCUG-CUUUCUAA
AALY01000001.1/401433-401027   GCGG-AG-G-G-G-C-G--GAUGGCCGCGGG-GU--C-UG------------------------------------------------------------------------------------------GCAA-----CA-G-G-C-CGCGAGGAAAGUCCGGACUC-C---ACA-AGGCAA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCCGGG-----------------------GCAA------CCCGAGGG-AA---AGC-GCCACAGAGA--ACAG-ACU-GCU----CC---G--GCA-----------------------------------------------------------------------------------------------------------------------------UGC-C----G--G---AGUGAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GGGG-G-G-C-UG-GUAA--CA-G-U-C-CCCG-C-AU----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-GAAU------------------------------AGGGA--U-CGCGCGCGGGGCCGGUCGGGC----------------------AACCGAUACCGCCCGCAGGCCGCCUU----GGCCCA------GCAGA---UC-C-----GGGU---U-----G---G-CAGC---------------------U--AGAGGCCG-C-A-UGGCAACAU-G--U-G-G-C-C--AAGAUGAAU-GGUCAUCU-----------------CGGGCAGCGUCUUUGGCGCU--------------------------------GUCUAUGACAGAAUCCGGCUUA--U-AGCCCCU-CCGCGCAU
ABCL01000002.1/247411-247824   GCGG-AG-G-G-C-C-G--GAUGGCCGCGGC-AC--C-U-------------------------------------------------------------------------------------------GCAA------G-G-G-U-GUCGAGGAAAGUCCGGACUC-C---ACA-AGACAA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCUGGG-----------------------GUAA------CCCAAGGG-AA---AGC-GCCACAGAGA--AGAG-ACC-GCC----CC---A--GA--------------------------------------------------------------------------------------------------------------------------GUGA-UC-U----G--A---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-G-A-C-GG-GCAA--CC-G-G-A-CCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGA--C-CGCGCGCGGGGGCUGGUCCUGGACCC------------UGGUCCGGGAUACCGCCCGCAGGCACGUCUU----GGCCC-------GGCGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--AGAGGGGC-G-U-UGGCAACAG-C--G-U-C-C-C--AAGAGGAAU-GGUCAUCC-----------------AGCCUCGGAUUACGGUCCG----------------------------------GGGUGGACAGAAUCCGGCUUA--C-AGGCUCU-CCGCGCCC
CP000377.1/2017757-2017331     GCAG-AG-A-G-C-C-G--GAUGGCCGCGUU-GG--G-GC------------------------------------------------------------------------------------------AUCU-----GC-C-C-C-CGCGAGGAAAGUCCGGACUC-C---CUG-AAACGA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGGCAGG-----------------------GCAA------CCUGACGG-AA---AGC-GCCACAGAAA--AGAG-ACC-GCC----UC---G--CCGCUCUGGAGG------------------------------------------------------------------------------------------------------UUCGCCAAAGGAUGCGA-C----G--G---GGUAAGGAUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCAC-C-G-C-UG-GCAA--CA-G-G-G-GUGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGC--C-UCCGCGCGGGCAGGUCGGGCA----------------------ACCGAAACCGCCGCUAGGGAUGUUUC----ACCCGA------GAGAG---GC-C-----GGGU---U-----G---G-CAGC---------------------U--AGA-GAUG-U-C-CGGCAACGG-G--C-A-U-C-C--CAGAAGAAU-GGUCAUCG-----------------AACCCUGUCUUUUGGGGCA----------------------------------GGGGGAACAAGAUCCGGCUUA--U-AGGCUCU-CUGCGCAA
AAMV01000002.1/534098-534529   GCGG-AG-G-G-C-C-G--GAUGGCCGCGGC-AU--C-CCCC----------------------------------------------------------------------------------------AAA------GG-G-G-U-GACGAGGAAAGUCCGGACUC-C---ACA-AGACAA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCUGGG-----------------------GUAA------CCCAAGGG-AA---AGC-GCCACAGAGA--AGAA-ACC-GCC----CG---U--CGCACCUGCGGUU-----------------------------------------------------------------------------------------------------CGCCAAGGGAGACUGCGCA----C--G---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-G-A-C-GG-GCAA--CC-G-G-A-CCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGA--C-CGCGCGUGGGGACAGGUCGGGC--------------------AACCGAUACCGCCCGCAGGCACGUCUU----GGCCC-------GGCGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--AGAGGGGC-G-U-UGGCAACAA-C--G-U-C-U-C--AAGAGGAAU-GGUCAUCC-----------------AACCCCGGAUCACGGUCCG----------------------------------GGGUGGACAGAAUCCGGCUUA--U-AGGCCCU-CCGCGCGC
BX248583.1/58173-58588         GAAG-CU-G-A-C-C-A--GGCAAUCGCUGC-UU--U-UCUAGACUGUUUUAUUUUUAUACUAUGAAA-----------------------------------AUUGGAGUAUGUUGAUAGUUAGUAAGUAUAG-----AG-A-A-A-GGAGAGGAAAGUCCGGGCUC-C---GUA--GGACA-A-AG-UG----------------CCAGG------------UAACU----------------CCUGGGAGAU-----------------------GUGA------AUCUACGA-CA---AGU-GCAACAGAAA--AAA--ACC-GCUA-AAUG---U--UAUUAU-------------------------------------------------------------------------------------------------------------------GAAAUUAAUA-A----U--AA-AAGUAAGGGUGAAAA----GGU---GU-G--G--U----------------------AAGAG-CGCACC--AUAC-A-A-U-UG-GUAA--CA-AUU-U-GUAG-U-AA----------------UGUAAAC-UCCACUU-GGAGCAAGGCU-AAAU------------------------------AGAAG--U-UCUAU------------------------------------------------------AGUAUAGUCC----GUACU---------GAA---CU-U-----GGGU---A-----A---G-CCGC---------------------U--GUA-GUUU-U-U-AUGUGAAUA-A--A-A-A-C-A--UAGAUGAAU-GAUUGCCC-----------------GU--------------------------------------------------------GACAGAACCCGGCUUA--U-AGGUCAG-CUUAUAUA
AAMW01000001.1/77138-77556     CAGG-GA-G-C-C-G-A--GGCAACCGCGUG-GU------------------------------------------------------------------------------------------------UUCG----------A-C-CGCGAGGAAAGUCCGGGCUC-C---ACG-AAGCAA-G-GG-UG----------------GCGGG------------UAACG----------------CCCGCCGGGUGAGGCU-----------UUCGGGCUGA------GCUCAGGG-AA---AGU-GCCACAGAGA--GUAU-ACC-GCCG--AUG---G--AGG------------------------------------------------------------------------------------------------------------------------UCGAACCU-C---AC--A---GGCAAGGGUGAAAG----GGU---GC-G--G--C----------------------AAGAG-CGCACC--GGGG-G-U-C-UG-GCAA--CA-G-G-C-UCCG-C-AU----------------GGCAAAC-CCCACCC-GGAGCAAGGCC-AAAU------------------------------AGGGG--C-CUCGCGCCCGACCAGAU------------------------------ACGGUCAGGGCAGGAGCGCUUC----GCUCCG------AGAGG---CC-C-----GGGU---U-----G---G-CUGC---------------------U--UGA-GCCG-C-G-UGGCAACAU-G--C-G-G-C-C--CAGAUGAAU-GGUUGCCG-----------------CCGCGGCGCUGGUCGAAAGAUAC-------------------------CGGUCGCGGAGACAGAACCCGGCUUA--U-GACGCUC-CCUGAUGC
AALZ01000008.1/147793-148204   GCGG-AA-G-G-C-U-G--GAUGGCCGCGGU-CU--U-G-------------------------------------------------------------------------------------------GCAA------C-A-G-G-GUCGAGGAAAGUCCGGACUC-C--CAGA--AGAAA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGGCGGG-----------------------GUAA------CCCGACGG-AA---AGC-GCCACAGAAA--ACAG-ACC-GCC----GC---U--UCGACGGGUCGG------------------------------------------------------------------------------------------------------GCAACCGAUACCACCGG-G----G--A---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-A-G-G-UG-GUAA--CA-U-C-U-CUGG-C-AA----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGA--C-CGCGCGCCGCGUCUGGC------------------------------AACAGGCAAGGCGGGGCCACUUC--UGCCCCA------GCAGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--GUAGCUGU-G-C-AGGCAACUG-C--A-U-G-G-U--CAGAGGAAU-GGUCAUCC-----------------CCUGUCGCAAGGCGG------------------------------------------GGACAAAAUCCGGCUUA--U-AGGCCUU-CCGCGCAU
AATQ01000007.1/49807-50210     GUGG-AG-G-G-C-U-G--GGCGGCCGCCGC-CU--U-CGGGG--------------------------------------------------------------------------------------UGACC-----CG-U-C-G-GGGGAGGAAAGUCCGGACUCAC---CGA--AGCGC-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGGCAGG-----------------------GCAA------CCUGACGG-AC---AGC-GCCACAGAGA--ACAG-ACC-GCC----GU---C--C---------------------------------------------------------------------------------------------------------------------------UUCG--G-G----G--C---GGUAAGGGUGAAAC----GGU---GG-A--G--U----------------------AAGAG-ACCACC--GGGG-G-A-C-GG-GCAA--CC-G-G-A-CCCG-C-AU----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGA--C-CUCGCGCGGGCAUGAUCCUU------------------------CGGGAUAUCACCGCAGGGCUGCUUC----GGCCCG------AGAGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--UGA-GCGC-G-C-GGGCAACCG-C--G-G-G-C-C--UAGAGGAAU-GGUCGCCG-----------------AGGGGCGGGGAGACCCGC------------------------------------UCUGAACAGAAUCCGGCUUA--C-AGGCCCU-CCACGCAU
CP000448.1/742047-741624       UAAG-UA-A-A-U-C-A--GAUAGUCGCAGG-CA--U-UU---------------------------------------------------------------------------------------------------AU-U-U-G-CCUGAGGAAAGUCGGAGCUC-C---AUA--GGGCA-G-GG-UG----------------CUGGA------------UAACA----------------UCCAGUGGGG-----------------------GUGA------CCCCAAGG-AA---AGU-GCCACAGAAA--GAA--ACC-GCC----GG---A--AAUGGAGACCAGAGCGGAGGACGGAAGUCGGAUGUCGGAAGA------------------------------------------CCGAUGUUUGAUUACGGAAGAAGGAAUUCCGGGUUCUGGUCUCCGUU-U----U--C---GGCAAGGGUGGAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCAU-U-C-A-G--GCGA---C-U-G-A-AUGG-C-UC----------------GGCAAAC-CCCACCU-GGAGCAAGACC-GAAU------------------------------AGGGG--A-ACAAU------------------------------------------------------GAGGCGGCCC----GUCUC---------GUU---CC-C-----GGGU---U----AG---G-UCGC---------------------U--UGA-GGUA-G-C-AGGUAACUG-C--U-G-U-C-C--CAGAUAGAU-GACUAUCU-----------------AA--------------------------------------------------------UACAGAACUCCGCUUA--U-AGAUUUA-CUUACUUU
AATR01000031.1/8560-8909       GCGG-AU-G-G-C-U-G--GGCGGCCGCGC----------------------------------------------------------------------------------------------------GAAA---------------GCGAGGAAAGUCCGGACUC-U---UUA-CAGCAA-U-GG-CG----------------GCGGG------------UAACA----------------CCCGCCUGGG-----------------------GUAA------CCCAAGGG-AA---AGC-GCCACAGAAA--AUAA-ACC-GCU----CA---C--U----------------------------------------------------------------------------------------------------------------------------AAA--C-G----U--G---AGUAAGGGUGAAAC----GGU---AG-G--G--U----------------------AAGAG-CCUACC--GCAG-U-A-U-UG-GUAA--CA-A-U-A-UUGG-C-AU----------------GGCAAGC-CCCGUCA-GGAGCAAAACC-AAGU------------------------------AGGAA--C-CGCGUGCCCUU------------------------------------------AUGGGCGGGGUCGCUGA--AGCCCCA------GCAGG---UU-C-----GGGU---------G---G-UUGC---------------------U--AGA-GCAU-U-A-UGGUAACAU-A--A-U-G-C-G--CAGAUGAAU-GGUCGCUC-----------------AC--------------------------------------------------------GACAAAAUCCGGCUUA--U-AGGCCAU-CCGCAUUG
CP000264.1/1178594-1178183     GUGG-AG-G-G-C-U-G--GAUGGCCGCGAG-GC--U-CUGUUUU----------------------------------------------------------------------------------UCGGAAU-----GG-G-G-U-GUCGAGGAAAGUCCGGACUC-C--CUGA--AGACA-A-GG-UG----------------CCGGG------------UAACG----------------CCCGGGCCUGGCUGUUUGGG--GCUUGCCCAGAACGG-----CUGGGACGG-AA---AGC-GCCACAGAAA--ACAA-ACC-GCU----UC---C--GCGCCC-------------------------------------------------------------------------------------------------------------------UCCGGGACGC-A----G--G---AGCAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GGGG-G-G-C-UG-GCAA--CA-G-C-A-CCCG-C-AU----------------GGCAAGC-CCCACCUGGGAGCAAUGCC-GAAU------------------------------AGGGA--C-CGCAUC----------------------------------------------------AUGGGGCGCUUC--ACCCCU--------GCGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--AGA-GUUU-G-C-GGGCAACCG-U--A-G-A-C-C--GAGAGGAAU-GGUCAUCC-----------------AGGCUGGGGUUACCCCG-------------------------------------GCUGGACAAAAUCCGGCUUA--C-AGGCUCU-CCACGCAU
AAYA01000002.1/458457-458060   GUGG-AG-G-G-C-C-G--GACGGCCGCCUU-GG--G---------------------------------------------------------------------------------------------GAAA--------C-C-C-CGGGAGGAAAGUCCGGACUC-G---CCA--AAGCACC-GG-UG----------------CCGGG------------UAACG----------------CCCGGGCAGG-----------------------GCAA------CCUGACGG-AA---AGC-GCCACAGAAA--ACAG-ACC-GCC----UG---U--CGC--------------------------------------------------------------------------------------------------------------------------CUGUCG-G----C--A---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GGGG-G-G-A-UG-GCAA--CA-U-C-G-CCCG-C-UU----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-GUGU------------------------------AGGGA--C-CUCGCGUCCGACUGAUCCCGCU--------------------UGCGGGAUAUCGGGACAGGGCGGCUUU----GGCCCG------AGAGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--AGA-GCCG-C-G-CGGCAACGU-G--C-G-G-C-C--CAGAGGAAU-GGUCGUCU-----------------GAGGGGGCAACCCCG-----------------------------------------ACAACAGAAUCCGGCUUA--C-AGGCCCU-CCGCGCAU
AP009389.1/933770-934210       UGAG-UA-A-A-U-C-A--GGUGAUCGCGGG-UG--C-CGGU---------------------------------------------------------------------------------------CAGGA-----CG-G-C-G-CCUGAGGAAAGUCCGAGCUC-C---GCA--GGGCA-G-GG-UG----------------CUGGG------------UAAUA----------------CCCAGUGGGG-----------------------GCGA------CCCCAAGG-AA---AGU-GCCACAGAAA-UGCAG-ACC-GCC----CG---G--AACAGAAGCCGGAUGCCAAAUGCCGGAGGAUCUUUGGGCUGAAGGC-----------------------------------AACUCCUUCCCCAAUUAGAUCUGCCGGCUGUCAGGCUCCCUGCUUUUGUU-A----C--G---GGCAAGGGUGGAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGG-C-C-G-G--GCGA---C-C-G-G-CCGG-C-UA----------------GGUAAAC-CCCACCU-GGAGCAAGACC-GAAU------------------------------AGGGG--A-GCGUGU-----------------------------------------------------GCGGCGGCCC----GUCGU--------UGCU---CC-C-----GGGU---C----AG---G-UCGC---------------------U--AGA-GGCG-G-C-UGGCAACAG-C--C-G-U-C-C--CAGAUAGAU-GAUCACCC-----------------AC--------------------------------------------------------GACAGAACUCGGCUUA--C--GAUUUG-CUCACUAU
AAWO01000052.1/3266-2896       AAAG-AU-G-G-G-C-A--GGUGGCCGCCCG-G--------U----------------------------------------------------------------------------------------CUAU------------C-CGGGAGGAAAGUCCGAGCAC-C---AUA--GGGCA-A-GG-CG----------------CUGGG------------UAACU----------------CCCAGUCCCG-----------------------GUGA------CGGGAAGG-AA---AGU-GCCACAGAAA--AAAA-ACC-GCC----CG---A------------------------------------------------------------------------------------------------------------------------------GAAA----U----C--G---GGUAAGGGUGAAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC--GCGU-U-U-C-UG-GUGA--CA-G-A-A-ACGG-C-AU----------------GGUAAAC-CCCGCCC-GGUGCAAGACC-AAAU------------------------------AGGGG--G-GCUUUUCCGUUGU--------------------------------------UCGGAAAGGAAUCGGCCC----GGUUC-------GUGCC---CC-C-----GGGU---A----AG---G-UCGC---------------------U--UGA-GGCC-U-C-GGGUAACCG-U--G-G-U-C-C--CAGAGUAAU-GGUCGCCA-----------------CUGCCGGAAGAUGGC-----------------------------------------AGGACAGAACUCGGCUUA--U-GUCCUGU-CUUUCGCA
M64290.1/94-492                CGAG-CC-G-G-G-C-G--GGCGGCCGCGUG-GG--G-GUCU----------------------------------------------------------------------------------------UCGG-----AC-C-U-C-CCCGAGGAACGUCCGGGCUC-C---ACA--GAGCA-G-GG-UG----------------GUGGC------------UAACG----------------GCCACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----GG---G--GAC-------------------------------------------------------------------------------------------------------------------------CUCGGUC-C----U--C---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGC-C-U-G-AG-GCGA--CU-C-A-G-GCGG-C-UA----------------GGUAAAC-CCCACUC-GGAGCAAGGUC-AAGA--------------------------------GGG--G-ACACCCCGGUGUCCCUG------------------------------CGCGGAUGUUCGAGGGCUGCUC----GCCCG--------AGUC---CG-C-----GGGU---A-----G---A-CCGC---------------------A--CGA-GGCC-G-G-CGGCAACGC-C--G-G-C-C-C--UAGAUGGAU-GGCCGUCG-----------------CCCCGACGACCGCGAGGUC---------------------------------CCGGGGGACAGAACCCGGCGUA--C-AGCCCGA-CUCGUCUG
ABCR01000003.1/366725-366320   GCGG-AA-G-G-C-U-G--GAUGGCCGCGGG-GG------------------------------------------------------------------------------------------------UCCG----------C-C-CCCGAGGAAAGUCCGGACUC-C---ACA-AGACAA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCCGGG-----------------------GAAA------CCCGAGGG-AA---AGC-GCCACAGAGA--ACAG-ACC-GCC----CC---G--CAGCUGC-----------------------------------------------------------------------------------------------------------------GAAAGCGUCUG-C---AC--G---GGUAAGGGUGAAAC----GGU---GG-A--G--U----------------------AAGAG-CCCACC--GCGG-G-G-C-UG-GCAA--CA-G-C-C-CCGG-C-AU----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-GAAU------------------------------AGGGA--U-CGCGCGCGGGGGUCUGGUCGGG-------------------CAACCGAUACCGCCCGCAGGGACGUCUU----GCCCC-------AGCGA---UC-C-----GGGU---U-----G---G-CAGC---------------------U--UGAGGUGU-C-G-UGGCAACAC-G--G-C-G-C-C--CAGACGAAU-GGUCAUCC-----------------AAGGGGGCGACCCCU------------------------------------------GGACAGAAUCCGGCUUA--C-AGGCCUU-CCGCGCAU
AE008923.1/912011-912437       GGAG-UC-G-G-C-C-A--GACAGUCGCGUC-AC--U-C-------------------------------------------------------------------------------------------GCAA------G-A-G-U-GCCGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-A-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGC-----------------------GCAA------GCCGACGG-AA---AGU-GCAACAGAAA--GAU--ACC-GCCU--ACG---U--CCCUCGUCACCCCUUUGCCGCCACUGAAACGUGCCAGCGAUG------------------------------------------CCUCGCAUCGCCAAGCGCGCUCGGAGGCCGCAAAGGGGUGGCGAGGG-G----C--C---GGUAAGGGUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGA-G-U-C-CG-GUAA--CG-G-A-C--CGG-C-AC----------------GGCAAAC-CCCACCU-GGAGCAAGACC-AAAU------------------------------AGGGA--U-CCAUU------------------------------------------------------GGCGUGGCCC----GCGCU---------GGA---UC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCGC-C-G-CGGUGACGU-A--G-C-G-C-C--UAGACGAAU-GACUGUCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGCCGG-CUCCGCCG
CP000020.2/2483732-2483324     UGAG-CU-G-A-C-U-C--GGUAAUCGCUGC-UU--C-AUUGAUGUCCU--------------------------------------------------------------------------UAGGGAGACUG-----GU-G-G-A-GGGGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCAA------GCCUACGA-CA---AGU-GCAGCAGAGA--GGAA-ACC-GCCG--AUG---G--CUUAAUCUUCUUUUAU----------------------------------------------------------------------------------------------UCUUCGGAGUAGAGAAGUAAG-C---AC--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGAC-G-U-C-UA-GUAA--UA-GUG-C-GUUG-C-AA----------------GGUAAAC-UCCACCC-GGAGCAAGAUC-AAAU------------------------------AGGCC--C-UCGCA-----------------------------------------------------UAGCAUUGCUC----GUGUU--------UGGG---GG-C-----GGGU---A-----G---A-UUGC---------------------U--UGA-GCCU-G-U-GAGCGAUUG-C--A-G-G-C-C--UAGACGAAU-GGUUACCA-----------------CCGCGCAAGCGG----------------------------------------------GACAGAACCCGGCUUA--U-AUGUCGG-CUCUAACU
CP000927.1/3973535-3973136     CCAG-AU-G-G-U-C-G--GGCGGCCGCGGU-CU--U-C-------------------------------------------------------------------------------------------GCAA------G-A-A-G-AUCGAGGAAAGUCCGGGCUC-C---ACG-GUGACA-A-GG-CG----------------GCGGG------------UAACG----------------CCCGCCGGGA-----------------------GCGA------UCCCAGGG-AU---AGC-GCCACAGAAA--GCAA-ACC-UCC----UC---C--C---------------------------------------------------------------------------------------------------------------------------UUCG--G-G----G--C---GGGAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-A-C-C-UG-GCAA--CA-G-G-G-ACGG-C-AU----------------GGCAAGC-CCCGCCU-GGAGCAAGACC-GAAU------------------------------AGGGA--C-CCCGCGCCGGCCUC------------------------------------GCGUCGGAUAGGCCGUCAC---UGGCUGA------GAGGG---UC-C-----GGGU---A-----G---G-UCGC---------------------G--AGA-ACCG-U-C-CAGCGAUGG-A--C-G-G-U-C--CAGAGGAAU-GGCCGUCU-----------------CGCGGUCGUCUUUCCUUCGGGAGG-----------------------GGCGGACGUCAGACAGAACCCGGCUUA--C-AGACCAU-CUGGUCCA
ABED02000025.1/24408-24071     CGAG-UG-G-A-A-C-A--UACGGCGGCGGG-GC--G-GC------------------------------------------------------------------------------------------UUUG-----AC-C-G-C-UCUGAGGAAAGUCCGGGCCU-C---ACA--GAGCA-C-GG-UA----------------ACUGC------------UAACG----------------GCAGCCGAGG-----------------------GUGA------CCUUAGGG-AA---AGU-GCAACAGAAA--ACAA-ACC-GCC----GC---A------------------------------------------------------------------------------------------------------------------------------GCAA----U----G--C---GGUAAGGAUGAAAC----GGC---GA-G--G--U----------------------AAGAG-CUCACC-AGCGC-A-U-G-G--GUGA---C-C-A-U-GCGG-C-UU----------------UGUAAAC-CCUACCG-GAAGCAACGCC-UAUA------------------------------U-GGG--A-CGUAC------------------------------------------------------AGCGCUGCUC----GCG-----------UGU---CC-C-----GAA----------G---G-CGGC---------------------A--CGA-GCCU-G-U-CAGCAAUGG-C--A-G-G-C-C--UAGACAGAU-CGUCGUUU-----------------AA--------------------------------------------------------UACAGAACCCGGCUUA--C-GGUCUAU-CUCGUUUU
CP000847.1/661512-661911       UAAA-CA-G-G-U-C-G--UGCAGUUGCGUG-AU--GAUAUA----------------------------------------------------------------------------------------GCAAAGCUGUA-G-A-U-CACGAGGAAAGUCCGGACUC-U---AUA-GAGGUA-U-GG-UG----------------CCGGU------------UAACC----------------UCCGGCAAAGUA-------------------UUAUUA------CUUUAGGG-AA---AGU-ACCACAGAAA--AUAU-ACC-GCU----GAAUUG--UAC-------------------------------------------------------------------------------------------------------------------------GUAAGUA-C----U--C---GGUAAGGGUGAAAA----GGU---AC-G--G--U----------------------AAGAG-CGUACC--GGUA-A-G-U-UG-GUAA--CA-A-A-U-UACG-C-AU----------------GGUAAAC-CCCACCA-AGAGCAAGAUC-AAAU------------------------------AGGCA--U-UACAGAACUUAUCAAGUU----------------------------CCCGGAUUAUCUCUAGCC---------GGCUU--------GUAA---UG-C-----GGGU---A-----G---A-UCGC---------------------U--UGA-GGUA-A-A-CGGUAACGU-U--U-A-U-C-C--UAGAUAAAU-AACUGCAA-----------------UGAAUUUAUAUUCA--------------------------------------------UACAGAAUCCGGCUUA--U-AGACCUU-AUUGUCAU
ABEE02000017.1/499481-499149   UAAG-UA-A-A-A-C-A--GACAAUCGCGUG-A--------G----------------------------------------------------------------------------------------AUAA------------U-CACGAGGAAAGUCCGUGCAC-C---AUA--GAGUA-G-AA-UG----------------CUGGA------------UAACG----------------UCCAGUGGGG-----------------------GCGA------CCCUAAGG-CU---AGU-GCAACAGAGA--UAU--ACC-GCC----AU---U-------------------------------------------------------------------------------------------------------------------------------UAU----A----A--U---GGUAAGGGUGGAAA----GGU---GA-G--G--U----------------------AAGAG-CUUACC-AGCAU-A-U-A-G--GAGA---C-U-A-U-AUGG-C-UA----------------UGUAAAC-CCCAUUC-GGUGCAAGAUC-AAGA--------------------------------UUG--A-ACUUUU-----------------------------------------------------GUAGUUGCUC----GCUAC---------GUU---CA-U-----AGGU---A-----G---A-UUGC---------------------U--UGA-ACAA-A-U-UGGCAACAA-U--U-U-G-U-C--UAGAUAGAU-GAUUGUCU------------------------AA-------------------------------------------------UACAGAACACGGCUUA--U-AGUUUUG-CUUAAUAU
CP001101.1/1048460-1048077     AAAC-CA-A-A-G-U-G--UGCAGUCGCCGU-AU--A-UCUU----------------------------------------------------------------------------------------UGAG-----GA-U-A-U-GCGGAGGAAAGUCCGAACAU-C---ACA--GGACA-G-GG-UG----------------CCGGC-----------CGAGAGUAUUA-----CUCAAGACCGGGAGUAGU------------------GGCGCAAGC-UCCUGCUACAG-AG---AGU-GCAACAGAAA--GUAU-ACC-GCC----CC---G--G----------------------------------------------------------------------------------------------------------------------------CUA--C-C----G--G---GGUAAGGGUGAAAC----GGG---GG-U--G--U----------------------AAGAG-ACCACC-AGACA-U-G-U-CA-GUAA--UG-A-C-C-UGUG-C-UA----------------UGAAAAC-CUC-CCC-GAUGCAAGGCU-GAAU------------------------------AGGGA--A-ACUUUUCCGAA-----------------------------------------AGGGAGAAGAGCUGUCC----GCUCAAUUUUUUGAGUU---UC-C-----GGGU---G-----A---G-CCGC---------------------A------------------------------------U--AAGAUAAAU-GACUGCAG-----------------UCUUGUCGAAAGGCAA----------------------------------------GGAACAGAAUUCGGCUUA--C-AGCUUUG-GUUUCUUU
CP000908.1/5193807-5193404     UCAG-CC-G-G-C-C-G--GGCAGCCGCUCC-GU--C---------------------------------------------------------------------------------------------GUCA--------G-A-C-GGGGAGGAAAGUCCGGGCUC-C---AUG-GAGAGG-C-GG-UG----------------CCGGA------------UAACC----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AC---AGU-GCCACAGAGA--GCAG-ACC-GCC----UU---G--CAAGGC-------------------------------------------------------------------------------------------------------------------CCGUCCUUCG-C----A--A---GGUCAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-A-C-G-CG-GCAA--CG-C-G-G-ACGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGG--C-GACACGCCUUCUCCGC--------------------------------GAGGAGGGGGCAGGCCCUCUCUCCAGGCUC--------GUCG---CC-C-----GGGU---U-----G---G-UUGC---------------------U--CGA-GGCG-G-C-CGGUAACGG-A--C-G-U-C-C--CAGAGGAAU-GGCUGCUA-----------------CGUCCGUGAGUUCAUCUCGC--------------------------------GGGCCCUACAGAACCCGGCUUA--C-AGGCCGG-CUGAUCCA
CP001098.1/1331603-1331257     UAAG-UU-G-G-C-C-G--AAUGGUCGCGGC-UA--U-AU---------------------------------------------------------------------------------------------------AU-A-U-A-GCCGAGGAAAGUCCGAGCUU-C---ACA--GGGCA-G-GG-UG----------------CUGGG------------UAACA----------------CCCAGUGGAG-----------------------GUGA------CUCCCAGG-AA---AGU-GCCACAGAAA--CAA--ACC-GCC----UU---A--CCUG-----------------------------------------------------------------------------------------------------------------------UUUAAUGG-U----A--A---GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGUGC-C-C-A-G--GUGA---C-U-G-G-GUAG-C-UA----------------GGUAAAC-CCCACCC-GAAGCAAGUCC-AUGU------------------------------AGGGG--G-AGUUA------------------------------------------------------AGGGUGGCCC----GCCCG---------UUC---CC-C-----GGGU---C----UG---G-ACGC---------------------U--AAA-GGUA-C-C-AGGCGACUG-G--U-A-U-C-U--CAGAUAGAU-GACCAUUC-----------------AA--------------------------------------------------------GACAGAACUCGGCUUA--C-AGGUCAA-CUUAUACU
CP000923.1/1357072-1357421     UGAG-UA-A-G-U-C-G--GAUGGCCGCGUG-CG--A----------------------------------------------------------------------------------------------UUU--------U-C-G-CACGAGGAAAGUCCGAGCUC-C---ACA--GGGCA-G-GG-UG----------------CCGGG------------UAAUA----------------CCCGGUGGAG-----------------------GCGA------CUCCAAGG-AA---AGU-GCAACAGAGA--UAU--ACC-GCC----UG---G--CACUCAA-----------------------------------------------------------------------------------------------------------------CUUGCUGAGUG-C----U--G---GGUAAGGGUGGAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGGGA-C-C-A-G--GCGA---C-U-G-G-UCUG-C-UC----------------UGCAAAC-CCCACCC-GGAGCAAGGC--GAAU------------------------------AGGAG--G-GAG--------------------------------------------------------UAGGUGGCCC----GCCGU--------UUCC---CU-C-----GGGU---U----AU---G-CCGC---------------------U--GGA-GGUG-U-C-AGGCAACUG-A--C-C-C-C-C--UAGAUAGAU-GGCCAUCC-----------------UC--------------------------------------------------------GACAGAACUCGGCUUA--C-AGACUUG-CUCACAUG
CP000849.1/247812-248205       AAAU-AG-G-U-C-G-U--GUAGUUGCGUGA-UU--U-UU-------------------------------------------------------------------------------------------AAA-----AA-A-U-U-ACGAGGAAAGUCCGGACUCU-A---UAG-AGGUAU-G-GU-GC----------------CGGGU------------AACGC----------------CCGGCGGAGUAA-------------------UAUUAC------UUUAGGGA-AA---GUG-CCGCAGAAAA--UAAA-CCG-CCA----UA---A--UAUA----------------------------------------------------------------------------------------------------------------------UUUUAUAUU-A----C--G---GUAAGGGUGAAAAG----GUG---UG-G--U--A----------------------AGAGC-ACACCG--GUAA-G-U-U-GG-UAAC--AA-G-U-U-ACGC-A-UG----------------GUAAACC-CCACCAA-GAGCAAAAUCA-AAUA------------------------------GGCGU--U-ACAGAGCUUUUAUAA---------------------------------GCUCCAGGGUAUCUCUAACCG----GUUUG--------UAAU---GC-G-----GGUA---G-----A---U-UGCU---------------------U--GAG-GUAA-A-C-GAUAACGUU-U--A-U-C-C-U--AGAUAAAUA-ACUACAAC-----------------GAGCUAUUUAUAGUUC----------------------------------------GUACAGAAUCCGGCUUAU--A-GACCUUA-UUUUGUC-
CP001097.1/1676001-1676408     AAAC-CGCA-A-G-U-G--UGCAGCCGCUGU-AU--A-ACU-----------------------------------------------------------------------------------------UCUG-----GU-U-A-U-GCAGAGGAAAGUCCGAACUU-C---ACA--GGGCA-G-GA-UG----------------CCGGUCGAG----AGCCGAAAGGCU---------CAAGCCCGGGGACAGC------------------AGGGAAAACCAGCUGUCACAG-AU---AGU-GCAACAGAAA--AUAU-ACC-GCU----CC---G--G---------------------------------------------------------------------------------------------------------------------------GAAA--C-C----G--G---UGUAAGGGUGAAAA----GGC---GG-U--G--U----------------------AAGAG-ACCACC-GGAUA-U-U-C-CG-GUAA--CG-G-A-A-UGUG-C-CU----------------GGCAAAC-CUC-UCC-GAAGCAAGGCU-AAAU------------------------------AGGAA--A-ACUUUUUUCCUUCGGGAAAAA---------------------AAGAGCGGCCCGUUCAAUUCCUUUUAC---AAGGAG--------AGUU---UU-C-----GGGU---A-----A---G-CCGC---------------------A------------------------------------U--CAGAUAAAU-GGCUGCAGCUUCA-------UAUCCCAGGGGAUAUGAUC--------------------------------------------CACAGAAUUCGGCUUA--C-AGCUUCG-GUUUCAGC
CP000820.1/6067977-6068392     CGAG-UU-G-G-C-C-G--GACGGUCGCGUC-GG--U-ACCGGGGCG------------------------------------------------------------------------------CGAGCCCGG-----GU-G-C-C-GCCGAGGAACGUCCGGGCUC-C---ACA--GGGCG-G-GG-UG----------------GUGGG------------UAACG----------------CCCACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAGA--ACAG-ACC-GCC----GG---U--GCC------------------------------------------------------------------------------------------------------------------------GUCAUGGC-G----C--C---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGC-C-C-G-GG-GUGA--CC-C-G-G-GCGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGGCC-AAGAGGCCCCGGCCGGU---CACGGUCGCGGGCUGCGCA--G-GCGUCC----------------------------------------------------GAGGGCUGCUC----GCCCG--------AGCC---UG-C-----GGGU---A-----G---G-CCGC---------------------U--GGA-GGCC-G-U-CGGCAACGG-C--G-G-U-C-C--UAGAUAGAU-GACCGUCA-----------------CCGGCAAGCCGCGAGGCGA----------------------------------CCCGGAACAGAACCCGGCGUA--C-AGGCCAA-CUCGUCCG
CP001110.1/1741219-1741621     AACC-GC-A-A-G-U-G--UGCAGUCGCCGU-GC--A-GCCC----------------------------------------------------------------------------------------AUCCG---GGC-U-G-U-GCAGAGGAAAGUCCGAACUU-C---ACA--GGGCA-G-GG-UG----------------CCGGU-----------CGAGAGUUGCAAA--ACUCAAGCCCGGGGAUAAC------------------GGCGCAAGCCGCUUGUCACAG-AA---AGC-GCAACAGAAA--ACAG-ACC-GCU----UC---G--G---------------------------------------------------------------------------------------------------------------------------GCAA--C-C----G--G---AGUAAGGGUGAAAC----GGG---GG-U--G--U----------------------AAGAG-ACCACC-AGACA-U-G-A-CA-GUAA--UG-G-C-A-UGUG-C-UU----------------GGCAAAC-CUC-CCC-GAAGCAAGGCU-AAAU------------------------------AAGAG--G-ACUUUUCCCCCAGGGGAAAA-----------------------AGAGCGGCCCGUUCAAUUCC--GCAA-----GGAG--------AGUU---CU-C-----GGGU---A-----A---G-CCGC---------------------A------------------------------------U--CAGAUAAAU-GGCUGCAG-----------------UCUUACCCGGUCUCCGGG-----------------------------------UAAUUCACAGAAUUCGGCUUA--U-AGCUUAC-GGUUUCAG
CP001124.1/580627-581051       CGAA-GC-A-GAC-C-A--GAUGGCCGCCGU-CC--A-CCGUAGCC-------------------------------------------------------------------------------UUUGGCGAA-----GG-U-G-G-AGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-U-GG-UG----------------CUGGA------------UAACG----------------UCCAGCGAGG-----------------------GUAA------CCUCAGGG-AA---AGU-GCCACAGAGA--GAAG-UCC-GCC----CC---C--CACACCCUGGCGACAGGGUCC-------------------------------------------------------------------------------------GCCGAAGCCUCGGCGAAGGCGGAAG-G----G--G---GGUAAGGGUGAAAG----GGU---GA-G--G--U----------------------AAGAG-CUCACC-GGGUU-C-G-G-CG-GCGA--CG-C-C-G-GAUG-C-CA----------------GGUAAAC-CCCACCA-GGAGCAAGACC-AAAU------------------------------AGGGA--A-GCGUU-----------------------------------------------------AAGGACGGCCC----GUCCG--------UGCU---UC-C-----GGGU---U-----G---G-UUGC---------------------U--UGA-GGGC-G-U-CGGUAACGG-C--G-C-U-C-C--UAGAUGAAU-GACCAUCG-----------------CCCGUCUCCGGGUAACCGGC--------------------------------UGCGGGAACAGAACCCGGCUUA--C-GGGCUGC-UUCGGCCA
CP000675.2/2025610-2025238     AGAG-UC-G-G-U-C-A--GGCAAUCGCUCU-UU--G-CC------------------------------------------------------------------------------------------UAAC-----AG-C-A-A-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-AG-UG----------------CCAGG------------UAACU----------------CCUGGGAGGU-----------------------GUGA------GCCUACGG-AA---AGU-GCCACAGAAA--AUAU-ACC-GCC----CA---C--UUUUCC-------------------------------------------------------------------------------------------------------------------UUUGGGAAUC-G----U--A---GGUAAGGGUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-A-U-UG-GUAA--CA-G-U-C-GUGG-C-AG----------------GGAAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGAA--U-CCAUUUGACUGCA-------------------------------------AGGUCCUAACGUAUGGCCC----AUACG---------GGA---UU-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GGCA-U-G-UGGUGACGC-A--U-G-U-C-C--CAGAUGAAU-GGUUGCCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGACCGA-CUCUAAUC
CP000859.1/2608080-2607688     GAAG-UU-G-C-G-C-A--GACGAUCGCUGA-AG--C-GGUCAAGGC------------------------------------------------------------------------------AUUGGCCUG-----CC-G-C-U-UUGGAGGAAAGUCCGAACAC-C---ACA--GGGCA-G-GG-UG----------------CUUCA------------UAACG----------------UGAAGUCAUG-----------------------GCGA------CAUGAAGG-AA---AGU-GCCACAGAAA--AGAU-ACC-GCC----AA---A--GGAG----------------------------------------------------------------------------------------------------------------------CGCUGCUCU-U----U--U---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGUUC-C-C-C-GG-GUGA--CC-G-G-G-GAAG-C-UA----------------GGUAAAC-CCCACCC-GGUGCAAGACC-AAAU------------------------------AGGGG--G-ACGUUU----------------------------------------------------GAGGGCGGCCC----GUCCA--------AGUC---CC-C-----GGGU---A-----G---G-UCGC---------------------A--UGA-GGCG-U-C-GGGCAACCG-G--C-GUC-C-C--GAGAGGAAU-GAUCGUCG-----------------GCCGGCAAGGGGUAACCCGC--------------------------------GCCGGACACAGAAUUCGGCUUA--C--GCGCAG-CUUCAACC
BA000016.3/2292224-2291878     CGAG-UA-A-G-C-C-A--GACAAUCGCUGC-UA--G-UC------------------------------------------------------------------------------------------UUAG-----AA-C-U-A-GGAGAGGAAAGUCCGAGCUC-C---AUA--GGGCA-G-GA-UG----------------CUGGA------------UAACG----------------UCCAGUGGAG-----------------------GUGA------CUCUAAGG-AU---AGU-GCAACAGAAA--UAA--ACC-GCC----UA---G--A---------------------------------------------------------------------------------------------------------------------------UUUA--U-C----U--A---GGUAAGGGUGGAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGGGU-A-U-A-G--GUGA---C-U-A-U-ACUG-C-UA----------------UGUAAAC-CCCAUCU-GGAGCAAGACC-AAAU------------------------------AGGAG--G-ACAUAU----------------------------------------------------AGGGGCUGCCC----GUCCC---------GUC---CU-C-----GGGU---G-----U---G-UCGC---------------------U--UGA-GCCU-A-U-CGGCAACGG-U--A-G-G-C-C--UAGAUAGAU-GAUUGUCA------------------------AA-------------------------------------------------UACAGAACUCGGCUUA--U-AGACUUAUCUCGUAUU
CP001348.1/631191-631544       UGAG-UA-A-G-C-C-A--GAUGAUCGCAGA-UA--C-UGCCU-------------------------------------------------------------------------------------GAAAAG-----GC-G-U-A-GAUGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-AUGG-UG----------------CCGGG------------UAACU----------------CCCGGUGAAG-----------------------GUGA------CUUUAAGG-AA---AGU-GCAACAGAGA--UAU--ACC-GCC----AU---A--UUAGG---------------------------------------------------------------------------------------------------------------------UUUGCCUUA-U----A--U---GGUAAGGGUGGAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC-AGCGA-C-U-U-G--GCGA---C-U-U-G-UCGG-C-UA----------------UGUAAAC-CCCAUCU-GGAGCAACACC-GUGG------------------------------A-GGG--A-CGCAAU-------------------------------------------------------GACUGCCC----GUC-----------AGU---CC-C-----GGGG---A-----G---G-UGGC---------------------U--UGA-GCCA-G-A-CAGAAAUGU-A--U-G-G-C-C--UAGAUAGAU-GAUCAUCA-----------------AA--------------------------------------------------------UACAGAACCCGGCUUA--U-AGACUUA-CUCAUACC
CP000943.1/324335-323926       UCAG-CC-G-G-C-C-G--GGCGGCCGCUCU-GC--C-CU---------------------------------------------------------------------------------------------------CG-G-G-C-AGGGAGGAAAGUCCGGGCUC-C---AUG-GAGAGA-C-GG-UG----------------CCGGA------------UAACA----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AC---AGU-GCCACAGAGA--GGAG-ACC-GCC----GG---G--CGGGCC-------------------------------------------------------------------------------------------------------------------GCGAGGCCCG-C---GC--C---GGUCAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-A-C-G-CG-GCAA--CG-C-G-G-ACGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGG--C-GACACGGGCGGGCCGA--------------------------------CGGCCCGCCCAGGCCUCUCCC---CAGGCC-------CGUCG---CC-C-----GGGU---U-----G---G-UUGC---------------------U--CGA-GGCG-G-C-CGGCAACGG-C--C-G-U-C-C--CAGAGGAAU-GGCCGCCA-----------------CGUCCGGGGGACCCGCGAGGGUC-------------------------CGCCGGGCCCUACAGAACCCGGCUUA--C-AGGCCGG-CUGAUCCC
AAUJ02000001.1/472894-473254   GAAG-UG-C-G-C-C-A--GACCGCCGCUGG-UA--C-UAGCCGAAAGGCCAACGC------------------------------------------------------------UUGCGUUGGGUCGAAAGA-----CC-G-U-A-CUGGAGGAACGUCCGGACUG-C---AUA--GGGCG-G-CG-UA----------------GCAGC------------UAACA----------------GCUGUCCACC-----------------------GUGA------GGUGAGGA-UC---AGA-GCAACAGAGA--CGAG-UCU-------------G--GCA-------------------------------------------------------------------------------------------------------------------------GGAGUGC-C----G--C------AAGGCAGACCA----ACC--------------------------------------AG----GGU----------------GAAA------------------CG----------------GGCAAUC-UCUACGC-GCAGCAAUACC-AAGU------------------------------AGGCA--C-ACGUUG----------------------------------------------------A--CGGGGCCC----CCGGA---------GUG---UG-C-----GGGU---A-----G---G-UAGC--------------------AC--CGA-GCCA-U-C-AGGCGACUG-A--U-G-G-C-C--AAGAUUAAU-GGCGGUCA-----------------CAUGGCGGGCAACCGUU--------------------------------------GUGCACAGAAUCCGGCUUA--U-CGGCGCA-CUUCACAC
CP000853.1/1386146-1386539     UGAG-UA-G-A-U-C-A--GAUGAUCGCGGA-CA--U-GG------------------------------------------------------------------------------------------UUUU-----CC-A-U-G-GACGAGGAAAGUCCGAGCUC-C---AUA--GGGUA-G-GG-CG----------------CUGGG------------UAACA----------------CCCAGUGGGG-----------------------GCGA------CCCCAAGG-AA---AGU-GCAACAGAGA--GAU--ACC-GCC----AG---A--UCCCUUGUUCAGUAGCAAUGCUGUU-----------------------------------------------------------------------------ACUUGGGUGAGAAUAGCUUUUGACAGCUA-U----C--U---GGUAAGGAUGGAAA----GGU---GA-G--G--U----------------------AAGGG-CUCACC-AGGGG-C-U-A-G--GUGA---C-U-A-G-UCUG-C-UA----------------UGUAAAC-CCCGUCU-GGAGCAAGACC-AAGU------------------------------AGGGA--C-UGAAAA----------------------------------------------------AGCGGCGACCC----GUCGU--------G------UC-CC---GUGGU---A-----G---G-UUGC---------------------U--UGA-GCCG-U-C-UGGUAACAG-C--C-G-G-C-C--UAGAUAGAU-GAUCGUCG-----------------AA--------------------------------------------------------UACAGAACUCGGCUUA--U-AGAUUUG-CUCACUUA
CP000830.1/2943463-2943080     GCGG-GG-G-G-C-U-G--GAUGGCCGCUUG-GG--C-CGAU----------------------------------------------------------------------------------------GUUU-----CG-G-U-U-CGAGAGGAAAGUCCGGACUC-C---ACG-AAGAGA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGGCGGA-----------------------GUGA------UCCGACGG-AA---AGC-GCCACAGAGA--AAAG-ACC-GCC----UG---C--C---------------------------------------------------------------------------------------------------------------------------ACAG--G-G----C--G---GGUCAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-G-G-C-UG-GUAA--CA-G-C-C-CCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAUGCC-AAAU------------------------------AGGGA--C-CUCGUCGCGUCGC--------------------------------------AAGGCGCGGGGCCGCUUC----AGCCC-------AGAGG---UC-C-----GGGU---U-----G---G-CAGC---------------------U--AGA-GCGG-C-C-GGGCAAUCG-G--U-C-G-C-C--CAGAGGAAU-GGUCAUCC-----------------ACGGGGGUCCGCCCCC----------------------------------------UGGACAGAAUCCGGCUUA--C-AGGCCCCUCCGCGCAU
AAQJ02000001.1/918442-918085   AGAG-UU-A-G-C-U-A--GACAGUCGCUGU-AA--U-AA-------------------------------------------------------------------------------------------UUA-----UC-A-U-U-ACAGAGGAAAGUCCGGGCUC-C---AUU--GGGCA-A-AG-UG----------------CCAGG------------UAAUG----------------CCUGGGAAGC-----------------------GCGA------GCUUACGG-AA---AGU-GCCACAGAAA--AUAG-ACC-GCC----UA---A--GAUUUAU-----------------------------------------------------------------------------------------------------------------AAUGAUGGGUC-U----C--A---GGUAAGGGUGAAAA----GGU---GU-G--G--U----------------------AAAAG-CACACC--GCAU-C-A-C-UG-GUAA--CA-G-U-G-GUGG-C-AA----------------GGUAAAC-CCCACUU-GGAGCAAGACC-AAAU------------------------------AGGAA--C-CUUUUA-----------------------------------------------------GACGCGGUCC----ACGUU---------AGG---UU-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GAUA-U-A-CGGUGACGU-A--U-G-U-C-C--UAGAUGAAU-GACUGUCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--U-CGGCUAA-CUCUUCUU
ABCC02000021.1/71166-70809     UGAG-UA-G-G-A-C-A--GGUGGCCGCUGC-CG--C-GAUACC------------------------------------------------------------------------------------GCAAGG-----CC-G-C-G-GGAGAGGAAAGUCCGGGCUU-C---ACA--GGGCA-G-GG-UG----------------CCAGA------------UAACG----------------UCUGGCGGAG-----------------------GCGA------CUCCAGGG-AC---AGU-GCAACAGAAA--UGU--ACC-GCC----UU---U--UUGGC---------------------------------------------------------------------------------------------------------------------UGCGGCCUU-A----A--A---GGUAAGGGUGGAAG----GGC---AG-U--G--U----------------------AAGAG-ACUACC--GCCC-G-U-C-UG-GUAA--CA-G-G-C-GGGG-CACA----------------UGUAAAC-CCCACUC-GAAGCAAGACC-GAAC------------------------------A-GGA--A-GCAUA-------------------------------------------------------UGGCUGCCC----GUCA----------GCU---UC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGCU-G-C-CGGCGACGG-C--A-G-U-C-C--UAGAUAGAU-GGCCAUUC-----------------AAC-------------------------------------------------------GACAUAACCCGGCUUA--U-CGUCCUG-CUCACAUA
CP001089.1/691698-691329       GGAG-UA-G-G-C-C-A--GAUGAUCGCUGU-CU--G-AC------------------------------------------------------------------------------------------CCAG-----GU-C-A-G-AGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-CG----------------CUGGG------------UAAUC----------------ACCAGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAGA--GAAG-UCC-GCC----CG---U------------------------------------------------------------------------------------------------------------------------------UUCG----A----C--G---GGUAAGGGUGAAAG----GGU---GA-G--G--U----------------------AAGAG-CUCACC-GGGUC-C-G-G-UG-GUGA--CA-C-C-G-GAUG-C-CA----------------GGUAAAC-CCCGCCA-GGAGCAAGGCC-GAAU------------------------------AGGGA--G-GCGUC-----------------------------------------------------AAGGGCGGCCC----GCCCG--------UGCC---UC-C-----GGGU---U-----G---G-CUGC---------------------U--UGA-GGUC-A-C-CGGUAACGG-U--G-A-U-C-C--UAGAGGAAU-GAUCAUCAUCU-----------GCCGUCGGGUAACCACCGGC--------------------------------------AGAAACAGAACCCGGCUUA--C--GGCCUG-CUCCAACC
CP001390.1/835755-836131       CGAA-GC-A-GAC-C-A--GGUGGUCGCCGC-CC------------------------------------------------------------------------------------------------GCAA----------G-G-GGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-U-GA-CG----------------CUGGA------------UAACG----------------UCCAGCGGGG-----------------------GCAA------CCCCAGGG-AA---AGU-GCCACAGAGA--GAAG-UCC-GCC----UG---U--CGGAA--------------------------------------------------------------------------------------------------------------------GCGUGCGAAG-A----C--A---GGUAAGGGUGAAAG----GGU---GA-G--G--U----------------------AAGAG-CUCACC-GGAUC-C-G-G-CG-GUGA--CG-U-C-G-GAUG-C-CA----------------GGUAAAC-CCCGUCA-GGAGCAAGACC-AAAU------------------------------AGGGA--A-GCGUC-----------------------------------------------------AAGGACGGCCC----GUCCG--------UGCU---UC-C-----GGGU---U-----G---G-UUGC---------------------U--UGA-GGCC-G-U-CGGUAACGA-C--G-G-U-C-C--UAGAUGAAU-GGCCGCCG-----------------CCUGCUUCAGGGAAACCUGU--------------------------------UGCAGGAACAGAACCCGGCUUA--U-GGGCUGC-UUCGGCCA
CP001037.1/1484900-1485316     AGAG-UA-G-A-C-G-CAGGCGGUUGCAGAU-CA--G-UCAU----------------------------------------------------------------------------------------AGUC----ACU-G-A-U-UUGAGGAAAGUCCGGGCUCC-CG-AAAG--ACCAA-A-CUUGC----------------UGGAU------------AACGU----------------CCAGUGCGAG-----------------------CGAU------CGUGAGGA-UA---GUG-CCACAGAAAG--AUA--CCG-CCA----GA---U--CAAUUAAAAAUUAAAAAUUAAAAAUCUAAA-------------------------------------------------------------------AUGAGUAAUUUUUAAUUUUACAUUUUUAAUUGAU-C----U--G---GUAAGGGUGCAAAG----GUG---CG-G--U--A----------------------AGAGC-GCACCA-GCAGU-A-U-C-G--AGAG---G-U-G-C-UGGC-U-CG----------------GUAAACC-CCGGUUGGGAGCAAGGCG---AUA------------------------------GG--A--A-CUACGG----------------------------------------------------UUGGUCUUUUA----CCAGUU-----CCGCUC---AA-U-----GAGA---G---------C-CGCU---------------------A--GAG-GCGU-U-U-GGUAACAAG-C--G-U-C-C-C--AGAUAGAUA-ACUGCCCU-----------------CGCAAGAGA-------------------------------------------------ACAGAACCCGGCUUAU--G-UACUGCU-CUUUCC--
CP000750.2/3654587-3654962     CGAG-UC-G-G-C-C-G--GGCGACCGCGUC-GG--C-CGGG----------------------------------------------------------------------------------------GCGAC---CCG-G-C-C-GCCGAGGAAAGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------GUGGC------------UAACA----------------GCCACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAGA--ACAG-ACC-GCC---ACC---C--CGA-------------------------------------------------------------------------------------------------------------------------GCGAUCG-G----G--G--CGGUAAGGGUGAAAC----GGU---GG-U--G--C----------------------AAGAG-ACCACC-AGCGU-G-C-C-GG-GUGA--CC-G-G-U-GCGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGACC-AGAC------------------------------A-GGC--A-GCGUUC----------------------------------------------------GAGGGCGGCCC----GCCCG--------AGCU---GC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GGCG-U-G-CGGCAACGC-A--C-G-U-C-C--UAGAGGGAU-GGUCGCCG-----------------CCCGCUCCCCGGAGCG---------------------------------------GGGCACAGGAUCCGGCUUA--C-AGGCCGG-CUCGUCCA
AE016828.2/103047-103388       AGAG-CC-A-G-C-C-A--AACAGUCGCUCA-AC------------------------------------------------------------------------------------------------GGUA----------G-U-UGGGAGGAAAGUCCGGGCUC-C---AUC--GGGCA-G-AG-UG----------------CCAGG------------UAACC----------------CCUGGGAGGC-----------------------GCGA------GCCUACGG-AA---AGU-GCAACAGAAA--GAAU-ACC-GCU----GC---C------------------------------------------------------------------------------------------------------------------------------GUCA----G----G--C---AGUAAGGGUGAAAU----GGU---GU-G--G--U----------------------AAGAG-CACACC--GCGU-U-G-G-UG-GUAA--CA-U-U-A-ACGG-CGAU----------------GGUAAAC-CCCACUC-GGAGCAAGGCC-AAAU------------------------------AGGAA--U-CCUGAU----------------------------------------------------UGUGUGGCCCA----CACAG--------UGGA---UU-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GGUA-C-A-UGGUGACAU-G--U-A-U-C-C--CAGAUAGAU-GACUGUUC------------------------AU-------------------------------------------------GACAGAACCCGGCUUA--U-CGGCUGG-CUCUCCAA
ABAX03000012.1/707980-707643   UUAG-UU-A-A-C-C-G--AAUGAUCGCGCC-AA--A-GU---------------------------------------------------------------------------------------------------CU-U-U-U-GGUGAGGAAAGUCCGGGCUU-C---GCA--GGGCA-G-GA-UG----------------CCGGA------------UAACG----------------UCCGGUAGGG-----------------------GUGA------CCCUCAGG-CU---AGU-GCAACAGAAA--UAA--ACC-GCC----GG---U------------------------------------------------------------------------------------------------------------------------------AUUA----G----C--C---GGUAAGGGUGGAAA----GGC---GG-G--G--U----------------------AAGAG-CCCACC--GCUU-G-G-C-UG-GUAA--CA-G-G-C-AAGG-CACA----------------UGUAAAC-CCCAUCC-GAAGCAAGGCA---GG------------------------------AGAAA--A-GCUAU------------------------------------------------------GGGCUUGCCC----GGUCC---------GCU---UU-U-----CGGU---G-----U---G-CCGC---------------------U--GGA-GCUU-G-C-UGGCAACAG-C--A-A-G-U-C--GAGAUAGAU-GAUCAUUU-----------------AA--------------------------------------------------------GACAGAACCCGGCUUA--U-AGAUUAG-CUAAAUUC
CP000878.1/1554059-1554452     GAAA-GC-A-G-G-A-G-AGGUGAUCACAAU-CA--A-GAUUUAUCGCGU------------------------------------------------------------------------UUCGCAAUAAAU-----GC-U-U-G-AUUGAGGAAAGUCCGGGCUC-CC-UGAU--GGUCA-A-GCUUG----------------CUGGG------------UAACU----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AU---AGU-GCCACAGAAA--CAC--ACC-GCC----GA---U--GGCUUAG-----------------------------------------------------------------------------------------------------------------UCCCACUCAGC-A----C--A---GGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UU----------------GGUAAAC-CCCGGCUAGGAGCAAGGC------------------------------------AAAGG--A-GCAUUA-----------------------------------------------------AUGGCCAUCU----AUGAU---------GCU---CC-U-----GAAA---A-----A--AG-CCGC---------------------U--UGA-GGUU-G-U-CGGUAACGG-C--A-G-U-C-C--CAGAUAGAU-GAUUACCC-----------------ACUAACCUUUUUAGGUA--------------------------------------GUGAACAGAACCCGGCUUA--U-GACCUGC-UUUCACCC
CP000409.1/594394-594001       CUAA-AU-G-G-U-C-A--UGCAGUUGCGUG-AU--G-AUAUAGC----------------------------------------------------------------------------------AAAGCUA-----UA-G-A-U-CACGAGGAAAGUCCGGACUC-U---AUA-GAGGUA-U-GG-UG----------------CCGGC------------UAAUC----------------UCCGGCAGAGUA-------------------UUAUUA------CUUUAGGG-AA---AGU-ACCACAGAAA--AUAU-ACC-GCC----GC---A--AU-------------------------------------------------------------------------------------------------------------------------------AU-U----U--C---GGUAAGGGUGAAAA----GGU---AC-G--G--U----------------------AAGAG-CGUACC--GGUA-A-G-U-UG-GUAA--CA-A-A-U-UACG-C-AU----------------GGUAAAC-CCCACCA-AGAGCAAGAUC-AAAU------------------------------AGGCA--U-UACAGAACUUGUGUUUCC----------------------------AAGUUCCCGGGUUAUCUCUAACC----GGCUU--------GUAA---UG-U-----GGGU---A-----G---A-UCGC---------------------U--UGA-GGUA-A-A-CGGUAACGU-U--U-A-U-C-C--UAGAUAAAU-AACUGCAA-----------------UGAAUUUCUAUUCA--------------------------------------------UACAGAAUCCGGCUUA--U-AGACC---UUAAAAAU
CP001251.1/1276985-1276628     GAAG-UA-G-A-U-C-A--GGCAACCGCGGA-AU--U---------------------------------------------------------------------------------------------GAGA--------G-A-U-UCCGAGGAAAGUCCGAACAC-C---AAA--GGGCA-G-GG-UG----------------CUGGG------------UAAUA----------------CCCAGUCAGG-----------------------GUGA------CCUGAAGG-AA---AGU-GCCACAGAAA--AUAA-ACC-GCC----CA---A--GGU-------------------------------------------------------------------------------------------------------------------------UUUUGCC-U----U--G---GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCAG-G-A-A-GG-GUGA--CC-U-U-C-CUGG-C-UU----------------GGCAAAC-CCCACCU-GGUGCAAGGCC-AAAU------------------------------AGGAG--G-GGUUG-----------------------------------------------------A--GGUGGCCC----GCC----------GACC---CU-C-----GGGU---U-----G---G-CCGC---------------------U--UGA-GGCA-A-G-AAGUAAUUC-U--U-G-C-C-C--UAGAUAGAU-GGUUGCCG-----------------CCCCAUAUAUAUGGG------------------------------------------GAACAGAAUUCGGCUUA--U--GAUCUG-CUUCUUCC
CP001146.1/1110111-1109756     GAAG-UA-G-A-U-C-A--GGCAACCGCGGA-AU--C---------------------------------------------------------------------------------------------GAAA--------G-A-U-UCCGAGGAAAGUCCGAACAC-C---ACA--GGGCA-G-GG-UG----------------CUGGG------------UAACA----------------CCCAGUCAGG-----------------------GCGA------CCUGAAGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----UA---G--GGU------------------------------------------------------------------------------------------------------------------------UCUUUACC-C----U--G---GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCAG-G-A-A-GG-GUGA--CC-U-U-C-CUGG-C-UU----------------GGCAAAC-CCCACCC-GGUGCAAGGCC-AAAU------------------------------AGGAG--G-GGUUG-----------------------------------------------------A--GGUGGCCC----GCC----------GACC---CU-C-----GGGU---U-----G---G-CCGC---------------------U--UGA-GGCA-A-G-AAGUAAUUC-U--U-G-C-C-C--UAGAUAGAU-GGUUGCCG-----------------CCCCUAUAUGGGG---------------------------------------------AACAGAAUUCGGCUUA--U--GAUCUG-CUUCUUCC
CP000304.1/1180839-1181198     AGAG-UU-G-A-U-C-G--GACAGUCGCUGU-CU--C-UUUUUGUU--------------------------------------------------------------------------------CCGGCAAG-----AA-G-G-G-AGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-A-AG-UG----------------CCAGG------------UAACG----------------CCUGGGAGGC-----------------------GUGA------GCCUACGG-AA---AGU-GCCACAGAAA--AUA--ACC-GCC---UAA---G--CGC-------------------------------------------------------------------------------------------------------------------------UUCGGCG-C----C------GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-G-G-C-UG-GCAA--CA-GUC-C-GUGG-C-UA----------------GGUAAAC-CCCACUU-GGAGCAAGACC-AAAU------------------------------AGGGA--U-CCAUU------------------------------------------------------GGCGUGGCCC----GCGCU---------GGA---UC-C-----GGGU---A-----G---G-UUGC---------------------U--AGA-GGCA-G-U-CAGUGAUGG-C--U-G-U-C-G--UAGAGGAAU-GGCUGUCC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--C-AGAUCGA-CUCUCCGA
CP001157.1/1278404-1278762     AGAG-UC-G-G-U-U-G--GACAGUCGCUGU-CC--C-AUAUUGU---------------------------------------------------------------------------------UCCUCAAU-----AU-G-G-G-AGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-AG-UG----------------CCAGG------------UAACG----------------CCUGGGAGGC-----------------------GCGA------GCCUACGG-AA---AGU-GCCACAGAAA--ACA--ACC-GCC---UAA---G--CGC-------------------------------------------------------------------------------------------------------------------------GCAAGCG-C----C------GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-G-G-C-UG-GCAA--CA-GUU-C-GUGG-C-UA----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGA--U-CCAUU------------------------------------------------------GGCGUGGCCC----GCGCU---------GGA---UC-C-----GGGU---A-----G---G-UUGC---------------------U--AAA-GGCG-G-C-CAGCGAUGG-U--C-G-U-C-G--UAGAGGAAU-GACUGUCC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--C-AGACCGG-CUCUCCCC
CP000712.1/4919241-4918866     AGAG-UC-G-A-U-C-G--GACAGUCGCUGC-CU--G-UUUUUGUUCCGCAAC-----------------------------------------------------------------UUUUUGUUGUGUGAGC-----AG-C-A-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-AG-UG----------------CCAGG------------UAACG----------------CCUGGGAGGC-----------------------GUGA------GCCUACGG-AA---AGU-GCCACAGAAA--AUA--ACC-GCC---UAA---G--CAC-------------------------------------------------------------------------------------------------------------------------UUCGGUG-C----C------GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-G-G-C-UG-GCAA--CA-GUU-C-GUGG-C-UA----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCAUCA-----------------------------------------------------GGCGUGGCCC----GCGUC---------GGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--AGA-GGCG-U-C-CAGUGAUGG-C--C-G-U-C-G--UAGAGGAAU-GACUGUCC-----------------UC--------------------------------------------------------GACAAAACCCGGCUUA--C-AGAUCGA-CUCUCCAC
BX897699.1/1251235-1250846     UCAG-UC-G-G-C-U-G--GGCAGCCGCGCU-UG--U-CAAUGC-----------------------------------------------------------------------------------CUAAAGG-----UG-G-C-A-GGUGAGGAAAGUCCGGGCUC-C---AUG-GAAAAA-C-GG-UG----------------CCGGG------------UAACA----------------CCCGGCGGGG-----------------------GCGA------CCCUAGGG-AA---AGU-GCCACAGAAA--GUAA-ACC-GCC----UA---U------------------------------------------------------------------------------------------------------------------------------UUUU----A----U--A---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCAC-A-U-U-CA-GUAA--UG-A-A-U-GUGG-C-AA----------------GGUAAAC-CCCACCG-GGAGCAAGACC-AAAU------------------------------AGAAA--U-GACGCGCAAGGCUU------------------------------------AACUUGCAGCCGGUUUCCG----GGCGA--------GUCA---UU-C-----GGGU---A-----G---G-UUGC---------------------A--AGA-GGCG-G-A-UGGUAACAU-C--C-G-U-C-C--CAGAUGAAU-GGUUGCCA-----------------UGUAAAGUGUACACUUU-------------------------------------ACCAUACAGAACCCGGCUUA--C-AGGCCGA-CUGAUUUU
CT573326.1/4810543-4810184     AGAG-UC-G-A-U-C-G--GACAGUCGCUGC-CG--U-CUUUUGU---------------------------------------------------------------------------------UCCGCAAG-----AG-G-C-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-AG-UG----------------CCAGG------------UAACG----------------CCUGGGAGGC-----------------------GCGA------GCCUACGG-AA---AGU-GCCACAGAAA--ACA--ACC-GCC---UAA---G--CGC-------------------------------------------------------------------------------------------------------------------------UUCGGCG-C----C------GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-A-C-UG-GCAA--CA-GUU-C-GUGG-C-UA----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCAUAC-----------------------------------------------------GGCGCGGCCC----GCGUC---------GGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--AGA-GGCG-U-C-CAGUGAUGG-C--C-G-U-C-G--UAGAGGAAU-GACUGUCC-----------------UC--------------------------------------------------------GACAAAACCCGGCUUA--C-AGAUCGA-CUCUCCAC
CP000934.1/1090630-1090999     GGAG-UU-G-G-C-C-A--GGCAAUCGCUCC-GC--G-CAUACCUUCCAU------------------------------------------------------------------------UGCUGGAUAAGG-----UG-C-G-CCGGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-AG-UG----------------CCAGG------------UAACA----------------CCUGGGAGGC-----------------------GUGA------GCCUACGG-AA---AGU-GCAACAGAGA--GUAG-ACC-GCC---CAA---G--CAC-------------------------------------------------------------------------------------------------------------------------GCAAGUG-C----C------GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-A-A-C-UG-GUAA--CA-GGC-U-GCGG-C-UA----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGG--U-CCAUU------------------------------------------------------GGUGUGGCCC----GCACU---------GGA---CC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGCC-U-G-UGGUGACAC-A--G-G-U-C-C--CAGAUGAAU-GAUUGCCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGCCGA-CUCCUUUA
CP001277.1/1731802-1732181     UAAG-UU-A-A-C-C-A--GACAGUCGCCGC-UU--C-UUUUGAUGUUUAUU--------------------------------------------------------------------AAAAAAACAAAAAA-----UA-G-A-A-GAGGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-G-AG-UG----------------CCAGG------------UAAUG----------------CCUGGGAGGC-----------------------GUGA------GCCUACGA-CA---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CCUGA--------------------------------------------------------------------------------------------------------------------AAUAUGAGGA-U----C--A---GGUAAGGGUGAAAU----GGU---GU-G--G--U----------------------AAGAG-CACACC--GCGC-G-U-U-UG-GUAA--CA-A-G-C-GUGG-C-AA----------------GGUAAAC-UCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGG--U-UCACAU-----------------------------------------------------AGUGCGGCUC----GUACU---------GAA---CU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCA-U-C-AAGCGAUUG-C--U-G-G-C-C--UAGAUGAAU-GACUGUCC-----------------AC--------------------------------------------------------GACAAAACCCGGCUUA--U-CGGUUAA-CUUACUUU
CP000680.1/1031226-1031573     AGAG-UC-G-A-U-C-G--GACAGUCGCUGC-CU--U-C-------------------------------------------------------------------------------------------GCAA------G-A-A-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCG-G-AG-UG----------------CCAGG------------UAAUG----------------CCUGGGAGGC-----------------------GUGA------GCCUACGG-AA---AGU-GCCACAGAAA--AUA--ACC-GCC---UAA---G--CGU-------------------------------------------------------------------------------------------------------------------------UUCGGCG-C----C------GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-G-G-C-UG-GCAA--CA-GUC-C-GUGG-C-UA----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCAUC------------------------------------------------------GGCGUGGCCC----GCGCU---------GGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--AAA-GGCG-U-G-CAGUGAUGU-A--C-G-U-C-G--UAGAGGAAU-GGCUGUCC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--C-AGAUCGA-CUCUCCUC
CP000075.1/4902542-4902185     AGAG-UC-G-A-U-U-G--GACAGUCGCUGC-CU--C-UUGUUGU---------------------------------------------------------------------------------UCCGCAAC-----AA-G-G-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCG-G-AG-UG----------------CCAGG------------UAACG----------------CCUGGGAGGC-----------------------GUGA------GCCUACGG-AA---AGU-GCCACAGAAA--AUA--ACC-GCC---UAA---G--CAC-------------------------------------------------------------------------------------------------------------------------UUCGGUG-C----C------GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-G-U-C-UG-GUAA--CA-GUU-C-GUGG-C-AA----------------GGUAAAC-CCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCUA-------------------------------------------------------GGCGUGGCCC----GCGCU---------GGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--AAA-GACG-U-C-CAGUGAUGG-C--C-G-U-C-G--UAGAGGAAU-GACUGUUC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--C-AGAUCGA-CUCUCCAC
CP000681.1/4300860-4300509     CGAG-UU-G-G-C-C-A--GACAGUCGCCGC-GU--U-C-------------------------------------------------------------------------------------------GUAA------G-A-A-C-GGGGAGGAAAGUCCGGGCUU-C---AAA--GAGCG-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GUGA------ACCGACGA-CA---AGU-GCAACAGAGA--GUAG-ACC-GCC---UGC---C--UGA-------------------------------------------------------------------------------------------------------------------------UUUAUCA-G----G--U--CGGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-G-G-C-UA-GCAA--UA-GUC-C-GUAG-C-AA----------------GGUAAAC-UCCACCC-GAAGCAAGACC-AAAU------------------------------AGGGU--U-CCGUAU-----------------------------------------------------GGCGUGGCUC----GCGUU---------GGA---AC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCCU-G-U-GAGCGAUUG-C--A-G-G-C-C--UAGAUGAAU-GACUGUCC-----------------AA--------------------------------------------------------GACAGGACCCGGCUUA--U-CGGCCAA-CUCACCUC
CP001339.1/815892-816249       GGAG-UC-G-G-C-C-G--GACAGUCGCUGC-GA--C-CUU--------------------------------------------------------------------------------------------------GU-G-U-C-GUGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGC-----------------------GCGA------GCCGACGG-AA---AGU-GCCACAGAAA--ACAU-ACC-GCCG--AUG---G--CUCGGAC-----------------------------------------------------------------------------------------------------------------CCGUUCCGGGA-U----C--A---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-G-UG-GCAA--CA-CUU-C-GCGG-C-AC----------------GGUAAAC-CCCACCC-GGAGCAAGGCC-AAAU------------------------------AGGGG--U-GCAUU------------------------------------------------------GGUGUGGCCC----GCACU---------GCA---CC-C-----GGGU---A-----G---G-CUGC---------------------U--CGA-GGCG-C-G-CGGUGACGC-G--C-G-U-C-C--CAGAUGAAU-GACUGUCC-----------------CA--------------------------------------------------------GACAGAACCCGGCUUA--C-AGGCCGA-CUCCCCAU
CR954246.1/2675114-2674750     GAGU-UA-G-C-C-A-A--GAUAAUCGCUGC-CU--G-UGACG-------------------------------------------------------------------------------------AAAAUG-----AU-C-A-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-AG-UG----------------CCAGU------------UAACG----------------GCUGGGGGGC-----------------------GCGA------GCCCACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCC----AA---U--C---------------------------------------------------------------------------------------------------------------------------UUCG--G-A----U--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGGC-C-G-C-UA-GUAA--UA-GUC-G-GUUG-C-AA----------------GGUAAAC-UCCACUC-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCUUAU-----------------------------------------------------GGCGUGGCCC----ACGUU---------GGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCA-U-A-GAGCGAUUU-A--U-G-G-C-C--UAGACGAAU-GAUUAUCA-----------------CUUUCUUCGGAAAG--------------------------------------------GACAGAACCCGGCUUA--U-ACGGCUA-ACUCACUC
CP000851.1/283404-283755       CGAG-UU-G-G-C-U-A--GACAGUUGCCGC-GU--U-C-------------------------------------------------------------------------------------------GCAA------G-A-A-C-GGGGAGGAAAGUCCGGGCUU-C---AAA--GAGCA-G-GG-UA----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GUGA------ACCGACGA-CA---AGU-GCAGCAGAGA--GGAG-ACC-GCC----UU---C--UUGA-----------------------------------------------------------------------------------------------------------------------UUUAUCAA-G----G--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-G-G-C-UA-GUAA--UA-GUU-C-GUAG-C-AA----------------GGUAAAC-UCUACCC-GAAGCAAGACC-AAAU------------------------------AGGGU--C-CCGUAU-----------------------------------------------------GGCGCUGCUC----GCGUU---------GGG---AC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCCU-G-U-GAGCGAUUG-C--A-G-G-C-C--UAGAUGAAU-AACUGUCC-----------------AC--------------------------------------------------------GACAGGACCCGGCUUA--U-CGGCCAA-CUCACCUA
CP001034.1/1292874-1293232     CAAG-UA-A-G-U-C-G--GGUAGUCGCGAG-GA--C-AG------------------------------------------------------------------------------------------UAAA-----CU-G-U-C-UUCGAGGAAAGUCCGAGCUC-C---GUA--GGGCA-G-GG-UG----------------CUGGG------------UAACA----------------CCCAGUGGGG-----------------------GCGA------CCCCCAGG-AA---AGU-GCCACAGAAA--CAA--ACC-GCC----AG---G--C---------------------------------------------------------------------------------------------------------------------------UUCA--A-U----C--U---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGG-C-C-A-G--GUGA---C-U-G-G-UCGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGACC-AAAU------------------------------AGGGA--A-GGGAUG----------------------------------------------------A--AGUGGCCC----GCUG---------ACCU---UC-C-----GGGU---U----UG---G-UCGC---------------------U--UGA-GGUG-U-C-AGGCGACUG-G--C-A-C-C-C--UAGAUAGAU-GACUGCCA-----------------CUCCCUCUAGGGGGA------------------------------------------GGACAGAACUCGGCUUA--C-AGACUUG-CUUGUAAA
CP000961.1/447682-448026       CGAG-UU-G-G-C-U-A--GACAGUUGCUGC-GU--U-C-------------------------------------------------------------------------------------------GCAA------G-A-A-C-GGGGAGGAAAGUCCGGGCUU-C---AUA--GAGCA-G-GG-UA----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GUGA------ACCGACGA-CA---AGU-GCAGCAGAGA--GGAG-ACC-GCC----AA---U--C---------------------------------------------------------------------------------------------------------------------------UUAG--G-A----U--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGGC-G-G-C-UA-GUAA--UA-G-U-C-GUUG-C-AA----------------GGUAAAC-UCUACCC-GAAGCAAGACC-AAAU------------------------------AGGGU--U-CCAGAC-----------------------------------------------------GGCGCGGCUC----GCGUU---------GGA---AC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCCU-G-C-GAGCGAUUG-C--A-G-G-C-C--UAGAUGAAU-AACUGUCC-----------------AC--------------------------------------------------------GACAAGACCCGGCUUA--U-CGGCCAA-CUCACCUA
CP000891.1/4952519-4952167     CGAG-UU-G-G-C-C-A--GACAGUCGCCGC-GU--U-C-------------------------------------------------------------------------------------------GCAA------G-A-A-C-GGGGAGGAAAGUCCGGGCUC-C---AAA--GAGCG-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GCGA------ACCGACGA-CA---AGU-GCAACAGAGA--GUAG-ACC-GCC----UG---C--CUGA----------------------------------------------------------------------------------------------------------------------UUUUAUCAG-G----U--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-G-G-C-UA-GCAA--UA-GUU-C-GUAG-C-AA----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGGU--U-CCGUAU-----------------------------------------------------GGCGUGGCUC----GCGUU---------GGA---AC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCCU-G-U-GAGCGAUUG-C--A-G-G-C-C--UAGAUGAAU-GACUGUCC-----------------AA--------------------------------------------------------GACAGGACCCGGCUUA--U-CGGCCAA-CUCACCUC
CP000941.1/425084-425433       GAAG-UC-G-G-C-U-G--GACAGUCGCGUC-AU--C-C-------------------------------------------------------------------------------------------GAGA------G-G-A-U-GCCGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-A-GG-UG----------------CCAGG------------UAACA----------------CCUGGGCGGC-----------------------GUGA------GUCGACGG-AA---AGU-GCAACAGAAA--GAU--ACC-GCCA-AUAU---U--CCU-------------------------------------------------------------------------------------------------------------------------UUCUAGG-A----U--U--CGGUAAGGGUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGA-G-U-U-CG-GUAA--CG-G-A-C--CGG-C-AC----------------GGCAAAC-CCCACCU-GGAGCAAGACC-AAAU------------------------------AGGGA--U-CCUAU------------------------------------------------------GGUGUGGCUC----GCGCU---------GGA---UC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCAC-C-G-UGGUGACGC-G--G-U-G-C-C--UAGAUGAAU-GGCUGUUC-----------------AU--------------------------------------------------------GACAGAACCCGGCUUA--U-AGGCCGA-CUUCACCG
CP000749.1/2967653-2967305     CAAG-UU-G-G-C-U-A--GGCAGUCGCCGC-UC--A-AUUU-------------------------------------------------------------------------------------------------AU-U-G-G-GGGGAGGAAAGUCCGGGCUU-C---GCA--GGGUA-A-AG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GUGA------GCCUACGG-AA---AGU-GCAGCAGAAA--AUAC-ACC-GCC---UAA---G--CAG-------------------------------------------------------------------------------------------------------------------------UUUACUG-C----C------GGUAAGGUUGAAAU----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-A-C-UG-GCAA--CA-GUU-C-GUGG-C-UA----------------GGUAAAC-CCCACUU-GAAGCAAGACC-AAAU------------------------------AGGAA--C-UCUUU------------------------------------------------------GGCGUGACCC----GCGCU---------GAG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--AAA-GACG-U-G-CAGUGAUGU-A--C-G-U-A-U--UAGAUGAAU-GACUGUCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGCCAA-CUUGCAAU
AE008691.1/1699443-1699089     UGAG-UA-A-G-U-C-G--GAUGGCCGCGGG-CG--A-GGCA----------------------------------------------------------------------------------------UUUG-----CC-U-C-G-CACGAGGAAAGUCCGAGCUC-C---ACA--GGGCA-G-GG-UG----------------CCGGG------------UAACA----------------CCCGGUGGAG-----------------------GCGA------CUCCAAGG-AA---AGU-GCCACAGAAA-UGUAG-ACC-GCC----UG---A--CGCUU---------------------------------------------------------------------------------------------------------------------UCAAAGGCG-U----C--G---GGUAAGGGUGCAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-C-G-G--GCGA---C-C-G-G-CUGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGGC--AAAU------------------------------AGGAG--G-GAGUA-----------------------------------------------------GGUGGC---CC----GCCAU--------UUCC---CU-C-----GGGU---U----AA---G-CCGC---------------------U--AGA-GGUA-U-C-AGGCAACUG-A--U-A-C-C-C--UAGAUAGAU-GGCCAUCU-----------------AA--------------------------------------------------------AACAGAACUCGGCUUA--C-GGACUUG-CUCACAUG
CP000472.1/2154687-2155030     CGAG-UU-G-G-C-U-A--GACAGUUGCCGC-GU--U-C-------------------------------------------------------------------------------------------GUAA------G-A-A-C-GGGGAGGAAAGUCCGGGCUU-C---AAA--GAGCA-G-GG-UA----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GUGA------ACCGACGA-CA---AGU-GCAGCAGAGA--GGAG-ACC-GCC----AA---C------------------------------------------------------------------------------------------------------------------------------UUCG----G----U--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGGC-G-G-C-UA-GUAA--UA-GUC-C-GUUG-C-AA----------------GGUAAAC-UCUACCC-GAAGCAAGACC-AAAU------------------------------AGGGU--C-CCGUAU-----------------------------------------------------GGCGCUGCUC----GCGUU---------GGG---AC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCCU-G-U-GAGCAAUUG-C--A-G-G-C-C--UAGAUGAAU-AACUGUCC-----------------AC--------------------------------------------------------GACAGGACCCGGCUUA--U-CGGCCAA-CUCACCUA
CP001336.1/4457100-4456711     AAAG-UU-A-A-U-C-A--GAUGGUCGCGGA-AG--U-AAGAAC-----------------------------------------------------------------------------------CGAAAGG-----UU-G-C-U-UCUGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-A-GG-UG----------------CUGGG------------UAACG----------------CCCAGUGGGA-----------------------GAAA------UCCUAAGG-AC---AGU-GCAACAGAGA--UAU--ACC-GCC----AA---A--CAGCGGCCGGUC------------------------------------------------------------------------------------------------------CGAUGACUGACUGAGCG-U----U--U---GGUAAGGGUGGAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC-GGCAG-C-C---UG-GUGA--CA---G-G-CUGG-C-CC----------------UGCAAAC-CCCACUU-GGAGCAAGACC-GAAU------------------------------AGGGA--G-ACUAU------------------------------------------------------AAAACGGCCC----GUUUU--------UGUC---UC-C-----GGGU---A----AG---G-UCGC---------------------U--UGA-GGCC-G-U-UGGUAACAA-C--G-G-U-C-C--CAGAUAGAU-GAUCAUCA-----------------CCUUCUGAAAGGAAG------------------------------------------GAACAGAACCCGGCUUA--U-AGAUUGG-CUUUGCAU
CP000821.1/5221598-5221247     CGAG-UU-G-G-C-C-A--GACAGUUGCCGC-GU--U-C-------------------------------------------------------------------------------------------GCAA------G-A-A-C-GGGGAGGAAAGUCCGGGCUU-C---AUA--GAGCA-G-GG-UA----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GUGA------ACCGACGA-CA---AGU-GCAGCAGAGA--GGAG-ACC-GCC----UG---C--UUGA-----------------------------------------------------------------------------------------------------------------------UUUAUCAA-G----U--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-G-G-C-UA-GUAA--UA-GUC-C-GUAG-C-AA----------------GGUAAAC-UCUACCC-GAAGCAAGACC-AAAU------------------------------AGGGU--U-CCAUAC-----------------------------------------------------GGCGCGGCUC----GCGUU---------GGA---AC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCCU-G-U-GAGCGAUUG-C--A-G-G-C-C--UAGAUGAAU-AACUGUCC-----------------AC--------------------------------------------------------GACAAGACCCGGCUUA--U-CGGCUUA-CUCUUUGG
AE004439.1/600938-601317       UGAG-UU-G-G-U-C-A--GACAAUCGCUGG-UU--U-AUUGAAGCCCUUAACCGUCUU------------------------------------------------------UAUGACGACCUAGUGGGACAA-----AU-A-G-A-CGAGAGGAAAGUCCGAGCUA-C---ACA--GGGCA-G-AG-UG----------------CCAGG------------UAACG----------------CCUGGGAGGC-----------------------GCGA------GCCUACGA-CA---AGU-GCAACAGAGA--GCAG-ACC-GCC----AG---U------------------------------------------------------------------------------------------------------------------------------UUCG----G----C--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAU-G-G-C-UG-GCAA--CA-GUA-C-AUGG-C-AG----------------GGUAAAC-UCCACUC-GUAGCAAGACC-AAAU------------------------------AGGAA--U-CCAA-------------------------------------------------------UGAGUGGCCC----GCUCA---------GGA---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCGU-A-U-GUGCGAAUG-U--A-C-G-C-C--UAGAGGAAU-GAUUGUCC-----------------GC--------------------------------------------------------GACAGAACUCGGCUUA--U-CGACCAA-CUCAGUAC
CP000447.1/420344-420697       CGAG-UU-G-G-C-C-A--GACAGUUGCCGC-GU--A-C-------------------------------------------------------------------------------------------GCAA------G-U-A-C-GGGGAGGAAAGUCCGGGCUU-C---AAA--GAGCG-G-GG-UA----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GUGA------ACCGACGA-CA---AGU-GCAACAGAGA--GGAA-ACC-GCC----AU---U--UUGGC---------------------------------------------------------------------------------------------------------------------CUAGGCUAA-G----A--U---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-G-G-C-UA-GUAA--UA-GUC-C-GUAG-C-AA----------------GGUAAAC-UCUACCC-GAAGCAAGACC-AAAU------------------------------AGGGU--U-CCGCAU-----------------------------------------------------GGCGCUGCUC----GCGUU---------GGA---AC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCU-G-U-GAGCGAUUG-C--A-G-G-C-C--UAGAUGAAU-AACUGUCC-----------------AC--------------------------------------------------------GACAGGACCCGGCUUA--U-CGGCCAA-CUCACCUC
CP001393.1/1102031-1102382     CGAG-CA-G-G-U-C-G--AACGGCUGCGCA-AG--G-GA-------------------------------------------------------------------------------------------AUA-----AC-C-C-U-UGUGAGGAAAGUCCGAGCUC-C---ACA--GGGCA-G-GG-UG----------------CUGGG------------UAACA----------------CCCAGUGGAG-----------------------GCGA------CUCCAAGG-AA---AGU-GCAACAGAAA--AGA--ACC-GCC----GU---C--CAUU-----------------------------------------------------------------------------------------------------------------------UUUGCAUG-G----A--U---GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCAG-U-C-A-G--GCGA---C-U-G-A-CUGG-C-UG----------------UGCAAAC-CCCACCC-GGAGCAAGACC-AAAU------------------------------AGGGG--A-ACAAU------------------------------------------------------GCAGUGGCCC----GCUGC---------GUU---CC-C-----GGGU---U-----G---G-UCGC---------------------A--AGAGGUCU-G-A-UGGCAACGU-C--A-G-A-C-CCAAAGAGAAAU-AGCCGUUC-----------------UC--------------------------------------------------------GACAGAACUCGGCUUA--C-AGACCUG-GUCGCACA
CU468230.2/2376950-2376596     GAAG-UG-A-G-C-C-G--GAUGGUCGCUGC-UG--U-GGAGGUCU-------------------------------------------------------------------------------CCGUGACUG-----AA-G-C-A-GGAGAGGAAAGUCCGGGCUU-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGCGGU-----------------------GAAA------GCCGACGG-AA---AGU-GCAGCAGAGA--GUAG-ACC-GCC----UC---A------------------------------------------------------------------------------------------------------------------------------UUCG----U----G--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-G-U-C-UG-GGAA--CA-GUU-C-ACGG-C-AU----------------GGCAAAC-CCCACCA-GAAGCAAGACC-AAAU------------------------------AGGAA--U-CCUA-------------------------------------------------------GGUGCGGCCC----GUACU---------GGA---UU-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCGU-A-U-GAGUGAUUG-U--A-C-G-C-C--UAGAGGAAU-GACCAUCC-----------------UC--------------------------------------------------------GACAGAACCCGGCUUA--U-AGGCUCA-CUUCACCU
BX571872.1/169334-168958       GGAG-UU-G-A-C-U-A--GACAGUCGCUGC-UU--U-AUCAUUAAUCC-------------------------------------------------------------------------UUUGGAUGAUAG-----AU-G-G-A-GGAGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------CCAGA------------UAACG----------------UCUGGGGGGU-----------------------GAAA------GCCCACGA-CC---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CUUACU-------------------------------------------------------------------------------------------------------------------UAAUGUAGGA-U----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-G-G-C-UG-GUAA--CA-GUU-C-GUGG-C-AC----------------GGUAAAC-UCCACUC-GGAGCAAGGCC-AAAU------------------------------AGGGG--U-UCAUUA-----------------------------------------------------GGUACGGCCC----GUAUC---------GAA---CC-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GCCA-G-U-GCGUAAGUG-C--U-G-G-C-C--UAGAUGAAU-GAUUGUCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGUCAA-CUUCACAA
BX950851.1/373518-373896       GGAG-UU-G-A-C-C-A--GACAGUCGCCGC-UU--C-ACUGCCGUCCCUU----------------------------------------------------------------------UCGGGGGAGACAG-----GU-G-G-A-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGAGGC-----------------------GCAA------GCCUACGA-CU---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CCCAC--------------------------------------------------------------------------------------------------------------------GCAAGUGGGA-U----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-A-C-UG-GCAA--CA-GUU-C-GUGG-C-AC----------------GGUAAAC-UCCACCC-GGAGCAAGGCC-AAAU------------------------------AGGGG--U-UCACAU-----------------------------------------------------GGUACGGCCC----GUACU---------GAA---CC-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GCCA-G-U-GAGUGAUUG-C--U-G-G-C-C--UAGAUGAAU-GACUGUCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--A-CGGUCAA-CUCCCUUC
AM260525.1/1710521-1710131     UCAG-UC-G-G-C-U-G--GGCAGCCGCGCU-UG--U-CCAAUGC----------------------------------------------------------------------------------UGAAAAG-----CG-G-C-A-GGUGAGGAAAGUCCGGGCUC-C---AUG-GAAAGA-C-GG-UG----------------CCGGG------------UAACA----------------CCCGGCGGGG-----------------------GUGA------CCCUAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----UA---U------------------------------------------------------------------------------------------------------------------------------UUUU----A----U--A---GGUAAGGGUGAAAG----GGU---GG-A--G--U----------------------AAGAG-CCCACC--GCAC-A-U-U-CA-GUAA--UG-A-A-U-GUGG-C-AA----------------GGUAAAC-CCCACCG-GGAGCAAGACC-AAAU------------------------------AGAAA--U-GACGUGCAAGAUUUAA--------------------------------UUUGCAGCCA------AUUUCC-GG-GCG--------AGUCA---UU-C-----GGGU---A-----G---G-UUGC---------------------A--CGA-GGCG-G-G-UGGUAACAU-C--C-G-U-C-C--CAGAUGAAU-GGUUGCCA-----------------UGUAAAGUACAAGCUUU-------------------------------------ACACUACAGAACCCGGCUUA--U-AGGCCGA-CUGAUAUU
CP001616.1/482441-482821       GGGG-UU-G-G-C-C-G--GGCAGUCGCCGU-CU--U-GUUGUUGUGCCU------------------------------------------------------------------------UCGGGUAGACAA-----AC-A-G-G-AGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGAGGC-----------------------GUAA------GCCUACGA-CC---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CCC-------------------------------------------------------------------------------------------------------------------------GCAAGGGAU----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-A-C-UG-GCAA--CA-GUU-C-GUGG-C-AC----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGCU--U-CCAU-------------------------------------------------------GUCGCGGCCC----GCGUC---------GGA---AG-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCU-G-C-GAGCGAUUU-C--A-G-G-C-C--UAGAGGAAU-GGCUGCCA-----------------CCGCGCAAGCGG----------------------------------------------AACAGAACCCGGCUUA--C-AGGCCAA-CCCCACUA
CU468135.1/3254372-3253993     GAAG-CU-G-A-C-C-A--GACAGUCGCCGC-UU--U-GUUGCCGUCCUCC---------------------------------------------------------------------UUCGGGGGAGACAG-----AC-A-G-A-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCAA------GCCCACGA-CC---AGU-GCAACAGAGA--GCAA-ACC-GCCGAUG-----G--CCUAC--------------------------------------------------------------------------------------------------------------------GCAAGUAGGA-U--------C-AGGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-C-UG-GCAA--CA-GUU-C-GUGG-C-AC----------------GGUAAAC-UCCACCC-GGAGCAAGGCC-AAAU------------------------------AGGGG--U-UCACCA-----------------------------------------------------GGUACGGCCC----GUACU---------GAA---CC-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GCCA-G-U-GAGCGAUUG-C--U-G-G-C-C--UAGAUGAAU-GACUGUCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--C-CGGUCAG-CUUCACAC
AP008232.1/411371-411749       GGAG-UU-G-A-C-C-A--GACAGUCGCCGC-UU--C-ACCAUCGUCCCCG----------------------------------------------------------------------CAAGGGGAAACAG-----GU-G-G-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGU-----------------------GCAA------ACCCACGA-CA---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CCCGC--------------------------------------------------------------------------------------------------------------------GCACGCGGGA-U----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-C-UG-GUAA--CA-GUU-C-GCGG-C-AC----------------GGUAAAC-UCCACCC-GGAGCAAGGCC-AAAU------------------------------AGGGG--U-UCACAU-----------------------------------------------------GGUACGGCCC----GUACU---------GAA---CC-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GCCA-G-C-GCGUGAGCG-C--U-G-G-C-C--UAGAUGAAU-GACUGUCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--A-CGGUCAA-CUCCACUC
CP000783.1/3478414-3478038     GAAG-CU-G-A-C-C-A--GACAGUCGCCGC-UU--C-GUCGUCGUCCUU------------------------------------------------------------------------UCGGGGAGACGG-----AC-G-G-A-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCAA------GCCUACGA-CC---AGU-GCAACAGAGA--GCAA-ACC-GCCG--AUG---G--CCCAC--------------------------------------------------------------------------------------------------------------------GCAAGUGGGA-U----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-U-C-UG-GCAA--CA-GUU-C-GCGG-C-AC----------------GGUAAAC-UCCACCC-GGAGCAAGGCC-AAAU------------------------------AGGGG--U-UCACAA-----------------------------------------------------GGUACGGCCC----GUACU---------GAA---CC-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GCCA-G-U-GAGCGAUUG-C--U-G-G-C-C--UAGAUGAAU-GACUGUCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--C-CGGUCAG-CUUCACAC
CR378673.1/179764-179382       GGAG-UU-G-G-U-C-A--GGCGAUCGCUGC-UU--C-GUUGAUGUCCU--------------------------------------------------------------------------UAGGGAGACUG-----AC-G-G-A-GGGGAGGAAAGUCCGGGCUC-C---AAA--GGGCA-G-GG-UG----------------CCAGA------------UAACG----------------UCUGGGGGGC-----------------------GCGA------GCCCACGA-CA---AGU-GCAGCAGAGA--GUAU-ACC-GCCG-AU-G--AC--UCG-------------------------------------------------------------------------------------------------------------------------CUUGCGA-GA--AC-----AGGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-G-C-UA-GUAA--UA-GUU-C-GUGG-C-AU----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGUC--C-CUAAU------------------------------------------------------GGCGCGGCCC----GCGUU---------GGG---GA-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCU-G-U-GAGCGAUUG-C--A-G-G-C-C--UAGAGGAAU-GGUUGCCA-----------------CUGCGAAAG-CAGC--------------------------------------------UACAAAACCCGGCUUA--U-AGACCAA-CUCCACCU
AE016827.1/976620-977008       CGAG-UU-G-G-U-C-A--GACAAUCGCUGG-UU--U-AUUGAAGCCCUUAACCGUAG-------------------------------------------------------UAAUACGACCUAGCGGGACAA-----GU-A-A-A-CGAGAGGAAAGUCCGAGCUA-C---AUA--GGGCA-G-AG-UG----------------CCAGA------------UAACG----------------UCUGGGAGGC-----------------------GUGA------GCCUACGA-CA---AGU-GCAGCAGAGA--GCAA-ACC-GCCG--AUG---G--CUC-------------------------------------------------------------------------------------------------------------------------GCAAGAG-A---UC--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAU-G-G-C-UG-GUAA--CA-GUA-C-AUGG-C-AG----------------GGUAAAC-UCCACUC-GUAGCAAGACC-AAAU------------------------------AGGAA--C-UCAAU------------------------------------------------------GGGUGUGC-C----CGCCC--------AGAG---UU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCGU-A-U-GUGCGAAUA-U--A-C-G-C-C--UAGAGGAAU-GAUUGUCC-----------------GC--------------------------------------------------------GACAGAACUCGGCUUA--U-CGACCAA-CUCAAUCU
CP001145.1/493991-493612       AAGA-GU-A-G-A-C-G-AGGCAGCCGCAAC-C-------------------------------------------------------------------------------------------------AAAA------------G-GUUGAGGAAAGUCCGAGCUC-C---ACA--GAGCA-G-GA-UG----------------CUGGG------------UAACA----------------CCCAGUGAGG-----------------------GCGA------CCUCAAGG-AG---AGU-GCCACAGAAA--ACAA-ACC-GCC----UA---C--CCAA-----------------------------------------------------------------------------------------------------------------------AUGUUUGG-G----U--A---GGUAAGGGUGAAAA----GGC---GG-G--G--U----------------------AAGAG-CCCACC--GCAG-C-A-C-UG-GCGA--CA-G-U-G-CUGG-C-AC----------------GGUAAAC-CCCAUCC-GGAGCAAGGCC-AAGC------------------------------A-GCC--A-GCUGUG----------------------------------------------------A--CCCUGCUC----GGCG---------AGCU---GG-C-----GGGU---A-----G---G-CCGC---------------------U--GGA-GCUU-G-C-UGGCAACAG-C--A-A-G-C-C--AAGAUAAAU-GGUUGCCA-----------------CCCACCAAAACUUUUGAAGGCAACGC--------------------GGUUUUGGUGGGAACAGAACUCGGCUUA--C-CGUCUAC-UCGUAGUU
AM236080.1/3479602-3479205     CCAG-UU-G-G-C-U-G--GGCAGCCGCGCU-UU--A-CCAAUGC---------------------------------------------------------------------------------CGAAAGGC-----GG-U-A-G-GGUGAGGAAAGUCCGGGCUC-C---ACG-GAAACA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGAGG-----------------------GCGA------CCUCAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----UG---U--CA-------------------------------------------------------------------------------------------------------------------------------UG-A----C--A---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCAU-C-U-C-CG-GCAA--CG-G-A-A-AUGG-C-AC----------------GGUAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGA--U-GACGCGGUAGGCCGAA-------------------------------AGGCCUUCCGGCUGGU-UUCCA---G-GCCA--------GUCA---UC-C-----GGGU---G-----G---G-UUGC---------------------G--UGA-GGCA-G-C-GUGCGAACG-C--U-G-U-C-C--CAGAGGAAU-GGCUGCCA-----------------CGUUCCGGUUCACGCCGG-----------------------------------AGCCAUACAGAACCCGGCUUA--C-AGGCCAA-CUGGCGAU
CP000698.1/4631397-4631021     CGAA-GU-A-GAC-C-A--GAUGGCCGCCGC-CC------------------------------------------------------------------------------------------------GCAA----------G-G-GGGGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-U-GG-CG----------------CUGGA------------UAACA----------------UCCAGCGGGG-----------------------GUGA------CCCCAGGG-AA---AGU-GCCACAGAGA--GAAG-UCC-GCC----UG---C--CGGAG--------------------------------------------------------------------------------------------------------------------CUUUGCGAAG-G----C--A---GGUAAGGGUGAAAG----GGU---GA-G--G--U----------------------AAGAG-CUCACC-GGGUC-C-G-G-CG-GUGA--CG-U-C-G-GAUG-C-CA----------------GGUAAAC-CCCGCCA-GGAGCAAGACC-AAAU------------------------------AGGGA--A-GCGUU-----------------------------------------------------AAGGACGGCCC----GUCCG--------UGCU---UC-C-----GGGU---U-----G---G-UUGC---------------------U--UGA-GGCC-G-U-CGGUAACGA-C--G-G-U-C-C--UAGAUGAAU-GGCCAUCG-----------------CCCGCGGUCGGGAAACUUGC--------------------------------AGCGGGAACAGGACCCGGCUUA--U-GGGCUGC-UUCGGCCA
CP000910.1/2951051-2950681     UGGG-GC-A-A-C-U-G--GGCGAUCGCGUG-UU--G-U-------------------------------------------------------------------------------------------GCAA------A-C-A-A-CCCGAGGAACGUCCGGGCUC-C---GAA--GAGCA-C-AG-UG----------------GUGGG------------UAACA----------------CCCACUCGGG-----------------------GUAA------CCCGCAGG-CC---AGU-GCCACAGAAA--AUAG-ACC-GCC----UC---U--GCA-----------------------------------------------------------------------------------------------------------------------------UGC-A----G--A---GGUAAGGGUGAAAC----GGC---GG-U--G--U----------------------AAGAG-ACCACC--GCUU-U-C-C-GG-GUGA--CC-G-G-A-AAGG-CUAA----------------GGUAAAC-CCCACUG-GGAGCAAGGCC-AGAC------------------------------A-GGG--C-ACGUUU----------------------------------------------------GAGGGCUGCUC----GCCCG--------AGUG---UC-C-----GGGU---A-----G---G-CUGC---------------------U--AGA-GGGC-G-U-CGGCAACGG-C--G-U-C-C-G--UAGAUGGAU-GAUCGUCG-----------------CUUCUAUGCUGGUAACGGCG--------------------------------UAGUAAGACAGAACCCGGCGUA--C-AGGUUGC-CCCAUCCG
CP000082.1/408052-408419       UUGG-UA-G-A-C-U-A--GGCAAUCGCCGC-UG--C-ACACUGGC--------------------------------------------------------------------------------AACAGAUU-----GA-G-C-A-GGGGAGGAAAGUCCGGGCUA-C---AUA--GGGCA-G-CG-UG----------------CCAGC------------UAACG----------------GCUGGGCAGG-----------------------GUAA------CUUGACGA-CC---AGU-GCAGCAGAGA--GUAG-ACC-GCC----UU---U--GUUAUC-------------------------------------------------------------------------------------------------------------------GCAAGAUAUC-A----U--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-G-G-C-UG-GCAA--CA-GUU-C-ACGG-C-AU----------------GGUAAAC-UCCACGC-GUAGCAAGACC-AAAU------------------------------AGGCA--U-CGGCAU-----------------------------------------------------GGCGCGGCCC----GCGUU---------CGA---UG-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCGU-A-C-GAGCGAUUG-U--G-C-G-C-C--UAGAGGAAU-GAUUGUCC-----------------AC--------------------------------------------------------GACAGAACCCGGCUUA--U-CGGUUUA-CCAACCUU
CP001197.1/295568-295205       GGAG-CC-G-G-A-C-G--GGCUGUCGUCGC-GG--G-CC------------------------------------------------------------------------------------------GCAA-----GG-C-C-C-GGGGAGGAAAGUCCGGGCUC-C---GCA--GGGCA-G-GA-CG----------------CUGGG------------UAACC----------------CCCAGGACGA-----------------------GCGA------UCGU-CGG-AC---AGG-GCCACAGAAA--ACAG-ACC-GCC----CG---G--CAGG-----------------------------------------------------------------------------------------------------------------------UUCGCCUG-C----C--G---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC-AGCUG-G-C-G-CG-GUGA--CG-C-A-C-CAGG-C-UC----------------GGUAACC-CCCGUCC-GGAGCAAGACC-AAAU------------------------------AGGGA--A-GCGUAC----------------------------------------------------GAGGCCUGCCC----GGCCC-------AUGCU---UC-C-----GGGU---C-----G---G-UUGC---------------------U--UGA-GGGC-G-U-CGGUAACGG-C--G-C-U-C-C--UAGAGGAAU-GACAGCCA-----------------CCCGCAAG----GG--------------------------------------------UACAGAACCCGGCUUA--C-AGUCCGA-CUCCCGAA
CP000633.1/2425356-2424957     CCAG-UC-G-G-C-C-G--GGCAGCCGCGCU-UU--A-CCAAUGC---------------------------------------------------------------------------------CGAAAGGC-----GG-U-A-G-GGUGAGGAAAGUCCGGGCUC-C---ACG-GAAACA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGAGG-----------------------GCGA------CCUCAGGG-AA---AGU-GCCACAGAAA--GCAG-ACC-GCC----CC---G--U----------------------------------------------------------------------------------------------------------------------------UUA--U-C----G--G---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGU-C-G-C-UG-GUGA--CA-G-G-G-ACGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGA--U-GACGCGGGUGCAACGC-------------------------------AAGUUGCGCUA-CAGCCGGUUUU-CGGGCCA--------GUCA---UC-C-----GGGU---G-----G---G-UUGC---------------------G--AGA-GGCG-G-U-GCGCAAGUA-U--C-G-U-C-C--CAGAUGAAU-GGCUGCCA-----------------CGUUCCGGGAAACCGGG-------------------------------------GCCAUACAGAACCCGGCUUA--C-AGGCCGA-CUGGUAUU
CP000628.1/2390520-2390121     CCAG-UU-G-G-C-C-G--GGCAGCCGCGCU-UU--A-CCAAUGC---------------------------------------------------------------------------------CGAAAGGC-----GG-U-A-G-GGGGAGGAAAGUCCGGGCUC-C---ACG-GAAACA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGAGG-----------------------GCGA------CCUCAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----UG---A--UCC-------------------------------------------------------------------------------------------------------------------------UU--GGA-U----C--G---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGU-C-U-C-UG-GCGA--CA-G-C-G-ACGG-C-AC----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--U-GACGCGGAGCGCGA------------------------------------AAGCGCUCCAGCCCGUUUC---CGGGCC-------GGUCA---UC-C-----GGGU---G-----G---G-UUGC---------------------A--UGA-GGCG-G-C-GCGCAAGCG-U--C-G-U-C-C--CAGAUGAAU-GGCUGCCA-----------------CGUUCCGGCCUCGGCCGG-----------------------------------AGCCAUACAGAACCCGGCUUA--C-AGGCCAA-CUGGCAAA
AB047586.1/419-800             GGAG-CU-G-A-C-U-G--GGUAGUCGCUGC-UU--U-GUUGAUGUCCU--------------------------------------------------------------------------UCGGGAGACUG-----AC-A-A-A-GGGGAGGAAAGUCCGGGCUU-C---AUA--GAGCA-A-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCAA------GCCUACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCCG--AUG---G--CCC-------------------------------------------------------------------------------------------------------------------------GUAAGGG-U---AC--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGAC-G-A-C-UA-GCAA--UA-GUU-C-GUAG-C-AG----------------GGUAAAC-UCCACCU-GAAGCAAGACC-AAAU------------------------------AGGCC--U-CCACA-----------------------------------------------------UUGCGUUGCUC----GCGUA--------AGGA---GG-C-----GGGU---A-----G---G-UUGC---------------------U--CGA-GCCA-G-U-GAGUGAUUG-C--U-G-G-C-C--UAGACGAAU-GGCUACCG-----------------CCGCGCAAGCGG----------------------------------------------AACAGAACCCGGCUUA--U-GUGUCGG-CUCCACCU
CP000148.1/443714-444093       CGAA-GC-A-G-AAC-A--GAUGACCGCUCU-CC--G-UU---------------------------------------------------------------------------------------------------CG-C-G-G-AGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-U-GG-UG----------------CUGGA------------UAACG----------------UCCAGCGGGG-----------------------GCGA------CCCCAGGG-AU---AGU-GCCACAGAGA--GAAG-UCC-GCC----UG---C--CGGAGC-------------------------------------------------------------------------------------------------------------------GUUAGCGAAG-G----C--G---GGUAAGGGUGAAAG----GGU---GA-G--G--U----------------------AAGAG-CUCACC-GGGUC-C-G-G-CG-GUGA--CG-U-C-G-GAUG-C-CA----------------GGUAAAC-CCCACCA-GGAGCAAGGCC-GAAU------------------------------AGGGA--A-GCGUU-----------------------------------------------------AAGGACGGCCC----GUCCG--------AGCU---UC-C-----GGGU---U-----G---G-CUGC---------------------U--UGA-GGCC-G-U-CGGUAACGG-C--G-G-U-C-C--CAGAGGAAU-GGUCAUCG-----------------CCCGCCAAGGGGUAACCCGC--------------------------------GGCGGGAACAGAACCCGGCUUA--U-GGGCUGC-UUCGGCCA
CP001056.1/940440-940784       CGAG-CA-A-A-A-C-G--UGCAAUCGCUGC-UG--G-GCU-------------------------------------------------------------------------------------------UG-----AC-C-C-A-GGAGAGGAAAGUCGGGGCUC-C---AUA--GGGCA-G-GG-UG----------------CUGGA------------UAACG----------------UCCAGUCAAG-----------------------GCGA------CUUGAAGG-AU---AGU-GCAACAGAGA--UAU--ACC-GCC----UA---A--G---------------------------------------------------------------------------------------------------------------------------UUUA--C-U----U--A---GGUAAGGGUGGAAA----GGC---GA-G--G--U----------------------AAGAG-CUCACC-AGCGU-G-A-U-G--GUGA---C-A-U-C-ACGG-C-UA----------------UGUAAAC-CCCACUU-GGAGCAAGACC-GAAU------------------------------AGAGA--G-GCAUUA----------------------------------------------------AGGGAUUGCCC----GUCCC---------GCC---UC-C-----GGGU---G-----C---G-UCGC---------------------U--UGA-GCUC-A-U-UGGCAACAA-U--G-A-G-C-C--UAGAUAGAU-GAUUGCUU-----------------AA--------------------------------------------------------UACAGAACCCCGCUUA--C-GGCUUGU-CUCGCAUA
CP001341.1/2464077-2463692     UGGG-AC-A-G-C-C-A--GGCGGCCGCGCG-UC--A-C-------------------------------------------------------------------------------------------GAAA------G-U-G-G-CUCGAGGAACGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------GUGGG------------UAACG----------------CCCACUCGGG-----------------------GUAA------CCCGCAGG-CA---AGU-GCCACAGAGA--AUAG-ACC-GCC----UG---C--GUUUUCCG---------------------------------------------------------------------------------------------------------------UUUUCGGAAAGC-G---GC--A---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCUU-C-C-C-GG-GUGA--CC-G-G-G-AAGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGGCC-AGAC------------------------------A-GGG--C-ACGUUU----------------------------------------------------GAGGGCUGCCC----GCCCG--------AGUG---UC-C-----GGGU---A-----G---G-CCGC---------------------U--AGA-GGGU-G-C-CGGCAACGG-U--A-C-C-C-G--UAGAUGGAU-GGCCGUCG-----------------CCCCCGUGACGGCAACGGCA--------------------------------CGGGGGAACAGAACCCGGCGUA--U-CGGUUGU-CCCAUCCG
CP000488.1/840996-840654       GAAG-UU-G-G-U-C-G--GAUGGUCGCUGG-AG--C-UU---------------------------------------------------------------------------------------------G-----AU-U-C-U-UCAGAGGAAAGUCCGGGCUC-C---AUA--GAGUA-A-AG-UG----------------CUAGC------------UAACA----------------GCUAGGUAUG-----------------------GUGA------CAUAACGG-AA---AGU-GCUACAGAGA-UUUAG-ACC-GCC----UA---U--U----------------------------------------------------------------------------------------------------------------------------UUU--A-A----U--A---GGUAAGGGUGAGAA----GGC---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-A-U-UG-GUGA--CA-A-C-C-GUGG-C-AA----------------GGUAAAC-CCCACUU-GGAGCAAGCUC-AAAU------------------------------AGGCU--G-AUGAUG----------------------------------------------------AC--GUUGCUC----GCU-G--------AGUU---GG-U-----GGGU---A-----G---A-GUGC---------------------U--AAA-GCGU-U-U-UGGCAACAA-A--A-C-A-C-G--UAGAUGAAU-GACCAUCU-----------------AU--------------------------------------------------------UACAGAACCCGGCUUA--U-AGACCGA-CUUCUUUU
AM494475.1/1549288-1548904     GUUG-AU-A-G-C-U-G--UAUGGCUACACA-AA--A-UU-------------------------------------------------------------------------------------------UAU-----AG-A-U-U-UGUGAGGAAAGUCCGAGCUC-C---AUA-AAAGCA-U-AG-UG----------------CUGGG------------UAACG----------------CCCAGCAGAA-----------------------GUAA------UUCUAGGG-AA---AGU-ACCACAGAGA--AUAU-ACC-GCC----AA---A--UAA---------------------------------------------------------------------------------------------------------------------------AUUAA-U----U--U---GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUUACC--GGUA-G-U-U-UA-GUAA--UA-A-A-U-UACG-C-AU----------------GGUAAAC-CCCACUA-GGAGCAAGACC-AAAU------------------------------AGAAG--C-AACAUAACUAA------------------------------------------UAAGU-UAGAAGGCGU----UUUUAUC----UAGUUG---CU-U-----GGGU---A-----G---G-UCGC---------------------U--UGA-GGUA-A-A-UAGUAAUAU-U--U-A-C-C-C--CAGAUAAAU-AGCCGUAA-----------------UUAAUAUAUUAAUUAAUA-----------------------------------UAUUUUACAGAACUCGGCUUA--U-AGGCUAU-CAAUACAA
CP000113.1/7099786-7100181     GGAG-CG-G-C-C-C-G--GGUGAACGCCGG-UC--A-CCGCA-------------------------------------------------------------------------------------GUCAUG-----GG-U-G-G-CGGGAGGAAAGUCCGAGCUC-C---AGA--GGGCA-G-GG-UG----------------CUGGC------------UAACG----------------GCCAGUCGAG-----------------------GCGA------CUCGCAGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----CG---U--UCC-------------------------------------------------------------------------------------------------------------------------GAAAGGG-G----C--G---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-C-C-G-GG-GUGA--CU-C-G-G-ACGG-C-UC----------------GGUAAAC-CCCACCU-GGAGCAAGAGC-CAAU------------------------------AGGAG--C-GCGUCCUCGCCGUA------------------------------------CGGAGGACAGGGAUGGCCC----GUCCC-------AUGCG---UU-C-----GGGU---U-----G---C-UCGC---------------------UGAUGA-GGCCCC-U-GGGCAACCA-G--G-G-C-C-C--UAGAUGAAU-GUUCACCG-----------------CCCAUCCCGAAAGGGGU--------------------------------------GGGAACAGAACUCGGCUUA--C-ACGGCCG-CUCCGGCG
CP001016.1/2691085-2690677     CCAG-UC-G-G-C-C-G--GAUGGCCACCGC---------------------------------------------------------------------------------------------------UCAG--------------GCGGAGGAAAGUCCGGGCUC-C---AUG-GAAACA-C-GG-UG----------------CCGGA------------UAAUG----------------UCCGGCGAGG-----------------------GUGA------CCUCAGGG-AA---AGC-GCCACAGAAA--GGAA-ACC-GCC----UC---G--CAACCGAGCC----------------------------------------------------------------------------------------------------------GAAAGGCGAGGACCG-C---GG--A---GGUAAGGGUGAAAG----GGU---GC-G--G--C----------------------AAGAG-CGCACC--GCGC-U-U-A-UG-GUGA--CA-U-G-A-GCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGG--C-GACAGGCAGCGAACCCAUU--------------------------CGAUGGGACGCUCAAAUCCGUUUC---CAGAUU--------GUCG---CC-C-----GGGU---U-----G---G-UUGC---------------------U--CGA-GGCG-G-C-UGGCAACAG-C--C-G-U-C-C--UAGAGGAAU-GGUCAUCA-----------------CGCAAGCGGUUUCGCCGCU----------------------------------UGCCUUACAGAACCCGGCUUA--C-AGGCCGA-CUGGUAUU
AP009384.1/5180043-5180420     CCAG-CC-G-G-C-C-G--GGCGGCCGCGGU-GC-------C----------------------------------------------------------------------------------------UUGU----------G-C-AUCGAGGAAAGUCCGGGCUC-C---ACG-GAGACA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCUAGGG-AA---AGU-GCCACAGAAA--UCAG-ACC-GCC----CG---C--GCG-----------------------------------------------------------------------------------------------------------------------------UGC-G----C--G---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGC-G-A-C-CG-GCAA--CG-G-A-A-GCGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAGGUC-GAAU------------------------------AGGGA--C-GGCACGGGCGCGC-------------------------------------AAGCGCCCAAUCCGGUCUU----CGGAU-------CGUCG---UC-C-----GGGU---U-----G---A-CUGC---------------------C--AGA-GGCG-C-C-GGGUAACCG-G--C-G-U-C-C--CAGAGGAAU-GGCCGCCA-----------------CGUGGGAGAAAUCCCG---------------------------------------CCAUACAGAACCCGGCUUA--C-AGGCCGG-CUGGUGCU
CP001189.1/3484775-3484361     CCAG-AU-G-G-U-C-G--GGCGGCCGCUGU-CG--C-GUGGA-------------------------------------------------------------------------------------UUUCCC-----AC-G-C-G-GUGGAGGAAAGUCCGGGCUC-C---ACG-GAGGAA-C-GG-UG----------------CCGGC------------UAACG----------------GCCGGCGGGG-----------------------GUGA------CCCCAGGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----CC---C--ACGGCAUUCCG--------------------------------------------------------------------------------------------------------GUUCGCCGGAGAUGGU-G----C--G---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-U-G-CG-GUAA--CG-C-A-G-GCGG-C-AG----------------GGCAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGAA--C-GGCAGACGGACCGCCUCG---------------------------CGCGGGGUCGUCGGGGGUCCCUCC----GCCCC--------GUCG---UU-C-----GGGU---U-----G---G-UCGC---------------------G--UGA-GGCG-C-G-CCGCAAGGC-G--C-G-U-C-C--CAGAGGAAU-GGUCGCCC-----------------CCCUUCAUCGAAGGU------------------------------------------GGACAGAACCCGGCUUA--C-AGACCAU-CUGGCCGU
CP000482.1/3637855-3637487     UGAA-GC-A-GGA-C-A--GACGGCCGCCGC-CG--A---------------------------------------------------------------------------------------------GGUA--------U-C-G-GGGGAGGAAAGUCCGGGCUC-C---ACA--GGGCG-C-GA-UG----------------CUGGA------------UAACG----------------UCCAGCGGGG-----------------------GUGA------CCCCAGGG-AA---AGU-GCCACAGAGA--GAAG-UCC-GCC----UG---C--C----------------------------------------------------------------------------------------------------------------------------ACG--C-G----C--A---GGUAAGGGUGAAAG----GGU---GA-G--G--U----------------------AAGAG-CUCACC-GGGUC-C-A-U-CG-GUGA--CG-G-U-G-GAUG-C-CA----------------GGUAAAC-CCCAUCG-GGAGCAAGACC-UAAU------------------------------AGGGG--G-GCGUC-----------------------------------------------------AAGGGUGGCCC----GCCCG--------UGCC---UC-C-----GGGU---U-----G---G-UUGC---------------------U--UGA-GGCU-G-C-CGGUAACGG-C--A-G-A-C-C--CAGAUGAAU-GGCCGUCG-----------------CCCGGGAAGGGGUAACCCGA--------------------------------CCCGGGAACAGAACCCGGCUUA--C-GGACUGC-UUCAGCCA
AB047591.1/293-732             GGAG-UU-G-A-C-U-G--GGUAGUCGCUGC-UU--U-GUUGAUGUCCUUCGGGAGACUGACGCUGAAGUCCU--------------------------UUGGGAGACUGGCGUUGACGUCCUUCGGGAGACUG-----AC-A-A-A-GGGGAGGAAAGUCCGGGCUC-C---AUA--GAGCA-G-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCAA------GCCCACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCC----GA---U--GGCCUCAUU------------------------------------------------------------------------------------------------------------UCUUCGGAAGGGGC-A----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGAC-G-G-C-UA-GCAA--UA-GUC-C-GUUG-C-AG----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGCC--U-CCACA-----------------------------------------------------UUGCGUUGCUC----GCGUA--------AGGA---GG-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GCCA-G-U-GAGCGAUUG-C--U-G-G-C-C--UAGACGAAU-GGCUACUA-----------------CCGCGCAAGCGG----------------------------------------------AACAGAACCCGGCUUA--U-AUGUCGA-CUCCACCU
CP001196.1/1207538-1207114     UCAG-UC-G-G-C-C-G--GACGGCCGCUCU-UG--C-AGGAUC------------------------------------------------------------------------------------GAAAGG-----UC-G-C-A-AGGGAGGAAAGUCCGGGCUC-C---AUC-GACAUA-C-GG-UG----------------CCGGA------------UAACA----------------UCCGGCGAAG-----------------------GCGA------CUUCAGGG-AA---AGU-GCCACAGAGA--ACGA-ACC-GCC----AC---G--CCCCC--------------------------------------------------------------------------------------------------------------------GCAAGGGUGG-C----U--C---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-C-U-C-CG-GCAA--CG-G-A-G-GCGG-C-AU----------------GGCAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-GGCACAGCGGAAAGUUCGUCUU--------------------CGGACGAUAACCCCGCGGGGUCAUGUC---GGACCC--------GCCG---UC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGCG-C-G-CAGCAAUCC-G--C-G-U-C-C--CAGAGGAAU-GGCCGUCA-----------------CGUCUGCAUGGUGCGAACCGU-----------------------------GCAGGCCCUCCAGAACCCGGCUUA--C-AGGCUGG-CUGACAUC
CP001280.1/3899599-3899981     CCAG-UC-G-G-C-C-G--GAUGGCCGCCGC-C-------------------------------------------------------------------------------------------------UCAG------------G-GCGGAGGAAAGUCCGGGCUC-C---ACA-GAGAAA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCUAGGG-AA---AGC-GCCACAGAAA--ACAG-ACC-GCC---AUC---C--GGC-------------------------------------------------------------------------------------------------------------------------UUGCGCC-G----G--A---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-G-C-A-UG-GCGA--CA-U-G-A-GCGG-C-AC----------------GGCAAGC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGG--C-GACGCGGGGCGC---------------------------------------AGGCCCCAGAUCCUUCUC---UGGAUC--------GUCG---CC-C-----GGGU---U-----G---G-UUGC---------------------U--CGA-GGCG-G-C-CGGUAACGG-C--C-G-U-C-C--CAGAGGAAU-GGCCAUCG-----------------CGCGCCGCGGACUCCGCGG----------------------------------CGCCUUACAGAACCCGGCUUA--A-AGGCCGG-CUGGCGCC
CP001087.1/3336133-3335754     CGGA-CC-A-G-A-CUA--GGCGAUCGCGGG-AU--C---------------------------------------------------------------------------------------------GAAA--------G-A-U-UUCGAGGAAAGUCCGAACAC-C---GCA--GGGCA-G-GA-CG----------------CUCCA------------UAACG----------------UGGAGUCGCA-----------------------GCAA------UGUGAAGG-AA---AGU-GCAGCAGAGA--AUAG-ACC-GCC----GG---G--CACCC---------------------------------------------------------------------------------------------------------------------CUUGGGGUG-C----C--C---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGUUU-U-C-C-AG-GUGA--CU-G-G-A-AAAG-C-UU----------------GGUAAAC-CCCGUCC-GGUGCAAGACC-AAAU------------------------------AGAGA--A-GCGUUU----------------------------------------------------GAGGGUUGCCC----GCCUG--------AGCU---UC-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-GGUG-C-A-CGGCAACGU-G--C-A-U-C-C--UAGAUGAAU-GAUCGCUG-----------------CCCCGGCAUCGGGUAACCGU-------------------------------GCAGGGGUACAGGAUUCGGCUUA--C-UGGCUGA-UCUGGCCG
CP000250.1/2253459-2253028     UCAG-UC-G-G-C-C-G--GACGGCCGCUCC-CG--C-ACCGGC-----------------------------------------------------------------------------------CGAAAGG-----CU-G-C-G-GGGGAGGAAAGUCCGGGCUC-C---AUC-GACAUA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAGA--CCGA-ACC-GCC----CC---G--CGAAGCC-----------------------------------------------------------------------------------------------------------------GCAAGGCGAAG-C----G--G---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-C-U-C-CG-GCAA--CG-G-A-G-ACGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-GGCAUCGCGGACAGUUCGCUCU--------------------CGGGCGAUAACUCCGCAGGGUGAUGUC---AAACCC--------GCCG---UC-C-----GGGU---A-----G---G-UUGC---------------------U--CGA-GGCG-C-U-GUGCAAACA-G--C-G-U-C-C--CAGAGGAAU-GGCCGUCG-----------------CGUAUCGCUCCGCCUCACGGCGA--------------------------GCGGUGCCCUCCAGAACCCGGCUUA--C-AGGCCGA-CUGAUACU
CP000860.1/536580-536991       CGAG-UA-A-A-C-C-A--GGUGAUCGCGGG-UA--C-CGUU-------------------------------------------------------------------------------------------------UG-G-U-A-UUCGAGGAAAGUCCGAGCUC-C---GCA--GGGCA-G-GG-UG----------------CUGGG------------UAACU----------------CCCAGUGGGG-----------------------GCGA------CCCCAAGG-AA---AGU-GCCACAGAAA--UGUGUACC-GCC----GU---G--CGUCGGAGCCGGUCGCCGGAGGUCUGGAAUCGGC-----------------------------------------------------------AAGCCUUCCGAGACGGACUUCCUGAGACCGGCGGCCGG-U----A--C---GGUAAGGGUGGAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGG-U-C-A-G--GUGA---C-U-G-G-CCGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGACC-AAAU------------------------------AGGGG--A-ACAAU------------------------------------------------------GGAGCGGCCC----GCUCC---------GUU---CC-C-----GGGU--UA-----G---G-UCGC---------------------U--AGA-GGCGUC-C-GGGCAACCG-G--C-G-U-C-C--CAGAUAGAU-GAUCAUCC-----------------AC--------------------------------------------------------GACAGAACUCGGCUUA--C-AGGUUUA-CUCGCCCG
CP000463.1/2310384-2309954     UCAG-UC-G-G-C-C-G--GACGGCCGCUCC-CG--C-UAUGGU-----------------------------------------------------------------------------------CGAAAGG-----CU-G-C-G-GGGGAGGAAAGUCCGGGCUC-C---AUC-GACAUA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCUAGGG-AA---AGU-GCCACAGAGA--ACGA-ACC-GCC----CC---G--CAAAGCC-----------------------------------------------------------------------------------------------------------------GCAAGGCGAAG-C----G--A---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-C-G-C-CG-GCAA--CG-G-C-G-AUGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-GGCAUCGCGGACAGUUCGCUUU--------------------CGGGCGAUAACUCCGCAGGGUGAUGUC---AAACCC--------GCCG---UC-C-----GGGU---A-----G---G-UUGC---------------------U--CGA-GGCC-A-U-GUGCAAACA-U--G-G-U-C-C--CAGAGGAAU-GGCCGUCG-----------------CGUAUCGGCUCGCGCAAGCGAG---------------------------ACGGUGCCCUCCAGAACCCGGCUUA--C-AGGCCGG-CUGACGUU
CP001389.1/2181601-2181204     CCAG-UU-G-G-C-C-G--GGCAGCCGCGCC-CC--G-CAGGUGC---------------------------------------------------------------------------------CGAAAGGC-----CG-C-G-G-GGUGAGGAAAGUCCGGGCUC-C---ACG-GAAACA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCU----CC---G--C-----------------------------------------------------------------------------------------------------------------------------UC--G-C----G--G---AGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGG-A-C-A-UG-GCGA--CA-U-G-G-ACGG-C-AC----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--U-GACACGGGCGCGCA-----------------------------------AGCGCCCAGCCGGU-UUCCA---G-GCCG--------GUCA---UC-C-----GGGU---G-----G---G-UUGC---------------------A--CGA-GGCU-G-U-GCGCAAGCG-C--A-G-U-C-C--CAGAUGAAU-GGCUGCCA-----------------CGUUCCGCUUCCUCGGAGGC-------------------------------GGAGCCAUACAGAACCCGGCUUA--C-AGGCCAA-CUGGCGAU
CU458896.1/1909668-1910072     CGAG-UU-G-G-C-C-G--GGCGGCCGCGGA-UC--A-CGAGAG------------------------------------------------------------------------------------AAAUCU-----CG-C-G-G-UUCGAGGAAAGUCCGGACUU-C---ACA--GAGCA-G-GG-UG----------------AUUGC------------UAACG----------------GCAAUCCGAG-----------------------GUGA------CUCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----AC---C--A---------------------------------------------------------------------------------------------------------------------------CUCG--U-G----G--U---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGG-A-C-C-GG-GUGA--CC-G-G-U-UCGG-C-UC----------------GGUAAAC-CCCACCC-GAAGCAAGGCC-AAAAGGCUGUGCG------------UGCACAGCUGCGGA--A-GUGUUC----------------------------------------------------GAGGGCUGCUC----GCCCG--------AGCU---UC-C-----GGGU---A-----G---G-CCGC---------------------U--CGA-GGUA-C-C-CGGCGACGGUG--U-A-C-C----CAGAUGGAU-GGUCGCCG-----------------CCGCGUGGCCGCGGCUAGCCCGU-------------------------GGCUGUGCGGAACAGGAUCCGGCUUA--C-AGGCCAA-CUCGUUCG
CP001185.1/1619726-1619403     UGAG-UG-G-A-G-C-G--AGGAGGCGCAGC-UU--U---------------------------------------------------------------------------------------------------------A-A-A-GCUGAGGAAAGUCCGGACUC-C---G-U--GGGCA-G-GG-UG----------------CCGGA------------UAACA----------------UCCGGAGGGA-----------------------GUGA------UCCC-UGG-AC---AGG-GCCAUAGAGA-AGAAA-ACC-ACC----A------------------------------------------------------------------------------------------------------------------------------------CUA------------U---GGUAAGGGUGGAAC----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGGUA-U-G-G-A--GUAA---U-C-C-A-UACG-C-UU----------------GGCAACC-CCCACCU-GGAGCAAGGUC-AAGC------------------------------AG-GG--U-U----------------------------------------------------------UGGGUGGCCC----GCCCU--------AUAA---CC------CGGGU---A-----G---A-CCGC---------------------U--UGA-GGAA-U-U-UGGUAACAA-A--U-U-C-C-C--AAGAUAGAU-GCCUCCAA-----------------A---------------------------------------------------------AACAGAAUCCGGCUUA--C-CGCUCCA-CUCAUUUU
AB047588.1/607-1060            GGAG-CU-G-A-C-U-G--GGUAGUCGCUGC-UU--U-GUUGAUGUCCUUCGGGAGACUGACGUCGAAGUCCCUUCGGGAGACUGACGUCGAAGUCCCUUUGGGAGACUGACGUUGACGUCCUUCGGGAGACUG-----AC-A-A-A-GGGGAGGAAAGUCCGGGCUU-C---AUA--GAGCA-A-GG-UG----------------CCAGG------------UAACG----------------CCUGGGGGGC-----------------------GCAA------GCCUACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCC----GA---U-GGCC-------------------------------------------------------------------------------------------------------------------------UUAGGGC-A----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGAC-G-A-C-UA-GUAA--UA-GUU-C-GUAG-C-AG----------------GGUAAAC-UCCACCU-GAAGCAAGACC-AAAU------------------------------AGGCC--U-CCACA-----------------------------------------------------UUGCGUUGCUC----GCGUA--------AGGA---GG-C-----GGGU---A-----G---G-UUGC---------------------U--CGA-GCCA-G-U-GAGUGAUUG-C--U-G-G-C-C--UAGACGAAU-GGCUACCG-----------------CCGCGCAAGCGG----------------------------------------------AACAGAACCCGGCUUA--U-GUGUCGG-CUCCACCU
CP000454.1/2736332-2735941     UGGG-UU-G-A-C-C-A--GGCGGCCGCGCG-UC--A-C-------------------------------------------------------------------------------------------GCAA------G-U-G-G-CUCGAGGAACGUCCGGGCUC-C---GCA--GAGCA-G-GG-UG----------------GUGGG------------UAACG----------------CCCACUCGGG-----------------------GUAA------CCCGCAGG-CC---AGU-GCCACAGAGA--ACAG-ACC-GCC----UG---C--CGCGGUCCGUG---------------------------------------------------------------------------------------------------------UCCGCACGGGCUGUG-A---AC--A---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCUU-C-C-C-GG-GUGA--CC-G-G-G-AAGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGGCC-AGAC------------------------------A-GGG--C-ACGUUC----------------------------------------------------GAGGGCUGCUC----GCCCG--------AGUG---UC-C-----GGGU---A-----G---G-CCGC---------------------U--GGA-GGGC-G-U-CGGCAACGG-C--G-U-U-C-G--UAGAUGGAU-GGCCGCUA-----------------UUCCCGCACCGGCAACGGCG--------------------------------CGGGAACACAGAACCCGGCGUA--U-CGGUCAA-CCCAUCCA
AM747720.1/3667865-3667454     AAAG-CA-G-G-C-C-A--GGCAGUCGCGGC-CU--C-GCCGUCU---------------------------------------------------------------------------------UCGGGCGC-----GC-G-G-G-GGCGAGGAAAGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------AUGGC------------UAACG----------------GCCAUCCGUG-----------------------GCGA------CACGCGGA-AC---AGG-GCAACAGAAA--GCAA-ACC-GCCG--AUG---G--CCCGGC------------------------------------------------------------------------------------------------------------------GCAAGCCGGGA-U----C--A---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-C-G-A-CG-GCGA--CG-UUC-G-CCGG-C-AC----------------GGUAACC-UCCACCC-GGAGCAAUUCC-AAGU------------------------------AGGCA--G-GCGCGCAUUUUC---------------------------------------GGAUGCAGGACGGGGCCC----CCGUC-------UCGUC---UG-C-----GGGU---A-----G---G-AAGC---------------------U--UGA-GCGC-G-U-CAGCAAUGG-C--G-C-G-C-C--UAGAGGAAU-GACUGCCA-----------------CGCGUUGCGUGCUUCGGUGCG------------------------------CGGCGUGCACAGAAUCCGGCUUA--U-CGGCCUG-CUUUGCCG
AP009493.1/6142372-6142780     CGAG-CC-G-G-G-C-G--GACGGCCGCGUG-AG--G-AUCC---------------------------------------------------------------------------------------CUCGG-----GA-C-C-U-CCCGAGGAACGUCCGGGCUC-C---ACA--GGGCA-G-GG-UG----------------GUGGC------------UAACG----------------GCCACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----CG---G--GAC-------------------------------------------------------------------------------------------------------------------------UCCGGUC-C----C--G---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGC-C-U-G-AG-GUGA--CU-C-A-G-GCGG-C-UA----------------GGUAAAC-CCCACCC-GGAGCAAGGUC-AAAAGGAGGCGCCCCGGA--AACGGGACGGCUCUGCGUG--A-ACGUUC----------------------------------------------------GAGGGCUGCUC----GCCCG--------AGUU---CA-C-----GGGU---G-----G---A-CCGC---------------------A--CGA-GGCC-G-G-CAGCAAUGC-C--G-G-C-C-C--UAGAUGGAU-GGCCGUCU-----------------CCCCGGCCGCCGCGAGGCGA--------------------------------CCGGGAGACAGAACCCGGCGUA--C-AGCCCGA-CUCGUCUG
AE017196.1/707035-706686       CUAG-GU-G-G-A-AUA--AGUAGCUGCUGU-UG--U-GUG-----------------------------------------------------------------------------------------AUAA-----AC-A-U-A-GCAGAGGAAAGUCCGGGCUC-C---AAG-GAAAAA-U-AG-UG----------------ACGGG------------UAAUG----------------CCCGCCGGAG-----------------------GUAA------CUCCAGUU-AU---AGG-GCUACAGAAA--AUU--ACC-GCC----UA---A--AA---------------------------------------------------------------------------------------------------------------------------UAU-UU-U----U--A---GGUAAGGGUGAAAA----GGU---GU-G--G--U----------------------AAGAG-CACACC--AUGG-C-A-A-UG-GCAA--CA-U-U-G-GUAG-U-CG----------------AGUAACC-AACACUA-GGAGCAAGAUU-AAAU------------------------------AGAAG--U-AGAUU-----------------------------------------------------UUAUGUUUUCC----UCAUA--------UCUA---CU-C-----GGGU---A-----A---A-UCGC---------------------A--UGC-GGUA-A-A-UGGUAACAU-U--U-A-C-U-C--CAGAUAAAU-AGCUACAU-----------------A---------------------------------------------------------AACAGAACUCGGCUUA--U-AUUUCAC-CUAGGCGU
CP000885.1/4346921-4346525     UGAG-UA-G-U-A-C-A--GAUGAUCGCGCC-GA--U-U----------------------------------------------------------------------------------------------U------A-A-U-C-GGUGAGGAAAGUCCGGGCUU-C---AUA--GGGCA-G-GG-UG----------------CCGGA------------UAACG----------------UCCGGUGGAG-----------------------GCGA------CUCUAAGG-CC---AGU-GCAACAGAAA--AUAA-ACC-GCC----UA---A--CCGCAGGUUAG---------------------------------------------------------------------------------------------------------AUAAUAACCGUUAGG-U----U--A---GGUAAGGGUGGAAU----GGC---GG-U--G--U----------------------AAGAG-ACCACC--GCUU-C-U-C-UG-GUAA--CA-G-A-G-AAGG-C-UG----------------UGUAAAC-CCCACUU-GAAGCAAGACC-AAACAAAUACC---------------UUUAUGGUAUGAG--A-GCGAU------------------------------------------------------ACGGCGGCCC----GUCGU---------GCU---CU-U-----AGGU---A-----G---G-UCGCGUUUUGUCUGGUAACGGGCAAA--UGA-GCUG-U-A-UGGUAACGU-A--C-A-G-U-C--AAGAUAGAU-GAUCAUCA-----------------AA--------------------------------------------------------UACAGAACCCGGCUUA--U-AGUACUA-CUCAACUU
AP009152.1/1651041-1650663     CAGG-UG-G-G-C-C-G--GGCGACCGCGCG-GC--G-UCGUCGU----------------------------------------------------------------------------------UCGCGAC-----GG-C-G-U-CUCGAGGAAAGUCCGGGCUC-C---GCA--GAGCA-G-GA-CG----------------GUGGG------------UAACA----------------CCCACUCGGG-----------------------GAAA------CCCGCAGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----CG---C--C----------------------------------------------------------------------------------------------------------------------------GCG--A-G----C--G---GGUCAGGGUGAAAA----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGC-G-C-C-GG-GUGA--CC-G-G-C-GCGG-C-UC----------------GGUAAAC-CCCGUCC-GGAGCAAGGCC-AUGC------------------------------A-GGG--C-GCGUUC----------------------------------------------------GAGGGCUGCUC----GCCCG--------AGCG---UC-C-----GGGU---A-----G---G-CUGC---------------------U--CGA-GCCG-U-G-CGGCAACGC-A--C-G-G-C-C--UAGAUGGAU-GGUCGUCA-----------------CCGCGGUGCGGGCAACCGG---------------------------------CCGCGGCACAGAACCCGGCUCA--C-AGGCCCA-CCUGUCCA
CP001043.1/2886567-2886154     AAAG-UA-G-G-C-C-A--GGCAGUCGCGGC-UU--C-GCUGGUU----------------------------------------------------------------------------------UCGGCUG-----GC-G-A-G-GGCGAGGAAAGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------AUGGC------------UAACG----------------GCCAUCCGUG-----------------------GCGA------CACGCGGA-AC---AGG-GCAACAGAAA--GCAA-ACC-GCCG--AUG---G--CCCGUC------------------------------------------------------------------------------------------------------------------GCAAGACGGGA-U----C--A---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-C-U-G-CG-GCGA--CG-C-A-GACCGG-C-AC----------------GGUAACC-UCCACCC-GGAGCAAUUCC-AAGU------------------------------AGGCA--G-GCGCGCAUCUUCG--------------------------------------AGAUGCAGGAUGGGGCCC----CCGUC-------UCGUC---UG-C-----GGGU---A-----G---G-AAGC---------------------U--UGA-GCGC-G-U-CAGCAAUGG-C--G-C-G-C-C--UAGAGGAAU-GGCUGCCA-----------------CGCGUGGGGCGCUUUCGGGCGC----------------------------GUCGCGUGCACAGAAUCCGGCUUA--U-CGGCCUG-CUUUGCCG
CP001096.1/4356479-4356935     UCAG-UC-G-G-C-C-G--GACGGCCGCUCC-GG--C-AAGUGC-----------------------------------------------------------------------------------CGAAAGG-----CC-G-C-C-GGGGAGGAAAGUCCGGGCUC-C---AUC-GACAUA-C-GG-UG----------------CCGGA------------UAACG----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAGA--ACGA-ACC-GCU----UC---C--UCUUUCUUCUCCCUCCCCCG---------------------------------------------------------------------------------------CUUGCGGGGGAGGGUCGGGGUGGG-G----G--C---AGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGU-C-G-C-CG-GCAA--CG-G-G-G-ACGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--C-GGCAUCGCGGAUAGUUCGCUGCU------------------CGCAGCGAUAACUCCGCAGGGCGAUGUC---AGGCUC--------GCCG---UC-C-----GGGU---A-----G---G-UUGC---------------------U--CGA-GGCG-C-U-GUGCAAACA-G--U-G-U-C-C--CAGAGGAAU-GGCCGUCG-----------------CGCAUCGCCUCCGCAAGGAAG-----------------------------CGGUGCCCUCCAGAACCCGGCUUA--C-AGGCCGG-CUGAUACU
AP009153.1/4390-3973           GUCA-CC-G-G-C-C-G--GAUGGUCGCGAA-AC--A-GGGGAACGAGCCU----------------------------------------------------------------------UCAUGGCCACGCC-----CG-U-G-U-UCCGAGGAAAGUCCGGGCUC-C---AUA--GGGCA-G-AU-CG----------------CCAGG------------UAACG----------------CCUGGGCGCAUAC-----------------GGCGUGAGCUGCAUGCGACGG-AC---AGU-GCAACAGAAA--GCAA-ACC-GCC----GU---C--UUC-------------------------------------------------------------------------------------------------------------------------GCGAGAA-G----G--C---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GCGC-G-U-C-CG-GCAA--CG-G-G-C-GUGG-C-UC----------------GGUAAAC-CCCGGUC-GGAGCAAGGCC-AAAU------------------------------AGGCG--G-UGAGAGACGGCCCG------------------------------------UCUCGACAGGAUGCUUUCG---GGCAUC--------GAGC---CG-C-----GGGU---A-----G---G-CUGC---------------------U--GGA-GCGU-G-U-UGGUGACGA-C--A-C-G-C-C--GAGAGGAAU-GACCAUCC-----------------GGUGCACCUCGGUGUA----------------------------------------CCGACAGAACCCGGCUUA--C-AGGCCGG-UGACAUCC
CP000812.1/706597-706925       GGAG-AG-A-G-G-C-G--GGUGGUCGCAGG-C--------------------------------------------------------------------------------------------------GCU------------G-CCUGAGGAAAGUCCGGACUC-C---ACA--GGGCA-G-GA-CG----------------CUGGG------------UAAUA----------------CCCAGGAGGA-----------------------GCGA------UCCU-CGG-AC---AGG-GCCAUAGAGACUUCAA-ACC-GCC----U-----------------------------------------------------------------------------------------------------------------------------------UGAA------------A---GGCAAGGGUGGAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGCAU-C-G-G-G--GUGA---C-C-C-G-AUGG-C-UC----------------GGUAACC-CCCGUUC-GGAGCAAGGCC-AAGC------------------------------AG-GG--G-UU----------------------------------------------------------GGGUGGUCC---CGCCC-G------AUAAC---CC------CGGGU---A-----G---G-CCGC---------------------U--UGA-GGAG-G-G-UGGUAACAC-C--C-U-U-C-C--AAGAUAGAU-GACCACCU-----------------GA--------------------------------------------------------GACAGAAUCCGGCUUA--C-GGCCUCU-CUCCGAUU
CP000084.1/39405-39051         CUAG-AU-G-A-A-C-G--ACUUAUCGCUUU-AA------------------------------------------------------------------------------------------------UUUA----------U-U-AAAGAGGAAAGUCCGGGCUC-C---GCA-AAGACA-C-AG-UG----------------CCAGA------------UAAUA----------------CCUGGCGGGG-----------------------GAAA------CCCUAGGG-AU---AGU-GCCACAGAAA--AUAU-ACC-GCC----AU-----------------------------------------------------------------------------------------------------------------------------------AAC---------A--U---GGCAAGGGUGAAAA----GGU---GU-G--G--U----------------------AAGAG-CGCACC--GGUU-CUA-U-UG-GUAA--CA-A-U-G-AACG-C--U----------------GGAAAAC-CCCACUG-GGAGCAAGACU-AAGU------------------------------AGAGA--U-GACAUUGUUGCA----------------------------------------AAACUAAAAGCCGUCUU---UGGCUA--------GUCA---UC-A-----GGGU---U-----A---G-UUGC---------------------A--UGA-GCUU-A-A-GAGUGAUCU-U--A-A-G-C-C--UAGAGAAAU-GAUAGGUU-----------------UAAAU-----------------------------------------------------GACAGAACCCGGCUUA--U-AGUUUGU-CUAGCAAA
AP008971.1/892181-891852       UGAC-UA-A-A-U-C-A--GAUAAUCGCAUG-AA--------------------------------------------------------------------------------------------------------------U-U-CAUGAGGAAAGUCCGUGCAC-U---AUA-GAGCGA-G-GA-UG----------------CUGGA------------UAACG----------------UCCAGUGGGG-----------------------GCGA------CCCUAAGG-CU---AGU-GCAACAGAGA--UAU--ACC-GCC----AU-----------------------------------------------------------------------------------------------------------------------------------UUA---------A--U---GGUAAGGGUGGAAA----GGU---AG-G--G--U----------------------AAGAG-CCUACC-AGCAU-A-A-A-G--GUGA---C-U-U-U-AUGG-C-UA----------------UGUAAAC-CCCAUUC-AGUGCAAAAUC-AAAU------------------------------AG-----G-AAUAAA----------------------------------------------------GACGGCUGCUC----GUCGU--------CUCC---GG-U-----AGGU---A-----G---A-UUGC---------------------U--UGA-ACUA-A-U-UGGUAACAA-U--U-A-G-U-C--UAGAUAGAU-GAUUAUCA-----------------AA--------------------------------------------------------UACAGAACACGGCUUA--U-AGAUUUG-GUCAUAAA
CP000850.1/4149263-4148852     CGAG-UC-G-A-C-C-G--GGCGGUCGCGUC-GG--U-GGGU----------------------------------------------------------------------------------------UUGG----CCC-G-C-C-GUCGAGGAACGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------GUUGC------------UAACG----------------GCAACCCGGG-----------------------GUGA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----GU---U--CCC-------------------------------------------------------------------------------------------------------------------------A-UCGGG-G----A--C---GGUAAGGGUGAAAC----GGU---GG-G--G--U----------------------AAGAG-CCCACC-AGCAC-C-C-C-GG-GUGA--CC-G-G-G-GUGG-C-UC----------------GGUAAAC-CCCACCC-GGAGCAAGGCC-AAGA------------------------------AGGGC--G-UCAUCUGCGGAGACGACGAC------------------------CCGCGCAGGCGAUCGAGGGCGGCCC----GUCCG-------AUGUC---UG-C-----GGGU---A-----G---G-CCGC---------------------U--GGA-GCCU-G-U-CGGUGACGG-C--A-G-G-C-C--GAGAUGGAU-GACCGCCG-----------------CCGGCGCGAACCCUCGGGUGC-----------------------------GCGCCGCGCACAGAAUCCGGCGUA--C-AGGUCGA-CUCGUCCG
CR767821.1/1094194-1094531     UCAG-GU-A-A-G-A-A--AGUAGUUGCUGU-AU--U---------------------------------------------------------------------------------------------UCAU--------A-A-U-GCAGAGGAAAGUCCGGACUC-C---AAG-GGAAAA-U-GG-UG----------------ACAGG------------UAACU----------------CCUGUCGGAG-----------------------GUAA------CUCUAGGU-AU---AGG-ACUACAGAAA--AUA--ACC-GCC----UU---A------------------------------------------------------------------------------------------------------------------------------CUAA----U----A--A---GGUAAGGGUGAAAA----GGU---GU-G--G--U----------------------AAGAG-CACACC--GUAC-U-U-A-UG-GCAA--CA-UAU-A-GUAG-C-UA----------------AGCAACC-ACCACCA-GGAGCAAGACU-AAA-------------------------------AGAGA--U-AUA--------------------------------------------------------UGUGUUUUCC---CUCACA--------AUUA---UC-U-----AGGU---A-----A---G-UCGC---------------------G--UGA-GGUA-G-A-UAGCAAUAU-U--U-A-U-C-C--CAGAUGAAU-AACUACAC-----------------A---------------------------------------------------------AACAGAAUCCGGCUUA--C--UCUUAC-CUGACCAU
CP001322.1/3925535-3925148     AGAG-GA-G-A-C-C-A--GGCGGCCGCCGG-GU------UU----------------------------------------------------------------------------------------CACC----------U-C-CCGGAGGAAAGUCCGAACAC-C---GCA--GGGCA-G-GG-UG----------------CUCCG------------UAACG----------------CGGAGUCGCG-----------------------GCAA------CGCGAAGG-CA---AGU-GCAACAGAAA--GUAU-ACC-GCC----UG---G--CAGUCUCGCU-----------------------------------------------------------------------------------------------------------UUUGAGCGGGCCUG-C----C--C---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGUUC-C-C-C-GG-GCGA--UC-G-G-G-GAAG-C-UG----------------GGUAAAC-CCCACCC-GGUGCAAGACC-AAAU------------------------------AGGGG--A-GCUCA-----------------------------------------------------UGCAGCGGCCC----GCUGU-------AGGCU---CC-C-----GGGU---A-----G---G-UUGC---------------------A--AGA-GGCG-U-C-GGGCAACCG-G--C-G-C-C-C-UUAGAUGAAU-GGCCGCCG-----------------CCCUGGCCGGGGCGACCCGA--------------------------------CCAGGGAACAGAAUUCGGCUUA--C--GGUUUC-CUUUGACC
AE016958.1/2182909-2182516     CGAG-UU-G-G-C-C-G--GGCGGCCGCGGC-UC--G-UAU--------------------------------------------------------------------------------------------------CC-C-G-A-GUCGAGGAAAGUCCGGACUU-C---ACA--GAGCA-G-GG-UG----------------AUUGC------------UAACG----------------GCAAUCCGAG-----------------------GUGA------CUCGCGGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----AC---C--C----------------------------------------------------------------------------------------------------------------------------UCG--C-G----G--U---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAC-C-C-C-GG-GUGA--CC-G-G-G-GUGG-C-UC----------------GGCAAAC-CCCACCC-GAAGCAAGGCC-AA----------------------------------GAA--G-GCCGUGCCGCCGGCACGGC--------------------------CGCGCAGGCGUCCGAGGGUUGCUC----GCCCG--------AGCC---UG-C-----GGGU---A-----G---G-CCGC---------------------U--CGA-GGCA-C-C-CGGUGACGGUG--U-G-U-C----CAGAUGGAU-GGUCGCCG-----------------CCGCGGCGCCGGUUUUCCGGC------------------------------GGCGCGGAACAGAAUCCGGCUUA--C-AGGCCAA-CUCGUCCG
CP000236.1/343907-343570       UCAG-GU-A-A-A-A-A--AGUAGUUGCUGU-AU--U---------------------------------------------------------------------------------------------GUAA--------A-G-U-ACAGAGGAAAGUCCGGACUC-C---AAG-GGAAAA-U-GG-UG----------------ACAGG------------UAAUC----------------CCUGUCGGAG-----------------------GUGA------CUCUAGGU-AA---AGG-GCUACAGAAA--AUA--ACC-GCC----UU---G-------------------------------------------------------------------------------------------------------------------------------UUA----C----A--A---GGUAAGGGUGAAAA----GGC---GU-G--G--U----------------------AAGAG-CACACC--GUAC-U-U-A-UG-GCAA--CA-UAU-A-GUAG-C-UA----------------AGUAACC-ACCACCA-GGAGCAAGACU-AAGA------------------------------AGAGG--U-AUU--------------------------------------------------------UGUGUUUUCC---CUCACA--------AUUA---CC-C-----AGGU---G-----A---G-UCGC---------------------G--UGA-GGUA-G-G-UAGCGAUAU-C--U-A-U-C-C--CAGAUGAAU-AACUACAU-----------------A---------------------------------------------------------AACAGAAUCCGGCUUA--U--UUUUAC-CUGGCAAG
AP009179.1/609781-610130       CAGG-UG-C-A-A-C-A--GGUAGUUGCUGG-UG--A-CA------------------------------------------------------------------------------------------UUUG-----UG-U-C-A-CGAGAGGAAAGUCCGGGCUG-C---AAGUGAGACA-G-GA-CU----------------CCAUC------------UAACG----------------GAUGGCCAGA-----------------------GUAA------UCUGAGGG-CA---AGU-GCAACAGAAA--GUAA-ACC-GCC----AG---A--C----------------------------------------------------------------------------------------------------------------------------UUU--G-U----U--U---GGUAAGGGUGAAAG----GGU---GG-G--G--C----------------------AAGAG-CCCACC-GGUGA-G-U-G-UG-GUAA--CA-C-G-C-UCAG-C-CA----------------GGUAAAC-CCUGUCC-GCAGCAAGAAG-UAUA------------------------------UGGU-------AUAAGUCU--------------------------------------------CACAA-GCCGUUCAG---UCGGC---------A---------C-----UCAU---A-----C---U-UCGC---------------------U--CGA-GCCU-G-C-UGGCAACAA-C--A-G-G-C-C--UAGAUAAAU-AACUACCC-----------------AAU-------------------------------------------------------GACAGAACCCGGCUUA--U-CGUUGCA-CCUAUUAU
CP001001.1/2506640-2506242     UCAG-CC-G-G-C-C-G--GGCAGCCGCUCC-GG--A-CGCG----------------------------------------------------------------------------------------CGAG-----CG-U-U-C-GGGGAGGAAAGUCCGGGCUC-C---AUG-GAGAGA-C-GG-UG----------------CCGGA------------UAACC----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AC---AGU-GCCACAGAGA--GCAG-ACC-GCC----CC---G--GA--------------------------------------------------------------------------------------------------------------------------UCCG-UC-C----G--G---GGUCAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-A-C-G-CG-GCAA--CG-C-G-G-ACGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGG--C-GGCGCGCCCUUCGCGA--------------------------------GAAGGGCAGGCCGGCUCUCCA----GGCCA--------GUCG---CC-C-----GGGU---U-----G---G-UUGC---------------------U--CGA-GGCG-G-U-CGGCAACGA-U--C-G-U-C-C--CAGAGGAAU-GGCUGCCA-----------------CGUCGGCGCGCGCGAGCGCU-------------------------------CCGGCCCUACAGAACCCGGCUUA--C-AGGCCGG-CUGAUCCA
CABC01000030.1/25678-26056     ACGG-AU-C-G-G-C-G--GACGGCCGCGUG-CC--C-CUGC-------------------------------------------------------------------------------------------------GG-G-G-G-UGCGAGGAAAGUCCGGGCAC-C---GCA--GAGCA-G-GA-UG----------------GUGGA------------CAACA----------------UCCACCCGGG-----------------------GCGA------CCCGCGGG-CC---AGU-GCCACAGAGA--GAAG-ACC-GCC----UC---C--GCGC----------------------------------------------------------------------------------------------------------------------CGUGUGCGC-G----G--C---GGUAAGGGUGAAAG----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGCGG-C-C-C-CG-GUGA--CG-G-G-G-CCGG-C-UC----------------GGUAAAC-CCCAUCC-GGUGCAAGGCC-GAAC------------------------------A-GGA--C-GCGUCA---------------------------------------------------CGAGGGCUGCUC----GCCCC--------AGCG---UC-C-----GGGU---U-----G---G-CCGC---------------------U--CGA-GCCC-G-U-CAGCGAUGG-C--G-G-G-C-C--CAGAUGGAU-GGCCGUCA-----------------CCUCGCGCGGGGCAACGCGC--------------------------------GCGAGGCACAGAACCCGGCUUA--C-AGCCGGU-CCGUCCCA
CP001079.1/890021-890352       CCAG-GU-G-G-A-G-A--AGUAGCCGCUGU-GC--C-GC---------------------------------------------------------------------------------------------------GU-U-G-U-ACAGAGGAAAGUCCGGACUC-C---AAG-GGAAGA-U-GG-UG----------------GCAGG------------UAACU----------------CCUGCCGGGG-----------------------GUAA------CCCUAGGU--U---AGG-GCCACAGAAA--AUU--ACC-GCC----UC-----------------------------------------------------------------------------------------------------------------------------------UAC---------G--A---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUGC-U-C-G-UG-GUGA--CA-CGU-A-GCAG-C-CA----------------GGCAACC-ACCACCA-GGAGCAAGGCU-AAGA------------------------------A-GGG--U-AUUGUG------------------------------------------------------UCUUCUCUC----AUG-----------UUA---CC-C-----GGGU---A-----A---G-UCGC---------------------U--UGA-GGUA-A-G-UAGCGAUGC-U--U-G-C-C-C--CAGAUGAAU-GGCUACAU-----------------A---------------------------------------------------------AACAGAAUCCGGCUUA--U--CUCCAC-CUGGUCCG
AP010918.1/2472230-2471802     UGAG-UU-G-G-C-U-G--GGCGGCCGCGGC-UC--G-CGUAGGGCUUGUGUGG----------------------------------------------------------------AUUCACGAGGUUCAGC-----GU-C-G-A-GUCGAGGAAAGUCCGGACUU-C---ACA--GAGCA-G-GG-UG----------------AUUGC------------UAACG----------------GCAAUCCGAG-----------------------GUGA------CUCGCGGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----AU---C--C----------------------------------------------------------------------------------------------------------------------------UCG--U-G----G--U---GGCAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAU-U-C-C-GG-GUGA--CC-G-G-G-GUGG-C-UA----------------GGCAAAC-CCCACCC-GAAGCAAGGCC-AAGAAGGCCGCACCG--------AAAGUGCGGCCGC-------------GCAGG------------------------------------------CGCUUGAGGGUUGCUC----GCCCG--------A---------GCCUGCGGGU---A-----G---G-CCGC---------------------U--CGA-GGCA-C-C-CGGUAACGGUG--U-G-U-C----CAGAUGGAU-GGUCGCCG-----------------CCGUGCCGCCGUUAGCUUGGCUGU------------------------GGCGGCGCGGAACAGAAUCCGGCUUA--C-AGGCCAA-CUCGUCCG
CP000235.1/215238-214901       UCAG-GU-G-G-A-G-U--UGUAGUCGCUGU-GC--U----U----------------------------------------------------------------------------------------UUUU--------U-G-C-ACAGAGGAAAGUCCGGACUC-C---AAG-AGAAGA-U-GG-UG----------------GCAGG------------UAACU----------------CCUGCCGGGG-----------------------GUAA------CUCUAGGU--U---AGG-GCCACAGAAA--ACU--ACC-GCC----CC---G-------------------------------------------------------------------------------------------------------------------------------UAA----A----G--G---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GUAC-U-C-G-UG-GUAA--CA-C-GCA-GUAG-C-AA----------------GGUAACC-ACUACCA-GGAGCAAGGCU-AAGA------------------------------A-GGG--C-AUUAU------------------------------------------------------GGCUUCUCUC----AUUUG---------UUG---CC-C-----GGGU---A-----A---G-CCGC---------------------A--UGA-GGCA-U-G-CAGCGAUGC-A--U-A-U-C-C--CAGAUGAAU-GACUACAU-----------------AA--------------------------------------------------------CACAGAAUCCGGCUUA----UCUCCAC-CUGACAUC
CP001029.1/5550002-5549599     UCAG-CC-G-G-C-C-G--GGCGGCCGCUCC-GU--C---------------------------------------------------------------------------------------------GUCA--------G-A-C-GGGGAGGAAAGUCCGGGCUC-C---AUG-GAGAGG-C-GG-UG----------------CCGGA------------UAACC----------------UCCGGCGGGG-----------------------GCGA------CCCCAGGG-AC---AGU-GCCACAGAAA--GCAG-ACC-GCC----CC---G--CCAAGG------------------------------------------------------------------------------------------------------------------CCCGUCCUUCG-C----G--G---GGUCAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-A-C-G-CG-GCAA--CG-C-G-G-ACGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGG--C-GACACGCCUUCUCCGCGA----------------------------GGGGAAGGCAGGCCCGCUCUCCA----GGCUC--------GUCG---CC-C-----GGGU---U-----G---G-UUGC---------------------U--CGA-GGCG-G-C-CGGCAACGG-C--C-G-U-C-C--CAGAGGAAU-GGCUGCCA-----------------CGUCCGUGGGCUUGCCCAC---------------------------------GGGCCCUACAGAACCCGGCUUA--C-AGGCCGG-CUGAUCCA
AE006914.1/739871-739357       CUAA-AU-G-G-U-C-G--UGCAGUUGCGUG-AU--A-AUAUAGC----------------------------------------------------------------------------------AAAGCUA-----UA-G-A-U-CACGAGGAAAGUCCGGACUC-U---AUA-GAGGUA-U-GG-UG----------------CCGGU------------UAACC----------------UCCGGCAGAGUA-------------------UUAUUA------CUUUAGGG-AC---AGU-ACCACAGAAA--AUAC-ACC-GCC----AA---G--UAUGAAUACGAAGAUCCUUCAAAAAGAGCUAGGAGUUCACAAGACGAGGAACGGAGCGUAUA---CUUAAUACGUGAGUACCGUAGUACUUGUGAAAUGACGCAGCCAAUUUUUGCAGUUGAUCGAGUAUU-U----U--U---GGUAAGGGUGAAAA----GGU---AC-G--G--U----------------------AAGAG-CGUACC--GGUA-A-G-U-UG-GUAA--CA-A-A-U-UACG-C-AU----------------GGUAAAC-CCCACCA-AGAGCAAGAUC-AAAU------------------------------AGGCG--U-UACAGAACUUAUCAAGUU----------------------------CCCGGGUUAUCUCUAGCC---------GGCUU--------GUAA---UG-C-----GGGU---A-----G---A-UCGC---------------------U--UGA-GGUA-A-A-CGGUAACGU-U--U-A-U-C-C--UAGAUAAAU-AACUGCAA-----------------UGAAUUGAUAUUCA--------------------------------------------UACAGAAUCCGGCUUA--U-AGACCUU-AUUGUCAU
CP000511.1/3845801-3845381     UGAG-CU-G-G-C-U-G--GGCGGCCGCGGC-AC------CC----------------------------------------------------------------------------------------CACA----------G-U-GUCGAGGAAAGUCCGGACUU-C---ACA--GAGCA-G-GG-UG----------------AUUGC------------UAACG----------------GCAAUCCGAG-----------------------GUGA------CUCGCGGG-AA---AGU-GCCACAGAAA--ACAG-ACC-GCC----UC---C--ACUGCGCCCCAAGCC------------------------------------------------------------------------------------------------UUCGGGCCCAAGGACGCUCC-G----G--A---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAU-C-C-C-GG-GUGA--CC-G-G-G-GUGG-C-UU----------------GGUAAAC-CCCACCC-GAAGCAAGGCC-AAGAAGGCCGCAACC--------UGGUUGCGGCCGC-------------GCAGG------------------------------------------CGUUCGAGGGUUGCUC----GCCCG--------A---------GCCUGCGGGU---A-----G---G-CCGC---------------------U--CGA-GGCA-C-C-CGGCGACGGUG--U-G-U-C----CAGAUGGAU-GGUCGCCG-----------------CCUCGCUGCCAGAGAUGGCC--------------------------------GUGAGGAACAGAAUCCGGCUUA--C-AGGCCGG-CUCAUCCG
CP001357.1/28262-27922         UAUG-CG-G-A-G-U-G--GGUAAACGCGGU-AU--U-UAA-----------------------------------------------------------------------------------------GUAA-----CU-A-A-U-ACUGAGGAAAGUCCGUACCU-C--UAAA--GGGCU-U-CA-UG----------------CAAGC------------UAACG----------------GCUUGAAGGC-----------------------GAAA------GCCUAUGG-AA---AGU-GCAGCAGAAA--AUAU-ACC-GCC----A------------------------------------------------------------------------------------------------------------------------------------AUU------------U---GGUAAGGGUGAAAA----GGC---AU-G--G--U----------------------AAGAG-CAUACC--GCAU-U-U-A-UG-GCGA--CA-U-G-A-AUGG-C-AG----------------UGUAAAC-CCCAUGA-GAGGCAAGAGC-AAAC------------------------------A-GAA--A-CGGAUU----------------------------------------------------GCCCUUUUCCU-----------------AUGU---UU-C-----AGGU---G-----G---C-UCGC---------------------U--AAA-GCAU-U-G-UAGUGAUAU-A--A-U-G-C-G--UAGAUAAAU-GUUUACCU-----------------UAAAU-----------------------------------------------------GACAGAAUACGGCUUA--U-AGCUCCG-CUUUUUAU
CP000848.1/666733-667249       CUAA-AU-G-G-U-C-G--UGCAGUUGCGUG-AU--A-AUAUAGC----------------------------------------------------------------------------------AAAGCUA-----UA-G-A-U-CACGAGGAAAGUCCGGACUC-U---AUA-GAGGUA-U-GG-UG----------------CCGGU------------UAACC----------------UCCGGCAGAGUA-------------------UUAUUA------CUUUAGGG-AC---AGU-ACCACAGAAA--AUAC-ACC-GCC----AA---G--UAUGAAUACGAAGAUCAACUUCAAAAAGAGCUAGGAGUUCACAAGACGAGGAACGGAGCGUAU-ACUUAAUACGUGAGUACCGUAGUACUUGUGAAAUGACGCAGCCAAUUUUUGCAGUUGAUCGAGUAUU-U----U--U---GGUAAGGGUGAAAA----GGU---AC-G--G--U----------------------AAGAG-CGUACC--GGUA-A-G-U-UG-GUAA--CA-A-G-U-UACG-C-AU----------------GGUAAAC-CCCACCA-AGAGCAAGAUC-AAAU------------------------------AGGCG--U-UACAGAACUUAUCAAGUU----------------------------CCCGGGUUAUCUCUAGCC---------GGCUU--------GUAA---UG-C-----GGGU---A-----G---A-UCGC---------------------U--UGA-GGUA-A-A-CGGUAACGU-U--U-A-U-C-C--UAGAUAAAU-AACUGCAA-----------------UGAAUUAAUAUUCA--------------------------------------------UACAGAAUCCGGCUUA--U-AGACCUU-AUUGUCAU
CP001620.1/804140-804595       UGAG-CC-G-G-C-C-G--GGUAAUCGCGGG-GG--C-GGAAUCGACAGCACAGCGAGUCUCUGCU---------------------------------------UGCAGAGACGGUGCCUGAUGCUGCGCAGA-----CC-G-U-C-GUCGAGGAAAGUCCGGACUC-C---ACA--GAGCA-C-GG-AU----------------GUUGC------------UAACA----------------GCAACCCAGG-----------------------GCGA------CCUGAGGG-CA---CGU-GCAACAGAAA--GUAG-ACC-GCC----UG---C--AGAC----------------------------------------------------------------------------------------------------------------------GCAAUAUCU-G----C--A---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAC-U-G-C-AG-GUGA--CU-G-U-G-GUGG-C-UA----------------GGUAAAC-CCUUCCG-GGAGCAAGGCA-UGAU-------------------------------GGCG--C-ACCAGUAUGGUGCGCCG-----------------------------GCGCGGGCGUUUGAGGGCUGCUC----GUCCA--------AGUC---CG-C-----GGGU---A-----A---G-CCGC---------------------G--UGA-GGCU-G-C-CAGCGAUGG-C--A-G-C-C-C--AAGAUAGAU-GAUUACCU-----------------CCCAUGCCAGGGGAGACCCCG------------------------------CAUGGCAGACAAAAUCCGGCUUA--U-AGGCCGG-CUCAUUCG
CP000683.1/680077-680596       CUAA-AU-G-G-U-C-G--UGCAGUUGCGUG-AU--G-AUAUAUAG--------------------------------------------------------------------------------CAAAGCUA-----UA-G-A-U-CACGAGGAAAGUCCGGACUC-U---AUA-GAGGUA-U-GG-UG----------------CCGGU------------UAACC----------------UCCGGCAGAGUA-------------------UUAUUA------CUUUAGGG-AC---AGU-ACCACAGAAA--AUAC-ACC-GCC----AA---G--UAUGAAUACGAAGAUCAACUUCAAAAAGAACUAGGAGUUCACAAGACGAGGAACGGAGCGUAUACUUAAUACGUGAGUACCGUAGGUACUUGUGGAAUGACGCAGCCAAUUUCUGAAGUUGAUCGAGUAUU-U----U--U---GGUAAGGGUGAAAA----GGU---AC-G--G--U----------------------AAGAG-CGUACC--GGUA-A-G-U-UG-GUAA--CA-A-A-U-UACG-C-AU----------------GGUAAAC-CCCACCA-AGAGCAAGAUC-AAAU------------------------------AGGCG--U-UACAGAACUUAUCAAGUU----------------------------CCCGGGUUAUCUCUAGCC---------GGCUU--------GUAA---UG-C-----GGGU---A-----G---A-UCGC---------------------U--UGA-GGUA-A-A-CGGUAACGU-U--U-A-U-C-C--UAGAUAAAU-AACUGCAA-----------------UGAAUUUCUAUUCA--------------------------------------------UACAGAAUCCGGCUUA--U-AGACCUU-AUUGUCAU
CP000107.1/922327-922662       UCAG-GU-A-A-A-A-G--AGUAGUUGCUGU-A-------CU----------------------------------------------------------------------------------------AACA------------U-ACAGAGGAAAGUCCGGACUC-C---AAG-GGAAAA-U-GG-UG----------------ACAGG------------UAAUC----------------CCUGUCGGGG-----------------------GUAA------CUUCAGGU-AA---AGG-GCUACAGAAA--AUA--ACC-GCC----UU---G------------------------------------------------------------------------------------------------------------------------------UUAA----C----A--A---GGUAAGGGUGAAAA----GGC---GU-G--G--U----------------------AAGAG-CACACC--GUAC-U-U-A-UG-GCAA--CA-UAU-A-GUAG-C-UA----------------GGCAACC-ACCACCA-GGAGCAAGACU-AAAA------------------------------UGAGG--U-AA---------------------------------------------------------UGUAUUUUCC---CUUACA--------AUUA---CC-A-----AGGU---G-----A---G-UCGC---------------------G--CGA-GUUA-G-G-UAGUGAUAC-C--U-A-U-C-C--CAGAUGAAU-AACUACAU-----------------A---------------------------------------------------------AACAGAAUCCGGCUUA--U--UUUUAC-CUGGCACA
AP009178.1/851649-851994       GUGG-CG-C-A-A-C-G--GAUAGCUGCUUG-G-------------------------------------------------------------------------------------------------GAAA------------C-CAAGAGGAAAGUCCGAGCUG-C---AGU-GAGGCA-G-GG-UU----------------CCACC------------UAACC----------------GGUGGCCAGCGAAGCC----------CUUUGGGAUAA------GCUGAGGG-AA---AGU-GCAACAGAAA--GCAG-ACC-GCC----GA---U-GGCC-------------------------------------------------------------------------------------------------------------------------UUUUGGC-A----C--A---GGCAAGGGUGAAAG----GGU---GA-G--G--U----------------------AAGAG-CUCACC--GCUU-C-U-G-UG-GCAA--CA-C-A-G-AAGG-C-AG----------------UGUAAAC-CCAACCC-GCAGCAAGUCG-CACC------------------------------UG-----------GU----------------------------------------------------UAAAGCCUCAC----AUUUU--------U---------------GAGU---G-----C---G-ACGC---------------------U--AGA-GCUU-A-G-UGGUGACAC-U--A-A-G-C-G--UAGAUAAAU-AGCUAUCC-----------------AC--------------------------------------------------------GACAGAACUCGGCUUA--C-AGUUGCG-CCACCUCU
AM260522.1/1224605-1224290     CGCA-UU-A-G-A-A----GAUGGUCGCUAU-U-------------------------------------------------------------------------------------------------UUAG------------A-AUAGAGGAAAGUCCGGGCUA-C---AUU--AGACA-A-AA-UU----------------CCAUC------------UAACG----------------GAUGGCUAGC-----------------------GCAA------GCUAAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----U-----------------------------------------------------------------------------------------------------------------------------------UUUA------------A---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--AAAG-C-U-A-AA-GCAA--UU-U-A-G-UUUG-U-UU----------------GGCAAAC-CCAAUUU-GUAGCAAGAAG-UGCA------------------------------UGGUA--A-GUCUA---------------------------------------------------------------A------------------AUU---GA-U-----ACGC---A-----C---U-UCGC---------------------U--UGA-GGAA-U-A-UUGCAAAAU-A--U-U-C-C-C--UAGAUAAAU-GACCAUCC-----------------AUU-------------------------------------------------------GACAGAACCCGGCUUA-----UUCUAA-UGCUUUAU
CT573073.1/410381-410766       AAAG-UA-G-A-C-G-A--GGUGAUCGCCGG-UU--A-UAAUGAAUCUU--------------------------------------------------------------------------CGGAUUUAUUA-----UU-G-G-A-CGGGAGGAAAGUCCGAGCUC-C---AUA--GGGCG-C-AG-UG----------------CUCCG------------UAACG----------------CGGAGUCCCG-----------------------GCGA------CGGGAAGG-AA---AGU-GCAACAGAAA--AUAU-ACC-GUC----UC---A--UCUU-----------------------------------------------------------------------------------------------------------------------UUUUUCGA-U----G--G---GAUAAGGGUGAAAU----GGC---GG-G--G--CCGAAAGG-------CUUAAUGUAAGAG-CCCACC--GCUC-C-G-G-CG-GCGA--CG-U-U-G-GAGG-C-AU----------------GGCAAAC-CCCACUG-GGAGAAAGGCC-AAAU------------------------------AGGGA--G-GGAU-------------------------------------------------------GAAGCUGCCC----GCUUCGC----UAUACC---UU-C-----GGGU---A-----G---G-CCGU---------------------U--AGA-UCUC-G-C-UGGCAACAA-C--G-A-G-G-C--UAGAUGAAU-GAUCACCC-----------------AC--------------------------------------------------------GACAAGACUCGGCUUA--U--UGUCUA-CUUUUACC
CP000661.1/2259552-2259157     GCGG-GU-G-G-C-C-G--GAUGACCGCGUG-CC------------------------------------------------------------------------------------------------UUCG----------G-G-CGCGAGGAAAGUCCGGACUC-C---AUG-AGACAA-G-GG-UG----------------CCGGG------------UAACG----------------CCCGGCCGGG-----------------------GCAA------CCCGAGGG-AA---AGC-GCCACAGAGA--AGAG-ACC-GCCC-CACC---G--GCC-------------------------------------------------------------------------------------------------------------------------GAAAGGC-C---CG--G---GGCAAGGGUGAAAC----GGU---GG-G--G--C----------------------AAGAG-CCCACC--GCGG-G-A-C-UG-GCAA--CA-G-G-A-CCGG-C-AC----------------GGCAAGC-CCCACCC-GGAGCAAUGCC-GAAU------------------------------AGGGG--U-CUCGCGCGGGGCUGAUCCGU------------------------CAGGAUAUCGCCGCAGGGAAGUCUC----AGCCCG------AGAGA---CC-C-----GGGU---U-----G---G-CAGC---------------------U--CGA-UCCC-G-U-CGGCAACGG-C--G-G-G-G-C--CAGAGGAAU-GGUCAUCG-----------------AAGGGGGCAACCCCG------------------------------------------GAACAGAAUCCGGCUUA--C-AGGCUGC-CCGCACAU
CP001349.1/5573628-5573218     UCAG-CC-G-G-C-C-G--GGCGGCCGCUCC-GC--C-UU---------------------------------------------------------------------------------------------------CG-G-G-U-GGGGAGGAAAGUCCGGGCUC-C---AUG-GAGAGA-C-GG-UG----------------CCGGA------------UAACC----------------UCCGGCGGGG-----------------------GUGA------CCCCAGGG-AC---AGU-GCCACAGAGA--GGAG-ACC-GCC----GC---------GCGCAC-------------------------------------------------------------------------------------------------------------CUCCGGGUGC-----CUUAG--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-A-C-G-CG-GCAA--CG-C-G-G-ACGG-C-AC----------------GGCAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGG--C-GACAGGCGCCGGCCUUC------------------------------GGGCCGGCGCGAGGCGUUCUCC---AGCCCC--------GUCG---CC-C-----GGGU---U-----G---G-UUGC---------------------U--UGA-GGCG-G-C-CGGCGACGG-C--C-G-U-C-C--CAGAGGAAU-GGCCGCCA-----------------CGUCCGGGGAGCCUUCGGGUUCC--------------------------GCCGGGCCCUACAGAACCCGGCUUA--C-AGGCCGG-CUGAUACU
BX294154.1/194145-193741       CGAG-UG-G-G-C-G-G--GGUGACCGCUGG-CA--C-GGUUCGCGGU----------------------------------------------------------------------------UCCCGCGUUU-----CC-G---G-CUGGAGGAAAGUCCGGGCUC-C---GAA--GGGCA-G-GA-UG----------------GUCGA------------UAACG----------------UCGACCGGUC-----------------------GUGA------GGCCAGGG-AA---AGU-GCAGCAGAGA--GCAG-ACC-GCC----GA---A--CGGUGACGCCG--------------------------------------------------------------------------------------------------------CUUGCGGUGUCAUGCG-U-----------GGUGAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGA-U-C-A-GG-GUGA--CU-U-G-A-UCGG-C-UC----------------GGUAAAC-CCCAUCC-GGAGCUAGACC-AAAC------------------------------A-GGG--U-GCAUCA---------------------------------------------------UCGAGGCGGCCC----GCCUCGUU--AUCGACA---UC-C-----GGGU---A-----G---G-UCGCA-------------------GU--GGA-GGCG-A-C-GAGCAAUCG-U--C-G-UGC-A--CAGAUAAAU-GGUCACCG-----------------UCGAUGCUCGCAUCG------------------------------------------GCACAGAACCCGGCUUA--C-AAGCCCA-CUCGUUUU
AE001439.1/590504-590821       CGCA-UU-A-G-A-A----GAUGGUCGCUAU-U-------------------------------------------------------------------------------------------------UUAG------------A-AUAGAGGAAAGUCCGGGCUA-C---AUU--AGACA-A-AA-UU----------------CCAUC------------UAACG----------------GAUGGCUAGC-----------------------GCAA------GCUAAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----UU-----------------------------------------------------------------------------------------------------------------------------------UUU---------A--A---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--AAAG-C-U-A-AA-GCGA--UU-U-A-G-CUUG-UUUG----------------GGCAAAC-CCAAUUU-GUAGCAAGAA--------------------------------------GCG--C-AUGGUA----------------------------------------------------A-G-UCUAAAU----UA------------AUA---CG-C-----GC---------------U-UCGC---------------------U--UGA-GGAA-U-A-UUGCAAAAU-A--U-U-U-C-C--CAGAUAAAU-GGCCAUCC-----------------AUU-------------------------------------------------------GACAGAACCCGGCUUA-----UUCUAA-UGCUUAAC
CP000360.1/1550317-1549892     CCGC-UG-G-G-C-C-G--GACGGCCGCUGC-UG--C-AUCGGUUUACGCCCGGU--------------------------------------------------------------UCGCCGGGGCCGUACUG-----AU-G-U-G-GGGGAGGAAAGUCCGAACUC-C---GCA--GAGUG-G-UG-UG----------------CCGGA------------UAACG----------------UCCGGGAGGGCG-------------------CCGUUAAGGGCGUUCGACGG-AA---AGU-GCCACAGAGA--ACAU-ACC-GCC----CG---C--C---------------------------------------------------------------------------------------------------------------------------GCAA--G-G----C--A---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GGGC-G-C-G-CA-GUGA--UG-C-G-C-GUUG-C-AU----------------GGCAAAC-CCCACAC-GGAGCAAGACC-AAAU------------------------------AGGGG--A-GAAGUUCGCGGGGCAAC-----------------------------UCGCGAUGCGUGCUGACUCGGUG----CGCCA--------AACU---UC-C-----GGGU---A-----G---G-UCGC---------------------U--UGA-GCCA-G-U-CAGUAAUGA-U--U-G-G-C-C--CAGAGGAAU-GGUCGUCC-----------------CGCCGGCGCAAGCCGG----------------------------------------UGGACAGAAUUCGGCUUA--U-AGGCCCG-GCGGCUAA
CT573213.2/2444154-2443740     CGAG-GU-G-G-C-C-G--GGCGGCCGCGUC-GG--C-ACCGGUU----------------------------------------------------------------------------------CACGCCG-----GU-G-C-C-GCCGAGGAAAGUCCGGGCUC-C---ACA--GGGCA-G-GG-CG----------------GUGGG------------UAACA----------------CCCACCCGGG-----------------------GCGA------CCCGCGGG-AC---AGU-GCCACAGAAA--ACAG-ACC-GCC----GG---U--GCCG-----------------------------------------------------------------------------------------------------------------------GUGACGGC-G----C--C---GGUAAGGGUGAAAC----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGC-C-C-A-GG-GUGA--CC-U-G-G-GCGG-C-UC----------------GGUAAAC-CCCGCCC-GGAGCAAGGUC-AGAAGGCCCGCGGCCGUA--ACCGGUCGCGAGCCGCGCA--G-GCGUUC----------------------------------------------------GAGGGCUGCCC----GCCCG--------AGUC---UG-C-----GGGU---G-----G---A-CCGC---------------------U--GGA-GGCU-G-U-CGGCAACGG-C--A-G-C-C-C--GAGAGAGAU-GGCCGCCA-----------------CCGGCGAGCCGCAAGGCGA---------------------------------CCCGGCCACAGGACCCGGCUUA--C-AGGCCAC-CUCGUCCG
CP001072.2/761860-761543       CGCA-UU-A-G-A-A----GAUGGUCGCUAU-U-------------------------------------------------------------------------------------------------UUAG------------A-AUAGAGGAAAGUCCGGGCUA-C---AUU--AGACA-A-AA-UU----------------CCAUC------------UAACG----------------GAUGGCUAGC-----------------------GUAA------GCUAAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----UU-----------------------------------------------------------------------------------------------------------------------------------UUU---------A--A---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--AGAG-C-U-A-AA-GCAA--UU-U-A-G-CUUG-UUUG----------------GGCAAAC-CCAAUUU-GUAGCAAGAAG--------------------------------------------CGCAUGG-------------------------------------------------UAA--GUCUAAAU---UGAU--A------CACG--------------------------C---U-UCGC---------------------U--UGA-GGAA-U-A-UUGCAAAAU-A--U-U-U-C-C--CAGAUAAAU-GGCCAUCC-----------------AUU-------------------------------------------------------GACAGAACCCGGCUUA-----UUCUAA-UGCUUAAC
AE000511.1/629821-630135       GCAU-UA-G-A-----A--GAUGGUCGCUAU-U-------------------------------------------------------------------------------------------------UUAG------------A-AUAGAGGAAAGUCCGGGCUA-C---AUU--AGACA-A-AA-UU----------------CCAUC------------UAACG----------------GAUGGCUAGC-----------------------GCAA------GCUAAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----U-----------------------------------------------------------------------------------------------------------------------------------UUUA------------A---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--ARAG-C-U-A-AA-GCAA--UU-U-A-G-CUUG-UUUG----------------GGCAAAC-CCAAUUU-GUAGCAAGAAG--------------------------------------------CGCAUGG-------------------------------------------------UAA--GUCUAAAU---UGAU--A------CACG--------------------------C---U-UCGC---------------------U--UGA-GGAA-U-A-UUGCAAAAU-A--U-U-U-C-C--CAGAUAAAU-GGCCAUCC-----------------AUU-------------------------------------------------------GACAGAACCCGGCUUA--U----UCUA-AUGCUCAA
CP000747.1/2646768-2646353     UCAG-AC-G-G-C-C-G--GGCGGUCGCGGC-CC--U-CC------------------------------------------------------------------------------------------UUCG-----GG-C-G-G-GUCGAGGAAAGUCCGGGCUC-C---ACG-ACGGCA-U-GG-CG----------------GCGGG------------UAACG----------------CCCGCCGGGG-----------------------GCGA------CCCCAGGG-AU---AGC-GCCACAGAAA--GCAA-ACC-GCC----CG---G--CGAAGC------------------------------------------------------------------------------------------------------------------CUCGUGCGGAG-C----A--G---GGUAAGGGUGAAAG----GGU---GG-G--G--U----------------------AAGAG-CCCACC--GGGU-C-G-C-UG-GUGA--CA-G-A-G-GCCG-C-AU----------------GGCAAGC-CCCGCCA-GGAGCAAGACC-GAAU------------------------------AGGGA--U-UCCGCGCCGGCGCCUCUCCUU---------------------CGGGAAAGGGGCCGGUAGGGCCGCCGC---CGGCCCG------AGGGA---UC-C-----GGGU---A-----G---G-UCGC---------------------G--AGA-ACCG-G-U-CCGCGAGGG-C--C-G-G-U-C--CAGAGGAAU-GAUCGCCG-----------------CGCUCCGCCCUCGGGCGG-----------------------------------GGCGGCACAGAACCCGGCUUA--C-AGGCCGU-CUGAUCCC
CR555306.1/867494-867067       GAAG-UU-C-G-C-C-A--GGCAGUCGCUGC-GU--G-CA------------------------------------------------------------------------------------------CUUG-----UG-U-G-C-GUGGAGGAAAGUCCGGGCCC-C---GCA--GAGCA-G-GA-UG----------------CCGGC------------UAACG----------------GCCGGGCGUC-----------------------GUGA------GGCGACGG-AA---AGU-GCAACAGAAA--GCAA-ACC-GCC----GA---U--GGCUCCGCGAGGAGAUCAGGCAAGGG---------------------------------------------------------------------------UGAAAUGGUGCGCAGCGCGCGUCGAGCGUC-G----UUGC---GGACGGGGUGCAAGC-CUCGU---CG-G--G--U----------------------AAGAG-CCCACC--GCAG-G-A-C-UG-GCGA--CA-G-G-A-CUGG-C-AC----------------GGCAAAC-CCCAUCC-GGGGCAAGGCC-AAAU------------------------------AGGGG--A-GCAAU------------------------------------------------------GGCGUGGCUC----GCGCU---------GUU---CC-C-----GGGU---A-----G---G-CUGC---------------------U--UGA-GCGC-C-G-CGGCAACGC-G--G-C-G-C-C--CAGAGGAAU-GACUGCCC-----------------GGUGCCUGUGAUGCGAGUCGC-----------------------------AGGCGCUCGACAGAACCCGGCUUA--U-CGGCGAA-CUUCCCAU
CP000552.1/1578074-1578455     GAAA-GC-A-G-G-A-G-AGGCAAUCGCAAA-AA--A-GUUUUAUUUCGU------------------------------------------------------------------------UUUGAAAAUAAA-----AC-U-U-U-UUUGAGGAAAGUCCGGGCUC-C--CAUA-UGGUCA-G-GCUUG----------------CUGGG------------UAAUU----------------CCCAGUGCGG-----------------------GCAA------CCGUGAGG-AU---AGU-GCCACAGAAA--CAU--ACC-GCCU--AAU---A--CUU--------------------------------------------------------------------------------------------------------------------------UCUUAG-U----A--U---GGCAAGGGUGCAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-A-U-U--GAGA---A-G-U-G-UUGG-C-UA----------------GGUAAAC-CCCGGCUGGGAGCAAGGCU-UAGU------------------------------GGAUU--U-AUGAC-----------------------------------------------------CAUUAGAAAAU----CUACU--------U---------------AUGA---G-----C---G-CCGC---------------------U--UGA-GGCU-GUG-AAGUAAUUC-C--A-G-U-C-C--UAGAUAGAU-GAUUGCCC-----------------AUCUUAAUUACGAU-------------------------------------------GAACAGAACCCGGCUUA--U-GACCUGC-UUUCUAAU
CP000976.1/763015-763362       GUUG-AU-A-U-C-C-A---GUCAUCGCUUA-AC--A-UACUGU-----------------------------------------------------------------------------------AUUUCAG-----UA-U-C-U-UGAGAGGAAAGUCCGAGCUC-C---AAUAAGAGCA-U-AA-UG----------------CUAGG------------UAAUG----------------CCUAGGAGUU-----------------------GAAA------GACUUAAG-AU---AGU-GUCACAGAAA--AUU--ACC-GCC----------------------------------------------------------------------------------------------------------------------------------------UUAG----------------GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC--GCUU-A-U-U-UA-GUGA--UA-A-A-U-AAGGUC-AA----------------GACAAAC-CUCAUUA-GGAGCAAAAUC-AAGU------------------------------AAACA--A-GCUUCC----------------------------------------------------UUAGCUCUUGA----GGGUA--------UGCU---UG-U-----GGGU---A-----G---A-UUGC---------------------A--UGA-UUUU-U-U-CAGUGAUGG-A--A-A-A-A-C--AAGAUAGAU-GAUGACAU-----------------AA--------------------------------------------------------UACAGAACUCGGCUUA--U--GGAUAU-CAACUUAA
CP000576.1/1518319-1518700     GAAA-GC-A-G-G-A-G-AGGCAAUCGCAAG-AA--A-GUUUUAUUUUGG------------------------------------------------------------------------AAACAAAAUAAA-----AC-U-U-U-CUUGAGGAAAGUCCGGGCUC-CC-AAAU--GGUCA-G-GCUUG----------------CUGGG------------UAAUU----------------CCCAGUGCGG-----------------------GCAA------CCGUGAGG-AU---AGU-GCCACAGAAA--CAU--ACC-GCCU--AAU---A--CUU--------------------------------------------------------------------------------------------------------------------------UAUAUG-U----A--U---GGCAAGGGUGCAAG----GGU---GU-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-A-U-U--GAGA---A-G-U-G-UUGG-C-UA----------------GGUAAAC-CCCGGCUGGGAGCAAGGCU-UAGU------------------------------AGAUU--U-AUGACC----------------------------------------------------A----UUACAC----AA-----------UCUA---CU-U-----UGAA---G-----C---G-CCGC---------------------U--UGA-GACU-GUG-AAGUAAUUC-C--A-G-U-C-C--UAGAUAGAU-GAUCGCCC-----------------AUCUUAAUUAAGAU-------------------------------------------GAACAGAACCCGGCUUA--C-GACCUGC-UUUCUAAU
BX548174.1/1533930-1534307     GAAA-GC-A-G-G-A-G-AGGCAAUCGCAAA-AA--U-GUUUUAUUUUG-------------------------------------------------------------------------UUUUGAAAAUAA-----AU-C-U-U-UUUGAGGAAAGUCCGGGCUC-C--CAUA-UGGUCA-G-GCUUG----------------CUGGG------------UAAUU----------------CCCAGUGCGG-----------------------GUAA------CCGUGAGG-AU---AGU-GCCACAGAAA--CAU--ACC-GCC----UA---A--UAC------------------------------------------------------------------------------------------------------------------------UUUAUGUA-U-----------GGCAAGGGUGCAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-A-U-U--GAGA---A-G-U-G-UUGG-C-UA----------------GGUAAAC-CCCGGCUGGGUGCAAGGCU-AA----------------------------------GUA--G-AUUUAU----------------------------------------------------G-----ACCAU----UAAAA--------AAUC---UA-C-----UUUU---A-----AG-CG-CCGC---------------------U--UGA-GGCU-GUG-AAGUAAUUC-C--A-G-U-C-C--UAGAUAGAU-GAUUGCCC-----------------AUCUUAUUAAGAUG--------------------------------------------AACAGAACCCGGCUUA--U-GACCUGC-UUUCUACU
CP000814.1/518663-518343       AAAG-CA-U-A-G-U-A--AAUGCUCGCUUC-U-------------------------------------------------------------------------------------------------UUUU------------A-GAAGAGGAAAGUCCGGGCUG-C--UAAA--GACAA-A-CA-UU----------------CCAUC------------UAACA----------------GAUGGCUAGG-----------------------GUAA------CCUAAGGG-AU---AGU-GCAACAGAAA--GAAA-ACU-ACC----AC----------------------------------------------------------------------------------------------------------------------------------GCAA---------G--U---GGAAAAGGUGAAAC----GGC---GG-G--G--U----------------------AAAAG-CCCACC-AGCGA-U-U-U-UG-GUAA--CA-A-U-U-UCGG-C-UA----------------UGUAAAC-CCAAUGU-GCAGCAAGAAG-GGAU--------------------------------GGU--U-AGCGUC----------------------------------------------------U-----UUGUU------------------UUA---AC-C------------------C---U-UCGC---------------------U--UGA-UUUU-G-U-UUGCAAAAA-C--A-A-A-A-C--UAGAUAAAU-GAGCAUUC-----------------AA--------------------------------------------------------GACAGAACUCGGCUUA--U-CGCUAUG-CUUUUUUA
CP001154.1/3111469-3111873     GAAG-UC-A-G-C-C-G--GACAGCCGCCGC-CC--G-CU---------------------------------------------------------------------------------------------------UG-C-G-G-GGGGAGGAAAGUCCGGGCUC-C---GCA--GAGCA-G-GA-UG----------------CCGGC------------UAACG----------------GCCGGGCGUC-----------------------GCGA------GGCGACGG-AA---AGU-GGAACAGAGA--GCAG-AACCGCC----GA---U--GGCCGGGGCAACCCGGCACAGGCAA----------------------------------------------------------------------------GGGUGAAAAGGUGGACUCCUUCACGGAGCC-G----C--C---GG---GUGCAAACC---CGGC---GC-G--G--U----------------------AAGAG-CGCACC--GCGG-A-C-G-UG-GCAA--CA-C-G-G-ACGG-C-AG----------------GCUAAAC-CCCAUCC-GGAGCAAGACC-AAAC------------------------------A-GGG--G-GCAUU------------------------------------------------------GACGUGGCUC----GCGUC---------GUC---CC-C-----GGGU---A-----G---G-UUGC---------------------U--GGA-GCGC-A-C-GGGUAACCG-U--G-C-G-C-C--UAGAGGAAU-GGCUGUCU-----------------GAGGUGGCAACACCCG----------------------------------------AACACAGAACCCGGCUUA--C-AGGCUGA-CUUCACCC
CP000792.1/844958-845284       CUGG-CA-C-G-G-U-A--AGCGGUCGCUUU-UG--C-AUC--------------------------------------------------------------------------------------------------UU-G-C-A-AAAGAGGAAAGUCCGAGCUG-C--GAUA--AGACA-A-AG-UU----------------CCAUC------------UAACG----------------GAUGGCUAGG-----------------------GAAA------CCUAAGGG-AU---AGU-GUAACAGAAA--GCAA-ACU-UCC----GC---C--------------------------------------------------------------------------------------------------------------------------------UU----G----G--C---GGUAAAGGUGAAAU----GGC---GG-G--G--U----------------------AAGAG-CCCACC-GGCAC-G-C-U-UG-GUAA--CU-U-G-C-GUGG-C-CA----------------UAUAAAC-CCAACUU-GCAGUAAGAAG-GGAU--------------------------------GGU--U-UUGGUC----------------------------------------------------U-------UAU-------A--------UUAAA---AC-C------------------C---U-UCGC---------------------U--AGA-GCUU-G-U-UUGUAAAAG-C--A-A-G-C-G--UAGAUAAAU-GAUCGCUC-----------------AA--------------------------------------------------------GACAGAACUCGGCUUA--A-CGCCGUG-CCUCCCUU
CP000111.1/1585720-1586099     GAAA-GC-A-G-G-A-G-AGGCAAUCGCAAA-AA--A-GUUUUAUUUUGU------------------------------------------------------------------------UUCCAAAAUAAA-----AC-U-U-U-UUUGAGGAAAGUCCGGGCUC-C--CACA-UGGUCA-G-GCUUG----------------CUGGG------------UAAUA----------------CCCAGUGCGG-----------------------GUAA------CCGUGAGG-AU---AGU-GCCACAGAAA--CAU--ACC-GCC----UA---A--UAC------------------------------------------------------------------------------------------------------------------------UUUAUGUA-U-----------GGCAAGGGUGCAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-A-U-U--GAGA---A-G-U-G-UUGG-C-UA----------------GGUAAAC-CCCGGCAGGGAGCAAGGCU-UA----------------------------------GUA--G-AUUUAU----------------------------------------------------GACCAUUACAC----A-------------AUC---UA-C-----UUUU---A-----AG-CG-CCGC---------------------U--UGA-GACU-GUG-AAGUAAUUC-C--A-G-C-C-C--UAGAUAGAU-GAUUGUCC-----------------AUCUGAAUUAAGAU-------------------------------------------GAACAGAACCCGGCUUA--U-GACCUGC-UUUCUAAU
CP001344.1/3702833-3702450     AGAG-UA-G-G-C-G-A--GGUGGUUGCGGA-UU--U-GUCU----------------------------------------------------------------------------------------AAGC----GAU-A-A-A-UCUGAGGAAAGUCCGGGCUU-CC-GAAA--GACCA-G-ACUUG----------------CUGGA------------UAACG----------------CCCAGUGCGA-----------------------GCGA------UCGUGAGG-AU---AGU-GCCACAGAAA--AAU--ACC-GCC----GA---U--GGGGCCUUUCU---------------------------------------------------------------------------------------------------------CACAGAUAAGGGCUC-A----C--A---GGUAAGGGUGCAAA----GGU---GU-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-A-U-C--GUGA---G-G-U-A-CUGG-C-UC----------------GGUAAAC-CCCGGUCGGAAGCAAGGUU-GAA---------------------------------GGG--A-CAAG-------------------------------------------------------GGUUGGUCUU----UUUCC---------UGU---CC-C-----GCGU---UU--GAA---A-CCGC---------------------U--AGA-GGCA-U-C-UGGUAACAG-U--U-G-U-C-C--CAGAUAGAU-AACCGCCC-----------------UGCUGGUCCGCCAGU-----------------------------------------GGAACAGAACCCGGCUUA--U--GUCCUG-CUCUUUCC
CP000048.1/758113-758459       GUUG-AU-A-U-C-C-A---GUCAUCGCUUA-AU--A-UGCUGC-----------------------------------------------------------------------------------AUUGAAG-----UA-U-U-U-UAAGAGGAAAGUCCGAGCUC-C---AAUAAGAGUA-U-AA-UG----------------CUAGG------------UAAUG----------------CCUAGGAGUU------------------------UAA------AACUUAAG-AG---AGU-GUCACAGAAA--AUU--ACC-GCC----------------------------------------------------------------------------------------------------------------------------------------UUAG----------------GGUAAGGGUGAAAA----GGU---GA-G--G--U----------------------AAGAG-CUCACC--GCUU-A-U-U-UA-GUGA--UA-A-A-U-AAGGUC-AA----------------GAUAAAC-CUCAUUA-GGAGCAAAAUC-AAAU------------------------------AAGCA--A-GCUUCC----------------------------------------------------UUAGCUCUUGA----GGGUA--------UGCU---UG-C-----GGGU---G-----G---A-UUGC---------------------A--UGA-UUUU-U-U-CAGUGAUGA-A--A-A-A-A-C--AAGAUAGAU-GAUGACAU-----------------AA--------------------------------------------------------UACAGAACUCGGCUUA--U--GGAUAU-CAACUUAA
BA000019.2/4950808-4950360     GAGA-GU-A-G-G-C-GUUGGCGGUUGCAGA-CC--A-GUUA---------------------------------------------------------------------------------------GCUUA-----AC-U-G-A-UUUGAGGAAAGUCCGGACUC-CC-GAAA--GACCA-G-ACUUG----------------CUGGA------------UAACG----------------UCCAGUGCGA-----------------------GCGA------UCGUGAGG-AU---AGU-GCCACAGAAA--AAU--ACC-GCC----AA---G--AUUGGGGACUGGGGACUAGGGGUUGGGGACUGGGGAA----------------------------------------------------GAAACUUCCCAAUCCCUAAUCCCCCAUACCCAAUACCCAACU-C----U--U---GGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-A-U-C--GAGA---G-G-U-A-CUGG-C-UC----------------GGUAAAC-CCCGGUUGGGAGCAAGGCC-GAA---------------------------------GGA--A-CUAU-------------------------------------------------------GGUUGGUCUU----UUACC---------AGU---UC-C-----GCUA---UCA-GAG--AG-CCGC---------------------U--AGA-GGCG-U-U-UGGUAACAA-A--C-G-U-C-C--CAGAUAGAU-AAUCGCCC-----------------UCGUGUAAAGCAAUUUACA----------------------------------CAGAGAACAGAACCCGGCUUA--C-CACCAAC-UCUCUCCU
CP001291.1/2949667-2949299     AGAG-UU-G-G-C-G-A--GGGGGUUGCGGA-UU--C-GUUU----------------------------------------------------------------------------------------UAAGC---GAC-G-A-A-UCUGAGGAAAGUCCGGGCUC-CC-GAAA--GACCA-A-ACUUG----------------CUGGA------------UAACG----------------CCCAGUGUAC-----------------------GCGA------GUGCGAGG-AG---AGU-GCCACAGAAA--CAU--ACC-GCC----UU-----------------------------------------------------------------------------------------------------------------------------------UUU---------U--A---GGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-A-U-C--GUGA---G-G-U-A-CUGG-C-UC----------------GGUAAAC-CCCGGUUGGGAGCAAGGUC-GGAG------------------------------GGACU--A-AGGUU------------------------------------------------------GGUCUUUUCC---CCGUCC---------CGU---UU-U-----AGGU---G-----A---A-CCGC---------------------A--AGA-GGUG-U-U-UGGUAACAA-A--C-A-U-C-C--CAGAUAGAU-AACUCCCC-----------------UCAUCGAUGGCAACAUCUA----------------------------------UGAAGAACAGAACCCGGCUUA--U--GUCCAA-CUCUCUCC
CP000951.1/518444-518058       AGAG-UU-A-G-C-G-C--GGCAGUUGCAGG-GU--U-GACAU--------------------------------------------------------------------------------------UGAGA-----UC-A-G-C-UCUGAGGAAAGUCCGGGCUC-CC-CAAA--GACCA-A-ACUUG----------------CUGGG------------UAACG----------------CCCAGUGCGC-----------------------GUGA------GCGUGAGG-AU---AGU-GCCACAGAAA--CAU--ACC-GCC----GA---A----GCUUAGCAUU-------------------------------------------------------------------------------------------------------AGGUUCGCCUAAUCUA-U----C--U---GGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-A-U-C--GUGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGUUGGGAGCAAGGAC-GGUG------------------------------GGAUG--A-UGGUU------------------------------------------------------GGUCUUUUUC----CGAUC--------CCAU---AA-U-----UUGG---A-----G---UGCCGC---------------------U--GGA-GGUG-G-C-UGGUAACAG-U--C-A-U-C-C--UAGAUAGAU-AACUGCCC-----------------UUUUGCGCUGCAAGA------------------------------------------GAACAGAACCCGGCUUA--U--GUCUAA-CUCUCCUG
CP000393.1/3464219-3463800     AAAA-GU-A-G-A-A-G-AGGCAGUUGCGGA-CU--C-AAUAC--------------------------------------------------------------------------------------UUAUU-----UA-G-G-G-UCUGAGGAAAGUCCGGGCUC-CC-AAAA--GACCA-A-GCCUG----------------CUGGA------------UAACG----------------CCCAGUGCGA-----------------------GUGA------UCGUGAGG-AU---AGU-GCCACAGAAA--AAU--ACC-GCC---AAA---G--UAGAUUAAUU----------------------------------------------------------------------------------------------------------AUUAUUGUUUAGUCA-C----U--UC-AGGUAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-U-G-U-C--GUGA---G-A-U-A-CUGG-C-UC----------------GGUAAAC-CCCGGCGGGGAGCAAGGUC-GAAG-------------------------------GAAC--A-AUGGUUGGUCUUUUUCCG---------------------------GUUCCAUUGCAUUAUAGAU---UU----AUUUG--------UAAU---GU-U-----UGGU---G-----U---A-CCGC---------------------A--AGA-GGUG-U-C-UGGUAACAG-G--C-A-U-C-C--CAGAUAGAU-AACUGCCC-----------------UCAAAGCUUGUUUGAGUU-----------------------------------GAGAGAACAGAACCCGGCUUA--C-UUCCUAC-UUUUUCCU
AM406670.1/935235-935677       GAAG-UU-C-G-C-C-A--GGCAGUCGCUGC-GU--G-CCA-------------------------------------------------------------------------------------------UG-----UG-U-G-C-GUGGAGGAAAGUCCGGGCCC-C---GCA--GAGCA-G-GA-UG----------------CCGGC------------UAACG----------------GCCGGGCGCC-----------------------GUGA------GGCGACGG-AA---AGU-GCAACAGAGA--GCAG-ACC-GCC----GA---U--GGCUCUUGUCGAGGAGUUCGCUCUUCGCGGAGCACA-------------------------------------------------------GGUAAGGGUGAAACGGUGCGGUGACGCGCGCAAGCGCGGC-G----C--C---GGUCGGAGCGCAAGCUUCGGC---GG-G-----U----------------------AAGAG-CCCACC--GCAG-G-A-C-UG-GCAA--CA-G-G-A-CUGG-C-AC----------------GGUAAAC-CCCAUCC-GGGGCAAGGCC-AAAU------------------------------AGGGG--A-GCAUU------------------------------------------------------GGCGUGGCUC----GCGUC---------GCU---CC-C-----GGGU---A-----G---G-CUGC---------------------U--AGA-GCGC-C-G-CGGUAACGC-G--G-C-C-C-C--CAGAGGAAU-GACUGCCC-----------------GGCGACUGCGGCUUGCCGCG-------------------------------GUCGUUCGACAGAACCCGGCUUA--U-CGGCGAA-CUUCCCAA
CP000932.1/724342-724668       CAAA-CA-U-A-G-C-A--AAUGAUCGCUUC-A--------U----------------------------------------------------------------------------------------UUUU------------U-GAAGAGGAAAGUCCGAGCUG-C---AAUAGGACAA-A-GA-UU----------------CCAUC------------UAAUG----------------GAUGGCUAGG-----------------------GUGA------CCUAAGGG-AA---AGU-GCAACAGAAA--GAAA-ACU-ACC----AU---A--U----------------------------------------------------------------------------------------------------------------------------UUU--A-U----A--U---GGAAAAGGUGAAAC----GGU---AG-A--G--U----------------------AAGAG-CCUACC-AGUAG-C-U-U-UG-GUAA--CA-A-A-G-CUAG-C-UA----------------UGUAAAC-CCAAUCU-GCAGCAAGAAG-GGGU------------------------------GG------------------------------------------------------------------UUUUUGUCUU----AUAAU--------A---------------UAAC---C-----C---U-UCGC---------------------U--UGA-GUUU-G-U-UUGCAAAAA-C--A-A-A-A-U--UAGAUAAAU-GAUCAUUC-----------------AA--------------------------------------------------------GACAAAACUCGGCUUA--U-AGCUAUG-UUUUACUU
BX571658.1/53597-53272         AGGG-CG-U-G-G-C-G--GACGGUUGCUUC-U-------GC----------------------------------------------------------------------------------------UCCA------------A-GAAGAGGAAAGUCCGAGCUG-C---AUU-GAGACA-G-GG-UU----------------CCAUC------------UAACG----------------GAUGGCUAUC-----------------------GUAA------GAUAAGGG-AA---AGU-GCAACAGAGA--AGAG-ACC-GCC----GA----------------------------------------------------------------------------------------------------------------------------------GUCA---------U--C---GGUAAGGGUGAAAC----GGA---GG-U--G--U----------------------AAGAG-ACCCCC--GGAG-U-C-C-UA-GCAA--UA-G-G-A-GUCG-C-AU----------------GGUAAAC-CCAACCC-GCAGCAAGAAG-GAUC------------------------------UGG---------UUA----------------------------------------------------A-AG-UCUCAA---AA-CU---------U---------C-----GAAU---C-----C---U-UCGC---------------------U--UUA-UCGC-U-A-UUGUGAAAU-A--GUC-G-A-A--UAGAUGAAU-AGCCGUCA-----------------U---------------------------------------------------------AACAGAACUCGGCUUA--C-GGCCACG-CCCCUCUC
CP000805.1/532010-532352       ACAG-AG-A-A-C-U-GCAGAUAGUCGCUGC-GG--G----------------------------------------------------------------------------------------------UUU--------C-U-C-GCAGAGGAAAGUCCGGACUC-C---UUC--GGAAA-U-GA-UG----------------CUAGU------------UAAUU----------------ACUAGGCAGCGGCUC------------UCUGCAGUGC-----CGCUGACAG-CA---AGC-GCCACAGAAA--AUAU-ACC-GCC----------------------------------------------------------------------------------------------------------------------------------------UUUG----------------GGUAAGGGUGAAAG----GGC---GA-G--G--U----------------------AAGAG-CUCACC--GCGU-U-U-U-G--GCGA---C-A-A-A-ACGG-C-AC----------------GGCAAGC-CUCAUCA-GGAGCAAGAUC-GAGC------------------------------A-GCA--A------------------------------------------------------------AGGAUAUUCC---GAUCCU--------GUUU---UG-C-----GGGU---U-----G---A-UUGC--------------------AU--AAA-UUUA-U-A-UAGCGAUAU-A--U-A-A-AGU--GAGACAGAU-GAUUAUCC-----------------UU--------------------------------------------------------GACAGAAUCCGGCUUA--C-CAGUUCU-CUGUUUUU
CP000435.1/208346-207956       AAAG-UA-G-G-C-G-A--GGUGAUCGCAAU-CG--A-UGGUUGUUGCCU------------------------------------------------------------------------UCGGGCUGCAGU-----CA-U-C-G-GUUGAGGAAAGUCCGGGCUC-CC-CGAU--GGCCA-G-GCUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAC--ACC-GCC----GA---U--GGCCGG-------------------------------------------------------------------------------------------------------------------UUCCGCCGGC-A----C--A---GGCAAGGGUGCAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAG-C-A-U-C--GAGA---G-G-U-G-CUGG-C-UC----------------GGUAAAC-CCCGGCUGGGAGCAAGGCC-UAGG------------------------------AACGA--C-GGGUGG----------------------------------------------------C--CAUCUUCC----CCG---------UUCCG---UC-U-----UUGU---G-----C---G-CCGC---------------------U--CGA-GGUC-G-U-CGGUAACGG-C--G-A-U-C-C--CAGAUAGAU-GAUCACCC-----------------CCCUUCCUUGGAAGGG----------------------------------------UGAACAGAACCCGGCUUA--U--GUCCUG-CUUUCAAC
CP000815.1/542171-541778       GAAA-GC-A-G-G-C-G-AGGUGAUCGCGAC-CA--G-AC------------------------------------------------------------------------------------------UUUG-----UU-C-U-G-GUUGAGGAAAGUCCGGCCUC-CU-UAAU--GACCA-G-GCUUG----------------CUGGG------------UAAUA----------------CCCAGUGCGG-----------------------GUAA------CCGUGAGG-AA---AGU-GCCACAGAAA--CAU--ACC-GCCA--AUG---A--CC-UCGGGA-------------------------------------------------------------------------------------------------------------AUUUUUCCAA-GG-U---AC--A---GGCAAGGGUGCAAA----GGU---GU-G--G--U----------------------AAGAG-CACACC-AGCAA-U-A-U-C--GAGA---G-A-U-A-UUGA-C-UU----------------GGUAAAC-CCCAGCCAGGAGUAAGGCC-UAGG------------------------------GACAA--C-GGUUGG----------------------------------------------------UCCA--UUUCC---C--UGU--------UCCG---CU-U-----UUGA---G-----U---G-CCGC---------------------U--UGA-GAUU-G-U-UGGUAACAG-C--A-G-U-U-C--CAGAUAGAU-GAUUACCC-----------------ACUUCCUCUGAAUCUUCGUCAG----------------------------UGGUAGUGAACAGAAUCCGGCUUA--C-GUCCUGC-UUUCAGAC
CP000090.1/512222-512564       AAAG-CA-G-G-C-C-A--GACAAUCGCUGC-UU--G-CAUCG--------------------------------------------------------------------------------------CAAGG-----UG-C-A-A-GGGGAGGAAAGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------UUGGC------------UAACA----------------GCCAUCCACG-----------------------GUAA------CGUGCGGA-AU---AGG-GCCACAGAGA--CGAG-UCUUGCC----GC---C--AGG-------------------------------------------------------------------------------------------------------------------------UUCGCCU-G----G--C---GGGAAGGGUGAAAC--------------------------------------------------------G---------------------------------C-------------------GGUAACC-UCCACCU-GGAGCAAUCCC-AAAU------------------------------AGGCA--G-GCAUCG----------------------------------------------------A--GGCGGCCC----GCU---------GAGCC---UG-C-----GGGU---A-----G---G-GAGC---------------------U--GGA-GCCG-G-C-UGGUAACAG-C--C-G-G-C-C--UAGAGGAAU-GGUUGUCA-----------------CGCGCCGCCGUGCCGCAAGGUGC--------------------------GGUGACGUGCACAGAAUCCGGCUUA--U-CGGCCUG-CUUUGCGC
CP000361.1/1308271-1307950     UAGG-UA-A-A-C-C-A--GACAAUAGCUUG-AA--A---------------------------------------------------------------------------------------------------------U-U-U-CAAGAGGAAAGUCCGGGCUG-C---AGU-GAAGUG-U-GG-UU----------------CCAUU------------UAAAU----------------AAUGGCUAGA-----------------------GUAA------UCUAAGGG-AU---AGU-GCAACAGAGA--GUAG-ACA-GCC----AA---U-------------------------------------------------------------------------------------------------------------------------------UUU----U----U--U---GGUGAUGGUGAAAC----GGU---AA-G--G--U----------------------AAGAG-CUUACC-AGCAA-A-U-U-GA-GUAA--UC-U-U-U-UUGG-C-UU----------------UGUAAAC-CCAACUU-GCAGCAAGAA--GACU------------------------------AGGUA--A-UUAC------------------------------------------------------------UUCAC-------------------AU---UU-U-----UGGU---C---------U-UCGC---------------------A--GGA-GUAC-U-A-AAGUAAUUU-A--G-U-A-C-C--UAGAUAAAU-UAUUGUCU-----------------UU--------------------------------------------------------GACAGAACGCGGCUUA--C--GGUUUA-CCUAACUU
CP000352.1/435682-436022       AAAG-CA-G-G-C-C-A--GACAAUCGCUGC-UU--G-CAUCG--------------------------------------------------------------------------------------CAAGG-----UG-C-A-A-GGGGAGGAAAGUCCGGACUC-C---ACA--GGGCA-G-GG-UG----------------UUGGC------------UAACA----------------GCCAUCCACG-----------------------GUAA------CGUGCGGA-AU---AGG-GCCACAGAGA--CGAG-UCUUGCC----GC---U--GGC-------------------------------------------------------------------------------------------------------------------------UUCGGCU-G----G--C---GGGAAGGGUGAAAC--------------------------------------------------------G---------------------------------C-------------------GGUAACC-UCCACCU-GGAGCAAUCCC-AAAU------------------------------AGGCA--G-ACGAUG----------------------------------------------------A--AGCGGCCC----GCC---------GAGUC---UG-C-----GGGU---A-----G---G-GAGC---------------------U--GGA-GCCG-G-C-CGGUAACGG-U--C-G-G-C-C--UAGAGGAAU-GGUUGUCA-----------------CGUUCCGGGCGCCGCAAGGCGU----------------------------GCGGGGCGCACAGAAUCCGGCUUA--U-CGGCCUG-CUUUGCUU
CP000767.1/1120671-1120353     UCGG-CA-C-G-G-U-A--AGUGAUCACUU----------------------------------------------------------------------------------------------------GAAA---------------AAGAGGAAAGUCCGAGCUG-C--GAUA--AGACG-A-AG-UU----------------CCAUC------------UAACG----------------GAUGGCUAGG-----------------------GCAA------CCUAAGGG-AA---AGU-GUAACAGAAA--GCAA-ACA-GCC----GC---U-------------------------------------------------------------------------------------------------------------------------------AAA----C----G--C---GGUAAAGGUGAAAC----GGC---GG-G--G--U----------------------AAGAG-CCCACC-AGCGC-G-C-U-UG-GCAA--CU-C-G-C-GCGG-C-UU----------------UAUAAAC-CCAACUU-GCAGCAAGAAG-GGAC------------------------------------------GGU----------------------------------------------------UUUAGUCUUAU----AUUUA--------A-----------------AC---C-----C---U-UCGC---------------------U--AGA-GCUA-A-A-UUGUAAAAU-U--U-A-G-A-G--UAGAUAAAU-GAUCACUC-----------------AC--------------------------------------------------------GACAGAACUCGGCUUA--U-CGCCGUG-CCUUAAUU
AE015925.1/236348-235953       CGGA-AG-A-G-A-A-A--GGCAACCGCUUU-UU--A-UAUCUCU----------------------------------------------------------------------------------AGUUAGG-----UA-U-A-C-UGAGAGGAAAGUCUGGACUU-C---AUA--AGAAG-A-GA-UA----------------CUGGA------------GAAAC----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAC-UCC-GCU----AU---A--AAAG-----------------------------------------------------------------------------------------------------------------------GGUCUUUU-U----A--U---AGACAGGCUGAAAA----UUC---CU-ACUU--U----------------------AAGAG-UAGGA---GCUA-U-U-A-AG-GUGA--CU-U-A-A-UAGA-C--A----------------UGCAAAC-CCUAUCU-GAAGCAAGA---GAAA------------------------------AA--------GUUUUUGUUUCUGCA-------------------------------UAGUGAGGGAU-AGUAUUCCUC----AUAAA---------C--------------UUUU---UC--AUA---A-UCGC---------------------U--UGA-GGGG-U-A-UAGUAAUAU-G--C-C-C-C-C--UAGAUGAAU-GGUUGCCC-----------------UCAAGAUGGUCUUUUCCAU---------------------------------CUUGUAGACAGAAUCCGGCUUA--C-UCUCUCU-UCCGAUAU
CP000828.1/1701275-1701688     AAGA-GU-A-G-G-A-GUAGGUGGUUGCGGA-CU--U-GA------------------------------------------------------------------------------------------GAUC-----GC-A-A-G-UCUGAGGAAAGUCCGGGCUC-UC-GAAA--GGCCA-G-ACUUG----------------CUGGG------------UAACG----------------CCCAGUGCGG-----------------------GUGA------CCGUGAGG-AG---AGU-GCCACAGAAA--CAU--ACC-GCC----GA---U--GGCUUGUUUCGCUA---------------------------------------------------------------------------------------------------CAGGAUAGCCAAACAUUC-A----C--A---GGUAAGGGUGCAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAA-C-G-U-C--GAGA---G-G-C-G-UUGG-C-UC----------------GGUAAAC-CCCGGUGGAGAGCAAGGC-A------------------------------------GAG--G-GCAAC------------------------------------------------------GGUUGGUCUU----UUCCC--------CGCU---CU-C-----GUUU---G----U-AGCG-CCGC---------------------U--UGA-GGCG-U-C-UGGUAACAG-G--C-G-U-C-C--CAGAUAGAU-AACUACCC-----------------UCUUUCGACCAAUCCUGGGCCAAUGUCC----------------GGGUGGAGAAAGAGAACAGAACCCGGCUUA--C-CGCCUGC-UCUUCCCU
CP000269.1/3436150-3435828     GAAG-UA-A-G-C-C-A-AGACAACCGCUGG-CU--G-UCAUU--------------------------------------------------------------------------------------UCGGU-----GA-U-G-G-CGGGAGGAAGGUCCGGACUC-C---AUA--GAGCA-G-GG-UG----------------ACGGU------------UAACG----------------GCCGUCCGCC-----------------------GUGA------GGCGAGGA-AU---AGG-GCCACAGAGA--CGAG--CG----------------UAU-------------------------------------------------------------------------------------------------------------------------UAAGUUA------------------CGGUGAAAC--------------------------------------------------------G---------------------------------C-------------------GGUAACC-UCCACUC-GGAGCAAUUCC-AAAU------------------------------AGGCA--C-GCGUUG----------------------------------------------------A--CGUUGCUC----GCGGA---------GCG---UG-C-----GGGU---A-----G---G-AAGC---------------------U--UGA-GCCG-U-G-GAGUAAUUC-A--C-G-G-C-C--UAGAGGAAU-GGUUGUCA-----------------UAACGCGUGGGUUCGCCCAU-------------------------------GCGUCGUAACAGAAUCCGGCCUA--U-CGGCUUG-CUUCAACU
CR848038.1/237165-236768       CGGA-AG-A-G-A-A-A--GGCAACCGCUUU-UU--G-UACCUUA----------------------------------------------------------------------------------ACUAAGG-----UA-G-A-U-UAAGAGGAAAGUCUGGACUU-C---AUA--AGAAA-A-GA-UA----------------CUGGA------------GAAAC----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAU-UCC-GCU----AU---A--AAAG-----------------------------------------------------------------------------------------------------------------------GGUCUUUU-U----A--U---AGACAGGCUGAAAA---U-UC---CU-A--UUUU----------------------AAGAA-UAGGA---GCUA-U-U-A-AG-GUGA--CU-U-A-G-UAGA-C--A----------------UGCAAAC-CCUAUCU-GAAGCAAGA------G------------------------------AAAAA--G-UUUUUGUUUCUGCA------------------------------------UAAUGAGAGGGAGGGUAUC----CCUCAU------G-AAC---UU-U-----UUCA---U-----A---A-UCGC---------------------U--UGA-GGGA-U-A-UAGUAAUAU-A--U-C-C-C-C--UAGAUGAAU-GGUUGCCC-----------------UCAAGAUGAGUUUUCUCAU---------------------------------CUUGUAGACAGAAUCCAGCUUA--C-CCUCUCU-UCCGAUAU
CR931997.1/806240-806707       CGAG-AC-G-G-C-C-G--GGCGAUCGCGGC-GC--A-CGGAACCACCCUG---------------------------------------------------------------------UACACGGGGCAGGC-----CG-G-G-C-GCGGAGGAAAGUCCGGACUC-C---ACA--GGGCAAC-GG-UG----------------GUUGC------------UAACA----------------GCAACCCGGG-----------------------GCGA------CCCGCGGG-AA--CAGU-GCCACAGAAA--ACAA-ACC-GCC----CG---C--C----------------------------------------------------------------------------------------------------------------------------ACG--C-G----C--G---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCAC-C-C-C-AG-GCGA--CU-G-G-G-GUGG-C-UA----------------GGUAAAC-CCCACCG-GGAGCAAGGUC-AAGG------------------------------U-GCC--C-GCACGCACGCCAUCCCAGAUGGUGC-------------ACCAGCGUGCGGCGUAGCUCUAGGGCUGCCC----GCCCAA------CAAUG---AG-C-----AGGU---A-----G---G-CCGC---------------------U--UGA-AGCC-A-C-CAGCAAUGG-U--G-G-G-C-U--CAGAUGGAU-GAUCGCCU-----------------CGUCCCACGCCUUCUUCGCGUGCCCCUCGCGGGCGCUGCGGAAAUGGACGGGGGAUAGGACAGAAUCCGGCUCA--U-AGGCCGU-CUCGGCGC
AM942444.1/1533990-1533532     CGAG-GC-G-G-C-C-G--GGUGGCUGCGGC-GC--G-GUGGAACCACCGGCCGGUG----------------------------------------------------------UUAUGCCGGCGGGUCAGGC-----CC-C-G-U-GUCGAGGAAAGUCCGGACUC-C---ACA--GAGCA-C-AG-UG----------------GUUGC------------UAACG----------------GCAACCCAGG-----------------------GUGA------CCUGCGGG-CA---AGU-GCAACAGAAA--GUAG-ACC-GCC----CG---C--CCACCGUUU-------------------------------------------------------------------------------------------------------------UUCGCGGUGUGCG-G----C--G---GGUGAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC-AGCGU-G-G-C-AG-GCGA--CU-G-U-C-GCGG-C-UA----------------GGUAAAC-CCCACUG-GGAGCAAGGUC-AAGG------------------------------AGCC------GCAC-GGCCCCGCCCGUCGCAGGG-------------CGGGGCGGGCGGCGUUGUCUGAGGGCUGCUC----GCCCG--------AUGA---AG-GA---CAGGU---G-----G---A-CUGC---------------------U--UGA-GGCG-C-C-CAGCAAUGGUG--C-G-U-C----CAGAUGGAU-GGUCACCU-----------------CGUGCCACCCCUCGUGGGUG--------------------------------GCAUCAGACAGAAUCCGGCUUA--G-AGGCCGC-CUCGACAC
AJ012174.2/7-392               GAGU-A----------A--GGCAACCGCUGU-UU--A-UAUUUCU----------------------------------------------------------------------------------CAAAAAA-----UA-U-A-A-AGAGAGGAAAGUCUGGACUU-C---AUA--AGAGA-A-GA-UA----------------CUGGA------------GAAAU----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAC-UCC-GCU----AU---A--AAA-------------------------------------------------------------------------------------------------------------------------UUUAUUU-U----A--U---AGACAGGCUGAAAA---UUCC---UA-C--U--U----------------------UAGGA-GUAGGA--GCCA-U-U-A-AG-GUGA--CU-U-A-A-UAGG-C--A----------------UGCAAAC-CCUAUCU-GAAGCAAGA------G------------------------------AAAAA--A-GCUUUUUGUGUCUG------------------------------------CAAAUGUGAGAGGAAUUCC----UCCCAU------AGGCU---UU-U-----UCGA---A---------A-UCGC---------------------U--UGA-GGGA-U-C-UAGUAAUAG-C--U-C-C-C-C--UAGAUGAAU-GGUUGCCC-----------------UUAGGAUAGUUCGCAAGAGCU-----------------------------AUCUUAUAGACAGAAYCCGGCUUA-------------CUCGCUC
CP000879.1/813666-813996       GAAG-UA-G-G-A-C-G--GUUGAUCGCGAG-UA--G-GCAUA--------------------------------------------------------------------------------------CUUGG-----GC-C-U-AUUUUGAGGAAAGUCCGGACUC-U----AA--GGGCA-A-GA-UA----------------CUGGU------------UAACA----------------ACCAGAGGGA-----------------------GUGA------UCCC-UGA-AU---AGG-GCCAUAGAAA-AGAAA-ACC-GCC----------------------------------------------------------------------------------------------------------------------------------------GAAA----------------GGCAAGGGUGGAAC----GGU---GA-G--G--U----------------------AAGAG-CUCACC-AGUGU-C-A-G-A--GCGA---U-C-U-G-GCAG-C-UU----------------GGUAACC-UCUAUCU-UGAGCAAGGUC-AAAC------------------------------AAGAA--G-GCCAGAGGUUGC----------------------------------------CCGCCGAGAGACU-UUA----GUGUC--------CGCC---UU-C----UGGGU---A-----G---A-CCGC----------------------------------------------------------G--UAGAUUAAU-GGUUAACU-----------------U---------------------------------------------------------UACAGAAUCCGGCUUA--U-AGUCCUA-CUGAUAUA
CP001100.1/2524217-2524610     GGCU-GU-A-U-C-U-U--GGCAAUCGCUGU-AU--U-GC------------------------------------------------------------------------------------------AUAG-----GC-A-A-U-GCAGAGGAAAGUCCGAACAU-C---AUA--GGGCA-G-GG-UG----------------CCGGA------------CAAGAUGUUUC----AUCAAGUUCGGGCAAAAAGG--------------CUGAAGAGCC---UUUUUGACAG-AA---AGU-GCAACAGAAA--GCAA-ACC-GCC----AU---U---CC--------------------------------------------------------------------------------------------------------------------------GUUGGA-A----U--U---GGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGGCA-A-U-G-UG-GUAA--CA-C-G-U-UGUG-C-UC----------------GGUAAAC-CUC-CCC-GGUGCAAGGCU-AAGU------------------------------AAGAA--A-GCUUCCUUUUGGGAAAGA----------------------------GCUGCCCGCUCAAUUUACUUC-G----GUAAA--------AGUU---UU-C-----GGGU---G-----A---G-CCGC---------------------A------------------------------------U--UAGAUAAAU-GGUUGCCG-----------------ACUGCUUCAUUAUUGAA-------------------------------------GUAGUACAGAAUUCGGCUUA--A-AAGAUGC-AGCUUUGC
CP001108.1/1643311-1643713     AUAC-CA-C-A-G-U-G--UGCAGUCGCUGU-UU--A-CCAU----------------------------------------------------------------------------------------UGCU-----GG-U-A-G-ACAGAGGAAAGUCCGAACAU-C---ACA--GGACA-G-GG-UG----------------CCGGCCGAGAGCUCUGCUCAAG----------------UCCGGGAGUACAG----------------GACUGAAAAC-CUGUACUACAG-AU---AGU-GCAACAGAAA--ACAG-ACC-GCU----CC---G--GAA-----------------------------------------------------------------------------------------------------------------------------UUC-C----G--G---AGUAAGGGUGAAAC----GGU---GG-U--G--U----------------------AAGAG-ACCACC-AGAUG-C-G-U-CA-GUAA--UG-G-C-G-CAUG-C-UU----------------GGCAAAC-CUC-CCC-GAUGCAAGGCU-AAAU------------------------------AGGGC--A-GCUUUUCCAAAAAGGAAAAA------------------------GAGCGGUCCGUUCAAUUCUG---AA----CAGAG--------AGUU---GC-C-----GGGU---G-----A---G-CCGC---------------------A------------------------------------U--CAGAUAAAU-GACUGCAA-----------------CUCUCCUCCGGUCACGACCGG------------------------------AAGAGAGAACAGAAUUCGGCUUA--C-AUCUGCG-GUAUCGGC
AJ012172.2/7-388               GAGU-A----------A--GGCAACCGCUUU-UU--A-UAUCUCU----------------------------------------------------------------------------------AGUUAGG-----UA-U-A-C-UGAGAGGAAAGUCUGGACUU-C---AUA--AGAAG-A-GA-UA----------------CUGGA------------GAAAC----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAC-UCC-GCU----AU---A--AAAG-----------------------------------------------------------------------------------------------------------------------GGUCUUUU-U----A--U---AGACAGGCUGAAAA----UUC---CU-ACUU--U----------------------AAGAG-UAGGA---GCUA-U-U-A-AG-GUGA--CU-U-A-A-UAGA-C--A----------------UGCAAAC-CCUAUCU-GAAGCAAGA---GAAA------------------------------AA--------GUUUUUGUUUCUGCA-------------------------------UAGUGAGGGAU-AGUAUUCCUC----AUAAA---------C--------------UUUU---UC--AUA---A-UCGC---------------------U--UGA-GGGG-U-A-UAGUAAUAU-G--C-C-C-C-C--UAGAUGAAU-GGUUGCCC-----------------UCAAGAUGGUCUUUUCCAU---------------------------------CUUGUAGACAGAAYCCGGCUUA-------------CUCGCUC
AJ012171.2/7-376               GAGU-A----------A--GGCAACCGCUUC-CU--G-UAUCUC-----------------------------------------------------------------------------------UAGUAGA-----UA-U-G-G-UAAGAGGAAAGUCUGGACUU-C---AUA--AGAAG-A-GA-UA----------------CUGGA------------GAAAC----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAC-UCC-GCU----AU---A---------------------------------------------------------------------------------------------------------------------------------A----U----A--U---AGACAGGCUGAAAA----UUC---CU-ACUU--U----------------------AAGAG-UAGGA---GCUA-U-U-A-AG-GUGA--CU-U-A-A-UAGA-C--G----------------UGCAAAC-CCUAUCU-GAAGCAAGA---GAAA------------------------------AAGUU--U-UUGUUUCUGC-------------------------------------------AUAAUGAGGAGCUCUG----UUCCU--------CAUA---AA-C-----UUUU---UC--ACA---A-UCGC---------------------U--UGA-GGGA-U-A-UAGUAAUAU-A--U-C-C-C-C--UAGAUGAAU-GGUUGCCC-----------------UCAAGAUGGUCUUUGCCAU---------------------------------CUUGUAGACAGAAYCCGGCUUA-------------CUCGCUC
AJ012177.2/7-395               GAGU-A----------A--GGCAACCGCUGA-GC--C-AGUUUUA---------------------------------------------------------------------------------GAAAAACU-----GC-G-U-A-UCAGAGGAAAGUCCGGACUU-C---GUA--AGAAA-A-GA-UG----------------CUGGA------------GAAAU----------------UCCAGGGGCC-----------------------GUAA------GGCUACGG-AA---AGU-GCAACAGAAA--ACAU-UCC-GCU----AU---A--AAUG-----------------------------------------------------------------------------------------------------------------------AUAUCAUU-U----A--U---AGACAGGCUGAAAA---AUCC---UA-C--U--U----------------------UAGGA-GUAGGA--GCUG-C-U-A-GG-GAGA--CC-U-G-G-UAGA-C--U----------------UGUAAAC-CCCAUCU-GAAGCAAGA--------------------------------------GAAA--A-AGUUAUUUGUCUCUGC--------------------------------AAAAUCCUUUCUAAUGAAAGG----CAUAA--------ACUU---UU-U-----CAUA---A-----------UCGC---------------------U--UGA-GGAG-U-A-CAGUAAUGU-G--C-U-C-C-C--UAGAUGAAU-GGUUGCCC-----------------ACAAGUAAGAAUUUCUUAUUCG----------------------------UACUUGUUGACAGAAYCCGGCUUA-------------CUCGCUC
CP001013.1/621331-621659       GAAG-CA-A-G-C-C-A--GACCGCCGCUGG-UG--C-CGGAUC-----------------------------------------------------------------------------------CGAAAGG-----UG-G-C-A-CUGGAGGAAGGUCCGGACUG-C---ACA--GAGCA-G-CG-UA----------------GGAGG------------UAACA----------------CCUCUCCACC-----------------------GCGA------GGUGCGGA-UC---AGA-GCAACAGAGA--CGAG--CC----------------GGU-------------------------------------------------------------------------------------------------------------------------UCAGUCC------------------GGGUGAAAC----------------------------------------------G---------------------------------------------------------------GGCAAUC-UCUACGC-GCAGCAACACC-AAAU------------------------------AGGCC--A-GCAUUG----------------------------------------------------A--AGCGGCUC----GCUGA---------GCU---GG-C-----GGGU---A-----G---G-UGGC--------------------AU--CGA-GCCG-G-GUGGGCGACCC-C--C-G-G-C-C--CAGAGGAAU-GGCGGUCA-----------------CGGCGGGGGGUCUUUCGGGAUC----------------------------GUCUGCUGCACAGAAUCCGGCCUA--U-CGGCUUG-CUUCACAC
CP000539.1/3943608-3943267     GAAG-CA-C-G-C-C-A--GACCGCCGCUGG-UG--C-AAUCUG-----------------------------------------------------------------------------------GGAAACC-----AG-G-C-A-CUGGAGGAACGUCCGGACUG-C---ACA--GGACA-G-CG-UA----------------GCAGC------------UAACG----------------GCUGCCCACC-----------------------GUGA------GGUGAGGA-UC---AGA-GCAACAGAGA--CGAG-UCC-CGG----GG---G------------------------------------------------------------------------------------------------------------------------------AGUG----C----C--U---GCGAAGGCAGACCA------------------------------------------CUGGG-------GG------------U-GAAA------------------CG----------------GGCAAUC-UCUACGC-GCAGCAAUACC-AAGU------------------------------AGGCC--A-GCGUUG----------------------------------------------------ACGUG--GUUC-----CGCG-------GAGCU---GG-C-----GGGU---A-----G---G-UAGC--------------------AC--CGA-GCCGUG-G-UGGUGACAC-C--C-G-G-C-C--CAGAUUAAU-GGCGGUCA-----------------CGCUGCGGGCAACCGCA--------------------------------------GUGCACAGAAUCCGGCUUA--U-CGGCGCG-CUUCACAC
CP000884.1/1619737-1620169     GAAG-CA-C-G-C-C-A--GACCGCCGCUGG-UG--C-AAUCGU-----------------------------------------------------------------------------------GGAAACA-----CG-G-C-A-CUGGAGGAACGUCCGGACUG-C---ACA--GGGCA-G-CG-UA----------------GCAGC------------UAACG----------------GCUGUCCACC-----------------------GUGA------GGUGAGGA-UC---AGA-GCAACAGAGA--CGAG-UCG-GGG---ACA---U--GUGCCGCCAACUUGGUGUUCUAUGGGGUG--------------------------------------------------------------------CCAGCGCAAGCUGGCGACGGAUGGCGCAAGCCAG-A----C--G---CCCA--GGCGAAAG-----CC---UG-G--G--CC--------------------CCAUAG-CCA----CCCGG-G-G-A-CGCGGAACGCG-U-C-C-CCGG-G-UGAA-----------ACGGGCAAUC-UCUACGC-GCAGCAAUACC-AAGU------------------------------AGGCA--C-ACGUUG----------------------------------------------------A--CGGGGCCC----CCG---------GAGUG---UG-C-----GGGU---A-----G---G-UAGC--------------------AC--CGA-GCCG-G-G-CGGCGACGC-C--C-G-G-C-C--CAGAUUAAU-GGCGGUCA-----------------CAUGCGGGCAACCGCG----------------------------------------UGCACAGAAUCCGGCUUA--U-CGGCGCG-CUUCACAC
AM902716.1/765617-766031       AAGA-CA-G-G-C-C-G--GGCAAUCGCGGU-GG--A-U-------------------------------------------------------------------------------------------GCAA------A-U-C-C-GUCGAGGAAGGUCCGGACUC-C---ACA--GGGCA-G-GG-UA----------------GCGGC------------UAACG----------------GCCGUCCGGCCGUGCCGGCAG-GCUUGCCUGCAGGCAC----GACCGAGGA-AC---AGG-GCCACAGAGA--CGAG-U----CUG--CGG---G--GCG-------------------------------------------------------------------------------------------------------------------------GGCGCGC-C-----------AG---UCGCGCACC----GGC---AC-G--G--C----------------------CAUCUCCGUGCC--GCGCGG-U-C-CG-GCAA--CG-G-G-CGGCGG-C-AUCGCAGGG-UGAAACGCGGCAACC-UCUAUCC-GGAGCAACACC-AAAU------------------------------AGGCA--U-GUGUGGGCCCCU---------------------------------------GGGCCCGAAGGGCGGCCC----GCCCG--------AGCA---UG-C-----GGGU---A-----G---G-UGGC---------------------U--ACA-GCGG-U-C-CAGCAAUGG-C--C-C-G-C-G--CAGAGGAAU-GAUUGCCC-----------------GCCGGGUUCGCCCGG-----------------------------------------CGUACAGAAUCCGGCCUA--C-AGGCCUG-UCUUGCAA
CP002156.1/1932954-1933325     UCAG-AU-G-G-C-C-G--GACGGCCGCAGG-U--------------------------------------------------------------------------------------------------CCU------------A-CCUGAGGAAAGUCCGGGCUC-C---CUG-GCGGCA-G-GG-UG----------------CCGGG------------UAACC----------------CCCGGCCGGA-----------------------GCGA------UCCGAGGG-AA---AGC-GCCACAGAGA--UCGA-ACC-GCC----UC---G--G---------------------------------------------------------------------------------------------------------------------------UCCG--C-C----G--A---GGUAAGGGUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCCG-C-A-U-CG-GCAA--CG-C-U-G-CGGG-C-AU----------------GGCAAGC-CCCACCU-GGAGCAAAACC-GAAU------------------------------AGGGA--U-GGGAGGGGCCCU----------------------------------------UGGGCCCGGGGGCGCCGC-CACCCCUU------ACCCA---UC-C-----GGGU---U-----G---G-UUGC---------------------U--UGA-GGCC-G-C-CCGCAAGGG-C--GCG-U-C-C--CAGAUGAAU-GGUCGUCC-----------------UCCGCCACGGCAGA--------------------------------------------GACAGAACCCGGCUUA--CGCGGCCGU-CUGACACU
CP001103.2/922253-922603       GGAG-UU-G-G-C-C-A--GGCAAUCGCCGC-UU--U-C-------------------------------------------------------------------------------------------GUAA------G-A-A-A-GGGGAGGAAAGUCCGGGCUC-C---AAA--GGGCA-G-GG-UG----------------CCAGA------------UAACG----------------UCUGGGCGGC-----------------------GUGA------GCCGACGA-CA---AGU-GCAGCAGAGA--GAAG-ACC-GCCU--AAG---C--AUG-------------------------------------------------------------------------------------------------------------------------UUUACAU-G----C--C---GGUAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAC-C-U-C-UG-GUAA--CA-G-A-GUGUGG-C-AA----------------GGUAAAC-UCCACCC-GGAGCAAGACC-AAAU------------------------------AGGAU--C-CCUCAA-----------------------------------------------------CGUGUGGCCC----GCAUG---------GGG---AU-C-----GGGU---A-----G---G-UUGC---------------------U--UGA-AUCA-G-U-GAGCGAUUG-C--U-G-A-U-C--UAGAGGAAU-GGUUGCCC------------------------AC-------------------------------------------------GACAGAACCCGGCUUA--C--GGCCAA-CUCCACUC
CP000613.2/663266-662837       CCAG-AC-G-G-C-C-G--GAUGGCCGCCCU-CC--G-GCAACGG---------------------------------------------------------------------------------GGAAACCC-----GC-C-G-G-GGGGAGGAAAGUCCGGGCUC-C---ACG-GAAGCA-C-GG-UG----------------CCGGG------------UAACG----------------CCCGGCGGGG-----------------------GCGA------CCCCAGGG-AA---AGU-GCCACAGAAA--GCAA-ACC-GCC----CA---U--GAUCCCCGCC----------------------------------------------------------------------------------------------------------UCCGGGUGGGACGGC-A----U--G---GGCAAGGGUGAAAG----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCGC-C-C-C-CG-GCGA--CG-G-G-G-GUGG-C-AU----------------GGUAAAC-CCCACCG-GGAGCAAGACC-GAAU------------------------------AGGGG--U-GGCACGGCCGGGAA------------------------------------ACCGGCCGAAGCGCGCUUC---CGCGCA--------GCCG---CC-C-----GGGU---G-----G---G-UCGC---------------------G--UGA-GGCG-U-C-CGGCAACGG-G--C-G-U-C-C--CAGAGGAAU-GGCCAUCC-----------------CCCGGAUACCGUCCAGCCCGCUGGA---------------------UACGGUCCGGCGGACAGAACCCGGCUUA--C-AGGCCGU-CUGGCGUC
AE008692.2/1079883-1079512     CCAG-AA-G-G-U-C-G--GGCGGCCGCCGG-UA--U-GUUU----------------------------------------------------------------------------------------UUG------AC-A-U-A-CGGGAGGAAAGUCCGGGCUC-C---AAG-GAGUAA-C-GG-UG----------------CCGGA------------UAACA----------------UCCGGCGAGG-----------------------GUGA------CCUCAGGG-AA---AGU-GCCACAGAAA--ACAA-ACC-GCU----UU---U--UAC-------------------------------------------------------------------------------------------------------------------------UUCGGUA-A---UA--A---AGUAAGGAUGAAAA----GGU---GC-G--G--U----------------------AAGAG-CGCACC--GCAU-U-U-C-CG-GUAA--CG-G-C-A-AUGG-C-AA----------------GGUAAAC-CCCACCG-GGAGCAAAACC-GAAU------------------------------AGGGA--U-GGCAUA----------------------------------------------------UGGGCUGGCUC----CGCCC-------CGUCA---UC-C-----GGGU---U-----G---G-UUGC---------------------U--GAA-GACC-G-G-AAGCAAUUC-C--G-G-U-U-U--UAGAUGAAU-GGUCGCCU-----------------AUCCAGCUUUGCUGG-----------------------------------------UGGACAGAACCCGGCUUA--U-AGACCUU-CUGGCGUA
#=GC SS_cons                   {{{{.{{.{.{.{.{.{..{{{{{{{,<<<<.<<..<.<<__........................................................................................____.....>>.>.>.>.>>>>,,,,AAA,AAAAA[[[.[...---..BBBB-.[.[[.[[................<<<<<............_____................>>>>><<<<<.......................____......>>>>->((.--...-((.(((,,,,,,,..,,,,.,<<.<<<....<<...<..<<<.........................................................................................................................____>>>.>....>..>...>>>-->>,,,,,,,....<<<...<<.<.._.._......................_____.>>>>>>..<<<<.<.<.<.<<.____..>>.>.>.>.>>>-.>.,,................)))--)).))]]]]].]]]],,,<<<<.----..............................--<<<..<.<<----....................................................-<<<<<_bbbb....>>>>>........->>>...>>.>.....----...-.....>...>.>>,,.....................,..,,,.<<<<.<.<.<<____>>>.>..>.>.>.>.,..,,,,,,,,,.}}}}}}}-.................--------------............................................-------aaaaaaaa-..}.-}}}}}}.}}}}::::
#=GC RF                        cgag.cc.g.g.c.c.g..ggcggucGCgcc.cc..c.ccuu........................................................................................aaaa.....gg.g.g.g.ggcGAGGAAAGUCCGGgCUc.C...AuA..GggCA.g.gg.uG................ccgGg............UAACg................cCcggcgggg.......................GugA......ccccAgGG.Aa...AGu.gCcACAGAAA..auAg.ACC.gCc....cg...c..ccc.........................................................................................................................uuauggg.g....c..g...gGcAAGGGUGAAAa....GGu...gc.g..G..U......................AAGAG.cgcaCC..Gcgc.c.c.c.cG.GuaA..Cg.g.g.g.gcgG.C.uu................gGcAAaC.CCCaccc.GgAGCAAggcc.AAAU..............................AGGgg..c.gcauuu....................................................acgggcugcuc....gcccg........agcg...cc.C.....GGGU...a.....g...g.ccGC.....................U..uGA.Gccg.g.c.cgGuAAcgg.c..c.g.g.C.C..uAGAugAAU.gaccgcca.................ucuauuuaaauuuu............................................aACAGAAcCCGGCUUA..c.aggccgg.cucgucau
//
# STOCKHOLM 1.0

#=GF AC   RF00011
#=GF ID   RNaseP_bact_b
#=GF DE   Bacterial RNase P class B
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Mifsud W; 0000-0002-9805-6461
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Brown JW, The Ribonuclease P Database, 9847214
#=GF SS   Published; PMID:9847214
#=GF GA   97.00
#=GF TC   97.10
#=GF NC   96.60
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00002
#=GF DR   URL; http://jwbrown.mbio.ncsu.edu/RNaseP/home.html;
#=GF DR   SO; 0000386; RNase_P_RNA;
#=GF DR   GO; 0008033; tRNA processing;
#=GF DR   GO; 0004526; ribonuclease P activity;
#=GF DR   GO; 0030680; dimeric ribonuclease P complex;
#=GF RN   [1]
#=GF RM   9759486
#=GF RT   Ribonuclease P: unity and diversity in a tRNA processing ribozyme.
#=GF RA   Frank DN, Pace NR
#=GF RL   Annu Rev Biochem 1998;67:153-180.
#=GF RN   [2]
#=GF RM   9847214
#=GF RT   The Ribonuclease P Database.
#=GF RA   Brown JW
#=GF RL   Nucleic Acids Res 1999;27:314.
#=GF CC   Ribonuclease P (RNase P) is a ubiquitous endoribonuclease, found in
#=GF CC   archaea, bacteria and eukarya as well as chloroplasts and mitochondria.
#=GF CC   Its best characterised activity is the generation of mature 5'-ends of
#=GF CC   tRNAs by cleaving the 5'-leader elements of precursor-tRNAs. Cellular
#=GF CC   RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its
#=GF CC   catalytic activity in the absence of the protein subunit, i.e. it is a
#=GF CC   ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown
#=GF CC   to retain its catalytic function, but is still essential for the catalytic
#=GF CC   activity of the holoenzyme. Although the archaeal and eukaryotic
#=GF CC   holoenzyme s have a much greater protein content than the bacterial ones,
#=GF CC   the RNA cores from all the three lineages are homologous -- helices
#=GF CC   corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular
#=GF CC   RNase P RNAs. Yet, there is considerable sequence variation, particularly
#=GF CC   among the eukaryotic RNAs.
#=GF WK   Ribonuclease_P
#=GF SQ   114


U64877.1/1-316               ---------------------------------------------------------------------------------------GAGGAAAGUCCGGG-CUAGCACAC-ACCUUAUGG-GUGUGUAGUGUUUGU-GCUAAGG--GAAAUCAUAACCUUAGGUA--UGUUG----UAUA-----AACA--UAACGGCAAACUA-GUUA-UA-GCUAAGGUG-UUUC------ACUACGUUAUAACUUAAA-UUAAA--GUGCCACAGAGACGAA-UCUAUU-UA-----------------------GAAA------------------------UAA-AUAGAGUGAAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAAUU---AGGUAGGGGCAC-A-UGAUG--UGUAG-------CAAUACAA-CAUCAUGC-AAGAU----------------UUGA-----AUC--UUGAGAUUAAUAGUCACAA---AAGAA----------------------GAAA-----------------------UUCUU---UACAGAACGCGGCUUA----------------------------
M19023.1/1-411               AUGCAGGAAAUGC-GGGUAGCCGCUGCCGCAAUCGUCUC----------------------------------GGCGAUUGGCGGUAGAGGAAAGUCCAGG-CUCGCCCAA-GC-UGAGAU-GCUUGGAGUGUUCGU-ACCUGGC--GCAA------GCCAGGGCAA-GUGAGGC--GCAA--GCCUCGC--UGACGGC---GUG-GAAA-GG-GCU--CUC--UCU-------GAG--GCCCGAGUACGC--UGAAA--GUGCCACAGAAACGUAGCUUUUC-UG-----------------------GCGA------------------------CAG-AAAAGAUGGAACG-CGGUAAACCCUGCGAGCGAGAAACCCAAAUU---UGGUAGGGGAAC-C-GUCCU--GAAGGAAUC---AAACGGAA-GGGACGGA-UGGUAUCUU------------CGGA-----UGC--CAUAGAUAGAUGGCUACCG---CUCUU--GGUGCGAGG-----------GAUA------CGUCCCGCUUGCAGCACGGGAG--AGACAGAACCUGGCUUAUAGCA----------UUUCCUGCUGGAU
BA000004.3/1843310-1843721   AUCAUAACCGUUC-AGGUAACCGCUGCAUCGCA----------------------------------------UGCG-----AUGUAGAGGAAAGUCCAUG-CUCGCACAG-GC-UGAGAU-GCUUGUAGUGUUCGU-GCCUAGC--GAAGUCAUAAGCUAGGGUA--GUCUGGUU-CUUAGAACUGGGC--UAACGGC--AAGG-UAAG-CA-CCUACGUUCAUCAU-----GAAUAUGGUGUGAUGCCUU-UGAAA--GUGCCACAGUGACGUAGUCCGUU-UG-----------------------GAAA------------------------CAG-ACGGAGUGGAACG-AGGUAAACCCCUCGAGCGAGAAACCCAAAAAU--UGGUAGGGGAAC-C-UUCUU--GAAGGAAAU---GAACGGA--GAGAAGGA-CGGAAGU--------------UUUA----CUUC--UGUAGACAGAUGGUUACCA---CCGGA--G-UACGAGG-----------UUCA-------UCACCGUUUGUAGUACGAAGG---AACAGAACAUGGCUUAUCGAA------------CGGGAAUGAGA
M19022.1/1-408               UGAAAUAACGUUC-AGGUAAUCGCUGCAUCA------------------------------------------UUUG-----AUGUAGAGGAAAGUCCAUG-CUCGCACGGUGC-UGAGAU-GCCCGUAGUGUUCGU-GCCUAGU--GAAAAAAUAAGCUAGGGCA--GCUUGGC--UUAU-AGCUUAGC--UGACGGC--GGGA-AAAACCA-CCUAAGUC--UUUG------GAUAUGGUCGAGUAUCCU--GAAA--GUGCCACAGUGACGAAGCUUUGC-UG-----------------------GAAA------------------------CAG-CAAAGGUGGAACG-CGGUAAACCCCACGAGCGAGAAACCCAAACAA--UGGUAGGGGAAC-U-GUCUC--AAAGGAAUC---UAACGGA--GAGACGGA-CGGUUACAU------------GCGU-----AAU--CGUAGAUAGAUGAUUACCG---CCUGA--G-UACGAGAU----------UAAA---------AUCGUUUGCAGUACAAAGG---UACAAAACAUGGCUUUACGAA----------CGUUGUUGAAACA
M19021.1/1-417               GUUAAUCAUGCUC-GGGUAAUCGCUGCGGCCGGUU--------------------------------------UCGG-----CCGUAGAGGAAAGUCCAUG-CUCGCACGGUGC-UGAGAU-GCCCGUAGUGUUCGU-GCCUAGC--GAAUCCAUAAGCUAGGGCA--GCCUGGC--UUCG--GCUGGGC--UGACGGC--GGGG-AAAG-AA-CCUACGUCCGGCUG-----GGAUAUGGUUCGAUUACCC-UGAAA--GUGCCACAGUGACGGAGCUCUAA-GG-----------------------GAAA------------------------CCU-UAGAGGUGGAACG-CGGUAAACCCCACGAGCGAGAAACCCAAAUGA--UGGUAGGGGCAC-C-UUCCC--GAAGGAAAU---GAACGGA--GGGAAGGA-CAGGCGGCGCA----------UGCA-----GCC--UGUAGAUAGAUGAUUACCG---CCGGA--G-UACGAGGCG---------CAAA---------GCCGCUUGCAGUACGAAGG---UACAGAACAUGGCUUAUAGAG----------CAUGAUUAACGUG
M13175.1/1-401               GUUCUUAACGUUC-GGGUAAUCGCUGCAGAU------------------------------------------CUUG--AAUCUGUAGAGGAAAGUCCAUG-CUCGCACGGUGC-UGAGAU-GCCCGUAGUGUUCGU-GCCUAGC--GAAGUCAUAAGCUAGGGCA--GUCU-----UUAG-----AGGC--UGACGGC--AGGA-AAAA-AG-CCUACGUC--UUCG------GAUAUGGCUGAGUAUCCU-UGAAA--GUGCCACAGUGACGAAGUCUCAC-UA-----------------------GAAA------------------------UGG-UGAGAGUGGAACG-CGGUAAACCCCUCGAGCGAGAAACCCAAAUUU--UGGUAGGGGAAC-C-UUCUU--AACGGAAUU---CAACGGA--GAGAAGGA-CAGAA----------------UGCU-----UUC--UGUAGAUAGAUGAUUGCCG---CCUGA--G-UACGAGGUG---------AUGA---------GCCGUUUGCAGUACGAUGG---AACAAAACAUGGCUUACAGAA----------CGUUAGACCACUU
U64878.1/1-308               ---------------------------------------------------------------------------------------GAGGAAAGUCCGGG-CUCGCACAU-UC-UGUGAU-GAAUGUAGUGUUUGU-GCUGGAU--GAAACGAUAAAUCCAGGCA--GC-------GUAA-------GC--UGACGGC---UGG-AGAA-GG-CCUGUGGU--GAAA------GCUAUGGCGGACUCCUU--UAAAA--GUGCCACAGAAACGAG-CUUUUC-GG-----------------------GAAA------------------------CCG-GAAAGAUGGAACG--GGUAAACCCCGCAAGCGAGAAACCCAAAUU---UGGUAGGGGAAU-C-UAAUCA-CGGCAAAAC---GAAGCCAGUGAUCGGAA-CGUG-----------------GAAA------CA--CGUAGAUAAAUGACUGCCA---CUUUC----------------------GCAA-----------------------GAGAG---UACAAAACACGGCUUA----------------------------
U64887.1/1-331               ---------------------------------------------------------------------------------------GAGGAAAGUCCGGG-CUCGCACAA-GC-UGAGAU-GCUUGUAGUGUUCGU-GCUUAGC--GAAAUCAUAAGCUAAGGUA--CUCU------UUU-----AGAG--UAACGGC--AGGA-AAAA-UG-ACUAAGGU--UUCG------ACUAUGUCAAAGUAUCCU-UGAAA--GUGCCACAGUGACGAAGCGAUGU-GG-----------------------GAAA------------------------CUC-CAUCGGUGGAACG-CGGUAAACCCCUCGAGCGAGCAACCCAAACAA--UGGUAGGGGCGC-U-CUUCU--AAAGGAAAU---GAACGAGU-AGAAGAGG-CAGAG----------------UUUA-----CUC--UGCAGAUAGAUGAUGACCG---UCACC--A-AUUUUUCCU---------GAAG-------------------AAUUGGUGA---UACAGAACGCGGCUUAU---------------------------
AF056391.1/4-345             ---------------------------------------------------------------------------------------GAGGAAAGUCCGGG-CUCGCACAU-CC-UGCGAU-GGAUGUAGUGUUCGU-GCCCGUU----CGUAAU--GGCGGGGCA--GUCAGCUU-UUUA---GCAGAU--UGACGGC--GGGG-AAAG-CAUCCUACAGCCAACUU-----GGCCAUGGUGCAAGUACCC-UGAAA--GUGG-AUAGAGACGAG-UCGUCG-GG-----------------------GAAA------------------------CUC-GACGAGUGGAACG-A-CUAAACCCCACGAGCGAGCAACUCAGUGU-----GUAGAGGCAC-C-UGGCU--GAGAGAAAU---GAAUCAA--UGCCGGGA-CGAUCGA--------------CAUA----UGAU--CGUAGAAAAAUGAUUGCCC---CUUCU--G-UGGGAGGCUGGGAAG---CCUA----------------GAACCACAUUGG---AACAGAAUCCGGCUUA----------------------------
U64882.1/1-342               ---------------------------------------------------------------------------------------GAGGAAAGUCCGGG-CUCGCACAU-CC-UGCGAU-GGAUGUAGUGUUCGU-GCCCGUU----CGUAAU--GGCGGGGCA--GUCAGCUU-UUUA---GCAGAC--UGACGGC--GGGG-AAAG-CAUCCUACAGCCAUCUU-----GGCCAUGGUGCAAAUACCC-UGAAA--GUGG-AUAGAGACGAG-UCGUCG-GG-----------------------GAAA------------------------CUC-GACGAGUGGAACG-A-CUAAACCCCACGAGCGAGCAACUCAGUGU-----GUAGAGGCAC-C-UGGCU--GAGAGAAAU---GAAUCGA--CGCUGGGA-CGAUCGC--------------CAUA----UGAU--CGUAGAAAAAUGAUUGCCC---CUUCU--G-UGGGAGGCUGGGAAG---CCAA----------------GAACCACAUUGG---GACAGAACCCGGCUUA----------------------------
U64883.1/1-328               ---------------------------------------------------------------------------------------GAGGAAAGUCCGGG-CCCGCGCAA-GC-UGAGAU-GCUUGUAGUGUUCGU-GCUAAGC-----CCAAUAAGCUUAGGGG--CCGU-----GUAA-----ACGG--CUACGGC--GGCC-AAAC-GC-GCUAAGGC--GUCA------GCUAUGCGCUAGUAGGUC-UGAAAA-GUGCCACAGUGACGAAACGAUCA-GG-----------------------GAAA------------------------CCU-GAGCGGUGGAACG--GGUAAACCCCGCGAGCGAGUAACCCAAACUUU-UGGUAGGGGCGU-U-UUGCC--AAGCAAAUU---GAAGCGAC-GGCAAUAC-AGCG-----------------GUAA------CG--CUGAGAUAGAUGAUGACUGAA-GGAGC--U-UGUGC-------------CUGA-------------------ACAAGUUCU-GGAACAACACACGGCUUAU---------------------------
D13066.1/58-413              GAGAU--UUUAUU-GGUCAAUCGCUGUAUUU------------------------------------------GAAA-AAGAAUAUAGAGGAAACUCCACG-CUUACACAA-UC-UGUGAU-GAUUGUAGUGUUUAU-GCUAAAU--GAAAAAAUAAAUUUAGGCA--GUAA-----UUAA-----UUAC--UGACGGC--AUAA-CUA---A-CCUAAGGC--UUU-------GCUAUGGU--GAUGUUAU---AAA--GUGCCACAGAGACGAAU---AAA-GA-----------------------GAAA------------------------UCU-U-GAAAUGGAACG-CGGUAAACCCCAUAAGUAAGAAACUCAAAUUU--UGGUAGAGGAAU-C-UGAUU--AAGAAAAUA---AGAAUCAA-AAUCAGAA-GUUA-----------------UUAU------UA--ACUAGAUAGAUGAUUGACG---CU-------------------------GAAA--------------------------AG---UACAAAACGUGGGUUAUAAAU-----------AAAAUCUCAUCA
U41756.1/1-291               -------AGCAUU-GGCUAACAGCUGCUU--------------------------------------------GAAA-----GAGUAGAGGAAAGUCCACG-CUAGCACAA-CC-UGCGAU-GGUUGUAGUGAUCAU-GCUAGGC-----CCAAUAAGCCUAGGC-------------UUA------------GACGAC---------------------------------------------------------UA--GUGCCACAGAGACGAGA---------------------------------AUU---------------------------------GUGAAACG-CGGUAAACUCCAUGAGUUAGAAACCCAAAUAU--UGGUAGGGGAAC-U-UUUCA--ACGGAAAUU---GAACCAA--AGAAAAGA-GUUGA----------------UUAA-----UCA--ACUAGAUAAAUUGUUAGCA---CCU------------------------GAGA-------------------------GGG---UACAAAACGUGGCUUAUAAAU-----GCUAAAACACUUGCGCGA
X69983.1/47-447              --------GCACA-AGUCAAUCGCAGGUAUAAUCAAAAUAUUAUUUUAUAAAUAUAAAUUAUAUUUUGA----UUAA-----UAUUUGAGGAAAGUCCGCG-CUAGCACUA-CC-UGUGAU-GGUAGUAGUGUUCAU-GUUGGGU-----CUAAUAAACCCAAGC-------------UUA------------GACGAC---------------------------------------------------------AA--GUGCCACAGAGACGAG-CUUAUU-UAUUAAAUUCUUCUUUUUCUAUAUUGAGA-----AUUACAAUUUUUUUCUUAAUAA-AUAAGGUGAAACG-CGGUAAACUCCAUGAGCUAGAAACCUAAAUUU--UGGUAAGGGAGC-C-CAAUU--UGAAGAAAA---AAAACUUC-GAUUGGGA-AGUUUUUUGAUAAGGUUAUUAUUAAAAGAAAAA--CUUAGAUAAAUGAUUGACU--------------------------------GA-------------------------------UACAGAACGCGGCUUAUUAGU------GCAAAAACAGCGUAAAA
X69982.1/45-449              -------UGCACA-AGUCAAUUGCAGAUAUAAUUAAAUAUAAUAAUUUUUUUAUAAUUGUUAUAUUUAACAAAUUUA-----UAUUUGAGGAAAGUCCGCG-CUAGCACUA-CC-UGAGAU-GGUAGUAGUGUUCAU-GUUGGAU-----CUAAUAAAUCCAAGC------------UUUA------------GACGAC---------------------------------------------------------CA--GUGCCACAGAGACGAG-UUUAUU-UAUUAAUUUGUUUAUAUU-------AAAAAAUAGUUUAGAAUUUUUAAAUUAAUAA-AUAAGGUGAAACG-CGGUAAACUCCAUGAGCUAGAAACCUAAAUUU--UGGUAAGGGAGC-C-CAAUU--UCGGGAAAC---AAACUUU--AAUUGGGA-AGUUCUAUUAUAAUAUU----UUUA-UAAAGAA--CUUAGAUAAAUGAUUGAUU--------------------------------AA-------------------------------UACAGAACGCGGCUUAUUAGUGCAAAAAAAACAGCGAAUCUGAA
AF151218.1/1-397             UGA----UAUUUC-GGGUAAUCGCUAUAU--------------------------------------------U--------AUAUAGAGGAAAGUCCAUG-CUCACACAG-UC-UGAGAU-GAUUGUAGUGUUCGU-GCUUGAU--GAAACAAUAAAUCAAGGCA-----------UUAA---UU------UGACGGC--AAUG-AAAU-AU-CCUAAGUC--UUUC------GAUAUGGAUAGAGUAAUU-UGAAA--GUGCCACAGUGACGUAGCUUUUA-UA-----------------------GAAA------------------------UAU-AAAAGGUGGAACG-CGGUAAACCCCUCGAGUGAGCAAUCCAAAUU---UGGUAGGAGCAC-U-UGUUU--AACGGAAUU---CAACGUAU-AAACGAGA-CACACUUCGC-----------GAAA-UGAAGUG-GUGUAGACAGAUGGUUAUCA---CCUGA--G-UACCAGUGUG--------ACUA------GUGCACGUGAUGAGUACGAUGG---AACAGAACAUGGCUUAUAGAA---------AUAUCACUACUAGU
U64885.1/1-349               ---------------------------------------------------------------------------------------GAGGAAAGUCCGGG-CUCACACAG-UC-UGAGAU-GAUUGUAGUGUUCGU-GCUUGAU--GAAACAAUAAAUCAAGGCA-----------UUAA---UU------UGACGGC--AAUG-AAAU-AU-CCUAAGUC--UUUC------GAUAUGGAUAGAGUAAUU-UGAAA--GUGCCACAGUGACGUAGCUUUUA-UA-----------------------GAAA------------------------UAU-AAAAGGUGGAACG-CGGUAAACCCCUCGAGUGAGCAAUCCAAAUU---UGGUAGGAGCAC-U-UGUUU--AACGGAAUU---CAACGUAU-AAACGAGA-CACACUUCGC-----------GAAA-UGAAGUG-GUGUAGACAGAUGGUUAUCA---CCUGA--G-UACCAGUGUG--------ACUA------GUGCACGUGAUGAGUACGAUGG---AACAGAACGCGGCUUAU---------------------------
U64886.1/1-331               ---------------------------------------------------------------------------------------GAGGAAAGUCCGGG-CUCGCACAG-GC-UGUGAU-GCCUGUAGUGUUCGU-GCUUAGC--GAAACAAUAAGCUAAGGUG--CUCU------AUU-----AGAG--UAACGGC--AGGA-AAAC-AA-GCUAAGGUU-UUUA------ACUAUGCUUAAGUAUCCU-UGAAA--GUGCCACAGUGACGAAGCGGAUA-GG-----------------------GAAA------------------------CUU-AUUCGGUGGAACG-CGGUAAACCCCUCGAGCGAGCAACCCAAACAA--UGGUAGGGGCGC-U-UUUUG--UUGGGAAUUAA-GAACGAGA-CAAAAAGG-CAG-G----------------UUAA-------C--UGCAGAUAGAUGGUUACCA---CAUUG--C-UUUU--------------UCUC--------------CCUGGAAAGUAGUG---UACAGAACACGGCUUAU---------------------------
AF295988.1/1-331             ---------------------------------------------------------------------------------------GAGGAAAGUCCGGG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGU--GAAUCAAUAAGCCUAGGGA--CAUCU----UUUU-----GAUG--UUACGGC--GGGC-AAAA-AG-GCUAAGUCU-UUAC-----GGAUAUGUCUGAAUAGCCC-UGAAA--GUGCCACAGUGACGUAGUUCUUG-GG-----------------------GAAA------------------------CCU-AAGAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GUUGGAAUC---CGAACAAUCUAUCCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAGA--U-AAGA--------------CCUA-------------------GUUAUCUCU-GGAACAAAACACGGCUUAU---------------------------
AF295989.1/1-302             ---------------------------------------------------------------------------------------GAGGAAAGUCCGGGACUCGCACCA-CC-UGAGAU-GGUGGUAGUGUUUGU-GCUCAGU--GAAUCAAUAAGCUGAGGUA--UAGA-----GGCA-----UCUA--UAACGGC--AGAC-CAAA-AU-CCUAAGGG--AA--------ACUAUGGAU--GGAGGCUAUAAAA--GUGCCACAGUGACGAAGUUCCUA-GG-----------------------GAAA------------------------CCU-AGGAAGUGGAACG-AGGUAAACCCCAUAAGCGAGAAACCCAAAAU---UGGUAGGGGAAC-U-CACAC--UACUGAAAU---GAAGGUA--ACGUGAGA-CGUUU----------------UUA------AAA--CGUAGAUAAAUGAUUAUC-------------------------------GCAA-------------------------------GUCANAACACGGCUUAU---------------------------
AJ511701.1/1-371             GUGCA--AUUUUU-GGAUAAUCGCAUGAAAA------------------------------------------GUUA--UUUUUUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGC--GAAACAAUAAGCCUAGGGA--CGGA-----UUAU-----UCCG--UUACGGC--GGAU-GAAA-CA-GCUAAGUC--UCUU------GAUAUGCUGGAGUAGGCC-UGAAA--GUGCCACAGUGACGUAGUUUUUG-UG-----------------------GAAA------------------------CAC-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-GAAUG--CGUGGAAAC---GAACAUUG-CAUUCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAAA--U-GGUA--------------CCUA-------------------GUCAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AF295987.1/1-332             ---------------------------------------------------------------------------------------GAGGAAAGUCCGGG-CUAGCACCG-GC-UGUGAU-GCUGGUAGUGUUUGU-GCUAGGC--GAACAAAUAAGCCUAGGGA--UGUGU----UUGA-----CACA--UUACGGC--GAGU-GAAA-AG-GCUAAGUC--CUUG------GAUAUGCCAGAGUAGCUC-UGAAA--GUGCCACAGUGACGAAGUUUUUA-UG-----------------------GAAA------------------------CGU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GUUGGAAAC---GAACAAGC-UAUCCUGA-CUGUU----------------GACA-----AAC--AGUAGACAGAUGAUUAUCGAA-GGAGA--U-AAUA--------------CCUA-------------------GUUAUUUCU-GGAACAAAACACGGCUUAU---------------------------
AJ511695.1/1-374             GUGCA--AUUUUU-GGAUAAUCGCGUAGUAUU-----------------------------------------GCAA----UACUAUGAGGAAAGUCCAUG-CUAGCACCG-GC-UGUGAU-GCUGGUAGUGUUUGU-GCUAGGC--GAACAAAUAAGCCUAGGGA--UGUGU----UUGA-----CACA--UUACGGC--GAGU-GAAA-AG-GCUAAGUC--CUU-------GAUAUGCCAGAGUAGCUC-UGAAA--GUGCCACAGUGACGAAGUUUUUA-UG-----------------------GAAA------------------------CGU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GUUGGAAAC---GAACAAGC-UAUCCUGA-CUGUU----------------GACA-----AAC--AGUAGACAGAUGAUUAUCGAA-GGAGA--U-AAUA--------------CCUA-------------------GUUAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AJ511705.1/6-366             -------AUUUUU-GGAUAAUCGCAUGGG--------------------------------------------AUAA------CCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGAC--GAAAAAAUAAGUCUAGGGA--CAUG-----GUGA-----CAUG--UUACGGC--GGAU-AAAA-UG-ACUAAGUC--UUCU------GAUAGGUCAGAGUUAUCC-UGAAA--GUGCCACAGUGACGUAGUUUUUA-UG-----------------------GAAA------------------------CGU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-GGAAA--GCUGGAAAC---GAACAGUC-UUUCCUGA-CUGC-----------------AUAA------GC--AGUAGACAGAUGAUUAUCG---AAGGC--G-GCAGAGC-----------CUAG-------------------UGUCGCUGG---AACAAAACAUGGCUUAUAGAA-----------------------
AM263198.1/1937764-1937383   -------ACGUUC-GGAUAAUCGCUGUUUUCUU----------------------------------------UUGA-----AAACAGAGGAAAGUCCAUG-CUCGCACGGUGC-UGUGAU-GCCCGUAGUGAUCGU-GCCUGGU--CAAACAAUAAGCCAGGGCAUUCCGG-----AUUU-----CCGGUUUGACGGC--AGGU-GAAU-GA-CCUAAGUC--UUCG------GAUAUGGUCUUAUAACCU-UGAAG--GUGCCACAGUGACGAAGUUCCGG-CA-----------------------GAAA------------------------UGCUCGGAAGUGGAACG-AGGUAAACCCCACGAGCGAGAAACUCAAACUUA-UGGUAGGGGCAC-U-UUUCC--CGAGGAAUCA--AGAACGAG-GGACGAGG-UACGAAUGA------------AUUU-----UCG--UGCAGAUAGAUGGUUAUCU---CUUUG--C-UAUU--------------ACCC--------------UGUAUAUAGUAAAG---AACAGAACAUGGCUUACAGAG-----------------------
AJ511677.1/6-374             -------AUUUUU-GGAUAAUCGCGUGGUAUUU----------------------------------------UAAU-----ACCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGU--GAAUCAAUAAGCCUAGGGA--CAUCU----UUUU-----GAUG--UUACGGC--GGGC-AAAA-AG-GCUAAGUCU-UUAC-----GGAUAUGUCUGAAUAGCCC-UGAAA--GUGCCACAGUGACGUAGUUCUUG-GG-----------------------GAAA------------------------CCU-AAGAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GUUGGAAUCC--GAACAAUC-UAUCCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAGA--U-AAGA--------------CCUA-------------------GUUAUCUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AJ511678.1/6-380             -------AUUUUU-GGAUAAUCGCGUGGUAAAUAUUGCAA---------------------------------UUUU-----AUCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGAC--AAAAAAAUAAGUCUAGGGA--UGUGC----UUUG-----CGCA--UUACGGC--GGAU-AAAA-UG-GCUAAGUC--UUU-------GAUAGGCCGGAGUAAUUC-UGAAA--GUGCCACAGUGACGUAGCUUUUA-UG-----------------------GAAA------------------------CAU-AAAAGGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GAAAA--GCUGGAAAAA--GAACGGUC-UUUUCUGA-CUGC-----------------AUAA------GC--AGUAGACAGAUGAUUAUCAAA-AAAGG--U-GGUA--------------CCUA-------------------GUCACCUUU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AJ511688.1/6-371             -------AUUUUU-GGAUAAUCGCGUGGUAUUC----------------------------------------UAAU-----ACCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGU--GAAUUAAUAAGCCUAGGGA--CAUC-----UUGU-----GAUG--UUACGGC--GAGU-GAAA-AG-GCUAAGUC--UUU-------GAUAUGCCUAAAUAGCUC-UGAAAA-GUGCCACAGUGACGUAGUUCUUG-AG-----------------------GAAA------------------------CUC-GAGAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAC-G-GGAUA--GUAGGAAUCC--GAACGAUC-UAUCCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAGA--U-AAGA--------------CCUA-------------------GUUAUCUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AJ511718.1/6-377             -------AUUUUU-GGAUAAUCGCAUGGUUGCAAGUAA-----------------------------------GUCU-----UCCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGC--GAAUCAAUAAGCCUAGGGA--CUUGA----UUUU-----CAAG--UUACGGC--GAGC-GAAC-UG-GCUAAGUC--UUCG------GAUAGGUUUUAGUAGCUC-UGAAA--GUGCCACAGUGACGGAGUUUUUA-GG-----------------------GAAA------------------------CCU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUG--GCCGGAAAC---GAACGGAC-CAUUCUGA-CUGC------------------UAU------GC--AGUAGACAGAUGAUUAUCGAA-GGAAG--U-GGUA--------------CCUA-------------------GUCACUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
BA000028.3/1789668-1789281   -------UUGCUC-AUGUAAUCGCUGCAUCCUU----------------------------------------UAGG-----AUGUAGAGGAAAGUCCAUG-CUCACACGA-GC-UGCGAU-GCUCGUAGUGUUCGU-GCUUGAC--GAAGUCAUAAGUCAAGGUA--GCUU-------UA-----AUGC--UAACGGC--AGAUAUGAU-AU-CCUAAGUUA-UCUUAAAGAUAAUAUGGAUUCAUU--CU-UGAAA--GUGCCACAGUGACGUAGCUAGAU-CG-----------------------GAAA------------------------CUU-UCUAGGUGGAACG-CGGUAAACCCCACGAGUGAGCAACCCAAAUUAA-UGGUAGGGGCAU-C-CUUUUAGUAGGGAAUU---AGAACCGA-AUAAGGGA-CAGAUU---------------AAUG-----AUC--UGUAGAUAGAUGAUUACGA---CCGGC--G-UACAAGG-----------UUGA-------CCACCGUUUGCAGUACAAUGG---UACAGAACAUGGCUUAUCGAG-----------------------
AAXV01000008.1/62968-62589   -------AAAUUC-UGGUAAUCGCUGCGGCGCUA---------------------------------------GACG-----UCGUAGAGGAAAGUCCAUG-CUCACACGGUAC-UGAGAU-GUCCGUAGUGUUCGU-GCUUACU--GAAAAAAUAAGGUAAGGCA--GCUG-----UUCA------GGC--UGACGGC--GGAA-GGAA-AA-CCUAAGUC--CUUG------GAUAUGGUUGACACUUCC-UGAAA--GUGCCACAGUGACGAAGCUUGCU-UG-----------------------GAAA------------------------CAU-GCAAGGUGGAACG-AGGUAAACCCCACGAGUGAGAAACCCAAAUUA--UGGUAGGGGCAC-U-CUCUU--GAAGGAAUU---GAACGGA--UAGAGGGA-CGGAG----------------CUUG-----CUC--UGUAGAUAGAUGAUUACUA---CCUGGUCG-UACGAGGCGCAAGCUGU-UUGA-------------------GUACUCAGG---AACAAAACAUGGCUUAUGGAA-----------------------
AJ511729.1/6-371             -------AUUUUU-GGAUAAUCGCGUGAGAAUAUUU-------------------------------------UAUU-----UUCAUGAGGAAAGUCCAUG-CUAGCACGG-GC-UGUGAU-GCCCGUAGUGUUUGU-GCUAGGU--GAAACAAUAAGCCUAGGGA--CGAG-------AA-----AUCG--UUACGGC--GGAC-GAAA-CA-GCUACGUC--UCUG------GAUAUGCUGGAAUAGUCC-UGAAA--GUGCCACAGUGACGUAGUUUUUG-CA-----------------------GAAA------------------------CGC-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAC-G-GAAUG--CGUGGAAAC---GAACAUAG-CAUUCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAAA--U-GAUA--------------CCUA-------------------GUUAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AP008934.1/1342447-1342821   -------UGUUUC-GGGUAAUCGCUAUAG--------------------------------------------CG-------AUAUAGAGGAAAGUCCAUG-CUCACACAA-UC-UGAGAU-GAUUGUAGUGUUCGU-GCUUGAU--GAAACAAUAAGUCAAGGCA-----------UUAA---GU------UGACGGC--AACG-AAAU-AA-CCUAAGUC--CUUA------GAUAAGGUUAGAUUAGUU-UGAAA--GUGCCACAGUGACGGAGCUUUUG-CA-----------------------GAAA------------------------UGC-AAAAGGUGGAACG-CGGUAAACCCCUCGAGUGAGCAAUCCAAAUU---AGGUAGGAGCAC-U-UAUUU--AACGGAAUU---CAACGUAU-AUAUAAGA-CAUACUUU-------------UAAA----AGUA--UGUAGACAGAUGGUUACCA---CCUGC--G-UACG--------------AGUGUUUCUAGUACACGUUAGCAGUACAAUGG---UACAAAACAUGGCUUACAGAA-----------------------
AJ511700.1/6-373             -------AUUUUU-GGAUAAUCGCGUGAAGAUUUGA-------------------------------------UAUU-----UUCAUGAGGAAAGUCCAUG-CUAGCACCG-GC-UGUGAU-GCUGGUAGUGUUUGU-GCUAGGC--GAAACAAUAAGCCUAGGGA--CGGA-----GCAA-----UCCG--UUACGGC--GACU-GAAA-AG-GCUAAGUC--UUUA------GAUAGGUCUGAAUAGGUC-UGAAA--GUGCCACAGUGACGUAGUUCUUC-UG-----------------------GAAA------------------------CAG-AAGAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAC-G-GAAUG--CGUGGAAAC---GAACAUAG-CAUUCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAGA--U-GGUA--------------CCUA-------------------GUCAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
CP000029.1/1061551-1061168   -------UAUUUC-GGGUAAUCGCUAUAG--------------------------------------------CA-------AUAUAGAGGAAAGUCCAUG-CUCACACAA-UC-UGAGAU-GAUUGUAGUGUUCGU-GCUUGAU--GAAACAAUAAAUCAAGGCA-----------UUAA---UU------UGACGGC--AAUG-AAAU-AA-CCUAAGUC--AUUG------GAUAUGGUUAGAAUAGUU-UGAAA--GUGCCACAGUGACGUAGCUUUUA-UA-----------------------GAAA------------------------UAU-AAAAGGUGGAACG-CGGUAAACCCCUCGAGUGAGCAAUCCAAAUU---GGGUAGGAGCAC-U-UGUUU--AGCGGAAUU---CAACGUAU-AGACGAGA-CGAUUUUUACGCGAAA-----GUAA----AAAU-AUGUAGACAGAUGGUUACCA---CCGAC--G-UACCAGU-----------GUAA---CUAGUACACAUUAUGAGUACAACGG---AACAGAACAUGGCUUACAGAA-----------------------
ABCF01000047.1/221-605       -------ACAUUC-AGGUAAUCGCUGCAACG------------------------------------------UUUG-----UUGUAGAGGAAAGUCCAUG-CUCGCACGGUGC-UGAGAU-GCCCGUAGUGUUCGU-GCCUAGC--CAAUUCAUAAGCUAGGGCA--GUCUGC---UUCU---GCAGAU--UGACGGC--AGGG-AAAA-CA-CCUAAGUCC-UAUG------GAUAUGGUGUGAAUACCU-UGAAA--GUGCCACAGUGACGGAGUCUUGC-AA-----------------------GAAA------------------------UUG-CAAGAGUGGAACG-AGGUAAACCCCACGAGCGAGAAACCCAAAAUA--AGGUAGGGGCAC-C-UUCUU--UGAGGAACU---CAACGAG--AAGAAGGA-CGAAACA--------------GUUG-----UUU--CGUAGAUAGAUGAUUGCCG---CCGGA--G-UACG--------------AGAU----GACCCAUCGCUUGCAGUACGAAGG---AACAAAACAUGGCUUACAGAA-----------------------
BA000026.2/520178-520527     -------UAAUGAUAGUUGGUUGCUAUAAG-------------------------------------------UUUC-----UUAUAGAGGAAAGUCCAUG-CUAGCACUA-UC-UGAGAU-GAUAGUAGUGUUUGUUGCAGGUAUAUAAAAAAUAAAACCUGGAA--GA-------UUUA----C--UC--UUACGAC--ACAA-CAA--AA-CCUAAAAUG-GUUG-----CAUUAUGGUUGAG--UUGU-AUAAA--GUGCCACAGAGACGAGC--AAAG-AA-----------------------GAAA------------------------UUC-UUGAUAUGAAACG-CGGUAAACUCCACAAGCUAGAAACCUAAAUU---UGGUAAGGGAAC-U-GGUUAU-AAAAGAAUU---CAAUUUUA-UAAACGGA-AGAAU----------------GUAU-----GUU--CUUAGAUAAAUAACCAACG----------U-CUAG--------------AUAA-------------------UAGA--------UACAGAACAUGGCUUAUUUCA-----------------------
AJ511703.1/6-386             -------AUUUUU-GGAUAAUCGCGUGAGGAGAAUU-------------------------------------GCUU-----CUCAUGAGGAAAGUCCAUG-CUAGCACAG-GC-UGUGAU-GCCUGUAGUGUUUGU-GCUAGGC--GAAACCAUAAGCCUAGGGA--CGAG-------AA-----AUCG--UUACGGC--AGUU-GAAA-UG-GCUAAGUC--CUUG------GAUAGGCCAGAGUAGGCU-UGAAA--GUGCCACAGUGACGGAGUCUUUC-UG-----------------------GAAA------------------------CAG-AGAGAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAAUUU--UGGUCGGGGCAU-G-GAGUA--CGCGGAAAC---GAACGUAG-UAUUCUGA-CUGCUAUCAGCUAGAGC----UGUU-----AGU--GGUAGACAGAUGAUUAUCGA--AGGAA--G-UGGU--------------CCUA------------------GUCACUUCUG--GAACAAAACAUGGCUUAUAGAA-----------------------
AJ511697.1/6-375             -------AUUUUU-GGAUAAUCGCGUAGUAUUU----------------------------------------UGAU-----ACUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGC--GAAAAAAUAAGCCUAGGGA--CGUAUG---AUGA-----UACG--UUACGGC--AGGU-AAAA-UG-GCUAAGUC--CUU-------GAUAUGCCAUAGUAACCU-UGAAA--GUGCCACAGUGACGAAGUUUCUA-GG-----------------------GAAA------------------------CCU-AGAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-AGAUAG-CUGGAAGAC---GAACAGAACUAUCUUGA-CUGC-----------------AACA------GC--AGUAGACAGAUGAUUAUCG---AGGAA--G-UUGG--------------UUCC---------------UAGUCAACUUCUG---AACAAAACAUGGCUUAUAGAA-----------------------
AJ511673.1/6-374             -------AUUUUU-GGAUAAUCGCGUAGUAUU-----------------------------------------GAUA----UACUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGC--GAAAAAAUAAGCCUAGGGA--GAUAG----CUAG----CUAUC--UUACGGC--AAGC-AAAA-GG-GCUAAGUC--UUUG------GAUAUGCCUGAAUAGCUU-UGAAA--GUGCCACAGUGACGUAGUUUCUA-GG-----------------------GAAA------------------------UCU-AGAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GUUGGAAUGA--GAACAAUC-UAUCCUGA-CUGC------------------UUU------GC--AGUAGACAGAUGAUUAUCGAA-AGAAA--C-AAUU--------------CCUA-------------------GUUGUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AE017198.1/1120310-1119944   -------AAUUUC-GAGCGAUCGCGGUUAGCUU----------------------------------------AUGC-----UAGCUGAGGAAAGUCCACG-CACGCACAA-GC-UGAGAU-GCUUGUAGUUUUUGU-ACUCAGC-----CCAAUAAGCUGGGGAA--CUUGUU---UUUA-----CAAG--UUACGGC---GGA-AAAA-GC-ACUAAAUCA-UUUU-----UGACAUGUGUGACUAUCCU-GAAAA--GUGCCACAGUGACGAAGCAGUGA-AG-----------------------GAAA------------------------CUU-UGCUGGUGGAACG-AGGUAAACCCUGCAAGCGGGCAACCCAAAUU---UGGUAGGGGCGCUU-UCGUC--UAAGUAAAU---GAACUAAA-GACGAGGU-CAUU------------------UUU------AA--UGAAGAUAGAUGGUCGCUG---AAAAU--A-GGAA--------------UUAA--------------CCAAAUCCUAUUGG---AACAGAACGUGGCUUAUAGAG-----------------------
AM406671.1/759051-759433     -------GUUUUC-GGAUAAUCGCGCGAUUCUUU---------------------------------------GUGA-----AUCGUGAGGAAAGUCCAUG-CUCGCGCGUUGC-UGAGAU-GCACGCAGUGAUUGU-GCUAGGU--CAAACAAUAAACCUAGGUA--GGAGC----GUCA-----UGCC--UAACGGC--UGGC-CAAA-AC-GCUAAGUC--UUUU------GAUAUGCGUGAGUAGCCUGUAAAA--GUGCCAUAGAGACGAG-UCUUAG-UG-----------------------GAAA------------------------CGC-UAAGAAUGGAACG-UGGUAAACCCCUCAAGCGAGCAACCCAAACUUA-UGGUCGGGGCAC-U-UGACU--AGCCCAAAU---GAAGGCGU-GGUCGAGG-CUGAAAUUA------------AGAA----UUUU--GGCAGACAGAUGAUUAUCGAA-GGGGA--G-AUUCAUUGA---------UAUG-------------------GAUUGAACU-GGAACAAAACAUGGCUUAUAGAA-----------------------
CP000002.3/2302344-2301958   -------ACGUUC-GGGUAAUCGCUGCAGAUUUU---------------------------------------ACAU-----CUGUAGAGGAAAGUCCAUG-CUCGCACGGUGC-UGAGAU-GCCCGUAGUGUUCGU-GCCUAGC--GAAGUCAUAAGCUAGGGCA--GCCUUG---CAGA-----AGGC--UGACGGC--AGGA-AAAA-AG-CCUACGUCC-UUUA----UGGAUAUGGCUGAGUAUCCU-UGAAA--GUGCCACAGUGACGAAGUCUCAC-UA-----------------------GAAA------------------------UGG-UGAGAGUGGAACG-CGGUAAACCCCUCGAGCGAGAAACCCAAAUUU--UGGUAGGGGAAC-C-UUCUG--GACGGAAAU---GAACGGA--AGGAAGGA-CAGAG----------------UUGA-----CUC--UGUAGAUAGAUGAUUACCA---CCCGA--G-UACGAGG-----------CUUA------GCAGCCGACGGCAGUACGACGG---AACAAAACAUGGCUUACAGAA-----------------------
AM285310.1/28714-28347       -------UAACAG-AACUAGUUGCUAUUAACUUC---------------------------------------UUGU-----UAAUAGAGGAAACUCCACG-CUCGCACAA-UC-UGUGAU-GAUUGUAGUGUUUGU-GCUAAUU--UAAUUCAUAAAAUUAGGCA--UAAG-----GUUA-----CUUA--UGACGGC--UGAA-AAAA-AU-CCUACGUUA-UUAU-UAAAUAAUAUGGAGUUUUUUCUA-UAAAA--GUGCCACAGAAACGAG-UUUUUA-AA-----------------------GAAA------------------------UUU-AAAAAAUGGAACG--GGUAAACCCCACAAGCGAGAAACCUAAAUUU--UGGUAAGGGAAC-U-UCUUG--UUUUGAAGC---AGAAAAAA-CAAGGGGA-UCAAUUU--------------AAUA-----AUU--GAUAGAUAAAUAACUAGUA---UUUUA--U-UUU-----------------AA-------------------GAAAUAAAA----ACAGAACGUGGGUUAUGAUG-----------------------
AAQK01006327.1/2314-1971     -------UUAAAU-CGACAGUCGCUGGCUACUU----------------------------------------AGAU-----AGUUAGAGGAAAGUCCAUG-CUCGCACAA-UC-UGUGAU-GAUUGUAGUGUUUGU-GCUAGAU--GAAUAAAUAAGUCUAGGCA--AGUU-------AU-----UGCU--UGACGGC--UGUU-UUGU-UU-GCUAAGGG--AA--------ACUAUGUAA-ACAAACUU-UAAAA--GUGCCACAGAGACGAA-UCUAUA-UG-----------------------GAAA------------------------CGU-AUAGGGUGGAACG--GGUAAACCCCACAAGCGAGAAACCCAAAUU---UGGUAGGGGAAC-C-GGCUG--GAAUGAAAC---GAAAGGA--AGGCUGGA-UAGCU----------------UUA------UGC--UAUAGAUAAAUGACUGUCA---CCAC-----------------------GCAA------------------------GUGG---AACAGAACAUGGCUUAUGAUU-----------------------
AJ511676.1/6-374             -------AUUUUU-GGAUAAUCGCGUAGUAUUU----------------------------------------CAAU-----ACUAUGAGGAAAGUCCAUG-CUAGCACCG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGC--GAAAAAAUAAGCCUAGGGA--UGCA-----GAAA-----UGCA--UUACGGC--GAAA-GAAC-GA-GCUAAGUC--UUCG------GAUAUGUUUUAGUAUUUC-UGAAA--GUGCCACAGUGACGCAGUUUCUA-UG-----------------------GAAA------------------------CGU-AGGAAAUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-GAAUA--GAUUGGAAACAAGAACGAGC-UAUUCUGA-CUGU------------------UAU------AC--GGUAGACAGAUGAUUAUCGAA-GGAGA--U-GAUA--------------CCUA-------------------GUCAUCUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AACY023573249.1/971-644      -------AAUGGA-AGAUGAUCGAGCGGU-----------------------------------------------------AACGUUAGGAAAGUCCAUA-CUAACACAG-AC-UUUUAUAGUUUGUAGUGUUUGU-GUCUAAG--GAAAAAAUAACUUAGAGUA--UC-------GAAA-------GA--UAACGGC--GAAU-UCAG-UG-UCUAAGGG--AA--------ACUAUGAUA--CUAAUUU-GUAAA--GUGCCACAGUGACGAAU--CAUU-UA-----------------------GAAA------------------------UAA-AUGG-GUGAAACG-AGGUAAACCCCACAAGUUAGAAACCCAAAUUU--UGGUAGGGGAAC-A-UUGAU--UUUUGAGAA---AAA------AUUGAUGC-UACAA----------------UU-------UUG--UAGAGAUAAAUGAUCAU-A---CCUAU------------------------UU-----------------------AUAGG---AACAGAAUAUGGCUUAUGCAC-----------------------
AAOX01000023.1/29612-29224   -------ACGUUC-GGGUAAUCGCUGCGGCAGCUU--------------------------------------GCUG-----CUGCAGAGGAAAGUCCAUG-CUCGCACGG-AC-UGAGAU-GUCCGUAGUGUUCGU-GCCUGGC--GAAGUCAUAAGCCAGGGCA--GCCGGGCG-AUUG---CGCGGC--UGACGGC--AGGG-AAAA-UG-CCUAAGUCC-UUCG-----GGAUAUGGCAUGAAUACCU-UGAAA--GUGCCACAGUGACGGAGCCUUUC-CA-----------------------GAAA------------------------UGG-GAAGGGUGGAACG-AGGUAAACCCCGCGAGCGAGAAACCCAAAUAA--UGGUAGGGGCAC-U-UUCUC--UGAGGAAAU---GAACAAG--GAGAAGGA-CAGAUU---------------UUAU-----AUC--UGUAGAUAGAUGAUUGCCG---CCUUA--G-UACG--------------AGAC-----UCAGGUCGAUUGCAGUACAAAGG---AACAAAACAUGGCUUACAGAA-----------------------
CR936503.1/911803-912163     -------AAUCUU-GAGUAAUCGCGGUCUACAU----------------------------------------CAGU-----AGGCUGAGGAAGGUCCAUG-CCCGCACAG-GC-UGAGAU-GCUUGUAGUGUUCGU-GCCUGGC-----CCAAUAAGCCAGGGUA--CCUU--------A-----AUGG--UAACGGC---GGA-AAAA-GC-GCUAAAAC--UUCG------GUCAUGCGUUAAUAUCC--UUAAAUAGUGCCACAGUGACGGAGCGUUUG-GG-----------------------GAAA------------------------CCC-AAACGAUGGAACG-AGGUAAACCCCGCGAGCGAGUAACCCAAACUU--UGGUAGGGGCGU-C-UCAUU--UAUGGAAAU---GAACUAAA-AAUGAGAG-UUC------------------GAAA-------G--AACAGAUAGAUGAUUACUGAA-GGAGC--U-UUCU--------------UCCU-----------------GGGGAAGUUCU-GGAACAAAACAUGGCCUAUAGAG-----------------------
AJ511707.1/6-373             -------AUUUUU-GGAUAAUCGCAUGUCGCUUUCU-------------------------------------UGGC-----GACAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGU--GAAAAAAUAAGCCUAGGGA--UGUCU----AUUU-----GACA--UUACGGC--GGAC-GAAA-GA-GCUAAGUC--UUUG------GAUAAGUUU--CUAGUCC-UGAAA--GUGCCACAGUGACGGAGUUCUUG-GG-----------------------GAAA------------------------CUC-AGGGAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAC-A-AGAUG--GCUGGAAUUC--GAACGGAC-CAUCUUGA-CUGC-----------------GCAA------GC--AGUAGACAGAUGAUUAUCGA--AGGGG--A-CAGG--------------CCUA-------------------GUGUCUCUG--GAACAAAACAUGGCUUAUAGAA-----------------------
L43967.2/406519-406179       -------GCUGUC-GGUUAGUUGCUGCUUUAAAGAUAUA----------------------------------UUUA-----AAGUAGAGGAAAGUCCAUG-CUUGCACUU-GC-UGGAAU-GCAAGUAGUGUUUGU-GUAAAUC--AAAGCGAUAAGAUUUAGGA--UGUG-----AUAG-----C-CA--UAACGAC-----A-UAAC-UAGUCUAAGGU--UAAU------ACUAUGAUGAUGUUU----UGAAA--GUGCCACAGAGACGAGC---UUG-GU-----------------------GAAA------------------------ACC-A-GGUAUGAAACG-CGGUAAACUCCACAAGCAAGAAACCUAAAUUU--UGGUAAGGGAAU-G-UUGCU--UUAAGAACA---AAUAAUUAAAGUAAUGA-CAGCA----------------AU-------UGC--UGUAGAUAAAUAACUGACU------------------------------UUAA-------------------------------AACAGAACAUGGCUUAUUGAC-----------------------
AJ511732.1/6-372             -------AUUUUU-GGAUAAUCGCGUGAAGAGUUCG-------------------------------------UCUU-----UUCAUGAGGAAAGUCCAUG-CUAGCACGG-GC-UGUGAU-GCCCGUAGUGUUUGU-GCUAGGU--GAAACAAUAAGCCUAGGGA--CGGA-----AGUA-----UCCG--UUACGGC--GACU-GAAA-UG-GCUAAGUC--UUU-------GAUAAGUCAAAAUAGGUC-UGAAA--GUGCCACAGUGACGUAGUUUUUG-CG-----------------------GAAA------------------------CGC-AGGAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAC-G-GAAUG--CGUGGAAAC---GAACGCAG-CAUUCUGA-CUG------------------GUAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAAA--U-GAUA--------------CCUA-------------------GUUAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AJ511689.1/6-374             -------AUUUUU-GGAUAAUCGCAUGUCACUUUUU-------------------------------------AGUU-----GAUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGU--GAAACAAUAAGCCUAGGCA--UGUCU----AUUU-----GACA--UGACGGC--GGAC-GACG-GA-GCUAAGUU--CUUG------GAUAUGUUC--CCAGUCC-UGAAA--GUGCCACAGUGACGGAGUCCUUG-AG-----------------------GAAA------------------------CUU-AAGGAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAAUUU--UGGUCGGGGCAC-G-AGAUG--GCUGGAAUCC--GAACGGAC-CAUCUUGA-CUGC-----------------GUAA------GC--AGUAGACAGAUGAUUAUCGAA-GGAGA--C-AGCA--------------CCUA-------------------G-UGUCUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
CP000387.1/1852793-1852426   -------AUUUUU-GGAUAAUCGCGUGGAAAUUUUA-------------------------------------GAUU-----UUCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGC--GAAGAAAUAAGCCUAGGGA--CGGA-----UUUU-----UCCG--UUACGGC--GACU-GAAA-GG-GCUAAGUC--UUUG------GAUAUGUCUGAUUAGGUC-UGAAA--GUGCCACAGUGACGUAGUUCUUU-UG-----------------------GAAA------------------------CAG-AAGAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-GAGUG--CGUGGAAGC---GAACAUAG-CACUCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAAA--U-GGUA--------------CCUA-------------------GUCAUUUCC-GGAACAAAACAUGGCUUACAGAA-----------------------
CP000414.1/621486-621858     -------AGUAUC-GGGUAAUUGCGCGUUAUAU----------------------------------------UUCU-----AACGUGAGGAAGGUCCAUG-CUCGUACAC-UC-UGAGAU-GGGUGUAGUGUUUGU-GCUGGGA--UAAAAAAUAAACCCAGGAA--CA-------GUGA-------UG--UUACGGC--AGUC-GAAA-GG-GCUAAGGC--UUAG------GCUAUGUCUGAAUAGGCU-CGAAG--GUGCCAUAGAAACGUAUAUGCUA-GU-----------------------GAAA------------------------GCU-AGUAUUUGAGACG-AGGUAAACCCCACAAACGGGCAACCCAAACUUU-UGGUAGGGGCGG-C-UGGCC--UAGUGAAAU---GAAGCGAU-GGUCGGUAUGGUUCGUU-------------UGAA----CGAA--CUUAGAUAGAUGAUUACCGAAGGUGUA--A-UGUU--------------ACCU-------------------GCAUUACACUGGAACAAAACAUGGCCUAUAGAU-----------------------
AP006627.1/2129636-2129255   -------GUCUUC-AGACAACCGCUGCGCAUU-----------------------------------------UUAU-----GUGUAGAGGAAAGUCCAUG-CUCGCACCG-GC-UGAGAG-GCCGGUAGUGUUCGU-GCCUAGU--UAAUCCAUAAGCUAGGGCA--GCUGC----UGUG-----CAGC--UGACGGC--AGGA-GAGA-UG-CCUACGUCCAAAUG------GAUAAGGCAUGCACUCCU-UGAAA--GUGCCACAGUGACGUAGUCUGCU-UG-----------------------GAAA------------------------CGG-GCAGAGUGGAACG-CGGUAAACCCCUCGAGCGAGAAACCCAAACAA--UGGUAGGGGCAU-U-UUUCAG-UCUGAAAAU---GAACGGAACUGAAAAAA-CGAA-----------------GCAA------UU--CGUAGAUAGAUGGUUGUCG---CCGGA--G-UACG--------------AGGC----UCAUCACCGUUUGUAGUACAAAGG---UACAGAACAUGGCUUAUCGAU-----------------------
AE016830.1/1121959-1122327   -------AUUUUC-GGGUGAUCGCGGUUUGCUU----------------------------------------UUGC-----AAGCUGAGGAAAGUCCAUG-CUCGCACAA-GC-UGAGAU-GCUUGUAGUGUUCGU-GCUUAGC--GAAAUCAUAAGCUAAGGUA--CUCU------UUU-----AGAG--UAACGGC--AGGA-AAAA-UG-ACUAAGGU--UUCG------ACUAUGUCAAAGUAUCCU-UGAAA--GUGCCACAGUGACGAAGCGAUGU-GG-----------------------GAAA------------------------CUC-CAUCGGUGGAACG-CGGUAAACCCCUCGAGCGAGCAACCCAAACAA--UGGUAGGGGCGC-U-CUUCU--AAAGGAAAU---GAACGAGU-AGAAGAGG-CAGAG----------------UUUA-----CUC--UGCAGAUAGAUGAUGACCG---UCACC--A-AUUU--------------UUCC--------------UGAAGAAUUGGUGA---UACAGAACAUGGCUUAUAGAA-----------------------
AJ511704.1/6-373             -------AUUUUU-GGAUAAUCGCGUGAGAGAUUC--------------------------------------UUCC-----CUCAUGAGGAAAGUCCAUG-CUAGCACAG-GC-UGUGAU-GCCUGUAGUGUUUGU-GCUAGGU--GAAUUCAUAAGCCUAGGGA--CUUGA----UGUU-----CAAG--UUACGGC--GGGU-GAAA-GA-GCUAAGUC--UUUG------GAUAGGUUCUAGUAACUC-UGAAA--GUGCCACAGUGACGUAGUUUUUA-GG-----------------------GAAA------------------------CCU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-GAAUA--CGUGGAAAC---GAACAUAG-UAUUCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAAA--U-GGUA--------------CCUA-------------------GUCAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AJ511671.1/6-373             -------AUUUUU-GGAUAAUCGCGUGAUAAUA----------------------------------------UUUU-----AUCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCCAGGC--GAACAAAUAAGCCUGGGGA--UGUGU----UUUG-----CACA--UUACGGC--GGAU-AAAA-UU-GCUAAGUC--UUCG------GAUAGGUGAGAGUCAUCC-UGAAA--GUGCCACAGUGACGUAGCUUUUA-UG-----------------------GAAA------------------------CAU-AAAAGGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GAAGA--GCCGGAAACA--GAACGGUC-UUUUCUGA-CUGC------------------AUA------GC--AGUAGACAGAUGAUUAUCGAA-GAAGG--U-GAGA--------------CCUA-------------------GUCAUCUUU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AJ511675.1/6-369             -------AUUUUU-GGAUAAUCGCGUAGCUUU-----------------------------------------UUAG-----GUUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGC--GAAAAAAUAAGCCUAGGAA--UGUC------UUU-----GACA--UUACGGC--GGAA-AAAA-AG-GCUAAGUC--GAAU------GAUAUGCCUGAGUAUUUC-UGAAA--GUGCCACAGUGACGCAGUUUCUA-UG-----------------------GAAA------------------------CGU-AGAAAAUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-GGAUAG-ACGGGAAAC---GAACCUUC-UAUCCUGA-CUG------------------UUUA-------C--AGUAGACAGAUGAUUAUCGAA-AGAAG--U-AAUA--------------CCUA-------------------GUUAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
CP000416.1/875033-874654     -------GAUCCU-GAGUAAUCGCGGUCGGCUU----------------------------------------AUGU-----CGGCUGAGGAAAGUCCAUG-CUCGCACAG-GC-UGCGAU-GCCUGUAGUGUUCGU-GCUCGGU--GAAAAAAUAAGCCGGGGGA--CGUUA----GCAA----UAGCG--UUACGGC--GGGA-AAAAACG-GCUAAGGC--UUCG------GCUAUGCUUGAGUAUCCC-UGAAAA-GUGCCACAGUGACGAUACGCCUA-GG-----------------------GAAA------------------------CCU-AGGCGGUGGAACG-CGGUAAACCCCUCGAGCGGGCAACCCAAACUUU-UGGUAGGGGCGC-U-UCACA--UAUGGAAUU---GAACGAAA-UGUGGGGG-GAGAG----------------GAAA-----CUC--UCGAGAUAGAUGAUUACUG---CCAGC--U-GAUC--------------GUUU---------GCCUGAAACGGUUGGGUGG---UACAAAACAUGGCUUACAGGG-----------------------
AJ511708.1/6-378             -------AUUUUU-GGAUAAUCGCGUAGUAUUU----------------------------------------UAAU-----ACUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGC--GAAAAAAUAAGCCUAGGAA--UGUAC----UUUA----GUACA--UUACGGC--GAGU-GAAA-UG-GCUAAGUC--CUUU------GAUAUGCCAAAGUAAGUC-UGAAA--GUGCCACAGUGACGCAGUUUUUA-UG-----------------------GAAA------------------------CGU-AAAAAAUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-GAAUAG-CAUGGAAAC---GAACAGGC-UAUUCUGA-CUGUAA---------------UACA-----AUC--AGUAGACAGAUGAUUAUCGAA-AGAAG--U-GGUU--------------CCUA-------------------GUCACUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
CP000413.1/1024282-1023914   -------AAUUUC-GAGCGAUCGCGGUUAGCUU----------------------------------------AUAC-----UAGCUGAGGAAAGUCCACG-CACGCACAA-GC-UGAGAU-GCUUGUAGUUUUUGU-ACUCAGC-----CCAAUAAGCUGGGGGA--CUUGUU---UUUA----GCAAG--UUACGGC---GGA-AAAA-GC-ACUAAAUCA-UUUU----UUGACAUGUGUGACUAUCCU-GAAAA--GUGCCACAGUGACGAAGCAGCAA-GG-----------------------GAAA------------------------CUU-UGCUGGUGGAACG-AGGUAAACCCUGCAAGCGGGCAACCCAAAUU---UGGUAGGGGCGC-UUUCGUC--UAAGUAAAU---GAACUAAA-GACGAAGU-CAUU------------------UUU------AA--UGAAGAUAGAUGGUCGCUGAA-GAUAA--G-AUUCA-------------ACCA-------------------AAUCUUAUU-GGAACAGAACGUGGCUUAUAGAG-----------------------
CP000423.1/1471802-1471437   -------GGUCCU-GAGUGAUCGCGGUCUGCUU----------------------------------------UUGC-----AGGCUGAGGAAAGUCCAUG-CCCGCACAA-GC-UGAGAU-GCUUGUAGUGUUCGU-GCUAAGC-----CCAAUAAGCUUAGGGG--CCGU-----GUAA-----ACGG--CUACGGC--GGCC-AAAC-GC-GCUAAGGC--GUCA------GCUAUGCGCUAGUAGGUC-UGAAAA-GUGCCACAGUGACGAAACGAUCA-GG-----------------------GAAA------------------------CCU-GAGCGGUGGAACG--GGUAAACCCCGCGAGCGAGUAACCCAAACUUU-UGGUAGGGGCGU-U-UUGCC--AAGCAAAUU---GAAGCGAC-GGCAAUAC-AGCG-----------------GUAA------CG--CUGAGAUAGAUGAUGACUGAA-GGAGC--U-UGUGC-------------CUGA-------------------ACAAGUUCU-GGAACAAAACAUGGCUUAUAGGG-----------------------
AJ511743.1/6-374             -------AUUUUU-GGAUAAUCGCGUGAGAAUAUUU-------------------------------------UAUU-----UUCAUGAGGAAAGUCCAUG-CUAGCACGG-GC-UGUGAC-GCCCGUAGUGUUUGU-GCUAGGU--GAAACAAUAAGCCUAGGGA--CGGA-----AAUA-----UCCG--UUACGGC--GACU-GAAA-UG-GCUAAGUCU-CUCU------GAUAAGUCAAACUAGGUC-UGAAA--GUGCCACAGUGACGUAGUUUUUG-UG-----------------------GAAA------------------------CGC-AAGAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAC-G-GAGUG--CGUGGAAAC---GAACAUAG-CAUUCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAAA--U-GAUA--------------CCUA-------------------GUUAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AACY020292620.1/1543-1207    -------CAUUGC-AGGCAACCG-AGCCA--------------------------------------------GCGA-----UGGUU-AGGAAAGUCCAUG-CUAGCACAG-GC-UGCGAUCGCCUGUAGUGAUUGU-GAUAGAG--GAAACCAUAACUCUAUGCA--CCC------GAGA------GGG--UGACGGC--UGAG-AAAG-AG-GCUUA-------UC---------AAGUCUUGAGUAUCUUUAAAA--GUGCCACAGAGACGAG-CUCUUU-UA-----------------------GCAA------------------------UAA-AAGAGGUGGAACG--GGUAAACCCCGCAAGCUAGAAACCCAAAUUU--UGGUAGGGGCAC-U-UGGCG--UGAGAAACU---GAACUUAA-CGCCGAGG-UACGA----------------UU-------UUG--UACAGAUAAAUGGUUGCCA---CCCUU----------------------UUUA-----------------------AAGGG---UACAGAACAUGGCUUAU-GCA-----------------------
AJ511669.2/6-373             -------AUUUUU-GGAUAAUCGCGUGGUACCUU---------------------------------------ACGU-----ACCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGU--GAAUUAAUAAGCCUAGGGA--CAUCU----UUUU-----GAUG--UUACGGC--GAGU-GAAA-AA-GCUAAGUC--UUUU------GAUAUGCUUGAAUAGCUC-UGAAAA-GUGCCACAGUGACGUAGUUCUUG-GG-----------------------AAAA------------------------CCC-GAGAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAC-G-GGAUA--GUAGGAAAC---GAACGAUU-UAUCCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAGA--U-AAGG--------------CCUA-------------------GUUAUCUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
CP000411.1/1021545-1021185   -------CAAAUC-GGAUGAUCGCGCGAUGA------------------------------------------AAGA-----CUCGUGAGGAAGGUCCAUG-CCCGCCCAA-UC-UGAGAU-GAUUGGAGUGUUUGU-ACUGAGC-----CCAAUAAGCGAAGGCA--GU-A-----UUUA-------AC--UGACGGC--UAGC-GAAA-GG-ACUAAAGC--UUA-------GCCAUGUCUGAUUAACUUAUAAAA--GUGCUAUAGCGACGAAU--AACC-GG-----------------------GAAA------------------------CCG-GGGAAGUGAGACG-ACGUAAACCCUGCAAGCGGGCAACCCAAACUUUUUGGUAGGGGCGG-U-CAAUU--UGGCUAAAU---GAAGUAAA-AAUUGACA-CCGGU----------------UUUA-----UCC--GGUAGAUAGAUGAUCGUCGAA-GAACG--U-GAUC--------------GCCA-------------------AUCUCGUUU-GGAACAUAACAUGGCCUAUAGAU-----------------------
AJ511698.1/6-387             -------AUUUUU-GGAUAAUCGCGUGAAGAGGAUC-------------------------------------UCUU-----UUCAUGAGGAAAGUCCAUG-CUAGCACAG-GC-UGUGAU-GCCUGUAGUGUUUGU-GCUAGGC--GAAUCCAUAAGCCUAGGGA--CGAG-------AA-----AUCG--UUACGGC--AGUC-GAAA-UG-GCUAAGUC--UUCG------GAUAGGUCAAAAUAGGCU-UGAAA--GUGCCACAGUGACGGAGUCUUUC-UG-----------------------GAAA------------------------CAG-AGAGAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAAUUU--UGGUCGGGGCAU-G-GAGUG--CACGGAAAC---GAACGUAG-UACUCUGA-CUGCUAGCAGAUUUAUGC---UGUU-----AGC--GGUAGACAGAUGAUUAUCGA--AGGAA--G-UGGU--------------CCUA------------------GUCACUUCUG--GAACAAAACAUGGCUUAUAGAA-----------------------
CP000233.1/856590-856964     -------AAUUUC-UGGUAAUCGCGGUCUAUGU----------------------------------------AUAU-----AGGCUGAGGAAAGUCCAAG-CUUGCACAG-GC-UGAGAU-GCCUGUAGUGAUCGU-ACUUGCU--GAAAAAAUAAGGCAAGGCA--CUGCU----UUUA-----GUAG--UGACGGC--AGAC-AAAA-GA-GCUAAGGU--UUCG------GCUAUGCUUGAGUAGUCU-UGAAAA-GUGCCACAGUGACGAAGUAAUAU-AG-----------------------GAAA------------------------CUG-UAUUAGUGGAACG-CGGUAAACCCUGCGAGCAGGUAACCCAAACUU--UGGUAGGGGCGC-U-UCAUG---AUGGAAAU---GAACUAAU-CAUGGGGG-CGAGUUU--------------UUUA-----ACU--CGGAGAUAGAUGAUUACCA---CCGAU--U-CUAA--------------UUUU------------CCUGAAUUAGAUGACG---UACAGAACGUGGCUUAUAGAG-----------------------
U00089.2/571800-571471       -------GCUGUC-GGUCAGUUGCUGCUC--------------------------------------------AAU------GAGUAGAGGAAAGUCCAUG-CUUGCACUU-GC-UGGAAC-GCAAGUAGUGUUUGU-GUAAAUU--GAACAAAUAAGAUUUAGGA--CGCU-----AAUA-----GACG--UCACGAC--UGGA-CUAG----UCUAAGGUC-UUUG------ACUAUGA--UGAUGUCCG--UAAA--GUACCACAGAGACGA---GCUUA-GU-----------------------GAAA------------------------ACU-AAGU-AUGAAACG-CGGUAAACUCCACAAGCAAGAAACCUAAAUUU--UGGUAAGGGAAU-G-UUACU--UUAAGAAAA---AUAAUUAA-AGUAAUGA-CAG-G----------------AUUA-------C--UGUAGAUAAAUAACUGACU------------------------------UUAA-------------------------------AACAGAACAUGGCUUAUUGGC-----------------------
AJ512493.1/6-377             -------AUUUUU-GGAUAAUCGCGUAGUAUUU----------------------------------------GUAU-----ACUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGC--GAAAAAAUAAGCCUAGGGA--CGUAUCU--UUGA-----UGCG--UUACGGC--AGGU-AAAA-UG-GCUAAGUC--UUUG------GAUAUGCCUGAGUAACCU-UGAAA--GUGCCACAGUGACGAAGUUUUCA-GG-----------------------GAAA------------------------CCU-GAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-AGAUAG-CUGGAAGUC---GAACAGAACUAUCUUGA-CUGC------------------UUU------GC--AGUAGACAGAUGAUUAUCG---AGGAA--G-UUGU--------------GUGC--------------CUAGUCAACUUCUG---AACAAAACAUGGCUUAUAGAA-----------------------
AJ511668.1/6-374             -------AUUUUU-GGAUAAUCGCGUAGUAUUC----------------------------------------CAAU-----ACUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGAUUGU-GCUAGGC--GAACAAAUAAGCCUAGGGA--UGUG-----CUUA-----UACA--UUACGGC--GAAG-AAAA-UG-GCUAAGUC--CUUG------GAUAUGCCAAAGUACUUC-UGAAA--GUGCCACAGUGACGAAGUUUUUA-UG-----------------------GAAA------------------------CGU-AAAAAAUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GUUGGAAAC---GAACAAGC-UAUCCUGA-CUGUU----------------AUUA-----GAC--AGUAGACAGAUGAUUAUCGAA-AGAGA--U-GAGA--------------CCUA-------------------GUCAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AE017263.1/229614-229950     -------UUUUAU-GGUCAAUCGCUGCAUUUUU----------------------------------------AUUA-----AUGUAGAGGAAACUCCACG-CUUGCACAA-UC-UGAGAU-GGUUGUAGUGAUUAU-GCUAGAC--GAAAAAAUAAGUCUAGGCA--AUAC-----GCAA-----GUAU--UGACGGC--AUAA-CUAA----CCUAAGGCU-UUUG------GCUAUGG--AGAUGUUAU---GAA--GUGCCACAGAGACGAGU---AUA-GG-----------------------GAAA------------------------CCU-U-GAAAUGGAACG-CGGUAAACCCCAUAAGUAAGAAACUUAAAUUU--UGGUAAAGGAAC-U-UGGCG--AACAGAAAU---GAAUGUA--AACCAGGA-GGAU------------------UAU------AU--CCUAGAUAGAUGAUUGACA---CC-------------------------GAAA--------------------------GG---UACAAAACGUGGGUUAUAGUA-----------------------
AJ511692.1/6-374             -------AUUUUU-GGAUAAUCGCGUAGUAUUC----------------------------------------AAAU-----ACUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGCGAU-GCCGGUAGUGUUUGU-GCUAGGC--GAAAAAAUAAGCCUAGGGG--GGUAGUC--UUUU----CUGCC--CUACGGC--GAGU-AAAA-UG-GCUAAGUC--GUAA------GAUAUGUCAGAAUAACUC-UGAAA--GUGCCACAGUGACGUAGUUUUUA-UG-----------------------GAAA------------------------CGU-AAAAAAUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GCUGGAAGU---GAACGGUC-UAUCCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAGA--U-GGUA--------------CCUA-------------------GUCAUCUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AJ511696.1/6-372             -------AUUUUU-GGAUAAUCGCGUGGUGUUU----------------------------------------AGAU-----ACCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGC--GAAAAAAUAAGCCUAGGGA--GGUA-----GCGA-----UACC--UUACGGC--GAUC-AAAA-GA-GCUAAGUC--UUU-------GAUAUGCUCAAGUAGAUC-UGAAAA-GUGCCACAGUGACGUAGUUUUUA-GG-----------------------GAAA------------------------CCU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GUUGGAAAC---GAACGAUC-UAUCCUGA-CUGC-----------------UUUU------GC--AGUAGACAGAUGAUUAUCGAA-GGUGG--C-AAGA--------------CCUA-------------------GUUGCCGCC-GGAACAAAACAUGGCUUAUAGAA-----------------------
CP000412.1/862723-863083     -------AAUUUC-GAGCAGUCGCGGCCGGCCUU---------------------------------------GAGC-----CGGCUGAGGAAAGUCCACG-CACGCACGG-GC-UGCGAU-GCCCGUAGUGAUCGU-AUUCAGC-----CCAAUAAGCUGGAGGA--GGCC------CCA-----GGCC--UCACGGC---AGA-GAAA-GC-GCUAAAGC--CUA-------GCCAUGCGUGAAUAUCU--UGAAA--GUGCCACAGUGACGGAGCAAGCC-GG-----------------------GAAA------------------------CCG-GUUUGGUGGAACG-AGGUAAACCCUGCGAGCGUGUAACCCAAAAUU--UGGUAGGGGCGU-CUCAACU--UAGGUAAAU---GAACCAAA-AGUUGGAC-UACAU----------------C--------AUG--UAGAGAUAGAUGGCUGCUGAA-ACCAG--C-CGCG--------------GCCG-------------------GCGGUUGGU-GGAACAGAACGUGGCUUAUAGAA-----------------------
AJ511693.1/6-372             -------AUUUUU-GGAUAAUCGCGUAGUAUU-----------------------------------------GUAA----UACUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGC--GAAACAAUAAGCCUAGGGA--UGUA------AAA-----UACA--UUACGGC--AGGU-AAAA-UA-GCUAAGUC--UUUU------GAUAUGCUAAAGUAACCU-UGAAA--GUGCCACAGUGACGAAGUUUUUA-UG-----------------------GAAA------------------------CGU-AAAAAAUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-GGAUAG-UUUGGAAAC---GAACGAAC-UAUCCUGA-CUGU-----------------UUAA------UC--AGUAGACAGAUGAUUAUCGAA-GGAAA--U-AAUC--------------CCUA-------------------GUUAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AJ511681.1/6-373             -------AUUUUU-GGAUAAUCGCAUGGUAGGA----------------------------------------AUCU-----ACCAUGAGGAAAGUCCAUG-CUAGCACCG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGC--GAACCAAUAAGCCUAGGGA--CGUA-----GCAA-----UGCG--UUACGGC--GAUU-GAAA-GA-GCUAAGUC--GCAA------GAUAUGUUCGAGUAGGUC-UGAAAA-GUGCCACAGUGACGGAGUUUUUA-UG-----------------------GAAA------------------------CAU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAAUUU--UGGUCGGGGCAU-G-GGAAA--GUCGGAAACA--GAACGAAC-UUUCCUGA-CUGC-----------------AUAA------GC--AGUAGACAGAUGAUUAUCG---AAGGU--G-GUAGUGC-----------CUAG-------------------UACCACUGG---AACAAAACAUGGCUUAUAGAA-----------------------
AJ511680.1/6-373             -------AUUUUU-GGAUAAUCGCGUAGUAUUC----------------------------------------AAAU-----ACUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GCUAGGC--GAACAAAUAAGCCUAGGGA--CAUAUA---AAUA-----UAUG--UUACGGC--GAGU-AAAA-UA-GCUAAGUC--UUUU------GAUAUGCUUGAGUAGCUC-UGAAA--GUGCCACAGUAACGAAGUUUUUA-UG-----------------------GAAA------------------------CGU-AAAAAAUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GUUGGAAAC---GAACAAGC-UAUCCUGA-CUGUU----------------U--------GAC--AGUAGACAGAUGAUUAUCGAA-GGAAA--U-GAUU--------------CCUA-------------------GUUAUUUCC-GGAACAAAACAUGGCUUAUAGAA-----------------------
CP000422.1/936616-936988     -------AAUCUC-GGGUAAUUGCGGUUAGCAU----------------------------------------CUGC-----UAACUGAGGAAAGUCCAUG-CUCGCACAA-GC-UGCGAU-GCUUGUAGUGUUCGU-GCCUGGU--GAAAAAAUAAGCUGGGGCA--UUUGC----UUUG-----CAAA--UGACGGC--AAGU-GAAC-AA-GCUAAAGCC-UUCG------GUCAUGCUUAAGUAGCUU-UGAAAA-GUGCCACAGAGACGAU-CUUAUU-AA-----------------------GAAA------------------------UUA-AUAAGUUGGAACG-CGGUAAACCCCUCGAGCGGGCAACCCAAACUA--UGGUAGGGGAGC-U-UCACA--UCUGGAAUU---GAACUAAA-UGUGGGGG-CAGAC----------------AUU------GUC--UGGAGAUAGAUGAUUACC----CAAAU--U-UAAA--------------UUUU-----------CCUGAGAAUUUAUUUUG---GACAAAACAUGGCUUAUAGAG-----------------------
AJ511687.1/6-387             -------AUUUUU-GGAUAAUCGCGUGGAGAGUUUA-------------------------------------UCUU-----UUCAUGAGGAAAGUCCAUG-CUAGCACAG-GC-UGUGAU-GCCUGUAGUGUUUGU-GCUAGGC--GAAACCAUAAGCCUAGGGA--CGAG-------AA-----AUCG--UUACGGC--GAGU-GAAU-AG-ACUAAGUU--UUCG------GAUAUGUUUUAGUAGCUC-UGAAA--GUGCCACAGUGACGAAGUCUCUC-UG-----------------------GAAA------------------------CAG-AGAGAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAAUUU--UGGUCGGGGCAU-G-GAGUG--CGCGGAAAC---GAACGUAG-UACUCUGA-CUGCUAGCAGCUUCUAGC---UGUU-----AGU--GGUAGACAGAUGAUUAUCGA--AAGAA--G-UGGU--------------CCUA------------------GUCACUUCUG--GAACAAAACAUGGCUUAUAGAA-----------------------
AJ511702.1/6-373             -------AUUUUU-GGAUAAUCGCGUGGUUAUU----------------------------------------GGUG-----ACCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCGGUAGUGUUUGU-GUUAGGC--GAAAAAAUAAGCCUAAGGA--UGUGG----UUAA-----CACA--UUACGGC--GGAU-AAAA-UC-ACUAAGUC--UUAU------GAUAUGUGAGAGUCAUCC-UGAAA--GUGCCACAGUGACGUAGUUUUUA-UG-----------------------GAAA------------------------CAU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAC-G-GAAAA--GCUGGAAGAA--GAACAGUC-UUUUCUGA-CUGC------------------AAA------GC--AGUAGACAGAUGAUUAUCAAA-GAAGA--U-AAUA--------------CCUA-------------------GUUAUCUUU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AAHK01009266.1/373-66        -------UUGCAC-AGCCAACUGCUGCAGAUUUU---------------------------------------AAUU-----AUGUAGAGGAAAAUCCGCU-CUAACACUU-GC-UGCGAU-GCAAGUAGUGUUCAU-GCUAGGC-----CCAAUAAGCCUAGGCA--GUUAUUUUGUAAA-----UAAU--UGACGAC---------------------------------------------------------CA--GUGCAACAGAGACGAG-CUUAUU-U-----------------------------------------------------AG-UUAAGGUGCAACG-AUGUAAACUCCAUGAGUUAGAAACCCAAAUUU--CGGUAGGGGAAC-C-UAGUU--AAGAUAAAU---GAAUUGA--GACUGGGA-AGUUU----------------UUU------AAA--CUUAGAUAAAUAGUUGGCA---CUGUA-------U--------------UUUU-----------------------UACAG---CACAAAAAGCGGUUUAUCGUG-----------------------
AJ511699.1/6-376             -------AUUUUU-GGAUAAUCGCAUGUCGCUUUUUUC-----------------------------------UGUC-----GGCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGU--GAAACAAUAAGCCUAGGGA--UGUCU----AUUU-----GACA--UUACGGC--GGAC-GAUG-AG-GCUAAGUC--CUUG------GAUAUGCCU--CUAGUCC-UGAAA--GUGCCACAGUGACGGAGCCUUUG-AG-----------------------GAAA------------------------CUC-AAGGGGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAC-G-AGAUG--GCUGGAAUGC--GAACGGAC-CAUCUUGA-CUGC-----------------GCAA------GC--AGUAGACAGAUGAUUAUCG---AAGGG--G-GUAGGAC-----------CUAG-------------------UACCUCUGG---AACAAAACAUGGCUUAUAGAA-----------------------
AJ511706.1/6-376             -------AUUUUU-GGAUAAUCGCGUGGUGCAUU---------------------------------------UGGU-----AUCAUGAGGAAAGUCCAUG-CUAGCACCG-GC-UGUGAU-GC-GGUAGUGUUUGU-GCUAGGU--GAAUCAAUAAGCCUAGGGA--CAUCUUUUUGGAA-----GGUG--UUACGGC--GAGC-GAAA-GG-GCUAAGUC--GUUA------GAUAGGUCUGAGUUGCUC-UGAAA--GUGCCACAGUGACGUAGUUUUUA-GG-----------------------GAAA------------------------CCU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GUUGGAAGAC--GAACAAUC-UAUCCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAGG--U-AAGA--------------CCUA-------------------GUUACCUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AAAK03000070.1/106-473       -------GUUUUC-GGGUAAUCGCGGUCUGACUU---------------------------------------GAUC-----AGGCUGAGGAAAGUCCAUG-CUCGCACAG-GC-UGUGAU-GCCUGUAGUGUUCGU-GCUUAGC--GAAACCAUAAGCUAAGGUA--CUCU-----UU-------GGAG--UAACGGC--AGGA-AAAC-AA-GCUAAGGC--UUCG------GCUAUGCUUAAGUAUCCU-UGAAA--GUGCCACAGUGACGAAGCGGCUG-GG-----------------------GAAA------------------------CCC-AUCCGGUGGAACG-CGGUAAACCCCUCGAGCGAGCAACCCAAACAA--UGGUAGGGGCGC-U-UUUUG--UCUGGAAGAA--GAACAGGA-CAAAAAGG-CAGU------------------AUA------AC--UGCAGAUAGAUGGUUACCG---CUUUG--U-UUUU--------------UCUC-------------CCUGGAAAAGCAAAG---UACAGAACAUGGCUUAUAGAA-----------------------
AJ511670.1/6-371             -------AUUUUU-GGAUAAUCGCGUAGUAUUU----------------------------------------UGAU-----ACUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGC--GAAAAAAUAAGCCUAGGGA--UGUG-----CUUG-----CACA--UUACGGC--GAAA-GAAC-UG-GCUAAGUC--UUU-------GAUAUGCCACAGUAUUUC-UGAAA--GUGCCACAGUGACGCAGUUUUUA-UG-----------------------GAAA------------------------CGU-GAGAAAUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAC-G-GGAUA--GUUGGAAAC---GAACAAGC-UAUUCUGA-CUGU-----------------UUAA------AC--AGUAGACAGAUGAUUACCGAA-GGAAU--U-AAUA--------------CCUA-------------------GUUAUUUCC-UGAACAAAACAUGGCUUAUAGAA-----------------------
AP006716.1/1492055-1492438   -------UAUUUU-GGGUAAUCGCUAUA---------------------------------------------GAAA------UAUAGAGGAAAGUCCAUG-CUCACACAG-UC-UGAGAU-GAUUGUAGUGUUCGU-GCUUGAU--GAAACAAUAAAUCAAGGCA-----------UUAA---UU------UGACGGC--AACG-AAAU-AA-CCUAAGUC--UUAU------GAUAUGGUUAAAUUAGUU-UGAAA--GUGCCACAGUGACGUAGCUUUCA-UA-----------------------GAAA------------------------UAU-GAAGGGUGGAACG-CGGUAAACCCCUCGAGUGAGCAAUCCAAAUU---UGGUAGGAGCAC-U-UGUUU--AGCGGAAUU---CAACGUAU-AAACGAGA-CAUCUUUAUUCGAAAU-----AUAA-----AGAUUUGUAGACAGAUGGUUACCA---CCGAC--G-UACC--------------AGUACAACUAGUGUACGUUAUGAGUACAACGG---UACAGAACAUGGCUUACAGAA-----------------------
AF242853.3/587-938           -------UGUUGC-AGUUGGUUGCUGUUUUAUU----------------------------------------UA-------AAGCAGAGGAAAGUCCAUG-CUCGCACAA-GC-UGUGAUUGCUUGUAGUGUUUGA-GUAAAUAAAUAAAAGAUAAAAUUUAGCA--GAUUAG---AAUU-----AGUC--UGACGGC--GGAA-AAGU-UG-CUAAAUUGC-UAAA-----ACAACAUGCAAAUUAUUCC-AUAAC--GUGCCACAGAGACGA--GUUGAGCUC-----------------------GAAA------------------------GAC-UCAGUAUGAAACG-CGGUAAACCCCUCAAGCGAGAAACCUAAAUU---UGGUAAGGGAAC-U-AAUAA--ACAAGAAAC---AGAAUUGU-UUAGAAGA-AUAAAAAUCA-----------AAUU-----UUU--AUUAGAUAAAUAACCAAUC--------------------------------AA-------------------------------GACAGAACAUGGCUUAUCGCA-----------------------
AJ511721.1/6-373             -------AUUUUU-GGAUAAUCGCAUGGUUGCUA---------------------------------------GUCU-----UCCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGU--GAAUCAAUAAGCCUAGGGA--CUUGA----UUUU-----CAAG--UUACGGC--GAGC-GAAC-UA-GCUAAGUC--UUAG------GAUAGGUUUUAGUAGCUC-UGAAA--GUGCCACAGUGACGGAGUUUUUA-GG-----------------------GAAA------------------------CCU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUG--GCUGGAAAC---GAACGGAC-CAUUCUGA-CUGC------------------UAU------GC--AGUAGACAGAUGAUUAUCGAA-GGAAG--U-GGUA--------------CCUA-------------------GUCACUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AJ511728.1/6-370             -------AUUUUU-GGAUAAUCGCGUGAAGAGUCG--------------------------------------UCUU-----UUCAUGAGGAAAGUCCAUG-CUAGCACGG-GC-UGUGAU-GCCCGUAGUGUUUGU-GCUAGGU--GAAACAAUAAGCCUAGGGA--CGAG-------AA-----AUCG--UUACGGC--GGAC-GAAA-CA-GCUACGUC--UCUG------GAUAUGCUGGAAUAGUCC-UGAAA--GUGCCACAGUGACGUAGUUUUUG-CG-----------------------GAAA------------------------CGC-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAC-G-GAAUG--CGUGGAAAC---GAACACAG-CAUUCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAAA--U-GAUA--------------CCUA-------------------GUUAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
CP000419.1/240600-240968     -------AUUUUC-GGAUAAUCGCAUGGUUGCAA---------------------------------------GUCU-----UCCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGU--GAAUCAAUAAGCCUAGGGA--CUUGA----UUUU-----CAAG--UUACGGC--GAGC-GAAC-CG-GCUAAGUC--UUCG------GAUAGGUUUUAGUAGCUC-UGAAA--GUGCCACAGUGACGGAGUUUUUA-GG-----------------------GAAA------------------------CCU-AAAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAC-G-GGAUG--GCCGGAAAC---GAACGGAC-CAUUCUGA-CUGC------------------UAU------GC--AGUAGACAGAUGAUUAUCGAA-GGAAG--U-GGUUA-------------CCUA-------------------GUCACUUCU-GGAACAGAACAUGGCUUAUAGAA-----------------------
CP000557.1/1480049-1480446   -------AUGUUC-GGGUAAUCGCUGCGGCCGGUU--------------------------------------UCGG-----CCGUAGAGGAAAGUCCAUG-CUCGCACGGUGC-UGAGAU-GCCCGUAGUGUUCGU-GCCUAGC--GAAUCCAUAAGCUAGGGCA--GUCUGGC--UUCG--GCUGGGC--UGACGGC--GGGG-AAAG-AA-CCUACGUCCGAAUG----CGGAUAUGGUUCGAUUACCC-UGAAA--GUGCCACAGUGACGGACCUCUAA-GG-----------------------GAAA------------------------CCU-UAGAGGUGGAACG-CGGUAAACCCCACGAGCGAGAAACCCAAAUGA--UGGUAGGGGCAC-C-UUCCC--GAAGGAAAU---GAACGGA--GGGAAGGA-CAGGCGACGCG----------UGUU-----GCC--UGUAGAUAGAUGAUUACCG---CCGGA--G-UACG--------------AGGC----GAAAAGCCGUUGGCAGUACGAAGG---UACAGAACAUGGCUUACAGAA-----------------------
AJ511694.1/6-387             -------AUUUUU-GGAUAAUCGCGUGAGGAGAAUU-------------------------------------UCUU-----UUCAUGAGGAAAGUCCAUG-CUAGCACAG-GC-UGUGAU-GCCUGUAGUGUUUGU-GCUAGGC--GAAACCAUAAGCCUAGGGA--CGAG-------AG-----AUCG--UUACGGC--AGUU-GAAA-UG-GCUAAGUC--UUCG------GAUAGGUCAGAGUAGGCU-UGAAA--GUGCCACAGUGACGGAGUCUUUC-UG-----------------------GAAA------------------------CGG-AGAGAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAAUUU--CGGUCGGGGCAU-G-GAGUG--CACGGAAAC---GAACGUAG-UACUCUGA-CUGCUAUCAGCUAUAGGC---UGUU-----AGU--GGUAGACAGAUGAUUAUCAA--AGGAA--G-UGGU--------------CCUA------------------GUCACUUCUG--GAACAAAACAUGGCUUAUAGAA-----------------------
AJ511684.1/6-374             -------AUUUUU-GGAUAAUCGCGUAGUAUUC----------------------------------------CAAU-----ACUAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGAUUGU-GCUAGGC--GAACAAAUAAGCCUAGGGA--UGUG-----CUUG-----CACA--UUACGGC--GGAG-AAAA-UG-GCUAAGUC--CUUG------GAUAUGCCAAAGUACUUC-UGAAA--GUGCCACAGUGACGUAGUUUUUA-UG-----------------------GAAA------------------------CGU-AAAAAAUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUA--GUUGGAAAC---GAACAAGC-UAUCCUGA-CUGUC----------------AACA-----GAC--GGUAGACAGAUGAUUAUCGAA-GGAGA--U-GAUG--------------CCUA-------------------GUCAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
CP000764.1/1387139-1387530   -------GCGUUU-GGGUAAUCGCUGCAACGUA----------------------------------------AACG-----UUGUAGAGGAAAGUCCAUG-CUCGCACGA-CC-UGAGAU-GGUCGUAGUGUUCGU-GCCUAGC--CAAUUCAUAAGCUAGGGUA--UUCUGGCC-GCGA-GGCUGGUU--UAACGGC--AGGG-AAAA-AA-CCUAAGUCC-UUUU-----GGAUAUGGUUUGACUACCU-UUAAA--GUGCCACAGUGACGAAGUCCUUG-AA-----------------------GAAA------------------------UGA-UAGGAGUGGAACG-AGGUAAACCCCACGAGCGAGAAACCCAAAUAA--UGGUAGGGGAAU-C-UUUUC--CAAGGAAAU---GAACGAUG-GAAAAGGA-CAGGUUUG-------------AGUA-----ACC--UGUAGAUAGAUGAUUACCA---CCGGA--G-UACG--------------AGGC-----GUGGGCCGUUUGUAGUACAAAGG---AACAGAACAUGGCUUACAGAA-----------------------
AJ511739.1/6-373             -------AUUUUU-GGAUAAUCGCGUGAGAAUAUUU-------------------------------------UAUU-----UUCAUGAGGAAAGUCCAUG-CUAGCACGG-GC-UGUGAU-GCCCGUAGUGUUUGU-GCUAGGU--GAAACAAUAAGCCUAGGGA--CGGA-----AGUA-----UCCG--UUACGGC--GGAC-GAAA-CA-GCUACGUC--UCUG------GAUAUGCUGGAAUAGUCC-UGAAA--GUGCCACAGUGACGUAGUUUUUG-UG-----------------------GAAA------------------------CAC-AAGAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAC-G-GAAUG--CGUGGAAAC---GAACGCAG-CAUUCUGA-CUG------------------GAAA-------C--AGUAGACAGAUGAUUAUCGAA-GGAAA--U-GAUA--------------CCUA-------------------GUUAUUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
BA000043.1/1581285-1581681   -------AUGUUC-GGGUAAUCGCUGCGGCCGGUU--------------------------------------UCGG-----CCGUAGAGGAAAGUCCAUG-CUCGCACGGUGC-UGAGAU-GCCCGUAGUGUUCGU-GCCUAGC--GAAUCCAUAAGCUAGGGCA--GUCUGGC--UUCG--GCUGGGC--UGACGGC--GGGG-AAAG-AA-CCUACGUCCGCAUG----CGGAUAUGGUUCGAUUACCC-UGAAA--GUGCCACAGUGACGCAGCUCUAA-GG-----------------------GAAA------------------------CCU-UAGAGGUGGAACG-CGGUAAACCCCACGAGCGAGAAACCCAAAUGA--UGGUAGGGGCAC-C-UUCCC--GAAGGAAAU---GAACGGA--GGGAAGGA-CAGGCGGCGUA----------CGCU-----GCC--UGUAGAUAGAUGAUUACCG---CCGGA--G-UACG--------------AGGC-----GAAAGCCGCUUGCAGUACGAAGG---UACAGAACAUGGCUUACAGAA-----------------------
AJ511716.1/6-373             -------AUUUUU-GGAUAAUCGCAUGGUUGCUU---------------------------------------GUCU-----UCCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGUGAU-GCCAGUAGUGUUUGU-GCUAGGU--GAAUUAAUAAGCCUAGGGA--CUUGA----UUUU-----CAAG--UUACGGC--GAGC-GAAC-UG-GCUAAGUC--UUCG------GAUAAGUUUUAGUAGCUC-UGAAA--GUGCCACAGUGACGGAGUUUUUA-GG-----------------------GAAA------------------------CCU-AGAAAGUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUAGGGGCAU-G-GGAUG--GCUGGAAAC---GAACGGAC-CAUCCUGA-CUGCU----------------U--------AGC--AGUAGACAGAUGAUUAUCGAA-GGAAG--U-GGUA--------------CCUA-------------------GUCACUUCU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AE017333.1/2302197-2301811   -------ACGUUC-GGGUAAUCGCUGCAGAUUUU---------------------------------------ACAU-----CUGUAGAGGAAAGUCCAUG-CUCGCACGGUGC-UGAGAU-GCCCGUAGUGUUCGU-GCCUAGC--GAAGUCAUAAGCUAGGGCA--GCCUUG---CAGA-----AGGC--UGACGGC--AGGA-AAAA-AG-CCUACGUCC-UUUA----UGGAUAUGGCUGAGUAUCCU-UGAAA--GUGCCACAGUGACGAAGUCUCAC-UA-----------------------GAAA------------------------UGG-UGAGAGUGGAACG-CGGUAAACCCCUCGAGCGAGAAACCCAAAUUU--UGGUAGGGGAAC-C-UUCUG--GACGGAAAU---GAACGGA--AGGAAGGA-CAGAG----------------UUGA-----CUC--UGUAGAUAGAUGAUUACCA---CCCGA--G-UACG--------------AGGC---UUAGCAGCCGACGGCAGUACGACGG---AACAAAACAUGGCUUACAGAA-----------------------
CP001176.1/1538131-1538521   -------ACGUUU-GGGUAAUCGCUGCAACGCC----------------------------------------AACG-----UUGUAGAGGAAAGUCCAUG-CUCGCACGG-CC-UGAGAU-GGCUGUAGUGUUCGU-GCCUAGC--CAAUUCAUAAGCUAGGGUA--UUCUGGCU-GUAA-GGCUGGUU--UAACGGC--AGGG-AAAA-AA-CCUAAGUCC-UUUC-----GGAUAUGGUUUGACUACCU-UUAAA--GUGCCACAGUGACGAAGUCCUUG-AA-----------------------GAAA------------------------UGA-UAGGAGUGGAACG-AGGUAAACCCCACGAGCGAGAAACCCAAAUAA--UGGUAGGGGAAU-C-UUUUC--CAAGGAAAU---GAACGACG-GGAAAGGA-CAGGUUU--------------UAUA-----ACC--UGUAGAUAGAUGAUUGCCA---CCGGA--G-UACGAGGCGUGGGCCGUUUGUA-------------------GUACAAAGG---AACAGAACAUGGCUUACAGAA-----------------------
AL591981.1/209188-208807     -------ACGUUC-GGAUAAUCGCUGUUUUCUU----------------------------------------UUGA-----AAGCAGAGGAAAGUCCAUG-CUCGCACGGUGC-UGUGAU-GCCCGUAGUGAUCGU-GCCUGGU--CAAACAAUAAGCCAGGGCAUUCCGG-----UUUU-----CCGGUUUGACGGC--AGGU-GAAU-GA-CCUAAGUC--UUCG------GAUAUGGUCUUAUAACCU-UGAAG--GUGCCACAGUGACGAAGUUCCGG-CA-----------------------GAAA------------------------UGCUCGGAAGUGGAACG-AGGUAAACCCCACGAGCGAGAAACUCAAACUUA-UGGUAGGGGCAC-U-UUUCC--CGAGGAAUCA--AGAACAAG-GGACGAGG-CGCAAAUGU------------AUUU-----UUG--CGCAGAUAGAUGGUUAUCU---CUUUA--C-UAUU--------------ACCC--------------UGUACGUAGUAAAG---AACAGAACAUGGCUUACAGAG-----------------------
CP001022.1/1294210-1294583   -------UGGUUC-GGACAAUUGCGGGGCACUU----------------------------------------CGGU-----GCUUUGAGGAAAGUCCAUG-CUCGCACAA-CC-UGCGAU-GGUUGUAGUGAUCGU-GCUACAC--GAAAAGAUAAGUGUAGGCA--GCGU-----C--------GUGC--UGACGGC--AGAA-GGAA-CG-CCUAAGUC--UUCG------GAUAUGGCCGAAACUUCU-UGAAA--GUGCCACAGUGACGGAGCCUUAC-UG-----------------------GAAA------------------------CAG-UAAGGGUGGAACG-AGGUAAACCCCACGAGCGAGAAACCCAAAUU---UGGUAGGGGAAU-U-UCCGG--AGCGGAACU---GAACGCG--AAGGAGAG-CGUAU----------------GUAA-----AUA--CGGAGAUAGAUGAUUGUCG---CCCAC--G-UGUGAGGG----------UCAA---------ACCGUUUGCAACACUAGGG---AACAGAACAUGGCUUACAGGA-----------------------
AE005176.1/1702167-1701784   -------GUUUUC-GGAUAAUCGCGCGAUUUUUUU--------------------------------------GUAA-----AUCGUGAGGAAAGUCCAUG-CUCGCGCGUUGC-UGAGAU-GCACGCAGUGAUUGU-GCUAGGU--CAAACAAUAAACCUAGGUA--GGAGC----GUCA-----UGCC--UAACGGC--UGGC-CAAA-AC-GCUAAGUC--UUUU------GAUAUGCGUGAGUAGCCUGUAAAA--GUGCCAUAGAGACGAG-UCUUAG-AG-----------------------GAAA------------------------CUC-UAAGAAUGGAACG-UGGUAAACCCCUCAAGCGAGCAACCCAAACUUA-UGGUCGGGGCAC-U-UGACU--AGCCAAAAU---GAAGGCGU-GGUCGAGG-CUGAAAUUAA-----------GAAU-----UUU--GGCAGACAGAUGAUUAUCGAA-GGGGA--G-AUUC--------------ACGA--------------AUGUGAAUUGAACU-GGAACAAAACAUGGCUUAUAGAA-----------------------
AAPZ02000002.1/258240-258615 -------AGUUUU-GGGUAAUUGAGCACAGCUU----------------------------------------AUGU-----UGUGUUAGGAAGGUCCAUG-CUCGCACAG-GC-UGCGAU-GCCUGUAGUGUUUGU-GCUCGCU--GAAAAAAUAAGGCGGGGCA--CCAU------UUU-----AUGG--UGACGGC--GGAA-AAAC-GG-ACUAAGGU--UUUA------ACUACGUCUUAGUAUUCC-UGAAAA-GUGCCACAGUGACGAUACAAUAU-UG-----------------------GAAA------------------------CGA-UAUUGGUGGAACG-CGGUAAACCCCUCAAGCGGUAAACCCAAACUA--CGGUAGGGGAGC-U-UUGGA--UAACAAAUU---GAAGUGAU-UCCAGGGG-AGAGUAUU-------------UCGA----UACU--CUGAGAUAGAUGAUUACCU---CGAUA--U-AAUUAUGCCU--------GAUA-------------------AUUAUAUUA--CGACAAAACAUGGCCUACAGAU-----------------------
CP000903.1/1529096-1529487   -------ACGUUU-GGGUAAUCGCUGCAACGCC----------------------------------------AACG-----UUGUAGAGGAAAGUCCAUG-CUCGCACGG-CC-UGAGAU-GGCUGUAGUGUUCGU-GCCUAGC--CAAGUCAUAAGCUAGGGUA--UUCUGGCU-GCAA-GGCUGGUU--UAACGGC--AGGG-AAAA-AA-CCUAAGUCC-UUUC-----GGAUAUGGUUUGACUACCU-UUAAA--GUGCCACAGUGACGAAGUCCUUG-AA-----------------------GAAA------------------------UGA-UAGGAGUGGAACG-AGGUAAACCCCACGAGCGAGAAACCCAAAUAA--UGGUAGGGGAAU-C-UUUUC--CAAGGAAAU---GAACGACG-GAAAAGGA-CAGGUUUU-------------CGUA-----ACC--UGUAGAUAGAUGAUUACCA---CCGGA--G-UACG--------------AGGC-----GUGGGCCGUUUGCAGUACAAAGG---AACAGAACAUGGCUUACAGAA-----------------------
CP000033.3/1133530-1133164   -------AAUUUC-GAGUAGGCGCGGCUAGCUU----------------------------------------UUGC-----UAGCUGAGGAAAGUCCACG-CACGCACAA-GC-UGCGAU-GCUUGUAGUGAUCGU-AUUCAGC-----UCAAUAAGCUGGAGGA--AAGUUA---UUUA-----ACUU--UUACGGC---GGA-AAAA-GU-GCUAAAUC--UUUG------GACAUGCAUUACUAUCC--UGAAA--GUGCCACAGUGACGUAGCAAAAU-CA-----------------------GAAA------------------------UGA-UUUUGGUGGAACG-AGGUAAACCCUGCGAGCGUGAAACCCAAAUUU--GGUGGGGGAGUU-U-CGAUC--UAAGGAAAU---GAACUAAA-GAUCGGGU-UAUUGCA--------------UUAG-----CAA--UAAAGAUAGAUGACUACUA---AUAGU--G-AUUUUGC-----------CAAG-------------------AAUCACUGG---AACAAAACGUGGCUUAUAGAA-----------------------
AF222894.1/355530-355892     -------GUAAAA-AGCUAAUUGCUGCAUUUUUUA--------------------------------------AAAA-----AUGUAGAGGAAAGUCCGUG-CUCACACUA-AC-UGUGAU-GUUAGUAGUGUUUGU-GUAUGUA--UAAUUAAUAAGGCAUAGCA--UA-------GGCA-------UA--UGACGGC--AAAU-UUUU-AA-GCUAAGUGA-UUUA---AAUUAUAUGUUU-AAAAAUUUAUAAAA--GUGCCACAGAGACGA--UUAAUC-AA-----------------------GAAA------------------------UUG-AUGAGAUGAAACGUUGGUAAACCCCACAAGUGAGAAACCUAAAUUU--CGGUAAGGGAAU-C-UAAUU--UAGUAAAUU---AAGAAAUUAAAUUAGGA-UAGAAUUG-------------UUUA---CAUUC--UAUAGAUAAAUAAUUAGCG---CUACA----------------------UUUU-----------------------UGUAG---AACAGAACACGGCUUAUUUUU-----------------------
CP001184.1/353627-353990     -------GUAAAA-AGCUAAUUGCUGCAUUUUUAA--------------------------------------AUAA-----AUGUAGAGGAAAGUCCGUG-CUCACACUA-AC-UGUGAU-GUUAGUAGUGUUUGU-GUAUGUA--UAAUUAAUAAAGCAUAGCA--UAGG--------------CGUA--UGACGGC--GAAU-UUUUUAA-GCUAAGUAA-UUUU--CUAUUAUAUGUUU-AAAAAUUC-ACAAA--GUGCCACAGAGACGA--UUAAUC-AA-----------------------GAAA------------------------UUG-AUGAGAUGAAACGUUGGUAAACCCCACAAGUGAGAAACCUAAAUUU--UGGUAAGGGAAU-C-UAAUU--UAGUAAAUU---AAGAAAUUAAAUUAGGA-UAGAAUAAAC-----------UUUA-----UUC--UAUAGAUAAAUAAUUAGCA---CUACA----------------------UUUU-----------------------UGUAG---AACAGAACACGGCUUAUUUUU-----------------------
ABAW02000019.1/236603-236264 -------CAUUAC-AGACAGUCGCUGGCU--------------------------------------------AUAA-----AGCUAGAGGAAAGUCCAUG-CUCGCACGA-UC-UGUGAU-GAUCGUAGUGUUUGU-GCAGAAU--GAAUACAUAAGUUCUGGCA--GCUG--------A-----UUGC--UGACGGC--UGAG-GGAA--G-CCUAAGAC--UUCG------GUUAUGGU--GUACCUCUGUAAAA--GUGCCACAGAAACGAG-UCGUAU-CG-----------------------GAAA------------------------CGA-UACGAAUGGAACG--GGUAAACCCCGCAAGCGAGAAACCCAAAUU---UGGUAGGGGAAU-C-CACUA--AAGUGAAAC---GAAACGG--CGGUGGGA-CGUGC----------------AU-------GCA--CGUAGAUAAAUGACUGUCA---CUCAU----------------------AUAU-----------------------AUGAG---CACAGAACAUGGCUUAU-GUA-----------------------
CP000408.1/396906-397270     -------AUUUUU-GGAUAAUCGCGUGGUAGUU----------------------------------------UUCU-----ACCAUGAGGAAAGUCCAUG-CUAGCACUG-GC-UGAGAU-GCCAGUAGUGUUUGU-GCUAGGC--GAAUCAAUAAGCCUAGGGA--CGCC-----CUUG-----GGCG--UUACGGC--GGUU-AAAA-UG-GCUAAGUC--UUUU------GAUAUGUCAGAGUAGAUC-UGAAA--GUGCCACAGUGACGAAGUUUUUA-UG-----------------------GAAA------------------------CGU-AAAAAAUGGAACG-CGGUAAACCCCUCAAGCUAGCAACCCAAACUU--UGGUCGGGGCAU-G-GGAUG--GAUGGAAAU---GAACAGA--AAUCCUGA-CUGU-----------------UUAG------AC--AGUAGACAGAUGAUUAUCG---AAGGU--G-GUAGAAC-----------CUAG-------------------UACCACUGG---AACAAAACAUGGCUUACAGAA-----------------------
CP001617.1/1571725-1572099   -------AAUUCU-GGGUAAUCGCGGUCGGCUU----------------------------------------AUGU-----CGGCUGAGGAAGGUCCAUG-CUCGCACAA-GC-UGCGAU-GCUUGUAGUGUUCGU-GCUCGGU--GAAAAAAUAAGCCGGGGUA--CCGA-----UUUA-----UCGG--UAACGGC--GGAA-AAAA-CG-GCUAAGGC--UUCG------GCUAUGCCCGAGUAUUCC-UGAAAA-GUGCCACAGUGACGAUACUCAAU-UG-----------------------GAAA------------------------CGG-UUGAGUUGGAACG-CGGUAAACCCCACGAGCGGGCAACCCAAACUA--CGGUAGGGGCGC-U-UCACA--UAAGGAACU---GAACUAAA-UGUGGGGG-GAGAUU---------------AGUA-----AUC--UCGAGAUAGAUGAUUACCG---CCUAG--U-UAAC--------------AGAC-----------CCUGUACUUUAACUAGG---UACAAAACAUGGCCUACAGGA-----------------------
FQ377874.1/508470-508809     -------UUUAUU-AGUCAAUCGCUGUAUUUGAAA--------------------------------------AAGA-----AUAUAGAGGAAACUCCACG-CUUACACAA-UC-UGUGAU-GAUUGUAGUGUUUAU-GCUAAAU--GAAAAAAUAAAUUUAGGCA--GUAA-----GUAA-----UUAC--UGACGGC----UU-AACU-AA-CCUAAGGC--UUU-------GCUAUGGUGAUGUUA----UUAAA--GUGCCACAGAGACGAAU---AAA-GA-----------------------GAAA------------------------UCU-U-GAAAUGGAACG-CGGUAAACCCCAUAAGUAAGAAACUCAAGUUU--UGGUAGAGGAAU-C-UGAUU--AAGAGAAUA---AGAAUUAA-AAUCAGAA-GUUA-----------------UUAU------UA--ACUAGAUAGAUGAUUGACG---CU-------------------------GAAA--------------------------AG---UACAAAACGUGGGUUAUAGAU-----------------------
#=GC SS_cons                 .......:::{{{.{{{{{{{{,<<<<<<____........................................____.....>>>>>>,,,,AAA,AAAAA.{{{{{<<<<.<<.______.>>>>>>,,,,,[[[[.[<<<<<<..__________>>>>>><<<..<<<<.....____.....>>>>..>>->((,..<<<<.----.<<.<<---<<<..____......>>>-->>>>----->>>>.,,,,,..<<<<<------------<<<<<<.<<.......................____........................>>>.>>>>>--------.->>>-->>))]]]]]}}}}},,,<<<______.._____>>>,,,<.<.<<<<<.._________...________.>>>>>>><.<<<<<_...............____.....>>>..>>>,,,,,,,,}}}}}}},...<<<<<..<.<<<_..............____...................>>>>>>>>>...,,,,,,,aaaaaaaa,}-}}}.......................
#=GC RF                      .......auuuuc.gGguaaucGCugcgguauu........................................uuua.....ccgcaGAGGAAAGUCCAuG.CucGCACgg.gC.UGuGAU.GcccGUAGUGUUcGu.Gcugggc..gAAauAAUAAgcccagGcA..ggcg.....uuua.....cgcc..UgACGGC..gggc.aAAa.gg.gCUAAguc..uuuu......gacAUGcccuaauagccc.UgAAA..GUgCCACAGuGACGaagcuucuc.ug.......................GAAA........................cag.agaagGUGgAACG.cGGuAAACCCCaCgAGCgaGaAACCcAAAuUU..UGGUAgGGGaAc.c.cgguc..uaagGAAau...gAAcuuaa.gaccggga.cggccu...............uuaa.....ggc..cguAGAuAgAUgauuacCa...ccgcc..g.ggca..............uuua...................gcccggcgg...aACAgAACaUGGCUUAcagaa.......................
//
# STOCKHOLM 1.0

#=GF AC   RF00012
#=GF ID   U3
#=GF DE   Small nucleolar RNA U3
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Marz M; 0000-0003-4783-8823
#=GF SE   Published; PMID:19875933; Gardner PP
#=GF SS   Published; PMID:19875933; Gardner PP
#=GF GA   34.00
#=GF TC   34.00
#=GF NC   33.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00100
#=GF DR   SO; 0001179; U3_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300259;
#=GF DR   snoopy; Homo_sapiens300287;
#=GF RN   [1]
#=GF RM   9016512
#=GF RT   The uRNA database.
#=GF RA   Zwieb C
#=GF RL   Nucleic Acids Res 1997;25:102-103.
#=GF RN   [2]
#=GF RM   10567566
#=GF RT   Nuclear retention elements of U3 small nucleolar RNA.
#=GF RA   Speckmann W, Narayanan A, Terns R, Terns MP
#=GF RL   Mol Cell Biol 1999;19:8412-8421.
#=GF RN   [3]
#=GF RM   19875933
#=GF RT   Comparative analysis of eukaryotic U3 snoRNA.
#=GF RA   Marz M, Stadler PF
#=GF RL   RNA Biol. 2010;6:503-507.
#=GF CC   Small nucleolar RNAs (snoRNAs) are involved in the processing and
#=GF CC   modification of rRNA in the nucleolus. There are two main classes of
#=GF CC   snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member
#=GF CC   of the box C/D class. Indeed, the box C/D element is a subset of the six
#=GF CC   short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C,
#=GF CC   C', and D. The U3 snoRNA secondary structure is characterised by a small
#=GF CC   5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C,
#=GF CC   C', and D), the two domains being linked by a single-stranded hinge. Boxes
#=GF CC   B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs,
#=GF CC   and boxes C' and D form the C'/D motif. The latter is functionally similar
#=GF CC   to the C/D motifs found in other snoRNAs. The 5' domain and the hinge
#=GF CC   region act as a pre-rRNA-binding domain. The 3' domain has conserved
#=GF CC   protein-binding sites. Both the box B/C and box C'/D motifs are sufficient
#=GF CC   for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary
#=GF CC   for nucleolar localisation, stability and hyper-methylation of U3 snoRNA.
#=GF CC   Both box B/C and C'/D motifs are involved in specific protein interactions
#=GF CC   and are necessary for the rRNA processing functions of U3 snoRNA.
#=GF WK   Small_nucleolar_RNA_U3
#=GF SQ   87


AAPY01491858.1/243-27          AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGAUC-GU-GUAGA--GCACCGA--------AAACC---ACGAG-------GAGGAG-GCGCA-GUGUUCUCU-CC-U-GA-GCGUGAAG--CCGGCUCU--UGGU------------GUCGCUUUGC--UGCGAC-----------UGCCU-UUUGCC--AUU-GAUGAUCGUUCUU---CCU---U-C-CC--GCAA-------GGG-UGGGU--AAGAGGGAGAGGA-CGC-AGUCUGAGUGGU
ABDC01538673.1/966-749         AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUCCGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAGA--GUACCGA--------AAACC---ACGAG-------GAGGAG-GCGCA-GUGUUCUCU-CC-U-GA-GCGUGAAG--CCGGCUCU--UGGU------------GUUGCUUCGC--UGCAAC-----------UGCCA-CUUGCC--AUU-GAUGAUCGUUCUU---CUC---U-C-UC--UUUAU------GGG-GGAGU--GAGAGGGAGAGGA-CGC-AGUCUGAGUGGU
AANN01155091.1/2770-2558       AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUACGU-UACUAGA----GAAGUUCC-UCUGAUC-GU-GUAGG--GCACCCG--------AAACC---ACGAG-------GAGGAG-GCACA-GCGUUCUCU-CC-U-GA-GCGUGAAG--CCAGCUCU--AGGU------------GUUGC-UUUU---GCAAC-----------UGCCU-UUUGCU--AUU-GAUGAUCGUUCUU---CUC---U-U-CC--UUU--------GGG-GGAG---AAGAGGGAGAGAA-CGC-AAUCUGAGUGGU
AALT01658977.1/9347-9135       AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUAUGU-UACUAGA----GAAGUUUC-UCUGAUC-GU-GUAGA--GCACCCG--------AAACC---ACGAG-------GAGGAG-CCAGA-GCAUCCUCU-CC-U-GA-GCGUGAAG--CCGGCUCU--AGGU------------GUUGC-UUCU---GCAAC-----------UGCCU-UUUGCC--AUU-GAUGAUCGUUCUU---CUC---U-U-CC--UUU--------GGA-AGGGU--GAGAGGGAGAGGA-UGC-AGUCUGAGUGG-
AAWR02012944.1/32312-32098     AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAGA--GCACCCG--------AAACC---ACGAG-------GAGGAG-GCGCA-GCGUUCUCU-CC-U-GA-GCGUGAAG--CCGGCUCU--UGGU------------GUUGC-UUCC---GCAAC-----------UGCCU-UUUGCC--AUU-GAUGAUCGUUCUU---CUC---U-U-CU--UUUU-------AGG-AGAGU--AAGAGGGAGAGGA-CGC-AGUCUGAGUGGU
AC198150.2/173553-173452       AAGAC--UCUACUUU--CA-GCGAUCA--UUUC-UA--UAGUUCAU-UACCAGA----GAAGUUUC-UCUGAAU-GU-GUAGA--GCACAAA--------AA-----------------------G-UAAAU------------------------------A--------AGGC-----------C---------A--U-----------------GCCU---------A------GAC------------------------AUGUU-----------------------------------------A-----
AY123429.1/65518-65421         AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUGGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAGA--GCACCAA--------AU----------------------AG----A------------------A-AGCUGAAA--CU------------------------------------G-------------------------------------GAUCCU-----------------------UUC-----------------------------------------------
ABRT010843960.1/380-596        AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUUGU-UACUAGA----GAAGUUUC-UUUGAUC-GU-GUAGA--GCACCGA--------AAACC---ACGAG-------GAGGAG-CCACA-GUGUUUUCU-UC-U-GA-GCGUGAAG--CCGGCGUU--UGGU------------GUGGUAGUCA-UUACAUC-----------UGCCA-UUUGCC--AUU-GAUGAUCGUUCUU---ACU---C-U-UC--UGUG-------GAA-GAGU---UAGAGGGGGAAAA-CGC-AUUCUGAGUGGU
AF176810.1/1-214               AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAGA--GCACCCG--------AAACC---ACGAG-------GAGGAG-AUAAA-GCGUUCUCU-UC-U-GA-GCGUGAAG--UCGGCUUU--GGGU------------GUUGC-UUCU---GCAGC-----------UGCCG-UUAGCC--AUU-GAUGAUCGUUCUU---CUU---U-U-CC--UUUUA------GGA-GAUG---AAGAGGGAGAGAA-CGU-AAUCUGAGUGG-
AAFC03030311.1/44174-43960     AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAGA--GCACCCG--------AAACC---ACGAG-------GAGGAG-AUAAA-GCGUUCUCU-UC-U-GA-GCGUGAAG--UCGGCUUU--UGGU------------GUUGC-UUCU---GCAGC-----------UGCCG-UUAGCC--AUU-GAUGAUCGUUCUU---CUU---U-U-CC-UUUU-------AGGA-GAUG---AAGAGGGAGAGAA-CGU-AAUCUGAGUGGU
X63743.1/815-1027              AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUUGU-UACUAGA----GAAGUUUC-UCUGACU-GU-GUAGA--GCACCCG--------AAACC---ACGAG-------GAGGAG-ACAGA-GUGUCCUUU-CC-U-GA-GCGUGAAG--CCGGCUUU--UAGU------------GCUGCAUUU---UGCAAC-----------UGCUA-UCUGCC--AUU-GAUGAUCGUUCUC---AAC---U-C-UC--UU---------GAG-GGUU---GAGAGGGAGAGGA-CAC-AGUCUGAGUGGU
J01884.1/1-215                 AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGACU-GU-GUAGA--GCACCCG--------AAACC---ACGAG-------GAGGAG-ACGUA-GCGUUCUCU-CC-U-GA-GCGUGAAG--CCGGCUCU--UAGU------------GUUGCUUCCG--UGCAAC-----------UGCUA-UUGGCC--AUU-GAUGAUCGUUCUC---GGU---C-C-UC--UCU--------GAG-GGGC---GAGAGGGAGAGAA-CGC-AGUCUGAGUGGU
X02722.1/550-763               AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGACU-GU-GUAGA--GCACCCG--------AAACC---ACGAG-------GAGGAG-ACGUA-GCGUUCUCU-CC-U-GA-GCGUGAAG--CCGGCUCU--UAGU------------GUUGCUUCC---UGCAAC-----------UGCUA-UUGGCC--AUU-GAUGAUCGUUCUC---GAG---C-C-UC--UCU--------GAG-GUUC---GAGAGGGAGAGAA-CGC-AGUCUGAGUGGU
AAIY01001061.1/928-1144        AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-GACUAGA----GAAGUUUC-UCUGACC-GU-GUAGA--GCACCGA--------AAACC---ACGAG-------GAGGAG-GCGCA-GCAUUCUCU-CC-U-GA-GCGUGAAG--CCGGCUCC--CGGC------------GCUGCCUCGC--UGCAGC-----------UGCCG-CUUGUC--AUU-GAUGAUCGUUCUU---CUC---U-G-CC--CUCG-------GGC-GGAGC--GAGAGGGAGAGAG-UGC-AGUCUGAGUGGC
AAKN02033252.1/474-691         AAGGC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUAUGU-UACUAGA----GAAGCUUC-UCUGACU-GU-GUAGA--GCACCAG--------AAACC---ACGAG-------GAGGAG-GCGUA-GUGUUCCUU-CC-U-GA-GCGUGAAG--CCGGCUCU--CGGC------------GCUGCUUCAG--UGCAGC-----------UGCCG-CUUGCC--AUU-GAUGAUCGUUCCU--GCUA---U-U-UC--CUCG-------GAG-AUAGC--AGGAGGGGAGGAA-CAC-AGUCUGAGUGGC
X02717.1/550-764               AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGACU-GU-GUAGA--GCACCCG--------AAACC---ACGAG-------GACGAG-ACAUA-GCGUCCCCU-CC-U-GA-GCGUGAAG--CCGGCUCU--AGGU------------GCUGCUUCUG--UGCAGC-----------UGCCU-CUUGCC--AUU-GAUGAUCGUUCUU---CUC---U-C-C---UUCG--------GG-AGGGU--AAGAGGGAGGGAA-CGC-AGUCUGAGUGGA
M23705.1/702-916               AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGACU-GU-GUAGA--GCACCCG--------AAACC---ACGAG-------GACGAG-ACGUA-GCGUUCCCU-CC-U-GA-GCGUGAAG--CCGGCUCU--AGGU------------GCUGCUUGAC--UGCAGC-----------UGCCU-CCUGCC--AUU-GAUGAUCGUUCUU---CCC---U-C-C---UUUG--------GG-AGGGU--GAGAGGGAGGGAA-CGC-AGUCUGAGUGGA
M23707.1/503-717               AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGACU-GU-GUAGA--GCACCCG--------AAACC---ACGAG-------GACGAG-ACGUA-GCGUUCCCU-CC-U-GA-GCGUGAAG--CCGGCUCU--AGGU------------GCUGCUUGAC--UGCAGC-----------UGCCU-CCUGCC--AUU-GAUGAUCGUUCUU---CCC---U-C-C---UUUG--------GG-AGGGU--GAGAGGGAGGGAA-CGC-AGUCUGAGUGGA
AC139728.3/90984-91194         AAGAC--UGUACUUU--CG-GGGAUCA--UUUC-UA--UAGUUCGU-CACUAGA----GAAGUUUC-UCUGAAU-GU-GUAGA--AUACCCU--------AAACC---AUGAG-------GAGGAG-GUGCA-GUGUUCUCU-CC-U-GA-GCAAUAC-----CUCUUC--UGGU------------AUUGCUUUU---AG-AAC-----------UGCCA-AUAGCC--AUU-GAUGAUUGUUCUU---CUC---U-U-C---CUUCA-------GA-AGAGU--AAGAGGGGGAGAA-CAC-AGUCUGAGUGGU
ACBE01421767.1/283-497         AGGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGAAU-GU-GUAGA--GUACCCG--------AAACC---ACGAG-------GAGGAG-GCGAA-GUGUUCUCU-CC-U-GA-GCGUGAAG--CUGGCUUU--UGGU------------GCUGU-CGUU---ACAGU-----------UGCCG-AUUGCC--AUU-GAUGAUCGUUCUU--UCUC---U-C-UC--UUU--------GGG-AGAGU--AAGAGGGAGAGAG-CAC-AGUCUGAGUGGU
AF020531.1/104-320             AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUGUGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAGA--GCACCGA--------AAACC---ACGAG-------GAAGAG-AAGUA-GCGUUUUCU-CC-U-GA-GCGUGAAG--CCGGCUUU-CUGGC------------GUUGCUUGGC--UGUAAC-----------UGCCG-UCAGCC--AUU-GAUGAUCGUUCUU---CUC---C-C-CG--UAU--------UGG-GGAGU--GAGAGGGAGAGAA-CGC-GGUCUGAGUGGU
M14061.1/277-493               AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUGUGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAGA--GCACCGA--------AAACC---ACGAG-------GAAGAG-AGGUA-GCGUUUUCU-CC-U-GA-GCGUGAAG--CCGGCUUU-CUGGC------------GUUGCUUGGC--UGCAAC-----------UGCCG-UCAGCC--AUU-GAUGAUCGUUCUU---CUC---U-C-CG--UAU--------UGG-GGAGU--GAGAGGGAGAGAA-CGC-GGUCUGAGUGGU
X14945.1/538-754               AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUGUGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAGA--GCACCGA--------AAACC---ACGAG-------GAAGAG-AGGUA-GCGUUUUCU-CC-U-GA-GCGUGAAG--CCGGCUUU-CUGGC------------GUUGCUUGGC--UGCAAC-----------UGCCG-UCAGCC--AUU-GAUGAUCGUUCUU---CUC---U-C-CG--UAU--------UGG-GGAGU--GAGAGGGAGAGAA-CGC-GGUCUGAGUGGU
ABGA01262676.1/1340-1125       AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAGA--GCACCGA--------AAACC---ACGAG-------GAAGAG-ACGUA-GCGUUUUCU-CC-U-GA-GCGUGAAG--CCGGCUUU--UGGU------------GUCGCUUCGU--UGCGAC-----------UGCCG-UCAGCC--AUU-GAUGAUCGUUCUU---CUC---U-U-C---UUAUU-------GG-AGAGU--AAGAGGGAGAGAA-CGC-GGUCUGAGUGGU
AANU01105435.1/2236-2452       AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUUGU-UACUAGA----GAAGUUUC-UCUGAAU-GU-GUAGA--GCACCGA--------AAACC---ACGAG-------GAAGAG-ACGUA-GUGUUCUUU-CC-U-GA-GCGUGAAG--UCCGCAUU--UGGU------------GUUGCUUCAC--UGCAAC-----------CGCCA-UUUGCC--AUU-GAUGAUCGUUCUU---CUC---U-C-CA--UUUU-------UGG-GGAGU--AAGAGGGAAAGAA-CAC-GGUCUGAGUGGU
AAGV020566442.1/1857-1640      AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUGUU-GACUAGA----GAAGGUUC-UCUGAAC-GU-GUAGG--GCACCGA--------AAGCC---ACGAG-------GAGGAG-GCGCA-GCGUUCUCU-CC-U-GA-GCGUGAAG--CCGGCUCU--AGGU------------GUUGCUUUUC--UGCAAC-----------UGCCU-UUUGCC--AUU-GAUGAUCGUUUUU---CUC---U-U-CC--UUUUU------GGA-UGAGU--AAGAGGGAGAGGA-CGC-AGUCUGAGUGGU
ABVD01644074.1/1753-1970       AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUUGU-UACUAGA----GAAGAUUC-UCUGACU-GU-GUAGG--GUACCGA--------AAACC---AUGAG-------GAAGAG-GUGUA-GCGUUCUCU-CC-U-GA-GCGUGAAG--GCGGCUUU--CGGU------------GUUGCUUUUC--UGCAAC-----------UGCUU-AUUGCC--AUU-GAUGAUCGUUCUG---CUU---U-U-CC-AUUU-------UGGG-AGAGU--UAGAGGGAGAGAA-CGC-AGUCUGAGUGGU
CABF01044723.1/2170-2355       GAGAU--CGUACUUC--UA-GGGAUCA--GUCC-UA--UAGUACGU-AUCACCA-----GGACGUC--AAACAA-AC-UAGAC--CCUGGCUA-----ACCCACC---GCGAU-------GAUGAU-CAGUG-CGGCCUAGU-CC-U-GA-GCGUGAAG--CAGGU-----GUGU------------GGCUGUCCGU--CUAGCU-----------GACUC-----CC--UAU-GGAGUUUGU---------------------CCGUG---------------------CGGACUUGG-CCG-CCUCCUUGU---
AAGD02005452.1/2742-2555       GAGAC--CAUACUAU-ACA-GAA-UCA--UUUC-UG--CAGUAUGU-AUCUCG------UAAUUCC--CAUCAA-AU-UGGUAGAGAUGC----------CAUCC---GCGAU-------GAGUGGGAGAC--GGGCGGGCC-GC---GA-GCGUGAAA-C-------------------------AGUCCU-UUCG---AGGAC----------U-----------------UGAUGACCGC----A-CGGA---G-C-CG-AUGAAUU---UUUGG-AGCCG-U----AGUGGCCAG-CUC--UUCUGAGCGGA
AY948622.1/2-186               GAGAC--CAUACUAU-ACA-GAA-UCA--UUUC-UG--CAGUAUGU-AUUUCG------UAAUUCC--CAUCAA-AU-UGGUAGAGAUUC----------CAUCC---GCAAU-------GAGUGGGAGAC--GGGCGAGCC-GC---GA-GCGUGAAA-C-------------------------AGUUC--UUCG----GAAC----------U-----------------UGAUGACCGC----A-CGGA---G-C-CG-AUGAAUU----UUGG-AGCCG-U----AGUGGCUUG-CUC--UUCUGAGCGGA
CAAC02000606.1/1368922-1368738 GAGAC--CAUACUAU-ACA-GAA-UCA--UUUC-UG--CAGUAUGU-AUCUCG------UAAUUCC--CAUCAA-AU-UGGUAGAGAUGC----------CAUCC---GCGAU-------GAAUGGGAGAC--GGGCUUGCC-GC---GA-GCGUGAAA-C-------------------------AGUUC--UUCG----GAAC----------U-----------------UGAUGACCGC----A-CGGA---G-C-CG-AUUCAUU----UUGG-AGCCG-U----AGUGGCUAG-CUC--UUCUGAGCGGA
ABKE01003568.1/5923-6108       GAAAU--CAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUAUGU-AUUUCA--------CAUGAUCCCUCAC-UCUGCUUUGAACAGG----------CAACC---GCGGU-------GAUUGGGAAAA--GAGCGAAGC-GC---GA-GCGUGAAA---------------------------AUGCC--UUCG----GGCU----------U------------------GAGGACCGC---GGACGCU---G-A-AA-GCUCA------CUUU-UGGUGGCC---UGCGCCUCG-CUC--AUCUGAGCGGU
AAQA01000362.1/29408-29193     GAGAU--CAUACUUC-ACA-GAA-UCA--UUUC-UG--UAGUAUGU-AUUUC--------UUCGCU----GUU-------AGCGAAAAUGCGACGGAGCGCAGCC---GCGAU-------GAUGUGGCAGG--GCGUCAUCU-CC-A-GA-GCGGGAAG----AAGU----GUGUCA--------UCCUCACUCCUA-CAGUGUGGG-------UG-UCAU---ACUU------GAUGACUGC---GUGGAGA---A-CCUU-GAAU-------UAGG-UUUUCCGGAA--GGAGUUGA-CGC-GUGCUGAGCGGU
ABLA01005111.1/2914-3134       GAGAC--UGUACUUC-UCA-GGA-UCA--UUUC-UG--UAGUACG--GUUUCCC----GGUGGGAG--UUCCAC-CU-UGCUC--GCCAAAG--------CACCC---GCGAU-------GACGAG-ACUCG-GCGUCGUCC-CC-U-GA-GCGUGAAG--CUCGCCGG--G--GU----------CGUCGCUGGAA--AGCAUUUUUGG-UGAUC-G--C-CCGGCG---UU-GAGGAACGUCGGC--U-GG---C-C-CC--CCUUG------GGG-GUC-G--GCCGCGGGGGCGA-CGC-UCUCUGAGCGGG
ABLG01002636.1/7043-6835       GGGAC--UGUACUUC-UCA-GGA-UCA--UUUC-UG--UAGUAUGU-AUUCCCU---UG--CGGAG-ACG-CAA-AC-UGCUUCA--CCAAG--------CACCC---UCGAU-------GAUGAG-UUUAG-GCGUUGUUC-CC-U-GA-GCGUGAAG--CUUGUUGG--GACGA---------UGCCAA--AAUU----UUGG-----------AUGUC-CUGACG---UU-GAUGAUCGU----C-AGCU---G-G-CC--CUUCG------GGU-CGGCG-A----UGGGGACAA-CGC-UCUCUGAGCGGG
CABB01004407.1/4482-4691       GGGAC--UGUACUUC-UCA-GGA-UCA--UUUC-UG--UAGUACGU-AUUCC----------UUUG--CGGAGA----CGCAAACUGCUUCACA---AAGCACCC---UCGAU-------GACGAGUUUAG--GCGUUGUCC-CC-U-GA-GCGUGAAG---CUUGUU---GGGAC---------GUUGCCAAAUUU--UUGGAUG---------C--CCU--GACGU-----UGAAGACCGU----CAGCUG---G-C-CC--UUUU-------GGG-UCGGCUA----UGGGGGCAA-CGC-UCUCUGAGCGGG
ABWE01000761.1/1590-1369       AUGAUCCUGUACUUUUACA-GGA-UCA--UUUC-UA--UAGUACCU--UCUUUU----CUACUUGACUUUCCUA-GU-AGACA--ACCUCCU--------UAACU---UUGAU-------GAUCGC-AUUCG-ACUUCAUGC-AU-U-GACUCGGGAUG--UCGGUGGUAGUGCU------------GUGCUCUCUU--UGGGAC-----------UGGCC-UCCUCC--GUU-GAUGAACGU---C---CGC---U-G-UC-GUUAUUCC--AAGAC-GGCGU--G---AGUGUGUGA-AGU-GAUAUGAGAAG-
AAQX01000976.1/70933-71158     AAGAC--CGUACUUUUACA-GGA-UCA--UUUC-UA--UAGUAC-U-CUCUAUU----CUACUUUC-UUUCCAA-AA-GUAGACAAUUUCAA--------UAACU---UUGAU-------GAUCGU-AUUCG-ACUUCAUUC-AU-U-GACUCGGGAUG--UCGGUGGU--UGCAGCG------CUGGGUUCUCUUU--UGGACU-----------CGGCC-CACCCC--AUU-GAUGAACGU---C---CGC---U-G-UC-GCUAUUCC--AAGGC-AGCGU--G---AGUGAGUGG-AGU-GAUAUGAGAAGU
AATU01001845.1/132925-132701   AAGAC--CGUACUUACACA-GGA-UCA--UUUC-UA--UAGUACC--UUCUUUU----CUACUUGACUUUCCUC-GU-AGACA--AUCUCAA--------UAACU---UUGAU-------GAUCGU-AUUGG-ACUUCAUUC-AU-U-GACUCGGGAUG--UCGGUGGU--UGCAGUG------CUGAGUUCUCUUU--UGAACU-----------UGGUC-UCCCCC--AUU-GAUGAACGU---C---CGC---U-G-UC-GCUAUUCC--AAGGC-AGCGU--G---AGUGAGUGG-AGU-GAUAUGAGAAGU
AAZO01005228.1/11835-12050     AAGAU--CAUACUUU-UCA-GGA-UCA--UUUC-UG--UAGUAUGA-AUAAUCUUUUG-AAGUCGU--AGACU----UCUGCGCACCA------------AAACC---AUGAU-------GACGAUUCAUG---ACAUCUGC-GCCU-GA-GCGUGAGG--CAGGCU----AUCGU----------UGAUCUUGUUU-AAGGAUCG---------A-CUUU---AGUC--AUC-GAUGACCGUUCAC--CACG---G-G-AG--CUCGU------CUC-UUGUG--GGAGGGUGUGGAU-GU--GAUCUGAGUGGG
AAQB01007950.1/85194-85386     AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--U-UACUUUC--ACAUUG-AA--AGAAAGCCACAUA--------CACCC---GCGUU-------GAUGAG-UUGGA-UCGUUCUAU-UC-GGCA-GCGUGAGGUAUUUCGCA---GUGCC----------C------UCUU-U------G--------GGGGCGC--AGCGU--UUC-GAUGAUCGC---------------------UCGGUAA--AA---------------CGAGUAGAA-CGA-AUUCUGAGUGGU
AADE01001755.1/10518-10738     AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--U-UACUUUC--GCACAA-AU--UGAAAGCCAAACA--------CACCC---GCGUU-------GAUGAG-UUAAA-UCGUCCUAU-UC-GGCA-GCGUGAGGUUUUGCCCA---GCGCCCUUUCUGGUGCGG-CACUUCG--GUGUCCGUGUCGUUCGGGGCGC--AGAGC--UUC-GAUGAUCGC---------------------UCGGUAA--AA---------------CGGAUAGAA-CGA-AUUCUGAGUGGU
AAFS01000539.1/44651-44431     AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--U-UACUUUC--GCACAA-AU--UGAAAGCCAAACA--------CACCC---GCGUU-------GAUGAG-UUAAA-UCGUCCUAU-UC-GGCA-GCGUGAGGUUUUGCCCA---GCGCCCUUUCUGGUGCGG-CACUUCG--GUGUCCGUGUCGUUCGGGGCGC--AGAGC--UUC-GAUGAUCGC---------------------UCGGUAA--AA---------------CGGAUAGAA-CGA-AUUCUGAGUGGU
AC023683.4/143519-143307       AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--A-UACUUUC--ACACUA-GC--UGAAAGCCAAGUG--------CACCC---GCGUU-------GAUGAG-UUGAA-UCGUUCUGU-CC-GGCA-GCGUGAGGAUUUGCCCA---GCACCCU-----UGUGGGAUGCACU---GCAUCCUUA----GCGGGGAGC--GGGGC--UUC-GAUGAUCGC---------------------UCGGUUU-GAA---------------CGGAUAGAG-CGA-AUUCUGAGUGGU
AAPP01018784.1/368929-369149   AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--A-UACUUUC--ACAUUA-GA--UGAAAGCUAAGCA--------CACCC---GCGUU-------GAUGAG-GUGAA-UCGUUCUAU-UC-GGCA-GCGUGAGGAUUUGUCCA---GCGGCCUUUGUGGUGUGG-CGCUUCG--GUGUCCGCAUCCUCCGGGUCGU--CGGGC--UUC-GAUGAUCGC---------------------UCGGUAA--CA---------------CGAAUAGAG-CGA-AUUCUGAGUGGU
AAKO01000685.1/22923-22714     AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--A-UACUUUC--ACACUA-GC--UGAAAGCCAAGUG--------CACCC---GCGUU-------GAUGAG-UUGAA-UCGUUCUAU-UC-GGCA-GCGUGAGGAUUUGCCCA---GUGUCCUUGUUGGUGC-------CUC--------GCAUCGUUCGGGACGC--AGGGC--UUC-GAUGAUCGC---------------------UCGGUAG-AAA---------------CGGAUAGAG-CGA-AUUCUGAGUGGU
AASR01018747.1/1648-1857       AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--A-UACUUUC--ACACUA-GC--UGAAAGCCAAGUG--------CACCC---GCGUU-------GAUGAG-UUGAA-UCGUUCUAU-UC-GGCA-GCGUGAGGAUUUGCCCA---GUGUCCUUUUUGGUGC-------CUC--------GCAUCGUUCGGGACGC--AGGGC--UUC-GAUGAUCGC---------------------UCGGUAG-AAA---------------CGGAUAGAG-CGA-AUUCUGAGUGGU
AAPQ01007051.1/481137-480929   AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--A-UACUUUC--ACACUA-GA--UGAAAGCUGAGUG--------CACCC---GCGUU-------GAUGAG-UUGAA-UCGUUCUAU-UC-GGCA-GCGUGAGGAUUUGUCCA---GUGUCCUUU-UGGUGC-------UUC--------GCAUCUUUCGGGACGC--AGGGC--UUC-GAUGAUCGC---------------------UCGGUAG-AAA---------------CGGAUAGAG-CGA-AUUCUGAGUGGU
AAEU02000386.1/7816-7607       AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--A-UACUUUC--ACACUA-GC--UGAAAGCCAAGCG--------CACCC---GCGUU-------GAUGAG-UUGAA-UCGUUCUAU-UC-GGCA-GCGUGAGGAUUUGUCCA---GUGUCCUUUGUGGUGC-------UUC--------GCACUGUUCGGGAUGC--AGGGC--UUC-GAUGAUCGC---------------------UCGGUAA-CCA---------------CGGAUAGAG-CGA-AUUCUGAGUGGU
AAPT01021465.1/320367-320151   AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--U-UACUUUC--ACACUA-UC--UGAAAGCACUUCA--------CACCC---GCGUU-------GAUGAG-GUGAA-UCGUUUUAU-UC-GGCA-GCGUGAGGUUUUGCGUG---AUGCCCUU---UGCGGUAUGACUUCG--GUUAU-CCGUG-UUGUGGGCGU--GGCGC--UUC-GAUGAUCGC---------------------UCGGUAA--CA---------------CGAAUAGAA-CGA-AUUCUGAGUGGU
AANI01014831.1/252349-252134   AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--U-UACUUUC--ACACUU-UC--UGAAAGCAAGUCA--------CACCC---GCGUU-------GAUGAG-AUGAA-UCGUUUUAU-UC-GGCA-GCGUGAGGAUUUGCGUG---AUGCUCUU---UGCGAUGUGAUUUU---AUCAC-UCGUU-UUGUGGGCGU--GGCGC--UUC-GAUGAUCGC---------------------UCGGUAA--CA---------------CGAAUAGAA-CGA-AUUCUGAGUGGU
AAPU01010213.1/13262-13048     AAGAC--UAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUCA---GUCUUCAC--U-UACUUUC--ACACAA-AA--UGAAAGCACACCA--------UACCC---ACGCU-------GAUGAG-AUGAA-UCGGUUUAU-UC-GGUA-GCGUGAGGAUUUGCGUU---AUGCCCUU---UACGUUGUGA-CUUG---UUGC-ACGUA-UGAUGGGUGU--AGCGC--UUC-GAUGAUCGC---------------------UCGGUCA--CA---------------CGAAUAAAA-CGA-AUUCUGAGUGGU
AAAB01008984.1/7337520-7337722 AAGAC--UGUGCUUC-AUA-GGA-UCA--UUUC-UA--UAGGCAA--GUUUUCAA--CUCACUUUC----ACUC------GAAAGUCGAGCUAU---UCCAACCC---ACGAU-------GAUGAG-GUGUA-GUGGCUGUC-CU-G-GA-GCGUGAAACUGUCGGAUC--UUGGC----------UGCGUC-UCU----GACGC-----------GUCG---AUCUGUGCUU-GAUGAUCGU---------------------AUCCAUUUGCA---------------AAGGGCAGA-CAC-AUUCUGAGUGGU
AAGE02018994.1/27034-27245     AAGAC--UGUGCUUC-ACA-GGA-UCA--UUUC-UG--UAGGCAA--GUUUUCACCACAAGUUUUUA-CCGAAA----GGAAAAGCUUUCC---------CACCC---ACGAU-------GAUGAGACAAUG-GUGGCCAGU-UU-G-GA-GCGUGAAA-CUUGGUUCA--GUGAGA-------CCAUUCGA-UUCU-U-UCGGAAG-------GACUUC---GGGCU--UUU-GAUGAUCGG-------------------CUUCCUUGCAAUA----------------AAACUGGC-CGC-GGUCUGAGUGGU
AADK01016831.1/3475-3676       AAGAC--CUUACUUC-AUA-GGA-UCA--UUUC-UA--UAGUAAGC--UCUUACC-GA-GAACUUC--ACACUA-C--GUGAA--UGAUCGA--------CAACC---ACGAU-------GAUGAG-GCGUG-GCGCGGCAU-CC-U-GA-GCGUGAGG--CAGGCA-------------------AUGGUU-AGCU---AACCA----------U-------UAGCC--AUC-AAUGAUCGUUCGC---UUC---C-U-U---UCAC--------AG-GGAA---GAGUGGGAUGUUGUCGC-UAUCUGAGUGGU
AAJJ01000071.1/125775-125565   AAGAU--CAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUAU---AUCUUCAC--A-UACUCUA--CACUCA-AA-CGUAGAGUUGACG---------CAACC---ACGAU-------GAUGAG-GGACA-GUCCUGUAU-CC-U-GA-GCGUGAGG--CAGAUU----UGUUU----------CAGGUU-GCAA---AACCUG---------G-CUCA---AGUC--AUC-GAUGAUCGUUCGC---AUG---A-G-C---UUUUU-------GC-UCAU---GUCAUGGAUGCAG-GAC-AGUCUGAGUGGU
AAZX01014918.1/8779-8564       AAGAU--CAUACUUC-ACA-GGA-UCA--UUUC-UG--UAGUAU---AUCUUCAC--A-GACUCUC--UACCCA-A--AGUAGGAGUCGAUG--------CAACC---ACGAU-------GAGGAG-ACGUA-GCUCUCCUU-CC-U-GA-GCGUGAGG--ACGACU----CGGAA----------UUCCGACUUUG--GUCGGAA---------U-ACC----AGUC--AUC-GAUGAUCGUUCAC--CUUU---U-G-CA-CUUU-------GUGC-AGAAG--GCAUGGGAGGAUG-GGC-UUUCUGAGUGGC
AASC02012716.1/1783-2004       AAGAU--CAUACUUU-UAG-GGA-UCA--UUUC-UA--AAGUAUGU-CUUGC--C--GAGAC-GUC--GA-GUA-AAAUCGAUCGGCACGU---------AAACC---ACGAU-------GACGAGAUUGC--GUCAGUUCC-UC-U-GA-GCGUGAAG--UUGAGGC---UGGCA---------UGACUACUGCUC-UCGUAGUC--------AG-GCCGU-GUCUC---GUUGAGGAUCGU----UCCUUU---CCU-CCCUCAGU-G----GGGA--CAAGGA----GGGGGAACU-GGC-AAUCAGAGUGGU
ABRM01002704.1/36840-37049     AAGAC--CGUACUAA-CUA-GGA-UCA--UUUC-UA--UAGUAUGC-GUCCU-------GUCAUUGUAAUUCUACAAAGACAACCCACC-----------GAACC---AUGAU-------GAUGAGCUGUU--GUGACAGCG-CC-U-GA-GCGUGAUG--CUAAUCAA------C---------UAGAGGCUUGC---AGUCUUU--------AG------UUGAUU----UAGAUGAUCGU----UCUGUC----CG-CC--UAUAA-----UGGUG-GAUAGA----GGGCGCUCU-CAC-CAGCUGAAUGGU
ABAV01026709.1/16104-16324     AAGAC--CGUACUUA-CUA-GGA-UCA--UUUC-UA--UAGUACGC-GUCCC-------GUCUUUG--UA-ACC-U--UACAGAGACAACCAC-----GAUACCC---ACGGU-------GACGAUGCAUA--GCGUGAUCC-UC-U-GG-GCGCGAAG--CACGUCGA-GGGC-------------AUUGCCUUGAUUGGCGAGU---------C--GCCACCGACG---AUUGAUGACCGU----UCCUCC---CUG-CC--UAUUAG----UGGCUGGGAGGG----GGAGGAUCA-CGC-AUUCAGAGUGGG
CU210853.5/178869-178983       AAGCC--UAUACUUC--CG-GGGAUCA--UUUC-UA--UAGUUUGU-GACCUAG----AAUAAAGG--UAGAAA-AC-UGCCU--GAUCCA------------------------------AGGA----AUA--------------------------------AAUAC-----------------C-----UUCAU--A---------------C------CCAUU----------------UCUU------------------ACUC-----------------AAGC-------------UCUCCUGG-----
AAWT01056012.1/14056-14278     AUGAC--CAGGCUUC--AAA-GGAUCUUGUCC-GUU--UAGUUUGU-GUCGCCA----G-AAUGUU--AUAAAA-UU-AUGAC-CCUGGGCA--------AAAGU---UCGAU-------GACGUA-UUGAUCAUAUUACCA-UU-UCGA-GCGUGAAC--AAGGCAAA--AGCU------------GUUGAGUCUU-ACUCAAC----------UUGGCA-UUUGUU--UAU-AAUGAUCGC--UU---AUU---G-A-UU-CUCAUU-----UGGU-CAAUG--AAG-GAAUGGUAA-UAUUUAUCAGAGGACU
AACT01045944.1/3617-3408       AAGAU--CAUACUUU--UA-GGGAUCA--UUUC-UA--UAGUGUGC-AUCUUGA-----AAACGUC--AUCAAA-UU-AUGAC-GAAACCUC--------AA-CU---ACGAUGAUGAGUUGU-AG-------GGAUUCCU--UC-U-GA-GCAUGAAG-CUUGGUU----CGUU------------GUAUCUUC----GGAUGU------------UGCG---AACU--AUU-AAGGAUUGUUCUU---GGA---U-U-UC--CGUUC-----CGAG-AUCU---GGGAGGA-AGGAA-UCUCCGGCUGAGUAGU
AABS01000023.1/32234-32026     AAGAU--CAUACUUU--UA-GGGAUCA--UUUC-UA--UAGUGUGU-AUCUUGA-----AAACGUC--GUCAUA-UU-GUGAC-GAUACGAC--------AA-CU---GCGAU-------GAUGAG-UCGCA-GGAUUCCCC-UC-UGGA-GCAUGAAG-CUUUACU----GUUU------------GUAGGUUC----AUUUAC------------AAAC---AGUG--AUU-GAGGAUUGUUUUC---AUU---G-C-UG--AUG--------UAGUUAAU---GAAAGGAGGAGAA-UCC-UUGCUGAGCGGU
ABJB010182825.1/511-296        AAGAU--CAUGCUUC-AUA-GGA-UCA--UUUC-UA--UAGGCUG--AUC----------GCCGAGUUUCAACC-GUAAACUCGGAACACCC-------UCAACC---ACGAU-------GAGGAG-UCGUA-GGGUCUCCA-CC-U-GA-GCGCGAAG--CCGGUC----AGGUG---------ACUUGGGUUUCC-UGCCUGGG--------UU--CCU----GCC--AUU-GAUGACCGUUCCC--ACCG---G-G-C---UUGGA------CGC-CCGC--UGGGAGGGUGGAGA-CUC-AUUCUGAGUGGC
ABEP02020740.1/7770-7551       AAGAU--CAUACUUU--UA-GGGAUCA--UUUC-UA--UAGUAUGU-GACCCGU----GCAUUCUC-ACGGAAA-CG-UGAAC-GCACGCAG--------AAGCC---ACGAU-------GACGAG-CGGUA-GCGUUCCCU-UC-U-GA-GCGCGAAG--CGGGUCGG--GAGU------------GGAGUCCCUG-GGGCUCC----------GGGCUC-CCGGCC--AUU-GAUGACCGUUCCU---UCC---C-C-UC--UUACG------GAG-GGCU---UGGAGGAAGGGAA-CGC-AUUCCGAGUGGU
AANH01009063.1/57627-57412     AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUUCU-GACUUGA----GAAAUGCGUUUCUAAU-UU-GUUUG--GUCUCGC--------UAACC---ACGAU-------GAAGAG-AUGGUGAUACUCUUC-CC-U-GA-GCGCGAAG--CGGGCGGA--CAGA------------CUUGAUUCAU--UUCAUA-----------CGCUG-UCCGCU--UUU-GAUGACCGUUCUU---UGU---C-U-C---CUCG--------GG-GACA---UAGAGGGGAAGAG-UAU-GUGCGGAGUGGU
CAAE01007620.1/23928-23713     AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCCU-GACUUGA----GAAAUGUGUUUCUAAA-GU-GUUG---GUCUCGC--------UAACC---ACGAU-------GAAGAG-GUGGUGAUGCUCCUC-UC-U-GA-GCGCGAAG--CGGGCAGA--GAAA------------CUUGAUUCAC--UUCAUG-----------UGUUC-UCUGCU--UUU-GAUGACCGUUCAG---CGC---C-U-C---CAUCC-------GG-GGCU---UUGAGGGGAGGAG-CAU-GAUCAGAGUGGU
BAAF04057796.1/1492-1276       AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUGCAU-AACUUGA----GAAAUGUGUUUCUAAA-GU-GAUUG--GUCUCGC--------UAACC---ACGAU-------GAAGAG-UUAGUGAUGCUUCAC-CC-U-GA-GCGCGAAG--CGUACUU---CAGUC----------AGUGAG-UUU----CUCACA---------AGACUG-U-CGUU--AUU-GAUGACCGUUCAC---UGC---U-U-AC--CUAG-------GUU-AGCA---GCGAUGGGUGAAG-UAU-GUGCCGAGUGGU
BX539315.5/55089-54874         AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUGUU-AACUAG-----GACAUGUGUUUCUAAA-GU-GUGGA--GUCUUCC--------AAACC---ACGAU-------GAUGA--UUCUUGAUACUCUUU-UC-U-GA-GCCUGAAU--CAGAUGCA--GAGA------------AAUGAUUUAA--UUCAUA-----------UUCUC-UGUAUC--UUU-GAUGAAUGUUCCU---UGU---U-G-U---CUCUU-------AC-AACAU--AGGAGGAAAAUAG-UAU-GAUCUGAGUGGU
AAVX01295013.1/566-347         AAGAC--UAUACUUU--UA-GGGAUCA--UUUC-UA--UAGUCUCUGAACUGA-----GAAAUGUUUUUCUGAA-CU-UGGUC-GGUUUCGC--------CAGCC---ACGAG-------GAGGA--GACAGAGCGGUUCCU-UC-U-GA-GCGUGAAG--CGGGCUGU--GGGU------------GUUGCCAUCU-GUGCAAG-----------AGCUC-ACAGCC--AUU-GAUGAUCGUUCUU---CCU---C-U-CC--UUUAU------GGG-GAGG---UGGAGGGAGGAAC-CGC-AUUCUGAGUGGU
ABGP01000303.1/727-514         AAGAC--UGUACUUU-CUA-GGA-UCA--UUUC-UA--UAGUACAC-GUCCC-------GUCUUUC--UU-CUC-CA-AAGAAGACAACCGCA------UCAACC---AUGAG-------GAGGAUUAAUA--ACGUUCUUU-CC-U-GA-GCGGGAAG--CGGGCGAU------A---------UUGUUCCAGUC---UGGAAUG--------AU------AUUGUC---AUUGAUGACCGU----UCUCGU---UGU--ACUAUUGCA----GU-AUUUCGGGA----GGGAAGGAA-CGU-AUUCUGAGUGGU
X07318.1/1-219                 AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGGUUGU-ACCUGGU----GAAAUGUG-CUCGAAA-GU-GUCUGAA--CUCAC--------AAACC---ACGAG-------GAAGAG-CGUCA-GUGUUUUCU-CC-U-GA-GCGUGAAG--UGAGCUCA--CAGU------------GCUGCUUCAU--UGUGGC-----------UGCUG-UUUGCU--AUU-GAUGAACGUUCUG---CUC---C-C-CU--UUAUUA----UUGG-GGAGA--UAGAGGGAGAGAA-CAC-AAGCUGAGUGG-
Z12613.1/694-913               AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGGUUGU-ACCUGGU----GAAAUGUG-CUCGAAA-GU-GUCUG-A-ACUCAC--------AAACC---ACGAG-------GAAGAG-CGUCA-GUGUUCUCU-CC-U-GA-GCGUGAAG--UGAGCUCA--CAGU------------GCUGCUUCAU--UGUGGC-----------UGCUG-UUUGCU--AUU-GAUGAACGUUCUG---CUC---C-C-CU--UUAUUA----UUGG-GGAGA--UGGAGGGAGAGAA-CAC-AGGCUGAGUGGU
ABQF01071364.1/398-185         AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UG--UAGUUGGU-CACUAGA----GGAGAGUG-AUCUUCC-CU-GAUCG--GCGUCAC--------AAGCC---ACGAG-------GAGGAG-CGAG--GUGUUCUCU-CC-U-GA-GCGCGAAG--CGGGCGGG--CGGU------------GCUGC-CUGC---GCAGG-----------GGCCG-CCCGCC--AUU-GAUGACCGUUCCC---GGC---C-C-U---CGCAG-----U-GG-GGCUC--GGGAGGGAGAGAG-CAC-GGGCUGAGUGGU
AAPN01410201.1/1404-1189       AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUAUGU-CACUAGA----GAAGUGAG-AAUGAAA-GU-GUGAA--GAGACGA--------AAGCC---ACGAG-------GAGGAG-UUUGA-GUGUUCUCU-CC-U-GA-GCGCGAAG--CGGGCUCG--CGGU------------GCUGCUUUG---AGCAGC-----------UGCCG-UUUGCC--AUU-GAUGACCGUUCCU---CCU---U-C-UC--UUCG-------GGG-AAGGU--UGGAGGGAGAGAA-CAC-AAGCUGAGUGGU
AAFR03045428.1/4614-4830       AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUAUGU-UACUAGA----GAAUUGUG-GCUGAAA-GU-GUAGC--ACGGAGG--------UAACC---ACGAG-------GAGGAG-CUGUA-GUGUUCUCU-UC-U-GA-GCGUGAAG--CUGGCUUG--UGGU------------GCUGCUUUCC--AGCAGC-----------UGCUA-CCUGCC--AUU-GAUGAUCGUUCUU---CUC---U-G-CU--UUU--------GGGCAGGGU--GAGAGGAAGAGAA-CGC-AAGCUGAGUGGC
ABRN01297802.1/8586-8380       CAGAC--UGUACUU---CA-GGGAUCA---UUC-UA--UAGU-CGU-UUCUAGA----GAAGUUCU--CUGAAU-GU-GUAGA--GCACUG---------AA---ACCACGAG-------GAGGAG-GU----GUGGUGUCUGUC-U-GA-GCAUGAAG--CUGGUUAU--UGGU------------GUUGC-UUCU---GCAGC-----------UGCCA-UUAGCC--AUU-GAUGAUCGCUCUU---CUC---U-U-CU--UUC--------GGG-AGAGU--GAGAGGGAGAGAA-UGC-CAUCUGAGUAAA
ABRP01111646.1/6212-5998       AAGAC--UAGACUUU--UA-GGAACCA--UUUC-UACAUAGUUUCU-UACUGGA----GAAAUUUC-UCUGAAC-GU-ACGGA--ACACCGG--------AAACC---AGGAG-------GAGGAG-GCGUG-GCGUUCCCU-CC-U-AA-GUGCGAAG--CGGGCUCU--UGGU------------GUUGC-UUCU---GCAAC-----------UAUCA-UUUGCC--AUU-GGUGACUGUUCUU---CUC---U-U-CC--CUU--------GGG-AGAGU--AAGAGGGAGGG-A-UGC-UGUCUGAGUGGU
AAQQ01377710.1/265-50          AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGAUC-GU-GUAGA--GUACCGA--------AAACC---ACGAG-------GAGGAG-UUGUA-GCGUUCCCU-UC-U-GA-GCGUGAAG--CAGGCACU--UGGU------------GUUGCUUUAC--UGCAAC-----------UGCCU-CUUGCC--AUU-GAUGAUCGUUCUU---CUC---U-C-C---UUUUA-------GG-AGAGU--AAGAGGGAGGGAA-CGC-AGUCUGAGUGGU
AAYZ01671298.1/83-298          AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUCUGU-GACUAGA----GAAGUUUC-UCUGAUC-GU-GUAGA--GCACCGA--------AAACC---ACGAG-------GAGGAG-UUUUA-GCAUCCUCU-CC-U-GA-GCGUGAAG--CUGGCUUU--UGGU------------GUUGCUUUUG--UGCAAC-----------UGCCA-CUUGCC--AUU-GAUGAUCGUUCUU---CUC---U-C-CU--UGU--------AGG-AGAGU--GAGAGGGGGAGGA-UGC-AGUCUGAGUGGU
AADA01318152.1/802-588         AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGCUUGC-CACUAGA----GAAGCUUU-UCUGGAC-GU-GUAGA--GCACCGG--------CAACU---GCGAG----------GAG-ACGCA-GUGUUCUCU-CC-U-GA-GCCUGAAA--CCAGCAAG-UUGGU------------GUUGCUUUGC--UGCAGC-----------UGCUG-UUUUCC--AUU-GAUGGA--UGAUU---CUUCCCU-U-CC--UCU--------GGG-AGAGC--AAGCGGGAGAGGA-CGC-AAUCUGAGUGCU
AL627390.7/149172-148958       AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUUGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAUA--GCACUGA--------AAACC---ACAAA-------GAAGAG-GUGCA-GCAUUAUCU-CC-U-AA-GUGUAAAG--CCGGCUCU--UGAU------------GUUGCUUUGC--UGCAAC-----------UGCCA-UUUGCC--AUU-GAUGAUCGUUCUU---UUC---U-U-CC--UUU--------GGG-AGACU--GGGAAGGAAAGGA-UGC-AAUCUGAGUGG-
AADA01192714.1/17868-18084     AAGAC--UAUACUUU--CA-GGGAUCA--UUUC-UA--UAGUUCGU-UACUAGA----GAAGUUUC-UCUGAAC-GU-GUAGA--GCACCGA--------AAGCC---ACGAG-------GAAGAG-ACAUA-GCGUUUUCU-UC-U-GA-GCGUGAAG--CCGGCUUU-AUGGU------------GUUGCUUAGC--UGCAAC-----------UGCCG-UCAGCC--AUU-GAUGAUCGUUCUU---CUC---U-C-C---ACUUG-------GG-GGAGU--AAGAGGGAGAGAA-CGC-GGUCUGAGUGGU
Z75549.1/30014-29830           GAGAC--CAUACUAU-ACA-GAA-UCA--UUUC-UG--CAGUAUGU-AUCUCG------UAAUUCC--CAUCAA-AU-UGGUAGAGAUGC----------CAUCC---GCGAU-------GAGUGGGAGAC--GGGCGAGCC-GC---GA-GCGUGAAA-C-------------------------AGUUC--UUCG----GAAC----------U-----------------UGAUGACCGC----A-CGGA---G-C-CG-AUGAAUU----UUGG-AGCCG-U----AGUGGCUUG-CUC--UUCUGAGCGGA
EU240276.1/1-214               AGGAC--UAUACUUU--CA-GGGAUCA--UUUC-UG--UAGUUGGU-AACUAGA----GGAGUGUG-AUCGAAA-GU-GUCCG--GCGUCAC--------AAACC---ACGAG-------GAGGAG-CAGC--GUGUUCUCU-CC-U-GA-GCGCGAAG--CGGGCGGG--CGGU------------GCUGC-UUGU---GCAGG-----------AGCCG-CCCGUC--AUU-GAUGACCGUUCCC---GUC---C-C-A---CUUGG-----U-UG-GGUCU--GGGAGGGAGAGAA-CAC-AGGCUGAGUGGU
M38249.1/859-675               GAGAC--CAUACUAU-ACA-GAA-UCA--UUUC-UG--CAGUAUGU-AUCUCG------UAAUUCC--CAUCAA-AU-UGGUAGAGAUGC----------CAUCC---GCGAU-------GAGUGGGAGAC--GGGCGAGCC-GC---GA-GCGUGAAA-C-------------------------AG-UU--CUUC-G--GAAC----------U-----------------UGAUGACCGC----A-CGGA---G-C-CG-AUGAAUU----UUGG-AGCCG-U----AGUGGCUUG-CUC--UUCUGAGCGGA
#=GC SS_cons                   <<<<<..<<<<<<--.-<<.<<<.___.._>>>.>>..->>>>>>-.>>>>>,,....,,,,,<<<..<<____.__.>>>>>.--------........--(((...((---.......------.-----.(((((((((.((.(.,,.<<<-----..--<<<<--..<<<<...........-<<<<<_____.._>>>>>..........-->>>>.-->>>>..---.------>>>..<<...<<<...<.<.<<.._____....._>>>.>>>>-..>>,.))))))))).))).-------)))))
#=GC RF                        aaGac..cauACUUu.AcA.GGa.UCA..UuUC.Ug..UAGUaugU.guCuugA....gaAaUuuc..ccaaaa.gU.gggaa.ggcaccca........aAaCC...aCGAU.......GAuGAG.augua.gcGuucucu.cC.u.GA.gCGUGAAG..cuggccau..cggc...........aguugcUUuuu..ugcaac..........uugccg.uuggcc..aUU.GAUGAUCGc..uc...cuc...u.c.cc..Uuuuu.....aggg.agagu..gaG.gGgagagaa.Cgc.auUCUGAGuGGu
//
# STOCKHOLM 1.0

#=GF AC   RF00013
#=GF ID   6S
#=GF DE   6S / SsrS RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Barrick JE
#=GF SE   Barrick JE
#=GF SS   Published; PMID:15811922
#=GF GA   48.00
#=GF TC   48.00
#=GF NC   47.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000376; RNA_6S;
#=GF RN   [1]
#=GF RM   10892648
#=GF RT   6S RNA regulates E. coli RNA polymerase activity.
#=GF RA   Wassarman KM, Storz G
#=GF RL   Cell. 2000;101:613-623.
#=GF RN   [2]
#=GF RM   15793584
#=GF RT   A highly conserved 6S RNA structure is required for regulation of
#=GF RT   transcription.
#=GF RA   Trotochaud AE, Wassarman KM
#=GF RL   Nat Struct Mol Biol 2005;12:313-319.
#=GF RN   [3]
#=GF RM   15811922
#=GF RT   6S RNA is a widespread regulator of eubacterial RNA polymerase that
#=GF RT   resembles an open promoter.
#=GF RA   Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR
#=GF RL   RNA. 2005;11:774-784.
#=GF RN   [4]
#=GF RM   28692405
#=GF RT   6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak
#=GF RT   in late exponential phase and gene deletion causes a high salt stress
#=GF RT   phenotype.
#=GF RA   Elkina D, Weber L, Lechner M, Burenina O, Weisert A, Kubareva E, Hartmann
#=GF RA   RK, Klug G
#=GF RL   RNA Biol. 2017; [Epub ahead of print]
#=GF CC   E. coli 6S RNA was the first non coding RNA to be sequenced, but its
#=GF CC   function was unknown until recently. It consists of 184 nucleotides that
#=GF CC   fold into an extended hairpin structure with a large single-stranded
#=GF CC   internal bulge. The 6S RNA specifically associates with RNA polymerase
#=GF CC   holoenzyme containing the sigma70 specificity factor. This interaction
#=GF CC   represses expression from a sigma70-dependent promoter during stationary
#=GF CC   phase [1]. 6S RNA homologs have recently been identified in most bacterial
#=GF CC   genomes [2,3]. Many Gram-positive species have two copies of 6S RNA. In
#=GF CC   Bacillus subtilis, both copies appear to interact with RNA polymerase
#=GF CC   holoenzyme containing the housekeeping sigma factor and be expressed
#=GF CC   during different stages of growth. In many proteobacteria, 6S RNA may be
#=GF CC   processed from a transcript encoding homologs of the E. coli YgfA protein
#=GF CC   which is a putative methenyltetrahydrofolate synthetase.
#=GF WK   6S_/_SsrS_RNA
#=GF SQ   149


CR543861.1/1111804-1111620   UUGUCUCUGGG-AUGCUCGCCAGCGAGUCAGAA----UCCCC-UGA-GCCGAUACUAUCACUUUA-----GGAUAGCGUUCUG---CAUAU-UUAGAGU-GU-AUGCCUAC---------------CCAGA---------GUAGGAA---AC---CCAGCAAG-U-AUG--CGUCGCU--UCCACCUUG-----AAC----UUAA---GGGU--UCAAG--GG-------UAAUGACAGGCAGCGGCAU--CUUCGGAGGCAUU
AB036820.1/118-302           GAGAUUAUGUA-CUCCACUCCGAUUACCUA--------GUUU-UGA--CCGAACAUUUUUUUAUAC----GGGAGCUUGCCCU--UUCCUU-UCUGCAU-AA-AUGCCCUC----------------AUUA---------GAGGCAC---UU---AUAAAGUC-A-GGA--AGAAAGC-ACCCACCUGC----CAUG---GUGCG---GGGU--UCA-A--AAC------GAAGGAAAGGA-GGGGAAGAAAUAAGAAAGAUAU
AL591979.1/136531-136336     GAAACCCUAAU-GUAUUCGAUAUAGUUCCUGAU----AUUUU-UGA-ACCGAACAAUUUUUUAUACC-UAGGGAGCUUGGAGU--UCCGGC-GCGGCGC-AC-AUGCCUU----------------CACAC----------GAGGAA---GU---GCAAACCG-U-UAG--ACAGAGC-ACCCACCUGCU--UUAAUUGAGAGCG----GGU--UCA-A--AGG-----AAGGGAAUCCUAAACGGUAC--GAUUGGGGUUUCU
BX842646.1/183093-182914     AGAAGGGUUCG-ACGG-CGUAAAGCUCUAUC------GAAAA-UAA-ACCUUACAAGCAUAUUUUU----GGGGACUGUCCC----UGACA-AUGGUGA-GC-AAGCUCAG---------------CUCGU--------ACUGAGAA---GC---CUAAAGUU-G-UUA--UCAUGGUUACCCACCUUAG---CUAA----AACA----GGU--UUACU-UUUU-------------CAGAGUGGUCUU---CGAGCCUUUUUU
AE017355.1/1531701-1531884   AAAUUCCUACG-GUGUACGUAGCUUAUGCAUG------UCU--UAA-ACCAAUAAGUUUAAUAU------GGAAGUUCAAUAU--UUAAAU-GUAGCUA-AC-AUGCCAUC---------------UUUUU-------AAGAAGGAA---GU---UACAAACA-U-UUG--UGAGAGC-AUCCACCUGU-----GAG----AGCA----GGU--UUAU---GGAC-----AUCUAGAGAGA-ACGGCAU--AUGUGGGGCUAUA
AE017355.1/1531497-1531679   CACAUCCUGCG-GUGUACGUAACUUAUUUA--------UGUCUAAA-ACCGAUGUUAGUUAUAC------GGAAGCUCAAUAUU-UAGUGA-CCAUC-A-UC-AAGCCUUC---------------CUUGU---------GGAGGAA---GA---UGUACGGU-A-ACU-GUGAGGGC-AUCCACCUGC----GAGU----AGCG----GGU-UUUUGG--ACAU-----U---UACGAGGAGCGGCAC--GUGCGGGG-GUCU
BX640434.1/259466-259282     UUGUCCCUGCC-GUGCUCGUGACUUGGCCAUACA---UUCUCU-GA-ACCUAUGUCUUACGGCAUAU--GGGUUGCGGGAGU----GUAGA-GCUGGAG----UGAUCGUCU-------------ACUCGU--------AGACGAACC-C-------GAUGCU-C-UUC--GGAUCGC-GACCACCUUG-----AAC----CUCA---GGGU--UC--G--AGAU-----GCCGGCC--UUGACGGCAC--AGGCGGGG-CAUC
CR522870.1/3243294-3243122   AUUCCCCUGUG-CUGUUGGUGAUUGCUAAAGUG----U-GU--UGA-GCCAACUCUCAAUAAAA------GGGCGUUGUCUCU---UGUCA-GU------AA-AGGUGAA----------------UCGGU----------GACGAA---UU--GGCUGAGCU-G-AUA--AUAUGAU-GCCCACCUAU----UAAU-----UUA----GGU--UUA----AC-------UAUCUUAGCGACACGGCAG---UGUGGGGGAUUU
U62615.1/1314-1495           AUCUGGCUGCG-ACGU-UGGUGACUGCCAACAAU---GUUUUUUGA--UCUAUACCUUUCGAAGUU----GGGCGCUCUCGCA--GAGCCG-ACGGC-A-GU-AGACCGAG---------------CUUGA---------CUCGGAA---AC---UUAAUGUU-G-GCC---GCAAGC-UCCCCCCUGG-----UUC---UCCCA----GG---UCG----AAAU-------CUGAGGUAAAACGGCGU---CGCGGUUAGAUC
AE017334.2/1507514-1507697   AAAUUCCUACG-GUGUACGUAGCAUAUGCAUG------UCU--UAA-ACCAAUAAGUUUAAUAU------GGAAGUUCAAUAU--UUAAAU-GUAGCUA-AC-AUGCCAUC---------------UUUUU-------AAGAAGGAA---GU---UACAAACA-U-UUG--UGAGAGC-AUCCACCUGU-----GAG----AGCA----GGU--UUAU---GGAC-----AUCUAGAGAGA-ACGGCAU--AUGUGGGGCUAUA
AL596168.1/332986-332791     GAAACCCUAAU-GUAUUCGAUAUAGUUCCUGAU----AUUUU-UGA-ACCGAACAAUUUUUUAUACC-UAGGGAGCUUGGAGU--UCCGGC-GCGGCGC-AC-AUGCCUU----------------CACAC----------GAGGAA---GU---GCAAACCG-U-UAG--ACAGAGC-ACCCACCUGCU--UUAAUUGAGAGCG----GGU--UCAAA--GGA------AGGGAAUCCUAAACGGUAC--GAUUGGGGUUUCU
BX571857.1/1685846-1685657   AGUCAUCUGAG-UUGUUCGUAAGUUUGCUUUU------UAAUUUGG-GCCUAACACUCUUUGAUCA---AGGGAGCCCAAUGGGUUUUCUU-GCAGCGU-AC-ACGCCUU----------------AUAUG----------AAGGAC---GU---ACAAAACA-A-GAA--ACAGGGC-ACCCACCUGU----AUAU----AACA----GG---CCGAA--UGAUCA-AGCUAUUAUAACU-ACGGCAA---UACGGAC-UCUA
AF029321.1/2323-2482         GGGGGUCUGCG-UUGUUCGU--GUAGGUUGAAA----GUGCCUCGA-GCCCGAUUUUGUUCUUAUA----GGGAGCCGUCAC----UGGUA-AC------------CU------------------CGAGU------------AG---------------GUU-A-UUA---CACGGC-GCCCACCUUA-----GCU-----UUA----GUC--UC-AG--G-ACA--CUAAGCAAAGCGUUACGGCAA--AUGCGGAUCUCCU
M12965.1/109-292             AUUUCUCUGAG-AUGUUCGCAAGCGGGCCAGU------CCCC-UGA-GCCGAUAUUUCAUACCACA---AGAAUGUGGCGCUC---CGCGG-UUGGUGA-GC-AUGCUCGG---------------UCCGU---------CCGAGAA---GC---CUUAAAAC-U-GCG--ACGACAC-AUUCACCUUG-----AAC-----CAA---GGGU--UCAAG--GG------UUACAGCCUGCG-GCGGCAU---CUCGGAGAUUCC
CR378673.1/72541-72721       UUGACCCUAGG-GUGUACGUCAGUGUGUCAAC------GUCCCCGA-GCCGAUAAGCAAAUAACCC----GGAUCAGCUUUU----AUUAG-CUAUUGU-GC-AAGCUCAG---------------CUCGA---------CUGAGAA---GC---C-UGCGGC-U-AAU--GUUGCUG-AACCACCUUG-----AAC----AUCU----GGU--UCAAG--GGCC------UAGAUGCGCA-ACGGCAC---CUUGGGG-CAUA
BX569692.1/257432-257250     CCUGAACUGCU-GUGUUGGUGACGGCCUUUUCUA---GUGCUCUGA--UCUGACUCUCUUUCGACU---UGGGGAGACUGUC----GUGAC-GGUGC-C-GU-AAACCGGC---------------CCUGU--------AGCCGGAA---AC---G--AAUCC-C-CAC--UUUGUUU-CCCCUUCUGG-----UUC---UUCCA----GG---UC-GA--CCAC-----U--GGGGCUCGCACGGCAC---GGUGGUUCACCC
AE017197.1/941600-941442     UCUUGGCUGCU-UGGUGCGUGAGCUUAAUAUUA----ACCUAGGACUACCACUAACUUUUA---------GGACAUCAUCUC----UGUCU-AACA----------CU------------------AAUUC------------AG----------U----UUA-G-AUA---UAUGAA-GUCCACCUUU-----ACA----UCAA----GGU-CUUUGA--AGGAU---U-----UUAAGUAACGGCCA--AAGCGGUCAUGUA
BX571871.1/85682-85868       AUUUCUCUGAG-AUGUUCGUUAACGGGGAAAGU------CCCCUGA-GCCGAUAUUUCAUACAUUAU--AGAAUGUGGUGCUC--CGUAGU-CUGGUGU-GC-AUGCUCGG---------------UCCAG---------CCGAGAA---GC---CUUAAAG--C-UGC-GACGCUGC-GUUCACCUUG-----AAC----CGAG----GGU--UCAAG--GG-------UUACUACCUGUAACGGCAU---CUUGGAGAAUCU
X01238.1/1-184               AUUUCUCUGAG-AUGUUCGCAAGCGGGCCAGU-------CCCCUGA-GCCGAUAUUUCAUACCACA---AGAAUGUGGCGCUC---CGCGG-UUGGUGA-GC-AUGCUCGG---------------UCCGU---------CCGAGAA---GC---CUUAAAAC-U-GCG--ACGACAC-AUUCACCUUG-----AAC-----CAA---GGGU--UCAAG--GG------UUACAGCCUGCG-GCGGCAU---CUCGGAGAUUCC
BX897700.1/1339934-1340092   GGUGUUCUGCG-CUUCUCGACAGGAAAUAACAU----AUCCUGAGA--CCUUAGUGAUCUCCAA------GGGAGCUGUCCCU---GAUCA-AG------------CC------------------CGUG-------------GG---------------CUU-U-UUC--AUAUGGC-GCCCACCUAU-----UUU-----GUA----GGU--UCCCG--GGAU-----CAACUUUUUCCAUCGGUCG--UUGUGGAUCACCA
BX572607.1/143813-143653     GCGAAGCUGCG-GGACGCGUCAGGAGCCAUAUA-----UCCCCGGG-GCCUUAUCGAUCCUUUC------GGGAACUGUCCC---------------------UGGCCGGGU-------------CCGUGG--------ACCCGGUC--A----------------------UAUGGU-GCCCACCUAC-----UUU----CGUA---GGGA-ACUCCG--GGAU-----CGAGUGCUUCA-ACGGUCA--CCGUGGCCUCGCA
BX897699.1/1644926-1645087   GGUGUUCUGCG-CCUCUCGACAGGAAAUAACAU----AUUCCUGAG-ACCUUAGUGAUUUCCAA------GGGAGCUGUCCC----UGA-----------------UUAAG---------------CUCGUG------GGCUUUU---------------------UCA---UAUGGC-GCCCACCUAU----UUAU-----AUA----GGU-UCCCAG--GGAU-----CAACUUUUUCCAUCGGUUG--UUGUGGAUCACCA
AF316874.1/3084-3280         UACAAGCUGCA-UUGUUCGU--AUCAUUAUUAA----GUUU--UAA--CCUUUAAGCUGUAAAA------GGGAGUUUUAUGA--UUGAAA-CUGAAAU-GGCAAGCCUCGU-------------UCUUUUAAUUAACAACGAGGACA-GAC---AGGCAAGU-U-UCU---GCGAAC-ACCCACUUUG-----AGG----AGUGG--UGGU--UUA----AGAC----UUUCUAGAGACGUACGGCAG--AGGCGGCUGAUAC
BX640420.1/116264-116080     UUGUCCCUGCC-GUGCUCGUGACUUGGCCAUACA---UUCUCU-GA-ACCUAUGUCUUACGGCAUAU--GGGUUGCGGGAGU----GUAGA-GUUGGAG----UGAUCGUCU-------------ACUCGU--------AGACGAACC-C-------GAUGCU-C-UUC--GGAUCGC-GACCACCUUG-----AAC----CUCA---GGGU--UC--G--AGAU-----GCCGGCC--UUGACGGCAC--AGGCGGGG-CAUC
BX950851.1/526655-526839     AUUUCUCUGAG-AUGUUUGUCAGCGGGCCAGU-------CCCCUGA-GCCGAUAUUUUAUACCAAAC--AGAAUGUAAUGCUC---UGCGG-UUGGUGC-GC-AAGCUCGG---------------UUCGU---------CCGAGAA---GC---CUUAAGAC-U-GCG--ACGUUAU-GUUCACCUUG-----AAC-----CAA---GGGU--UCAAG--GG------UUACAGCCUGCG-GCGGCAU---CUCGGAGAUCCC
AJ235273.1/69980-69822       UCUUGGCUGCU-UGGUGCGUGAGCUUAAUAUUA----ACCU--AGG-ACUACCACUAACUUUUA------GGACAUCGUCUC----UGUCU-AAUAC---------UC------------------AUUCA------------GU---------------UUA-G-AUA---UAUGAA-GUCCACCUUU-----ACA----UCAA----GGU--CUUUG-AAGG--------AUUUUAAGUAACGGCCA--AAGCGGUCAUGUA
AP009389.1/1081845-1082030   AAUACCCUGCU-GUGUGCGUGAUCAGCCUUGAA-----GUUU-UGA-GCCAACACCAUUAGAAA------GGGAGCCCGGACU--CUGAAU-GUGGCUU-GU-AUGCCUCU---------------CAUGC---------AGAGGAA---AC---AAAAAGCA-U-UCA--GGAGGGC-ACCCACCUGU----UGAG----AGCA----GGU--UCAAA-AAACU-----UUUGGGGAUC--ACGGCAU--GAGUGGGGUUUUU
AP008232.1/3464584-3464767   AUUUCUCUGAG-GUGUUCGCCAGCGGGUCAGU------CCCU-UGA-GCCGAUAUUUCAUACCACA---AGAAUGUGGCUAUU---CCUGA-CCGGUGC-GC-AUGCUCGG---------------CUUGU---------CCGAGAA---GC---CUUAAGGU-C-UCG--ACGCUAC-GUUCACCUUG-----AAC----CAAG----GGU--UCA-A--GGGU-----UACAGCCUGCG-GCGGCAU---CUCGGAGAUCCU
AAKK02000137.1/3410-3226     UUUACCCUGGG-GUGUGCGUCAGCAGGAUUUAA-----GUCCCUGA-GCCGAUAAGCAAUACCUAA----GGGUUAGUAUUU----GGUAA-CUAUUGA-GC-AAGCUCGG---------------CAUGU--------ACCGAGAA---GC---C-UACGGU-U-GUC--AUUGCUG-AUCCGCCUUG-----AAC---CAGCU----GGU--UCAAG--GGC------CACAAUCCUCA-ACGGCAC---CCUGGGGUAUUC
BA000031.2/2733820-2734004   UUUACCCUGGG-GUGUUCGUCAGGCGGAUUUAA-----GUCCCUGA-GCCGAUAAGCAAUACCAAA----GGGUUAGUACUU----GAUAG-CUAUUGA-GC-AAGCUUGG---------------CAUGC--------ACCGAGAA---GC---C-UACGGU-U-AUC--AUUGCUG-AUCCGCCUUG-----AAC---CAGCU----GGU--UCAAG--GGC------CACAAUCCUCA-ACGGCAC---CCUGGGGUAUUC
AM286415.1/3711867-3712050   AUUUCUCUGAG-GUGUUCGUCAGCGGGUCAGU------CCC-CUGA-GCCGAUAUUUAAUACCAAC---AGAAUGUAGUGCCU--CCGUAA-CCGGUGC-GC-AUGCUCGG----------------UCCG---------CCGAGAA---GC---CUUAAGGU-U-GCG--ACGCUGC-GUUCACCUUG-----AAC----CAUG----GGU--UCAA---GGGU-----UACAGCCUGCG-GCGGCAU---CUCGGAGAUCCC
CP000302.1/950450-950269     UGCUCCCUGGG-AUAUUCGCCAGCUGGUAAU-------GUCCCUGU-GCCGAUAAUUUUUAAACCA----GGGUGAAUGUUUU---UACUG-ACAUUGC-GC-AUGCUCAG---------------CUUGU--------ACUGAGAA---GC---CUUAGGA--G-GUA--AUCAUUU-ACCCGCCUUG-----AAC----CUAC----GGU--UCAAG--GGCU-------ACACCGGCA-GCGGUAU---UUUGGGGAGCAU
AACK01000017.1/27996-27815   ACUUGCCUGAG-GUGUGCGUUACUCGUUAC--------GUCCCUGA-GCCGAUAAUUUGAAACUUU----GAGUUGGACAUCU---AAAUG-CCGGUGA-GC-AGGCUUAC---------------CUUGA---------GUAAGAA---GC---CUAAAGGC-A-AUU--AAGUUCG-ACUCCCUUGA-----ACC----UUCU----GGU--UCAAG--GAC------CACCACAAGUA-ACGGCAC---UUCGGGUUCUUU
BX936398.1/3749921-3750103   AUUUCUCUGAG-GUGUUUGCCAGCGGGCCAGU------CCC-CUGA-GCCGAUAUUUAAUACCAAU---AGAAUGUAGUGCUC---CGUAA-CCGGUGA-GC-AUGCUCGG----------------UCCG---------CCGAGAA---GC---CUUAAGGU-U-GCG--ACGCUGC-GUUCACCUUG-----AAC----CAAG----GGU--UCAA---GGGU-----UACAGCCUGCG-ACGGCAC---CUCGGAGAUCCC
AACY023937400.1/581-403      AACUUCCUGGG-GUGUGCGCCAGUCGGUGAU-------GUCCCUGA-GCCGAUACGCACAACCAC-----GGGGGUUGCACGU---UGGGG-CCGGUGU-GC-AUGUCCG----------------CCUGA----------CGGAAA---GC---CUUAACGC-C-UCC---UGCAAC-CUCCACCUUG-----AAC---UUUCG----GGU--UCAAG--GGCU-------AAACCGACA-GCGGCAC---GCCGGGAAGUCA
CP000746.1/718947-718765     GAUUACCUGAG-AUGCUCGCCAGCGGGUUAC-------GUCCCUGA-GCCGAUACUUACAUACUUC----GAGUUGGUUCUC----UACUG-UUGGUGU-GC-AGGCUUAG---------------UUUCA---------CUAAGAA---GC---CUAAAAAC-G-GUU--ACAACUG-ACUC-CCUUG-----AAC----CGUC---GGGU--UCAAG--GACC-----GACCACCCACG-ACGGCAU---CUCGGGGCCUAA
CP000232.1/1712162-1711978   UUUACCCUGCG-AUGUUCGUGAAGAGCCGUGCA-----GUUU-UGA-GCCAACACCAAAACUUA------GGGAACCUGACAU--CCGGGC-AUGGCUU-GC-AGGCCCCA---------------GUUUC--------CAGGGGAA---GC---AAAAAGUG-U-CCG--UGGAGGU-ACCCACCUGC----UGAG----AGCA----GGU--UCAAA--AAC------CACGGCAUUC--ACGGCAU--UUGUGGGGUUUUA
AE017143.1/796107-795926     CACUACCGGGG-GUGUUCGUUAUUAGUUAC--------GUCCCUGA-GCCGAUAAUUGAAAACUUU----GAGUUGAACAUCU---AAUCG-CUGGUGA-GC-AAGCUUAC---------------CUUGA---------GUAAGAA---GC---CUAAAAGC-U-AUU--AAGCUUA-ACUC-CCUUG-----AAC----CAUU---UGGU--UCAAG--GGC------CUUCACUGAUA-ACGGCAC---UCCGGGUAUCUU
CP000117.1/5398416-5398599   GUUGCACUGCG-ACGUUGGUGACUGCCAUCAAG----U-UUUUUGA-UCUAUGUCUUUAAGAAAAA----GGGAACCAAACGU---CUCUC-GUGGC-A-GU-AUACCGGG---------------CUUGU--------ACCCGGAA---AC---UUUAAACG-A-GGA-AAAUCGGU-ACCCACCUGG-----UUU----AACC----AGG--UCAUA--AA---------CUUAGGUAAAACGGCGU---UGCGGUGAACUC
CP000521.1/1200632-1200448   CUGUCUCUGGG-AUGUUCGCCAGCCGGUCUGAU----U-CCCCUGA-GCCGAUAUCAUCUCUUUA-----GGAUGGUGUUCUG---CAUAU-UUAGAGC-GU-AUGCCUAC---------------CCCGA---------GUAGGAA---AC---CCAGCAAG-U-AUG--CGUCACC--UCCACCUUG-----AAC----UUUA---GGGU--UCAAG--GG-------UAACGACAUGCAGCGGCAU--CUUCGGAGCAUUU
AAOH01000006.1/92254-92072   UGUUCUCUGAG-AUGCAGGUCAGUGGGUUAA-------GUCCCUGA-GCCGAUAAAUUUUUUGUUA----GGGACGCAGUUU----AUUAG-CUAUUGU-GC-AAGCUCGG---------------CAUGU--------ACCGAGAA---GC---C-UGCGGC-U-AGU--UGUUGUG-UUCCGCCUUG-----AAC----CUUA---GGGU--UCAAG--GGC------UGACACCCGCA-ACCGCAU---CUUGGAGACACU
CP000436.1/730391-730576     GAUUACCUGAG-AUGUUUGCCGGCGGAUUAA-------GUCCCUGA-GCCGAUACUGAAAACUUAA---UGAAUUGGCGUCC----UGUUG-UUGGUGU-GU-AUGCUUGC--------------UAGCCA--------UGCAAGAA---AC---CUAAAAAC-A-AUA--UUAGCCG-AUUC-CCUUG-----AAC----CGUA---GGGU--UCAAG--GACC-----GAACAUCCGCA-GCGGCAU---CUCGGGGCUAUU
CP000644.1/2821324-2821506   AAUUCCCUGGG-AUGUGCGUCAGCCGGUUCAA------GUCCCCGA-GCCGAUAAUCAUACCCAAC---AGGGGAUCGGCCU----UCUGG-CUAUUGC-GC-AUGCUCGG---------------CACGA---------CCGAGAA---GC---C-UGCGGU-C-AGA---UUCGAU-UCCCGCCUUG-----AAC----CUAC----GGU--UCAAG--GGC------CCAAACCGGCA-ACGGCAU--CUCCGGGGUACCA
BA000043.1/2585765-2585579   ACCGUCCUAAU-GUGUUCGUCGGAUCACUGAU------CGUUUUGA--CCGAACAGUUUAUGAUCC----GGGAGCUCGGGGU--UUCCAA-GCGGCGU-GC-ACGCCUCU--------------UCGUCA--------CAGGGGAA---GC---AUAAACCU-U-GGA--ACAGGGC-ACCCACCUAUG---GGAG----AGCG----GGU--UCAAA--ACG--------AAGGCAUCG-ACGGCAC--GAUUGGGACUGGC
AAOU01000016.1/1661-1842     UUAACCCUGGG-GUGUGCGUCAGUGAAUGAAC------GUCCCCGA-GCCGAUAAGCAAAUACCCA----GGAUCUGCUUUU----AUUAG-CUAUUGA-GC-AUGCUCAG---------------CUCGA---------CUGAGAA---GC---C-UACGGU-U-AAU--GUUGCCG-AUCCACCUUG-----AAC----UUCU----GGU--UCAAG--GGC------AUUAUUUCGCA-ACGGCAC---CUUGGGGAACUU
AE016827.1/441283-441084     GAUUUCCUGAG-GUGUUCGUCAGCGGGUUAC-------GUCCCUGA-GCCGAUACUUACAUACUCU---AGAAUUGGUUCUC----UAUAG-UUGGUGA-GC-AUGCUUGCCCUGACCUUCGAGGUCCUGA--------UGCAAGAA---GC---CUAAAAAC-A-GUU--ACGACCG-AUUC-CCUUG-----AAC----CGUC---GGGU--UCAAG--GACC-----GACCACCCACA-ACGGCAU---CUCGGGGUCUUC
DQ163568.1/634-454           AUAUCUCUAGG-AUGUUUGCCAGCGGGUCAGU-------CCCCUGA-GCCGAUAUUGAAUAUAAAA----AAAUAUGGUGUU----CUUAA-CUCGUGA-GC-AUGCUUGG----------------UUCG---------CCAGGAA---GC---CUAAAGGU-U-AUG--ACGCUAU-AUUCACCUUG-----AAC----CAAG----GGU--UCAAG--GG-------CCAAAGCUCGCAGCGGCAU---CUUGGAGACCCC
CP000557.1/2605605-2605418   ACCGUCCUGAU-GUGUUCGUCGGGUCACCCAU------CGUUUUGA--CCGAACAGUCGAUGAUCC----GGGAGCCCGGGGU--UUCCAA-GCGGCGU-GC-AUGCCUCUU-------------CGUUGC--------AGGGGGAA---GC---GCAAACCU-U-GGA--ACAGGGC-ACCCACCUAU-----GUGG--GAGCG----GGU--UCAAA--ACG--------AAGGCAUCG-ACGGCAC--GAUUGGGACUGGU
BA000004.3/1350679-1350867   AGAGUCCUGAG-GUGUACGUGCAUAACUGUAC------GUUU-UGA-GCCAACACUUUUGAAUAA-----GGGAGCUUGUUGU--CUCCUC-AUGGAUU-AC-AUGCCCUU--------------UCUCAUA-----GAUGAGGGAC---GU---AAGAAGUG-A-UGA--GCAGAGC-ACCCACCUGC----CGAG----GGCA----GGU--UCA-A--AAC------CAAAGUUUUCG-ACGGCAC--AUUUGGGACUCUU
AAZW01000077.1/13609-13792   UUUACCCUGGA-GUGUUUGUCAGAGGAUUCAC------GUCCCCGA-GCCGAUAAGCAAUCCCUAA----GGGUUAGUACUU----GAGUG-CUAUUGA-GC-AUGCUCGG---------------CCCGA---------CCGAGAA---GC---C-UACGGU-A-AUC--AUUGCUG-AUCCGCCUUG-----AAC---UCGCU----GGU--UCAAG--GGCC-----AUCUAUUCUCA-ACGGCAC---UUUGGGGUAUCC
CP000507.1/3260662-3260842   UGCUCCCUGGG-UUGUGCGCCAGCUGGUAAU-------GUCCCUGU-GCCGAUAUUUUUGACUUUA----GGGCAGGUGUUU----UACCG-ACAUUGA-GC-AGGCUCGG---------------CUCGU--------ACCGAGAA---GC---CUUAGGA--A-GUA--AUCGCAG-GCCCGCCUUG-----AAC----CUAC----GGU--UCAAG--GGCU-------ACACCGGCA-GCGGCAU---UCCGGGGAGCAU
CP000606.1/3644460-3644640   UGCUCCCUGUG-GUGUGCGUGAGUCGGUUAU-------GUCCCUGU-GCCGAUAUUUACAAACUCA----GGGUGAAUGUUU----UGAUG-ACAUUGC-GC-AAGCUCGG---------------CGCGA--------ACCGAGAA---GC---CUUAGG---A-UUU-GAUCAUUU-ACCCGCCUUG-----AAC----CUAC----GGU--UCAAG--GGCU-------ACACCGGUA-ACGGCAU---CUUGGGGAGCAA
CP000075.1/336144-335966     UGCUCCCUGGA-GUGCUUGCCAGUCGGUCAU-------GUCCCUGA-GCCGAUACGCACAACCAC-----GGGGGUUGCACGU---UGGGG-UUGGUGU-GC-AUGUCCG----------------CUCGA----------CGGAAA---GC---CUUAAAAC-C-UCC---UGCAAU-CUCCACCUUG-----AAC---UUUCG----GGU--UCAAG--GGCU-------AAACCGACA-GCGGUUC---GUCGGGGAGUCC
CP000002.3/2770276-2770080   AAAGUCCUGAU-GUGUUUGUUGUACACCUA--------GUUU-UGA--CCGAACAUUUUUUUACUU----GGGAGUUCGAUGU--UUCCGA-AUGGAGC-AA-AUGCCUCUUAU--------CACUCGUGUGC----UCAGGAGGAC---UU---GCAAAGUU-U-GGA--ACAGAAC-ACCCACCUGC----CGAG----AGCG----GGA--UCA-A--AACGA---AGGAAUACGACA-ACGGCAC--AAUCGGGACUUUU
AAWL01000035.1/260-442       AGUGCCCUGCU-GUGUUCGU--GUAAGCCCGGA-----UGUUUUGA-GCCAACACAUACACUAU------GGGAGCCUAACUC---UGAUU-AUGGCAU-GU-AUGCCCCAUA-----------CUCUUUU---------GGGGGAC---AC---AUAAAGUA-A-UCA--GGAGGGC-ACCCACCUGC----CGGG----GGCA----GGU--UCAAA--ACA--------ACGGCAAU--ACGGCAU---GGUGGGGACUUA
AE017340.1/2235806-2235990   GGUUUCCUGGG-GUGUUUGCCAGCAGGCUUAU------GUCCCUGA-GCCGAUGCUUGUAUUAAAA----GGGGAUCACUGGC------CU-GCCAUGA-GC-AAGCCCGG---------------CUUGA--------ACCGGGAA---GC---CUACGGCA-G-AUACCAUUUGCU-CCCCGCCUUG-----AAC----CAAU---GGGU--UCAAG--GGC------UACAGCCAGCA-GCGGCAC---CUUGGGAAGCCA
CP000764.1/1419388-1419571   CACAUCCUGCG-GUGUGCGUAACUCAUUUAU-------GUCU-AAA-ACCGAUGUUAGUAAUAA------GGAAGCUCAACAU--UUAGUU-AUUAUAA-UC-AAGCCUUC---------------CUUGU---------GGAGGAA---GA--UGUAUGGUA-A-CUG--UGAGGGC-AUCCACCUGC-----GAG---UAGCG----GGU--UUUUG--GAC------AUUUAGGAGGA-ACGGCAC--GUGCGGGGGUUUU
AADV02000115.1/4181-4364     GGAAAGCUGCU-GUGUUGGUGACUGCCAAUAAA----GUUUUUUGA--UCUAUGCUUUGAGUUUAA----GGGCGUUAACCA----GCUAU-CGUGGUA-GU-AAACCGAG---------------CUUGU--------ACUCGGAA---AC---AGAAACGA-UAAGC--GGUCGAU-ACCCACCUGG----UUCU----UCCA----GG---UCAUA--AACU---------GAGGUAAAACGGCAC---GGCGGUUUUUCA
AASA01000055.1/2997-3188     UCUUGCCUGGG-GUGUGCGUUACGAGUUAC--------GUCCCUGA-GCCGAUAAUUUGAAACUUU----GAGUUGGACAUCU---AAC-G-CUGGUGA-GC-AAGCUUACCCUAA-----UUUAAUUAGG--------AGUAAGAA---GC---CUAAAAGC-A-GUU--AAGUUUG-ACUC-CCUUG-----AAC----CGAC---UGGU--UCAAG--GACC-------AUUACUGGUAGCGGCAU---CUCGGGUCUUUA
CP000448.1/929295-929469     AAACCCCUGCU-GUGUGCGUGAAUAGCUGUUA------AGUU-UUU-GCCAACACAAAAAUUAA------GGGAACCUAUCUC---CGCCU-AUGGCUU-GU-AAGCCCGC----------------UUCU---------GUGGGAC---AC---AUUAAAUA-U-GCG--GGAGGGC-ACCCACCUGC-----UAA-----GCA----GGU--UAA-A--ACU--------ACGGCAUC--ACGGCUC---GGUGGGGUUUUU
AAVW01000041.1/27531-27348   GUUGCACUACG-ACGUUGGUGACUGCCAUCAAG----U-UUUUUGA-UCUAUGUCUUUAAAGAAAA---GGGAAGCUAACAA----GUCUC-GUGGC-A-GU-AAACCGGG---------------CGUGU--------ACCCGGAA---AC---UUAAAACGAA-GAA--AGUCGGC-ACCCACCUGG-----UUU----AACC----AGG--UCAUA--AA---------CUUAGGUAAAACGGCGU---UGCGGUGAACUU
ABCF01000001.1/315152-315339 UACAAGCUGCG-UUGUACGUAAUGAUAAUAA-------AGUUUUAA--CCUUUAAACUGUAAUA------GGGAGUUUUACAU---CGAAG-CCGGAAU-GUCAGGCCGCC---------------AUGGA--------UAGCGGAA--GAC---AAGAACGU-U-UCU---GCAAAC-ACCCACUUUG-----AGG----AGUGG--UGGU--UUAAA--ACUU----UCUUAGACGAUUUACGGCAA--AUGCGGCCUACAU
BA000022.2/1886880-1887065   AAGUAACUACC-GCGUUGGUGACUGCCAACAAC----GUUUUUUGA--UCUAUGCUUGAAAAAUAA----GGGUGUCUCUGUG--CAUUCUGCGUGGUA-GU-AGACCGGG---------------CUCGU--------ACCCGGAA---AC---GAAAACGA-G-AAU--UGAUGAC-UCCCCCCUGG----UUAC----ACCA----GG---UCAUA--AACU---------GAGGUAAAACGGCGU---GGUGGUGCUUCU
AAWF01000047.1/25976-26166   UUUACCCUGGGGGGGUUCGUCAGCGGAUUUAU------GUCCCUGA-GCCGAAUAAGCAACAUAAC---AGGGUUGGUAUUGG---GGUAG-CUAUUGA-GC-AAGCUCGG---------------CUUGU-------ACCCGAGAA---GC---C-UGCGGU-U-ACC--AUUACUGAUCCCGCCUUG-----AAC----CUGA---UGGU--UCAAG--GGCU-----ACGAUCCUUCA-ACGGCAU--UCCCGGGGUUCCC
CP000612.1/811548-811737     UUUACCCUGCU-UUGUGCGUGGGUUAUCUGG-------GGUUUUGA-GCCAACAUUUUGCAAAAC-----GGGAGUCCGGUUU--CACGCA-AGGAAAU-GU-AGACCUUA--------------CAUUGU--------AUAAGGAA---AC---AGGAAACU-G-CGG---AAGGGC-ACCCACCUGUU---GGAG----AACA----GGU--UCAAAAAACCU-----UAGGUAACAAACACGGCAU---GGUGGGGUUUCC
AAOX01000042.1/20660-20846   AGAGUCCUAAU-GUGUUCGU--UGUUUCACCUG----ACAUUUUGA--CCUAACAUUAUUCCUUC-----GGGAGCCCGGAUU---UCCUU-GCGGCGU-AA-ACGCCUCU----------------GGCU---------AGGGGAC---UU--ACAAAAGC--G-GGA--AUAGGGC-ACCCACCUGC----UGAG----UGCG----GGU--UCAAA--ACGAA---GGCAUCCAAGGCGACGGCAC--AAUUGGGACUCUU
CP000097.1/1017959-1018142   CAUGAACUGCU-GUGUUGGUGAAGGCCUUUUCUA---GUGCUCUGA-UCUGACUCUCUUUCGACUU----GGGGAGGCUGUC----GUGAC-GGUGA-C-GU-AAACCGGC---------------CUUGU--------AGCCGGAA---AC-----GAAGCC-C-CAC--UUUGACU-CCCCUUCUGG----UUAA----CUCC----AGG--UCG-A--CCAC-------AAUCGGUCACACGGCAU---GGUGGUUCACCC
CP000407.1/2019501-2019694   GAACUGCUGUG-GUAUACGA--AUUCAUACCUA----UGUGU-UGA--CCGACUAUUUUUGUAUUAC-UAGGGAGACAAAGAU--CCUCUA-ACAGUAU-GC-AAGCUGG----------------CACAC----------CCAGAA---GC--AACUAAGUU-A-GAA--ACGCGUC-ACCCACCUGC----UUUU----AGCGUGCGGGA--UCA-A--UACA-----AUCCAUGGAUAACCGGUACCAAUACAGCAUUUUU
AF269334.1/1264-1454         AGUCAUCUGUG-GUGUUCGUAAGUUUGCUUU-------UUAUUUGG-GCCUAACACUCUUUGAUCA----GGGAGCCCAAUAGGUUUUCUC-GCAGCGC-AC-ACGCCUC----------------UAUAG----------GAGGAC---UU---GCAAAACG-A-GAA--ACAGGGC-ACCCACCUGU----AUAU----AGCA----GG---CCGAA--UGAUCAAGCUAUUUAUAACU-ACGGCAU--CAACGGACUCUAU
AATP01000004.1/128564-128407 GGCGGGCUGGC-CGGUUCGACAGGCGUAACUAU-----UCCCCGGG-GCCUUAGUCAUUCCACA------GGGAGCUGUCCCU---GCCCU-UG------------CC------------------CGUG-------------GG---------------CUC-G-GGC--ACACGGC-GCCCACCUAC-----UUU-----GUA----GGU--UCCCG--GGAU-----CGACUUCGACCAUCGGCCG---GCUGGCUCGCCA
BA000028.3/1102945-1103130   UACAAGCUACA-UUGUUCGU-----AUUAAUAU----AAGUUUUAA--CCUCUAAUGUUGGAAUA-----GGGAGUUUUACAU---CGAAA-UUGGAAU-GCCGAGCCGCC---------------GUUGA---------AGCGGAA--GGC---AGGAAGUU-U-UCU---GCGAAC-ACCCACUUUG-----CGA----AGUGG--UGGU--UUAAA--ACUU----UUUAUUACAAGAUACGGCAA--AUGUGGCCUGUAU
AATN01002095.1/1924-2110     CGUCCUCGGCC-GUGUUCGAUAGCGGAUUCUUACA-UUUGCCCUGA-CCCUAAUUAACGACCCC------GGGCUCGUUACU----CCUUG-UUGGUGU-GC-AUGUCCGC---------------CCCGG-------UUGCGGAAA---GC---C-CGAUGC-G-AGG--UUCGCUG-GCCCACCUGA-----UCC-----UUG----GGA--UCAAG--GUC------GUUUGGUCCGCAACGGCAC---GGCGGAGGACUC
CP000110.1/1358428-1358245   AUUGAACUGCU-GUGUUGGUGACGGCCUUUUUCU--AGUGCUCUGA-UCUGACUCUCUUUCGACUU----GGGGAGACUGUC----GUGAC-GGUGA-C-GU-AGACCGGC---------------CAUGC--------AGCCGGAA---AC---GAAACCC----CAC--UUUGUCG-CCCCUUCUGG-----UUC----UUCC----AGG--UCG-A--CCAC-------UGGGGCUCGCACGGCAU---GGCGGUUCACCU
AAOK01000003.1/289953-289770 CUUGGACUACU-CAGUUGGUGAGAGCCUUUUUCU--AGUGCUCUGA-UCUGACUCUCUUUCGACUU----GGGGCAACUGUC----GUGAU-GGUGC-C-GU-AGACCGGC---------------CUCGU--------AGCCGGAA---AC-----GAAGCC-U-CAC--UUUGUCG-CCCCUUCUGG-----UAA----CUCC----AGG--UCG-A--ACAC-------UGGGGCUUGCACGGCUG---GGUGGUUCACCC
AP006716.1/1327404-1327594   AGUCAUCUGUA-UUGUUCGUACGUUUGCUUU-------UUAUUUGG-GCCUAACACUUUUUGAUCA----GGGAGCCCAAUAGGUUUUCUU-GCAGCGC-AC-ACGCCUC----------------AAUUG----------GAGGAC---UU---GCAAAACA-A-GAA--ACAGGGC-ACCCACCUGU----AUAU----AGCA----GG---CCGAA--UGAUCAAGCUUUUUAUAACU-ACGGCAA--UCACGGACUCUAC
AANO01000007.1/70904-70723   CUCGGACUGCU-GUGUUGGUGACUGCCUUUCAC----AGUUUCUGA-UCUGACUCCCUCUUCGACG---UGGGUGGUCUGUC----GCGAC-GGUGA-C-GU-ACACCGGC---------------CUCGU--------UGCCGGAA---AC-----GAAGCC-C-CGC--UUUGACU-GCUCCUCUGG-----UAC----UACC----AGG--UCGAA--CACU---------GGGGCAAGACGGCAC---AGCGGUUCACCC
AANP01000003.1/193518-193701 AGCGGACUGCC-GUGUUGGUGACAGCCUUUCUCU--AGUGCUCUGA-UCUGACUCUCUGUCGACUU----GGGGCGACUGUC----GUGAC-GGUGC-C-GU-AGACCGGC---------------CCAGC--------AGCCGGAA---AC-----GAAUCC-C-CAC--UUUGUUA-CCCCUUCUGG-----UUC----AUCC----AGG--UCG-A--UCAC-------UGGGGCUCGCACGGCAC---GGCGGUUCACCC
AP008934.1/1179168-1179359   AGUCAUCUGUA-GUGUUCGUAAGUUUGCUUCAU----AUU---UGG-GCCUAACACUCUUUGAUCC----GGGAGCCCAAUGGGUUUUCUU-GCAGCGC-AC-ACGCCUC----------------AUUUA--------G-GAGGAC---UU---GCAAAACA-A-GAA--ACAGGGC-ACCCACCUGU----UAUA----AGCA----GGC--CGAA---UGAUCA-AGCAUUUUAUAACUACGGCAC--UAACGGACUCUAU
AE013598.1/1156001-1155818   CGUUCUCUGCU-GUAAACGACAGCGUGCAAAACA--UUCGCCUUGU-CCCUUAAUUACGACCAC------GGGGGCGCGACG-----GAGC-CGGGUGU-GC-AGGUCCGC---------------CUUGU--------AGCGGGAA---GC---CCGAUGGC-C-UC---ACAACGU-CCCCA-CUUG-----AAC----CCCG----GGU--UCAAG--GUC------GUUUCGCCCGCAUCGUCAU---GGCGGAGAAUGC
CP000576.1/657516-657700     AGAUUACUGGA-UCUUUGGUUAAGUUCUUCUUUA--UGUGCUCUGA-UCUGACUCUCUUUCGACAU----GAGGAGACUGUC----GUGAU-GCGGU-A-GU-AAACCGAU---------------CUUGU--------AAUCGGAA---AC---G-AAAGCC---CAC--UUUGAAU-CCUCUUCUGG-----CAU----UUCC----AGG--UCGAU--GCAG-------CAGAGAACUGACGGGGA---UCCGGUAUUACC
CP000419.1/1793770-1793575   AAAUUGCUGUG-GUAUACGA--AUCCACAUAUA----AGUGU-UGA--CCGACUAAUUUUUGUAUUA-UCGGGAGACAGAGGU--CUAUUA-ACAGUGU-GC-AGGCUGG----------------CUCAC----------CCAGAA---GCA-ACUGAAGUU-A-GUA--GCGAGUC-GCCCACCUGCUUUUUUACG--UCGCG----GGU--UCA-A--UACA-----AACUGUGGAUCAUCGGUACCAAUACAGCA-UCCA
AAAM03000019.1/57691-57877   CGUUCUCUGCU-GUGAACGACGGCGCGUGCAAACAUUUAGCCUUGU-CCCUUAAUCACGACCAA------GGAGGCGCGAC-----GAUAC-CGGGAGU-GC-AAGUCUGC---------------CUUAG-------GAGCGGAAA---GC---C-CAAUGG-U-AUU--UCAACGC-CUCCA-CUUG-----AAC----CACU----GGU--UCAAG--G-UC-----GUUUCGCGAGCAUCGUCAU---AGCGGAGAAUGC
CP000553.1/685817-685998     CCAGUACUGCU-UUGUUGGUAUAGGCCUUCUCAA---GUGCUCUGA-UCUGACUCUCUUUCGAUUU----GGGGAAGCUGUC----GUGAA-AGUGA-C-GU-AUACCAG----------------CUUGU--------U-CUGGAA---AC-----GAAGCU-C-CAC--UUUGAAU-CCCCCUCUGG-----UUC----UUCC----AGG--UCGAU--GC-------UUCUUGGGCCUUACGGCAA---AGCGGUACUUCC
AE017126.1/924642-924462     AGAGAACUGUU-UUGUUGGUGAUGACCUUUUAAG---UGC-UCUGA-UCUGACUCUUUUUCGACUU----GAGGAGACUGUU----GUUAU-CGUGA-A-GU-AAACCAGU---------------CAUGC--------AACUGGAA---AU-----GGAUCA-U-UAC--UUUGACU-CCUCUUCUGG-----CUU----AUCC----AGG--UCGAA--CGCU---------UAGGUCACACGGCAA---AAUGGUUCUAUA
CP000463.1/5354265-5354106   GCGAGGCUGCG-CUGCGCGUCAGGAGCCAAUA------UCCCCGGG-GCCUUAUCGAUCCUUAA------GGGAACUGUCCC----UGG-----------------CCGGG---------------UCCGUG------GACCCGG---------------------UCA---CAUGGU-GCCCACCUAC-----UUU----CGUA---GGGA-ACUCCG--GGAU-----CGAGCGCUUCA-ACGGCAG--CUGUGGCUUCGCG
BA000039.2/659756-659570     GUUUAGCUGCG-ACGUUGGUGACUGCCAAUAUUG---UUUUG-UGA--UCUACACUUGCAAAACAUU--UGGGAAUCAAUAC----UGUGG-GCGGC-A-GU-AAACUGGU---------------CUUUG--------AGCCAGAA---AC--UUCUAAGUC-U-GCA-GUUAGUAU-UCCCCCCUAGU---UUUU----ACUA----GG---UCA-U--AAAC--------UGAGGUAAAACGGCGU---CGCGGUUAGACU
AAUA01000002.1/251304-251487 GUCGGACUGCU-GUGUUGGUGACGGCCUUUUCUA---GUGCUCUGA-UCUGACUCUCUAUCGACUU----GGGGCGACUGCC----GUGUC-GGUGC-C-GU-AAACCGGC---------------CUUGU--------AGCCGGAA---AC---GAAUCCCC-A-CUU---UUGUUA-CCCCUUCUGG-----UUC----UUCC----AGG--UCG-A--UCAC-------UGGGGCUCGCACGGCAU---GGUGGUCCCCCA
BA000040.2/1665066-1665226   GCGAGGCUGCG-ACGCGCGUCCGGAGCCAUAUA-----UCCCCGGG-GCCUUAUCGAUCCUUUA------GGGAACUGUCCCU--G-------------------GCCGGG---------------CCCGUG------GGCCCGGAC------------------------AUAUGGU-GCCCACCUAC-----UUU----CGUA---GGGA-ACUCCG--GGAU-----CGAGUGCUUCA-ACGGCGU--CCGCGGCUUCGCA
CP000524.1/206871-206710     GGUGUUCUGCU-CUUCUCGACAGGAAAUACAGAC---AUUCCCGGG-GCCUUAUUGAUUCCUAA------GGGAGCUGUCCCU---GAGAA-AG------------CC------------------CGUG-------------GG---------------CUU-U-UUC--AUAUGGC-GCCCACCUAC-----UUG----UGUA----GGU--UCCCG--GAAU-----CAGACUUUUCCAUCGGUCG--CUGCGGUUCACCA
CP000148.1/31807-31627       UUCUCUCUGCC-AUGCGCGUCAGGCUGAUAU-------GCCC--CA-GCGGAACAUUUACGUAAGA---CGG--GGGUUCUUU---CUACC-GUGGUGU-GC-UGCCCCA----------------UCAUG----------UGGGAUU-UGC---CUGAAGCG-G-UAC--AGAGCCU--GCCACCUGU-----AAG---GAACU----CGC--UGU-G-AGGCC-----CUUACAAGCCA-ACGGCAU---GGUGGAGGGAUU
AAXV01000007.1/159165-159357 UAAAGGCUGCA-UUGUUCGUAUAAUAUUAA--------GUUU-UAA--CCUUUAAGCUGUAAAA------GGGAGUUUUAUUA--UUGGAG-UUGGAAU-GACGGGCCUCACA-----------CUACUGUG------CAUGAGGAUA-AGC---AGGAAAAC-U-UCU---GCGAAC-ACCCACUUUG-----AGG----AGUGG--UGGU--UUA-A--AACUU---UCUAUAAUAACU-ACGGCAU--ACGCGGCUUUUUA
AM236080.1/4231502-4231344   UGCGGUCUGCG-CCUCUCGACAGGAACCACAA------UCCCUGGG-GCCAUACUCGAUCCAAA------GGGAGCUGUCCCU--G-------------------GCCAGG---------------CCCGUG------GGCCUGGAC------------------------ACACGGC-GCCCACCUAC-----GUU----UGUA----GGC--ACCCA--GGAU-----CGUAAACAUCCAUCGGUGG--UCGUGGAUCGCAC
CP000115.1/2966805-2966646   GCGAGGCUGCG-CCGCGCGUCAGAAGCCACAA------UCCCCGGG-GCCUUAUCGAUCCUUAA------GGGAACUGUCCCU---GGUCG-GG------------UC------------------CGUG-------------GA---------------UCC-G-GCC--AUAUGGU-GCCCACCUAC-----UUU----CGUA---GGGA-ACUCCG--GGAU-----CGAGCGCUUCA-ACGGCGG--UCGCGGCUUCGCG
CT978603.1/1256376-1256194   UUCGGACUGCU-GUGUUGGUGUUUGCCCUGCCAA--GUGUUCU-GA-UCUGACUCCCUUUUCGACU---UGGGGGAGAUGUC----CCGGA-AGUGA-C-GU-AGACCGGC---------------CCAGU--------AGCUGGAA---AC-----GAAGCU-C-CGC--UUUUCUC-CCCCUUCUGG-----UUU----AUCC----AGG--UC--G--AACC-----UCAGGUCAUC--ACGGCAC---GGCGGUCCACCC
AAMY01000003.1/191244-191085 GCGAGGCUGCG-ACGCGCGUCAGGAGCCACAA------UCCCCGGG-GCCUUAUCGAUCCUUAA------GGGAACUGUCCCU--G-------------------GCCGGG---------------UCCGUG------GACCCGGAC------------------------AUAUGGU-GCCCACCUAC-----UUU----CGUA---GGGA-ACUCCG--GGAU-----CGAGCGCUCCA-ACGGCGA--UUGCGGCUUCGCG
CP000111.1/646219-646403     AAGUCACUGGA-UCUUUGGUUAAGUUCUUCUUUA--UGUGCUCUGA-UCUGACUUUCUUUCGACGU----GAGGAGACUGUC----GUGAU-GCGGU-A-GU-AAACCGAU---------------CUUGU--------AAUCGGAA---AC---G-AAAGCC---CAC--UUUGAAU-CCUCUUCUGG-----CUU----UUCC----AGG--UCGAU--GCAG-------CAGAGAACUGACGGGGA---UCCGGUAAACCU
AACV01012376.1/1014-1199     CGUUCUCUGCG-GUACUCGACGGCAUGUGCAAACA-UUCGCCUUGU--CCCUUAAGAACGACACC-----GGGAGCGCGAC-----AGCGC-CGGGAGU-GC-AGGUCCGC---------------CUUGU--------AGCGGGAA---GC---C-CGAUGG-U-UCU--CCAGCGU-UCCCACUUGA-----GCC----CCCG----GGU--UCAAG--GUC------GUUUCGCAUGCAUCGACAU---UGCGGAGAAUGC
CP000390.1/3466517-3466361   AGCGGUCUGCG-CCUCGCGACAGGAAUUCAAU------UCCCCGGG-GCCUUAUCGAUCCUCUA------GGGAGCUGUCCCU---GGCCU-UG------------CC------------------CGUG-------------GG---------------CUU-G-GCC--ACACGGC-GCCCACCUAC-----UUU-----GUA----GGU--UCCCG--GGA------UCGGUCAUUCCAUCGGUUG--UCGUGGAUCGCUG
CP000482.1/2822559-2822381   UUCUCCCUGUC-CUGUUCGACGGCUGUAGU--------GCC--CGG-GCGGAAUAAACAAUGAAC-----GGGAGACCAUUC----UUGUC-GUGGUGU-GC-UGCCCCA----------------UUGCG----------UGGGAUU-UGC---CUGAAGCG-G-CAU---AUGGUC-GCCCACCUGU----UAAG---GAACU----CGC--CGGA---GGUC-----CUUUUAGGUUG-ACGGCAG---GACGGGGAGAGU
CP000781.1/3399714-3399867   GCGGGGCUGCG-GGGCACGUUAGGAGACAUU-------UCCCCGGG-GCCUUAUCGAUCCUUAA------GGGAGCUGUCCCU--G-------------------ACCUCGU-------------CCCUGG--------ACUUGGAC------------------------ACACGGC-GCCCACCUAC-----GUU-----GUA----GGU--UCCCG--GGAU-------CGAACUCCG-ACGGCUU--CUGUGGCUCCGCA
AM167904.1/3157669-3157484   UUGUCCCUGCG-GUGCUCGUGACUUGGCCAUACA---UUCUCU-GA-ACCGAUGCUUUUCGGCAUAC--UGGUUGCGGGAGU----GUCGA-GCGGG-U-GU-GA-UCGUCU-------------CUUUGC--------UGACGA-----AC---CCGAUGCU-C-UUC--GGAUCGC-GACCACCUUG-----AAC----CUAU---GGGU--UC--G--AGAU-----GCCGGCC--UAGACGGCAC--UUGCGGGGCAUCU
BA000012.4/3164455-3164300   GACGGUCUGUG-CUUCCCGGCAGGAGAACAUUU-----UCCCCGGG-GCCUUAACGAUCCUUA-------GGGAGCUGUCCCU---GGGAA-GA------------CC------------------CGUG-------------GG---------------UUU-U-CUC--ACACGGC-GCCCACCUAC-----UUU-----GUA----GGU--UCCCG--GGAU-----CGCUCUCUCCA-CCGGUUG---UGUGGAUCGUCA
CP000435.1/1304306-1304119   AGAGAACUGCU-GUGUUGGUGACAGCCUUUCUCU--AGUGCUCUGA-UCUGACUCUCUUUCGACAU----GGGGUGACUGUC----GUGCU-GGUGC-C-GU-AAACCGGU---------------CUCGU--------AACCGGAA---ACG-AAUCCUCUC-G-AAA--UCUUUCG-CCCCUUCUGG-----UAA----CUCC----AGG--UCG-A--CCAC-------AGAUUGGCGCACGGCAU---GGUGGUUCAACC
CP000319.1/3880876-3880716   GCGAGGCUGCG-ACGCGCGUCAGGAGCCACACA-----UCCCCGGG-GCCUUAUCGAUCCUUCA------GGGAACUGUCCCU---GGCCG-GG------------UC------------------CGUG-------------GA---------------UCC-G-GUC--AUAUGGU-GCCCACCUAC-----UUU----CGUA---GGGA-ACUCCG--GGAU-----CGAGCGCUCCA-ACGGCGA--UUGCGGCUUCGCA
CU234118.1/1211196-1211357   GCGAGGCUGCG-ACGCGCGUCCGGAACCAACAU----AUCCCCGGG-GCCUUAUCGAUCCUUAA------GGGAACUGUCCCU--G-------------------GCCAGG---------------UCCGUG------GACCUGGAC------------------------AUAUGGU-GCCCACCUAC-----UUU----CGUA---GGGA-ACUCCG--GGA------UCGAGCGUUUCAACGGCGA--UUGCGGCUUCGCU
CP000283.1/4650246-4650087   GCGAGGCUGCG-UUUCGCGUCAGGAGCCAUAA------UCCCCGGG-GCCUUAUCGAUCCUUAA------GGGAACUGUCCC----UGG-----------------CCGGG---------------UCCGUG------GACCCGG---------------------UCA---CAUGGU-GCCCACCUAC-----UUU----CGUA---GGGA-ACUCCG--GGAU-----CGAGCGCUUCA-ACGGUCA--UCGUGGCUUCGCA
AAAP01001314.1/649-805       GCGGGGCUGCA-GAGUUCGUCAGGAGAACUU-------UCCCCGGG-GCCUUAUCGACUCCCUC------GGGAGCUGUCAC----UGG-----------------CCUCG---------------UCCGUG------GACUUGG---------------------CCA--ACACGGC-GCCCACCUAC-----UCU-----GUA----GGU-AUCCCG--GGAU-------CGACACUCCAACGGCUC--ACGUGGCUCCGCA
CP000738.1/2752042-2751884   UGCGGUCUGCA-CUUCUCGACAGGAACCACAA------UCCCCGGG-GCCAUACACGAUCUCAA------GGGAACUGUCCCU--G-------------------GCCGGA---------------CCCGUG------GGUCCGGAC------------------------AUACGGU-GCCCACCUAC-----CUA-----GUA----GGU--ACCCG--GGAU----CGUAAAAAAUCCAUCGGUCG--UUGUGGAUCGCGC
AAPJ01000002.1/435351-435507 GACGGGCUGCG-CGGUGCGCCAGGAGUAACAUA-----UUCUCGGG-GCCUUAGUCAUUCCUA-------GGGAGCUGUCCCU---GCCUU-GG------------CC------------------CGUGG------------GC---------------CUG-G-GGC--ACACGGC-GCCCACCUAC-----UCU-----GUA----GGU--UCCCG--GGAU-----CGACAUCUCCA-UCGGCCG---GGUGGCUCGUCA
CP000552.1/686863-687046     UAAGUACUGGA-UCUUUGGUUAAGUUCUUCUUUA--UGUGCUCUGA-UCUGACUCUUUUUCGACUU----GAGGAGACUGUC----GUGAU-GUAGA-C-GU-AAACCAAU---------------CAUGU--------AAUUGGAA---AC---G-AAAACC---CAC--UUUGACU-CCUCUUCUGG-----CUU----UCCC----AGG--UCGAC--GCUC--------AGAGGACUGACGGGGA---UUCGGUGUAAAG
CP000698.1/4969602-4969428   UUCUCUCUGCC-CUGUUCGUGAGGUUAGUAC-------GCCC--CU-GCGGAAUAAUCGAAGAAC-----GGGAGCCUUUUU----AAACU-GUGGUGU-GC-UGCCC------------------CUUGC------------GGGAUUUGC---CUGAAGCA-G-UGU---AAAGGA-GCCCACCUAU-----UAGG--GAACU----CGC--UGU-G-AGGCC---------CCGAACCAACGGCAU---GGUGGAGAGAAU
CP000133.1/3679725-3679567   UGCGGUCUGCG-CCUCUCGACAGGAACCACAA------UCCCUGGG-GCCAUACUCGAUCCAAA------GGGAGCUGUCCCU---GUCUG-GG------------CU------------------CGUGG-------------G---------------CCU-G-GAC--ACACGGU-GCCCACCUAC-----GUU----UGUA----GGC--GCCCA--GGAU-----CGUAAACAUCCAUCGGUCG--UCGUGGAUCGCAC
AAUW01000002.1/210754-210600 UUGCGGCUGCC-CGAUACGUCAGGAACAUUA-------UCCCCGGG-GCCUUACGCAUUCCCUU------GGGAGCUGUCCCU---GCGCU-GGGCC-----------------------------GUGGU-----------------------------CCG-U-UGC--AAACGGC-GCCCACCUAC-----AUA-----GUA----GGU-UUCCCG--GGA------UUGCAAAUCCA-ACGGUCG---GGCGGCUGCACG
CP000774.1/2293600-2293756   CGGGAUCUGCC-CGGCGCGUUAGGAACACAUA------CUCUCGGG-GCCUUACGGUCCUCAA-------GGGAGCUGUCCCU---GAGGG-AGACU-----------------------------GUGGU-----------------------------CUU-C-UUC--ACACGGC-GCCCACCUAC-----GUU----AGUA----GGU--CUCCG--GGG------AACGAAGUUCCGACGGCCG--UGGCGGACCCACU
CP000943.1/3397496-3397653   GCGGGGCUGCG-GGGUGCGUCAGGAGACACAUA-----UCCCCGGG-GCCUUAUCGACUCCCUC------GGGAGCUGUCCCC-----------------GC----CCUGG---------------UCCGUG------GACCGGG-----GC---A----------------CACGGC-GCCCACCUAC-----GCU-----GUA----GGU-UUCCCG--GGAU-------CGAUCCUCCAACGGCUU--UCGUGGCUCCGCG
CP000563.1/698015-697835     UGCUCCCUGGG-AUGCAUGCCAACUGGUAAU-------GUCCCUGU-GCCGAUAAUUUUUAUCUCA----GGGUGAAUGCUU----UACUG-ACAUUGU-GC-AUGCUCGG---------------CUUGU--------ACCGAGAA---GC---CUUAGGA--G-GUA--AUCAUUU-ACCCGCCUUG-----AAC----CUAC----GGU--UCAAG--GGCU-------ACACCGGUA-GCGGCAU---UCUGGGGAGCAU
AE007870.2/814010-813852     UGCGUUCUGCG-CUUCCCGACAGGAACCACA-------AUCCCUGGGGCCAUACUCGAUCCAAA------GGGAGCUGUCCC------------------UG---GCCAGU---------------CCUGUG------GGACUGGA----CA--------------------CACGGC-GCCCACCUAC-----UUU----UGUA----GGC-ACCCAG--GAUC-----GUAAAUCUCCA-UCGGUCG--CCGCGGAUCGCAC
CP001233.1/2595247-2595430   UUUACCCUGGG-GUGUUCGUCAGCGGAUUUAU------GUCCCUGA-GCCGAUAAGCAACAUAACA----GGGUUGGUAUUG----GGUAG-CUAUUGA-GC-AAGCUCGG---------------CUUGU--------ACCGAGAA---GC---C-UGCGGU-U-ACC--AUUACUG-AUCCGCCUUG-----AAC----CUGA---UGGU--UCAAG--GGC------UACGAUCCUCA-ACGGCAU---CCCGGGGUUCUC
CP000924.1/1101622-1101804   AAAGCCCUGUG-GUGUACGUGAGGUCCGGUGAA-----AGUU-UGA-GCCAACACCAAUAAUAA------GGGAGCCUGGGCU--UUGGCA-GUGGAAU-AU-AGGCCGU----------------CUUCG--------A-ACGGAA---AU---AUGAAGCU-G-CCA--AGAGGGC-ACCCACUUUG----UGAG----UCCG----GGU--UCAAA-AACU------ACCGGGAGGC--ACGGCAC---UAUGGGGUUUUU
AAGD02002558.1/1673-1492     ACAACUCUAGG-GUGUUCGCCAGUACGUCUAUU----CCCC--UG---CCGAUACUUAAACUUAU-----GGAUGUGUUCUG----UAUAU-UUUGAGU-GU-AUGCCCAC---------------CUUGA---------GUGGGAA---AU---CCAUUAAG-U-GUA---CGUCGC-GUCCACCUUG-----AACU--CUUCG----GGU--UCA----GGGU-----AACGACCAUGCAACAGCAU--CUCGGGAGUGUUU
AL009126.3/2096113-2095927   AAGAAGCUACU-UUGUGCGU--AUUGUUAAUU------AAGUUUUA-ACCUUUAAGCUGUAAUA------GGGAGUUUUAUAU--C-GAAG-CCGGAAUGUC-AUGCCUCC---------------AUUGC---------AGAGGAC---GA--CAGGAACGU-U-UC---UGCAAAC-ACCCACUUUG-----AGG----AGUGG--UGGU-UUAAAA--CUU------UCUUACUUGCAUACGGCAAG-ACGUAGCGAAAGC
CP001124.1/290243-290062     CUCUCUCUGCC-CUGUCCGUGAGGUUACUAAC------GCCC--CU-GCGGAAUAAUUUAUUGAAC----GGGUGACUGUUU----CGACC-GUGGUGA-GC-UGCCCCA----------------UUGCG----------CGGGAAU-UGC---CUAAAGCG-G-UCC---ACAGGA-GCCCACCUGA-----AUGG--GAACU----CGC--UGU-G-AGGC------CCCCGAAACCA-ACGGCAC---GGCGGAGAGAGU
CP000826.1/4345485-4345667   AUUUCUCUGAG-AUGUUCGCCAGCGGGCCAGU------CCC-CUGA-GCCGAUAUUUAGUACCAAC---AGAAUGUGAUGAUC---CGCGA-UCGGUGU-GC-AUGCUCGG---------------CCCG----------CCGAGAA---GC---CUUAAGAU-U-GCG--ACAGCAC-GUUCACCUUG-----AAC----CAUG----GGU--UCAA---GGGU-----UACAGCCUGCG-ACGGCAU---CUCGGAGAUUCC
AL009126.3/2814682-2814490   AAAGUCCUGAU-GUGUUAGUUGUACACCUA--------GUUU-UGA--CCGAACAUUUUUUUGAUU---UGGGAGCCCGCAUU---UUUAA-AUGGCGU-AC-AUGCCUCUUU----------UCAUUCGGU------AAAGAGGAC---UU---ACAAGAUU-U-AAA--AGAGGGC-ACCCACCUGC----UGAG----AGCG----GGU--UCA-A--AAC-A--AAGGAAAGCUGCA-ACGGCAC--UAUUGGGACUUUA
CP000057.2/971464-971661     AAUUACCUGGA-GUGUUCGUCAGUAGGCUAU-------GUCCCUGA-GCCGAUACUUUAAAUCUUA---UAAAUUGGUUUCC----UAUCG-UUGGUGU-GU-AGGCUUAACCUUUGA-CUCGUUCAUUGG--------GCUAAGAA---AC---CUGAAAAC-G-GUA--UCAACUG-AUUU-CCUUG-----AAC----CGUC---GGGU--UCAAG--GAC------UACUGCCCGCA-GCGGCAC---UCUGGGUCCUAU
CP000020.2/2339101-2339281   UUUACCCUGGA-GUGUUUGUAGGCGGAUCUAU------GUCCCUGA-GCCGAUAAGCACAAAUUA-----GGGUUAGUACUU----GUUUG-CUAUUGA-GC-AUGCUCGG---------------CUUGU--------ACUGAGAA---GC---C-UACGGU-A-AAC--UUUGCUG-AUCCGCCUUG-----AAC----CUAG----GGU--UCAAG--GGCU-------ACGACCACU-ACGGCAC---UUUGGGGUAUUC
AE008691.1/1726945-1726768   AAGUUCCUGUG-GGGUUUGUAGCGGGCUAAUUU-----GUUU-UCA-CCCAACGCAACCCAUAC------GGGAAUCCGGGUU---CAUCA-GUGGAUG-AA-AUGCCUGG----------------GAAA---------CCAGGAC---UU---CAGAAGCU-G-GUG--ACAGGGU-ACCCACCUGC-----GAG----AGCA----GGG-AUGA-A--AAC----------AUAGCCGUACGGCUC---CGUGGGUAAAGU
CP000903.1/1546247-1546430   AAAUUCCUACG-GUGUACGUAGCUUGUGUAU-------GUCU-UAA-ACCAAUAAGUAUAAUGC------GGAAGUUCAAUAU--UUAAAU-GUAGAUA-GC-AGGCCAUC---------------UUUUU-------AAGAAGGAA---GU---UACAAACA-U-UUG--UGAGAAC-AUCCACCUGU-----GAG----AGCA----GGU--UUAUG--GAC------AUCUAUAGAUA-ACGGCAU--AUGUGGGACUAUA
CP000878.1/704395-704578     UUUGGACUACC-UUGUUGGUGAAGACCUUCCUUA--AGUGCUCUGA-UCUGACUCUUUUUCGACUU----GUGGAGACUGUC----GUGAC-GGUGA-A-GU-AAACCAGU---------------CUAGU--------AACUGGAA---AU---G-GAACC--U-CGC--UUUGACU-CCUCUUCUGG-----UUA----AUCC----AGG--UCGAU--GCUC--------UGAGGUCUCACGGCAA---GGUGGUCUUGUA
CP000050.1/1085473-1085290   CGUUCUCUGCU-GUGAACGACGGUGUGCAAAACA--UUCGCCUUGU--CCCUUAAUUACGACCAC-----GGGGGCGCGACG-----AAGC-CGGGAGU-GC-AAGUCCGC---------------CUUGU--------AGCGGGAA---GC---C-CGACGG-C-CU--AACAACGU-CCCCA-CUUG-----AAC----CCCG----GGU--UCAAG--GUCG-----UUUCGCACAC-AUCGUCAU---GGCGGAGAAUGC
BX548174.1/652620-652804     UACAUACUGGA-UCUUUGGUCAAGUUCUUCUUUA--UGUGCUCUGA-UCUGACUCUUUUUCGACUU----GAGGAGACUGUC----GUGAU-GUAGA-C-GU-AAACCAAU---------------CCUGU--------AAUUGGAA---AC---G-AAAGCC---CAC--UUUGACU-CCUCUUCUGG----CUUU----UCC-----AGG--UCG-A-UGCAU-------CAGAGAACUGGCGGGGA---UUCGGUGUUACC
AE004439.1/1932211-1932030   GAUUACCUGAG-GUGUUUGCCAGUGGGUUAU-------GUCCCUGA-GCCGAUACUUUUAUUUUAU----GAAUCGGUUUCU----AAUUG-UUGGUGU-GC-AUGCUUAG---------------CUUGA---------CUAAGAA---GC---CUAAAAAU-A-GUU--AUAACUG-AUUC-CCUUG-----AAC----CGUU---GGGU--UCAAG--GACU-----G--AGACUUGCAGCGGCAU---CUCGGGUUCUUC
CP000821.1/4485692-4485873   UGCUCCCUGGU-AUACGCGUCAGUCGGCAAU-------GUCCCUGU-GCCGAUAUUUACAAACCCA----GGGUGAAUGCUU----UAUUG-ACAUUGU-GC-AAGCUCGG---------------CUCGU--------AUCGAGAA---GC---CUUAGGAU---AUA--AUCAUUU-ACCCGCCUUG-----AAC----CUAC----GGU--UCAAG--GGC------UUACGCCGGCA-ACGGUAU---UUUGGGGAGCAA
BA000034.2/1725130-1725326   ACAUUGCUGUG-GCAUACGA-AUCCACAUCUAA-----GUGU-UGA--CCGACUAUUUCUUUGUAUUUUCGGGAAACAAAGAC---UCUUU-CUAGUCU-GC-AAGCCGU----------------UUCAC----------GCGGAC---GCAACUUCCAAGA-A-AGA--GCGCGUU-ACCCACCUGCU--UAUAC----UGCGC--GGGC--UCA-A--UAC-A---AAAACGUGGAUCACCGGUGCCAAUACAGCAUUCUU
AE005176.1/34739-34931       AAAGCACUGG-AAUGUGCGAGCUCUUUCAUUUU----U----UUGA--CCGACUAUAUUUGUAUUGCAUAGGG-GUUCAUGAGA-CAUUCG-GUAGCGUA---AUACCUCG---------------AACGAA-----AGUAGGGGAA--G-----CUGAUGC--G-AAG--CGAGAAC-ACCCACCUGGC---GUUU---UAGCG----GGU--UCAA---UAC------ACGGAAGAGCAUACGGCAUUCAAUCAGUGUUUUU
AE008923.1/4015282-4015465   CGUUCUCUGCG-GUAAACGACAGCGUGCAAAACA--UUCGCCUUGU--CCCUUAAUUACGACCAC-----GGGGGCGCGAC-----GAAGC-CGGGUGU-GC-AAGUCCGC---------------CUUGU--------AGCGGGAA---GC---C-CGAUGG-C-CUC--ACAACGU-CCCCA-CUUG-----AAC----CCCG----GGU--UCAAG--GUCG-----UUUCGCCCGC-AUCGUCAC---GGCGGAGAAUGC
CP000923.1/1508100-1508282   AAAGCCCUGUG-GUGUACGUGAGGUCCGGUGAA-----AGUU-UGA-GCCAACACCAAUAAUAA------GGGAGCCUGGGCU--UUGGCA-GUGGAAU-GU-AGGCCGU----------------CUUUG--------A-ACGGAA---AC---AUGAAGCU-G-CCA--AGAGGGC-ACCCACGUUG----UGAG----GACG----GGU--UCAAG-AACU------ACCGGGAAGC--ACGGCAC---UAUGGGGUUUUU
BX548175.1/727040-727223     CUUGAACUGCU-GUGU-UGGUGACGGCCUUUUUCU-AGUGCUCUGA-UCUGACUCUCUUUCGAUUU----GGGGAGGCUGUC----GUGAA-GGUGA-C-GU-AGACCGGA---------------CUUGC--------UUCCGGAA---AC---G--AAGCC-C-CAC--UUUGCUU-CCCCUUCUGG-----UUC---UUCC-----AGG--UCG-A--ACAC-----U--GGGGCUCGCACGGCAU---GGCGGUUCACCU
CP001037.1/5114015-5113832   GUUGCACUACG-ACGUUGGUGACUGCCAUCAAG----U-UUUUUGA-UCUAUGCCUUUAAUGACAA----GGGAGUCAACUG----UUCUC-GUGGC-A-GU-AUACCGGG---------------CAUGU--------ACCCGGAA---AC---UUUAAACG-A-GGA-AUUUAGGU-UCCCACCUGG----AUAA----ACCC----AGG--UCAUA--AA---------CUUAGGUAAAACGGCGU---CGCGGUGAACUU
AM939562.1/1-159             GGCGAUCUGCG-CUUCCCGACAGGAACCACAA------UCCCCGGG-GCCAUACACGAUCUCAA------GGGGACUGUCCCU--G------------G-------CCGGA---------------CCCGUG------GGUCCGG------------GCA------------UACGGU-GCCCACCUAC-----CUA-----GUA----GGU--ACCCG--GGAU----CGUAAAUCAUCCAUCGGUCG--UCGUGGAUCGCAC
AE008917.1/324738-324896     GGCGAACUGCG-CUUCCCGACAGGUGUAACAGC----AUCCCCGGG-GCCUUAUUGAUCUCUAA------GGGAGCUGUCCCU---GUGAA-GG------------CU------------------UGCGG-------------G---------------CUU-U-CGC--AUAUGGC-GCCCACCUAC-----UUU-----GUA----GGU--UCCCG--GGAU-----CAAUCACUACCAUCGGCCG--UCGUGGU-CGCCG
CP000851.1/4051647-4051828   UGCUCCCUGGG-AUAUUCGCUAGCUGGUAAU-------GUCCCUGU-GCCGAUAAUUACAAACCCA----GGGUGAAUGUUU----UACUG-ACAUUGU-GC-AAGCUCGG---------------CUCGU--------ACCGAGAA---GC---CUUAGGA--G-GUA--UUCAUUU-ACCCGCCUUG-----AAC----CUAC----GGU--UCAAG--GGCU-----ACACCAGCGG--UCGGUAU---UCUGGGGAGCAA
CP001390.1/479177-479352     UUCUCUCUGCC-CUGUUCGUGAGGUAUUAAA-------GCCC--CU-GCGGAAUAAUCAUUGAAC-----GGGCGCCUUUUU----AAGCU-GUGGUGU-GC-UGCCCC-----------------UUUGC-----------GGGAAU-UGC---CUGAAGCA-G-CAU--UAAAGGA-GCCCACCUGU-----UAGG--GAACU----CGC--UGU-G-AGGCC----------CCGACCAACGGCAU---GGUGGAGAGAUA
AE008691.1/1234385-1234567   AAAACCCUGUG-GUGUUCGUGUGACCCGGUGAA-----AGGU-UGA-GCCAACACCAAAAAUAA------GGGAGCCUGGGCU--UUGGCA-GUGGAUU-GU-AGGCCGC----------------CUCGU--------C-GCGGAA---AC---AUGAAGCU-G-CCA--AGAGGGC-ACCCACUUUG----UGAG----GACG----GGU--UCAAA-ACCU------ACCGGUAGGC--ACGGCAC---UAUGGGGUUUUU
CP002469.1/514264-514080     UUUACCCUGGA-GUGUUUGUCAGCCGGAUUAAA-----GUCCCUGA-GCCGAUAAGCAACACCAAA----GGGUUGGUACUU----GAUCG-CUAUUGA-GC-AAGCUUGG---------------CCCGU--------ACCGAGAA---GC---C-UACGGU-A-AUC--AUUGCCG-AUCCGCCUUG-----AAC---CAGCU----GGU--UCAAG--GGC------CACAAUCCGCG-ACGGCAC---UCUGGGGUAUCC
CP002222.1/2091393-2091580   AAAUUACUAAG-GUGUGCGCAUUGCUCUAAACAA---AGUGU--UG--CCGAACAAUUAAUACUACU-UUGGGAUGUCCGUUA--GCUAAU-UCCAU-A-AC-AUGCCUU----------------AUCCU----------UUGGUA---GU----UAGCGAA-U-UAG-UCAGAACG-UCCCACCUGCC---UUAA----AGCG----GG---UCA-A--UAC-----UGAAGGGCGAUUAACGGCAC--CACUAGUUUUUCC
CP003056.1/2576832-2577026   UACAAGCUGCG-UUGUACGUAAUAUUAAUA--------AAGUUUUA-ACCUUUAAACUGUUAUA------GGGAGUUUAACAU--UAUUGC-GGGAAUG-CC-GAGCCUUUUG----------CCGUUUGGC------AGGGAGGAU---GG---CAGGAACG-C-UUU--UGCGGAC-ACCCACUUUG-----AGG----AGUG---UGGUUCUAAAA--CUUU-----CUUAGUUUGAUUACGGCAA--CUGCGGCACAUAC
AP010655.1/1905876-1906069   GAAUUGCUGUG-GCAUACGA--AUUCACAUCUA----AGUGU-UGA--CCGACUAUUUUUUUGUAUUAUCGGGAAACAAAAGU--CUUCUG-ACAGUAU-GC-AGGCCGU----------------UUCAC----------GCGGAA---GCA-ACUAAAGUC-A-GAG---CGAGUU-GCCCACCUGCU---UAAG----CGUGC--GGGU--UCA-A--UACA-----AAACGUGAAUCAUCGGUGCCAAUACAGCAUUUUC
AY345075.1/252-94            UAUUAGCUGCU-UGGUUCGUGAGCUUAAUAUUA----ACCU--AGG-ACUACCACUAACUUUUA------GGACAUCGUCCCU---GUCUA-AU----A-------CU------------------AAUUC------------AG---------------UUU-A-GAU--AUAUGAA-GUCCACCUUU-----ACA----UAAA----GGU--CUUU-GAAGG--------AUUUUAAGUAACGGCCA--AAGCGGUCAUGUA
#=GC SS_cons                 :<<<<<<<<<<.<<<<-<<<-------------.....<<<<-<<<.<<<----------------....<<<-<<<<<----...<<<<<.<<-----.<<.---<<<<<..............._____........_>>>>>--...>>...----->>>.>.>>>..-->>>>>.->>>------.....---....----....>>>..>>>->..>>>-.....------------>>>>>>>...>>>>>>>>>>::
#=GC RF                      aaauccCUGcg.gUGUUCGucAguugcuuauaa.....guccCUGA.gCCgAuaauuUuuuuaauu....GGGagcccuaucU...uucaa.gugGuGu.Gc.AaGCCugg...............CUUGu........AccaGGAA...gC...cuaAAacu.u.gaa..acagggc.aCCCACCUgg.....aAc....agCa....GGu..UCAAg..gacu.....uaaugacgaCaaaCGGCAc...cgCGGggauuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00014
#=GF ID   DsrA
#=GF DE   DsrA RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:9770508
#=GF GA   60.00
#=GF TC   61.50
#=GF NC   57.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000378; DsrA_RNA;
#=GF DR   GO; 0045727; positive regulation of translation;
#=GF DR   GO; 0009299; mRNA transcription;
#=GF RN   [1]
#=GF RM   7534408
#=GF RT   A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of
#=GF RT   Escherichia coli.
#=GF RA   Sledjeski D, Gottesman S
#=GF RL   Proc Natl Acad Sci USA 1995;92:2003-2007.
#=GF RN   [2]
#=GF RM   9770508
#=GF RT   DsrA RNA regulates translation of RpoS message by an anti-antisense
#=GF RT   mechanism, independent of its action as an antisilencer of transcription.
#=GF RA   Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S
#=GF RL   Proc Natl Acad Sci USA 1998;95:12462-12467.
#=GF RN   [3]
#=GF RM   15913835
#=GF RT   Micros for microbes: non-coding regulatory RNAs in bacteria.
#=GF RA   Gottesman S
#=GF RL   Trends Genet 2005;21:399-404.
#=GF RN   [4]
#=GF RM   28934467
#=GF RT   The important conformational plasticity of DsrA sRNA for adapting multiple
#=GF RT   target regulation.
#=GF RA   Wu P, Liu X, Yang L, Sun Y, Gong Q, Wu J, Shi Y
#=GF RL   Nucleic Acids Res. 2017;45:9625-9639.
#=GF CC   DsrA RNA regulates both transcription, by overcoming transcriptional
#=GF CC   silencing by the nucleoid-associated H-NS protein, and translation, by
#=GF CC   promoting efficient translation of the stress sigma factor, RpoS. These
#=GF CC   two activities of DsrA can be separated by mutation: the first of three
#=GF CC   stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but
#=GF CC   not for anti-H-NS action, while the second stem-loop is essential for
#=GF CC   antisilencing and less critical for RpoS translation. The third stem-loop,
#=GF CC   which behaves as a transcription terminator, can be substituted by the trp
#=GF CC   transcription terminator without loss of either DsrA function. The
#=GF CC   sequence of the first stem-loop of DsrA is complementary with the upstream
#=GF CC   leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with
#=GF CC   the RpoS message might be important for translational regulation.
#=GF WK   DsrA_RNA
#=GF SQ   5


M15749.1/155-239           AACGCAUCGGAUUUCCCGGUGUAACGAAUU-UUCAAGUGCUUCUUGCAUUAGCAAGUUUGAUCCCGA-CUCCUGC-GAGUCGGGAUUU
CP000653.1/2739273-2739189 CCCACAUCAGAUUUCCUGGUGUAACGAAUU-UACAAGUGCUUCUUGCAUAAGCAAGUUCAUCCCGGU-CAUCCCC-AUGGCCGGGAUU
CP000468.1/2032638-2032552 AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUAAGCAAGUUUCAUCCCGA-CCCCCUCAGGGUCGGGAUUU
CP000857.1/1802194-1802277 CUCACAUCAGAUUUCCUGGUGUAACGAAUU-UUCAAGUGCUUCUUGCAUAAGCAAGUUUGAUCCCG--ACCCGUA-GGGCCGGGAUUU
CP001383.1/2080784-2080698 AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUAAGCAAGUUUCAUCCCGACACCCUCA-GGGUCGGGAUUU
#=GC SS_cons               :::<<<<<<<_____>>>>>>>,,,<<<<<.<<<<<<<<_____>>>>>>>>->>->>>-<<<<<<<.-<<____.>>->>>>>>>::
#=GC RF                    aaCaCauCaGAUUUCCuGguGuAACgaauu.uuuaaGugCUUCUugCuuaagCaaGuucaauCCcGa.cccCuuc.ggGuCgGGauUU
//
# STOCKHOLM 1.0

#=GF AC   RF00015
#=GF ID   U4
#=GF DE   U4 spliceosomal RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Zwieb C, The uRNA database, PMID:9016512
#=GF SS   Published; PMID:2339054; Griffiths-Jones SR
#=GF GA   46.00
#=GF TC   46.00
#=GF NC   45.90
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.40 -Z 549862.597050 CM SEQDB
#=GF CL   CL00007
#=GF DR   SO; 0000393; U4_snRNA;
#=GF DR   GO; 0000244; spliceosomal tri-snRNP complex assembly;
#=GF DR   GO; 0000353; formation of quadruple SL/U4/U5/U6 snRNP;
#=GF DR   GO; 0017070; U6 snRNA binding;
#=GF DR   GO; 0005687; U4 snRNP;
#=GF DR   GO; 0046540; U4/U6 x U5 tri-snRNP complex;
#=GF RN   [1]
#=GF RM   9016512
#=GF RT   The uRNA database.
#=GF RA   Zwieb C
#=GF RL   Nucleic Acids Res 1997;25:102-103.
#=GF RN   [2]
#=GF RM   11163207
#=GF RT   Crystal structure of the spliceosomal 15.5kD protein bound to a U4 snRNA
#=GF RT   fragment.
#=GF RA   Vidovic I, Nottrott S, Hartmuth K, Luhrmann R, Ficner R
#=GF RL   Mol Cell 2000;6:1331-1342.
#=GF RN   [3]
#=GF RM   9452384
#=GF RT   A spliceosomal recycling factor that reanneals U4 and U6 small nuclear
#=GF RT   ribonucleoprotein particles.
#=GF RA   Raghunathan PL, Guthrie C
#=GF RL   Science 1998;279:857-860.
#=GF RN   [4]
#=GF RM   2339054
#=GF RT   The spliceosomal snRNAs of Caenorhabditis elegans.
#=GF RA   Thomas J, Lea K, Zucker-Aprison E, Blumenthal T
#=GF RL   Nucleic Acids Res 1990;18:2633-2642.
#=GF CC   U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent
#=GF CC   spliceosome. It forms a duplex with U6, and with each splicing round, it
#=GF CC   is displaced from U6 (and the spliceosome) in an ATP-dependent manner,
#=GF CC   allowing U6 to re-fold and create the active site for splicing catalysis.
#=GF CC   A recycling process involving protein Prp24 re-anneals U4 and U6.
#=GF WK   U4_spliceosomal_RNA
#=GF SQ   170


AAIY01144063.1/2359-2499       AGCUUUGCGC-AGUGGCAA-UAUCGUAGCCAGUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCG--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AC193264.3/174224-174084       AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AADD01128634.1/1009-869        AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AAFR03070450.1/4019-4159       AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AAPN01043183.1/815-675         AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AAHY01048392.1/24763-24623     AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
ABDC01319198.1/612-472         AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AANG01100342.1/1096-956        AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AALT01138445.1/833-693         AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AANU01246434.1/3940-4080       AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AANN01193588.1/6106-6246       AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AACN010181221.1/232-92         AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AAFC03029538.1/15458-15318     AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-CAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AAPY01772888.1/1357-1497       AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCG--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AAYZ01170597.1/2807-2947       AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCG--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUU-----------------------------------------------------------------CGGAGA
AB168678.1/1-141               AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCG--UGA-CG-ACUUG---------------------------CAAU--AU--AGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
K00476.1/2-142                 AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUAA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
BAAE01269333.1/2018-1878       AUCUUUGCGC-AGUGGCAG-UAUCGUAGCCUAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUA------CCCAAUAC--CCCGCCU--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--AUGGCAAUUUUUG--ACGGUCUCUA-----------------------------------------------------------------AGGAGA
AAZO01005801.1/5213-5353       AGCUUUGCGC-AGUGGCGA-UAUCGUAACCAAUGAAGGUUU--ACUGAGGUGCGAUUA--UUGCUAGUUGAAAACUUAU------ACCAAUAC--CCCGCC---UAG-GA-AAUGUG--------------------------UAAU-ACC--AUU-UC-CUA---UGGCAAUUUUUG--AAAGCUUCUA-----------------------------------------------------------------AGGAAG
BC124577.1/1-141               AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCUAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUA------CCCAAUAC--CCCGCC---GUGACG-ACUUG----------------------------AAA--UA-UAGU-CGGCAC---UGGCAAUUUUUG--ACAGUCUUCU-----------------------------------------------------------------CGAAGA
AANH01001405.1/82396-82256     AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCUAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAGUUGAAAACUUUA------CCCAAUAC--CCCGCCU--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--AUGGCAAUUUUUG--ACGGUCUCUA-----------------------------------------------------------------AGGAGA
ABAV01003454.1/17582-17444     AGCUUUGCGC-AGUGGCAU-UACCGUAGCUGAUGAGGUUCA--UCCGAGGCGCGGUUA--UUGCUGAUUGAAAACUUUU------CCCAAUAC--CCCGCG---AGA-CG-ACUUG----------------------------AAA--CA-UAGU-CG-GCU---UUGCAAUUUUUG--AAGGUCUUCA-----------------------------------------------------------------AGAAGG
AAZX01000257.1/602-462         AUCUCUGCGC-AGUGGCGA-UAUCGUAACCAAUGAGGUUCU--ACCGAGGUGCGAUUA--UUGCUAGUUGAAAACUUUU------ACCAAUAC--CCCGCCA--AGA-CG-AUGUG----------------------------AAA--UA-CCAU-CG-GCU--ACGGCAAUUUUUG--ACAGCCCUUA-----------------------------------------------------------------CGAGGG
AAGE02020535.1/44175-44035     AGCUUUGCGC-AGUGGCGA-UAUCGUAACCAAUGAGGUUUA--ACCGAGGUGCGAUUA--UUGCUAGUUGAAAACUAAU------ACCAAUAC--CCCGCCU--UGG-GG-ACGUG----------------------------AAA--UA-CCGU-CCGCUA---CGGCAAUUUUUG--ACAACCCCGA-----------------------------------------------------------------AAGGGG
AAVX01087583.1/989-849         AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCGAUGAGGUCUA--ACCGAGGCGCGAUUA--UUGCUUAUUGAAAACUUUU------CCCAAUAC--CCCGCCG--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUG-----------------------------------------------------------------CGGAGA
K03095.1/1-139                 AGCUUAGCGC-AGUGGCAA-UACCGUAACCAAUGAAGCCUC--CCUGAGGUGCGGUUA--UUGCUAGUUGAAAACUUUA------ACCAACC---CACGCC---AUG-GG-ACGUG----------------------------AAA--UA-CCGU-CC-ACU--ACGGCAAUUUUUG--GAAGCCCUUA-----------------------------------------------------------------CGAGGG
AACT01063233.1/31971-31831     AGCUUUGCGC-AGUGGCAG-UAACAUAGCCAAUGAGGUUUA--UCCGAGGCGUGUUUA--UUGCUAGUUGAAAACUAUA------CCCAAUAC--CCCGCC---CUG-UC-GACGUG--------------------------AAAC-ACC--GUC-GG-CUG---UGGCAAUUUCUG--ACGGGUUCUC-----------------------------------------------------------------CGGAAC
AAWU01039949.1/7621-7481       AGCUUUGCGC-AGUGGCGA-UAUCGUAACCAAUGAGGUACA--UCCGAGGUGCGAUUA--UUGCUAGUUGAAAACUAAU------ACCAAUAC--CCCGCCA--UGG-GG-ACGUG----------------------------AAA--UA-CCGU-CCGCUA---CGGCAAUUUUUG--AAAACCCCGA-----------------------------------------------------------------AAGGGG
AAAB01008933.1/1598961-1598821 AGCUUUGCGC-AGUGGCGA-UAUCGUAACCAAUGAGGUACA--ACCGAGGUGCGAUUA--UUGCUAGUUGAAAACUAAU------ACCAAUAC--CCCGCCU--UGG-GG-ACGUG----------------------------AAA--UA-CCGU-CCGCUA---UGGCAAUUUUUG--CAAACCCCGA-----------------------------------------------------------------AAGGGG
X15933.1/1-149                 AUCUUUGCGCUUGGGGCAA-UGACGCAGCUAGUGAGGUUCUA-ACCGAGGCGCGUCUA--UUGCUGGUUGAAAACUAUUU-----CCAAAC----CCCCUCU--UAG-GC-UUGAG---------------------------GUAA--CU--CAA-GC-CUU---UGAGAAUUUCUG--GAAGGGCUCCCUUAGGGU---------------------------------------------------------AAAGUC
AC084591.1/18183-18321         AGCUUUGCGC-UGGGGCGA-UAACGUGACCAAUGAGGCUUU--GCCGAGGUGCGUUUA--UUGCUGGUUGAAAACUUUU------CCCAAUUG--CCCGCG---AUG-UC-CCCUG----------------------------AAA--CAUGGGU-GA-CAU---ACGCAAUUUUUG--AACGCCUCUA------------------------------------------------------------------GGAGG
CU302335.1/69797-69946         AUCUUUGCGCUUGGGGCAA-UGACGCAGCUAAUGAGGUUAUA-ACCGAGGCGCGUCUA--UUGCUGGUUGAAAACUAUUU-----CCAAAC----CCCCUCU--UAG-GC-UUGAG---------------------------GCAA--CU--CAA-GC-CUU---CGAGAAUUUCUG--GAAGGACUCCUUUUGGGGU--------------------------------------------------------AAAGUC
AABS01000042.1/351938-351798   AGCUUUGCGC-AGUGGCGG-UAUCGUAGCCUAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAGUUGAAAACUAUU------CCCAAUAC--CCCGCC---CUG-UC-GACGUG--------------------------AAAA-ACC--GUC-GG-CUG---UGGCAAUUUCUG--AUGUGUUCUC-----------------------------------------------------------------AGGAAC
AADK01043685.1/1410-1272       AACUUUGCGC-AGAGGCAA-UAUCGUAACCAAUGAGGUUAA--UCCGAGGUGCGAUUA--UUGCUAGUUGAAAACUUUA------C-CAAUAC--CCCGCC---UUG-UG-GACGUG--------------------------AAAC-ACC--GUC-CG-CUA---UGGCAAUUUUUG--GAAGGCCGUA------------------------------------------------------------------AAGGC
AACG02000302.1/224-363         AGCUUUGCGC-AGUGGCAG-UAACAUAGCUGAUGAGGUUCA--UCCGAGGCGUGUUUA--UUGCUAGUUGAAAACUAUA------CCCAAUAC--CCCGCC---CUG-UG-GACGU---------------------------AUAA--AC-CGUU-CG-CUG---UGGCAAUUUCUG--AUGGGUUCCC-----------------------------------------------------------------CGGAAC
AACA01000783.1/223-362         AGCUUUGCGC-AGUGGCAG-UAACAUAGCUGAUGAGGUUCA--UCCGAGGCGUGUUUA--UUGCUAGUUGAAAACUAUA------CCCAAUAC--CCCGCC---CUG-UG-GACGU---------------------------AUAA--AC-CGUU-CG-CUG---UGGCAAUUUCUG--AUGGGUUCCC-----------------------------------------------------------------CGGAAC
AAPU01010717.1/67287-67148     AUCUUUGCGC-AGAGGCGA-UAUCGUAACCAAUGAAGUUCU--ACUGAGGUGCGAUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCCGCCA--UGG-GG-ACGUG----------------------------AAA--UA-CCGU-CCACUA---CGGCAAUUUUUG--GAA-GCCCGA-----------------------------------------------------------------AAGGGC
AAPQ01007039.1/986580-986441   AUCUUUGCGC-AGAGGCGA-UAUCGUAACCAAUGAAGUUCU--ACUGAGGUGCGAUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCCGCCA--UGG-GG-ACGUG----------------------------AAA--CA-CCGU-CCACUA---CGGCAAUUUUUG--GAA-GCCCGA-----------------------------------------------------------------GAGGGC
AAFS01000180.1/63195-63056     AUCUUUGCGC-AGAGGCAU-UAUCGUAACCAAUGAAGUUCU--ACUGAGGUGCGAUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCCGCCA--UGA-GG-ACGUG----------------------------AAA--UA-CCGU-CC-GCU--ACGGCAAUUUUUG--GAA-GCCCGU-----------------------------------------------------------------GAGGGC
AAIZ01004033.1/4883-4744       AUCUUUGCGC-AGAGGCAU-UAUCGUAACCAAUGAAGUUCU--ACUGAGGUGCGAUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCCGCCA--UGA-GG-ACGUG----------------------------AAA--UA-CCGU-CC-GCU--ACGGCAAUUUUUG--GAA-GCCCGU-----------------------------------------------------------------GAGGGC
AANI01016129.1/182015-181878   AACCUUGUGC-AGUGGCAA-UAUCGCAAACAAUGAGGUCACA-ACCGAGUUGCGAUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAA--CUCGCC---CUG-UG-UGAGC----------------------------CAC--GC--UCA-CG-UUG---AGGCAAUUUUUU--UAG-GCUCGA-----------------------------------------------------------------AAGAGC
AAJJ01000336.1/45867-45727     AGCUUUGCGC-AGUGGCAG-UAUCGUAACCGAUGAGGUAAA--UCCGAGGUGCGAUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCCGCCA--UGU-GC-ACGUG----------------------------AAA--UA-CCGU-GC-GCU--ACGGCAAUUUUUG--GAAGCCUCUA-----------------------------------------------------------------CGGGGG
AAAA02007064.1/44912-44768     AUCUUUGCGCUUGGGGCAA-UGACGCAGCUAGUGAGGUUAU--ACCGAGGCGCGUCAA--UUGCUGGUUGAAAACUAUUU-----CCAAAC----CCCCUC---UGC-GG-CCC-----------------------------AUCC------GGG-CC-UCA----GAGAAUUUCUG--GAAGGGCUCCCUAACUAGGGU------------------------------------------------------AAAGCC
AAKO01002834.1/25643-25504     AUCUUUGCGC-AGUGGCAA-UACCGUAACCAAUGAAGUCCU--CCUGAGGUGCGGUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCCGCCA--UGG-GG-ACGUG----------------------------AAA--UA-CCGU-CCACUA---CGGCAAUUUUUG--GAA-GCCCGA-----------------------------------------------------------------GAGGGC
AAEU02000313.1/218060-217921   AUCUUUGCGC-AGUGGCAA-UACCGUAACCAAUGAAGUCCU--CCUGAGGUGCGGUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCCGCCA--UGG-GG-ACGUG----------------------------AAA--UA-CCGU-CCACUA---CGGCAAUUUUUG--GAA-GCCCGA-----------------------------------------------------------------GAGGGC
AASS01015485.1/140-1           AUCUUUGCGC-AGUGGCAA-UACCGUAACCAAUGAAGUCCU--CCUGAGGUGCGGUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCCGCCA--UGG-GG-ACGUG----------------------------AAA--UA-CCGU-CCACUA---CGGCAAUUUUUG--GAA-GCCCGA-----------------------------------------------------------------GAGGGC
X07113.1/1-150                 AUCUUUGCGCUUGGGGCAA-UGACGUAGCUAGUGAGGUUCUA-ACCGAGGCGCGUCUA--UUGCUGGUUGAAAACUAUUU-----CUAAAC----CCCCUCUU-AGG-CU-UGAGU----------------------------UUA--AC--UCA-AG-CCU--UUGAGAAUUUCUG--GAAGGACUCCUUCGGGGU---------------------------------------------------------AAAGUC
AAPP01015712.1/40466-40605     AUCUUUGCGC-AGUGGCAA-UACCGUAACCGAUGAAGUUCU--ACUGAGGUGCGGUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCCGCCA--UGG-GG-ACGUG----------------------------AAA--UA-CCGU-CCACUA---CGGCAAUUUUUG--CAA-GCCCGA-----------------------------------------------------------------GAGGGC
AM479189.1/4511-4661           AUCUUUGCGCUUGGGGCAA-UGACGCAGCUAGUGAGGUUCUA-ACCGAGGCGCGUCAA--UUGCUGGUUGAAAACUAUUU-----CCAAAC----CCCCUCC--UUG-GC-CUGGGU--------------------------UACG--CC--CAG-GC-CAU---CGAGAAUUUCUG--GAAGGGCUCCCUAAGGGGU--------------------------------------------------------AAAGCC
AASG02000802.1/49546-49696     AUCUUUGCGCUUGGGGCAA-UGACGCAGCUAGUGAGGUUCUA-ACCGAGGCGCGUCUA--UUGCUGGUUGAAAACUAUUU-----CCAAAC----CCCCUCAU-UGG-CC-UGGGU----------------------------UUG--GC--CCA-GG-CCA--UUGAGAAUUUCUG--GAAGGGCUCCCUUAGGGGU--------------------------------------------------------AAAGCU
AAPT01020986.1/3963-4102       AUCUUUGCGC-AGAGGCGA-UAUCGUAACCAAUGAAGUUCU--ACUGAGGUGCGAUUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCUGCCA--UGG-GG-ACGUG----------------------------AAA--UA-CCGU-CCGCUA---CGGCAAUUUUUG--GAA-GCCCGA-----------------------------------------------------------------GAGGGC
AARH01003623.1/42069-42219     AUCUUUGCGCUUGGGGCAA-UGACGCAGCUAGUGAGGUUCUA-ACCGAGGCGCGUCAA--UUGCUGGUUGAAAACUAUUU-----CCAAAC----CCCCUCAU-UGG-CC-UGGGU----------------------------UUG--GC--UCA-GG-CCA--UUGAGAAUUUCUG--GAAGGGCUCCCCUCGGGGU--------------------------------------------------------AAAGCC
X67145.1/194-344               AUCUUUGCGCUUGGGGCAA-UGACGCAGCUAAUGAGGUUCUA-ACCGAGGCGCGUCUA--UUGCUGGUUGAAAACUAUUU-----CCAAAC----CCCCUCCU-AGG-CC-UAAGC----------------------------UUG--UC--UUA-GG-CCU--UCGAGAAUUUCUG--GAAGGGCUCCCUUUGGGGU--------------------------------------------------------AAAGCC
AP004858.3/49137-48993         AUCUUUGCGCUUGGGGCAA-UGACGCAGCUAGUGAGGUUAU--ACCGAGGCGCGUCAA--UUGCUGGUUGAAAACUAUUU-----CCAAAC----CCCCUU---UGC-GG-CCC-----------------------------AUCC------GGG-CC-UCA----GAGAAUUUCUG--GAAGGGCUCCCUAACUAGGGU------------------------------------------------------AAAGCC
AAQA01000004.1/379392-379252   AGCUUUGCGC-AGUGGCGA-UAACGUGACCAAUGAGGCUUA--GCCGAGGUGCGUUUA--UUGCUGGUUGAAAACUUUCA-----CCCAAUUG--CCCGCC---GCA-GC-UCCUG---------------------------AAAA--AU--GGAUGC-UGU---AGGCAAUUUUUG--AACGCCCCGC-----------------------------------------------------------------ACGGGG
AP006099.1/69439-69589         AUCUUUGCGCUUGGGGCAA-UGACGCAGCUUAUGAGGUUCUA-ACCGAGGCGCGUCUA--UUGCUGGUUGAAAACUAUUU-----CCAAAC----CCCCUCU--UAG-GC-CUGGG---------------------------UUCA--CC-CCUG-GC-CUU---CGAGAAUUUCUG--GAAGGGCUCCCUUUGGGGU--------------------------------------------------------AAAGCU
AAWT01050999.1/11219-11362     GUUUUUGCGC-AGGUGCAA-UACACCAUCAAGUGAGGAUAAU-UCCGAUGAGGUGUUU--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCUAUUAGU-UU-UACUG---------------------------AUCA--UA--GUA-AA-ACU-UUUAGCAAUUUUUA--AAGGUCCGAC------------------------------------------------------------------AAGGA
AATT01000006.1/24344-24478     AUUCUUGCAC-GGGAGCAU-UAUCCAUAACUGUGAAGUUACG-ACUGAGUUUGGAUUA--UUGCUGAUUGAAAACUAAU------UCCAAUC---GGCUCU---UGA-CG-CCCUA------------------------------C--UG--GGG-CG-GCA----AGGAAUUUUUG--GACCCAUUAC-----------------------------------------------------------------UUAAUA
AAQB01006409.1/413450-413312   AUCUUUGCGC-AGCGGCAA-UUUCGUAACCAAUGAAGGCA---ACUGAGGUGCGAAUA--UUGCUAGUUGAAAACUUUA------ACCAAUAC--CCCGCCC--AGG-GG-ACGUG----------------------------AAA--UA-CCGU-CC-ACU--AAGGCAAUUUUUG--GAA-GCCCGA-----------------------------------------------------------------GAGGGC
AP007155.1/2359336-2359191     AUCCUAGUGC-ACGGGCAA-UACACGUAUCAGUGAGGAGACA-UCCGAGAUCGUGUUU--UUGCUAGUUGAAAACUAUUUU----UUUGAC----CGCUCU---AGU-UG-GCC-----------------------------UUCG------GGU-CG-GCU----AGGAAUUUUUG--AAAACAAACUGCCCUGGCUCA------------------------------------------------------UAUUUG
AAIH02000036.1/105327-105472   AUCCUAGUGC-ACGGGCAA-UACACGUAUCAGUGAGGAGACA-UCCGAGAUCGUGUUU--UUGCUAGUUGAAAACUAUUUU----UUUGAC----CGCUCU---AGU-UG-GCC-----------------------------UUCG------GGU-CG-GCU----AGGAAUUUUUG--AAAACAAACUGCCCUGGCUCA------------------------------------------------------UAUUUG
AACW02000210.1/206231-206366   AUUCUUGUGC-UAGGGCAA--AACCACGAAAGUGAGGUUCAU-ACUGAUUCUGGUUUA--UUGCUGGUUGAAAACUACU------ACCAAUG---CCCGUC---UGC-AG-UGCUC---------------------------UUCG--GG--GCG-CG-GCA----G-CAAUUUUUU--GAAGGCUCAG-----------------------------------------------------------------UAGGGC
AC192395.1/10098-9958          AGCUUUGUGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUGUA--UCUGAGACUCGAUUA--UUGCUAUUUGAAAACUUUU------CCCAGUAC--CCCGCCA--UGA-CA-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
CAAJ01010632.1/7788-7919       AUCCUUGCGGGAGGGGCAU-UAUCGCUGUAAAUGACGACUA--ACGGAUACGCGAUUA--UUGCUAGUUGAAAACUACU------C-CAAUU---CCCGU----CUC-GA-UGCUU---------------------------GAAA--AA--GCA-GA-GAG------CAAUUUUUG--UAGCCUUUUU-------------------------------------------------------------------AAAG
CAAI01006665.1/11117-11248     AUCCUUGCGGGAGGGGCAU-UAUCGCUGUAAAUGACGACUA--ACGGAUACGCGAUUA--UUGCUAGUUGAAAACUACU------C-CAAUU---CCCGU----CUC-GA-UGCUU---------------------------GAAA--AA--GCA-GA-GAG------CAAUUUUUG--UAGCCUUUUU-------------------------------------------------------------------AAAG
AAKM01000017.1/282531-282664   AUCUUUGCGGGAGGGGCAU-UAUCGCUGUAAAUGACGACUA--ACGGAUACGCGAUUA--UUGCUAGUUGAAAACUACU------C-CAAUU---CCCGUC---UC--GA-GGCUU---------------------------GAAA--AA--GCU-----GA---GGGCAAUUUUUG--UAGCCUUUGC-----------------------------------------------------------------AUGAAG
AABL01000640.1/15189-15058     AUCCUUGCGGGAGGGGCAU-UAUCGCUGUAAAUGACGACUA--ACGGAUACGCGAUUA--UUGCUAGUUGAAAACUACU------C-CAAUU---CCCGU----CUC-GA-UGCUU---------------------------GAAA--AA--GCA-GA-GAG------CAAUUUUUG--UAGCCUUUUW-------------------------------------------------------------------AAGG
L22250.1/171-310               AGCUUUGCGC-AGAGGCGA-UAACGUGACCAAUGAGGCUCA--GCCGAGGUGCGUUUA--UUGCUGGUUGAAAACUUUCA-----CCCAAUU---GCCCGC---CGCGGC-GCCUG----------------------------AAA--CA-UGGC-GG-CCG---UACGAAUUUUUG--AACGCCCUGA-----------------------------------------------------------------AGGGGG
AAFU01001086.1/4264-4401       AUCCAAGUGC-AGGGGUUU-UACGUGUAUCAGUGAGGAUUCG-UCCGAGAUCACGUUU--UUGCUAGUUGAAAACUACAUA----CCUGAC----CGCUCC---UGU-UG-GGU-----------------------------UUCG------ACC-UG-ACA----GGGAAUUUUUG--GAACCCUUCCUCU--------------------------------------------------------------CGCAGG
X58844.1/1-130                 NACCUCGCGACAGGGGCAA-UAUAGCAGCAAGUGACGGUUA--ACUGAUGCGCUAUUA--UUGCUAGUUGAAAACUACU------U-CAAU----AAGUGG---AAA-CG-ACGCU---------------------------------UG--CGU-CG-GGU----CCCAAUUUCUG--GAAGGUCGUA-------------------------------------------------------------------UGAC
AAYL01000045.1/85592-85722     AUCCUUGCGGUAGGGGCAA-UGUCGCUGCAAGUGACGCCUA--GCGGAUGCGCGAUGA--UUGCUAGUUGAAAACUACU------C-CAAUU---CCCGU----UCG-CC-GACCC---------------------------GAAA--GG--GUC-GG-CGG------CAAUUUCUG--GGG-CCCCCC-------------------------------------------------------------------GGGG
AAXJ01014857.1/1040-1174       AUCCUUGCGGGAGGGGCAA-UAGCGCUAUCUAUGACGCCUU--GCGGAGAUGCGCUUU--UUGCUAGUUGAAAACUACU------C-CAAUUC--CCGUCG---CGA-GA-UUC-----------------------------UAAC------GGA-UC-CCG---UCGCAAUUUUAG--GGCGCCUCGC-----------------------------------------------------------------AUGAGG
AANS01000355.1/46407-46542     AUCUUUGCGGGAGGGGCAG-UAUCGCUGUAAAUGACGACGA--ACGGAUACGCGAUUA--UUGCUAGUUGAAAACUACU------C-CAAUU---CCCGU----CUC-GA-UGCUU---------------------------GAAA--AA--GCA-GA-GAG------CAAUUUUUG--UAGCCUUUCUUU---------------------------------------------------------------AUAAAG
AATM01000105.1/197284-197424   AUCUUUGUGC-ACGGGUAU-UACGCUUAUCAGUGAGGAUCCUUUCCGAGAUGGCGUUA--UUGCUAGUUGAAAACUACAAC----CCUGAC----CGCUCC---GAC-UC-AUGCU-----------------------------UU--UG--CGU-GU-UUC----GGGAAUCUUUG--GAAAAAAAUCCAG--------------------------------------------------------------CAUUUU
AAGT01000338.1/12653-12519     AUCUUAGUGC-AUGGGUUU-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGCGUUU--UUGCUAGUUGAAAACUAUAAC----CAUGAC----CACUCC---AGG-UU-GGC-----------------------------UUCG------GCU-GG-CCU----GGGAAUCUUUG--GAACCAAAAC-----------------------------------------------------------------AUCUUC
AAXI01000285.1/23727-23857     AUCCAAGUGC-UCGGGCUU-UACGCUUACCAGUGAGGAUUCG-UCCGAGGUAGCGUUU--UUGCUAGUUGAAAACUACAAC----UAUGAC----CGCUCC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-ACU----GGGAAUUUUUG--UAACAAACUG-----------------------------------------------------------------UA----
AAID01000631.1/14812-14946     AUCUUAGUGC-AUGGGUUU-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGCGUUU--UUGCUAGUUGAAAACUAUAAC----CAUGAC----CACUCC---AGG-UU-GGC-----------------------------UUCG------GCC-GG-CCU----GGGAAUCUUUG--GAACCAAACA-----------------------------------------------------------------UCUUCU
CU329671.1/467615-467481       AUCUUUGUGC-ACGGGUAU-UACGCUUAUCAGUGAGGAACUUUUCCUAGAUGGCGUUA--UUGCUAGUUGAAAACUAUUAC----CCUGAC----CGCUCC---AAC-UC-U-------------------------------CGUU-A------A-GA-GUU--UUGGGAAUAUUUG--GAAACCAACU-----------------------------------------------------------------UAUUGC
AAXT01000001.1/1022888-1022758 AUCCUUGCGGAAGGGGCAA-UAUCGUUGCAAGUGACGCUUA--GCGGAUGCGCGAUAA--UUGCUGGUUGAAAACUACU------C-CAAUU---CCCGU----CUA-UC-AUUUC---------------------------GAAA--GA--UUU-GU-UAG------CAAUUUUUG--UAG-CCUCCC-------------------------------------------------------------------GGGG
AAFT01000065.1/55802-55646     AUCUUUAUGC-AGGGGCAU-UACGUGUAUCAGUGAGGAUUCG-UCCGAGAUCAUGUUU--UUGCUGGUUGAAAACUAUAA-----CCUGAC----AACUCCU--UGG-UA-GACCUUGCCUU---------------------GUGC-UUG--GGC-UG-CCC---GGGGAAUUUUUG--GAUUUGCCUGAUUUUGCUUU-------------------------------------------------------GUGGCA
ABAS01000010.1/147598-147449   AUCCUAGUGC-UCGGGCAG-UUCGAUUACCAGUGAGGAUUUCAUCCGAGGUAUCGAUU--UUGCUAGUUGAAAACUACCUAG---UUUGAC----CACUUC---AAC-UG-GCCUG---------------------------------CG--GGU-CG-GUU----GGGAAUUUUUG--AUCACUCAAUUCUCUUACUCUGU----------------------------------------------------GGAGAG
AACM02000196.1/54942-55125     AUCCGAGUGC-AAGGGCGU-UAUCCAUCUCAAUGAGGCUUU--GCCGAGAGUGGAUUU--UUGCUAGUUGAAAACUAUAC-----ACUGAC----CGCUCC---UAC-UU-GGG-----------------------------UUCG------CCU-GG-GUA----GGGAAUUUUUG--GAACACUUUUCCUAUGGAAACUUUUCUUUCAUUGCGAUCGGUCCUUUAUGAACUGGCGCGA--------------AGAAGG
AAVQ01000002.1/194294-194149   AUCUUUAUGC-AGGGGCAU-UACGUGUAUCAGUGAGGAUUCG-UCCGAGAUCAUGUUU--UUGCUGGUUGAAAACUAUAA-----CCUGAC----AGCUUCU--UAG-UG-AUCUAGCCU-----------------------UGUG-CUA-UGAA-UG-CUA---AGGGAAUUUUUG--GAGAACUAUC-----------------------------------------------------------------AUUUGA
ABAR01000001.1/643558-643722   AUCCUAGUGC-UCGGGCAG-UUCGAUUACCAGUGAGGAUUUCAUCCGAGGUAUCGAUU--UUGCUAGUUGAAAACUACCUAG---UUUGAC----CACUUC---AAC-CG-GCCUG---------------------------------CG--GGU-CA-GUU----GGGAAUUUUUG--AUCUCACUGAAUUUUCGCUCAGCUAGUACUUGUUACUA-------------------------------------CUAGUG
CAAL01000681.1/399056-398923   AUCCUUAUUC-AGGGGCAA-UAUCGCUGUAAGUGACGUACCA-ACGGAUACGCGA-GA--UUGCUAAUUGAAAACUACU------C-CAAU----GCGAGU---GUA-CG-ACUUC---------------------------CUUG-UGA--AGU-CG-UUC----ACCAAUUUCUG--AAGGGUCGAA-------------------------------------------------------------------AGAC
BX842620.1/46696-46842         AUCCAAGUGC-AGGGGUUU-UACGCGUAUCAGUGAGGAUUCG-UCCGAGAUCGCGUUU--UUGCUAGUUGAAAACUACAUA----CCUGAC----CGCUCU---CAG-UU-GGC-----------------------------UUCG------GCU-GG-CUG----GGGAAUUUUUG--GCAACCCACAAUCCUUUCUCGG-----------------------------------------------------ACUGGA
AAFO01000045.1/228200-228380   GUCUUUAUGC-AGGGGCAU-UACGUGUAUCAGUGAGGAUUCG-UCCGAGAUCAUGUUU--UUGCUGGUUGAAAACUUAAA-----CCUGAC----AACUUC---UUG-AA-UGCUAUAGUAUU--------------------UUAC-UUG-UGUG-UU-UAA----GAGAAUUUUUG--GAACCAUUUUUUUUCAUAAUCAUCAAACAUGUGGGAAAUCACGA-------------------------------AUAAUG
AACQ01000084.1/105435-105615   GUCUUUAUGC-AGGGGCAU-UACGUGUAUCAGUGAGGAUUCG-UCCGAGAUCAUGUUU--UUGCUGGUUGAAAACUUAAA-----CCUGAC----AACUUC---UUG-AA-UGCUAUAGUAUU--------------------UUAC-UUG-UGUG-UU-UAA----GAGAAUUUUUG--GAACCAUUUUUUUUCAUAAUCAUCAAACAUGUGGGAAAUCACGA-------------------------------AUAAUG
AAJN01000077.1/141935-142086   AUCCUAGUGC-AAGGGUUU-UACACGUGUCAGUGAGGAGACA-UCCGAGACCGUGUUU--UUGCUAGUUGAAAACUACCUAG---UUUGAC----CGCUCC---AGA-UG-GCC-----------------------------UUCG------GGU-CG-UCU----GGGAAUUUUUG--AAAAACACACUGCCCUGACUCCUCGU-------------------------------------------------UUGUGG
AACD01000007.1/178412-178544   AUCCUGGUGC-AAGGGUUU-UACACGUGUCAGUGAGGAGCCA-UCCGAGACCGUGUUU--UUGCUAGUUGAAAACUACCUA----GUUGAC----CGCUCC---AAU-UG-GCCUU---------------------------------AG--GGU-CG-GUU----GGGAAUUUUUG--AACACUUAAA-------------------------------------------------------------------GAAA
CR382130.1/2966271-2966119     AUCUUUAUGC-UCGGGCAU-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUAU--UUGCUGGUUGAAAACUUAAC-----CAUGAC----CGCUCU---CUA-UU-GCCUUGUGGCUUGC------------------CACA-GUC--GGC-UU-UAG----AGGAAUUUUUG--GAACCUCAAGAUCGA------------------------------------------------------------AGUGAG
AM269959.1/11788-11936         AUCCUGGUGC-ACGGGUUU-UACACGUGUCAGUGAGGAGACA-UCCGAGACCGUGUUU--UUGCUAGUUGAAAACUACCUAG---UUUGAC----CGCUCU---CCU-UG-GUC-----------------------------UUCG------GAU-CG-GGG----AGGAAUUUUUG--AAAAAAAAGAUGCCAUGCCUUCA----------------------------------------------------AAUUUU
AAFM01000021.1/757822-757672   AUCUUUAUGC-AGGGAUAU-UACGUGUAUCAGUGAGGAUUCG-UCCGAGAUCAUGUUU--UUGCUAGUUGAAAACUACAA-----CCUGAC----AGCUCCU--UGA-UG-UGGUAUCCUU----------------------GUGG--UA-UCUG-CG-UCC---AGGGAAUUUUUG--GAACUUUUUUUUUUC------------------------------------------------------------AUUGAA
AACY020397167.1/942-809        AUCCUUGCGGAAGGGGCAA-UCGCGCUACCAGUGACGCCUA--GCGGAGGUGCGCGGU--UUGCUAGUUGAAAACUACU------C-CAAUU---CCCGUC---AAG-UU-UGAUC---------------------------GUCA--GG--UCA-UU-CUU----G-CAAUUUUUA--GGCGGGCUUC-------------------------------------------------------------------GGCC
AAKE03000003.1/920249-920379   AUCCUGGUGC-ACGGGUUU-UACACGUGUCAGUGAGGAGACA-UCCGAGACCGUGUUU--UUGCUAGUUGAAAACUACCUA----GUUGAC----CGCUUC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-ACU----GGGAAUUUUUG--AAAAAAAAGU-----------------------------------------------------------------UG----
AB189720.1/1-134               --CUUUGCGGGAGGGGCAG-UAUCGCUGUAAAUGACGACUA--ACGGAUACGCGAUUA--UUGCUAGUUGAAAACUACU------C-CAAUU---CCCGU----CUC-GA-UGCUU---------------------------GAAA--AA--GCA-GA-GAG------CAAUUUUUG--UAGCCUUUCUUU---------------------------------------------------------------AUAAAG
AAGK01000002.1/935734-935865   AUCCUUGCGGAAGGGGCAU-UCUCGUUGCAAGUGACGCCUA--GCGGAUGCGCGAUAA--UUGCUAGUUGAAAACUACU------C-CAAU----UCCCGA---CUU-UC-AUUAC---------------------------GCAA--GU--UUU-GA-AAG---C---AAUUUUUG----UGGCCCUU-----------------------------------------------------------------AGGGGC
AAHF01000007.1/1275121-1274962 AUCCUGGUGC-ACGGGUUU-UACACGUGUCAGUGAGGAGACA-UCCGAGACCGUGUUU--UUGCUAGUUGAAAACUACCU-----GUUGAC----CGCUUC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-GCU----GGGAAUUUUUG--AAAAAAAGUUGCCCUGACAUCCUAAGUCUUGGUGUC---------------------------------------AGUUUU
AC198144.2/107120-106981       AGUUUUGCAC-AGUGGCAG-UACCGUAGCCAAUGAGAUUUA--UCCAAGACGCGAUUA--UUGCUAAUUGAAAAUUUUC------C-CAAUAC--CCCACCA--UGA-UG-ACUUG----------------------------AAA--UA-UAAU-CA-GCA--CUGGCAAUUUUUG--ACACUCUCUA-----------------------------------------------------------------CGGAGA
ABDB01000004.1/78964-78804     AUCCUGGUGC-ACGGGUUU-UACACGUGUCAGUGAGGAGACA-UCCGAGACCGUGUUU--UUGCUAGUUGAAAACUACCUA----GUUGAC----CGCUUC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-GCU----GGGAAUUUUUG--AAAAAAAGUUGCCCUGACAUCCUAAGUCUUGGUGUC---------------------------------------AGUUUU
AAEE01000007.1/708153-708014   AGCCUUACGCAAGGGGAGA-UAUCGUUACAAAUGACGCUCA--GCGGAUGUGCGAUUU--CUGCUAGUUGAAAACUACA------C-CAAUUUA-AACUUCUA-UUA-UU-CUAUU---------------------------CUCU--AA--UAG-AU-UAA---UGGCAAUUUCUG----GGGCCCUC-----------------------------------------------------------------UAGGGC
AAEL01000435.1/3438-3299       AGCCUUACGCAAGGGGAGA-UAUCGUUACAAAUGACGCUCA--GCGGAUGUGCGAUUU--CUGCUAGUUGAAAACUACA------C-CAAUUUA-AACUUCUA-UUA-UU-CUAUU---------------------------CUCU--AA--UAG-AU-UAA---UGGCAAUUUCUG----GGGCCCUC-----------------------------------------------------------------UAGGGC
AAGI01000165.1/170050-170233   UGCUAGGUGC-UCGGGCUU-UACGCUUACCAGUGAAGAUUCG-UCUGAGGUAGCGUUU--UUGCUAGUUGAAAACUACAAC----UAUGAC----UGCUCC---AGU-UG-GCC-----------------------------UUCG------GGU-CG-GCU----GGGAAUUUUUG--AAACCUUUACACUUUUUUGUGCUUUUCGUUGAUUUUUGCGGCCUUGAGCUGCAUGAUCG----------------AAGAAG
AAPO01000090.1/100324-100179   AUCUUUAUGC-AGGGGCAU-UACGUGUUUCAGUGAGGAUUCG-UCCGAGAUCAUGUUU--UUGCUGGUUGAAAACUUUAAA----CCUGAC----AGCUUC---UCA-AU-GUUGGUGUCCUUGU------------------GAUA-UUU--GAU-GU-UGA----GAGAAUUUUUG--GAAACUUUUU-----------------------------------------------------------------UUA---
AAQQ01631221.1/1703-1837       AGCUUUGUGC-AGUGGCAG-UAUUGAAGCCAAUGAAGUCCA--UCUGAGGCACAAUUA--UUGCUAAUUGAAAACUUUU------C-CAGUACC-CCACCA---UGA-CA-ACUUU---------------------------UAAU--AU--AGU-CG-GCA---UUGGCAUAAUUU--AAAAAAAAAA-----------------------------------------------------------------UA----
CR382124.1/1170861-1171036     AUCCUUAUGC-ACGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUA--UUGCUGGUUGAAAUUUAUUUUUAACCAUGACC---UCCUCC---UCA-UA-ACGUAUUGUGUCUUUCAUUUUA----------CACA--UG--UGU-UA-UGC---AGGGAAUUUUUG--GAACCUACCUUUUUUUCCUUCUUC---------------------------------------------------AAGAAG
AAKD03000006.1/347523-347653   AUCCUGGUGC-ACGGGUUU-UACACGUAUCAGUGAGGAGACA-UCCGAGAUCGUGUUU--UUGCUAGUUGAAAACUACCUA----UUUGAC----UGCUCC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-GCU----GGGAAUUUUUG--AAGAAAAAGG-----------------------------------------------------------------UU----
AAWC01000056.1/46279-46148     AUCUUUGUGC-UCGGGCAAGUGAUUAAUCCAGUGAAGUGUAU-ACUGAGGAUAAUCAA-AUUGCUGGUUGCAAACUAUU------ACCAAA----UGCUUC---CAU-CG-CCCUG---------------------------------CG--GGG-UU-GUU---GGGGAAUUUCUG----AGCCCCCA-------------------------------------------------------------------GGGG
ABCN01001426.1/26711-26844     AUCCUUGCGCUUGGGGCAG-UGUCGCAGACUGUGAGGUCUA--ACCGAGUCGCGAC-A--GUGCCAGUUGAAAACUUAU------UCCAUC----CCCGUC---GGU-CGUCGUUC---------------------------UUCG--GA--ACG-CU-UCC----G-CAAUUUCUG--UCGGGCCUUU-------------------------------------------------------------------UGGC
AANV02000065.1/936-807         AUCCUUGCGC-UAGGGCAA-UAUUCU-UUUAAUGA--CUGCA-AAGGAAGAGGAAUGA--UUGCUAGUUUAAAACUAAAU-----CCAAGC----GCCGAG---AAA-CA-GUG------------------------------ACU------UGC-UG-UUU----CUCAAUUUUUG--AACUCGAAUU-----------------------------------------------------------------UAUUUG
AAIM02000062.1/67925-68097     AUCCAAGUGC-AUGGGCGU-UUUCCUUCUCCGUGAAGCGAUAAGCUGAGAGAGGAAUU--UUGCUAGUUGAAAACUAUAC-----ACUGAC----CGCUCC---UUG-UU-GGG-----------------------------UUCG------CCU-GG-CAA----GGGAAUUUUUG--GAACUUUCAUUUUCUUUCAUUGCGACCAGUUCUUGAUGGACUGCCGUG---------------------------AAGAAG
AATU01001408.1/348748-348878   AUCUUUGUGCUUGGGGCAA-UACGAUAGUGUGUGAAGCUCU--GCUGAUGCAUCGUGA--UUGCUAGUUGAAAACUACU------C-CAACA---CCCGUG---AGA-AG-GCC------------------------------ACU------GGC-CA-GCU---C--CAAUUUCUG--UUUUAUCUCC-----------------------------------------------------------------CACUAU
AF270843.1/940-1107            AUCCUUAUGC-ACGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUU--UUGCUGGUUGAAAUUUAAUUAUAAACCAGACC---GUCUCC---UCA-UG-GUCUACUAUGGGUGUUCGCUUUUGAACA----CUUC--AA--GAC-UA-UGU---AGGGAAUUUUUG--GAAUAUUUUC-----------------------------------------------------------------UCAUAU
AAQX01001192.1/50846-50711     AUCUUUGUGCUUGGGGCAA-UACGAUAGUGUGUGAAGCUCU--GCUGAUGCAUCGUGA--UUGCUAGUUGAAAACUACU------C-CAACA---CCCGUG---AGA-AG-GCC------------------------------ACU------GGC-CG-GCU---CCAAUUUCUGUU--UUAUCUCCCAAUU--------------------------------------------------------------CGGGAG
AARE01001618.1/3212-3345       AUCCAAGUGC-ACGGGUUU-UACGUU-ACCGGUGAAGGUUCG-CCUGAGGCAACGUUU--UUGCUAGUUGAAAACUACCAU----UAUGAC----CGCUCC---AGU-UG-GUCUC------------------------------U--GU--GAU-CG-GCU----GGGAAUAUUUG--GAAACCAGAA------------------------------------------------------------------UUUGG
AADM01000245.1/23026-22856     AUCCUUAUGC-ACGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUA--UUGCUGGUUGAAAUUAACAUUUAA-CCUGACC---CGCUCCU--CAU-AG-UUUUAAGUGUCUUUU-----------------UACA-CUG--UAG-CU-AUG--UAGGGAAUUUUUG--GAAUAUUUAUAUUUUGUACUCUUG---------------------------------------------------CAAAAC
ABBC01001255.1/19365-19501     AUCCGAGUGC-ACGGGUCU-UACGUU-UCCAGUGAAGGUUCG-CCUGAGGCAACGUUU--UUGCUAGUUGAAAACUACAAAC---UUAGAC----CGCUCC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-GCU----GGGAAUUUUUGAAAAAAUUUAUC-----------------------------------------------------------------UUUAAA
AATX01000107.1/49292-49428     AUCCGAGUGC-ACGGGUCU-UACGUU-UCCAGUGAAGGUUCG-CCUGAGGCAACGUUU--UUGCUAGUUGAAAACUACAAAC---UUAGAC----CGCUCC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-GCU----GGGAAUUUUUGAAAAAAUUUAUC-----------------------------------------------------------------UUUAAA
AASO01000240.1/58-194          AUCCGAGUGC-ACGGGUCU-UACGUU-UCCAGUGAAGGUUCG-CCUGAGGCAACGUUU--UUGCUAGUUGAAAACUACAAAC---UUAGAC----CGCUCC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-GCU----GGGAAUUUUUGAAAAAAUUUAUC-----------------------------------------------------------------UUUAAA
ABBB01000091.1/60646-60782     AUCCGAGUGC-ACGGGUCU-UACGUU-UCCAGUGAAGGUUCG-CCUGAGGCAACGUUU--UUGCUAGUUGAAAACUACAAAC---UUAGAC----CGCUCC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-GCU----GGGAAUUUUUGAAAAAAUUUGUC-----------------------------------------------------------------UUUAAA
CP000582.1/123212-123076       AUCUUUGCGCAUGGGGUUA-UAUCCAAAGCUGUGAAGUCUUA-ACUGAGCUUGGAAUA--UUGCUGGUUGAAAACUAAA------UUCCAUA---CCCCGU---GAC-GG-UCGCG-----------------------------CA--CG--CG--UC-GUC----ACGAAUUUCUG--CAGGCGCACCA----------------------------------------------------------------CACGCG
AAIW01000278.1/37304-37168     AUCCAAGUGC-ACGGGUCU-UACGUU-UCCAGUGAAGGUUCG-CCUGAGGCAACGUUU--UUGCUAGUUGAAAACUGCAAAU---UUAGAC----CGCUUC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-GCU----GGGAAUUUUUG--AACAACUUUCAC---------------------------------------------------------------AAAAGU
AACI02000576.1/2356-2546       AUCCUUAUGC-ACGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUU--UUGCUGGUUGAAAUUUAAUUAUAAACCAGACC---GUCUCC---UCA-UG-GUCGCUUAUCGGUGUUCGCUUUUGAAUA----CUUC--AA--GAC-UA-UGU---AGGGAAUUUUUG--GAAUUUUUUUCUUAUUUAUCGAUAUUUAAACUU------------------------------------------UCAAAA
AACF01000119.1/10356-10566     AUCCUUAUGC-AAGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUU--UUGCUGGUUGAAAUUUAAUUAAA--CCAGACC---UGCUCC---UCA-UU-GUCGCCAGUUAGAUGUUCGCUUCAUG------AACAUCUC-AGAU-AA-UGU---AGGGAAUUUUUG--GAAUACUUUUAUUUUCUAAUCAUGAAUUUUCCCAUCAAGAUAACCGAUGAGAGA---------------------AGGAGU
AAJI01000076.1/250-381         AUCCAAGUGC-ACGGGUUU-UACGUU-ACCAGUGAAGGUUCG-CCUGAGGCAACGUUU--UUGCUAGUUGAAAACUACAACU---ACUGAC----CGCUCC----AU-GU-UGGUC---------------------------UUCG--GA--UCG-GC-------UGGGAAUUUUUG--AACAAAAGCA-----------------------------------------------------------------AU----
AABZ01000001.1/29367-29202     AUCCUUAUGC-ACGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUU--UUGCUGGUUGAAAUUUAAUUAUAAACCAGACC---GUCUCC---UCA-UG-GUCGUUUAUCGGUGUUCGCUUUUGAAUA----CUUC--AA--GAC-UA-UGU---AGGGAAUUUUUG--GAAUAUUUCU-----------------------------------------------------------------UUUA--
U18778.1/15676-15446           AUCCUUAUGC-ACGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUU--UUGCUGGUUGAAAUUUAAUUAUAAACCAGACC---GUCUCC---UCA-UG-GUCAAUUCGGUGUUCGCUUUUGAAUA------CUUC--AA--GAC-UA-UGU---AGGGAAUUUUUG--GAAUACCUUUUUUCAUUACCGAUAUUCAUUCUUUCAAAGGGACUGUUUAUUUUUCUUUGGAAGUAAUAUCAAAAAAUAGGU
AAEG01000006.1/103924-103694   AUCCUUAUGC-ACGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUU--UUGCUGGUUGAAAUUUAAUUAUAAACCAGACC---GUCUCC---UCA-UG-GUCAAUUCGGUGUUCGCUUUUGAAUA------CUUC--AA--GAC-UA-UGU---AGGGAAUUUUUG--GAAUACCUUUUUUCAUUACCGAUAUUCAUUCUUUCAAAGGGACUGUUUAUUUUUCUUUGGAAGUAAUAUCAAAAAAUAGGU
AABY01000063.1/21244-21029     AUCCUUAUGC-ACGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUU--UUGCUGGUUGAAAUUUAAUUAUAAACCAGACC---GUCUCC---UCA-UG-GUCAAUUCUGUGUUCGCUUUUGAACA------CUUC--AG--GAC-UA-UGU---AGGGAAUUUUUG--GAAUACUUUUUUUUCGUUUACCGAUAUUCAUUCUUUCAAAGAAACUUUUCAUCUUUCUUU---------------GGAAGU
AADS01000270.1/32451-32584     AUUCUUGUGC-UCGGGCACGUACUGUCGCCAGUGAGGUCUUU-ACCGAGGCACAGUCU-UUUGCUGAUUGCAAAUUACACA----UCCGAA----CACGUC---UGU-UG-GC------------------------------UUCG-------GC-CU-UCA----G-CAAUUUUUG--GAAAAACCCU-----------------------------------------------------------------UCACUU
AE017356.1/390372-390503       GUCCUUGUGCUAGGGUUAG-AGCUUCUGACAGUGAGGAGAAA-UCCGAGUCGAAGCAA--UUGCUGAUUGCAAAAAAUA------UCCUA-----CACGUA---AUG-UC--CAUC---------------------------GUAA--GG--UGU-GA-CAU---U--CAAUUUCUG--GCA-AAGUAC-------------------------------------------------------------------ACUU
AAEY01000066.1/357595-357726   GUCCUUGUGCUAGGGUUAG-AGCUUCUGACAGUGAGGAGAAA-UCCGAGUCGAAGCAA--UUGCUGAUUGCAAAAAAUA------UCCUA-----CACGUA---AUG-UC--CAUC---------------------------GUAA--GG--UGU-GA-CAU---U--CAAUUUCUG--GCA-AAGUAC-------------------------------------------------------------------ACUU
AACO02000129.1/36387-36520     GUCCUUGUGCUAGGGUUAG-AGCUUCUGACAGUGAGGAGAAA-UCCGAGUCGAAGCAA--UUGCUGAUUGCAAAAAAUA------UCCUA-----CACGUA---AUG-UC--CAUC---------------------------GUAA--GG--UGU-GA-CAU---U--CAAUUUCUG--GCAACG-UAC-----------------------------------------------------------------ACAUCG
AAZN01000370.1/73687-73536     AUCCUUAUGC-AUGGGAAA-UACACAUUUCAGUGAGGAUUCG-UCCGAGAUUGUGUUU--UUGCUGGUUGAAAUUUAAA------UUUAAUUUUAACCUGA---CCC-UU-CUCCUCAUAGU---------------------CAAC-UAU--UAU-AA-UGGAUAUUCGCUUUAUUG--AAUAUCUUUU-----------------------------------------------------------------AAAAGA
AAFP01000576.1/27349-27217     GUCCUUGUGCUAGGGUUAG-AGCUUCUGACAGUGAGGAGAAA-UCCGAGUCGAAGCAA--UUGCUGAUUGCAAAAAAUA------UCCUA-----CACGUA---AUG-UC--CAUC---------------------------GUAA--GG--UGU-GA-CAU---U--CAAUUUCUG--GCAAAGUACA-------------------------------------------------------------------CUCU
AANW02001764.1/480-354         CGCCUUGCGC-UCGGGCAA-UAUCUA-UUUAAUGA--CAGAA-AUGGAAAGUAGAUGA--UUGCUAGUUUAAAACUAAA------UCCAGC----CCAGGU-----A-CC-ACGUG----------------------------UCU--UG--CGU-CG-G------ACCAAUUUUUG--UACUCGUUUU-------------------------------------------------------------------AAUC
AACP01000036.1/91007-91135     AGC---------GAGGCAGGCGCUUCAUCCAGUGAGGUCUUU-ACCGAGGAGAAGCUU-AUUGCUGAUUGCAAAUUACC------UAUAUUG---CACGUCCU-UGC-UG-UCA------------------------------CCA------UGA-CG-GCC---UGGCAAUUUUUG--GCACCCAUCC------------------------------------------------------------------UUUGG
X13840.1/1-118                 ---UUUGCGCUUGGGGCAA-UAUUAUAGCGCGUGA--CCGAA-AGGGAUGCAUAAUUA--UUGCUAGUUGAAAACUAAU------C-UAAUG---GCUGCG-------GU-GACCC---------------------------CUCG--UG--GUC-AGG------CUGCAAUUUUUG--AAA------------------------------------------------------------------------AA----
D63682.1/100-232               AUCUUUGUGC-UCGGGCACGCGAUGGCGACGUUGAAGGAA---ACUGAGUCCCAUCUA-AUUGCUGGUUGCAAACUAAA------UUCCACA---CUCUUC----AC-UG-CACUC---------------------------UUCG--GA--GUC-UU-------UGGGAAUUUCUG----CCCGCCUA-----------------------------------------------------------------ACGGCG
AC149882.2/166659-166543       GUCUUUGCGC-AGUGGCAG-UAACAUAGCCAAUAAGGUCAA--ACCGAGGCGUGAUUA--UUGCUAAUUG-----------------UGAU----GAAGCU---UAU-UG-U--------------------------------ACA--------G-CA-CUG---CGGAAUAUGUUG--GCGCUUUAUA-----------------------------------------------------------------AAUAAA
AC190402.1/26804-26930         GGAACUGAGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCGGAGGUGUGAUCA--UUGCUAAUUGAAAACUUUUC-----UAUAAA----GGAACUG--GUC-UG-UAGUU---------------------------UAAA--AA--AAA-AA-AAU---CAGU--------------GUCACA-----------------------------------------------------------------AAGGAC
DQ451048.1/205-341             AGCUUUGCAU-AGUGGUAG-UACUGUAGCCAUUGAAGUUUU--UCAGAGGUGUGAUUA--UUGCUAAUUGAAAACAGGGA-----AACGAAG---CUCCUG---UCC-UG-UUUAA---------------------------UCUG--UA-UAAA-UG-UAA---UUUGUACUU-----GAGCCCCUUU-----------------------------------------------------------------ACUGGG
AL590450.1/23479-23642         GUCCUUACGC-AGG---AG-GCCUCU-AUCGAUGACGUUCAC-ACGGAGAUAGAGAGA--UUGCUAGGUUGGAA--AUC------CAAACC----ACUGCA---AAU-UC-AAGUCUUAUGUCUUUCGUGGCAUGAGCCCCCUCUCA-AGC--UUU-GGGAGG---AUGCAAUUUUUG--GAGUAGGCUUUUG--------------------------------------------------------------AAGCCU
ABIT01000802.1/5235-5099       AUCCGAGUGC-ACGGGUCU-UACGUU-UCCAGUGAAGGUUCG-CCUGAGGCAACGUUU--UUGCUAGUUGAAAACUACAAAC---UUAGAC----CGCUCC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-GCU----GGGAAUUUUUGAAAAAAUUUGUC-----------------------------------------------------------------UUUAAA
AAZY02000012.1/107951-108083   AGUCUUGCGCCAGGGGCAA-UGUCGUUGCAGGUGACGCCGA--GCGGAUGCGCGACUA--UUGCUAGUUGAAAACUACA------C-CAAUU---CCCUUC---UAU-CG-GCCCU----------------------------CUG--UG--GUC-UG-GU-----GGAAAUUUCUG----GGGCCCUG-----------------------------------------------------------------AGGGGC
AAKN02007150.1/17728-17588     AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCG--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACGGUCUCUA-----------------------------------------------------------------CGGAGA
M15957.1/271-411               AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AL844502.1/365248-365383       AUCUUUGCGGGAGGGGCAG-UAUCGCUGUAAAUGACGACUA--ACGGAUACGCGAUUA--UUGCUAGUUGAAAACUACU------C-CAAUU---CCCGU----CUC-GA-UGCUU---------------------------GAAA--AA--GCA-GA-GAG------CAAUUUUUG--UAGCCUUUCUUU---------------------------------------------------------------AUAAAG
AASC02060889.1/1492-1632       AGCUUUGCGC-AGUGGCGG-UACCAUAGCCAAUGAGGUUUU--ACCGAGGCGUGGUUA--UUGCUAGUUGAAAACUACU------CCCAAUAC--CCCGCAC--GGG-CU-GGCCU---------------------------UCAC--AG--GUU-AG-CUU--AGUGCAAUUUUUU--ACGGCUCUUA-----------------------------------------------------------------CGGGAG
AM055942.3/1615661-1615791     AUCCUUGCGGUAGGGGCAA-UGUCGCUGCAAGUGACGCCUA--GCGGAUGCGCGAUGA--UUGCUAGUUGAAAACUACU------C-CAAUU---CCCGU----UCG-CC-GACCC---------------------------GAAA--GG--GUC-GG-CGG------CAAUUUCUG--GGG-CCCCCC-------------------------------------------------------------------GGGG
AC189493.2/83218-83068         AUCUUUGCGCUUGGGGCAA-UGACGCAGCUAAUGAGGUACUA-ACCGAGGCGCGUCUA--UUGCUGGUUGAAAACUAUUU-----CCAAAC----CCCCUCC--UGG-GC-CUAAG---------------------------CUUG-UCU--UGG-GC-CUU---CGAGAAUUUCUG--GAAGGGCUCCCUCCGGGGU--------------------------------------------------------AAAGCU
AACE03000002.2/368765-368919   AUCCUUAUGC-ACGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUA--UUGCUGGUUGAAAUUUUUAA-----CCUGAC----CGCUCC---UCA-UA-GUUUAAUGUGUCUUUUUUA-------------CACU-AUA-UGGC-UA-UGC---AGGGAAUUUUUG--GAAUUAUCCU-----------------------------------------------------------------CUGAUG
AAGF03001264.1/335958-336087   AACCUCGCGACAGGGGCAA-UAUAGCAGCAAGUGACGGUUA--ACUGAUGCGCUAUUA--UUGCUAGUUGAAAACUACU------U-CAAU----AAGUGG---AAA-CG-ACGCU---------------------------------UG--CGU-CG-GGU----CCCAAUUUCUG--GAAGGUCGUA-------------------------------------------------------------------UGAC
ABRQ01104616.1/4922-4782       AGCUUUGCGC-AGUGGCAA-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCG--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--UUGGCAAUUUUUG--ACGGUCUCUA-----------------------------------------------------------------CGGAGA
CR382136.2/1404151-1404006     AUCUUUAUGC-AGGGGCAU-UACGUGUAUCAGUGAGGAUUCG-UCCGAGAUCAUGUUU--UUGCUGGUUGAAAACUAUAA-----CCUGAC----AGCUCCU--UAU-UA-UUAUGGCUUU----------------------AUGC-UUU--UGA-UA-UUA---AGGGAAUUUUUG--GAAUUCUUCU-----------------------------------------------------------------UUUAGA
AAWR02035467.1/41938-42078     AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCC---GUGACG-ACUUG----------------------------AAA--UA-UAGU-CGGCAC---UGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------CGGAGA
AAGD02002631.1/646-784         AGCUUUGCGC-UGGGGCGA-UAACGUGACCAAUGAGGCUUU--GCCGAGGUGCGUUUA--UUGCUGGUUGAAAACUUUU------CCCAAUUG--CCCGCG---AUG-AC-CCCUG----------------------------AAA--CAUGGGU-GU-CAU---ACGCAAUUUUUG--AACGCCUCAA------------------------------------------------------------------GGAGG
AAGJ04107959.1/2135-2275       AUCUUUGCGC-AGAGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCGCGAUUA--UUGCUAGUUGAAAACUUAU------CCCAAUAC--CCCGCU---CUGACG-ACGUG----------------------------AAA--UA-CCGU-CGGCUG---UAGCAAUUUUUC--CAGAUCUCCA-----------------------------------------------------------------AGGAGA
ABEG02000949.1/11902-11764     AGCUUUGCGC-UGGGGCGA-UAACGUGACCAAUGAGGCUUU--GCCGAGGUGCGUUUA--UUGCUGGUUGAAAACUUUU------CCCAAUUG--CCCGCG---AUG-AC-CCCUG---------------------------AAAC-ACG--GGU-GU-CAU---ACGCAAUUUUUG--AACGCCUCCA------------------------------------------------------------------GGAGG
AACS02000001.1/566465-566333   UCUCUUGUGC-UCGGGCAUGUGCUGUCGCCAGUGAGGUUUCU-ACCGAGGCACAGCCUAUUUGCUGAUUGCAAAUUACACA----UCCGAA----CCCGU----CUC-UU-AGC-----------------------------UUCG------GCU-AU-GAG------CAAUUUUUG--GAAAAAUUUC-------------------------------------------------------------------ACUU
AE016817.6/721964-721809       AUUCUUAUGC-ACGGGAAA-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGUGUUA--UUGCUGGUAAAAUAAUAUAAAC---CAUGACC---CGCUCC---UCA-UG-GUCAUAGAUGUCCUAGUAC-------------AUCG--CG--GAC-UA-UGU---AGGGAAUUUUUG--GAAUGACACA-----------------------------------------------------------------AUUAUA
AAPE02005503.1/37803-37943     AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUUA--UCCGAGGCACGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCC---GUG-AC-AACUUG--------------------------AAAU-AUA--GUU-GG-CAC---UGGCAAUUUUUG--ACAGUCUCUA-----------------------------------------------------------------UGGAGA
AAEC03000003.1/2600987-2601123 AUCCGAGUGC-ACGGGUCU-UACGUU-UCCAGUGAAGGUUCG-CCUGAGGCAACGUUU--UUGCUAGUUGAAAACUACAAAC---UUAGAC----CGCUCC---AGU-UG-GUC-----------------------------UUCG------GAU-CG-GCU----GGUAAUUUUUGAAAAAAUUUAUC-----------------------------------------------------------------UUUAAA
ADTU01005844.1/39857-39997     AGCUUUGCGC-AGUGGCGA-UAUCGUAACCAAUGAGGUUCU--ACCGAGGUGCGAUUA--UUGCUAGUUGAAAACUUUU------ACCAAUAC--CCCGCCA--UGA-CG-AUGUG----------------------------AAA--UA-CCAU-CG-GCU--ACGGCAAUUUUUG--AAAGUUUCUG-----------------------------------------------------------------CGGAAA
AAIL02000028.1/1015369-1015502 AUCCAAGUGC-ACGGGCGU-UUUCCUUCUCCGUGAAGCGAUAAGCUGAGAGAGGAAUU--UUGCUAGUUGAAAACUAUAC-----ACUGAC----CACUCC---UGG-UU-GGG-----------------------------UUCG------CCU-GG-CCA----GGGAAUAUUUG--GAACCCUUCA------------------------------------------------------------------CAAGC
AAWZ02025418.1/39904-40044     AGCUUUGCGC-AGUGGCAG-UAUCGUAGCCAAUGAGGUUAA--UCCGAGGCGCGAUUA--UUGCUAAUUGAAAACUUUU------CCCAAUAC--CCCGCCA--UGA-CG-ACUUG----------------------------AAA--UA-UAGU-CG-GCA--CUGGCAAUUUUUG--ACAGUCUCUG-----------------------------------------------------------------CGGAGA
AAQY02000456.1/44132-43994     AUCUUUGUGCUUGGGGCAA-UACGAUAGUGUGUGAAGCUUU--GCUGAUGCAUCGUGA--UUGCUAGUUGAAAACUACU------C-CAACA---CCCGUG---GGA-AG-GCC------------------------------ACU------GGC-CG-GCU---C--CAAUUUCUG--UUUUAUCUCCCCUCUUGC---------------------------------------------------------GGGGGU
AACU03000146.1/753634-753781   AUUCUAGUGC-ACGGGUUU-UACGCAUAUCAGUGAGGAUUCG-UCCGAGAUUGCGUUU--UUGCUAGUUGAAAACUACAUA----CCUGAC----CACUCC---AUG-CG-GGC-----------------------------UUCG------GCU-UA-CAU----GGGAAUUUUUG--GAACCAAAAGAUCUCAUUGAGGA----------------------------------------------------UUUUUG
Z74042.2/30433-30295           AGCUUUGCGC-UGGGGCGA-UAACGUGACCAAUGAGGCUUU--GCCGAGGUGCGUUUA--UUGCUGGUUGAAAACUUUU------CCCAAUUG--CCCGCG---AUG-UC-CCCUG----------------------------AAA--CAUGGGU-GG-CAU---ACGCAAUUUUUG--AAAGCCUCUA------------------------------------------------------------------GGAGG
AFQF01001265.1/35199-35370     AUCCAAGUGC-AUGGGCGU-UUUCCUUCUCCGUGAAGCGAUAAGCUGAGAGAGGAAUU--UUGCUAGUUGAAAACUAUAC-----ACUGAC----CGCUCC---UUG-UU-GGG-----------------------------UUCG------CCU-GG-CAA----GGGAAUUUUUG--GAACUCUUUAUUUUCUUUCAUUGCGACCAGUUCUUGAUGGACUGCCG----------------------------UGAAGA
#=GC SS_cons                   ::::::::::.::::::<<.-<<<<<-<<<____________._____>>>>>>>>--..>>,,,,<<<<__________.....__>>>>,...,,,<<<...<<<.<<.<<<<<...........................____..>>..>>>.>>.>>>...->>>,,,,,,,,..,,,,<<<<__.................................................................__>>>>
#=GC RF                        AUCcUUGuGC.AgGGGcAa.UaccccugcCAGUGAGGaUucg.uCcGAGgcgggguUa..uUGCUAgUugAAAACUAuuu.....cccaAca...ccCgcc...uca.ug.gccuc...........................uuca..ga..ggc.ca.uga...aggcAAUUUUUG..gAAuccccuu.................................................................aagggg
//
# STOCKHOLM 1.0

#=GF AC   RF00016
#=GF ID   SNORD14
#=GF PI   U14
#=GF DE   Small nucleolar RNA SNORD14
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Mifsud W; 0000-0002-9805-6461
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   64.00
#=GF TC   64.10
#=GF NC   63.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300888;
#=GF DR   snoopy; Homo_sapiens300754;
#=GF DR   snoopy; Saccharomyces_cerevisiae300053;
#=GF RN   [1]
#=GF RM   8668536
#=GF RT   An essential domain in Saccharomyces cerevisiae U14 snoRNA is absent in
#=GF RT   vertebrates, but conserved in other yeasts.
#=GF RA   Samarsky DA, Schneider GS, Fournier MJ
#=GF RL   Nucleic Acids Res 1996;24:2059-2066.
#=GF CC   U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of
#=GF CC   eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop
#=GF CC   region (known as the Y-domain) which is essential for function. A similar
#=GF CC   structure, but with a different consensus sequence, is found in plants,
#=GF CC   but is absent in vertebrates [1].
#=GF WK   Small_nucleolar_RNA_SNORD14
#=GF SQ   18


X96815.1/716-841       -----UCACGGUGAUGAAAGA--------CUGGUUCCUUA--ACAUUCGCAGUUUCCACGGUA-GGAGUAC---------GCUUACGAAC-CCAUCGUUA-GUACUCUCGGUGACCGCUCUUCUUUAGAGACCUUCCUA-GGAUGUCUGAGUGA-----
Z49897.1/2330-2421     -----UCACAGUGAUGA-CUGGU----------UUCCAAU---CAUUCGCAGUUUCUACCAGAA--------AGCUUU--GCCU------------------------------GGUGUUGGCU--AGUAACCUUCCUU-GGAUGUCUGAGUGA-----
Z49897.1/1656-1746     -----UCACAGUGAUGA-CUGGU----------UUCCAAU---CAUUCGCAGUUUCUACCAGAA--------AGCUUU--G-CU------------------------------GGUGUUGGCC--UGUAACCUUCCUU-GGAUGUCUGAGUGA-----
AC006597.2/8154-8065   -----UCACUGUGAUGA-UGGUU----------UUCCAA----CAUUCGCAGUUUCCACCAGAA--------AGGUUUU--CCU-----------------------------UAGUGUUGGGU----AAACCUUCCUU-GGAUGUCUGAGUGA-----
D88010.1/2919-3009     -----UCACUAUGAUGA-UUGGU----------UGCCAGA---CAUUCGCAGUUUCCACCAGAA--------AUGUUUUU-CCU------------------------------UAUGUUGGCC----AGUUCUUCCUU-GGAUGUCUGAGUGA-----
Z49896.1/3386-3480     -----UCGCUGUGAUGAACUU-----------GUUCCAAAG-CCAUUCGUAGUUUCCACCAGAU---------GCCGAAAGGCU------------------------------GAUGAUGGCC--UAGCACCUUCCUU-GGAUGUCUGAGCGA-----
Z49896.1/1591-1686     -----UCGCUGUGAUGAAUGUGA----------UUCCAAAG-CCAUUCGUAGUUUCCACCAGAU--------GUCU-CACGACU------------------------------UAUGAUGGUU--UAUUACCUUCCUU-GGAUGUCUGAGCGA-----
Z49896.1/2359-2452     -----UUGCUAAGAUGAAUACGA----------UUCCAAAG-CCAUUCGUAGUUUCCACCAGAU---------GUCGUAAGACU------------------------------CAUGAUGGCUC----UACCUUCCUU-GGAUGUCUGAGCGA-----
Z35302.1/1-124         ---UAUGGCAAUGAUGAUGAAAGAUAAGGCUUGUUUCUCA--ACAUUCGCAGUAGCCGCCUAAGAGCUUUCGCCACGCCAGGCU----------------CGAGAGCU----------UGUGCUGUUGAAUCCUUCCUU-GGAUGUCUGAGCCAUA---
Y11048.1/1341-1463     ----AUGGCAAUGAUGUUGAAGUUAAAGGCUUGUUUCUCA--ACAUUCGCAGUAGCCGCCUAAGAGCUUUCGCCCUGCCAGGCU----------------UGAGAGCU----------UGUGCUGUUUAAUCCUUCCUU-GGAUGUCUGAGCCAUA---
AP002485.2/15585-15700 --------CAAUGAUGAUAAAUUU-AAGGCUUGUUUCUCAUAACAUUCGCAGUUGCCGCCUAAGAGCUUUCGCCCUGCCAGGCU----------------UGAGAGCU----------AAUGCUGUUAAUUCCUUCCUU-GGAUGUCUGAGC-------
Y11048.1/1797-1925     UGCAUUGCAAGUGAUGACAAAAUC-AAGGCUUGUUUCUCG--ACAUUCGCAGUUGCCGCCUAAGAGCUUUCGCCCUGCCAGGCU----------------UGAGAGGU----------AGUGCUGCCAAAUCCUUCCUU-GGAUGUCUGACGCAAUGCA
Z35299.1/1-129         UGCAUUGCAAGUGAUGAUGAAGUC-AAGGCUUGUUUCUCU--ACAUUCGCAGUUGCCGCCUAAGAGCUUUCGCCCUGCCAGGCU----------------UGAGAGCU----------AGUGCUGCCAAAUCCUUCCUU-GGAUGUCUGAUGCAAUGCA
AJ310377.1/341-211     UGCAUGGCAAAUGAUGCUAAAAGC-AAGGCUUGUUUCUCAUAACAUUCGCAGUUGCCGCCUAAGAGCUUUCGCCUUGCCAGGUU----------------UGAGAGCU----------AAUGCUGCUAAUUCCUUCCUU-GGAUGUCUGAUGCAAUGCA
AF332622.1/717-819     --------UAAUGAUGCUAAAA-----------UUUCUCAUAGCAUCUGCAGUUACUGCCUAAUAGCUUUCGCCCUGCCAGGCU----------------UGAGAGCU----------AGUGCUGUUAAAUCCUUCGUU-GAAUG-C--AUA-------
Z35301.1/1-128         CGGU-GCCCUAUGAUGACAAAAUC-AAGGCUUGUUUCUCU--ACAUUCGCAGUUGCCGCCUAAGAGCUUUCGCCCUGCCAGGCU----------------UGAGAGCU----------AAUGCUGCAGAAUCCUUCCUU-GGAUGUCUGAGGGCCGCCG
Z35303.1/11-130        --------CUCUGAUGAUACAAUUGAAGGCUUGUUUCUCUAAACAUUCGCAGUGGCCGCCUAAG--------AUCUUUC-GCCU----UCGCCA----GG--------CUUGAGAGAUAAUGCUGCUUUAUCCUUCCUU-GGAUGUCUGAGAUC-----
U29583.1/543-654       ---UCAACAGGUGAUG---AAAU----------UUCCAUUGAACAUUCGCAGUUUCC-CCGGA--GCGGCA------------UACGAAC-CCA-AUUU--UGCCGC--------AGAUGUCGUGCAUAGUCCUUCCUUUGGAUGUCUGAUGUUG----
#=GC SS_cons           .....<<<<--------------......-----------..----------------------<<<<<<<.____________.................>>>>>>>......-------------------------.---------->>>>.....
#=GC RF                .....ucgcagUGAUGAuaaaau......CUuGUUuCuca..ACAUUCGCAGUUuCCaCCuaAgaGcgcuc.accUgccAGgCU.................gagcgCu......aaugauuGCUguuaAauCCUUCCUU.GGAUGUCUGAgcga.....
//
# STOCKHOLM 1.0

#=GF AC   RF00017
#=GF ID   Metazoa_SRP
#=GF PI   SRP_euk_arch; 7SL; CeN107
#=GF DE   Metazoan signal recognition particle RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19838050
#=GF SS   Published; PMID:19838050
#=GF GA   70.00
#=GF TC   70.00
#=GF NC   69.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.49 -Z 549862.597050 CM SEQDB
#=GF CL   CL00003
#=GF DR   URL; http://rnp.uthscsa.edu/rnp/SRPDB/SRPDB.html;
#=GF DR   SO; 0000590; SRP_RNA;
#=GF DR   GO; 0006617; SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition;
#=GF DR   GO; 0005786; signal recognition particle, endoplasmic reticulum targeting;
#=GF RN   [1]
#=GF RM   11839493
#=GF RT   Towards the structure of the mammalian signal recognition particle.
#=GF RA   Wild K, Weichenrieder O, Strub K, Sinning I, Cusack S
#=GF RL   Curr Opin Struct Biol 2002;12:72-81.
#=GF RN   [2]
#=GF RM   10678824
#=GF RT   Crystal structure of the ribonucleoprotein core of the signal recognition
#=GF RT   particle.
#=GF RA   Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA
#=GF RL   Science 2000;287:1232-1239.
#=GF RN   [3]
#=GF RM   11243816
#=GF RT   Structural and energetic analysis of RNA recognition by a universally
#=GF RT   conserved protein from the signal recognition particle.
#=GF RA   Batey RT, Sagar MB, Doudna JA
#=GF RL   J Mol Biol 2001;307:229-246.
#=GF RN   [4]
#=GF RM   12520023
#=GF RT   SRPDB: Signal Recognition Particle Database.
#=GF RA   Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T
#=GF RL   Nucleic Acids Res 2003;31:363-364.
#=GF RN   [5]
#=GF RM   12140321
#=GF RT   Prediction of signal recognition particle RNA genes.
#=GF RA   Regalia M, Rosenblad MA, Samuelsson T
#=GF RL   Nucleic Acids Res 2002;30:3368-3377.
#=GF RN   [6]
#=GF RM   19838050
#=GF RT   Kinship in the SRP RNA family.
#=GF RA   Rosenblad MA, Larsen N, Samuelsson T, Zwieb C
#=GF RL   RNA Biol. 2009;6:508-516.
#=GF CC   The signal recognition particle (SRP) is a universally conserved
#=GF CC   ribonucleoprotein. It is involved in the co-translational targeting of
#=GF CC   proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S
#=GF CC   RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP
#=GF CC   consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54
#=GF CC   proteins. Eukaryotic and archaeal 7S RNAs have very similar secondary
#=GF CC   structures, as represented by this family. Eight helical elements fold
#=GF CC   into the Alu and S domains, separated by a long linker region [1,2]. The
#=GF CC   Alu domain is thought to mediate the peptide chain elongation retardation
#=GF CC   function of the SRP [1]. The universally conserved helix which interacts
#=GF CC   with the SRP54 M domain mediates signal sequence recognition [2,3]. In
#=GF CC   eukaryotes and archaea, the SRP19-helix 6 complex is thought to be
#=GF CC   involved in SRP assembly and stabilises helix 8 for SRP54 binding [1]. The
#=GF CC   Signal Recognition Particle Database (SRPDB) [4] provides compilations of
#=GF CC   SRP components, with phylogenetic data and structural illustrations. Many
#=GF CC   sequences below the threshold for this family are clearly closely related,
#=GF CC   but are most likely to be SRP RNA derived pseudogenes. The human genome in
#=GF CC   particular is known to contain a large amount of SRP RNA related sequence,
#=GF CC   including Alu repeats. While the threshold of this family is set high so
#=GF CC   as to minimise the number of hits to such regions, it is likely that some
#=GF CC   remain.
#=GF WK   Signal_recognition_particle_RNA
#=GF SQ   91


AL627171.1/120155-119857       GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGUGGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGAGCAA--CAUAGCGAG---ACCCCGUCUC-U-----
AAQA01001314.1/4979-5279       GCCGGGCGUUG-----UGGC---GAGCGCUUGUAA-UCC----AAGUGAC-----UG-GGAGGC----AUGUGGUGGCG-GAUGGAGU--GAGAGGAGGA-GUCCUG-GCUGA---UGCUUG----GCGGUGGC--------------------------------GACCGAGC-GU-CCAGGCCA-AGCGU-GGCGUCGACAAGGUGUCGAG-AUAGGAGUGUCAUCGGUACCUGGUCG-CAUAAUGAGGGGCGUAC--GGCUCAGGGCCGAAAGGCAGCAGGCAAAAGU-CCCCGCGUC-AUGACAG-UGGCC-GG-AUAGC-GCUUGC--------GAGUCGU----CGGU----AUUAGU-C-AG---CCUUGUCAA--UACCUCCAG---ACCCAUCG----CUUUU
ABEP02026228.1/63371-63072     GCUGGGCGUGG-----UGGC---GCGCGCCUGUAA-UCC-----AGCUAC-----CU-GGAGGC----UGGGGUUGGUG-GACCGCUU--GAUGCCGGGG-GUUCUG-CGGCG----UGCUGU---CCUAUGGC--------------------------------GAUCGGGC-GU-CCACGCUA-AGUUC-GGCAUCGAUAUGGUUACCCC-GGGGGAGCCC-AGGGCAACCAGGUCG-UCUAAGGAGGGACGCAC-CGGCCCAGGUUGGAAACAAAGCAGGCAAAAGU-CCCCGUGUC-GA-UCAG-UAGCG-GG-AUCGC-GCCCGU--------GAAUAGG----CACUG----CGUCU-C-AG---CCCGGCCAA--UAUAGUGGG---ACCCAAUUCU-UCUU--
M20910.1/127-406               ------CGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGUGGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGAGCAA--CAUAGCG----------------------
X01055.1/13-289                -----------------GGC---GUGUGCCUGUAA-UCC-----AGCUAC-----UU-GGAGGC----UUGGGCUGUCG-GAUCGCUU--GAGUCCAUGA-GUUCUG-GGCUG----CACUGA---GCUAUGUC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGUAUCAAUAUGGUUUUCCU-GGGGGAGCCU-CGGAUCACCAGGUUGCUCUAAGGAGGGGUGAAC-CGGCCUAGGUCGGAAACGGAGCAGGUCAAAAC-CCCCGUGCC-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CGGUG----CAGAA-C-AG---CCUGAACAA--CACAGCGAG---AC---------------
X04249.1/67-346                ------CGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGUGGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGAGCAA--CAUAGCG----------------------
X02067.1/61-359                GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGUGGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGAGCAA--CAUAGCGAG---ACCCCGUCUC-U-----
AC099934.14/67547-67847        GCCGGGCGCGG-----UGGC---GCACGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGACAGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UUU---
AL139099.3/76053-75753         GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UUU---
Z30973.1/7231-6933             ACCGAGCGUCG-----UGGC---GGGCGCUUGUGA-GUC-----AGCUUC-----UU-GACGGU----AGAUAAGUGUG-GAUGGAGU--GAGAGGAGGA-GUCCUG-UGUAU---GUCGUUG---UCAACGUC--------------------------------GACCGAGC-GU-CCGUGCCA-AGCGC-UGCGUCACCAGGGGAUGACU-GUCGGAAGAU-GGUCAGUCCCGGGUG-CAUAAGGAGUGGUGGAU--GGUUCAGGACCGAAAGGUAGCAGACAAAAGC-CACCGCGCG-GU-GCAG-UGGCC-GG-ACUGC-GCUUGU--------GAGUUGA----CACG----UAUACA-C-AG---CCUUCUCAA--UACCUUCAG---ACCACUUGUU-UUU---
Z34533.1/38793-39082           -------GUCG-----UGGC---GGGCGCUUGUGA-GUC-----AGCUUC-----UU-GACGGU----AGAUGAGUGUG-GAUGGAGU--GAGAGGAGGA-GUCCUG-UGUAU---GUCGUUG---UCAACGUC--------------------------------GACCGAGC-GU-CCGUGCCA-AGCGC-UGCGUCACCAGGGGAUGACU-GUCGGAAGAU-GGUCAGUCCCGGGUG-CAUAAGGAGUGGUGGAU--GGUUCAGGACCGAAAGGUAGCAGACAAAAGC-CACCGCGCG-GU-GCAG-UGGCC-GG-ACAGC-GCUUGU--------GAGUUGA----CACG----UAUACA-C-AG---CCUUCUCAA--UACCUUCAG---ACCACUUGUC-A-----
X04248.1/1-299                 GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-U-----
U40756.1/3688-3391             GCCGGGUACGG-----UGGC---GCGUGCCUGUAA-UCC----AAGCUAC-----UG-GGAGGC----UGAGGCUGGCG-GAUCGCUU--GAGCUCAGGA-GUUCUG-GGCUU----CAGCGG---ACUAUGUC--------------------------------GAUCGGGU-GU-CCGUACUA-AGUUC-GGUAUCGAUAUGGUGCUCCU-GGGGGAGCCC-GGGAUCACCAGGUCG-CCUAAGGAGGGGUGCCC-CGGCCCAGGUCGGAAACGAAGCAGGUCAAAGC-CCCCGUGCC-GC-UCAG-UAGUG-GG-AUCGC-GCCCGU--------GAAUAGA----CGCUG----UAGUU-C-AA---CCUGAGUAA--CACAGCGGG---ACUCAGUCUU-U-----
X01037.1/5-292                 GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG--------------------
AC126244.3/141271-141559       -----------------GGC---GCACGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGACAGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UUU---
AE001572.2/236401-236699       ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAUCUACUGCGUAGCG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GUGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGA----CUGC----CGUUAU-C-AG---CCCAACCGA--UAUGGUUGG---ACCACAAUCU--UUU--
AAWT01054001.1/400-696         GCCGGACGUAG-----CGGU---GUGCGUCUGUAA-UCC-----AACUAC-----UA-GGAGGC----CGGGUAUAUG--AAUGGUUU--GAGAUGAGGA-GUUCUG-UGAGC----AUUGCG---CCUAUGUA--------------------------------GAUCGGAU-GU-CCACAGUA-AGCUU-GGCGUCAACAUGGUUAUAUU-GUCGGAGGAU-AGAAUACCCAGGUUG-UUUAAUGAGAGAGGUAA-CGGCUCAGGGGAGAAAUCCUGCAGGCAAAACU-CUCCACGUC-AU-UCGG-UAUUG-GG-AUAGC-AUCUGU--------GAAUAGA----GCAGU----GUUGG-C-AG---CCUCAUCAA--UAUGACCAG---ACUCGUACCU--UU---
AATT01000260.1/65731-65425     GUUGGGUACAG----UCGC----GUGUGCCUGUAA----C--CGAAGC--C--GG------GAC-------UGGGAUAUGAAU----------GUACG---CGCUGUGG--GAUUUCGGGCC------------UUGGUUGUUCUUCGGAACAGUUUGGUCUUGCAGAGAGUCA-GUCCAUG-AUGAACU--UUGAGUUCAACAUUGGCACUCUUGCGGAAGCAGG-GUGUCGAGGUUG--UUAAAGA-GCUGUGGAA-AGCGUGAGGCUAGAAAUAGAGCAGCGAAAAGC-AGCCGCUUGA---AGUGGUGU-UGCGGAUAGC-UGGCUUGA----GA-------GAUUCGCCUUGGCUUG-CCA-CGUCG-AGUAUCAGAC--------UUCC--AUCCC----UU----
AC084446.1/16506-16208         ACCGGGUGUCG-----UGGC---GGGCGCCUGUGA-GUC-----AGCUUC-----UU-GACGGU----AGACAAGUGUG-GAUGGAGU--GAAGGGAGGA-GUCCUG-UGGGU---GUUGUCG---GCAACGGC--------------------------------GACCGAGC-GU-CCGUGCCA-AGCGC-UGCGUCGCCAGGGGUCUCCG-GUCGGAAGGC-UGGCGGUCCCGGGCG-CAUAAGGAGUGGUGCAC--GGCUCAGGGCCGAAAGGCAGCAGGCAAAAGC-CACCGCGCG-GU-GCAG-UGGCC-GG-AUAGC-GCUUGU--------GAGUUGU----CGCU----CGCCCA-C-AG---CCUCUCUGA--UACCUUCAG---ACCACUUGUC-AUU---
AAGD02010404.1/8312-8015       ACCGGGCGUCG-----UGGC---GGGCGUCUGUGA-GUC-----AGCUUC-----UU-GACGGU----AGACAAGUGUG-GAUGGAGU--GAAGGGAGGA-GUCCUG-UGGGU---GUUGUCG---GCAACGGC--------------------------------GACCGAGC-GU-CCGCGCCA-AGCGC-UGCGUCGCCAGGGGUCACUC-GUCGGAAGAC-GGGCGGUCCCGGGUG-CAUAAGGAGUGGUGGAU--GGCUCAGGGCCGAAAGGCAGCAGGCAAAAGC-CACCGCGCG-GU-GCAG-UGGCC-GG-AUAGC-GCUUGC--------GAGUUGU----CACU----CUCCCA-C-AG---CCUCUCUGA--UACCUUCAG---ACCGCUUGUC-AU----
AADD01137907.1/9486-9773       --------CGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUC---------
AABS01000318.1/14425-14147     -------------------------GCGCCUGUAA-UCC-----AGUUAC-----UU-GGAGGC----UUGGGUUGGAG-GACGGCGU--GAGAUUGGGA-GCCCUG-UGGCG----CUCUGC---CCUAUGUC--------------------------------GAUCGGGC-GU-CCGCGCUA-AGCUC-GGCGUCAAUAUGGACAUCCC-GGGGGAGCUU-GGGGUGGCCAGGUUG-UCUAAGGAGGAACGAAC-CGGGCGAGGCCCGAAAGGGAGCAGCCAAAAGUUCCC-ACGUU-GA-UCAG-UAGCG-GG-AUAGC-GCCUGU--------GAAUAGG----CGGAG----UGUCA-C-AG---CCCAGUCAA--UAUCGCAGG---ACCCGAUCCU-------
AAGE02003358.1/57464-57166     ACUGGGAGCG------UGGC----GUCUCCUGUAA-CGU-----GGCUGC-----UC-ACGGG-U--C-GGGUUACGG--ACUGAUUU--GAGGUUGGGGUCCACUGUGUGCCG--GGUAAG----UCCAUGUU--------------------------------GACGGGAC-GU-CCGCACUA-AGCUG-ACCGUCAAUAUGGGUGCAAU-GGGGGAGCCC-GAUGCAUUCAGGUUG-GCUAAAGAGAGAUGAAC-CGAGCGAGGGGUGAAAACCAGCAGCUAAAAGU-CUCCGCGGU-AA-GCAG-UAGUG-GG-AUCGC-GUCCCG--------GAGUGGA----CUUC----CGGUGC-C-AG---CCUGACCAA--UAUAGUCAC---ACUGUAAUCU-UUU---
AADC01117130.1/255294-255577   GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAG------------------------
AC157822.2/121901-122184       -----------------------GCACGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGACAGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-U-----
AAPN01002588.1/4286-4586       GCCGGGCGCGG-----UGGC---GCGCGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGCUCAGGA-GUUCUG-GGCUG----CAGUCC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGUAUCAAUAUGGUGAUCCU-CCGGGAGCGG-AGGGUUACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCC-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGU----UGCUG----CAGUC-U-AG---CCUGGGCAA--GAUAGUGAG---ACACGGUCUC-UUU---
AADB02016073.1/179675-179377   GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-U-----
X00952.1/3-299                 ACUGGAAGGU------UGGC----AGCUUCUGUAACUCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAUCUACUGCGUAGCG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GUGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGA----CUGC----CGUUAU-C-AG---CCCAACCGA--UAUGGUUGG---ACCACAAUCU-------
AAQB01008633.1/175519-175220   ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAAUCACUGUGUAGCG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GACAUCAAUAUGGGUGCCAU-GGAGGAGUCC-ACGGCAUUCAGGUUG-GCCAAGGAGGGACGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGUU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGAA----CUGC----CGUUAU-C-AG---CCCAACCAA-UUAUGGUUGG---ACCACAAUCU--UUU--
AASC02036016.1/26997-26697     GCUGGGAGUUG-----UGGC---GUGCUCCUGUAA-UCC-----AGCUAC----UUU-GGAGGC----UUGAGUCGGAG-GACGGUUU--GAGUGCGGGG-GUUCUG-CUCUC----GGGCGU---GCCAUGUC--------------------------------GAUCGGGU-GU-CCGCACUA-AGCCC-GGCAUUAAUAUGGUGAUCUU-GUAGGAAUAC-GAGAUUUCCAGGUUG-ACUAAGGAGGGACGAAC-CGGCCCAGGGGGGAAACCCAGCAGGCAAAAGUCCCC-GUGUC-GC-GCAG-UAGUG-GG-AUCGC-ACCCGU--------GAAUGGG----CGUUC----GUUGG-C-AG---CCCGUCCGA--UAUAAUCGG---ACCCGGCUCU--UAUU-
DQ285765.1/1-290               GCCGGGCGCGG-----UGGC---GCACGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGACAGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---AC---------------
X01056.1/2-295                 ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAUCUACUGCGUAGCG--GACCAG----CUCAUGUU----------------------------------CGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GUGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAACCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGA----CUGC----CGUUAU-C-AG---CCCAACCGA--UAUGGUUGG---ACCACAAUCU-------
AAHX01044897.1/9186-8886       GCCGGGCGCGG-----UGGC---GCACGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGACAGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UUU---
BX000700.38/167765-167484      GCCGGGUUCAG-----UGGU---GCGCGCCUGUAA-UCC----AAGCUAC-----UG-GGAGGC----UGAGGCUG-CG-GAUCGCUU--GAGCUCAGGG-CUUCUG-GACUG----CAGUGG---ACUAUGUU--------------------------------GAUCAGGU-GU-CCACACUA-AGUUC-GGUAUCGAUAUGGUGCUCCU-GGGGGAGCUU-GGGACCACCAGGUCG-UGUUAUGAGGGGUGAAC-CGGCCCAGGUCGGCGACGGAGCAGGUCAAAUC-CCCCGUGCU-GA-UCAG-UAGUG-GG-AUCAC-ACCUGA--------GAAUAGA----CACUG----CAGUG-C-AG---CCUGAGUGA--CACAG------------------------
AAFR03019305.1/83084-83384     GCCGGGCGUGG-----UGGC---GCGCGCCUGUAG-UCC----UAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----CUGUGU---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCCC-CUGGGAACGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCC-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----UACUC-C-AG---CCUGGGCAA--GAUAGUGAG---ACACGGUCUC-UUU---
AADB02016074.1/2338757-2339036 ------CGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGUGGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGAGCAA--CAUAGCG----------------------
AAPU01011054.1/166427-166722   ACUGGAAGGU------UGGC----AUCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGGAUCACUGUGUAGUG--GACCAG-----CCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCGA-GGAGGAGUCC-ACGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGU----CUGC----CAUUAC-C-AG---CCUUGCCAA----UUGUUGG---ACCACAAUCU--UUU--
AAPP01019528.1/176323-176606   ------------------GC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAUUCACUGUGUAGCG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-AAGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGAA----CUGC----CGUUAU-C-AG---CUCAACCAA--CAUGGUUGG---ACCACAAUCU-------
AAAB01008834.1/1158888-1159185 ACCGGGAGCG------UGGC----GUCUCCUGUAA-CGC-----GGCUAC-----UC-GUGGGU---C-GGAUUACGG--ACUGAUUU--GAGGGCGGGAG-UCCUGUGUGCUG--GACCAG----GCCAUGUU--------------------------------GACGGGGC-GU-CCGCACUA-AGCUG-GCCGUCAAUAUGGGUGUCAC-GGAGGAGUCC-GAGACAUUCAGGUUG-GCUAAGGAGAGACACAC-CGAGCGAGGGGUGACAACCAGCAGCUAAGAGU-CUCCGCGGC-AA-GCAG-UAGUG-GG-AUCGC-GUCCCG--------GAGUGGA----CUGC----CAGUGC-C-AG---CCCGACCAA--CACAGUCAC---ACUGUAAUCUUUU----
ABGA01125459.1/6006-5706       GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UUU---
ABBA01018109.1/65364-65664     GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UUU---
AANU01127736.1/6578-6278       GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UAG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCUGUCUC-UUU---
ABKE01001214.1/10841-11139     ACGGAGUGUCG-----UGGC---GGGCACUUGUGA-GCC-----AGCCUC-----UA-GGCCGU----AGAUUAUGGUG-GAGAGAGU--GAGGGAGGGA-UCCCUG-GUCGG---AAUUCGG---UCUACGAC--------------------------------GACCGGGC-GU-CCGUGCCA-AGCGA-UGCGUCACUAGGGGGUAAGA-CUCGGAAGGG-UCUCUCUCCCGGGUG-GAAAAGGACAACCGUAU--GGCUCAGGCCCGAAAGGGAGCAGGCAAAAGG-UUGCGCGCG-UUGACAG-UGGCC-GG-AUAGC-GUCUGC--------GAGUAAA----UCGA----UCUGAA-C-AG---CCCUUCUAA--UACCUCUCG---ACCCAUAAUC-GC----
ABBA01018120.1/60549-60270     ------CGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGUGGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGAGCAA--CAUAGCG----------------------
BX649540.7/48309-48605         GCCGGGCGCAG-----UGGC---GUGCGCCUGUAA-UCC----AAGCUAC-----UG-GGAGGC----UGAGGCUGGCG-GACCGCUU--GAGCUCAGGG-GUUCUG-GGCUG----CAGUGG---ACUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGUAUCGAUAUGGUGCUCCU-GGGGGAGCCU-UGGACUACCAGGUCG-UCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAGACGGAGCAGGUCAAAGC-CCCCGUGCC-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGA----CACUG----CAGUG-C-AG---CCUGAGUAA--UACAGCGGG---ACUCAGUCUU-------
ABGA01125411.1/4305-4605       GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGUGGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGAGCAA--CAUAGCGAG---ACCCCGUCUC-UUU---
AL590449.1/138985-139146       --------------------------------------------------------------------------------------------------------------------------------------GGG--------------------------CAGUAAGCAUG-GGCCUGG-AUGAUCU-C-CUUGUGGGCAG-UUGGGGAG-CCUGUAGGGG-UGCUCCAC-CUGCCA--UUAAAGCGGAGGGGAA-CGCAUGAGGGCGGAAACGCAGCAAUGAGUACC-UCCUGCAGG-GU-AGAGUCGC-C--AGCAGAC-CAUGCCAG---UCC-------------------------------------------------------------------UUUU--
CU179657.6/159276-158995       GCCGGGUUCAG-----UGGC---GCGCGCCUGUAA-UCC----AAGCUAC-----UG-GGAGGC----UGAGGUUG-CG-GAUUGCUU--GAGCUCAGGG-CUUCUG-GACUG----CAGUGG---ACUAUGUU--------------------------------GAUCGGGU-GU-CCACACUA-AGUUC-GGUAUUGAUAUGGUGCUCCU-GGGGGAGCUU-GGGACCACCAGGUCG-UGUAAUGAGGGGUGAAC-CGGCCCAGGUUGGCGACGGAGCAGGUCAAAUC-CCCCGUGCU-GA-UCAG-UAGUG-GG-AUCAC-ACCUGA--------CAAUAGA----CACUG----CAGUG-C-AG---CCUGAGUGA--CACAG------------------------
AABS01000247.1/111722-112007   ----------------UGGC---GUGCGCCUGUAA-UCC-----AGUUAC-----UU-GGAGGC----UUGGAUUGGAG-GACGGCGU--GAGAUUGGGA-GCCCUG-UGGCG----CUCUGC---CCUAUGUC--------------------------------GAUCGAGC-GU-CCGCGCUA-AGCUC-GGCGUCAAUAUGGACAUCCC-GGGGGAGCUU-GGGGUGGCCAGGUUG-UCUAAGGAGGAACGAAC-CGGGCGAGGCCCGAAAGGGAGCAGCCAAAAGUUCCC-ACGUU-GA-UCAG-UAGCG-GG-AUAGC-GCCUGU--------GAAUAGG----CGGAG----UGUCA-C-AG---CCCAGUCAA--UAUCGCAGG---ACCCAAUCCU--U----
ABSL01047197.1/65379-65676     -CCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-U-----
AAPQ01006440.1/468195-468493   ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAUCUACUGCGUAGCG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GUGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGA----CUGC----CGUUAU-C-AG---CCCAACCAA--UAUGGUUGG---ACCACAAUCU--UUU--
AAIZ01001735.1/77926-78223     ACUGGAAGGU------UGGC----AUCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-AGAUUGUGG--GAUGGCCU--GAGGCUGGGAAUCACUGUGUAACG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GCGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGAA----CUGC----CGUUU--CCAG---CCCA-CCAA--CAUGGUUGG---ACCACAAUCU--UUU--
AAGV020686351.1/312-612        GCCGGGCGCGG-----UGGC---GCGCGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCAGAGG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----CAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----UACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UUU---
AE014297.2/2648223-2648520     ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAUCUACUGCGUAGCG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GUGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGA----CUGC----CGUUAU-C-AG---CCCAACCGA--UAUGGUUGG---ACCACAAUCU--UU---
ABFJ01001344.1/60274-60571     -----------AUUGGGCA-UAA----GCCUGUAA----ACACCUUUACCAGUGU------AAU-----CGUUGCCGG-AAGGAACGUUG-UGAGGGCAGG------AUACUUG-GGCAUGGCA-U--------UGUCU----------------------GUGUCGAUCUGGCUGUCCUUG-UGG-AAGCG-GCUGUGGCU-AAGGGCCAUUCGACGGAGGUCGGGUAGUCCUUCAGCC-UUGAAG-AAGCUGGCAC-UGGCACAGGGAGGAAACUCAGCACGCAAAACA-GUUCGCAGU-UG-UUAG-CCA--GAGGAUGGCAGCCG--UGAGCAGA-------G-UGCCGUGAUCCAG--------C-CUGUCCGACAGUCAACGAACCU-U-UUUGCUC---------
AABS01000744.1/970-1238        -----------------GGC---GUGCGCCUGUAA-UCC-----AGUUAC-----UU-GGAGGC----UUGGAUUGGAG-GACGGCGU--GAGAUUGGGA-GCCAUG-UGGCG----CUCUGC---CCUAUGUC--------------------------------GAUCGGGC-GU-CAGCGCUA-AGCUC-GGCGUCAAUAUGGACAUCCC-GGGGGAGCUU-GGGGUGGCCAGGUUG-UCUAAGGAGGAACGAAC-CGGGCGAGGCCCGAAAGGGAGCAGCCAAAAGUUCCC-ACGUU-GA-UCAG-UAGCG-GG-AUAGC-GCCUGU--------GAAUAGG----CGGAG----UGUCA-C-AG---CCCAGUCAA--UAUC-------------------------
AB021174.1/1-298               GCCGGGCGCGG-----UGGC---GCGCGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCCGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UCGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCUGUCUC-------
AC091616.2/101009-101306       GCCGGGCGCGG-----UGGC---GCACGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGACAGGAG-GAUCGAUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCC-GUCUC-U-----
AANI01013436.1/5754-6049       ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGGAUCACUGUGUAGUG--GACCAG-----CCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCGC-GGAGGAGUCC-ACGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AA-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGA----CUGC----CACUAU-C-AG---CCUUGCCAA----UUGUUGG---ACCACAAUCU--UUU--
AAFC03032873.1/73555-73855     GCCGGGCGCGG-----UGGC---GCGCGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGCUCAGGA-GUUCUG-GGCUG----CAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----UACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UUU---
AADC01117175.1/34409-34130     ------CGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGUGGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGAGCAA--CAUAGCG----------------------
ABAV01015674.1/42152-42450     GCCGGGCAUUG-----UGGC---GCAUGCCUGUAA-UCC-----AGCUGC-----UU-GGAGGC----UAGAGAUGUUG-AAUGGCUU--GAGGUGUGGA-UUCCUG-AUGGC----GGUCGU---GCUAUGUC--------------------------------GAUCGGGU-GU-CCGCGCUA-AGUCG-GGCGUCAAUAUGGUGCCUUA-AGAGGAGUCU-CGAGUCACCAGGUUG-GUUAAAGAGGAGCGUAC-CGGCCCAGGGUGGAAACACAGCAGGCAAAAGC-UCCCGCGUU-CG-ACAG-UAGUG-GG-AUAGC-ACCUGU--------GAAUAGA----CGGCC----GUCAA-C-AG---CCAUGCCAA--GAUAGUCGA---ACUCAUCUCU-CUU---
AACT01037627.1/49101-48816     -----------------GGC---GUGCGCCUGUAA-UCC-----AGUUAC-----UU-GGAGGC----UUGGGUUGGAG-GACGGUGU--GAGAUUGGGA-GCUCUG-UGGCGC-UC---UGU---CCUAUGUC--------------------------------GAUCGGGC-GU-CCGCGCUA-AGCUC-GGCGUCAAUAUGGGCAUUCC-AGGGGAGCCC-GGAGUGGCCAGGUUG-UCCAAGGAGGAACGCAC-CGGGCGAGGCCCGAAAGGGAGCAGCCAAAAGUUCCC-ACGUU-GA-UCAG-UAGCG-GG-AUAGC-GCCUGU--------GAAUAGG----CGGAG----CGUUG-C-AG---CCCAGUCAA--UAUCGCGGG---ACCCAAUCCU--UU---
BX469912.5/75439-75158         GCCGGGUUCAG-----UGGC---GCGCGCCUGUAA-UCC----AAGCUAC-----UG-GGAGGC----UGAGGCUG-CG-GAUCGCUU--GAGCUCAGGG-UGUCUG-GGCGG----CAGUGG---ACUAUGUC--------------------------------GAUUGGGU-GU-CUGCACUA-AGUUC-GGUAUUGAUAUGGUGCUUCU-GGGGGAGCUC-GGGACCACCAGGUUG-AGUAAGGAGGGGUGAAC-CGGCCCAGGACGGAGACGGAGCAGGUCAAAGC-CCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUAA--------GAAUAGA----CACUG----CAGUG-C-AG---CCUGAGCAA--CACAG------------------------
AC002512.1/76040-75743         ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAUCUACUGCGUAGCG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GUGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGA----CUGC----CGUUAU-C-AG---CCCAACCGA--UAUGGUUGG---ACCACAAUCU--UU---
AACT01025682.1/5142-5415       ---------UG-----UGGC---GUGCGCCUGUAA-UCC-----AGUUAC-----UU-GGAGGC----UUGGGUUGGAG-GACGGUGU--GAGAUUGGGA-GCUCUG-UGGCG----CUCUGU---CCUAUGUC--------------------------------GAUCGGGC-GU-CCGCGCUA-AGCUC-GGCGUCAAUAUGGGCAUUCC-AGGGGAGCCC-GGAGUGGCCAGGUUG-UCCAAGGAGGAACGCAC-CGGGCGAGGCCCGAAAGGGAGCAGCCAAAAGUUCCC-ACGUU-GA-UCAG-UAGCG-GG-AUAGC-GCCUGU--------GAAUAGG----CGGAG----CGUUG-C-AG---CCCAGUCAA--UAUCGC-----------------------
AAGE02003358.1/52368-52666     ACUGGGAACG------UGGC----GUCUCCUGUAA-CGU-----GGCUGC-----UC-ACGGGU---C-GGGUUACGG--ACUGAUUU--GAGGUUGGGGUCCACUGUGUGCCG--GGUAAG----UCCAUGUU--------------------------------GACGGGAC-GU-CCGCACUA-AGCUG-ACCGUCAAUAUGGGUGCAAU-GGGGGAGCCC-GAUGCAUUCAGGUUG-GCUAAAGAGAGAUGAAC-CGAGCGAGGGGUGAAAACCAGCAGCUAAAAGU-CUCCGCGGU-AA-GCAG-UAGUG-GG-AUCGC-GUCCCG--------GAGUGGA----CUUC----CGGUAC-C-AG---CCUGACCAA--UACAGUCAC---ACUGUAAUCU-UUU---
CAAE01015003.1/876675-876973   GCCGGGUACGG-----UGGC---GCGUGCCUGUAA-UCC----AAGCUAC-----UG-GGAGGC----UGAGGCUGGCG-GACCGUUU--GAGCUCAGGA-GUUCUG-GGCUG----CAGCGG---ACUAUGUC--------------------------------GAUCGGGU-GU-CCGCACUA-AGCUC-GGUAUCGAUAUGGUGCUCCU-GGGGGAGCCC-GGGACCACCAGGUCG-CCUAAGGAGGGGUGCAC-CGGCCCAGGUCGGAAACGAAGCAGGCCAAAGC-CCCCGUGCC-GC-UCAG-UAGUG-GG-AUCGC-GCCCGU--------GAAUAGA----CGCUG----UAGUU-C-AG---CCUGAGCAA--CAUAGCGGG---ACUUAGUCUU-UU----
AC095014.1/156446-156743       ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAUCUACUGCGUAGCG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GUGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGA----CUGC----CGUUAU-C-AG---CCCAACCGA--UAUGGUUGG---ACCACAAUCU--UU---
AAHY01101031.1/13005-13305     GCCGGGCGCGG-----UGGC---GCACGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGACAGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UUU---
AAEU02000003.1/117581-117283   ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-CGAUUGUGG--GAUGGCCU--GAGGCUGGGAUUUACUGCGUAGCG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GUGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGA----CUGC----CGUUAU-C-AG---CCCAACCAA--UAUGGUUGG---ACCACAAUCU--UUU--
CR925739.5/105084-104803       GCCGGGUUCAG-----UGGC---GCGCCCCUGUAA-UCC----AAGCUUC-----UG-GGAGGC----UGAGGCUG-CG-GAUCGCUU--GAGCUCAGGG-CUUCUG-GGCUG----CAGUGG---ACUAUGCC--------------------------------GAUCAGGU-GU-CUGCGCUA-AGUUC-GGUAUCGAUAUGGUGCUCCU-GGGGGAGCUC-AGGACCACCAGGUUG-UCUAAGAAGAGGUGAAC-CGACCCAGGUCGGAGACGGAGCAGGUCAAAUC-CCCUGUGCU-GA-UCAG-UAGUG-GG-AUCGC-ACCUGU--------GAAUAGA----CACUG----CAGUU-C-AG---CCUGAGCAA--CACAG------------------------
AACT01038002.1/337-622         -----------------GGC---GUGCGCCUGUAA-UCC-----AGUUAC-----UU-GGAGGC----UUGGGUUGGAG-GACGGUGU--GAGAUUGGGA-GCUCUG-UGGCGC-UC---UGU---CCUAUGUC--------------------------------GAUCGGGC-GU-CCGCGCUA-AGCUC-GGCGUCAAUAUGGGCAUUCC-AGGGGAGCCC-GGAGUGGCCAGGUUG-UCCAAGGAGGAACGCAC-CGGGCGAGGCCCGAAAGGGAGCAGCCAAAAGUUCCC-ACGUU-GA-UCAG-UAGCG-GG-AUAGC-GCCUGU--------GAAUAGG----CGGAG----CGUUG-C-AG---CCCAGUCAA--UAUCGCGGG---ACCCAAUCCU--UU---
ABKP02019894.1/56541-56248     ACCGGGAGCG------UGGC----GUCUCCUGUAA-CGC-----GGCUAC-----UC-GUGGGU---C-GGAUUACGG--ACUGAUUU--GAGGGCGGGAG-UCCUGUGUGCUG--GACCAG----GCCAUGUU--------------------------------GACGGGGC-GU-CCGCACUA-AGCUG-GCCGUCAAUAUGGGUGUCAC-GGAGGAGUCC-GAGACAUUCAGGUUG-GCUAAGGAGAGACACAC-CGAGCGAGGGGUGAAAACCAGCAGCUAAGAGU-CUCCGCGGC-AA-GCAG-UAGUG-GG-AUCGC-GUCCCG--------GAGUGGA----CUGC----CAGUGC-C-AG---CCCGACCAA--UAAAGUCAC---ACUGUAAUC--------
AASW01050803.1/456-158         ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAUCUACUGUGUAGCG--GACUAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GUGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-ACAGC-GUACCG--------GAGUGAA----CUGC----CGUUAU-C-AG---CCCAACCGA--UAUGGUUGG---ACCACAAUCU--UUU--
AC095014.1/154373-154076       ACUGGAAGGU------UGGC----AGCUUCUGUAA-UCA-----CGCUUC-----UG-UGAGGU---C-UGAUUGUGG--GAUGGCCU--GAGGCUGGGAUCUACUGCGUAGCG--GACCAG----CUCAUGUU--------------------------------GACGGAAC-GU-CCGCACUA-AGCUU-GCCAUCAAUAUGGGUGCCAU-GGAGGAGUCC-GUGGCAUUCAGGUUG-GCUAAGGAGGGAUGAAC-CGGGCCAGGGGUGAAAACCAGCAGCCAAGAGU-UCCCGUGGU-AG-GCAG-UAGUG-GG-AUAGC-GUACCG--------GAGUGGA----CUGC----CGUUAU-C-AG---CCCAACCGA--UAUGGUUGG---ACCACAAUCU--UU---
AADD01137944.1/11247-10949     GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGUGGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGAGCAA--CAUAGCGAG---ACCCCGUCUC-U-----
AACW02000088.1/106193-106487   ACUGGAAAGUG----UAAC----GUCUUUCUGUAA----G--CAGAGU--U--GC------AGUCUAUAAAAGGAUGAAUUCAUCUGU-U---GAUGG-----------AAUC---ACGGUAUAUUCAACGCUUUG----------------------------UCGAAAUUAG-UGUCUUC-CAGAGUC--UAGUGU-CAACAUUCUAGUUCGGGCGUAGGCCUGAGUUAGGAGGUUG--UUCAAUA--CUGGGGAACCGCCCGAGGGUAGCAAUACAGCAGGGAAAACU-CAGAGCACUGGC--ACGGCUG-U-AAGAUAGC-ACAAUGGA---GAAGUGAUUGGAUAUACUA------------------CCAUU-------GCGGGUGGGA-ACUACCUUUUUUU---
CR854846.8/26167-26463         GCCGGGCUCGG-----UGGC---GCGCGCCUGUAA-UCC----AAGCUAC-----UG-GGAGGC----UGAGGCUG-CG-GAUCGCUU--GAGCUCAGGG-CUUCUG-GGCUG----CAGUGG---ACUAUGUC--------------------------------GAUCGGGU-GU-CCACACUA-AGUUC-GGUAUCGAUAUGGUGCUCCC-GGGGGAGCUU-GGGACCACCAGGUCG-UCUAAGGAGGGGUGAAC-CGACCCAGGUCGAAGACGGAGCAGGUCAAAAC-CCCCGUGCC-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGA----CACUG----CAGUG-C-AG---CCUGAGCAA--CACAGGGAG---ACGCAGACUU-U-----
ABIR02000767.1/132257-131958   GCCGGGCGUUG-----UGGC---GAGCGCUUGUAA-UCC-----AGCUAC-----UU-GGAGGC----UUGGACCAGUG-GAUGUCUU--GAGAGCGGGA-GUUCUG-UGCCU---GGUUGUG---CUCAUGUU--------------------------------GACCGAGC-GU-CCGCAUCA-AGCAU-GGCGUCAACAUGGUUGAUUC-UGAGGAGUCA-GAGCCGACCAGGUUC-GUCAAAGAGGGUCGGAC-CGGCCGAGGGCGGAAACGCAGCAGGCAAAAGU-CCCCGCGUC-AGCGCAG-UGAUG-GG-AUAGC-GCUCGC--------GAAUAAG----CCGC----CGGGUA-C-AG---CCCGCUCAA--GAAACUCAG---ACCUGGUCCUUA-----
FO080694.1/33862-33564         ACCGAGCGUCG-----UGGC---GGGCGCUUGUGA-GUC-----AGCUUC-----UU-GACGGU----AGAUAAGUGUG-GAUGGAGU--GAGAGGAGGA-GUCCUG-UGUAU---GUCGUCG---UCUACGUC--------------------------------GACCGAGC-GU-CCGUGCCA-AGCGC-UACGUCACCAGGGGAUAACU-GUCGGAAGGC-GGUUAGUCCCGGGUG-CAUAAGGAGUCGUGGAU--GGUUCAGGACCGAAAGGUAGCAGACAAAAGC-GACCGCGUG-GU-GCAG-UGGCC-GG-ACCGC-GCUUGU--------AAGUUGA----CACA----CAUACA-C-AG---CCUUCUCGA--UACCUUCAG---ACCACUUAUC-AUU---
AAGJ04048628.1/48554-48851     ACUGGGCGUUG-----UGGC---GUGCGCCUGUAA-UCC-----AGUUAC-----UU-GGAAGU----CGGGGUUGGUG-GAUCGUUU--GAGAGCGGGA-GUCCUG-UAUGU----CGUCGC---UCUAUGGC--------------------------------GAUCGGGC-GU-CCAUGCUA-AGCUC-GGCAUCGAUAUGGUUGAUUG-GUCGGAGGAC-UGGCCAACCAGGUCG-UCUAAGGAGGGACGUAC-UGGCCCAGGGCGGAAACGCAGCAGGCAAAAGU-CCCCGUGUG-GA-GCAG-UAGUG-GG-AUAGC-GCCUGU--------GAAUAGG----CGGCG----GCUUG-C-AG---CCCGUUCAA--CAUAGUGAG---ACCCAAUCCU-UU----
AADN03004790.1/7381-7092       GCCGGGCGCGG-----UGGC---GCACGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGCCCGCCG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----CAGUGC---GCUAUGCC--------------------------------GAGCGGGC-GU-CCGCGCUA-AGGCC-GGCAUCAAUAUGGUGAGCCC-CGGGGAGCCG-AGGCACACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCC-GG-UCAG-UAGCG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CAGCG-U-AG---CCUGGGCAA--CACAGAGAG---AC---------------
CABG01000014.1/282857-283153   GCUGGGCGUGG-----UGGC---GUGCGCCUGUAA-UCU-----AGCUAC-----UU-GGAGGC----CAGGGUGCGG--GAUUUCGU--GGGACCGGGA-GUUCUG-GCAUA----UGGGUG---CUCAUGUU--------------------------------GAUCGGGC-GU-CCACGCUA-AGCAC-GGCGCCGAUAUGGAUGAGCU-GUCGGAGGAC-GGGUUGUCCAGGUCG-UCUAAGGAGGGGCGGAC-CGGCCCAGGGGGGAAACCCAGCAGGCAAAAGU-CCCCGCGUG-GU-GCGG-UAGCG-GG-AUAGC-GCCUGU--------GAAUGGU----GUCC----AUGUGA-C-AG---CCCGGUUGG--CGCGUGAAG---ACCGCCUCCU-UU----
AY948606.1/2-300               ACCGAGCGUCG-----UGGC---GGGCGCUUGUGA-GUC-----AGCUUC-----UU-GACGGU----AGAUAAGUGUG-GAUGGAGU--GAGAGGAGGA-GUCCUG-UGUAU---GUCGUUG---UCUACGUC--------------------------------GACCGAGC-GU-CCGUGCCA-AGCGC-UACGUCACCAGGGGAUAACU-GUCGGAAGGC-GGUUAGUCCCGGGUG-CAUAAGGAGUCGUGGAU--GGUUCAGGACCGAAAGGUAGCAGACAAAAGC-GACCGCGUG-GU-GCAG-UGGCC-GG-ACCGC-GCUUGU--------GAGUUGA----CACA----CAUACG-C-AG---CCUUCUCGA--UACCUUCAG---ACCACUUAUC-AUU---
AACN010616031.1/232-530        GCCGGGCGCGG-----UGGC---GCGCGCCUGUAG-UCC----CAGCUAC----UCG-GGAGGC----UGAGGCAGGAG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----CAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-U-----
FO081379.1/1858-1566           ACCGGGCGUCG-----UGGC---GGGCGUCUGUAA-GCC-----AGCUUC-----UU-GGCGGU----AGAUAAGUGUG-GAUGGAGU--GAAGGGAGGA-GCCCUU-UGGGU---GUUGCUG---GCAACGGC--------------------------------GACCGAGC-GU-CCGUGCCA-AGCGC-UGCGUCGCUAGGGGUCAUCU-GGCGGAAGGC-GGGCGGUCCCGGGCG-CAUAAGGAGCGGUAUAC--GGCUCAGGGCCGAAAGGCAGCAGGCAAAAGC-CUCCGCGCG-GU-GCAG-UGGCC-GG-AUAGC-GCUUGC--------GAGUUGU----CGCU----CACCCA-C-UG---CCUCUCUGA--UACCUUUAG---ACCACUU----------
AAGE02003358.1/100111-100407   ACUGGGAGC-G-----UGGC---G-UCUCCUGUAA-CGU-----GGCUGC-----UC-ACGGGU----CGGGUUACGG--ACUGAUUU--GAGGUUGGGGUCCACUGUGUGCCG--GGUAAG----UCCAUGUU--------------------------------GACGGGAC-GU-CCGCACUA-AGCUG-ACCGUCAAUAUGGGUGCAAU-GGGGGAGCCC-GAUGCAUUCAGGUUG-GCUAAAGAGAGAUGAAC-CGAGCGAGGGGUGAAAACCAGCAGCUAAAAGU-CUCCGCGGU-AA-GCAG-UAGUG-GG-AUCGC-GUCCCG--------GAGUGGA----CUUCC----GGUGC-C-AG---CCUGACCAA--UACAGUCAC---ACCGUAACCU--U----
AB073218.1/1-299               GCCGGGCGCGG-----UGGC---GCACGCCUGUAG-UCC----CAGCUAC-----UCGGGAGGC----UGAGCCCGCCG-GAUCGCUU--GAGCCCAGGA-GUUCUG-GGCUG----CAGUGC---GCUAUGCC--------------------------------GAGCGGGC-GU-CCGCGCUA-AGGCC-GGCAUCAAUAUGGUGAGCCC-CGGGGAGCCG-AGGCACACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCC-GG-UCAG-UAACG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CAGCG-U-AG---CCUGGGCAA--CAUAGCGAG---ACCCUGUCUC--C----
AB061847.1/1334-1035           GCCGGGCGCGG-----UGGC---GCGUGCCUGUAG-UCC----CAGCUAC-----UCGGGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UU----
AADA01294667.1/15052-14753     GCCGGGCGCGG-----UGGC---GCGUACCUGUAG-UCC----CAGCUAC-----UCGGGAGGC----UGAGGCUGGAG-GAUCGCUU--GAGUCCAGGA-GUUCUG-GGCUG----UAGUGC---GCUAUGCC--------------------------------GAUCGGGU-GU-CCGCACUA-AGUUC-GGCAUCAAUAUGGUGACCUC-CCGGGAGCGG-GGGACCACCAGGUUG-CCUAAGGAGGGGUGAAC-CGGCCCAGGUCGGAAACGGAGCAGGUCAAAAC-UCCCGUGCU-GA-UCAG-UAGUG-GG-AUCGC-GCCUGU--------GAAUAGC----CACUG----CACUC-C-AG---CCUGGGCAA--CAUAGCGAG---ACCCCGUCUC-UU----
#=GC SS_cons                   (((<<<<<<<<.....____...>>>>>>>>,,,,.<<<...._______.....__.>>>)))....-((((((((((.-(((((((..(((((((((-.---(((.(((((...-(((((-...(((((((-................................--((((((.((.((-(((((.(((((.(((((<<<<<<<<<<<<<<<.<<<____>>>.>>>>>>>>>>>>>>>.<<___>><<<<<<<---.<<<<<----<<<____>>>---->>>>>->>>.>>>>))))).)).)))-.))))).)).---)).))))))........)))))))....)))))...-))))).).))...)))))))))..--)))))))...)))))))))).::....
#=GC RF                        gCcGGGcgcgg.....uGgC...gcgcgCCUGUAA.ucc....aagcUaC.....Ug.ggagGc....ugggggggggg.ggucgcgu..gcggccggGA.guucug.ggccg...gcagcgu...cccaugcc................................GAccgggc.Gu.Ccgcgcua.ggcuc.ggcGUcgacauggggccccc.ggcGGAGgcc.gggggccccaggucg.ccuAAggaGgggcGaAc.cggcccAGGgcgGAAAcgcAGCAggcagAAgc.ccCcGCgcc.ga.gccG.uagcg.gG.AUagC.gcccgg........gaauggg....cgcug...Ccggcc.c.ag...Cccggccga..uAacgcgac...accccccccc.UU....
//
# STOCKHOLM 1.0

#=GF AC   RF00018
#=GF ID   CsrB
#=GF DE   CsrB/RsmB RNA family
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD; Bateman A; Gardner PP;
#=GF GA   71.00
#=GF TC   71.40
#=GF NC   70.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00106
#=GF DR   SO; 0000377; CsrB_RsmB_RNA;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   97362239
#=GF RT   The RNA molecule CsrB binds to the global regulatory protein CsrA and
#=GF RT   antagonizes its activity in Escherichia coli.
#=GF RA   Liu MY, Gui G, Wei B, Preston JF 3rd, Oakford L, Yuksel U, Giedroc DP,
#=GF RA   Romeo T
#=GF RL   J Biol Chem 1997;272:17502-17510.
#=GF RN   [2]
#=GF RM   7665490
#=GF RT   Identification of a global repressor gene, rsmA, of Erwinia carotovora
#=GF RT   subsp. carotovora that controls extracellular enzymes,
#=GF RT   N-(3-oxohexanoyl)-L-homoserine lactone, and pathogenicity in soft-rotting
#=GF RT   Erwinia spp.
#=GF RA   Cui Y, Chatterjee A, Liu Y, Dumenyo CK, Chatterjee AK
#=GF RL   J Bacteriol 1995;177:5108-5115.
#=GF RN   [3]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF RN   [4]
#=GF RM   23251905
#=GF RT   Crp induces switching of the CsrB and CsrC RNAs in Yersinia
#=GF RT   pseudotuberculosis and links nutritional status to virulence.
#=GF RA   Heroven AK, Sest M, Pisano F, Scheb-Wetzel M, Steinmann R, Bohme K, Klein
#=GF RA   J, Munch R, Schomburg D, Dersch P
#=GF RL   Front Cell Infect Microbiol. 2012;2:158.
#=GF RN   [5]
#=GF RM   29091941
#=GF RT   CsrB, a noncoding regulatory RNA, is required for BarA-dependent
#=GF RT   expression of biocontrol traits in Rahnella aquatilis HX2.
#=GF RA   Mei L, Xu S, Lu P, Lin H, Guo Y, Wang Y
#=GF RL   PLoS One. 2017;12:e0187492.
#=GF RN   [6]
#=GF RM   18052890
#=GF RT   Dynamic regulation of GacA in type III secretion, pectinase gene
#=GF RT   expression, pellicle formation, and pathogenicity of Dickeya dadantii
#=GF RT   (Erwinia chrysanthemi 3937).
#=GF RA   Yang S, Peng Q, Zhang Q, Yi X, Choi CJ, Reedy RM, Charkowski AO, Yang CH
#=GF RL   Mol Plant Microbe Interact. 2008;21:133-142.
#=GF RN   [7]
#=GF RM   18441056
#=GF RT   Regulatory network controlling extracellular proteins in Erwinia
#=GF RT   carotovora subsp. carotovora: FlhDC, the master regulator of flagellar
#=GF RT   genes, activates rsmB regulatory RNA production by affecting gacA and hexA
#=GF RT   (lrhA) expression.
#=GF RA   Cui Y, Chatterjee A, Yang H, Chatterjee AK
#=GF RL   J Bacteriol. 2008;190:4610-4623.
#=GF RN   [8]
#=GF RM   26462993
#=GF RT   Cross-talk between a regulatory small RNA, cyclic-di-GMP signalling and
#=GF RT   flagellar regulator FlhDC for virulence and bacterial behaviours.
#=GF RA   Yuan X, Khokhani D, Wu X, Yang F, Biener G, Koestler BJ, Raicu V, He C,
#=GF RA   Waters CM, Sundin GW, Tian F, Yang CH
#=GF RL   Environ Microbiol. 2015;17:4745-4763.
#=GF CC   The CsrB RNA binds to approximately 18 copies of the CsrA protein
#=GF CC   Pfam:PF02599. CsrA proteins are found in a wide variety of bacteria. The
#=GF CC   CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18
#=GF CC   copies and has been suggested to bind CsrA. The Csr regulatory system has
#=GF CC   a strong negative regulatory effect on glycogen biosynthesis,
#=GF CC   glyconeogenesis and glycogen catabolism and a positive regulatory effect
#=GF CC   on glycolysis [1]. In other bacteria such as Erwinia caratovara the RsmA
#=GF CC   protein has been shown to regulate the production of virulence
#=GF CC   determinants, such extracellular enzymes [2]. RsmA binds to RsmB
#=GF CC   regulatory RNA which is also a member of this family [2]. RsmB RNA was
#=GF CC   shown to be upregulated by GacS/A system, and increase downstream T3SS
#=GF CC   gene expression.[6] FlhDC, the master regulator of flagellar genes, also
#=GF CC   activates rsmB RNA production.[7] A regulatory network have been revealed
#=GF CC   connecting rsmB, FlhDC and T3SS.[8] Plays role in the biocontrol activity
#=GF CC   of Rahnella aquatilis HX2 (a biocontrol agent producing antibacterial
#=GF CC   substance).[5]
#=GF WK   CsrB/RsmB_RNA_family
#=GF SQ   38


AAYV01000020.1/39993-39672   GAUCUGGCGGAGAGGGAACGCAUCUGGAAGAUGUG-----------------------------------------------UCUUCAG-GAC-GAAGA-ACA-CAGGGA-CUGCUUAGGACGAGUGAAGG--GACGUUUCAGGAU-GAAACAAGGGACACCUCCAGGAUGGAGAUUGAGAGCC-AGUU-CA-GGAUGA-UU-GGUG-GGUUAGGAUAGCC------------UA-AGGAUUAACG-------------CCGGGAUGGUGUA--U-----A-A--CAU-UGCGAUGG--------AUUGC-UGGUUAGUAUAACCAUA-CGGAAAAGUUUUCAGGGAU-UGAGCAGGGAGCAUC-AAUUUUAGCUGGAUUGCUAUAAAACGAAUUGAGGGG-UACUG--GUAAAACAGUA--C-CCCUUUUUUGUGCC
CP000826.1/4199485-4199142   GAUACGGUGGAGCUGGAAAGCAUCAGGAUGAUGCAGCUUCAG---G-AUGAAGAAGU--------------------GGAUGCGCUCAGUGAA-GAGCG-----AAGGAC-GGCGUCAGGA-GAUGCUCAG--GAUGUUUCAGGAUUGAAACCAGGGACACCUCCAGGAUGGAGAUUGAGAGCU-GGCA-CA-GGAUGG-UU-GGCG-GGUCAUGAAGACUGAG--GAACCGCGUCAGGACGAUG--CUA----------CAGGACAGAG-----CCAGGA-UGG----------------------UUU-UGGUCAGGAUGGCCGCA--GGAAAAGUUUUCAAGGAU-UGAGCAGGGAGCACA-CUGUGUAGCGGGACUGCUAUAAAACGAACC-GAGGG-CACUG--UUAGCGCAGUG--C-CCUCAACUUUUUAU
AF076153.1/1958-2313         GAGUCGUACAACGAAGCGAACGUCAGGAUGAUGACGCUUCAG---C-AGGAC------------------------------ACGCCAG-GAU-GGUGUUACA-AGGAAA-GGCUUCAGGAUGAAGCAAAGUGGAAAGCGCAGGAU-GCGUUAAAGGACACCUCCAGGACGGAGAACGAGAGCC-GA-U-CA-GGAU-GUUC-GGCG-GGUCUGGAUGACCAGG--GA--CGCUUCAGGAAGAAG--CUA----UCACAUCGGGC-GAUGUG--CGCAGGA-UGCAAA-CGUUCAGG-----AUGAACA----GGCCGUAAGGUCACA--GGAAAAGUUGUCACGGAU--GAGCAGGGAGCACG-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UUUAUACAGUG--C-UCCCUUUUUUUUGU
AL627276.1/270587-270233     GAGUCGUACAACGAAGCGAACGUCAGGAUGAUGACGCUUCAG---C-AGGAC------------------------------ACGCCAG-GAU-GGUGUUACA-AGGAAA-GGCUUCAGGAUGAAGCAAAGUGGAAAGCGCAGGAU-GCGUUAAAGGACACCUCCAGGACGGAGAACGAGAGCC-GA-U-CA-GGAU-GUUC-GGCG-GAUCUGGAUAACCAGG--GA--CGCUUCAGGAUGAAG--CUA----UCACAUCGGGC-GAUGUG--CGCAGGA-UGUAAA-CGUUCAGG-----AUGAACA----GGCCGUAAGGUCACA--GGAAAAGUUGUCACGGAU--GAGCAGGGAGCACG-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UUUAUACAGUG--C-UCCCUUUUUUUGU-
CP000247.1/2917922-2917563   GAGUCAGACAACGAAGUGAACAUCAGGAUGAUGACACUUCUG---A-AGGAC------------------------------ACACCAG-GAU-GGUGUUUCA-GGGAAA-GGCUUCUGGAUGAAGCGAAGAGGAUGACGCAGGAC-GCGUUAAAGGACACCUCCAGGAUGGAGAAUGAGAACC-GG-U-CA-GGAUGAUUC-GGUG-GGUCAGGAAGGCCAGG--AA--CACUUCAGGAUGAAG---UA----UCACAUCGGGGUGGUGUG--AGCAGGA-AGCAAU-AGUUCAGG-----AUGAACGA-UUGGCCGCAAGGCCAGA--GGAAAAGUUGUCAAGGAU--GAGCAGGGAGCAAU-AAAAGUAGCCGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UGAAUACAGUG--C-UCCCUUUUUUUAUU
CP000653.1/3538029-3537674   AUGCCGACACGAGAAGCGAACAUCAGGAUGAUGACGUUUUUC---A-CCGAGG---------------------------AUACGUCAG-GAU-GGCGCUGCA-G--GAA-GGCUUAAGGAUGAAGCAAAAAGGAUCACGCAGGAC-GCGU-AAGGGACACCUCCAGGAAGGAGAAAGAGAACC-GG-U-CA-GGAU-GCCC-GGUG-GGUCAGGAAGAUCAGG---A--CGUUUCGGGAUGAAA--CAU----UCACAUCAGGAUGAUGUG--AGCAGGA-UGCGCG-GUUUACGG-----ACGACCA----GGCCCUCGGGCCACA--GGAAAAGUUGUCACGGAC--GAGCAGGGAGCACA-AAUUGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UUUAUACAGUG--C-UCCCUUUUUUUGUU
CP000647.1/3438829-3438471   ACGUCGCGAAAUGAAGCGAACAUCAGGAUGAUGGCGCUUCUG---C-AGGAC------------------------------CCGCCAG-GAC-GGCGUUGCA-GGGACA-GGCUUCAGGAUGAAGCAAGG--AUAACGC-AGGAU-CGCGUAAUGGACACCUCCAGGAUGGAGAACGAGAGCC-GC-U-CA-GGAUGA-AC-GGUG-GAUCAGGAAGAUCGGG--AC--AAACUUAUGGAUAAG--UCAU--UUCGCAUCGGGGUGGUGUGAAAGCAGGA-UGCACG-UGUUUAUG----GAUGAACAU--GGUCAGGA-GACCUCA--GGAAAAGUUUUCAAGGAC--GAGCAGGGAGCACC-AAU-GUAGCGGGACUGCUGCAAAACGAACC-GGGAG-CACUG--UUUAUACAGUG--C-UCCCUUUUUUUAUU
BX950851.1/1144364-1144719   CGUUACUGCACUCGGGCUGUUUUCAGGAAGAGACAUUGUUUU-----AGGAAGAAA---------------------CAGCCGCUUCAG-GAA-GAAGC-GCG-G-------UUUUCAGGAAGAAACACG------AUUUCAGGAU-GAAAUCAGGGACACCUCCAGGAAGGAGACCGAGAGCC-GA-U-UA-GGAAUG-UC-GGUG-GGGCAGGA-GCCUAAA---G--GGAUUGA--AUCACG---GA----AGAUA-CAGGAUGGAAAC--GUCAGGA-CGAAAG-UGGGACGCCAGCAAGGAUUGU-GGGUCAGGAUGACCAAAAAGGAAAAGUUUUCACGGAU--GAGCAGGGAUGCAA-AUGUGUAGCGGGAUAGCUAUAAAACGAACC-GGGGG-UGCUG--AGCAAUCAGUA--C-CCCCAACUUUUUGC
X79474.1/346-702             GUUUCAGGAAGAAGCGUUGUUUUCAGGAAGAUAAACAGUUUU---C-AGGAAGAUA---------------------AACAGUUUUCAG-GAA-GAAGA-ACA-G-------UUUUCAGGAAGAAACAUGA------UUUCAGGAU-GAAAUCAGGGACACCUCCAGGAAGGAGACCGAGAGCC-GA-U-UA-GGAAUA-UC-GGUG-GGGCAGGA-GCCUAAA---G--GGAUUGA--AUCACG---GA----AGAUA-CAGGAUGGAAAC--GUCAGGA-AGAAAG-UGGGACGCCAGCAAGGAUUGU-GGGUUAGGACGACCAAAAAGGAAAAGUUUUCACGGAU--GAGCAGGGAUGCAA-AUGUGUAGCGGGAUAGCUAUAAAACGAACC-GGGGG-UACUG--AGCAAUCAGUA--C-CCCCAAUUUUUUGC
L13457.1/235-574             -----------------UCGUUUUAGGAAGAAACGAUCGUUU---C-AGGAAGAAG---------------------CGUUGUUUUCAG-GAA-GAAGA-ACG-G-------UUUUCAGGAAGAAACAUGG------UUUCAGGAU-GAAAUCAGGGACACCUCCAGGAAGGAGACCGAGAGCC-GA-U-UA-GGAAUA-UC-GGUG-GGGCAGGA-GCCUAAA---G--GGAUUGA--AUCACG---GA----AGAUA-CAGGAUGGACAC--GUCAGGA-AGAAAG-UGGGACGCCAGCAAGGAUUGU-GGGUUAGGACGACCAAAAAGGAAAAGUUUUCACGGAU--GAGCAGGGAUGCAA-AUGUGUAGCGGGAUAGCUAUAAAACGAACC-GGGGG-UACUG--AGUAAUCAGUA--C-CCCCAAUUUUUUGC
AM286415.1/3595708-3595388   GAUCUGGCGGAA-AGGACGGUAUCAGGAUGGUGCCA-----------------------------------------------CUUCAG-GAU-GAAGG-ACU-CAGGGA-CUGCUUAGGAUGAGUGAAGG--GAUGUUUCAGGAA-GAAACAAAGGACACCUCCAGGAUGGAGAUUGAGAGCC-AG-UCCA-GGAUGA-UU-GGUG-GGUUAGGAUAACU-------------UCAGGAUUGGC-------------ACUGGGAUGGU------GUAGGACAAC-----GCGACGG--------AUUGC-UGGUUAGGAUAACCGCA-CGGAAAAGUUUUCAAGGAU-UGAGCAGGGAGCAUC-ACUUUUAGCUGGAUUGCUAUGAAACGAAUAGAGGGG-UACUG--GUAAAACAGUA--C-CCCUUUUUUUAUCC
ABKX01000001.1/604476-604836 GAGUCAGACAGCGAAGUGAACAUCAGGAUGAUGACACUUCUG---A-AGGAC------------------------------ACGCCAG-GAU-GGUGUUUCA-GGGAAA-GGCUUCUGGAUGAAGCGAAGAGGAUAACGCUGGAU-GCGUUAAAGGACACCUCCAGGAUGGAGAAUGAGAGCC-AG-U-CA-GGAUGAUUU-GGCG-GGUCAGGAAGGCCAGG--GA--CGCUUCAGGAUGAAG--UAA----UCACGCCGGGGUGGUGUG--UGCAGGA-AGCAAU-AGUUCAGG-----AAGAACGA-UUGGCCGCAAGGCCAGA--GGAAAAGUUGUCAAGGAU--GAGCAGGGAGCAAC-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UGAAUACAGUG--C-UCCCUUUUUUUAUU
CU928158.2/283863-284220     GAGUCGCACAGUGAAGUGAACGUCAGGAAGAUGGCGCUUCAA---A-AGGAC------------------------------ACACCAG-GAC-GGUGC-UAC-AAGGAA-GACUUCAGGACGAAGUAUAAAGGAAAACGCAGGAU-GCGUUAAGGGACACCUCCAGGACGGAGAACGAGAGCU-GA-A-CA-GGAUGG-UC-AGUG-GGUCAGGAAGGCCAGG---A--UGCUUCAGGAUGAAG--UAA----UCACACCGGGGUGGUGUG--UGCAGGA-UGCGCG-AGUUCAGG-----ACGAACAA-CAGGUCGCAAGACCACA--GGAAAAGUUGUCACGGAU--GAGCAGGGAGCAAC-AAAUGUAGCUGGAAUGCUGCAAAACGAAUC-GGGAG-CACUG--UUUAUACAGUG--C-UCCCUUUUUUUAUU
CP000880.1/4597967-4598323   GAGUCGUACAACGAAGCGAACGUCAGGAAGAUGGCGCUUCUG---C-AGGAC------------------------------ACGCCAG-GAG-GGCGUUACA-UGGAAA-GGCUUCAGGAUGAGGCAAAGUGGAAAGCGCAGGAU-GCGUUAAAGGACACCUCCAGGACGGAGAACGAGAGCC-GA-U-UA-GGAUGG-UC-GGCG-GGUCUGGAUGACCAGG--GA--CGCUUCGGGAUGAAG--CUA----UCACAUCGGGGCGAUGUG--CGCAGGA-UGCAAA-CGUUCAGG-----AUGAGCA----GGCCGCAGGGUCACA--GGAAAAGUUGUCACGGAU--GAGCAGGGAGCAUG-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UUUAUACAGUG--C-UCCCUUUUUUUGUU
CP000783.1/487241-487598     CGGAGUGGCGCUGAAGCGAACAUCAGGAUGAUGGCGCUUCAA---AAAGGAC------------------------------ACGCC-G-GAG-GGCGA-UUC-AGGGAA-GGCUUCAGGAUGAAGCGAAA-GGACGGCGCAGGA--GCGCUGAGGGACACCUCCAGGAAGGAGAAUGUGAGCC-GG-U-CA-GGAUUA-CC-GGUG-GGUCAGGAAGACCAGGGACA--CGCAUCAGGAUGAUG---CACCAGUGACAUCAGGACGAUGUG--GGCAGGA-CGC-----GUAAACG--------GACGU-AAGGUCGAAAGGCCGCA--GGAAAAGUUGUCACGGAC--GAGCAGGGAGCACCGAAAAGUAGCCGGACUGCUGCGAAACGAACC-GGGAG-CACUGUGUUAUCACAGUG--C-UCCCUUUUUUUAUG
CP000822.1/3859356-3858998   GAGUCGCACAACGAAGCGAACGUCAGGAUGAUGGCGCUUCAG---C-AGGAC------------------------------ACGCCAG-GAU-GGUGUUACA-AGGACA-GGCUUCAGGAUGAAGCAAAGUGGAAAACGCCGGAU-GCGUUAAGGGACACCUCCAGGACGGAGAACGAGAGCC-GG-G-CA-GGAUGU-UC-GGUG-GGUCAGGAUGGCCAGG---A--UACUUCAGGAUGAAGUCGAU----UCACAUCGGGGUGAUGUG--AGCAGGA-UGCAAAUUGUUCAGG-----AUGAGCA----GGUCGCAAGACCACA--GGAAAAGUUGUCACGGAU--GAGCAGGGAGCACC-AAAAGUAGCCGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UUUUUACAGUG--C-UCCCUUUUUUUUAU
AF031251.1/1-360             GAGUCAGACAACGAAGUGAACAUCAGGAUGAUGACACUUCUG---C-AGGAC------------------------------ACACCAG-GAU-GGUGUUUCA-GGGAAA-GGCUUCUGGAUGAAGCGAAGAGGAUGACGCAGGAC-GCGUUAAAGGACACCUCCAGGAUGGAGAAUGAGAACC-GG-U-CA-GGAUGAUUC-GGUG-GGUCAGGAAGGCCAGG--GA--CACUUCAGGAUGAAG---UA----UCACAUCGGGGUGGUGUG--AGCAGGA-AGCAAU-AGUUCAGG-----AUGAACGA-UUGGCCGCAAGGCCAGA--GGAAAAGUUGUCAAGGAU--GAGCAGGGAGCAAC-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CGCUG--UGAAUACAGUG--C-UCCCUUUUUUUAUU
FJ465142.1/214-524           GAGGCUCAGGAAAAAGAUAUCGUCAGGAUGAUGAUAAGCCAU---G-AGGCAGG--------------------------AACGUAACG-GAGCUUACG-GCACAAGGAA-GGUUUCAGGAUGAAACAGG---AUCGCUC-AGGAU-UGAGCAAGGGACACCUCCAGGAUGGAGAAUGAGAACCC-CCU-CA-GAAGAG-G-UGGUG-GGCCAGGA-UGCU--------------AAGGA-U--------------ACA----------------UCAGGA-CGA----------------------UGC-GCGACAGGAGUUCGCAC-UGGACAAGUUGUCAUGGAA--GAGCAGGGAGCAUU-AAC-GUGGCGGGAUGGCUGCA-AACGAACC-GGGAG-CACUG--UUUAUACAGUG--C-UCCCUUUUUUUGUG
BX936398.1/3550390-3550069   GAUCUGGCGGAGAGGGAACGCAUCUGGAAGAUGUG-----------------------------------------------UCUUCAG-GAC-GAAGA-ACA-CAGGGA-CUGCUUAGGACGAGUGAAGG--GACGUUUCAGGAU-GAAACAAGGGACACCUCCAGGAUGGAGAUUGAGAGCC-AGUU-CA-GGAUGA-UU-GGUG-GGUUAGGAUAGCC-------------UAAGGAUUAAC-------------GCCGGGAUGGUGUA--U-----A-A--CAU-UGCGAUGG--------AUUGC-UGGUUAGUAUAACCAUA-CGGAAAAGUUUUCAGGGAU-UGAGCAGGGAGCAUC-AAUUUUAGCUGGAUUGCUAUAAAACGAAUUGAGGGG-UACUG--GUAAAACAGUA--C-CCCUUUUUUUGUUU
CP001164.1/3751312-3750953   GAGUCAGACAACGAAGUGAACAUCAGGAUGAUGACACUUCUG---A-AGGAC------------------------------ACACCAG-GAU-GGUGUUUCA-GGGAAA-GGCUUCUGGAUGAAGCGAAGAGGAUGACGCAGGAC-GCGUUAAAGGACACCUCCAGGAUGGAGAAUGAGAACC-GG-U-CA-GGAUGAUUC-GGUG-GGUCAGGAAGGCCUGG--GA--CACUUCAGGAUGAAG---UA----UCACAUCGGGGUGGUGUG--AGCAGGA-AGCAAU-AGUUCAGG-----AUGAACGA-UUGGCCGCAUGGCCAGA--GGAAAAGUUGUCAAGGAU--GAGCAGGGAGCAAC-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UGAAUACAGUG--C-UCCCUUUUUUUAUU
ABVY01000012.1/18391-18747   GUUUUAGGAAGAAACAGUCGUUUCAGGAAGAAGCGUUGUUUU---C-AGGAAGAUA---------------------AACAGUUUUCAG-GAA-GAAGA-ACA-G-------UUUUCAGGAAGAAACAUG------AUUUCAGGAU-GAAAUCAGGGACACCUCCAGGAAGGAGACCGAGAGCC-GA-U-UA-GGAAUA-UC-GGUG-GGGCAGGA-GCCUAAA---G--GGAUUGA--AUCACG---GA----AGAUA-CAGGAUGGAAAC--GUCAGGA-AGAAAG-UGGGACGCCAGCAAGGAUUGU-GGGUUAGGACGACCAAAAAGGAAAAGUUUUCACGGAU--GAGCAGGGAUGCAA-AUGUGUAGCGGGAUAGCUAUAAAACGAACC-GGGGG-UACUG--AGCAAUCAGUA--C-CCCCAAUUUUUUGC
ABAT01000014.1/43523-43202   GAUCUGGCGGAGAGGGAACGCAUCUGGAAGAUGUG-----------------------------------------------UCUUCAG-GAC-GAAGA-ACA-CAGGGA-CUGCUUAGGACGAGUGAAGG--GACGUUUCAGGAU-GAAACAAGGGACACCUCCAGGAUGGAGAUUGAGAGCC-AGUU-CA-GGAUGA-UU-GGUG-GGUUAGGAUAGCC-------------UAAGGAUUAAC-------------GCCGGGAUGGUGUA--U-----A-A--CAU-UGCGAUGG--------AUUGC-UGGUUAGUAUAACCAUA-CGGAAAAGUUUUCAGGGAU-UGAGCAGGGAGCAUC-AAUUUUAGCUGGAUUGCUAUAAAACGAAUUGAGGGG-UACUG--GUAAAACAGUA--C-CCCUUUUUGUGCCC
CAAT01000037.1/31831-32186   GAGUCGUACAACGAAGCGAACGUCAGGAUGAUGACGCUUCAG---C-AGGAC------------------------------ACGCCAG-GAU-GGUGUUACA-AGGAAA-GGCUUCAGGAUGAAGCAAAGUGGAAAGCGCAGGAU-GCGUUAAAGGACACCUCCAGGACGGAGAACGAGAGCC-GA-U-CA-GGAUGU-UC-GGCG-GAUCUGGAUAACCAGG--GA--CGCUUCAGGAUGAAG--CUA----UCACAUCGGGC-GAUGUG--CGCAGGA-UGUAAA-CGUUCAGG-----AUGAACA----GGCCGUAAGGUCACA--GGAAAAGUUGUCACGGAU--GAGCAGGGAGCACG-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UUUAUACAGUG--C-UUCCCUUUUUUUGU
CAAQ01004577.1/1374-1732     GAGUCGUACAACGAAGCGAACGUCAGGAUGAUGACGCUUCAG---C-AGGAC------------------------------ACGCCAG-GAU-GGUGUUACA-AGGAAA-GGCUUCAGGAUGAAGCAAAGUGGAAAGCGCAGGAU-GCGUUAAAGGACACCUCCAGGACGGAGAACGAGAGCC-GA-U-CA-GGAUGU-UC-GGCG-GAUCUGGAUAACCAGG--GA--CGCUUCAGGAUGAAG--CUA----UCACAUCGGGC-GAUGUG--CGCAGGA-UGUAAA-CGUUCAGG-----AUGAACA----GGCCGUAAGGUCACA--GGAAAAGUUGUCACGGAU--GAGCAGGGAGCAACGAAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGA-GCACUG--UUUAUACAGUGUC-UUCCCUUUUUUUGUU
AP008232.1/3356002-3355655   UAAGCAAGGAACGCCCACUGAACCAGGAUUGUGCCG-----C---A-CGGAC------------------------------AGCGCAGGGAA-GGGUUAGUG-CAGCAACGGCCUCAGGAAGAAGCCCG---CAAAUUUCAGGAU-GAUACUCAGGACACCUCCAGGAUGGAGAAUGUGAGCU-GG-U-AACGGAACG-CC-AGCGAAGCAGGGACUGCU-------------GCAGGACAUAC--GUU----UGAUAACGUAGGCGUGGC--GCAAGGA-UGGGUU-UUGCCAAC-----AUGGAUUG-UUGCAAUGUUAUCUUGU--AUAACAAGUGUUAUGGAGGUAGGCAGGGAGCAUA-AAC-GUAGCGGGAUUGCUAUAAAACGAACC-GGGGG-UACUG--UGUAAACAGUA--C-CCCCUUUUCUUUGA
ABVX01000043.1/11742-12098   UGUUUUAAGGAUAAACACUGUUUUAGGAAGAAACAGUCGCUU---C-AGGAAGAAG---------------------CGUUGUUUUCAG-GAA-GAAGA-ACA-G-------UUUUCAGGAAGAAACAUG------GUUUCAGGAU-GAAAUCAGGGACACCUCCAGGAAGGAGACCGAGAGCC-GA-U-UA-GGAAUA-UC-GGUG-GGGCAGGA-GCCUAAA---G--GGAUUGA--AUCACG---GA----AGAUA-CAGGAUGGAAAC--GUCAGGA-AGAAAG-UGGGACGCCAGCAAGGAUUGU-GGGUUAGGACGACCAAAAAGGAAAAGUUUUCACGGAU--GAGCAGGGAUGCAA-AUGUGUAGCGGGAUAGCUAUAAAACGAACC-GGGGG-UACUG--AGCAAUCAGUA--C-CCCCAAUUUUUUGC
AAMJ02000040.1/17166-16807   GAGUCAGACAACGAAGUGAACAUCAGGAUGAUGACACUUCUG---C-AGGAC------------------------------ACACUAG-GAU-GGUGUUUCA-GGGAAA-GGCUUCUGGAUGAAGCGAAGAGGAUGACGCAGGAC-GCGUUAAAGGACACCUCCAGCAUGGAGAAUGAGAACC-GG-U-CA-GGAUGAUUC-GGUG-GGUCAGGAAGGCCAGG--GA--CACUUCAGGAUGAAG---UA----UCACAUCGGGGUGGUGUG--AGCAGGA-AGCAAU-AGUUCAGA-----AUGAACGA-UUGGCCGCAAGGCCAGA--GGAAAAGUUGUCAAGGAU--GAGCAGGGAGCAAC-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UGAAUACAGUG--C-UCCCUUUUUUUAUU
CP000034.1/2780478-2780119   GAGUCAGACAACGAAGUGAACAUCAGGAUGAUGACACUUCUG---A-AGGAC------------------------------ACACCAG-GAU-GGUGUUUCA-GGGAAA-GGCUUCUGGAUGAAGCGAAGAGGAUGACGCAGGAC-GCGUUAAAGGACACCUCCAUGAUGGAGAAUGAGAACC-GG-U-CA-GGAUGAUUC-GGUG-GGUCAGGAAGGCCAGG--GA--CACUUCAGGAUGAAG---UA----UCACAUCGGGGUGGUGUG--AGCAGGA-AGCAAU-AGUUCAGG-----AUGAACGA-UUGGCCGCAAGGCCAGA--GGAAAAGUUGUCAAGGAU--GAGCAGGGAGCAAC-AAAUGUAGCUGGAAUGCUGCGAAACUAACC-GGGAG-CACUG--UGAAUACAGUG--C-UCCCUUUUUUUAUU
CP000964.1/999311-999670     AAGUCGCGAAAUGAAGCGAACAUCAGGAUGAUGGCGCUUCUG---C-AGGAC------------------------------CCGCCAG-GAU-GGCGUUGCA-AGGACA-GGCUUCAGGAUGAAGCAAGG---AUAACGCAGGAACGCGU-AAUGGACACCUCCAGGAUGGAGAACGAGAGCC-GC-U-CA-GGAUGA-AC-GGUG-GAUCAGGAAGAUCGGGA-CA--AACUUAAGGAUAAGUC-AUU----UCGCAUCGGGGUGGUGUGAAAGCAGGA-UGCGCG-AGUUUAUG----GAUGAACAU-UGGUCAGGA-GACCUCA--GGAAAAGUUUUCAAGGAC--GAGCAGGGAGCACC-AAU-GUAGCGGGAAUGCUGCAAAACGAACC-GGGAG-CACUG--UUUAUACAGUG--C-UCCCUUUUUUUAUU
FM200053.1/2930345-2929990   GAGUCGUACAACGAAGCGAACGUCAGGAUGAUGACGCUUCAG---C-AGGAC------------------------------ACGCCAG-GAU-GGUGUUACA-AGGAAA-GGCUUCAGGAUGAAGCAAAGUGGAAAGCGCAGGAU-GCGUUAAAGGACACCUCCAGGACGGAGAACGAGAGCC-GA-U-CA-GGAUGU-UC-GGCG-GGUCUGGAUGACCAGG--GA--CGCUUCAGGAUGAAG--CUA----UCACAUCGGGC-GAUGUG--CGCAGGA-UGUAAA-CGUUCAGG-----AUGAACA----GGCCGUAAGGUCACA--GGAAAAGUUGUCACGGAU--GAGCAGGGAGCACG-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UUUAUACAGUG--C-UCCCUUUUUUUUUG
CU468135.1/3038137-3037797   CAGGAAGAGGUAAAGGAUACCUCCAGGAUGGAGACGCGCCGG---AAAGGAUAUUCGGCAGUUAUGGAUGAUGCCAGGAUCACUAUCGG-GAU-GAUAGAGCA-GGGACA-GGCUUCGGGAUGAAGCGCAG--GAGACCUCAGGAA-GAGGUAAAGGACACCUCCAGGACGGAGAAUGUGAGCC-GU-A-CA-GGAUUG-UA-GGCG----------UUCAGGG---A--UGUCAAAGGAUUACC-----------------------------GUCAGGA-AGA----------------------UGUUUGCUCAGGAGAGCGAAA--GGAAUAGUUUUCAAGGAU--GAGCAGGGAGCAUA-AAG-GUAGCUGGACCGCUGCG-AACGAACC-GGGGG-CACUG--UGUAAACAGUG--C-CCCUUUUUUUGUUG
CP001063.1/2875622-2875981   GAGUCAGACAACGAAGUGAACAUCAGGAUGAUGACACUUCUG---C-AGGAC------------------------------ACACCAA-GAU-GGUGUUUCA-GGGAAA-GGCUUCUGGAUGAAGCGAAGAGGAUGACGCAGGAC-GCGUUAAAGGACACCUCCAGGAUGGAGAAUGAGAACC-GG-U-CA-GGAUGAUUC-GGCU-GGUCAGGAAGGCCAAG--GA--CACUUCAGGAUGAAG---UA----UCACAUCGGGGUGGUGUG--AGCAGGA-AGCAAU-AGUUCAGG-----AUGAACGA-UUGGCCGCAAGGCCAGA--GGAAAAGUUGUCAAGGAU--GAGCAGGGAGCAAC-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CGCUG--UGAAUACAGUG--C-UCCCUUUUUUUAUU
ACDJ01000018.1/54365-54009   GAGUCGCACAACGAAGAGAACAUCAGGAUGAUGGCUCUUCGC---C-AGGAC------------------------------ACACCAG-GAC-GGUGUUGCA-AGGACA-GGCUUCAGGACGAAGCAAAGAGGAAGACGCUGGAU-GCGUUAAAGGACACCUCCAGGAUGGAGAAUGAGAGCC-GG-U-CA-GGAUGU-UC-GGCG-GGUCUGGAUGGCCAGG---A--UACUUCAGGAUGAAG--UUU----UCACAUCGGGGUGAUGUG--AGCAGGA-UGCAGA-AGUUCAGG-----AUGAACAC---GGUCGCAAGACCACA--GGAAAAGUUGUCAAGGAU--GAGCAGGGAGCACU-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UUUUUACAGUG--C-UCCCUUUUUUUAUU
AALD02000009.1/85062-85382   GAUCUGGCGGAGAUGGAUGGUAUC-GGAUGCUACCA-----------------------------------------------CUUCAG-GAU-GAAGA-AUA-UAGGGA-CUGCUUAGGACGAGUGAAGG--GACGUUUCAGGAU-GAAACAUUGGACACCUCCAGGAUGGAGAUUGAGAGCCGGU-U-CA-GGAUGG-AU-GGUG-GGUUAGGAUAACU-------------UCAGGAUUAGC-------------ACCGGGAUGGU------GUAGGACAAC-----GCUACGG--------AUUGC-AGGUUAGGAUAACCAAA-CGGAAAAGUUUUCAAGGAU-UGAGCAGGGAGCAUC-ACUUUUAGCGGGAUCGCUAUGAAACGAAUCGAGGGG-UACUG--GUAAAACAGUA--C-CCCUUUUUUUAUUC
ABWL02000021.1/191679-192035 GAGUCGCACAACGAAGAGAACAUCAGGAUGAUGGCUCUUCGC---C-AGGAC------------------------------ACACCAG-GAC-GGUGUUACA-AGGACA-GGCUUCAGGAUGAAGCAAAGUGGAAAGCGCGGGAU-GCGUUAAAGGACACCUCCAGGAUGGAGAAUGAGAGCC-GG-U-CA-GGAUGU-UC-GGCG-GGUCAGGAUGGCUAGG---A--CACUUCAGGAUGAAG--UUU----UCACAUCGGGGUGAUGUG--AGCAGGA-UGCAAA-CGUUCAGG-----AUGAACAA---GGUCGCAAGACCACA--GGAAAAGUUGUCACGGAU--GAGCAGGGAGCACU-AAAAGUAGCUGGAAUGCUGCGAAACGAACC-GGGAG-CACUG--UUUUUACAGUG--C-UCCCUUUUUUUAUU
AALE02000003.1/44248-43927   GAUCUGGUGGAGAAGGACGGUAUCAGGAUGGUGCCA-----------------------------------------------CUUCAG-GAU-GAAGA-ACA-CAGGGA-CUGCUUAGGAUGAGUGAAGG--GAUGUUUCAGGAU-GAAACCAAGGACACCUCCAGGAUGGAGAUUGAGAGCC-AGUU-CA-GGAUGA-UU-GGUG-GGUUAGGAUAACC------------UU-AGGAUUGACG-------------CCGGGAUGGU------GUAGGACAAC-----GCGACGG--------AUUGC-UGGUUAGGAUAACCACA-CGGAAAAGUUUUCAAGGAU-UGAGCAGGGAGCAUC-AAUUUUAGCUGGAUUGCUAUGAAACGAAUUGAGGGG-UACUG--GUAAAACAGUA--C-CCCUUUUUUUAUCU
AALF02000009.1/41628-41307   GAUCUGGCGGAGAAGGACGGUAUCAGGAUGCUACCA-----------------------------------------------CUUCAG-GAU-GAAGA-ACA-CAGGGA-CUGCUUAGGAUGAGUGAAGG--GACGUUUCAGGAU-GAAACCAAGGACACCUCCAGGAUGGAGAUUGAGAGCCGGU-U-CA-GGAUGA-AU-GGUG-GGUUAGGAUAACC-----------UC--AGGAUUAGC-------------AUCGGGAUGGU------GUAGGA-AAC----UGCGAUGG--------AUUGC-UGGUUAGGAUAACCAUA-CGGAAAAGUUUUCAUGGAU-UGAGCAGGGAGCAUC-ACUUUUAGCGGGAUAGCUAUGAAACGAAUUGAGGGG-UACUG--GUAAAACAGUA--C-CCCUUUUUUUAUGC
ABWM02000033.1/161632-161274 ACGCCGACACGAGAAACGAACAUCAGGAUGAUGGCGUAUCUCAGCA-AGGAC------------------------------UCGUCAG-GAA-GGCGCUGCA-G--GAA-GGCUUCAGGAUGAAGCAAAGUGGAUAACGCAGGAU-GCGU-AAGGGACACCUCCAGGAAGGAGAACGAGAGCC-GG-U-CA-GGAUGG-UC-GGUG-GGUCAGGAAGGCCAGG---A--CGUUUCAGGACGAAA--CAC----ACACAUCAGGAUGAUGUG--AGCAGGA-UGCAAC-GGUUAACG-----GAUAACCA-ACGCCCUUCGGGCAUCA--GGAAAAGUUGUCACGGAU--GAGCAGGGAGCACG-AAUUGUAGCUGGAAUGCUGCGGAACGAACC-GGGAG-CACUG--UUUAUACAGUG--C-UCCCUUUUUUUAUU
#=GC SS_cons                 ::::::::::::::::::::<<<_______>>>,,,,,,,,,...,.,,,,,..............................<<<<<__.___.>>>>>,,,,.,,,,,,.,<<<<<_____>>>>>,,,,..,,,<<<<<_____.>>>>>,,,,,,,,,<<<<_____>>>>,,,,,,,<<<.<<.<.__._____>.>>.>>>,.<<<_______>>>,,,...,..,,<<<<_____>>>>...,,....,,,,,,,,,,,,,,,,,,..,<<____._>>,,,.,,,,,,,,.....,,,,,,,,.,,,,,,,,,,,,,,,,,..,,,,,,,,,,<<______..>>,,,,,,,,,,,,.,,,,<<<<<______>>>>>,,,,,,,,,,.<<<<<.<<<<<..______>>>>>..>.>>>>::::::::::
#=GC RF                      gAgucggagaaagaaGauaacauCAGGAUGaugacgcuUCug...a.AGGAc..............................ccgcCAG.GAu.GgcgguaCA.agGaaA.GgcuUcAGGAugAagcaaaG..GAugccgCAGGAU.GcggcaAaGGACACCUCCAGGAuGGAGAauGAGAgCC.gg.u.cA.GGAuga.cc.GGcG.GGccAGGAuggCCAgG...A..cgcuucAGGAUgaag...ua....ucAcAuCgGGaUGgUGug..agCAGGA.aGcaau.uGuuaagg.....AuGAaugu.ugGucaGgAugaCcaaA..GGAAAAGUUuUCAaGGAU..GAGCAGGGAGCAua.AAauguAGCuGGAuuGCUacgAAACGAACC.GGGgG.cACUG..uuuAuACAGUg..C.cCCCUUUUUUUuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00019
#=GF ID   Y_RNA
#=GF PI   Y1; Y2; Y3; Y5
#=GF DE   Y RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Griffiths-Jones SR, Published; PMID:18087752, Gardner PP
#=GF SS   Published; PMID:10606662
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000405; Y_RNA;
#=GF RN   [1]
#=GF RM   10606662
#=GF RT   Conserved features of Y RNAs: a comparison of experimentally derived
#=GF RT   secondary structures.
#=GF RA   Teunissen SW, Kruithof MJ, Farris AD, Harley JB, Venrooij WJ, Pruijn GJ
#=GF RL   Nucleic Acids Res 2000;28:610-619.
#=GF RN   [2]
#=GF RM   7489501
#=GF RT   Caenorhabditis elegans embryos contain only one major species of Ro RNP.
#=GF RA   Van Horn DJ, Eisenberg D, O'Brien CA, Wolin SL
#=GF RL   RNA 1995;1:293-303.
#=GF RN   [3]
#=GF RM   10766734
#=GF RT   Ro ribonucleoproteins contribute to the resistance of Deinococcus
#=GF RT   radiodurans to ultraviolet irradiation.
#=GF RA   Chen X, Quinn AM, Wolin SL
#=GF RL   Genes Dev 2000;14:777-782.
#=GF RN   [4]
#=GF RM   18087752
#=GF RT   Evolution of the vertebrate Y RNA cluster.
#=GF RA   Mosig A, Guofeng M, Stadler BM, Stadler PF
#=GF RL   Theory Biosci. 2007;126:9-14.
#=GF RN   [5]
#=GF RM   24022222
#=GF RT   5'-YRNA fragments derived by processing of transcripts from specific YRNA
#=GF RT   genes and pseudogenes are abundant in human serum and plasma.
#=GF RA   Dhahbi JM, Spindler SR, Atamna H, Boffelli D, Mote P, Martin DI
#=GF RL   Physiol Genomics. 2013;45:990-998.
#=GF CC   Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in
#=GF CC   association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins
#=GF CC   are well conserved, but the function of the Ro RNP is not known. In humans
#=GF CC   the RNA component can be one of four small RNAs -- hY1, hY3, hY4 and hY5.
#=GF CC   These small RNAs are predicted to fold into a conserved secondary
#=GF CC   structure containing three stem structures. The largest of the four, hY1,
#=GF CC   contains an additional hairpin. This family includes a significant number
#=GF CC   of annotated pseudogenes and the model is expected to discriminate poorly
#=GF CC   between real and Y RNA related pseudogenes.
#=GF WK   Y_RNA
#=GF SQ   104


AAQQ01567293.1/1826-1938       GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUUGAACUCCUUGUUCUACUCUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
AADA01181485.1/19721-19833     GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUCGAACUCCUUGUUCUACUCUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
AADD01087484.1/3854-3742       GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUCGAACUCCUUGUUCUACUCUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
AANG01401391.1/4351-4239       GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUCGAACUCCUUGUUCUACUCUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
AANU01114500.1/5407-5295       GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUCGAACUCCUUGUUCUACUCUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
CAAA01202596.1/1204-1315       GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUUGAACUCCUGUU-CUACACUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
ABDC01640458.1/594-706         GGCUGGUCCAAAAGUAGUGA--G---UUAUCUCACUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUUGAACUCCUUGUUCUACUCUUUCCCC-ACUU-CUCACUACUGCACUUGACUAGUC-----UUAA
AAFC03099238.1/121707-121818   GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUCGAACUCCUCGUUCU-ACUCUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
AAHX01030026.1/7139-7028       GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUUGAACUCCUGUU-CUACACUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUCU
AAFR03014070.1/33365-33253     GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAAUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUCGAUCUCCUUGUUCUCUCUUUCCCUC-CCUU-CUCACUACUGCACUCGACUAGUC-----UUUU
AAPY01074605.1/4054-3942       GGCUGGUCUAAAGAUAGUGA--G---UUAUCUCAAAUGAGUGUU-CA-----AAGUCAGUUAC--------------AGGUUGAACUCCUUGUUCUACUAUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUAA
AAPN01172659.1/53662-53775     GGCUAGUCCGAAGGUAGUGA--G---UUAUCACAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUCGAUAUCCCUGUUCUCUCUUCCUCCCACCUU-CUCACUACCGUAUUUGACUAGUC-----UUUU
CU104669.1/59726-59616         GGCUUGUCCAAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU--------CAGUCAGUUAC--------------AGAUUGAACUCCUUGUUCUACUCUUUACCU-ACUU-CUCACUAUUGCACUUGACUAGUC-----UUUC
AAYZ01133136.1/1346-1235       GGCUGGUCCGAAGGUAGUGA--G---CCAUCACAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGGUCGAACUCCUCGUUC-AACAAUUCCCC-CCUC-CUCACUACUGCACUUGACUGGUC-----UUUU
AC198789.3/79648-79760         GGCUGGUUCGAAGGUAGUGA--C---UUAUCUUAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUAAAACUCUCUGUUCUACUCUUUCCCA-CCUU-CUCACUACUACACUUGACUAGUC-----UAAA
AC193857.1/159000-159109       GGCUGGUCUGAAGGUAGUGA--G---UUAUCUCAAUUGACUGUU--------CAGUCAGUUAC--------------AGAUCAAACUCCUUGUUCUACUCUUUCCCC-ACUU-CUCACUA-UGCACUUGACUAGUC-----UUAA
CT954295.2/106374-106485       GGUUGGUCUGAAUGUAGUGA--G---UUAUCU--------------------CAAUGGACUGUUCACAGUCUGUUACAGAUAGAACUCCUUGU-UCUAUUCCUUCCC-CUGU-CUUACUGCUGCACCUGACUUGUC-----AAAA
AANN01713410.1/1087-1200       GGCUGGUCCGAAGGUAGUGA--G---UUAUCACAAUUGGUUCUA--------CAGUCAGUUACAGC-----------UCGAACUCCUCCUUGUACUCCUUGUUCUAC-CCUC-CUCACUGCUGCACUUGACUGGUC-----UUUU
AAIY01602616.1/513-618         GGCUGGUCCAAAGGUAGUGA--G---AUC-----------------------UCACAACGAUUGCUUACAGUC----AGUUACUGUUCGACCUAUUUAUCUACCCCC-CCCC-CUCACUACUGCACUUGACUAGUC-----UUAA
AC128639.13/157491-157374      GGCUGGUCCAAAGGUAGUUA--G---UUGAGUUAUCUCAGUUGG-UUGUUCAUAGGCAGUAAC--------------AGAUCAAACUCCUUAUUCUUCUCUGUCCCC-UCUU-CUCAAUACUGCACUUGACUAGUC-----UAAA
AALT01276434.1/528-629         GGCUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAAUUAAUUGAUCAC----------AGCCAAUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACCAGCC-----UAAA
AAFC03099238.1/126186-126085   GGCUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAAUUAAUUGAUCAC----------AGCCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACUAGCC-----UUUU
AANG01401391.1/458-559         GGCUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAAUUAAUUGAUCAC----------AGCCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACUAGCC-----UUUU
AAPN01172659.1/46022-46123     GGCUGGUCCGAGUGCAGUGG--AAU-UUA-----------------------UAAUUAAUUGAUCAC----------AGUCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACUAGUC-----UUUU
ABBA01033605.1/1707-1808       GGCUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACUAGCC-----UUUU
AAQQ01087250.1/2676-2575       GGCUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACUAGCC-----UUUU
AALT01190817.1/1596-1495       GGCUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAAUUAAUUGAUCAC----------AGCCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACCGGCC-----UUUU
AACN010300925.1/452-553        GGCUGGUCCGAGUGCAGUGGU-GC--UUA-----------------------CAAUUAAUUGAUCAC----------AGCCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACCGGCC-----UUUU
AAPY01489510.1/220-119         GGCUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AGCCAGUUACAGAUUCCUUUGUUCCUUCUC-UACU-CCCACUGCUUCACUUGACUAGCC-----UUUU
AANU01114500.1/1882-1983       GGUUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACCAGCC-----UUUU
AANN01151837.1/1360-1259       GGUUGGUCCGAGUGCAGUGGU-G---UUUACACU------------------UAAUUGAUCAC--------------AGCCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACUAGCC-----UUUU
L27532.1/94-195                GGCUGGUCCGAUUGCAGUGG--UAC-UUA-----------------------UAAUUAAUUGAUCAC----------AGUCAGUUACAGGUUUCUUUGUUCUUUCUC-CACU-CCCACUGCUUCACUUGACUAGUC-----UUUU
ABDC01154708.1/21315-21214     GGUUGGUCCAAGUGCAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AGUCAGUUACAGAUUACUUUGUUCCUUCUC-CAUU-CCCACUGCUUCACUUGACCAGCC-----UUAA
AC190269.3/73147-73248         GGCUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCUACUGCUUCACUUGACUAGCC-----UAAA
AAFR03014070.1/16387-16488     GGCUGGUCCGAUUGCAGUGG--UAA-CUC-----------------------UAAUUAAUUGAUUAC----------AGUCAGUUACAGAUUUCUUUGUUCUUUCUC-CGCU-CCCACUGCUUCACUUGACUAGUC-----UUUU
AC198096.2/48526-48425         GGCUGGUCCAAGUGCAAUGG--UGU-UUA-----------------------CAACUAAUUGAUAAC----------AACCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-UCCACUGCUUCACUUGACUAGCC-----UUAA
AAYZ01133135.1/2712-2813       GGCUGGUCCGAGUGCAGUGGU-GC--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGGUUUCUUUGUUCCUUCUC-CACC-CCCACUGCUUCACUUGACCGGUC-----UUUU
AC166248.20/29722-29823        GGUUGGUCCGAGAGUAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGAUUUCUUUGUUCCUUCUC-CGCU-CCCACUGCUUCACUUGACCAGCC-----UUUU
L15431.1/36-136                GGCUGGUCCGAAGGCAGUGGUUG---CCA-----------------------CCAUUAAUUGAUUAC----------AGACAGUUACAGACUUCUUUGUUCUUCUCC-CC-U-CCCACUGCUUCCCUUGACUAGCC-----UUUU
AC199101.3/202469-202368       GGCUGGUCCAAGUGCAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCAUUGUGUCACUUGGCUAGCC-----UAAA
CU104658.1/43354-43455         GGCUGGUCAGAGUGUAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAAUUACAGAUUUCUUUUUUCCUUCUC-CACU-CCCACUGCUUCGCUUGACUAGCC-----UUUA
AAIY01627550.1/131-32          GGCUGGUCCGAGUGCAGUGG--GG--UCA-----------------------CAACUAAUGAUCAC-----------AGCCAGUUACAGGUUCCUUUGUUCUUUCUC-CACC-UCCACUGCUUCACUUGACCGGUC-----UUAA
AB172890.1/1859-1960           GGCUGGUCCAAGUACAGUAGU-GU--UUA-----------------------CAACUAUAUGAUCAC----------AACCAGUUACAGAUUUCUUUGUUCCUUCUC-CAUC-CCCACUGCUUUACUUGACUAGCC-----AAAA
DQ375698.1/52-152              GGCUUGUCC-AGUGCAGUGGU-GC--UUA-----------------------CAGCUAAUUGAUCAC----------AACCAGUUAUAGAUGUCUUUGUUUCUUCUC-GACU-CCCACUGCUUCACUUCACUAGCC-----UUAA
AC091754.4/85523-85426         GGCCC----GAGUGCAGUGG--UGG-UUACACU-------------------UAAUUGAUCAC--------------AACCAGUUACAGAUUUUUUUGUUCCCUCUC-CACU-UCCACUGCUUCACUGUAAGAGCC-----UAAC
BAAE01083756.1/1191-1090       GGUUGGUCCGACGGCAGUGG--GAU-UUACAAUUGA----------------UUGCCACAGUC----------------ACAGAAAACUUCUACGUUGCUUCUCUCC-CC-U-CUCACUGCCGACCUUGACUAGCC-----UUUU
AAVX01633839.1/220-328         GGCCGGUCCGAUGGUAGUGG--G---UUA-----------------------UCGUUGAUAUUUGCUUACAGAGUC-AGUUACAGAUUUCCUUGUUCUCUCUUCCCC-CCUU-CUCACUGCUUCACUUGACUGGUC-----CUUU
CAAE01014565.1/1750315-1750419 GGCUGGUCCGAUGGCGGUGA--GA--UUUCAAUUGA----------------UUGCUACAGUG--------------AGUUACAGAACCUCUAUGUUUCUUCUCUCC-CCUCCCUCACCGCCGGCCUUGACUAGCU-----UUUG
AC073140.5/117955-118049       GGCUGGUCCGAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACAACC-C----CCCACUGCUAAAUUUGACUGGC------UUUU
AANU01114497.1/4433-4527       GGCUGGUCCGAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACAACC-C----CCCACUGCUAAAUUUGACUGGC------UUUU
AAQQ01087252.1/3999-3905       GGCUGGUCCGAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGAUAUACAACC-C----CCCACUGCUAAAUUUGACUGGC------UUUU
AAFC03099237.1/8865-8959       GGCUGGUCCGAUGGUAGUGG--G---UUA-----------------------CCAGAACUUAUUAA-----------CGUUAGUGUCACUAAAGUUGGUAUACAACC-C----CCCACUGCUAAAUUUGACUGGC------UUUU
AAPY01593018.1/4000-3906       GGCUGGUCCGAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACCACC-C----CCCACUGCUAAAUUUGACUGGC------UUUU
ABDC01601884.1/580-486         GGCUGGUCCAAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUUCAACC-C----CCCACUGCUAAAUUUGACUGGC------UUUU
AC191785.1/102750-102844       GGCUGGUCCAAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACAAGC-C----CCCACUGCUAAAUUUGACUGGU------UUUU
AAIY01183764.1/1055-959        GGCUGGUCCGAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACAAAC-CC-C-CCCACUGCUGAAUUUGACUGGC------UUUU
AAYZ01133134.1/5808-5901       GGCUGGUCCGAUGGUAGUGG--G---UUA-----------------------UCAGAACUUAUUA------------ACAUUAGCUCACUAAAGUUGGUAUACAACC-C----CCCACUGCUAAAUUUGACUGGC------UUUU
CU104657.1/45296-45390         GGCUGGUCCGAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------UGUGUCACUAAAAUUGGUAUACAACC-U----CCCACUGCUAUAUUUGACUGGC------UAAA
AAPN01172659.1/41108-41201     GGCUGGUCCGAUAGUAGUGG--G---UGC-----------------------CCAGAACUCUUUA------------AUAUAGUUUCACUAAACUUGGUAUAUUCCA-C----CUCACUGCUAAACUUGACUGGCC-----UUU-
L27536.1/95-191                GGCUGGUCCGAAAGUAGUGG--G---UUAUC---------------------ACAGAAAUUAUUAC-----------AGUUAGUUUCACUAACCUUUCUAAGUUCCA-C----CCCACUGCUAACCUUGACUGGUC-----UUU-
AALT01150475.1/801-706         GGCUGGUCCGAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACACU------------------AGGAUCACUAAAGUUGGUAUUCUACC-CC---CCCACUGCUGAAUUUGACUGGC------UUUU
AAFR03014070.1/4048-4144       GGCUGGUCCGAUGGCAGUGG--U---UUA-----------------------CCAGAACUUAUUGAU----------AUUAGUUUCACAACAAGUUAAUAUAUUCCA-CC---CCCACUGCUAAAUUUGACUGGCC-----UUU-
AAHY01783012.1/356-450         GGCUGGUCCGAUGGUAGUGG--G---UCAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACAACC-C----CCCAUUGCUAAAUUUCACUGGA------UUAA
AANN01541484.1/11468-11369     GGCUGGUCCGAAGGUAGUGG--G---UUA-----------------------UCAGAAAAACUAUUAA---------CGUUAGUGUCACUAAAGUUGGUAAACAACC-CCCC-CCCACUGCUGGAUUUGACUGGC------UAAA
AB173926.1/570-476             GGCUGGUCUGAUGGUAGUGA--G---UAAUUAGAAU----------------GUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACAACU-C----CCCACUGCUAAAUGUGACU-GUC-----UGAA
BAAF04056104.1/511-600         GGCUGGUCCGAUGGCAGUGG--A------------------------------AAUCGAAAGC--------------AUUUGCAACAGUCUACGUCUCUUCUCUACU-CC-C-UUCACUGCCAACCUUGACUAGC------UUUU
AC188094.1/125458-125557       GGCUGGUCCAAGGGCAGAGGU-GU--UUA-----------------------CAACUAACUGAUCAC----------AGCCAGUUACAGAUUUCUUUGUCCUUUUCC-AC-G-CCCACGGCUUCAUUUGACUAGCC-----UAA-
ABDC01212300.1/2415-2498       AGUUGGUCCGAGGGUUGUGG--G---UUA-----------------------UUGUUAAGCUG-----------------------------AUUUAACAUUGUCUC-CC---CCCACAACCACGCUUGACUAGCUUUGUGUUUU
AANU01114493.1/23713-23796     AGUUGGUCCGAGUGUUGUGG--G---UUA-----------------------UUGUUAAGUUG-----------------------------AUUUAACAUUGUCUC-CC---CCCACAACCGCGCUUGACUAGCUUGACGUUUU
AADD01087475.1/2469-2552       AGUUGGUCCGAGUGUUGUGG--G---UUA-----------------------UUGUUAAGUUG-----------------------------AUUUAACAUUGUCUC-CC---CCCACAACCGCGCUUGACUAGCUUGCUGUUUU
AANG01401364.1/3093-3176       AGUUGGUCCGAGGGUUGUGG--G---UUA-----------------------UUGUUAAGUUG------------------------------UUUAACAGUGUCUC-CC-C-CCGACAACCAUACUUGACUGGCUUUGCCUUUU
AAPY01099160.1/404-321         AGUUGGUCCGAGGAUUGUGG--G---UUA-----------------------UUGUUAAGCUG------------------------------AUUAACAUUGUCUC-CC-U-CCCAUAUCCAUACUUGACUAGCUAUGCGCUUG
AALT01071660.1/743-660         AGUUGGUCCGAGGGAUGUGA--G---UGA-----------------------UUGUUAAACUG------------------------------AUUAACAUUGUCUC-CU-G-CUCACAACCACAUUUGACUAGCUGGGAUUUUU
AAYZ01133133.1/1470-1552       GGUUGGUCCGCGAGCUGUGG--G---UUG-----------------------UUGUUAAGCUG------------------------------UUUAACAUUGUCUC-CC---CCCACAACCACAUUUGACCGGCUUUGCCUUUU
AANN01447405.1/373-290         AGUUGGUUCAAGAGUUGUGG--U---UUA-----------------------UUGUUAAGCUG------------------------------UUUAACAUUGUCUG-CC-A-UCCACAACCGCAUUUGACUGACUUAAGAUUUU
U94705.1/86-167                AGUUGGUCCGAAGGUUGUGG--G---UUA-----------------------UCGUUAUUGAU-------------------------------UUAAUAUUGUCUC-CC---CCCACACCCCCUCUUGACUAGCUUUGUUUUUU
AAIY01754109.1/639-719         AGUUGGUCCGAAGGUUGUGG--G-----------------------------UUGUUAAGCUA------------------------------UUUAGCAUUGUCUC-CC-A-CCCACAACCAUACCUGACUAGCUUUGCCUUUU
AAPN01172659.1/37408-37498     AGUUGGUCCGAGAGUUGUGG--G---UUA-----------------------UUGUUACAUUU----------------------GAUUCGAAUGGAACAUUGUCUC-CC---CCCACAACUGAGUUUGACUGGCUUUGCUUUUC
AAHY01053143.1/11743-11662     AGUUGGUCUGG-GGUUGUGG--G---UUA-----------------------UUGUUAAAUUG------------------------------UUUAACACUGUUUC-CC---CCCAUACCCAUGCUUGACUAACGUGGGGAAAU
AAFR03014070.1/19826-19746     AGUUUGUCUGGGAGUUGUGG--G---UUA-----------------------UUGAUCAUUAA-------------------------------U-AUCAUAUUCUA-CC---CCCACCACUGUGUUUGACUGGCUUUCUUUUUC
L15432.1/36-131                GGUUGGUCCGAAAGUUGUGG--G---UUAUCCAAAUCAUU------------CAGUUAGUAUC------------------------------ACUAACCUUCUAUU-UCAC-CCCACUGCUGACCUUGACUGGCCAAUUUUUUA
AAKN02032250.1/45001-45095     GGCUGGUCCGAUGGCAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACCACC-C----CCCACUGCUAAAUUUGACUGGC------UUUA
L32608.1/283-377               GGCUGGUCCGAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACAACC-C----CCCACUGCUAAAUUUGACUGGC------UUUU
AAWR02036108.1/19259-19341     AGUUGGUCCGAAGGUUGUGG--G---UUA-----------------------UUGUUAAACUG------------------------------AUUAACAUUGUCUC-CC---CCCACAACCGUGUUUGACUGGCUGCGUGUUUU
AAKN02015288.1/137209-137126   AGUUGGUCCGAAGGCUGUGG--G---UUA-----------------------UUGUUAUACAU-----------------------------GGUUAACAUUGUCUC-CC---CCCACACCCGUGCUUGACUAACUGAGUGUUUU
CAAK05049532.1/4055-3950       GGCUGGUCCGAAGGCGGUGG--G---UUAGUCA-------------------CAAUUGAUUGCUACAGUC-------AGUUACAGAACUCCUUGUUUCUUCUCUCCC-CUCU-CCCACCGCUGAACUUGACCAGCC-----UUU-
AAWR02036109.1/33571-33459     GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGCU-CA-----CAGUCAGUCAC--------------AGAUCGAACUCCUUGUUCUACUCUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
AAKN02015288.1/122513-122624   GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU-C------ACAGUCAGUAC--------------AGAUUGAACUCCUUGUUCUACUCUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
ABVD01627856.1/93-188          GGCUGGUCCGAUGGUAGUGG--G---UUA-----------------------UCAGAACUUAUUAA-----------CAUUAGUGUCACUAAAGUUGGUAUACAACC-CC---CCCACUGCUGAAUUUGACUGGC------UUUU
V00584.1/39-151                GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUUCA------CAGUCAGUUAC--------------AGAUCGAACUCCUUGUUCUACUCUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
ABDC01454694.1/1407-1507       GGUUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGAUU-CUUUGUUCCUUCUC-CACU-CCCACUGCUCCACUUGACCAGCC-----UUUA
AAGV020140146.1/661-580        GGUUGGUCCGAGGCUUGUGG--G---UUA-----------------------UUGUUAAACUG------------------------------UUUAGCAUUGUCUC-CC---CCCACAACCACAUUUGACUAACUAAGCUUUU-
AAWZ02001015.1/5911-5815       GGCUGGUCCGAAAGUAGUGG--G---UUACC---------------------ACAGAAAUUAUUAC-----------AGUUAGUUUCACUAACCUUUCUAAGUUCCA-C----CCCACUGCUAACCUUGACUGGUC-----UCC-
AC205306.6/147779-147685       GGCUGGUCCGAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACAACC-C----CCCACUGCUAGAUUUGACUGGC------UUUU
AADN03001926.1/468172-468061   GGCUGGUCCGAAGGUAGUGG--G---GUGUCUCAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUUGAUCUCCUCGUUCUCUCUUUCCCCC-CU-U-CCCACUACUGCACUUGACUAGUC-----UUUU
AAQR03087348.1/2666-2565       GGCUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGAUUCCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUAGACUAGCC-----UUUU
AABR05113607.1/617-718         GGUUGGUCCGCGAGUAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACCAGCC-----UUUU
AAQR03087347.1/3330-3442       GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCACUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUUGAACUCCUUGUUCUACUCUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
AC205306.6/121485-121597       GGCUGGUCCGAAGGUAGUGA--G---UUAUCUCAAUUGAUUGUU-CA-----CAGUCAGUUAC--------------AGAUUGAACUCCUUGUUCUACUCUUUCCCC-CCUU-CUCACUACUGCACUUGACUAGUC-----UUUU
V00585.1/39-140                GGCUGGUCCGAGUGCAGUGGU-GU--UUA-----------------------CAACUAAUUGAUCAC----------AACCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACUAGCC-----UUUU
BL000002.1/147953394-147953488 GGCUGGUCCGAUGGUAGUGG--G---UUAUCAGAAC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUACAACC-C----CCCACUGCUAAAUUUGACUGGC------UUUU
AAPE02039776.1/102994-103096   GGCUGGUCCGAGUGCAGUGGU-GU-CUUA-----------------------CAACUAAUUGAUCAC----------AGCCAGUUACAGAUUUCUUUGUUCCUUCUC-CACU-CCCACUGCUUCACUUGACUAGCC-----UUUU
AADN03001926.1/477473-477373   GGCUGGUCCGAUGGCAAUGG--CAU-UUAUAA--------------------UAAUUGAUCAC--------------AGUCCGUUACAGAUUUCUUUGCUCUUUCUC-CACU-CCCACUGCUGCAUUUGACUAGUC-----UUUU
AAQR03087350.1/1071-976        GGCUGGUCCGAUAGUAGUGG--G---UUAUCAGAGC----------------UUAUUAACAUU------------------AGUGUCACUAAAGUUGGUAUUCAACC-CC---CCCACUGCUAAAUUUGACUGGC------UUUU
#=GC SS_cons                   <<<<<<<<-<<--<<<<<<<..<...-----.....................-<<<-<<____.............._________________>>->>>-------.----.>>>>>>--->>-->>>>>>>>>>.....::::
#=GC RF                        GGCuGGUCCGAagguaGUGG..G...UUAuc.....................uuguuAguuau..............AGauaguuauacuuuuucUuacauuuuCcC.CcuU.CCCACugCUacACUUGACUaGCC.....UUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00020
#=GF ID   U5
#=GF DE   U5 spliceosomal RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Zwieb C, The uRNA database, PMID:9016512; PMID:18390578
#=GF SS   Published; PMID:2339054; Griffiths-Jones SR
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000395; U5_snRNA;
#=GF DR   GO; 0000244; spliceosomal tri-snRNP complex assembly;
#=GF DR   GO; 0000353; formation of quadruple SL/U4/U5/U6 snRNP;
#=GF DR   GO; 0005682; U5 snRNP;
#=GF DR   GO; 0046540; U4/U6 x U5 tri-snRNP complex;
#=GF RN   [1]
#=GF RM   9016512
#=GF RT   The uRNA database.
#=GF RA   Zwieb C
#=GF RL   Nucleic Acids Res 1997;25:102-103.
#=GF RN   [2]
#=GF RM   8702566
#=GF RT   Domain analysis of human U5 RNA. Cap trimethylation, protein binding, and
#=GF RT   spliceosome assembly.
#=GF RA   Hinz M, Moore MJ, Bindereif A
#=GF RL   J Biol Chem 1996;271:19001-19007.
#=GF RN   [3]
#=GF RM   2339054
#=GF RT   The spliceosomal snRNAs of Caenorhabditis elegans.
#=GF RA   Thomas J, Lea K, Zucker-Aprison E, Blumenthal T
#=GF RL   Nucleic Acids Res 1990;18:2633-2642.
#=GF CC   U5 RNA is a component of both types of known spliceosome. The precise
#=GF CC   function of this molecule is unknown, though it is known that the 5' loop
#=GF CC   is required for splice site selection and p220 binding, and that both the
#=GF CC   3' stem-loop and the Sm site are important for Sm protein binding and cap
#=GF CC   methylation.
#=GF WK   U5_spliceosomal_RNA
#=GF SQ   180


AAFC03028536.1/14883-14999     AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUCUUUACCC--------AAUUUUUUGA------GGCCUCGUUUUU---AACGAGGCU
AANU01096983.1/4726-4842       AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GCAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-ACUCU-------GAGUCUUAACCC--------AAUUUUUUGA------GGCCUUGUAUUU---UGCAAGGCU
M10270.1/1-117                 AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACNAAAGA-UUUCCG----UGG-A--GA-GGAACA-ACUCU-------GAGUCUUAAACC--------AAUUUUUUGA------GGCCUUGUCUUG---AGCAAGGCU
AAFR03051183.1/13754-13869     AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-GUUAA-------GAGUUUUUACCU--------AAUUUUUUGA------GGCCUCGUUUU----UGCGAGGCU
AALT01479958.1/1552-1436       AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUUUUUACCC--------AAUUUUUUGA------GGCCUUGCUUUU---AGCAGGGCU
AC083892.19/144818-144933      AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUCUUACACU--------AAUUUUUUGA------GGCCUUGCUUU----AGCAAGGCU
AANG01141002.1/575-691         AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUCUUAAAAC--------AAUUUUUUGA------GGCCUUGCACUU---AGCGAGGCU
ABDC01046604.1/3549-3664       AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUUUUAUACC--------AAUUUUUUGA------GGUCUUGCUUU----AGCAAGACU
AAQQ01236639.1/2054-2171       AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUCUGAAACC--------AAUUUUUUGA------GGCCUUGUUUUUC--AGCAAGGCU
AAIY01547840.1/3111-2996       AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GCAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-ACUCU-------GAGUCUUAAACC--------AAUUUUUUGA------GGCCUUGCUUA----UGCAAGGCU
AAYZ01307320.1/25593-25710     AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUCUUUACCC--------AAUUUUUUGA------GGCCUUGCAUUAU--UGCAAGGCU
AC068213.7/527-412             AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GCAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-ACUCU-------GAGUCUUAACCC--------AAUUUUUUGA------GGCCUUGCUUU----GGCAAGGCU
AANN01833323.1/1168-1053       AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUACAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUUUAUACCU--------AAUUUUUUGA------GGCCUUGUUCU----UACAAGGCU
AAPY01334745.1/473-358         AUACUCUGGUU-U-CU-CUUCA-------------------------------------AAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUUUGUAACU--------AAUUUUUUGA------UGCCUUGCUUU----GGCAGGGCU
AAPN01296676.1/948-833         AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GCAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-GUUAU-------GAGUUUGUAACU--------AAUUUUUUGA------GGCCUCGUUUU----UACGAGGCU
CAAE01011816.1/72155-72041     UCACUCUUGUU-U-CA-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GU-GGAACA-AUUAA-------GAGUUUUACUC---------AAUUUUUUGA------UGCCCUGCGUC----UGCGGGGCU
K03164.1/1-115                 AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-ACCAC-------GAGUGUCGUGG---------AAUUUUUUGA------GGCUCCGCUUC----GGCGGAGCU
AAVX01303608.1/479-595         AUGCUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAGCA-UUUAC-------GAGUUUUUAACCC-------AAUUUUUUUA------GGCUCUGCACC----AGCAGAGCU
BAAF04017217.1/172-285         ACUCUU--GUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-ACAA--------GAGAUUUACUC---------AAUUUUUUGA------UGCCUUGCUUCAC--AGCGAGGCU
X63789.1/2235-2348             UAUCACAGAAC-U-CA-GCUCA-------------------------------------UUAC-GAUUUAAUUUUUCGCCUUUUACUAAAGA-UUACCG----UGA-G--CU-GGGUUU-UUCAA------UGUGAAUUAUUAA--------AAUUUUUGCA-------GGAUUCUUUU------GAAUCCU
X06020.1/401-515               AUACUCUGGUU-U-CU-CUUCAA------------------------------------AUUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACG-ACCAU-------GAGUUUCGUUCA--------AUUUUUUGAA------GCCUGGUUCAC------ACCAGGU
K03096.1/1-119                 AUACUCUGGUU-U-CU-CUUCAA------------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-CUCUA------AGAGUCUAAAACU--------AAUUUUUUAG------UCAGUCUUGUCG---CAAGACUGG
AC174762.1/131410-131525       ACACUCUAGUU-U-CU-CUUCA-------------------------------------GAUC-GCAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAAC--ACUAU-------GAGUUUUAACU---------AAUUUUUUGA------UGCCCUGCUUCAC--UGCGGGGCU
AASG02001471.1/28708-28826     AGCCGC-GCGG-U-AA-GCACA-------------------------------------AAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--CU-UGCCGC-AAAUA-------GCGGCAUACGCC--------AAUUUUUGGAGG----GUUCUCUUUUCUC--GGAGAGGAU
AM454615.1/12361-12244         AGCCAC-GUGG-U-GG-GCACA-------------------------------------AAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--CU-CUCCAC-AUUUA-------GUGGCAUACGCU--------AAUUUUUGGAG-----AGUCCUCUUCUAC--UAGAGGGCU
AP004339.3/129793-129675       AGCUGC-GUGG-U-GA-GCACA-------------------------------------AAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--CG-CGCCAC-AUUAA-------GCAGCAUACGCU--------AAUUUUUGGAGGG---CGCCCUCUCUCA---GAGAGGGCC
AAAA02022467.1/54175-54057     AGCUGC-GUGG-U-GA-GCACA-------------------------------------AAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--CG-CGCCAC-AUUAA-------GCAGCAUACGCU--------AAUUUUUGGAGGG---CGCCCUCUCUCA---GAGAGGGCC
ABAV01004466.1/10927-10807     UCACUCUGGUU-U-UC-CUUCA-------------------------------------GAGC-GCAAAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GG-AGAACA-ACAUA-----AUGAGUCUAUAAACU-------AAUUUUUUGU------UGCCCUGCCUUAU--GGCGGGGCU
CAAJ01000127.1/3421-3534       GGUGUGUGUAC-U-UA-CUACA-------------------------------------UAAC-GAAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-A--GG-AGGUAC-UUUAA------AUACAAUACCACA--------AAUUUUUGUC-------ACGUCAUUUU------UGGCGUG
CAAI01002944.1/2056-1943       GGUGUGUGUAC-U-UA-CUACA-------------------------------------UAAC-GAAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-A--GG-AGGUAC-UUUAA------AUACAAUACCACA--------AAUUUUUGUC-------ACGUCAAUAU------UGGCGUG
AAJJ01001278.1/15201-15319     UCACUCUGGUU-U-CC-CUUCA-------------------------------------GUGC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GG-GGAACA-AUUCA----AAUGAGUCUAUGAAA--------AUUUCUUGAU------UGCCCGGCGAA----AGCUGGGCG
X15935.1/3-121                 AGCCAU-GUGA-U-AA-GUACA-------------------------------------AAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-A--CU-UUUCAC-UAACA-------GUGGCAUACGAU--------AAUUUUUGAA------UGAGCUCUCAUGUUUGAGAGCUCU
AC158186.2/4528-4644           AAGCCGUGUGG-U-CA-GCGCA-------------------------------------AAAC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--UU-GGCCAC-AUAAU-----AGCGGCAUAUCCA---------AAUUUUUGGA------ACGCUUCCUCA----CGGAGGCAC
AC007202.3/14338-14454         AGCCGU-GUGG-U-GA-AUACA-------------------------------------AAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--UU-CUCCAC-GCUAA-------ACGGCAUACACC--------AAUUUUUGGAGGAG--UAACUUCAUCU------GAAGUUU
AATU01003637.1/103086-103202   UUCCGCUGAGU-U-AA-UUUCA--------------------------------------UUC-GUAUUAAUCUUUCGCCUUUUACUAAAGA-UUACCG----UGG-A--AU-UGACUC-ACAAA-----AUGCGGCUUCGACC--------AAAUUUCUGG-------ACCCCUCCUUG---UGAGGGGAA
Z14994.1/1543-1661             AGCUGC-GCAG-U-GG-GCACA-------------------------------------AAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--CC-CGCUGC-AAUUA-------GCAGCAUACGCA--------UAUUUUUGGA------GGGUUCUCUCUUUUGUGAGAAGCC
AADK01028234.1/592-479         UAUCUCUGGUU-U-CC-CUUCA-------------------------------------AAAC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GG-GGAACA-CUCAA-------AUGAGUCUAUAA--------UAUUUUUGAU------GCCCUGACUUG------UCAGGGU
AASM01000961.1/2142-2261       GGUGUGUGUAC-U-UA-CUACA-------------------------------------UAAC-GAAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-A--GU-AAGUAU-GUUAA------AUACAAUAUACCACG------AAUUUUUGUC-------GCGCCUAUUAAG--UUAGGUGCU
AARH01001853.1/639606-639489   AGCCGU-GCGG-U-AG-ACACA-------------------------------------AAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--UU-UGCCGC-AAAUC-------ACGGCAUACGCU--------AAUUUUUGAA------GGGGUUCUCCGACG-GCGAGCCCU
AC146755.23/40564-40682        AGCCGU-GUGA-U-GA-UGACA-------------------------------------UAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-C--AA-CGUCAC-UUUUA-------ACGGCAUACGUU--------AGUUUUUGGA------AGAGCCCUCUUAAUUGAGGGCUCU
AAZO01006170.1/89711-89592     CACCUCAUGUU-U-CC-CUUCA-------------------------------------UAAC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GG-GGAACA-AUAGU-------GAGACUUUAGGUC-------AAUUUUUGUGG-----AGCCUGUAUAUAC--GUACAGGCC
AAZX01000523.1/17560-17680     UCACUCUGGUU-U-CC-CUUCAUU-----------------------------------ACAC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GG-GAAACA-CUUGA------UGAGUCUAUAGACUU------AUUUUUUGUG------UGCCCAACGAA----AGUUGGGCC
X74440.1/1-120                 ACACGCGGCUU-U-CU-CGGCA-------------------------------------GAUC-GAAUUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-C--GG-GGAUGC-AUAUU------UGCGUCUUUUGAUCG------AAUUUUUUGC------GGCCACUCUUUA---UGAGUGGCU
EF647601.1/94040-94158         AGCCAC-GCAG-U-GA-GCACA-------------------------------------UAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--CG-CGUUGC-AAUUA-------GUGGCAUACGCU--------AAUUUUUGGA------GGGAUUUUCUUAACUGAAGAUCCC
AABL01000519.1/10755-10640     GGUGUGUGUAC-U-UA-CUACA-------------------------------------UAAC-GAAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-A--GG-AGGUAC-UUUAA------AUACAAUACCACA--------AAUUUUUGU--------CACGUCAAUUU---GGCGUGUGU
AAKM01000004.1/1465347-1465233 GGGUAU-GUAC-U-UA-CUACA-------------------------------------UAAC-GUAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-A--GU-AGGUAC-AAUAA-------AUACGUUAUACCACA-----AAUUUUUGU--------CGUGCC--UUC---CGGGCGCGU
AAWU01000380.1/47408-47286     UUACUCUGGUC-U-CU-CUUCAAU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGGACA-CUCUA-----AUGAGUCUAAACUA--------AAUUUUUGUU------CGUCUCGAUCCUUA-ACUGGGUCG
AAPT01020503.1/50561-50682     CUACUCUGGCU-U-CU-CUUCAGU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAGCA-CUCUA-----AUGAGUCUAAAAUA--------AUUUUUUGCA------GUGCCUGAUUCCC--AUCGGGCCA
CR855038.1/57351-57233         AGCUGC-GCAG-U-GG-GCACA-------------------------------------AAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--CU-CGCUGC-AAAUA-------GCAGCAUACUCU--------AAUUUUUUGAGGG---GAUUUCCAGCAU---UUGGAGAAC
AAGE02022633.1/4541-4666       UUACUCUGGUC-U-CU-CUUCAAA-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGGACA-CUCUA-----AUGAGUCUAAAAUA--------AAUUUUUGUCUUGUCCAACCCCGCUAA----UCCGGGGUU
AAQX01002881.1/912-1027        UUCCGCAAAAU-U-AA-CUACA--------------------------------------UUC-GUAUUAAUCUUUCGCCUUUUACUAAAGA-UUACCG----UGU-G--GU-UGGUUU-ACUAA-----AUGCGGCUUCAACC--------AAUUUCUGU--------GCCCCUCCUUG---CGAGGGGAA
AACY020397167.1/1194-1084      AUCACA-GCGU-U-CA-CUUCA-------------------------------------UUAC-GCACCAAUCUUUCGCCUUUUACUAAAGG-UUGCCG----UGA-A--AG-GGACGC-AUCAA-------UGUGACUUCAUC--------AAUUUUUGC--------GGGACCUUCG------GGUCCCA
AACT01019277.1/3233-3346       UUACUCUGGCU-U-CU-CUUCA---------------------------------------UC-GUAUGAUUCUUUCGCCUUUUACUAAAGA-AUUCCG----UGG-A--GG-GGAGCA-UUUCA-----AUGAGUCUUAAACU--------AUUUUUCUUA------ACCUGACUUGU------GUCAGGU
AASV01046355.1/666-787         UCACUCUGGUU-U-CU-CUUCAAU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-CUCUA-----AUGAGUCUAAACUA--------AAUUUUUGUU------AAGGCAUGAUAAC--UUAUGUUAU
AAEU02000660.1/100051-99931    UUACUCUGGUU-U-CU-CUUCAAU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-CUCUA-----AUGAGUCUAAAAUA--------AUUUUUUGUA------GUGCCCGGUGAC---UUCGGUUGC
AAPQ01007319.1/728227-728345   UUACUCUGGUU-U-CU-CUUCAAU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-CUCUA-----AUGAGUCUAAACAU--------AAUUUUUGUU------UAGAGCC--CCG---CAGGCGUUU
AAPP01015704.1/527093-527216   CAACUCUGGUU-U-CU-CUUCAAU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGGACA-CACUA-----AUGAGUCUAGACUC--------AAUUUUUUGAUAG---GGCCCUGCUGCU---UGCGGGGCC
AACW02000228.1/444426-444540   UACUUCUGUCU-U-GU-GCUCA-------------------------------------UAUC-GGAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--UG-CGGGAC-ACUAA------AGAAGAUUACCCG--------AAUUUUUUGG------UAAAACCCUCU------CUUUUUC
AAAB01008944.1/3738569-3738447 GCACUCUGAUC-U-CU-CUUCAAC-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGGAUA-CUCUA-----AUGAGUCUAUAGAG--------AAUUUUUGUC------CGUCUCGAUUCCGU-AAGGAGUCG
AAKO01001397.1/16278-16396     UUACUCUGGUU-U-CU-CUUCAAU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-CUCUA-----AUGAGUCUAAACAC--------AAUUUUUGCU------UAGAGCC--CCG---AUGGCGUUU
AAPU01010615.1/222531-222648   UUACUCUGGCU-U-CU-CUUCAGU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAGCA-CUCUA-----AUGAGUCUAAAUUG--------AAUUUUUUGA------UUGUGUCUGAC------GGCGUUU
X01693.1/1-112                 AUCACA-GAAC-U-CA-GCUCA-------------------------------------AUAC-GCUUUAAUUUUUCGCCUUUUACUAAAGA-UUACCG----UGG-G--CU-GGGUUC-UACAA-------UGUGAAUUAUUA--------AAAUUUUUG--------AGGAUU--GUG---UGAAUCCUA
AAYL01000045.1/86345-86236     AUCGCA-GCGG-U-UG-UCACA-------------------------------------GAAC-GCAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-G--AC-AUCCGCAUCAAA-------UGCGAAUCAAG---------AAUUUUUGAC-------GGCGUC--UC------GACGCCA
AANI01017247.1/37618-37740     UCACUCUGGCU-U-CU-CUUCAGU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAGCA-CUCUA-----AUGAGUCUAAAAU---------AAUUUUUGCUAG----UGCCCGAUUGCAA--AAUUGGGCC
AY462110.1/1391-1506           GGCGACUGGGC-G-UU-UCUCA--------------------------------------ACC-AAACUAUCCCCUCGCCUUUUACUAGGGG-AUACCG----UGG-G--AG-ACGCCA-CUCAA------UGUCGCAUUAGCC--------AAUUUUUCAG------CACUCAGUACC----AUCUGAGCC
AADS01000442.1/10516-10633     AGCGGCAGAGG-G-CA-GCACA--------------------------------------AAC-AGACAACGCCCUCGCCUUUUACUAGGGC-GUUCCG----UGU-G--CU-GCCCUC-ACAUC----AAUGCCGCUUAGCC---------AAUUUUUCAG------CCCUCAGCUUCG---UCCUGAGAU
AF271469.1/310-194             CGACUCUGGUU-U-CU-CUUCA-------------------------------------UUAC-GCACAAGCCUUUCGCCUUUUACUAAAGA-CUUCCG----UGG-A--GA-GGAACA-CUUAC-------GAGUUCAACGUA--------UUUUUGGAAG------GGCUUUGCUUCU---GGCAGAGCC
AAQB01006740.1/366264-366386   UUACUCUGGCU-U-CU-CUUCAGU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGUGCA-CUCUA-----AUGAGUCUAUUUAG--------AAUUUUUCACUG----UGCCUGACUACC---AGUCGGGCA
AADE01000447.1/59086-59201     UUACUCUGGCU-U-CU-CUUCAAU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGGGCA-CUCUA-----AUGAGUCUAAACUG--------AAUUUUUUCA------UAGUUCC--------UGGCGACUU
AB202073.1/931-819             UGACUCUGGUU-U-CU-CUUCA-------------------------------------AAAU-GCACAAGUCUUUCGCCUUUUACUAAAGA-CUUCCG----UGG-A--GA-GGGACG-UUCAA-------GAGUUUAAGUU----------AUUUUUGGU------GGGCUUU--GCC---GUAAGGCUG
AABS01000112.1/71173-71286     UUACUCUGGCU-U-CU-CUUCA---------------------------------------GC-GCAUGAUUCUUUCGCCUUUUACUAAAGA-AUUCCG----UGG-A--GG-GGAGCA-UUUCA-----AUGAGUCUUUAACU--------AUUUUUCUAC------ACCCGACUUAG------GUCGGGA
AAIZ01003066.1/82049-82166     UCACUCUGGUU-U-CU-CUUCAAU-----------------------------------UGUC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGGACA-CUCUA-----AUGAGUCUAAACUA--------AAUUUUUGUU------UAGUGCCUGGU------GACAUCU
AAQA01000616.1/21218-21104     UUUGUCUUGCU-C-UC-CUGCAUUU----------------------------------GACC-GAGAAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGC-A--GG-AGAGUA-UUUAU-------GAUUGUUAACAU--------AUUUUUUGGA------AGCCCUU--UA------AGGGGCU
AY705674.1/1315-1203           UAGCUCUGGUC-U-CU-CUUCA-------------------------------------AAAC-GUAUAAUUCUUUCGCCUUUUACUAAAGA-AUUCCG----UGG-A--GA-GGGACA-CUCUU-----AUGAGUAUUUG-----------AAUUUUUCUG------UAGCUCCAAAC------GGAGCAG
Z69659.1/6667-6789             AAACUCUGGUU-C-CU-CUGCAUUU----------------------------------AACC-GUGAAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGC-A--AA-GGAGCA-UACAU------UGAGUAUUAUAUAC-------AAUUUUUGGA-------GUCCCCUCGAAAG-AGCGGGACA
CAAL01001847.1/78328-78213     AUCACC-GAGC-U-CA-ACCUA-------------------------------------UUAC-GUGCUAAUUUUUCGCCUUUUACUAAAGA-UUACCG----UGG-G--UU-GGGCUC-AUACC-------GGUGACUUACAG--------AAAUUUUUAG------AGGUCGAAAGAC---CCCCAACCA
L22251.1/140-257               CAGCUCUGGUU-C-CU-CUGCAUC-----------------------------------CACC-GAGAAAUUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGC-A--GA-GGAACG-UUUAU-------GAGUAUACGCC---------AAUUUUUGGA------GUCCCAGCUUCG---GCUAGGGAC
AAXJ01002433.1/2315-2426       UAUCACAGCGG-U-CA-UCUCA-------------------------------------AAGC-GAAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-GGCAU-GACUGC-ACACA------UGUGAACUUACAC--------AAUUUUUGCG-------GAGCGU----------AUGCUCC
AAXT01000002.1/226294-226405   AUAGCA-GCGG-U-CG-CCGCA-------------------------------------UUUC-GCAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGC-G--GC-GUCCGCAUUCAA-------UGCAUCUUUUCU--------AAUUUUUUC--------UGGCGCUCCG------GCGCCUA
AAFP01000428.1/22975-22864     AGCGGG-GGAU-C-AA-ACACA-------------------------------------AAUC-GAAUAAAUCUCUCGCCUUUUACUAGAGA-UAUCCG----UGU-A--UU-UGGUCC-GCAAA-------CCCGCGUUCAA---------AUUUGUUCCA------CACCCAUUUCC------UUGGGCU
AE017344.1/587581-587470       AGCGGG-GGAU-C-AA-ACACA-------------------------------------AAUC-GAAUAAAUCUCUCGCCUUUUACUAGAGA-UAUCCG----UGU-A--UU-UGGUCC-GCAAA-------CCCGCGUUCAA---------AUUUGUUCCA------CACCCAUUUCC------UUGGGCU
AAEY01000021.1/77428-77539     AGCGGG-GGAU-C-AA-ACACA-------------------------------------AAUC-GAAUAAAUCUCUCGCCUUUUACUAGAGA-UAUCCG----UGU-A--UU-UGGUCC-GCAAA-------CCCGCGUUCAA---------AUUUGUUCCA------CACCCAUUUCC------UUGGGCU
AAFI02000148.1/105951-105837   CGCUUCCGACU-U-CG-GUUCAA------------------------------------UAAC-GAAAAAGAUUUUCGCCUUUUACUAAAAUACUUCCG----UGA-A--CC-GAAGUC-AUAAA------GGCAGCUUUCACU--------AUUUUUUUG--------AAUAGGUCUU------CCUAUUC
DQ001173.1/3-117               CGCUUCCGACU-U-CG-GUUCAA------------------------------------UAAC-GAAAAAGAUUUUCGCCUUUUACUAAAAUACUUCCG----UGA-A--CC-GAAGUC-AUAAA------GGCAGCUUUCACU--------AUUUUUUUG--------AAUAGGUCUU------CCUAUUC
AAGK01000001.1/548506-548395   UACGCA-GUAG-U-CG-UCGCA-------------------------------------UCAC-GCACCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGC-G--GC-GUCUACAUUUAA-------UGCUAUUUAUCU--------AAUUUUUCU--------UGGCGCUCAG------GCGCCUA
AACO02000021.1/6655-6544       AGCGGG-GGUU-C-AA-ACACA-------------------------------------AAUC-GAAUAAAUCUCUCGCCUUUUACUAGAGA-UAUCCG----UGU-A--UU-UGGUCC-GCAAA-------CCCGCGUUCAA---------AUUUGUUCCA------CACCCAUUUCU------UUGGGCU
AATT01000070.1/145415-145303   CUUCUCUGAGG-C-CU-UCGCA-------------------------------------AAAC-GUACAACUCUUUCGCCUUUUACUAAAAA-GUUCCG----UGUAG--GG-GGCCUC-ACAUG-------GAGAAUGUCUCC--------AAUUUUUCCC------AUACCUU--------GGAGGGUUA
X00386.1/1-104                 AUCACA-GUGU-U-CA-CUUCA--------------------------------------ACC-GAAUCAAUCUUUCGCCUUUUACUAAAGG-UUGCCG----UGA-A--UG-GGACAC-AUCAA-------UGUGAAUCUCUC--------AAUUUUUGAG-------GGC-------U---CU---GCCC
AAWT01083394.1/3003-2887       UAACUCUUGUU-U-CA-UUUCAAUAUACG------------------------------AAAC-GUUUAAAUCUUUCGCCUUUUACUAAAGA-UUUUCG----UGG-A--AU-GGAACA-AUUAA-----AAGAGUUUUAAAC---------ACUUUUUAA--------AGCCCUC---------AGGGUUA
AF095839.1/891-776             CAGCACCGCCU-G-CU-ACUUA-------------------------------------CAUC-GCAUUUAUCUUUCGCCUUUUACUAAAGA-UAGCCG----UGA-G--UGAGCAGGC-ACUGC------GGUGCAUUGACCC--------AAUUUUUGGA------GCCCCCUCAAA------AGGGCAA
X16573.1/258-372               GUCAAA-GCAC-U-UU-GCAAAAGC----------------------------------UAAC-GUAUCUGUUUCUUGCCUUUUACCAGAAA-CAGCCG----UUU-G--UA-AGGUGU-GCUAA-------UUUGACUGUAU---------AGUUUUUGUA------AUCUUUUUCUU------GAAACAU
AAFU01001022.1/48358-48247     UUGGAG-UAGG-C-CC-GCUCA-------------------------------------GACC-GAACUCAUUUCCUGCCUUUUACCGGAUG-UGACCG----UGA-G--UU-GGCCUA-AAAUA-------CUCCAUUCCCC---------AAUCUUUGGA------AACACCUCUCU------GGGUAUC
ABCN01002017.1/34559-34665     CGCGAC-GAGC-U-GA-ACGCG-------------------------------------UAGC-GAAUAUCUCUUUCGCCUUUUACUAAAGA-GAUCCG----CGA-G--UU-UUGCUC-ACGCA-------GUCGCAUAUCCU--------UCUUUUUGUG------GGGC-----UU----UU---GCCC
AAFB02000352.1/4039-4148       AUCUUC--ACU-A-CU-AACAA-------------------------------------AAUC-GAUCUUAUCUUUCGCCUUUUACUAAAGA-UAACCG----U-G-U--UA-GUAGAU-UUACU-------GAAGAUGAAGG---------AAUUUUUGGA------GGGUCUAUUCA------AGGACCA
AACM02000265.1/29897-29783     UCGGAGUGGGA-C-C--UCCCA---------------------------------------UC-GAACUCACCUCUUGCCUUUUACCAGAUG-UGACCG----UGG-G--AUUGGCCCA-ACAGA-------CUCCAUUCAUCU--------AAUCUUUGGA------AACCAUUCAUCU---AGAAUCUCU
CR382132.1/1370879-1370995     AACAACGGAGG-U-CG-ACAUC--------------------------------------GAC-GUACAUGGCUCUUGCCUUUUACCAGAGC-CAUCCG----GGU-G--UC-GU-CUC-UACAA-------GUUGUUUUUCU---------AGUUUUUGGA------AACUUCUUCUUAUGGAGACAAGUG
AANV02000637.1/5704-5595       AUCUUC--ACU-A-CU-AGCAA-------------------------------------AAUC-GAUCUUAUCUUUCGCCUUUUACUAAAGA-UAACCG----U-G-U--UA-GUAGAU-UCACU-------GAAGAUGAAGG---------AAUUUUUGGA------GGGUCUGUUCA------AGGACCA
AATM01000006.1/4956-4838       GUCAAA-GCAU-U-UC-ACAAAAUC----------------------------------UAUC-GCAUCUAUUUCUUGCCUUUUACCAGAAA-UAGCCG----UUU-G--UG-AGGUGU-GUGAA-------UUUGACUGUAC---------AAUUUUUGCUAC----UGUUUCCCUAA----CGGGGGACU
AAIM02000161.1/229078-228967   UCGGAGUGGGA-C-C--UCCCA---------------------------------------UC-GAACUCACCUCUUGCCUUUUACCAGAUG-UGACCG----UGG-G--AUUGGCCCA-ACAGA-------CUCCAUUCACCU--------AAUCUUUGGA------AACCAUUCGUC------UAGGGAC
AARE01001511.1/1260-1149       AUGGAGUGGGA-C-GA-GCUAG-------------------------------------CUCA-GAAUCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG----UGG-C--UU-CGCCCA-UUAAA-------CUCCACUUAAC---------AAUCUUUGGA-------AUGUCUAACA------AGACACA
AAJI01001476.1/13492-13374     AUGGAGUGGAA-C-AG-GCUAG-------------------------------------CUCA-GAAUCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG----UGG-C--UC-UGUCCA-AAAUA-------CUCCAAUACUCG--------AAUCUUUGGA------CACUUUCCUAUUCG-ACAAUAGUU
AF529186.1/1009-894            A-ACUCUGGCA-U-CU-CCUCAC------------------------------------UUGC-GGACAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGU-G--GA-GGUGCA-GCACA-----AUGAGUCUAUAGAGU-------CAUUUUUGCA------CUGCCCC----G---ACGCGGCUU
AAEE01000007.1/707570-707686   ACACCGUACUG-A-UG-UGAUA-------------------------------------UCUC-GUACCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-C--AC-AUCAGC-UUGGU-------AGUUAUUACCAGGUCAU---AAUAUUUGG--------GGAGUUUCUA------CACUCCG
AAEL01000435.1/2854-2970       ACACCGUACUG-A-UG-UGAUA-------------------------------------UCUC-GUACCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-C--AC-AUCAGC-UUGGU-------AGUUAUUACCAGGUAAU---AAUAUUUGG--------GGAGUUUCUA------CACUCCG
AAWC01002764.1/14312-14199     CAUGCU-CUGU-U-UG-GUCUCAU-----------------------------------AUUC-GAACGUCCCCCUCGCCUUUUACUAGGGA-GACCCG----GGG-A--CC-AGGCAG-GUCAA-------AGCAUGCCCAC---------AAUCUUUCGU------GACCACCCUCA------GGUGGGA
AAFT01000039.1/59328-59208     GACGCCAGAAGAU-CA-GUUUCUU-----------------------------------AAGC-GUACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGA-A--CU-GUCUUU-GCUAA------UGGUGUUUUUUUU--------CAUUUUUUGG------AACUCUCCCAUG---UGCUAAAUC
Z11883.1/951-834               AGCCAC-GCAG-U-GA-GCACA-------------------------------------GAAC-GAACAGUUCUUUUGCCUUUUACUAAAGA-AUACCC---AUGU-G--CA-CUCUGC-AAAUA-------GUGGGUUAUGCC--------UAUUUUUGGA------GGGGUUCUCUCUA--UUGAGUGCC
AAKE03000008.1/776195-776083   GAGGAGUGGGA-C-AA-GCUAG-------------------------------------CUCA-GAACCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UGCCCA-ACAUA-------CUCCUCUUCUC---------AAUCUUUGGA-------CCUUUCCAUC----GACAUAGCU
AAHF01000006.1/1883955-1883843 GAGGAGUGGGA-C-AA-GCUAG-------------------------------------CUCA-GAACCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UGCCCA-ACAUA-------CUCCUCUUCUC---------AAUCUUUGGA-------CCUUUCCAUC----GACAUAGCU
ABDB01000059.1/258270-258158   GAGGAGUGGGA-C-AA-GCUAG-------------------------------------CUCA-GAACCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UGCCCA-ACAUA-------CUCCUCUUCUC---------AAUCUUUGGA-------CCUUUCCAUC----GACAUAGCU
AATX01000063.1/152569-152455   AGGAGU-GGGA-C-AA-GCUAG-------------------------------------CUCA-GAAUCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UUGCCC-AAUAC-------ACUCCGCUCCUC--------AAUCUUUGGA------AUCACUAUCGAC---AAUAGUCGG
ABBB01000033.1/420348-420462   AGGAGU-GGGA-C-AA-GCUAG-------------------------------------CUCA-GAAUCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UUGCCC-AAUAC-------ACUCCGCUCCUC--------AAUCUUUGGA------AUCACUAUCGAC---AAUAGUCGG
AASO01001658.1/2059-1945       AGGAGU-GGGA-C-AA-GCUAG-------------------------------------CUCA-GAAUCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UUGCCC-AAUAC-------ACUCCGCUCCUC--------AAUCUUUGGA------AUCACUAUCGAC---AAUAGUCGG
ABBC01000392.1/6892-7006       AGGAGU-GGGA-C-AA-GCUAG-------------------------------------CUCA-GAAUCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UUGCCC-AAUAC-------ACUCCGCUCCUC--------AAUCUUUGGA------AUCACUAUCGAC---AAUAGUCGG
AAXI01000301.1/8428-8544       UGUGCA-GUGC-GAGG-AUUUG--------------------------------------UAC-GAACUCAUUUCUUGCCUUUUACCAGAAG-UGACCG----CGA-G--UC-CCGCAC-AACAC-------UGCACUUACUC---------AAUCUUUGGA------AACAACUCGCCCCA-UCAGGGGUU
AAVQ01000002.1/3936-3813       AUCGCCAGGAGAU-CA-AUUUCAA-----------------------------------AAUC-GUACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGA-A--UU-GUCUUC-AAUAC---AAAUGGUGUAUCAACU--------AGUUUUUGGA------AACCUUUCCACU---UCAAAUCAC
AAGI01000327.1/72210-72324     UGUGCA-GUGC-GAGG-AUUUG--------------------------------------UAC-GAACUCAUUUCUUGCCUUUUACCAGAAG-UGACCG----CGA-G--UC-CCGCAC-AACAC-------UGCACUUACUC---------AAUCUUUGGA------ACAAAAACGUCG---AGGAUUCGA
AAKD03000017.1/303987-303868   GAGGAGUGGGA-C-AA-GCUAG-------------------------------------CUCA-GAACCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UGCCCA-AAAUA-------CUCCUCUUCUC---------AAUCUUUGGACUUAUCCAUCGACACAG----CUGUCGAUU
AM270115.1/128938-128823       GAGGAGUGGGA-C-AA-ACUAG-------------------------------------CUCA-GAACCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--UU-UGCCCA-AAAGA-------CUCCUCUCAUC---------AAUCUUUGGA------AUCACCCAUCGAC--ACAGCUGUC
AANW02001233.1/8188-8079       UGUCGC--UUC-UACU-AACUG-------------------------------------UUUC-AUACUUAUCUUUCGCCUUUUACUAAAGA-UAACUG-----AG-U--UG-GAGAAU-UAACA-------GCGACACAAAA---------AAUUUUUGGA-------GGGUUCAUUC------GGACCUG
AP007155.1/1026766-1026646     GAGGAGUGGGA-C-AA-GCUAG-------------------------------------UUCA-GAACCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--UU-UGCCCA-CAAUA-------CUCCUCUACUG---------AAUCUUUGGACCUUU-CAAUCGACACAGU--UGUCGAUUU
AAIW01000368.1/11893-11779     AGGAGU-GGGA-C-AA-GCUAG-------------------------------------CUCA-GAAUCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UUGCCC-AAAAU-------ACUCCGCUCCUC--------AAUCUUUGGA------AGAACUCUCGAC---UACAGUCAG
AAJN01000094.1/53887-53768     GAGGAGUGGGA-C-AA-GCUAG-------------------------------------UUCA-GAACCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UGCCCA-GAAUA-------CUCCUCUCCUC---------AAUCUUUGGAAUUCUCCAUCGACACAG----CUGUCGAUU
AANS01001320.1/16875-16995     GGUGUGUGUAC-U-UAGGGACA-------------------------------------UAAC-GAAGCAAUCGUUCCCCUUUUACUAAAGA-UUGCCG----UGU-A--GU-AAGUAU-GUUAA------AUACAAUAUACCACG------AAUUUUUGUC-------GCGCCUAUUAAG--UUAGGUGCU
AAFM01000003.1/226344-226452   CGCCAG--AAGAU-CA-AUAUC-------------------------------------UAUC-GUACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGU-A--UU-GUCUUU-AU----------AUGGUGCUCGCU--------AUUUUUUGGA-------ACCUUCUCAU------GAUGCUU
AL590450.1/114088-114197       ACCCCUGGCCG-C-CU-CGCCG-------------------------------------AUAA-GUACGAGUCUUUUGCCUUUUACUGAAGA-CUCCCA----UGG-C--CA-GGCAG------U-------AGUGCCCACCAC--------AAUUUUUGGA------AUGCUGA--CUA---GCUCAGCUU
AC004395.1/1702-1592           ACGGGU-GUGU-G-GG-CCUAG-------------------------------------CUCA-GAAUCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG------U-G--GG-CCACGC-AAAAU-------ACCCUACUACCU--------AAUCUUUGGA------AUCAUCUAUCG------ACAUAGU
AACD01000010.1/103824-103714   ACGGGU-GUGU-G-GG-CCUAG-------------------------------------CUCA-GAAUCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG------U-G--GG-CCACGC-AAAAU-------ACCCUACUACCU--------AAUCUUUGGA------AUCAUCUAUCG------ACAUAGU
AAPO01000006.1/285980-286104   AUCGCCAGGAGAU-CA-AUUCC--------------------------------------AAC-GAACAUGGUUCUUGCCUUUUCCCAGAAC-CAUCCG----GGA-A--UU-GUCUCC-CGUUAGUCAAAUGGUGUAUCAAUUAUCU----AAUUUUUGGA------AUAUUUAUCAU------UUAGUUU
AAIH02000216.1/25877-25996     GAGGAGUGGGA-C-AA-GCUAG-------------------------------------UUCA-GAACCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--UU-UGCCCA-CAAUA-------CUCCUCUACUG---------AAUCUUUGGACCUUUCCAUCGACACAG----UUGUCGAUU
AAGT01000497.1/29058-28944     UCGGAGUGGGA-C-A--AGCUA-------------------------------------GCUCAGAAUUCAUUUCUUGCCUUUUACCAGAGA-UGACCG----UGG-C--UCAUGCCCA-UAAUA-------CUCCAUUCAUCA--------AAUAUUUGGA------ACAAACCUUUC------UGAUUAC
X87329.1/2199-2085             GGGAGC-AGGC-C-AA-GCUCAAC-----------------------------------CAAC-GCAUUCAUUUCCUGCCUUUUACCGGAUG-UGACCG----UGA-G---U-UGGCCU-ACAAU-------GCUCCCAUUCU---------AAUCUUUGGAAA----CCUCUGGACAC------CCAGAUU
AAFO01000011.1/73327-73206     CGCCAG-AAGA-U-CA-AUUUCAAUAUAC------------------------------CUAC-GUACAUGGUUCUUGUCUUUUCCCAGAAC-CAUCCG----GGA-A--UU-GUCUUC-AUUCA-------AUGGUGUAUCA---------AAUUUUUACU------UUUUGGAAAAUU---GUUUCAAGA
AACQ01000039.1/46591-46712     CGCCAG-AAGA-U-CA-AUUUCAGUUUAC------------------------------CUAC-GUACAUGGUUCUUGUCUUUUCCCAGAAC-CAUCCG----GGA-A--UU-GUCUUC-AUUCA-------AUGGUGUAUCA---------AAUUUUUACU------UUUUGGAAAAUU---GUUUCAAGA
CR382125.1/1422292-1422448     ACGUCUGGCGA-U-CA-GUAUCAAUGGGGGCGUUCCAGCUUUUUACUGGUUUGCCCUCGUUUC-GAACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGU-A--CU-GUCCCA-ACUAU-------GGACUCAAUACUCUGUCU--AAUUUUUGGC------AGCCUUUUUUU------AAAGAAA
AAID01003647.1/370-250         UCGGAGUGGGA-C-A--AGCUA-------------------------------------GCUCAGAAUUCAUUUCUUGCCUUUUACCAGAGA-UGACCG----UGG-C--UCAUGCCCA-UGAUA-------CUCCAUUCUUCA--------AAUCUUUGUAACACACCUUCUGAUUAU------UCAGAGA
AC091619.3/67508-67375         AGACUCUG----U-CU-CAACAAAAACAAAAAAAAAGAUAUGG----------------UCAU-UAUUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUGU-------GAGUUCACCACC--------AAAUUUUUUG------ACGUCCUGCUU----AGAGGGGGC
AACA01000117.1/2098-2219       UUUGUU-GCCU-A-CA-GAACUUA-----------------------------------UAAC-GAACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGU-G--CU-GUCUCC-ACUUA-------AACAGGUAAAGCUGUC----CGUUACUGUG------GCUCCUCGCAUU---UUUUGGAAC
AACG02000018.1/45887-45766     UUUGUU-GCCU-A-CA-GAACUUA-----------------------------------UAAC-GAACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGU-G--CU-GUCUCC-ACUUA-------AACAGGUAAAGCUGUC----CGUUACUGUG------GCUCCUCGCAUU---UUUUGGAAC
AC189540.1/19288-19170         AAGUAUGCCAG-A-GC-GUAAA-------------------------------------UUUU-UCACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--UU-CUCCAC-GCUAA-------GUGGCAUACGCC--------UAUUUUUGGA------GGGUCCUGCUUUCG-AGUGGGCCC
AACI02000988.1/1421-1535       UUUGUU-GCCU-A-CA-GAACUUA-----------------------------------UAAC-GAACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGU-G--UU-GUCUCC-AUUAA-------AACAGGCAAAG-----------CUGUCCGU------UACUGUGAACUU---GUCGCAUUU
AACH01000658.1/4206-4082       UUUUAUUGCCU-A-UA-GAACUUA-----------------------------------UAAC-GAACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGU-G--UU-GUCUCC-AAAGA--AACAGGUAAAGCUGUCCG-------UUACUGUGAG------CUUGCCAUAUUU---UUUGGAAAU
DQ028748.1/5155-5269           UCCAGCGAUGC-C-CA-CCUCU-------------------------------------UACG-UUAUACAUCAUUCGCCUUUUACUAACGA-UGUCAC-----GG-A--GU-GCGCAU-CUAAU-------GUUGAGACUUCU--------AGAAUUUCUU------UCCACUCUACU----UCGAGUAUA
AADM01000037.1/36531-36659     AUUUUGGGCUG-C-UA-ACUCA-------------------------------------UAAC-GAACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGU-G--UU-GUCUUU-UCCGG----GGGCAAGUUUUACAGUGCUGCUUACUUUUUGGA------ACUUUUCCCAUUU--UUGUUAGAU
AABY01000025.1/44800-44680     AUUGCC--UAU-A-GA-ACUUA-------------------------------------UAAC-GAACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCGGGUGUUG-C--CU-CUAUAG-AAACA-------GGUAAAGCUGUC--------CGUUACUGCCAG----CUUGCCAUAUUU---UUUGGAAAU
CR380948.1/197408-197529       CAUGCG-GUGG-C-UA-ACUUA-------------------------------------UAUC-GAACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGU-G--UU-GUCUCC-AUUUU-------CUCUAAAACAGGUAGCGC--UGUCCUUGGG------CUUCGUCCUUGU---CCUCCGAAC
AAFD02000027.1/316326-316217   GUGCCU-GUUG-G-UA-AACUA-------------------------------------AAAU-ACCACCAUCUCUUGCAUUUUUCCAGAGA-UGGCAG----UGG-U--UU-GCCAAU-UCAUU------AGGGCCACACGCC--------AAUCUUUGCA-------GCCCCGU---------CGGGGUU
AAKN02051087.1/45335-45220     AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUCUUAAACC--------AAUUUUUUGA------GGCCUUGCUCC----AACAAGGCU
AAGV020174570.1/3903-4018      AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GAAACA-ACUCU-------GAGUCUUUGACC--------AAUUUUUUGA------GGCCUUGUUAC----GGCAAGGCU
AASC02039457.1/2620-2506       GUACUCUGGUU-U-CU-CUUCA-------------------------------------CAAC-GAAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAGCA-AUAUA-----AUGAGUCUAUAGAC--------UAUUUUUCAA------GCCCUACUUU-------GUAGGGU
ABIS01000186.1/30072-30186     AGGAGU-GGGA-C-AA-GCUAG-------------------------------------CUCA-GAAUCCAUUUCUUGCCUUUUACCAGAGA-UGGCCG-----UG-G--CU-UUGCCC-AAUAC-------ACUCCGCUCCUC--------AAUCUUUGGA------AUCACUAUCGAC---AAUAGUCGG
AABX02000002.1/78945-78831     CUGGAG-UGGG-C-CU-GCUCA--------------------------------------UAC-GAACUCAUCUCCUGCCUUUUACCGGAUG-UGACCG----UGA-G--UU-GGCCCA-AAAUA-------CUCCAAUACCCU--------AAUCUUUGGAACC---CAUCUGGACAU------CCAGAAU
AP009663.1/4379-4498           AGCCUC-GCAU-U-AA-GCACA-------------------------------------AAGC-GAACUAUUCUUUCGCCUUUUACUAAAGA-AUACCG----UGU-G--CU-UGUUGC-AAUAA-------AAGGCAGACGCU--------AAUUUUUUGAAGGG--AUUCUUUCAUUU---GAAAGGAAC
AAWR02001149.1/42020-41905     AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GCAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUUUCAAACC--------AAUUUUUUGA------GGCCUUGUUCU----AACAAGGCU
BX890568.8/147618-147503       ACACUCAUGUU-U-UU-CCUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-G--GA-AGAAC--ACUAU-------GAGUAUAAACU---------AAUUUUUUGA------UGCCCUGCCGAUA--GGCGGGGCU
AC110235.13/80163-80048        AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-ACUCU-------GAGUCUUAAACC--------AAUUUUUUGA------GGCCUUGUUUC----GGCAAGGCU
AAGD02000134.1/1661-1782       UAACUCUGGUU-C-CU-CUGCAUUU----------------------------------GACC-GUGAAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGC-A--AA-GGAGCA-AACAC------UGAGUAUUAUAAAC-------AAUUUUUGGA-------GUCCCCUCGAAAG-AGCGGGAC-
AM055942.3/1616414-1616305     AUCGCA-GCGG-U-UG-UCACA-------------------------------------GAAC-GCAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-G--AC-AUCCGCAUCAAA-------UGCGAAUCAAG---------AAUUUUUGAC-------GGCGUC--UC------GACGCCA
CAAC02000457.1/1551549-1551428 UAACUCUGGUU-C-CU-CUGCAUUU----------------------------------GACC-GUGAAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGC-A--AA-GGAGCA-AAUAC------UGAGUAUUACUAUC-------AAUUUUUGGA-------GCCUCCUCGAAAG-AGCGAGGC-
CR382134.2/219036-219157       AUCACCAGAAGAU-CA-AUUUCAA-----------------------------------AAUC-GUACAUGGUUCUUGCCUUUUACCAGAAC-CAUCCG----GGA-A--UU-GUCUUC-ACUAC------UGGUGUUUUCACU--------AUUUUUUGGA------ACCUUUUUCUUUA--UAUUAAGAU
AAFN02000018.1/172560-172433   AUCGCCAGAAGAU-CA-AUUUCGUUC---------------------------------AAUC-GUACAUGGUUCUUGUCUUUUCCCAGAAC-CAUCCG----GGA-A--UU-GUCUUC-AUUCA-----AUGGUGUAUCAAAUUUUA----AUUUUUUGGA------ACCCCCCUUUCA---UUAUGAUAU
AE016817.6/459194-459336       UCGCCCCGGAGAU-CA-GUGUCAGAAAGCGCCAUUGGCGCAAUCUA-------------UAUC-GAACAUGUUUCUUGCCUUUUACCAGAAA-CAUCCG----GGC-A--CU-GUCUCC-GCCUA-----UGGGGCCGGUAGCGGCAC----AAUUUUUGGA-------ACCUUUAGAUA---AACAC----
ABDG02000015.1/1095640-1095526 UUGGAGUGGGA-C-C--UCCCA---------------------------------------UC-GAAUUCACCUCUUGCCUUUUACCAGAUG-UGACCG----UGG-G--AUUGGCCCA-GCAGA-------CUCCAUUUCAAU--------AAUCUUUGGC------AUUACCUCAUCU---GGAUGUUCC
AADG06003819.1/2345-2227       GUACUCUGGUU-U-CC-CUUCAGA-----------------------------------CCAC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GG-GGAACA-AUUGA------UGAGUCUGAAUUA--------AUUUUUUGUG------UGCCCGACAUA----AGUUGGGCC
AFQF01001308.1/86869-86981     UCGGAGUGGGA-C-C--UCCCA---------------------------------------UC-GAACUCACCUCUUGCCUUUUACCAGAUG-UGACCG----UGG-G--AUUGGCCCA-ACAGA-------CUCCAUUCACCU--------AAUCUUUGGA------AACCAUUCGUCU---AGAGACU--
AACU03000132.1/1014141-1014032 AGGAGU-GCGA-C-GA-GCUC----------------------------------------AC-AUGCCCGUUUCUUGCCUUUUACCAGACA-CGGCCG-----GA-G--AU-CG-CGC-CUUAU-------ACUCCACUUCU---------AAUCUUUGGA------AAACCAAUUGAA---CUCGCGUUC
CAAB02011239.1/13744-13857     CACUCUU-GUU-U-CA-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GU-GGAACA-ACA---------AGAGUUUAACUC--------AAUUUUUUGA------UGCCCUGCCUCG---UGCGGGGCU
AACN010031598.1/2460-2578      AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUCUUAACUC--------AAUUUUUUGA------GGUCCUGUUUUUUA-AGCAGGACU
AAWZ02006407.1/13458-13573     AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-UUUAU-------GAGUUUUUCUCA--------AAUUUUUUGA------GGCUCCACUCU----UGUGGAGCU
AACS02000007.1/597289-597173   CGCAGCAGUGG-G-AA-CGUCA--------------------------------------AAC-AGACAAUCCCCUCGCCUUUUACUAGGGG-AUUCCG----UGC-C--GC-UCCCAC-ACUAU----AAUGCUGCGUUUC----------AAUCUUUGGA------AACUCUCUCCUC---GAAGGAGUC
ABDF02000090.1/29527-29640     UUGGAGUGGGA-C-C--UCCCA---------------------------------------UC-GAACUCACCUCUUGCCUUUUACCAGAUG-UGACCG----UGG-G--AAUGGCCCA-ACAGA-------CUCCAUUUCAAU--------AAUCUUUGGC-------AUUACCUCAUC---UGGAUGGUU
AAGW02002965.1/6736-6851       AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUCUUAACCC--------AAUUUUUUGA------GGCCUUGCACU----AGCAAGGCU
AAGJ04035404.1/487-369         UUACUCUGGUU-U-UU-CUGCA-------------------------------------AUAC-GCAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGC-A--GA-GGAACA-CAUUG-----AUGAGUCUAUAAAG--------AUUUUUCUUC------GGCUUGCCUACA---CGGCAAGCC
AAIL02000016.1/31650-31761     UUGGAGUGGGA-C-C--UCCCA---------------------------------------UC-GAACUCACCUCUUGCCUUUUACCAGAUG-UGACCG----UGG-G--AUUGGCCCA-ACAGA-------CUCCAUUCAAAC--------AAUCUUUGGC------ACUUCCUCAUC------UGGAGCU
AAQR03026016.1/3436-3551       AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-ACUCU-------GAGUCUGAAACC--------AAUUUUUUGA------GGCCUUGUUUC----GGCAAGGCU
AE014187.2/1889353-1889471     GGUGUGUGUAC-U-UA-CUACA-------------------------------------UAAC-GAAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGU-A--GU-AAGUAU-GUUAA------AUACAAUAUACCACG------AAUUUUUGUC-------GCGCCUAUUAAG--UUAGGUGC-
AAPE02065766.1/2803-2918       AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GUAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUGU-------GAGUUUUCACUC--------AAUUUUUCGA------GGCCUCGUUCU----UACGAGGCU
AACZ03099104.1/4171-4286       AUACUCUGGUU-U-CU-CUUCA-------------------------------------GAUC-GCAUAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGG-A--GA-GGAACA-AUUCU-------GAGUCUUAACCC--------AAUUUUUUGA------GGCCUUGCUUU----GGCAAGGCU
AAQY02000250.1/229279-229396   UUCCGCAAAGU-U-AA-UUUCA--------------------------------------UUC-GCAUCAAUCUUUCGCCUUUUACUAAAGA-UUGCCG----UGG-A--AU-UGACUU-ACUAA-----AUGCGGCUUCAACC--------AAAUUUCUGG------AUCCCUCCUUGU---GAGGGGAAC
ABEG02003930.1/15093-15214     UAACUCUGGUU-C-CU-CUGCAUUU----------------------------------AUCC-GAGAAAAUCUUUCGCCUUUUACUAAAGA-UUUCCG----UGC-A--AA-GGAGCA-AUCUC------UGAGUAUUACAAUC-------AAUUUUUGGA-------GUCCCCUCGAAAG-AGCGGGAC-
#=GC SS_cons                   ::<<<<--<<<.<.<<.<<<<<.....................................----.----<<<<<<<<___________>>>>>.>>>---....>>>.>..>>.>>>>>-.-----.......>>>>--------........---------<......-<<<<<<____....__>>>>>>>
#=GC RF                        auccccuGggg.c.ca.cuaca.....................................uauC.GAAcaagucUcUcGCCUUUUACuAgAga.cuuCCG....ugu.a..gu.ggccca.auuaa.......gggguuuaaacu........AAUUUUUGga......agcccuuuuuu....uuaagggcu
//
# STOCKHOLM 1.0

#=GF AC   RF00021
#=GF ID   Spot_42
#=GF PI   Spot42
#=GF DE   Spot 42 RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:12101127
#=GF GA   80.00
#=GF TC   81.00
#=GF NC   79.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000389; spot_42_RNA;
#=GF RN   [1]
#=GF RM   12101127
#=GF RT   Spot 42 RNA mediates discoordinate expression of the E. coli galactose
#=GF RT   operon.
#=GF RA   Moller T, Franch T, Udesen C, Gerdes K, Valentin-Hansen P
#=GF RL   Genes Dev 2002;16:1696-1706.
#=GF RN   [2]
#=GF RM   2452153
#=GF RT   DNA polymerase I activity in Escherichia coli is influenced by spot 42
#=GF RT   RNA.
#=GF RA   Polayes DA, Rice PW, Dahlberg JE
#=GF RL   J Bacteriol 1988;170:2083-2088.
#=GF RN   [3]
#=GF RM   11804583
#=GF RT   Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction.
#=GF RA   Moller T, Franch T, Hojrup P, Keene DR, Bachinger HP, Brennan RG,
#=GF RA   Valentin-Hansen P
#=GF RL   Mol Cell 2002;9:23-30.
#=GF CC   The physiological role of Escherichia coli Spot 42 (spf) RNA has remained
#=GF CC   obscure, even though the 109-nucleotide RNA was discovered almost three
#=GF CC   decades ago. Spot 42 seems to have a regulatory role on the galactose
#=GF CC   operon [1]. It is proposed that Spot 42 acts by an antisense mechanism
#=GF CC   where the RNA binds to the galK translation initiator region [1]. Changes
#=GF CC   in Spot 42 levels are implicated in affecting the adjacent DNA polymerase
#=GF CC   I levels [2]. The Hfq protein has been shown to interact with several
#=GF CC   small regulatory RNAs in E. coli, and the protein is required for OxyS,
#=GF CC   DsrA, RprA and Spot 42 RNA regulation [3].
#=GF WK   Spot_42_RNA
#=GF SQ   19


BX571860.1/72921-73037       AGUUAUUGGCGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UACUUC---AC--GUAAUCGGAU------UUAGCUGAAUA--UUAGCUGCCCCAGUCA-AU-U-U---UGACUGGGGCAUUUUUUU
CP000247.1/4255583-4255701   AGUUAGUCGCGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UACUUC---AC--GUAAUCGGAU------UUGGCUGAAUAUUUUAGCCGCCCCAGUCA-GU-A-A---UGACUGGGGCGUUUUUUA
ABCD01000004.1/974798-974681 AGUUAUAGACGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UACUUC---AC--GUAAUCGGAU------UUGGCUGUAUA--UUAGCCGCCCCAGUCA-UU-UAU---UGACUGGGGCGUUUUUUG
ABCH01000019.1/86688-86803   AUUAGGACGCGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UGUUUC---AC--GUUAUUGGAU------UAGGCUGAU----UCAGCCGCCCCAGUCA-GUAU-U---UGACUGGGGCGUUUUUUC
AP008232.1/3889649-3889530   AGUUAUCGGCGUAGGGUACACAGAGGU-AAGAUGUUCUAUCUUUCAGGCCUUU---UACUUC---AC--GUAAUCGGAC------UUGGCUAAGUA--UUAGCUGCCCCAGUCA-UU-U-A--AUGACUGGGGCGUUUUUUA
AAKK02000018.1/66975-67090   AUUAAUACUCGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UGUUUC---AC--GUUAUUGGAU------UAGGCUGAU----UCAGCCGCCCCAGUCAGCU-U-U---UGACUGGGGCGUUUUUUA
BX950851.1/28750-28867       AGUUAAAGACGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UACUUC---AC--GUAAUCGGAU------UUGGCUGAAUA-UUUAGCCGCCCCGCUCA-GU-U-U---UGAGCGGGGCGUUUUUUA
AAPH01000038.1/53476-53588   AGUUAAUGACGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UGUUUC---AC--GUUAUUGGAU------UUGGCUGAU----UCAGCCGCCCUGGUCG-AU-------UGACCAGGGCGUUUUUUC
CP000644.1/4423458-4423345   AGUUAGCGACGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UAUUUC---AC--GUAAUUGAAU------GUGGCUG---A--AUAGCUGCCCCGAUGA-GU-A-U---UCGUCGGGGUGUUUUUUU
CP000447.1/4706489-4706607   UAUAUUCGUCGUAGGGUA--CAGAGGUUAAGAUGUUCAAUCUUUCAAACCUUUAUUUCACUA---GC--GAUAGUG-AC------UAGCCAAA-----UUCGGCGCCCCAGCAA-CU-U-A-GGUUGCUGGGGCUUUUUUUU
CP000606.1/4421493-4421612   UAUUCUCUGCGUAGGGUA--CAGAGGUUAAGAUGUUCUAUCUUUCAGACCUUUUUUUAUUUC---AC--GUUAAGUGAA------AAGCCAAAU----UCUGGCGCCCCAGCAA-GU-U-A--CUUGCUGGGGCUUUUUUUC
CP000507.1/104126-104012     UAUUCUCGGCGUAGGGUA--CAGAGGUUAAGAUGUUCUAUCUUUCAGACCUU----UAUUUC---AC--UUGAUAGUGA------U-GCCAAAUAA--U--GGCGCCCCAGCAU-CU-CGU---AUGCUGGGGCUUUUUUUA
CP000302.1/4342007-4342125   UAUUCUCGGCGUAGGGUA--CAGAGGUUAAGAUGUUCAAUCUUUCAAACCUUU-UUUAAAUC---ACUAGCAAUAGUGA------CAGCCAAA-----UAUGGCGCCUCAGUAA-GC-G-A---UUACUGGGGCUUUUUUUU
CP001485.1/616399-616514     AUUAGCUCGCGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UGUUUC---AC--GUUAUUGGAU------UAGGCUGAU----UCAGCCGCCCCAGUCACCA-U-U---UGACUGGGGCGUUUUUUA
CP000563.1/62559-62444       UAUUCUCUGCGUAGGGUA--CAGAGGUUAAGAUGUUCUAUCUUUCAGACCUU----UAUUUC---AC--UUAUAGUGAU------GAGCCAAAU----UCUGGCGCCUCAGCAA-CU-UGU---UUGCUGAGGCUUUUUUUU
CP000851.1/113522-113395     UAUUCUCGGCGUAGGGUA--CAGAGGUUAAGAUGUUCUAUCUUUCAGACCUUU---UUUUUACGUUC--GCUAUUUUAUAGUGAAUGGCCAAAU----UAUGGCGCCUCAGCAA-AU-C-UAAUUUGCUGGGGCUUUUUUUC
CP000821.1/106228-106110     UAUUCUCUGCGUAGGGUA--CAGAGGUUAAGAUGUUCUAUCUUUCAGACCUUU--UUAUAUC---AC-UGUUAUAGUGA------ACAGCCAAAUU--AUGGC-GCCCCAGCAA-UU-U-A---UUGCUGGGGCUUUUUUUC
BA000037.2/199033-199150     AUUAGUACGCGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UGUUUC---AC--GUUAUUGGAU------UAGGCUGAU----UCAGCCGCCCCAGUCA-GG-U-UAUUUGACUGGGGCGUUUUUUA
AALD02000020.1/6958-7075     AGUUACAGAUGUAGGGUA--CAGAGGU-AAGAUGUUCUAUCUUUCAGACCUUU---UACUUC---AC--GUAAUCGGAU------UUGGCUAUAUA--UUAGCCGCCCCAGUCA-CU-UGU---UGACUGGGGCGUUUUUUA
#=GC SS_cons                 ::::::::<<<<-<<<<<..-<<<<<<.<<<<<<___>>>>>>---->>>>>>...>>>>>-...>>..>>,,,,,,,,......,,<<<<<<_....>>>>>><<<<<<<<<<.__._._...>>>>>>>>>>::::::::
#=GC RF                      aaUuaucggcGuAgggua..CagaGGu.aaGaugUUCuauCuuUCAGaCCuuu...uaccuc...aC..gcuAuuggAu......uaGgCugau....ucaGcCGCCcCaGcca.aU.u.u...uggCuGgGGCuUUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00022
#=GF ID   GcvB
#=GF DE   GcvB RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Bateman A, PMID:17974919, Daub J
#=GF SS   Published; PMID:17974919
#=GF GA   42.00
#=GF TC   45.00
#=GF NC   41.60
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000379; GcvB_RNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   10972807
#=GF RT   The gcvB gene encodes a small untranslated RNA involved in expression of
#=GF RT   the dipeptide and oligopeptide transport systems in Escherichia coli.
#=GF RA   Urbanowski ML, Stauffer LT, Stauffer GV
#=GF RL   Mol Microbiol 2000;37:856-868.
#=GF RN   [2]
#=GF RM   17974919
#=GF RT   A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich
#=GF RT   elements inside and upstream of ribosome-binding sites.
#=GF RA   Sharma CM, Darfeuille F, Plantinga TH, Vogel J
#=GF RL   Genes Dev. 2007;21:2804-2817.
#=GF RN   [3]
#=GF RM   19379489
#=GF RT   Small noncoding RNA GcvB is a novel regulator of acid resistance in
#=GF RT   Escherichia coli.
#=GF RA   Jin Y, Watt RM, Danchin A, Huang JD
#=GF RL   BMC Genomics. 2009;10:165.
#=GF RN   [4]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF RN   [5]
#=GF RM   25630703
#=GF RT   Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge
#=GF RT   of the  GcvB small RNA.
#=GF RA   Miyakoshi M, Chao Y, Vogel J
#=GF RL   EMBO J. 2015;34:1478-1492.
#=GF CC   The gcvB gene encodes a small untranslated RNA involved in expression of
#=GF CC   the dipeptide and oligopeptide transport systems in Escherichia coli.
#=GF CC   Included several unknown homologues in alignment (Bateman A pers obs). It
#=GF CC   base-pairs with SorC. This interaction triggers the degradation of GcvB by
#=GF CC   RNase E, alleviating the GcvB-mediated mRNA repression of other amino
#=GF CC   acid-related transport and metabolic genes [5].
#=GF WK   GcvB_RNA
#=GF SQ   27


U00096.2/2940718-2940923   ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-GUUCUGGUGAA----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCAUGGUAGCAA--------------------------AGCUACC----------UUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCUAAU-------------UGCGGUGCUUUUUUUU
U29581.1/24251-24456       ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-GUUCUGGUGAA----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCAUGGUAGCAA--------------------------AGCUACC----------UUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCUAAU-------------UGCGGUGCUUUUUUUU
BX571861.1/50378-50183     ACUUC-CUAAGCC--GGAACGAAAAGUGA--AUCAGCUU-A-----ACGCUAUGAAA----CUUUU----GGCUUUGUGGUUGUGAUG--------UUGUGUUUGCAA----GUUGUCUGGGAA---ACCGGACCCU-GUAGCUC-------------------------AAGCUACU---------GUUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUUUUUAA---UGCACCGCAG---------------UUGCGGUGCUUUUUUUU
BX950851.1/1137282-1137085 ACUUC-CUGGGCC--GGAACGAAAAGUGCG-GAGGGG--------UGACCUGAGGUG----CUUUU----GGCUUGUG-GUUGUGAUG--------UUGUGUUUGCUAUUUUUUUGUCUGCUUC--UUGCAGAUGU-GGUAGCGA--------------------------GUCUACC---------CUAUU--CACUUCCUGUACAUUUACCCUGUCUGUCUAAAGUGA-UUUUUUAUG-UAGCACCGCAA--------------AUUGCGGUGCUUUUUUU-
AL627277.1/14855-15060     ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-GUUCUGAUGGG----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCACGGUAGCGA--------------------------GACUACC----------CUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCAUAU-------------UGCGGUGCUUUUUUUU
AAZG01000006.1/28699-28507 UUCUU-AAAAUAC--CGCCAUACUUAAUG--AUUGGUAA-UUC-C-UUACUAGUUAAUGAGUUUCA----GACUUAAG---UAUGAUG--------UUGUGUUUGCAU----AUAGUUCGGGAA---ACCGAACUUGAGUAACAAU------------------------UUGUUACU----------CAUUU--ACUUCCUGUAUAUUAUUAAACC-----------GAUUUGGUUAA---AUCGCCGCUCCAU-----------UGAGCGGCGUUUUUUUCA
CP000671.1/1207671-1207862 UCCUU-ACAAUAC--AACCAUACUUAAUG--AUUGGUAA-UUC-C-UUACUAGUUAAUGAGUUUCG----GACUUAAG---UAUGAUG--------UUGUGUUUGCAU----AUAGUUCGGGUA---ACCGAACUUGAGUAACAAA-----------------------UAUGUUACU----------CAUUU--ACUUCCUGUAUAUUAUUAAACC-----------GAUUUGGUUAA--ACGCUGCUCUCAUU--------------GAGUGGCGUUUUUUU
AAYT01000006.1/48084-48288 ACUUCCCCUAGCC--GGAACGAAAAGUAGG-UUUGGUAU-CCCAG-GUACUGAAAUG----CUUUU----GGCUUUGUGGUGGUGAUG--------UUGUGUUUGCAA----AUGGUCUGGUAU---GCCAGACAU-AGUAGCUA--------------------------AGCUACUG-------CUUUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUG-C---AGCACCGU-UAUU-----------UUGGCGGUGCUUUUUUU-
CP000647.1/3469834-3470041 ACUUC-CUGAGCC--GGAACGAGAAGCUUUUUUUGGAAU-GCG-U-GUUCCAUCAAG----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGUUUU---UGCAGACCCUGGUAGCAA--------------------------AGCUACC----------CCUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUAAUG-U---AGCACCGC-AACG-------------CGCGGUGCUUUUUUUU
AE017220.1/3095018-3095215 ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-GUUCUGAUGGG----CUUUU----GGCUUACG-GUUGUGAUG--------UUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCACGGUAGCGA--------------------------GACUACC----------CUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCAUAU-------------UGCGGUGCUUUUUUUU
AAZF01000004.1/84336-84525 UCUUA-AAAUAUC--GC-CAUACUUAAUG--AUUGGUAA-UUC-C-UUACUAGUUAAUGAGUUUCA----GACUUAAG---UAUGAUG--------UUGUGUUUGCAU----AUAGUUCGGGAA---ACCGAACUUGAGUAACAAU------------------------UUGUUACU----------CAUUU--ACUUCCUGUAUAUUAUUAAACC-----------GAUUUGGUUAA--ACGCUGCUCUC--------------AUUGAGUGGCGUUUUUUU
CP000653.1/3547890-3548097 ACUUC-CUGAGCC--GGAACGAAAAGCUUUUUUUGGAAU-GCG-U-GUUCUGAAGGG----CUUUU----GGCUUGCG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCUAU----UCAGAUCAUGGUAGCAA--------------------------AGCUACC---------CUUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCUAUU-------------UGCGGUGCUUUUUUUU
AE016827.1/873502-873689   GCGUA-CUU--------AAUGAUUAAGCAA-UUCCUUUU-UCA-U-AAAGAGUUUCA----UUCUU------AUUAAG---UAUUAUG--------UUGUGUUUGCAU----AUUGUUCGGGAA---ACCGAACGCAAGUAACUU--------------------------AGUUACU----------UAUUUA-ACUUCCUGUAUAUUUUUAAACC---UAAUUUUGGG-UUCGUA-A---UGCACCGCUCUUUG---------UG-AGCGGUGUUUUUUUAU
CP000746.1/1862334-1862531 ACUUA-AUGACUG--GUAAUUCCUUAAUUG-AUU------AAG-A------GUUGAA----UCUUU----UAGUUAAG---UAUUAUG--------UUGUGUUUGCAU----AUUGUUUGGGUA---ACCAAACAAAAGUAAUUAAUCCUU--------------CUAUUUAAUUACU----------UAUUA--ACUUCCUGUAUAUUUACUACCU----AAUUUUAGG-UUAUU------GGCACCGCGCUUAAACUCCAAAAAAGUGCGGUGUUU------
CP000266.1/2950132-2950337 ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-AUUCUGGUGAA----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCAUGGUAGCAA--------------------------AGCUACC----------UUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCUAAU-------------UGCGGUGCUUUUUUUU
AE017143.1/818099-817906   ACUGA-AAUAGUUUAGUGUUUAUUCGUGUU-CUUUAAUG-C-----UAUUAAAUCCA----UCUAUUUCAAAUUUAAG---UAUGAUG--------UUGUGUUUGCAU---AUUGGUCUAGGCA---ACUAGACUAGAGUAACAGU-----------------------UAAGUUACU----------CAUUU-CACUUCCUGUAUAUUUAAACCUUUU---------GG-UUUAU-U------AACCGCCUAAUU----------UAGGCGGUUUUUUUACUU
BA000037.2/879563-879356   GCAAC-GCUAGCC--UGAACGGCUUGAUUU-CUU----------U------GUAAAU----CAAUU----GGCUUAGUUGUUGCGAUG--------UUGUGUUUGCAA--------ACUCGUAU--UUCGAGU---UAGGUAGAUUUCUACCGUAG----UGUUUUGUCCAACUCCCUGUG---ACAAAACCUAUACUUCCUGUAUUUAUUUUUGACCUGUCU------G-UCAAAUUUG-UUACACCGCCUAUU------------AGGCGGUGUUUUUUUAU
BA000031.2/725281-725072   GCAAC-ACGAGCC--UGAACGGC--------UUGAUUUC-CUU-G-GAAAUCAA----------UU----GGCUUCGUUGUUGCGAUG--------UUGUGUUUGCAA--------ACUCGUAU--UUCGAGU---UAGGUAGAUUUCUACCAUGA---UGUUUUGUCCACACUCCCUGUG---ACAAAACAGAUACUUCCUGUAUUUAUUUUUGACCUGUCU------G-UCAAAUUUG-UUACACCGCCUUUU-----------UAGGCGGUGUUUUUUUAU
AAND01000021.1/495-707     CAGCA-GCUAGCC--UGAACGGC--------UUGAUUCU-CUC-U-AGAAUCAA----------UU----GGUUUAGCUCCUGCGAUG--------UUGUGUUUGCAA--------ACUCGUUCUUUUCGAGU---UGGGUAGAGUUCUACCAAAUG--UUUUGUUGCAGUUCUAUACUGAAACGAGGCAUGU--ACUUCCUGUAUUUAUUUUGACC-UGUCU------G-UCAAAUUUGUUUACACCGCCUUAU------------GGGCGGUGUUUUUUUAU
AAZW01000011.1/773-985     CAGCA-GCUAGCC--UGGACGGC--------UUGAUUCU-CUC-U-AGAAUCAA----------UU----GGCUUAGCUCCUGCGAUG--------UUGUGUUUGCAA--------ACUCGUACUUUUCGAGU---UGG-GUAGAGUUCUACCAAAUGUUUUGUUGCAGUUAUACACUGAAA-CGAGGCAUCU--ACUUCCUGUAUUUAUUUUGACC-UGUCU------G-UCAAAUUUGUUUACACCGCCUAUA------------CGGCGGUGUUUUUUUAU
CP000826.1/4206206-4206404 ACUUC-CCGGGCC--GGAACGAAAAGGGA--GUGGGUGUCGAG-G-ACGCCGAUGAA----CUUUU----GGCUUGUG-GUUGUGAUG--------UUGUGUUUGCAA----AUUGUCUGGCAA---UCCAGACGU-GGUAGCUA--------------------------AGCUACU----------GUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUG-C---AGCACCGCAA-UC-----------UUUGCGGUGCUUUUUUU-
CP001113.1/3119655-3119860 ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-GUUCUGAUGGG----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCACGGUAGCGA--------------------------GACUACC----------CUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCAUAU-------------UGCGGUGCUUUUUUUU
AE004439.1/652195-651997   -CCUCUAAAAUGC--GCGCAUACUUAAUG--AUUGGUAA-UUC-C-UUACUGGUUAAG-AGUUUCG----GACUUAAG---UAUGAUG--------UUGUGUUUGCAU----AUUGUUUGGGAA---ACCAAACAG-AGUAACUUAUC--------------------UUAAGUUACU----------UAUUUUCACUUCCUGUAUAUUUAUUUUAGACCCUU--------UUGGUUA----AACACCGCUCU--A---------UCGAGCGGUGUUUUUUUAU
AALD02000009.1/78108-77906 ACUUC-CCAAGCC--GGAACGAAAAGUAGG-UUUAGUAU-CCA-G-GUACUGAAAUG----CUUUU----GGCUUUGUGGUUGUGAUG--------UUGUGUUUGCAA----AUGGUCUGGUGU---GCCAGACAU-AGUAGCUA--------------------------AGCUACUG-------UUUUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUG-C---AGCACCGCCA--UU----------UUCGCGGUGCUUUUUUU-
FR729477.2/4274443-4274241 ACUUC-CCAAGCC--GGAACGAAAAGUAGG-UUUAGUAU-CCA-G-GUACUGAAUUG----CUUUU----GGCUUUGUGGUUGUGAUG--------UUGUGUUUGCAA----AUGGUCUGGUAU---GCCAGACAU-AGUAGCUA--------------------------AGCUACUGU------UUUUUUU-CACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUG-C---AGCACCGCU-AUU-----------UUCGCGGUGCUUUUUUU-
FM954972.2/2569880-2570092 CAGCA-GCUAGCC--UGAACGGC--------UUGAUUCU-CUC-U-AGAAUCAA----------UU----GGUUUAGCUCCUGCGAUG--------UUGUGUUUGCAA--------ACUCGUUCUUUUCGAGU---UGGGUAGAGUUCUACCAAAUG--UUUUGUUGCAGUUCUAUACUGAAACGAGGCAUGU--ACUUCCUGUAUUUAUUUUGACC-UGUCU------G-UCAAAUUUGUUUACACCGCCUUAU------------GGGCGGUGUUUUUUUAU
AE017042.1/3133288-3133493 ACUUCCCCUAGCC--GGAACGAAAAGUAGG-UUUGGUAUCCCA-G-GUACUGAAAUG----CUUUU----GGCUUUGUGGUGGUGAUG--------UUGUGUUUGCAA----AUGGUCUGGUAU---GCCAGACAU-AGUAGCUA--------------------------AGCUACUG-------CUUUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUG-C---AGCACCGUUAUUU------------UGGCGGUGCUUUUUUUU
#=GC SS_cons               :::::.:::<<<<..--<<----<<<<<<-.<<<<<<<<.___._.>>>>>>>>>>>....>>>>>....>>>>,,,,.,,,,,,,,,........,,,,,,,,,,,,....,<<<<<<<<___..._>>>>>>>>,<<<<<<___........................__>>>>>>..........,,,,,.,,,,,,,,,,<<<<<______________.....__.__>>>>>,...<<<<<<<<_____...........___>>>>>>>>:::::::
#=GC RF                    aCuuc.auuAgcc..ggaacGAcaagcucu.uucggucu.uuc.u.agaccgaagag....cuuuu....ggcUUAag.gUUgUGAUG........UUGUGUUUGCAa....augGuCUgguaa...accAGaCcaugGuagcaau........................uagcuaCc..........uaUUU.CACUUCCUGUacauuUauucugucUGUCu.....Ga.UUaauguu...agCACCGCcuuuU...........uuuGCGGUGcuUUUUUuU
//
# STOCKHOLM 1.0

#=GF AC   RF00023
#=GF ID   tmRNA
#=GF PI   10Sa_RNA; SsrA
#=GF DE   transfer-messenger RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19617710
#=GF SS   Published; PMID:19617710
#=GF GA   47.00
#=GF TC   47.00
#=GF NC   46.80
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 16.62 -Z 549862.597050 CM SEQDB
#=GF CL   CL00001
#=GF DR   SO; 0000584; tmRNA;
#=GF DR   URL; http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=S14.001;
#=GF DR   GO; 0006401; RNA catabolic process;
#=GF RN   [1]
#=GF RM   8972778
#=GF RT   Phylogenetic analysis of tmRNA secondary structure.
#=GF RA   Williams KP, Bartel DP
#=GF RL   RNA 1996;2:1306-1310.
#=GF RN   [2]
#=GF RM   8990402
#=GF RT   Probing the structure of the Escherichia coli 10Sa RNA (tmRNA).
#=GF RA   Felden B, Himeno H, Muto A, McCutcheon JP, Atkins JF, Gesteland RF
#=GF RL   RNA 1997;3:89-103.
#=GF RN   [3]
#=GF RM   11752287
#=GF RT   The tmRNA Website: invasion by an intron.
#=GF RA   Williams KP
#=GF RL   Nucleic Acids Res 2002;30:179-182.
#=GF RN   [4]
#=GF RM   12140330
#=GF RT   BRUCE: a program for the detection of transfer-messenger RNA genes in
#=GF RT   nucleotide sequences.
#=GF RA   Laslett D, Canback B, Andersson S
#=GF RL   Nucleic Acids Res 2002;30:3449-3453.
#=GF RN   [5]
#=GF RM   12520048
#=GF RT   tmRDB (tmRNA database).
#=GF RA   Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J
#=GF RL   Nucleic Acids Res. 2003;31:446-447.
#=GF RN   [6]
#=GF RM   19617710
#=GF RT   Variations on the tmRNA gene.
#=GF RA   Mao C, Bhardwaj K, Sharkady SM, Fish RI, Driscoll T, Wower J, Zwieb C,
#=GF RA   Sobral BW, Williams KP
#=GF RL   RNA Biol. 2010;6:355-361.
#=GF CC   Bacterial tmRNA, also known as 10Sa RNA or SsrA, is named for its dual
#=GF CC   tRNA and mRNA-like properties. Its role is to liberate the mRNA from a
#=GF CC   stalled ribosome. To accomplish this part of the tmRNA is used as a
#=GF CC   reading frame that ends in a translation stop signal. The broken mRNA is
#=GF CC   replaced in the ribosome by the tmRNA and translation of the tmRNA leads
#=GF CC   to addition of a proteolysis tag to the incomplete protein enabling
#=GF CC   recognition by a protease. Recently a number of permuted tmRNA genes have
#=GF CC   been found encoded in two parts. tmRNAs have been identified in eubacteria
#=GF CC   and some chloroplasts but are absent from archaeal and eukaryote nuclear
#=GF CC   genomes.
#=GF WK   Transfer-messenger_RNA
#=GF SQ   477


AF389977.1/33-350              --------G-------------ACAAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUC-GCAG-------------------------------------CUUAAUA--------------------ACCUGCGCUGAGC---------------------------------------------------------------------CCUUCUC-------------CCCC--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------UGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAUUCGAGCUA---GUCAAUGCGU----GGCG---UGUCU--CUC---C-GC----AGCGUGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUUGGA-CGGG-------------------------G
AAFX01035522.1/635-271         GGGGCUG---ACAGGAAU--CGACAGUAGAGU---G----UAUC-AUGUCAG-UAAG-CAUGCCGGGGA---AUGGUGGUU----UACCCCGUUAUCAA---AUGAUUACCG------ACCAAUAAUUGGCGAAACUCGUUUC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUUGGCUGCCU--------------------------------------AAUUCA----------------------AGGAA-UUAGCG-------------------------------------------------------------------U-GCCUU--------------CAUGC--UAAGG------GUUUGAUA----UCUGC-----UAAAA-----------------------------------------------------------CCCGGUGC-------AUUCAUCAAUG----------------------------------------CAGGUUAAGC-CA--AAGGGAUG----------------------U-CCCGACCGG--------A--GGCCGACAAUCCAGGGAACCGGAUGUCAUCACGU----UGUUGCAGU---A-CCAGAUGGCAUCUUAAAUCCG-------------------------------------------------------AUCUGCAAA----UA---AGCAUGUA--G-AAAGCUGAUGUGGG-----C--UUUAGCUGGA-CGGGGGUUCAAUUCCCCC-CGGCUCCACCA
CP000114.1/1000313-999964      GGGGUCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGUAUAU-UUCG-CGACUCAUC------GGCA-----------GAUGUAA-----------AAUGCCA--GUUAAAUAUAACUGCAAAAAAUACAAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAUUAGCUGC--------------------------------------CUAAAA---------------------AACAGCCUGCGU---------------------------------------------------------------------GAUCUU--------------CACA---AGAUU------GUUUGC-------GUUU-----UGCU-----------------------------------------------------------AGAAGGUCUUAU---UUAUCAGCAAACUAC---------------------------------GUUUGGCUA------C----UGUCUAG---------------------------UUAGUUAAAAA-GAG---A-UUUAUAGACU--CGCUAUGUGA-----GGGCU-UGAGUUAUGU----G-UC-----AUCACCUAGUUAAA---------------------------------------------------U-CAAUACAUAACC---UA---UAGUUGUA---GACAAAUAUAUUA-------GCAGAUGUUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUAU
CP000013.1/46893-46531         GGGGAUGU--UUUGGAUU--UGACUGAAAAUGC--U-----AAU-AUUGUAA-GUUG-CAGGCAGAGG-----GAAU----------CUCUUAAAA------------CUUC------UAAAAUAAAUGCAAAAAAUAAUAAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUACAAGCUC---------------AAACCUUGUAA-------UGGCUGCU----UAAGUUAGC----------------------------------------------------------------------------------AGAGAG------------UUUCGU-UGAAUUU-----GGCUUUG-----AGGUUC---ACUUAU----------------------------------------------------------ACUCUUUUCG------ACAUCGAAGCU--------------------------------------UGCUUAAAAAUGU-----UUUCAAGU---------------------UAAUUUUUAGGGA------CU-UUUGUACUUGAGA-----GCAAUUUGGUGGUUUG----CUAGUAUUU--CC-AAACCAU---AUUGCUUAAGU---------------------------------------------------A----AAAUGCUAG--AUA---AGCUUGUA--G-AAGCUUAUAAUAU------U--GUUUUUAGGA-CGCGGGUUCAAUUCCCGC-CAUCUCCAUUU
AF375582.1/1-310               ---------------------------CACAG---U-----UCG-AGCUUGA-AUUG-CGUUUCGUAG-----GUUACGU-------CUACGUUAA--------AACGUUACA--GUUAAAUAUAACUGCUAAAAACGAAAACAACU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUACGCUUUAGCUGC--------------------------------------CUAAAA----------------------ACAGUUAGCG-U-------------------------------------------------------------------AGAUCCU--------------CUCG---GCAUC------GCCCAU-------GUGC----UCGAG-----------------------------------------------------------UAAGGGUCUCAA----AUUUAGUGGGAUAC---------------------------------GUUAAACUUUU----C----CGUCUGU---------------------------AAAGUUUAAAA-GAG---A-UCAUCAGACU--AGCAAUACAG-A--AUGCC---UGUCA-CUC----G-GCA---AGCUGUAAAGCGAAACC------------------------------------------------UC-AAAUGAGUUGAC---UA---UGAACGUA---GAUUUUUAAGUGU-------CGAUGUG-------------------------------------
AE000657.1/1153844-1153501     GGGGGCGG--AAAGGAUU--CGACGGGGACA----GGC-GGUC--C--CCGA-GGAG-CAGGCCGGG-------UGGCU---------CCCGUAAC----------AGCCGC---------UAAAACAGCUCCCGAAGCUGAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUCGCUCUCGCUGCCU-----------------------------------AAUUAAAC----------------------GGCAGCG--------------------------------------------------------------------------CGUCC--------------CCGGU---AGGUU----UGCGGGUG-----GCCU-----ACCGGA------------------------------------------------------------GGGCGUCAGA------GACACCCGC-------------------------------------UCGGGCUACUCGGU-----CGCACGGG---------------------GCUGAGUAGCU-------GACACCUAACCCGUGCU------ACCCUCGG-GGAGCU----UGCCCGUG----G-GCGACCCGAGGGGAAAUCCUGA--------------------------------------------------A-----CACGGGC----UA---AGCCUGUA--G-AGCCUCGGAUGUGGCC-GCC---GUCCUCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCA---
AE003849.1/2602997-2603351     GGGGGUGCA--CUGGCUU--CGACGGGGGUCACAA------A-A-UCAC--U-UGGUGCAUGCCGAGG----GGGCCGCUU-----UCCUCGUAAAUC-----C-AGCAGCA-----AACUUAUAGUUGCCAACGAAGACAACUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUGUAGCC------------------------------------GCUUAA------------------------GGCUUAAGC-----------------------------------------------------------------------CUCGA--A----------ACUG-----CUUGUG-----UCCGUGCU---CGCAG--------CG--------------------------------------------------------------UAGAGUCAU------CAUCACGGAA------------------------------------CCGCUGAG---ACGU---GGCCGUCUGCC-----------------CAUC----CUCGGUUAAA---U---CUAGCAGACUG----GUUUCCGGGU----GCGCU-UUGCCU--GUC---G-UGC---UGCCCGGCGACGAGAC--------------------------------------------------CUAACGGCG-AGGA---UA---AGCAUGUA--GGGCCG---GGGAUG------GAGUACUUUCGGA-CGGCGGUUCGAUUCCGCC-CACCUCCACCA
CP000282.1/3471683-3472071     GGGGGCGA--UUAGGAUU--CGACGCCGGUAACAA--------A-ACCCG---AAGUGCAUGUCGUGA----GGGUAGCCA-----AUCACGUAAAUC----CAAAGCUGCA-----AAUUAUCAGUUGCCAAUGAUGACAACUACG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGCUCAACUAGCUGC--------------------------------------GUAA------------------------GUAGCUUUUUGUUACACCAUCUAG-------------------------------------------CGGUACGCCGCUAGCGGU----------------------UUUUAA----CAAGGUG---------------------C--------------------------------------------------------CAGUACCGCGUUAA-CGACUGUCA-CUUAGAAC----------------------------UGGAUCGCAGUG---AAGC---CU-GCCUGGG-------------------GUG---GAUCAGCUAAA-CU-----UUUACAGGAUC---GCGCUUUUCG-----UCC---CGCCC--GCU---G-GG----CUGUAAAGCGUUAAAU--------------------------------------------------CAAUAAGC--GGUU--CUA---AGCAUGUA--GAGCUG--ACGGCGG-------AGUACUGACGGA-CGGGGGUUCAAAUCCCCC-CGCCUCCACCA
FM211192.1/809064-809432       GGGGCUGA---AAGGUUU--CGACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGUUGCAGC-------AAUAUAAGCGCCGAUUCAUAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUAUGCUCUCGC--------------------------------------UGCCUA---------------------AGCGAUGGCUAGU-------------------------------------------------------------------CUGUCAG--------------------ACCGGGAA---CGCCCUCGU----CCCGGA--GC-----------------------------------------------------------------CUGGCAUCAG------CUAGAGGGAU-C--------------------------------UACCGAUGGGUU---------CGGUCGC----------------------G-G-GACUCGUCGGGA-CAC---CAACCGCGACUG---GGAUCGU--CAUCCUGGC--UAGUUCGCGUG---A-UCAGGA------GAUCCGAGUAGA----------------------------------------------GGC----AUAGCGAAC---UA---CGCACGGA----GAAGCCUUGAGGGA-----AAUGC-CGUAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCACCG
CP000884.1/5167730-5167353     GGGGCUGUC--CUGGUUU--CGACGUGGGUUCGGG-------AC-CGGU-GU-GGUG-CAUGUCGAGC-----UUGAGUGA----C-GCUCGUAAAUC-----UCCAUUCAA------AAAACUAACUGCAAACGACGAACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUCGCCG-------------------------------------CUUAAA----------------------UCCGGUGAG------------------------------------------------------------------------CCUUGCA------------ACAGCA-C-----------GCUGAUG--------------GGCUGGGCAAGGGGGUAGC---------------------------------AAUACCUCCCGGCUGCAAGGGA-----AUUUACAUCAGCUG-----------------------------------GCUGCGUGCUG----------GGCUUC--------------------UU---AGUACGUGGCAA-GAU--CCAAGGAAGCUGG---CAUCCCGGGU----AGCG---UGCGC--CUG---C-GC----GACUUGGGAGGCGAGAC------------------------------------------------UCAAAACAGA-ACGC---UA---AACAUGUA---GAUCUGC--CCGGC------GAAGGCUUGCGGA-CGCGGGUUCAAUUCCCGC-CAGCUCCACCA
FM209186.1/4965959-4966311     GGGGCCGAU--UAGGAUU--CGACGCCGGUAACAA------A-A-CUUG----AGGGGCAUGCCGAGCU---GGUAGCAG------AACUCGUAAAUU-----CGCUGCUGC----AAACUUAUAGUUGCCAACGACGACAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUAGCUGC--------------------------------------UUAA-----------------------UGCGGCUAG------------------------------------------------------------------------CAGUCGC------------------UAGGGGAU-----GCCUGU-A----AACCCG--AA----------------------------------------------------------------ACGACUGUCAG----AUAGAACAGGAUC-------------------------------------GCCGCC----AAG---UUCGCUGUAG------------------ACGU----AACGGCUAAA-A-----CUCAUACAGCUC---GCUCCAAGC----ACCCU----GCCA--CUC---G-GG----CGGCGCGGAGUUAACU--------------------------------------------------CAGUAGAGC-UGGC---UA---AGCAUGUA--GAACCG--AUAGCGG-------AGAGCUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
CP000305.1/3257923-3258286     GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUG------GCCUCGUAAA--------AAACCGCA----AAAAAAAUAGUUGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAGCUC----------------------------------G---UGUGG---AAAC---CUUGCCUGGG-------------------GUG---GAAGCAUUAAA-AC-----UAAUCAGGAUA---GUUUG-UCAG---UAGCG---UGUCC--AUC---C-GCA---GCUGG-CCGGCGAAU---------------------------------------------------GUAAUGAU-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AY316313.1/1114-752            GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AAGA01018978.1/816-458         GGGGAUGUU--CUGGCUU--CGACGCUGGUGAUGA------A-A-CUCAA---UGAUGCAUGUCGAGAG---UGUAUGUC------CUCUCGUUAAUC-----A-AACAUAU----AUUGUUAUAGUCGCAAACGACGAAACUUAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUAGCAG-------------------------------------CUUAAAC--------------------C-CUGCUU--------------------------------------------------------------------------ACUUAGU------------UG------CUGAUC----ACCUACA------GUUGG-------UUA-----------------------------------------------------------ACUAAGUUGAAGCGUCCGCAUGUAGGCU----------------------------------C--GCCACA---AGUG---AUUGUCUCAA------------------UUGC--U--UGGGUUCAA-A------AGUAGAGAAUC---GUCCAAUCC----AUCCU----GACU--GUC---G-GA----UCGGUGCGGAUUAAAU--------------------------------------------------UUAAAGACAGAAAC---UA---AACAUGUA---GAUUC--AUGAGCG------UAAUGCUGGCGGA-CGCGGGUUCAACUCCCGC-CAUCUCCACCA
AE000512.1/531684-532039       GGGGGCGA---ACGGGUU--CGACGGGGAUGGAG---------U-CCCCUGG-GAAG-CGAGCCGAGGU---CCCCACCU-------CCUCGUAAAA-------AAGGUGGGA---CAAAGAAUAAGUGCCAACGAACCUGUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUGUUGCCGCUUA--------------------------------------AUAGA-----------------------UAAGCGGC-------------------------------------------------------------------------CGUCC--------------UCUCC---GAAGU----UGGCUGGG-----CUUC-----GGAAGA------------------------------------------------------------GGGCGUGAGA------GAUCCAGCC--------------------------------------UACCGAUUCAGCUU----CGCCUUCC--------------------GGCCUGAAUCGG-------GAAAACUCAGGAAGGC-------UGUGGGAGAGGACACC-C-UGCCCGUGG---G-AGGUCCCUCCCGAGAGCGAA--------------------------------------------------------AACACGGGC----UG---CGCUCGGA--G-AAGCCCAGGGGC-------CUCCAUCUUCGGA-CGGGGGUUCGAAUCCCCC-CGCCUCCACCA
EF508371.1/55977-55668         ------------------------AUUUUGGAAAGA-----AUA-GUAUUAU-GAUG-CAAGUCAAGA----UUGAGCUC------AUCUUGUUAAUA-----A--AGCUCA----UCAUAAAUAAAUGCAAAUAAUAUUGUACCUUUUUCUCGUAAGGUCGCUUUAGUUUAAGAUUGUUUUCCUCAUUGGAGACUUGAUUAAUCUAUAAAAAUAAGUUAAAGCUAAAACAUUGGAAGAAAUUUAGCUUAUAAAUAAAAUUCCGUUCUCAUAACUUUAGUGGGUAAAAAAAUACUUUCUUUGAGUAUUGAACAAAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUA---AACUUGU------GAAUGAGUGUGCUACGUAA-GCUGAAAUGGA-CGUGG------------G-----------U
CP000302.1/1448027-1447673     GGGGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCA---AGGAGCAUGUCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----CCGUUAUAGUUGCAAACGACUCUAACUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUCUCUAGC-AGC--------------------------------------UUAG------------------------GCUAGCUAG-----------------------------------------------------------------------CCAUCUG-------------ACCC--AGGUUUC-----UCAA-AUG----GG-CG-----GGGUAU--------------------------------------------------------AC-AGAUGGUCAU---AUAACAU-UUGAUA-------------------------------------GCGAGG--GAACU---CC-GUCCGGG-------------------GGU---GAACCGCGAAA-CA-----GUACCGGACUC---GCCAUGUAGC----AUCC---UGUCU--UUC---G-GA----GACUGCCUGGUUAAC---------------------------------------------------UAAAAGAG--AGAC---UA---AACAUGUA--GCGCCG--AGGAUGU-------AGGCUUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
AM167904.1/1413101-1412696     GGGGCCGAU--CCGGAUU--CGACGUGGGUCAUGA-------AA-CAGU-UC-AGGG-CAUGUCGAGC-----ACCAGUAC------GCUCGUAAAA-------CCACUGGA----AACAAUACAAACGCCAACGACGAGCGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCUCUCGCCGC--------------------------------------UUAA------------------------GCGGUGAGC-----------------------------------------------------------------------CGCUGCA------------CUGAUC-U-----------GUCCUUG--------------GGUCAGGCGGAGGAAGCAACUCCCGUAAGGGAGCCAUCGCCUAAAGGGGCAACCCUUGAACCGCA-GCAGUGUU-----AUUCACAAGGAAUC----------------------------------GGUCUGCGCUGG----------GGUCAC---------------------A---CGGUUCAGGCUU-AAA---UUACGUGAAUCG----CUUCGGUCC----GGCC---CGUUG--AUC---G-GCU---AAGUCCGGGGUUAAAUC------------------------------------------------CAAAUAGAU--CAAC---UA---AGCAUGUA---GAACUGA--CUGCG------GAGGGCUUGCGGA-CGGGGGUUCAAUUCCCCC-CGGCUCCACCA
BA000033.2/839013-839374       GGGGACGUU-CAUGGAUU--CGACAGGGGUCCCC--------CG-AGCUCAU-UAAG-CGUGUCGGAG-----GGUUGU--------CUUCGUCAUCAA--CACACACAGUU------UAUAAUAACUGGCAAAUCAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------CUAAUC----------------------GCA-CUCUGC----------------------------------------------------------------------AUCGCC-------------UAACA---GCAUU------UCCUAU-------AUGC-----UGUUA-----------------------------------------------------------ACGCGAUUCAA---C-CUUAAUAGGAUAU---------------------------------GCUAAACACUG----C----CGUUUGA------------------------A-GUCUGUUUAGAA-GAAA-CU-UAAUCAAGCU--AGCAUCAUGUU-----GGU---UGUUUAUC-----A-CUU----UUCAUGAUGCGAAA---------------------------------------------------C-CUUUCGAUAAAC---UA---CACACGUA---GAAAGAUGUGUAU-------CAGGACCUCUGGA-CGCGGGUUCAAAUCCCGC-CGUCUCCAUUA
AF389952.1/44-364              --------G-------------ACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGGAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAU--------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGACC----------------------------------G---CGCGG---AUGU---CCUGCCUGGG-------------------GCU---GAAGUGCUAAA-AC-----UAAUCAGGCUA---GUUCG-UUAG---UGGCG---UGUCU--GUC---C-GCA---GCUGG-CGUGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUGCCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
AY364898.1/1-307               ------------------------AAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUAGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------CGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUCAAUUCGU----GGCG---UGUCU--CUC---C-GC----AGCGGGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUU----------------------------------
AE017355.1/4856870-4856516     GGGGACGUU--ACGGAUU--CGACAGGGAUAGUU--------CG-AGCUUAG-GUUG-CGAGUCGAGG-----GGAUCG-------GCCUCGUUAA---------AACGUCA----AAGCCUAUAAUUGGCAAACAAAACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUUUCUUUAGCUGC--------------------------------------UUAAUU----------------------GCACUAAAG-----------------------------------------------------------------------GUUCCU--------------CCCU---CCAUC------GUCCAU-------GUGG----UAGGG-----------------------------------------------------------UAAGGGACUCAA----ACUAAGUGGACUAC---------------------------------GCCGGAGUUCG----C----CGUCUGA---------------------------GGACAAAGGAA-GAG--AA-CAACCAGACU--AGC-AACUUGG---AAGCC---UGUCGAUA-----G-GCC---GAAGAGUUCGCGAAACG------------------------------------------------CU--AAUAUAUCGAC---UA---CACUCGUA---GAAGCUUAAGUGCC-------GAUAUUUUUGGA-CGUGGGUUCGACUCCCAC-CGUCUCCACCA
CP001157.1/4355963-4356314     GGGGCCGAU--UAGGAUU--CGACGCCGGUAACGA------A-A-CUUG----AGGGGCAUGCCGAGUU---GGUGGCAG------AACUCGUAAAUC-----CACUGCUAC----AAACUCAUAGUUGCCAACGACGACAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUGGCGGC--------------------------------------UUAA-----------------------UGCC-CCAG------------------------------------------------------------------------CAGUCUC------------------CAGGGGAU-----GCCUGU-A----AACCCG--AA----------------------------------------------------------------GAGACUGUCAG----AUAGAACAGGAUC-------------------------------------GCCGCC----AAG---UUCGCUGUAG------------------ACGU----AACGGCUAAA-A-----CUCAUACAGCUC---GCCCAAAGC----ACCCU----GCCC--GUC---G-GG----CCGCAAUGGGUUAACU--------------------------------------------------CAAUAGACA-GGGC---UA---AGCAUGUA--GAACCG--AUAGCGG-------AGAGCUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
AE009951.2/1209564-1209221     GGGGAUGC--AAAGGUUU--CGACGGGGUUG----U-----GAG-GUUAUAG-GUAG-CAAGUCAGGC-------UUGUCG------CUGUGAGAG---------ACUAAACA---CAUCUUUUAGAUGGAAACAAAGAUUAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUAGCUG--------------------------------------CUUAGU--------------------U-CAGCUA---------------------------------------------------------------------------CACCU--------------UGGAU--AACUUA----UUCUAUAC-----GGGUU----UUUCAA------------------------------------------------------------AGGUGUUG------ACUAGUAUAGAU-------------------------------------CACCAUAAAUGA-U----UUCUCUA----------------------A-G-UUUAUGG--------G--ACAUUUUAGAGGA----UAGUUUUAGUUAGCCC-----UGUUUACGG------GAGUAAUUAUUACGAAAUUU---------------------------------------------------A---AUAGUAAAC----UA---AACUUGUA--G-AAGCUUAUGGUCA------UUAUGAUUUCGGA-CACGAGUUCGACUCUCGU-CAUCUCCACCA
CP000255.1/854460-854821       GGGGACGUU-CAUGGAUU--CGACAGGGGUCCCC--------CG-AGCUCAU-UAAG-CGUGUCGGAG-----GGUUGU--------CUUCGUCAUCAA--CACACACAGUU------UAUAAUAACUGGCAAAUCAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------CUAAUC----------------------GCA-CUCUGC----------------------------------------------------------------------AUCGCC-------------UAACA---GCAUU------UCCUAU-------GUGC-----UGUUA-----------------------------------------------------------ACGCGAUUCAA---C-CUUAAUAGGAUAU---------------------------------GCUAAACACUG----C----CGUUUGA------------------------A-GUCUGUUUAGAA-GAAA-CU-UAAUCAAACU--AGCAUCAUGUU-----GGU---UGUUUAUC-----A-CUU----UUCAUGAUGCGAAA---------------------------------------------------C-CUAUCGAUAAAC---UA---CACACGUA---GAAAGAUGUGUAU-------CAGGACCUUUGGA-CGCGGGUUCAAAUCCCGC-CGUCUCCAUAU
CP000260.1/1058342-1058686     GGGGUUGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCAUGU-UUUG-CGUCCCAUC------GGCA-----------GAUGUAA-----------AUUGCCA--GUUAAAUAUAACUGCAAAAAAUACAAACUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUUUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCUAGCGU---------------------------------------------------------------------GACUUC--------------UACA---AGAUU------GCUUGU-------GUCC-----UGU------------------------------------------------------------UAGAAGUCUCAA-----AAUAGCAAGCUAC---------------------------------GGUUACGAAA-----U----UGUCUAG---------------------------UUUCGUGACAA-GAG---A-UUGAUAGACU--CGCAAACUAA-----UGGCU-UGAGUUAUGU----G-UC-----UUUAGUUUGUUAAA---------------------------------------------------U-GAAGACAUAACC---UA---UGGACGUA---GACAAAUAUGUUG-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CAGCUCCA---
AE015929.1/564585-564945       GGGGACGUU-CUUGGAUU--CGACAGGGGUCCC---------CG-AGCUUAU-UAAG-CGUGUCGGAG-----GGUUGG--------CUCCGUCAUCAAC-ACAUUUCGGUU------AAAUAUAACUGACAAAUCAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------GUAAUA----------------------GCCACUGC------------------------------------------------------------------------AUCGCCU-------------AACA---GCAUC------UCCUAC-------GUGC-----UGUU-----------------------------------------------------------AACGCGAUUCA----ACCCUAGUAGGAUAU---------------------------------GCUAAACACUG----C----CGCUUGA------------------------A-GUCUGUUUAGAU-GAAA-UA-UAAUCAAGCU--AGUAUCAUGUU-----GGU---UGUUUAUU-----G-CUU----AGCAUGAUGCGAAA---------------------------------------------------A-UUAUCAAUAAAC---UA---CACACGUA---GAAAGAUUUGUAU-------CAGGACCUCUGGA-CGCGGGUUCGAAUCCCGC-CGUCUCCAUUA
AACY020564110.1/11913-12262    GGGGGCGA---UCGGUUU--CGACGAAAUAUGCAU-------CU-UUCU-AA-AUGG-CAUGCCGAGU-----CCCAGAA-------UCUCGUAAAU-------AAUCUGGA----AAAACCAUAAAUGCCGAUAACGGCUAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUGGCCGCUGCU--------------------------------------UAA-------------------------GUAAGUGGUC----------------------------------------------------------------------CGUCCUU----------------AG--UUUAGUG---CGUCUAUGG----CUUAA----CU--------------------------------------------------------------AAAGGGCGUC-----AAAUACAUAGACU-------------------------------------GGUUCUGGUUGU-------GUCUGUG--------------------AU---AUCAGGAUGAGA-A------UUAAACAGACU--GUGUUUAUAAU----AGUU--UUGUCA--UCA---G-GA---CAGUUAUAAGCAAGAU---------------------------------------------------UAAUCUGAU-UGAC---UA---AGCGUGUA---GAUAUUUUUUUAGG-------UUCUAUCUCGGA-CGGGAGUUCGAUUCUCCC-CGCCUCCACAA
CP000946.1/1157423-1157061     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000800.1/2905926-2906288     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----UGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AY040838.1/1-298               ------------------------GGGGAACGUGU------UUG-CUUGGG---AUG-CGAGCCGGGUU---GCCGCCAG-------GACCGUAAA--------AAGGGCGG----AAGGCUUUAAUUGCCGAAGAUA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUACGCUUUAGCUG------------------------------------C-UUAAU---------------------UGCAGUCGAA------------------------------------------------------------------------CCUCUU----------------CUC-CUCUGU------GCUCUC-G----GUGA-----GGAUG------------------------------------------------------------UAAGGGGUCAUU--U---AAGAGAGC--U---------------------------------GGCUUCGACCAAU--------UCUCGG----------------------A----GGUCCAAGCGA-G-----AUUUAUCGAAUA---GCCUGACCAA-----CCU--CUGUCUGCCGU---G-CGG----AAGG-AAGGCGAAAU--------------------------------------------------CUAAAACGACAGAC---UA---CGCUCGUA---GUGUCCUUUGUGGG-------CAUUUCUUC----------------------------------
L43967.2/406542-406929         GGGGAUGUU--UUGGGUU--UGACAUAAUGCUGA-------UAG-ACAAACA-GUA--GCAUUGGGGU-----AUGC----------CCCUUACA-------------GCGCU--AGGUUCAAUAACCGACAAAGAAAAUAACGAAGUGUUGGUAGAUCCAAAUUUGA------------------------------------------------------------------------------------------------------------------------------UCAUUAACCAACAAGCAAGUGUUAACUUUGCUUUUG-------------------------------------CAUAA------------------------GUAGAUACUAAAG-----------------------------------------------------------------CUACAGCUG--------------------GUGAAU-----AGUCAUAG----UUUGC---------------------------------------------------------------------UAGCUGUCAUAG-UU----UAUGACUC------------------------------------GAGGUUAAAU-----------CGUUC----------------------A---AUUUAACCUUUA-AAA--AU---AGAACUUG---UUGUUUCC-----AUGAU---UGUUU-UGUG---A-UCA---AUUGGAAACAAGACAAA------------------------------------------------AA--UCCACA-AAAC---UA---AAAUGUA----GAAGCUGUUUGUUG------UGUCCUUUAUGGA-AACGGGUUCGAUUCCCGU-CAUCUCCACCA
AL009126.3/3451071-3450712     GGGGACGUU--ACGGAUU--CGACAGGGAUGGAU--------CG-AGCUUGA-GCUG-CGAGCCGAGA-----GGCGA---------UCUCGUAA----------ACACGCAC---UUAAAUAUAACUGGCAAAACUAACAGUUUUAACCAA--------------------------------------------------------------------------------------------------------------------------------------------------------------AACGUAGCAUUAGCUGC-CU----------------------------------------AAUA----------------------AGCGCAGCG----------------------------------------------------------------------AGCUCUU--------------CCUG---ACAUU------GCCUAU-------GUGU----CUGUG-------------------------------------------------------------AAGAGCAC-----AUCCAAGUAGGCUAC---------------------------------GCUUGCGUUC-----C----CGUCUGA---------------------------GAACGUAAGAA-GAG---A-UGAACAGACU--AGC-UCUCGGA---AGGCC---CGCCCGCA-----G-GCA---AGAAGAUGAGUGAAACC------------------------------------------------AU-AAAUAUGCAGGC---UA---CGCUCGUA---GACGCUUAAGUAAU------CGAUGUUUCUGGA-CGUGGGUUCGACUCCCAC-CGUCUCCA---
BX640413.1/282336-281950       GGGGCCGAU--CCGGAUU--CGACGUGGGUCAUGA-------AA-CAGC-UC-AGGG-CAUGCCGAGC-----ACCAGUAA------GCUCGUUAAU-------CCACUGGA-----ACACUACAAACGCCAACGACGAGCGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCUCUCGCCGC--------------------------------------UUAA------------------------GCGGUGAGC-----------------------------------------------------------------------CGCUGCA------------CUGAUC-U-----------GUCCUUG--------------GGUCAGGCGGGGGAAGGCAACUUCCC------------------AGGGGGCAACCCCGAACCGCA-GCAGCGAC-----AUUCACAAGGAAUC----------------------------------GGCCACCGCUGG----------GGUCAC---------------------A---CGGCGUUGGUUU-AAA---UUACGUGAAUCG----CCCUGGUCC----GGCC---CGUCG--AUC---G-GCU---AAGUCCAGGGUUAAAUC------------------------------------------------CAAAUAGAU--CGAC---UA---AGCAUGUA---GAACUGG--UUGCG------GAGGGCUUGCGGA-CGGGGGUUCAAUUCCCCC-CGGCUCCACCA
AY911524.1/1-307               ------------------------AGGGAUAGUU--------CG-AGCUUAG-GUUG-CGAGUCGAGG-----GGAUCG-------GCCUCGUUAA---------AACGUCA----AAGCCUAUAACUGGCAAACAACAAAACAA-C------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCUUUAGCUGCU---------------------------------------UAAU-----------------------AGCGCUUAGCG---------------------------------------------------------------------GUUCCU--------------CCCU---CCAUU------GCCCAU-------GUGG----UAGGG-----------------------------------------------------------UAAGGGACUCAC----UUUAAGUGGGCUAC---------------------------------GCCGGAUUCCA----C----CGUCUGA---------------------------GGAAGAAGGAA-GAG--AA-CAACCAGAC----UAGCUCAUCGG-ACGCCC----GUCAGCAGG---C-AGA---AGAAUGAGCGAAUCGC--------------------------------------------------G--AAUAUGUUGAC---UA---CACUCGUA---GAAGCUUAAGUGCC-------GAUGUUUCU----------------------------------
U68077.1/21-338                --------N---------------GCCGGUGACGA--------A-CCCUU---GGGUGCAUGCCGAGA----UGGCAGCGA-----AUCUCGUAAAUC----CAAAGCUGCA-----ACGUAAUAGUCGCAAACGACGAAAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCACUGGCGGC--------------------------------------GUAA------------------------GCCGUUCCAGU---------------------------------------------------------------------CGUCCUG--------------------GCUGAGG---CGCCUAUAA---CUCAGUA--GCAACAUC---------------------------------------------------------CCAGGACGUCA----UCGCUUAUAGGCU--------------------------------------GCUCCGU-UCACC---AGAGCUCACU-------------------GGU--G-UUCGGCUAAG-A------UUAAAGAGCUC---GCCUCUUGCA-----CCC---UGACC--UUC---G-GG----UCGCUUGAGGUUAAAU--------------------------------------------------CAAUAGAA--GGACA-CUA---AGCAUGUA--GACCUC--AAGGCCU-------AGUGCUGGCGGA-------------------------------
AL157959.1/1166057-1165698     GGGGGCGAC-CUUGGUUU--CGACGGGGGUUGCGA-------AG-CAGA-UG-CGGG-CAUACCGGGG-----UCUCAGAU------UCCCGUAAAA-------CACUGAAU------UCAAAUAGUCGCAAACGACGAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUAGCCG-------------------------------------CUUAA-------------------------GGCUAGC------------------------------------------------------------------------CGUUGCA------------GCAGUC------------GGUCAAUG--------------GGCUGUGUGGCGA---------------------------------------------AAGCCACCGCAACGUC--A--UCUUACAUUGACUG-----------------------------------GUUUCCUGCC---------GGGUUAUU---------------------U---GGCAGGAAAUGA-GAU---UUAAGGUAACUG---GUUUCCAAAA----GGCC---UGUUG--GUC---G-GC----AUGAUGGAAAUAAG-AUUUU------------------------------------------CAAAU---AGACA-CAAC---UA---AGUAUGUA---GAACGC--UUUGUA------GAGGACUUUCGGA-CGGGGGUUCGAUUCCCCC-CGCCUCCA---
AY911519.1/1-337               ------------------------GUGGGUCGCGA-------AA-CAAC-UC-AGGG-CAUGCCGAGC-----ACCAGUAC------GCUCGUUAAA-------CCACUGGA-----ACACUACAAACGCCAACGACGAGCGU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCUCUCGCCGCU---------------------------------------UAA-------------------------GCGGUGAGC----------------------------------------------------------------------CGCUGCA------------CUGAUC-U-----------GUCCUUG--------------GGUCAGGCGGAGGAAGGCAACUUCCCA----------------GGGGGGCAACCCUCGAACCGCA-GCAGCGAC-----AUUCACAAGGAAUC----------------------------------GGUUUGAACUGG----------GGUCACA------------------CGGUUCAAAUUUAAAU----------UACGUGAAUCG----CUCUGGUCC----GGCC---UGUCG--GUU---G-GCU---AAGUCCAGGGUUAAAA-------------------------------------------------CCAAAUAGAU-CGAC---UA---CGCAUGUA---GAACUGG--UUGCG------GAGGGCUUGC----------------------------------
CP000159.1/1402196-1401828     GGGGAUGA--CACGGCUU--CGACGUGUAGUAA--GC---GUGC-AG-CAGA-CUGA-CCUGCCGAGCA---GCCUGAUUC-----GCUUCGUAAAA------CCUGUCAGG------AACUGUAACUGCGGACGAUUAUUCG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCGAUGGCGGCG---------------------------------------UAAC-----------------------AGCCCCCAUC-----------------------------------------------------------------------UGUCUC-------------GCGUC--GCUCCU-----GGCCCUU-----GGGGA-----GCGU------------------------------------------------------------GAGACAUCGA-----CAAAAAGGGUG--------------------------------------UAGCCGCCGCGUUCU--CCGACUGCG---------------------GAUGCGCCGGU--------GAAAUCUAAUCAGUCUC-AGCGCCGCCC-U-GGCCU-----UGUGAAUG-------GGCAGACGGGCGACGUGAACCGC----------------------------------------------CAA---UGCAUUCAC----UA---UGCAGGUA--G--AGGUUUGCCUGUG----CG--GCUACACGGA-CCCGGGUUCGACUCCCGG-CAUCUCCACAA
U68081.1/20-350                --------N--------N------GGGGACGUGGA-------AG-CCGU--A-GCGG-CAGGUCGAGG----CGCCGCUGG------CCUCGUAAA---------AAGCGGC----ACAAAAGUAAUUGCCAACAACGAUUAC---G------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUACGCUUACGCUG-------------------------------------CCUAAUA--------------------A-CAGCG-AGGC-AAUGACCGU--------------------------------------------------UUAACGGUCGCGCCGAU-------------CAGGG--CCAUG------CCUGAUA-----A--------CCCUG------------------------------------------------------------AUUGGCGAC-------ACUUAUCAGG-------------------------------------CUGGCGAAAACCGG------CUCUCGCC-------------------GGGGUUUUUCGCGAGGA-GUU---UACCGGCGGGAU--UGCUGCGUUGU-----GCC---UGGUC--AGG---G-GC---CAACAGCGCGGUGAAAU--------------------------------------------------ACAUACUU--GACC---UA---AACCUGUA---GAUGCUUC-GUGUG------GAAUGUUCUCGGA-------------------------------
AAAM03000041.1/33267-32913     GGGGGUGCA--CUGGCUU--CGACGGGGGUCACAA------A-A-UCAC--U-UGGUGCAUGCCGAGG----GGGCCGCUU-----UCCUCGUAAAUC-----C-AGCAGCA-----CACUUAUAGUUGCCAACGAAGACAACUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUAUAGCC------------------------------------GCUUAA------------------------GGCUUAAGC-----------------------------------------------------------------------CUCGA--A----------ACUG-----CUUGUG-----UCCGUGCU---CGCAG--------CG--------------------------------------------------------------UAGAGUCAU------CAUCACGGAA------------------------------------CCGCUGAG---ACGU---GGCCGUCUGCC-----------------CACC----CUUGGUUAAA---U---CUAGCAGACUG----GUUUCUGGGU----GCGCU-UUGCCU--GUC---G-UGC---UGCCCGGCGACGAGAC--------------------------------------------------CUAACGGCC-AGGA---UA---AGCAUGUA--GGGCCG---GGGAUG------GAGUACUUUCGGA-CGGCGGUUCGAUUCCGCC-CACCUCCACCA
AF389985.1/19-332              --------G-------------ACAGGAUUCACGA--------A-ACCCU---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----CAGUUAUAGUUGCAAACGACGAUAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGCAGC--------------------------------------UUAG-----------------------GCUAGCUAG------------------------------------------------------------------------CCAUCUG-------------ACAC--AGGUCUC-----UCAA-AUG----GG-CG-----GUGUAU--------------------------------------------------------AC-AGAUGGUCAU---CUUACAU-UUGAUA-------------------------------------GCGAGG--GAACU---CC-GUCCGGG-------------------GGU---GAACCGCGAAA-UA-----GUACCGGACUC---GCCCGAUGAA----AUCC---UGUCU--UUC---G-GA---GUUUAUUCGGGUUAAU---------------------------------------------------UAAAAGAG--AGAC---UA---AGCAUGUA--GUGCCU--UGGAUGU-------AGGUGUUCUGGA-CGCG-------------------------G
CP000454.1/2985502-2985134     GGGGAUGA---UCGGUUU--CGACGAUGUUAGU--------CGC-GACAGGU-GAAG-CGGGCCGAGG-----AUGCAGA-A--UUAUCUCGUAAACG----CUGUCUGCAA------AACAAUAAGUGCCAAACAAACGCGCACUGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------CU-UCGCUCUCGCUGC--------------------------------------CUA------------------------AGCAGUAAGAC-AG-----------------------------------------------------------------UCCGUCAG--------------------CCCGGGAU---UGCUAUC-G---UCCCGGU--UC-----------------------------------------------------------------CUGGCGUCAU------UAAGAUAGCCAC--------------------------------UGCUGUUUACCU---------UCGUCAU----------------------U-G-GGGUGAACGGGA-CU----CUUAGAUGACUG---GGCCCGGAUCA-GCUACU---UGUUUGCAGG---A-------------UAGCUGGGGCCGA--------------------------------------------GAAAAUCCGACGCAAAC---UG---CGCCCGGA----GAAGCCCUGACAA-------CACGACAUCGGA-CGGGGGUUCAAUUCCCCC-CAUCUCCACCA
AE016822.1/1400978-1400585     GGGGAUGA---UCGGUUU--CGACAUUGUCUGC--------GUG-AGUAUGA-GAAG-CGGGUCGAGG-----ACGCAUG-G--UUAUCUCGUUAACG----AUCCAUGCAA-------AAAAUAAGUGCCAAUUCCAAGAGCACUGUCU-----------------------------------------------------------------------------------------------------------------------------------------------------------------CGGCCAAGGCCGACUUCGCCCUC-----------------------------GCGGCGUAAGUUCA--------------CCUCAGCCAUCUGAAGAG-----------------------------------------------------------------GCCGUCAG--------------------ACCGGGAA--CUGUUCUCUA----CCCGGA--GC-----------------------------------------------------------------CUGGCGUCAG------UGAGAGAACU-C---------------------------------GCUUCUGCGUU---------GAGUAUC----------------------A-G-GGCGCAGAGGGA-CUU---CAACUGAUACUA---GGCCCGC---CGGAACAG--GUGCCAGCGAC---A-CGUUCCG-----GGGCCGAGAAAG----------------------------------------------CGA----CACACUGGC---UA---CGCCCGUA----GAAGGCAUAUGAC-------CACAGCAGUGGA-CGGGGGUUCGAUUCCCCC-CAUCUCCACCA
AF389974.1/19-336              --------G-------------ACAAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUC-GCAG-------------------------------------CUUAAUA--------------------ACCUGCGCUGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------CGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUCAAUGCGU----GGCG---UGUCU--CUC---C-GC----AGCGUGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUUGGA-CGGG-------------------------G
CP000958.1/1102376-1102007     GGGGGCGAC--CUGGUUU--CGACAGGGGUUGUGA-------AG-CGG--CU-AGGG-CAUGUCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AAAUCGUAACUGCAAACGACGAUACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUGGCAGCC---------------------------------------UAAG-----------------------GGCCGCCGU-----------------------------------------------------------------------CCUCUGC------------CUAGUU-C-----------ACUGACG--------------GGCUAGUGUCGCAAGACCG---------------------------------GUAGCAAUACCGC-CAGAGGUC-----AUUUACGUCAGUUA----------------------------------AGCCCUGUCGGC-----------GUCGC--------------------GA----CGCCAGGGUCG-AAA--AUCUAGCGAAUCG----CCGUAGUGC----AGCG---UGUUC--GUC---C-GCG----UCGCUGCGGUUAAAU--------------------------------------------------CAAAAGACU-GGAC---UA---AACAUGUA---GAACUAG--UCGUG------GAGCGCUUCUGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
AF375579.1/1-299               ---------------------------CAUUG---------UCG-CGCAUGA-ACUG-CAACUGGUGG-----UGAUG---------UCACCUAA---------AUCCAUCGCA-GAUAAAUAUAACUGCUAAAAAUAACACUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCACUCGCUGC--------------------------------------CUAAAC---------------------ACCAGCUUGCGU---------------------------------------------------------------------AGCUGAU--------------GAU---CGUUC------GCCGAU-------GGCG-----GCC------------------------------------------------------------UGAAGCUCUAAA----CCUCAGUCGGAUAC---------------------------------GUUUUUAUG-----------GUGGCUU----------------------U----ACAUAAAAAAA-GAG---AUUUUAAAGCAC--CGCAAAUUUCU---GCUGUU-UGAGACUGGC----U-UU-----GGAAAUUUGUUAAACU------------------------------------------------AG----AGAAAGUCC---UA---UGGUUGUA---GACGUUGAUGUAG-------CAAGGUG-------------------------------------
BX248356.1/37148-37532         GGGGCUGAU-UUUGGUUU--CGACUGCGUGCAU--------UAA-GCUAGGG-GAAG-CGUGCCGGUG-----CAGGCUA-GA-GACCACCGAUUUUAAGCGUCGUAGCAAA-------UAUAUAAGCGCAGAGAACACUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCCCUCGC--------------------------------------UGCCUAAUU---------------UGCAGCGACCUGCGUG------------------------------------------------------------------UCUGUCAG--------------------CCUAGAUU---CGUCUCUGG----UUUAGU--GU-----------------------------------------------------------------CUGGCAUCGA------UUAAGAGACU-U---------------------------------GCUGGUUUGUUG--------UGUCAACG---------------------G---GGCAAACUGGGA-CUU---UCACCGAUGACU--GGGCUCAU--CAUCCGGGU--GUGUUCGUCCA---A-GCCGGA------GAGCCGAGUAGA----------------------------------------------GAU-CCACGCGCGAAC---UG---CGCACGGA----GAAGCCCUAGCGA-------GGUGACGUAGGA-CCCGGGUUCAAUUCCCGG-CAGCUCCACCA
AY846305.1/1-307               ------------------------GCUGGUGAUGA------A-A-CUCAA---UGAUGCAUGUCGAGAG---UAUAUGUC------CUCUCGUUAAUC-----C-AACAUAU----AUUGUUAUAGUCGCAAACGACGAAAAUUAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUAGCAG-------------------------------------CUUAAAC--------------------C-CUGUUU--------------------------------------------------------------------------ACUUGGU------------UG------CUGAUC----ACCUACA------GUUGG-------UCA-----------------------------------------------------------ACUAAGUUGAAGCGUCCGCAUGUAGGAU----------------------------------C--GCCACA---AGGG---AUUGUCUCAA------------------UCCU--U--UGGGUUCAA-A------AGUAGAGACUC---GGCUAAUCC----AUCCU----GACU--GUC---G-GA----UCGGUGCAGACUAAAA--------------------------------------------------UUAAAGACAGAAAC---UA---AACAUGUA---GAUUC--AUGAGCG------UAAUGCUGGC----------------------------------
CP001113.1/2846103-2846465     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000507.1/2868249-2868604     GGGGGCGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACUCC---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAGUUAUAGUUGCAAACGACGAUAACUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUGGC-UGC--------------------------------------UUAA-----------------------UUAGCGCCAG-----------------------------------------------------------------------CCAUCUA-------------CCAC--AGGUCUC-----GCAC-AUG----GG-CA-----GUGGAU--------------------------------------------------------UU--GAUGGUCAC---CUUACAUCGUGCUA-------------------------------------GCGAGG--GAACC---UU-GUCUGGG-------------------GGU---GAACCGCGAAA-CA-----GUUCCAGGCUC---ACCGUUAGAA----AUCC---UGUCU--UUC---G-GA----GUUCGAGCGGUUAAA---------------------------------------------------UAAAAGAG--AGAC---UA---AGCAUGUA--GCGCCU--UGAGCGU-------AGGUUUUUCGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
AF389949.1/19-338              --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGGGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAU--------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGU---CCUGCCUGGG-------------------GCU---GAAGUGCUAAA-AC-----UAAUCAGGCUA---GUUCG-UUAG---UGGCG---UGUC---UGU---C-GCA---GCUGG-CGUGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
U68075.1/21-331                --------N---------------AAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUAGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------CGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUCAAUUCGU----GGCG---UGUCU--CUC---C-GC----AGCGGGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUUGGA-------------------------------
AJ629111.1/506-157             GGGGUAGUU--CCGGAAU-UCGACAGGUUAUU---------ACA-AGCAUGG-AUUG-CGUUCCCGUU-------------------UGUCGGGUU--------AAAGACUG-----CAGAUAUAACUGCAAAAAAUAAUGAACCAU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUACGCAUUAGCUGC--------------------------------------CUAAUC----------------------GCAG-UAGCG---------------------------------------------------------------------UAGCCCUU--------------UGU---UGA--------GUCCAC-------GGCA-----ACAU-----------------------------------------------------------UCUCGGCCUAAU-------UAGUGGAUUAG--------------------------------CUGCUGGCAUUU----A----UGUUCGG---------------------------AAUAAAAGCAG-UGAAACAAGAAUCGAACU--AGCUCUCGAUU-----UGG--AAGUUAGCAA----C-CU-----AAUCUUGAGCGAAA---------------------------------------------------U--UACUUGUUAAC---UA---UGAGCGUA---GAUAUUUAUGUGAU------UGGAUAAUUUGGA-CAUGGGUUCGACUCCCAU-CUACUCCAUAU
ABGK02000007.1/123731-124089   GGGGAUGU--UUUGGAUU--UGACUGAAAAUGU--U-----AAU-AUUAUAA-GUUG-CAGGCAGAGG-----GAAU----------CUCUUAAAA------------CUUC------UAAAAUAAAUGCAAAAAAUAAUAAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUACAAGCUC---------------AAAUCUUGUAA-------UGGCUGCU----UAAGUUAGC----------------------------------------------------------------------------------AGAGGG------------UUUUGU-UGAAUUU-----GGCUUUG-----AGGUUC---ACUUAU----------------------------------------------------------ACUCUUUUCG------ACAUCAAAGCU--------------------------------------UGCUUAAAAAUGU-----UUUCAAGU---------------------UGAUUUUUAGGGA------CU-UUUAUACUUGAGA-----GCAAUUUGGUGGUUUG----CUAGUAUUU--CC-AAACCAU---AUUGCUUAAUA--------------------------------------------------------AAAUACUAG--AUA---AGCUUGUA--G-AAGCUUAUAGUAU------U--AUUUUUAGGA-CGCGGGUUCAAUUCCCGC-CAUCUCCA---
AE016958.1/3520218-3519851     GGGGCUGA---AAGGUUU--CGACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-CU-GACCACCGUAAGCG----UCGUUGCAAA-------UAGAUAAGCGCCGAUUCACAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGACAGCUAGU-------------------------------------------------------------------CCGUCAG--------------------CCCGGGAA---CGCCCUCGA----CCCGGA--GC-----------------------------------------------------------------CUGGCGUCAG------CUAGAGGGAU-C--------------------------------CACCGAUGAGUU---------CGGUCGC----------------------G-G-GACUCAUCGGGA-CAC---CAACAGCGACUG---GGAUCGU--CAUCCUGGC--UUGUUCGCGUG---A-CCAGGA------GAUCCGAGUAGA----------------------------------------------GGC----AUAGCGAAC---UG---CGCACGGA----GAAGCCUUGAGGG------AAUGC-CGUAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCACCG
CP000503.1/3307740-3308087     --GGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCU---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----CAGUUAUAGUUGCAAACGACGAUAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGCAGC--------------------------------------UUAG-----------------------GCUAGCUAG------------------------------------------------------------------------CCAUCUG-------------ACAC--AGGUCUC-----UCAA-AUG----GG-CA-----GUGUAU--------------------------------------------------------AC-AGAUGGUCAU---CUUACAU-UUGAUA-------------------------------------GCGAGG--GAACU---CC-GUCCGGG-------------------GGU---GAACCGCGAAA-UA-----GUACCGGACUC---GCCCGAUGAA----AUCC---UGUCU--UUC---G-GA---GUUUAUUCGGGUUAAU---------------------------------------------------UAAAAGAG--AGAC---UA---AGCAUGUA--GUGCCU--UGGAUGU-------AGGUGUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCC------U
ACAT01000012.1/45784-45462     --------A--------G--------GCAUAG---------UUG-AGCUUGA-AUUG-CGUUUCGUAG-----GUUACGG-------CUACGUUAA--------AACGUUACA--GUUAAAUAUAACUGCUAAAAACGAAAACAAUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUUCGCUUUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCUAGCG-A-------------------------------------------------------------------AGAUCCU--------------CCCG---GCAUC------GCCCAU-------GUGC----UCGGG-----------------------------------------------------------UCAGGGUCCUAA----UCGAAGUGGGAUAC---------------------------------GCUAAAUUUUU----C----CGUCUGU---------------------------AAAAUUUAGAA-GAG---C-UUACCAGACU--AGCAAUACAG-A--AUGCC---UGUCA-CUC----G-GCA---CGCUGUAAAGCGAACCU------------------------------------------------UU-AAAUGAGU-GUC---UA---UGAACGUA---GAGAUUUAAGUGG-------CAAUAUGUUUGGA-CGC--------------G-----------G
BX571856.1/883681-884042       GGGGACGUU-UCUGGAUU--CGACAGGGGUCCCC--------CG-AGCUCAU-UAAG-CGUGUCGGAG-----GGUUGU--------CUUCGUCAUCAA--CACACACAGUU------UAUAAUAACUGGCAAAUCAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------CUAAUC----------------------GCA-CUCUGC----------------------------------------------------------------------AUCGCC-------------UAACA---GCAUU------UCCUAU-------GUGC-----UGUUA-----------------------------------------------------------ACGCGAUUCAA----CCUUAAUAGGAUAU---------------------------------GCUAAACACUG----C----CGUUUGA------------------------A-GUCUGUUUAGAA-GAAA-CU-UAAUCAAGCU--AGCAUCAUGUU-----GGU---UGUUUAUC-----A-CUU----UUCAUGAUGCGAAA---------------------------------------------------C-UUUUCGAUAAAC---UA---CACACGUA---GAAAGAUGUGUAU-------CAGGACCUCUGGA-CGCGGGUUCAAAUCCCGC-CGUCUCCAUAU
CP000088.1/2912337-2911966     GGGGGUGA---UCGGUUU--CGACUUCGAUGGU--------UGU-UGUAGGG-GAAG-CGGGCCGAGG-----AGAGCGG-ACGCAGCCUCGUUAAAAAU-GCGACCGCGAA-------AAAAUAAGUGCCAACUCUAAGCGCACU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGUUCGCUCUCGC--------------------------------------UGCUUG--------------------A-UCGAGAGU-GAC------------------------------------------------------------------UCUGUCGG--------------------CCUGGGAG---CGUCUCCGA----CCCAGU--GU-----------------------------------------------------------------CCGGCAUCGU------UGAGGAGACU-U--------------------------------GCCGGUCAGAUC---------AGGCCAC----------------------A-G-GAUCUGACUGGG-ACA--UGCUCUGUGGCUG---GGCCUGU---C-GGCGAC--UUGUCUGCGUG---A-GCGCCG------GGGCCGAGGAGA----------------------------------------------ACG---CUGAGCAGAC---UG---CGCCCGGA----GAAGCCCUGCUGC-------AGCAUCGAAGGA-CGCGGGUUCGAUUCCCGC-CACCUCCACGC
AC165062.2/759-1127            GGGGGCGAC--CUGGCUU--CGACGGGGAGAGAGA-------AU-UCGA-GA-GCG--CGUGCCGAGG-----UCCCCGACA---A-CCUCGCUAAU-------CCUCGGGA----AAAAAAUCAAACGCCAACGAUAACUCG---UA---------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCGUUGGCCGCCUAAA--------------------------------------GAGA------------------------UUUAGGUAGCC---------------------------------------------------------------------CGUUGGC--------------------GUCCGU----GGGGCCUACAACGCGGAC---------------------------------------------------------------------GCCGACGCCA-U-CUACAGCAGGCUAGCCGAU--------------------------CACUCUUGUUCAGGGG--------CGGCCGGCG-------------------AAACUCUCUGAA-----------------CUGGUCC--AAUCCGGAU-------CCU----GUCA--GUC---G-GA---GCUGGUGAGGAUGAGAAAGC-------------------------------------------CGUAGCAUAGAC--UGAC---UA---CGCACGUA---GUGGUCUC-GUAGG------ACCUAUUCUCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
CP000857.1/2842992-2843354     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AJ867055.1/1-397               GGGGAUGA---UCGGUUU--CGACAGCGGCUGU--------CGA-AGCAGGG-GAAG-CGUGUCGAGG----AAGCGGCC-A--UGAUCUCGUAAACC----ACAGGCCGAA-------AAAAUAAUCGCCAACACCAAGCGCGAUUCCUCCCAG-------------------------------------------------------------------------------------------------------------------------------------------------------CAGGCCUUCGCCCUCGCUGCCUGA--------------------------------------UC--------------------------UCAGGUAGCGAAGCGAGCCUCC-----------------------------------------------UACUAAGGGAGUGUCAG--------------------CCCGGGGC---UGUUCCCGA----CCCGGA--UC-----------------------------------------------------------------CUGGCAUCAG------CUAGGGGACU-A---------------------------------AACCUUGAUCC---------CGGUCAC----------------------G-G-GGUGAAGAGGGA-AAC--CAAACAGUGACUG---GGCCCGU---C-GGAGAC--UUGUCCGCGUG---A-UCUCCG------GGGCCGAGAAA-----------------------------------------------AUC----GAAGCGGAC---UG---CACACGGA----GAAGCCCUGAUUC-------CGCACCGUUGGA-CGCGGGUUCGAUUCCCGC-CAUCUCCAC--
CP000027.1/1361697-1362048     GGGGACGC---GUGGUUU--CGACAGGGAAGG---U-----AGG-CUACUGG-AUUG-CAGGCUGAGG----UGCCAUCC------ACCUCAUUAAA-------CAGGUGGC-----AAAAAACAACUGGCGAACGUGAACUC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUUCUUGCUGGCU------------------------------------AAAUA-------------------------AGACAGCA-------------------------------------------------------------------------CAUCC--------------UGCUU--GGCCC------CACCUCAA---CGGGUC----AGGUU------------------------------------------------------------UGGGUGCCGA----UUAGUUGAGGUG---------------------------------------CCGUUUCCCCAA------CGCCGA----------------------UGAGGGGGACG--------AAAGAAAUAUCGGCU-----GGUUUGGCUAAAUUAG------GCCGGCAA-------AAGCUAGCCAGACAAGAUUA--------------------------------------------------A---AUAGACGGA----UA---AUCCUGUA--GUAGAUCCUGG-GUC------A-CCUUUUCUGGACGGGGAGUUCGACCCUCCCCCGUCUCCACCA
CP001138.1/2786701-2787063     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000568.1/3242301-3242687     GGGGGCGUA--UUGGUUU--CGACGGGAUUGU---------UGA-AGCUUGA-GUAG-CGGGUAGAGGA--UUCUCGUUG------GCCUCUUUAAAA-----AACGAGAAA-----CUAAAAUAAACGCUAACGAAGAUAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUUUAGCUGCU-----------------------------------GCCUAAU-A------------------UAGGCAGCC--------------------------------------------------------------------------CGUCAG---------------UCCA--GGGU-------UCCUGC-------GCCU----UGGGU-AGCUGGCG-------------------------------------------UCAUUAAGUCAGGCCUUUU---G----AGUGGGAAGGUUAAA----------------------CUCUAGAACUGUCAC-AGUG------GUAGCCUU--------------------GA-GCU-GUGAUGGAUU-UU------A-AAGGCUAC---UGAUAUCCAA-----AGC--CUGCCC--AUG---G-GCG----UUGGGUUGAGGGAAUU-----------------------------------------------UUUAAAACAU--GGGC---UG---CACCCGGA---GAAGCUCUUGUGGA-------UACGAUUUCGGA-CAGGGGUUCGACUCCCCU-CGCCUCCACCA
BA000016.3/1526404-1526044     GGGGGCGUU--UUGGCUU--CGACGGGGGUAAG--------AUG-GGUUUGA-UAAG-CGAGUCGAGGG---AAGCAUGGU-----GCCUCGAUAAUA-----AAGUAUGCA----UUAAAGAUAAACGCAGAAGAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUUGCAUUAGCAGC--------------------------------------UUAAUUU------------------AGCGCUGCU--------------------------------------------------------------------------CAUCCUU--------------CCUC--AAUU-------GCCCAC-------GGUU----GAGAG-----------------------------------------------------------UAAGGGUGUCAUUUAA---AAGUGGGGA------------------------------------ACCGAGCCUAGC-------AAAGCUUU--------------------GA-GCUAGGAACGGAAU-UU------AUGAAGCUUA---CCAAAGAGAA-----AGU--UUGUCU--GUG---G-ACG----UUCUCUGAGGGAA-UU------------------------------------------------UUAAAACACA-AGAC---UA---CACUCGUA---GAAAGUCUUACUGG-------UCUGCUUUCGGA-CACGGGUUCGACACCCGU-CGCCUCCACCA
BX927150.1/150689-151065       GGGGCUGA--CAUGGUUU--CGACUACGUUGAU--------UUA-GCCAGGG-GAAG-CGUGCCGGUG-----AAGGCUG-GA-GACCACCGUAAGCG----UCGCAGCAAA-------CCAAUAAGCGCCGAGAAGUCUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCCCUCGC--------------------------------------UGCAUA---------------------AGCAAGCGACCGCGU---------------------------------------------------------------GUCUGUCAG--------------------CCUAGGGA---AGUCCCUGA----CCUAGA--UC-----------------------------------------------------------------CUGGCAUCGA------CUAAGGGACU-U---------------------------------GCUGUUCAAUCG--------CGUCAGCG---------------------G---GGUUGAACAGGA-CUU---UUACCGUUGACU--GGGCUCAU--CAUCCGGAA--GUGUUCGUCCU---A-GCCGGA------GGGCCAAGCAGA----------------------------------------------GAU-CUUUGCGCGAAC---UG---CGCACGGA----GAAGCCCUGGCGA-------GGUGACGUAGGA-CCCGGGUUCAAUUCCCGG-CAGCUCCACCG
CP000057.2/1702657-1703022     GGGGCUGAU-UCUGGAUU--CGACGGGAUUAGCGA--------A-GCCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAU-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUUUAGC---------------------------------------------------------------------CUUCGCG-------------CUCCA--GCUUCC-----GCUC-GU------AAGA----CGGGGAU--------------------------------------------------------AACGCGGAGUCAAA--CCAAAAC-GAGAUC----------------------------------G---UGUGG---AAGCC--ACCGUUUGAG-------------------GAU--CGAAGCACUAAA-UU-----GAAUCAAACUA---GCUUA-AGUU---UAGCG---UGUCU--GUC---C-GC----AUGCU-UAAGUGAAA---------------------------------------------------UUAAAGAC-GAGAC---UA---AACGUGUA--GUGCUG--AAGGUAG-------AGUAAUUUCGGA-CGGGGGUUCAACUCCCCC-CAGCUCCACCA
AE017226.1/246562-246212       GGGGAUGU--UCCGGUUU--CGACCGGAAAGA---C----GGAG-GCUUAAG-C-UG-CAGGCGGAGU-----GCCGA---------UCUCCUGAU-----------UCGGCA---AACACUAUAACUGCCGAAAAUAACGAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGUUUCGAUUACGCC---------------------------------------UUAGC----------------------UGCAUAAUCG-----------------------------------------------------------------------CGGAA--------------UCUGC--UUUGCA----CUGCUCCGA----GCGGG----GCAUGA------------------------------------------------------------UUCCGACGC-----CAAUCGGGGCU--------------------------------------UGCUUUUUAGCGG-----CGUGUAA----------------------ACGUUAAAAGGG-------AC-UUUU-UUUACAC-------UAAGGAUUCGACGCU----UUCGGUGCU---G-CUACCGGAUCCCUACAACCAC------------------------------------------------------CUCGCACCGA----UA---AGCCUGUA--G--ACGCUUCUGAUUC-----C--CUUUUCGGGA-CGGGGGUUCAAUUCCCCC-CAUCUCCAUCA
BA000031.2/674768-674401       GGGGCUGAU-UUAGGAUU--CGACGGGAAUUCAGA--------A-GUCUG---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------CCCUGCUCAGAGC---------------------------------------------------------------------UCUCUCG-------------CCCU--AGCUUCC-----GCAC-GU------AAGA----CGGGGAAU-------------------------------------------------------AACGAGAGAUCAAA--CCCAAAC-GCGCUA-------------------------------------GCCCGG---AUUCU-CCCGCCUGAGA-------------------GAU---GAACGGCGAAU-UA-----UAAUUCAGGAU--AGUCAUUCAUU----AGCG---UGUCG--GUU---C-GC----AGGUGGAUGGUGAAU---------------------------------------------------UUAAAGAU--CGAC---UA---AGCAUGUA--GUACCA--AUGAUGA-------AAGGUUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AM743169.1/1945390-1945037     GGGGGUGCA--UUGGUUU--CGACGGGGGUUGUGA------A-G-UCGCC---UGGCGCAUGCCGAGG----GGGUAGCUU-----UCCUCGUAAAUC-----C-AGCUGCA-----AAACUCUAGUUGCCAACGACGACAACUA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUGGCC------------------------------------GCUUAA------------------------GGCCUAAGC-----------------------------------------------------------------------CUCGAAA-------------C------CGCUUGU---GUCCAUG-C----UCGCG--------G------------------------------------------------------------UGUAGAGUCAC------UAUCAUGGAA------------------------------------UCGCGCUG----GGUG--GCUGCCUGUC------------------AGUC----CGGCACUAGA---A---CACAACAGGCUG---GUUCCCGGAU----GCGCU-UUGCAC--GCC---G-UGC---UGUUCGGGGACGAGAU--------------------------------------------------CCAACGGU--GAGC---UA---AGCAUGUA--GUGCUG---GGGAUG------GAGUGCCUUCGGA-CGGCGGUUCAAUUCCGCC-CACCUCCACCA
AE000511.1/838812-838427       GGGGCUGAC--UUGGAUU-UCGACAGAUUUCUUGU------C-G-CAC--AG-AUAG-CAUGCCAAGC-----GCU-----------GCUUGUAAAA------C-----AGCA---ACAAAAAUAACUGUAAACAACACAGAUUACGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCAGCUUACGCUAAAGC----------------------------------UGCGUGAGUUAA---------------UCUCCUUUU---GGAG-------------------------------------------------------------------CUGGAC---------------UGAUU--AGAAUU-----UCUAGC------GUUUU----AAUCG--------------------------------------------------------------CUCCAUAACC--U--UAAGCUAGACG----------------------------------CUUUUAAAAGGU-----------GGUU----------------------C-G-CCUUUUAAACUA-AGA--AACAAGAACUC-----UUGAAACUAUCUCAAGGUUUUAGAAAGUUGG---A-CCAG-AGCUAGUUUUAAGGCUAAA----------------------------------------------AAACCAACCAAUUUUC---UA---AGCAUUGU--AGAAGUUUGUGUUUAGG---GCAAGAUUUUUGGA-CUGGGGUUCGAUUCCCCA-CAGCUCCACCA
AACY020561232.1/2642-2986      GGGGGCGUA-UUAGGCUU--UGACGUCUACCACGG--------A-ACCCA---AAGUGCAUACCGAGC-----ACGAACAU-----AACUCGUAAAAU-----AUUGUUUAA-----AACAAAUAGUUGCAAAUAAUUACAACUA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAGUUUGGCAG-------------------------------------CUUAA-------------------------UGCC-AAC-----------------------------------------------------------------------CUGUUAU-------------CAUU--UGUGAC------CUAC-AA------CAUU-----UG--------------------------------------------------------------AUAACGGUCAU---U----UUAGUAGGA----------------------------------U--AUACUCUACCAG------AGCCCA----------------------CU----UGUAGAGCGA-AU-----UUAAGGGCUUA---GCUUAGUGUG-----UCU---UGAUC--AUC---A-GG---CUACACCAAAGUGAAUU--------------------------------------------------AAAUUGAU--GAAU--CUA---AGUAUGUA--GAGACU--AGGGGAA-------AGUGAUGACGGA-CGUGGGUUCAAAUCCCGC-CGCCUCCACCA
AY040837.1/1-317               ------------------------AGGAUCACGAA--------G-GCUUG---UGGAGCAUGUCGAGG-----UGCGGUUU-----GCCUCGUUAAA-------CAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------CCCUGCUAAGAGC---------------------------------------------------------------------GCUCCUG-------------CCCU--AGCUUCC-----GCUU-GU------AAGA----CGGGGAAU-------------------------------------------------------AACAGGGGUUCAAA--CCCAAAC-GAGAUA-------------------------------------GCGAGG--GAUUCU-UUGACUAGAGA-------------------GAU---GAACCGCGAAA-UA-----GAAUUCUGGUA--UGUAUUAGCAU----AGCG---UGUCA--AUU---C-GC----AGUGACGAUACGAGA---------------------------------------------------AUAAAGAU--UGAC---UA---AACAUGUA--GCGCCA--UCUGUUA------GACUGAUUUU----------------------------------
D12501.1/1355-1717             GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP001144.1/2922578-2922940     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000148.1/1848574-1848929     GGGGGUGUA--CAGGUUU--CGACGGGGAUAGGAA--------A-CUAA-AG-GUUG-CAUGCCGAGG-----UCCGGGCUG---G-CCUCGUUAAA------AAGCCCGGG-----GCGAAUUACACGCCGAUAAUUACGAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCCGUAGCAG-------------------------------------CUUAAUA--------------------CCCUGCUACCGAU---------------------------------------------------------------------CCGCCGA-------------GCCUC--UCCCAC------GGGUGA-----A---------------------------------------------------------------------------GAUGGAU--------CGUUAUUUCAGUG-------------------------------GGAUAGU-CAAGGGGA------GUGCCCG---------------------CGGCCCCAAGGCGAAA-CU----UUAGCAGGAUCG---CUUCCCGGAA----AUCC---CUGCC--AGG---G-GA---GAGUCGGGCGGCUAAA---------------------------------------------------UCAAAUCCU-GGCA---UA---AGCAUGUA---GACGCCUU-CUGUG------UAUGAUCUUCGGA-CGCGGGUUCGACUCCCGC-CACCUCCACCA
AE000516.2/3464130-3463763     GGGGCUGA---ACGGUUU--CGACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGUUGCGAC-------CAAAUAAGCGCCGAUUCACAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGACGGCUAGU-------------------------------------------------------------------CUGUCAG--------------------ACCGGGAA---CGCCCUCGG----CCCGGA--CC-----------------------------------------------------------------CUGGCAUCAG------CUAGAGGGAU-C--------------------------------CACCGAUGAGUC---------CGGUCGC----------------------G-G-GACUCCUCGGGA-CAA---CCACAGCGACUG---GGAUCGU--CAUCUCGGC--UAGUUCGCGUG---A-CCGGGA------GAUCCGAGCAGA----------------------------------------------GGC----AUAGCGAAC---UG---CGCACGGA----GAAGCCUUGAGGG------AAUGC-CGUAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCACCG
CP000964.1/1196116-1195754     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCUGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-UC-----UAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCU--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUGCCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
U68074.1/1-363                 GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AL766848.1/13776-13427         GGGGUCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGUAUAU-UUUG-CGACUCAUC------GGCA-----------GAUGUAA-----------AAUGCCA--GUUAAAUAUAACUGCAAAAAAUACAAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAUUAGCUGC--------------------------------------CUAAAA---------------------AACAGCCUGCGU---------------------------------------------------------------------GAUCUU--------------CACA---AGAUU------GUUUGC-------GUUU-----UGCU-----------------------------------------------------------AGAAGGUCUUAU---UUAUCAGCAAACUAC---------------------------------GUUUGGCUA------C----UGUCUAG---------------------------UUAGUUAAAAA-GAG---A-UUUAUAGACU--CGCUAUGUGA-----GGGCU-UGAGUUAUGU----G-UC-----AUCACCUAGUUAAA---------------------------------------------------U-CAAUACAUAACC---UA---UAGUUGUA---GACAAAUAUAUUA-------GCAGAUGUUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUAU
AE016826.1/200304-199938       GGGGCUGAU-AUUGGAUU--UGACAAAAUUAUUGA--------A-AACUG---AUGUGCAUGCCGAGG------AUGGUUU-----GCCUCGUUAAA-------AAACCAUA------AAAAAUAGUAGCAAAACAAAAUCAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------AUCUGAAUAAAGC---------------------------------------------------------------------CCUUCUU-------------UUAA---ACAUAU-----UCUC-UU-----AAUGU-----UUAAUUU------------------------------------------------------AUAUAGAAGGUUA----AUCUAAA-GAGAUC--------------------------------------GCAACU-CAAAUC--UAUUUUGAAA------------------GAUUUUUUGUUGCUAAAU-AA----AAACUUCAAAAU---AUAUA-UCUA---UAAUG---AGUCU--AUA---C-------AUCGA-UAGAUAAGA---------------------------------------------------AAAGAUAA-UAGAC---UA---AGCAUGUA--GUAUCU--GAAGUCG------UAAAAAUUUUGGA-CGCGGGUUCGAAUCCCGC-CAGCUCCAAAA
CP000526.1/2566848-2567217     GGGGGCGAC--CUGGUUU--CGACAGGGGUUGUGA-------AG-CGG--CU-AGGG-CAUGUCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AAAACGUAACUGCAAACGACGAUACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUGGCAGCC---------------------------------------UAAG-----------------------GGCCGCCGU-----------------------------------------------------------------------CCUCUGC------------CUAGUU-C-----------ACUGACG--------------GGCUAGUGUCGCAAGACCG---------------------------------GUAGCAAUACCGA-CAGAGGUC-----AUAUACGUCAGUUA----------------------------------AGCCUGUCCGGC-----------GUCAC--------------------GA----CGGACAGGUCG-AAA--AUCAAGUGAAUCG----CCGUAACGG----AGCG---UGUUC--GUC---C-GCG----ACGUCACGGUUAAAU--------------------------------------------------CAAAUGACA-GAAC---UA---AACAUGUA---GAACUGG--UCGUG------GACCGCUUCUGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
AE017143.1/71003-70637         GGGGCUGAU-UCUGGAUU--CGACGGGAUUAGCGA--------A-GUCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUUUAGC---------------------------------------------------------------------CUUCGCG-------------CCCUA--GCUUUC-----GCUC-GU------AAGA----CGGGGAG--------------------------------------------------------CACGCGGAGUCAAA--CCAAAAC-GAGAUC----------------------------------G---UGUGG---ACGCU--UCGGCUUGUA-------------------GAU--CGAAACACCAAA-UU-----GAAUCAAGCUA---GUUUA-UUUC---UUGCG---UGUCU--GUC---C-GCU---GGAGA-UAAGCGAAA---------------------------------------------------UUAAAGAC-CAGAC---UA---AACGUGUA--GUACUG--AAGAUAG-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
FM204884.1/1203181-1203529     GGGGUUGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCCUAU-UUUG-CAACUCAUC------GGCA-----------GAUGUAAA----------AAUGCCA--GUUAAAUAUAACUGCAAAAAAUAACACAAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUUUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCCGGCGU---------------------------------------------------------------------GACUUC--------------UAUA---GGAUU------GUUUGU-------GUCU-----UAU------------------------------------------------------------UAGAGGUCUCAA-----AACAGCAAGCUAC---------------------------------GUUUAGGUGA-----U----UGUCUAG---------------------------UCACCUAAAAA-GAG---A-ACCCUAGACU--CGCAGGCUG--A--UGGCU--UGAGUUAUGU----G-UCC-----UUGGUCUGUUAAAG--------------------------------------------------U--AAGACAUAACC---UA---UGGUUGUA---GACAAAUAGGUUA-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CAGCUCCAUCA
AF389947.1/19-339              --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGGGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAU--------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGU---CCUGCCUGGG-------------------GCU---GAAGUGCUAAA-AC-----UAAUCAGGCUA---GUUCG-UUAG---UGGCG---UGUCU--GNC---C-GCA---GCUGG-CGUGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
AAFX01088509.1/935-572         GGGGGUGAC-CCCGGUUU--CGACGUGGGUUACAA-------AG-CAGU-GC-AGGGGCAUACCGAGG-----ACCAGUCA------CCUCGUAAAA-------CAACUGGA----AAAAGUAUAGUCGCAAACGACGAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUCUAGCCG-------------------------------------CUUAAUA---------------------CCGGCUGGA------------------------------------------------------------------------CGCUGCA------------CCGAAG------------GGCCUUCG--------------GUCGGGCAGGGC----------------------------------------------AACCUGCAGCAGCGUC-----AUAAAGAGAGGAUC-----------------------------------GUGCCGUACC---------GGGUUACU---------------------U---GAUACAGCAUUA-AAU---CCAAGGUAACUC---GCCUUGCCUC----AGCC---UGCCG--GUU---G-ACG---GUUGCAAGGUCAAAU---------------------------------------------------CAAAUAACC-AGGC---UA---AGUAUGUA---GAACUG--UCUGUA------GAGGGCUUGCGGA-CGGGGGUUCGAUUCCCCC-CACCUCCACCA
AE014184.1/278117-278485       GGGGAUGA---CUGGUUU--CGACGCUGUUUGU--------GUA-CUCGUGG-GAAG-CGGGUCGAGG-----AUGCGAG-G--UUGUCUCGUUAACG----AUCCUCGCAA-------AAUAUAAGUGCCAACUUAAAGCGCACU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUCUAAGUCUUGCU--------------------------------------GCUU-----------------------AAGCG---CUUAGA-----------------------------------------------------------------UCUGUCGG--------------------UAUAGGGC--UUGUCUUCGG---CCCUGUA---U-----------------------------------------------------------------CCGGCAUGGU-----UUUAGAGGACU-U---------------------------------GCCGCGUGUUUG--------CCGCUUG----------------------C-GUGAACAC-CGGGA-CUU---UAUUGCAAGCUG---GGCCUGU---UGAUUUAG--AUUCCGCUGCA---A-AGAAUCA-----GGGCUGAGUAUA----------------------------------------------ACG--GUUUUAGCGGA---UA---CACCCGUA----GAAGUCACGGGCU-------CCAUGCCGCGGA-CGGGGGUUCGAUUCCCCC-CAUCUCCACUG
CP000083.1/3996724-3997073     GGGGCGGAU-CUAGGAUU--CGACAAGAUUCAUGA--------A-ACUCA---AGGUGCAUGCCCAGG-----GGCGGUUU-----GCCUGGUAAA--------AAGCCGCA-----AAACUAUAAUUGCUAACGACGAUACGUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCACUAGCCG-------------------------------------CUUAG--------------------------GC--UAG-----------------------------------------------------------------------CCAUCG--------------CCUUG-AAAUCUC-----UCCU-AUU----GGUU-----AGAGGA----------------------------------------------------------U-CGAUGGUCAC---CCCAAAU-AGGAUA-------------------------------------GCGA-GG-GAAGC---AC-GCUUGAG-------------------GCU---GAACCGCGAAA-UA-----GUAUCAAGCUC---ACCAUGACGA----AGCC---UGUCG--CUU---G-GC----GUCUAAUUGGUUAAA---------------------------------------------------UAAAUGAG--CGAC---UA---AGCAUGUA--GUACCG--AGAACGU-------AGGCUUUUUGGA-CGGGGGUUCGAUUCCCCC-CCGCUCCACCA
CR936503.1/1274331-1273962     GGGGCCGUU--ACGGAUU--CGACAUGUGUAG---------GUG-AGCGUGA-AUUG-CACUUCGUAG-----GUUACGU-------CUGCGUUAAC-------AACGUUACA--GUUAAUUAUAACUGCAAACAAUAACAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUGUAGCUGC--------------------------------------CUAAACA------------------CCAGCA-UAGCG----------------------------------------------------------------------UGAUCCG--------------UCUG---ACUUC------ACCCAA-------GGGU-----UAGAU----------------------------------------------------------CCGGGUCUCAAA-----UUAAUUGGGUUAC---------------------------------GUUAAAUGCCG----C----CGUUUGA---------------------------AGUGUUUAAAA-GAG---A-UUUUCAAGCU--AGUUAGUCCAUC-CGAGCCU-CUGUUGAAC-----G-GCG--UUUUGGGCUAGCGAAUUU------------------------------------------------CU-AAAUAGUUCGAC---UA---UGAGUGUA---GAGAUUGACGUGG-------CAAUGCGCAUGGA-CGCGGGUUCAACCCCCGC-CGGCUCCAUUG
U68076.1/21-329                --------N---------------GGAAUUCAAGA--------A-GCCCG---AGGUGCAUGUCGAGG-----UGCGGUUU-----GCCUCGUAAAA-------AAGCCGCAA---UUUAAAGUAAUCGCAAACGACGAUAACUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUCUCUAGC-AGC--------------------------------------UUAG------------------------GCUGGCUAG-----------------------------------------------------------------------CGCUCCU-------------UCCA--UGUAUUC-----UUG--UGG----AC--------UGGAUU--------------------------------------------------------UU-GGAGUGUCAC---CCUAACACCUGAUC-------------------------------------GCGACGG-AAACC---CU-GGCCGGG-------------------GUU---GAAGCGUUAAA-AC-----UAAGCGGCCUC---GCCUUUAUCU----ACCG---UGUUU--GUC---C-GG----GAUUUAAAGGUUAAU---------------------------------------------------UAAAUGAC--AAUA--CUA---AACAUGUA--GUACCG--ACGGUCG-------AGGCUUUUCGGA-------------------------------
AE001437.1/832978-833336       GGGGGCGCU-UUUGGUUU--CGACGGGGAUGAUG-------UUA-CGUUUGA-GAAG-CGAGUCGAGGG--AACCUGUGGA-----CCCGCGUUAAAA-----AACUAUAGGC--CUUAAAAAUAAAGGAUAACGAAAAUAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUAGCUUUAGCUG--------------------------------------CGUAGU------------------------CAGCUAA------------------------------------------------------------------------CGUCAGC---------------CUG--AGAG-------UCCCGC-------GACU----CAGAG------------------------------------------------------------UCUGGCGUCGA-------CAGCGGGGAA------------------------------------CCGAGCCUUAC-------AAAGCUUU--------------------GA-GUAAGGAACGGAAU-UU------AUGAAGCUAC---UGAAGUGAAA-----AGC--UUGUUU--GUA---G-GCG----UUUCAUGGAGGGAAUG------------------------------------------------UUAAAAUAC--AAAC---UG---CACUCGGA---GAUGCUUAAAUGAA-------ACCAUUUUCGGA-CAGGGGUUCGAUUCCCCU-CGCCUCCACUA
CP000447.1/1293358-1293003     GGGGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCA---AGGAGCAUGUCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----CCGUUAUAGUUGCAAACGACUCUAACUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUCUCUAGC-AGC--------------------------------------UUAG------------------------GCUAGCUAG-----------------------------------------------------------------------CCAUCAA-------------CCAC--ACGUUUC-----GCAC-GUG----GA-CA-----GUGGAU--------------------------------------------------------UC-UGAUGGUCAUA--UUACAGU-GUGCUA-------------------------------------GCGAGG--GAACU---CC-GUCCGGG-------------------GGU---GAACCGCGAAA-CA-----GUACCGGACUC---ACCAAGUAGC----AUCC---UGUCU--UUC---G-GA----GACUGCUUGGUUAAA---------------------------------------------------UAAAAGAG--AGAC---UA---AACAUGUA--GUGCCG--AGGAUGU-------AGGCUUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
CP000469.1/3545784-3546138     GGGGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCU---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUUAA--------AAGCCGCA-----AAGUUAUAGUUGCAAACGACGAUAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGCCGC--------------------------------------UUAA-----------------------UGCCGCUAG------------------------------------------------------------------------CCAUCUA-------------CCAC--ACGUUUC-----GCAC-AUG----GG-CA-----GUGGAU--------------------------------------------------------UU--GAUGGUCAU---CUCACAUCGUGCUA-------------------------------------GCGAGG--GAACC---CU-GUCCGGG-------------------GGU---GAACCGCGAAA-CA-----GUACCGGACUC---ACCGUGUGGG----AUCC---UGUCU--UUC---G-GA----GUUCAAACGGUUAAA---------------------------------------------------CAAUAGAA--AGAC---UA---AGCAUGUA--GCGCCU--UGGAUGU-------AGGUUUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
AM747720.1/3241218-3241587     GGGGGCGAC--CUGGUUU--CGACAGGGGUUGUGA-------AG-CGG--CU-AGGG-CAUGUCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AAAUCGUAACUGCAAACGACGAUACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUGGCAGCC---------------------------------------UAAG-----------------------GGCCGCCGU-----------------------------------------------------------------------CCUCUGC------------CUAGUU-C-----------ACUGACG--------------GGCUAGUGUCGCAAGACCG---------------------------------GUAGCAAUACCGA-CAGAGGUC-----AUUUACGUCAGUUA----------------------------------AGCCCUGUCGGC-----------GUCGC--------------------GA----CGCCAGGGUCG-AAA--AUCUAGCGAAUCG----CCGUAGUGC----AGCG---UGUUC--GUC---C-GCG----UCGCUGCGGUUAAAU--------------------------------------------------CAAAAGACU-GGAC---UA---AACAUGUA---GAACUAG--UCGUG------GAGCGCUUCUGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
AF389956.1/20-341              --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AGGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-UC-----UAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCU--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
AE017180.1/1874135-1874490     GGGGGUGUA--CAGGUUU--CGACGGGGAUAGGAA--------G-CUGA-UG-GUUG-CAUGCCGAGG-----UCCGGGCUG---G-CCUCGUUAAA------AAGCCCGGG-----GCGAAUUACACGCCGAUAAUUACGAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUGUAGCAG-------------------------------------CUUAAUA--------------------ACCUGCUACCGAU---------------------------------------------------------------------CCGCUGA-------------GCCUC--UCCCAC------GGGUGA-----A---------------------------------------------------------------------------GAUGGAU--------CGUCAUUUUAGUG-------------------------------GGAUAGUUGCGGGGAG------GGUCCAC---------------------GGCCCCAAGGCGAAAC-C-----UUAGUGGAAUCG---CUUCCCGGAA----AUCC---CUGCC--AGG---G-GA---GAGUCGGGCGGCUAAA---------------------------------------------------UCAAAUCCU-GGUA---UA---AGCAUGUA---GACGCCUU-CGGUG------UAUGAUCUUCGGA-CGCGGGUUCGACUCCCGC-CACCUCCACCA
AACY020562586.1/58305-57951    GGGGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCU---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUUAA--------AAGCCGCA-----AAGUUAUAGUUGCAAACGACGAUAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGCCGC--------------------------------------UUAA-----------------------UGCCGCUAG------------------------------------------------------------------------CCAUCUA-------------CCAC--ACGUUUC-----GCAC-AUG----GG-CA-----GUGGAU--------------------------------------------------------UU--GAUGGUCAU---CUCACAUCGUGCUA-------------------------------------GCGAGG--GAACC---CU-GUCCGGG-------------------GGU---GAACCGCGAAA-CA-----GUACCGGACUC---ACCGUGUGGG----AUCC---UGUCU--UUC---G-GA----GUUCAAACGGUUAAA---------------------------------------------------CAAUAGAA--AGAC---UA---AGCAUGUA--GCGCCU--UGGAUGU-------AGGUUUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
ABDX01000004.1/6714-7074       GGGGGCGUU--UUGGCUU--CGACGGGGGUAAG--------AUG-GGUUUGA-UAAG-CGAGUCGAGGG---AAGCAUGGU-----GCCUCGAUAAUA-----AAGUAUGCA----UUAAAGAUAAACGCAGAAGAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUUGCAUUAGCAGC--------------------------------------UUAAUUU------------------AGCGCUGCU--------------------------------------------------------------------------CAUCCUU--------------CCUC--AAUU-------GCCCAC-------GGUU----GAGAG-----------------------------------------------------------UAAGGGUGUCAUUUAA---AAGUGGGGA------------------------------------ACCGAGCCUAGC-------AAAGCUUU--------------------GA-GCUAGGAACGGAAU-UU------AUGAAGCUUA---CCAAAGAGAA-----AGU--UUGUCU--GUG---G-ACG----UUCUCUGAGGGAA-UU------------------------------------------------UUAAAACACA-AGAC---UA---CACUCGUA---GAAAGUCUUACUGG-------UCUGCUUUCGGA-CACGGGUUCGACACCCGU-CGCCUCCACCA
AAUJ02000001.1/3848858-3848484 GGGGCUG-U-CCUGGUUU--CGACGUGGGUUCGGG-------AC-CGGU-GC-GGUG-CAUGUCGAGC-----UUGAGUGA----U-GCUCGUAAAUC-----UCCAUUCAA------AAAACUAACUGCAAACGACGAACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUCGCCG-------------------------------------CUUAA-----------------------UCCGGUGAG------------------------------------------------------------------------CCUUGCA------------ACAGCA-C-----------GCUAGUG--------------GGCUGGGCAAGGGGGUAGC---------------------------------AAUACCUCCCGGCUGCAAGGG---A--AUUUACAUUAGCUG-----------------------------------GCUGGAUACCG----------GGCUUC--------------------UU---GGUAUUCGGCGA-GAU--UUAAGGAAGCUGG---CUACCCAGAC----AGCG---UGUGC--CUG---C-GG----GGUUUGGGUGGCGAGAU------------------------------------------------UCAAAACAGA-GCAC---UA---AACAUGUA---GAUCUGU--CCGGC------GAAGGCUUACGGA-CGCGGGUUCAAUUCCCGC-CAGCUCCA--C
AM180252.1/573061-573436       GGGGACGCA--CUGGUUU--CGACGGGGAUGUGGA-------AA-CCA--AA-GUGG-CAGGUCGAGG----CGCCGCUGG------CCUCGUAAA---------AAGCGGC----AACAAUGUAAUUGCAAACAACAAUUAC---G------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUACGCUCUUGCUG-------------------------------------CAU--------------------------AAGUAAUAGCGUACCUGGCUAU-----------------------------------------------UUAAAUAGCCACGUCAAU---------------CCU--GCUGAU----GUCUGAUA-------AGC----UGG--------------------------------------------------------------UGCGGCGAC-------AAUCAUCAGG-------------------------------------CUAGCAGCCUAUUG-----UGUUUACU---------------------GGAUAGUCUGCGAAAU-UA----UUACAGUAAACU--UGUUUUGAUCU-----GCC---UGGCU--AAG---G-GC---UAGAAUCAAAAUAAGAU--------------------------------------------------GUAAACUU--AGCC---UA---AACCUGUA---GAUACUU--UGUGUG-----GAACUUUCUCGGA-CGCGGGUUCGAUUCCCGC-CGUCUCCACCA
CP001219.1/1222516-1222879     GGGGGCGA---CCGGCUU--CGACGCAGGUCGCGA------A-G-CCUU----CGGUGCAUGCAGAGC-----UGCGGUU------CGCUCUUAAAAC-----U-GGUCGCA-----GAUUCAUAAUUGCCAACGACAGCAAUUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUCGCUGCU---------------------------------------UA-------------------------AGCAGUGAG-----------------------------------------------------------------------CCCUCUG-------------CC-----CGGAUUU---GUCUGUG-G----AUCC--------GG-AGCCGAA---------------------------------------------AGGCGCGCGGAGGGUCAU-----GAAACACGGAA------------------------------------UCGUGCGC---AUUC---UA--GUCUGU------------------GGGA--U-GCGCGCUAAA---U--UAAAGCAGAAUC----GCCAUGUCGU---CAUCC---UGUCU--GUC---G-GAG---GGCGGUGCGGUUAAAG-------------------------------------------------CCAAAAGAC--AAAC---UA---CGCAUGUA--GAUCCG---GUGGUCU-----AGGUA-CUGCGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
AF269873.1/1626-1987           GGGGACGUU-CUUGGAUU--CGACAGGGGUCCCC--------CG-AGCUUAU-UAAG-CGUGUCGGAG-----GGUUGG--------CUCCGUCAUCAAC-ACAUUUCGGUU------AAAUAUAACUGACAAAUCAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------GUAAUA----------------------GCCACUGC------------------------------------------------------------------------AUCGCCU-------------AACA---GCAUC------UCCUAC-------GUGC-----UGUUA-----------------------------------------------------------ACGCGAUUCAA---C-CCUAGUAGGAUAU---------------------------------GCUAAACACUG----C----CGCUUGA------------------------A-GUCUGUUUAGAU-GAAA-UA-UAAUCAAGCU--AGUAUCAUGUU-----GGU---UGUUUAUU-----G-CUU----AGCAUGAUGCGAAA---------------------------------------------------A-UUAUCAAUAAAC---UA---CACACGUA---GAAAGAUUUGUAU-------CAGGACCUCUGGA-CGCGGGUUCGAAUCCCGC-CGUCUCCAUUA
CP000783.1/602363-602000       GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----UAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC-CGGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
BX248344.1/299881-299514       GGGGCUGA---ACGGUUU--CGACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGUUGCGAC-------CAAAUAAGCGCCGAUUCACAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGACGGCUAGU-------------------------------------------------------------------CUGUCAG--------------------ACCGGGAA---CGCCCUCGG----CCCGGA--CC-----------------------------------------------------------------CUGGCAUCAG------CUAGAGGGAU-C--------------------------------CACCGAUGAGUC---------CGGUCGC----------------------G-G-GACUCCUCGGGA-CAA---CCACAGCGACUG---GGAUCGU--CAUCUCGGC--UAGUUCGCGUG---A-CCGGGA------GAUCCGAGCAGA----------------------------------------------GGC----AUAGCGAAC---UG---CGCACGGA----GAAGCCUUGAGGG------AAUGC-CGUAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCACCG
CP000316.1/1861517-1861903     GGGGCUGCA--CUGGUUU--CGACGCGGGUACGGA-------CG-CGCA-GU-GGGG-CAUGCCGAGC------UUAGUGU------GCUCGUAAAA------CUGACUAAA-----ACAAACUAACUGCAAACGACGAACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUCGCUG-------------------------------------CUUAAUA--------------------ACCAGUGAG-------------------------------------------------------------------------CCCUACA------------ACAGCA-G-----------GCCGAUG--------------GGCUGGGCAAGGGGUCUUUAGCGC-----------------------AAGUUGAAGGCUCCCGGCUGUAGGGUC-----AUACACAUCGGCUG-----------------------------------GCCUGGUACCG----------GGCACC--------------------UU---GGUAUCAGGCGA-GAC--AAUAGGAUGCUGG---CAACCUGUAU----AGCG---UGCUG--CUG---C-GC----GAUACGGGAAGUGAGAC------------------------------------------------UCAAAUCAGA-CGGC---UA---AGCAUGUA---GAACUAC--GCGAA------GAAGGCUUGCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AE006470.1/660570-660973       GGGGAUGA--CAGGCUAU--CGACAGGAUAGG---U-----GUG-AGAUGUC-GUUG-CACUCCGAGUUUCAGCAUGGACG-----GACUCGUUAAAC-----AAGUCUAUG-----UACCAAUAGAUGCAGACGAUUAUUCG---UA----------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCAAUGGCUGCCUGA--------------------------------------------UUAGCAC------AAGUUAAU-UCAGA-AGCCA--------------------------------------------------------------------U--------------------CGUCC-UGCGGUGAAUGCGCUUACUCUGAAGCCGCC---GGAUGGCAUAACCCGCGCUUGA---------------------------GCCUACGGGUUCGCGC------------------AAGUAAGC----------------------------------------UCCGUACAUUCA----UGCCCGAG--------------------GGGGUGUGCGGG--------U--AACCAAUCGGGAU-----AAGGGGA-CGAACGC----UGCUGGCGGU-----GUAAUCGGACCACGAAAAACC-------------------------------------------------------AACCACCAG---AGA---UGAGUGUG--G-UAACUGCAUCGAGC-----A--GUGUCCUGGA-CGCGGGUUCAAGUCCCGC-CAUCUCCACCA
CP000480.1/2169257-2169625     GGGGCUGA---ACGGUUU--CGACUUCGAGCAU--------CGA-AUCCAGG-GAAG-CGUGCCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGUUGCAAC-------CAAUUAAGCGCCGAUUCCAAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCCCUCGC--------------------------------------UGCCUA---------------------AGCGACGGCUGGU-------------------------------------------------------------------CUGUCAG--------------------ACCGGGAG---UGCCCUCGG----CCCGGA--UC-----------------------------------------------------------------CUGGCAUCAG------CUAGAGGGAC-C--------------------------------CACCCACGGGUU---------CGGUCGC----------------------G-G-GACCUGUGGGGA-CAU--CAAACAGCGACUG---GGAUCGU--CAUCUCGGC--UUGUUCGUGUG---A-CCGGGA------GAUCCGAGUAGA----------------------------------------------GAC----AUAGCGAAC---UG---CGCACGGA----GAAGCCUCGAGGA------CAUGC-CGUAGGA-CCCGGGUUCAAUUCCCGG-CAGCUCCACCA
CP000086.1/1835164-1834795     GGGGGCGAC--CUGGUUU--CGACAGGGGUUGUGA-------AG-CGG--CU-AGGG-CAUGUCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AAAACGUAACUGCAAACGACGAUACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUGGCAGCC---------------------------------------UAAG-----------------------GGCCGCCGU-----------------------------------------------------------------------CCUCUGC------------CUAGUU-C-----------ACUGACG--------------GGCUAGUGUCGCAAGACCG---------------------------------GUAGCAAUACCGA-CAGAGGUC-----AUAUACGUCAGUUA----------------------------------AGCCUGUCCGGC-----------GUCAC--------------------GA----CGGCCAGGUCG-AAA--AUUGAGUGAAUCG----CCGUAACGG----AGCG---UGUUC--GUC---C-GCG----ACGUCACGGUUAAAU--------------------------------------------------CAAACGACA-GAAC---UA---AACAUGUA---GAACUGG--UCGUG------GACCGCUUCUGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
AY911520.1/1-342               ------------------------GCCGGUUGCGA------A-C-CUUU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA--ACUUUCUAUAGUUGCCAAUGACGAAACCUACGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAUACGCUCUCGCUGC--------------------------------------GUAA------------------------GCAGCCUUAGCCCUUCCCUCCUGGU-----------------------------------------ACCUUCGGGUCCAGCAAUCAU------------------CAGGGGAU-----GUCUGU-A----AACCCA--AA----------------------------------------------------------------GUGAUUGUCAU----AUAGAACAGAAUC-------------------------------------GCCGUG----CAG---UACGUUGUGG------------------ACGA----AGCGGCUAAA-A-----CUUACACAACUC---GCCCAAAGC----ACCCU----GCCC--GUC---G-GG----UCGCUGAGGGUUAACU--------------------------------------------------UAAUAGACA-CGGC---UA---CGCAUGUA--GUACCG--ACAGCAG-------AGUACUGGC----------------------------------
AARF01000086.1/11864-12230     GGGGGCGUU-UUUGGAUU--CGACGGGGAUAGUU--------CG-AGCAUGG-GUAG-CGGGUAGUGG-----GGACGCG------UCCGCUUUAUC--------AACGCUAAC-GCCAAAUUUAAACGGCAAACAACAAAACAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUACGCUUUAGCAG-------------------------------------CUUAAUA--------------------ACCUGCUUGCGU----------------------------------------------------------------------GCUCCU--------------GCUUU--GCAUC------GCCCAU-------GUGC----CAAGU------------------------------------------------------------UAGGGGCUCAA----CUUUAGUGGGCUAC---------------------------------GCUGUCUAGUCU---C----CGCCUGA--------------------------GGCUA-GCUGAA-GAA--GA-CAAUCAGGCU---GACCUGUGAGA-AAGCCG----GUUACGGGG---C-GGG----CUUACAGGUGACAU---------------------------------------------------U--AAAACCGUGAC---UA---CACCCGUA---GAAGCCUAUGUGGC-------GUUAUCUUUGGA-CACGGGUUCGACUCCCGU-CGCCUCCAUAU
BX294141.1/117195-117574       GGGGGCGA--CUUGGAAU--CGACCG-GAUGUCA-A-----GAA-GCGUAUG-CCUG-CGUGUCGUGGU--UGAUCAGUUG-----GCCACGUAAA--------AAGCUGAUCA-AAAACUUUUAGUUGCAGAAGAAAACUUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUGGCCGCCU-------------------------------------AAUUAC-----------------------AGGUAGCCCGGA-------------------------------------------------------------------C-UGAUG--------------GGGAU-CGCCGAUG--UCGCC-UGA--------------AUGUC-------------------------------------------------------------CGUCACAAUG---UCGGAUCGUGGC--------------------------------------CCGUCUUACUCAAG---ACGCGGGUCGCUAAA---------CAAGAUUUGAGU-UAGCGG------AU-UCGGGAGCCUGUC--AGGUAGCGCCCGAUGAAGC-----GAAAAGGA--AU-CUUCGAGAUUCCACAAA-----------------------------------------------------------UAGCUUGAC----UA---CACAUGUA--G-ACGGCAU-CGUGGA----UG--CAUCGCGGGA-CGGGAGUUCAAUCCUCCC-CGCCUCCACUU
AE017334.2/4834863-4834509     GGGGACGUU--ACGGAUU--CGACAGGGAUAGUU--------CG-AGCUUAG-GUUG-CGAGUCGAGG-----GGAUCG-------GCCUCGUUAA---------AACGUCA----AAGCCUAUAAUUGGCAAACAAAACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUUUCUUUAGCUGC--------------------------------------UUAAUU----------------------GCACUAAAG-----------------------------------------------------------------------GUUCCU--------------CCCU---CCAUC------GUCCAU-------GUGG----UAGGG-----------------------------------------------------------UAAGGGACUCAA----ACUAAGUGGACUAC---------------------------------GCCGGAGUUCG----C----CGUCUGA---------------------------GGACAAAGGAA-GAG--AA-CAACCAGACU--AGC-AACUUGG---AAGCC---UGUCGAUA-----G-GCC---GAAGAGUUCGCGAAAUG------------------------------------------------CU--AAUAUAUCGAC---UA---CACUCGUA---GAAGCUUAAGUGCC-------GAUAUUUUUGGA-CGUGGGUUCGACUCCCAC-CGUCUCCACCA
BX640447.1/241865-242251       GGGGCCGAU--CCGGAUU--CGACGUGGGUCAUGA-------AA-CAGC-UC-AGGG-CAUGCCGAGC-----ACCAGUAA------GCUCGUUAAU-------CCACUGGA-----ACACUACAAACGCCAACGACGAGCGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCUCUCGCCGC--------------------------------------UUAA------------------------GCGGUGAGC-----------------------------------------------------------------------CGCUGCA------------CUGAUC-U-----------GUCCUUG--------------GGUCAGGCGGGGGAAGGCAACUUCCC------------------AGGGGGCAACCCCGAACCGCA-GCAGCGAC-----AUUCACAAGGAAUC----------------------------------GGCCACCGCUGG----------GGUCAC---------------------A---CGGCGUUGGUUU-AAA---UUACGUGAAUCG----CCCUGGUCC----GGCC---CGUCG--AUC---G-GCU---AAGUCCAGGGUUAAAUC------------------------------------------------CAAAUAGAU--CGAC---UA---AGCAUGUA---GAACUGG--UUGCG------GAGGGCUUGCGGA-CGGGGGUUCAAUUCCCCC-CGGCUCCACCA
AF375575.1/1-309               ---------------------------CGUAG---------AUU-CGCAUUG-ACUG-CGAUUCGUAG-----GUUACGU-------CUACGUAAA--------AACGUUACA--GUUAAAUAUAACUGCAAAUAACAAAAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAUUAGCUGC--------------------------------------UUAAU-U-------------------UAGCGCAUGCG----------------------------------------------------------------------UUGCUCUU-------------UGUC---GGUUU------ACUCGU-------GGCU-----GAC------------------------------------------------------------ACUGAGUAUCAA----CUUUAGCGAGUUAC---------------------------------GUUUAACUAUC----U----CACCUGA---------------------------AUAGUUGAAAA-GAG--UC-UUAACAGGUU--AGCUAGCUCAUC-CUAGCC--CUGUUAUAU-----G-GCG--UUUUGAGCUAGUGAAGU-------------------------------------------------UC-AAGUAAUAUAAC---UA---UGAUCGUA---GAGGUCAGUGACG-------GAAUGCG-------------------------------------
U68082.1/21-356                --------N---------------AGAUUUCUUGU------C-G-CGC--AG-AUAG-CAUGCCAAGC-----GCU-----------GCUUGUAAAA------C-----AGCA---ACAAAAAUAACUGUAAACAACACAGAUUACGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCAGCUUACGCUAAAGC----------------------------------UGCGUGAGUUAA---------------UCUCCUUUU---GGAG-------------------------------------------------------------------CUGGAC---------------UGAUU--AGAAUU-----UCUAGC------GUUUU----AAUCG--------------------------------------------------------------CUCCAUAACC--U--UAAGCUAGACG----------------------------------CUUUUAAAAGGU-----------GGUU----------------------C-G-CCUUUUAAACUA-AGA--AACAAGAACUC-----UUGAAACUAUCUUAAGGUUUUAGAAAGUUGG---A-CCAG-AGCUAGUUUUAAGGCUAA-----------------------------------------------AAACUAACCAAUUUUCUAAGC---AUUGUAGA---AGUUUGUG--UUUAGG---GCAAGAUUUUUGGA-------------------------------
CP001037.1/6023908-6024297     GGGUCCGU--CACGGUUU--CGACAGGUUGGCGAAC-----GCU-GCUCUGU-GAUU-CAGGUCGAGA----G-UGAGUC-U---CCUCUCGGAAAUC----AAAGGCUCAAA---CAAAAAGUAAAUGCGAAUAACAUC------GUUAA----------------------------------------------------------------------------------------------------------------------------------------------------------------CUUUGCUCGUAAGGAUGCU-------------------------------------CUAG------------------------UAGCUGCCUAAACACCUCUUAU-------------------------------------------------AGGUUCGAGC-------------------GUCUUU--AGUUUG----ACUCCGUUA---AGGACU----GAAGACC---------------------------------------------------------A--AACCCC-----------AACGGAUG-----------------------------------CUCUAGUAAGCGUU------CUCUGGU------------------------UGGCUUGCUAGCUA-AG----AUUAAAUCAGAG--A---------------------------------------------------------AUCCUACGUUCGGGAUAAUGAACGA--UUCCCGCCUUGAGGGUCAGAAAGGC----------------UA---AACCUGU----GAAUGAGCGGGGGGUC--AAUACCCAAUUUGGA-CAGCAGUUCGACUCUGCU-CGGAUCCACUA
AF389962.1/19-339              --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCGCGUAAA--------AAGCCGCA------AUAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
AE007317.1/773607-773954       GGGGUCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCAUAU-UUUG-CGACUCGUG------UGGC-----------GACGUAA-----------ACGCUCA--GUUAAAUAUAACUGCAAAAAAUAACACUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUCUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCAGGCGU---------------------------------------------------------------------GACCCG---------------AUUU--GGAUU------GCUCGU-------GUUC-----AAU------------------------------------------------------------GACAGGUCUUAU----UAUUAGCGAGAUAC---------------------------------GAUUAAGCC------U----UGUCUAG---------------------------CGGCUUGAUAA-GAG---A-UUGAUAGACU--CGCAGUUUCU-----AGACU-UGAGUUAUGU----G-UC-----GAGGGGCUGUUAAAA--------------------------------------------------U--AAUACAUAACC---UA---UGGUUGUA---GACAAAUAUGUUG-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUUA
AF481102.1/4584-4321           GGGGAUGAC-AGGGAUU---CGACA-CGGGGCAAG------GGA-UGGG--G-UGC--CAUGCCGAAC------AGCCCAA-----CGUUAG--------------GGGC---------ACGAAAGGUGCACC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGUAAUA----------------------GGUUCACC-----------------------------------------------------------------------AUUGUGG-------------CUAAC-------------GAUUGCAU---------------CGA-------------------------------------------------------------CGCGUUAGUC-A-GAAGAGCAGUGGUAU----------------------------------A---GUGC------------GAAGGUA------------------------C-ACUGAGGGACUA-GG----CUGACGGUCAUA-------------------------GUGC--GAC----------------------------------------------------------------------------------UGU--AAAC---AA---AGCAUGUU---GUGCAC--CCCACA------CCUCCCUGCUGGA-CGUGGGUUCAAUUCCCAC-CAUCUCCAGGC
AB003477.1/1390-1783           GGGGCUGU--AAUGGUUU--CGACGUGUUGGUGAAU-----CCU-UCACCGU-GAUU-CAGGCCGAGA----G-GGAGUC-C---ACUCUCGUAAAUC-----CAGGCUCA-A---CCAAAAGUAACUGCGAACAACAUC------GUUCC----------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCUCGUAAGGCUGCU-------------------------------------CCUG-------------------------UAGCUGCUUAAACGCCACAAACU--------------------------------------------UUCUGGCUCGAGC-------------------GUCUAG--UCGUAG----ACUCCGUUA---AUACGC----CUAGACUU-------------------------------------------------------AA--ACCCCC-----------AACGGAUG-----------------------------------CUCGAGUGGCGGC-------CUCAGGU------------------------CCGUCCUCUCGCUA-AG----CAAAAACCUGAG--C---------------------------------------------------------AUCCCGCCAACGGGGAUAAUCGUUG-GCUCCCGCACAGUGGGUCAACCGUGC----------------UA---AGCCUGU----GAACGAGCGGAAAGUU--ACUAGUCAAUGCGGA-CAGCGGUUCGAUUCCGCU-CAGCUCCAUUU
CP000058.1/4804338-4804725     GGGGCCGAU--UUGGAUU--CGACGCCGGUGAUGA------A-A-CUUU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA--ACUUUCUAUAGUUGCCAAUGACGAAAACUACG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGCUCAACUAGCUGC--------------------------------------GUAA------------------------GCAGCCUAGCCGCACUUCUGGUA--------------------------------------------GCUUCGGCUCCAGCAAUCAU------------------CAGGGGAU-----GUCUGU-A----AACCCA--AA----------------------------------------------------------------AUGAUUGUCAU----AUAGAACAGAAUC-------------------------------------GCCGUG----CAG---UACGCUGUGG------------------ACGA----AUCGGCUAAA-A-----CUUACACAGCUC---GCCCAAAGC----ACCCU----GCCC--GUC---G-GG----UCGCUGAGGGUUAACU--------------------------------------------------UAAUAGACA-CGGC---UA---CGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
CP000017.1/983425-983772       GGGGUUGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCAUGU-UUUG-CGUCCCAUC------GGCA-----------GAUGUAA-----------AUUGCCA--GUUAAAUAUAACUGCAAAAAAUACAAACUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUUUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCUAGCGU---------------------------------------------------------------------GACUUC--------------UACA---AGAUU------GCUUGU-------GUCC-----UGU------------------------------------------------------------UAGAAGUCUCAA-----AAUAGCAAGCUAC---------------------------------GGUUACGAAA-----U----UGUCUAG---------------------------UUUCGUGACAA-GAG---A-UUGAUAGACU--CGCAAACUAA-----UGGCU-UGAGUUAUGU----G-UC-----UUUAGUUUGUUAAA---------------------------------------------------U-GAAGACAUAACC---UA---UGGACGUA---GACAAAUAUGUUG-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CAGCUCCAUCA
AF389955.1/19-340              --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGAUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AGGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-UC-----UAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCU--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
AF389966.1/18-338              --------G-------------ACGGGAUU-GUGA--------A-GCCUU---AGGAGCAUGCCGAGG-----GGCGGUUU-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CUUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAAGUCAAA--CCCAAAA-GAGCUC----------------------------------G---UGUGG---AUGU---CUUGCCUGGG-------------------GCU---GAAGCACUAAA-AC-----UAAUCAGGAUA---GUUUG-GUAA---UGGCG---UGUCU--AUC---C-GCA---GUUGC-CCGGCGAAU---------------------------------------------------GUAAAGAU-AUGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUUCGGA-CGCG-------------------------G
CP000918.1/834786-835133       GGGGUCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCAUAU-UUUG-CGACUCGUG------UGGC-----------GACGUAA-----------ACGCUCA--GUUAAAUAUAACUGCAAAAAAUAACACUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUCUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCAGGCGU---------------------------------------------------------------------GACCCG---------------AUUU--GGAUU------GCUCGU-------GUUC-----AAU------------------------------------------------------------GACAGGUCUUAU----UAUUAGCGAGAUAC---------------------------------GAUUAAGCC------U----UGUCUAG---------------------------CGGCUUGAUAA-GAG---A-UUGAUAGACU--CGCAGUUUCU-----AGACU-UGAGUUAUGU----G-UC-----GAGGGGCUGUUAAA---------------------------------------------------A-UAAUACAUAACC---UA---UGGUUGUA---GACAAAUAUGUUG-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUUA
CP000725.1/1316530-1316182     GGGGUCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCAUAU-UUUG-CGACUCAUCU-----AGCG-----------GAUGUAA-----------AACGCCA--GUUAAAUAUAACUGCAAAAAAUAAUACUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUUUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCGGGCGU---------------------------------------------------------------------GACCCG---------------AUUC--GGAUU------GCUUGU-------GUCU-----GAU------------------------------------------------------------GACAGGUCUUAU----UAUUAGCAAGCUAC---------------------------------GGUAGAAUC------U----UGUCUAG---------------------------UGAUUUUACAA-GAG---A-UUGAUAGACU--CGCUUGAUUU-----GGGCU-UGAGUUAUGU----G-UC-----AAAAUCAAGUUAAAA--------------------------------------------------C--AAUACAUAGCC---UA---UGGUUGUA---GACAAAUGUGUUG-------GCAGAUGUUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUAU
AF022186.2/109751-109498       GGGGCUG---AAAGGAUAUUCGACAUAUUAAUUU-CGUGCGCUA-------U-GAUG-CAAGCCGAGA------AUGCUU------AUCUCGUAAAAAA--GCA--GAC-------AAAGAAAUAAAUGCAAACAAUAUUAUUGAAAUUAGCAAUAUUAGAAAACCAGCUCUAGUAGUCUAGC-----------------------------------------------------------------------------------------------CUGAUUCAGUUAUUUCUAAAUUAUUUAUGUUAUGUUAU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUA---AGCUUGU------AGUAACUAUCUAGUG-UACAAUUUCUAUGGA-CGUGGGUUCAAUUCCCAC-CAGCUCCACAA
AF137379.1/195547-195873       GGGGUUGU--CAUGGAAU--CGACGUCUCUUCUAAG----AACG-AAAGGUU-AAAG-CAGGUCGAGG------UCGAAGAU---GGACUCGUACUCU----CCACUUCAUU----GCUUGAUUGCAUGCUAAUCAGAUUCUUCCUUUCUCUCGCCGGGUAGCCGUUGCUGCUUAAGCGAGUUUCUAGUGC-------------------------------------------------------------------------------CACUUUGUCACUAGUUUGUAUUAUGAGUUUCACACUCACUUCAAUG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGGUGAUAGAUACUACAUAUCAC----UCCUGCUUAGAGGGUCAUCUAAGC----------------UA---AACCAUGU---GAAUAUAACCUUUCGG--GCCUCGAGAGACGGA-AGUGAGUUCAAUUCUCAC-CAACUCCACCA
CP000431.1/6908166-6908497     -----------------C------UGCGUACGU--------UGA-GGUAGGG-GAAG-CGUGUCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGCUGCAAA-------CAUAUAAGCGCCGAUUCCAAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCACUCGC--------------------------------------UGCCUA---------------------AGUAGCGACUGCGU----------------------------------------------------------------GUCUGUCAG--------------------UCCGGGUU---CGCCCUCGG----CCCGGG--UA-----------------------------------------------------------------CUGGCAUCAG------CUAGAGGGCU-U--------------------------------UACCGUUCGACU---------CGGUCGC----------------------G-G-AGUCGAAUGGGA-CAA--CCAACAGCGACUG---GGAUCGU--CAUCCUGGC--UUGUUUGCGAG---A-CUGGGA------GAUCCAAGUAGA----------------------------------------------GAC----AUAGCAAAC---UG---CACACGGA----GAAGCCCUAGCUU-------UGCUGCGGAGGA-CCCGG------------G-----------U
ACFI01000164.1/26695-26328     GGGGCUGA---AAGGUUU--CGACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-CU-GACCACCGUAAGCG----UCGUUGCAAA-------UAGAUAAGCGCCGAUUCACAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGACAGCUAGU-------------------------------------------------------------------CCGUCAG--------------------CCCGGGAA---CGCCCUCGA----CCCGGA--GC-----------------------------------------------------------------CUGGCGUCAG------CUAGAGGGAU-C--------------------------------CACCGAUGAGUU---------CGGUCGC----------------------G-G-GACUCAUCGGGA-CAC---CAACAGCGACUG---GGAUCGU--CAUCCUGGC--UUGUUCGCGUG---A-CCAGGA------GAUCCGAGUAGA----------------------------------------------GGC----AUAGCGAAC---UG---CGCACGGA----GAAGCCUUGAGGG------AAUGC-CGUAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCACUG
AM181176.4/5798308-5798704     GGGGCCGUU--UAGGAUU--CGACGCCGGUCGCGA------A-A-CUUU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA--ACUUCUUAUAGUUGCCAAUGACGAAAACUACGGCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------AGGAAUUCGCUCUCGCUGC--------------------------------------GUAA------------------------GCAGCCUUAGCCCUGAGCUUCUGGU-----------------------------------------ACCUUCGGGUCCAGCAAUCAC------------------CAGGGGAU-----GUCUGU-A----AACCCA--AA----------------------------------------------------------------GUGAUUGUCAU----AUAGAACAGAAUC-------------------------------------GCCGUG----CAG---UACGUUGUGG------------------ACGA----AGCGGCUAAA-A-----CUUACACAACUC---GCCCAAAGC----ACCCU----GCCC--UUC---G-GG----UCGCUGAGGGUUAACU--------------------------------------------------UAAUAGAAA-CGGC---UA---CGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
AY846304.1/1-313               ------------------------GGAAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAGAUAGUCGCAAACGACAAUCAGUAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAGCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAAC---CUAGCUUGGG-------------------GUU---GAAGCGUUAAA-UA-----UAAUCAAGCUA---GCUUA-UUUG---UGGCG---UGUCU--GUU---C-GCA---GCAAG-UAAGUGAAA---------------------------------------------------UUAAAGAC--AGAC---UA---AGCAUGUA--GUGCCG--CGGAUGU-------AGGAAUUUC----------------------------------
AF440350.1/2-322               -----------------------CAGGGAUAGUU--------CG-AGCUUGA-GUUG-CGAGUCGGGG-----GGAUCGU-------CCUCGUUAUCAA---CGUCAAAGCC------AAUAAUAACUGGCAAAGAAAAACAAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUAGCUUUCGCUGC--------------------------------------CUAAUAA------------------GCAGUAGCAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------GCCCAU-------GUGC----UACGG-----------------------------------------------------------AAAGGGUCUCAC----UUUAAGUGGGCUAC---------------------------------ACUAAAUAAUC----U---CCGUCUGG--------------------------GGUUAGUUAGAA-GAG--CU-UAAUCAGACU--AGC-UGAAUGG---AAGCC---UGUUACCG-----G-GCU---GAUGUUUAUGCGAAAU-------------------------------------------------AC-UAAUACGGUGAC---UA---CGCUCGUA---GAUAUUUAAGUGC-------CCAUAUUUCUGG--------------------------------
AACY022163104.1/800-460        GGGGGUGAA--CUGGCUU--CGACUUUGAAGCGAG--------C-CUCU-CA-GUAG-CGAGCUGAGG-----GUCCUAGG----G-CCUCAUUAAAA-----ACGUAGGAA------AAAAAAGAUAACUGCCAAACCUAAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUGGCCGUAGCAG------------------------------------C-UUAAU-----------------------UGUUGCU-------------------------------------------------------------------------CGUCGA--------------CUAUC-----GGG-------GCUCCCA-CCUCG------GAUAGU-----------------------------------------------------------AUCGGCGU----------CGAAAUG--------------------------------------UGGGAUGCUAAGUUA----G-AUUACC---------------------GGC-UAGCUUUCAAGA-UUU--AA---GGUAAAA----ACUAUUGAGAA-UUUGUU----UCUG-GUGA---C-UC-----UCUCAAUAGU---------------------------------------------------------AUUUCAC-CAGA---UG---CGCUCGGA---GAAGCUG-UUGGGU-------AGCUUAAAAGGA-CCGGGGUUCGACUCCCCG-CACCUCCACCA
FM180568.1/2999022-2999384     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AF389957.1/21-334              --------C---------------GGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AGGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----UAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCU--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC-UG-AC---UA---AGCAUGUA--GUGCCG--AGGAUGU-------AGGAAUUUC--G------------------------------G
AE005176.1/1457456-1457098     GGGGGCGUU--ACGGAUU--CGACAGGCAUUG---------UCG-CGCAUGA-ACUG-CAACUGCUGA-----GGGAU----------CAGGAUA---------AUCAUCCGCA-GAUAAAUAUAACUGCUAAAAAUAAUACACAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUACGCAAUGGCAGC--------------------------------------CUAAAC----------------------AGCACCA-UGCG-------------------------------------------------------------------UGCCUGA--------------UUUU---UGCUC------UCUGAU-------GGCA-----AUU------------------------------------------------------------UGACGGCCUAAA---CUUUUAGUCAGAUAC---------------------------------GUUGUUGUG-----------GAGGCUU----------------------G----ACGCAGCAAAA-GAG---AUUUAAAGCCCC---GCAAAAUGUC---GCUGUU-UGAGACUGGC----U-UU-----GGCAUUUUGUUAAAUU------------------------------------------------UG----AGAAAGUCC---UA---UGGUUGUA---GACGUUGAUGUAG-------CAAGGUGUUUGGA-CAGGGGUUCGACUCCCCU-CGCCUCCAUUG
AE015924.1/2226462-2226056     GGGGCUGA---CCGGCUU--UGACAGCGUGA----U----GAAG-CGGUAUG-UAAG-CAUGUAGUGCG--UGGGUGGCUU------GCACUAUAAUC-----UCAGACAUC----AAAAGUUUAAUUGGCGAAAAUAACUAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUCGCUGCGUAAUCGAAGAAUAGUAGAUUAGACGCUUCAUCGCCGCCAAAGU--------------------G-GCAGCGACGAG--------------------------------------------------------------------A-CAUCGC-------------CCGAG--CAGCUU----UUUCCCGA-----AGUAG----CUCGAUG--------------------------------------------------------GUGCGGUGCUGA-----CAAAUCGGGAA--------------------------------------CCGCUACAGGAU-------GCUUCC----------------------U-GCCUGUGGUCA------GA-UCGAACGGAAGA----UAAGGAUCGUGCAUUGGG---UCGUUUCAG----C-CU-CCGCUCGCUCACGAAAAUU-------------------------------------------------CC---AACUGAAAC----UA---AACAUGUA--G-AAAGCAUAUUGAUU-----C--CAUGUUUGGA-CGAGGGUUCAAUUCCCUC-CAGCUCCACCA
CP000438.1/4749731-4750083     GGGGCCGAU--UAGGAUU--CGACGCCGGUAACAA------A-A-CUUG----AGGGGCAUGCCGAGCU---GGUAGCAG------AACUCGUAAAUU-----CGCUGCUGC----AAACUUAUAGUUGCCAACGACGACAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUAGCUGC--------------------------------------UUAA-----------------------UGCGGCUAG------------------------------------------------------------------------CAGUCGC------------------UAGGGGAU-----GCCUGU-A----AACCCG--AA----------------------------------------------------------------ACGACUGUCAG----AUAGAACAGGAUC-------------------------------------GCCGCC----AAG---UUCGCUGUAG------------------ACGU----AACGGCUAAA-A-----CUCAUACAGCUC---GCUCCAAGC----ACCCU----GCCA--CUC---G-GG----CGGCGCGGAGUUAACU--------------------------------------------------CAGUAGAGC-UGGC---UA---AGCAUGUA--GAACCG--AUAGCGG-------AGAGCUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
AM286415.1/1116549-1116169     GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGAG------GCCUCGUAAA--------AAACCGCA----AAAAAAAUAAUUGCAAACGACUCGCAAUACGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------AUCUGCUGCUUUAGCAG-------------------------------------CUUAAUCA-------------------GCCUAAGAAACUGAAG--------------------------------------------------------------AUUCCCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAGAUC----------------------------------G---CGUGG---ACAC---CUUGCCUGGG-------------------GUG---AAAGCGUUAAA-CC-----CAAUCAGGAUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUAA-CCGGCGAAU---------------------------------------------------GUAAUGAC-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGCGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AAFX01004374.1/206-561         GGGGGCG---AUCGGUUU--CGACGGGGGUCG---C-----GAA-AUCGCCU-GGAG-CAUGCCGAGGG---CGUCAUCU------UCCUCGUUAA-------UCCGGUGGCA---AAAAACUCAGACGCCAACGACGACGUC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUGUAGCCG---------------------------------------CUUA-----------------------AGGCUUAAGC-----------------------------------------------------------------------CCCGA--------------ACCCA--CUUGUG------CCUGUGC---UCGUGG-----AUGUA--------------------------------------------------------------GGGUCA------CUAUCACGGGAUC--------------------------------------GCUGCUGGUUGC----CGUCCGU----------------------CGGCCAGCGGUU-------AA-CCUAAAACGGGC---UGGUCCUUCGGUGCGCU-----UUGCACGCCG--U----GU-UGCCGCGGGACGAGACCA------------------------------------------------AA---ACGGCGCGC----UA---AGCAUGUA--G-CGCCGGG-GAUGUA-----G--CGCCUUCGGA-CGGGGGUUCAAUUCCCCC-CGCCUCCACCA
AE017285.1/1922270-1922621     GGGGGCGCA--CUGGUUU--CGACGGGGACGUAGA-------AG-CCG--GA-GUUG-CAGGCCGAGG----CGCCGCUGG------CCUCGUAAA---------AAGCGGC----ACAAAAGUAAUUGCCAACAAUUACGAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUCUGGCUG-------------------------------------CUUAAUU--------------------GACGGCCA--------------------------------------------------------------------------CGUCGA-------------ACCGGU--UCACG------CCUGAUA-----G--------ACCGGU----------------------------------------------------------G--AGACGU------AACUUCAUCAGGC-------------------------------------UGGCAUCUGACGG------CGCUCGC--------------------CGCGAAGGGUGCGAGAA-A-A---ACAGGUGAGCUG---GUCGAAGGUU-----GCC---UGGUC--GGG---G-GC-G-AAACCU-GAGAUGACGA--------------------------------------------------UUGUACUC--GACC---UA---AGCCUGUA---GACGCUUC-GUGUG------GAACAUUCUCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
CT573326.1/791766-791375       GGGGCCGAU--UAGGAUU--CGACGCCGGUAGCGA------A-A-CUCU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA--ACUUUCUAUAGUUGCCAAUGACGAAAACUACGAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCUACGCUCUCGCUGC--------------------------------------GUAA------------------------GCAGCUGAGCCCGCUCUCCUGGUA-------------------------------------------GCUUCGGCUCCAGCAAUCAU------------------CAGGGGAU-----GCCUGU-A----AACCCG--AA----------------------------------------------------------------AUGAUUGUCAU----ACAGAACAGGAUC-------------------------------------GUCGUG----CAG---CACGUUGGGG------------------GCGA----AGCGACUAAA-A-----CUUACCCAACUC---AUCCAAAGC----ACCCU----GCCC--GUC---G-GG----CGGCUGCGGAUUAAAU--------------------------------------------------CAGUAGACA-CGGC---UA---AGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
CP000513.1/208739-208388       GGGGGCGUU-CUUGGAUU--CGACGGGGAUUGCGA------G-G-CUCG----AGGUGCAUGUCGAGA-----AUGAGAGA-----AUCUCGUUAAAU-----A-CUUUCAA-----AACUUAUAGUUGCAAACGACGACAACUA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUUUAGCGG-------------------------------------CUUAA------------------------UUCCCGCUUU----------------------------------------------------------------------CGCUUAC-------------C------UAGAUUU---GUCUGUG-G----GUUUA--------C-----------------------------------------------------------CGUAAGCGACAU------UAACACAGAA------------------------------------UCGCUGGU----UAA---CGCGUCCGCU------------------GUUA----AUCGGUUAAA-------UUAAGCGGAAUC---GCUUGUAAAA----UGCC---UGAGC--GUU---G-GC----UGUUUAUGAGUUAAAC-------------------------------------------------CUAAUUAACU-GCUC---UA---AACAUGUA--GUACCA---AAAGUU------AAGGAUUCGCGGA-CGGGGGUUCAAAUCCCCC-CGCCUCCACCA
AACV01028831.1/1594-1241       GGGGGUGCA--UUGGUUU--CGACGGGGGUUGUGA------A-G-UCGC--C-UGGCGCAUGCCGAGG----GGGUAGCUU-----UCCUCGUAAAUC-----C-AGCUGCA-----AAACUCUAGUUGCCAACGACGACAACUA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUGGCC------------------------------------GCUUAA------------------------GGCCUAAG------------------------------------------------------------------------CCUCGA-A----------ACCG-----CUUGUG-----UCCAUGCU---CGCGG--------UG--------------------------------------------------------------UAGAGUCAC------UAUCAUGGAA------------------------------------UCGCGCUG----GAC---GGCUGCCUGUC-----------------AGUC----CGGCACUAGA---A--CACAACAGGCUG----GUUCCCGGAU----GCGCU-UCGCGC--ACC---G-UGC---UGUUCGGGGACGAGAU--------------------------------------------------CCAACGGU--GAGC---UA---AGCAUGUA--GUGCUG---GGGAUG------GAGUGCCUUCGGA-CGGCGGUUCAAUUCCGCC-CACCUCCACCA
AF375567.2/1-295               ---------------------------UGUUG---------UCG-CGUAUGA-GCUG-CGAUUAGUG------AGACGU---------CACUCUA---------AACCGUCGCA-GAUAAAUAUAACUGCUAAAAAUACACAAAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUUUAGCUGC--------------------------------------CUAAAC---------------------CACAGCCGGCGU---------------------------------------------------------------------GCCAGA--------------CUUU---CGUUC------GCCUAU-------GACG-----AUU------------------------------------------------------------UGAUGGCCUAA-----U-UUAGUAGGAUAC---------------------------------GCUUUUGUG------G----UGUCUUG---------------------------ACAUGAAAGAA-GAG---A-UUAAGAGACU--CGCCAGCUGAC---UUUGUU-CGAGGAUUGU----C-UU-----GUCAGUUGGGUAAAU--------------------------------------------------U--UAGACAGUCCC---UA---UGAUUGUA---GACGCUGAUAUAG-------CAAGGCA-------------------------------------
CR522870.1/569610-569245       GGGGGCGAA--ACGGCUU--CGACGGGGAUGUAUA------A-G-CUCU-AC-GUUG-CAUGUCGAGC----AACUGCCA-------GCUCGUAAAA------A-AGGCGGAA---ACUAAUAUAAUCGCAGACGAUUAUAAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCAGUA--GCAG-------------------------------------CUUAAUA--------------------A-CUGUCAUACUG--------------------------------------------------------------------CCGUCUC--------------UCCAG--UCCUCC-----GCUCAU------GAGGG----UUGGG-U---------------------------------------------------------CCGAGGCGUC--G--ACCAAAAUGAGC--U---------------------------------AGCAAUCGGGUGGU---------GUUCU---------------------GGUCGCCCCGGCGCGA-AAA--UAUACAGAAUA-----GCGUUAUAGU---A-UCC--CUGUUC-CGAC---G-GA----AGCUAAAUCGCGAAA---------------------------------------------------ACUAAGUGG-GAAC---UA---AACAUGUA---GAUACGAG-AGGGG-------AGCAUUUGCGGA-CGCGGGUUCGACUCCCGC-CGCCUCCACCA
AE017282.2/2818519-2818874     GGGGGCGAC--AUGGCUU--CGACGUGGAUCGCGA------A-A-CCUG----AGGUGCAUGCCGAGG----UGCAGAUG------ACCUCGUAAAUC-----C--AUCUGCA---AACCAAAUAAACGCCAACGACGACGUUUA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCACUGGCCG-------------------------------------CUUAA----------------------GCCGGCCGG-------------------------------------------------------------------------CCUCUGA--------------UCAGCAGCUCGC-----UUACAA-G----CGGCU----G----------------------------------------------------------------GUUGGGGGUAA----CCCAAUUGUAAGC-----------------------------------UCGCGCU---GAAGU---CU--GUCCGG------------------GGCC---GAAGCGCUAAA-A-C---CCAACGGAAUC----GCCGUCCGU----CUUCC--CUGCCA--CUC---G-GG----UAGCGUCCGGCUAAAU--------------------------------------------------CAAUAGAG--UGGA---UA---CGCAUGUA--GAACCG--AUGGCAG-------AGGAUUUGCGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
ABIN01000090.1/11435-11114     -----------------G----ACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-CC-GACCACCGUAAGCG----UCGUUGCAAA-------CAGAUAAGCGCCGAUUCACAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGACAGCUAGU-------------------------------------------------------------------CCGUCAG--------------------ACCGGGAA---CGCCCUCGA----CCCGGA--GC-----------------------------------------------------------------CUGGCGUCAG------CUAGAGGGAU-C--------------------------------CACCGAUGAGUC---------CGGUCGC----------------------G-G-GACUUAUCGGGA-CAC---CAACAGCGACUG---GGAUCGU--CAUCUCGGC--UUGUUCGCGUG---A-CCGGGA------GAUCCGAGUAGA----------------------------------------------GGC----AUAGCGAAC---UG---CGCACGGA----GAAGUCUUGAGGG------AAUGC-CGUAG--------------------------------G
AF389948.1/19-339              --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGAUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCUCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAU--------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGU---CCUGCCUGGG-------------------GCU---GAAGUGCUAAA-AC-----UAAUCAGGCUA---GUUCG-UUAG---UGGCG---UGUCU--GUC---C-GCA---GCUGG-CGUGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUGCCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
AE004969.1/862950-863312       GGGGGCGAC-CUUGGUUU--CGACGGGGGUUGCGA-------AG-CAGA-UG-CGGG-CAUACCGGGG-----UCUCAGAU------UCCCGUAAAA-------CACUGAAU------UCAAAUAGUCGCAAACGACGAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUAGCCG-------------------------------------CUUAA-------------------------GGCUAGC------------------------------------------------------------------------CGUUGCA------------GCAGUC------------GGUCAAUG--------------GGCUGUGUGGUGA---------------------------------------------AAGCCACCGCAACGUC--A--UCUUACAUUGACUG-----------------------------------GUUUCCAGCC---------GGGUUACU---------------------U---GGCAGGAAAUAA-GAC---UUAAGGUAACUG---GUUUCCAAAA----GGCC---UGUUG--GUC---G-GC----AUGAUGGAAAUAAG-AUUUU------------------------------------------CAAAU---AGACA-CAAC---UA---AGUAUGUA---GAACGC--UUUGUA------GAGGACUUUCGGA-CGGGGGUUCGAUUCCCCC-CGCCUCCACCA
BX950851.1/927307-926945       GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCAA--------A-GCCCA---AGGUGCAUGCCGAGG-----GGCGGUUU-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGGGCUAAA-UC-----UAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCU--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--ACGGUAG-------AGUAGUUCCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AE001273.1/21082-20663         GGGGGUGU--AAAGGUUU--CGACUUAGAA-----A-----UGA-AGCGUUA-AUUG-CAUGCGGAGGG---CGUUGGCUG-----GCCUCCUAAA--------AAGCCGAC----AAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGCUU---------------------------------------------------------------------------------------------------------------------------------------CGCUGAUCUCGAAGAUCUAAGAGUAGCUGCUU-------------------------------------AAUUAGC--------------------A-AAGUUGUUACCUAAAUAC------------------------------------------------------GGGUGACC-CGGUG--------------UUCGC--GAGCU-----CCACCAGA-----GGUUU----UCGAA------------------------------------------------------------ACACCGUCA------UGUAUCUGGU---------------------------------------UAGAACUUAGGUCCU-UUAAUUCUCGA-------------------GGAAAUGAGUUUGA------AA-UUUAAUGAGAGU------CGUUA-GUCUCUAUAG---GGGUUUCUAG---C-UGAGGAGACAUAACGUAUAGU---------------------------------------------------A---CCUAGGAAC----UA---AGCAUGUA--G-AGGUUAGCGGGGAG-----U--UUACUAAGGA-CGAGAGUUCGACUCUCUC-CACCUCCAUAG
CP000046.1/875955-876313       GGGGACGUU-CAUGGAUU--CGACAGGGGUCCCC--------CG-AGCUCAU-UAAG-CGUGUCGGAG-----GGUUGU--------CUUCGUCAUCAA--CACACACAGUU------UAUAAUAACUGGCAAAUCAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------CUAAUC----------------------GCA-CUCUGC----------------------------------------------------------------------AUCGCC-------------UAACA---GCAUU------UCCUAU-------GUGC-----UGUUA-----------------------------------------------------------ACGCGAUUCAA---C-CUUAAUAGGAUAU---------------------------------GCUAAACACUG----C----CGUUUGA------------------------A-GUCUGUUUAGAA-GAAA-CU-UAAUCAAACU--AGCAUCAUGUU-----GGU---UGUUUAUC-----A-CUU----UUCAUGAUGCGAAA---------------------------------------------------C-CUAUCGAUAAAC---UA---CACACGUA---GAAAGAUGUGUAU-------CAGGACCUUUGGA-CGCGGGUUCAAAUCCCGC-CGUCUCCA---
BX571857.1/837496-837857       GGGGACGUU-CAUGGAUU--CGACAGGGGUCCCC--------CG-AGCUCAU-UAAG-CGUGUCGGAG-----GGUUGU--------CUUCGUCAUCAA--CACACACAGUU------UAUAAUAACUGGCAAAUCAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------CUAAUC----------------------GCA-CUCUGC----------------------------------------------------------------------AUCGCC-------------UAACA---GCAUU------UCCUAU-------AUGC-----UGUUA-----------------------------------------------------------ACGCGAUUCAA----CCUUAAUAGGAUAU---------------------------------GCUAAACACUG----C----CGUUUGA------------------------A-GUCUGUUUAGAA-GAAA-CU-UAAUCAAGCU--AGCAUCAUGUU-----GGU---UGUUUAUC-----A-CUU----UUCAUGAUGCGAAA---------------------------------------------------C-CUUUCGAUAAAC---UA---CACACGUA---GAAAGAUGUGUAU-------CAGGACCUCUGGA-CGCGGGUUCAAAUCCCGC-CGUCUCCAUAU
CP000108.1/2092429-2092029     GGGGAUGA--CAGGCUUU--CGACAGGGUAGG---U-----GUA-AGGUGGC-GUUG-CACUCCGAGUUUCAGCAUGGAUG-----GACUCGUUAAAG-----AAGUCUAUG----CAACCUUUAGAUGCAGACGAUUAUUCG---UA----------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCAAUGGCUGCCUAA--------------------------------------------UUAGCAA------AAGUUAAU-UAACC-AGCCA--------------------------------------------------------------------U--------------------CGCUC-UUCAGCGGAGGCGCUUACUCCAAGGCUGUU--AGAGUGGCAUAAUUCGCGCUU------------------------------GAGCUCUGCUCGCGC------------------AAGUAAGC----------------------------------------UCCGUUUUGUAU----UGCCUGAU--------------------GUGCUUAGCGGG--------U--AUUUAUUCGGGAU------AGUAAGUU-GAACG----UUACAAGUG----U-CGUACCAACUUAUGAAUCUUA-------------------------------------------------------AACACUUGA----GA---UGAGUGUG--G-UAGCGUUAUCAAGC-----A--AUAUUCUGGA-CGCGGGUUCGAAUCCCGC-CAUCUCCACCA
BX571870.1/186841-187204       GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCGCAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CUUGCCUGGG-------------------GUU---GAAGCGUUAAA-UC-----UAAUCAGGCUA---GUUUG-UGAG---UGGCG---UGUCU--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAU-UAGAC---UA---AGCAUGUA--GUACCA--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AF389945.1/20-340              --------G-------------ACAGGAUUUGCAA--------A-GCCCU---AGGAGCAUGCCGAGG-----GGCGGUUU-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUUGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GUUC-UU------AAGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAACUC----------------------------------G---CGUGA---AUAC---CUUGCCUGGG-------------------GUU---GAAGCGCUAAA-AU----CUAAUCAGGCUA---GUUUG-UCAG---UGGCG---UGUCC--GUU---C-GCA---GCUGA-CCGGCGAAU---------------------------------------------------GUAAAGAU--GGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUCU-GA-CGCG-------------------------G
BX640432.1/247325-247711       GGGGCCGAU--CCGGAUU--CGACGUGGGUCAUGA-------AA-CAGC-UC-AGGG-CAUGCCGAGC-----ACCAGUAA------GCUCGUUAAU-------CCACUGGA-----ACACUACAAACGCCAACGACGAGCGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCUCUCGCCGC--------------------------------------UUAA------------------------GCGGUGAGC-----------------------------------------------------------------------CGCUGCA------------CUGAUC-U-----------GUCCUUG--------------GGUCAGGCGGGGGAAGGCAACUUCCC------------------AGGGGGCAACCCCGAACCGCA-GCAGCGAC-----AUUCACAAGGAAUC----------------------------------GGCCACCGCUGG----------GGUCAC---------------------A---CGGCGUUGGUUU-AAA---UUACGUGAAUCG----CCCUGGUCC----GGCC---CGUCG--AUC---G-GCU---AAGUCCAGGGUUAAAUC------------------------------------------------CAAAUAGAU--CGAC---UA---AGCAUGUA---GAACUGG--UUGCG------GAGGGCUUGCGGA-CGGGGGUUCAAUUCCCCC-CGGCUCCACCA
CP000462.1/1578060-1577701     GGGGCUGAU-UCUGGAUU--CGACAAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAU-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUC-GCAG-------------------------------------CUUAAUA--------------------ACCUGCGCUGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------CGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUCAAUUCGU----GGCG---UGUCU--CUC---C-GC----AGCGGGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUGCCA--AGGAUGU-------AGUAAUUUUGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
CR378665.1/70600-70233         GGGGCUGAU-UCAGGAUU--CGACAGGAUCAAGAA--------G-GCUUG---UGGAGCAUGCCGUGG-----GGCGGUUG-----GCCACGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUUC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCU-AGCGC---------------------------------------------------------------------ACUUCUA-------------CCCU--AGCUUCC-----GCUU-GU------AAGA----CGGGGAAU-------------------------------------------------------CAUAGAAGUUCAAA--CCCAAAC-GAGAUA-------------------------------------GCGAGG--GAACCU-UUGACUAGAGA-------------------GGU---GAACCGCGAAA-UA-----GAAUUCUGGUA--UGUAUUUACAU----GGCG---UGUCU--GUU---C-GC----AGUGUACUUACGAGA---------------------------------------------------AUAAAGAU--AGAC---UA---AGCAUGUA--GCGCCU--AUGGUUG------GAUUGCUCUUGGA-CGCGGGUUCAAAUCCCGC-CAGCUCCACCA
AAKK02000007.1/7330-7697       GGGGCUGAU-UUAGGAUU--CGACGGGAAUUCAGA--------A-GUCUG---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCAGAGC---------------------------------------------------------------------UCUCUCG-------------CCCU--AGCUUCC-----GCAC-GU------AAGA----CGGGGAAU-------------------------------------------------------AACGAGGGAUCAAA--CCCAAAC-GCGCUA-------------------------------------GCCCGG---AUUCU-CCCGCCUGAGA-------------------GAU---GAACGGCGAAU-UU-----UAAUUCAGGCU--AGUCAUUCAUU----AGCG---UGUCG--GUU---C-GC----AGGUGGGUGGCGAAA---------------------------------------------------UUAAAGAU--CGAC---UA---AGCAUGUA--GUACCA--AUGAUGA-------ACGGUUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AM849034.1/2211870-2211495     GGGGAUGA---UCGGUUU--CGACAUUGCCUGA--------AUG-ACUGCGA-GAAG-CGGGUCGAGG-----AUGCAGG-G--CUAUCUCGUAAACG----CUCUCUGCAA-------AAUACAACUGCCAAUAACAAGCAGUCGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUUUGUUCUCGCUG--------------------------------------CCUA-----------------------AGCGAGCGCACUAACA-------------------------------------------------------------GGACCGUCGA---------------------CCCGGUG--AUGCUCUCUA---UCCGGUA--AG-----------------------------------------------------------------UCGGCGUCAG-----AAAAGGGAGCU-C---------------------------------GCUGCGCGGUC---------GUGCCUC----------------------A-G-GGCCGCGCGGGA-CUC---GAACUGAGGCUG---GGCCCGU---CGGAUCAG--AUGCCAGGAGC---A-AGUUCCG-----GGGCCGAGCAGG----------------------------------------------ACG--CCUUUCCUGGA---UA---CACCCGUA----GAAGGCGCAGGAU-------UACAGCAGUGGA-CCGGGGUUCGAUUCCCCG-CAUCUCCACCA
CP000750.2/3144288-3144653     GGGGAUGA---CAGGUUU--CGACGUUGGUCGU--------CGA-GCCAGGG-GAAG-CGGGUCGAGG-----AUGCAUG-G--UCAUCUCGUCAACG----AUCCAUGCAA------ACCAAUAGGUGCCGAUUCCAAGCGCACC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGUUCGCCCUCGC--------------------------------------CGCCUG---------------------AGCGAGCGCGA-C------------------------------------------------------------------UCUGUCAG--------------------CCCGGGUG---AGCUCCCGC----CCCGGG--UC-----------------------------------------------------------------CUGGCAUCGA------CUAGGGGGCU-C---------------------------------ACCUCUCACCG---------AGGUCGC----------------------G-U-AGGUGAGAGGGA-CAA---UCAACGCGGCUG---GGCCCGG---C-GAUGAC--AUGCCUGUAUG---A-GCAUCG------GGGCCGAGCAGA----------------------------------------------CCG---CUGAACAGGA---UG---CACCCGGA----GAAGCCCUGGUAC-------CACGCUGACGGA-CGCGGGUUCGAUUCCCGC-CAUCUCCACUC
ACKV01000008.1/12419-12062     GGGUCUGUU-UUUGGAAU-UCGACAGGUCGUU---------UAG-AGCAUUG-AUUG-CGUUUCGCCA-------UCCG---------GGCGCAA---------AACGGGC-A---GAAAUUUUAACUGCAAAAAACGAAAACUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCUAUCGCUGC--------------------------------------CUAAAA---------------------ACCAGUGAUGCG--------------------------------------------------------------------UAGCUUAA-------------UCUU---GGUU-------GCUGGC-------GUCU-----GAGG------------------------------------------------------------UUAGGCCAUAA---A---AGGCCAGAUCG---------------------------------UACUGCUUCUU----A----CAUCUGG---------------------------AAAAGCAGUAU-UAA--AU-CAAUCAGGUU--AGUUAUAUUGAA--GAGCC--UUGAGCUAU-----G-GCA---GACAAUAUAAUGAACU-------------------------------------------------AC-AAAUAAUAGCCC---UA---UAAACGUA---GAUAUUGGUGUAU-------CGGGCGAUUUGGA-CAGGGGUUCGACUCCCCU-CAGAUCCAUUU
CP000090.1/2828530-2828889     GGGGCCGAC--CUGGUUU--CGACGUGGGUUGCGA-------AG-CAGU-GG-AGGG-CAUACCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AUGCAAUAACUGCUAACGACGAACGU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCACUGGCAGCC---------------------------------------UAAG-----------------------GGCCGCCGU-----------------------------------------------------------------------CCUCGCA------------CUGGCU-C-----------GCUGACG--------------GGCUAGGGUUCGC--------------------------------------------AAGAACCA-GCGAGGUC-----AUUUACGUCAGAUA----------------------------------AGCCCCGUCGGU-----------GUCAC--------------------GA----CUGCGGGGACG-AAA--ACCAAGUGACUCG----CCGUCGUAG----AGCG---UGUUC--GUC---C-GCG----AUGCGGCGGUUAAAU--------------------------------------------------CAAAUGACA-GAAC---UA---AGUAUGUA---GAACUCU--CUGUG------GAGGGCUUGCGGA-CGCGGGUUCGAUUCCCGC-CGGCUCCACCA
AF375577.1/1-309               ---------------------------CGUAG---------AUU-CGCAUUG-ANUG-CGAUUCGUAG-----GUUACGU-------CUACGUAAA--------AACGUUACA--GUUAAAUAUAACUGCAAAUAACAAAAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAUUAGCUGC--------------------------------------UUAAU-U-------------------UAGCGCAUGCG----------------------------------------------------------------------UUGCUCUU-------------UGUC---GGUUU------ACUCGU-------GGCU-----GAC------------------------------------------------------------ACUGAGUAUCAA----CUUUAACGAGUUAC---------------------------------GUUUAACUACC----U----CACCUGA---------------------------AUAGUUGAAAA-GAG--UC-UUAACAGGUU--AGCUAGCUCAUC-CUAGCC--CUGUUAUAU-----G-GCG--UUUUGGGCUAGUGAAGU-------------------------------------------------UC-AAGUAAUAUAAC---UA---UGAUCGUA---GAGUUCAGUGACG-------GAAUGCG-------------------------------------
S67602.1/1-411                 GGGGAUGUC--AUGGAUU--UGACAGGAUAUCU--------UUA-GUACAUA-UAA--GCAGUAGUGUU---GUAGACUAU----AAAUACUACUA----------GGUUUA---------AAAAAACGCAAAUAAAAACGAAGAAACUUUUGAAAUGCCAGCAUUUA-----------------------------------------------------------------------------------------------------------------------------UGAUGAAUAAUGCAUCAGCUGGAGCAAACUUUAUGUU------------------------------------U--GCUUA--------------------AUAACUACUAGUUU-------------------------------------------------------------------AGUUAUAGUAUUUCACGAAUU-------AUAGAUA--UUUUAAGCU------UUAU---------------------------------------------------------------------UUAUAACCGUAUUAC-CCAAGCUUAA-------------------------------------UAGAAUAUAU----G----AUUGCAA----------------------U-AAAUAUAUUUGAAA-UC------UAAUUGCAA-----AUGAUAUUU----AACCUUUAGUUAAUUUU---A-GUU----AAAUAUUUUAAUUA-------------------------------------------------------GAAAAUUAAC---UA---AACUGUA----GAAAGUAUGUAUUA-------AUAUAUCUUGGA-CGCGAGUUCGAUUCUCGC-CAUCUCCACCA
AACY020396050.1/454-188        GGGGGCGAC--C-GGUUU--CGACAUUUUAGAAUG------A-AAUCUUA---GAUUGCAUGUAGAGC-----UUAGUA--------ACUCUUAAA--------ACUUCUAA----ACUAUAUUAAGUGCCGAUAAUGGCCAAAU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCUUUUG------------------------------------CUUAAUUG--------------------C-UAAAGUCCAUCA-------------------------------------------------------------------UCAGUAGA------------C-------GUUUCUCA-UCGUUCGCU-----GAAU------------------------------------------------------------------------GGUGUCAUA------AAAAUGAGA-------------------------------------UAGUUUA---UU-UU---UC-UGCUUCG------------------GUUUA-A--UAAAUGAAU---C---CUUAGAAGAUA-G-CUAUAUGCCUG---UUUGU----------UCU--UG-UA-----CUGUCAUGUA---------------------------------------------------------------G--------------------------------------------U-----------G------------------------------A
CP001233.1/872109-871743       GGGGCUGAU-UCAGGAUU--CGACGGGAAUUUUGC--------A-GUCUG---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------CCCUGCUCAGAGC---------------------------------------------------------------------CCUUCCU-------------CCCU--AGCUUCC-----GCUU-GU------AAGA----CGGGGAAA-------------------------------------------------------UCAGGAAGGUCAAA--CCAAAUC-AAGCUG-------------------------------------GCGUGG---AUUCC-CCCACCUGAGG-------------------GAU---GAAGCGCGAGA-UC-----UAAUUCAGGUU--AGCCAUUCGUU----AGCG---UGUCG--GUU---C-GC----AGGCGG-UGGUGAAA---------------------------------------------------UUAAAGAU--CGAC---UA---AGCAUGUA--GUACCA--AAGAUGA-------AUGGUUUUCGGA-CGGGGGUUCAACUCCCCC-CAGCUCCACCA
AL646052.1/943228-942872       GGGGCCGAC--CUGGUUU--CGACGUGGGUUGCGA-------AG-CAGU-AG-CGGG-CAUACCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----ACGCAAUAACUGCUAACGACAACCGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACCAGCUGGCCG-------------------------------------CUUAAUU--------------------GCGCGCC-GU------------------------------------------------------------------------CCUCGCA------------CUAGCU-U-----------GCCGAUA--------------GGCUAGGGCCGC----------------------------------------------AAGGCCACGCGAGGUC-----AUUCAUAUCGGAUC----------------------------------GCUUCGGCCGGU----------GUCACG--------------------AC-----GGCCGGGGUU-AAC---UCCAAGUGACUC---GUCGUCGCGC----AGCG---UGUUC--GUC---C-GC----GUCGCGCCGGUUAAAU--------------------------------------------------CAAAUGACU-GAAC---UA---AGUAUGUA---GAACGCU--CUGUA------GAGGACUUGCGGA-CGCGGGUUCGAUUCCCGC-CGGCUCCA---
CP000423.1/1024842-1024479     GGGGGUGUA--AUGGUCU--CGACAUUGCUUU---------UCG-CACAUGC-AGUG-CACCUCGGAG-----GCU-CGG-------CUCCGUCAUC-------AACGGAACA---GUUAAUAUAACUGCAAAGAACGAAAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUUUAGCUGC--------------------------------------UUAAUAA------------------CCAGC--UAGCG-----------------------------------------------------------------------UGAUCCU-------------UCCG---ACUUC------GCUCAA-------GGGU-----CGGGU----------------------------------------------------------CUGGGUCUCAAA------UUAUUGAGCUAC---------------------------------GGUUAAUGUUG----C----CACCUGA---------------------------GGCAUUAACAA-GAG---A-CUAGUAGGUU--AGCUGCGUUGUG-UUAGCC--UUGCUGGCU-----G-GCG--CGACAUCGCGGCGAAUU-------------------------------------------------UU-AAAUAAGUCAGC---UA---UAGGUGUA---GAGCUGCAUGUAG-------CAGGGGUGAUGGA-CAGGAGUUCGAUUCUCCU-CACCUCCAUUA
BX936398.1/1359891-1359528     GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUG------GCCUCGUAAA--------AAACCGCA----AAAAAAAUAGUUGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAGCUC----------------------------------G---UGUGG---AAAC---CUUGCCUGGG-------------------GUG---GAAGCAUUAAA-AC-----UAAUCAGGAUA---GUUUG-UCAG---UAGCG---UGUCC--AUC---C-GCA---GCUGG-CCGGCGAAU---------------------------------------------------GUAAUGAU-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
BA000037.2/823422-823056       GGGGCUGAU-UUAGGAUU--CGACGGGAAUUUUGC--------A-GUCUG---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------AACUGCUCAGAGC---------------------------------------------------------------------CCUCUCG-------------CCCU--AGCUUCC-----GCUU-GU------AAGA----CGGGGAAU-------------------------------------------------------CACGAGGGGUCAAA--CCAAAUC-AAGCUG-------------------------------------GCGUGG---AUUCC-CCCACCUGAGG-------------------GAU---GAAGCGUAAGA-UA-----UAAUUCAGGUU--AGCUAUUCAUU----CGCG---UGUCG--GUU---C-GC----AGGUGG-UAGUGAAA---------------------------------------------------UUAAAGAU--CGAC---UA---AGCAUGUA--GUACCA--AUGAUGA-------AUGGUUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
CP000075.1/4999820-5000211     GGGGCCGAU--UUGGAUU--CGACGCCGGUGAUGA------A-A-CUUU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA--ACUUUCUAUAGUUGCCAAUGACGAAACCUACGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAUACGCUCUCGCCGC--------------------------------------GUAA------------------------GCGGUGCUAGCCUUCCUUCUGGUA-------------------------------------------GCUUCGGCUCCAGCAAUCAU------------------CAGGGGAU-----GCCUGU-A----AACCCG--AA----------------------------------------------------------------AUGAUUGUCAU----AUAGAACAGGAUC-------------------------------------GUCGCC----UAG---UACGUUGUGG------------------ACGA----AGCGACUAAA-A-----CUUACACAACUC---GCCCAAAGC----ACCCU----GCCC--GUC---G-GG----UCGCUGAGGGUUAACU--------------------------------------------------UAAUAGACA-CGGC---UA---AGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
CP001050.1/750995-750675       --------C---------------GGGGGUUGCGA-------AG-CAGA-UG-CGGG-CAUACCGGGG-----UCUCAGAU------UCCCGUAAAA-------CACUGAAU------UCAAAUAGUCGCAAACGACGAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUAGCCG-------------------------------------CUUAA-------------------------GGCUAGC------------------------------------------------------------------------CGUUGCA------------GCAGUC------------GGUCAAUG--------------GGCUGUGUGGCGA---------------------------------------------AAGCCACCGCAACGUC--A--UCUUACAUUGACUG-----------------------------------GUUUCCAGCC---------GGGUUACU---------------------U---GGCAGGAAAUAA-GAC---UUAAGGUAACUG---GUUUCCAAAA----GGCC---UGUUG--GUC---G-GC----AUGAUGGAAAUAAG-AUUUU------------------------------------------CAAAU---AGACA-CAAC---UA---AGUAUGUA---GAACGC--UUUGUA------GAGGACUUUCGGA-CGGGG------------G-----------U
CP000020.2/2237433-2237799     GGGGCUGAU-UCAGGAUU--CGACGGGAAUUUUGA--------A-ACCCG---AGGAGCAUGUCGUGG-----GGCGGUUG-----GCCACGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUGAGAGC---------------------------------------------------------------------UCUCCUG-------------CCCU--AGCUUCU-----GCUU-GU------AAGA----CGGGGAAU-------------------------------------------------------AACAGGGGAUCAAA--CCCAAAC-GAGCUA-------------------------------------GAACGG---AUUCU-CCCGCCUGAGA-------------------GAU---GAACUUCGAAU-UA-----UAAUUCAGGAU--AGCCAUAAGAU----AGCG---UGUCG--GUU---C-GC----AGUUUUACGGUGAAA---------------------------------------------------UCAAAGAU--CGAC---UA---AACAUGUA--GCGCCA--ACGGUGA-------ACGAUUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AE014295.3/206548-206944       GGGGGCGA---UCGGUUU--CGACGGUGACCUGU-------UCG-CUGCAGG-GAAG-CGUGCCGAGA----ACGCCGGG-U---CCGCUCGUGGAUG-----ACCCCGGCA-----AAAGAAUAAGUGCUAAAUCUAACCGCACUGAGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------UCGCUCUCGCUGCCUGAUU---------------------------------------UUU------------------------AGUCAGGAUUAACCAGUGAG---------------------------------------------------CAGCCGCUCCGUUCA--------------------CUCCUCCU---CGUCUUUGG----GAGGAU--GC-----------------------------------------------------------------UGAGCGUCGU------UUAGAAGACU-U--------------------------------GCUGAUGCAGUU---------GAGCCUC----------------------A-G-GGCUGCAUCGGG-ACU--UUAACUGCGGAUA---UGCUCGC---C-AUCAGU---UGUCUGCGAC---A-UCGAUG------GGGGCAGAAAAAUC-----------------------------------------GCCAACUUGGCCAGCAGAC---UA---CGCACGUA----GAAGACUGUGGGC-------UCGGUCAUCGGA-CCGGGGUUCAAUUCCCCG-CGCCUCCACCA
CP000514.1/3730537-3730902     GGGGACGA--CUUGGCUU--CGACGCCGGUGACGA--------A-CCCUU---GGGUGCAUGCCGAGA----UGGCAGCGA-----AUCUCGUAAAUC----CAAAGCUGCA-----ACGUAAUAGUCGCAAACGACGAAAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCACUGGCGGC--------------------------------------GUAA------------------------GCCGUUCCAGU---------------------------------------------------------------------CGUCCUG--------------------GCUGAGG---CGCCUAUAA---CUCAGUA--GCAACAUC---------------------------------------------------------CCAGGACGUCA----UCGCUUAUAGGCU--------------------------------------GCUCCGU-UCACC---AGAGCUCACU-------------------GGU--G-UUCGGCUAAG-A------UUAAAGAGCUC---GCCUCUCGCA-----CCC---UGACC--UUC---G-GG----UCGCUUGAGGUUAAAU--------------------------------------------------CAAUAGAA--GGACA-CUA---AGCAUGUA--GACCUC--AAGGCCU-------AGUGCUGGCGGA-CGCGGGUUCAAUUCCCGC-CGUCUCCACCA
CP000611.1/3480490-3480123     GGGGCUGA---ACGGUUU--CGACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGUUGCGAC-------CAAAUAAGCGCCGAUUCACAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGACGGCUAGU-------------------------------------------------------------------CUGUCAG--------------------ACCGGGAA---CGCCCUCGG----CCCGGA--CC-----------------------------------------------------------------CUGGCAUCAG------CUAGAGGGAU-C--------------------------------CACCGAUGAGUC---------CGGUCGC----------------------G-G-GACUCCUCGGGA-CAA---CCACAGCGACUG---GGAUCGU--CAUCUCGGC--UAGUUCGCGUG---A-CCGGGA------GAUCCGAGCAGA----------------------------------------------GGC----AUAGCGAAC---UG---CGCACGGA----GAAGCCUUGAGGG------AAUGC-CGUAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCACCG
CP000746.1/1403027-1402661     GGGGCUGAU-UCUGGAUU--CGACGGGAUUGGCGA--------A-GCCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAU-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUUUAGC---------------------------------------------------------------------CUUCGCU-------------CCCCA--GCUUCC-----GCUC-GU------AAGA----CGGGGAU--------------------------------------------------------CAAGCGGAGUCAAA--CCUAAAC-GAGAUC----------------------------------G---UGUGG---ACGCU--UCGGCUUGGA-------------------GAU--CGAAACACUAAA-UU-----GAAUCAAGCUA---GUUUA-UUCU---UCGCG---UGUCU--GUC---C-GCA---GGGGA-UAAAUGAAG---------------------------------------------------UUAAAGAC-CAGAC---UA---AACGUGUA--GUGCUG--AAGGUAG-------AGUAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP001048.1/1357396-1357033     GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUG------GCCUCGUAAA--------AAACCGCA----AAAAAAAUAGUUGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAGCUC----------------------------------G---UGUGG---AAAC---CUUGCCUGGG-------------------GUG---GAAGCAUUAAA-AC-----UAAUCAGGAUA---GUUUG-UCAG---UAGCG---UGUCC--AUC---C-GCA---GCUGG-CCGGCGAAU---------------------------------------------------GUAAUGAU-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
CP000383.1/1433554-1433957     GGGGUCGA---CAGGAAU--UGACAGGUUGAGU--GA---UUAC--G-UGUG-UAAG-CAUGCAGGCUC---AUGGGAUGA-----GAGCCUUAAAAG-----AUAGUUCCG------AACAAUAAUUGGCGAAGAAUCUUAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCCAUGGCUGCUUAAUUACGAACUAA------GUUUGUAAUAAUGAGCGUUGAGUGGAGCUGUUAAGAACAGCACC--CGGCCA--------------------------------------------------------------------------CAUCUC--------------ACAC---GGCUUC---UGUUCUGC-----GGGCU----GUGA--A--------------------------------------------------------CUGAGAUGUCG------AACAGCAGGAC--------------------------------------UAGGGGAGUACA------AGUUGCG-----------------------GGUGCUUCGC--------G--AAAUUAAGUAACU----AAGGUUAUAGUUGGG------UGCCGGUG-------ACCUGCUACAGCUCGAAAAUG--------------------------------------------------A---ACAUCCGGC----UA---AGCAUGUA--G-AAGAUUCGAUAGUG-----G-CCUUCUCUGGA-CGAGAGUUCGAAUCUCUC-CGACUCCACAC
AACY023318861.1/904-508        GGGGCCGUU--UAGGAUU--CGACGCCGGUCGCGA------A-A-CUUU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA--ACUUCUUAUAGUUGCCAAUGACGAAAACUACGGCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------AGGAAUUCGCUCUCGCUGC--------------------------------------GUAA------------------------GCAGCCUUAGCCCUGAGCUUCUGGU-----------------------------------------ACCUUCGGGUCCAGCAAUCAC------------------CAGGGGAU-----GUCUGU-A----AACCCA--AA----------------------------------------------------------------GUGAUUGUCAU----AUAGAACAGAAUC-------------------------------------GCCGUG----CAG---UACGUUGUGG------------------ACGA----AGCGGCUAAA-A-----CUUACACAACUC---GCCCAAAGC----ACCCU----GCCC--UUC---G-GG----UCGCUGAGGGUUAACU--------------------------------------------------UAAUAGAAA-CGGC---UA---CGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
AY911527.1/1-311               ------------------------GGGAUUUGCGA--------A-GCCCU---AGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------CCCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---ACGU---CCUGCCUGGG-------------------GCU---GAAGCGUUAAA-CU-----CAAUCAGGCUA---GUCUG-UCAG---UAGCG---UGUCC--AUC---C-GCA---GCUGG-CCGGCGAAU---------------------------------------------------GUAAAGAU-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUUC----------------------------------
AE015451.1/5390009-5390407     GGGGCCGAU--UAGGAUU--CGACGCCGGUAGCGA------A-A-CUCU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA---ACUUUUAUAGUUGCCAAUGACGAAAACUACGGCG-----------------------------------------------------------------------------------------------------------------------------------------------------------------CGGAGUACAAGCUGGCUGC--------------------------------------GUAA------------------------GCAGUCCUCUUGACCCGUUGCUUCUG--------------------------------------GUAGCUUCGGCUCCAGCAAUCAC------------------UAGGGGAU-----GCCUGU-A----AACCCG--AA----------------------------------------------------------------CUGAUUGUCAU----ACAGAACAGGAUC-------------------------------------GUCGCG----UAG---CACGUUGUGG------------------GCGA----AGUGACUAAA-A-----CUUACACAACUC---AUCCAAAGC----ACCCU----GCCC--GUC---G-GG----CGGCUGCGGAUUAAAU--------------------------------------------------CAGUAGACA-CGGC---UA---AGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
AY442269.2/10-369              GGGGCUGAU-UCUGGAUU--CGACAAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGCUAAU-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUG-GCAG-------------------------------------CUUAAUA--------------------ACCUGCGCAGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCAUGC-----CUGU-GU------CCUA----GGGAAU-----------------------------------------------------------CGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUCAAUUCGU----GGCG---UGUCU--CUC---C-GC----AGCGGGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUGCCA--AGGAUGU-------AGUAAUUUUGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
U00089.2/571825-572211         GGGGAUGUA--GAGGUUU--UGACAUAAUGUUGA-------AAG-GAAAACA-GUU--GCAGUGGGGU----AUGCCCCUUA---CAGCUCUA-------------GGUAUA----------AUAACCGACAAAAAUAACGACGAAGUUUUGGUAGAUCCAAUGUUGA------------------------------------------------------------------------------------------------------------------------------UCGCUAACCAACAAGCAAGUAUCAACUACGCUUUCG------------------------------------CUUAGAACA-------------------UACUAAAGCU------------------------------------------------------------------------ACACGAA--------------------UUGAAU----CGCCAUA-G----UUUGG---------------------------------------------------------------------UUCGUGUCACAG-UU-----UAUGGCUC------------------------------------GGGGUUAACU--------GGUUCAA----------------------C----UUAAUCCUUAA---------AUUAUGAACUU-AUCGUUUACUU----GUUU----GUCU-UAUG---A-UCU--AAAGUA-AGCGAGACAUU------------------------------------------------AA--AACAUA-AGAC---UA---AACUGUA----GAAGCUGUUUUACC------AAUCCUUUAUGGA-AACGGGUUCGAUUCCCGU-CAUCUCCACCA
AM942759.1/2050903-2051269     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAGAUAGUCGCAAACGACAAUCAAUAU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCCUAGAGC---------------------------------------------------------------------CUUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAU--------------------------------------------------------AAAGAGGAGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CUAGCUUGGG-------------------GUU---GAAGCGUUAAA-UU-----UAAUCAAGCUA---GCUUA-UUUG---UGGCG---UGUCU--GUC---C-GCA---GCAAG-UAAGUGAAU---------------------------------------------------UUAAAGAC-UAGAC---UA---AGCAUGUA--GUGCCG--CGGAUGU-------AGAAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
ABDU01000062.2/17115-16758     GGGGGCGUU--UUGGCUU--CGACGGGGGUAAG--------AUG-GGUUUGA-UAAG-CGAGUCGAGGG---AAGCAUGGU-----GCCUCGAUAAUA-----AAGUAUGCA----UUAAAGAUAAACGCAGAAGAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUUGCAUUAGCAGC--------------------------------------UUAAUUU------------------AGCGCUGCU--------------------------------------------------------------------------CAUCCUU--------------CCUC--AAUU-------GCCCAC-------GGUU----GAGAG-----------------------------------------------------------UAAGGGUGUCAUUUAA---AAGUGGGGA------------------------------------ACCGAGCCUAGC-------AAAGCUUU--------------------GA-GCUAGGAACGGAAU-UU------AUGAAGCUUA---CCAAAGAGAA-----AGU--UUGUCU--GUG---G-ACG----UUCUCUGAGGGAA-UU------------------------------------------------UUAAAACACA-AGAC---UA---CACUCGUA---GAAAGUCUUACUGG-------UCUGCUUUCGGA-CACGGGUUCGACACCCGU-CGCCUCCA---
AM933173.1/2786912-2787274     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000252.1/1802340-1801985     GGGGGCGUU--ACGGUUU--CGACGGGGAUAGUUG--------A-AGCU-GU-AGAAGCGUACCGAGG-----UUCCUACAG---G-CCUCGUUAAAC-----AGGUAGGAA------AACAAUACUCGCAAACGACUACGAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCAUUAGCCG-------------------------------------CUUAGUC--------------------GGCUAACGUUCUU---------------------------------------------------------------------UCU--GA-------------UUUUU--CCUGUC------GGAUCA---------------------------------------------------------------------------------GAGGGGG--------CGUAAUUUCAGGC------------------------------AGGAUAGUCCUAACCUU------UUCCUGU---------------------GGGGAACAGGGCGAAA-UU----CACAUGGGAUAG---CAAUCAGUAA----AGCC---UGCCU--UUG---G-GC---GUUACAGAGUGCGAAUG-------------------------------------------------ACAAAACAA--AGGA---UA---CGUACGUA---GAAACUGC-AGUGG-------AAUAUUUUCGGA-CGCGGGUUCGACUCCCGC-CGCCUCCACCA
AE015925.1/760011-760435       GGGGGUGU--AUAGGUUU--CGACUUGGAA-----A-----UGA-AGUGUUA-AUUG-CAUGCGGAGGG---CGUUGGCUG-----GCCUCCUAAA--------AAGCCGAC----AAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGUUU---------------------------------------------------------------------------------------------------------------------------------------CUCUGACCUCACCGAGGAAAGAUUAGCUGCUU-------------------------------------AAUUAGCA-------------------A-AAGUUGUUGUCUAGAUAACCU-------------------------------------------------CUAGAUAACC-CGGUG--------------CUCAU--AGACU-----CCACCAGA-----GGUUU----GUGAA------------------------------------------------------------ACACCGUCA------UCUAUCUGGU---------------------------------------UGGAAUCUACCUUCU-CUAAUUCUCAA-------------------GGAGGUUUAUUCGA------G--AUUAUUGAGAGU------CGUUG-GCUUCCAUAG---AUGUUCUUAG---C-UGAGGAAGUUCAAUGUAUGAU------------------------------------------------------UACUAGGGAC----UA---AGCAUGUA--G-AGGUUAGCAGGGAG-----U--UUACUAAGGA-CGAGAGUUCGAGUCUCUC-CACCUCCAUUU
AM039952.1/1753447-1753051     GGGGGUGCA--CUGGUUU--CGACGGGGGUCGCGA------A-G-UCGC--U-UGGCGCAUGCCGAGG----GGGCAGCUU-----UCCUCGUUAAUC-----C-AGCAGCA-----AACUUUUAGUUGCCAACGAUGACAACUA-CGGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------UCGGACUCCGCUAUCGCCG-------------------------------------CUUAAU-----------------------UGGCUUUAGUUGUAGUUCUACAGC------------------------------------------CGCCUAAGGCGAACCCCCGA-A----------CCUA-----CUUGUG-----CCCGUGCU---CGUAGG-------UG--------------------------------------------------------------UAGGGUCAU------UAUCACGGAA------------------------------------CCAUCGGU----AGU---GGCUGCCUGUC-----------------AGCU----ACCGGUCAGA---U---AAAGCAGGCUG----GUUUCCAGGU----GCGCU-UUGCCA--ACC---G-UGC---UGCCUGGAAACGAGAU--------------------------------------------------CUAACGGA--GGGC---UA---AGCAUGUA--GUGCUG---GGGAUG------GAGUGCUUCCGGA-CGGCGGUUCGAUUCCGCC-CACCUCCACCA
AACY023480922.1/1342-1077      ----------------------------------A----------------C-AAUA-CAAGUCGAGA------AUGGGA------AUUUCUCGUUAAA--AUU-UCUCAAAA---AAA-UAAUAAAUGCAAAUAACAUUUUAAAAUUCUUUACCAAGUCUCCGGUAGUAGCAUUCGCUUAGAACCUUUGGUUUCACAUUAGUCUAAUCUUAAUCU-----------------------------AAUAUGAAAAUAUUUAAGAUGCAGCUAAAAAAUAAAUUUAGCUAAGAACCCUACGCAAUCAAAUGUAUGUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAACAGAACUUGG------AAUACUAUUGACUAAUAUA-AUCUAAUUGGA-CGUGG------------G-----------U
CP000437.1/22848-22428         GGGGGCGAA-UAUGGUUU--CGACAUGAAUGUCAA------A-A-UCUA----AGGUGCAUGCCGAGG----AAGUACCGU----AACCUCGUUAAUA-----A-CAGUACAAAUGCCAAUAAUAACUGGCAACAAAAAAGCAAACCGCGUAGCGGCUAACG------------------------------------------------------------------------------------------------------------------------------------------ACAGCAACUUUGCUGCUGUUGCUAAAGCUG-------------------------------------CCUAG----------------------UCUAGCUUAAUAACCUA-------------------------------------------------------------GAUGCGCACGGA----------UAUGA----UAGUCU----UUCUUAUGA----CACUAUC-UAUACAU-----------------------------------------------------------CCGUUCAUAUU-----CCGCAUAAGA---------------------------------------CGGUCU--UUGCU---UUUUGUCUGG------------------GAGUU-A-AGGCUGUAU--------UUAACAGACUC----GCUA-ACUAUU--ACCCU---GGCUA--AUU---G-GGG---AAUAGUCAAGCUAAAC-------------------------------------------------UCAAAUAGAU-UAGC--CUA---AGCAUGUA--GAUCCA---AAGAUC------UAGAGUUUGUGGA-CGCGGGUUCAAAUCCCGC-CGCCUCCACCA
AF440342.1/1-322               ----------------------ACAGGGAUAGUU--------CG-AGCUUGA-GUUG-CGAGUCGGGG-----GGAUCGU-------CCUCGUUAUUAA---CGUCAAAGCC------AAUAAUAACUGGCAAAGAAAAACAAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUAGCUUUCGCUGC--------------------------------------CUAAUAA------------------GCAGUAGCAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------GCCCAU-------GUGC----UACGG-----------------------------------------------------------UAAGGGUCUCAC----UUUAAGUGGGCUAC---------------------------------ACUAAAUAAUC----U---CCGUCUGG--------------------------GGUUAGUUAGAA-GAG--CU-UAAUCAGACU--AGC-UGAAUGG---AAGCC---UGUUACCG-----G-GCU---GAUGUUUAUGCGAAAU-------------------------------------------------GC-UAAUACGGUGAC---UA---CGCUCGUA---GAUAUUUAAGUGC-------CGAUAUUUCUGG--------------------------------
BA000008.3/138204-137782       GGGGGUGU--AUAGGUUU--CGACUUGAAA-----A-----UGA-AGUGUUA-AUUG-CAUGCGGAGGG---CGUUGGCUG-----GCCUCCUAAA--------AAGCCAAC----AAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUUAGCUU---------------------------------------------------------------------------------------------------------------------------------------GUUUGACUCAGUAGAGGAAAGACUAGCUGCUU-------------------------------------AAUUAGCA-------------------A-AAGUUGUUAGCUAGAUAAUCU-------------------------------------------------CUAGGUAACC-CGGUA--------------UCUGC--GAGCU-----CCACCAGA-----GGCUU----GCAAA------------------------------------------------------------AUACCGUCA------UUUAUCUGGU---------------------------------------UGGAACUUACUUUCU-CUAAUUCUCAA-------------------GGAAGUUCGUUCGA------G--AUUUUUGAGAGU------CAUUG-GCUGCUAUAG---AGGCUUCUAG---C-UAAGGGAGUCCAAUGUAAACA---------------------------------------------------A--UUCUAGAAGA----UA---AGCAUGUA--G-AGGUUAGCAGGGAG-----U--UUGUCAAGGA-CGAGAGUUCGAGUCUCUC-CACCUCCA---
AF440336.1/1-322               ----------------------ACAGGGAUAGGU--------CG-AGCUUGA-GUUG-CGAGCCGGGG-----GGAUCGG--------CCCGUCAUCAA---CGUCAAAGCC------AAUAAUAACUGGCAAACAAAACAACAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUAGCUUUCGCUGC--------------------------------------CUAAUAG------------------CAGUCUGAAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------ACCCAU-------GUGC----UACGG-----------------------------------------------------------UAAGGGUCUCAC---UUUUAAGUGGGUUAC---------------------------------GCUGGCUUAUC----U---CCGUCUGG--------------------------GGCAAACGAGAA-GAG--CA-UAAUCAGACU--AGC-UAGAUAG---AGCCC---UGACGCCG-----G-GCA---GACAUCUAUGCGAAAU-------------------------------------------------CC-AAAUACGGCAAC---UA---CGCUCGUA---GAUGCUCAAGUGC-------CGAUAUUUCUGG--------------------------------
ABYE01000001.1/21079-20663     GGGGGUGU--AAAGGUUU--CGACUUAGAA-----A-----UGA-AGCGUUA-AUUG-CAUGCGGAGGG---CGUUGGCUG-----GCCUCCUAAA--------AAGCCGAC----AAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGCUU---------------------------------------------------------------------------------------------------------------------------------------CGCUGAUCUCGAAGAUCUAAGAGUAGCUGCUU-------------------------------------AAUUAGC--------------------A-AAGUUGUUACCUAAAUAC------------------------------------------------------GGGUGACC-CGGUG--------------UUCGC--GAGCU-----CCACCAGA-----GGUUU----UCGAA------------------------------------------------------------ACACCGUCA------UGUAUCUGGU---------------------------------------UAGAACUUAGGUCCU-UUAAUUCUCGA-------------------GGAAAUGAGUUUGA------AA-UUUAAUGAGAGU------CGUUA-GUCUCUAUAG---GGGUUUCUAG---C-UGAGGAGACAUAACGUAUAGU---------------------------------------------------A---CCUAGGAAC----UA---AGCAUGUA--G-AGGUUAGCGGGGAG-----U--UUACUAAGGA-CGAGAGUUCGACUCUCUC-CACCUCCA---
AY911522.1/1-341               ------------------------GCCGGUAGCGA------A-A-CUCU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA--ACUUUCUAUAGUUGCCAAUGACGAAACCUACGGCGAG--------------------------------------------------------------------------------------------------------------------------------------------------------------GAAACCUACGCUCUCGCAGC--------------------------------------GUAA------------------------GUGACCUUUGCUUCUGGUAGC------------------------------------------------UUCGGCUCCAGCAAUCAC------------------UAGGGGAU-----GCCUGU-A----AACCCG--AA----------------------------------------------------------------CUGAUUGUCAU----ACAGAACAGGAUC-------------------------------------GUCGCG----UAG---CACGUUGUGG------------------GCGA----AGUGACUAAA-A-----CUUACACAACUC---AUCCAAAGC----ACCCU----GCCC--GUC---G-GG----CGGCUGCGGAUUAAAU--------------------------------------------------CAGUAGACA-CGGC---UA---CGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGC----------------------------------
AL583919.1/121055-121420       GGGGCUGA---AAGGUUU--CGACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGUUGCAGC-------AAUAUAAGCGCCGAUUCAUAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUAUGCUCUCGC--------------------------------------UGCCUA---------------------AGCGAUGGCUAGU-------------------------------------------------------------------CUGUCAG--------------------ACCGGGAA---CGCCCUCGU----CCCGGA--GC-----------------------------------------------------------------CUGGCAUCAG------CUAGAGGGAU-C--------------------------------UACCGAUGGGUU---------CGGUCGC----------------------G-G-GACUCGUCGGGA-CAC---CAACCGCGACUG---GGAUCGU--CAUCCUGGC--UAGUUCGCGUG---A-UCAGGA------GAUCCGAGUAGA----------------------------------------------GGC----AUAGCGAAC---UA---CGCACGGA----GAAGCCUUGAGGGA-----AAUGC-CGUAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCA---
CP000117.1/3231376-3230987     GGGUCCGU--AACGGUUU--CGACAGGUUGGCGAAC-----GCU-ACUCUGU-GAUU-CAGGUCGAGA----G-UGAGUC-U---CCUCUCGCAAAUC-----AAGGCUCAAA---ACAAAAGUAAAUGCGAAUAACAUC------GUAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------AUUUGCUCGUAAGGACGCU-------------------------------------CUAG------------------------UAGCUGCCUAAUUAGCCUCUUA------------------------------------------------CAGGUUCGAGC-------------------GUCUUC--GGUUUG----ACUCCGUUA---AGGACU----GAAGACC---------------------------------------------------------A--ACCCCC-----------AACGGAUG-----------------------------------CUCUAGCAAGUGUU------CUCUGGU------------------------UGGCUUGCUAGCUA-AG----AUUUAAUCAGAG--C---------------------------------------------------------AUCCUACGUUCGGGAUAAUGAACGA--UUCCCGCCUUGAGGGUCAGAAAGGC----------------UA---AACCUGU----GAAUGAGCGGGGGGUC--AAUACCCAAUUUGGA-CAGCAGUUCGACUCUGCU-CGGAUCCACUA
CU928145.2/2978730-2979092     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000285.1/3454289-3454668     GGGGGCG-A-CAUGGCUU--CGACGCCGGUGACAA--------U-CCCUG---AGGUGCAUGCCGAGA----GCGUAACGU-----AUCUCGUAAAUC----CAACGUUACG-----AUUAAAUAGUCGCAAACGACGACAACUACGCU--------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGG-CGCGCUGGCAG-------------------------------------CGUAA--C-------------------AACUGCUAG-------------------------------------------------------------------------CUUCUAGUCC-------GGCCCGG-AGGUGAUGU---GCCCAUU-C----AUCACC---GAUGGG-----------------------------------------------------------AUACGAGCUCA-----GACUGAUGGGA------------------------------------UCGCGGU----UGGC---CCUGUCCUCG------------------UGUC--A--GCCGCUAAA-AC-----UUAGAGGAAUC---GCGUCGCUGG----AUCC---UGCCC--GUC---G-GA----GCCAGGGACGUUAAAU--------------------------------------------------CAGAAGAC--GGAC--CUA---AGCAUGUA--GAGCCG--AUGGGUG-------AGUGCCGGCGGA-CGGGGGUUCAAUUCCCCC-CGCCUCCACCA
BA000022.2/3317157-3316759     GGGGCCGC--AAUGGUUU--CGACAGGUUGGCGAAA-----GCU-UGCCCGU-GAUA-CAGGUCGAGA----G-UGAGUC-U---CCUCUCGCAAAUC----AAAGGCUCAA----AAAAAAGUAACUGCGAAUAACAUC------GUCAG----------------------------------------------------------------------------------------------------------------------------------------------------------------CUUCAAACGGGUAGCCAUA-------------------------------------GCAG------------------------CCUAGUCUGUAAAAGCUACAUUUUCU----------------------------------------UGUCAAAGACCGUUU-------------------ACUUCU--UUUCUG----ACUCCGUUA---AGGAUU----AGAGGU----------------------------------------------------------U--AACCCC-----------AACGGAUG-----------------------------------CUUUGUUUGGCUCUU-----CUCUAGU------------------------UAGCUAAACAAUCA-AGA---CUCAGACUAGAG--C---------------------------------------------------------AUCCCACCAUCAGGGAUAAUCGAUG--GUCCCCGUCCUAGGGCUAGAAGGAC----------------UA---AACCUGU----GAAUGAGCGGAAAGUU--AAUACCCAGUUUGGA-CAGCAGUUCAAUUCUGCU-CGGCUCCAUUU
AF389983.1/18-335              --------G-------------ACGGGACACUCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAU-------AAACCGCA------AAAAAUAGUCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCGGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUAU-GUC----CUAG------GGGAU-----------------------------------------------------------UGGAAGGUCAU---CUUUCAU-AGGAUC-------------------------------------GCGUGG---AAGC---CUUGUCUGGG-------------------GUG---GAAGCGUUAAA-AC-----UAAUCAGACUA---GUUAUUCAGU----GGCG---UGUCG--GUC---C-GC----AGCUGGGUGGCGAAU---------------------------------------------------GUAAAGAU-UCGAC---UA---AGCAUGUA--GUACUG--AGGAUGU-------AGGUUUUUCGGA-CGCG-------------------------G
Y15063.1/86-434                GGGGGUGA--AACGGUCU--CGACGGGGGUCG---C-----CGA-GGGCGUG-GCUG-CGCGCCGAGG----UGCGGGUG------GCCUCGUAAAA---------ACCCGC----AACGGCAUAACUGCCAACACCAACUAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUCGCGGC--------------------------------------UUAAUG----------------------ACCGCGA--------------------------------------------------------------------------CCUCG--------------CCCGG--UAGCCC----UGCCGGG------GGCUCA---CCGGA-----------------------------------------------------------AGCGGGGACAC-------AAACCCGGC--------------------------------------UAGCCCGGGGCCA-----CGCCCUC----------------------UAACCCCGGGC-------GAAGCUUGAAGGGGGC-----UCGCUCCUGG--CCGCC----CGUCCGCG----G-GCCAAGCCAGGAGGACACGCG---------------------------------------------------A---AACGCGGAC----UA---CGCGCGUA--G-AGGCC-CGCCGUAG-----A--GACCUUCGGA-CGGGGGUUCGACUCCCCC-CACCUCCACCA
CP000016.1/678009-678400       GGGGCUGAU-UUUGGAUU--CGACGGAGUAUCUUG------U-U-AUUUA---AAGUGCAUGCCGAGG-----UGAGGCAG-----GCCUCGUAAA--------AAGCCUCA------AAAGAUAAAUGCAAAUAAUACUACAUAUAGA-------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAUCU--GUUGCUUUAGC----------------------------------AGCUUAAAUC------------------AGACUAAUAUUCUGAAG--------------------------------------------------------------GUUCCCUCUCG------------UUUCA---AUAUUU-----ACUCUUA-----GAUAU-----UAAAAAAU----------------------------------------------------AAAUAGAGAGGCCAUA--UAAAUAA-GAGUGC-------------------------------------GCGUAA----AUG---CUUGCUUUUG------------------GCU-----UAACGUUAAG-UA-----UA-AAAAGCUA---GUUGGUUAGU----GAUU----GGUC-UUGA---U-AUA---UCUACGCCAAUUAAAU--------------------------------------------------GUAAUUCA-AGACC---UA---AGCAUGUAGGUUACUA--AAAAUAA------AAAGAAUUCUGGA-CGCGGGUUCGAACCCCGC-CAGCUCCACCA
AF389965.1/19-342              --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG------GCGGUUG-----GCCUCGUAAA--------AAGCCGCAA--AAAAAAUAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCUGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AGGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-UC-----UAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCU--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGC--------------G-----------G
CP000538.1/1278617-1278259     GGGAGCGAC--UUGGCUU--CGACAGGAGUAAGUC--------U-GCU-UAG-AUGG-CAUGUCGCUU-----UGGGCA--------AAGCGUAAAA------A---GCCCAA---AUAAAAUUAAACGCAAACAACGUUAAAUUCGCUC------------------------------------------------------------------------------------------------------------------------------------------------------------------CUGCUUACGCUAAAGCUG-------------------------------------CGUAAGU--------------------U-CAGUUG-AGC----------------------------------------------------------------------CUGAAAU-------------UUAAG--UC---------AUACUAU-----CUAG-----CUUAA------------------------------------------------------------UUUUCGGUCAUU--U-UUGAUAGUGUA------------------------------------GCCUU-GCGUU-----------UGAC----------------------A-A-GCGUUGAGGUGA-AA-----UAAAGUCUUA----GCCUUGCUUUU-GAGUUU--UGGAAG-AUGA---G-CG------AAGUAGGGUGAAG---------------------------------------------------U--AGUCAU-CUUUG-CUA---AGCAUGUA---GAGGUCUU-UGUGG------GAUUAUUUUUGGA-CAGGGGUUCGAUUCCCCU-CGCUUCCACCA
AE017221.1/336629-336977       GGGGGUGA--AACGGUCU--CGACGGGGGUCG---C-----CGA-GGGCGUG-GCUG-CGCGCCGAGG----UGCGGGUG------GCCUCGUAAAA---------ACCCGC----AACGGCAUAACUGCCAACACCAACUAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUCGCGGC--------------------------------------UUAAUG----------------------ACCGCGA--------------------------------------------------------------------------CCUCG--------------CCCGG--UAGCCC----UGCCGGG------GGCUCA---CCGGA-----------------------------------------------------------AGCGGGGACAC-------AAACCCGGC--------------------------------------UAGCCCGGGGCCA-----CGCCCUC----------------------UAACCCCGGGC-------GAAGCUUGAAGGGGGC-----UCGCUCCUGG--CCGCC----CGUCCGCG----G-GCCAAGCCAGGAGGACACGCG---------------------------------------------------A---AACGCGGAC----UA---CGCGCGUA--G-AGGCC-CGCCGUAG-----G--GACCUUCGGA-CGGGGGUUCGACUCCCCC-CACCUCCACCA
CP000249.1/937591-937964       GGGGGUGA---CCGGCUU--CGACUCCGGACGU--------CGA-GGCAGGG-GAAG-CGGGCCGAGG-----AUGAGCG-G--UUAUCUCGUUAACG----AUCCGUUCAG------AACAACAGCUGCCAACAAGACGCAGCCCAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------UACCCCCACUUACGCG--------------------------------------CUCGC-----------------------CGCUUAAGAGGGACUA----------------------------------------------------------GGUAGUCGUCAG--------------------CCUGGGAG---AGCCUCCGG----CCCAGA--AU-----------------------------------------------------------------CUGACGUCGC------UAGGAGGAUC-----------------------------------ACCGGCUGACC---------UGGUCGC----------------------G-G-GGUCGGUCGGGA-CAU--CAAACAGCGACUG---AGCCUA----U-GUCGGC--UUGCCUGCGUG---U-CCGACG------AGGCUGAGAAA-----------------------------------------------CAA----GUAGCAGGA---UG---CGCCCGGA----GAAGCCCUGUGUC-------GGGGCCGGAGGA-CGCGGGUUCGAUUCCCGC-CACCUCCACAA
AAAA02039738.1/1593-1956       GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-GCCCU---AGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------CCCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGU---CCUGCCUGGG-------------------GCU---GAAGCGUUAAA-CU-----CAAUCAGGCUA---GUCUG-UCAG---UAGCG---UGUCC--AUC---C-GCA---GCUGG-CCGGCGAAU---------------------------------------------------GUAAAGAU-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
CP001175.1/161039-161408       GGGGAUGUU--ACGGAUU--CGACAGGGAUAGUU--------CG-AGCUUGA-GUUG-CGAGUCGGGG-----GGAUCGU-------CCUCGUUAUCAA---CGUCAAAGCC------AAUAAUAACUGGCAAAGAAAAACAAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUAGCUUUCGCUGC--------------------------------------CUAAUAA------------------GCAGUAGCAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------GCCCAU-------GUGC----UACGG-----------------------------------------------------------UAAGGGUCUCAC----UCUAAGUGGGCUAC---------------------------------ACUAGUUAAUC----U---CCGUCUGG--------------------------GGUUAAAUAGAA-GAG--CU-UAAUCAGACU--AGC-UGAAUGG---AAGCC---UGUUACCG-----G-GCC---GAUGUUUAUGCGAAAU-------------------------------------------------GC-UAAUACGGUGAC---UA---CGCUCGUA---GAUAUUUAAGUGC-------CGAUAUUUCUGGA-CGUGGGUUCGACUCCCAC-CAUCUCCAUAU
CP000419.1/583008-583357       GGGGCCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCAUAU-UCUG-CGACUCGUG------UGGCG-----------ACGUUA-----------ACGCUCA--GUUAAAUAUAACUGCAAAAAAUACUAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUGUAGCAGC--------------------------------------CUAAAC---------------------ACCUGCUCGCGU---------------------------------------------------------------------GACUUC--------------UAGC---AGAUU------GCUUAU-------GUUU-----GUU------------------------------------------------------------UAGAGGUUUUAU---UGAUUUAUAAGCUAC---------------------------------GUUCGAUCA------U----UGCCUAG---------------------------CUGGUCGAAAA-GAG---A-UUUAUAGGCU--CGCAUAUAGA-----AGGCU-UGAGUUAUGU----G-UC-----GUCUAUCUGUUAAAU--------------------------------------------------G-AAAGACAUAACC---UA---UGGUCGUA---GACGAAUAUGUUG-------GCAGAUGCUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUAA
CP000820.1/7030866-7030492     GGGGGUGA---CCGGCUU--CGACUCCGGACGU--------CGA-GGCAGGG-GAAG-CGGGCCGAGG-----AUGAGCG-G--UUAUCUCGUUAACG----AUCCGUUCAG------AACAACAGCUGCCACUAAGACGCAGCCUGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------UAGCUCCACUUUCGCC--------------------------------------CUCGC-----------------------GGCCUGAGUAGAGACCA---------------------------------------------------------ACUAGCCGUCAG--------------------CCUGGGAG---UUCCUCCGG----CCCAGG--AU-----------------------------------------------------------------CUGGCGUCGA------CAGGAGGAUC-----------------------------------ACCGUCCCACC---------CGGUCGC----------------------G-G-GGUAGGUCGGGA-AAU--CUAACAGCGACUG---AGCCUG----C-GCCGGC--UUGCCUGCGGG---A-CCGGCG------GGGCUGAGAAA-----------------------------------------------AAA----CAAGCAGGC---UG---CGCCCGGA----GAAGCCCUGUGUC-------GGGGCCGGAGGA-CGCGGGUUCGAUUCCCGC-CACCUCCACCA
BA000018.3/843797-844158       GGGGACGUU-CAUGGAUU--CGACAGGGGUCCCC--------CG-AGCUCAU-UAAG-CGUGUCGGAG-----GGUUGG--------CUUCGUCAUCAA--CACACACAGUU------UAUAAUAACUGGCAAAUCAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------CUAAUC----------------------GCA-CUCUGC----------------------------------------------------------------------AUCGCC-------------UAACA---GCAUU------UCCUAU-------GUGC-----UGUUA-----------------------------------------------------------ACGCGAUUCAA----CCUUAAUAGGAUAU---------------------------------GCUAAACACUG----C----CGUUUGA------------------------A-GUCUGUUUAGAA-GAAA-CU-UAAUCAAGCU--AGCAUCAUGUU-----GGU---UGUUUAUC-----A-CUU----UUCAUGAUGCGAAA---------------------------------------------------C-CUUUCGAUAAAC---UA---CACACGUA---GAAAGAUGUGUAU-------CAGGACCUCUGGA-CGCGGGUUCAAAUCCCGC-CGUCUCCAUAU
AE017194.1/4827856-4827502     GGGGACGUU--ACGGAUU--CGACAGGGAUAGUU--------CG-AGCUUAG-GUUG-CGAGUCGAGG-----GGAUCG-------GCCUCGUUAA---------AACGUCA----AAGCCUAUAAUUGGCAAACAAAACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUUUCUUUAGCUGC--------------------------------------UUAAUU----------------------GCACUAAAG-----------------------------------------------------------------------GUUCCU--------------CCCU---CCAUC------GUCCAU-------GUGG----UAGGG-----------------------------------------------------------UAAGGGACUCAA----ACUAAGUGGACUAC---------------------------------GCCGGAGUUCG----C----CGUCUGA---------------------------GGACAAAGGAA-GAG--AA-CAACCAGACU--AGC-AACUUGG---AAGCC---UGUCGAUA-----G-GCU---GAAGAGUUUGCGAAAUG------------------------------------------------CU--AAUAUAUCGAC---UA---CACUCGUA---GAAGCUUAAGUGCC-------GAUAUUUUUGGA-CGUGGGUUCGACUCCCAC-CGUCUCCACCA
CP000112.1/1988490-1988131     GGGGGCGCA--CUGGUUU--CGACGGGGAUAAAGA-------AG-CCG--GA-GUGG-CAGGUCGAGG----CGCCGCUGG------CCUCGUUAA---------AAGCGGC----ACAAAUGUAAUUGCCAACAACGAUUAC---GAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCAAUGGC-AGCCU----------------------------------------AAUU----------------------AGGCUUGCCG----------------------------------------------------------------------CACUG--------------AUUGGC-U-GACG------UCAGAUA-----C--------GCCGA-------------------------------------------------------------CCAGUGAC-----AAACUUAUCCGAC-------------------------------------UGGCACCCAAAGC------CGUCUGU--------------------CGCAGCGGGUGUAAGAU-UUU---UUAAGACAGACU---UGCCGCCGGU----AGCC---CGAUC--AGG---G-GC-AUCACCGGAUGGCGAGC-U-------------------------------------------------UGAAUACCU--GAUC---UA---AACCUGUA---GAAGCUUC-GAGUG------GACUGUUCUCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
CP000284.1/1198789-1199149     GGGGCCGAC--CAGGUUU--CGACGUGGGUUGCAA-------AG-CAGC-GC-AGGG-CAUACCGAGG-----CCUAGUCA------CCUCGUAAAU-------AAACUAGA----ACAAGUAUAGUCGCAAACGACGAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUCUAGCCG-------------------------------------CUUAAUC---------------------CCGGCUGGA------------------------------------------------------------------------CGCUGCA------------CCGGAA------------GGCCUCUC--------------GGCCGGGCGGGU-----------------------------------------------AACCGCAGCAGCGUC-----AUUUAGAGAGGAUC-----------------------------------GUGUUGUAUU---------GGGUUACU---------------------U---AAUACAACAUUA-AAU---CCAAGGUAACUC---GCCUGCUGUU----CGCU---UGCUC--GUU---G-GUG---GGCAU-CAGGUUAAAU--------------------------------------------------CAAACAACA-CAGC---UA---AGUAUGUA---GAACUG--UCUGUG------GAGGGCUUGCGGA-CGGGGGUUCGAUUCCCCC-CGGCUCCACCA
AF400065.1/3312-3681           GGGGCCGUU--ACGGAUU--CGACAUGUGUAG---------GUG-AGCGUGA-AUUG-CACUUCGUAG-----GUUACGU-------CUGCGUUAAC-------AACGUUACA--GUUAAUUAUAACUGCAAACAAUAACAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUGUAGCUGC--------------------------------------CUAAACA------------------CCAGCA-UAGCG----------------------------------------------------------------------UGAUCCG--------------UCUG---ACUUC------ACCCAA-------GGGU-----UAGAU----------------------------------------------------------CCGGGUCUCAAA-----UUAAUUGGGUUAC---------------------------------GUUAAAUGCCG----C----CGUUUGA---------------------------AGUGUUUAAAA-GAG---A-UUUUCAAGCU--AGUUAGUCCAUC-CGAGCCU-CUGUUGAAC-----G-GCG--UUUUGGGCUAGCGAAUUU------------------------------------------------CU-AAAUAGUUCGAC---UA---UGAGUGUA---GAGAUUGACGUGG-------CAAUGCGCAUGGA-CGCGGGUUCAACCCCCGC-CGGCUCCAUUG
ABIZ01000001.1/2235966-2236321 GGGGGCGU--UCUGGUUU--CGACGGAUUGCU---------AGA-AGUGGAG-GCUG-CAUGCCGCGGA---UGAUUCGUU----GGCCGCGUUACCA-----AUUCGGAUCA---AACAAACUAAAUGCGAACUCUAACGAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUGCCCUCG-------------------------------------CCGCUUAA-------------------U-UGACGGUGA------------------------------------------------------------------------CGUU----------------CCUC--CAGUGA-----AGUCUGUG----AAUUG----GAGG---------------------------------------------------------------GGCGACU------ACUUACAGGCU---------------------------------------GGCCAAAAGAGC-----GGGCGACC--------------------GGCU-CCGAGGCGA------GAUCUACAGGCCGCU-------GGGUGGACGGUAUCC----UGGCAGUAG-----GAGACUGGACAUCGAGAUCAA-------------------------------------------------------AUUAUUGCC----UG---AGCAUGGA--GACGCUUU-CAUGGA------A-GGUGGUUCGGA-CAGGGGUUCAACUCCCCU-CGCCUCCACCA
AE009952.1/3388875-3389238     GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUG------GCCUCGUAAA--------AAACCGCA----AAAAAAAUAGUUGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAGCUC----------------------------------G---UGUGG---AAAC---CUUGCCUGGG-------------------GUG---GAAGCAUUAAA-AC-----UAAUCAGGAUA---GUUUG-UCAG---UAGCG---UGUCC--AUC---C-GCA---GCUGG-CCGGCGAAU---------------------------------------------------GUAAUGAU-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
CP000151.1/1084016-1083647     GGGGGCGAC--CUGGUUU--CGACAGGGGUUGUGA-------AG-CGG--CU-AGGG-CAUGUCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AAAUCGUAACUGCAAACGACGAUACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUGGCAGCC---------------------------------------UAAC-----------------------GGCCGCCGU-----------------------------------------------------------------------CCUCUGC------------CUAGUU-C-----------ACUGACG--------------GGCUAGUGUCGCAAGACCG---------------------------------GUAGCAAUACCGC-CAGAGGUC-----AUUUACGUCAGUUA----------------------------------AGCCCUGUCGGC-----------GUCGC--------------------GA----CGCCAGGGUCG-AAA--ACCUAGCGAAUCG----CCGUAGUGC----AGCG---UGUUC--GUC---C-GCG----UCGCUGCGGUUAAAU--------------------------------------------------CAAAUGACU-GAAC---UA---AACAUGUA---GAACUAG--UCGUG------GAGCGCUUCUGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
AE017198.1/812877-813243       GGGGAUGUU-UUGGGAUU--CGACAGGCGUAG---------AUU-CGCGUUG-ACUG-CGAUUCGUAG-----GUCACGU-------CUACGUUAAA-------AACGUCACAG-UUAAAUUAUAACUGCAAAUAACGAAAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAGUAGCUGC--------------------------------------UUAGUC-----------------------AGCCUGCG----------------------------------------------------------------------UGAUCCAA-------------AGAU---GGAUU------GCUCGU-------GUCU-----AUC------------------------------------------------------------UACGGGUCUUAC---CAUUUAACGAGCUAC---------------------------------GUUUAACUACU----U----ACCUUAA---------------------------UAGUUAGAAAU-AAG---A-UUCUUAGGUU--AGUUUUGAUAGU-UUAGCC--CUGUUAUAU-----G-GCG--UUUUAUCAAAGCGAAUU-------------------------------------------------UU-AAGUAAUAUAAC---UA---UGAUCGUA---GAUGUUAACGACG-------AAAUACGUUUGGA-CAGGGGUUCAAUUCCCCU-CAUCUCCAUAG
AF375587.1/1-302               ---------------------------GGUUCCA--------UG-AGCUAGU-UAAG-CGUGUCGGAG-----GGUUGU--------CUUCGUCACCAA--CACACACAGUU-------AUAAUAACUGGCAAAGAAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------GUAAUA----------------------GCA-CUCUGC----------------------------------------------------------------------AUCGCC-------------UAACG---GUAUC------UCCUAU-------GUAC-----CGUUA-----------------------------------------------------------ACGCGAUUCAA---CCUAUAGUAGGAUAC---------------------------------GCUAGGCACUG----C----CGUUUGA------------------------A-GUCUGCCUAGAA-GAG--AU-UAAUCAAACU--AGCAUAAUGAC-----GGA---UGUCUAUC-----A-CCU----CCCAUUAUGCGAAA---------------------------------------------------C-CUAUUGAUAGAC---UA---CGCACGUA---GAAGUGCUAGUAU-------CAGAACC-------------------------------------
CP000232.1/284252-284609       GGGGGCGUA--AUGGUUU--CGACGGGGGUAGC--------AUU-GGCAGUA-GUAG-CCAGGCGAGAU---C-CCACCG-------GCUCGUUAA--------ACGGUGGAA---CGGCUAUUAAGUGCCGACGAUAAUUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCUCUGGCUGCUUA-----------------------------------------AU-U-------------------AAAAAGUAGCC-----------------------------------------------------------------------CAUCCG---------------UCUG--GUCCU------GGCCUGCG----GGGAC----CAGUA------------------------------------------------------------CCGGGUGUCAAA-UC--UAGCAGGCU-------------------------------------ACCGGCAAGGCCCC------GGCCCG----------------------GGGGCC-UGAAGGGAA-UCU---C-AAGCGGGCUG--GCCCGAGGGU------AUC--CGGUUU--CCG---G-GA----GACCCGACGGCGAGAU-------------------------------------------------UGAAAACGG--AAAC---UA---UCCUGGUA---GAAGCUACUGUGGA-------UGUACCUUCGGA-CGGGGGUUCGACUCCCCC-CGCCUCCACCA
CP000033.3/728512-728880       GGGGAUGUU-UUGGGAUU--CGACAGGCGUAG---------ACC-CGCAUUG-ACUG-CGAUUCGUAG-----GUUACGU-------CUACGUAAA--------AACGUUACA--GUUAAAUAUAACUGCAAAUAACAAAAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAUUAGCUGC--------------------------------------UUAAU-U-------------------UAGCGCAUGCG----------------------------------------------------------------------UUGCUCUU-------------GACC---AGUUU------ACUCGU-------GACU-----GGUU-----------------------------------------------------------UUCGAGUAUCAA----CUUUAGCGAGUUAC---------------------------------GUUUAACUACC----U----CACCUGA---------------------------AUAGUUAAAAA-GAG--UC-UUAACAGGUU--AGCUGGUUCAUA-CUAGCC--CUGUUAUAU-----G-GCG--UUUUGAACUAGUGAAGU-------------------------------------------------UU-AAGUAAUAUAAC---UA---UGAUCGUA---GAGGUUAAUGACG-------AGAUGCGUUUGGA-CAGGGGUUCAAUUCCCCU-CAUCUCCAUAG
AF375578.1/1-295               ---------------------------UGUUG---------UCG-CGUAUGA-GCUG-CGAUUAGUG------CGGCGC---------CACUCUA---------AACCGCCGCA-GAUAAAUAUAACUGCUAAAAAUACACAAAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAGUAGCUGC--------------------------------------CUAAAC---------------------CACAGCCUGCGU---------------------------------------------------------------------GCCUGA--------------CUUU---CGCUC------GCCUAU-------GGCG-----AUU------------------------------------------------------------UGAUGGCCUAA------UUUAGUAGGAUAC---------------------------------GAUUUGACG------G----UGUCUUG---------------------------ACGUCAGAGAA-GAG---A-UUAAGAGACU--CGCAAGUUAAC---UUUGUU-CGAGGAUUGU----C-UC-----GUUAGCUUGUUAAAU-------------------------------------------------UU---AGACAGUCCC---UA---UGAUUGUA---GACGCUGAUAUAG-------CAAGGCA-------------------------------------
CP000352.1/785856-785497       GGGGCCGAC--CUGGUUU--CGACGUGGGUUACAA-------AG-CAGU-GG-AGGG-CAUACCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AUGCAAUAACUGCUAACGACGAACGU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCACUGGCAGCC---------------------------------------UAAG-----------------------GGCCGCCGU-----------------------------------------------------------------------CCUCGCA------------CUGGCU-C-----------GCUGACG--------------GGCUAGGGUUCGC--------------------------------------------AAGAACCA-GCGAGGUC-----AUUUACGUCAGAUA----------------------------------AGCUUCGGGA--------------GUGU--------------------CA-CGGGCCCGAGGACG-AAA--ACCUAGUGACUCG----CCGUCGUAG----AGCG---UGUUC--GUC---C-GCG----AUGCGCCGGUUAAAU--------------------------------------------------CAAAUGACA-GAAC---UA---AGUAUGUA---GAACUCU--CUGUG------GAGGGCUUGCGGA-CGCGGGUUCGAUUCCCGC-CGGCUCCACCA
CP001147.1/1166175-1165826     GGGGGCGA---AAGGACU--CGACGGAGGUA----G-----UGA-GGGCUAA-GCUG-CAUGCCGUGG----UUCCUGCC------ACCACGUAAAA------CAGGUAGGG-----AAAACACAACUGCCAACAACGAAUUG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUCGCUGCUU-------------------------------------AAUUAA-----------------------AAGCAGC--------------------------------------------------------------------------CGUCU--------------UCCCA--AGUUCU-----GCUCUGA-----GGCUU----GGGCA-------------------------------------------------------------AGGCGUCA------UAAAUCAGAGC---------------------------------------UAUCCUAAGGCAC----AAACCCGA---------------------UGCCUUAGGGA--------G---AGCUAAGGGUU----GUAGGAGCUUAGAGAGCC----UGUGGAAG----G-GCGAGCUAACUUCCGAAUCCUA--------------------------------------------------A---AACUUCCAC----UA---AGCAUGUA--G-AUGCUUAGAAGUA------G--CACCUUCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
CP001229.1/18285-18635         GGGGGCGA--UACGGGUU--CGACGGCAAGAGC--------AGG-CA-AAGG-GAAG-CAUGCCGUAG-----AAGGCC-------ACUACGUAAAA---------AACCAA-------AACAAAACAAUUCCCGAACGCGAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUCGCUCUCGCUGCU-----------------------------------UAAUUAAC----------------------GCAGCGA--------------------------------------------------------------------------CGUCC--------------UACCC---GGUUU----GCCUGUA------GGCU-----GGGAUA------------------------------------------------------------GGGCGUAAG-------ACAUACAGG-------------------------------------AUAGGAGGUUGCCAA----CCUCCCCU--------------------GAGGUAACCUCC-------GAAACUCUACGGGGAUA------GCUU-CUC-UCCUCC----UGCCUGUG----G-GAAA-GAGAGAAGC-GAAACUC--------------------------------------------------A---AACACAGGC----UA---AGCAUGUA--G-AUGCCCUACUGCUU----AGGCUCUUGUCGGA-CGGGGGUUCGAUUCCCCC-CGCCUCCACUC
CP000325.1/2679105-2678738     GGGGCUGA---ACGGUUU--CGACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGAUGCAAC-------UAGAUAAGCGCCGAUUCACAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGACGGCUAGU-------------------------------------------------------------------CUGUCGG--------------------ACCGGGAA---CGCCCUCGC----CCCGGA--CC-----------------------------------------------------------------CCGGCAUCAG------CUAGAGGGAU-C--------------------------------AACCGAUGAGUU---------CGGUCGC----------------------G-G-GGCUCAUCGGGA-CAU---CAACAGCGACUG---GGAUCGU--CAUCCUGGC--UAGUUCGCGUG---A-CCAGGA------GAUCCGAGCAGA----------------------------------------------GAC----AUAGCGGAC---UG---CGCACGGA----GAAGCCUUGAGGG------AAUGC-CGUAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCACAA
ABVK02000009.1/94035-94264     --------------------------------A-----------------------C---------------------------------CGUAAAA---------ACCCGC----AAAACCACAAAGGCCAACAAGCCUGCU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUCGCGGC--------------------------------------UUAAUG----------------------ACCGCGA--------------------------------------------------------------------------CCUCG--------------CCCGG--UAGCCC----UGCCGGG------GGCUCA---CCGGA-----------------------------------------------------------AGCGGGGACAC-------AAACCCGGC--------------------------------------UAGCCUGGGGCCA-----CGCCCCC----------------------UAACCCCAGGC-------GAAGCGCAAGGGGGCU------CGCCCCUGG--CCGCC----CGUCCGCG----G-GCCAAGCCAGGGGGACACCCA---------------------------------------------------A---AACGCGGAC----UA---CGCGCG----U----------------------------------------------------------------
AACY020561358.1/221-575        GGGGGCGAC--C-GGUUU--CGACGGGGUAAGAUA------A-U-GAUAA---GAUUGCAUGCAGAGG-----UUCGGGA------UCCUCUUUAAU------AUCCCCGAA----AUAUCAAUAAAUGCCGAUUACGGCUACAU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCAGCUGCUUA------------------------------------AUUAGC------------------------UCUGCCCGCUC--------------------------------------------------------------------UGGAUUAA--------------------GUUUGUCUGUGGUUUAAUC----UAAG------------------------------------------------------------------------AGCGUCAUA------AACGCAGAC-------------------------------------UGGUCCCU---GGAU---UU-GUUUACUA-----------------GAA-----AGGGAUAAGA-U-G---UUUUGUAAAC--U-GGUUGAUAUAU----GGGU---UGUUA--UUU---G-UCC---GCUAUAUCAAUGAGAA-------------------------------------------------UAAAUCAGA--UGAC---UA---UGUAUGUA--GACGUU--UUGUUAG------AAUCUAUCUCGGA-CGGGAGUUCGAAUCUCCC-CGCCUCCACAU
AE001439.1/801377-800995       GGGGCUGAC--UUGGAUU-UCGACAGAUUUCUUGU------C-G-CAC--AG-AUAG-CAUGCCAAGC-----GCU-----------GCUUGUAAAA------C-----AGCA---ACAAAAAUAACUGUAAACAACGCAGAUUACGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCAGCUUACGCUAAAGC----------------------------------UGCGUGAGUUAA---------------UCUCCUUUU---GGAG-------------------------------------------------------------------CUGGAC---------------UGAUU--AGAAUU-----UCUAGC------GUUUU----AAUCG--------------------------------------------------------------CUCCAUAACC--U--UAAGCUAGACG----------------------------------CUUUUAAAAGGU-----------GGUU----------------------C-G-CCUUUUAAACUA-AGA--AACAAGAACUC-----UUGAAACUAUCUCAAGGUUUUAGAAAGUUGG---A-CCAG-AACUAGUUUUAAGGCUAAA----------------------------------------------AAGCUAAUCAAUUUUC---UA---AGCAUUGU--AGAAGUUUGUGUUUAGG---ACAAGAUUUUUGGA-CUGGGGUUCGAUUCCCCA-CAGCUCCA---
BA000028.3/2479403-2479040     GGGGACGUU--ACGGAUU--CGACAGGGAUAGAU--------UG-AGCUCAG-GUUG-CACGUCGAGG-----UUACG---------GCUCGUA----------AAACGUUAUG-CCUAAAUAUAACUGGCAAAGAAACUAAUCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCUGUUUUAGCAGC--------------------------------------UGCGUAA------------------GUAGCC-UAAAA--C-------------------------------------------------------------------GAUCCUU--------------CCUG---GCAUC------GCCCGU-------GUGG-----CAGAU----------------------------------------------------------UGAAGGGUCUCA---AAUUAAGCGGGCUAU---------------------------------GCUACGAUCCU----C----CGCCUGG------------------------G-GAUUUGUAGAUG-AAU---C-UAAUCAGGCU--AGC-UCCAUGA---AAGCC---UGUUGGUA-----G-GCC---AACAUGAGAGCGAAUG--------------------------------------------------A-UAAUAUACCAAC---UA---CGCGUGUA---GAAGCCUGAGUGG-------CGAUAUCCUUGGA-CGAGGGUUCGACUCCCUC-CGUCUCCACCA
AACY020564764.1/1738-2092      GGGGGCGAC--UUGGCUU--CGACAGCAGAUACAA--------A-CCCU-CA-AGUG-CAUGUCGAGA-----AGGUAGUAA---U-UCUCGUAAAU------AAAUUGCUGC--AAACUUGUUAGUUGGCGAAAACGCAGAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUAGCCG------------------------------------C-UUAAU-----------------------UGGCUAA-------------------------------------------------------------------------CUGUCC-------------UUGGUA---ACGUG------CUCGUGC----GC-------CUCCAA------------------------------------------------------------AGACAGAC-----GACUACACGAGAUGC---------------------------------UGGAAUUGUU-----------CUUCUC----------------------A-U-UGACAAUUUCUU-AAGAAUUAAAUUGAGAU----CGUUUUUUGA----UCCC---UGUUU--AUC---G-GG-----UGUAAAAGAUUAAAU--------------------------------------------------UAAUAGAUA-AAAC---UA---AACAUGUA---GAUCUUG--UGGCA------GAGUACUGAUGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
CP000109.2/1520762-1521119     GGGGAUGCA--CUGGUUU--CGACGGGGAGUACAA------A-G-UUUA----GGAUGCAUGUCGUGC-----CUGAAUGA-----UGCACGUAAAUC-----UUUAUUUCAA---UUUGUUAUAGUUGCAAACGACGAUAACUA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGCGG-------------------------------------CUU-A--A-------------------UCCCGCUAG-------------------------------------------------------------------------CGCAGAC--------------------UGGGAC----CGUUGUUCG----UGGCA----C-----CC-------------------------------------------------------AGCUCUGUGUCGA-----CUCACACGGAA------------------------------------UCGUCGG---GUCUU---AUGUGUUUGGA-----------------UAAGA-C--UUGACUAAA---C---UUAACAAACUC----GCUUAAUGUG----AUCC--CUGCUG--GCC---G-GG----CAGCAUUAAGUUAAAA--------------------------------------------------UAAUAGAC--CAAA---UA---AACAUGUA--GAGUUU---UAAAUG------GAGGCUUCUCGGA-CGGCGGUUCGACUCCGCC-CAUCUCCACCA
AAAA02043629.1/984-1362        GGGGCUGCC--CUGGUUU--CGACGUGGGUUCGGA-------AU-CGGU-GU-GGUG-CAUGUCGAGC-----UUGAGUGG----C-GCUCGUAAAUC-----UGCAUUCAA------CAAACCAACUGCAAACGACGAACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUCGCCG-------------------------------------CUUAAAC--------------------ACCGGUGAG-------------------------------------------------------------------------CCUUGCA------------ACAGCA-C-----------GCUGACG--------------GGCUGGGCAAGGGGGCCGC---------------------------------AAGGCCUCCCGGCUGCAAGGU---U--AUUCACGUCAGCUG-----------------------------------GCCUCCUGCCG----------GGUACC--------------------UU---GGCAUGGGGCGA-GAU--CCAAGGGUGCUGG---CCUUCCUUGC----AGCG---UGCGA--CUG---C-GC----GGCGUGGAAGGUGAGAU------------------------------------------------CCAAAACAGA-CCGC---UA---AACAUGUA---GAUCUGC--CCGAA------GAAGGCUUGCGGA-CGCGGGUUCAAUUCCCGC-CAGCUCCACCA
CP000024.1/560365-560714       GGGGUCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCAUAU-UCUG-CGACUCGUG------UGGCG-----------ACGUUA-----------ACGCUCA--GUUAAAUAUAACUGCAAAAAAUACUAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUGUAGCAGC--------------------------------------CUAAAC---------------------ACCUGCUCGCGU---------------------------------------------------------------------GACUUC--------------UAGC---AGAUU------GCUUAU-------GUUU-----GUU------------------------------------------------------------UAGAGGUUUUAU---UGAUUUAUAAGCUAC---------------------------------GUUCGAUCA------U----UGCCUAG---------------------------CUGGUCGAAAA-GAG---A-UUUAUAGGCU--CGCAUAUAGA-----AGGCU-UGAGUUAUGU----G-UC-----GCCUAUCUGUUAAAU--------------------------------------------------G-AAAGACAUAACC---UA---UGGUCGUA---GACGAAUAUGUUG-------GCAGAUGCUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUAA
CP001164.1/3579710-3580072     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGACGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
BA000007.2/3475602-3475964     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGACGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AF389958.1/19-340              --------G-------------ACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCUGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AGGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----UAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCU--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GCGCCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
AE004091.2/901872-901522       GGGGCCGAU--UAGGAUU--CGACGCCGGUAACAA------A-A-CUUG----AGGGGCAUGCCGAGCU---GGUAGCAG------AACUCGUAAAUU-----CGCUGCUGC----AAACUUAUAGUUGCCAACGACGACAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUAGCUGC--------------------------------------UUAA-----------------------UGCGGCUAG------------------------------------------------------------------------CAGUCGC------------------UAGGGGAU-----GCCUGU-A----AACCCG--AA----------------------------------------------------------------ACGACUGUCAG----AUAGAACAGGAUC-------------------------------------GCCGCC----AAG---UUCGCUGUAG------------------ACGU----AACGGCUAAA-A-----CUCAUACAGCUC---GCUCCAAGC----ACCCU----GCCA--CUC---G-GG----CGGCGCGGAGUUAACU--------------------------------------------------CAGUAGAGC-UGGC---UA---AGCAUGUA--GAACCG--AUAGCGG-------AGAGCUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCA--C
AAFL01000002.1/28456-28814     GGGAGCGAC--UUGGCUU--CGACAGGAGUAAGUC--------U-GCU-UAG-AUGG-CAUGUCGCUU-----UGGGCA--------AAGCGUAAAA------A---GCCCAA---AUAAAAUUAAACGCAAACAACGUUAAAUUCGCUC------------------------------------------------------------------------------------------------------------------------------------------------------------------CUGCUUACGCUAAAGCUG-------------------------------------CGUAAGU--------------------U-CAGUUG-AGC----------------------------------------------------------------------CUGAAAU-------------UUAAG--UC---------AUACUAU-----CUAG-----CUUAA------------------------------------------------------------UUUUCGGUCAUU--U-UUGAUAGUGUA------------------------------------GCCUU-GCGUU-----------UGAC----------------------A-A-GCGUUGAGGUGA-AA-----UAAGGUCUUA----GCCUUGCUUUU-GAGUUU--UGGAAG-AUGA---G-CG------AAGUAGGGUGAAG---------------------------------------------------U--AGUCAU-CUUUG-CUA---AGCAUGUA---GAGGUCUU-UGUGG------GAUUAUUUUUGGA-CAGGGGUUCGAUUCCCCU-CGCUUCCACCA
AAFZ01002114.1/680-1094        GGGGGCGUA--UUGGAUU--CGACGCCGGUUACAA------A-A-CUUG----AGGUGCAUGCCGAGA----UGGUGACCA-----AUCUCGUUAAUC----CAAAGUCGCA----AACCUUAUAGUUGCCAACGACGACAACUACGCACUCGCUGCUUAU--------------------------------------------------------------------------------------------------------------------------------------------ACACCAGUAGAGCGC----------------------------------------------------------------------------------------------------------------------------------------------------------------CAUCUGA------------C-UG----GAGCCGU---GCUUAUG-C----GUCCAGC-GCUUCAUCUGCCCCCGGGCCUCAAAAC-------------------CCAGGGCAGCGGCGAAGCAUUCAGGUGUCAU-----AACUCAUAAGA------------------------------------UCGCGAU---GACCC---AC--GUCUGG------------------GGGUG-A--CUCGCUAAA-ACC--UAAACCAGAAUC----GCCAUUUCACA--UGCCC---UGCCG--GCC---G-GG----CAGUGAGAGGUUAAAU-------------------------------------------------AUAAUAGACC-GAAC---UA---AGCAUGUA--GAGCCG---AUAGCA------GCGGACUGACGGAC-GCGGGUUCAAUUCCCGC-CGCCUCCACCA
CP000246.1/1709063-1708703     GGGGGCGUU--UUGGCUU--CGACGGGGGUAAG--------AUG-GGUUUGA-UAAG-CGAGUCGAGGG---AAGCAUGGU-----GCCUCGAUAAUA-----AAGUAUGCA----UUAAAGAUAAACGCAGAAGAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUUGCAUUAGCAGC--------------------------------------UUAAUUU------------------AGCGCUGCU--------------------------------------------------------------------------CAUCCUU--------------CCUC--AAUU-------GCCCAC-------GGUU----GAGAG-----------------------------------------------------------UAAGGGUGUCAUUUAA---AAGUGGGGA------------------------------------ACCGAGCCUAGC-------AAAGCUUU--------------------GA-GCUAGGAACGGAAU-UU------AUGAAGCUUA---CCAAAGAGGA-----AGU--UUGUCU--GUG---G-ACG----UUCUCUGAGGGAA-UU------------------------------------------------UUAAAACACA-AGAC---UA---CACUCGUA---GAAAGUCUUACUGG-------UCUGCUUUCGGA-CACGGGUUCGACACCCGU-CGCCUCCACCA
AM263198.1/2430862-2430542     -----------------------CAGGGAUAGUU--------CG-AGCUUGA-GUUG-CGAGUCGGGG-----GGAUCGU-------CCUCGUUAUCAA---CGUCAAAGCC------AAUAAUAACUGGCAAAGAAAAACAAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUAGCUUUCGCUGC--------------------------------------CUAAUAA------------------GCAGUAGCAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------GCCCAU-------GUGC----UACGG-----------------------------------------------------------UAAGGGUCUCAC----UCUAAGUGGGCUAC---------------------------------ACUGGCUAAUC----U---CCGUCUGA--------------------------GGUUAGUUGGAA-GAG--CU-UAAUCAGACU--AGC-UGAAUGG---AAGCC---UGUUACCG-----G-GCC---GAUGUUUAUGCGAAAU-------------------------------------------------GC-UAAUACGGUGAC---UA---CGCUCGUA---GAUAUUUAAGUGC-------CGAUAUUUCUGG--------------------------------
AE002160.2/343251-342834       GGGGGUGU--AAAGGUUU--CGACUUAGAA-----A-----UGA-AGCGUUA-AUUG-CAUGCGGAGGG---CGUUGGCUG-----GCCUCCUAAA--------AAGCCGAC----AAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGCUU---------------------------------------------------------------------------------------------------------------------------------------CGCUGAUCUUAAUGAUCUAAGAGUUGCUGCUU-------------------------------------AAUUAGC--------------------A-AAGUUGUUACCUAAGUAC------------------------------------------------------UGGUAACC-CGGUG--------------UUCGC--GAGCU-----CCACCAGA-----GGUUU----UCGAA------------------------------------------------------------ACGCCGUCA------UUUAUCUGGU---------------------------------------UAGAAUUAGGGCCUU-UUAACUCUCAA-------------------GGGAACUAAUUUGA------AU-UUUAAUGAGAGU------CGUUG-GUCUCUAUAG---AGGUUUCUAG---C-UGAGGAGAUAUAACGUAAAAU---------------------------------------------------A--UUCUAGAAAC----UA---AGCAUGUA--G-AGGUUAGCGGGGAG-----U--UUACUAAGGA-CGAGAGUUCGAAUCUCUC-CACCUCCA---
AAFX01031538.1/449-804         GGGGGCGC--ACCGGUUU--CGACGGGAUUG----A----AUCG-UUGUGGG-AAGG-CGUGCCGGGUU---CCGAGC---------UCCCGUAAA---------ACGAUCGG---AAAACAACAACUGCCAACAACACGCAG---UU----------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCAUACGCUGCCUAA---------------------------------------UUAA-----------------------UUAGGUAGC------------------------------------------------------------------------CGCUG--------------CGGUC--UCUGGC------UCCUGU-----CUGGA----GGCCUG-----------------------------------------------------------UCGGCGUCU------UAAUGCAGGAU---------------------------------------GGGCCUAACGCU-----UCGGUCCG--------------------GAGCGGACAGCCGA------GA-UCAAUCGGGCUAA--------GCCGACCGGCUCU----UGCCGGUUC---C-UCACCGGUCGGACGAAAACCA---------------------------------------------------C---CGAAUCGGA----CA---CGCACGUA--GUCUUUUC-AUGGCGG-----A--CUUUCUCGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
AF375585.1/1-302               ---------------------------GGUUCCA--------UG-AGCUAGU-UAAG-CGUGUCGAAG-----GGUUGU--------CUUCGUCACCAA--CACACACAGUU-------AUAAUAACUGGCAAAGAAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------GUAAUA----------------------GCA-CUCUGC----------------------------------------------------------------------AUCGCC-------------UAACG---GUAUC------UCCUAU-------GUAC-----CGUUA-----------------------------------------------------------ACGCGAUUCAA---CCUAUAGUAGGAUAC---------------------------------GCUAGGCACUG----C----CGUUUGA------------------------A-GUCUGCCUAGAA-GAG--AU-UAAUCAAACU--AGCAUAAUGAC-----GGA---UGUCUAUC-----A-CCU----CCCAUUAUGCGAAA---------------------------------------------------C-CUAUUGAUAGAC---UA---CGCACGUA---GAAGUGCUAGUAU-------CAGAACC-------------------------------------
AY364895.1/1-307               ------------------------AAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUAGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------CGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUCAAUUCGU----GGCG---UGUCU--CUC---C-GC----AGCGGGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUU----------------------------------
CR954246.1/2232366-2232010     GGGGCUGA--UUAGGAUU--CGACGGAAUUCAAGA--------A-GCCCA---AGGUGCAUGUCGAGG-----UGCGGUUU-----GCCUCGUUAAA-------CAGCCGCAA---CCUAAAGUAAUCGCAAACGACGAUAACUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUCUCUAGC-GGC--------------------------------------UUAG------------------------GCCAGCUAG-----------------------------------------------------------------------CGCUCCU-------------UCUA--UGUAUUC-----UUG--UGG----AC--------UAGAUU--------------------------------------------------------UU-GGAGUGUCAC---CCUAACACCUGAUC-------------------------------------GCGAUGG-AAACC---CU-GGCCGGG-------------------GUU---GAAGCGUUAAA-AC-----UAAGCGGCCUC---GCCUUUAUUU----ACCG---UGUUU--GUC---C-GG----GACUUAAAGGUUAAU---------------------------------------------------UAAAUGAC--AAUA--CUA---AGCAUGUA--GUACCG--ACGGUCG-------AGGCUUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
ABGI02000002.1/57019-57380     GGGGAUGU--UUUGGAUU--UGACUGAAAAUGU--U-----AAU-AUUAUAA-GUUG-CAGGCAGAGG-----GAAU----------CUCUUAAAA------------CUUC------UAAAAUAAAUGCAAAAAAUAAUAAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUACAAGCUC---------------AAAUCUUGUAA-------UGGCUGCU----UAAGUUAGC----------------------------------------------------------------------------------AGAGGG------------UUUUGU-UGAAUUU-----GGCUUUG-----AGGUUC---ACUUAU----------------------------------------------------------ACUCUUUUCG------ACAUCAAAGCU--------------------------------------UGCUUAAAAAUGU-----UUUCAAGU---------------------UGAUUUUUAGGGA------CU-UUUAUACUUGAGA-----GCAAUUUGGUGGUUUG----CUAGUAUUU--CC-AAACCAU---AUUGCUUAAUA--------------------------------------------------------AAAUACUAG--AUA---AGCUUGUA--G-AAGCUUAUAGUAU------U--AUUUUUAGGA-CGCGGGUUCAAUUCCCGC-CAUCUCCACUU
AADV02000210.1/4102-3717       GGGGCCGC--AACGGCUU--CGACAGGCUGGCGAAA-----UCC-AAAUUGU-GAUU-CAGGUCGAGA----G-UGAGUC-U---CCUCUCGUAAAUA----CAAGACUCAAA---ACAAUAGUAACUGCGAACAACAUC------GUAA------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUCAAGCGCGUAGCAG--------------------------------------UAG-------------------------CUGCGUAGAACUCUCUCAUA---------------------------------------------------GAGUCGCUU-------------------ACCUCU--GACCUG----ACUCCGUUA---AGGACUC---GGAGGUA--------------------------------------------------------CC--AACCCC-----------AACGGAUG-----------------------------------CCCUUAAUAGCUAC------CUCUGGU------------------------UGGCUGUUGAGCUA-AG----ACUACACCAGAG--C---------------------------------------------------------AUCCCACCGUUCGGGAGAAUGAGCG--GUUCCCGUCUGAGGGUCAGAAAGAC----------------UA---AGCCUGU----GAAUGAGCGGUAGGUC--AAUACCCAGUCUGGA-CAGCAGUUCGACUCUGCU-CGGCUCCAUUC
FM211044.1/4405-4768           GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUUGCAAACGACAACGAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GUAG-------------------------------------CUUAAUA--------------------ACCUGCAUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGGGAGGUCAAA--CCUAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CUUGCCUGGG-------------------GUU---GAAGCGUUAAA-UC-----UAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCU--AUC---C-GCA---GCUGG-CAAGUGAAU---------------------------------------------------GUAAAGAU-UAGAC---UA---AGCAUGUA--GUACCA--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AE017283.1/1467918-1467548     GGGGAUGA---CUGGUUU--CGACUUGGAAUGGU-------UGU-UCCAGGA-GAAG-CGGGCCGAGG-----ACCCAGG-G--UCAACUCGUUAACG----AUCCUUGGAA------ACCUAUAAGUGCCGAGAACACUCGCACU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUUCGCUCUCGC--------------------------------------UGCCUGA------------------UCAGUGAUCGAAGG----------------------------------------------------------------------GUCAG--------------------CCCGGAUG--UAGCCUUCCG----UCCGGA--UC-----------------------------------------------------------------CUGGCCUCGU------UUAGAAGGCU-U--------------------------------GCCGUACAGCUG---------UGGUCAC----------------------G-G-GGGCUGUACGGG-ACG---UUUACGUGACUG---GGCUUGU---C-UGCACC--AUGUCGGUGUG---A-GUGCAG------GAGCCGAGCAAU----------------------------------------------AAC-GACAGCAUCGAC---UG---CGCCCGGA----GAAUGUCUGGACG-------GUCUUUCAAGGA-CGCGGGUUCAAUUCCCGC-CAUCUCCACUA
AE017340.1/1771213-1770855     GGGGCUGAU--CUGGAUU--CGACGGGAUACACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGAGGCAG-----GCCUCGUAAA--------AAGCCUCA-----ACCUAAUAGUUGCAAACGACGACAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUC-UAGCGG-------------------------------------CUUAA--U------------------AACCCGCUAAGC------------------------------------------------------------------------CCAUCC-------------CCCG--GCGCUUU-----GUCU-GCG----AG-AC-----CGGACC--------------------------------------------------------AG-GAUGGCUCAAA--CUAAUGU-AGACUC-------------------------------------GCGUGG--AGGCU---UU-GUCCGGA-------------------GCU---GAAGCGUUAAA-AC-----CAAUCGGACUC---GUCAGUUGUG---AAGCC---UGUCA--GUC---G-GC---GU-CACACUGAUUAAC---------------------------------------------------UAAAAGAC--UGAC---UA---AGCAUGUA--GGACCG--AGGAUGU-------AGGUAUUGCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AE006468.1/2843947-2844309     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP001275.1/249350-249702       GGGGAUGA---CUGGAUU--CGACAGGGCCG----U-----AGG-UGCGAGG-AUUG-CAGGUCGAGG----UCGCCCACG-----AACUCGUAAAA--------AGGGGCA-----GCCAAGUAACUGGCGAGCGCGAACUC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUGGCUGCGU-------------------------------------AAUUC------------------------ACGCAGCCA------------------------------------------------------------------------CGUCU--------------GCCCG--GACCCU----UCCCUGGU-----GGGUU----CGGAGC------------------------------------------------------------GGGCGCCGC------AAGACCGGGG------------------------------------U-GCCCCUGGCCCAA------GCGCCGG--------------------UGCGGGCCAGGUCA------AGCGUGAUCCGGCUCG----GCUGACCGGGAUCC-------UGUCGGUG--------GGAGCCUGG-CAGCGACAGU-------------------------------------------------AG---AACACCGAC----UA---AGCCUGUA--GCAUAUCCUCG-GCUG-----A--ACGCUCUGGA-CGGGGGUUCGACUCCCCC-CAUCUCCACCA
AF389946.1/19-339              --------G-------------ACAGGAUUUGCAA--------A-GCCCU---AGGAGCAUGCCGAGG-----GGCGGUUU-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUUGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GUUC-UU------AAGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAACUC----------------------------------G---CGUGA---AUAC---CUUGCCUGGG-------------------GUU---GAAGCGCUAAA-AU----CUAAUCAGGCUA---GUUUG-UCAG---UGGCG---UGUCC--CUC---C-GCA---GC-GU-GUUGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUUGGA-CGGG-------------------------G
AF389968.1/19-336              --------G-------------ACAAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUC-GCAG-------------------------------------CUUAAUA--------------------ACCUGCGCUGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------CGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUCAAUUCGU----GGCG---UGUCU--CUC---C-GC----AGCGGGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUUGGA-CGGG-------------------------G
CP000569.1/2059595-2059960     GGGGCUGAU-UCUGGAUU--CGACGGGAUUAGCGA--------A-GUCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCAUAGC---------------------------------------------------------------------CUUAUCG-------------CCUCA--GCUUCC-----GCUC-GU------AAGA----CGAGGGC--------------------------------------------------------AACGAUAAGUCA-C--CCAAAAC-GAGAUC----------------------------------G---UGUGG---ACGCC--GCCGUUUGAG-------------------GAU--CGAAACACUAAA-UU-----GAAUCAAACUA---GCUUA-UUUC---UUGCG---UGUCU--GUC---C-GCU---GGAGG-UAAGUGAAA---------------------------------------------------UUAAAGAC-CAGAC---UA---AACGUGUA--GUGCUG--AAGAUGG-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AL591983.1/115220-114851       GGGGAUGUU--ACGGAUU--CGACAGGGAUAGUU--------CG-AGCUUGA-GUUG-CGAGUCGGGG-----GGAUCGU-------CCUCGUUAUCAA---CGUCAAAGCC------AAUAAUAACUGGCAAAGAAAAACAAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUAGCUUUCGCUGC--------------------------------------CUAAUAA------------------GCAGUAGCAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------GCCCAU-------GUGC----UACGG-----------------------------------------------------------UAAGGGUCUCAC----UCUAAGUGGGCUAC---------------------------------ACUAGUUAAUC----U---CCGUCUGG--------------------------GGUUAAAUAGAA-GAG--CU-UAAUCAGACU--AGC-UGAAUGG---AAGCC---UGUUACUG-----G-GCC---GAUGUUUAUGCGAAAU-------------------------------------------------GC-UAAUACGGUGAC---UA---CGCUCGUA---GAUAUUUAAGUGC-------CGAUAUUUCUGGA-CGUGGGUUCGACUCCCAC-CAUCUCCAUAU
CP001132.1/1107491-1107854     GGGGGCGA---CCGGCUU--CGACGCAGGUCGCGA------A-G-CCUU----CGGUGCAUGCAGAGC-----UGCGGUU------CGCUCUUAAAAC-----U-GGUCGCA-----GAUUCAUAAUUGCCAACGACAGCAAUUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUCGCUGCU---------------------------------------UA-------------------------AGCAGUGAG-----------------------------------------------------------------------CCCUCUG-------------CC-----CGGAUUU---GUCUGUG-G----AUCC--------GG-AGCCGAA---------------------------------------------AGGCGCGCGGAGGGUCAU-----GAAACACGGAA------------------------------------UCGUGCGC---AUUC---UA--GUCUGU------------------GGGA--U-GCGCGCUAAA---U--UAAAGCAGAAUC----GCCAUGUCGU---CAUCC---UGUCU--GUC---G-GAG---GGCGGUGCGGUUAAAG-------------------------------------------------CCAAAAGAC--AAAC---UA---CGCAUGUA--GAUCCG---GUGGUCU-----AGGUA-CUGCGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
AF389950.1/20-340              --------G-------------ACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCA-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAU--------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGU---CCUGCCUGGG-------------------GCU---GAAGUGCUAAA-AC-----UAAUCAGGCUA---GUUCG-UUAG---UGGCG---UGUC---UGU---CCGCA---GCUGG-CGUGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
CR954253.1/581189-581550       GGGGAUGUU-UUGGGAUU--CGACAGGCGCAG---------ACC-CGCGCUG-GUUG-CGAUUCGUAG-----GUUACGU-------CUACGUUAA--------AACGUUAAACAGUUUAAAUUAACUGCAAACGAAAACUC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUACGCUGUAGCUGC--------------------------------------UUAGU-----------------------UCAGCCCAG----------------------------------------------------------------------CUGCCAAU-------------AGAC---UGCCU------GCCCGU-------GGCG-----GUC------------------------------------------------------------UUGCGGUAUCAA---CAUU--ACGGGAUAC---------------------------------GCUUGCCUAUC----A----CACCUGA---------------------------AUAAGCGAGAA-GAG---A-CUAACAGGUU--AGCCGUGGCUGU-UUGGCC--CUGUCAUAU-----G-GCG--UUUUGCCCCGGUGAAGU-------------------------------------------------UU-AAAUAAUAUGAC---UA---UGAUCGUA---GAGAUUAGUGACG-------GGAUGCGUUUGGA-CAGGGGUUCAAUUCCCCU-CAUCUCCAUCU
AY082650.1/2-330               -------------------------GGUUGGCGAAA-----GCU-AAUCUGU-GAUG-CAGGUCGAGA----G-UGAGUC-G---CCUCUCGGAAAUA-----CAGGCUCAAA--UCUAAAUAUAGAUGCAAACAACAUC------GUAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------AUUCGAGCGUCAAGCAGUA-------------------------------------UUUG------------------------CUUAAGCCCAACUGAGGC---------------------------------------------------------UUGCUC-------------------GCUUUU--AGUCCG----ACUCCGUUA---ACGGCU-----AAAACG---------------------------------------------------------A--AACCCC-----------AACGGAUG-----------------------------------CACCUUUUAGUUAC------UUUCGGU------------------------UGACUAAUUGCGUA-AAG---ACUUCACCGAAA--C---------------------------------------------------------AUCCUACUAUCAGGGAUAAUUGAUA-GUUCCAGUUCUUGGGAUUAUAAGAAC----------------UA---AACCUGU----GAAUGAGCAGAAUGUC--AUUAUCCAGUC-----------------------------------
CU928160.2/2822548-2822910     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AADL01000160.1/2071-2429       GGGGGCGA---UCGGGUU--CGACGGGGAUG----A----GAAA-GC-AAGG-ACAG-CAUGCCGAGG----UCCCAGG-------UCCUCGUAAAA-------CCUUUGGG----AAAAAGACAACUGCCAACGAAGAGCUG---G------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUCUCGCUGCUUAAU--------------------------------------CUAAA---------------------CAAUUAAGUGAGC--------------------------------------------------------------------G-CGCUU--------------AUCGG-AUUUUGC-----GCCUGUC-----CGGGU----CCGAA--------------------------------------------------------------GGCGUGGA------GAAGGCAGGA--------------------------------------UCGCCAAGGGAACA----UGCCUGG----------------------GUUCCUGAGGU--------UAAACCCUUACAGGC----UCGCUGAUGACGGG-UA-----CGCCCCUCU--U----UCCCGUCGUUGGUCAGACUU--------------------------------------------------G---AACAGGGGC----UA---AGCAUGUA--G-CGGUUCUUGGCGG------A-CUGUUUCCGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
CP000323.1/2008654-2008296     GGGGAUGUU--CUGGCUU--CGACGCUGGUGAUGA------A-A-CUCAA---UGAUGCAUGUCGAGAG---UAUAUGUC------CUCUCGUUAAUC-----A-AACAUAU----AUUGUUAUAGUCGCAAACGACGAAAAUUAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUAGCAG-------------------------------------CUUAAAC--------------------C-CUGUUU--------------------------------------------------------------------------ACUUGGU------------UG------CUGAUC----AUCUACA------GUUGG-------UCA-----------------------------------------------------------ACUAAGUUGAAGCGUCCGCAUGUAGAAG----------------------------------C--GCCACA---AGUG---AUUGUCUCAA------------------UUGC--U--UGGGUUUAA-A------AGUAGAGAAUC---GUCCUAUCC----AUCCU----GACU--GUC---G-GA----UCGGUGCGGACUAAAA--------------------------------------------------CCAAAGACAGAAAC---UA---AACAUGUA---GAUUC--AUGAGCG------UAAUGCUGGCGGA-CGCGGGUUCAACUCCCGC-CAUCUCCACCA
CR543861.1/914849-915208       GGGGAUGUU-AUUGGCUU--CGACGCUGGUGAUGA------A-G-CUCAU---AGAUGCAUGCCGAGAG---CGCAUUUU------CUCUCGUAAAU--------AAAAUUUG--CAUUUUAAUAGUCGCAAACGACGAAACUUAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUAGCUGCCU----------------------------------------AA------------------------GGGCAGUUUGUCCGCUUCCUAGAAU-----------------------------------------ACUUGUGGUUUAGGAACCCGA------------------CCGUAG-------------CG----CACGCA--CA----------------------------------------------------------------CAAGUCCGUAU---AGAGUCA-AGCCUC-------------------------------------------------------------G--------------------GGG----CUUUAUACCA-A-----ACUUAGAGGAUC---GCAUCUUGU----ACCCU----GUUC--GUC---G-GG----UCACUGGGUGUUAAAA--------------------------------------------------CAAUAGACGAUAUC---UA---AGCAUGUA--GUAUUC--UCGAGUG------UAGUGCUGGCGGA-CGCGGGUUCAACUCCCGC-CAUCUCCACCA
AL111168.1/1293658-1293303     GGGAGCGAC--UUGGCUU--CGACAGGAGUAAGUC--------U-GCU-UAG-AUGG-CAUGUCGCUU-----UGGGCA--------AAGCGUAAAA------A---GCCCAA---AUAAAAUUAAACGCAAACAACGUUAAAUUCGCUC------------------------------------------------------------------------------------------------------------------------------------------------------------------CUGCUUACGCUAAAGCUG-------------------------------------CGUAAGU--------------------U-CAGUUG-AGC----------------------------------------------------------------------CUGAAAU-------------UUAAG--UC---------AUACUAU-----CUAG-----CUUAA------------------------------------------------------------UUUUCGGUCAUU--U-UUGAUAGUGUA------------------------------------GCCUU-GCGUU-----------UGAC----------------------A-A-GCGUUGAGGUGA-AA-----UAAAGUCUUA----GCCUUGCUUUU-GAGUUU--UGGAAG-AUGA---G-CG------AAGUAGGGUGAAG---------------------------------------------------U--AGUCAU-CUUUG-CUA---AGCAUGUA---GAGGUCUU-UGUGG------GAUUAUUUUUGGA-CAGGGGUUCGAUUCCCCU-CGCUUCCA---
AE017220.1/2861122-2861484     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AAFA03000004.1/17757-17410     GGGGUUGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCUUGU-UCUG-CAACUCAUC------GGCA-----------GAUGUAAA----------AAUGCCA--GUUAAAUAUAACUGCAAAAAAUACAAACAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAUUAGCAGC--------------------------------------UUAAUA---------------------ACCUGCCUGCGU---------------------------------------------------------------------GACCAG--------------UCGC---GAAUU------GCUUGU-------GUUU-----GCU------------------------------------------------------------GAUUGGUCUUAA-----AAUAGCAAGCUAC---------------------------------GUUGGGAUUG----------AGUCAGG---------------------------CAGUUCCAAAA-GAG---A-UUUACUGACU--CGCUUGGUCU-----AGGUU-UGAGUUAUGU----A-UC-----GAGUUCAAGUUAAAG--------------------------------------------------C--AAGACAUAACC---UA---UGGUUGUA---GACGAAUAAGUUA-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CAGCUCCAUAU
AM180355.1/3687738-3687389     GGGGGCGUA--AAGGUUU--CGACGUGGGUUU---------GGA-ACUUGAG-GCUG-CAUGUCGUGU----UACUCUGG------GUCACGUAAAA-------ACUGGGGAA--CUUUAAAAUAAACGCAGACGAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCGAUAGCAGC--------------------------------------CUAGU----------------------UGCUGCU--------------------------------------------------------------------------CGUCCC--------------UCUUA--GUCC-------UCCUGC-------CGAC----UAAGA------------------------------------------------------------CUGGACGUCAUU--A----UGCAGGGA------------------------------------ACUACUUUAGG---G----GUGUCUCG---------------------A-C-UUGAAGUAG-AU-UA------AUUGGGACUG--GCUAAGCAUAG-----AGC--CUGCCA--CUU---G-GCG----CUAUGUGAGGUGAGAU-----------------------------------------------AUUAGUGAAGU-UGGC---UA---AGCAUGUA---GAUGCAGCAAGGAA-------AAGAUUUGCGGA-CAGGGGUUCGACUCCCCU-CGUCUCCACCA
CP000034.1/2587105-2587467     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGACGU-------AGGAAUUCCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
BX908798.1/630473-630069       GGGGGUGU--UACGGUUU--CGACUAGGAA-----G-----UGA-AAAAUUG-AUUG-CAUGCGGAGGA---UAUCGGUUG-----GCCUCCUAAA-------AAAACCGGU----AAAACAAUAAAUGCUAACAAUAGCAAUAAAAUUGCAAAAGUUGACUUC-------------------------------------------------------------------------------------------------------------------------------------CAGGAAGGGACUUUUGCUAGAGCUGCGUAAGAC-------------------------------------CUAACA-----------------------GUCUUG-GUAGC-------------------------------------------------------------------C-CGAUAG--------------UCUG--AAACU-----GGACCGAG-----GGUUU----UAGAAU-----------------------------------------------------------CUAUCGUCA------UUUUCUUGGU---------------------------------------AUGAAUUCUUUUUCU-CGCCGCUUCUA-------------------GGGAAAAGUUUUCA------AGAUUAAAUGAAGCA-------AACUAACUUCGAUUG---UUGCGUUCUG---C-AUAG-GAGUUAGGGAUUUU---------------------------------------------------------ACAGAACGA----UA---AGCAUGUA--G-UGGUCAAUUCGUAA-----U--UUGCCAAGGA-CGAGAGUUCAAUUCUCUC-CACCUCCAAUU
AARY02000146.1/1226-857        GGGGAUGUU--ACGGAUU--CGACAGGGAUAGUU--------CG-AGCUUGA-GUUG-CGAGUCGGGG-----GGAUCGU-------CCUCGUUAUCAA---CGUCAAAGCC------AAUAAUAACUGGCAAAGAAAAACAAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUAGCUUUCGCUGC--------------------------------------CUAAUAA------------------GCAGUAGCAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------GCCCAU-------GUGC----UACGG-----------------------------------------------------------UAAGGGUCUCAC----UCUAAGUGGGCUAC---------------------------------ACUAGUUAAUC----U---CCGUCUGG--------------------------GGUUAAAUAGAA-GAG--CU-UAAUCAGACU--AGC-UGAAUGG---AAGCC---UGUUACUG-----G-GCC---GAUGUUUAUGCGAAAU-------------------------------------------------GC-UAAUACGGUGAC---UA---CGCUCGUA---GAUAUUUAAGUGC-------CGAUAUUUCUGGA-CGUGGGUUCGACUCCCAC-CAUCUCCAUAU
AE014613.1/2734487-2734849     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
U00096.2/2753615-2753977       GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000932.1/1225993-1225635     GGGGACGAC--UUGGCUU--CGACAGGAGUAGAGU--------G-GCC-UUG-GUGG-CAUGUCGCUU-----UGAGCA--------AAGCGUAAAA------A---GCUCAA--AUUAAAAUUAAACGCAAACAACGUUAAAUUCGCUC------------------------------------------------------------------------------------------------------------------------------------------------------------------CUGCUUAUGCUAAAGCUG-------------------------------------CGUAAGU--------------------U-CAGUUG-AGC----------------------------------------------------------------------CUGAAUU------------UUAAGU-G-----------AUACUAU-----C----U--AGCUUAG-----------------------------------------------------------AAUUUGGUCAUU--U-UUGAUAGUGUA------------------------------------GAUUGAAAUU------------UGAC----------------------A---AAUUUUAAUUGA-AA----UUAAAGUCUUA----GUCUAGCUUG----AAAUUUUGGAAG-GUGA---G-UUU------GGCUAGAUGAAU---------------------------------------------------U--UUUCAC-CUUUG-CUA---AGCAUGUA---GAUGCCGU-GGUUG------UUUUAUUUUUGGA-CAGGGGUUCAAUUCCCCU-CGUCUCCACCA
AE005672.3/821929-822276       GGGGUCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCAUAU-UUUG-CGACUCGUG------UGGC-----------GACGUAA-----------ACGCUCA--GUUAAAUAUAACUGCAAAAAAUAACACUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUCUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCAGGCGU---------------------------------------------------------------------GACCCG---------------AUUU--GGAUU------GCUCGU-------GUUC-----AAU------------------------------------------------------------GACAGGUCUUAU----UAUUAGCGAGAUAC---------------------------------GAUUAAGCC------U----UGUCUAG---------------------------CGGUUUGAUAA-GAG---A-UUGAUAGACU--CGCAGUUUCU-----AGACU-UGAGUUAUGU----G-UC-----GAGGGGCUGUUAAAA--------------------------------------------------U--AAUACAUAACC---UA---UGGUUGUA---GACAAAUAUGUUG-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUUA
AE016877.1/5030657-5030303     GGGGACGUU--ACGGAUU--CGACAGGGAUAGUU--------CG-AGCUUAG-GUUG-CGAGUCGAGG-----GGAUCG-------GCCUCGUUAA---------AACGUCA----AAGCCUAUAAUUGGCAAACAAAACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUUUCUUUAGCUGC--------------------------------------UUAAUU----------------------GCACUAAAG-----------------------------------------------------------------------GUUCCU--------------CCCU---CCAUC------GUCCAU-------GUGG----UAGGG-----------------------------------------------------------UAAGGGACUCAA----ACUAAGUGGACUAC---------------------------------GCCGGAGUUCG----C----CGUCUGA---------------------------GGACAAAGGAA-GAG--AA-CAACCAGACU--AGC-AACUUGG---AAGCC---UGUCGAUA-----G-GCC---GAAGAGUUCGCGAAAUG------------------------------------------------CU--AAUAUAUCGAC---UA---CACUCGUA---GAAGCUUAAGUGCC-------GAUAUUUUUGGA-CGUGGGUUCGACUCCCAC-CGUCUCCACCA
AE014299.1/1538496-1538142     GGGGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCU---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAGUUAUAGUUGCAAACGACGAUAACUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGC-CGC--------------------------------------UUAA-----------------------UGCCGCUAG------------------------------------------------------------------------CCAUCUA-------------CCAC--ACGCUUU-----GCAC-AUG----GG-CA-----GUGGAU--------------------------------------------------------UU--GAUGGUCAU---CUCACAUCGUGCUA-------------------------------------GCGAGG--GAACC---CU-GUCUGGG-------------------GGU---GAACCGCGAAA-CA-----GUACCGGACUC---ACCGUGUGGG----AUCC---UGUCU--UUC---G-GA----GUUCAAACGGUUAAA---------------------------------------------------CAAUAGAA--AGAC---UA---AGCAUGUA--GCGCCU--UGGAUGU-------AGGUUUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
CP000444.1/3388384-3388738     GGGGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCU---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUUAA--------AAGCCGCA-----AAGUUAUAGUUGCAAACGACGAUAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGCCGC--------------------------------------UUAA-----------------------UGCCGCUAG------------------------------------------------------------------------CCAUCUA-------------CCAC--ACGUUUC-----GCAC-AUG----GG-CA-----GUGGAU--------------------------------------------------------UU--GAUGGUCAU---CUCACAUCGUGCUA-------------------------------------GCGAGG--GAACC---CU-GUCCGGG-------------------GGU---GAACCGCGAAA-CA-----GUACCGGACUC---ACCGUUUGGG----AUCC---UGUCU--UUC---G-GA----GUUCAAACGGUUAAA---------------------------------------------------CAAUAGAA--AGAC---UA---AGCAUGUA--GCGCCU--UGGAUGU-------AGGUUUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
CP001022.1/2340046-2339688     GGGGACGUU--ACGGAUU--CGACGGGGGUAGUU--------CG-GUCUUCU-GUGG-CGUGUCGAGG-----GGUCG--------GCCUCGUUAAA--------ACGCAUC------AGCCAUAACUGGCAAAACUAACACA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAACUCGCAGCAGCU---------------------------------------UAAU-----------------------AGCUACUACG----------------------------------------------------------------------GAUCCU--------------AGCA---GCCGU-----CGCCUGGU------CGGC-----UGAUUU---------------------------------------------------------CUAGGGUCUCA----CUUUAAACAGGCUAC---------------------------------GCUUGGACCCU----U---CCGUCUGG--------------------------AGGGAAAGAGAA-GAGA-UG-GAAUCAGACU--GGUCGGACGGA----CGCC---UGUCAAUU-----G-GCA---GCCUG-ACGACGAGAU-------------------------------------------------CC-CAAUAAAUUGAC---UA---CACACGUA---GAAGCUUAAGUAUA------CGAUGCCUUCGGA-CGUGGGUUCGACUCCCAC-CGUCUCCAUAC
AE009442.1/2447459-2447813     GGGGGUGCA--CUGGCUU--CGACGGGGGUCACAA------A-A-UCAC--U-UGGUGCAUGCCGAGG----GGGCCGCUU-----UCCUCGUAAAUC-----C-AGCAGCA-----CACUUAUAGUUGCCAACGAAGACAACUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGCC------------------------------------GCUUAA------------------------GGCUUAAGC-----------------------------------------------------------------------CUCGA--A----------ACUG-----CUUGUG-----UCCGUGCU---CGCAG--------CG--------------------------------------------------------------UAGAGUCAU------CAUCACGGAA------------------------------------CCGCUGAG---ACGU---GGCCGUCUGCC-----------------CACC----CUUGGUUAAA---U---CUAGCAGACUG----GUUUCCGGGU----GCGCU-UUGCCU--GUC---G-UGC---UGCCCGGCGACGAGAC--------------------------------------------------CUAACGGCC-AGGA---UA---AGCAUGUA--GGGCCG---GGGACG------GAGUACUUUCGGA-CGGCGGUUCGAUUCCGCC-CACCUCCACCA
CP000805.1/277716-278069       GGGGAUGA--CUAGGUUU--CGACUAGGGAUG---U----GGGG-UGUUGCG-C-UG-CAGGUGGAGU-----GUCGA---------UCUCCUGAU-----------UCGGC----GCCUUUAUAACUGCCAAUUCUGACAGU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGACUACGCG---------------------------------------CUCGC----------------------CGCGUAAUCG-----------------------------------------------------------------------CGGGCC-------------UGUG---UUUGCG----CUGCUCUGA----GCGAA-----CAUAU----------------------------------------------------------CGGCCCGACGC-----CAAACGGAGCU--------------------------------------UGCUCUUACGUUG-----UGCACGGC---------------------GGACGUAGGGGG-------AC-UUUUGUCUGUGC-------UAAGACUCUGGCGCG----UGCGGUGCAG-GC-CUAGCAGAGUCCGACAAACGC----------------------------------------------------AGUACGCACCGC----UA---AACCUGUA--G--GCGCGCAGCACUC-----G--CUCUUUAGGA-CGGGGGUUCGAUUCCCCC-CAUCUCCACAA
AP006627.1/3123303-3122949     GGGGACGUU--UUGGAUU--CGACAGGGAUAGGU--------CG-AGCUUGC-GUUG-CGAGCCGAGG-----GGUCG--------GCCUCGUAA----------AAACGCAC---AAGCCAAUAACUGGCAAAGAAAACAAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACUUCGCUCUAGCU---------------------------------------GCAUA----------------------AGCUA-AGCG---------------------------------------------------------------------GUCUCUC--------------CUCU---CCAUC------GCCCAU-------GUGG----AGUGG-----------------------------------------------------------CUGAGACUCAA-----CUUUAGUGGGAUAC--------------------------------GCCU-UUCUCCC----C---CCGCCUGA---------------------------GGGAGA-AGGA-AGAG-AC-UAAUCAGGCU--AGC-UGCACGG---AGGCC---UGUCUUUG-----G-GCU---GAAGUGCUAGCGAAAU-------------------------------------------------AC-GAAUACAAAGAC---UA---CGCUCGUA---GAAGCGUAAGUGU-------CGUUAUCUCUGGA-CGUGGGUUCAAUUCCCAC-CGUCUCCAUAU
AE000513.1/863322-863670       GGGGGUGA--CCCGGUUU--CGACAGGGGAACUG---------A-AGGUGAU-GUUG-CGUGUCGAGG----UGCCGUUG------GCCUCGUAAAC--------AAACGGCA--AAGCCAUUUAACUGGCAACCAGAACUAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUCGCU-------------------------------------GCUUA------------------------AGUGAGA--------------------------------------------------------------------------UGACG-------------ACCGUG--CAGCCC----GGCCUUU------GGCGU----CGCGG------------------------------------------------------------AAGUCACUAAA------AAAGAAGGC--------------------------------------UAGCCCA-GGCGAU----UCUCCAU----------------------A-GCCGACGGC--------GA-AACUUUAUGGAG---CUACGGCCUG-CGAGAACC----UGCCCACU----G-GUGAGCGCCGGCCCGACAAUCA--------------------------------------------------A---ACAGUGGGA----UA---CACACGUA--G-ACGCA-CGCUGGA------CGG-ACCUUUGGA-CGGCGGUUCGACUCCGCC-CACCUCCACCA
FM204883.1/989840-989492       GGGGUUGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCCUAU-UUUG-CAACUCAUC------GGCA-----------GAUGUAAA----------AAUGCCA--GUUAAAUAUAACUGCAAAAAAUAACACAAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUUUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCCGGCGU---------------------------------------------------------------------GACUUC--------------UAUA---GGAUU------GCUUGU-------GUCU-----UAU------------------------------------------------------------UAGAGGUCUCAA-----AACAGCAAGCUAC---------------------------------GUUUAGGUGA-----U----UGUCUAG---------------------------UCACCUAAAAA-GAG---A-ACCCUAGACU--CGCAGGCUG--A--UGGCU--UGAGUUAUGU----G-UCC-----UUGGUCUGUUAAAG--------------------------------------------------U--AAGACAUAACC---UA---UGGUUGUA---GACAAAUAGGUUA-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CAGCUCCAUCA
CP000951.1/28953-29348         GGGGCCGC--AACGGUUU--CGACAGGUUGGCGAAA----GCUU-CCACUGU-GAUG-CAGGUCGAGA----G-UGGGUC-U---CCUCUCGCAAAUC----AAAGAUCCAAA---CAAAAUGUAACUGCGAACAACAUC------GUUCC----------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCUCGCAAAGCUGCU-------------------------------------GCUG----------------------------UAGCUUAAUAAGAACACCUUA------------------------------------------ACUUAGGUUCGAGC-------------------AUUCAU--AAUUCG----ACUCCGUUA---AGGAUU----AUGACUA---------------------------------------------------------A--ACCCCC-----------AACGGAUG-----------------------------------CUCUCUAGGAAUAC------AUCUGGU------------------------UUGCACUAGAGCUA-AG----ACUAGACCAGAG--A---------------------------------------------------------UUCUUGGCGACUCGGAACAAGCAGUCGUUCCCGUUCUGAGGAUUAGAAGAAC----------------UA---AACCUGU----GAAUGAGCUAGGGGUG--AAUACCCAGUUUGGA-CAGCAGUUCGACUCUGCU-CGGCUCCAUUU
AM260479.1/857346-857004       --------C--------G----ACGUGGGUUACAA-------AG-CAGU-GG-AGGG-CAUACCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AUGCAAUAACUGCUAACGACGAACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCACUGGCCG-------------------------------------CUUAAUU--------------------GC--GGCCGU------------------------------------------------------------------------CCUCGCA------------CUGGCU-C-----------GCUGACG--------------GGCUAGGGUCGC----------------------------------------------AAGACCACGCGAGGUC-----AUUUACGUCAGAUA----------------------------------AGCUCCGGAAGG----------GUCACG--------------------AA-----GCCGGGGACG-AAA---ACCUAGUGACUC---GCCGUCGUAG----AGCG---UGUUC--GUC---C-GC----GAUGCGCCGGUUAAAU--------------------------------------------------CAAAUGACA-GAAC---UA---AGUAUGUA---GAACUCU--CUGUG------GAGGGCUUACGGA-CGCGGGUUCGAUUCCCGC-CGGCUCCACCA
AF375568.1/1-292               ---------------------------CAUUA---------UGA-GGCAUAU-UCUG-CGACUCGUG------UGGCG-----------ACGUUA-----------ACGCUCA--GUUAAAUAUAACUGCAAAAAAUACUAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUGUAGCAGC--------------------------------------CUAAAC---------------------ACCUGCUCGCGU---------------------------------------------------------------------GACUUC--------------UAGC---AGAUU------GCUUAU-------GUUU-----GUU------------------------------------------------------------UAGAAGUUUUAU---UGAUUUAUAAGCUAC---------------------------------GUUCGAUCA------U----UGCCUAG---------------------------CUGGUCGAAAA-GAG---A-UUUAUAGGCU--CGCAUAUAGA-----AGGCU-UGAGUUAUGU----G-UC-----GCCUAUCUGUUAAAU--------------------------------------------------G-AAAGACAUAACC---UA---UGGUCGUA---GACGAAUAUGUUG-------GCAGAUG-------------------------------------
AE016830.1/1067257-1066891     GGGGGCGUU--ACGGAUU--CGACAGGCAUAG---------UUG-AGCUUGA-AUUG-CGUUUCGUAG-----GUUACGG-------CUACGUUAA--------AACGUUACA--GUUAAAUAUAACUGCUAAAAACGAAAACAAUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUUCGCUUUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCUAGCG-A-------------------------------------------------------------------AGAUCCU--------------CCCG---GCAUC------GCCCAU-------GUGC----UCGGG-----------------------------------------------------------UCAGGGUCCUAA----UCGAAGUGGGAUAC---------------------------------GCUAAAUUUUU----C----CGUCUGU---------------------------AAAAUUUAGAG-GAG---C-UUACCAGACU--AGCAAUACAG-A--AUGCC---UGUCA-CUC----G-GCA---CGCUGUAAAGCGAACCU------------------------------------------------UU-AAAUGAGU-GUC---UA---UGAACGUA---GAGAUUUAAGUGG-------CAAUAUGUUUGGA-CGCGGGUUCGACUCCCGC-CGUCUCCAUUU
AF389978.1/4-353               ---GCUGAU-UCUGGAUU--CGACGGGACACUCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAU-------AAACCGCA------AAAAAUAGUCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCGGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUAU-GUC----CUAG------GGGAU-----------------------------------------------------------UGGAAGGUCAU---CUUUCAU-AGGAUC-------------------------------------GCGUGG---AAAC---CUUGUCUGGG-------------------GUG---GAAGCGUUAAA-AC-----UAAUCAGACUA---GUUAUUCAGU----GGCG---UGUCG--GUC---C-GC----AGCUGGAUGGUGAAU---------------------------------------------------GUAAAGAU-UCGAC---UA---AGCAUGUA--GUACUG--AGGAUGU-------AGGUUUUUCGGA-CGCGGGUUCAACUCCCGC-CAGC-------
CP001485.1/2749147-2749513     GGGGCUGAU-UCAGGAUU--CGACGGGAAUUUUGC--------A-GUCUG---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------CCCUGCUCAGAGC---------------------------------------------------------------------CCUUCCU-------------CCCU--AGCUUCC-----GCUU-GU------AAGA----CGGGGAAA-------------------------------------------------------UCAGGAAGGUCAAA--CCAAAUC-AAGCUG-------------------------------------GCGUGG---AUUCC-CCCACCUGAGG-------------------GAU---GAAGCGCGAGA-UC-----UAAUUCAGGUU--AGCCAUUCGUU----AGCG---UGUCG--GUU---C-GC----AGGCGG-UGGUGAAA---------------------------------------------------UUAAAGAU--CGAC---UA---AGCAUGUA--GUACCA--AAGAUGA-------AUGGUUUUCGGA-CGGGGGUUCAACUCCCCC-CAGCUCCACCA
ABKK02000034.1/88935-88586     GGGGGCGUA--AAGGUUU--CGACGUGGGUUU---------GGA-ACUUGAG-GCUG-CAUGUCGUGU----UACUCUGG------GUCACGUAAAA-------ACUGGGGAA--CUUUAAAAUAAACGCAGACGAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCGAUAGCAGC--------------------------------------CUAGU----------------------UGCUGCU--------------------------------------------------------------------------CGUCCC--------------UCUUA--GUCC-------UCCUGC-------CGAC----UAAGA------------------------------------------------------------CUGGACGUCAUU--A----UGCAGGGA------------------------------------ACUACUUUAGG---G----GUGUCUCG---------------------A-C-CUGAAGUAG-AU-UA------AUUGGGACUG--GCUAAGCAUAG-----AGC--CUGCCA--CUU---G-GCG----CUAUGUGAGGUGAGAU-----------------------------------------------AUUAGUGAAGU-UGGC---UA---AGCAUGUA---GAUGCAGCAAGGAA-------AAGAUUUGCGGA-CAGGGGUUCGACUCCCCU-CGUCUCCACCA
CP000422.1/600623-600255       GGGGUCGUU--AUGGAUU--CGACAGGUAUGG---G-----UCG-AGCCAUG-ACUG-CAUUUCGUAG-----GUUACGG-------CUACGUAAA--------AACGUUC-A--GUUUAUUAUAACUGCAAAAAAUAAUAACAAUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUACGCUUUAGCUGC--------------------------------------CUAAUA---------------------GUAGCUUGACG---------------------------------------------------------------------UAGAUCCG-------------CCUA---GUCUC------GUCCAU-------GGGC-----UAGAU----------------------------------------------------------ACGGGUCCUAAA-----UGAAGUGGACUUG--------------------------------CGCUUAAGUACU---------GGCCUGG---------------------------GUGCUUAAGAA-GAG--GA-UUUACAGACU--AGCGUUUUAAUG--AAGCC--CCGACAUAC-----G-GCG---UCUUAUUUCGCGAAAU-------------------------------------------------UU-AAGUAGUAUGAA---UA---UGAAUGUA---GAUGUCAUGGUGG-------CGACAUGCUUGGA-CGCGGGUUCGACUCCCGC-CGACUCCAUUU
CP001146.1/1187989-1187640     GGGGGCG---AUUGGUUU--CGACAGGGAGUAC--A-----AGG-AUCAAAA-GCUG-CAAGCCGAGG-----UGCCGUU------ACCUCGUAAAA------C-AACGGCA------AAAAAGAAGUGCCAACACAAAUUUA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAUUAGCUGCU---------------------------------------UAAUU--------------------U-AGCAGCUA-------------------------------------------------------------------------CGCUC--------------UUCUA--ACCCG------GGCUGGC-----AGGGU----UAGAA-------------------------------------------------------------GGGUGUCAUA----AUGAGCCAGCUG--------------------------------------CCCCUUCCGAC------UCCCCUA----------------------A-G-GAAGGG---------A--AAGAUGUAGGGGA--UAGGUGCUUACAGAAUCC-----UGCGGGAG------GGAGUCUGUAAGUGCCGAAAAGU-----------------------------------------------UAA---AACUCCCGC----UA---AGCUUGUA--G-AGGCUUUUGAUUC------U-UGCUCUCUGGA-CGCGGGUUCGACUCCCGC-CGCCUCCACCA
AM408590.1/3422820-3422453     GGGGCUGA---ACGGUUU--CGACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGUUGCGAC-------CAAAUAAGCGCCGAUUCACAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGACGGCUAGU-------------------------------------------------------------------CUGUCAG--------------------ACCGGGAA---CGCCCUCGG----CCCGGA--CC-----------------------------------------------------------------CUGGCAUCAG------CUAGAGGGAU-C--------------------------------CACCGAUGAGUC---------CGGUCGC----------------------G-G-GACUCCUCGGGA-CAA---CCACAGCGACUG---GGAUCGU--CAUCUCGGC--UAGUUCGCGUG---A-CCGGGA------GAUCCGAGCAGA----------------------------------------------GGC----AUAGCGAAC---UG---CGCACGGA----GAAGCCUUGAGGG------AAUGC-CGUAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCACCG
AF389975.1/19-336              --------G-------------ACAAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAGUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUC-GCAG-------------------------------------UUUAAUA--------------------ACCUGCGCUGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------CGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUCAAUGCGU----GGCG---UGUCU--CUC---C-GC----AGCGUGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUUGGA-CGGG-------------------------G
CP000803.1/22872-22452         GGGGGCGAA-UAUGGUUU--CGACAUGAAUGUCAA------A-A-UCUA----AGGUGCAUGCCGAGG----AAGUACCGU----AACCUCGUUAAUA-----A-CAGUACAAAUGCCAAUAAUAACUGGCAACAAAAAAGCAAACCGCGUAGCGGCUAACG------------------------------------------------------------------------------------------------------------------------------------------ACAGCAACUUUGCUGCUGUUGCUAAAGCUG-------------------------------------CCUAG----------------------UCUAGCUUAAUAACCUA-------------------------------------------------------------GAUGCGCACGGA----------UAUGA----UAGUCU----UUCUUAUGA----CACUAUC-UAUACAU-----------------------------------------------------------CCGUUCAUAUU-----CCGCAUAAGA---------------------------------------CGGUCU--UUGCU---UUUUGUCUGG------------------GAGUU-A-AGGCUGUAU--------UUAACAGACUC----GCUA-ACUAUU--ACCCU---GGCUA--AUU---G-GGG---AAUAGUCAAGCUAAAC-------------------------------------------------UCAAAUAGAU-UAGC--CUA---AGCAUGUA--GAUCCA---AAGAUC------UAGAGUUUGUGGA-CGCGGGUUCAAAUCCCGC-CGCCUCCACCA
AF389981.1/19-335              --------G-------------ACGGGACACUCGA--------A-ACCCA---AGGUGCAUGCCGAGG------UCGGUAG-----GCCUCGUUAAU-------AAACCGCA------AAAGAUAGCCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCGGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUAU-GUC----CUAG------GGGAU-----------------------------------------------------------UGGAAGGUCAU---CUUUCAU-AGGAUC-------------------------------------GCGUGG---AAAC---CUUGUCUGGG-------------------GUG---GAAGCGUUAAA-AC-----UAAUCAGACUA---GUUAUUCAGU----GGCG---UGUCG--GUC---C-GC----AGCUGGAUGGUGAAU---------------------------------------------------GUAAAGAU-UCGAC---UA---AGCAUGUA--GUACUG--AGGAUGU-------AGGUUUUUCGGA-CGCG-------------------------G
CP000247.1/2763346-2763708     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
BX571661.1/326505-326873       GGGGUCGAC--UUGGAUU-UCGACGGGAGCUAAAU--------A-GCC-UCG-GUUG-CAUGUCGGCA-----UGGGCA--------CGCCGUAAAAC-----U---ACCCG----CAAUCAAUAAACGCAAACAACGCAAACUACGCUC------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGCUUACGCCAAAGCUG-------------------------------------CGUAAGUC-------------------UAACUCUUCGGAG--------------------------------------------------------------------CCGUCAAG------------CCUCAC--AAU--------GCUAAC-----------U--AGUGGGG----------------------------------------------------------AUUUGGCGUAA------CUUUGUUAGC--C--------------------------------GCUCUCUCGUCUC---------AUCCGA----------------------A-----GCGAGGGAAA-AG-------AUUAGGAUUG-CCCAUCACUUCC--GCCUU----GGGG-GCUU---G-AG----CAAAGCGAUGGAAAGA--------------------------------------------------GCUUUCAAC-CCCAU-CUA---AGCAUGUA---GAGACUGG-GGUGGG-----UUUGGCUUUCGGA-CUGGGGUUCGAUUCCCCA-CGACUCCACCA
AL939114.1/192486-192090       GGGGAUGA---UCGGUUU--CGACAGCGGCUGU--------CGA-AGCAGGG-GAAG-CGUGUCGAGG----AAGCGGCC-A--UGAUCUCGUAAACC----ACAGGCCGAA-------AAAAUAAUCGCCAACACCAAGCGCGAUUCCUCCCAG-------------------------------------------------------------------------------------------------------------------------------------------------------CAGGCCUUCGCCCUCGCUGCCUGA--------------------------------------UC--------------------------UCAGGUAGCGAAGCGAGCCUCC-----------------------------------------------UACUAAGGGAGUGUCAG--------------------CCCGGGGC---UGUUCCCGA----CCCGGA--UC-----------------------------------------------------------------CUGGCAUCAG------CUAGGGGACU-A---------------------------------AACCUUGAUCC---------CGGUCAC----------------------G-G-GGUGAAGAGGGA-AAC--CAAACAGUGACUG---GGCCCGU---C-GGAGAC--UUGUCCGCGUG---A-UCUCCG------GGGCCGAGAAA-----------------------------------------------AUC----GAAGCGGAC---UG---CACACGGA----GAAGCCCUGAUUC-------CGCACCGUUGGA-CGCGGGUUCGAUUCCCGC-CAUCUCCAC--
AY599475.1/1932-1567           GGGGCUGAU-UCUGGAUU--CGACGGGAUUAGCGA--------A-GCCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAU-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUUUAGC---------------------------------------------------------------------CUUCGCG-------------CUCCA--GCUUCC-----GCUC-GU------AAGA----CGGGGAU--------------------------------------------------------AACGCGGAGUCAAA--CCAAAAC-GAGAUC----------------------------------G---UGUGG---AAGCC--ACCGUUUGAG-------------------GAU--CGAAGCACUAAA-UU-----GAAUCAAACUA---GCUUA-AGUU---UAGCG---UGUCU--GUC---C-GC----AUGCU-UAAGUGAAA---------------------------------------------------UUAAAGAC-GAGAC---UA---AACGUGUA--GUACUG--AAGGUAG-------AGUAAUUUCGGA-CGGGGGUUCAACUCCCCC-CAGCUCCACCA
CP000414.1/273277-273583       ---------------------------UCGUU---------UAG-AGCAUUG-AUUG-CGUUUCGCCA-------UCCG---------GGCGCAA---------AACGGGC-A---GAAAUUUUAACUGCAAAAAACGAAAACUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCUAUCGCUGC--------------------------------------CUAAAA---------------------ACCAGUGAUGCG--------------------------------------------------------------------UAGCUUAA-------------UCUU---GGUU-------GCUGGC-------GUCU-----GAGG------------------------------------------------------------UUAGGCCAUAA---A---AGGCCAGAUCG---------------------------------UACUGCUUCUU----A----CAUCUGG---------------------------AAAAGCAGUAU-UAA--AU-CAAUCAGGUU--AGUUAUAUUGAA--GAGCC--UUGAGCUAU-----G-GCA---GACAAUAUAAUGAACU-------------------------------------------------AC-AAAUAAUAGCCC---UA---UAAACGUA---GAUAUUGGUGUAU-------CGGGCGAUUUGGA-CAG---------------------------
CU468135.1/1085284-1084904     GGGGCUGAU-UCUGGAUU--CGACAGGAUUUGCGA--------A-GCCCU---AGGAGCAUGCCGAGG-----GGCGGUUU-----GCCUCGUUAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUUCGCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUGCUGCUUUA-GCAG-------------------------------------CUUAAU-----------------------CAGCUUAAUAAACUGA----------------------------------------------------------AGGUGUCCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--ACUAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CUUGCCUGGG-------------------GUU---GAAGCGUUAAA-UC-----CAAUCAGGCUA---GUUUG-UUAG---UAGCG---UGUCC--GUU---C-GCA---GCUAA-CCGGCGAAU---------------------------------------------------GUAAUAAC-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUCUGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000266.1/2915116-2914754     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AF440335.1/1-316               ------------------------AAGCACAG---U-----UCG-AGCUUGA-AUUG-CGUUUCGUAG-----GUUACGU-------CUACGUUAA--------AACGUUACA--GUUAAAUAUAACUGCUAAAAACGAAAACAACU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUACGCUUUAGCUGC--------------------------------------CUAAAA----------------------ACAGUUAGCG-U-------------------------------------------------------------------AGAUCCU--------------CUCG---GCAUC------GCCCAU-------GUGC----UCGAG-----------------------------------------------------------UAAGGGUCUCAA----AUUUAGUGGGAUAC---------------------------------GUUAAACUUUU----C----CGUCUGU---------------------------AAAGUUUAAAA-GAG---A-UCAUCAGACU--AGCGAUACA--G-AAUGCC---UGUCACUC-----G-GCA---AGCUGUAAAGCGAAACC------------------------------------------------UC-AAAUGAGUUGAC---UA---UGAACGUA---GAUUUUUAAGUGU-------CGAUGUGUUU----------------------------------
CP000359.1/2118878-2119225     GGGGGUGA--CCCGGUUU--CGACAGGGGAACUG---------A-AGGUGAU-GCUG-CGUGUCGAGG----UGCCGUUG------GCCUCGUGAAC--------AAACGGCA---AAGCCAUUAACUGGCAACCAGAACUAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUCGCU-------------------------------------GCUUA------------------------AGUGAGA--------------------------------------------------------------------------CAGUG-------------ACCGCC--GAGCCC----GGCCUUU------GGCGC----GGCGC------------------------------------------------------------GAACUGAACCA------AAAGAAGGC--------------------------------------UAGCCCC-GGCGAG----GUUCCAU----------------------A-GCCGCAGGC--------GA-AACUCCAUGGAA---AUACGGUCUGGG-CGAGCC----UGCCCGCU----G-GCGCUCCCCGACCCGACAACAA--------------------------------------------------A---AAAGCGGGC----UA---CACACGUA--G-ACGCA-CGCUGGA------AGG-ACUCUUGGA-CGGCGGUUCGACUCCGCC-CACCUCCACCA
AP006841.1/1350686-1351083     GGGGUUGA---CUGGUUU--UGACAGCGGGC----A----GAAA-UGGUGGG-UAAG-CAUGCAGUGCG--UCGGUGAUU------UGCACUUUAAUC-----UCAGUUAUC----AAAAUUUUAUCUGGCGAAACUAAUUAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUUGCUGCUUAAUCGAAU---------CAUAGUAGAUUAGC-UUAA--UCCAGGCACCAGGUGCCAGGA-CGAGA----------------------------------------------------------------------------CAUCAC-------------UCGGA--AGCUGU----UGCUCCGA-----AGCAU----UCCGGUU--------------------------------------------------------CAGUGGUGCAGU-----UACAUCGGGGA--------------------------------------UAGUCAGAAGUG-------GCCUUG-----------------------CGCUUCUGAU--------GA-AACUUUAAAGGAU---AAGGCAGGAAUUGAU-------GGCUUUGG--------UUCUGCUCCUGCACGAAAAAC------------------------------------------------UU---AGGCAAAGA----UA---AGCAUGUA--G-AAAGCUUAUGAUUU-----C--CUCGUUUGGA-CGAGGGUUCGAAUCCCUC-CAGCUCCACUU
CP000679.1/1245181-1244816     --GGGCGUGUUUUGGAAU-UCGACGGGGGCAGU--------CGG-AUUCCAA-AUAG-CGGGUAGUGGU--UUUCUCGGUA------CCACUAUAAA------AAACCGAGA----AGAAAAAUAACUGCAGACAAAGCUGA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACU-CGCUUUAGCUG------------------------------------C-AUAAG-AU-----------------AAGCAGCUAA-------------------------------------------------------------------------CGUCCG----------------CCG--GAGGUG----CCCACGG-------CCUC----CGAGU-------------------------------------------------------------CGGGCGCCAAC-CC-----ACGUGGG------------------------------------GCACCGAAAGU---A----AGGUCGCCUGA---------------GCCUUACUUUUGGGUC------A---AAUCUCAGGCUG---GGGAAGAAAA-----AGC--CUGUCA--GUG---G-GCG----UUUUCUUCCCGAGAAU-----------------------------------------------UUAAGUACAC--UGAC---UG---CACCCGGA---GAAGUUUGGAGUUC-------GAUGCCUUCGGA-CGGGGGUUCAAAUCCCCC-CGCCUCCACCA
BA000004.3/3652617-3652257     GGGGACGUU--CUGGAUU--CGACAGGAAUAGGU--------CG-AGCUUAA-GUGG-CGAGCCGAGG-----UGGCG--------AACUCGUUAA---------AACGCC-A---UCGCCAAUAACUGGCAAAGAAAACAACAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUCGCAUUAGCUGC--------------------------------------CUAA--G------------------CUAGCAAAUGCG-----------------------------------------------------------------------GUUCCG--------------CCCU---CCAUC------GCCCAU-------GUGG----UAGGU-----------------------------------------------------------GUCGGGACUCAC----UUUUAGUGGGCUAC--------------------------------GCCUCUCACCCU----C----CGUCUGU---------------------------GGGUGAAGGAA-GAG--AU-UUAUCAGACU--AGC-CUUACGG---AAGCC---UGUCGCUG-----G-GCU---GAAGUAACGGCGAAAU-------------------------------------------------GC-GAAUACAGUGAC---UA---CGCUCGUA---GAAGCUUAAGUACU------CGUUAUUUCUGGA-CGUGGGUUCGAUUCCCAC-CGUCUCCAUUU
CP000473.1/5294752-5294401     GGGGGCGU--AACGGAUU--CGACGGGAUUG----A----AUCG-UGGUGGG-GAGG-CGUGCCGGGUU---CCGAGC---------UCCCGUAAA---------ACGAUCG----GAAAACAUAACUGCCAACACGCAGUUU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAUACGCUGCUUAA---------------------------------------UUAA-----------------------UUAAGUAGC------------------------------------------------------------------------CGUUC--------------CAGCC--ACUGA-------GCCUGC-----GCGGU----GGUGAG-----------------------------------------------------------UGAACGUCA------UUUUGCAGGA---------------------------------------UAGGCCAAGAGCU-----UCGGUCCG--------------------GAGCUGGCGGCUGA------GACUCAAUCGGGCUAA-----GCUGCCACC-GC-CCU----UGCCGGUUC---A-GG----GGUGGCCGCCGACAAC-------------------------------------------------CA---UGAGCCGGA----UA---CGCACGUA--GUUCUCUCCAGUACG------G-GCUUUUUCGGA-CGGGGGUUCAACUCCCCC-CGCCUCCACCA
AP009324.1/869435-869796       GGGGACGUU-CAUGGAUU--CGACAGGGGUCCCC--------CG-AGCUCAU-UAAG-CGUGUCGGAG-----GGUUGG--------CUUCGUCAUCAA--CACACACAGUU------UAUAAUAACUGGCAAAUCAAACAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCAGUAGCUGC--------------------------------------CUAAUC----------------------GCA-CUCUGC----------------------------------------------------------------------AUCGCC-------------UAACA---GCAUU------UCCUAU-------GUGC-----UGUUA-----------------------------------------------------------ACGCGAUUCAA----CCUUAAUAGGAUAU---------------------------------GCUAAACACUG----C----CGUUUGA------------------------A-GUCUGUUUAGAA-GAAA-CU-UAAUCAAGCU--AGCAUCAUGUU-----GGU---UGUUUAUC-----A-CUU----UUCAUGAUGCGAAA---------------------------------------------------C-CUUUCGAUAAAC---UA---CACACGUA---GAAAGAUGUGUAU-------CAGGACCUCUGGA-CGCGGGUUCAAAUCCCGC-CGUCUCCAUUA
CP000608.1/1828487-1828067     GGGGGCGAA-UAUGGUUU--CGACAUGAAUGUCAA------A-A-UCUA----AGGUGCAUGCCGAGG----AAGUACCGU----AACCUCGUUAAUA-----A-CAGUACAAAUGCCAAUAAUAACUGGCAACAAAAAAGCAAACCGCGUAGCGGCUAACG------------------------------------------------------------------------------------------------------------------------------------------ACAGCAACUUUGCUGCUGUUGCUAAAGCUG-------------------------------------CCUAG----------------------UCUAGCUUAAUAAUCUA-------------------------------------------------------------GAUGCGCACGGA----------UAUGA----UAGUCU----UUCUUAUGA----CACUAUC-UAUACAU-----------------------------------------------------------CCGUUCAUAUU-----CCGCAUAAGA---------------------------------------CGGUCU--UUGCU---UUUUGUCUGG------------------GAGUU-A-AGGCUGUAU--------UUAACAGACUC----GCUA-ACUAUU--ACCCU---GGCUA--AUU---G-GGG---AAUAGUCAAGCUAAAC-------------------------------------------------UCAAAUAGAU-UAGC--CUA---AGCAUGUA--GAUCCA---AAGAUC------UAGAGUUUGUGGA-CGCGGGUUCAAAUCCCGC-CGCCUCCACCA
CR626927.1/1289246-1289643     GGGGUUGA---CUGGUUU--UGACAGCGGGC----A----GAAA-UGGUGGG-UAAG-CAUGCAGUGCG--UCGGUGAUU------UGCACUUUAAUC-----UCAGUUAUC----AAAAUUUUAUCUGGCGAAACUAAUUAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUUGCUGCUUAAUCGAAU---------CAUAGUAGAUUAGC-UUAA--UCCAGGCACCAGGUGCCAGGA-CGAGA----------------------------------------------------------------------------CAUCAC-------------UCGGA--AGCUGU----UGCUCCGA-----AGCAU----UCCGGUU--------------------------------------------------------CAGUGGUGCAGU-----UACAUCGGGGA--------------------------------------UAGUCAGAAGUG-------GCCUUG-----------------------CGCUUCUGAU--------GA-AACUUUAAAGGAU---AAGGCAGGAAUUGAU-------GGCUUUGG--------UUCUGCUCCUGCACGAAAAAC------------------------------------------------UU---AGGCAAAGA----UA---AGCAUGUA--G-AAAGCUUAUGAUUU-----C--CUCGUUUGGA-CGAGGGUUCGAAUCCCUC-CAGCUCCACUU
AF440351.1/1-322               ----------------------ACAGGGAUAGUU--------CG-AGCUUGA-GUUG-CGAGUCGGGG-----GGAUCGU-------CCUCGUUAUCAA---CGUCAAAGCC------AAUAAUAACUGGCAAAGAAAAACAAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUAGCUUUCGCUGC--------------------------------------CUAAUAA------------------GCAGUAGCAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------GCCCAU-------GUGC----UACGG-----------------------------------------------------------UAAGGGUCUCAC----UCUAAGUGGGCUAC---------------------------------ACUGGCUAAUC----U---CCGUCUGA--------------------------GGUUAGUUGGAA-GAG--CU-UAAUCAGACU--AGC-UGAAUGG---AAGCC---UGUUACCG-----G-GCC---GAUGUUUAUGCGAAAU-------------------------------------------------GC-UAAUACGGUGAC---UA---CGCUCGUA---GAUAUUUAAGUGC-------CGAUAUUUCUGG--------------------------------
ABGQ01000005.1/122398-122710   --------A--------C------AGGAGUAAGUC--------U-GCU-UAG-AUGG-CAUGUCGCUU-----UGGGCA--------AAGCGUAAAA------A---GCCCAA---AUAAAAUUAAACGCAAACAACGUUAAAUUCGCUC------------------------------------------------------------------------------------------------------------------------------------------------------------------CUGCUUACGCUAAAGCUG-------------------------------------CGUAAGU--------------------U-CAGUUG-AGC----------------------------------------------------------------------CUGAAAU-------------UUAAG--UC---------AUACUAU-----CUAG-----CUUAA------------------------------------------------------------UUUUCGGUCAUC--U-UUGAUAGUGUA------------------------------------GCCUU-GCGUU-----------UGAC----------------------A-A-GCGUUGAGGUGA-AA-----UAAAGUCUUA----GCCUUGCUUUU-GAGUUU--UGGAAG-AUGA---G-CG------AAGUAGGGUGAAG---------------------------------------------------U--AGUCAU-CUUUG-CUA---AGCAUGUA---GAGGUCUU-UGUGG------GAUUAUUUUUGGA------------------------------C
AE017042.1/1136978-1137341     GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUG------GCCUCGUAAA--------AAACCGCA----AAAAAAAUAGUUGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAGCUC----------------------------------G---UGUGG---AAAC---CUUGCCUGGG-------------------GUG---GAAGCAUUAAA-AC-----UAAUCAGGAUA---GUUUG-UCAG---UAGCG---UGUCC--AUC---C-GCA---GCUGG-CCGGCGAAU---------------------------------------------------GUAAUGAU-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AF389984.1/19-335              --------G-------------ACGGUACACUAGA--------A-AACCA---AGGUGCAUACCGAGG-----UGCGGUAG-----CCUUCGUUAAU-------AAACCGCA------AAAGAUAGUCGCAACGACGAAACGCAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------UGCUGCUAGGACU---------------------------------------------------------------------CCUUCUN-------------NACU--AGCUUGC-----UUAU-GUC----CUAG------GGGAU-----------------------------------------------------------UGAAAGGUCAU---CUUUCAU-AGAGAC-------------------------------------GCGUGG---AAGC---CCUGUCUGGG-------------------GUG---GAAGCGUCAAA-AC-----UAAUCAGGCAA---GUUAUGCAAU----GGCG---UGGCG--GAC---C-GG----AGCUGGGUGGCGAAU---------------------------------------------------GGAAAGAU-UCGAC---UA---AGCAUGUA--GUACUG--AGGAUGU-------AGUAUUUUCGGA-CGCG-------------------------G
AF389951.1/19-338              --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGUCGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAU--------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGU---CCUGCCUGGG-------------------GCU---GAAGUGCUAAA-AC-----UAAUCAGGCUA---GUUCG-UUAG---UGGCG---UGUCU--GUC---C-GCA---GCUGG-CGUGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUGCCG--AGGAUGU-------AGGAAUUUCGGA-CGUG-------------------------G
AF389942.1/19-340              --------G-------------ACAAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------CCCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAU--------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CAUGG---AAGU---CCUGCCUGGG-------------------GCU---AAAGUGCUAAA-UC-----UAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--AUC---C-GCA---GCUGA-CCGGCGAAU---------------------------------------------------GUAAAGAU-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGCAAUUUCGGA-CGGG-------------------------G
CP000605.1/230962-231358       GGGGGCGA---UCGGUUU--CGACGGUGACCUGU-------UCG-CUGCAGG-GAAG-CGUGCCGAGA----ACGCCGGG-U---CCGCUCGUGGAUG-----ACCCCGGCA-----AAAGAAUAAGUGCUAAAUCUAACCGCACUGAGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------UCGCUCUCGCUGCCUGAUU---------------------------------------UUU------------------------AGUCAGGAUUAACCAGUGAG---------------------------------------------------CAGCCGCUCCGUUCA--------------------CUCCUCCU---CGUCUUUGG----GAGGAU--GC-----------------------------------------------------------------UGAGCGUCGU------UUAGAAGACU-U--------------------------------GCUGAUGCAGUU---------GAGCCUC----------------------A-G-GGCUGCAUCGGG-ACU--UUAACUGCGGAUA---UGCUCGC---C-AUCAGU---UGUCUGCGAC---A-UCGAUG------GGGGCAGAAAAAUC-----------------------------------------GCCAACUUGGCCAGCAGAC---UA---CGCACGUA----GAAGACUGUGGGU-------UCGGUCAUCGGA-CCGGGGUUCAAUUCCCCG-CGCCUCCACCA
AAEW02000005.1/94749-94397     GGGGGCGCC--AAGGUUU--CGACGGGGAUUGGAA--------G-CUA--AG-GUUG-CAUGUCGGAG-----UGGGCAGG------CUCCGUUAAAAA---GCCCAUCUUA---------UACAAACGCCGAUACUGACGUU---U------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGUACGCACUGGCAG-------------------------------------CUUAA----------------------GUCUGCCA--------------------------------------------------------------------------CGUCU--------------CUAGUC--UCUUCG-----CCUGCGGGU--UU----------CUAG-------------------------------------------------------------CGACGUCAA---U---UUAGUAGG-------------------------------------CUGGUUGUUGUUC-------AAGUCCGUG-----------------GUU---CAACAGCGAGAU-CU-----AAACGGAAUCG--CCACAUGUAAG----AGCC---UGUCU--GUG---G-GG---GCUGCAUGCGGUUAAAU-------------------------------------------------UUAAAACAC--AGAC---UA---CACAUGUA---GACGCCUU-AAGUG------AAAGAUUUUCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
CP000471.1/1522615-1522980     GGGGGUGAA--CUGGCUU--CGACGGGGUGUGGAA-------CG-GUUA-GC-AAGG-CGACUCGGAA------UGGUAC-------CUACGUAC---------AGGACCAA-----ACUUUACAAUUGCCAAUGACGAGCAC---UACG-----------------------------------------------------------------------------------------------------------------------------------------------------------------CUCCGGCUUUUGCAGCUGC------------------------------------A-UAAA------------------------GUAGUUGUACAAAGC------------------------------------------------------------GGGGU------------------------------CUG-----AACC---------CGG-----------GCCCGGCAACAGAAGCUUUUAG---------------CGGGGUUAAGCCGGAACUGUGU-AGGCCGGU------GUAAAUCCAGGG------------------------------------ACACCCAGUUCUCC-------GAGGUAA-------------------CGGG-G---------------------------------GCUAUGUGGU-----CA-----GCCA-GCCU---G-AG---ACGCCACAAAGCAGUA--------------------------------------------------------GGGU-UGGCA-AAA---UGGUCGUGA-UUCCUUCU--AGCUUA----AUACAUAUUUCGGA-CCGGGGUUCGACUCCCCG-CACCUCCACCA
AE017262.2/2463848-2463523     --------C--------G----ACAGGGAUAGUU--------CG-AGCUUGA-GUUG-CGAGUCGGGG-----GGAUCGU-------CCUCGUUAUCAA---CGUCAAAGCC------AAUAAUAACUGGCAAAGAAAAACAAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUAGCUUUCGCUGC--------------------------------------CUAAUAA------------------GCAGUAGCAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------GCCCAU-------GUGC----UACGG-----------------------------------------------------------UAAGGGUCUCAC----UCUAAGUGGGCUAC---------------------------------ACUAGUUAAUC----U---CCGUCUGG--------------------------GGUUAAAUAGAA-GAG--CU-UAAUCAGACU--AGC-UGAAUGG---AAGCC---UGUUACCG-----G-GCC---GAUGUUUAUGCGAAAU-------------------------------------------------GC-UAAUACGGUGAC---UA---CGCUCGUA---GAUAUUUAAGUGC-------CGAUAUUUCUGGA------------------------------C
AM421808.1/996334-995972       GGGGGCGAC-CUUGGUUU--CGACGGGGGUUGCGA-------AG-CAGA-UG-CGGG-CAUACCGGGG-----UCUCAGAU------UCCCGUAAAA-------CACUGAAU------UCAAAUAGUCGCAAACGACGAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUAGCCG-------------------------------------CUUAA-------------------------GGCUAGC------------------------------------------------------------------------CGUUGCA------------GCAGUC------------GGUCAAUG--------------GGCUGUGUGGCGA---------------------------------------------AAGCCACCGCAACGUC--A--UCUUACAUUGACUG-----------------------------------GUUUCCUACC---------GGGUUACU---------------------U---GGCAGGAAAUAA-GAC---UUAAGGUAACUG---GUUUCCAAAA----GGCC---UGUUG--GUC---G-GC----AUGAUGGAAAUAAG-AUUUU------------------------------------------CAAAU---AGACA-CAAC---UA---AGUAUGUA---GAACGC--UUUGUA------GAGGACUUUCGGA-CGGGGGUUCGAUUCCCCC-CGCCUCCACCA
AY319520.1/1371-1009           GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AAGD02010331.1/701-1059        GGGGAUGUU-AUUGGCUU--CGACGCCGAUGAUGA------A-G-CUCAU---AGAUGCAUGCCGAGAG---CGCAUUUU------CUCUCGUAAAUC-----A-AAUUUGC-----AUAUUUUAGUCGCAAACGACGAAUCUUAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUAGCUGCCU----------------------------------------AA------------------------GGGCAGCUU-----------------------------------------------------------------------GUCCGC-------------UU----CACUGAAU-----ACUUGU-G----GUCAGUGGACCCGAC-----------------------------------------------------------UGUAGCGCA------CGCACACAAGUCC-------------------------------------GUAUAA---AGUC---AA-GCCUCGG-------------------GGC--U---UUAUACUA-AA-----CUUAGAGGAUC---GCGUUUUGU----ACCCU----GUUC--GUC---G-GG----UCACUUAAUGUUAAAA--------------------------------------------------UAAUUGACGAUAUC---UA---AGCAUGUA--GUAUUC--UCGAGUG------UAGUGUUGGCGGA-CGCGGGUUCAACUCCCGC-CAUCUCCACCA
AAGP01000004.1/107195-107571   GGGGAUGA---UCGGUUU--CGACGUCGGACAC--------UGC-GACGGGA-GAAG-CGGGCCGAGA-----AUGUAGA-G--UCAUCUCGUUAAUG----UCCUCUGCAA------AACAAUAGGUGCUAAGUCUAAUAACCGCACCG------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUUCGCCCUCGCUGCCU--------------------------------------GAUU------------------------AGGC--CGAGCUGCG-------------------------------------------------------------AAUCCGUCAG--------------------UCUAGAGU---UGCUUCC-A---CUCUAGG--UC-----------------------------------------------------------------CUGGCGUCGC------UUAGGGAGCCAC--------------------------------UGCUUCAGAUAU---------UUGUUGA----------------------G-G-GUAUCUGAGGGA-CU----UUUACUCAACUC---CGUUCGUUGGU-CC-ACA---UGUUCGUGUG---A-------------GGGCCAGAACCUA-------------------------------------------AGAAACUACUUCACGAAC---UG---CGCCCGGA----GAAGUCCUGACAA-------UCUGCCGACGGA-CGCGGGUUCGAUUCCCGC-CAUCUCCACCC
AE016825.1/2186992-2187356     GGGGGCGA--CCUGGUUU--CGACGGGGGUUGCGA-------AG-CAGA-UG-AGGG-CAUACCGGGA-----UUUCAGUC----A-CCCCGUAAAA-------CGCUGAAU------UUAUAUAGUCGCAAACGACGAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUCUGGCAG-------------------------------------CCUAACG--------------------GCCGGCCAGA------------------------------------------------------------------------CACUACA------------ACGGUU------------CGCAGAUG--------------GGCCGGGGGCGUC---------------------------------------------AAAACCCUGUAGUGUC--A--CUCUACAUCUGCUA-----------------------------------GUGCUGUUCC---------GGGUUACU---------------------U---GGUUCAGUGCGA-AAU---AAUAGGUAACUC---GCCAAAGUCC----AGCC---UGUCC--GUC---G-GC----GUGGCGGAGGUUAA-AUCC--------------------------------------------AAAU----GACA-CGAC---UA---AGUAUGUA---GAACUC--ACUGUA------GAGGACUUUCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
AE009948.1/922761-922412       GGGGUCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGUAUAU-UUCG-CGACUCAUC------GGCA-----------GAUGUAA-----------AAUGCCA--GUUAAAUAUAACUGCAAAAAAUACAAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAUUAGCUGC--------------------------------------CUAAAA---------------------AACAGCCUGCGU---------------------------------------------------------------------GAUCUU--------------CACA---AGAUU------GUUUGC-------GUUU-----UGCU-----------------------------------------------------------AGAAGGUCUUAU---UUAUCAGCAAACUAC---------------------------------GUUUGGCUA------C----UGUCUAG---------------------------UUAGUUAAAAA-GAG---A-UUUAUAGACU--CGCUAUGUGA-----GGGCU-UGAGUUAUGU----G-UC-----AUCACCUAGUUAAA---------------------------------------------------U-CAAUACAUAACC---UA---UAGUUGUA---GACAAAUAUAUUA-------GCAGAUGUUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUAU
AE004439.1/906024-905658       GGGGCUGAU-UCUGGAUU--CGACGGGAUUAGCGA--------A-GCCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAU-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCAUAGC---------------------------------------------------------------------CUUCUCU-------------CCCCA--GCUUCC-----GCUC-GU------AAGA----CGGGGAU--------------------------------------------------------CAAGAGGAGUCAAA--UUCAAAC-GAGAUC----------------------------------G---CGUGG---ACGCC--UCCGCUUGAG-------------------GAU--CGAAGCGUUAAA-UU-----GAAUCAAGCUA---GUUUA-UCUA---UCGCG---UGUCU--GUC---C-GCA---GUGGG-UAAAUGAAA---------------------------------------------------UUAAAGAC-GAGAC---UA---AACGUGUA--GUACUG--AAGGUAG-------AGUAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
BX248583.1/610694-611086       GGGGCUGAU-UUAGGUUU--CGACUGAAUGUCUUU------G-U-GUUUG---CAGUGCAUGUCGAGG-----GGAGAUAG-----GCCUCGUAAAA-------AAAUCUCA------AAAAAUAAUUGCAAAAAAUAAAUAUAAUGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCUG--UUGCAUUAGCA-----------------------------------GCUUAAUU--------------------GGGUUAAUAACCUAAAG-------------------------------------------------------------GUUCCCUCUUA------------AUUUU---UUUGUU-----ACUCUUA-----ACAAG-----AAAAUCAUUA-------------------------------------------------UCUCAUAAGAGGUCUA---UAAAUAA-GAGCGC-------------------------------------UCAUUA---UAAA---GU-GC-CUAAC-----------------UCUA----UAAUGAUAAG-AAUA-AAAAUUAGAGCUA---AUUGAUUAAU----UGAC--AUGAUC-UUAA---G-UC----AUUUU-UCAAUAAAA---------------------------------------------------U--AUUAA-AGAUC---UA---AACAUGUA--GUAUCU-GGAAAAUA------UAAGAAUUCUGGA-CGCGGGUUCGAAUCCCGC-CAGCUCCAUUU
CP000487.1/460574-460214       GGGGGUGAC--UUGGCUU--CGACAGGAGUAGUGG------AGU-CAC---G-GCGG-CAUGCAGCUU-----UGGGCA--------AAGCUUAAAA------A---GCCCAA--AAUAAAAUUAAACGCAAACAACGUUAAAUUCGCUC------------------------------------------------------------------------------------------------------------------------------------------------------------------CUGCUUACGCUAAAGCUG-------------------------------------CGUAAGU--------------------C-CAGUUG-AGC----------------------------------------------------------------------CCUGCG--------------AAACU-UCA---------AUGCUAU-----CUAG-A--AGCUUU-------------------------------------------------------------AGCGGGUAAU---UUUUGAUAGCUUA------------------------------------GAUUAAAGAAU-----------UGAC----------------------G-A-AUCUAUAAUUGA-AA-----UUUAGUCUUA----GCUUAGCUAA---ACGCUU-UGGGAA-GUGA---G-CG------AAGCUAAGUGAAA---------------------------------------------------C--UCUCAC-UUCUG-CUA---AGCAUGUA---GAGGCU---AUGAAU----CUAUUAUUUUUGGA-CUGCAGUUCGAUCCUGCA-CACCUCCACCA
AE013218.1/203736-203361       GGGGCUGUU-UUUGGAUU--CGACAAAGUUAUCAA------A-A-AAGUA---AAGUGCAUGCCGAGG-----AACGGUUU-----GCCUCGAUAAA-------AAACCGUA-----AAAAAAUAGCUGCAAAUAAUAAACAAAAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUA-GCAG-------------------------------------CUUAAAA--------------------AACUGUAUAAAGC---------------------------------------------------------------------CCUUUCA-------------UCUCU--GACUUC-----UCUC-UU-----GAGAA----CGAGAAAUU----------------------------------------------------UUUAAGAAAGGCCGAC--AUUUAAA-GAGAAA----------------------------------A--AUGUGA---GCAC---UAUGCUUGAU------------------AGUG----ACACAAAAUU-AA----UUUUUCAAGCUA---UAAGC-UUA------AAA---UGAGU-UUUU---C-CAAA-UUAAGC-AAUGAAAAA---------------------------------------------------AUAAAGAA--AAAC---UA---AGCAUGUA--GUAUCU--UUAUUUA------UAGAAAUUUUGGA-CGCGGGUUCAAAUCCCGC-CAGCUCCAAAA
CP001091.1/2116748-2117113     GGGGCUGAU-UCUGGAUU--CGACGGGAUUAGCGA--------A-GUCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCAUAGC---------------------------------------------------------------------CUUAUCG-------------CCUCA--GCUUCC-----GCUC-GU------AAGA----CGAGGGC--------------------------------------------------------AACGAUAAGUCA-C--CCAAAAC-GAGAUC----------------------------------G---UGUGG---ACGCC--GCCGUUUGAG-------------------GAU--CGAAACACUAAA-UU-----GAAUCAAACUA---GCUUA-UUUC---UUGCG---UGUCU--GUC---C-GCU---GGAGG-UAAGUGAAA---------------------------------------------------UUAAAGAC-CAGAC---UA---AACGUGUA--GUGCUG--AAGAUGG-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AACT01039607.1/1457-1864       GGGGGUGAU--UCGGAUU--CGACGACGGUAUCGA------A-C-CCUU-AG-GUG--CAUGCCGAGG----GCGUAGUGG----U-UCUCGUUAAUCA---AAACACUACA----AACCUAUUAGUUGCCACAUUGACAACUACUGGAAGUGC----------------------------------------------------------------------------------------------------------------------------------------------------------AAACGACGAGUUCUUUGACGCUCGUCU---------------------------UCGUGCUUAAUCG-------------------U-AGCUAAACCCUACGAG-----------------------------------------------------------CUUCCCAGUCCGU-----------CCGGCU-------------CGUCUGC-----U--------GGCUGGUU------------------------------------------------------UUUCGGACUGUCA-U--CGUAAGCGG----------------------------------------ACUCGCCACGU-UCAGCAGGUCUCUGGC-------------------UGA-------CGGGUUA-AAA---C-UUGUGG-GAAU-CGCGCUGCAGA----ACCC---CGACC--ACU---G-GGU--CGCUGU-GGUGUUAAAU--------------------------------------------------UUAAACGUG-GAUC---UA---AGCAUGUA---AA-GCCGA-AGGCU------GAGAGCUGGCGGA-CGCGGGUUCGACUCCCGC-CGCCUCCACCA
AF440353.1/1-310               ------------------------GGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------GG-A----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CUUGCCUGGG-------------------GUU---GAAGCGUUAAA-CU-----UAAUCAGGAUA---GUUUG-UUGG---UGGCG---UGUCU--GUC---C-GCA---GCUGG-CAAAUGAAU---------------------------------------------------UCAAAGAC-UAGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGAAAUUUC----------------------------------
DQ250622.1/1-313               --------------------------GAAUUAGAU------A-G-CUCU-AG-CUG--CAUGCCGACUU--GUGUUA----------UGUCGUAAAA------C----UAGCA--UAUAAAUAUAAACGCAAACAACGCAAAUUACGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCUGCUUACGCUAAAGU----------------------------------UGCGUAAGUUUA--------------AUUAGCUUUU---GGAG-------------------------------------------------------------------CUGUUUU--------------UGAAC--AAGGAU-----UCUAGC--------GA-----CUUUU-----------------------------------------------------------CAAAAACAUCAU---U--UUAGCUAGAUG----------------------------------CGCCUUGCA------------CUACCGA---------------------A-----UGCAAGUUUA-AG----U--UUAGGU---UGCCUUGAAGCA-U--UAUU----UUUGGAAGUU---U-GGU--G---UUUUUAAGAAA----------------------------------------------------GAUUUAAAAUCCAA--AUA---AGCAUGUA--UAUCGGCU-GUUGUUG----GUCUAGUUU------------------------------------
CP000916.1/157231-156875       GGGGGCGA---ACGGGUU--CGACGGGGAUGGAG---------U-CCCCUGG-GAAG-CGAGCCGAGGU---CCCCACCU-------CCUCGUAAAA-------AAGGUGGGA---ACACGAAUAAGUGCCAACGAACCUGUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUGUUGCCGCCUA--------------------------------------AUAGA-----------------------UAGGCGGC-------------------------------------------------------------------------CGUCC--------------UCUCC---GGAGU----UGGCUGGG-----CUCC-----GGAAGA------------------------------------------------------------GGGCGUGAGG------GAUCCAGCC--------------------------------------UACCGAUCUGGGCU---CCGCCUUCC--------------------GGCCCGGAUCGG-------GAAGGUUCAGGAAGGC-------UGUGGGAAGCGACACC-C-UGCCCGUGG---G-GGGUCCUUCCCGAGACACGA--------------------------------------------------------AACACGGGC----UG---CGCUCGGA--G-AAGCCCAGGGGC-------CUCCAUCUUCGGA-CGGGGGUUCGAAUCCCCC-CGCCUCCACCA
CP000720.1/3263983-3264346     GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUG------GCCUCGUAAA--------AAACCGCA----AAAAAAAUAGUUGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAGCUC----------------------------------G---UGUGG---AAAC---CUUGCCUGGG-------------------GUG---GAAGCAUUAAA-AC-----UAAUCAGGAUA---GUUUG-UCAG---UAGCG---UGUCC--AUC---C-GCA---GCUGG-CCGGCGAAU---------------------------------------------------GUAAUGAU-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AF389963.1/19-339              --------G-------------ACGGGAUUUGCGA--------A-GCCCU---AGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------CCCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGU---CCUGCCUGGG-------------------GCU---GAAGCGUUAAA-CU-----CAAUCAGGCUA---GUCUG-UCAG---UAGCG---UGUCC--AUC---C-GCA---GCUGG-CCGGCGAAU---------------------------------------------------GUAAAGAU--UGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUUCGGA-CGGG-------------------------G
CP000103.1/2481035-2480674     GGGGGCGA--CUUGGCUU--CGACGUGGGUUGCAA-------AA-CAGA-GC-AGGG-CAUACCGAGG-----ACCAGUUA------CCUCGUAAAU------ACAUCUGGA-----AACCAAUAGUCGCAAACGACGAAAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUCUAGCCG-------------------------------------CUUAAAU---------------------CCGGCUGGA------------------------------------------------------------------------CUCCGCA------------CCGGUG------------GGCCUCAA--------------CGCCGGGUCUGGC---------------------------------------------AACAGACAGCGGAGCC------AUUAACGAGGAUC-----------------------------------GCGCCCGGUA---------GGGUUACU---------------------U---UACAGGGCGUUA-AAC---AAUAGGUGACUC---GCCUGCCAUC----AGUC---CGCCG--GUU---G-AC----GGAUGCCAGGUUAA-AUU---------------------------------------------AAAA----AACA-UGGC---UA---AGUAUGUA---GAACUG--CCUGUA------GAGGGCUUGCGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
BA000003.2/202977-202609       GGGGCUGUU-UUUGGAUU--UGACAAAAUUAUCAA------C-A-AAGUA---AAGUGCAUGCCGAGG-----AACGGUUU-----GCCUCGAUAA--------AAGCCGUA-----AAAAAAUAAUUGCAAAUAAUAAACAAAAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUA-GCAG-------------------------------------CUUAAAA--------------------AACUGAAUAAAGC---------------------------------------------------------------------CCUUCCU-------------UCUUA--UCCUCC-----UUCU-CU------UAG-G--AUGAGAAA--------------------------------------------------------ACAGGAAGGUCAG---A--AAAA-GAGAAA----------------------------------A--ACGUGG---AUAU---CAAGCUUGAC------------------GAUA----ACACGAAGUA-GU----UUUUUCAAGCUA---UAUAC-CUAA---U-AUG---UGUUU--UUC---C-AAAU-UAGGUA-AUGAAUUCA---------------------------------------------------AUAAAGAA-AAAAC---UA---AGCAUGUA--GGGCUU---UAUUAG------UAGAAAUUUUGGA-CGCGGGUUCGAAUCCCGC-CAGCUCCAAAA
AF389979.1/19-336              --------G-------------ACGGGACACUCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAU-------AAACCGCA------AAAAAUAGUCGCAAACGACGAAACCUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCGGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUAU-GUC----CUAG------GGGAU-----------------------------------------------------------UGGAAGGUCAU---CUUUCAU-AGGAUC-------------------------------------GCGUGG---AAAC---CUUGUCUGGG-------------------GUG---GAAGCGUUAAA-AC-----UAAUCAGACUA---GUUAUUCAGU----GGCG---UGUCG--GUC---C-GC----AGCUGGAUGGUGAAU---------------------------------------------------GUAAAGAU-UCGAC---UA---AGCAUGUA--GUACUG--AGGAUGU-------AGGUUUUUCGGA-CGCG-------------------------G
AAZI01000003.1/34098-33733     GGGGCUGAU-UCUGGAUU--CGACGGGAUUAGCGA--------A-GCCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAU-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUUUAGC---------------------------------------------------------------------CUUCGCG-------------CUCCA--GCUUCC-----GCUC-GU------AAGA----CGGGGAU--------------------------------------------------------AACGCGGAGUCAAA--CCAAAAC-GAGAUC----------------------------------G---UGUGG---AAGCC--ACCGUUUGAG-------------------GAU--CGAAGCACUAAA-UU-----AAAUCAAACUA---GCUUA-AGUU---UAGCG---UGUCU--GUC---C-GC----AUGCU-UAAGUGAAA---------------------------------------------------UUAAAGAC-GAGAC---UA---AACGUGUA--GUACUG--AAGGUAG-------AGUAAUUUCGGA-CGGGGGUUCAACUCCCCC-CAGCUCCACCA
AAWO01000065.1/2096-1738       GGGGGCGA---UCGGGUU--CGACGGGGAUG----A----GAAA-GC-AAGG-ACAG-CAUGCCGAGG----UCCCAGG-------UCCUCGUAAAA-------CCUUUGGG----AAAAAGACAACUGCCAACGAAGAGCUG---G------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUCUCGCUGCUUAAU--------------------------------------CUAAA---------------------CAAUUAAGUGAGC--------------------------------------------------------------------G-CGCUU--------------AUCGG-AUUUUGC-----GCCUGCC-----CGGAU----CCGAA--------------------------------------------------------------GGCGUGGA------GAAGGCAGGA--------------------------------------UCGCCAAGGGAACA----UGCCUGG----------------------GUUCCCGAGGU--------UAAACCCUUACAGGC----UCGCUGAUGACGGG-UA-----CGCCCCUCU--U----UCCCGUCGUUGGUCAGACUU--------------------------------------------------A---AACAGGGGC----UA---AGCAUGUA--G-CGGUUCUUGGCGG------A-CUGUUUCCGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
CP000408.1/1368887-1368534     GGGGUUGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCUUGU-UCUG-CAACUCAUC------GGCA-----------GAUGUAAA----------AAUGCCA--GUUAAAUAUAACUGCAAAAAAUACAAACAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAUUAGCAGC--------------------------------------UUAAUA---------------------ACCUGCCUGCGU---------------------------------------------------------------------GACCAG--------------UCGC---GAAUU------GCUUGU-------GUUU-----GCU------------------------------------------------------------GAUUGGUCUUAA-----AAUAGCAAGCUAC---------------------------------GUUGGGAUUG----------AGUCAGG---------------------------CAGUUCCAAAA-GAG---A-UUUACUGACU--CGCUUGGUCU-----AGGUU-UGAGUUAUGU----A-UCG-----AGUUCAAGUUAAAGUU---------------------------------------------AAAG-CAAGACAUAACC---UA---UGGUUGUA---GACGAAUAAGUUA-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CAGCUCCAUAU
CP000113.1/2426740-2427105     GGGGGCGAC--CUGGUUU--CGACGGGGGCAUUGA-------AG-UUC--GA-GACG-CGUGCCGAGC----UUGUCAGGU----A-GCUCGUAAAUU----CAACCCGGCA-----AAGACACAAAAGCCAACGACAACGUUGAGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCGCGCU---GGCUG-------------------------------------CCUAAAA--------------------A-CAGCCCAUAGUGC----------------------------------------------------------------GCGGUCCCCC------------CGCCCU--CG---------GCCUGU---------------GGGGU-------------------------------------------------------------UGGGACAGACCGUCAUAAUGCAGGC--U---------------------------------GGCUGCCGAGGGU---------GCCUG----------------------G-ACCCGAGGUGGCGA-GAU---CUUCCCAGGACC---GGCUCUGAGU----AUCC---CGUCC--GUG---G-GA---GCCUCAGGGACGUAG----------------------------------------------------CAAAUCGC--GGAC---UA---CGCACGUA---GGGUCGAA-GAGCG------GACGGCUUUCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACUG
CP000425.1/1442760-1442402     GGGGGCGUU--ACGGAUU--CGACAGGCAUUG---------UCG-CGCAUGA-ACUG-CAACUGCUGA-----GGGAU----------CAGGAUA---------AUCAUCCGCA-GAUAAAUAUAACUGCUAAAAAUAAUACACAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUACGCAAUGGCAGC--------------------------------------CUAAAC----------------------AGCACCA-UGCG-------------------------------------------------------------------UGCCUGA--------------UUUU---UGCUC------ACUGAU-------GGCA-----AUU------------------------------------------------------------UGACGGCCUAAA---CUUUUAGUCAGAUAC---------------------------------GUUGUUGUG-----------GAGACUU----------------------G----ACGCAGCAAAA-GAG---AUUUAAAGUCCC---GCAAAAUGUC---GCUGUU-UGAGACUGGC----U-UU-----GGCAUUUUGUUAAAUU------------------------------------------------UG----AGAAAGUCC---UA---UGGUUGUA---GACGUUGAUGUAG-------CAAGGUGUUUGGA-CAGGGGUUCGACUCCCCU-CGCCUCCAUUA
AF389943.1/19-339              --------G-------------ACAGGAUUUGCAA--------A-GCCCU---AGGAGCAUGCCGAGG-----GGCGGUUU-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUUGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GUUC-UU------AAGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAACUC----------------------------------G---CGUGA---AUAC---CUUGCCUGGG-------------------GUU---GAAGCGCUAAA-AU----CUAAUCAGGCUA---GUUUG-UCAG---UGGCG---UGUCC--GUU---C-GCA---GCUGA-CCGGCGAAU---------------------------------------------------GUAAAGAU--GGAC---UA---AGCAUGUA--GUGCCG--ACGGUGU-------AGUAAUUCUGGA-CGCG-------------------------G
AF389960.1/19-341              --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG----GGCUGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--AGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
AP006618.1/4642707-4642340     GGGGCUGA---ACGGUUU--CGACUGCGUACGU--------UGA-UUCAGGG-GAAG-CGUGUCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGCUGCAAC-------CAAUUAAGCGCCGAUUCUCAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGAAGCGUCU--------------------------------------------------------------------CUGUCGG--------------------CCCGGGAU--AUGCCCUCGG----UCCCGG--UG-----------------------------------------------------------------CCGGCAUCAG------CUAGAGGGCU-C---------------------------------ACCGUCCGCCU---------CGGUCGC----------------------G-G-AGACGGACGGGA-CAU--CCAACAGCGACUG---GGAUCGU--CAUCUCGGC--UUGUUCGCGUG---A-CCGAGA------GAUCCGAGCAGA----------------------------------------------GAC----ACAGCGAAC---UG---CACACGGA----GAAGCCCUGAAGA-------CGCGGCGGAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCACGA
CP000116.1/1005311-1004945     GGGGCCGAC--CUGGCUU--CGACGUGGGUCGCAA-------AG-CAGC-GU-AGGG-CAUACCGAGG-----GUCAGAGC----A-CCUCGUAAAU------CCAACUGAA-----AAACUUUAGUCGCAAACGACGAAAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCCCUGGCCG-------------------------------------CUUAAGG--------------------UCCAG----G------------------------------------------------------------------------ACUCACA------------CUAGCC-U-----------GUUCAUG--------------GGCUAGGCCGGGUC-------------------------------------------AAACCGGCAGUGAGUU---A--AUUCACAUGAAAUC-----------------------------------GCGCUUGUCCG---------GGUCGCU---------------------U---GGGCAGGUGCUA-AAU---CCAAGGCGGCUC---GGCGAAAUCC----AGCC---UGUUC--GGC---G-GG----CGUGAUGGAGCUUAAAGC----------------------------------------------UUAAAAACACC-GGAC---UA---AGUAUGUA---GAACUGC--CUGUA------GAGGGCUUGCGGA-CGCGGGUUCGAUUCCCGC-CGGCUCCACCA
AACY020409485.1/2045-2389      GGGGGCGUA-UUAGGCUU--UGACGUCUACCACGG-------AA-CCUA-AA-GUG--CAUAUCGAGC----AUGAACAUA------ACUCGUUAAA------UACUGUUUA----AAACAAAUAGUUGCAAAUAAUUACAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAUAGUUUGGCAG-------------------------------------CUUA-------------------------AUGCCAAC------------------------------------------------------------------------CUGUUAU----------------CA--UUUGUG-----ACCUACA-----ACAUU----UG---------------------------------------------------------------AUAACGGUC-----AUUUUAGUAGGA------------------------------------UAUACUCUACCAG---------CGCCC----------------------A-CUUGUAGAGUGAAU--------UUAAGGGCU----UAGCUUAAUGU----GUCU---UGAUC--AUC---A-GG-C-UACAUUAAAGUGA---AU------------------------------------------------UAAAUUGAUG-AAUC---UA---AGUAUGUA---GAUACUA--AGGGA------AAGUGAUGACGGA-CGUGGGUUCAAAUCCCGC-CGCCUCCACCA
BA000019.2/3247-2858           GGGUCCGU--AACGGUUU--CGACAGGUUGGCGAAC-----GCU-ACUCUGU-GAUU-CAGGUCGAGA----G-UGAGUC-U---CCUCUCGCAAAUC-----AAGGCUCAAA---ACAAAAGUAAAUGCGAAUAACAUC------GUUAA----------------------------------------------------------------------------------------------------------------------------------------------------------------AUUUGCUCGUAAGGACGCU-------------------------------------CUAG------------------------UAGCUGCCUAAAUAGCCUCUUU------------------------------------------------CAGGUUCGAGC-------------------GUCUUC--GGUUUG----ACUCCGUUA---AGGACU----GAAGACC---------------------------------------------------------A--ACCCCC-----------AACGGAUG-----------------------------------CUCUAGCAAGUGUU------CUCUGGU------------------------UGGCUUGCUAGCUA-AG----AUUUAAUCAGAG--C---------------------------------------------------------AUCCUACGUUCGGGAUAAUGAACGA--UUCCCGCCUUGAGGGUCAGAAAGGC----------------UA---AACCUGU----GAAUGAGCGGGGGGUC--AAUACCCAAUUUGGA-CAGCAGUUCGACUCUGCU-CGGAUCCACUA
AY911521.1/1-340               ------------------------GCCGGUUGCGA------A-A-CUUU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA--ACUUCCUAUAGUUGCCAAUGACGAAACCUACGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAUACGCUCUCGCUGC--------------------------------------GUAA------------------------GCGGCGCUAGCCUUCCUUCUGGUA-------------------------------------------CCUUCGGGUCCAGCAAUCAU------------------CAGGGGAU-----GUCUGU-A----AACCCG--AA----------------------------------------------------------------AUGAUUGUCAU----ACAGAACAGAAUC-------------------------------------GCCGUG----CAG---UACGUUGUGG------------------ACGA----AGCGGCUAAA-A-----CUUACACAACUC---GCCCAAAGC----ACCCU----GCCC--GUC---G-GG----UCGCUGAGGGUUAACU--------------------------------------------------CAAUAGACA-CGGC---UA---CGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGC----------------------------------
BA000034.2/1107458-1107805     GGGGUUGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCAUGU-UUUG-CGUCCCAUC------GGCA-----------GAUGUAA-----------AUUGCCA--GUUAAAUAUAACUGCAAAAAAUACAAACUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUUUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCUAGCGU---------------------------------------------------------------------GACUUC--------------UACA---AGAUU------GCUUGU-------GUCC-----UGU------------------------------------------------------------UAGAAGUCUCAA-----AAUAGCAAGCUAC---------------------------------GGUUACGAAA-----U----UGUCUAG---------------------------UUUCGUGACAA-GAG---A-UUGAUAGACU--CGCAAACUAA-----UGGCU-UGAGUUAUGU----G-UC-----UUUAGUUUGUUAAA---------------------------------------------------U-GAAGACAUAACC---UA---UGGACGUA---GACAAAUAUGUUG-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUCA
FJ619521.1/691-1004            ------A----------------CGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAA-UAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU-----AGG-A----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAAACU-----UAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC-U-GAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUC--G------------------------------G
AP008232.1/3071644-3072027     GGGGCUGAU-CCUGGACU--CGACGGGAUUUGCGA--------A-ACCUA---AGGUGCAUGCCGAGG-----UGAGGCUG-----GCCUCGUAAA--------AAACCUCA-----AAAAAAUAAUUGCAAACGACUCGCAAUUCGAAU------------------------------------------------------------------------------------------------------------------------------------------------------------------CUAACGCUGCUUUAGCAG-------------------------------------CUUAAUCA-------------------GCUUAAUAACCUGAAG--------------------------------------------------------------AUUCCCUCUCU-------------CCCUA--GCCUCC-----UCUC-UU------AGGA----CGGGGAU--------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGU---CCUGCCUGGG-------------------GCU---GAAGCGUUAAA-AC-----UAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGA-CAGGUGAAU---------------------------------------------------GUAAAGAC-UGGAC---UA---AGCAUGUA--GUGCCG--AAGGCGU-------AGAAAUUCCGGA-CGCGGGUUCAAAUCCCGC-CAGCUCCACCA
CP000127.1/1307217-1307577     GGGGGCGAC--CUGGCUU--CGACGCGGGUAGCAA------A-A-CCUA----AGGGGCAUGCCGAGG-----UGCAGUG------ACCUCGUUAAUC-----A-CGCUGCA-----ACAUUAUAGUUGCCAACGACGACAACUA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCACUCGCUG-------------------------------------CUUAA--A------------------ACCCAGUAGGGUGC---------------------------------------------------------------------CGUCUGA------------C-UG----AAGCCGU---GCUUGUG-C----GUUCAG---A-----U---------------------------------------------------------UUCAGGCGUCGA-----UUCUCACAAGA------------------------------------UCGCGGU---GAAGU---UC--UCCCAG------------------GGCAG-A--CCCGCUAAA-A-C--UUUACUGGGAUC----GCCGUAUGUU----UUCC--UUGCCC--GUC---G-GG----UAGCAUGCGGUUAAA---------------------------------------------------UUAAUGACU-GGGC---UA---UGCAUGUA--GAACCG---AAGGCG------GAGUACUUGUGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
CP000702.1/403790-403470       -----------------C------GGGGAUGGAG---------U-CCCCUGG-GAAG-CGAGCCGAGGU---CCCCACCU-------CCUCGUAAAA-------AAGGUGGGA---CAAAGAAUAAGUGCCAACGAACCUGUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUGUUGCCGCUUA--------------------------------------AUAGA-----------------------UAAGCGGC-------------------------------------------------------------------------CGUCC--------------UCUCC---GAAGU----UGGCUGGG-----CUUC-----GGAAGA------------------------------------------------------------GGGCGUGAGA------GAUCCAGCC--------------------------------------UACCGAUUCGGGCU---UCGCCUUCC--------------------GGCCUGAAUCGG-------GAAAUUUCAGGAAGGC-------UGUGGGAGAGGACACC-C-UGCCCGUGG---G-GGGUCCCCCCUGAAAUCGAA--------------------------------------------------------AACACGGGC----UG---CGCUCGGA--G-AAGCCCAGGGGC-------CUCCAUCUUCGGA-CGGGGGUUC--------G-----------A
CR848038.1/730177-730601       GGGGGUGU--AUAGGUUU--CGACUUAGGA-----A-----UGA-AGUGUUA-AUCG-CAUGCGGAGGG---CGUUGGCUG-----GCCUCCUAAA--------AAGCCGAC----AAAACAAUAAAUGCCGAACCUAAGGCUAAAUGCGAAAUUAUCAGUUU---------------------------------------------------------------------------------------------------------------------------------------CUCUGAACUCUCUGAGCAAAGAUUAGCUGCUU-------------------------------------AAUUAGCA-------------------A-AAGUUGUUAUUUAGAUAACCU-------------------------------------------------CUAGAUAACC-CGGUC--------------UUCAU--GGACU-----CUACCAGA-----GGUUU----GUGAA------------------------------------------------------------GUACCGUCA------UCUAUCUGGU---------------------------------------UGGAAUCUACCUCCU-CUAAUUCUCAA-------------------GGGGGUUUAUUCGA------G--AUUAUUGAGAAU------CGUUG-GUUUCCAUAG---AUGUUCUUAG---C-UGAGGAAAUGCAACGUUAGAC------------------------------------------------------UACUAGGGAC----UA---AGCAUGUA--G-AAGUUAGCAGGGAG-----U--UUACUAAGGA-CGAGAGUUCGAGUCUCUC-CACCUCCAUAC
AACY022720378.1/378-32         GGGGGCGAA--UAGGGUU--CGACGUUUCUACUGG------A-C-UCCG----AAGCGCAUGCCAAGA----UUGUAGUAA-----UUCUUGUAAAAC-----A-UACUACA----AAAAAAAUAGUUGCAAAUAACGACAACUA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUUUAGCAG-------------------------------------CUUAA-------------------------UGCUAA-------------------------------------------------------------------------CCGAUG---------------------CAAGAAU---UGACUGU-G----GUUCGA--AG-----------------------------------------------------------------CAUCGGCUAA-----ACACACAGUC-------------------------------------UAGCCAAGC---UAU---AUUGCUUGGA------------------UAUA---GUUUGGUAA---------AA-CUUAAUCAA---GCUAGCUUUUA--UGCCC---UGCUC--UUC---G-GG-----UGAUAAAAGUUAAAA-------------------------------------------------AUAAUAGAAU-GAGC---UA---UGCAUGUA--GAAGUU--AGGCUGA-------AGGAUUGACGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
CP000393.1/7574767-7575164     GGGGCAUU--AACGGUUU--CGACAGGGUGGUGAAA-----UCU-GCUUUGU-GAUG-CAGGCCGAGA----G-UGAGUC-U---UCUCUCGAAAAUC----CUGGACUCAA----AAAAUAAUAAGUGCAAACAACAUU------GUACC----------------------------------------------------------------------------------------------------------------------------------------------------------------UUUUGCUCGUAAGCAAGUA-------------------------------------GCUG------------------------CUCUAGCUUAAUUGCAAAAACACCUC-----------------------------------------UUAUAGGUUCGAGC-------------------GUCUGU--GGUUUG----ACUCCGUUA---AUAAUU----GCAGACU---------------------------------------------------------U--AACCCC-----------AACGGAUG-----------------------------------CUCUAGCAAUUUUU------CUCUGGU------------------------U-ACCUGCUAGUUA-AG----AUUUAACCAGAG--C---------------------------------------------------------AUCCCACUAUCCGGGAUAAUGGAUAGUCCCAGCUCUGAGGGUUAAGAAGGGC----------------UA---AACCUGU----GAAUGAGUGAAGGGUG--AAUAGCCAUUUUGGA-CAUGGGUUCGACUCCCAU-AUGCUCCAUAC
FM872308.1/21676-21257         GGGGGUGU--AAAGGUUU--CGACUUAGAA-----A-----UGA-AGCGUUA-AUUG-CAUGCGGAGGG---CGUUGGCUG-----GCCUCCUAAA--------AAGCCGAC----AAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGCUU---------------------------------------------------------------------------------------------------------------------------------------CGCUGAUCUCGAAGAUCUAAGAGUAGCUGCUU-------------------------------------AAUUAGC--------------------A-AAGUUGUUACCUAAAUAC------------------------------------------------------GGGUGACC-CGGUG--------------UUCGC--GAGCU-----CCACCAGA-----GGUUU----UCGAA------------------------------------------------------------ACACCGCCA------UGUAUCUGGU---------------------------------------UAGAACUUGGGUCCU-UUAAUUCUCGA-------------------GGAAAUGAGUUUGA------AA-UUUAAUGAGAGU------CGUUA-GUCUCUAUAG---GGGUUUCUAG---C-UGAGGAGACAUAACGUAUAGU---------------------------------------------------A---CCUAGGAAC----UA---AGCAUGUA--G-AGGUUAGCGGGGAG-----U--UUACUAAGGA-CGAGAGUUCGACUCUCUC-CACCUCCAUAG
AM884176.1/343330-342911       GGGGGUGU--AAAGGUUU--CGACUUAGAA-----A-----UGA-AGCGUUA-AUUG-CAUGCGGAGGG---CGUUGGCUG-----GCCUCCCAAA--------AAGCCGAC----AAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGCUU---------------------------------------------------------------------------------------------------------------------------------------CGCUGAUCUCGAAGAUCUAAGAGUAGCUGCUU-------------------------------------AAUUAGC--------------------A-AAGUUGUUACCUAAAUAC------------------------------------------------------GGGUGACC-CGGUG--------------UUCGC--GAGCU-----CCACCAGA-----GGUUU----UCGAA------------------------------------------------------------ACACCGUCA------UGUAUCUGGU---------------------------------------UAGAACUUGGGUCCU-UUAAUUCUCGA-------------------GGAAAUGAGUUUGA------AA-UUUAAUGAGAGU------CGUUA-GUCUCUAUAG---GGGUUUCUAG---C-UGAGGAGACAUAACGUAUAGU---------------------------------------------------A---CCUAGGAAC----UA---AGCAUGUA--G-AGGUUAGCGGGGAG-----U--UUACUAAGGA-CGAGAGUUCGACUCUCUC-CACCUCCAUAG
AAFJ01000006.1/109216-108858   GGGGACGAC--CUGGCUU--CGACAGGAGUAGUUU------G-A-CUA--GG-AUGG-CAUACCGCUU-----UGGGCA--------AAGCGUAAAA------A---GCCUAA---AUAAAAUUAAACGCAAACAACGCGAAAUUUGCUC------------------------------------------------------------------------------------------------------------------------------------------------------------------CUGCUUACGCUAAAGUUG-------------------------------------CGUGAGU--------------------U-CAGUUG-AGC----------------------------------------------------------------------CUAGAGC------------UUGAGU-G-----------AUACUAU-----C----U--AGCUUAA-----------------------------------------------------------GUUUUAGUCAUC--U-UUGGUAGUGUA------------------------------------GUUUUAAGAC-----------UUGACG---------------------C---ACCUUAAAGUGA-AG-----UUUAGUCUA-----GUCAAAUUUGU-AAGUUU--UGGAAG-AUGA---G-CG------GAAUUUGAUGAAA---------------------------------------------------G--AGUCAU-CUUUG-CUA---AGUAUGUA---GAGGUCUU-UUUUG------GGCUAUUUUUGGA-CAGGGGUUCAAUUCCCCU-CGUCUCCACCA
AY616521.1/1-382               GGGGAUGA---UCGGUUU--CGACAGGGGAUGU--------UGA-AACAGGG-GAAG-CGAGCCGAGG----AACGCGGC-AA-UGAUCUCGUUAACCA---CGUGUCGCAA------AAAAAUAAUCGCCAACUCUAAGCGCGAUUCCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAGUUCGCUCUCGCUGC------------------------------------CUAAUAA-----------------------GCACCGAUAGCGCU--------------------------------------------------------------UGGGUGUCAG--------------------ACCGGGG----AGUUCCCGA----CCCGGA--CC-----------------------------------------------------------------CUGGCAUAAU------CUAGGGAACU-C--------------------------------AACCGUCCGCCC---------GGGCUGC----------------------G-G-GGGCGGAUGGGA-AAU--CAAACAGCAGCUG---GGCCUGU---U-GGCGGC--UUGUCCGCGUG---A-CCGCCA------GGGCCGAGAAA-----------------------------------------------AGC----ACAGCGGAC---UG---CGCUCGGA----GAAGCCCUGAAUU-------AACUCCACUGGA-CCCGGGUUCGAUUCCCGC-CAUCUCCACCA
AF389969.1/4-355               --GGCUGAU-UCUGGAUU--CGACAAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUC-GCAG-------------------------------------CUUAAUA--------------------ACCUGCGCUGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------CGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUCAAUUCGU----GGCG---UGUCU--CUC---C-GC----AGCGGGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUUGGA-CGGGGGUUCAACUCCCCC-CAGC------A
CP000076.1/938686-938293       GGGGCCGUU--UAGGAUU--CGACGCCGGUUGCGA------A-A-CUUU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA--ACUUCCUAUAGUUGCCAAUGACGAAACCUACGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUUACGCUCUCGCUGC--------------------------------------GUAA------------------------GCAGCCUUAGCCCUUCCCCCCUGGU-----------------------------------------ACCUUCGGGUCCAGCAAUCAU------------------CAGGGGAU-----GUCUGU-A----AACCCA--AA----------------------------------------------------------------AUGAUUGUCAU----AUAGAACAGAAUC-------------------------------------GCCGUG----CAG---UACGUUGUGG------------------ACGA----AGCGGCUAAA-A-----CUUACACAACUC---GCCCAAAGC----ACCCU----GCCC--GUC---G-GG----UCGCUGAGGGUUAACU--------------------------------------------------CAAUAGACA-CGGC---UA---AGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
L42023.1/1357929-1357564       GGGGCUGAU-UCUGGAUU--CGACGGGAUUAGCGA--------A-GCCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAU-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUUUAGC---------------------------------------------------------------------CUUCGCG-------------CUCCA--GCUUCC-----GCUC-GU------AAGA----CGGGGAU--------------------------------------------------------AACGCGGAGUCAAA--CCAAAAC-GAGAUC----------------------------------G---UGUGG---AAGCC--ACCGUUUGAG-------------------GAU--CGAAGCACUAAA-UU-----GAAUCAAACUA---GCUUA-AGUU---UAGCG---UGUCU--GUC---C-GC----AUGCU-UAAGUGAAA---------------------------------------------------UUAAAGAC-GAGAC---UA---AACGUGUA--GUACUG--AAGGUAG-------AGUAAUUUCGGA-CGGGGGUUCAACUCCCCC-CAGCUCCACCA
CP000026.1/2661750-2662112     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGCGG---AUGC---CCUGCCUGGG-------------------GUU---GAGGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000446.1/3323222-3323576     GGGGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCU---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUUAA--------AAGCCGCA-----AAGUUAUAGUUGCAAACGACGAUAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGCCGC--------------------------------------UUAA-----------------------UGCCGCUAG------------------------------------------------------------------------CCAUCUA-------------CCAC--ACGUUUC-----GCAC-AUG----GG-CA-----GUGGAU--------------------------------------------------------UU--GAUGGUCAU---CUCACAUCGUGCUA-------------------------------------GCGAGG--GAACC---CU-GUCCGGG-------------------GGU---GAACCGCGAAA-CA-----GUACCGGACUC---ACCGUGUGAG----AUCC---UGUCU--UUC---G-GA----GUUCAAACGGUUAAA---------------------------------------------------CAAUAGAA--AGAC---UA---AGCAUGUA--GCGCCU--UGGAUGU-------AGGUUUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
AACY020346596.1/19837-19483    GGGGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCU---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUUAA--------AAGCCGCA-----AAGUUAUAGUUGCAAACGACGAUAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGCCGC--------------------------------------UUAA-----------------------UGCCGCUAG------------------------------------------------------------------------CCAUCUA-------------CCAC--ACGCUUC-----GCAC-AUG----GG-CA-----GUGGAU--------------------------------------------------------UU--GAUGGUCAU---CUCACAUCGUGCUA-------------------------------------GCGAGG--GAACC---CU-GUCCGGG-------------------GGU---GAACCGCGAAA-CA-----GUACCGGACUC---ACCGUUUGGG----AUCC---UGUCU--UUC---G-GA----GUUCAAACGGUUAAA---------------------------------------------------CAAUAGAA--AGAC---UA---AGCAUGUA--GCGCCU--UGGAUGU-------AGGUUUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
ACIY01000561.1/557-191         GGGGACGUU--ACGGAUU--CGACAGGCACAG---------UCG-AGCUUGA-AUUG-CGUUUCGUAG-----GUUACGU-------CUACGUAAA--------AACGUUACA--GUUAAAUAUAACUGCUAAAAACGAAAACAACU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUACGCUUUAGCUGC--------------------------------------CUAAAA----------------------ACAGUUAGCG-U-------------------------------------------------------------------AGAUCCU--------------CUCG---GCAUC------GCCCAU-------GUGC----UCGAG-----------------------------------------------------------UAAGGGUCCUAA----CUUUAGUGGGAUAC---------------------------------GUUUCAACUUU----C----CGUCUGU---------------------------AAGUUGAAAAA-GAG---A-ACAUCAGACU--AGCGAUACAG-A--AUGCC---UGUCA-CUC----G-GCA---AGCUGUAAAGUGAAUCC------------------------------------------------UU-AAAUGAGUUGAC---UA---UGAACGUA---GAUUUUUAAGUGG-------CGAUGUGUUUGGA-CGCGGGUUCGACUCCCGC-CGUCUCCAUUG
CP000001.1/4909622-4909268     GGGGACGUU--ACGGAUU--CGACAGGGAUAGUU--------CG-AGCUUAG-GUUG-CGAGUCGAGG-----GGAUCG-------GCCUCGUUAA---------AACGUCA----AAGCCUAUAAUUGGCAAACAAAACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUUUCUUUAGCUGC--------------------------------------UUAAUU----------------------GCACUAAAG-----------------------------------------------------------------------GUUCCU--------------CCCU---CCAUC------GUCCAU-------GUGG----UAGGG-----------------------------------------------------------UAAGGGACUCAA----ACUAAGUGGACUAC---------------------------------GCCGGAGUUCG----C----CGUCUGA---------------------------GGACAAAGGAA-GAG--AA-CAACCAGACU--AGC-AACUUGG---AAGCC---UGUCGAUA-----G-GCC---GAAGAGUUCGCGAAACG------------------------------------------------CU--AAUAUAUCGAC---UA---CACUCGUA---GAAGCUUAAGUGCC-------GAUAUUUUUGGA-CGUGGGUUCGACUCCCAC-CGUCUCCACCA
AE016853.1/5086183-5086570     GGGGCCGAU--UUGGAUU--CGACGCCGGUGAUGA------A-A-CUUU----AGGUGCAUGCCGAGUU---GGUAACAG------AACUCGUAAAUC-----CACUGUUGCA--ACUUUCUAUAGUUGCCAAUGACGAAAACUACG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGCUCAACUAGCUGC--------------------------------------GUAA------------------------GCAGCCUAGCCGCACUUCUGGUA--------------------------------------------GCUUCGGCUCCAGCAAUCAU------------------CAGGGGAU-----GCCUGU-A----AACCCA--AA----------------------------------------------------------------AUGAUUGUCAU----AUAGAACAGGAUC-------------------------------------GUCGCC----UAG---UACGUUGUGG------------------ACGA----AGCGACUAAA-A-----CUUACGCAACUC---GCCCAAUGC----ACCCU----GCCC--GUC---G-GG----UCGCUGAGGGUUAACU--------------------------------------------------UAAUAGACA-CGGC---UA---CGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
AF440349.1/1-322               ----------------------ACAGGGAUAGUU--------CG-AGCUUGA-GUUG-CGAGUCGGGG-----GGAUCGU-------CCUCGUUAUCAA---CGUCAAAGCC------AAUAAUAACUGGCAAAGAAAAACAAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUAGCUUUCGCUGC--------------------------------------CUAAUAA------------------GCAGUAGCAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------GCCCAU-------GUGC----UACGG-----------------------------------------------------------UAAGGGUCUCAC----UCUAAGUGGGCUAC---------------------------------ACUAGUUAAUC----U---CCGUCUGA--------------------------GGUUAAAUAGAA-GAG--CU-UAAUGAGACU--AGC-UGAAUGG---AAGCC---UGUUACCG-----G-GCU---GAUGUUUAUGCGAAAU-------------------------------------------------GC-UAAUACGGUGAC---UA---CGCUCGUA---GAUAUUCAAGUGC-------CGAUAUUUCUGG--------------------------------
AY129337.1/100059-100495       GGGCCUGA--CAAGGUUU--CGACUGGUCGAUGG-A-----CAA-CUGAACA-G----CGGGCGAGUGU--UGGCCGCACU----UCUACUCUGAGUG-----A-ACGCGGC-----AACUGAUAAACGCAACCGACACGGAUGCAACGGUGACCGACGCCGAGAU---------------------------------------------------------------------------------------------------------------------------------CGAGGCCUUCUUUGCUGAAGAGGCUGCCGCUCUCG---------------------------------------UC-------------------------UGAAGGAACCAGCCUGGCUCAGCGUGCUGCUGUGCAGCGGCCAGGCUUCAUCUCUAACAGCAGCGAACGGACAUGAGGGAGCGCAAAC-----------CCUCGU--CCCAAAC---AUCAUGAA-----UGCG-----UCGCA------------------------------------------------------------CGGGCUCCAG-------CGUCAGGGG-------------------------------------CCAGAGGUGGG--------------------------------------------------------------------------AAACGGU--GUGAAACUCC----UGUCCUGG----G-GA---UCACCGACCGAUACGC---------------------------------------------------C--AAACCAGGAC----UA---CGCCCGU---------AGAACGCAGUG--AGAAAGACACCAGGA-CAGGGGUUCGAGUCCCCU-CAGGUCCACGU
CP000082.1/1764614-1764256     GGGGAUGUU--CUGGCUU--CGACGCUGGUGAUGA------A-A-CUCAA---UGAUGCAUGUCGAGAG---UAUAUGUC------CUCUCGUUAAUC-----A-AACAUAU----AUUGUUAUAGUCGCAAACGACGAAAAUUAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUAGCAG-------------------------------------CUUAAAC--------------------C-CUGUUU--------------------------------------------------------------------------ACUUGGU------------UG------CUGAUC----AUCUACA------GUUGG-------UCA-----------------------------------------------------------ACUAAGUUGAAGCGUCCGCAUGUAGAAG----------------------------------C--GCCACA---AGUG---AUUGUCUCAA------------------UUGC--U--UGGGUUUAA-A------AGUAGAGAAUC---AUCCUAUCC----AUCCU----GACU--GUC---G-GA----UCGGUGCGGACUAAAA--------------------------------------------------CCAAAGACAGAAAC---UA---AACAUGUA---GAUUC--AUGAGCG------UAAUGCUGGCGGA-CGCGGGUUCAACUCCCGC-CAUCUCCACCA
AF389964.1/19-339              --------G-------------ACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUGC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUAAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAAU-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----UAAUCAGGCUA---GUUUG-UCAG---UGGCG---UUCC----UC---C-GCA---GCUGG-CCAGCGAAU---------------------------------------------------GUAAAGAC-UGGAC---UA---AGCAUGUA--GUGCCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
BX842656.1/106010-105665       GGGGGCGUA--CUGGCUU--CGACGUGGGUGCUGA-------AG-CAU--AA-GGAG-CAUACCGGGG----CGGAUGAGG----A-CCUCGUUAAA------A--ACGUCC-----ACUUUGUAAUUGGCAACGAU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCACUUGCAG-------------------------------------CUUAA--------------------------UUAAGCAGC---------------------------------------------------------------------ACGAUCA--------------ACCU--UGUGGU-----GGUUCCG------CACU----UGG---A---------------------------------------------------------UUGAUCGU-------CAUUUAGGGACC-------------------------------------UCGGCGUGUUGGGU-----UUUCUCCA---------------------G-CAGACAUGCUUAAA-UU-----UACUGGGGGAG--AGGUCUUAGGG----AUUU---UGUCU--GUG---G-AA---GCCCGA-GGACCAAUC---------------------------------------------------UAAAACAC--UGAC---UA---AGUAUGUA---GCGCCUUA-UCGUG------GAUCAUUUGCGGA-CGGGGGUUCAAUUCCCCC-CGCCUCCACCA
CP000909.1/2590220-2589860     GGGGAUGC--UCUGGUUU--CGACAGGGAGU----G-----AAC-GCCGUAG-ACUG-CAGGUCGUGC-----CGCCCA-------GUCACGUAAAA---------GGGGCA-----AGGCAACAACUGCCAACACCAACACU---CGGGCCCA---------------------------------------------------------------------------------------------------------------------------------------------------------GGCUCGCCUGGCCCUCGCCGCUU-------------------------------------AAUAA------------------------UAGCGGCG-------------------------------------------------------------------------CGCUCG--------------CCGU---AGCUC----CCCCGAU------GGUU-----ACGGGU-----------------------------------------------------------CGAGCGUCA--------GCAGUCGGG------------------------------------UGCUCCGGUAACGCC-----U-GCCUG----------------------AGCGUUAUCGG--------CUAAGAGAUCAGGCU-----GGCCCAACGGUCGCUU-----UGCCACUCG------UGCGACUG-CGGGUGAGAUGA--------------------------------------------------A---ACGAGGGGC----UA---AACCUGUA--G-AUGUCUGCGGUCU------A--GCUUUCUGGA-CGGGGGUUCGACUCCCCC-CAUCUCCACCA
AE017125.1/1767632-1768000     GGGGCUGA---UUGGCUU-UCGACAGGAGCAAAGA------G-A-CUU--AA-GUG--CAUGUGAGCU-----GGUA----------AGCUCUAAAA------C----UACCA--CAAAUAAAUAAACGCAAACAACGCAAAUUACGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCAGCUUACGCAAAAGU----------------------------------CGCGUAAGUUUA--------------UCACACUUUU---GGAG-------------------------------------------------------------------UCGGCUU-------------AAGAAC--UUCUAA-----UCUAGC------UAGAA----UCUUU------------------------------------------------------------CAAGCUGUAAU---C--UUUGCUAGAUG----------------------------------CUCUUUUUGU----------CAUACCUU---------------------A----GCAAAAAGAAA-AGA---A--UAAGGU---UGCUUGUGGGAU-U--UAUC----UUGGGGUGUU---G-GAU--A----ACCACGAAAAGA-------------------------------------------------AA--ACAAUA-CCUA--CUA---AACAUGUA---GAUUCUU--AAGAAG----CUCAAGCUUUUGGA-CUGGGGUUCAACUCCCCA-CAGCUCCACCA
CP000270.1/3815315-3815684     GGGGGCGAC--CUGGUUU--CGACAGGGGUUGCGA-------AG-CGG--CU-AGGG-CAUGUCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AAAACGUAACUGCAAACGACGAUACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUGGCAGCC---------------------------------------UAAG-----------------------GGCCGCCGU-----------------------------------------------------------------------CCUCUGC------------CUAGUU-U-----------ACUGACG--------------GGCUAGAGUCGCAAGACCG---------------------------------GUAGCAAUACCGA-CAGAGGUC-----AUAUACGUCAGUUA----------------------------------AGCCUUGGUGGU-----------GUCAC--------------------GA----CAUCCGGGUCG-AAA--AUCUAGUGAAUCG----CCGUAGUGC----AGCG---UGUUC--GUC---C-GCG----UCGCUACGGUUAAAU--------------------------------------------------CAAAUGACA-GAAC---UA---AACAUGUA---GAACUGG--UCGUA------GAGUGCUUCUGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
AE002098.2/1031164-1030805     GGGGGCGAC-CUUGGUUU--CGACGAGGGUUGCGA-------AG-CAGA-UG-CGGG-CAUACCGGGG-----UCUCAGAU------UCCCGUAAAA-------CACUGAAU------UCAAAUAGUCGCAAACGACGAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUAGCCG-------------------------------------CUUAA-------------------------GGCUAGC------------------------------------------------------------------------CGUUGCA------------GCAGUC------------GGUCAAUG--------------GGCUGUGUGGCGA---------------------------------------------AAGCCACCGCAACGUC--A--UCUUACAUUGACUG-----------------------------------GUUUCCUACC---------GGGUUACU---------------------U---GGCAGGAAAUAA-GAC---UUAAGGUAACUG---GUUUCCAAAA----GGCC---UGUUG--GUC---G-GC----AUGAUGGAAAUAAG-AUUUU------------------------------------------CAAAU---AGACA-CAAC---UA---AGUAUGUA---GAACGC--UUUGUA------GAGGACUUUCGGA-CGGGGGUUCGAUUCCCCC-CGCCUCCA---
AF389973.1/20-337              --------G-------------ACAAGAUUCACGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUC-GCAG-------------------------------------CUUAAUA--------------------ACCUGCGCUGAGC---------------------------------------------------------------------CCUUCUA-------------CCCU--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------CGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUCAAUUCGU----GGCG---UGUCU--CUC---C-GC----AGCGGGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---CGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUUGGA-CGGG-------------------------G
ABQK01000005.1/2431625-2431263 GGGGACGUU--ACGGAUU--CGACAGGGAUGGAU--------CG-AGCUUGA-GCUG-CGAGCCGAGA-----GGCGA---------UCUCGUAA----------ACACGCAC---UUAAAUAUAACUGGCAAAACUAACAGUUUUAACCAA--------------------------------------------------------------------------------------------------------------------------------------------------------------AACGUAGCAUUAGCUGC-CU----------------------------------------AAUA----------------------AGCGCAGCG----------------------------------------------------------------------AGCUCUU--------------CCUG---ACAUU------GCCUAU-------GUGU----CUGUG-------------------------------------------------------------AAGAGCAC-----AUCCAAGUAGGCUAC---------------------------------GCUUGCGUUC-----C----CGUCUGA---------------------------GAACGUAAGAA-GAG---A-UGAACAGACU--AGC-UCUCGGA---AGGCC---CGCCCGCA-----G-GCA---AGAAGAUGAGUGAAACC------------------------------------------------AU-AAAUAUGCAGGC---UA---CGCUCGUA---GACGCUUAAGUAAU------CGAUGUUUCUGGA-CGUGGGUUCGACUCCCAC-CGUCUCCAUAC
AF137379.1/97379-97053         GGGGUUGU--CAUGGAAU--CGACGUCUCUUCUAAG----AACG-AAAGGUU-AAAG-CAGGUCGAGG------UCGAAGAU---GGACUCGUACUCU----CCACUUCAUU----GCUUGAUUGCAUGCUAAUCAGAUUCUUCCUUUCUCUCGCCGGGUAGCCGUUGCUGCUUAAGCGAGUUUCUAGUGC-------------------------------------------------------------------------------CACUUUGUCACUAGUUUGUAUUAUGAGUUUCACACUCACUUCAAUG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGGUGAUAGAUACUACAUAUCAC----UCCUGCUUAGAGGGUCAUCUAAGC----------------UA---AACCAUGU---GAAUAUAACCUUUCGG--GCCUCGAGAGACGGA-AGUGAGUUCAAUUCUCAC-CAACUCCACCA
FM211187.1/775852-776199       GGGGUCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GGCAUAU-UUUG-CGACUCGUG------UGGC-----------GACGUAA-----------ACGCUCA--GUUAAAUAUAACUGCAAAAAAUAACACUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUCUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCAGGCGU---------------------------------------------------------------------GACCCG---------------AUUU--GGAUU------GCUCGU-------GUUC-----AAU------------------------------------------------------------GACAGGUCUUAU----UAUUAGCGAGAUAC---------------------------------GAUUAAGCC------U----UGUCUAG---------------------------CGGCUUGAUAA-GAG---A-UUGAUAGACU--CGCAGUUUCU-----AGACU-UGAGUUAUGU----G-UC-----GAGGGGUUGUUAAAA--------------------------------------------------U--AAUACAUAACC---UA---UGGUUGUA---GACAAAUAUGUUG-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUUA
AP010918.1/3415454-3415133     -----------------G----ACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGUUGCGAC-------CAAAUAAGCGCCGAUUCACAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGACGGCUAGU-------------------------------------------------------------------CUGUCAG--------------------ACCGGGAA---CGCCCUCGG----CCCGGA--CC-----------------------------------------------------------------CUGGCAUCAG------CUAGAGGGAU-C--------------------------------CACCGAUGAGUC---------CGGUCGC----------------------G-G-GACUCCUCGGGA-CAA---CCACAGCGACUG---GGAUCGU--CAUCUCGGC--UAGUUCGCGUG---A-CCGGGA------GAUCCGAGCAGA----------------------------------------------GGC----AUAGCGAAC---UG---CGCACGGA----GAAGCCUUGAGGG------AAUGC-CGUA--G------------------------------G
CP000002.3/3469669-3469314     GGGGACGUU--ACGGAUU--CGACAGGGACGGAU--------CG-AGCUUGA-GCUG-CGAGCCGAGA-----GGCGA---------UCUCGUAA----------AAACGCAC---CUAAAUAUAACUGGCAAAUCUAACCAGAACU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------UAGCACUAGCUGC-CU----------------------------------------AAUU----------------------AGCGCAGCG----------------------------------------------------------------------AGCUCUU--------------GCCC---GCAUC------GCCUAU-------GUGC----CGGUU-----------------------------------------------------------AAGAGCCCAUAA-----CGAAGUAGGCUAC--------------------------------GCUUGC--GCCC----C----CGUCUGA---------------------------GGGCGCAGGAA-GAG--AC-UCAUCAGACU--AGC-UCUCCUA---GGGCC---CGCCCGCA-----G-GCA---CGAAGAUGAGCGAAACU------------------------------------------------AA--AUAUGCAGGGC---UA---CGCUCGUA---GACGCUGAAGCAAU------CGACGUUUCUGGA-CGUGGGUUCGACUCCCAC-CGUCUCCAUCU
CP001358.1/1443619-1443282     --------A--------C------GGGGACGUGGA-------AG-CCGU--A-GCGG-CAGGUCGAGG----CGCCGCUGG------CCUCGUAAA---------AAGCGGC----ACAAAAGUAAUUGCCAACAACGAUUAC---G------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUACGCUUACGCUG-------------------------------------CCUAAUA--------------------A-CAGCG-AGGC-AAUGACCGU--------------------------------------------------UUAACGGUCGCGCCGAU-------------CAGGG--CCAUG------CCUGAUA-----A--------CCCUG------------------------------------------------------------AUUGGCGAC-------ACUUAUCAGG-------------------------------------CUGGCGAAAACCGG------CUCUCGCC-------------------GGGGUUUUUCGCGAGGA-GUU---UACCGGCGGGAU--UGCUGCGUUGU-----GCC---UGGUC--AGG---G-GC---CAACAGCGCGGUGAAAU--------------------------------------------------ACAUACUU--GACC---UA---AACCUGUA---GAUGCUUC-GUGUG------GAAUGUUCUCGGA-CGGGG------------G-----------U
AL954747.1/2785135-2784776     GGGGGCGA--UCCGGUUU--CGACGUGGGUUGCAA-------AG-CAGC-GC-AGGG-CAUACCGAGG-----UUCAGUAC------CCUCGUAAAA-------CAGCUGAA-----AAAAAAUAGUCGCAAACGACGAAAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUAGCCG-------------------------------------CUUAAU----------------------CCGGCUAAA------------------------------------------------------------------------CUCCACA------------CCGGUG------------GGCCUCAA--------------CGCCGGGUCUGGC---------------------------------------------AACAGACAGUGGAGUC------AUUAACGAGGAUC-----------------------------------GCGUUUUGCA---------GGGUUACU---------------------U---UGCAGAGCGCUA-AAA---AAUAGGUAACUC---GCCUGUCAUC----AGCC---UGCCG--GUU---G-GC----GGAUGCCAGGUCAA-AUU---------------------------------------------AAAU----AACA-UGGC---UA---AGUAUGUA---GAACUG--UCUGUA------GAGGACUUGCGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
AF389961.1/19-340              --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GCC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--AGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
AE014075.1/3018179-3018541     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-ACA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--URAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGAAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
AE001363.1/138493-138068       GGGGGUGU--AUAGGUUU--CGACUUGAAA-----A-----UGA-AGUGUUA-AUUG-CAUGCGGAGGG---CGUUGGCUG-----GCCUCCUAAA--------AAGCCAAC----AAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUUAGCUU---------------------------------------------------------------------------------------------------------------------------------------GUUUGACUCAGUAGAGGAAAGACUAGCUGCUU-------------------------------------AAUUAGCA-------------------A-AAGUUGUUAGCUAGAUAAUCU-------------------------------------------------CUAGGUAACC-CGGUA--------------UCUGC--GAGCU-----CCACCAGA-----GGCUU----GCAAA------------------------------------------------------------AUACCGUCA------UUUAUCUGGU---------------------------------------UGGAACUUACUUUCU-CUAAUUCUCAA-------------------GGAAGUUCGUUCGA------G--AUUUUUGAGAGU------CAUUG-GCUGCUAUAG---AGGCUUCUAG---C-UAAGGGAGUCCAAUGUAAACA---------------------------------------------------A--UUCUAGAAGA----UA---AGCAUGUA--G-AGGUUAGCAGGGAG-----U--UUGUCAAGGA-CGAGAGUUCGAGUCUCUC-CACCUCCAUUA
CP000468.1/2914707-2915069     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000388.1/2078693-2078337     GGGGCUGAU-UUUGGAUU--CGACAAGAUUCUUGA--------G-GCUUU---AGGUGCAUGCAGAGG-----AGCGGUUU-----GCCUCUUAAA--------AAGCCGCA-----UUUAAAUAGUCGCAAACGACGAAAACUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAG-CCGC--------------------------------------UUAA--U-------------------AACCGGCUAAGCCCU-----------------------------------------------------------------UC--------------------CACUC-AUACUCU-----UUCU-GCU----AG-UA-----GAGGUU---------------------------------------------------------C-GGAAGGUCA----UCCCAGC-AGAAUA-------------------------------------GCGAGG--GAACC---UU-GUCUAAG-------------------GGU---GAACCGCGAAA-UA-----GUAUUAGGCCC---GCUAUGAGAA----AUCC---UGUCU--GCC---G-GA---GUUCGAAAUAGUUAAA---------------------------------------------------UAAAAGAC--AGAA---UA---AGCAUGUA--GUACCG--ACGGUUA-------ACGUUUUUUGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CU928163.2/3048497-3048859     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGACGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CP000312.1/1455328-1455014     ----------------------ACGGGGGUAAG--------AUG-GGUUUGA-UAAG-CGAGUCGAGGG---AAGCAUGGU-----GCCUCGAUAAUA-----AAGUAUGCA----UUAAAGAUAAACGCAGAAGAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUUGCAUUAGCAGC--------------------------------------UUAAUUU------------------AGCGCUGCU--------------------------------------------------------------------------CAUCCUU--------------CCUC--AAUU-------GCCCAC-------GGUU----GAGAG-----------------------------------------------------------UAAGGGUGUCAUUUAA---AAGUGGGGA------------------------------------ACCGAGCCUAGC-------AAAGCUUU--------------------GA-GCUAGGAACGGAAU-UU------AUGAAGCUUA---CCAAAGAGAA-----AGU--UUGUCU--GUG---G-ACG----UUCUCUGAGGGAA-UU------------------------------------------------UUAAAACACA-AGAC---UA---CACUCGUA---GAAAGUCUUACUGG-------UCUGCUUUCGGA------------------------------C
AE015928.1/5798212-5798608     GGGGUUGA---CUGGAUU--UGACAGCGGGC----A----GAAA-UGGUAGG-UAAG-CAUGCAGUGGG--UCGGUAAUU------UCCACUUAAAUC-----UCAGUUAUC----AAAACUUUAUCUGGCGAAACUAAUUAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCUUGCUGCUUAAUCGAAU---------CACAGUAGAUUAGC-UUAA--UCCAGGCACUAGGUGCCAGGA-CGAGA----------------------------------------------------------------------------CAUCAC-------------UCGGA--AGCUGU----UGCUCCGA-----AGCAU----UCCGGUU--------------------------------------------------------CAGUGGUGCAGU-----AACAUCGGGGA--------------------------------------UAGUCAGAAGCG-------GCCUCG-----------------------CGUUUUUGAU--------GA-AACUUUAGAGGAU---AAGGCAGGAAUUGAU-------GGCUUUGG--------UUCUGCUCCUGCACGAAAAU-------------------------------------------------UU---AGGCAAAGA----UA---AGCAUGUA--G-AAAGCUUAUGAUUU-----C--CUCGUUUGGA-CGAGGGUUCGAUUCCCUC-CAGCUCCACCU
BA000043.1/3063829-3063478     GGGGACGAU--CCGGAUU--CGACAGGGGUAGGU--------CG-AGCUUAA-GCGG-CGAGCCGAGG-----GGGACG-------UCCUCGUAAAA--------ACGUCAC----CUAAAGAUAACUGGCAAACAAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGCUUUAGCUGCCU----------------------------------------AAUU---------------------GCUGCAGCUA-----------------------------------------------------------------------GCUCCU--------------CCCG---CCAUC------GCCCGC-------GUGG-----CGUUC----------------------------------------------------------GAGGGGCUCAUA-----UGAAGCGGGCUAC---------------------------------GCCCAAAUCCG----C----CGCCUGA---------------------------GGAUGAGGGAA-GAG--AC-GAACCAGGCU--AGC-CGCCGGG---AGGCC---UGUCGGUA-----G-GCG---GAACGGACGGCGAAGC--------------------------------------------------G-AAAUAUACCGAC---UA---CGCUCGUA---GAUGCUUAAGUG-G------CGAUGCCUCUGGA-CGUGGGUUCGACUCCCAC-CGUCUCCAUUU
AY082653.1/1-337               ------------------------AGGUUGGCGAAC-----GCU-GCUCUGU-GAUU-CAGGUCGAGA----G-UGAGUC-U---CCUCUCGCAAAUC----CAAGGCUCAAA---ACAAAAGUAAAUGCGAACAAUAUC------GUAAA----------------------------------------------------------------------------------------------------------------------------------------------------------------AUUUGCUCGUAAGGAAGCC-------------------------------------CUAG------------------------UUGCUGCCUAAUAGCCUCUUAU-------------------------------------------------AGGUCCGAGC-------------------GUCUUU--AGUCCG----ACUCCGUUA---AGGGCU----AGAGAC----------------------------------------------------------C--AACCCC-----------AACGGAUG-----------------------------------CUCUAGCAAGUAUU------CUCUGGU------------------------UGACUUGCUAGCUA-AG----ACUUAAUCAGAG--C---------------------------------------------------------AUCCUACGUUCGGGAUAAUGAACGA--UUCCCGCCUUGAGGGUCAGAUAGGC----------------UA---AACCUGU----GAAUGAGCGGAGGGUC--AAUACCCAAUUU----------------------------------
AE008691.1/989409-989759       GGGGGUGUG--UUGGUUU--CGACGGGGGCGGU--------CGA-GGUAAAA-GUAG-CGAGCCGAGUU---CUCCACCA-------GCUCGUAAAA-------AAGGUGGA-----AAAAAAUAAACGCAGACAGAGAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCGCUUACGCUGCCU----------------------------------------AAU-U-------------------AAAGGCGGC-------------------------------------------------------------------------CGUCCAG---------------CCU--GAAAU------GCCCAC------GUUUC----AGGA-------------------------------------------------------------CUGGGCGUCAA---A--AGAGUGGG---G---------------------------------AACUGGUUUUGCC--U----GCGCCUCG---------------------G-GGCAAAACCGGA---------AUAAUGAGGCUA---CCGAAGCGGU-----UAUC-CUGUCG--CUG---G-GAG--A-ACCG-CUGAGGGAAAG------------------------------------------------CUAAAACAG--CGAC---UG---CGCUCGGA---GAAGCUUUUACCGG-------GACGCCUUCGGA-CCGGGGUUCGAAUCCCCG-CACCUCCACCA
CP000681.1/1371577-1371222     GGGGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCU---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----CAGUUAUAGUUGCAAACGACGAUAACUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGC-AGC--------------------------------------UUAG------------------------GCUAGCUAG-----------------------------------------------------------------------CCAUCUG-------------ACAC--AGGUCUC-----UCAA-AUG----GG-CG-----GUGUAU--------------------------------------------------------AC-AGAUGGUCAU---CUUACAU-UUGAUA-------------------------------------GCGAGG--GAACU---CC-GUCCGGG-------------------GGU---GAACCGCGAAA-UA-----GUACCGGACUC---GCCCGAUGAA----AUCC---UGUCU--UUC---G-GA---GUUUAUUCGGGUUAAU---------------------------------------------------UAAAAGAG--AGAC---UA---AGCAUGUA--GUGCCU--UGGAUGU-------AGGUGUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
CP000386.1/1626790-1626431     GGGGGCGA--UCCGGCUU--CGACGGGAGCGGAC-------AGC-GUCCGGU-GAGA-CGAGCCGAGU----UCGCCGGA------GACUCGUAAA-------ACGCCGGCAC---CUAAACAUACACGCCAACGACAGA------GA----------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUGGCGCUGGCUGCCU-----------------------------------AAAACCAC--------------------U-GGCAGCC-------------------------------------------------------------------------CGUCGG---------------------UCCGGGC---GGCCCACGG----CCCGGU--UU-----------------------------------------------------------------CCGGCGUCGG------UUAGUGGGCUU----------------------------------ACCUCCCGGGCUCC------GGCCC--------------------------GGGGUCCGGGGGGG-ACA--CCACAGCAGGGCU----AGCCC----C-UCUGCG----GCGCCCCGGU-CC-GCAGAG---GCCGGUGAAGCUA-------------------------------------------------AA----CCGG-GUGC---GA---CGCUCGUA--CAAUCUCCCGGAUGG-------CGCGCUCGCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACUG
CP000142.2/2135368-2135011     GGGGGUGAC--ACGGUUU--CGACGGGGAUUGGA--------AG-CGA--AG-GUGG-CAUGCCGGGGA---CGCCAGUUG----G-CCUCGUUAAA------A-AACUGGC----AUACAUACAAACGCCGAUACUGACGUU---U------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGUACGCACUGGCAG-------------------------------------CUUAAUU--------------------GCUGCCUCGUCUU---------------------------------------------------------------------GAGUUCC-------------UUCGC--CUGCGC-----GG-------------------------------------------------------------------------------------AGCUUAAAG-A--CGUCAAUUGAG--------------------------------------UGGGCUAGUUUCGG------UGAGCGU---------------------UCGCGGUGCCGAAGCG-AAAU-UUAAGCGAACUCG---CCUGAUACAC----AUCC---UGUCG--ACG---G-GA---GUUGUAUCCGGUUAAAC-------------------------------------------------UCAAAACAU--CGAC---UA---CGCAUGUA---GAAGCCUU-AUGUG------AAAGAUUUUCGGA-CGCGGGUUCGAUUCCCGC-CACCUCCACCA
CP000436.1/1530051-1529685     GGGGCUGAU-UUUGGAUU--CGACGGAAUUAGCGA--------A-GCCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAU-------AAACCGCA-----AAACAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCAUAGC---------------------------------------------------------------------CUUCACU-------------CCCUA--GCUUUC-----GCUC-GU------AAGA----CGGGGAU--------------------------------------------------------AAAGUGGAGUCAAA--UCCAAAC-GAGAUC----------------------------------G---UGUUG---AAGCC--GCCGCUUUAG-------------------GAU--CGAAGCAUUAAA-UU-----GAAUAAAGCUA---GUUUU-UUGA---UGGCG---UGUCU--GUC---C-GCA---GUCAA-UUUACGAAA---------------------------------------------------UUAAAGAU-UAGAC---UA---AACGUGUA--GGACUG--AAGGUAG-------AGUAAUUUCGGA-CGGGGGUUCAACUCCCCC-CAGCUCCACCA
CP000967.1/3496947-3497343     GGGGGUGCA--CUGGUUU--CGACGGGGGUCGCGA------A-G-UCGC--U-UGGCGCAUGCCGAGG----GGGCAGCUU-----UCCUCGUUAAUC-----C-AGCAGCA-----AACUUUUAGUUGCCAACGAUGACAACUA-CGGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------UCGGACUUCGCUAUCGCCG-------------------------------------CUUAAU-----------------------UGGCUUUAGUUGUCGUUCUACAGC------------------------------------------CGCCUAAGGCGAACCCCCGA-A----------CCUA-----CUUGUG-----CCCGUGCU---CGUAGG-------UG--------------------------------------------------------------UAGGGUCAU------UAUCACGGAA------------------------------------CCAUCGGU----AGU---GGCUGCCUGUC-----------------AGCU----ACCGGUUAGA---U---AAAGCAGGCUG----GUUUUCAGGU----GCGCU-UUGCCA--ACC---G-UGC---UGCCUGGGAAUGAGAU--------------------------------------------------CUAACGGA--GGGC---UA---AGCAUGUA--GUGCUG---GGGAUG------GAGUGCUUCCGGA-CGGCGGUUCGAUUCCGCC-CACCUCCACCA
AM946015.1/984321-984670       GGGGUUGUU--ACGGAUU--CGACAGGCACUA---------UGA-GGCAUGU-UUUG-CAACUCAUC------GGCA-----------GAUGUAAA----------AAUGCCA--GUUAAAUAUAACUGCAAAAAAUACAAACUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCUUUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCUAGCGU---------------------------------------------------------------------GACUUC--------------UUCA---AGAUU------GCUUGU-------GUCC-----UGA------------------------------------------------------------UAGAAGUCUCAA----AAACAGCAAGCUAC---------------------------------GACUAAAGCC-----U----UGUCUAG---------------------------AGCCUUAGUAA-GAG---A-UUUAUAGACU--CGCUAAGUAA-----UGGCU-UGAGUUAUGU----G-UC-----CUUACUUAGUCAAAA--------------------------------------------------C--AAGACAUAACC---UA---UGGUUGUA---GACAAAUAUGUUG-------GCAGGUGUUUGGA-CGUGGGUUCGACUCCCAC-CAGCUCCAUUA
AY082651.1/2-338               -------------------------GUGGAGUGAAA-----GCU-GCUCCGU-GAUU-CAGGCCGAGA----G-UGAGUU-G---UCUCUCGUCAAUC----CCCAACUCAAA---AAAAAAGUAAAUGCGAACAACAUC------GUUCC----------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCUCGUAAAGCGGCU-------------------------------------CCUG------------------------UAGCUGCCUAAAAACCUCUAGC------------------------------------------------AGGUUUGAGCG-------------------GUCUAU--AGCUUG----ACUCCGUUA---AAGGCU----ACAGACA---------------------------------------------------------A--ACCCUC-----------AACGGAUG-----------------------------------CUCUAGUAAGGUUU------CUCUGGU------------------------U-ACUUGCUAGUUA-AG----ACUCAACCUGAG--U---------------------------------------------------------AUCCUGUCAUCCGGGAUAAUGGAUG-GUCCCCGCCCAGAGGGUUAAAUGGGC----------------UA---CGCCUGU----GAAUGAGCGGUAGGCG--AAUACCUCUGC-----------------------------------
AY491435.1/1-310               ------------------------GGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CUCAAAA-GAGAUC----------------------------------G---CGCGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGUGCUAAA-AC-----UAAUCAGGCUA---GUUCG-UUAG---UGGCG---UGUCU--GUC---C-GCA---GCUGG-CGUGCGAAU---------------------------------------------------GUAAAGAC--AAAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUC----------------------------------
ABGO01000552.1/2485-2074       GGGGGCGA--UCUGGUAU--CGACCGGGU-GU---C----GGAA-GUGUUCG-GUGG-CGUGUCGUGGU--UGAUCAGCUG-----GCCACGUAAA--------AAGCCGAU----CAAAAUUUAACUGCUGAACCGCAGUAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCCUCGCGGCUU------------------------------------AAGUGCCG--------------------A-GAGCCGUU-------------------------------------------------------------------------------------------CUGGCA--GCUUC------GCCUGA------GAGG-----UGCUAG----------------------------------------------------------U-CCGGAC--------GCAAGUCAGGCUCGCGGGAACUCGAGGAGAGGGGACAACCACCCGAUCCGCCUCGGCGGC--------CGUUCCUGCUAAAAAAAUCUGGCCGAUAGUUGUGUCGGGGUC-----CCGCUCGUAGGAACCCGGUAACAACGAACGUGCGGCGG-CCCGUUAAACGGUGC-GCCGCAGGAA------------------------------------------------------------------UAUACGAGC----UA---CACACGUA--G-AUGCCGG-CGCGGA-----A-GCGCCUCGGGA-CCGGGGUUCGAUUCCCCG-CGCCUCCACUC
AY491434.1/1-311               ------------------------GGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUU-----GCCUCGUUAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUCUGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----UGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----UAAUCAGGCUA---GUUCG-UUAG---UGGCG---UGUCU--GUC---C-GCA---GCUGG-CGUGCGAAU---------------------------------------------------GUAAAGAC--AAAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGAAAUUUC----------------------------------
CP000606.1/1467345-1466990     GGGGGCGAU-UCUGGAUU--CGACAAGAUUCACGA--------A-ACCCU---AGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----CAGUUAUAGUUGCAAACGACGAUAACUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGC-AGC--------------------------------------UUAG------------------------GCUAGCUAG-----------------------------------------------------------------------CCAUCUU-------------GCUC--ACGUUUC-----UCAA-AUG----GG-CA-----GAGUAU--------------------------------------------------------UA-AGAUGGUCACC--UUUACAU-UUGAUA-------------------------------------GCGAGG--GAACC---AU-GUUCAGG-------------------GGU---GAACCGCGAAA-CA-----GUACUGAACUC---GCCAAUAACA----AUCC---UGUCU--UUC---G-GA----GUGUUGUUGGUUAAC---------------------------------------------------CAAUAGAA--AGAC---UA---AGCAUGUA--GCGCCG--AGGAUGU-------AGGCUUUUUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
CP000416.1/1289472-1289843     GGGGCCGUU--CUGGAUU--CGACUGGUAUAG---G-----UUG-CGCCCCA-ACUG-CACUCCGUAG-----CGG-CAU-------CUACGUUAA--------AAGGUCC-AG-UUUAAUUAUAACUGCAAAAAAUAAUAACAAUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUACGCUUUAGCUGC--------------------------------------UUAAUA---------------------GGCGCUUAACG---------------------------------------------------------------------UAGAUCCU-------------CCUA---GGCUU------GUCCGU-------GGUC-----UAGAU----------------------------------------------------------CUGGGUCCUAAA-----UUUAACGGACUUA--------------------------------CGCUAACGACUC----C----CACCUGA---------------------------AGUACGUUAGA-AGAG-AA-AAAUCAGGUU--AGCUGUUCAUGU--GGGCC--CUGACAGGC-----G-GCA---AGUUGGGCAGUGAAACC------------------------------------------------UU-AAGUAGUCUGAA---UA---UGAGUGUA---GACGUUGGGGUGG-------CAAUAUGCUAGGA-CGCGGGUUCGAUCCCCGC-CGGCUCCAUAU
AAAL02000007.1/78420-78066     GGGGGUGCA--CUGGCUU--CGACGGGGGUCACAA------A-A-UCAC--U-UGGUGCAUGCCGAGG----GGGCCGCUU-----UCCUCGUAAAUC-----C-AGCAGCA-----CACUUAUAGUUGCCAACGAAGACAACUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUCUAGCC------------------------------------GCUUAA------------------------GGCUUAAGC-----------------------------------------------------------------------CUCGA--A----------ACUG-----CUUGUG-----UCCGUGCU---CGCAG--------CG--------------------------------------------------------------UAGAGUCAU------CAUCACGGAA------------------------------------CCGCUGAG---ACGU---GGCUGUCUGCC-----------------CACA----CUUGGUUAAA---U---CUAGCAGACUG----GUUUCCGGGU----GCGCU-UUGCCU--GUC---G-UGC---UGCCCGGCGACGAGAC--------------------------------------------------CUAACGGCC-AGGA---UA---AGCAUGUA--GGGCCG---GGGAUG------GAGUACUUUCGGA-CGGCGGUUCGAUUCCGCC-CACCUCCACCA
CP000141.1/258392-258750       GGGGGCGUA--AAGGGUU--CGACGGGGGAGCGA-------AGG-GCCGAAA-GUAG-CGAGGCGAGGA---CCCCAUCUU-----ACCUCGUUAAA------AAUGGUGGG-----AAAAGAUAACUGCCAACGAAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUACGCUUUAGCUG------------------------------------C-UUAAU-A------------------ACGCAGCUA--------------------------------------------------------------------------CGUCCUG---------------ACG--GAAGCU----UGCCCGG-G----GCUUC----UGU--------------------------------------------------------------CGGGGCGUGACC--G---GACCGGGC--U---------------------------------GGCUUAUGAAGGG--------UGUCCCG---------------------G-CUCUUCAUAAGCGA-G-A--UUUUACGGGAUA----GCCCGAUUGU-----GGC--CUGCCG--GUA---G-GCA----CCAAUCGGGUGAAAG-------------------------------------------------CAAAAAUAC--CGGC---UG---CCCUCGGA---GAAGCUUUCGGUUC-------UUGUCCUCCGGACGGUGGGUUCGAUUCCCCC-CGCCUCCACCA
CP001215.1/4837167-4836853     --------A--------C------AGGGAUAGUU--------CG-AGCUUAG-GUUG-CGAGUCGAGG-----GGAUCG-------GCCUCGUUAA---------AACGUCA----AAGCCUAUAAUUGGCAAACAAAACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUUUCUUUAGCUGC--------------------------------------UUAAUU----------------------GCACUAAAG-----------------------------------------------------------------------GUUCCU--------------CCCU---CCAUC------GUCCAU-------GUGG----UAGGG-----------------------------------------------------------UAAGGGACUCAA----ACUAAGUGGACUAC---------------------------------GCCGGAGUUCG----C----CGUCUGA---------------------------GGACAAAGGAA-GAG--AA-CAACCAGACU--AGC-AACUUGG---AAGCC---UGUCGAUA-----G-GCC---GAAGAGUUCGCGAAAUG------------------------------------------------CU--AAUAUAUCGAC---UA---CACUCGUA---GAAGCUUAAGUGCC-------GAUAUUUUUGGA-CGUGG------------G-----------U
CP001145.1/429109-429461       GGGGGCGAA--AAGGUCU--CGACGGCGAGUCG---------GA-GCCUUGA-GCUG-CAGGCAGGGUU---GGCUGCCA-------CACCUUAAAA-------AGGGUAGCAA-GGCAAAAAUAAAUGCCGAACCAGAAUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCACUAGCUGCUUA-----------------------------------------AU----------------------GUAAGCAGC------------------------------------------------------------------------CGCUCUC---------------CAA--ACUGA------GGCUGC-A----UAAGU----UUGG-------------------------------------------------------------AAGAGCGUCAACCCA-UGCAGCGGC---------------------------------------UCUUAAGCAGU--------GGCACCAG------------------CUGUUUAAGGGUGAAAAG-A--------GUGGUGCUG---GGCAGUGC-------GGUU-GGGCUU--CCU---G-GGC-----UGCACUGUCGA--GA-----------------------------------------------CUUCACAGGA--GGGC---UA---AGCCUGUA---GACGCGAAAGGUGG-------CGGCUCGUCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
AE008923.1/1746069-1745673     GGGGGUGCA--CUGGUUU--CGACGGGGGUCGCGA------A-G-UCGC--U-UGGCGCAUGCCGAGG----GGGCAGCUU-----UCCUCGUUAAUC-----C-AGCAGCA-----AACUUUUAGUUGCCAACGAUGACAACUA-CGGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------UCGGACUUCGCUAUCGCCG-------------------------------------CUUAAU-----------------------UGGCUUUAGUUGUAGUUCUACAGC------------------------------------------CGCCUAAGGCGAACCCCCGA-A----------CCUA-----CUUGUG-----CCCGUGCU---CGUAGG-------UG--------------------------------------------------------------UAGGGUCAU------UAUCACGGAA------------------------------------CCAUCGGU----AGU---GGCUGCCUGUC-----------------AGCU----ACCGGUCAGA---U---AAAGCAGGCUG----GUUUCCAGGU----GCGCU-UUGCCA--ACC---G-UGC---UGCCUGGGAACGAGAU--------------------------------------------------CUAACGGA--GGGC---UA---AGCAUGUA--GUGCUG---GGGAUG------GAGUGCUUCCGGA-CGGCGGUUCGAUUCCGCC-CACCUCCACCA
BA000030.3/6202757-6203145     GGGGAUGA---UCGGUUU--CGACAGCGGCUGU--------UGA-AGCAGGG-GAAG-CGUGUCGAGG-----AAGCGGC-AA-UGAUCUCGUAAACCA---UAUGUCGCAA-------AAAAUAAUCGCCAAUACCAAGAGCGAUUCCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------AGUCCUUCGCCCUCGCUGC------------------------------------CUAAUAA-----------------------GCAGUGAGUGAGGGACCC------------------------------------------------------UUAAUGGGUGUCAG--------------------CCCGGGAG---UGUUCCCGA----CCCGGA--CC-----------------------------------------------------------------CUGGCAUAAU------CUAGGGGACU-A--------------------------------AACCAUCGAGCC---------CGGUCAC----------------------G-G-GGUUCGAUGGGA-AAU--CAAACAGUGACUG---GGCCCGU---C-GGCGAC--UUGUUCGCGUG---A-UCGCCG------GGGCCGAGAAA-----------------------------------------------AUC----GCAGCGAAC---UG---CACACGGA----GAAGCCCUGAUUC-------UGCACCGGUGGA-CGCGGGUUCGAUUCCCGC-CAUCUCCACGA
AF389976.1/18-333              --------G-------------GCAAGAUUCACGA--------A-ACCAA----GGUGCAUGCCGAGG-----UGCGGUAG-----GCCUCGUUAAC-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUC-GCAG-------------------------------------CUUAAUA--------------------ACCUGCGCUGAGC---------------------------------------------------------------------CCUUCUC-------------CCCU--AGCUUGC-----CUGU-GUC----CUAG------GGAAU-----------------------------------------------------------UGGAAGGUCAU---CCUUCAC-AGGAUC-------------------------------------GUGUGG---AAGU---CCUGCUCGGG-------------------GCG---GAAGCAUUAAA-AC-----CAAUCGAGCUA---GUAA-UGCGU----GGCG---UGUCU--CUC---C-GC----AGCGUGUUGGCGAAU---------------------------------------------------GUAAAGAG--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGUAAUUUUGGA-CGGG-------------------------G
AAGX01000013.1/8741-9125       GGGGAUGUU--UUGGGUU--UGACAUAAUGCUGA-------UAG-ACAAACA-GUA--GCAUUGGGGU-----AUGC----------CCCUUACA-------------GCGCU--AGGUUCAAUAACCGACAAAGAAAAUAACGAAGUGUUGGUAGAUCCAAAUUUGA------------------------------------------------------------------------------------------------------------------------------UCAUUAACCAACAAGCAAGUGUUAACUUUGCUUUUG-------------------------------------CAUAA------------------------GUAGAUACUAAAG-----------------------------------------------------------------CUACAGCUG--------------------GUGAAU-----AGUCAUAG----UUUGC---------------------------------------------------------------------UAGCUGUCAUAG-UU----UAUGACUC------------------------------------GAGGUUAAAU-----------CGUUC----------------------A---AUUUAACCUUUA-AAA--AU---AGAACUUG---UUGUUUCC-----AUGAU---UGUUU-UGUG---A-UCA---AUUGGAAACAAGACAAA------------------------------------------------AA--UCCACA-AAAC---UA---AAAUGUA----GAAGCUGUUUGUUG------UGUCCUUUAUGGA-AACGGGUUCGAUUCCCGU-CAUCUCCA---
CP000100.1/989730-989337       GGGGCUGU--AAUGGUUU--CGACGUGUUGGUGAAU-----CCU-UCACCGU-GAUU-CAGGCCGAGA----G-GGAGUC-C---ACUCUCGUAAAUC-----CAGGCUCA-A---CCAAAAGUAACUGCGAACAACAUC------GUUCC----------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCUCGUAAGGCUGCU-------------------------------------CCUG-------------------------UAGCUGCUUAAACGCCACAAACU--------------------------------------------UUCUGGCUCGAGC-------------------GUCUAG--UCGUAG----ACUCCGUUA---AUACGC----CUAGACUU-------------------------------------------------------AA--ACCCCC-----------AACGGAUG-----------------------------------CUCGAGUGGCGGC-------CUCAGGU------------------------CCGUCCUCUCGCUA-AG----CAAAAACCUGAG--C---------------------------------------------------------AUCCCGCCAACGGGGAUAAUCGUUG-GCUCCCGCACAGUGGGUCAACCGUGC----------------UA---AGCCUGU----GAACGAGCGGAAAGUU--ACUAGUCAAUGCGGA-CAGCGGUUCGAUUCCGCU-CAGCUCCAUUU
CP000570.1/2853082-2853451     GGGGGCGAC--CUGGUUU--CGACAGGGGUUGUGA-------AG-CGG--CU-AGGG-CAUGUCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AAAACGUAACUGCAAACGACGAUACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUGGCAGCC---------------------------------------UAAG-----------------------GGCCGCCGU-----------------------------------------------------------------------CCUCUGC------------CUAGUU-C-----------ACUGACG--------------GGCUAGUGUCGCAAGACCG---------------------------------GUAGCAAUACCGA-CAGAGGUC-----AUAUACGUCAGUUA----------------------------------AGCCUGUCCGGC-----------GUCAC--------------------GA----CGGACAGGUCG-AAA--AUCAAGUGAAUCG----CCGUAACGG----AGCG---UGUUC--GUC---C-GCG----ACGUCACGGUUAAAU--------------------------------------------------CAAAUGACA-GAAC---UA---AACAUGUA---GAACUGG--UCGUG------GACCGCUUCUGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
CP000439.1/15626-15294         GGGGGCGAA-UAUGGUUU--CGACAUGAAUGUCAA------A-A-UCUA----AGGUGCAUGCCGAGG----AAGUACCGU----AACCUCGUUAAUA-----A-CAGUACAAAUGCCAAUAAUAACUGGCAACAAAAAAGCAAACCGCGUAGCGGCUAACG------------------------------------------------------------------------------------------------------------------------------------------ACAGCAAUUUUGCUGCUGUUGCUAAAGCUG-------------------------------------CCUAG----------------------UCUAGCUUAAUAACCUA-------------------------------------------------------------GAUGCGCACGGA----------UAUGA----UAGUCU----UUCUUAUGA----CACUAUC-UAUACAU-----------------------------------------------------------CCGUUCAUAUU-----CCGCAUAAGA---------------------------------------CGGUCU--UUGCU---UUUUGUCUGG------------------GAGUU-A-AGGCUGUAU--------UUAACAGACUC----GCUA-ACUAUU--ACCCU---GGCUA--AUU---G-GGG---AAUAG------------------------------------------------------------------------------------------------------------------C------------------------------------------U
BA000035.2/872709-873084       GGGGCUGA--CAUGGUUU--CGACUACGUUGAU--------UGA-GCCAGGG-GAAG-CGUGCCGGUG-----AAGGCUG-GA-GACCACCGUGAGCG----UCGCAGCAAA-------CCAAUAAGCGCCGAGAAGACUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCCCUCGC--------------------------------------UGCCUA---------------------AGUAGCGACCGCGU----------------------------------------------------------------GUCUGUCAG--------------------CCCGGGGA---UGUCCCUGC----CCCGGA--UG-----------------------------------------------------------------CUGGCAUCGA------CUAAGGGACU-U---------------------------------GCUAUCCAACCG--------CGUCAGCG---------------------G---GGUUGGAUGGGA-CUU---CUACCGCUGACU--GGGCCCAU--CAUCCGGAU--GUGUUCGUCCU---A-GCCGGA------GGGCCAAGCAGA----------------------------------------------GAU-CGCUGCACGAAC---UG---CGCACGGA----GAAGCCCUGGCAA-------AGUAGCGUAGGA-CCCGGGUUCAAUUCCCGG-CAGCUCCACGA
AY204390.2/768-425             ------------------------GGGGAUG----A----GAAA-GC-AAGA-AUCG-CAUGCCGAGGA---CUCCUGGC------UCCUCGUAAAU------CAUCCGGGA----AACAACACAACUGCCAACAACGAAAUG---G-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CACUUGC-UGCCUGAU--------------------------------------CUAAAA----------------------GUCAGGUGAGCU------------------------------------------------------------------AG-CGUCU--------------ACCGG-UACCAGU-----GCCUGUC-----CUGGU----CCGGA--------------------------------------------------------------GGCGUCGA------GAUGACAGGA--------------------------------------UGGCUUCCGGAACC----CGCCUGG----------------------GUUCCGCUAGC--------GACACAGAUCCAGGC----UCGCGGCGAAAAGGGUG-----UGUCCUUUC-------UCCCUCUAGUGGCCAGACAA--------------------------------------------------A---AAAAAGGGC----UA---AGCAUGUA--G-UGGUUCUUAGCGG------A-CUGUUUCCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
CU928164.2/2932788-2933150     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA------AAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AAGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC----UUAAUCAGGCUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUGG-CAAGCGAAU---------------------------------------------------GUAAAGAC--UGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCGGGUUCAACUCCCGC-CAGCUCCACCA
CR628336.1/182379-182784       GGGGGCGAC--CUGGCUU--CGACGUGGGUUGCAA------A-A-CCGG----AAGUGCAUGCCGAGA-----AGGAGAU------CUCUCGUAAAUA-----A-GACUCAA----UUAAAUAUAAAUGCAAACGAUGAAAACUUUGCUGG---------------------------------------------------------------------------------------------------------------------------------------------------------------UGGGGA---AGCUAUCGCUG-------------------------------------CCUAA-----------------------UAAGCACUUUAGUUAAACCAUCACUGUGUAC-------------------------------UGGCCAAUAAACCCAGUAUCCCGUUC------------GACC----GAGCCC-----GCUUAU-C----GGUAU----------CG------------------------------------------------------AAUCAACGGUCAUA-----AGAGAUAAGC-------------------------------------UAGCGUC---CUAAU---CU--AUCCCG------------------GGUU--A-UGGCGCGAAA---C---UCAGGGAAUC-----GCUGUGUAUC----AUCC---UGCCC--GUC---G-GA----GGAGCCACAGUUAAAU-------------------------------------------------UCAAAAGACA-AGGC---UA---UGCAUGUA--GAGCUA---AAGGCA------GAGGACUUGCGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
CP000671.1/854998-854633       GGGGCUGAU-UCUGGAUU--CGACGGGAUUAGCGA--------A-GCCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAU-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUUUAGC---------------------------------------------------------------------CUUCGCG-------------CUCCA--GCUUCC-----GCUC-GU------AAGA----CGGGGAU--------------------------------------------------------AACGCGGAGUCAAA--CCAAAAC-GAGAUC----------------------------------G---UGUGG---AAGCC--ACCGUUUGAG-------------------GAU--CGAAGCACUAAA-UU-----GAAUCAAACUA---GCUUA-AGUU---UAGCG---UGUCU--GUC---C-GC----AUGCU-UAAGUGAAA---------------------------------------------------UUAAAGAC-GAGAC---UA---AACGUGUA--GUACUG--AAGGUAG-------AGUAAUUUCGGA-CGGGGGUUCAACUCCCCC-CAGCUCCACCA
CP001019.1/668126-667767       GGGGGCGAC--CAGGCUU--CGACGUGGAUCCUGA------A-A-CCCG----AGACGCAUGUCGAGCC---GGCAACGAA-----GGCUCGUAAAUC----CAUCAGUUGC----AAACAGAUAGUUGCAAACGAUAGUAAUUA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUCCAAGAAGCUUA-----------------------------------CGCAUA------------------------AAGCUUCUU-----------------------------------------------------------------------CCGUUGC------------U-------GGGAUU----CGCUUAUAG----AUCCCU---A----------------------------------------------------------------CCAACGGCCAU----AGCAUAUAAGC-------------------------------------UCGCCCUCA---AGC---AU-GGCUCAU-------------------GAC--UUGAAGGUUAAA-------CAGAAGAGCUC---GCAGUCAAUUU----CCCC---UGCAC--GUC---G-GG-----CGAUUGACUGUUAAA--------------------------------------------------UCAUAGACG-AUGC---UA---AGCAUGUA--GUGUCA--ACGGCGG-------AUGAUUUACGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCAUCA
AY485228.1/1-386               GGGGAUGA---UCGGUUU--CGACAGCGGAUGU--------CGA-AGCAGGG-GAAG-CGUGUCGAGG-----AAGCGGC-CA-UGAUCUCGUAAACCA---CAGGCCGAAA-------ACAAUAAUCGCCAACACCAAGCGCGAUUCCUC---------------------------------------------------------------------------------------------------------------------------------------------------------------CUCGUUCGCCCUCGCUGCCU--------------------------------------AAU-------------------------UAGCAGCUAGCGAACUCU------------------------------------------------------CAUAGGAGUGUCAG--------------------CCCGGGGC---UGUUCCCGA----CCCGGA--UC-----------------------------------------------------------------CUGGCAUCGA------CUAGGGGACU-A---------------------------------AACCUUGAUCC---------CGGUCAC----------------------G-G-GGUGAAGAGGGA-AAC--CAAACAGUGACUG---AGCCCGU---C-GGAGAC--UUGUCCGCGUG---A-UCUCCG------GGGCCGAGAAA-----------------------------------------------AGC----GAAGCGGAC---UG---CACACGGA----GAAGCCCUCCUUC-------CGCACCGUUGGA-CGCGGGUUCGAUUCCCGC-CAUCUCCACCA
AY552545.2/118125-117779       GGGGGCGAA--UAGGGUU--CGACGUUUCUACUGG------A-C-UCCG----AAGCGCAUGCCAAGA----UUGUAGUAA-----UUCUUGUAAAAC-----A-UACUACA----AAAAAAAUAGUUGCAAAUAACGACAACUA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCUUUAGCAG-------------------------------------CUUAA-------------------------UGCUAA-------------------------------------------------------------------------CCGAUG---------------------UAAGAAU---UGACUGU-G----GUUUGA--AG-----------------------------------------------------------------CAUCGGCUAA-----ACACACAGUC-------------------------------------UAGCCAAGC---UAU---AUUGCUUGGA------------------UAUA---GUUUGGUAAAA-C-----UUAAUCAAGCUA---GCUUUUAUGC-----CCU----GCUC--UUC---G-GG-----UAAUAAAAGUUAAAA-------------------------------------------------ACAAUAGAAU-GAGC---UA---AGCAUGUA--GAAGUU--AGGCUGA-------AGGAUUAGCGGA-CGCGGGUUCAAUUCCCGC-CGCCUCCACCA
AF389959.1/19-340              --------G-------------ACGGGAAUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGGGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----UAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--AGAC---UU---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
CP000880.1/216939-216618       --------G-------------ACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCUUCC-----GCUC-UU------AAGA----CGGGGAUC-------------------------------------------------------AAAGAGAGGUCAAA--CCCAAAA-GAGAUC----------------------------------G---CGUGG---AUGC---CCUGCCUGGG-------------------GUU---GAAGCGUUAAA-AC-----GAAUCAGGCUA---GUCUG-GUAG---UGGCG---UGUCC--GUC---C-GCA---GGUGC-CAGGCGAAU---------------------------------------------------GUAAAGAC--AGAC---UA---AGCAUGUA--GUACCG--AGGAUGU-------AGGAAUUUCGGA-CGCG-------------------------G
AE008922.1/1711297-1710901     GGGGGUGCA--CUGGUUU--CGACGGGGGUCGCGA------A-G-UCGC--U-UGGCGCAUGCCGAGG----GGGCAGCUU-----UCCUCGUUAAUC-----C-AGCAGCA-----AACUUUUAGUUGCCAACGACGACAACUA-CGGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------UCGGACUUCGCUAUCGCCG-------------------------------------CUUAAU-----------------------UGGCUUUAGUUGUAGUUCUACAGC------------------------------------------CGCCUAAGGCGAACCCCCGA-A----------ACUA-----CUUGUG-----CCCGUGCU---CGUAGA-------UG--------------------------------------------------------------UAGGGUCAU------UAUCACGGAA------------------------------------CCGCCGGU----AGU---GGCUGCCUGUC-----------------AGCU----AUCGGUUAGA---U---CAAGCAGGCUG----GUUUUCAGGU----GCGCU-UUGCCC--GCC---G-UGC---UGCCUGGGAACGAGAU--------------------------------------------------CUAACGGA--GGGA---UA---AGCAUGUA--GUGCUG---GGGAUG------GAGUGCUUCCGGA-CGGCGGUUCGAUUCCGCC-CACCUCCACCA
FM242711.1/2481648-2481323     --------C--------G----ACAGGGAUAGUU--------CG-AGCUUGA-GUUG-CGAGUCGGGG-----GGAUCGU-------CCUCGUUAUCAA---CGUCAAAGCC------AAUAAUAACUGGCAAAGAAAAACAAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUAGCUUUCGCUGC--------------------------------------CUAAUAA------------------GCAGUAGCAUAG--C-------------------------------------------------------------------UGAUCCU--------------CCGU---GCAUC------GCCCAU-------GUGC----UACGG-----------------------------------------------------------UAAGGGUCUCAC----UCUAAGUGGGCUAC---------------------------------ACUAGUUAAUC----U---CCGUCUGG--------------------------GGUUAAAUAGAA-GAG--CU-UAAUCAGACU--AGC-UGAAUGG---AAGCC---UGUUACCG-----G-GCC---GAUGUUUAUGCGAAAU-------------------------------------------------GC-UAAUACGGUGAC---UA---CGCUCGUA---GAUAUUUAAGUGC-------CGAUAUUUCUGGA------------------------------C
CP000614.1/1042603-1042234     GGGGGCGAC--CUGGUUU--CGACAGGGGUUGUGA-------AG-CGG--CU-AGGG-CAUGUCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AAAACGUAACUGCAAACGACGAUACG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUGGCAGCC---------------------------------------UAAC-----------------------GGCCGCCGU-----------------------------------------------------------------------CCUCUGC------------CUAGUU-C-----------ACUGACG--------------GGCUAGUGUCGCAAGACCG---------------------------------GUAGCAAUACCGA-CAGAGGUC-----AUAUACGUCAGUUA----------------------------------AGCCUUGGCGGC-----------GUCGC--------------------GA----CGUCCGGGUCG-AAA--ACUUAGCGAAUCG----CCGUAGUGC----AGCG---UGUUC--GUC---C-GCG----UCGCUGCGGUUAAAU--------------------------------------------------CAAAUGACU-GAAC---UA---AACAUGUA---GAACUAG--UCGUG------GAGCGCUUCUGGA-CGCGGGUUCGAUUCCCGC-CGCCUCCACCA
AY911518.1/1-343               ------------------------AGGGUGGUGAAA-----UCU-GCUUUGU-GAUG-CAGGUCGAGA----G-UGAGUC-U---UCUCUCGCAAAUA----CCGGGCUCAA----CAAAUAAUAAGUGCAAACAACAUU------GUACC----------------------------------------------------------------------------------------------------------------------------------------------------------------UUUUGCUCGUAAGCAAGUA-------------------------------------GCUG----------------------------UAGCUUAAUUGCCGAAACGCCU----------------------------------------CUUAUAGGUUCGAGC-------------------GUCUGU--GAUUUG----ACUCCGUUA---AGGAUU----GCAGACU---------------------------------------------------------U--AACCCC-----------AACGGAUG-----------------------------------CACUAGCUCACUGC------CUCUGGU------------------------C-GGCUGCUGGUUA-AG----ACUUCACCGGAG--A---------------------------------------------------------AUCCCGCCAUCUGGGAUAAUGGAUGGUCCCCGCCUUCAGGGUUAAGAUAGGC----------------UA---AACCUGU----GAAUGAUCGAAGAGUG--AAUAGCCACUUU----------------------------------
BA000039.2/236043-236428       GGGGCUGA--AACGGCUU--CGACGUCCUAGUGAAA-----GUU-GGGCUGU-GAUG-CAGGUCGAGA----G-UGGACU-A---UCUCUCGUUAAUC----CAGAGUCCAAG---CCAAAAGUAACUGCGAACAACAUC------GUUCC----------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCGCUCGUAAAGCUGCU-------------------------------------GCGG---------------------------UAGCCUAAGACCUCUAAAC-------------------------------------------------AGGUUCGAGC-------------------ACUCGU--UGUCCG----ACUCCGUUA---AGGGC-A---GCGGGU----------------------------------------------------------U--AACCCC-----------AACGGAUG-----------------------------------CGCUAGACAGUUCU------CUCUGGU------------------------GGGCUGUUUAGCAA-AG----ACUCGACCAGAG--C---------------------------------------------------------AUCCUACUGUUCGGGAUAAGGAACA--GUCCCCGCCUGAGGGUCAAAAAGGC----------------UA---AGCCUGU----GAAAGAGCAGUCGAUG--AAUAGCUAGGGCGGA-CACGGGUUCGACUCCCGU-CAGCUCCAUUA
CP000555.1/2388964-2388593     GGGGCCGAC--CUGGUUU--CGACGUGGGUGCGGA-------AU-UGGA-GU-GGUG-CAUGCCGAGC-----AUCAGUGA------GCUCGUAAAU------CCAGCUGAA-----ACAAACCAACUGCGAACGACGAACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCCCUCGCCG-------------------------------------CUUAAAC--------------------ACCGGUGAG-------------------------------------------------------------------------CGUCUCA------------ACGGCA-G-----------GCCGAUG--------------GGCCGGGCCCAAGCCGC------------------------------------AAGGUGGAAGGCUGAGACGUC-----AUGCACAUCGGCUG-----------------------------------GUUGCUCGUCG----------GGUCAC--------------------UC---GGCGUUCAACGA-GA----CUCAGUGACUGG---CGUUGUCCGU----AGCG---UGCUU--CUG---C-GC----GACGGCGGCGUGAGAC-------------------------------------------------UCAAAUCAGA-CAGC---UA---AGCAUGUA---GAUCUAC--CUGAG------GAUGGCUUGCGGA-CGGGGGUUCGAUUCCCCC-CGGCUCCACCA
CP000563.1/1487294-1486939     GGGGGCGAU-UCUGGAUU--CGACAGGAUUCACGA--------A-ACCCU---GGGAGCAUGCCGAGG-----GGCGGUUG-----GCCUCGUAAA--------AAGCCGCA-----CCGUUAUAGUUGCAAACGACUCUAACUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUCUCUAGCAGC--------------------------------------UUAG-----------------------GCUAGCUAG------------------------------------------------------------------------CCAUCUG-------------ACAC--AGGUCUC-----UCAA-AUG----GG-CA-----GUGUAU--------------------------------------------------------AC-AGAUGGUCAU---CCUACAU-UUGAUA-------------------------------------GCGAGG--GAACU---CC-GUCCGGG-------------------GGU---GAACCGCGAAA-UA-----GUACCGGACUC---GCCCGAUGAA----AUCC---UGUCU--UUC---G-GA---GUUUAUUCGGGUUAAU---------------------------------------------------UAAAAGAG--AGAC---UA---AGCAUGUA--GUGCCU--UGGAUGU-------AGGUGUUCUGGA-CGCGGGUUCAAGUCCCGC-CGCCUCCACCA
CP001472.1/1452760-1452409     GGGGGCGU--CACGGUUU--CGACGGGAUU-----GA---CUG--CGGCAAA-GAGG-CAUGCCGGGG----GGUGGGC--------ACCCGUAAU---------CGCUCGC----AAAACAAUACUUGCCAACAACAAUCUG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUCGCAGCUUA---------------------------------------AUUAA--------------------A-UAAGUUGC-------------------------------------------------------------------------CGUCC--------------UCUGA--GGCUUC------GCCUGU-----GGGCC----GAGGCA------------------------------------------------------------GGACGUCA------UACAGCAGGCU---------------------------------------GGUUCCUUCGGC-----UGGGUCUG--------------------GGCCGCGGGGAUG-------A--GAUCCACGGACUA-----GCAUUCUGCGUAUCUU----GUCG-CUUC--UA-AG---CGCAGAGUGCGAAACCUA-----------------------------------------------AAG----GAAUGCGAC---UG---AGCAUGGA--G-UCUCUUUUCUGAC------A-CCAAUUUCGGA-CGCGGGUUCGACUCCCGC-CGCCUCCACCA
CP002276.1/842782-842417       GGGGCUGAU-UCUGGAUU--CGACGGGAUUAGCAA--------A-GCCCA---AGGUGCACGUCGAGG-----UGCGGUAG-----GCCUCGUAAAU-------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAACAAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUA-GCAG-------------------------------------CUUAAUA--------------------ACCUGCAUUUAGC---------------------------------------------------------------------CUUCGCG-------------CUCCA--GCUUCC-----GCUC-GU------AAGA----CGGGGAU--------------------------------------------------------AACGCGGAGUCAAA--CCAAAAC-GAGAUC----------------------------------G---UGUGG---AAGCC--ACCGUUUGAG-------------------GAU--CGAAGCACUAAA-UU-----GAAUCAAACUA---GCUUA-AGUU---UAGCG---UGUCU--GUC---C-GC----AUGCU-UAAGUGAAA---------------------------------------------------UUAAAGAC-GAGAC---UA---AACGUGUA--GUACUG--AAGGUAG-------AGUAAUUUCGGA-CGGGGGUUCAACUCCCCC-CAGCUCCACCA
ACEQ02000004.1/72943-73304     GGGGGCGAC-CUUGGUUU--CGACGGGGGUUGCGA-------AG-CAGA-UG-CGGG-CAUACCGGGG-----UCUCAGAU------UCCCGUAAAA-------CACUGAAU------UCAAAUAGUCGCAAACGACGAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUAGCCG-------------------------------------CUUAA-------------------------GGCUAGC------------------------------------------------------------------------CGUUGCA------------GCAGUC------------GGUCAAUG--------------GGCUGUGUGGCGA---------------------------------------------AAGCCACCGCAACGUC--A--UCUUACAUUGACUG-----------------------------------GUUUCCAGCC---------GGGUUACU---------------------U---GGCAGGAAAUGA-GAC---UUAAGGUAACUG---GUUCCCUAAA----GGCC---UGUCG--GUC---G-GC----AUGACGGGGAUAAG-AUUC-------------------------------------------CAAAU---AGAUA-CGAC---UA---AGUAUGUA---GAACGC--UUUGUA------GAGGACUUUCGGA-CGGGGGUUCGAUUCCCCC-CGCCUCCACCA
CP000094.2/879220-878831       GGGGCCGUU--UAGGAUU--CGACGCCGGUUGCGA------A-A-CUCU----AGGUGCAUGCCGACUU---GGUAACAG------AAGUCGUAAAUC-----CACUGUUGCA--ACUACUUAUAGUUGCCAAUGACGACCAAUACG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGCUGCUCUCGCUGC--------------------------------------UUAA----------------------UUGCAGCUGACAUGCACUCCUGGUA--------------------------------------------CCUUCGGGUCCAGCAAUCAU------------------CAGGGGAU-----GUCUGU-A----AACCCA--AA----------------------------------------------------------------AUGAUUGUCAU----AUAGAACAGAAUC-------------------------------------GCCGUG----CAG---UACGUUGUGG------------------ACGA----AGCGGCUAAA-A-----CUUACACAACUC---GCCCAAAGC----ACCCU----GCCC--GUC---G-GG----UCGCUGAGGGUUAACU--------------------------------------------------UAAUAGACA-CGGC---UA---CGCAUGUA--GUACCG--ACAGCGG-------AGUACUGGCGGA-CGGGGGUUCAAAUCCCCC-CGGCUCCACCA
CP002222.1/2211225-2211552     --------A--------G--------GUAUAG---U-----UUG-AGUUCG-GAUUG-CGCUUCGUAG-----GUUGCGU-------CUACGUAAA--------AACGCUC-AGUUUAAAUUAUAACUGCAAAAAAUAAUAACAAUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUACGCUUUAGCUGC--------------------------------------CUAAUA---------------------AGCGCUUAACG---------------------------------------------------------------------UAGAUCCU-------------CCCA---GGAUC------GUCCAU-------GUUC-----UGGAU----------------------------------------------------------CUGGGUCCUAAA-----UUUAGUGGACUUA--------------------------------CGCUCAAAGCUU----C----CACCUGG---------------------------AGUUGCGAGAA-GAG--AC-UAAUCAGGUU--AGUCAUUGCUGG--GUGCC--CUGUCAUAC-----G-GCG---UUUGCAAUGAUGAAAU-------------------------------------------------UU-AAAUAGUAUGAA---UA---UGAGCGUA---GAUAUCCGAGGGG-------CAAUAUGCUUGGA-CGC--------------G-----------A
AALD02000010.1/63425-63045     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGAG------GCCUCGUAAA--------AAACCGCA----AAAAAAAUAAUUGCAAACGACUCGCAAUACGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------AUCUGCUGCUUUAGCAG-------------------------------------CUUAAUCA-------------------GCCUAAGAAACUGAAG--------------------------------------------------------------AUUCCCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAGAUC----------------------------------G---CGUGG---ACAC---CUUGCCUGGG-------------------GUG---AAAGCGUUAAA-CC-----CAAUCAGGAUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUAA-CCGGCGAAU---------------------------------------------------GUAAUGAC-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGCGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
CP002409.1/1444210-1443840     GGGGAUGA---CUGGUUU--CGACUUGGAAUGGU-------UGU-UCCAGGA-GAAG-CGGGCCGAGG-----ACCCAGG-G--UCAACUCGUUAACG----AUCCUUGGAA------ACCUAUAAGUGCCGAGAACACUCGCACU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUUCGCUCUCGC--------------------------------------UGCCUGA------------------UCAGUGAUCGAAGG----------------------------------------------------------------------GUCAG--------------------CCCGGAUG--UAGCCUUCCG----UCCGGA--UC-----------------------------------------------------------------CUGGCCUCGU------UUAGAAGGCU-U--------------------------------GCCGUACAGCUG---------UGGUCAC----------------------G-G-GGGCUGUACGGG-ACG---UUUCCGUGACUG---GGCUUGU---C-UGCACC--AUGUCGGUGUG---A-GUGCAG------GAGCCGAGCAAU----------------------------------------------AAC-GACAGCAUCGAC---UG---CGCCCGGA----GAAUGUCUGGACG-------GUCUUUCAAGGA-CGCGGGUUCAAUUCCCGC-CAUCUCCACUA
CP001802.1/3669401-3669073     -----------------G----ACUGUGUGCGC--------CGA-GGUAGGG-GAAG-CGUGUCGGUG-----CAGGCUG-GA-GACCACCGUUAAGCG---UCGCGGCAAC-------CAAUUAAGCGCCGAUUCCAAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCCCUCGC--------------------------------------UGCCUG---------------------AUCAGCGACGGCUA----------------------------------------------------------------GUCUGUCGG--------------------CCCGGGUU--GUGUUCCCGA---ACCCGGA--UG-----------------------------------------------------------------CCGGCAUCAU------CUCAGGGAAC-U--------------------------------CACCGUGUUCGC---------CGGUCGC----------------------G-G-ACGGACACGGGA-CAG--CAAACAGCGACUG---GGAUCGU--CAUCUCGGC--UUGUUCGCGUG---A-CCGGGA------GAUCCAAGUAGA----------------------------------------------GAC----AUAGCGGAC---UG---CACACGGA----GAAGCCCUACUGA-------CUCGACACAG--------------------------------G
CP001794.1/3173387-3173036     GGGGACGAU--CCGGAUU--CGACAGGGGUAGGU--------CG-AGCUUAA-GCGG-CGAGCCGAGG-----GGGACG-------UCCUCGUAAAA--------ACGUCAC----CUAAAGAUAACUGGCAAACAAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGCUUUAGCUGCCU----------------------------------------AAUU---------------------GCUGCAGCUA-----------------------------------------------------------------------GCUCCU--------------CCCG---CCAUC------GCCCGC-------GUGG-----CGUU-----------------------------------------------------------CGAGGGGCUCAU----AUGAAGCGGGCUAC---------------------------------GCCCAAAUCCG----C----CGCCUGA---------------------------GGAUGAGGGAA-GAG--AU-GAACCAGGCU--AGC-CGCCGGG---AGGCC---UGUCGGUA-----G-GCG---GAACGGACGGCGAAGC--------------------------------------------------G-AAAUAUACCGAC---UA---CGCUCGUA---GAUGCUUAAGUG-G------CGAUGCCUCUGGA-CGUGGGUUCGACUCCCAC-CGUCUCCAUUU
AJ749949.2/1737798-1738218     GGGGGCGAA-UAUGGUUU--CGACAUGAAUGUCAA------A-A-UCUA----AGGUGCAUGCCGAGG----AAGUACCGU----AACCUCGUUAAUA-----A-CAGUACAAAUGCCAAUAAUAACUGGCAACAAAAAAGCAAACCGCGUAGCGGCUAACG------------------------------------------------------------------------------------------------------------------------------------------ACAGCAACUUUGCUGCUGUUGCUAAAGCUG-------------------------------------CCUAG----------------------UCUAGCUUAAUAAUCUA-------------------------------------------------------------GAUGCGCACGGA----------UAUGA----UAGUCU----UUCUUAUGA----CACUAUC-UAUACAU-----------------------------------------------------------CCGUUCAUAUU-----CCGCAUAAGA---------------------------------------CGGUCU--UUGCU---UUUUGUCUGG------------------GAGUU-A-AGGCUGUAU--------UUAACAGACUC----GCUA-ACUAUU--ACCCU---GGCUA--AUU---G-GGG---AAUAGUCAAGCUAAAC-------------------------------------------------UCAAAUAGAU-UAGC--CUA---AGCAUGUA--GAUCCA---AAGAUC------UAGAGUUUGUGGA-CGCGGGUUCAAAUCCCGC-CGCCUCCACCA
AALE02000007.1/199748-200110   GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGUG------GCCUCGUAAA--------AAACCGCA-----AAAAAAUAGUCGCAAACGACGAAAACUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACUA-GCAG-------------------------------------CUUAAUA--------------------CCCUGCUUAGAGC---------------------------------------------------------------------CCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--ACUAAAA-GAGCUC----------------------------------G---UGUGG---AAAC---CUUGCCUGGG-------------------GUG---GAAGCAUUAAA-AC-----UAAUCAGGAUA---GUUUG-UCAG---UGGCG---UGUCC--AUC---C-GCA---GCUGG-CCGGCGAAU---------------------------------------------------GUAAUGAU-UGGAC---UA---AGCAUGUA--GUACCG--ACGGUGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AP010655.1/886656-887004       GGGGUCGUU--ACGGAUU--CGACAGGCAUUA---------UGA-GACCUAU-UUUG-CGACUCAUCU-----AGCG-----------GAUGUAA-----------AACGCCA--GUUAAAUAUAACUGCAAAAAAUACAAAUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACGCAGUAGCUGC--------------------------------------CUAAAA---------------------ACCAGCCUGUGU---------------------------------------------------------------------GAUCAA--------------UAAC---AAAUU------GCUUGU-------GUUU-----GUU------------------------------------------------------------GAUUGGUCUUAU----UGUUAACAAGCUAC---------------------------------GUUAGAACU------G----AGUCAGG---------------------------CUGUUCUAAAA-GAG---U-UCUACUGACU--CGCAUCGUUA-----GAGUU-UGAGUUAUGU----A-UU-----GUAACGGUGUUAAA---------------------------------------------------U-AAACACAUAACC---UA---UAGUUGUA---GACAAAUGGGUUA-------GCAGAUGUUUGGA-CGUGGGUUCGACUCCCAC-CGGCUCCAUUA
ACCD01000005.1/64762-65142     GGGGCUGAU-UCUGGAUU--CGACGGGAUUUGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGAG------GCCUCGUAAA--------AAACCGCA----AAAAAAAUAAUUGCAAACGACUCGCAAUACGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------AUCUGCUGCUUUAGCAG-------------------------------------CUUAAUCA-------------------GCCUAAGAAACUGAAG--------------------------------------------------------------AUUCCCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAGAUC----------------------------------G---CGUGG---ACAC---CUUGCCUGGG-------------------GUG---AAAGCGUUAAA-CC-----CAAUCAGGAUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUAA-CCGGCGAAU---------------------------------------------------GUAAUGAC-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGCGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
AALF02000019.1/36194-36574     GGGGCUGAU-UCUGGAUU--CGACGGGAUUCGCGA--------A-ACCCA---AGGUGCAUGCCGAGG-----UGCGGAG------GCCUCGUAAA--------AAACCGCA----AAAAAAAUAAUUGCAAACGACUCGCAAUACGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------AUCUGCUGCUUUAGCAG-------------------------------------CUUAAUCA-------------------GCCUAAGAAACUGAAG--------------------------------------------------------------AUUCCCUCUCU-------------CCCUA--GCCUCC-----GCUC-UU------AGGA----CGGGGAU--------------------------------------------------------CAAGAGAGGUCAAA--CCUAAAA-GAGAUC----------------------------------G---CGUGG---ACAC---CUUGCCUGUG-------------------GUG---AAAGCGUUAAA-CC-----CAAUCAGGAUA---GUUUG-UUAG---UGGCG---UGUCC--GUC---C-GCA---GCUAA-CCGGCGAAU---------------------------------------------------GUAAUGAC-UGGAC---UA---AGCAUGUA--GUGCCG--ACGGCGU-------AGUAAUUUCGGA-CGGGGGUUCAAAUCCCCC-CAGCUCCACCA
CP001644.1/873842-873513       --------C--------G----ACGUGGGUUGCGA-------AG-CAGC-GG-AGGG-CAUACCGAGG-----ACCCGUCA------CCUCGUUAAU-------CAAUGGGA-----AUGCAAUAACUGCUAACGACGAACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCACUGGCAG-------------------------------------CCUAAGG--------------------GCCGCCG--U------------------------------------------------------------------------CCUCGCA------------CUGGCU-C-----------GCUGACG--------------GGCUAGGGUCGC-----------------------------------------------AAGACCAGCGAGGUC-----AUUUACGUCAGAUA----------------------------------AGCUUUAGGUGA----------GUCACG--------------------GG-----CCUAGAGACG-AAA--ACUUAGUGAAUCG---C-CGUCGUAG----AGCG---UGUUC--GUC---C-GC----GAUGCGGCGGUUAAAU--------------------------------------------------CAAAUGACA-GAAC---UA---AGUAUGUA---GAACUCU--CUGUG------GAGGGCUUGCGGA-CGCGGGUUCGAUUCCC-------------G
HE572590.1/3532494-3532127     GGGGCUGA---ACGGUUU--CGACUUCGCGCAU--------CGA-AUCAAGG-GAAG-CGUGCCGGUG-----CAGGCAA-GA-GACCACCGUAAGCG----UCGUUGCGAC-------CAAAUAAGCGCCGAUUCACAUCAGCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACUACGCUCUCGC--------------------------------------UGCCUA---------------------AGCGACGGCUAGU-------------------------------------------------------------------CUGUCAG--------------------ACCGGGAA---CGCCCUCGG----CCCGGA--CC-----------------------------------------------------------------CUGGCAUCAG------CUAGAGGGAU-C--------------------------------CACCGAUGAGUC---------CGGUCGC----------------------G-G-GACUCCUCGGGA-CAA---CCACAGCGACUG---GGAUCGU--CAUCUCGGC--UAGUUCGCGUG---A-CCGGGA------GAUCCGAGCAGA----------------------------------------------GGC----AUAGCGAAC---UG---CGCACGGA----GAAGCCUUGAGGG------AAUGC-CGUAGGA-CCCGGGUUCGAUUCCCGG-CAGCUCCACCG
CP001635.1/1754992-1755347     --------G-------------ACGUGGGUUCGGA-------GU-CGCA-GC-GGGG-CAUGUCGAGC------UGAAUGC------GCUCGUAAAA------CAGAUUCAA-----ACAAACUAACUGCAAACGACGAACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCACUCGCUG-------------------------------------CUUAAUU--------------------GCCAGUGAG-------------------------------------------------------------------------CCUUGCA------------ACAGUU-G-----------GCCGAUG--------------GGCUGGGCAAGGGGGUCUGGAGC-------------------------AAUCCUGACCUCCCGGCUGCAAGGAU-----AAUUACAUGGGCUG-----------------------------------GCUCCGAUCCG----------GGUACC--------------------UU---GGGUCGGGGUGA-GAA--AAUAGGGUGCUGG---CGUCCGGUUU----AGCG---UGUGA--CUG---C-GC----GACUCCGGAAGCGAGAC------------------------------------------------UCAAAUCAGA-UCAC---UA---AACAUGUA---GAACUGC--GCGAU------GAAGGCUUGCGGA-CGGGGGUUCAAAUCCC-------------C
CP001221.1/176574-176921       GGGGACGAA-AUUGGUUU--CGACUGUUGUUG---C-----CAG-GGGUUAU-GUGG-CGUGUAGAGGU---UGUAGGC-------UCCUCUAAAA----------ACCUUC-----AAACAAUAACCGCUAAUAACGAAUUA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUUAGCAG--------------------------------------CUUAAUC-------------------U-CUGCUA---------------------------------------------------------------------------CGGAA--------------CUUUA--GUUUUU-----UCUCUCG-----AAUUC----UAAAUG------------------------------------------------------------UUCUGACAA-----UGAUCGGGAGG--------------------------------------CGAUUCUUUUGGU-----UUUUGGUU---------------------CCUAAAAGAGU-------UUGUAUUUGAGCCGAA-------UAGGAAAGAGAGUCC----UGUCUGAGG--GU-GAACCUCUUUCCGAAAUUUUA-------------------------------------------------------UACACAGAC----UA---CACACGUA--G--AGGCUGAUCUGGG-----G--CGCAAUAGGA-CGCGGGUUCGAACCCCGC-CGUCUCCAA--
CP002420.1/1268682-1269044     GGGGGCGAC-CUUGGUUU--CGACGAGGGUUGCGA-------AG-CAGA-UG-CGGG-CAUACCGGGG-----UCUCAGAU------UCCCGUAAAA-------CACUGAAU------UCAAAUAGUCGCAAACGACGAAACU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UACGCUUUAGCCG-------------------------------------CUUAA-------------------------GGCUAGC------------------------------------------------------------------------CGUUGCA------------GCAGUC------------GGUCAAUG--------------GGCUGUGUGGCGA---------------------------------------------AAGCCACCGCAACGUC--A--UCUUACAUUGACUG-----------------------------------GUUUCCUACC---------GGGUUACU---------------------U---GGCAGGAAAUAA-GAC---UUAAGGUAACUG---GUUUCCAAAA----GGCC---UGUUG--GUC---G-GC----AUGAUGGAAAUAAG-AUUUU------------------------------------------CAAAU---AGACA-CAAC---UA---AGUAUGUA---GAACGC--UUUGUA------GAGGACUUUCGGA-CGGGGGUUCGAUUCCCCC-CGCCUCCACCA
AL935263.2/2243186-2243557     GGGGAUGUU--CUGGAUU--CGACAGGUAUAG---U-----UUG-AGUUCGG-AUUG-CGCUUCGUAG-----GUUGUGU-------CUACGUAAA--------AACGCUC-AGUUUAAAUUAUAACUGCAAAAAAUAAUAACAAUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUACGCUUUAGCUGC--------------------------------------CUAAUA---------------------AGCGCUUAACG---------------------------------------------------------------------UAGAUCCU-------------CCCA---GGAUC------GUCCAU-------GUUC-----UGGAU----------------------------------------------------------CUGGGUCCUAAA-----UUUAGUGGACUUA--------------------------------CGCUCAAAGCUU----C----CACCUGG---------------------------AGUUGCGAGAA-GAG--AC-UAAUCAGGUU--AGUCAUUGCUGG--GUGCC--CUGUCAUAC-----G-GCG---UUUGCAAUGAUGAAAU-------------------------------------------------UU-AAAUAGUAUGAA---UA---UGAGCGUA---GAUAUCCGAGGGG-------CAAUAUGCUUGGA-CGCGAGUUCGACUCUCGC-CAUCUCCAUUA
AE017283.1/1466571-1466231     ----------AGCGUUUU--C----CGGACGGUUG--------U-UCCAGGA-GAAG-UGGGGUGAGG----GCCCAGGGU----CAACUUGUUAACG-----AUCGUUGGG-----AAUCUAUAAGUGCCGAGAAUACUCGCAC-UG----------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUUCGCUCUUGCUG--------------------------------------CCUGAU------------------------CAGUGAUCGAA------------------------------------------------------------------GG-GUCAG---------------------------------CCCGGA----------U---U-----------------------------------------------------------------CUGGUUUCGU------UGCGAUGACUU----------------------------------GCCGCCCAGUU---G-----UUGUCGUG---------------------G-U-GACUGGGCGGAA-UUA---UUUCUACGAUCG--AGUUUG-UUUG----CACC--AUGUCGGUGUG---A-GUGC-AGGAGC-CGAGCAAUAAC-----------------------------------------------GAC---AGCAU-CGAC---UG---CGCCCGGA----AAAUGUCUGGACG-------GUCUUUCAAGGA-CGUGGGUUCAAUUCCUGC--CUCUCCACUA
#=GC SS_cons                   [[[[[[[,...,,,,,,,..,((((((((((((--......-((.(((((((.((((.(((((AAAAA.....<<<<<<<......_aaaaa______.....__>>>>>>>....,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.......................................................................................................................................................................,,.,,,,<<<<<<<<<......................................____........................>>>>>>>>>.......................................................................<<<<<<..............<<<<...<<<<__.....BBBBBBB....._>>>>....->>>>.............................................................>>>>>>,,,......,,,bbbbbbb,....................................<<<<<<<<<_........._CCCCCC......................_..._>>>>>>>>>,,.,.....,,,,,cccccc,...<<<<<<<<<<....-<<<..._DDDD..DDD...>.>>....->>>>>>>>>>,,,,,..................................................,...,ddd,.dddd...,,...,)))))--...-)))))))))))))......-)))))))))))).,<<<<<_______>>>>>.]]]]]]]::::
#=GC RF                        GGGGcUGA...auGGuUU..CGACgggggugauaA......aaa.cuccuug.aaug.CAuGcCGAGg.....ggcgguu......acCUCGUAAAua.....aAaaccgcc....aAAAAAAUAAaUGCaAAcaAcAAuaacuAcu.......................................................................................................................................................................ug.uCgcucucgccgc......................................uUAA........................gcggcgaga.......................................................................ccuccc..............uccc...ccguuu.....GCCcguu.....gacgg....gggga.............................................................gggaggUcA......uaAaacGGGaU....................................ccccgcaacg.........cgguugc......................g...gguugcggggaA.a.....uuaaaagaacug...gccucuggau....agcc...UGucc..gUc...g.gc....gauccagaggcgAAaa..................................................c...Agaca.aGAC...UA...AgCaUGUA...Gaaaucaagggggg......aagcacuuucGGA.CGgGGGUUCGAuUCCCcC.CAgCUCCACCa
//
# STOCKHOLM 1.0

#=GF AC   RF00024
#=GF ID   Telomerase-vert
#=GF DE   Vertebrate telomerase RNA
#=GF AU   Machado Lima A
#=GF SE   Machado Lima A
#=GF SS   Published; PMID:10721988; Machado Lima A
#=GF GA   70.00
#=GF TC   70.30
#=GF NC   68.20
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.69 -Z 549862.597050 CM SEQDB
#=GF CL   CL00004
#=GF DR   SO; 0000390; telomerase_RNA;
#=GF DR   GO; 0007004; telomere maintenance via telomerase;
#=GF DR   GO; 0003720; telomerase activity;
#=GF DR   GO; 0000333; telomerase catalytic core complex;
#=GF RN   [1]
#=GF RM   10721988
#=GF RT   Secondary structure of vertebrate telomerase RNA.
#=GF RA   Chen JL, Blasco MA, Greider CW
#=GF RL   Cell 2000;100:503-514.
#=GF RN   [2]
#=GF RM   11842102
#=GF RT   Analysis of the structure of human telomerase RNA in vivo.
#=GF RA   Antal M, Boros E, Solymosy F, Kiss T
#=GF RL   Nucleic Acids Res 2002;30:912-920.
#=GF RN   [3]
#=GF RM   15811851
#=GF RT   Comparative functional study of the viral telomerase RNA based on natural
#=GF RT   mutations.
#=GF RA   Fragnet L, Kut E, Rasschaert D
#=GF RL   J Biol Chem. 2005;280:23502-23515.
#=GF CC   Telomerase is a ribonucleoprotein reverse transcriptase that synthesises
#=GF CC   telomeric DNA. Telomerase RNAs differ greatly in sequence and structure
#=GF CC   between vertebrates, ciliates and yeasts, but they share a 5' pseudoknot
#=GF CC   structure close to the template sequence. Vertebrate telomerase RNAs have
#=GF CC   a 3' H/ACA snoRNA-like domain. This family also contains viral telomerase
#=GF CC   RNAs from the Gallid herpes viruses as described in [3].
#=GF WK   Telomerase_RNA_component
#=GF SQ   37


AF221915.1/120-667       -----------------UCA-----CAUUGCU--GCGGGGUGGAGGC---GUUUUU--AACUAACCCUAA-UGCAGAGUAA--GUGG--CUGG---------------GCCUUCCUCACACUGCCUCCCGCUG----------CGUGAAACCUCGCUGUUUUCUUGGCUAACUUUCAGCGAGGUGAGGCAAGGCGGCAAA----------------------------------------------------AAAAAGUUGGGAG------------CAGCAACGGCAAGCAAA---AAAAAAGUUCCAGC-CGAG------GCC-UCCUCACCA-CGCGGC--C---UG----GGUCUGAGGGUAACAUGGCCCUGCGGGAGAGAGCCAACACGGG---------GGGGCCCCGGUCCGGCUAACAGGGCAGGAG----GUCGGCCCCAAUUGCCUCA-------GGCCC----AGCC--ACUCC-------GGGCCGCGAUCAGCCC-GGGCUUU----CCCUACUUU-GGGGCCC-AAUGCUGUCGCGAAGAGU-UCG-GCUCUGUCAGCCC---GGCU------GGGUC-------CGGGUG-GGGGC--CGGC--ACAGAGGGACACACCGGGCCGGGGCGCCGAGGAUAGCUACCGCCCGCAGG-GAUAGUAAAUAUCCGUGACCAGU-GGC--------CUCGGUGGCUGCG--UCUCCC-GGAGCAAU-GGGA-CC--CGCAAGGCU--GCC--C-UGGUCAUACACGC
AF221933.1/121-679       -----------------UCA-----CAUUGCU--GCGGGGUGGAGGC---GAUUUU--AACUAACCCUAA-UGCAGAGUAA--GUGG--CUGG---------------GCCUUCCUCACACUGCCUCCCGCUG----------CGCGAAACCUCGCUGUUUUCUUGGCUAACUUUCAGCGAGGUGAGGAGAGGCGGCAAA-------------------------------------------------AAAAAAAGGUUGGGAG------------CAGCAGCGGCAAACAAAA--AAAAAAGUUCCAGC-CGAG------GCC-UCCUCACCCCCGCGGC--C---UG----GGUCUGAGGGUAACACGGCCCUGCGGGAGAGAGGCAACACGG----------GGGCCCCCGGUCCGGCGAACAGGGCAGGAG----GUCGGUCCCAAUCGCCUCACA-----GGCCC----AGCC--ACUCC-------GGGCCGCGGUCAGCCC-GGGGCUUUCCCCCCCACCAUGGGGGCCC-AAUGCUGCCGCGAAGAGU-UCG-GCUCUGUCAGCCC---GGCU------GGGCC-------AGGGUG-GGGGC--CGGC--ACAGAGGGACACACCGGGCCGGGGCGCCGGGGAUAGCUACCGCCCGCAGG-GAUAGCAAAUAUCCGUGACCAGU-GGU--------CUCGGUGGCUGCG--UCUCCC-GGAGCAAU-GGGA-CC--CGCAAGGCU--GCC--C-UGGUCAUACACAU
AF221919.1/107-614       GUGCGGACGGGCUGCGUGGGC------GGGUCG---GUCC--GUCCU----GGCAC--AUCUAACCCUAAAUGCGCGCUGGUUGAAGUGGCUU----------------CUCC-------UGGGCGA-U--------------------CGCUCGCUGUUUUUGUGGCUGGCUUUCAGCGGGCU--GGAGGAGCCGGG--------------AGCGGAGGCGGAGGACCGAG----------------------------------------------------------CC-----AAAAACGUC--AGC-CG--------AGG-CC-----GGGC--GGCCC----------CG-----------------CUCGUGGCCCGUCCGCACUGUCCGGGCCAGGCCCCGGCCCGAACCCCCUGGAGACAACUCCCGCAGGGUCUGCGCUGCGCCGCGGAGC-----CCCG-GCU-GCCC--ACGUAG------AGGCGGCGG-CCGUCUCGGGGCCCCUG--CGUG--CGGGGCGCCC-ACUGCGGCCGCCAAGAG-CUCGU-CUCUGUCAGCCUC--GGGUGCACG--UGGG---CCCGCGGUCG-AGCCCUAAGGCC----------------GGGCGUGGGG-CUG-----------GGGUCGCAGG-GAGAGUAA----CCGUGAGCCGGC-GCCC-------AGCCUUCAGGGCG--CUCCCUCGAGCUAU-GGGA-GC-UGCCC---CCGGGC--AC-GGCUCGGACACCC
AF221914.1/112-589       ----------------------GUCCA--GCU--GCG-GG-GGAG--ACAGUGUCGCUCUCUAACCCUAAUGUGGGGGCAA-CGCGGG--------------------CCCUU-UGUUUAAAG--UCCCGCUGU---------CGGGAGCCCUCGCUGUUUUCUUGGCUAACUUUCAGCGAUGG--CGAAAGGGCCCAGC-----------------------------------------------------AAAGGUUGGGAAGCGUGAUUUAUUGUUGGUGGGCAGAGAG----AAAAAAGUUUAAGC-CGCGGCCUC---C-UCC----CCG-GCGGC--CCA--GGAC-CC-----------------CCUGUU-GCAACGUGCGGAAUGGCG----------------------------------------GCCUCGGCCC-----CCCUGCU---GCACGCCCA---GCCG--UUU---------AGGCCGCGGUCAGCGC-CGGUUUC-CACGCCAGUGU-GGGGCUUG--AUGCUGUCGCGAAGAG-UUCGU-CUCUGUUAGCC----UGGCA-----GGGUGUGC-----UACGCA-GGGU--CGGGGU--------------------------GCGGAG------------GGCAGG-GAGAUUAAAUAG-CUUGACCAGA-CGC-----UAUGGCCUGUACUGCA--UUUCCC-AGAGCUGU-GGGA-CC--UGCAAAUCU--GCG--C-UGGUCAUACAUUU
AF221935.1/112-602       ----------------------GUCCA--GCU--GC--GG-GGAG--AAAGUGUCGUUCUCUAACCCUAAUGCGAGGGCAA-UGCGGG--------------------CCCUU-UGUUUAAAG--UCCCGUUGUCGCGCGAAGCGGGAGCCCUCGCUGUUUUCUUGGCUAACUUUCAGCGAUGG--UGAAAGGGCCUAGC-----------------------------------------------------AAAGGUUGGGAAGCGUGAUUUAUUGUUGGUGGGCAGAGAG----AAAAAAGUUUCAGC-CGCGGCCUC---C-UCC----CCG-GCGGC--CCA--GGAC-CC-----------------CCUGUU-GCAACGUGCGAAAUGGCG----------------------------------------GCCUCGGCCC-CCACCUUUGCUC--GCAUGCCCA---GCCG--AGU---------AGGCCGCGGUCAGCGC-CGGCUUC-CACGCCAGUGU-GGGGCUUG--AUGCUGUCGCGAAGAG-UUCGU-CUCUGUCAGCC----UGGCA-----GGGGGUGC-----UACGCA-GGGU--CGGGGU--------------------------ACGGGG------------GACAGG-GAGAUUAAAUAG-CUUGACCAGA-CGC-----UAUAACCUGUACUGCA--UCUCCC-AGAGCUGU-GGGA-CC--UGCAAAUCU--GCG--C-UGGUCAUACAUUU
AF221908.1/136-584       -AAUCAGCGUUUAAAGCUCAA-----UGUGGA--CGGAGG-UCUCU----GUUU----CGCUAACCCUAAUACACUGGCUUCAGGGCGAUG-----------------GCUCU--------------------UCGCGGCGG-------UGCCUGUUGUUUUACUUGCUGACUUUCAGCGGGCA-CGG-AGAGCAAGC---------------------------------------------------------------------------------GUAGACGACGACUA----AAAAACGUC--AGC-UG---------GG-AGACU--CCUCCGUUCGC----A-----CAGCCCGA-----------CCUGCUCCAUUGCCCAAGAGC--------------------------------------------CCCGGGUUUU-CUCUGUGGAA---UGUAUCAGGCGCUCCCCGGUCUGUCUGUCUGGGGCCGCGGUCGGCA--------------UCAU--------------CUGCUGUCGCGAAGAG-UUCGU-CUCUGUUAGCCCU-UGGGGGC----CCUGGUGCG----GAG-U--GGAGAGUCCGGG-----------------------UCUGGG--------------GGGUCGG-GAGAACAAAAG-----GGGGCG-CGCUGGUGCUCAGGCUCAGUCAUGC--UUUCCC-UUAGUUGU-GGGAUAU--GCGU---GUUCAGCCA--GUCCCCGACAUGU
AF221913.1/109-520       -----------------UU---AAUUAGAGGGAUUGGAAG-GUUCC----GCUUA---UGCUAACCCUAAUAUUGGGGGUCUGUUGAAAA------------------CCUCU----UUAAGAUA------------------------UGCGUGUUGUUUUAUUGGCUGACUUUCAGCGCGCA-UUG-AGAGGAGUU---------------------------------------------------------------------------------GCUGCCCAGGACUA----AAAAAUGUC--AGC-UG---------GG-AGU---CCUUCCUCUCCC----UUAUU--------------------UCUGCCUCACAACCU-GGA-------------------------------------------------CUCUUUA------UUUA------GCGGUG-----CCCC-AUUUGUCG-----AGGCCGCAGUCAGUCU-UGUUCUU------------------AUACGCUGCUGUUGCGAAGAG-UUCGU-CUCUGUCAGCCUCC-GGGG-------CAACGC---CUUGAAUU--UGGA--GAG-----------------------------CCUGGGAAUGUAACAAGGGGUAGG-GAAAAUAACGA-----GAGCUGA-GUUG-----GCUUCUCCUG--UGC--UGUUCC-UGAGCUGU-GGAACUU--GCA-A-UCG-CAGU--C-GGCUCUGACACUU
AF221926.1/103-507       -----------------ACA-----GUGGGAA--UAGGAG-GG------AGUCUAUAUUUCUAACCCUAAUAUACCCGGU--UCAGG---------------------GCUCU-----UA-----------UGUGG-------------CGCUCGUUGUUUUGCCGGUUGCCUUUCAGCGGGCG-AA--AGAGCUCAG---------------------------------------------------------------------------------AGAAGCGAGGACCA----AAAAACGGC--AGCCGCGGG----------CC----CUCCUGUUCCC----AC----CAU----------------CCCAGCUUUUCCACACUGCGC-----------------------------------------------CUGGGUU-CUCACUCAAGUGU--UCGGCAG----CUUCC-ACUUACG-----AGGCCGCGGUCUACC------------GCUGUCAC------------UGGUAGUCGCGAAGAG-UUCGU-CUCUGUCAGCCUU-GGGAG------CCGCGGA--CGGAGUAUGA-GGUC--CAG----------------------------UAAUGAG-----------AGCAGGG-AAGAGUAAAGC-----GAGCCGC-GCUA------CUUGUCCUAUCUGC-C-GCUCC-UAAGCUGU-GGGGCG-U-GUAG-GGUA-CACA-A--GGCUCCGACAUUC
AF221940.1/103-499       -----------------CCA-GCGGUA--AUA--GGAGAGU--UCUA---UCC-----UUCUAACCCUAA-UGCACAGACCCCUCGCU--------------------GCUCU--UCA-------------------------------UGCUCGUUGUUUUUCUCGCUGACUUUCAGCGGGCG-AA--AGAGCAAUG---------------------------------------------------------------------------------GAAGCUCAGGACUA----AAAAACGUC--AGC-CG--------UAG-G------CUUUCCUAU------AGCCGCAGG----------------CCUGCC-UGUCAGUG-UGC------------------------------------------------GCGGCCUCU-GCUCGCAA-UGU--CCGCAG-----CGCC-UUCCUAUG-----AGGCCGCAGUCUGCC------------AAUACCCC------------GGGCAGCCGCGAAGAG-CUCGU-CUCUGUCAGCCUUU-GGCG-------CUGCGG--CGGAGUGGG-GGAGG--CCGC----------------------------UGAU--------------GGCAGCUGAGAAUAAAGC-----GAGCCCA-GCUG---CCCCGCUCUGUUCCACUG---CCCC-UGAGCUGU-GGGGU---UGGUGAAUUG-CAGC-A-UGGCUCCGACAACU
AF221934.1/121-565       -------------------U--CUCUCC-GGAGAGGGGCGG--UUUC---UCUGUC--UUCUAACCCUAAUGCGGUGCUUCGGCAGAA--------------------GCUCUC----CACUGCGUA----------------------CGCUCACUGUUUUUCUAGCUAACUUUCAGUGAGCA-GGG-AGAGCGAAGUC-----------------------------------------------------------------------CAGUUUC-ACGACAACGGAGA-----AAAAAUGUU--AGC-UG--------GGG-A----A-CGUCCCUUU--CCC-GAGAG--------------------CCCGCGCCGUCCUUUUUCUUCCU-----------------------------------------CGGGCCCGUUGG-CAUAGCC-------CCUGGCCU---CCUCGCUCUAU-------AGGCCGCGGUCAGCUC-GGGCCCC---AGCUCCGGCAGGGGUUCC-ACUGCUGCCGCGAAGAG-UUCGC-CUCUGUCAGCCU--UGAGG-U----GGCCGGG------AUAGAAUAGGC--GGGCUCG-------------------------CGGCAGC----------GCGCGGGAAAGAGCAAAU---GGUGAACUG-G-GUGC------CUGUUGGGGUCGCG---UCCC-UGAAGAGU-GGGA-AG-UGCGA--UCUGUGU-UCCU-GUUCAGACACAC
AF221927.1/113-556       -----------------UCU--CUCU---GGAGCGGGGCGA--UUUC---UCUUCC--UUCUAACCCUAAUGCGGUGCUUAGGCGACA--------------------GUUCU-------------CCGGGUG----------------CGCUCGCUGUUUUUCUGGCUAACUUUCAGCGAGCGGAG--AGAGCGAAGCC---------------------------------------------------------------------GUGGUUUACGACGAUAGAGGAGA-----AAAAAUGUU--AGC-UG--------GGG-A----A-CGUCCCUUU--CCCG-AGAG--------------------CCCGCGCCAUCCU----CUUCCU-----------------------------------------CGGGCCCAUUGGCGAUAGCC-------CCCGGC-CUC-CCUCGCUCACC-------AGGCCGCGGUCAGCCC-GGGCCCU---GGCUCUGCUAGGGCGUCC-AAUGCUGCCGCGAAGAG-UUCGU-CUCUGAUUGCCU--UGAGG-UA----GCCGGG------CUCGAAUAGGU--GGGCUCG-------------------------CGGCGAU----------GCGCAGGAAAGAGCAAAACA--GUGAACUG-G-GCGU------GUGCUGGGGUCGCG---UCCC-UGAAGUGU-GGGA-UG-UGCGA--UCUGUCCGC-U-UGUUCAGACAUUG
AF221910.1/112-554       -----------------UGU-CAUUCCGGAGA--GGGGCG--UUUUC---UUCUUU--CUCUAACCCUAAUGUAUUGCUUGGGCAGCA--------------------GCUCU-------CUCGGUA----------------------UGCUCGCUGUUUUGCUGGCUAACUUUCAGCGAGCA--G--AGGGCGAAGUC-----------------------------------------------------------------------GAAUUUCG--GACAAGGGAGA-----AAAAAUGUU--AGC-CG--------GGG-AA-----CGCCCCUUUCCC----GAAUG-------------------CCCGUGCCGUCCUUCCUCU-CCUC----------------------------------------UGGGCCCGUUGGCGAUAGCCCCC-------GGCCUC--CCUCGCUCCUU-------AGGCCGCGGUCAGUCC-GGGCCCU---UGCUCUGGCAUGAGGUCC-AUUGCUGCCGCGAAGAG-UUCGU-CUCUGUCAGCCU--UGAGG-U----GGCC------AGCAUGGAAUUGGC--GGGCUUG-------------------------UGGCGGC----------GCGCGGGAAAAAGCAAAU---GGUGAACUA-G-GUGC------GUGUUGUGGUCGUG---UUCC-UGAAGCGU-GGAA-UG-UGCGA--UCUGUGCGC-U-AGUUCAUACACAC
AF221932.1/102-549       ----GGGUUGAGGAGGGUACG---CCCGGGA---GGGCGGU-GGUCU---GUUCUG--UUCUAACCCUAACUGAUAAG---------------GGCGUAGGC-GCCGUGCUUU--------UGU-UCCC--------------------CGCGCGUUGUUUUUCUCGCUGACUUUCAGCGGGCG--GGAAAAGCCUCG--GUCUA-CCGCC-GUCUACCG-AUAGCCU--------------------------------------------------GGAGCAAA----CAA----AAAAAUGUC--AGC-CGC-------CGG-CC---GCUCGCCCCUCCC----GGG---AA-----------------CCUGCAGUGGCUC-----------------------------------------------------GCC-CGCCC-----AGC--------CCCGC--UC--CCCGC--CUGG-------AGGCCGCGGUCGGCCU-GGGGCUUC----UCCG---GAGGUUCCC-GCUGCCGCCGCGAAGAGU-UGG-GCUCUGUCAGCC---GCGGG-UCCC---GCGGG------AACCAA-GGGC--GAGGC---------------------------UGGGGCC-UCCUGA---ACGCAGG-GAGAGAAA-----CG-GAGC---GGUUCC-------CCGCGUGCGUGCGC-UUCCC-UGAGUUGU-GGGA--UGUGCGC--UC-GGGGCUC-A-GCUCCGACAGGU
AF221923.1/106-554       ----GGGUUGAGGAUGGCGCC---CCCGGGUC--GGGCAGU-GGUCU---UUUUUG--UUCUAACCCUAACUGGCAAG---------------GGCGUAGGU-GCUGUGCUUU--------UGU-UCCC--------------------CGCGCGUUGUUUUUCUCGCUGACUUUCAGCGGGCG--GGAAAAGCCCUG--GCCUA-CCGCC-GUCUACCG-AUAGUUU--------------------------------------------------GGAGCAAA----CAA----AAAAAUGUC--AGC-CGC-------UGG-CC---GCUCACCCCUCCC----GGG---AA-----------------CCUGUGGUGGCUC-----------------------------------------------------GCC-CGCCC-----AGC--------CCCGCG-C---CCCGC--CUGG-------AGGCCGCGGUCGGCCU-GGGGCUUC----UCCG---GAGGUUCCC-AUUGCCGCCGCGAAGAGU-UAG-GCUCUGUCAGCC---GCGGG-UCC---UGCGGG------AACCAA-GGGC--GAGGC---------------------------UUAGGCC-UCCUGA---ACGCAGG-GAGAGAAA-----UG-GAGC---GAUUCC-------CCGAGUACGUGUGC-UUCCC-UGAGUUGU-GGGAU--GUGCGU--CC-GGGACUC-A-GCUCCGACAGGU
AF221918.1/97-547        ----GGGCUGAGGAGGGUGGG---CUCGGGAG--GGGCC-C-GGUCA---UUUCUC--AUCUAACCCUAACUGAGCAG---------------GGCGUAGGC-GCCGCGCUUU--------UGUUUCCC--------------------CGCGCGCUGUUUUUCUCGCUGACUUUCAGCGCGUG--GGAAAAGCCUUG--GCCUA-CCGCC-GUCCACCGUUCAUUUC--------------------------------------------------GCAGUAAA----CA-----AAAAAUGUC--AGC-CGC-------UGG-CC--GGUUCGCCCUUCCC----GGG---GA-----------------CCUGCGGUGGCUC-----------------------------------------------------GCC-CGCCC--------------GGCCCCCG-UGC-CCCGC--CUG--------AGGCCGCGGUCGGCCC-GGGGCUUC----UCCG---GAGGUGCCC-AAUGCCGCCGCGAAGAGU-UAG-GCUCUGUCAGCC---GCGGG-UCCCU-CGGGGGCC----AA-----GGGC--GAGGC---------------------------GCAGGCC-GUCUGG---CCGCAGG-GAGAGGAA-----CG-GAGC-G-GGUCCC-------CCAGCGUGGUGCGC-UUCCC-UGAGCUGU-GGGA-C-UUGCAC--CC-GGGACU-CG-GCUCAAACACGC
AF221929.1/92-517        -----------------UGGG---CC-GGGAG--GGGUGGU-GGUCU---UCCCU---GUCUAACCCUAAG-GUGAAGAG-------------GACGUGGGU-GCCGUGUUUU--------UCGCUCC---------------------CGCACGCUGUUUUUCUCGCUGACUUUCAGCGUGCAGA---AAAGCCUUG--GCCUA-CCGUC-GGUUAUUGUCUAAUUA--------------------------------------------------GAAGCAAA----CA-----AAAAAUGUC--AGC--G--------UGG-CC--GGGCCGCCCCUCCC----GGA---UA-----------------CCUGCGGCGGCUC-----------------------------------------------------GUC-C-ACCG--------------GCCCCCG-AGC-CCCGC--CU---------AGGCCGCGGCCGGCGC-GGGGCUUC----CCUG---GAGGCGCCC-AUGGCCGCCGCGAAGAG-UUCGU-CUCUGUCAGCU---GCGGG-UCGCC-CGGGGGC--CG-------CGG--GAGAGUC---------------------------CCAGGCC---UUGG---CCGCAGG-GAGAGAAA-----CG-GAGC--AGGUCCU---------CGCGCGGUGCAC-UCCCC-UGAGCUGU-GGG-AA-GUGCAC--C--GGGAC-G-G-GCUCCUACAAGC
AF221937.1/99-545        ----GGGUUGAGAAUGGUGGG---CC-GGGAG--GGGAGGU-GGGCA---UGUUUU--GUCUAACCCUAACUAGGAGGAG-------------GACGUAGGC-GCCGUGCUUU--------UGU-UCCC--------------------CGCGCGCUGUUUUUCUCGCUGACUUUCAGCGUGCGGA---AAAGCCUUG--GCCUG-CCGUC-GACCACUGUCUAAUUA--------------------------------------------------AAAGCAAA----CA-----AAAAAUGUC--AGC--G--------UGG-CC--GGUCCGCCCCUCCC----GGG---UA-----------------CCUGCGGCAGCUC-----------------------------------------------------GCC-CGGCUG--------------GCCCCCG-AGC-CCCGC--CCA--------GGGCCACGGCUGGCGC-GGGGCUUC----UCCG---GGAGCGCC--AUGGCCGCCGCGAAGAG-UUCGU-CUCUGUCAGCC---GCGGG-UCGCG-CGGGGGC--CG-------CGG--GGGAGUC---------------------------CUAGGCC-GAGUGG---CCGCAGG-AAGAGAAA-----CG-GAGCC-U-GUCCC-------UGUGCACGGGGCGC-UUCUC-UGAGCUGU-GGGAA--GUGCCC--C--GAGAC-U-CGGCUCCUACAAGC
AF221930.1/94-546        -----------GGCCGGCGUGCCUGGGAGGGG---GGGCU--GGUC----CCACUC--UUCUAACCCUAAGGGUGUCG---------------GCUGUAGGC-GCCGUGCUUU----UUA---CUUCCC--------------------CGCGCGCUGUUUUUCUGGCUGGCUUUCAGCGAGCGGAA--AAAGCUUUG--GUCUA--CAGGCCACUCACUUUGUAUCCC-------------------------------------------------GAAACCAAAUU-GAAAAAAAAAAAUGCC--AGC-UCC--------GG-CC-----GGUCCACCCCU----CCCGGGGU-----------------CCUGCGGCCCGGCC----------------------------------------------------GCC-CGCCCGAAC------------CCCCCGCGA--CCCGC--CUG--------AGGCCACGGCCGGCCC-GGGGCCUC----UGCG---GAGGUGCCC-AUUGCCGCCGCGAAGAGU-UAG-GCUCUGUCAGCC---GCGGGAUCC--GCGCGGG---C--------CGGGCC-GCGGC-------------------------------CGGACGCCGAU--CCGCAGG-GACAGCAA-----CG-GAAC-C-GGCCCC-------UUCGCCCUGUGCGC-UUCCC-GGAGCUGU-GGGA--UGAGCAC--CC-GGGGUC-G--GCUCCUACAGUU
AF221909.1/98-496        --------------------------------------GA--CGCGC----GCCUC--UUCUAACCCUAAAAACUG-GA--------------GCUGUAGGU-GUUGCUCUUU-------------CAGCGU-----------------CGCCCGCUGUUUUUCUCGCUGGCUUUCAGCGGGCC-AG--AAAGUUCAG--ACCUCU-CAGCAGAUCGUCGCGUCGUUC--------------------------------------------------UCAACCA-----CA-----AAAAAUGCC--AGCGCAAA------GCG-CG-----UC-------------------AGCCUAGAAC---------CUUGCGGCCCCG-------------------------------------------------------GGCCGCCC----------------AGCCCC-GCA-CCCGC--CUUG-------AGGCCGCGGUUGGCCU-GGAG-UUC----UCCG---GA---CUCC-GCUGCCGCCGCGAAGAG-UUCGU-CUCUGUCAGCC---GCGGAGUAUCA-GGGGCU--G----------GGGCCAGGCC--------------------------------CGGAC-AGCG---UCGCAAG-UACAGUAA-----CG-GAGC-U-GGUCCU-----UGUUCG----GUG-GC--UUCCCUGAGCUGUAGGAA---GUACAC--CC-AGAGCUCG--GCUCCUACAACC
AF221928.1/95-476        ----------------------------------------------------------GUCUAACCCUGAAUUCUGAGA--------------GCUGUGGGU-ACUGUGCUUU--------CGU--CUC--------------------CGCCCGCUGUUUUUCUCGCUGACUUCCAGCGGGCG--GG-AAAGUCCAG--ACCUG--CAGCGGGCCAUCGCGCGUUUU--------------------------------------------------CCA-CCA-----CAA----AAAAAUGUC--AGCGCUGG-GCUCA--------------------------------UGUGCCU-------GGAGCCUUGCGGCC----------------------------------------------------------GGCCGCCC----------------AGCCCC-GCA-CCCGC--CUG--------AGGCCGCGGUCGGCCU-GGAG--UC----CUCG---GG---CUCC-GCUGCCGCCGCGAAGAG-CUAGA-CUCUGUCAGCC---GCGGGGCGUCA-GGGGCU--G----------GGGCGAGCCC--------------------------------CGGC--AGCG---CCGCAAG-CAGAGAAA-----CG-GAGC-U-GGUCCC--------GUGAACGGUG-AC-UUCCC-UGAGUUGU-GGGAAAUG--CAC--CA-GGAACUCG--GUUCCCACAACC
AC121792.3/109554-109950 ----------------------------------------------------------ACCUAACCCUGAUUUUCAUUA--------------GCUGUGGGU-UCUGGUCUUU--------UGUU-CUC--------------------CGCCCGCUGUUUUUCUCGCUGACUUCCAGCGGGCC-AGG-AAAGUCCAG--ACCUG--CAGCGGGCCACCGCGCGUUCC--------------------------------------------------CGAGCCU-----CAAAA--ACAAACGUC--AGCGCAGGAGCUCC--------------------------------AGGUUCGCCG----GGAGCUCCGCGGCGCCG-------------------------------------------------------GGCCGCCC---------------AG-UCCCGUA--CCCGC--CUAC-------AGGCCGCGGCCGGCCU-GGGG--UC----UUAG---GA---CUCC-GCUGCCGCCGCGAAGAG-CUCGC-CUCUGUCAGCC---GCGGG-GCGC-CGGGGGCU-G----------GGGCCAGGCC---------------------------------GGGCGAGCG---CCGCGAG-GACAGGAA-----UG-GAAC-U-GGUCCC---CGUGUUCG----GUGU-C-UUACC-UGAGCUGU-GGGAA--GUGCAC--CC-GGAACUCG--GUUCUCACAACC
AF221916.1/94-481        ----------------------------------------------------------GUCUAACCCUAU-UGUUAU-A--------------GCUGUGGGU-UCUGUUCUUU--------UGUU-CUC--------------------CGCCCGCUGUUUUUCUCGCUGACUUUCAGCGGGCC-UGG-AAAGUUCAG--ACCUG--CAGCGGGUCACCGCGCAUUCU--------------------------------------------------GGAACCU-----CA-----AAAAAUGUC--AGCGUAGGAGCUCU--------------------------------GGUGCC--------AGAGCUCCGCGGCGCUG-------------------------------------------------------GGCCGCCC-A--------------GCCCGGUA---CCCGC--CUGG-------AGGCCGCGGACGGCCU-GGGG--UC----UUAG---AA---CUCC-GCUGCCGCCGUGAAGAG-CUAGU-CUCUGUUAGCU---ACGGG-GC---ACCGGGC--GCUG-------GGGUCAGGCC-------------------------------GGGAGAGCG-----CCGCAAG-GACAGUAA-----CG-GAAC-U-GGUCCC---UGAGUUCG----GUG-GC-UUUCC-UGAGAUGU-GGGAA--GUGCAC--CU-GGAACUCA--GUUCCUACAACC
AY058901.1/1-397         ----------------------------------------------------------ACCUAACCCUGAUUUUCAUUA--------------GCUGUGGGU-UCUGGUCUUU--------UGUU-CUU--------------------CGCCCGCUGUUUUUCUCGCUGACUUCCAGCGGACC-AGU-AAAGUCCAG--ACCUG--CAGCGGGCCACCGCGCGUUCC--------------------------------------------------CGAGCCUCAAAAAC-------AAACGUC--AGCGCAGGAGCUUC--------------------------------AGGUUCGCCG----GGAGCUCCGCGGCGUCG-------------------------------------------------------GGCCGCCC-A-------------G-UCCCG-UA--CCCGC--CUAC-------AGGCCGCGGCCGGCCU-GGGG--UCUUAGGA---C-------UCC-GCUGCCGCCGCGAAGAG-CUCGC-CUCUGUCAGCC---GCGGG-GCGC--CGGGGGC--------UG--GGGCCAGGCC---------------------------------GGG-CGAGCG--CCGCGAG-GACAGGAA-----UG-GAACU--GGUCCC-------CGUGUUUGGUGU--CUUACC-UGAGCUGU-GGGAAGU--GCAC--CC-GGAACU--CGGUUCUCACAACC
U85256.1/1-451           ----GGGUUGCGGAGGGUGGG---CCUGGGAG--GGGUGGU-GGCCA---UUUUUU--GUCUAACCCUAACUGAGAAG---------------GGCGUAGGC-GCCGUGCUUU--------UGCU-CCC--------------------CGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGA---AAAGCCUCG--GCCUG-CCGCC-UUCCACCGUUCAUUCU--------------------------------------------------AGAGCAAA----CA-----AAAAAUGUC--AGC-UGC-------UGG-CC--CGUUCGCCCCUCCC----GGG---GA-----------------CCUGCGGCGGGUC------------------------------------------------------GCCUGCCC-A-------------GCCCCCGAAC--CCCGC--CUGG-------AGGCCGCGGUCGGCCC-GGGGCUUC----UCCG---GAGGCACCC-ACUGCCACCGCGAAGAGU-UGG-GCUCUGUCAGCC---GCGGG-UCUC-UCGGGGGC-GA---------GGGCG-AGGU----------------------------UCAGGCCUUUCAGG---CCGCAGG-AAGAGGAA-----CG-GAGC-G-AGUCCC-------CGCGCGCGGCGCG-AUUCCC-UGAGCUGU-GGGA----CGUGCACCC-AGGACU-CG-GCUCACACAUGC
AF221912.1/98-564        ----GGG-AGUGGAGGGUGGG---CCCGGGAC--GGGCG-C-GGACC---CGGUA---AUCUAACCCUGACUCACAAGA--------------GGCGUAGGC-GCCGUGCUUU--------UGCU-CCC--------------------CGCGCGCUGUUUUUCUCGCUGACUUUCAGCGUUCGGA---AAAGCCCUGUGGCCUA-UCGCC-AUCCACCAUCCUUUCU--------------------------------------------------GGAACAAACAGACAAAAAAAAAAAUGUC--AGC-UGC-------UGG-UC--CGUUCGCUCCUCCC----GGG---C------------------CCUGCGGUGGCCGCCAGCCC----------------------------------------------GCC-CUCUC-A--------------UCCCCCGCGU-CCCGC--CUAG-------AGGCCGCGGUCGGCCC-GGGGCUUC----UCCG---GAGGUGCCC-AUUGCCGCCGCGAAGAGU-UAG-GCUCUGUCAGCC---GCGGG-CUCU-CGGGGGG--------CCCA-GGG-C-GAGGU---------------------------UUAGGCC-UCGUGG---CCGCAGG-GACAGCAA-----CG-GAGC-G-GGUCCC------CGCGAGCCUGUGCGCG-UCCC-UGAGCCGU-GGGA--CUUGCAC--CG-GGGACU-UU-GCUCGGACAAUC
AF221939.1/99-544        ----GGGUUGUGGAGGGUGGG---CCUGGGAG--GGGAAGC-GGUCA---GUUUUU--GUCUAACCCUAACUGAGAAG---------------GGCGUAGGC-GCCGCGCUUU--------UGUUUCC---------------------CGCACGCUGUUUUUUUCGCUGACUUUCAGCGGGCGGA---AAAGCCUCG--GCCUA-CCGCC-GUCCACCGUACAGUUU--------------------------------------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-UGC-------UGA-CU--UGCUCGCCCCUCCC----AGG---AC-----------------CCUGCGGUGGCUC-----------------------------------------------------GCCUC-CUU-AG--------------CCCCCGCGU-CCCGC--CUAG-------AGGCCGCGGUCGGCCC-GGGGCUUC----UCCG---GAGGCACCC-AUUGCCGUCGCGAAGAGU-UGG-GCUCUGUCAGCC---GCGGG-UCCCUUGGGGG-------GGCCGA-GGG-C-GAGGC------------------------------------UCUGA---CCGCAGG-GAGAGAAA-----CGGGAGC--AGGUCCC-------CGCGCGCGGUGCGC-UUCCC-UGAGCUGU-GGGA-C-UUGCAC--CC-GGGACUG-G-GCUCAGACACAU
AF221931.1/99-541        ----GGGUUGCGGAGGGUGGG---CUCGGGAG--GGGUGGC-GGUCA---UUUUCU--GUCUAACCCUAACUGAAACG---------------GGCGUAGGC-GCUGCGCUUU--------UGUU-CCC--------------------CGCACGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGA---AAAGCCUUG--GCCUA-CUGCC-ACACACCAUCCAGUUU--------------------------------------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-GGC-------UGG-CC--UGCUCGCCCCUCCC----GGG---AG-----------------CCUGCGGCGACUC-----------------------------------------------------GCC-CGCUU-A--------------GCCCCCGCAU-CCCGC--CUGG-------AGGCCGCGGUCGGCCC-GGGGCUUC----UCCG---GAGGCACCC-AUUGCCGUCGCGAAGAGU-UGG-GCUCUGUCAGCC---GCGGG-ACCCUUGGGGGC---------CAA-GGGC--GAGGC------------------------------------UCUGG---CCGCAGG-GAGAGAAA-----CG-GAGC--GGGUCCC-------CUCGCGCGGUGCGC-UUCCC-UGAGCUGU-GGGA-C-UUGCAC--CC-GGGACUA-G-GCUCACACACAC
AF221917.1/99-542        ----GGGUUGCGGAGGGUGGG---CCUGGGAG--GGGUGGC-GGUCG---UUUUAU--GUCUAACCCUAACUGAGAAG---------------GGCAUAGGC-GCUGCGCUUU--------UGUU-CCC--------------------CGCACGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGA---AAAGCCUCG--GCCUA-CUGCC-AUCCACCAUCCAGUUU--------------------------------------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-CGC-------CGG-CC--UGCUCGCCCCUCCC----GGG---AU-----------------CCUGCGGUGGCUC-----------------------------------------------------GCC-CGCUU-A--------------GCCCCCGCGU-CCCGC--CUGG-------AGGCCGCGGUCGGCCC-GGGGCUUC----UCCG---GAGGCACCC-AUUGCCGUCGCGAAGAGU-UGG-GCUCUGUCAGCC---GCGGG-ACCUUUGGGGGC---------CAA-GGGC--GAGGC------------------------------------UCUGG---CCGCAGG-GAGAGAAAA----CG-GAGC--GGGUCCC-------CUUGCGCGGUGCGC-UUCCC-UGAGCUGU-GGGA-C-UUGCAC--CC-GGGACUA-G-GCUCACACACAU
AF221936.1/98-540        ----GGGUUGCGGAGGGUGGG---CCCCGGGU--UGGUGGC-AGCCA---UUUCUC--AUCUAACCCUAAUUGAGACA---------------GGCGUAGGC-GCUGUGCUUU--------UGGUUAC---------------------CGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGA---AAAGCCUCG--GCCUA-CCGCC-AUCCACCAUCCAGUCU--------------------------------------------------GCAACAAA----CA-----AAAAAUGUC--AGC-CGC-------UGG-CU--CGCUCACCUCUCC-C---GGG---AA-----------------CCUGCGGUGGUCC-----------------------------------------------------GCC-CGCCC-AG-------------CC-CCAGUGC-CCCGC--CUG--------AGGCCGCGGUCGGCCC-GGUGCUUC----UCCG---GAGGUGUCC-AUUGCCGCCGUGAAGAGU-UGG-GCUCUGUCAGCC---GCGGG-UCGCUC-GGUGG-------GCCGA-GG-C-A-UGGC------------------------------------UGUAA---CCGCAGG-GAAAGGAA-----CG-GAGUGG-GGUCCC-------CGCGCGCGGUGCGC-UUCCC-UGAGCUGU-GGGA-C-UUGCAC--CC-GGGACU-CG-GCUCAGACAUCC
AF221920.1/99-541        ----GGGUUGCGGAGGGUGGG---CCCAGGAG--CGGUGGC-GGCCA---UUUUUUAAGUCUAACCCUAACUGAAAGA---------------GGCGUAGGC-GCUGCGCUUU--------UGCUUCA---------------------CGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGA---AAAGCCUCG--GCCUA-CCGCC-AUCCACCAUCCAGUCU--------------------------------------------------GAAACAAA----CA-----AAAAAUGUC--AGC-CUC-------UGG-CU--CGCUCACUGCUCC-C---GGG---AA-----------------CCUGCGGUGGUUC-----------------------------------------------------GCC-CGCCC-A--------------GCCCCCGCGC-CCCGC--CUG--------AGGCCGCGGUCGGCCC-GGGGCUUC----UCCG---GAGGCGCCC-AUUGCCGCCGCGAAGAGU-UGG-GCUCUGUCAGCC---GCGGG-UCCCUCGGGGGC---------CAA-GG-C--GAGGC------------------------------------UCUGA---CCGCAGG-GAAAGGAA-----CG-GAGU-U-GGUCCC-------CGCGCGCUGUGCGCUU-CCC-UAAGCUGU-GGG--CUGUGCAC--CU-GGGACUCG--GCUCAGACACUU
AF221921.1/98-548        ---------------GGCGGG--UUGCGGGAGC-UGCGAG-CGGCCG-----UCUC--GUCUAACCCUAAA-GAGAAA---------------GGCGUAGGU-GCUUGGCCUU---------GGCGACU--------------------CGCCCGCUGUUUUU-UGGCUGGCUUUCAGCGGGUGAA---GAGGCCCAAG-ACCUA-CCGCC-ACCCACCGUCUAGUGUCUUAAGGGCACAAAGUCCUGCCCGCCACCCUUCGA---------------GGAGCGAAA---CCC----AAAAAAGUC--AGC-CCC-------UGG-CCG-CCUCUCGCCCUCUC----GCAA---------------------CCCGC--CU----------------------------------------------------------CCG-UCCC-A--------------GCCUC--CAUCCCCGC--CCC--------AGGCCGCGGUCGGUCC-GGG-CUUC----UUCG---GAAGU-CCC-GUUGCCGUCGCGAAGAG-UUCGC-CUCUGUCAGCC---GCGGG-GCU-U--GGGGC---------CA--GGGA---CGG----------------------------------GACCCUGU-CC--GCAGG-GAGAGAAA-----CU-GGAGCCGGG-CCC---------UCCACGGUGC-C--UCCC-CGAGCUGU-GGGAUC-U-GCAC--CC-GGGACU--CGAACCCUACACUU
AF221925.1/98-540        ----GGGUGGGGGAGAGUGGG---UCUGGGCG--GGGCGGC-GGUCA---CGUUUU--GUCUAACCCUAACUGAGCUG---------------GGCGGAGGC-GCCGCGCUUU--------UGCU-CCC--------------------CGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGA---AAAGCCUCG--GUCUA-CCGCC-ACUUACCAUCCAGUCU--------------------------------------------------GGAGUAAA----CA-----AAAAAUGUC--AGC-CGC-------UGG-CU--CGCUCGCCCCUCCC----GGG---AC-----------------CCUGCGACGGCUC-----------------------------------------------------GCC-CGCCC-A--------------GCCCCCGCGC-CCCGC--CUGG-------AGGCCGCGGUCGGCCC-GGGGCUUC----UCCG---GAGGCGCCC-AAUGCCGCCGCGAAGAGU-UGG-GCUCUGUCAGCC---GCGGG-UGCCUCGGGGGC---------CAG-GGAC--GAGGC------------------------------------UCUGG---CCGCAGG-GAGAGGAA-----CG-GAGC-G-GGUCCC-------CGCGCGCGGUGCGC-UUCCC-UGAGCUGU-GGGA-C-GUGCAC--CC-GGGACU-CG-GCUCAAACACGU
AF221906.1/96-545        ----GGGUUGCGGAGGGAGGG---CCCGGGAG--GGGUGAG-CGUCC---AUUAUC--GUCUAACCCUAACUGAGAUG---------------GGCGUAGGC-GCCGCGCUUU--------UGCUUCC---------------------CGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGA---AAAGCCUCG--GCCUA-CUGCC-GUCUACUGUCGUAUCU--------------------------------------------------GGAGCAAA----CA-----AAAAAUGUC--AGC-CGC-------UGG-UC--CGCUCGCCCCAUCC----GGG---AA-----------------CCUGCGGUGGCUC-----------------------------------------------------GUC-CGCCC-U------------GCCCCCGCGC---UCCGC--CUAG-------AGGCCGCGGUCCGCCC-GGGGCUUC----UCCG---GAGGCACCC-AAUGCAGCCGCGAAGAGU-UAG-GCUCUGUCAGCC---GCGGA-UCC--CGCGGGGGC-------CAA-GGGU--GAGGC---------------------------UUAGGCC--GCGGG---CCGCAGG-AAGAAAAA----CC--GAGC-G-AGUUCU-------CACGCGCGGUGCGCUU-CCC-UGAGCUGU-GGG-UC-GUGCGC--CU-GGGACU-CG-GCUCAGACACGU
AF221911.1/104-513       ------------------CCG---CUGCGGCGGCAGGUGGG-GGCUC----AGUCU--UUCUAACCCUAAGCGAAAUGUGACC------------------------C-CUCC-------------CCGCUGCAGC-------------CGUCCGCUGUUUUACUCGCUGACUUUCAGCGGACG-GGG-GGAGCGGGU--------------------------------------------------------------------------------GGAGACGCCAACCA-----AAAAACGUC--AGC-GAG-------GGGCCC----UCCCCUCCCACG----CCG---AC-----------------CUGGGCCUGUGG----------------------------------------------------UGGGGCCCGCC-----AGCGAAGU-CCCCGCCGC-----CCCGCCCCGGUG-----AGGCCGCGGUCAGCC--GGC---------UCGC---------GCC-ACUGCUGCCGCGAAGAG-UUCGU-CUCUGUCAGCCU--CGGGG------GCGGCCGGG---GUGGAAG-GGCG--GGUCCCG--------------------------AGCCCGUC--------GGCC-GG-GAGAGCAAA---CGU-GAGCGGCAGCCCC--------UGCGCCACCGC-CCUCCCC-UAAGCUGU-GGGGCCC--GCGG--UC-GGGGC--UGCGCUCAGACACGC
AF221924.1/105-538       ------------------CGC---GUGGCGGA--UGGGGA--GGCUC---CAGUCU--CACUAACCCUAAU----------------------GGC-U--GCCGCCGUGCUCC-------------CCGCACC----------------CGUCCGCUGUUUUAUUCGCUGACUUUCAGCGGACG-GGG-GGAGCC-------------GCCUGGGGGGGA---------------------------------------------------------AGGGGUUUGCAAUCA-----AAAAACGUC--AGC-GAC-------GGG-UC-----UCCCCAGCC-CAGCCCGC---C------------------CUGGGGUCUCCGUCCCCCCACGCAGCC-------------------------------------GGGGGCCUGCC------GCGGAG----GCUCCCUC---CGCCGCACUUCACGG---AGGCCGCGGUCGGCC--GGUG-UCC-----------------GCC-ACUGCCGCCGCGAAGAG-UUCGU-CUCUGUCAGCCU--CGGCG-GCGGUGGGGAGC------GAGAG--GGC-UC-GUCCCC-------------------------GCGCCGGGG--------ACCCCAG-CAGAGCAAAA---CG-GAGC-G-GCGUC---CUCGGCACAGCCGCCGCGC-UUCCC-UCAACCGU-GGGA--UGCGCGG--AC--GGCGC-C--GCUUCGACACCC
AY312571.1/605-1069      -----------------ACGC-------GUGGC-GGGUGGAAGGCUC---CGCUGU--GCCUAACCCUAAUCGGGGGAAUUGAUGGU------GCUGUC----GCCGCGCUCC-----------CUCCGCC------------------CGCCCGCUGUUUUACUCGCUGACUUUCAGCGGGCG-AGA-GGAGCCGCCC-CGGGGGGGAGGCGGGCGGCGGGAGGGGGCCGGGGCGCCGCGGCGGUGGGGGUCGGGGGGGGGAGAGAAAGGGCCGAAAGGGGCUCCGCGGCCAA---AAAAACGUC--AGC-GAG-------GGG-UC--CGCUCGCCCCGAU-C---------CGC---------------CCUGGGG-UC------------------------------------------------------------------------------------CCCGC------UCG--CG---------UGGCCGCGGUCGGCC--GGCACCC------------------GCC-AUUGCCGCCGCGAAGAG-UUCGC-CUCUGUCAGCCU--CGGCG-GCGC-GCGGG----------------------------------------------AGGUGCGGCGCGCGGCCCCGCG-C-CCCCAG-CAGAGCAAA----CGGGAGC-G-GCGCC---CCCGGGGUAACCCCCGCGC-UCCCC-UGCGCCGU-GGGG-C-GCGCGG--AC--GGCGU-C--GCUCCCACACGC
AF147806.2/247-692       -----------------ACAC-------GUGGC-GGGUGGAAGGCUC---CGCUGU--GUCUAACCCUAAUCGGAGGUAUUGAUGGUA------CUGUC----GCCGCGCUCC-------------CUC--------------------CGCCCGCUG-UUUACUCGCUGACUUUCAGCGGGCU-AGG-GGAGCCGCCC--------CAGGGGGCGCCGCGGGGGGGAGGGGGUGGGGCGGACGCGGGAGAAAGGACCGAAAGGGGCUCCAC--------GGCAAACAAAAAAAA--AAAAACGUC--AGC-GAG-------GGG-UC--CUCUCGCCCCCAU-C---------CGC---------------CCUGGGG-UC------------------------------------------------------------------------------------CUCG-----CCCGC-------------AGGCCGCGGUCGGCC--GGCACCC------------------GCC-AUUGCCGCCGCGAAGAG-UUCGC-CUCUGUCAGCCUCGGCGGG-GCC---CGGG-----AGAUGCGGA----------------------------------------GCGCGGC-CCCGCG-C-CCCCAG-CAGAGCAACA---CGGGAGC-G-GCGCC---CCCGGGGCAACCCCCGCGC-CCCCC-UGCGCCGU-GGGG-C-GCGCGGAC----GGCGU-C--GCUCCCACACGC
#=GC SS_cons             .................::::...<<<<<<<<..<<<<<<-.<<<<<...------..-----------------------..----....................-<<<<<........--------....................<<<<<<<<<________AAAAAAAAA>>>>>>>>>.---.>>>>>----..............--------.-------..................................................---------------....--aaa-aaa..aaa.---.......>>>.>>.....>>>>>>>>>>>....>>>...,,.................(((((((--------.---...............................................(((((((((.-....---.......(((((((-...(((((.,,,,,.......,,,,<<<<<-<<<<--.<<<_____....____...______>>>.--->>>>>>>>>,<<<<._____.>>>>,,,,,,,,..))))).---..)))))))......-----..))))..)))))...........................-------..-----...))))))).,,,,,,,,,....,,.<<<<<<.<<<<<<......---------<<<<<-.-<<<<.________.>>>>.--.>>>>>..--.>>>>>>.>.>>>>>::::::::
#=GC RF                  .................ucag...cccGggcg..ggGgggu.ggccc...uuuUuu..uUCUAACCCUAAuugagaaguua..gaGg....................ugCucu........uGuuUCCc....................cGCcCGCUGUUUUucUcGCUGACUUUCAGCGgGCg.AgG.agaGccuag..............ggccaccg.guaguuu..................................................ggagcaaaaagACaA....AAAAAuGUC..AGC.cgc.......ggg.cc.....cccCcccgccC....ggg...ag.................CcuGcggcaucucug.aau...............................................ggcccgccc.a....ucu.......cccccgcu...cCCgc.aCUuu.......AGGCCGCGGUCgGCCc.GGggCUUC....uccg...gaGGugcCC.AuUGCcGCCGCGAAGAG.UUCGU.CUCUGUCAGCCU..gcGGg.ucc..gcggggg......gagug..gggc..gggcc...........................ucggggg..ucuga...ccgCagG.gAgAGuAAA....CG.GAgccg.gggccc......gugcguuccgcGcgC.uUCCC.UGAGCUGU.GGGA.cu.cgCgc..uC.gggccc.c.ggcUCauACAcuc
//
# STOCKHOLM 1.0

#=GF AC   RF00025
#=GF ID   Telomerase-cil
#=GF DE   Ciliate telomerase RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   McCormick-Graham and Romero, PMID:7739888; Griffiths-Jones SR, Moxon SJ
#=GF SS   Published; PMID:7958872; PMID:7739888, Moxon SJ
#=GF GA   41.00
#=GF TC   42.40
#=GF NC   40.70
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00004
#=GF DR   SO; 0000390; telomerase_RNA;
#=GF DR   GO; 0007004; telomere maintenance via telomerase;
#=GF DR   GO; 0003720; telomerase activity;
#=GF DR   GO; 0000333; telomerase catalytic core complex;
#=GF RN   [1]
#=GF RM   7739888
#=GF RT   Ciliate telomerase RNA structural features.
#=GF RA   McCormick-Graham M, Romero DP
#=GF RL   Nucleic Acids Res 1995;23:1091-1097.
#=GF RN   [2]
#=GF RM   7958872
#=GF RT   Telomerase RNAs of different ciliates have a common secondary structure
#=GF RT   and a permuted template.
#=GF RA   Lingner J, Hendrick LL, Cech TR
#=GF RL   Genes Dev 1994;8:1984-1998.
#=GF CC   Telomerase is a ribonucleoprotein reverse transcriptase that synthesises
#=GF CC   telomeric DNA. Telomerase RNAs differ greatly in sequence and structure
#=GF CC   between vertebrates, ciliates and yeasts, but they share a 5' pseudoknot
#=GF CC   structure close to the template sequence.
#=GF WK   Telomerase_RNA_component
#=GF SQ   20


U22349.1/199-360     UUAUACCCGC----AU-AUCAUUCAG--ACCC-UUUAU---GGAA---CUGUC-AUUC--AACCCCAAAAAUCUAGUGCA-AAUAUUGUCUU---AAUUACUUAGGCUAAAAG--AAAUAAGUAUUAAA-------GCGGG-----AC-----AAGGC----------AUCGA--CAUUUGAUACA-AAU--AUU-----------------------------------------GAUCA-AUG-GAU-GUCUU----AUU-UUU
U10565.1/50-238      AGUUUCUCGA---UAA-UUGA-UCUG--U----AGAAU----------CUGUC-AAGCAAAACCCCAAAACCUUA-CACU-GAGAGC-AUUU---AGCCUGAUUACUCUUUAAA-UCAAAUCAGGCAAU------AGAGAGAA---ACUCG--AGAGGUGAAAACCCCACA----GCAUUCUGAAA-UGU--AUUUGGGAGU----------------AAUCUCAUA---------UUAGUUUGC-UGU-CCUCU--CAUCU-UUU
AJ132318.1/1-175     -GACAAUUGCU--GUA-UUCAUUCUCCUUUCUCGAUAG---AGAU-UGGAGUC-AUAC--AACCCCAGAAACC-AUUCCU-UAUA-C-CUUGAG-UAUUGCUGAAUUC-------AGUUUAGCGUGCAUGCUCUUGGCUAU-----UCUCA--UAGUGA---------UUGUCA-AAUUUGGAGUU-ACUU-AUU-----------------------------------------CGUCA-AUU-CAA-UAUUU----AUG-ACG
U10567.1/1-190       AGCUGGUGGA----AG-UGCG-UCAG-----U-CAUAG--CA------CUGUCAACAA--AACCCCAAAACCGUA-AACU-CAGAGC-AAUU---CGCCUGGUUCCUCUUUAAAGCAAAACCAGGAGGU-------UCCGCCAGCUACC----AGAGGACGAAG----UGG----GCUAAGUGAAA-UGAAAAUUUGAGAGU---------------UUCUCUCCA----------UCACUUAGCCCCG-CCUCU-CAUUCU-UUU
U22350.1/52-211      UUAUACCCGC---AAA-UUCAUUCAG--GUCU-GUAAU---AGAU---CUGUC-AUUC--AACCCCAAAAAUCUAGUGCA-AAUAUUACCUU---CACCAAUUAGGUA-------UAAUCAAUGGUAUC-------GCGGG-----ACAA---AAGACU---------AUCGA--CAUUUGGUA-C-ACU--AUU-----------------------------------------UAUCA-AUG-GAU-GUCUU----AUU-UUU
U10569.1/29-216      GUUCGGCGGA----AA-UCCG-UCAG----C--UAUAA---CG-----CUGUCAAGAA--AACCCCAAAACCGUA-AAAU-GAGAGC-AAUU---CGCCUGGUUCCUCUUUAAAGUCAAACCAGGAGGC-------UCCGCCGG--ACU----AGAGGUCGAAA----AGG----ACUGAGUAAAAUACUGCAUUUGAGAGU---------------UUCUCUCCA----------UUGCAAAGU-CCUCCCUCU--CUUCU-UUU
U22352.1/508-657     UUAAUCCCGC---UAU-UGCAUUCCA-------UUUCG--A---------GUC-AUUC--AACCCCAAAAUUCUAGUACACACUAAAGCU------UGCCUUUGGGCA-------UAUCAGGGGCA----------GCGGGAGA--AUU----UAGAAU---------UUCGA--CAUGUGGUA-C-ACU--AUU-----------------------------------------UAUCUCAUG-GAGAUUCUA----AUU-UUU
AF417611.1/281-444   AUAUCCCCGC---AAA-UUCAUUCUG--UUU--GCAUU---CAAA---CAGUC-AUUC--AACCCCAAAAAUCUAGACCA-AAUAUUGUCUU---CCCUUCUUGGCACA------AACAAAGAAGAGAC-------GCGGG-----AUA----AAGAUA---------CUCCGA-CGAUUGAUA-C-AAU--AUU-----------------------------------------UAUCA-ACGGGAG-GUCUU-ACUUUU-UUU
AF399707.1/2181-2345 UUAUACCCGC---UUAAUUCAUUCAG--AUCU-GUAAU---AGAA---CUGUC-AUUC--AACCCCAAAAAUCUAGUGCU-GAUAUAACCUU---CACCAAUUAGGUUC------AAAUAAGUGGUAAU-------GCGGG-----ACAA---AAGACU---------AUCGA--CAUUUGAUA-C-ACU--AUU-----------------------------------------UAUCA-AUG-GAU-GUCUU-AUUUUU-UUU
U45437.1/191-400     UGACAAUUGCU--GUA-UUCAUUCUCCUUUCU-CGAUA---GGAAUUGGAGUC-AUAC--AACCCCAGAAACC-A-UCCU-UAUA-C-CUUGA--GUAUGCUGAAUUCC--------GUUAGCGUAGCU---CUUGGCUAU-----UCUCA--UAGUG----------AUUGCAUAUUUGGAGU-U-ACUU-AUUCGUCAAUUCAAUUAAAAUUCA----UGACGAACCUAAAAGUACUCUGAAU-GGU-UAUUU-UUUAUA-AUU
U22354.1/216-379     UUAUACCCGC---ACA-UUCACUCAA--AUCU-GUAAU---AGAC---UUGUC-AUUC--AACCCCAAAAAUCUAGUGCA-AAUAUUACCUU---CGCCAAUUAGGUA-------CAAUUAAUGGUUCU------CGCGGG-----ACAA---AAGACU---------AUCGA--CAUUUGAUA-C-AUU--AUU-----------------------------------------UAUCA-AUG-GAU-GUCUU-AUUUUU-CUU
U10570.1/72-259      GUUCGGCGGA----AA-UCCG-UCAG----C--UAUAA---CG-----CUGUCAAGAA--AACCCCAAAACCGUA-AAUU-GAGAGC-AAUU---CGCCUGGUUCCUCUUUAAAGUUAAACCAGGAAGC-------UCCGCCGA--ACU----AGAGGUCGAUA----AGG----GCUGAGUAAAAUACUGCAUUUGAGAGC---------------UUCUCUCCA----------UUGCAAAGU-CCUCCCUCU--CUUCU-UUU
M33461.1/140-346     GGAUAUAGGG---UAG-UUC-UCCAU---UGA-CUAAUCCGUCAA-AUCUGUC-AAACAAAACCCCAAAACCG-AUCAAU-AGGUGC-GUUUAGCUUGAUUACACCUCUU-----AAAUGAAAUCUUGC-----AAUUCUG---GAGAGCUUGAGAGGUGAAACCCCCACA----GUUAGGUCA-AACAUA-GUUUGAGAUU--------------UGUAUCUCAUA---------UGCUCUAGC-UGU-CCUCUCAUCUUU-UUG
U10566.1/72-260      AGUUUCUCGA---UAA-UUGA-UCUG--U----AGAAU----------CUGUC-AAGCAAAACCCCAAAACCUUA-CACU-GAGAGC-AUUU---AGCUUGAUUACUCUUUAAA-UUAAAUCAGGCAAU------AGAGAGAA---ACUCG--AGAGGUGAAAACCCCACA----GCAUUCUGAAA-UGU--AUUUGGGAGU----------------AAUCUCAUA---------UUGGUUUGC-UGU-CCUCU--CAUCU-UUU
AF417609.1/192-355   AUAUCCCCGC---AAA-UUCAUUCUG--UUU--GCAUU---CAAA---CAGUC-AUUC--AACCCCAAAAAUCUAGACCA-AAUAUUGUCUU---CCCUUCUUGGCACA------AACAAAGAAGAGAC-------GCGGG-----AUA----AAGAUA---------CUCCGA-CGAUUGAUA-C-AAU--AUU-----------------------------------------UAUCA-ACGGGAG-GUCUU-ACUUUU-UUG
U10568.1/27-212      AGUCGGCGGA----AA-UCAG-UCAG-----U-CAUAG--CG------CUGUCAACAA--AACCCCAAAACCGUA-AAAU-UAGAGC-AAUU---CGCCUGGUUCCUCUUUAAAGCAAAACCAGGAGGC-------UCCGCCG---ACUCA--GAGGGC---------ACUGUGGGCUGAGCAAAA-UGAAAAUUUGAGAGU---------------UUCUCUCCA----------UUGCUUAGC-CCU-ACCUC--UAUCU-UUU
U22351.1/80-240      UUAUACCCGC---AUU-UUCAUUCAG--AUCU-UUAAU---GGAG---CUGUC-AUUC--AACCCCAAAAAUCUAGUGCA-ACUACUGCCUU---AACUACUUAGGCA-------AAAUAAGUCGUAAA-------GCGGG-----AC-----AAGGC----------AUCGA--CAUUUGAUACA-AAU--AUU-----------------------------------------GAUCA-AUG-GAU-AUCUU-AUUUUU-UAU
AF417610.1/218-380   GUAUCCCCGC---AAC-UCCAUUCAG--UUC--GAAAU---UGAA---CUGUC-AUUC--AACCCCAAAAAUCUAGUAAAAAAUAUUGCC-G---AAACUUUCAGGCAU------UAAGGAAAGUAAA--------GCGGG-----AU-----CAGAUA---------CUCCGA-CUUGUGAUA-C-ACU--AUU-----------------------------------------UAUCACAUGGGAG-AUCUA--UUUUUAUUU
U22353.1/53-206      UUAUACCCGC---AAA-UUCACUCAA--AUCU-GUAAU---AGGU---UUGUC-AUUC--AACCCCAAAAAUCUAGUGCA-AAUAUUACUUU---CGCCAAUUAGGUA-------UAAUAA-UGGUAA--------GCGGG-----AC-----AAGAC-----------UCGA--CAUUUGAUA-C-ACU--AUU-----------------------------------------UAUCA-AUG-GAU-GUCUU----UUU-UCU
AF417612.1/228-392   AGAUACCUCCUGUGGA-UCCAUUCAG--GAUU-AAUGA---AAUC---CUGUC-AUUC--AACCCCAAAAAUCUUGUCAA-AUUAUUGCC-U---CGUCUUUUGGGCAC------AAACAAAAGUCACG-----CAGGAGG-----UU-----CAGACA---------UUCGA--CAUAAGAUA-C-ACU--AUU-----------------------------------------UAUCUUAUG-GAAGGUCUA----GUU-UUU
#=GC SS_cons         :::::(((((...,,,.,,,,,,<<<..-<<<._____...>>>-...>>>,,.,,,,..,,,,,,,,,,,,,,,,,,,,.,,,,,,.,,,,...,<<<<<<<<_____......___>>>>>>>>,,,......,))))).....----...<<<<<-.........<<<--..<<<-<<<<<.-.----.----<<<<__..................>>>>--..........>>>>>->>>.>>>.>>>>>..:::::.:::
#=GC RF              ugAUacccGc...uaA.UUCAUUCag..uucu.uaaAu...agaa...cuGUC.AuaC..AACCCCAAAAaCcUAguacU.aAuAgc.cuUU...cuccucuuaacUCu......aAAuaagaggaaau......agCggg.....aCuC...aagggu.........aucGa..gcuuuGaua.a.AcUu.AUUUGaGAgU..................UCuCaa..........uauCauagc.gau.cccuu..uuuUU.UUU
//
# STOCKHOLM 1.0

#=GF AC   RF00026
#=GF ID   U6
#=GF DE   U6 spliceosomal RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Griffiths-Jones SR; ; PMID:18390578
#=GF SS   Published; PMID:2339054; Griffiths-Jones SR
#=GF GA   44.00
#=GF TC   44.00
#=GF NC   43.90
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00009
#=GF DR   SO; 0000396; U6_snRNA;
#=GF DR   GO; 0000244; spliceosomal tri-snRNP complex assembly;
#=GF DR   GO; 0000353; formation of quadruple SL/U4/U5/U6 snRNP;
#=GF DR   GO; 0030621; U4 snRNA binding;
#=GF DR   GO; 0005688; U6 snRNP;
#=GF DR   GO; 0046540; U4/U6 x U5 tri-snRNP complex;
#=GF RN   [1]
#=GF RM   9016512
#=GF RT   The uRNA database.
#=GF RA   Zwieb C
#=GF RL   Nucleic Acids Res 1997;25:102-103.
#=GF RN   [2]
#=GF RM   1960724
#=GF RT   Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some
#=GF RT   possible snRNA-snRNA base-pairing interactions.
#=GF RA   Orum H, Nielsen H, Engberg J
#=GF RL   J Mol Biol 1991;222:219-232.
#=GF RN   [3]
#=GF RM   2339054
#=GF RT   The spliceosomal snRNAs of Caenorhabditis elegans.
#=GF RA   Thomas J, Lea K, Zucker-Aprison E, Blumenthal T
#=GF RL   Nucleic Acids Res 1990;18:2633-2642.
#=GF CC   U6 snRNA is a component of the spliceosome which is involved in splicing
#=GF CC   pre-mRNA. The putative secondary structure consensus base pairing is
#=GF CC   confined to a short 5' stem loop, but U6 snRNA is thought to form
#=GF CC   extensive base-pair interactions with U4 snRNA [2]. This model hits a
#=GF CC   large number of sequences in vertebrate genomes, which appear to be U6
#=GF CC   derived pseudogenes or repeats. This family has a high significance
#=GF CC   threshold to minimise this problem, but many annotated pseudogenes remain.
#=GF WK   U6_spliceosomal_RNA
#=GF SQ   188


AB010698.1/46416-46518           GUC-CC---------------UUCG-------GG--G-AC--AUCUGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAUAAA--UCGAGAAAU------------GGUCCAAAUUUUU
AARH01001853.1/272694-272592     GUC-UC---------------UUCG-------GA--G-AC--AUCUGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAUUUUU
X60506.1/390-492                 GUC-CC---------------UUCG-------GG--G-AC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAUUUUU
AC146705.11/15272-15374          GUC-CC---------------UUCG-------GG--G-AC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAUUUUU
AASG02002949.1/2307-2409         GUC-CC---------------UUCG-------GG--G-AC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAUUUUU
AACV01009611.1/38269-38167       GUC-CC---------------UUCG-------GG--G-AC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAUUUUU
AAAA02013555.1/2292-2394         GUC-CC---------------UUCG-------GG--G-AC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAUUUUU
CR855100.1/43897-43999           GUC-CC---------------UUCG-------GG--G-AC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAUUUUU
X52315.1/1-103                   GUC-UC---------------UUCG-------GA--G-AC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAUUUUU
X51447.1/262-364                 GUC-CC---------------UUCG-------GG--G-AC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAAUUUU
AAXJ01018701.1/864-762           ACC-CC---------------UUCG-------GG--G-GU--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAGU------------GUAAAAAGUUUUU
AAQA01000086.1/111608-111711     GUU-CAU--------------UCCG------AUG--A-AC--AUAUAC---UAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAAAUUUUU
L26849.1/150-253                 GUU-CAU--------------UCCG------AUG--A-AC--AUAUAC---UAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAAAUUUUU
X51387.1/158-259                 GUU-CU---------------UCCG-------AG--A-AC--AUAUAC---UAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAAAUUUUU
AANU01133867.1/371-269           ACC-CC---------------CUCG-------GG--G-GU--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAGU------------GUAAAAAGUUUUU
X63066.1/363-465                 GCC-CC---------------UUCG-------GG--G-AC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAUUUUU
AAAB01008807.1/5121648-5121542   GUC-CUUGC------------UUCG-----GCAG--G-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAWU01008690.1/11499-11605       GUC-UUUGC------------UUCG-----GCAA--G-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAGE02013372.1/83708-83814       GUC-UUUGC------------UUCG-----GCAA--G-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AABU01002774.1/16804311-16804417 GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAGH01007200.1/1053-947          GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AADE01001799.1/12821-12927       GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAEU02000254.1/81013-80907       GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAPQ01001284.1/654-760           GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAPP01016905.1/3608-3714         GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAQB01008633.1/461913-461807     GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AANI01001778.1/524-630           GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAIZ01003051.1/11867-11761       GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAPT01019380.1/23511-23405       GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAPU01011102.1/63061-63167       GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AABS01000051.1/274751-274857     GUA-CUAGC------------UUCG-----GCAG--U-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCAUAUUUUU
AAHY01132583.1/7739-7845         GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCAUAUUUUU
AAFC03115769.1/4330-4436         GUG-CUCGC-----------UUUGG------CAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGU------------GUUCCAUAUUUUU
AAPY01153714.1/3278-3172         GUG-CUCGC-----------UUUGG------CAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGU------------GUUCCAUAUUUUU
AALT01529386.1/701-595           GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGU------------GUUCCAUAUUUUU
AAYZ01436191.1/1883-1777         GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGU------------GUUCCAUAUUUUU
BAAB01141103.1/711-817           GUA-CUUGC------------UUCG-----GCAG--U-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAZX01000860.1/13921-13815       GUA-CUUGC------------UUCG-----GCAG--U-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AACY022149992.1/529-635          GUA-CUUGC------------UUCG-----GCAG--U-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AATU01006594.1/28185-28081       GAC-CAC--------------UUCG------GUG--G-UC--AUCCGU---AAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAUAAA--UCGAGAAGU------------AUCGCACUUUUUG
ABAV01046662.1/5606-5712         GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAAAUUUUU
AAFR03037834.1/2280-2178         GUG-CU---------------UCAG------CAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACAA-GGAUGACAUGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
ABDC01230141.1/8073-7967         GUG-CUUGC-----------UUUGG------CAG--C-AC--AUAUAC---UAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---UGUGAAGU------------GUUCCAUAUUUUU
AANN01390182.1/1050-1156         GUG-CUUGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
M31687.1/705-811                 GUG-CUUGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
AACT01041609.1/35558-35664       GUA-CUUGC------------UUCG-----GCAG--U-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCUUAUUUUU
AANG01770494.1/575-681           GUG-CUCAC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACAA-GGAUGACACGCAAAUU---UGUGAAGU------------GUUCCAUAUUUUU
AAQQ01629113.1/2249-2143         GUG-CUCGC-----------UUUGG------CAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
ABBA01062195.1/38876-38770       GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
AAIY01587713.1/2016-2122         GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
AAPN01022574.1/939-833           GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
CR956385.13/177771-177665        GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
U43841.1/336-439                 AUC-CAC--------------UUCG------GUG--G-AA--AUCCCA---UAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCUCAUA---CGAGAAGU------------UAAAAAGUUUUUU
AANV02000039.1/44432-44535       AUC-CAC--------------UUCG------GUG--G-AA--AUCCCA---UAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCUCAUA---CGAGAAGU------------UAAAAAGUUUUUU
AAFB02000174.1/3561-3664         AUC-CAC--------------UUCG------GUG--G-AA--AUCCCA---UAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCUCAUA---CGAGAAGU------------UAAAAAGUUUUUU
CAAI01006173.1/984-1090          GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACCCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
BAAF04101838.1/670-565           GCA-CUAGU-----------UCUCU-------AG--U-GC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCUCAUUUUU
AAVX01043085.1/4211-4317         GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUG
AC148181.3/26639-26533           GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-CU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACAUGCAAAUU---CGUGAAGU------------GUUUCAUAUUUUU
CT573239.9/51807-51913           GUG-CUUGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUCUUUUA
AAYL01000007.1/235430-235323     GGC-CUCC-------------UUCG-----GGAG-UG-CC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAGU------------GUAACCAAUUUUU
CAAE01010022.1/48689-48584       GUG-UUAC-------------UUCG-----GUAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCUUCAUUUUU
AF529186.1/459-564               GUA-UCUC-------------CUCG-----GAGG--U-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCAUAUUUUC
AAXT01000001.1/1039074-1039179   GGC-CUC--------------UUCG------GAG-UG-CC--AUCAGA---AAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCUCAAA--UCGAGAAGU------------GUAAAAACGAUUU
DQ666642.1/4-106                 UUG-CU---------------UCGG------CAG--U-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AAWT01067003.1/344-451           GUG-UGUUG-----------CUUCG-----GCUU--C-AC--AUAUAU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCAUAUUUUU
AANH01010141.1/91130-91025       GUG-UUAU-------------UUCG-----AUAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCUCAUUUUC
AB220565.1/723-829               GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGAAAAUU---UGUGAAGC------------GUUCCAUAUUUAA
AAGK01000002.1/918046-917941     GGC-CUC--------------UUCG------GAG-CG-CC--AUCAGA---AAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCUCAAA--UCGAGAAGU------------GUAAAACCCAUUU
AC136964.2/84202-84308           GUG-CUCGC-----------UUUGG------CAG--C-AC--CUAUAU---UAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGUGCAA-GGAUGACACACAAAUU---UGCGAAGC------------GUUCCAUAUUUUU
X71486.1/1-101                   GUG-C----------------UUCG--------G--C-AC--AACUGU---UAAAA-UU--GGAAAA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAUAAA--UCGAGAAAU------------GGUUCCAAAUUUU
AACM02000382.1/262414-262518     UGU-CUC--------------UUCG------GAG--A-CA--AUAUGG---UCAAA-CA--GUAAAA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACAA-GGAUGACACAUUCAAA--UCUAGAGAA------------GCUCAAAUUUUUU
AC146661.3/155499-155393         GUG-CUCGC-----------UUUGG------CAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGA------------AAAAAAAAAAUCA
CAAL01001232.1/21304-21406       GAC-CC---------------UUCG-------GG--G-UC--AUCCGU---CAAAU-UU--GGAACG-UAA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGUAA-GGAUGACACGCAUUAA--GCGAGAUGG------------UAGCUCAUUUUUU
AC087806.3/115795-115689         GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUAAAA
L25920.1/3-109                   GUA-CUCGC------------UUCG-----GCGG--U-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU--UCGUGAAGC------------GUUCCAUA-UUUU
CU326409.1/117472-117365         GUG-CUCAC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGUGCAAAGAAUGACACGCAAAUU---CUUGAAGA------------GUUCCAUAUUUUU
AC188110.1/71045-71151           GUG-CUUGC-----------UUUGG------CAG--C-AC--AUGUAU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-UCCUGUGCAA-GGAUGACACGCAAAUU---CCUGAAGC------------CUUCCACAUUUUU
CR382132.1/1089192-1089093       GUC-C----------------UUCG--------G--G-AC--AUAUGG---UCAAU-UU--GAAAAA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCAUAA-GGAUGACACGCUUUAC---AAAGAGAU------------UUAAACCGUUUUU
DQ068047.1/3306-3202             GUC-CN---------------UUCG-------GG--G-AC--AUCCGA---UAAAN-NU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GNAUGACACGGCACAAAAUCGAGAAAU------------GGUCCAAUUUUUU
AC189844.3/58074-58180           AUG-CUCAC------------UUCG-----GCAG--C-AC--AUAUAU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGCUGACACGCAAAUU---UAUGAAGC------------GUUCCAUAUUUAA
AF095841.1/1-107                 GUG-CUCGC-----------UUUGG------CAG--C-AC--UUACAC---UAAAA-UU--GGAAUG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCACGGU-CCCUGGGCAA-GGAUGACACACAAGUU---CGUGAAGC------------GUUCCAUAUUUUU
AASM01002098.1/3099-2992         GGCUCUC--------------UUCG------GAGAUG-CC--GUUUGU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACAUGACGU--UCGAGAAGG------------AAUGUAAUUUUUU
X58843.1/3-106                   AAC-CC---------------GAAA-------GG--G-UC--AUCCGU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCGAAGGAUGACACGCUCAAA--GCGAGAAGG------------AUUCCCCAUUUUU
CAAJ01009065.1/446-339           GGCUCUC--------------UACG------GAGAUG-CC--GUUUGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACAUGACGU--UCGAGAAGG------------AAUGUAAAUUUUU
AAFU01001153.1/10970-11070       GCC-C----------------UUCG--------G--G-GC--AUUUGG---UCAAU-UU--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUACUC---AAAGAGAC------------GCUACCAAUUUUU
AABL01000365.1/9537-9644         GGCUCUC--------------UACG------GAGAUG-CC--GUUUGC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACAUGACGU--UCGAGAAGG------------AAUGUAAAUUUUU
AADS01000210.1/17114-17228       GUC-CCC--------------UUCG------GGG-UG-AC--AUACGA---AAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACAA-GGAUGACACGCUUUCC--CGGAGUGGUAGAC---CUACGGGUCUCAAUAUUU
AAPO01000024.1/134030-133927     ACU-AUC--------------UUCG------GAU--A-GU--ACAUUU---GUCAA-UU--UUAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUUGU-CCUUGCAUAA-AGAUGACACGCUUUAC---AAAGAGAU------------UUACAGUUUUUUU
AAWC01002368.1/53508-53403       GCC-CAC--------------UUCG------GUG--GUGC--AUACGU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACAA-GGAUGACACAUGUAGU--CAGAAUGGA------------UUCACCUAUGGGU
CT990557.10/71286-71393          GUG-CCCUU-----------UUUGG------UAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA---ACAGUGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUAACACGCAAAUU---CGUGAUGC------------AUUCCAUAUUCUU
AAFM01000021.1/681699-681594     ACU-AUCG-------------UUCG-----CGAU--A-GU--ACAUUU---GUCAA-UU--UUAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUUGU-CCUUGCAUAA-AGAUGACACGCUUUAC---AAAGAGAU------------UUACCAUUUUUUU
AAFT01000065.1/268653-268548     ACU-AUUG-------------UUCG-----CAAU--A-GU--ACAUCU---GUCAA-UU--UUAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUUGU-CCUUGCAUAA-AGAUGACACGCUAUAC---AAAGAGAU------------UUACCAUUUUUUU
AAEY01000056.1/129419-129306     GCC-ACC--------------UUCG------GGU-CG-GC--AUAAGA----AAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUUGC-CCCUGCAUAA-GGAUGACAAACUCGAG--CAGAGAGGAGGUU---CUUCGGAACCAAAUAUUU
AACO02000104.1/123353-123240     GCC-ACC--------------UUCG------GGU-CG-GC--AUAAGA----AAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUUGC-CCCUGCAUAA-GGAUGACAAACUCGAG--CAGAGAGGAGGUU---CUUCGGAACCAAAUAUUU
AE017348.1/872264-872377         GCC-ACC--------------UUCG------GGU-CG-GC--AUAAGA----AAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUUGC-CCCUGCAUAA-GGAUGACAAACUCGAG--CAGAGAGGAGGUU---CUUCGGAACCAAAUAUUU
AAFP01000223.1/16410-16523       GCC-ACC--------------UUCG------GGU-CG-GC--AUAAGA----AAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUUGC-CCCUGCAUAA-GGAUGACAAACUCGAG--CAGAGAGGAGGUU---CUUCGGAACCAAAUAUUU
CP000496.1/1065610-1065505       ACU-AUCC-------------UUCG-----GGAU--G-GU--ACACUU---GUCAA-UU--UUAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUUGU-CCUUGCAUAA-AGAUGACACGCUUUAC---AAAGAGAU------------UUAACAUUUUUUU
AAID01000554.1/5500-5599         ACA-AU---------------UUCA-------AU--A-GU------GG---UCAAU-UU--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUCAAU--CAAAGAGAA------------GCUACCAAUUUUU
X14196.1/133-285                 UGA-UC---------------UUCG-------GA--U-CA--CUUUGG---UCAAA-UU--GAAACG-AUA----CAGAGAAGAUUGUAAGUAACAAUAUUUACCAAGGUU-------CGAGUCAUACUAACUCGUUGUUUAGAGCAUGGC-CCCUGCACAA-GGAUGACACUGCGACA--UUGAGAGAA------------AACCCAUUUUUUU
AAZN01000268.1/119544-119646     GUA-CCC--------------UCCG------UGG----AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAAUAAGUUUUU
AACW02000046.1/25302-25425       GAC-ACGCUCA-------UUGAGCC------UCU--G-UC--ACUUAU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACAA-GGAUGACACUAAAUCU--CUGAGAAGGAAGCUCUACGGAGCAACAUUUUUUU
CU104654.2/178130-178232         GUA-CUCGC-----------UUUGG------CAG--C-AC--AUAUAU---UAAAA-UA--GGAACG-AUA----CAGAGAAGAUC---------------------------------------------------------AGCAUGGU-CCCUGCACAA-----GACAUGCAAAUU---CAUGAAGC------------AUUCUAUAUUUUU
EF419774.1/1-102                 GCU-CUC--------------UUCG------GAG--AUGC-CGUUUGU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACAUGACGU--UCGAGAAGG------------AAUG-----UAAU
AACI02000106.1/4087-4199         GUC-CGCGGAGUA----ACCCUUCG-------UG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAUUUCGUUUUU
CR382126.1/1858703-1858820       GUC-CAUAUUACCCUCCGUGGUUUU------AUG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAAGAUUUUUUU
AACH01000157.1/7933-7821         GUU-CGCGAAGUA----ACCCUUCG-------UG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAAUUCGUUUUU
AATM01000137.1/47790-47943       CGA-UC---------------UUCG-------GA--U-CA--CUUUGG---UCAAA-UU--GAAACG-AUA----CAGAGAAGAUUGUAAGUACCCCCCUAAGGUCGUGAG------UUCGAGUUCCACUAACACCCGUCUAGAGCAUGGC-CCCUGCACAA-GGAUGACACUGCGACA--UUGAGAGAA------------ACCCAAUUUUUUU
Z73279.1/2843-2955               GUU-CGCGAAGUA----ACCCUUCG-------UG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAUUUCGUUUUU
AACA01000433.1/2210-2322         GUU-CGCGAAGUA----ACCCUUCG-------UG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAUUUCGUUUUU
AAEG01000112.1/87347-87459       GUU-CGCGAAGUA----ACCCUUCG-------UG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAUUUCGUUUUU
AABY01000279.1/8828-8716         GUU-CGCGAAGUA----ACCCUUCG-------UG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAUUUCGUUUUU
AACG02000194.1/7974-8086         GUU-CGCGAAGUA----ACCCUUCG-------UG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAUUUCGUUUUU
AACF01000007.1/86925-87036       GUC-CCGAGGCA-----ACCCCUCG-------UG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAUUCGUUUUUU
AADM01000279.1/397-288           GCU-CAU--------------UUCGGUGGGCGUG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUACAAGUUUUUU
AF083031.2/127905-127809         GAU-CU---------------UUUG------GAU--A-UU--CCAUCA---UAAAU-UU--AAUACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGUAA-GGAUGACAUGAAAAUC---UA------------------CUGGUAGUAUUUU
AC144401.2/82868-82974           GUG-CUUGC-----------UUUGG------CAA--C-AC--AUAUAC---UAAAA-UU--UGAAAC-AUA----CAGAAAAGAUU---------------------------------------------------------GGCAUAGC-CCCUCUGCAA-GGAUGUCGUGCAAAUU---CCUGAAGC------------AUUCCAUAUUUUA
AANW02001116.1/942-1048          UAG-UCUGGG---------AAAUCG-------GA--C-UA--CUAAUC---UAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAAAAC-CCCUGCGCAA-GGCCGG-UUACUUCUA---CGAGAAGU------------UAAGGAAUUUUUU
AY953942.1/4-110                 CCU-CCGGGC----------AACCG-------GC--A-GG--CAUCCA---AAUUA-UG--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGU-CCCUGCGUAA-GGAUGACCGUAAAGCA---AUCAAGAA------------GAAAAACAUUUUU
AJ416571.1/12089-11984           AGG-CC---------------CUCA------CGG--C-UUUAAAAUGC---GUCAC-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUAGC-CCCUACGCAA-GGAAGACACGCACAAA--UCGAGAAAU------------AGCCCAAAGCGGA
AATT01000229.1/70559-70673       GGA-UUC--------------UUCG------GGA--C-CU--CAUCAA---AAUAA-UU--GGAUAC-AAA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGCUCCCUGUGCAA-GGAUGACACGCAAAAC--UUGAGUGGAUUGC---CCUUCUGGGCAAGUUUUU
AL590448.1/66612-66503           GUA-GUU--------------UUCU-------AC--C-GC--CAUUG-------AU-UU--GGAACA-ACA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGUAA-GGACGACAUGUAUAAC--UUGAGAGGUCGCUG--GAUGUAGAUCCGGCUUUU
AY136823.1/430-532               UGG-AC---------------AUAU-------GC--U-CG--ACAUUG---CUAAA-UU--GGAACG-AUA----CAGAGACGAU----------------------------------------------------------AGCAUGUC-CCCUGCGCAA-GGAUGACGUUACAAAU---CGAGAUAUU----------CGUUUUAGGCUUUU
AF305715.1/117-214               GCC-CC---------------UUCG------GGG--G-AC--AUCCAC----AAAC-UG--GAAAUU-CAA----CAGAGAAGAUU---------------------------------------------------------AGCACUCU-CCCUGCGCAA-GGCUGAUGUCAAUCUU---CGAGAGAU------------AUAGC----UUUU
X82228.1/412-509                 GCC-CC---------------UUCG------GGG--G-AC--AUCCAC----AAAC-UG--GAAAUU-CAA----CAGAGAAGAUU---------------------------------------------------------AGCACUCU-CCCUGCGCAA-GGCUGAUGUCAAUCUU---CGAGAGAU------------AUAGC----UUUU
AAFI02000006.1/10321-10427       CCU-CCGGGC----------AACCG-------GC--A-GG--CAUCCA---AAUUA-UG--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------ACCAUGGU-CCCUGCGUAA-GGAUGACCGUAAAGCA---AUCAAGAA------------GAAAAACAUUUUU
AF053588.1/116-223               UGC-AG---------------UUUG-------CU--G-CG--CUAUUA------GU-UU--GGAACA-ACA----CUGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGACGGCAUCUUUCUU---UGAGAGGUGUGC---UGGGCUCGCCCAGCUUUU
AAJI01001561.1/684-795           GCU-CAUAUA---------UAUACC------CAG--A-GC--AUUUGG---UC-AA-UU--GAAACG-AUAU--ACGGAGAAGAUU---------------------------------------------------------UGCAUGGC-CUCUGCUCUAAGGAUGACACGCUCAAU--CAAAGACAA------------GCUACAAGUUUUU
AACQ01000098.1/66592-66693       UAG-UUGCGC----------GUUCG------GAA--C-UU--GUC---------AA-CU--UUAAAA-UUA----CAGAGAAAAUU---------------------------------------------------------AGCAUUUC-CCCUGCAUAA-GGACGGAACGCUUUAC---AAAGAGAU------------UUACCAUUUUUUU
AAFO01000026.1/267271-267372     UAG-UUGCGC----------GUUCG------GAA--C-UU--GUC---------AA-CU--UUAAAA-UUA----CAGAGAAAAUU---------------------------------------------------------AGCAUUUC-CCCUGCAUAA-GGACGGAACGCUUUAC---AAAGAGAU------------UUACCAUUUUUUU
AAIM02000091.1/125555-125392     GCC-AGCGGG---------CAACCG-------CU--G-GC--CUAUGG---UCCAA-CU--GAAAAU-AUA----CAGAGAAGAUGUAAGUGUUUACCCCCAAAUUCUAGCGU---UCGAGCACUCACUAACAGUUCCAUAGUAGCAUGGC-CCCUGCACUAAGGAUGACACAUGUAAU--CAAAGAGAC------------GCAAACCAUUUUU
X78552.1/318-415                 GCC-CC---------------UUCG------GGG--G-AC--AUCCAC----AAUC-UG--GAAAUU-CAA----CAGAGAAGAUU---------------------------------------------------------AGCACUCU-CCCUGCGCAA-GGCUGAUGUCAAUCUU---CGAGAGAU------------AUAGC----UUUU
X79014.1/475-572                 GCC-CC---------------UUCG------GGG--G-AC--AUCCA-----CAAC-CU--GGAACU-UCA---ACAGAGAAGAUU---------------------------------------------------------AGCACUCU-CCCUGCGCAA-GGCUGAUGUCAAUCUU---CGAGAGAU------------AUAGC----UUUU
X78551.1/329-426                 GCC-CC---------------UUCG------GGG--G-AC--AUCCAC----CACC-UG--GAAAUU-CAA----UAGAGAAGAUU---------------------------------------------------------AGCACUCU-CCCUGCGCAA-GGCUGAUGUCAAUCUU---CGAGAGAU------------AUAGC----UUUU
AC149301.1/92055-91961           GUU-CC---------------UUCA-------GG--G-AC--AUCCAA---UAAAA-UU--GG-------------AGAGAAGAUA---------------------------------------------------------UGCACAGC-CCAUGUGCAA-GGAUGACAUGCACAAA--CCGAGAGUU------------GGUGUGCACAUAC
AAEE01000007.1/553473-553580     GGU-UCUCC-----------UUGCG------GGA--A-CC--CGAUUC---UAAAA-UU--GGCUUU-AAAA--ACAGAGAAGAUU---------------------------------------------------------AGCAA-AC-CCCUGCGUAA-GGCUGGUUUCAUUCGC---CGAAAGGU------------AUAACCAAUUUUU
AAEL01000070.1/7754-7647         GGU-UCUCC-----------UUGCG------GGA--A-CC--CGAUUC---UAAAA-UU--GGCUUU-AAAA--ACAGAGAAGAUU---------------------------------------------------------AGCAA-AC-CCCUGCGUAA-GGCUGGUUUCAUUCGC---CGAAAGGU------------AUAACCAAUUUUU
X82229.1/194-291                 GCC-CC---------------UUCG------GGG--G-AC--AUCCA-----CAAC-CU--GGAACU-UCA---ACAGACAAGAUU---------------------------------------------------------AGCAUUCU-CCCUGCGCAA-GGCCGAUGUCAAUCUU---CGAGAGAU------------AUAGC----UUUU
AAHK01000939.1/1885-1993         CCU-UCGUGU----------CAAAG------CGA--A-GG--ACAUCC---ACAAU-CU--GGAAAU-UCA---ACAGAGAAGAUU---------------------------------------------------------AGCACUCU-CCCUGCGCAA-GGCUGAUGUCAAUCUU---CGAGAGAU------------AUGGCUUUUCUGU
CP000581.1/336841-336949         GUC-UUAUC------------UUCGG----AUAU--G-AC--ACCUGA---UAAAC-UG--GAAAAAAAUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGUGAGUGUUCGC---UCGGACGC------------UCGCGCCGCGCAC
AC152105.2/17973-17865           GUC-UUAUC------------UUCGG----AUAU--G-AC--ACCUGA---UAAAC-UG--GAAAAAAAUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGUGAGUGUUCGC---UCGGACGC------------UCGCGCCGCGCAC
AC092562.4/129660-129562         UCG-CU---------------UGCG------CAG--C-GC--AUACAC---UGAAA-CU--CGAACG-AUA----CAG---GGAUU---------------------------------------------------------AGCA-GGC-CUCUGUACAA-GGAUGGCACGCCACUU---UGUGAAAU------------GUUCCAUAUAGAA
AAXI01000109.1/30199-30115       CGC-CG---------------CGCA------GCG--G-CG--CCGCU-------------------------------AGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUCAAU--CAAAGAGAA------------GCUACCAUUUUUU
DQ103593.1/29389-29298           GUU-UU---------------AAAG-------AA--A-UC--UUAUUC---UGUAC-UU--G---------------GAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGCUAUUCAAGCU---AAUUUGUA------------UUUACUAAAUUAA
AP004520.1/55775-55881           GUA-CA---------------AUCA------GUU--U-AU--CUAAAA---UAAAU-UUUGGGAACU-AUAUAUACUGAGAAGAUU---------------------------------------------------------AGCAUGGC-ACCUGCAUA---UAUGACACACACUUU---AAAAAAAA------------UUGGGUUAUUUAU
AAHC01000890.1/7726-7624         GUU-GCUAU-----------GUUCU------GGC--U-AC--UUUCAU----------U--UCAACG-AUA----CAGAGAAAUUU---------------------------------------------------------AGCAUGGU-CCUUGGACAA-AGAUGACCCUAAUAUCA-CCUUUGAGU------------GCACAAAAUGUUU
AAHF01000007.1/1651650-1651551   GCC------------------UUCG-----------G-GC--AUUUGG---UCAAU-UU--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACAAAGGAUGACACGCUCAAU--CAAAGAGAA------------GCUACCAGUUUUU
U58510.1/7462-7568               UUU-UAAUC------------UGCG------UUC--A-CG--CAUCUU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAUAAU--CCGAGAUUA------------GGUUCCUUUAUUU
ABAR01000008.1/592107-592006     AUG-CC---------------UUCG-------GG--C-AU----UUGG---UCAAU-UU--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUCAAU--CAAAGAGAA------------GCUACCAGUUUUU
AP007171.1/1600650-1600749       GCC------------------CUCG------A----G-GC--AUCCGG---UCAAU-UU--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACAA-GGUUGACACGCUUUAU--CAAGGAGAU------------GCUAAACUUUUUU
AARE01000569.1/1814-1714         GUG-CC---------------UUCG-------GG--C-AU--UUGGUC------AA-UU--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUCAAU--CAAAGAGAA------------GCUACCAGUUUUU
AASO01000114.1/1873-1980         GCC-UUUCU------------GCCU------UCG--G-GC--AUUUGG---UCUUA-UU--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUCAAU--CAAAGAGAA------------GCUCCAAGUUUUU
AAIW01000495.1/17855-17954       GCC------------------UUCG-----------G-GC--AUUUGG---UCUUA-UU--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUCAAU--CAAAGAGAA------------GCUCCAAGUUUUU
X04788.1/1-98                    CUU-CG--------------------------GG--G-AC--AUCCGA---UAAAA-UU--GGAACG-ACA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAAU------------GGUCCAAAUUUU-
AAGI01000262.1/1755-1855         GCC------------------UCCG-----------G-GC--ACCAGU---CAAUU-UU--GAAAAACAUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUCAAU--CAAAGAGAA------------GCUACCAUUUUUU
AY102720.1/4016-3910             AUA-AUCUA------------AAAU-------AU--C-AU--UCAAAU---CAAAC-CU-GGGAACG-AUU----GAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CUCUGCACAA-GGAUGACACGCAUAAA--UCGAGAAAU------------GUUCCAAAUAAAG
X57046.1/441-540                 GCC-C----------------UUCG------G-G--G-AC--AUCCAC----AAAC-UG--GAAAUU-CAA----CAGAGAAGAUU---------------------------------------------------------AGCACUCU-CCCUGCGCAA-GGCUGAUGUCAAUCUU---CGAGAGAU------------AUAGCUUUUCGGU
AC148038.3/33473-33580           UUU-ACCAG------------ACAG-----CCGG--A-AG--AGGGAG---AGGGU-UA--GGAAAG-ACU---UCAAGGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GAAAGACACAGAAAUU---CGCGAAGC------------ACUCCAUGCUCUU
AAZY02000001.1/305276-305169     CUC-ACC--------------UUCG------GGU--G-AG--UCUAAAUUCUAAAA-UU--GGCUUU-AAAA--ACAGAGAAGAUU---------------------------------------------------------AGCAA-AC-CCCUGCGUAA-GGCUGGUUUCAUGAGC---CGAUAGGU------------AUAACCAAUUUUU
CR380959.2/1159577-1159689       GUC-CUUGAAGUA----ACCCUUCU-------UG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAUUCGUUUUUU
CAAC02000605.1/61448-61549       GUU-CU---------------UCCG-------AG--A-AC--AUAUAC---UAAAA-UU--GGAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUACCAAAUUUUU
M10329.1/1-108                   GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU--------------------------------------------------------UAGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
CR382136.2/1319844-1319739       ACU-AUCCU------------UCUG------GAU--A-GU--ACAUUU---GUCAA-UU--UUAACA-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUUGU-CCUUGCAUAA-AGAUGACACGCUUUAC---AAAGAGAU------------UUAACCAUUUUUU
X12565.1/540-652                 GUU-CGCGAAGUA----ACCCUUCG-------UG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUAUUUCGUUUUU
AASC02049566.1/23588-23693       GUA-CUGUU------------CACG------CAG--U-AC--AUAUAC---UAAAA-UU--GGAAAG-AUA----CAGAGAAGACU---------------------------------------------------------AGCAUGGC-CCCUGCAUAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
AC121317.7/68985-69092           GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAAAUU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
AAPN01095965.1/240-347           GUG-CUCGC------------UUCGG----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
AAFD02000024.1/69022-69131       GUC-CCCGGU---------UCGCCG------GGU--G-AC--AUUAAA---CAAAC-GC--UUAAAU-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGU-CCCUGUGCAA-GGAUGACACGCAUAAU--CGAAGAGAA------------GCAAACCUUUUUU
AABX02000022.1/362974-363076     CGC-CC---------------UUCG-------GG--G-CA--AUUUGG---UCAAU-UU--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUACUC---AAAGAGAC------------GCUACCAAUUUUU
ABPA01000003.1/180549-180442     GGC-CUCC-------------UUCG-----GGAG-UG-CC--AUCCGA---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCACAAA--UCGAGAAGU------------GUAACCAAUUUUU
AACE03000008.2/905684-905797     GUC-CAAGACAUU----UCGGUGUU------UUG--G-AC--AUUUGG---UCAAU-UU--GAAACA-AUA----CAGAGAUGAUC---------------------------------------------------------AGCAGUUC-CCCUGCAUAA-GGAUGAACCGUUUUAC---AAAGAGAU------------UUACUUCAUUUUU
FR796420.1/621391-621294         GCC-CC---------------UUCG------GGG--G-AC--AUCCAC----AACC-UG--GAAAUU-CAA----CAGAGAAGAUU---------------------------------------------------------AGCACUCU-CCCUGCGCAA-GGCUGAUGUCAAUCUU---CGAGAGAU------------AUAGC----UUUU
AAFN02000036.1/11182-11077       GUG-AAAGU-----------CGCCG------GUU--C-GG--AACUUG---UCAAA-UU--UAAAAU--UA----CAGAGAAAAUU---------------------------------------------------------AGCAUUUC-CCCUGCAUAA-GGACGGAACGCUUUAC---AAAGAGAU------------UUACAACAUUUUU
AAGV020896327.1/1288-1181        GUG-CUCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAAAUU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---UGUGAAGC------------GUUCCAUAUUUUU
AATU01006589.1/7799-7695         AAC-CAC--------------UUCG------GUG--G-UC--AUCCGU---AAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAUAAA--UCGAGAAGU------------AUCGCACUUUUUG
AFQF01002057.1/12805-12639       GCC-AGCGGG---------UAACCG-------CU--G-GC--CUAUGG---UCACA-UU--GAAACG-AUA----CAGAGAAGAUGUAGGUGUUCUUCCCCCCUAAGUUCCAGCGUUCGAGCACGCACUAACAUCUCUAUAGUAGCAUGGC-CCCUGCACUAAGGAUGACACAUGUAAU--CAAAGAGAC------------GCAACCCAUUUUU
CAAA01180605.1/4-106             -----UCGC------------UUCG-----GCAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
ABDF02000090.1/1201765-1201660   GAA-GAG--------------GUCG-----CCUG--U-UC--GAAUCG---CUGAC-GU--UGCAAC-AGA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGUAAGUUGAACU---CCUGAACC------------AUACUCUGGUCAA
AACU03000132.1/2986497-2986398   GCC------------------UUCG-----------G-GC--AUUUGG---UCAAU-UU--GAAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUCAAU--CAAAGAGAA------------GCUCAACAUUUUU
AAIL02000075.1/131155-131066     GUU-CGA--------------AUCG-------CU--A-AC--AGGUCA----------------------A----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACUAAGGAUGACACGCUCACU--CAAAGAGAA------------GCUAAACAUUUUU
X76546.1/281-387                 GUG-UUAGC------------UUCG-----GCAA--C-AC--AUCUAU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCAUAUUUUU
CAAB02029384.1/647-542           GUG-UUAC-------------UUCG-----GUAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCUUCAUUUUC
AAEX03005034.1/14917-14815       GUG-CU---------------UCGG------CAG--C-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAUU---CGUGAAGC------------GUUCCAUAUUUUU
AC242743.1/25579-25465           GUC-CCC--------------UUCG------GGG-UG-AC--AUACGA---AAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCACAA-GGAUGACACGCUUUCC--CGGAGUGGUAGAC---CUACGGGUCUCAAUAUUU
BAAB01206473.1/1073-967          GUA-CUUGC------------UUCG-----GCAG--U-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
M24606.1/401-507                 GUU-CUUGC------------UUCG-----GCAG--A-AC--AUAUAC---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACGCAAAAU---CGUGAAGC------------GUUCCACAUUUUU
AL844509.2/1632740-1632633       GGCUCUC--------------UUCG------GAGAUG-CC--GUUUGU---UAAAA-UU--GGAACG-AUA----CAGAGAAGAUU---------------------------------------------------------AGCAUGGC-CCCUGCGCAA-GGAUGACACAUGACGU--UCGAGAAGG------------AAUGUAAUUUUUU
AC188639.6/7118-7225             GUG-CUUGC------------UUCU-----GCAGGAC-AU--AAACAC---UAAAA-UU--GGAAUG-AUA----AAGAGAAGAUU---------------------------------------------------------AGGAUGGC-CCCUGUGCAA-GGAUGACACACAA-UU---UGUGAAAC------------GUUCCAUAUUUUU
#=GC SS_cons                     <<<.<<_..............____......_>>..>.>>..::::::...:::::.::..::::::.:::....:::::::::::.........................................................::::::::.::::::::::.::::::::::::::::...::::::::............:::::::::::::
#=GC RF                          guc.ccc..............UUCG......ggg..g.ac..aUaUgg...UaAAa.UU..GgAACg.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCaCAA.GGAUGACACguauaau...agAGAgau............guaccauaUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00027
#=GF ID   let-7
#=GF DE   let-7 microRNA precursor
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.69 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000002;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11533718
#=GF RT   Control of developmental timing in animals.
#=GF RA   Rougvie AE
#=GF RL   Nat Rev Genet 2001;2:690-701.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the microRNAs (miRNA) let-7 and mir-98. let-7 was
#=GF CC   identified from a study of developmental timing in C. elegans [1], and was
#=GF CC   later shown to be part of a much larger class of non-coding RNAs termed
#=GF CC   miRNAs [2]. Both miRNAs let-7 and mir-98 have now been predicted or
#=GF CC   experimentally confirmed in a wide range of species (MIPF:MIPF000002).
#=GF CC   miRNAs are transcribed as ~70nt precursors (modelled here) and
#=GF CC   subsequently processed by the Dicer enzyme to give a ~22nt product. The
#=GF CC   extents of the hairpin precursors are not generally known and are
#=GF CC   estimated based on hairpin prediction. The products are thought to have
#=GF CC   regulatory roles through complementarity to mRNA. The involvement of Dicer
#=GF CC   in miRNA processing suggests a relationship with the phenomenon of RNA
#=GF CC   interference. This family also includes the miR-98 precursor from human,
#=GF CC   which may be a let-7 homologue.
#=GF WK   let-7_microRNA_precursor
#=GF SQ   63


Z70203.2/12451-12379           UCCGGU-GAGGUAGUAGGUUGUA-UAGUU----UGG------AAUAUUA--CCA-----CCGGUG--AACUAUGCAAUUUUCUACCUU-ACCGGA
AC048341.22/3536-3622          CCUGGCUGAGGUAGUAGUUUGUG-CUGUUGGUCGGGUU---GUGACAUU-GCCC--GCUGUGGAGAUAACUGCGCAAGCUACUGCCUU-GCUAGU
AC018755.3/119936-120011       CCGGGCUGAGGUAGGAGGUUGUA-UAGUU----GAGG------AGGACA-CC-C-----AAGGAGAUCACUAUACGGCCUCCUAGCUU-UCCCCA
AL049853.1/18009-17931         UUGGGGUGAGGUAGUAGGUUGUA-UAGUUUG--GGGC---------UCU-GCCC--UGCUAUGGGAUAACUAUACAAUCUACUGUCUU-UCCUGA
AP000962.2/118093-118168       CCGGGUUGAGGUAGUAGGUUGUA-UGGUUU--AGAGU---------UAC-ACCC-----UGGGAGUUAACUGUACAACCUUCUAGCUU-UCCUUG
AF210771.1/1883-1955           UACGGU-GAGGUAGUAGGUUGUA-UAGUUU--AGAAU---------AUU-ACUC-----UCGGUG--AACUAUGCAAGUUUCUACCUC-ACCGAA
AL158152.18/38291-38377        UCAGAGUGAGGUAGUAGAUUGUA-UAGUUGU-GGGGUA---GUGAUUUU-ACCC-UGUUCAGGAGAUAACUAUACAAUCUAUUGCCUU-CCCUGA
AL158152.18/40779-40863        CUAGGAAGAGGUAGUAGGUUGCA-UAGUUUU-AGGGCA---GGGAUUUU-GCCC---ACAAGGAGGUAACUAUACGACCUGCUGCCUU-UCUUAG
AL158152.18/37901-37981        -UGGGAUGAGGUAGUAGGUUGUA-UAGUUUU-AGGGU---------CAC-ACCCACCACUGGGAGAUAACUAUACAAUCUACUGUCUU-UCCUAA
AC094021.2/47340-47253         CCAGGCUGAGGUAGUAGUUUGUA-CAGUUUG-AGGGUC--UAUGAUACC-ACCC-GGUACAGGAGAUAACUGUACAGGCCACUGCCUU-GCCAGG
AP001359.4/114553-114478       CCAGGUUGAGGUAGUAGGUUGUA-UAGUUU--AGA----------AUUA-CAUC----AAGGGAGAUAACUGUACAGCCUCCUAGCUU-UCCUUG
AF480570.1/1-79                -----GUGAGGUAGUAAGUUGUA-UUGUUGU-GGGGUAGGGAUAUUAGG-CCCC--AAUUAGAAGAUAACUAUACAACUUACUACUUU-C-----
BX005154.6/63678-63599         GCAGGCUGAGGUAGUUGGUUGUA-UGGUUUU-GCAUC-----AUAAUCA-GCCU-------GGAGUUAACUGUACAACCUUCUAGCUUUCCCUGC
AY866046.1/496-584             CCAGGGUGAGGUAGUAAGUUGUA-UUGUUGU-GGGGUAG-GGAUAUUAG-GCCC-CAAUUAGAAGAUAACUAUACAACUUACUACUUU-CCCUGG
AC117784.13/47755-47833        UUGGGGUGAGGUAGUAGGUUGUA-UGGUUUU--GGGC---------UCU-GCCC--CGCUCUGCGGUAACUAUACAAUCUACUGUCUU-UCCUGA
AAVX01008163.1/128-212         CUGGGUAGAGGUAGUAGGUUGCA-UAGUUUG-AGGGCA---GGGAUUUU-GCCC---CAAAGGAGAUAACUAUACAACCUGCUGCCUU-UCCUGG
BAAE01218263.1/598-683         ACAGGGUGAGGUAGUAGGUUGUG-UGGUUUC-AGGGUU---GUGAUUUU-ACCC--CAUAAGGAGCUAACUAUACAACCUACUGCCUU-CCCUGG
CAAE01014991.1/464883-464800   UCAGGGUGAGGUAGUAGGUUGUA-UAGUUUG-GUGGG-----UGGGAUU-GCCC--ACUCAGGUGAUAACUAUACAGUCUAUUGCCUU-CCCUGA
AANG01619101.1/1216-1136       GUGGGAUGAGGUAGUAGAUUGUA-UAGUUUU-AGGGU--------CAUA-CCCC--AUCUUGGAGAUAACUAUACAGUCUACUGUCUU-UCCCAC
AANH01007764.1/36699-36614     ACAGGGUGAGGUAGUAGGUUGUG-UGGUUUC-AGGGUU---GUUAUUUU-ACCC--CAUCGGGAGUUAACUAUACAACCUACUGCCUU-UCCUGG
AAYZ01324012.1/2457-2541       ACGGGGUGAGGUAGUAGGUUGUG-UGGUUUC-AGGGCG---GUGAUGUC-GCCC---CUCAGCAGAUAACUAUACAGCCUACUGCCUU-CCCUGA
AAFR03057393.1/4201-4115       GCGGGGUGAGGUAGUAGGUUGUG-UGGUUUC-AGGGUA---GUGAUUUU-GCCC-CAAUCAGAAGAUAACUAUACAACCUACUGCCUU-CCCUGA
AAPY01378069.1/2181-2093       CUGGGGUGAGGUAGUAAGUUGUA-UUGUUGU-GGGGUUGGGAUUGUAGA-CCCC--AAUUAGAAGAUAACUAUACAACUUACUACUUU-CCCUGG
AAPN01341034.1/3404-3318       GCGGGAUGAGGUAGUAGGUUGUG-UGGUUUC-AGGGGA---GUGAUUUUGCCCC--AAUCAGAAGAUAACUAUACAGCCUACUGCCUU-CCCUGG
AAIY01003579.1/1841-1762       GUAGGAUGAGGUAGUAGAUUGUA-UAGUUGU-AGGUC---------AUA-ACCC--AUCUUGGAGAUAACUAUACAGUCUACUGUCUU-UCCCAC
AANN01347783.1/1229-1152       UUGGGGUGAGGUAGUAGGUUGUA-UAGUUUG--GGGC---------CCU-GCCC--UGCUAUGGGU-AACUAUACAAUCUACUGUCUU-UCCUGA
AAZX01015868.1/1070-988        CCUGGGUGAGGUAGUAGGUUGUA-UAGUGGG-GAAUG------AAAAUU-CGUC--AUUAUGGAAUCCACUGUACAACUUGCUAACUU-UCCCGG
AALT01443655.1/3068-3143       CCAGGUUGAGGUAGUGGGUUGUA-UAGUUCA-G---------AAUCACA-------UCAAGGGAGAUAACUGUACAGCCUCCUAGCUU-GCCUUG
AANU01169061.1/33054-33138     CUAGGAAGAGGCAGCACGUUGCA-UAGUUCU-AGGGA----AGGCACUU-UUCC--CACUUGGGGGUAACUGUAUGCCCUGCUGCCUG-UCUUAG
AABS01000138.1/96907-96982     GCAAGUUGAGGUAGUAGGUUAUAUCAGUUGA-U---------UAUAUGA--------ACCAGGAGAUAACUGUAUAGCCCACUAGCUU-ACUUGC
AAGD02006482.1/22892-22821     UCUGGU-GAGGUAGUAGGUUGUA-UAGUU----UAGA-----------A-UCUU--ACCUUGGUG--AACUAUGCAAGUUUCUACCUC-ACCAGA
AACT01004141.1/13602-13519     AUAACAUGAGGUAGUAGGUUAUG-CAGUUUG-GCGAC----AAUAUUUC-GUUG---CAAAGGAGAUAACUGUGUAACUUGCUGGCUC-UUUUAU
AAZO01005184.1/23361-23435     CAGGGU-GAGGUAGUAGACUGUA-UAGUA----AAGA---------AUU-ACAU--CAUUUGGAGG-UACUGUACAAUCUGCUAACUU-UCCCUG
AANI01016295.1/2335-2404       GCAAAUUGAGGUAGUAGGUUGUA-UAGUAGU-A-------------UUU----------AUAGAGCAUACUAUACAGCGUGCUAGCUUUCUUUGC
AAPT01004257.1/151-220         GCAAAUUGAGGUAGUAGGUUGUA-UAGUAGU-A-----------------------UCUAUCUAGCAUACUAUACAGCUUGCUAGCUUUCUUUGC
AAQA01000457.1/25368-25290     GCUCGAUGAGGUAGUAGGUUGUA-UAGUU----AUGA------GUUGUA-CCAU---AAUCGGAGA-AACUGUCCAGCCUGCUAGCUUGCCGUGC
AAJJ01000960.1/12168-12093     UCUGUUUGAGGUAGUAGGUUGUA-UAGUA----AGUA---------UUA-CACC--UAUUGGGAG--UGCUGUACAGCCUGCUAACUUUCCCAGA
AAPP01015675.1/360249-360318   GCAAAUUGAGGUAGUAGGUUGUA-UAGUAGC-A-----------------------ACUAAGAAUCGUACUAUACAAUGUGCUAGCUUUCUUUGC
AAPU01010514.1/89793-89724     GCAAAUUGAGGUAGUAGGUUGUA-UAGUAGU-A-----------------------CUUAUAGACCAUACUAUACAGCGUGCUAGCUUUCUUUGC
AABU01002759.1/2931025-2930956 GCAAAUUGAGGUAGUAGGUUGUA-UAGUA----GUAA-------------UUAC--ACAUCA-----UACUAUACAAUGUGCUAGCUUUCUUUGC
AAQB01006449.1/358437-358507   GCAAAUUGAGGUAGUAGGUUGUA-UAGUAGU-A---------------A-------UUAUUCAAUCAUACUAUACAAUGUGCUAGCUUUCUUUGC
AAFS01000369.1/71461-71393     GCAAAUUGAGGUAGUAGGUUGUA-UAGUAGU-A------------------------CUUCAGAUCGUACUAUACAAUGUGCUAGCUUUCUUUGC
ACBE01248169.1/7760-7844       CGGGGU-GAGGUAGUAGGUUGUG-UGGUUUC-AGGGCA---GUGAUGUU-GCCC--CCUCGGAAGAUAACUAUACAACCUACUGCCUU-CCCCGA
AAKN02054092.1/95811-95899     CUGGGGUGAGGUAGUAAGUUGUA-UUGUUGU-GGGGUAAGGAUUUAAGG-CCCC--AUUAAGAAGAUAACUAUACGACUUACUACUUU-CCCUGG
AAGW02075197.1/23048-23132     UCGGGGUGAGGUAGUAGGUUGUG-UGGUUUC-AGGGCA---GCGGUGUC-GCCC---CUCAGCAGAUAACUAUACAGCCUACUGCCUU-CCCCGA
AABR05153093.1/1773-1848       CCAGGCUGAGGUAGUAGGUUGUA-UAGUUUA-G---------AGUUACA-------ACAAGGGAGAUAACUGUACAGCCUCCUAGCUU-UCCUUG
CAAE01013731.1/39581-39496     ACGGGGUGAGGUAGUAGGUUGUG-UGGUUUC-AGGGUG---GUGAUAUU-GCCC--AAUCAGGAGAUAACUAUACAACCUACUGCCUU-CCCUGG
AY866050.1/490-568             UUGGGGUGAGGUAGUAGGUUGUA-UAGUUU--GGGGC---------UCU-GCCC--UGCUAUGGGAUAACUAUACAAUCUACUGUCUU-UCCUGA
AY866357.1/820-906             UCAGAGUGAGGUAGUAGAUUGUA-UAGUUGU-GGGGUA---GUGAUUUU-ACCC-UGUUCAGGAGAUAACUAUACAAUCUAUUGCCUU-CCCUGA
AF274345.1/1758-1830           UCCGGU-GAGGUAGUAGGUUGUA-UAGUU----UGGA-------AUAUU-ACCA-----CCGGUG--AACUAUGCAAUUUUCUACCUU-ACCGGA
AY866017.1/450-525             CCAGGUUGAGGUAGUAGGUUGUA-UAGUUUA-G---------AAUUACA-------UCAAGGGAGAUAACUGUACAGCCUCCUAGCUU-UCCUUG
AY866355.1/408-489             GUGGGAUGAGGUAGUAGGUUGUA-UAGUUUU-AGGGU---------CAC-ACCCACCACUGGGAGAUAACUAUACAAUCUACUGUCUU-UCCUAA
AC231658.3/113295-113375       GUGGGAUGAGGUAGUAGAUUGUA-UAGUUUU-AGGGU--------CAUA-CCCC--AUCUUGGAGAUAACUAUACAGUCUACUGUCUU-UCCCAC
AY866150.1/447-522             CCGGGUUGAGGUAGUAGGUUGUA-UGGUUUA-G---------AGUUACA-------CCCUGGGAGUUAACUGUACAACCUUCUAGCUU-UCCUUG
AY866290.1/298-385             CCAGGCUGAGGUAGUAGUUUGUA-CAGUUUG-AGGGUC--UAUGAUACC-ACCC-GGUACAGGAGAUAACUGUACAGGCCACUGCCUU-GCCAGG
EU624487.1/1401-1470           GCAAAUUGAGGUAGUAGGUUGUA-UAGUAGU-A---A-------------U-------UACACAUCAUACUAUACAAUGUGCUAGCUUUCUUUGC
HM625839.1/191-271             UUGGGGUGAGGUAGUAGGUUGUA-UAGUUUG-AGGGU---------UUA-ACCC-UUGCUGUCAGAUAACUAUACAACUUACUGUCUU-UCCCGA
AY866352.1/767-853             UCAGAGUGAGGUAGUAGAUUGUA-UAGUUGU-GGGGUA---GUGAUUUU-ACCC-UGUUUAGGAGAUAACUAUACAAUCUAUUGCCUU-CCCUGA
HM625839.1/1002-1087           ACAGGGUGAGGUAGUAGGUUGUG-UGGUUUC-AGGGUU---GUAAUUUU-GCCC--CAUCAGGAGAUAACUAUACAACCUACUGCCUU-CCCUGA
AY866020.1/478-553             CCAGGCUGAGGUAGUAGGUUGUA-UAGUUUA-G---------AAUUACA-------UCAAGGGAGAUAACUGUACAGCCUCCUAGCUU-UCCUUG
AC147162.2/101359-101275       CUAGGAAGAGGUAGUAGGUUGCA-UAGUUUU-AGGGCA---GAGAUUUU-GCCC---ACAAGGAGUUAACUAUACGACCUGCUGCCUU-UCUUAG
AY866019.1/258-334             CCAGGUUGAGGUAGUAGGUUGUA-UAGUUUA-G---------AAUUACA-------UCAAGGGAGAUAACUGUACAGCCUCCUAGCUUUCCCUGG
AY866051.1/437-516             UGGGGGUGAGGUAGUAGGUUGUA-UAGUUUG-GGGGC---------UCU-GCCC--UGCUAUGGGAUAACUAUACUAUCUACUGUCUU-UCCUGA
#=GC SS_cons                   <<<<<<-<<<<<<<<<<<<<<<<.<<<<<--.-<<<<....._______.>>>>..----------->>>>>>>>>>>>>>>>>>>>>.>>>>>>
#=GC RF                        ccaGGcUGAGguAGuAgguUGuA.uaGUuuu.agggc.....ugauuuu.gccc..aauuaGGAGaUaACuaUaCAaccUaCUacCUU.gCCugg
//
# STOCKHOLM 1.0

#=GF AC   RF00028
#=GF ID   Intron_gpI
#=GF DE   Group I catalytic intron
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Eddy SR
#=GF SS   Published; PMID:2197983
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Intron;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000587; group_I_intron;
#=GF DR   GO; 0000372; Group I intron splicing;
#=GF RN   [1]
#=GF RM   2197983
#=GF RT   Self-splicing of group I introns.
#=GF RA   Cech TR
#=GF RL   Annu Rev Biochem 1990;59:543-568.
#=GF RN   [2]
#=GF RM   8781224
#=GF RT   Crystal structure of a group I ribozyme domain: principles of RNA packing.
#=GF RA   Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Kundrot CE, Cech TR,
#=GF RA   Doudna JA
#=GF RL   Science 1996;273:1678-1685.
#=GF CC   Group I catalytic introns are large self-splicing ribozymes. They catalyse
#=GF CC   their own excision from mRNA, tRNA and rRNA precursors in a wide range of
#=GF CC   organisms. The core secondary structure consists of 9 paired regions
#=GF CC   (P1-P9). These fold to essentially two domains - the P4-P6 domain (formed
#=GF CC   from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain
#=GF CC   (formed from the P8, P3, P7 and P9 helices). The secondary structure
#=GF CC   mark-up for this family represents only this conserved core. Group I
#=GF CC   catalytic introns often have long ORFs inserted in loop regions. The
#=GF CC   window size for this search is chosen to minimise search time and catch
#=GF CC   the small examples. A larger window size will find more matches.
#=GF WK   Group_I_catalytic_intron
#=GF SQ   12


V01416.1/43-384    AUGACUCUCUAAAUAG-CAAUAU----------------UUACCUUUGGAGGGAAAAGU------UAUCAGGCAUGCACCUGGU----------------------------AGCUA-------GUCUUUAAACCAAUAGAUUGCAUCGGUUUAAAA---------------------------------------------------------------GGC-AAGACCGUCAAAUUG-CGGGAAAGGGGUCAACA-----------------------------------------------------------GCCGUUCAGUACCAAGUCUC-AGGGGAAACUUUGAGAUGGCCUU-GCA-------A-AGGGUAUGGUAAUAAGCUGACGGAC----------------AUGGUCCUAACCACGCAGCCAAGUCCUAA-GUCAAC-AGAUCUUC--------------------UGUUGAUAUGGAUGCAGUUCACAGACUA-----------------------------------------------------AAUGUCGGUCGGGGAAGAUG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAUUCUUCUCAUAAGAUAUAGUCG-GACCUCUCCUUAAUGGGAGCU
X03106.1/43-386    AUGACUCUCUAAAUUG-CAAAAU----------------UUACCUUUGGAGGGAAAAGU------UAUCAGGCCUGCACCUGAU----------------------------AGCUA-------GUCUUUAAACCAAUAGAUUGCAUCGGUUUAAUA---------------------------------------------------------------GGC-AAGACCGUCAAAUUG-CGGGAAAAGGGUCAACA-----------------------------------------------------------GCCGUUCAGUACCAAGUCUC-AGGGGAAACUUUGAGAUGGCCUU-GCA-------A-AGGAUAUGGUAAUAAGCUGACGGAC----------------AGGGUCCUAACCACGCAGCCAAGUCCUAA-GUCAAC-AUUUCGG---------------------UGUUGAUAUGGAUGCAGUUCACAGACUA-----------------------------------------------------AAUGUCGGUCGGGGAAGAAUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGUAUUCUUCUCAUAAGAUAUAGUCG-GACCUCUCCUUAAUGGGAGCU
M86534.1/28-414    -UAACAAGGUUUUUU--AUUGGUUCUUCUGCAGUGCGC-CAAAGGAAGCCUUAG-CAGC------CUGAAAGGGUGUAUCUCCGCGACUAUAAAUAAAAAGGGGAUUUUAAAUGCUA-------GUCUGAUAAAAAAA----------------------------------------------------------------------------------GGCG-ACAUUGCCAAAUUG-CGGGAAGUCCCUAAA-------------------------------------------------------------GAUU-CAACUACUAAGCAGCUUGUGGAAACACAGUUGUGGCCGAG--UUAAUAGCCCUGGGUAUAGUAACAAUGUUGAAUAUGACUCUUAAUUGAGG-AAAUGGGUGAUC-CGCAGCCAAAUCCUAAGGACAUUU---------------------------UAUUGUCUAUGGAUGCAGUUCACAGGCCA-----------------------------------------------------GAUGGCAAUGGGUAUCCUAGUGGGAUAUAUAUA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAUGGAUGCUUAAGAUAUGGUCG-AGCUUCUCUCGAAAGAGAG--
M55084.1/84-519    CUACGGACUUAAU----------------------------UGUAUUGAGC-CUUGGUAUGGAAA-----------------------------------------------CAUAUUAAG-UG----------------------------------------------------------------------------------------------------AAAACUUUCAAAUUC-AGAGAAA-CCCUAGA---AUUU-------------------------------------------------------------------------------------------------------------------------------------------------------UAAAUGGGCAAUC-CUGAGCCAAAUCCUUCUUUCCGA-AAACAAAAAACUAAAAGUUC---------AGAAAAAAAGGAUAGGUGCAGAGACUC-----------------------------------------------------AAUGGAAGCUAUUCUAACAAAUGGAGUUGACAACAUUCAAUUGAU-UAAUGAAGAUUUCUAACUUCUAUUUGUAAAUUGUAACUAUUUUUUUUAGUUUUGAUUCGAUCACAAUUGAAACGAAACAUUAGAAUCAAAUCAAUUCCAACUGGAAGAAAAAAUGGUGAAUAUUCAUUGAUCAAAUCAGUCACUCCACCAAAAUAUGAUGGAUCUUUUGAAUAACUGAUUAAUC--------------------------------------------------------AGACGAGAAUAAAGAUAGAGUCC-CAUUCUACAUGUCAAUACCGA
M16898.1/110-597   CUACGGACUUAAU----------------------------UGGAUUGAGC-CUUGGUAUGGAAA-----------------------------------------------CUUACUAAG-UG----------------------------------------------------------------------------------------------------AUCACUUUCAAAUUC-AGAGAAA-CCCUGGA---AUUAACA----------------------------------------------------------------------------------------------------------------------------------------------------AAAAUGGGCAAUC-CUGAGCCAAAUCCUGUUUUCCGA-AAACAAACAAAGGUUC-------------AGAAAAAAAGGAUAGGUGCAGAGACUC-----------------------------------------------------AAUGGAAGCUAUUCUAACAAAUGGAGUUAAAUGCGUUGGUAGAGG-AAUCUUUACAUCGAAACUUCAGAAAGAAAAAGAAUGAAGUGAAGGAUAAACGUAUAUACAUACGUAUUGAAUACUAUAUCAAAAUCAAAUGAUUAAUGAUGACCCGAAUCUGUAUUUUUUCUAUAAAAAAUAGAAGAAUUGGUGUGAAUCGAUUCUACAUUGAAGAAAGAAUCGAAUAUUCAUUGAUCAAACCAUUCACUCCAUAGUCUGAUAGAUCUUUUGAAGAACUGAUUAAUC---GGACGAGAAUAAAGAUAGAGUCC-CGUUCUACAUGUCAAUACCGG
X13486.1/3718-4075 CAAUACGCUUC-----------------------------AAAUGGGGCCGUUAGAUA---GAAA------------------------------------------------UAUCUAAAUG----------------------------------------------------------------------------------------------------AACAUCUGGCUGUAUG-CUGGGAACUCCUUAUUAUAAAUUCAAAAA-AAAGAAAAAAAAGAAACGAGAGCUUUUUUGAAUAAGUAAUUUAAAUAUAUAAAACGACUUAUUUAAGUUUUAAG------------------------------UAAAUAAGUAAAACUGUUUUAUA-------------------ACGGACAAUC-AGCAGGGAAGUCCUAUGACUU---------------------------------UAAAAGUUAUGACCCCUCAACGACUA-----------------------------------------------------CACGCCGGACACCCAAUAAAAAAUAAGUAUUAUACGUAAACACGC-UACGCGUGUUUACUAAUAUAAUAAU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUAUUUAGGGUGAUGAUAUAGUCUACU-ACUUAUGUAAACAUAAGG
Z17234.1/2424-2842 ACGUCGGGAUUUU---------------------------AAAUAGUCCCCCUUUAUA---GUGA------------------------------------------------UAUAAAGGU----UCUCUUUUUAAGAGAAUAAGGAGCCAGAACGCCCGCGUUGUAAACAACGCGGGGCGUUCAGGUUAACCCUGCUUAUUUUAUAAGUGAGUUCCGA---AAAAUUGGGUGAAUUGCCAAGGAC-GCUAAGU---UAAAAGCUACU-CGACUCGCUUAGCGAGUCGAGUAUUAAGCCUUU---------------------------------------------------------------------------------------------------------------AAUACGCCAACU-UGCAGCCAAGUCUAACGAAUUUUCGAA--------------------------AAGGUAGUUAGAAAGGUUCAACGACUAGGGCUUGAGU-ACGAAAUAUCAAUAACAGCCC-------CACG----------AGCGCCCAACAACUUAGGAUUCUGUACGAAAAGUACUCGCCCGCU-GCUUUGCCGCGGGCG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGCAUAAGUUGAAGACAUAGUCUGAA-CUGUAAAGAAAUUUACAG
Z17234.1/2999-3375 GAAGUUUGCUC----------------------------UUUUUGGGCUAGCUAAUAU---GUGA------------------------------------------------GUAUUAGUGAUA--------------------------------------------------------------------------------------------------AAAACUGGGUGAAUUGUCAAGAAG-ACUAACG---UCUAUGUUUAU-UAUAUUUUAAAUUUAAUAACUGUAG-----------------------------------------------------------------------------------------------------------------------ACCAUGUUAACU-UGCAGCGAAGCUUAUCGAAUGGUAAAUAAC-------------------------AGUAGAUAAGAACGUUCAACGACUAGAAAGUGAAG-AUUACCAACUAAUAAACUUUC-------CACG----------AGCGCCCAGCAACUUUUGUUUAUAUUUAUAACAGGCCCGCGGCUU-UGCCGCGGGCGUAGCAUCAAAUUAAUUAAAUUGUAUUUUUGAUGCGCGGCCAGCAACUAAGCUGGCAAAUAU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAACCAAGUUGAAGACAUAGUCUGAA-CUGUAAAGAAAUUUACAG
Z17234.1/4409-4687 UGUCCAGGCUUA---------------------------GUUGUAGGCCUCCUAUUAG---GCAA------------------------------------------------CUAAUGGGCUAA----------------------------------------------------------------------------------------------------CAUUGGGUGAAUUG-CAUGAAA-GCUAAGGC--GUAAC-------------------------------------------------------------------------------------------------------------------------------------------------------GCUAUGCUAACC-UGCAGCGAAUUACAUCGACUGAUAUUAAUAUAAA---------------------AAUAGAUGUACACGUUCAACGACUAGCGAGUGAUGUAAAUCAGUCAAAUAAUCUCGC-------CACG----------AGCGCCCGACAUCUUGAUAUUUACUUAGACCCCCGCUUAAGUAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAUGGCCAAGAUGAUGACAUAGUCUGAG-CAACGUGGAAACACGUUG
V00178.1/106-548   CUACGGACUUGAU----------------------------UGUAUUGAGC-CUUGGUAUGGAAA-----------------------------------------------CCUGCUAAG-UG----------------------------------------------------------------------------------------------------GUAACUUCCAAAUUC-AGAGAAA-CCCUGGA---AUGA-------------------------------------------------------------------------------------------------------------------------------------------------------AAAAUGGGCAAUC-CUGAGCCAAAUCCCUUUUUUGAA-AAACAAGUGGUUCUCAAACUAGAACCC--AAAGGAAAAGGAUAGGUGCAGAGACUC-----------------------------------------------------AAUGGAAGCUGUUCUAACGAAUCGAAGUAAUAACGAUUAAUCACA-GAACCCAUAUUAUAAUAUAGGUUCUUUAUUUUAUUUUUAGAAUGAAAUUAGGAAUGAUUAUGAAAUAGAAAAUUCAUAAUUUUUUUUUAGAAUUAUUGUGAAUCUAUUCCAAUCAAAUAUUGAGUAAUCAAAUCCUUCAAUUCAUUGUUUUCGAGAUCUUUUAAUUUUAAAAAGUGGAUUAAUC--------------------------------------------------------GGACGAGGAUAAAGAGAGAGUCC-CAUUCUACAUGUCAAUACUGA
FJ572425.1/448-150 CUACGGACUUAAU----------------------------UUAAUUGAGC-UUUAGUAGAGAAA-----------------------------------------------UUUACUAAA-UG----------------------------------------------------------------------------------------------------AUUGUUUUCAAAUUC-AGGGAAA-CCUAGGU---UGCAAAAAAAAAGAUUAA------------------------------------------------------------------------------------------------------------------------------------------AAUUAGGUAAUC-CUGAGCCAAAUUUUGUUUACU-----------------------------------AAAACAAAAGAGGUGCAGAGACUC-----------------------------------------------------AAAGAAAACUAUCCUAACGAAAUGUUUUAUCAUUUUUAUAAAAAAAUUGGAUUAAUAUAUUAAUUAAUAAUAAUA---UUAUUAAACCCUUUUUUCAUUUAAAAAAUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACGAGGAUAAAGAUAGAGUCC-GUUUUUACAAGUUACUUUUAA
AY262145.2/209-414 GCUUAUGAGUUAACGUA---------------------A-GUCAAGCUCAUGUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUCUGCCUAA-AA-CGGGAAACUCUCAC------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAGACAAUC-CGUUGCUAAAUCAGCAGUA----------------------------------------GCUGUAAAUGCCCAACGACUAUCCCUGAUGAAUGUA-----------AGGGAGUAGGGUCA---AGCGACCCGAAACGGCAGACAACUCUAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGUUGAAGAUAUAGUCUGAA-CUGCAUGGUGACAUGCAG
#=GC SS_cons       ::::<<<<<<<<<...........................____>>>>>>>>>,,,<<<..____..............................................._>>>,,,,,.,.....................................................................................................,,(((((-((,,,<<.<<<<---.<<<<<__...____........................................................................................................................................................__>>>>>--->>.>>>><<---<<<<----<<<<<_.______.......................>>>>>--->>>>--->>,,,A,AAAAA.....................................................,,))-))))),<<<<<<<<<_________________________._______________.................................................................................................................................................................................................................................>>>>>>>>>,,,,,,,,aaaaaa.,,,,,<<<<<____>>>>>::
#=GC RF            cuAugagcuUaau...........................auauauuGagcucauaagc..GaAA...............................................cgcuaUAAG.U.....................................................................................................AAauCuGuCaAAUUG.CGgGAAA.cCcuaga...auaA........................................................................................................................................................AAuugGgCAAUc.CGCAGCCAAauCcuaaGuuucuu.AAAcaa.......................agaaaAAugGgaaAgGUUCAaAGACUA.....................................................AAuGgCaGacAgccuacauuaugGAuuUAaaaacguUcaauuaau.uaucuuugauuugua.................................................................................................................................................................................................................................aauguaggcUgAAGAUAUAGUCu.aaucUcucauGAAAaugagaG
//
# STOCKHOLM 1.0

#=GF AC   RF00029
#=GF ID   Intron_gpII
#=GF DE   Group II catalytic intron
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   PMID:11726522
#=GF SS   Predicted; PFOLD
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Intron;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000603; group_II_intron;
#=GF DR   GO; 0000373; Group II intron splicing;
#=GF RN   [1]
#=GF RM   11377794
#=GF RT   The ins and outs of group II introns.
#=GF RA   Bonen L, Vogel J
#=GF RL   Trends Genet 2001;17:322-331.
#=GF RN   [2]
#=GF RM   11726522
#=GF RT   Control of branch-site choice by a group II intron.
#=GF RA   Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM
#=GF RL   EMBO J 2001;20:6866-6876.
#=GF RN   [3]
#=GF RM   12870716
#=GF RT   Group II introns: structure and catalytic versatility of large natural
#=GF RT   ribozymes.
#=GF RA   Lehmann K, Schmidt U
#=GF RL   Crit Rev Biochem Mol Biol 2003;38:249-303.
#=GF CC   Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi,
#=GF CC   plants and protists, and also in mRNA in bacteria. They are large
#=GF CC   self-splicing ribozymes and have 6 structural domains (usually designated
#=GF CC   dI to dVI. This model and alignment represents only domains V and VI. A
#=GF CC   subset of group II introns also encode essential splicing proteins in
#=GF CC   intronic ORFs. The length of these introns can therefore be up to 3kb.
#=GF CC   Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing
#=GF CC   with two transesterification steps. The 2' hydroxyl of a bulged adenosine
#=GF CC   in domain VI attacks the 5' splice site, followed by nucleophilic attack
#=GF CC   on the 3' splice site by the 3' OH of the upstream exon. Protein machinery
#=GF CC   is required for splicing in vivo, and long range intron-intron and
#=GF CC   intron-exon interactions are important for splice site positioning. Group
#=GF CC   II introns are further sub-classified into groups IIA and IIB which differ
#=GF CC   in splice site consensus, distance of bulged A from 3' splice site, some
#=GF CC   tertiary interactions, and intronic ORF phylogeny [1].
#=GF WK   Group_II_intron
#=GF SQ   92


AF074613.1/60570-60649  UUGAGCCGUAUGCCGG---GAAA--CUGGCACGUACGGUUCUU------------------------AG-GGGGC---------------------------------------------------------------------------GGUGAUGCAGUAAUGCAUCACUGCUACC-CGAUCGU
X03834.1/1418-1494      GGGAGCCGGAUGAGA---AGAAA-C-UCUCAUGUCCGGUUCUGU----------------------AGU-AGAGA------------------------------------------------------------------------------UGGAAUAGGGAAAUAACCAUCAACU-AU--AAC
M68929.1/41010-41093    GUGAGCCGUGUAAUGG---GCAA--CUAUUUCGCACGGUUCGG------------------------AG-GGCACUUC---------------------------------------------------------------------AGUAAGCCCUACAAGGGCUGAAGUCUUGACC-CC--UAU
AJ316582.1/9914-9993    AGGAGCCGAAUGAAAC---CAAA--GUUUCAUGUUCGGUUUUGA----------------------AUU-AGAGA---------------------------------------------------------------------------CGUUAAAAAUAAUGAAUCGACGUCGACU-AU--AAC
X07106.1/2899-2978      UUGAGCCGGAUGAUGA---AAAA--UUAUCAUGUCCGGUUCUUU----------------------CGG-GGGAU---------------------------------------------------------------------------GAAUUGAAUCUAUAAGAAUUCACCUAUC-CU--AAU
X01088.1/1893-1955      GAGAGCUUUUUGCGGG---GAAA--CUUGCAAGUAAAGUUUGG------------------------GG-GGAGG-------------------------------------------------------------------------------------------CGGGCGUCGACC-CA-ACCU
U77945.1/1848-1919      AACCGCCGUGUACG-----GAAC----CGUACGCACGGUGGUG------------------------UG-AGAGG----------------------------------------------------------------------------ACGGCGGGUGUGAAUCCGCCUCCUACU-CG---AU
AB022308.1/6486-6569    GAACGCCGUAUGCUG----GAAA--CUCGCCUGUACGGUGUGA-----------------------AGU-GGGGGAAA---------------------------------------------------------------------AGCUGGAGAUAACUUCAAAAGCUUACCUAUC-AC--UAU
X62341.1/1274-1336      GAGAGCUUUUUGCGGG---GAAA--CUUGCAAGUACAGUUUGG------------------------GG-GGAGA-------------------------------------------------------------------------------------------CGGGCGUCGACC-CA-ACCU
L43910.1/323-456        AAGAGCGCAGUACAAC---GGGG-AGUUGUAUGCUGCGUUCGG------------------------GA-AGGAUGAAUCGCUCCCGAAAAGGGAGUCUAUUG-------------------AUUCUCUCCCCAAUUGGUUGGAUCGUAGAGCGCAGUACAAGGGGCGAUGAUUUACU-UC---AC
AJ316582.1/98150-98072  AGGAGCCGUGUGAGAU---GAAA--GUCUCAUGCACGGUUUUGAA--------------------UGAG-AGAAA------------------------------------------------------------------------------GAAGUGAGGAAUCCUCUUUUCGACU-CU--GAC
AF314856.1/1250-1311    ACGAGCCACAUGCAGG---GAAA--CUUGCACGUGUGGUUCUG------------------------GCCGGGGA-------------------------------------------------------------------------------------------CCCCGGUAUACU-GU---AC
X71404.1/2822-2898      AGGAGCCGUAUGAGGU---GAAA--GUCUCAAGUACGGUUUUG-----------------------AAG-ACCAG-----------------------------------------------------------------------------CAGGAUUGGUGACAGUCUUGCUGAGU-UU--AAU
V00712.1/1227-1289      GAGAGCUUUUUGCGGG---GAAA--CUUGCAAGUCAAGUUUGG------------------------GG-GGAGG-------------------------------------------------------------------------------------------CGGGCGUCGACC-CA-ACCU
X17395.1/1934-1994      GAGAGCUUUUUGCGGG---GAAA--CUUGCAAGUACAGUUUGG------------------------GG-GGAGG-------------------------------------------------------------------------------------------CGGGCGUCGACC-CU---AC
AB027572.1/1941-1862    AGGAGCCGAAUGAAAU---CAAA--AUUUCAUGUUCGGUUUUGA----------------------AUU-AGAGA---------------------------------------------------------------------------CGUUAAAAAUAAUCAACCAACGUCGACU-AU--AAC
AF235045.1/658-731      GAAAGCCGUAUUCGAU---GAAA--GUCGUAUGUACGGCUUGG------------------------AG-GGAGA------------------------------------------------------------------------------UCUUUCAUAUCUUUCGAGAUCCACC-CU---AC
X63625.1/1815-1875      GAGAGCUUUUUGCGGG---GAAA--CUUGCAAGUACAGUUUGG------------------------AG-GGAGG-------------------------------------------------------------------------------------------CGGGCGUCGACC-CA---AC
AF143423.1/825-965      GUGAGCCGUGUGAUGG---GAAA--CCUCCCCGCACGGUUCGGAGAGCACUUAAUUAGAAUGUUCCUGG-GGGGUACCACAUCAUUGCAAGGGUA-----------------------------------ACAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACUUCCGACC-CU---GU
Z00044.2/23180-23109    UUGAGCCGGAUGAAAG---GAAA--CUUUCACGUCCGAUUUUGA----------------------AGG-GGGGG-----------------------------------------------------------------------------------AGAUCCUAUAGAAUCCUAUC-CC--AAU
AJ130737.1/1761-1840    UUGAGCCGUAUGCGGG---GAAA--CUUGCACGUGCGGUUCUUU---------------------GAGG-GGGGG----------------------------------------------------------------------------GAGCUUGCUCGAAAGAGCCUACCUAUC-CC--GAU
X07106.1/1306-1373      UUGAGCUGUACGAGAU---GAAA--GUCUCAUAUACAGUUCUU-----------------------AGG-GGGGU--------------------------------------------------------------------------------------UUAAUAGUUUACCUAUC-UC--AAU
AJ131144.1/1753-1833    UUGAGCCGUAUGCGAG---GAAA--CUUGCACGUGCGGUUCUUUGC-----------------UUUGAG-GGGGG-------------------------------------------------------------------------------AAAGCUUGAAAGAGCCUAUCCAUC-CU--GAU
U41288.1/3118-3192      UUGAGCCGUAUGCGAU---GAAA--GUUGCACGUACGGUUCUU-----------------------ACC-GGGGG-------------------------------------------------------------------------------AAAGCUUGAGAGAGCCUACCUAUC-GG--AAC
X04336.1/3210-3313      GAGAGCCGUAUGCAGG---GAAA--CUUGCACGUACGGUUCGG------------------------AG-GGAGGUCUCUCGUUGCCAG------------------------------------------------UUCUAAUCUAUUGAUAAGGAUCACGGUGCGGGUUAUCGACC-CU---AC
AJ277126.1/9249-9325    AGGAGCCGUAUGAAUG---GAGA--CAUUCACGUACGGUUUUGG----------------------AGU-AGCAG------------------------------------------------------------------------------GAUAUAUGGUAACAUGUACUUGACU-AU--AAG
AJ277126.1/6413-6487    GUGAGCCGUGUGCGAU---GAAA--GUCGCAAGCACGGUUCUG-----------------------AUG-GGGGG-------------------------------------------------------------------------------AAAACGAGAGAUCGUCUACCUAUC-CA--ACU
AJ277126.1/35792-35885  GAGAGCCCGGUGCGGU---GAAA--GUCGCACGCCGGGUUCGG------------------------GG-AGAACUCUCUGUAA----------------------------------------------------------CUAAAAUAUUUCGGUAUCACGUUAUGGUUAGUCACU-CC---AC
X72287.1/717-859        GUGAGCCGUGUGAUGG---GAAA--CCUUCCCGCACGGUUCGG------------------------AG-AGCACUGAAUUAGAAUGAGAGGUUCACCACCACAUCAU---------UGCAUGCAAGGGGAGCUCGCUCGAUUCGCAAAUUGGUCCGACUCGUAAUUCACUUCUGACU-CC---GU
X55026.1/77786-77867    GAGAGCCGUAUGAUGG---GAAA--CUAUCACGUACGGUUCGG------------------------GA-AAAGGUAU----------------------------------------------------------------------AUAUACUGAUAAGAGGUAUACGUAUCUAGU-UC---AU
AJ316582.1/78387-78450  UUGAGCUGUACGAGAU---GAAA--GUCUCAUAUACGGUUCUC-----------------------AGA-GGGGG------------------------------------------------------------------------------------------AGUUCCGCCUAUC-UC--AAU
X60045.1/1000-1142      GUGAGCCGUGUGAUGG---GAAA--CCUUCCCGCACGGUUCGG------------------------AG-AGCACUGAAUUAGAAUGAGAGGUUCACCACCACAUCAU---------UGCAUGCAAGGGGAGCUCGCUCGAUUCGCAAAUAGGUCCGACUCGUAAUUCACUUCUGACU-CU---GU
AJ131145.1/1727-1802    UUGAGCCGUAUGCGAG---GAAA--CUUGCACGUGCGGUUCUUU---------------------GAGG-GGGGG--------------------------------------------------------------------------------AAGCUUGAAAGAGCCUACCCAUC-CC--GAU
AF080083.1/1551-1683    GAGAGCCGUGUGAUGG---GUGA--CUAUCCAGCACGGUUCGG------------------------AG-AGCACUUUUAGUCUGCGUUGGUGAAUGAAAGCC-------------------CCCCCCCAUCAAGCAAGAAAGAAGCGGCUCUUCCCACGGCGGAGUCACCAUUGACU-CU---AU
AJ130746.1/1754-1835    UUGAGCCGUAUGCGAA--GGAAA--CUUGCACGUGCGGUUCUUUGC-----------------UUUGAG-GGGGG-------------------------------------------------------------------------------AAAGCUUGAAAGAGCCUAUCCAUC-CU--GAU
AF065404.1/6521-6444    UUGAGCCGUAUGUGCU---GAAA--GGUACAAGUACGGUUCUU------------------------AG-GGGAG---------------------------------------------------------------------------AAAGAGUUGGUAACACCUCUGACUUACC-CG--ACU
AJ277126.1/33096-33168  GCGAGCCGUAUGAUGG---GAAA--CUAUCACGUACGGUUCUG------------------------AG-GGCAA--------------------------------------------------------------------------------GGUAUAUUCUAAAUGCCUUGACCCCU---AC
X03481.1/524-600        AGGAGCCGUAUGAGGU---GAAA--AUCUCAUGUACGGUUCUG-----------------------UAG-AGUGG-----------------------------------------------------------------------------CAGUAAGGGUGACUUAUCUGUCAACU-UU--UCC
AJ131136.1/1732-1807    UUGAGCCGUAUGCGAG---GAAA--CUUGCACGUGCGGUUCUUU---------------------GAGG-GGGGA--------------------------------------------------------------------------------AAGCUUGAAAGAGCCUAUCCAUC-CC--GAU
X86563.2/93178-93102    AGGAGCCGUAUGAGGU---GAAA-A-UCUCAUGUACGGUUCUG-----------------------UAG-AGGGA-----------------------------------------------------------------------------CAGUAAGGAUGACUUAUCUGUCGACU-UU--UCC
AJ131147.1/1719-1794    UUGAGCCGUAUGCGAG---GAAA--CUUGCACGUGCGGUUCUUU---------------------GAGG-GGGAA--------------------------------------------------------------------------------AAGCUUGAAAGAGCCUAUCCAUC-CC--GAU
AF143425.1/760-901      GUGAGCCGUGUGAUGG---GAAA--CCUCCCCGCACGGUUCGGAGAGCACUU------CAUUCGAAUGG-GGUGAACCACCACAUCAUUGCAAGGGUAA----------------------------CAGAGCUCGCUCGAUUCGCAGAUUGGUUUGACCCGGAAUUCACUUUCGACC-CU---GU
AF029891.1/4522-4594    UUGAGCCGUAUGCCAU---GAAA--GUGGCACGUACGGUUCUG-----------------------AGG-GGGGG-------------------------------------------------------------------------------AAAGUCUGAGAGGACCUACCUAUC-CC----A
Z00044.2/45483-45410    AGGAGCCGUAUGAGGU---GAAA--AUCUCACGUACGGUUCUGG----------------------AAC-GGAGA---------------------------------------------------------------------------------UUCUUUCAAUUGAAUGACGACC-GU--AAC
V00694.1/5204-5294      GAGAGCCGUAUGAUAU---GAAA--GUAUCACGUACGGUUCGG------------------------AG-AGGGCUCUUUUA-------------------------------------------------------------UAUGAAUGUUAUUACAUUCAGAUAGGUUUGCUACU-CU---AC
X04465.1/116516-116403  GAGAGCACAGUACGAU---GAAA--GUUGUAAGCUGUGUUUGG------------------------GG-GGGAGUUAUUGUCUAUCAAAGGCC--------------------------------------UCUAUGGUAAAAUAAAUCAAUAAAGUCUAAGAGACGAUGGCUUACC-CU---GU
U13767.1/4803-4881      GGGAGCCGUGUGCAGC---GAAA--GUUGCACGCACGGAUCUAA----------------------CAG-AGAGG----------------------------------------------------------------------------GACGGGGAAUAAUAUCCCCUCUCGACU-CU--AAC
AF143421.1/868-1007     GUGAGCCGUGUGAUGG---GAAA--CCUCCCCGCACGGUUCGGAGAGCACUUAAUUAGAAUGUUCCUGG-GGGUACCACAUCAUUGCAAGGGUAA------------------------------------AAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACUUCCGACC-CU---GU
M68929.1/120754-120816  GGGAGCCGGAUGAGGG--AGAAA-UUUCUCACGUCCGGAUCUU------------------------UG-AGAGC-------------------------------------------------------------------------------------------CUCCGGGCUACU-CU---CU
X73671.1/1293-1367      UUGAGCCGUAUGCGAU---GAAA--GUUGCACGUACGGUUCUU-----------------------AAG-AGGGG-------------------------------------------------------------------------------AAAAUGAGUGAUCAUCUACCUAUU-CU--AAC
AJ277126.1/8230-8302    UUGAGCCGUGUGCGUU---GAAA--GAUGCAUGCACGGUUCUU-----------------------AGG-GGGGG---------------------------------------------------------------------------------AAAGCCGGUAACCGUACCUAUC-CC--AAU
Y12731.1/1118-1260      GUGAGCCGUGUGAUGG---GAAA--CCUUCCCGCACGGUUCGG------------------------AG-AGCACUUAAUUAGAAUGAGAGGUUCACCACCACAUCAU---------UGCAUGCAAGGGGAGCUCGCUCGAUUCGCAAAUAGGUCCGACUCGUAAUUAACUUCUGACU-CC---GU
M36911.1/2445-2539      GAGAGCCGUAUGCGGU---GAAA--GUCGCACGUACGGUUCGG------------------------AG-GAGAGUUUUUGGUU---------------------------------------------------------UCUAAGGUCUAUAUAGACUAAGGACUGGCUGCUUAUC-CU---AC
X86563.2/124917-124799  AAGAGCGCAGUACAAC--GGGGA--GUUGUAUGCUGCGUUCGG------------------------GA-AGGAUGGAUCGCUCCCGAAAAGGAGU----------------------------------CUAUUGAUUCUCUCCCAAUUGGUUGGAUCGUAGGGGCGAUGAUUUACU-UC---AC
Z69899.1/2926-3021      GAGAGCCGUAUGCGGU---GAAA--GUCGCACGUACGGUUCGG------------------------AG-GAGAGUUGUUGGUU---------------------------------------------------------UCUAAGGUUUCUUUAGACUAAGGACUGGCUGCUUAUC-CU--ACA
X57546.1/2817-2907      GAGAGCCGUAUGAUAU---GAAA--GUAUCACGUACGGUUCGG------------------------AG-AGGGCUCUCUUA-------------------------------------------------------------UAUGAUUGUUAUUACAAUCAGAUAGGUUUGCUACU-CU---AC
AF143424.1/944-1083     GUGAGCCGUGUGAUGG---GAAA--CCUCCCCGCACGGUUCGGAGAGCACUUCAUUCUAAUGUUCCUGG-GGGUACCACAUCAUUGCAAGGGUAA------------------------------------CAGAGCUCGAUUCGCAGAUUGGUUCGACCCGGAAUUCACUUCCGACC-CU---GU
X17375.2/29364-29438    UUGAGCCGUGUGCGGU---GAAA--GUCGCAUGCACGGUUCUA-----------------------CUG-GGGGG-------------------------------------------------------------------------------AAAGCCUGAGAGGGCCUACCUAUC-CA--ACU
Z00044.2/84143-84067    AGGAGCUGGAUGAGA---AGAAA--CUCUCACGUCCGGUUCUGU----------------------AGU-AGAGA------------------------------------------------------------------------------UGGAAUUCAGAAACAACCAUCAACU-AU--AAC
Z00044.2/44465-44397    CUGAGCCGUAUGAGG-UAAGAAA--UUCUCAAGUACGGUUCUA-----------------------AGG-GAAGG---------------------------------------------------------------------------------------AAUUGAACUACCUAUU-CC--GGC
Y08501.2/135699-135828  UCGAGCCGUAUGAAGG---GAAA--CUCUCACGUACAGUUUGUUUU-----------------UUUUGG-GGGGGGCAGGAGCCCGACAGGGUCCCCC------------------------------ACUGACUUGGCCCGGGCCUAAGUUAAAGUGAAGUGGUGGGCCUACCCAUC-CC--AAC
X97295.1/1333-1451      GAGAGCGCAGUACAAC--GGAGA--GUUGUAUGCUGCGUUCGG------------------------GA-AGGAUGAAUCGCUCCCGAAAAGGAAU----------------------------------CUAUUGAUUCUCUCCCAAUUGGUUGGACCGUAGGUGCGAUGAUUUACU-UC---AC
Y18999.2/2881-2957      UUGAGCCGGAUGAGGG---GCGA--CUCUCAUGUCCGGUUCUU------------------------AG-GGGAC---------------------------------------------------------------------------GGCGGCGCAGUAAUGCGCUGCUGUUACC-CG---AC
AF029891.1/9161-9235    UUGAGCCGUAUGCGAU---GAAA--GUCGCACGUACGGUUCUU-----------------------AGA-GGGGG-------------------------------------------------------------------------------AAAGUUCGAGAGGACCUACCUAUC-UC--AAC
M68929.1/49817-49892    UUGAGCCGUAUGCGG----GAAA-ACUCGCACGUACGGUUCUU-----------------------AGG-GGGGG------------------------------------------------------------------------------GAAAGCUUGAGAGGGCCUACCUAUC-CC--GAC
L36897.1/2659-2743      GAAAGCCGUAUGAUGG---GAAA--CUAUCACGUACGGUUUGG------------------------GA-AAGGCUCUU-------------------------------------------------------------------UAACACGUGGCAACAUAGGUUAAUUUGCUAUU-UC---AU
Y08501.2/169475-169584  GUGAGCCUAGUGAUAG---GAGA--CUAUCUAGCUUGGUUCGG------------------------AG-AGCACUUGUUGGGUUAAAAACU-----------------------------------------UUUUUUGUUGCUAAAUGUUACAGCCUAAAUGCUGAACUAUUGACU-CU----A
M81726.1/5191-5288      GUGAGCCGUAUGAUGG---GCAA--CUAUCUCCUGCGGUUCGG------------------------AG-AGGACUCAGCUGUUAG------------------------------------------------------UUAGUACCCCCGUCGGUUUCGGGGUGGACCCUUUUACU-CU---AU
AF200692.2/21112-21025  GAGAGCCGGAUGCGCU---GAAA--GGUGCACGUCCGGUUCGG------------------------GG-AGGAGAGGCA-----------------------------------------------------------------GGGAAAUAGUCCGACUACGCCCUGCCUCUUACU-CU--UAC
X05422.1/3488-3558      UUGAGCCGUACGAGA---UGAAA-U-UUUCAUAUACGGUUCUC-----------------------GGA-GGGGG-----------------------------------------------------------------------------------AGUCGGGCUAGUUACCUAUC-UC--AAU
AJ277126.1/2879-2953    UUCAGCCGUGUGCGGU---GAAA--GUCGCACGCACGGUUGUG-----------------------AGG-GGGGG-------------------------------------------------------------------------------AAAAUCUGUGAAGAUCUACCUAUC-CC--GAU
Z00028.1/5121-5234      GAGAGCACAGUACGAU---GAAA--GUUGUAAGCUGUGUUCGG------------------------GG-GGGAGUUAUUGCCUAUCGUUGUCC--------------------------------------UCUAUGGUAGAACCCGUCGGGGAGGCCUGAGAGGCGGUGGUUUACC-CU---GU
Z72500.1/3161-3251      GAAAGCCGUAUGAGGG---GAAA--CUUUCACGUACGGUUUGG------------------------AG-GAAAGUCGGGAA-------------------------------------------------------------GCUCUAAGGUAUUUGCUAUGAACUCUCGGCUCAUC-CU---AC
AB042240.3/88332-88259  GAAAGCCGUAUUCGAU---GAAA--GUCGUAUGUACGGCUUGG------------------------AG-GGAGA------------------------------------------------------------------------------UCUUUCCUAUCUUUCGAGAUCCACC-CU---AC
AJ315331.1/53-130       AGGAGCCGUAUGAGAU---GAAA--AUCUCACGUACGGUUCUGU----------------------AAU-AGCGA-----------------------------------------------------------------------------UGGGCACAGUGAUGUUAUCAUCGACU-AU--GAU
X02819.1/3326-3410      GAGAGCCGUAUAAUUA--CGAAA--GUAUCCCGUACGGUUCGG------------------------UG-ACGAGCCG---------------------------------------------------------------------UGUCAACCCUGCAAAGGGAAUGCGUCUUAGUUCA---AU
U41288.1/27369-27451    GAGAGCCGUAUGCGGU---GAAA--GUUGCACGUACGGUUCGG------------------------UG-GGAGGUUU---------------------------------------------------------------------CUUAUAUCCCUCGUGGAGUAGGCUAUCGACC-CA---AC
AF243383.1/10225-10322  CAGAGCCGUAUACUCC---GAGA--GGGGUACGUACGGUUCCC------------------------GA-AGAGGGUGGUGCAAAC------------------------------------------------------CAGUCACAGUAAUGUGAACAAGGCGGUACCUCCCUACU-UC---AC
M15176.1/580-656        AGGAGCUGGAUGAGA---AGAAA-C-UCUCAUGUCCAGUUUUGU----------------------AGU-AGAGA------------------------------------------------------------------------------UGGAACUAAGAAGGAACCAUCGACU-AU--AAC
V00166.1/1829-1941      GAGAGCACAGUACGAU---GAAA--GUUGUAAGCUGUGUUCGG------------------------GG-GGGAGUUAUUGUCUAUCGUUGGC---------------------------------------CUCUAUGGUAGAAUCAGUCGGGGGACCUGAGAGGCGGUGGUUUACC-CU---GC
Z00044.2/12705-12618    GAGAGCCAAAUGAAUC---GAAA--GAUUCAUGUUUGGUUCGG------------------------GA-AGGGAUUAUG-----------------------------------------------------------------GAAUUUUGGAAAGGAAUGGAAAAAUAAUCUACUUUC---AU
M68929.1/7762-7915      GAGAGCCGUAUGCGAG---GAGA--CUUGCACGUACGGUUCGG------------------------AG-GAAGGCCAUUGAUACCUAAUGAAAAUAUCACCAUGACUAAGGUAUAAGCCGCGCCUUGAAAGUCCAGAGGACUUGGUUUUAUUGGGUAGUUGAGGUUGGUGGCCCAUC-UC-UUAC
X77508.1/2333-2408      GGGAGCGGUAUGAGCC---GAGA--GGUUCACGUACCGUUCUG------------------------CG-AGAGG----------------------------------------------------------------------------CUGCGGGGGAGGUUCCUGCGGCCUACU-CA---CC
X04465.1/8-84           AGAAGCCGUAUGAAAU---GAAA--AUAUCAAGUACGGUUUUG-----------------------UAA-AGUGA-----------------------------------------------------------------------------CAAUUUAGGUAACUUAUUUGUCAACU-UU--UCC
AY248839.1/1808-1884    GGGAGCGGUGUGAAUC---GAGA--GGUUCACGCACCGUUCUG------------------------CG-AGAGG---------------------------------------------------------------------------CCGGCUGGUGAAACUCCUCCGGCCUACU-CA---CC
AM087200.3/1962-1851    GAAAGCCGUGUGCA--A-UGAAAAG--UGCAAGCACGGCUUGG------------------------GG-AGGGAUCUUUACUUGUUUAUUUA----------------------------------------AUUUAAGAUUAACAUUUAUUUUAUUUAACAAGGAACUUAUCUACU-CC---AU
AC145820.20/76117-76030 GAGAGCCAAAUGAAUU---GAAA--GAUUCAUGUUUGGUUCGG------------------------GA-AGAGAUCAUA-----------------------------------------------------------------GACAUUUUGAAAUGAAUGGAAAGAGAAUCUACUUUC---AU
AB281599.1/897-973      AGGAGCCGUAUGAAUG---GAGA--CAUUCACGUACGGUUUUGG----------------------AGU-AGCAG------------------------------------------------------------------------------GAUAUAUGGUAACAUGUACUUGACU-AU--AAG
FM992111.1/3630-3713    GAACGCCGUAUGCGGU---GAAA--GUCGCACGUACGGUGUGA-----------------------GGC-GGGGGAAA---------------------------------------------------------------------AGUUGGAGAUAACAUCAAAUUCUUACCUAUC-GU---AC
AM489440.1/2183-2254    AACCGCCGUAUGCGG-------A--GCCGCAUGUACGGUGGUG------------------------UG-AGAGG----------------------------------------------------------------------------ACGGCGGGAGUGAUCCCGCCUCCUACU-CG---AU
DQ787115.1/750-834      GAACGCCGUAUGCGGU---GAAA--GUCGCACGUACGGUGUGG-----------------------AGC-GGGGGAAA---------------------------------------------------------------------AAUUGGAGAUAACAUCAAAGAUUUACCUAUC-GC--UAU
EF165030.1/2861-2955    GAACGCCGUGUGCGGG---GAAA--CUCGCACGCACGGUGUGA-----------------------AGC-GGGGAAAAAUAGC-----------------------------------------------------------CCCUCCGGGUAAUGCCGAGGGUGACUAUUACCUAUC-GC--UAU
#=GC SS_cons            ::<<<<<<<<-<<<<<...____..>>>>>--->>>>>>>>--........................<<.<<-<<________...........................................................______________________________>>-->>.>>...::
#=GC RF                 GaGAGCCGuaUGcggg...GAAA..cccgCACGuaCGGUUCGG........................gG.GGgGgucauugau...........................................................ucgcaaaUuguuuggacuuggaauugacuacCuACC.Cc...Au
//
# STOCKHOLM 1.0

#=GF AC   RF00030
#=GF ID   RNase_MRP
#=GF DE   RNase MRP
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Published; PMID:12088147, Griffiths-Jones SR, Daub J
#=GF SS   Published; PMID:7678563
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00002
#=GF DR   SO; 0000385; RNase_MRP_RNA;
#=GF DR   GO; 0006364; rRNA processing;
#=GF DR   GO; 0000171; ribonuclease MRP activity;
#=GF DR   GO; 0000172; ribonuclease MRP complex;
#=GF RN   [1]
#=GF RM   7678563
#=GF RT   Secondary structure of RNase MRP RNA as predicted by phylogenetic
#=GF RT   comparison.
#=GF RA   Schmitt ME, Bennett JL, Dairaghi DJ, Clayton DA
#=GF RL   FASEB J 1993;7:208-213.
#=GF RN   [2]
#=GF RM   12088147
#=GF RT   Phylogenetic analysis of the structure of RNase MRP RNA in yeasts.
#=GF RA   Li X, Frank DN, Pace N, Zengel JM, Lindahl L
#=GF RL   RNA 2002;8:740-751.
#=GF RN   [3]
#=GF RM   16087735
#=GF RT   Identification and analysis of ribonuclease P and MRP RNA in a broad range
#=GF RT   of eukaryotes.
#=GF RA   Piccinelli P, Rosenblad MA, Samuelsson T
#=GF RL   Nucleic Acids Res. 2005;33:4485-4495.
#=GF RN   [4]
#=GF RM   16083861
#=GF RT   Secondary structure probing of the human RNase MRP RNA reveals the
#=GF RT   potential for MRP RNA subsets.
#=GF RA   Walker SC, Avis JM
#=GF RL   Biochem Biophys Res Commun. 2005;335:314-321.
#=GF RN   [5]
#=GF RM   16998185
#=GF RT   Inventory and analysis of the protein subunits of the ribonucleases P and
#=GF RT   MRP provides further evidence of homology between the yeast and human
#=GF RT   enzymes.
#=GF RA   Rosenblad MA, Lopez MD, Piccinelli P, Samuelsson T
#=GF RL   Nucleic Acids Res. 2006;34:5145-5156.
#=GF CC   RNase MRP is an enzymatically active ribonucleoprotein with two distinct
#=GF CC   roles in eukaryotes. In mitochondria it plays a direct role in the
#=GF CC   initiation of mitochondrial DNA replication. In the nucleus it is involved
#=GF CC   in precursor rRNA processing, where it cleaves the internal transcribed
#=GF CC   spacer 1 between 18S and 5.8S rRNAs. Despite distinct functions, RNase MRP
#=GF CC   has been shown to be evolutionarily related to RNase P. Like eukaryotic
#=GF CC   RNase P, RNase MRP is not catalytically active without associated protein
#=GF CC   subunits.
#=GF WK   RNase_MRP
#=GF SQ   66


D30745.1/2839-3111               -GGCAU----UCU-GA---AG-ACC-UGAAG----UCUAGGC--AACGUAC-------GGGAGACGU-------------------------------------------------------AGUUCUUC--------------AAUCACAUGACGCCUAG-GG--GAAAGUCCCCGGAU----------------CUCGGG--UA--------------GAAAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGCGCU--------------------------ACUA--------------UGGCGUGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUAA---UCCCG-C-CCUGC----------UGUCCAUAUCAA-CCCGCCAAGAA--------------------------------------------------------------------------------------------------------------GCUC--CCA----GAGC---------------CGAGCGGC-------UUGGAU--UAGG-GCG-G------------GAU--------------CUCUCAUCAGUCACCAUAGUAAC--------------UCAGGU--AGCGCGGCAACG-----------------------------------------------------UCCACGCUAACUAAACGGGGCUCA-UUC----UC--A-G-A-----AUG-CU
Z11844.1/494-766                 -GGCAU----UCU-GA---AG-ACC-UGAAG----UCUAGGC--AACGUAC-------GGGAGACGU-------------------------------------------------------AGUUCUUC--------------AAUCACAUGACGCCUAG-GG--GAAAGUCCCCGGAU----------------CUCGGG--UA--------------GAAAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGCGCU--------------------------ACUA--------------UGGCGUGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUAA---UCCCG-C-CCUGC----------UGUCCAUAUCAA-CCCGCUAAGAA--------------------------------------------------------------------------------------------------------------GCUC--CCA----GAGC---------------CGAGCGGC-------UUGGAU--UAGG-GCG-G------------GAU--------------CUCUCAUCAGUCACCAUAGUAAC--------------UCAGGU--AGCGCGGCAACG-----------------------------------------------------UCCACGCUAACUAAACGGGGCUCA-UUC----UC--A-G-A-----AUG-CA
J03151.1/847-1116                -CUCGC----UCU-GA---AG-GCC-UGUUU----CCUAGGC--UACAUAC-------GAGGGACA---------------------------------------------------------UGUUCCU----------------UAUCCUUUCGCCUAG-GG--GAAAGUCCCCGGAC----------------CACGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------ACAC----------------GCGCGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----UUCCC-C-CGCAA----------GUCAC-UGUUAG-CCCGCCAAGAAGCGACCCCUCCGGG------------------------------------------------------------------------------------------------GC-----------GAGC---------------UGAGCGGC---------GUGC--AGCG-GGG-C------------GUC--------------AUCCGUCAG-CUCACAUAGUGAC--------------GCAGGC--AGUGCGACCUGG-----------------------------------------------------CUCGCACCAACCACACGGGGCUCA-UUC----UC--A-G-C-----GCG-GC
J05014.1/2-272                   GCUCGC----UCU-GA---AG-GCC-UGUUU----CCUAGGC--UACGUAC-------GGGGGACCU--------------------------------------------------------UGUUCCU----------------UAUCCUUUCGCCUAG-GG--GAAAGUCCCCGGAC----------------CAUGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------ACAC----------------GCGCGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGC----UUCCC-C-CGCAA----------GUCAC-UGUUAG-CCCGCCAAGAAGCGACCCCUCCGGG------------------------------------------------------------------------------------------------GC-----------GAGC---------------UGAGCGGC---------GUGC--GGCG-GGG-U------------GUC--------------AUCCGUCAG-UUCUCCUAGUGAC--------------GCAGGC--AGUGCGACCUUG-----------------------------------------------------UACGCACCAACCACACGGGGCUCA-UUC----UC----G-C-----GCG-GC
L22578.1/704-978                 -UUCGU----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACAUAC-------GGAGGACUA--------------------------------------------------------GUUCCUU-------------------GUUUGCGCCUAG-GG--GAAAGUCCCCGGAC----------------CGUGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUGC---------------------------CCGU----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----UUCCC-C-UGCUU----------CUCACGACUAAA-CCCGCCAAGAAGCGAUCCU------------------------------------------------------------------------------------------------------ACCC--UGG----GGGU-------GGGGAAGCCGAGCGGC---------GUGU--UGCG-GGG-U------------GUC--------------AUCCGUCAGCUUCUAAUAGUUAC--------------GCAGGC--AGUGCCU--CCA-----------------------------------------------------UGCGCACCAACCUCACGGGGCUCA-UUC----UC--A-G-C-----ACG-UC
M29212.1/2-265                   -UUCGU----GCU-GA---AG-GCC-UGUAU----CCUAGGC--UACACAC-------UGAGGACUC-------------------------------------------------------UGUUCCUC----------------CCC-UUUCCGCCUAG-GG--GAAAGUCCCCGGAC----------------CUCGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUGC---------------------------AUAC----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----AUUCC-C-CGCUU----------CCCACUCCAAAG-UCCGCCAAGAA--------------------------------------------------------------------------------------------------------------GCGA--UUC----CCGC---------------UGAGCGGC---------GUGG--CGCG-GGGGC------------GUC--------------AUCCGUCAGCUCCCUCUAGUUAC--------------GCAGGC--AGUGCGU--GUC-----------------------------------------------------CGCGCACCUACCACACGGGGCUCAAUUC----UC--A-G-C-----GCG-GC
M29916.1/746-1008                -UUCGU----GCU-GA---AG-GCC-UGUAU----CCUAGGC--UACACAC-------UGAGGACUC-------------------------------------------------------UGUUCCUC----------------CCC-UUUCCGCCUAG-GG--GAAAGUCCCCGGAC----------------CUCGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUGC---------------------------AUAC----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----AUUCC-C-CGCUU----------CCCACUCCAAAG-UCCGCCAAGAA--------------------------------------------------------------------------------------------------------------GCGU--AUC----CCGC---------------UGAGCGGC---------GUGG--CGCG-GGGGC------------GUC--------------AUCCGUCAGCUCCCUCUAGUUAC--------------GCAGGC--AGUGCGU--GUC-----------------------------------------------------CGCGCACCAACCACACGGGGCUCA-UUC----UC--A-G-C-----GCG-GC
Z25280.1/704-978                 -UUCGU----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACAUAC-------GGAGGACUA--------------------------------------------------------GUUCCUU-------------------GUUUGCGCCUAG-GG--GAAAGUCCCCGGAC----------------CGUGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUGC---------------------------CCGU----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----UUCCC-C-UGCUU----------CUCACGACUAAA-CCCGCCAAGAAGCGAUCCU------------------------------------------------------------------------------------------------------ACCC--UGG----GGGU-------GGGGAAGCCGAGCGGC---------GUGU--UGCG-GGG-U------------GUC--------------AUCCGUCAGCUUCUAAUAGUUAC--------------GCAGGC--AGUGCCU--CCA-----------------------------------------------------UGCGCACCAACCUCACGGGGCUCA-UUC----UC--A-G-C-----ACG-UC
AAQX01001105.1/73112-73390       GAACAC----GAU-UU---AG-AAU-UGCGAAG--UCAAGUG--G--------------GCCCCUCU-------------------------------------------------------CGGGGGGC-------------------------GGCUUG-GG--GAAAUUCCCCGGACA---------------CCAGGG--CA--------------GAGAG--------------UG----CC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCGU---------------------------CCAA----------------GCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACU---CCCUCAG-CGAUG----------AAGCU---------UGGCGGAGAGGGCCCGUCUC----------------------------------------------------------------------------------------------------GGCG---------GGUU---------------GGAGUCAU--------CGGCGGAUUCG-CGA-G------------GAC--------------UGAUGGUCA-UACUAACAGUUAU--------------GCAAUU--GGCUCAGCGGCAUAUGGCGGACGUCGUGCCGUCGCCGC---------------------------UUGGAGCUAACCCGACGGGGAUUA-CUC----AU--G-U-U-----GUG-UU
ABCN01002927.1/686-416           AGGCGCAG--UGC-GG---AG-GGC-CAC-C----UCGGUGU--CACUUAC-------GGCAGGAGUCGAGGGGCUGCUGCUUUGAGCGCGGCCCCCGGCUGGGCGCU--------------GCAUCCAU----------------GUAUUGAGCACAUCGGGC--GAAAGUCCCCGGGCG---------------ACGGGG--CA--------------GAGAG--------------UG----CC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCCC---------------------------GCAA----------------GGGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGA----CCCCC-G-CGCG------------UCGU-------------------------------------------------------------------------------------------------------------------------------------U-UUU----------------------------------------ACGA---CCG-CGG-G-------------GC--------------AGCUCGCCA-UAGCAACAGUUAU--------------GUGGCC--AGUGGGG-AUAC-----------------------------------------------------AACCCACCAACACAACGGGGCUUA-CUC----CC--G-C-A--CUGACG-CU
AP006493.2/385670-385231         GGGAAGACUCUGC-UA---AG-CGU-UCCUCGUUAUCAGAGCGCUACGUAC-------GGUUUACGGGAGGGUCCUGGAUUAGCCCCUAAACCAGGCUCGGUGCGAACAGGUGCGCCCUGAUUCGAUGCC----------------AGCCGUUUGGCUCUGGGU--GAAAGUCCCCGGACA---------------GUAGGU--CA--------------GAGAG--------------UG----UCGGUGGUAAGCAAAGCUGGGCGUUUCAGGUCGCGCACACUUCU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUCGCG--------------------------GGAC---------------UGCAACC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACAGAA--CCCCA-A-UAAGA----------GCGGGAGUGCUG-CGCGACAGUGAACGUCGCUUGUCGAUGGUGCAGCGCUGGAACCUGCUG-------------------------------------------------------------------------CCGC--GUU----GGGG---------------UGCUUGCG---------CCCC--AUGU-UUG-G---------CAGCGG--------------CAGCCUGCA-CUGAAUCAGCAAU--------------GGAACG--AGCGAGAGCGACCGUCCUUCAUGGACGGC------------------------------------GACUCGUGAACACAAUGGGGCUUA-CUC----UG--G-C-AGUGUGCUC-CC
AABU01002774.1/15978705-15978349 UUGAGUC---UUC-CA---UG-CUU-GUCUC----UCGGGGC--CACAAAA-------CGAGUUCCU-------------------------------------------------------GGUAACUC---------------AACUGAUAAUGCCCUGGGC--GAAAGUCCCCGGGC----------------CUAGGA--UA--------------GAAAG--------------UA----UCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGUGUAAAAAGUGUGCACAAAACACCCACCACCCCUGUGGUGGGUGGUGCAUUCGCCUAU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUCUGCGGAAUUUCGCCUGGC----------GUAU---------GGAUGAAGAG--------------------------------------------------------------------------------------------------------------GAUU--U------UAUC---------------CGAAUCCU--------UACGC---GCCAGGUUG-------UCUGCGGA-----------AAUCUGCCAGAGUAAUCUUAGAUAUG--------------GACGAGUU-GGUAGGACUCGGCGGGUGGUGUUCACACACUUUCUCGUCUGAGAA-------------------ACCGCCUACACAGAAUGGGGCUUA-CAU----UG--G-G-A----AACU-CG
AACT01041809.1/6950-7211         CUGCAC----UUG-GA---AG-ACU-UGCUA----UCUAAGU-----------------CAUUAUGG-------------------------------------------------------GCAAAAGG----------------GACCCUAUGGCUUAG-GG--GAAAGUCCCCGGAC----------------ACUGGG--UA--------------GAGAG--------------UA----CCUG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGUGUA--------------------------ACCC-------------CCCACACCU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUCUA--AACCA-C-CUGGGGUUA------UACACCUUGGAC-CAAGCUAAGAU--------------------------------------------------------------------------------------------------------------GCA----------UUGC---------------GGAGCUUG--------UGGGU--ACGG-UUG-G------------GCU--------------UAGUC-----GAAGCACAGUCAU--------------GCAAGU--GGCUAGUUGUAA-----------------------------------------------------UGCUAGCUAACUCAAUGGGGCUCA-CUC----UC--C-A-A-----GUG-CA
AAYL01000122.1/26509-26132       GGGAGC----AGCAAG---CA-AGU-UGCAU----CAUAGCG--UUCCGAC-------GAGGGCUUUUGAGACUUCGCUGUGGGCGUCCGCGCGCAGUGCGUCGACCACGCAGUCUCCAA--UAUGCUCU--------------------UUACAAGCUAUGGG--GAAAGUCUCCGUGCC---------------AUGGGG--UC--------------GAGAG--------------GA----UCGAUGAGAAAUUCGUGGACGCCUCUCAGCUACAGUC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCCUGA---------------------------UGUG----------------UUGUGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGU----CUCCU-C-UGUGA----------CAGGCUUCUUGC-CUGGAGAAGAGGCAGCGCGAC----------------------------------------------------------------------------------------------------GGCU--GGA----GGUU---------------GAUUGCAG-------UUGCCG--CUUA-CAU-G------------CGG--------------GCUCUUCCAAGGCUUGAGUUCAU--------------GCGACU--GGUGGGACUGUCUUCCCGAGGAC------------------------------------------GUUCCGCUAACAGAAUGGAGCUUA-UGU----CUUCG-C-U-----GUU-CC
AAXT01000002.1/573795-573558     GAUACG----GUC-GC---GA-AGC-UACUU----CGUAGUG--AACACAC-------GGGUU-----------------------------------------------------------G---AGCC---------------------UAUACACUACGGG--GAAAGUCUCCGUGCGU--------------UUAAUG--CC--------------UAGAG--------------GG----CA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGGG---------------------------GAAU----------------CUCCAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGGAU---GCUGC-G-AAU-------------GUUAUUUU-------------AC--------------------------------------------------------------------------------------------------------------UCGA--CAU----UUGC---------------UGC-------------UUCAC--UAUU-UGC-C-------GUUUGGCC--------------AGACCAUUA-AACCGAUAGUCAA-------------UGUAGCU--AGCGCC------------------------------------------------------------UGGCGCUGACUCAAUGGAGCUUA-UCU----GC--GUA-C-----CGU-AU
AADA01035511.1/14292-14554       GUUCGU----GCU-GA---AG-GCC-UGUAU----CCUAGGC--UACACAC-------UGGGGACUC-------------------------------------------------------UGUUCCUC----------------CCC-UUUCCGCCUAG-GG--GAAAGUCCCCGGAC----------------CUCGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------AUAC----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----AUUCC-C-CGCUU----------CCCACUCCAAAG-UCCGCUAAGAA--------------------------------------------------------------------------------------------------------------GCGU--UUC----CCGC---------------UGAGCGGC---------GUGG--UGCG-GGGGC------------GUC--------------GUCCGUCAG-CUCCUCUAGUUAC--------------GCAGGC--AGUGCGU--GUC-----------------------------------------------------CGCGCACCAACCACACGGGGCUCA-UUC----UC--A-G-C-----GCG-GC
ABDC01137536.1/1679-1414         GGUCGC----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACAGAC-------GGAGGACUA--------------------------------------------------------GUUCCUC----------------AUU-CUUCUGCCUAG-GG--GAAAGUCCCCGGAC----------------CUCCGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------ACGC----------------GCACGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----AUCCC-U-CAGCUU---------UCCACUGUAAGG-ACCGCCAAGAA--------------------------------------------------------------------------------------------------------------GCGA--AUC----CCGC---------------UGAGCGGC------GUGGCGG--CGUG-GGG-U------------GUC--------------ACCCGUCAGCUAAUGCUAGUUAC--------------GCAGGC--AGUGCGU--CUU-----------------------------------------------------CGCGCACCAACCACACGGGGCUCA-UUC----UC--A-G-U-----GCG-GC
AANU01164883.1/1953-2212         GGUCGU----GCU-GA---AG-GCC-UGUAU----CCUAGGC--UACAAAC-------UGGGGACUA-------------------------------------------------------CGUUCCUC-------------------CCCCCUGCCUAG-GG--GAAAGUCCCCGGAC----------------CUCCGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUGC---------------------------AUAA----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACAU--UCCCC-C-UUC-------------CCACUGUAAAG-UCCGCCAAGAA--------------------------------------------------------------------------------------------------------------GCGU--GGC----CCGC---------------UGAGCGGC---------GUGG--UGCG-GGG-U-----------AGUC--------------GUCCGUCAG-CUCUUCUAGUUAC--------------GCAGGC--AGUGCGU--CUU-----------------------------------------------------GGCGCACUAACCACACGGGGCUCA-UUC----UC--A-G-C-----GCG-GC
AANN01822319.1/784-1041          GCUUAC----GCU-GA---AG-GCC-UGUUU----CCUAGGC--AACAAAC-------GGAGGACUU--------------------------------------------------------GUUCCUC-------------------GCUCUCGCCUAG-GG--GAAAGUCCCCGGAC----------------CACAGG--CA--------------GAAAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUGC---------------------------GCAU----------------GCACGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----UGUCC-C-UGCUU----------CUCAC-CUUAAG-UCCGCCAAGAA--------------------------------------------------------------------------------------------------------------GCCC--GCC----GGGC---------------CGAGCGGC---------GUGU--UGUA-GGGAU------------GUC--------------AUCCGUCAG-CAGUUCUAGUCAC--------------GCAGGC--AGUGCAU---UC-----------------------------------------------------CGUGCACCAACCAAACGGGGCUCA-UUC----UC--A-G-C-----GCA-GC
AY953321.1/41-313                GCGCGU----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACAGAC-------GGAGGACUU--------------------------------------------------------GUUCCUU-------------------AUUUGCGCCUAG-GG--GAAAGUCCCCGGAC----------------CCUUGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------GCGU----------------GCACGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAC----UUUCC-C-UGCUU----------UGCACUGUAACG-UCCGCCAAGAA--------------------------------------------------------------------------------------------------------------GCGAUCCGU----UUGC-----CGCGGGGAGCCGAGCGGC---------GUGU--GGCG-GGG-C------------GUC--------------GUCCGUCAACUCUAUCUAGUUAC--------------GCAGGC--AGCGCGC-CUGG-----------------------------------------------------UGCGCGCCAACCACACGGGGCUCA-UUC----UC--A-G-C-----GCG-GC
AAPY01565803.1/1823-1547         GCUUGU----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACGUAC-------GGGGGACU---------------------------------------------------------GGUUCCC----------------GAU--UUGUGCCUAG-GG--GAAAGUCCCCGGAC----------------CUUGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------GCCU----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAC----UGCCC-U-CGCUU----------UUCACGAAUUAA-UCCGCCAAGAAGCGAACCAAGGUC-------------------------------------------------------------------------------------------------UCUUG-GGG----UAGC---------------UGAGCGGC---------GUGU--GGCG-GGGGU------------GUC--------------AUCCGUCAGCCCUACCUAGUUAC--------------ACAGGC--AGUGCGUGCCUG-----------------------------------------------------CGCGCACCAACCACACGGGGCUCA-UUC----UC--A-G-C-----GCG-GC
AAYZ01073739.1/1951-1685         GUUCGC----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACAUAC--------GGGGACUU--------------------------------------------------------GUUCCUC----------------AUCUUCUC-GCCUAG-GG--GAAAGUCCCCGGAC----------------CUCCGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------GCAU----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----UCACC-C-CGCCC----------CCCAC-GGCUAG-UCCGCCAAGAAGCUCCCUGCU----------------------------------------------------------------------------------------------------GGAC--AGG----GCGC---------------CGAGCGUU---------GUGG--UGCG-GGG-C------------GUC--------------GUCCGUCA--CGGUCACAGUUAC--------------GCAGGC--AGCGCGC---CC-----------------------------------------------------CGCGCGCCAACCACACGGGGCUCA-UUC----UC--A-G-C-----GCG-GA
AANG01432228.1/1130-848          GUUCGU----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACAAAC-------GGGGGACUU--------------------------------------------------------GUUCCUU-------------------AUUAACGCCUAG-GG--GAAAGUCCCCGGAC----------------CGCGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUGC---------------------------AUGC----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----CUUCC-C-UGUGU----------UUCACUGUAAAG-UCCGCCAAGAAGCGACCCCCCCCCC------------------------------------------------------------------------------------------------CGUA--UAC----GGCG--------GGGGAGCUGAGCGGC---------GUGU--UGCA-GGG-G---------UGUGUC--------------CUCAGUCAG-CUCUCCUAGUUAC--------------GCAGGC--AGUGCGU--UUG-----------------------------------------------------UGCGCACCAACCACACGGGGCUCA-UUC----UC--A-G-U-----GCG-GC
AAQQ01544511.1/981-703           GUGCGU----GCU-GA---AG-GCC-UGU-U----CCUAGGC--UACAAAC-------GAGGGACU---------------------------------------------------------AGUUCCU----------------UACCUUUCCGCCUAG-GG--GAAAGUCCCCGGAC----------------CUCCGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUGC---------------------------GCUC----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC-----CUUC-C-CGCCA----------GUCACUGGCUUA-UCCGCCAAGAAGCGAUCCCGCCGCGUGC---------------------------------------------------------------------------------------------GACG--GGG----GAGC---------------UGAGCGGC---------GUGU--GGCG-UGGGC------------GUC--------------GUCCGUCAU-CUCUCCUAGUAAC--------------GCAGGC--AGUGCGUGCUUU-----------------------------------------------------CGCGCACCAACCGCACGGGGCUCA-UUC----UC--A-G-C-----GCG-GC
AALT01554760.1/622-340           GUCCGU----GCU-GA---AG-GCC-UGUUG----CCUGGGC--UACAAAC-------GGAGGACUG-------------------------------------------------------UGUUCCU-----------------ACUCCCUUCGCCCAG-GG--GAAAGUCCCCGGAC----------------CUCCGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUGC---------------------------GCGU----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAC----CUUCC-C-CGCAU----------CUCACAAAUAAC-UCCGCUAAGAAGCGAGCCGGCCCCUCUCCGG------------------------------------------------------------------------------------------GCUG---GG----GAGC---------------CGAGCGGC-------GUGUGG--CGGC-GGG-G------------GUC--------------AUCCGUCAU-CUGACCUAGUUAC--------------GCAGGC--AGCGCGC--GCC-----------------------------------------------------CGCGUGCCAACCGAACGGGGCUCA-UUC----UC--A-G-C-----ACG-GC
AAPN01196855.1/605-343           AGUGGCGA--GCU-GA---AA-GUC-UGUUG----CCUAGGC--UACGAGC-------UGGGGACU---------------------------------------------------------GGUUCCC----------------ACC-UGAGCGCCUAG-GG--GAAAGUCCCCGGAC----------------CCCGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGCGC---------------------------GCAG----------------GCGCGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGGG------CCG-C-CUCGU----------UCGCUCUCUUAG-GCCGCCGAGAC--------------------------------------------------------------------------------------------------------------GCCU--C------UGGU---------------UGAGCGGU--------GAGCG--UGGG-GCG-G------------CCU-------------ACUCAGUCAAGUUUGCAUAGUUAU--------------ACAGGC--AGUGCGC--ACA-----------------------------------------------------GGUGCACCAACUCAACGGGGCUCA-AUC----UC--A-G-C---AAGCC-AG
AAIY01269613.1/2336-2072         UUUCGU----GUU-GA---AG-GCCCUGUUU----CCUAGGC--UACAGAC-------GGAGGACUU--------------------------------------------------------GUUCCU--------------------GGAACCGCCUAG-GG--GAAAGUCCCCGGAC----------------CUCGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGCGC---------------------------GAAC----------------GUGCGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGC----CGACC-C-GCC-------------GCUCACGGUCC-UCCGCCAAGAGGCGAGCCUGCGG--------------------------------------------------------------------------------------------------GC-----------GAGC---------------UGAGCGGC---------GUGG--CGGC-GGG-C------------GGC--------------CCUCCGUCAGCGGAGCGAGUGAC--------------GCAGGC--AGCGCGC-UGCA-----------------------------------------------------CGCGCGCCAACCACACGGGGCUCA-UUC----UC--A-G-C-----ACG-GC
AAFR03028712.1/851-1131          AGGCGCUU--GCU-GA---AG-GCC-UGUUA----CCUAGGC--UACGUAC-------GGGGGACAU--------------------------------------------------------GUUCCCC-------------------AUCUGCGCCUAG-GG--GAAAGUCCCCGGAC----------------CAAUGG--CA--------------GAAAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGCAC---------------------------GCAC----------------GUGCGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUGG---CCUAU-G-UCGCA----------GCUCCAUAUCUC-CCUGCCAAGAAGUUCUUCAACCUC-------------------------------------------------------------------------------------------------GGUU--GAA----GCAC---------------UGAGCGGA--------GGGAG-CGCGA-UGA-G-----------GCCG-----------CCCUUAGUCAAGAACUGGAUAGUUAC--------------GCAGGC--AGUGCGU---CA-----------------------------------------------------UGCGCACCAACUCCACGGGGCUCA-UUC----UC--A-G-C-----GCG-UC
AABS01000030.1/66301-66051       CUGCAC----UUG-GA---AG-ACU-UGCUA----UCUAAGU--CACUAUG-------GACAU-----------------------------------------------------------C---AUAU----------------GAUCCUAUGGCUUAG-GG--GAAAGUCCCCGGAC----------------AUUGGG--UA--------------GAAAG--------------UA----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGGGGUU--------------------------UGAA----------------ACCCCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACCUG--AUCCA-AACCACCUGGGUGUAAAAGCUC--AUGAU-CAAGCUAAGAU--------------------------------------------------------------------------------------------------------------GCG----------UUGC---------------GGAGCUUG--------UGGGU--AUGG-UUG-G------------GCU--------------UAGUC-----GUAGCAUAGAUAU--------------GCAAGU--AGUU----CACA---------------------------------------------------------AAC----ACAAUGGGGCUCA-CUC----UU--C-A-A-----GUG-UA
AAKO01000389.1/32662-32318       UGAGUC----UUC-CA---UG-CUU-GUCUC----UCGGGGC--CACAAAA-------CGAGUUCCU-------------------------------------------------------GGUAACUC---------------CACUGAUAAUGCCCUGGGC--GAAAGUCCCCGGGC----------------CUAGGA--UA--------------GAAAG--------------UA----UCUAGGUGUAAAAAGUGCAUCCAUCAUCCUGUGGUGGUGGUGCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCC--------------------------UAUA------------UUCUGCGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUU----UCGCC-U-GGC-------------GUAU---------GGAUGAAGAG--------------------------------------------------------------------------------------------------------------GAUU--U------UAUC---------------CGAAUCCU--------UACGC---GCC-AGG-U------------UGU--------------CUGCGGAAAUCUGCCAGAGUAAA---------UCUUAGAUAUG--GACGAGUUGGUAGGACUCGCCGGGUUGGUGUUCCACACUUUCUCGGCUGAGAA------------ACCGCCUACACAGAAUGGGGCUUA-CAU----UG--G-G-A-----AAC-UC
AASV01011901.1/1905-1558         UGAGUC----UUC-CA---UG-CUU-GUCUC----UCGGGGC--CACAAAA-------CGAGUUCCU-------------------------------------------------------GGUAACUC---------------CACUGAUAAUGCCCUGGGC--GAAAGUCCCCGGGC----------------CUAGGA--UA--------------GAAAG--------------UA----UCAAGGUGUAAAAAGUGCAUCCAUAUCAUCCUGUGUUGGUGGUGCA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCC--------------------------UAUA------------UUCUGCGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUU----UCGCC-U-GGC-------------GUAU---------GGAUGAAGAG--------------------------------------------------------------------------------------------------------------GAUU--U------UAUC---------------CGAAUCCU--------UACGC---GCC-AGG-U------------UGU--------------CUGCGGAAAUCUGCCAGAGUAAA---------UCUUAGAUAUG--GACGAGUUGGUAGGACUCGCCGGGUUGGUGUUCCCACACCCUCUCGGCUGAGAA-----------ACCGCCUACACAGAAUGGGGCUUA-CAU----UG--G-G-A-----AAC-UU
AATU01002697.1/96756-97056       GAACAC----GAU-UU---AG-AAU-UGCGAAG--UCAAGUG--G--------------GUCUUCAUCCUGGUGCACCAUGUGCUAGAG---------------------------------CUGGAGGC-------------------------GGCUUG-GG--GAAAUUCCCCGGACA---------------CCAGGG--CA--------------GAGAG--------------UG----CC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCGU---------------------------CUAA----------------GCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACU---CCCUCAG-CGAUG----------AAGCU---------ACGCGGAGAUGGCUCACUUC----------------------------------------------------------------------------------------------------GGUG---------GGCC---------------GGAGCUUU--------CGGCGGAUUCG-UGA-G------------GAC--------------UGAUGGUCA-UACUAAAAGUUAU--------------GCAAUU--GGCUCAGCGGCACAUGGCGGACGUCGUGUCGUCGUCGC---------------------------UUUGAGCUAACCCGACGGGGAUUA-CUC----AU--G-U-U-----GUG-UU
AAPQ01006809.1/690372-690710     UGAGUC----UUC-CA---UG-CUU-GUCUC----UCGGGGC--CACAAAA-------CGAGUUCCU-------------------------------------------------------GGUAACUC---------------CACUGGUAUUGCCCUGGGC--GAAAGUCCCCGGGC----------------CUAGGA--UA--------------GAAAG--------------UA----UCAAGGUGUAAAACGUGCAUCCCUCAGGUUGAUGAGUUCUUGCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCC--------------------------UAUA------------UUCUGCGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUU----UCGCC-U-GGC-------------GUAU---------GGAUGAAGAG--------------------------------------------------------------------------------------------------------------GAUC---------UAUC---------------CGAAUCCU---------UUGC---GUC-AGG-U------------UGU--------------CUGCGGAAAUCUGCCAGAGUAUC-----------UUAGAUAUG--GACGAGUUGGUAGGACUCGCCGGGCGGAGUUCACGCUCUCUCGGCUGAGAA--------------ACCGCCUACACAGAAUGGGGCUUA-CAU----UG--G-G-A-----AAC-UC
AAEU02000441.1/179185-179529     UGAGUC----UUC-CA---UG-CUU-GUCUC----UCGGGGC--CACAAAA-------CGAGUUCCU-------------------------------------------------------GGUAACUC---------------CACUGAUAAUGCCCUGGGC--GAAAGUCCCCGGGC----------------CUAGGA--UA--------------GAAAG--------------UA----UCAAGGUGUAGAAAGUGCAUCACACACUUUGUUGAGUGAGUUUUGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCC--------------------------UAUA------------UUCUGCGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUU----UCGCC-U-GGC-------------GUAC---------GGAUGAAGAG--------------------------------------------------------------------------------------------------------------GUUU--U------UUUC---------------CGAAUCCU--------UACGC---GCC-AGG-U------------CGU--------------CUGCGGAAAUCUGCCAGAGUAUC-----------UUAGAUAUG--GACGAGUUGGUAGGACUCGCCGGGCGGAGUUCACGCUCUUCUCGGCCGAGAA-------------ACCGCCUACACAGAAUGGGGCUUA-AAU----UG--G-G-A-----AAC-UU
AAPP01019595.1/1014493-1014830   CGAGUU----UUU-CA---UG-CUU-GUCUC----UCGGGGC--UACAAAC--------GAGUUCCU-------------------------------------------------------GGUAACUC---------------UAUGCAUCGUGCCCUG-GG--UAAAGUCCCCGGGU----------------CUAGGA--UA--------------GAAAG--------------UA----UCAAGGUGUAAAAUGUGCGUUUUUGUGCGCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGCC--------------------------UAUA------------UUUCGCGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUC----UCGCC-A-GGC-------------GUAG---------UGAUGAAGAA--------------------------------------------------------------------------------------------------------------GGAUU-CGAAAGGAUCC---------------UGAAUCC----------UUGC--CGUC-CGG-U------------UGU--------------CUGCGGAAAUCUGCCAGAGUUCU------UCACCUCAGAUAUG--GACGAGUUGGUAGGACCUUUCCCCUCUAACUCCUCGGAGUGGGGGGAAGGAU-------------ACCGCCUACACGGAAUGGGGCUUA-CAU----UG--A-G-A-----AAU-UU
AAQB01008982.1/155948-156306     UGAGUU----UUU-CA---UG-CUU-GUCUC----UCGGGGU--AACACGA-------CGAGUUCCU-------------------------------------------------------GGUAACUC----------UUUAUAAAUAUUUACACCCUG-GG--UAAAGUCCCCGGGC----------------CUAUGA--UA--------------GAAAG--------------UA----UCAAGGCGUAAAAAGUGUAUAUAGAGAGGGAUUUAUAUUUCUCUUUACAUAU----------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUCGCCUA------------------------UAUU--------------CCGCGGAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUC-------GC-CUUGCGU----------UGCGACGAAGAA-GGAACGAAGUCCGCAA---------------------------------------------------------------------------------------------------------GGAUU-UCU----CUCC---------------CGAGUCCU--UUGCGUUUGGU--UGUC-UGC--------------GGA--------------AAUGUGCCAAAUAUAUCAGAUAU-------------GGACGAG--UUGGCAAUCAUCAAAUGCCACGUGUAUUUGGUG--------------------------------UUUGUCUACACGGAAUGGGGCUUA-CGU----UG--A-G-A-----AAU-UU
Z14231.1/277-602                 CAUGAC----CAAAGA------AUC-GUCACAAA-UCGAAGCU-UACAAAAU------GGAGUAAAAUUUU---------------------------------------------------UUUUACUC----------------AGU-AAUAUGCUUUG-GGUUGAAAGUCUCCCACCAAUUCGUAUGCGGAAAACGUAA--UGAGAUUUAAAAAUUUUAAAUUGUUUAAAUCAACUCA----UU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGGAGGAUGCC---------------------CUUG----------GGUAUUCUGCUUCUUGAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUG-------GU-A-CCU-------------CU---------------------------------------------------------------------------------------------------------------------------------------A-UUG---C--------------------------------------AG----GG-UAC--------------UGGUGUUUUCUUCGGUACUGGAUUCCGUUUGUAUGGAAUCUAAACCAUAGUUAUGACGAU---UGCUCUUUCCCGUGCUGGA---------------------------------------------UCGAGUA--ACCCAAUGGAGCUUA-CUA---UUC--U-U-G-----GUCCAU
EF424786.1/14-398                --UGAG----CUC-GA---AC-GAU-CGUGG----UUGAAGCA-GUCAUAC--------AGGAAUUU-------------------------------------------------------UUAUUCCU----------------CUAAACA--GCUUUA-GG--GAAAGUCCCCGGACU---------------CUUGCG--UCUUGAUCUCCAUG--GAGAU-------UGGGACAGG----CGGUAACGUGCUGACUUGAAGAAUCAGCGGUUUCAUUAAUGGCGCUAGUUUUUCCUUUAGCCUUUGUACUUUAAACCUCAAGAGAUAUAACU------------------------------------------------------------------------------------------------------------------------------CCUUGUCCA------------------------GAAU----------GAGUAGAUAAGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUA----CAGUC-U-AUGAG----------UUGUGUUUCUUG-AGCGUCUAGUGUACGAA--------------------------------------------------------------------------------------------------------CGGU--AUG----GUUG---------------AUUACGCC-------AUUUCU--GAAU-UGU-G------------GUU--------------UUUCGUCGU-AGUUGAUAGUUAU--------------ACGGUC--GCAUCCA--UUU-----------------------------------------------------GUUGAUGUAUCACAAUGGGGCUUA-GUC----UC--G-U-G-----CUC-A-
AADM01000056.1/42358-42674       CAUGGU----CAAAGA------GUC-GUCACUAA-UCGAAGC--U-UGCAC-------AAUGGGCAU--------------------------------------------------------GUCCUAU----------------CUUUUUUAAGCUUUG-GGUCGAAAGUCUCCCACCUGUC------------CGUAUG--CG--------------GAAAA--------------CG----CAAUGAGAUUUAAAAAUAUUUUUAAAUUGUUUAAAUCCACUCAUUAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGUGCA--------------------------UUCG---------------UGCACUC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCU---GUCCC-G-CGG-------------GAUC-------------------------------------------------------------------------------------------------------------------------------------C-UGG---------------------------------------UGGUC---UCG-UGG-UGACUUCGGUACUGGA----ACUGUAUUUCUUGAGUUCU-AAACCAUAGUUAU--------------GACGAUU-GCUGCGUGUUUGGCCUUGUCC--------------------------------------------AGCGCAGUAACCCAAUGGAGCUUA-CUA---UUC--U-U-G-----GCUCAU
AY090596.1/3-377                 UGUAGU----CGAAGA------AUC-GUCACUGA-UCGAAGCU-UACAUAAGGAAC--GGAUUUUAUCUGUUCAAUUGAA------------------------------------------AUGAUAUC----------------AUUUCUAUAGCUUUG-GGUAGAAAGUCUCCGACCAGUC------------CGUAAG--CG--------------GAAA---------------CG----UAAUGAGAUUUAAAAACUUUUCAAAUGUUUAAAUCAACUCAUUAAUCGUGUUGGUUUUCUGUC------------------------------------------------------------------------------------------------------------------------------------------------------------ACGGU---------------------------UUCU----------------AUCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGG---CUGUU-U-UAGAA----------GCCUCUGUG---------------------------------------------------------------------------------------------------------------------------------U-CUU----------------------------------------GGGU--ACUG-AAG-U----------AUUUC--------------UUUACUUU--AAACGAAAGUUAU--------------GACGAU--UGCCCGAGCGUUUUUAUCUCUUUUUUUGUUACUUCUGUUUACAGGGGUGAUUAGGGAGGAGGUAGCUUGGGU-AACCCAAUGGAGCUUA-CUU----UC--U-C-G-----GCUCAC
AACM02000363.1/288058-287605     CCCUCG----CUC-AA---UA-GAU-CGCUAU---UCGAAGCU-CACAAAC-------AGAGACACUGCGAUUUAUCGC-------------------------------------------AGCGUCUC-------------AAUCUCUUUAUUGCUUUGGGA--GAAAGUCCCCGGACGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUCGU---------------------------UUCG----------------ACGAAGUUUGCGGAAACGCGCCGCCAUAGAAGCACUGCGGUUGACCUUUGCGCCCAGGCCCUCGCCCUGCACUGGCCCUGCCCUCCGCUACAUCUGCUUGCCAACGGCCUUUGUCUCAACGGUCUUUGCCGCCCUCGGUCCUCUUGGAUGAAGAUAUGAGUCCGCUGUCGAGGUGCGGUGAGUUCUGGACGGACGGGUUGUCUGGCGGGUGGAUGGUGGGC-------------------------------------------------------AGAC------GCU-U-AGU-------------GCUC---------GUGCA-----------------------------------------------------------------------------------------------------------------------U-GUG--------------------------GCAUC---------GGGU--CGCU-UAG-G------------AUU--------------UGUUGUCGA-GAUUGACAGGUAU--------------GCGAUU--GCCUAGC--GAA-----------------------------------------------------AGCUUGGUUACUCAAUGGGGCUCA-UUC----UU--GAU-G-----CGA-GG
AAHF01000005.1/2298545-2298918   UCCUCG----CUC-AA---AG-GAU-CGCAU----UCAAAGCU-CACACAC-------AGAGUACCUACCG----------------------------------------------------GGUAUUCUCAUUCCUCUGCCAGGAGGAACCUAGCUUUGGGA--GAAAGUCCCCGGACA---------------CCCUG---------------------------------------------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGAUC---------------------------CUCG----------------GAUCCG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGGC-------AG-G-CAAUG----------CGGAA--ACGCG-CCGCCAUAGAAGCAAUUUGAUAGCGGCUAACUGCCCUACUCCCUCCCGGCGCCCGUGCCUAUAUCUGACGCUGUUCGCGGUGGAA------------------------------------ACAA--UGA----UGGUAUAGCGGGGUGUCGGAGAGGGGU------UGUUUCA--UUGG-GUU--------------GCC--------------UUUCGUCGUGUUUGGAUAGUCAU--------------GCGAUU--GCCCUGAUCCUCCUUUGGAGGC-------------------------------------------UUUUGGGUAACUCAAUGGGGCUCA-UUC----UU--GAG-G-----CGA-GG
AL451109.1/35066-34571           CCCUCG----UCC-GA---CA-AAU-CGCUAU---UCGAAGCU-UCCACAC-------GGAGAGAUCACGCUUUUUUUGCGCG---------------------------------------CUUCUUUC---------------AUUUCCUCGAGCUUUGGGA--GAAAGUCCCCGGACAUUCGUUCG-------CUUGCGAACG--------------GAUUG--------------CGGAAACG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCCGCCAUAGAA--------------------GCAC---------------UGCGGCUGAUCUCGGCCGCCCAGUUCCUCGUCUGUCUUGCCCAGCCCUGCCCGUCACACCAAAGUCGACCUCGUCUGCUUCUCCAGGGAGGGUG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCAU----CUUCC-G-AGC-------------UCGGGGACCACAUGGACGAAGAUAUGAGUCCGCGCCUCGGGUGACGAGUUUGAUGCCUGAUCUGGGGAGCUGGGGUCGAUGGCGGGUUCAGCCGCUUGGGUGG------------------------------UCCG--GAC----UUGG---------------GGCGUUUU-------GACGGU--GGCU-CGA-G------------AGG--------------UUUCGUCACGAUACCACAGAUAU--------------GCGAUU--GCU-CGCUCUUGUUUCUCUUCGGGGAAGCUGC---------------------------------GGCGAAGUUACUCGACGGGGCUUA-UUC----UU--G-GUG-----CGA-GG
CP000500.1/1045694-1046146       ACGUCCAUG-GUC-AA---AG-AUU-UGUUU----UCGAGGC--U-CACAA-------AAGGAUCCU-------------------------------------------------------CGGAUCUU--------------------CAUAUGCCUUG-GG--GAAAGUCUCCUGCCA---------------CAUAAG--CG--------------GAAA---------------CG----CAGUGGAUUUACCAAUCCACUUGAGAGGAUUGUGGAAUAAAAUCAGAAGUUGUCAAUUCCAGCGAUGUUAAAGUUGUGAUUAUAUCUACAGUGGAGUUGCUAAUUCGUCUAUGGAUCUUGUCUCUUUCGAGCUCUGGCAAUGAAAGUGUUCUGAUUGGUCAGAAUGAGUUGUUGAAGUUGUUCCUUUUAUUUUUUUCACAAUCACCUCUCAUUGUCCCAGUUGGUC-------------------------UUUA--------------UCCCAUCU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGUG----AUUUC-C-UUUCA----------GAGGA-------------------------------------------------------------------------------------------------------------------------------------A-CUG----------------------------------------UUCG--GCAA-UGG-G------------AAU--------------UUGUUUCCU-AAACGAUAGUUAU-------------AACAAGU--GAUCAAC--AAC-----------------------------------------------------UGUUGAUUAACCCAAUGGAGCUUA-CUC----UU--G-A-C-CCAUGGA-CG
CR382125.1/739090-739470         UUUUGUA---GUC-GAA--GA-AUC-GUCACUGA-UCGAAGCU-UACAUAAGGAAC--GGAUUUUAUCUGUUCAAUUGAA------------------------------------------AUGAUAUC----------------AUUUCUAUAGCUUUG-GGUAGAAAGUCUCCGACCAGUC------------CGUAAG--CG--------------GAAA---------------CG----UAAUGAGAUUUAAAAACUUUUCAAAUGUUUAAAUCAACUCAUUAAUCGUGUUGGUUUUCUGUC------------------------------------------------------------------------------------------------------------------------------------------------------------ACGGU---------------------------UUCU----------------AUCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGG---CUGUU-U-UAGAA----------GCCUCUGUG---------------------------------------------------------------------------------------------------------------------------------U-CUU----------------------------------------GGGU--ACUG-AAG-U----------AUUUC--------------UUUACUUU--AAACGAAAGUUAU--------------GACGAU--UGCCCGAGCGUUUUUAUCUCUUUUUUUGUUACUUCUGUUUACAGGGGUGAUUAGGGAGGAGGUAGCUUGGGU-AACCCAAUGGAGCUUA-CUU--UCUC--G-G-C---UCACG-AA
AACD01000075.1/118622-118263     UCCUCG----CUC-AA---AG-GAU-CGCAU----UCAAAGCU-UACACAC-------AGAGAAUUUUC-----------------------------------------------------CAGUUCUC-UCCUCUUCUACCAAGAAGAGUCUUGCUUUGGGA--GAAAGUCCCCGGAC----------------ACCCUG--UCUUUCGUCUCUGGC-GAUAG-----------ACAGG----CA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUGCG---------------------------GAAA----------------CGCG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGC------CAU-A-AAAGC----------AAUUU---GAUA-GCGGCUGACUGCCCUAUUCCCUACCGGUGCUGAGUGCGUACUCGACGCACACUGUGUGGAAACAAUG------------------------------------------------------GGGU--AUA----CCUC---------------UGUGCCGG---------AGAG-GGGUU-UAU-U------------GGG---------UUGCCUUUCGUCGUGUUUGGAUAGUCAU--------------GCGAUU--GCUCAGCUACUGAGUU-------------------------------------------------AGCUGGGUAACUCAAUGGGGCUCA-UUC----UU--GAG-G-----CGA-GG
CU329670.1/1234461-1234849       UUUGAG----CUC-GA---AC-GAU-CGUGG----UUGAAGCA-GUCAUAC--------AGGAAUUU-------------------------------------------------------UUAUUCCU----------------CUAAACA--GCUUUA-GG--GAAAGUCCCCGGACU---------------CUUGCG--UCUUGAUCUCCAUG--GAGAU-------UGGGACAGG----CGGUAACGUGCUGACUUGAAGAAUCAGCGGUUUCAUUAAUGGCGCUAGUUUUUCCUUUAGCCUUUGUACUUUAAACCUCAAGAGAUAUAACU------------------------------------------------------------------------------------------------------------------------------CCUUGUCCA------------------------GAAU---------GGAGUAGAUAAGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUA----CAGUC-U-AUGAG----------UUGUGUUUCUUG-AGCGUCUAGUG--------------------------------------------------------------------------------------------------------------UACG--AAC----GGUA---------UGGUUGAUUACGCC-------AUUUCU--GAAU-UGU-G------------GUU--------------UUUCGUCGU-AGUUGAUAGUUAU--------------ACGGUC--GCAUCCA--UUU-----------------------------------------------------GUUGAUGUAUCACAAUGGGGCUUA-GUC----UC--G-U-G-----CUC-AA
AAJI01002466.1/2910-2420         AACUCU----UCG-CUCAAAG-AAU-CGCAU----UCAAAGCU-UACGCACAGGAGAGGGAAGAGAAUAGCCCUUCACGGAAUUAUUUUAUU------------------------------CUCUCUUC----------AUACCGCAACUACUAGCUUUGGGA--GAAAGUCCCCGGACACCCUGCACCCCCGUCUUAAAA--CC--------------GCGAG--------------GG----UU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUCACA--------------------------ACAA----------------GCCAGGCACUGCGGAAACGCGCCGCCAUAGAAGCAUUUCUCAUUGCGGCUUACGCCUUUUUCCCUUCCCUUCUCUUUUCUCACUCUUCUUUUAGAAGGGAUGAGGAAAGAAAGAAGGGCUCGUCGCUG----------------------------------------------------------------------------------------------------------------------------------------------------UUCC----UACCC-G-ACUCU----------GGAAGUUUUUAU-UCUGCAGAGAAAACAAUG-------------------------------------------------------------------------------------------------------GUGG--UUU----GGAC-------------GGGAUGGGGC---------CAUU--UUGG-CGA-G------------GGA-----UAGGUUGCCAUUCGUCGUGUUUCGAUAGUCAU--------------GCGAUU--GCUUGGUUUCGCAUGUGUAUAUUAUAUGUGUGA--------------------------------AAUCAAGUAACUCGAUGGGGCUUA-UUCAUGAGG--C-G-A-----GGA-GU
AY090608.1/5-320                 CAUGGU----CAAAGA------AUC-GUCACUGU-UCGAAGCU-UGCAAAACU-----GGAGUGGUUC------------------------------------------------------AUACACUC----------------AAU--CAAUGCUUUG-GGUAGAAAGUCUCCGACCAGAC------------CGUAUG--CG--------------GAAAA--------------CG----UAAUGAGAUUUAAAAAUUUUACAAUCUUUAAAUCAACUCAUUAAGUGGACU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGGAUA--------------------------CUUG---------------UAUUUUC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCC----CGCUU-U-CCA-------------ACCUGUAU-----------------------------------------------------------------------------------------------------------------------------ACUCC-UUU----GAGU---------------UGC-----AGUGCUUUUCGGU--AUGG-GAA-U------------CUC--------------GCUAGAUUUCAAACCAUAGUUAU--------------GACGAU--UGUUCAGUUUUU-----------------------------------------------------GCUGAAU-AACCCAAUGGAGCUUA-CUU---UUC--U-U-G-----GCUCAU
X65942.1/199-444                 UUGUCA----CUG-GA---CG-AAG-UGA-A----UGGGUCA--UAU------------GGGCUUGU-------------------------------------------------------CCAAGUUC-------------------------CGACCC-AG--GAAAGUCCCCGGGCCACU------------UAUCCG--CA--------------GAGA---------------UG----CG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUCG---------------------------GUAA----------------CGAGAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUC----UUGCG-G-UGG-------------AGAG-AUUCAA-AUUGCUGAGAC--------------------------------------------------------------------------------------------------------------GCGU---------GUGU---------------GGAGCUUA---UGUGGUCUCU---CCG-CCGAU------------GAU--------------AUCAUGGCC-GUUCGACAGUUAU--------------UCACCU--C---UUCCUCUA-----------------------------------------------------UGGAC--UAACUGAACGGGGCUUA-CGU----UU--C-A-A-----UGA-CA
AAWR02025203.1/483-217           GUCCGU----GCC-GA---AG-GCC-UGUUU----CCUAGGC--UACAUAC-------GGGGGACU---------------------------------------------------------GGUUCCU----------------GAC--AAGUGCCUAG-GG--GAAAGUCCCCGGAC----------------CGCGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------GCGC----------------GCACGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGG-----CCGC-C-CGCCC----------GUCACUGUCUAG-GCCGCCGAGACGCGACCCCACG---------------------------------------------------------------------------------------------------GCGG--G------GAGC---------------CGAGCGGC---------GUGC--GGCG-GGC-G------------GCC--------------GUCCGUCAG-CUCCUCCAGUUAC--------------GCAGGC--AGUGCGC--CUU-----------------------------------------------------CGCGCGCCAACCACACGGGGCUCA-UUC----UC--G-G-C-----GCG-GC
AY948627.1/1-183                 GCAUGA----CGG-CA---AG-GCG-AGUAC----UCGCAGC--CACGAAA--------CGUUCCCU-------------------------------------------------------GUUGAGCG----------------CGCUA----ACUGUGAGC--GAAAGUCCCUGGAC----------------CACUGG--CA--------------GAAAG--------------UG----UC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCUC---------------------------UAGG----------------UUGGGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUC---------------------------------------------------------------------------------------------------------------------------------------------------------------------U-UUG--------------------------------------------------------------------GAG--------------UUUUAGUC--AUAGCACAGAGAC--------------GCUCCU--U----------------------------------------------------------------A------GAACAGCAUAGGGCCUA-CUC----UG--AUC-G-----UCA-UG
AAGV020433745.1/900-619          GUUCGU----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACAAAC-------GGAGGACUU--------------------------------------------------------GUUCCUU----------------UAC-UUUCCGCCUAG-GG--GAAAGUCCCCGGAC----------------CUCCGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------GCGU----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAGA----CCUCC-U-CACGG----------UUCACUGUAAAG-CCCGCUAAGAAGCGACCCCGCUCCCUG----------------------------------------------------------------------------------------------GGUG--GGG----GAGC---------------UGAGCGGC---------GUGA-GAGCG-GGGAC------------GUC--------------AUCCGUCAGCAUUUCCUAGUUAC--------------GCAGGC--AGCGCGUCGUGC-----------------------------------------------------UGCGCGCCAACCGCACGGGGCUCA-UUC----UC--A-G-C-----GCG-UU
AAKN02030431.1/17344-17064       GAUCGC----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACACUC-------GGGGGACUU--------------------------------------------------------GUUCCUC----------------AUC-UAGUUGCCUAG-GG--GAAAGUCCCCGGAC----------------CUUGGG--CA--------------GAAAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUGC---------------------------UCAC----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----CCUCC-C-CGCCC----------UUCAC-ACUUAG-CCCGCCAAGAAGCAAACCC------------------------------------------------------------------------------------------------------GCUCU-UUG----GAAC-------GGGAAUGCUGAGCGGC---------GUGU--UGCG-GGA-C------------GUC--------------AUCCGUCAG-CUGUCAUAGUGAC--------------GCAGGC--AGUGCGCACAUGGG---------------------------------------------------UGCGCACCAACCAAACGGGGCUCA-UUC----UC--A-G-C-----GCG-GC
AAQR03015324.1/19728-19463       GGUCAU----GCU-GA---AG-GCC-UGUUU----CCUCGGC--UACAUGC-------AGGGGACU---------------------------------------------------------GGUUCCU----------------UGUUCUUCUGCCUAG-GG--GAAAGUCCCCAGAC----------------CUCAGG--CA--------------GAGAG--------------UG----UG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------AUGC----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGACA---UCCUU-C-CAUUU----------CUCACUCUUAAAACCCACCAAGAA--------------------------------------------------------------------------------------------------------------GCGA--AUC----UCGC---------------CAAGCGGA---------GUGG--UGCG-GAG-G-----------CAUC--------------GUCUGUCAG-CUCCACUAGUUAA--------------GCAGGC--AGUGAGUGUCUU-----------------------------------------------------AGCGCUCCAACCACAUGGGGCUCA-UUC----UC--A-G-C-----GCG-GC
AAQY02000199.1/360008-360290     GAACAC----GAU-UU---AG-AAU-UGCGAAG--UCAAGUG-----------------GGCCCCUCCCCG---------------------------------------------------GGGGGGGC-------------------------GGCUUG-GG--GAAAUUCCCCGGACA---------------CCAGGG--CA--------------GAGAG--------------UG----CC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCGU---------------------------CCAA----------------GCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACU---CCCUC-GGCGAUG----------AAGCU---------UUGCGGAGAUGGCUCCGCUUC---------------------------------------------------------------------------------------------------GGCG---------GGCC---------------GGAGCUUU--------CGGCGGAUUUG-CGA-G------------GAC--------------UGAUGGUCA-UACUAAAAGUUAU--------------GCAAUU--GGCUCAGCGGCUUAUGGCGGACGUCGUGCCGUCGCUGC---------------------------UUGGAGCUAACCCGACGGGGAUUA-CUC----AU--G-U-U-----GUG-UU
AAGW02033514.1/33245-32971       GUUCGU----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACAUAC-------GGGGGACUC--------------------------------------------------------GUUCCUU----------------AUC--UUCCGCCUAG-GG--GAAAGUCCCCGGAC----------------CAUGGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------GCAU----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAGA----CUCCC-C-CGCGU----------CCCAC-CGAUAG-UCCGCCAAGAAGCGAACCCGCCCCGGGGGCG------------------------------------------------------------------------------------------GCA----------GAGC---------------CGAGCGGC---------GUGG--UGCG-GGG-C------------GUC--------------CUCCGUCAG-CUCUCAUAGUUAC--------------GCAGGC--AGCGCGC--CCC-----------------------------------------------------GGCGCGCCAACCGCACGGGGCUCA-UUC----UC--A-G-C-----ACG-GC
ABDF02000003.1/1755298-1754855   CCUUUG----CUC-AA---CA-AAU-CGCCAU---UCGAAGCU-UACAAAC-------GGAGAUGCUGCUUGCC------------------------------------------------AGCGCCUC--------------GUGAGAUCACGGCUUUGGGA--GAAAGUCCCCGGACGUCUCCUUUUCGG---AGCAUG--CG--------------GAAA---------------CG----CG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGCCAUAGAA--------------------GCAC---------------UGCGG--CUGACCUCCGCGCCUUGGCCCAGCUGAGGCAUCUGCCCUGCCUGCUGCU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAUC---CGUCU-U-UGCGA----------GACAU---------UUGCCAACCCUGUUUCUGCGCCUCUGGCCCCCAUGGAUGAAGAUAUGAGUCCGAGCUGGAUAGCUGUGGGAGCAGGGCCGCGUCGAUGUCGACCAAGGGUGGAUGGUAGGCGGACGUUUUGGUG--UCU----CGGC---------------UGCGGUAU---------CGGG--UGCA-GAG-G------------AUU--------------UGUUGUCGA-GGUCGAUAGUUAU--------------GCGAUU--GCCCGGC--GCA-----------------------------------------------------AGCUUGGUUACUCGAUGGGGCCCA-UUC----UU--G-AUG-----CAA-AG
ABDG02000029.1/789960-790403     CCUUCG----CUC-AA---CA-AAU-CGCCAU---UCGAAGCU-UACACAC-------GGAGAUUCUGCUCUGC------------------------------------------------AGCAUCUC--------------UUCCAAACACAGCUUUGGGA--GAAAGUCCCCGGACGUCUCCU---------UUUUG---------------------GAG---------------------C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUGCG---------------------------GAAA----------------CGCG--CCGCCAUAGAAGCACUGCGGCUGACCUCCGCGCCUUGGCCCAGCUGCCGCAUCUGCCCUGCCUGCUGCUAAAUCCGUUUCUCACGAGGCACUGUCAAACCCUAAUCUUGCGUCUCUGGCCCCUAUGGAUGAAGAUAUGAGUCCGUGCUGGAAGGCUGCGGGAUUGGGGUGGCGACGCUGAAUGGAGAUGGAUGGCAGGUGGACGU-----------------------------------------------------------------UGUC----AUGUC-U-GCCG------------GCUG-------------------------------------------------------------------------------------------------------------------------------------U-GGU--------------------------------------AUCGGG---UGC-AGA-G------------GAU--------------UUGUUGUCGAGGUCGAUAGUUAU--------------GCGAUU--GCCUGGC--GCA-----------------------------------------------------AGCUUGGUUACUCGAUGGGGCCCA-UUC----UU--G-AUG-----CGA-AG
AAIL02000096.1/26104-26605       CCUUUG----CUC-AA---CA-AAU-CGCCAU---UCGAAGCU-CACACAC-------GGAGAUGCUCUUUUCGAAGAGCAUCU--------------------------------------CGCACCUC----------------AAAAAACAAGCUUUGGGA--GAAAGUCCCCGGACGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUCCUCU--------------------------UCUA---------------CGAGGAGCAUGCGGAAACGCGCCGCCAUAGAAGCACUGCGGCUGACCUCCGCGCCUUGGCCCAGCCGCGGCAUCUGCCCUGCCUACUGCUAAAUUCGUCCUUCUUUGUCCUCUUUUUUUCCGGCACGAACCUUGUUUUCCCUUUCGUUUCUGUUGCCGGCCGCUUAUGGAUGAAG------------------------------------------------------------------------------------------------------AUAC----GAGUC-C-GAG-------------CUGGGAGCGCA-ACGACUGGGAAUAGGGGUGAGUUUGGAGAGGGGACGAAGGGGUUGGAUGGUAGGUGGACGUUUC---------------------------------------------------------GAUG--UUC----UUUC---------------GCGGUUGU----GGUAUCGGG---UGC-AGA-G------------GAU--------------UUGUUGUCGAGGUCGAUAGGUAU--------------GCGAUU--GCCCGGCUGUGUCACAGC-----------------------------------------------AGCUUGGUUACUCGAUGGGGCCCA-UUC----UU--G-AUG-----CAA-AG
AAPE02045418.1/25573-25844       GUUCGC----GCU-GA---AG-GCC-UGUUG----CCUAGGC--UACGUAC-------GGAGGACUC-------------------------------------------------------GGUUCCUC-------------------AUUUGCGCCUAG-GG--GAAAGUCCCCGGAU----------------CUCUGG--CA--------------GAGAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------GCAU----------------GCACGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAC----UUCCU-C-CGCUU----------CUCCU-UGUCAA-UCCGCCAAGACGCGA----------------------------------------------------------------------------------------------------------GCCC--GUU----AGGC-------GGGGGAGCCGAGCGGU---------GUGC--GGCG-GGG-U---------GUUGUC--------------AUCCGUCAU-CUCCUCUAGUUAC--------------GCAGGC--GGUGCGU----C-----------------------------------------------------CGCGCACUAACCACACGGGGCUCA-UUC----UC--A-G-C-----GCG-GC
AE016817.6/339559-339280         AGGCAUG---UCC-GA---AGAAUC-GUCACAA--UCGAAGCU-UACCAAGG------CCGGCAGCU-------------------------------------------------------AGCUGCCG----------------GUCCGCCAUGCUUUG-GG--GAAAGUCUCCGACCAGGC------------UGUAUG--CG--------------GAAA---------------CG----CAGCGAGAUUUAAAAACUUAUUUUUACAUCCACUC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUAGG---------------------------GCUG----------------CCUGGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCC----CUUUC-U-CCUGG----------GGCGC-----------------AA--------------------------------------------------------------------------------------------------------------GCUC---------CAGU---------------GAC------------UUUCGG--UAGC-GGG-G------------CCC--------------UGUGGGCGCCGAGCGAUAGUUAU--------------GACGAU--UGCGCA------------------------------------------------------------CCGCGU-AACGCAAUGGAGCUUA-UUC----UC--G-G-G---CCAUG-CC
AADN03004103.1/140439-140725     -GGAUGU---UCU-GA---AG-ACC-UGCUC----UCUAGGC--CACGCAC-------GGAGGACGUCUGUUCCUCG---------------------------------------------AGGGCCGU-------------------GUGCCCGCCUAG-GG--GAAAGUCCCCGGAC----------------CGCGGG--CA--------------GAGAG--------------UG----CCG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCGCC---------------------------GCC-----------------GGCGCCC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUC-----CGCC-C-CGCA------------GCCC-ACGCAC-GCCGCUGAGAC--------------------------------------------------------------------------------------------------------------GCUC---CC----GGGC---------------CGAGCGGG--------UGAGC---GCG-GGG-C------------GGG--------------CAUUCGUCA-CGGCCACAGACAC--------------GCAGGU--AGUGCGGAGGCGCGUCCCGCGAGCCGGGGCC----------------------------------GCAGCACCAACAGAACGGGGCUCA-CUC----UC--A-G-G----CCAU-C-
AACS02000003.1/1671152-1670746   CUGCCG----CUG-GA---AG-AAU-CGCUG----UCGCAGCU-CACGUAC-------UGAGAGCCUCGA----------------------------------------------------GCUCUCUC--------------------AUUCUGCUGUG-GG--GAAAGUCCCCGGAGG-------------------UG--CA--------------GAGAA---UAUCCUCGUUCUG----CA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUGGAAA--------------------------GCUG------------CCGAUUCCAAGCGCAUCGGUCCAGGGACGUUGGGAUGGCGAAGGUCGAUUUGGAUGCGUUCUAAGUUCGCGUUAGCGGUCUCGUUUGCAUCCUCCGCUUCGUCCACUCUGCUGCUCAGCUGAAGCCUUGUCGCGUCGGUGAAGGCGGGAAUGCGCAA---------------------------------------------------------------------------------------------------------------------------AGAUAUG-AGCGC-G-UUUCU----------UGCUC---------------------------------------------------------------------------------------------------------------------------------GGCA---------UGAC--------------------------------GGGG--UAAC-GGC-U--------GGGCAUC--------------UUGUUGCUCAUAGUCAUAGUUAU--------------GCGAUU--GUAGACUUGCGCAAG--------------------------------------------------CGGUCGUUAACUCAAUGGGGCUCA-CUC----UC--C-A-A-----CGG-CA
AAGU03018545.1/59131-59409       GCUCGU----GCU-GA---AG-GCC-UGUUU----CCUAGGC--UACAGAC-------GGAGGACUA--------------------------------------------------------GUUCCUC----------------AUUUCUCACGCCUAG-GG--GAAAGUCCCCGGAC----------------CUUGGG--CA--------------GAAAG--------------UG----CC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGUGC---------------------------UCAU----------------GCACGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGU----CAUCC-C-GUC-------------UCAC-AGUAAG-CCCGCCAAGAAGCAACCCCGCCAUCUGCG--------------------------------------------------------------------------------------------GCUG---GC----UAGC---------------UGAGCGGC---------GUGA--UAGC-GGGGU------------GUC--------------GUCCGUCUA-CUGUGCUAGUUAC--------------GCAGGC--AGUGCGUCUUCCG----------------------------------------------------UGCGCACCAACCAAACGGGGCUCA-UUC----UC--A-G-U-----GCG-GC
AACU03000132.1/743038-743599     CCCUCG----UCC-AA---AC-GAU-CGCCA----UCGAAGCA-CAUAUAGCAC----GGAGAUGAAUGGCUAAUCCC--------------------------------------------AUCGUCUC---------------AUUUACAUUUGCUUUG-GG--GAAAGUCCCCGGACAC--------------CAUCAG--CG--------------GAAA---------------CG----CG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGCCAUAAAA----------------------GCAC----------------UCGCGGCUUAGCCCUGCCGACUGUUUUACCUCGCGCCUGGUCUUUAUUUGGUUCUUUUUGCCAACCCUCCCGUUUUUGGACGGUUUCCAUUUCUUCCCCUCGGUCUUCUUACCCAGUCGUUGUCUUGAUUCGCCUUUCUUCGGCCCUCGCCGCCCCCAAUGGACGAAGAUAUGAGUCCGCGCUUCGAGUGGUUUGGGUUAGGCUGUCAGGCAAUUGCUGGCUCUGGCUGUCGAGGUAGGGGUCUUGGUGUAAUGGGGAAGGCGGGGGAGUUAUCUUAAAGGUUGGGUCU-A-UGGGA----------AACGC-------------------------------------------------------------------------------------------------------------------------------------U-AUA----------------------------------------GUCU--UGCA-UGG-G--------AGUUCUU--------------CGUCAGUUU-UACUGAAAGUUAU--------------GCGAUU--CAACCUCGUCCGCUCUGAGUACCUCUGGGGAAAACGAGUGG------------------------CUUGGUUUAACACGAUGGGGCUUA-CUC----UU--G-GUG-----CGA-GG
#=GC SS_cons                     :[[[[[....[[[.[[...,,.(((.(((,,....<<<<<<<-.-------.......-<<<<<<<___....................................................._>>>>>>>................--------->>>>>>.>,..,,AAA,AAAA,,,,,...............,,,,<<..<<.............._____..............>>....>>........................................................................................................................................................................................................................<<<<<<_..........................____..............._>>>>>>..............................................................................................................................................................................................................................................................................,<<<....---<<.<.<<<--..........-<<<<.........<<<<------..............................................................................................................<<<<..___....>>>>...............--->>>>-.........>>>>..->>>.>>>.-............>>>..............,,,,,,,,,.,,,,,,,,,,,,,..............))))))..,<<<<<<________.................................................._>>>>>>,,,,,,,,,aaaaaaa,.,,,....]]..].].].....]]].]]
#=GC RF                          cccucc....ccc.gA...AG.aau.cGCuu....UCGAaGCU.UACAcAc.......GGaGauccUuc.....................................................aggauCuC................auuaauuauGCuUUG.GG..GAAAGUCCCCGGACa...............CuuggG..Cg..............GAAAG..............cG....Cc........................................................................................................................................................................................................................ccgcgcu..........................ucaa...............ugcgcgg..............................................................................................................................................................................................................................................................................Agac....cuucc.c.cgcga..........gccac.........ccgCcAAGAa..............................................................................................................Gccc..uuu....gggC...............uGaGcggu.........gugg..ugcg.ggg.G............guc..............uUucgUccu.aaucgAuAGUUAU..............GCgauu..Ggcccgcuuuucuuu..................................................agcgggcUAACuCAAUGGGGCUUA.cUC....Uc..g.g.g.....gga.gg
//
# STOCKHOLM 1.0

#=GF AC   RF00031
#=GF ID   SECIS_1
#=GF PI   SECIS
#=GF DE   Selenocysteine insertion sequence 1
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Gautheret D, PMID:12458087
#=GF SS   Published; PMID:12458087
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001274; SECIS_element;
#=GF DR   GO; 0001514; selenocysteine incorporation;
#=GF RN   [1]
#=GF RM   8634917
#=GF RT   A novel RNA structural motif in the selenocysteine insertion element of
#=GF RT   eukaryotic selenoprotein mRNAs.
#=GF RA   Walczak R, Westhof E, Carbon P, Krol A
#=GF RL   RNA 1996;2:367-379.
#=GF RN   [2]
#=GF RM   12458087
#=GF RT   A survey of metazoan selenocysteine insertion sequences.
#=GF RA   Lambert A, Lescure A, Gautheret D
#=GF RL   Biochimie 2002;84:953-959.
#=GF CC   The incorporation of selenocysteine into a protein sequence is directed by
#=GF CC   an in-frame UGA codon (usually a stop codon) within the coding region of
#=GF CC   the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in
#=GF CC   the 3' UTR that is required for the distinction of UGA stop from UGA
#=GF CC   selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60
#=GF CC   nt in length and adopts a hairpin structure which is sufficiently
#=GF CC   well-defined and conserved to act as a computational screen for
#=GF CC   selenoprotein genes [2].
#=GF WK   SECIS_element
#=GF SQ   61


X13710.1/946-1008         U-UUUCAUC--UAUGAGGGUGUUUCCUCUAAA--CCUACG---AGG-----------GAGGAA-C-A-CCUGAU---CUUA-----CAGAAAA
X12367.1/703-764          G-UUUUUCC---AUGACGGUGUUUCCUCUAAA--UUUAC----AUG-----------GAGAAA-C-A-CCUGAU-UUCCAG------AAAAAU
X03920.1/1172-1235        G-GUUCUUC--CAUGAUGGUGUUUCCUCUAAA--UUUGC----ACG-----------GAGAAA-C-A-CCUGAU-UUCCAG-----GAAAAUC
X13684.1/700-760          U-UUUGCCC---AUGAAGGUGUUCCCUCUAAA--CCUAC----GUG-----------GAGGAA-U-G-CCUGAU-GUCCAG-------GAAAA
AF532927.1/678-740        A-UUUUAUC--CAUGAAAGUGUUUCCUCUAAA--CCUAU----GUG-----------GAGGAA-C-A-CCUGAU-GUCCAG------GAAAAU
L37762.1/2940-3006        C-UCGCUAU---AUGACGAUGGCAAUC-UCAA--AUGUU----CAU--U--------GGUUGC-C-A-UUUGAU--GAAAUCAGUUUUGUGUG
X53463.1/847-903          U-UCACAGA---AUGAUGGCACCUUCC-UAA---ACCCU----CAU-----------GGGUGG-U-G-UCUGAG--AGGC--------GUGAA
X58295.1/1384-1453        U-GGCGUCUU-CAUGAGGGAGGGGCCC--AAA-GCCCUUG--UGGG--C--------GGACCU-C-C-CCUGAG---CCUGUCUGAGGGGCCA
X84742.1/5239-5302        G-UGUCUCU---AUGAAGGAGGGGCCC-GAAG-CCCUUGU---GGG--C--------GGGCCU-C-C-CCUGAG---CCCG----UCUGUGGU
X71973.1/730-791          C-CGGCACU--CAUGACGGCCUGCCUG-CAAA--CCUGC----UGG--U--------GGGGCA-G-A-CCCGAA-AAUCCA-------GCGUG
AB030643.1/4176-4241      C-CGGCACU--CAUGAAGGUCUGCCUG-AAAA-CCAGCCU--GCUG-GU--------GGGGCA-G-U-CCUGAG-GACCUG-------GCGUG
AF274027.1/835-900        C-CGGCACU--CAUGAAGGUCUGCUUG-AAAA-CCAGCCU--GCUG-GU--------GGGGCA-G-U-CCUGAG-GACCUG-------GCGUG
L24896.1/600-665          C-CGGCACU--CAUGACGGUCUGCCUG-AAAA-CCAGCCC--GCUG-GU--------GGGGCA-G-U-CCCGAG-GACCUG-------GCGUG
AB017534.1/661-726        C-CCGGUGCC-UAUGACGGUCUGUCUG-AAAA-CCAGCCC---CUG-GU--------GGGGCA-G-A-CCUGAG-AACCUG-------GCGUG
X76008.1/2709-2772        C-UGGCACC--CAUGACAGUCUGCCUA-AAAA-CCAGCC----CUG-GU--------GGGGCA-G-A-CUCGAG-AACCUG-------GCGUG
L12743.1/694-758          C-UGGCACC--CAUGACAGUCUGCCUA-AAAA-CCAGCCC---CUG-GU--------GGGGCA-G-A-CUCGAG-AACCUG-------GCGUG
AF333036.1/2190-2249      C-AUGCGUC--CAUGAAGUCACUGGCC-UCAA-GCCCAA----GUG-GU--------GGGCAG-U-G-ACAGAA---GA---------GCUGC
AF166127.1/1919-1981      G-CCGGAUG---AUGACGACCUGGGUG-GAAA-CCUACCC-UGUGG--G--------CACCCA-U-G-UCCGAG---CCCC-------CUGGC
AF072865.1/1887-1947      G-UCAGAUG---AUGACGGCCUGUGCA-GAAA-CCCCCAC-GUGGG--C--------UGC-CA-G-G-UUUGAA---CCC--------CUGGC
AF136399.1/1808-1868      G-UCAGAUG---AUGAUGGCCUGGGCA-GAAA-CCCCAUG--UGGG--C--------CGCCCA-G-G-UUUGAA---CCC--------CUGGC
AB022283.1/1669-1729      G-CCAGAUG---AUGAGGACCUGUGCG-GAAA-CCCCCCG--CGGG--C--------UGCCCA-U-G-UCUGAG---CCC--------CUGGC
AF053984.1/1951-2017      G-AUGCGUC--CAUGAAGUCACCAGCC-CCAA-GCCCCUC---GUG-GU--------GGGUGG-U-G-AUGGAA-CCGUCA-----AAGCAGU
S48220.1/1731-1788        U-AUUUGUU--UAUGAUGGCCACAGCC-UAAA--GUACA----CAC-----------GGCUGU-G-A-CUUGAU---UCA--------AAAGA
AL645723.11/192421-192359 U-AUUUGUG--UAUGAUGGUCACAGUG-UAAA--GUUCC----CAC-----------AGCUGU-G-A-CUUGAU--UUUUA----AAAAUGUC
X57999.1/1526-1586        A-UAUUUGUU-UAUGAUGGUCACAGUG-UAAA--GUUCA----CAC-----------AGCUGU-G-A-CUUGAU--UUUUA-------AAAAU
Y11110.1/1218-1277        U-AUUUGUC---AUGACAGUCACAGCA-UAAA--GCGCA----GAC-----------GGCUGU-G-A-CCUGAU--UUUAG------AAAAUA
Y11109.1/927-987          U-GUUUAUU--AAUGACGGCUACAGAU-UAAA--CCUUU----AGC-----------CUCUGG-A-G-CCAGAU--GCAUU------CAAACA
Y11109.1/1272-1330        G-UUUCUCA---GUGAAGGCUACAGAU-UAAA--CCUCU----GGC-----------CUCUGG-A-G-CCAGAU--GCAUU-------GAAAC
AL049837.4/130674-130738  G-UGUGCGG---AUGAUAACUACUGAC-GAAA-GAGUCAU-CGACU--C-------AGUUAGU-G-G-UUGGAU---GUAG------UCACAU
AF093774.1/5851-5916      G-UGUGCGG---AUGAUAACUACUGAC-GAAAGAGUCAUC---GAC--C-----UCAGUUAGU-G-G-UUGGAU---GUAG------UCACAU
AF096875.1/5504-5568      G-UGUGCGA---AUGAUAACUACUGAC-GAAA-GAGCUGU-CUGCU--C-------AGUCUGU-G-G-UUGGAU---GUAG------UCACAC
AF125575.1/5781-5843      G-UGUGUUU---AUGAAGAGCACUAAC-AAAA-GAGUAAU-UGACU--C-------AGUUGGU-G-U-UCAGAU--GCU---------CUCAC
S79854.1/1605-1666        C-ACUGCUG---AUGACGAACUAUCUC-UAAC-UGGUCUU--GACC--A-------CGAGCUA-G-U-UCUGAA---UU-G-------CAGGG
Y11273.1/1139-1211        U-AUUUCUU--UGUGAUGACCGAUUUU-GAAA-UGGGUUU---CUC--UAAUGCCAGGAAAUC-GUG-UCUGAU---GUUG-----UCAAGUA
L28111.1/1299-1365        G-UGUUUGCA-AAUGACGACCGAUUUU-GAAA-UGGUCUCACGGCC--A-------AAAACUC-GUG-UCCGAC---AUC--------AACCC
Y11111.1/1260-1324        G-UGUCUCU---GUGAAGUUCGGUUUU-UAAA-AGGGUCA---UCC--A-------GAAAACC-G-ACACUGAU--GUUUC------CGACAC
M63574.1/1465-1528        G-UUACAUU--GAUGAGAACAGAAACA-UAAA--CUAUGA-CCUAG-G---------GGUUUC-U-G-UUGGAU--AGCUC-------GUAAU
AF322071.1/1577-1642      A-UGUGGUCUUUAUGAAGGCAGGUGCA-GAAA-CUAUGCA---CUA-GU--------GGUGUC-U-G-UCUGAU--GUUUG-------GCCAU
D25220.1/1493-1556        C-UUGCGUU--AAUGAGAACAGAAACG-AAAA--CUAUAA-CCUAG-G---------GGUUUC-U-G-UUGGAU--GGUUG-------GCAAC
D88033.3/5711-5774        C-UUGCGUU--AAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G---------GGUUUC-U-G-UUGGAU--GGUUG-------GCAAC
AF021345.1/10097-10160    G-UUACAUU--AAUGAGAACAGAAACA-UAAA--CUAUGA-CCUAG-G---------GGUUUC-U-G-UUGGAU--AGCUU-------GUAAU
AL833145.1/1479-1545      U-UUGCUUU--AAUGAGAAUAGAAACG-UAAA--CUAUGA-CCUAG-G---------GGUUUC-U-G-UUGGAU-AAUUAG-----CAGUUUA
AB032826.1/1401-1464      ACUUGCGUU--AAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G---------GGUUUC-U-G-UUGGAU--GGUUG-------GCAA-
U43286.1/2054-2120        C-UCUGUUA---AUGACGUCUCUCCCUCUAAA-CCCCAUU-AAGGA--C--------UGGGAG-A-G-GCAGAGCAAGCCU-------CAGAG
U43285.1/2009-2075        C-UCUGAUA---AUGAUGUCUCUCCCU-CUAA-CUCCCAGUAAGGA--C--------UGGGAG-A-G-GCUGAACAAACCU-------CAGAG
AC092237.1/57223-57161    C-AUUCAACU-UAUGAGGAUUAUUUCU-UAAA-GGCCUCU---GGC--U-------CGGAAAU-A-G-UCUGAA---CCU--------UAUUG
U67171.1/375-442          G-ACGCUUC---AUGAUAGGAAGGACU-GAAA-AGUCUUG-UGGAC--A-----CCUGGUCUU-U-C-CCUGAU--GUUCU------CGUGGC
U25264.1/366-432          G-CCGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUCA-AAGAC--C-----UGUGGUCUU-U-C-UUCGAU--GUUCU-------GCGGC
AF241527.2/359-424        G-CCGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUUA---GAC--C-----UGUGGUCUU-U-C-CUCGAU--GUUCC------UGCGGC
AC002327.1/156204-156268  C-UCAGCAG--GAUGAUGAGAAGGGCU-GAAA-UGCUGCC--AAAC--C-------AGGUCCU-U-U-UCUGAU--GGUGG-------CUGGG
AF380118.1/366-433        G-ACGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUUG-UGGAC-GC------CUGGUCCU-U-C-CCUGAU--GUUCU------CAUGGC
U67853.1/375-442          G-ACGCUUC---AUGACAGGAAGGACU-GAAA-UGUCUCU-UGGAC-GC------CUGGUCCU-U-C-CUUGAU--GUUCU------CACGGC
AF390544.1/1076-1142      U-UUGCAUU--AAUGAGGAUUACACAG-AAAA-CCUUUGU--UAAGGGU--------UUGUGUCG-A-UCUGCU--AAUUG-------GCAAA
AF288740.1/1291-1357      U-UUGCAUU--AAUGAGGAUUACACAG-AAAA-CCUUUGU--UAAG-GA-------CUUGUGU-AGA-UCUGAU--AAUUG-------GCAAA
BC003127.1/865-928        G-UCACUGC---AUGAUCCGCUCUGGU-CAAA-CCCUUCC---AGG--C------CAGCCAGA-G-U-GGGGAU--GGUCU-------GUGAC
AF195142.1/461-524        G-UCACCGA---AUGAUCUGCUCUGGU-CAAA-UCCUUCU---AUG--C------CAGCCAGG-G-U-GGUGAU--GACCC-------GUGAC
AF195141.1/689-759        G-ACUGACAU-UAUGAAGGCCUGUACU-GAAG-ACAGCAA--GCUG--U-------UAGUACA-G-A-CCAGAU--GCUUU--CUUGGCAGGC
AY119185.1/838-902        G-AGCC-CU---AUGAUCGAUGAUUGG-CAAA-UCCUCUC--GAGG--A-------ACCGAUC-G-U-UGAGAA--CCCCU-----UUGCCUU
AY060611.1/560-627        G-UGGCGCU--UAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GC--------GGGCAA-U-U-GCUGAU---UACG---AUUAACCAC
AF201385.1/3055-3117      G-CCAGAUG---AUGACGACCUGGGUG-GAAA-CCUACCC-UGUGG--G--------CACCCA-U-G-UCCGAG---CCCC-------CUGGC
AF148217.1/2209-2272      G-AGGCAGCUUUGUGACGACCUUUGGC-UAAA-CUCCAUC--GUGA-GC--------GCCUCU-G-G-UCUGAU---GC---------GCCUC
#=GC SS_cons              <.<<<<---..------<<<<<<<<<<.----.-<<<___.._>>>..-........>>>>>>.>.>.>>----..-----.......>>>>>
#=GC RF                   g.ucucaUu..uAUGAuGaccgguccu.uAAA.ccucuuu..ggag..c........gggacc.g.g.uCUGAU..gcuuG.......gagac
//
# STOCKHOLM 1.0

#=GF AC   RF00032
#=GF ID   Histone3
#=GF DE   Histone 3' UTR stem-loop
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:17998288
#=GF SS   Published; PMID:17998288
#=GF GA   25.00
#=GF TC   25.00
#=GF NC   24.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.68 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0006398; mRNA 3'-end processing by stem-loop binding and cleavage;
#=GF RN   [1]
#=GF RM   7899087
#=GF RT   The sequence of the stem and flanking sequences at the 3' end of histone
#=GF RT   mRNA are critical determinants for the binding of the stem-loop binding
#=GF RT   protein.
#=GF RA   Williams AS, Marzluff WF
#=GF RL   Nucleic Acids Res 1995;23:654-662.
#=GF RN   [2]
#=GF RM   10571029
#=GF RT   Formation of the 3' end of histone mRNA.
#=GF RA   Dominski Z, Marzluff WF
#=GF RL   Gene 1999;239:1-14.
#=GF RN   [3]
#=GF RM   17998288
#=GF RT   Early evolution of histone mRNA 3' end processing.
#=GF RA   Dávila López M, Samuelsson T
#=GF RL   RNA. 2008;14:1-10.
#=GF CC   The mRNAs of metazoan histone genes lack a poly-A tail. 3' end processing
#=GF CC   occurs at a site between a highly conserved stem-loop (modelled by this
#=GF CC   family) and a purine rich region around 20 nts downstream (the histone
#=GF CC   downstream element, or HDE). The stem-loop is bound by a 31 kDa stem-loop
#=GF CC   binding protein (SLBP - also termed the histone hairpin binding protein,
#=GF CC   or HBP). Together with U7 snRNA binding of the HDE, SLBP binding nucleate
#=GF CC   s the formation of the processing complex. The histone 3' UTR stem-loop is
#=GF CC   also involved in nucleocytoplasmic transport of the mRNA, and in stability
#=GF CC   regulation and translation efficiency in the cytoplasm.
#=GF WK   Histone_3'_UTR_stem-loop
#=GF SQ   46


CAAE01014536.1/93243-93288     ACAACGGCUCUUUUAAGAGCCACCACAUGU-GACCGAAAGAGCAUUU
AC084589.1/5032-4987           CCAACGGCCCUCUUUAGGGCCACGAAUCACAUGAAUCCAAAUUGAU-
AL662809.14/46720-46765        CCAACGGCUCUUUUCAGAGCCACC-CACAGAGUCAGAAAAAGUGUCU
M74534.1/508-553               CCAAAGGCUCUUUUCAGAGCCACC-CACGCUGUCAAGGGAAGAGCCU
AAGE02005905.1/5861-5816       AAAACGGCCCUUUUCAGGGCCACUAGAGCAUUCCCUAAAAGAGUUG-
AAAB01044800.1/486-531         CAAACGGUCCUUUUCAGGACCACAAUACAUUACUCA-AGAGCUGUGU
AY128653.1/651-696             CAAAAGGCCCUUUUCAGGGCCCCCAAACUGUCACAGAAAG-AGCUGU
ABAV01048734.1/586-541         AAAACGGCUCUUUUAGGAGCUACCACAUGCAAAAAAGUCAAUAGCC-
Z81128.2/25556-25511           CCAACGGCCCUCUUUAGGGCCACAAAUGAUAAAUCCAAACAGUCCG-
CR354435.20/79242-79197        CCAAAGGCUCUUUUCAGAGCCACCUCAGUGUAUCAGAAAAGUGUAA-
CAAI01002844.1/301-346         UUUGAGGCUUCACUAGAAGCCAUUA-CUAGAUACUUACAAACAAUGU
ABPA01000184.1/11471-11515     UUUUAGGCUUCACUAGAAGCCACC-AACGUUUACUUCGGACGUCAU-
AABL01000137.1/776-821         UUUGAGGCUUCACUAGAAGCCAUUA-CUAGAUACUUACAAACAAUGU
AC084502.1/4081-4126           CCAACGGCCCUCUUUAGGGCCACAAAUAAC-ACGAAUCCUAAAAUAU
AF361948.1/1198-1243           CUUUAGGCUUCACUAGAAGCCACC-AAAACUAUUUUUCCCGCCAAGU
AAGE02005905.1/11272-11317     CAAACGGCCCUUUUCAGGGCCACCAAACACACUCAUCAAGGAGUUG-
CAAE01014565.1/1508968-1508923 ACAACGGCUCUUUUAAGAGCCACU-CACUUUCUACUAAGAGCAGCGU
AAAB01008948.1/3301455-3301500 CAAACGGCCCUUUUCAGGGCCACC-AAUUGUGUUGAAAAGAACUUAU
AAEL01000068.1/8576-8621       GAACAGGUGGCACUAGCCACCAUA-AAUUUUGAGAUAAAAGUUUUAG
AL589879.21/31985-31940        CUAAAGGCCCUUUUCAGGGCCAUC-CAAUUAAUCCUCCAAAGGGUUG
AE014134.5/21504391-21504346   CAAUCGGUCCUUUUCAGGACCACCAUUCAGUUUUUAAAAGGAGGAA-
AAEL01000015.1/38686-38731     UGACAGGCGUUACUAGACGCCACA-AAUAGUUUAUGUUGCUCUUUGG
AE014134.5/21406015-21406060   UAAUCGGUCCUUUUCAGGACCAAAAACCAGAUUCAAUGAGAUAAAA-
Z83245.4/30945-30900           CCAACGGCCCUCUUUAGGGCCACAAAUGUGAUAAUAUCCCAUGUAA-
AL009179.1/138662-138707       CCAAAGGCUCUUUUCAGAGCCACC-CACAUGCGCGCUGAAAAGAUCU
ABCN01000686.1/16677-16632     AACUCGGUGUUUCUCAACACCACC-UAGACAAAGAAUCGGAUGUGCU
AAFD02000019.1/418583-418538   ACACUGGAUUUUAUAAAAUCCACU-CAUCAAUCAAAGAACUUCUUAU
ABEP02040002.1/589-545         ACCCCGGCCCUUCUCAGGGCCACA-CACAUAUCCCAGAAAGAUCUA-
AAEE01000004.1/565730-565685   GAACAGGUGGCACUAGCCACCAUA-AAUUUUGAGAUUAAAGUUUUAG
AABS01000176.1/158056-158011   AAAACGGCUCUUUUCAGAGCCACC-UAUUUAUACAAAGAGAUGAAGU
M61155.1/597-642               CCAAAGGCUCUUUUAAGAGCCACCACGUUGCCACUGGGGAGAGCUG-
CR855729.2/461-505             ACAAAGGCUCUUUUCAGAGCCACC-GACACUUUCUGGGAAUGAGCU-
AAEE01000003.1/1110682-1110637 UGACAGGCGUUACUAGACGCCACA-AAUAGUAUAUGUUGCUCUUUGG
ABEP02004286.1/1361-1316       ACCCCGGCCCUUUUCAGGGCCACC-CAAAUGUCUAAGAAAGAGCUGU
AAFD02000019.1/419847-419892   AAACUGGAUUUUCUAAAAUCCACC-CACUUUCCAAAGAACUAAGAUU
V01355.1/567-612               CAAACGGCUCUUUUCAGAGCCACCAAAUAAUCAAGAAAGAAUACUG-
AAHC01037550.1/201-246         UAAUUGGAUUUUUUGAAAUCCACC-UGCAGUAGGAUAAAGGAGAUGU
AAFI02000005.1/2443043-2442999 CCAAAGGUGUUUUUUAACACCACA-CAAAAAACCAAUUUCUUUUCA-
ABAV01054220.1/1227-1272       CAAACGGUUCUUUUAGGAACCACCACAUAUGACAAGAGUCAUGUCC-
AL844505.1/445330-445375       UUUAAGGCUUCACUAGAAGCCAUUAUAUAUAAUAUACACAUAUAUA-
AAGK01000004.1/1341571-1341616 ACCCAGGCUUCACUUGAAGCCAUA-AUCAUACACUAAUUUUUUAUCA
CR354435.20/94861-94817        CCAAAGGCUCUUUUAAGAGCCACC-CAUUUCAUCUGUGAAAGAGCA-
AAGK01000004.1/1343635-1343680 ACCCAGGCUUCACUUGAAGCCAUA-AUCAUACACUAAUUUUUUACCA
AAGJ04044602.1/134-89          CAAACGGCUCUUUUCAGAGCCACCACA-ACCCCAAGAAAGAAUCAUU
CAAB02006192.1/1863-1818       CCAAAGGCUCUUUUAAGAGCCACU-CACAUCUUGUAAAGAGUAGAAU
CAAB02016978.1/7350-7306       ACAAAGGCUCUUUUAAGAGCCACAACA-AGUCUGUUCAAGGAGCAU-
#=GC SS_cons                   :::::<<<<<<____>>>>>>:::.::::::::::::::::::::::
#=GC RF                        ccAAaGGCUCUUUUaAGAGCCACc.aAcAuuuacaaaaAaauuuUgU
//
# STOCKHOLM 1.0

#=GF AC   RF00033
#=GF ID   MicF
#=GF DE   MicF RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Noncoding RNAs Database
#=GF SS   Predicted; Bateman A
#=GF GA   70.00
#=GF TC   71.30
#=GF NC   69.60
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://biobases.ibch.poznan.pl/ncRNA;
#=GF DR   SO; 0000383; MicF_RNA;
#=GF DR   GO; 0006950; response to stress;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   11601842
#=GF RT   MicF: an antisense RNA gene involved in response of Escherichia coli to
#=GF RT   global stress factors.
#=GF RA   Delihas N, Forst S
#=GF RL   J Mol Biol 2001;313:1-12.
#=GF CC   The micF gene is a stress response gene found in Escherichia coli and
#=GF CC   related bacteria that post-transcriptionally controls expression of the
#=GF CC   outer membrane porin gene ompF. The micF gene encodes a non-translated 93
#=GF CC   nt antisense RNA that binds its target ompF mRNA and regulates ompF
#=GF CC   expression by inhibiting translation and inducing degradation of the
#=GF CC   message. In addition, other factors, such as the RNA chaperone protein
#=GF CC   StpA also play a role in this regulatory system. Expression of micF is
#=GF CC   controlled by both environmental and internal stress factors. Four
#=GF CC   transcriptional regulators are known to bind the micF promoter region and
#=GF CC   activate micF expression.
#=GF WK   MicF_RNA
#=GF SQ   4


Y15844.1/543-450 CGCUAUCAUCAUUAACUUUAUUUAUUACCGUCAUUCACU--UCUGAAUGUCUGUUUACCCCUAUUUCAACCGAAUGCUUCGCAUUCGUUUUUUUUA
Z33506.1/97-4    CGCUAUCAUCAUUAACUUUAUUUAUUACCGUCAUUCAGU--UCUGAAUGUCUGUUUACCCCUAUUUCGACCGGAUGCUUCGCAUCCGGUUUUUUUU
L24960.1/158-73  CGCUAUCAUCAUUAUUUUCAUU-AUUACCUUCAUUAUCCGAAGAUAAUUUCUGCAUACC-----UUUAACCGGCUUC----UGGCCGGUUUUUUAU
AF039309.1/94-1  CGCUAUCAUCAUUAACUUUAUUUAUUACCGUCAUUCACU--UCUGAAUGUCUGUUUACCCCUAUUUCAACCGGAUGCUUCGCAUUCGGUUUUUUUU
#=GC SS_cons     ::::::::::::::::::::::::::::::::<<<<<<_.._>>>>>>-------------------<<<<<<<<<<___>>>>>>>>>>::::::
#=GC RF          CGCUAUCAUCAUUAacUUuAUUUAUUACCgUCAUUcagu..ucugAAUgUCUGuuUACCCCUAUUUcaAcCGgaugCUUCGcaucCGgUuUUUUuu
//
# STOCKHOLM 1.0

#=GF AC   RF00034
#=GF ID   RprA
#=GF DE   RprA RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Noncoding RNAs Database
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   70.00
#=GF TC   70.20
#=GF NC   69.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 36 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://biobases.ibch.poznan.pl/ncRNA;
#=GF DR   SO; 0000387; RprA_RNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   11251852
#=GF RT   Regulation of RpoS by a novel small RNA: the characterization of RprA.
#=GF RA   Majdalani N, Chen S, Murrow J, St John K, Gottesman S
#=GF RL   Mol Microbiol 2001;39:1382-1394.
#=GF RN   [2]
#=GF RM   12410838
#=GF RT   Regulation and mode of action of the second small RNA activator of RpoS
#=GF RT   translation, RprA.
#=GF RA   Majdalani N, Hernandez D, Gottesman S
#=GF RL   Mol Microbiol 2002;46:813-826.
#=GF CC   Translational regulation of the stationary phase sigma factor RpoS is
#=GF CC   mediated by the formation of a double-stranded RNA stem-loop structure in
#=GF CC   the upstream region of the rpoS messenger RNA, occluding the translation
#=GF CC   initiation site. Clones carrying rprA (RpoS regulator RNA A) increased the
#=GF CC   translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory
#=GF CC   RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three
#=GF CC   stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in
#=GF CC   the positive regulation of RpoS translation. RprA also appears to bind to
#=GF CC   the RpoS leader [2]. RprA is non-essential [1]. The Y. pestis homologue
#=GF CC   was detected by similarity to the E. coli gene (pers obs. Bateman A).
#=GF WK   RprA_RNA
#=GF **   Founds Erwinia and Photorhabdus homologues
#=GF SQ   13


BX950851.1/2106268-2106157   ACGGAGCUAG-UAUUA-ACCUACUGUUUGU-CAAUGA-GGUUUCCUCCUCGUCAGAGC-UAGUAAC-GAAUUGCUGUGUGUAGUCUUUGCCCAUCCC--CUGAGAUGGGCCUUUUUUUUC
U00096.2/1768396-1768503     ACGGUUAUA--AAUCA-ACAUAUUGAUUUA-UAAGCAUGGAAA--UCC-CCUGAGUG--AAACAAC-GAAUUGCUGUGUGUAGUCUUUGCCCAUCUC--CCACGAUGGGCUUUUUUUUAA
BX571867.1/288515-288628     AGUGGGCUAUGAACGAGACGUUUAUUUCUCCUUUUGAUGGUUC--UAC-U-UGUUAG--AAACGCCUAUAUUGCUGUGUGUAGUCCUUGCCUAUCACGCCCAUGAUAGGCUUUUUUUUUC
AL627271.1/108510-108617     ACGGUUAUA--AAUCA-ACACAUUGAUUUA-UAAGCAUGGAAA--UCC-CCUGAGUG--AAACAAC-GAAUUGCUGUGUGUAGUCUUUGCCCGUCUC--CUACGAUGGGCUUUUUUUUUU
AAYT01000004.1/252910-253019 AAGGCGCUU--AAAUA-AACCAUUUAAUGA-UAGCUUAUUUAA--ACG-UCUGUGAUC-UAGUACAUGUAUUGCUGUGUGUAGUCUUUGCCUGUCAC--CUAAGACAGGCUUUUUUUUUG
AACY022447626.1/334-227      AUGGCUUUA--GAUCA-ACACAUUGAUUUA-UAAGCAUGGAAA--UCC-CCUGAGUG--AAACAAC-GAAUUGCUGUGUGUAGUCUUUGCCCAUCUC--CCACGGUGGGCUUUUUUUUGU
AM286415.1/2382209-2382313   ----AUUUA--AAUAA-AUUAUCUCAUAAU-GACUUAUUUAAA--UAUCUGUAAUCG--AAUAUAA-GUAUUGCUGUGUGUAGUCUUUGCCUGUCAC--CUAAGACGGGCUUUUUUUUUA
AP008232.1/2390532-2390429   GCGUGU-----UAUUA-GCUCUAUGAUUUAGUAAUGAUUUUAA--UG---CUACCCG--GCAUGACAGAAUUGCUGUGUGUAGUCUUUGCCCAUCUU---UAAGAUGGGCUUUUUUUUAU
CP000826.1/2374322-2374212   AUAUUGCUU--CAAAU-ACCUGAUUUAAAG-CAAGAUUUCCAA--ACA-AUGUAAUGCCAUACAUGUGAAUUGCUGUGUGUAGUCUUUGCCCGUCUC--CUAUGAUGGGCUUUUUUUUAU
CP000857.1/2421525-2421632   ACGGUUAUA--AAUCA-ACACAUUGAUUUA-UAAGCAUGGAAA--UCC-CCUGAGUG--AAACAAC-GAAUUGCUGUGUGUAGUCUUUGCCCGUCUC--CUACGAUGGGCUUUUUUUUUA
AALC02000001.1/49739-49635   GUUUAAAUA--AAUCA-UUUCAGAAUGAUU-UACUUAAAUAUC--UG----UAAUCG--AAUAUAC-GUAUUGCUGUGUGUAGUCUUUGCCUAUCAC--UUAAGAUGGGCUUUUUUUUUG
AALD02000007.1/58628-58520   AGGCGUUUA--AAUAA-AUCAUUUCAUAAU-GACUUAUUUAAA--UAUCUGUAAUCG--AAUAUAC-GUAUUGCUGUGUGUAGUCUUUGCCUGUCAC--CUAAGACGGGCUUUUUUUUUG
AALF02000003.1/16089-16192   AUUUAAAUA--ACUCA-UUUUCAAGUGAGU-UAUUUAAAUAUC--UG----UAAUCG--AAAU-AC-GUAUUGCUGUGUGUAGUCUUUGCCUGUCAU--CUAAGACGGGCUUUUUUUUAC
#=GC SS_cons                 :<<<<____.._____.____>>>>,,,,,.,,,,<<-<<___..__>.>->>,,,,..,,,,,,,.,,,,<<<___>>>,,,,,,,,<<<<<<<__..____>>>>>>>::::::::::
#=GC RF                      AcguuucUA..aAuuA.Acuuaaugauuuu.uAaucaUggaaa..Ucc.ccugauuG..AAauaac.GaAUUGCUGUGUGUAGUCUUUGCCcgUCaC..CUAaGAcgGGCUUUUUUUUuu
//
# STOCKHOLM 1.0

#=GF AC   RF00035
#=GF ID   OxyS
#=GF DE   OxyS RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Noncoding RNAs Database
#=GF SS   Published; PMID:11804582
#=GF GA   75.00
#=GF TC   75.10
#=GF NC   74.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://biobases.ibch.poznan.pl/ncRNA;
#=GF DR   SO; 0000384; OxyS_RNA;
#=GF RN   [1]
#=GF RM   9774350
#=GF RT   The Escherichia coli OxyS regulatory RNA represses fhlA translation by
#=GF RT   blocking ribosome binding.
#=GF RA   Altuvia S, Zhang A, Argaman L, Tiwari A, Storz G
#=GF RL   EMBO J 1998;17:6069-6075.
#=GF RN   [2]
#=GF RM   11804582
#=GF RT   The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs.
#=GF RA   Zhang A, Wassarman KM, Ortega J, Steven AC, Storz G
#=GF RL   Mol Cell 2002;9:11-22.
#=GF CC   OxyS is a small untranslated RNA which is induced in response to oxidative
#=GF CC   stress in Escherichia coli. This novel RNA acts as a global regulator to
#=GF CC   activate or repress the expression of as many as 40 genes, including the
#=GF CC   fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s)
#=GF CC   subunit of RNA polymerase [1]. OxyS is bound by the Hfq protein, that
#=GF CC   increases the OxyS RNA interaction with its target messages [2].
#=GF WK   OxyS_RNA
#=GF SQ   5


AL627279.1/144216-144327   AGAACGGAGCGGUUUCUCGUUUAACCCUUGAAGACACCGCCCGUUCAGAGGGUAUCUCUCGAACCCGAAAUAACUAAAGCCAACGUGAACUUUUGCGGACCUC--UGGUCCGCU
M34102.1/107-1             GAAACGGAGCGGCACCUCUUUUAACCCUUGAAGUCACUGCCCGUUUCGAGAGUUUCUC---AACUCGAA-UAACUAAAGCCAACGUGAACUUUUGCGGAUCUCCAGGAUCC---
X16531.1/107-1             GAAACGGAGCGGCACCUCUUUUAACCCUUGAAGUCACUGCCCGUUUCGAGAGUUUCUC---AACUCGAA-UAACUAAAGCCAACGUGAACUUUUGCGGAUCUCCAGGAUCC---
U87390.1/56-165            GAAACGGAGCGGCACCUCUUUUAACCCUUGAAGUCACUGCCCGUUUCGAGAGUUUCUC---AACUCGAA-UAACUAAAGCCAACGUGAACUUUUGCGGAUCUCCAGGAUCCGCU
CP001127.1/4210197-4210086 AGAACGGAGCGGUUUCUCGUUUAACCCUUGAAGACACCGCCCGUUCAGAGGGUAUCUCUCGAACCCGAAAUAACUAAAGCCAACGUGAACUUUUGCGGACCUC--UGGUCCGCU
#=GC SS_cons               <<<<<<<-<<<<-<<-<<___________>>->>-->>>>>>>>>>>,,<<<<_____..._>>>>,,,.,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<_____>>>>>>>:
#=GC RF                    ggaaCGGAGCgGuacCuCuUUUAACCCUUGaAguCACcGCCCGuuccGAGgGuuUCUC...AaCcCGAA.UAACUAAAGCCAACGUGAACUUUUGcGGacCUCcAuGguCCgCU
//
# STOCKHOLM 1.0

#=GF AC   RF00036
#=GF ID   RRE
#=GF DE   HIV Rev response element
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Published; PMID:12177299
#=GF GA   104.00
#=GF TC   104.00
#=GF NC   103.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000388; RRE_RNA;
#=GF DR   GO; 0051169; nuclear transport;
#=GF DR   GO; 0005515; protein binding;
#=GF DR   GO; 0005634; nucleus;
#=GF RN   [1]
#=GF RM   12177299
#=GF RT   RNA molecules with structure dependent functions are uniquely folded.
#=GF RA   Le SY, Zhang K, Maizel JV Jr
#=GF RL   Nucleic Acids Res 2002;30:3574-3582.
#=GF CC   The Rev response element (RRE) is encoded within the HIV-env gene. Rev is
#=GF CC   an essential regulatory protein of HIV that binds an internal loop of the
#=GF CC   RRE leading, encouraging further Rev-RRE binding. This RNP complex is
#=GF CC   critical for mRNA export and hence for expression of the HIV structural
#=GF CC   proteins.
#=GF WK   HIV_Rev_response_element
#=GF SQ   65


AF025758.1/1519-1855 ACUAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUGUACUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAUUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGAAUUUGGGGCUGCUCUGGAAAACUCAUUUGCACCACUAACAUGACCUGGA
U36876.1/1534-1870   ACCAAGGCAAAGAGAAGAGUGGUGCAAAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUGUGCUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCACUGACGCUGACGGUACAGGCCAGACUAUUACUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGGAAUUUGGGGUUGCUCUGGAAAACUCAUUUGCCCCACUACUGUGCCUUGGA
U36859.1/1501-1837   ACCAAGGCAAAAAGAAGAGUGGUGCAGAGAGAGAAAAGAGCAGUGGGA---AUAGGAGCUGUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGAAUUUGGGGUUGCUCUGGAAGACUCAUUUGCACCACUGCUGUGCCUUGGA
U36862.1/1501-1837   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAGAAAAGAGCAGUGGGA---AUAGGAGCUGUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGAAUUUGGGGUUGCUCUGGAAGACUCAUUUGCACCACUGCUGUGCCUUGGA
AF256208.1/7739-8078 ACCAAGGCAAAGAGAAGAGUGGUGCAAAGAGAAAAAAGAGCAGUGGGAAUAAUAGGAGCUAUGCUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAAGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGGGUUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF256204.1/7738-8077 ACCAAGGCAAAGAGAAGAGUGGUGCAAAGAGAAAAAAGAGCAGUGGGAAUAAUAGGAGCUAUGCUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAAGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGGGUUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AJ006287.1/7294-7633 ACCAAGGCAAAGAGAAGAGUGGUGCAAAGAGAAAAAAGAGCAGUGGGAAUAAUAGGAGCUAUGCUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCACCUCACAGUCUGGGGCAUCAAGCAGCUCCAAGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGGGUUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF256209.1/7744-8083 ACCAAGGCAAAGAGAAGAGUGGUGCAAAGAGAAAAAAGAGCAGUGGGAAUAAUAGGAGCUAUGCUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAAGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAAUUCAUUCGCACCACUGCUGUGCCUUGGA
AF256205.1/7729-8068 ACCAAGGCAAAGAGAAGAGUGGUGCAAAGAGAAAAAAGAGCAGUGGGAAUAAUAGGAGCUAUGCUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAAGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF256206.1/7745-8081 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUGUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAAGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
L02317.1/7251-7587   ACCACGGCAAAGAGAAGAGUGGUGCAAAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUCUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGUUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
U08445.1/1467-1806   ACCAGGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGAGCACUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAACAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUAGGGAUUUGGGGAUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
U08446.1/1488-1827   ACCAAGGCAAAGAAAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGAGUACUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAACAGCUCCAGGCAAGAAUCCUGGCUAUGGAAAGAUACCUAAAGGAUCAACAGCUCCUAGGGAUUUGGGGAUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF358142.1/1495-1831 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAGACUCAUUUGCACCACUGCUGUGCCUUGGA
AF358140.1/1495-1831 AUCAAGACAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAGACUCAUUUGCACCACUGCUGUGCCUUGGA
AF358141.1/1495-1831 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAACAGCUCCAGGCAGGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAGACUCAUUUGCACCACUGCUGUGCCUUGGA
K02013.1/7312-7648   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCACGGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
U12033.1/1920-2256   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCACACGGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUAUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
L42371.1/1489-1825   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCACGGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAUCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAACAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
U26942.1/7087-7423   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGAUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAACAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF070521.1/7699-8035 ACCAAGGCAAAGAGAAGAGUCGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUCAUUGUCUGGUAUAGUGCAUCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAACAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
L31963.1/7756-8092   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF358145.1/1495-1831 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCGGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGAA
AF321145.1/1327-1663 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUGCAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
K02011.1/1705-2041   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGGCCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF033819.3/7265-7601 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCCUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
Z11530.1/7741-8077   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACCCAUUUGCACCACUGCUGUGCCUUGGA
M14100.1/1972-2308   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUACUUUGCACCACUGCUGUGCCUUGGA
U12034.1/1916-2252   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUAUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
U12036.1/1506-1842   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUAUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAUAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF189159.1/1480-1816 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGGCGCUGACGGUACAGGCCAGACAAUCAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUCUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF042101.1/7738-8074 ACUAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---CUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUAACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUCUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGACUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGAAUUUGGGGUUGCUCUGGGAAACUCAUUUGCACCACUACUGUGCCUUGGA
AF038399.1/7833-8169 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAAGCAAGAAUCCUAGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUAGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF491741.1/1986-2322 ACCAGGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGG---GAUGGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAGUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAGCAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGAAUUUGGGGCUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
U84819.1/1740-2073   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGC---A---CUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAAGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AJ418481.1/1498-1834 ACUAAGGCAAAAAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGCGGGA---CUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAGGGGAUCAACAGCUCCUGGGUAUUUGGGGUUGCUCUGGAAAACUCAUCUGCACCACUGCUGUGCCUUGGA
AF025754.1/1489-1825 ACUAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGCGGGA---CUAGGAGUUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAACAGCUCCAGGCGAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
U79722.1/1497-1833   ACCAGGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGU---AACGCUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAUUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUAGGAAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUACUGUGCCUUGGA
M38430.1/1673-2009   ACCAGGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---CUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCACGGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGAGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUACUGUGCCUUGGA
AJ417428.1/1504-1840 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---CUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAAAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGACCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AJ417427.1/1474-1810 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---CUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAAAACAAUUUGCUGAGGGCUAUUGACGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGACCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AJ417426.1/1480-1816 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGCGGGA---CUAGGAGCUGUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAAAACAAUUUGCUGAGGGCUAUUGACGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGACCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
L08657.1/1501-1840   ACCAAGGCAAAGAGAAGAGUGGUACAGAGAGAAAAAAGAGCAGUGGGAACGAUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAAGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAACAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUAGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
U34604.1/7723-8059   ACCAGGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCGUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUAACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUCUGCACCACUGCUGUGCCUUGGA
AF112547.1/1447-1786 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGAAUGUUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUAACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAAUAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAAUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUCUGCACCACUACUGUGCCUUGGA
AF217162.1/1537-1873 ACUAAGGCAAAAAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUGUGUUCCUUGGGUUCUUAGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUAACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUCUGCACCACUACUGUGCCUUGGA
AF217172.1/1552-1888 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUGUGUUCCUUGGGUUCUUAGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUAACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGACCAACAGCUCCUGGGAAUUUGGGGUUGCUCUGGAAAGCUCAUCUGCACCACUACUGUGCCUUGGA
AF217173.1/1552-1888 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUAUGUUCCUUGGGUUCUUAGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUAACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUCUGCACCACUACUGUGCCUUGGA
AJ286340.1/1537-1876 ACCAAGGCAAGGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGAACAAUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACAAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUCUGCUGAAGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUAGGGAUUUGGGGUUGCUCUGGAAAACUCAUCUGCACCACUACUGUACCUUGGA
AF025749.1/1498-1837 ACCAGGGCAAGGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGAACAAUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUAGGGAUUUGGGGUUGCUCUGGAAAACUCAUCUGCACCACUGCUGUGCCUUGGA
AF025764.1/1500-1839 ACCAAGGCAAAGAGAAGAGUGGUCCAAAGAGAAAAAAGAGCAGUGGGAACAAUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUAACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUCUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AJ418536.1/1522-1861 ACCAAGGCAAAGAGAAGAGUGGUGCAAAGAGAAAAAAGAGCAGUGGGAACAAUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAUUGACGCUGACGGUACAGGCCAGAUUAUUAUUGUCUGGUAUAGUGCAGCAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUAGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACUACUGCCGUGCCUUGGA
U69587.1/7276-7615   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGAACAAUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCCGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
U69585.1/7273-7612   ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAGGAGCAGUGGGAACAAUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCCGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AF003887.1/7736-8075 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGAACAAUAGGAGCUAUGUUCCUUGGGUUCUUGGGAGCAGCGGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUAGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUGCUGUGCCUUGGA
AJ418528.1/1477-1813 ACCCAGGCAAAGCGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGACA---UUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUACAGGAUCAACAGCUCCUGGGGAUUUGGGGCUGCUCUGGAAAACUCAUCUGCACCACUGCUGUGCCUUGGA
AJ418529.1/1477-1813 ACCCAGGCAAAGCGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGACA---UUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUACAGGAUCAACAGCUCCUGGGGAUUUGGGGCUGCUCUGGAAAACUCAUCUGCACCACUACUGUGCCUUGGA
AJ418523.1/1489-1825 UCCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGACA---UUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUACAGGAUCAACAGCUCCUGGGGAUUUGGGGCUGCUCUGGAAAACUCAUCUGCACCACUGCUGUGCCUUGGA
AJ418521.1/1489-1825 UCCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGACA---UUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGACAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUACAGGAUCAACAGCUCCUGGGGAUUUGGGGCUGCUCUGGAAAACUCAUCUGCACCACUGCUGUGCCUUGGA
AF025760.1/1479-1815 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUUUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUCUGGGGUUGCUCUGGAAAACUCAUCUGCACCACUACUGUGCCUUGGA
AF025756.1/1480-1816 ACUAAGGCAAAGAGAAGAGUGGUGCAAAGAGAAAAAAGAGCAGUAGGA---AUAGGAGCUGUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUACUGUGCCUUGGA
AF025751.1/1486-1822 ACCAAGGCAAAAAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUGUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUAGGGAUUUGGGGUUGCUCUGGAAAACUCAUUUGCACCACUACUGUGCCUUGGA
AJ418518.1/1549-1885 ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUGUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAGCUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAGGGAUCAGCAGCUCCUGGGGAUUUGGGGUUGCUCGGGAAAACUCAUCUGCACCACUGCUGUGCCUUGGA
M77230.1/717-1053    ACCAAGGCAAAGAGAAGAGUGGUGCAGAGAGAAAAAAGAGCAGUGGGA---AUAGGAGCUGUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCAAUAACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUGAGGGAUCAACAGCUCCUGGGGAUAUGGGGUUGCUCUGGAAAACUCAUCUGCACCACUGCUGUGCCUUGGA
AF041133.1/1483-1819 ACCAAGGCAAAGAGAAGAGUGGUGCAGAAAGAAAAAAGAGCAGUGGGG---AUAGGAGCUGUGUUCCUUGGGUUCUUGGGAGCAGCAGGAAGCACUAUGGGCGCAGCGUCACUGACGCUGACGGUACAGGCCAGACUAUUAUUGUCUGGUAUAGUGCAACAGCAGAACAAUUUGCUGAGGGCUAUUGAGGCGCAACAGCAUCUGUUGCAACUCACAGUCUGGGGCAUCAAGCAGCUCCAGGCAAGAGUCCUGGCUGUGGAAAGAUACCUAAAGGAUCAACAGCUCCUGGGAAUUUGGGGUUGCUCAGGAAAACUCAUCUGCACCACUGCUGUGCCUUGGA
#=GC SS_cons         :[[[[[[[[--------[[[[[[[-[[[[[[-----[[[[[[[[[---...[[[[[[[[[----[[[[[[[[[[[[[----[[[[[[,,,,((((((<<--<<<<<<<<_____>>>>>>->>--->>,<<<<<<<<<___>>>>>>>>>,)))))),,<<<<<<<____>>>>>>>((((((,,,<<<--<<<<<<<___>>>>>>>-->>>,,<<<<<<<<<<________>>>>>>>>>>,,))))))]]]]]]---]]]]-]]]]]-]]]]-----]]]]]]]]]--------]]]]]]]]]------]]]-]]]-]]]]]]]----]]]]]]]]:
#=GC RF              AccaaGGCaAAGAGAAGaGuGGuGcagaGaGAAAAAaGaGcagccggA...ccaGGaGcuuUGuuccuugGGuucuuGGGAgCaGccGGAAGcacuauGGGcGcaGcGucAAUgaCgCugACgGUACaGgCcaGacaaUUAuuguCugGcAuagugCAacaGcagaAcAAucugCugaGGgcuAUUGaGGcGcaacaGcAUCuguugCAACuCAccGccuGGgGcAUcAAgcAgCcCCaggCgAGagcCCuggCuGcGGAaagaUaCCcaAaggaUcAAcagCuCCuggGgAUUUGGggcugCuCuGGAAAACuCAucuGCaCCaCugcUGuGCCuuggA
//
# STOCKHOLM 1.0

#=GF AC   RF00037
#=GF ID   IRE_I
#=GF PI   IRE I; IRE; ferritin
#=GF DE   Iron response element I
#=GF AU   Stevens S
#=GF AU   Gardner P; 0000-0002-7808-1213
#=GF AU   Brown C
#=GF SE   Leipuviene, R. and Theil, E.C.
#=GF SS   Published; PMID:17849083
#=GF GA   34.00
#=GF TC   34.00
#=GF NC   33.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.44 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   GO; 0010039; response to iron ion;
#=GF DR   SO; 0004725; regulatory_region;
#=GF RN   [1]
#=GF RM   3685996
#=GF RT   Identification of the iron-responsive element for the translational
#=GF RT   regulation of human ferritin mRNA.
#=GF RA   Hentze MW, Caughman SW, Rouault TA, Barriocanal JG, Dancis A, Harford JB,
#=GF RA   Klausner RD
#=GF RL   Science. 1987;238:1570-1573.
#=GF RN   [2]
#=GF RM   18160403
#=GF RT   Ferritin L and H subunits are differentially regulated on a
#=GF RT   post-transcriptional level.
#=GF RA   Sammarco MC, Ditch S, Banerjee A, Grabczyk E
#=GF RL   J Biol Chem. 2008;283:4578-4587.
#=GF RN   [3]
#=GF RM   11903622
#=GF RT   Repression of Manduca sexta ferritin synthesis by IRP1/IRE interaction.
#=GF RA   Zhang D, Albert DW, Kohlhepp P, D-Pham DQ, Winzerling JJ
#=GF RL   Insect Mol Biol. 2001;10:531-539.
#=GF RN   [4]
#=GF RM   12429122
#=GF RT   Structured RNA upstream of insect cap distal iron responsive elements
#=GF RT   enhances iron regulatory protein-mediated control of translation.
#=GF RA   Nichol H, Winzerling J
#=GF RL   Insect Biochem Mol Biol. 2002;32:1699-1710.
#=GF RN   [5]
#=GF RM   10070739
#=GF RT   An atypical iron-responsive element (IRE) within crayfish ferritin mRNA
#=GF RT   and an iron regulatory protein 1 (IRP1)-like protein from crayfish
#=GF RT   hepatopancreas.
#=GF RA   Huang TS, Melefors O, Lind MI, Soderhall K
#=GF RL   Insect Biochem Mol Biol. 1999;29:1-9.
#=GF WK   Iron_response_element
#=GF SQ   61


Y09188.1/1-35                CU-G-UCUCUUGCUUCAACAGUGUUUGGACGGA-ACAG
M14211.1/193-227             GG-G-UUUCCUGCUUCAACAGUGCUUGGACGG-AACCC
AY032659.1/108-140           UC----GCC-UUCUGCACCAGUGUGUGUAAAGGCCUGA
AB099065.2/27-62             CG-G-UUUCCUGCUUCAACAGUGCUUGAACGGNAACCG
AANN01127411.1/370-404       CU-G-UUUCUUGCUUCAACAGUGUUUGGACGG-AACAG
AAIY01636926.1/362-328       CU-G-UGUCCUGCUUCAACAGUGUUUGAACGGA-ACAG
ABGA01194773.1/10307-10273   GG-G-CUUCCUGCUUCAACAGUGCUUGAACGGAA-CCC
ABRN01304445.1/359-393       CU-G-UCUCUUGCUUCAACAGUGUUUGAACAGA-ACAG
AAPN01199084.1/201-236       CG-G-UUUCCCGCUUCAACAGUGCUUGGACGGAAGCCG
AAQQ01605438.1/3746-3780     CU-G-CUUCUUGCUUCAACAGUGUUUGGACGGAA-CAG
BAAE01241509.1/2881-2846     GA-A-GUUCUUGCUUCAACAGUGUUUGAACGGAACUUC
D15071.1/10-45               CG-G-UUUCCUGCUUCAACAGUGCUUGGACGGAACCCG
AB371410.1/64-99             CG-G-UUUCUUGCUUCAACAGUGCUUGGACGGAAGCCG
ABDC01086142.1/996-1030      CU-G-UCUCCGGCUUCAACAGUGUUUGGACGGA-ACAG
AAGV020889339.1/949-914      UG-G-UUUCCUGCUUCAACAGUGCUUGAACGGAACCCA
AAWR02009010.1/38752-38718   UG-G-UUUCCUGCUUCAACAGUGCUUGAACGG-AACCG
AB073371.1/2-37              CG-G-UCUCCUGCUUCAACAGUGCUUGGACGGAGCCCG
ABVD01450449.1/988-1023      UG-G-GUUCCUGCUUCAACAGUGCUUGAAUGGAACCCA
ABRT010002577.1/1339-1305    CU-G-UCUCUUACUUCAACAGUGUUUGGAUGGA-ACAG
AF266195.1/11-46             GA-G-AUUCUUGCUUCAACAGUGUUUGAACGGAAUUUC
ABQO010588503.1/1800-1767    GG-G-UUUCCUGCUUCAACAGUGCUUGAACGG-A-CCC
ABRP01011077.1/2966-3000     UU-G-UCUCUUGCUUCAACAGUGUUUGGACAGA-ACAG
ABRR01372656.1/429-395       CU-G-UCUCUUGUUUCAACAGUGUUUGGACAGA-ACAG
AAFR03019774.1/239510-239545 GA-G-GUUCUUGCUUCAGCAGUGUUUGGACGGAACCUC
BT075303.1/10-45             AG-G-UUACCUGCUUCAACAGUGCUUGAACGGCAACCU
BX934496.1/23-58             CG-G-GUUCCUGCGUCAACAGUGCUUGGACGGAACCGG
AAPY01271888.1/1826-1792     CG-G-UUUCCUGCAUCAACAGUGCUUGAACGG-AACCG
M55010.1/4-39                AG-A-GUUCUUGCUUCAACAGUGUUUGAACGGAACCCU
AANG01554495.1/4632-4598     CU-G-UCCCUUGCUUCAACAGUGUUUGGACAGA-ACAG
ABRO01415732.1/1669-1703     CU-G-UGUCUUGCUUCAACAGUGUUUGGACAG-CACAC
AANH01004160.1/35803-35838   GG-A-GUUCUUGCUUCAACAGUGUUUGAACGGAACUUU
AANU01126896.1/12416-12450   CU-G-UAUCUUGCUUCAACAGUGUUUGGAUGGA-ACAG
BT047622.1/7-41              -G-G-GUUCUUGCUUCAACAGUGAUUGAACGGAACUCC
ABRQ01098844.1/1724-1759     CG-G-UGUCCUGCUUCAACAGUGCUUGAACGGAACCCG
AALT01281908.1/825-859       CU-G-UCUCUUGCUUCAACAAUGUUUGGACGGA-GCAG
BC152596.1/22-57             GA-G-GUUCUUGCUUCAACAGUGAUUGAACGGAACUUC
AAYZ01376712.1/735-701       CU-G-UGUCUUGCUUCAACAGUGUUUGAAUGGA-ACAG
AF285177.1/2-35              UG----UUCCUGCUUCAACAGUGCUUGGACGGAACCCG
AJ276505.2/120813-120779     CU-G-UGUCUUGCUUCAACCGUGUUUGGACGGA-ACAG
BT073905.1/31-66             GA-A-GUUCUUGCUUCAACAGUGAUUGAACGGAACUCC
DQ437112.1/26-59             AG----UUCUUGCUUCAACAGUGAUUGAACGGAACACU
AAHY01029141.1/15302-15336   CU-G-UGUCUUGCUUCAACAGUGUUUGGACGAA-ACAG
AF068225.2/1-36              CG-G-UGUUUUGCUUCAACAGUGUUUGAACGAGCAUCG
DQ659631.1/11-46             GU-U-GUUCUUGCUUCAACAGUGUUUGAACGGAACUUC
BC063337.1/26-62             CGCA-GUUCUUGCUUCAACAGUGCUUGAACGGAACUCG
EF628371.1/43-77             GA-G-GGUCUUGCUUCAACAGUGAUUGAACGGA-ACUC
ABAV01011851.1/25472-25507   CC-G-UUUUGUGCUUCAACAGUGAUUGAACCGAAACAG
BT081799.1/21-57             CC-GAGUUCUUGCUUCAACAGUGAUUGAACGGAGCCGG
ABQF01062964.1/539-575       CC-GCGUUCUCGCUUCAACAGUGCUUGAACGGAACCGG
AAVX01381105.1/393-360       UG----UUCUCGCUUCAACAGUGCUUGAACGGAACUGG
AY260753.1/1-34              ---G-UUACCUGCUUCAACAGUGCUUGAACGGCAACCU
AY277900.1/12-47             CG-A-UGUUAUGCUUCAACAGUGAUUGAACGAGCAUCG
AY550979.1/1-34              UG----GUUUUGCUUCAACAGUGAUUGAACGAGCAUCG
AAGE02004546.1/6487-6454     AG-G-UGUUUUGCUUCAACAUUGUUUGAACGA-C-CGU
AAWZ02023447.1/15493-15528   UG-G-GUUCUUGCUUCAACAGUGUUUGAACGGGACCCG
AL592437.7/34848-34882       CU-G-UUCCUUGCUUCAACAGUGUUUGGAUGG-AACAG
AAGU03011944.1/23235-23201   CU-G-UUUCUUGCUUCAACAGUGCUUGGACGG-AGCAG
AAGW02057904.1/76866-76900   CU-G-UGUCUUGCCUCAACAGUGUUUGAACGGA-ACAG
AAQR03095747.1/6073-6108     CA-G-UUUCCUGCUUCAACAGUGCUUGGACGGAAACGG
AAHX01094585.1/10740-10774   CU-G-UAUCUUGCUUCAACAGUGUUUGGACAGA-ACAG
AAPE02030929.1/24760-24794   UG-G-UUUCCUGCUUCAACAGUGCUUGGACGG-AACCA
#=GC SS_cons                 <<.<.<<<<<-<-<<<<<<___>->>>>>>>>>>>>>>
#=GC RF                      Cg.G.uUUCUUGCUUCAACAGUGUUUGAACGGAAaCcG
//
# STOCKHOLM 1.0

#=GF AC   RF00038
#=GF ID   PrfA
#=GF DE   PrfA thermoregulator UTR
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD
#=GF GA   88.00
#=GF TC   109.40
#=GF NC   81.40
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   12230973
#=GF RT   An RNA thermosensor controls expression of virulence genes in Listeria
#=GF RT   monocytogenes.
#=GF RA   Johansson J, Mandin P, Renzoni A, Chiaruttini C, Springer M, Cossart P
#=GF RL   Cell 2002;110:551-561.
#=GF CC   In Listeria monocytogenes, virulence genes are maximally expressed at 37
#=GF CC   degrees C, almost silent at 30 degrees C and controlled by PrfA, a
#=GF CC   transcriptional activator whose expression is thermoregulated. It has been
#=GF CC   shown that the untranslated mRNA (UTR) preceding prfA, forms a secondary
#=GF CC   structure, which masks the ribosome binding region [1]. This family also
#=GF CC   contains UTRs from other closely related bacteria. The secondary structure
#=GF CC   of this motif forms a hairpin. The Shine-Dalgarno (SD) sequence is partly
#=GF CC   masked by the most conserved stem of the secondary structure. It is
#=GF CC   thought that at 37 degrees C the SD sequence is unmasked [1].
#=GF WK   PrfA_thermoregulator_UTR
#=GF SQ   11


AL591974.1/4468-4339 UGUAAAAAACAUCAUUUAGCGUGACUUUCUUUCAACAGCUAACAAUUGUUGUUACUGCCUAAUG---UUUUUAGGGUA-UUUUAAAAAAGGGCGAUAAAAAACGAUUGGGGGAUGA-GACAUGAACGCUCAAGCA
M24199.1/139-10      UGUAAAAAACAUCAUUUAGCGUGACUUUCUUUCAACAGCUAACAAUUGUUGUUACUGCCUAAUG---UUUUUAGGGUA-UUUUAAAAAAGGGCGAUAAAAAACGAUUGGGGGAUGA-GACAUGAACGCUCAAGCA
M55160.1/297-426     UGUAAAAAACAUCAUUUAGCGUGACUUUCUUUCAACAGCUAACAAUUGUUGUUACUGCCUAAUG---UUUUUAGGGUA-UUUUAAAAAAGGGCGAUAAAAAACGAUUGGGGGAUGA-GACAUGAACGCUCAAGCA
X54618.1/1184-1313   UGUAAAAAACAUCAUUUAGCGUGACUUUCUUUCAACAGCUAACAAUUGUUGUUACUGCCUAAUG---UUUUUAGGGUA-UUUUAAAAAAGGGCGAUAAAAAACGAUUGGGGGAUGA-GACAUGAACGCUCAAGCA
X61210.1/159-288     UGUAAAAAACAUCAUUUAGCGUGACUUUCUUUCAACAGCUAACAAUUGUUGUUACUGCCUAAUG---UUUUUAGGGUA-UUUUAAAAAAGGGCGAUAAAAAACGAUUGGGGGAUGA-GACAUGAACGCUCAAGCA
X72685.1/1303-1435   UGUAAAAAACAUUAUUUAGCGUGAUUUUCUAUCAACAGCUAACAAUUGUUAUUAGUGCCUAGCGCAAUCAUAAGGAUAAUUUUUCAAAAAGGCUAUAAAAA-CGAUUGGGGGAUGA-AAAAUGGACGCUCAAGCA
X97014.1/5134-5003   AAGUAAAUACAUGGCAGAGAGUCG-UUUCUAACAAAAACUAACAAUUGUUAUUGCUGUCUAAGCU--UCAAAAGGGUAAUUUUAAAAUGGGAAGUUAAAGAACAAUUGGAGGAUGACGAUGUGAGCACUAAAGCA
AJ002742.1/161-290   UGUAAAAAAUAUUAUUUAGCGUGACUUUCUUUCAACAGAUAACAAUUGUUGUUACUGCCUAAUG---UUUUUAGGGUA-UUUUAAAAAAGGGCGAUAAAAAACGAUUGGGGGAUGA-GACAUGAACGCUCAAGCA
AJ132962.1/66-198    UGUAAAAAACAUUAUUUAGCGUGAUUUUCUAUCAACAGCUAACAAUUGUUAUUAAUGCCUAGCGCAAUCAUAAGGAUAAUUUUUCAAAAAGGCUAUAAAAA-CGAUUGGGGGAUGA-AAAAUGGACGCUCAAGCA
AJ132963.1/66-198    UGUAAAAAACAUUAUUUAGCGUGAUUUUCUAUCAACAGCUAACAAUUGUUAUUAAUGCCUAGCGCAAUCAUAAGGAUAAUUUUUCAAAAAGGCUAUAAAAA-CGAUUGGGGGAUGA-AAAAUGGACGCUCAAGCA
AJ132964.1/66-198    UGUAAAAAACAUUAUUUAGCGUGAUUUUCUAUCAACAGCUAACAAUUGUUAUUAAUGCCUAGCGCAAUCAUAAGGAUAAUUUUUCAAAAAGGCUAUAAAAA-CGAUUGGGGGAUGA-AAAAUGGACGCUCAAGCA
#=GC SS_cons         :::::::::::::::::<<<<---------------------<<<<<<<<-------<<______.._______________________>>------->>->>>>>>--------.-------->>>>::::::
#=GC RF              UGuAAAAAACAUuAUUuAGcGUgAuUUUCUaUCAAcAGCUAACAAUuGUuaUUAcUGcCUAaugu..UuaUaAGGgUAAUUUUaaAAAAgGgcgAUAAAaAACgAUUGGGGGAUGA.gAaAUGaACgCUcAAGCA
//
# STOCKHOLM 1.0

#=GF AC   RF00039
#=GF ID   DicF
#=GF DE   DicF RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   48.00
#=GF TC   49.50
#=GF NC   46.00
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF RN   [1]
#=GF RM   7508908
#=GF RT   Division inhibition gene dicF of Escherichia coli reveals a widespread
#=GF RT   group of prophage sequences in bacterial genomes.
#=GF RA   Faubladier M, Bouche JP
#=GF RL   J Bacteriol 1994;176:1150-1156.
#=GF RN   [2]
#=GF RM   1372677
#=GF RT   Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense
#=GF RT   RNA. Division does not require a fixed number of FtsZ molecules.
#=GF RA   Tetart F, Bouche JP
#=GF RL   Mol Microbiol 1992;6:615-620.
#=GF RN   [3]
#=GF RM   2477663
#=GF RT   Genetic evidence that DicF, a second division inhibitor encoded by the
#=GF RT   Escherichia coli dicB operon, is probably RNA.
#=GF RA   Bouche F, Bouche JP
#=GF RL   Mol Microbiol 1989;3:991-994.
#=GF RN   [4]
#=GF RM   28874523
#=GF RT   Escherichia coli responds to environmental changes using enolasic
#=GF RT   degradosomes and stabilized DicF sRNA to alter cellular morphology.
#=GF RA   Murashko ON, Lin-Chao S
#=GF RL   Proc Natl Acad Sci U S A. 2017;114:E8025.
#=GF CC   DicF RNA is an antisense inhibitor of cell division gene ftsZ [1]. DicF
#=GF CC   and Hfq are necessary to reduce FtsZ protein levels, leading to cell
#=GF CC   filamentation under anaerobic conditions.[4]
#=GF WK   DicF_RNA
#=GF SQ   5


AF370716.1/3656-3603       UGUGUGUAGUACUUGGCGGCAUCAGUUUUUCUUAGUCCUUUCUGAUGU-CCGCCC
BA000007.2/1165782-1165731 UUCUGGUGACAUUUGGCGGUAUCAGUUUUACUCCGUA---ACUGCUCUGCCGCCC
BA000007.2/2250671-2250722 UUCUGGUGACGUUUGGCGGUAUCAGUUUUACUCCGUG---ACUGCUCUGCCGCCC
BA000007.2/2201445-2201496 UUCUGGUGACGUUUGGCGGUAUCAGUUUUACUCCGUG---GCUGCUCUGCCGCCC
D84432.1/195877-195831     UUUGUGU-GUCUUUGGUGGCAUCAGU---AAUCUAAU---AC-GAUUUGCCACCU
#=GC SS_cons               ::::::::::::::<<<<<<<-<<<<___________...>>>>--->>>>>>>:
#=GC RF                    UUuuuGUGauaUUUGGCGGuAUCAGuUUUACUCcGUu...aCUGaUcUgCCGCCC
//
# STOCKHOLM 1.0

#=GF AC   RF00040
#=GF ID   rne5
#=GF DE   RNase E 5' UTR element
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, Moxon SJ
#=GF SS   Published; PMID:10817759
#=GF GA   180.00
#=GF TC   182.80
#=GF NC   170.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   10817759
#=GF RT   An evolutionarily conserved RNA stem-loop functions as a sensor that
#=GF RT   directs feedback regulation of RNase E gene expression.
#=GF RA   Diwa A, Bricker AL, Jain C, Belasco JG
#=GF RL   Genes Dev 2000;14:1249-1260.
#=GF CC   This family represents a conserved element found in the 5' UTR of RNase E
#=GF CC   mRNA. RNase E is a key regulatory enzyme in the pathway of mRNA
#=GF CC   degradation in E. coli that is able to auto-regulate the degradation of
#=GF CC   its own mRNA in response to changes in RNase E activity. This rne 5' UTR
#=GF CC   element acts as a sensor of cellular RNase E concentration enabling tight
#=GF CC   regulation of RNase E concentration and synthesis.
#=GF WK   RNase_E_5'_UTR_element
#=GF SQ   6


BX950851.1/2038367-2038030 UUUCCCACGCGGA--UUUCCGAUAAACAAGGGGAAAUU---GCGAAGUUAC----------------------------------------------------------------------------------UAAAU--UUGCCUGAUAACGCACAC-ACGCAGCAAUGGCGUAAGACGU-AAUGCGAA-AUCAAGCAG-UUAGCGGGCUGUGGAUUGCAGC-UUGGCCGGCAAAU---GGAAUCAGAUCUGG-CGACAU-UAU--UCAGAAGCUGUUCCCUCAGUA-AAUGCGCUGU-UUUC-CAUCAGGAAA-UACAGGCU-ACCGA-AACA-UGCGUCUCUAUGCA--GGCGACAACCGGGAGGUUGACGUCCCUGCGAUAAGCCACGAGGCCAUCGGUUC--ACUCCGGUCAUGCGGUUCU-----UUUUGUCCGCAGCUCUAUCAAUAA
AL627269.1/129907-129570   GUUUCCGCACCGAAACUUGU--UAAA---ACAAAAAGUUUAGCGGAAUAAC----------------------------------------------------------------------------------CCAUU--UUGUCUGA-CCGAUCAUCAACGCAGCAAUGGCGUAAGACGUAUUGAUUUU--UCAGACAG-UUAGCGGGCUGCGGGUUGCAGUCCUUACCGGUAGAU---AGGAUCUUCUCUGG-AGAGUAAUGC--CCAGG-CUGCUUCCCUGAUA--AUUGCGCUGUGUUUC-CGUAU-GAAA-UACAGGCA-ACCGA-CACUCUGCGCCUCUUUGAGCUGACGAUAACCGUGAGGUUGGCGACGCGA--AAUAGUCACGAGGCCAUCGGUUCAUGC-CCGGUAA-GGCGUCAC-----CAU-GCCCGCAGCUUAGUCGUCAA
AF259267.1/37-374          AAUUCUACGUUGA--UUCUCGUUAGACC-AAGAGACUU---GUGGAAUAAU----------------------------------------------------------------------------------AAACU--UUGCCUGAUCACACAAAA-ACGCGGCAAUGGCGUAAGACGU-AAUGUGAA-AUCAAGCAA-UUAGCGGGCUGCGGGUUGCAGC-UUGGCCGGCAAGU---GGGUAAAGCUCUGU-UGUCUUAAAU--UCAGAAGC-UACCCUUUAUAUAAAAGCGCUGUUUUUC-AGAAC-GAAA-CACAGGCUUACCGA-AAUAAUGCGCCCCUAUGCA--GGCGACAACCGUGAGGUUGACGGCUUAGCUAGAAGACUCGGGGCCAUCGGUUU--AC-CCGGUCAUGAGGUUAU-----UUU-GCCCGCAGUUCUAACGCCAA
AF259268.1/36-432          CUGCCAA----GA--UGUU---UAAA----AACGAAAA----UUGGCUUUGCUAUGUUAGCUUUAGGUGUUUUUGCACUUUCAGCUAUAAUUAUUUUUAGCUAGUAGAAUACAAGUUAGACGUAAUACUGUAGGAAUUUAUUAUUUGAUGGCGU-AACGAUGCUGCAAUGGCGUAAGACAUCUA-AC-AAGAUCAAGUAAAUUAGCGAGCAACGAA-UUUU-----AGCU-UAUUGGGUUGGG-AGUCUCCGUUUUCUAAGAAAU-UUACGGCA--UCCUGAUUA----AGAACGCUGAAUUUUUAAUCUAAAAA--UCAGGUUCACCGAAUACUGCGCGUCUCUAUACG--AACGACUGCCGAGAGGUAGACGGCUUUG-UAAAAAUCAUGAGGCCAUCGGUUUACAGU--AGCU-----CUUUC-----U----UUCGCUGCUCUUU--AUUA
BX571868.1/245396-245719   CAGUUUU--UUAA--UCCU---GAAU----GGCGAAGU----UAAACGUUU----------------------------------------------------------------------------------GUUCU--UCAUUUGAUUGCACAAAA-ACGCAGCAAUGGCGUAAGACGU-ACUGGGAA-AUCAAAUAA-UUAGCGGGCUACGGGUAGCAGA-U-UACUGGAAU-----CGGAUCAAAUCAGCUUCAUUUAUAUUUGCAGA--UUAUUCCUAGAAA--AGGGUACUGU-UUUC-UAAGU-GAAAAUUCAGACCUGCCGA-AAAUAUGCGUCUCUAUACA--AACGACAACCGGGAGGUUGGCGGAUUUG-UAAAAGACACGAGACCAUCGGU-U--A--CCAGUC----GCUCAUCUAUAUUU-GCCCGUAGCUCUAUAACUAA
AF259269.1/38-376          CUUUCCGCGUUGA--UUCUCGUUAAACA-GGGAAAACG---GUGGAAUUAU----------------------------------------------------------------------------------AAAAU--UUGUCUGAUCGCGCAAAA-ACGCAGCAAUGGCGUAAGACGU-AAUGCGAA-AUCAAACAA-UUAGCGGGCUGCGGGUUGCAGC-UUGGCCGGCAAAU---GGAAUCAGAUCUG-UCGACGUAAAU---CAGAGGCUAUUCCCCUAGUA-AAAGUGCUGUCUUUC-ACAAA-GAAA-AGCAGGCUUACCGA-GAUAAUGCGCCCCUAUGCA--GGCGACAACCGUGAGGUUGACGACUUUGCGAGAAGACACGGGGCUUUCGGUUUA-ACUCCGGCCAUGAGGUUAU-----UUU-GCCCGCAGCUUUGUCGAUAA
#=GC SS_cons               ::<<<<<<-----..<<<<<..____...>>>>>----...>>>>>>,,,,..................................................................................,,,,,..<<<<<<<<---<<<<---.<<<--<<____>>------>>>.-->>>>--.->>>>>>>>.-----(((((((((((------.-(((((((,,,,,...<<<<<----<<<<<___________..>>>>>---->>>>>,,,,,,..,,<<<-<<<<-<<<<._____.>>>>.->>>>>>>,<<<<<.--------<<<<<------..--<<-<<<<<____>>>>>->>------.---------->>>>>-->>>>>,,,.,,,))))))).--------.....---.))))))))))):::::::::
#=GC RF                    cugcccgCguuGA..cgccc..UAAA...gggcgAAau...GcgggcUuau..................................................................................aaAuU..uugccUGAUugcgcaAAc.AcGCaGCAAUGGCGUAAGACgU.aaugcgAA.AUCAggcaa.UUAGCGgGCugCGGguUgcaGu.uuggCcGGaauau...gGgaccauacCgggUugaauuAaAU..cccGgaauugucCcuuuAua..AagGcGCUGuaUUUc.aauau.gAAA.uaCAGgCcuaCCGA.aAcuauGCGcCuCUAUaca..aaCGACaaCCGuGAGGuuGaCGgCuUuG.uAaAAguCAcGaGgCCAUCGGuUUA.AcUCCgGcca.GaggUuau.....UuU.gcCCGcaGCuCUaUcgaUaA
//
# STOCKHOLM 1.0

#=GF AC   RF00041
#=GF ID   Entero_OriR
#=GF DE   Enteroviral 3' UTR element
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:9862969
#=GF SS   Predicted; PFOLD
#=GF GA   80.00
#=GF TC   83.20
#=GF NC   78.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0039703; RNA replication;
#=GF RN   [1]
#=GF RM   9862969
#=GF RT   Structural requirements of the higher order RNA kissing element in the
#=GF RT   enteroviral 3'UTR.
#=GF RA   Wang J, Bakkers JM, Galama JM, Bruins Slot HJ, Pilipenko EV, Agol VI,
#=GF RA   Melchers WJ
#=GF RL   Nucleic Acids Res 1999;27:485-490.
#=GF CC   This RNA structure is found in the 3' UTR of various enteroviruses. The
#=GF CC   overall structure forms the origin of replication (OriR) for the
#=GF CC   initiation of (-) strand RNA synthesis [1]. Pseudoknots have also been
#=GF CC   predicted in this structure [1].
#=GF WK   Enteroviral_3'_UTR_element
#=GF SQ   60


AY302558.1/7298-7418 AAGUGGUUAGAUUCUUUCUAAA--UUAGAG-GCAAUUUGAA----AUAAUUUAAA-UUAGCUCAACCCUACUGCACUUACCGAACUAGAUAACGGUGUAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AF231765.1/7280-7400 AAGUGGUUGGACUCCUUUUAGA--UUAGAG-ACAAUUUGAA----AUAAUUUAGA-UUGGCUUAACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
D00627.1/7329-7452   AAGUGGUUGGACUCUUUCUAAA--UUAGAG-ACAAUUUGAA----CUGAUUUGAA-UUGGCUCAACCCUACUGUACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAGG-------
AF311939.1/7276-7397 AAGUGGCUAGACUCUUUUUAAAU--UAGAGCACAAUUUGGU----UUAAUUCCAA-UUGGCUUAACCCUACCACACUCACCGAACUAGAUAACGGUGUGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AF465517.1/7298-7418 AAGUGGUUAGAUUCUUUCUAAA--UUAGAG-GCAAUUUGAA----AUAAUUUAAA-UUAGCUCAACCCUACUGCACUUACCGAACUAGAUAAUGGUGUAGUAGGGGUAAAUUCUCCGCGUUCGGUGCGG----------
AY186748.1/7251-7372 AAGUGGUUGGACUCUUUUUAAA--UUAGAG-ACAAUUUGAA----ACAAAUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGG---------
AY302541.1/7317-7437 AAGUGGUUGGACUCUUUCUAAA--UUAGAG-ACAAUUUGAU----UUUAUUUGAA-UUGGCUCAACCCUACUGCACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AF029859.2/7278-7397 AAGUGGUUGGACUCCUUCUAAAA-UUAGAGCACAAUUAGUA--------GAUUAAAUUGGCUUAACCCUACCGCAUGAACCGAACUUGAUAAAAGUGCGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
X84981.1/7301-7420   AAGUGGUUGGACUCCUUCUAAA--GUAGAG-ACAAUUUGAU----CUAACUUGAA-UUGGCUUAACCUUACUGCACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCG-----------
AF114383.1/7280-7400 AAGUGGUUGGACUCUUUCUAAA--UUGGAG-ACAAUUUGAG----AUAAUUUGAA-UUGGCUUAACCCUACCGCACUAACCGAACUAGAUAACGGUGCGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
K02709.1/1396-1514   AAGUGGUUGGACUCCUUUUAGA--UUAGAG-ACAAUU-GAA----ACAAUUUAGA-UUGGCACAACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCG-----------
X92886.1/7332-7451   AAAUGGUUGGACUCCUUUUAAGA-UUAGAGCUCAAUUUGUA-----AUUUAUAA--UUGGCUUAACCCUACCGCAUGAACCGAACUUGAUACAAGUGCGGUAGGGGUAAAUUCUCCGCAUUCGGUGCG-----------
U16283.1/7297-7417   AAGUGGUUAGAUUCUUUCUAAA--UUAGAG-GCAAUUUGAA----AUAAUUUAAA-UUAGCUCAACCCUACUGCACUUACCGAACUAGAUAAUGGUGUAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
D10582.1/4105-4224   AAGUGGUUGGACUCUUUUUAAA--CUAGAG-ACAAUUUGAA----CUAAUUUGAA-UUGGCUUAACCCUACUGCACUUACCGAACUAGAUAACGGUGUAGUAGGGGUAAAUUCUCCGCAUUCGGUGCG-----------
AJ577590.1/7312-7433 AAGUGGUUAGACUCCUUCUAAAAAUUAGAGUACAAUUAAUG------AACUAUAA-UUGGCUUAACCCUACCGCAUGAACCGAACUUGACAAAAGUGCGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302553.1/7308-7428 AAGUGGUUAGACUCUUUCUAAA--UUGGAG-GCAAUUUGAA----AUAAUUUAAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302545.1/7315-7435 AAAUGGUUGGACUCUUUUUAAA--UUAGAG-ACAAUUUGAA----AUAAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGAUAACGGUACGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
S76772.1/7276-7397   AAGUGGCUAGACGCUUUUUAAAU--UAGA-CACAAUUUGGU----UUAAUUCCAA-UUGGCUUAACCCUACUGCACUCACCGAAGUAGAUAACGGUGUGGUCGGGGUAAAUUCUCCGCAUUCGGUGCGGA---------
AJ577594.1/7312-7433 AAGUGGUUAGACUCCUUCUGAAA-UUAGAGUACAAUUAAUG------AACUUCAA-UUGGCUCAACCCUACCGCAUGAACCGAACUUGACAAAAGUGCGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGG---------
AY302557.1/7274-7394 AAGUGGUUGGACUCCUUCUAAA--UUAGAG-ACAAUUUGAU----CUAAUUUGAA-UUGGCUUAACCCUACUGCACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302549.1/7306-7426 AAGUGGCUGGAUUCCUUCUAAA--UUAGAG-GCAAUUCGAU----UAAAUCUGAA-UUGGCUUAACCCUACUGCGCUAACCGAACUAGAUAAUGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
X77708.1/7303-7433   AAAUGGCUGGAUUCCUUUUAAA--UUAGAG-ACAAUUUGAA----AUAAUUUAAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGACAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGAAAAAAAAAAA
AF311938.1/7320-7445 AAGUGGCUAGACUCUUUUUAGAU--UAGAGUACAAUUAUAUAAUUUUAAUUUUAA-UUGGCUUAACCCUACCACACUUACCGAACUAGACAACGGUGUGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AF230973.1/7287-7416 AAAUGGUUGGACUCUUUUUAGA--UUAGAG-ACAAUUUGAA-----UAAUUUAAA-UUGGCUUAACCCUACUGCAUUAACCGAACUAGACAACAAUGCAGUAGGGGUAAAUUUUCCGCGUUCGGUGCGGAAAAAAAAAA
AF465516.1/7307-7427 AAGUGGUUGGACUCUUUUUAAA--UUAGAG-ACAAUUUAAA----CUAAUUUGAA-UUGGCUUAACCCUACUGCACUAACCGAACUAGAUAACGGCGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302540.1/7330-7450 AAAUGGUUGGAUUCCUUCUAAA--UUAGAG-GCAAUUUACA----UUAAUUGAAA-UUGGCUUGACCCUACUGCACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
D16364.1/7281-7401   AAGUGGUUGGACUCCUUUUAAAA-UUAGAGCACAAUUAGUC------AAUCAUAA-UUGGCUCAACCCUACCGCAUGAACCGAACUUGAUAAAAGUGCGGUAGGGGUAAAUUCUCCGUAUUCGGUGCGG----------
AF328683.1/7272-7392 AAGUGGUUGGACUCCUUCUAAAU-UUAGAGUACAAUUAGUA-----GAUUAC-AA-UUGGCUUAACCCUACUGCACGAACCGAACUUGAUAUAAGUGCGGUAGGGGUAAAUUCUCCGCGUUCGGUGCGG----------
AF083069.1/7313-7433 AAAUGGUUGGACUCUUUCUGAA--UUAGAG-ACAAUUUGAA----AUAAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302560.1/7291-7411 AAAUGGUUGGACUCCUUCUAAA--UUAGAG-ACAAUUUGAA----ACAAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302552.1/7307-7427 AAAUGGUUGGACUCUUUCUAAA--UUGGAG-ACAAUUUAAA----ACAAUUUGAA-UUGGCUUGACCCUACUGUACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AF524867.1/7334-7453 AAAUGGUUGGACUCUUUUUAAGU--UAGAG-ACAAUUUGGU----ACAACUUAAA-UUGGCUUAACCCUACCGCACUUACCGAACUAGACAAUGGUGCGAUAGGGGUAAAUUCUCCGCAUUCGGUGCG-----------
AF039205.1/7278-7398 AAGUGGUUGGAUUCCUUCUAAA--UUAGAG-ACAAUUCGAU----AAAAUUUGAA-UUGGCUUAACCCUACUGCGCUAACCGAACUAGACAACGGCGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302544.1/7313-7433 AAAUGGUUGGACUCUUUCUAAA--UUGGAG-ACAAUUUGAA----AUAAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGAUAAUGGUGCAGUAGGGGUAAAUUUUCCGCAUUCGGUGCGG----------
X67706.1/7281-7402   AAAUGGUUGGACUCCUUUUAGAU--UAGAG-GCAAUUUCAA----UUGAUUAGAA-UUGGCUUAACCCUACCGCACCAACCGAACUAGACAACGGUGCGGUAGGGGUAAAUUAUCCGCAUUCGGUGCGGG---------
AY302556.1/7274-7394 AAAUGGUUGGACUCCUUCUAAA--UUGGAG-ACAAUUUGAA----AUAAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGACAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302548.1/7313-7433 AAGUGGUUGGACUCUUUCUAAA--UUAGAG-ACAACUUGAA----AUAAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGACAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AF317694.1/7290-7410 AAGUGGUUGGACUCCUUCUAAA--GUAGAG-ACAAUUUGAU----CUAAUUUGAA-UUGGCUUAACCCUACUGCACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AJ245864.1/1369-1498 AAGUGGUUGGACUCCUUCUAGAA-GUAGAGCACAAUUUGUA-----AAUUACAA--UUGGCUCAACCCUACCGCAUGAACCGAACUUGACAAAAGUGCAGUAGGGGUAAAUUCUCCCGAUUCGGUGCGGAGGAGAAAA-
AJ577589.1/7312-7433 AAGUGGUUAGACUCCUUCUAAAA-UUAGAGCAUAAUUAACA------AAUUAUAA-UUGGCUUAACCCUACCGCAUGAACCGAACUUGAUAAAAGUGCGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGG---------
X05690.1/7275-7395   AAAUGGUUGGAUUCCUUUUAAA--UUAGAG-ACAAUUUGAA----ACAAUUUAAA-UUGGCUUAACCCUACUGCACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCGUUCGGUGCGG----------
AY429470.1/7281-7401 AAGUGGUUAGACUCCUUUUAAAA-UUAGAGCACAAUUAGUC------AAUCAUAA-UUGGCUCAACCCUACCGCAUGAACCGAACUUGAUAUAAGUGCGGUAGGGGUAAAUUCUCCGUAUUCGGUGCGG----------
AY302551.1/7291-7412 AAGUGGUUGGACUCCUUUUAAAA-UUAGAG-ACAAUUUGAU----AUAAUUUGAA-UUGGCUUAACCCUACUGCACUAACCGAACUAGACAAUGGUGCGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AF524866.1/7334-7453 AAAUGGUUGGACUCCUUUUAAGA-UUAGAGCUCAAUUUGUA------AUUUAUAA-UUGGCUUAACCCUACCGCAUGAACCGAACUUGAUACAAGUGCGGUAGGGGUAAAUUCUCCGCAUUCGGUGCG-----------
AY302543.1/7296-7416 AAAUGGUUGGACUCUUUUUAAA--UUAGAG-ACAAUUUGAA----AUGAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGAUGACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302555.1/7300-7420 AAAUGGUUGGACUCUUUUUAAA--UUGGAG-GCAAUUUGAA----UUAAUUUGAA-UUGGCUUAACCCUACUGUAUCAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302547.1/7306-7426 AAGUGGUUGGACUCUUUCUAAA--UUGGAG-ACAAUUUGAU----CUGAUUUGAA-UUGGCUUAACCCUACUGCACUAACCGAACUAGACAACGGUGCAGUAGGGGUAAAUUCUCCGCGUUCGGUGCGG----------
AF241359.1/7291-7411 AAAUGGUUGGACUCUUUUUAAA--UUAGAG-ACAAUUUGAA----AUAAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302539.1/7289-7410 AAAUGGUUGGACUCCUUUUAAAA-UUAGAG-ACAAUUUGAG----AUAAUUAAAA-UUGGCUUAACCCUACUGCACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AJ493062.2/7295-7415 AAAUGGCUAGAUUCUUUUUAGAU--UAAAGCACAAUUUGGU----UUAAUUCUAA-UUGGCUCAACCCUACCACACUCACCGAACUAGACAACGGUGUGGUAGGGGUAAAUUCUCCGCAUUCGGUGCG-----------
AJ245863.1/1369-1498 AAGUGGUUGGACUCCUUUUAAAA-UUAGAGCGCAAUUAGUC------AAUCAUAA-UUGGCUCAACCCUACCGCAUGAACCGAACUUGAUAAAAGUGCGGUAGGGGUAAAUUCUCCGUAUUCGGUGCGGAGGAGAAAA-
U57056.1/7280-7400   AAGUGGUUGGACUCUUUCUAAA--UUAGAG-ACAAUUUGAU----CUGAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGACAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302550.1/7303-7424 AAAUGGUUAGACUCCUUCUAAAA-UUAGAG-ACAAUUUGAU----ACAAUUUGAA-UUGGCUUAACCCUACUGCACUAACCGAACUAGACAAUGGUGCGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302542.1/7313-7437 AAGUGGCUGGAUUCCUUUUAAGU--UAGAG-ACAAUUCACA----ACAAUUGAAA-UUGGCUUAACCCUACUGCACUAACCGAACUAGACAACGGCGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGGAGG------
M16560.1/7270-7389   AAGUGGUUGGACUCUUUUUAAA--UUAGAG-ACAAUUUGAA----CUAAUUUUAA-UUGGCUUAACCCUACCGCACUAACCGAACUAGAUAACGGUGCAGUGGGGGUAAAUUCUCCGCAUUCGGUGCG-----------
AF085363.1/7286-7411 AAGUGGUUGGACUCUUUUUAAA--UUAGAG-ACAAUUUGAA----CUAAUUUGAG-UUGGCUUAACCCUACUGCAUCAACCGAACUAGACAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAGGAG-----
AJ276224.1/7310-7431 AAAUGGCUGGAUUCUUUUUAAAU--UAGAGUACAAUUUGGU----UAAAUUCCAA-UUGGCUUAACCCUACCACACUCACCGAACUAGAUAACGGUGUGGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302554.1/7312-7432 AAAUGGUUAGACUCAUUCUAAA--UUAGAG-ACAAUUUGAG----AUAAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY302546.1/7274-7394 AAAUGGUUGGACUCCUUCUAAA--CUAGAG-ACAAUUUGAA----AUAAUUUGAA-UUGGCUUAACCCUACUGUACUAACCGAACUAGAUAACGGUGCAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
AY036578.1/7306-7426 AAGUGGUUGGAUUCCUUUUGAA--CUAGAG-ACAAUUUGAU----ACAAUUUGAA-UUGGCUUAACCCUACUACACUUACCGAACUAGACAGCGGUGUAGUGGGGGUAAAUUCUCCGCAUUCGGUGCGG----------
#=GC SS_cons         ::::::::::::::::::::::..:<-<<<.-<<<<<<<<<....____>>>>>>.>>>->>>-><<<<<<<<<<<<_AAAAAA_________>>>>>>>>>>>>,,,,,,,,,<<<<_aaaaaa>>>>..........
#=GC RF              AAgUGGUUgGAcUCuUUuUAAA..uuAgaG.ACaauucgaa....auAAuucgaa.uuGGCucAaCCCuaCcGcaccaACCGAACUaGAuAAcggugCgGuaGGGGUAAAUUCUCCGCAUUCGGUGCGG..........
//
# STOCKHOLM 1.0

#=GF AC   RF00042
#=GF ID   CopA
#=GF DE   CopA-like RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   60.00
#=GF TC   66.30
#=GF NC   57.50
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.46 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   2421250
#=GF RT   Structural analysis of an RNA molecule involved in replication control of
#=GF RT   plasmid R1.
#=GF RA   Gerhart E, Wagner H, Nordstrom K
#=GF RL   Nucleic Acids Res 1986;14:2523-2538.
#=GF RN   [2]
#=GF RM   11894917
#=GF RT   Post-transcriptional control of expression of the repA gene of plasmid R1
#=GF RT   mediated by a small RNA molecule.
#=GF RA   Light J, Molin S
#=GF RL   EMBO J 1983;2:93-98.
#=GF RN   [3]
#=GF RM   11502000
#=GF RT   Real time kinetic studies of the interaction between folded antisense and
#=GF RT   target RNAs using surface plasmon resonance.
#=GF RA   Nordgren S, Slagter-Jager JG, Wagner GH
#=GF RL   J Mol Biol 2001;310:1125-1134.
#=GF RN   [4]
#=GF RM   28854680
#=GF RT   The CTX-M-14 plasmid pHK01 encodes novel small RNAs and influences host
#=GF RT   growth and motility.
#=GF RA   Jiang X, Liu X, Law COK, Wang Y, Lo WU, Weng X, Chan TF, Ho PL, Lau TCK
#=GF RL   FEMS Microbiol Ecol. 2017; [Epub ahead of print]
#=GF CC   In several groups of bacterial plasmids, antisense RNAs regulate copy
#=GF CC   number through inhibition of replication initiator protein synthesis.
#=GF CC   These RNAs are characterised by a long hairpin structure interrupted by
#=GF CC   several unpaired residues or bulged loops. In plasmid R1, the inhibitory
#=GF CC   complex between the antisense RNA (CopA) and its target mRNA (CopT) is
#=GF CC   characterised by a four-way junction structure and a side-by-side helical
#=GF CC   alignment [3].
#=GF WK   CopA-like_RNA
#=GF SQ   37


AB011549.2/72471-72383       AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-CUC--AGUCGCCAAAC-UUUCUGAAGAUUAUCGGGGUUUUUGCUU
AB024946.1/39191-39282       AUAGCUGAAUUGUUGGCUAUACGGUUUUUA-GAUGGCCCCGGUAAUCUU-UCUGUACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUUGCUU
AB040415.1/24427-24516       AUAGCCUGAUUGGUGGCUAUACAGUUU--AAGUAGGCCCCGUUAAUCUU-U-CGUUCCCGCCAAGA-AAUGAGAAGAUUAUCGGGGUUUUUGCUU
V00351.1/909-819             AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-UUCGUAUUCGCCAAAG-UUGAAGAAGAUUAUCGGGGUUUUUGCUU
X02302.1/564-474             AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-UUCGUACUCGCCAAAG-UUGAAGAAGAUUAUCGGGGUUUUUGCUU
X55895.1/565-474             AUAGCUGAAUUGUUGGCUAUACGGUUUUUA-GAUGGCCCCGGUAAUCUU-UCUGCACUCGCCAAAG-UUAGAGAAGAUUAUCGGGGUUUUCGCUU
Y13308.1/1294-1207           AUAGAGCAACAGC-UUCUAUACAGUUUU-AAGUAGGCCCCGGUAAUCUU-CGA--CUCCGCCAAGAAUUGA--AAGAUUUCCGGGGUUUUUGCUU
AF053946.1/59545-59456       AUAGAGCAACAGC-UUCUAUACAGUUUU-AAGUGGGCCCCGGUAACCUU-CUCG-CCUCGCCAAAG-AUGAGGAAGUUUAUCGGGGUUUUUGCUU
AF177050.1/3124-3034         AUAGCUUGAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-UUCUGACUCGCCAAAG-UUGAAGAAGAUUAUCGGGGUUUUUGCUU
AF348706.1/209069-208980     AUAGCUUGAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-U-CUGACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUUGCUU
AJ009980.1/414-326           AUAGAGCAACAGC-UUCUAUGCAGUUU--AUGAAGGCCCCGUUAAUCUU-UUCCU-UCCGCCAAGA-UUGAAGAAGAUUAUCGGGGUUUUUGCUU
AJ009981.1/403-317           AUAGAGCAACAGC-UUCUAUACAGUUU--AGGUAAGCCCCGGUAAUCUU-C--UACGUCGCCAAACAUUGA--AAGAUUAUCGGGGUUUUGUCUU
AY091607.1/5757-5846         AUAGCUGAAUUGUUGGCUAUACGGUUUUUAGAUGG-CCCCGGUAAUCUU-U-CUA-GUCGCCAAAC-UUGAAGAAGAUUAUCGGGGUUUUCACUU
J01762.1/1156-1066           AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUU-UUCGUACUCGCAAAAG-UUGAAGAAGAUUAUCGGGGUUUUUGCUU
M16167.1/665-575             AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGACCCCGGUAAUCUU-CUCCUCGUCGCCAAAC-UAGAUGAAGAUUAUCGGGUUUUUUGCUU
M16168.1/1216-1126           AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGAUCCCGGUAAUCUU-CUCCUCGUCGCCAAAC-UAGAUGAAGAUUAUCGGGGUUUUUGCUU
AF401292.1/3686-3599         AUAGAGCAACAGC-UUCUAUGCGGUUUU-UAGAUGGCCCCGGUAAUCUU-CUU--CGUCGCCAAACAUAGA--AAGAUUAUCGGGGUUUUCGCUU
CP000244.1/1306-1218         AUAGCUGAAUUGUUGGCUAUACGGUUUC-UUGUUAGCCCCGGUAAUCUU-CUU--CGUCGCCAAACAUAGA--AAGAUUAUCGGGGUUUUUGCUU
M13472.1/235-144             AUAGCUGAAUUGUUGGCUAUACGGUUU--AAGUGGGCCCCGGUAAUCUUCUUCGCAGUCGCCAAAC-UUGACGAAGAUUAUCGGGGUUUUUGCUU
AF135182.4/22566-22477       AUAGAGCAACAGC-UUCUAUACAGCUUU-GAGUGAGCCCCGUUAAUCUU-U-CGUCUCCGCCAAGA-AAUGAGAAGAUUAUCGGGGUUUUUGCUU
DQ381420.1/54109-54021       AUAGCUGAAUUGUUGGCUAUGCGGUUUU-AUG-GGGCCCCGGUAAUCUU-U--CUAGUCGCCAAAC-UUGAAGAAGAUUAUCGGGGUUUUCGCUU
AJ698720.1/112849-112760     AUAGAGCAACAGC-UUCUAUACAGUUU--AAGUAGGCCCCGUUAAUCUU-CUCUUAGUCGCCAAAC-CUGGUGAAGAUUAUCGGGGUUUUUGCUU
CP000035.1/176755-176665     AUAGCUUGAUUGUUGGCUAUACGGUUUU-UAGAUGGCCCCGGUAAUCUU-U-CUCACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUUGCUU
AY517905.1/24841-24927       AUAGCCUGAUUGGUGGCUAUACAGUUU--AAGUAGGCCCCGUUAAUCUU-CGU---CCCGCCAAGAAAUGA--AAGAUUAUCGGGGUUUUUGCUU
AJ851089.1/21862-21772       AUAGAGCAACAGC-UUCUAUGCAGUUUC-UUGUUAGCCCCGGUAAUCUU-CUCUUAGUCGCCAAAC-CUGGUGAAGAUUAUCGGGGUUUUUGCUU
M26937.1/556-467             AUAGAGCAACCGC-UUCUAUGCAGUUUC-UUGUUAGCCCCGAUAAUCUU-U-CUCACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUCACUU
AY214164.3/3313-3404         AUAGAGCAACAGC-UUCUAUGCGGUUUC-UUGUUAGCCCCGUUAAUCUUCUUCUCAGUCGCCAAAC-UUGCUGAAGAUUAUCGGGGUUUUCACUU
M27528.1/169-82              AUAGCUGAAUUGUUGGCUAUGUGGUUUU-AUGGGG--CCCGAUAAUCUU-U--CUAAUCGCCAAAC-UUGAAGAAGAUUAUCGGGGUUUUCACUU
ABAN01000047.1/12752-12665   AUAGCCUGAUUGGUGGCUAUACAGUUU--AGGUAAGCCCCGGUAAUCUU-CUU--CGUCGCCAAACAUUGA--AAGAUUAUCGGGGUUUUGUCUU
AB255435.1/103133-103043     AUAGCUGAAUUGUUGGCUAUACGGUUUU-UAGAUGGCCCCGGUAAUCUU-U-CUGACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUCACUU
AAJT02000104.1/9003-9093     AUAGCUGAAUUGUUGGCUAUACGGUUUC-UUGUUAGCCCCGGUAAUCUU-U-CUCACUCGCCAAAG-UUAAAGAAGAUUAUCGGGGUUUUCACUU
AAJX02000085.1/4103-4193     AUAGCUGAAUUGUUGGCUAUACGGUUUU-AUG-GGGCCCCGGUAAUCUU-CUCUUAGUCGCCAAAC-UUCUCGAAGAUUAUCGGGGUUUUUGCUU
AAJW02000029.1/47300-47209   AUAGCUGAAUUGUUGGCUAUACGGUUUU-UAGAUGGCCCCGUUAAUCUU-CUCUUAGUCGCCAAAC-UUGCUGAAGAUUAUCGGGGUUUUCACUU
AAJT02000054.1/33351-33263   AUAGCUGAAUUGUUGGCUAUACGGUUUU-UAGAUGGCCCCGGUAAUCUU-CUU--CGUCGCCAAACAUAGA--AAGAUUAUCGGGGUUUUCGCUU
CP001123.1/1907-1997         AUAGAGCAACAGU-UUCUAUGUUGUCU--AAAUUGCCCCCGAUAAUCUU-UUUACUGGUCCAAAAAGUGAAACAAGAUUAUCGGGGGUUGUUUUU
AAMK02000010.1/115535-115445 AUAGAGCAACAGC-UUCUAUGCAGUUUC-UUGUUAGCCCCGUUAAUCUU-UCUGGACUCGCCAAAG-UUAGAGAAGAUUAUCGGGGUUUUCACUU
CP001143.1/36115-36202       AUAGCCUGAUUGGUGGCUAUACAGUUU--AAGUAGGCCCCGUUAAUCUU-CUG--UCCCGCCAAGAAUAGA--AAGAUUAUCGGGGUUUUUGCUU
#=GC SS_cons                 <<<<<__________>>>>>--------.<<<<<<<<<<<<<<<<<<<<.________________.______>>>>>>>>>>>>>>>>-->>>>
#=GC RF                      AUAGcuuAAuuGuUggCUAUACgGUUUu.aaGcgggCCCCGgUAAUCUU.uucuuaguCGCCAAAa.UugaaGAAGAUUAcCGGGGuucUugCuu
//
# STOCKHOLM 1.0

#=GF AC   RF00043
#=GF ID   Plasmid_R1162
#=GF DE   R1162-like plasmid antisense RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   55.00
#=GF TC   65.10
#=GF NC   52.40
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0060908; plasmid copy number maintenance;
#=GF RN   [1]
#=GF RM   2430262
#=GF RT   Copy-number of broad host-range plasmid R1162 is regulated by a small RNA.
#=GF RA   Kim K, Meyer RJ
#=GF RL   Nucleic Acids Res 1986;14:8027-8046.
#=GF CC   The copy-number of the broad host-range plasmid R1162 is controlled by the
#=GF CC   amounts of two proteins, encoded by cotranscribed genes comprising a
#=GF CC   region of the plasmid called RepI. RepI is negatively regulated by a 75
#=GF CC   base RNA that is complementary to a segment of the RepI message [1].
#=GF WK   R1162-like_plasmid_antisense_RNA
#=GF SQ   8


Y19120.1/3371-3442     CGGCGCAUGGCGGGG-CA----UCCCCGCCAGCGCUUGACCAUCAACCGCCUGCAAAGGAGGCAAACCAAUGGCUAC
Z47410.1/1220-1294     CGGCGCAGGGCGGGG-GUAGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGCAAAGGAGGCAAUC-AAUGGCUAC
AF325537.2/5765-5838   CGGCGCGAGCCGGAG-UGUCAGUCCCCGGCAGCGCCUAACCACGCCAGUUCUGGAAAGGAGAACAGC--AUGGCUUU
AJ271879.1/3249-3322   CGGCGCAGGGCGGGG-GUGGUGACCCCGCCAGCGCCUAACCACCAACUGCCUGAACAGGAGGCAAUC--AUGGCUAC
AJ871969.4/3379-3450   CGGCGCAUGGCGGGG-AU----GCCCCGCCAGCGCCUGACCAUCAACCGCCUGCAAAGGAGGCAAACCAAUGGCUAC
Z78058.1/1759-1831     UAGCGCUU-AUGGGG-UA-GUGACCCCGCCAGCGCCUAACCACCAACUGCCUGCAAAGGAGGCAAUC-AAUGGCUAC
M73777.1/788-859       CGGCGC-GGCAGGGG-AUUGCGGCCCCGGCAGCGCCUAACCACAAC-UGUCUGAAAAGGAGACAAGC-A-UGGCUUU
AY428550.1/11023-11096 CGGCGC-GGCAGGGUGCGGGAACACCCGGCAGCGCCUAACCAUAACCGUUCUACACAGGAGAACAGC--AUGGCUUU
#=GC SS_cons           :<<<<<--<<<<<<<._______>>>>>>>->>>>>---<<<-----<<<<<-<___>->>>>>---.-->>>::::
#=GC RF                CGGCGCagGgcGGGG.uuuguGaCCCCgcCAGCGCCUAACCAccAacugcCUGcAAAgGAGgcaAuC.AAUGGCUac
//
# STOCKHOLM 1.0

#=GF AC   RF00044
#=GF ID   Phage_pRNA
#=GF DE   Bacteriophage pRNA
#=GF AU   Finn RD; 0000-0001-8626-2148
#=GF SE   Finn RD
#=GF SS   Predicted; ILM
#=GF GA   40.00
#=GF TC   61.90
#=GF NC   35.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   12206459
#=GF RT   Structure and function of phi29 hexameric RNA that drives the viral DNA
#=GF RT   packaging motor: review.
#=GF RA   Guo P
#=GF RL   Prog Nucleic Acid Res Mol Biol 2002;72:415-472.
#=GF RN   [2]
#=GF RM   11562164
#=GF RT   Cryoelectron-microscopy image reconstruction of symmetry mismatches in
#=GF RT   bacteriophage phi29.
#=GF RA   Morais MC, Tao Y, Olson NH, Grimes S, Jardine PJ, Anderson DL, Baker TS,
#=GF RA   Rossmann MG
#=GF RL   J Struct Biol 2001;135:38-46.
#=GF RN   [3]
#=GF RM   11130079
#=GF RT   Structure of the bacteriophage phi29 DNA packaging motor.
#=GF RA   Simpson AA, Tao Y, Leiman PG, Badasso MO, He Y, Jardine PJ, Olson NH,
#=GF RA   Morais MC, Grimes S, Anderson DL, Baker TS, Rossmann MG
#=GF RL   Nature 2000;408:745-750.
#=GF RN   [4]
#=GF RM   10957642
#=GF RT   Purification, crystallization and initial X-ray analysis of the head-tail
#=GF RT   connector of bacteriophage phi29.
#=GF RA   Badasso MO, Leiman PG, Tao Y, He Y, Ohlendorf DH, Rossmann MG, Anderson D
#=GF RL   Acta Crystallogr D Biol Crystallogr 2000;56:1187-1190.
#=GF RN   [5]
#=GF RM   3107124
#=GF RT   A small viral RNA is required for in vitro packaging of bacteriophage phi
#=GF RT   29 DNA.
#=GF RA   Guo PX, Erickson S, Anderson D
#=GF RL   Science 1987;236:690-694.
#=GF RN   [6]
#=GF RM   2125049
#=GF RT   Phylogenetic analysis and secondary structure of the Bacillus subtilis
#=GF RT   bacteriophage RNA required for DNA packaging.
#=GF RA   Bailey S, Wichitwechkarn J, Johnson D, Reilly BE, Anderson DL, Bodley JW
#=GF RL   J Biol Chem 1990;265:22365-22370.
#=GF CC   During replication of linear dsDNA viruses, the viral genome is packaged
#=GF CC   into the pre-formed viral procapsid. The packaging of DNA into the
#=GF CC   procapsid requires a molecular motor which using ATP as energy to
#=GF CC   accomplish the energetically unfavourable motion. In some bacteriophage,
#=GF CC   an RNA (pRNA) molecule is a vital component of this motor [1]. Structural
#=GF CC   analyses of the packaging motor have demonstrated that the pRNA molecule
#=GF CC   has fivefold symmetry when attached to the prohead [2-4]. The pRNA is
#=GF CC   thought to be bound by the capsid connector protein (PFAM:PF05352) [4].
#=GF CC   Only the first 120 bases of the pRNA are essential for packing the viral
#=GF CC   DNA [5,6]. The pRNA is proposed to be comprised of two domains, one
#=GF CC   corresponding to the first 120 bases and the second to the remaining 50
#=GF CC   bases [6]. Nuclear cleavage occurs in the single strand region linking
#=GF CC   these two domains [6].
#=GF WK   Bacteriophage_pRNA
#=GF SQ   3


V01121.1/318-75    AAUGGUACGGUACUUCCAUUGUCAUGUGUAUGUUGGGGAUUAAACCCUGAUUGAGUUCAGCCCACAUACUUUGUUGAUUGGUUGUCAAUCAUGGCAAAAGUGCACGCUACUUUGAUAACCUUUUACAUGCGACACAGACGAAGCGCUAAAACGUGGGAUUCUGUGUCGUUUUAUGUUGUUCAUUGACAAACCUAUCUAGUAGGUCUAUAGAUUGAUAUAUUAAGUAGUAGUUUCCCUCCCUGAU
V01155.1/318-75    AAUGGUACGGUACUUCCAUUGUCAUGUGUAUGUUGGGGAUUAAACCCUGAUUGAGUUCAGCCCACAUACUUUGUUGAUUGGUUGUCAAUCAUGGCAAAAGUGCACGCUACUUUGAUAACCUUUUACAUGCGACACAGACGAAGCGCUAAAACGUGGGAUUCUGUGUCGUUUUAUGUUGUUCAUUGACAAACCUAUCUAGUAGGUCUAUAGAUUGAUAUAUUAAGUAGUAGUUUCCCUCCCUGAU
M11813.1/4883-5126 AAUGGUACGGUACUUCCAUUGUCAUGUGUAUGAUGGGGAUUAAACCCUGAUUGAGUUCAGCCCACAUACUUUGUUGAUUGGUUGUCAAUCAUGGCAAAAGUGCACGCUACUUUGAUAACCUUUUAAAUGCGACACAGACGAAGCGCUAAAACGUGGGAUUCUGUGUCGUUUUAUGUUGUUCAUUGACAAUCCUAUCUAGUAGGACUAUAGAUUGAUAUAUUAAGUAGUGAUCUCCCUGCCCGAU
#=GC SS_cons       ::<<<__________>>>,,,,,,,,,,<<<<<----<<<<<_____>>>>>----------->>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,((((((-((((,,,,,<<<_____________________>>><<<<<<<<____________>>>>>>>>,,,,,,,,,,,,<<<<<<___>>>>>>,,,,,,,,,,,,,))))))))))<<<_________>>>::
#=GC RF            AAuGGUACGGUACUUCCaUUGUCAUGUGuauGuUGGGgauuaAACCCugauuGAGUUCAGCCCaCauaCUUUGUUGAUUGGUUGUCAAUCAUGGCAAAAGUGCACGCuaCuuUgauaACCUUuuacAUGCGACACAGACGAAGCGCuaaaaCgugggAUUCUGUGUCGUuuuauGuuGUUCAUUGACAAaCCuauCUAguaGGuCUAUAGAUUGAUAuauuaaGuaGuggUuUCCCUcCccgAU
//
# STOCKHOLM 1.0

#=GF AC   RF00045
#=GF ID   SNORA73
#=GF PI   U17
#=GF DE   Small nucleolar RNA SNORA73 family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR; Cervelli et al, PMID:11821910
#=GF SS   Published; PMID:11821910
#=GF GA   74.00
#=GF TC   74.20
#=GF NC   73.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00078
#=GF DR   snoRNABase; U17a;
#=GF DR   snoRNABase; U17b;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300899;
#=GF DR   snoopy; Homo_sapiens300294;
#=GF RN   [1]
#=GF RM   8903340
#=GF RT   5'ETS rRNA processing facilitated by four small RNAs: U14, E3, U17, and
#=GF RT   U3.
#=GF RA   Enright CA, Maxwell ES, Eliceiri GL, Sollner-Webb B
#=GF RL   RNA 1996;2:1094-1099.
#=GF RN   [2]
#=GF RM   11821910
#=GF RT   Comparative Structure Analysis of Vertebrate U17 Small Nucleolar RNA
#=GF RT   (snoRNA).
#=GF RA   Cervelli M, Cecconi F, Giorgi M, Annesi F, Oliverio M, Mariottini P
#=GF RL   J Mol Evol 2002;54:166-179.
#=GF CC   U17 (SNORA73A and SNORA73B) also known as E1 belongs to the H/ACA class of
#=GF CC   small nucleolar RNAs (snoRNAs). Vertebrate U17 is intron-encoded and
#=GF CC   ranges in length from 200-230 nucleotides, longer than most snoRNAs. It is
#=GF CC   one of the most abundant snoRNAs in human cells and is essential for the
#=GF CC   cleavage of pre-rRNA within the 5' external transcribed spacer (ETS) [1].
#=GF CC   This cleavage leads to the formation of 18S rRNA. Regions of the U17 RNA
#=GF CC   are complementary to rRNA and act as guides for RNA/RNA interactions,
#=GF CC   although these regions do not seem to be well conserved between organisms
#=GF CC   [2].
#=GF WK   Small_nucleolar_RNA_SNORA73
#=GF SQ   66


AJ006836.1/1091-1295       CCAACGUG-GA-U-A--UCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCUAGUG--GC-GA-ACGGGAGCUUA--GGGCAUU----GCC-CGGUGAUGUAC-AGUCCC-UUUCCACAACGUUGGAGAUGAAGC-------UG-----GGCUUUCGAG---------UC---UGC-GCCUGCAUAUUC-------CUACGACUUCUCAGAGU-CCC-GUGG-ACCAUGACUGAGGAGACAAACCAUGCAGG--AAACAAAA
X94942.1/2747-2965         CCGACGUG-GA-C-A--UCCA-GCGAG-CUG------CUCUC--C--UGGCUCUGUCCUGGUG--GC-GU-AUGGGAGCGUA--GCUUU-U----CAG-CAGAGACGUAC-AUUCCC-GUUCCACACCGUCGGAGAGAAAGC-----UCUGUCCCCGGC-CUCUGGCUGGCGUGGAC--GAGCGUCCUGUAUAUUC-------CUACAUCUUCCCAGAGU-CCUACUGG-GCCGUUACUGGGGAGCUAAACCAUGCAGU--GCACAUCA
X94942.1/2086-2300         CCGACGUG-GA-C-A--UCCA-GCGAG-CUG------CUCUC--C--UGGCUCUGUCCUGGUG--GC-GU-AUGGGAGCGUA--GCUUUCA------G-CAGAGACGUAC-AUUCCC-GUUCCACACCGUCGGAGAGAAAGC-----UCUGUCCCCGGC-CUCUGGCUGGCGUGGAC--GAGCGU-CUGUAUAUUC-------CUACAUCUUCCCAGAGU-CCUACUGG-ACCGUUACUGGGGAGCUAAACCAUGCA----GUGCACAU
X94942.1/1504-1721         CUGACGUG-GA-C-A--UCCA-GCGAG-CUG------CUCUC--C--UGGCUCUGUCCUGGUG--GC-GU-AUGGGAGCGUA--GCUUU-U----CAG-CAGAGACGUAC-AUUCCC-GUUCCACACCGUCAGAGAGAAAGC-----UCUGUCCCCGGC-CUCUGGCUGGCGUGGAC--GAGCGUCCUGUAUAUUC-------CUACAUCUUCCCAGAGU-CCUACUGG-ACCGUUACUGGGGAGCUAAACCAUGCAGU--GCACA-UU
AL513497.21/8055-8258      CCAACGUG-GA-U-A--CCCU-GGGAG-GUCA-----CUCUCCCC--AGGCUCUGUCCAAGUG--GC-AU-AGGGGAGCUUA--GGGCUCU----GCC-CCAUGAUGUAC-AGUCCC-UUUCCACAACGUUGAAGAUGAAGC-------UGGGCCUCGU---------------GUC---UGC-GCCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CCU-GUGG-ACAAUGACUGGGGAGACAAACCAUGCAGG--AAACAUAU
X71081.1/6865-7085         CCAACGUG-GA-U-A--UCUC-AUGAG-GUUA-----CUCA---U--GGGCUCUGUCUUGGUG--GC-GU-AUGGGAGCGUC--GCCCUGUG-AGGCG-CAGUGACGUAU-AAUCCC-CUUCCACAACGUUGGAGAACAAGC------AUGUCCCUAGCCUUCG-GCUGGUGUGGGC---AGCACCCUGUAUAUUC-------CUACAACUUCCCAGAGC-CC--UCGG-GCAAUGACUGAGGAGACAAACCAUGCAGGACACACAAAU
X71081.1/3489-3711         UCAAUGUG-GA-U-A--UCCU-GUGAG-GUUA-----CUCUC-AU--GGGCUCUGUCCAAGUG--GC-GU-AUGGGAGCGUAGUGCUUUAU---GGCG-CAGUGACGUAC-AAUCCC-UUUCCACAACAUUGAAGAACAAGC------AUGUCCUCGGCCAUUAGGCUGUUGUGGGC---AGCGUCCUGUAUAUUC-------CUACAACUUCCCAAAGC-CAA-AAUG-GCUCUUACUGGGGAGACAAACCAUGCAGG--UUACAUCU
X71081.1/4425-4646         CCAAUGUG-GA-U-A--UCCU-UAGAG-GUCU-----CUCU---U--GGGCUCUGUCCAGGUG--GC-GU-AUGGGAGCAUAUAGCCCUUAA-AGGUG-CAGUGACGUAU-AAUCCC-CUUCCACAACAUUGGAGAACAAGC------AUGUCCCCAGCCAUUAGGCGGGUGUGGGC---AGCAUCCUGUAUAUUC-------CUAAAACUUCCCAGAGC-CC--UUGG-GCAAUAUCUGGGGAGACAAACCAUGCGGG--AUACAUUU
X71081.1/1462-1682         CCAACGUG-GA-U-A--UCUC-AUGAG-GUUA-----CUCUC-AU--GGGCUCUGUCUUGGUG--GC-GU-AUGGGAGCGUC--GCCCUGUG-AGGCG-CAGUGACGUAU-AAUCCC-CUUCCACAACGUUGGAGAACAAGC------AUGUCCCCGGCCAUUCGGCUGGUGUGGGC---AUCACCCUGUAUAUUC-------CUACAACUUCCCAGAGC-CC--UCGG-GCAGUGACUGAGGAGACAAACCAUGCAGG--AUACA-UU
X71081.1/9191-9412         CCAACGUG-GA-U-A--UCUC-AUGAG-GUUA-----CUCUC-AU--GGGCUCUGUCUUGGUG--GC-GU-AUGGGAGCGUC--GCCCUGUG-AGGCG-CAGUGAUGUAU-AAUCCC-CUUCCACAACGUUGGAGAACAAGC------AUGUCCCCGGCCAUUCGGUUGGUGUGGGC---AGCACACUGUAUAUUC-------CUACAACUUCCCAGAGC-C-G-UCGG-GCAGUGACCGGGGAGACAAACCAUGCAGG--AUACAUUA
L16792.1/3-205             C-AACGUG-GA-U-A--CCCC-GGGAG-GUCA-----CUCUCCCC--AGGCUCUGUCCAAGUG--GC-AU-AGGGGAGCUUA--GGGCUCU----GCC-CCAUGAUGUAC-AGUCCC-UUUCCACAACGUU-AGGAAUGAAG------CUGGGCCUCGU---------------GUC---UGC-GCCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CCU-GUGG-ACAAUGACUGGGGAGACAAACCAUGCAGG--AAACAUAU
AJ310189.1/1-223           CCAACGUG-GA-C-A--UCCA-GUGAG-GUUG-----CUCUCGCA--UGGCUCUGUCCAUGUG--GC-GU-AUGGGAGCGUA--GCACUUC---AGUG-UAGUGACGUAC-AGUCCC-GUUCCACGACGUUGGAGAGCAAGC-----UUUGUCCCCGGCCCUCCGGCUGGUGAGGAC---GGCGUUCUGUAUAUUC-------CUACAUCUUCCCAGAGC-CCU-UUGG-GCCAUGACUGGGGGGCUAAACCAUGCAGU--GUACAACU
AJ306558.1/1-213           UCAACAUG-GA-C-A--UCCG-UUGAG-GUUA-----CUUG------UGGGUCUGUCCAAGUG--GU-AU-AUGGGAGUAUA--GCCCUAA----GUG-CAGUGAUGUAC-AGUCCC-CUUCCACAGUGUUGAAGAGCAAGC-----CCUGUCCCUGGUUCUAGAGCUGAUGAGGGC---AGACUCCUUUAUAUUC-------CUAUAACUUCUCA--GU-CU--CUAG-ACAAUUACUGAGGAGA--AACCAUGCAGG--GUGCAACU
AJ306559.1/1-212           CCAAUAUA-GU-C-A--UCCA-UUGAG-GUUA-----CUCG------UGGCUCUGUCCAAGUG--GU-AU-AUGGGAGCGUA--GCCCUAA----CUG-CAAUGAUGUAC-AAUCCC-CUUCCACAGUGUUGAAGAGUAAGC------CUGUCUUUGGUUCUAGAGCUGAUGAGAGC---AGCAUCCUUUAUAUUC-------CUAUAACUUCUCC--GU-CU--CUAG-ACAAUUACUGAGGAGA--AACCUUGCAGG--GUGUAAGA
AJ306560.1/1-214           CCAAUAUG-GU-C-A--UCCA-UUGAG-GUUA-----CUCA------UGGCUCUGUCCAAGUGGUGU-AU-AUGGGAGCAUA--GCCCUAA----GUG-CAGUGAUAUAC-AAUCCC-CUUCCACAGUGUUGAAGAGCAAGC------CUGUCUCUGGUUCUAGAGCUGAUGAGAAC---AGCAUUCUAUAUAUUU-------UUAUAACUUCUCA--GU-CU--CUAG-ACAAUUACUGAGGAGA--AACCAUGCAGG--UUACAACU
AJ306561.1/1-211           CCAAUGUG-GU-C-A--UCCA-UCGAG-GUUA-----CUAG------UGGCUCUGUCCAGGUG--GU-AU-AUGGGAGCAUA--GCCCUAA----GUG-CUGUGGUGUGC-AGUCCC-CCUUC-CAGUGUUGAAGAGCGAGU------CUGUCUCUGGUUCUAGAGCUGACGAGGAC---AGCAUCCUAUAUAUUU-------UUAUAACUUCUCA--GU-CU--CUAG-ACAGUUACUGAGGAGA--AACCAUGCAGG--GUGCAACU
AJ306562.1/1-220           CUACUAUA-GU-C-C--UCCA-UUGUG-GUUA-----CUUG------UGGCUCUGUCUCUGUG-UGU-GU-GUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUG-UGUUCC-CUUCCACGGUGUUGAAGAGUAAGC------CUGUCCUUGGUUUUAGAGUCAAUAAGGGC---AGCAAUCUUUAUAUUC-------CUAUAACUUCUCA--GU-CU--CUAG-ACAGUUACUGAGGAGG--AACCAUGCAGG--AUGAAACU
AJ306563.1/1-220           CCAAUGUG-GU-C-A--UCCA-UUGAG-GUUA-----CUAG------UGGCUCUGUCCAAGUG--GU-AU-UUGGGAGCAUA--GCUCUAA----GUG-CAGUGGUGUAC-AAUCCC-CUUCCACAGUGUUGUAGAGCAAGU-----CCUGUCUCUGGUUCUAGAGCUGACGAGGAC---AGCAUCCUAUAUAUUUCUAUUUUUUAUAACUUCUCA--GU-UA--AUUG-GUAGUGACUGAGGAGA--AACCAUGCAGA--GUGCAACU
AJ306564.1/1-212           CCAAUAUG-GU-C-A--UCCA-UUGAG-GUUA-----CUUG------UGUCUCUGCCCAAGUG--GU-AU-AUGGGAGCAUA--GCCCUAA----GUG-CAGUGAUGUAC-AAUCCC-CUUCCACAGUGUUGAAGAGCAAGC------CUGUCUCUGGUUCUAGAGCUGAUGAGGAC---AGCAUCCUACAUAUUU-------UUAUAACUUCUCU--GU-CU--CUAG-AUAAUUACUGAGGAGA--AACUAUGCAGG--UUGCAACU
AJ306565.1/1-215           CCAACAUG-GU-C-C--UCCA-UUGAG-GUUA-----CUCA------UGGCUCUGUCCAAGUG--GC-AU-AUGGAGGCAUA--GCCCUAA----GUG-CAGUGAUGCAC-AAUACC-CUUCCAUAGU-UGGAAGAGCAAAC------CUAUCUCUGGCUCUACAACUGAUGAAGUC---AGAAUCCUGUAUAUUC-------CUAAAACUUCUCAUAGU-CU--UUAG-GUGAUUACUGAGGCGAAAAACCAUGCAGG--AUGUAAUU
D00591.1/3109-3311         CCAACGUG-GA-U-A--CCCU-GGGAG-GUCA-----CUCUCCCC--AGGCUCUGUCCAAGUG--GC-AU-AGGGGAGCUUA--GGGCUCU----GCC-CA-UGAUGUAC-AGUCCC-UUUCCACAACGUUGAAGAUGAAGC-------UGGGCCUCGU---------------GUC---UGC-GCCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CCU-GUGG-AUAAUGAUAGGGGAGACAAACCAUGCAGG--AAACAUAU
AJ310188.1/1-225           CCAACGUG-GA-C-A--UCCG-GUGAG-GUUG-----CUCUCGCA--UGGCUCUGUCCUUGUG--GC-GU-UUGGGAGCGUA--GUACUUCA-CAGUA-CUGUGACGUAC-AGUCCC-GUUCCACGACGUUGGAGAGCAAGC-----UUUGUCCCCGGCCUUCGGGCUGGUGAGGAG---GGUGUUCUGUAUAUUC-------CUACAUCUUCCCAGAGC-CCU-UUGG-GCCAUGACUGGGGGGCUAAACCAUGCAGU--GUACAACC
BX276180.5/20672-20892     CCAACGUG-GA-C-A--UCCC-GUGAG-AUGC-----CUCUCAUG--UGGCUCUGUCCAUGUG--GC-GU-AUGGGAGCGUA--GCACUUC---GGUG-UUGUGACGUAC-AGUCCC-GUUCCACGACGUUGGAUAGCAAGC------UUGUCCCCGGC-CUCUGGCUGGUGUGGAC---UACGUCCUGUAUAUUC-------CUACAUCUUCCCAGAGC-CCU-UUGG-GCCAUUACUGGGGAGGUAAACCAUGCAGU--GCACACUA
AJ493422.1/1-216           CCAAUAUG-GU-A-A--UCCG-UUGAG-GUUA-----CUUG------UGGCUCUGUCCAAGUG--GU-AU-AUGGGAGCAAA--GCCCUAA----GUG-CAAUGGUGUAC-AAUCCC-CUUCCACAGUGUUGAAGAGCAAGC------CUGUCUCUGAUUCUAGAGCUGAUGUGGAU---AGCAUCCUAUAUAUUUUA---UUUUAUAACUUCUCA--GU-CU--CUAG-ACAAUUACUGAGGAGA--AACCAUGCAGG--GUGCAACU
AJ493416.1/1-215           CCAGCAUG-GU-C-A--UCCA-UUGAA-GUUA-----CUCA------UGGCUCUAGCCAAGUG--GC-AU-AUGGGAGCAUA--GCCCUUA----GUG-CAGCGAUGUAC-CAUCCC-CUUCCACAAU-UGGCAGAGCAAGC------CUGUCCCUGGUUCUAGAGCUGAUGGGGAU---AGAAUCCUGUAUAUUC-------CUAUAAUUUUUCAUUGU-CU--UUAG-ACGUUUACUGAAAAGAGAAACCAUGCAGG--GGGCAAUU
AAVX01060057.1/357-135     CCAAUGAG-GG-C-G--UCCAUGGGAG-UUCG-----CUCUC--CCGUGGCUCUGUCCGAGUG--GC-GU-AUGGGAGCGUA--GGCCUCU---GGGC-CCUUGACGUAC-AGUCCC-AUUCCACAGCGUUGGAGAGAGUGC------CUGUCCCCGGCCCUUGGGCUGGUGAGGAC---AGCAGCCUGUAUAUUC-------CUAUACCUUCUCAGAGU-CCA-GCGG-GCAAUGACUGAGGAGAUAAACCAUGCAGG--GUACAAUU
AJ493420.1/1-215           CCAACAUG-GU-C-A--UCUG-UUGAG-GUUA-----CUCA------UGGCUCCGUCCAAGUG--UC-AU-AUGGGAGUAUA--GCCCUAA----GUG-CAGUGAUGUGC-AAUCCC-CUUCCACAGU-UGGAAGAGCAAAC------CUGUCCCUGGUUCUAGAGCUGAUGGGGAC---AGAAUCCUGUAUAUUC-------CUAUAAUUUCUCAUUGU-CU--UUAG-ACAAUUACUGAGACGAGAGACCAUGCAGG--GUGCAGCU
AAFC03094567.1/12296-12093 CCAACGUG-GA-U-A--CCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCAGGUG--GC-GA-ACGGGAGCGUA--GGGCUCU----GCU-CAGUGACGUAC-AGUCCC-UUUCCACAACGUUGGAGAUGAAGC-------UGGGCCUUGA---------------GUC---UGC-GCCUGCAUAUUC-------CUACAGCUUCUCAGAGU-CCU-GUGG-ACAAUGACUGAGGAGACAAACCAUGCAGG--AAACAUCU
ABDC01498416.1/762-965     CCAACGUG-GA-U-A--CCCU-GGGAG-GUCA-----CUCUGCCC--AGGCUCUGUCCAGGUG--GC-AU-AGGGGAGCAUA--GGGCUCU----GCC-CCGUGACGUAC-AGUCCC-UUUCCACAACGUUGGAGAUAAAGC-------UGGGCUUUGU---------------GUC---UGC-GCCUGCAUAUUC-------CUACGACUUCCCAGAGU-CCU-GUGG-ACAAUGACUGGGGAGACAAACCAUGCAGG--AAACAUGU
AANU01100867.1/8151-8355   CCAACGUG-GA-U-A-CACCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCAAGUG--GC-GU-AGGGGAGCAUA--GGGCUCU----GCC-CCGUGAUGUAC-AAUCCC-UUUCCACAACGUUGGAGAUAAAGC-------UGGGCCUUGA---------------GUC---UGC-GCCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CCU-GUGG-ACAAUGACUGGGGAGACAAACCAUGCAGG--AAACAACC
AANH01008512.1/7650-7868   CCGACGUG-GU-C-A--UCCA-GCGAG-GUCA-----CUCUC--C--UGGCUCUGUCCUGGUG--GC-GUUAUGGGAGCGUA--GCGCUCA------G-CUGAGACGUAC-AAUCCC-GUUCCACAGCGUCGGAGACAAAGC-----UCUGACCCCGGC-CUCCGGUCGGUGGGGAC--GAGCGUCCUGCAUAUUC-------CUACAUCUUCCCAGAGU-CCU-UUGG-GCCGUGACUGGGGGGCUAAACCAUGCAGU--GCACAACA
AAHX01040057.1/46568-46771 CCAACGUG-GA-U-A--CCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCUAGUG--GC-GU-ACGGGAGCAUA--GGGUACU----GCC-CGAUGAUGUAC-AGUCCC-UUUCCACAACGUUGGAGAUGGAGC-------UGGGCUUCGA---------------GUC---UGC-GCCUGCAUAUUC-------CUACGACUUCUCAGAGU-CCU-GUGG-ACCGUGACUGAGGAGACAAACCAUGCAGG--AAACAAAA
AAQQ01135328.1/378-177     CCAACGUG-GA-U-A-CUCUC-GGGAG-GUCU-----CUCCC--C--GGGCUCUGUCCAGGUG--GC-AU-AGGGGAGCAUA--GGGCUCU----GCC-CCAUGAUGUAC-AGUCCC-UUUCCACAACGUUGGAGAUGAAGC-------UGGGCUUUAU---------------GUC---UGC-ACCUGCAUAUUC-------CUACGACUUCUCAGAGU-CU--GUGG-ACUAUGACUGAGGAGACAAACCAUGCAGG--AAACAAAA
AAYZ01245006.1/2687-2890   CCAACGUG-GG-C-A--UCCC-GGGAG-GUCA-----CUCUCCCC--GGGCCCUGUCCUGGUG--GC-AC-AUGGGAGCUGA--GGGCUCU----GCC-CCGUGACGUAC-AGUCCC-CUUCCACGACGUUGGAGAGAAAGC------CGGGCCUUCGG---------------GUC---UGC-GCCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CC--AUGG-ACCGUGACUGGGGAGACAAACCAUGCAGG--AAACAGCU
AACN010016018.1/3148-3351  CCAACGUG-GA-U-A-CUCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCAGGUG--GC-GU-AUGGGAGCUCA--GGGCUCU----GCC-CCGUGACGUAC-AGUCCC-UUUCCACAACGUUGGAGAUGAAGC------CGGGCUUGAGU-----------------C---UGC-GCCUGCAUAUUC-------CUACAGCUUCUCAGAGU-CCU-GUGG-ACCAUGACUGAGGAGACAAACCAUGCAGG--AAACAUCU
AAPY01775264.1/1451-1654   CCAACGCG-GA-U-A--CCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCUGGUG--GC-AU-AGGGGAGCAUA--GGGCUCU----GUC-CCGGGAUGUAC-AGUCCC-UUCCCACGGCGUUGGAGAUGAAGC-------UGGGCUCCGC---------------GCC---CGC-ACCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CCU-AUGG-ACAGUGACUGGGGGGACAAACCAUGCAGG--AAACACCU
AALT01627737.1/266-63      CCAACGUG-GA-U-A--UCCC-GGGAG-GUCA-----CUCUCCCC--GGGCAAUGUCCAGGUG--GC-GU-AGAGGAGCAUA--GGGUUCU----GCC-CUGUGAUGUAC-AGUCCC-UUUCCACACCGUUGGAGAUCAAGC------CGGGCCUCGAG----------------UC---UGC-GCCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CCU-CUGG-ACCAUGACUGGGGAGACAAACCAUGCAGG--AAACACAC
AAIY01303410.1/717-923     CCAACGUG-GA-U-A-CUCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCAGGUG--GC-AU-GGAGGAGCACAGGGCUCAGU----GCC-CCGUGAUGUAC-AGUCCU-UUCCCACAACGUUGGAGAUCAAGC-------CGGGCCUGGA---------------GCC---UGC-GCCUGCAUAUUC-------CUACAGCUUCUCAGAGU-CCU-GUGG-ACAAUGACUGAGGAGACAAACCAUGCAGG--AAACAUGU
BAAF04042643.1/3742-3957   CCGACGCG-GA-C-G--UCCA-GAG-A-GUUA-----UGCUC--C--UGGUUCUGUCCGGGUG--GC-GU-AUGGGAGCGUA--GCUCU------GAG-CUGAGACGUAC-AUUCCC-GUUCCACAGCGUCGGACAGAAAGC-----UCCGCCCCCGGC--CUCAGCUGGUGAGGGC--GGGCGUCCUGCAUAUUC-------CUACACCUUCCCAGAGU-CCU-UUGG-GCCGUUACUGGGGAGCUAAACCAUGCAGU--GCACAGAU
AAFR03060641.1/7668-7867   CCAACGAG-GA-U-A--UCC---UGAG-GUCA-----CUCCU--C--CGGCUCUGUCCAGGUG--GC-AA-AAGGGAGCUUA--GGGCUUU---UGCC-CUGUGAUGUAC-AGUCCC-AUUCCACAACGUUGGAUAUCAAGC-------UGGGCUUUGU---------------GUC---UGC-ACCUGCAUAUUC-------CUAAACCUUCUCAGAGU-CU--UUGG-ACUAUGACUGAGGAGACAAACCAUGCAGG--AAACAAUU
AJ493419.1/1-213           UCAAGGUA-GU-C-G--CCCG-GUGAG-UGGA-----CUAU------UGGGUCUGUCCAAGCG--GU-AU-AUAGGAGAGUG--GCCGGUU----GUG-CCGUGAUGUAC-AGUCCCCCUUCCUCAGUGUUGAAGAGCAAGC------CUGUCCUUGGUCCUAGAGCUGAUGAGGGC---AGCAUCCUUUAUAUUC-------CUAUAACUUCUCA--GU-CU--CUAG-ACAAUUACUGAGGAGA--AACCAUGCAGG--GUGCAACA
AANN01441289.1/1208-1009   CCGACGCG-GA-U-A--CCC---UGGG-GUCG-----CUCUC-CC--AGGCUCUGUCCGGGUG--GC-GG-C-GGGAGCGCA--GGGCUCU----GCC-CCAUGACGUAC-AGUCCC-UUUCCACGGCGUCGGAGAUGAAGC------CGGGCCCUGAGUCCAC--------------------GCCUGCAUAUUC-------CUACAGCUUCUCAGAGU-CCC-ACGG-GCCGUGACUGAGGAGACAAACCAUGCAGG--AAACAGUU
AAPN01430738.1/56-260      CCAACAGG-GA-C-A--CCCG-GGGAGGGUCGUUGCCCUCCC-----CGGCUCUGUCCAAGCG--GC-GU-AUGGGAGCGUA--GGGGUCA----CCC-C-GUGACGUAC-AGUCCC-GUUCCGUGCUGUUGGAGAUCAAGC------CGGGCUUCGUG----------------UC---UGC-GCCUGCAUAUUC-------CUACUGCUUCUCUGAGC-CC--CCGG-GCCGUGACAGAGGAGAGAAACCAUGCAGG--AUACAAGC
AJ493421.1/1-189           CCACUAUA-GU-C-C--UCCA-UUGAG-GUUA-----CUUG------UGGCUCUGUCUCUGUG-UGU-GU-AUGUGUG-------------------------------U-AAUUCC-CUUCCACGGUGUUGAAGAGUAAGC------CUGUCCCUGGUUUUAGAGUCAAUAAGGGC---AGCAAUCUUUAUAUUC-------CUAUAACUUCUCC--GU-CU--CUAG-ACAGUUACUGAGAAGG--AACCAUGCAGG--AUGAAGCU
AAKN02028629.1/12706-12503 CCAACGUG-GA-U-A--CCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCAGGUG--GC-AU-AGGGGAGCAUA--GGGCUCU----GCC-CCGUGAUGUAC-AGUCCC-UUUCCACGACGUUGGAGAAGAAGC------CGGGCCUUGUG----------------UC---UGC-GCCUGCAUAUUC-------CUACAACUUCUCAGAGU-CCU-UUGG-ACAGUGACUGAGGAGAUAAACCAUGCAGG--AAACAGUC
AAGV020314116.1/757-553    CCAACGUG-GA-U-A--CCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCAGGUG--GC-GC-AGGGGAGCACA--GGGCUCU----GCC-CAGUGAUGUAC-AGUCCC-AUUCCACAACGUUGGAGAGGAAGC------CGGGCUCUCGA----------------GC---CCCCACCUGCAUAUUC-------CUACAGCUUCUCUGAGU-CUU-AUUG-ACAAUGACUGAGGAGAAAAACCAUGCAGG--AAACAUAU
AAGU03057465.1/82998-83202 CCAACGUG-GA-U-A-UUCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCUGGUG--GC-GC-AGGGGAGCAUA--GGGCUCU----GCC-CCUUGAUGUAC-AAUCCC-UUUCCACGACGUUGGAGAUAAAGC------CGGGCCUUGAG----------------UC---UGC-GCCUGCAUAUUC-------CUACAGCUUCUCAGAGU-CGU-GCAG-ACAAUGACUGAGGAGACAAACCAUGCAGG--AAACAUGU
AAPE02043788.1/16918-17121 CCAACGUG-GA-U-A--CCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCAGGUG--GC-GC-AGGGGAGCAUA--GGGCUCU----GCC-CCGUGAUGUAC-AGUCCC-UUUCCACAACGUUGGAGAGAAAGC------CGGGCCUUGAG----------------UC---UGC-GCCUGCAUAUUC-------CUACAGCUUCUCAGAGU-CCU-GUGG-ACGAUGACUGAGGAGACAAACCAUGCAGG--AAACAUCU
AAWZ02033754.1/83541-83751 CCAAUGGG-GA-U-A--UCUGGGAGAG-GUCGC---GCUCUC--U--CAGCGCUGUCCGCGUG--GC-AU-GUGGGAGCGUA--GGCCUCU---GGGC-CGGUGAUGUAC-AGUCCC-CUUCCACACCAUUGGAGAGCAAGA------CGGGCCUCCUC-----------GGAGGUC---UGCAGCCUGCAUAUUC-------CUACUGCUUCUCUGAGC-CU--UUUG-GCCGUGACUGAGGAGACAAACCAUGCAGG--AGACAUUG
AACZ03060756.1/41573-41365 CCAACAUG-GA-U-A--GCCU-GGGAG-GUCA-----CUCUCCCC--AGGCUCUGUGGAAGUG--GU-GU-UGGGGAGCAUA-GACGUUUGGUCCAUG-AAGUACAGUAC-AGCCCC-UUUCCACAAUGUUGGAGAUGAAGC-----UGGGUCUCCUGU-----------------C---UGC-GCCUGCAUAUUC-------CUAUAGCUUCCCUGAGU-CCU-GUGG-AUGAUGACUGGUGAGACAAAUCGUGCAGG--AAACAUGU
AADN03008159.1/12923-13127 CCAACGAG-GG-C-A--UCCG-GAGAA-GUAG-----CUCUCUCU--CGGCUCUGUCCGUGUG--GC-GC-ACGGGAGCGUA-GGCCUUCG----GGC-CCGAGACGUAU-AUUCCC-CUUCCACAUCGUUGGAGAACAAGC-------UGGGCCUCGA---------------GCC---UGCAGCCUGCAUAUUC-------CUACUGCUUCUCUGAGC-CC--UCGG-GCAGUGACAGAGGAGAUAAACCAUGCAGG--AAACACAU
AAGW02062793.1/5976-5774   CCAACGUG-GA-C-A--CCCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCAGGUG--GC-AC-AGGGGAGCACA--GGGCUCU----GCC-CGAUGACGUAC-AGUCCC-UUCCCACGCCGUUGGAGAGGAAGC------GGGCCUCGAGU-----------------C---UGC-GCCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CCU-GUGG-ACAAUGACUGGGGAGACAAACCAUGCAGG--AAACAGCU
AAQR03135364.1/9001-9204   CCAACGUG-GA-U-A--UCCU-AGGAG-GUCA-----CUCUACCC--AGGCUCUGUCCAAGUG--GC-AU-AGGGGAGCAUA--GGGCUCU----GAC-CCGUGAUGUAC-AGUCCC-UUUCCACACCGUUGGAGAUGAAGC-------UGGGCCUUGA---------------GUC---UGC-ACCUGCAUAUUC-------CUACGACUUCCCAGAGU-CCU-AUGG-ACAAUGACUGGGGAGAGAAACCAUGCAGG--AAACAGCC
AJ493417.1/1-212           CCAAUAUA-GU-U-A--UCCG-UUGAG-GUUA-----CUCG------UGGCUCUGUCCAAGUG--GU-AU-AUGGGAGCGUA--GCCCUAA----CUG-CAAUGAUGUAC-AAUCCC-CUUCCACAGUGUUGAAGAUCAAGC------CUGUCUUUGAUUCUAGAGCUGAUGAGAGC---AGCAUCCUUUAUAUUC-------CUAUAACUUCUCC--GU-CU--CUAG-ACAAUUACUGAGGAGA--AACCUUGCAGG--GCGCAACU
FJ915988.1/4-119           CCC--------------------------UUU------------C-----C-------AC------------------------------A----ACG-UU------------------------------GGAGAUAAAGC------UGG-GCCUUGA---------------GUC---UGC-GCCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CCU-GUGG-ACAAUGACUGGGGAGACAAACCAUGCAGG--AAACAACC
L22738.1/523-728           CCAACGUG-GA-U-A-CACCC-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCAAGUG--GC-GU-AGGGGAGCAUA--GGGCUCU----GCC-CCAUGAUGUACAAGUCCC-UUUCCACAACGUUGGAAAUAAAGC-------UGGGCCUCGU---------------GUC---UGC-GCCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CCU-GUCG-ACAAUUACUGGGGAGACAAACCAUGCAGG--AAACAGCC
U64695.1/8-117             CCA----G-G------------------CUCU----------------------GUCCAAGUG--GC-AU-AGGGGAGCUUA--GGGCUCU----GCC-CCAUGAUGUAC-AGUCCC-UUUCCACAACGUUGAAGAUGAAGC-------UGGGCCUCGU---------------GUC---UGC------------------------------------------GC----------------------------------CUGCAUAU
AY948718.1/2-221           UCGACAUGUGAC-UA--GCGA-UCCUC-UUCG-----GGGUU-GA--UUGCUUU-UCUUAGUG--GA-GC-AUCGGGG------GCUUUCU----GUA-AAGU------U-GACUCC-GAUCCACCUUGUCGUAUACCAACAGUCUGUGUGGCCCUCUAC-CGCUAUUUGAGAUGCCCGGGCUGGAUUGCAUAUUC-------CU-UAUCCUUCCGUAGAUCCU-AUGGGUCCGUGACGGUUAGGACAAACCAUGCAAA--UUACAAAU
U64697.1/3-117             UCUCCCCG-GG-C----------------UCU----------------------GUCCUAGUG--GC-GU-ACGGGAGCAUA--GGGCACU----GCC-CAAUGAUGUAC-AGUCCC-UUUCCACAACGUUGGAGAUGAAGC-------UGGGCUUCGA---------------GUC---UGC------------------------------------------GC----------------------------------CUGCAUAU
L07382.1/2-208             CCAACGUG-GA-U-ACACCCU-GGGAG-GUCA-----CUCUCCCC--GGGCUCUGUCCAAGUG--GC-GU-AGGGGAGCAUA--GGGCUCU----GCC-CCAUGAUGUACAAGUCCC-UUUCCACAACGUUGGAAAUAAAGC-------UGGGCCUCGU---------------GUC---UGC-GCCUGCAUAUUC-------CUACAGCUUCCCAGAGU-CCU-GUCG-ACAAUUACUGGGGAGACAAACCAUGCAGG--AAACAGCC
AJ493423.1/1-212           UCAACAUA-GU-C-A--UCCG-UUGAG-GUUA-----CUUA------UGGGUCUGUCCAAGUG--GU-AU-AUGGGAGUAUA--GCCCUAA----GUG-CAGUGAUGUAC-AGUCCC-CUUCCACAGUGUGGAAGAGCAAGC------CUGUCCCUGGUUCUAGAGCUGAUGAGGGC---AGCAUCCUUUAUAUUC-------CUAUAACUUCUCA--GU-CU--CUAG-ACAAUUACUGAGGAGA--AACCGUGCAGG--GUGCAACU
AJ493425.1/3-138           -------G-GU-U-A---CUA-G------------------------UGGCUCUGUCCAAGUG--GU-AU-UUGGGAGCAUA--GCUCUAA----GUG-CAGUGGUGUAC-AAUCCC-CUUCCACAGUGUUGUAGAGCAAGU------CUGCCUCUGGUUCUAGAGCUGACGAGGAC---AGCAU--------------------------------------C-CU----------------------------------AUAUAUUU
X94942.1/3702-3921         CCGACGUG-GA-C-A--UCCA-GCGAG-CUG------CUCUC--C--UGGCUCUGUCCUGGUG--GCAGU-AUGGGAGCGUA--GCUUU-U----CAG-CAGAGACGUAC-AUUCCC-GUUCCACACCGUCGGAGAGAAAGC-----UCUGUCCCCGGC-CUCUGGCUGGGGUGGAC--GAGCGUCCUGUAUAUUC-------CUACAUCUUCCCAGAGU-CCUACUGG-ACCGUUACUGGGGAGCUAAACCAUGCAGU--GCACAAAC
AJ493424.1/16-138          UCUGCCC---------------------------------------------------AAGUG--GU-AU-AUGGGAGCAUA--GCCCUAA----GUG-CAGUGAUGUAC-AAUCCC-CUUCCACAGUGUUGAAGAGCAAGC------CUGUCUCUGGUCCUAGGGCUGAUGAGGAC---AGCAU--------------------------------------C-CU----------------------------------AUAUAUUU
AJ493418.1/1-212           CCAAUAUG-GU-C-A--UCAA-UUGAG-GUUA-----CUCA------UGGCUCUGUCCAAGUG--GU-AU-AUGGGAGCAUA--GCCCUAA----GUG-CAAUGAUGUAC-AAUCCC-CUUCCACAGUGUUGAAGAGCAAGC------CUGUCUCUGGUUCUAGAGCUGAUGAGGAC---AGCAUCCUAUAUAUUU-------UUAUAACUUCUCA--GU-CU--CUUG-ACAAUUACUGAGGAGA--AACCAUGCAGG--GUGCAACU
U64698.1/3-117             UCUCCCCG-GG-C----------------UCU----------------------GUCCUAGUG--GC-GU-ACGGGAGCUUA--GGGCACU----GCC-CGGUGAUGUAC-AGUCCC-UUUCCACAACGUUGGAGAUGAAGC-------UGGGCUUCGA---------------GUC---UGC------------------------------------------GC----------------------------------CUGCAUAU
#=GC SS_cons               (((((((<.<<.<.<..-<<<.-<<<<.____.....>>>>-..-..>>>--->>>>>,,<<<..<-.--.--<<<<<-<<<..<<_____....___.__>>-->>>->.-->>>>.--->>>>,)))))))---------......-----------------------------...-----<<<<<<<----.......------<<<<<<---<<.<<_.__>>.>>------->>>>>>------->>>>>>>..::::::::
#=GC RF                    cCaAcguG.Ga.c.A..uCcc.gcgaG.GUua.....Cucgc..c..ggGCUCUguCCaaGUG..Gc.gU.AUGGGaGCaua..gcucUcu....Gug.CaguGAuguAC.AauCCC.uUUCCACAacgUuGgAGAgcAAGC......cUGuCCCUgGuucUagaGcUgauGaGGuC...aGCaucCUGcAUAUUC.......CUAuAaCuuccCAgAGu.CcU.uUgG.aCaaUgACUGgggaGAcAAACCAUgCAGg..auACAaaU
//
# STOCKHOLM 1.0

#=GF AC   RF00046
#=GF ID   snoR30
#=GF DE   Small nucleolar RNA R30/Z108
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   60.00
#=GF TC   61.30
#=GF NC   58.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00073
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics. Identification of 140 Candidates for Small
#=GF RT   Non-Messenger RNAs in the Plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol 2002;12:2002-2013.
#=GF CC   snoR30 is a C/D box small nucleolar RNA which acts as a methylation guide
#=GF CC   for 18S ribosomal RNA in plants.
#=GF WK   Small_nucleolar_RNA_R30/Z108
#=GF SQ   6


AJ505639.1/22-116      GGAGAUUACGAUGAGGAUGUACAGCUCCCUCUUCUGAUUAAGCUGAAGAGAAUUGCUGGCAGAAUCGAACCUAAAUCACUAGCCACUACUGAGUU-
AY013245.2/64306-64401 GGCUGUUGCGAUGAGGAUAUUAUGCUCCCUCUUCUGAAGGCAUUGAGGACGCUCGCUGGCAGAAUCGAACCAAUUAUUAAAGCCACCACUGAGUAA
AY013245.2/62208-62303 CGCUGUUGCGAUGAGGAUAUUAUGCUCCCUCUUCUGAAGGCAUUGAGGACGCUCGCUGGCAGAAUCGAACCAAUUAUUAAAGCCACCACUGAGUAA
AY013245.2/60110-60205 GGCUGUUGCGAUGAGGAUAUUAUUCUCCCUCUUCUGAAGGCAUUGAGGACGCUCGCUGGCAGAAUCGAACCAAUUAUUAAAGCCACCACUGAGUAA
AY013245.2/55895-55990 GGCUGUUGCGAUGAGGAUAUUAUGCUCCCUCUUCUGAAGGCAUUGAGGACGCUCGCUGGCAGAAUCGAACAAAUUAUUAAAGCCACCACUGAGUAG
AJ307929.1/7-102       GUCUAUUGCGAUGAGGAUAUUAAGCUCCCUCUUCUGAAGGCAUUGAGGACACUCGCUGGCAGAAUCGAACCAAUUAACAAAGCCACCACUGAGUAA
#=GC SS_cons           :::::<<<<___________________________________________________________________________________>>>>
#=GC RF                GGcuguugCGAUGAGGAUAUuAuGCUCCCUCUUCUGAaggcAUUGAgGAcgcUcGCUGGCAGAAUCGAACcaAuuauuAaAGCCACcACUGAGuaa
//
# STOCKHOLM 1.0

#=GF AC   RF00047
#=GF ID   mir-2
#=GF DE   mir-2 microRNA precursor
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   45.00
#=GF TC   45.10
#=GF NC   44.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000049;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679672
#=GF RT   An extensive class of small RNAs in Caenorhabditis elegans.
#=GF RA   Lee RC, Ambros V
#=GF RL   Science 2001;294:862-864.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the microRNA (miRNA) precursors mir-2 and mir-13
#=GF CC   (MIPF:MIPF0000049). mir-2 has now been predicted or experimentally
#=GF CC   confirmed in a wide range of species. The miRNAs are transcribed as ~70nt
#=GF CC   precursors (modelled here) and subsequently processed by the Dicer enzyme
#=GF CC   to give a ~22nt product. In this case the mature sequence comes from the
#=GF CC   3' arm of the precursor. The extents of the hairpin precursors are not
#=GF CC   generally known and are estimated based on hairpin prediction. The
#=GF CC   products are thought to have regulatory roles through complementarity to
#=GF CC   mRNA. The involvement of Dicer in miRNA processing suggests a relationship
#=GF CC   with the phenomenon of RNA interference. miRNAs are numbered based on the
#=GF CC   mature sequence. This family also contains the mir-13 precursor which,
#=GF CC   despite giving rise to a distinct mature sequence appears to be related in
#=GF CC   sequence.
#=GF WK   mir-2_microRNA_precursor
#=GF SQ   56


AC007769.3/76981-76908           AAUGUCAUCAAAAAGGG-CU-GAAGAAA--GAUA---UUUCUGCAUU-----UGAAUCGUAUCACAGCCAGCUUUGAUGGGCAUUG
AC007769.3/76625-76559           CAUGUCGUUAAAA-UGU-UU-G-UGAACU-UAU--------GUAUUC-----ACAAUCAUAUCACAGCCA-UUUUGACGAGUUUGG
AC023719.4/66771-66704           UAACGCGUCAAAA-UGA-CU-G-UGAGC--UAUG---UGGAUUUG--------ACUUCAUAUCACAGCCA-UUUUGACGAGUUUGU
Z83731.1/29638-29566             AAAGCCAUCAAAG-CGG-UG-GUUGAUG--UGUU---GCAAAUUAUG-----ACUUUCAUAUCACAGCCAGCUUUGAUGUGCUGCC
AC092220.1/147044-147112         ACUGUCUUCAAAG-UGG-CA-G-UGACA--UGUU---GUCAACAA--------UAUUCAUAUCACAGCCAGCUUUGAGGAGCGUUG
AC005128.1/19054-19128           UCAUUCUUCAAAG-UGG-UU-G-UGAAA--UGUU---UGCCUUUUUAUGC--CUAUUCAUAUCACAGCCAGCUUUGAGGAGCGACG
AAIZ01000548.1/11193-11126       CAUGUCGUUAAAA-UGU-UU-G-UGACCU-UAUG---U----ACUCU-----UGAAUCAUAUCACAGCCA-UUUUGACGAGUUUGG
AAAB01008807.1/11606679-11606749 CAGGUCGUAAAAA-UGG-UU-G-UGCCG--UGUC---GAUUUAAGAA-----AAGUUCAUAUCACAGCCA-UUUUGACGAGUUUGA
AAZO01007079.1/41194-41254       CCACUCA-CAAAG-UGG-CU-G-GGGUA--UGUU---G---------------AAUUCAUAUCACAGCCAGCUUUGAUGAGCGGGA
AADK01013541.1/4027-3962         GAUCCUGUCAAAG-CGG-CG-G-UGAAA--UGU--------CUCCUC-----CCUUUCAUAUCACAGCCA-CUUUGAUGUGGUCGG
AADE01000834.1/22052-21985       UAACCCAUCAAA--CGG-UU-G-UGAAA--UGUU---GCAUUUAU-------CAAAUCAUAUCACAGCCA-UUUUGAUGAGUUUCG
AAIZ01000548.1/11570-11497       AGUGUCAUCAAAAAUGG-CU-GAAGAAA--GAUA---UAUUUGCAUU-----UGAAGCGUAUCACAGCCAGCUUUGAUGGGCAUUG
AAGH01000244.1/1102-1034         UAACUCCUCAAAG--GG-UU-G-UGAAA--UGUC---GACUAUUA-U-----CUACUCAUAUCACAGCCA-UUUUGAUGAGUUUCG
AAPU01010520.1/77495-77569       UGAGCUCUCAAAG-AGG-CU-G-UGAAA--UGCAUUUUGAAAGCUUU-----GCGAGCAUAUCACAGCCAGCUUUGAUGAGCUUAG
AANI01013749.1/162155-162082     UGCGCUCUCAAAG-UGG-UU-G-UGAAAUGCAUU---UGAAAGCUUU-----GCGCGCAUAUCACAGCCAGCUUUGAUGAGCUUAG
AANI01017189.1/98316-98382       CAUGUCGUUAAAA-UGC-CU-G-UGACCU-UAU--------GUAUUU-----UAUAUCAUAUCACAGCCA-UUUUGACGAGUUUGG
BAAB01090954.1/2653-2589         CCACUCGUAAAAA-UGG-CU-G-UGUCG--UGUA---G-------CA-----ACCCUCAUAUCACAGCCAUUUUUGACGAGUUGGG
AAGE02012793.1/16205-16139       AGACUC-UCAAAG-UGG-CU-G-UGAAA--UGGU---U----UUAUU-----UUGCUCAUAUCACAGCCAGCUUUGAUGAGCUGGA
AAPU01011022.1/363976-364043     UAACUCUUCAAGG--GG-UU-G-UGAAA--UGUA---GCCAUUAU-------CAAGUCAUAUCACAGCCA-UUUUGAUGAGUUUCG
AASU01000880.1/461-389           UGGGCUCUCAAAG-UGG-UU-G-UGAAA--UGCA---UUUCCGCUUUG----CGCGGCAUAUCACAGCCAGCUUUGAUGAGCUUAG
AAZX01013101.1/18721-18788       CCGAUCGUCAAAU-UGG-UU-G-UGGCG--UGUU---G----UCUAG-----AUUUUCAUAUCACAGCCAUUUUUGACGAGUUGGA
AAGE02012793.1/17697-17627       CGGAUCGUAAAAA-UGG-UU-G-UGCUG--UGUU---GUUACGCUCG-----AAAUUCAUAUCACAGCCA-UUUUGACGAGUUCGA
AAIZ01000971.1/3321-3388         ACGCUCUUUAAAG-UGG-CG-G-UGACG--UGUU---GGUAAUAA--------UAUUCAUAUCACAGCCAGCUUUGA-GAGCGUUG
AAWU01020422.1/10643-10573       CCACUC-UCAAAG-UGG-CU-G-UGAAA--UGGU---UCCUCCAGAA-----AUCGCCAUAUCACAGCCAGCUUUGAAGAGCGAUA
AAWU01020422.1/10370-10299       AGACUCA-CAAAG-UGG-CA-G-UGAAA--UGGU---ACUGUGUUUGA----UAUCGCAUAUCACAGCCAGCUUUGAUGAGCUGGA
AAQB01006412.1/121627-121699     GAGCUCA-CAAAG-UGG-UU-G-UGAAAUGCAUU---AUUUGCUUUA-----UCCAGCAUAUCACAGCCAGCUUUGAUGAGCUCUG
AANI01016575.1/52926-52998       UGGCGCGUCAAAA-UGA-CU-G-UGAGCUAUGUU---GUUGCAUUUG-----CCAUUCAUAUCACAGCCA-UUUUGACGAGUUUGA
AAIZ01004769.1/8926-8993         UUACGCGUCAAAA-UGA-CU-G-UGAGC--UAU------GUGUUUUU-----GAUCUCAUAUCACAGCCA-UUUUGACGAGUUUGA
AAPT01019328.1/229098-229026     AAUGUCAUCAAAAAGGG-CU-G-AGAAU--GAUA---UAUCUGCAAU-----UGAAUCGUAUCACAGCCAGCUUUGAUGGGCAUUG
AAQA01003088.1/958-1028          CGACACGUCAAAG-UGGUCA-G-UGAUG--UGUC---GCAAAAUG-------AAAUUCAUAUCACAGCCAGCUUUGAUGUGUUGUG
AAPU01010520.1/76994-77067       UCAUUCUUCAAAG-UGG-UU-G-UGAAA--UGUU---UGCUUUUUCUGC---CUACUCAUAUCACAGCCAGCUUUGAGGAGCGACA
AAJJ01001714.1/2416-2480         CAAGUCGUCAAUU-UGG-UU-G-UGAAC--UCU---------UAAUU-----UAAACGAUAUCACAGCCA-CUUUGAUGAGCUUGG
AAQB01008610.1/296847-296776     UAACUCUUCAAGG-GGG-UU-G-UGAAA--UGUU---GCCAUUUUAUU----CAACUCAUAUCACAGCCA-UUUUGAUGAGUUUCG
AAEU02000279.1/215063-215137     UCAUUCUUCAAAG-UGG-UU-G-UGAAA--UGUU---UGCCUUUUUCUGC--CUAUUCAUAUCACAGCCAGCUUUGAGGAGCGACG
AAAB01008807.1/11607145-11607220 UGUCUC-UCAAAG-UGG-CU-G-UGAAA--UGGU---GCACUUUCGAUCCGAUAUCUCAUAUCACAGCCAGCUUUGAUGAGCUAGG
AAPT01021140.1/8903-8975         UGGCGCGUCAAAU-UGA-CU-G-UGAGCUAUGUU---GUUGCAGUUG-----UAAUUCAUAUCACAGCCA-UUUUGACGAGUUUGA
AAQB01006881.1/26688-26760       GGUCGCGUCAAAA-UGA-CU-G-UGAGC--UAUG---UUAACCGGUCAG---AAAUUCAUAUCACAGCCA-UUUUGACGAGUUCGA
AAPU01011022.1/363722-363794     AGUGUCAUCAAAAAGGG-CU-G-AGAAU--GAUA---UUUCUGUAAU-----UGAAUUGUAUCACAGCCAGCUUUGAUGGGCACUG
AAQB01008610.1/296699-296630     CAUGUCGUUAAAA-UGU-UU-G-UGACUU-UAUG---UUGUGUCU-------CUAUUCAUAUCACAGCCA-UUUUGACGAGUUUGG
AAPP01015718.1/156815-156885     GGGCUCA-CAAAG-UGG-UU-G-UGAAA--UGCA---UUUCCAUUUU-----GCCCGCAUAUCACAGCCAGCUUUGAUGAGCUUAG
AAPP01016552.1/52617-52684       CAGCGCGUCGAAA-UGA-CU-G-UGACU--UAUG---CGUAUUUG--------AUGUCAUAUCACAGCCA-UUUUGACGAGUUUGG
AAPP01019563.1/1782-1715         UAACUCCUCAAAG--GG-CU-G-UGAAA--UGUU---GCCAUUAU-------CUACUCAUAUCACAGCCA-UUUUGAUGAGUUUCG
AAPP01019563.1/1637-1570         CAUGUCGUUAAAA-GGC-UU-G-UGACCU-UAUG---U----AUUUC-----GCAAUCAUAUCACAGCCA-UUUUGACGAGUUUGG
AAPU01011022.1/364143-364209     CAUGUCGUUAAAA-UGU-CU-G-UGACCG-UAU--------GUAUUC-----ACUAUCAUAUCACAGCCA-UUUUGACGAGUUUGG
AAZX01013101.1/19937-20004       UCGCCCGUCAGAG-UGG-UU-G-UGAUA--UGGU---G----CUAUU-----GAACGCAUAUCACAGCCAGCUUUGAUGUGCGUAA
AAPU01009688.1/35644-35576       UUGCGCGUCAAAU-UGA-CU-G-UGAGC--UAUG---UUUAUGAG-------AUUAUCAUAUCACAGCCA-UUUUGACGAGUUUGA
BAAB01090954.1/2518-2450         UCGCUCA-CAAAG-UGG-UU-G-UCG----UAUG---CGUUUUUACU-----UUGGCCAUAUCACAGCCAGCUUUGAUGAGCGAUG
AAJJ01001714.1/2663-2727         UCGCUCAUCAAC--UGG-AU-G-UGAAA--UGG---------AUUUG-----UAGCUCAUAUCACAGCCAGCUUUGAUGAGCGCUA
AASC02030054.1/11043-11110       CCUGACGUCAAGG-CGG-UU-G-UGAUG--UGGU---G----ACACC-----AUGAGCAUAUCACAGCCAGCUUUGAUGACAGGGA
AAGD02006756.1/79087-79015       AAGCCCGUCAAAG-UGG-CUCG-UGUUA--UGUU---GAAUCUUGAA-----GUAAUCAUAUCACAGCCAGCUUUGAUGUGCUUCC
AASC02030054.1/10795-10859       CAAGGCAUCAAAG-UGA-UU-G-UGAUG--UGU----------UUCA-----ACAAUCAUAUCACAGUCAGCUUUGAUGAGCUUGA
AADG06000036.1/25868-25935       CCGCUCA-CAAAG-UGG-UU-G-UGAUA--UGCU---GAUACGAG--------CGUUCAUAUCACAGCCAGCUUUGAUGAGCGUGG
AEKZ01001510.1/6921-6860         CGAUACAUCAAAU-UGG-UU-G-UGGAA--UGU------------UU-----CGAGUCAUAUCACAGCCA-UUUUGAUGAGCUUGG
ABEG02006312.1/20409-20483       AAGCACGUCAAAG-UGG-CGCG-UGUUA--UGUC---GGAAAUAUGAAA---AGGAUCAUAUCACAGCCAGCUUUGAUGUGCUUGA
AEKZ01001510.1/5353-5287         CCUCCCAUCAGAG-UGG-UU-G-UGA----UGUG---GUAACUUG--------GACUCGUAUCACAGCCAGCUUUGAUGAGCGGAA
AEKZ01001510.1/6572-6502         CCAAUCGUCAAAU-UGG-UU-G-UGGCG--UGUU---GCUUUUCU-A-----GAUUUCAUAUCACAGCCAUUUUUGACGAUUUGGA
#=GC SS_cons                     ::::<<<<<<<<<.<<<.<<.<.<<<--..<<<_...__________.....______>>>>>>>>>>>>->>>>>>>>>::::::
#=GC RF                          uaacuCgUCAAAg.uGG.cU.G.UGAaa..UGuu...guuauuuuuu.....uaaaUCaUAUCACAgCCaGcUUUGAcGaGcUugG
//
# STOCKHOLM 1.0

#=GF AC   RF00048
#=GF ID   Entero_CRE
#=GF PI   CRE
#=GF DE   Enterovirus cis-acting replication element
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:11044080
#=GF GA   55.00
#=GF TC   55.00
#=GF NC   49.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0039703; RNA replication;
#=GF RN   [1]
#=GF RM   11044080
#=GF RT   Identification of an RNA hairpin in poliovirus RNA that serves as the
#=GF RT   primary template in the in vitro uridylylation of VPg.
#=GF RA   Paul AV, Rieder E, Kim DW, van Boom JH, Wimmer E
#=GF RL   J Virol 2000;74:10359-10370.
#=GF RN   [2]
#=GF RM   10775595
#=GF RT   Identification of a cis-acting replication element within the poliovirus
#=GF RT   coding region.
#=GF RA   Goodfellow I, Chaudhry Y, Richardson A, Meredith J, Almond JW, Barclay W,
#=GF RA   Evans DJ
#=GF RL   J Virol 2000;74:4590-4600.
#=GF CC   The first step in the replication of the plus-stranded poliovirus RNA is
#=GF CC   the synthesis of a complementary minus strand. This process is initiated
#=GF CC   by the covalent attachment of UMP to the terminal protein VPg, yielding
#=GF CC   VPgpU and VPgpUpU. A small RNA hairpin in the coding region of protein 2C
#=GF CC   as the site in PV1(M) RNA that is used as the primary template for the in
#=GF CC   vitro uridylylation [1-2].
#=GF WK   Enterovirus_cis-acting_replication_element
#=GF SQ   56


X92886.1/4415-4475   AAUGAGCAACUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGUUUACUCCUU
Y14459.1/4345-4405   AAUUUUAGGAUACAUACAGUUCAAGAGCAAGCAACGGAUUGAGCCUGUAUGUCUCCUGAUU
AF029859.2/4361-4421 GAUGAGCAACUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAGCCUGUAUGUUUACUUCUC
AF039205.1/4361-4421 AAUGAGUAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGCUUGCUACUA
AF081485.1/4369-4429 GAUGAGCAAUUACAUACAAUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGUUUGUUCCUA
AF083069.1/4396-4456 GAUGAGUAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAGCCUGUAUGUUUGCUCCUA
AF085363.1/4369-4429 GAUGAGCAAUUACAUACAAUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGUUUGCUCCUA
AF114383.1/4363-4423 AAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAGCCUGUAUGUUUGCUCCUA
AF119795.2/4397-4457 AAUGAAUAAUUACAUGCAGUUCAAGAGCAAACACCGUAUUGAACCUGUAUGCCUAAUCAUC
AF162711.1/4398-4458 AAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAGCCUGUAUGUUUACUCCUA
AF177911.1/4399-4459 GAUGAACAACUACAUGCAGUUCAAGAGCAAACACCGUAUUGAACCCGUAUGUUUGAUCAUU
AF201894.1/4325-4385 GAUGAAUAACUACAUACAGUUCAAGAGCAAAUCAAGGAUUGAACCCGUAUGUUUAUUAAUC
AF231763.1/4363-4423 GAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGUUUGCUCCUG
AF241359.1/4374-4434 GAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAGCCUGUAUGUCUGCUCUUA
AF268065.1/4364-4424 GAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGUCUCUUGCUC
AF302996.1/4397-4457 AAUGAAUUAUUACAUGCAGUUCAAGAGCAAACACCGAAUUGAACCUGUAUGUCUUAUUAUU
AF304459.1/4399-4459 AAUGAAUAAUUACAUGCAGUUCAAGAGCAAACACCGUAUUGAACCUGUAUGCCUAAUUAUC
AF311938.1/4403-4463 AAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAGCCUGUAUGUUUACUGCUA
AF311939.1/4359-4419 AAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGCCUAUUGCUA
AF316321.2/4400-4460 AAUGAACAAUUACAUGCAGUUCAAGAGCAAACACCGUAUUGAACCUGUAUGUCUCAUCAUU
AF405666.1/4444-4504 AAUAAACAACUACAUACAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGUCUGUUGGUA
AF405669.1/4445-4505 CAUCAAUAACUACAUACAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGUUUGUUAGUG
AF405682.1/4444-4504 CAUUAAUAAUUACAUACAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGUUUGUUAGUA
AF462418.1/4444-4504 CAUAAAUAAUUACGUACAGUUCAAGAGCAAGCACCGUAUUGAGCCAGUAUGUUUGUUAGUG
AF462419.1/4444-4504 CAUAAAUAAUUACGUACAGUUCAAGAGCAAGCACCGUAUUGAGCCAGUAUGUUUGUUAGUA
AF504533.1/4287-4347 GAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGUUUACUCCUG
AF504534.1/666-726   GAUGAGCAACUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUCUGUUUAUUGCUG
AF504536.1/666-726   GAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUCUGUUUAUUGCUG
AJ132960.1/4445-4505 CAUUAACAACUACAUACAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGUUUGCUAGUG
AJ132961.1/4445-4505 UAUUAACAACUACAUACAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGCUUGCUAGUG
AJ276224.1/4393-4453 GAUGAGCAACUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUCUGUCUUUUGCUC
AJ293918.1/4440-4500 AAUUAACAAUUACAUACAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGCUUGUUAGUG
AJ295172.1/4347-4407 ACUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAGCCCGUAUGUUUGCUCCUA
AJ295214.1/163-223   GAUGAGCAACUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUCUGUCUCUUGCUU
AJ416942.1/4444-4504 CAUUAACAACUACAUACAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGUUUGCUAGUA
AY036578.1/4389-4449 AAUGAGCAACUACAUACAGUUCAAGUCCAAAUGCCGCAUUGAACCUGUCUGUCUUCUGCUC
AY036579.1/4390-4450 GAUGAGUAACUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCCGUAUGUCUGCUCUUG
AY056701.1/4247-4307 AAUUAAUAAUUACAUACAGUUCAAGAGCAAACACCGGAUUGAACCAGUAUGUCUAUUAGUG
D00435.1/4364-4424   GAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUCUGUCUCUUGCUC
D00538.1/4407-4467   AAUAAACAAUUAUAUACAGUUCAAGAGCAAACACCGUAUUGAGCCAGUAUGUAUGCUCGUU
D00625.1/4443-4503   GAUUAACAACUACGUACAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGUUUGUUGGUG
D00627.1/4412-4472   GAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAGCCUGUAUGUUUGCUCCUA
D00820.1/4386-4446   AAUUAACAACUACAUACAGUUCAAGUCCAAAUCUCGCAUUGAACCAGUAUGUUUGAUAAUA
D10582.1/1188-1248   GAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGUCUACUUCUA
D90457.1/4467-4527   CAUUAACAACUAUAUCCAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGUAUGUUGAUA
K01392.1/4435-4495   CAUUAAUAAUUACAUACAGUUCAAGAGCAAACACCGUAUUGAGCCAGUAUGUUUGUUAGUG
M16560.1/4353-4413   AAUGAGUAACUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGCUUGCUCUUG
U05876.1/4404-4464   GAUGAAUAACUACAUGCAGUUCAAGAGCAAACACCGUAUUGAACCUGUAUGUCUCAUCAUC
U22521.1/4397-4457   GAUGAAUAACUACAUGCAGUUCAAGAGCAAACACCGUAUUGAACCUGUAUGCUUGAUCAUC
U22522.1/4400-4460   AAUGAAUAAUUACAUGCAGUUCAAGAGCACACACCGUAUUGAACCUGUAUGUCUCAUCAUC
U57056.1/4363-4423   GAUGAGUAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAGCCUGUAUGUCUGCUCCUG
V01148.1/4439-4499   UAUUAACAACUACAUACAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGUUUGCUAGUA
X04468.1/4439-4499   GAUUAACAAUUACAUACAGUUCAAGAGCAAACACCGUAUUGAACCAGUAUGUUUGUUAGUA
X05690.1/4358-4418   AAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGCUUGCUUUUG
X67706.1/4364-4424   AAUGAGUAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAACCUGUAUGUUUGCUUCUG
X84981.1/4384-4444   GAUGAGCAAUUACAUACAGUUCAAGUCCAAAUGCCGUAUUGAGCCUGUAUGUCUACUCCUA
#=GC SS_cons         ::::::::::::<<<<<-<<<<<<---<_______>-->>>>>>-->>>>>::::::::::
#=GC RF              aAUgAacAAuUACAUACAGuUCAAGagCAAAuaCCGUAUUGAaCCuGUAUGUuUguUaaUa
//
# STOCKHOLM 1.0

#=GF AC   RF00049
#=GF ID   SNORD36
#=GF PI   U36
#=GF DE   Small nucleolar RNA SNORD36
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300968;
#=GF DR   snoopy; Oryzias_latipes300058;
#=GF RN   [1]
#=GF RM   8764399
#=GF RT   Intron-encoded, antisense small nucleolar RNAs: the characterization of
#=GF RT   nine novel species points to their direct role as guides for the
#=GF RT   2'-O-ribose methylation of rRNAs.
#=GF RA   Nicoloso M, Qu LH, Michot B, Bachellerie JP
#=GF RL   J Mol Biol 1996;260:178-195.
#=GF RN   [2]
#=GF RM   9703018
#=GF RT   Evolution of U24 and U36 snoRNAs encoded within introns of vertebrate
#=GF RT   rpL7a gene homologs: unique features of mammalian U36 variants.
#=GF RA   Gilley J, Fried M
#=GF RL   DNA Cell Biol 1998;17:591-602.
#=GF CC   U36 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U36 is encoded within the intron of rpL7a, and
#=GF CC   has two regions of complementarity to 18S and 28S ribosomal RNA. This
#=GF CC   complementarity suggests that U36 acts as a 2'-O-ribose methylation guide
#=GF CC   [1,2]. This family also contains snoR47, which has been shown to be
#=GF CC   homologous to U36 [2], and plant Z100 snoRNA.
#=GF WK   Small_nucleolar_RNA_SNORD36
#=GF SQ   59


X52138.1/4300-4372           UUGCA-AUGAUGU---------GAAUCUCU-CACUGAAUUC----AACCUUGAAGU--GCGAAUC--CAUGAGCUUUUUAACCCUGA-GCAAU
X52138.1/3930-4011           CAGCAGUCGAUCGUCA---AAAUUUCUUCGGCCUCGAAAUUCA--CUCGUCGAAGAG-UCAAA----ACCGAGCUUUUUAACACUGA-GUCAG
AB052962.1/8100-8020         GGCCAAAUGAUGCU-----AAAAUAUGUUUUUGCUGAGUCU----UUCUUUGAAGAC-UAACAAA--AUCGAGCUUUUUAAAACUGAUGGUUG
AB052962.1/8576-8491         GAGCAGAUGAUGUUAA---AUACUAGUUGAUCACUGAGAUCUUG-AUCUUUGAUGUC-UAAAAAA--AUCGAGCUUUUUAAAACUGAUGCUUA
AB052962.1/8393-8310         GAGCAUGUGAUGUU-----ACAAGGAGAUGCUACUGAGAUGUUAUAUCGUUGAAGUC-UCUAAAA---CCGAGCUUUUUAAAACUGAUGCUUG
AB052962.1/7854-7779         GAGCAGAUGAUGAU-----AUAUUAUGUUUGUACUGAUU-------UAUUUGAUGUC-UAAAAA----UCGAGCUUUUUAAAACUGAUGCUCA
AJ003043.1/58-131            GUGCA-GUGAUGU------GUGAAUUUCUUCACCUGAAAAU-----AUUGUGAAGAG-U--AA----AUCGAGCUUUUUAACCCUGAGUCGCA
AJ003044.1/85-155            UUGCA-AUGAUGU--------CAAUCUUU-GA-CUGAAGUG-----ACCUUGAAGU--GC-AAUU--ACUGAGCUUUUUAACCCUGA-GCAAU
AJ003047.1/146-218           AUGCA-GUGAUGAC-----UUGAAUUUCUUCACCUGAAACC----UUCAGUGAUGC-----UUU----UUGAGCUUUUUAACCCUGA-GCAUU
AJ003048.1/56-132            UGGCA-AUGAUGU------UUGAAUUUCUUCACCUGAAGUCUC--UAUGUAGAUCA----AAACA--GACGCGCUUUUUAACCCUGA-GCAGG
D14522.1/2533-2609           UGGCA-GUGAUGU------AUGAAUUUCUUCACCUGAGCU-----CAAAGUGAAGAG-CGAAAUA--GACGAGCUUUUUAACCCUGA-GCUUU
D14522.1/2979-3051           UUGCG-AUGAUGU------AUGAAUUUCUUCACCUGAAUC-----AACAAUGAAGA--GCAAA-----AUGAGCUUUUUAACACUGA-GCAAU
X61923.1/2456-2529           UUGCA-AUGAUCU--------CAAUCUCU-CA-CUGAAUUC----AACCUUGAAGUU-GCGAAUC--CAUGAGCUUUUUAACCCUGA-GCAAU
X61923.1/2094-2169           UAGCAGUCGAUGU------CAAAAUUUCUUGGCUCGAAAUU-----ACUGUGAAGAG-U-AAA----AUCGAGCUUUUUAAGAGUGAGUCAGC
X97585.1/1-72                UUGCA-AUGAUGU------AUGAAUUUCUUCACCUGAAUC-----AACAAUGAAGA--GCAAA-----AUGAGCUUUUUAACACUGA-GCAA-
X52138.1/4693-4760           UUGCCAAUGAUGGUU----AAGAAUUUCUUCACCGUAAUA-----AACCAUGUGGU--------------CAGCAUUGCAU--CUGAGGCAAA
X97587.1/1-68                UUGCCAAUGAUGGUU----AAGAAUUUCUUCACCGUAAUA-----AACCAUGUGGU--------------CAGCAUUGCAU--CUGAGGCAAA
AJ003045.1/47-114            UUGCCAGUGAUGCUU----AGGAAUUUCUUCACCUGAAUC-----AACUAUGUGGU--------------CACACUGUUGU--CUGAGGCAAA
AJ003041.1/119-186           UUGCCAAUGAUGGUU----AAGAAUUUCUUCACCUGAAUA-----AACCAUGUGGU--------------CAGCAUUGCAU--CUGAGGCAAA
X61923.1/2849-2915           UUGCCAAUGAUGGUU----AAGAAUU-CUUCACCGUAAUA-----AACCAUGUGGU--------------CAGCAUUGCAU--CUGAGGCAAA
AAPN01441764.1/86-160        UUGCA-AUGAUGU------AUGAAUUUCUUCACCUGAAA------AAGAAUGAAGA--GCAAAUA--CACGAGCUUUUUAACCCUGA-GCAAA
CAAE01014533.1/198985-199061 UUGCA-AUGAUGU------UUGAAUUUCUUCACCUGAAGUC-----ACUGUGUAGA--UCAAAACA-GACGAGCUUUUUAACCCUGA-GCAAG
AAFR03046637.1/96037-96114   UUGCA-AUGAUGU------GUGAAUUUCUUCACCUGAAUUAA---UAGCAUGAAGA--AUAAAUA--CACGAGCUUUUUAACCCUGA-GCAAA
AAVX01327471.1/645-571       CUGCA-AUGAUGUA-----AUGAAUUUCUUCACCUGAAA------AAUCAUGUGGA--CCCAAA---AAUGAGCUUUUUAACCCUGA-GCAGA
BAAE01095776.1/2764-2836     AUGCA-AUGAUGUU-----CAGAAUUUCUUCACCUGAAACU----UUCUAUGAUGGU-U--------UUUGAGCUUUUUAACCCUGA-GCAUU
AACN010181918.1/540-615      UUGACAAUGAUGC------AGGAAUUUCUUCACCUGGAAUC-----UCUGUGAAGA--GUAAA----AUCGAGCUUUUUAACCCUGAGUCACA
AANG01443883.1/11459-11530   UUGCA-AUGAUGU--------GGAUUUCU--CACUGAAUUC----AACUUUGAAGU--GCAAAA---CAUGAGCUUUUUAACCCUGA-GCAGU
AAFC03123178.1/4890-4818     UUGCA-AUGAUGU--------GAACUUCUU--ACUGAAUUA----AACCUUGAAGU--GCAAACA--CAUGAGCUUUUUAACCCUGA-GCAAU
DQ179615.1/241-315           AUGCA-GUGAUGAC-----UCGAAUUUCUUCACCUGAAACU----CACUUUGAUGC--UUUUU-----UUGAGCUUUUUAACCCUGA-GCAUU
AAPY01744257.1/192-267       GUUGCGAUGAUGU------AUGAAUUUCUUCACCUGAAA-------CCAGUGAAGAG-UAAAAA---UCCGAGCUUUUUAACACUGAGUCACA
AB170956.1/1-73              UUGCA-AUGAUGU----------GAAUCUGUCACUGAAUUC----AACCUUGAAGU--GCAAAUC--CAUGAGCUUUUUAACCCUGA-GCAAC
AANN01562901.1/9381-9310     UUGCA-AUGAUGU---------AAGUUCCUUU-CUGAAUAA----GACCUUGAAGU--GCAAAA---UAUGAGCUUUUUAACCCUGA-GCAAU
AANU01042861.1/167-239       UUGUA-AUGAUGU--------GAAUCUCU--CACUGAAUUC----AACCUUGAAGU--GCAAAUC--CGUGAACUUUUUAACCCUGA-GCAAU
AAHX01020526.1/115928-115858 UUGCA-AUGAUGU--------GAAUCUUUU--GCUGAAGUG-----ACCUUGAAGU--GUAAUU---CCUGAGCUUUUUAACCCUGA-GCAAU
AANH01004750.1/5716-5649     AUGCA-AUGAUGAC-----AUGAAUUUCUUCAACUGACAAC--------CUGAUGC--U--------UUUGAGCUUUUUAACCCUGA-GCAUU
AAQQ01357120.1/2206-2280     UUGCA-AUGAUGC----------AAGCCUUUUGCUGAAUUA----GACCUUGAAGUGCAUAUAUA--CUUGAGCUUUUUAACUCUGA-GCAAU
AAYZ01032719.1/7569-7496     UUGCA-GUGAUGC---------AACUUUUUCA-CUGAAUUA----AACCUUGAGAUG-UCAGCUA--CAUGAGCUUUUUAUCCCUGA-GCAAU
AAIY01548945.1/1459-1387     UUGCC-AUGAUGA----------CAGUCAUUCCCUGAAUUA----ACCCUUGAAGC--ACAAACA--CAUGAGCUUUUUACCCCUGA-GCAGC
ABDC01438530.1/394-460       UUGCCAAUGAUGGUU----AAGAAUUUCUUCACCUGAAUA-----AACCGUGUGGU-----CA----------CAUUUUAU--CUGAGGCAAA
AALT01069898.1/1169-1103     UUGCCCGUGAUGGUU----AAGAAUUUCUUCACCUGAAUCG-----UCUAUGUGGU------------CAGAG-----UAUGGCUGAGGCAAA
CU019641.4/7292-7367         CUGCA-AUGAUGUC-----UUGAAUUUCUUCACCUGAAUUC-----AAACUGAAGA--UCAAAA---UACGAGCUUUUUAACCCUGA-GCAAC
AJ869502.1/145-222           UGGCA-AUGAUGUU-----AUGAAUUUCUUCACCUGAGCUC-----AAAAUGAAGA--GCAAAAUA-GACGAGCUUUUUAACCCUGA-GCUCU
AJ890708.1/10-87             YGGCA-AUGAUGUU-----AYGAAUUUCUUCACCUGAGCUC-----AAAGUGAAGA--GCAAAAUA-GACGAGCUUUUUAACCCUGA-GCUUU
AADA01110910.1/1989-2062     UUGCA-GUGAUGU-------AAAAUUUCUUCGCCUGAAAUU-----ACUGUGAAGA--GUAAA----ACCGAGCUUUUUAACACUGAGUCAAC
DQ402459.1/113-188           UGGCA-GUGAUGU------AUGAAUUUCUUCACCUGAGCUC-----CAAGUGAAGA--GCAAAAUA-GACGAGCUUUUUAACCCUGA-GCUU-
AB124893.1/2122-2044         GCCAA-AUGAUGCU-----AAAAUAUUUUAUUGCCGAGUCU----UUCAUUGAAGAC-UAACAAA--AUCGAGCUUUUUAAAACUGA-UGGUU
AARH01001851.1/156318-156401 GAGCAGAUGAUGAGGAUUUUAAUAUUUUGAUUGCUGAUUAA-----UCCAUGAAGCU-UCAAAA---UUCGAGCUUUUUAAAACUGAUGCUCA
AM430325.2/739-654           GGGCAGAUGAUGAAAGAU-AUUAGUAAUUGUUACUGAUAAAU---CUCCAUGAAGCU-UCAAAAA--UUCGAGCUUUUUAAAACUGAUGCCCA
AAZX01011108.1/1884-1957     UUCGU-AUGAUGAC-----AAUUUUUAUUUUAAUUGAAGAA-----ACCAUGAUUU--UUUAU-----UUGAGCUUUUUAACACUGA-CGAAU
AB124892.1/2883-2799         GAGCAGAUGAUGUUAA---UACUAACUAGAUCACUGAGAUCUUG-GUCUUUGAUGU--CUAAAAA--AUCGAGCUUUUUAAAACUGAUGCUUA
AADK01024041.1/3927-3853     CCAAA-GUGAUGU------ACAAAAAUACU--UCCGAAU------AACCAUGUGGU--UAAAAAAUACACGAGCUUUUUAACACUGA-UUGGU
AAXJ01000523.1/18490-18569   UUCCG-AUGAUGACUUU--ACGGAAAUCCAACACUGAAUU------CUCGUGUUGA--GUAAAUCC-AACGAGCUUUUUAACCCUGA-GGAAA
AB124887.1/2162-2084         GCCCA-AUGAUGCU-----AAAGUAUGGUAUUGCUGAGUCU----UUCUUUGAAGAC-UAACAAA--AUCGAGCUUUUUAAAACUGA-UGGUU
AAGV020591270.1/136-208      UUGCA-AUGAUGU--------GAAUCUCU--CACUGAAUCA----AACCGUGAAGU--GCAAAUC--UAUGAGCUUUUUAACCCUGA-GCAAU
AAKN02024174.1/61920-61992   UUGCA-AUGAUGU--------GAAUCUCU--CACUGAAUUA----CGCCAUGAGGUG-UGAAUC---CAUGAGCUUUUUAACCCUGA-GCAGU
AAWR02025921.1/949-1023      -UGGCGAUGAUGC------AUGAAUUUCUUCACCUGGAAUC-----ACCGUGAAGA--GUAAAA---UCCGAGCUUUUUAACCCUGAGUCAU-
AAQR03116520.1/21832-21896   -UGCCAAUGAUGGUU----AAGAAUUUCUUCACCUGAAUA-----AACUAUGUGGU-----CA----------CUUCGUAU--CUGAGGCAA-
AAGJ04050995.1/5140-5064     CCGCA-AUGAUGU------AAGAAUUUCUUCACCUGAAAUAA---UUUCAUGAAGA--UCACAC---AUAGAGCUUUUUAAAACUGA-GCGGA
AAGU03081536.1/6716-6644     -UGGCGAUGAUGA------UGAUAAUUUUUCACCUGAAGUG-----ACCAUGAGGG--GUGAA-----UUGAGCUUUUUAACACUGAGUCAC-
#=GC SS_cons                 <<<<_.________.....______________________....___________..______...____________________.>>>>:
#=GC RF                      uuGCA.AUGAUGuU.....AagAAUUUCUUcacCUGAAuua....aaCcuUGAaGu..ucAAAa...auCGAGCUUUUUAACaCUGA.GCaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00050
#=GF ID   FMN
#=GF PI   RFN
#=GF DE   FMN riboswitch (RFN element)
#=GF AU   Vitreshchak A
#=GF AU   Gelfand M
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Vitreshchak A
#=GF SS   Published; PMID:12456892
#=GF GA   74.00
#=GF TC   74.20
#=GF NC   73.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0010181; FMN binding;
#=GF RN   [1]
#=GF RM   12136096
#=GF RT   Regulation of riboflavin biosynthesis and transport genes in bacteria by
#=GF RT   transcriptional and translational attenuation.
#=GF RA   Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS
#=GF RL   Nucleic Acids Res 2002;30:3141-3151.
#=GF RN   [2]
#=GF RM   10529804
#=GF RT   A conserved RNA structure element involved in the regulation of bacterial
#=GF RT   riboflavin synthesis genes.
#=GF RA   Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA
#=GF RL   Trends Genet 1999;15:439-442.
#=GF RN   [3]
#=GF RM   12456892
#=GF RT   An mRNA structure that controls gene expression by binding FMN.
#=GF RA   Winkler WC, Cohen-Chalamish S, Breaker RR
#=GF RL   Proc Natl Acad Sci U S A 2002;99:15908-15913.
#=GF CC   The RFN element is a highly conserved domain that is found frequently in
#=GF CC   the 5'-untranslated regions of prokaryotic mRNAs that encode for flavin
#=GF CC   mononucleotide (FMN) biosynthesis and transport proteins. This element is
#=GF CC   a metabolite-dependent riboswitch that directly binds FMN in the absence
#=GF CC   of proteins. In Bacillus subtilis, the riboswitch most likely controls
#=GF CC   gene expression by causing premature transcription termination within the
#=GF CC   5' untranslated region of the ribDEAHT operon and precluding access to the
#=GF CC   ribosome-binding site of ypaA mRNA [3].
#=GF WK   FMN_riboswitch
#=GF SQ   144


U27202.1/210-335             AAUAAUCUUCAGGGCAGGGUGAAAUUCCCGAUCGGCGGUA----------------------------------------AAGUCCGCGA-GCCGAACGA----------------------------------------------------AAAAGGUUUGGCAGGAACCGGUGAGAUUCCGGUACCGACAG-UAUAGUCUGGAUGGAAGAAGAUGAAA-
M64472.1/901-1048            GCUUAUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAAAUCAACUCAGUUGA-------------------------AAG-CCGCGA-GCGCUUUGGGUGCGAA---------------------------------------------CUCAAAGGACAGCAGAUCCGGUGUAAUUCCGGGGCCGACGGUUAGAGUCCGGAUGGGAGAGAGUAACG-
AJ009832.1/4549-4670         GAUCGCUCUCGGGGCAGGGUGGAAUUCCCGACCGGCGGUGA---------------------------------------AAGCCCGCGA-GCC----------------------------------------------------------CCCUUCUGGGGGUUGACCCGGUGGAAUUCCGGGGCCGACGGUGAAAGUCCGGAUGGGAGAGAGCGAAG-
AL939108.1/337004-336876     CAGCGCACUCCGGGGUCGGUGAAAGUCCGAACCGGCGGUUA---------------------------------------CAGUCCGCGA-CCCGGUCGCC---------------------------------------------------UCCAGCGACCGGUUGACCAGGUGAAAUUCCUGGACCGACGGUUAAAGUCCGGAUGGGAGGCAGUGCGC-
L09228.1/7992-8136           UUGUAUCUUCGGGGCAGGGUGGAAAUCCCGACCGGCGGUAGUAAAGCACAUUUGCUUUA---------------------GAGCCCGUGA-CCCGUGUGC----------------------------------------------------AUAAGCACGCGGUGGAUUCAGUUUAA-GCUGAAGCCGACAGUGAAAGUCUGGAUGGGAGAAGGAUGAU-
X51510.1/938-1082            UGUAUCCUUCGGGGCAGGGUGGAAAUCCCGACCGGCGGUAGUAAAGCACAUUUGCUUUA---------------------GAGCCCGUGA-CCCGUGUGC----------------------------------------------------AUAAGCACGCGGUGGAUUCAGUUUAA-GCUGAAGCCGACAGUGAAAGUCUGGAUGGGAGAAGGAUGAU-
X95955.1/376-523             UGUAUCCUUCGGGGCUGGGUGAAAAUCCCGACCGGCGGUAAUAAGGCGCUCCUGCGCUUUA-------------------CAGCCCGUGA-CCCGUAUGC----------------------------------------------------AUCUGUAUACGGUGGAUUCAGUGAAAAGCUGAAGCCGACAGUGAAAGUCUGGAUGGGAGAAGGAUGAG-
AJ010128.1/362-218           CAGCAUCUUCGGGGUCGGGUGAAAUUCCCAACCGGCGGUGAUGAAGUGCAAACUUCU-----------------------AAGUCCGUGA-CCCGUUUUCA---------------------------------------------------ACUCGAAAACGGUGGAUCUAGUGAAACUCUAGGGCCGACAG-UAUAGUCUGGAUGGGAGAAGGAUAUGU
AF269345.1/3001-2863         UAUUUCUUUCGGGGCAGGGUGAAAUUCCCAACCGGCAGUAAAUU------------------------------------GAGCCUGCGA-CCCACUAAUAUUGUUUU--------------------------------------------UGAUGUUAGUGGCUGAUCUAGUGUGAAUCUAGAGCCGACAGUUAGAGUCUGGAUGGGAGAAAGAAGUU-
AL591981.1/267609-267487     GUUCAUCUUCGGGGCAGGGUGCAAUUCCCGACCGGUGGUUA---------------------------------------AAGUCCACGA-UCUGC--------------------------------------------------------UUUUUUAGCAGUUGACUCUGGUGUAAUUCCAGGACCGACAG-UAUAGUCUGGAUGGGAGAAGAUGUUG-
AL596170.1/284996-284874     GUUCAUCUUCGGGGCAGGGUGCAAUUCCCGACCGGUGGUUA---------------------------------------AAGUCCACGA-UCUGC--------------------------------------------------------UUUCUUAGCAGUUGACUCUGGUGUAAUUCCAGGACCGACAG-UAUAGUCUGGAUGGGAGAAGAUGUUG-
AL766851.1/11027-10882       AGGUGUCUUCAGGGCAGGGUGUAAUUCCCGACCGGCGGUAAUCGCUUCCAACUUAUUUGUCAGUUGUGAAGCAU------CAGUCCGCGA-GC------------------------------------------------------------------GAAAGCUGAUGUGGUGAGAUUCCACAACCGACAG-UAAAGUCUGGAUGGGAGAAGACAAAG-
AL766847.1/1-103             ------CUUCGGGGUCAGGUGAAAAUCCUAACCGGCGGUA----------------------------------------UAGUCCGCGA-GC---------------------------------------------------------------UUUCGAGCAUGAACUGGUGUGAUUCCAGUACCGACAG-UAAAGUCUGGAUGAGAGAAG-------
AF269712.1/1300-1435         AUUCAUCUUCGGGGUAGGGUGUAAUUCCCAACCGGCAGUAAUCU------------------------------------AAGCCUGCGA--CGACAACGUAUUAAU---------------------------------------------UUUUGCUUUGUCUUGAUUCAGUGAGAGUCUGAAGCCGACAG-UAUAGUCUGGAUGGGAGAAGAUGGAG-
AP008934.1/1304561-1304696   AUUCAUCUUCGGGGUAGGGUGCAAUUCCCAACCGGCAGUAAAUA------------------------------------AAGCCUGCGA-CCCAUUUUAUUAUAU----------------------------------------------AUAAUAAAAUGGCUGAUCUAGUGAAAAUCUAGAGCCGACAG-UAAAGUCUGGAUGGGAGAAGAUGGAG-
CP000705.1/931807-931947     AAUUUUCUUCGGGGCAGGGUGAAAUUCCCAACCGACGGUAACAAGUACGCUUG---------------------------GAGUCCGUGA-CCCGUUAGCAU--------------------------------------------------UUAUGUUAACGGUUGAACCAGUGAAAAUCUGGUACCGACAG-UAUAGUCUGGAUGGGAGAAGAAAACU-
CP000046.1/1565491-1565357   AUUCAUCUUCGGGGUCGGGUGUAAUUCCCAACCGGCAGUAAAUA------------------------------------AAGCCUGCGA-CCUGCUAGUAUGUA-----------------------------------------------UCAUAUUAGUGGCUGAUCUAGUGAGAUUCUAGAGCCGACAG-UAUAGUCUGGAUGGGAGAAGAUGGAG-
CP000703.1/1951702-1951567   UAAUUCUUUCGGGGCAGGGUGAAAUUCCCAACCGGCAGUAAAUA------------------------------------AAGCCUGCGA-CCUGCUAAUAUGUU-----------------------------------------------UCAUAUUAGUGGCUGAUCUAGUGAGAUUCUAGAGCCGACAGUUAAAGUCUGGAUGGGAGAAAGAAUGU-
ABCH01000022.1/43466-43613   UUUUAUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAAAUCAAUGUUUGAU--------------------------AAGCCCGCGA-GCGCUUAACUUUAUGG---------------------------------------------AGUUAAGGUCAGCAGAUCUGGUGAGAAUCCAGAGCCGACGGUUAAAGUCCGGAUGGGAGAGGAUAAUG-
ABDQ01000002.1/179883-180005 UAGUAUCUUCAGGGCAGGGUGUAAUUCCCGACCGGCGGUUA---------------------------------------AAGUCCGCGA-GCUUU--------------------------------------------------------AUUUUUAUAUGGCUGAUUUGGUGAAACUCCAAAACCGACAG-UAAAGUCUGGAUGAGAGAAGGUAUAG-
ABCF01000046.1/1602-1738     AUUCGUCUUCGGGGCAGGGUGUAAUUCCCGACCGGCGGUAAUGAAUGAUUUCAUUCU-----------------------AAGCCCGCGA-GCC----------------------------------------------------------UGUUGUUUGGGCAGGAUUUGGUGAGAUUCCAAAGCCGACAG-UAUAGUCUGGAUGGGAGGAGAUGAAG-
AAEK01000025.1/41573-41430   AGCAUCCUUCGGGGUCGGGUGAAAUUCCCAACCGGCGGUGAUGAAGUGCAAACUUCU-----------------------AAGUCCGUGA-CCCGUUUUCA---------------------------------------------------AAUCGAAAACGGUGGAUCUAGUGAAAUUCUAGGGCCGACAG-UAUAGUCUGGAUGGGAGAAGGAUAUG-
AAOX01000016.1/69993-70130   GUCUAUCUUCGGGGCAGGGUGAAAUUCCCGACCGGCGGUGAUGAGGCAAGUUGCUCU-----------------------AAGCCCGCGA-GC-----CU----------------------------------------------------GUUUUAUUGGGCAGGAUUUGGUGAGAUUCCAAAGCCGACAG-UACAGUCUGGAUGGGAGAAGAUGGAG-
CP000771.1/1532327-1532468   GGGUACUCUCGGGGCAGGGUGAAAUUCCCGACCGGCGGUGA---------------------------------------AAGCCCGCGA-GCCUUCCGAAAGUUUUUAAGUUU--------------------------------------UUUGUAGGAAGGUUGAUCCGGUGGAAUUCCGGAGCCGACGGUGAAAGUCCGGAUGGGAGAGAGUACCA-
CP000382.1/2191386-2191265   UAGUAUCUUCAGGGCAGGGUGUAAUUCCCGACCGGCGGUUA---------------------------------------AAGUCCGCGA-GC-----UA----------------------------------------------------UACUUGGUAUGGCUGAUUUGGUGAGAUUCCAAAACCGACAG-UAAAGUCUGGAUGAGAGAAGGUAUAG-
CP000557.1/2349127-2348995   UACAUCCUUCGGGGCAGGGUGAAAUUCCCGACCGGCGGUGAUGAGGCCGAAGCCUCU-----------------------CAGCCCGCGA-GCC--------------------------------------------------------------GUAUAGGCACGAUCCGGUGCGAUUCCGGAGCCGACAG-UAUAGUCUGGAUGGGAGAAGGAUGAA-
AE017333.1/2382202-2382069   AUCAAUCUUCGGGGCAGGGUGAAAUUCCCUACCGGCGGUGAUGAGCAAGCGCUCU-------------------------AAGCCCGCGA-GC-----------------------------------------------------------CUUUUUAUGGGCAGGAUUCGGUGCGAUUCCGAAGCCGACAG-UAUAGUCUGGAUGGGAGAAGAUGGAG-
ABAH01000018.1/164932-164783 AAUAAUCUUCAGGGCAGGGCGAAAUUCCCUACCGGCGGUAACUGCUUAUAGCAG--------------------------AAGCCCGCGA-GCGCUUUCUAAUAAAAAU-------------------------------------------AGAAAGGUCAAGCAGAUUUGGUGUAAUUCCAAAGCCGACAGUUAAAGUCUGGAUGAAAGAAGAUUGAG-
AAOJ01000002.1/922614-922474 AUUAAUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAUACUUUUCAAGU----------------------------GAGCCCGCGA-GCGCUCGAUAU--------------------------------------------------UUUCGAGGUCAGCAGAUCUGGUUAGAAGCCAGAGCCGACGGUUAUAGUCCGGAUGAGAGAGAAUUGAG-
AE000512.1/1804292-1804171   AAACGCUCUCGGGGCAGGGUGGAAUUCCCGACCGGCGGUGA---------------------------------------AAGCCCGCGA-GCC----------------------------------------------------------CUCUCAGGAGGGUUGACCCGGUGGAAUUCCGGGGCCGACGGUGAAAGUCCGGAUGGGAGAGAGCGUGA-
CP000716.1/48959-48841       UAGAGUCCUCGGGGCAGGGUGAAAGUCCCGACCGGCGGUGA---------------------------------------AAGCCCGCGA-GC-------------------------------------------------------------CCGUUAAGGGUUGAUCCGGUGAAAUUCCGGAGCCGACGGUUAAAGUCCGGAUGGGAGAGGACAAUG-
AAKK02000001.1/258130-258269 AAUUGUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAUACUUUUCAAGU----------------------------GAGCCCGCGA-GCGCUCGAUU---------------------------------------------------CGUCGAGGUCAGCAGAUCUGGUGAGAUGCCAGAGCCGACGGUUAUAGUCCGGAUGAAAGAGAAUAAGA-
BA000043.1/1793427-1793295   AUUCAUCUUCGGGGCAGGGUGAAAUUCCCGACCGGCGGUGAUGAGGCGCUUGGCCUCU----------------------CAGCCCGCGA-GCCGC---------------------------------------------------------------AAGGCAGGAUCCGGUGCGAGUCCGGAGCCGACAG-UAUAGUCUGGAUGGGAGAAGAUGAAG-
AAML04000003.1/43960-44077   GAAGAUCUUCGGGGCAGGGUGAAAUUCCCUACCGGCGGUA----------------------------------------UAGCCCGCGA-AC------------------------------------------------------------UACUUAGGUGGUUGAUUUGGUGAGAUUCCAAAGCCGACAG-UAAAGUCUGGAUGAGAGAAGAUAUUU-
AACY022395047.1/599-750      GCUUAUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAAAUCAACCAUAGCGUUGA----------------------AAGCCCGCGA-GCGCUUUCUGUGAAAG---------------------------------------------CAGAAAGGUCAGCAGAUCCGGUGUAAUUCCGGGGCCGACGGUUAAAGUCCGGAUGGGAGAGAGUAACG-
BA000016.3/704095-704210     AAAAUUCUUCAGGGCAGGGUGAAAUUCCCUACCGGCGGUA----------------------------------------AAGCCCGCGA-GC--------------------------------------------------------------UAGUUUAGCAUGAUUCGGUGAAAUUCCGAGGCCGACAG-UAAAGUCUGGAUGAAAGAAGAAUAUC-
AP006716.1/1452644-1452770   AUUCAUCUUCGGGGUAGGGUGCAAUUCCCAACCGGCAGUAAAUU------------------------------------AAGCCUGCGA-CCCGCUU-------------------------------------------------------CUUUGAAGUGGCUGAUUCAGUGGAAAUCUGAAGCCGACAG-UAUAGUCUGGAUGGAAGAAGAUGGAG-
CP000673.1/3663447-3663329   UAUAAUCUUCAGGGCGGGGUGAAAUUCCCCACCGGCGGUA----------------------------------------UAGCCCGCGA-GC-----------------------------------------------------------UGCGUGUUCAGCAUGAUUCAGUGAAAUUCUGAAGCCGACAG-UAAAGUCUGGAUGGGAGAAGAUAGAA-
CP000653.1/3761427-3761277   GCUUAUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAAAUCAGCCUUGCGCUGA-----------------------AAGCCCGCGA-GCGCUUUGGGUGAAAA---------------------------------------------CCUAAAGGUCAGCAGAUCCGGUGUAAUUCCGGAGCCGACGGUUAGAGUCCGGAUGGGAGAGAGUAACG-
AAER01000019.1/1243-1104     GUCUAUCUUCGGGGCAGGGUGAAAAUCCCGACCGGCGGUGAUGAACUAUUUAUGAUUUUGUUCU----------------AAGCCCGCGA-GCC--------------------------------------------------------------GUUAAGGCAGGAUUUGGUGUGAUUCCAAAGCCGACAG-UAUAGUCUGGAUGGGAGAAGAUGGAG-
AE001437.1/2971922-2971806   AAUGAUCUUCAGGGCAGGGUGAAAUUCCCUACCGGCGGUA----------------------------------------UAGCCCGCGA-GC-------------------------------------------------------------CUUUUUAGGUAUGAUCCGGUUUGAUUCCGGAGCCGACAG-UAAAGUCUGGAUGAAAGAAGAUAUAU-
CP000647.1/3779064-3778913   GCUUAUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAAAUCAACCAUGGCGUUGA----------------------AAGCCCGCGA-GCGCUUCCCGUGACUA---------------------------------------------CGGGAAGGUCAGCAGAUCCGGUGUAAUUCCGGGGCCGACGGUUAAAGUCCGGAUGGGAGAGAGUAACG-
AAEW02000005.1/32930-33076   CCCUAUUCUCAGGGCGGGGUGAAAUUCCCCACCGGCGGUGACUCCUUGUGAG----------------------------AAGCCCGCGA-GCGCCUUUAUUAUUGGG--------------------------------------------AUAAAGGGUCAGCAGAUCUGGUGAGAUUCCAGAGCCGACGGUUAUAGUCCGGAUGAAAGAGGAUAUUC-
CP000141.1/1316951-1316827   UACUACCUUCGGGGUCAGGUGGAAUUCCUAACCGGCGGUA----------------------------------------AAGCCCGCGA-GUCCGUA------------------------------------------------------AAAAUUUACGGAUAGAUCCGGUGAAAUUCCGGAGCCGACAGUUAAAGUCUGGAUGGGAGAAGGUAUUA-
AM236080.1/2884220-2884370   AAAUGUUCUCGGGGCGGGGUGUAAUUCCCCACCGGCGGUAUCAGGAGCAAUCCUG-------------------------GAGCCCGCGA-GCGCUUCCGGCACCUCCUG------------------------------------------UCGGAAGGUCAGCAGAUCCGGUGAGAUGCCGGAGCCGACGG-UAUAGUCCGGAUGGAAGAGGACAACA-
CP000764.1/1319447-1319591   GUCUAUCUUCGGGGCAGGGUGAAAAUCCCGACCGGCGGUAAUGAAUGAGUAUAUGAAUAUGUGAGUUCU-----------AAGCCCGCGA-GCC--------------------------------------------------------------GUUAAGGCAGGAUUUGGUGCGAUUCCAAAGCCGACAG-UACAGUCUGGAUGGGAGAAGAUGGAG-
AE015927.1/318413-318527     AAAUAUCUUCAGGGCGGGGUGUAAUUCCCCACCGGCGGUA----------------------------------------UAGCCCGCGA-GCCGC---------------------------------------------------------------AAGGCAUGAUUCGGUGUAACUCCGAAGCCGACAG-UAAAGUCUGGAUGAAAGAAGGUAUAA-
ABCR01000011.1/7978-7832     GAGCGUUCUCAGGGCGGGGUGGAACUCCCCACCGGCGGUAAGCAUCUGUAUUGUGC------------------------AAGCCCGCGA-GCGCCUCUCUUAU------------------------------------------------GAGGGGGUCAAGCAGAUCAGGUGAAAUUCCUGAGCCGACGGUUAAAGUCCGGAUGGAAGAGAACGUGC-
AAVO02000007.1/6177-6291     AGAUAUCUUCAGGGCAGGGUGAGAUUCCCUACCGGCGGUA----------------------------------------AAGCCCGCGA-GC---------------------------------------------------------------CGAGAGGCAUGAUCCGGUGAGAUUCCGGGGCCGACAG-UACAGUCUGGAUGGAAGAAGAUGAUA-
CP000721.1/562620-562737     AUAUAUCUUCAGGGCAGGGUGUAAAUCCCUACCGGCGGUA----------------------------------------UAGCCCGCGA-GC------------------------------------------------------------UUUUAAGAAAGCAGAUUCGGUGUAACUCCGAGGCCGACAG-UAUAGUCUGGAUGAAAGAAGGUAACC-
AANE01000019.1/87182-87037   UUUCGUUCUCGGGGCGGGGUGAAAUUCCCCACCGGCGGUAAGAACUUAGGUUU---------------------------AAGCCCGCGA-GCGUCUAAUCGUAUA----------------------------------------------GAUUAGAGUCAGCAGAUCUGGUGUGAUUCCAGAGCCGACGGUCAUAGUCCGGAUGAUAGAGAGCGUGU-
CP000411.1/1598055-1598186   UAAAUUCUUCGGGGCAGGGUGUGAUUCCCAACCGACGGUAACAACAUUUUGUUG--------------------------AAGUCCGUGA-CCCGC------------------------------------------------------------GCAAGCGGUUGACCCAGUGAAACUCUGGGACCGACAG-UAUAGUCUGGAUGGGAGAAGAAAUAG-
AAOU01000004.1/94074-94215   AUUAAUUCUCAGGGCGGGGUGGAAUUCCCCACCGGCGGUGUACUUUUUUAAGU---------------------------GAGCCCGCGA-GCGCUCGAUAU--------------------------------------------------UUUUGAGGUCAGCAGAUCUGGUUAGAAGCCAGAGCCGACGGUUAUAGUCCGGAUGAGAGAGAAUUUAA-
AM180355.1/1973352-1973231   CUUAAUCUUCGGGGUAGGGUGAAAUUCCCAAUCGGCGGUA----------------------------------------UAGCCCGCGA-GCCAA--------------------------------------------------------GGUAAAACUUGGUUGAUUUGGUUAAAUUCCAAAGCCGACAG-UAAAGUCUGGAUGGAAGAAGAUAUUU-
CP000416.1/1625123-1624989   UGAUUUCUUCGGGGCAGGGUGAAAUUCCCGACCGACGGUGACAACUUAAAGUUG--------------------------AAGUCCGUGA-CC-----CA----------------------------------------------------CGUUUAACGUGGUUGACCCAGUGUGAGUCUGGGACCGACAG-UAUAGUCUGGAUGGGAGAAGAAACGA-
CP000724.1/1065003-1065119   UAUAAUCUUCAGGGCAGGGUGUAAUUCCCGACCGGCGGUA----------------------------------------AAGUCCGCGA-GC-------------------------------------------------------------CACAAUGUGGUUGACUUGGUGAAACUCCAAGACCGACAG-UAAAGUCUGGAUGGAAGAAGAACAGU-
DQ645592.1/49-179            CGAUUUCUUCGGGGCAGGGUGCAAUUCCCGACCGACGGUAACAACGUAAGUUG---------------------------AAGUCCGUGA-CCCGC------------------------------------------------------------GUGAGCGGUGGACCCAGUGCAAGUCUGGGACCGACAG-UAUAGUCUGGAUGGGAGAAGAAAAUU-
CP000262.1/317676-317799     AAGUGUCUUCAGGGCAGGGUGUGAUUCCCGACCGGCGGUGACUAGUAACUAG----------------------------AAGUCCGCGA-GC------------------------------------------------------------------GCAAGCUGAUGUGGUGUAACUCCACAACCGACAG-UAUAGUCUGGAUGAGAGAAGACCGGG-
AAQL01001388.1/1132-1015     UAACGUCUUCAGGGCAGGGUGCAAGUCCCUACCGGCGGUUA---------------------------------------UAGCCCGCGA-GC-------------------------------------------------------------CUUAUAUGGCAUGACUUGGUGAGAUUCCAAGGCCGACAG-UACAGUCUGGAUGGAAGAAGAUUUAA-
CP000422.1/1801122-1800990   AGAUUUCUUCGGGGCAGGGUGUAAUUCCCGACCGACGGUAACAACCAAGGGUUG--------------------------AAGUCCGUGA-CC-----------------------------------------------------------CGCGAGUAGCGGUGGACCUAGUGAGAGUCUAGGACCGACAG-UAUAGUCUGGAUGGGAGAAGAAACGU-
BA000012.4/6017355-6017207   UAAAGUUCUCAGGGCGGGGUGAAAGUCCCCACCGGCGGUAAGGGCCUCAAACCC--------------------------AAGCCCGCGA-GCGCUUUCCAAGACAAU--------------------------------------------UGGAAAGGUCAGCAGAUCCGGUGUGAUUCCGGAGCCGACGGUUAGAGUCCGGAUGAAAGAGGACGAAA-
AP008232.1/481423-481583     GCUUAUUCUCAGGGCGGGGUGCAAUUCCCCACCGGCGGUAAACCUGGCUAAAGUAUUGCACAGG----------------AAGCCCGCGA-GCGCUCAGGUUGCAUUGCA------------------------------------------GUCUGAGGUCAGCAGAUCCGGUGUAAUUCCGGGGCCGACGGUAAUAGUCCGGAUGGGAGAGAGUAACG-
CP000759.1/1217787-1217947   GCUUGUUCUCGGGGCGGGGUGAAACUCCCCACCGGCGGUAUGAAGCGAAAGUUUC-------------------------GAGCCCGCGA-GCGCCUGAAAAGAUGCCGAUUCGGCUUU---------------------------------GUUCAGGGUCAGCAGAUCCGGUGAGAUGCCGGAGCCGACGGUUAAAGUCCGGAUGGAAGAGAGCGAAU-
CP000023.1/268469-268591     AAGGGUCUUCGGGGCAGGGUGAAACUCCCGACCGGCGGUGAUUCUUUGGAU-----------------------------AAGUCCGCGA-GC------------------------------------------------------------------GCAAGCUGAUGAGGUGUAAUUCCUCAACCGACAG-UAUAGUCUGGAUGGAAGAAGACCAGU-
CP000376.1/319904-319773     UUCCAUUCUCAGGGCGGGGUGAAAUUCCCCACCGGCGGUUA---------------------------------------UAGCCCGCGA-GCGCCACCUCUAC------------------------------------------------GGGGUGGGUCAGCAGAUCCGGUGGAAUUCCGGGGCCGACGGUCAUAGUCCGGAUGGGAGAGAAUGUAC-
AATE01006899.1/660-546       AAAUAUUUUCAGGGCGGGGUGAAAUUCCCCACCGGUGGUA----------------------------------------AAGCCCACGA-GCCGU---------------------------------------------------------------AAGGCAUGAUUUGGUGAAAUUCCAAAGCCGACAG-UAUAGUCUGGAUGAAAGAAAAUUCUU-
CP000414.1/807573-807710     UUUAAUCUUCGGGGCAGGGUGUAAUUCCCGACCGACGGUGAUGGUGAAUAACCU--------------------------CAGUCCGUGA-CCCGCGA-------------------------------------------------------UAUUUUCGCGGUUGACACAGUGAAAUUCUGUGACCGACAGUUAAAGUCUGGAUGGGAGAAGAUUUGA-
AAYC01000017.1/60436-60586   CGCCGUUCUCAGGGCGGGGUGAAAUUCCCCACCGGCGGUAAGCAGGCCUAGUCCCGU-----------------------AAGCCCGCGA-GCGGCUUCCGGUCAUC---------------------------------------------UGGAAGUGUCAGCAGAUCUGGUGCAAUUCCAGAGCCGACGGUUACAGUCCGGAUGGAAGAGAAGGUAC-
AAXV01000008.1/126859-126734 GAUGUUCUUCGGGGUAGGGUGAAAUUCCCAAUCGGCGGUGAUGAAGCAAUUCA---------------------------AAGUCCGUGA-GC------------------------------------------------------------------GCAAGCUGAUUUGGUGCAAAUCCAAAACCGACAGUGAUAGUCUGGAUGGGAGAAGAACAAA-
AE017263.1/670666-670782     UAACAUUUUCGGGGCAAGGCGAAAUUCCUUACCGAUGGUAA---------------------------------------UAGUCCAUGA-ACC--------------------------------------------------------------UUAAUUGGUUGAUUCAGUGAAAUUCUGAAACCGACGG-UAUAGUCCGGAUGGUAGAAAAUGUCA-
CP000749.1/1531976-1531815   CUUCGUUCUCGGGGCGGGGUGUAAUUCCCCACCGGCGGUAAAGACUUUACAUAAGUUAAAUUCU----------------AAGCCCGCGA-GCGCCUUCAAGAAACUUUUC-----------------------------------------UUUUAGGGUCAGCAGAUCUGGUGUAAUUCCAGAGCCGACGGUUAUAGUCCGGAUGAUAGAGAGCGCGU-
AAMR01000023.1/75758-75608   UUUUAUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAUGUCCUUAGCAAAAUCUAAAGAU-----------------AAGCCCGCGA-GCGCUCGAUU---------------------------------------------------CGUCGAGGUCAGCAGAUCUGGUGAGAUGCCAGAGCCGACGGUUAUAGUCCGGAUGAGAGAGAAUGAAA-
CP000261.1/324694-324818     AAGUGUCUUCAGGGCAGGGUGUGAUUCCCGACCGGCGGUGACUAAGUAACUAG---------------------------AAGUCCGCGA-GC------------------------------------------------------------------GCAAGCUGAUGUGGUGUAACUCCACAACCGACAG-UAUAGUCUGGAUGAGAGAAGACCGGG-
CP000155.1/1396507-1396361   ACUUAUUCUCAGGGCAGGGUGAAAUUCCCUACCGGCGGUAUGUCCCCCGUGGAC--------------------------GAGCCCGCGA-GCGCCUGCUGCAGUA----------------------------------------------CAGCAGGGUCAGCAGAUCCGGUGAGAGGCCGGAGCCGACGGUGACAGUCCGGAUGGGAGAGAAUAAGG-
AAPG01000027.1/38942-39095   CACUAUUCUCAGGGCGGGGUGAGAUUCCCCACCGGUGGUAAUUUGUAAAACGUUACAA----------------------CAGCCCACGA-GCGCUUUAUAUUGAAAAA-------------------------------------------UAUAAAGGUCAGCAGAUCCAGUGAAAACCUGGAGCCGACGGUUAAAGUCCGGAUAAAAGAGAAUGAAU-
ABDX01000009.1/107577-107694 AAAAGUCUUCAGGGCGGGGUGUAAGUCCCCACCGGCGGUA----------------------------------------AAGCCCGCGA-GC------------------------------------------------------------UAGUUUUUAGCAUGAUUCGGUGAAAUUCCGAGGCCGACAG-UAUAGUCUGGAUGAAAGAAGAUGAGU-
CP000232.1/950178-950293     AACGUCCUUCGGGGUUAGGUGUAAUUCCUUACCGGCGGUA----------------------------------------AAGCCCGCGA-GCCGU---------------------------------------------------------------UAUGGCAGACCCGGUGAAAUUCCGGGGCCGACAGUAAAAGUCUGGAAGGGAGAAGGAGGUU-
CP000521.1/970595-970445     CAUCG-CUUCAGGGCGGGGUGUAAUUCCCCACCGGUGGUAAAGUUAAUUUUUAUUGUUAAAUUAAC--------------AAGCCCACGA-GCUUAAAUU----------------------------------------------------AUGUAAUUUGAGCAGAUUUGGUGAAACUCCAAAGCCGACGG-UAUAGUCCGGAUGAAAGAAGACGACG-
AAWP01000010.1/3949-3809     CAAUGUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAUACUCUUUUGAGU---------------------------GAGCCCGCGA-GCGCUCGAUU---------------------------------------------------CGUCGAGGUCAGCAGAUCUGGUGAGAUGCCAGAGCCGACGGUUAUAGUCCGGAUGAAAGAGAAUAAGA-
AASA01000089.1/10476-10358   UUUAAUCUUCAGGGCAGGGUGAAAUUCCCGAUCGGCGGUA----------------------------------------AAGUCCGCGA-GC-----------------------------------------------------------CGAGCAAUCGGCAGGAUUUGGUGAAAUUCCAAAACCGACAG-UAUAGUCUGGAUGAAAGAAGAGUCAA-
BA000028.3/3348439-3348301   UGUAUUCUUCGGGGCAGGGUGUAAUUCCCGACCGGCGGUGACAAGUCAUCAGAACUUG----------------------AAGUCCGUGA-CCCGCUU----------------------------------------------------------UUAUGCGGUGGAUCUAGUGAGAAUCUAGAGCCGACAGUAAUAGUCUGGAUGGGAGAAGAAUAGC-
AM263198.1/2000161-2000041   GUUCAUCUUCGGGGCAGGGUGCAAUUCCCGACCGGUGGUUA---------------------------------------AAGUCCACGA-UCUGCUUUU----------------------------------------------------AGCAGUUGAC------UCUGGUGUAAUUCCAGGACCGACAG-UAUAGUCUGGAUGGGAGAAGAUGUUG-
ABCB02000018.1/8466-8595     AGCUGUCUUCGGGGCGGGGUGAAAGUCCCCACCGGCGGUAACCCUUUCAAACAUGGG-----------------------AAGCCCGCGA-GC-----------------------------------------------------------------UGCUUGCUGAUCUGGUGAGAUUCCAGAGCCGACGG-UAUAGUCCGGAUGGAAGAAGAAAAGA-
BA000004.3/1634615-1634762   UUUAUCCUUCGGGGCUGGGUGGAAAUCCCGACCGGCGGUGAUGAAGCGAAUGCUUCU-----------------------UAGUCCGUGA-CCCGGUUGCUGAU------------------------------------------------AUCAGUAAGCGGUGGACCUGGUGAAAAUCCGGGACCGACAGUGAAAGUCUGGAUGGGAGAAGGAAACG-
CP000230.1/2551172-2551329   GCUUGUUCUCAGGGCAGGGUGAAACUCCCGACCGGCGGUAAUCCUUCCCUUUCACGGGGGGGA-----------------CAGCCCGCGA-GCGCCCUUUGCCGGUGGU-------------------------------------------GAAGGGGUCCAGCAGAUCCGGUGCGAAGCCGGAGCCGACGG-UAUAGUCCGGAUGGAAGAGAACGAGG-
AASE01000003.1/858-707       ACCUGUUCUCAGGGCGGGGUGAAAAUCCCCACCGGCGGUAUACCGGCUGUUAAUCCGGA---------------------AAGCCCGCGA-GCGCUUUCGAUUAUU----------------------------------------------UCGAAAGGUCAGCAGAUUUGGUGAAACUCCAAAGCCGACGGUUAUAGUCCGGAUGAAAGAGGAUAGCG-
AAZD01000001.1/551093-550916 UCGCAUUCUCAGGGCAGGGUGAAAUUCCCUACCGGUGGUA----------------------------------------AAGCCCACGA-GCGUUUAAAAGUGCGGUCAAUUUUUGGCAAAUUUUUCUUGCUAAAUUGUCCUGAUUUUCACUUUUAAAGUCAGCAGAUUUGGUGAAAUUCCAAAGCCGACAG-UAAAGUCUGGAUGAAAGAGAAUAAAA-
AE016827.1/145278-145429     GGGCAUUCUCAGGGCAGGGUGAAAUUCCCUACUGGUGGUA-UAUGUUUACAU----------------------------AAGCCCACGA-GCGCCUAUUUUUAUGUGAUGUAG--------------------------------------AAUUAGGGUCAGCAGAUUUGGUGAGAUUCCAAAGCCAACAGUUAAAGUCUGGAUGAAAGAGAAUAAAA-
CP000491.1/171669-171797     GCGUGUUCUCGGGGCGGGGUGCAAUUCCCCACCGGCGGUUA---------------------------------------CAGCCCGCGA-GCGCCUGCAAU--------------------------------------------------CCGCAGGGUCAGCAGAUCCGGUGAAACUCCGGGGCCGACGG-UAUAGUCCGGAUGAAAGAGAAUGGAC-
CP000114.1/817263-817377     GAAUUUCUUCGGGGUCAGGUGAAAAUCCUAACCGGCGGUA----------------------------------------UAGUCCGCGA-GC---------------------------------------------------------------UUUCGAGCAUGAACUGGUGUGAUUCCAGUACCGACAG-UAAAGUCUGGAUGAGAGAAGAAUUCA-
AP006627.1/1930361-1930511   ACUCAACUUCGGGGCAGGGUGUAAAUCCCGACCGGCGGUGAUAAGGCAAUCGCCUUU-----------------------UAGUCCGUGA-CCCGCAUAAGCAUUAC---------------------------------------------UCGUGCGUGCGGUGGAUCUGGUGCAAAUCCAGAGCCGACAGUAAUAGUCUGGAUGGGAGAAGUUCGAG-
CP000133.1/2799767-2799909   CGCCGUUCUCAGGGCGGGGUGAAAGUCCCUACCGGCGGUAUGCAGUUUCGAUUGC-------------------------GAGCCCGCGA-GCGCCUUCCU---------------------------------------------------CGGAAGGGUCAGCAGAUCAGGUGAGAUGCCUGAGCCGACGGUCAUAGUCCGGAUGAAAGAGAACGUGC-
CP000746.1/533105-533234     CCGCAUUCUCAGGGCAGGGUGAAAUUCCCUACUGGCGGUC----------------------------------------AAGCCCGCGA-GCGUUUGUUAUA-------------------------------------------------AGGCAAAGUCAGCAGAUUUGGUGAAAUUCCAAAGCCAACAGUUACAGUCUGGAUGAAAGAGAGUAAAC-
CP000152.1/1720041-1720197   GAACGUUCUCGGGGCGGGGUGAAAUUCCCCACCGGCGGUAAUCGCGCGAUUGCGCG------------------------UAGCCCGCGA-GCGCUUGCCGGCACGCAUGUGCC--------------------------------------CGGCAAGGUCAGCAGACCCGGUUGGAUUCCGGGGCCGACGGUCAAAGUCCGGAUGAGAGAGAGCGGGG-
AP008230.1/4208512-4208661   ACGAACCUUCGAGGCAGGGUGAAAUUCCCGACCGGCGGUAAUAAUUGCCCGUGCAAUU----------------------CAGCCCGCAA-CUCAGUGCAGCUCCA----------------------------------------------GUGCUGCACCGACUGACUUGGUGAGACUCCAAGGCCGACGG-UAUAGUCCGGAUGGGAGAAGGUACAA-
CP000387.1/1760462-1760315   UGAUGUCUUCAGGGCAGGGUGAGAUUCCCGACCGGCGGUAAUUUUUGGAUUGGAAUUUUUUUCUCCAUGUCAAAUC----AAGUCCGCGA-GC------------------------------------------------------------------GCAAGCUGAUGUGGUGAGAUUCCACAACCGACAG-UAUAGUCUGGAUGGGAGAAGACGAGA-
AAXB02000021.1/33038-32924   CGAAAUCUUCAGGGCAGGGUGCGAUUCCCUACCGGCGGUA----------------------------------------AAGCCCGCGG-GC---------------------------------------------------------------CGAGAGGCAUGAUCCGGUGUGAUUCCGGAGCCGACAG-UAUAGUCUGGAUGAAAGAAGAUGAUG-
AE017143.1/943036-943169     UUUAAUCUUCAGGGCAGGGUGAAAUUCCCGAUCGGUGGUA----------------------------------------AAGUCCGCGA-GCCGAACUUCGAUUAAC--------------------------------------------AUCAAGUUUAGCAGGAACUAGUGAAAUUCUAGUACCGACAG-UAUAGUCUGGAUGGAAGAAGAGCAGA-
CP000679.1/895035-894907     UCCAUCCUUCGGGGCGGGGUGAAAUUCCCCACUGGCGGUAA---------------------------------------AAGCCCGCGA-GCAAAAGCCU---------------------------------------------------UUCUGGCUUUUGCAGAACCGGUGGAAUUCCGGUGCCAACGGUUACAGUCCGGAUGGGAGAAGGAAUGG-
AE017221.1/684544-684423     CACCUCCUUCGGGGCGGGGUGGAAGUCCCCACCGGCGGUGA---------------------------------------AAGCCCGCGA-AGC----------------------------------------------------------CCCUAAAGGGGCCCGACCCGGUGGAAUUCCGGGGCCGACGGUGAAAGUCCGGAUGGGAGAAGGAGGGC-
CP000423.1/1361659-1361777   GUUCGUCUUCAGGGCAGGGUGCAAUUCCCGACCGGCGGUA----------------------------------------UAGUCCGCGA-CCCGC------------------------------------------------------------UUAUGCGGUGGAACCGGUGUGACUCCGGUACCGAUAGUGAUAGUCUAGAUGGAAGAAGAUGGGG-
AAZF01000001.1/50869-51046   GCGCAUUCUCAGGGCAGGGCGAAAUUCCCUACCGGUGGUA----------------------------------------AAGCCCACGA-GCGUUUAAAAGUGCGGUCAAUUUCAGGCAAGUUUUUUCUGCGAAAUUGCCCUGACAUUCAUUUUUAAAGUCAGCAGAUUUGGUGAAAUUCCAAAGCCGACAG-UAAAGUCUGGAUGAAAGAGAAUAAAA-
BX640436.1/209532-209685     GUACGUCUUCAGGGCGGGGUGCAAUUCCCCACCGGCGGUAUGCCACGCAAUGUGGC------------------------GAGCCCGCGA-GCGCCCUGCGUUGGCAACAG-----------------------------------------CGCAGGGGUCAGCAGACCUGGUGAGAUGCCAGGGCCGACGGUCAUAGUCCGGAUGAGAGAAGAUGUGC-
AE009951.2/10346-10461       UAAAGUCUUCAGGGCAGGGUGAAAUUCCCGACCGGUGGUA----------------------------------------CAGUCCACGA-AAG--------------------------------------------------------------CAUUUGCUUUGAUUUGGUGAAAUUCCAAAACCGACAG-UAGAGUCUGGAUGGGAGAAGAAUUAG-
CT573326.1/621066-620925     AAGGGUCUUCAGGGCGGGGUGAAAGUCCCCACCGGCGGUAA-AUCGAAAGAU----------------------------GAGCCCGCGA-GCGCCCCGGCCAU------------------------------------------------GCCGGGGGUCAGCAGAUCUGGUGAGAUUCCAGGGCCGACGGUCAUAGUCCGGAUGAAAGAAGGCGUUU-
CP000612.1/832798-832653     ACUUGUUCUCAGGGCGGGGUGAAAGUCCCUACUGGCGGUAUCCAGUUCACACUGG-------------------------GAGCCCGCGA-GCGCUCCUUAUUAU-----------------------------------------------AUAGGAGGACAGCAGAUCUGGUGAAAAGCCAGGGCCAACGG-UAUAGUCCGGAUGAAAGAGGAUAAGG-
CP000009.1/1075963-1076120   AGACGUUCUCAGGGCGGGGUGAAAUUCUCCACCGGCGGUAUUGGCGGAUUUCUCCGCCU---------------------CAGCCCGCGA-GCGCCUUCCGGAUUUCGGUUC----------------------------------------GGAAGGGACAAGCAGAUCCGGUGAGACUCCGGAGCCGACGGUUAGAGUCCGGAUGGAAGAGAACGCAG-
AE016825.1/4551002-4551150   UUACGUCUUCGGGGCGGGGUGCAACUCCCCACCGGCGGUAUGGCGCGCAAGCGCC-------------------------GAGCCCGCGA-GCGCCUUUGCCUGACG---------------------------------------------GCAAAGGGUCAGCAGAUCUGGUGAAACGCCAGAGCCGACGGUAAUAGUCCGGAUGAGAGAAGACGACG-
CP000362.1/544510-544358     GCGUAUUCUCAGGGCGGGGUGAAAUUCCCCACCGGCGGUAUGUGGGGCGUGACCUUAC----------------------GAGCCCGCGA-GCGGCCUUUCCCGAACU--------------------------------------------GAAGGGUUUCAGCAGAUCUGGUGAGAUGCCAGAGCCGACGGUCAUAGUCCGGAUGAAAGAGAAUGCGA-
CP000728.1/3149843-3149956   AGUAUCCUUCAGGGUUGGGUGAAAUUCCCUAUCGGCGGUA----------------------------------------UAGCCCGCAA-GC----------------------------------------------------------------CAUAAGGCAGAUUCGGUUAAAUUCCGAAGCCGACAG-UAUAGUCUGGAUGAAAGAAGGUAAAU-
AY246427.1/2402-2556         UUCUGUUCUCAGGGCGGGGUGAAACUCCCCACCGGCGGUAAGAGUUUCGGCUC---------------------------GAGCCCGCGA-GCGCCUUCCCUCGUGUCCAAGCGG-------------------------------------GGGAAGGGUCAACAGAUCCGGUGCGAUUCCGGAGCCGACGGUUAAAGUCCGGAUGGAAGAGAAUGAGU-
CP000626.1/213449-213587     CAAUAUUCUCAGGGCGGGGCGAAAUUCCCCACCGGUGGUA-UGCCGCAAGGC----------------------------GAGCCCACGA-GCGCUCGAUU---------------------------------------------------CGUCGAGGUCAGCAGAUCUGGUGAGAAGCCAGAGCCGACGGUUACAGUCCGGAUGAGAGAGAAUGACA-
BX950851.1/1001970-1002170   GCUUAUUCUCAGGGCGGGGUGUAAUUCCCCACCGGCGGUAAACCAGUGAACGUAUGAACGAAUAAGGUUCUGCGCACUGGAAGCCCGCGA-GCGCUCAGGCUGUGUUUUCCGAUAUCAAUUGUCGGUUUUCGCA------------------ACAUGAGGUCAGCAGACCCGGUGUAAUUCCGGGGCCGACGGUUAAAGUCCGGAUGGGAGAGAGUAACG-
L47648.1/1826-1960           AUCAAUCUUCGGGGCAGGGUGAAAUUCCCUACCGGCGGUGAUGAGCCAAUGGCUCU------------------------AAGCCCGCGA-GC-----------------------------------------------------------UGUCUUUACAGCAGGAUUCGGUGAGAUUCCGGAGCCGACAG-UACAGUCUGGAUGGGAGAAGAUGGAG-
ABED02000028.1/57463-57577   AGAAAUCUUCAGGGCAGGGUGCGAUUCCCUACCGGUGGUA----------------------------------------CAGCCCACGA-GCCGU---------------------------------------------------------------AAGGCAUGAUUCGGUGAAACUCCGAAGCCGACAG-UACAGUCUGGAUGAAAGAAGAUACCA-
ABCC02000026.1/45214-45328   UAAUAUCUUCAGGGCAGGGUGCAAUUCCCUACCGGUGGUA----------------------------------------CAGCCCACGA-GCCGC---------------------------------------------------------------AAGGCAUGAUUCGGUGAAACUCCGAAGCCGACAG-UACAGUCUGGAUGAAAGAAGAUGGAA-
AE005176.1/1307881-1307745   AAAUAUCUUCAGGGCACCGUGUAAUUCGGGACCGGCGGUAAAUAGGGCUUUGACCUUAU---------------------GACUCCGCGAUUCGCUAC-------------------------------------------------------------GGCGAUUGAAGCAGUGAGAAUCUGCUAGCGACAG-UAAAGUCUGGAUGGAAGAAGAUGAAC-
CP000826.1/4751561-4751400   GCUUAUUCUCAGGGCGGGGUGCAAGUCCCCACCGGCGGUAAAUCACCUUCUACGGUGA----------------------AAGCCCGCGA-GCGCUCAGCCAGUCUCUUGCAGUUUG-----------------------------------GUUAGAGGUCAGCAGAUCCGGUGUAAUUCCGGGGCCGACGGUUAUAGUCCGGAUGGGAGAGAGUAACG-
CP001581.1/209561-209677     UUAUAUCUUCAGGGCGGGGUGUAAUUCCCCACCGGCGGUA----------------------------------------AAGCCCGCGA-GC-------------------------------------------------------------UAUUUUUAGCAUGAUUCGGUUAAAUUCCGAAGCCGACAG-UAAAGUCUGGAUGGAAGAAGAUUAUA-
CP001348.1/3959917-3960045   UAAUAUCUUCAGGGCAGGGUGCGAUUCCCUACCGGCGGUAAUGUACUAUUUAGUAU------------------------UAGCCCGCGA-GCG-----------------------------------------------------------------UUUUGCAGACAUGGUGUGAUUCCAUGGCCGACAG-UACAGUCUGGAUGAAAGAAGAAACAG-
ACOM01000004.1/361838-361724 AUAUAUCUUCAGGGCAGGGUGAAAAUCCCUACUGGCGGUA----------------------------------------CAGCCCGCGA-GC---------------------------------------------------------------UAUUUUAGCAGAUUCGGUGUAAUUCCGAAGCCAACAG-UAUAGUCUGGAUGAAAGAAGGUAACC-
CP000923.1/23974-24088       UAAAACCUUCAGGGAUCGGUGAAAUUCCGUACCGGCGGUA----------------------------------------UAGCCCGCGA-GC----------------------------------------------------------------CUUUUGGCAGACUCGGUGAAAUUCCGAGGCCGACAGUUAAAGUCUGGAUGGGAGAAGGAGAAA-
CP001022.1/2287514-2287654   UUCCAUCUUCAGGGCAGGGUGAAAUUCCCGACCGGCGGUAAACAGGCGAUUCGCCUG-----------------------AAGCCCGCGA-GCGAAUA------------------------------------------------------GGGCGCUAUUUGCUGAUUCUGUGUAACUCAGGAGCCGACAG-UAUAGUCUGGAUGGGAGAAGAUGGCG-
AE007869.2/1872198-1872348   GGUUGUUCUCAGGGCGGGGUGCAAUUCCCCACCGGCGGUAUCGGGAUUUGUCCCG-------------------------GAGCCCGCGA-GCGCUUCCGGUCUCCAAAG------------------------------------------CCGGAAGGUCAGCAGAUCCGGUGAGAGGCCGGAGCCGACGG-UAUAGUCCGGAUGGAAGAGGACAAGG-
CP001111.1/691560-691705     AAACGUCUUCAGGGCGGGGUGCGAUUCCCCACCGGCGGUAGGUGCGCAAGCAC---------------------------GAGCCCGCGA-GCGCUCCGGCCUUACC---------------------------------------------GCCGGGGGUCAGCAGAUCCGGUCCAAUGCCGGAGCCGACGG-UAUAGUCCGGAUGAAAGAAGACGGUG-
AE016828.2/594013-594149     AAGCGCCUUCAGGGCGGGGUGGAAGUCCCCACCGGCGGUAAGUUUCUUUGAAAU--------------------------AAGCCCGCGA-GUCUC--------------------------------------------------------UAUUUUAAGAGACAGAUCUGGUUAAAUUCCAGAGCCGACGGUCAGAGUCCGGAUGAGAGAAGGUAUGC-
AE008922.1/837066-837234     GAACGUCUUCAGGGCGGGGUGCGAUUCCCCACCGGCGGUAUGCAUGCGCAAGCGUGU-----------------------GAGCCCGCGA-GCGCUUCGCUGCCGAUCUCUCGCUGAGAGCACGGC--------------------------GGUGAAGGUCAGCAGAUCCGGUGCGAUGCCGGGGCCGACGG-UAUAGUCCGGAUGAAAGAAGACGGCC-
CP001098.1/1089819-1089940   AAAUGCUAACGGGAUACGGUGAGAUUCCGAACCGGUGGUGA---------------------------------------AAGUCCACAA-GC-----CA----------------------------------------------------UAUUUAUUAUGGUUGAUUUGGUGAAAUUCCAAAACCGACAG-UAUAGUCUGGAAGGGAGUUAGCAUUG-
CP000919.1/179511-179397     AACUAUCUUCAGGGCAGGGUGCAAUUCCCUACCGGUGGUA----------------------------------------UAGCCCACGA-GC---------------------------------------------------------------CGAAAGGCAUGAUUUGGUGAAAUUCCAAAGCCGACAG-UAUAGUCUGGAUGAAAGAAGAUAAAA-
CP000903.1/3971775-3971918   AACAUCCUUCGGGGUCGGGUGAAAUUCCCAACCGGCGGUGAUGAAGCGAUAGCUUCU-----------------------AAGUCCGUGA-CCCGUUUUCA---------------------------------------------------ACGCGAAAACGGUGGAUCUAGUGAAACUCUAGGGCCGACAG-UAUAGUCUGGAUGGGAGAAGGAUAUG-
ABAX03000010.1/110704-110590 UAGGAUCUUCAGGGCAGGGUGAAAUUCCCUACCGGUGGUA----------------------------------------CAGCCCACGA-GCCGC---------------------------------------------------------------AAGGCAUGAUUCGGUGAAACUCCGAAGCCGACAG-UACAGUCUGGAUGAAAGAAGAUAGUG-
AE008691.1/541539-541640     ---------CGGGGCAGGGUGGAAUUCCCGACCGGCAGUGA---------------------------------------AAGCCUGCGA-GCC------------------------------------------------------------GCAUAUGCGGUUGACUCGGUGAAAUUCCGAGGCCGACGGUAAAAGUCCGGAUGGGAG----------
AL591688.1/2398173-2398337   AAGCGUUCUCAGGGCGGGGUGAAAUUCCCCACCGGCGGUAGCGAACACAGGAUCGGGAAUGGUCGGUGGUCG--------GAGCCCGCGA-GCGCUUCGCAUUUCG----------------------------------------------UGCGAAGGUCAGCAGAUCCGGUCGAAUUCCGGAGCCGACGGUUAUAGUCCGGAUGGAAGAGAGCAAGC-
AE005176.1/1021729-1021845   AUAAAUCUUCAGGGCAGGGUGUAAUUCCCUACCGGCGGUA----------------------------------------UAGCCCGCGA-GC-------------------------------------------------------------UGCUUGCAGCAUGAUUCGGUGAAACUCCGAGGCCGACAG-UAUAGUCUGGAUGAAAGAAGAUAAUA-
AE004439.1/1582210-1582055   GCGCAUUCUCAGGGCAGGGUGAAAUUCCCUACCGGUGGUAAAUGUAUAACAU----------------------------AAGCCCACGA-GCGUUUACUAUUUCAUGUCACAAGAGA----------------------------------UAGUAAAGUCAGCAGAUUUGGUGAGAAUCCAAAGCCGACAG-UAUAGUCUGGAUGAAAGAGAAUAAGC-
CP000873.1/673354-673517     GCUUGUUCUCGGGGCGGGGUGAAACUCCCCACCGGCGGUAUGAAAAGCAAUUUUC-------------------------AAGCCCGCGA-GCGCCUGAAAUGGAAGCCGAUUCGCAUGCCA------------------------------UUUCAGGGUCAGCAGAUCCGGUGAGAUGCCGGAGCCGACGGUUAAAGUCCGGAUGGAAGAGAGCGAAU-
ABCA03000041.1/6063-5943     AAUCUGUUUCAGGGCGGAGUGAAAUUCUCCACCGGUGGUA----------------------------------------AAGUCCACGA-GC-----GC----------------------------------------------------AAAGUAUUUGUGCCGAUUCGGUGAAAUUCCGAAACCGACGG-UAUAGUCCGGAUGAAAGAAUCAGAAA-
CP000909.1/2997673-2997805   GAAGACCUUCGGGGCAAGGUGAAAUUCCUGAUCGGCGGUAAUGGUGGCGUGCCCACAC----------------------AAGCCCGCGA-GCCGU---------------------------------------------------------------AAGGCAGGACCCGGUGUGAUUCCGGGGCCGACGG-UAUAGUCCGGAUGGGAGAAGGUCGGC-
CP001336.1/3015833-3015947   GAAUACCUCUGGGGAUUGGUGAAAUUCCAUACCGGCGGUC----------------------------------------AAGCCCGCGA-GC---------------------------------------------------------------CAUUAUGGCAGAUCUGGUGUAAUUCCAGAGCCGACAG-UAAAGUCUGGAUGAGAAGAGGAAAUU-
CP000853.1/2675114-2674995   AUGAUUCUUCAGGGCAGGGUGAAAUUCCCGACCGGCGGUA----------------------------------------UAGUCCGCGA-CUC----------------------------------------------------------GAUAUACAUCGAUUGAACUGGUGAGAUUCCAGUACCGACAG-UAAAGUCUGGAUGGGAGAAGAAAAAG-
ABDE02000001.1/586343-586474 AUAAGUCUUCGGGGCGGGGUGAAAUUCCCUACCGGCGGUGA---------------------------------------AAGUCCGCGA-ACUUCGGGAACACG-----------------------------------------------GUGUUUCCGGAGCCGAUCCGGUGCGAUUCCGGAACCGACAG-UAAAGUCUGGAUGAAAGAAGGCUGAC-
CP001645.1/912076-912231     GUACGUCUUCAGGGCGGGGUGAAAUUCCCCACCGGCGGUAUGCGGACCGUGUGUCCGU----------------------GAGCCCGCGA-GCGCCUUGCAUGCGCCUGCA-----------------------------------------UGCAGGGGUCAGCAGAUCCGGUGAAAUGCCGGGGCCGACGGUCAGAGUCCGGAUGGAAGAAGAUGUGC-
AE016796.2/1572120-1571980   UUUUAUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAUACCGAAUGAGGU---------------------------GAGCCCGCGA-GCGCUCGAUU---------------------------------------------------CGUCGAGGUCAGCAGAUCUGGUGAGAGGCCAGAGCCGACGGUUAUAGUCCGGAUGAGAGAGAAUGAAA-
CP003056.1/1405866-1406005   AUUUUCCUUCGGGGCAGGGUGCAAUUCCCGACCGGCGGUGAUGAGGAAACUCA---------------------------AAGCCCGUGA-CCCGUAUUC----------------------------------------------------UCCGGAAUGCGGUGGAUUUGGUGAAAUUCCAAAGCCGACAGUGACAGUCUGGAUGGGAGAAGGAUCAA-
#=GC SS_cons                 ::((((((((,,,,,,<<<_______>>>,,,,,<<<<_______________...........................____>>>>,,.,,,,,,,,,,...................................................,,,,,,,,,,,,,,,,<<<<<_______>>>>>,,,,,<<<.______>>>,,,,,,,))))))))::.
#=GC RF                      aaucguccUCaGGGCaGGGUGaAAUUCCCuACCGGCGGUAAuuaauuaaauuu...........................aAGcCCGCGA.gCguuuaaaa...................................................uuuuaaagucagcaGAuccGGUGaaAuUCCggaGCCGACgG.UAuAGUCcGGAUGgaAGAggacgaaa.
//
# STOCKHOLM 1.0

#=GF AC   RF00051
#=GF ID   mir-17
#=GF DE   mir-17 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   45.00
#=GF TC   47.10
#=GF NC   44.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science 2001;294:853-858.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the microRNA (miRNA) precursor mir-17, family,
#=GF CC   which includes mir-20, mir-91, and mir-103. miRNAs are transcribed as
#=GF CC   ~70nt precursors (modelled here) and subsequently processed by the Dicer
#=GF CC   enzyme to give a ~22nt product. In this case the mature sequence comes
#=GF CC   from the 3' arm of the precursor. The extents of the hairpin precursors
#=GF CC   are not generally known and are estimated based on hairpin prediction. The
#=GF CC   products are thought to have regulatory roles through complementarity to
#=GF CC   mRNA. The involvement of Dicer in miRNA processing suggests a relationship
#=GF CC   with the phenomenon of RNA interference. miRNAs are numbered based on the
#=GF CC   sequence of the mature RNA.
#=GF WK   mir-17_microRNA_precursor_family
#=GF SQ   54


AY866334.1/211-294   CCCUGCCGGGGCUAAAGUGCUGACAGUGCAGAUAGUGGUCCUCUCCG-UGCUACCGCACUGUGGGUACUUGCUGCUCCAGCAGGG
AY866338.1/212-295   CCCUGCCGGGGCUAAAGUGCUGACAGUGCAGAUAGUGGUCCUCUCCG-UGCUACCGCACUGUGGGUACUUGCUGCUCCAGCAGGG
AY866337.1/226-309   CCCUGCCGGGGCUAAAGUGCUGACAGUGCAGAUAGUGGUCCUCUCCG-UGCUACCGCACUGUGGGUACUUGCUGCUCCAGCAGGG
AY866340.1/206-289   CCCUGCCGGGGCUAAAGUGCUGACAGUGCAGAUAGUGGUCCUCUCCG-UGCUACCGCACUGUGGGUACUUGCUGCUCCAGCAGGG
AY866336.1/211-294   CCCUGCCGGGGCUAAAGUGCUGACAGUGCAGAUAGUGGUCCUCUCCG-UGCUACCGCACUGUGGGUACUUGCUGCUCCAGCAGGG
AY866335.1/233-316   CCCUGCCGGGGCUAAAGUGCUGACAGUGCAGAUAGUGGUCCUCUCCG-UGCUACCGCACUGUGGGUACUUGCUGCUCCAGCAGGG
AY866339.1/221-304   CCCUGCUGGGGCUAAAGUGCUGACAGUGCAGAUAGUGGUCCUCUCCG-UGCUACCGCACUGUGGGUACUUGCUGCUCCAGCAGGG
AY866342.1/235-318   CCCUGCUGGGGCUAAAGUGCUGACAGUGCAGAUAGUGGUCCUCUCCG-UGCUACCGCACUGUGGGUACUUGCUGCUCCAGCAGGG
AY866341.1/221-303   CCCUGCCGGGGCUAAAGUGCUGACAGUGCAGAUAG-UGUCCUCUCCG-UGCUACCGCACUGUGGGUACUUGCUGCUCCAGCAGGG
AY866360.1/935-1017  UCCUAGCAGUACCAAAGUGCUCAUAGUGCAGGUAG-UUUUGGCAUGACU-CUACUGUAGUGUGGGCACUUCCAGUACUCUUGGAU
AY866367.1/317-399   UCCUAGCAGUACCAAAGUGCUCAUAGUGCAGGUAG-UUUUGGCAUGACU-CUACUGUAGUGUGGGCACUUCCAGUACUCUUGGAU
AY866363.1/941-1023  UCCUAGUAGUACCAAAGUGCUCAUAGUGCAGGUAG-UUUUGGCAUGACU-CUACUGUAGUGUGGGCACUUCCAGUACUCUUGGAU
AY866366.1/584-666   UCCUAGUAGUACCAAAGUGCUCAUAGUGCAGGUAG-UUUUGGCAUGACU-CUACUGUAGUGUGGGCACUUCCAGUACUCUUGGAU
AY866368.1/942-1024  UCCUAGUAGUACCAAAGUGCUCAUAGUGCAGGUAG-UUUUGGCAUGACU-CUACUGUAGUGUGGGCACUUCCAGUACUCUUGGAU
AY866362.1/366-448   UCCUAGUAGUACCAAAGUGCUCAUAGUGCAGGUAG-UUUUGGCAUUACU-CUACUGUAGUGUGGGCACUUCCAGUACUCUUGGAU
AY866365.1/896-978   UCCUAGUAGUACCAAAGUGCUCAUAGUGCAGGUAG-UUUUGGCAUGACU-CUACUGUAGUAUGGGCACUUCCAGUACUCUUGGAU
AY866361.1/908-990   UCCUAGUAGUACCAAAGUGCUCAUAGUGCAGGUAG-UUUUGGCAUGACU-CUACUGUAGUAUGGGCACUUCCAGUACUCUUGGAU
AY866364.1/939-1021  UCCUAGUAGUACCAAAGUGCUCAUAGUGCAGGUAG-UUUUGGCAUGACU-CUACUGUAGUAUGGGCACUUCCAGUACUCUUGGAU
AY866359.1/938-1020  UCCUAGUAGUACCAAAGUGCUCAUAGUGCAGGUAG-UUUUGGCAUGACU-CUACUGUAAUAUGGGCACUUCCAGUACUCUUGGAU
AY866310.1/634-712   CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUCAUGAGCACUUAAAGUACUGC--UAG
CR390304.1/91-169    CUCUUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUCACUA-A-U-CUACUGCAUUAUAAGCACUUAAAGUACUGC--UAG
AY866311.1/905-983   CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AB176708.1/1503-1581 CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AY866315.1/896-974   CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AY866317.1/659-737   CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AY866309.1/827-905   CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AY866314.1/942-1020  CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AY866312.1/881-959   CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AL138714.9/658-736   CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AY866313.1/926-1004  CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AY866318.1/924-1002  CUUCUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AY866316.1/888-966   CUUUUGUAGCACUAAAGUGCUUAUAGUGCAGGUAG-UGUUUAGUU-A-U-CUACUGCAUUAUGAGCACUUAAAGUACUGC--UAG
AY866365.1/502-582   CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAG-CUUUUUGAG-A-U-CUACUGCAAUGCAAGCACUUCUUACAUUACCAUGG
AY866366.1/190-270   CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAG-CUUUUUGAG-A-U-CUACUGCAAUGCAAGCACUUCUUACAUUACCAUGG
AY866361.1/514-594   CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAG-CUUUUUGAG-A-U-CUACUGCAAUGCAAGCACUUCUUACAUUACCAUGG
AY866363.1/547-627   CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAG-CUUUUUGAG-A-U-CUACUGCAAUGCAAGCACUUCUUACAUUACCAUGG
AY866360.1/541-621   CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAG-CUUUUUGAG-A-U-CUACUGCAAUGCAAGCACUUCUUACAUUACCAUGG
AY866368.1/548-628   CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAG-CUUUUUGAG-A-U-CUACUGCAAUGCAAGCACUUCUUACAUUACCAUGG
AY866359.1/544-624   CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAG-CUUUUUGAG-A-U-CUACUGCAAUGCAAGCACUUCUUACAUUACCAUGG
AY866364.1/545-625   CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAG-CUUUUUGAG-A-U-CUACUGCAAUGCAAGCACUUCUUACAUUACCAUGG
AF480549.1/1-81      CCUUGGCCAUGUAAAAGUGCUUACAGUGCAGGUAG-CUUUUUGAG-A-U-CUACUGCAAUGUAAGCACUUCUUACAUUACCAUGG
AY866313.1/472-553   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUACGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AY866316.1/431-512   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AY866317.1/203-284   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AY866318.1/470-551   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AL138714.9/204-285   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AY866310.1/184-265   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AY866315.1/442-523   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AY866309.1/373-454   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AY866314.1/488-569   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AY866311.1/449-530   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AF480562.1/1-82      UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AB176708.1/1049-1130 UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
AY866312.1/427-508   UCAGAAUAAUGUCAAAGUGCUUACAGUGCAGGUAG-UGAUAUGUGCA-U-CUACUGCAGUGAAGGCACUUGUAGCAUUAUGGUGA
#=GC SS_cons         :::::<<<<<<<--<<<<<<<<-<<-<<<<<-<<<.___________._.>>>>>>>>->>->>>>>>>>--->>>>>>>:::::
#=GC RF              cCuuaguaGuGcuAAAGUGCucAcAGUGCaGGUAG.ugUUuuguucA.U.CUACuGCAuUguggGCACUUguagCaCuacuaugg
//
# STOCKHOLM 1.0

#=GF AC   RF00052
#=GF ID   lin-4
#=GF DE   lin-4 microRNA precursor
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   47.00
#=GF TC   47.00
#=GF NC   46.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000303;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11533718
#=GF RT   Control of developmental timing in animals.
#=GF RA   Rougvie AE
#=GF RL   Nat Rev Genet 2001;2:690-701.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the microRNA (miRNA) lin-4 (MIPF:MIPF0000303).
#=GF CC   lin-4 was identified from a study of developmental timing in C. elegans
#=GF CC   [1], and was later shown to be part of a much larger class of non-coding
#=GF CC   RNAs termed miRNAs [2]. miRNAs are transcribed as ~70nt precursors
#=GF CC   (modelled here) and subsequently processed by the Dicer enzyme to give a
#=GF CC   ~22nt product. The extents of the hairpin precursors are not generally
#=GF CC   known and are estimated based on hairpin prediction. The products are
#=GF CC   thought to have regulatory roles through complementarity to mRNA. The
#=GF CC   involvement of Dicer in miRNA processing suggests a relationship with the
#=GF CC   phenomenon of RNA interference.
#=GF WK   lin-4_microRNA_precursor
#=GF SQ   12


U01837.1/538-607         GCCUGCUCCCUGAGACCUC--AAG-UGUGAGCGCACUGUUGAUGCUUCACGCCU-GGGCUCUCUGGGUACCAGG
U01829.1/524-593         GCCUGUUCCCUGAGACCUC--AAG-UGUGAGCGUUCUGAACAUGCUUCACGCCU-GGGCUCUCCGGGUACCAGG
U01830.1/508-577         GCCUGUUCCCUGAGACCUC--AAG-UGUGAGUGUACUAUUGAUGCUUCACACCU-GGGCUCUCCGGGUACCAGG
U01838.1/544-613         GCCUGCUCCCUGAGACCUC--AAG-UGUGAGCGUACUGUAGAUGCUUCACACCU-GGGCUCUCUGGGUACCAGG
AC122451.3/2004-1935     GCCUAGUCCCUGAGACCCU--AACUUGUGAGGUAU-UUUAGUAACAUCACAAGUCAGGUUCUU-GGGACCUAGG
AC006590.11/38290-38358  GCUGAUUCCCUGAGACCCU--AACUUGUGACUUUU-AAUACCAGUUUCACAAGUUUUGAUCUCC-GGUA-UUGG
AP001359.4/67794-67724   UCUCAGUCCCUGAGACCCU--AACUUGUGAUGUUUACCGUUUAAAUCCACGGGUUAGGCUCUU-GGGAGCUGCG
AC018755.3/120411-120479 UCUAGGUCCCUGAGACCCUUUAACCUGUGAGG----ACAUCCAGGGUCACAGGUGAGGUUCUU-GGGAGCCUGG
AP000962.2/168508-168577 UCCUAGUCCCUGAGACCCU--AACUUGUGAGGUAU-UUUAGUAACAUCACAAGUCAGGCUCUU-GGGACCUAGG
AB232081.1/345-415       UCUCAGUCCCUGAGACCCU--AACUUGUGAUGUUUACCGUUUAAAUCCACGGGUUAGGCUCUU-GGGAGCUGCG
AY865912.1/459-528       UCCUAGUCCCUGAGACCCU--AACUUGUGAGGUAU-UUUAGUAACAUCACAAGUCAGGCUCUU-GGGACCUAGG
EU624487.1/1700-1768     GCUGAUUCCCUGAGACCCU--AACUUGUGACUUUU-AAUACCAGUUUCACAAGUUUUGAUCUCC-GGUA-UUGG
#=GC SS_cons             :<<<<--<<<-<<<<-<<<..-<<<<<<<<________________>>>>>>>>->>>->>>>.>>>--->>>>
#=GC RF                  gCcuggUCCCUGAGACCcc..AAcuuGUGAgguuUcuuuaguagcuUCACaagUuggGcUCUC.GGGaaCcagG
//
# STOCKHOLM 1.0

#=GF AC   RF00053
#=GF ID   mir-7
#=GF DE   mir-7 microRNA precursor
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   60.00
#=GF TC   61.20
#=GF NC   59.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.76 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000022;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science 2001;294:853-858.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the microRNA (miRNA) precursor mir-7. This miRNA
#=GF CC   has been predicted or experimentally confirmed in a wide range of species
#=GF CC   (MIPF:MIPF0000022). miRNAs are transcribed as ~70nt precursors (modelled
#=GF CC   here) and subsequently processed by the Dicer enzyme to give a ~22nt
#=GF CC   product. In this case the mature sequence comes from the 5' arm of the
#=GF CC   precursor. The extents of the hairpin precursors are not generally known
#=GF CC   and are estimated based on hairpin prediction. The products are thought to
#=GF CC   have regulatory roles through complementarity to mRNA. The involvement of
#=GF CC   Dicer in miRNA processing suggests a relationship with the phenomenon of
#=GF CC   RNA interference. miRNAs are numbered based on the sequence of the mature
#=GF CC   RNA.
#=GF WK   mir-7_microRNA_precursor
#=GF SQ   57


AC005523.1/3567-3652         GGUCU-A-GUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUCU----GA-UGUA-CUA------CGACAACA-AGUCACAGCCGGCCU-CAUAGCGCA-G-ACUC
AC007837.4/16002-16089       GAGUG-C-AUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUG----GU-CUUUGGUAA-----UAACAAUA-AAUCCCUUGUCUUCU-UACGGCGUG-C-AUUU
AC013489.17/21820-21733      CGGCU-G-GCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGU----CU-UACUGCGC-----UCAACAACA-AAUCCCAGUCUACCU-AAUGGUGCC-A-GCCA
AC026385.19/122238-122323    GAGCC-A-GUGCUAUGUGGAAGACUUGUGAUUUUGUUGUUCU----GA-UAU-GAUA------UGACAACA-AGUCACAGCCAGCCU-CAUAGCGUG-G-ACUC
AL354733.15/170740-170651    GGCCU-A-GUUCUGUGUGGAAGACUAGUGAUUUUGUUGUUUU----UA-GAUAACUAAA---UCGACAACA-AAUCACAGUCUGCCA-UAUGGCACA-G-GCCA
AL929155.4/163041-163131     UAUUU-U-GGGCAUUAUGGAAGACUAGUGAUUUUGUUGUUGUG-ACGU-CAUCAGUAC-----UGACAACA-AGUCACAGUCUGCCU-CAGUGACCA-G-AAUC
AY866134.1/241-328           UGGCU-G-GCCCCGUCUGGAAGACUAGUGAUUUUGUUGUUGU----CU-UACUGCGCU-----CAACAACG-AAUCCCAGUCUGCCG-AAUGGUGCC-A-GCCA
AAKN02016044.1/62776-62689   UGGCC-A-GUCCUGUCUGGAAGACUAGUGAUUUUGUUGUUGU----CU-CACUGUGCC-----CAACAACA-AGUCCCAGUCUGCCG-CACAGUGCU-G-GCCU
ABRO01186159.1/4332-4419     UGGCC-G-GCUCUGUCUGGAAGACUAGUGAUUUUGUUGUUGU----GU-CUCUCUGUU-----AAACAACA-AAUCCCAGUCUGCCG-CACGGAGCC-G-GCCC
AAWR02000553.1/2779-2692     GGGCC-A-GCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGU----CU-UGCUGCGCC-----CAACAACA-AGUCCCAGUCUGCCG-CAUGGUGCG-G-GCCA
AAYZ01309177.1/4256-4167     GGCCU-U-GUUCUGUGUGGAAGACUAGUGAUUUUGUUGUUUUU--AGA-UAACGGAAU-----CGACAACA-AAUCACAGUCUACCA-UAUGGCACA-G-GCCA
ACBE01190514.1/4195-4108     CGGCU-C-GCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGU----UU-CGCUGCACC-----CAACAACA-AGUCCCAGUCUGCCU-CAUGGUGCU-G-GCCA
ABQO010287123.1/6780-6691    GGCCU-G-GCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUCUC--UAA-CAUAAAGAU-----UGACAACA-AAUCCCAGUCUGCCU-CAUGGUGCC-U-GGCC
AAQQ01635886.1/1135-1220     CGGCU-A-GCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGU----UU-CACCUCU-------CAACAACA-AGUCCCAGUCUGCCG-CAUGGUGCU-G-GCCC
AAPN01102459.1/801-712       GGCCG-G-GCCCCGUCUGGAAGACUAGUGAUUUUGUUGUUCU----CU-AGCUGACCGC---ACGACAACA-AAUCCCAGUCUGCCU-GACGGUGCC-C-GGUG
ABRQ01582202.1/711-627       GGUCU-A-GUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUCU----GA-UAUA--AAA-----UGACAACA-AAUCACAGCCUGCCU-CAUAGCG-U-G-GACU
AAVX01096348.1/698-611       GGUCU-G-GUUCUGUGUGGAAGACUAGUGAUUUUGUUGUUUU----UG-ACAGUUGAA-----UGACAACA-AAUCACAGUCUGCCA-UAUAGCGCA-G-GUCA
AC192790.3/173758-173847     GGUCU-A-GUUCUGUGUGGAAGACUAGUGAUUUUGUUGUUUU----UA-GAUAAUUAAA---UUGACAACA-AAUCACAGUCUGCCA-UAUGGCACA-G-AUCA
AAIY01692482.1/225-309       GGUCU-A-GUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUCU----GA-UAUC--CAU-----UGACAACA-AGUCACAGCCGGCCU-CACAGCG-U-G-GACU
AAFC03123320.1/10424-10510   CAGCC-A-GCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGU----CU-CCU-GCGCU-----CAACAACA-AGUCCCAGUCUGCCG-CAUGGUGCU-G-GCCA
ABVD01329072.1/528-444       GGUCU-A-GUGCUGUAUGGAAGACUAGUGAUUUUGUUGUUCU----AA-UAUA-CUA------UGACAACA-AGUCACAGCCGGCCU-CACAGCA-U-G-GACU
AAGV020344978.1/2692-2781    CGGCC-A-GUACCACCUGGAAGACUAGUGAUUUUGUUGUUGU----CU-CACUGUGCGC---UCAACAACA-AGUCCCAGUCUGCCG-CAUGGUGCU-G-GCCA
AAPT01021600.1/45421-45508   AAAUG-C-AUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUG----GU-CUUUGUUAA-----UAACAAUA-AAUCCCUUGUCUCCU-AACGGCGCG-C-AUUG
AAFR03051817.1/35977-36061   GGUCA-A-AUGCUGUAUGGAAGACUAGUGAUUUUGUUGUUGU----AA-UAUA--UAA-----AGACAACA-AAACACAGCCUGCCU-UACAGCGUG---GACA
ABRP01204078.1/2652-2739     UGGCC-U-GCCCCGUCUGGAAGACCGGUGAUUUUGUUGUUGU----CU-CUCUGUGCU-----CAACAACA-AGUCCCAGUCUGCCA-CGCGGUGCG-G-GCCC
BAAE01231804.1/1152-1241     UGGCU-G-CUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUUU----UA-GUUAGAUUAA---CCGACAACA-AAUCACAGUCUGCCA-AACGGCACA-G-GCUC
ABQF01047217.1/12512-12598   GGCCU-G-GCUCUGUGUGGAAGACUAGUGAUUUUGUUGUUGU----GU-UUGUAAAGG-----UGACAACA-AAUCAUAGCCUGCCA-UACAGC-CC-A-GGCU
AANI01014458.1/93584-93497   AAAUG-C-UUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUG----GU-CUCUGCUAA-----UAACAAUA-AAUCCCUUGUCUUCU-UAUGGCGCG-C-AUUC
ABRR01350609.1/1944-1861     GGUCU-A-GUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUCU----GA-UAUA-CUA------UGACAACA-AGUCACAG-CUUCCU-CAUAGCG-U-G-GACU
AALT01636026.1/624-710       UGGCC-A-GCCCCAUCUGGAAGACUUGUGAUUUUGUUGUUGU----UU-CUCUG-AAU-----CAACAGCA-AAUCCUGGUCUGCCU-CAUGGUGCA-G-GUCC
AANN01185580.1/744-658       CAGCC-C-GCCCCGUCUGGAAGACUAGUGAUUUUGUUGCUGU----CU-CACCGGUU------CAACAACA-AGUCCCAGUCUGCCC-UACGGUGUG-G-GCCC
AANH01008709.1/44998-44909   UGUGC-G-ACGCGCUGUGGAAGACUAGUGAUUUUGUUGUUCU----AA-GCUCACGUCC---CUGACAACA-AGUCCCAGUCUACCU-CAGCGAGUC-C-CGCU
ABEP02016699.1/38749-38660   UGCUG-U-GUUCUGUAUGGAAGACUAGUGAUUUUGUUGUUGU----GUGUCUUGCAAA-----CAACAGUA-AAUCACAGUCUUCCU-UACGGUGCAUC-GGCA
AAPU01010038.1/141440-141353 GAGUG-C-UUGCCGUAUGGAAGACUAGUGAUUUUGUUGUUUG----GU-CUCUGCUAA-----UAACAAUA-AAUCCCUUGUCUUCU-UAUGGCUCG-C-AUUG
ABPK01033505.1/392-306       CUGGU-G-GUGCUGAGUGGAAGACUAGUGAUUUUGUUGUGAC----GC-UGAU-CAAA-----GAACAACA-AGUCCCAGUCUGCCU-CUCAGCACA-A-GCAG
AAQB01006270.1/683084-682994 GAAUG-C-AUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUG----GU-CUUUAAUAAA--AUUAACAAUA-AAUCCCUUGUCUUCU-UAUGGCGUG-U-AUUU
CAAE01014344.1/111036-111123 GGUCC-G-GAGCAGCGUGGAAGACUAGUGAUUUUGUUGUUUG----GU-GUCA-AAAU-----UGACAACA-AAUCAUUGUCUUCCU-CACUGCCCC-GAGACG
AAJJ01000341.1/22410-22324   UGAAU-G-GUGUUGUGUGGAAGACUAGUGAUUUUGUUGUUCU----AA-UUUUUACG------UAACAAGG-AAUCACUAAUCAUCC-CACAAAGCC-G-UUCG
ABPJ01060011.1/287-197       AGUGU-A-GUAUGCUGUGGAAGACUAGUGAUUUUGUUGUUGUA--AAU-UCAUGUUUU-----UGACAACAGAGUCACAGUCUACCU-CGGUAUUCC-A-CACC
ABJB010540838.1/8437-8350    GGGGC-C-CUCCCGUCUGGAAGACUAGUGAUUUUGUUGUUCU----GU-CAAACUUGG-----AAACAAGA-AAUCACUAUC-UCCG-AACGGUGGGCG-CCCU
ABKQ02022271.1/23171-23083   UGGCAAA-ACAUUGUAUGGAAGACUAGUGAUUUUGUUGUUUG----GC-UUAUGAUAC-----UAACAAUA-AAUCUCUCGUCUUUC-UACAAAGUU-U-GCCC
AADK01002696.1/14030-14114   CGCUU-C-GUGUUGUAUGGAAGACUAGUGAUUUUGUUGUUUU----UG-U----UGAC-----UAACAAGA-AAUCACUAAUCUGCC-UACAAAGCG-ACAGCA
AAGE02031115.1/46027-46113   CGCAA-U-AUUUUGUAUGGAAGACUAGUGAUUUUGUUGUUUU----GC-UUACGAUAA-----UAACAAUA-AAUCUCAAGUCUUUC-UACAAAGU--U-UGCU
AAWU01000135.1/11357-11271   CGCAA-U-AUUUUGUAUGGAAGACUAGUGAUUUUGUUGUUUG----GC-UUAAGAUAG-----UAACAAUA-AAUCUCCAGUCUUUC-UACAACGU--U-UGCU
AAZO01007227.1/5979-6065     AGGCU-GGGUAUCUUGUGGAAGACUAGUGAUUUUGUUGUUCU----UU-AUUC--GAG-----UAACAAGG-AAUCACUAAUCAUCC-CAAGAUGGU-G-GCUG
AAZX01009358.1/3771-3685     UGAGC-G-UCGUUGUAUGGAAGACUAGUGAUUUUGUUGUUCU----AC-UUAAGAUG------UAACAAGG-AAUCACUAAUCAUCC-UACAAAGAC-G-CUCG
AASC02043326.1/70059-69973   CCUCU-G-UUGUGGUCUGGAAGACUAGUGAUUUAGUUGUUUU----AU-UGAUGGA-------GAACAAUU-AAUCACAAUCUUCUAUGACCACGGC-A-GAUG
AAPE02054819.1/5435-5349     CGGCC-A-GCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGU----CU-CGCUGCAU------CAGCAACA-AGUCCCAGUCUGCCG-CAUGGUGUG-G-GCCC
AABR05010615.1/3754-3839     AGACC-A-GCCCUGUCUGGAAGACUAGUGAUUUUGUUGUUGU----GU-CUGUGUC-------CAACAACA-AGUCCCAGUCUGCCA-CAUGGUGUU-G-GUCA
AEKZ01001356.1/15440-15354   CGAGC-G-CCGUUGCAUGGAAGACUAGUGAUUUUGUUGUUCU----AC-UUUCGAUA------UAACAAGG-AAUCACUAAUCAUCC-UACAAAGGC-G-CUCG
AAGU03052362.1/9289-9201     CGGCU-A-GCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGU----CU-CAUUACCGU----UCAACAACA-AGUCCCAGUCUGCCG-UAUGGUGCA-G-GCCA
ABLF02009125.1/21254-21349   CCGUUAA-CUGUCGUAUGGAAGACUAGUGAUUUUGUUGUUUUAAAA---AAAAAGUAUUUUCCUAACAAGA-AGUCUCUAGUCUUCU-UACGAAAGU-A-UCGA
CAAB02001092.1/24281-24369   UGUCU-G-CUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUUU----UA-GUUAGAUCAA---CUGACAACA-AAUCACAGUCUGCCA-AACAGCA-C-A-GGCU
AAQR03058470.1/10486-10573   CGGCU-G-GCUCCAUCUGGAAGACUAGUGAUUUUGUUGUUGU----CU-UACUGUGCU-----CAACAACA-AGUCCCAGUCUGCCG-CAUGGUGCG-G-GCCA
AAEX03002316.1/288375-288462 UGGCU-C-GCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGU----CU-CACUGCAUC-----CAACAACA-AGUCCCAGUCUGCCA-CAUGGUGCU-G-GCCA
AAWZ02033338.1/5865-5776     UGCCC-U-GCUUCUUAUGGAAGACUAGUGAUUUUGUUGUUCU----GU-AGUUCAUCUC---ACGACAACA-AGUCACAGUCUGCCU-UAUGGGGCC-U-GGCC
AAGJ04110086.1/1195-1104     UACCU-C-UGGCCCUUUGGAAGACUAGUGAUUUUGUUGUUGUGAAUG--UCAAAGAA-----CUAACAAAA-AAUCACUGUCGGCCACUGGGGACAG-A-GGUC
#=GC SS_cons                 :<<<<.<.<<<<<<<<-<<-------<<<<<-<<<<<<<<__....__._________....._>>>>>>>.>>>>>>------>>-.>>>>>>>>>.>.>>>:
#=GC RF                      uggcc.c.gccccguaUGGAAGACUAGuGAuUUUgUUGUuuU....gu.uuuugauau.....uaACAAcA.AaUCaCaguCugCCu.uacggggcg.g.gcca
//
# STOCKHOLM 1.0

#=GF AC   RF00054
#=GF ID   SNORD25
#=GF PI   U25
#=GF DE   Small nucleolar RNA SNORD25
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   39.00
#=GF TC   40.00
#=GF NC   38.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00049
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300709;
#=GF DR   snoopy; Homo_sapiens300169;
#=GF RN   [1]
#=GF RM   11266566
#=GF RT   Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana.
#=GF RA   Qu LH, Meng Q, Zhou H, Chen YQ, Liang-Hu Q, Qing M, Hui Z, Yue-Qin C
#=GF RL   Nucleic Acids Res 2001;29:1623-1630.
#=GF RN   [2]
#=GF RM   8559254
#=GF RT   A mammalian gene with introns instead of exons generating stable RNA
#=GF RT   products.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Nature 1996;379:464-466.
#=GF CC   U25 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U25 is found in gene clusters in plants [1], and
#=GF CC   within the U22 snoRNA host gene (UHG) in mammals [2]. U25 is thought to as
#=GF CC   a 2'-O-ribose methylation guide for ribosomal RNA. This RNA has also been
#=GF CC   named snoRNA R73 in some plants.
#=GF WK   Small_nucleolar_RNA_SNORD25
#=GF SQ   12


U40654.1/666-735       --CCCCUAUGAUGAGGACC-UUUUCACAGACCUGUA--------CUGAUAUAU----------CUGUGAGGAUAAGUAACUCUGAGGAGGC
U40580.1/750-817       --UUCCUAUGAUGAGGACC-UUUUCACAGACCUGUA--------CUGAGCU------------CCGUGAGGAUAAAUAACUCUGAGGAGAU
L36587.1/100-167       --UUCCUAUGAUGAGGACC-UUUUCACAGACCUGUA--------CUGAGCU------------CCGUGAGGAUAAGUAACUCUGAGGAGAU
AL662969.3/86874-86961 CAUGGCGGUCUUGAGC-CC--UAACAGACCUGAAAUAAUUAUUGCGGAUAUGAUUGCUUAAUUCAGAGCACAUCUAAGGGACUGAGUUGCC
AL662969.3/87797-87884 GGCAACAGUGAUGAGU-CC--UUACAGACCUGUAAUGAUUCUUGCGGGAAUGAUCGCUUGAUUCAAAGAACAUCUAAGGGACUGAGUUAUC
AJ276573.1/1-85        AAGAACAGUGAUGAGU-CAGUUUACAGACCUGUAAUGA---UUGCGGUAAUGAUCGCAUUA--UUAUGAACAUCUAAGGGACUGAGUUCUU
AL662969.3/87631-87717 UUUGACGGUGAUUAGC-CC--UAACAGACCUGUAAUGAUUCUUGCGGAUACGAUCGCUUGAU-CAAAGAACAUCUAAGGGACUGAGUAAUA
AL662969.3/86448-86535 UGUGGCAGUGAUGAGC-CC--UAACAGACCUGUAAUGAUUCUUGUGUAUAUGAUCGCUUGAUUCAAAGAACAUCUAAGGGACUGAGUUGUC
AY103180.1/27-114      CAUGGCGGUCUUGAGC-CC--UAACAGACCUGAAAUAAUUAUUGCGGAUAUGAUUGCUUAAUUCAGAGCACAUCUAAGGGACUGAGUUGCC
AJ532527.1/1-87        UUUGACGGUGAUUAGC-CC--UAACAGACCUGUAAUGAUUCUUGCGGAUACGAUCGCUUGAU-CAAAGAACAUCUAAGGGACUGAGUAAUA
AJ532528.1/4-91        GGCAACAGUGAUGAGU-CC--UUACAGACCUGUAAUGAUUCUUGCGGGAAUGAUCGCUUGAUUCAAAGAACAUCUAAGGGACUGAGUUAUC
AJ532526.1/1-86        -GUGGCAGUGAUGAGC-CC--UAACAGACCUGUAAUGAUUCUUGUGUAUAUGAUCGCUUGAUUCAAAGAACAUCUAAGGGACUGAGUUGU-
#=GC SS_cons           :<<<<<__________.__.._________________________________________.______________________>>>>>:
#=GC RF                ugcucCaGUGAUGAGc.CC..UuACAGAccUGUAAUGAUUcUUGCGGAuAUGAUCGCUUgAU.CaaaGAAcAUcUAAGGGACUGAGgagcc
//
# STOCKHOLM 1.0

#=GF AC   RF00055
#=GF ID   SNORD96
#=GF PI   snoZ37
#=GF DE   Small nucleolar RNA SNORD96 family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, Daub J
#=GF SS   Predicted; PFOLD
#=GF GA   43.00
#=GF TC   43.50
#=GF NC   42.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF CL   CL00072
#=GF DR   snoRNABase; U96a;
#=GF DR   snoRNABase; U96b;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300073;
#=GF DR   snoopy; Homo_sapiens300641;
#=GF RN   [1]
#=GF RM   12523999
#=GF RT   Plant snoRNAs: functional evolution and new modes of gene expression.
#=GF RA   Brown JW, Echeverria M, Qu LH
#=GF RL   Trends Plant Sci 2003;8:42-49.
#=GF RN   [2]
#=GF RM   11266566
#=GF RT   Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana.
#=GF RA   Qu LH, Meng Q, Zhou H, Chen YQ, Liang-Hu Q, Qing M, Hui Z, Yue-Qin C
#=GF RL   Nucleic Acids Res 2001;29:1623-1630.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA Z37 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Z37 acts as a methylation guide for 5.8S
#=GF CC   ribosomal RNA. This family contains a putative snoRNA found in the intron
#=GF CC   of the receptor for activated C kinase (RACK1) gene in mammals (S.
#=GF CC   Griffiths-Jones, pers. obs.). This family also includes human snoRNAs U96a
#=GF CC   (SNORD96A) and U96b (SNORD96B) and the apicomplexan snoRNA snr39b.
#=GF WK   Small_nucleolar_RNA_Z37
#=GF SQ   9


AJ132685.1/1-77      -AUCCUAGUGAUGACAAGACGAC-AUUGUCAA-C-CAAUCCCCCACAAGGGAAUGAG-------------GACAUG-------UCCUGCA-AUUCUGAAUGG---
AF295529.1/5361-5441 GAUCCUAGUGAUGACAAGACGAC-AUUGUCAA-C-CAAUCCCCCACAAGGGAAUGAG-------------GACAUG-------UCCUGCA-AUUCUGAAUGGGUU
AF146043.1/3911-3989 GAUCCUGGUGAUGACCA-AUGAC-AUUGUCAG-C-CAAUCC-CCACAUGGGAAUGUG-------------GACAUG-------UCCUGCA-AUUCUGAAGGGAUU
AJ240068.1/1-85      UAGCC-AAUGAGGACAU-CAGAUUAUAAAAGAACACCAUCUUUCGGGACUGAUUAA---------------CAUUGAUGAUACUUCUGCA-AUUCUGA--GGCUA
AC096691.6/4089-3994 UGGCC-GGUGAAGAAAA-CCUCG-AUUAAAAA-CACCAUCUUUCGGGGCUGAUCGGCCGCCGCUCGGCG-GCCAUGCUGCCA-UUCUGCA-AUUCUGA--GGCCA
AJ242537.1/1-95      -AGCC-GAUGUGGAUAU-CAGAUUAUAAAAGAACACCAUCUUUCGGGACUGAUUGACUUCU--UUUGAA-GUUUUGCUGAUACUUCUGCA-AUUCUGA--GGCU-
AC096691.6/4322-4224 CGACG--GUGAUGAAAAACCGCA-AGAAAAACACACCAUCUUUCGGGGCUGAUUUGGCGCCGCCGCGCGUGCAAUGAUGCUAAUUCUGCA-AUUCUGA--UGUCC
AC096691.6/3905-3812 GGACC-UGUGAUGAAAU-CUGGA-ACCAAAAA-UACCAUCUUUCGGGACUGAUUUGGCUU---UCAGCA-GCCAUGUUGUCACUUCCAAG-AUCCUGA--GGUCU
AJ010681.1/2-84      CUAUU-UAUGAUGAUUU-CCC----UUAAUUU-UACCAUCUUUCGGGUCUGAAUUAA-------------GAUGUGUUGAUAUUAUGGGAUAUACUGA--AAUAG
#=GC SS_cons         <<<<<.___________._____.________.________________________.............____________________._______..>>>>>
#=GC RF              cggCc.aGUGAuGAaAa.CcGaa.AUuAAaaa.CACCAUCUUUCGGGaCUGAuUgag.............GacaUGuUGaUAcUuCUGcA.AUUCUGA..gGccg
//
# STOCKHOLM 1.0

#=GF AC   RF00056
#=GF ID   SNORA71
#=GF PI   U71
#=GF DE   Small nucleolar RNA SNORA71
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   60.00
#=GF TC   60.40
#=GF NC   59.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; U71a;
#=GF DR   snoRNABase; U71b;
#=GF DR   snoRNABase; U71c;
#=GF DR   snoRNABase; ACA39;
#=GF DR   snoRNABase; ACA60;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300703;
#=GF DR   snoopy; Homo_sapiens300484;
#=GF RN   [1]
#=GF RM   9106664
#=GF RT   The family of box ACA small nucleolar RNAs is defined by an evolutionarily
#=GF RT   conserved secondary structure and ubiquitous sequence elements essential
#=GF RT   for RNA accumulation.
#=GF RA   Ganot P, Caizergues-Ferrer M, Kiss T
#=GF RL   Genes Dev 1997;11:941-956.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [3]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [4]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the H/ACA class of snoRNAs which bind
#=GF CC   a number of proteins (including dyskerin, Gar1p and Nop10p) to form snoRNP
#=GF CC   complexes. This class of snoRNAs are thought to guide the sites of
#=GF CC   modification of uridines to pseudouridines by forming direct base pairing
#=GF CC   interactions with substrate RNAs [2]. This family includes U71 (SNORA71),
#=GF CC   ACA39 (SNORA39) and ACA60 (SNORA60) [1,3]. U71 and ACA60 are predicted to
#=GF CC   guide the pseudouridylation of U406 and U1004 in 18S rRNA respectively
#=GF CC   [4]. There is currently no target RNA identified for ACA39 [3].
#=GF WK   Small_nucleolar_RNA_SNORA71
#=GF SQ   40


AL080249.26/93236-93103      ACCUGUAUUC-GAAAGUGAUCGUGGGCU---GCC-UGUGCCCUGGUCAUUGAUAGUGCAGGGAAAGAAAUCGCGGAAAGUGCUU--CCCCGUGUUUGGAGGGUCCGCUCCUGU-CCCUUUCAAACUCUGGAGCU-UUCUCACA
AL080249.26/89041-88908      CCCUGCAUUC-GAAAGUGAUCAUGAGCU---GCC-CGUGCCCUGGUCAUUGGUAGUGCAGGGAGAGGAACUGCCGAGAGCACUU--CCCCGUGUUUGGAGGGUCCACUCCUGU-CUCUUCCAAACCCUGGAGCU-UUCCCACA
AL049868.20/4397-4528        GCCUGCAUUC-GUAAGUGAUCACGGGCU---GCC-CGUGUCCUGGUCAUUGGUAGUGCAGGCAGAGGAAAUGCGGGAAAGGUUG----CUGUGUUUGGAGGGUCCACAUCUUCACCCUCCUGUCCCAGGAGC-U-UUCCUACA
AL663063.14/208893-208763    CCCUGUAUUC-GAAAGUGAUUGUGGGCU---GCC-GGUGCCCUGGUCAUUGAUACUGCAGGGAGAGGA--UGCCGAAAGCCUUU--CCCCGUGUUUGGAGGAUC-ACACUUGU-CCUUGCCAAACCCUGGUGCU-UUCGAACA
AL080249.26/84574-84441      CCCUGUAUUC-GAAAGUGAUCGUGGGCU---GCC-UUUGCCCUGGUCAUUGAUAGUGCAGGGAGAGGAAUCAAUGAAAGCGCUU--CCCCGUGUUUGAAGGGUCCACUCCUAU-CCCUUCCAAACUCUGGAGCU-UUCGUACA
AL844513.8/2453-2322         CCCUGUAUUC-GAAAGUGAUUGUGGGCU---GCC-UGUGCCCUGGUCAUUGAUACUGCAGGGAGAGGA--UUUGGAAAGCCUUU--CCCCGUGUUUGGAGGAUCCACACUCGU-CCUUGCCAAACCCUGGUGCU-UUCCCACA
AC012560.5/166192-166076     CCCUAUAUUC-GAAAGUUAUC--------------------CUGGUCAUUGACAGUGCAGGGAGAGAAACUGCUGAAAGCAUUC--CCCCUUGUUUGGAGGGUCCACUCCUGU-CCCUUCUAAACUCUGGAGUU-UUC-CACA
Y11166.1/2-135               UCCUGUAUUC-GAAAGUGAUCGUGGGCU---GCC-UUUGCCCUGGUCAUUGAUAGUGCAGGGAGAGGAAUCAAUGAAAGCGCUU--CCCCGUGUUUGAAGGGUCCACUCCUAU-CCCUUCCAAACUCUGGAGCU-UUCGUACA
Y11165.1/2-135               UCCUGCAUCC-GAAAGUGAUCAUAGGCU---GCC-UGUGCCUAGGUCAUUGAUAGUGCAGGGAGAGGAA-CGCUGAAAGAGGUUGUCCCCGUGUUUGGAGGGUCCACC-CUAU-CCCAUCCGAACCCUGAAGCU-UUCACACA
AL049868.20/5683-5816        ACCUGCAUUC-AAAAAUGAUCACGGGCU---GCC-UGUGCUCUGGUCAUCAAUAACGCAGGGAGAGGAAUUGCUGAAAGCCGUU--UCCCGUGUUUGGAGGGUUCACACCUGU-CCCUUUCAAAUGCUGGCGCU-UUCACACA
AL080249.26/81016-80889      UCUUGUAUCC-AAAAGUGAUCAUGGGUU---GCC-UGUGUCCCGAUCAUUAACAGUGCAGGGGUAGGA-GUGCUGAAAGACAUCUUCCCUGCGUU-----GGUCCAG-CCU-U-CCCUUUCAAACCCUGGAGCU-UUCCCACG
AL844513.8/20746-20878       CCCUGCGUUC-GUAAGUGAUCA-GGGAU---ACC-CAUGCCCUGACCAUUGGUAGUGCAGGCAGAGGAAAUGUGGAAAGAACUG--UCCCGUGCUUGGAAGGUCCACACCCAUGCCUUCCAAUGC-UGGGAGCU-UUCCCACA
AL844513.8/22058-22190       ACCUGCAUUUAGAAGCCGACCAUGGGCU---GCG-UGUGCUCUGGCCAUACAUGAUGCAGGGAGAGGAGUUGCUGAAGGCCGUU--UCCCGUGUUUGAAGGGUCCACUCCU---CCCUCUCAAAUGCUGGCGCU-UUCACACA
AL671877.15/121417-121547    CCCUGUGUUG-GAAAGGGAUUGUGGGCU---UCC-CAAACCCUAGGCACGGAUACUGCAGGGAGAGGA--UGCUAAAAGCCAU---CCUCAUGUUUGGAAGGUCCACUCCUAU-CCUUACCAGAUCCUGGUGCU-UUUGAACA
AAFC03065128.1/84445-84577   CCCUGCAUUC-GAAAGUGACCGUGGGCU---GCC-UGUGCCCUGGUCAUUGAUAGUGCAGGGAGAGGAAUUGCCGAAAGCCUUU--CCCCGUGUUUGGAGGGUCCAU-CCUGU-CCCUUGCAAACCCUGGCGCU-UUCGCACA
ABDC01049949.1/1444-1311     CCCUGCAUUC-GAAAGUGAUCGUGGGCU---GCC-CGUGCCCUGGUCAUUGAUAGUGCAGGGAGAGGAAUUGCCGAAAGCGUUU--CCCCGUGUUUGGAGGGUCUCUACCUGU-CCCUGCCAAACUCUGGAGCU-UUCGUACA
AAQQ01612056.1/1105-972      CCCUGUAUUC-GAAAGUGAUCAUGGGCU---ACC-CGUGCCCUGGUCAUUGAUAGUGCAGGGAGAGGAAUUGCUGAAAGCAUUU--CCCCGUGUUUGGAGGGUCUGCAUUUGU-CCCUUUCAAACUCUGGAGCU-UUUGUACA
AAIY01076031.1/281-413       CCCUGCAUCC-GAAAGUGACCGUGGGCU---GC--AGUGUCCCGGUCAUUGAUAGUGCAGGGAGAGGAAUUGUGGAAAGCCUUU--CCCCGUGUUUGGAGGGUCUGCUCCUGU-CCCUCCCAGACCCUGGAGCU-UUCCCACA
AACN010969629.1/514-381      ACCUGCAUUC-GAAAGUGAUCGUGGUCU---GUC-GGUGUCCUGGUCAUUGAUAGUGCAGGGAGAGGAGUCGCUGAAAGCGCUU--CCCCGUGUUUGGAGGGUCCACUCCUGU-CCCUUCCAAACUCUGGAGCU-UUCCCACA
AAYZ01018555.1/15409-15276   CCCUGUGUUC-GAAAGUGAUCGUGGGCU---GCC-CGUGCCCUGGUCAUUGAUAGUGCAGGGAGAGCAGCUGUGGAAAGCGCUU--CCCCGUGUUUGGAGGGUCCAGCGCCGU-CCCUUGCAAACCCUGCAGCU-UUCCCACA
AANG01536992.1/6162-6029     ACCUGCAUUC-AGAAGCGAUCACGGGCU---GUC-UGUGCUCUGGUCAUUGAUAAUGCAGGGAGAGGAAUUGUUGAAAGCAGUU--UCCCGUGUUUGGAGGGUCCACACCCAU-CCCUUUCAAAUGCUGGCGCU-UUCGCACA
AAPY01644280.1/277-144       CCCUGCAUUC-GAAAGUGAUCGUGGGCU---GCC-UGUGCCCUGGUCAUUGAUAGUGCAGGGAGAGAAAUCGCUGAAAGACGUUU-CCCCGUGUUUGGAGGGUCUAC-GCUGU-CCCUUUCAAACCCUGGAGCU-UUCCCACA
AAFR03012018.1/46758-46625   CCCUGCAUUC-GAAAGUGAUCAUGGUCU---AAC-UGUGACCUGGUCAUUGAUAGUGCAGGGAAAGAAACUCCUGAAAGGGUUU--UCCCGUGUUUGAAGGGUCAGCAUCCGG-CCCUUGCAAACCCUGUACCU-UUCACACA
AC204094.7/48016-48149       CCCUGCAUUA-GAAAGUGAUUAUGGGCU---GCC-CGUGCCCUGGUCAUUGGUGGUGCAGGGAGAGGAACUGCCGGGAGCACUU--CCCCGUGUUUGGAGGGUGCGCUCCUGU-CUCUCCCAACCCCUGGAGCU-UUCCCACA
AANN01284973.1/2107-1975     ACCUGCAUUC-GAAAGUGAUCACGGGCU---GCC-UGUGCCCUGGUCAUUGAUAGUGCAGGGAGAGCAACUGCCAAAAGCGUUU--CCCCGUGUUUGGAGGGUCUCC-CCUGU-CCCUUCUGAACCCUGAAGCU-UUCUCACA
AALT01492391.1/658-788       CCCUGUAUUC-GAAAGUGAUCGCUGGCU---GCC-UGUGCCCCGGUCAUUGAUAGUGCAGGGAGAGAAGUUGAUGAAAGCCUUU--CCCCGUGUUUGGGGGGUC---UCCUGU-CCCUUCCAGACCCUGGUGCU-UUCGUACA
AAPN01179880.1/5427-5298     ACCUGCAUUC-GAAAGUGAUUAUGGUAU---UC--UGUGACCUGGUCAUUGAUAGUGCAGGGAGAGAAACUUAAGAAAGUUUUU--C-CCGUGUUUGGAGGGUCCAC--CUGU-CCCAUCCAAACCCUGUAACU-UUCUAACA
CR387128.1/228-359           ACCUGCAUUC-GAAAGUGAUCGUGGUCU---GCUGCGUGGCCCGGUCAUUGAUAGUGCAGGGAGAGGA--ACACGAAGGCGUUU--C-CCGUGUUUGGUUGGGUCUGUGCUAU-CCCUCCCAAACCCUGUAGCG-UUCGGACA
BAAF04008472.1/3151-3275     UCCUGUAUC--GAAAGUGACCAUGGCGU---GCA-UGUUGCCAGGUCAUUGAUAGUACAGGAAAAUCAAAG--UGAGAGCAUUU--UCCCGUGUUUGAAAGAUC------UGU-UCUUUUUGAACCCUGGCGCU-CUCAGACA
CAAE01007124.1/64860-64738   ACCUGUAUC--GAAAGUGAUCAUGGUAA---CCU-UGUAGCCAGGUCAUCGAUAGUACAGGAAGAGCAACCA--GAGAGCUUUU--C-CCGUGUUUGUGGGA-------CUGU-UCCCAUCAAACCCUGGCGCU-CUCAUACA
AAGV020906997.1/1383-1250    ACCUGCAGUC-AAAAGUGAUCGUGGGCU---GCC-UGUGUCCUGGUCAUGGAUAAUGCAGGGAGAGGAAUUGUGGAAAGCAGUU--UCCCGUGUUUGGAGGGUCCACACCUGU-CCCUUUCAAAUGCUGGCGCU-UUCACACA
AAWR02026629.1/185142-185275 ACCUGCAUUC-AAAAGUGAUCACGGGCU---GUC-UGUGCUCUGGUCAUUGAUAACGCAGGGAAAGGAAUUGUUGAAAGCAGUU--UCCCGUGUUUGGAGGGUCCACACCUGU-CCCUUUCAAAUGCUGGCGCU-UUCACACA
AAKN02039430.1/137812-137680 CCCUGUAUUC-GAAAGUGAUCGUGGGCU---GCC-UGUGCCCUGGUCAUUGAUAGUGCAGGGAGAGGAACUGGUGAAAGCCUUU--CCCCGUGUUUGGAAGGUCUACUGCUGU-CCUAC-CAGACCCUGGUGCU-UUCCCACA
AAGU03041653.1/32279-32147   CCCUGCAUUC-GAAAGUGACCCUGGGCU---GC--UGUGUCCUGGUCAUUGAUAGUGCAGGGAGAGGAAUUGCUGAAAGCAUUU--CCCCGUGUUUGGAGGGUCCACUCCUGU-CCCUUCCAGACCCUGGAGCU-UUCCUACA
AAPE02044131.1/16931-16800   UCCUGCAUUC-GAAAGUGAUCGUGGGCU---GC--UGUGCCCUGGUCAUUGAUAGUGCAGGGAGAGGA-UUGCUGAAAGGAGUUUUCCCCGUGUUUGAAGGGUCCAG--CUGU-CCCUUCCAAACCCUGGAACU-UUCACACA
AABR05107765.1/1187-1319     ACCUGCAUUUGGAAGCCGACCACGGGCU---GCC-UGUGCUCUGGUCAUCCAUAAUGCAGGGAGAGGAGUUGCUGAAAGCCAUU--UCCCGUGUUUGAAGGGUCCACUCCU---CCCUCUCAAAUGCUGGUGCU-UUCACACA
AAQR03049938.1/1492-1359     CCCUGCAUUU-GAAAGUGAUCAUGGGCU---GCC-GGUGCCCUGGUCAUUGAUAGUGCAGGGAGAGGAAUCGCUGAAAGCAUUU--CCCCGUGUUUGGAGGGCCCUCACCUGU-CCCUUACAAACCCUGGAGCU-UUCUCACA
CAAB02005448.1/182818-182944 UCCUGUAUC--GAAAGUGAUCAUGGCGU---GCU-UGUGGCCAGGUCAUUGAUAGUACAGGAAGAAUAA-CG-UGAGAGCCUUU--C-CCGUGUUUGUUGGA---GCUUGCGU-UCCUCUCAGACCCUGAUGCU-CUCUCACA
AAGW02060088.1/86654-86522   CCCUGCAUUC-GAAAGUGAUCGUGGGCU---GCC-CGUGCCCUGGUCAUUGAUAGUGCAGGGAGAGCAGCUGCUGAAAGCGCUU--CCCCGUGUUUGGAGGGUCCGCGCCG-U-CCCUGCCGAACCCUGGAGCG-UUCGCACA
AAWZ02028738.1/2354-2489     ACCUGCAUUC-GAAAGUGAUUGUGGCCUUUCCUC-UGUGGCCUGGUCAUUGAUACUGCAGGAAGAGAA-UUCCUGAAAGCAUUU--CCCGUGUUUGGGGGGGCUCGUUGCCAU-CCUUU-CCAGACCCUGAGCUCUUCAGACA
#=GC SS_cons                 <<<<<<<<<-.---<<<<<<<<-<<<<_...___.___>>>>>>>>>>>>--->>>>>>>>>---------<-<<<<<<<----..------<<<<<<<<<<___________.>>>>>->>>>>------>>>.>>>>>:::
#=GC RF                      cCCUGcacuc.GAAaguGauCgUGGgcU...gCc.uGUgcCCcGguCauuGAUagugCAGGgAGAGgAAuugccGAaaGcauUU..cCCCGUGuuuGgagGGUcCacucCUgU.CCcucuCaaaCcCUGgagCu.uUCgcACA
//
# STOCKHOLM 1.0

#=GF AC   RF00057
#=GF ID   RyhB
#=GF DE   RyhB RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   55.00
#=GF TC   55.20
#=GF NC   54.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.95 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0010039; response to iron ion;
#=GF DR   GO; 0046677; response to antibiotic;
#=GF RN   [1]
#=GF RM   11917098
#=GF RT   A small RNA regulates the expression of genes involved in iron metabolism
#=GF RT   in Escherichia coli.
#=GF RA   Masse E, Gottesman S
#=GF RL   Proc Natl Acad Sci U S A 2002;99:4620-4625.
#=GF RN   [2]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF RN   [3]
#=GF RM   15913835
#=GF RT   Micros for microbes: non-coding regulatory RNAs in bacteria.
#=GF RA   Gottesman S
#=GF RL   Trends Genet 2005;21:399-404.
#=GF RN   [4]
#=GF RM   15937163
#=GF RT   Characterization of the small untranslated RNA RyhB and its regulon in
#=GF RT   Vibrio cholerae.
#=GF RA   Davis BM, Quinones M, Pratt J, Ding Y, Waldor MK
#=GF RL   J Bacteriol. 2005;187:4005-4014.
#=GF RN   [5]
#=GF RM   29467745
#=GF RT   Small Non-coding RNA RyhB Mediates Persistence to Multiple Antibiotics and
#=GF RT   Stresses in Uropathogenic Escherichia coli by Reducing Cellular
#=GF RT   Metabolism.
#=GF RA   Zhang S, Liu S, Wu N, Yuan Y, Zhang W, Zhang Y
#=GF RL   Front Microbiol. 2018;9:136.
#=GF RN   [6]
#=GF RM   28245801
#=GF RT   Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7
#=GF RT   EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory
#=GF RT   RNA RyhB and  a peptide, RyhP.
#=GF RA   Neuhaus K, Landstorfer R, Simon S, Schober S, Wright PR, Smith C, Backofen
#=GF RA   R, Wecko R, Keim DA, Scherer S
#=GF RL   BMC Genomics. 2017;18:216.
#=GF CC   The RyhB 90-nt RNA down-regulates a set of iron-storage and iron-using
#=GF CC   proteins when iron is limiting; it is itself negatively regulated by the
#=GF CC   ferric uptake repressor protein, Fur (Ferric uptake regulator). RyhB RNA
#=GF CC   levels are inversely correlated with mRNA levels for the sdhCDAB operon,
#=GF CC   encoding succinate dehydrogenase, as well as five other genes previously
#=GF CC   shown to be positively regulated by Fur by an unknown mechanism. These
#=GF CC   include two other genes encoding enzymes in the tricarboxylic acid cycle,
#=GF CC   acnA and fumA, two ferritin genes, ftnA and bfr, and a gene for superoxide
#=GF CC   dismutase, sodB [1]. This ncRNA gene was also identified in a screen and
#=GF CC   called SraI and it was found to be expressed only in stationary phase
#=GF CC   [2].First sRNA shown to mediate persistence to antibiotics in E.coli.[5]
#=GF CC   It may act both as an RNA-RNA interaction based regulator and as a
#=GF CC   transcript encoding for a small protein.[6]
#=GF WK   RyhB
#=GF **   Gained 4 new members by re-searching and changing structure
#=GF SQ   26


AY183121.1/21-87             GAAAGCACGACAUUGCUCACAUUGCUUCCAGUGUUUUUUA-AGCCAGC---UCGGGUGCUGGCUUUUUUUU
AL627281.1/157209-157273     GAAAGCAUGACAUUGCUCACAUUGCUUCCAGUUUUAUUUU-GGCCAGC---UUU--UGCUGGCUUUUUUUU
BX571867.1/241263-241198     AAAAGCACGACAUUGCUCACAUUGCUUCCAGUGUUUUUU--AGCCAGC---UCGGGUGCUGGCUUUUUUUU
BX950851.1/2247640-2247706   GAGAGCACGACAUUGCUCACAUUGCUUCCAGUAUUAUUUU-AGCCAGC---CUACGUGCUGGCUUUUUUUU
AY008264.2/541-607           AAAAGCACGACAUUGCUCACAUUGCUUCCAGUGUUUUUUA-AGCCAGC---UCGGGUGCUGGCUUUUUUUU
X76000.1/258-323             GAGAGCACGACAUUGCUCACAUUGCUUCCAGUAUUAUUUU-AGCCAGC---CGACGUGCUG-CUUUUUUUU
BX950851.1/4651440-4651375   GAAGGCACGACAUUGCUCACAUUGCUUCCAGUAUUAUUU--AGCCAGC---UCGGGUGCUGGCUUUUUUUU
BX571859.1/98959-98893       GAAAGCACGACAUUGCUCACAUUGCUUCCAGUGUUUACUUUAGCCAGC---CAAG-UGCUGGCUUCUUUUU
CP000038.1/3861605-3861541   GAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUU--AGCCAGC---CGGG-UGCUGGCUUUUUUUU
BA000037.2/195620-195685     UUUGACACGACAUUGCUCACAUUGCUUCCAGUGUAAUUUA-UAGCUUU---AUGGUU-AAGCUGCCGUAUU
AAUU01000182.1/409-344       UUUGACACGACAUUGCUCACAUUGCUUCCAGUGUAAUUUU-UAGCUUU---UUGG-UAAAGCGAAUCAAAA
CP000653.1/1810151-1810088   UUUAGUACGACAUUGCUCACAUUGCUUCCAGUAUUUCUU--GCCCACU---UUU--UAGUGGGCUUUUUUU
CP000647.1/1404566-1404503   UUCAGUACGACAUUGCUCACAUUGCUUCCAGUAUUUU----UGCCCGC---ACUUGUGCGGGCUUUUUUUA
AM286415.1/4382210-4382145   GAAGGCACGACAUUGCUCACAUUGCUUCCAGUGUUUACUU-AGCCAGC---CGGG-UGCUGGCUUUUUUUU
AAYS01000010.1/87292-87356   AAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUU--UUA-AGCCAGC---UCGGGUGCUGGCUUUUUUGU
AAZW01000010.1/62530-62465   UUUGACACGACAUUGCUCACAUUGCUUCCAGUGUAAUUUA-UAGCUUU---UAGG-UAAAGCUGUGGUAUU
AAWP01000024.1/10163-10098   UUUGACACGACAUUGCUCACAUUGCUUCCAGUGUAAUUUA-UAGCUUC---UUGGUU-AAGCUGCCAUACA
AP008232.1/4010678-4010614   GGGAGCACGACAUUGCUCACAUUGCUUCCAGUA--AUUUC-AGCCAGC---UUGUGCGCUGGCUUUUUUUG
CP000653.1/4158664-4158599   GAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUACUUU-AGCCAGC---UUAA-CGCUGGCUUUUUUUU
AAKK02000018.1/63583-63648   UUUGACACGACAUUGCUCACAUUGCUUCCAGUGUAAUUUA-UAGCUUC---UUGGUU-AAGCUGCUCUAUU
AP008232.1/2523068-2523004   AUGGGCACGGCAUUGCUCAUAUUGCUUCCAGUAUUAUUU--AGCCAGC---AGGG-UGCUGGCUUUUUUUU
AACY022459113.1/47-108       GAAGGCACGACAUUGCUCACAUUGCUUCCAGUUAAGG----GGCCAGU---UUU--UACUGGCCCUCUUUU
CP000644.1/197460-197521     GAAGGCACGACAUUGCUCACAUUGCUUCCAGUUAUA-----GGGCCAG---UUCU-UCUGGCCCUCUUUUU
CP000026.1/1645920-1645987   UUCGGUACGACAUUGCUCACAUUGCUUCCAGUAUUAUUU--GCCCGCCUCACCGAGU-GCGGGCUUUUUUU
CP001113.1/3689979-3689915   GAAAGCACGACAUUGCUCACAUUGCUUCCAGUAUUAUUUU-GGCCAGC---UUU--UGCUGGCUUUUUUUU
AALD02000007.1/113336-113399 GAAAGCACGACAUUGCUCACAUUGCUUCCAGUGUUUA----GGCCGGC---UCGGGUGCUGGCCCUUUUUU
#=GC SS_cons                 ::::::<<<<----<<_______>>->>-->>--------.<<<<<<<...______>>>>>>>:::::::
#=GC RF                      gaaaGCACGACAUUGCUCACAUUGCUUCCAGUaUUaUUUu.ggcCagc...uugggUgcuGgccUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00058
#=GF ID   HgcF
#=GF DE   HgcF RNA (Pab35)
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD
#=GF GA   70.00
#=GF TC   120.30
#=GF NC   34.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   12032319
#=GF RT   Noncoding RNA genes identified in AT-rich hyperthermophiles.
#=GF RA   Klein RJ, Misulovin Z, Eddy SR
#=GF RL   Proc Natl Acad Sci U S A 2002;99:7542-7547.
#=GF RN   [2]
#=GF RM   18304947
#=GF RT   Combined in silico and experimental identification of the Pyrococcus
#=GF RT   abyssi H/ACA sRNAs and their target sites in ribosomal RNAs.
#=GF RA   Muller S, Leclerc F, Behm-Ansmant I, Fourmann JB, Charpentier B, Branlant
#=GF RA   C
#=GF RL   Nucleic Acids Res. 2008;36:2459-2475.
#=GF CC   The HgcF ncRNA gene was identified computationally in AT-rich
#=GF CC   hyperthermophiles. The genes were named hgcA through hgcG ("high GC"). It
#=GF CC   was also identified as Pab35 H/ACA snoRNA with rRNA targets.[2] 
#=GF WK   HgcF_RNA
#=GF SQ   4


AF468962.1/1-168           GCCGACAGCGAGGGUACAAUA----CCCUCGCAAGGGCUCGGUCAACCCGCCCCCGCAAGGU-UUCGGGUUCGAUGAGCGGGGUGUGCUCACGCCGAGCCUACAGGGCCGG-UGCAUCCGCCCGCGGGAUCAAUGACCGCUGGGUCUCUGUUGCCGGCCCACAAAAGUAUUUUA
AJ248284.1/11131-11298     GCCGACAGCGAGGGUACAAU-----CCCUCGCAGGGGCUCGGUCUACCCGCCCCCGCAAGGUGUUCGGGUUCGAUGAGCGGGGUGUGCUCACGCCGAGCCCACAGGGCCGG-UGCAUCCGCCCGCGGGAUCAAUGACCGCCGGGUCUCUGUUGCCGGCCUACAGCAAAAAUUUA
BA000001.2/1531413-1531580 GCCGACAGCGAGGGUACAAUA----CCCUCGCAAGGGCUCGGUCAACCCGCCCCCGCAAGGU-UUCGGGGUCGAUGAGCGGGGUGUGCUCACGCCGAGCCUACAGGGCCGG-UGCAUCCGCCCGCGGGAUUAAUGACCGCUGGGUCUCUGUUGCCGGCCCACAAUAAAGUUUAA
AP006878.1/1107433-1107263 GCCGACAGCGAGGGGACAGUCAGUCUCCUCGCA-GGGCUCGGUACAACCGCCUCCGCAAGGU-AUCGGGUUCCGUGAGCGGAGCGUGCUCACGCCGAGCCCACAGGGCCGGGAGCAUCCACCCGCGGGAGCAGUGACCGC-GGGCCUCUGUACCCGGCCCACAUUUCGAUGCCC
#=GC SS_cons               :::::::<<<<<<<_______....>>>>>>>,,<<<<<<<<----<<<<<-<<<<______.__>>>>-------->>>>>----------->>>>>>>>---<<<<<<<.--------<<<<<<<_________>>>>->>>--------->>>>>>>::::::::::::::
#=GC RF                    GCCGACAGCGaGGGuACAaUa....CCCuCGCAagGGCuCGGUcaAcCCGCCcCCGCAAGGU.uUCGGguUCgaUGAGCGGgGuGUGCUCACGCCGaGCCcACAGGGCCGG.uGCAUCCgCCCGCGGGAucAaUGACCGCuGGGuCUCUGUugCCGGCCCACAauaaaauuuua
//
# STOCKHOLM 1.0

#=GF AC   RF00059
#=GF ID   TPP
#=GF PI   THI
#=GF DE   TPP riboswitch (THI element)
#=GF AU   Vitreshchak A
#=GF AU   Gelfand M
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Vitreshchak A
#=GF SS   Published; PMID:12376536; Moxon SJ
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.95 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0030976; thiamine pyrophosphate binding;
#=GF RN   [1]
#=GF RM   12376536
#=GF RT   Comparative genomics of thiamin biosynthesis in procaryotes. New genes and
#=GF RT   regulatory mechanisms.
#=GF RA   Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS
#=GF RL   J Biol Chem 2002;277:48949-48959.
#=GF RN   [2]
#=GF RM   11470904
#=GF RT   A conserved RNA structure (thi box) is involved in regulation of thiamin
#=GF RT   biosynthetic gene expression in bacteria.
#=GF RA   Miranda-Rios J, Navarro M, Soberon M
#=GF RL   Proc Natl Acad Sci U S A 2001;98:9736-9741.
#=GF RN   [3]
#=GF RM   12410317
#=GF RT   Thiamine derivatives bind messenger RNAs directly to regulate bacterial
#=GF RT   gene expression.
#=GF RA   Winkler W, Nahvi A, Breaker RR
#=GF RL   Nature 2002;419:952-956.
#=GF RN   [4]
#=GF RM   12756322
#=GF RT   Metabolite-binding RNA domains are present in the genes of eukaryotes.
#=GF RA   Sudarsan N, Barrick JE, Breaker RR
#=GF RL   RNA 2003;9:644-647.
#=GF RN   [5]
#=GF RM   14675766
#=GF RT   Thiamine-regulated gene expression of Aspergillus oryzae thiA requires
#=GF RT   splicing of the intron containing a riboswitch-like domain in the 5'-UTR.
#=GF RA   Kubodera T, Watanabe M, Yoshiuchi K, Yamashita N, Nishimura A, Nakai S,
#=GF RA   Gomi K, Hanamoto H
#=GF RL   FEBS Lett 2003;555:516-520.
#=GF RN   [6]
#=GF RM   16728979
#=GF RT   Structural basis for gene regulation by a thiamine pyrophosphate-sensing
#=GF RT   riboswitch.
#=GF RA   Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ
#=GF RL   Nature. 2006;441:1167-1171.
#=GF RN   [7]
#=GF RM   23950988
#=GF RT   A genome-wide survey of highly expressed non-coding RNAs and biological
#=GF RT   validation of selected candidates in Agrobacterium tumefaciens.
#=GF RA   Lee K, Huang X, Yang C, Lee D, Ho V, Nobuta K, Fan JB, Wang K
#=GF RL   PLoS One. 2013;8:e70720.
#=GF RN   [8]
#=GF RM   17307816
#=GF RT   Ligand binding and gene control characteristics of tandem riboswitches in
#=GF RT   Bacillus anthracis.
#=GF RA   Welz R, Breaker RR
#=GF RL   RNA. 2007;13:573-582.
#=GF CC   Vitamin B(1) in its active form thiamin pyrophosphate (TPP) is an
#=GF CC   essential coenzyme that is synthesised by coupling of pyrimidine and
#=GF CC   thiazole moieties in bacteria. The previously detected thiamin-regulatory
#=GF CC   element, thi box [1] was extended, resulting in a new, highly conserved
#=GF CC   RNA secondary structure, the THI element, which is widely distributed in
#=GF CC   eubacteria and also occurs in some archaea. Analysis of operon structures
#=GF CC   identified a large number of new candidate thiamin-regulated genes, mostly
#=GF CC   transporters, in various prokaryotic organisms [2]. The THI element is a
#=GF CC   riboswitch [3] that directly binds to TPP to regulate gene expression
#=GF CC   through a variety of mechanisms in archaea, bacteria and eukaryotes [4,5].
#=GF WK   TPP_riboswitch
#=GF SQ   109


BX842649.1/277414-277318       ACCUGACGCUAGGGGUGUUGGUGAAUU-----------------------------------------------CACCG-ACUGAGAA------------------------------------------------------------UAA-CCCUUUGA-ACCUGA-UAGAGAUAAUGCUCGCG-CAGGGA--AGCAAGAAUAGAAAGAU
Z82044.1/19193-19300           AAUAGUUACUGGGGGUGCCCGCUU---------------------------------------------------UCGG-GCUGAGAGAGAAGGCAAG---------------------------------------------CUUCUUAA-CCCUUUGG-ACCUGA-UCUGGUUCGUACCAGCG-UGGGGA--AGUAGAGGAAUUGUUUU
BX571861.1/7126-7022           GCCAUCUCAACGGGGUGCUGGCUGUUUAAAACA-----------------------------------------GCCUU-GCUGAGAGU-----------------------------------------------------------AAA-CCCGCCGA-ACCUGA-UCCGGCUAAUACCGGCG-UAGGGA-UUUGAGCUGCUAACUAUU
AF104225.1/570-680             CGUUACCACAGGGGGGGCUUC-------------------------------------------------------UUA-GCUGAGAUUGAGUCCACGUGUUUUUGG------------------------------------AUUCUGA--CCCUUUGA-ACCUGU-UC--GUUAAUACGAGCG-UAGGGA-UUGUGGCGAUUGCAUUUC
AY123045.1/16666-16547         AGUCCCUGUCAGGGGAGUCUCGCCA-------------------------------------------------GAGAG-ACUGAGAGGCUAAUAGCGAUUUUCGCGGC----------------------------------UUAGC-GA-CCCUUAGA-ACCUGA-CCCAGCUGAUACUGGCG-UAGGAA--GACUCGUAUCUUGAUGA
AB118748.1/319-422             UGGAGGGGUACCGGGUGUACGAGGCAGAGUCCG-----------------------------------------GUCGU-UCUGAGAUU-----------------------------------------------------------AUA-CUGUCAUA-ACUUGA-UCUAGAUAAUACUAGCG-AAAGGA--CAUGCGUGGCAUUGAUU
AF070520.1/2088-2190           GCGCAUUCCGAGGGGAGCACUAGA---------------------------------------------------CGGU-GCUGAGAUGGCGUU-------------------------------------------------GAGCCGGA-CCCUUGA--ACCUGA-UCCGGGUCAUGCCGGCG-UAGGAA--CGGAAAGAAGGCCGCCA
BX927152.1/148798-148691       AUACUAGGCACGGGGUGCCAACCGGAUGGAAAAAUUC-------------------------------------CGGAG-GCUGAGAAA-----------------------------------------------------------ACA-CCCGUUGA-ACCUGC-UCUAGCUCGUACUAGCG-AAGGGA--UGGCCUUAACGUGGCUA
AL627265.1/128216-128117       CCGAACUCAACGGGGUGCCGCGCUCAU-----------------------------------------------GCGCGCGCUGAGAAA-----------------------------------------------------------AUA-CCCGUCGA-ACCUGA-UCCGGAUAAUGCCGGCG-AAGGGA-UUUGAGGCUACCUCUCAA
AB042239.3/9807-9660           AGGCGUCACAAGAGGAGCUU---------------------------------------------------------UU-GCUGAGAAUGACCUCCAGUUUUAAGUAAAUUCCAUAACAUUGGAGUUUUGCGCAAAGUCUGGGUGUCUAAA-CUCUUUGA-ACCUGA-ACAAGGUAAUGCUUGCGUAAGGGA--UGUGCAGAAAUAAGUGG
X54035.1/52-153                GAUGACCACAAGGGGAGCAUU-------------------------------------------------------AAA-GCUGAGAGUGAGCGGUUUC--------------------------------------------GUUC-UGA-CCCUUUGA-ACCUG--U-UAGUUAACGCUGGCG-UAGGGA--UGUGGCAAAUGCAAUAG
AD000014.1/41361-41472         GGGUACCCACGCGGGAGCGCAACGCCG-----------------------------------------------AGUGC-GCUGAGAGGACGGCUCGGGG-------------------------------------------CCGUC-GA-CCGUACGA-ACCUGA--CCGGGUAAUGCCGGCG-UAGGGA--GUUGCAAAUGACCAUCA
BX640423.1/313922-313811       AGGAUCACGCAGGGGUACUCGCUGUCCCGCCUUCAAGGCCGGC-------------------------------AGCGU-GUUGAGAG------------------------------------------------------------AGU-CCCUUCGU-ACCAG--UACGGAUAAUGCCGAUG-CUGGGA--GCGUAUUCCAGUUGCCG
AL596164.1/123476-123581       AAGAAAAACUAGGGGGGCCGAU-----------------------------------------------------UCUG-GCUGAGAUAGGAAGGUAAUGC------------------------------------------UUUCUGA--CCCUUUGA-ACCUG--U-UUGUUAGUGCAAGCG-UAGGGA--AGUGAAUGUGAAAGUGA
AK068703.1/2083-2217           UGUUAGGAGGUGGGGUGCCUGUAUUCUCAACGAUCUGAAGGCCUCUUGGCCUGGAUUGUUGUGA----------AUUGG-GCUGAGAA------------------------------------------------------------AGU-CCCUUUGA-ACCUGA-ACAGGAUAAUGCCUGCG-AAGGGA-GUGUGCAUUUCUACUUUU
AL445066.1/239884-239777       AACUAGGCGAGGGGGAGCUCCAUA--------------------------------------------------AGGGG-GCUGAGAGGAUCCGGAU----------------------------------------------GGAUCGA--CCCCUGGA-ACCUGA-UCCGGGUAAUACCGGCG-GAGGGA-AUCGUAUGAUGAAUGAGA
BX572604.1/199848-199986       GCCCGUUCCGAGGGGGGCUCCGAC--------------------------------------------------GAGGA-GCUGAGAUACCGCACGCUCGCCGCUUCGCUCCGCGAGGCACAGAGACC---------------GCGGUGA--CCCUUUGA-ACCUGA-UCCGGGUCAUGCCGGCG-AAGGGA-CAGGGAUGCAUCAGACAG
M33642.1/428-524               GUGUACAUCAA----UGUCAAGAAGAGGAGA-------------------------------------------GCGUG-GCUGAGAUU-----------------------------------------------------------AUA-C-GGCGAA-ACUUGA-UCUGGAUAAUACCAGCG-AAAGGA--UCAUGCUCUCCUCCCCC
AJ002571.1/43977-43865         GGAAAGCACUAGGGGUGCUGU------------------------------------------------------UUUG-GCUGAGAUAAAGCGCGGAAGAAACGC-------------------------------------GCUUUGAU-CCCUUAUG-ACCCGA-UCUGGAUAAUACCAGCG-UGGGGA--AGUGCAGGUUGACCGAA
AC084406.7/91434-91300         AAGUUGCACCAGGGGUGCCUGUAUUCUCAACGAUCUGAAGGCCUCUUGGCCUGGAUUGUUGUGA----------AUUGG-GCUGAGAA------------------------------------------------------------AGU-CCCUUUGA-ACCUGA-ACAGGAUAAUGCCUGCG-AAGGGA-GUGUGCAUUUCUACUUUU
AL583918.1/33385-33496         AAAAAACCACGCGGGAGCACACACCA------------------------------------------------AGUGC-GCUGAGAGGACGGAUCGGGG-------------------------------------------CCGUC-GA-CCGUAUGA-ACCUGA--CCGGGUAAUGCCGGCG-UAGGGA-GAUGAAUAAUGACUGAAA
AL583918.1/38806-38668         ACUUCAGUACACGGGAGUCCCCAGGCAGUCCGAAUCU-------------------------------------GCGGG-GCUGAGAGUGGGCACAGCCAGAGUGACUGAACCU-----------------------------ACCCUUA--CCCUCCCACACCUGA-UCCGGGUCAUGCCGGCG-AAGGGA-GGUUCAAGAUGCCGUCAG
AB033416.1/2076-2219           UCAUGCAUGAGCCGGUGCCCAUUCUUCUCCCAUCAGCAUGGUCAGUUCAAACUGGUCGUGUUGAUGAUAGGGGGAUGUG-GCUGAGAUU-----------------------------------------------------------AUA-CGGCAAA--ACUUGA-UCUGGAUAAUACCAGCG-AAAGGA--UCAUGUCAUCUCCCCUA
AF264948.1/14680-14561         GGUUCCUGUCAGGGGAGUCUCGCCA-------------------------------------------------GAGAG-ACUGAGAGGCUGAUAGCGAUUUUCGCGGC----------------------------------UUAGC-GA-CCCUUAGA-ACCUGA-CCCAGCUGAUACUGGCG-UAGGAA--GACUCGUAUCUUGAUAA
M73546.1/221-329               UUUAACCACUAGGGGUGUCCUUCA--------------------------------------------------UAAGG-GCUGAGAUAAAAGUGUGA---------------------------------------------CUUUUAGA-CCCUCAUA-ACUUGA-ACAGGUUCAGACCUGCG-UAGGGA--AGUGGAGCGUAUUUGUG
AF269819.1/1816-1718           AUUUGCUACUAGGGGAGCCAA-------------------------------------------------------AAG-GCUGAGAUGAAUG--------------------------------------------------UAUUCAGA-CCCUUAUA-ACCUGA-UUUGGUUAAUACCAACG-UAGGAA--AGUAGUUAUUAACUAUU
BX842573.1/168419-168309       GGGUACCCACGCGGGAGCGCACGCCG------------------------------------------------AGUGC-GCUGAGAGGACGGCUCGGGG-------------------------------------------CCGUC-GA-CCGUACGA-ACCUGA--CCGGGUAAUGCCGGCG-UAGGGA--GUUGCAAAUGACCAUCA
BX842573.1/159140-159250       CCCUGUAGACACGGGAGUCCCGGGAG------------------------------------------------CGGGG-UCUGAGAGUGGGCGCGCCU--------------------------------------------GCCCUUA--CCGUCAC--ACCUGA-UCCGGAUCAUGCCGGCG-AAGGGA-GGUCAAGGAUGGCGUCCG
AL766847.1/94269-94358         AUAGGACAUUUGGGGUGCGUA-------------------------------------------------------ACA-GCUGAGAUU-----------------------------------------------------------AUA-CCCAUUGA-ACUUGA-UACAGUUAGUACUGUCG-AAGGGA--AAUGUGUGCCAUUACAA
AF269570.1/1830-1729           UAGUAUCAUUAGGGGUGCAAUUCA---------------------------------------------------AUUU-GCUGAGAGAAAGUCU------------------------------------------------ACUUUCAA-CCCUUGA--ACCUG--U-UGGUUAGCACCAGCG-UAGGAA--AGUGAGCAAUAUUGAUA
AL939124.1/163164-163269       AUAUUCCGACAGGGGAGCGCCA-----------------------------------------------------CAGC-GCUGAGAGUGCGGCACCGG--------------------------------------------CCGCA-GA-CCCUCCGA-ACCUGG-CCCAGGUCAUUCUGG-G-UAGGGA-GAUCGGUCACCACUCGAG
M16495.1/2120-2233             GCCAUCUUGUCGGAGUGCCAACCGUCGAACGAC-----------------------------------------GCGAG-GCUGAGACCGUUA--------------------------------------------------AUUCGGGA-UCCGUGGA-ACCUGA-UCAGGCUAGCACCUGCG-AAGGGA-AACAAGGGUAACUUGCGG
AL939111.1/162719-162830       CAAGGCACUCGCGGGAGCCCGGACGC------------------------------------------------ACCGG-GCUGAGAGGGAGGCUGGCG--------------------------------------------GCCUCCGA-CCGUACGA-ACCUGA-UCCGGGUCAUGCCGGCG-AAGGGA--GGGGCUGGACGCCCAUG
BX569689.1/134905-135013       AAACACCACUAGGGGUGCCUCGAUCGGUUUUCUGGUCG------------------------------------ACGGG-GCUGAGAUC-----------------------------------------------------------ACA-CCCUCUGA-ACCUGA-CCCGGGUCAUGCCGGCG-AAGGGA--AGUGACCAGCGUGAUCG
AY316746.1/2276-2378           CUCCAUUCCGAGGGGAGCGCCGGG---------------------------------------------------CGGC-GCUGAGACGGCGGU-------------------------------------------------GAGCCGGA-CCCUUGA--ACCUGA-UCCGGGUCAUGCCGGCG-UAGGAA--CGGAACGAGGCUGCCCU
BX248354.1/27456-27566         AGUGUCCCCCGCGGGCGCCCGAGC---------------------------------------------------ACGG-GCUGAGAUUGCGCUGAUGCU-------------------------------------------GUGCAAGCACCGUUUGA-ACCUG--UCUGGUUAACACCAGCG-AAGGAA-GAGAGGAGCGCGAGCCUA
AB087258.1/15478-15568         CCGACUUAGUCGGGGUGCUGAU-----------------------------------------------------AACA-GCUGAGAUA-----------------------------------------------------------AUA-CCCGUGA--ACCUGA-UACAGUUAAUACUGACG-UAGGAA--ACUAAUGGUCUUACUCC
AF159589.1/4059-4150           ACCUUCACAAAGGGGAGCCA--------------------------------------------------------UUG-GCUGAGAACGGGGAA------------------------------------------------ACCCGGA-CCCUUCGA--ACCUGU-UC--GUUAAUGCGAGCG-UAGGGA-UUUGUGAAUGGU------
U64312.1/2271-2374             UAGUUCCACUAGGGGUGUCAGUUU--------------------------------------------------GUCUG-ACUGAGAGAGGGA--------------------------------------------------AGCCUCAA-CUCUUAAA-ACCUGA-UCUAGCUUGUACUAGCG-UAGGGA--AGUGGUGGCACAUUCUA
AL672115.1/15647-15763         CGCAUUCACCAGGGGAGUCCCGGC--------------------------------------------------AAGGG-GCUGAGAUACUGCUGGCUUUCGCGGC-------------------------------------GCAGUGA--CCCGUUGA-ACCUGA-UCCAGUUCAUACUGGCG-UAGGGA-CGGUGCAAGCGCUUUGCG
AF109218.1/4405-4502           UAAAAUUGCUAGGGGCGCCUU-------------------------------------------------------UUG-GCUGAGAUAGUUU---------------------------------------------------GACUAGA-CCCUUAUA-ACCUGA-UUUGGUUCGUACCAACG-UAGGAA--AGUAGUAUAUUCAGAAU
AF264021.1/2226-2360           AAGUUGCACCAGGGGUGCCUGUAUUCUCAACAAUCUGAAGGGCCCUUGGCCUGGAUUGUUGUGA----------UAUGG-GCUGAGAA------------------------------------------------------------AGU-CCCUUUGA-ACCUGA-ACAGGAUAAUGCCUGCG-UAGGGA-GUGUGCAUUUCUAUUUUG
AL596168.1/251336-251226       CGUUACCACAGGGGGGGCUUC-------------------------------------------------------UUA-GCUGAGAUUGAAUCCGCGUGUUUUUGG------------------------------------AUUCUGA-CCCUUUGA--ACCUGU-UC--GUUAAUACGAGCG-UAGGGA-UUGUGGCGAUUGCAUUUC
AF217503.1/595-688             ACAUGGCAUCGAUGGACUGGGU-----------------------------------------------------UCGU-UCUGAGAUU-----------------------------------------------------------AUA-CGGCUAAA-ACUUGA-UCUGGAUAAUACCAGCGAAAAGGG-UCAUGCCUUCUCUCGUUC
AK120238.1/2075-2184           CUAUGUUAGGAGGUGGCCUCUUGGCCUGGAUUGUUGUGA-----------------------------------AUUGG-GCUGAGAA------------------------------------------------------------AGU-CCCUUUGA-ACCUGA-ACAGGAUAAUGCCUGCG-AAGGGA-GUGUGCAUUUCUACUUUU
AF004408.1/427-558             ACCAUUCACCAGGGGUGCCCCGGC--------------------------------------------------AAGGG-GCUGAGAUUCUGCUGAACAAUACGGCUUUGCCUGUUGUGG-----------------------CGCGGUGA-CCCGUUGA-ACCUGA-UCCAGUUCAUACUGGCG-UAGGGA-CGGUGCGGACCUGCGGCU
BX571860.1/177712-177587       ACUUUCUUGUCGGAGUGCCUAGCGUAAGCUGUUUUAUCGCAGCAUA----------------------------CACAG-GCUGAGACCGUUA--------------------------------------------------AUUCGGGA-UCCGCGGA-ACCUGA-UCGGGUUAAUACCCGCG-AAGGGA--ACAAGAGUAAUCAACCG
AY102616.1/4667-4777           GGCAGUCCCCACGGGCGCCCGAGC---------------------------------------------------ACGG-GCUGAGAUCGCGCUGAUUSUG------------------------------------------CGCGAGCA-CCGUUUGA-ACCUG--UCCGGUUAGCACCGGCG-AAGGAA-GAGAGGAAUGGUGCAAUG
U81371.1/247-152               AAAAAACUAUUAGGGUGCCCGUAG--------------------------------------------------UAUGG-GUUUAGAAA-----------------------------------------------------------AAA-CCUUUUGG-ACUUGA-UAUGGAUCAUACCAGCU-UAGGAA-AGUAGUGUAAUUUUUUCC
BX248356.1/234808-234920       ACGAGAUGCCCGG-GUGCCAUGUGCUUGCUGU------------------------------------------ACGUG-GCUGAGACGGCUGUU------------------------------------------------UGGCCGAA--CCGUAGA-ACCUGA-UCUGGGUAAUACCAGCGAUAGGAA--GACUUCAUACUGUGACU
BX248356.1/232868-232999       UUUAUAAAUCACGGGUGCUGGACGGCAUACGUUUGCC-------------------------------------ACAAA-GCUGAGACAGGGCGAGAAGACGUGCACG-----------------------------------UCCCUGAA-CCGUUGA--ACCUGA-UCCGGGUAAUACCGGCGAUAGGAA--GAAUAAUGAACCGAUCG
AC005496.3/78625-78498         CAAAAGCACCAGGGGUGCUUGAACCAGGAUAGCCUGCGAAAAGGCGGGCUAUCCGGG-----------------ACCAG-GCUGAGAA------------------------------------------------------------AGU-CCCUUUGA-ACCUGA-ACAGGGUAAUGCCUGCG-CAGGGA-GUGUGCAGUUUUUUUUUU
AK119882.1/1-98                UUGAAUGACUCGGGGUGCCCCUUUUCAC----------------------------------------------AAAGG-GCUGAGAA------------------------------------------------------------AUA-CCCGUACC-ACCUGA-UCUGGAUAAUGCCAGCG-UAGGGA--AGUCAGAUGCCUGCCCG
AL445064.1/126097-125991       CUGGUGUGGUGGGGGAGCUCCAUA---------------------------------------------------AGGG-GCUGAGAGGAUCCGGAU----------------------------------------------GGAUC-GAUCCCUGGA--ACCUGA-UCCGGGUAAUACCGGCG-GAGGGA-AAUUAUGGAAAAAAAUAG
CP000557.1/594796-594903       GACAUCCACUAGGGGGGCCUUUAG---------------------------------------------------AAAG-GCUGAGAUCAAAGUGUGC---------------------------------------------CUUUGAGA-CCCUUAGC-ACCUGA-UCUGGGUAAUACCAGCG-UAGGGA--AGUGGAGAGGAGCUACA
CP000141.1/198028-198135       AACGGCCACUGGGGGUGCCGGUCAA-------------------------------------------------AACCG-GCUGAGAGGGAGAGU------------------------------------------------UCUCCCAA-CCCUUUGA-ACCUGA-UCCGGGUAAUACCGGCG-UAGGGA-AAGUGGGGUAACUGGAAG
AP006627.1/829775-829676       AAGAACCACUAGGGGAGCCAU-------------------------------------------------------CUG-GCUGAGAAAAGCGC-------------------------------------------------UGCUUUGA-CCCUUUGA-ACCUGA-UCUGGCUUGUACCAGCG-UAGGGA--AGUGGAGAACAAUUGCU
BA000043.1/643262-643369       AUCAUCCACUAGGGGGGCCUUUAG---------------------------------------------------AAAG-GCUGAGAUCAAAGUGUGC---------------------------------------------CUUUGAGA-CCCUUAGC-ACCUGA-UCUGGGUAAUGCCAGCG-UAGGGA--AGUGGAGGAGCAGCACA
AACY022101973.1/389-487        UAUAAGUCCAAGGGGUGCCAA-------------------------------------------------------UUG-GCUGAGAUGGUUU--------------------------------------------------UAACCAAU-CCCUUUGA-ACCUGA-UCCGGUUAAUACCGGCG-UAGGAA--UGGAUUUUCUCUACAGC
AARF01000324.1/6363-6261       UUUUUUCACUAGGGGCGCCCGU-----------------------------------------------------ACGG-GCUGAGACAGAAUGG------------------------------------------------UUUCUGGA-CCCUUUGA-ACCUGA-UCUGGAUUAUACCAGCG-UAGGAA--AGUGGGAAUGCAUGAAU
AAMD01000032.1/31845-31737     CGUUGUCGCUAGGGGUGCCCCCGU--------------------------------------------------CAGGG-GCUGAGAUGGCCGUGGAC---------------------------------------------CGGCCAGA-CCCUUUGA-ACCUGA-ACCGGGUCAUACCGGCG-GAGGGA--AGCGGCGGGCGCUCCAA
CP000510.1/2895423-2895324     CAAAUAUAGUCGGGGGGCCUG-------------------------------------------------------AAG-GCUGAGAUCGCAUA-------------------------------------------------GUGCGAAA-CCCGUUGA-ACCUGA-UUCAGUUAAUACUGGCG-UAGGGA--ACUAUAAGUCUUGUUUU
AAEK01000033.1/47712-47817     UUUAUCCACUAGGGGGGCCUAUUA----------------------------------------------------UAG-GCUGAGAUCAAAUGGGA----------------------------------------------AUUUGAGA-CUCUUAGU-ACCUGA-UCUGGUUAAUGCCAGCG-UAGGGA--AGUGGAAAAGACAUUGC
CP000076.1/627657-627761       CGGUUCUUGUCGGGGUGCCUUGCU--------------------------------------------------AUGAG-GCUGAGAUCGGAUA-------------------------------------------------AUCCGGAU-CCCGUUGA-ACCUGA-UCAGGUUAGCGCCUGCG-UAGGGA--ACAAGAUUUCUCGUCAC
ABCF01000004.1/41916-42024     CAAAACCACUGGGGGAGCCUUUUA----------------------------------------------------AAG-GCUGAGAUUAAAGUGUACUA-------------------------------------------CUUUAAGA-CCCUUUGA-ACCUGA-UCUAGUUCAUACUAGCG-GAGGGA--AGUGUAGUCUGAAUGAU
CP000489.1/34903-34800         CUCAUACACUUGGGGAGCCUCGCA---------------------------------------------------CGAG-GCUGAGAGGUGCCG-------------------------------------------------GGCACCGA-CCCAUCGA-ACCUGA-UCCGGGUCAUGCCGGCG-UAGGGA--AGGGUAGAGUGAAGCGG
AE015929.1/2101479-2101588     UUUAACCACUGGAAGUGCCUUUGU--------------------------------------------------UUAAG-GCUGAGAGUAAAGAACUGA--------------------------------------------CUUUAUAA-UUCCUGGA-ACCUGA-UCCAGUUCAUACUGGCG-UAGGGA--AGUGGCGACGCUCAAUU
CP000568.1/733772-733877       UCAUCACGCUAGGGGUGCCAU------------------------------------------------------UGUG-GCUGAGAAAGAGACUUAAG--------------------------------------------UCUCUUAA-CCCUUUGA-ACCUGA-UGCGGUUAGUACCGCCG-GAGGGA--AGCGGAAAAUAUUGUUU
CP000771.1/338574-338685       UAAUGCCUGGAGGGGAGCUCCAAAAU------------------------------------------------GCGGG-GCUGAGAGGAAGGAGUCAAU-------------------------------------------CCUUC-GA-CCCUUCGA-ACCUGA-UCCGGGUAAUACCGGCG-GAGGGA--CCAGGUGACUCAAAAAU
AE017180.1/640928-640827       AUAGUCUGCUGGGGGAGUUCUU-----------------------------------------------------GGGA-ACUGAGACGGGCAA-------------------------------------------------CGCCCGAA-CCCUUUGA-ACCUGA-UCCGGUUUAUACCGGCG-UAGGGA--AGCGGCCAGAAACAAUC
CP000764.1/2008349-2008244     UCUAUCCACUAGGGGUGCCGAU-----------------------------------------------------AUUG-GCUGAGAUUAAAGUUUAU---------------------------------------------CUUUGAGA-CCCUUAGU-ACCUGA-UCUGGUUCGUACCAGCG-UAGGGA--AGUGGAAAUGACAAAAU
AP006716.1/943397-943499       UAAUGCUACUAGGGGAGCCAUAGU--------------------------------------------------AAAUG-GCUGAGAUGAUUA---------------------------------------------------AUUCAGA-CCCUUAUA-ACCUGA-UUUGGUUAGUACCAACG-UAGGAA--AGUAGUUAUGUAAAUGU
AALZ01000004.1/372786-372686   AUCUAUCCGUCGGGGUGCCCUA-----------------------------------------------------GGGG-GCUGAGAGGUGCG--------------------------------------------------UGCACCGA-CCCGUCGA-ACCUGA-UCCGGGCAAUACCGGCG-UAGGGA--ACGGGUAUCUUUGUGCA
CP000002.3/1271349-1271457     GUUUUCCACUAGGGGAGUCCUUGA--------------------------------------------------UAAGG-GCUGAGAUAAAAGUUUGA---------------------------------------------CUUUUAGA-CCCUCAUA-ACCUGA-ACAGGUUCAAACCUGCG-UAGGGA--AGUGGCACGGUAUUUGA
CP000058.1/628566-628670       GCGUUCUUGUCGGGGUGCCUUGCU--------------------------------------------------GUGAG-GCUGAGAUCGGUUA-------------------------------------------------AACCGGAU-CCCGUUGA-ACCUGA-UCAGGUUAGCGCCUGCG-UAGGGA--ACAAGAUUUCUCGUCUC
CP000716.1/1578877-1578987     AGAAAACCCGAGGGGAGCUCCAUAAG------------------------------------------------CCGGG-GCUGAGAGGAAGGCGGAAG--------------------------------------------UCUUC-GA-CCCUUAGA-ACCUGA-ACCGGGUAAUACCGGCG-GAGGGA--CGGGUAGAGAAAAUUUC
AALV01000001.1/1015631-1015532 UAAGAUACCUCGGGGGGCCUG------------------------------------------------------ACAG-GCUGAGAUGUGCG--------------------------------------------------CGCACGGA-CCCGUUGA-ACCUGA-ACCGGUUAACACCGGCG-GAGGGA--AGGUCUGGAUACACCUC
AP008934.1/816596-816694       AAACGCUACUAGGGGAGCCAG-------------------------------------------------------UUG-GCUGAGAUGAUUA--------------------------------------------------AAUUCAGA-CCCUUACA-ACCUGA-UUUGGUUAAUACCAACG-UAGGAA--AGUAGUUUAAUCUAAAG
CT573326.1/5282526-5282420     AUGUUCUUGUCGGGGUGCCUUGAAG-------------------------------------------------CAAAG-GCUGAGAUCGCAAAG------------------------------------------------UUGCGGAU-CCCGUUGA-ACCUGA-UCAGGUUAGCGCCUGCG-UAGGGA--ACAAGAUUGCUCUCAUU
AE017221.1/302202-302311       GGGGCAGGCUAGGGGUGCCCGAAUG-------------------------------------------------GAAGG-GCUGAGAGCUGGGUUUCU---------------------------------------------CCCAGCAA-CCCUUGGA-ACCUGA-UCCGGGUAAUGCCGGCG-GAGGGA--AGCCUAUGCGGAAGACC
AE004439.1/1459568-1459465     GCACUUUAGUCGGGGUGCUUUGUAACCAAAUUGU----------------------------------------ACAAA-GCUGAGAU-----------------------------------------------------------GAUA-CCCGUGA--ACCUGA-UACAGCUAACACUGACG-UAGGAA--ACUAAUUAUGCCAAUAA
AE008691.1/1681524-1681422     CUCAAGUGCUAGGGGAGCCAGA-----------------------------------------------------AAUG-GCUGAGAGGGGAUUC------------------------------------------------GUUCCCGA-CCCUUAGA-ACCUGA-CCAGGGUAAUGCCUGCG-AAGGGA--AGCACGUUUUAUUGAGU
AE008691.1/2399659-2399556     UAUGUCCGCUGGGGGAGCCUGA-----------------------------------------------------AAAG-GCUGAGACGGCAGAA------------------------------------------------AUGCCGAA-CCCUUGGA-ACCUGA-UGAGGGUAAUGCCUCCG-UAGGGA-AUGCGGGCUCAAAAGGCA
CP000114.1/913402-913491       AUAGGACAUUUGGGGUGCGUA-------------------------------------------------------ACA-GCUGAGAUU-----------------------------------------------------------AUA-CCCAUUGA-ACUUGA-UGCAGUUAGUACUGUCG-AAGGGA--AAUGUGUGCCAUUACAA
AE007869.2/2541937-2541826     GCCAUUCACCAGGGGUGUCCCGUC--------------------------------------------------AAGGG-GCUGAGAUUCUGCUUUCAU--------------------------------------------GCGCAGUGACCCGUUGA-ACCUGA-UCCAGUUCAUACUGGCG-UAGGGA-CGGUGCAAAGACCUGAUG
BX548175.1/178356-178459       GCAAAACACUAGGGGUGCCAUUCAGCAAUCGCU-----------------------------------------GAGUG-GCUGAGAUC-----------------------------------------------------------ACA-CCCUCCGA-ACCUGA-UACGGGUUGUGCCGGCG-CAGGGA--AGUGAAAUGACGUGAUC
AE004439.1/444121-444213       GACUCUUAGUCGGGGUGCUAUUGC---------------------------------------------------GUUA-GCUGAGAU-----------------------------------------------------------GAUA-CCCGUGA--ACCUGA-UGCAGUUAAUACUGACG-UAGGAA--ACUAGCAGUCAAUAUUG
AM039952.1/4100743-4100646     CCGCCGAAGUGGGGGUACCGCAGCGUG-----------------------------------------------CUGCG-GUUGAGAU------------------------------------------------------------AGU-CCCUUCGA-ACCUGA-UCCGGCUGAUACCGGCG-UAGGGA-AGCUUCGUCAGAUGCGAU
AL009126.3/1607367-1607468     GAUUCAUCCUAGGGGUGCUUUG-----------------------------------------------------CGAA-GCUGAGAGAGACUU-------------------------------------------------UGUCUCAA-CCCUUUUG-ACCUGA-UCUGGAUCAUGCCAGCG-GAGGGA--AGCGGUGAAAAGCGGAG
AL009126.3/1242262-1242370     UUUAACCACUAGGGGUGUCCUUCA--------------------------------------------------UAAGG-GCUGAGAUAAAAGUGUGA---------------------------------------------CUUUUAGA-CCCUCAUA-ACUUGA-ACAGGUUCAGACCUGCG-UAGGGA--AGUGGAGCGGUAUUUGU
CP000050.1/1019813-1019911     CCGCCGAAGUGGGGGUACCACAGCACUG----------------------------------------------CUGCG-GUUGAGAU------------------------------------------------------------AGU-CCCUUCGA-ACCUGA-UCCGGCUCAUACCGGCG-UAGGGA-AGCUUCGUUAGAUGCGCU
CP000830.1/937748-937645       CAACAACCGUUGGGGUGCCCGAUU---------------------------------------------------CAGG-GCUGAGAGGCGCAC-------------------------------------------------UGUGCCGA-CCCAUGGA-ACCUGA-UCCGGGCAAUACCGGCG-UAGGGA--ACGGUCAUCGUGGCAAU
CP000919.1/639572-639660       UAAAGACAUUUGGGGUGCUU--------------------------------------------------------UAG-GCUGAGAU-----------------------------------------------------------GAUA-CCCAUUGA-ACCUGA-UACAGUUAAGACUGGCG-AAGGGA--AAUGUGAAAUGUUUUUU
CP000918.1/2145369-2145290     UACAGUCUGAGAGGAAGUGU--------------------------------------------------------UAA-ACU----UC------------------------------------------------------------GA-CCGC-----ACCUGA-UCUGGGUAAUGCCAGCG-GAGGGA-ACGAUACUUAGUCUAAU-
AE007870.2/312774-312876       AGCUCUUCCGAGGGGAGCACCAGA---------------------------------------------------CGGU-GCUGAGAUGGUGGU-------------------------------------------------GAACCGGA-CCCUUGA--ACCUGA-UCCGGGUCAUGCCGGCG-UAGGAA--CGGAACUGUCGUGCGCU
AL009126.3/3179105-3179206     GAUGACCACAAGGGGAGCAUU-------------------------------------------------------AAA-GCUGAGAGUGAGCGGUUU---------------------------------------------CGUUCUGA-CCCUUUGA-ACCUG--U-UAGUUAACGCUGGCG-UAGGGA--UGUGGCAAAGUCAAAUG
AL766847.1/75304-75206         AAAUACACAAGGGAGUGCCU--------------------------------------------------------UGA-GCUGAGAUUGCAGAU------------------------------------------------AUGCAAAA-UCCUCUA--ACCUGA-UCUCGUUAGGACGAGCG-UAGGAA--UUGUGGUUUGAAUUGGU
CP000936.1/749906-749994       UAGAGACAUUUGGGGUGCUU--------------------------------------------------------UAA-GCUGAGAU-----------------------------------------------------------GAUA-CCCAUUGA-ACCUGA-UACAGUUAAGACUGGCG-AAGGGA--AAUGUGAAACGUUUUUU
AE008691.1/2140374-2140272     UCAAAGUGCUAGGGGAGCCAGA-----------------------------------------------------AAUG-GCUGAGAGGGGAUUC------------------------------------------------GUUCCCGA-CCCUUAGA-ACCUGA-CCAGGGUAAUGCCUGCG-AAGGGA--AGCACGUUUUACGGAAU
AE014074.1/464992-464896       UAUUUCACAAAGGAGUGCUU---------------------------------------------------------UG-GCUGAGAUCGCAA--------------------------------------------------UUGCGAAA-UCCUGAGG-ACCUGA-UCUUGUUAGUACAAGCG-UAGGGA--UUGUGACCAAUAAUCAA
CP000425.1/327513-327414       UAUUUGCACAAUGGGUCUAUUGACAAGUCUG-------------------------------------------UCAGU-AGCGAGAA------------------------------------------------------------AUA-CCAUCUG--ACCUGA-UCUGGGUAAUGCCAGCG-UAGGAA--UGUGUUAAGACAAUCGU
AE007317.1/646024-645926       AACAACCACUAGGGGUGCGU--------------------------------------------------------AAA-GCUGAGAUUAACGAC------------------------------------------------UGUUAGAU-CCCUCUG--ACUCAA-UCUAGGUAAUGCUAGCU-GAUGGA--AGUGGAAAUGAUAAUGG
CP001488.1/228163-228057       CAAAAUUCGUUGGGGUGCCUUGAA---------------------------------------------------AGAG-GCUGAGAGACGCAUUCU----------------------------------------------CACGUCAA-CCCAUUGA-ACCUGA-UCCGGGUAAUACCUGCG-UAGGGA--ACGGAGUUUGGCGCGUC
AE008691.1/1524796-1524694     CUCAAGUGCUAGGGGAGCCAAA-----------------------------------------------------AAUG-GCUGAGAGGGGAUUC------------------------------------------------GUUCCCGA-CCCUUAGA-ACCUGA-CCAGGGUAAUGCCUGCG-AAGGGA--AGCACGUUUUACGAAAU
BX548174.1/1543261-1543163     AAAUAUAACUAGGGGUGCUAAGUCAAUU----------------------------------------------ACUUA-GCUGAGAUC-----------------------------------------------------------AUA-CCCUUCGA-ACCUGA-AACAGUUAAAACUGACG-CAGGAA--AGUUUCAAUUUGAUCGA
AL591688.1/3532865-3532978     GCUGCUCUAACGGGGUGCCCUGGCCGGCUUUGCGA---------------------------------------CCAUG-GCUGAGAGGCUUC---------------------------------------------------GAGCCAA-CCCGCGGA-ACCUGA-UCCGGCUCAUACCGGCG-GAGGGA--UUAGAAGCGAUCGGACC
AL935263.2/202700-202607       UCAUAGCAACUGGGGUGCCAU------------------------------------------------------CACG-GCUGAGAUA-----------------------------------------------------------AUA-CCCAUUGA-ACCUGAAUCUGGACAAUGCCAGCG-CAGGGAGCAAUGCUUUUAUUUGGGG
AL935263.2/99249-99354         UUUAAACACUAGGGGUGUCCAAAA---------------------------------------------------AUGG-GCUGAGAUGGUGCUGUAA---------------------------------------------GUACCGAU-CCCUUUGA-ACCUG--U-AAGCUCAAACUUGCG-UAGGAA--AGUGUCACAGCUAAUGU
CP003056.1/3348160-3348049     UCAAACUACUAGGGGUGCCCGGAUUU------------------------------------------------GGCGG-GCUGAGAGAAAAACCGGCG--------------------------------------------UUUUUCAA-CCCUUUGG-ACCUGA-UCCGGAUCAUACCGGCG-UAGGAA--AGUAGGAAUUUGUAAAA
#=GC SS_cons                   :::::[[[[[((((,,<<<<<___..................................................__>>>.>>,,,,,<<<<<<_.................................................>>>>>>,,.)))),,,,.,<<<<-.-<<<<______>>>>--.>>>>,,..]]]]]::::::::::::
#=GC RF                        aaauaccacuaGGGGuGCcccuau..................................................aaggg.GCUGAGAugggccu.................................................ggcccaaA.CCCuUuGA.ACCUgA.UCcGGaUAAUaCCgGCG.uAGGGA..aguggauauauauuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00060
#=GF ID   HgcE
#=GF DE   HgcE RNA (Pab105)
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   66.20
#=GF NC   34.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.16 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   12032319
#=GF RT   Noncoding RNA genes identified in AT-rich hyperthermophiles.
#=GF RA   Klein RJ, Misulovin Z, Eddy SR
#=GF RL   Proc Natl Acad Sci U S A 2002;99:7542-7547.
#=GF RN   [2]
#=GF RM   18304947
#=GF RT   Combined in silico and experimental identification of the Pyrococcus
#=GF RT   abyssi H/ACA sRNAs and their target sites in ribosomal RNAs.
#=GF RA   Muller S, Leclerc F, Behm-Ansmant I, Fourmann JB, Charpentier B, Branlant
#=GF RA   C
#=GF RL   Nucleic Acids Res. 2008;36:2459-2475.
#=GF CC   The HgcE ncRNA gene was identified computationally in AT-rich
#=GF CC   hyperthermophiles. The genes were named hgcA through hgcG ("high GC").It
#=GF CC   was also identified as a part of Pab105 H/ACA snoRNA with rRNA targets.
#=GF CC   [2] 
#=GF WK   HgcE_RNA
#=GF SQ   4


AF468961.1/1-132         GGCGCGCGAUGAACG-AGGUGACGUCUCCGGGCGGACAGGGCCCGGCCUUCGGGGCCGCCUGAGGGAGCCGAGAAGGGCAGACGAUGAAGGCGGGCGGAUAAGCCGGGCCCUCAAAGGGUUUUGAUUCUAA--UU
AJ248287.2/141310-141179 GGCGCGCCAUGAACG-AGGCGACGUCGCCGGGCGGACAGGGCCCGGUCUCCGGGGCCGCCUGAGGUUGCCGACAACGGCGGGCAAUGAGGGCGGGUGGAUAAGCCGGGCCU--AUACCACUUCAAUUCUAACCUU
BA000001.2/592118-592247 GGCGCGCAAUGAACG-AGGUGACGUCGUCGGGCGGACAGGGCCCGGUCUCCGGGGCCGCCUGAGGUUGCCGAGAAUGGCGUUCAAUGAAGGCGGGCGGAUAAUCCGGGCCU--AAAGAACUUUAAUUCUAA--CU
AP006878.1/465164-465039 GGCCCACAGUGAAGGGAUGAGACGAUGCCGGGCGGACAGGGCCCGGUCUCCGGA-CCGCUGGAGGGGGUCUCU---GGCCGUCAAUGAGAGCGGG-GGAUCAGCCGGGCCC--ACACCGAUUGGUUUCUGU--UA
#=GC SS_cons             :::::::::::::::.::::::::::::::::::::::<<<<<<<<<--<<----<<<<<<------<<<______>>>--------->>>>>>-->>---->>>>>>>>>..::::::::::::::::::..::
#=GC RF                  GGCgCgCaaUGAAcG.AgGuGACGucgcCGGGCGGACAgGGCCCGGcCUcCGGgGCCGCcuGAGGuuGcCgauAAuGgCaguCAAUGAagGCGGGcGgAUaAgCCGGGCCc..AaAgaauUUuaaUUCUaa..Uu
//
# STOCKHOLM 1.0

#=GF AC   RF00061
#=GF ID   IRES_HCV
#=GF PI   HCV_IRES
#=GF DE   Hepatitis C virus internal ribosome entry site
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Published; PMID:12212848
#=GF GA   110.00
#=GF TC   110.50
#=GF NC   109.70
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00017
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   12023841
#=GF RT   The hepatitis C virus internal ribosome-entry site: a new target for
#=GF RT   antiviral research.
#=GF RA   Gallego J, Varani G
#=GF RL   Biochem Soc Trans 2002;30:140-145.
#=GF RN   [2]
#=GF RM   12212848
#=GF RT   Domains on the hepatitis C virus internal ribosome entry site for 40s
#=GF RT   subunit binding.
#=GF RA   Lytle JR, Wu L, Robertson HD
#=GF RL   RNA 2002;8:1045-1055.
#=GF RN   [3]
#=GF RM   11350030
#=GF RT   The internal ribosome entry site (IRES) of hepatitis C virus visualized by
#=GF RT   electron microscopy.
#=GF RA   Beales LP, Rowlands DJ, Holzenburg A
#=GF RL   RNA 2001;7:661-670.
#=GF CC   Protein translation of most eukaryotic mRNAs requires association of
#=GF CC   Met-tRNA, several initiation factors, and GTP with the 40S ribosomal
#=GF CC   subunit. The ribosome can only bind the capped mRNA after binding the
#=GF CC   initiator tRNA. Translation of hepatitis C virus (HCV) mRNA is initiated
#=GF CC   by a different mechanism from the usual 5' cap-binding model [2]. This
#=GF CC   alternate mechanism relies on the direct binding of the 40S ribosomal
#=GF CC   subunit by the internal ribosome entry site (IRES) in the 5' UTR of HCV
#=GF CC   RNA. HCV IRES adopts a complex structure, and may differ significantly
#=GF CC   from IRES elements identified in picornaviruses. A small number of
#=GF CC   eukaryotic mRNA have been shown to be translated by internal ribosome
#=GF CC   entry [3].
#=GF WK   Hepatitis_C_virus_internal_ribosome_entry_site
#=GF SQ   79


D37841.1/1-365   GCCAGCCCCUUAACGGGGCGACACUCCACCAUGAUCACUCCCCUGU-------------------GAG-GAACUACUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUAGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUCCAUUGGAUCAA-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUCCUAAACCUCA
M84754.1/1-364   GCCAGCCCCCGAUUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGU-----------------GAG-GAACUACUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUGGUAAACCUCA
AY190500.1/1-181 -----------------------------------------------------------------U-G--------------------------------------------------------------CAGC--CUCCAGGGCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-GGGAUGACCGGGU-CCUUUC--UUGGAAU-A-ACCCGCUC-AAUG-CCCGGA-AAUUUGGGCGUG-CCCC-CGCGAG-AUCACUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGC---------C-U---------------------U--------GUGG-----------------------------------------
AB030907.1/1-364 GCCCGCCCCCUGAUGGGGGCGACACUCCGCCAUGAAUCACUCCCCUGU-----------------GAG-GAACUACUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUACAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGAAAGACUGGGU-CCUUUC--UUGGAUA-A-ACCCACUC-UAUG-UCCGGU-CAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGCCUCGUAGACCGUGCACCAUGAGCACAAAUCCUAAACCUCA
L29598.1/1-191   -----------------------------------------------------------------G-A-G--------------U---------------------G------------------UUGUACAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGAUGACCGGGU-CCUUUC--UUGGAUUAA-ACCCGCUC-AAUG-CCCGGA-GAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-AAAGGCCUUGUGGU-------------------------------------------------------------------------------
X78860.1/2-193   -----------------------------------------------------------------G-GCG--------------UUA---------------------------GUAUNAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACCGCUAG-----------------------------CCGAGUAGUGU-U--------------GG----GU---CGCGAAAGG-----------------------------------------
U23386.1/2-279   -----------------------------------------------------------------G-GCG--------------U---------------------U------AGUAUAUA--GUGCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGAUGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-AGUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUUCCAAAACCCCA
Z77063.1/1-197   -----------------------------------------------------------------A-U-G--------------GCG------------------UU------AGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGCGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGC---------C-U---------------------------------------------------------------------------
AY146052.1/3-208 ---------------------------------------------------------------------G--------------CCA-------------UGGCGUU------AGUAUGAG--UGUCGUGCAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGU-------------------------------------------------------------------------------
AF041270.1/1-191 -----------------------------------------------------------------C-C-------------------------------------UC-----------------------------CCGG------------------G----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGAAGACUGGGU-CCUUUC--UUGGAUA-A-ACCCACUC-UAUG-CCCGGC-AAUUUGGGCAUG-CCCC-CGCAAG-AAUGCUAGCCGA-GUAGG-GU-UGGGUCGGG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUGGCGAGUGC-C-------------------------------------------------
AF057152.1/1-238 -------------------------------------------------------------------------------------AA-------AGCGCCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGCG----AG-AGCC-UAUUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCG-GGGGUGACCGGGU-CCUUUC--UUGGAGC-A-ACCCGCUC-AAUG-ACUCCA-GAAUUGGGCGUG-CCCC-CGCAGG-AUCACUAGCCGA-GUGGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUACGUGCCUGAUAGGGUGCUU------GC---------G-----------------------------------------
D49758.1/1-361   GCCAGCCCCUUACGGGGCGACACUCCACCAUGAUCACUCCCCUGU--------------------GAG-GAACUACUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGAUCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCAAAACCCCA
AY344020.1/1-344 GGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUUCCUGUCUUCAC--------------G-CAG---------------AA-------AGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUCC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGAAGG----UCUCGUAGUUCGUGCUUCAUGAAAAUCCUCAACCUCA
AJ438620.1/1-256 UGUUUUCAC--------------------------------------------------------G-CAG---------------AA-------AGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUNCACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUA-A-ACCCGNUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGN-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------G---CUCGAGAGU---------------------------------------GA
AF041297.1/1-191 -----------------------------------------------------------------C-C-------------------------------------UC-----------------------------CCGG------------------G----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGAAGACUGGGU-CCUUUC--UUGGAUA-A-ACCCACUC-UAUG-CCCGGC-AAUUUGGGCGUG-CCCC-CGCAAG-AAUGUUAGCCGA-GUAGU-AG-UGGGUCGGG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGGGAGUGC-C-------------------------------------------------
AJ007824.1/1-227 ----------------------------------------------------------------------------------------------UGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUUGARCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-RGGAYGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-RAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-U--------G----------------CCUGAUAGG-----------------------------------------
U23750.1/1-270   UAU--------------------------------------------------------------G-A-G--------------U---------------------G------------------UCGUACAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACAGGGU-CCUUUC--UUGGAUC-A-ACCCUCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUCCUAAACCCCA
L29612.1/1-231   ------------------------------------------------------------------------------------UUA---------------------------UUAUGAG--UGUCGAACAGC--CUCCAGGAUCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUUCACCGGAAUCGCC-GGGAUGACCGGGU-CCUUUC--UUGGAAUCA-ACCCGCUC-AAUG-CCCGGA-AAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGG--------------------------------------------
U81280.1/1-231   -----------------------------------------------------------------G-CAG---------------AA-------AGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUACAGC--CUCCAGG-CCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGAAGACUGGGU-CCUUUC--UUGGAUA-A-ACCCACUC-UGUG-CCCGGC-CAUUUGGGCGUG--CCC-CGCAAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-AAAGGCCUUGUGGUAC-U--------G----------------CCUGAUAGG-----------------------------------------
AB047641.1/1-363 ACCCGCCCCUAAUAGGGGCGACACUCCGCCAUGAAUCACUCCCCUGU------------------GAG-GAACUACUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUACAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGAAGACUGGGU-CCUUUC--UUGGAUA-A-ACCCACUC-UAUG-CCCGGC-CAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACAACUCCUAAACCUCA
AF506627.1/1-230 AUCCCUGUGAGGAACUUCUGUCUUCAC--------------------------------------G-C-G--------------GAA-------AGCGCCUAGCCAUGGCGUUAGUACGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCCUCCCGGG---AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUUUC--UUGGAAU-A-ACCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCGAG-AUCACUAG-----------------------------CCGAGUAGUGU-U------------------------------GGGU-----------------------------------------
Z84266.1/1-249   UUCAC------------------------------------------------------------G-CAG---------------AA-------AGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC--CCCUCCCG----GG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGUCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCGUGAUAGGGU---------G---CUCGAGAGU-----------------------------------------
D13449.1/1-185   U----------------------------------------------------------------G-U-G--------------C----------------------------------------------AGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUCCACCGGAAUCGCC-GGGAUGACCGGGU-CCUUUC--UUGGAACUA-ACCCGCUC-AAUG-CCCGGA-AAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGC---------C-U---------------------U--------GUGG----------------------------------------U
D16614.1/3-283   AU---------------------------------------------------------------G-GCG--------------UUA---------------------------GUACGAG--UGUCGUGCAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUAGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-GGGGUGACCGGGU-CCUUUC--UUGGAAUCA-ACCCGCUC-AAUA-CCCGGA-AAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAUUUCCUAAACCUCA
L12355.1/1-336   ACCAUGGAUCACUCCCCUGUGAGGAACUUCUGUCUUCAC--------------------------G-C-G--------------GAA-------AGCGCCUAGCCAUGGCGUUAGUACGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUUUC--UUGGAGC-A-ACCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCGAG-AUCACUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACACUUCCUAAACCUCA
AY172639.1/1-295 -----------------------------------------------------------------A-G-----------------AA-------AGCGUUUACCCAUGGCGUUAGUAUGAG--UGUUGUACAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUCCACCGGAAUCUCC-AGGACGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-AAUG-CCUGGA-AAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUCCUAAACCUCA
AF041311.1/1-191 -----------------------------------------------------------------C-C-------------------------------------UC-----------------------------CCGG------------------G----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGU-GU-GGGGUCGCG-AAAGGCCUGGUGGUAC-UACCUGAUAGGGUGCUGGCGAGUGC-C-------------------------------------------------
AF041303.1/1-191 -----------------------------------------------------------------C-C-------------------------------------UC-----------------------------CCGG------------------G----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUUCAACGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGAAAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGGGAGUGC-C-------------------------------------------------
Z84276.1/1-250   UUCAC------------------------------------------------------------G-CAG---------------AA-------AGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUACAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUCUC--UUGGAAU-A-ACCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCGAG-AUCACUAGCCGA-GUAGU-GU-UGGGCCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------G---CUCGAGAGU-----------------------------------------
AF077233.1/1-250 UUCAC------------------------------------------------------------G-CAG---------------AA-------AGCGUCUAGCCAUGGCGUUAGUACGAG--UGUCGUGCAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUUUC--UUGGAGC-A-UCCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCAAG-AUCACUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------G---CUCGAGAGU-----------------------------------------
AF041282.1/1-191 -----------------------------------------------------------------C-C-------------------------------------UC-----------------------------CCGG------------------G----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGAAGACUGGGU-CCUUUC--UUGGAUA-A-ACCCACUC-UAUG-CCCGGC-CAUUUGGGCGUG-CCCC-CGAAAG-ACUGCUAGCCGA-GUAGC-GU-GGGGUCGCG-AAAGGCCUGGUGGUAC-UGCCUGAUAGGGUGCUGGGGAGUGC-C-------------------------------------------------
AF057148.1/1-238 -------------------------------------------------------------------------------------AA-------AGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUACAGC--CUCCAGGCCCCCC-CCUCCCGCG----AG-AGC-AUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUU-AC-CGAAAGACUGGGU-CCUUUC--UUGGAUACA-ACCCACUC-AUUGCCCGGUC-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUU------GC---------G-----------------------------------------
D37839.1/1-362   ACCUGCCUCUUUCGAGGCGACACUCCACCAUGAGUCACUCCCCUGUGAGGAACUUCUGUCUUCACG-C-G--------------GAA-------AGCGUCUAGCCAUGGCGUUAGUACGAG--UGUCGUGCAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-GGGAUGACCGGGU-CCUUUC--UUGGAAC-A-ACCCGCUC-AAUG-CCCGGA-AAUUUGGGCGUG-CCCC-CGCGAG-AUCACUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUCCUAAACCCCA
D50466.1/1-362   ACCCGCCCCUUAUUGGGGCGACACUCCACCAUGAUCACUCCCCUGU-------------------GAG-GAACUACUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGAACAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGACGACCGGGU-CCUUUC--UUGGAUA-A-ACCCGCUC-AAUG-CCCGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUCCUAAACCUCA
AY145903.1/2-211 -----------------------------------------------------------------U-UAG--------------CCA-------------UGGCGUU------AGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCCUCCCGGGAGA----GCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACGCGUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGU-------------------------------------------------------------------------------
AY311400.1/1-215 UCAC-------------------------------------------------------------G-C-G--------------GAA-------AGCGUCUAGCCAUGGCGUUAGUACGAG--UGUCGUGCAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-GGGACGACCGGGU-CCUUUC--UUGGAAC-A-ACCCGCUC-AAUG-CCCGGA-AAUUUGGGCGUG-CCCC-CGCGAG-AUCACUAG-----------------------------CCGAGUAGUGU-U--------------GG----GU---CGCGAAAGG-----------------------------------------
AF506647.1/1-238 AUCCCUGUGAGGAACUUCUGUCUUCAC--------------------------------------G-C-G--------------GAA-------AGCGCCUAGCCAUGGCGUUAGUACGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUUUC--UUGGAGC-A-ACCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCGAG-ACCGCUAG-----------------------------CCGAGUAGUGU-U--------------GG----GU---CGCGAAAGG-----------------------------------------
AF506639.1/3-232 CCAU-------------------------------------------------------------G-GCG--------------UUA---------------------------GUGUGAG--UGUCGUACAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGAAGACUGGGU-CCUUUC--UUGGAUA-A-ACCCACUC-UAUG-CCCGGC-CAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-ACAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------G---CUUGCGAGA-----------------------------------------
D84264.2/1-361   GCCAGCCCCUAAUGGGGCGACACUCCACCAUGAUCACUCCCCUGU--------------------GAG-GAACUACUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACUCCC-CCUCCCGGG----AG-AGCCAUAGUAGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGAUGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-GAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCAAG-AUUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUCCAAAACCCCA
Z36522.1/3-205   -----------------------------------------------------------------A-U-G--------------GCG------------------UU------AGUACGAG--UGUCGUGCAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-GGGUUGACCGGGU-CCUUUC--UUGGAAC-U-ACCCGCUC-AAUG-CCCGGA-AAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-AAAGGCCUUGUGGU-------------------------------------------------------------------------------
U38285.1/1-202   --------------------------------------------------------------------------------------A-------AGCGCCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAG-----------------------------CCGAGUAGUGU-U--------------------GG---GUCGCGA-------------------------------------------
AF216795.1/3-205 -----------------------------------------------------------------A-U-G--------------GCG------------------UU------AGUACGAG--UGUCGAACAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCCCC-AGGACGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-CAUG-CCUGGG-UAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGU-------------------------------------------------------------------------------
D28833.1/2-211   --------------------------------------------------------------------------------------------------------------------------------------------A------------CCGGUG----AG-UAC-A---------CCGG------------------AAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUUCCAAAACCCCA
AY190452.1/1-181 UGCA-------------------------------------------------------------G-G--------------------------------------------------------------------CUUCAGGACCCCC-AGUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGC---------C-U-------------------------UGUGG---------------------------------------------
AJ437144.1/1-237 -------------------------------------------------------------------------------------AA-------AGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCCCCCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAA-CGCU-AGGGUGACCGGGU-CCUUUC--UUGGAGC-A-ACCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------G---CUUGA---------------------------------------------
AF077229.1/1-285 UUCAC------------------------------------------------------------G-CAG---------------AA-------AGCGUCUAGCCAUGGCGUUAGUACGAG--UGUCGUGCAGC--CUCCAGGCCCCCC--CUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUUUC--UUGGAAC-A-ACCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCGAG-AUCACUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------G---CUCGAGAGU-----GGCCCUCCUCGUUUAGGUCUCGUAGACCGUGCACCU
U59514.1/2-304   CACUCCCCUGU------------------------------------------------------GAG-GAACUACUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGAGCCCC-CCUCCCGAGU---AG-CGAGAUC-UGGGCGUCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUA-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGG------------------------UCUCGUAGACCGUGCAC
AY145966.1/2-232 ---------------------------------------------------------------------G--------------CCA-------------UGGCGUU------AGUAUGAG--UGUCGUGCAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUUUC--UUGGAAC-A-ACCCGCUC-AAUA-CCCGRA-AAUUUGGGCGUG-CCCC-CGCGAG-AUCACUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------G---CUUGCGAGU-----------------------------------------
AY163831.1/1-177 -----------------------------------------------------------------U-C--------------------------------------------------------------------CCGG-------------------G---AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCU-AGGGCGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUAGA-AAUUUGGCCGUG-CCCC-CGCGAG-AUCACUAGCCGA-GUAGU-GUUUGGGUCGCU-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------------------------------------------------------------
AF511949.1/1-364 ACCAGCCCCCUGAUGGGGGCGACACUCCACCAUGAAUCACUCCCCUGU-----------------GAG-GAACUACUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUACAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAUUCCUAAACCUCA
X91421.1/2-204   CAC--------------------------------------------------------------G-GCG--------------UUA---------------------------GUACGAG--UGUCGUGCAGC--CUCCAGCGCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACGCGAAUCGCC-GGGGUGACCGGGU-CCUUUC--UUGGAAC-A-ACCCGCUC-AAUA-CCCGGA-AAUUUGGGCGUG-CCCC-CGCGAG-AUCACUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGC---------C-U---------------------U--------GUGG-----------------------------------------
Z84281.1/1-249   UUCAC------------------------------------------------------------G-CAG---------------AA-------AGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUACC-GGAAAGACUGGGU-CCUUUC--UUGGAUA-A-ACCCACUC-UAUG-UCCGGU-CAUUUGGGCGUG-CCCC-CGCAAG-ACUG-UAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------G---CUCGAGAGU-----------------------------------------
AY434109.1/2-197 -----------------------------------------------------------------U-GAG--------------U---------------------G------------------UUGUACAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUUCACCGGAAUCGCC-GGGACGACCGGGU-CCUUUC--UUGGAACAA-ACCCGCUC-AAUG-CCCGGC-AAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGC-GU-UGGGUUGCG-AAAGGCCUUGUGGUAC-U---------------------------------G-----------------------------------------
AF165050.1/1-352 UUGGGGGCGACAUUCCACCAUAGAUAAUUCCCCUGUGA---------------------------G-G-AAUUACUGUUUUAACGCAGAA----AGCGUUUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--UUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGAUGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCUAAACCCCA
AJ006317.1/1-229 C----------------------------------------------------------------G-U-G--------------C----------------------------------------------AGC--CUCCAGG--CCCC-CCUCUAGGG----AGCAGCCAUAGUGGUGUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGA-CGGGU-CCUUUC--UUGGAGC-A-ACCCGCUC-AAUA-CCCAGA-AAUUUUGGCGUGCCCCC-CGCAAG-AUCACUAGCCCAAGUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCAAGUGCCCCCGGGAGG---------------------------------UCUCGUAA
AY344021.1/1-348 GGCGACACUCCACCAUAGAUCACUCUCCCUGU---------------------------------GAG-GAACUACUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-AANNNUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGUNCUCGUAGACCGUGCAUCAUGAGCACAAAUCCUUAACCUCA
AY145968.1/2-232 ---------------------------------------------------------------------G--------------CCA-------------UGGCGUU------AGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUUUC--UUGGAGU-A-ACCCGCUC-AAUA-CCCAGR-AAUUUGGGCGUG-CCCC-CGCGAG-ACCGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------G---CUUGCGAGU-----------------------------------------
AF506679.1/1-231 UUCCCUGUGAGGAACUUCUGUCUUCAC--------------------------------------G-C-G--------------GAA-------AGCGCCUAGCCAUGGCGUUAGUACGAG--UGUCGUGCAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGAUGACCGGGU-CCUUUC--UUGGAAC-A-CCCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCAAG-AUCACUAG-----------------------------CCGAGUAGUGU-U----------------------------GGGUCG-----------------------------------------
AF041281.1/1-191 -----------------------------------------------------------------C-C-------------------------------------UC-----------------------------CCGG------------------G----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGAAGACUGGGU-CCUUUC--UGGGAUA-A-ACCCACUC-AAUG-CCCGGC-CAUUUGGGCGUG-CCCC-CGAAAG-AUUGUUAGCCGA-GUAGC-GU-GGGGUCGCG-AAAGGCCUGGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-C-------------------------------------------------
L38354.1/1-261   C----------------------------------------------------------------G-U-G--------------C----------------------------------------------ARC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGMGUK-CCCC-CGCGAG-ACUGCUARCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACACUUCCUAAACCUCA
AJ006327.1/1-227 ---------------------------------------------------------------------G--------------CCA-------------UGGCGUU------AGUAUGAG--UGUCGCGCAGC--CUCCAGGACCCCC-CCUCCAGGG----AG-AGCCAUAGUGGUCUGCGGAGCCGGUGAGUACACCGGAAUUGCC-AGGAUGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUU------GC---------------------------------------------------
AF057155.1/1-236 -------------------------------------------------------------------------------------AA-------AGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGCG----AG-AGC-AUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-GGGGAUACCGGGU-CCUUUC--UUGGAUA-A-ACCCGCUC-AAUG-CCUGGA-AAUU-GGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUGGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUU------GC---------G-----------------------------------------
AF057147.1/1-240 -------------------------------------------------------------------------------------AA-------AGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGUACAGC--CUCCAGGCCCCCC-CCUCCCGCG----AG-AGC-AUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUACC-GGGAAGACUGGGU-CCUUUC--UUGGAUACA-ACCCGCUC-AAUG-CCUGGACGAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGUUGU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUU------GC---------G-----------------------------------------
L29576.1/1-230   ------------------------------------------------------------------------------------UUA---------------------------GUAUGAG--UGUCGUGCAGC--CUCCAGGAUCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGAUGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-AGUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGG--------------------------------------------
AY188114.1/3-196 -----------------------------------------------------------------G-A-G--------------U---------------------G------------------UCGUGCAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUUUC--UUGGACC-A-ACCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCAAG-AUCACUAUCCGA-GUAAU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-U---------------------------------G-----------------------------------------
AY163827.1/1-253 -----------------------------------------------------------------U-U-UAAGUA---------GAA-------ACUGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGGGCAGCCUGCCAAGGACUCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUCAA-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU---------G---CUCGAGAGU-----------------------------------------
X78865.1/2-193   -----------------------------------------------------------------G-GCG--------------UUA---------------------------GUAUGAG--UGUUGUACAGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-GGGAUGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-AAUG-CCCGGA-AAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAG-----------------------------CCGAGUAGUGU-U--------------GG----GU---CGCGAAAGG-----------------------------------------
D45193.1/1-363   ACCUGCUCUCUAUGAGAGCAACACUCCACCAUGAACCGCUCCCCUGU------------------GAG-GAACUUCUGUCU---UCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAG--UGUUGUACAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-GGGAUGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-AAUG-CCCGGA-AAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUCCUAAACCUCA
AY163829.1/1-223 CUGUGAGGAACUUCUGUCUUCAC------------------------------------------G-C-G--------------GAA-------AGCGUCUAGCCAUGGCGUUAGUACGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGUCCUUUUC--UUGGAGC-AAACCCGCUCCAAUG-CCCAGA-GAUUUGGGCGAG-CCCCACGCGAG-AUCGCUAG-----------------------------CCG------AG-U------------------------------GAGU-----------------------------------------
D13451.1/2-185   -----------------------------------------------------------------G-U-G--------------C----------------------------------------------AGC--CUCCAGGCCCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-GGGAUGACCGGGU-CCUUUC--UUGGAACUA-ACCCGCUC-AAUG-CCCGGA-AAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGU-------------------------------------------------------------------------------
X78867.1/2-193   -----------------------------------------------------------------G-GCG--------------UUA---------------------------GUAUGAG--UGUCGAACAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGAUGACCGGGU-CCUUUC--UUGGAUU-A-ACCCGCUC-AAUG-CCCGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAG-----------------------------CCGAGUAGUGU-U--------------GG----GU---CGCGAAAGG-----------------------------------------
AF041285.1/1-191 -----------------------------------------------------------------C-C-------------------------------------UC-----------------------------CCGG------------------G----AG-AGCCAUGGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGAAGACUGGGU-CCUUUC--UUGGAUA-A-ACCCACUC-UAUG-CCCGGC-CAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGS-GU-UGGGUUGCG-AAAGGCCUUGKGGKAC-UGCCUGAUAGGGUGCUUGGGAGUGC-C-------------------------------------------------
AF134759.1/1-181 -----------------------------------------------------------------U-G--------------------------------------------------------------CAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-GGGGAGACCGGGU-CCUUUC--UUGGAAC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCAAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGC---------C-U---------------------U--------GUGG-----------------------------------------
AY190402.1/3-181 ----------------------------------------------------------------------------------------------------------------------------------CAGC--CCCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCC-GGGAUGACCGGGU-CCUUUC--UUGGAUA-A-ACCCGCUC-AAUG-CCCGGA-AAUUUGGGCGUG-CCCC-CGCGAG-ACCGUUAGCCGA-GUAGU-GU-UGGGUCGCA-AAAGGC---------C-U---------------------U--------GUGG-----------------------------------------
U23749.1/1-261   C----------------------------------------------------------------G-U-G--------------C----------------------------------------------AGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGCGACCGGGU-CCUUUC--UUGGAAC-A-ACCCGCUC-AAUA-CCCAGA-GAUUUGGGCGUG-CCCC-CGCAAG-ACCACUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGGUCUCGUAGACCGUGCAACAUGAGCACACUUCCUAAACCUCA
AF506666.1/2-232 CCCUGUGAGGAACUUCUGUCUUCAC----------------------------------------G-C-G--------------GAA-------AGCGCCUAGCCAUGGCGUUAGUACGAG--UGUCGUGCAGC--CUCCAGGACCCCC-CCCUCCCGGG---AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUCGCU-GGGGUGACCGGGU-CCUUUC--UUGGAGC-A-ACCCGCUC-AAUA-CCCAGA-AAUUUGGGCGUG-CCCC-CGCGAG-ACCGCUAG-----------------------------CCGAGUAGUGU-U---------------------------GGGUCGC-----------------------------------------
AJ006314.1/1-234 -----------------------------------------------------------------A-A-----------------------------------CCAU-----------------------------CCUU-GUAUCCCC-CCUCCCUGU----AG-AGCAA-AGUGGUCUCCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUCAA-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGUCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGUGCUUGCGAGUGC-CCCGGGAGG------------------------UCUCGUAAACCGUGCCC
AY163830.1/1-251 UUCAC------------------------------------------------------------G-CAG---------------AA-------ACCGUCUAGCCAUGGCGUUAGUAUGAG--UGUCGGGCAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGUCAAAGUCGACCGAAU-CCUUUG--UUUUAUC-A-AACCCCUC-GAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAGCACUGUUAGCCGA-GUAAU-GU-UGGGUCCCGUAAAGGCCUUGAGGUAC-UGCCUGAUAGGGU---------G---CUCGAGA-------------------------------------------
AY163822.1/1-254 UUCAC------------------------------------------------------------G-C-A--------------AGAA------AACGUCUAGCCAUGGCGUUAGUAUGAGUGUCAGUGCAAGC--CUCCAGGACCCCC-CCUCCCGGG----AG-AGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCC-AGGACGACCGGGU-CCUUUC--UUGGAUC-A-ACCCGCUC-AAUG-CCUGGA-GAUUUGGGCGUG-CCCC-CGCGAG-ACUGCUAGCCGA-GUAGU-GU-UGGGCCGCG-AAAGGCCUUGUGGUAC-UGCCUGAUAGGGU--------GG---CUCGAGAGU-----------------------------------------
#=GC SS_cons     :::..............................................................<.<.<..............-<<.......<<<<<<_______>>>>>>--------..>>---------..>->>---------.{{{{{{{{{....[[.-[[[[(((((((((((((,,<<<<<<____>>>>>><<<<-<<.<<<--<<-<<<<<.______.._______._.>>>>>->>.----.>>>>>-.>>>>,<<<____.>>>).)))-)).)))))))<<<<-.-<-<<.<_._____>>>-.>->>>>,,,,]]]]-].]<<<______>>><<__....__>>.}}}}}}}}}.........................................
#=GC RF          uuc..............................................................g.g.g..............uca.......agcGccUAGccauggCgcuAGUAuGAG..ugUcGugcAGC..cUccAGGacCCCC.cCucccggg....aG.AgCCauagcgguCugCGGAACCGGuGAGUACaCCGGaaucGCc.gGGauGaCcGGgu.CCUUUC..UUGGAuc.A.acCCgCuC.AAUg.CCcgGA.gauuUGGGCGUG.CCCC.CGcgaG.accgcuaGCCcA.GuAGc.GU.UGGGUCgCG.aAgGGCCuuGuGGuAC.ugCCUGAUAGGGcGcuu....GugC.cccgggaGg.........................................
//
# STOCKHOLM 1.0

#=GF AC   RF00062
#=GF ID   HgcC
#=GF DE   HgcC family RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   51.00
#=GF NC   45.60
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   12032319
#=GF RT   Noncoding RNA genes identified in AT-rich hyperthermophiles.
#=GF RA   Klein RJ, Misulovin Z, Eddy SR
#=GF RL   Proc Natl Acad Sci U S A 2002;99:7542-7547.
#=GF CC   The HgcC ncRNA gene was identified computationally in AT-rich
#=GF CC   hyperthermophiles. The genes were named hgcA through hgcG ("high GC").
#=GF CC   HgcC is of unknown function. Two other homologues were detected called
#=GF CC   HhcA and HhcB after "homologue of hgcC" [1]. This family contains a large
#=GF CC   number of putative archaeal matches to the 3' end of the known ncRNAs.
#=GF CC   Many of these partly overlap coding regions.
#=GF WK   HgcC_family_RNA
#=GF SQ   5


AF468965.1/1-126         GAGGGUAGCUCUGACUCUGCCCG-----AUGAC---ACCAACCUGCCCUGUGACCUAUCGGCGACGAUAAGUAGCAGGGUGUU---------------------------------------CCGUGUUGGAACCUCCACCCUUUAGGU-GGAGAGAAGAUCAG---UUAAAAUUCC
AF447577.1/1-129         GAGGGCUG-UCUGACCCAGCCCG-----AUGAG---CUGAACCUGCCCUGUGACCUACCGGCGACGGUAGGGAGAAGGGUGUU---------------------------------------CCCCGUGGGAACCUCCGAGCUUUAGCUCGGAGAGGAGGUCAGCUUUUAACAUUUC
AF468966.1/1-127         GAGGGUGCCUCUGACCGUGCCCG-----AUGAC---ACCAACCUGCCCAAUGAAGCACGGGCGACCGUGGGGA---GGGUGUU---------------------------------------CCCUGUGGGAACCCUCGCCAUUCACGGCGAGGAGGAGGUCAGCUCCUCCACGUUC
L77117.1/951852-951980   GAGGGCUG-UCUGACCCAGCCCG-----AUGAG---CUGAACCUGCCCUGUGACCUACCGGCGACGGUAGGGAGAAGGGUGUU---------------------------------------CCCCGUGGGAACCUCCGAGCUUUAGCUCGGAGAGGAGGUCAGCUUUUAACAUUUC
AE009950.1/754818-754978 GUGGUCUUUAC-GCCCAAGGGAGGGGUAAUGGGCCUGAGACCGGGCCC-UCGGGC------CGAAC---CGAAACC-GGUG--ACGGGAGUAGGUGGAUGAGAGCCCGCAAACCUCUCCCCGCCC-GUUGAAAGCCUCGCCCUUCAAGGCGGGGAGGAGGUCAGGAGG-AGAUAACC
#=GC SS_cons             ::::::::::((((((,,,,,,,.....,,,,,...,,,,,,,,<<<<<------<<<<<____>>>>>------>>>>>,,,.......................................<<<___>>>,,,<<<<<<<<____>>>>>>>>,,,,)))))):::::::::::::
#=GC RF                  GaGGgcuuuuCuGaCCaaGcccG.....AUGag...aagAaCcugCCCuuuGaaccaccGGCGACgguggGaAacaGGGuGUU.......................................cCcuGUgGgAAcCccCGcccUUuAgggCGggGAGGAGGuCaGcuuuUAaauuuuC
//
# STOCKHOLM 1.0

#=GF AC   RF00063
#=GF ID   SscA
#=GF DE   SscA RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD
#=GF GA   60.00
#=GF TC   64.80
#=GF NC   37.10
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF RN   [1]
#=GF RM   12032319
#=GF RT   Noncoding RNA genes identified in AT-rich hyperthermophiles.
#=GF RA   Klein RJ, Misulovin Z, Eddy SR
#=GF RL   Proc Natl Acad Sci U S A 2002;99:7542-7547.
#=GF CC   The SscA ncRNA gene was identified computationally in AT-rich
#=GF CC   hyperthermophiles using QRNA [1]. SscA stands for Secondary Structure
#=GF CC   Conserved A. SscA is 97 nucleotides in length and is of unknown function.
#=GF CC   This RNA is currently restricted to pyrococcal species.
#=GF WK   SscA_RNA
#=GF SQ   5


AF468964.1/1-97            GAGCUCAAUGAAGCCCCCUCAACUAAAGGCGGGUUUCCCGCCUGAGGGGGCUGAUGUGCGAAAGCUUUAAAAAGUAAGUUCAAAAGUAGGGUUAGGC
AJ248285.1/36503-36598     CGAGCAAAUGAGGCUUCCUCCUCUGU-GGCGGGUUUCCCGCCGGAGGGAGCCGAUGUCCGAAAAUUUUAAAAGGCUAUCCCAAAAGUAGGGUUAGGC
X59857.1/513-608           GAGCUCAAUGAAGCCCCCUCAACUAAAGGCGGGUUUCCCGCCUGAGGGGGCU-AUGUGCGAAAGCUUUAAAAAGUAAGUUCAAAAGUAGGGUUAGGC
BA000001.2/1327888-1327793 AGGGAAAAUGAGGCUUCCUUCAGUUU-GGCGGGUUUCCCGCCGAAGGAAGCCGAGAUCCGAAAGUUUUAAAAGAUCUCCUCAAAAGUAGGGUUAGGC
AP006878.1/263953-263858   AGAACUCAUGAGGUCCCCCCGAAAAC-GGCGGGUUUCCCGCCCGAGGGGGCCGAGGUUCGAAAGAUUUAAAAAGCCAUCCUAGUCAACGAGACUAGA
#=GC SS_cons               :::<-------<<<<<<<<<<-----.<<<<<<___>>>>>>>>>>>>>>>>----->:::::::::::::::::::::::::::::::::::::::
#=GC RF                    agaguaaAUGAgGcccCCucgAauau.GGCGGGUUUCCCGCCcgaGGgggCcGAuGUcCGAAAGuUUUAAAAaGuaAucucAAaaguaGgGuUagGc
//
# STOCKHOLM 1.0

#=GF AC   RF00064
#=GF ID   HgcG
#=GF DE   HgcG RNA (Pab40)
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD
#=GF GA   77.00
#=GF TC   77.90
#=GF NC   76.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17.62 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   12032319
#=GF RT   Noncoding RNA genes identified in AT-rich hyperthermophiles.
#=GF RA   Klein RJ, Misulovin Z, Eddy SR
#=GF RL   Proc Natl Acad Sci U S A 2002;99:7542-7547.
#=GF RN   [2]
#=GF RM   18304947
#=GF RT   Combined in silico and experimental identification of the Pyrococcus
#=GF RT   abyssi H/ACA sRNAs and their target sites in ribosomal RNAs.
#=GF RA   Muller S, Leclerc F, Behm-Ansmant I, Fourmann JB, Charpentier B, Branlant
#=GF RA   C
#=GF RL   Nucleic Acids Res. 2008;36:2459-2475.
#=GF CC   The HgcG ncRNA gene was identified computationally in AT-rich
#=GF CC   hyperthermophiles. The genes were named hgcA through hgcG ("high GC") [1].
#=GF CC   HgcG is of unknown function. hgcG is significantly similar to a region of
#=GF CC   the Archaeoglobus fulgidus genome. In a recent experimental screen for
#=GF CC   ncRNAs in A. fulgidus, this locus was identified as the second-most
#=GF CC   abundant transcript (Afu-4) (T.-H. Tang, J.-P. Bachellerie, H. Huber, M.
#=GF CC   Drungowski, T. Elge, J. Brosius, and A. Hüttenhofer, personal
#=GF CC   communication in [1]).It was also identified as Pab40 H/ACA snoRNA with
#=GF CC   rRNA targets.[2]
#=GF WK   HgcG_RNA
#=GF SQ   5



CP001857.1/451659-451932   -----AUUACAAAAGGCUGAUCGAGAAAAUUUAAUAGUUAGAGAGACAUACUAUAUA--UUGCCCCAGG-CGGGAUGAAGGGGCUGAGUGGGCGCAUGCCCUCAAUGAAGCCACUUGCGAACUUGGGGCGACAGGCGGUGUC---GAGACGUCCCCUUCGGAGAGAGUAUACGCUUUC--GAUGA-----UGUAGGGGCAACCCCGACACCGCA-----CAACCCCGA-UGGGUCAGCGGUCUUGAGCG-GGCAUUUGCCUUCGAUGAGAGACCGUGUUAGCGUUCGGGGAACAUCUCA
AF468963.1/1-277           CUCAUAAUCUCUUUUUUUGAAGUCAACAUUAUAAACGUCUUA---AUGUAAAAUAAUUAACGCCCCCGCAAGCGAGGGCUUGGCUGAU------------CUUAAUGAGGCCAGGUGCGACGCGGGGGCAACA-GCCCGGCCUCAGCGAGGUCCCCUCGGGAGGUGCCUUCCGCGUCACGGAGUGCCGUGACCGGGGGUAACCCUGGCCGGGCA-----CAGGCCCACCUGGGUUAGCCCGCCUGAGAAUGCAUACAUGCUACGAUGAGGGCGGGUGUUA-CGGGUGGGCCACAUAUAA
AJ248284.1/75232-75504     UUCAUUUUUGCUUCUUCCAUAGUCACUAUUAUAAAACUUCGG--GUCUUAUUCUCAU--AUGCCCCCGCAAGCGAGGGCCUGGUCGA--------------UUAGUGAGACCAGGUGCGACGCGGGGGCUACA-GCCCGGCCUCAGCGAGGUCCCCUCGGUAGGUGCCUUCCGCGUCACGGAGCGCCGUGACCGGGGGUAACCCUGGCCGGGCA-----CAGGCCCGUCUGGGUUAGCCCGCCUGAUCAUGCCGUUG-GCUUAGAUGAAGGCGGGUGUUA-CGGGCGGGCUACAGAUUC
AP006878.1/462004-462277   CUGAUGGAAGCGAUUGCAGACCAUCAAUUUAUAAACCUGUCA---GUGGAGAAUAAA--AUGCCCCUGC--GCGAGGACCCCGGGGA---------------GAAUGAACCGGGGGGCGAUGCGGGGGCAACA-GCCCGGCCUCAGCGAGGUCCCCGCGGGAGG-GCCUUCCGCGUCCCGGAGCACGAUGACCGCGGGAAACCCAGGCCGGGCACAGUUCUGGCCCGCCAGGGUUAGCCCGCCCAAGGGUGGCGUACGCCUUCGAUGAGGGCGGGAGUUA-CCGGCGGGCCAUAUUCUC
BA000001.2/1597364-1597639 UUCAAGUGAUAAUUACCUGAGGUCAACAUUAUAAAUGCUUAA--GAUGUAAUUUUAC-AAUGCCCCCGCAAGCGAGGGCUUGGCCGAG------------CUUAAUGAGGCCAGGUGCGACGCGGGGGCGACA-GCCCGGCCUUAGCGAGGUCCCCUCGGGAGGCGCCUUCCGCGUCACGGAGUGCCGUGACCGGGGGUAACCCUGGCCGGGCA-----CAGGCCCGUCUGGGUUAGCCCGCCCAAUUUUGCCGAGG-GCUUAGAUGAGGGCGGGUGUUA-CGGGCGGGCCACAGAUAA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::..:::::::::::::..::<<<<<<<<---------<<<<<<<___............________>>>>>>>------>>>>>>>>,,,,.((((((((,,,,<<<<<___>>>>>,,,,,,,,,,,<<--<<<<<<<____>>>>>>>->>,,,,,,,,,,))))))))-.....--<<<<<<<<<<------<<<<<<<------<<<___>->>-------->>>>>>>-----.>>>>>>>>>>::::::::
#=GC RF                    uUcAuauuauaauuuuCuGAagucaAaAuUaUAAaagUuugA..GauguAauaUaaa..aUGCCCCcGcAaGcGAgGacccgGccGAg............CUuAAUGAggCcggguGCGAcgCgGGGGCaACA.GCccgGcCUcAGcGaGGUCCCCuCgGGAGgugccuUcCGCguCacgGAguaCcguGaccGgGGGuAACCCuGgCcggGCA.....CAggCCCGcCcGGGUUAGCccgCccgAguaUGgcguuggcCUUcGAUGAggGcggGUGUUA.CgGgCGGGccAcAuaUua
//
# STOCKHOLM 1.0

#=GF AC   RF00065
#=GF ID   snoR9
#=GF DE   Small nucleolar RNA snoR9
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Bateman A
#=GF SS   Published; PMID:12032319
#=GF GA   90.00
#=GF TC   98.20
#=GF NC   75.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032319
#=GF RT   Noncoding RNA genes identified in AT-rich hyperthermophiles.
#=GF RA   Klein RJ, Misulovin Z, Eddy SR
#=GF RL   Proc Natl Acad Sci U S A 2002;99:7542-7547.
#=GF CC   snoRNA R9 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. R9 was identified in a computational
#=GF CC   screen in AT-rich hyperthermophiles [1]. R9 was found to overlap with the
#=GF CC   smaller snoRNA R19 which is currently a member of Pyrococcus C/D box
#=GF CC   snoRNA family Rfam:RF00095.
#=GF WK   Small_nucleolar_RNA_snoR9
#=GF SQ   5


AF468960.1/1-128         GGGCCCGGUU-CCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGACCGGGCCCACA--AUGGGAUGAUGACCUUUUGCUUUACUGAACACAUGAUGACCACGCCCUUCGCUGAC-CUAAAUAUUUGAC
AJ248283.1/230575-230449 GGGCCCGGCU-CCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGGCCGGGCCUACA--G--UUAUGAUGAACUUUUGCUUUGCUGAUGUGGUGAUGAGCACGCCCUUCGCUGAUACUCUCUCGUCCAU
BA000001.2/215834-215709 CGGCCCGGUU-CCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGACCGGGCCGACA--GG-GGAUGAAGAGCUUUUGCUUUGCUGAGCAGAUGAUGACCACGCCCUUCGCUGAC-CU-GCUAUUUGAC
AP006878.1/47908-47779   GGGCCUGGCGUCCCGCCCUCCCCGGGGAAACGUGAACCGGGGCUUCCUGCCAGGCCUACACCGGGGGAUGAAGAGCUUUUGCUUUGCUGAC--UGUGAUGAGCACGCCCUUCACUGACCCCGUAUCAGCUCU
AE009950.1/163991-163864 GGGCCCGGUU-CCCGCCCUCUCCGGGGAAUCGUGAACCGGGGGUUCCGACCGGGCCCACA--AUGGGAUGAUGACCUUUUGCUUUACUGAACACAUGAUGACCACGCCCUUCGCUGAC-CUAAAUAUUUGAC
#=GC SS_cons             <<<<<<<<<<.---<<<<---<<<<___________>>>>>>>>--->>>>>>>>>>:::..::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::
#=GC RF                  gGGCCcGGcc.CCCgCCCUCuCCGGGGAAuCGUGAACCGGGGGuUCCggCCgGGCCcACA..guGggAUGAuGAaCUUUUGCUUUgCUGAacauaUGAUGAcCACGCCCUUCgCUGAc.CuauaUauuugau
//
# STOCKHOLM 1.0

#=GF AC   RF00066
#=GF ID   U7
#=GF DE   U7 small nuclear RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Marz M; 0000-0003-4783-8823
#=GF SE   Griffiths-Jones SR; Published; PMID:18267300
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR
#=GF GA   34.00
#=GF TC   34.00
#=GF NC   33.90
#=GF TP   Gene; snRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.34 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000274; snRNA;
#=GF RN   [1]
#=GF RM   7937126
#=GF RT   3' end processing of mouse histone pre-mRNA: evidence for additional
#=GF RT   base-pairing between U7 snRNA and pre-mRNA.
#=GF RA   Spycher C, Streit A, Stefanovic B, Albrecht D, Koning TH, Schumperli D
#=GF RL   Nucleic Acids Res 1994;22:4023-4030.
#=GF RN   [2]
#=GF RM   2825355
#=GF RT   Identification of the human U7 snRNP as one of several factors involved in
#=GF RT   the 3' end maturation of histone premessenger RNA's.
#=GF RA   Mowry KL, Steitz JA
#=GF RL   Science 1987;238:1682-1687.
#=GF RN   [3]
#=GF RM   18267300
#=GF RT   U7 snRNAs: a computational survey.
#=GF RA   Marz M, Mosig A, Stadler BM, Stadler PF
#=GF RL   Genomics Proteomics Bioinformatics. 2007;5:187-195.
#=GF CC   Animal histone pre-mRNAs are spliced by a different mechanism than nuclear
#=GF CC   pre-mRNAs and self-splicing introns. This processing involves the U7
#=GF CC   snRNP, which contains only one RNA species: U7. The 5' end of U7 RNA is
#=GF CC   thought to base-pair to a conserved spacer element downstream of the
#=GF CC   cleavage site in histone pre-mRNA. This family contains a number of
#=GF CC   annotated U7 pseudogenes.
#=GF WK   U7_small_nuclear_RNA
#=GF SQ   49



M17910.1/2-64                -NNGUG-UUACAGCUCUUUUAGAAUUUGUCUAGUA-GGCUU-UCU--GGCUUUUC-ACC--GGA-AA--GCCCCU
AAFC03061782.1/74685-74624   -CAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-GGCUU-UCC--GGU-UUGC-ACC--GGA-AA--GCCCCU
AAQQ01624215.1/522-461       -AAGUG-UUGCAGCUCUUUUAGAAUUUGUCUAGCA-GGCUU-UCU--GGC-AGUU-GCC--GGA-AA--GCCCCU
AAIY01793969.1/208-147       -UAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-CGUUU-UCU--GGU-UUCU-ACC--AGA-AA--GCCCCC
AANU01190095.1/9982-9921     -CAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-GGCUU-UCC--GGU-AUUU-GCU--GGA-AA--GCCCCU
AAHX01112961.1/18874-18935   -AAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGUA-GGUUU-UCU--GAC-UUCG-GUC--GGA-AA--ACCCCU
AANG01081017.1/1107-1168     -UAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-GGUUU-UCC--GGU-UUUU-ACC--GGA-AG--GCCCCC
AAFR03067202.1/16722-16783   -CAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGUA-GGUUU-UCC--GGU-GUUU-GCC--GGG-AA--GCCCUC
BX001019.7/126828-126773     -UGAAAAUA---GCUCUUUUAGUAUUUGUCCAGUA-GGUUU-CCU-----AUAAAA-----AGG-AA--GCCCAU
BX935168.2/176-235           -CAGUGAUUUCAGCUCUUUUAGUAUUUGUCCAGCA-GGUUU-CCC--GC--CCC---GC--GGG-AA--GCCCCA
AAIY01149668.1/205-144       -UAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-GGUUU-UCU--GGU-UUUU-ACC--AGA-AA--ACCCCC
BX001019.7/132397-132343     -GGAAAAUA---UCUCUUUUACUAUUUGUCCAGUA-GGUUU-CCU-----UUAAA------AGG-AA--GCCCAU
U47924.1/155825-155887       -CAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGUA-GGCUU-UCU--GGCUUUUU-ACC--GGA-AA--GCCCCU
AANH01001136.1/46489-46433   --GAAUCUAUAUGCUCUUUAGAUAUUUUUCUAGUA-GGUUU-CUC-----GUAAA------GAG-AA--GCCCUC
Z54313.1/9464-9520           -AAGUG-UUACAGCUCUUUUACUAUUUGUCUAGCA-GGUUC-UUA--C---UCU----G--UAG-GA--GCCACA
X54748.1/482-543             -AAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-GGUUU-UCU--GAC-UUCG-GUC--GGA-AA--ACCCCU
AANN01093499.1/887-826       -CAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-GGUCU-UCC--GGU-UCCU-ACC--GGA-AG--GCCCCC
X64404.1/2361-2417           -AAGUG-UUACAGCUCUUUUACUAUUUGUCUAGCC-GGUUU-UUA--C---UCU----G--UUG-GA--GCCACA
CR388102.8/23123-23068       -UGGAAAAUU--GCUCUUUUAGUAUUUGUCUAGCA-GGCUU-CCU-----UUAAA------AGG-AA--GCCCAC
BAAF04048895.1/511-566       -GGAAACUUU--GCUCUGAAGAUAUUUGUCUAGCA-GGUUU-CUC-----AUAAA------GAG-AA--GCCCCU
AAIZ01011560.1/1330-1264     -AAAU-UUUUAAUCUCUUUGA-AAUUUAUCUUGGU-GGGACCCUU--UUGUCAAGGCAAUUGAGUGU--UCCCGA
AY310908.1/332-396           -AAAU-UUUUAUUCUCUUUGA-AAUUUGUCUUGGU-GGGACCCUU---UGUCUAGGCA-UUGAGUGU--UCCCGU
AAPU01011493.1/10145-10080   -AAAUAUUUUUAUCUCUUUGA-AAUUUGUCCUGGU-GGGACCCUU---UGCCUUGGCA-CUGAGUGU--UCCGAA
AAEU02000134.1/355158-355222 AAAA--UUUUAUUCUCUUUGA-AAUUUGUCUUGUU-GGGACCCUU---UGUCUAGGCA-UUGAGUGU--UCCCGU
AANI01017320.1/19268-19203   -AAAUAUUUUUAUCUCUUUGA-AAUUUGUCCUGGU-GGGACCCUU---UGCUUAGGCA-UUGAGUGU--UCCGAA
AAQB01007746.1/175188-175252 -AAAU-UUUUAAUCUCUUUGA-AAUUUGUCCUGUU-GGGACCCUU---UGUCUAGGCA-UUGAGUGU--UCCCCA
AAPQ01006552.1/12257-12321   -AAAU-UUUUAUUCUCUUUGA-AAUUUGUCUUGGU-GGGACCCUU---UGUCUAGGCA-UUGAGAGU--UCCCGG
AAPP01019312.1/138204-138140 AAAA--UUUAAAUCUCUUUGA-AAUUUGUCUUGGU-GGGACCCUU---UGCUUAGGCA-UUGAGAGU--UCCCGA
ABDC01308671.1/824-763       -AAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-GGUCU-UCC--GGU-CCUU-ACC--GGA-AG--GCCCAA
AADA01187858.1/23944-23883   -CAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-GGCUU-UCC--AGU-UUUU-GCU--GGA-AA--GCCCAA
AAPY01117698.1/5611-5672     -GAGUG-UUACGUCUCUUUUAGAAUUUGUCUAGCA-GGUUU-UCC--AGU-UUUU-ACU--GGA-AA--GCCCCC
AALT01385751.1/743-682       -CAGUG-UUAUAGCUCUUUUAGAAUUUGUCUAGCA-GGUUU-UCC--GGU-UGCU-ACC--AGA-AA--GCCAAG
AAYZ01241424.1/853-915       -CAGUG-UUACAGCUCUUUUCGAAUUUGUCAAGCA-GGCUU-UCC--GGU-UUGU-ACU--GGA-AA-GGCCCAC
AAPN01194339.1/1321-1260     -GCCAU-UUCAAGCUCUUGUAGAAUUUGUCUAGUA-GGUUU-UCC--AGU-AUUG-GCU--GGA-AA--GCCCUU
AAGL01003173.1/340-403       -UAGUG-UUACAGCUUUUUUAGAAUUUGUCUAGCA-GGCUU-UCU--GGU-UUUC-ACC--AUA-AAAUGCCCCA
AC199101.3/50895-50842       -CAGUG-UUACAGUUCUUA--------GUCUAGCA-GGCUU-UCU--GGU-UUUU-GCC--AGA-AA--GCCCCA
U28353.1/287-347             -AGCUA-AUACAGCUUUUAGA-AUUUUGUCUAGCA-GGUUU-UCU--GAA-UUUG-GUU--GGA-AA--ACCUAU
AAWR02029200.1/6316-6377     -CAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGUA-GGUCU-UCC--GGU-UUUU-UCC--GGA-AG--GCCCCC
AAKN02052151.1/67960-68021   -AAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGUA-GGUUU-UCU--GGU-GUUU-GCC--GGA-AA--ACCCAU
AAGV020207087.1/1970-1909    -CAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGUA-GGUCU-UCU--GGC-GCUU-GCC--GGA-AG--GCCCUC
M13311.1/229-296             -GAGAGACCAUUUAUCUUUCA-AGUUUCUCUAGAAGGGUCU-CGCGUCC-GAAGUC-GGUGGCG-AG-UGCCCAA
AAQR03168143.1/79369-79430   -GAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-GGUUU-UCC--GGU-CUCU-ACC--GGA-AA--ACCCCC
AAGJ04113203.1/935-873       ---GAG---AGUUAUCUUUCA-AGUUUCUCUAGCAGGGUCU-CGC-AUCCGAAGUCGGA-CGCG-AG-UGCCCAA
AAGU03036159.1/12300-12360   -UAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGUA-GGUCU-UCU--AG-UUUUU--CU--GGA-AG--ACCCUU
AACN010370619.1/1124-1185    -UAGUG-UUACAGCUCUUUUAGAAUUUGUCUAGCA-GGUUU-UCC--GGU-CCUC-ACC--GGA-AA--GCCCCC
AAWZ02028238.1/54909-54970   -CAGUGAUUUCAGCUCUUUUAGUAUUUGUCCAGCA-GGCUU-UCU--GC--AGUUA-GC--GGA-GA--GCCACC
CAAB02008541.1/44851-44905   --GAAUGAUU--GCUCUUUAGAUAUUUCUCUAGUA-GGCUU-UUC-----AUACA------GAG-AA--GCCCCC
AAGW02051582.1/13062-13123   -CAGUG-UUACAGCUCUUUUCGAAUUUGUCUAGCA-GGCUU-UCC--GGU-UUUC-ACC--GGA-AA--GCCCCC
AAPE02007016.1/5346-5408     -CAGUGCUUACAGCUCUUUUUGAAUUUGUCCAGCA-GGUCU-UCC--GGC-UCGU-CCC--GGA-AG--GCCCUC
#=GC SS_cons                 .:::::.::::::::::::::::::::::::::::.<<<<<.<<<..<<<_____.>>>..>>>.>>..>>>:::
#=GC RF                      .aAGUG.UUAcAGCUCUUUuAGAAUUUGUCUAGcA.GGuuU.ccc..gguuuuuu.acc..ggg.Aa..gCCCaa
//
# STOCKHOLM 1.0

#=GF AC   RF00067
#=GF ID   SNORD15
#=GF PI   U15
#=GF DE   Small nucleolar RNA SNORD15
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR; Plant snoRNA database, PMID:12520043
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR, Daub J
#=GF GA   75.00
#=GF TC   75.00
#=GF NC   74.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.42 -Z 549862.597050 CM SEQDB
#=GF CL   CL00045
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300760;
#=GF DR   snoopy; Homo_sapiens300742;
#=GF RN   [1]
#=GF RM   8319909
#=GF RT   A small nucleolar RNA is processed from an intron of the human gene
#=GF RT   encoding ribosomal protein S3.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Genes Dev 1993;7:1176-1190.
#=GF RN   [2]
#=GF RM   7984408
#=GF RT   Different forms of U15 snoRNA are encoded in the introns of the ribosomal
#=GF RT   protein S1 gene of Xenopus laevis.
#=GF RA   Pellizzoni L, Crosio C, Campioni N, Loreni F, Pierandrei-Amaldi P
#=GF RL   Nucleic Acids Res 1994;22:4607-4613.
#=GF RN   [3]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [4]
#=GF RM   12520043
#=GF RT   Plant snoRNA database.
#=GF RA   Brown JW, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Huttenhofer A,
#=GF RA   Kastenmayer JP, Green PJ, Shaw P, Marshall DF
#=GF RL   Nucleic Acids Res 2003;31:432-435.
#=GF CC   U15 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U15 is encoded within the introns of ribosomal
#=GF CC   protein S1 in Xenopus and S3 in human and Fugu. snoR75 from Arabidopsis
#=GF CC   [3] and homologues in rice and other plants are alternatively known as
#=GF CC   U15, and, despite a significantly shorter sequence length, appear to be
#=GF CC   related [4].
#=GF WK   Small_nucleolar_RNA_SNORD15
#=GF SQ   11



L16016.1/866-1013    CUUCGAUGAAGAGAUGAUG-ACGAGUCUGACUUGGGGA--UGUUCUCUUUGCCCAGGUGGCCUACUCUGUGCUGCGUUCUG--UGGCACAG----UUUAA-AGAGCCCUGG-UUGAAGUAAUUU-CCUAA--AGAUGACUUAGAGGCAUUUGUCUGAGA-AGG
AY043296.2/720-867   CUUCGAUGAAGAGGUGAUG-ACGAGUCUGAGUAGGAAG--UGUUGUCUUUGUCCAAGA-UGCCUCACUAUGCUGCGUUCUG--UGGCACAG----CUGAA-AGCACUGUGGUCAAAAGAAACUU-CCUAA--AGAUGACCAAGAGGCAUUUGUCUGAGA-AGG
Z34530.1/4257-4400   CUUCAGUGAUGAUUUGAUG-ACGAGUCUGACUUCCU------CCUUUCAUGCCCCAUU-CAGCUAAAGGAGCUGCGUUCUGCAUGUUGCUUU-UGCUGUU-GGGUCCUCAU--AACAAAGUUGU-AU-----GAAGACUCUUGAGGCAUUUGUCUGAGA-AGA
Z34530.1/6444-6594   CUUCAGUGAUGAGACGAUCGACGAGUCAGAAGGACCAUCAAUGUAGUGUGUCUCGUGA-GUGUCACGUUCUCUGCGAGCUG--UGUUUCCGG--CCGCCAUGCAUCAGCUU-----UGCCCCUU-CUUACCUGAUCGAUAUGGAGGCAUUCGC-UGAGACAGG
X97794.1/3225-3370   CUUCAGUGAUGAUACGAUG-ACGAGUCGGAACAAAGC----CGUCUUGUUCUGGGGGUUCGUGGUUCAGCUCUACGUUCUG--UGGUUCUG----UUCC--AGUUCCUCAG--UUCAGGGUCUU-UUUCUCUUGAAGACAUAGAGGCAUUUGUCUGAGA-AGG
X97794.1/2144-2293   CUU-GGUGAAGAUAAGAUG-ACGAGUCGGAAUAGGACA--GAUCCUGCUUCUGCCGGUCACUGGUUCAGGUCCACGUUCUG--UGGGUUUC----UACC--AGUUCUUCAGAGUGGGUCGUCCCUCUUCAUUUGAAGACACUGAGGCAUUUGUCUGAGA-AGG
Z34530.1/8157-8303   CUUCAGUGAUGAGACGAUG-ACGAGUCAGAAAGGAC-------CAGCAAUGUAGUGUG-UCCUGCUCAGUGUCACGUUCUG--UGCCGCUCUGUUUGGU--UGCACUGCAU-CAGCUUUGUCCU-UCUUACUGAUUGAUAUAGAGGCAUUUGUCUGAGA-AGG
L15557.1/1-146       CUUCAGUGAUGACACGAUG-ACGAGUCAGAAAGGUC-------ACGUCCUGCUCUUGG-UCCUUGUCAGUGCCAUGUUCUG--UGGUGCUGU--GCACG--AGUUCCUUUGGCAGAAGUGUCCU-AUUUAUUGAUCGAUUUAGAGGCAUUUGUCUGAGA-AGG
AY043296.2/3945-4089 CUUCAGUGAUGACACGAUG-ACGAGUCAGAAUGGCC-------ACGUCUUGCUCUUGG-UCCCUGUCAGUGCCAUGUUCUG--UGGUGCUG----UACAU-GGUUCCCUUGGCAAAAGUGUCCU-GCGCACUGAUUGAUUUAGAGGCAUUUGUCUGAGA-AGG
Z34530.1/10197-10341 CUUCUGUGAUGAUACGAUG-ACGAGUCUGAGUGGGU------AAAUCGUUUUCCAGUGGUCUCUGUCUGUAUCACGUUCUG--UGCUGUAG------CUG-AGCCCCACUGAGUCAAGAUUGCC-CUUGGCUUGAUGUGCUUGAGGCAUUUGUCUGAGA-AGG
X80988.1/3-147       CUUCUGUGAUGAUACGAUG-ACGAGUCUGAGUGGGU------AAAUCCUUUUCCAGUGGUCUCUGUCUCCAUCACGUUCUG--UGCUGUAG------CUG-AAGCCCACUGAGUCAAGAUUGCC-CUUGGCUUGAUGUCCUUGAGGCAUUUGUCUGAGA-AGG
#=GC SS_cons         <<<<_______________.________________......________________.______________________..________...._____.__________.____________.________________________________>>.>>:
#=GC RF              CUUCaGUGAUGAuAcGAUG.ACGAGUCuGAaugggu......uuauucUUguuCaggu.ucuuuaucugugCuaCGUUCUG..UGgugCug....uucua.aGuuCcuCug.caaaaGagUcuU.cUUaaCUgaauGAuaUaGAGGCAUUUGUCUGAGA.AGG
//
# STOCKHOLM 1.0

#=GF AC   RF00068
#=GF ID   SNORD21
#=GF PI   U21
#=GF DE   Small nucleolar RNA SNORD21
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR, Daub J
#=GF GA   63.00
#=GF TC   64.00
#=GF NC   62.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300771;
#=GF DR   snoopy; Danio_rerio300117;
#=GF RN   [1]
#=GF RM   7937132
#=GF RT   U21, a novel small nucleolar RNA with a 13 nt. complementarity to 28S
#=GF RT   rRNA, is encoded in an intron of ribosomal protein L5 gene in chicken and
#=GF RT   mammals.
#=GF RA   Qu LH, Nicoloso M, Michot B, Azum MC, Caizergues-Ferrer M, Renalier MH,
#=GF RA   Bachellerie JP
#=GF RL   Nucleic Acids Res 1994;22:4073-4081.
#=GF RN   [2]
#=GF RM   8603691
#=GF RT   SnoRNA U21 is also intron-encoded in Drosophila melanogaster but in a
#=GF RT   different host-gene as compared to warm-blooded vertebrates.
#=GF RA   Renalier MH, Nicoloso M, Qu LH, Bachellerie JP
#=GF RL   FEBS Lett 1996;379:212-216.
#=GF CC   U21 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U21 is encoded within an intron of the gene for
#=GF CC   ribosomal protein L5 in mammals [1], but within introns of the ADP
#=GF CC   ribosylation factor gene in Drosophila [2]. U21 snoRNA has a 13 nt region
#=GF CC   of complementarity with an invariant region of eukaryotic 28S ribosomal
#=GF CC   RNA.
#=GF WK   Small_nucleolar_RNA_SNORD21
#=GF SQ   5


Z35312.1/944-1038  GCUGAAUGAUGAUAUCCCACUAACUGAGCAGUCAGUAGUUGGUCCUUUGGUUGCAUAUGAUGCGAU-AAUUGUUUCAAGACGGGACUGA-UGGCAGC
Z35311.1/728-821   GCC-AAUGAUGACACCACACUAACUGAGCAGUUAGUAGUUGGUCCUUUGAUUGCAUGUGAUGUAAU-CAUUGUUUCAAGACGGGACUGA-AGGCGGC
D10737.1/4698-4793 GCUAUGUGAUGAUACCCCAAUGUCUGACCACUCCGUAGUAGGUCCAUGGUGUGUAAAUGAUGGACUGCGUAGUUUCAAGACGGGACUGA-UGGCAGC
Z35416.1/1-94      -CUAUGUGAUGAUACCCCAAUGUCUGACCACUCCGUAGUAGGUCCAUGGUGUGUAAAUGAUGGACUGCGUAGUUUCAAGACGGGACUGA-UGGCAG-
S62079.1/541-624   UCUAUAUGAUGUUAACAGCUUGU------AAUGAUUA-----UGCAUUGUGAUUAUUCAAGUUUAU--UUUGUUUCAAGACGGGACUGACUAUAUUA
#=GC SS_cons       <<<<______________________________________________________________.______________________.>>>>:::
#=GC RF            gccauaUGAUGAUAcCacAaUguCUGAgCAaUcagUAGUuGGUcCaUuGugUguAuaUGAuguaaU.caUuGUUUCAAGACGGGACUGA.uggcagc
//
# STOCKHOLM 1.0

#=GF AC   RF00069
#=GF ID   SNORD24
#=GF PI   U24
#=GF DE   Small nucleolar RNA SNORD24
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR, Daub J
#=GF GA   41.00
#=GF TC   41.20
#=GF NC   40.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300797;
#=GF DR   snoopy; Oryzias_latipes300056;
#=GF RN   [1]
#=GF RM   7651828
#=GF RT   U24, a novel intron-encoded small nucleolar RNA with two 12 nt long,
#=GF RT   phylogenetically conserved complementarities to 28S rRNA.
#=GF RA   Qu LH, Henry Y, Nicoloso M, Michot B, Azum MC, Renalier MH,
#=GF RA   Caizergues-Ferrer M, Bachellerie JP
#=GF RL   Nucleic Acids Res 1995;23:2669-2676.
#=GF RN   [2]
#=GF RM   8764399
#=GF RT   Intron-encoded, antisense small nucleolar RNAs: the characterization of
#=GF RT   nine novel species points to their direct role as guides for the
#=GF RT   2'-O-ribose methylation of rRNAs.
#=GF RA   Nicoloso M, Qu LH, Michot B, Bachellerie JP
#=GF RL   J Mol Biol 1996;260:178-195.
#=GF RN   [3]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF RN   [4]
#=GF RM   9703018
#=GF RT   Evolution of U24 and U36 snoRNAs encoded within introns of vertebrate
#=GF RT   rpL7a gene homologs: unique features of mammalian U36 variants.
#=GF RA   Gilley J, Fried M
#=GF RL   DNA Cell Biol 1998;17:591-602.
#=GF RN   [5]
#=GF RM   11606788
#=GF RT   Position within the host intron is critical for efficient processing of
#=GF RT   box C/D snoRNAs in mammalian cells.
#=GF RA   Hirose T, Steitz JA
#=GF RL   Proc Natl Acad Sci U S A 2001;98:12914-12919.
#=GF CC   U24 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs [1]. C/D box snoRNAs have been shown to act as
#=GF CC   methylation guides for a number of RNA targets [2,3]. U24 is encoded
#=GF CC   within an intron of the gene for ribosomal protein L7a in mammals, chicken
#=GF CC   and Fugu [4]. The U76 snoRNA is found in an intron of the uRNA host gene
#=GF CC   (UHG) growth arrest specific 5 (GAS5) transcript gene [5]. snoRNAs Z20 and
#=GF CC   U76 snoRNAs show clear similarity to U24.
#=GF WK   Small_nucleolar_RNA_SNORD24
#=GF SQ   14


AJ224036.1/1-85      GGCCG--GUG-AUGUAAUCAAAAUAUUUGCUACUCUUGA-UGAAGAAUUUCUUCA-----GUUGAUG-AUAUUU--ACCACCAAGAUC---UCUGA-GGCC
AJ240063.1/2-93      GGCCA--GUG-AUGUAAUAAAAAUAUUUGCUACUCUUGA-UGAAGAACUUUGUUCUUUCAGUUGAUG-AUUGGUUUACCACCAAGAUC---UCUGA-GGCC
AJ003046.1/33-102    UGCAU--AUG-AUGUAA--CGA-UAUU-GCU-AUCUUAA-UGACGAU-------------GAUGACA-AUAU----CCCACCAAGAUC---GCUGA-UGCA
Y15171.1/2155-2227   UGCAU--AUG-AUGUAAA-CGAAUAUUUGCU-AUCUUAA-UGACGAU-------------GAUGACA-AUAU----CCCACCAAGAUC---GCUGA-UGCA
AF141346.1/1275-1356 UGCCACAAUG-AUGACA---GUUUAUUUGCUACUCUUGAGUGCUAGAAU-----------GAUGAGG-AUCUUA--ACCACCAUUAUCUUAACUGA-GGCA
AJ224032.1/2-84      UGCCACAAUG-AUGACAU-CA--UAUUUGCUACUCUUGACAGCUGGGGU-----------GACGAUAGCUUUAA--ACCACCAUGAUUAUAACUGA-GGCA
Z48765.1/1-75        UGCAG--AUG-AUGUAAA-AGAAUAUUUGCU-AUCUGAG-AGAUGGU-------------GAUGACA-UUUUAA--ACCACCAAGAUC---GCUGA-UGCA
AJ222770.1/4-73      UGCAA--UUG-AUGAAA------UAUUUGCUUAUGAUCA-AUAA-----------------AUGAUU-CUUUUAUUAUCACCAAGAUC---GCUGAGUGCU
Z48763.1/1-75        UGCAG--AUG-AUGUAAA-AAAAUACUUGCU-AUCUGAA-UGGUAGU-------------GCUGACA-UACAUU--AUCACCAAGAUC---UCUGA-UGAA
X61923.1/1387-1462   UGCAG--AUGAAUGUAAA-AGCCUAUUUGCU-AUCUGAG-AGAUGUG-------------GAUGACA-UUUUAA--ACCACCAAGAUC---GCUGA-UGCA
D14522.1/1637-1711   UGCAG--AUG-AUGUGAA-AAAAUACUUGCU-AUCUGAA-UGGUAGU-------------GCUGACA-UACAUA--ACCACCAAGAUC---GCUGA-UGCA
AJ003042.1/135-208   UGCAG--AUG-AUGUGAC-AGAAUAUUUGCU-AUCAGAU-GAGUGGU-------------GAUGACA-CUAGA---ACCACCAAGAUC---GCUGA-UGCA
AF270677.1/360-430   UGCAA--GUG-AUGCAA------AAGUAUGUUACCUGGA-AGAUGGU-------------GAUGACA-CUUUAA--ACCACCAAGAUC---GCUGA-UGCA
Z48760.1/109-198     UUCAA--AUG-AUGUAAU-AACAUAUUUGCUACUUCAGA-UGGAACUUUGAGUUCCGAA-UGAGACA-UACCAAUUAUCACCAAGAUC---UCUGA-UGAA
#=GC SS_cons         <<<<_..___._______.____________________._______............._______.______..____________..._____.>>>>
#=GC RF              uGCaa..AUG.AUGuAAu.AaaAUAUUUGCUAaUCUugA.uGauGgu.............GaUGAca.aUuuaA..ACCACCAAGAUC...gCUGA.uGCa
//
# STOCKHOLM 1.0

#=GF AC   RF00070
#=GF ID   SNORD29
#=GF PI   U29
#=GF DE   Small nucleolar RNA SNORD29
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Moxon SJ; Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   48.00
#=GF TC   49.10
#=GF NC   47.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300713;
#=GF DR   snoopy; Oryctolagus_cuniculus300345;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   8962077
#=GF RT   A small nucleolar RNA requirement for site-specific ribose methylation of
#=GF RT   rRNA in Xenopus.
#=GF RA   Tycowski KT, Smith CM, Shu MD, Steitz JA
#=GF RL   Proc Natl Acad Sci U S A 1996;93:14480-14485.
#=GF RN   [3]
#=GF RM   8559254
#=GF RT   A mammalian gene with introns instead of exons generating stable RNA
#=GF RT   products.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Nature 1996;379:464-466.
#=GF CC   U29 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_SNORD29
#=GF SQ   10


AJ532522.1/1-93        UUGGCGAUGAUGAUACUCUUUUACCCAGCUCAUUAUGAGACUUCCCUUUGUGGGUUGUCUUGGAUAUGAACUUUUCCUUUGUAUCUGAGCUUA
AJ532523.1/1-92        UCUGCAAUGAUGAUACCUUUUUACUCAGCUCAUUAUGAGACUUCCCUUUGUGGGUUGUUUGGGAUAUGAACUUUCCCUUA-UACCUGAGCAGA
AC087551.3/49489-49580 UCUGCAAUGAUGAUACCUUUUUACUCAGCUCAUUAUGAGACUUCCCUUUGUGGGUUGUUUGGGAUAUGAACUUUCCCUUA-UACCUGAGCAGA
U72863.1/1-65          -UUGCUGUGAUGAAAC-----UAACUAGCUCACUUUGA-----AUAAGCGUGAAAAG------CUUUGAACU-----------CCUGAGCAUC
U72864.1/1-65          -UUGCUGUGAUGAAAC-----UAACUAGCUCACUUUGA-----AUAAACGUGAAAAG------CUUUGAACU-----------CCUGAGCAUC
U72865.1/1-65          -UUGCUGUGAUGAAAC-----UAACUAGCUCACUUUGA-----UUAAGCAUGAAAAG------CUUUGAACU-----------CCUGAGCAUC
U72862.1/1-65          -UUGCUGUGAUGAAAC-----UAACUAGCUCACUUUGA-----UUAAACAUGAAAAG------CUUUGAACU-----------CCUGAGCAUC
U72866.1/1-65          -UUGCUGUGAUGAAAC-----UAACUAGCUCACUUUGA-----AUAAACAUGAAAAG------CUUUGAACU-----------CCUGAGCAUC
U40580.1/2415-2479     -UUUCUAUGAUGAAUC-----AAACUAGCUCACUAUGA-----CCGACAGUGAAAAU------ACAUGAACA-----------CCUGAGAAAC
U40654.1/1763-1827     -UUUCUAUGAUGAAUC-----AAACUAGCUCACUAUGA-----CUGCUAAUGAAAAC------ACAGGAACA-----------CCUGAGAAAC
#=GC SS_cons           .:<<<___________....._________________.....______________......_________..........._____>>>::
#=GC RF                .UuGCuAUGAUGAaAC.....UAaCuAGCUCAcUaUGA.....ccauuuGUGaaaaG......AUaUGAACU...........CCUGAGCaua
//
# STOCKHOLM 1.0

#=GF AC   RF00071
#=GF ID   SNORD73
#=GF PI   U73
#=GF DE   Small nucleolar RNA SNORD73
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR
#=GF GA   42.00
#=GF TC   43.50
#=GF NC   41.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300904;
#=GF DR   snoopy; Gallus_gallus300084;
#=GF RN   [1]
#=GF RM   9573378
#=GF RT   A novel snoRNA (U73) is encoded within the introns of the human and mouse
#=GF RT   ribosomal protein S3a genes.
#=GF RA   Rebane A, Tamme R, Laan M, Pata I, Metspalu A
#=GF RL   Gene 1998;210:255-263.
#=GF CC   U73 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U73 is encoded within the introns of ribosomal
#=GF CC   protein S3a and contains a 12nt region of complementarity to a conserved
#=GF CC   sequence in 28S ribosomal RNA. U73 is therefore thought to function as a
#=GF CC   2'-O-ribose methylation guide for pre-rRNA.
#=GF WK   Small_nucleolar_RNA_SNORD73
#=GF SQ   25


X87373.1/2786-2857           AAUGAAUGAUGACAAAAUGUUUCAGUCCCAAAUGAUACA----UACUGAUUA---------UACCAUUAUAUUUAUC-CUGACAUU
Z83331.1/1-70                -AUGAGUGAUGACAAGAUGUUUCGGUCCCAAAUGAAGCC----UACUGAU-----------UACCGUUACAUUUAUUGCUGACAUU
Z83334.1/4297-4361           AAUAAGUGAUGAAAAAA-GUUUCGGUCCCAGAUGAUGGC----CAGUGAU-----------AACA---ACAUUUUU--CUGAUGUU
Z83332.1/1-68                AACAUGUGAUGAGAAACUGUUUCGGUCCCAGUUGAUGGC----CACUGAU-----------AACAUU-ACAUUUUU--CUGAUGUU
ABDC01207740.1/266-338       AAUGAAUGAUGACAAAAUGUUUCGGUCCCAAAUGAUACA----UACUGAUUA---------UACCGUUACAUUUAUUUCUGACAUU
AAFR03015790.1/81555-81626   AAUGAAUGAUGACAAAAUGUUUCGGUCCCAAAUGAUACA----UAAUGAUUA---------UACCAUUGCAUUUUUU-CUGACAUU
AANN01335782.1/6831-6759     AAUGAAUGAUGACAAAAUGUUUCGGUCCCAUAUGAUUGA----CACUGAUUA---------UACCGUUACAUUAAUUUCUGACAUU
AAPY01415118.1/566-638       AAUGAAUGAUGACAAAAUGUUUCGGUCCCAGAUGAUACA----UCCUGAUUA---------UACCGUUACGUUUGUUUCUGACAUU
AANU01092345.1/982-915       AAUGAAUGAUGACAAAAUGUUUCGGUCCCAAAUGAUACA----UACUGAUUA---------UACCGU----UUUAUC-CUGACAUU
AADA01146743.1/18872-18792   AAUGAAUGAUGACAAAAUGUUUCAGUCCCAAAUGAUACA----UACUGAUUAUACCGUUAAUACCGUUAUAUUUAUC-CUGACAUU
AALT01646974.1/1083-1015     AAUAUGUGAUGACAAAU-GUUUCGGUCCCAGAUGAUGUC----CAGUGAU-----------AAGAUUUAACAUUUUU-CUGAUGUU
AAPN01216197.1/78-7          GAUGUGUGAUGACAAAAUGUUUCGGUCCCAAAUGACAUU----CCAUGAUUU---------GACUGUUGCAUUUUUC-CUGACAUC
AAFC03040637.1/33937-34005   AAUAAAUGAUGACAAAU-GUUUCGGUCCCAUAUGAUGUC----UGAUGAUA----------AAACUUAACAUUUUU--CUGAUGUU
AANG01715464.1/5580-5656     AAUGAAUGAUGACAAAAUGUUUUGGUCCCAAAUGAUACUGAUAUACUGAUUA---------UACUGUUAGGUUUAUUUCUGACAUU
AAIY01412025.1/395-466       AAUGAAGGAUGACAAAAUGUUUCGGUCCCAAAUGAU-CG----UACUGAUUA---------UACCGUUAUGUUUGGUUCUGACAUU
AAYZ01412487.1/510-573       AAUAAGUGAUGAAAAAU-GUUUUGGUCCCAGAUGAUGAU----CGGUGAU-----------AA-----AUCUUUUUU-CUGAUGUU
AAGV020149726.1/1505-1438    AAUACAUGAUGAGAAAAUGUUUCGGUCCCAGCUGAUGUA----CACUGAU-----------AACUUA-ACAUUUUU--CUGAUGUU
AAKN02042687.1/370083-370151 UAUAAGUGAUGAAAAAAUGUUUUGGUCCCAGUUGAUGUC----CACUGAU-----------AACUGUUACAUUUUU--CUGAUGUU
AAWR02018749.1/70987-70916   AAUAGAUGAUGACAAUGUGUUUCGGUCCCAUAUGAUGUC----CGGUGAUAA---------AACUGUUAACAUUUUU-CUGAUGUU
AACN010254564.1/1689-1617    AAUGAGUGAUGACAAAAUGUUUCGGUCCCAAAUGAUACA----UAUUGAUUA---------UACCGCUACAUUUACUUCUGACAUU
FM165399.1/8-78              AAUGAAUGAUGACAAAUUGUUUCGGUCCCAGAUGACACG----AAAUGAUUU---------UAAUUUUCCCAUUUU--CUGACAUU
AAGW02045887.1/126797-126862 AAUAAGUGAUGAAAAAA-GUUUCGGUCCCAGAUGAUGUC----CGAUGAU-----------AA--AUUACAUUUUU--CUGAUAUU
AAGU03067685.1/34741-34675   AAUAAAUGAUGAAAAACUGUUUCGGUCCCAGCUGAUGUC----CUGUGAU-----------AACU--UGCAUUUUU--CUGAUGUU
AAPE02001569.1/58035-58105   AAUAAGUGAUGACAAAAUGUUUCGGUCCCAAAUGAUGUC----CAGUGAUAA---------AACUUAAACAUUUUU--CUGAUGUU
AABR05088915.1/40283-40214   AAUGUGUGAUGAGAAAAUGUUUCGGUCCCAGUUGAUGAC----CACUGAUA----------AUAACUCACAUUUUU--CUGAUGUU
#=GC SS_cons                 <<<<___________________________________...._________.........________________.____>>>>
#=GC RF                      AAuGAaUGAUGAcAAAAUGUUUCGGUCCCAaAUGAUaca....uAcUGAUUA.........uACugUUAcAUUUuUu.CUGACaUU
//
# STOCKHOLM 1.0

#=GF AC   RF00072
#=GF ID   SNORA75
#=GF PI   U23
#=GF DE   Small nucleolar RNA SNORA75
#=GF AU   Bachellerie JP
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR
#=GF GA   80.00
#=GF TC   80.10
#=GF NC   78.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300788;
#=GF DR   snoopy; Homo_sapiens300068;
#=GF RN   [1]
#=GF RM   9106664
#=GF RT   The family of box ACA small nucleolar RNAs is defined by an evolutionarily
#=GF RT   conserved secondary structure and ubiquitous sequence elements essential
#=GF RT   for RNA accumulation.
#=GF RA   Ganot P, Caizergues-Ferrer M, Kiss T
#=GF RL   Genes Dev 1997;11:941-956.
#=GF RN   [2]
#=GF RM   12457565
#=GF RT   The expanding snoRNA world.
#=GF RA   Bachellerie JP, Cavaille J, Huttenhofer A
#=GF RL   Biochimie 2002;84:775-790.
#=GF RN   [3]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   U23 belongs to the H/ACA class of snoRNAs. snoRNAs bind a number of
#=GF CC   proteins (including dyskerin, Gar1p and Nop10p in the case of the H/ACA
#=GF CC   class) to form snoRNP complexes. This class are thought to guide the sites
#=GF CC   of modification of uridines to pseudouridines by forming direct base
#=GF CC   pairing interactions with substrate RNAs [3]. Targets include ribosomal
#=GF CC   and spliceosomal RNAs as well as the Trypanosoma spliced leader RNA (SL
#=GF CC   RNA) as possibly other, still unknown cellular RNAs [3]. U23 can direct
#=GF CC   the pseudouridylation of U97 in human 18S rRNA (Bachellerie JP, Ganot, P
#=GF CC   unpublished data). U23 is encoded within intron 12 of the nucleolin gene
#=GF CC   in human, mouse, rat chicken, and Xenopus laevis.
#=GF WK   Small_nucleolar_RNA_SNORA75
#=GF SQ   6


AJ009730.1/1-133    GCUUUCUCA-UGAGCUCCUCUCUGCCGAU----CAGUGGCGUUGUAUGGAUUCGCACGAGAAGAAGAGACUAA--UCAC-AAAUUGAACAGGCACC----CCCC-UAAUCUCAACAGGUG-------UUGCCCAUGUCUG----CUGUGAAACAAUU
AJ009731.1/1-129    UUCUUCUCA-UGAGCUCCUCUCUGUCAAUC---CAGUGGCAGUGUAUGGAUUCGCACGAGAAGUAGAGUGA-U--UCAC-AGUUU-AACAGGUGUUU---CCAC-UG-------CAUUGG----GACAUGCCCAUGUCUG----AUGUGAGACAUUC
AJ009728.1/1-142    CACUUCUCAAUGAGCUCCUUCCUGCCGACAUAUCCAUGGCAGCCUAUGGAUUCGCACGAGAAGGACAUAAACAGCUCAGUAGU---GGCACGC--UCA--CAACCUGGU-UAUACAUCAGUUGUGAUUAACCACUUACUGU----UCU---ACAAGU
M55022.1/344-480    AUCUUCUCAUUGAGCUCCUUUCUGUCAAC----CAGUGACAGAUUAUGGAUUCGCACGAGAAGAAGAGAAAGU--UCAC-AGAACUAGCAC----UUAAUCUUC-UG-UUUUUGCAGGAG-------AUCUAUUUGGCUGUUAUGUGUGAGACAUUC
X07699.1/9946-10078 AUCUUCUCAUUGAGCUCCUUUCUGUCCAU----CAGUGAUAGAUUAUGGAUUCGCACGAGAAGAAGAGAGAAU--UCAC-AGAACUGGCAC----UUAU-CUUC-UG-UUUUUGCAGAAG--------UAUAUUUGGCUGU--UGUGUGAGACAUUA
AJ007015.1/1-137    GUCUUCUCAUUGAGCUCCUUUCUGUCUAU----CAGUGGCAGUUUAUGGAUUCGCACGAGAAGAAGAGAGAAU--UCAC-AGAACUAGCAUUAUUUUAC-CUUC-UG-UCUUUACAGAGG--------UAUAUUUAGCUGU--AUUGUGAGACAUUC
#=GC SS_cons        ::<<<<<<-----<<<<<---<<<<<___....____>>>>>----->>>--->>-->>>>>>----------..<<<<.<<-----------..---..<<<<.<<.______>>>>>>.......--------------...>>>>>>:::::::
#=GC RF             auCUUCUCAuUGAGCUCCUuUcuGcCaAu....CAGUGgCaguuUAUGGAUUCGCACGAGAAGaAgAgAaAau..uCAc.AcaauuagCAcgc..UuA..Cccc.UG.UuUuuaCAgggG.......uuauauuUguCUGU...gUgUGagACAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00073
#=GF ID   mir-156
#=GF DE   mir-156 microRNA precursor
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   62.00
#=GF TC   62.00
#=GF NC   61.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000008;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12101121
#=GF RT   MicroRNAs in plants.
#=GF RA   Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP
#=GF RL   Genes Dev 2002;16:1616-1626.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the plant microRNA (miRNA) precursor mir-156. This
#=GF CC   miRNA has now been predicted or experimentally confirmed in a range of
#=GF CC   plant species (MIPF:MIPF0000008). Animal miRNAs are transcribed as ~70nt
#=GF CC   precursors and subsequently processed by the Dicer enzyme to give a ~22nt
#=GF CC   product. In plants the precursor sequences may be longer, and the carpel
#=GF CC   factory (caf) enzyme appears to be involved in processing. In this case
#=GF CC   the mature sequence comes from the 5' arm of the precursor, and both
#=GF CC   Arabidopsis and rice genomes contain a number of related miRNA precursors
#=GF CC   which give rise to almost identical mature sequences. The extents of the
#=GF CC   hairpin precursors are not generally known and are estimated based on
#=GF CC   hairpin prediction. The products are thought to have regulatory roles
#=GF CC   through complementarity to mRNA.
#=GF WK   mir-156_microRNA_precursor
#=GF SQ   10


AL606594.4/122244-122157 GUGACAGAAGAGAGUGAGCACACGGCCGGGC---GUGACGGCACCGGCGGGCG-UGCCGU---CGCGG-------CCGCGUGCUCACUGCUCUUUCUGUCAU
AC003058.3/76991-76907   GCGACAGAAGAGAGUGAGCACACAU---GGCU--CUUUU--------UCUAGCAUGCUCA---UGCUCGAAAGCUCUGCGUGCUUACU-CUCUUCUUGUCUC
AP002816.1/72598-72685   CUGACAGAAGAGAGUGAGCACACACGGUGCUUU-CUUA--------GCAUGCAAGAGCCA---UGCUGGGA-GCUGUGCGUGCUCACU-CUCUAUCUGUCAG
AP003332.4/36088-35998   GUGACAGAAGAGAGUGAGCACACGUGGUUGUUUCCUUGC-------AUAAAUGAUGCCUA---UGCUUGGA-GCUACGCGUGCUCACUUCUCUCUCUGUCAC
AF149413.1/10006-9915    GUGACAGAAGAGAGUGAGCACACAUGGUGGCUUUCUUGC-------AUAU-UUGAAGGUUCCAUGCUUGAA-GCUAUGUGUGCUCACU-CUCUAUCCGUCAC
AL163812.1/61753-61850   GUGACAGAAGAGAGUGAGCACACAUGGUGGUUU-CUUGCAUGCUU-UUUUGAUUAGGGUUUCAUGCUUGAA-GCUAUGUGUGCUUACU-CUCUCUCUGUCAC
AP002836.1/25247-25339   CUGACAGAAGAGAGUGAGCACACAUGGUGACUUUCUUGC-------AUGCUGAAUGGACUCA-UGCUUGAA-GCUAUGUGUGCUCACUUCUCUCUCUGUCAG
AL022198.1/47163-47082   CUGACAGAAGAGAGUGAGCACAUGCAGGCACU--GUUAU-------GUGU-CUAUAACUU---UGCGU-------GUGCGUGCUCACCUCUCUUUCUGUCAG
AL391222.1/7873-7786     UUGACAGAAGAGAGUGAGCACACAAAGGGGAA--GUUGUAUAAAA-GUUUUGUAUAUGGU---UGCUU-------UUGCGUGCUCACU-CUCUUUUUGUCAU
AL161579.2/181456-181372 CUGACAGAAGAGAGUGAGCACACAAAGGCACU---UUGC-------AUGUUCGAUGCAUU---UGCUUCUC----UUGCGUGCUCACUGCUCUAUCUGUCAG
#=GC SS_cons             <<<<<<<<<<<<<<<<<<<<<-<<<_______.._____.......______________...________.___>>>->>>>>>>>>.>>>->>>>>>>>>
#=GC RF                  guGACaGaaGAGaGUGAGCACACacgGuggcU..cUUgc.......aUauuuuAugcauu...UGCUuGaA.GCUguGcGUGCUCACu.CUCUuuCuGUCac
//
# STOCKHOLM 1.0

#=GF AC   RF00074
#=GF ID   mir-29
#=GF DE   mir-29 microRNA precursor
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   51.00
#=GF TC   52.90
#=GF NC   50.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000009;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the microRNA (miRNA) precursors mir-29. This miRNA
#=GF CC   has been predicted or confirmed in a wide range of species
#=GF CC   (MIPF:MIPF0000009). Animal miRNAs are transcribed as ~70nt precursors and
#=GF CC   subsequently processed by the Dicer enzyme to give a ~22nt product. In
#=GF CC   this case the mature sequence comes from the 3' arm of the precursor. The
#=GF CC   extents of the hairpin precursors are not generally known and are
#=GF CC   estimated based on hairpin prediction. The products are thought to have
#=GF CC   regulatory roles through complementarity to mRNA.
#=GF WK   mir-29_microRNA_precursor
#=GF SQ   10


BC058715.1/4089-4150     CUGA--CCGAUUUCUCCUGGUG-UUCAGAGU-----CUGUUUUUGUCUAGCACCAUUUGAAAUCGG--UUAU
BX323868.6/63999-64062   AUGA--CUGAUUUCCUUUGGUG-CUUAGAGU---CCCAUCUGUCAUCUAGCACCAUUUGAAAUCGG--UUAU
CR749762.6/80332-80264   GCGUGACUGAUUUCCUCUGGUG-UUCAGAGUGGACUGGGUUU--UUCUAGCACCAUUUGAAAUCGGUCGUGC
BX001041.6/158851-158788 UUGA--CCGAUUUCUUUUGGUG-UUCAGAGU---CUUUUGGGGUUUCUAGCACCAUUUGAAAUCGG--UUAC
BX465862.7/161280-161350 CAGAUGCUGGUUUCACAUGGUGGUUUAGAUGUGUUCUACCAA-AGUCUAGCACCAUUUGAAAUCAGUGUUCU
AC024913.33/28763-28700  AUGA--CUGAUUUCUUUUGGUG-UUCAGAGU---CAAUAGAAUUUUCUAGCACCAUCUGAAAUCGG--UUAU
AY865998.1/352-415       AUGA--CUGAUUUCUUUUGGUG-UUCAGAGU---CAAUAUAAUUUUCUAGCACCAUCUGAAAUCGG--UUAU
BX001041.6/159008-158937 UGGAAGCUGGUUUCAAGUGGUGUUUUAGAGUGCUGAUCAAAUGAAUCUAGCACCAUUUGAAAUCAGUGUUCU
AF480543.1/5-76          UGGAAGCUGGUUUCACAUGGUGGCUUAGAUUUUUCCAUCUUUGUAUCUAGCACCAUUUGAAAUCAGUGUUUU
AF480542.1/5-75          AGGAAGCUGGUUUCAUAUGGUGGUUUAGAUUUAAAUAGUGAU-UGUCUAGCACCAUUUGAAAUCAGUGUUCU
#=GC SS_cons             <<<<--<<<<<<<<---<<<<<.---<<<<______________>>>>-->>>>>--->>>>>>>>-->>>>
#=GC RF                  agGaaGCuGaUUUCauuUGGUG.UUuAGAcUuuucuauuuauuugUCUAGCACCAUUUGAAAuCaGUguUcu
//
# STOCKHOLM 1.0

#=GF AC   RF00075
#=GF ID   mir-166
#=GF DE   mir-166 microRNA precursor
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, Daub J
#=GF SS   Predicted; PFOLD
#=GF GA   60.00
#=GF TC   60.50
#=GF NC   59.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.06 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000004;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12101121
#=GF RT   MicroRNAs in plants.
#=GF RA   Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP
#=GF RL   Genes Dev 2002;16:1616-1626.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the plant microRNA (miRNA) precursor mir-166. This
#=GF CC   miRNA has now been predicted or experimentally confirmed in a wide range
#=GF CC   of plant species (MIPF:MIPF0000004). Animal miRNAs are transcribed as
#=GF CC   ~70nt precursors and subsequently processed by the Dicer enzyme to give a
#=GF CC   ~22nt product. In plants the precursor sequences may be longer, and the
#=GF CC   carpel factory (caf) enzyme appears to be involved in processing. In this
#=GF CC   case the mature sequence comes from the 3' arm of the precursor, and both
#=GF CC   Arabidopsis and rice genomes contain a number of related miRNA precursors
#=GF CC   which give rise to almost identical mature sequences. The extents of the
#=GF CC   hairpin precursors are not generally known and are estimated based on
#=GF CC   hairpin prediction. The products are thought to have regulatory roles
#=GF CC   through complementarity to mRNA.
#=GF WK   mir-166_microRNA_precursor
#=GF SQ   31



ABEU01003209.1/178750-178656 GCUGUGAGGAAUGCCGCAUGGACCGAAGCUAUGUGCU-CCAUCUU---------------------------------------------------------------------------------------------AACGUGGUGGUAUUGAUAC---UACGUU-UCGGACCAGGCUUCAUUCCCCUCAGC
AC148816.3/87512-87332       GGUGUUUGGAAUGAGGUUUGUUCCAAGAUCAUCACAC-AUCAUGUUUCUUCUUCCCUUUCAAUAAUUCUUGAUUAAUUUAUGUUCAUACA--------UCUAUAUAUAUAUCUAUAUAUAUUAUCAAGUCAUUACAUGCAUGGGAUGAGAUAUUGAG---AGUGAUCUCGGACCAGGCUUCAUUCCUCACACC
AY551234.1/11-145            GGUGUCUGGAAUGGAGGCUGAUCCAAGAUCAUUGCUU-GGUGCAAAAUACUAGGGCAUUGUUGUAAG------------------------------------------------------UGCCAUUAGUUCUUUUUUGUUUCCGAGUUUGUUAUC---GAGGAUCUCGGACCAGGCUUCAUUCCUCACACC
AY551231.1/31-172            GUUAAGGGGUUUGUUGUCUGGUUCAAGGCCUCCUGCU-GUCCUACAUCACAUUUUUUUUUCUUUGUUCUGA-----------------------------------------------AUUUCUGAUGGAUGUGUGUGUGCAUGAUGCAUGGCUGGU---GGUGACCUCGGACCAGGCUUCAUUCCCUUUAAC
AY501432.1/1-124             --UGAGUGGAAUGUUGUCUGGUUCAAGGUCUUGCUUUCCGAUUUGAGAAUGAUCCAUGCUUGC---------------------------------------------------------------AUGUGUAGGUUUUUUUGUUCCUCAGAUCUAC---AAGAUC-UCGGACCAGGCUUCAUUCCCCUCAGG
AY664417.1/307265-307178     GUUGAGGGGAAUGUCGUCUGGCGCGAGA------------------------------------------------------------------------------------------------------CCGUACCGGACGACGUGCUCUCGGUUG---GACGGUCUCGGACCAGGCUUCAUUCCUCCCAAC
AP004125.3/115130-115014     GUUAAGGGGUUUGUUGUCUGGCUCGAGG-CAUCCGGG-ACUCCGGUUUCUCCUUU-----------------------------------------------------------------------CCUACUGGAGGCGCCUAAUUUCCGGCGAGCU---CGGAGCCUCGGACCAGGCUUCAAUCCCUUUAAC
AY551233.1/12-120            CUUGUGGGGAAUGUUGGCUGGCUCGAGGUAUCCACAU-CUUAAUUCCUCU--------------------------------------------------------------------------------CCGGCGAUCGAGCCGGCUCGGGCGUGU---GGAAGCGUCGGACCAGGCUUCAUUCCUCGCAAG
AC148487.14/34671-34762      GUUCAGGGGAAUGGUGUCUGAUUCGAGACCAU--------------------------------------------------------------------------------------------------UCGUCACAAGUAAACAGUAGCCUUGAG---AAUGAUCUCGGACCAGGCUUCAUUCCCCCUAGC
CT009488.4/103389-103285     GCUGAGAGGAACGCAGUCUGGCUCGAGGAAUGCUCAG-AUCUGUUU------------------------------------------------------------------------------------UGAUCUGAUCGAUAUGUUCAUAUCUAA---UUAAUUCUCGGACCAGGCUUCAUUCCUCCCAUC
CT009488.4/103549-103459     GUUGAGGGGAAUGUUGCCUGGCUCAAGGCUUUUCAUA-GUUU--------------------------------------------------------------------------------------------------GAUCUAUCUACUAUGAU---UAAGGCUUCGGGCCAGGCUUCAUCCCCCUCAAA
AY664413.1/238586-238494     GUUGAGGGGAAUGUCGUCUGGCGCGAGACCGUA-------------------------------------------------------------------------------------------------CCAGACGACGUGCUCUCUCGGUCGUCG---GACGGUCUCGGACCAGGCUUCAUUCCCCCCAAC
AC140029.19/70482-70585      GUUGAGAGGAACGUUGUCUGGCUCGAGGUGAUGGAGA-UGGAAGA-------------------------------------------------------------------------------------GUACUCUCUACUCACUCAUCACUAACU---UUCAAUCUCGGACCAGGCUUCAUUCCCCCCAGC
AC155889.2/42101-41932       GUUGAUGGGAAUGUUGUUUGGCUCGAGGUAAUAACUA-ACUCAAUUUCUUUGUCUUUGAAAGCUUUUCUUUGUUUCACUCUUUU--------------------UGAUUCUUAGAAAGUUGAAACUAAGUGAGCUUUAAAGGUUUGAUUUUGAUGUG--UGAUUAUCUCGGACCAGGCUUCAUUCCUACCAAC
AY551232.1/7-113             GUUAAGGGGAUUGUUGUCUGGUUCAAGGUCUCCACAU-UGUGCAAAAU----------------------------------------------------------------------------------GUUCAUUCAUGGAGGCACAGGAUGCUU---GGUGAUCUCGGACCAGGCUUCAAUCCCUUUAAC
AY599420.1/1-187             --UGAGGGGAAUGUUGUCUGGCUCGAGGUCACCAACU-AGAUCCAUAAACUCCAUAUUAUGCUUUUUUGAAUAUAAAGAUUAGUUUUUCUUUUCUUUUCACUAGGAAAAUUUAAAGAUUAGUUGAUUAUAUUAAAAAGGGUUUAUGGAUCAUGAGUU---AGUGUUGUCGGACCAGGCUUCAUUCCCCCCAAU
AY551230.1/23-201            UUUGAGGGGAAUGUUGUCUGGCUCGGGGCUACUUUUA-AUUUCUCUCUCUUUUGAUAUCUUCUUUUCUCGAUCUCCUAGCUUGAUCUUU----------UGAUCUCUCAAAUCGAUCUUAAGAAAAAGAUCAGUCAAAGAGAUGAGAGUAGAUGUCU---GUAGAUCUCGGACCAGGCUUCAUUCCCCCCAAA
AC140029.19/70272-70377      UUUGAGGGGAAUGUUGGCUGGCUCGAGGCUUUUCAGU-UUCACAAAGGAAGU-----------------------------------------------------------------------------------UCAGUCUUAAUUGUAUGAACUA---UAAGGCUUCGGACCAGGCUUCAUUCCCCUCAAA
AB005234.1/57935-58034       GUUUAGAGGAAUGUUGUUUGGCUCGAGGUCAUGGAGA-GUA-----------------------------------------------------------------------------------------AUUCGUUAACCCAACUCAAAACUCUAA---AUGAUUCUCGGACCAGGCUUCAUUCCCCUCAAC
AB016875.1/40211-40311       GUUCAGGUGAAUGAUGCCUGGCUCGAGACCAUUCAAU-CUCA----------------------------------------------------------------------------------------UGAUCUCAUGAUUAUAACGAUGAUGAU---GAUGAUGUCGGACCAGGCUUCAUUCCCCUCAAC
AC144592.26/52711-52605      UUUGAGGGGAAUGUUGUCUGGCUCGAGGACGCUUUCU-UCUCGAUCUAAUGC----------------------------------------------------------------------------------AAAUUUGUGGUCAUGGAUUGUAA---AGUAUUCUCGGACCAGGCUUCAUUCCCCCCAAU
AC025296.10/95861-95981      UCUGAGUGGAAUGUUGUCUGGUUCAAGGUCUCAUGCA-CCUUGCGGUUUUGAGGA-----------------------------------------------------------------------UGAUUUGUGCAAGGUUUUUCAUUCCUCUCAUCCGUGGGAUCUCGGACCAGGCUUCAUUCCCCUCAGA
AC005819.3/30684-30829       UUUGAGGGGACUGUUGUCUGGCUCGAGGACUCUGGCU-CGCUCUAUUCAUGUUGGAUCUCUUUCGAUCUAACA-------------------------------------------AUCGAAUUGAACCUUCAGAUUUCAGAUUUGAUUAGGGUUUU---AGCGUCUUCGGACCAGGCUUCAUUCCCCCCAAU
AF013294.1/57881-58026       GUUGUGGGGAAUGUUGUUUGGAUCGAGGAUAUCAUAA-ACGCAUACACAUGUUUAUAUGUUAUGAUGCAUUAU-------------------------------------------AUGACUGAUGUAAUGUACAUAUAUAUACAUACAUGCCACAU---GGUAUCGUCGGACCAGGCUUCAUCCCCCUCAAC
AL590346.1/42078-42188       GUUGAGAGGAAUAUUGUCUGGCUCGAGGUCAUGAAGA-AGAUCGGUAGAUUG------------------------------------------------------------------------------AUUCAUUUUAAAGAGUGAAAUCCCUAA---AUGAUUCUCGGACCAGGCUUCAUUCCCCCCAAC
AL138642.1/84877-84998       UUUGAGGGGACUGUUGUCUGGCUCGAGGACUCUUAUU-CUAAUACAAUCUCAUUUGAAU-------------------------------------------------------------------ACAUUCAGAUCUGAUGAUUGAUUAGGGUUUU---AGUGUCGUCGGACCAGGCUUCAUUCCCCCCAAU
AL590346.1/40100-40217       GUUGAGAGGAUUGUUGUCUGGCUCGAGGUCAUGAAGA-AGAGAAUCACUCGAAUU-----------------------------------------------------------------------AAUUUGGAAGAACAAAUUAAGAAAACCCUAG---AUGAUUCUCGGACCAGGCUUCAUUCCCCCUAAC
AC023628.3/19945-19835       GUUGAGGGGAAUGUUGUCUGGAUCGAGGAUAUUAUAG-AUAUAUACAUGUGU------------------------------------------------------------------------------AUGUUAAUGAUUCAAGUGAUCAUAGAG---AGUAUCCUCGGACCAGGCUUCAUCCCCCCCAAC
AB016871.1/77005-76861       UUUGAGGGGAAUGUUGUCUGGCACGAGGCCCUUAACUUAGAUCUAUAUUUGAUUAUAUAUAUAUGUCUCUUC---------------------------------------------UUUAUUCAUUAGUCUAUACAUGAAUGAUCAUUUUACGGUU---AAUGACGUCGGACCAGGCUUCAUUCCCCUCAAU
GQ418834.1/83-169            GUUGAGAGGAAUGUCGUCUGGCCUGAG-------------------------------------------------------------------------------------------------------AUCGUACCACAGUGGUGGGUACACGUG---GACGGUCUCGGACCAGGCUUCAUUCCCCUCAAC
GQ418889.2/316-450           GGUGUUUGGAAUGCAGUUUGAUCCAAGAUCUGCCUAU-AUAUAUGGUGUGUAUAUCAUAUCUUGUGAU-----------------------------------------------------AUGGGGGAUAUGCAACAGGUGUGUGAC-AGGGGUAG---GUAGAUCUCGGAUCAGGCUUCAUUCCUCACACC
#=GC SS_cons                 <<<<<<<<<<<<<--<<<<<<--<<<___________._________________________..............................................................._______________________________..._______>>>-->>>>>>-->>>>>>>>>>>>>
#=GC RF                      guUGaGgGGAAUGUUGUCUGGCUCGAGGuCauuaaau.auuucuauuuaUuuUuuuuUauuuU...............................................................aaauuuauauuagauuuauuauuauauuuau...aguGaUCUCGGACCAGGCUUCAUUCCcCuCAac
//
# STOCKHOLM 1.0

#=GF AC   RF00076
#=GF ID   mir-181
#=GF DE   mir-181 microRNA precursor
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   52.00
#=GF TC   56.40
#=GF NC   50.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000007;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF RN   [2]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA 2003;9:175-179.
#=GF CC   This family represents the microRNA (miRNA) mir-181 which has been
#=GF CC   predicted or experimentally confirmed in a wide number of vertebrate
#=GF CC   species (MIPF:MIPF0000007). miRNAs are transcribed as ~70nt precursors
#=GF CC   (modelled here) and subsequently processed by the Dicer enzyme to give a
#=GF CC   ~22nt product. In this case the mature sequence comes from the 5' arm of
#=GF CC   the precursor. The extents of the hairpin precursors are not generally
#=GF CC   known and are estimated based on hairpin prediction. The products are
#=GF CC   thought to have regulatory roles through complementarity to mRNA. The
#=GF CC   involvement of Dicer in miRNA processing suggests a relationship with the
#=GF CC   phenomenon of RNA interference. miRNAs are numbered based on the sequence
#=GF CC   of the mature RNA.
#=GF WK   mir-181_microRNA_precursor
#=GF SQ   19


AC122794.3/125701-125775     UUUGGGGGAACAUUCAAC-CUGUCGGUGAGUUUGGGCAG--CUCAGAC-----AAACCAUCGACCGUUGAGUGGACCCCGAGG
AL158075.11/55107-55180      CUCCAAGGAACAUUCAACGCUGUCGGUGAGUUUGGGAUU--UGAA--A-----AAACCACUGACCGUUGACUGUACCUUGGGG
AL136321.5/86569-86494       CUUCAGUGAACAUUCAACGCUGUCGGUGAGUUUGGAAUU--AAAAUCA-----AAACCAUCGACCGUUGAUUGUACCCUAUGG
AC020916.8/87858-87932       UUUGGGGGAACAUUCAAC-CUGUCGGUGAGUUUGGGCAG--CUCAGGC-----AAACCAUCGACCGUUGAGUGGACCCUGAGG
AANN01489271.1/1239-1164     CUCCAAGGAACAUUCAACGCUGUCGGUGAGUUUGGGAUU--UGGAAAA-----AAACCACCGACCGUUGACUGUACCUUGGGA
AAPN01119455.1/4934-5009     CUUCAGUGAACAUUCAACGCUGUCGGUGAGUUUGGAAUU--AAAGUAG-----AAACCAUCGACCGUUGAUUGUACCCUGCGG
AAYZ01097726.1/658-732       CUCCAAGGAACAUUCAACGCUGUCGGUGAGUUUGGGAUG--UGGA-AA-----AAACCACCGACCGUUGACUGUACCGUGGGG
AALT01219307.1/2594-2520     UUCCAAGAAACAUUCAACGCUGUCGGUGAGUUUGGGAUC--UGAA-AA-----AAACCACUGACCGUUGACUGUACCUUGGGG
AAFR03041358.1/50589-50664   CUUCAGUGAACAUUCAACGCUGUCGGUGAGUUUUUAGAU--UUAAAAG-----AAACCAUCGACCGUUGACUGUGCCUUGAGG
AAVX01605662.1/457-382       UUUCAGGGAACAUUCAACGCUGUCGGUGAGUUUGAUGCU--AUUGGAG-----AAACCAUCGACCGUUGAUUGUACCUUGUAU
BAAE01046132.1/387-313       UCACGGGGAACAUUCAACGCUGUCGGUGAGUUUGUGCUA--CAAU-CA-----AAACCAUCGACCGUUGACUGUACCCUGAGA
CAAE01007899.1/3116-3043     CAACGGUGAACAUUCAACGCUGUCGGUGAGUUUGACACU--GAAC--G-----AAACCAUCGACCGUUGACUGUACCCCGAGG
AANH01010005.1/225761-225835 CCACGGUGAACAUUCAACGCUGUCGGUGAGUUUGAGCUU--UGAC-CA-----AAACCAUCGACCGUUGACUGUACCCUGAGG
AAIY01460174.1/553-632       CUCCAGAGAACAUUCAACGCUGUCGGUGAGUUUGGGAUU--UGAAAAA-AAAAAAACCACUGACCGUUGACUGUACCUUGAGG
CAAK05046427.1/2246-2169     CCUCAGUGAACAUUCAACGCUGUCGGUGAGUUUGAGCUAAAUGGAAAA-----AAACCAUCGACCGUUGAUUGUACCCUGCGG
AAHX01021242.1/19646-19566   CUCCAUGGAACAUUCAACGCUGUCGGUGAGUUUGGGAUU--CAAAAACAAAAAAAACCACCAACCGUUGACUGUACCUUGGGA
CAAB02002969.1/44553-44625   CUUUGGGGAACAUUCAACGCUGUCGGUGAGUUUUGUCUC--CGAA--------AAACCAUCGACUGUUGAGUGUACCCUGACA
AEQU010205162.1/1456-1381    CUUCAGUGAACAUUCAACGCUGUCGGUGAGUUUGGGAUU--AAAGUGA-----AAACCAUCGACCGUUGAUUGUACCCUCCAG
AADN03007326.1/16297-16223   CUUCAGUGAACAUUCAACGCUGUCGGUGAGUUUGAGAA---CUAAGAA-----AAACCAUCGACCGUUGACUGUACCUUGAGG
#=GC SS_cons                 ::<<<<<<--<<-<<<<<---<<<<<<<-<<<<______.._______.....>>>>>>>>>>>->>>>>->>-->>>>>>::
#=GC RF                      cUcCaggGAACAUUCAACGCUGUCGgUGAGUUUGggauu..uaaaaaa.....AAACCAcCGACCGUUGAcUGUACccuGgGg
//
# STOCKHOLM 1.0

#=GF AC   RF00077
#=GF ID   SraB
#=GF PI   sraB
#=GF DE   SraB RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD
#=GF GA   130.00
#=GF TC   133.90
#=GF NC   127.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF CC   This RNA was discovered in E. coli during a large scale screen [1]. This
#=GF CC   ncRNA was found to be expressed only in stationary phase [1]. The function
#=GF CC   of this RNA is unknown.
#=GF WK   SraB_RNA
#=GF SQ   5


M29698.1/90-258              UAGGCAUAUUUUUUUCCAUCAGAUAUAGCGUAUUGAUGAUAGCCAUUUUAAACUAUGCGCUUCGUUUUGCAGGUUGAUGUUUGUUAUCAGCACUGAACGAAAAUAAAGCAGUAACCCGCAAUGUGUGCGAAUUAUUGGCAAAAGGCAACCACAGGCUGCCUUUUUCUUU
CP000034.1/1873400-1873232   UAGGCAUAUUUUUUUCCAUCAGAUAUAGCGUAUUGGUGAUAGCCAUUUUAAACUAUGCGCUUCGUUUUGCAGGUUGAUGUUCGUUAUCAGCACUGAACGAAAAUAAAGCAGUAACCCGCAAUGUGUGCGAAUUAUUGGCAAAAGGCAACCACAGGCUGCCUUUUUCUUU
ABEJ01000009.1/157589-157755 GGGGCAUAUUUUUU-CCCUCAGAUAUAGCGUAAUGAUGAGAGCCAUCUUAAACUAUGCUCUUCGGUCUUCAAGCCUGUCAUACUGACUCGUCUUGAGCGAAAAUAAGUCUGUAACCCGCAAUGUGUGCGAAUUAU-GGCAAAAGGCAACCGCAGGCUGCUUUUCUUUGA
AE014075.1/1290089-1290256   UAGGCAUAUUUUUUUCCAUCAGAUAUAGCGUAUUGAUGAUAGCCAAUUUAAACUAUGCGCUUCGUUUUGCUGACUGGCAACUU-UGCCAGCACUGAACGAAAAUAAGGCUGUAACCCGCAAUGUGUGCGAAUUAUUGGCAAAAGGCAACCGCAGGCUGCCUUUUUCUUU
CP001144.1/2091931-2091764   GGGGCAUAUUUUUU-CCCUCAGAUAUAGCGUAAUGAUGAGAGCCAUCUUAAACUAUGCUCUUCGGUCUUCAAGCCUGUCAUACUGACUCGUCUUGAGCGAAAAUAAGUCUGUAACCCGCAAUGUGUGCGAAUUAUUGGCAAAAGGCAACCGCAGGCUGCCUUUUUCUUU
#=GC SS_cons                 :::::::::::::::::<<<<_______________>>>>,,,,,,,,,,,,,,,,,,,,<<<<<<---<<<-<<<<<<_____>>>>>>-->>>>>>>>>,,,,,,,,,<<<<--<<<<_____>>>>-->>>>,,,,<<<<<<<<-<<___>>->>>>>>>>:::::
#=GC RF                      uaGGCAUAUUUUUUUCCcuCaGAUAUAGCGUAuUGAuGagAGCCAuuUUAAACUAUGCgCuuCGuuuUgCaggcuggucaUuuUgaccaguacuGaaCGaaAAUAAggCuguaaCCCGCaAUGUGuGCGAAuuauUGGCaaaaGGCaACCgCAGGCuGCCuuuuUcUuu
//
# STOCKHOLM 1.0

#=GF AC   RF00078
#=GF ID   MicA
#=GF PI   SraD; MicA
#=GF DE   MicA sRNA
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Predicted; Barquist LE
#=GF SS   Predicted; Udekwu KI; WAR
#=GF GA   41.00
#=GF TC   42.30
#=GF NC   38.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.57 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0006950; response to stress;
#=GF RN   [1]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF RN   [2]
#=GF RM   16204185
#=GF RT   Hfq-dependent regulation of OmpA synthesis is mediated by an antisense
#=GF RT   RNA.
#=GF RA   Udekwu KI, Darfeuille F, Vogel J, ReimegÃ¥rd J, Holmqvist E, Wagner EG
#=GF RL   Genes Dev 2005;19:2355-2366.
#=GF WK   MicA_RNA
#=GF SQ   17



U00096.2/2812824-2812895   GAAAGACGCGCA---UUUGUUAUCA-----UCAUCCCUGAAUU----CAG-AGA-UG------AA-AUUUU-GGCCACU--CA-CG------AGUGGCC--UUUU
CP002433.1/3353571-3353642 GAAAGACGCGCA---UUUGUUAUCA-----UCAUCCCUGACAA----CAG-AGA-UG-UU---A---A-UUCGGCCACA--GU-GA------UGUGGCC--UUUU
AM286415.1/966505-966434   GAAAGACGCGCA---UUUGUUAUCA-----UCAUCCCUGUUAU----CAG-AGA-UG-UU---A---AUUU-GGCCACA--GC-AA------UGUGGCC--UUUU
CP001655.1/1140070-1139991 GAAAGACGCGCA---UUUAUUAUCA-----UCAUCCCUAUUAU---C-AG-AGA-UG-UUU------CUUUC-GCCACCCGGUAACAA-UCGGGUGGC--AUUUU
FN392235.1/3058834-3058911 GAAAGACGCGUA---UUUGUUAUCAUCAUCUCAUCCCUGACAA----CAG-AGA-UG-UU---A---AUUUAGGCCACA--GU-GA------CGUGGCC--UUUU
FQ312003.1/2989429-2989501 GAAAGACGCGCA---UUUGUUAUCA-----UCAUCCCUGUUUU----CAG-CGA-UG------AA-AUUUU-GGCCACU--CCGUG------AGUGGCC--UUUU
FN667742.1/1133198-1133128 G-AAGAUGCGCAAAA-UUGUUAU-------U-AUCCCUAUUCU---CUA--AGA-UACUUU--A-----UUCGGCCACC---UCC-------GGUGGCC-AUUUU
AP008232.1/941056-940984   GAAAGAUGCGCA---UUUGUUAUCA-----UCAUCCCUGUUAA----CAG--GAAUG-UU---A---AUUUA-GCCACA--GUUUC------UGUGGCC--UUUU
FN545200.1/16759-16830     GCAAGACGCG-AAAA-UUGUUAU--------CAUCC-UAUUCU---CUA--AGA--GAUUU-UA---UUUU-GGCCACU--UUAA-------AGUGGCC-AUUUU
CP002272.1/1084358-1084286 GAAAGACGCGCA---UUUGUUAUCA-----UCAUCCCUGACUU----CAG-AGA-UG------AAAUGUUU-GGCCACA--GU-GA------UGUGGCC--UUUU
FN667741.1/3206853-3206924 G-AAGACGCGCAAAA-UUGUUAU--------CAUCCCUAUUUU---CUA--AGA--GAUUU-UA----UUUCGGCCACC--ACU--------GGUGGCC-AUUUU
CP002910.1/3807171-3807244 GAAAGACGCGCA---UUUAUUAUCAU--CAUCAUCCCUGA-AU----CAG-AGA-UG------AA-AGUUU-GGCCACA--GU-GA------UGUGGCC--UUUU
CP002038.1/3695450-3695529 GAAAGACGCGCA---UUUAUUAUCA-----UCAUCCCUAUUAU----CAG-AGA-UG-UUU------CUUU-GGCCACC-CGAUGACAAUCGAGUGGCC--UUUU
ABXV02000042.1/18924-18998 GAAAGACGCGCAA-A-UUGUUAU--------CAUCCCUAAUUCU-CUAAG-AGA-U--UUUUUA----UUU-GGCCAC---UUAAU-------GUGGCCACUUCU
AC192956.2/2979-2910       GCAAGACGCGCA---UUUGUUAU--------CAUCCUUAGGUU---AUAC-AGA-UG-UUU-U-----UUU-GGCCACA--UA-AU------AGUGGCC--UUUU
AJ628152.1/358-278         GAAAGACGCGCA---UUUAUUAUCA-----UCAUCCCUAAUUAUCAUUAUCAGA-U-AUUU---C--UUUU-GGCCACAUUACUCA------UGUGGCC--UUUU
AM942759.1/433511-433436   G-AAUACGCGCAAAA--UGUUAU--------CAUCCCUAUUUC--UCUA-UAGA---AUUU--A-----UUCAGCCACA--CAAAUUU-UAGUGUGGCU--UUUU
#=GC SS_cons               ::::::::::::...::::::::::.....:<<<<-<<<____..._>>>.->>.>>.---..-...----.<<<<<<<.._____......>>>>>>>..::::
#=GC RF                    GAAAGACGCGCA...UUUGUUAUCA.....UCAUCCcUguuuu...ucAg.AGA.UG.UUU..A...uUUU.GGCCACc..guaaa......gGUGGCC..UUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00079
#=GF ID   OmrA-B
#=GF PI   SraE_OmrA_OmrB; OmrA-B; SraE_RygA_RygB; SraE
#=GF DE   OmrA-B family
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   40.00
#=GF TC   42.90
#=GF NC   37.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli
#=GF RA   Argaman, L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF RN   [2]
#=GF RM   11445539
#=GF RT   Identification of novel small RNAs using comparative genomics and
#=GF RT   microarrays
#=GF RA   Wassarman, KM, Repoila F, Rosenow C, Storz G, Gottesman S
#=GF RL   Genes Dev 2001;15:1637-1651.
#=GF RN   [3]
#=GF RM   16359331
#=GF RT   Remodelling of the Escherichia coli outer membrane by two small regulatory
#=GF RT   RNAs
#=GF RA   Guillier M, Gottesman S
#=GF RL   Mol Microbiol. 2006;59:231-247.
#=GF RN   [4]
#=GF RM   20407422
#=GF RT   Two antisense RNAs target the transcriptional regulator CsgD to inhibit
#=GF RT   curli synthesis.
#=GF RA   Holmqvist E, Reimegard J, Sterk M, Grantcharova N, Romling U, Wagner EG.
#=GF RL   EMBO J. 2010;29:1840-1850.
#=GF WK   OmrA-B_RNA
#=GF SQ   23


CP000653.1/3580539-3580454   CCCAGAGGUAUUGAUUGGUGAGA--AUUCUAAGUACG--------G-AAU-CGU-ACUCA-----------UCUCUUGCACCAGCCUGCGCA--G--AUGCGCAGGUUUUUUUU
U00096.2/2974211-2974124     CCCAGAGGUAUUGAUUGGUG--AGAUUAUUCGGUACG--------CUCUU-CGU-ACCCUG---------U-CUCUUGCACCAACCUGCGCG--G--AUGCGCAGGUUUUUUUU
CP000822.1/3911889-3911803   CCCAGAGGUAUUGAUUGGUGAGA--UUAUUCGGUACG--------CUCUU-CGU-ACCUG-----------UCUCUUGCACCAACCUGCGCG--G--AUGCGCAGGUUUUUUUU
CP001063.1/2822249-2822336   CCCAGAGGUAUUGAUUGGUG--AGAUUAUUCGGUACG--------CUCUU-CGU-ACCCUG---------U-CUCUUGCACCAACCUGCGCG--G--AUGCGCAGGUUUUUUUU
CP001120.1/3152846-3152760   CCCAGAGGUAUUGAUUGGUGAGA--UUAUUCGGUACG--------CUCUU-CGU-ACCUG-----------UCUCUUGCACCAACCUGCGCG--G--AUGCGCAGGUUUUUUUU
CAAU01003337.1/82-1          CCCAGAGGUAUUGAUUGGUGAGA--UUAUUCGGUACG--------CUCUU-CGU-ACCUG-----------UCUCUUGCACCAACCUGCGCG--G--AUGCGCAGGU-----UU
BAAW01009601.1/708-621       CCCAGAGGUAUUGAUUGGUG--AGUUUUUUAAGUACG--------CUNUU-CGU-ACUGAU---------U-AUCUUGCACCGACCUGCGCG--G--AUGCGCAGGUUUUUUUU
CP000964.1/876436-876523     CCCAGAGGUAUUGAUAGGUG--AGUUUCUUAGGUACG--------CUCUU-CGU-ACUGAA---------C-GUCUUACACCGACCUGCGCG--G--AUGCGCAGGUUUUUUUU
ABVY01000003.1/33440-33350   CCCAGAGGUAUUGAUUGGUG--A--UAUAUCGAUGUG--------CUCUG-UAC-AUUGAAAC-----CAUUUGAUUACACCAACCUACGCG--G--AUGCGUAGGUUUUUUUU
BX950851.1/4090604-4090514   CCCAGAGGUAUUGAUUGGUG--A--UACAUCGAUGUA--------CUCUG-UAC-AUUGAAAU-----CAUUUGAUUACACCAACCUACGCG--G--AUGCGUAGGUUUUUUUU
CP000647.1/3563356-3563275   CCCAGAGGUAUUGAUAGGUG---------GAGUCAAC--------GUCAC-GUU-GACCAC---------UUUACUUACACCAGCCUGCGCA--G--AUGCGCAGGUUUUUUUU
AAYT01000006.1/84649-84555   CCCAGAGGUAUUAAUUGGUG--A--AUAAUCAACAUUCGCUGUGUAUCAAAGAUCGUUU-----------UUUAUUUGCACCGACCUACGCA--G--AUGCGUAGGUUUUUUUU
AM286415.1/3638400-3638306   CCCAGAGGUAUUAAUUGGUG--A--GUAAUCAACAUA--------CGCUG-UGU-GUUAAAGCCA-GUUUUUUAUUUGCACCGACCUACGCA--G--AUGCGUAGGUUUUUUUU
CP000826.1/4240050-4239958   CCCAGAGGUAUUGAUUGGUG--A--GAAAUCAGCAUA--------CUCUG-UAU-GUUGAAGCC---AUUUUCAAUUGCACCAACCUACGCG--G--AUGCGUAGGUUUUUUUU
AP008232.1/3424551-3424460   CCCAGAGGUAUUGAUUGGUG--A--GAAAUCAACAUA--------CUCUG-UAU-GUUGAAAC----CAUUUCAGUUGCACCAACCUACGCG--G--ACGCGUAGGUUUUUUUU
CU928158.2/2838351-2838269   CCCAGAGGUAUUGAUAGGUG---------GUGUCAAC-------UAUAAA-GUU-GACCAC---------UUGAAUUACACCAACCUGCGCA--G--AUGCGCAGGUUUUUUUU
CP000266.1/2983711-2983630   CCCAGAGGUAUUGAUAGGUG--A-------AGUCAAC--------UUCGU-GUU-GAGCAC---------AUGAAUUACACCAGCCUGCGCA--G--AUGCGCAGGUUUUUUUU
CP000783.1/443904-443986     CCCAGAGGUAUUGAUAGGUG---------AAGUCAGC-------GACUUA-GCU-GAUCAC---------AACACUUACACCAACCUGCGCG--G--AUGCGCAGGUUUUUUUU
AACY022553564.1/811-729      CCCAGAGGUAUUGAUAGGUG---------AAAUCAAC-------UUUCGG-GUU-GAUCAC---------UAGAAUUACACCAGCCUGCGCA--G--AUGCGCAGGUUUUUUUU
AL627277.1/51364-51280       CCCAGAGGUAUUGAUAGGUG--G-------AAUCAAC-------GUCAUU-GUU-GAUCAC---------ACGAAUUACACCAACCUGCGUAGAG--AUGCGCAGGUUUUUUUU
CP000880.1/4544687-4544771   CCCAGAGGUAUUGAUAGGUG--G-------AAUCAAC-------GUAGUC-GUU-GAUCAC---------ACGAAUUACACCAACCUGCGUA--GAAAUGCGCAGGUUUUUUUU
AALC02000012.1/55476-55571   CCCAGAGGUAUUAAUUGGUG--A--GUAAUCAACAUA--------CGCUG-UGU-GUUAAAAACCAGUUUUUGAUUUGCACCGACCUACGCA--G--AUGCGUAGGUUUUUUUU
ABWM02000033.1/204261-204176 CCCAGAGGUAUUGAUUGGUGAGA--AUUCUUAGUACG--------G-UUU-CGU-ACUCA-----------UCUCUUGCACCAACCUGCGCG--G--AUGCGCAGGUUUUUUUU
#=GC SS_cons                 :::::::::::::::<<<<<..<..------<<<<<<........_____.>>>.>>>---.........->------>>>>><<<<<<<<_.._..__>>>>>>>>:::::::
#=GC RF                      CCCAGAGGUAUUGAUuGGUG..a..uuaauaggcacg........cucuu.cgu.gccuAa.........uuuaaUUgCACCaaCCUgCGCa..G..AUGCGcAGGuUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00080
#=GF ID   yybP-ykoY
#=GF PI   SraF
#=GF DE   yybP-ykoY manganese riboswitch
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Barrick JE, Breaker RR
#=GF SS   Predicted; Barrick JE, Breaker RR
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   44.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.53 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0030145; manganese ion binding;
#=GF RN   [1]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF RN   [2]
#=GF RM   15096624
#=GF RT   New RNA motifs suggest an expanded scope for riboswitches in bacterial
#=GF RT   genetic control.
#=GF RA   Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M,
#=GF RA   Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR
#=GF RL   Proc Natl Acad Sci U S A 2004;101:6421-6426.
#=GF RN   [3]
#=GF RM   25794618
#=GF RT   The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory
#=GF RT   element.
#=GF RA   Dambach M, Sandoval M, Updegrove TB, Anantharaman V, Aravind L, Waters LS,
#=GF RA   Storz G
#=GF RL   Mol Cell. 2015;57:1099-1109.
#=GF RN   [4]
#=GF RM   25794619
#=GF RT   Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches.
#=GF RA   Price IR, Gaballa A, Ding F, Helmann JD, Ke A
#=GF RL   Mol Cell. 2015;57:1110-1123.
#=GF CC   This RNA was originally discovered in E. coli during a large scale screen
#=GF CC   and was named SraF [1]. The family was later found to exist upstream of
#=GF CC   related families of protein genes in many bacteria, including the the yybP
#=GF CC   and ykoK genes in B. subtilis. The specific functions of these proteins
#=GF CC   are unknown, but this structured RNA element may be involved in their
#=GF CC   genetic regulation as a riboswitch [2].
#=GF WK   yybP-ykoY_leader
#=GF SQ   29



AL954747.1/2722783-2722598   -------------C----------U-----------G-UUACAA-UUUGCCGGUCAUUGGGGAGUAGCCGCUCU----UC-------GUUU-C--------------------------------------------GAAGGGGCUUACGUCAACAUACUUGACC----GGCA------GGUCAUGGCGUAAGC-GGUUCUAAGCC-UGGCA----AGACCUUUGACCACAAUGCCUCCGAUUU----------------------------------------------------------------GGCCGGGGAGGCGUUGUGGUCAAUCGUCUGUA-AAC-CGGCCGGAGAACAUU---------
CU207211.1/3280200-3280389   CUGCUAUCAUUCGC----------C-----------C-C------------GAACAUUGGGGAGUAGCCGGCCU----UA------------GUCA---------------------------------------ACUAAGGGAUCUGCGUCAACAUUCUUGGCC----CGCA------GGCCAUGGUGCAGAUAGUCGCAAGAC----UUG----GCGAGACCAUCGCUCAAAUGACGACCGCAUGGGCCGGGGU----------------------------------------CGCUGUUUGCGCUUUGGUUAUUAUUCCGGCCCCAGAAAGUU--------------------------------
AEGR01000046.1/5080-4892     U------------UG-------UU---------------AGAAU-GCGCCCCGUCAUUGGGGAGUAGCCG-CUCU--UCA------C-----CGC-----------------------------------------GAAGAG-GCUUGCGUCAACACACUUGGUC----CAUC-----GGACCAUGGCGCAGGC-AGCUCCUGGCC-UGGCA----AGACCUUUGACCACGAAGCCUCCGUUUUGGCCGGGGAUG------------------------------------------CGUCGUGGUCAAUCGUCUCUGUACACCGGCCUUGGACAUU--------------------------------
CP000269.1/3948088-3948277   ------------------------------------------------------------------------CUGCUAU----------CAUUACGCCUGAACAUUGGGGAG-------UAGCCGGCCUUUGGCAACAAAGGAAUCUGCAUCAACACUCUUGGCA----CGCA------UGCCAUGGUGCAGAU-AGUCGCAAGA----CUU----GGCGAGACCAUUGAUCAAGUGACGACCGCAUG-------------------------------------------------------GGCCGGGGUCGUUGUUUGGUCUUUGGUUAUUCGUCCG-GCCCGAGA--AAGUC-------------
FP929140.1/858523-858335     ------------------------------------------------------------------------CU----GA-------UAUACUUCGCUGGUCAUUGGGGAG---------UAGCCGAUCUUCGCACUGAAGAUGCUUACGUCAACACACUUGGCC----CACA------GGCCAUGGCGUAAGC-GGUUCACACGC--UUGG----CAAGACCUUUGACCACAACGCCUCCGUAUUAAGGCU-----------------------------------------------GGGGAUGCGUCGUGGUCAAUUGUGUCUAAUCCAGCCUGAGA-AUC-GU----------------------
CP001013.1/98070-98260       -------------------------------------------------------------------------UC--GC--------UAUA-CUCGCGGCGCUUUCGUCAUUGG---GGAGUAGCCGCCCUGCGCCCGCAGGGGUUCGCGUCAACACACUUGACC----CUCA-----CGGUCAUGGCGCGAAC-AGCUCCAGAGC-CUGGC----AAGACCUUUGACCACACUGCCUCCGGAAGGGCCG---------------------------------------------------GGGAUGCCGUGUGGUCUCUGGUAUUCGCUGGCCCUUGGA-GAU-C-----------------------
AM406670.1/393403-393588     -------------------------------------------------------------------------UC--GC---------UAAUAUCCGCGCCUUCAUUGGGGAG----UAGCCGCCCUUCACCGUGGUGAAGGGGCUUGCGUCAACACACUUGGCC----GUCC------GGCCAUGGCGCAAGCAGUUCCUGGAC---UUGG----CAAGACCUUUGAUCACGAUGCCUCUGGUAUGG-------------------------------------------------------CCGGGGAGGCGCGUGGUCAUCGGUUGUACCGGCCAGG-GAU-CAU---------------------
CP000155.1/3815875-3815690   ------------------------------------------------------------------------UUG---CA-------UUAG-UAUGCCCGGCGUCACUGGGG------AGUAGCCUCUCUUCGCCCUGAAGAGGUUUGCGUCAACAUACUUGGCC----CACA------GGCCAUGGCGUAAAC-GGUUCCAUA-----ACU----UGGCAAGACCUUUGACUAUGCCGCACCGGUUGGGC-------------------------------------------------CGGGGCGUGGCGUAGUCAUAUGGUUAAUCCGGCCCA------------G--GAGAUUU-----------
ABSP01053999.1/668-852       C------------CGGUAGAAUCGC-----------G-C------------GGUCAUUGGGGAGUAGUCGCCCUC---UA-------CCCAG-----------------------------------------------AGGGGCUUGCGUCAACAUACUUGACC----GAUU------GGUCAUGGCGCAAGC-GGUUUCCUAG---CUUG----GCGAGACCUUUGACCAUAUCGCCUUCGGACUGGCCG------------------------------------------------GAGAAGCGGUGUGGUCAUUUGUCUUCUUCCGGCCAGGGAGCAC--C-----------------------
CP000555.1/403908-404093     A------------A----------UCGCGGCUCCCAC-C------------CGUCAUCGGGGAGUAGCCG-CCCU--GCA-------UCC--GUU-----------------------------------------GCAGGG-GCUCGCGUCAACACACUUGGCC----UGCA------GGCCAUGGUGCGAGC-AGCUUCCACAG--CCUG----GCAAGACCUUUGACCGCACAGCCUCCGCGUGGCC----------------------------------------------------GGAGAGGCCGUGUGGUCAUUGCGUCAUCCGGCCCAGGA-CCU-C-----------------------
CP000089.1/2431458-2431642   U------------C----------G-----------A-UAGAAUGUUCCUGAGUCAUUGGGGAGUAGCCGC-UCU--UCA-------AU---CU-------------------------------------------GAAGAGGCUUGCGUCAACAUACUUGGUC----AUUC------GACCAUGGCGUAAGC-GGUUUCUGCUU--GGCA----AGACCUUUGACCAUACUGCCUUCCGAAUGGCCGG---------------------------------------------------GGAGGUGGUGUGGUCAUUCGUCGAAUUCCGGCCAAGGAA-ACC-------------------------
CP000450.1/221379-221198     CUGGUA--CAAUUU----------U-----------C-A------------GGUCAUUGGGGAGUAGCCACUCUU---U--------AUCACA---------------------------------------------AAGAGGCUUACAUCAACAUACUUGACC----CACA------GGUCAUGGUGUAGGC-AGCCCUUCGCC-UGGCA----AGACCUUUGACUGCGAUGCUUCCACUAGGCCGGAGA-----------------------------------------------UGUAUCGUGGUCAAUCGUCUUUUCCGGCCAGGAAAUUC--------------------------------
AFQG01000103.1/17144-17325   C------------CGAUAUAAUCUA-----------G-C------------CAUCACUGGGGAGUAGCCGCUCA-----U-------UUUCC-----------------------------------------------UGAGGUUUACGUCAACAUACUUGAUG----CAUG------CAUCAUGGCGUAAAC-AGCGAUAUCGC-UUGGC----AAGACCUUUGAUCACUUUUUUCCGUUCAGACCGGA-------------------------------------------------GGAAAAGGUGAUCAUUCGUCUAUUGUCCGGUCGCGGUAUU-GA--------------------------
ADNR01000005.1/164179-163991 C------------CGUUAGAAUCGC-----------C-C------------GGUCACUGGGGAGUAGCCUUCCUU---CA-------UCCU-UU-------------------------------------------GAAGGAGAACGCGUCAACAUACUUGGCC----UCGU-----AGGUCAUGGCGCGUUC-GACCGUGUCG---GUUU----GGCGAGACCAUUGACGCACUGCCUCGUUCUGGUCGGAC-------------------------------------------GGGCGGCGGUGCGUCAUUGGUUUGUCAUCUACGUCCGACCGC------------------------------
ADGO01015088.1/632-820       ------------------------------------------------------------------------CGU--GU-----------AUGCUCCCGCCCCGUCAUUGGGGAGUAACCUCCUGCGGCGUUACGCCGCC-GGGCUUACAUCAACACACUUGGCC----GGUU-----GGGCCAUGGUGUAAGC-GGCUUCAGUG---CUUG----GUGAGACCUUUGAUCAUGUCGUUCCGGUAUGGGC----------------------------------------------------CGCGGACGGCGUGGUCAAUUGUGUCCUCCGGCCCUGAACGCU-------------------------
ABCT01000004.1/172288-172470 CGGUUA-ACAUACC----------A-----------U-C------------ACUCAUUGGGGAGUAGCCUC-CUU--UU-------CUCGA-----------------------------------------------AAAGGGCUUGCAUCAACAUACUUGGCC----CAAA------AGCCAUGGUGCAAGC-GGUUUCCACA---CUUG----GCAAGACCUUUGACUGCAUUUCCACCGCUUCGGCC--------------------------------------------------UGGGUGGAAUGUGGUCAUUUGGUUCUCAAGGCCGUGGAA-UUU-------------------------
CP000270.1/4748060-4747865   C------------CGUUAGAAUCCC-----------C-C------------GGUCACUGGGGAGUAGCCUUCCUU---CA-------UCGU-UU-------------------------------------------GAAGGAGAACGCGUCAACAUACUUGGCC----UUGC-----AGGUCAUGGCGCGUUC-GGCCGUGUCG---GUUU----GGCGAGACCAUUGACGCACUGCCUCGUUCUGGUCGGACGGGC-----------------------------------GGCGGUGCGUCAUUGGUUUGUCGUCUACGUCCGACCGUGGAGUUG-------------------------------
CP001052.1/4299894-4299707   C------------CGUUAAAAUCCC-----------C-C------------GGUCACUGGGGAGUAGCCUUCCUU---CA-------UCCAUU--------------------------------------------GAAGGAGAGCGCGUCAACAUACUUGGCC----UGCG------GGUCAUGGCGCGUUC-GACCGGGUCG---GUUU----GGCGAGACCAUUGACGCACUGCCUCGUUCUGGUCGGACG-----------------------------------------GGCGGCGGUGCGUCAUUGGUUUGUUAUCGACGUCCGACCGC--------------------------------
CR555306.1/995584-995774     ------------------------------------------------------------------CCGG-UAG----AA-------UUCG-CGCCGUCAUCAGGGAGUA-----------GCCGCCUGCGAGCCUUCGCAGGGACCACGUCAACAGACUUGCGC----G--U-----CGCGCAUGGCGUGGCCAGCCUUCGGGCCUGGCGA----GACUUUUGGCUGCAUGCCCUCCGAUUUUUC-----------------------------------------------------------GGGCCCGGGAGGCGUGCGGUCAUCGGUCAUCAGCC-GGC-CCGG--AGAACCUG----------
CP002021.1/2050633-2050454   ACAC------UAAA----------A-----------A-U------------AGUCAUUGGGGAGUAGCUG-CCCU---C--------CGAAUGCG-----------------------------------------AGAGGG-ACCUGCGUCAACAUACUUGCCU----CACA------AGGCAUGGCGCUGGU-GAU--UCCAU---AUUU----GGCAAGACCUUUGACCGAAGCGCCUCCGUUGGGCC--------------------------------------------------GGAGAAGCGUUCGGUCAUUGUGUUCUUCCGGCCCGGAGU-CAU-C-----------------------
AACY020053177.1/876-690      ------------------------------------------------------------------UUGU-UAU----AA-------UUUAAAUGUCACUAGGGAGUAGC-----------UUCUCUUCUCUACAGAAGAU-GGCUUACAUCAACAUACUUGAGC----UUAG------GCUUAUGGUGUAAGC-GGUUUAAAU-----ACU----UGGCAAGACUUUUGACUACAAACACUUACUUAGGCUG----------------------------------------------UGGGUGCGUUGUAGUCAUUUGUUUAUGUCACAGCCUAGAGG-ACU-------------------------
CP001616.1/2283380-2283567   ------------------------------------------------------------------UCG--UUA----UA-------CUGC-GCCGGUCAUUGGG---------------------GAGUAGCCUCCUUUAGGGUUUGCAUCAACAGACUUGACC----CUCA-----CGGUCAUGGUGCAAAC-AGUGAUUCGU---CAUU----AAAACGGAUACACCUGGCAAGACCUUUGACCAUACCCUGUGCG----------------------------------GCCGGACAGGUGUGUGGUCAAUGGAAGUUUUCCGGCCAUGGAGUAUC-----------------------------
AEWG01000141.1/70250-70056   -------------------------------------------------------------------------C----UA-------GAAUC-----------------------------------------------GCG-CCCGCACUCGUCAUCGGGGAGUAGCC----GCCCUGCCGCCCGG---CAGG-GGUCCGCGCC----AAC----ACGCUUGGCCCUCAGGGGCCAUGGUCCGGACAGCCCCCAGCCUGGCAAGACCGCUGACUGCGCCGCCUCCGAAUGGGCCGGGGUCGCGGCGUGGUCAAGCUCCGGUCAUGCCGGCCCGUAUCGG-AUU-------------------------
CP000103.1/662385-662565     C------------A----------A-----------GU-AGAAU--AUUCCGGUCAUCGGGGAGUAGCUU-CCUUC-CG-------UCGA--AU------------------------------------------AGAAGG-GCUUGCAUCAACAUACUUGACC-----CGU------GGUCGUGGUGCAAGG-AGUUCGUGCCU-GGCAA----GACCUUUGACCACAUUGUCUCCGGAAGGGCGGG-----------------------------------------------------GAGAAGCCUGGUCUCGCUUCUUGUCCGGCCUGGAGCGU-A---------------------------
AF270169.1/2621-2476         A------------A----------A-----------A-C------------UGUCAGAGGGGAGUAACUUGAGAA---UA-------GUUAUUGAAUGCAUUUAAA-------------------CCGAUAAUAACUAUUCAACACUUUGUCGUCAUUACGAAGA----UAAG------UCUUCCGGUAAAGUG-GGCAAA-----------AAU--------------------------------------------------------------------------------------------------------------------------AUU-GCU-AAGU--GAGACCUUUGCUAUUAAA
AL591977.1/131463-131588     A------------C----------A-----------A-A------------UGUCAGAGGGGAGUAGCG-CUGAU---UA------GCUUUUU--------------------------------------------AAUCAGGAUAAAGUCGUCAUUACAUGAU---AGAGA-----UAUCAUCGGUUUUAUC-ACAUUUA----------ACUU------------------------------------------------------------------------------------------------------------------------UAAA-UGU-UAGC--GAGACCUUUGCCUUUACG
AF109909.2/85-201            U------------U----------A-----------C-G------------GAGUAAAGGGGAGUAGCG-UCAG----G--------GAAA-----------------------------------------------CCUGAAACAAAGUCGUCAUUACAUGGA----GUAU------UCCAUCGGCUUUGUU-GGCAUAA----------UGA-------------------------------------------------------------------------------------------------------------------------UUAU-GCU-UAGC--AAGACCUUUGCCAUAUUU
Y14370.1/1315-1188           C------------A----------U-----------U-U------------UGUCAGAGGGGAGUAACUUAAGAA---UCAUGACCGUAUAAAU------------------------------------------GAUUCGACACUUUAUCGUCAUUACGAAG-----AUAU-------CUUCCGGUAAAGUG-GGCAAU-----------UAA--------------------------------------------------------------------------------------------------------------------------AUU-GCU-UAGU--GAGACCUUUGCUAUUUAU
AL596167.1/48063-48187       A------------C----------A-----------A-A------------UGUCAGAGGGGAGUAGCG-CUGAU---UA------GCUUUUA---------------------------------------------AUCAGGAUAAAGUCGUCAUUACAUGAU---AGAGA-----UAUCAUCGGUUUUAUC-ACAUUUA----------ACUU------------------------------------------------------------------------------------------------------------------------UAAA-UGU-UAGC--GAGACCUUUGCCUUUAUG
#=GC SS_cons                 :............:..........:...........:.:............:::::::::::::::::::.<<<_...__......._______..........................................___>>>,<<<<<<<<<<-------<<<<<....____......>>>>>>>>>>>>>>>.<<<<<<<___...____....__________________________________...................................................___________________________________>>>>.>>>.........................
#=GC RF                      c............c..........a...........c.c............gGUCAuuGGGGAGUAGCcg.ccuU...UA.......uuuauuU..........................................ugAaggGGcuugCgUCAACAUACUUGgcC....caca......GgcCAUGGcGcaagC.Gguuccagcc...guuu....gggcauuccucucacguaCcgCCgucuggucGGC...................................................GggGgGgGguggggguuuugUuuugcccgcgccuaugga.acU.........................
//
# STOCKHOLM 1.0

#=GF AC   RF00081
#=GF ID   ArcZ
#=GF PI   ArcZ_RNA; SraH
#=GF DE   ArcZ RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD
#=GF GA   66.00
#=GF TC   67.00
#=GF NC   65.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF CC   This RNA was discovered in E. coli during a large scale screen [1]. SraH
#=GF CC   expression is highly abundant in stationary phase, but low levels could be
#=GF CC   detected in exponentially growing cells as well [1]. The function of this
#=GF CC   RNA is unknown.
#=GF WK   ArcZ_RNA
#=GF SQ   9


X53315.1/2472-2365         GUGCGGCCUGAAA-AACAGUGCUGUGCC--CUUGUAACUCAUCAUAAUAAUUUAC---GGCGCAGCCAAGAUUUCCCUGGUGUUGGCGCAGUA-UUCGCGCACCCCGGUCUAGCC
CP000653.1/3944323-3944431 GUGCGGCCUCAUUCU-UAAGGCAGCGUCCAUGCGAAA-ACAACACAAAGAA-UCA---GGCGCGGCCACGAUUUCCCUGGUGUUGGCGCAGUAUUUCGCGCACCCCGGUUUAUCC
CP000647.1/3973082-3973190 GAGCAAUCCACUU-C-UUCGGUUGCGCCA-CGUAACA-ACAUCACUCAAAC-AACACUGGCUCAACCACCAGUUCCCUGGUGUUGGCGCAGUA-UUCGCGCACCCCGGUCUGUCC
AL627278.1/138905-139009   GUGCGGCCUGAAA-A-CAGGACUGCGCC--UUUGACA-UCAUCAUAAUAAG-CAC---GGCGCAGCCACGAUUUCCCUGGUGUUGGCGCAGUA-UUCGCGCACCCCGGUCAAACC
CP000468.1/3643167-3643274 GUGCGGCCUGAAA-AACAGUGCUGUGCCC-UUGUAAC-UCAUCAUAAUAAUUUAC---GGCGCAGCCAAGAUUUCCCUGGUGUUGGCGCAGUA-UUCGCGCACCCCGGUCUAGCC
BA000007.2/4092930-4093037 GUGCGGCCUGAAA-AACAGUGCAGUGCCC-UUGUAAC-UCAUCAUAAUAAUUUAC---GGCGCAGCCAAGAUUUCCCUGGUGUUGGCGCAGUA-UUCGCGCACCCCGGUCUAGCC
CP000946.1/537783-537676   GUGCGGCCUGAAA-AACAGUGCUGUGCCC-UUGUAAC-UCAUCAUAAUAAUUUAC---GGCGCAGCCAAGUUUUCCCUGGUGUUGGCGCAGUA-UUCGCGCACCCCGGUCUAGCC
CP001113.1/3472442-3472546 GUGCGGCCUGAAA-A-CAGGACUGCGCC--UUUGACA-UCAUCAUAAUAAG-CAC---GGCGCAGCCACGAUUUCCCUGGUGUUGGCGCAGUA-UUCGCGCACCCCGGUCAAACC
CP000826.1/4809172-4809277 AUGUUUAGGAAUUCU-CUACAACCUGCUC-GACCAGA-ACAUUAAAACCAA-UAC----GCAGGUUCACAAUUUCCCUGGUGUUGGCGCAAUA-UUCGCGCACCCCGGCCUAGGU
#=GC SS_cons               :::::::::::::.:.::::<<<<<<<<_._______._____________.___...>>>>>>>>------------<<<----<<<<____.___>>>>>>>:::::::::::
#=GC RF                    GUGCggccuaAaa.a.cagugcuGcGCCc.uuuuAaA.uCAUCAuAAuaAu.uAC...GGCgCagcCAcgAUUUCCCUGGUGUUGGCGCAGUA.UUCGCGCACCCCGGUCUAgcC
//
# STOCKHOLM 1.0

#=GF AC   RF00082
#=GF ID   SraG
#=GF DE   SraG RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   52.90
#=GF NC   39.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF RN   [2]
#=GF RM   27495318
#=GF RT   The small RNA SraG participates in PNPase homeostasis.
#=GF RA   Fontaine F, Gasiorowski E, Gracia C, Ballouche M, Caillet J, Marchais A,
#=GF RA   Hajnsdorf E
#=GF RL   RNA. 2016;22:1560-1573.
#=GF CC   This RNA was discovered in E. coli during a large scale screen [1].
#=GF CC   Evidence was found for specific cleavage of this RNA [1].
#=GF WK   SraG_RNA
#=GF SQ   7


Y10692.1/1974-1797         CUUCACACUGCAUCCUCGCGACUAAUGACAACCCUUAACCCCCAUGA-GU---UAAAGUCUCUCAUUAGCCGCGCGAACCUCUGCACCGGAAGAUCCUAUGU-UUUAAAAAUA---UAGAACAACAAUAUACUAGCGUAUUUUAUCAUUGCUUCU--UAGAAAAAAGGGGCC-AAUUUGGCCCUUUCUC
X01073.1/600-431           --UC-UGC-GCAUCCUCGCGACUAAUGACAACCCUAACCCAGCUCUAUGUGGGUAAAGCCUCUCAUUAGCCGCGCGAACCUCUGCAACGGAAGAUCAUUC-----AUAGC------AACAAUA-CAUUAGUUUCCAGUGA-AU-UGCUGCCGUCAGCUUGAAAAAAGGGGCC-ACUCAGGCCCCCUUUU
X76069.1/670-501           CUUCAUGC-ACAUCCUCGCGACUAAUGACAGGUCUCAUUCCU--UUAAG------CA--CUCUCAUUAGCCGCGCGAACCUCUGUAACCGAAGAGCCUUACCCAAAAAUC------AUCAUUAGCAUUCUUAUGCUGCUACAUAUGAUGAUUUCU-CAGAAGAAAAGGGGCC-AUAUAUGGCCCCUUUC
BX936398.1/570028-569847   CUUCACACUGCAUCCUCGCGACUAAUGACAAUCCUUAACUUUCAUUAAGU---UAAAGUCUCUCAUUAGCCGCGCGAACCUCUGCAUUGGAAGAUCCUAUUU-AUAAAUCUUAUAUAAUAAUAACAAUAUACUAACGUAUUCUAUCAUUACUUCU--UAGAAAAAAGGGGCC-AACUUGGCCCCUUUCU
BX571874.1/71730-71899     CUCCAUGCCACAUCCUCGCGACUAACGACAGGUCUUACUCCC--UUAAG------CA--CUCUCAUUAGCCGCGCGAACCUCUGUAACUGAAGAGCCUAAAC-AAAAACC------ACCACCAGCAUUUUUGUGCUGUUAUCUAUGAUGGCUUCU-CAGAAGAAAAGGGGCC-CUAUAUGGCCCCUUUC
BX950851.1/784001-783834   CUUUGCACUACAUUCUCACGACUAAUGACAACCCUUAUCUUGCUUAUGCAGA-UAAAGCCUCUCAUUAGCCGCGCGAACCUCUGUAAUGAAAGAUCCUAU------------------UAACAACAAUACACUACUCUGUUUUGCUAAUGCUUCC--UAGAAGAAAGGGGCCAAAAGAGGCCCCUUUCC
CP001120.1/3466753-3466920 CUUC-UGC-GCAUCCUCGCGACUAAUGACAACCCUAACCCUG--AUAUGGG--UAAAGCCUCUCAUUAGCCGCGCGAACCUCUGCAACGGAAGAUCAUUC-----AUAGC------AACAAUA-CAUUAGUUUCCAGCGA-AU-UGCUGCCAUCUGCUGGAAAAAAGGGGCC-AUGAAGGCCCCCUCUU
#=GC SS_cons               <<<<-<<--<<<----<<<<-<<<<<<<______________________..._________>>>>>>>--->>>>------>>>-->>>>>>,,,,,<<__._______......______________________>>,,,,,,,,,,,,,,,.,,,,,,,,,,<<<<<<._____>>>>>>:::::
#=GC RF                    CUuCAcgCugCAUCCUCGCGACUAAuGACAAccCUuAuccuuCuuuAaGu...UAaAGuCUCUCaUUAGCCGCGCGAACCUCUGcAacgGaAGAuCcUucuu.auAaAuc......AacAauAaCAuUauuuUacuGUgaUaUAUgAUgaCuUCu.CuagAAAAAAGGGGCc.AuauagGCCCCuUUUc
//
# STOCKHOLM 1.0

#=GF AC   RF00083
#=GF ID   GlmZ_SraJ
#=GF PI   SraJ
#=GF DE   GlmZ RNA activator of glmS mRNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Gardner P; 0000-0002-7808-1213
#=GF SE   Published; PMID:18351803
#=GF SS   Published; PMID:18351803
#=GF GA   40.00
#=GF TC   40.40
#=GF NC   37.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00011
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF RN   [2]
#=GF RM   18351803
#=GF RT   Two seemingly homologous noncoding RNAs act hierarchically to activate
#=GF RT   glmS mRNA translation.
#=GF RA   Urban JH, Vogel J
#=GF RL   PLoS Biol. 2008;6:e64.
#=GF RN   [3]
#=GF RM   18334534
#=GF RT   The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of
#=GF RT   glmS expression and is subject to regulation by polyadenylation in
#=GF RT   Escherichia coli.
#=GF RA   Reichenbach B, Maes A, Kalamorz F, Hajnsdorf E, Gorke B
#=GF RL   Nucleic Acids Res. 2008;36:2570-2580.
#=GF RN   [4]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   This RNA was discovered in E. coli during a large scale screen [1]. The
#=GF CC   sraJ gene was expressed in early logarithmic phase, but its level
#=GF CC   decreased with cell growth [1]. Specific cleavage products of this RNA
#=GF CC   were found [1]. The function of this RNA is unknown. Identified in
#=GF CC   Yersinia pseudotuberculosis as Ysr248/153/sR016 [4].
#=GF WK   GlmZ_RNA
#=GF SQ   21


AM286415.1/218914-219136   GUAGAUGCUCAUCCCACUUAUUAUGAUAGCCUGGUUUUUAUAGCCAAUUUAGCUUCAUAAACCCA-GGGAUGACGC-AGAGCCGAUUUUAGGGUGCCUAUUGUCCAUGUAAACGAUGUUGAAUAUCUU------------CAUCA--CAUACCGGGCAUAACGUUGAGUGAGGCACCGACAU-UGUUGUCUGU-AGACCUGAAAA---UUUCAGACGCUUGCCCUUAU-----CGGCAAGCGUUUUUUU
BX571874.1/204902-204687   GUAGAUGCUCAUCCUAUUUCUUAUGAUUGCAUAU-----------------GCUUCAUAAACCCA-GGGAUGAUGC-AGAGCCGAUUAU-CGGUGCCUAUUGUCCAUGUCACAGAUGAGUAAGAUAUAACCCUCUUU--UCAUCG--CCGACCGGACUCAACGUUGAGUGAGGCACU-AUCC-----GUCUGU-AGACCUGAUUGU--AUUUGUACACCUAUCUUUAUUUUUAAGGUAGGUGUUUUUUU
BX950851.1/4684949-4684740 GUAGAUGCUCAUUCCACCUUCUAUGCUUGCUUCG-----------------GCUUCAUAAUCCUG-GGAAUGACGC-AGAGCCAAUUUUGAGGUGCCUAUCGUCCAACUC-CAGAUGAAGAUGCAAAUCU---------CCAUCGGGCUUUCCGGACAUAACGUUGAGUGAGGCACC-AUUC-UGUUGUCUGACAGACCUGAUA----UUUUCAACGCUUACCGUUUA----UCGGUAAGCGUUUUUUU
CP000038.1/4195535-4195740 GUAGAUGCUCAUUCCAUCUCUUAUGUUCGCCUUA---------------GUGCCUCAUAAACUCC-GGAAUGACGC-AGAGCCGUU--UACGGUGCUUAUCGUCCA-CUGACAGAUGUCGC--UUAUGCC---------UCAUCAGACACCAUGGACACAACGUUGAGUGAAGCACC--CAC-UGUUGUCAUACAGACCUG--------UUUUAACGCCUGCUCCGUA-AUAAGAGCAGGCGUUUUUUU
CP000647.1/4707421-4707632 GUAGAUGCUCAUUCCAUCUCUUAUGUUCGCCUUC---------------GUGCCUCAUAAACUCC-GGAAUGAUGC-AGAGCCGUUCUUACGGUGCUUAUCGUCCA-CUGACAGAUGUCGCAUUUAUGCC---------UCAUCAAACACCAUGGACAUUACGUUGAGUGAAGCACCCAAUU-UGUUGUCAAACAGACCUG--------UUUUAACGCCUGCCCUGAU-UUCAGCGCAGGCGUUUUUUU
CP000653.1/4326971-4326771 GUAGAUGCUCAUUCCACCUCUUAUGUUCGCCUUA---------------GUGCCUCAUAAACUCA-GGAAUGACGC-AGAGCCAUU--UACGGUGCUUAUCGUCCA-CCGACAGAUGUCGC--UUCGGCC---------UCAUCAAACACCAUGGACACAACGUUGAGUGAAGCACCAAAUA-UGUUGUCGAAUAGAUCUG---------UUUAACGCCUGCUUUU-------UAGCAGGCGUUUUUUU
CP000720.1/222226-222448   GUAGAUGCUCAUCCCACUUAUUAUGACAGCUUGGCCAUUAAGGCUAAUUUAGCUUCAUAAACCCA-GGGAUGACGC-AGAGCCGAUUUUAGAGUGCCUAUUGUCCAUGUAACCGAUGU-UGAGUAAUG-----------UCAUCA--CAUACCGGGCAUAACGUUGAGUGAGGCACUGAUAU-UGUUGUCUAUC-GACCUGAAAA---UUUUAGACACUUGCCCUUUU-----CGGCAAGUGUUUUUUU
M90498.1/3570-3743         GUAGAUGCUCAUUCCAUCUCUUAUGUUCGCCUUA---------------GUGCCUCAUAAACUCC-GGAAUGACGCGAGAGCCGUU--UACGGUGCUUAUCGUCCA-CUGACAGAUGUCGC--UUAUGCC---------UCAUCAGACACCAUGGACACAACGUUGAGUGAAGCACCCACUU--GUUGUCAUACAGACCUG-------------------------------------------UUUUA
U00096.2/3984455-3984661   GUAGAUGCUCAUUCCAUCUCUUAUGUUCGCCUUA---------------GUGCCUCAUAAACUCC-GGAAUGACGC-AGAGCCGUU--UACGGUGCUUAUCGUCCA-CUGACAGAUGUCGC--UUAUGCC---------UCAUCAGACACCAUGGACACAACGUUGAGUGAAGCACCCACUU--GUUGUCAUACAGACCUG--------UUUUAACGCCUGCUCCGUA-AUAAGAGCAGGCGUUUUUUU
ABAT01000008.1/60360-60582 GUAGAUGCUCAUCCCACUUAUUAUGACAGCUUGGCCAUUAAGGCUAAUUUAGCUUCAUAAACCCA-GGGAUGACGC-AGAGCCGAUUUUAGAGUGCCUAUUGUCCAUGUAACCGAUGUUGAGUAAUGU------------CAUCA--CAUACCGGGCAUAACGUUGAGUGAGGCACUGAUAU-UGUUGUCUAUC-GACCUGAAAA---UUUUAGACACUUGCCCUUUU-----CGGCAAGUGUUUUUUG
CP000034.1/3676029-3675823 GUAGAUGCUCAUUCCAUCUCCUAUGUUCGCCUUA---------------GUGCCUCAUAAACUCC-GGAAUGACGC-AGAGCCGUU--UACGGUGCUUAUCGUCCA-CUGACAGAUGUCGC--UUAUGCC---------UCAUCAGACACCAUGGACACAACGUUGAGUGAAGCACC-CACU-UGUUGUCAUACAGACCUG--------UUUUAACGCCUGCUCCGUA-AUAAGAGCAGGCGUUUUUUA
CP001138.1/4061393-4061600 GUAGAUGCUCAUUCCAUCUCUUAUGUUCGCCUUC---------------UGGCCUCAUAAACUCA-GGAAUGAUGC-AGAGCCGUU--UACGGUGCUUAUCGUCCA-CUGACAGAUGUCGC--UUACGCC---------UCAUCAAACACCCUGGACACAACGUUGAGUGAAGCACCCCUUUAUGUUGUCAUACAGACCUG--------UUUUGACGCCUGCCUCUUA--ACCGGGCAGGCGUUUUUUU
CP001120.1/4151577-4151784 GUAGAUGCUCAUUCCAUCUCUUAUGUUCGCCUUC---------------UGGCCUCAUAAACUCA-GGAAUGAUGC-AGAGCCGUU--UACGGUGCUUAUCGUCCA-CUGACAGAUGUCGC--UUACGCC---------UCAUCAAACACCCUGGACACAACGUUGAGUGAAGCACCCCUUUAUGUUGUCAUACAGACCUG--------UUUUGACGCCUGCCCCUUA--ACCGGGCAGGCGUUUUUUU
CP001144.1/4170255-4170462 GUAGAUGCUCAUUCCAUCUCUUAUGUUCGCCUUC---------------UGGCCUCAUAAACUCA-GGAAUGAUGC-AGAGCCGUU--UACGGUGCUUAUCGUCCA-CUGACAGAUGUCGC--UUACGCC---------UCAUCAAACACCCUGGACACAACGUUGAGUGAAGCACCCCUUUAUGUUGUCAUACAGACCUG--------UUUUGACGCCAGCCCCUUA--ACCGGGCAGGCGUUUUUUU
CP000826.1/198017-198236   GUAGAUGCUCAUUCCACCUCUUAUGUUUGCCUUA----------------GGCUUCAUAAACCCUGGGAAUGACGC-AGAGCCGAU-UUAAGGUGCCUAUUGCCCACCAGAACGAUGUCAGCGUUGCUUGCAGCCGCAGACAUCA--CACUCCGGGCAUAACGUUGAGUGAGGCACCGCCCC-UGUUGUCCUA--GACCUGAUUGCUUUUUUAUACACUUGCCACCG------CGGCAAGUGUUUUUUU
AAMJ02000024.1/58014-57808 GUAGAUGCUCAUUCCAUCUCUUAUGUUCGCCUUA---------------GUGCCUCAUAAACUCC-GGAAUGACGC-AGAGCAGUU--UACGGUGCUUAUCGUCCA-CUGACAGAUGUCGC--UUAUGCC---------UCAUCAGACACCAUGGACACAACGUUGAGUGAAGCACCCACUU--GUUGUCAUACAGACCUG--------UUUUAACGCCUGCUCCGUA-AUAAGAGCAGGCGUUUUUUU
CU928164.2/3094769-3094563 GUAGAUGCUCAUUCUAUCUCUUAUGUUCGCCUUA---------------GUGCCUCAUAAACUCC-GGAAUGACGC-AGAGCCGUU--UACGGUGCUUAUCGUCCA-CUGACAGAUGUCGC--UUAUGCC---------UCAUCAGACACCAUGGACACAACGUUGAGUGAAGCACC-CACU-UGUUGUCAUACAGACCUG--------UUUUAACGCCUGCUCCGUA-AUAAGAGCAGGCGUUUUUUU
AALE02000016.1/52978-53200 GUAGAUGCUCAUCCCACUUAUUAUGACAGCCUGGUUUUUAUAGCCAAUUGUGCUUCAUAAACCCA-GGGAUGAUGC-AGAGCCGAUUUUAGGGUGCCUAUUGUCCAUGUAAACGAUGUUGAAUAUCUU------------CAUCA--CAUACCGGGCAAAACGUUGAGUGAGGCGCCGACAU-UGUUGUCUGU-AGACCUGAAAA---UUUUAGACGCUUGCCCCUAU-----CGGCAAGCGUUUUUUU
AALC02000029.1/13844-13630 GUAGAUGCUCAUCUCACUUAUUAUGACAGCCUGGCUUUAUAG-------CCACUUCAUAAACCCA-GAGAUGAUGC-AGAGCCGAUUUUAGGGUGCCUAUUGUCCAUGUAAACGAUGUUGAAUAUCUU------------CAUCA--CAUACCGGGCAUAACGUUGAGUGAGGCGCC-AACA-UGUUGUCUGU-AGACCUGAAAA---UUUUAGACGCUUGCCGAAAA-----CGGCAAGCGUUUUUUU
AALD02000050.1/26165-26384 GUAGAUGCUCAUCUCACUUAUUAUGACAGCUUGGUCUUACCGCCAAUU-UAGCUUCAUAAACCCA-GAGAUGAUGC-AGAGCCAAUUUUAGGGUGCCUAUUGUCCAAGUAAACGAUGUUGAAUACCUU------------CAUCA--CAUACCGGGCAUAACGUUGAGUGAGGCGCCGACAU--GUUGUCGUA--GACCUGAAGA---UUUUAGACGCUUGCCGAAAA-----UGGCAGGCGUUUUUUU
AALF02000074.1/688-908     GUAGAUGCUCAUCUCAUUUAUUAUGAUAGCGUGGUGUUAUAGCCAACU-UAGCUUCAUAAACCCA-GAGAUGAUGC-AGAGCCGAUUUUAGGGUGCCUAUUGUCCAUGUAAACGAUGUCGAAUAUCUU------------CAUCA--CAUACCGGGCAUAACGUUGAGUGAGGCGCCGACAU-UGUUGUCUGU-AGACCUGAAAA---UUUUAGACGCUUGCCUUUC------CGGCAAGCGUUUUUUU
#=GC SS_cons               <<---<<<<<<<<<<-----<<<<<---<<____...............__>>-->>>>>-----.>>>>>>>->>.>-->>,,,,,,,,,(((((((,,,<<<<--------<<<<_____________........._>>>>-..------>>>>,,,<<_____>>,))))))),,,,,.,,,,<<<_____>>>,,,,,,,...,,,,,<<<<<<<<<<<____.....>>>>>>>>>>>:::::
#=GC RF                    GuAGAUGCUCaUcCCAuuUcuUaUGuUuGCcUua...............uuGCuUCAuAaACuCa.GGgAuGAuGC.AGAgCCGaUUuUAcGGuGCcUAUuGuCCAucUaAcaGaUGUcgaauuuauucc.........uCAuCA..CAuacuGGaCAuAaCGUUGAGuGAgGCaCCgauuu.UGUUGUCuuacAGACCUGAaaa...uUUUagaCGCcuGCccuuua.....ggGCagGCGucUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00084
#=GF ID   CsrC
#=GF PI   SraK
#=GF DE   CsrC RNA family
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD
#=GF GA   61.00
#=GF TC   64.70
#=GF NC   58.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 16.55 -Z 549862.597050 CM SEQDB
#=GF CL   CL00106
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   12694612
#=GF RT   A novel sRNA component of the carbon storage regulatory system of
#=GF RT   Escherichia coli.
#=GF RA   Weilbacher T, Suzuki K, Dubey AK, Wang X, Gudapaty S, Morozov I, Baker CS,
#=GF RA   Georgellis D, Babitzke P, Romeo T
#=GF RL   Mol Microbiol 2003;48:657-670.
#=GF RN   [2]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF CC   The 245 nucleotide sRNA of Escherichia coli, CsrC, was discovered using a
#=GF CC   genetic screen for factors that regulate glycogen biosynthesis. CsrC RNA
#=GF CC   binds multiple copies of CsrA Pfam:PF02599, a protein that
#=GF CC   post-transcriptionally regulates central carbon flux, biofilm formation
#=GF CC   and motility in E. coli. CsrC antagonises the regulatory effects of CsrA,
#=GF CC   presumably by sequestering this protein. The discovery of CsrC is
#=GF CC   intriguing, in that a similar sRNA, CsrB, performs essentially the same
#=GF CC   function. Both sRNAs possess similar imperfect repeat sequences (18 in
#=GF CC   CsrB, nine in CsrC), primarily localised in the loops of predicted
#=GF CC   hairpins, which may serve as CsrA binding elements. Transcription of csrC
#=GF CC   increases as the culture approaches the stationary phase of growth and is
#=GF CC   indirectly activated by CsrA via the response regulator UvrY [1]. This RNA
#=GF CC   was also discovered in E. coli during a large scale screen [2]. The gene
#=GF CC   called SraK, was highly abundant in stationary phase, but low levels could
#=GF CC   be detected in exponentially growing cells as well [2].
#=GF WK   CsrC_RNA_family
#=GF SQ   4



CP000647.1/4572620-4572875 CAACGGCGGGGAUGCUGAAAGGAUUAG-GACUC-AGGACGAGGAGUCAGGAAGCGCCAGGAGGCGAAGACCACAGGAUAGUCAGGAUGACGCGCGUCUUGGAGACGUU-UUACAGGGAAAAGGAAGAA-ACAGGGACCGUUGGACGCUAAGGGAAAGACAGGGUGAGUCGUUAGCGAACAGGGAAAGAAGAGCCCGUUAAGGGUGGUCAGUGA-GGAAAAAGGCGACAGAGUAAUCUGUCGCCUUUUUUCUUUGCUUGCUU
CP000653.1/4458195-4457944 CCACGGCGAGGAUGCCAUCAGGAUUA-UGACUUAAGGAUGA-GGGUC-AGGAGCGCCAGGAGGCGAAGACU-CAGGAUUACAAGGACGACA--CGCC-AGGAGGCG-UUUAAAAGGGAAAUGGAACCGUAUCACGGAUGAUUG-CGCUAAAGGAUAAACAGGGUUAGUUGUUGGCGAACAGGGAUUGUAAAACCCGUUUAGGGUGGUGAGUCAGGAAAAAAGGCGACAGAUUGCUCUGUCGCCUUUUUUCUUUGCUUGCUU
CP001127.1/4088494-4088746 AUAG--CGAGGACGCUAACAGGAUCAACGACUC-AGGAUGA-GGGUC-AGGAGCGCCAGGAGGCGAAGACA-CAGGAUUGUCAGGAAGACAAACGUC-CGGAGACGUUAGUAAAAGGAAAUGGAAACA-ACAUGGAAUGUUCCAGGCUAAGGGAAAAACAGGGCGUGUUGAUAGCCAACAGGGAUGGUGGAACCCGUUAAGGGUCGUGAGUCAAGAAAAAAGGCGGCAGAUUACUCUGUCGCCUUUUUUCUUUGCUUGCUU
DQ328981.1/142-396         ACAUAGCGAGGACGCUAACAGGAUCAACGACUC-AGGAUGA-GGGUC-AGGAGCGCCAGGAGGCGAAGACA-CAGGAUUGUCAGGAAGACAAACGUC-CGGAGACGUUAGUAAAAGGAAAUGGAAACA-ACAUGGAAUGUUCCAGGCUAAGGGAAAAACAGGGCGUGUUGAUAGCCAACAGGGAUGGUGGAACCCGUUAAGGGUCGUGAGUCAAGAAAAAAGGCGGCAGAUUACUCUGUCGCCUUUUUUCUUUGCUUGCUU
#=GC SS_cons               ::::<<<<____>>>>,,,,,,,,,,,<<<<<<._______.>>>>>.>,,,,<<<<____>>>>,,<<<<.______>>>>,,,,,,,,,,<<<<<.____>>>>>,,,,,,,,,,,,,,,,,,,<<.<<<<<--<<<<<<<________>>>--->>>>-->>>>>>>,,,,,,,<<_______>>,,,<<<<_____>>>>,,,,,,,,,,<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>:::::::::::
#=GC RF                    auAugGCgaGGAcGCcaacAGGAUuAacGaCcc.AGGAuGA.ggGuC.gGgAGCGCCAGGAGGCGAAgacc.CAGGAUggucAGGAaGACaaaCGuC.uGGAGaCGuUauuAaAaGGAAAuGGAAacg.acccgGacuGuuccAcGCUAAgggaaAaaCagGGcgggucguUaGCgAaCAGGGAuaGuagAaCCCGUUaAGGGugGUgAGUcAaGaaaaaaGGCGaCaGauUacuCuGuCGCCuuuuuuCUUUGCUUGCUU
//
# STOCKHOLM 1.0

#=GF AC   RF00085
#=GF ID   SNORD28
#=GF PI   U28
#=GF DE   Small nucleolar RNA SNORD28
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR
#=GF GA   50.00
#=GF TC   53.80
#=GF NC   49.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300712;
#=GF DR   snoopy; Oryctolagus_cuniculus300343;
#=GF RN   [1]
#=GF RM   8559254
#=GF RT   A mammalian gene with introns instead of exons generating stable RNA
#=GF RT   products.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Nature 1996;379:464-466.
#=GF RN   [2]
#=GF RM   8962077
#=GF RT   A small nucleolar RNA requirement for site-specific ribose methylation of
#=GF RT   rRNA in Xenopus.
#=GF RA   Tycowski KT, Smith CM, Shu MD, Steitz JA
#=GF RL   Proc Natl Acad Sci U S A 1996;93:14480-14485.
#=GF CC   U28 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U28 is encoded within the U22 snoRNA host gene
#=GF CC   (UHG) in mammals [1] and is thought to act as a 2'-O-ribose methylation
#=GF CC   guide for ribosomal RNA.
#=GF WK   Small_nucleolar_RNA_SNORD28
#=GF SQ   20


U40580.1/1686-1760         GUCAGAUGAUUUG-AAUUGAUAAG--------CUGAUG-UUCUGUGAGGU--ACAAAAGUUAAUAGCAUGUUAGAGUUCUGAUGGCA
U40654.1/1539-1614         GUCAGAUGAUUUG-AAAUGAUGACAC------UGAACA-CUCCGUGAAG---GUGUGAAUUUAUAGCAUGUUAGAGUUCUGAUGGCA
U72860.1/1-83              UCCAAGUGAUGACUGAAUGAAGUCUCGUUCGUCUGAAA-AUCUUUGAAG---AAUACUCCUUUUAGCAUGGUGGAGUUCUGAUGGAA
U72861.1/1-83              UCCAAGUGAUGACUGAAUGAAGUCUCGUUCGUCUGAAA-AUCUUUGGAG---AAUACUCCUUUUAGCAUGGUGGAGUUCUGAUGGAA
AAFC03036502.1/31461-31386 GUCAGAUGAUUUG-AAUUGAUAAUGC-------UGAUC-CUCUGUGAGGU--ACCACAGUUAAUAGCAUGUUAGAGUUCUGAUGGCA
AAYZ01222735.1/190-115     GUCAGAUGAUUAGAGACAAUCAAA--------CUGAUG-UUCUGUGAGGC--CUGACAAUUAAUAGCAUGUUAGAGUUCUGAUGGCA
AAPN01030027.1/6432-6357   GCCAGAUGAUUUC-AAUCCUUAUUUU------CUGAUG-CUCCGUGAGG---UACAGAUAUCAUAGCAUGUUAGAGUUCUGAUGGCA
AADA01343082.1/14302-14228 UUCAGAUGAUUUG-AAUUGAUAAG--------CUGAGG-UUCUGUGAGGA--AUGACAGUUAAGAGCAUGUUAAAGUUGUUAUGAAA
AAQQ01777657.1/182-256     GUUAAAUGAUUUG-AAUUGAUGAG--------UUGAUG-CUCUGUAAGGU--AUAACAGUUAAUAGCAUGUAAGAGUUCUGAUGAAA
AAHX01009401.1/27224-27301 GUCAGAUGAUUUG-AAUUGAUACA--------CUGAUAACUCCGUGAAGGUGUGAAUUUAUUAUAGCAUGUUAGAGUUCUGAUGGCA
AANU01129693.1/3021-2947   UUCAGAUGAUUUG-AACUGAUAAG--------CUGAGG-CUCUAUGAGGA--AUGACAGUUAAGAGCAUAUUAAAGUUGUUAUGAAA
AAFR03060925.1/35237-35160 GUCAGAUGAUUUG-AAUCUUGGCUUA------CUGAUG-CUCUAUGAGGGU-CCACAUUCUUAUAGCAUGUUAGAGUUCUGAUGGCA
AALT01210120.1/1142-1213   GUCAGAUGAUUUG-AAUCGAUAAUGC-------UGAUC-CUCUGUGAGG---UACAA---UAAUAGCAUGUUAGAGUUCUGAUGACG
AANN01152481.1/1044-1114   GUCAGAUGAUUUG-AAUUUGUUUG--------CUGAUC-UCCUGUGAGG---CUCAA---UAAUAGCAUGUUAGAGUUCUGAUGGCA
AAWR02037725.1/17609-17535 GUCAGAUGAUUUG-AAUUGAUAUG--------CUGAUC-CUCCGUGAGGU--ACGACAGUUAAUAGCAUGUUAGAGUUCUGAUGGCA
AAGV020553791.1/4484-4559  GUCAAAUGAUUUG-AAAUAAUAAUGC-------UGAUG-CUCUGUGAGGU--AUGACAGUUAAUAGCAUGUUAGAGUUCUGAUGACA
AAQR03143594.1/7481-7555   GUCAGAUGAUUUG-AAUUGAUAUG--------CUCAUG-CUUUGUGAGGU--AUAUCAGUCAAUUGCAUGUUAGAGUUCUGAUGGCA
AAPE02052744.1/3482-3556   GUCAGAUGAUUUG-AAUUGUUAUG--------CUGACG-CUCUGUGAGGU--AUGACAGGUAAUAGCAUGUUAGAGUUCUGAUGGCA
AAGW02063721.1/6922-6997   GUCAGAUGAUUAG-AGCUGAUAAAGC-------UGACG-CUUGGUGAAGU--GUGACAGUUAAUAGCAUGUUAGAGUUCUGAUGGCA
AACN010068463.1/1169-1095  GUCAGAUGAUUUG-AAUAGAUAUG--------CUGAUC-CUCUGUGAGGU--ACAACAAUUAAUAGCAUGUUAGAGUUCUGAUGACA
#=GC SS_cons               <<<<_________.____________......______.___________..______________________________>>>>:
#=GC RF                    gcCAGAUGAUUUG.AAuUGAUauuuc......CUGAug.cUCUGUGAGGu..auaAcaguUaAUAGCAUGUUAGAGUUCUGAUGgcA
//
# STOCKHOLM 1.0

#=GF AC   RF00086
#=GF ID   SNORD27
#=GF PI   U27
#=GF DE   Small nucleolar RNA SNORD27
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR, Moxon SJ, Daub J
#=GF SS   Predicted; Moxon SJ, Daub J
#=GF GA   52.00
#=GF TC   53.20
#=GF NC   51.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.44 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300711;
#=GF DR   snoopy; Oryctolagus_cuniculus300342;
#=GF RN   [1]
#=GF RM   8559254
#=GF RT   A mammalian gene with introns instead of exons generating stable RNA
#=GF RT   products.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Nature 1996;379:464-466.
#=GF RN   [2]
#=GF RM   8962077
#=GF RT   A small nucleolar RNA requirement for site-specific ribose methylation of
#=GF RT   rRNA in Xenopus.
#=GF RA   Tycowski KT, Smith CM, Shu MD, Steitz JA
#=GF RL   Proc Natl Acad Sci U S A 1996;93:14480-14485.
#=GF CC   U27 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U27 is encoded within the U22 snoRNA host gene
#=GF CC   (UHG) in mammals [1] and is thought to act as a 2'-O-ribose methylation
#=GF CC   guide for ribosomal RNA. This family also contains several related snoRNAs
#=GF CC   from yeast and plants.
#=GF WK   Small_nucleolar_RNA_SNORD27
#=GF SQ   8



JN899102.1/2-75          ACUCCAUGAUG-AACGGU-AAA-AU-GACAAGCAUAUGCCUGAACUCAAAAAAGUG-A-U--GUCAUCUUAACU-ACUGAGA-A-
FJ916003.1/1-69          ACUCCGUGAUG-AACAC--AAA-AU-GACAAGCAUAUGGCUGAACUU--AUAAGUG-A-U--GUCAUCUUACUA--CUGAGA---
U72858.1/1-73            UGUCAAUGAUG-AAUAA--AAU-ACAGACAAGCAUAUGUCUGAAUCU---UAUGUG--UU--GCCAUCUUAAUUUUCUGAGA-AA
U40580.1/1298-1369       ACUCCAUGAUG-AACAC--AAA-AU-GACAAGCAUAUGGCUGAACUU--UCAAGUG-A-U--GUCAUCUUACUA--CUGAGAAGU
U72859.1/1-73            UGUCAAUGAUG-AAUAA--AAA-ACAGACAAGCAUAUGUCUGAAUAU---UAUGUG--UU--UCCAUCUUAAUUUUCUGAGA-AA
AK095849.1/803-874       ACUCCAUGAUG-AACAC--AAA-AU-GACAAGCAUAUGGCUGAACUU--UCAAGUG-A-U--GUCAUCUUACUA--CUGAGAAGU
U40654.1/1205-1271       --UUAAUGAUGAACAAUGUAAAU---GACAAGCAUAUGGCUGAGUUG--CAAUGAU------GUCAUCUUACUA--CUGAAA---
CR382139.2/220781-220859 AAUAAAAGAUGAGCUUGAAAAA-AAAGACAAGCAUAUGUCUGAAUCU-UUAAUGAAGA-GAAACUUUUUCGUGU--CUGAUA-UU
#=GC SS_cons             <<<<_______._____..___.__._____________________.._______._._..____________..____>>.>>
#=GC RF                  acUcaAUGAUG.AAuaa..AAA.Au.GACAAGCAUAUGuCUGAAuuU..uaAuGug.A.U..guCAUCUUAauu..CUGAgA.gu
//
# STOCKHOLM 1.0

#=GF AC   RF00087
#=GF ID   SNORD26
#=GF PI   U26
#=GF DE   Small nucleolar RNA SNORD26
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR
#=GF GA   44.00
#=GF TC   45.50
#=GF NC   43.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00050
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300710;
#=GF DR   snoopy; Oryctolagus_cuniculus300341;
#=GF RN   [1]
#=GF RM   8559254
#=GF RT   A mammalian gene with introns instead of exons generating stable RNA
#=GF RT   products.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Nature 1996;379:464-466.
#=GF RN   [2]
#=GF RM   8962077
#=GF RT   A small nucleolar RNA requirement for site-specific ribose methylation of
#=GF RT   rRNA in Xenopus.
#=GF RA   Tycowski KT, Smith CM, Shu MD, Steitz JA
#=GF RL   Proc Natl Acad Sci U S A 1996;93:14480-14485.
#=GF CC   U26 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U26 is encoded within the U22 snoRNA host gene
#=GF CC   (UHG) in mammals [1] and is thought to act as a 2'-O-ribose methylation
#=GF CC   guide for ribosomal RNA.
#=GF WK   Small_nucleolar_RNA_SNORD26
#=GF SQ   17


U40580.1/1015-1089         CUACGGGGAUGAUUUUACGAACUGAACUCUCUCUUUCUGAUGGAUUAGUGGAGAAAACAGAAA--AU--UCUGAGUAGC
U40654.1/922-996           CUACGGGGAUGAUAUGAA-AACUGAACUCUCUCUUUCUGAUGGUUUAGUGGAGAAAACAAAAA--UUC-UCUGAGUAGC
U72857.1/1-72              CUGCACUGAUGAUACCUA----UGAACUCUCUCUUACUGAGCUUCCAGUGGAGACA-GACUUU--AUAAUCUGAGUUGC
U72856.1/1-73              CCGCACUGAUGAUACCUA----UGAACUCUCUCUUACUGAGCUUCCAGUGGAGACAAGACUUU--AUAAUCUGAGUGGC
AAFC03036502.1/32216-32141 CUACGGGGAUGAUUUCAAAAACUGAACUCUCUCUUUCUGAUGGAUUAGUGGAGAAAACAUAAA--AAC-UCUGAGUAGC
AADA01100603.1/10491-10415 CUACGGGGAUGAUUUUACGAACUGAACUCUCUCUUUCUGAUGGAUUAGUGGAGAAAACACAGA--AAAUUCUGAGUAGC
ABDC01493902.1/1788-1712   CUACGGUGAUGAUUUUAAGAAUUGAACUCUCUCUUUCUGAUGAAUUAAUGGAGAAAGCACAAA--AAAUUCUGAGUAGC
AANU01214137.1/3030-3103   CUACGGGGAUGAUUUUACAAACUGAACUCUCUCUUUCUGAUGGAUUAGUGGAGAAAACAAAAA--UU---CUGAGUAGC
AAQQ01114995.1/2785-2859   CUACAGGGAUGAUUUACG-AUUUGAACUCUCUCUUUCUGAUGGUUUAGUGGAGAAAAUGUAAA--AGU-UCUGAGUAGC
AANG01067642.1/1437-1362   CUACGGGGAUGAUACUAAGGAUUGAACUCUCUCUUUCUGAUGGAGUAGUGGAGAAAGCCUAAG--AGU-UCUGAGUAGC
AAHX01009401.1/26618-26692 CUACGGGGAUGAUUUAGA-AGCUGAACUCUCUCUUUCUGAUGGUUUAGUGGAGAAAUCAAAAA--UAC-UCUGAGUAGC
AAWR02037725.1/18353-18278 CUACGGGGAUGAUUUCAAGCACUGAACUCUCUCUUUCUGAUGGCUUAGUGGAGAAAACGUAAA--AAC-UCUGAGUAGC
AAQR03147715.1/12858-12933 CUACGGUGAUGAUUUUAAAAACUGAGCUCUCUCUUGCUGAUGUGUUAGUGGAGAAA-GCGUAA--AAAUUCUGAGUAGU
AAPE02052744.1/2739-2810   CUACGGGGAUGAUAAAAA---CUGAACUCUCUCUUUCUGAUGGAUUGGUGGAGAAGUGUAUAC--AU--UCUGAGUAGC
AAGW02063721.1/6273-6346   CUACGGGGAUGAUUGCGACACUUGAACUCUCUCUUGCUGAGGGGCUAGUGGAGAAAAUGCAAA--UU---CUGAGCAGC
AAWZ02032435.1/13011-12937 CUACAGAGAUGAGAAACA----UGAACUCUCUCUUUCUGAAGCUUCAGUGGAGAAAAACAUUAGCAGAUUCUGAGUAGC
AACN010068463.1/1948-1873  CUACGGGGAUGAUACUAGGAAUUGAACUCUCUCUUUCUGAUGGGUUGGUGGAGAAA-AUGUAA--AGAUUCUGAGUAGC
#=GC SS_cons               <<<<___________________________________________________________..___._____>>>>:
#=GC RF                    CuaCGGgGAUGAUuuuaAgAacUGAACUCUCUCUUuCUGAuGguUUAGUGGAGAAAacaaaaa..Aua.UCUGAGuaGC
//
# STOCKHOLM 1.0

#=GF AC   RF00088
#=GF ID   SNORD30
#=GF PI   U30
#=GF DE   Small nucleolar RNA SNORD30
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   40.00
#=GF TC   40.30
#=GF NC   39.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.95 -Z 549862.597050 CM SEQDB
#=GF CL   CL00052
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300559;
#=GF DR   snoopy; Danio_rerio300011;
#=GF RN   [1]
#=GF RM   8559254
#=GF RT   A mammalian gene with introns instead of exons generating stable RNA
#=GF RT   products.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Nature 1996;379:464-466.
#=GF RN   [2]
#=GF RM   8962077
#=GF RT   A small nucleolar RNA requirement for site-specific ribose methylation of
#=GF RT   rRNA in Xenopus.
#=GF RA   Tycowski KT, Smith CM, Shu MD, Steitz JA
#=GF RL   Proc Natl Acad Sci U S A 1996;93:14480-14485.
#=GF CC   U30 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U30 is encoded within the U22 snoRNA host gene
#=GF CC   (UHG) in mammals [1] and is thought to act as a 2'-O-ribose methylation
#=GF CC   guide for ribosomal RNA.
#=GF WK   Small_nucleolar_RNA_SNORD30
#=GF SQ   20


U40580.1/2651-2720           GUUUGUGAUGACUUA-----CAUGGAAUCUCGUUCGGCUGAUGACUU-GCUGUUGAGACUCUGAAAUCUGAUUUUC
U40654.1/2012-2080           AUAUAUGAUGACUUU-----CAUAGAAUCUCGUUCGGCUGAUGA-UU-GCUGUUGAGACUUGGAAAUCUGAUUUUU
U72867.1/2-74                CGGACUGAUGAAUUUAAUCUCAUGGAAUCUCAUUCGUCUGAAUAAUU--CUGAUGAGACU-UAUUAUCUGACUGUU
AAPY01121463.1/445-514       AUACAUGAUGACUUC-----CAUGGAAUCUCGUUCGGCUGAUUACUU-GCUGCUGAGACUAGGAAAUCUGAUUUUC
ABDC01628854.1/804-734       AUAUAUGAUGACUUA-----CAUGGAAUCUCGUUCGGCUGAUGACUUGGCUGUUGAGAAUUGGAAAUCUGAUUUUG
AAPN01443316.1/1715-1647     GGAUGUGAUGAAUUU-----CUUGGAAUCUCGUUCGGCUGAACU-CU-GCUGUUGAGACUUGGAAAUCUGAUUGUC
AAFC03074495.1/38320-38251   AUAUGUGAUGAUUUA-----CAUGAAAUCUCAUUUAGCUGAUGGUUU-GCUAUUGAGACUCGGAAAUCUGAUUUUC
AAQQ01114996.1/551-618       AUAUAUGAUGACUU-------AUGGAAUCUCGUUCGGCUGAUGUUUU-GCUGUUGAGACUCGGAAAUCUGAUUUCC
AALT01366508.1/975-909       AUAUGUGAUGACUUA-----C--UGAAUCUCGUUCGGCUGAUGAUUU-GCUG-UGAGACUCGGAAAUCUGAUUUCC
AL954715.13/174735-174666    ACUUAUGAUGAUUUUC----AUUGGAAUCUCGUUCGUCUGAAUUCCU-GCUGAU-AUCUUUUAAAUACUGAUGUUA
AAKN02039313.1/10149-10218   CUGUGUGAUGACUUA-----CAUGGAAUCUCGUUCGGCUGAAGGCUU-GCUGUUGAGACUUGGAAAUCUGAUUUCU
AAWR02037725.1/16602-16533   AUAUGUGAUGACUUA-----CAUGGAAUCUCGUUCGGCUGAUAACUU-GCUGUUGAGACUCGGAAAUCUGAUUUUC
AAGV020553791.1/5459-5527    CUGUAUGAUGACUUA-----CAUGGAAUCUCGUUCGGCUGAUUC-UU-GCUGUUGAGACUUGGAAAUCUGAUUUUC
AAQR03147716.1/783-852       GCAUGUGAUGACUUA-----CAUGGAAUCUCGUUCGGCUGAUGGCUU-GCUGUUGAGACUUGGAAAUCUGAUCUCU
AAPE02052744.1/4472-4541     AUAUAUGAUGACUGA-----CAUGGAAUCUCGUUCGGCUGAUGACUU-GCUGUUGAGACUCGGAAAUCUGAUUUUC
AAGU03076505.1/369-438       CUAAAUGAUGACUUA-----CAUGGAAUCUCGUUCGGCUGAUAACUU-GCUGUUGAGACUCGGAAAUCUGAUUUUU
AAEX03011662.1/176419-176488 AUCCAUGAUGACUUA-----UGUGGAAUCUCGUUCGGCUGAUAACUU-GCUGUUGAGACUCGGAAUUCUGACUUUC
AAWZ02032435.1/11668-11600   UUUCAUGAUGAAUUUGC---UUUGGAAUCUCGUUCGGCUGAAUU-UC-GCUGUUGAGAAG--CAAAUCUGAGUCUU
AC004998.2/93755-93686       AUACAUGAUGACUUA-----CAUGGACUCUCAUUCAGCUAAUGACUU-GCUGCUGAAACAUGGAAAUCUGAUUUUU
AAGW02063721.1/7855-7923     AUGUAUGAUGACUUA-----C-UGGAAUCUCGUUCGGCUGAUGGCUU-GCUGUUGAGACUCGGAAAUCUGACUUCU
#=GC SS_cons                 :::::::::::::::.....:::::::<<<<<--<<<<_________.>>>>->>>>>::::::::::::::::::
#=GC RF                      aUauaUGAUGAcUUa.....CAUGGAAUCUCGUUCGGCUGAuuacUU.GCUGuUGAGACUuGGAAAUCUGAUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00089
#=GF ID   SNORD31
#=GF PI   U31
#=GF DE   Small nucleolar RNA SNORD31
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00053
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300715;
#=GF DR   snoopy; Loxodonta_africana300011;
#=GF RN   [1]
#=GF RM   8559254
#=GF RT   A mammalian gene with introns instead of exons generating stable RNA
#=GF RT   products.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Nature 1996;379:464-466.
#=GF RN   [2]
#=GF RM   8962077
#=GF RT   A small nucleolar RNA requirement for site-specific ribose methylation of
#=GF RT   rRNA in Xenopus.
#=GF RA   Tycowski KT, Smith CM, Shu MD, Steitz JA
#=GF RL   Proc Natl Acad Sci U S A 1996;93:14480-14485.
#=GF CC   U31 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U31 is encoded within the U22 snoRNA host gene
#=GF CC   (UHG) in mammals [1] and is thought to act as a 2'-O-ribose methylation
#=GF CC   guide for ribosomal RNA.
#=GF WK   Small_nucleolar_RNA_SNORD31
#=GF SQ   26


U40580.1/2987-3057         CUCACCAG-UGAUGAGUUGAAU--ACCGCCCCAGUCUGAUCAAUGUGUGACUGAAA-GGUAU-UUUCUGAGCUGUG
U40654.1/2265-2331         CUCACCC--UGAUGAACUGAAU--ACCGCCCCAGUCUGAUAGC--UGUGGA-GAAA-GGUAU-UUUCUGAGUUGUG
U72868.1/1-67              AAGACC---UGAUGAUCUCUAUU-ACCGCCCCAGUCUGAUUA-UAUGUGACUGAAU-GGUAU-CUUCUGA--UUGC
U72869.1/1-64              AAGACC---UGA---UCUCUAUU-ACCGCCCCAGUCUGAUUA-UCUGUGACUGAAU-GGUAU-CUUCUGA--UUGC
ABDC01628854.1/541-473     CUCACCAG-UGAUGAGUUGAAU--ACCGCCCCAGUCUGAUCAC--UGUGACUGAAA-GGUAU-UUUCUGAACUGAG
AAQQ01114996.1/830-898     CUCACCAG-UGAUGAGUUGAAU--ACCGCCCCAGUCUGAUCAU--UGUGACAGAAA-GGUAC-ACUCUGAGUUGUG
AANG01643015.1/1946-1878   CUCACCAG-UGAUGAAUGCAAU--ACCGCCCCAGUCUGAACAC--UGUGACUGAAA-GGUAU-UCUCUGAGCUGUG
AAPY01121463.1/746-813     CUCACCAG-UGAUGAGUUGA-U--ACCGCCCCAGUCUGAUCAC--UGUGACUGAUA-GGUAU-UUUCUGAGCUGUG
AAFC03036502.1/30234-30167 CUCACCAA-UGAUGAGUUCAAU--ACCGCCCCAGUCUGAUCAC--UAUGACUGAAA-GGUAU--UUCUGAGCUGUG
CAAE01014779.1/63527-63596 CCCACCAAAUGAUGAGUACGUU--ACCGCCCCAGUCUGAUAA-CUCGUGACUGAUG-GGUAU-UUUCUGA-CUGAA
AAPN01030027.1/4732-4665   AAUAUUCUGUGAUGAA-UCUAU--ACCGCCCCAGUCUGAUCAU--UGUGACUGAAA-GGUA--AUUCUGAGCUGUC
AANU01261827.1/873-941     AUCACCAG-UGAUGAGAUGAAU--ACUGCCCCUUUCUGAUCAA--UAUGCGUGAAA-GAUAU-UUUCUGAGCUGUG
AANN01835099.1/8950-8883   AUUACUAG-UGAUGAAUUCAUU--GCCACCC-AGUCUGAUCGC--UGUGACUGAUA-GGUAU-UUCCUGAGCUGUG
AAFR03060925.1/33935-33869 CCCACCAG-UGAUGAGACGAUU--ACCGCCCCAGGCUGAUUCC--UGUGACUGAUA-GGUU--GUUCUGAG-UGGG
AAZX01004141.1/32507-32574 AUUUAUAA-UGAUGACAUCCAU--ACCGCCCCAGUCUGAGUUC--UGUGACUGAUU-CGGAU--UACUGAUAAAAA
AAJJ01000083.1/51812-51744 AACGUAACGUGAUGAUUUACUU--ACCGCCCCAGUCUGAAAUC--GGUGACUGAUU-GGUUU--UUCUGAUUUGUU
AAVX01289320.1/180-247     CUAAAUA--UGAUGAGCCUGUU--AUCGCCCCAGUCUGAUUG-UUGGUGACUGAAACGGUAA-CCUCUGA--UUCA
AANH01007201.1/24133-24067 UUUUGAUG-UGAUGA--UUAUU--ACCGCCCCAGUCUGAUAA-UUCAUGACUGAUU-GGUU--ACUCUGAUCAAAU
AAKN02039313.1/10431-10499 CUCACCAG-GGAUGAA-UUGAAU-ACCGCCCCAGUCUGAUCAC--UGUGACAGAAA-GGUAU-UUUCUGAGUUGAG
AAGV020553791.1/5789-5856  CUCACCAG-UGAUGAGUUGAAU--ACCGCCCCAGUCUGAAAAC--UAUGACUGAAA-GGUAU--UUCUGAGCUGUG
AL954715.13/177135-177065  AUAGGU-G-UGAUGAUUUUAGAUUACCGCCCCAGUCUGAUUUA--UCUGACUGAUU-GGUACCCCUCUGAACCUUU
AAWR02037725.1/16273-16205 CUCACCAG-UGAUGAGUUCAAU--ACCGCCCCAGUCUGAUUAC--UGUGACUGAAA-GGUAU-UCUCUGAGCUGUG
AAGU03076505.1/711-778     AUCACCAG-UGAUGAGUUGAAU--ACCGCCCCAGUCUGAUCAC--UGUGACUGAAA-GGUAU--UUCUGAGCUGUG
AAGW02063721.1/8086-8154   CUCACUAG-UGAUGAGUCUGAU--ACCGCCCCAGUCUGAUCAC--UGUGACUGAAA-GGUAU-UUUCUGACCUGUG
AL138914.9/114073-114005   ACCACCAG-UGAUGAGUUGAAU--ACUGCCCCAGUCUGAUCAA--CAUGCGUGAAA-GAUAU-UUUCUGAGCUGUG
AAQR03118152.1/8663-8595   UUUACCAG-UGCUGAGUUGAAU--ACCACCCCAGUCUGAUAAC--UGUGACUGAAA-AGUAU-UUUCUGAACUGAG
#=GC SS_cons               ::<<____._____________..___________________..___________._____._________>>::
#=GC RF                    aUcaccAG.UGAUGAguUuaaU..ACCGCCCCAGUCUGAUuac..UGUGACUGAaa.GGUAU.uUUCUGAgCugug
//
# STOCKHOLM 1.0

#=GF AC   RF00090
#=GF ID   SNORA74
#=GF PI   U19
#=GF DE   Small nucleolar RNA SNORA74
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR
#=GF GA   71.00
#=GF TC   72.40
#=GF NC   70.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.50 -Z 549862.597050 CM SEQDB
#=GF CL   CL00043
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300550;
#=GF DR   snoopy; Loxodonta_africana300332;
#=GF RN   [1]
#=GF RM   9106664
#=GF RT   The family of box ACA small nucleolar RNAs is defined by an evolutionarily
#=GF RT   conserved secondary structure and ubiquitous sequence elements essential
#=GF RT   for RNA accumulation.
#=GF RA   Ganot P, Caizergues-Ferrer M, Kiss T
#=GF RL   Genes Dev 1997;11:941-956.
#=GF RN   [2]
#=GF RM   8657112
#=GF RT   Characterization of the intron-encoded U19 RNA, a new mammalian small
#=GF RT   nucleolar RNA that is not associated with fibrillarin.
#=GF RA   Kiss T, Bortolin ML, Filipowicz W
#=GF RL   Mol Cell Biol 1996;16:1391-1400.
#=GF RN   [3]
#=GF RM   9630250
#=GF RT   Human U19 intron-encoded snoRNA is processed from a long primary
#=GF RT   transcript that possesses little potential for protein coding.
#=GF RA   Bortolin ML, Kiss T
#=GF RL   RNA 1998;4:445-454.
#=GF CC   U19 belongs to the H/ACA class of snoRNAs. snoRNAs bind a number of
#=GF CC   proteins (including dyskerin, Gar1p and Nop10p in the case of the H/ACA
#=GF CC   class) to form snoRNP complexes. This class are thought to guide the sites
#=GF CC   of modification of uridines to pseudouridines by forming direct base
#=GF CC   pairing interactions with substrate RNAs [1]. Targets may include
#=GF CC   ribosomal and spliceosomal RNAs but the exact functions of many snoRNAs,
#=GF CC   including U19, are not confirmed. Co-precipitation of U19 snoRNA with
#=GF CC   RNase MRP RNA suggests that U19 may be involved in pre-rRNA processing
#=GF CC   [2].
#=GF WK   Small_nucleolar_RNA_SNORA74
#=GF SQ   24




AM055743.1/3-203             UCCAGCAGUAGUCAGCCAUCC-GGACAGAACCGU-UCCUGUGAUGGUGU----UACACUGCUGGGAGAGGAAUGUCUUGUCUUCA-UC-CGGU-UGCCUG-CGC-CACUGUUCUGGUGG--CG-UCUGGCACUGGUGCAAGACAGAGCUGUGCUUCCC-CGAGAGUGUGCUAAGCAUUCACUUUGGCUGCUUAGUUCUAGUCUGGGAGCAGACAGA
X94290.1/2-199               UCCAGCGGUUGUCAGCUAUCCAGGCUCAUGUGGU-GCCUGUGAUGGUGU----UACACUGUUGGAAGAGCAA-ACACUGUCUUUA-UUGAGGU-UUGGCUCCAAGCACUGUUUUGGUGU--UG-UAGCUGAGUACCUUUGGGCAGUGUUUUGCACCUC-UGAGAGUGGAAUGACUCC------UGUGGAGUUGAUCCUAGUCUGGGUGCAAACAAU
X94291.1/4-200               UCCAGCAGUUGUCAGCUAUCCAGGCU-GUGUGGU-GCCCGAGAUCGUGU---GUACACUGUUGGAAGAGUAA-ACACUGCCUUAC-UA-AGGG-UCGGCUCCCAGCACUGUUUUGGUGU-CUG-GUGCUGAGUACUUUCAGGCA--GUAUUGCAUCCC-UGAGAGUGGAAUGACUCCU-----UGUGGAGUUGGUCCUGGUCUGGGUGCAAACAAU
AC007318.4/80306-80504       UCCAGCAGUCGUUAGCUCUCCUGGCUAGUGUGAU-GCCUGUGAUGGUGU----UUCACUGUUGGAACAGCAA-GCACUGUCUUAA-UUGAGGC-UUGGCUCCGGGUGCUGUUUUGGUGU-GGG-GCCAAGUAUACCUUUGGGCAGUGUUUUGCACUUC-UGAGAGUGAAAUGACUCC------UGUGGAGUCGGUCCUAAUCUGAGUGCAAACAAU
AAPY01563514.1/105-305       UCCAGCAGUUGUCAGCUGUCCAGGCUAGUGUGAU-GCCUGUGAUGGUGU----UACACUGUUGGAAGAGUAA-GCACUGUCUUUA-UUGAGGU-UUGGCUAUAAGCACUGUUUUGGUGU--GA-UAGCCAAGAACCUUUGGGCAGUGUUUUGCACCUC-UGAGAGUGGAGUAACUCCUCC---UGUGGAGUUGGUCCUAGUCUGGGUGCAAACAAU
ABDC01187956.1/1054-1254     UCCAGCGGUUGUCAGCUGUCCAGGCUAGUGUGAU-GCCUGUGAUGGUGU----UACACUGUUGGAAGAGCAA-GCACUGUCUUUA-UUGAGGU-UUGGCUCUAAACACUGUUUUGGUGU--UU-UGGCUGAGUACCUUUGGGCAGUGUUUUGCACCUC-UGAGAGUGGAAUGACUCCUCC---UGUGGAGUUGGUCCUAGUCUGGGUGCAAACAGU
AAFC03054672.1/53430-53231   UCCAGCAGUUGUCAGCUAUCCAGGCUAGCGUGAU-GCCUCAGAUGGUGU----UACACUGUUGGAAGAGCAA-GCACUGCCUUUA-UUGAGGU-CUGACUUCA-GCACUGUUUUGGUGU--UG-UGGCUGAGUACCUCUGGGCAGUGUUUUGCACCUC-UGAGAGUGGAGUAACUCCUCC---UGUGGAGUUGGUCCUAGUCUGGGUGCAAACAGU
AAHX01094506.1/6494-6298     UCCAGCAGUUGUCAGCUGCCCAGGCU-GUGUGGU-GCCUGUGAUUGUGU----UACACUGUUGGAAGAGCAA-AGGCUGCUUUAG---AAGGG-UUGGCUCCAAGCACUGUUUUGGUGU-UUG-GUGCUGAGUACCUUCAGGCAGUGUAUUGCAUCCC-UGAGAGUGGAAUGACUCCU-----UGUGGAGUUGGUCCUAGUCUAGGUGCGAACAAU
AANU01291338.1/2812-2616     UCCAGCAGUCGUUAGCUCUCCUGGCUAGUGUGAU-GCCUGUGAUGGUGU----UUCACUGUUGGAACAGUAA-GCACUGUCUUCA-UUGAGGC-UUGGCUGCAGCUGCUGUUUUGGUG---UG-GGGCCAAGUACCUUUGGGCAGUGUUUCGCACCUC-UGAGAGUGAAAUGACUCC------UGUGGAUUAAGUCCUAAUCUGAGUGCAAACAAU
AAYZ01095122.1/948-1147      UCCAGUGGUUGUCAGCUAUCCAGGCUUGUAUGAU-GCCUGGGAUGGUGU----UACACUGCUGGAAGAGCAA-GCACUGGCUCCA-CUGAGGU-UUGGCCCCCUGCACUGUUUUGGUGC--UG-GGGUCAAGAACUCUGAG-CAGUGUUUUGCACCUC-UGAGAGUGGAAUGACUCCUCC---UGUGGAGUUAGUCCUAGUCUGGGUGCAAACAGU
AANG01341556.1/2951-3150     CCCAGCGGUUGUCAGCUAUCCAGGCCAGCAUGAU-GCCUUGGAUGGUGU----UACACUGUUGGAAGAGCAA-ACGCUGACCUUC-UUGAGGU-CUGGCUUCAAGCACUGUUUUGGUGU--UG-UGGCU-GAUACUCUUGGGCAGUGUUUUGCACCUC-UGAGAGUGGAGUAACUCCUCC---UGUGGAGUUGGUCCUAGUCUGGGUGCAAACAAU
AAIY01482875.1/1763-1565     CCCAAUGGUUGUCAGCUAUCCAGGCUAGCACGAU-GCCUGUGAUGGUGU----UACACUGUUGGAAGAGCAA-GCGCUGCCC--A-GUGGGGU-CUGGCUCCAAGCGCUCUUUCCGUG--GUG-UGGUCACGUACCUUUGGGCAGCGUUUUGCACCUA-UGAGAGUGGAAUGACUUCUCC---UGUGGAGUUGGUCCUAGUCUGGAUGCAAACAUU
AANN01586748.1/5755-5951     CCCAGUGGUUGUCAGCUACCAAGGCUAAUGU----GCCUUGGGUGGUGU----UACACUGCUGGAAGAGCAA-UCAUUGCCUUGA-AUGACGU-AUGAGUCUGAGCACUGUUUUAGUGU--GA-UGACAGU--ACCUUGGGGCAAUGCCUUGCACCUCUUGAGAGUGGAAUGACUCCUCC---UGUGGAGUUGGUCCUAGUCUGGGUGCAAACAUA
AALT01149980.1/2859-2663     CCCAGUGGUUGUCAGCUGUCUGGGCUAAUAU----GCCUCGGAUGGUGU----UACAGUGCUGGGAGAACAA-GCACUGCCUUAU-UUGGGGU-GUGGCUGCAG-CGCUGUUCUGGUGC--UG-UGGCCCAGUUCCUGUGGGCAGUGUUUUGCACCCC-UGAGAGUGGAGUGGCUCCUUU---UCUGGAGUUAGUCCUAGUCUGGGUGCAUACAGU
AAFR03013214.1/49626-49426   CCCAGUGACUGUCAGCUGUCCAGGCC-ACACCAU-GCCUGUGACGGUGU----UACAUUUCUGGGAGAGAAAUGCACUGUCGCCA-CCAAGGUCUUGUCACAUGGCACUGUUUUAGUGU--CC-AGGCUGACUGCCUUA-GAUAGUGCUUUGCACCAC-UGAGAGUGGAUUAACUUCCUU---UAUGAAGUUAGUCCUAGUCUAGGUGCACACAUG
AAPN01274425.1/450-652       UCCAGCGGCUGUCAGCUGUCCAGGUGGGCGCGGU-ACCUGCGAUAGCGU----UACACCGCUGGGACAUCAGGGCGCCGUCC-AG-ACGACCC-UCCGCCUCCGCCGCUGUUUUAGCGU-CGG-GUCCGG-CUGGGCCCGGGCGGCGCUUUGCGUUCC-CGAGAGUGGACGGACUCUUGCC-CCGUAGAGUCGGCCCUAGAUUGGAUGCAAACAUC
AAGV020172193.1/944-1145     ACCAGCAGUUGUCAGCUUUCCAGGCCAGUGUGAU-GCCUGUGAUGGUGU----UACACUGUUGGAAGAGGAA-GCACUACCUUUA-CUGUGGU-CUGGCCCCAAGCACUGUUUUGGUG--AUGAGGGCAAGUACCUAUAGGGCAGUGUUUUGCACCUC-UGAGAGUGGAGUGGCUCCCUU---UGUGGGCUUGGUCCUAGUCUGGGUGCAAACAGU
AAWR02002418.1/85269-85068   UCCAGCGGUUGUCAGCUAUCCAGGCUAGUGCGAU-GCCUUGGAUGGUGU----UACACUGGUGGAAGAGUAA-ACGCUGCCUUAUGCUGAGGU-AUGGCUCCAAGCACUGUUUUGGUGU--UG-UGGCUGAGUACCUUUGGGCAGUGUUUUGCACCUC-UGAGAGUGGAGUAACUCCUCC---UGUGGAGUUGGUCCUAGUCUGGGUGCAAACAAU
AAEX03007822.1/4715-4915     CCCAGCGGUUGUCAGCUAUCCAGGCUAGUAUGUU-GCCUUGGAUGGUGU----UACACUGUUGGAAGAGCAA-ACACUGCCUUUA-UUGAGGU-CUGGCUCCGAGCACUGUUUUGGUGU--UG-CAGCUAAGUACUCUUGGGCAGCGUUUUGCACCUC-UGAGAGUGGAAGAACUCCUCC---UGUGGAGUUGGUCCUAGUCUGGGUGCAAACAGU
AAPE02012926.1/123904-123704 UCCAGCGGUUGUCAGCUAUCCAGGCUAGUGUGAU-GCCUUGGAUGGUGU----UACACUGUUGGAAGAGCAA-GCGCUGCCUUUA-AUGAGGU-CUGGCUCCAAGCACUGUUUUGGUGU--UG-UGGCCGAGUACCUUUGGGCAGUGUUUUGCACCUC-UGAGAGUGGAAUAACUUCUCC---UGUGGAGUUAGUUCUAGUCUGGGUGCGAACAAU
AAQR03052918.1/1813-2007     CCCAGCAGUUGUCAGCCCUCCAGGCUCACGUGAUGGGCUG-CAGGGCUGAUGCUGCACCGUUGGAAGAGCCA-GUGUU----------GAGGU-UUGGCUCCGAUCACUGUUUUGGUG---CU-GGGCAGAAUACCUUUGGACAAUGUUUUCCACCUC-CAAGAGUGGAAAGCCUCCUCC---AGAGGAGUUGGUCCUAAUCUGAGUAUAAACAAU
AACZ03012574.1/18342-18538   UCCAGCAGUUGUUAGCUCUCCUGGCUAGUGUGAU-GCCUGUGAUGGUGU----UUCACUGUUGGAACAGCAA-GCACUGUCUUAA-UUGAGGC-UUGGCUCCGGGUGCUGUUUUGGUG---UG-GGGCCAAGUGCCUUUGGGCAGUGUUUUGCACUUC-UGAGAGUGAAAUGACUCC------UGUGGAGUCAGUCCUAAUCUGAGUGCAAACAAU
AAGW02027745.1/13500-13299   CCCAGCGGUUGUCAGCUGUCCAGGCUUGUAUGAU-GCCUGUGAUGGUGU----UACACUGUUGGGAGAGCAA-ACACUGUCUACA-CU-GGGU-UUGGCUCCGAGCACUGUUCUGGUGUGUUG-UGGGCAAGAACCCUUAGGCAGUGUUUUGUGCCUC-UGAGAGUGGAAUGACUCCUCC---UGUGGGGUUGGUCCUAGUCUGGGUACAAACAAU
AAGU03004652.1/77489-77687   CCCAAUGGUUGUCAGCUAUCCAGGCUAGUGUGAU-GCCUGGGGUGGUGU----UACACUGUUGGGAGAACAA-GUGCUGCCUUUG-UUGAGGU-CUGGCUCCAAGCACUGUUUUGGUGU--UG-AGGUUAG-UACCUUUCGGUAGCAU-UUGCACCUC-UGAGAGUGGAGUGACUCCUCC---UGUGGAGUUGGUCCUAGUCUGGGUGCAAACAAU
#=GC SS_cons                 <<<<<<<<<-<<--<<<<<<<<<<<_________.>>>>>->>>>>>--....->>>>>>>>>>>,,,,,,,.<<<<<<<<<---.--<<<<<.<<<<<<-<<<-<<<<_____>>>>>..>>.->>>>>>-->>>>>->>>>>>>>>,<<<<<<<<-.-------<<<-<<<<<<<___...___>>>>>>>->>>------>>>>>>>>:::::
#=GC RF                      cCCAgcgGuUGuCAgCcguCcaGGcuagugugaU.gCCuguGacgGuGU....UaCaCcgcUGGgAGAGcAA.gcgcuGcCcUua.uuggggu.ucggccccgggCaCcGUUUUgGuGc..cg.uggccgagUaccccugGgCagcgcUuugCacccC.UGAGAGUGgaaugacuccUcc...UGUggagucaGucCUAGUCUggguGcaaACAau
//
# STOCKHOLM 1.0

#=GF AC   RF00091
#=GF ID   SNORA62
#=GF PI   E2
#=GF DE   Small nucleolar RNA SNORA62/SNORA6 family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   80.00
#=GF TC   80.10
#=GF NC   79.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00040
#=GF DR   snoRNABase; E2;
#=GF DR   snoRNABase; ACA6;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300694;
#=GF DR   snoopy; Homo_sapiens300658;
#=GF RN   [1]
#=GF RM   8586453
#=GF RT   The gene for human E2 small nucleolar RNA resides in an intron of a
#=GF RT   laminin-binding protein gene.
#=GF RA   Selvamurugan N, Eliceiri GL
#=GF RL   Genomics 1995;30:400-401.
#=GF RN   [2]
#=GF RM   9144174
#=GF RT   Three small nucleolar RNAs that are involved in ribosomal RNA precursor
#=GF RT   processing.
#=GF RA   Mishra RK, Eliceiri GL
#=GF RL   Proc Natl Acad Sci U S A 1997;94:4972-4977.
#=GF RN   [3]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [4]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [5]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the H/ACA class of snoRNAs which are
#=GF CC   predicted to guide the sites of modification of uridines to pseudouridines
#=GF CC   [3]. This family includes human snoRNAs E2 (SNORA62), ACA6 (SNORA6) and M2
#=GF CC   and mouse MBI-136. In humans both E2 and ACA6 are encoded in the introns
#=GF CC   on the same host gene (LAMR1)[1,3]. E2 is involved in the processing of
#=GF CC   eukaryotic pre-rRNA and has regions of complementarity to 28S rRNA [2].
#=GF CC   ACA6 is predicted to guide the pseudouridylation of residue U3616 of 28S
#=GF CC   rRNA [5].
#=GF WK   Small_nucleolar_RNA_SNORA62
#=GF SQ   18


AF375472.1/1-148       --UGCACACUAUUAAAGCUCAG-GGUGGAG-GCCAGUCU-UGGCUCAUGAACUUCUGAGUGUCGGAAGUGUGCUAUAUCAA------UGGCAGGAU-UUUCGCUAACACCAGUAGAG-CU----UGCCUCUAUGACUGGAGUUUGGUAGUACUCGCUGCCACAUA-
AJ609429.1/1-149       --UGCACACUAUUAAAGCUCAG-GGUGGAG-GCCAGUCU-UGGCUCAUGAACUUCUGAGUGUCGGAAGUGUGCUAUAUCAA------UGGCAGGAU-UUUCGCUAACACCAGUAGAG-CU----UGCCUCUAUGACUGGAGUUUGGUAGUACUCGCUGCCACAUAG
U64700.1/1-155         -UUGCACACAGUUAGAACUUGG-AGCUGAG-GCCUU-UUCA-GCCAAUGAACU-CUGAGUGUAGGAUGUGUGCUACAUUAAC----AUGGCAGACU-UUUCGCUAACGCCACAAGGAGCUUUAGAGCUCCAGUGACUGGAGUUUGAUAGUAAUUCUUGCCACAGCU
L22739.1/569-721       UGUGCACAUUGUUAGAGCUUGG-AGUUGAG-GCUACUGACUGGCCGAUGAACUCGCAAGUGUAGGUAGUGUGCUACAUGAG------GGGCAAG-U-UUUCGCUAACACCACAAGGGUCUC---UGGCCCAAUGAGUGGAGUUUGAUAGUAAUUCUUGCUACAAGU
AC099332.2/52634-52482 UGUGCACAUUGUUAGAGCUUGG-AGUUGAG-GCUACUGACUGGCCGAUGAACUCGCAAGUGUAGGUAGUGUGCUACAUGAG------GGGCAAG-U-UUUCGCUAACACCACAAGGGUCUC---UGGCCCAAUGAGUGGAGUUUGAUAGUAAUUCUUGCUACAAGU
U36484.1/569-721       UGUGCACAUUGUUAGAGCUUGG-AGUUGAG-GCUACUGACUGGCCGAUGAACUCGCAAGUGUAGGUAGUGUGCUACAUGAG------GGGCAAG-U-UUUCGCUAACACCACAAGGGUCUC---UGGCCCAAUGAGUGGAGUUUGAUAGUAAUUCUUGCUACAAGU
AK055991.1/796-948     UGUGCACAUUGUUAGAGCUUGG-AGUUGAG-GCUACUGACUGGCCGAUGAACUCGCAAGUGUAGGUAGUGUGCUACAUGAG------GGGCAAG-U-UUUCGCUAACACCACAAGGGUCUC---UGGCCCAAUGAGUGGAGUUUGAUAGUAAUUCUUGCUACAAGU
U43901.2/6709-6861     UGUGCACAUUGUUAGAGCUUGG-AGUUGAG-GCUACUGACUGGCCGAUGAACUCGCAAGUGUAGGUAGUGUGCUACAUGAG------GGGCAAG-U-UUUCGCUAACACCACAAGGGUCUC---UGGCCCAAUGAGUGGAGUUUGAUAGUAAUUCUUGCUACAAGU
L07383.1/1-153         UGUGCACAUUGUUAGAGCUUGG-AGUUGAG-GCUACUGACUGGCCGAUGAACUCGCAAGUGUAGGUAGUGUGCUACAUGAG------GGGCAAG-U-UUUCGCUAACACCACAAGGGUCUC---UGGCCCAAUGAGUGGAGUUUGAUAGUAAUUCUUGCUACAAGU
AF375473.1/1-156       CACGCACACAGUUGGAACUUGGGAGCUGAGAGCCAACCUGUGGCCAAGGAACU-CUCAGUGUAGGAUGUGUGCUACAGUAAC----AUGGCAGGAC-UUAC-UGACAGCCU-GAGGGCCUUU-GUGGCCCAAUGAAAGGAGUUUGGUAGUCAAUCUUGCCACAGU-
U43901.2/4011-4161     GCUGCACACUAUUAAAGCUCAG-GGUGGAG-GCCAGUCU-UGGCUCAUGAACUUCUGAGUGUCGGAAGUGUGCUAUAUCAA------UGGCAGGAU-UUUCGCUAACACCAGUAGAG-CU----UGCCUCUAUGACUGGAGUUUGGUAGUACUCGCUGCCACAUAG
FJ915979.1/1-150       -CUGCACACUAUUAAAGCUCAG-GGUGGAG-GCCAGUCU-UGGCUCAUGAACUUCUGAGUGUCGGAAGUGUGCUACAUUAA------UGGCAGGAU-UUUCGCUAACACCAGUAGAG-CU----UGCCUCUAUGACUGGAGUUUGGUAGUACUCGCUGCCACAUAC
EU240299.1/1-156       CUUGCACACAGUUGGAACUUGG-AGCUGAG-GCCAUCCUGUGGCCAAGGAACUCUCAAGCGUAGGAUGUGUGCUACAGUAAC----AUGGCAGGAC-UUAC-UGACAGCCU-GAGGGCCUUU-GUGGCCCAAUGAAAGGAGUUUGGUAGUCAAUCUUGCCACAGUU
EU094012.1/1-161       CCCGCACACGGUUAGAGCUUGG-AGCUGAG-GCCGGUCUCCGGCCGAUGAACUACCGAGUGUAGGUCGUGUGCCACAGCGAAG--GACGGCGGGUUUUUUCGCUAACGCCACGAGGCCCUCG-GUGGGCCGACGAGUGGAGUUUGAUAGUGACAUCUGCCACAGGU
EU094008.1/1-155       CCCGCACACUAUUAAAGCUCAG-AGCUGAG-GCCGGUUCCGGGCCUAUGAACUCCUGAGUGUCGGAAGUGUGCCACAGUAAA---GCGGGCAGGAU-UUUCGCUAACACCAGGAGAG-CU----CGCCUCCGUGACUGGGGUUUGAUAGUACUCGCUGCCACACGC
EU240300.1/1-158       -UUGCACACUGUUAAAGCUUGA-UGCUGAG-GUCAGUUCCUGACCAAUGAGCUCUCAAGUGUCGGAAGUGUGCUACAACAAAGCUGUUGGCAGGGU-GCUUGCUAAUGCCAGGAGAGGAGC---UGCCUCUAUGAUUGGAGUUUGAUAGCA-GCCCUGCCACAUGC
AF375474.1/1-156       CUUGCACACUGUUAAAGCUUGA-UGCUGAG-GUCAGUUC-UGACCAAUGAGCUCUCAAGUGUCGGAAGUGUGCUACACAAAGC-UGUUGGCAGGGU-GCUUGCUAAUGCCAGGAGAGGAGC---UGCCUCUAUGAUUGGAGUUUGAUAGCA-GCCCUCCGACAUG-
AF357422.1/1-130       -------------------UGG-AGUUGAG-GUCACACGCUGGUCGAUGAACUCACAAGUGUAGGUAGUGUGCUAAAAGAN------UGGCAAGGU-UUUCGCUAACACCCCAC-----UC---UGGUCCAGUGAGUGGGGUUUGAUAGUAACCUUUGCUACAAAA
#=GC SS_cons           :::<<<<<<<------------.-------.<<<<_____>>>>---------------------->>>>>>>---------....--<<<<<---.-----------<<<<--<<<<<__..._>>>>>----->>>>---------------->>>>>::::::
#=GC RF                uuUGCACAcugUUAgAGCUUGG.aGuUGAG.GccagUuucuggCCaAUGAACUcucaAGUGUaGGaagUGUGCUAcAuuAaa....augGCAgGaU.UUUCGCUAAcaCCagaAGgGcCUc...UGgCcCaAUGAcuGGAGUUUGaUAGUAauuccUGCcACAugu
//
# STOCKHOLM 1.0

#=GF AC   RF00092
#=GF ID   SNORA63
#=GF PI   E3
#=GF DE   Small nucleolar RNA SNORA63
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR
#=GF GA   90.00
#=GF TC   90.00
#=GF NC   89.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300555;
#=GF DR   snoopy; Homo_sapiens300073;
#=GF RN   [1]
#=GF RM   9144174
#=GF RT   Three small nucleolar RNAs that are involved in ribosomal RNA precursor
#=GF RT   processing.
#=GF RA   Mishra RK, Eliceiri GL
#=GF RL   Proc Natl Acad Sci U S A 1997;94:4972-4977.
#=GF CC   E3 belongs to the H/ACA class of snoRNAs and is involved in the processing
#=GF CC   of eukaryotic pre-rRNA and has regions of complementarity to 18S rRNA. E3
#=GF CC   is encoded in introns in the gene for protein synthesis initiation factor
#=GF CC   4AII [1].
#=GF WK   Small_nucleolar_RNA_SNORA63
#=GF SQ   8


U64705.1/82-210    AAGCAGGAUUUU-ACUACAAUAUGGCUGCUCAGUGCUGUGUUGUCGUUCCCCCUGCUCAGAACAA--UUGUUU-CUUAACUAUACCUGUCUGCUGUCUACCUGUAG--CAGCCAGGGACGCUUGGUCUCAUACAU
U64706.1/79-207    AAGCAGGAUUUA-ACUACAAUAUAGCUGCUCAGUGCUGUGUUGUCGUUCCCCCUGCUCAGAAUAA--UUGUUU-CUUAACUAUACCUGUCUGCCAUCUGCCUGUAG--CAGCCAGGGACGCUUGGUCUCAAACAU
U12212.1/198-329   ACGCAGGAUUCAGACUAGAAUAUAGCUGUUAAGUGCUGUGUUGUCAUUCUCCCUGCUUAAAAUAAAGUUUUUUUCUUAACUAUACCUGUCUGCUAU-CUGCUGUAG--CAGCCAGGGAUGCUUGGUUUCAUACAU
U64704.1/88-217    AAGCAGGAUUCAGACUACAAUAUAGCUGUUUAGUGCUGUGUUGUCGUUCCCCCUGCUCAAAGUAAGGUUGUUU-CUUA-CUAUACCUGUCUGCUCUAUCCCUGUAG--CAGCCAGGGACGCUUGGUCUCAUACA-
L07384.1/2-133     AAGCAGGAUUCAGACUACAAUAUAGCUGCUAAGUGCUGUGUUGUCGUUCCCCCUGCUUAAAAUAAAGUUGUUU-CUUAACUAUACCUGUCUGCUAUUCUCCUGUAG--CAGCCAGGGACGCUUGGUCUCAUACAU
X56953.1/3592-3718 AUGCAGGUACAG--UUACAAUAAAACUG--AAGUGUUCUAUUGUCGUUCCCCCUGCUUAAAGCAU--UUGAUA-CAUUACUAUCUCUGCCCUAGCUCUACC-AUAGCUAAGGCAGAGACGCUUGGUUUCAAACAU
U64707.1/102-229   AAGCAGGAUAAG--UUAUGAUAUAGCUGUGCAGUGCUGUAUUAUCGUUCCCCCUGCUUAAAGAAAA-AUGUUUCCUU--CUAUCCCUACCUGCUUAGUUCCCACAG--CAGGUAGGGACGCUGGGUUUCAUACAU
U64708.1/2-124     -UGCAGGAUUAG--UUACAAUAUAUCUGGGCAGUGCUGUGUUGUCGUUCCCCCUGCUAGAAAGUAAGUUGAUUCCUU--CUAUUCCUGGCUGUUCU----CUAUAG--CAGACAGGAACGCUUGGUCUCAAACA-
#=GC SS_cons       ::<<<<<-----.---<<<<<<<<<<________>>>>>>>>>>------->>>>>----------.------.----------<<<<-<<<<____________>..>>>->>>>:::::::::::::::::::
#=GC RF            AaGCAGGAUuaa.AuUAcaAuAcagCUGuuaAGUGcugUgUugUCGUUCCCCCUGCUuAAAauAAA.UUGuUU.CUUaACUAUaCCUGuCugcuaUuuucCUaUAg..caGcCAGGGACGCUUGGUuUCAuACAU
//
# STOCKHOLM 1.0

#=GF AC   RF00093
#=GF ID   SNORD18
#=GF PI   U18
#=GF DE   Small nucleolar RNA SNORD18
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR
#=GF GA   41.00
#=GF TC   41.00
#=GF NC   40.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF CL   CL00047
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300894;
#=GF DR   snoopy; Homo_sapiens300399;
#=GF RN   [1]
#=GF RM   7507233
#=GF RT   Two different snoRNAs are encoded in introns of amphibian and human L1
#=GF RT   ribosomal protein genes.
#=GF RA   Prislei S, Michienzi A, Presutti C, Fragapane P, Bozzoni I
#=GF RL   Nucleic Acids Res 1993;21:5824-5830.
#=GF RN   [2]
#=GF RM   11726521
#=GF RT   Release of U18 snoRNA from its host intron requires interaction of Nop1p
#=GF RT   with the Rnt1p endonuclease.
#=GF RA   Giorgi C, Fatica A, Nagel R, Bozzoni I
#=GF RL   EMBO J 2001;20:6856-6865.
#=GF CC   U18 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. It is encoded in introns of ribosomal protein L1
#=GF CC   in Xenopus and human, and in introns of elongation factor 1 beta in yeast.
#=GF CC   Related snoRNAs in Arabidopsis and rice have been named R63 and Z106
#=GF CC   respectively. Factors involved in the processing of the intronic snoRNA
#=GF CC   have recently been elucidated [2].
#=GF WK   Small_nucleolar_RNA_SNORD18
#=GF SQ   16


AJ307927.1/2-83      GGAACAUGAUGAAGAACCAUU-----GGUCCGUGUUUCUGA---------UCAUCUCG-UGAUGAAACUA-CAA----UGAAGCACUCAUACUUCUGAUUCC
Z75111.1/1-65        UGGCAGUGAUGAUCA-CA--------AAUCCGUGUUUCUGA---------CAAGCGAU-UGAC--GAUAGAAAA----------------CCGGCUGAGCCA
AB061820.1/2178-2249 CAGUAGUGAUGAAAUUCCACUUCAUUGGUCCGUGUUUCUGA-----------ACCACA-UGAUUUUCUCG-GAU-----------------GUUCUGAUGCU
X61926.1/688-775     AAGCUAUGAUGACCA-AAAUU-----GGUCCGUGUUACUGA--GCGGAUUAAGACCCC-AGCAAACGAAGAGAA-----ACCCAAUUUUUAAUUCUGAUUUU
U12981.1/1-88        -GUGAAUGAUGAAUU-UAAUUCUUU-GGUCCGUGUUUAUGA-UGGGAAGUAAGACCCC-CGAUAUGAGUGACAA---------AAGAGAUGUGGUUGACUAU
X06552.1/2863-2934   GCUUUAUGAUGAGCU-CCACUUCUAUGGUCCGUGUUUCUGA----------UGCAUCA-UGAUCUCUGUG-GAA-----------------GUUCUGAUCAG
X96517.1/284-381     UUAAAAUGAUGAUCU-CAAUCUUU--GGUCCGUGUUUAUGAGGUGGCCUCAAGACCCA-CCGCAUGAGUGACAAAGAAGAUUUAAAUCUUAUAUCUGACAAU
AB061820.1/3401-3472 UCAAAAUGAUGAGAUUCCACUUAAUUGGUCCGUGUUUCUGA-----------AACACA-UGAUAUUUGUG-GAA-----------------AUUCUGACUUG
AB061820.1/4174-4242 UUGUUAUGAUGAGAU-UCCACUUAA-GGUCCGUGUUUCUGA-----------AACAAA-UGAU-UUUGUG-GAA-----------------GUUCUGAUUUA
X06552.1/5485-5556   UGUUAAUGAUGAGUU-CCACUUCAUUGGUCCGUGUUUCUGA----------AACCUUA-UGAUCUAAGUG-GAA-----------------GUUCUGACUGA
X75488.1/49-119      UGGAUAUGAUGAGCU-CCACUUCAU-GGUCCGUGUUUCUGA-----------ACCGAAGUGAUAUCAAUG-GAA-----------------GUUCUGAUUAC
M15678.1/1373-1441   UGUUAAUGAUGAGCU-CCACUUCAU-GGUCCGUGUUUCUGA------------CCUUA-UGAUCUGAGUG-GAA-----------------GUUCUGAUAUA
X06552.1/4707-4777   UAUACAUGAUGAUUU-CCACUUCUAUGGUCCGUGUUUCUGA-----------AACUCA-UGAUAUUUGUG-GAA-----------------GUUCUGAUUUA
X06552.1/2182-2251   UCGAUAUGAUGAGUU-CCACUUCAU-GGUCCGUGUUUCUGA-----------ACCUAG-UGAUAUUAAUG-GAA-----------------GUUCUGAUUUC
M15678.1/705-773     UAUACAUGAUGAUCU-CCACUUCU--GGUCCGUGUUUCUGA-----------AACUCA-UGAUCUUUGUG-GAA-----------------GUUCUGACUUA
X75486.1/57-126      UGAAUAUGAUGAGUU-CCACUUCAU-GGUCCGUGUUUCUGA-----------ACCCAG-UGAUAAUAAUG-GAA-----------------GUUCUGAUUUA
#=GC SS_cons         <<<<___________._________._______________.........________.___________.___................________>>>>
#=GC RF              uuaaaAUGAUGAucU.CcAuUUcuU.GGUCCGUGUUUCUGA.........aAAaCuCa.UGAUaUuagUG.gAA................agUUCUGAuuaa
//
# STOCKHOLM 1.0

#=GF AC   RF00094
#=GF ID   HDV_ribozyme
#=GF DE   Hepatitis delta virus ribozyme
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, Daub J
#=GF SS   Published; PMID:9783582
#=GF GA   50.00
#=GF TC   55.00
#=GF NC   49.00
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://subviral.med.uottawa.ca/cgi-bin/species.cgi?fkLongueur=2;
#=GF DR   SO; 0000374; ribozyme;
#=GF RN   [1]
#=GF RM   9783582
#=GF RT   Crystal structure of a hepatitis delta virus ribozyme.
#=GF RA   Ferre-D'Amare AR, Zhou K, Doudna JA
#=GF RL   Nature 1998;395:567-574.
#=GF RN   [2]
#=GF RM   3184270
#=GF RT   Characterization of self-cleaving RNA sequences on the genome and
#=GF RT   antigenome of human hepatitis delta virus.
#=GF RA   Kuo MY, Sharmeen L, Dinter-Gottlieb G, Taylor J
#=GF RL   J Virol 1988;62:4439-4444.
#=GF RN   [3]
#=GF RM   2430299
#=GF RT   Structure and replication of the genome of the hepatitis delta virus.
#=GF RA   Chen PJ, Kalpana G, Goldberg J, Mason W, Werner B, Gerin J, Taylor J
#=GF RL   Proc Natl Acad Sci U S A. 1986;83:8774-8778.
#=GF CC   The hepatitis delta virus (HDV) ribozyme is necessary for viral
#=GF CC   replication and is thought to be the only catalytic RNA known to be
#=GF CC   required for viability of a human pathogen. The ribozyme acts to process
#=GF CC   the RNA transcripts to unit lengths in a self cleavage reaction. The
#=GF CC   ribozyme is found to be active in vivo in the absence of any protein
#=GF CC   factors and is the fastest known naturally occurring self-cleaving RNA
#=GF CC   [1].
#=GF WK   Hepatitis_delta_virus_ribozyme
#=GF SQ   33


AF425644.1/679-767 AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAA-GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA
AF425645.1/687-774 GUGGCCGGCAUGGUC-CCA--------GCCUCCCCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA
AB037947.1/685-775 GUGGCCGGCAUGGCC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACGAUCCGA--GGGGA-CUG--U-CCCU-C----UC-GAGAAUCGGCAAA---UGGGGCCCC
AB037948.1/685-775 GUGGCCGGCAUGGCC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACGAUCCGA--GGGGA-CUA--U-CCCU-C----UC-GAGAAUCGGCAAA---UGGGGCCCC
X77627.1/679-767   AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAG-GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA
L22063.1/691-781   GUGGCCGGCAUGGCC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACGAUCCGA--GGGAG-CUA--C-UCCU-C----UC-GAGAAUCGGCAAA---UGGGGCCCC
AJ309877.1/318-405 GUGGCCGGCAUGGUC-CCA--------GCCUCCUCGUUGGCGCCGGCCGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA
M84917.1/684-773   GUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U-CCUC-C----UC--GGUAAUGGCGAA---UGGGACCCA
X85253.1/682-769   AUGGCCGGCAUGGUC-CCA--------GCCUCCUUCGUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA
U81988.1/679-767   AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--C--CCC-C----UC--GGUAAUGGCGAA---UGGGACCCA
AF209859.1/689-775 -UGGCCGGCAUGGUC-CCA--------GCCUCCUCGUCGGCGCCGGCCGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA
M28267.1/687-775   AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U--CCC-C----UC--GGUAAUGGCGAA---UGGGACGCA
AF104263.1/681-769 AUGGCCGGCAUGGUC-CCA--------GCCUCCCCGGUGGCGCCGGCUGGGCAACAUUCCGAA-GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA
AF104264.1/691-778 GUGGCCGGCAUGGUC-CCA--------GCCUCCCCCGUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----UC--GGUAAUGGCGAA---UGGGACCCA
M92448.1/681-769   AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--AGGGA-CCG--U--CCC-U----UC--GGUAAUGGCGAA---UGGGACCCA
X04451.1/684-772   AUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U--CCC-C----UC--GGUAAUGGCGAA---UGGGACCCA
AJ584845.1/918-825 UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGC-GGUCCGACCUGGG---CAU-CCGAA-GGAGGACAGAAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCAGU
AJ309880.1/911-818 UCGGGUCGGCAUGGCAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAUCCGUA--GGAGGACAG-AC--GUC-C----UACUCG-GAUGGCUAAGGGAGAGCCAGU
EF514905.2/675-762 GUGGCCGGCAUGGU--CCA--------GCCUACUCGCUGGCGCGGGCUGGGCAACAUUCCGA--GGGGA-CCC--G--UCC-C----UC--GGUAAUGGCGAA---UGGGACCCA
L22063.1/906-814   UCGGGUCGGCAUGGGAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGUAAGGAGA-GCG--UAGCUC-C---CUC--GG--AUGGCAAAGGGAGAUCCACC
AB221936.1/165-71  UCGGGUCGGCAUGGCAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGUA-GGAGG-ACRRAC--GUC-CUACCUC--GG--AUGGCUAAGGGAGAGCCAGU
AB118827.1/904-812 UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGU-GGUCCGACCUGGG---CAU-CCGAA-GGAGG-ACAAAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCAGU
AM183327.1/684-771 GUGGCCGGCAUGGUC-CCA--------GCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGA--GGGGA-CCG--U---CC-C----CC--GGYAAUGGCAGA---UGGGACCCA
AB037949.1/902-810 UCGGGUCGGCAUGGGAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGUAAGGAGG-ACG--U-AGUC-C--CCUC--GG--AUGGCAAAGGGAGAUCCACC
AJ584849.1/902-810 UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGU-GGUCCGACCUGGG---CAU-CCGAA-GGAGGACAG-AC--GUC-C--ACUC--GG--AUGGCUAAGGGAGUGCCAGC
AM183332.1/902-810 UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGC-GGUCCGACCUGGG---CAU-CCGUA-GGAGG-ACGGAC--GUC-C--ACUC--GG--AUGGCGAAGGGAGAGCCAGU
AB221996.1/162-71  UCGGGUCGGCAUGGCAUCUCC------ACCUCCUCAC-GGUCCGACCUGGG---CAU-CCGAA-GGAGG-ACA-AC--GUC-C--CCUC--GG--AUGGCUAAGGGAGAGCCAGU
AJ309877.1/537-443 UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGC-GGUCCGACCUGGG---CAUCCGUAA-GGAGGACAG-AC--GUC-C----UACUCG-GAUGGCUAAGGGAGAGCCACU
EF514904.1/897-798 UCGGGUCGGCAUGGCAUCUCCACCUCCACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGAA-GGAGGAGCGGAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCCAG
U19598.1/901-809   UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGC-GGUCCGACCUGGG---CAU-CCGUA-GAGAG-ACGAAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCAGU
AF104264.1/907-816 UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGC-GGUCCGACCUGGG---CAU-CCGUA-GGAGG-ACGAAC--GUCAC----UC--GG--AUGGCUAAGGGAGAGCCAGU
AM183330.1/903-811 UCGGGUCGGCAUGGCAUCUCC------ACCUCCCCGU-GGUCCGACCUGGG---CAU-CCGAA-GGAGGACGG-AC--GUC-C--ACUC--GG--AUGGCUAAGGGAGUGCCGGC
X04451.1/902-810   UCGGGUCGGCAUGGCAUCUCC------ACCUCCUCGC-GGUCCGACCUGGG---CAU-CCGAA-GGAGG-ACGCAC--GUC-C--ACUC--GG--AUGGCUAAGGGAGAGCCACU
#=GC SS_cons       ::<<<<<<<--AAAA-AAA--......<<<_BB____.>>>>>>>>>>bb-...<<<<<<<<-.<<<-<.___..>..->>.>....>>..>>.>>>>::::::::aaaaaaa::
#=GC RF            uugGgcgGgaauGuCAuCuCC......gCCUCCuCGc.GGccCcgcCuGGG...CauuCcGaA.GGgGg.ccG..c..gcC.C....uC..gG.aauGGCuAAGGGaGaGaCacu
//
# STOCKHOLM 1.0

#=GF AC   RF00095
#=GF ID   snoPyro_CD
#=GF PI   CD_sno_Pyro
#=GF DE   Pyrococcus C/D box small nucleolar RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.00 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://rna.wustl.edu/snoRNAdb/;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Oryctolagus_cuniculus300306;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science 2000;288:517-522.
#=GF RN   [2]
#=GF RM   10736225
#=GF RT   Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs:
#=GF RT   lessons from the Pyrococcus genomes.
#=GF RA   Gaspin C, Cavaille J, Erauso G, Bachellerie JP
#=GF RL   J Mol Biol 2000;297:895-906.
#=GF CC   Computational screens have identified C/D box snoRNAs in a number of
#=GF CC   archaeal genomes [1,2]. This family represents several related snoRNAs
#=GF CC   from Pyrococcus. These RNAs are thought to act as guides for the
#=GF CC   2'-O-ribose methylation of ribosomal RNA.
#=GF WK   D_box_small_nucleolar_RNA
#=GF SQ   25



AF254836.1/1-50            --AA-UGAUGAGACCG-GCACUAA-CUGAGUU----GUGAUGAGCACUC-GGUUGGCUGA---
AJ248283.1/127068-127123   GCCAAUGAUGAGACCG-GCACUAA-CUGAGUU----GUGAUGAGCACUC-GGUUGGCUGAGAC
AF254829.1/1-52            --GA-UGAUGAGCCUUCCCCUCAC-CUGAGU----GGUGAUGAGCACACCGGUAGGCUGA---
AF254824.1/1-52            --GA-UGAUGAGUUUUUCCCUCACUCUGAGCC----GUGAUGAGGAG-CCGAUGCUCUGA---
AJ248283.1/230633-230690   AGGGAUGAUGAGUUUUUCCCUCACUCUGAGCC----GUGAUGAGGAG-CCGAUGCUCUGACCU
AJ248285.1/75109-75163     UGCGAUGAUGAUAACU-CCCUGAC-CUGAAA----GGUGAUGAGGA--CCGGUUCACUGAGCU
AF254839.1/3-58            AGGAAUGAUGAGAUUU-GCUACCA-CUGAGCA----GUGAUGAGCCCUGCCG-UUACUGACCU
AJ248286.2/47940-47881     GGGAGUGAUGAGGUUC-GCUAGAG-CUGAAGGAUUGAUGAUGAGACCCAGGG-UAUCUGACCG
AJ248284.1/94572-94515     UCGAGUGAUGAGCCCG-CGCAGCG-CUGAGCA--AGAUGAUGAAGAUUUUA-AGUGCUGACGC
AJ248283.1/258067-258122   GAAGAUGAUGAGCUCG-GCAGGUC-CUGAGGA----GUGAUGAGGAUCUUG-AGUGCUGAUUC
AJ248287.2/1331-1388       AGCGAUGAUGUAGAUUAGCCCCGA-CUGAGUU----GUGAUGAGGCUGGCCCAUCGCUGAGCU
AJ248285.1/162300-162244   AGUGAUGAUGAUUAAA-CCCGUUG-CUGAGA----GGUGAUGAGGGGACCGACUAGCUGAACA
AJ248284.1/11081-11026     GCGGAUGACGAGCCUU-GCCCAGC-CUGAAA----GGUGAUGAUGUCGGUA-UUAGCUGACGC
AE009950.1/1345505-1345452 GAGA-UGAUGAGAACU-CCCUGAU-CUGAGC----GGUGAUGAGGA--CCGGUGAUCUGAAAA
AE009950.1/552381-552326   GGCGAUGACGAAGGGU-GACGUCC-CUGAGU----GGUGAUGAAGCCCGCG-AUAGCUGAGCA
AE009950.1/1798444-1798389 UGAGAUGAUGAACUCG-GCAGGUC-CUGAAG----GAUGAUGAGGAUCUUG-AGUGCUGAUCA
AE009950.1/477349-477406   AGGGAUGAUGAGAUUU-GCUACCU-CUGAAAAU-A-AUGAUGAACCCUGCCG-UUACUGACCG
AE009950.1/581261-581204   GGCGAUGAUGUAGAUUAGCCCCGA-CUGAGC----GGUGAUGAAGCUGGCCCAUCGCUGAGUC
AE009950.1/1666263-1666208 GCGGAUGAUGUGCCUU-GCCCAGC-CUGAAA----GGUGAUGAUGUCGGUA-UUAGCUGACGC
AE009950.1/164062-164119   GGGGAUGAUGAGUUUUUCCCUCACUCUGAUUA----GUGAUGAGGAG-CCGAUGCACUGACCU
AE009950.1/1374522-1374577 GUAGAUGAUGAGGCCA-UCCC-CU-CUGAUCU----GUGAUGAGUGGGUGAGCUGGCUGAUAC
AE009950.1/1374434-1374489 AGGGAUGAUGAAGUUC-GCUAGAC-CUGAGGA----GUGAUGAGCCCUAGGG-UAUCUGACCA
AF013497.1/174-230         CUGA-UGAUGAUCCUUCCCCUCAA-CUGAGA----GGUGAUGAGCACACCGGUAGGCUGAGGU
AE009950.1/10963-10908     GUCGAUGACGAAACCG-GCACUAU-CUGAAU----GAUGAUGAGCACUC-GGUUGUCUGAGAC
AE009950.1/1550992-1550936 AAAGAUGAUGAACCCG-CGCAGCU-CUGAAGG---GAUGAUGAGGAUCUUA-AGUGCUGAUCU
#=GC SS_cons               <<<_____________._______._______..._________________________>>>
#=GC RF                    gggGAUGAUGAGcuUu.GCCacac.CUGAGua...GGUGAUGAGGacucCGGuUaGCUGAccc
//
# STOCKHOLM 1.0

#=GF AC   RF00096
#=GF ID   U8
#=GF PI   CeN21; CeR-2
#=GF DE   U8 small nucleolar RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Griffiths-Jones SR, Gardner PP
#=GF SS   Published; PMID:11675000; Gardner PP
#=GF GA   41.00
#=GF TC   41.40
#=GF NC   40.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300007;
#=GF DR   snoopy; Homo_sapiens300380;
#=GF RN   [1]
#=GF RM   11675000
#=GF RT   The U8 snoRNA gene family: identification and characterization of
#=GF RT   distinct, functional U8 genes in Xenopus.
#=GF RA   Peculis BA, DeGregorio S, McDowell K
#=GF RL   Gene 2001;274:83-92.
#=GF RN   [2]
#=GF RM   9199304
#=GF RT   The sequence of the 5' end of the U8 small nucleolar RNA is critical for
#=GF RT   5.8S and 28S rRNA maturation.
#=GF RA   Peculis BA
#=GF RL   Mol Cell Biol 1997;17:3702-3713.
#=GF RN   [3]
#=GF RM   20460460
#=GF RT   A small nucleolar RNA functions in rRNA processing in Caenorhabditis
#=GF RT   elegans.
#=GF RA   Hokii Y, Sasano Y, Sato M, Sakamoto H, Sakata K, Shingai R, Taneda A, Oka
#=GF RA   S, Himeno H, Muto A, Fujiwara T, Ushida C
#=GF RL   Nucleic Acids Res. 2010;38:5909-5918.
#=GF CC   U8 is a member of the C/D class of snoRNA which contain the C (UGAUGA) and
#=GF CC   D (CUGA) box motifs. U8 is the RNA component of a small complex (the U8
#=GF CC   snoRNP) which is required for accumulation of mature large subunit
#=GF CC   ribosomal RNAs, 5.8S and 28S rRNAs. U8 RNA has been identified in human,
#=GF CC   mouse, rat and Xenopus.
#=GF WK   U8_small_nucleolar_RNA
#=GF SQ   55


AL807389.7/15376-15244       ACAUCAGU-GAGGU-ACAUCCUUACCUGU-U-ACCUUAG-CAAU-AAGGUU-A--CAGAU----------CAUGAUGAUU-GGAUU-CUAUGAAUACG----U---GAUU-AUAUACCG-U-AUU-UG-U----------UUAGG-GA-CUG---CAACC---CCUUUACG---AAUCCUG--UCUGAC
M11057.1/2-139               UCGUCAG--GAGGU-UAAUCCUUACCUGU-C-CCUCCU---UUC-GGAG-G-G--CAGAU--AG----AAAAUGAUGAUU-GGAGCUUGCAUGAUCUG---CU---GAUU-AU--AGCA-U-UUC-CG-U-GUA-----AUCAGG-AC-CUG--ACAACA---UCCUGAUU---GCUUCUA--UCUGAU
L13416.1/2-139               UCGUCAGU-GAGGU-UAAUCCUUACCUGU-U-CCU-C----UCC-G--G-G-A--GAAAC--AG----CACAUGAUGAAU-GGAGG-AGACUGAGUCG---CU---GAUU-AC-UC-UG-UACUC-CGGU-CCU-----GUCUGG-UG-CGA---CAACACUUACCAGGCA---GGAUCAU--UCUGAU
AF375054.1/1920-2053         UUGUCAGU-GAGGU-UAAUCCUUACCUGU-U-CCUU-C---UCCG---G-G-A--GAAAC--AG----CACAUGAUGAAU-GGAGG-AGACUGAGUCG---CU---GAUU-AC-UC-UGUA-CUC-CG-G-UCC----UGUCUGG-UG-UG------ACA--UUCCAGUCU---GGGUCAU--UCUGAU
X04239.2/3-137               UCGUCAG--GAGGU-UAAUCCUUACCUGU-C-CCUCCU---UUC-GGAG-G-G--CAG---UAG----AAAAUGAUGAUU-GGAGCUUGCAUGAUCUG---CU---GAUU-A----GCA-U-UUC-CA-U-GCA-----AUCAGG-AC-CUG--ACAACA---UCCUGGUU---GCUCCUA--UCUGAU
AAHX01064560.1/8360-8495     UCGUCAG--GAGGU-UAAUCCUUACCUGU-U-CCUCCU---CUC-GGAG-G-G--CAGAU--AG----AAAAUGAUGAUU-GGAGCUUGCAUGAUCUG---CU---GAUU-A----GCA-U-UUC-CG-U-GUA-----AUCAGG-AC-CUG--ACAACA---UCCUGAUU---GCUCCUA--UCUGAU
BC047810.1/2-134             GCAUCAGU-GAGGU-UAAUCCUUACCUGU-U-GUCUUA---GAA-AUAA-G-A--CUA---CAG----CACAUGAUGAUU-GAAUU-CUAUGAAUACG----U---GAUU-AUAUUCUG-U-AUU-CU-U----------AAAGG-GU-UUG---CAACA---CCUUUAUG---AAUCCUG--UCUGAU
AANN01499785.1/973-1107      UCGUCAGU-AAGGU-UAAUCCUUACCUGU-U-CCUCC----UCU-GGAG-G-G--CAGAU-ACG----AACAUGAUGAUU-GGAGUACACAUGAUUCG----U---GAUU-A----ACG-A-CUC-UG-U-GUA-----GUCAGG-GC-UUG---CAACA---CCCUGAUU---GCUCCUA--UCUGAU
AAIY01080613.1/1330-1464     UCGUCAGU-AAGGU-UAAUCCUUACCUGU-U-CCUCCU---UUU-GGAG-A-A--CAGAG--AU----AAAAUGAUGAUU-GGAGCUCUCAUGAUACG----U---GAUU-A----GCG-U-CUC-CG-U-GUG-----AGCAGG-AC-UUG---CAACA---UCCUGUUU---GCUCCUA--UCUGAU
CAAE01014577.1/304763-304628 UCGUCAGU-GAGGU-ACAUCCUUACCUGU-U-ACUUCAG-AAAU-GAAG-UUG--CAG----------AAAAUGAUGAAU-GGAGGCUGCAUGAGGAA----U---GAUU-AU--AUGU-C-CUC-UG-G-CAU-----GUCGGG-AC-CAG---CAACU---CCCUGCAU---GACCCAU--UCUGAU
AAIY01100313.1/3582-3448     UCGUUAGU-AAGGU-UAAUCCUUACCUAU-U-CCUCCU---UUU-GGAG-A-A--CAGAG--GU----AAAAUGAUGAUU-GGAGCUCACGUGAUACG----U---GAUU-A----GCG-U-CUC-UG-U-GUG-----AGCAGG-AC-UUG---CAACA---UCCUGUUU---GCGUCUA--UCUGAU
AALT01649851.1/389-254       UCGUCAGG-UAGGA-UAAUCCUUACCUGU-U-CCUCUU---UUC-AGAG-G-G--CAGAU--AG----AAAAUGAUGAUU-GGAGUUCGCAUGAUACG----U---GAUU-A---UACG-U-CUC-UG-C-GUG-----AUUAGG-GC-CUG---CAACA---CCCUAAUC---GCUCCUA--UCUGAU
AAYZ01129993.1/2422-2291     UCGUCAGG-UGGGU-UAAUCCUUACCUGU-U-CCUCCU---UCG-GGAG-G-G-----AU--AG----AACAUGAUGAUU-GGAGUUCGCAUGAUGCG----U---GAUU-A----GCG-U-CUC-UG-C-GUA-----AUCAGG-AC-UUG---CAACA---CCCUGAUU---GCUCCUA--UCUGAU
AAFC03091925.1/8345-8480     UCGUCAGG-UAGGA-UAAUCCUUACCUGU-U-CCUCCU---UUU-GGAG-G-G--CAGAA-UAG----AACAUGAUGAUU-GGAGCUCGCAUGAUUCG----U---GAUU-A----ACG-G-CUC-UG-C-GUA-----AUCAGG-AC-UUG---CAACA---CCCUGAUU---GCUCCUA--UCUGAU
AALT01511605.1/346-480       UUGUCAAG-UAGGA-UAAUCCCUACCUGU-U-UCUCUU---UUC-AGAG-G-G--CAGAU--AG----AACAUGAUGAUU-GGAGCUUGCAUGAUUUG----U---GAUU-A----ACA-U-CUC-UG-U-GUG-----AUUAGG-GC-UCA---AAACA---CCCUAAUU---GCUCUUU--UCUGAU
AAPY01311180.1/1652-1518     UCGUCAGG-UGGGA-UAAUCCUUACCUGU-U-CCUCCU---UCG-GGAG-G-G--CAGAU--AG----AACAUGAUGAUU-GGAGUCCGCAUGAUACG----U---GAUU-A----GCG-U-CUC-UG-C-GUA-----AUCAGG-AC-UUG---CAACA---CCCUGAUU---ACUCCUA--UCUGAU
AACN010131197.1/1439-1574    UCGUCAGG-UAGGA-UAAUCCUUACCUGU-U-CCUCCC---UCG-GGAG-G-G--CAGCU-CGG----AACAUGAUGAUU-GGAGCUCGCAUGAUUCG----U---GAUU-A----GCG-U-CUC-UG-C-GUA-----GUCGGG-AC-UUG---CAACA---CCCCGGCU---GCUCCUA--UCUGAU
AADC01102901.1/15489-15356   CUGUCAGG-UGGGA-UAACCCUUCCCUGU-U-CCUCCG---UUU-GGAG-G-G--CAGAU--AG----AACAUGAUGACU-GGAGA-UGCAUGAAAUG----U---GACU-A----AUG-U-CUC-UG-U-GUA-----AUCAGG-AC-UUG---CAACA---CCCUGAUU---GCUCCUA--UCUGAU
AAFR03058570.1/10411-10547   UCGUCAGU-ACGGU-ACAUCCUUACCUGU-U-GCUCCU--UCUU-GGAG-A-A--CAGU----------AAAUGAUGAUU-GGAGCCUGCAUGACACG----U---GAUU-A----GUG-U-CUC-UG-CAGCA-----ACUCGG-AG-AUG--GCGACAAACUCCUUGUU---GCUCCUU--UCUGAU
AAPY01187975.1/2595-2462     UGGUCAGG-U-GGA-UAAUCCUUACCUGU-U-CCUCCU---UCG-GGAA-G-G--CAGAU--AG----AACAUGAUGAUU-GGAGUUCGCGUGAUACG----U---GAUU-A----GCG-U-CUC-UG-C-GUC-----AUCGGG-AC-UUG---CAACA---CCCUGCUU---GCUCCUA--UCUGAU
AANU01204695.1/188-54        UCGUCAGG-UGGGA-UAAUCCUUACCUGU-U-CCUCUU---U-U-GGAG-G-G--CAGAU-UAG----AACAUGAUGAUU-GGAGAAUGCAUGAAACG----U---GAUU-A----ACG-U-CUC-UG-C-GUA-----AUCAGG-AC-UUG---CAACA---CCCUGAUU---GCUCCUA--UCUGAU
AANH01002299.1/69986-69854   UCUUCAGU-GAGGU-GCAUCCUUACCUGU-U-ACUCCCUACCAA-GGAG-U-A-UCAGAU----------CAUGAUGAAU-GGGGA-AUCAUGAGAUA----U---GAUU-A----AAA-U-CUC-CA-U--CU-----UAUAGG-GA-AAG---CAACA---CCCUAUUA---GAUCCAU--UCUGAU
ABDC01455897.1/606-470       UCGUCAGG-UGGGA-UAAUCCUUACCUGU-U-ACUCCU---UUU-GGAG-U-G--CAGAU-GAG----AAAAUGAUGAUU-GGAGUUCGCAUGAUACG----U---GAUU-A---UACG-U-CUC-UG-C-GUA-----AUCAGA-GC-CUG---CAACA---CUCUGAUU---GCUCCUA--UCUGAU
AANH01002299.1/71546-71414   UCUUCAGU-GAGGU-ACAUCCUUACCUGU-U-ACUCCCUACCAA-GGAG-U-A-UCAGAG----------CAUGAUGAAU-GGGGA-AUCAUGAGAUA----U---GAUU-A----AUA-U-CUC-UG-U--CU-----UUUAGG-GA-AAG---CAACA---CCCUACUA---GAUCCAU--UCUGAU
AC090233.16/1998-1865        UCAUCAGG-UGGGA-UAAUCCUUACCUGU-U-CCUCGU---UUU-GGAG-G-G--CAGAU--AG----AACAGGAUAAUU-GGAGUUUGCAUGAUCCA----U---GAUU-A----AUG-U-CUC-UG-U-GUA-----AUCAGG-AC-UUG---CAA-A---CUCUGAUU---GUUCAUA--UCUGAU
AANU01222760.1/36-167        UCCACAGG-UGAGA-UCAUUCUUACCUGU-U-CCUCCU---UUU-GGAG-G-G--CAG----AG----UUCAUGAUGACU-AGAGUUCACACGAUAUG----U---GAUU-A----AU--U-CUC-UG-C-AUA-----AUCAGG-AU-CUG---CAACA---UCCUGAUU---GCUCCUA--CCUGAU
AANN01834300.1/641-507       UAGUCAAA-AAGGU-UAAUCCUUCUCUGU-U-CCUCC----UCU-GGAG-G-G--CAGAU-ACA----AACAUGAUAAUU-GGAAUACACAUGAUUCU----U---GAUU-A----ACG-A-CUC-UG-U-GUA-----GUCAGG-GC-UCU---CAAUA---CCCUGAUU---GCUCCUA--UUUGAU
AAPN01229839.1/4639-4773     UUGUUGGU-AGGUU-AUAUCCUCACCUGU-U-UCUCCU---UCG-GGAG-A-G--UGGAU---------AUAUGAUGAUU-GGAGUUCGCAUGACACG----U---GAUU-A----GUG-U-CUC-CG-C-GAC----GAUUGGG-GAGCUG--ACAACA---CCCCAAUU---GUUCCUA--UCUGAU
ABDC01473394.1/1460-1596     UCAUCAGA-UGGGA-UAAUCCUUACCGGU-U-CCUCCU---UAU-GGAG-G-G--CAGUU-UAG----CAAAGGAUGAUU-GGAGUUUGCGUGAUACA----U---GAUU-A---UAUG-U-CUC-UG-C-AUA-----AUCAGG-AC-UUG---CGACA---CCCUGAUU---GCUCCUA--UCUGAU
AAFC03037687.1/47949-48084   UUGUCAGG-UAAGA-UACUUCUUACCUGU-U-CCUCUU---UUU-GGAG-G-G--CAGAA-UAG----AAUGUGAUGAUU-GGAGCUCGAAUGAUUUA----U---GAUU-A----AGG-G-CUC-UC-C-AUA-----AUCAGG-AC-UUG---CAACA---CCCUGACU---ACACCUA--UCUGAU
AAQQ01061167.1/707-577       CCUUCAGG-UGGGA-CAAUCCUUAUCUAU-U-CCUCCU---UUU-GGAG-G-G--CAGAU--GG----AACAGGAUGAUU-GGAGUU-----UGUAUG---GU---GAUU-A----GUG-U-CUA-UG-A-AUA-----AUAAGG-AC-UUG---CAACA---CUCUGAAU---GCUCCUA--UCCGAU
BAAF04059230.1/8769-8901     UCUUCAGU-GAGGU-ACAUCCUUACCUGU-U-ACUCCC---UCC-GGGG-A-G--UUU---CAG----UACAUGAUGAAU-GGAGU-AUUAUGAGACA----U---GAUU-A----AUG-U-CUC-CC-U-CUU-----AGAAGG-AA-CGG---CAACA----CCUCCUA--AGAGCCAU--UCUGAU
AANG01229970.1/274-411       UUAUCAGG-CUGGA-UAAUCUUUACCUGU-U-CUACUU---UUU-GGAG-G-G--CAGAU-UAG----AACAUGAUGACU-GAAGUUUGCAUGAUUUG----U---GAUU-A----GAG-U-CUC-UG-C-AUGC---AGUCAGG-AC-UUC---CCACA---CACUGAUU---GAUCCUA--UUUGAU
ABAV01000378.1/3928-3794     UCAUCAGUAUAGGG-UGAUCCUUACCUGU-C-GCCCUC-----C-GGGG-C-A--CAGUA-AGG----AACAUGAUGAUU-GGUAC-AAGAUGAUCCUC--AU---GAGU-U----A--UC-CUA-UC-G-GA-----GCUCGGG-GC-UUG---CAACA---CCCCUUGU---AUCUAAC--UCUGAA
ABAV01000378.1/2725-2598     UCAUCGGUAUAGGG-UGAUCCUUACCUGU-C-GCCCUC-----C-GGGG-C-A--CAGUA-AGG----AACAUGAUGAUU-GGUAC-AAGAUGAUCCUC--AU---GAGU-U----------AUC-CU-A----------UCGGG-GC-UUG---CAACA---CCCCUUGU---AUCUAAC--UCUGAA
AACT01012532.1/19787-19929   UCAUCAGU-UCGGG-UGAUCCUUACCUGU-U-GUCCUU--AAAU-GGAC-U-U--CAGAU-AAG----UACGUGAUGACA-AUGGGUAUUAUGAGUUUA--AU---GACU-UA-UAAAC-A-CCCUAG-U--CG-----GGUAGC-GG-UCG---CAACAA-CCGUUAUCU---G-GCAUG--UCUGAG
AABS01000060.1/236915-237057 UCAUCAGU-UCGGG-UGAUCCUUACCUGU-U-GUCCAU---AUA-UGGA-C-U-UCAGAU-AAG----UACAUGAUGACACUGGGUUUAUGAGUUUGA----U---GACU-UA-UAAUA-U-CCC----U-UGCCUUGUACUGGU-AA-------CAACA---CACCAGUG---CUUGGUAUGUCUGAG
AAGV020416759.1/1200-1066    UCGUUAGG-AGGGU-UAAUCCUGACCUGU-U-CCUCCU---UCG-GGAG-G-G--CAGAU-UGG----AACGUGAUGAUU-GGAGUUCGCAUGACACG----U---GAUU-A----GCG-U--UC-UG-C-GUA-----AUCGGG-AC-CUG---CAACA---UCCUGGUU---ACUCCUA--UCUGAU
AAWR02013423.1/11935-11801   UCGUCAGG-UAGGA-UAAUCCUUACCUGU-U-CCUCCU---U-U-GGGG-G-G--CAGAU-UGG----AAAAUGAUGAUU-GGAGUGCGCAUGAUUCG----U---GAUU-A----GCG-U-CUC-UG-C-GUA-----AUCAGG-AC-UUG---CAACA---CCCUGAUU---GCUCCUG--UCUGAU
AY948613.1/4-125             UCUUCAGU-AUGGG-UCAA------UC---UC---UGA---UCUGCA-----ACU-GA-----------AUAUGAUGAGUUCGGGCGAUGAUCUUCUG----U---GAUU-A-----CA-U-CGC-AC-G-GCG-----AGGUGGGAA--CG---CAAUA---CCCGCCUGCCAGCCCGAU--UCUGAA
AAGD02012178.1/8300-8179     UCUUCAGU-AUGGG-UCAA------AU--AU----UGA---UCUGCA-----ACU-GA-----------AUAUGAUGAGUUCGGGCGAUGAUCCUCUG----U---GAUU-A-----CA-U-CGC-AG-G-GCG-----AGUUGG-GA-ACG---CAAUA---CCUGACUGCCAGCCCGGU--UCUGAC
CAAC02000550.1/78098-78219   UCUUCAGU-AUGGG-UCAA------AU--AU----UGA---UCUGCA-----ACU-GA-----------AUAUGAUGAGUUCGGGCGAUGAUCUUUCG----U---GAUU-A-----CA-U-CGC-AC-G-GCG-----AAGUGG-GA-ACG---CAAUA---CCUGCUUGCCAGCCCGAU--UCUGAA
ABRM01022647.1/3897-3760     UCAUCAGU-AUGGUGUAAUCCUUACCUGU-UGACUGCU---ACG-GCAG-UCA-UCAGUA-AGG----CAAAUGAUGACU-AGGGC-AGUAUGAUUCC----UCACGAAUUA----CAC-G-CUC-GG-G-CCU-----A-GAGA-C--------UAACA---CCCUCUUA---GGUCACA--UCUGAC
ABGP01000229.1/181888-181746 CUAUCAGU--AGGG-UGAUCCUUACCUGU-U-GUCUCUU-AAAU-GAGA-C-A--CAGAUUAAGGAUACACAUGAUGAUC-CGAGA--GUAUGACUAUUCCAU---GAAU-U----AAA-A-CUC-UC-G-CAU-----AGCAGA-GC-CGG---CGACG--ACUUUGUUA---UG--GUU--GCUGAC
AAGU03065714.1/19846-19711   UCGUCAGU-AAGGU-UAAUCCUUACCUGU-U-UCUCCU---UUC-GGAG-A-G--CAGAU--UU----AAAAUGAUGAUUUGGAGCUCGCAUGAUCCG----U---GAUU-A----ACG-U-UUC-CG-C-GUG-----AUCAGG-AC-CAG---CAACA---UCCUGAUU---GCUCCUA--UCUGAU
AAGJ04048535.1/1460-1326     UCAUCAGU-UAGGAAUAAUCCUUUCCUGU-U-ACCUCU---UCG-GAGG-U-A--GCAAG-AUG----AAGAUGAUGAGA-UGUCU-UGGAUGAUCAA----U---GAUU-A----------CUC-CA-U-GGG-----AGUGGG-GA-AUAUGACAACC---CCCCAUAA---CCCCAUC--UCUGAU
AAWZ02027083.1/21917-21784   UCGUCAGU-GAGGU-AUAUCCUGACCUGU-U-CCUCCU---CCG-GGAG-A-A-ACAGUG---------AAAUGAUGAAU-GGAGGCAGCAUGAGACA----U---GAUU-A----GAG-U-CUC-CC-G-CUG-----GCCGGG-GA-ACG---CAACG---CCCCGGCC--UGCUCCUU--UCUGAU
AAGW02049536.1/12481-12615   UCGUCAGG-UGGGA-UAAUCCUUACCUGU-U-CCUCCU---UUU-GGAG-G-G--CAGAU--AG----AACAUGAUGAUU-GGAGUUCGCAUGAUGCG----U---GAUU-A----GCG-U-CUC-UG-C-GUA-----AUCAGG-AC-UUG---CAACA---CCCUGAUU---GCUCCUA--UCUGAU
ABEG02006923.1/5128-5250     UCAUCAGU-AUGGG-UCAA------UC---UC---UGA---UCUGCA-----ACU-GA-----------ACAUGAUGAAAACGGGCGAUGAUCCUUUG---GU---GAUU-A-----UA-A-CGC-AC-G-GCG-----AGGAGG-GA-ACG---CAAUA---CCCACCUGUCUGCCCGAA--UCUGAG
CAAB02006582.1/60764-60629   UCUUCAGU-GAGGU-AUAUCCUUACCUGU-U-ACUUCAG-AAAU-GAAG-UUG--CAG----------AAAAUGAUGAAU-GGAGGCAGCAUGAGGAA----U---GAUU-AU--AUGU-C-CUC-UG-U-CAU-----GUUGGG-AA-CAG---CAACA----CCCUUCA---UGACCCA-UUCUGAU
AAQR03080591.1/4516-4654     UCAUCAGG-UGGGA-UAAUCCUUACCUGU-U-UCUCCU---UCU-GGAG-A-A--CAGAU-UAG----AAAAUGAUGAUUUGGAGCUCGCAUGAAACG----U---GAUU-A---UGCG-U-CUC-UG-C-GUA-----GCCAGG-AC-UUG---CAACA---CCCUGGUU--CGCUCCUG--UCUGAU
AAPE02044542.1/1658-1522     UCGUCAGG-UAGGA-UAAUCCUUACCUGU-C-CCUCCU---UUU-GGAG-G-G--CAGAU-UGG----AACAUGAUGAUU-GGAGAUCGCAUGAUUCG----U---GAUU-A----AUG-U-CUC-UG-C-GUA-----AUCAGG-AC-UUG---UAACA---CCCUGAUU---GCUCCUA-AUCUGAU
AAPE02026241.1/78551-78416   UGAUCAGA-UAGGA-UAAUUCUUACCUGU-U-CCACCU---CUU-GGAG-G-G--CAGAA-CAG----AACAUGAUGACU-GGAGUUUGCAUGAUUCG----U---GAUU-A----AGG-U-CGC-UG-C-GUG-----GUCAGG-UG-UUG---CAACA---CCCUGAUU---GCUACAC--CCUGAU
ABLE03026268.1/26329-26208   UCUUCAGU-AUGGG-UCAA------UU---UC---UGA---UCUGCA-----ACU-GA-----------AUAUGAUGAGUUCGGGCAAUGAUUCUUUG----U---GAUU-A-----CA-U-UGC-AC-G-GCG-----AGGUGG-GA-ACG---CAAUA---CCUGCCUGUCAGCCCGAU--UCUGAA
AC193927.3/112672-112539     UCGUCAGG-UAGGA-UAAUCCUUACCUGU-U-CCUCCU---U-C-GGAG-G-G--CAGAU-UAG----AACAUGAUGAUU-GGAGU-UGCAUGAAACG----U---GAUU-A----ACG-U-CUC-UG-C-GUA-----AUCAGG-AC-UUG---CAACA---CCCUGAUU---GCUCCUU--UCUGAU
#=GC SS_cons                 ::::::::.:::::.::::::::::<<<-.<.<<<<<_...___.>>>>.>.>..>>>,,..,,....,,,,,,,,,,,,.,,,,,,,,,,,<<-<<<....<...____.>....->>.>.->>.--.-.<<<.....<<<<<<.__.___..._____..._>>>>>>>...>>:::::..::::::
#=GC RF                      UCaUCAGU.uaGGu.UaAUCCUUACcuGU.u.ccuccu...uuu.ggag.g.a..CagAu..aG....aAcAUGAUGAuU.gGaGuuagcAUgauacg....U...GAUU.A....acg.u.Cuc.ug.u.gcu.....aucaGG.aa.uuG...CAACA...CCCugaua...gcuCcua..UCUGAu
//
# STOCKHOLM 1.0

#=GF AC   RF00097
#=GF ID   snoR71
#=GF DE   Plant small nucleolar RNA R71
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300245;
#=GF RN   [1]
#=GF RM   12523999
#=GF RT   Plant snoRNAs: functional evolution and new modes of gene expression.
#=GF RA   Brown JW, Echeverria M, Qu LH
#=GF RL   Trends Plant Sci 2003;8:42-49.
#=GF CC   R71 is a member of the C/D box family of snoRNAs containing the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Multiple nearly identical copies of this snoRNA
#=GF CC   have been identified in Arabidopsis, and it is thought to function as a
#=GF CC   2'-O-ribose methylation guide for 18S ribosomal RNA.
#=GF WK   Plant_small_nucleolar_RNA_R71
#=GF SQ   25


AJ429536.1/1-107           AAGCCAUGAUGAGGGCAUUGGUUGGUGUAACCUUUGAAACGCUCCCAUGCUUCACAGAAGCUUUCACCAGUCUUCUGUGAGAAACCAGAAA-UCUCAUUUCGGAGUCU
AJ429540.1/1-107           AAGCCAUGAUGAGGGCAUUGGUUGGUGUAACCCUUGAAACGCUCCCAUGCUUCACAUAAGCUUUCACCAGUCUUCUGUGUAAAACCAGAAA-UCUCAUUUCUCAGUCU
AJ429544.1/1-107           AAGCCAUGAUGAGGGCAUUGGUUGGUGUAACCCUUGAAACGCUCCCAUGCUUCACAGAAGCUUUCACCAGUGUUCUGUAAAAAGCCAGAGA-UCUCAUUUCUGAGUCU
AJ429547.1/1-107           AAGCCAUGAUGAGGGCAUUGGUUGGUAUAACCCUUGAAACGCUCCCAUGCUUCACAAAAGCUUUCACCAGCCUUCUGUAAAAAACCAGAAA-UCUCAUUUAUGAGUCU
AJ429549.1/1-107           AAGCCAUGAUGAAGGCAUUGGUUGGUAUAACCCUUGAAACGCUCUCAUGCUUCACAGAAGCUUUCACCAGUCUUCUAUGAAAAGCCAGAGA-UCUCAUUUCUGAGUCU
AJ429551.1/1-106           AAGCCAUGAUGAGGGCAUUGGUUGGUGUAACCCUUGAA-CGCUCCCAUGCUUCACAUGAGCUUUCACCAAUUUUUGGUGAAAAACCAGAAA-UCUCAUUUCUGAGUCU
AJ429553.1/1-107           AGGCCAUGAUGAGGGCAUUGGUUGGUGUAACCCUUGAAACGUUCCCAUGCUUCACAGAAGCUUUCACCACUCUUCUGUGAAAAACCAGAAA-UCUCAUUUCUGAGUCU
AJ429554.1/1-107           AAACCAUGAUGAGGGAAUUGGUUGGUGUAACCCUUGAAGCGCUCCCAUGCUUCAUAGAAGCUUUCACUAGUCUUCUGUGAAAAACCAGAAA-UCUCAUUUCUGAGUCU
AJ429555.1/1-107           AAGCCAUGAUGAGGGCAUUGGUAGGUAUAACCCUUGAAACGCUCCCAUGCUUCACAGAAGCUUUCACCAGUCUUCUGUGAAAAACCAGAAA-UCUCAUUUCUGUGGCU
AJ429559.1/1-107           AAGUCAUGAUGAGGACAUUGGUUAAUGUAACCCAUGAAACGCUCCAAUGCUUCACAGAAGCUUUCACCAGUCUUCUGUGAAAAACCAGAGA-UCUCAUUUUUGAGUCU
AJ429560.1/1-107           AAGCCAUGAUGAGGGCAUCGAUUGGUGUAACCCUUGAAACCUUCCCAUGCUUCACAGAAGCUUUCGCCAGUCUUCUGUGAAAAACCAGAAA-UCUGAUUUCUGAGUCU
AJ429570.1/1-107           AAGCCAUGAUGAGGGCAUUGGUUGAUGUAACCCUUGAAACGUUCCUAUGCUUCAUAGAAGCUUUCACCAGUCUUCUGUUAAAAACCAGAGA-UCUCAUUUUUGAGUUU
AJ429576.1/1-107           AAGCCAUGAUGAGGGCAUUGGUUGGUGUAACCCUUUAAACGCUUCCAUGCUUCACAGAAGCUUUCAUCAGUCUUCUGUGAGAAACUAGAAA-UCUCAUUUCUGAGUCU
AJ429577.1/1-107           AAGCCAUGAUGAGGGCAUUGGUUGGUGUAACCCUUGAAAUGCUCCCAUGCUUCACAAUAGCUUUCACCAGCCUUCUGUAAAAAAACAGAGA-UCUCAUUUCUGAGUCU
AJ429579.1/1-107           AAGCCAUGAUGAGGGCAUUGGUUGGUGUAACCCUUGAAACGCUCCCAUGCUUCACAGAAGCUUUCACCAGCCUUCUAUAAAAAGACAGAGA-ACUCAUUUCUGGCGUU
AJ429580.1/1-107           AAGCCAUGAUGAGGGCAUUGGGUUGUAUAACCCUUAAAACGCUCCCAUUCUUCACAGAAGCUUUCACCAGCCUUCUGUAAAAAGCCAGAGA-UCUCAUUUCUGAGUCU
AJ429590.1/1-107           AAGCCAUGAAGAGGGCAUUGGUUGGUGUAACCCUUGAAGCGCUCCCAUGCUUCACAGAAGCUUUCACCAGUCUUAUGUGAAAAACCCGAAA-UCUCAUUUCUGAGUCU
AJ429592.1/1-107           AAGCCAUGGUGAGGGCAUUGGUUGGUGUA-CCCUUGAAACGCUCCCAUACUUCACAGAAGCUUACACCAGUCUUCUGUGAAAAACAAGAAAAUCUCAUUUCUGAGUCU
AJ429598.1/1-107           AAGCCAUGAUGAGGGCAUUGGUUGGUGUAACCUUUGAAACGCUCCCAUGCUUCACAUAAACUUUCACCAGCCUUCUGUGAAAAACCAGAGA-UCUCAUUUCUGAGUCU
AJ429599.1/1-107           AAGCCACGAUGAGGGCAUUGGUUGGUGUAACCCUUGAAACGCUCACAUGCUUCACAGAAGCUUUCACCAGUCUUUUGUAAAAAGCCAGAAA-UCUCAUUUCUGAGUCC
AJ429603.1/1-107           AAGCCAUGAUGAGGGCAUUGGUUGGUAUAACCCUUAAAACACUCUCAUGCUUCACAGAAGCUUUCACCAGCUUUCUGUAAAAAGCCGGAGA-UCUCAUUUCUGAGUCU
AASG02000366.1/60456-60350 AAUCCGUGAUGUGGGCAGCAUUUCAAAAUAUCUUUAAACCUCUCCCAUGCAUCAUACAUGCUUUCAUCAUCAAGCUGCACAAAAUAAGAUA-UUUCAUUUCUAAGUUU
AACV01016926.1/9115-9221   AUCCCAUGAUGAGGACAGGCGGGCACGUACUCCUGCAGACGCUCCCAUGCUUCUAGAAUAGACUCAUCUCUUGUCUGUUGGAAACUAGAAA-UCCUUCGACUAAGGGC
AC131249.44/54676-54782    AGGCCAUGGUGGGGACAAAGUCUAAGCAUUUCCUUGAAACGCUCCCACGCCUCAUAGAGAGAUUCCCCAUCUUUUUGAUUGAAACGUGUGA-UUUGGUCUCUGAGCUU
AC189405.2/13263-13369     AAACCAUGAUGAGGGCAUUGAGACCAAUAGCCCUUGAACCUCUCCCAUGCUUCACUGAAGCUCUCUAGAUCUUUCUGUUGAAACCCAGAGA-UUUCGUUCCUGAUUUU
#=GC SS_cons               <-<<<<--------------------------------------------------<<-<__________>->>-----------------.--------->>->>->
#=GC RF                    AAgCCAUGAUGAGGGCAuuGguUggugUAacCCUUgAAACGCUCCCAUGCUUCAcAgaagCUUUCAcCAgccuuCUGUaaAAAACcAGAaA.UCUcAUUUCUGAGccU
//
# STOCKHOLM 1.0

#=GF AC   RF00099
#=GF ID   SNORD22
#=GF PI   U22
#=GF DE   Small nucleolar RNA SNORD22
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   50.00
#=GF TC   51.20
#=GF NC   49.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300716;
#=GF DR   snoopy; Loxodonta_africana300333;
#=GF RN   [1]
#=GF RM   8559254
#=GF RT   A mammalian gene with introns instead of exons generating stable RNA
#=GF RT   products.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Nature 1996;379:464-466.
#=GF RN   [2]
#=GF RM   7985025
#=GF RT   Requirement for intron-encoded U22 small nucleolar RNA in 18S ribosomal
#=GF RT   RNA maturation.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Science 1994;266:1558-1561.
#=GF CC   U22 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U22 is encoded within the U22 snoRNA host gene
#=GF CC   (UHG) in mammals [1] and has also been identified in Xenopus [2]. U22 is
#=GF CC   thought to as a 2'-O-ribose methylation guide for ribosomal RNA.
#=GF WK   Small_nucleolar_RNA_SNORD22
#=GF SQ   49


L36588.1/797-921             UCCCAAUGAAGAAA-C-UUUCA-CAUGUCUUACUCUCUGUCCUAGUCCCAGAGCCUGUAAA-GGU-GAACC--ACUGGG-ACUGGCUGGGG-GAGAA-GA-G-GA-------AGAUUUGUUCC-AGAAGGAA-CUGUCU-GA-GGGAU
U40654.1/2537-2662           UCCCCAUGAAGAAA-U-GUUCA-CACGUCCUACUUCCUGUCCUAGCUCCAGAGCCUGAAAA-GGU-GAACCC-ACUGGG-GCUGGCUGGGG-GAAAA-GA-G-GA-------AACUUUGUUCC-AGAAGGAA-CUGUCU-GA-GGGAU
L36586.1/1-125               CCCCAAUGAUGAAA-C-CUUCA-CAUGUCCGACCAGCUG-CCUGUUGCCAGAGCCUGAAAA-GGU-GAACCC-ACUGGC-UCAA-CAGCUG-GAGAG-GAAG-GA-------UGACUUGUUCC-AGCUGGAA-CUGUCU-GA-GGGGG
AAPY01121463.1/1034-1159     UCCCAAUGAGGAAA-C-AUUCA-CAAGUCUUACUUCCUGUCCUAGUCCCAGAGCCUGUAAA-GGU-GAACCC-ACUGGG-GCUGGCUGGGG-GAGAA-GA-G-GA-------GAGUUUGUUCC-AGAAGGAA-CUGUCU-GA-GGGAU
AAFC03078397.1/65055-64930   UCCCAGUGAAGAAA-U-ACUCA-CAAGUCUUACUUCCUGUCCUAGUCCCAGAGCCUGUAAA-GGU-GAACCC-ACUGGG-GCUGGCUGGGG-GAGAA-GA-G-GA-------AAGCUUGUUCC-AGAGGGAA-CUGUCU-GA-GGGAU
AALT01366508.1/388-263       UCCCCAUGAAGAAA-C-UCUCA-CAUGUCUUACCACCUGUCCUAGUCCCAGAGCCUGCAAA-GGU-GAACCC-ACUGGG-ACUGGCUGGGG-GAAAA-GA-G-GC-------AAGCUUGUUCC-AGCAGGAA-CUGUCU-GA-GGGAU
AANG01643015.1/1637-1513     UCCCAGUGAAGAAA-C-AGUCA-CAUGUCUUACUUCCUGUUCUAGUCCCAGAGCCUGUAAA-GGU-GAACCC-ACUGGG-ACUGGCUGGGG-GAAAA-GA-G-GA-------AG-CUUGUUCC-AGAAGGAA-CAGUCU-GA-GGGAU
AAQQ01778534.1/11110-11236   UCCCAAUGAAGAAA-CAUUUCA-CACGUCUUACUUCCUGUCCGAGUCCCAGAGCCCGUAAA-GUU-GAACCC-ACUGAG-GCUGGCUGGGG-GAGAA-GA-G-GA-------GAACUUGUUCC-AGAAAGAA-CUGUCU-GA-GGGAU
AAIY01598195.1/1116-1239     CCCCAAUGAGGAAA-C-AAUCA-C--GUCUUACCUCCUGUCCUAGCCCCAGAACCUGAAAA-GGU-GAACCA-ACUGGG-GCUGGCUGGGG-GAGGA-GA-G-GA-------GAACUUGUUCC-AGAAGGAA-CUGUCU-GA-GGGGU
AANN01771733.1/150-274       UUCCGGUGACGAAA-C-ACCCA-AAUGUCUCACCUCCUGUCCUAGUCCCAGAGCCUGCAAA-GGU-GAACCC-ACUGGG-ACUGGCUGGGG-GAAAA-GA-G-GA-------A-AUUUGUUCC-AGAAGGAA-CUGUCU-GA-GGGAC
AAHX01067412.1/3590-3714     UCCCUAUGAAGAUA---UUUCA-CACGUCUUACUUCCUGUCCUAGCUCCAGAGCCUGAAAA-GAC-GAACCC-ACUGGG-GCUGGCUGGGG-GAAAA-GA-G-GA-------CGUUUUGUUCC-AGAAGGAA-CUGUCU-AA-UGGAU
AAFR03060925.1/34734-34608   UACCCAUGAGGAAAGC-AAACA-AAUGUCUUAACCCCAGUCCUGGCCCCAGAGCCAGUAAU-GGU-GAACCC-ACUGGG-GCUGGCUGGGG-GAAAA-GA-G-GA-------AGCCCUGUUCC-UGAAGGAA-CUGUCU-GA-GGUAC
AAPN01030027.1/4474-4348     UCCUAAUGAAGAAAAC-CAGCA-CCUGUCUUACUCCUUGUCCUGGCCCCAGAGCCUGCAAA-GGC-GAACCC-ACUGGG-GUCGGCUGGGG-GAGAA-GA-U-GA-------UAAUCUGUUCC-AGCGGGAA-CAGUCU-GA-GGGAC
ABDC01628854.1/204-73        UCCCGAUGAAGAAAAC-AUUCA-CACGUCUUACUUCCUGUCCCAGUCCCAGAGCCUGUAAA-GGU-GAACCCCACUGAG-ACUGGCUGGGAAGAGAA-GA-G-GA-------AAGUUUGUUCCCAGAAGGAAACUGUCUUGA-GGGAC
AAYZ01222734.1/7580-7461     UCCCAAUGAGGAAA-C-GCUCA-CACGUC-UACUGCCUGUCCU-GUCCCAGAG-CUGCAAA-GCU-GAAUCC-GCUGGG--CUG-CUGGGG-GAAAA-GA-G-GA--------GACCUGUUCC-AGAACGAA-CUGUCU-GA-GGGAC
AANN01745912.1/3227-3101     UCCUGGUGAAAAAAAC-ACCCA-AAUGUCUUACCUCCUGUCCUAGUCCCAGAGCCUACAAA-GGU-GAACCC-ACUGGG-ACUGGCUGGGA-GAAAA-GA-G-AA-------AAUUCUAUUCC-AGAAGGAA-CUGUCU-GA-GGGAU
AANN01594760.1/149-275       UUCCGGUGAAGAAA-C-ACCCG-AAUGUCUUACCUGCUGUCCUAGUCCCAAAGCCUGCAAA-GGU-GAACCC-ACUGGG-ACUGGCUGGGG-GAAAAAGA-G-GA-------AAUUUUCUUCC-AGAAAGAA-CUGUCU-GA-GGGAU
AAPN01030027.1/6198-6073     UACUAAUGAGGAAA-U-CCACA-CCUGUCUUAGCUCCUG-UCCAGUUCCAGAGCCUGCAAA-GGC-GAACCC-ACUGGA-AUUGGCAGGGGAGAGAG-GA-A-GA-------UAAAAUGUUCC-UGAGUGAA-CAGUCU-GA-UGUGC
AACN010068463.1/589-463      UGCCGGUGAGGAGAGC-AAGCAUCCUGUCUUACCCCCUG-UUCAGUUCCAGAGCCAGUAAU-GGU-GAACCC-ACUGGG-ACUGACUGGGA-GAGAG-GA-U-GA-------GAAUUUGUUCC-AUAGGGAA-CAGUCU-GA-GGCAC
AAIY01637421.1/214-337       CCCCAAUGAGGAAA-C-AAUCA-U--GUCUUACCUCCUGUCCUAG-CCCAGACCCUGAAAA-GGC-GAACCC-ACUGGG-GCUGGCUUGGG-GAGGA-GA-G-GA-------GAACUUGUUCC-AGAAGGAA-CUGUCU-GACGGAGU
AANN01377676.1/604-730       ACCUGGUGAAGAAA-C-ACUCA-AAUAUCUUACCUCCUGUCCUAGUCCCAGAGCCUGCAGA-AGU-GAACCU-ACUGGG-ACUGGCUGGGG-GAAAA-AA-GAGG-------ACUUUUGUUCC-AGCAGGAA-CUGUCU-GA-GGGAU
AAQQ01123516.1/263-146       UCCCAAUGAAGAAA-C-AUUCA-C--GUCUUACUUCCUU-UCUGGUCCCAGAAUUGGUAAA-GGU-GAAUCC-ACUAGG-GCUGGCUGUGA-GAGAA-GA-G-CA-------AAAUUUGUUCC-AGAAAGAA-CU------A-AGGAA
AAIY01097218.1/1827-1953     CCCCAAUGAGGAAA-CAAAUCA-CAUAUCUUACCUCCUGUCCUAUCCACAGAACCUGAAAA-GGU-GAACCC-ACUGGG-ACUGGCUCGGG-GAGGA-GA-G-GA-------GAACUUGUUCC-AGAAGGAA-UUAUUU-GA-GGGGU
AAIY01144874.1/932-1057      CCCCAGUGAGGAAA-CAAAUCA-CACGUCUUACCUC-UGUCCUAGCCCUAGAACCUGAAAA-GAU-GAACCC-ACUGGG-GCUGGCUGGGG-GAGGA-GA-G-GA-------GAACUUGUUCC-AGAAGGAA-CUGUCU-GA-GGGGG
AAFC03036502.1/31098-30972   UGCCAAUGAGGAAAGC-AGACAUCCUGUCUUAC-CCCUGUUCUAGCCCCAGAGCCAGUAAU-GGU-GAACCC-ACUGGG-GCUAACUGGGA-GAAAG-GA-U-GA-------AAUUUCAUUCC-AUAAGGAA-UUGUCU-GA-GGUAC
AAFC03008319.1/22385-22262   UCCCAGUGAAGAAA-C-AUUCA-U--GUCUUAUUCCCUGUCCUAGUCCCAUAGCCUGUAAA-GGU-GAACCC-ACUGGG-GUUGGCUGGGG-GAGAA-GA-G-GA-------AAGUUCAUUCC-AGAAGGAA-CUGUCU-GA-GGGAU
AAFC03046819.1/4214-4340     UCCCAGUGAAAAAA-C-AUUCA-CACAUCUUACCUCUUGUUCUAGUUCCAGAAACUGUAAA-GGU-GAACCU-ACUGGGGGCUGGCUUGAG-GAGAA-AA-G-GG-------AAUCUUGUUCC-AGAAGGAA-CUUUAU-GA-GGGAU
AANN01760072.1/317-185       UCUCGGUGAAGAAA-C-ACCCA-AAUGUUUUACCUCCUGUCCUAGUCCCAGAGCCUGCAAA-GGU-GAACCC-ACUGAG-ACUGGCUGGAG-GUGAA-GG-G-GGGAAGAGGAAAUUUGUUCC-AGAAGGAA-CUGUCU-GA-GGGAU
AAFR03060925.1/33405-33283   ACCCAAUGAAGAAG-A-CAUCA-CCUGUCUUACUCCCUGACCU-GCCCCAGAACCUGCAAA-GGUUGAACCC-ACUGGG-GCUGGCUGGGA-GGCAG-GA-G-GA-------A-ACAUGUUCC-AGA--GAA-CUGUCU-GA-GGGAC
AANG01067642.1/236-110       UGCCAAUGAAGAGAGC-AAGCAUCCUGUCUUAC-CCCUGUUCUAGCCCCAGAGCCAGUAAU-GGU-GAACCC-ACUGGG-GCUAACUGGGU-GAGAG-GA-U-GA-------GAAUUUGUUCC-AUAAGGAA-CUGUCU-GA-GGUAC
AAGV020947826.1/639-513      UGCUUGUGAGGAAC-A-AACAU-CUUGUCUUAACCCCUCUUCUGGUCCCAGAGCUGGUAAAUGGU-GAACAC-ACUGGG-GCUAACUGGGA-GAGAG-GA-C-GA-------GAACUUGUCCC-GUAAGGAA-CUGUCU-GA-GGUAC
AAWR02028294.1/11708-11833   UCCCAGUGAAGAAA-C-AUUCA-CACGUCUUACCUCCUGUCCUAGUUCCAGAGCCUGUAAA-GCU-AAACCC-ACUGGG-GCUGGCUGGGG-GAAAA-GA-G-GA-------AAGCUUGUUCC-AGAAGGAA-CUGUCU-GA-GGGAU
AAKN02039313.1/10812-10937   UCCCAGUGAUGAAA-U-AGUCA-CGAGUCUUACUUCCUGUCCUAGUCCCAGAGCCUGUAAA-GGU-GAACCC-ACUGGG-GCUGGCUGGGG-GAAAA-GA-G-GA-------AAAUUAGUUCU-AGAAGGAA-CUGUCU-GA-GGGAU
AAGV020553791.1/4921-5046    UGCCAGUGAGGAGC-A-AACAU-CUUGUCUUAAUCCCUGUUAUGGCCCCAGAGCCAGUAAU-GGU-GAACCC-ACUGGG-GCUAACUGGGA-GAGAU-GA-U-GA-------UAACUUAUUCC-AUAAGGAA-CUGUCU-GA-GGUAC
AAWR02024301.1/189133-189008 UCCCAGAGAAGAAA-C-AGUCA-CAAGUCUUACCUCUUGUCCUAGUCCCAGAGCCUGUAAA-GGA-GAGCCC-ACUGGG-ACUGGCUGGGA-GAGAG-GA-G-GA-------AAGUUUGUUCU-AAAAGGAA-CUGUCU-GA-GGGAA
AAWR02037725.1/17168-17042   UGCCAGUGAGGAGAGC-AAGCAUCCUGUCUUAACCCCUG-UUUAGCCCCAGAGCCAGUAAU-GGU-GAACCC-ACUGGG-GCUAACUGGGA-GAGAG-GA-U-GA-------AAACUUGUUCC-AUAAGGAA-CGGUCC-GA-GGUAC
AAGV020553791.1/6057-6182    UCCCCGUGAAGAAA-C-AUUCA-CAUGUCUUACCUUCUGUCCUAGUCCCAGAGCCUGUAAA-GGU-GAACCC-ACUGGG-GCUGGCUGGGG-GAUAA-GA-G-GA-------GCAUUUGUUCC-AGAUGGAA-CUGUCU-GA-GGGAU
AAGW02063721.1/7289-7413     UGCCAAUGAGGAAC-A-GACAU-CCUGUCUUACUCCCUGUUUUAAUCCCAGAGCCAGUAAU-GGU-GAACCC-ACUGGG-GUGA-CUGGGA-GAUGG-GA-U-GA-------GAACUGGUUCU-GUAAGGAA-CUGUCU-GA-GGUGC
AAQR03147716.1/1396-1521     UCCCAAUGAAGAAA-C-AUUCA-CAUGUCUUACUUCCUGUCUUAGCUCCAGAGCCUGUGAA-GGU-GAACCC-ACUGGG-GCUAGCUGGGG-GAGAA-GA-G-GA-------AAGUUGGUUCC-AGAAGGAA-CUGUCU-GA-GGGAC
AAGW02014061.1/4738-4858     UCCCAGUGAGGAAA------CA-CAUAUGUUACUUCCUGUCCUAUUCCUAGAGCCUGUAAA-GGU-GG-CCC-ACUGGG-GCUGGC-UGGGAGGAAA-GA-G-GA-------AAGUGUGUUGC-AGAAGGAA-CUGUCC-GA-GGGAU
AAPE02052516.1/20735-20858   UCCUACUGAGGAAA-C-AUGCA-CAUGUCUUGCCUCCUGUCCUAGUCCCCGAGCCAGUAAA-GGG-GACCCC-ACAGGG-GCUGGCUGGGG-AAGAA-GA-G-GA---------GUUUUUUCU-AGAAGGAA-CUGUCG-AA-GGGAU
AAPE02052744.1/5032-5157     UCCCAGUGAAGAAA-C-CUUCA-CAUGUCUUACCUCCUGUCCUUGUCCCAGAGCCUGUAAA-GGU-GAACCC-ACUGGG-GCUGGCUGGGG-GAGAA-GA-G-GA-------AAGCUUGUUCC-AGAAGGAA-CUGUCU-GA-GGGAU
AAGW02063721.1/8555-8680     UCCCAGUGAGGAAG-C-ACUCA-CACGUCUUACUUCCUGUCCUAGCCCCAGAGCCUGUAAA-GGU-GAACCC-ACUGGG-GCUGGCUGGGA-GAAAA-GA-G-GA-------AAGUGUGUUCC-AGAAGGAA-CUGUCU-GA-GGGAC
AAGU03076505.1/1052-1177     UCCCGAUGAAGAAA-C-AUGUA-CACGUCUUACCUCCUGUCCUGGUCCCAGAGCCUGUAAA-GGU-GAACCC-ACUGGG-GCUGGCUGGGG-GAGAG-GA-G-GA-------GAGCUUGUUCC-AGAAGGAA-CAGUCU-GA-GGGAU
AAEX03003011.1/78557-78681   UCCCAGUGAAGAAA-C-AGUCA-CAUGUCUUACCUCCUGUCCUAGUCCCAGAGCCUGUAAA-GGU-GAACCC-ACUGGG-GCUGGCUGGGG-GAAAG-GA-G-GA-------A-ACUUGCUCC-AGAAGGAA-CUGUCU-GA-GGGAU
AAPE02052744.1/3923-4049     UGCCAGUGAGGAGAGC-AAACAUCCUGUCUUAC-CCCAGUACCAGCCCCAGAGCCAGUAAU-GGU-GAACCC-ACUGGG-GCUAACUGGGA-GAGAG-GA-U-GA-------GAACCUGUUCC-GUAAGGAA-CUGUCU-GA-GGUAC
AAGU03059936.1/81070-80947   UCCCAGUGAGGAAA-C-ACUGA-CACGUCUUCCCUCCUGUCCUGGUCCCAGAGCCUGUAAA-GGC-GAGCCC-AUUGGG-GCUGGCUGGGG-G-GAA-GA-G-GA-------GAGCUUAUUCC-AGAAGGAA-C-GUCU-GA-GGGGU
AAPE02019237.1/15702-15578   UCUCAGUGAGGAAA-C-AUUCG-CAUGUCUUAACUCCUGUCCUAGUCCCAGAGCCUGUAGA-GGU-GAACCC-ACUGGG-GCUGGCUGGG--GAGAA-GA-G-GA-------AAGUUUGUUCC-AGAAGGAA-CUGUCU-AA-GGCAG
AAWZ02032435.1/8771-8645     UCCCAAUGAUGA-U-C-UCUCA-UACGUCUUACUAUCUGUUUUGGGGCUAGAACCUGCAAA-GGUUGAACCC-ACUAGC-ACCAGCAGAUG-GGAAA-GA-G-GA-------AACUUGGCUCC-GGAAGGAA-CAGUCU-GAUGGGAU
#=GC SS_cons                 <<<<__________._._____.______________________________________.___.______.______.___________._____.__._.__.......___________.________.______.__.>>>>:
#=GC RF                      ucCcaaUGAaGAAA.C.auuCA.cauGUCUUACcuCCUGUcCUAGUCCCAGAGCCUGuAAA.GGU.GAACCC.ACUGGG.gCUGGCUGGGg.GAgAA.GA.G.GA.......aAauUUGUUCC.AGAAGGAA.CUGUCU.GA.gGgau
//
# STOCKHOLM 1.0

#=GF AC   RF00100
#=GF ID   7SK
#=GF DE   7SK RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:18193315
#=GF SS   Published; PMID:1646389
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00013
#=GF DR   SO; 0000274; snRNA;
#=GF RN   [1]
#=GF RM   11864590
#=GF RT   Transcription: surprising role for an elusive small nuclear RNA.
#=GF RA   Blencowe BJ
#=GF RL   Curr Biol 2002;12:R147-149.
#=GF RN   [2]
#=GF RM   1646389
#=GF RT   Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant
#=GF RT   human small RNP of unknown function.
#=GF RA   Wassarman DA, Steitz JA
#=GF RL   Mol Cell Biol 1991;11:3432-3445.
#=GF CC   7SK was discovered as an abundant small nuclear RNA in the mid-70s but a
#=GF CC   possible function has only recently been suggested [1]. Two independent
#=GF CC   studies have found that 7SK RNA binds the CDK9/cyclin T complex (known as
#=GF CC   elongation factor P-TEFb). P-TEFb activates transcription by
#=GF CC   phosphorylating the C-terminal domain of RNA polymerase II. This process
#=GF CC   is negatively regulated by the 7SK RNP. The secondary structure of 7SK RNA
#=GF CC   shown here was proposed by Wasserman and Steitz on the basis of chemical
#=GF CC   modification and enzymatic cleavage experiments [2]. This family contains
#=GF CC   a number of annotated pseudogenes and 7SK derived repeats. The threshold
#=GF CC   is artificially high to minimise the pseudogene count.
#=GF WK   7SK_RNA
#=GF SQ   45


X04236.1/1-328               NGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGC-GGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCAUCC---CCGA--UAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUU--UCU
AM773430.1/1-329             GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGA--UAG-AGAC------GGU-ACCGU--------------------UCAUCGGUCAAGGGUAUACG--GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAG--CUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUGCAGACACAUCCAAGUGAGGCACUGC-AUGUG-GCAGUCUGCCUUUCUUU
K02909.1/1-330               GGAUGUGA-GG-C-GAUCUGGCUGCGACAUCUG-UCA-CC--CUAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGA-AUAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCA-UU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUUUCUUU
AM773429.1/1-314             GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCUAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGUGC-------GCUCGG-UCGAAGAGGAUGGCUGUCC---CCGA--UAG-AGAA------GC--ACCGA--------------------ACUCCGUUCAAGAGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAG--------------CUU------CAAGU-ACGUAGGGUAGUCAAG-CU-CCAAAUCUUCAAGCACAUCCAAGUGUGGCGCUGC-ACGUG-GCAGUCUGCCUUCCUUU
AM773436.1/1-322             GGAUGUGC-CGGGCGAUUUGGCAGCGACACCUUCUCACCAU-CCAUUGAUCGCUAGGGCAAGU----UCGGCU-GAUCUGGC-UGCAUAGAUCGGU-GUCCCC---UCAU-CGGCGCUCAUCCGUGUUCGUCCCUCCCGAUGCUCUGC-------GCUCGG-UGGCAGCGGACUCCGACCC---CCGA----G-GGAC-----CGGC-AACGGCUUCUUC-------------GUCGAGGUCGCGGGUUUAGGC-GUAGCGAC--GGCUCCCUGCUAGA----CCA---AACUCC-----AC-GGGCGAGGCGA-GUAGG-CGA--GCUGGAA-----CU-C--CGACUACAGCAUCCACAUCCAGA-UCGGCACUGC-ACGUG-GCAGUCUGCCUGU-UUU
AM773431.1/1-311             GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCUAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUC-CGU-UCCAUGUGUGUCCCUCCCGAAGCCCCGC-------GCUCGG-UGCUAGUGGACGUAU-CCC---GGCG----G-ACGA------GC--AUCGUU-------------------------------GGUAUACCA-GUAGCUG----CUCCCCUGCUAGAACCUCCA---AACAAG--CUCAA-GGCCCAUUU---GUAGGAGAAACGUAGGGAAGUCAAG-CU-CCAAGACUUCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCGUAAUUU
AM773433.1/1-328             GGAUGUGCAGGUG-GAAUUGGCCGCGACUCCCA-UCA-CUC-CCAUUGAUCGCUAGCGCUAGGA---UCGGCU-GAUCUGGUUGGU-UAGAUGGGGCGUCCCCCGUUC--CCCGCACGGAUCCGCGUCCGGCCUCGCCGAUGCCCCGC-------GCUCGGAUCGACGGCCGAGAGGCUCA---CCGC-ACGCACCAC------GCU-CACGG--------------------CUACGGCGCACGGGUUUAACCACGGAGCUGCGAGUACCCACUUAGACC----A---AAC-CCCGGAGAC-GGCGACGGC-G-AUA--------AGAGGGAAGCACGC-UCUGCACCAUAUGUUGCACAUCCAAC-ACGGCGCUGC-ACGUG-GCAGUUUGCCUU--GUU
AM773435.1/1-303             GAGCGUGU-GU-CAG----------GAGACA---CGU-CUG-ACAUUGAUCGCUAUGAUCUUAU---ACGGCUUGAUCUGUCUAG--AUUGGUUGU-UUCC---------ACCACACCAUUCCGAUAGUUGAGCUCCCGCUGCACCCCCGGGGACGCACGG-UCGAGC-UCUGUUCAAAAUUGC-UGG--UCGUAGAG------UU--UGCAUGGCUCGGCGGCCAAUGGGGUUAUUUCUGUUAGGGCUUCUCU-CUAUUUCCG-CGUAACGGGGAAGUUCGUUUU---CAGAAACCAUUUG-AAUUUAUGU---C-----------------GC--------------------------UCCAUUGGAGGCAUUAC-ACGUG-GUAAUCUGCCUUUCUUU
AB179256.1/1-294             GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCUUCG-----GUCAA-------GGG--UAU-ACGA------GU--A-------------------------------------------------GCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUUUCUUU
X05490.1/245-574             GGAUGUGA-GG-C-GAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCAUCC---CCGA--UAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUGCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUUUCUUU
M63671.1/163-493             GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGA-AUAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCUCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCA-UU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCUUUCUUUU
AM773432.1/1-316             GGGUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCUAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCC--UU--CCCUCACAGCUCCAUGUGCGUCCCUCCCGAAGCUCAGC-------GCUCGG-UCGCAGAGGA---UGACCC---CCUA----G-AAGA------GGA-CCGCU--------------------CCGCCGGUCUAGGGUAUAUGACGUAGCUAC--ACUCCCCUGCUAGG----CUA---AAC-----CUCCA-AGACCAUUU---GUAGGAUG-ACGUAGGGAAGUCAAG-CU-CCAAGACUUCAGACACAUCCAAGUCAGGCACUGC-ACGUG-GCAGUCUGCCGUUCUUU
X04992.1/244-574             GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCAUCC---CCGA--UAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCA-UU--UGUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUUUCUUU
AM773434.1/1-304             --------------GGUUU------G--GCAUC-ACC-CCGUCCAUAGAUCGCCCCCGUAGUGUGUUUCGGCC-GAUCUGGCUGGUUCCGUGUUGC-CUCCGCC--ACAU---CCGCAUCUCUUCCACCGGCUCUCCCGACGCCUCGC-------GCUCGG-UCGAGAGUCUACCUCCUCC---CCGA----G-UCAACCCCCUGU--GAUUG--------------------CCGAAAGGUUGGGUGAAAAGC-GUAGCUGCA-GCCCCUGAUG----UUCUCCA---CUGCUAGGGUCAG-AGAGCGUCG---UGUCGAGC-GC-------AGCAAAG-C---CAAGACGCCACACACAUCCAAU-ACGGCGCUGCCACGCGGGCAGCCUGCCAU---UU
AANU01242908.1/30859-31189   GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCAUCC---CCGC--UAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUUUCUUU
AANN01178127.1/1580-1911     GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGGCCUUCC---CCGA-AUAG-AGAC------GG--ACCGG--------------------UCUUCGGUCGAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUUUCUUU
AAQQ01045895.1/3447-3777     GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGA--UAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUUCUUU
AANG01281180.1/2213-2543     GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGA--UAG-AGGA------GG--ACCGU--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUUCUUU
AAFC03074072.1/524-194       GGAUGUGA-GG-GCGAUCUGGUUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCAUCC---CCGC--UAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUUCUUU
AAYZ01141529.1/1312-1642     GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCAUCC---CCGC--UAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUUUGUUU
AALT01379588.1/2052-2383     GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGGCCUUCC---CCGA-AUAG-AGAC------GG--ACCGG--------------------UCUUCGGUCGAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUUCUUU
ABDC01305949.1/10171-10507   GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGC--UAG-AGGA------GG--ACCGGUCUUCG--------------GGUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCAAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUCCUUU
AAIY01588576.1/908-1238      GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UUGAAGAGGACGACCUUCC---CCGA--UAGAAGGA------AG--ACCGU--------------------CCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAG-UCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUUUCUUU
AAFR03002426.1/49563-49241   GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGA--UAG-AGGC------GU--ACCGU--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGA-----------ACAAGCUCCCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUCCUUU
AANH01005129.1/138410-138730 GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCUAGGUUUGAUU---UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGUGUCCCUCCCGAAGCCCAGC-------GCUCGG-UGGCAGAGGACGAGGUCCC--CCCCG----G-CGGA-----CGA------------------------------CCAUCCAUCGGUGUACCA-GUAGCUAC--GCUCCCCUGCUAGAACCUCCA---AACAAG--CUCAA-GGCCCAUUU---GUAGGAGAAACGUAGGGAAGUUAAG-C--UCCAAGCGUCAGGCACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUCCUUU
BAAF04042483.1/6479-6795     GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCUAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGGUCCAUGAGAGUCCCUCCCGAAGCUCUGC-------GCUCGG-UGGCAGCGGACGGUG-UCC---CCCA----G-CGGU------GG--ACGACC------------------------AUUCAUCGGUAUACCA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACA--AGCUCAA-GGCCAA-------UAGGAGAAACGUAGGGAAGUCAAG-C--UCCAAGCUUCAGACACAUCCAACUGCGGCGCUGC-ACGUG-GCAGUCUGCCUUCCUUU
AC147455.3/128369-128676     GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--UCAUUGAUCGCCAGGGUUGAU----UCAGCU-GAUCUAGCUGGC-UAGGCAGGU-GUCCCCU--UCCUCCCUCACCACUCUGUACACGUCCCUCCAGAAGCUGUGU-------GCUCAG-UUGAAGAAGAAGGCUUUC----CCAGAAUAG-AGAU------GG--ACCUG--------------------UCUUAGGUCGAGGGUAUAUGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGAAAC---------UGAUU-AU-------UGACAAU-U---CAAGAAUAGAUUUACUUUAAUAUAA---UUUUC----UG-GGAUGCUC--UUUCUUU
AC188405.3/136382-136062     AAACGUGA-GG-ACAAUCUGGCUGUGACAUCCA-UCA-CC--CCACUGAUCUCCAGCGUUGAU----UCAGCU-GAUC-AGUGGGC-UGAGCAGGU-GUCCCCU--UUCUCCCUCACCAUUCCAUGUGCGUUCCUCCCAGAACUGCAC-------ACCUGG-UCAAAGAGGAAGGCCUUUC---CUGA--UAA-AGG-------AG--GACCA--------------------UUCUCAGUCAAGGGUAUGUGA-GUACCUGU--UCUCCCCUGCCAGAAUCUCAAACGAGCUCUCUGUAAA-AAUCACAAG---AUUUUAUU-GUGCAUGGUAGC--AU-G-----AGUCUGUAAUCCCAGCUACCAGCUACUCAG----GUG-GCUGAG-GUAGUGGGAU
CU104670.1/27701-28003       GGAUGUGA-GG-GUGAUCUGGCUAUGACAUCUG-UCA-CC--CCAGUGAUUGCCACUAUUGAU----UCUGCU-GAUCUAGCUGGC-UAGGU-GGU-GUCCCCU--UCCUCCCUCACCACUCCAUGUGCAUCCCUCCUGAAGCUGUGU-------GCUCAG-UUGAAGAGGAGGACCAUCC---CCAA--UAG-AGGA------GG--ACCAG--------------------UCUUCGGCUAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAAUCUCCA---AACAAGCUCUCAA-GGUCCA---------GAGAC-AAGAUGUGAACUUCAU-GUCUCAA----------------UUGAUGAUCAC------GUG-GUUGUGUGGUGGUGCAG
AACY021333937.1/619-306      AGAUAUGA-GA-GCUAUCUGGCUGUGACAUCUG-UCA-CC--CCACUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGAUGGCU-GUCCCCU--UCCUCCCUCACCCCUCCAUGUGUGUCCCUCCCAAAACUGCAU-------GCUCGU-UCGAAGAGGACAACCAUCC---CCAA--UAG-AGGA------GG--ACCAG--------------------UCUUUGGUCGAGGGUAUAUGA-GUAGCUGC--ACUCCUCUGCCAGAAUCUCCA---AACAAGCUCUCAA-GAAUAC--------ACACAU-AAGC-----AGUU-AG-UAUAGACAGUUGCUAUUACAUUCAUAA-----GUUUG-UUCUG-UAAAUA-AGGUUUUUAU
AC129097.27/184193-183893    GGAUGUGA-GG-GUGAUCUGGCUGCCACAUCUG-UCA-CC--CCAUUGAUCACCAGGGUUGAU----UCGGCU-GAUCUGGCUGAC-UGGGCGGGU-AUCCCCU--UCCUCCCUCACUGCUCCGUGUGUGUCCCUCCAGAAGCUGUGC-------GCUCAG-UGGAAGAGGAUGACCAUCC---CCGA--UAG-AGGA------GG--AUCGG--------------------UCUUCAGUCAAAGGUAUAAGA-GUAGCUGC--GCUCCCCUGCUAGGACCUCCA---AACAAGCUAUCAG-AAUGUUAUU---UUUCU------GUCUUAUGUCCAAC-CCCUCAUUAAAAUGUUCAUAGUAAAA------------ACAUA---------------UUU
CT737198.8/109814-109510     GGAUGUAA-GG-GCGAUCUGGCUGUGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----CUGGCU-GACCUGGCUGGC-UCGGCGGGU-AUCCCCU--UCCUCCCACACUGCUCCAUGUACGUCCCUCCAGAAGCUGCAC-------GCACAG-UCGAAGAGCAUGACCAUCC---CCUA--UAG-AGGA------GG--ACUGU--------------------UCUUCGGUCAAGGGUAUACCA-GUAGCUGU--GCAGCCCUGCUAGAACCUCUC---AACAAGCUCUCAA-GGA---CU-------AGA-----GUGAGAAUG---AGACAGACUUACUUUCUUCAUGAUGCACAUGAGUC-------AUUG--------GUCCAUAUGU
AC200272.4/46787-47106       GGAUGUGA-GG-GCGAUCUGGCUGUGACAUCUA-UCA-CC--UCCUUGAUCACCACGGCUGAU----UUGGCU--AUCUGGCUGGC-CAGGCGGGU-GUCCCCU--UCCUCCCUCACUACUCCACGUGUGUCCCUCCCGAAGAUGUGC-------GCUCAG-UUGAAGAAGAUGACUAUCU---CCCA--UAG-ACGA------GA--ACCAG--------------------UCUUUGGUCAAGGGUAUAUGA-GUAGGUGC--ACUCCCCUGCUAGAACCUCCA---AAUAAACUCUCAA-GAACUAGGG---AGAGGAGA-GUGAA----AAUUAAC-CUAGUUACAAUGAUUGUAUCCUUACAUUC---UUUGAUAAAUU-UCAAAA----UACUUCU
AC196701.9/116655-116349     AGAUAUGA-GG-GCGAUCUGACUGUGACAUCUG-UCA-CU--CUAUUGAUCACCAGGGUUGAU----UCGGCU-GAUCUAGCUAGC-UAGGCAGGA-GUCCCCU--UCCUCCCUCACCACUCCAUGUGCUUCCCUCUUGAAGCUGUGC-------ACUCGG----------------U--------------G-AAAG------GA--UGCCA--------------------UCUUCAGUCAAGGGUAUACAA-GUAGCUGC--ACUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAAAAGA-ACAUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCUGAAUGAGUUGCUGC-AUGUG-GCAGUCUGCCUUUCUUU
AAWR02010297.1/23760-24090   GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGA--UAG-AGGA------GG--ACCGU--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUUUCUUU
AADA01266996.1/7335-7665     GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCAUCC---CCGA--UAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUUUGCCUUUCUUU
CAAE01015006.1/595427-595745 GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCUAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGGUCCAUGUGUGUCCCUCCCGAAGCUCCGC-------GCUCGG-UGGAAGAGGACGAGG-UCC----UCG--CGG-CGGA-----CGA------------------------------CCGUUCCUCGGUGUACCA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAG--CUCAA-GGCCCAUUU---GUAGGAGAAACGUAGGGAAGUUAAG-C--UCCAAGCGUCAGACACAUCCAAUUGCGGCGCUGC-ACGUG-GCAGUCUGCCUUCCUUU
AAQR03066699.1/17270-17600   GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGA--UAG-AGGA------GG--ACCGU--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAG-CUCUCAAGGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-AUGUG-GCAGUCUGCCUUUCUUU
AJ890104.1/1-319             GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCUAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGGUCCAUGUGUGUCCCUCCCGAAGCUCCGC-------GCUCGG-UGGAAGAGGACGAGG-UCC----UCG--CGG-CGGA-----CGA------------------------------CCGUUCUUCGGUGUACCA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAG--CUCAA-GGCCCAUUU---GUAGGAGAAACGUAGGGAAGUUAAG-C--UCCAAGCGUCAGACACAUCCAAUUGCGGCGCUGC-ACGUG-GCAGUCUGCCUUACUUU
AAGW02018299.1/84405-84735   GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCAUCC---CCGC--UAG-AGGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUUCUUU
AAEX03008397.1/4832-5162     GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCAUCC---CCGA--UAG-AGGA------GG--ACCGU--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUUCUUU
AJ890101.1/1-329             GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGA--UAG-AGAC------GGU-ACCGU--------------------UCAUCGGUCAAGGGUAUACG--GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAG--CUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUGCAGACACAUCCAAGUGAGGCACUGC-AUGGG-GCAGUCUGCCAUUGUUU
AAPE02026038.1/9966-10297    GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCC--UCCUCCCUCACCGAUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCCCCCCCGA----G-GAGA------GG--ACCGG--------------------UCUUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUCCUUU
AAGU03002674.1/25068-24736   GGAUGUGA-GG-GCGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUGAU----UCGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGC-------GCUCGG-UCGAAGAGGACGACCUUCC---CCGA--UAG-AGGA------GAGGACCGU--------------------CCAUCGGUCAAGGGUAUACGA-GUAGCUGC--GCUCCCCUGCUAGAACCUCCA---AACAAGCUCUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUAGUCAAG-CUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGC-ACGUG-GCAGUCUGCCUUCCUUU
AAWZ02020286.1/110315-110000 GGAUGUGA-GG-GUGAUCUGGCUGCGACAUCUG-UCA-CC--CCAUUGAUCGCCAGGGUUAAU----UUGGCU-GAUCUGGCUGGC-UAGGCGGGU-GUCCCCU--UCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCAC-------GCUCGG-UGGAAGAGGAUGACA-UCC---CAGG--UAU-AGAA------GA--AGUGUACUGAGGUCUCCAG------UCUUUGGUCCCGGGUAUACGA-UAG-CUGC--GCUCUCUUGCUAGAACCUCCA---AACAAG--CUCAA-GGUCCAUUU---GUAGGAGA-ACGUAGGGUACUC-AG-A----------------------UAUUAUAGAAUUGU-ACUUU--CAGUUC-CUAUUAAUA
#=GC SS_cons                 <<<-<<<<.<<.<-<<---<<----<<<<<<<<.<<-.<<..<<<--<<<<<<<_________....__>>>-.>>>>>>>-->>-.-->>>>>>>.>>>->>-..>>-->>>>>>>--->>>,,,,,,,((((((<<<<-<<_____.......>>>>>>.<<<----<<<______>>>...->>>..,,).)))-......))..,,,,,....................,,,,,,,,,,,,,,,,,,,,,.,,,<<<--..-<<-<<<<<<------<<<<-...-<<<<<_______.______>>>...>>->>>>-.-->>>>>>->>--->>.>,.,,,,,,,,,,,,,,,,,,,,<<<-<<<<<<<<<<._____.>>>>>-->>>>>-->>>
#=GC RF                      GGAUGUGa.GG.gcGAUCUGGCUGCGAcacCcg.ucA.Cc..CCAUUGAUCGCcAgGGUUGau....UCgGCU.GAUCUGGCUgGC.UaggcgGgu.gUCCCCU..UCCUcCCuCACcgcUCCaUGUgCGccccucCcGaaGCUgCGC.......GCuCgG.ucgAAGaggaagaccaucc...Ccga..Uag.agga......gg..aaCgg....................UcuUcgguCaaGGGUAUAuga.GUAgcugC..gcucCCcugCUAGAaCcUccA...AacaagCucUcAa.GGuccacuu...guAggAga.AcGcagGGuagucAag.cu.cCAAgAcuucAuaCACAUCCAaaugaGgCgcUGC.AcGUG.GCAgccUGcCucUcuuU
//
# STOCKHOLM 1.0

#=GF AC   RF00101
#=GF ID   SraC_RyeA
#=GF DE   SraC/RyeA RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Predicted; PFOLD
#=GF GA   37.00
#=GF TC   37.20
#=GF NC   36.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00105
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol 2001;11:941-950.
#=GF RN   [2]
#=GF RM   11445539
#=GF RT   Identification of novel small RNAs using comparative genomics and
#=GF RT   microarrays.
#=GF RA   Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S
#=GF RL   Genes Dev 2001;15:1637-1651.
#=GF CC   This RNA was discovered in E. coli during a large scale screens [1-2]. The
#=GF CC   function of this RNA is unknown. This RNA overlaps RFAM:RF00111 on the
#=GF CC   opposite strand suggesting that the two may act in a concerted manner.
#=GF WK   SraC/RyeA_RNA
#=GF SQ   13


AL627272.1/127686-127830     AAUUAAAAAAAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAAU-C-GCCUUGCUCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU
CP000653.1/2601613-2601758   AGAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAUAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAACUAC-GCCUGACACUCUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUCC
AE017042.1/1756200-1756347   AAUUAAAAAAAGACCGAAUACGAUUCCUGAUAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGUAUUAAU----GUAGGCUUAUU-CAGCCGCACUUCUUAAGCGUAGCCGAGUACCGACAUUUCGCCAACCUU
CP000034.1/1046100-1046244   AAUGAAAAAAAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU
CP000647.1/2580976-2581120   AGAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAGU-C-GCCUUGCACUAUAAGAAUAGUUUAACG-CGUCAGCUUUUCCAGUCC
AM286415.1/1991675-1991530   AAUUAAAAAGAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUGUU-CAGCCAUACUCUUUAAGAGUAGUCGAGGU-CAUGUGUUUCGCCAACUU
CU928145.2/2074283-2074427   AGAUAAAAAGAGACCGAACACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU
CP000970.1/1336993-1336849   AGAUAAAAAGAGACCGAACACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUUAGU-U-GCCUUGCUCUUUAAGAAUAGAUGACGA-CGCCAGAUUUUCCAGUUU
AM933172.1/1226335-1226191   AAAUAAAAAGAGACCGAAUACGAUUCCUG-UAUUCGGUCCAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAU----GCAGGCUAAAU-C-GCCUUGCCCUUUAAGAAUAGAUGACGA-CGCCAGGUUUUCCAGUUU
AALD02000029.1/37435-37580   ACUUAAAAAGAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUGUU-CAGCCGUACUACUUAAGCGUAGUCGAGUA-CAUGUGUUUCGCCAACUU
AALC02000009.1/70496-70641   AGAUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUAUUUAGCCAACUU
AALF02000003.1/121616-121765 AAUUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAUGGCUCUUGGGACAGAGCCGUGCGCUAAAAGUUGGCAUUAAUUAACGUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUGUUUAGCCAACUU
AALE02000013.1/38-183        AGUUAAAAAAAGACCGAAUACGAUUCCUA-UAUUCGGUCUAGGGAAAGGGCUCUUGGGAGAGAGCCGUGCGCUAAAAGUUGGCAUUAAC----GUAGGCUUAUU-CAGCCGUACUCCUUAAGCGUAGUCGAGUA-CAUGUGUUUCGCCAACUU
#=GC SS_cons                 :::::::::::<<<<<<<<<<_______>.>>>>>>>>>,,,,,,,<<<<<<<<______>>>>>>>>,,<<_________>>,,,,,,....,,,<<<_____._.>>>::::::::::::::::::::::::.::::::::::::::::::
#=GC RF                      AauUAAAAAaAGaCCGaauacGAUUCCUg.uauuCGGuCuAGGGAAauGGCuCuUGGGAgaGaGCCguGCGCUAAAAGUUGGCAUUAAu....GuAGGCUuAuU.c.GCCuuaCucuUUAAGaaUAGuuGAguA.CgucaguUUuuCcAauUU
//
# STOCKHOLM 1.0

#=GF AC   RF00102
#=GF ID   VA
#=GF DE   VA RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Bateman A, Moxon SJ
#=GF SS   Published; PMID:8809020, Moxon SJ
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   36.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   95176559
#=GF RT   Human and simian adenoviruses: phylogenetic inferences from analysis of VA
#=GF RT   RNA genes.
#=GF RA   Kidd AH, Garwicz D, Oberg M
#=GF RL   Virology 1995;207:32-45.
#=GF RN   [2]
#=GF RM   6297772
#=GF RT   Adenovirus VAI RNA is required for efficient translation of viral mRNAs at
#=GF RT   late times after infection.
#=GF RA   Thimmappaya B, Weinberger C, Schneider RJ, Shenk T
#=GF RL   Cell 1982;31:543-551.
#=GF RN   [3]
#=GF RM   6201722
#=GF RT   Adenovirus VA RNAI: a positive regulator of mRNA translation.
#=GF RA   Svensson C, Akusjarvi G
#=GF RL   Mol Cell Biol 1984;4:736-742.
#=GF RN   [4]
#=GF RM   2583126
#=GF RT   Adenovirus VAI-RNA regulates gene expression by controlling stability of
#=GF RT   ribosome-bound RNAs.
#=GF RA   Strijker R, Fritz DT, Levinson AD
#=GF RL   EMBO J 1989;8:2669-2675.
#=GF RN   [5]
#=GF RM   7555067
#=GF RT   Structure, function, and evolution of adenovirus virus-associated RNAs.
#=GF RA   Mathews MB
#=GF RL   Curr Top Microbiol Immunol 1995;199:173-187.
#=GF RN   [6]
#=GF RM   8809020
#=GF RT   Secondary and tertiary structure in the central domain of adenovirus type
#=GF RT   2 VA RNA I.
#=GF RA   Ma Y, Mathews MB
#=GF RL   RNA 1996;2:937-951.
#=GF CC   The VA (viral associated) RNA is found in adenovirus. It plays a role in
#=GF CC   regulating translation.
#=GF WK   VA_RNA
#=GF SQ   54


U52574.1/118-289       GGCUCG-ACUCCGUGGCCUGGGGGA---ACG--UG--AACGGGUUG--GGUCGCG-GUGUA-C---CC-CGGUUCGAGUCCAAAGCUAAGCAAUCACACUCGG-AUC-G-GCCGGA-GCC--GCGGCU-AAC----GUG-GUAUUGGCUAUCCCGUC----UCG---------------------ACCCA-----------GCC-GA--CGAA------U-AUCCAGGGU-ACG-GAGUAGAGU-CGUU
U52574.1/363-537       GGCUCG-CGCCCGUAGUCUGGAGAAUC-AGU--CG--CCAGGGUUGC--GUUGCG-GUAUG-C---CCCCGGUUCGAGCCUAAGCGCGGC---------UCGU-AUCGG-CCGGUU-UCC--GCGACA-AGC----GAG-GGUUUGGCAGCCCAGUC-AUUUCC------------------AAGACCCC-----------GCCAGC--CGAC------UUCUCCAGUUU-ACG-GGAGCGAGC-CCUU
U52566.1/115-274       GGCUCUUCCUCCGUAGCCUGGCGGA---ACG--CA--AACGGGUUA--GGCCGCGUGUGUA-C---CC-CGGUUCGAGUCCCC----------------UCGA-AUCAG-GCUGGA-GCC--GCGACU-AAC----GUG-GUAUUGGCACUCCCGUC----UCG---------------------ACCCG----------AGCCCGA--UAGC--------CGCCAGGAU-ACG-GCGGAGAGC-CCUU
AY163756.1/10432-10590 GACUCG-ACUCCGUAGCCUGGAGGA---ACG--UG--AACGGGUUG--GGUCGCG-GUGUA-C---CC-CGGUUCGAGACUUGUAC-------------UCGA-GCC-G-GCCGGA-GCC--GCGGCU-AAC----GUG-GUAUUGGCACUCCCGUC----UCG---------------------ACCCA-----------GCCUAC--AAAA--------AUCCAGGAU-ACG-GAAUCGAGU-CGUU
U52558.1/333-482       GGCUCG-CGCCCGUAGUCUGGAGAAG--CAU--CG--CCAGGGUUGA--GUCGCG-GCAGA-A---CC-CGGUUCGA------------------------GG-A---------CG-GCC--GCGGCG-AGC----G-G-GACUUGGUCACCCCGCC-GAUUUA------------------AAGACCCA---------CAGCCAGC--CGAC------UUCUCCAGU-U-ACG-GGAGCGAGC-CCCC
U52541.1/115-274       GGCUCUUCCUCCGUAGCCUGGCGGA---ACG--CA--AACGGGUUA--GGCCGCGUGUGUA-C---CC-CGGUUCGAGUCCCC----------------UCGA-AUCAG-GCUGGA-GCC--GCGACU-AAC----GUG-GUAUUGGCACUCCCGUC----UCG---------------------ACCCA----------AGCCCGA--UAGC--------CGCCAGGAU-ACG-GCGGAGAGC-CCUU
U52533.1/372-529       GGCUCGCUCCCUGUAGCC-GGAGGGUU-AUU--U-UCCAAGGGUUGA--GUCGCG-GGAC--C---CC-CGGUUCGAGUC-------------------UCGG-GCC-G-G-CCGG-ACU--GCGGCG-AAC----GGG-GGUUUGCCU-CCCCGUC----AUG-----------------CAAGACCCC-----------GCUUGC--AAAU------UCCUCC-GGAA-ACA-GGGACGAGC-CCCU
U52533.1/117-273       GGCACU-CUUCCGUGGUCUGGUGGAUAAAUU--CG--CAAGGGU--AUCAUGGCG-GACGA-C---CGG-GGUUCGAACC-------------------CCGG-AUCCG-GC--CG-UCC--GCCGUG-AUCC---AUG-CGGUUACCGCCCGCGU----GUCG--------------------AACCCA----------GGUGUGC-----------GA-CGUCAG-ACAACG-GGGGAGCGCUCCUU
AY530878.1/10419-10580 GGCUCG-ACUCCGUGGCCUGGAGGCU--AAG--CG--AACGGGUUG--GGCUGCGCGUGUA-C---CC-CGGUUCGAAUC-------------------UCGA-AUCAG-GCUGGA-GCC--GCAGCU-AAC----GUG-GUACUGGCACUCCCGUC----UCG---------------------ACCCA----------AGCCUGC--UAAC---GAAACCUCCAGGAU-ACG-GAGGCGGGU-CGUU
AY530878.1/10641-10813 GGCUCG-CUGCCGUAGUCUGGAGAAAG-AAU--CG--CCAGGGUUGC--GUUGCG-GUGUG-C---CC-CGGUUCGAGCCUCAGCGC------------UCGGCGCC-G-GCCGGAUUCC--GCGGCU-AAC----GUG-GGCGUGGCUGCCCCGUC-GUUUCC------------------AAGACCCC--------UUAGCCAGC--CGAC------UUCUCCAGU-U-ACG-G-AGCGAGC-CCCU
U52553.1/333-482       GGCUCG-CGCCCGUAGUCUGGAGAAG--CAU--CG--CCAGGGUUGA--GUCGCG-GCAGA-A---CC-CGGUUCAA------------------------GG-A---------CG-GCC--GCGGCG-AGC----G-G-GACUUGGUCACCCCGCC-GAUUUA------------------AAGACCCA---------CAGCCAGC--CGAC------UUCUCCAGU-U-ACG-GGAGCGAGC-CCCC
U10680.1/24-195        GGCUCG-ACUCCGUGGUCUGGGGGA---ACG--UG--AACGGGUUG--GGUCGCG-GUGUA-C---CC-CGGUUCGAGUCCAAAGCUAAGCGAUCACGCUCGG-AUC-G-GCCGGA-GCC--GCGGCU-AAC----GUG-GUAUUGGCUAUCCCGUC----UCG---------------------ACCCA-----------GCC-GA--CGAA------U-AUCCAGGGU-ACG-GAGUAGAGU-CGUU
U10680.1/268-440       GGCUCG-CGCCCGUAGUCUGGAGAAUC-AGU--CG--CCAGGGUUGC--GUUGCG-GUAUG-C---CC-CGGUUGGAGCCUAAGCGCGGC---------UCGU-AUCGG-CCGGUU-UCC--GCGACA-AGC----A-G-GGUUUGGCAGCCCCGU-UAUUUCC------------------AAGACCCC-----------GCCAGC--CGAC------UUCUCCAGUUU-ACG-GGAGCGAGC-CCUU
U03015.1/24-172        GGCUCU-UCUCCGUGGUCUAGUGGAAA-AUU--UG--CAAUGGU--AUGUUGGCG-GAGC-UC---ACG-GGUUCGA------------------------A--ACCCG-CCGG-C-UCU--GCCAGC-AUCG---GGG-UGAUUGGUCGUCACGUC----UCG--------------------AACCUA-----------GCC-GG--CGAA--------CCCUAG-AU-ACG-GAGGAGAGU-CUUU
M14082.1/179-349       GACUCC-UCUCCGUAGCUUGGGGGUU--AGGU-CG--CAAGGGU-GC-GGUGGCG-GGGAA-C---CC-CGGUUCGA------------------------A--ACC-G-GCCGGA-UCC--GCCACU-CCC----GAC-G--C-GGCGGCCCCGC----GUCCACGACCCCACCAGAGGCCGAGACCCA-----------GCC-GC---GACGCGCGCA-CCCCAA-AU-ACG-GAGGGGAGU-CUUU
L06496.1/76-247        GACUUU-CCUCCGUAGCCUGGGGGA---CAGACCG--CCAGGGU-GCA-GUGGCA-AACAA-C---CCCCGGUUCGA------------------------G--ACC-G-GCUGGA-UCU--GCCACU-CCC----GAC-G----CGCCGGCCGUGC---GUCC------------ACGACGGAAACCCCGCCGAGACCUAGCC-GC--GGUCCAUGGAU-CUCCAG-AU-ACG-GAGGGGAGU-CUUU
AF108105.1/10236-10396 GGCUCUUCCUCCGUAGCCUGGCGGA---ACG--CA--AACGGGUUA--GGCCGCGCGUGUA-C---CC-CGGUUCGAGUCCCC----------------UCGA-AUCAG-GCUGGA-GCC--GCGACU-AAC----GUG-GUAUUGGCACUCCCGUC----UCG---------------------ACCCG----------AGCCCGA--UAGC--------CGCCAGGAU-ACGCGGGAAGAGC-CCUU
U03007.1/36-206        GACUCC-UCUCCGUAGUCUGGAGGUU--AGGU-CG--CAAGGGU-GC-GGCGGCG-GGGAA-C---CC-UGGUUCGA------------------------A--ACC-A-GCUGGA-UCC--GCCGUC-CCG----AUG-CGCUUGGCC-CCGCAUCCACGACG------GCCCCGGGCGUCGAGACCCA-----------GCC-GC--GAUA-CGCACA-CCCCAA-AU-ACG-GAGGGGAGU-CUUU
U52545.1/333-482       GGCUCG-CGCCCGUAGUCUGGAGAAG--CAU--CG--CCAGGGUUGA--GUCGCG-GCAGA-A---CC-CGGUUCGA------------------------GG-A---------CG-GCC--GCGGCG-AGC----G-G-GACUUGGUCACCCCGCC---GAUA----------------UAAAGACCCA---------CAGCCAGC--CGAC------UUCUCCAGU-U-ACG-GGAGCGAGC-CCCC
U52537.1/115-274       GGCUCUUCCUCCGUAGCCUGGCGGA---ACG--CA--AACGGGUUA--GGCCGCGCGUGUA-C---CC-CGGUUCGAGUCCCC----------------UCGA-AUCAG-GCUGGA-GCC--GCGACU-AAC----GUG-GUAUUGGCACUCCCGUC----UCG---------------------ACCCG----------AGCCCGA--UAGC--------CGCCAGGAU-ACG-GCGGAGAGC-CCUU
U52537.1/333-482       GGCUCG-CGCCCGUAGUCUGGAGAAG--CAU--CG--CCAGGGUUGA--GUCGCG-GCAGA-A---CC-CGGUUCGC------------------------GG-A---------CG-GCC--GCGGCG-AGC----G-G-GAAUUGGUCACCCCGCC-UAUUUA------------------AAGACCCA---------CAGCCAGC--CGAC------UUCUCCAGU-U-ACG-GGAGCGAGC-CCCC
U52573.1/114-286       GACUCU-UCUCCGUAGCCUGGAGGAU--AGAC-CG--CCAGGGU-GC-GGUGGCG-AACAA-C---CCCCGGUUCGA------------------------G--ACC-G-GCUGGA-UCC--GCCACU-CCC----GAC-G--C-GCCGGCCCCGU----GUCC------------ACGACGGAAACCCCGCCGAGACCUAGCC-GC--GGUCCCCGGAU-CUCCAG-AU-ACG-GAGGGGAGAUCUUU
U52565.1/119-278       GGCUCG-UCUCCGUGGCCUGGAGGCU--AAG--CG--AACGGGUUG--GGCUGCGCGUGUA-C---CC-CGGUUCGAAUC-------------------UCGG-AUCAG-GCUGGA-GCC--GCAGCU-AAC----GUG-GUACUGGCACUCCCGUC----UCG---------------------ACCCA----------GGCCUGC-ACAAA------ACCUCCAGGAU-ACG-GAGGCGGGU-CGUU
U52565.1/354-525       GGCUCG-CGCCCGUAGUCUGGAGAAUC-AAU--CG--CCAGGGUUGC--GUUGCG-GUGUG-C---CC-CGGUUCGAGUCUUAGCGCG-----------CCGG-AUCGG-CCGGUU-UCC--GCGACA-AGC----GAG-GGUUUGGCAGCCCCGUC--AUUUC-----------------UAAGACCCC-----------GCCAGC--CGAC------UUCUCCAGUUU-ACG-GGAGCGAGC-CCUC
AF534906.1/10629-10785 GGCACU-CUUCCGUGGUCUGGUGGAUAAAUU--CG--CAAGGGU--AUCAUGGCG-GACGA-C---CGG-GGUUCGAGCC-------------------CCGU-AUCCG-GC--CG-UCC--GCCGUG-AUCC---AUG-CGGUUACCGCCCGCGU----GUCG--------------------AACCCA----------GGUGUGC-----------GA-CGUCAG-ACAACG-GGGGAGCGCUCCUU
U10684.1/21-181        GGCUCG-ACUCCGUGGCCUGGAGCU---AAG--CG--AACGGGUUG--GGCUGCGCGUGUA-C---CC-CGGUUCGAAUC-------------------UCGA-AUCAG-GCUGGA-GCC--ACAGCU-AAC----GUG-GUACUGGCACUCCCGUC----UCG---------------------ACCCA----------AGCCUGC--UAAC---GAAACCUCCAGGAU-ACG-GAGGCGGGU-CGUU
M14785.1/5430-5577     GACUCC-CUUCCGUGGUUUGGUGGAAA-AGU--CA--CAAGGGU--ACCAUAGCG-AGGAA-C---CC-CGGUUCGA------------------------A--ACC-G-GCAGGA-UCC--GCUAUG-AGCACAAGUG-A----GGCGCUUGCGC----GUUG--------------------AACCCG-----------GCC-AA--GGAC--------CCCCAG-AC-ACG-GAGAGGAGU-CUUU
U10676.1/26-173        GACUCC-CCUCUGUGGCCUGGCGGAAA-AGU--CA--CAAGGGU--ACCACAGCG-AGGAA-C---CC-CGGUUCGA------------------------A--ACC-G-GCAGGA-UCC--GCUGUG-AGC----GUA--UAUAGGGCGUC-UGC--GCGUAG--------------------AACCCA-----------GCC-AA--AGAC--------CCCCAG-AC-ACG-GAGAGGAGU-CUUU
J01917.1/10866-11023   GGCUCGCUCCCUGUAGCC-GGAGGGUU-AUU--U-UCCAAGGGUUGA--GUCGCA-GGAC--C---CC-CGGUUCGAGUC-------------------UCGG-GCC-G-GCCG-G-ACU--GCGGCG-AAC----GGG-GGUUUGCCU-CCCCGUC----AUG-----------------CAAGACCCC-----------GCUUGC--AAAU------UCCUCC-GGAA-ACA-GGGACGAGC-CCCU
M10281.1/2-159         GGCACU-CUUCCGUGGUCUGGUGGAUAAAUU--CG--CAAGGGU--AUCAUGGCG-GACGA-C---CGG-GGUUCGAACC-------------------CCGG-AUCCG-GC--CG-UCC--GCCGUGUAUC----CUGACGGUUACCGCCCGCGU----GUCG--------------------AACCCA----------GGUGUGC-----------GA-CGUCAG-ACAACG-GGGGAGCGCUCCUU
U52540.1/115-274       GGCUCUUCCUCCGUAGCCUGGCGGA---ACG--CA--AACGGGUUA--GGUCGCGUGUGUA-C---CC-CGGUUCGAGUCCCC----------------UCGA-AUCAG-GCUGGA-GCC--GCGACU-AAC----GUG-GUAUUGGCACUCCCGUC----UCG---------------------ACCCG----------AGCCCGA--UAGC--------CGCCAGGAU-ACG-GCGGAGAGC-CCUU
AY339865.1/10876-11033 GGCUCGCUCCCUGUAGCC-GGAGGGUU-AUU--U-UCCAAGGGUUGA--GUCGCG-GGAC--C---CC-CGGUUCGAGUC-------------------UCGG-ACC-G-GCCG-G-ACU--GCGGCG-AAC----GGG-GGUUUGCCU-CCCCGUC----AUG-----------------CAAGACCCC-----------GCUUGC--AAAU------UCCUCC-GGAA-ACA-GGGACGAGC-CCCU
AY339865.1/10621-10777 GGCACU-CUUCCGUGGUCUGGUGGAUAAAUU--CG--CAAGGGU--AUCAUGGCG-GACGA-C---CGG-GGUUCGAGCC-------------------CCGU-AUCCG-GC--CG-UCC--GCCGUG-AUCC---AUG-CGGUUACCGCCCGCGU----GUCG--------------------AACCCA----------GGUGUGC-----------GA-CGUCAG-ACAACG-GGGGAGUGCUCCUU
AY487947.1/10357-10516 GGCUCG-ACUCCGUGGCCUGGAGGCU--AAG--CG--AACGGGUUG--GGCUGCGCGUGUA-C---CC-CGGUUCGAAUC-------------------UCGA-AUCAG-GCUGGA-GCC--GCAGCU-AAC----GUG-GUACUGGCACUCCCGUC----UCG---------------------ACCCA----------GGCCUGC-ACAAA------ACCUCCAGGAU-ACG-GAGGCGGGU-CGUU
AY487947.1/10575-10742 GGCUCA-CUGCCGUAGAUUGGAGAAG--AAU--CG--CCAGGGUUGC--GUUGCG-GUGUG-C---CC-CGGUUCGAGACCGC----------------UCGG-GUC-G-GCCGAAUUCC--GCGGCU-AAC----GAG-GGCGUGGCUGCCCCGUC-GUUUCC------------------AAGACCCC-------AUAAGCCAGC--CGAC------UUCUCCAGU-U-ACG-G-AGCGAGC-CCCU
M86665.1/672-843       GACUUU-CCUCCGUAGCCUGGAGGA---CAGACCG--CCAGGGU-GCA-GUGGCA-AACAA-C---CCCCGGUUCGA------------------------G--ACC-G-GCUGGA-UCU--GCCACU-CCC----GAC-G--C-GCCGGCCGUGC----GUCC------------ACGACGGAAACCCCGCCGAGACCUAGCC-GC--GGUCCCUGGAU-CUCCAG-AU-ACG-GAGGGGAGU-CUUU
U52544.1/333-482       GGCUCG-CGCCCGUAGUCUGGAGAAG--CUU--UG--CCAGGGUUGA--GUCGCG-GCAGA-A---CC-CGGUUCGC------------------------GG-A---------CG-GCC--GCGGCG-AGC----G-G-GACUUGGUCACCCCGCC-GAUUUA------------------AAGACCCA---------CAGCCAGC--CGAC------UUCUCCAGU-U-ACG-GGAGCGAGC-CCCC
AF394196.1/10420-10579 GGCUCG-ACUCCGUGGCCUGGAGGCU--AAG--CG--AACGGGUUG--GGCUGCGCGUGUA-C---CC-CGGUUCGAAUC-------------------UCGA-AUCAG-GCUGGA-GCC--GCAGCU-AAC----GUG-GUAUUGGCACUCCCGUC----UMG---------------------ACCCA----------AGCBUGCACCAAC-------CCUCCAGGAU-ACG-GAGGCGGGU-CGUU
AF394196.1/10641-10799 GGCUCGUCUGCCGUAGUCUGGAGAAG--AAU--CG--CCAGGGUUGC--GUUGCG-GUGUG-C---CC-CGGUUCGA------------------------G--GCC-G-GCCGGAUUCC--GCGGCU-AAC----GAG-GGCGUGGCUGCCCCGUC-GUUUCC------------------AAGACCCC--------AUAGCCAGC--CGAC------UUCUCCAGU-U-ACG-G-AGCGAGC-CCCU
U52536.1/115-274       GGCUCUUCCUCCGUAGCCUGGCGGA---ACG--CA--AACGGGUUA--GGCCGCGUGUGUA-C---CC-CGGUUCGAGUCCCC----------------UUGA-AUCAG-GCUGGA-GCC--GCGACU-AAC----GUG-GUAUUGGCACUCCCGUC----UCG---------------------ACCCG----------AGCCCGA--UAGC--------CGCCAGGAU-ACG-GCGGAGAGU-CCUU
U52564.1/354-525       GGCUCG-CGCCCGUAGUCUGGAGAAUC-AAU--CG--CCAGGGUUGC--GUUGCG-GUGUG-C---CC-CGGUUCGAGUCUUAGCGCG-----------CCGG-AUCGG-CCGGUU-UCC--GCGACA-AGC----GAG-GGUUUGGCAGCCUCGUC--AUUUC-----------------UAAGACCCC-----------GCCAGC--CGAC------UUCUCCAGUUU-ACG-GGAGCGAGC-CCUC
U10683.1/23-181        GGCUCUUCCUCCGUAGCCUGGCGGA---ACG---A--AACGGGUUA--GGCCGCGCGUGUA-C---CC-CGGUUCGAGUCCCC----------------UCGA-AUCAG-GCUAAA-GCC--GCGACU-AAC----GUG-GUAUUGGCACUCCCGUC----UCG---------------------ACCCA----------AGCCCGA--UAGC--------CGCCAGGAU-ACG-GUGAAGAGC-CUUU
U10683.1/239-388       GGCUCG-CGCCCGUAGUCUGGACAAG--CAU--CA--CUAGGGUUAA--GUUACA-GCAGA-A---CC-CGGUUCGC------------------------GG-A---------CG-GCC--GCGGCA-AGC----G-G-GACUUAGUUACCCCGCC-AAUUUA------------------AAGACCCG---------CAGCCAGC--CGAC------UUUUCCAGU-U-ACG-GGAGCGAGC-CCCC
AY530876.1/10428-10594 GGCUCG-ACUCCGUGGCCUGGAGGCU--AAG--CG--AACGGGUUG--GGCUGCGCGUGUA-C---CC-CGGUUCGAGUCCCUGC--------------UCGA-AUCAG-GCUGGA-GCC--GCAGCU-AAC----GUG-GUACUGGCACUCCCGUC----UCG---------------------ACCCA----------AGCCUGC--UAAC---GAAACCUCCAGGAU-ACG-GAGGCGGGU-CGUU
M35961.1/2-156         GGCACU-CUUCCGUGGUCUGGUGGAUAAAUU--CG--CAAGGGU--AUCAUGGC--GUGGA-CGACCGG-GGUUCGAACC-------------------CCGG-AUCCGU----GA-UCCAUGCGGUU-ACC----GUC-C----GCCGCCCGUGC----GUCG--------------------AACCCA----------GGUGUGC-----------GA-CGUCAG-ACAACG-GGGGAGCGCUCCUU
U52543.1/115-274       GGCUCUUCCUCCGUAGCCUGGCGGA---ACG--CA--AACGGGUUA--GGCCGCGUGUGUA-C---CC-CGGUUCGAAUCCCC----------------UCGA-AUCAG-GCUGGA-GCC--GCGACU-AAC----GUG-GUAUUGGCACUCCCGUC----UCG---------------------ACCCG----------AGCCCGA--UAGC--------CGCCAGGAU-ACG-GCGGAGAGC-CCUU
U10674.1/256-426       GGCUCG-CGCCCGUAGUCUGGAGAAUC-AAU--CG--CCAGGGUUGC--GUUGCG-GUGUG-C---CC-CGGUUCGAGUCUUAGCGC------------GCGG-AUCGG-CCGGUU-UCC--GCGACA-AGC----GAG-GGUUUGGCAGCCUCGUC--AUUUC-----------------UAAGACCCC-----------GCCAGC--CGAC------UUCUCCAGUUU-ACG-GGAGCGAGC-CCUC
U52567.1/117-264       GACUCC-CUUCCGUGGCUUGGUGGAAA-AGU--CA--CAAGGGU--ACCAUAGCG-AGGAA-C---CC-CGGUUCGA------------------------A--ACC-G-GCAGGA-UCC--GCUAUG-AGC----GUA-AGUGAGGCGCUUGCGC----GUUG--------------------AACCCG-----------GCC-AA--AGAC--------CCCCAG-AC-ACG-GAAAGGAGU-CUUU
L05511.1/76-247        GACUCU-UCUCCGUAGCCUGGAGGAU--AGAC-CG--CCAGGGU-GC-GGUGGCG-AACAA-C---CCCCGGUUCGA------------------------G--ACC-G-GCUGGA-UCC--GCCACU-CCC----GAC-G--C-GCCGGCCCCGU----GUCC------------ACGACGGAAACCCCGCCGAGACCUAGCC-GC--GGUCCCCGGAU-CUCCAG-AU-ACG-GAGGGGAGU-CUUU
U52542.1/333-482       GGCUCG-CGCCCGUAGUCUGGAGAAG--CAU--CG--CCAGGGUUGA--GUCGCG-GCAGA-A---CC-CGGUUCAA------------------------GG-AC--G--------GCC--GCGGCA-AGC----G-G-GACUUGGUCACCCCGCC-GAUUUA------------------AAGACCCA---------CAGCCAGC--CGAC------UUCUCCAGU-U-ACG-GGAGCGAGC-CCCC
U52534.1/362-535       GGCUCG-CGCCCGUAGUCUGGAGAAUC-AGU--CG--CCAGGGUUGC--GUUGCG-GUAUG-C---CC-CGGUUGGAGCCUAAGCGCGGC---------UCGU-AUCGG-CCGGUU-UCC--GCGACA-AGC----GAG-GGUUUGGCAGCCCCGU-UAUUUCC------------------AAGACCCC-----------GCCAGC--CGAC------UUCUCCAGUUU-ACG-GGAGCGAGC-CCUU
U52570.1/118-276       GACUCG-ACUCUGUAGCCUGGAGGA---ACG--UG--AACGGGUUG--GGUCGCG-GUGUA-C---CC-CGGUUCAAGACUUGUAC-------------UCGA-GCC-G-GCCGGA-GCC--GCGGCU-AAC----GUG-GUAUUGGCACUCCCGUC----UCG---------------------ACCCA-----------GCCUAC--AAAA--------AUCCAGGAU-ACG-GAAUCGAGU-CGUU
U10681.1/21-180        GGCUCG-ACUCCGUGGCCUGGAGGCU--AAG--CA--AACGGGUUG--GGCUGCGCGUGUA-C---CC-CGGUUCGAAUC-------------------UCGA-AUCAG-GCUGGA-GCC--GCAGCU-AAC----GUG-GUACUGGCACUCCCGUC----UCG---------------------ACCCA----------GGCCUGC-ACAAA------ACCUCCAGGAU-ACG-GAGGCGGGU-CGUU
X03000.1/10423-10594   GGCUCG-ACUCCGUGGCCUGGGGGA---ACG--UG--GACGGGUUG--GGUCGCG-GUGUA-C---CC-CGGUUCGAGUCCAAAGCUAAGCAAUCACACUCGG-AUC-G-GCCGGA-GCC--GCGGCU-AAC----GUG-GUAUUGGCUAUCCCGUC----UCG---------------------ACCCA-----------GCC-GA--CGAA------U-AUCCAGGGU-ACG-GAGUAGAGU-CGUU
#=GC SS_cons           ((((((.((((((((--((((((---..---..--..---((((,,,.<<<<<<<.<<<<-.-...<<.-<<<<______...................__>-.>>>.>.>--->>.>>>..>>>>>>.,,,....<<<.<___________>>>>,...,,,,....................,))))-..........-------..----......-.))))))--).))).))))))))).):::
#=GC RF                GgCuCg.cccCCGUgGuCUGGagGAu..Aau..CG..caAGGGUUGa.ggccGCG.GcccA.C...CC.CGgUuCGAguC...................uCgg.AcC.G.GCuGgg.gCC..GCggcc.AaC....gcg.guauUGgCaacCccgcC...gUcg....................aACCCa..........aGCcuGc..ugac......u.cuCCAGgAc.ACG.GgggcGaGc.CuUU
//
# STOCKHOLM 1.0

#=GF AC   RF00103
#=GF ID   mir-1
#=GF DE   mir-1 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   44.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679672
#=GF RT   An extensive class of small RNAs in Caenorhabditis elegans.
#=GF RA   Lee RC, Ambros V
#=GF RL   Science 2001;294:862-864.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the microRNA (miRNA) mir-1 family. miRNAs are
#=GF CC   transcribed as ~70nt precursors (modelled here) and subsequently processed
#=GF CC   by the Dicer enzyme to give a ~22nt product. In this case the mature
#=GF CC   sequence comes from the 3' arm of the precursor. The extents of the
#=GF CC   hairpin precursors are not generally known and are estimated based on
#=GF CC   hairpin prediction. The products are thought to have regulatory roles
#=GF CC   through complementarity to mRNA. The involvement of Dicer in miRNA
#=GF CC   processing suggests a relationship with the phenomenon of RNA
#=GF CC   interference. miRNAs are numbered based on the sequence of the mature RNA.
#=GF CC   This family also contains the mir-206 from human, which appears to be
#=GF CC   related to mir-1.
#=GF WK   mir-1_microRNA_precursor_family
#=GF SQ   66


AC103987.5/56357-56281         ACUCAGA-GUACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUAC-AAUGC-UAUGGAAUGUAAAGAAGUAUGUAUUUUUGGU
AL391221.15/79486-79562        UCCCGAGGCCACAUGCUUCUU-UAUAUCCCCAUA-UG-GA----UUAC-UUUGC-UAUGGAAUGUAAGGAAGUGUGUGGUUUCGGC
AC087074.1/69936-70014         UGCCGAG-CUGCAUACUUCCU-UACAUGCCCAUA-CU-GUAC-UGUGA-AUGGA-UAUGGAAUGUAAAGAAGUAUGUAGAACGGAA
AL449263.6/21373-21297         GCUUGGG-AAACAUACUUCUU-UAUAUGCCCAUA-UG-GA---CCUGC-UAAGC-UAUGGAAUGUAAAGAAGUAUGUAUCUCAGGC
AL672157.5/42188-42264         GCUUGGG-ACACAUACUUCUU-UAUAUGCCCAUA-UG-AA---CCUGC-UAAGC-UAUGGAAUGUAAAGAAGUAUGUAUUUCAGGC
AAVX01149879.1/956-880         ACCUGAA-ACACAUACUUCUU-UAUAUGCCCAUA-UG-AA---CCUCA-CAAGC-UAUGGAAUGUAAAGAAGUAUGUAUUUCUGGU
AAGD02012398.1/27745-27823     UGCCGAG-CUGCAUACUUCCU-UACAUGCCCAUA-CU-AUAU-CAGUA-AUGGA-UAUGGAAUGUAAAGAAGUAUGUAGAACGGUU
CR589876.7/166160-166084       GCUUGGU-AGACAUACUUCUU-UAUAUGCCCAUA-UG-AA---CAAGA-GCAGC-UAUGGAAUGUAAAGAAGUAUGUAUCCCAGGU
AAHY01004442.1/497-572         CCCCAGG-CCACAUGCUUCUU-UAUAUCCUCAUA-GA-UA----UCUC-AGCAC-UAUGGAAUGUAAGGAAGUGUGUGGUUUUGGC
DQ066649.1/1-73                UCAGA---GUACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUAC-AAUGC-UAUGGAAUGUAAAGAAGUAUGUAUUUUUG--
CAAE01014981.1/12786-12709     CCUUAGU-GUACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUAUGAUAAC-UAUGGAAUGUAAAGAAGUAUGUAUUCUUGGU
AANG01241232.1/1165-1238       GCUUGGG-AAACAUACUUCUU-UAUAUGCCCAUA-UG-GA------CC-UAAGC-UAUGGAAUGUAAAGAAGUAUGUAUUUCAGGC
AANH01005371.1/151669-151592   CCUUGGU-GCACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUAUGAUAGC-UAUGGAAUGUAAAGAAGUAUGUAUUCCUGGU
AC140316.3/155249-155325       ACUCAGA-GCACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUUC-AGUGC-UAUGGAAUGUAAAGAAGUAUGUAUUUUGGGU
AAPN01089888.1/1993-2069       GCUCAGA-GUACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUAA-AAAGC-UAUGGAAUGUAAAGAAGUAUGUAUUUUUGGC
AAPN01163915.1/14813-14737     GCUUGAG-GAACAUACUUCUU-UAUAUCCCCAUA-UG-AA---CCUGG-CAAGC-UAUGGAAUGUAAAGAAGUAUGUAUUUCAGGU
AAFR03005394.1/95017-95093     GCUUGAG-AAACAUACUACUU-UAUAUGCCCAUA-UG-AA---CGUGC-UAAGC-UAUGGAAUGUAAAGAAGUAUGUAUUUCCGGU
AAHX01093471.1/12884-12808     ACUCAGA-GCACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUAG-AAUGC-UAUGGAAUGUAAAGAAGUGUGUAUUUUGGGU
DQ066650.1/1-72                UCAGA---GCACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUAG-AAUGC-UAUGGAAUGUAAAGAAGUGUGUAUUUUG---
BAAF04064761.1/1030-1106       GCUUGGG-GGACAUACUUCUU-UAUAUGCCCAUA-UG-AA---CACGA-GCAAC-UAUGGAAUGUAAAGAAGUAUGUAUCCCAGGU
AANU01221577.1/6692-6768       ACUCAGA-GUACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUAC-AAGGC-UAUGGAAUGUAAAGAAGUAUGUAUUUUGGUA
DQ520618.1/109-184             CCCAAGG-CCACAUGCUUCUU-UAUAUCCCCAUA-CG-GA----UUAC-UUUGC-UAUGGAAUGUAAGGAAGUGUGUGGUUUCGGC
AAVX01053845.1/1717-1792       GCCUGGA-ACACAUACUUCUU-UAUAUACCCAUA-UG-AA----CUUA-ACAGC-UAUGGAAUGUAAAGAAGUAUGUAUUUUUGGU
AC147912.2/160163-160239       GUUUGGA-GUACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUAC-AAUGC-UAUGGAAUGUAAAGAAGUAUGUAUUUUUAUC
AL929326.9/101067-101144       ACUUGGU-GUACAUACUUCUU-UAUGUGCCCAUA-UG-AAC--AUAUA-AAAGC-UAUGGAAUGUAAAGAAGUAUGUAUUCUUGGU
CAAE01015266.1/460-536         GCCUGGG-GGACGUACUUCUU-UAUAUGCCCAUA-UG-GA---CAUGA-GCAAG-UGUGGAAUGUAAAGAAGUAUGUAGCCCAGGU
AAVX01164741.1/393-468         UCCAAAA-CUGCAUACUUCUU-CAUAUGCCCAUA-UG-AA----AUGC-UUUGC-UAUGGAAUGUAAAGAAGUAUGUAUUUUUGGG
AALT01502699.1/11495-11572     ACUCAAGAGUACAUACUUCUU-UAUGUACCCAUA-UG-AA---CAUAG-AAUGC-UAUGGAAUGUAAAGAAGUAUGUACUUUUGGU
AALT01102453.1/1268-1343       GCCAAGA-UGACAUGCUUCUU-UAUAUCCCCAUA-CG-GA----UCUC-UUGGC-UAUGGAAUGUAAGGAAGUGUGUGGUUUUGGC
AAFR03002451.1/41335-41260     UCUGAGG-CAACAUGCUUCUU-UAUAUCCCCAUA-UG-AA----UUAU-GCUGC-UAUGGAAUGUAAGGAAGUGUGUGGUUUCGGG
AAPN01261137.1/2838-2913       UCCGAGA-CAACAUGCUUCUU-UAUAUCCCCAUA-UG-GA----UUAC-GCUGC-UAUGGAAUGUAAGGAAGUGUGUGGUUUCGGG
AAPN01136163.1/2517-2440       CCCCGGG-CCACACACUUCUU-CAUAUGCCCAUA-GG-GAG--CUGCC-CGAAC-UAUGGAAUGUUAAGAAGUGUGUGUUCUUGGG
DQ066652.1/2-78                CUUUAGG-GCACAUACUUCUU-UAUAUGCCCAUA-CU-GA---AUGAA-AAUGC-UAUGGAAUGUUAAGAAGUAUGUAACCUAAGG
BAAF04038301.1/61-138          CCCUGGG-GUACAUACUUCUU-UAUGUACCCAUA-UG-AAG--AUAUG-AAAGC-UAUGGAAUGUAAAGAAGUAUGUAUUCUCGGU
AANN01270542.1/4439-4364       CCCAAAG-CCACAUGCUUCUU-UAUAUCCCCAUA-UG-GA----UUAC-UUUGC-UAUGGAAUGUAAGGAAGUGUGUGGUUUUGUC
AAYZ01364871.1/459-535         GCUUGGG-AGACAUACUUCUU-UAUACGCCCAUA-UG-GA---CUUGC-UGCAC-UAUGGAAUGUAAAGAAGUAUGUACCCCAGGC
AAZX01000650.1/30055-30128     GCGUCUG-UUCCGUGCUUCCU-UACUU-CCCAUA-GU-GC-----ACG-UGACG-UAUGGAAUGUAAAGAAGUAUGGAGCCGCGCU
AAQB01006401.1/151186-151263   UUGAGAG-UUCCAUGCUUCCU-UGCAU-UCAAUAGUA-UA---UUAAA-UAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC
CAAE01015003.1/757237-757162   CUUGUAA-GGACAUGCUUCCU-UAUAUCCCCAUA-UU-AA----UACA-CCACU-UAUGGAAUGUAAGGAAGUGUGUGGUUACGAG
AAKO01002808.1/45325-45400     UUGAGAG-UUCCAUGCUUCCU-UGCAU-UCAAUA-GU-UA---UACUC-AAGCA-UAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC
BAAB01105211.1/2094-2168       GCGCAAG-UUCCGUGCUUCCU-UACUU-CCCAUA-GU-CA----UUGU-AAUCA-UAUGGAAUGUAAAGAAGUAUGGAGCUGCGCG
AANU01232204.1/19432-19506     UAGCUGG-UUGCUUACUUGUU-UGUAUUCCCAGG-UG-AA----CUGU-GAGCU-CUUGGAA-GCAAAGAAGUAUGUCUUUGAUGU
AAPT01020974.1/21428-21504     UUGAGAG-UUCCAUGCUUCCU-UGCAU-UCAAUA-GU-AU---AUAAA-UAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC
AAFS01000978.1/39458-39534     UUGAGAG-UUCCAUGCUUCCU-UGCAU-UCAAUA-GU-AU---AACAU-AAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC
AANI01016241.1/6126-6050       UUGAGAG-UUCCAUGCUUCCU-UACAU-UCAAUA-GU-AUU--CAAAU-AAGCA-UAUGGAAUGUAAAGAAGUAUGGAGCGAAAUC
BX276101.6/115878-115803       CUUGUGA-AGACAUGCUUCCU-UAUAUGCCCAUA-UU-AA----UGCU-CAAGU-UAUGGAAUGUAAGGAAGUGUGUGGUUUCAGG
AAZO01007144.1/49277-49350     UUACUAG-GUCCGUGCUUCCU-UACUU-CCCAUA-UA-GU---GUUUG-UUU---UAUGGAAUGUAAAGAAGUAUGGAGCCUGUAC
AAJJ01000046.1/50771-50844     UCGCGAG-UUCCGUGCUUCCU-UACUU-CCCAUA-GU-GC-----UUU-AAACG-UAUGGAAUGUAAAGAAGUAUGGAGCGAACGC
AAAB01008964.1/1830748-1830826 GCGAAAG-UUCCAUGCUUCCU-UGCAU-UCAAUA-GU-AUGUUUGUAA-AACCC-UAUGGAAUGUAAAGAAGUAUGGAGCGAUUGG
AANH01006842.1/36647-36722     CUCGCGA-GGACAUGCUUCCU-UAUAUCCCCAUA-UC-AA----UACA-CCACU-UAUGGAAUGUAAGGAAGUGUGUGGUCUCAAG
AAWU01006939.1/25735-25811     GCGAAAG-UUCCAUGCUUCCU-UGCAU-UCAAUA-GU-GAU--CUUUG-AAACG-UAUGGAAUGUAAAGAAGUAUGGAGCGCUCGG
AAGE02025061.1/66260-66336     UCGAAAG-UUCCAUGCUUCCU-UGCAU-UCAAUA-GU-GA---UUCUG-AAAGCAUAUGGAAUGUAAAGAAGUAUGGAGCGCUCGG
AAGV020639359.1/176-251        CCCCGGG-AGACAUACUUCUU-UAUAUGCCCAUA-UG-GA----GCUC-GGAGC-UAUGGAAUGUAAAGAAGUAUGUAUCUCAGGC
CAAK05040482.1/7048-7123       -AUUGAGACGACAUACUUCCU-UAUAUCCCCAUA-UU-CA----GAAU-UAAUC-UAUGGAAUGUAAGGAAGUGUGUGGCUUCAGU
AAWZ02024324.1/1768-1847       UCUUGAGCCUACAUACUUCUU-CAUAUGCCCAUA-UG-GAGU-CGGCC-AGAUU-UAUGGAAUGUUAAGAAGUAUGUAUCGUUGGG
AAWZ02009612.1/57865-57941     -GUUGAGAGCACAUACUUCUU-UAUGUACCCAUA-UG-AA---GAUAC-AAUGU-UAUGGAAUGUAAAGAAGUAUGUAUUUUUGAU
AAGJ04155449.1/4343-4264       CAUGCCA-UAACAUACUUCUU-UAGAAUUCCAUA-CU-GAAUCUCCUC-AACUC-UAUGGAAUGUAAAGAAGUAUGUAUUGAAACU
ABEG02003477.1/15436-15515     UGCCGAG-CUGCAUGCUUCUUCUACAUGCCCAUA-CU-AUAU-CGUAA-AUGGA-UAUGGAAUGUAAAGAAGUAUGUAGAACGGAA
AADN03008235.1/118591-118669   CCCAACC-CUACAUACUUCUU-CAUAUGCCCAUA-UG-GAGU-CGGCC-GGCGU-UAUGGAAUGUUAAGAAGUAUGUAUCCUCGGG
AAPE02049319.1/6122-6197       GCCUGGG-AGACAUACUUCUU-UAUAUGCCCAUA-UG-AC----CUGG-GAAGC-UAUGGAAUGUAAAGAAGUAUGUAUUUCAGGU
AAWZ02017015.1/31896-31821     -UUUGAGAUUACAUGCUUCUU-UAUAUCUCCAUA-UG-AA----UUGC-CUUGC-UAUGGAAUGUAAGGAAGUGUGUGGUUUCAAG
AEKZ01016876.1/452-379         GAUGCUG-UUCCGUGCUUCCU-UACUU-CCCAUA-GU-GG----AUGC-GACG--UAUGGAAUGUAAAGAAGUAUGGAGCUGCGCC
AADN03007856.1/168402-168478   GCUUGAG-AGACAUACUUCUU-UAUAUGCCCAUA-UG-AA---CCUGG-CAAUC-UAUGGAAUGUAAAGAAGUAUGUAUUUCAGGU
FO081495.1/23097-23019         UACCGAG-CUGCAUACUUCCU-UACAUGCCCAUA-CU-AUAU-CAUAA-AUGGA-UAUGGAAUGUAAAGAAGUAUGUAGAACGGGG
DQ520617.1/109-184             -CCCAAGGCCACAUGCUUCUU-UAUAUCCCCAUA-CGGAU-----UAC-UUUGC-UAUGGAAUGUAAGGAAGUGUGUGGUUUCGGC
AADN03003607.1/193091-193166   UAUGAGA-UGACAUGCUUCUU-UAUAUCCCCAUA-UG-GA----UUAG-GCUGC-UAUGGAAUGUAAGGAAGUGUGUGGUUUCAGG
#=GC SS_cons                   :::::::.<<<<<<<<<<<<<.<<<<<-<<-<<<.__.__..._____._____.>>>>>->>>>>>>>>>>>>>>>>>:::::::
#=GC RF                        ucuugaG.cuaCAUaCUUCuU.UAuAUgCCCAUA.ug.aA...cuuaa.aaagc.UAUGGAAUgUAAaGAAGuAUGuaguuuaggu
//
# STOCKHOLM 1.0

#=GF AC   RF00104
#=GF ID   mir-10
#=GF DE   mir-10 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   33.00
#=GF TC   33.00
#=GF NC   32.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000033;
#=GF DR   MIPF; MIPF0000025;
#=GF DR   MIPF; MIPF0000268;
#=GF DR   MIPF; MIPF0000271;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679672
#=GF RT   An extensive class of small RNAs in Caenorhabditis elegans.
#=GF RA   Lee RC, Ambros V
#=GF RL   Science 2001;294:862-864.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the microRNA (miRNA) mir-10 family, which contains
#=GF CC   mir-10, mir-51, mir-57, mir-99 and mir-100. mir-10, mir-99 and mir-100
#=GF CC   have now been predicted or experimentally confirmed in a wide range of
#=GF CC   species (MIPF:MIPF0000033, MIPF:MIPF0000025). mir-51 and mir-57 have
#=GF CC   currently only been identified in the nematode Caenorhabditis elegans
#=GF CC   (MIPF:MIPF0000268, MIPF:MIPF0000271). miRNAs are transcribed as ~70nt
#=GF CC   precursors (modelled here) and subsequently processed by the Dicer enzyme
#=GF CC   to give a ~22nt product. In this case the mature sequence comes from the
#=GF CC   5' arm of the precursor. The extents of the hairpin precursors are not
#=GF CC   generally known and are estimated based on hairpin prediction. The
#=GF CC   products are thought to have regulatory roles through complementarity to
#=GF CC   mRNA. The involvement of Dicer in miRNA processing suggests a relationship
#=GF CC   with the phenomenon of RNA interference. miRNAs are numbered based on the
#=GF CC   sequence of the mature RNA.
#=GF WK   mir-10_microRNA_precursor_family
#=GF SQ   36


U77364.1/4186-4260       CUAUAUAUACCCUGUAGAACCGAAUUU-GUGUGGUACCC----ACAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU
U92575.1/1530-1608       CUAUAUCUACCCUGUAGAUCCGGAUUU-GUGUAAAAAUCAUUAAAGCAAUCACAAAUUCGCUUCUAGGGGAGUAUAUAGU
AL645782.2/32556-32631   CUAUAUAUACCCUGUAGAUCCGGAUUU-GUGUAAACAGA---CGCACAGUCACAAAUUCGUAUCUAGGGGAGUAUGUAGU
AL645798.2/23515-23586   CUAUAUAUACCCUGUAGAUCCGAAUUU-GUGUGAAUA-------UACAGUCGCAAAUUCGUGUCUUGGGGAAUAUGUAGU
AC095014.1/143527-143452 CCACGUCUACCCUGUAGAUCCGAAUUU-GUUUUAUACUA---GCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUG
AC018755.3/119760-119832 UGGCACCCACCC-GUAGAACCGACCUU-GCGGGGCCUUC-----GCCGCACACAAGCUCGUGUCUGUGGGUCCGUGUCGG
AC122451.3/49344-49273   UGACAUAAACCC-GUAGAUCCGAUCUU-GUGGUGAAGUG------GACCGCGCAAGCUCGUUUCUAUGGGUCUGUGGCAG
AF480571.1/6-77          UGGCAUAAACCC-GUAGAUCCGAUCUU-GUGGUGAAGUG------GACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG
AF480538.1/6-75          UGCCACAAACCC-GUAGAUCCGAACUU-GUGGUAUUA--------GUCCGCACAAGCUUGUAUCUAUAGGUAUGUGUCUG
AY866139.1/146-221       CUGUAUAUACCCUGUAGAUCCGAAUUU-GUGUAAGGAAU---UUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU
AY866144.1/478-552       CUAUAUAUACCCUGUAGAACCGAAUUU-GUGUGGUAUCC----AUAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU
AY866067.1/466-535       UGCCACAAACCC-GUAGAUCCGAACUU-GUGGUGUUA--------GUCUGCACAAGCUUGUGUCUAUAGGUAUGUGUCUG
AY866142.1/143-218       CUGUAUAUACCCUGUAGAUCCGAAUUU-GUGUAAGGAAU---UUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU
AY866146.1/472-546       CUAUAUAUACCCUGUAGAACCGAAUUU-GUGUGGUAUCC----GUAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU
AY866063.1/457-526       UGCCACAAACCC-GUAGAUCCGAACUU-GUGGUAUUA--------GUCCGCACAAGCUUGUAUCUAUAGGUAUGUGUCUG
AY866140.1/97-172        CUGUAUAUACCCCGUAGAUCCGAAUUU-GUGUAAGGAAU---UUUGUGGUCACAAAUUCGUAUUUAGGGGAAUAUGUAGU
FJ485603.1/59-134        CCACGUCUACCCUGUAGAUCCGAAUUU-GUUUUAUACUA---GCUUUAAGGACAAAUUCGGUUCUAGAGAGGUUUGUGUG
AY866143.1/135-210       CUGUAUAUACCCUGUAGAUCCGAAUUU-GUGUAAGGAAU---UUUGUGGUCACACAUUCGUAUCUAGGGGAAUAUGUAGU
AY866062.1/453-522       UGCCACAAACCC-GUAGAUCCGAACUU-GUGGUAUUA--------GUCCGCACAAGCUUGUAUCUAUAGGUAUGUGUCUG
AY866060.1/443-512       UGCCACAAACCC-GUAGAUCCGAACUU-GUGGUAUUA--------GUCCGCACAAGCUUGUAUCUAUAGGUAUGUGUCUG
FJ746716.1/41-116        CUAUAUAUACCCUGUAGAUCCGGAUUU-GUGUAAACAGA---CGCACAGUCACAAAUUCGUAUCUAGGGGAGUAUGUAGU
AY866064.1/423-492       UGCCACAAACCC-GUAGAUCCGAACUU-GUGGUAUUA--------GUCCGCACAAGCUUGUAUCUAUAGGUAUGUGUCUG
AY866059.1/508-579       UGGCAUAAACCC-GUAGAUCCGAUCUU-GUGGUGAAGUG------GACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG
AY866145.1/442-516       CUAUAUAUACCCUGUAGAACCGAAUUU-GUGUGGUAUCC----AUAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGU
AY866066.1/468-537       UGCCACAAACCC-GUAGAUCCGAACUU-GUGGUGUUA--------AUGUGCACAAGCUUGUGUCUAUAGGUAUGUGUCUG
AY866058.1/523-594       UGGCAUAAACCC-GUAGAUCCGAUCUU-GUGGUGAAGUG------GACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG
AY866055.1/522-593       UGGCAUAAACCC-GUAGAUCCGAUCUU-GUGGUGAAGUG------GACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG
AY866057.1/503-574       UGGCAUAAACCC-GUAGAUCCGAUCUU-GUGGUGAAGUG------GACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG
AY866065.1/465-534       UGCCACAAACCC-GUAGAUCCGAACUU-GUGGUAUUA--------GUCCGCACAAGCUUGUGUCUAUAGGUAUGUGUCUU
AY866141.1/176-251       CUGUAUAUACCCUGUAGAUCCGAAUUU-GUGUAAGGAAU---UUUGUGGUCACAAAUUCGUAUCUAGGGGAAUAUGUAGU
AY866061.1/472-541       UGCCACAAACCC-GUAGAUCCGAACUU-GUGGUGUUA--------GUCUGCACAAGCUUGUGUCUAUAGGUAUGUGUCUG
AY866056.1/508-579       UGGCAUAAACCC-GUAGAUCCGAUCUU-GUGGUAAAGUG------GACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG
AY866054.1/508-579       UGGCAUAAACCC-GUAGAUCCGAUCUU-GUGGUGAAGUG------GACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG
AY866053.1/524-595       UGGCAUAAACCC-GUAGAUCCGAUCUU-GUGGUGAAGUG------GACCGCACAAGCUCGCUUCUAUGGGUCUGUGUCAG
Z68760.4/2906-2832       GUCCGUCUACCC-GUAGCUCCUAUCCAUGUUACUGGUC----AAAAAGUGAACAUGGAAGCAGGUACAGGUGCACGGCGA
Z36753.2/18689-18616     GCUCGUCUACCCUGUAGAUCGAGCUGU-GUGUUUGAAAC----AAUCAUACACGAGCUAGACUACAAGGUGCACGAACA-
#=GC SS_cons             :<<<<<<--<<<---<<<<<<<<<<<<.<<<________...._______>>>>>>>>>>>>>>>-->>>-->>>>>>::
#=GC RF                  ugacAuaUACCCUGUAGAucCGAacuU.GUGuuauaauc....auguaugCACAaguUCGuaUCUAuGGGuauaUgucgg
//
# STOCKHOLM 1.0

#=GF AC   RF00105
#=GF ID   SNORD115
#=GF PI   snoHBII-52; HBII-52
#=GF DE   Small nucleolar RNA SNORD115
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   39.00
#=GF TC   39.00
#=GF NC   38.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300124;
#=GF DR   snoopy; Homo_sapiens300324;
#=GF RN   [1]
#=GF RM   11106375
#=GF RT   Identification of brain-specific and imprinted small nucleolar RNA genes
#=GF RT   exhibiting an unusual genomic organization.
#=GF RA   Cavaille J, Buiting K, Kiefmann M, Lalande M, Brannan CI, Horsthemke B,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Proc Natl Acad Sci U S A 2000;97:14311-14316.
#=GF CC   HBII-52 is a member of the C/D class of snoRNAs, which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. HBII-52 is encoded in a tandemly
#=GF CC   repeated array with another C/D snoRNA, HBII-85, in the Prader-Willi
#=GF CC   syndrome (PWS) region of chromosome 15. HBII-52 is exclusively expressed
#=GF CC   in the brain but is absent in PWS patients. HBII-52 lacks any significant
#=GF CC   complementarity with ribosomal RNAs, but does have an 18-nt region of
#=GF CC   conserved complementarity to serotonin 2C receptor mRNA.
#=GF WK   Small_nucleolar_RNA_SNORD115
#=GF SQ   32


AF250841.1/161569-161650     GGGUCAAUGAUGAGAACCUUAUAUUGUCCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/103788-103869     GGGUCGAUGAUGAGAACCUUAUAUUGUCCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/130987-131068     GGGUCAGUGAUGAGAACCUUAUAUUGUCCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/92869-92950       GGGUCAAUGAUGAGAACCUUAUAUUGUUCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/118634-118715     GGGUCGAUGAUGAGAACCUUAUAUUGUCCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUAUGCUGAGGCCC
AF250841.1/122288-122369     GGGUCAAUGAUGAGAACCUUAUAUUGUCCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGUCCC
AF250841.1/127912-127992     -GGUCGAUUAUGAGAACCUUAUAUUGUCCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCCCAAUAGGAUUACGCUGAGGCCC
AF250841.1/99908-99988       GGGUCGAUGAUGAGAACCUUAUAUUG-UCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/120455-120535     GGGUCGAUGAUGAGAACCUUAUAUUU-UCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/89204-89285       GGGUCGAUGAUGAGAACUUUAUAUUGUUCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/144757-144838     GGGUCAAUGAUGAGAACCUUAUAAUGUUCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/139479-139560     GGGUCAGUGAUGAGAACCUUAUAUUGUCCUGAAGAAAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACACUGAGGCCC
AF250841.1/87299-87379       GGGUCAAUGAUGAGAACCUUAUAUUGUCCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUUAGUAGGAUUACGCUGAGG-CC
AF250841.1/107292-107372     GGGUCGAUGAUGAGAAACUUAUAUUG-UCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/116729-116810     GGGUCGAUGAUGAGAACCUUAUAUUGUCCUGAAGAGAGGUGAUGACUUAAAAAU--CAUUCUCAAAAGGAUUAUGCUGAGGCCC
AF250841.1/137573-137654     GGGUCAAUGAUGAGAACCUUAUAUUGUUCUGAAGAGAGGUGAUUAUUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/143208-143289     GGGUCAAUGAUGAGAACCGUAUAUUGUCCUGAAGAGCGGUGAUGACUUAAAAAU--AAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/96678-96759       GGGUCAAUGAUGAGAACCUUACAUUGUUCUGAAGAGAGAUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/141337-141417     GGGUCAAUGAUGAGAACCUGAUAUUGCCCUGAAGAGAGAUGAUGACUUAAAAAU--CAUGUUCAAUAGGAUUACGCUGAGG-CC
AF250841.1/85007-85088       GGGUCGAUGAUGAGAAGCUUCUGUUUUCUUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUAUGCUGAGGCCC
AF250841.1/124166-124247     GGGUCAAUGAUGAGAACCCUAUAUUGUGUUGAAGAGAGGUGAUGACUUAAAAUUACCAUGCUC--AAUGAUUACGCUGAGGCCC
AF250841.1/182151-182226     GGGUCAAUGAUGAGA------UGUUACCUUGAAGAGAAAUGAUGACGUAAAAAU--UAAGUUCAGUUGGAUUACGCUGAGGCCC
AAHX01307617.1/398-475       GGGUCAAUGAUGACAACC---GAAAGUCAAGAACAGA-AUGAUGACAUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/176878-176958     GGGGCAAUAUGGAGA-UGUUAUAUUGUCUUCGACAGGGAAGAUGACAUAAAAAU--UAUGUUCAAUAGGAUUAUGUGGAGACUU
ACBE01194089.1/12712-12632   GGGUCAAUGAUGAGA-ACUCAUAUGGUCUCGAAGACAGAUGAUGACCUAAAAAU--UAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/105693-105774     GGGUCGAUGAUGAGAACCUUAUAUUAUCCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AF250841.1/159716-159797     GGGUCGAUGAUGAGAACCUUAUAUUGUUCUGAAGAGAGGUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACGCUGAGGCCC
AC221015.2/7612-7547         ----------UGACAACC---CAAUGUCAUGAAGAAAGGUGAUGACAUAAAAUU--CAUGCUCAAUAGGAUUACGCUGAGG---
AAYZ01655861.1/973-1050      GGGUCAAUGAUGAGA------UCCCAUACUGAAGGAAGGUGAUGACUUAAAAAAGUCAUGCUCAAUAGGAUUACGCUGAGGCCC
AAGW02050368.1/58895-58815   GGGUCGAUGAUGAGA-CCUCAUACUGUCUUGAAGAGAGAUGAUGACUUAAAAAU--CAUGCUCAAUAGGAUUACACUGAGGCCC
AAEX03002193.1/106182-106102 GGGUCAGUGAUGAGAAUU-CAUAUUGUCUCGAAGAGAGAUGAGGACUUAAAAAU--CAUGCUCAAUAGGAUUAUGCUGAGGCCC
AAGU03082779.1/104733-104813 GGGUCAAUGAAGACA-CCUCAACUUGUCUCGAAGAGAGAUGAUGACAUAAAAAU--CAUGCUCAAUAGGAUCCCGCUGAGGCCC
#=GC SS_cons                 <<<<<<-<<_____________________________________________.._________________>>->>-->>>>
#=GC RF                      GGGuCaAuGAUGAGAAccUUAUAUUGUcuUGAAGAGAGgUGAUGACuUAAAAAU..cAUGCUCAAUAGGAUUACgCuGAGgCCC
//
# STOCKHOLM 1.0

#=GF AC   RF00106
#=GF ID   RNAI
#=GF DE   RNAI
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Published; PMID:7535193
#=GF GA   47.00
#=GF TC   47.00
#=GF NC   46.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0060910; negative regulation of DNA replication initiation involved in plasmid copy number maintenance;
#=GF RN   [1]
#=GF RM   7523833
#=GF RT   PcnB is required for the rapid degradation of RNAI, the antisense RNA that
#=GF RT   controls the copy number of ColE1-related plasmids.
#=GF RA   He L, Soderbom F, Wagner EG, Binnie U, Binns N, Masters M
#=GF RL   Mol Microbiol 1993;9:1131-1142.
#=GF RN   [2]
#=GF RM   7688127
#=GF RT   The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of
#=GF RT   ColE1-type plasmids in vivo and degradation of RNAI decay intermediates.
#=GF RA   Xu F, Lin-Chao S, Cohen SN
#=GF RL   Proc Natl Acad Sci U S A 1993;90:6756-6760.
#=GF RN   [3]
#=GF RM   7535193
#=GF RT   Surprises at the 3' end of prokaryotic RNA.
#=GF RA   Cohen SN
#=GF RL   Cell 1995;80:829-832.
#=GF CC   RNAI is an antisense repressor of the replication of some E. coli
#=GF CC   plasmids, including ColE1. Plasmid replication is usually initiated by
#=GF CC   RNAII, which acts as a primer by binding to its template DNA. The
#=GF CC   complementary RNAI binds RNAII prohibiting it from its initiation role.
#=GF CC   The rate of degradation of RNAI is therefore a major factor in control of
#=GF CC   plasmid replication. This rate of degradation is aided by the pcnB
#=GF CC   (plasmid copy number B) gene product, which polyadenylates the 3' end of
#=GF CC   RNAI targeting it for degradation by PNPase. Please note: This family
#=GF CC   contains subsequences annotated as human (Z96734), Arabidopsis (AB003142),
#=GF CC   Xenopus (X91243) and S. pombe (L25927, L25928), which match with highly
#=GF CC   significant scores. These eukaryotic matches are almost certainly the
#=GF CC   result of vector contamination.
#=GF WK   RNAI
#=GF SQ   10


AF156893.2/4598-4498 CGAAUUUGGUUACUGCGCUCCUCCA-AGCCAG-UUACCUCGGUUCAAAGAGC-GCCAAC-UCCUCGAACCUUCGAAAAAACCGCCC---GCCAAGGCGGUUUUUUCGU
AJ132618.1/824-723   CGAAUUUGGUGGCAGCGGUCUUGUACACCCUG-UUACCACGGUUCAGAAGUUCCCCAAC-UUACUGAACCUUCGAAAAA-CCACCU---CCCCAGGUGGUUUUUUCGU
D21263.1/151-50      CGAAUUUGGUGGCAGCGGUCUUGUACACCCUG-UUACCACGGUUCAUAAACUUGCCGGU-UUAAUGAACCUUCGAAAAA-CCACCU---UGCCGGGUGGUUUUUUCGU
S42973.1/3-107       AGUAUUUGGUAUCUGCGCUCUGCUGAAGCCAG-UUACCUUCGGAAAAAGAGUUGGUAGC--UCUUGAUCCGGCAAACAAACCACCGCUGGUAGCGGUGGUUUUUUUGU
U65460.1/39-143      AGUAUUUGGUAUCUGUGCUCUGCUGAAGCCAGAUUACCUCGGUUAGAUAAUCUGCCAGGAUUAGCUAACCUUCGAAAAAACCACCU---GCCAGGGUGGUUUUUUCGU
U80803.1/804-704     CAGAUUUGGUUACUGCGUUCCUCCA-AGCCAG-UUACCGCGGUUCAAAGAGUUGGUAGC-UCUGAGAACCUUCGAAAAA-CCGCCU---UGCAGGGCGGUUUUUUCGU
X63534.1/2865-2765   UAGAUUUGGUUACUGCGCUCCUCCA-AGCCAG-UUACCGCGGUUCAAAGAGUUGGUAGC-UCAGAGAACCUUCGAAAAA-CCGCCU---UGCAGGGCGGUUUUUUCGU
X80302.1/245-141     AGUAUUUGGUAUCUGUGCUCUGCUGAAGCCAGAUUACCUCGGUUAGAUAAUCUGCCAGGAUUAGCUAACCUUCGAAAAAACCACCU---GCCAGGGUGGUUUUUUCGU
Y17716.1/6521-6420   CGUAUUUGGUGGCAGCGGUCUUGUACACCCUG-UUACCACGGUUCAGAAGUUCCCCAAC-UUACUGAACCUUCGAAAAA-CCACCU---CCCCAGGUGGUUUUUUCGU
Y17846.1/1185-1085   -AGAUUUGGUGGCAGCGGUCUUGUACACCCUG-UUACCACGGUUCAGAAGUUCCCCAAC-UUACUGAUCCUUCGAAAAA-CCACCU---CCCCAGGUGGUUUUUUCGU
#=GC SS_cons         :::::::<<<<<<<<-<<<_______>>>>>>.>>>>>,,<<<<<<<<<<<<_____>>.>>>>>>>>>>--<<<<<<<.<<<<<<...____>>>>>>>>>->>>>:
#=GC RF              aguAUUUGGuggCuGcGcuCuucuaaagCCaG.ccaCCucGGuucggggagcugccAgc.uccccgaaCCuuCGaaaaa.CCgCCc...uccagGGcGGuuuUuuCGU
//
# STOCKHOLM 1.0

#=GF AC   RF00107
#=GF ID   FinP
#=GF DE   FinP
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Published; PMID:9917389
#=GF GA   45.00
#=GF TC   50.80
#=GF NC   43.10
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00016
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   9917389
#=GF RT   Degradation of FinP antisense RNA from F-like plasmids: the RNA-binding
#=GF RT   protein, FinO, protects FinP from ribonuclease E.
#=GF RA   Jerome LJ, van Biesen T, Frost LS
#=GF RL   J Mol Biol 1999;285:1457-1473.
#=GF RN   [2]
#=GF RM   14633993
#=GF RT   FinO is an RNA chaperone that facilitates sense-antisense RNA
#=GF RT   interactions.
#=GF RA   Arthur DC, Ghetu AF, Gubbins MJ, Edwards RA, Frost LS, Glover JN
#=GF RL   EMBO J 2003;22:6346-6355.
#=GF CC   The FinOP system regulates the transfer of F-like plasmids. FinP encodes
#=GF CC   an antisense RNA product that is complementary to part of the 5' UTR of
#=GF CC   the traJ mRNA. The traJ gene encodes a protein required for transcription
#=GF CC   from the major transfer promoter, pY. The FinO protein is essential for
#=GF CC   effective repression, acting by binding to FinP and protecting it from
#=GF CC   RNase E degradation.
#=GF WK   FinP
#=GF SQ   6


AE006471.1/61593-61518 GACACAUAGGAACCUCCUCA--AAGGAUUCUAUGGACAGUCGAUGCAGGGAGU-GACAG-CUCCCUGUAUCGGCGAUUUA
X55896.1/1041-966      CACACAUAGGAACCUCCUCA--AAGGAUUCUAUG-ACAGUCGAUGCAGGGAGG-GACAAGCUCCCUGCAUCGGCGAUUUU
U01159.2/1039-961      GAUACAUAGGAACCUCCUCACAAAGGAUUCUAUGGACAGUCGAUGCAGGGAGUUCACGU-CUCCCUGCAUCGGCGAUUUU
X55894.1/1036-958      GAUACAUAGGAACCUCCUCACAAAGGAUUCUAUGGACAGUCGAUGCAGGGAGGAGAGAA-CUCCCUGCAUCGGCGAUUUU
AF389529.1/1113-1037   GAUACACAGGAGCCUCCUCA--AAGGAUUCUAUGGGUAGUCGAUGCAGGGAGG-GACCAACUCCCUGCAUCGGCGAUUUA
M20941.1/217-140       GAUACAUAGGAACCUCCUCUCAAAGGAUUCUAUGGACAGUCGAUGCGGGGAGGUCGCU--CUCCCUGCAUCGGCGAUUUU
#=GC SS_cons           ::::<<<<<<<-<<<________>>>->>>>>>>----<<<<<<<<<<<<<<_______.>>>>>>>>>>>>>>::::::
#=GC RF                gAuACauaGgaACCuCCUCAcAAaGGAuuCuauGGAcAGuCGauGCaGGGaGgugAcaa.CuCCCuGCauCGgCGAUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00108
#=GF ID   SNORD116
#=GF PI   snoHBII-85; HBII-85
#=GF DE   Small nucleolar RNA SNORD116
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   35.00
#=GF TC   35.20
#=GF NC   34.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300268;
#=GF DR   snoopy; Homo_sapiens300125;
#=GF RN   [1]
#=GF RM   11106375
#=GF RT   Identification of brain-specific and imprinted small nucleolar RNA genes
#=GF RT   exhibiting an unusual genomic organization.
#=GF RA   Cavaille J, Buiting K, Kiefmann M, Lalande M, Brannan CI, Horsthemke B,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Proc Natl Acad Sci U S A 2000;97:14311-14316.
#=GF CC   HBII-85 is a member of the C/D class of snoRNAs, which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. HBII-85 is encoded in a tandemly
#=GF CC   repeated array with another C/D snoRNA, HBII-52, in the Prader-Willi
#=GF CC   syndrome (PWS) region of chromosome 15. Unlike most other snoRNAs, HBII-85
#=GF CC   is expressed prevalently in the brain (but is absent in PWS patients) and
#=GF CC   lacks any significant complementarity with ribosomal RNA.
#=GF WK   Small_nucleolar_RNA_SNORD116
#=GF SQ   48


AF250841.1/1-91              -GAUCGA-UGAUGACUUC------------CAUA-UAUACAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACUGUCAUC-CUCGUCG--AACUGAGGU-CC
AF250841.1/1142-1233         GGAUCGA-UGAUGACUUC------------CACA-UAUACAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACCGUCAUC-CUCGUCG--AACUGAGGU-CC
AF250841.1/2261-2352         GGAUCGA-UGAUGACUUC------------CAUA-UGUACAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACCGUCAUC-CUCGUCG--AACUGAGGU-CC
AF250841.1/4124-4215         GGAUCGA-UGAUGACCUC------------AAUA-CAUGCAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACCGUCGUC-CUCGUCA--AACUGAGGU-CC
AF250841.1/6375-6466         GGAUCGA-UGAUGACUUU------------UAUA-CAUGCAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACCGUCAUC-UUCGUUG--AACUGAGGU-CC
AF357429.1/1-91              --AUCUAAUGAUGAUUCC------------CAGU-CAAACAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAAA---ACUCUG--UACUGCCACU-CUCAUCG-GAACUGAGGU---
AF250841.1/18857-18939       GGAUCGA-UGAUGACUUA------------AAAA-AAUGGAAACCUU-GGAAA-UCUGAA-CAAAAUGAGUGACCAAGACAC----UUCUGU-------------GAGCUGAGGU-CC
ABDC01398238.1/4428-4519     GGAUUGA-UGAUGACUGC------------CAAA-UACACAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACCGUCAUC-CUCAUCG--AACUGAGGU-CC
AAPY01232258.1/5937-5846     GGAUCGA-UGAUGACUUC------------CAAA-UAUACAUUCCUU-GGAAA-UCUGAA-CAAAAUGAGUGAGA---AAUCUC--AACCGUCAUC-CUCAUCG--AACUGAGGU-CC
AADA01034022.1/1285-1194     GGAUCAA-UGAUGACUUC------------CAUA-UAUACAUUCCUU-GGAAA-GCUGAA-UAAAAUGAAUGAAA---ACUCUA--UACCAUCAUC-CUCAUUG--AACUGAGAU-CC
AANU01099493.1/38672-38581   GGAUCAA-UGAUGACCUU------------UAUA-CAUGCAUUCCUU-UGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACCGUCAUC-CUCAUUG--AACUGAGGU-CU
AAHX01488397.1/97-6          GGAUCGA-UGAUGAUUUC------------CAAU-AAAACAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCAA--UACCGCCACU-AUCAUCG--GACUGAGGU-CC
AAQQ01456141.1/5775-5684     GGAUCGA-UGAUGACUCC------------CACA-AAAACAUUCCUU-GGAA--GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACCGUCUCU-CUCAUCG-AAACUGAGGU-CC
AANG01483763.1/818-910       GGAUCGA-UGAUGACUCC------------CUCA-ACAGCAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAGA---ACUCCC--UACCGUCUUU-CUCGUCG-AAACUGAGGU-CC
AALT01596458.1/2542-2634     GGAUCGA-UGAUGAUUCU------------CCCA-AAAGCAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAGA---ACUCAA--UACCGCCGUU-CUCCUCG-ACGCUGAGGU-CC
AAYZ01347451.1/903-994       GGAUCGA-UGAUGACUCC------------CGCA-AAUACAUUCCUU-GGAA--GCUGAA-CAAAAUGAGUGAAA---ACCCCA--UACCGUCGUU-CUCAUCG-UGACUGAGGU-CC
AAFC03091868.1/2550-2641     GGAUCGA-UGAUGACUCC------------CACA-AAUGCAUUCCUU-GGAAA-UCUGAA-CAAAAUGAGUGAGC---CAUCAC--UACCGU-CUC-CUCAUCG-GAACUGAGGU-CC
AANN01224462.1/353-254       GGAUCGA-UGAUGACUCCCCACU-------CACA-CCAGCAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAGA---ACCCCC--CUCCGUCUAU-CUCAUCGGUUUCUGAGGU-CC
AAPY01669616.1/1268-1177     GGAUCGA-UGAUGACCCC------------UAAA-UAUACAUUCCUU-GGAAA-UCUGAA-CAAAAUGAGUGAAA---AAUCUC--AACCGUCAUC-UUCAUCG--AACUGAGGU-CC
AAHY01310504.1/454-361       GGAUCUA-UGAUGAUUCC------------CAGU-CAAACAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAAA---ACUCUG--UACCGUCACU-CUCAUCG-GAACUGAGGU-CC
ABDC01398238.1/23-115        GGAUUGA-UGAUGACUCGC-----------CAAA-UACACAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACCGUUGUC-CUCAUCG--AACUGAGGU-CC
AANU01099489.1/3375-3284     GGAUCAG-UGAUGACUUC------------CACA-CAUGCAUUCCUU-GGAAA-GCUAAA-CAAAAUGAGUGAAA---ACUUUA--UACCGUCAUC-CUCUUCA--AACUGAGGU-CU
AAQQ01436445.1/4768-4861     GGAUCGA-UGAUGAGUCC------------UCCA-AUAACAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAAA---ACCCAC--UACCGUCUCG-CUCAUCG-UGACUGAGGU-CC
AACN010755929.1/369-463      GGAUCGA-UGAUGACUCC------------CUCAAUCUGCAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAGA---ACUCCC--UGCCGUCAUU-CUCAUCG-CAACUGAGGU-CC
AAYZ01347450.1/1628-1722     GGAUCGA-UGAUGACUCCA-----------CCGU-CAAACAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAAA---ACUCAC--UACCGUCGUU-CUCAUCG-UGACUGAGGU-CC
AALT01318476.1/1421-1515     GGAUCGA-UGAUGAUUUCCU----------CUCA-AAAGCAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAGA---ACUCAA--UACCACCGUU-CUCCUCG-ACGCUGAGGU-CC
AANN01351369.1/524-427       GGAUCGA-UGAUGACUCCCCAUU-------CACA-CCAGCAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAGA---ACCCCC--U-CCGUCUAU-CUCAUCG-GUUCUGAGGU-CC
AAIY01112162.1/1182-1273     AGAUUGA-UCAUUAUUUC------------UACA-UAGACAUUCCUU-GGAAA-UCUGAA-CAAAAUGAGUGAAA---AAUCGC--UAGCAUUUUG-CUUAGAA--CUUUGUAAC-AU
AAFC03091868.1/16020-16110   GGAUUG--UGUUGACUCC------------CACA-AAUGCAUUCCUU-GGGAG-UUUGAA-CAAAAUGAGUGAGC---AGUCCU--UGUGGUCUUC-UCAUUAG--AAUUAAGUU-CC
AAIY01349944.1/1943-1852     AGAUCGA-UGUUGCCUCC------------CCCG-UCAGCAUUCCUCAGGAAA-GCUGAA-C-AAGUGAGUGACA---ACUCCC--UGCCGUCUUG-UUCAUCA--CACUGAGGU-GC
AANG01731207.1/964-1052      AGAUUGA-UGAUGACUCCCUC---------CUCA-ACUGCAUUCUUU-U-AAA-GCUGCACAAACCUGAGUGAGA---ACUCAC--UACCGUCAUU-CUCAUC---------AGUGCU
AAGV020589273.1/2304-2397    GGAUCGA-UGAUGGCACC------------CUAA-UCAGCAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAGA---AAUCCC--UACCAUCUCCUCUCAUUG--AACUGAGGU-CC
AAWR02044478.1/21086-21178   GGAUCGA-UGAUGACUCC------------CUCA-AAUGCAUUCCUU-GGAAA-UCUGAA-CAAAAUGAGUGAGA---ACUCAC--UACCGUCGUU-CUCGCCG-AGACUGAGGU-CC
AAWR02044478.1/23872-23965   GGAUCGA-UGAUGACUCC------------CUCA-UAUGCAUUCCUU-GGAAAAUCUGAA-CAAAAUGAGUGAGA---ACUCAC--UACCGUCGUU-CUCAUCG-AAACUGAGGU-CC
AAKN02054628.1/81515-81606   GGAUCGA-UGAUGACACU------------CAUA-AAUGCAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---AACCUA--UACCGUCAUU-CUCAUCG--AACUGAGGU-CC
AAKN02054628.1/38229-38322   GGAUCGA-UGAUGAUGCC------------CCAA-AAAACAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAGA---GCUCUA--AUCCGUCACU-CUCGUCG-UGACUGAGGU-CC
AAGV020534921.1/55-148       GGAUCGA-UGAUGACAUC------------CUAA-UUAGCAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAGA---AAUCCC--UACUGUCUCCUCUCAUCA--AACUGAGGU-CC
AAGW02050371.1/89345-89252   GGAUCGA-UGAUGACUCC------------CCCA-UAAACAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAGA---ACUCAC--AACCGUCAUU-CUCAUCG-UGACUGAGGU-CC
AAGU03082774.1/120551-120642 AGAUCAA-UGAUGAAAUC------------CAUA-UAUACAUUCCUU-GGAAA-UCUGAA-CAAAAUGAGUGAAA---AACCCC--UACCGUCUUG-CUCAUCG--ACCUGAGGU-CC
AAQR03178255.1/31971-31881   GGAUCGA-UGAUGACUGC------------CA-A-GAAACAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACCGUCGUC-CUCAUCG--AACUGAGGU-CC
AACZ03100820.1/66450-66362   GGAUC----AAUGACUUC------------CAUA-UAUACAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---ACUCUA--UACCGUCAUC-CUCGUUG--AACUGAGGU-CC
AABR05008878.1/9310-9218     GGAUCGA-UGAAGAUUUC------------CUAC-AAAACAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAAA---AAUCAA--UACCGCCACU-AUCAUCG-UUACUGAGGU-CC
AAGU03082769.1/17552-17644   GGAUUGA-UGAUGACUGC------------UAUC-UAAACAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAAA---ACUCCU--UACCGUCUCA-CUCAUUG--AACUGAGGU-CC
AAPE02056879.1/9277-9183     AGAUCGA-UGAUGAC-CC------------CAAA-AAUGCAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGAGA---ACUCAUACUGUCGUCAUU-CCCAUCAAAAACUGAGGU-CC
AAGW02050371.1/57929-57838   GGAUUGA-UGAUGACUCC------------UGCA-GAUACAUUCUUU-GGAA--GUUGAA-CAAAAUGAGUGAAA---ACCCCA--UACCAUCAUU-CUCUUCA-UUACUGAGGU-CC
AAQR03178255.1/11035-10944   GGAUCGA-UGAUGACUUC------------CAGA-UAUGCAUUCCUU-GGAAA-GCUGAA-CAAAAUGAGUGACA---ACUCUA--UACCGUCGUC-CUCAUCG--AACUGAGGU-CC
AAEX03002194.1/47404-47310   GGAUCGA-UGAUGACUCC------------UUCAAUUUGCAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAGA---ACUCCC--UACUGUCGUU-CUCGUCA-AAACUGAGGU-CC
AAPE02055916.1/40801-40693   GGAUCGA-UGAUGACUCCUCCAAAAAAAACCAAA-CCAACAUUCCUU-GGAAAAGCUGAA-CAAAAUGAGUGAGA---ACUACACCCGUCGUCGUU-CUCAUCGGUAACUGAGGU-CC
#=GC SS_cons                 <<<<<--.----------............----.----<<<<<-<<.<____.______.>>>--->>>>>---...------..----------.-------..------>>>.>>
#=GC RF                      GGAuCGA.UGAUGACUcC............caaA.uauaCAuUCCUU.GGAAA.GCUGAA.CAAAAUGAgUGAaA...AcUCua..UacCGUCaUu.CUCaUcG..aACUGAGgU.CC
//
# STOCKHOLM 1.0

#=GF AC   RF00109
#=GF ID   Vimentin3
#=GF DE   Vimentin 3' UTR protein-binding region
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Published; PMID:9241253
#=GF GA   36.00
#=GF TC   36.20
#=GF NC   35.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   9241253
#=GF RT   RNA-protein interactions within the 3' untranslated region of vimentin
#=GF RT   mRNA.
#=GF RA   Zehner ZE, Shepherd RK, Gabryszuk J, Fu TF, Al-Ali M, Holmes WM
#=GF RL   Nucleic Acids Res 1997;25:3362-3370.
#=GF RN   [2]
#=GF RM   11377416
#=GF RT   Perinuclear mRNA localisation by vimentin 3'-untranslated region requires
#=GF RT   a 100 nucleotide sequence and intermediate filaments.
#=GF RA   Bermano G, Shepherd RK, Zehner ZE, Hesketh JE
#=GF RL   FEBS Lett 2001;497:77-81.
#=GF CC   The 3' UTR of the vimentin mRNA contains a Y shaped structure which has
#=GF CC   been shown to have protein binding activity [1]. The same region has been
#=GF CC   implicated in the control of mRNA localisation to the perinuclear region
#=GF CC   of the cytoplasm, possibly at sites of intermediate filament assembly [2].
#=GF CC   The identity of the proteins involved and the localisation mechanism are
#=GF CC   not known.
#=GF WK   Vimentin_3'_UTR_protein-binding_region
#=GF SQ   19


AJ493266.1/1523-1589 AAAAAAAGUGAAAAAA-----------UAA-CAGCUUUAAAGUGCCUU-U--CUGCAGU--UAUCUG--AGAGCGCCAGAUAGAGU
BC087987.1/1512-1585 UACCUGUUUUAAAGUUUGAAGA-----AAACCAGCUUUCAAGUGCCUU-U---UGCAGU--AAAUUGG-AGAGCACAAGAUAGGGA
X16843.1/1495-1568   GGUGUGUUUUAAACUUUGAAGA-----AAACCAGCUUUCAAGUGCCUU-U---UGCAGU--CAAUUGG-AGAGCGCAAGAUAGGGA
BC054161.1/1500-1573 GUUGUGUUUUAAAAUUUGAAGA-----AAACCAGCUUUCAAGUGCCUU-U---UGCAGU--UAAUUGG-GGAGCGCAAGAUAGGGA
BC054327.1/872-945   GGUGUGUUUUAAACUUUGAAGA-----AAACCAGCUUUCAAGUGCCUU-U---UGCAGU--CAAUUGG-AGAGCGCAAGAUAGGGA
BC045233.1/1484-1557 GUUGUGUUUUAAAAUUUGAAGA-----AAACCAGCUUUCAAGUGCCUU-U---UGCAGU--UAAUUGG-AGAGCGCAAGAUAGGGA
AF447708.1/1750-1826 UUCAAAUUUGAAAUAUUUUGCACACUUAUA----CUUUCAAGUGCCUU-U--CUACACAUUUUUCCA--UGAGCACAGGAUGGUUA
V00447.1/86-155      UUCAUGUCUUAAAGGAAG---------AAA-CAGCUUUCAAGUGCCUU-U--CUCCAGU-UUUUCCA--UGAGCGCAAGAUUAUUA
M18895.1/303-367     UCCAUAUCUUAAAG-------------AAA-CAGCUUUCAAGUGCCUU-U--CUGCAGU--UUUUCA--GGAGCGCAAGGAAUUAA
X62952.1/1534-1599   AUCGUAUCUUAGAAA------------AAA-GAGCUUUCAAGUGCCUU-UA-CUGCAGU---UUUCA--GGAGCGCAAGAUAGAUC
L13263.1/1457-1521   UCCAUAUCUUAAAG-------------AAA-CAGCUUUCAAGUGCCUU-U--CUGCAGUU-UUUUCA--GGAGCG-AAGAUAGAUU
M16718.1/1402-1467   UUCGUAUCUUAAGG-------------AAA-CAGCUUUCAAGUGCCUU-UA-CUGCAGU--UUUUCA--GGAGCGCAAGUAAGAUU
AB169770.1/1641-1705 UCCAUAUCUUAAAG-------------AAA-CAGCUUUCAAGUGCCUU-U--CUGCAGU--UUUUCA--GGAGCGCAAGAUAGAUU
M26251.1/1935-2000   AUCGUAUCUUAGGA-------------AAA-CAGCUUUCAAGUGCCUU-UA-CUGCAGU--UUUUCA--GGAGCGCAAGAUAGAUU
X87227.1/1201-1266   UUUGUAUCUUAAGG-------------AAA-CAGCUUUCAAGUGCCUU-UA-CUGCAGU--UUUUCA--GGAGCGCAAGAUACAUU
AB188279.1/1604-1668 UCCAUAUCUUAAAG-------------AAA-CAGCUUUCAAGUGCCUU-U--CUGCAGU--UCUUCA--GGAGCGCAAGAUAGAUU
K00927.1/229-294     UUCGUAUCUUAAGG-------------AAA-CAGCUUUCAAGUGCCUU-UA-CUGCAGU--UUUUCA--GGAGCGCAAGAUAGAUU
S76850.1/1539-1604   GUAAAAUAGAAAAA-----------------CAGCUUUAAAGUGCCUU-UUUUUGCAUU--GCCACAUUAGAGCGGUCUGUUGAUA
BC053115.1/1499-1568 AAAGAAAAGAAAAGAA-----------AAA-CAGCUUUAAAGUGCCUUCU--UUGCAUU--GCCACAUUAGAGCGGUCUGUUAUUA
#=GC SS_cons         ::::((((((<<<___...........___.____>>>,,,<<<<-<<.<..-<<____..____>>..>>>>>>>))))))::::
#=GC RF              uucauaucuuAAAgau...........AAA.CAGCUUUCAAGUGCCUU.u..CUgCAgU..UuuucA..aGAGCGCaagauaGaUa
//
# STOCKHOLM 1.0

#=GF AC   RF00110
#=GF ID   RybB
#=GF DE   RybB RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Gottesman S, Storz G
#=GF SS   Predicted; PFOLD
#=GF GA   40.00
#=GF TC   41.60
#=GF NC   38.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11445539
#=GF RT   Identification of novel small RNAs using comparative genomics and
#=GF RT   microarrays.
#=GF RA   Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S
#=GF RL   Genes Dev 2001;15:1637-1651.
#=GF CC   This ncRNA was identified in a large scale screen of E. coli [1]. The
#=GF CC   function of this short RNA is unknown. The exact 5' and 3' ends of this
#=GF CC   RNA are uncertain.
#=GF WK   RybB_RNA
#=GF SQ   8


BX571864.1/148819-148741   ACUGCUUUUCUUUGAUAUCCCCAUAUUGAGGA-ACCCGAUAGUCAAUCC-AU-UUUGGUUCGAGACU-AUCGGGU-UUUUUUAU
AP008232.1/1511362-1511284 ACUGCUUUUCUUUGAUGUCCCCAUUUUGAGGA-GCCCAAGCGUCCCGCC-UA-UUAGGUUCAAGACG-CUUGGUU-UUUUUAUU
AE017042.1/1382184-1382264 ACUGCUUUUCUUUGAUGUCCCCAUAUUGAGGA-GCCCGGUAGUCCCGCC-UUCUUAGGUUCAAGACUAACCGGGU-UUUUUCUU
AACY020520751.1/570-648    ACUGCUUUUCUUUGAUGUCCCCAUUUUGUGGA-GCCCGAUAAUCCCGCC-UU-UUAGGUUCAAGAUU-AUCGGGU-UUUUUGUU
AACY022102840.1/831-905    ACUGCUUUUCUUUGAUGUCCCCAAUUUGUGGA-GCCCAUCAACCCCGCC-GU-UUUGGUUCAAGGUU-GAUGGGU-UUU----U
BX950851.1/3019344-3019423 ACUGCUUUUCUUUGAU-UCCCCUUAUUGAGGAAGCCCAUCGUUCCCGCC-UU-UCAGGUUCAAGAGC-GAUGGGCGUUUUCUUU
CP000026.1/1968331-1968409 ACUGCUUUUCUUUGAUGUCCCCAUUUUGUGGA-GCCCAUCAACCCCGCC-AU-UUCGGUUCAAGGUU-GGUGGGU-UUUUUGUU
CP000826.1/1795684-1795605 ACUGCUUUUCUUUGAUGUCCCCAUUUUGUGGA-GCCCGUUAGUCCCGCCUAU-UUAGGUUCAAGACU-AGCGGGU-UUUUUAUU
#=GC SS_cons               :::::::::::::::::::::::::::::::<.<<<<<<<<<<<_____.__.__________>>>>.>>>>>>>.>:::::::
#=GC RF                    ACUGCUUUUCUUUGAUGUCCCCAUuUUGaGGA.gCCCgccaguCCCGCC.uU.UUaGGUUCAAGacu.ggcGGGu.UUUUUuUU
//
# STOCKHOLM 1.0

#=GF AC   RF00111
#=GF ID   SdsR_RyeB
#=GF PI   RyeB;
#=GF DE   SdsR_RyeB RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Gottesman S
#=GF SS   Predicted; PFOLD
#=GF GA   38.00
#=GF TC   38.90
#=GF NC   36.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00105
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11445539
#=GF RT   Identification of novel small RNAs using comparative genomics and
#=GF RT   microarrays.
#=GF RA   Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S
#=GF RL   Genes Dev 2001;15:1637-1651.
#=GF RN   [2]
#=GF RM   22180532
#=GF RT   A conserved RpoS-dependent small RNA controls the synthesis of major porin
#=GF RT   OmpD.
#=GF RA   Frohlich KS, Papenfort K, Berger AA, Vogel J
#=GF RL   Nucleic Acids Res. 2012;40:3623-3640.
#=GF RN   [3]
#=GF RM   27407104
#=GF RT   The target spectrum of SdsR small RNA in Salmonella.
#=GF RA   Frohlich KS, Haneke K, Papenfort K, Vogel J
#=GF RL   Nucleic Acids Res. 2016; [Epub ahead of print]
#=GF RN   [4]
#=GF RM   26811318
#=GF RT   Small RNA Regulation of TolC, the Outer Membrane Component of Bacterial
#=GF RT   Multidrug Transporters.
#=GF RA   Parker A, Gottesman S
#=GF RL   J Bacteriol. 2016;198:1101-1113.
#=GF CC   This ncRNA was identified in a large scale screen of E. coli [1]. The
#=GF CC   exact 5' and 3' ends of this RNA are uncertain. This RNA overlaps
#=GF CC   RFAM:RF00101 on the opposite strand suggesting that the two may act in a
#=GF CC   concerted manner. The homologous sRNA in S. enterica was shown to regulate
#=GF CC   synthesis of major porin OmpD. A study using Salmonella identified 20
#=GF CC   targets of this sRNA including transcriptional regulator, CRP, global
#=GF CC   DNA-binding factors, StpA and HupB, the antibiotic transporter protein,
#=GF CC   TolC, and the RtsA/B two-component system (TCS), and validated their
#=GF CC   post-transcriptional control by SdsR/RyeB RNA. SdsR (sigma-S-dependent
#=GF CC   sRNA).
#=GF WK   RyeB_RNA
#=GF SQ   17


AL627272.1/127789-127690     AGGC---GAUUU-A--GCCU-GCAUUAA-UGCCAACUUUUAGCGCACGGCUCUCUCCCAAGAGCCAU-UUCCCUGGACCGAAU--A-CA---GGAAUCGUAUUCGGUCUUUUUUU
BX936398.1/2014814-2014915   CGGCU--GAAUA-A--GCCU-ACAUUAA-UACCAACUUUUAGCGCACGGCUCUCUCCCAAGAGCCAU-UUCCCUAGACCGAAU--AUCA---GGAAUCGUAUUCGGUCUUUUUUU
CP000507.1/2477672-2477759   A------------------U-CCCCUUU-UGCGACCGAAUAGCGCACGGCUCUUU---AUGAGCCAU-UCCCCUGGGCCCAAA--A-CAAUUGGAAUAGUUUUGGGCCUUUUUUU
CP000469.1/2083537-2083442   AAG------CGC-A---CUG-CAUGGCG-CUUUCAUCUGUAGCGCACGGCUC--UUCAACGAGCCAU-UCCCCUAGGCCCAAACAG-CU---GGAAUCGUUUUGGGCCUUUUUUU
BX571868.1/65482-65383       AAAUUGUAAGUU-GUUUUUC-GUCUCAA-UGAC-ACUUUUAGCGCACGGCUCU----UAAGAGCCAUUUUCCCUAGGCCGAGU--A-GA---GGAGU-CAACUCGGCCUUUUUUU
AM286415.1/1991571-1991671   UGGCU--GAACA-A--GCCU-ACGUUAA-UGCCAACUUUUAGCGCACGGCUCUCUCCCAAGAGCCAU-UUCCCUAGACCGAAU--A-UA---GGAAUCGUAUUCGGUCUCUUUUU
AP008232.1/2147389-2147489   AGGA---CAUCA-AAAGCCU-ACAAAAA-UGCCAACUUUUAGCGCACGGCUCUCUC-CAAGAGCCAU-UUCCCUGGACAGAAU--A-UA---GGAAUCGUAUUCGAUUUUUUUAU
AAOJ01000002.1/106646-106742 AGUG---UAAUC-A--AACU-CCAUUUA-C-UAACCAGUUAGCGCAAGGCUCUUACG--AGAGCCAU-UCCCCUAGGCCCGAG--A-CA---GGAGUCGUUUCGGGCUAUUUUUU
BX950851.1/2786787-2786689   GGGC---UAGUACA--GCUU-GUAUAAA-UGCCAACUUUUAGCGCACGGCUCU--CCCAAGAGCCAU-UUCCCUAGACUGAAU--A-CA---GGAAUCGUAUUCAGUCUUUUUUU
CP000606.1/1812213-1812114   UGAG---AUGAA-A--UUC--GAGGCAA-UCUCAAACAGUAGCGCACGGCUCU--GCAAAGAGCCAU-UCCCCUAGACCCAGA--A-CAAUUGGAAUAGUUUUGGGUCUUUUUUU
CP000961.1/2442838-2442748   A------------------G-AGAGUAA-UUCUCACCAGUAGCGCACGGCUCUUUAAACAGAGCCAU-UCCCCUGGACCCAAA--A-CAAUCGGAAUAGUUUUGGGUCUUUUUUU
CP000886.1/1142953-1143052   AGGC---GAUUU-A--GCCU-GCAUUAA-UGCCAACUUUUAGCGCACGGCUCUCUCCCAAGAGCCAU-UUCCCUGGACCGAAU--A-CA---GGAAUCGUAUUCGGUCUCUUUUU
CP000821.1/3200789-3200891   AGAG---AGUUA-A--UUCC-CGCGAGG-AUCUCACCAGUAGCGCACGGCUCUUUAAACAGAGCCAU-UCCCCUGGACCCAGA--A-CAAUUGGAAUAGUUUUGGGUCUUUUUUU
CP000826.1/2129617-2129710   AAG-------------CCUU-GCACAAAAUGCCAACUUUUAGCGCACGGCUCUCUCCCAAGAGCCAU-UUCCCUAGACCGAAU--A-UA---GGAAUCGUAUUCGGUCUUUUUUU
CP000038.1/1385102-1385194   UAAG------------CCUG-CAUUAA--UGCCAACUUUUAGCGCACGGCUCUCUCCCAAGAGCCAU-UUCCCUGGACCGAAU--A-CA---GGAAUCGUAUUCGGUCUUUUUUU
CP000946.1/1992711-1992810   AGGC---AACUA-A--GCC-UGCAUUAA-UGCCAACUUUUAGCGCACGGCUCUCUCCCAAGAGCCAU-UUCCCUGGACCGAAU--A-CA---GGAAUCGUGUUCGGUCUCUUUUU
AALF02000003.1/121709-121620 AC----------------GU-UAAUUAA-UGCCAACUUUUAGCGCACGGCUCUGUCCCAAGAGCCAU-UUCCCUAGACCGAAU--A-UA---GGAAUCGUAUUCGGUCUUUUUUU
#=GC SS_cons                 :<<<..._____._..>>>,.,,,,,,,.,,,,,,,,,,,,,,,,,,<<<<<<______>>>>>>--.------<<<<<<<<<..<.<_...______>>>>>>>>>>>::::::
#=GC RF                      aggc...aAuua.A..gccu.acauuaA.UgccAACuuuUAGCGCACGGCUCUuUcccAAGAGCCAU.UuCCCUaGgCCgaau..a.cA...GGAAUcguauucGGcCuUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00112
#=GF ID   CyaR_RyeE
#=GF PI   RyeE
#=GF DE   CyaR/Rye RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Gottesman S, Storz G, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   47.00
#=GF TC   49.00
#=GF NC   45.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11445539
#=GF RT   Identification of novel small RNAs using comparative genomics and
#=GF RT   microarrays.
#=GF RA   Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S
#=GF RL   Genes Dev 2001;15:1637-1651.
#=GF RN   [2]
#=GF RM   18399940
#=GF RT   Systematic deletion of Salmonella small RNA genes identifies CyaR, a
#=GF RT   conserved CRP-dependent riboregulator of OmpX synthesis.
#=GF RA   Papenfort K, Pfeiffer V, Lucchini S, Sonawane A, Hinton JC, Vogel J
#=GF RL   Mol Microbiol. 2008;68:890-906.
#=GF RN   [3]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   This sRNA was originally identified in a large scale screen of E. coli. It
#=GF CC   was shown to bind Hfq and called RyeE [1]. This sRNA has since been
#=GF CC   characterised as a post-transcriptional regulator of the 18 kDa OmpX porin
#=GF CC   in Salmonella [2]. Phylogenetic and mutational analyses suggest that a
#=GF CC   conserved RNA hairpin of this sRNA which features a C-rich apical loop,
#=GF CC   acts to sequester the Shine-Dalgarno sequence of ompX mRNA and inhibits
#=GF CC   translational initiation [2]. The expression of this sRNA has been shown
#=GF CC   to be tightly controlled by the cyclic AMP receptor protein, CRP and has
#=GF CC   been renamed CyaR (cyclic AMP-activated RNA)[2]. CyaR appears to be highly
#=GF CC   conserved amongst enterobacteria and the cyaR gene is frequently located
#=GF CC   downstream of the yegQ gene.
#=GF WK   RyeE_RNA
#=GF SQ   17


AAYT01000003.1/317658-317745 CCGAGUACAAUCAAUAACUAAA-AAAGU-----GUUA-AGUAAUACUAGGAACCACCUCCUUGGCUAGCCCAAUCUCCCUUGGGCUGGCCUUUUC
BX571868.1/175508-175592     GAAAAAUAAAAAAUUAAAAAAG-UUUUA-----C----AGUAAGACUAGGAACCACCUCCUUGGCCGGCUCAAUCUCCCUUGAGCUGGCCUUUUC
CP000468.1/2259167-2259252   UCGCUGAAAAACAUAACCCAUAAAAUGC-----U----AGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACGCAGGCUUAUUU
CP000653.1/2911593-2911677   CCGCUGAAAAACAUAACCCAUA-AAUGC-----U----AGCUGUACCAGGAACCACCUCCUUAGCCUGCGUAAUCUCCCUUACGCAGGCUUAUUU
CP000647.1/2775701-2775785   UCGCUGAAAAACAUAACCCAUA-AAUGC-----U----AGUUGUACCAGGAACCACCUCCUUAGCCUGCGUAAUCUCCCUUACGCGGGCUUAUUU
AACY021413777.1/498-414      UCGCUGAAAAACAUAACCCAUA-AAUGC-----U----AGCUGUACCAGGAACCACCUCCUUAGCCUGCGUAAUCUCCCUUACGCGGGCUUAUUU
CP000034.1/2056399-2056484   UCGCUGAAAAACAUAACCCAUAAAAUGC-----U----AGCUGUACUAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU
AM286415.1/1229660-1229572   UCGAGUACAAUCAAGAACUAAA-AAAGU-----UUUAAAGCAAGACUAGGAACCACCUCCUUGGCCAACCCAAUCUCCCUUGGGCUGGCCUUUUC
DQ077535.1/279-363           GCGCUGAAAAACAUAACCCAUA-AAUGC-----U----AGCUGUACCAAGAACCACCUCCUUGGCCUGCGUAAUCUCCCUUACGCAGGCUUAUUU
BX950851.1/3574694-3574778   AAAACAUAGAACAAAAAAUAAG-CGUAG-----U----GAUACUACUAGGAACCACCUCCUUGGCCAGCUCAAUCUCCCUUGAGCUGGCUUUUCU
CP000266.1/2176798-2176883   UCGCUGAAAAACAUAAUCCAUAAAAUGC-----U----AGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU
CP000826.1/3938239-3938328   CUGCUUAAAACUAAGAACGAAA-AAUAUUUGCAU----AGCAAUACUAGGAACCACCUCCUUAGCCGGUCCAAUCUCCCUUGGACUGGCUUUUUC
CP001063.1/1042605-1042520   UCGCUGAAAAACAUAACCCAUAAAAUGC-----U----AGCUGUACCAGGAACCACCUCCUUAGCCUGUGUAAUCUCCCUUACACGGGCUUAUUU
CP001120.1/2278718-2278802   GCGCUGAAAAACAUAACCCAUA-AAUGC-----U----AGCUGUACCAGGAACCACCUCCUUGGCCUGCGUAAUCUCCCUUACGCAGGCUUAUUU
CP001127.1/2252673-2252757   GCGCUGAAAAACAUAACCCAUA-AAUGC-----U----AGCUGUACCAGGAACCACCUCCUUGGCCUGCGUAAUCUCCCUUACGCAGGCUUAUUU
FR718724.1/33582-33670       UCGAGUACAAUCAAGAACUAAA-AAAGU-----UUUAAAGCAAGACUAGGAACCACCUCCUUGGCUAGCCCAAUCUCCCUUGGGCUGGCCUUUUC
AALF02000004.1/243202-243290 UCGAGUACAAUCAAGAACUAAA-AAAGU-----UUUAAAACAAGACUAGGAACCACCUCCUUGGCUAGCCCAAUCUCCCUUGGGCUGGCCUUUUC
#=GC SS_cons                 ::::::::::::::::::::::.:::::.....:....:::::::::<<<<______>>>>-<<<<<<<<<<<______>>>>>>>>>>>:::::
#=GC RF                      ucGauuAAAAacAuaAaCuAaA.AAUgu.....U....AGcaauACuAGGAACCACCUCCUUgGCCcGcgcAAUCUCCCUUgcgCgGGCcUuUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00113
#=GF ID   SIB_RNA
#=GF PI   QUAD; QUAD_RNA
#=GF DE   Short Intergenic Abundant RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Gottesman S, Storz G
#=GF SS   Predicted; PFOLD
#=GF GA   56.00
#=GF TC   59.30
#=GF NC   55.70
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.02 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   11445539
#=GF RT   Identification of novel small RNAs using comparative genomics and
#=GF RT   microarrays.
#=GF RA   Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S
#=GF RL   Genes Dev 2001;15:1637-1651.
#=GF CC   This family contains multiple ncRNA from E. coli that were identified in a
#=GF CC   large scale screen of E. coli, were they were called candidates 43,55 and
#=GF CC   61 [1]. These RNAs have also been identified by other groups and called
#=GF CC   QUAD RNAs.
#=GF WK   Sib_RNA
#=GF SQ   17


AL627278.1/13975-13826     UUGACGCUGCUUUUUUUUCGACCUAAAGUAAAG-GAAUAAGGGUGAGAGGG----GAUCUCUCCC-CCCU-----CUGA---UUGGCUGUUAGUAAGCUGGGAAACUUAUCAGUAACAGAACAAUCAGUAUGAUGACCUGGUGCAUCAU-AACCCUU-UCCUUAUU
U00096.2/3193297-3193148   UUGACGCUGUUGUUUUUUCAACCUAGAGUAAAG-GAACAAGGGUAA--GGG--AGGAUUUCUCCC-CCCU-----CUGA---UGAGUUGUUAGUAAGUCGGGAAACUUAACAGUAACAACACAACCAGUAUGAUGACGAGCUUCAUCAU-AACCCUU-UCCUUAUA
U00096.2/3054837-3054987   UUGACAUCGUUGAUUCUUUGACCUAAUUU--AGUGAGUAAGGGUAA--GGG--AGGAUUGCUCCUCCCCUGAGA-CUGA---CUGU----UAAUAAGCGCUGAAACUUAUGAGUAACAGUACAAUCAGUAUGAUGACAAGUCGCAUCAU-AACCCUUCUCCUUCAA
AL627277.1/109438-109590   UUGACAGCGUCGCUUUUUUGACCUAAAUUUCUC-GGUGAAGGGUGA--GGG--AGG--CGAACCU-CCCUC----CUGCGUACUCACUGUUAAUAUGCUGGGCAAGCGAUGAUUAACAGGAUCAGCAGCAUGAUGACGUAUCUCAUCAUCGUCCCUU-UCCUUUUU
AE005174.2/2899260-2899403 UUGACAUUCUGAACGUGAAGGCAUACUUUC-AG-GAGUGAGGGUAG--AGC--GGGGUUUCCCCC-GCCC------UGG---UAGUCU--UAGUAUGCUGGGUAGCUAAUCACUAA--GAAGCACCACGAUGAUGAGUAUCUUCAUCAU-GACCCUU-UCCUUAUU
AE014073.1/2983210-2983360 UUGACAUCGUUGAUUCUUUGACCUAAUUU--AGUGAGUAAGGGUAA--GGG--AGGAUGACUCCU-CCCUUGAGACUGA---CUGU----UAAUAAGCUCCGAAACUUAUCAGUAACAGUACAAUCAGUAUGAUGACAAGUCGCAUCAU-AACCCUUCUCCUUUAA
AE014075.1/2440196-2440338 UUGACAAUUGGACCGUGAAGGCAUACUUUC-AG-GAAUGAGGGUUG--AGC--GGGGUUUCCCCC-GCCC------UGG---UAGUCU--UAGUAAGCCGGGAAGCUUAUGACUAAGAGCA---CCACGAUGAUGAUCCACUUCAUCAU-GACCCUU-UCCUUAUU
AE005174.2/3861252-3861402 UUGACAUCGUUGAUUCUUUAACCUAAUUU--AGUGAGUAAGGGUAA--GGG--AGGAUGACUCCUCCCCUGAGA-CUGA---CUGU----UAAUAAGCUGGCAAACUUAUCAGUAACAGUACAAUCAGUAUGAUGACAAGUCGCAUCAU-AACCCUUCUCCUUCAA
AE014075.1/2439868-2440010 UUGACAACAAGGGUUGAGUGACAUAAUUUC-AG-GAGUGAGGGUAGA-GCG----GGGUUUUCCC-CGCC-----CUGG---UAGUCU--UAGUAUGCUGGGUAGCUAAUGACUAAGAGCA---CCACGAUGAUGAGUAGCUUCAUCAU-GACCCUU-UCCUUAUU
CP001063.1/1057530-1057382 UUGACACUAAGGGCGGAGUGACAUAAUUUC-AG-GAGUGAGGGUUA--GGGAGAGGUUUCCCCCU-CCCC-----CUGG---GGUUCU--UAGUAAGCCUGGAAGCUAAUCACUAAGAGUAUCACCAGUAUGAUGACGUGCUUCAUCAU-ACCCCUU-UCCUUAUU
AE006468.1/3362474-3362324 UUGACGCUGCUUUUUUUUCGACCUAAAGUAAAG-GAAUAAGGGUGA--GAG--GGGAUCUCUCCCCCCCU-----CUGA---UUGUCUGUUAGUAAGCUGCGAAACUUAUCAGUAACAGAACAAUCAGUAUGAUGACCUGGUGCAUCAU-AACCCUU-UCCUUAUU
CP000247.1/2190729-2190871 UUGACAAUUGGACCGUGAAGGCAUACUUUC-AG-GAGUGAGGGUAG--AGC--UGGGUUUCCCCC-GCCC------UGG---UAGUCU--UAGUAUGCUGGGUAGCUAAUCACUAAGAGCA---CCACGAUGAUGAGUAUCUUCAUCAU-GACCCUU-UCCUUAUU
CP000247.1/2190401-2190543 UUGACACUAAGGGCGGAGUGACAUAAUUUC-AG-GAGUGAGGGUAG--AGC--GGGGUUUCCCCC-GCCC------UGG---UAGUCU--UAGUAAGCUGGCCAGCUAAUGACUAAGAGCA---CCACGAUGAUGAGUCGCUUCAUCAU-GACCCUU-UCCUUAUU
FM200053.1/824841-824696   UUGACAUUAUUCUUGAUGUGGCUUAACGUC-AG-GAGUGAGGGUAA--GGG--AGGAUUCCUCCU-CCCC-----CUGG----UGUCU--UAGUAAGCUGGUAGGCUAAUCACUAAGAGUAUCACCAGUAUGAUGACUACCUUCAUCAU-AACCCUU-UCCUUAUU
CP000266.1/3155500-3155351 UUGACGCUGAUUUUUUUUCAACCUAAAGUAAAG-GAACAAGGGUGA--GGG--AGGAUUUCUCCC-CCCU-----CUGA---UUGGCUGUUAAUAAGCUGCGAAACUUACGAGUAACAACACAAUCAGUAUGAUGACGAGCUUCAUCAU-AACCCUU-UCCUUCUG
U00096.2/2151634-2151776   UUGACAAUCUUAUCGUGAAGGCAUACUUUC-AG-GAGUGAGGGUAG--AGC--GGGGUUUCCCCC-GCCC------UGG---UAGUCU--UAGUAAGCGGGGAAGCUUAUGACUAAGAGCA---CCACGAUGAUGAGUAGCUUCAUCAU-GACCCUU-UCCUUAUU
CP000038.1/3226619-3226769 UUGACAUCGUUGAUUCUUUAACCUAAUUU--AGUGAGUAAGGGUAA--GGG--AGGAUUGCUCCUCCCCU-----GUGA---CUGACUGUUAAUAAGCUGGGAAACUUAUGAGUAACAGUACAAUCAGUAUGAUGGCAAGUCGCAUCAU-AACCCUUCUCCUUCAA
#=GC SS_cons               ::::::::::::::::::::::::::::::.((.((--((((((,,..<<<..____________.>>>,.....<<<<...______..__________________________________>>>><<<<<<<________>>>>>>.>)))))).))))::::
#=GC RF                    UUGACAuuguuguUuuuuuGACcUAAuuUc.AG.GAgUaAGGGuaA..GGg..aGGaUuuCuCCu.cCCu.....CUGg...uuguCU..UAgUAaGCuggGaAaCUuAUgAgUAAcAGuAcaAcCAGuAUGAUGAcuaguuuCAUCAU.aaCCCUu.UCCUUaUu
//
# STOCKHOLM 1.0

#=GF AC   RF00114
#=GF ID   S15
#=GF DE   Ribosomal S15 leader
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Ji Y
#=GF SS   Published; PMID:8955900
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045974; regulation of translation, ncRNA-mediated;
#=GF RN   [1]
#=GF RM   8955900
#=GF RT   Pseudoknot and translational control in the expression of the S15
#=GF RT   ribosomal protein.
#=GF RA   Benard L, Philippe C, Ehresmann B, Ehresmann C, Portier C
#=GF RL   Biochimie 1996;78:568-576.
#=GF CC   The E. coli Ribosomal S15 gene 5' UTR can form two alternative structures.
#=GF CC   One that is a series of three hairpins, The other includes a pseudoknot.
#=GF CC   This structure causes translational regulation of the S15 protein. The
#=GF CC   alignment of this family contains only the final two hairpins which are
#=GF CC   conserved in other species, and also includes the complete region that
#=GF CC   forms the alternate structures.
#=GF WK   Ribosomal_S15_leader
#=GF SQ   78


CP000076.1/977408-977537     UAUAGAUACAGGGAUUUGUCCCUGGCCUGUUGAAACUGUUCUU---GAACAGUUUCC-UGAUAUAA---GGAUUGCC---CACAUGGCACUCAGCGUUGAAGAAAAAGCUCAGAUCGUAACCGACUACCAGCAAGCUGUU
CP000075.1/4969964-4969852   CGGCCUGUUGGAAAC-----GUUUCUCCGGAAACGCUUCC----------------U-UGCACAAAA--GGAUUGCC---CACAUGGCACUCAGCGUUGAAGAAAAAGCUCAGAUCGUAACCGACUACCAGCAAGCUGUU
CP000058.1/4774465-4774353   CGGCCUGUUGGAAAC-----GUUUCUCCGGAAGCGCUUCC----------------U-UGAACAAAA--GGAUUGCC---CACAUGGCACUCAGCGUUGAAGAAAAAGCUCAGAUCGUAACCGACUACCAGCAAGCUGUU
AE004969.1/192921-193035     UGGCAAACUUGU-------------CCGAAUCCCAUUUGGGGUU--CUUUUUAUUUU-UC---------GGAGUUUUUCCAUUAUGGCACUGACCGUAGAACAAAAAGCACAAAUCGUUAAAGAUUUCCAACGUAAAGAA
AE002098.2/639696-639820     GUUGUCUUCAGGCUUGGCAAACUUGUCUGAAUCCCUAUGGGGA---UUCUUAUAUUU-UU---------GGAGUUUUC--AUUAUGGCACUGACCGUAGAACAAAAAGCACAAAUCGUUAAAGAUUUCCAACGCAAAGAA
CR378664.1/324022-324139     GGUGUCGGCUGAAUC-----AGAGAUUGGCGACACAAAUUAAA---AACAUCUAGUA-UU---------AGGAAGAG----UUAUGUCUCUGAAUGCAGAAACUAAAGCAGCUAUCGUUGCUGAAUACGCACAAUGCGAA
BA000031.2/2575966-2575847   CGUGUCGGCUGAAUC-----AGAGAUUGGCUGGCACAAACAUUAA-CUUACUCUUAU-UA---------GGAGAGAA----UUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUGCAGAAUACGCACAAUCUGAA
BA000037.2/2744699-2744580   CGUGUCGGCUGAAUC-----AGAGAUUGGCUGGCACAAAUAUUAA-CCUACUCUUAU-UA---------GGAGAGAA----UUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUGCUGAUUACGCACGUGGCGAA
BX950851.1/783487-783603     UUGGGUGGCUGAAUU-----AGAGAUCGGCGCCUGUUUUUU-----UAUCUAUAAUG-UU---------GGAGUAUU---ACAAUGUCUCUAAGUGUUGAAGCUAAAGCUAAAAUCGUAGCAGACUUCGGUCGUGGCACU
AE016827.1/652723-652843     UGUCGUAGCUGAAUU-----AGAGAUCGGCAAACGAUGUACUAUU-AACUUACUUUU-UA---------GGAGUAAU---AAAAUGUCUCUAAGCGUAGAAAAAAAAGCUGCAAUCGUAGCUGAAUUCGGUCGUGAUGCA
BX936398.1/569499-569617     UUGGGUUGCUGAAUU-----AGAGAUCGGCGCCUGUCUUAAUU---CAUUUAUAUAU-UU---------GGAGUUGU---AUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUGCUGACUUCGGUCGCGGUACU
U18997.1/92494-92380         UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUUUCAU-------UCUAUAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA
X13270.1/1684-1798           UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUUUCAU-------UCUAUAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA
X13775.1/1684-1798           UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUUUCAU-------UCUAUAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA
M14425.1/90-204              UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUUUCAU-------UCUAUAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA
X00761.1/90-204              UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUUUCAU-------UCUAUAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA
BA000007.2/4054239-4054125   UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUUUCAU-------UCUAUAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA
J02638.1/90-204              UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUUUCAU-------UCUAUAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA
X01073.1/87-201              UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUUUCAU-------UCUAUAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA
U00096.2/3309764-3309650     UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUUUCAU-------UCUAUAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA
AE005174.2/4121455-4121341   UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUUUCAU-------UCUAUAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCAACAGCUAAAAUCGUUUCUGAGUUUGGUCGUGACGCA
BX571874.1/72249-72130       UUGGGUGGCUGAAUU-----AGAGAUCGGCACCUGUAAUUUUAU--UUUAUAUGUUU-UU---------GGAGUUGU---AAUAUGUCUCUAAGUACUGAAGCAAAAGCGCAAAUUAUUGCUGAAUUUGGUCGUGAUGUG
CP000026.1/3260707-3260592   UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUCUCAU------UCUUAAAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUUCUGAGUUCGGUCGUGACGCA
AL627278.1/101763-101648     UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUCUCAU------UCUUAAAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUUCUGAGUUCGGUCGUGACGCA
AF399929.1/155-270           UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUCUCAU------UCUUAAAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUUCUGAGUUCGGUCGUGACGCA
AE017220.1/3407979-3407864   UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUCUCAU------UCUUAAAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUUCUGAGUUCGGUCGUGACGCA
Y10692.1/1450-1568           UUGGGUUGCUGAAUU-----AGAGAUCGGCGCCUGUCUUAAUU---UAUCUAUAUAU-UU---------GGAGUUGU---AUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUGCUGACUUCGGUCGCGAUGCC
X76069.1/151-270             UUGGGUGGCUGAAUU-----AGAGAUCGGCACCCGUAAUUUUAA--UUUAUGUAUUU-UU---------GGAGUUGU---AAUAUGUCUCUAAGUACUGAAGCAAAAGCGCAAAUUAUUGCUGAAUUUGGUCGUGAUGCG
CP000563.1/3795357-3795244   CCCUCUGGCUGAGUU-----AGUGAUCGGCUAGAGAUUCA-------UAUUAUUUAU-UU---------GGAGAUAU----ACAUGUCACUAAGUACUGAAGUAAAAGCAAAAAUUUUGGCUGAUUUUGGCCGUUGUGAA
CP000444.1/1261147-1261260   CCCUCUGGCUGAGUU-----AGUGAUCGGCUAGAGAUUCA-------CAUUUUAUAU-UU---------GGAGAGAC----ACAUGUCACUAAGUACUGAAGCGAAAGCAAAGAUCCUGGCUGAAUUUGGCCGUGGCGCA
AACY021269637.1/318-197      UGACCUACCUGUAAA-----UGUGCACGGGUAGGCCAAUCUUUU--UAAUUGCACAU-UA---------UGAGGAAAAG-AAAAUGGCUCUUAGUCCAACUGAAAAAGCAGCAAUUGUUACUGACUACCAACGUGAAGAA
AACY020346007.1/913-799      UGGGAUAGCUGAAUU-----AGAGAUCGGCAUCCUUUCAU-------UCUUAACACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCUACCGCUAAAAUCGUUUCUGAGUUUGGUCGUGAUGCA
AAOJ01000019.1/50021-49903   GGUGUCGGCUGAAUC-----AGAGAUUGGCGGCACAAAUUAAAA--CAUCUUUGUAU-UA---------GGAAUGAG----UUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUGCAGAAUACGCACAAUGUGAA
CP000302.1/1150814-1150928   CCCUCUGGCUGAGUU-----AGUGAUCGGCUGGAGAUACA------UUCUAUAUAUU-UU---------GGAGAUAC----ACAUGUCACUAAGUACUGAAGCAAAAGCAAAAAUCCUAGCUGAUUUCGGCCGUUGUGAA
AAWF01000035.1/36295-36175   CGUGUCGGCUGAAUC-----AGAGAUUGGCUGGCACAAACUUAAACCUCAAACUCUU-UA---------GGAGAGAA----UUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUGCUGAAUAUGCACGUUGCGAA
AAZW01000011.1/111600-111481 CGUAGCGGCUGAAUC-----AGAGAUUGGCUGCUACAAAUAUUA--AACUACUCUUA-UC---------AGGAGAGA---AUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUGCAGAAUACGCGCGCUCUGAA
CP000238.1/662084-661969     CUUUAUGGCUAAAUU-----AGAGAUUGAUGCCUAUCUAU------UUUAUAUUAAU-UU---------GGAUUAUU---AUAAUGUCUCUAAGUUUUAAUACGAAAGCCAAAAUAAUUGCUGAUUUUGGCAGAAAUAAU
AE017143.1/1451380-1451500   UGUCAUAGCUGAGUU-----AGAGAUCGGCUAUUGAUGUA-------UUAUCAACCC-UGAAAAAA---AGGAUAUA---AAUAUGUCUCUAAGCGUAGAAGCAAAAGCAAAGAUCGUGUCUGAAUUUGGCCGUGAUGCA
AACY020025610.1/990-1108     UGGGCUGUCUGUAAU-----UAUGCACGGGCAUCCUGAAUU-----AACAAUUGCAUAUU---------GGAGUAAUU--AUCAUGGCACUAAGUGCAGAAGAGAAAGCAAAAAUCUUAGCAGACUUUGGACAGGGCGAU
CP000507.1/1165215-1165328   CUUCUUGGCUGAGUU-----AGUGAUCGGCUGAGACAAUU-------UACUGAUAUU-UU---------GGAGAUAU----UCAUGUCACUAAGUACUGAAGCUAAAGCAAAAAUCCUGGCUGAGUUUGGCCGUGGUGAA
AAWP01000061.1/18567-18448   CGUAGCGGCUGAAUC-----AGAGAUUGGCUGCUACAACUUUAAA-CCUACUCUUAU-UA---------GGAGAGAA----UUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUGCAGAAUACGCACAAGGCGAA
CP000606.1/3348589-3348478   CUCUUUGGCUGAGUU-----AGUGAUCGGCUGAAGUUUCU---------AUCUAUUU-UU---------GGAGAAAA----AAAUGUCACUAAGUAAAGAAGUAAAAGCACAAAUCCUGGCUGAUUUCGGUCGUGGUGAA
CP000746.1/1989106-1989226   UAUCGUCGCUGAAUU-----AGAGAUCGGCGAACGAUGUAUCGUU-AACUUGCUUUU-CUA--------GGAGUAAA----AAAUGUCUCUAAGCGUAGAACAAAAAGCUGCAAUCGUUGCAGAAUUCGGUCGUGAUGCA
AACY020349371.1/3302-3417    UUUCACGGCUGAAUU-----AGAGAUUGGCUGUGAACCUU------UAAACACUCUA-CU---------GGAGUAAU---ACCAUGUCUCUAAAUGCUGAGAUCAAAGCUCAAAUCGUUGCUGACAACGCUCGUUGCGCC
AP008232.1/678028-678144     GCGGGUGGCUGAAUU-----AGAGAUCGGCGCCCAUCUAUU-----UCACAAUCAUU-UU---------GGAGUGUU---AUAAUGUCUCUAAGUGUUGAAGCGAAAGCGAAAAUUGUUUCUGAUUUCGGCAGUGAUGCC
CP000447.1/1160052-1160165   CACUCUGGCUGAGUU-----AGUGAUCGGCUUGAGAUACA-------UUUACUUUUU-UU---------GGAGAUAC----ACAUGUCACUAAGUGCUGAAACAAAAGCAAAAAUUUUGGCUGAUUUUGGUCGCUGCGAA
L42023.1/1554761-1554645     ACUUCCGUCAUAAAU-----CCAUUUUUGAAUUGCUAUUUGA----UCGCUCUUUUU-UA---------GGAGUAAA----AAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUGCUGAAUUUGGUCGUGAUGCG
CP000647.1/3935217-3935102   AGGGGUCGCUGAAUU-----AGAGAUCGGCACCCUUUCUU------UCUUUUAAUUU-UU---------GGAGUUAU---AAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUUCUGAGUUUGGUCGUGGCGAA
CR954246.1/1037269-1037385   CGUUUUGGCUGAAUU-----AGUGAUCGGCUAAAGCACCUUUU---AAAUUUAAUUU-UU---------GGAGUUAU-----UAUGUCACUAAGCAAUCAAGAAAAAAUCGAUAUCAUUGCUAAAUUCGCACGUGCUGAA
AC192955.1/73895-74009       UGGGGUUGCUGAAUU-----AGAGAUUGGCGCCCAUCUUA-------UUUUAAUUAU-UC---------GGAGUAUU---AUAAUGUCUCUAAGUGUUGAAGUGAAAGCUAAAAUUAUUGCUGAUUUCGGUCGUAAUGCU
AASA01000067.1/80679-80559   UGUCGUAGCUGAGUU-----AGAGAUCGGCUAUUGAUGUA-------UUAUCAACCC-UUAACAAA---AGGAAAUU---AAAAUGUCUCUAAGCGUAGAAGCAAAAGCAAAAAUCGUUGCUGAAUUUGGUCGUGAUGCA
CP000653.1/3906672-3906558   UGGGGUUGCUGAAUU-----AGAGAUCGGCACCCUUUCAU------UCUUUAUAUUU-UU---------GGAGUUCA----UCAUGUCUCUAAGCGUUGAAGCUAAAGCUAAAAUCGUUUCCGAGUUCGGUCGUGGUACU
CP000569.1/1169320-1169443   UGUCCUAGCUGAGUU-----AGAGAUCGGCUACGGAUGUA-------UUAUCAACCC-UUAACGAAAAAAGGAUAUU---AAAAUGUCUCUAAGCGUAGAAGCAAAAGCAAAAAUCGUUGCUGAAUUUGGUCGUGAUGCA
AAOH01000006.1/367267-367382 CGUUUUGGCUGAAUU-----AGUGAUCGGCUAAAGCAUCUUU----UAAAUUUAUUU-UU---------GGAGUCAU-----UAUGUCACUAAGUACUCAACAAAAAGCUGAAAUUCUAGCUAAAUUCGCACGCGCUGAA
AAOU01000003.1/127548-127665 GGUGCCGGCUGAAUC-----AGAGAUUGGCGGCACAAAUUAA----AACAUCUUGUA-UU---------AGGAAUGA---GUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUGCAGAUUACGCACAAUGUGAA
AAZI01000003.1/93153-93274   UGUCAUCGCUGAGUU-----AGAGAUCGGCGAAUGAUGUAUUAAC-AACACUACCUU-UUA--------GGAGUAAA---AAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCAAUCGUUGCUGAAUUUGGUCGUGAUGCG
AAND01000050.1/13253-13134   CGUAGCGGCUGAAUC-----AGAGAUUGGCUGCUACAAAUAUA---AACUUACUCUUAUCA--------GGAGAGAU----UUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUGCAGAAUACGCACAAUCUGAA
AACY024062024.1/98-217       GUUGGCCGGGUUAGCAU---AGCGCCACCCGGCACCCUUUCU----UUCUUUUAAAU-CU---------GGAGUUUU---AAAAUGUCUCUAAGCGUUGAAGCUAAAGCAAAAAUCGUUUCUGAGUUUGGUCGUGGCGAA
ABCQ01000011.1/16156-16042   UCUUAUAGCUGAACG-----AGUGGUCGGCUAUGAGCUAU--------UUAUCUAUA-UU---------GGAGACUCC--ACUAUGUCAUUAAACGCUGAAGCUAAAGCAGCUAUCGUUGCAGAUUUCGCACGCCAAGAA
AE017340.1/1019832-1019719   UAUCGAUGCUGAAUU-----AGUGAUUGGCGUCGAUCAUU------UUGACAAAACU-UA---------GGAGUUAG-----CAUGUCACUAACUGUUGAACAGAAAGCUGAGAUUUUAAAAGAAUUUGGCCAAGGCGAG
CP000388.1/2032735-2032850   UGGCAUGGCUGAAUU-----AGUGAUCGGCCUGCUGUAUUU-----UAGCUCUUAUA-UU---------GGAGAAAG----UUAUGUCACUAACUACUCAAGAAACUGCAGCAAUCAUUGCUGAUUAUGGCGUAAAAGAA
CU207211.1/1844328-1844211   UCGUUGUUCACGGUG-----UGUGGGGUGAGAACUCUGUGCA----UCGCAUGUGAA-AG---------GUAAUUCA---AUCAUGUCUCUCGAAAAAACAAGCAAAGCUGCCAUCGUUGCAGAUAACGCACGUGGCGCA
AE016825.1/1555422-1555541   UGGGUUUUCCGGCUCGCCGCACUUGUCGGGUUUUCAAACC--------CCUAUUGAA-AC---------GGAGCAAUC--CAAAUGGCAAUGACCGCCGCUCAAAAAGCAGAAAUCGUUAAAGGCUUCCAACGCGCUGAA
CP000680.1/3978377-3978281   UGAGACUGCUG---------------CGGCAGUUUCCAGA------------------UG---------AGAGGAAGCC-AACAUGGCACUCAGCGUUGAAGAAAAAGCCCAGAUCGUAAACGAGUACAAGCAAGCUGAA
Y18132.1/190-286             UUGGACCCCGCA-------------UGCGGGAUCCGUUAU------------------CA---------GGAGAAGC---CACAUGGCCCUCAGCGUUGAAGAAAAAGCUCAGAUCGUUGCCGAAUAUCAGCAAACCGCC
CP000821.1/4128138-4128023   CACUUUAGCUGAGUU-----AGUGAUUGGCUAAAGCUUAU------UAAUGCAUUAU-UU---------GGAGAGAC---AAAAUGUCACUAAAUGCUGAACAAACUGCAACAAUCCUGGCUGAAUUCGGUCGUAGUGAA
CP001157.1/4317828-4317721   GUCCGACGCCGC------------AUUGGCCCGCACGGUU------UCCCGACAGAG-AG---------GAUGCCCA----UCAUGGCACUCACCGUUGAAGAAAAAGCCCAGAUCGUCAACGAGUACAAGCAAGCUGAA
CP000961.1/4345047-4344931   CGCUUUAGCUGAGUU-----AGUGAUUGGCUAAAGAUUUAU-----UAAUGCAUUAU-UU---------GGAGAGAC---AACAUGUCACUAAAUGCUGAACAAACUGCAUCUAUCCUGGCUGAAUUCGGUCGUUGUGAA
CP001139.1/514873-514992     CGUAGUGGCUGAAUC-----AGAGAUUGGCUACUACAAAUAUUA--AACUACUCUUA-UC---------AGGAGAGA---AUUAUGUCUCUGAAUGCAGAAACUAAAGCAGCAAUCGUUGCUGAAUACGCACAAUCUGAA
CP000436.1/508973-508852     UGUCAUCGCUGAGUU-----AGAGAUCGGCGAAUGAUGUAU-----UAUCAACCCUU-UUAGUAUAA--GGAAUGUU-----UAUGUCUCUAAGUACAGAAAAAAAAGCAGCUAUUGUUGCUGAAUUUGGUCGUGAUGCG
CP000851.1/3751621-3751505   CCCUUUGGCUGAGUU-----AGUGAUCGGCUAAAGAUUUUUU----AAUGUAAUAUU-UU---------GGAGAUAG----AAAUGUCACUAAGUGUUGAAGCUAAAGCUCAAAUCCUAGCUGAAUUUGGUCGUUGUGAA
CP000886.1/3412197-3412082   UGGGAUCGCUGAAUU-----AGAGAUCGGCGUCCUCUCAU------UCUUAAAUACU-UU---------GGAGUUUU---AAAAUGUCUCUAAGUACUGAAGCUACAGCUAAAAUCGUUUCUGAGUUCGGUCGUGACGCA
CP000057.2/1535723-1535843   UAUCAUCGCUGAGUU-----AGAGAUCGGCGAAUGAUGUAUUAAC-AACACUACCUU-UUA--------GGAGUAAA----AAAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUGCUGAAUUUGGUCGUGAUGCG
AE004439.1/352235-352355     UGUCGUAGCUGGAUU-----AGAGAUCGGCUAGCGAUGUAUUUU--UAACUUAACUU-UUA--------GGAGUUAU---CAAAUGUCUCUAAGUACAGAAAAAAAAGCAGCGAUCGUUGCUGAAUUUGGUCGUGAUGCA
CP000503.1/1219554-1219667   CCCUCUGGCUGAGUU-----AGUGAUCGGCUAGAGAUUCA-------UACUAUAUAU-UU---------GGAGAGAC----ACAUGUCACUAAGUACUGAAGCGAAAGCAAAAAUCCUGGCUGAAUUUGGCCGCGGCGAA
CP002276.1/1040102-1039987   ACUUCCGUCAUAAAU-----CCAUUUUUGAAUUGCUAUUUGA----UCGCUCUUUUU-UA---------GGAGUAAA-----AAUGUCUCUAAGUACUGAAAAAAAAGCAGCAAUCGUUGCUGAAUUUGGUCGUGAUGCG
CP000094.2/917832-917934     UGUUGAAACUGUUUU-----UGA-AACAGUUUCCUGAUAA------------------AA---------GGAUUGCC----UCAUGGCUCUCGACGUUCAAGAAAAAGCUCAAAUCGUUGCCGACUACCAGCAAGCCGUU
AALF02000011.1/47337-47457   UUGGGUUGCUGAAUU-----AGAGAUCGGCGCCUGUUUUAAUUUA-UCUAUAUAUAU-UU---------GGAGUUGU---AUCAUGUCUCUAAGUGUUGAAGCGAAAGCUAAAAUUGUUGCUGACUUCGGUCGCGGUGCC
#=GC SS_cons                 ::::::<<<<<<___....._____>>>>>>----------.....----------<.<<.........<<<<____..._______>>>>>>>::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      ugugaUcgCuGaAUU.....AGaGAuCgGcgaccauuuuuu.....uuuuuauuuuu.uu.........GGaGUuau...AaaAUGUCuCUaagUGcUGAAGaaAAAGCaaAAAUCGUUgCuGAaUUCGguCGuGauGaA
//
# STOCKHOLM 1.0

#=GF AC   RF00115
#=GF ID   McaS
#=GF PI   IS061;
#=GF DE   McaS/IsrA RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22289118
#=GF GA   42.00
#=GF TC   42.10
#=GF NC   38.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -n -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF CL   CL00106
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0005515; protein binding;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   12069726
#=GF RT   A bioinformatics based approach to discover small RNA genes in the
#=GF RT   Escherichia coli genome.
#=GF RA   Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB
#=GF RL   Biosystems 2002;65:157-177.
#=GF RN   [2]
#=GF RM   23666921
#=GF RT   Dual function of the McaS small RNA in controlling biofilm formation.
#=GF RA   Jorgensen MG, Thomason MK, Havelund J, Valentin-Hansen P, Storz G
#=GF RL   Genes Dev. 2013;27:1132-1145.
#=GF RN   [3]
#=GF RM   22289118
#=GF RT   A small RNA that regulates motility and biofilm formation in response to
#=GF RT   changes  in nutrient availability in Escherichia coli.
#=GF RA   Thomason MK, Fontaine F, De Lay N, Storz G
#=GF RL   Mol Microbiol. 2012;84:17-35.
#=GF RN   [4]
#=GF RM   26609136
#=GF RT   Ribonucleoprotein particles of bacterial small non-coding RNA IsrA (IS61
#=GF RT   or McaS) and its interaction with RNA polymerase core may link
#=GF RT   transcription to mRNA fate.
#=GF RA   van Nues RW, Castro-Roa D, Yuzenkova Y, Zenkin N
#=GF RL   Nucleic Acids Res. 2016;44:2577-2592.
#=GF CC   This family consists of several bacterial RNA genes which are found
#=GF CC   between the abgR and ydaL genes in Escherichia coli and Shigella
#=GF CC   flexneri.[1] It was discovered using a computational screen of the E. coli
#=GF CC   genome.[1] Subsequent characterisation of ISO61 region has revealed that
#=GF CC   the reverse strand is actually a CsrA binding ncRNA called McaS and that
#=GF CC   it has a role in biofilm formation control.[2] Furthermore, it has been
#=GF CC   shown that McaS(IsrA) exists as a ribonucleoprotein particles (sRNPs),
#=GF CC   which involve a defined set of proteins including Hfq, S1, CsrA, ProQ and
#=GF CC   PNPase.[4]
#=GF WK   IS061_RNA
#=GF SQ   4



CP000036.1/1703842-1703937 ACCGGCGCAGAGGAGACAAUGCCGGACUUAAGACGCGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGACUCUAUUUUUUUAU
U00096.3/1405751-1405656   ACCGGCGCAGAGGAGACAAUGCCGGAUUUAAGACGCGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGACUCUAUUUUUUUAU
CP000034.1/1309299-1309204 ACCGGUCACCAGGACCCCAGGCCGGAUUUAAGACGAGGAUGCACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGGCUCUAUUUUUUUAU
CP011132.1/1732716-1732810 ACCCGCCACACGGAAUAAUAACGGGAACACAUG-AAGGAUAAACUGCUGUGUGUACUGUAGAGUCUGGCGGAUGUCGACAGGCUCUAUUUUUUUAU
#=GC SS_cons               :<<<<<<____________>>>>>>,,,,,,,<<<<<<________>>>>>>-----<<<<<<<<<<-<<_____>>->>>>>>>>>>::::::::
#=GC RF                    ACCgGccaaaaGGAaacaaggCcGGAuuuaAgaCgcgGAUgcACUGCugcGuGUACUguaGaGuCuGGCGGAUGUCGACaGaCuCuauUUUUUUAU
//
# STOCKHOLM 1.0

#=GF AC   RF00116
#=GF ID   C0465
#=GF DE   C0465 RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Hershberg R
#=GF SS   Predicted; PFOLD
#=GF GA   40.00
#=GF TC   42.50
#=GF NC   35.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   12202758
#=GF RT   Transcriptome analysis of Escherichia coli using high-density
#=GF RT   oligonucleotide probe arrays.
#=GF RA   Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C
#=GF RL   Nucleic Acids Res 2002;30:3732-3738.
#=GF CC   This family consists of a number of bacterial RNA genes of 78 bases in
#=GF CC   length which are found between the tar and cheW genes in E. coli and
#=GF CC   Shigella flexneri. The function of this RNA is unknown.
#=GF WK   C0465_RNA
#=GF SQ   8


AE005174.2/2649880-2649955 GGGAAACUUUAUUGCUGAUGCCACCCGCCGCGAAAUUGAAAU--AAAACCCGAUGCGCAGAUCAUCGGGUUCAUUUCA
CP000247.1/1882367-1882444 GGGAAACUUUAUUGCUGAUGCCACCCGCCGCGCAAUUGAAAUAAAAAACCCGAUGCGCAGAUCAUCGGGUUCAUUUCA
BA000007.2/2574669-2574744 GGGAAACUUUAUUGCUGAUGCCACCCGCCGCGAAAUUGAAAU--AAAACCCGAUGCGCAGAUCAUCGGGUUCAUUUCA
FM180568.1/2069466-2069543 GGGAAACUUUAUUGCUGAUGCCACCCGCCGCGAAAUUGAAAUAAAAAACCCGAUGCGCAGAUCAUCGGGUUCAUUUCA
AE014075.1/2122192-2122269 GGGAAACUUUAUUGCUGAUGCCACCCGCCGCGCAAUUGAAAUAAAAAACCCGAUGCGCAGAUCAUCGGGUUCAUUUCA
AAJX02000031.1/11199-11122 GGGAAACUUUAUUGCUGAUGCCACCCGCCGCGAAAUUGAAAUAAAAAACCCGAUGCGCAGAUCAUCGGGGUCAUUUCA
CP000948.1/2061334-2061411 GGGAAACUUUAUUGCUGAUGCCACCCGCCGCGAAAUUGAAAUAAAAAACCCGAUGCGCAGAUCAUCGGGUUCAUUUCA
AAJV02000029.1/42474-42551 GGGAAACUUUAUUGCUGAUGCCACCCGCCGCGAAAUUGAAAUAAAAAACCCGAUGCGCAGAUCAUCGGGGUCAUUUCA
#=GC SS_cons               <<____>>,,,<<<<----<<_____>>->>>>---<<<<<<----<<<<<<<<<_______>>>>>>>>>->>>>>>
#=GC RF                    gGGAAACuUUAuuGCUGAUGCCACCCGCCGCgaAAUuGaaauAAAAaaCCCGauGCGCAGAUCauCGGGuuCauuuCa
//
# STOCKHOLM 1.0

#=GF AC   RF00117
#=GF ID   C0719
#=GF DE   C0719 RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Hershberg R
#=GF SS   Predicted; ILM
#=GF GA   50.00
#=GF TC   69.30
#=GF NC   34.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.27 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   12202758
#=GF RT   Transcriptome analysis of Escherichia coli using high-density
#=GF RT   oligonucleotide probe arrays.
#=GF RA   Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C
#=GF RL   Nucleic Acids Res 2002;30:3732-3738.
#=GF CC   This family consists of a number of bacterial RNA genes, of 222 bases in
#=GF CC   length, which are found between the yghK and glcB genes in both Shigella
#=GF CC   flexneri and Escherichia coli. The function of this RNA is unknown.
#=GF WK   C0719_RNA
#=GF SQ   9


U28377.1/75750-75971       UAUAGGCGUUAUACUUUACAGCAACAGUACGCCGCUAACGCAAUUGCUACCUCUGGCAUAACAAGUAUAUCGGGUAAGGGUUUCUGUUCCGCACACGCAGACGCAGAGUAUCGUUAAGAUGUCCAUAUUGUUGUUUUAGGCCCGCUAGUAAUGCGCUACGGGUAUUUAAUAUUGUUAAACCCUGAUAAUCGCUCCGGUUAUUUCCGGGAUAAAUGUACUACC
AE014075.1/3536017-3536238 UAUAGGCGUUAUACUUUACAGCAACAGUACGCUGCUAACGCAAUUGCUACCUCUGGCAUAACAAGUAUAUCGGGUAAGGGUUUCUGUUCCGCACACGCAGGCGCAGAGUAUCGUUAAGAUGUCCAUAUUGUUGUUUUAGGCCCGCUAGUAAUGCGCUACGGGUAUUUAAUAUUGUUAAACCCUGAUAAUCGCUCCGGUUAUUUCCGGGAUAAAUGUACUACC
CP000266.1/3095124-3095345 UAUAGGCGUUAUACUUUACAGCAACAGUACGCCGCUAACGCAAUUGCUACCUCUGGCAUAACAAGUAUAUCGGGUAAGGGUUUCUGUUCCGCACACGCAGGCGCAGAGUAUCGUUAAGAUGUCCAUAUUGUUGUUUUAGGCCCGCUAGUAAUGCGCUACGGGUAUUUAAUAUUGUUAAACCCUGAUAAUCGCUCCGGUUAUUUCCGGGAUAAAUGUACUACC
CP000247.1/3216088-3216309 UAUAGGCGUUAUACUUUACAGCAACAGUACGCUGCUAACGCAAUUGCUACCUCUGGCAUAACAAGUAUAUCGGGUAAGGGUUUCUGUUCCGCACACGCAGGCGCAGAAUAUCGUUAAGAUGUCCAUAUUGUUGUUUUAGGCCCGCUAGUAAUGCGCUACGGGUAUUUAAUAUUGUUAAACCCUGAUAAUCGCUCCGGUUAUUUCCGGGAUAAAUGUACUACC
CP000468.1/3397884-3398105 UAUAGGCGUUAUACUUUACAGCAACAGUACGCCGCUAACGCAAUUGCUACCUCUGGUAUAACAAGUAUAUCGGGUAAGGGUUUCUGUUCCGCACACGCAGGCGCAGAGUAUCGUUAAGAUGUCCAUAUUGUUGUUUUAAUCCCGCUAGUGAUGCGCUACGGGUAUUUAAUAUUGUUAACCCCUGAUAAUCGCUCCGGUUAUUUCCGGGAUAAAUGUACUACC
CP000948.1/3217125-3217346 UAUAGGCGUUAUACUUUACAGCAACAGUACGCCGCUAACGCAAUUGCUACCUCUGGCAUAACAAGUAUAUCGGGUAAGGGUUUCUGUUCCGCACACGCAGACGCAGAGUAUCGUUAAGAUGUCCAUAUUGUUGUUUUAGGCCCGCUAGUAAUGCGCUACGGGUAUUUAAUAUUGUUAAACCCUGAUAAUCGCUCCGGUUAUUUCCGGGAUAAAUGUACUACC
AP009240.1/3380501-3380722 UAUAGGCGUUAUACUUUACAGCAACAGUACGCCGCUAACGCAAUUGCUACCUCUGGCAUAACAAGUAUAUCGGGUAAGGGUUUCUGUUCUGCACACGCAGGCGCAGAGUAUCGUUAAGAUGUCCAUAUUGUUGUUAUAGGCCCGCUAGUAAUGCGCUACGGGUAUUUAAUAUUGUUAAACCCUGAUAAUCGCUCCGGUUAUUUCCGGGAUAAAUGUACUACC
AAJV02000002.1/76508-76729 UAUAGACGUUAUACUUUACAGCAACAGUACGCCGCUAACGCAAUUGCUACCUCUGGCAUAACAAGUAUAUCGGGUAAGGGUUUCUGUUCCGCACACGCAGGCGCAGAGUAUCGUUAAGAUGUCCAUAUUGUUGUUUUAGGCCCGCUAGUAAUGCGCUACGGGUAUUUAAUAUUGUUAAACCCUGAUAAUCGCUCCGGUUAUUUCCGGGAUAAAUGUACUACC
AAJU02000009.1/7241-7020   UAUAGGCGUUAUACUUUACAGCAACAGUACGCCGCUAACGCAAUUGCUACCUCUGGCAUAACAAGUAUAUCGGGUAAGGGUUUCUGUUCCGCACACGCAGGCGCAGAGUAUCGUUAAGAUGUCCAUAUUGUUGUUUUAAUCCCGCUAGUGAUGCGCUACGGGUAUUUAAUAUUGUUAACCCCUGAUAAUCGCUCCGGUUAUUUCCGGGAUAAAUGUACUACC
#=GC SS_cons               :::::<<<<<__________________________>>>>>,,,<<<<<____>>>>>--------------------------(((((((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<__________________>>>>>>>,,,,,,<<<<<<<<___>>>>>>>>,,))))))):::::::::::
#=GC RF                    UAUAGGCGuuAUACUUUACAGCAACAGUACGCcGCUaaCGCAAUuGCuaCCUCugGCaUAACAAGUAUAUCGGGUAAGGGUUUCuguuCCGCACACGCAGgCGCAGAGUAUCGUUAAGAUGUCCAUAUUGUUGUUUUAggCCCGCuaguaauGCGCUACGGGUAUUUAAUauuguuaAaCCCUgauaauCGCUCCGguuauuUCCGGgauaAAUGUACUACC
//
# STOCKHOLM 1.0

#=GF AC   RF00118
#=GF ID   rydB
#=GF DE   rydB RNA
#=GF AU   Barquist L; 0000-0003-4732-2667
#=GF SE   mafft; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   59.20
#=GF NC   37.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.5 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11445539
#=GF RT   Identification of novel small RNAs using comparative genomics and
#=GF RT   microarrays.
#=GF RA   Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S
#=GF RL   Genes Dev 2001;15:1637-1651.
#=GF CC   This family consists of several bacterial sequences from E. coli, Shigella
#=GF CC   flexneri and Salmonella species. This RNA gene was discovered by an RNA
#=GF CC   screen [1] between the ydiC and ydiH in E. coli. This gene is only 67
#=GF CC   bases in length and is composed of a hairpin like structure. The function
#=GF CC   of this RNA is unknown.
#=GF WK   rydB_RNA
#=GF SQ   7


U00096.2/1762792-1762732   G-CCCC-UUCAAGAGCUAAGCC------ACUGAGAGUGCCGGAGAUAAGCGCCGGAUGGGGUAGAAACC
CP002433.1/2598598-2598658 G-CCCC-UUCAAGAGCUAAGCC------AUUAUGAGUGCCGGAGAUAAGCGCCGGGUGGGGCAUAAACU
ACXA01000019.1/45860-45915 G-CCCC-UUCAAGAGCUAAGCC------AAUGUGAGUGCCGGAGAUAAGCGCCGGAUGGGGUCC-----
FP236843.1/1318988-1319049 GCCCCC-UUCAAGAGCUAAGCC------AAUGCGAGUGCCGGAGAUAAGCGCCGGAUGGGGAGCAGUAU
CP000822.1/1642857-1642796 -ACCCC-UUCAAGAGCUAAGCCU-----GAAAUGAGUGCCGGAGAUAAGCGCCGGGUGGGGCAACGAAC
CP002206.1/1693433-1693371 G-UCCC-UGACAGAGCUACCACC----UUAACUGAGUGCCGGAGAUAAGCGCCGGGAGGGACGUACUUU
AP008232.1/1966284-1966350 --CCCCAUUGCAGAGCUAAAACCGCCGUCGGGUGAGUUCCGGAGAUAAGCGCCGGGUGGGGACAACUUC
#=GC SS_cons               :.((((.,,,,,,,<<<______.....______>>>,<<<<-<_____>->>>>,,))))::::::::
#=GC RF                    G.CCCC.UUcaAGAGCUAAgcCc.....aaugUGAGUGCCGGAGAUAAGCGCCGGgUGGGGcaaAauuu
//
# STOCKHOLM 1.0

#=GF AC   RF00119
#=GF ID   C0299
#=GF DE   C0299 RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Hershberg R
#=GF SS   Predicted; PFOLD
#=GF GA   40.00
#=GF TC   52.20
#=GF NC   32.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   12202758
#=GF RT   Transcriptome analysis of Escherichia coli using high-density
#=GF RT   oligonucleotide probe arrays.
#=GF RA   Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C
#=GF RL   Nucleic Acids Res 2002;30:3732-3738.
#=GF CC   This family consists of a group of Shigella flexneri and Escherichia coli
#=GF CC   RNA genes which are 78 bases in length and are found between the hlyE and
#=GF CC   umuD genes. The function of this RNA is unknown.
#=GF WK   C0299_RNA
#=GF SQ   5


U73842.1/82-4              GCCACGUGAGCACAAGAUAAGAGAACGAAAAAUCAGCAGCCUAUGCAGCGACAAAUAUUGAUAGCCUGAAUCAGUAUUG
CP000034.1/1125398-1125476 GCCGCGUGAGCACAGGAUAAGAGAACGAAAAAUCAGCAGUCUAUGCAGCGACAAAUAUUGAUAGCCUGAAUCAGUAUUG
CP001063.1/1218217-1218295 GCCACGUGAGCACAGGAUAAGAGAACGAAAAAUCAGCAGUCUAUACAGCGACAAAUAUUGAUAGCCUGAAUCAGUAUUG
CU928145.2/1326462-1326540 GCCACGUGAGCACAGGAUAAGAGAACGAAAAAUCAGCAGUCUAUGCAGCGACAAAUAUUGAUAGCCUGAAUCAGUAUUG
CP000970.1/1991085-1991007 GGCGCGUGAGCACAGGAUAAGAUAACGAAAAAUCAGCAGUCUAUGCAGCGACAAAUAUUGAUAGCCUGAAUCAGUAUUG
#=GC SS_cons               <<--<<<<-<<----<<<_____________>>>---->>->>>>-->>----<<<<<<<<<_______>>>>>>>>>:
#=GC RF                    GCCaCgugAgCACAgGauAAGAgAACGAAAAauCAGCAGcCuauGCAGCGACAaauauuGauAGCCUGAauCaguauuG
//
# STOCKHOLM 1.0

#=GF AC   RF00121
#=GF ID   MicC
#=GF PI   IS063
#=GF DE   MicC RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Hershberg R
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   51.90
#=GF NC   45.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   12069726
#=GF RT   A bioinformatics based approach to discover small RNA genes in the
#=GF RT   Escherichia coli genome.
#=GF RA   Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB
#=GF RL   Biosystems 2002;65:157-177.
#=GF RN   [2]
#=GF RM   15466019
#=GF RT   MicC, a second small-RNA regulator of Omp protein expression in
#=GF RT   Escherichia coli.
#=GF RA   Chen S, Zhang A, Blyn LB, Storz G
#=GF RL   J Bacteriol 2004;186:6689-6697.
#=GF RN   [3]
#=GF RM   29211019
#=GF RT   Dual Regulation of the Small RNA MicC and the Quiescent Porin OmpN in
#=GF RT   Response to Antibiotic Stress in Escherichia coli.
#=GF RA   Dam S, Pages JM, Masi M
#=GF RL   Antibiotics (Basel). 2017; [Epub ahead of print]
#=GF CC   MicC (previously known as IS063 [1]) is located between the ompN and ydbK
#=GF CC   genes in E. coli. This family of Hfq-associated sRNA is thought to be a
#=GF CC   regulator of OmpC expression. MicC inhibits the 30S ribosome binding
#=GF CC   through a conserved 22 bp RNA duplex near the start codon of the ompC
#=GF CC   mRNA. Along with Rfam:RF00033 it may act in conjunction with EnvZ-OmpR
#=GF CC   two-component system to control the OmpF/OmpC protein ratio in response to
#=GF CC   a variety of environmental stimuli [2]. The expression of micC was shown
#=GF CC   to be increased in the presence of beta-lactam antibiotics. The metabolic
#=GF CC   activity of E.coli expressing either OmpC or OmpF was strongly inhibited
#=GF CC   upon exposure to beta-lactams [3].
#=GF WK   MicC_RNA
#=GF SQ   8


AL627270.1/60166-60286     CCUGUUAUAUGCCUUUAUUGUCAC---AUAUUCAUUUUGUCGUUGGGCCAUUGC---GUUAACCU-UUGCUUUCCAGCGUAUAAAUUGACAAGCCCGAAC-GGAU----GUUCGGGCUUUUUUUGUCUA-UGGA
AJ277528.1/288-168         CGUGUUAUAUGCCUUUAUUGUCAC----GUUUAUUUUUC--GUUGACGUAUUGAUA-GCUAUUAU-UAAUUAGCCAGCGAAUAAAUUGACAAGCCCGAACAACCC----GUUCGGGCUUUUUUUUGGGU-UCCA
CP000034.1/1341223-1341344 CGGGUUAUAUGCCUUUAUUGUCAC---AGAUUUUAUUUUCUGUUGGGCCAUUGC---AUUGCUAC-UGAUUUUCCAACAUAUAAAAAGACAAGCCCGAAC-AGUC----GUCCGGGCUUUUUUUUAGAAUUGGA
AACY022965012.1/342-461    CGUGUUAUAUGCCUUUAUUGUCAC---GUUUUAUUUUUC--GUUGGUAUAUUGAUG-GUAAUUAU-UAAUUAGCCAGCGAAUAAAUUGACAAGCCCGAAC-AACU----GUUCGGGCUUUUUUUUGG--UUCCA
EF682131.1/218-344         UGGGUUAUAUGCCUUUAUUGUCAUUUAAAAUUUAUAUUGUUGCCGUCUCAUUCAUAUCGAAUGAU-UAAUUCGUCGGAAAAU-----GACAAGCCCGAAUAGUUUUACUAUUCGGGCUUUUUUUAUUGC-GCCA
CP000647.1/1603837-1603960 CGCGUUAUAUGCCUUUAUUGUCAUGCCAAUAAUUUAUUGUUGCCGUCUCAUUCUGC-GGAAUGAUGUUGUUUAUCGGUAAAA----CGACAAGCCCGAACGUUGU----GUUCGGGCUUUUUUUAUGGA-CAAA
AE006468.1/1745789-1745671 CCUGUUAUAUGCCUUUAUUGUCAC---AUAUUCAUUUUGUCGCUGGGCCAUUGC---GUUAACCU-UUGCUUUCCAGCGUAUAAAUUGACAAGCCCGAAC-GGAU----GUUCGGGCUUUUUUUGU---UUCCA
CP001509.3/1412677-1412798 CGGGUUAUAUGCCUUUAUUGUCAC---AGAUUUUAUUUUCUGUUGGGCCAUUGC---AUUGCCAC-UGAUUUUCCAACAUAUAAAAAGACAAGCCCGAAC-AGUC----GUCCGGGCUUUUUUUUUAGAAUUGG
#=GC SS_cons               ::::::<<<<<____>>->>>,,,...,,,,,,,,,,,,,,<<<<<<_________.________.______>>>>>>---------<<-<<<<<<<<<<.____....>>>>>>>>>>>>::::::::.::::
#=GC RF                    CguGUUAuAUGCCUUUAUUgUCAc...AaaUUuuUuUUguugcuGgcuCAUUgaua.guuAuuAU.UaaUUugcCagcaaAUAAAuuGACAAGCCCGaAC.auuu....GUuCGGGCUUUUUUUuugga.uccA
//
# STOCKHOLM 1.0

#=GF AC   RF00122
#=GF ID   GadY
#=GF PI   IS183
#=GF DE   GadY
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Hershberg R, INFERNAL
#=GF SS   Predicted; ILM
#=GF GA   45.00
#=GF TC   55.40
#=GF NC   33.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   12202758
#=GF RT   Transcriptome analysis of Escherichia coli using high-density
#=GF RT   oligonucleotide probe arrays.
#=GF RA   Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C
#=GF RL   Nucleic Acids Res 2002;30:3732-3738.
#=GF RN   [2]
#=GF RM   15466020
#=GF RT   GadY, a small-RNA regulator of acid response genes in Escherichia coli.
#=GF RA   Opdyke JA, Kang JG, Storz G
#=GF RL   J Bacteriol 2004;186:6698-6705.
#=GF CC   This family represents a GadY RNA (previous named IS183 in [1]). GadY can
#=GF CC   form base pairs with the 3' UTR of its target mRNA gadX, this pairing is
#=GF CC   thought to confer increased stability to the transcript, allowing
#=GF CC   accumulation of gadX (a transcriptional regulator of the acid response)
#=GF CC   and therefore increased expression of downstream acid resistance genes
#=GF CC   [2].
#=GF WK   GadY
#=GF SQ   5


AF311305.1/31-144              CUUACUGAGAGCACAAAGUUUCCCGUGCCAACAGGGAGUGUUAUAACGGUUUAUUAGUCUGGAGACGGCAGACUAUCCUCUUCCCGGUCCCCUAUGCCGGGUUUUUUUUAUGUC
U00039.1/79120-79233           CUUACUGAGAGCACAAAGUUUCCCGUGCCAACAGGGAGUGUUAUAACGGUUUAUUAGUCUGGAGACGGCAGACUAUCCUCUUCCCGGUCCCCUAUGCCGGGUUUUUUUUAUGUC
CP000036.1/3510427-3510540     CUUACUGAGAGCACAAAGUUUCCCGUGCCAACAGGGAGUGUUAUAGCGGUUUAUUAGUCUGGAGACGGCAGACUAUCCUCUUCCCGGUCCCCUAUGCCAGGUUUUUUUUAUGUC
CP000468.1/3964436-3964548     CUUACUGAGAGCACAAAGUUUCCCGUGCCAACAGGGAGUGUUAUAACGGUUUAUUAGUCUGGAGACGGCAGACUAUCCUCUUCCCGGUCCCCUAUGCCGGG-UUUUUUUAUGUC
AAKB02000001.1/2320614-2320501 CUUACUGAGAGCACAAAGUUUCCCGUGCCAACAGGGAGUGUUAUAACGGUUUAUUAGUCUGGAGACGGCAGACUAUCCUCUUCCCGGUCCCCUAUGCCGGUUUUUUUUUAUGUC
#=GC SS_cons                   :::<<<<--<<<<<------<<<<<<____>>->>>>>>>>>---->>>>,,,,<<<<<<<_______>>>>>>>,,,,,,,<<<<<<_______>>>>>>:::::::::::::
#=GC RF                        CUUaCuGAGagCaCAAAGUUuCCCGuGCCAaCAGGGaGuGuuAUAACgGuUUAUuaGuCuGGAGACGGCaGaCuaUCCUCUUcCcGGuCCCCUAUgCCgGgUUUUUUUUAUGUC
//
# STOCKHOLM 1.0

#=GF AC   RF00124
#=GF ID   IS102
#=GF DE   IS102 RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Hershberg R
#=GF SS   Predicted; PFOLD
#=GF GA   46.00
#=GF TC   47.70
#=GF NC   43.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   12202758
#=GF RT   Transcriptome analysis of Escherichia coli using high-density
#=GF RT   oligonucleotide probe arrays.
#=GF RA   Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C
#=GF RL   Nucleic Acids Res 2002;30:3732-3738.
#=GF CC   This family consists of a group of Shigella flexneri and Escherichia coli
#=GF CC   RNA genes which are 208 bases in length and are found between the yeeP and
#=GF CC   flu genes. The function of this RNA is unknown.
#=GF WK   IS102_RNA
#=GF SQ   5


AF200692.2/35693-35898     ACGAUCGAUACCUAUUUUACCGAUCGUUAAUAUCGAUCGUUAUGCUAAUAAUAACUCCUGUUAGCAACGUGCGCAGAUACACA--CAGACAUGAGAUUCAGGGAACAACAGAGCCACACGUCAGAAACUUCCGUCAGCCGGACCUCCGGCACUGUAACCCUUUACCUGCCGGUAUCCACAUCUGUGGAUACCGGCUUUUUUAUUCACC
AF233272.1/74-277          ACGAUCGAUAUCUAUUUUAUCGAUCGUUUAUAUCGAUCGAUAAGCUAAUAAUAACCUUUGUCAGUAACAUGCACAGAUACGUA--CAGA-AAGACAUUCAGGGAACAACAGAACCACAAUUCAGAAACUCCCA-CAGCCGGACCUCCGGCACUGUAACCCUUUACCUGCCGGUAUCCACGUUUGUGGGUACCGGCUUUUUUAUUCACC
X16664.4/58046-58251       ACGAUCGAUACCUAUUUCACCGAUCGUUAAUAUCGAUCGUUAUGCUAAUAAUAACUCAUGUUAGCAACGUGCGCAGAUACACA--CAGUCAUGAGAUUCAGGGAACAACAGAGCCACACGUCAGAAACUUCCGUCAGCCGGACCUCCGGCACUGUAACCCUUUACCUGCCGGUAUCCACAUCUGUGGAUACCGGCUUUUUUAUUCACC
U24429.1/2410-2615         ACGAUCAAUAUCGAUUUAAUCGAUCGUUUAUAUCGAUCGAUUAGCUAAUAAUAACCUUUGUCAGUAACAUGCACAGAUAUGUUACCAGA-AAGACAUUCCGGGAACAACAGAACCACAAUUCAGAAAUUCCCA-CAGCCGGACCUCCGGCACUGUAACCCUUUACCUGCCGGUAUCCACGUUUGUGGGUACCGGCUUUUUUAUUCACC
AE014075.1/1225384-1225586 ACGAUCGAUAACUAUUUAAUCGAUCGUUUAUAUCGAUCGUUAUGCUAAUAAUAACACCCGUUAGCAAUGUAUGCAGACAC--A--CAGACAUGAGAUUCAGGGAACAACAGAGCCACACGUCAGAAACUUCCAUCAGCCGGAUCUGCGGCACUGUAACCCUUCACCUGCAGGUAUCCACAUUUGUGGAUACCGGC-UUUUUAUUCACC
#=GC SS_cons               :::::::::::::::::<<<<<<<<<_______>>>>>>>>>,,,,,,,,,,,,,,,,,<<<-<<_______>>->>>,,,,,..,,,,,,,,,,,,,,,<<<---------------------------------<<<<<____>>>>>------->>>,,,,,,,<<<<<<<<<<<<<__>>>>>>>>>>>>>:::::::::::::
#=GC RF                    ACGAUCgAUAuCuAUUUcauCGauCGUUuAUAUCGauCGauguGCUAAUAAUAACuuuUgucAGcAAcgUgcgCAgacAcaua..CAGAcAuGAgAUUCaGGGAACAACAGAgCCACAagUCAGAAAcUuCCaUCAGCCGgAcCUcCGGCACUGUAACCCUUUACCUGCcGGuauCCaCaUuuGuGGauaCCgGCUUUUUUAUUCACC
//
# STOCKHOLM 1.0

#=GF AC   RF00125
#=GF ID   IS128
#=GF DE   IS128 RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Hershberg R
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   94.30
#=GF NC   43.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   12202758
#=GF RT   Transcriptome analysis of Escherichia coli using high-density
#=GF RT   oligonucleotide probe arrays.
#=GF RA   Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C
#=GF RL   Nucleic Acids Res 2002;30:3732-3738.
#=GF CC   This family consists of a number of bacterial RNA genes of 209 bases in
#=GF CC   length. The IS128 RNA gene is present in Escherichia coli and Shigella
#=GF CC   flexneri and where it is found between the sseA and sseB genes. The
#=GF CC   function of this RNA is unknown.
#=GF WK   IS128_RNA
#=GF SQ   5


D10496.1/1236-1444           UUUAGCGUAUUAUCGACA--CCGGCCCUUUCCGCCG-UGUUCGGUAAUAAAAUAACCUGGCUUAUUAGUCCGAAUUCAGACAAAUAUAAAUAAAUCCUGCUCAAAAUUAAAA-AUUCUAACCGGUAAAAGAUAUUACUUAAACAUGUAAAUUCACUUUCCUUUAAAAAACAAAAAACCGCCAAAAUCAGGCGGUUUUUUGUUGCUGGUCCGGU
CP000034.1/2517112-2517324   AAAACCACCCCAGCGACGUUCAUAGAAUGGCGCAAUAUGUUCGAUAUUAAAAUGACCUGGCUUAUUAGUCCGAAUUCAGACAAAUAUAAACAAAUCCUGCUCAAUAUUAAAAUAUACUAACCGGUAAAAGAUAUUACUUAAAAAUGUAAAUUCACUUUUCUUUAAAAAACAAAAAACCGCCAAAAUCAGGCGGUUAUUUGUUGCCGGUUUGGU
AE014073.1/2632255-2632463   UUUAGCGUAUUAUCGACA--CCGGCCCUUUCCGCCG-UGUUCGGUAAUAAAAUAACCUGGCUUAUUAGUCCGAAUUCAGACAAAUAUAAACAAAUCCUGCUCAAAAUUAAAA-AUUCUAACCGGUAAAAGAUAUUACUUAAACAUGUAAAUUUACUUUCCUUUAAAAAACAAAAAACCGCCAAAAUCAGGCGGUUAUUUGUUGCUGGUCCGGU
AAMJ02000005.1/115409-115619 AAAACCACCCCAGCGACGUUCAUAGAAUGGCGCAAUAUGUUCGAUAUUAAAAUAACCUGACUUAUUAGUCCGAAUUCAGACAAAUAUAAACAAUUUUCGCUUAAUAUUAAAA-AUACUAACCGAUAAAAGAUAUUACUUGAACAUGUAAAUUCACUUUC-UUUAAACAACAAAAAACCGCCAAAAACAGGCGGUUAUUUGUUGCCGGUUUGGU
AAJV02000013.1/31054-31262   UUUAGCGUAUUAUCGACA--CCGGCCCUUUCCGCCG-UGUUCGGUAAUAAAUUAACCUGGCUUAUUAGUCCGAAUUCAGACAAAUAUAAACAAAUCCUGCUCAAAAUUAAAA-AUACUAACCGGUAAAAGAUAUUACUUAAACAUGUAAAUUCACUUUCCUUUAAAAAACAAAAAACCGCCAAAAUCAGGCGGUUAUUUGUUGCUGGUCCGGU
#=GC SS_cons                 :::::::<<<<<<<<<<<..-<<<<_______>>>>.>>->>>>>>>>>-------[[[[,,<<<<-<<<-<____>->>>->>>>,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,((((((,,,,<<--<<<<________>>>>-->>,,,,,,,,,,,,,,<<<<<<-<<<<<<<_______>>>>>>>->>>>>>))))))]]]]:
#=GC RF                      uuuAgCauauuacCGaCa..CcggcaaUuuCcgccg.uGUuCGguaauaAAAUAACCuggCUuauuAGuCCGAAUUCAGaCAaauaUAAAcAAaUccuGCUcAAaAUUAAAA.AUaCUAaCCgGuAAAAGaUAuuaCUUAAAcAUGuaaAUuCACUUUcCUUUAAAaaaCaaaAaaCCGCCAAAAuCAGGCGGuuAuuuGuugCcGGuccgGU
//
# STOCKHOLM 1.0

#=GF AC   RF00126
#=GF ID   ryfA
#=GF DE   ryfA RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Hershberg R
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   80.50
#=GF NC   77.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11445539
#=GF RT   Identification of novel small RNAs using comparative genomics and
#=GF RT   microarrays.
#=GF RA   Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S
#=GF RL   Genes Dev 2001;15:1637-1651.
#=GF RN   [2]
#=GF RM   11553332
#=GF RT   Computational identification of noncoding RNAs in E. coli by comparative
#=GF RT   genomics.
#=GF RA   Rivas E, Klein RJ, Jones TA, Eddy SR
#=GF RL   Curr Biol 2001;11:1369-1373.
#=GF CC   This family consists of a number of bacterial RNA genes of 305 bases in
#=GF CC   length. The ryfA RNA gene is present in E. coli, Shigella flexneri and
#=GF CC   Salmonella species where it is found between the ydaN and dbpA genes. The
#=GF CC   function of this RNA is unknown.
#=GF WK   ryfA_RNA
#=GF SQ   9


AL627275.1/82154-82449       CCGGCCCCCUUCGCCGUCUC--G--CAAACGGGCACUGGCUUCAGGAGAGGAUGUUCCAUGGCCGUA--AGCGCAGGCACACCACAGUGCCUG-CUAUCACGGCAUUAUCGCCAGCGGUGCUGCCGUGAUGCGGUCUUCGCAAGGACCGCAACAUGAAGGUACGAUGCUUUUGUGUCGUGCUUCUUGUUUCUGGCACGUUGUGUCUUCACGCAGA------CAGAAGCU------ACCCAGGU----AAUUCUGUUCCCGUAACGCUCAACGUCCAGAGCAG---GUAAGCCAGG-AGGCCGCCCUGUUGGGCGGCUUUCUUU
D10496.1/1576-1876           GCGGCCCUUUCCGCCGUCUC--G--CAAACGGGCGCUGGCUUUAGGAAAGGAUGUUCCGUGGCCGUA--AAUGCAGGU---UCACAGCGCUUC-GUAUCGCGGCAAUAUCGCCAGUGGUGCUGUCGUGAUGCGGUCUUCGCAUGGACCGCACAAUGAAGAUACGGUGCUUUUGUAUCGUACUUAUUGUUUCUGGUGCGCUGUUAACCGAGGUAAAUAAUAACCGGAGUC------UCUCCGGC----GACAAUUUACUGGUGGUUAACAACCUUCAGAGCAGCAAGUAAGCCCGA-AUGCCGCCCUUU-GGGCGGCAUAUUUU
BA000007.2/3374508-3374812   AUGGCCCUUUUCGCCGUCUC--G--CAAACGGGCGCUGGCUUUAGGAAAGAAUGUUCCAUGACCGUA--AAUACAGGCACCCCACAGUGCUUG-CUAUCGCGGCAAUAUCGCCAGUGGUGCUGUCGUGAUGCGGUCUUCGCAUGGACCGCACAAUGAAGAUACGGUGCUUCUGUAUCGUACUUAUUGUUUCUGGUGCGCUGUUAACCGAGGUAAAUAAUAACCGGAGUC------UCUCCGGC----GACAAUUUACUGGUGAUUAACAACCUUCAGAGCAGCAGGUAAGCCCGA-AUGCCGCCCUUUGGGGCGGCAUAUUUU
AM286415.1/1482585-1482285   CUGGGCCUUUUCGCCGCCCUAAG--CAAGCGGGCAUCGGUUUAAGGAAAGGAGUUCCAACGGCCGUA--AACACAGGCACACUCUCGUGCUUG-UAUUCACGGCAGUGUCGCCGAUGGUGCUGGCGUGAAGCGGUCUAAGCAUGGACCGCACAAUGAA---ACGAUACUUUUGUAUUGUGCUCGUUGUAUUUGGUGCGUUGUUAACAUCCUGGAA------UGGGGGUUGGAGUAUUUUCAAC----AACUCAAUCACGGUAAUCAUCAACACAUCAGGCAA---GUAAAAUAGG-UAGCCGUCCUUCGGGGCGGCUUUCCUU
AE006468.1/2674933-2675228   CCGGCCCUUUCCGCCGUCUC--G--CAAACGGGCGCUGGCUUCAGGAGAGGAUAACCCAUGGCCGUA--AGCGCAGGCACACCGUAGUGCCUG-CUAUCACGGCAUUAUCGCCAGCGGUGCUGCCGUGAUGCGGUCUUCGCAAGGACCGCAACAUGAAGGUACGAUGCUUUUGUGUCGUGCUUCUUGUUUCUGGCACGUUGUGUCUUCACGCAGA------CAGAAGCU------ACCCAGGU----AAUUCUGUUCCCGUAACGCUCAACGUCCAGAGCAG---GUAAGCCAGG-AGGCCGCCCUGUUGGGCGGCUUUCUUU
CP000826.1/5119938-5119642   GUGGGCUUUUCCGCCACCUU--AAGCAAGUGGGCAUCGGUUUUGGGGAAAGGAUUCCAAUAGCCGUA--AAUGCAAGCACGACCCGGUGCUUGUCUUUCACGGCAAUAUCGCCGGUGGUGUUGCCGUGAAGCGGUUUGAGCAUGGACCGCACAAUGAA---ACGAUACUUUUGUGUUGUGCUCGUUGUAUCUGGUGUGAUGUUGUCGUCUGGAAA------GGGAAGUUG----GAAUCUCUCCGACAACGUUAUUUCAGUAACAAUCUAUCACCAGAGCAA---GUAAGCCAGA-UGGCCGC---UUG--GCGGCCAUCUUU
AAMJ02000005.1/115092-115377 CUGGUU-----CGCGGCCUG--U--CCAGCAGGU--UGACUUGUG--------------UUGCCGGAGCAACGCAGGCACCCCACAGUGCUUG-CUAUCGCGGCAAUAUCGCCAGUGGUGCUGUCGUGAUGCGGUCUUCGCAUGGACCGCACAAUGAAGAUACGGUGCUUUUGUAUCGUACUUAUUGUUUCUGGUGCGCUGUUAACCGAGGUAAAUAAUAACCGGAGUC------UCUCCGGC----AACAAUUUACUGGUGGUUAACAACCUUCAGAACAGCAGGUAAGCCCGA-AUGCCGCCCUUUGGGGCGGCAUAUUUU
CP001383.1/2676708-2677012   GCGGCCCUUUCCGCCGUCUC--G--CAAGCGGGCGCUGGCUUAAGGAAAGGAUGUUCCGCGACCGUU--AGAGCAAGCGCGUCUCAGCGCUUG-CUAUCGCGGCAAUAUCGCCAGUGGUGCUGUCGUGAUGCGGUCUUCGCAUGGACCGCACAAUGAAGAUACGGUGCUUCUGUAUCGUACUUAUUGUUUCUGGUGCGCUGUUUUCCCAAGUAAAUAAUAACCGGAGUC------UCUCCGGC----GACAAUUUACUGGUGGUUAACAACCUUCAGAGCAGCAAGUAAGCCCGA-AUGCCGCCCUUUAGGGCGGCAUAUUUU
AALF02000048.1/2586-2886     GCGGACCUUUUCGCCGCCUUAAG--CAAGCGGGCAUCGGUUUAAGGGAAGGAUAUCCAUUGGCCGUA--AC-GCAAGUGCAACCCUGUACUUG-UAUUCACGGUAGUAUCACCGGUGGUGCUGGCGUGAAGCGGUCUAAGCAUGGACCGCACAAUGAA---ACGGUACUUUUGUAUUGUGCUCGUUGUAUUUGGCGCAUUGUUAACAUCCGGGAA------UGGGGGUUGGCGUAUUUUCAAC----AACUCAAUCACGGUGAUAAUCAACACGUCAGGCAA---GUAAGCCCGGUAAGCCGCCCUGCGGGGCGGUUUUCCUU
#=GC SS_cons                 ::::::((((((,<<<<___.._..___>>>><<____>>,,,,)))))),,,,,,,,,,,(((,,,..,,,,<<<<<<<______>>>>>>>.,,<<<<<<<<<-<<<<<____>>>>>->>>>>>>>><<<<<<<______>>>>>>><<<<<<<---<<<<<<<<____>>>>>>>>->>>>>>>,,,,)))((-(((((,,,,,,,,,,,,......,,<<<<__......_>>>>,,,....,,,,,,,,,,,<<<________>>>,,,,,)))))...)),,,,,,<<.<<<<<<<<<____>>>>>>>>>->>::
#=GC RF                      guGGcCcuuucCGCcGcCUu..g..CAAgCgGGCauuGGCUUuaGgaaagGAuaUuCaaUggCCGUA..AauGCAgGcaCacCacaGugCcUG.cuaUCaCGgCAauauCgCCaGcGgugCUGcCGuGAuGCGGUCuucGCAugGACCGCACaAugAAGauACGauaCUUUUGuauCGUaCUcaUuGUuUcUGGcgCGcUGuuaacuuauGuAAA......caggagUu......ucuccggc....AAcuauaUuccgGUaauuAuCAACcuucagagCAg...GuAAGcCagg.agGCCGCCCUuUgGGGCGGCcuuccUU
//
# STOCKHOLM 1.0

#=GF AC   RF00127
#=GF ID   t44
#=GF DE   t44 RNA
#=GF AU   Barquist L; 0000-0003-4732-2667
#=GF SE   Infernal; LocaRNA
#=GF SS   Predicted; LocaRNA; Barquist L
#=GF GA   44.00
#=GF TC   44.10
#=GF NC   43.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   12202758
#=GF RT   Transcriptome analysis of Escherichia coli using high-density
#=GF RT   oligonucleotide probe arrays.
#=GF RA   Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C
#=GF RL   Nucleic Acids Res 2002;30:3732-3738.
#=GF CC   This family consists of a number of bacterial RNA genes of between 135 and
#=GF CC   170 bases in length. The t44 gene has been identified in several species
#=GF CC   of enteric bacteria but homologs have also been identified in Pseudomonas
#=GF CC   and Coxiella species. The t44 gene is found between the map and rpsB genes
#=GF CC   in all species in the full alignment apart from Shigella flexneri. The
#=GF CC   function of this RNA is unknown.
#=GF WK   t44_RNA
#=GF SQ   78


AAKV01000050.1/100479-100392   CUUUUU-----CGGAGCAC-AAACCCACACAUGC-AUCGACA--CGA-UG-GCCUGGGUGCCCGCA------------------------------------AGGGU-UGGU--CAUUG-GGAUGCGUGGAGGC-CUAAC
AAMX01000008.1/91346-91432     UUCACU-----UUAAAUUU--AAACCACACAUAU-AUCGACA--CAU-AC-CACGGGGUGCCCAAU------------------------------------CGGGU-CGUG--CUAUG-GGGUAUAUGGAGGC-UUAAC
AAOS02000031.1/20362-20470     CUCAUA------UGUGUAA--AUAACACACACGU-GUCGACA--CAU-AC-ACCGGGGUGCCCUAAAGUUUUUGAUUG---------UUAUCAAUCGCUUAUGGGGU-CGGUG-UUAUG-GGACACGUGGAGGC------
AAWF01000098.1/4178-4263       CUAAUU---------GUUU--AAAUCACACACAU-UCCGACA--CGU-AU-UCCGGGGUGCUCCAA----------------------------------GUGGAGU-CGGAU-AUACG-GGGGAUGUGGAGGC-CUAAC
ABIC01000015.1/4541-4627       UUUAUU-----AAAU-ACU--AAAUCACACACGU-AUCGACA--CAU-UC-UUCGGGGUGCCUGUA------------------------------------UAGGU-CGAAG-AUAUG-GGAUGCGUGGAGGU-CUAAC
ABWL02000017.1/22454-22540     CUCACU-----UUGUGU-A--ACAACACACACGU-AUCGGCA--CAU-AU-UCCGGGGUGCCCUUU------------------------------------GGGGU-CGGUA-AUAUG-GGAUGCGUGGAGGC-UUAAC
ABXW01000041.1/29063-28959     CUCAAU-----UG--UGUA--AUAACACACACGA-AUCGGCA--CAU-GC-GCCGGGGUGCUCUUAUGCGUUUA-----------------GACGCAGCUUUAGAGU-CGGUA-GCAUG-GGAUUCGUGGAGGC-AUAAC
ADAQ01000013.1/1119434-1119349 CUUAAU-----UUAU---U--AACUCACACACAU-AUCGGCA--CAU-AC-GCCGGGGUGCCCUUG-----------------------------------AAGGGU-CGGAU-GUAUG-GGAUAUGUGGAGGC-CUAAC
AE017340.1/902573-902479       CUUGUAU---GUAAAUUAU--AAUCCACACAUAC-AUCGACA--CAU-AA-GGCGGGGUGCUUGUCUA------------------------------AGAACAGGU-CGGC--UUAUG-GGAUGUAUGGAGGC-UUAAC
AEIU01000081.1/55138-55226     CUAUAU---------UUUU--AAAUCACACACAU-UUCGACA--CAU-AU-UCCGGGGUGCCAAUG-A------------------------------AAAAUUGGU-CGGAA-UUAUG-GGGAAUGUGGAGGC-CUAAC
AEVG01000068.1/7046-7139       UUUAUU-----UUUUAACACUAAAACACACACAU-AUCGCAAGCUAA-UG-AUCGGGGUGCUACGU----------------------------------AAGUGGU-UGAUU-UAUUA-GGAUAUGUGGAGGC-UAAAC
AFOZ01000017.1/101703-101797   CUAAAU----------ACU--AAAUCACACACGU-GUCGACA--CAU-UC-UUCGGGGUGCCCUCAGUUAU------------------------UCACUGCGGGGU-CGAAG-ACAUG-GGAUACGUGGAGGU-CUAAC
AGBG01000016.1/22679-22766     CUUCAU------UGUUCCA--AAUCCACACAUGC-GCCGGCA--CGU-GC-AGCGGGGUGCCCCGA----------------------------------AAGGGGU-UGCU--GUUCG-GGGCGCAUGGAGGC-CCAAC
AGVO01000017.1/7947-8029       CUUAAU-----------CA--AUAACACACACAC-AUCGACA--CCU-GU-ACCGGGGUGCCCCUU-----------------------------------UGGGGU-CGGUU-ACAUG-GGAUGUGUGGAGGC-CUAAC
AP008232.1/3348455-3348359     CUCAAU-----UGUG--UU--AUUACACACACGU-AUCGGCA--CAU-GC-GCCGGGGUGCUCUGAAUCA-------------------------CAAGGUCGGGGU-CGGCC-GUAUG-GGAUACGUGGAGGC-AUAAC
BX950851.1/1154267-1154370     CUCACU-----UUGUGUAA--AUAACACACACAU-GUCGGCA--CGU-UC-GCCGGGGUGCUCCUGAGGUGUU--------------------UCACCGGAUGGGGU-CGGCG-UAAUG-GGACAUGUGGAGGC-AUAAC
CAEI01000138.1/246930-247020   CUCACU-----AUGUGUAA-UAAAACACACAUGU-AUCGACA--CAU-AC-GCCGGGGUGCCUUGA----------------------------------AAGAGGU-CGGUU-GUAUG-GGAUACAUGGAGGC-CCAAC
CP000127.1/881323-881413       CUUUUA-----AAGCAAAC-AAAAUCACACGCGC-AUCGGCA--CAU-ACUAUCGGGGUGCCUUUG----------------------------------GUCAGGU-CGGU--AUAUG-GGAUGCGCGGAGGA-AUAAC
CP000155.1/5396487-5396400     UUGAAA-------CCAUAA--AAAACACACAUGC-GUCGACA--CAU-GU-UUCG-GGUGCCGCUC--------------------------------AAAUGCGGU-UGGA--GCAUG-GGAUGCAUGGAGGU-UAAAC
CP000472.1/3726575-3726485     CUAAAU-----GAAAAUAC-UAAAUCACACACAU-AUCGACA--CAU-UC-UUCGGGGUGCCCCUA----------------------------------ACCGGGU-CGAAG-AUAUG-GGAUAUGUGGAGGU-CUAAC
CP000680.1/3380207-3380131     CUU---------------A--AACCCACACACGU-AUCGACA--CGG-UU-UCCUGGGUGCCCGCA------------------------------------AGGGU-UGGA--AGCUG-GGAUACGUGGAGGC-CUAAC
CP000826.1/4190821-4190717     CUCACU-----UUGUGUAA--AUAACACACACGU-AUCGGCA--CAU-CC-GCCGGGGUGCCCUGAGGUGAUU-------------------UAUCACCGCCAGGGU-CGGCG-UUAUG-GGAUACGUGGAGGC-AUAAC
CP000931.1/3626103-3626013     CUAUUG-----AUAAAUAC-UAAAUCACACACAU-AUCGACA--CGU-UC-UUCGGGGUGCCCUAA----------------------------------AUAGGGU-CGAAG-AUAUG-GGAUAUGUGGAGGU-CUAAC
CP000961.1/4024468-4024382     CUUGUA-----AAUA--CU--AAAUCACACACGU-GUCGACA--CAU-UC-UCCGGGGUGCCUCUA-----------------------------------GAAGGU-CGGAG-AUAUG-GGAUACGUGGAGGU-CUAAC
CP001277.1/1225298-1225206     CUUACU-----CUGUGUUA--AACACACACACUG-GUCGACA--CAU-AA-UCCGGGGUGCCCAGA-U------------------------------AUUUUGGGU-CGGUA-UUACG-GGACUGGUGGAGGU-AUAAC
CP001836.1/1029852-1029951     CUCACU-----AUGUG--U--AUAACACACACGU-GUCGACA--CAU-UC-GCCGGGGUGCCUGUAAUGGUU----------------------UUUCCAUUCUGGU-CGGUG-UAAUG-GGACACGUGGAGGC-AUAAC
CP002080.1/1188520-1188613     UUUGAUAGGUGGAGUAAAA--AAUCCGCACAUAU-AUCGUCA--CAU-UA-CUCUGGGUGCCUGUA----------------------------------AAAGGGU-GGAG---AAUGCGGAUAUAUGGAGGC-CUAAC
CP002209.1/1043144-1043233     CUGUAAA--GUGACUUUAU--AAACCACACACGU-ACCGGCA--CAU-GC-UCCGGGGUGCCCGAA------------------------------------AGGGU-CGGA--ACAUG-GGGUGCGUGGAGGC-UUAAC
CP002433.1/875789-875879       CUCAUU-----AUGUGUAC-UAAAACACACAUGU-AUCGACA--CGU-AC-ACCGGGGUGCCUCGU----------------------------------AAGAGGU-CGGUU-GUAUG-GGAUACAUGGAGGC-CCAAC
CP002505.1/926093-926195       CUUAUU-----AACGUAAGUAAUAACACACACGU-AUCGACA--CAU-AC-GCCGGGGUGCCUUGGGAAUU-----------------------CGUUCUGCAGGGU-CGGUU-GUAUG-GGAUACGUGGAGGC-AUAAC
CP002727.1/3691202-3691116     CCCCGA-----AAGCCUAA--ACCCCACACACGU-AUCGACA--CGA-UU-UCCUGGGUGCCCGCA------------------------------------AGGGU-UGGA--AAUUG-GGAUGCGUGGAGGC-CUAAC
CP002824.1/2502080-2502167     CUCAUA-----UUGUGUAA--AUAACACACACGU-AUCGGCA--CAU-AU-UCCGGGGUGCCCUUU------------------------------------GGGGU-CGGUA-AUAUG-GGAUACGUGGAGGC-AUAAC
CU468135.1/994867-994971       CUCACU-----AUGUGUAA--AUAACACACACGU-AUCGACA--CCU-AC-GCCGGGGUGCCUUGCAGGCUUG-------------------AAAAAGCCGAUGGGU-CGGUU-GUAUG-GGAUACGUGGAGGC-UUAAC
FN543093.2/863227-863313       CUCACU-----UUGUGU-A--AUAACACACACGU-AUCGGCA--CAU-AU-UCCGGGGUGCCCUUC------------------------------------GGGGU-CGGUA-AUAUG-GGAUACGUGGAGGC-AUAAC
FN543502.1/205184-205270       CUCACA-----UUGUGU-A--AUUACACACACGU-AUCGGCA--CAU-AU-UCCGGGGUGCCCUUC------------------------------------GGGGU-CGGUA-AUAUG-GGAUACGUGGAGGC-AUAAC
FP236843.1/972473-972580       CUCAUU-----AUGUGUAA--AUAACACACAUGU-AUCGACA--CAU-AC-UCCGGGGUGCCUGAACGCCUGCGU----------------AAGCAGUCUGCCGGGU-CGGUU-GUAUG-GGAUACAUGGAGGC-UUAAC
FR719195.1/33819-33715         CUCACU-----AUGUGUAA--AUAACACACACGU-AUCGAUA--CCU-GG-GCCGGGGUGCCCUGCUGGUUCA-------------------AAAGAGCCGACGGGU-CGGUU-GCCAG-GGAUACGUGGAGGC-UUAAC
U00096.2/189760-189846         CUCACU-----UUGUGU-A--ACAACACACACGU-AUCGGCA--CAU-AU-UCCGGGGUGCCCUUU------------------------------------GGGGU-CGGUA-AUAUG-GGAUACGUGGAGGC-AUAAC
FN667741.1/606445-606567       CUCAUU------UGUGUAA--AUAACACACACGG-AUCGACA--CAU-AC-ACCGGGGUGCUCUCAUGUGGUUCGCUCUUCUAUGAAUAGCUUCGCAGUCAAAGAGU-CGGUG-UUAUG-GGAUCUGUGGAGGC-AUAAC
ABCH01000022.1/1806-1707       AUUAAC-----UUUAAU-U--AAAUCACACACAU-UUCGUCA--CAU-GU-UCCGGGGUGCUUGAGUAAUC-----------------------AUUCAUACCAAGU-CGGAU-UCAUG-GGAAAUGUGGAGGC-CUAAC
AFHI01000071.1/69976-69878     CUGCAA-----UUAACUAA--ACAACACACAUAC-AUCGACA--CAU-AA-UCCGGGGUGCUGUAACUCA-------------------------UUGAGUUUCGGU-CGGUU-UUAUG-GGGUGUAUGGAGGC-CCAAC
AFPO01000011.1/81906-82008     AUAUUA-----AACUCUAA--AUUACACACACAU-AUCGGCA--CAU-GG-UGCGGGGUGCUUGGAUUGCUUA--------------------AAUGCAAUGCGGGU-CGCA--ACAUG-GGAUAUGUGGAGGC-AUAAC
BADT01000100.1/45785-45887     CACAAU-----UUGAUUUU--AACACACACACGU-AUCGUCA--CAU-AC-ACUUGGGUGCAUUUGAAGUUU---------------------AAAUACUUCGAUGU-UGGUG-CUAUG-GGAUAUGUGGAGGC-CUAAC
CP000733.1/589357-589449       AUAAAA-----GUGCGGCA-AAAUACACACACUU-AUCGGCA--CAU-GA-UCCCGGGUGCCCUGU-U------------------------------UCGACGGGU-CGGG--UCAUG-GGGUAGGUGGAGGU-UUAAC
CP000282.1/3292836-3292740     AUUUCU-----UAAACUAU--ACGUCACACAUAU-AUCGGCA--CAC-UU-GUCUGGGUGCCCUAGCUGU--------------------------UAAAGCGGGGU-UGGC--UUGUG-GGAUAUAUGGAGGC-CUAAC
CAED01000090.1/7765-7666       CCCGUC-----AGCACUUA--AACCCACACACGU-GUCGACA--CGA-UG-ACCUGGGUGCCCCGAGUUGC-----------------------GAAAUUCGCGGGU-UGGU--CAUUG-GGAUACGUGGAGGC-CCAAC
CP002667.1/2015218-2015305     AAAGGU-----UUAAUUUU--AAUUCACACACAU-AUCGACA--CUA-ACAAUCGGGGUGCC------------------------------------AAAC--GGU-CGGUUGUUUAG-GGAUAUGUGGAGGC-UAAAC
AAOE01000005.1/109417-109505   CUGGGC----AUUAACUUA--ACUUCUCACAUGC-UUCGACA--CAU-GG-UUCUGGGUGCCCGAA-----------------------------------AGGGGU-UGGA--UCAUG-GGAAGUGUGGAGGC-CUAAC
CP001616.1/2308831-2308744     AUCAAU-----UAAUCUUA-AAUACCACACACAC-AUCUAUA-ACCC-GC-UCCGGGGUGCC-----U------------------------------ACAU--GGU-CGGA--GUGAG-GGAUGUGUGGAGGC-CCAAC
AGFD01000016.1/11082-11168     AUUUUG-----CAAAAUAC--AUUCCACACACGC-GUCGGCA--CAU-UG-AGCUGGGUGCCCUUU------------------------------------GGGGU-CACU--GAAUG-GGGCGCGUGGAGGC-UCAAA
CP001339.1/1247493-1247587     CACACA-----UUACCCUG--AAACCGCACAUGC-GCCGGCA--CAU-CC-AGUCGGGUGCCCGUUGAG----------------------------ACAGACGGGU-UUCU--GGAUG-GGGCGCAUGGAGGC-UCAAC
ACZG01000002.1/1335833-1335917 AUGACG------CGCUUUA--AAUACACACACGU-UUCGGCA--CAU-AU-GAUAGGGUCCCUUU-------------------------------------GUGGG-UUUC--GUAUG-GGAAGCGUGGAGGA-AUAAC
AFOC01000010.1/22937-23032     CGCAGU-----C--CACCA--AAUCCGCACAUAC-AUCGACA--CAU-GU-ACCGGGGUGCUCAGCAGCA-------------------------UUGCUGCGGGGU-CGGG--GCAUG-GGGUGUAUGGAGGC-CUAAC
AGFC01000002.1/162303-162210   CUUUAU-----UUUU--AU--UGUCCACACACGU-GUCGACA--CAU-GC-GGCUGGGUGCCUGGGAAU---------------------------UCGCUCCGGGU-UGUC--GCGUG-GGAUGCGUGGAGGU-CCAAC
AGFB01000003.1/389490-389585   CAACGA-----AAACCCUA--AAUCCACACACGU-AUCGGCA--CGG-UC-UGUCGGGUGCCCGCCCUU---------------------------CGCGGUCGGGU-UUCA--GGCCG-GGAUACGUGGAGGC-UCAAC
AFWV01000006.1/258813-258731   CGGAAA-----AUGU---------CCGCACACGC-AUCGACA--CAA-CC-GGCCGGGUGCCUGGU---------------------------------AAACAGGU-UGCC--GCUUG-GGAUGCGUGGAGGC-CCAAC
CP001321.1/308378-308481       AUUUUU-----UAUUCACU--AAAUCACACACAU-AUCACAAACUAA-AC-AUCGGGGUGCUGUUUUUCUAU----------------------UAAGAGAAACGGU-CGAUG-ACUUA-GGAUAUGUGGAGGC-AAAAC
ADCF01000001.1/1009193-1009281 UUUAAU-----CAAACUUACUAAAACACACACAU-AUCAGUA-AGGC-UAAAUCGGGGUGCC------------------------------------AAAC--GGU-CGAU--UGGCU-GGAUAUGUGGAGGC-UAAAC
CP002154.1/793801-793904       UGUUAU-----UUGCAUAA--ACAACACACACGU-AUCGGCA--CAU-GU-GCCGGGGUGCCGUCGGACGCGA--------------------AUGCGUGCGGUGGU-CGGCG-UCAUG-GGAUACGUGGAGGC-AUAAC
AFWJ01000287.1/223-329         AACAAA-----CUAUUUCU-UAAAUCACACACGU-ACCGACA--CAU-GA-UCCGGGGUGCUCACUUACUUAGA------------------UAUAAGAAGCUGAGU-CGGAC-GCAUG-GGGUAUGUGGAGGC-CUAAC
CP001707.1/2064144-2064042     AGUCAU-----AAACCUAA--ACUACACACGCAA-AUCGACA--CAU-UU-GCCGGGGUGCUCAGUCGGAUUA--------------------AAGCUGGCUUGGGU-CGGG--AAAUG-GGAUUUGCGGAGGC-UUAAC
ADBS01000001.1/255440-255547   CUAAAC-----UAUUUUUA--AUCAUUCACACAU-AUCGUCA--CAU-UC-UCCGGGGUGCUCCUUAGCUUUCGC----------------AAAGCUUUAGUGGGGU-CGGCU-GAAUG-GGAUAUGUGGACGC-CUAAC
ACLE01000064.1/30116-30002     AUUCAA-----UUGUGUUA--AUGACACACACAA-AUCGACA--CAU-AC-GCCGGGGUGCUCUUAUGUAAAGGUUUA----------AUCUUUACAGCUGAUGAGU-CGGUC-GUAUG-GGAUUUGUGGAGGAAAUAAC
CP001614.2/1047131-1047226     CUGUAA-----UUUAUUUA--AAGUCGCACAUAU-ACCGUCA--CAU-CU-GCCUGGGUGCCGUGCCUU---------------------------UGGGCUUCGGU-UGGC--UGGUG-GGGUAUAUGGAGGC-CUAAC
CP000510.1/3669645-3669541     AAGACG-----UUCUUCAA--AUAACACACACAC-GUCGACA--CGU-CA-CUCGGGGUGCCUGAUUUCAAAU-------------------GAUUUGAAAUUCGGU-CGAGU-GUAUG-GGAUGUGUGGAGGC-CUAAC
CP000544.1/1582321-1582219     CUGACU-----GAACCACU-GAAUCCACACAUAC-GCCGACA--CAU-UC-GACCGGGUGCCCGGCGGCUGC----------------------GCAGCAAUCGGGU-UGUC--GGAUGCGGGCGUAUGGAGGC-UCAAC
CP000949.1/4506989-4506877     ACCCCG-----UCUGCUCA--AACCCACACACGU-GUCGACA--CGA-UG-ACCUGGGUGCCCCGCAUUCUCGAAGUU----------CUUGUUCAGGUGCGUGGGU-UGGU--CAUUG-GGAUACGUGGAGGC-CCAAC
CP001905.1/1592657-1592551     CUCGCG-----GAACCU-U--AAUCCACACACGC-AUCGACA--CGG-UC-UGUCGGGUGCCCGCCAGGAGGCUU---------------CGGUCUCGUGCUCGGGU-UUCA--GAUCG-GGAUGCGUGGAGGC-UCAAC
ABSJ01000026.1/71623-71529     UAUUUU-----UAACUUUG--AGUCCACACAUACGACCGUCA--CAC-UC-GAAUGGGUGCCGCGCCU-----------------------------AAAAAGCGGU-UUUC--GAGUG-GGGUGUAUGGAGGC-CCAAC
AGIB01000088.1/187287-187181   ACUAUC-----AAGCCUUA--AAAACACACAUGC-ACCGGCA--CAU-GG-UCCCGGGUGCCGCUGGCAGCGUU-----------------UAACGCGGUCAACGGU-CGGAU-CCAUG-GGGUGCGUGGAGGC-CUAAC
FN545250.1/29195-29090         CUUAAC-----UGUG--UU--AUAACACACACAG-AUCGGCA--CAU-UU-UCCGGGGUGCUCUUAUGUAGGAAA---------------GCCUACAGCUAAUGAGU-CGGG--GAAUG-GGAUCUGUGGAGGC-AUAAC
AAPG01000059.1/7565-7464       UAUAAA-----AGUCACUA--AUCACACACACGU-AUCGACA--CGU-AA-CUCGGGGUGCUGUUUUUAACU----------------------UGUUAAAGAUGGU-CGAGU-UUAUG-GGGUACGUGGAAGC-UUAAC
AAVT01000006.1/21231-21323     AAUAAA-----UCCACUAA--AAUCCGCACAUAU-ACCGUCA--CAA-AG-GUCAGGGUGCUCUGUUA------------------------------AGUCAGGGU-UGAU--CGAUG-GGGUAUAUGGAGGC-CUAAC
AAQH01000009.1/27881-27980     UAGAAA-----AUAUACAU--AAUCCGCACAUAU-AUCGGCA--CAU-UG-UUCAGGGUGUCUUAAAAACU-----------------------CAGUUUUUAGGAU-UGGA--UAAUG-GGAUAUAUGGAGGC-UUAAC
ABBZ01002027.1/249-338         GUUGCC-----UGAGUACA--AAAACACACAUAC-ACCGUCA--CAG-AG-AUUGGGGUGCUCAUA---------------------------------GCCAGAGU-CAAU--CUUUG-GGGUGUGUGGAGGC-GUAAC
ABQB01000355.1/7827-7930       AAAUUU-----AUUUUAUU--AAAACACACAUAU-ACCGACA--CUUCGU-AUCGGGGUGUUCAGUUCAAUUU--------------------AGGUUGGUCUGAAU-CGAU--ACAAG-GGGUAUAUGGAGGC-CUAAC
ABXQ01000055.1/1503-1401       UAGAUG-----AGAACUAA--AUGACACACACAU-AUCGACA--CCU-GU-UCCAGGGUGCCCUUCGGCCAUU--------------------UUUGGCACGCGGGUUUGGA--GCAGG--GAUAUGUGGAGGA-CUAAC
CP000746.1/834991-835076       AAUUUA-----UUUUAGUA--AUAACACACACAU-AUCGUUC-GGGU-AA-AUCGGGGUGCC------------------------------------AAAC--GGU-CGGU--UUACU-UGGUAUGUGGAGGC-UCAAC
#=GC SS_cons                   ::::::.....::::::::..::::::::<<<<<.<<<----..<<<.<<.<<<<----<<<<<______..........................______>>>>>.>>>>..>>>>>.->>>>>>>>:::::.:::::
#=GC RF                        cUuauu.....uuauuuaa..AaaaCACACACgu.auCGaCA..Cau.gc.gcCgGGGUGCcccuauuuu..........................agaaaagggGU.cGgc..gcauG.GGauacGUGGAGGC.uUAAC
//
# STOCKHOLM 1.0

#=GF AC   RF00128
#=GF ID   GlmY_tke1
#=GF PI   tke1
#=GF DE   Glm Y RNA activator of glmS mRNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Gardner P; 0000-0002-7808-1213
#=GF SE   Published; PMID:17854828
#=GF SS   Published; PMID:17854828
#=GF GA   33.00
#=GF TC   33.30
#=GF NC   32.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00011
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11553332
#=GF RT   Computational identification of noncoding RNAs in E. coli by comparative
#=GF RT   genomics.
#=GF RA   Rivas E, Klein RJ, Jones TA, Eddy SR
#=GF RL   Curr Biol 2001;11:1369-1373.
#=GF RN   [2]
#=GF RM   18351803
#=GF RT   Two seemingly homologous noncoding RNAs act hierarchically to activate
#=GF RT   glmS mRNA translation.
#=GF RA   Urban JH, Vogel J
#=GF RL   PLoS Biol. 2008;6:e64.
#=GF RN   [3]
#=GF RM   18334534
#=GF RT   The small RNA GlmY acts upstream of the sRNA GlmZ in the activation of
#=GF RT   glmS expression and is subject to regulation by polyadenylation in
#=GF RT   Escherichia coli.
#=GF RA   Reichenbach B, Maes A, Kalamorz F, Hajnsdorf E, Gorke B
#=GF RL   Nucleic Acids Res. 2008;36:2570-2580.
#=GF RN   [4]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   This family consists of a number of bacterial RNA genes of around 167
#=GF CC   bases in length. The tke1 RNA gene is present in Escherichia coli,
#=GF CC   Shigella flexneri, Yersinia pestis and Salmonella species where it is
#=GF CC   found between the yfhK and purL genes. The function of this RNA is
#=GF CC   unknown.
#=GF WK   GlmY_RNA
#=GF SQ   17


AP008232.1/3036799-3036631   AGUCGCUCAUUCACCUUGAUAUGAC-AGCGUCACACGCUAGGCAAUACGACCGCUCCAUAUCUG-CCGAAUGAUGCCAAUG--UAUGGUGCCUACUGUCCAACGUAACCGUUAAUCGCUGCCUUGGCGG---CGAUUAACAAUCACAGGGCGACACGUUGAGUGAGGCACCUCCUA
CP000720.1/1353391-1353555   AGUUGCUCAUUCACCUUUUUAUGAU-AGCCCCGCAAUUAAGCGGAU-GAUGCGCUUCAUAAGCCUCCGAAUGAUGCCUAAG--ACUGGUGCCUAUCGUCCACCUAAACCGACAUUGUGU-----GAAAGC--ACAUUAUCAAACAUCGGACGACACGUUGAGUGAGGCACCGCCUA
BX950851.1/3645067-3644897   UGUUGCUCAUUCAACUGGUUAUGAUUGCGUUG-CUAACUGGCAAAU-AUUUUCGCUCAUAACAUCUGGAAUGAUGCCAAAAGAAAGGGUGCCUAUCGUCCACCAGA-CCGAUAACAGGGCGU--GAAAACGAACUUUAUCAAGCAUCGGACGACACGUUGAGUGAGGCACCGCCUA
AM286415.1/1156074-1156238   AGUUGCUCAUUCACCUCUUUAUGAU-AGUCCCGCCGUACAGCGGAA-UAUGCACUUCAUAAGCCACCGAAUGAUGCCUAAG--ACUGGUGCCUAUCGUCCACCCAAACCGAUAUUGUGU-----GAAUGC--ACAUUAUCAAACAUCGGACGACACGUUGAGUGAGGCGCCGCCUA
CP000034.1/2545199-2545064   AGUGGCUCAUUCACCGACUUAUGUC-AGC----CCCUUCGG------GACGUGCUACAUAAAAU-UCGAAUGACGCACAA---CAAGGUGCCUGCCGUCCAACUU--CUGAUAUCA--------GCGUA---GCUAU----------G--CGAAACGUCGAGUUAGGCACCGCCUU
CP000653.1/3309706-3309558   AGUGGCUCAUUCACCCUCUUAUGUC-AGC----CCCUUCGG------GACGCGCUACAUAAACU-UCGAAUGACGCACAA---AAAGGUGCCUGCCGUCCAACUA--CUGAUUAUU--------GCGUAA--GCUUUAUCAGGCUCCGGGCGAAACGUCGAGUAAGGCACCGCCUC
CP000647.1/3167027-3166880   AGUGGCUCAUUCACCUUCUUAUGUC-AGC----CCCUUCGG------GACGCGCUACAUAAACU-UCGAAUGACGCACAA---ACAGGUGCCUGCCGUCCAACUC--CUGAUAACA--------GCCUG---GCUUUAUCAGACAUCGGGCGAAACGUCGAGUAAGGCACCGCCUC
BX571870.1/111637-111479     AGUUGCUCAUUCAGCUUCUUAUGUC-GGCC---CACAUUAGGUGGA-GAAAUGCCACAUAAACUAUCGAAUGAUGCCAGAG--UAAGGUGCCUACCGUCCAACUCA-GUGAUAUC---------GCUUUCGAGCCUUAUCAAACAUCGGGCGACACGUGGAGUGAGGCACCACCUA
CP001127.1/2708954-2708807   AGUGGCUCAUUCACCUUCUUAUGUC-AGC----CCCUUAGG------GAUGCGCUACAUAAACU-UCGAAUGACGCACAA---CAAGGUGCCUGCCGUCCAACUU--CUGAUAAUA--------GCGUA---GCUUUAUCAACCUCCGGGCGAAACGUCGAGUUAGGCACCGCCUU
CU928164.2/2865839-2865692   AGUGGCUCAUUCACCGACUUAUGUC-AGC----CCCUUCGG------GACGUGCUACAUAAAAU-UCGAAUGACGCACAA---CAAGGUGCCUGCCGUCCAACUU--CUGAUAUCA--------GCGUA---GCUAUAUCAACCCUCGGGCGAAACGUCGAGUUAGGCACCGCCUU
CP000948.1/2781127-2780980   AGUGGCUCAUUCACCGACUUAUGUC-AGC----CCCUUCGG------GACGUGCUACAUAAAAU-ACGAAUGACGCACAA---CAAGGUGCCUGCCGUCCAACUU--CUGAUAUCA--------GCGUA---GCUAUAUCAACCAUCGGGCGAAACGUCGAGUUAGGCACCGCCUU
CP001120.1/2764535-2764388   AGUGGCUCAUUCACCUUCUUAUGUC-AGC----CCCUUAGG------GACGCGCUACAUAAACU-UCGAAUGACGCACAA---CAAGGUGCCUGCCGUCCAACUU--CUGAUAACA--------GCGUA---GCUUUAUCAACCUCCGGGCGAAACGUCGAGUUAGGCACCGCCUU
CP000826.1/4043314-4043147   AGUUGCUCAUUCAACUAUUUAUGAC-GGCCCC-GUAUUUAGACGGAAUUGUUGCCUCAUAAGCCUCCGAAUGAUGCCAAAGA-AAUGGUGCCUAUCGUCCAACCAAACCGAUAACAGACGC---GCAAGC--GCUUUAUCAAGCAUCGGGCGACACGUGGAGUGAGGCACCGCCUG
AALE02000007.1/162365-162202 AGUUGCUCAUUCA-CUUUUUAUGAU-AGUCCCGCCGUAAAGCGGAA-UAUGCGCUUCAUAAGCCACCGAAUGAUGCCUAAG--ACUGGUGCCUAUCGUCCACCUAAACCGAUAUUGUGU-----GAAUGC--ACAUUAUCAAACAUCGGACGACACGUUGAGUGAGGCGCCGCCUA
AALC02000019.1/46319-46483   AGUUGCUCAUUCACCUCUUUAUGAU-AGUCCCGCUGUUAAGCGGAA-UAUGCGCUUCAUAAGCCACCGAAUGAUGCCUAAG--ACUGGUGCCUAUCGUCCACCUAAACCGAUAUUGUGU-----GAAUGC--ACAUUAUCAAACAUCGGACGACACGUUGAGUGAGGCACCGCCUA
AALF02000019.1/601-438       AGUUGCUCAUUCAACUUAUUAUGAU-AGUCCCGCGAUUAAGCGGAA-UAUGCGCUUCAUAAACCAUCGAAUGAUGCCUAAG--ACUGGUACCUAUCGUCCACCAAA-CCGAUAUCGUGU-----GAAUUC--ACUUUAUCAAACAUCGGACGACACGUUGAGUGAGGUACCGCCUA
AALD02000010.1/100030-100194 AGAUGCUCAUUCACCUUUUUAUGAU-AGUCCCGCUGUUAAGCGGAA-UAUGCGCUUCAUAAGCCAUCGAAUGAUGCCUAAG--ACUGGUACCUAUCGUCCACCUAAACCGAUAUCGUGU-----GAAUAC--ACAUUAUCAAACAUCGGGCGACACGUUGAGUGAGGUACCGCCUA
#=GC SS_cons                 ::::<<<<<<<<------<<<<<<-.<<<___._____________._____>>>>>>>>>------>>>>>>->>-----..---(((((((,,<<<<<------.-<<<<<<_____.....______..___>>>>>>------>>>>>,<<<_____>>>))))))):::::
#=GC RF                      AGUuGCUCAUUCAcCUuuuUAUGac.aGcccc.CuauuuaGcagAa.uaugcgCuuCAUAaacuauCGAAUGAuGCcuAAG..aauGGuGCCUauCGuCCAaCuaA.CuGaUAacaugu.....Gaauac..aCuuUAuCaAaCAUCGGaCGAcACGUuGAGUgAGGCaCCGCCUa
//
# STOCKHOLM 1.0

#=GF AC   RF00129
#=GF ID   mir-103
#=GF DE   mir-103/107 microRNA precursor
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   51.00
#=GF TC   71.50
#=GF NC   39.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11914277
#=GF RT   miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.
#=GF RA   Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L,
#=GF RA   Rappsilber J, Mann M, Dreyfuss G
#=GF RL   Genes Dev 2002;16:720-728.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family consists of the mammalian microRNA (miRNA) precursors mir-103
#=GF CC   and mir107. Animal miRNAs are transcribed as ~70nt precursors and
#=GF CC   subsequently processed by the Dicer enzyme to give a ~22nt product. In
#=GF CC   this case the mature sequence comes from the 3' arm of the precursor. The
#=GF CC   extents of the hairpin precursors are not generally known and are
#=GF CC   estimated based on hairpin prediction. The products are thought to have
#=GF CC   regulatory roles through complementarity to mRNA. The involvement of Dicer
#=GF CC   in miRNA processing suggests a relationship with the phenomenon of RNA
#=GF CC   interference. miRNAs are numbered based on the sequence of the mature RNA.
#=GF WK   Mir-103/107_microRNA_precursor
#=GF SQ   28


AF480550.1/3-80              CUCUGCUUUCAGCUUCUUUACAGUGUUGCCUUGUGGCAUGGAGUUCAAGCAGCAUUGUACAGGGCUAUCAAAGCACAG
AF480544.1/1-78              UUGUGCUUUCAGCUUCUUUACAGUGCUGCCUUGUAGCAUUCAGGUCAAGCAACAUUGUACAGGGCUAUGAAAGAACCA
AF480545.1/1-78              UACUGCCCUCGGCUUCUUUACAGUGCUGCCUUGUUGCAUAUGGAUCAAGCAGCAUUGUACAGGGCUAUGAAGGCAUUG
AL808128.4/93326-93403       UCGUGCUUUCAGCUUCUUUACAGUGCUGCCUUGUAGCAUUCAGGUCAAGCAGCAUUGUACAGGGCUAUGAAAGAACCA
AL353194.13/56360-56437      UUGUGCUUUCAGCUUCUUUACAGUGCUGCCUUGUAGCAUUCAGGUCAAGCAGCAUUGUACAGGGCUAUGAAAGAACCA
AAFC03055169.1/1823-1900     UUGUGCUUUCAGCUUCUUUACAGUGCUGCCUUGUAGCAUUCAGGUCAAGCAGCAUUGUACAGGGCUAUGAAAGAACUA
AADA01185334.1/2106-2183     UUGUGCUUUCAGCUUCUUUACAGUGCUGCCUUGUAGCAUUCAGGUCAAGCAGCAUUGUACAGGGCUAUGAAAGAACCA
AAIY01564143.1/1613-1536     UACUGCCUUCGGCUUCUUUACAGUGCUGCCUUGUUGCAUAUGGAUCAAGCAGCAUUGUACAGGGCUAUGAAGGCACUG
AALT01572385.1/2705-2628     UGGUGCUUUCAGCUUCUUUACAGUGCUGCCUUGUAGCAUUCAGGUCAAGCAGCAUUGUACAGGGCUAUGAAAGAACCA
AY866089.1/459-536           UACUGCCCUCGGCUUCUUUACAGUGCUGCCUUGUUGCAUAUGGAUCAAGCAGCAUUGUACAGGGCUAUGAAGGCAUUG
AAYZ01392126.1/2884-2961     UGGUGCUUUCAGCUUCUUUACAGUGCUGCCUUGUAGCAUUCGGGUCAAGCAGCAUUGUACAGGGCUAUGAAAGAACCA
AAFR03012611.1/75832-75909   UAUUGUCUUCGGCUUCUUUACAGUGCUGCCUUGUUGCAUAUGGAUCAAGCAGCAUUGUACAGGGCUAUGAAGACAUUG
AAPN01020470.1/19947-20024   CCUUGCCCUCGGCUUCUUUACAGUGCUGCCUUGUUGCAUAUGGAUCAAGCAGCAUUGUACAGGGCUAUGAGGGCAUUG
AAVX01046194.1/322-245       CCGUGCCUUCGGCUUCUUUACAGUGCUGCCUUGUGACGUGAAGAUCAAGCAGCAUUGUACAGGGCUAUGAAGGCACAG
AY866109.1/455-532           CUCUGCUUUCAGCUUCUUUACAGUGUUGCCUUGUGGCAUGGAGUUCAAGCAGCAUUGUACAGGGCUAUCAAAGCACAG
AANG01590200.1/990-913       CUCUGCUUUCAGCUUCUUUACAGUGUUGCCUUGUGGCAUGGAGUUCAAGCAGCAUUGUACAGGGCUAUCAAAGCAUAG
AAQQ01203378.1/2844-2767     CUUUGCUUUCAGCUUCUUUACAGUGUUGCCUUGUGGCAUGGAGUUCAAGCAGCAUUGUACAGGGCUAUCAAAGCACAG
BX000534.11/124450-124373    GUGUGCUCUGAGCUUCUUUACAGUGUUGUCUUGUGGCAUGGAGAUCAAGCAGCAUUGUACAGGGCUAUCACAGCACAC
CAAE01014634.1/190187-190110 CCCUGCUCUCAGCCUCUUUACGGUGCUGCCUUGUGGCAUCUUGAUCAAGCAGCAUUGUACAGGGCUAUGAAGGCGUGG
BAAF04036119.1/2342-2265     GUGUGCUGUGAGCUUCUUUACAGUGUUGCCUUGUGGCAUGGCGAUCAAGCAGCAUUGUACAGGGCUAUCACUGCAUGC
AANH01004124.1/31115-31038   CUUUGCGUUCAGCCUCUUUACGGUGCUGCCUUGUGGCGUCUCGAUCAAGCAGCAUUGUACAGGGCUAUGAAGGCUCAG
AAKN02020745.1/252670-252593 CUUUGCUUUCAGCUUCUUUACAGUGUUGCCUUGUGGCAUGGAGAUCAAGCAGCAUUGUACAGGGCUAUCAAAGCACAG
AAHX01000199.1/3575-3652     CUCUGCUUUAAGCUUCUUUACAGUGUUGCCUUGUGGCAUGGAGUUCAAGCAGCAUUGUACAGGGCUAUCAAAGCACAG
CAAE01014532.1/20132-20209   GUCUGCUGUGAGCUUCUUUACAGUGUUGCCUUGUGGCAUGGCGAUCAAGCAGCAUUGUACAGGGCUAUCACCGCACAC
AAGU03041265.1/97195-97118   UGGUACUUUCAGCUUCUUUACAGUGCUGCCUUGUAGCAUUCAGGUCAAGCAGCAUUGUACAGGGCUAUGAAAGAACCA
AEYP01079605.1/31042-30965   UUGUGCUUUCAGCUUCUUUACAGUGCUGCCUUGUAGCAUUCAGGUCAAGCAGCAUUGUACAGGGCUAUGAAAGAACCG
AAWZ02019300.1/85184-85261   CGCUGCCUUCAGCUUCUUUACAGUGCUGCCUUGUUGCUUAUGGAUCAAGCAGCAUUGUACAGGGCUAUGAAGGCAUUG
AADN03006660.1/6818-6895     UGCUGCCUUCGGCUUCUUUACAGUGCUGCCUUGUUGCAUAUGGAUCAAGCAGCAUUGUACAGGGCUAUGAAGGCACUG
#=GC SS_cons                 :::::<<<<<-<<-----<<<<<<<<<<<___________________>>>>>>>>>>>---->>--->>>>>:::::
#=GC RF                      uuuUGCcuUcAGCUUCUUUACAgUGcUGCCUUGUaGCAUuuaGaUCAAGCAgCAuUGUACAGGGCUAUgAagGcAcag
//
# STOCKHOLM 1.0

#=GF AC   RF00130
#=GF ID   mir-192
#=GF DE   mir-192/215 microRNA precursor
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   54.00
#=GF TC   54.40
#=GF NC   52.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA 2003;9:175-179.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the human microRNA (miRNA) precursors mir-192 and
#=GF CC   mir-215. Animal miRNAs are transcribed as ~70nt precursors and
#=GF CC   subsequently processed by the Dicer enzyme to give a ~22nt product. In
#=GF CC   this case the mature sequence comes from the 5' arm of the precursor. The
#=GF CC   extents of the hairpin precursors are not generally known and are
#=GF CC   estimated based on hairpin prediction. The products are thought to have
#=GF CC   regulatory roles through complementarity to mRNA. The involvement of Dicer
#=GF CC   in miRNA processing suggests a relationship with the phenomenon of RNA
#=GF CC   interference. miRNAs are numbered based on the sequence of the mature RNA.
#=GF WK   Mir-192/215_microRNA_precursor
#=GF SQ   41


AC103590.2/170923-170819     AUUCAGAAAUGGUAUACAGGAAAAUGACCUAUGAAUUGACAGACAAUAUAGCUGAG-----UUUGUCUGUCAUUUCUUUAGGCCA-AUAUUCUGUAUGACUGUGCUACUUC
AL445435.11/13794-13690      AUUCAGAAAUGGUAUACAGGAAAAUGACCUAUGAAUUGACAGACAAUAUAGCUGAG-----UUUGUCUGUCAUUUCUUUAGGCCA-AUAUUCUGUAUGACUGUGCUACUUC
AP001187.5/97046-96937       GCCGAGACCGAGUGCACAGGGCUCUGACCUAUGAAUUGACAGCCAGUGCUCUCGUCUCCCCUCUGGCUGCCAAUUCCAUAGGUCA-CAGGUAUGUUCGCCUCAAUGCCAGC
AC000159.6/81460-81569       GCCGAGACCGAGUGCACAGGGCUCUGACCUAUGAAUUGACAGCCAGUGCUCUCGUCUCCCCUCUGGCUGCCAAUUCCAUAGGUCA-CAGGUAUGUUCGCCUCAAUGCCAGC
AACN010376920.1/1185-1295    GCUGAGAUCGAGUGCACAGGGCUCUGACCUAUGAAUUGACAGCCAGUGCUCUCAUCUCUCCUCUGGCUGCCAAUUCCAUAGGUCACAAGGUAUGUUCGCCUCAAUGCCAGC
AAHX01009308.1/1254-1145     GUCAAGAUGGAGUGCACAGGGCUCUGACCUAUGAAUUGACAGCCAGUACUCUGAUCUCGCCUCUGGCUGCCAGUUCCAUAGGUCA-CAGGUAUGUUCGCCUCAAUGCCAGC
AC127556.4/107222-107331     GCCAAGAUGGCGUGCACAGGGCUCUGACCUAUGAAUUGACAGCCAGUACUCUUUUCUCUCCUCUGGCUGCCAAUUCCAUAGGUCA-CAGGUAUGUUCACCUCAAUGCCAGC
AADA01191401.1/22670-22775   AUUCAGAAAUGGUAUACGGGAAAAUGACCUAUGAAUUGACAGACAAUAUAGCCUGA----GUUUGUCUGUCAUUUCUUUAGGCCA-AUAUUCUGUAUGACUGUGCUACUUC
AAYZ01125558.1/348-240       GGUGAGACCGAGUGCACAGGGCUCUGACCUAUGAAUUGACAGCCAGUGC-CCCGUCUGCCCUCUGGCUGCCAAUUGCAUAGGUCA-CAGGUAUGUUCGCCUCAAUGCCAGC
AAIY01186786.1/2491-2595     AUCAAGAAACAGCGCACAGGAAAAUGACCUAUGAAUUGACAGACAAUAUGGCCAAG-----CUUGUCUGUCAUUUCUGUAGGCCA-AUAUUCUGUAUGUCUCUGCUACUUC
AANN01720898.1/1196-1090     GCAGAGACAGAGUGCGCAGGGCUCUGACCUAUGACUUGACAGCCAGUGCCCUC---UCCCCUCUGGCUGCCAAUUCCAUAGGUCA-CAGGUAUGUUCACCUCAAUGCCAGC
AAFC03085979.1/1681-1785     AUUCAGAAAUGGUGUACAGGAAAAUGACCUAUGAAUUGACAGACAACGUGACUAAG-----UCUGUCUGUCAUUUCUGUAGGCCA-AUGUUCUGUAUAUCUCUGCGACUUC
AAPN01160419.1/4341-4444     AGGAAGAAAUGGUGUACAGGAAAAUGACCUAUGAAUUGACAGACAGUAUAUUUAGA------UUGUCUGUCAUUUCUGUAGGCCA-AAGUUCUGCAUGCCUUCACUGCUCC
AANG01032370.1/112-8         ACUCAGAAAUGGUGUACAGGAAAAUGACCUAUGAACUGACAGACAAUUUGCCUAAG-----UCUGUCUGUCAUUUCUGUAGGCCA-AUAUUCUGUAUAUCUCUUCUACUUC
AAFR03023364.1/184964-184859 AGUAAGAAAUGGUGUGUAGGAAAAUGACCUAUGAAUUGACAGACAUUAUAUUUAAA----GUUUGUCUGUCAUUUCUGUAGGCCA-AUGCCUUGUAUGUCUGUGCUGCUUC
AAPY01700927.1/1101-997      AUUAACAAAUGGUAUACAGGAAAAUGACCUAUGACUUGACAGACAAUGUGGCUAGU-----UCUGUCUGUCAUUUCCGUAGGCCA-AUAUUCUGUAUAUCUCUGCUGCUUC
BX248510.4/109218-109112     GUUAAG-UCUAGGACACAGGGUGAUGACCUAUGAAUUGACAGCCAGUGUUUGCAGUCC--AGCUGCCUGUCAGUUCUGUAGGCCA-CUGCCCUGUUUAUCCUACUAAACAC
BAAE01291848.1/722-616       GAAAAGAGUUUGGGCACAAGGUGAUGACCUAUGAAUUGACAGCCAGUUACUUCUAAC---ACCUGCCUGUCAGUUCUGUAGGCCA-CUGCUGCGUUUGUCCUCCUGAGCAC
AANH01000564.1/249533-249430 GAAGAGCGAUGGGACACAAAGCGAUGACCUAUUAAUUGACAGCCAGUGGUUGUAAA----CUCUGCCUGUCAGUUCUCUAGGCCA-CUGCUGUGUUU--CUCCCUCCCGAA
CAAE01014650.1/773661-773759 CCUGGG-------ACACGAGGUGAUGACCUAUGAAUUGACAGCCAGUAACUGGAGC----CUCUGCCUGUCAGUUCUGUAGGCCA-CUGCUGCGUCCGUCCCCCUUCUCUA
AALT01482191.1/6358-6456     GGGAGGAGCGGGAC-ACAGGAACAUGACCUAUGAACUGACAGACAGUGGCUCG--------CCUGCCUGUCACUUCCAUAGGCCA--AAUUCUGU-GGCCCACUGGCACUU
AY866321.1/496-600           AUUCAGAAAUGGUAUACAGGAAAAUGACCUAUGAAUUGACAGACAAUACAGCUGAG-----UUUGUCUGUCAUUUCUUUAGGCCA-AUAUUCUGUACAACUGUGCUACUUC
AY866319.1/760-864           AUUAAGAAAUGGUAUACAGGAAAAUGACCUAUGAAUUGACAGACACUAUAGCUGAG-----UUUGUCUGUCAUUUCUUUAGGCCA-AUAUUCUGUAUGACUGUGCUACUUC
AY866322.1/453-557           AUUCAGAAAUGGUAUACGGGAAAAUGACCUAUGAAUUGACAGACAAUAUAGCUGAG-----UUUGUCUGUCAUUUCUUUAGACCA-AUAUUCUGUAUGACUGUGCUACUUC
AAHY01149687.1/2360-2462     AGCAUC-AACGGUGUACAGGAGAAUGACCUAUGAUUUGACAGACCGUGCAGCUGUG-----UAUGUCUGUCAU-UCUGUAGGCCA-AUAUUCUGUAUGUCACUGCUACUUA
AANN01206173.1/3045-3149     UCACAGACAUGGUGUACAGGAAAAUGACCUAUGAAUUGACAGAUAAUGUGGCUGAG-----CUUGUCUGUCAUUUCUGUAGGCCA-AUAUUCUGUAUUCCACUGCUGCUUC
AAIY01704218.1/882-773       GCCCAGACCGAGUGCACAAGUCUCUGACCUAUGAAUUGACAGCCAGUGCCUUGGGCUCCCCUCUGGCUGCCAAUACCAUAGGUCA-CAGGUAUGUUUGCCUCCAUGCCAGC
AAKN02018928.1/14074-14177   UUACCG-AGUGGGGUGCAGGAGUAUGACCUACAAAUUGACAGACGAUGUGCCUGAG-----UCUGUCUGUCACUUCUGUAGGCCA-ACAUCCUGUACUCCGCCUCAACCCC
AAKN02038532.1/88187-88078   CCCAAGACCGAGUGCACAGGGCUCUGACCUAUGAAUUGACAGCCAGUGCUGUCAGCUCCCCUCUGGCUGCCAAUUCCAUAGGUCA-CAGGUAUGUUCGCCUCAAUGCCUGC
AAGV020435009.1/397-505      GCCGAGACCGAGUGCACAGGGCUCUGACCUAUGAAUUGACAGCUAGUGCUGUUGUCCGC-CUCUGGCUGCCAAUUCCAUAGGUCA-CAGGUAUGUUCGCCUCAAUGCCAGC
AAWR02033463.1/86334-86230   AUUAAGAAAUGGUAUACAGGAAAAUGACCUAUGAAUUGACAGACAAUAUGACUAAG-----UUUGUCUGUCAUUUCUGUAGGCCA-AUAUUCUGUAUAUCUCUGCUACUUC
CAAB02009490.1/73889-73791   CUUGGG-------ACGUGAGGUGAUGACCUAUGAAUUGACAGCCAGUAACUGGAGC----CUCUGCCUGUCAGUUCUGUAGGCCA-CUGCUACGUUUGUCCCCUUGACCUG
AAHX01077280.1/19936-20038   ACCAUG-ACCGGUGUACAGGACAAUGACCUAUGAUUUGACAGACAGUGUGGCUGCG-----UGUGUCUGUCAU-UCUGUAGGCCA-AUAUUCUGUAUGUCUCUCCUCCUUA
AAPE02028384.1/76917-77021   ACUAACAAAUGGUGUACAGGAAAAUGACCUAUGAAUUGACAGACAGUGUGGCUAAG-----UGUGUCUGUCAUUUCUGUAGGCCA-AUAUUCUGUAUAUCUCGACGACUUC
AAGW02025725.1/27838-27734   AAAGAGAAUUGGUAUAUAGGAAAUUGACCUAUGAAAUGACAGAUGAUAUGGCUAAA-----UUUGUCUGUCAUUUCUGUAGGCCA-AUAUUCUGUAUACCUCUGCUGCUUC
AAGU03077813.1/8708-8606     ACUCAGAAACGGUGUACAGGAAAAUGACCUAUGAACUGACAGACAAUAUGGCUAAG-----UUUGUCUGUCAUUUCUGUAGGCCA-ACAUUCUGUAUGUCUG--CUACUUC
AADN03003271.1/75837-75734   AGUAAGAACUGGUGUCCAGGAAAAUGACCUAUGAAUUGACAG--ACUGCUUUCAAA----AUGUGCCUGUCAUUUCUAUAGGCCA-AUAUUCUGUGCACUUUUCCUACUUU
AAWZ02006025.1/14732-14632   AAAUGGAG-----GCUUAGGGUAAUGACCUAUGAUUUGACAGACUGUGCUUUCUAU----GUCUGCCUGUCAUUUCUGUAGGCCA-AUACUCUGUACGCCCUCACUACUCU
AAEX03018351.1/31201-31097   ACUAAAAAAUGGUGUACAGGAAAAUGACCUACGAAUUGAUAGACAAUUUGGCUAAG-----UUUGUCUGUCAUUUUUGUAGGCCA-AUAUUCUGUAUAUCUCUUCUGCUUC
AAQR03078873.1/354-250       GUUCAGAGGUGGUAUACAGGAAAUUGACCUAUAAACUGACAGAUAAUACGGCUCCA-----UUUGUCUGUCAUUUCUGUAGGCCA-AUAUUCUGCAUGUCUUUGCUACUUC
AAPE02049461.1/327-218       GCCGAGACCCAGUGCACAGGGCUCUUCCCUAUGAAUUGACAGCCAGGUCUCUUGUUUCCCCUCUGGCUGCCAAUGGCAUAGGUGA-CAGGUAUGUUCCCCUUAAAUCCCAG
#=GC SS_cons                 :::<<<-------<-<<<------<<<<<<<-<<<<<<<<<<<<<<__________....__>>>>>>>>>>>>>>-->>>>>>>.------>>>->-->>>:::::::::
#=GC RF                      auucaGAaaugGUguaCAGGaaaaUGaCCUAUgAAuUGaCAGcCAgUguuuuuaaa....cUcUGgCUGuCAaUUcUgUAGGcCA.auauUcUGuacguCuguauuaCuuc
//
# STOCKHOLM 1.0

#=GF AC   RF00131
#=GF ID   mir-30
#=GF DE   mir-30 microRNA precursor
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   45.00
#=GF TC   46.90
#=GF NC   43.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science 2001;294:853-858.
#=GF RN   [2]
#=GF RM   11914277
#=GF RT   miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.
#=GF RA   Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L,
#=GF RA   Rappsilber J, Mann M, Dreyfuss G
#=GF RL   Genes Dev 2002;16:720-728.
#=GF RN   [3]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family consists of the mammalian microRNA (miRNA) precursor mir-30a.
#=GF CC   Animal miRNAs are transcribed as ~70nt precursors and subsequently
#=GF CC   processed by the Dicer enzyme to give a ~22nt product. In this case the
#=GF CC   mature sequence comes from both the 3' (miR-30) [1] and 5' (mir-97-6) [2]
#=GF CC   arms of the precursor. The extents of the hairpin precursors are not
#=GF CC   generally known and are estimated based on hairpin prediction. The
#=GF CC   products are thought to have regulatory roles through complementarity to
#=GF CC   mRNA. The involvement of Dicer in miRNA processing suggests a relationship
#=GF CC   with the phenomenon of RNA interference. miRNAs are numbered based on the
#=GF CC   sequence of the mature RNA.
#=GF WK   mir-30_microRNA_precursor
#=GF SQ   49


AL606904.12/11306-11245        UGUAAACAUCCUUGACUGGAAGCUGUAAGGUGUU--GAGAGGAGCUUUCAGUCGGAUGUUUACA
AL354914.9/34109-34170         UGUAAACAUCCUUGACUGGAAGCUGUAAGGUGUU--CAGAGGAGCUUUCAGUCGGAUGUUUACA
AF159227.7/97022-97081         UGUAAACAUCCCCGACUGGAAGCUGUAAGACAC----AGCUAAGCUUUCAGUCAGAUGUUUGCU
AF480569.1/10-70               UGUAAACAUCCUCGACUGGAAGCUGUGAAGCCA---CAGAUGGGCUUUCAGUCGGAUGUUUGCA
AAFR03044146.1/42124-42063     UGUAAACAUCCUUGACUGGAAGCUGUAAGGUGCU--UGGAGGAGCUUUCAGUCGGAUGUUUACA
AAFC03016105.1/17756-17816     UGUAAACAUCCUCGACUGGAAGCUGUGAGGCUG---CAGAAAGGCUUUCAGUCGGAUGUUUGCA
AAYZ01071033.1/327-268         UGUAAACAUCCUCGACUGGAAGCUGUGACCCAC----AGAUGGGCUUUCAGUCGGAUGUUUGCA
AANN01559436.1/74-14           UGUAAACAUCCUCGACUGGAAGCUGUGAACUCU---CAAAUGGGCUUUCAGUCGGAUGUUUGCA
AAPN01350711.1/16343-16283     UGUAAACAUCCUUGACUGGAAGCUGGAAGGUGC---CGAAGGAGCUUUCAGUCGGAUGUUUACA
AAQQ01060122.1/527-468         UGUAAACAUCCCCGACUGGAAGCUGUAGGACAC----AGCUGAGCUUUCAGUCAGAUGUUUGCU
AAVX01474940.1/155-214         UGUAAACAUCCUCGACUGGAAGCUGUGAGGGGC----CAAUGGGCUUUCAGUCGGAUGUUUGCA
CR356236.12/41533-41474        UGUAAACAUCCUUGACUGGAAGCUGGUGCACAU----GAUGGAGCUUUCAGUCGGAUGUUUGCA
CAAE01014597.1/2003600-2003540 UGUAAACAUCCUUGACUGGAAGCUGGUGUUUAG---UUCUGGGGCUUUCAGUCGGAUGUUUGCA
AANH01002293.1/5342-5405       UGUAAACAUCCUUGACUGGAAGCUGUGGUUUUGGACGUCAAGGGCUUUCAGUCGGAUGUUUGCA
BAAE01224429.1/689-751         UGUAAACAUCCUUGACUGGAAGCUGGGAUUUUGU-CAGUGUGGGCUUUCAGUCGGAUGUUUGCA
AAFR03002164.1/5580-5641       UGUAAACAUCCUCGACUGGAAGCUGUGAAGCAGC--AGAUGGGGCUUUCAGUCGGAUGUUUGCA
AAYZ01122954.1/1089-1030       UGUAAACAUCCCCGACUGGAAGCUGUAAGAAGC----GGCUAAGCUUUCAGUCAGAUGUUUGCA
CAAE01014785.1/265034-265091   UGUAAACAUCCCCGACUGGAAGCUGUCACUCAG------CAGAGCUUUCAGUCUGAUGUUUACC
BAAE01018124.1/650-593         UGUAAACAUCCCCGACUGGAAGCUGUGUCUGCG------CAGAGCUUUCAGUCUGAUGUUUGCA
AANH01002465.1/73021-72964     UGUAAACAUCCCCGACUGGAAGCUGUCCAUCUG------CAGAGCUUUCAGUCCGAUGUUUGCU
BX323874.4/7995-7933           UGUAAACAUCCCCGACUGGAAGCUGUGCUACGCG-GAAAACGAGCUUUCAGUUGGAUGUUUGCU
AAPN01319291.1/18051-18110     UGUAAACAUCCCCGACUGGAAGCUGUAAAAUAC----CUUCAAGCUUUCAGUCAGAUGUUUGCU
AAVX01365666.1/262-201         UGUAAACAUCCCCGACUGGAAGCUGUAAAACAGC--AGCUCCAGCUUUCAGUCCGAUGUUUGCG
AC108837.9/196937-196996       UGUAAACAUCCCCGACUGGAAGCUGUAAGCCAC----AGCCAAGCUUUCAGUCAGAUGUUUGCU
AAWR02021647.1/29439-29380     UGUAAACAUCCCCGACUGGAAGCUGUGAGACAU----GGCUAAGCUUUCAGUCAGAUGUUUGCU
AAKN02041734.1/70427-70486     UGUAAACAUCCCCGACUGGAAGCUGUACAACAC----AGCUGAGCUUUCAGUCAGAUGUUUGCU
AAWR02021647.1/25105-25048     UGUAAACAUCCUA--CACUCAGCUGUACUACAU----GGAUUGGCUGGGAGGUGGAUGUUUACU
AY866282.1/409-468             UGUAAACAUCCUACACUCUCAGCUGUGGAAAGU----AAGAAAGCUGGGAGAAGGCUGUUUACU
ABQF01000883.1/17684-17743     UGUAAACAUCCUACACUCUCAGCUGUGGAAACU----AAGAAAGCUGGGAGAAGGCUGUUUACU
AY865841.1/453-510             UGUAAACAUCCUA--CACUCAGCUGUAAUACAU----GGAUUGGCUGGGAGGUGGAUGUUUACU
AY865844.1/508-565             UGUAAACAUCCUA--CACUCAGCUGUAAUACAU----GGAUUGGCUGGGAGGUGGAUGUUUACU
AY866283.1/417-476             UGUAAACAUCCUACACUCUCAGCUGUGGAAAGU----AAGAAAGCUGGGAGAAGGCUGUUUACU
AY866284.1/445-504             UGUAAACAUCCUACACUCUCAGCUGUGGAAAGU----AAGAAAGCUGGGAGAAGGCUGUUUACU
AY865845.1/456-513             UGUAAACAUCCUA--CACUCAGCUGUAAUACAU----GGAUUGGCUGAGAGGUGGAUGUUUACU
AY865843.1/517-574             UGUAAACAUCCUA--CACUCAGCUGUAAUACAU----GGAUUGGCUGAGAGGUGGAUGUUUACU
AY865842.1/515-572             UGUAAACAUCCUA--CACUCAGCUGUAAUACAU----GGAUUGGCUGGGAGGUGGAUGUUUACU
AY865846.1/450-507             UGUAAACAUCCUA--CACUCAGCUGUAAUACAU----GGAUUGGCUGGGAGGUGGAUGUUUACU
AY865840.1/481-538             UGUAAACAUCCUA--CACUCAGCUGUAAUACAU----GGAUUGGCUGGGAGGUGGAUGUUUACU
CAAB02003142.1/36971-37033     UGUAAACAUCCUUGACUGGAAGCUGGGGUUUAAA-UUGUGAAGGCUUUCAGUCGGAUGUUUACA
AAGW02018778.1/56781-56722     UGUAAACAUCCUCGACUGGAAGCUGUGAGGCGC----AGACGGGCUUUCAGUCGGAUGUUUGCA
AAEX03008842.1/69098-69041     UGUAAACAUCCCCGACUGGAAGCUGGAAGACAG------CAAAGCUUUCAGUCAGAUGUUUGCU
AAWZ02024328.1/46503-46564     UGUAAACAUCCUUGACUGGAAGCUGUGCAAGGCU--CAAAGGGGCUUUCAGUCGGAUGUUUACA
AADN03008176.1/18084-18145     UGUAAACAUCCUUGACUGGAAGCUGUGAGGUGUC--AGCGGGGGCUUUCAGUCGGAUGUUUACA
AAWZ02018601.1/2233-2179       UGUAAACAUCCCCGACUGGAAGCUGUAAAUUUC---------AGCUUUCAGUCAGAUGUUUGCU
AADN03002007.1/424995-424939   UGUAAACAUCCCCGACUGGAAGCUGUAGCAGCU-------UGAGCUUUCAGUCAGAUGUUUGCU
AAEX03008842.1/64830-64773     UGUAAACAUCCUA--CACUCAGCUGUAGUACAU----GGAUUGGCUGGGAGGUGGAUGUUUACU
AAGW02013551.1/32871-32814     UGUAAACAUCCCCGACUGGAAGCUGUAAAACAA------CUAAGCUUUCAGUCAGAUGUUUGCU
AAQR03067152.1/13148-13089     UGUAAACAUCCUCGACUGGAAGCUGUGAGGCAU----GGACGGGCUUUCAGUCGGAUGUUUGCA
AAWZ02015179.1/23146-23207     UGUAAACAUCCUCGACUGGAAGCUGUGAAGCAGU--AGAUGAAGCUUUCAGUCGGAUGUUUGCA
#=GC SS_cons                   :<<<<<<<<<<--<<<<<<<<<<<_________...._____>>>>>>>>>>>>>>>>>>>>>:
#=GC RF                        UGuAAACAUCcUcGACuGgaAGCuGUaauacau....ggaugaGCUuuCaGUCgGAUGUUUgCu
//
# STOCKHOLM 1.0

#=GF AC   RF00132
#=GF ID   snoR24
#=GF DE   Small nucleolar RNA R24
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics. Identification of 140 Candidates for Small
#=GF RT   Non-Messenger RNAs in the Plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol 2002;12:2002-2013.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snoR24 is a C/D box small nucleolar RNA which acts as a methylation guide
#=GF CC   for 18S ribosomal RNA in plants [1].
#=GF WK   Small_nucleolar_RNA_R24
#=GF SQ   12


AF317982.1/2-94          --AUCAGUGAUGAGAAAGCUAACACGUAAGAAGAGGUACUCCUUUGUGGUGUAUUUCUUCUAUGAAAUAUAUUUGUUACGCUUGGCUUCUGAGAU--
AL161574.2/196824-196728 CUAUCAGUGAUGAGAAAGCUAACACGUAAGAAGAGGUACUCCUUUGUGGUGUAUUUCUUCUAUGAAAUAUAUUUGUUACGCUUGGCUUCUGAGAUAA
AJ532534.1/5-96          GCAGCUGUGAUGAGACG--UAACACAUAAGAAGGCCAAACCGAUCAAUUGG---UUCUUCGAUGAAAUAUAUUUGUUACGCUUGGCUUCUGAGCUGA
AJ532535.1/5-95          GCUGCUGUGAUGAGCCG--UAACACAUAAGAAGGCC-AACCGAUCAAUUGG---UUCUUCGAUGACAAAUACUUGUUACGCUUGGCUUCUGAGCAGA
AF326224.1/1-93          --AGCUGUGAUGAGAAAGCUAACACGUAAGAAGGGGUACUCCUUUGUGGGGUGUUUCUUCAAUGAAAUACAUUUGUUACGCUUGGCUUCUGAGCU--
AJ532530.1/1-91          ACUGCUGUGAUGAGCCG--UAACACAUAAGGAGGCC-AACCGAUCAAUUGG---UUCUUCAAUGAAAUACUCUUGUUACGCUUGGCUUCUGAGCAUU
AJ532532.1/14-104        GCAGCUGUGAUGAGCCG--UAACACAUAAGGAGGCC-AACCGAUCAAUUGG---UUCUUCAAUGAAAUACUCUUGUUACGCUUGGCUUCUGAGCAUU
AL161574.2/197138-197042 UGAGCUGUGAUGAGAAAGCUAACACGUAAGAAGGGGUACUCCUUUGUGGGGUGUUUCUUCAAUGAAAUACAUUUGUUACGCUUGGCUUCUGAGCUAA
AJ532533.1/1-91          GCUGCUGUGAUAAGCCG--UAACACAUAAGAAGGCC-AACCGAUCAAUUGG---UUCUUUGAUGAAAUACUCUUGUUACGCUUGGCUUCUGAGCGAC
AJ532531.1/1-77          GCUGCUGUGA----------------UAAGAAGGCC-AACCGAUCAAUUGG---UUCUUUGAUGAAAUACUCUUGUUACACUUGGCUUCUGAGCGUC
AL161574.2/197366-197270 UGAGCUGUGAUGAGAAAGCUAACACGUAAGAAGAGGUAUUCCUUUGUGGGGUAUUUCUUCAAUGAAAUACAUUUGUUACGCUUGGCUUCUGAGCUAU
AL161574.2/196988-196892 UUAGCUGUGAUGAGAAAGCUAACACGUAAGAAGAAGUACUCCUUUGUGGUGUAUUUCUUCAAUGAAAUACAUUUGUUACGCUUGGCUUCUGAGUUAA
#=GC SS_cons             ::<<<_______________________________________________________________________________________>>>::
#=GC RF                  ucagCUGUGAUGAGaaaGCUAACACaUAAGAAGgcguAauCguUuauuugGUaUUUCUUCaAUGAAAUAcauUUGUUACGCUUGGCUUCUGAGcuaa
//
# STOCKHOLM 1.0

#=GF AC   RF00133
#=GF ID   SNORD33
#=GF PI   snoZ195
#=GF DE   Small nucleolar RNA Z195/SNORD33/SNORD32 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, Daub J, INFERNAL
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   44.00
#=GF TC   44.00
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.26 -Z 549862.597050 CM SEQDB
#=GF CL   CL00054
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300755;
#=GF DR   snoopy; Oryzias_latipes300077;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [3]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF RN   [4]
#=GF RM   8764399
#=GF RT   Intron-encoded, antisense small nucleolar RNAs: the characterization of
#=GF RT   nine novel species points to their direct role as guides for the
#=GF RT   2'-O-ribose methylation of rRNAs.
#=GF RA   Nicoloso M, Qu LH, Michot B, Bachellerie JP
#=GF RL   J Mol Biol. 1996;260:178-195.
#=GF CC   Members of this family belong to the C/D box class of small nucleolar RNA
#=GF CC   which contain C (UGAUGA) and D (CUGA) box motifs. This family includes
#=GF CC   plant snoRNA Z195, human snoRNAs SNORD33 (U33) and SNORD32 (U32). snoRNA
#=GF CC   U33 is found in intron 4 of the ribosomal protein L13a gene in humans and
#=GF CC   is also present in mice. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs.
#=GF CC   Although the selection of the target nucleotide requires the antisense
#=GF CC   element and the conserved box D or D' of the snoRNA, the methyltransferase
#=GF CC   activity is supposed to reside in one of the protein components [3].
#=GF WK   Small_nucleolar_RNA_Z195/SNORD33_family
#=GF SQ   72


X94599.1/95-179                GCG-GCCG-GUGAUGAGA---ACUUCU-CCC---ACUCACAUUC-GAG-------U--UUCCCG--ACCAUGAGAUGAC---UCCACAUGCACUACC-AUCUGAGGCC-AC
AC149479.1/42125-42034         GAA-AAAACAUGAUGAUG---UUUUAU-CGU---AAUAGUUUCU-GUGAUCAAAU--UACCAUG--AUGAUGAUUUAAU----GAACAUGCACUACC-AUCUGAUUUC-UC
AC140545.26/107636-107561      AAG-AGAA-AUGAUGAUA---UU-UAU-CCA---UACG---GUU-CUG-------U--UUUU------CAUGAUGAAAC----AAACAUGCACUACC-AUCUGAUCUC-UC
AC148239.7/93638-93563         AAG-AGAA-AUGAUGAUA---UA-UAU-CCA---UACG---GUU-CUG-------U--UAU-AG--AUGAUGAAACAA-------ACAUGCACUACC-AUCUGAUCUC-UU
AP006687.1/74108-74032         AAG-AGAU-AUGAUGAUU---UU-UAU-CCA---UCUA----UU-CUG-------U--AUUUGA--A---UGAUGAUUA---AUAACAUGCACUACC-AUCUGAUCUC-UU
Z70231.1/1-81                  ----AGAA-GUGAUGAUG---UCUUAU-CCA---UACCACAUGU-CUG-------C-AUCUCAU--AUGAUGAUUAAUC--UACAUCAUGCACUACC-AUCUGAUCU----
Z70230.1/1-81                  ----AGAA-GUGAUGAUA---CUUAAU-CCA---UACCAUAUUU-CUG-------C-AUCUCAG--AUGAUGAUCAAUC--UACAUCAUGCACUACC-AUCUGAUCU----
AJ490441.1/2-87                GGG-AGAA-GUGAUGAUA---UUAUAU-CCA---UACCACAUUU-CUG-------C-AUUCACU--AUGAUGAUCAUUA---ACUUCAUGCACUACC-AUCUGAUCUC-CU
AJ490443.1/2-87                GGG-AGAA-GUGAUGAUA---UUAUAU-CCA---UACCACAUUU-CUG-------C-AUUUGCU--AUGAUGAUCAUUA---AAUUCAUGCACUACC-AUCUGAUCUC-CC
AJ490453.1/3-89                AGG-AGAA-GUGAUGAUG---UCUUAU-CCA---UACCAAAUGU-CUG-------C-AUCUCAG--AUGAUGAUUAAUC--UACAUCAUGCACUACC-AUCUGAUCUC-CU
AJ490446.1/2-88                AGG-AGAA-GUGAUGAUG---UCUUAU-CCA---UACCACAUGU-CUG-------C-AUCUCAU--AUGAUGAUUAAUC--UACAUCAUGCACUACC-AUCUGAUCUC-CU
AJ490451.1/1-87                GGG-AGAA-GUGAUGAUA---CUUAAU-CCA---UACCACAUUU-CUG-------G-AUCUCAG--AUGAUGAUCAAUC--UACAUCAUGCACUACC-AUCUGAUCUC-CC
AJ490454.1/1-87                GGG-AGAA-GUGAUGAUA---CUUAAU-CCA---UACCACAUUU-CUG-------C-AUCUCAG--AUGAUGAUCAAUC--UACAUCAUGCACUACC-AUCUGAUCUC-CC
AJ490448.1/1-87                GGG-AGAA-GUGAUGAUA---CUUAAU-CCA---UACCACAUUU-CUG-------C-AUCUCAG--AUGAUGAUCAAUC--UACAUCAUGCACUACC-AUCUGAUCUC-CC
AAIY01734223.1/1230-1313       GUG-GCCA-GUGAUGAGG---ACUUCU-CCC---ACUCAAGUUC-GAG-------U--UUC-UG--ACAAUGAGAUAAC---CUCACAUGCACUACC-AUCUGAGGCC-AC
ABDC01307395.1/1742-1826       GUG-GCCA-GUGAUGAGG---ACUUCU-CCC---ACUCAUGUUC-GAG-------U--UUCCCU--ACCAUGAGACAAC---UCUACAUGCACUACC-AUCUGAGGCC-AC
AASG02001565.1/26848-26768     GUG-AAGC-GUGAUGAUG---UU-UAU-CCA---UAUA---AUU-CUG-------U-CGUCAAA--AUGAUGAUCACUA----AUACAUGCACUACC-AUCUGAUUUC-UC
AANH01003941.1/78292-78209     CCU-GUCA-GUGAUGAUU---CCUUAA-CCC---UGUU--GUUC-GAG-------U-UUAAAUG--ACAAUGAGACUAC---CUUACAUGCACUACC-AUCUGAGACA-UG
AC149868.2/112534-112451       GCA-GCUU-GUGAUGAGA---CA-UCU-CCC---ACUCAUGUUC-GAG-------U--UGCUCG--ACUAUGAGAUGAC---UCUACAUGCACUACC-AUCUGAGGCU-GU
AABS01000019.1/331927-332014   GUG-GCCA-AUGAUGAUGAAUAUAUAC-CCA---AAUU---UUC-GAAU----UU-CUUUUAAGAAAUUCUGAGAUAAC-----AACAUGCACUACC-AUCUGAGG-C-AC
CR352220.19/173911-173998      UUU-GUCG-GUGACGAGC---UCGCAA-CCACAGUUCAGUAUUC-GAG-------U--UUAACG--ACCAUGAGAAUAC---UUUACGUGCACUACC-AUCUGAGACA-AA
AANH01003941.1/78564-78483     UCU-GUCG-UUGAUGAUA---CA-UUU-ACA---GCUU-UGCUU-GAG-------U--UUAACG--ACCAUGAGAAAAC----UCUCAUGCACUACC-AUCUGAGACA-GA
AAYZ01277821.1/2630-2712       GCG-GCCC-GGGAUGAGG---ACGUGU-CCC---ACUCGUGUUC-GAG-------U--UUCCCG--ACCAUGAGAUGAC-----UACAUGCACUACC-AUCUGAGGCC-GC
AAFC03008223.1/5479-5395       GUA-GCCA-GUGAUGAAG---ACUUCU-CCC---ACUCGUGUUC-GAG-------U--UUCCCG--ACCGUGAGAUGAC---UCCACAUGCACUACC-AUCUGAGGCC-AC
AASG02001667.1/16436-16515     ACG-AGGU-GUGAUGAUA---CU-UAC-CCA---G----CAUUU-CUG-------C--UAUUGG--AUGAUGAAUAUAU----AUACAUGCACUACC-AUCUGAUCUCUGU
AAPN01363609.1/433-515         UGG-GUCU-GUGAUGAUG---ACUUUC-ACU---U---UAUUUC-GAG-------U--CUCACG--ACCUUGAGAUCAC--AGCUCCAUGCACUACC-AUCUGAGACC-CC
AC068667.6/43044-43128         GGG-AGGA-AUGAGGAUG---UA-AUU-CCA---UACG-UCUGC-AAA-------U-CUGAAAU--ACAGUGUUGAUAC--AAUGACAUGCACUACC-AUCUGACCUC-UG
AANN01156148.1/162-242         GCG-GCCG-CUGAUGAGG---AU-UGU-CCC---CUCG-UGUUC-GAG-------U--UGGCCG--ACCAUGAGACCAC-----CGCAUGCACUACC-AUCUGAGGCC-GC
AARH01011741.1/11937-12014     AGG-AGGC-GUGAUGAUA---UG-UAU-CCA---C----UUUUC-CUG-------C--AUUAAG--AUGAUGAAUUUUA-----UACAUGCACUACC-AUCUGAUCUC-UC
AAPN01017316.1/2006-2089       CCG-GUCU-GUGAUGACG---AC-UGU-CCA---CUUU-AUUUC-GAG-------U--CUCCCG--ACCUUGAGAUCAC--AUCUCCAUGCACUACC-AUCUGAGACC-GU
AAPY01734679.1/2365-2450       CUG-GCCA-GUGAAGAGG---ACUUCUCCCA---CUCAAUGUUC-GAG-------U--UUCCCA--ACUAUGAGAUGAC---UCCACAUGCACUACC-AUCUGAGGCC-AC
AAVX01117381.1/1131-1057       GAU-GUCU-GUGAUGAAU---UU------------CUGUGAUCC-GAG-------A--UUUCU----CAAUGAGAAUAC---CUCACAUGCACUACC-AUCUGAGACG-UA
AAFR03057352.1/10961-10875     GAG-A-CU-GUGAUGAUA--AUGCUUA-CCA---AAGCACGUUC-GAG-------U--UUGGCG--ACCAUGAGAUGAAA-AGCUCCAUGCACCUCC-AUCUGAGCUC-UC
CR626962.9/3088-3166           UUU-GUCA-GUGAUG-------UUUUU-CCA---CAGUAAGUAU-GAG-------U--UUAACG--ACCAUGAGUCCAC-----UUCAUGCACUACC-AGCUGAGACA-AA
AARH01005007.1/196478-196562   AAG-AAAAUAUGAUGAUG---CU-UAU-CAU---AGAAAAUUCU-GUC-------A-UCAAACC--AUGAUGAUCUCAA----AAACAUGCACUACC-AUCUGAUUUC-UC
CAAE01015019.1/2071491-2071408 GAUCGUCU-GUGAUGUU-----CUUAA-CCA---CUAU-AAUUC-GAG-------U-UUCAAUG--ACAAUGAGACAAC---CCUACAUGCACUACC-AUCUGAGACA-UC
EF057238.1/465-554             GGG-UGAA-GUGAGGAAU---CUCAAU-CCA---UAAACCAAUCUCUGC-----AU-CUUCANC--AUGAUGAUUGCCA--AAUUACAUGCACUACC-AUCUGAUCCC-CC
AALT01618522.1/2257-2340       GAG-GCUA-GUGAUGAGG---UU-UCU-CCC---ACUCAUGUUC-GAG-------U--UACCCA--ACCAUGAGAUGAC---UCCACAUGCACUACU-AUCUGAGGCC-GC
AAFC03123213.1/1402-1318       GAG-GCCA-GUGAUGAGG---ACUUUU-CCC---ACUCAUGUUC-AAG-------U--UUCCUG--CUCAUGAGAUGAG---UCCACAGGCACUGCC-AUCUGUGGCC-AC
AACT01064400.1/2634-2719       UGU-GUCG-GUGAUGAUG---AUUCAA-CCA---CAAACU-AUC-GAA-------UCCUCUACG--GAGGUCAUGUGAC---CAACCAUGCACUACC-AUCUGAGACA-CA
AC148689.1/105527-105613       UGG-AUCG-GUGAUGAGCA-CCAAUCA-CCA---UCUUUCGUUU-GAG-------U--UUCACG--GCCAUGAGACCAA----CCCCAUGCACUGCUGCUCUGAGACC-UG
BAAF04045040.1/28023-28103     UUU-GUCU-GUGAUG--------UUUU-CCC---ACUUGUAUUU-GAG-------U-UUCAUUG--ACCUUGAAAACAU---UGUACAUGCACUACC-AUCUGAGACA-AG
AABS01000019.1/332865-332952   UGU-GUCA-GUGAUGAUG--UGUUUAA-CCA---CAAACCAAUC-GAA-------UUCUCCUCG--GAGGUCAUGUGAC---CAACCAUGCACUACC-AUCUGAGACG-CA
AANU01228070.1/2462-2548       UGG-AUCG-GUGAUGAGCA-ACAAUCA-CCA---UCUUUCGUUU-GAG-------U--UUCAUG--GCCAUGAGACCAA----CCCCAUGCACUGCUGCUCUGAGACC-CG
Z69622.1/1-81                  -GA-GUCC-AUGAUCAGCA-ACACUCA-CCA---UCUUUCGUUU-GAG-------U--CUCACG--ACUGUGAGAUCAA-----CCCAUGCACCGC---UCUGAGACU-C-
X51528.1/2850-2930             -GA-GUCC-AUGAUCAGCA-ACACUCA-CCA---UCUUUCGUUU-GAG-------U--CUCACG--ACUGUGAGAUCAA-----CCCAUGCACCGC---UCUGAGACU-C-
X94598.1/86-166                -AG-GUCA-GUGAUGAGCA-ACAUUCA-CCA---UCUUUCGUUU-GAG-------U--CUCACG---CCAUGAGAUCAA----CCCCAUGCACCGC---UCUGAGACC-U-
AB028893.1/3145-3226           -AG-GUCA-GUGAUGAGCA-ACAUUCA-CCA---UCUUUCGUUU-GAG-------U--CUCACG--GCCAUGAGAUCAA----CCCCAUGCACCGC---UCUGAGACC-U-
AAYZ01277821.1/2136-2216       -AG-GUCC-GUGAUGAGCA-ACAGUCA-CCA---UCUUUCGUUU-GAG-------U--CUCACG--ACCGUGAGAUGAC-----CCCAUGCACCGC---UCUGAGACC-U-
AANN01390155.1/7437-7356       -AG-GUCG-GUGAUGAGCA-ACAAUCA-CCA---UCUUUUGUUU-GAG-------C--CUCACG--GCCAUGAGAUCAA----CUCCAUGCACUGC---UCUGAGACC-U-
AAIY01734223.1/661-741         -UG-GUCA-GUGAUGAGCA-AAAAUCA-CCA---UCUUUCGUUU-GAG-------U--CUCACG--ACCAUGAGACCAA-----CCCAUGCACCGC---UCUGAGACC-U-
AAPN01363609.1/114-195         -GG-GCCA-GUGAUGAGGA-ACAUUCA-CCA---UCUUUCGUUC-GAG-------U--CUCGCG--ACUGUGAGACCAA----CUCCAUGCACCGC---UCUGAGGCC-U-
CU104665.1/51425-51506         -GG-AUUG-GUGAUGAGCA-ACAAUCA-CCA---UCUUUCGUUU-GAA-------U--CUCAUG--GCCAUGAGACCAA----CCCCAUGCACUGC---UCUGAGACC-U-
AAFR03057352.1/11592-11512     -GG-GCCG-GUGACGAGGA-AUCUUCA-CCA---UCUUUCGUUC-GAG-------U--CUCGCG--ACUAUGAGACCAA-----ACCAUGCACCGC---UCUGAGGCC-C-
AC196948.9/127722-127638       -GG-AUCG-GUGAUGAGCA-ACAAUCA-CCA---UCUUUCGUUU-GAG-------U--UUCAUG--GCCAUGAGACCAA----CCCCAUGCACUGCUGCUCUGAGACC-C-
AM455011.2/14193-14117         AAG-GGGC-GUGAUGAUG---UU-UUU-CCA---U----AGUUU-CUG-------U--CAUUGG--AUGAUGAAUAAAA------ACAUGCACUACC-AUCUGAUCCU-AU
AAWR02030682.1/6128-6212       UCG-GCCA-GUGAUGAGG---ACUUCU-CCC---ACUCGUGUUC-GAG-------U--UUCCCA--ACCAUGAGAUGAC---UCCACAUGCACUACC-AUCUGAGGCC-GC
AAWR02030682.1/5418-5499       -AG-GUCG-GUGAUGAGCA-ACAAUCA-CCA---UCUUUCGUUU-GAG-------U--CUCACG--ACUGUGAGAUCAA----CCCCAUGCACCGC---UCUGAGACC-A-
AAXL01012888.1/722-638         GCA-GCUU-GUGAUGAGG---AUGUCU-CCC---ACUCAUGUUC-GAG-------U--UGCCUG--ACUAUGAGACGAC---UCUACAUGCACUACC-AUCUGAGGCU-GG
AASC02049677.1/912-987         ACU-GUCA-GUGAUG------CAACAU-CCA---CAGCGCAUUG-AUG-------C--UUUG--------UGAAAACAA---CCUACAUGCACUACC-AUCUGAGACA-GG
Z69623.1/1-80                  --A-GCUU-GUGAUGAGA---CA-UCU-CCC---ACUCAUGUUC-GAG-------U--UGCUCG--ACUAUGAGAUGAC---UCUACAUGCACUACC-AUCUGAGGCU---
EU094086.1/1-80                --G-GCCA-GUGAUGAGGA-ACAUUCA-CCA---UCUUUCGUUC-GAG-------U--CUCGCG--ACUGUGAGACCAA----CUCCAUGCACCGC---UCUGAGGCC---
AB028893.1/3795-3879           GCG-GCCG-GUGAUGAGA---ACUUCU-CCC---ACUCACAUUC-GAG-------U--UUCCCG--ACCAUGAGAUGAC---UCCACAUGCACUACC-AUCUGAGGCC-AC
AAGU03011894.1/10157-10073     GUG-GCCA-AUGAUGAAG---ACUUCU-CCC---GCUUGUGUUC-GAG-------U--UUCCCG--ACCAUGAGAAGAC---UUUACAUGCACUACC-AUCUGAGGCC-AC
AAPE02058383.1/14842-14760     CAG--UCC-GUGAUGAGGA-GCAAUCA-CCA---UCUUUCGUUU-GAG-------U--CUCACG--ACCAUGAGAUCAA----CCCCAUGCACCGC---UCUGAGACC-UG
AAWZ02025901.1/38197-38282     UGG--UCU-GUGAUGAUG---AC-AUU-CCA---CCAUUAGUUC-GAG-------U--CUCAAG--ACCAUGAGACAACAACUCUUCAUGCACUACC-AUCUGAGAAC-CA
AABR05007347.1/14414-14334     -GA-GUCU-GUGAUGAGCA-AUAAUCA-CCA---UCUUUCGUUU-GAG-------U--CUCACG--ACUGUGAGAUCAA-----CCCAUGCACCGC---UCUGAGACU-U-
AAPE02058383.1/14093-14009     GUG-GCCC-GUGAUGAGG---ACUUCU-CCC---ACUCAAGUUC-GAG-------U--UUCCCA--ACCAUGAGAUGAC---UCCACAUGCACUACC-AUCUGAGGCC-AC
AACN010024681.1/2613-2697      GUG-GCCA-GUGAUGAGG---ACUUCU-CCC---ACUUGUAUUC-GAG-------U--UUCCUG--ACUAUGAGAUGAC---UCCACAUGCACUACC-AUCUGAGGCC-AC
CAAB02000993.1/58900-58981     UCU-GUCA-GUGAUGAUA---UGUUUG---U---UUUUUUGCUU-GAG-------U--UUAGCG--ACCAUGAGAAAAC----UCACAUGCACUACC-AUCUGAGACG-GA
CAAB02000993.1/59174-59256     CAU-GUCU-GUGAUGUG----C-UUAA-CCA---AUAU-AAUUC-GAG-------U-UUCAUUG--ACAAUGAGACAAC---CUCACAUGCACUACC-AUCUGAGACA-UC
AAWZ02025901.1/35982-36065     GUG-GUCU-GUGAUGAUG---CC-UUU-CCA---CCAUUAGUUC-GAG-------U--GUCAUG--GCCAUGAGAUAAC---UCUACAUGCACUACC-AUCUGAGGCC-AC
#=GC SS_cons                   <<<.<<<_._________...______.___...__________.___......._..______.._____________..._______________.______>>>>.>>
#=GC RF                        gcg.guca.GUGAUGAug...uuuUau.CCA...uauuaugUUc.GAG.......U..UUcacG..AccAUGAgauaAc...ucuaCAUGCACUACC.AUCUGAgacc.gc
//
# STOCKHOLM 1.0

#=GF AC   RF00134
#=GF ID   snoZ196
#=GF DE   Small nucleolar RNA Z196/R39/R59 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   55.00
#=GF TC   56.50
#=GF NC   54.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.25 -Z 549862.597050 CM SEQDB
#=GF CL   CL00054
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics. Identification of 140 Candidates for Small
#=GF RT   Non-Messenger RNAs in the Plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol 2002;12:2002-2013.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [3]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science. 1999;283:1168-1171.
#=GF RN   [4]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF CC   This family includes plant snoRNA snoZ196 and yeast snoRNAs R39 and R59.
#=GF CC   Members of this family belong to the C/D box class of snoRNA which contain
#=GF CC   C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs. snoZ196 acts as a methylation guide for 18S ribosomal RNA in plants
#=GF CC   [1].Although the selection of the target nucleotide requires the antisense
#=GF CC   element and the conserved box D or D' of the snoRNA, the methyltransferase
#=GF CC   activity is supposed to reside in one of the protein components [4].
#=GF WK   Small_nucleolar_RNA_Z196/R39/R59_family
#=GF SQ   22


AC140545.26/107249-107163      UGCAAUCUAUGAUGC-AAUUUUUAUAU--CCUUACUAUU--CUG-AU-UUCCGUGA--UUAUUCAGAA-----AUAUCACCAUCUUUCG--GCUGAGA-UUGCA
AC150706.4/102309-102395       UGCAAUCUAUGAUGC-AAUUAAUAU----CCUUACUAUU--AUGAUUUCCCCGUGA--UUAAUAAAAU-----AUAUCACCAUCUUUCG--ACUGAGA-UUGCA
Z70229.1/1-81                  ---AGCCUGUGAUGC-AAAAGG-------ACCCAUGAAA--CUGAAU-UACACUGAAUUAAUUCCAAAC----AAAUCACCAUCUUUCGG-GCUGAGG-UU---
AP006687.1/73908-73825         UGCAAUCAAUGAUGA-AAUUUC-------CUUAAUAUA---AUGAAUAUAUUGUGA--UUAUUAUACC-A---AGAUCACCAUCUUUCG--GCUGAGA-UUGCA
X67711.2/2410-2494             UGCAGCCUGUGAUGGCAAAAGU-------ACCCAUUAAA--CUGAAU-UACACUGA--UUAUUCCAAAC----AAAUCACCAUCUUUCG--GGCGAGG-UUGGC
AC068667.6/43175-43262         UGCAAUCAGUGAUGA-AAUUAUG------UCAAAUUCA---AUGAUUAUACAAUGA--UUAUUAUAAUCACU-AGAUCACCAUCUUUCG--GCUGAGA-UUGCU
Z70693.1/1-77                  ---AACCUGUGAUGU-AAAUUA-------ACCCAUUUA---CUGAAC-UACGUUGA--UUAUUUCAGU-A---AAAUCACCAUCUUUCG--GCUGAGG-UU---
AC068667.6/51559-51646         UGCAAUCAGUGAUGA-AAUUAUG------UCAAAUUCA---AUGAUUAUACAAUGA--UUAUUAUAAUCACU-AGAUCACCAUCUUUCG--GCUGAGA-UUGCA
AJ490449.1/1-82                -GCAGCCUGUGAUGC-AAAAGU-------ACCCAUUAAA--CUGAAU-UACACUGA--UUAUUCCAAAC----AAAUCACCAUCUUUCG--GCUGAGG-UUGC-
AC134045.2/133476-133559       UGCAGCCUGUGAUGC-AAAAGU-------ACCCAUUAAA--CUGAAU-UACACUGA--UUAUUCCAAAC----AAAUCACCAUCUUUCG--GCUGAGG-UUGCU
AJ490447.1/1-83                UGCAACCUGUGAUGU-AAAUUA-------ACCCAUUUA---CUGAAC-UACGUUGA--UUAUUUCAGU-A---AAAUCACCAUCUUUCG--GCUGAGG-UUGCA
AJ490452.1/1-84                UGCAACCUGUGAUGC-AAAACU-------ACCCAUUAAA--CUGAAU-UACACUGA--UUAUUACAAAC----AAAUCACCAUCUUUCG--GCUGAGG-UUGCA
AY220647.1/3-86                UGCAAUCUAUGAUGC-AAAUAA-------UCCCAUUUG---CUGAAU-CACUGUGA--UUAUUGCAAUAA---AAAUCACCAUCUUUCG--GCUGAGA-UUGCA
AJ490445.1/2-85                UGCAAUCUAUGAUGC-AAAUAA-------UCCCAUUUG---CUGAAU-CACUGUGA--UUAUUGCAAUAA---AAAUCACCAUCUUUCG--GCUGAGA-UUGCA
AY220646.1/6-89                UGCAAUCUGUGAUGC-AAAUAA-------UCCCAUUUG---CUGAAU-CACUGUGA--UUAUUGCAAUCA---AAAUCACCAUCUUUCG--GCUGAGA-UUGCA
AJ490442.1/2-85                UGCAAUCUGUGAUGC-AAAUAA-------UCCCAUUUG---CUGAAU-CACUGUGA--UUAUUGCAAUCA---AAAUCACCAUCUUUCG--GCUGAGA-UUGCA
D25232.1/916-1003              CUUUCUUAAUGAUGA-AAACUAU------UCCUUAUUC---UCGACUAGUCUUUGA--CAAUGCUGUCGUU--UAAUCACCAUCUUUCG--GCUGACUAGUAAA
X53575.1/491-574               AUAUGAAAAAGAUGA-ACCUUU-------CACUCUUGGA--UUG-CU-AGUUUCGA--CGAUGCUGCUCC---AAAAUACCAUCUUUCG--GCUGAUU-CAUAU
Z73554.1/1068-1155             CUUUCUUAAUGAUGA-AAACUAU------UCCUUAUUC---UCGACUAGUCUUUGA--CAAUGCUGUCGUU--UAAUCACCAUCUUUCG--GCUGACUAGUAAA
AAFW02000099.1/355930-355833   CUCAUUUUAUGAUGA-AAAUCCAUUGUAUCCCAAUACAUAUUCGACUAGUCAUUGA--CGAUGCUGUCGUAACUUAUCACCAUCUUUCG--ACUGAUU-AUAAG
X62627.1/916-1013              CUCAUUUUAUGAUGA-AAAUCCAUUGUAUCCCAAUACAUAUUCGACUAGUCAUUGA--CGAUGCUGUCGUAACUUAUCACCAUCUUUCG--ACUGAUU-AUAAG
AACU03000099.1/1424175-1424089 UCAAGGAAAUGAUGG-ACAACA-------UACCCUUUG---C-GACUAGACUCUGU--CGAUGCUGUUGCA--AAAUUACCAUCUUUCGGGUCUGACC-CUUGA
#=GC SS_cons                   <<<<<<<________.______.......__________..______.________..____________...________________.._____>>.>>>>>
#=GC RF                        ugcagccuAUGAUGa.AAAuua.......uCCcAUUuaa..cUGAaU.uaCuuUGA..uuAUucuaaucu...AaAUCACCAUCUUUCG..GCUGAgg.cugca
//
# STOCKHOLM 1.0

#=GF AC   RF00135
#=GF ID   snoZ223
#=GF DE   Small nucleolar RNA Z223
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   45.00
#=GF TC   46.70
#=GF NC   44.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Monodelphis_domestica300018;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics. Identification of 140 Candidates for Small
#=GF RT   Non-Messenger RNAs in the Plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol 2002;12:2002-2013.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snoRNA Z223 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs identified in rice. C/D box small
#=GF CC   nucleolar RNAs are known to act as a methylation guides for 18S ribosomal
#=GF CC   RNA in plants [1].
#=GF WK   Small_nucleolar_RNA_Z223
#=GF SQ   5


AC105364.2/52337-52244 GUUUGGCAAUGAUGAAACAAACUUUCAGCUUACCAUGCCAGUUCUGCUUCUGAGAAUUCAUGACAGAUAAAGCUG-AUAUAGAUCUGAACUGAAU
AC003027.1/47945-47851 GAUUGGCUGGGAUGAUGAAUUGUAACAGCUUGAUACGCCAGUUCUGCUUCAGAUAAUUCUUGAUCGAAAAAGCUGUAUUCUUAUCCGAGCCUUUC
AP003829.2/17857-17764 GUUUGGCAAUGAUGAUACAAACUUUCAGCUUACCAUGCCAGUUCUGCUUCUGAGAAUUCAUGACAGAUAAAGCUG-AUAUAGAUCUGAGCUGAAU
AP003829.2/19099-19006 GGUUGGCAGUGAUGAUACAAACUUUCAGCUUACAAUGCCAGUUCUGCUUCUGAGAAUACAUGACAGAUAAAGCUG-AUAUAUAUCUGAGCCUUUU
AC090488.3/74979-75072 GUUUGGCAAUGAUGAUACAAACUUUCAGCUUACCAUGCCAGUUCUGCUUCUGAGAAUUCAUGACAGAUAAAGCUG-AUAUAGAUCUGAACUGAAU
#=GC SS_cons           <<<<<<<____________________________________________________________________.____________>>>>>>>
#=GC RF                guucgGcaauGAUGAUAcAaacUuuCAGCUUAcuAUGCCAGUUCUGCUUCuGAgAAUUCaUGAcaGAuAAAGCUG.AUaUauAUCUGAgCcgaac
//
# STOCKHOLM 1.0

#=GF AC   RF00136
#=GF ID   SNORD81
#=GF PI   U81
#=GF DE   Small nucleolar RNA SNORD81
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   50.60
#=GF NC   49.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00050
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300706;
#=GF DR   snoopy; Homo_sapiens300132;
#=GF RN   [1]
#=GF RM   9819378
#=GF RT   Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene
#=GF RT   and a member of the 5'-terminal oligopyrimidine gene family reveals common
#=GF RT   features of snoRNA host genes.
#=GF RA   Smith CM, Steitz JA
#=GF RL   Mol Cell Biol 1998;18:6897-6909.
#=GF CC   U81 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U81 acts as a guanine methylation guide and is
#=GF CC   found in intron 11 of the gas5 gene in mammals [1]. This RNA has also been
#=GF CC   called Z23 snoRNA.
#=GF WK   Small_nucleolar_RNA_SNORD81
#=GF SQ   22


AJ224028.1/3-79              CAGAAUAC--AUGAUGAUCUCAAUCCAACUUGAACUCUCUCACUGAUUACUUGAUGACAAU---------AA--AAUAUCUGAUAUUCUG
AJ224035.1/1-76              CAGAAUAC--AUGAUGAUCUCACA-CAACUUGAACUCUCUCACUGAUUACUUGAUGAUAGU---------AA--AAGAUCUGAUGUUCUG
AL606750.13/40184-40260      CAGGACAC--AUGAUGAUCUCACCCCAACUUGGACUCUCUCACUGAUUACUUGAUGACAGU---------AA--AAGACGUGAUAUUCUG
ABDC01278790.1/3802-3878     CAGAAUAC--AUGAUGAUCUCACUGCAACUUGAACUCUCUCACUGAUUACUUGAUGACAAC---------AA--AAGAUCUGAUAUUCUG
AANU01240317.1/3294-3218     CAGAAUAC--AUGAUGAUCUCAGUCCAGCUUGAACUCUCUCACUGAUUACCUGAUGACAAU---------AA--AAGAUCUGAUAUUCUG
AAPY01728088.1/9340-9415     CAGAAUAU--AUGAUGAUCUCACC-AAACUUGAACUCUCUCACUGAUUACUUGAUGACAAU---------AA--AAGAUCUGAUAUUCUG
AAYZ01154866.1/3472-3396     CAGAAUAC--AUGAUGAUCUCACCUCAGCUUGAACUCUCUCACUGAUAACCUGAUGGAGAU---------AA--CAGAUCUGAUAUUCUG
AALT01063557.1/160-231       CAGAAUAU--AUGAUGAUCU-----CAACUUGAACUCUCUCACUGAUGACUUGAUGACAGU---------AA--AUGAUCUGAUAUUCUG
AAFC03120161.1/30906-30982   AAGAAUAU--GUGAUGAUCUCAGCCCAACUUGAACUCUCUCACUGAUGCCUUGAUGAUGUU---------CA--AAGAUCUGAUAUUCUU
AADA01033599.1/12200-12125   CA-AAUAC--AUGAUGAUCUCUCCUCAGUUUGAACUCUCUCACUGAUCACUUGAUGACAAU---------AA--AAGAUCUGAUAUUGUG
AANN01159637.1/259-333       CAGAAUAC--AUGAUGAUCUCAAA----CUUGAACUCUCUCACUGAUCACUUGAUGUUAGA---------AAAUAAGAUCUGAUAUUCUG
AAIY01534871.1/472-399       CAGAAUAC--AUGAUGAUC-CACCCCAACUUGAACUCUCUCACUGAUAACUUGAUGAUAAU-------------GGGAUCUGAUAUUCUG
AANU01265424.1/25442-25518   UUGGAUAU--AUGAUAAUCUCACUCCAACUUUAACUCUCUCACUGAUUAUUUGAUAAUAAU---------AA--CAGGUCAGAUAUCCUG
AAIY01210190.1/1318-1402     UUAAAUAC--AUGAUGAUCU-ACCCCAACUUGAACUCUCUCACUGAUAACUUGAUGAUAAUGGGAAGGAAAA--AAAAAAGAGUACUUAA
AAIY01244248.1/1113-1040     CACAAUAU--AUGACGGUC-CAUCCCAACUUGACCUCUCUCACCAGUUACUUGAUGAUAAU-------------CGGAUCUGAUAUUCUG
AANU01202269.1/48062-48138   UUGGAUAU--AUAAUAAUCUCACUCCAACUUAAACUCUCUCACUGAUUAUUUGAUAAUAAU---------AA--CAGGUCAGAUAUUUUG
AAGV020273689.1/3634-3710    CAGAAUAC--AUGAUGAUCACACCCCAACUUGAACUCUCUCACUGAUUAUGUGAUGACGAU---------AA--AAGAUCUGAUAUUCUG
AAKN02037311.1/43777-43853   UGGAAUAC--AUGAUGAUCUCACCUCAGCUUGAACCCUCUCCCUGUUUACUGGAUGAUGAG---------CA--AAGAUCUAAUGUUCUA
AAGU03036956.1/70179-70252   CAGAAUAC--AUGAUGAUC-CACCCCAACUUGAACUCUCUUACUGAUUACUUGAUGAUGAU-------------AAGAUCUGAUAUUCUG
AAEX03005203.1/132526-132602 CAGAAUAC--AUGAUGAUCUCAUUGCAACUUGAACUCUCUCACUGAUCAUUUGAUGAUUUU---------AA--AAGAUCUGAUAUUCUG
AAPE02018271.1/28237-28161   CAGAAUAC--AUGAUGAUCUCAACCCAACUUGAACUCUCUCACUGAUUACUUGAUGAUGAA---------AG--AAGAUCUGAUAUUCUG
AAWZ02040398.1/3978-3901     GAAUAGAUUAAUGAUGAUAACCUAGC--CUUGAACUCUCUCUCUGACUAGAUGAUGGAAAA---------UAC-AAGGUCUGAUCUAUUC
#=GC SS_cons                 <<<<<<<_..___________________________________________________.........__.._________>>>>>>>
#=GC RF                      cagaAuAc..AUGAUGAUCUCAcccCAACUUGAACUCUCUCACUGAUuAcUUGAUGAuAAU.........AA..AAGAUCUGAUaUucug
//
# STOCKHOLM 1.0

#=GF AC   RF00137
#=GF ID   SNORD83
#=GF PI   U83
#=GF DE   Small nucleolar RNA SNORD83
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   35.00
#=GF TC   35.30
#=GF NC   34.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; U83;
#=GF DR   snoRNABase; U84;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300916;
#=GF DR   snoopy; Oryzias_latipes300094;
#=GF RN   [1]
#=GF RM   10684929
#=GF RT   Characterisation of the U83 and U84 small nucleolar RNAs: two novel
#=GF RT   2'-O-ribose methylation guide RNAs that lack complementarities to
#=GF RT   ribosomal RNAs.
#=GF RA   Jady BE, Kiss T
#=GF RL   Nucleic Acids Res 2000;28:1348-1354.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   U83 (SNORD83) and U84 (SNORD84) are members of the C/D class of snoRNA
#=GF CC   which contain the C (UGAUGA) and D (CUGA) box motifs. They act as guanine
#=GF CC   methylation guides but lack complementarity to ribosomal RNA [1]. U83 and
#=GF CC   U84 are spliced from introns 5 and 4 of the BAT1 gene in mammals.
#=GF WK   Small_nucleolar_RNA_SNORD83
#=GF SQ   7


Z34846.1/492-568       GCCACAUGAUGUUUUCAUUUUGAAAAGUGAGAGCUUUGCGCA--GUGACGACUUUUAUC-AUCACCCUUGACUGAUGGCU
AJ314857.1/13267-13341 GCCAAAUGAUGUGUG---UUUGAUAUAGGAGCACUGUGUGCA--AGGACGACCCUCAUCUAUCACCCAUGACUGAUGGCU
AF387339.1/12156-12229 GC-AAAUGAUGUGUG---UUUGAUAUAGGAGCACUGUGUGCA--AGGACGACCCUCAUCUAUCACCCAUGACUGAUGGCU
BC024859.1/809-885     GCCACAUGAUGUUUGCAUUUGGGAA-GUGAGCGCUCUGCGCA--GUGCUGACCCUUAUCUAUCACCCUUGACUGAUGGCU
AJ243199.1/1-78        GCCAUAUGAUGUUUUCUUUUCGAAAGGUGAGCGCUUUGCGCA--GUGAUGACCCUCAUCUAUCACCCUUGACUGAUGGCU
AJ314857.1/8059-8137   GCCACAUGAUGUUUGCAAUUGGGAA-GUGAGCGCUCUGCGCGCGGUGCUGACCCUUAUCUAUCACCCUUGACUGAUGGCU
AJ251914.1/37947-38024 GCCACAUGAUGUUUUCAUUUUGAAAAGUGAGAGCUUUGCGCA--GUGACGACUUUUAUCUAUCACCCUUGACUGAUGGCU
#=GC SS_cons           <<<<--------------------------<<<<___>>>>-..------------------------------->>>>:
#=GC RF                GCCAcAUGAUGUuUgCAuUUuGAaAuguGAGcGCUuUGCgCA..guGauGACccUuAUCUAUCACCCuUGACUGAUGGCU
//
# STOCKHOLM 1.0

#=GF AC   RF00138
#=GF ID   SNORD16
#=GF PI   U16
#=GF DE   Small nucleolar RNA SNORD16
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   45.00
#=GF TC   45.50
#=GF NC   41.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00046
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Oryzias_latipes300068;
#=GF DR   snoopy; Gasterosteus_aculeatus300109;
#=GF RN   [1]
#=GF RM   8335006
#=GF RT   A novel small nucleolar RNA (U16) is encoded inside a ribosomal protein
#=GF RT   intron and originates by processing of the pre-mRNA.
#=GF RA   Fragapane P, Prislei S, Michienzi A, Caffarelli E, Bozzoni I
#=GF RL   EMBO J 1993;12:2921-2928.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   U16 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U81 acts as a guanine methylation guide and is
#=GF CC   found in an intron of ribosomal proteins L1 gene in animals [1]. This
#=GF CC   snoRNA was independently named MBII-98 in mouse [2].
#=GF WK   Small_nucleolar_RNA_SNORD16
#=GF SQ   5


AF357363.1/1-90  ---------GUCGUAAUUUGCGUCUUACUCUGUUCACAGCGACAGUUGCCUGCUGUCAGUAUGCUGGUUCAGAAGGUUGACGAACAU--UGUUACUGAGCA
X67692.1/35-134  UGCUAUGAUGUCGUAAUUUGCGUCUUACUCCACAUCAUGCGACAGUUGCCUGCUGUCAUUAAGCUGGUGUGGGUGACUGACGAAUAUC-GCGUUCUGAGCA
Z70298.1/1-100   UGCAAUGAUGGUGUAAUUUGCGUCUUACCUGUUAUUCAGUGACGGUUGCCUGCUGUCAUUAAGCUGGUGCCGAGGGCUGACGAUAAAACAAGU-CUGAGCA
X72205.1/148-246 UGCAAUGAUGUCGUAAUUUGCGUCUUACUCUGUUCUCAGCGACAGUUGCCUGCUGUCAGUAAGCUGGUACAGAAGGUUGACGAAAAU--UCUUACUGAGCA
X67691.1/37-137  UGCUAUGAUGUCGUAAUUUGCGUCUUACUCCACAUCAAGCUACAGUUGCCUGCUGUUAUUAUGCUGAUGUGGAUGACUGACGAACAUCAGCGUUCUGAGCA
#=GC SS_cons     <<<-----------------<<<<-----<<<<<----<<<<<<<_______>>>>>----->>--->>>>>------>>>>------.--------->>>
#=GC RF          uGCaAUGAUGucGUAAUUUGCGuCUUACUccgcauuaAGcgaCaGUUGCCUGCuGucAuUAagCUGGugcggAaGgcUGaCGAaaAua.ucgUuCUGAGCa
//
# STOCKHOLM 1.0

#=GF AC   RF00139
#=GF ID   SNORA72
#=GF PI   U72
#=GF DE   Small nucleolar RNA SNORA72
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   43.00
#=GF TC   43.60
#=GF NC   41.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300854;
#=GF DR   snoopy; Homo_sapiens300439;
#=GF RN   [1]
#=GF RM   9106664
#=GF RT   The family of box ACA small nucleolar RNAs is defined by an evolutionarily
#=GF RT   conserved secondary structure and ubiquitous sequence elements essential
#=GF RT   for RNA accumulation.
#=GF RA   Ganot P, Caizergues-Ferrer M, Kiss T
#=GF RL   Genes Dev 1997;11:941-956.
#=GF CC   U72 is a member of the H/ACA class of snoRNAs. The snoRNA gene is located
#=GF CC   in intron 4 of the ribosomal L30 protein gene in human, mouse and chicken.
#=GF WK   Small_nucleolar_RNA_SNORA72
#=GF SQ   29


AC016710.7/58672-58803       CUGUGAAUA-UUCUCUGUGUUCUGAUU-AUGUGAGAGCCAGGACAGGCUA--AACAUUUGCUACAUUA-A--GACCAUGC-AU-G-UGU-AC-CCAGAUGUAG-CCCA-U-UCC---CUAGCUCUGGUCUUAUAAAUGCUGGUGAUAAAC
AC068057.5/62929-63057       CUGAGAAUA--UCUUGCUGUUCUGAUU-UUGUAAU----AGGACAGGCUAUAAAGAUUGGCUAUAUUA-A--GGCCACGC-AC-A-UGU-CC-CCAGACUUAA-UUCU-U-UCC---CUAGGUCUGGUUUUAUAAACUCUGGUAAUAAAC
Y11167.1/1-132               CUGCGAAUA-UUCUCGCUGUUCUGAUU-UUGUAAUAGUCAGGACAGGCUA--AACAUUCGCUAUAUUA-A--GACCAUGC-AU-G-UGU-CC-CCAAACCUAG-UUCU-U-UCC---CUAGGUCUGGUUUCAUAAAUGCUGGUGAUAAAC
AB070559.1/4340-4471         CUGCGAAUA-UUCUCGCUGUUCUGAUU-UUGUAAUAGUCAGGACAGGCUA--AACAUUCGCUAUAUUA-A--GACCAUGC-AU-G-UGU-CC-CCAAACCUAG-UUCU-U-UCC---CUAGGUCUGGUUUUAUAAAUGCUGGUGAUAAAC
K02928.1/2768-2899           CUGCGAAUA-UUCUCGCUGUUCUGAUU-CUGUGAUAAUCAGGACAGGCUA--GACAUUCGCUAUAGUA-A--GACCAUGC-AU-G-UGU-CC-CCAGACCUAG-UUCU-U-UAC---UUCAGUCUGGUUAUCUAAAUGCUGGUGACAGAC
AAFC03098910.1/11107-10976   CUGCGAAUA-UUCUCGCUGUUCUGAUU-UUGUAAUAAUCAGGGCAGGCUA--AACAUUUGCUAUAUUA-A--GACCAUGC-UU-G-UGU-CU-CCAGACCUAG-UUCU-U-UGC---CUAGCUCUGGUUUUAUAAAUGCUGGUGAUAAAC
AAXP01034212.1/334-203       AUGCGAAUA-UUCUCGCUGUUCUGAUU-UUGUGAUAAUCAGGACAGGCUA--AACAUUCGCUAUAGUA-C--GACCAUGC-AU-G-UGU-CC-CCAGACCUAG-UUCU-U-UAC---CUGGGUCUGGUUUUCUCAAUGCUGGUGACAAGC
AANG01555395.1/438-569       ACGUGAAUA-UUCUCACUGUUCUGAUU-UUGUAAUAAUCAAGGCAGGCUA--AACAUUCACUAUAUUA-A--GACCAUGC-AU-G-UGU-CC-CCAGACUUAG-UUCU-U-UCC---CUAGGUCUAGUUUUAUCAAUGCUGGUGAUAAAC
AAYZ01041827.1/849-718       AUGCGAAUA-UUCUCGCUGUUCUGAUU-UUGUGAUAAUCAGGGCAGGCUA--AACAUUCGCUAUAUUA-A--GACCACGC-AU-G-UGU-CC-CCAGGCCUAG-UUCU-C-UCC---CUAUGUCUGGUCUUAAAAAUGCUGGUGAUAACA
AAIY01108263.1/1452-1321     CUGCGAAUA-UUCUCGCUGUCCUGGUU-UUGUGGUAGCCAGGGCAGGCUA--ACCAUUCGCUAUAUUA-A--GACCAUGC-AU-G-UGU-CC-CCAGGCUGAG-UUCU-C-UCC---CUGAGCCUGGUUUUAUCAAUGCUGGUGAUAAGU
AAQQ01581071.1/816-683       CUGCGAACA-UUCUCGCUGUUCUGAUUUUUGUAAUAAUCAGGGCAGGCUA--AACAUUCGCUAUAUUA-A--GGCCAUGC-AC-GGUGU-CC-CCAGACCUAG-UUCU-U-UCC---CUGGGUCUGGUUUUAUAAGUGCUGGUGAUAAAC
AAPY01748840.1/1712-1581     UUGCACAUA-UUCUCGCUGUUCUGAUU-CUGUAAUAAUCAGGACAGGCUA--AACAUUUGCUAUAUUA-A--GACCAUGC-AU-G-UGU-UC-CCAGAUCUAG-UUCU-U-GCC---UUACGUCUGGUUUUAUAAAUACUGGUGAUAAGG
AANN01813189.1/3411-3542     CUGCGAAUA-UUCUCGCUGUUCUGGUU-UUAUAAUGAUCAGGGCAGGCUA--ACCAUUCGCUACAUUA-A--GACCACGC-AU-G-UGU-CC-CCAGACCUAG-UUCU-U-UAC---CUAGUUCUGGCUAUCUAAAUGCGGGUGAUAAAC
AANU01195292.1/4548-4679     UUAUGAAUA-UUCUCGCUAUUCCGAUU-UUGUAAUAAUCAGGACAGGCUA--AACAUUCACAAUAUUA-A--GACCAUGC-AU-G-UAU-CC-CUAGACCUAG-UUAU-U-UCC---CCAGGUCUGGUUUCAUAAAUGCUGGUGAUAAAA
AALT01398624.1/708-842       CUGCGAAUA-CUCUCACUGUUCUGAUU-UUGUAAUAAUCAGGACAGGCUA--AAUGUUCGCUAUAAUA-A--GACUAUGC-AU-G-UGU-GU-CCAGACCCAG-UUUU-U-ACCCACCUAGGUCUGGUCUUAGAAAUGCUGGUGAUGGGG
AADA01209429.1/176-307       CUGCAGAUA-UUCUCACUGUUUUGAUU-UUGUAAUAGUCAGGACAGGCUA--ACCAUUCACUUUAUUA-A--GACCAUGC-AU-A-UAU-CC-CCAGAACUAG-UUCU-U-UCC---CGAGGUCUAGUUUUAUAAAUGUUGCUGAUAAAC
ABDC01290390.1/8627-8496     AUGAGACUA-UUAUUACUGUUCUGGUU-UUCUAAUAAUCAGGACAGGCUA--AACAUUUACUACGUUA-A--GACCAUGC-AU-G-UGU-CU-CCAGAAAUCG-UUCU-U-UUC---CUAGGUUUAGUUUUAUAAAUGAUGGUGAUAAAC
AAFR03006590.1/214693-214826 UUGCGAAUA-UUCUCGCUGGCCUGAUA-UUACUGUGAUCUGGUCAGGCUA--GACAUUCGCUAGAUUA-A--GACCAUGC-AUUG-UGC-CU-CCAGAACUAG-UUCUCU-UCC---CUAGUUUUGGUUUUAUAAAUGCUGGUAACAAAC
AAPN01328295.1/4552-4420     CUGCGAAUA-UUCUCGCUGGCCUGAUA-UGCCCGUGAUCAGGUCAGGCUA--GACAUUCGCUAUAUUG-A--GACCCAGC-AUUG-UGU-CC-CCGGGAUUAG-UCCU-U-GCC---CUAAUCCUGGUUUUGCAAAUGCUGGUGACAAAU
AAWR02021228.1/73400-73267   CUGCGAAUA-UUCUCGCUGUUCUGAUU-UUGUAAUAAUCAGAGCAGGCUA--AACAUUCGCUAUAUUA-AAAUACCAUGC-AU-G-UGU-CC-CCAGACCUAG-UUCU-U-UCC---CUAGAUCUGGUUUUAUAAAUGCUGGGGAUAAAC
AAGV020308595.1/1886-1753    CUGCGAAUA-UUCUCGCUGUCCUGAUU-UUGUGAUAAUCAGGGUAGGCUA--AACAUUCGCUAUAUUAGA--AACCAUGC-AU-G-UGU-CC-CCAGACCUAG-UUUU-U-CUC--UCUAGGGCUGGUUUUUAGAAUGCUGGUGAUAAAC
AAKN02004273.1/7647-7778     CUGCAAAUA-UUCUCGCUGUUCUGAUU-GUGUCAUAAUCAGGGCAGGCUA--AACAUUUGCUAUAGUA-A--GACCAUGC-AU-G-UGU-CC-CCAGACCUUG-AUCU-U-UCC---CUAGGUCUGGUUUUAUAAAUGCUGCUGAUAAAU
AAGW02012549.1/93789-93658   UUGCGAAUA-UUCUCGCUGUUCUGGUU-UUGCAAUAAUCAGGGCAGGCUA--AACAUUCGCUAUAUUA-A--AACCAUGC-AU-G-UGU-CC-CCAGGCCUAG-UUCU-U-UCC---CUAUGUCUGGUUUUAUAAAUGCUGGUGAUAAAA
AAGU03022950.1/49520-49389   UGGCGAAUA-UUCUCGCUGUCCUGAUU-UUGUGAUAAUCAGGGCAGGCUA--AACAUUCGCUAUAGUA-A--AACCAUGC-AU-G-UGU-CC-CCAGACCUAG-UUCU-U-UAC---CUAGGUCUGGUUUUAUAAAUGCUGGUGAUAAAC
AAWZ02016254.1/5828-5695     AUGCGAAUAAUUCUCGCUGUCCUGAUA-UUUCCGUGAUCAGGGCAGGCUA--GACAUUCGCUAUAUUA-U--UACUAUGCGGU-G-UGU-CC-CCAGGGUUGG-UUCC-UCUCC---CUAGUCCUGGUUUU-UAACUGCAAGUAACAUGU
AAPE02005562.1/2578-2447     UUGCGAAUA-AUCUCCCUGUUCUGAUU-UUGUAAUAAUCAGGGCAGGCUA--CACAUUCGCUAUAUUA-A--GACCAGGC-AU-G-UGU-GC-CCAGACCUAG-UUCU-U-UCC---CUGGGUCUGGUUUUAUAAAUGCUGGUGAUAAAC
AAQR03071705.1/5015-4884     GUGCAAAUA-UUCUCGCUGUUCUGAUU-UUAUAAUAAUCAGCACAGGCUA--AACAUUUGCUAUAUAA-A--AACCAGGU-GU-G-UGUCCC-C-AGACCUAG-UUCU-U-UUC---CUAGGUUUGGUUUUAUAAAUGCUGUUGAUAAAC
AACN010571460.1/421-552      CUGUGAACA-UUCUCGCUGUUCUGAUU-UUGUAAUAAUCAGGGCAGGCUA--AACAUUCACUAUAUUG-A--GACUAUGC-AC-G-UGU-CC-CCAGACCUAG-UUCU-U-UCC---CUAGGUCUGGUUUUAUCAAUGCUGGUGAUAAAC
D14521.1/3447-3581           AUGCGAAUA-UUCUCGCUGCCCUGAUA-UUCCGGUGAUCAGGGGAGGCUA--GACAUUCGCUAUAUUA-A--AACUAUGC-AUUG-UGU-CCUCCAGGACUGGACUGC-U-GCU---CUAGUACUGGCUUUGAAAAUGCUAGUGACAUAC
#=GC SS_cons                 ::<<<----.------<<<<<<<<<<<._______>>>>>>>>>>>----..------>>>-------.-..-<<<<-<<.--.-.---.--.<<<<<<<<<<.____._.___...>>>>>>>>>>---------->>>>>>:::::::
#=GC RF                      cUGcgAAUA.UUCUCgCUGucCUGauu.UUgUaAUaauCAGgaCAGGCUA..AACAUUcgCUAUAUUA.A..gaCcaUGc.AU.G.UGU.cC.CCAGaccuaG.UUcU.U.ucC...CuagguCUGGUUUUauAAAUgCugGuGAUAAAc
//
# STOCKHOLM 1.0

#=GF AC   RF00140
#=GF ID   Alpha_RBS
#=GF DE   Alpha operon ribosome binding site
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Published; PMID:11504736
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11504736
#=GF RT   Translational repression of the Escherichia coli alpha operon mRNA:
#=GF RT   importance of an mRNA conformational switch and a ternary entrapment
#=GF RT   complex.
#=GF RA   Schlax PJ, Xavier KA, Gluick TC, Draper DE
#=GF RL   J Biol Chem 2001;276:38494-38501.
#=GF CC   The bacterial alpha operon ribosome binding site is surrounded by this
#=GF CC   complex pseudoknotted structure. Translation of the mRNA produces 4
#=GF CC   ribosomal protein products, one of which (S4) acts as a translational
#=GF CC   repressor by binding to the nested pseudoknot region. The mechanism of
#=GF CC   repression is thought to involve a conformational switch in the pseudoknot
#=GF CC   region and ribosome entrapment [1].
#=GF WK   Alpha_operon_ribosome_binding_site
#=GF SQ   39


BX950851.1/4490615-4490505 UAGCUGCAAC-AUU--A-UUUGAGUAUCCUGAAAACGGGCUUUUCAGAAU---GGUG---UUGCCGU----AUA-------AAAUUGU-AGGAGUGCA--UAG--UGGCCCGUAUAGCAGGCAUUAACAUUCCUGAU
CR378663.1/343377-343482   AGAAUUGUAC-CAC--C-ACUGCGUAUCCUA--AACGGGCUCUGCA-------GUGG---UUAUUCU----UGU-------AAAGUACUAGGAGUGAA--UAG--UGGCCCGUAUUGCAGGCAUUAACAUUCCUGAU
BX571874.1/272731-272618   UCACAGUAAC-ACU--G-UUUGAGUAUCCUGAAAACGGGCUUUUCAGAAU---GGUG---UUGCGGU--AAAUA-------AAUAAUUUAGGAGUGCA--UAG--UGGCCCGUAUAGCAGGCAUUAACAUUCCUGAU
AB032408.1/554-653         AACUGUCGUC-UGU--C----GAGUAUCCU---ACCGGGCUUUUC--------ACAG---AUGACC-----AUU-------AACUAUUGAGGAGUGCA--UAG--UGGCCCGUAUCGCUGGCAUUAACAUUCCUGAU
AE005174.2/4244784-4244673 GUCUGUGCGU-UUC--CAUUUGAGUAUCCUGAAAACGGGCUUUUCAGCAU---GGAA---CGUACAU----AUU-------AAAUAGU-AGGAGUGCA--UAG--UGGCCCGUAUAGCAGGCAUUAACAUUCCUGAU
BX936398.1/4386785-4386675 UGACUGCAAU-GCU--A-UUUGAGUAUCCUGAAAACGGGCUUUUCAGAAU---GGUA---UUGCUGU----AUA-------AAAUAGU-AGGAGUGCA--UAG--UGGCCCGUAUAGCAGGCAUUAACAUUCCUGAU
CP000753.1/256694-256792   AUCUGUUGAC-UGU--C----GAGUAUCCU---UUCGGGCUUUUC--------GCAG---UUGGCC-----UUU-------AACUUUA-AGGAGUGCA--UAG--UGGCCCGUAUCGCUGGCAUUAACAUUCCUGAU
CP000510.1/4332491-4332391 AAUUAUCAUU-UGU--C----GAGUAUCCU---ACCGGGCUUUUC--------ACAA---AUGAAUC----GUU-------AACUUUUAAGGAGUGCA--UAG--UGGCCCGUAUCGCUGGCAUUAACGUUCCUGAU
AASA01000095.1/13106-12993 GUCCUGAUAU-ACU--G-UUUGAGUAUCCUGA-AACGGGCUUUUCAAGAU--CAGUA---UAUCAAU-AAACUU-------AAAUAAU-AGGAGUGCA--UAG--UGGCCCGUAUUGCAGGCAUUAACAUUCCUGAU
CP000746.1/527966-528079   UCCUUGGCAU-ACU--G-UUUGAGUAUCCUGA-AACGGGCUUUUCAAGAU--CAGUA---UGUCAAA----UUA----GUUAAAAUAU-AGGAGUGCA--UAG--UGGCCCGUAUUGCAGGCAUUAACAUUCCUGAU
CP000503.1/201038-201135   AUCUGUCAAC-UGU--C----GAGUAUCCU---UUCGGGCUUUUC--------GCAG---UUGGCCU----UUA-------ACUUA---AGGAGUGCA--UAG--UGGCCCGUAUCGCUGGCAUUAACAUUCCUGAU
CP000302.1/206996-207093   AUUUGUCAUC-UGU--C----GAGUAUCCU---UUCGGGCUUUUC--------CCAG---AUGACCU----UUA-------ACUUA---AGGAGUGCA--UAG--UGGCCCGUAUCGCUGGCAUUAACAUUCCUGAU
AAND01000066.1/1798-1686   AAAGAAGUAG-UAUGCC-GCAGCGUAUCCAU--AACGGGCUUUGCUGCGG---AUAA---UUCUUUU---AUGA-------ACCCCCUUAGGAGUGAA--UAA--UGGCCCGUAUAGCCGGCAUUAACAUUCCUGAU
CP000388.1/1197645-1197749 CAAUUUUGUC-AUC--G-GGUAAGUAUCCU---AUCGGGCUUUUUAGGCU---GAUG---ACAUAA-----------------ACUAUGAGGAGUACUGUUAA--UGGCCCGUAUCGCUGGCAUUAACAUCCCUGAG
AAPS01000075.1/7302-7409   AGUAGUAUUC-CGC--A----GCGUAUCCAU--AACGGGCUUUGCU-------GCGG-CUAAUUCUU----UUA----UAGAAACACUUAGGAGUGAA--UAA--UGGCCCGUAUAGCAGGCAUUAACAUUCCUGAU
CP000606.1/189900-189999   AAUCGUCAUC-UGU--C----GAGUAUCCU---ACCGGGCUUUUC--------ACAG---AUGGCC-----UUU-------AACUUAUGAGGAGUGCA--UAG--UGGCCCGUAUCGCUGGCAUUAACAUUCCUGAU
AAVS01000029.1/44999-45109 UGAUUUGGUC-UUC--G-UUUGAGUAUCCU---UACGGGCUUUUCAAACUUUUGAUU---ACCAAAU----UCG-------AAUAUAGGAGAUGUGU---UAG--UGGCCCGUAUUGCUGGCAUUAACGUCCCUGAU
AAMX01000030.1/15346-15445 UUCGGCAAUC-GGU--U----GAGUAUCCU---AACGGGCUUUUCA-------ACUG---A-AGCCU----ACA-------AAAAAAGGAGACGUGU---UAG--UGGCCCGUAUCGCUGGCAUUAACGUUCCUGAC
AAOH01000018.1/3700-3591   AAGUUUGAUU-AUU--G-GUUGAGUAUCCU---AACGGGCUUUUCAACAA-AAUAUA---GUCAAAU----UCU-------UUUAUAGGAGAUGUGU---UAG--UGGCCCGUAUAGCUGGCAUUAACGUCCCUGAU
AE017340.1/2033365-2033265 UUCGGCAAUC-GGU--U----GAGUAUCCU---AACGGGCUUUUCA-------ACUG---A-AGCCU----ACA-------AACUGAAGGAGACGUGU--UAG--UGGCCCGUAUCGCUGGCAUUAACGUUCCUGAC
CP000436.1/76674-76792     UCCUUGAUAU-ACU--G-UUUGAGUAUCCUGA-AACGGGCUUUUCAAGAU--CAGUA---UAUCAAA----UUUAAUCAAUAAAAUAAUAGGAGUGCA--UAG--UGGCCCGUAUUGCAGGCAUUAACAUUCCUGAU
AE016827.1/1995725-1995612 UCCUUG-CAC-ACU--G-UUUGAGUAUCCUGAAAACGGGCUUUUCAAGAU--CAGUG---UGUCAAA----UUA-----AUUAGAAAAUAGGAGUGCA--UAG--UGGCCCGUAUUGCAGGCAUUAACAUUCCUGAU
CP000507.1/262573-262670   AACUGUCACC-UGU--C----GAGUAUCCU---UUCGGGCUUUUC--------ACAG---GUGGCCU----UUA-------ACUUA---AGGAGUGCA--UAG--UGGCCCGUAUAGCUGGCAUUAACAUUCCUGAU
ABCH01000098.1/5690-5799   AAGAAGUAGCACUC--C-GCAGCGUAUCCAU--AACGGGCUUUGCU-------GCGG---CUAUUCU----UUU----UAAGAAACACUAGGAGUGAA--UAA--UGGCCCGUAUAGCAGGCAUUAACAUUCCUGAU
AC202195.2/54176-54062     UGACUACAAC-GUC--G-UUUGAGUAUCCUGAAAACGGGCUUUUCAGCAU---GACG---UUGUGGUGUAAAUU-------AAAUAAU-AGGAGUGCA--UAG--UGGCCCGUAUAGCAGGCAUUAACAUUCCUGAU
AE017143.1/1639695-1639584 UCCUGAUAUA-CUG--U--UUGAGUAUCCUGA-AACGGGCUUUUCAAGAU---CAGU---AUAUCAU-AAACUU-------AAAUAAU-AGGAGUGCA--UAG--UGGCCCGUAUUGCAGGCAUUAACAUUCCUGAU
AE003852.1/2754033-2753923 AAGAAGUAGUAUAC--C-GCAACGUAUCCUC--GACGGGCUUUGUUGCGG---GUAA---UUCUUUG----AUG-------AAAGUACUAGGAGUGCA--UAG--UGGCCCGUAUAGCAGGCAUUAACAUUCCUGAU
CP000083.1/621277-621382   AAAGAGAAUG-GUU-------GGGUAUCCU---AACGGGCUUUCCAACCA--AAGUA---AUUUUAA----UUA-------UAAAUAGGAGAUGUGAU--UAG--UGGCCCGUAUCGCUGGCAUUAACAUCCCUGAU
CR954246.1/2987868-2987758 UGAUUUGGUC-UUC--G-UUUGAGUAUCCU---UACGGGCUCUUCAAACA---GAUGAUUACCAAAU----UCG-------AAUAUAGGAGAUGUGU---UAG--UGGCCCGUAUUGCUGGCAUUAACGUCCCUGAU
AE016853.1/702273-702368   UUAUCUCGCG-CCC--U------AUUUCUU-------GGCUUCCG--------GGGC---GUAGGUA---GCUG-------UCAAUUGGAGUCCCACU--GAA--UGGCCCGUAUUGCAGGCGUUAACAUUCCAGAU
CP000058.1/5216672-5216577 UUAUCUCGCG-CCC--U------AUUUCUU-------GGCUUCCG--------GGGC---GUAGGUA---GCUG-------UCAAUUGGAGUCCCACU--GAA--UGGCCCGUAUUGCAGGCGUUAACAUUCCAGAU
BX640422.1/15958-16066     GCACCGACCC-GCG--U-CACAAGCAGCGUC--AA--GGCUAACCCAGUU---AGCG---GUACGCA----ACG-------GAUUUAUUCAAGGAACA-GUCA--UGGCCCGUAUUGCUGGCAUUAACAUUCCGCCG
BX640437.1/48199-48307     GCACCGACCC-GCG--U-CACAAGCAGCGUC--AA--GGCUAACCCAGUU---AGCG---GUACGCA----ACG-------GAUUUAUUCAAGGAACA-GUCA--UGGCCCGUAUUGCUGGCAUUAACAUUCCGCCG
AM286690.1/459188-459298   CGGCGUAGCG-CUA--G-ACUCUGCCGCCU---UUCGGCGCCUAUGAGCC---UGGC---GCCACCC----GUU-------UUGUGAAUCGGAGAUAU--UCGGAUGGCCCGUAUUGCAGGCGUUAACAUCCCGGAA
CP000089.1/376642-376729   UUA---------------AUCCCCUGUCCAG--UUCGGCAUUCGUUAAUU---------------------UUC-------GAAAUAG-UGGAGUGAU-UCAA--UGGCCCGUAUUGCAGGGGUAAACAUUCCGAAC
AE004439.1/1587789-1587675 UCCUUGACAC-UUU--G-UUUGAGUAUCCUGAAAACGGGCUUUUCAAGAU--CAAAG---UGUCAAC----UUA----GUUAAAUAAU-AGGAGUGCA--UAG--UGGCCCGUAUUGCAGGCAUUAACAUUCCUGAU
CP000671.1/1599422-1599308 UCCUUGAUAU-UCU--G-UUUGAGUAUCCUGAAAACGGGCUUUUCAAGAU--CAGAA---UAUCAAA----UUA----AUUAAAAUAU-AGGAGUGCA--UAG--UGGCCCGUAUUGCAGGCAUUAACAUUCCUGAU
AE016795.3/754813-754706   AGAAGUAGUA-UCC--C-GCAGCGUAUCCGA--CACGGGCUUUGCUGC-----GGAU---AAUUCUU----UUA-------UGAAACCUAGGAGUGAA--UAA--UGGCCCGUAUUGCAGGCAUUAACAUUCCUGAU
CP001103.2/3079659-3079554 CAAUUUAGUC-GAC--G-GAUAAGUAUCCU---AUCGGGCUUUUUAGGUC---GUCG---ACAAAUA----AAC-------AAG-----AGGAGUGCUGUUAA--UGGCCCGUAUCGCUGGCAUUAACAUUCCUGAG
#=GC SS_cons               :::<<<<<<<.<<<.._._________AAA_..__BBBB____CCC____...>>>>...>>>>>>:....:::.......:::::::::::::::::..:::..:::bbbb::::::aaa::::::::::::ccc:
#=GC RF                    uaauggcgcc.ccc..g.uuuGaGUAUCCUg..aACGGGCUUUuCaAgau...gggg...gcgccau....uUu.......aAauuauuAGGAGUGcA..UAG..UGGCCCGUAUuGCaGGCAUUAACAUUCCUGAU
//
# STOCKHOLM 1.0

#=GF AC   RF00142
#=GF ID   snoZ118
#=GF DE   Small nucleolar RNA Z118/Z121/Z120
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   48.00
#=GF TC   48.50
#=GF NC   46.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   This family consists of several snoRNA Z118, Z121 and Z120 sequences which
#=GF CC   are members of the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. This family seems to be found exclusively in rice. C/D
#=GF CC   box small nucleolar RNAs are known to act as a methylation guides for 18S
#=GF CC   ribosomal RNA in plants [1].
#=GF WK   Small_nucleolar_RNA_Z118/Z121/Z120
#=GF SQ   7


AJ490481.1/1-105 UGUUUGCCUUGAUGAUUCCUACAAGGACGGUAUCUGAGUAAGGU---UCUUGAAAGAGUACUCCUUAUGUGAUUACAUCCAAAACUGAUC--AGAGAU-UCUGAGUAAACA
AJ490483.1/1-108 UGUUUGCUGUGAUGACAUCUACAAGGACGGUAUCUGAGUAAGGUGGCUCUUGAAAGAGUACUCCUUGCGUGAUUACAUCCAAAACUGAUC--AGAGAU-UCUGAGCAAACA
AJ490484.1/1-108 UGUUUGCCAUGAUGAUUCCUACAAGGACGGUAUCUGAGUGAGGAACCUCUUGAAAGAGAGCUCCUCACAUGAUUAUAUCCAAAACUGAUC--AGAGAU-UCUGAGCAAACA
AJ490485.1/1-108 UGUUUGCUGUGAUGAUUCCUACAUGGACGGUAUCUGAGUGAGGAACUACUUGAAAGAGUAUUCCUCACAUGAUUACAUCCAAAACUGAUC--AAAGAU-UCUGAGCAAACG
AJ490486.1/1-108 UGUUUGCUGUGAUGAUUCCUACAUGGACGGUAUCUUAGUAAGGAACCACUUGAAAAGGUGGUCCUCACGUGAUUACAUCCAAAACUGAUC--AGAGAU-UCUGAGCAAACA
AJ490480.1/1-92  ---UUGCUGUGAUGACAUCUAAUAGGACGGUAUCUGAGCGACGGA--UCU----------AUCCUCGCGUGAUUAUA-CCUAAACUGAGACUAAAAAUGUCUGAGCAA---
AJ490482.1/2-99  UAAUUGCUGUGAUGACAUCUACAAGGACGGUAUCUGAGCGAUGGA--UCU----------AUCCUCACGUGAUUAUA-CCUAAACUGAGACUAAAAAUGUCUGAGCAAAAC
#=GC SS_cons     <<<<<<<------------------------------<<<<<<___________________>>>>>>----------------------..------.----->>>>>>>
#=GC RF          uguUUGCugUGAUGAuuuCUAcAaGGACGGUAUCUGAGugAgGaAccuCUUGAAAgAGuaaUCcUcaCgUGAUUAuAUCCaAAACUGAuc..AaAgAU.UCUGAGCAAaca
//
# STOCKHOLM 1.0

#=GF AC   RF00143
#=GF ID   mir-6
#=GF DE   mir-6 microRNA precursor
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   58.00
#=GF TC   58.00
#=GF NC   55.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00083
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11914277
#=GF RT   miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.
#=GF RA   Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L,
#=GF RA   Rappsilber J, Mann M, Dreyfuss G
#=GF RL   Genes Dev 2002;16:720-728.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family consists of the microRNA (miRNA) precursor mir-6 which appears
#=GF CC   to be Drosophila specific. Animal miRNAs are transcribed as ~70nt
#=GF CC   precursors and subsequently processed by the Dicer enzyme to give a ~22nt
#=GF CC   product. In this case the mature sequence comes from the 3' arm of the
#=GF CC   precursor. The extents of the hairpin precursors are not generally known
#=GF CC   and are estimated based on hairpin prediction. The products are thought to
#=GF CC   have regulatory roles through complementarity to mRNA. The involvement of
#=GF CC   Dicer in miRNA processing suggests a relationship with the phenomenon of
#=GF CC   RNA interference. miRNAs are numbered based on the sequence of the mature
#=GF CC   RNA.
#=GF WK   Mir-6_microRNA_precursor
#=GF SQ   24


AE013599.4/15548587-15548511   UAAUGUAGAGGGAAUAGUUGCUG-UGCUGUAAG---UU-------AAUAUACC------AUA--UCUAUAUCACAGUGGCUGUUCUUUUUGUACCU
AANI01014795.1/39849-39929     UAACCGC-AGGGAACUGCUGCUGCUGAUAUACUGUAUA-------GAUUAUAU------CGA-UUCCAUAUCACAGUGGCUGUUCUUUUUGGUUGC
AAPU01010225.1/182992-182911   UAACCGC-AGGGAACUGCUGCUGCUGAUAUACUAUAUG-------UAUUUGUC------AGUACUCUAUAUCACAGUGGCUGUUCUUUUUGGUUGC
AAPT01006453.1/3535-3614       UAACCAC-AGGGAACUGCUGCUGCUGAUAUACA---AC-------CAUAUUUAUAC---ACG--ACUAUAUCACAGUGGCUGUUCUUUUUGGUUGC
AAIZ01001618.1/40271-40349     AAAAAGA-AGGGAACGGUUGCUGCUGAUGUAGU---UC-------AAGUUUCGC-----ACA-AUUUAUAUCACAGUGGCUGUUCUUUUUUGUUUG
AAST01030396.1/2689-2767       AAAAAGA-AGGGAACGGUUGCUGAUGAUGUAGU---UC-------GAAACUCUC-----ACA-AUUUAUAUCACAGUGGCUGUUCUUUUUUGUUUG
AADE01001895.1/3626-3699       GAAGUAG-AGAGAAUAGUUGCUG-UGCUAUAUG---UC-------CUUCGACUC-----UA-----UAUAUCACAGUGGCUGUUCUUUUUGUACCU
AAGH01003023.1/9218-9292       UAACCCC-AGGGAACUUCUGCUGCUGAUAUAUUA--UU-------GAAAAACU------CC-----UAUAUCACAGUGGCUGUUCUUUUUGGUUGC
AAPP01018770.1/57378-57462     UAGCCCC-AGGGAACUGUUGCUGCUGAUAUAUUA--UUCUCCCAAAAAAAAAA------UCA--CCUAUAUCACAGUGGCUGUUCUUUUUGGCUGC
AAPP01018770.1/57538-57612     AAAAAGA-AGGGAACGGUCGCUGCUGAUGUAG-----U-------UAUUCGCA------UCA--UUUAUAUCACAGUGGCUGUUCUUUUUUGUUUG
AAPU01010225.1/182811-182733   AAAGAGA-AGAGAACGUUCGCUGUUGAUGUAGU---CG-------AAUUCAUUUA----AUC--UUUAUAUCACAGUGGCUGUUCUUUUUUGUUUA
AAPT01020768.1/61474-61396     AAAAGGA-AGAGAACGCUCGCUGCUGAUGUAGU---UC-------AUGAUUCAA-----AUA-UUUUAUAUCACAGUGGCUGUUCUUUUUUGUUUA
AAPP01018770.1/57233-57304     UAAAGUAGAGAGAAUAGUGGCUG-UGCUGUA---------------AGUUUCA------AAA--UCUAUAUCACAGUGGCUGUUCUUUUUGCACCU
AAPT01006453.1/3396-3470       AAUGUAA-AGAGAAUAGAUGCUG-UGCUGUAUG---UU-------GAACGUAU------UG---UCUAUAUCACAGUGGCUGUUCUUUUUGUACCA
AAIZ01001618.1/40125-40208     CAACCGC-AGGGAACCGCUGCUGCUGAUAUAUUA--UC-------CACCCAUCUUUGACAUU--UCUAUAUCACAGUGGCUGUUCUUUUUGGUUGC
AAPQ01007044.1/1204728-1204655 UAACCCC-AGGGAACCUCUGCUGCUGAUAUAUU---AU-------UGAAAACU------CC-----UAUAUCACAGUGGCUGUUCUUUUUGGUUGC
AANI01014795.1/40023-40100     AAAAGGA-AGAGAACGUUCGCUGUUGAUGUAGU---CG-------ACCUUUGU------ACU-CUUUAUAUCACAGUGGCUGUUCUUUUUUGUUUA
AASS01023484.1/3760-3836       UAAAGUAGAGGGAAUAGUUGCUG-UGCUAUAAG---UU-------UAUAUACC------GUA--UCUAUAUCACAGUGGCUGUUCUUUUUGUACCU
AAQB01006291.1/70803-70723     AAAAAGA-AGGGAACGGUUGCUGUUGAUGUAGU---AU-------ACCAUUUUGUUUA-ACA--A-UAUAUCACAGUGGCUGUUCUUUUUUGUUUA
AAEU02000463.1/591819-591743   UAACGUAGAGGGAAUAGUUGCUG-UGCUGUAAG---UU-------AAUAACAA------AUA--UCUAUAUCACAGUGGCUGUUCUUUUUGUACCU
AAIZ01000060.1/36338-36263     UUAUCUA-AGGAAAUAGUAGCCG-UGAUUUAAC---AU-------AACAAAUC------CUU--UACAUAUCACAGUUGCUGUUUCUUUUAGAUAG
AAEU02000463.1/591680-591606   UAACCGC-AGGGAACCUCUGCUGCUGAUAUAUUA--UU-------GAGAAACU------UC-----UAUAUCACAGUGGCUGUUCUUUUUGGUUGC
AANI01014795.1/39694-39769     UAAAGUAGAGAGAAUAGACGCUG-UGCUGUAUG---UU-------UUGCGUAU-------GG--UCUAUAUCACAGUGGCUGUUCUUUUUGUACCU
AAQB01006291.1/71126-71052     UAAAGUAGAGAGAAUAGUUGCUG-UGUUUU-AU---GC-------CCUUUUCA------AUU--UC-AUAUCACAGUGGCUGUUCUUUUUGUGCCU
#=GC SS_cons                   ::::::<.<<<<<<<<<<<<<<<-<<<<<<<<_...__.......________......_>-..-->>>>>>>>>>>>>>>>>>>>>>>:::::::
#=GC RF                        uAAacua.AGgGAACaGuuGCUGcUGaUaUAgu...uu.......aAuauauu......aca..UcUAuAuCACAGUggCuGUUCuUUuUgGuUuu
//
# STOCKHOLM 1.0

#=GF AC   RF00144
#=GF ID   mir-199
#=GF DE   mir-199 microRNA precursor
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   58.00
#=GF TC   59.10
#=GF NC   56.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11914277
#=GF RT   miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.
#=GF RA   Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L,
#=GF RA   Rappsilber J, Mann M, Dreyfuss G
#=GF RL   Genes Dev 2002;16:720-728.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family consists of the microRNA (miRNA) precursor mir-199 which
#=GF CC   appears to be specific to humans. Animal miRNAs are transcribed as ~70nt
#=GF CC   precursors and subsequently processed by the Dicer enzyme to give a ~22nt
#=GF CC   product. In this case the mature sequence comes from the 3' arm of the
#=GF CC   precursor. The extents of the hairpin precursors are not generally known
#=GF CC   and are estimated based on hairpin prediction. The products are thought to
#=GF CC   have regulatory roles through complementarity to mRNA. The involvement of
#=GF CC   Dicer in miRNA processing suggests a relationship with the phenomenon of
#=GF CC   RNA interference. miRNAs are numbered based on the sequence of the mature
#=GF CC   RNA.
#=GF WK   mir-199_microRNA_precursor
#=GF SQ   40


AC007229.1/16746-16645       UGGAUAGC-CGGCCCCGCCAACCCAGUGUUCAGACUACCUGUUCAGGAGGCUCUCAAUGUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCUUGGGUGAGCG
AL137157.7/19246-19147       UGGAGAUC-CUGCUCCGUCGCCCCAGUGUUCAGACUACCUGUUCAGGACAAUGCCG-U-UGUACAGUAGUCUGCACAUUGG-UUAGACUGGGCAAGGGAGAGCA
AL590708.18/146131-146032    AGGACACCUCCACUCCGUCUACCCAGUGUUUAGACUAUCUGUUCAGGAC--UCCCAAAUUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCU-GGGUUAGAC
AANH01004681.1/136443-136347 UAGUCGCC-C-AGCCCGCCUGCCCAGUGUUCAGACUACCUGUUCAGGAAGUAGUGG--UUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGCC--GGGGAAGCA
CAAE01011305.1/260-162       CUCACUCC-CCACCCUGCCUGCCCAGUGUUCAGACUACCUGUUCAUCAG--ACUCAAGCUGAACAGUAGUCUGCACAUUGG-UUAUGCAGAGUU-GGGACACAC
CAAE01014575.1/64714-64811   UGUCCACC-C-AGCCCGCCUGCCCAGUGUUCAGACUACCUGUUCAGGAAGUAGUGG--UUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGCCC-GGGUAAGCA
ABDC01156515.1/926-826       CAGACAGC-CGGCCCCGCCGGCCCAGUGUUCAGACUACCUGUUCAGGGGCUGCUGCACGCGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCUCGGC-GAGCG
CAAA01166376.1/6652-6752     UGAACAGC-CAUCCCCGCCAUCCCAGUGUUCAGACUACCUGUUCAGGAGGCUGGGACA-UGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCUUGGGCCAGCA
AAHX01020762.1/284-188       AGGAUACC-U--CCCCGUCUACCCAGUGUUUAGACUACCUGUUCAGGAC--UCCCAAAUUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCU-GGGUUAGAC
BAAF04076833.1/4729-4828     AAGGCAUC-CUGCUCCGUCAUCCCAGUGUUCAGACUACCUGUUCAGAAUCUUCCUG--GUGUACAGUAGUCUGCACAUUGG-UUAGACUGUGCAUGGAAGUAUC
AAFR03049221.1/24866-24967   UCAAAUUC-CAGCCCCACCAGCCCAGUGUUCAGACUACCUGUCCAGGAGAUUGCAAAGGUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCUUGGAAAAGCA
CT563248.9/85109-85010       ACUAUCUC-CUGCUCCGUCAUCCCAGUGUUCAGACUACCUGUUCAGGAUCAUACUG--GUGUACAGUAGUCUGCACAUUGG-UUAGACUGUGCAUGGACUCCCG
AAQQ01144563.1/4013-4113     CGAGUAGC-CGGCCCCGCCAUCCCAGUGUUCAGACUAG-UGUUCAGGAGGCUCUGAAUGUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCUUGAACAAACG
BAAE01013242.1/84-183        CCCUCCCC-CCAUCCCGCCUGCCCAGUGUUCAGACUACCUGUUCAGGAAGUAGUGG--UUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGUUAGGGAAGUGCG
BX088529.6/78677-78581       UUGCCUCC-C--CCUCGCCUGCCCAGUGUUCAGACUACCUGUUCAUCAUGCUGCAG--CUGAACAGUAGUCCGCACAUUGG-UUAGGCUGGGCU-GGGACACAC
AAFR03046507.1/3724-3626     AACAGACU-CCACUCCGUCUACCCAGUGUUUAGACUAUCUGUUCAGGAC--UCCAAUAUUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCU-GGGCUACAC
AANG01185125.1/363-262       CGGACAGC-CGGCCCCGCCCACCCAGUGUUCAGACUACCUGUUCAGGGGGUUCAGAAUGUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCUCGGGUAAGCG
AANH01005434.1/24491-24590   CGCAACUC-CGGCUCCGUCCACCCAGUGUUCAGACUACCUGUUCAUUAUCAUACUG--GUGUACAGUAGUCUGCACAUUGG-UUAGACUGGGCAUGGACCGUCU
AANH01004317.1/876-974       CCGCCCCC-CCCCCCUGCCUGCCCAGUGUUCAGACUACCUGUUCAUCCGGCUACAG--CUGAACAGUAGUCUGCACAUUGG-UUAGGCUGGGCU-GGGACACGC
CAAE01014542.1/504358-504259 CCUCCACC-CGGCUCCGUCCACCCAGUGUUCAGACUACCUGUUCAUUGUCAUACUG--GUGUACAGUAGUCUGCACAUUGG-UUAGACUGGGCACGGACCCUCG
BAAF04061048.1/5562-5661     CUCCAUUC-CGGCUCCGUCCACCCAGUGUUCAGACUACCUGUUCAUUGUCAUACUG--GUGUACAGUAGUCUGCACAUUGG-UUAGACUGGGCCGGGCUCUCCU
AAVX01256932.1/291-390       AAAAGGUC-CUGCUCCGUCGGCCCAGUGUUCAGACUACCUGUUCAGGACAAUAUUG--UUGUACAGUAGUCUGCACAUUGG-UUAGAUUGGGCAUGGGAAAGCA
BAAF04022833.1/5094-5192     UCUAUCCC-CCACCCCGCCUGCCCAGUGUUCAGACUACCUGUUCCUCCA--GCUAUAACUGAACAGUAGUCUGCACAUUGG-UUAGGCUAGACU-GGGAGCCAC
BAAE01184372.1/319-221       UCUAUCCC-CCACCCCGCCUGCCCAGUGUUCAGACUACCUGU-UCCUCCAGCUACAACUGA-ACAGUAGUCUGCACAUUGG-UUAGGCUAGACU-GGGAGCCAC
AAYZ01174210.1/140-40        GACACCUC-CCACUCCGUCUACCCAGUGUUUAGACUAUCUGUUCAGGAC--UCCCAAAUUGUACAGUAGUCUGCACAUUGGUUUAGGCUGGGCUGGGCUAGACC
CU929237.12/85511-85412      CCUCGUGC-CCGCUCUGCUUUCCCAGUGUUCAGACUACCUGUUCAGGGC--GUAGAGAUUGUACAGUAGUCUGCACAUUGG-UUAGGCUGAGUGAGGGCUGCAC
CU138550.14/80968-81064      UGGACGCC-C-GUCCCGCCUGCCCAGUGUUCAGACUACCUGUUCAGGAA--UUAGUGUUUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGAU--GGGGAUGCU
AAKN02056464.1/56517-56417   CGGACA-C-CGGCCCCGCCGGCCCAGUGUUCAGACUACCUGUUCAGGCGCCUCUGCAUGUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCUCGGGCGUGCA
AAWR02017790.1/21207-21308   UGGACAGC-CGGCCCCGCCCGCCCAGUGUUCAGACUACCUGUUCAGGGGGCUCCGAAUGUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCCUGGGCAGCGG
AAHX01170648.1/717-621       UGAAUAGC-CAACCCUGCCAUCCCAGUGUUC---CUCG-UGUUCAGGAGACCAAGACA-UGUACAGUAGUCAGCACAUUGG-UUAGGCUGGGCUUGGGUCAGCA
CAAB02006614.1/142324-142226 UUCACUCC-CCGUCCUGCCUGCCCAGUGUUCAGACUACCUGUUCAUCAG--ACUAAAGCUGAACAGUAGUCUGCACAUUGG-UUAAGCUGGGUU-GGGACACAC
AAWZ02011103.1/105677-105577 AGGAGA-C-CAGCCCCGCCUUCCCAGUGUUCAGACUACCUGUUCAGGAAGCUACAAAGGUGUACAGUAGUCUGCACAUUGG-UUAGACUGGGCUUGGGUGAGCA
AAQR03140752.1/13262-13361   GAGACAGC-CAGCCAUGCCAGCCCAGCGUUCAGACCACCUGUGCAGGAG--CCUCUGAGUGCACAGUAGUUUACACAUUGG-UUCGGCCAAGCCAGGUGAGCAG
AAGU03050830.1/254-354       CAGACAGC-CGGCCCCGCCAACCCAGUGUUCAGACUACCUGUUCAGGGG-UUCUGAAUGUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCUCGGGCGAUCG
CAAB02001273.1/56306-56405   AGAAGCUC-CUGCUCCGUCAUCCCAGUGUUCAGACUACCUGUUCAGGAUUUUACUG--GUGUACAGUAGUCUGCACAUUGG-UUAGACAGUGCAUGGAAGUGCA
AAWZ02037129.1/4059-4158     ACCAAAUC-CUGCUCCGUCGCCCCAGUGUUCAGACUACCUGUUCAGGACAAUGCUG--UUGUACAGUAGUCUGCACAUUGG-UUAGACUGGGCAAGGAAACGCA
AAPE02018251.1/211838-211739 UGGAGCUC-CUGCCCCGUCGGCCCAGUGUUCAGACUACCUGUUCAGGACAAUGCCG--UUGUACAGUAGUCUGCACAUUGG-UUAGACUGGGCAAGGCACAGCA
AAWZ02032658.1/17347-17445   AGAGCCUC-C-ACUCCGUCUGCCCAGUGUUCGGACUACCUGUUCAGGAC--UACGAGAUUGUACAGUAGUCUGCACAUUGG-UUAGGCUGUGCUGGGAUAUACC
AGAI01054814.1/40458-40555   -AGAGGCU-CCACUCCGUCUGCCCAGUGUUCAGACUACCUGUUCAGGAC--UACGAGAUUGUACAGUAGUCUGCACAUUGG-UUAGGCUGUGCU-GGGAUACAC
AAPE02052565.1/37992-38093   UGGACAGC-CAGCCCCGCCAACCCAGUGUUCAGACUACCUGUUCAGGGGGCUCUGAAUGUGUACAGUAGUCUGCACAUUGG-UUAGGCUGGGCUUGGGCCAGCA
#=GC SS_cons                 ::::::<<.<-<<<<-<<<---<<<<<<<-<<<<<<<-<<<<-<<______________>>->>>>>>>>>>>->>>>>>>.--->>>->>>>-->>>::::::
#=GC RF                      uagacacC.CugccCCGcCugCCCAgUGUUCaGACUACCUGUUCaggauauuauuaaauuGUACAGUAGUCuGCACAuUGG.UUAGgCUGggcuuGGgaaagca
//
# STOCKHOLM 1.0

#=GF AC   RF00145
#=GF ID   snoZ105
#=GF PI   snoR7
#=GF DE   Small nucleolar RNA Z105
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Wilkinson AC; 0000-0001-7406-0151
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   45.00
#=GF TC   45.40
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   This family consists of several snoRNA Z105 sequences which are members of
#=GF CC   the C/D class of snoRNA which contain the C (UGAUGA) and D (CUGA) box
#=GF CC   motifs. This family seems to be found exclusively in plants. C/D box small
#=GF CC   nucleolar RNAs are known to act as a methylation guides for 18S ribosomal
#=GF CC   RNA [1].
#=GF WK   Small_nucleolar_RNA_Z105
#=GF SQ   11


AAAA02011125.1/45898-45831 UUGGCAUGAUGAGGAA----ACCUUACGUUUAU--CUGAUCUAUUUGAUGAUA--AAUU-CCUCCUACUCAUUCUGA
AJ489950.1/1-67            UUGGCAUGAUGAGGAA----AACCGAUGUUUUUG---GAUCUAUUUGAUGAUA--AAUU-CCUCCUACUCAUUCUGA
AC189189.1/52925-52858     AAGGCAUGAUGAGGAU-----UGUUU-AUUGUCAUCUGAUUUUC-UGA--UGAAUCAAUACCUCCUACUCAUUCUGA
AL049862.1/41945-41876     AAGGCAUGAUGAGGAU-----UGUUUUAUUGUCAUCUGAUUCUCAUGA--UGAAUAUAUACCUCCUACUCAUUCUGA
AARH01002622.1/16153-16085 AGGCAAUAAUGAUGAA-----AGAUUUAA-AUUAUCUUAUAUGUAUGA--UGAUUCAACACCUCCUACUCAUUCUGA
AC193778.1/40019-39952     GCAUAAUGAUGAUGCA---------AAAUUUGUUCCGAUUAUUCAUGAAUGGAAUACCAACCUCCUACUCAUUCUGA
AP006540.1/42483-42559     CUGGCAUGAUGAUGAUAAUUACGAUUGAUUUUGUAUGAUUAUUCAUAUGAUUAAUACAAUCCUCCUACUCAUUCUGA
AASG02002047.1/5497-5426   GCAUAGUGAUGAUGAA-----CUUGAAAUUUCCCGAUGAUUUUCAUGACAGGAAUAACAACCUCCUACUCAUACUGA
ABCN01006793.1/11445-11379 -UGGCU--AUGAGGAA-------ACACCUGUCUGAUCAUUUGAACUGAUGAGACCAAUCACCUCCUACUCAUUCUGA
FN596742.1/723319-723247   UUGGUAUGAUGAUGAAC---AUAACA-AUUAUUUUCUGAUGAUUCUUGAUUGAAUAAUAACCUCCUACUCAUUCUGA
AP003829.2/81303-81234     UUGGCAUGAUGAGGAA----AUCAAUCGUUUCUAACUGAUCCACUGGAUGAGA--AAUU-CCUCCUACUCAUUCUGA
#=GC SS_cons               :::::<<<<-------.....----------<<--<__________>---->>--------------->>>>:::::
#=GC RF                    uuGGcAUGAUGAuGAA.....ugauauAUUUucuucUgAUuUucaUgAugugaAUAAuaACCUCCUACUCAUUCUGA
//
# STOCKHOLM 1.0

#=GF AC   RF00147
#=GF ID   SNORD34
#=GF PI   U34
#=GF DE   Small nucleolar RNA SNORD34
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD, Griffiths-Jones SR
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.84 -Z 549862.597050 CM SEQDB
#=GF CL   CL00055
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300754;
#=GF DR   snoopy; Loxodonta_africana300497;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   snoRNA U34 is found in intron 5 of the ribosomal protein L13a gene in
#=GF CC   humans. U34 is a member of the C/D class of snoRNA which contain C
#=GF CC   (UGAUGA) and D (CUGA) box motifs, and functions in directing site-specific
#=GF CC   2'-O-methylation of 25S rRNAs. Although the selection of the target
#=GF CC   nucleotide requires the antisense element and the conserved box D or D' of
#=GF CC   the snoRNA, the methyltransferase activity is thought to reside in one of
#=GF CC   the protein components [1]. U34 snoRNA has homologues in mouse,
#=GF CC   Arabidopsis (annotated as snoR4) and in several copies in rice
#=GF CC   (alternatively named snoZ181) [2]. This family also contains a putative
#=GF CC   homologue in Drosophila (Griffiths-Jones SR, pers. obs.).
#=GF WK   Small_nucleolar_RNA_SNORD34
#=GF SQ   14


AJ490415.1/1-86      UGAUGCCUAUGAUGACUUGCAAGAU-UAUUGCCUACAUUGUUUGACAAGUAUCUUUGUGAUAUU-AAUUG--CAAGUA----CCUGAGGCUUGA
X51528.1/3627-3692   ---CGUCUGUGAUGUUCUGC------UAUUACCUACAUUGUUUGAGCCUCAU----GAAAACC---------CCACUG----GCUGAGACGC--
Z69624.1/1-66        ---CGUCUGUGAUGUUCUGC------UAUUACCUACAUUGUUUGAUGCUCAU----GAAAGAA---------CCACUG----GCUGAGACGC--
AJ490417.1/3-83      UUUA-CCUAUGAUGAGUUGCGAAAUUUAUUGCCUACAUUGUUUGAUUAACCU----GUGAGAAA-AUUUG--CAACAU-----CUGAGGAUAAA
AJ490418.1/3-83      UUUA-CCUAUGAUGAGUUGUGAAAUUUAUUGCCUACAUUGUUUGACUAACCU----GUGAGAAA-AUUUG--CAACAU-----CUGAGGAUAAA
AJ490420.1/1-84      UUCUGCCAAUGAUGAGUUGCAACAU-UAUUGCCUACAUUGUUUGACAAACAAAUUCAUGAUAAA-AAA-G--CAACAA-----CUGAGGCUUAA
AB028893.1/4087-4152 ---CGUCCAUGAUGUUCCGCAAC------UACCUACAUUGUUUGAUCCUCAU----GAAAGCA---------GCACUG----GCUGAGACGC--
AJ490419.1/2-84      UUUAACCUAUGAUGAGUUGCAAAAUUUAUUGCCUACAUUGUUUGACUAACCU----GUGAGAAACAAUUG--CAACAU-----CUGAGGAUAAA
AJ490416.1/2-87      CUCUGCUUAUGAUGAGUUGCAAUAUCUUUUGCCUACAUUGUCUGACAAAUGUUGUCAUGAUAAU-AUUUG--CAACCU-----CUGAGGCAUAA
FM991913.1/3-63      -----UCUGUGAUGUUCUGC------UAUUACCUACAUUGUUUGAGCCUCAU----GAAAACC---------CCACUG----GCUGAGA-----
X94600.1/100-170     UGGCGUCCAUGAUGUUCCGCAAC------UACCUACAUUGUUUGAUCCUCAU----GAAAGCA---------GCACUG----GCUGAGACGCCA
AF317962.1/1-82      A-AGGCCUAUGAUGAUU--CAAA---UUUUGCCUACAUUGUUUGAUAAACCA----AUGAUAUA-ACUUGUACAAAAUGUUUUCUGAGGCCU-U
JN899108.1/1-65      ---CGUCCGUGAUGUUCCGC------GAUUACCUACAUUGUUUGAUCCUCAU----GAAAACA---------GCACUG----GCUGAGACG---
EU094083.1/1-74      AG-GGCCGAUGAUGCUGUUCAA------UUACCUACAUUGUUUGAUUUUCCU----GUGAGAAA-ACA-G--CUAUAU-----CUGAGGCCCCU
#=GC SS_cons         <<-<<<<________________...__________________________....________._____..______...._____>>>>->>
#=GC RF              uuucGCCuAUGAUGauuUGCAAa...UAUUgCCUACAUUGUUUGAuaaaCaU....GuGAuAaA.AuUUG..CaAcau....gCUGAGGCguaa
//
# STOCKHOLM 1.0

#=GF AC   RF00149
#=GF ID   snoZ103
#=GF DE   Small nucleolar RNA Z103
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   44.00
#=GF TC   44.20
#=GF NC   43.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   This family consists of several snoRNA Z103 sequences which are members of
#=GF CC   the C/D class of snoRNA which contain the C (UGAUGA) and D (CUGA) box
#=GF CC   motifs. This family seems to be found exclusively in plants. C/D box small
#=GF CC   nucleolar RNAs are known to act as a methylation guides for 18S ribosomal
#=GF CC   RNA [1].
#=GF WK   Small_nucleolar_RNA_Z103
#=GF SQ   12



FN596005.1/903411-903317  AUGGAUGUGAUGAUUAUUUCCCCAGAUGAACGACGUUGAUUAUACUGUGCUAUUUCU---UUCUCU-U----UUUGAGA---UUCC-AAGCCAUUAC-UCUGAUCCAU
AC151822.29/114914-115009 AUGGGUGUGAUGAUUAUUUCCCCAGAUGAUCGAAACUGAACAUACUGUGCGAUUUUG----UUUCUCU----UUGGAGA---AAUC-AAGCCAAAUAAUCUGAUCCAU
AC207704.1/39109-39009    AUGGAUGUGAGGACUAUUUCCCCAGAUGAUCGAAGGUGAUAUAACUGUGCUAAUAAA-AUUUCUCCAU----UCAUGGAGAAAUUC-AAGCCAAUAU-UCUGAUCCAU
AJ307919.1/1-98           AUGGAAGUGAAGAUCCUUUCCCCAGAUGAUCGACUACGAUUAUACUGUGCGCAAAUG-UAAUCCCUUU----UCG--GA-GGAUUC-AAGCCAGAAA-UCUGAUCCAU
AJ307921.1/1-95           GAGGAUAUGAUGAUCCUUUCCCCAGAUGAUCGACAAUGAACAUACCGUGCGAUUGUU----UU-CUCU----UAGGAGAU--AAUC-AAGCCAGAAA-UCUGAUCCUC
AJ307916.1/3-96           GAGAAUAUGAUGAUCCUUUCCCCAGAUGAUCGACAAUGAACAUACUGAGCGCUAUUA----UUUCUCC----UUUGAGA----ACC-AAGCCAGUAU-UCUGAUUCUC
AJ307922.1/3-97           GAGGAUAUGACGAUCCUUUCCCCAGAUGAUCGACGAUGAGCAUAAUGUGCGCUAUUG----UU-CUCU----UAAGAGAU--AAUC-AAGCCAGAAC-UAUGAUUCUC
Y11049.1/893-999          UUUGAUGUGACGAUCCUUUCCCCAAAUUACCGACUUUGAUUAUACUGUGCGAUUUUU-CGAGUUCUGUCUCCUCGGAGAUGGCUCUUAAGCCAGAUAUUCUGAUCGAA
AJ307917.1/1-107          UUUGAAGUGAUGAUCCUUUCCCCAAAUUAUCGACUAUGAUUGUACUGUGCGAUUUUUGCAAGCUCU-UCUCUUCGGAGAAGGCUUCUAAGCCAGUAGUUCUGAUCAAA
AJ307923.1/3-96           GAGAAUAUGAUGAUCCUUUCCCCAGAUGAUCGACAAUGAACAUACUGAGCGCUAUUA----UUUCUCU----UUUGAGA----ACC-AAGCCAGUAU-UCUGAUUCUC
AJ309196.1/135-35         AUGGAAGUGACGAUCCUUUCCCCAGAUGAUCGACUAUGAUUAUACAGUGCGCACAAG-UGACCCCUCU----UCGAGGA-GGAUUCCAAGCCAGAAU-UCUGAUCCAU
AJ307918.1/2-99           AUGGAAGUGAGGAUCCUUUCCCCAGCUGAUCGACUAUGAUUAUACUGUGCGCAAAUG-UAAUCCCUCU----UCA--GA-GGAUUC-AAGCCAGAAA-UCUGAUCCAU
#=GC SS_cons              <<<<<____________________________________________________.__________...._______.______.__________._____>>>>>
#=GC RF                   gugGAuGUGAuGAUccUUUCCCCAGAUGAUCGACuaUGAuuAUACUGUGCGauuuuu.uaauuUCUcU....UcggAGA.ggauUC.AAGCCAgaAa.UCUGAUCcac
//
# STOCKHOLM 1.0

#=GF AC   RF00150
#=GF ID   SNORD42
#=GF PI   U42
#=GF DE   Small nucleolar RNA SNORD42
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   39.00
#=GF TC   39.20
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300937;
#=GF DR   snoopy; Danio_rerio300150;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snoRNA U42 is found in intron 3 of the ribosomal protein L23a (RPL23a)
#=GF CC   gene in humans and is also present in mice. U42 is a member of the C/D
#=GF CC   class of snoRNA which contain C (UGAUGA) and D (CUGA) box motifs. Most of
#=GF CC   the members of the box C/D family function in directing site-specific
#=GF CC   2'-O-methylation of substrate RNAs. Although the selection of the target
#=GF CC   nucleotide requires the antisense element and the conserved box D or D' of
#=GF CC   the snoRNA, the methyltransferase activity is supposed to reside in one of
#=GF CC   the protein components [1].
#=GF WK   Small_nucleolar_RNA_SNORD42
#=GF SQ   7


AJ224023.1/1-67           GUGCA-UAUGAUGGA-AAAGUUUUAA-UCUCC-U-----GACACUUGUGAUGUCUUCAAAGGAACCACU--GAUGCAC
AC004807.1/1740-1672      GUGCA-UAUGAUGGAAAAAAUCUGAAGUCUCC-U-----GAGACCUGUGAUGUCUUCAAAGGAACCACU--GAUGCAC
AC124016.3/72783-72715    UAGCA-UAUGAUGGA-AAAAUCUUAA-UCUUC-U-----GAGACUUGUGAUGUCUUCAAAGGAACCACUUCAAUGCAA
Z75890.1/1272-1207        -AGCCCUAAAAUGGAAAAAAUUUAAA-AUUAC-UUA---GACAA-UGUGAUGUCAUCAAAGGAACC-CU--AA-GUA-
AL591070.19/168628-168690 -UGCA-AAUGAUGGA-AAA--CUCAA-UGUUU-G-----GAAAAGAAUGACACCAACAAAGGAACCACU--GAUGCU-
X96641.1/1-62             -GGCU-AAUGAUGGAAAAA-----------UCAUUAUUGGAAAAGAAUGACAUGAACAAAGGAACCACU--GAAGUG-
AF001689.1/3146-3209      GGGGU-AAUGAUGGAAAAA-----------UCAUUAUUGGAAAAGAAUGACAUGAACAAAGGAACCACU--GAAGUGC
#=GC SS_cons              <<<<<.____________________._____._.....______________________________..__>>>>>
#=GC RF                   guGCa.uAUGAUGGAAAAAAUcUuAA.UcUuC.U.....GAaAagugUGAugUcauCAAAGGAACCACU..GAuGCac
//
# STOCKHOLM 1.0

#=GF AC   RF00151
#=GF ID   SNORD58
#=GF PI   U58
#=GF DE   Small nucleolar RNA SNORD58
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   42.00
#=GF TC   42.00
#=GF NC   41.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00064
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300308;
#=GF DR   snoopy; Oryzias_latipes300096;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell. 1996;85:1077-1088.
#=GF CC   snoRNA U58 is found in introns 1, 3 and 6 of the ribosomal protein RPL17
#=GF CC   gene in humans. U58 is a member of the C/D class of snoRNA which contain C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs. U58A and U58B are predicted to guide 2'O-ribose methylation of the
#=GF CC   large 28S rRNA subunit on position G4198 [2]. Although the selection of
#=GF CC   the target nucleotide requires the antisense element and the conserved box
#=GF CC   D or D' of the snoRNA, the methyltransferase activity is supposed to
#=GF CC   reside in one of the protein components [1].
#=GF WK   Small_nucleolar_RNA_SNORD58
#=GF SQ   33


AB061824.1/2400-2464         CUGCAGUGAUGAC-UUUCUUGGGACACCUUUGGA-------UUUACCGUG------AAAAUU--AA--UA-------A--A----U---UCUGAGCAGC
AB061824.1/4441-4504         UUGCUGUGAUGAC-UAUCUUAGGACACCUUUGGA-------AUAACUAUG------AAAG-A--AA--AC-------U--A----U---UCUGAGCAAC
X96657.1/1-65                CUGCAGUGAUGAC-UUUCUUAGGACACCUUUGGA-------UUUACCGUG------AAAAUU--AA--UA-------A--A----U---UCUGAGCAGC
AAIY01536853.1/1851-1915     CUGCUGUGAUGAC-UUUCUUAGGACACCUUUGGA-------UUAACCAUG------AAAAUG--AU--AA-------C--A----U---UCUGAGCAGC
AAPN01258164.1/1657-1721     UUGCUGUGAUGAC-AAUCUUAGGACACCUUUGGA-------UUAACCGUG------AAAAGA--AA--UA-------U--A----U---UCUGAGCAAU
AAQQ01338041.1/131-195       CUGCAGUGAUGCC-UUUCUUAGGACACCUUUGGA-------UUUACCAUG------AAAACU--AA--UA-------C--A----U---UCUGAGCAGC
AAHX01095982.1/12960-12896   UUGCUGUGAUGAC-UAUCUUAGGACACCUUUGGA-------UUAACCGUG------AAAUAA--AA--CA-------U--G----U---UCUGAGCAAC
AALT01408031.1/140-204       UUGCUGUGAUGAC-UAACUUAGGACACCUUUGGA-------AUAACCGUG------AAAGGA--AA--AC-------U--G----U---UCUGAGCAAC
AAPY01347359.1/2969-3033     CUGCAAUGAUGCC-AUUCUUAGGACACCUUUGGA-------UUUACCAUG------AAAAGU--AA--UA-------A--A----U---UCUGAGCAGC
AAFC03127110.1/4122-4059     UUGCUGUGAUGAC-UAACUUAGGACACCUUUGGA-------AUAACCAUG------AAAG-G--AA--GC-------U--A----U---UCUGAGCAAC
CAAA01155521.1/5239-5175     CUGCAGUGAUGAC-UAUCUUAGGACACCUUUGGA-------UUUACCGUG------AAAAGA--AG--UA-------A--C----C---UCUGAGCAGC
AANG01178038.1/399-335       CUGCAGUGAUGCG-UUUCUUAGGACACCUUUGGA-------UUUACCAUG------AAAACU--AA--UC-------A--G----U---UCUGAGCAGU
AANN01073482.1/2128-2192     CUGCGGUGAUGCU-UCUCUUAGGACACCUUUGGA-------UUUACCGUG------AAAACA--AA--CC-------A--G----U---UCUGAGCAGC
AAFR03048153.1/100411-100345 UUGCUAUGAUGAC-AAUCUUAGGACACCUUUGGA-------AUAACCAUG------AAAAAA--AA--CA-------UGUA----U---UCUGAGCAAC
AACN010483159.1/1092-1027    UUGCUGUGAUGAC-CAUCUUAGGACACCUUUGGA-------UUAACCAUG------AAAAGA--AAC-UG-------U--G----U---UCUGAGCAAC
BAAE01163555.1/431-365       CUGCAGUGAUGAC-CUUCUUAGGACACCUUUGGA-------AUAAAGAUG------AAAAGACGAA--AG-------A--A----A---UCUGAGCAGU
AAYZ01159458.1/15862-15800   UUGCAGUGAUGAC--AUCUUAGGACACCUUUGGA-------AUAGCCGUG------AAAG-C--AA--AC-------U--C----U---GCUGAGCAAC
AANU01182853.1/6230-6295     CUGCGAUGAUGGCAUUUCUUAGGACACCUUUGGA-------UUAAUCAUG------AAAACA--AC--UA-------C--U----C---UCUGAGCAGC
AAVX01050025.1/2444-2515     CUGCAAUGAUGAC-AAUCUUAGGACACCUUUGGA-------UUAAUCAUG------AAAACA--AA--UAGUUUUUUA--A----A---UCUGAGCUGC
CAAE01014575.1/25624-25559   CUGCGGUGAUGAC-UAUCUUAGGACACCUUUGGA-------UAAACGAUG------AAACUA--CU--CA-------U--G----UG--UCUGAGCACC
CR339054.14/98042-98112      GUACAGUGAUGAC-AUUCUUAGGACACCUUUGGA-------GGUUAUGACUAAUGAAAAGAA--AA--CA-------U--G----U---UCUGAGUACU
AANH01013632.1/7026-6959     UGGCUGUGAUGA--UGUCUUAGGACACCUUUGAA-------UUACGCAUG------AAAAUG--AC--UA-------U--UAAAGA---UCUGAGCUUC
AAGD02000363.1/27898-27965   GAGUUGUGAUGAC-UUACUUAGGACACCUUUGGAGGGUUUCGGUCCGCUG------AAAAGA--AA--AA-------U--A----G---U----ACGCC
AAWR02022472.1/27920-27857   UUGCUGUGAUGAC-UAACUUAGGACACCUUUGGA-------ACAACCGUG------AAAG-A--AU--AC-------U--A----U---UCUGAGCAAC
AAKN02020102.1/53794-53858   UUGCUGUGAUAAC-UAUCUUAGGACACCUUUGGA-------AUCACCAUG------AAAGGA--AA--AC-------U--A----U---UCUGAGCAAC
AAGV020207207.1/1491-1555    CUGCAGUGAUGAC-UUUCUUAGGACACCUUUGGA-------UUUACCAUG------AAAAUG--AA--CA-------A--G----U---UCUGAGCAGU
CAAB02002186.1/4011-3945     UUGCACUGAUGAC-CA-CUUAGGACACCUUUGGA-------UGAACCAUG------AAAACA--AA--CC-------G--U----UGAACCUGAGCAGC
AAGU03013227.1/18191-18255   UUGCAGUGAUGAC-AAUCUUAGGACACCUUUGGA-------UUAACCAUG------AAAAAA--AA--AA-------U--A----U---UCUGAGCAAC
AAQR03027268.1/131-194       UUGCUAUGAUGAC-UAUCUUAGGACACCUUUGGA-------UUAACCGUG------AAAG-G--AA--AC-------U--A----U---UCUGAGCAAC
AAPE02009055.1/16093-16157   CUGCAGUGAUGUC-UUUCUUAGGACACCUUUGGA-------UUGACCAUG------AAAACC--AA--UC-------A--A----U---UCUGAGCAGC
AL121809.6/172081-172016     CUGUGAUGAUGGCAUUUCUUAGGACAAUUUUGGA-------UUAAUUAUG------AAAACA--AC--UA-------C--U----C---UCUGAGCAAU
EU240248.1/1-67              UUGCUGUGAUGAC-UUUCUUAGGACACCUUUGGA-------UUCAAUGUG------AAAAGA--AACUUG-------U--A----U---UCUGAGCAAU
AAGW02032386.1/7736-7673     UUGCUGUGAUGGC-UAUCUUAGGACACCUUUGGA-------AUAACCGUG------AAAG-G--AA--AU-------U--G----U---UCUGAGCAAC
#=GC SS_cons                 <<<<_________.____________________......._________......______..__..__......._.._...._..._____>>>>:
#=GC RF                      cuGCaGUGAUGAC.uuUCUUAGGACACCUUUGGA.......uUaAccaUG......AAAAuA..AA..uA.......u..a....u...UCUGAGCagC
//
# STOCKHOLM 1.0

#=GF AC   RF00152
#=GF ID   SNORD79
#=GF PI   U79
#=GF DE   Small nucleolar RNA SNORD79
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   47.00
#=GF TC   47.10
#=GF NC   45.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00069
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   9819378
#=GF RT   Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene
#=GF RT   and a member of the 5'-terminal oligopyrimidine gene family reveals common
#=GF RT   features of snoRNA host genes.
#=GF RA   Smith CM, Steitz JA
#=GF RL   Mol Cell Biol 1998;18:6897-6909.
#=GF CC   snoRNA U79 or Z22 is found in intron 7 of the gas5 gene in humans and is
#=GF CC   also present in mice. U79 is a member of the C/D class of snoRNA which
#=GF CC   contain C (UGAUGA) and D (CUGA) box motifs. Most of the members of the C/D
#=GF CC   box family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs. Although the selection of the target nucleotide requires
#=GF CC   the antisense element and the conserved box D or D' of the snoRNA, the
#=GF CC   methyltransferase activity is supposed to reside in one of the protein
#=GF CC   components [1].
#=GF WK   Small_nucleolar_RNA_SNORD79
#=GF SQ   28


AF141346.1/2553-2637         UACUGUUAGUGAUGA-UU-UU-AAAAUUAAAGCAGAUGGGAAUCCCUCUGAGAAAGAAAAUGGAGAUUAAU---CUU--AAACUGAAACAGUA
AK025846.1/2178-2094         UACUGUUAGUGAUGA-UU-UU-AAAAUUAAAGCAGAUGGGAAUCUCUCUGAGAAAGAAAAUGGAGAUUAAU---CUU--AAACUGAAACAGUA
X67268.1/1201-1284           UACUGUUAGUGAUGAUCA-AU-AAAGUUAAA-CAGAUGGGAAUCUCUCUGAAUAAGA--UUGAAGAUUGAUU--GUU--AAGCUGAAACAGUA
AL591203.15/10289-10373      UACUGUUAGUGAUGA-UU-UU-AAAAUUAAAGCAGAUGGGAAUCUCUCUGAGAAAGAAAAUGGAGAUUAAU---CUU--AAACUGAAACAGUA
AJ224027.1/1-88              UACUGUUAGUGAUGAUUU-UA-AAAUUAAAAGCAGAUGGGAAUCUCUCUGAGAAAGAAAAUGGGAGAUUAAUC-CUU--AACCUGAAACAGUA
AJ224034.1/1-84              UACUGUUAGUGAUGAUCA-AU-AAAGUUAAA-CAGAUGGGAAUCUCUCUGAAUAAGA--UUGAAGAUUGAUU--GUU--AAGCUGAAACAGUA
AC143509.11/60126-60044      UACUGUUAGUGAUGA-UU-UU-AAAAUUAAAGCAGAUGGGAAUCUCUCUGA--AAGAAAAUGGAGAUUAAU---CUU--AAACUGAAACAGUA
AAQQ01328837.1/1386-1467     UGCUGUUAAUGAUGA--U-UU-AAAGUUGAAACAGAUGGGAAUCUCUCUGAAAGAGA--AUGAAGAUUAAC---UUU--AAACUGAAACAGUA
AAPY01728088.1/8475-8559     UGCUGUUAGUGAUGAUUUGUA-AAAGUUAAAACAGAUGGGAAUCUCUCUGAAAGAGA--AUGAAGAUUAAU---UUU--AAACUGAAACAGUA
ABDC01278790.1/2991-3074     UGCUGUUAGUGAUGAUUU-UC-AAAGUAACAACAGAUGGGAAUCUCUCUGAAAGAGA--AUGAAGGUUAAU---UUG--GAACUGAAACAGUA
AAFC03120161.1/29694-29774   UACUGUUGGUGAUGAUUU-UU-AUAAUAAAA-CAGAUGGGAAUCUCUCUGAAAAAGA--AUGAAGUUUUUA-----A--AAACUGAAACAGUA
AANG01024596.1/846-762       UACUGUUAGUGAUGAUUU-UUGAAAUUAAAAACAGAUGGGAAUCUCUCUGAAAAAGA--GUGAAGAUUUCU---UAA--ACGCUGAAACAGUA
AAFR03026464.1/110086-110006 UACUGUUGGUGAUGAUUU-CU-AUAUUAAAA-CA-AUGGGAAUCUCUCUGAAAGAGA--AUGAGGAUU--UU--CUU--UUUCUGAAACAGUA
AACN010598678.1/574-650      UGCUGUUAGUGAUGAUUU-UU-GAAA------UAGAUGGGAAUCUCUCUGAAAAAGA--GUGAAGAUUUUU----AA--AAACUGAAACAGUA
AAPN01008930.1/65324-65247   UGCUGUUCAUGAUGAUUU-GU-UAAAAUCAA-----UGGGAAUCUCUCUG---AAGAGAAUGAAGCCAGUU---UUU--AUACUGAAACAGUA
AAYZ01154866.1/4201-4119     GGCUGUUGAUGAUGA--C-AU-ACAGUUAAAACAGAUGGGAAUCUCUCUGAAAGAGG--AUGAGGACACCAC--UCU--ACACUGAAACAGUG
AANN01730354.1/1087-1011     UGCUGUUAAUGAUGA--------AUUUUUAAAUAGAUGGGAAUCUCUCUGAAGAAGA--GUGAUGAUUACA----AA--ACUCUGAAACAGUG
AAIY01534871.1/1182-1105     UGCUGUUGAUGAUGA-CU-AU-AAAU--------GAUGGGAAUCUCUCUGA--AAGAAAAUGAAGACUUAAUAUUGG--AAACUGAAACAGUA
CAAE01014995.1/850833-850752 AACUGUUAAUGAUGA--U-CU-UGUUUUAAAAACAAUGGGAAUCUCUCUGAAUUAGA--GUGAAAGAUGAC---UUU--UAACUGACACAGUA
BAAE01161713.1/2896-2976     AACUGUUGAUGAUGAUUC-UU-GUUGUGAAA--CAAUGGGAAUCUCUCUGAGAAA-A--GUGAAGAGGACU---UUU--GUUCUGAUGCAGUG
AANH01003589.1/57785-57715   AACUGUAAAUGAUGA-----------------UACUUGGGAAUCUCUCUGAAAAAAG--UGAAAGACUAACUU-UUU--UUACUGAUACAGAA
AAVX01500816.1/492-570       AGCAGAUAUUAAUGAUGU-GA-AAAGCAU-------UGGGAAUCUCUCUGACAAAAA--GUGAAAGAGACGUG-UUG--UUGCUGAAGCUGCG
AAHX01076292.1/14169-14085   UACUGUUAGUGAUGAUCA-AU-UAAGUUAAAACAGAUGGGAAUCUCUCUGAACAACA--UUGGAGAUUGAUU--GUU--AAGCUGAAACAGUA
CU467861.6/35168-35250       GACUGUUUAUGAUGAUUG-UU-AAAUGAAAC---AAUGGGAAUCUCUCUGAAUUAGA--CUGAAAGAGACAUC-UUU--AUGCUGAAACAGUG
AAGV020273689.1/2404-2485    UGCUGUUGAUGAUGGUUU-UU-UAAAUUAAA--AAAUGGGAAUCUCUCUGAAAGAGA--GUGAAGAUGAAU---AUU--UAACUGAAACAGUA
AAWR02036950.1/20384-20300   UGCUGUUAGUGAUGAUUU-UU-GAAAAUAA--CAGAUGGGAAUCUCUCUGAAAAACA--AUGAAGAUUAAUU--UUUAAAAACUGAAACAGUA
AAWZ02040398.1/4745-4667     UACUGUUAAUGAUGAUAU-UG-UAUGAAACA----AUGGGAAUCUCUCUGAAAGUUA--AUGAUGAAAGAA----UU--AUACUGAAACAGUA
AADN03005691.1/152043-151965 UACUGUUCAUGAUGAUUA-GU-UCUACACAA-----UGGGAAUCUCUCUGAAAGAGA---CUGAGGAGGACU--CUU--GAUCUGAAACAGUA
#=GC SS_cons                 <<<<<<<___________.__._________._________________________..____________...___.._______>>>>>>>
#=GC RF                      uaCUGUuaaUGAUGAUuU.uU.aAAauuAAA.cAgAUGGGAAUCUCUCUGAAAaAgA..aUGAAGauuaau...uUU..aaaCUGAaACAGua
//
# STOCKHOLM 1.0

#=GF AC   RF00153
#=GF ID   SNORD62
#=GF PI   U62
#=GF DE   Small nucleolar RNA SNORD62
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   39.00
#=GF TC   40.30
#=GF NC   37.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00068
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300200;
#=GF DR   snoopy; Echinops_telfairi300872;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   snoRNA U62 is found in both humans and mice. U62 is a member of the C/D
#=GF CC   class of snoRNA which contain C (UGAUGA) and D (CUGA) box motifs. Most of
#=GF CC   the members of the box C/D family function in directing site-specific
#=GF CC   2'-O-methylation of substrate RNAs. Although the selection of the target
#=GF CC   nucleotide requires the antisense element and the conserved box D or D' of
#=GF CC   the snoRNA, the methyltransferase activity is supposed to reside in one of
#=GF CC   the protein components [1].
#=GF WK   Small_nucleolar_RNA_SNORD62
#=GF SQ   14


AL929554.20/7608-7693        UCUUAGUGACAUAAUUCUAAUAGUUUGUUCCGACCUUCCACUGUGGACUCAAUAGCAGGG-AGAUGAAGAGGACAGUGAUUGCAUGA
AL358781.19/94752-94837      UCUCAGUGAUGUAAUUCCAAUAGAUCCUUCUGACCCUCCACUGUGGACUCAAUAGCAGGG-AGAUGAAGAGGACAGUGACUGAGAGA
U72851.1/1-86                UCUCAGUGAUGUAAUUCCAAUAGAUCCUUCUGACCCUCCACUGUGGACUCAAUAGCAGGG-AGAUGAAGAGGACAGUGACUGAGAGA
AAQQ01700835.1/2928-2843     CCUCAGUGAUGUAAUUCCAAUAGAUCCUUCUGACCCUCCACUGUGGACUCAACGGCAGGG-GGAUGAAGAGAACAGUGACUGAGAGG
AAFC03050704.1/42408-42493   UCUCAGUGAUGCGAUUCCAAUAGAUCCUUCUGACCCUCCACUGUGGACUCAAUAGCAGGG-AGAUGAAGAGGAACGUGACCGAGAGA
AAIY01713494.1/2654-2739     UCUCAGUGAUGUAAUUCCAAUAGACCCUUCUGACCCUCCUCUGUGCACUCAGUCGCAGUG-AGAUGAAGAGGACUGUGAUUGAGAGA
ABDC01183880.1/1070-986      UCUCAGUGAUGUACUUCCAGUAGAUCCUUCUGACC-UCUACUGUGGACUCAAUAGCAGGG-AGAUGAAGAGGACAGUGCCGGAGAGA
AANG01443650.1/3792-3875     UCUCAAUGAUGCGAUUCCAAUAGAUCCUUCUGACCCUCCACUGUGGACUCAAC-GCAGGG-GG-UGAAGAGGAACGUGACUGAGAGA
AAFR03046596.1/196392-196475 UCUCUAUGAUGUA-UUCCAAUAGAUCCUUCUGACCCUUCAAUGUGUACUCAGUAAAAGGG-AAAUGAAGAG-ACAAUACCUGAGAGA
AAPN01120941.1/11917-12002   UCUCUAUGAUGUA-UUCCAAUAGAUCCUUCUGACCCUCCAGUGUGCAUUCCAAAGAAGGGGAAAUGAAGAGAUGUGUGACUGAGAGA
AAGU03017565.1/79846-79761   UCUCAAUGAUGUAAUUCCAAUAGAUUCUUCUGACCCUCCACUGUGGGCUCAAUAGCAGGG-AGAUGAAGAGGAGAGUGACUGAGAGA
AAQR03116815.1/24501-24416   UCUCAGUGAUGUGUUUCCAAUAGAUCCUUCUAAUCCUGCACUGUGGACUCAAUAGCAGGG-AGAUGACGAGGACAGUGACUGAGAGA
AAPE02052684.1/3793-3708     UCUCAAUGAUGGAAUCCCAAUAGAUCCUUCUGACCCUCCACUGUGGACUCAAUAGCAGGG-AGAUGAAGAGGAACGUGGCUGAGAGA
AAEX03006829.1/5987-5905     UCUCCGUGAUGUAAUUCCAAUAGAUCCUUCUGACC--CCCCCGUGGACUCAAU-GCAGGG-GGAUGAAGAGGAAAGUGACUGAGAGA
#=GC SS_cons                 <<<<________________________________________________________.______________________>>>>
#=GC RF                      uCUCagUGAUGUAAUUCCAAUAGAUCCUUCUGACCCUCCAcUGUGgACUCAAUAGcAGGG.AGAUGAAGAGGAcaGUGACUGAGAGa
//
# STOCKHOLM 1.0

#=GF AC   RF00154
#=GF ID   SNORD63
#=GF PI   U63
#=GF DE   Small nucleolar RNA SNORD63
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   43.00
#=GF TC   43.20
#=GF NC   40.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300732;
#=GF DR   snoopy; Echinops_telfairi300783;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   snoRNA U63 is found in both humans and mice. U63 is a member of the C/D
#=GF CC   class of snoRNA which contain C (UGAUGA) and D (CUGA) box motifs. Most of
#=GF CC   the members of the box C/D family function in directing site-specific
#=GF CC   2'-O-methylation of substrate RNAs. Although the selection of the target
#=GF CC   nucleotide requires the antisense element and the conserved box D or D' of
#=GF CC   the snoRNA, the methyltransferase activity is supposed to reside in one of
#=GF CC   the protein components [1].
#=GF WK   Small_nucleolar_RNA_SNORD63
#=GF SQ   23


U72852.1/1-68                GUGCAAUGAUGUAUU---UUAU---U---CAACACAUCAUUCUGAA---A---G----AACG--U--GUG---GAAAAC----UAAUGACUGAGCACA
AC114820.4/4566-4635         GUGCGAUGAUGCAUU---UUAU---U---CAACACAUCAUUCUGAA---A---A----UAGA--U--GUGU-AGAGAAA----UGAUAACUGAGCACA
AANU01297394.1/4437-4506     GUGCGAUGAUGUAUU---UUAU---U---CAACACAUCAUUCUGAA---A---G----AACA--U--AUGU-GGAAAAA----UAAUGACUGAGCACA
AAHX01094491.1/84642-84714   GUGCAAUGAUGCAUU---UUAU---UAAUCAACACAUCAUUCUGAA---A---G----CAGA--U--GUGU-AGAGAAG----UAAUAACUGAGCACA
ABDC01145604.1/562-488       GUGCAAUGAUGCAUU---UUAUUCAU---CAACACAUCAUUCUGAA---A---G----CACAGAU--GUGU-AGAAUAC----UAAAGACUGAGCACA
AAIY01452900.1/1303-1232     GUGCAGUGAUGCAGA---UACA---U---CAACACAUCAUUCUGAA---A---AGA--CAGA--U--GUGU-AGAAAAU----AAAUGACUGAGCACA
AAYZ01034644.1/1632-1557     GUGCAAUGAUGCAUU---UUAG---UUAUCAACACAUCAUUCUGAACUCA---U----GAGA--U--GUGU-GUAAAAU----UAAUGACUGAGCACA
AALT01139724.1/447-521       GUGCAGUGAUGCAUUACAUUAA---U---CAACACAUCAUUCUGAA---A---AGA--CAGA--U--GUGU-AGAAAAC----UAAUGACUGAGCAUG
AAPY01036059.1/4348-4272     GUGCAAUGAUGCAUU---UUAUUCAU---CAACACAUCAUUCUGAA---AAGCA----CAGA--U--GUGU-AGAAGACU---UAAUGACUGAGCACA
AANN01251366.1/699-626       GUGCAGUGAUGCAUU---UUAUUCAU---CAACACAUCAUUCUGAA---A---A----UACA--G--AUGUGUGGAAAA----UUAGUACUGAGCACA
AAFC03118698.1/18323-18252   GUGCAAUGAUGCAUU---GUA----U---CAACCCAUCAUUCUGAU---A---AGA--UAGG--U--AUGU-GGAAAACU---UAAUGACUGAGCACA
AAPN01346672.1/2000-1929     GUGCCGUGAUGGAUU---UAACGA-U---CGACACAUCAUUCCGAA---A---C----GAGC--G--GUGU-GGACAGC----UAAUGACUGAGCACA
AAQQ01034281.1/3854-3783     GUGCAAUGAUG--UU---UUUG---U---CAACACAUCAUUCUGAA---G---GAAAAAGUA--U--GUGA-UGACAUC----CUAUGACUGAGCACA
AAVX01073374.1/1163-1089     GUGCUGUGAUGUUAU---CAUA---U---CAACACAUCAUUCUGAU---G---CA---AAAC--C--AUGG-AGAGAAUCAUCCAAUAACUGAGCACA
AAWR02002436.1/59167-59241   GUGCGAUGAUGCAUU---UUAC---UCAUCAACACAUCAUUCUGAA---A---GGA--CAGG--U--GUGU-GGAAAAC----UAAUGACUGAGCACA
AAGV020172891.1/1027-959     GUGCAGUGAUGUAUU---U--G---C---CAACACAUCAUUCUGAA---G---A----AAAA--U--GUGU-GGUAACUU---CUGUGACUGAGCACA
AAKN02009865.1/21186-21114   GUGCAGUGAUGCAUU---UUAU---U---CAACACAUCAUUCUCAA---A---G----UACA--GAAGUGU-GGAAAACU---UAAUGACUGAGCACA
AAWZ02014064.1/15185-15118   GUGCUGUGAUGCAAU---UAUA---U---CAACGCCUCAUUCUGAA---A---U----GUUA--U--GUG---GAAGAU----UGAUGACUGAGCAUG
AAGU03004619.1/27324-27253   GUGCAAUGAUGUAUU---U--G---C---CAACACAUCAUUCUGAA---G---AAAAGUAUG--U--GUGG-UGACUUU----UUAUCACUGAGCACA
AAGW02027768.1/36469-36543   GUGCAGUGAUGCAUU---UUAU---UUAACAACACAUCAUUCUGAA---CUC-A----CAGA--U--GUGU-GGAGAAC----UAAUGACUGAGCACA
AAPE02012939.1/106680-106754 GUGCAAUGAUGCAUU---CUAUUCAU---CAACACAUCAUUCUGAA---A---AGA--CAGG--U--GUGU-AGAAAGU----UAAUGACUGAGCACG
AACN011074855.1/103-177      GUGCAAUGAUGGAUU---UUAU---UUAUCAACACAUCAUUCUGAU---A---AGA--UAGG--U--GUGU-GGAAAAC----UAAUGACUGAGCACA
AADN03006685.1/295418-295487 GUGCCAUGAUGUAAU------G---U---CAACACAUCAUUCUGAA---G---AG---GAAU--U--GUGU-GGAGACCUU--CUGUAACUGAGCACA
#=GC SS_cons                 <<<<___________...____..._..._________________..._..._....____.._..____._______....__________>>>>:
#=GC RF                      GUGCaaUGAUGcAUU...UUAu...U...CAACACAUCAUUCUGAA...A...a....uAga..U..GUGU.aGAaAAc....UaAUgACUGAGCACA
//
# STOCKHOLM 1.0

#=GF AC   RF00155
#=GF ID   SNORA66
#=GF PI   U66
#=GF DE   Small nucleolar RNA SNORA66
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   45.00
#=GF TC   45.80
#=GF NC   43.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF CL   CL00038
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300772;
#=GF DR   snoopy; Gallus_gallus300121;
#=GF RN   [1]
#=GF RM   10902565
#=GF RT   Pseudouridine in RNA: what, where, how, and why.
#=GF RA   Charette M, Gray MW
#=GF RL   IUBMB Life 2000;49:341-351.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snoRNA U66 is found in both humans and mice. U66 is a member of the H/ACA
#=GF CC   class of snoRNA which contain H (ANANNA) and ACA box motifs. H/ACA box
#=GF CC   snoRNAs are involved in the conversion of uridines to pseudouridines
#=GF CC   (5-ribosyluracil) a constituent of structural RNAs (transfer, ribosomal,
#=GF CC   small nuclear, and small nucleolar) [1,2].
#=GF WK   Small_nucleolar_RNA_SNORA66
#=GF SQ   25


U66590.1/515-647           GUGCAAACUCGAUCACUAGCUCUGCGUGAUGUGGCAGAAGCAAAGGGAACCACGUUUGCAAAAGUAACUGUGGUGAUGGAAAUGUG----UAC-CCUCAGA-----CACUACUGAGGUGGUUCUUU-CUAUC-CUAGUACAGCUC
Y11160.1/1-133             GUGCAAACUCGAUCACUAGCUCUGCGUGAUGUGGCAGAAGCAAAGGGAACCAGGUUUGCAAAAGUAACUGUGGUGAUGGAAAUGUG---UUAG-CCUCAGA-----CACUACUGAGGUGGUUCUUU-CUAUC-CUAGUACAG-UC
AL162740.13/8947-9079      GUGCAAACUCGAUCACUAGCUCUGCGUGAUGUGGCAGAAGCGAAGGGAACCAGGUUUGCAAAAGUAACUGUGGUGAUGGAAAUGUG---UUAG-CCUCAGA-----CACUACUGAGGUGGUUCUUU-CUAUC-CUAGUACAG-UC
ABDC01226271.1/3744-3876   GUGCAAACUCGAUCACUAGCUCUGCCUGAUGUGGCAGAAGCUAAGGGAACCAGGUUUGCUAAAGUAAUUAUGGUGAUAGAAAUGUA---CUAG-CCUCAGA-----UGUUACUGAGGUUGCCCAUU-CUAUC-UUAGUACAG-UA
AAFC03018486.1/23431-23299 GUGCAAACUCGAUCACUAGCUCUGCAUGAUGUUGCAGAGGUGAGGGGAACCAGGUUUGCUAAAGUAAUUGUGGUGAUAGAAAUGUA---UUAG-CCUCGGA-----UGCUACCGAGGUGGCUCAUU-CUAUC-CCAGUACAU-UG
AANN01696725.1/1146-1278   GUGCAAACUCGAUCACUAACUCUGCAUGAAGUUGCAGAAGUGAGGGGAACCAGGUUUGCUAAAGUAAUUGUGGUGAUAGAAAUGUA---UUCG-UCUCAGA-----AGCUACUGAGGUGGCCUAUU-CUAUC-CUAGUACAG-UA
AAIY01307005.1/635-766     UUGCAAACUCGAUCACUAGCUCUGCAUGAUGUUGCAGAAGC-AAGGGAACCAGGUUUGCUAAAGUAACUGUGGGGAUAGUAAUGGU---UUAG-CCUCAGG-----GACUACUGAGGUGGCCAGUU-CUGUC-CUACUACAG-UA
AALT01388369.1/2073-2205   GUGCAAACUCGAUCACUAACUCUGCAUGAUGUUGCAGAUGUGAGGGGAACCAGGUUUGCUAAAGUAACUGCAGUGAUAGAAAUGGG---UUAA-CCUCAGC-----UCCUACUGAGGUUGCUUACU-CUAUC-CUACUACAG-GG
AAHY01047828.1/11585-11454 GAGCAAACUCGAUCACUAGCUCUGCAUAAUGUGGCAGCAGCUGAGGGAACCAGGUUUGCUAGAGUAAUUGUGGUGACAGCAAUGUG---CCAA-CCUCAGA-----AGCUACUGAGGUGCCCAUU--CUGUU-ACAGUACAG-UC
AAPY01329497.1/3482-3350   GUGCAAACUCGAUCACUAGCUCUGCGUGAUGUGGCAGACGCUAAGGGAACCAGGUUUGCUAAAGUAAUUUUGGUGAUAGAAAUAUGUAGUUAG-CCUCAA-------GCUAUUGAGGUGGCCCAUU-CUAUC-CU-GUACAG-UA
AACN010836164.1/579-715    GUGCAAACUCGAUCACUAGCUCUGCAUGAUGUUGCAGAAGUGAGGGGAACCAGGUUUGCUAAAGUAAUUGUGGUGAUAGAAAUGUA---UUAG-CCUCAGAAGGU-ACUUACUGAGCUGACCUAUU-CUAUC-CCAUUACAG-UG
AAYZ01225442.1/5165-5033   GUGCAAACUCGAUCACUAGCUCUGCGUCCUGUGGCAGAAGCGAGGGGAACCAGGUUUGCUAAAGUAAUUGUGGGGCUAGCACCGUG---UGAA-CCUCGGA-----AGCUGCUGAGGUGGCCCGGG-CUACC-CCAGGACAG-UG
AAFR03054727.1/32552-32414 UUGCAAACUCGAUCACUAGCUCUGCAUGAUGUUGCGGAAGCAAGGGGAACCAGGUUUGCUAAAGCAAUUAUGGUGAUAGAAAUUGA---UUUG-CCUCAGAAUUGACAUUUUUGAGGCGCCUCAUU-CUAUCCCUAAGACAA-GA
AAQQ01616572.1/7440-7572   UACAAAAAUCUGUCACUAGCUCUGCAUGACAUGGCAGAAACUAAGGGAACAGUGUUUGAUAGAGUAAUUGCAAGAAUAGGAAUGUA---UUAG-CCUCAGA-----AGUUACUGAGGUGGCCCAUU-CUAUC-CUAGCACAG-UG
AAPN01052944.1/4883-4749   UUGCAAACUCGAUCACUAGCUCUGCAUGGUGUUGCAGAAGCAAGGGGAACCAGGUUUGCUAAAGAAAGUGAGGAGAUGGAAAUCUU---UCGG-CCUUAGAGG---AAAUGUCGGGGCUGUCUUUU-CUCUC-UCCCUACAC-GC
AAGV020115838.1/5847-5715  GUGCAAACUCGAUCACUAGCUCUGCAUGAAGUUGCAGAAGCAAGGGGAACCAGGUUUGCUAAAGUAAUUGUGGUGAUAGAAAUGUA---UUAG-CCUCAGG-----AACUACUGGGGUGGCCCAUU-CUAUC-CUAAUACAG-UG
AAHX01077750.1/82061-82192 GUGCAAACUCGAUCACUAGCUCUGCAUGAUGUGGCAGCAGCUAAGGGAACCAGGUUUGCUAGAGUAACUGUGGUGAUAGCAAUGUA---CCAA-CCUCAGG-----AGCUACUGAGGUGCCCAUU--CUGUC-CCAGUACAG-UC
AAKN02004094.1/14527-14659 GUGCAAACUCGAUCACUAGCUCUGCAUGAUGUGGCAGAAGCUAAGGGAACCAGGUUUGCUAAAGUAAUUGUGGUGAUAGGACUGUA---UUAG-CCUCAGA-----AGCUACUGGGGUAGUUCGUU-CUAUC-CUCAUAUAG-UA
AAWR02017339.1/20769-20637 GUGCAAACUCGAUCACUAACUCUGCAUGAUGUUGCAGAAGUGAAGGGAACCAGGUUUGCUAAAGUAAUGGUGGUGAUAGAAACAUA---UUAG-CCUCAGA-----AGCUACUGAGGUGGCCCAUU-CUAUC-CCAGUACAG-CG
AAWZ02025313.1/15384-15520 UUGCAAACUCGAUCACUGGCUCUGCAUGCUGUGGCAGAAGCAAGGGGAAC-AGGUUUGCAAAAGUAAAUAUGGUAACAGAACCAUA---CCAG-CCUUAGAACAGACAAUACUAAGGCUGUUUAGU-CUGUG-CCAUGACAA-AA
EU240237.1/1-137           UUGCAAACUCGAUCACUAGCUCUGCAUGAUGUUGCAGAAGCAAGGGGAAC-AGGUUUGCUAAAGUAAACAUGGUAAUAGAACCAUA---UUAG-CCUUAGAAAUCAAAUGAUUGGGGCUGUUAAUU-CUAUA-CCAUGAUAA-GG
AAQR03022939.1/230-98      GUGCAAACUCGAUCACUGGCUCUGCAUGAUGUGGCAGGAGCUAAGGGAACCAGGUUUGCUAAAGUAAUUAUGGUGAUAGGAAUGUA---UUA-ACCUCAGA-----UGUUACUGAGGUUGCCCAU-UCUAUC-CUAGUACAG-GA
AAGW02001465.1/25324-25192 GUGCAAACUCGAUCACUGGCUCUGCAUGAUGUGGCAGUAGCAAAGGGAACCAGGUUUGCAAAAGUAACUGUGGUGAUAGAAAUGUU---UUAG-CCUCAGA-----AGCUGCUGAGGUGGCCCAUU-CUAUC-CCAGUACAG-UG
AAGU03072105.1/7465-7334   CUGCAAACUCGAUCACUAGCUCUGCAUGAUGUUGCGGAAGCGAGGGGAACCAGGUUUGCUAAAGUAAUUGUGGUGAUAGAAAUGAU----UAG-CCUCAGG-----AGCUACUGAGGUGGCCCUUU-CUAUC-AUAAUACAG-UA
AAPE02024807.1/25186-25054 GUGCAAACUCGAUCACUAACUCUGCAUGAUGUUGCAGAAGUGAAGGGAACCAGGUUUGCUAAAGUAAUUGUGGUGAUAGAAAUGUA---UUAG-CCUCAGA-----AGCUACUGAGGUGGUUCAUU-CUAUC-CUAGUACAG-UG
#=GC SS_cons               ::<<<<<<-------------<<<<________>>>>---------------->>>>>>---------------<<<<<<<-----...----.<<<<<<_....._____>>>>>>------->>.>>>>>.:::::::::.::
#=GC RF                    gUgCAAACUCGAUCACUAGCUCuGCAUGAUGUuGCaGAAGCaAaGGGAACCAGGUUUGcUAAAGUAAuUgUGGugauaGaaAUgUa...UUAg.CCuCaGA.....agcUACuGaGGUgGcccauu.Cuauc.cuAguACAg.ua
//
# STOCKHOLM 1.0

#=GF AC   RF00156
#=GF ID   SNORA70
#=GF PI   U70
#=GF DE   Small nucleolar RNA SNORA70
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300833;
#=GF DR   snoopy; Homo_sapiens300594;
#=GF RN   [1]
#=GF RM   10902565
#=GF RT   Pseudouridine in RNA: what, where, how, and why.
#=GF RA   Charette M, Gray MW
#=GF RL   IUBMB Life 2000;49:341-351.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snoRNA U70 seems to be exclusive to mammals and is a member of the H/ACA
#=GF CC   class of snoRNA which contain H (ANANNA) and ACA box motifs. H/ACA box
#=GF CC   snoRNAs are involved in the conversion of uridines to pseudouridines
#=GF CC   (5-ribosyluracil) a constituent of structural RNAs (transfer, ribosomal,
#=GF CC   small nuclear, and small nucleolar) [1,2].
#=GF WK   Small_nucleolar_RNA_SNORA70
#=GF SQ   43


AC087315.21/91175-91310      CUGCAGCCAAUUGAGUUGACCGAGCUCUUUUCCUCCU--GGGGGCC-UGGUGUGCAAUGGCUGCAAACAGCA----GAUUCCUUGGUAGUGUA-UGCAGCCUGCUUC-----UUGUAUGGGUUGCCUCUAAGGGACCUUGAAGGCAGCC
AC016708.11/153795-153929    CUGCAGCCAAUUAAGCCAACUGAGUUCCUUUCCUUGU--GGGGGCC-CAGUGUGCAAUGGCUGCACACAGCA----GCUUCCUUGGUAGUGUA-CACAGCCUGUUGG-----UUGUAUGGGUUGCUC-UGAGGGACCUUGGAGACAGGC
Z98941.2/67921-68052         CUACAGCCAACUCAGCUGGCUGAGUUCCUCGCCUCAU--GGGGGA--C-GUGUGCAAUGGCUGCAAACAGCA----GCUUCCUUGGUGGUGUA-UGCAGCCUGUUUC-----UUGUAU-GGCUGCUC-UAAGGGACCUUGGAGACAGGC
AL078599.19/69814-69946      CUGCAGUCAAUUAAGCCAGCUGUACUCCUUUCCUCAC--AGGGGCU-CGGUGU--AAUGGCUGCAAACAACA----GCCUCCUUUGUUGUAUA-CACAGCUUGUUUC-----UUGUAUGGGUUGCUC-UAAAGAACAUAGGAGACAGCC
AC091826.3/12688-12823       CUGCAGCCAAUUGAGUUGACCGAGCUCUUUUCCUCCU--GGGGGCU-UGGUGUGCAAUGGCUGCAAACAGCA----GAUUCCUUGGUAGUGUA-UGCAGCCUGCUUC-----UUGUAUGGGUUGCCUCUAAGGGACCUUGAAGGCAGCC
L44140.1/70716-70850         CCGCAGCCAAUUAAGCCGACUGAGUUCCUUUCCUCAU--GGGGACC-CAGUGUGCGAUGGCUGCACACAGCA----GCUUCCUUGGUAGUGUA-CGCAGCCUGUUGG-----UUGUAUGGGUUGCUC-UAAGGGACCUUGGAGACAGGC
AC087763.10/29854-29985      CUGCAGCCAAUUGAGCUGAUGGAGUUCCUUUCCUCCU---GGGGCC-CAGUGUGCAAAAGCUGCAAACAGCA----GCUUCCUUGGUAGUGUA-CGCAGCCUGUUUC-----UUAUAUGGGUUGCUC-UAAGGGACCUUGGAGACAG--
AC010653.10/163838-163972    CUGCAGACAGUUAAGCCAACUGAGUUCCUUUCCUCAG--GGAGGCC-CAGUGUACAAUGGCUGCCCACAGCA----GCUUCCUUGGUAGCGUA-CUCAGCCUGUUUC-----UUGUAUGGGUUGCUC-UAAGGGACCUUAGAGACAGGC
AC099676.2/79107-79241       CUGCAGCCAAUUAAGCCGACUGAGUUCCUUUCCUCAU--GGGGGCC-CAGUGUGCAAUGGCUGUAAAUAGCA----GCUUCCUUGGUAGUGUA-UGCAGCCUGUUUG-----UUGUAUGGGUUGCUC-UAAGGGACCUUGGAGACAGUC
AK027197.1/1806-1940         CCGCAGCCAAUUAAGCCGACUGAGUUCCUUUCCUCAU--GGGGACC-CAGUGUGCGAUGGCUGCACACAGCA----GCUUCCUUGGUAGUGUA-CGCAGCCUGUUGG-----UUGUAUGGGUUGCUG-UAAGGGACCUUGGAGACAGGC
AF280893.1/300-434           CUGCAGCCAAUUAAGCCGACUGAGUUCCUUUCCUCAU--GGGGGCC-CAGUGUGCAAUGGCUGCACACAGCA----GCUUCCUUGGUAGUGUA-CGCAGCCUGUUGG-----UUGUAUGGGUUGCUC-UAAGGGACCUUGGAGACAGGC
AC091980.4/116511-116645     CUGCAGCCAAUUAAGCCGACUGAGUUCCUUUCCUCAU--GGGGGCC-CAGUGUGCAAUCGCUGCAAACAGCA----GCUUCCUUGGUAGUAUA-UGCAGCCUGUUUA-----UUGUACGGGUUGCUC-UACGGGACCUUGGAGACAGGC
AC015550.19/39913-40054      CUGCAGCCUAUUAAGCCAACUGAGUUCCUUUCCUCAUGGGGGGGCC-CAGUGUGCAAUGGCUGCAAACAGCA----GCUUCCUUGGUAGUGUA-UGCAGCCUGUGUGUUGUAUUGUAUGGGUUGCUC-UAAGGGACCCUGGAGACAGUC
AANU01093797.1/1642-1508     CUGCAGCCAAUUAAGCUGACUGAGUUCCUUUCCUCAU--GGGGGCC-CAGUGUGCAGUCGCUGCAAACAGCA----GCUUCCUUGGUAGCGUA-UGCAGCCUGUUUA-----UUGUAUGGGUUGCUC-UAAGGGACCUUGGAGACAGGU
ABDC01316020.1/528-394       CUGCAACCAAUUAAGCCGACCGUGCUCCUUUCCUCAU--GGGGGCC-CGGUGUGCAGUGGCUGCAAACAGCA----GCCUCCUUGGUAGUGUA-UGCAGCCUGUUGC-----UUGUAUGGGCUGCUC-UAAGGGACCUCGGAGACAGUC
AAPY01616042.1/3216-3350     CUGCAGCCAAUUAAGCCGACUGUGCCCCUUUCCUCAU--GGGGGCC-CGGUGUGCAGUGGCUGCAAACAGCA----GCCUCCUGGGUAGUGUA-UGUAGCCUGUUGU-----UUGUACGGGUUGAUC-UAAGGGACCUUGGAGACAGCC
AANN01176057.1/635-502       CUGCAGCCAAUUAAGCCGACCGUGUUCUUUUCCCCGU---GGGACC-CGGUGUGCAAUGGCUGCAAACAGUA----GCCUCCAUGGUAGUGUA-UGCAGCCUGUUCC-----UUGUAUGGGUUGCUC-UAAGGGACCCUGGAGACAGCC
AAQQ01376438.1/1342-1476     CUGCAGCUAAUUAAGCCGACUGGGUUCCUUUACUUGU--GGUGGCC-CAGUGUGCAAUGGCUGCAAACAGCA----AUCUCCUUGGUAGUGUA-UGCAGCCUGUUGC-----UUGUAUGGGUUGCCC-UAAGGGACCUUGGAGACAGCA
AANG01186285.1/4494-4361     AUGCAGCCAAUUAAGCCGACUGUGCUCU-UUCCCCAU--GGGAGCC-CAGUGUGCAAUGGCUGCAAACAGUA----GCCUCCUUGGUAGUGUA-UGCAGCCUGUUGA-----UUGUACAGGUUGCCC-UAAGGGACCUUGGAGACAGCC
AAFC03117345.1/12835-12701   UCGCAGCCAAUUAAGCCGACUGUGCUCUUUUCCCCAU--GGGGGCC-CAGUGUGCAAUGGCUGCAGAUAGCA----GCCUCCUUGGUAGUGUA-UGCAACCUGUUGC-----CUGUACAGGUUGCCC-UAAGGGACCUUGGAGACAACU
AAYZ01032687.1/2795-2661     CUGCAGCUAAUUAAGCUGACCAGCUCUCUUGCUUCAU--GGUCGCC-UGGUGUGCAAUGGCUGCAGACAGCA----GCCUCCUUGGUAGUGUA-UGCAACCUGUUGC-----UUGUAUGGGUUGCUC-UAAGGGACCUUGGAGACAGUC
AC146536.3/15523-15389       CUGCAGCCAAUUAAGCCGACCGGCCCCCUCUUCCCAU--GGGGGCC-UGGUUUGCAAUGGCUGCAGACAGCA----GCCUCCUUGGUAGUGUA-UGUGGCCUGUUGC-----CUGUACAGGUUGCCC-UAAGGGACCUUGGAGACAGCC
AC171202.1/60024-60158       CUGCAGCCAAUUAAGCCGACCAGGUUCCUUUCCUCAU--AGGAGUC-UGGUGUGCAAUGGUUGCAAACAGCA----UCCUCCUUGCUAGUGUA-UGCAGCCUGCUGA-----AUGUGCAGGCUGCCC-AAAGGGACCUUGGAGACAGUC
AC094668.10/151055-150920    GUGCAGCUAAUUAAGCCGAUCAAGUCCCUUUCCCCAU--GGGGACUUUGGUGUGCAAUGGUUGCAAACAGCA----GCCUCCUUGGUAGUGUA-UGUAGCCUAUUGU-----CUAUAUGGGUUACCU-CAAGGGACCUUGGAAACAGUU
AAIY01539099.1/1373-1506     CUGCAGCCAAUUAAGCCGACCGUCCUCC--UCCUCGU--GGGGGC--CGGUGUGCAAUGGCUGCAUACAGCAA---GCCUCCUUGGUAGUGUA-UGCAGCCUAUUGGU----AUGUAUAGGCUGCCC-UAAGGGACCUUGGAGACAACC
AC188383.3/28408-28274       AUAAACAAAAGAACACCAAUUGUGCUCCUUUCCUCCU--GGGGGAC-CAGUGUGCAAUGGCUGCAAAUAGCU----GUUUCCUUGGUAACAUA-UGCAGCCUGUUGC-----UUGUAUGGGUUGCAC-UAAGAAACCUUAAAAACAGCC
AAPN01429039.1/3992-3859     CCGCAGACAAUUAAGCCGACUGGCCCCUGCCUCUGUC--GAGGGC--CAGUGUGCAAUGGCUGCGCACAGCA----AACUCCUCGGUUGUGUA-CGUGCCCCGUUCC-----CUGUAUGGGGCGCCC-UAAGGGACCUUGGAAACAGCA
AALT01612972.1/579-716       GGGCAGCUAAUUAAGCCGACCGUGCUCUCUGCCCUGU---GGGGCC-CGGUGUGCAAUGGCUGCCGACAGCAAGCGGCUCCCUGGGUAGUGUA-CGCAGCCUGUGGC-----UUGUACAGGCUGUGA-GAAGGGACCCGGGAGACAGUC
AAFR03063535.1/61733-61867   CUGCAGCCAAUUAAGCCGACCAACCCUACAGCGCCAGU-GUGGGCU-UGGUGUGCAAUGGUUGCAGACAUGA-----AUUCCCUGGUUGUGUG-CGUACCUUGUUUU-----CCAUGCAAGGUAUUC-UAAGGGACCUCGGAAACACUU
BAAE01006004.1/1189-1321     CUGCAGCUUAUUAAGCCGACUG--GUUGUGUUCUCGU--ACAUCUC-CAGUGUGCAAAGGCUGCAGACAG-A----GACUCUUUGGUUGUGUA-UGUCCUCAGCUGUG----AGGUGCUGAGUGCUU-UAAGGGACCACUGAGACAAAA
BX005483.3/13546-13679       CUGCAGCUUAUUAAGCCGACUGGACAGGUUGUGUGUA---CUUGUG-UGGUGUGCAAAGGCUGCAGACAGUA-----AAUCUUUGGUUGUGUA-UGAGCCUAGCUGGG----UAGUGCUGGGCCCUU-UAAGGGACCAUUGAAACAUGC
AAVX01014055.1/2170-2306     UUGCAGUUAAUUAAGCCGACUAGCCCUCUGUACCUGU--GGGAGGC-UGGUGUGCAAUGGCUGCAUACAGCA-----AGUCACUGGUUGUGUAACGCGCUUUGUCUUUC---CCGUGCAAAGUGCUC-CAAGGGACCUCUGAGACAUUG
BT028157.1/1611-1743         CUGCAGCUUAUUAAGCCGACUGGUCUCG--CUGCUGU--GCGGUUC-UGGUGUGCAAAGGCUGCAGACAGUA-----ACUCUGUGGUUGUGUA-UGUCCUCAGCUGGG----AGGUGCUGAGUGCUU-UAAGGGACCGCUGAGACAGAU
CAAE01007638.1/65573-65441   CUGCAGCUUAUUAAGCCGACUGGUUCUG--CUGUGGU--GCGGUUC-UGGUGUGCAGAGGCUGCAGACAGUG-----ACUCUCUGGUUGUGUA-UGUCCUCAGCUGGG----AGGUGCUGAGUGCUU-UAAGGGACCACUGAGACAAAC
AAKN02055764.1/8030-7896     CUGCAGUCAAUUAAGCUGACUGGGCGCCUUUGCUGGU--GGGUGCC-CAGUGUGCAGUGGCUGCAGACAGCA----ACCUCUUCAGUAGUGUA-UGCAGCCUGUUAC-----UUACAUGGGCUGCUU-CAAGGGACCUUGGAGACACUG
AAWR02040662.1/1564-1698     CUGCAGCCAAUUAAGCCGACCGGGUCCUUUUCCCCAU--GGGGGCC-CGGUGUGCACUGGCUGCAAACAGCA----GCCUCCUUGGUAGUGUA-UGCAGCCUGUUGC-----UUGUAUGGGUUGCCC-UAAGGGACCUUGGAGACAGCC
AAGU03086870.1/50019-49887   CUGCAGCCAAUUAAGCCGACUGUCCUCCUUUCCUGU----GGGGGC-CAGUGUGCAAUGGCUGCAAACAGCA----GCUUCCUCGGUAGUGUA-UGCAACCUGUUGC-----AUGUACGGGUUGCCC-UAAGGGACCUUGGAGACAGCA
AAWZ02016917.1/38377-38243   CUGCAGUCAAUUAAGCCGACCAGCCCCUGUUGCUAUC---AGUGGA-UGGUGUGCAAUGACUGCACACAGCAA---ACUCCCUUGGUUGUGUA-CGUGCUCCGUUCC-----UUGUACAGAGUACCU-UAAGGGACCUUGGGAACACCU
AAQR03004950.1/109138-109004 UUGCAACUAAUUAAGCUGACCGUGCUCCUUUCCUCAU--GGGGGCC-UGGUGUGCAUUGGCUGCAAAUAGCA----GCCUCCUCGGUAGUGUA-UGCAGCCUGUUGC-----UUGUAUAGGUUGCUC-UAAGGGACCUUGGAGACAUUC
AAPE02051464.1/590-456       CUGCAGCCAAUUAAGCCGACCAUGCUCUUUUCCCCAU--GGGAGCC-UGGUGUGCAAUGGCUGCAAACAGCA----GCAUCCUUGGUAGUGUA-CGCAACCUGUUGC-----UAGUAUGGGUUGCCU-UAAGGGACCUUGGAUACAGCC
AAGW02082198.1/7521-7387     CUGCAGCUAAUUAAGCCGACCAGCUCCCUUUCUUCAU--GGGGGCC-UGGUGUGCAAUGGCUGCAAACAGCA----GCCUCCUUGGUAGUGUA-UGCAACCUAUUGU-----UUGUAUGGGUUGCCC-UAAGGGACCUUGGAGACAGCC
AACZ03012393.1/17375-17241   CUGCAGCCAAUUAAGUUGACUGAAUUCCUUUCCUUAU--GGGGGUC-CAGUGUGCAAUGGCUGUAAACAGCA----GCUUCCUUGGUAGUGUA-UGUGGCCUGUUUG-----UUGUAUAGGUUGCUC-UAAGGGACCUUGGAGACAGGC
AC203193.13/227086-227219    CUGCAGCCACUUAAGCCGACUGUGCUCU-UUCCCCAU--GGGGGCC-CAGUGUGCCAUGGCUGCAAACAGUA----GCCUCCUUGGUAGUGUA-UGCAGCCUGUUGA-----UUGUAUGGGUUGCCC-UAAGGGACCCUGGAGACAGCC
#=GC SS_cons                 :<<<<-------------<<<<--<<<<_________.._>>>>--.>>>>->>>>----------------....--------<<<------.--<<<<<<_____.....______>>>>>>---.------>>>::::::::::::
#=GC RF                      cuGCAGccAAUUAAGCCGACcGagccccUUUcCUcaU..Gggggcc.CgGUGUGCaAUGGCUGCAaACAGCA....GcuUCCUUGGUaGUGUA.uGcagCCcGUUgc.....uUGUAugGGcugCuc.UAAGGGACCUUgGAGACAguc
//
# STOCKHOLM 1.0

#=GF AC   RF00157
#=GF ID   SNORD39
#=GF PI   SNORD55; U39; U55
#=GF DE   Small nucleolar RNA SNORD55/SNORD39
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00057
#=GF DR   snoRNABase; U55;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Gallus_gallus300101;
#=GF DR   snoopy; Loxodonta_africana300339;
#=GF RN   [1]
#=GF RM   8764399
#=GF RT   Intron-encoded, antisense small nucleolar RNAs: the characterization of
#=GF RT   nine novel species points to their direct role as guides for the
#=GF RT   2'-O-ribose methylation of rRNAs.
#=GF RA   Nicoloso M, Qu LH, Michot B, Bachellerie JP
#=GF RL   J Mol Biol 1996;260:178-195.
#=GF RN   [2]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF RN   [3]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [4]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA U39 (SNORD55), also described as U55 in [2], is a member of the C/D
#=GF CC   class of snoRNA which contain C (UGAUGA) and D (CUGA) box motifs [1]. U39
#=GF CC   guides the methylation of 2'-O-ribose residues in 28S ribosomal RNA [1].
#=GF WK   Small_nucleolar_RNA_SNORD39
#=GF SQ   20


Z69627.1/1-79              CGCG----GAUGAUGACACCUGGG-UA-UGCUGCACACUCCCGACUGCGUCGUGGGGAAGCCAACCUUGGAGAGCUGAGCG-UGCG
X97586.1/1-79              CGCG----GAUGAUGACACCUGGG-UA-UGCUGCACACUCCCGACUGCGUCGUGGGGAAGCCAACCUUGGAGAGCUGAGCG-UGCG
Z69626.1/1-80              CGUG----UAUGAUGACAACUCGG-UAAUGCUGCAUACUCCCGAGUGCGCGGUGGGGAAGCCAACCUUGGAGAGCUGAGCG-UGCG
X67247.1/516-595           CGUG----UAUGAUGACAACUCGG-UAAUGCUGCAUACUCCCGAGUGCGCGGUGGGGAAGCCAACCUUGGAGAGCUGAGCG-UGCG
ABDC01293119.1/5116-5195   CGCG----CAUGAUGACACCUGGG-AAAUGCUGCAGACUGCCGAGUGCGCAGUGGGGAAGCCAACCUUGGAGAGCUGAGCG-UGCG
AAYZ01156353.1/1156-1235   CGUG----GAUGAUGACACAUCGG-UAAUGCUGCAAACUCCCGACUGCGCGGUGGGGAAGCGAACCUUGGAGAACUGAGCG-UGCG
AACN010104974.1/1832-1911  CGUG----GAUGAUGACACCUUGG-UAAUGCGGAAAACUCACGAGUGCGCAGUGGGGGAGCCAACCUUGGAGAGCUGAGCG-UGCG
AAQQ01563043.1/4065-3986   CGUG----UAUGAUGACACUUUGG-UAAUGCUGCAUAUUGCCGACUAAGCAGUGGGGAAGCCAACCUUGGAGAGCUGAGCG-UGCG
AANG01007069.1/975-1054    UGUG----GAUGAUGACACCUUGA-UAAUGCUGUAAACUCCCGAGUGCGCAGUGGGGGAACCAACCUUGGAGAGCUGAGCG-UGCG
AAFC03118868.1/9582-9503   CGUG----CAUGAUGACACCUUGG-AAAUGCUGUGACCUCCCGACUGCGCUGUGGGGGAGCUAACCUUGGAGAGCUGAGCG-UGCG
AALT01192495.1/2222-2300   CGUG----UGUGAUGACACCUUGG-AAAUGCUGU-GACUCCCGACUGCGCAGUGGGGAAUCCAACCUUGGAGAGCUGAGCG-UGCG
AAPY01083429.1/2409-2332   CGUG----G-UGAUGACACCUUGG-UAAUGCUGCAGACUUCCGAGU-CGCUAUGGGGAAGCCAACCUUGGAGAGCUGAGCG-UGCG
AAIY01208130.1/1083-1160   CGUG----CAUGAUGACACCUCGG-UGAUGCUGCAAGUCCCCGAGUGUGCGGUGGGGAAGCCAACCUUGGAGAACUGAG---UGCG
AANN01103332.1/900-824     CGUG----UAUGAUGACACCUUCA-UGAUGCUGC---UUGCCGAGUACGCCGUGUGGAGGCCAACCUUGGAGAGCUGAGCG-UGCG
AAFR03051186.1/1825-1744   GGCGC---GCUGAUGACACCUUGGUUACUGCUGC-AAACACCGAGAUCCUGGUGGGGAUGCAAACCUUGGAGAGCUGAGCGCCGCC
AAKN02055181.1/85916-85995 CGUG----UAUGAUGACACCUCGG-UAACGCUGCGUACUCCCGACUGAGCGGUGGGGAAGCAAACCUUGGAGAGCUGAGCG-UGCG
AADN03005642.1/12445-12361 UGAGUCUCAAUGAUGAAGCUUCUCUGACUGCUGCAUAAAGCUGAGUGUGCUGUGCGGAUGCCAACCUUGGAGAGCUGAGGA-CUCA
AAQR03170566.1/2412-2334   CGCG----CAUGAUGACACCCAGG-AA-UGCUGCAGACUGCCGAUCGUGCAGUGAGGAAGCCAACCUUGGAGAGCUGAGCG-UGCG
AAPE02035687.1/21542-21465 CGCG----CAUGAUGACAGCCUAG-GACUGCUGUGAAACGCCGAU--CUCGGUGGGGAAGCCAACCUUGGAGAGCUGAGCG-CGCC
AAGU03058132.1/19657-19736 CGUG----CAUGAUGACACCUCGG-UAAUGCUGCAAAUCCCCGAGUGCGCGGUGGGGAAGCCAACCUUGGAGAGCUGAGCC-CGCG
#=GC SS_cons               <<<<....________________.________________________________________________________.>>>>
#=GC RF                    cGcg....uAUGAUGACACCUugG.uAaUGCUGcAaAcucCCGAgUGcGCaGUGgGGAAGCcAACCUUGGAGAGCUGAGCG.cgCg
//
# STOCKHOLM 1.0

#=GF AC   RF00158
#=GF ID   SNORD82
#=GF PI   U82
#=GF DE   Small nucleolar RNA SNORD82
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   43.00
#=GF TC   43.60
#=GF NC   42.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300790;
#=GF DR   snoopy; Loxodonta_africana300468;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   snoRNA U82 or Z25 is found in both humans and mice. U82/Z25 is a member of
#=GF CC   the C/D class of snoRNA which contain C (UGAUGA) and D (CUGA) box motifs.
#=GF CC   Most of the members of the box C/D family function in directing
#=GF CC   site-specific 2'-O-methylation of substrate RNAs. Although the selection
#=GF CC   of the target nucleotide requires the antisense element and the conserved
#=GF CC   box D or D' of the snoRNA, the methyltransferase activity is supposed to
#=GF CC   reside in one of the protein components [1].
#=GF WK   Small_nucleolar_RNA_SNORD82
#=GF SQ   27


AJ011568.1/1-67              ---ACAAAUGAUGAAUAACAAAGGGACUUAAUACUGAAAC--CAGAUGUUAC--A-UUGUAG---U-GUGCUGAU-GUGC-
AJ010666.1/3-73              AGCACAAAUGAUGAAUAACAAAGGGACUUAAUACUGAAAC--CAGAUGUUAC--A-UUGUAG---U-GUGCUGAU-GUGCU
AJ010668.1/1-72              AGCACAAGUGAUGACUAACAAAGGGACUUAAUACUGAAACAUCUGGGAUUGA--A-AUGCAG---U-AUGCUGAU-GUGC-
AANU01127039.1/4502-4571     AGCACAAAUGAUGAAUGACAAAGGGACUUAAUACUGAAAC--AUGAUGUUAC--A-UUGCAG---U-GUGCUGAU-GUGC-
AAFC03048025.1/7281-7350     AGCACAAGUGAUGAACAAUAAAGGGACUUAAUACUGAAAC--CUGAUGUUAU--A-UUUCAA---U-GUGCUGAU-GUGC-
AAHY01008130.1/13032-13101   AGCACAAGUGAUGAGUGACAAAGGGACUUAAUACUGAACC--AUGGGGUUGA--A-AUGAAA---U-AUGCUGAU-GUGC-
ABDC01394633.1/4013-3944     AGCACAGCUGAUGAAUGACAAAGGGACUUAAUACUGAAAC--CUGAUGUUAC--A-CUAUAA---C-GUGCUGAU-GUGC-
AAPY01196747.1/4564-4494     AGCACAAAUGAUGAUUGAUAUAGGGACUUAAUACUGAAAC--CUGAUGCUAC--AUUUGCAA---U-GUGCUGAU-GUGC-
AANN01153174.1/741-809       AGCACAAAUGAUGAACAACAAAGGGACUUAAUACUGAAUC--CUGAUGUUAC--A--UGCAA---U-GUUCUGAU-GUGU-
DQ082279.1/50-118            UGCACAAGUGAUGAACAGCAAAGGGACUUAAUACUGAAAC--CUGAUGUGAU--A-UUGUGA---U-GU-CUGAU-GUGC-
DQ082274.1/48-116            CGCACAAGUGAUGAACANCAAAAGGACUUAAUACUGAAGC--CUGAUGUGAU--A-UUGUGA---U-GU-CUGAU-GUGC-
DQ082283.1/48-116            UGCACAAGUGAUGAACAGUAAAGGGACUUAAUUCUGAAAC--CUGAUGUGGU--A-CUGUGA---U-AU-CUGAU-GUGC-
AACN010538567.1/321-386      UGCACAAGUGAUGAACAACAAAGGGACUUAAUACUGAUAC--CUGAUGUAAU--A-C----G---A-UGUCUGAU-GUGC-
DQ082281.1/50-118            GGCACAUGUGAUGAACAGCAAAGGGACUUAAUGCUGAAAC--UUGAUGUGAU--A-UUGUGA---U-GU-CUGAU-GUGC-
DQ082267.1/48-116            CGCACAAGUGAUGAACAGCAGAGGGACUUAAUACUGAAGC--CUGAUGUGAU--A-CUGUGA---U-GU-CUGAU-GUGC-
AAYZ01252946.1/1426-1358     AGCACGAAUGAUGAGUGACACAGGGACUUAAUACUGACAC--CUGCUGAUCC--A-CA-CAA---U-GUGCUGAU-GUGC-
AAIY01679901.1/6951-6880     GGCACAAAUGAUGAACCACAAAGGGACUUAAUACUGAUCAUCUUGAUGUGAC--U-UAAUGA---U-CAGCUGAU-GUGC-
AALT01279658.1/62-131        AGCACA-AUGAUGAAUGACAAAGGGACUUAAUGCUGAGAC--UUGAUGUCAC--A-UUCUUGA--U-AUUCUGAU-GUGU-
AAPN01359272.1/5048-4977     AGCACAAAUGAUGAGC-CUAAAGGGACUUAAUACUGAAAC--CUGAUGUAACUAA-AUAAUA---U-AUGCUGAUCGUGC-
AAFR03061959.1/16901-16829   GGCACAAGUGAUGAUCCACAUAGGGACUUAAUUCUGAAGC--CUGAUGCAAU--G-CUUGCUAUAU-AUGCUGAU-GUGC-
AAPY01815621.1/1796-1726     GACACAAAUGAUGUUUGACACAGGGACUUAAUACGGAAAC--CUGAUACUAC--A-UUUGCAA--U-GUGCUGAU-GUGC-
AAWR02034600.1/40585-40516   AGCACAAGUGAUGAACAGCAGAGGGACUUAAUGCUGAAAC--GUGAUGUCUC--A-CUAGGA---C-AUGCUGAU-GUGC-
AAGV020353737.1/642-575      AGCACAAAUGAUGAACAAGAAAGGGACUUAAUACUGAGAC--CUGAUGUUAC--A-UUGU-----G-AUACUGAU-GAGC-
AAPE02003570.1/32933-32864   AGCACAAGUGAUGAACAAAAAAGGGACUUAAUACUGAAAC--CUGAUGUUAC--A-UUGCAG---U-AUGCUGAU-GUGC-
AAEX03014432.1/47184-47119   UGCACAAGUGAUGAACAACAAAGGGACUUAAUACUGAGAC--CUGAUGUGAU--A-C----G---A-GGUCUGAU-GUGC-
AADN03005880.1/228335-228267 AGCACAAAUGAUGAUUA--UAAGGGACUUAAUACUGAAAU--GUGAUGUGAU--U-UUUGAG---CAGAACUGAU-GUGC-
AAQR03030108.1/1210-1278     GGCACAAAUGAUGAAUGACAA-GGGACUUAAUACUGAAAC--CUGAUGUUAC--A-UUACAA---U-GUGCUGAU-GUGC-
#=GC SS_cons                 :<<<<<__________________________________..__________.._.______..._._______>.>>>>.
#=GC RF                      aGCACAAaUGAUGAauaACAAAGGGACUUAAUACUGAAAC..cUGAUGUuAc..A.uUguaa...U.gUGCUGAU.GUGC.
//
# STOCKHOLM 1.0

#=GF AC   RF00159
#=GF ID   snoZ168
#=GF DE   Small nucleolar RNA Z168/Z174
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   36.00
#=GF TC   36.60
#=GF NC   34.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   This family consists of several snoRNA Z168 and Z174 sequences which are
#=GF CC   members of the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. This family seems to be found exclusively in rice. C/D
#=GF CC   box small nucleolar RNAs are known to act as a methylation guides for 18S
#=GF CC   ribosomal RNA in plants [1].
#=GF WK   Small_nucleolar_RNA_Z168/Z174
#=GF SQ   6


AJ490388.1/4-85 GGGCCGAUGAUGUGAACCAUGCUCCUACGGUCUA--AACCUGU-GGGGAGGAUUUCCAAACCAUA-UUUCCCAAGAGCUGAGGCCU
AJ490400.1/1-82 GGGCCGAUGAUGCGAACCAUGCUCCUAUGGUCUA--GACCUGU-GAGGAGGAUUUCCUAAACAUA-UUUCCCAAGAGCUGAGGCCC
AJ490397.1/1-82 -GGCCGAUGAUGCUAACAAUGCUCCUAUGGUCUUUGACUAAGA-GCUGAGGAUUCUCUAAGAAUG-UUUCCCAAGAGCUGAGGCC-
AJ490385.1/4-84 GGGCCGAUGAUGCAAACCUUGCUCCUACGGUCUA--A-CCUGU-GGGGAGGAUUUGUAAAGUAUA-UUUCCCAAGAGCUGAGGCCC
AJ490394.1/1-82 -GGCCGAUGAUGCUAAUCAUGCUCCUAUGGUCUUG-ACCAAGAAGCUGAGGAUUCUCUAAGAAUG-UUUCCCAAGAGCUGAGGCC-
AJ490395.1/1-83 GGGCCGAUGAUGCGAACCAUGCUCCUAUGGUAGA--CCCCUGU-GCGGAGGAUUUCCUAAACAUAAUUUCCCAAGAGCUGAGGCCC
#=GC SS_cons    :<<<<_____________________________.._______._____________________._______________>>>>:
#=GC RF         GGGCCGAUGAUGCuAACcAUGCUCCUAuGGUcUa..acCcuGu.GcgGAGGAUUuuCuAAgaAUa.UUUCCCAAGAGCUGAGGCCc
//
# STOCKHOLM 1.0

#=GF AC   RF00160
#=GF ID   snoZ159
#=GF DE   Small nucleolar RNA Z159/U59
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   39.00
#=GF TC   39.00
#=GF NC   38.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00065
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300085;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   This family consists of several snoRNA Z159 or U59 sequences which are
#=GF CC   members of the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. This family seems to be found exclusively in rice. C/D
#=GF CC   box small nucleolar RNAs are known to act as a methylation guides for 18S
#=GF CC   ribosomal RNA in plants [1].
#=GF WK   Small_nucleolar_RNA_snR54
#=GF SQ   10


AB092809.1/7232-7313 GCCUCCGAUGAUGAA-CAACUGUGU--GUUUUU-UUCUGA-GUUGUUU--------------CCAUGC-UGAAAA-UAUAGUGGAGACCUGAACUGAGGAGGC
AJ490357.1/1-86      GUCUCCGAUGAUGAUGUAUUUUUAU--ACUUUCGUUCUUCUGAAGUUG--------------UAAUGUGGAAGAACAAUU-UGGAGACCUGAACUGAGGGGUU
AJ490358.1/3-88      GUCUCCGAUGAUGAUGUAAAUUUAU--ACUUUCGUUCUUCUGAAGUUG--------------CAAUGUGGAAGAACUAUU-UGGAGACCUGAACUGAGGGGUU
AJ490364.1/1-93      GACUCA-AUGAUGAUGCAUUUUUAU--ACUUUUGUUCUUCUGAAGUUACAAACUUG------CAAUGUGGAAGAACAAUU-UGGGGACCAGAACUGAUGGGGU
AJ490360.1/3-101     GUCUCUGAUGAUGAUUAAAAAUGAUUAACUUUCGUUCUUCUGAUGC-GCUUUUCUCAUGGCGCGCUGCGGAAG--CAAUC-UGGAGACCUGAACUGAGGAGAC
AJ490365.1/1-93      GACUCA-AUGAUGAUGCAUUUUUAU--AUUUUUGUUCUUCUGAAGUUACAAACUUG------CAAUGUGGAAGAACAAUU-UGGGGACCAGAACUGAUGGGGU
AJ490363.1/3-101     GUCUCUGAUGAUGAUUAAAAAUGAUUAACUUUCGUUCUUCUGAUGC-GCUUUUCUCAUGGCGCGGUGCGGAAG--CAAUC-UGGAGACCUGAACUGAGGAGAC
AY112816.1/10-95     GUCUCCGAUGAUGAUGUAAAUUUUU--ACUUUCGUUCUUCUGAAGUUG--------------CAAUGUGGAAGAACUAUU-UGGAGACCUGAACUGAGGGGGU
AJ490361.1/3-88      GUCUCCGAUGAUGAUGUAAAUUUUU--ACUUUCGUUCUUCUGAAGUUG--------------CAAUGUGGAAGAACUAUU-UGGAGACCUGAACUGAGGGGGU
AJ490366.1/1-83      GUCUCCGACGAUG---UAAAUUUAU--ACUUUCGUUCUUCUGAAGUUGG-------------CAAUGUGGAAGAACUAUC-UGGAGACCUGAACUG-GGGGUU
#=GC SS_cons         ::<<<<___________________..______________________.............__________________.________________>>>>::
#=GC RF              GuCuCcGAUGAUGAUguAaauUuaU..AcUUUcGUUCUUCUGAaGUUgc.............CaAUGuGGAAGAACaAUu.UGGAGACCUGAACUGAgGaGgu
//
# STOCKHOLM 1.0

#=GF AC   RF00161
#=GF ID   nos_TCE
#=GF DE   Nanos 3' UTR translation control element
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Published; PMID:10882131
#=GF GA   60.00
#=GF TC   63.80
#=GF NC   39.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0008595; anterior/posterior axis specification, embryo;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   10882131
#=GF RT   Overlapping but distinct RNA elements control repression and activation of
#=GF RT   nanos translation.
#=GF RA   Crucs S, Chatterjee S, Gavis ER
#=GF RL   Mol Cell 2000;5:457-467.
#=GF CC   The Nanos protein in Drosophila is required for correct anterior/posterior
#=GF CC   patterning in the Drosophila embryo. Translation of the nanos mRNA is
#=GF CC   repressed in the bulk cytoplasm and activated in the posterior region.
#=GF CC   Repression is mediated by a translation control element (TCE) in the 3'
#=GF CC   UTR of the mRNA. This element forms a Y-shaped structure, part of which is
#=GF CC   recognised by the Smaug protein leading to translational repression [1].
#=GF WK   Nanos_3'_UTR_translation_control_element
#=GF SQ   9


AF252722.1/810-873       NGGAGCAGAGGCUCUGGCAGCUUUUGCAGCGU-UUAUAUAACAAGAAAUAUAUAUACGCAUUCCG
M72421.1/2491-2554       UGGAGCAGAGGCUCUGGCAGCUUUUGCAGCGU-UUAUAUAACAUGAAAUAUAUAUACGCAUUCCG
U24695.1/2509-2569       UGGA--AGAAGCUCUGGCAGCUUUUUAAGCGU-UUAUAUAAGA-GUUAUAUAUAUGCGCGUUCCA
AAEU02002047.1/7785-7722 AGGAGCAGAAGCUCUGGAAGCUUUUGUAGCGU-UUAUAUAACAAGAAAUAUAUAUACGCCUUCCG
AB194436.1/924-862       AGAACAAGAAGCUCUGGCAGCUUCUACAGCGC-UUAUAUAAUCAGAAAUAUAUAUGCGCG-UUCU
AB194434.1/965-904       GAACU-AGAAGCUCUGGAAGCUUCUUAAGCGUUUUAUAUAAUCAGAAAUAUAUAUGCGC--GUUC
AB194435.1/926-863       AGGAUUUGAAGCUCUGGCAGCUUCUGCAGCGC-UUAUAUAGUCAGAAAUAUAUAUUCGCGUUCGA
AB194415.1/11664-11723   GUCA----AAGCUCUGGCAGCUUCUUAAGCGU-UUAUAUAGUCAGAAAUAUAUAUGCGCGAUCAU
AB194432.1/908-846       AGAAAUCGAAGCUCUGGCAGCUUCUUAAGCGU-UUAUAUAGUCAGAAAUAUAUAUGCGCG-UUCA
#=GC SS_cons             ((((,,<<<<<<<_____>>>>>>>,,,<<<<.-<<<<<<________>>>>>>->>>>,,))))
#=GC RF                  cggauuaGAAGCUCUGGcAGCUUCuuaAGCGc.UUAUAUAAucAGAAAUAUAUAUgCGCgUuccg
//
# STOCKHOLM 1.0

#=GF AC   RF00162
#=GF ID   SAM
#=GF PI   S_box
#=GF DE   SAM riboswitch (S box leader)
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Grundy F, Henkin T, PMID:10094622
#=GF SS   Published; PMID:10094622
#=GF GA   44.00
#=GF TC   44.00
#=GF NC   43.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00012
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   10094622
#=GF RT   The S box regulon: a new global transcription termination control system
#=GF RT   for methionine and cysteine biosynthesis genes in gram-positive bacteria.
#=GF RA   Grundy FJ, Henkin TM
#=GF RL   Mol Microbiol 1998;30:737-749.
#=GF RN   [2]
#=GF RM   12910260
#=GF RT   An mRNA structure that controls gene expression by binding
#=GF RT   S-adenosylmethionine.
#=GF RA   Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR
#=GF RL   Nat Struct Biol 2003;10:701-707.
#=GF RN   [3]
#=GF RM   12702767
#=GF RT   The riboswitch-mediated control of sulfur metabolism in bacteria.
#=GF RA   Epshtein V, Mironov AS, Nudler E
#=GF RL   Proc Natl Acad Sci U S A 2003;100:5052-5056.
#=GF RN   [4]
#=GF RM   15215334
#=GF RT   Comparative genomics of the methionine metabolism in Gram-positive
#=GF RT   bacteria: a variety of regulatory systems.
#=GF RA   Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS
#=GF RL   Nucleic Acids Res 2004;32:3340-3353.
#=GF RN   [5]
#=GF RM   16810258
#=GF RT   Structure of the S-adenosylmethionine riboswitch regulatory mRNA element.
#=GF RA   Montange RK, Batey RT
#=GF RL   Nature. 2006;441:1172-1175.
#=GF CC   The SAM riboswitch is found upstream of a number of genes which code for
#=GF CC   proteins involved in methionine or cysteine biosynthesis in Gram-positive
#=GF CC   bacteria. The SAM riboswitch acts at the level of transcription
#=GF CC   termination control. The predicted structure consists of a complex
#=GF CC   stem-loop region followed by a single stem loop terminator region. An
#=GF CC   alternative and mutually exclusive form involves bases in the 3' segment
#=GF CC   of helix 1 with those in the 5' region of helix 5 to form a structure
#=GF CC   termed the anti-terminator form [1]. This entry represents the conserved
#=GF CC   core of the complex structure involving helices 1-4.
#=GF WK   SAM_riboswitch_(S_box_leader)
#=GF SQ   433


AF027868.1/5245-5154           UUUCUAUCCAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC-UCGGCAACA-------UU-----------------------------------------------------------AU--------UGUGCCA-AUUC--CAG-CAAGC-------GCUA-----------------------GCU-UG-A-AA-GAUAGGAA
AF269983.1/571-671             ACCUUAUUUUGAG-AAG-C-UG-----------------AGGGA-UUUGG-CCCAU--AGAA-GCU-UCAGCAACC-G-ACU-UUA---------------------------------------------------------AAUAGC-AC--GGUGCUA-AUAC--CAA-CGAG--------CAA-------------------------CU-CG-A-AU-GAUAAGUA
AJ000974.1/281-386             AACUUAUCAAGAG-CGG-C-UG-----------------AGGGA--CUGG-ACCUA--UGAA-GCC--CGGCAACC-U-GCA-UAG---------------------------------------------------------UUUGUA-A---GGUGCUA-CUUC--CAG-CAAAAUG-----AAUUC--------------------CAUUU-UG-A-AA-GAUAAGGG
AL596164.1/95936-95817         CUCUUAUCGAGAG-CGG-C-AG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CGGCAACC-U-AAC-UUUAUUUAA-----------------------------------------------GCGUAAAGUG-AA--GGUGCUA-AUUC--CAG-CAAAAUGG---UGUAUU-------------------CCGUUU-UG-G-UA-GAUAAGAG
AL591974.1/109385-109266       CUCUUAUCGAGAG-CGG-C-AG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CGGCAACC-U-AAC-UUUAUUUAA-----------------------------------------------GCAUAAAGUG-AA--GGUGCUA-AUUC--CAG-CAAAAUGG---UGUAUU-------------------CCGUUU-UG-G-UA-GAUAAGAG
U52812.1/691-829               CUCUUAUCCCGAGCUGG-C-GG-----------------AGGGA--CAGG-CCCUA--UGAA-GCC--CAGCAACC-G-GUU-UCUCUGUUAUUUAUUAUG----------------------------UUCAAUUGAGUGAGACAACC-AA--GGUGCUA-ACCU-GUUG-CAAGGUU-----GUAUG-------------------AUUCCU-UG-A-GC-GAUAAGAG
AL596169.1/221462-221354       CUCUUAUCCAGAG-CGG-U-AG-----------------AGGGA--CUGA-CCCUU--UGAA-GCC--CAGCAACC-U-ACA-CAUAU-------------------------------------------------------AAGUGA-AA--GGUGCUA-AUCU-GUUG-CAGGAGU----AAUAU----------------------CUCC-UG-A-AC-GAUGAGAG
AL591980.1/66651-66543         CUCUUAUCCAGAG-CGG-U-AG-----------------AGGGA--CUGA-CCCUU--UGAA-GCC--CAGCAACC-U-ACA-CAUAU-------------------------------------------------------AAGUGA-AA--GGUGCUA-AUCU-GUUG-CAGGAGU----AUUAU----------------------CUUC-UG-A-AC-GAUGAGAG
AL596172.1/176254-176136       AUCUUAUCCAGAG-UGG-U-GG-----------------AGGGA--AAUG-CCCUG--UGAA-ACC--CAGCAACC-U-AAA-CAAUAAUUC----------------------------------------------AUUAUGUGUUU-AA--GGUGCUA-AGUC--AUG-CAGAACAA---CGAUU---------------------UGUUC-UG-A-AA-GAUGAGAA
AL591983.1/96176-96058         AUCUUAUCCAGAG-UGG-U-GG-----------------AGGGA--AAUG-CCCUA--UGAA-GCC--CAGCAACC-U-AAA-CAAUAAUUC----------------------------------------------AUUAUGUGUUU-AA--GGUGCUA-AGUC--AUG-CAGAACAA---CUAAU---------------------UGUUC-UG-A-AA-GAUGAGAA
AL596170.1/192-86              CUCUUAUUAUGAG-UGG-U-AG-----------------AGGGA--CUGG-CCCGU--UGAA-ACC--CAGCAACC-U-UUC-AAUUC------------------------------------------------------GUUGAAA-A---GGUGCUA-AAUC--CUG-CGAAGUG-----UGAU----------------------GCUU-CG-A-GA-GAUAAGAG
AL591980.1/89597-89491         CUCUUAUAAUGAG-UGG-U-AG-----------------AGGGA--CUGG-CCCGU--UGAA-ACC--CGGCAACC-U-UUC-AAUAC------------------------------------------------------GUUGAAA-A---GGUGCUA-AAUC--CUG-CGAAGUG-----UGAU----------------------GCUU-CG-A-GA-GAUAAGAG
AL939119.1/177986-178133       CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-UACGG-CCCGA--UGAA-GCC-CCGGCAACC-C-UCC-AGUCGGUUCUUGUCACACGGA----------------------CGUGGCGAGGCUCCCGGCUAGGG-AA--GGUGCCA-AAUC--CGU-CUCACGGC---GAGAUGC------------------GUCGUG-AG-G-AA-GAUGAGGA
AB090330.1/380-279             UACUUAUCAAGAG-CGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--CAGCAACC-U-AUA-UGAAA------------------------------------------------------AUAUAUA-A---GGUGCUA-AAUC--CUG-CAGCA--------UA------------------------AGC-UG-A-GA-GAUGAGGA
U36379.1/1-106                 AUCCU-----GAG-UGG-U-GG-----------------AGGGA-CAUGGACCCAA--UGAA-ACC--CAGCAACC-U-CUU-UUUUA------------------------------------------------------UAAAAGA-AA--GGUGCCA-AACCGUUUG-CAGACA------AAUA----------------------GGUC-UG-A-AC-GAUAAGAG
L42943.1/254-144               CUCUUAUCCUGAG-UGG-U-GG-----------------AGGGA-CAUGGACCCAA--UGAA-ACC--CAGCAACC-U-CUU-UUUUA------------------------------------------------------UAAAAGA-AA--GGUGCCA-AACCGUUUG-CAGACA------AAUA----------------------GGUC-UG-A-AC-GAUAAGAG
AF270301.1/145-36              CUCUUAUCCUGAG-UGG-U-GG-----------------AGGGA-CAUGGACCCAA--UGAA-ACC--CAGCAACC-U-CUU-UAUU--------------------------------------------------------UAAAGA-AA--GGUGCCA-AACCGUUUG-CAGACAA-----AUAU----------------------GGUC-UG-A-AC-GAUAAGAG
AJ002571.1/38016-37861         CUCUUAUCGAGAGUUGG-G-CG-----------------AGGGA--UUGG-CCUUU--UGAC-CCCAACAGCAACC-G-ACC-GUAAUACCAUUGUGAAAUGGGGCGCACUGC-----UUUUCGCGCCGAGACUGAUGUCUCAUAAGGC-AC--GGUGCUA-AUUC--CAU-CAGAU--------UGU-----------------------GUC-UG-A-GA-GAUGAGAG
AL596163.1/172398-172500       UUCUUAUCCAGAG-UGG-U-GG-----------------AGGGA-AUCGG-CCCAG--UGAA-ACC--CGGCAGCG-G-AGC-GC----------------------------------------------------------AAGUUC-----UAUGCUA-AUUC-CGAU-CAGAAG------UAAU----------------------AUUC-UG-G-CA-GAUAAGUA
AL591973.1/137133-137235       UUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA-AUCGG-CCCAG--UGAA-ACC--CAGCAGCG-G-AGC-GC----------------------------------------------------------AAGUUC-----UAUGCUA-AUUC-CGAU-CAGAAG------UAAU----------------------AUUC-UG-G-CA-GAUAAGUA
AL596165.1/180914-180814       UUCUUAUCACGAA-AGG-U-GG-----------------AGGGA--CUGG-CCCUU--UGAA-GCC-UUAGCAACC-G-GAA-UUU---------------------------------------------------------AUUUUC-AC--GGUGCUA-AUUC--CAG-CAGUA--------UA------------------------UUC-UG-A-AA-GAUAAGUC
AL596166.1/166748-166844       AACUUAUCAAGAA-AGG-U-GG-----------------AGGGU-UCUGG-CCCAG--UGAA-GCC-UUGGCAACC-G-GAC-UU-------------------------------------------------------------UUC-AC--GGUGCCA-AAUC--CAG-CAGU---------AUC------------------------AC-UG-A-CA-GAUAAGGC
AL591976.1/242770-242867       AACUUAUCAAGAA-AGG-U-GG-----------------AGGGU-UCUGG-CCCCG--UGAA-GCC-UUGGCAACC-G-GAU-UU-------------------------------------------------------------UUC-AC--GGUGCCA-AAUC--CAG-CAGG--------UAAC------------------------AC-UG-A-CA-GAUAAGGC
AE017333.1/969726-969839       UUCUUAUUCAGAG-AGG-C-GG-----------------AGGGA-AUUGG-CCCUG--UGAA-ACC-UCGGCAGCG-G-GUU-CUGCAUA--------------------------------------------------CAGCAGAAU-AC--UGUGCCA-CAUC--CAA-CAAGCCG-----UACG----------------------GGCU-UG-G-AA-GAUAAGAA
BX571856.1/15939-16037         UUCUUAUUGUGAG-AAG-U-UG-----------------AGGGA-CUUGG-CCCUG--UGAU-ACU-UCAGCAACC-G-ACU-UU----------------------------------------------------------AUAG-C-AC--GGUGCUA-AAAC--CAA-CGAGUU---------------------------------ACU-CG-A-AU-GAUAAGUA
AE017225.1/3092372-3092274     UUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CAGCAACC-G-CGA----------------------------------------------------------------UGC-A---GGUGCUA-AUUC--CAG-CAGAACA-----AAUU---------------------UGUUC-UG-G-GA-GAUAAGAC
AP006716.1/475254-475360       CUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--UGUG-CCCUA--AGAA-GCC--CAGCAACC-G-UCG-UUU---------------------------------------------------------AACGAA-AU--GGUGCUA-AUUC--ACA-UAAAGUAG---ACAAU----------------------ACUU-UA-A-GA-GAUAAGAG
AP006716.1/507636-507743       GACUUAUCCAGAG-AAG-U-GA-----------------AGGGA-UUUGG-CCCAA--UGAA-ACU-UCAGCAACA-G-ACU-UAAAAG----------------------------------------------------ACAAAAGU-AC--UGUGCUA-ACUC-CAAA-GAGGU----------A----------------------UGCC-UC-A-AA-GAUAAGUG
BA000028.3/2365513-2365403     CUCUUAUUCAGAGUUGG-U-GG-----------------AGGGA--CAGA-CCCGA--UGAA-GCC--CAGCAACC-A-UCA-CUACU-------------------------------------------------------GGUGAA-AA--GGUGCUA-AUCU-GAUG-CAAGGAUA---AUAGU----------------------UCCU-UG-A-AC-AAUAAGAG
AE017225.1/177275-177161       CUCUUAUCAAGAG-UGG-C-GG-----------------AGGGA--CUGG-CCCGA--UGAU-GCC--CGGCAACCGA-GCU-UAUGACG---------------------------------------------------UAUAAGCU-AA--GGUGCUA-AUUC--CUG-CAAAAUG-----AGUUU-------------------UCGUUU-UG-G-AA-GAUAAGAG
AP008934.1/131883-131770       CUCUUAUUAAGAGUGAG-U-GG-----------------AGGGA-CUUGG-CCCUA--UGAA-ACU-CCAGCAACA-G-CAG-UC----------------------------------------------------------AUAUGC-GA--UGUGCUA-AAUC--CAA-CAACUCA-----GUAUGAC---------------GAUUGAGU-UG-A-AA-GAUGGGAA
AE017225.1/1375419-1375524     UUCUUAUAAAGAG-AGG-C-GG-----------------AGGGA--CUGG-CCCUA--CGAU-GCC-UCGGCAGCGGA-CUC-GAUUU-------------------------------------------------------UAGAGU-GC--UGUGCCA-AAUC--CAG-CAAGCAU-----GUG-------------------------CU-UG-A-AA-GAUGAGAA
CP000046.1/900604-900707       CUCUUAUCGAGAG-UGG-U-GG-----------------AGGGA--UGUG-CCCUA--CGAA-GCC--CGGCAACC-G-UCU-UAU---------------------------------------------------------AUAGAA-AU--GGUGCCA-AUUC--ACA-UAAAGUU-----UUAA-----------------------CUU-UU-G-AA-GAUGAGAG
BA000043.1/974636-974744       UUCUUAUCAAGAGCAGG-C-GG-----------------AGGGA--CGAG-CCCAA--UGAA-GCC--CGGCAACC-G-GCU-UGGCGCG---------------------------------------------------CGCCAAGC-AC--GGUGCUA-AUUC--UUG-CAGCG--------GAA----------------------ACGC-UG-A-GA-GAUAAGAA
CP000001.1/185418-185523       UACUUAUCCAGAG-AGG-U-AG-----------------AGGGA--CUGG-CCCUA--UGAC-ACC-UCAGCAGCG-G-GUU-CUGUAA-----------------------------------------------------UAGGAAC-AC--CGUGCUA-AUUC--CAG-CAAG---------CAA----------------------GUCU-UG-A-AA-GAUAAGUG
CP000001.1/3927237-3927096     CUCUUAUCAAGAGCAGG-U-GG-----------------AGGGA-UUUGG-CCCGA--UGAA-GCC--CAGCAACC-G-ACC-GUAAUACCAUUGUGAAAUGG------------------------GGCGUUUAUGACGCCAAAAGGC-AC--GGUGCUA-AUUC--CAG-CAGAAAG-----UAAAA--------------------CUUUC-UG-G-CA-GAUAAGAG
CP000046.1/2381002-2380907     CACUUAUCUAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC-UCGGCAACA--------UCUC-------------------------------------------------------GAA--------UGUGCCA-AUUC--CAG-UAACC-------GUAA----------------------UGGU-UU-G-AA-GAUAAGCA
BA000028.3/3162073-3162182     CUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA-AUAGG-CCCUG--CGAA-GCC--CGGCAACC-U-GUA-GCAAUU----------------------------------------------------GCUAUUGA-AA--GGUGCUA-AAUC--CUA-CAGACU------UCAU----------------------CGUC-UG-G-AA-GAUAAGAG
AE017355.1/3872413-3872520     UUCUUAUCAAGAGCAGG-U-GG-----------------AGGGA--CGAG-CCCGA--CGAA-ACC--CGGCAACC-G-AUC-UACAUAA---------------------------------------------------UUGUAGAC-AC--GGUGCUA-AUUC--UCG-CAGC---------AUU----------------------ACGC-UG-A-CA-GAUAAGGA
AP006840.1/2688754-2688649     GGUUCAUCGAGAG-UGG-C-GG-----------------AGGGA--CUGG-CCCCA--UGAU-GCC-ACGGCAACC-U-CUC-CCGCG-------------------------------------------------------GGGAGA-AC--GGUGCCA-AAUC--CAG-CGGAC-------ACUC----------------------GGUC-CG-A-GA-GAUGAAGC
AE017333.1/1735574-1735680     AACUUAUCAAGAG-CGG-U-GG-----------------AGGGA--CUGG-UCCGA--UGAA-ACC--CGGCAACC-U-GCG-UGUGA-------------------------------------------------------AGCGUA-A---GGUGCUA-CUUC--CAG-CAAAAUG-----CCCU---------------------CAUUU-UG-A-GA-GAUAAGGA
AE017355.1/4749676-4749569     CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA-CUGUG-CCCUG--UGAA-GCC--CGGCAACC-G-UCA-ACUUA------------------------------------------------------UGUUGAA-AU--GGUGCCA-AUUC--CUG-CAAAGC------AAAU----------------------GCUU-UG-A-GA-GAUGAGAG
CP000029.1/480767-480869       CUCUUAUCGAGAG-AGG-U-GG-----------------AGGGA--UGUG-CCCUA--AGAA-GCC--CGGCAACC-G-UCU-AAA---------------------------------------------------------AUAGAA-AU--GGUGCCA-AUUC--ACA-UAAAGUA-----UAAC------------------------UU-UA-G-AA-GAUGAGAG
BA000043.1/883132-883242       UUCUUAUCAAGAG-AAG-C-GG-----------------AGGGA-ACUGG-CCCAA--UGAA-GCU-UCAGCAACC-A-GCC-GCCCG-------------------------------------------------------GCGGCC-A---GGUGCUA-AAUC--CAG-CGAAUUGA--GCAUUC----------------------AAUU-CG-G-CA-GAUAAGAA
AP006627.1/604071-603968       UUCUUAUUAAGAG-GAG-C-AG-----------------AGGGA--CUGG-CCCAA--UGAU-GCU-UCAGCAACC-C-CGC-CAU---------------------------------------------------------GAGCGG-AA--GGUGCUA-AUUC--CAG-CAGGA-------CUAC----------------------GUCC-UG-G-GA-GAUAAGAG
AE017355.1/1833727-1833836     UUCUUAUUAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUU--CGAA-GCC-UCAGCAACC-UGAUU-UAUGU-------------------------------------------------------GAUAUA-AA--GGUGCUA-AAUC--CUG-UAGGAUA-----UAAA---------------------AGUCC-UA-A-UA-GAUAAGAA
AP006627.1/3104693-3104588     UUCUUAUCGAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCAA--UGAA-ACC--CGGCAACC-G-CAA-GUU---------------------------------------------------------CGCUUG-AA--GGUGCUA-AAUC--CUG-CAAAGCA-----UAUG---------------------GGCUU-UG-G-GA-GAUGAGAG
AE017334.2/197187-197081       AUUGUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUU--UGAA-ACC-UCGGCAGCA-G-GUU-CAUUU-------------------------------------------------------UUGAAU-AC--UGUGCCA-CUUC--CUG-CAAGCU------UUAU----------------------AGCU-UG-A-AA-GAUAGAAU
BA000043.1/972359-972191       CUCUUAUCAAGAGUUGG-C-UG-----------------AGGGA-AUUGG-CCCAA--UGAA-GCC--CAGCAACC-G-ACC-GUAAUACUAUCGUGAGAUAGGGCGCACGCCAAGGGCGGCGCCGGAAGCGUCAUGCUUCCGCAGGGC-AC--GGUGCUA-AGUC--CAA-CAGAAAGACCGAUGUC----------------------UUUC-UG-A-AA-GAUAAGAG
BA000043.1/2876470-2876356     CUCUUAUCCCGAGCCGG-U-GG-----------------AGGGA--CAGG-CCCGA--UGAA-GCC--CAGCAACC-G-UCA-CAACUGUA------------------------------------------------CAUGUGUGAA-AU--GGUGCUA-ACCU-GUGG-CAAGGCG-----CAGU-----------------------CCU-UG-A-AC-GAUAAGAG
BA000028.3/2134366-2134264     AACUUAUCCAGAG-UGA-C-GG-----------------AGGGA-ACAGG-ACCUA--CGAU-GUC-ACAGCAACC-U-ACC-UU----------------------------------------------------------UACGGA-GU--GGUGCUU-CUUC--CUG-CAGAA--------UUU----------------------UUUC-UG-A-AA-GAUAAGGU
BA000004.3/3590821-3590709     CUCUUAUCAUGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CAGCAACC-G-CCA-AGCAGCAAA-----------------------------------------------UCGCUUGGAA-AA--GGUGCUA-AUUC--CUG-CAAAG-------CGAU----------------------GCUU-UG-A-GA-GAUGAGAG
AE017333.1/1487506-1487363     CUCUUAUCGAGAGUUGG-G-UG-----------------AAGGA--CUGG-CCUAA--UGAU-CCCAACAGCAACC-G-ACC-GUAAUACCAUUGUGAAAUGGGG--------------------CGCGAAUCUCUGCGCCGCUAGGGC-AC--GGUGCUA-AUUC--CAU-CAGACUU-----UGAA-----------------------UUC-UG-A-GA-GAUAAGAG
AE017180.1/2700118-2700220     UUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--AAGG-CCCUG--UGAA-ACC-ACAGCAACC-G-GUC-CGGUAG----------------------------------------------------CGGACGCC-A---GGUGCUA-AAUC--CUG-CCCGA----------------------------------AAG-GG-A-GC-GAUGAGAG
AE017334.2/4074410-4074519     UUCUUAUCUAGAG-AGG-U-AG-----------------AGGGA--CUGG-CCCUA--UGAC-GCC-UCAGCAACC-A-UUA-ACAUU------------------------------------------------------UGUUAAU-AA--GGUGCUA-AUUC--CAG-CAAAUUG----CGAAA----------------------AAUU-UG-A-CA-GAUGAGAA
AE017225.1/4554904-4554783     CUCUUAUCCCGAGCUGG-C-GG-----------------AGGGA--CAGG-CCCGA--UGAA-GCC--CAGCAACC-U-CAC-UUGUAGUGGU--------------------------------------------AAAUACAGGUGA-AU-AGGUGCUA-AAACCUGUG-CGAGGCU-----ACAG----------------------GUCU-CG-A-AC-GAUAAGAG
BA000043.1/3025512-3025403     CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--UGUG-CCCAA--UGAA-GCC--CGGCAACC-G-UCA-GCGCAU----------------------------------------------------GUGCUGAA-AU--GGUGCCA-AUUC--ACA-CAAAGCG-----GCCU----------------------GCUU-UG-A-GA-GAUAAGAG
BA000028.3/3200638-3200530     AUCUUAUCCUGAG-AGG-U-GG-----------------AGGGA-AAUGG-CCCAA--AGAA-GCC-UCGGCAACA-G-GUU-CUAGC-------------------------------------------------------UUGAAU-AC--UGUGCCA-AAUC--CAU-CAAGUAU-----UCUA----------------------UGCU-UG-G-UA-GAUAAGAG
AP006627.1/3008449-3008342     CUUUUAUCCAGAGAUGG-C-GG-----------------AGGGA--CAGG-CCCGA--AGAA-GCC--CAGCAACC-A-ACA-CGUAA-------------------------------------------------------CGUGUA-AA--GGUGCUA-A--C--CUG-CAGAAUG-----CUCGG--------------------CGUUC-UG-G-AA-GAUAAGAG
AE017333.1/4014357-4014466     UCCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUG--UGAA-ACC--CGGCAACC-G-CUG-UCUAU-------------------------------------------------------GACAGA-AU--GGUGCUA-AAUC--CUU-AAGAGCA-----UGUUC-------------------GUGCUC-UU-G-AA-GAUAAGGA
AE017225.1/320618-320724       UUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--CGAU-ACC-UCAGCAACG-G-GUU-UUUUU-------------------------------------------------------AAUAC------CGUGCUA-ACUC--CAG-CAAGCCAU---AUAAA----------------------GGCU-UG-G-AA-GAUGAGAA
AE017333.1/3063716-3063609     AGCUUAUAAAGAG-AGA-U-GG-----------------AGGGA--CUGG-CCCGG--UGAA-AUC-UCAGCAACC-U-GCA-GC----------------------------------------------------------AGUGCA-A---GGUGCUA-AAUC--CAG-CAGAAUG-----UCAGGC------------------GCAUUC-UG-A-AA-GAUAAGUU
AE017355.1/1384699-1384807     AGCUUAUCAAGAG-AAG-C-GG-----------------AGGGA-ACUGG-CCCGG--CGAA-GCU--CGGCAACC-U-GCU-UAUAG-------------------------------------------------------AAAGCA-A---GGUGCUA-AAUC--CAG-CAAAAUG-----GAAUC--------------------CAUUU-UG-A-AA-GAUAAGGU
AP006840.1/138157-138265       CUCUUAUCAAGAG-AAG-C-GG-----------------AGGGA-CCUGG-CCCGA--UGAA-GCU-UCGGCAACCAG-CCU-GCGUC------------------------------------------------------ACCAGGC-AA--GGUGCCA-AGUC--CAG-CCGGGCA-----UACU-----------------------ACC-GG---GA-GAUAAGAG
AE017333.1/1292148-1292264     UUCUUAUCACGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUU--UGAA-ACC-UCAGCAACC-G-GUC-UGCACUGACGA-------------------------------------------CGUCAGUGCACC-AA--GGUGCUA-AAUC--CAG-CAAGCGG-----AUG-------------------------CU-UG-G-AA-GAUAAGAA
AE017355.1/768972-768867       GUCUUAUCAAGAGCAGG-U-GG-----------------AGGGA--UGAG-CCCUA--CGAA-GCC--CGGCAACC-G-ACC-CAUUU-------------------------------------------------------AUGGGC-AC--GGUGCUA-AUUC--UUA-CAACA-------CAUU----------------------GUGU-UG-A-AA-GAUAAGAG
BA000045.2/2730826-2730714     GACUUAUCCAGAGCAGG-C-GU-----------------AGGGA-ACAGG-CCCGG--UGAC-GCC-ACGGCAACCGC-CCA-CUAGC-------------------------------------------------------AACGGG-AAAAGGUGCCA-AUUC--CUG-CGGUUCC-----UCAC----------------------GAAC-CG-G-AA-GAUAAGUC
CP000029.1/1935501-1935405     AACUUAUCAAGAG-AAG-U-GG-----------------AGGGA--CUGG-CCCAA--AGAA-GCU-UCGGCAACA-------UUGUA-------------------------------------------------------UCA--------UGUGCCA-AUUC--CAG-UAACCGA-----GAA------------------------GGU-UA-G-AA-GAUAAGGU
AP006627.1/1705479-1705377     UUCUUAUCCAGAG-AGA-U-GG-----------------AGGGA-UUUGG-CCCUU--UGAA-GUC-UCAGCAACC-G-GCC-UUU-----------------------------------------------------------GGCA-AU--GGUGCUA-AUUC--CAA-UAGGUAA-----UGUA------------------------CC-UA-G-GA-GAUAAGAA
AE017334.2/2953356-2953255     UUCUUAUCACGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC-UCGGCAGCG-G-AUU-CGUUA-------------------------------------------------------UGAAUA-C---UGUGCCA-AUUC--CAG-CAAGG----------U----------------------AACU-UG-A-AA-GAUAAGAA
AE017355.1/2515876-2515991     UACUUAUCCAGAG-AGG-U-GG-----------------AGGGA--ACGG-CCCUA--UGAA-ACC-UCAGCAACC-C-CUA-UGUAAA----------------------------------------------------UGCAUAGG-AA--GGUGCUA-AUUC--C-G-CAGAGAA-----CACGUUG----------------UGUUUUU-UG-G-AA-GAUAAGAG
AP006627.1/1563582-1563686     CUCUUAUAACGAG-AAG-C-GG-----------------AGGGA--CUGG-CCCAA--UGAA-GCU-UCAGCAACC-A-UUC-AUUGC-------------------------------------------------------GAUGAA-AA--GGUGCUA-AAUC--CAG-CAAAGGG-----AAC-------------------------UU-UG-G-CA-GAUAAGGG
BA000004.3/910192-910088       UUCUUAUCCAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUG--UGAA-GCC--CGGCAACC-U-CUU-UUUU--------------------------------------------------------UAAAGA-A---GGUGCCA-AUUC--CAG-CAGAACA-----UGAU----------------------GUUC-UG-A-AA-GAUAAGAA
AE017225.1/4074580-4074471     CUCUUAUUGAGAG-CGG-U-GG-----------------AGGGA--AAGG-CCCUG--UGAA-ACC--CGGCAACC-U-UCA-AACGAAA---------------------------------------------------UGUUUGAA-AC--GGUGCUA-AUAC--CUG-CAAAAC------GAAU----------------------GUUU-UG-C-AU-AAUAAGAG
BA000028.3/1319041-1319141     UACUUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCGC--UGAA-ACC-UCAGCAAC--A-GAA-CGCAU-------------------------------------------------------CUGUCU------GUGCUA-AAUC--CUG-CAAGC--------AAU----------------------AGCU-UG-A-AA-GAUAAGUU
BA000028.3/727026-727131       GACUUAUCAAGAG-AGA-U-GG-----------------AGGGA--UUGG-CCCGA--UGAA-GUC-UCAGCAACC-A-GCC-UAGAU-------------------------------------------------------AAGG-U-AU--GGUGCUA-AUUC--CAA-UAGGCUU-----ACAA-----------------------GCC-UU-A-AA-GAUAAGAA
AE009951.2/1317653-1317567     UAACCAUCCAGAG-AAA-C-GG-----------------AGGGA--CUGG-CCCAA--UGAU-GUU-UCAGCAACC-U-ACU-UA----------------------------------------------------------AAUGUG-U---GGUGCUA-AUUC--CAG-----------------------------------------------A-GA-GAUGGAGA
AP008934.1/276954-277060       CUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--UGUG-CCCGA--UGAA-ACC--CAGCAACC-G-UCG-AUUU--------------------------------------------------------UUCGAA-AU--GGUGCUA-AGUC--ACA-AAAAGUU-----AUUU---------------------AACUU-UU-G-GA-GAUGAGAG
AP006840.1/278272-278389       CUCUUAUCCAGAGUAGG-C-UG-----------------AGGGA--CUGG-CCCGA--UGAC-GCC-ACGGCAACC-G-GCA-CGUCUCCC------------------------------------------------CAGGCGUGCA-GC--GGUGCCA-AUUC--CUG-GGGAGGG-----CUCCG--------------------CCCUC-CC-G-AA-GAUGAGAG
AE017333.1/3302616-3302509     CUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--AGUG-CCCUA--UGAA-ACC--CGGCAACC-A-UCA-ACACG------------------------------------------------------UGUUGAA-AU--GGUGCCA-AUUC--ACG-CGAAGCG-----UUAU----------------------GCUU-UG-A-AA-GAUGAGAG
AP008934.1/15667-15765         AUCUUAUUUCGAG-AAG-C-UG-----------------AGGGA-CUUGG-CCCAG--UGAU-GCU-UCAGCAACCGG-CUG-UGU------------------------------------------------------------AGU-AC--GGUGCUA-AAAC--CAA-CGA----------UAC----------------------AC-U-CG-A-AU-GAUAAGUA
CP000001.1/5213243-5213138     GUCUUAUCAAGAAAAGG-U-GG-----------------AGGGA--CAGG-CCCGA--UGAA-ACC-UUGGCAACA-G-CCG-UAU---------------------------------------------------------AACGGA-AU--UGUGCCA-AAUC--CUG-CAGGUAA-----UAAA-----------------------UCC-UG-A-GA-GAUAAGAA
AE017355.1/388363-388251       UCUUUAUCAAGAG-AGG-C-AG-----------------AGGGA--CCGG-CCCUU--UGAA-GCC--CAGCAACC-U-CAG-UUUAUA----------------------------------------------------CAAACUGA-AU-AGGUGCUA-AUUC--CUG-CAAAAUG-----CAUUG--------------------CAUUU-UG-A-AA-GAUAAAAC
BA000028.3/2437307-2437208     CUCUUAUCUAGAG-CGG-U-GG-----------------AGGGA--CUGG-CCCUU--UGAA-ACC-GCGGCAACC-U-UCA-UAAUU-------------------------------------------------------AAAUGA-AA--GGUGCCA-AUUC--CUG-CA-----------GAA----------------------AA---UG-A-AA-GAUGAGAG
AP008934.1/1011112-1011223     CUCUUAUCCUGAG-UGG-C-GG-----------------AGGGACAUGGA-CCCAA--UGAA-GCC--CAGCAACC-U-CUU-CUUAA------------------------------------------------------UUGAAGA-AA--GGUGCCA-AACCGUUUG-CAGACAA-----AUAG----------------------CGUC-UG-A-AC-GAUAAGAG
BA000004.3/1699957-1700066     UUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--ACGG-CCCGA--AGAA-ACC-UCAGCAACC-A-GCC-ACGAUC-----------------------------------------------------CUGUGGU-CA--GGUGCUA-AUUC--CUG-CAAGCAU-----UAUU----------------------UGCU-UG-A-GA-GAUAAGAG
BA000028.3/2708645-2708539     UUCUUAUCAUGAG-AGG-C-GG-----------------AGGGA-AAUGG-CCCAA--CGAA-ACC-UCGGCAACA-G-GUU-CUUAU-------------------------------------------------------UAGAAU-AC--UGUGCCA-AUUC--CAU-CAAGC-------AAAU----------------------UGCU-UG-A-AA-GAUAAGAG
AP008934.1/318535-318643       AACUUAUCCAGAG-AAG-U-UG-----------------AGGGA-AUUGG-CCCUG--UGAA-GCU-UCAGCAACAGA-CUU-UGUAA-------------------------------------------------------AGAAGU-AC--UGUGCUU-CGUC--CAA-CAAGUAA-----UACU-----------------------ACU-UG-A-AA-GAUAGGUG
BA000004.3/3427467-3427355     CUCUUAUCCAGAGUUGG-U-GG-----------------AGGGA--CAGG-CCCGA--AGAA-ACC-CCAGCAACC-A-ACA-CCUGUUAAA-----------------------------------------------CAAAGGUGAA-AA--GGUGCUA-A--C--CUG-CAAGG-------CGUU----------------------GCCU-UG-A-AA-GAUAAGAG
AE006470.1/606189-606295       CUAUCAUCCAGAA-AGG-C-GG-----------------AGGGA--CUGG-CCCUG--CGAA-GCC-UUGGCAACC-U-UCA-UUCCA-------------------------------------------------------CAUGAG-C---GGUGCCA-AAUC--CAU-CCCGGAG-----GAAA----------------------UCCG-GG-A-AA-GAUGAUGU
AP006716.1/417999-418100       GUCUUAUUAAGAGUGAG-U-GG-----------------AGGGA-AUUGG-CCCUA--UGAA-GCU-CCAGCAACU-G-CGC-UUU-----------------------------------------------------------GCGU-GA--GGUGCUA-AAUC--CAA-CAGG---------AGU----------------------UUCC-UG-A-AA-GAUAAGAA
BA000028.3/3466520-3466401     CUCUUAUUGAGAG-UGG-C-UG-----------------AGGGA--CUGG-CCCUG--UGAC-GCC--CGGCAACC-G-UUC-AUCGUAAUUC---------------------------------------------CAGUGAUGAAU-A---GGUGCUA-AAUC--CUG-CAAAAUACG-GACAGU----------------------AUUU-UG-A-GA-AAUAAGAG
BA000016.3/2500083-2499978     CUCUUAUCCAGAG-AGG-U-GG-----------------AGGGAAAAAGG-CCCUA--UGAA-ACC--CGGCAACC-A-GUG-AGAA--------------------------------------------------------AUCACU-AC--GGUGCCA-AUUC--CGG-UAAAG-------AAAU----------------------UCUU-UA-C-AA-GAUGAGAG
AP008934.1/1948647-1948540     CUCUUAUCACGAG-AGG-U-GG-----------------AGGGA--UGUG-CCCUU--UGAA-GCC--CGGCAACC-G-UCU-GUA---------------------------------------------------------ACAGAA-AU--GGUGCCA-AUUC--ACA-UAAAGUU-----CAUAG-------------------AAACUU-UA-G-AA-GAUGAGAG
CP000088.1/254824-254964       UGCUCAUCCAGAG-GGG-U-GG-----------------AGGGA-CACGG-CCCUG--UGAA-GCC-CCGGCAACC-A-UCC-CGGUGGACGUUGCUCGUC-----------------------------AGGUGCGAGGCGGCCGGGA-CA--GGUGCCA-ACUC--CGU-CCCACUG-----UCAAGGU----------------GGCAGUG-GG-G-AA-GAUGAGGG
AP006627.1/1701649-1701759     AACUUAUCAAGAG-UGG-C-GG-----------------AGGGA-CCUGA-CCCAA--UGAA-GCC--CGGCAACC-A-GUU-UAUUU------------------------------------------------------GUAAACC-AC--GGUGCUA-CAUU--CAG-CAGAGCA-----GCUUU--------------------UGUUC-UG-A-AA-GAUAAGUG
AE017333.1/3080753-3080616     CUCUUAUCCCGAGCUGG-U-GG-----------------AGGGA--CAGG-CCCAA--UGAA-ACC--CAGCAACC-G-GUU-UCUCUUAUUAAUGGAAAA----------------------------AAACAGUUUCUGAGACAACU-AC--GGUGCUA-ACCU-GAUG-CAAGGUGU---UCAAU----------------------ACCU-UG-A-GC-GAUAAGAG
AE017333.1/1489705-1489804     UUCUUAUCAAGAGCAGG-C-AG-----------------AGGGA--CAAG-CCCGA--UGAA-GCC--CGGCAACC-G-ACU-UUU---------------------------------------------------------UAAG-C-AC--GGUGCUA-AUUC--UUG-CAGCU----------G----------------------ACGC-UG-A-GA-GAUAAGGA
AE017180.1/1014096-1014202     AACUUAUCAAGAG-CGA-C-CG-----------------AGGGA--CAGG-CCCGG--UGAC-GUC-GCGGCAACC-U-CCC-CAU---------------------------------------------------------GGGGGG-AA--GGUGCCA-AUUC--CUG-CGAGACC-----GACA---------------------GGUUU-CG-G-GA-GAUAAGGA
AP006840.1/1830606-1830721     CUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA-ACUGG-CCCGA--UGAA-ACC--CGGCAACC-C-AGG-ACGCUGCG-------------------------------------------------GGGCGUCCG-AA--GGUGCCA-ACUC--CAC-CGGCGGC-----CUCAC--------------------GCCGC-CG-G-AA-GAUAAGAG
AP006716.1/14213-14314         AACUUAUUAAGAG-AAG-U-GG-----------------AGGGA-CACGG-CCCUG--AGAA-ACU-UCAGCAACC-G-GCG-AUGCA-------------------------------------------------------UACG-C-AC--GGUGCUA-CUAC--CAA-CGAGAU---------------------------------ACU-CG-A-AU-GAUAAGUA
AE017333.1/1207733-1207622     UUCUUAUCAAGAG-AGG-C-AG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC-UCAGCAACC-G-GUG-AAUGAAUA-------------------------------------------------UUCAUGACC-AA--GGUGCUA-AAUC--CAG-CAAGC-------AGCC----------------------UGCU-UG-G-AA-GAUAAGAA
BA000028.3/1098099-1097993     UUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCAA--GGAA-GCC-UCGGCAACA-G-ACU-UAUUUG----------------------------------------------------AUUAAGUA-C---UGUGCCA-AUUC--CAG-UAGCGUA-----AUU-------------------------GC-UA-G-AA-GAUGAGAA
BA000043.1/745485-745383       UUCUUAUCAAGAG-AGG-G-GG-----------------AGGGA--CUGG-CCCGG--UGAA-CCC-UCAGCAACC-U-GGC-CCG---------------------------------------------------------CGGCCA-A---GGUGCUA-AAUC--CAGACAGGCGG-----AAG-------------------------CC-UG-G-AA-GAUAAGAA
AP006627.1/1983212-1983311     UUCUUAUCAAGAG-AAG-U-GG-----------------AGGGA--AUGG-CCCAA--UGAA-GCU-UCAGCAACC-A-GCC-AAC---------------------------------------------------------CAUGGU-CA--GGUGCUA-AAUC--CAG-CAG----------UUU----------------------AU-C-UG-C-AA-GAUAAGAG
CP000001.1/334370-334474       UUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--CGAU-ACC-UCAGCAACG-G-GUU-UUUU-----------------------------------------------------------AAU-AC--CGUGCUA-ACUC--CAG-CAAGCCU-----AUAA---------------------GGGCU-UG-G-AA-GAUGAGAA
AP006627.1/951406-951512       GACUUAUCAAGAG-CGA-C-UG-----------------AGGGA-UUAGG-CCCAA--UGAC-GUC--CAGCAACC-U-CCC-GUU---------------------------------------------------------ACGGGG-AA--GGUGCCA-AUUC--CUG-CAGAAUG-----GGAU---------------------CAUUC-UG-A-AA-GAUAAGCC
AP006716.1/2100177-2100072     UUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--UGUG-CCCUA--UGAA-GCC--CGGCAACC-G-UCU-AGUU--------------------------------------------------------AUAGAA-AU--GGUGCCA-AUUC--ACA-UAAAGUU-----GAUU----------------------ACUU-UA-G-AA-GAUGAGAG
AP008934.1/616628-616728       AACUUAUCAAGAG-AAG-U-GG-----------------AGGGA--CUGG-CCUGU--GGAU-ACU-UCGGCAACA-U-GAU-UAU------------------------------------------------------------GCG-----UGUGCCA-AUUC--CAG-UAGCAUC-----AUUU----------------------AUGC-UA-G-AA-GAUAAGAA
BA000004.3/1348816-1348929     GACUUAUCGAGAG-AGG-C-AG-----------------AGGGA--CUGA-CCCGA--UGAU-GCC--CGGCAACC-C-GUU-UGUUAGCC-------------------------------------------------AAGCAAACG-AA--GGUGCUA-AUUU--CAG-CAGAAUG-----AUUU---------------------CAUUC-UG-G-AA-GAUAAGCG
CP000141.1/2169978-2169874     CUCUUAUCAAGAG-UGG-C-GG-----------------AGGGA--CUGG-CCCAA--UGAA-GCC--CGGCAACC-G-GCC-AUAUU------------------------------------------------------UUUGGCA-AU--GGUGCCA-AUUC--CUG-CGGAU--------UAA----------------------AUUC-CG-G-GA-GAUAAGAG
AM412317.1/1193313-1193415     UUCUUAUCAAGAG-CGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CGGCAACCAG-UAU-AUAUU-------------------------------------------------------UUAUAC-AU--GGUGCUA-AAUC--CUG-CAG---------AUUU----------------------AA-C-UG-A-AA-GAUGAGAA
AM180355.1/1724139-1724245     GUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUU--UGAA-ACC--CGGCAACC-A-GUA-UAUUUU-----------------------------------------------------AUAUACA-UU--GGUGCUA-AAUC--CUG-CAACUAA-----UAUA------------------------GU-UG-A-UA-GAUGAGUA
AAWL01000001.1/327573-327687   CUUUCAUCAAGAGCUGG-C-UG-----------------AGGGA--CUGG-CCCGA--UGAC-GCC-GCGGCAACC-A-UCG-CAUCUUU--------------------------------------------------GGGUGCGAA-AC--GGUGCCA-AUUC--CUG-CAGAACG-----GAUA---------------------AGUUC-UG-A-CA-GAUGAGGG
AAJM01000461.1/236-129         UUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCUUA--UGAA-ACC-UCAGCAACAGG-UCU-GCUUA------------------------------------------------------AGUAGAC-AC--UGUGCUA-AUUC--CAG-CGGGUGA-----UAAU------------------------CC-UG-A-UA-GAUGAGAG
CP000728.1/2062169-2062064     CUCUUAUCAAGAG-UGG-C-GG-----------------AGGGA-UCAGG-CCCUG--UGAA-GCC--CGGCAACA-G-CUA-GUUGA------------------------------------------------------ACCUAGA-AA--UGUGCUA-AUUC--CUG-CAGUG--------GAU----------------------UCAC-UG-A-GA-GAUGAGGG
CP000568.1/2679822-2679717     ACCUUAUCAAGAG-AGG-C-GG-----------------AGGGA-AUGGG-CCCUA--UGAA-ACC--CGGCAACC-G-GCA-GA----------------------------------------------------------AUUGUA-UC--GGUGCCA-AUUC--CUA-CAGGAUG-----UAAA---------------------AGUCC-UG-A-CA-GAUGAGGA
AP008230.1/4549598-4549497     UUCUCAUCCAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC-G-GCC-UAU---------------------------------------------------------AUGGCA-GU--GGUGCUA-AUUC--CAG-CAGGAUU-----AUU-------------------------CC-UG-G-AA-GAUGAGCA
CP000726.1/3620086-3619976     UUCUUAUCCAGAG-CGG-C-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--CGGCAACCAC-UAA-GGUGUUUU------------------------------------------------AUUACUUUAA-AC--GGUGCUA-AUUC--CAG-CAGG---------UUA----------------------AACC-UG-G-UA-GAUAAGAU
AAOX01000018.1/27020-26864     CUCUUAUCAAGAGCAGG-C-AG-----------------AGGGA-CUUGG-CCCGA--UGAU-GCC--CAGCAACC-G-ACC-GUAAUUCCAUCGUGAGAUGGGGCGCAAU---------CCUUGCGCCGGAGAAUUCCUCCAUAAGGC-AC--GGUGCUA-AUUC--CAG-CAGAAAG-----CUUGG--------------------CUUUC-UG-G-CA-GAUAAGAG
AAXV01000005.1/126573-126679   UUCUUAUCAAGAG-AGA-C-GG-----------------AGGGA--UCGG-CCCGA--UGAA-GUC-UCAGCAACC-A-GCU-CA----------------------------------------------------------AUCAGU-AU--GGUGCUA-AUUC--CUU-UUGGCAA-----AAUCU--------------------AAGCC-UG-A-AA-GAUGAGAA
AAOX01000014.1/12064-12163     UUCUUAUCCAGAG-AGG-U-AG-----------------AGGGA--CUGG-CCCUA--UGAC-ACC-UCGGCAGCG----GA-CUGAU-------------------------------------------------------GAAC-------CGUGCCA-AUUC--CAG-CAGGC-------AGAU----------------------UGCC-UG-A-AA-GAUAAGAA
CP000612.1/2418052-2417945     UACUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--CGGCAACC-G-GCC-AUUGG-------------------------------------------------------AUGGCG-GC--GGUGCCA-ACUC--CUG-CAGGACU-----UUUA---------------------GUUCU-UG-A-GA-GAUAAGGU
CP000673.1/1716322-1716209     UUCUUAUCAAGAG-AGA-C-GG-----------------AGGGA--CUGG-CCCUA--UGAU-GUC--CGGCAACCAG-AAG-AUUUU-------------------------------------------------------UAUUUC-AU--GGUGCUA-AUUC--CAG-CAGGUAU-----UAAUAUG----------------AAAAGCC-UG-A-UA-GAUAAGAG
CP000673.1/2974771-2974666     GCUUUAUCAAGAG-CGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--CAGCAACC-A-GUA-UUGUUUU---------------------------------------------------UUAAUACA-UU--GGUGCUA-AUUC--CUA-CAGCU----------U----------------------AAGC-UG-A-AA-GAUAGGGG
AM180355.1/174147-174250       ACCUUAUCAAGAG-AGG-C-UG-----------------AGGGA--UAGG-CCCUG--UGAA-GCC--CAGCAACC-A-CCC-AAA---------------------------------------------------------UGGGAA-AA--GGUGCUA-AUUC--CUA-CAAGACA-----AAAG-----------------------UCU-UG-A-AA-GAUGAGGU
CP000724.1/4004549-4004448     AACUUAUCAAGAG-AAA-C-UG-----------------AGGGA--CUGG-CCCGA--UGAU-GUU-UCAGCAACCAC-ACA-UAU------------------------------------------------------------GUG-AC--GGUGCUA-AAUC--CAG-CAGAACA-----UAGU------------------------UC-UG-G-GA-GAUGAGAA
AAXV01000010.1/2942-2843       UUCUUAUCAAGAG-AAG-C-AG-----------------AGGGA--CUGG-CCCAA--UGAA-GCU-UCAGCAACC-A-ACU-UUUU-----------------------------------------------------------GUC-A---GGUGCUA-AAUC--CAG-AAGACCG-----UUGA-----------------------GUC----G-AA-GAUGAGAA
CP000724.1/763663-763763       GCCUUAUCAAGAG-UGA-U-GG-----------------AGGGG-AAGGG-CCCGA--UGAA-AUC--CGGCAACC-A-UAG-AG-------------------------------------------------------------UGU-AU--GGUGCUA-AGUC--CCU-CAGAAU------UUUG----------------------GUUC-UG-A-AA-GAUGAGGA
AAXV01000011.1/30443-30546     UUCUUAUCAAGAG-AGA-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-AUC-UCGGCAGCG-G-AAC-UAUUA-------------------------------------------------------AGUUAC-----UGUGCCA-AAUC--CAG-CAAGCAA-----UGUU------------------------CU-UG-A-UA-GAUAAGAG
AAOX01000002.1/320062-320165   UUCUUAUCAAGAG-AGA-C-GG-----------------AGGGG-UAUGG-CCCGA--AGAA-GUC-UCGGCAGCA-G-GUU-CAU---------------------------------------------------------CCGGAC-AC--UGUGCCA-AAUC--CAU-CAGGC--------AAA----------------------GGCC-UG-G-CA-GAUAAGAA
ABCB02000018.1/9340-9436       CCCUUAUCAAGAG-AGG-C-GG-----------------AGGGA-ACAGA-CCCUG--UGAU-GCC--CGGCAACC-U-GCG-GUUU-----------------------------------------------------------GCA-A---GGUGCCA-AUUU--CUG-CGG----------GAA----------------------AA-C-CG-G-AA-GAUGAGGU
CP000685.1/4776282-4776182     UACUUAUCCAGAA-AGA-C-UG-----------------AGGGA-AUAGG-CCCAA--UGAA-GUC-UUAGCAACC-U-GUU-GC----------------------------------------------------------CGAAUA-A---GGUGCUA-AAUC--CUU-CCGC---------UAU----------------------AAGC-GG-G-CA-GAUAAGAA
CP000557.1/1285675-1285779     GUCUUAUCAAGAG-UGG-G-CG-----------------AGAGA-ACGGG-CUUGA--UGAC-CCC-ACAGCAACC-U-GCC-GCU-----------------------------------------------------------GGCA-A---GGUGCUA-AAAC--CCG-CAAAGCG-----AGUU---------------------CGCUU-UG-G-AU-GAUAAGAA
AE015927.1/303338-303443       CUCUUAUCGAGAG-AGG-U-GG-----------------AGGGA-AAGGG-CCCUA--UGAA-ACC--CGGCAACC-A-AUA-UUUUUA----------------------------------------------------GAAGUAUU-AA--GGUGCCA-AUUC--CUG-CAGAA----------A----------------------GUUC-UG-C-AA-GAUAAGAG
AE001437.1/453563-453665       UUCUUAUCAAGAG-UGA-C-GG-----------------AGGGA--UAGG-CCCUA--UGAA-GUC--CGGCAACA-U-CCA-AUUAU-------------------------------------------------------UUUGGA-GA--UGUGCUA-AUUC--CUA-CAGG---------UUU----------------------AUCC-UG-A-GA-GAUGAGAA
CP000673.1/503077-503184       UUCUUAUCAAGAG-CGG-C-GG-----------------AGGGA--UAGG-CCCUA--UGAA-GUC--CGACAACC-G-ACA-UUUUG-------------------------------------------------------UGCAUC-----GGUGUCA-AUUC--CUA-CAGAGUG-----UGUUA-------------------AUACUC-UG-A-AA-GAUAAGAA
AAOX01000055.1/439-545         UUCUUAUCGAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUG--UGAU-ACC--CGGCAGCC-G-CUG-ACUUA-------------------------------------------------------GUCAGA-AU--GGUGCUA-AAUC--CAG-CAAAGCG-----CAAU----------------------GCUU-UG-G-CA-GAUAAGAU
CP000612.1/107660-107768       CUCUUAUCCUGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CAGCAACCAU-UCG-GUUAA------------------------------------------------------GCCCGGA-CU--GGUGCUA-AUUC--CUG-CAGAAGA-----UAUU----------------------CUUC-UG-G-CA-GAUAAGAG
AAWL01000002.1/146610-146509   UACUCAUCAAGAGUUGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC-GCGGCAACCAU-UUG-GCAAG-------------------------------------------------------UCCAAA-AC--GGUGCCA-AUUC--CGG-CG-----------UAC----------------------GG---CG-C-GA-GAUGGGGA
AP008230.1/4551167-4551265     CUCUUAUCAAGAG-AGG-C-GG-----------------AGGGA--CUGG-CCCCA--UGAA-GCC--CGGCAACC-U-ACA-UAU------------------------------------------------------------GUG-A---GGUGCUA-AAUC--CAGAGAACC--------AUC----------------------AGGU-UC-G-AA-GAUAAGAG
CP000673.1/1915422-1915314     UUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAU-GCC--CGGCAACC-U-GAA-UGUAUU----------------------------------------------------UACAUUCA-AU--GGUGCUA-AUUC--CAG-CAGGUAA-----UAUA-----------------------ACC-UG-A-AA-GAUGAGAG
AP009389.1/1533734-1533850     CUCUUAUCCGGAG-UGG-C-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--CGGCAACC-U-UUG-GGUAUAUAG----------------------------------------------GCGUACCCAAA-AA--GGUGCUA-AUUC--CUG-CAGGAGA-----UUUA---------------------UCUUC-UG-A-CA-GAUAAGGG
CP000673.1/3104226-3104112     UUCUUAUCAAGAG-AGG-C-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CAACAACC-G-GCA-UUUAUUU--------------------------------------------------CAAUAUGUA-UC--GGUGUUA-AUUC--CUG-CAGAGUU-----AAUUU-------------------AUACUC-UG-A-AA-GAUGAGAA
AAOX01000006.1/30687-30791     CUCUUAUCCAGAG-AGG-C-GG-----------------AGGGA-AUUGG-CCCUA--UGAA-GCC-UCGGCAGCA-G-ACU-CCUUG-------------------------------------------------------CGAG-A-AC--UGUGCCA-AAUC--CAA-CAAGCGG-----AAG-------------------------CU-UG-G-AA-GAUGAGAG
AE015927.1/1456770-1456662     AGCUUAUUAAGAG-CGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--CGGCAACC-U-GUA-UAUGUGUUU-----------------------------------------------GCAUAUUAUA-A---GGUGCUA-AAUC--CUG-CGGUG----------U----------------------AAAC-CG-A-GA-GAUGAGGA
AE017194.1/1084280-1084386     UUCUUAUGUUGAG-AAG-U-GG-----------------AGGGA--CGGG-CCCUA--UGAA-ACU-UCGGCAACC-U-CGU-AUG---------------------------------------------------------AGACGA-AA--GGUGCCA-AAUC--CUG-CAGGUGA-----AGAA---------------------ACACC-UG-A-AA-GAUAAGAG
AE017194.1/3299167-3299061     UUCUUAUUAAGAG-AGA-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-AUC-UCAGCAACA-G-GCU-AUA---------------------------------------------------------AAAGUA-C---UGUGCUA-AGUC--CAG-CAAACGU-----AUGAA--------------------GCGUU-UG-G-AA-GAUGAGGG
AE015927.1/1226200-1226097     AUCUUAUCAAGAG-CGG-U-UG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CAGCAACC-U-AUA-CACAA-------------------------------------------------------AGUAUA-AA--GGUGCUA-ACUC--CAG-CAGGA--------AAU----------------------UUCC-UG-A-AA-GAUAAGAA
AAXV01000007.1/42365-42470     CUCUUAUCAAGAG-UAG-C-UG-----------------AGGGA--CUGG-CCCUA--UGAA-GCU--CGGCAACC-U-CCU-UUUAU-------------------------------------------------------AAAGGA-A---GGUGCUA-AAUC--CUG-CAAACGA-----AAUU----------------------CGUU-UG-A-UA-GAUAAGAG
AAOX01000002.1/340881-340984   CACUUAUCUAGAG-UGG-C-UG-----------------AGGGA--CUGG-CCCAU--CGAA-GCC--CGGCAACC-U-GCU-AAAA-----------------------------------------------------------GCA-A---GGUGCCA-AUUC--CAG-CAAAAUG-----UCCAG--------------------CAUUU-UG-G-GA-GAUAAGGU
AAXG02000006.1/101826-101729   GCCUUAUCAAGAG-CGG-U-GG-----------------AGGGA--ACGG-CCCGA--UGAA-ACC--CGGCAACC-U-GCG-CAU---------------------------------------------------------UGCGCA-A---GGUGCCA-AAUC--CGG-CGA----------GAG----------------------AA-U-CG-A-AA-GAUGAGGA
CP000673.1/818867-818971       AACUUAUUAAGAG-AGG-C-GG-----------------AGGGA--AAGG-CCCUA--UGAA-GUC--CGGCAACC-A-GCA-UUAUG------------------------------------------------------UAAUGUA-UU--GGUGCUA-AAUC--CUG-CAGCAUU-----GUA-------------------------GC-UG-A-AA-GAUGAGGU
AE001437.1/1976371-1976471     UUCUUAUCAAGA--AGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--UGACAACC-G-GCA-AAU------------------------------------------------------------GUA-C---GGUGUUA-AUUC--CUG-CAAAACU-----UAUU---------------------UGUUU-UG-A-AA-GAUAAGAA
AE001437.1/2914841-2914733     GUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CAACAACCAG-CAU-UUUUUAA---------------------------------------------------UUAGAUGU-AU--GGUGUUA-AUUC--CUG-CAAAGUU-----AAU-------------------------UU-UG-A-GA-GAUAAGAG
CP000232.1/2070462-2070570     CUCUUAUCGAGAGCUGG-C-GG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CGGCAACC-G-GCC-UCUUAGA---------------------------------------------------ACCCAGGU-AC--GGUGCCA-AUUC--CUG-CAGGA--------UUU----------------------CUCC-UG-G-CA-GAUGAGAG
AAEW02000009.1/42224-42117     GUGUUAUCACGAG-UGG-U-GG-----------------AGGGA--AUGG-CCCUU--UGAA-ACC-ACAGCAACCGG-UCC-UGACGUU--------------------------------------------------CAGGAUGAC-A---GGUGCUA-AUUC--CAC-CCCCG----------C----------------------AAGG-GG-A-CA-GAUGAGAC
AAWL01000026.1/22109-22215     CUCUUAUCAAGAG-CGG-U-GG-----------------AGGGA--CUGG-CCCUG--UGAA-GCC-GCGGCAACC-G-GCA-GCAA--------------------------------------------------------UGCGUC-U---GGUGCCA-AAUC--CAG-CAGAAUC-----UUCG---------------------GAUUC-UG-G-AA-GAUGAGAG
CP000724.1/968949-968838       CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACCAC-GAA-UUGUUUU--------------------------------------------------UGCAAUUCG-AA--GGUGCUA-AUUC--CAA-CAACAC------UUAU----------------------GUGU-UG-A-AA-GAUGAGAG
ABCF01000005.1/97205-97306     UUCUUAUCGAGAG-AGG-C-AG-----------------AGGGA--CUGG-CCCUG--UGAA-GCC-UCGGCAGCGGA-CUA-UU----------------------------------------------------------UAUAGU-AC--CGUGCCA-AAUC--CAG-CAAGC---------AU----------------------GUCU-UG-G-GA-GAUAAGAA
AAXV01000019.1/61222-61331     AUCUUAUCAAGAG-AAG-C-AG-----------------AGGGA-UUUGG-CCCGA--UGAC-GCU-UCAGCAACC-U-CUA-ACAAA------------------------------------------------------UGUUAGA-AA--GGUGCUA-AUUC--CAG-CAAAGGU-----UUUU----------------------CCUU-UG-A-GA-GAUAAGAG
AAOX01000038.1/20734-20635     UUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC----GG-CAAUA-------------------------------------------------------GAAC-------GGUGCUA-AUUC--CAG-CAGAGCA-----UGAU-----------------------CUC-UG-G-CA-GAUAAGUU
CP000612.1/3367128-3367031     UGCUCAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC-------UCACG-------------------------------------------------------UAA--------GGUGCCA-AGUC--CUG-CGGGAAG-----AAUA----------------------UUCC-UG-A-CA-GAUGAGGU
BA000028.3/3200764-3200871     UUCUUAUCGAGAG-AAG-C-UA-----------------AGGGA-CCUGG-CCUGU--UGAC-GCU-UCAGCAACC-U-CUA-UCUCC-------------------------------------------------------AUUAGA-AA--GGUGCUA-CCUC--CAG-CAAGAU------GUAU----------------------GUCU-UG-A-AA-GAUAAGAG
AAOX01000006.1/96737-96624     UUCUUAUCAAGAG-AGG-C-AG-----------------AGGGU--AUGG-CCCUG--UGAA-GCC-UCAGCAACC-U-UCA-AUGGAUA---------------------------------------------------AUAUUGAA-AA--GGUGCUA-AUUC--CUG-CAGGUCC-----UUUAU--------------------GGGCU-UG-A-AA-GAUAAGAA
BA000028.3/2856865-2856757     UCCUUAUCAAGAGUCGG-G-GG-----------------AGGAA-UCUGG-UCCAU--UGAU-CCC-GCAGCAACCAG-UUA-CAAUG------------------------------------------------------AAGUAAC-AU--GGUGCUC-AUUC--CAG-CAAGC--------GUA----------------------GGCU-UG-A-UA-GAUGAGAA
CP000673.1/3384182-3384086     UUCUUAUUUUGAG-AGA-C-GG-----------------AGGGA--CUGG-CCCUA--UGAU-GUC--CGGCAACC-U-GAA-UAU------------------------------------------------------------UUA-A---GGUGCUA-AUUC--CAG-CAGG---------UAU----------------------UACC-UG-A-GA-GAUAAGAA
CP000382.1/316300-316411       AUCUUAUCAAGAG-UGG-U-UG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CGGCAACA-A-CUA-AUUUUCAU------------------------------------------------UUAAAUUAGU-AA--UGUGCUA-AUUC--CAG-CAGGA-------AAUU----------------------UUCC-UG-A-AA-GAUAAGAG
AE001437.1/1073888-1073785     UCCUUAUCAAGAG-AAA-C-GG-----------------AGGGA--CUGG-CCCAA--UGAU-GUU-UCAGCAACC-A-AGG-UUUU--------------------------------------------------------AUACUU-AU--GGUGCUA-AUUC--CAG-CAGGA--------UAU----------------------UUUC-UG-A-AA-GAUGAGGA
ABDQ01000003.1/211832-211918   UGCUUAUCUAGAG-UGG-C-GG-----------------AGGGA--CUGG-CCCUU--UGAA-GCC--CAGCAACC-U-AUA-UUU---------------------------------------------------------AUUAUG-U---GGUGCUA-AUUC--CAG-----------------------------------------------A-CA-GAUGAGGA
CP000232.1/1354284-1354167     CUCUUAUCGAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CGGCAACC-C-GCU-CUCCUGGUUU---------------------------------------------CUCCGGGGGCG-AC-AGGUGCCA-AUUC--CUG-CAGGGCA-----GAAG----------------------GCCC-UG-A-GA-GAUAAGGG
AAXV01000007.1/124740-124627   CUCUUAUCAAGAG-CGG-C-GG-----------------AGGGA--UAGG-CCCUA--UGAU-GCC--CGGCAACC-A-GUA-GGUGAUG---------------------------------------------------AACUUACU-AA--GGUGCUA-AUUC--CUA-CAGAUUC-----UUACU-------------------UGGAUC-UG-G-CA-GAUAAGGG
ABCF01000016.1/2236-2349       CUCUUAUCGAGAG-CGG-C-GG-----------------AGGGA-UUAGG-CCCGA--UGAA-GCC--CGGCAACC-U-ACA-GGCAGUUU-------------------------------------------------CUGCUUGGA-AA--GGUGCUA-CAUC--CUA-CAGGCUC-----AAUG----------------------AGUC-UG-G-AA-GAUAAGAG
CP000612.1/2872894-2873007     UUCUUAUCCAGAG-AGG-C-UG-----------------AGGGA--CUGG-CCCUG--AGAC-GCC--CGGCAACC-U-UCU-UAGGCAUU------------------------------------------------UAUCUAAGAA-A---GGUGCUA-AUUC--CUG-CAGAAGA-----AUAA---------------------UCUUC-UG-A-AA-GAUAAGGA
AP009389.1/251789-251896       UUCUUAUCGAGAG-AAG-G-GG-----------------AGGGA--CGGA-CCCAA--UGAA-CCU-UCGGCAACC-U-UCA-GGCUUGA--------------------------------------------------AGGCCUGAA-AA--GGUGCCA-AUUU--CCG-CCGGG----------U----------------------AACC-GG-A-GA-GAUAAGAA
CP000142.2/516461-516352       UCUUUAUCGAGAG-UGG-U-GG-----------------AGGGA--UAGG-CCCUG--UGAA-ACC-ACAGCAACC-G-AUU-CGCCGGC--------------------------------------------------GCGAAUGUC-A---GGUGCUA-AUUC--CUA-CCCCUUC-----AACA------------------------GG-GG-A-GA-GAUGAGGA
AE015927.1/2676955-2676853     UUCUUAUCAAGAG-AGG-C-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CGGCAACC-A-AAA-AUAAU-------------------------------------------------------AAUUUU-AA--GGUGCCA-AUUC--CAG-CAGG---------UGA----------------------AACC-UG-A-CA-GAUAAGAC
CP000232.1/1204935-1204832     GGCUUAUCGCGAG-AGG-U-GG-----------------AGGGA--GGGC-CCCGA--UGAA-ACC--CGGCAACC-C-CGC-UAUUU-------------------------------------------------------AGCCGG-AA--GGUGCCA-AGUG--CCG-CAGGA--------AAC----------------------CUCC-UG-G-AA-GAUAAGUU
CP000673.1/1916685-1916789     UUCUUAUCAAGAG-AGG-U-AG-----------------AGGGA--CUGG-CCCUG--UGAU-ACC--CGGCAACC-U-UAU-UG----------------------------------------------------------UUUUCA-AU--GGUGCUA-AUUC--CAG-CAGGCAU-----GUAU---------------------UUGCU-UG-A-CA-GAUGAGAA
AAOX01000005.1/171326-171162   CUCUUAUCGAGAGCAGG-C-GG-----------------AGGGA-UUUGG-CCCGA--UGAA-GCC--CAGCAACC-G-ACC-GUAAUUCCGUUGUGAAACGGGGCGCAGCAA----GAUUUGCGCCGGUAUGUAAAUACCUUUAAGGC-AC--GGUGCUA-AUUC--CAA-CAGAGGA-----GAUUUU-----------------UCUUUUC-UG-G-GA-GAUAAGAG
AAXV01000033.1/3690-3784       CUCUUAUCAAGAU-AGG-U-GG-----------------AGGGA-CUUGG-CCCAA--UGAA-GCC-UCGGCAACC-------GAAAC-------------------------------------------------------AUA--------GGUGCCA-CUUC--CAA-CCGAU----------G----------------------UAUC-UG-A-GA-GAUAGGAG
AAOX01000002.1/320243-320340   CACUUAUCCAGAG-AGG-C-GG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC-UCGGCAGCAGG-UCU-GUU------------------------------------------------------------GAC-AC--UGUGCCA-AUUC--CA--CCGGU----------A----------------------UACC-GG-A-AA-GAUAAGCA
CP000482.1/3869976-3869870     UGCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--AAGG-CCCUG--UGAA-ACC-ACAGCAACC-G-GCC-GUCAU-------------------------------------------------------GGCGCC-A---GGUGCUA-AUUC--CUG-CCGUCAG-----GCAA----------------------AGAU-GA-G-AG-GGUGUGCU
CP000698.1/4591678-4591570     GCUUUAUCGAGAG-UGG-U-GG-----------------AGGGA--AAGG-CCCUG--UGAA-ACC-ACAGCAACC-G-GUU-CGCGAAA--------------------------------------------------GCGAAUGCC-A---GGUGCUA-AAUC--C---UGCCGAC-----UGAC----------------------CAGG-C--G-AA-GAUGAGGU
AL009126.3/3997775-3997881     ACCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAU-ACC--CGGCAACC-G-CUG-UUUCA-------------------------------------------------------AACAGA-AU--GGUGCUA-AAUC--CUU-AAGAACA-----UUGC----------------------GUUC-UU-G-CA-GAUGAGGC
CP001097.1/2001878-2001771     CUAUCAUCGAGAA-AGG-U-GG-----------------AGGGA--CUGG-CCCUG--AGAA-GCC-UUGGCAACC-G-UCA-CGCAC-------------------------------------------------------AGUGAU-U---GGUGCCA-AUUC--CAU-CCCGGAC-----UGCG---------------------AGCCG-GG-A-GA-GAUGAUGG
CP001336.1/1583758-1583658     CUCUUAUCCAGAGUAGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC-G-ACA-UGAAA-------------------------------------------------------AUG--C-AC--GGUGCUA-AAUC--CUG-CAG---------GAAA----------------------UA-C-UG-G-GA-GAUGAGAG
CP001022.1/2707752-2707649     CACUUAUCCAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--CGAA-ACC-UCGGCAACA-G-ACU-CAUUA-------------------------------------------------------UGAG-C-AC--UGUGCCA-AUUC--CAU-CAGAC--------AAU----------------------UGUC-UG-A-GA-GAUGAGUC
AL009126.3/1258304-1258424     UUCUUAUCGUGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUU--AGAA-ACC-UCAGCAACC-G-GCU-UGUUUUGCAU--------------------------------------------UUGCAAAGCGCC-AA--GGUGCUA-AAUC--CAG-CAAGCGU-----UUUUU--------------------AUGCU-UG-G-AA-GAUAAGAA
AE008691.1/500243-500352       CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA-AAGAG-CCCGA--UGAA-ACC--CGGCAACC-U-GUC-CUUUU-------------------------------------------------------AAGGAU-AA--GGUGCCA-AUUC--UCU-CAGAAGA-----UUUUU--------------------UCUUC-UG-A-AA-GAUGAGGG
CP001390.1/1543852-1543744     UGCUUAUCAAGAG-UGG-U-GG-----------------AGGGA-AAAGG-CCCUG--UGAA-ACC-ACAGCAACC-G-GUU-GAUCCGAAA-----------------------------------------------GGACGGCGUC-A---GGUGCUA-AAUC--CUG-CCCAU-----------------------------------UG-GG-U-AAAGAUGAGAG
ABDU01000083.2/79240-79352     UUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUG--UGAA-ACC--CAGCAACC-U-AUG-GUAUAAGUAUU-------------------------------------------UUUUAUGUCAUA-AC--GGUGCUA-AAUC--CUG-CAG----------GUU----------------------UA-C-UG-A-UA-GAUAAGUA
AL009126.3/1424683-1424527     CUCUUAUCGAGAGUUGG-G-CG-----------------AGGGA-UUUGG-CCUUU--UGAC-CCCAAAAGCAACC-G-ACC-GUAAUUCCAUUGUGAAAUGGGGCGCAUUU------UUUUCGCGCCGAGACGCUGGUCUCUUAAGGC-AC--GGUGCUA-AUUC-CAUU-CAGAU-------CUG------------------------AUC-UG-A-GA-GAUAAGAG
ABDT01000114.2/68234-68332     CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA-UAGGG-CCCAG--UGAA-ACC--CGGCAACC-U-GUA-UAU------------------------------------------------------------ACA-A---GGUGCCA-AUUC--CUG-UAGAU--------GUA----------------------AUUC-UA-C-AA-GAUAAGAA
CP001089.1/3288078-3288187     UUCUUAUCAAGAG-CGA-C-CG-----------------AGGGA--CUGG-CCCGG--UGAC-GUC-GCGGCAACC-C-GCC-UGA---------------------------------------------------------AAAGGU-AC--GGUGCCA-AUUC--CAG-CAAAGCC-----GCACAG------------------CGGUUU-UG-A-CA-GAUAAGGA
CP000879.1/1211576-1211465     UCCUUAUCGAGAG-AGG-C-GG-----------------AGGGA--CUGG-CCCGA--AGAA-GCC--CGGCAACC-U-GCA-UAAUUUAAC----------------------------------------------AAAAUUAUGCA-AU--GGUGCUA-AAUC--CUG-CAGAG---------AA----------------------AUUC-UG-G-GA-GAUAAGGA
ACOM01000005.1/822103-822219   AACUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CGGCAACC-G-ACA-UUUAGUUCAU--------------------------------------------UUACUAUAUGUG-AC--GGUGCUA-AUUC--CUG-CAGUUUA-----UUUA-----------------------AAC-UG-G-UA-GAUGAGAG
AE008691.1/2076682-2076573     CUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC-G-GCA-CGUA--------------------------------------------------------AGUGCU-U---GGUGCCA-AUUC--CUG-CAGGUUGG--GGUUACC--------------------CAGCC-UG-A-GA-GAUGAGAG
CP001098.1/2431377-2431263     CAAUCAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--AGAA-GCC--CGGCAACC-U-ACC-UGAGUUU--------------------------------------------------AGCAAGGUA-A---GGUGCCA-AAUC--CUG-CAUUCUG-----GGGAAU------------------CCGGAG-UG-A-GA-GAUGAGGG
CP000909.1/4069333-4069227     UGCUCAUCGAGAU-GGG-C-UG-----------------AGGGA--CUGG-CCCGA--UGAC-GCC--CGGCAACC-C-CCG-CCA------------------------------------------------------------GGG-AA--GGUGCCA-AAUC--CAG-CGGCAAU-----GGAUAU-----------------CAUUGGC-CG-A-AA-GAUGAGAG
AL009126.3/3364503-3364397     CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--AGUG-CCCUA--UGAA-GCC--CGGCAACC-A-UCA-ACACU-------------------------------------------------------GUUGAA-AU--GGUGCCA-AUUC--ACA-CGAAGC------GUUC---------------------AGCUU-UG-A-AA-GAUGAGAG
CP001022.1/2804795-2804898     UUUUUAUCGCGAG-AGA-C-GG-----------------AGGGA--CUGG-CCCGA--UGAU-GUU-UCGGCAGCG-G-ACG-AUUAA-------------------------------------------------------AUCGUA-C---UGUGCCA-AAUC--CAG-CAAGCUG-----CGG-------------------------CU-UG-A-GA-GAUAAGAA
CP001089.1/3739157-3739264     UGCUUAUCAAGAG-UGG-U-GG-----------------AGGGAUAAG-G-CCCGA--UGAA-ACC-ACAGCAACC-G-GCC-CUGCGACAA-----------------------------------------------ACAGGGCGCC-A---GGUGCUA-AAUC--CUG-----CCG-----CAAG----------------------GC------G-AA-GAUGAGCG
CP001022.1/2309368-2309263     CUCUUAUCGAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC-G-CGG-AAUUU-------------------------------------------------------AUUCCG-AAGUGGUGCUA-AUUC--CAG-CAGAC--------GAU----------------------UGUC-UG-C-AA-GAUGAGAG
AP008230.1/5317569-5317463     UUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CAGCAACC-G-GUA-UUCGGA----------------------------------------------------UGAAUACA-AC--GGUGCUA-AUUC--CUG-CGAUG--------GAA----------------------GCAU-UG-A-UA-GAUGAGAG
Y09476.1/38002-37885           UUCUUAUCAAGAG-AAG-C-AG-----------------AGGGA--CUGG-CCCGA--CGAA-GCU-UCAGCAACC-G-GUG-UAAUGGCGAU---------------------------------------------CAGCCAUGACC-AA--GGUGCUA-AAUC--CAG-CAAGCUC-----GAAC----------------------AGCU-UG-G-AA-GAUAAGAA
AACY020322622.1/575-479        UACUUAUCAAGAA-AGG-U-GG-----------------AGGGA-AAAGG-CCCUU--UGAA-ACC-UUAGCAACC-C-CAAAUU-------------------------------------------------------------AGG-AA--GGUGCUA-AAUC--CAG-AU----------GUAA----------------------AA---AU-C-AA-GAUAAGAG
CP001124.1/432444-432343       UGCUUAUCUAGAG-UGG-U-GG-----------------AGGGA--AAGG-CCCUG--CGAA-GCC-ACAGCAACC-G-GCC-CAGAAA----------------------------------------------------UGGGCGAC-A---GGUGCUA-AAUC--CUG-----CCG-----AAAG----------------------GC------G-AA-GAUGAGAA
CP001110.1/965443-965552       CUAUCAUCCAGAA-AGG-U-GG-----------------AGGGA--CUGG-CCCUG--AGAA-GCC-UUGGCAACCGU-CAU-UGCUC-------------------------------------------------------UAAUGA-GC--GGUGCCA-AUUC--CAU-CCCGGCA-----UAAA---------------------GACCG-GG-A-AU-GAUGAUGG
CP001022.1/2977132-2977031     UUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUU--UGAA-GCC-UCAGCAACAGG-UCG-AAA------------------------------------------------------------GAC-AC--UGUGCUA-AUUC--CUG-CGGGUGU-----UGUA------------------------CC-CG-A-UC-GAUAAGCU
ABDT01000037.2/9251-9359       UACUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUG--UGAA-ACC--CGGCAACC-A-AUA-UUUAUUA--------------------------------------------------GAUGAUAUG-A---GGUGCCA-AAUC--CUG-CAGUUUU-----UAUG------------------------AC-UG-G-UA-GAUAAGGU
CP001022.1/449125-449227       CUCUUAUCGUGAGUUGG-C-AG-----------------AGGGA-AUUGG-CCCGA--AGAC-GCC-GCAGCAACC-G-ACC-AUCC-----------------------------------------------------------GGC-AC--GGUGCUA-CAUC--CAA-CAGAC--------AUU----------------------CGUC-UG-A-GA-GAUAAGAG
CP001022.1/2949654-2949549     UUCUUAUCAAGAG-AAG-U-CG-----------------AGGGA--ACGG-CCCGA--AGAC-ACU-UCAGCAACC-C-CGC-GCG---------------------------------------------------------UAGCGG-AA--GGUGCUA-CUUC--CUA-AAAGGAA-----UUUU----------------------UCCU-UU-G-AA-GAUAAGAG
CP000853.1/102837-102950       CUUUUAUCGAGAG-AGG-U-GG-----------------AGGGA--AAGG-CCCUA--UGAA-ACC-UCGGCAACC-U-GCA-AACGUAU--------------------------------------------------UUGUUUGAA-AA--GGUGCCA-AUUC--CUA-CUCUAAG-----UGAA---------------------CUUAG-AG-A-GA-GAUAAGAG
AL009126.3/1426876-1426976     UUCUUAUCAAGAGCAGG-C-AG-----------------AGGGA--CGAG-CCCGA--UGAA-GCC--CGGCAACC-G-ACU-UAU---------------------------------------------------------AAAG-C-AC--GGUGCUA-AUUC--UUG-CAGCU--------AGC-----------------------GGC-UG-A-GA-GAUAAGAU
CP000875.1/2997482-2997580     CUCUCAUCGAGAU-GGG-C-AG-----------------AGGGA--CUGG-CCCGA--CGAA-GCC--CGGCAACC-C-CAU-UAUU-----------------------------------------------------------UGG-AA--GGUGCCA-AAUC--CUG-CAGG---------UUC----------------------GGCC-UG-A-UA-GAUGAGUU
CP001022.1/2505940-2506043     UACUUAUCGAGAG-CGA-C-CG-----------------AGGGA-UUAGG-CCCAA--CGAC-GUC--CGGCAACC-A-CCU-UUAA-----------------------------------------------------------GGA-AC--GGUGCCA-CAUC--CUA-CAGAAUG-----UUUC----------------------AUUC-UG-A-GA-GAUAAGUU
AL009126.3/3999166-3999272     UCCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUG--CGAU-ACC--CGGCAACC-G-CUG-UUU---------------------------------------------------------AACAGA-AU--GGUGCUA-AAUC--CUU-UAGAGCA----AUGAU---------------------UGCUC-UU-G-AA-GAUAAGGU
CP000875.1/1061086-1061193     AACUCAUCCAGAG-GGG-U-GG-----------------AGGGA--UCGG-CCCUA--UGAA-ACC-CCGGCAACC-G-CAG-GCAGCAA---------------------------------------------------UGCUUGGA-CU--GGUGCUA-AGUC--CGA-CAGA---------AUC----------------------AUUC-UG-G-AA-GAUGAGGG
AE008691.1/1750369-1750270     CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC-A-GCC-UU----------------------------------------------------------AGGGCA-U---GGUGCCA-AUUC--CUG-CAGCG-------GUUU-----------------------CGC-UG-A-AA-GAUGAGAG
ABDT01000031.2/132-23          UUUUUAUCAAGAA-AGA-C-AG-----------------AGGGA--CUGG-CCCUA--UGAA-GUC--UAGCAACC-U-GAA-UUAUUA----------------------------------------------------AUUAAUUU-AA--GGUGCUA-AUUC--CAG-CAGAUAU-----UUUA----------------------UAUC-UG-A-AA-GAUAAGAA
AL009126.3/3129333-3129195     CUCUUAUCCCGAGCUGG-C-GG-----------------AGGGA--CAGG-CCCUA--UGAA-GCC--CAGCAACC-G-GUU-UCUCUGUUAUUUAUUAUG----------------------------UUCAACUGAGUGAGACAACC-AA--GGUGCUA-ACCU-GUUG-CAAGGUU-----GUAUG-------------------AUUCCU-UG-A-GC-GAUAAGAG
AP008955.1/3935954-3935848     UUCUUAUCCAGAG-AGG-U-GG-----------------AGGGU--CUGG-CCCGA--UGAA-GCC--CGGCAACC-G-UUG-CAUAU-------------------------------------------------------UGCAAC-AA--GGUGCCA-AUUC--CUG-CGAGACG-----UUUC----------------------GUCU-CG-A-AA-GAUAAGAA
ACML01000054.1/24739-24633     CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--UCGG-CCCUA--UGAA-ACC-UCGGCAACC-C-CUA-UUUUA-------------------------------------------------------UUUAGG-AA--GGUGCCA-AUUC--CUU-UAGAAUU-----UA-A----------------------AUUC-UA-A-AA-GAUAAGAA
AP009049.1/1342262-1342152     UUCUUAUCCAGAG-UGG-C-GA-----------------AGGGA--CUGG-CCCUA--UGAU-GCC--CAGCAACC-U-GAA-UGAUUUUU-------------------------------------------------CAUCAUUCA-AC--GGUGCUA-AUUC--CAG-CAGGUAU-------AA----------------------AACC-UG-A-AA-GAUGAGAA
ACDK01000006.1/20557-20663     GUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--CAGCAACC-A-AGA-AUUUUAA--------------------------------------------------UCGAUUCUU-AA--GGUGCUA-AAUC--CUG-CAGGA----------A----------------------AUCC-UG-G-UA-GAUAAGAG
CP000924.1/750630-750734       CUCUUAUCGAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC-G-GCA-UUUUAU-----------------------------------------------------AUGCGUC-UU--GGUGCCA-AUUC--CAG-CAGCG---------UU----------------------UCGC-UG-A-AA-GAUGAGAG
ACMX01000011.1/17693-17806     CUCUUAUCCAGAG-AGG-C-GG-----------------AGGGA--CUGG-CCCUA--UGAU-GCC--CGGCAACCGA-GCU-UAUGAAU---------------------------------------------------UAUAAGCU-AA--GGUGCUA-AUUC--CUG-CAAAACG-----AUUUU--------------------CGUUU-UG-G-AA-GAUAAGAG
CP000448.1/1653165-1653067     CUCUUAUCCAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC-G-CCU-GAA-----------------------------------------------------------AGGU-AU--GGUGCCA-AAUC--CUG-CAGGA---------GG----------------------AUCC-UG-G-CA-GAUGAGAG
ABEZ02000013.1/193212-193110   ACCUUAUCAAGAG-AGG-C-UG-----------------AGGGA--CAGG-CCCUA--UGAA-GCC--CAGCAACC-A-CUU-GG----------------------------------------------------------AAAAGG-AA--GGUGCUA-AAUC--CUG-CUAGAGA-----GAA-----------------------UUCU-AG-A-AA-GAUGAGGU
CP000764.1/3033666-3033778     UUCUUAUCUAGAG-AGG-U-AG-----------------AGGGA--CUGG-CCCUA--UGAC-ACC-UCAGCAACC-A-UUA-ACAAAC----------------------------------------------------UUGUUAAU-AA--GGUGCUA-AUUC--CAG-CAAAUUA-----UCAAA--------------------UAAUU-UG-A-GA-GAUAAGAA
CP001078.1/2736261-2736158     UUCUUAUCGAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CGGCAACCAA-UAU-AUUAU-------------------------------------------------------AUAUAU-AA--GGUGCUA-AAUC--CUG-CAGUA---------AG----------------------UAAC-UG-A-UA-GAUAAGGG
CP000923.1/995529-995640       CUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC-G-GCA-UUUAU------------------------------------------------------AUGCGUC-U---GGUGCCA-AAUC--CUG-CAGGUUA-----GAUUAU-----------------UCUAACC-UG-A-GA-GAUGAGAG
ACMW01000090.1/86610-86722     UUCUUAUCUAGAG-AGG-U-AG-----------------AGGGA--CUGG-CCCUA--UGAC-ACC-UCAGCAACC-A-UUA-ACACGU----------------------------------------------------UCGUUAAU-AA--GGUGCUA-AUUC--CAG-CAAAUUG-----UGAAA--------------------AGAUU-UG-A-CA-GAUAAGAA
ABWP01000002.1/3034-3135       ACCUUAUCAAGAG-AGG-C-UG-----------------AGGGA--CAGG-CCCGA--UGAA-GCC--CGGCAACC-A-CCC-AUA---------------------------------------------------------AGGGAA-AA--GGUGCUA-AUUC--CUA-CAGGA--------UUU----------------------AUCC-UG-A-AA-GAUGAGGU
ACMV01000059.1/168768-168876   AGCUUAUCAAGAG-AAG-C-GG-----------------AGGGA-ACUGG-CCCUA--CGAA-GCU--CAGCAACC-U-GCU-UAUAA-------------------------------------------------------GAAGCA-A---GGUGCUA-AGUC--CAG-CAAAAUG-----GCAUC--------------------CAUUU-UG-A-AA-GAUAAGGU
CP000813.1/1116941-1116823     UUCUUAUCAAGAG-AGG-C-AG-----------------AGGGA--CUGG-CCCUG--UGAA-GCC-UCAGCAACC-G-GUG-UAGUAGAAAUCU-----------------------------------------AUUUUCUAUGACC-AA--GGUGCUA-AAUC--CAG-CAAGC--------AAC----------------------UGCU-UG-G-AA-GAUAAGAA
CP000727.1/1728869-1728972     UACUUAUCAAGAG-AGG-C-GG-----------------AGGGA--CUGG-CCCUG--UGAA-GCC--CAGCAACC-U-AUA-UGAAAG----------------------------------------------------UGAAUAUA-A---GGUGCUA-AAUC--CUG-CAGCA----------U----------------------AAGC-UG-A-GA-GAUGAGGA
ACMP01000006.1/18282-18169     CUCUUAUCAAGAG-UGG-C-GG-----------------AGGGA--CUGG-CCCGA--UGAU-GCC--CGGCAACCGA-GCU-UAGAACU---------------------------------------------------UAUAAGCU-AA--GGUGCUA-AUUC--CUG-CAGAACG-----AUUUU--------------------CGUUU-UG-G-AA-GAUAAGAG
CP001615.1/763985-763879       CUCUUAUCAAGAG-AGG-C-UG-----------------AGGGA--CUGG-CCCUA--UGAC-GCC--CAGCAACC-G-CGG-AGCAA-------------------------------------------------------UCCGAA-AU--GGUGCUA-AUUC--CAG-CAAGGUG-----AGAA----------------------ACCU-UG-A-CA-GAUGAGAG
ABRX01000004.1/223227-223118   CUCUUAUCAAGAG-AGG-C-AG-----------------AGGGA--CUGG-CCCUA--UGAC-GCC--CGGCAACCGU-UUC-UACUA-------------------------------------------------------UAGAAA-UU--GGUGCUA-AUUC--CUG-CAAAGCU-----GUUAC--------------------AGCUU-UG-A-CA-GAUAAGAG
CP001034.1/2889251-2889136     UCCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--CGGCAACC-G-GCA-GCAGCUAA------------------------------------------------UCCUGCUGUA-AA--GGUGCCA-AAUC--CUG-CAGAAGU-----GUAUU--------------------ACUUC-UG-A-CA-GAUAAGGA
CP001056.1/749334-749442       AUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CGGCAACC-A-AAU-GAUUACU---------------------------------------------------UAUCAUUU-AU--GGUGCUA-AAUC--CUG-CAACUU-------AUG----------------------GAGU-UG-A-UA-GAUGAGAG
ACJM01000005.1/12852-12955     CUCUUAUCAAGAGAAGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACCGG-ACA-CGC------------------------------------------------------------GUC-GC--GGUGCUA-AUUC--CAG-CAGGGAG-----UGAA----------------------ACCC-UG-A-UA-GAUAAGAG
ABDP01000004.1/161395-161294   CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGAAAAGGG-CCCUA--UGAA-ACC--CGGCAACC-A-GUG-AUA---------------------------------------------------------UUCACU-AA--GGUGCCA-AUUC--CUG-CAG---------UAUU----------------------AU-C-UG-C-AA-GAUAAGAG
CP000922.1/2445298-2445193     CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--UGUG-CCCGA--UGAA-ACC--CGGCAACC-G-UCA-GCGCU-------------------------------------------------------GCUGAA-AU--GGUGCCA-AUUC--ACA-CAAAGCG-----UU-U----------------------GCUU-UG-A-GA-GAUAAGAG
CP001393.1/1215384-1215507     UUCUUAUCAAGAG-UGG-C-GG-----------------AGGGA--CUGG-CCCAA--UGAA-GCC--CGGCAACC-G-GAA-AAAGGUAGGG--------------------------------------------GUGCCCUUUUUC-UU--GGUGCCA-AUUC--CAG-CAGGUAU-----UUUUUUA----------------AAAUACC-UG-G-CA-GAUAAGAA
CP000930.2/1734610-1734715     CUCUUAUCAAGAGUUGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CGGCAACCAG-CAG-GUUUU-------------------------------------------------------UCCUGC-AU--GGUGCCA-AUUC--CUG-CAGGG--------GAA----------------------ACCC-UG-A-AA-GAUAAGAC
CP000679.1/1731346-1731467     UUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCAA--UGAA-GCC--CGGCAACC-G-GAA-AAAGGUAUGG--------------------------------------------GUGCCCUUUUUC-UU--GGUGCCA-AUUC--CAG-CAGGUAU-----UUUUAA------------------AAUACC-UG-G-CA-GAUAAGAA
ABDA02000002.1/27359-27468     CUCUUAUCUAGAG-AGG-U-GG-----------------AGGGA-CUGUG-CCCUG--UGAA-ACC--CAGCAACC-A-UCA-AUUUUU----------------------------------------------------ACAUUGAA-AU--GGUGCUA-AUUC--CUG-CAAAGCA------AAU----------------------GCUU-UG-A-GA-GAUGAGAG
ACLX01000083.1/11419-11532     UUCUUAUCUAGAG-AGG-U-AG-----------------AGGGA--CUGG-CCCUU--UGAC-GCC-UCAGCAACC-A-UUA-ACAUUCA--------------------------------------------------UUCGUUAAU-AA--GGUGCUA-AUUC--CAG-CAAAUUG-----UGAA---------------------AGAUU-UG-A-CA-GAUGAGAA
BAAZ01010499.1/873-972         CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA-UAGGG-CCCGA--UGAA-ACC--CGGCAACC-U-GUA-UUU------------------------------------------------------------UCA-A---GGUGCCA-AUUC--CUG-UAGAUAG-----A--U----------------------UAUC-UA-C-AA-GAUAAGAG
ABKW02000003.1/317079-316978   CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGAAAAGGG-CCCUA--UGAA-ACC--CGGCAACC-A-GUG-AUA---------------------------------------------------------UUCACU-AA--GGUGCCA-AUUC--CUG-CAG---------UGCU----------------------AU-C-UG-C-AA-GAUAAGAG
CP001348.1/101863-101963       UCCUUAUCAAGAG-AGG-U-GG-----------------AGGGA-AUGGG-CCCGA--UGAA-ACC--CGGCAACCAG-C-A-UUU---------------------------------------------------------UUU-GC-AU--GGUGCCA-AUUC--CUG-CAGGC---------UA----------------------UGCC-UG-G-AA-GAUGAGGG
ABVH01000010.1/37660-37766     CGCUUAUCAAGAG-CGA-G-GG-----------------AGGGA--CUGG-CCCGA--UGAA-CUC--CGGCAACC-U-GCU-UCAU--------------------------------------------------------UUAGCA-A---GGUGCCA-AUUC--CAG-CAAAAUG-----GAUUC--------------------CAUUU-UG-G-AA-GAUAAGAC
CP000560.1/1082099-1081978     UUCUUAUCAAGAG-AAG-C-CG-----------------AGGGA--CUGG-CCCGA--CGAC-GCU-UCAGCAACC-G-GUG-UAGUGGUUUAC------------------------------------------CCAAACCAUGACC-AA--GGUGCUA-AAUC--CAG-CAAGCUA-----AAAA---------------------CAGCU-UG-G-AA-GAUAAGAA
CP000721.1/1647224-1647332     AACUUAUCAAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--AGAA-ACC--CAGCAACCGG-UAA-AUUUUAU---------------------------------------------------AGAAUUAC-UU--GGUGCUA-AAUC--CUG-CAGCG--------UAA----------------------GAGC-UG-G-UA-GAUAAGGU
ACMR01000082.1/17402-17507     UUCUUAUAAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUU--UGAA-ACC-UCAGCAACC-U-AAU-AU----------------------------------------------------------UACAUA-AA--GGUGCUA-AAUC--CUG-UAGGAUC-----UAAA---------------------AGUCC-UA-A-AA-GAUAAGAA
ACLP01000020.1/71764-71658     CUCUUAUCAAGAG-UGG-U-GG-----------------AGGGA--UGUG-CCCUA--CGAA-ACC--CAGCAACC-G-UCA-UUG---------------------------------------------------------UAUGAC-AU--GGUGCUA-AUUC--ACA-UAAAGUU-----AAUCA--------------------UACUU-UA-G-AA-GAUGAGAG
ACLW01000047.1/255928-256033   UUCUUAUUAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUU--CGAA-GCC-UCAGCAACC-U-UAU-GUG---------------------------------------------------------AUAUAA-A---GGUGCUA-AAUC--CUG-UAGGAUC-----UAAA---------------------AGUCC-UA-A-UA-GAUAAGAA
ACNG01000055.1/75164-75269     UUCUUAUUAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUU--CGAA-GCC-UCAGCAACC-U-AAU-GU----------------------------------------------------------GAUAUA-AA--GGUGCUA-AAUC--CUG-UAGGAUA-----UAAA---------------------AGUCC-UA-A-UA-GAUAAGAA
AP009484.1/63878-63783         UGCUUAUCCAGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CGGCAACC-U-AUU-A--------------------------------------------------------------AUU-UA--GGUGCUA-AUUC--CAG-CAGGU---------AU----------------------AUCC-UG-A-AA-GAUAAGGU
ABFU01000060.1/128844-128955   CUCUUAUCGAGAG-CGG-C-GG-----------------AGGGA-AUAGG-CCCUG--UGAA-GCC--CGGCAACC-A-UCA-AGCGAAUU-------------------------------------------------UUGCUUGAA-AA--GGUGCUA-AUUC--CUA-CAGGUAA-----UC------------------------UACC-UG-G-AA-GAUAAGAG
AAML04000010.1/122381-122487   AUCUUAUCAAGAG-UGG-C-AG-----------------AGGGA--CUGG-CCCUG--UGAA-GCC--CGGCAACC-A-GUA-UAUUUA----------------------------------------------------AUUAUACA-UU--GGUGCUA-AAUC--CUG-CAGCA--------UUU----------------------AUGC-UG-A-AA-GAUGAGUA
ABFD02000009.1/97533-97428     UUCUUAUCCAGAG-UGG-U-GA-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CAGCAACC-A-GUA-UAUUUU----------------------------------------------------UAUAUACA-UU--GGUGCUA-AAUC--CUG-CAGUA---------UU----------------------AUAC-UG-A-AA-GAUGAGUC
AARM02000086.1/6918-7038       CUCUUAUCGAGAG-CGG-C-AG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CGGCAACCUA-ACU-UUAUUUAA------------------------------------------------GCGUAAAGUG-AA--GGUGCUA-AUUC--CAG-CAAAAAUG---G--UGUAU----------------UCCGUUU-UG-A-UA-GAUAAGAG
ABSQ01002824.1/631-738         GCCUUAUCAAGAG-CGG-U-GG-----------------AGGGA--UAGG-CCCUA--UGAA-ACC--CGGCAACC-A-UAG-UGUGAA-----------------------------------------------------UACACGU-UU--GGUGCUA-AAUC--CUA-CAGAAUA-----UU-U----------------------AUUC-UG-A-AA-GAUGAGGA
ACFR01000002.1/115417-115315   CUCUUAUCGAGAG-AGG-U-GG-----------------AGGGA--UGUG-CCCUA--UGAA-GCC--CGGCAACC-G-UCU-GAU---------------------------------------------------------AUAGAA-AU--GGUGCCA-AUUC--ACA-UAAAGUU-----CA------------------------ACUU-UA-G-AA-GAUGAGAG
AM295250.1/465274-465380       CUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--UGUG-CCCUG--CGAA-ACC--CGGCAACC-G-UCU-UUA-U-------------------------------------------------------AUAGAA-AU--GGUGCCA-AUUC--ACA-AAAAGUU-----GAAC---------------------UGCUU-UU-G-AA-GAUGAGAG
AARL02000014.1/678-559         CUCUUAUCGAGAG-CGG-C-AG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CGGCAACC-U-AAC-UUUAUGUAA-----------------------------------------------GCGUAAAGUG-AA--GGUGCUA-AUUC--CAG-CAAAAUG-----GUGUAU-----------------UCCGUUU-UG-G-UA-GAUAAGAG
ABKL02000024.1/81090-81192     AUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACC--CGGCAACC-A-GUA-UAUUU------------------------------------------------------AUAUACA-AU--GGUGCUA-AAUC--CUG-CGGCG----------A----------------------AAGC-UG-A-GA-GAUGAGUA
ACND01000092.1/77021-76920     UUCUUAUCACGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAU-ACC-UCGGCAGCGGA-U-U-CGUUA-------------------------------------------------------GGA-AU-AC--UGUGCCA-AUUC--CAG-CAAGG----------U----------------------AACU-UG-A-AA-GAUAAGAA
ACMS01000020.1/866-971         CUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUA--CGAU-ACC-UCAGCAACG-G-GUU-UUU-----------------------------------------------------------UAAU-AC--CGUGCUA-AUUC--CAG-CAAGCUU-----AAAGU--------------------AAGCU-UG-G-AA-GAUGAGAA
ACMM01000043.1/11026-11131     UACUUAUCCAGAG-AGG-U-AG-----------------AGGGA--CUGG-CCCUA--UGAC-ACC-UCAGCAGCG-G-GUU-CUGUAG-----------------------------------------------------UAGGAAC-AC--CGUGCUA-AUUC--CAG-CAAGC---------AA----------------------GUCU-UG-A-AA-GAUAAGUG
ACLY01000071.1/41239-41095     CUCUUAUCAAGAGCAGG-U-GG-----------------AGGGA-UUUGG-CCCGA--UGAA-GCC--CAGCAACC-G-ACC-GUAAUACCAUUGUGAAAUGGGG--------------------CGUAUAUUUACGACGCCAAAAGGC-AC--GGUGCUA-AUUC--CAG-CAGAAAG-----UAUA---------------------CUUUC-UG-G-UA-GAUAAGAG
CP000817.1/560536-560639       CUCUUAUGAAGAG-CGG-C-GG-----------------AGGGA--AGUG-CCCUA--UGAA-GCC--CGGCAACC-A-UCA-CAU---------------------------------------------------------AGUGAA-AA--GGUGCCA-AAUC--ACC-CAAAGAU-----U-UU----------------------UCUU-UG-A-AA-GAUGAGAG
ACMT01000176.1/7164-7023       CUCUUAUCAAGAGCAGG-U-GG-----------------AGGGA-UUUGG-CCCGA--UGAA-GCC--CAGCAACC-G-ACC-GUAAUACCAUUGUGAAAUGGG-----------------------GCGUUUAUUUACGCCAAAAGGC-AC--GGUGCUA-AUUC--CAG-CAGAAAG-----UUUA---------------------CUUUC-UG-G-CA-GAUAAGAG
ACNK01000182.1/46147-46039     UUCUUAUCAAGAG-AGA-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-AUC-UCAGCAACAG--GCU-AUAUC-------------------------------------------------------AAAGU--AC--UGUGCUA-ACUC--CAG-CGAACGC-----AAUAG--------------------GCGUU-UG-A-AA-GAUGAGGA
CP000148.1/765280-765385       UUCUUAUCACGAG-CGA-C-CG-----------------AGGGA--CUGG-CCCUA--UGAC-GUC-GCGGCAACC-C-CCC-GC----------------------------------------------------------AAGGGG-AC--GGUGCCA-AAUC--CUG-CGGAACG-----GCAA---------------------CGUUC-CG-G-GA-GAUAAGGA
ACME01000005.1/38827-38723     AUUGUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCUU--UGAA-ACC-UCGGCAACA-G-GUU-CAUU--------------------------------------------------------UUGAAU-AC--UGUGCCA-CUUC--CUG-CAAGCUU-----U--A----------------------UGCU-UG-A-AA-GAUAGAAU
ABMW01084009.1/100-6           CAUUUAUCAAGAG-UGG-C-AG-----------------AGGGU--CAGG-CCCUG--UGAA-GCC--CAGCAACC-U-ACA-UUU------------------------------------------------------------GUA-A---GGUGCUA-AAUC--CUG-CGGUA---------------------------------UAAC-CG-A-AA-GAUAAGUU
ABGD02000008.1/40601-40696     ACCUUAUAAAGAG-CGG-C-GG-----------------AGGGA--CUGG-CCCUG--UGAA-GCC--CGGCAACC-U-GCA-UAU-----------------------------------------------------------UGCA-A---GGUGCCA-AAUC--CAG-CGGUA---------------------------------UGAC-CG-A-GA-GAUGAGGA
CP001099.1/664814-664922       CUAUCAUCCAGAA-AGG-C-GG-----------------AGGGA--CUGG-CCCUG--CGAA-GCC-UUGGCAACC-U-UCA-UAUCAC-----------------------------------------------------CUAUGAG-A---GGUGCCA-AAUC--CAU-CCCGGAG-----GAAU----------------------UCCG-GG-A-AA-GAUGAUGU
ACMJ01000013.1/79549-79437     CCUUUAUCAAGAG-AGG-C-AG-----------------AGGGA--CCGG-CCCUU--UGAA-GCC--CAGCAACC-U-CAG-UUUAUAA---------------------------------------------------GAACCGAA-UA--GGUGCUA-AUUC--CUG-CAAAAUG-----CAUUG--------------------CAUUU-UG-G-AA-GAUAAAAC
CP001337.1/4323854-4323960     UGCUCAUCGAGAU-GGG-C-UG-----------------AGGGA--CUGG-CCCGA--UGAC-GCC--CGGCAACC-C-CCA-ACA------------------------------------------------------------GGG-AA--GGUGCCA-AAUC--CAG-CGGCAAU-----GAAGAA-----------------CAUUGGC-CG-A-AA-GAUGAGAG
ACGB01000028.1/29135-29031     UGCUCAUCAAGAG-UGG-C-GG-----------------AGGGA--AUGG-CCCUA--UGAA-CCC-ACAGCAACC-A-UGG-CCUCA-------------------------------------------------------UGGCCA-AC--GGUGCUA-AAUC--CUG-CAAUG--------UAA----------------------UGAU-UG-U-AA-GAUGAGAG
ACMZ01000099.1/4914-5019       UUCUUAUCAAGAGCAGG-U-GG-----------------AGGGA--CGAG-CCCGA--CGAA-ACC--CGGCAACC-G-AUC-UACAAU-----------------------------------------------------CGUAGAC-AC--GGUGCUA-AUUC--UCG-CAGCA---------UU----------------------AUGC-UG-A-CA-GAUAAGGA
AASE01000018.1/36798-36683     CUAUCAUCGAGAA-AGG-U-GG-----------------AGGGA--CUGG-CCCUG--AGAA-ACC-UUGGCAACCGU-CAA-UUCAUAAU-------------------------------------------------GAAGUAUGA-AC--GGUGCCA-AUUC--CAU-CCCGGUA-----UAAA---------------------GGUCG-GG-A-AA-GAUGAUGG
ACOK01000109.1/19481-19381     ACCUUAUCAAGAG-CGG-C-GG-----------------AGGAA-ACAGG-UCCUG--UGAA-GCC--CGGCAACC-U-GAC-UAUUU-------------------------------------------------------CGGUCA-A---GGUGCUA-AUUC--CUG-CGG----------UUU----------------------AU-C-CG-G-AA-GAUGAGGA
ACJB01000070.1/16733-16623     CUCUUAUCCUGAG-UGG-U-GG-----------------AGGGACAUGGA-CCCAA--CGAA-ACC--CAGCAACC-U-CUU-UUUAG-------------------------------------------------------UAAAGA-AA--GGUGCCA-AACCGUUUG-CAGACAU-----AUAU----------------------CGUC-UG-A-AC-GAUAAGAG
AP008971.1/1262692-1262597     AUCUUAUUAAGAG-UAG-U-GG-----------------AGGGA-AUGGG-CCCUA--UGAA-ACU--CAGCAACC-U-AUU-AA-------------------------------------------------------------AUU-A---GGUGCUA-AAUC--CCA-CAGGA----------A----------------------AUCC-UG-A-AA-GAUAAGUU
ACNI01000057.1/7157-7272       UACUUAUCCAGAG-AGG-U-GG-----------------AGGGA--ACGG-CCCUA--AGAA-ACC-UCAGCAACC-C-CUA-UGCAAU----------------------------------------------------UUUAUAGG-AA--GGUGCUA-AUUC--C-G-CAGAGAA-----CACGAUG----------------UGUUUUU-UG-A-AA-GAUAAGAG
CP000975.1/1171211-1171325     CUCUUAUCGAGAG-CGG-U-GG-----------------AGGGA--CUGG-CCCUG--UGAA-ACC-GCGGCAACC-G-GAA-AAGAGAGU-------------------------------------------------CUUUUCGUC-AA--GGUGCCA-AUCC--CAG-CCCUUUG-----AAGC---------------------GUAAG-GG-A-AG-GAUGAGAG
ACLA01000020.1/206857-206751   ACCUCAUCCAGAG-CAG-C-GG-----------------AGGGA--AUGG-CCCGA--UGAA-GCU-GCGGCAACCAU-GGC-AAUGU-------------------------------------------------------GUGCCA-AC--GGUGCCA-AUUC--CUA-UAGGCGG-------AG----------------------CGCC-UA-U-GA-GAUGAGAG
ACLT01000057.1/24072-24187     UACUUAUCCAGAG-AGG-U-GG-----------------AGGGA--ACGG-CCCUA--AGAA-ACC-UCAGCAACC-C-CUA-UGCAAU----------------------------------------------------UUUAUAGG-AA--GGUGCUA-AUUC--C-G-CAGAGGA-----CACGAUG----------------UGUUUUU-UG-A-AA-GAUAAGAG
CP000860.1/973047-972931       CUCUUAUCGAGAG-UGG-C-GG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CGGCAACCAG-UCG-GUGGCGGU------------------------------------------------GGUCACCGGC-CA--GGUGCUA-AUUC--CUG-CGGGAGA-----UCGAU--------------------UCUUC-UG-G-GA-GAUAAGAG
ACMD01000102.1/19238-19132     UUCUUAUCAAGAG-AGA-U-GG-----------------AGGGA--CUGG-CCCGG--UGAA-AUC-UCAGCAACAGG-CUA-AAA-----------------------------------------------------------AAGC-AC--UGUGCUA-AUUC--CAG-CAAACGU-----AAAAG--------------------GCGUU-UG-G-AA-GAUGAAGG
ACMU01000050.1/34307-34422     UACUUAUCCAGAG-AGG-U-AG-----------------AGGGA--ACGG-CCCUU--UGAA-ACC-UCAGCAACC-C-CUA-UGUAAU----------------------------------------------------UACAUAGG-AA--GGUGCUA-AUUC--C-G-CAGAGGA-----CACUAUG----------------UGUCUUU-UG-A-AA-GAUAAGGG
ACEC01000115.1/2240-2146       GUCUUAUCAAGAG-UGG-U-GG-----------------AGGUA-ACAGG-ACCUG--UGAA-GCC--CGGCAACC-------UUUUG-------------------------------------------------------AGU----AA--GGUGCCA-AAUC--CUG-CGGCU---------------------------------AUGC-CG-A-AA-GAUGAGAA
CP001364.1/4661646-4661757     CACUCAUCCAGAG-CGG-U-GG-----------------AGGGA--CCGG-CCCGU--UGAA-ACC-GCAGCAACCCU-CGU-AUGCGUCG------------------------------------------------CCGCAUACGA-AC--GGUGCUA-AGUC--CGG-CAGAG---------GU----------------------GUUC-UG-G-AA-GAUGAGCG
CP001145.1/871363-871477       UUCUUAUCCAGAG-CGG-U-GG-----------------AGGGA--AAGG-CCCGA--AGAA-GCC--CGGCAACC-A-GCG-AGGGAGAA-------------------------------------------------AACCGAGC--AU--GGUGCCA-ACUC--CUU-CUGCACC-----AAGUC-------------------UGGUGC-AG-G-AA-GAUAAGAA
CP000492.1/2010009-2009901     CUGUCAUCGAGAA-AGG-U-GG-----------------AGGGA--CUGG-CCCUG--AGAA-ACC-UUGGCAACC-G-UCA-UUGCA------------------------------------------------------AUAUGAU-U---GGUGCCA-AUUC--CAU-CCCGGAU-----UACU---------------------GGCCG-GG-A-GA-GAUGAUGG
AAFX01122557.1/25-152          UGCUCAUCCAGAG-AGG-U-GG-----------------AGGGA--CCGG-CCCUG--AGAA-ACC-UCGGCAACC-G-CGA-AGCGC-------------------------------------------------------AGUCGC-U---GGUGCCA-AAUC--CGG-CAGAAGU-----UCUCCGGCAGGGUG-GCCGGGAGACAUUUC-UG-G-AA-GAUGAGGA
CT573074.1/54619-54740         AUCUUAUCCGGAG-UGG-C-AG-----------------AGGGA--CUGG-CCCUG--UGAA-GCC-ACAGCAACC-G-GCC-UGUUCAGAUUAC----------------------------------------GUCUGAACAUGGUG-CA--GGUGCUA-AUUC--CUG-UCUCAAG-----UUU-----------------------UUGG-GA-A-AA-GAUAAGAU
ABCM01000001.1/92975-92873     UACUUAUCCAGAA-AGA-C-UG-----------------AGGGA--AAGG-CCCUG--UGAU-GUC-UUAGCAACC-U-GUU-GAU----------------------------------------------------------UAAUA-A---GGUGCUA-AUUC--CUG-UCCGCAA-----CG-U----------------------AGCG-GA-G-AA-GAUAAGUG
AM263198.1/870267-870363       AUCUUAUCAAGAA-AGG-U-GG-----------------AGGGU-UCUGG-CCCGA--UGAA-GCC-UUGGCAACC-G-GAU-U--------------------------------------------------------------UUC-AC--GGUGCCA-AAUC--CAG-CAGUU----------A----------------------ACAC-UG-A-CA-GAUAAGGC
ACKT01000016.1/194512-194407   ACCUCAUCCAGAG-CAG-U-GG-----------------AGGGA--AUGG-CCCGA--UGAA-GCU-GCGGCAACC-A-UGA-CGACU-------------------------------------------------------GGGUCA-AC--GGUGCCA-AUUC--CUU-UAGGCGG-------AC----------------------UGCC-UA-U-GA-GAUGAGAG
CP001100.1/1493806-1493922     CUGUCAUCAAGAA-AGG-U-GG-----------------AGGGA--AAGG-CCCUG--CGAA-ACC-UUGGCAACCGC-UCA-AAUAAA----------------------------------------------------AAUGUGAG-UU--GGUGCUA-AUUC--CUA-CCCGGUG-----UAAACU-----------------ACCAGCG-GG-A-UA-GAUGACGG
CP000239.1/1201745-1201635     UCUUUAUCCAGAG-CAGAC-UG-----------------AGGGA-UCAGG-CCCAA--CGAA-GCU-GCGGCAACC-G-GCG-GAAGC------------------------------------------------------CUCCGCU-AC--GGUGCCA-ACUC--CUG-CGGUUAG-----UCAG----------------------UAAC-CG-A-AA-GAUAAAGG
ACIH01000230.1/3738-3609       AUCUUAUCAAGAGCAGG-U-GG-----------------AGGGA--CUAG-CCCGA--UGAU-ACC--CGGCAACC-G-GCG-AUGAAAC---------------------------------------------------CCAUCGCA-GC--GGUGCUA-AUUC--UUG-CAGGACCGU-CC----GUUUCGAAC----GCUGGACGGCUUC-UG-A-GA-GAUGAGAG
ACIK02000010.1/282585-282485   AACUCAUCAAGAG-UAG-U-GG-----------------AGGGA--UAGG-CCCUG--UGAA-GCU-ACAGCAACCAU-UCC-AA----------------------------------------------------------GAGGAA-AA--GGUGCUA-AUUC--CUA-UGACA----------A----------------------AUGU-CG-U-UA-GAUGGGAG
CP000607.1/1332223-1332114     CUAUCAUCGAGAA-AGG-U-GG-----------------AGGGA--CUGG-CCCUG--AGAA-GCC-UUGGCAACCGU-CAU-UCCUG-------------------------------------------------------UAAUGA-UU--GGUGCCA-AUUC--CAU-CCUGGCA-----GGGA---------------------CGCCG-GG-A-AA-GAUGACGG
CP001101.1/884104-884209       CUAUCAUCCAGAA-AGG-U-GG-----------------AGGGA--GUGG-CCCUG--AGAA-GCC-UUGGCAACC-G-UCA-GU----------------------------------------------------------AGUGAU-U---GGUGCCA-AUUC--CAA-CCCGGAC-----AAGCA--------------------GUGCG-GG-G-AA-GAUGAUUG
CP000108.1/1604667-1604787     CUAUCAUCCAGAA-AGG-U-GG-----------------AGGGA--CUGG-CCCAA--AGAA-GCC-UUGGCAACC-G-UUA-UUGUACU---------------------------------------------------GCAAUAAU-A---GGUGCCA-AUUC--CAU-CCUUAAC-----AUGGUAACU------------ACCUGUUAA-GG-A-AC-GAUGAUGG
ABIB01000001.1/287097-286995   UCGUUAUCAAGAA-AGG-C-UG-----------------AGGGA-AUAGA-CCCGA--UGAA-GCC-UUAGCAACC-C-UUU-ACAC--------------------------------------------------------AUAAAG-AA--GGUGCUA-CAUU--CUA-CUGCG----------C----------------------AAGC-GG-A-UA-GAUAACAA
AAOG01000001.1/142958-142849   AUGUUAUCAAGAA-AGG-C-GG-----------------AGGGA-UUAGA-CCCAU--UGAA-GCC-UUAGCAACC-C-UUU-AGUA--------------------------------------------------------AUAAAG-AA--GGUGCUA-AAUU--CUA-CUCAAUU-----AUUCG--------------------UAAUU-GG-A-UA-GAUAACAA
AANC01000003.1/237429-237533   AUGUUAUCAAGAA-AGG-C-GG-----------------AGGGA-AUAGA-CCCUA--UGAA-GCC-UUAGCAACC-C-UUU-CUCC--------------------------------------------------------CGAAAG-AA--GGUGCUA-CAUU--CUA-UCUGU--------UUU----------------------UGCA-GA-A-UA-GAUAACGC
ACBZ01000203.1/8528-8629       CUCUUAUUCAGAG-UGG-U-GG-----------------AGAUAUUAAGG-AUCAG--UGAA-ACC-ACGGCAACC-C-CUG-AC----------------------------------------------------------AAAAGG-AA--GGUGCCA-ACCU--GAG-CGAAG----------A----------------------AAUU-CG-A-AC-AAUAAGAG
CP001108.1/778657-778762       CUGUCAUCCAGAA-AGG-U-GG-----------------AGGGA--CUGG-CCCUG--AGAA-GCC-UUGGCAACC-G-UCA-UU----------------------------------------------------------CGUGAU-U---GGUGCCA-AUUC--CAA-CCCGGAG-----AGCU---------------------GUCCG-GG-A-AAAGAUGAUGG
CU207366.1/381646-381752       UCGUUAUCAAGAA-AGG-U-UG-----------------AGGGA-UUAGA-CCCUG--UGAA-ACC-UUGGCAACC-C-UCC-UGUAA-------------------------------------------------------UGGGAG-AA--GGUGCUA-CGUU--CUA-CCACGCC-----A--G----------------------UCGU-GG-A-UA-GAUAACUC
ACIN02000013.1/199862-199965   CUCUUAUUCAGAG-UGG-C-GG-----------------AGAGU-GAAGG-CUCUG--UGAA-GCU-ACGGCAACC-C-CUG-AA----------------------------------------------------------AGAUGG-AA--GGUGCCA-ACCU--GAG-CGAAGU-------UUU----------------------ACUU-CG-A-GC-AAUAAGAG
AARI02000249.1/265-361         AACUUAUCAAGAA-AGG-U-GG-----------------AGGGU-UCUGG-CCCCG--UGAA-CCU--UGGCAACC-G-GAA-GU-------------------------------------------------------------UUC-AC--GGUGCCA-AAUC--CAG-CAGGU----------A----------------------ACAC-UG-A-CA-GAUAAGGC
ACHB01000100.1/57340-57454     GAUUUAUAAAGAA-GUG-G-CG-----------------AGAGA--CUGG-CUCAA--UGAC-CCA-CUGGCAACC-U-UCA-AAAAAC-----------------------------------------------------GUUUGAA-AA--GGUGCCA-AUUC--CUG-UCCAAAG-----CAAUGU-----------------UGCUUUG-GA-G-CA-UAUAAAUG
ABIL02000006.1/144101-144004   ACCUUAUUUAGAG-CGG-U-GG-----------------AGUGA-AUAGG-CACUA--UGAA-ACC--CGGCAACC-G-GCA-AA-------------------------------------------------------------GGU-AC--GGUGCUA-AUAC--CUA-CGGGA---------UU----------------------UUUC-CG-A-AU-GAUGAGUA
CP000096.1/692601-692748       CUAUCAUCGAGAA-AGG-U-GG-----------------AGGGA--CUGG-CCCUG--AGAA-GCC-UUGGCAACC-G-UCA-UUGACCGUCAGUGAUUCAAUGGAUUG-------------CAUUGAUUCAUGUAUUGAGGUAAUGAU-U---GGUGCCA-AUUC--CAU-CCCGGUU-----GAAG----------------------GCCG-GG-A-AA-GAUGA-AG
AAPR01000022.1/22928-22828     GAUUUAUAAAGAA-GAG-G-CG-----------------AGAGA--CAGG-CUCCG--CGAC-CCU--CGGCAACC-U-CAA-CAAAG-------------------------------------------------------UGUUGA-AA--GGUGCUA-AUUC--CUG-CCC----------GAC----------------------AA-G-GG-A-CA-UAUAAAUU
ABRU01000018.1/11937-11821     CACUCAUCAAGAC-CGG-C-UG-----------------AGGGA-UUAGG-CCCUU--UGAC-GCC-GGGGCAACC-A-UCG-GGUUUCA--------------------------------------------------CCACCCGAA-AC--GGUGCCA-ACUC--CUG-CGGGGUC-----CUUCG-------------------GGGUCG-CG-A-GA-GAUGAGUG
ABVW01000002.1/44661-44766     UAGUUAUCAAGAA-AGG-U-GG-----------------AGGGA-UUAGA-CCCUG--UGAA-GCC-UUAGCAACC-C-UUU-GUAUUG-----------------------------------------------------UUCAAAG-AA--GGUGCUA-CAUU--CUA-UCUCA----------U----------------------UUGA-GA-A-UA-GAUAACCG
ACDH01000015.1/29225-29312     AUACCAUCAAGAG-AGA-U-UG-----------------AGGGA--CUGG-CCCGU--UGAA-AUC-UCAGCAACC-U-GCU-UUU---------------------------------------------------------UAAGUG-U---GGUGCUA-ACUC--CUG-----------------------------------------------A-GA-GAUGGAAU
AAWS01000061.1/3106-3001       GAUUUAUAAAGAA-GCG-C-UG-----------------AGAGA-GUAGG-CUCGA--UGAA-GCG-CUGGCAACC-U-GCU-AC----------------------------------------------------------ACAGUA-A---GGUGCUA-AGUC--CUA-CCUAAUU-----UAUU---------------------CAUUA-GG-A-AA-GAUAAAUC
ABED02000029.1/620487-620585   GACUUAUCAAGAG-CGG-C-UG-----------------AGGGG-ACAGG-CCCUG--UGAA-GCC--CGACAACC-U-GCG-CGA-G-------------------------------------------------------AGCGUA-A---GGUGCCA-AAUC--CUG-CGGGA----------------------------------AAC-CG-G-AA-GAUAAGAG
ABOU02000055.1/96522-96420     CUCUUAUUCAGAG-CAG-U-GG-----------------AGAUACAAAGG-AUCUA--AGAA-GCU-GCGGCAACC-C-CAC-AUUAU-------------------------------------------------------AAA-GG-AA--GGUGCCA-ACCU--GAG-CGAGU---------------------------------UACU-CG-A-AC-AAUAAGAG
ACEX01000437.1/2744-2885       CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA--ACGG-CCCGU--UGAA-GCC-CCGGCAACC-C-UCC-AGCUGGUCUCGCGUCCUGU---------------------------AGCGAGGCUCCCAGCUCGGG-AA--GGUGCCA-AUUC--CGU-CUCGUGG-----CGAAAUG----------------CGUCCCG-AG-G-AA-GAUGAGGA
AAXX01000001.1/747308-747200   UUGUUAUCACGAA-AGC-U-GG-----------------AGGGA-AUAGA-CCCUA--UGAA-AGC-UUAGCAACC-U-CUC-GCCCU-------------------------------------------------------UGCGGA-AA--GGUGCUA-CAUU--CUA-UUCCGAU-----ACUA----------------------UCGG-AA-G-CA-GAUAACGU
ABOX02000046.1/18955-19074     AUCUCAUGAAGAG-UGG-U-UG-----------------AGGGA--CUGG-CCCUA--CGAA-ACC-ACGGCAACC-G-GCU-GGGACGCG------------------------------------------------AUUUCCAGUG-CA--GGUGCCA-AGUC--CAG-CUCGAGC-----ACCAUU------------------AGCUCGGGG-A-AA-AAUGAGAA
CP001275.1/371734-371625       CGCUCAUCUCGAG-CGG-U-GG-----------------AGGGA--ACGG-CCCGA--CGAA-ACC--CGGCAACCA--GCG-CAGGCC----------------------------------------------------ACUGCGC--CA--GGUGCCA-AUGC--CGG-CGGAGCG-----GGAA---------------------AGCUC-CG-C-AC-GAUGAGCG
ABWO01000038.1/8212-8308       CUCUUAUUCAGAG-UGG-U-GG-----------------AGGUA-AAAGG-AUCUA--UGAA-GCC-ACGGCAACC-C-CGG-GAA------------------------------------------------------------CGG-AA--GGUGCCA-ACCU--GAG-CGAGU----------------------------------AAU-CG-A-AC-AAUAAGAG
ACDD01000058.1/73-160          AUACCAUCCAGAG-AAG-C-GG-----------------AGGGA--CUGG-CCCGA--UGAU-GCU-UCAGCAACC-U-ACU-GUU---------------------------------------------------------AGAGUG-U---GGUGCUA-AUUC--CAG-----------------------------------------------A-CA-GAUGGAGA
AAVO02000010.1/47842-47944     CUUUUAUUCAGAG-UGG-U-GG-----------------AGAUACAAAGG-AUCUG--AGAA-GCC-ACGGCAACC-C-CUU-UAUGU-------------------------------------------------------AUGAGG-AA--GGUGCCA-ACCU--GAG-CGAGA----------------------------------CAU-CG-A-AC-AAUAAGAG
AAVL02000036.1/100921-100817   CUCUUAUUAAGAGUUGG-C-GG-----------------AGAUA-CAAGG-AUCUG--UGAU-GCC-ACGGCAACC-C-CCG-AUUAU-------------------------------------------------------GAUGGA-A---GGUGCCC-ACCG--GAG-CAAUG---------CA----------------------AUAU-UG-A-UC-AAUAAGAG
ABYX01000149.1/176896-177023   AGCUCAUCCAGAG-GGA-C-UG-----------------AGGGA--ACGG-CCCGU--UGAA-GUC-CCGGCAACC-C-UCC-UGCCGACCGCGA-----------------------------------------GGUCACGGUGGGG-AA--GGUGCCA-AUUC--CGU-CUUGCGG-----CGAAAUG----------------CGUCGCG-AG-G-AA-GAUGAGGA
CP001472.1/3934139-3934250     AUUUCAUGAAGAG-UGG-C-UG-----------------AGGGA--CGGG-CCCUG--UGAC-GCC-ACGACAACC-G-GCU-CGAGCAA---------------------------------------------------UUCGGGAC-AU-CGGUGUCA-ACUC--UCU-CCUGCG------UAAC----------------------GGCG-GG-G-AA-CAUGAGAU
CT573213.2/7305357-7305472     GGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA--ACGG-CCCAG--UGAA-GCC-CCGGCAACC-A-CCC-GCAUCCG--------------------------------------------------AUGCGUGGC-A---GGUGCUA-AUUC--CGA-CCCGUGG-----CAGGUU------------------GCCCCG-GG-A-AA-GAUGAGGA
ABVR01000040.1/301449-301548   CUCUUAUUCAGAG-UGG-U-GG-----------------AGGUACAAAGG-ACCUG--CGAA-GCC-ACGGCAACC-C-CGG-UA----------------------------------------------------------AGCCGG-AA--GGUGCCA-ACCU--GAG-CGAGC----------------------------------AAU-CG-A-AC-AAUAAGAG
CP000386.1/1121068-1121189     CCCGCAUCAAGAG-CGG-U-GG-----------------AGGGA-ACUGG-CCCAG--CGAA-GCC-GCGGCAACC-G-GCG-GGGGGCCCU-----------------------------------------------UACCCCCGUG-A---GGUGCCA-AUUC--CAG-CAGGUCU-----CCCCGAG----------------GGGGGCC-UG-A-AA-GAUGUGGG
BA000030.3/4858626-4858480     CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-UACGG-CCCGA--UGAA-GCC-CCGGCAACC-C-UCC-AGCCGGUCUUGUCACGUUGAU-----------------------GUGGCGAGGCUCCCGGCUCGGG-AA--GGUGCCA-AAUC--CGU-CUCACGG-----CGAAGUG----------------CGUCGUG-AG-G-AA-GAUGAGGA
CP000885.1/4762158-4762063     CUCUUAUUCAGAG-UGA-C-GG-----------------AGAGU-AAAGA-CUCAG--UGAA-GUC-ACGGCAACC-C-CCU-AU-------------------------------------------------------------GGG-AA--GGUGCUA-AGUU--GAG-CGAGC----------------------------------AAU-CG-A-AC-AAUGAGAG
ACEZ01000126.1/65345-65190     AGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-AACGG-CCCGA--UGAA-GCC-CCGGCAACC-C-UCC-AGUCGGUACUCGUAGGUCACUGGCG--------------ACCACUUCGCGAGGCUCCCGACUAGGG-AA--GGUGCCA-AAUC--CGU-CUCACGG-----CGAGAUG----------------CGUCGUG-AG-G-AA-GAUGAGGA
CP000159.1/648790-648906       CAUUCAUCCAGAA-GGG-U-GA-----------------AGGGA-GCAGG-CCCGA--UGAA-GCC-CUGGCAACC-G-CCG-UCGGCACC------------------------------------------------CCCCGACGGA-AA--GGUGCCC-CAUC--CUG-CCUCGAC-----UGCU---------------------GUCGA-GG-A-AA-GAUGAGUG
AM420293.1/1589093-1588966     AGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA--ACGG-CCCGU--UGAA-GCC-CCGGCAACC-A-UCU-CGGCGUAUCGCGCAUUC------------------------------CGCGAGGCCGCCGGCGAAA-AA--GGUGCCA-AUUC--CGA-CCCGU----------C----------------------CGCG-GG-A-CA-GAUGAGGA
ACIP02000004.1/237213-237114   CUCUUAUUCAGAG-UGG-U-GG-----------------AGAUACAUAGG-AUCCG--UGAA-GCC-ACGGCAACC-C-CCA-AAG-----------------------------------------------------------CGGU-A---GGUGCCA-ACCU--GAG-CGAGU----------A----------------------UGUU-CG-A-AC-AAUAAGAG
AAXA02000011.1/106110-106208   CUCUUAUUCAGAG-CAG-U-GG-----------------AGGUACAAAGG-ACCUG--UGAA-GCU-GCGGCAACC-C-CCG-GUU-----------------------------------------------------------CGGG-AA--GGUGCCG-ACCU--GAG-CGAGU----------------------------------AAU-CG-A-AC-AAUAAGAG
CP000383.1/165474-165365       GAUUUAUAAAGAA-GAG-G-GG-----------------AGAGA-ACGGG-CUCUU--UGAA-CCU-CUAGCAACC-U-CCG-GGAGCA----------------------------------------------------AAUCCAGA-AA--GGUGCUA-AUUC--CUGACCUGA--------AUA----------------------AACA-GG-G-CA-UAUAAAUU
AARG01000011.1/103271-103357   UAACCAUCGAGAG-AAA-C-UG-----------------AGGGA--CUGG-CCCUA--UGAA-GUU-UCAGCAACCUG-UCA-UCA------------------------------------------------------------GAU-GU--GGUGCUA-AUUC--CAG-----------------------------------------------A-UA-GAUGGAAG
ACET01000016.1/116829-116743   AUACCAUCAAGAG-AGA-U-UG-----------------AGGGA--CAGG-CCCGA--AGAU-AUC-UCAGCAACC-U-ACU-GA----------------------------------------------------------AAUGUG-U---GGUGCUA-ACUC--CUG-----------------------------------------------U-UA-GAUGGAAG
ACII01000156.1/15700-15599     CUUUUAUUCAGAG-UGG-U-GG-----------------AGAUACAAAGG-AUCUG--CGAA-GCC-ACGGCAACC-C-CUG-UUUG--------------------------------------------------------UGUAGG-AA--GGUGCCA-ACCU--GAG-CGAGU----------------------------------GAU-CG-A-AC-AAUAAGAG
ACEW01000347.1/17844-17982     CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-CACGG-CCCGU--UGAA-GCC-CCGGCAACC-C-UCC-AGUCGGUUCUCGCCAGC-------------------------------GCGAGGCCCCGGCUAGGG-AA--GGUGCCA-AUUC--CGU-CUCAUGG-----CGAAGUG----------------CGCCAUG-GG-G-AA-GAUGAGGA
AAVP02000024.1/12932-13029     CUCUUAUUCAGAG-CAG-U-GG-----------------AGAUACAAAGG-AUCUG--AGAA-GCU-GCGGCAACC-C-CUG-AAC------------------------------------------------------------AGG-AA--GGUGCCA-ACCU--GAG-CGAGU----------------------------------CAU-CG-A-AC-AAUAAGAG
ABJH01000081.1/1215-1362       CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-AACGG-CCCGU--UGAA-GCC-CCGGCAACC-C-UCC-AGCCGGUCUCGUCGCGCACAG----------------------CGCAGCGGGGCUCCCGGCUCGGG-AA--GGUGCCA-AUUC--CGU-CUCAUGG-----CGAAACG----------------CGUCAUG-AG-G-AA-GAUGAGGA
ACEV01000067.1/336881-337014   CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA--ACGG-CCCGA--CGAA-GCC-CCGGCAACC-G-GCG-UGCAGCCUGUCAUCCCGCG--------------------------AUCGCGGGGUAGCUGACGACC-AC--GGUGCCA-AUUC--CGG-CCCGC--------UUC----------------------GGCG-GG-G-CA-GAUGAGGA
ABWN01000022.1/104834-104735   UGCUUAUUCAGAG-UGA-U-GG-----------------AGAUACAUAGG-AUCUG--UGAA-GUC-ACGGCAACC-C-CCU-UGG------------------------------------------------------------CGG-AA--GGUGCCA-ACCU--GAG-CGAAA----------G----------------------UAUU-CG-A-GC-AAUAAGUG
AANA01000001.1/1389418-1389294 ACGUUAUCACGAA-AGG-C-AG-----------------AGGGA-UUAGA-CCCAG--UGAA-GCU-UUGGCAACC-U-CUC-AGAA--------------------------------------------------------AUGAGA-AA--GGUGCUA-CAUU--CUA-CAAUCUA-----UUUCGAUAUUUU-----AUCAAAUAGCUAU-UG-A-CA-GAUAACAG
AAPD01000001.1/936074-936181   AAAUUAUCAAGAA-AGG-A-CG-----------------AGGGA-ACAGA-CCCAU--CGAC-UCC-UUAGCAACC-C-UUA-ACGCU------------------------------------------------------CGUUAAG-AA--GGUGCUA-CAUU--CUG-CCCAU--------UUA----------------------AUUG-GG-AUGA-GAUGAUAC
ABVK02000003.1/176687-176823   CUCUUAUCCAGAG-CGG-U-GG-----------------AGGGU--ACGG-CCCUG--UGAA-ACC-GCGGCAACC-U-CCC-GCUCCUUCCGUUCCAU--------------------------------GGCCGGAAGCGGGCGGGG-CU--GGUGCCA-ACGC--CGG-CCCGGGCGGGGG----AA-----------------ACGCCCG-GG-A-AC-GAUAAGAG
CP000249.1/5255171-5255287     GGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA--ACGG-CCCAG--CGAA-GCC-CCGGCAACC-A-CCC-GCAUCCC--------------------------------------------------GUGCGCGGC-A---GGUGCUA-AUUC--CGG-CCUGGUG-----GCAGAC-----------------UGCCCCG-GG-A-AA-GAUGAGGA
AAYG02000021.1/57727-57823     CUCUUAUUCAGAG-CAG-U-GG-----------------AGGUACAAAGG-ACCUG--UGAA-GCU-GCGGCAACC-C-CGU-CA-------------------------------------------------------------AGG-AA--GGUGCCG-ACCU--GAG-CGAGC----------------------------------AAU-CG-A-AC-AAUAAGAG
ABJF01000395.1/4781-4624       CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-CACGG-CCCGU--UGAA-GCC-CCGGCAACC-C-UCC-AGUCGGUUCUCGCGAUCGCCCGCACG------------GCGACACCAGCGAGGUCCCCGGCUAGGG-AA--GGUGCCA-AUUC--CGU-CUCAUGG-----CGAAGUG----------------CGCCAUG-GG-G-AA-GAUGAGGA
CP000820.1/215210-215091       GGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA--ACGG-CCCAG--CGAA-GCC-CCGGCAACC-A-CCG-UCGCAUCC-------------------------------------------------AUGCGCGGC-A---GGUGCUA-AUUC--CGA-CCCGGGA-----CGCAGCC---------------GGCUCCCG-GG-A-AA-GAUGAGGA
ABLU01106369.1/97-6            CAGUUAUUAAGAA-AGG-C-AG-----------------AGGGA-UUAGA-CCCGU--UGAA-GCC-UUAGCAACC-C-UUU-AUUC--------------------------------------------------------AUAAAG-AA--GGUGCUA-CAUU--CU----------------------------------------AC------C-AA-AAUAUUUU
ACEU01000265.1/7365-7210       CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-UACGG-CCCGU--UGAA-GCC-CCGGCAACC-C-UCC-AGCCAGUCUCCGCGCGGUUCACCGA--------------UACCGCCACCGAAGGCCCUGGCUCGGG-AA--GGUGCCA-AUUC--CGU-CUCGCGG-----CGAGAUG----------------CGCCGCG-GG-G-AA-GAUGAGGA
CP000112.1/2490976-2491083     AACUCAUGAAGAG-GAC-G-AG-----------------AGGGG-UCUGG-CCCGA--UGAC-CGU-CCGGCAACC-U-GCC-CGC---------------------------------------------------------AAGGCA-A---GGUGCCA-AAGC--CAG-CCACGGU-----GAGAU--------------------GCCGC-GG-U-GC-CAUGAGGU
ABYC01000290.1/27042-27199     CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-CACGG-CCCGU--UGAA-GCC-CCGGCAACC-C-UCC-GGUCGGUACUCCCGGCGCGUGUUCCA------------CCCGCGUCCGCGAGGCUCCCGGCUCGGG-AA--GGUGCCA-AUUC--CGU-CUCGCGG-----CGAGAUG----------------CGUCGCG-AG-G-AA-GAUGAGGA
ACES01000173.1/1604-1473       ACCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-UACGG-CCCGA--CGAA-GCC-CCGGCAACC-A-CCC-GCACGUUCGAUG----------------------------------------ACGAGCGGCGCGGA-CA--GGUGCCA-AUUC--CGU-CCCCGCC-----GCAGGGUG--------------CGAUGCGG-GG-A-AA-GAUGAGAG
AP008226.1/728125-727989       CUCUUAUCCAGAG-CGG-U-GG-----------------AGGGU--ACGG-CCCUG--UGAA-GCC-GCGGCAACC-U-CCC-GCCCCUUCCGUUCCAU--------------------------------GGCCGGAUGCGGGCGGGG-CU--GGUGCCA-ACGC--CGG-CCCGGGCGGGGG----AA-----------------ACGCCCG-GG-G-AC-GAUAAGAG
AP008957.1/5227167-5227072     CCACCAUCCAGAG-UGG-C-UG-----------------AGAGA-CCUGG-CUCGA--UGAU-GCC-GCAGCAACC-C-GCU-UCGUUU----------------------------------------------------GCGCAGUG-UG--GGUGCUA-CCGC--CAG----------------------------------------G------A-CC-GAUGGAGG
ABXP01000190.1/1560-1672       GUUUUGUACAGUUUGGG-U-AAC---------------CAGGGA-AAGAG-CCCGA--UGAA-ACC--CGGCAACCUG-UCC--UUUU-------------------------------------------------------AAGGAU-AA--GGUGCCA-AUUC--UCU-CAGAAGA-----UUUUU--------------------UCUUC-UG-A-AA-GAUGAGGG
ABYA01000312.1/4381-4534       AGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-CACGG-CCCGA--UGAA-GCC-CCGGCAACC-C-UCC-AGCCGGUUCUCGUGUCGAUCGUUGUGCGCGCACAGCCGAUCGCACCCGCGAGGCUCCCGGCUAGGG-AA--GGUGCCA-AAUC--CGU-C------------UCA----------------------CG----G-C-GA-GAUGCGUC
CP001638.1/2955292-2955189     UUCUUAUCAAGAG-AGG-U-GG-----------------AGGGA--CUGG-CCCAA--UGAA-GCC--CGGCAACC-G-GUU-GUU----------------------------------------------------------UCAAC-AU--GAUGCUA-AUUC--CAG-CAGAGCG-----AAUU----------------------GCUC-UG-A-GA-GAUAAGAA
CP002040.1/5022556-5022415     UGCUCAUCCAGAG-GGG-U-GG-----------------AGGGA--CCGG-CCCUG--CGAA-GCC-CCGGCAACCAU-UCC-AGCAUGUGACACCCGCGA-----------------------------ACCCGCGGGACGGCUGGGA-CA--GGUGCCA-ACUC--CGG-CCUGGGG-----ACAAGGU---------------GUCCGCCA-GG-A-AA-GAUGAGGG
CP001700.1/9422701-9422569     CGCUCAUCCAGAG-GAG-C-UG-----------------AGGGA--CCGG-CCCUA--CGAC-GCU-CCGGCAACC-A-UCC-GUUCUGCCACCU----------------------------------------CAUCGUGGCACGGC-GC--GGUGCCA-ACUC--CGG-CCCACCC-----GGCAGCCGC------------CGAGCCGUG-GG-A-AA-GAUGAGGA
ADJS01002320.1/1580-1477       UACUCAUCGAGAG-CAG-C-GG-----------------AGGGA-UUUGG-CCCCA--UGAU-GCU-GCAGCAACC-A-UUC-UAUAU-------------------------------------------------------AGGGAA-AA--GGUGCUA-AUUC--CAU-CAGCA----------U----------------------UUGC-UG-G-CA-GAUGAGAG
CP001825.1/900813-900915       GCCUUAUCAAGAG-AGG-U-GG-----------------AGGGA-GACGG-CCCUG--UGAA-GCC--CGGCAACC-A-GCG-CCCAG------------------------------------------------------GAGCGCC-A---GGUGCCA-AUUC--CGG-CGAGG----------U----------------------CACU-CG-C-AA-GAUAAGGG
ACIE02000025.1/96603-96517     AAUCCAUAGAGAG-AGA-U-GG-----------------AGGGA--CAGG-CCCUU--UGAU-AUC-UCAGCAACC-U-GCU-UUU----------------------------------------------------------AAGUG-U---GGUGCUA-AUUC--CUG-----------------------------------------------A-UA-GAUGGUUU
CP003056.1/960835-960734       GCCUUAUCAAGAG-AGG-C-GG-----------------AGGGA-CUUGG-CCCGA--UGAA-ACC-UCAGCAACCAG-CCC-AUAC-----------------------------------------------------------GGC-AC--GGUGCUA-AAUC--CAA-CAGGU----------A----------------------UACC-UG-A-AAAGAUAAGGA
CP002637.1/1789046-1788942     CACUCAUCAAGAG-CAG-U-GG-----------------AGGGA--CUGG-CCCUA--UGAA-ACU-GCGGCAACC-G-UUG-GCGUA------------------------------------------------------GGCCAAA-AA--GGUGCCA-AUUC--CUA-UAGGU---------AU----------------------UGCC-UA-U-GA-GAUGGGAG
ABJG02000470.1/2764-2919       CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-AACGG-CCCGU--UGAA-GCC-CCGGCAACC-C-UCC-AGCCAGUCUCCGCGCGGUUCACCGA--------------UACCGCCACCGAAGGCCCUGGCUCGGG-AA--GGUGCCA-AUUC--CGU-CUCGCGG-----UGAGAUG----------------CGCCGCG-AG-G-AA-GAUGAGGA
CP003029.1/2215558-2215432     AGCUCAUCCAGAA-GGG-U-GG-----------------AGGGA-CCAGG-CCCUG--UGAA-GCC-CUGGCAACC-G-CCC-CGUUGAUCGUCGG--------------------------------------GAGACGACGUGGGGA-AA--GGUGCCA-AUUC--CUG-CCUCGCA-----CGAC---------------------CGCGA-GG-G-GA-GAUGAGCU
CP001814.1/9846218-9846077     UGCUCAUCCAGAG-GGG-U-GG-----------------AGGGA--CCGG-CCCUG--CGAA-GCC-CCGGCAACCCU-CCC-GGUUCAAGACUCGUUUUU-----------------------------CUGACGAGGUCGGCCGGGA-CA--GGUGCCA-AUUC--CGG-UCUGUGA-----CCAGGGU----------------GGUCGCA-GACG-AA-GAUGAGGG
CP002157.1/228642-228537       CCGUUAUCAAGAA-AGG-C-GG-----------------AGGGA-CUAGA-CCCAA--UGAA-ACC-UUGGCAACC-C-UUU-ACU---------------------------------------------------------UUAAAG-UA--GGUGCUACAUUC--UAU-UACGCC-------UAU----------------------GGCG-UG-A-AA-GAUAACAG
ACCR02000003.1/83189-83082     CUCUUAUCUAGAG-CGG-C-AG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--CGGCAACC-U-AAC-UUUUU-------------------------------------------------------UUAGUG-AA--GGUGCUA-AUUC--CAG-CAACAUU-----UCUA---------------------AAUGU-UG-A-CA-GAUAAGAG
ACDB02000007.1/188296-188209   UAACCAUCAAGAG-AAA-C-UG-----------------AGGGA--CUGG-CCCUA--GGAC-GUU-UCAGCAACC-U-GCU-UAA---------------------------------------------------------AAAGUG-U---GGUGCUA-AUUC--CAG-----------------------------------------------A-AA-GAUGGAUA
CP001681.1/4562963-4563072     UGCUUAUAGAGAA-AGA-U-GG-----------------AGGGA-UUAGA-CCCUG--CGAA-GUC-UUGGCAACC-U-GUG-CUU------------------------------------------------------------ACA-A---GGUGCUA-CAUU--CUA-CAGGAAA-----UGCAGCU---------------GUACUUCC-UG-A-CA-GAUAAGUG
CP001699.1/4958750-4958860     UUCUUAUCAAGAA-AGG-C-AG-----------------AGGGA-AAUGG-CCCUG--UGAA-GCC-UUAGCAACCAU-CCG-GAACCAC--------------------------------------------------CAAACCGGA-AA--GGUGCUA-CAUC--CAG-CCCGC---------AU----------------------AGCG-GG-A-AA-GAUAAGUC
CP001968.1/2913390-2913281     AACUUAUCGAGAG-UAG-U-GG-----------------AGGGA-CAAGG-CCCUG--UGAA-GCU-ACAGCAGCC-G-GUU-AGCAUUAAA-----------------------------------------------AGCUGAUGUC-U---GGUGCUA-AUUC--CGA-CC----C-----UAUG----------------------GA---GG-A-GA-GAUAAGUC
ABTR02000001.1/1201751-1201854 CUCUUAUCGAGAG-AGG-C-GG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CGGCAACC-U-GCC-CGUA--------------------------------------------------------AGGGCAUGA--GGUGCCA-ACAC--CAG-CGACC--------GAC----------------------AGGU-CG-A-GU-GAUAAGAG
ABJJ02000300.1/30118-29960     CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA-UACGG-CCCGA--UGAA-GCC-CCGGCAACC-C-UCC-AGUCGGUUCUCGUAGCGAUCGCUGACG-----------AUCGUCUCCGCGAGGCUCCCGACUCGGG-AA--GGUGCCA-AAUC--CGU-CUCACGG-----CGAGAUG----------------CGUCGUG-AG-G-AA-GAUGAGGA
ABWK02000020.1/271385-271488   CUCACAUCCAGAG-CGG-C-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC-GCGGCAACC-A-UUG-ACUUC-------------------------------------------------------GUCAAA-AC--GGUGCCA-AUUC--CUU-UAGGU---------CC----------------------GGCC-UA-U-AA-GAUGAGAG
CP001649.1/963759-963659       UACUCAUGUAGAG-GAU-G-CG-----------------AGGGAAAUCGG-CCCGU--CGAC-CAU-CCGGCAACC-U-GCU-UCA---------------------------------------------------------GCAGCA-A---GGUGCCA-AUGC--CUU-CCCGU---------------------------------UACG-GG-A-CC-CAUGAGAG
CP001720.1/3787367-3787476     CUCUUAUCCGGAG-UGG-U-GG-----------------AGGGA--CUGG-CCCGA--UGAA-ACC--CGGCAACC-U-UCU-GAGAACU---------------------------------------------------AAUCAGAA-A---GGUGCUA-AUUC--CUG-CAGAGGA-----UUUU----------------------CUUC-UG-A-CA-GAUAAGAG
CP001685.1/832315-832217       AACUUAUCAAGAG-UGA-UACU-----------------AGGGA--CCGG-CCCGUUUUGAGUAUC--CAGCAACC-U-GUA-UUA------------------------------------------------------------ACA-A---GGUGCUA-AUUC--C-G-GCAUG----------U----------------------GAAU-GC-G-AA-GAUAAGAA
CP001818.1/1579334-1579230     CUCUUAUCAAGAG-UGG-C-GG-----------------AGGGA--CUGG-CCCGA--UGAA-GCC--CGGCAACC-U-GCA-GAGCACG---------------------------------------------------UCUCUGCG-U---GGUGCCA-ACAC--CUG-CGGCG----------A----------------------AAGC-CG-A-GU-GAUAAGAG
CP003056.1/3328132-3328032     UUCUUAUCCAGAG-AGG-U-GG-----------------AGGGA--AAGG-CCCUU--UGAA-GCC-UCGGCAACA-G-GUU-GAAA-----------------------------------------------------------AAC-AC--UGUGCCA-AUUC--CUG-CAGAC--------AAU----------------------CGUC-UG-A-AA-GAUAAGAG
CP001778.1/452900-453004       ACUUCAUCAAGAG-CGG-U-CG-----------------AGGGA--ACGG-CCCUG--CGAC-ACC-GCGGCAACC-A-CCC-AUC-----------------------------------------------------------CGGG-CA--GGUGCCA-AAUC--CGU-CCGGCGU-----GACC---------------------GCGCC-GG-G-AA-GAUGAGGC
CP001743.1/842385-842265       GCCUUAUCCAGAG-CAG-C-GGACAGGGCAACUGCCCGACGGGA--ACGG-CCCGA--UGAA-GCU-GCGGCAACCU--GCC-AAA-----------------------------------------------------------GGC--AA--GGUGCCA-AUUC--CGG-CCCGGCC-----UCUG---------------------CGCCG-GG-A-AA-GAUAAGGG
CP001794.1/1767716-1767554     U---UAUCAAGAGUUGG-C-UG-----------------AGGGA-AUUGG-CCCAA--UGAA-GCC--CAGCAACC-G-ACC-GUAAUGCUAUCGUGAGAUAGGGCGCACGCCAAGGGCGGCGCCGGAAGCGUCAUGCUUCCGCAGGGC-AC--GGUGCUA-AGUC--CAA-CAGAAAG-----ACCGAU-----------------GUCUUUC-UG-A-AA-GAUA---A
CP001793.1/5775580-5775452     AUCUUAUCAAGAGCAGG-U-GG-----------------AGGGA--CUAG-CCCUA--UGAA-ACC--CGGCAACCG--GCG-GCAAC-------------------------------------------------------AUCGC--AC--GGUGCUA-AUUC--UUG-CAGGAGA-----UACGACGAUUGUAUAAGCCGUUGUAUAGCC-UG-A-CA-GAUGAGAG
CP001736.1/1289540-1289681     UGCUCAUCCAGAG-GGA-C-UG-----------------AGGGA-UACGG-CCCGU--UGAA-GUC-CCGGCAACCCU-CCC-CGUGGAGGCCCCGUCCU-------------------------------GGGGCCGCUCGCGGCGGA-AC--GGUGCCA-AAUC--CGU-CCCACGC-----CGAGAUCC--------------GGCGCCCG-GG-G-AA-GAUGAGGA
ACDG02000015.1/15379-15466     AUACCAUCAAGAG-AGA-U-UG-----------------AGGGA--CAGG-CCCUA--AGAU-AUC-UCAGCAACC-U-ACU-GGA---------------------------------------------------------AAAGUG-U---GGUGCUA-ACUC--CUG-----------------------------------------------U-CA-GAUGGAAG
AAXU02000001.1/3185191-3185093 AGCUUAUCGAGAA-AGA-C-UG-----------------AGGGA--AGGG-CCCGA--CGAC-GUC-UUAGCAACC-U-GUA----------------------------------------------------------------ACC-AA--GGUGCUA-AUUC--CCA-UCCCGAA-----UA-U----------------------UCGG-GA-A-UA-GAUGAGCG
CP001631.1/1935400-1935293     GAAUCAUCGAGAG-CGG-U-GU-----------------AGGGA--CGGG-CCCUG--UGAU-ACC-GCGGCAACCAG-U-U-CGAUAC----------------------------------------------------GUCGA-AC-CA--GGUGCCA-AU------G-CCCGAGC-----GAUGG--------------------CGGCG-GG-A-GG-GACGAUGU
CP001738.1/890419-890560       CGCUCAUCCAGAG-GGG-U-GG-----------------AGGGA--CCGG-CCCUG--UGAA-GCC-CCGGCAACC-C-UCC-CGGUGCUGACGCUCUCGCG--------------------------ACCUGCGAGGCCGGCCGGGAC-AG--GGUGCCA-AUUC--CGG-CCCGCGA-----CCAAGG-----------------UGGCGCG-GG-A-CA-GAUGAGGA
ABJI02000433.1/3689-3816       CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA--ACGG-CCCGU--UGAA-GCC-CCGGCAACC-C-UCC-CGCCGACCGCGA-----------------------------------------GGUCACGGUGGGG-AA--GGUGCCA-AUUC--CGU-CUCGUGG-----CGAAGUG----------------CGUCACG-AG-G-AA-GAUGAGGA
ABYU02000037.1/4945-4847       CUCUUAUUCAGAG-UGA-U-GG-----------------AGAUACAUAGG-AUCUG--UGAA-GUC-ACGGCAACC-C-CGC-AUG-----------------------------------------------------------GCGG-AA--GGUGCCA-ACCU--GAG-CGA-----------AU----------------------AA-U-CG-A-AC-AAUAAGAG
ACDZ02000006.1/93274-93376     UACUUAUCAAGAG-UGA-G-UG-----------------AGGGA-UAAGG-CCCGG--UGAA-CUC--CAGCAACC-U-AAU-CAA-U-------------------------------------------------------UGAUUA-A---GGUGCUU-UCCU--UAG-CAAAG--------UUU----------------------ACUU-UG-A-GC-GAUGAGGU
CP003056.1/1844232-1844126     AACUUAUCAAGAG-AGG-G-GG-----------------AGGGA--CUGG-CCCGA--GGAA-ACC-UCAGCAACAGA-UUC-UUUUU-------------------------------------------------------GGGAAU-AC--UGUGCUA-AUUC--CAG-CAAGCGU-----CAAG------------------------CU-UG-G-AA-GAUAAGUU
ACBY02000020.1/258141-258043   AACUUAUCAAGAG-UGG-C-AG-----------------AGGGG-ACAGG-CCCUG--UGAA-GCC--CGACAACC-U-ACA-CAAA--------------------------------------------------------UGUGCA-A---GGUGCCA-AUUC--CUG-CGGGG----------------------------------AAC-CG-A-AA-GAUAAGCG
CP001656.1/5519557-5519455     UUCUUAUCAAGAGCAGG-C-GG-----------------AGGGA--CUAG-CCCGA--UGAA-GCC--CGGCAACC-G-GCG-UAA------------------------------------------------------------G-C-AC--GGUGCUA-AUUC--UUG-CGGAAAC-----AUUA---------------------GUUUC-UG-A-GA-GAUGAGGG
CP001791.1/1324400-1324509     UUCUUAUCCAGAG-CGG-C-GG-----------------AGGGA--CUGG-CCCUA--UGAA-GCC--CGGCAACC-A-UCA-CGAAA-------------------------------------------------------GUGGAA-----GGUGCCA-AUUC--CAA-CAGAGCG-----UAUUCG-----------------UACGCUU-UG-A-CA-GAUAAGAG
ACJX02000007.1/318260-318153   CUCUUAUCCAGAG-CGG-C-GG-----------------AGGGA--CUGG-CCCUG--CGAA-GCC--CGGCAACCU--GCU-UACCCUU--------------------------------------------------UGGGGAGC--GU--GGUGCCA-AAAC--CUG-CAACC--------GAA----------------------AGGU-UG-A-AU-GAUGAGAG
CP001739.1/1846920-1847007     AUAUCAUCAAGAG-GAA-C-UG-----------------AGAGA--CAGG-CUCUG--UGAC-GUU-CCAGCAACC-U-ACG-UAA---------------------------------------------------------AUCGUG-U---GGUGCUA-AUUC--CUG-----------------------------------------------A-AA-GAUGAAAA
CP001619.1/3294664-3294557     GAUUUAUAAAGAA-GAG-G-CG-----------------AGAGA-AUGGG-CUCAA--CGAA-CCU-CUGGCAACCUG-CUA-CCACA------------------------------------------------------UCGGAGA-AA--GGUGCUA-AUUC--CCA-CCUAA--------GUU----------------------AUUA-GG-A-GA-UAUAAACU
CP001867.1/829496-829625       CACUCAUCCAGAG-GGG-C-AG-----------------AGGGA-CACGG-CCCGA--CGAA-GCC-CCGGCAACCGC-CGC-ACCGCGCGU----------------------------------------------CAGCGCAGCGG-AA--GGUGCCA-AUUC--CGU-CCCGCGC-----GGCUCGACG-----------GCCCGAUGCG-GG-G-AA-GAUGAGGA
ACLF03000006.1/44662-44769     CACUCAUCACGAG-GGG-U-GG-----------------AGGGA--ACGG-CCCGC--UGAU-ACC-CCAGCAACC-A-GUC-GGUCU-------------------------------------------------------UCGACC-A---GGUGCUA-CGUC--CGU-CCCGGAG-----UCCG---------------------CUCCG-GG-G-AA-GAUGACCU
CP003056.1/732327-732208       UUCUUAUCAAGAG-AGG-U-UG-----------------AGGGA--AUGG-CCCGA--UGAA-GCC-UCAGCAACC-U-UCA-AUGCUUUU------------------------------------------------ACGCAUUGAA-AA--GGUGCUA-AGUC--CUG-CAAGUUAUGGGAUCAU----------------------AACU-UG-A-AA-GAUAAGAA
CP001823.1/1231295-1231405     CUCUUAUCCAGAG-UGG-U-GG-----------------AGGGA--ACGG-CCCGA--CGAA-GCC--CGGCAACC-G-ACG-GAUCGCA--------------------------------------------------CGGUCCG-C-GC--GGUGCCA-AUUC--CGG-CAGCGGC-----GUUG----------------------CCGC-UG-A-GA-GAUGAGAG
CP001769.1/5132553-5132446     UACUUAUCCAGAA-AGA-C-GG-----------------AGGGA-CCGGA-CCCGA--UGAU-GUC-UUGGCAACC-A-ACC-AGCCC-------------------------------------------------------AGGGGA-AU--GGUGCCA-AUUU--CCU-CCCGCCA-----GC-C----------------------AGCG-GG-G-UA-GAUAAGGU
ACCL02000003.1/136176-136276   CUCUUAUUCAGAG-UGG-U-GG-----------------AGAUACAGAGG-GUCUG--UGAA-GCC-ACGGCAACC-C-CGC-AU----------------------------------------------------------AGACGG-AA--GGUGCCA-GCCU--GAG-CGA----------UUA----------------------AU-U-CG-A-AC-AAUAAGAG
ACKQ02000002.1/742513-742620   AUGUUAUCAAGAA-AGG-U-UG-----------------AGGGA-UUAGA-CCCUG--UGAA-ACC-UUAGCAACC-C-UUU-GCGCA------------------------------------------------------AGUAAAG-AA--GGUGCUA-CGUU--CUA-CCAAAA-------UAA----------------------UUUU-GG-A-CA-GAUAACUU
ACIQ02000024.1/9596-9700       AUCUUAUUCAGAGACGG-U-GG-----------------AGCUACAUAGG-AGCGA--AGAA-GCC-GCAGCAACC-C-CGG-AAA------------------------------------------------------------CGG-AA--GGUGCUA-ACCU--GAG-CGAACAA------UUU----------------------GUUU-CG-A-AC-AAUAAGAC
ACHA02000006.1/124772-124667   CGCUUAUAGAGAA-AGG-C-AG-----------------AGGGA-CUAGA-CCCAA--UGAA-GCC-UUGGCAACCU--GUC-UUG---------------------------------------------------------GAGAC--AA--GGUGCUA-CAUU--CUA-CCCCACC-----UAAA----------------------AAAG-GG-A-AA-GAUAAGCG
CP001630.1/1349393-1349277     CGCUCAUCCAGAG-GGG-C-AG-----------------AGGGA--UCGG-CCCGA--AGAA-GCC-CCGGCAACC-U-GUC-ACCAGUCAUCA-------------------------------------------GACUGGGUGAUC-AC--GGUGCCA-AUUC--CGA-CCCGC--------GAA----------------------AGCG-GG-A-AA-GAUGAGGA
CP001661.1/2331226-2331122     AACUUAUCACGAG-CGA-C-CG-----------------AGGGA--CUGG-CCCCA--UGAC-GUC-GCGGCAACC-U-CCC-GUA-----------------------------------------------------------AGGG-AA--GGUGCCA-AAUC--CAG-CGAAGCG-----GCGA---------------------CGCUU-CG-G-AA-GAUAAGGA
CP002043.1/113014-112896       GUCUUAUCCAGAG-CAG-C-GG-----------------AGGGA--ACGG-CCCUG--UGAA-GCU-GCGGCAACC-U-GCG-GAGGCCUUCU--------------------------------------------AAAGCGCCUACU-AA--GGUGCCA-AUUC--CGA-CCCGGUG-----GCCA----------------------UCCG-GG-A-AA-GAUAAGGA
#=GC SS_cons                   ((((((((,,,,,.,<<.<.--.................-<<<_..____.>>>--..----.>>>.,,<<<-<<<.<.<<_._____.......................................................___>>>.--..>>>>>>,.,,,,..,,,.<<<<___.....____......................__>>.>>.,.,,.))))))))
#=GC RF                        cucUuAUcaAGAG.aGG.c.gG.................AGGGA..cuGG.CCCua..UGAA.gCC.uCgGCAACC.c.ccu.auaau.......................................................auaggg.Aa..GGUGCcA.AuUC..Cug.Ccggaua.....uuuu......................uucc.gG.a.aA.gAUaAgag
//
# STOCKHOLM 1.0

#=GF AC   RF00163
#=GF ID   Hammerhead_1
#=GF DE   Hammerhead ribozyme (type I)
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:9632772
#=GF GA   34.00
#=GF TC   34.00
#=GF NC   33.90
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.88 -Z 549862.597050 CM SEQDB
#=GF CL   CL00010
#=GF DR   SO; 0000380; hammerhead_ribozyme;
#=GF RN   [1]
#=GF RM   11024185
#=GF RT   Hammerhead-mediated processing of satellite pDo500 family transcripts from
#=GF RT   Dolichopoda cave crickets.
#=GF RA   Rojas AA, Vazquez-Tello A, Ferbeyre G, Venanzetti F, Bachmann L, Paquin B,
#=GF RA   Sbordoni V, Cedergren R
#=GF RL   Nucleic Acids Res 2000;28:4037-4043.
#=GF RN   [2]
#=GF RM   10899150
#=GF RT   Distribution of hammerhead and hammerhead-like RNA motifs through the
#=GF RT   GenBank.
#=GF RA   Ferbeyre G, Bourdeau V, Pageau M, Miramontes P, Cedergren R
#=GF RL   Genome Res 2000;10:1011-1019.
#=GF CC   The hammerhead ribozyme is one of the smallest catalytic RNAs. These RNAs
#=GF CC   have an endonuclease function, and most often are autocatalytic.
#=GF CC   Structurally it is composed of three base paired helices, separated by
#=GF CC   short linkers of conserved sequence. These helices are called I, II and
#=GF CC   III. We have classified hammerhead ribozymes into three types based on
#=GF CC   which helix the 5' and 3' ends of the sequence join. This family are the
#=GF CC   type I hammerheads. The conserved uridine-turn links helix I to helix II
#=GF CC   and usually has the sequence CUGA. Helix II and III are linked by a
#=GF CC   sequence CGAAA. The cleavage reaction occurs between helix III and I, and
#=GF CC   is usually a C. Hammerhead ribozymes are found in plant viroids and other
#=GF CC   small replicating satellite RNA species. Hammerhead ribozymes have been
#=GF CC   found in animals as well as plants.
#=GF WK   Hammerhead_ribozyme
#=GF **   seedtax: Viroids; Eukaryota
#=GF SQ   29


AF404068.1/70-185            CUUUCCAUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUUAAUAAAAGUUCACCACGACUCCUCCUUCUCU--CACAAGUCGAA---ACUCAGAGUC---GGAAAG
AF404052.1/70-187            CUUUCCCUGAAGUGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUUUAAUAAAAAGUUCACCACGACUCCUCCUUCUCUCACAAGUCGAA---ACUCAGAGUC---GGAAAG
AF404073.1/70-162            CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAACGACUCCUCCUUCUCU-------------------------CACAAGUCGAA---ACUCAGAGUC---GGAAAG
AF404040.1/70-186            CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUUUAAUAAAAGUUCACCACGACUCCUCCUUCUCU-CACAAGUCGAA---ACUCAGAGUC---GGAAAG
AF404041.1/70-183            CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUAUAAAAGUUCACCACGACUCCUCCUUCUCU----CACAAGUCGAA---ACUCAGAGUC---GGAAAG
X52041.1/178-64              CUUUCCCUGAAGAGACGAAGUGAUCAAGAGAUUGAAGACGAGUGAACUAAUUUUUUUAAUAAAAGUUCACCACGACUCCUCCUUCUCU---CACAAGUCGAA---ACUCAGAGUC---GGAAAG
AF213692.1/353-397           AUCCAGCCGAUGAGUUCCA------------------------------------------------------------------------AACAGGACUAA---ACGC-GCUUC---UUGGAU
AF213693.1/184-228           AUCCAACCGAUGAGUCCCA------------------------------------------------------------------------AAUAGAACGAA---ACCU-GCGUC---CUGGAU
AF036741.1/118-165           AUCCAGCCGACGAGUCCCA------------------------------------------------------------------------AAUAAAACGAA---ACGC-GCGUCAAAGUGGAU
X15619.1/121-168             AUCCAGCUGACGAGUCCCA------------------------------------------------------------------------AAUAGGACGAA---ACGC-UCGUCAAAAUGCAU
AF036393.1/119-166           AUCCAGCUGACGAGUCCCA------------------------------------------------------------------------AACAGGACGAA---ACGA-GAGUCAAACUGCAU
AF036390.1/118-165           AUCCAACUGACGAGUGCCC------------------------------------------------------------------------AAUAGGAGGAA---ACGC-GCGUCAAACUGCAU
AF036752.1/118-162           AUCCAGCUGACGAGUCCCA------------------------------------------------------------------------AAUAGGACUUG---ACGC-GCGUC---CUGGAU
AF036751.1/118-161           AUCCAGCUGACGAGUCCCA------------------------------------------------------------------------AAUAGGACGA----ACGC-ACUUC---CUAGAU
AF036748.1/120-164           AUCCAGCUGACGAGUCCUA------------------------------------------------------------------------AAUAGGGUGAA---ACGC-GCGUC---CUGGAU
AF036746.1/113-157           AUCCAGCUGACCAGUCGGA------------------------------------------------------------------------AAUAGGACGAA---ACGC-GCGUC---CUGGAU
AF036754.1/91-138            AUCCAGUUGACGAGUCCCA------------------------------------------------------------------------AAUUGGACGAA---ACGC-GCGUCAAACUGGAU
AF036749.1/121-167           AUU-AACAGACGAGUCCCA------------------------------------------------------------------------AAUAGGACGAAGUGACGC-GCGUC---CUGGAU
AF036400.1/123-167           AUCCAGCUGACGAGUGCCA------------------------------------------------------------------------AAUAGGACGAA---AUGU-GCAUC---CUGGAU
AF036755.1/118-162           AUCCNGCUGACGNGUCCCA------------------------------------------------------------------------AAUAGGACGGA---AGGC-GCGUC---CCGGAU
L07513.1/246-290             AUCUAGCUGACGAGUCCCG------------------------------------------------------------------------AAUAGGAGGAA---GUGC-UCGUU---CAAUAU
AF036398.1/58-102            AUCUUUCUGACGAGUUUCA------------------------------------------------------------------------AAUAGGACGAA---ACGC-GUGUC---AUGGAU
X15620.1/19-62               GGCUAGCAGUGGAAUCC-A------------------------------------------------------------------------AAUAGGACGAA---ACGC-GCGUC---CUGGAU
AF036395.1/119-163           CCCUGGCUGACGAGUCCCA------------------------------------------------------------------------AACAGGACGAA---ACGC-GCGUC---CUGGAU
D87493.1/3564-3609           GCACUUCUGAAGAGUCCCAU-----------------------------------------------------------------------GCUAGGACGAA---ACAG-CCUUC---CAGUAC
D87492.1/2147-2192           CAAUUGCUGAGGAGUCCCAU-----------------------------------------------------------------------AAUAGGACGAA---ACGG-CCGUC---CAGUGC
D87492.1/743-788             GCACUGCUGAGGAGUCCCAC-----------------------------------------------------------------------AAUAGGACGAA---ACGA-CCGUC---CAGUAC
M98271.1/8-53                CGACUGCUGAGGAGUCCCAC-----------------------------------------------------------------------AAUAGGGCGAU---ACGG-ACGUC---CAGUGC
HE601624.1/39306472-39306516 AUCUAAAUGACGAGUCCUA------------------------------------------------------------------------AAUGGAACUAA---ACAC-AUGUG---UUUGAU
#=GC SS_cons                 ((((((,,,,,,,<<<<___.......................................................................____>>>>,,,...<<<<.>>>>,...))))))
#=GC RF                      cUuuccCUGAaGAGuCcaAG.......................................................................AAUAgGaCGAA...ACgC.GcGUC...ggaaAg
//
# STOCKHOLM 1.0

#=GF AC   RF00164
#=GF ID   s2m
#=GF DE   Coronavirus 3' stem-loop II-like motif (s2m)
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   PMID:9568965; Griffiths-Jones SR, Moxon SJ
#=GF SS   Published; PMID:15630477
#=GF GA   40.00
#=GF TC   40.30
#=GF NC   37.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://athena.bioc.uvic.ca/sars/map/s2mmotif_main.html;
#=GF DR   SO; 0000233; mature_transcript;
#=GF RN   [1]
#=GF RM   9568965
#=GF RT   A common RNA motif in the 3' end of the genomes of astroviruses, avian
#=GF RT   infectious bronchitis virus and an equine rhinovirus.
#=GF RA   Jonassen CM, Jonassen TO, Grinde B
#=GF RL   J Gen Virol 1998;79:715-718.
#=GF RN   [2]
#=GF RM   15630477
#=GF RT   The structure of a rigorously conserved RNA element within the SARS virus
#=GF RT   genome.
#=GF RA   Robertson MP, Igel H, Baertsch R, Haussler D, Ares M Jr, Scott WG
#=GF RL   PLoS Biol 2005;3:e5.
#=GF CC   The s2m motif is found in the 3' UTRs of astrovirus, coronavirus and
#=GF CC   equine rhinovirus genomes [1]. Its function is unknown, but various viral
#=GF CC   3' UTR regions have been found to play roles in viral replication and
#=GF CC   packaging.
#=GF WK   Coronavirus_3'_stem-loop_II-like_motif_(s2m)
#=GF SQ   38


AF257226.1/425-467     GGAGACCGCGGCCACGCCGAGU-AGGAUCGAGGGUACAGUCUCC
AY338174.1/29515-29557 UUUCAUCGAGGCCACGCGGAGU-ACGAUCGAGGGUACAGUGAAU
Y15938.2/2354-2396     GAAAGCCGAGGCCACGCCGAGU-AGGAACGAGGGUACAGCUUUC
L06253.1/392-434       CAGUGCCGGGGCCACGCGGAGU-ACGAUCGAGGGUACAGCACUA
AB046864.1/2311-2353   CUUUCCCGAGGCCACGGCGAGU-AGCAUCGAGGGUACAGGAAUG
AB037273.1/2393-2435   GGAAGCCGCGGCCACGCCGAGU-AGGAUCGAGGGUACAGCUUCC
AY188195.1/190-232     GGGAGCCGCGGCCACGCCGAGU-AGGAUCGAGGGUACAGCUCCC
AY188187.1/197-239     GGAGACCGCGGCCACGCCGAGU-AGGAACGAGGGUACAGUCUCC
AJ619582.1/83-125      CAGUGCCGAGGCCACGCGGCGU-ACGAUCGAGGGUACAGCACUA
AF111995.1/1596-1638   CAGUGCCGGGGCCACGCGGCGU-ACGAUCGUGGGUACAGCACUA
S68561.1/2636-2678     GGAAGCCGCGGCCACGCCGAGU-AGGAACGAGGGUACAGCUUCC
AY536760.3/1545-1587   UUUCAUCGUGGCCACGCGGAGU-ACGAUCGAGGGUACAGUGAAU
AB033998.1/6702-6744   CUUUCCCGAGGCCACGGCGAGU-AGCAUCGAGGGUACAGGAAAG
AJ619592.1/83-125      CAGUGCCGGGGCCACGCGGAGU-ACGACCGAGGGUACAGCACUA
AJ619584.1/73-115      CAGUGCCGAGGCCACGCGGAGU-ACGAUCGAGGGUACAGCACUA
AF111997.1/1443-1485   CAGUGCCGGGGCCACGCGGAGU-ACGAUCGAGGGUACAGCACAA
U52595.1/1520-1562     CAGUGCCGGGGCCACGCGGAGU-ACGAUCGAGGGUACAGCACUU
AY188199.1/190-232     GGGAGCCGCGGCCACGCCGAGU-AGGAUCGAGGGUACAGCUCCU
AJ619594.1/83-125      CAGUGCCGAGGCCACGCGGGGU-ACGAUCGAGGGUACAGCACUA
AY641576.1/27283-27325 CAGUGCCGGGGCCACGCUGAGU-ACGACCGAGGGUACAGCACUA
AY188190.1/197-239     GGAGACCGCGGCCACGCCGAGU-AGGACCGAGGGUACAGUCUCC
AY179509.1/6505-6548   ACUACCCGAGGCCACGCCGAGUUAGGAUCGAGGGUACAGGUAGU
Y15937.2/6358-6400     CAAUCCCGAGGCCACGCCGAGU-AGGAUCGAGGGUACAGGAUUG
L06252.1/368-410       CAGUGCCAGGGCCACGCGGAGU-ACGAUCGAGGGUACAGCACCA
Z66541.1/2326-2368     GGAAGCCGCGACCACGCCGAGU-AGGAUCGAGGGUACAGCUUCC
AF361253.1/8721-8763   ACUCGCCGAGGCCACGCCGAGU-AGGACCGAGGGUACAGCGAGU
AY304457.1/197-239     GGAAGCCGCGGCCACGCCGAGU-AGGCACGAGGGUACAGCUUCC
AJ619583.1/83-125      CAGUGCCGANGCCACGCGGGGU-ACGAUCGAGGGUACAGCACUA
U52600.1/1419-1461     CAGUGCCGAGGCCACUCGGAGU-ACGAUCGAGGGUACAGCACUA
AY304452.1/197-239     GGAAGCCGCGGCCACGCCGAGU-GGGAACGAGGGUACAGCUUCC
AY188191.1/197-239     GGAGACCGCGGCCACGCGGAGU-AGGAUCGAGGGUACAGUCUCC
AY304470.1/197-239     GGAAGCCGCGGCCACGCGGAGU-AGGAUCGAGGGUACAGCUUCC
AY304462.1/197-239     GGAGACCGCGGCCACGCCGAGU-AGGAACGAGGGUACAGUCUCU
AJ278335.1/370-412     CAGUGCCAGGGCCACGCGGAGU-ACGAUCGAGGGUACAGCACUA
U15136.1/2344-2382     GAA-GCCGCGCCCACGCCGAGU-AGGAUCGAGGGUACAG---UC
Y15936.2/6871-6913     UGAUGCCGAGGCCACGCCGGGU-AGGAUCGAGGGUACAGCAUCG
AF056197.1/2428-2470   GAGAGCCGAGGCCACGCCGAGU-AGGAUCGAGGGUACAGCUCUC
AJ619580.1/109-151     CAGUGCCGAGGCCACGCGGAGA-ACGAUCGAGGGUACAGCACUA
#=GC SS_cons           :<<<<<----<<<-<<<<____._>>-->>-->>>--->>>>>:
#=GC RF                cgguGCCGaGGCCACGCcGAGU.AgGAUCGAGGGUACAGCacca
//
# STOCKHOLM 1.0

#=GF AC   RF00165
#=GF ID   Corona_pk3
#=GF DE   Coronavirus 3' UTR pseudoknot
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Published; PMID:10482585
#=GF GA   36.00
#=GF TC   36.70
#=GF NC   35.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   10482585
#=GF RT   A phylogenetically conserved hairpin-type 3' untranslated region
#=GF RT   pseudoknot functions in coronavirus RNA replication.
#=GF RA   Williams GD, Chang RY, Brian DA
#=GF RL   J Virol 1999;73:8349-8355.
#=GF CC   Coronaviruses are plus-strand RNA viruses with ~30kb genomes. The 3' UTR
#=GF CC   region of coronavirus genomes contains a conserved ~55nt pseudoknot
#=GF CC   structure which has been shown to be necessary for viral genome
#=GF CC   replication [1]. The mechanism of cis-regulation is unclear, but this
#=GF CC   element is postulated to function in the plus-strand.
#=GF WK   Coronavirus_3'_UTR_pseudoknot
#=GF SQ   14


X00509.1/2201-2262     ACACUCUCUAUCAGAAUGGAUGUCUUGCUG-UCAUAACA-GAUA-GAGAAG-GUUGUGG-CUGCCCU
AF207902.1/31022-31083 ACACUCUCUAUCAGAAUGGAUGUCUUGCUG-UCAUAACA-GAUA-GAGAAG-GUUGUGG-CAGACCC
AF058944.1/9309-9370   GCACUCUCUAUCAGAUUGGAUGUCUUGCUG-CUAUAAUA-GAUA-GAGAAG-GUUAUAG-CAGACUA
M36656.1/1479-1540     GCAUUCUCUAUCAGAAUGGAUGUCUUGCUG-CUAUAAUA-GAUA-GAGAAG-GUUAUAG-CAGACUA
X90577.1/1000-1062     CUACUCUUGUACAGAAUGGUAAAC-ACGUG-UAAUAGGAGGUAC-AAGCAACCCUAUUG-CAUAUUA
X66717.1/2272-2334     CUACUCUUGUACAGAAUGGUAAGC-ACGUG-UAAUAGGAGGUAC-AAGCCACCCUAUUG-CAUAUUA
X90576.1/809-871       CUACUCUUGUACAGAAUGGUAAGC-ACGUG-UAAUAGGAGGUAC-AAGCAACCCUAUUG-CAUAUUA
D13096.1/9359-9422     CUACUCUUGUACAGAAUGGUAAGCCAAGUGUCAAUAGGAGGUAC-AAGCAA-CCUAUUG-CAUAUUA
X90572.1/1000-1062     CUACUCUUGUACAGAAUGGUAAGC-ACGUG-UAGUAGGAGGUAC-AAGCAACCCUAUUG-CAUAUUA
X90578.1/1000-1062     CUACUCUUGUACAGAAUGGUAAGC-ACGUG-UGAUGGGAGGUAC-AAGCAACCCCAUUA-CAUAUUA
X66718.1/795-857       CUACUCUUGUACAGAAUGGUAAGC-ACGUG-UAAUGGGAGGUAC-AAGCAACCCCAUUG-CAUAUUA
Z35758.1/8161-8224     CUACUCUUAUACAGAAUGGUAAGC-ACGUG-UAAUAGGAGGUAAUAAGCAACCCUAUUG-CAUAUUA
X51325.1/1443-1505     CUAGUCUUAUACACAAUGGUAAGC-CAGUGGUAGUAAAG-GUAU-AAGAAA-UUUGCUACUAUGUUA
AF353511.1/27820-27882 UUGGUCUUGCACACAACGGUAAGC-CAGUGGUAAUGUCA-GUGC-AAGAAG-GAUAUUACCAUAGCA
#=GC SS_cons           ::::AAAAAAAA::::::::::::.::<<<.<<<<<<<_.aaaa.aaaa__.>>>>>>>.>>>::::
#=GC RF                cUACUCUUguACAGAAUGGUAAgC.aagUG.uaAUAggA.GUac.AAGaAA.ccUAUug.CAuAuUA
//
# STOCKHOLM 1.0

#=GF AC   RF00166
#=GF ID   PrrB_RsmZ
#=GF DE   PrrB/RsmZ RNA family
#=GF AU   Filiatrault M
#=GF AU   Gardner P; 0000-0002-7808-1213
#=GF SE   Filiatrault M
#=GF SS   Predicted; Filiatrault M, Gardner P
#=GF GA   38.00
#=GF TC   39.40
#=GF NC   37.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00106
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0006401; RNA catabolic process;
#=GF DR   GO; 0006109; regulation of carbohydrate metabolic process;
#=GF RN   [1]
#=GF RM   10869066
#=GF RT   A regulatory RNA (PrrB RNA) modulates expression of secondary metabolite
#=GF RT   genes in Pseudomonas fluorescens F113.
#=GF RA   Aarons S, Abbas A, Adams C, Fenton A, O'Gara F
#=GF RL   J Bacteriol 2000;182:3913-3919.
#=GF RN   [2]
#=GF RM   28400281
#=GF RT   The Pseudomonas transcriptional regulator AlgR controls LipA expression
#=GF RT   via the noncoding RNA RsmZ in Pseudomonas protegens Pf-5.
#=GF RA   Li M, Yan J, Yan Y
#=GF RL   Biochem Biophys Res Commun. 2017;487:173-180.
#=GF CC   PrrB RNA is able to phenotypically complement gacS and gacA mutants and is
#=GF CC   itself regulated by the GacS-GacA two-component signal transduction system
#=GF CC   [1]. Inactivation of the prrB gene in Pseudomonas fluorescens F113
#=GF CC   resulted in a significant reduction of 2, 4-diacetylphloroglucinol (Phl)
#=GF CC   and hydrogen cyanide (HCN) production, while increased metabolite
#=GF CC   production was observed when prrB was overexpressed [1]. The prrB gene
#=GF CC   sequence contains a number of imperfect repeats of the consensus sequence
#=GF CC   5'-AGGA-3', and sequence analysis predicted a complex secondary structure
#=GF CC   featuring multiple putative stem-loops with the consensus sequences
#=GF CC   predominantly positioned at the single-stranded regions at the ends of the
#=GF CC   stem-loops. This structure is similar to the CsrB and RsmB regulatory RNAs
#=GF CC   Rfam:RF00018 [1], suggesting this RNA also interacts with a CsrA-like
#=GF CC   protein.
#=GF WK   PrrB/RsmZ_RNA_family
#=GF SQ   37


AB054812.1/583-450         UGUGCACAGGGACAU--GCACAGGCUUUC-AGG-AUGAAGGCCAG----GGACAUCGC-AAGA-A-GCGAUUUCAUC-AGGAUGAUGUUU-G-GGACAAGCAGGGACUACGGAAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
AACY021828384.1/217-351    UGUGUCCACGGAUUG--GCAC-AGCCAUCAAGGAACGAUGGUUUGA-AGGACCGUCGC-AGGA-U-GCGAU-UCAUC-AGGAUGAUGA-A-AAGGA-AUACAGGGACUA-GGGAAAAAAUGUGGGCGGGUCAU---ACCGCCCCUUUUUUU-
AE015451.1/1822025-1822158 UGUGCACAGGGACAU--GCACAGGCUUUC-AGG-AUGAAGGCCAG----GGACAUCGC-AAGA-A-GCGAUUUCAUC-AGGAUGAUGUUU-G-GGACAAGCAGGGACUACGGAAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
AJ556798.1/345-475         UGUGUCGACGGACAG--ACAC-GCCCUUCAAGG-AAGAGGGGAAC----GGACAUCGC-AGGA-C-GCGAU-UCAUC-AGGACGAUGA-A-AAGGA-AUACAGGGAAUA-GGGAAAAAAUGUGGGCGGGUCAU---ACCGCCCCUUUUUUC-
AE016853.1/1728435-1728566 UGUGCCAACGGACAG--GCACAGGCCAUCAAGG-AUGACGGUC-A----GGACAUCGC-GGGA-A-GCGAU-UCAUC-AGGACGAUGACA-AGGGA-AUACAGGGAUUA-AGGACAAAAUGUGGGCGGGUCAU---ACCGCCCCUUUUUUU-
AF208000.1/1460-1590       UGUGCCAACGGACAG--GCACAGGCCAUCAAGG-AUGAAGGCC-G----GGAUAUCGC-GGGA-U-GCGAU-UCAUC-AGGAUGAUGACU-AGGGA-AUACAGGGAUCA-AGGA-AAAAUGUGGGCGGGUCAU---ACCGCCCCUUUUUUU-
AF245440.2/2236-2364       UGUGUCGACGGAUAG--ACAC-AGCCAUCAAGG-ACGAUGGUCAG-----GACAUCGC-AGGA-A-GCGAU-UCAUC-AGGACGAUGA-A-AAGGA-ACACAGGGACUA--GGGAAAAAUGUGGGCGGGUCAU---ACCGCCCCUUUUUUU-
AACY023002312.1/182-314    CGUGCUUAGGGAUAA--GCACAGGUCAUC-AGG-ACGAUGAUCAG----GAACAUCGC-AAGA-A-GCGAU-UCAUC-AGGAUGAUGGGC-UUGGAAAUAAAGGGACUAGGGAAUAAAA-GUGGGCGGCGCAA---GCCGCCCCUUUUUUU-
CP000712.1/4650676-4650543 UGUGCACAGGGACAU--GCACAGGCUUUC-AGG-AUGAAGGCCAG----GGACAUCGC-AAGA-A-GCGAUUUCAUC-AGGAUGAUGUUU-G-GGACAAGCAGGGACUACGGAAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
AE004091.2/4057660-4057541 UGCGUACAGGGA-AC--ACGCAACCCCGAAGG---AUCGGGGAAG---GGACGUCGCC-AGGG-A-GGCGAUUCAUC-AGGAUGAUGA-----CG------AGGGACU-----GAAGAGUG-GGCGGGGUAAU--ACCCCGCCCCUUUUUUU
Y19122.1/2240-2373         UGUGCACACGGACAU--GCACAGGCUUUC-AGG-GAGAAGGCCAA----GGACAUCGC-AAGA-A-GCGAUUUCAUC-AGGACGAUGUUU-G-GGACAAUCAGGGACUACGGAAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
CT573326.1/4468854-4468722 UGUGUCUACGGACUG--ACACAGGCUUUCAAGG-AUGGAGGCCAA----GGACAUCGC-AGGA-U-GCGAU-UCAUC-AGGAUGAUGAUU-G-GGACAAACAGGGACUAC-GGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
CP001157.1/1671953-1672091 CGUGUCGACGGAGCG--ACGCGGGUUGUCACGG-ACGAUGACCAU----GGAUUUCGC-AGGACG-GCGAA-UCAUC-AGGAUGAUGAGCCAGGGAAAAAAGGGAAAAAAGGACUGAAGAGCAGGCGAGGUUAU-CCUCGCCU-CUUUUUUU
D26134.1/2614-2729         UGCGUACAGGGA-AC--ACGCAACCCCGAA-G---AUCGGG-AAG---GGACGUCGCC-AGGG-A-GGCGAUUCAUC-AGGAUGAUGA-----CG------AGGGACU-----GAAGAGUG-GGCGGGGUAAU--ACCCCGCUUUUUUUU--
CP000076.1/1382689-1382817 UGUGUCGACGGAUAG--ACAC-AGCCAUCAAGG-ACGAUGGUCAG-----GACAUCGC-AGGA-A-GCGAU-UCAUC-AGGACGAUGA-A-AAGGA-ACACAGGGACUA--GGGAAAAAUGUGGGCGGGUCAU---ACCGCCCCUUUUUUU-
CP001157.1/116864-117005   UGUGCCGACGGAUCG--GUACCGGCUGACCAGG-AUGGCGGCCAA----GGACUUCGC-AGGAGA-GCGAUCCCAUC-AGGACGAUGACUCAACGGAAGAAAGGCAGUAUUCCGCGAAGAACGGCGAGAGCGAUCCUCUCGCCGUUUUUUAU
AF178851.1/1737-1855       UGUGCACACGGACAU--GCACAGGCUUCC-----AGGAGAGCCAA-----GACAUCGC-AAGA-C-GCGAU-UCAUC--AGAAGAUGUUU--NGGACAAGCAG--ACUA-----CGAAAUUUUGGCGGUUCA----ACCGCCCUUUUUUG--
EF587266.1/3410-3543       UGUGUCGACGGACAG--ACAC-GCCCGUCAAGG-ACGAUGGGAAGG-AAGGACAUCGC-AGGA-C-GCGAU-UCAUC-AGGAUGAUGA-A-UAGGA-UUAAAGGGAUUA-GGGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
CP000438.1/1500350-1500469 UGCGUACAGGGA-AC--ACGCAACCCCGAAGG---AUCGGGGAAG---GGACGUCGCC-AGGG-A-GGCGAUUCAUC-AGGACGAUGA-----CG------AGGGACU-----GAAGAGUG-GGCGGGGUAAU--ACCCCGCCCCUUUUUUU
CP000304.1/1688217-1688349 CGCGCUCAGGGAUUA--GCGC-GGCCCUCAGG--ACGAGGGUCAG----GACCAUCGC-AGGA-C-GCGAUGUCAUCCAGGACGAUGAGA-AGGGA--UACAGGGAACAGGGAAGGAGGCG-GGCGGGGUCAA---CCCCGCCCCUUUUUUU
CP000744.1/1543125-1543244 UGCGUACAGGGA-AC--ACGCAGCCCCGAAGG---AUCGGGGAAG---GGACAUCGCC-AGGG-A-GGCGAUUCAUC-AGGAUGAUGA-----CG------AGGGACU-----GAAGAGUG-GGCGGGGGAAU--ACCCCGCCCCUUUUUUU
AB039965.1/3562-3429       UGUGCACAGGGACAU--GCACAGGCUUUC-AGG-AUGAAGGCCAG----GGACAUCGC-AAGA-A-GCGAUUUCAUC-AUGAUGAUGUUU-G-GGACAAGCAGGGACUACGGAAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
AF170100.1/568-449         UGCGUACAGGGA-AC--ACGCAACCCCGAAGG---AUCGGGGAAG---GGACGUCGCC-AGGG-A-GGCGAUUCAUC-AGGACGAUGA-----CG------AGGGACU-----GAAGAGUG-GGCGGGGUAAU--ACCCCGCCCCUUUUUUU
CP000075.1/1558056-1558186 UGUGCCAACGGACAG--GCACAGGCCAUCAAGG-AUGAAGGCC-G----GGAUAUCGC-GGGA-U-GCGAU-UCAUC-AGGAUGAUGACU-AGGGA-AUACAGGGAUCA-AGGA-AAAAUGUGGGCGGGUCAU---ACCGCCCCUUUUUUU-
AY355347.1/1922-2054       UGUGCCGACGGAUCG--ACAC-AGUGCUCAAGG-AUGAGUGCUCAG--GGACAAUCGC-AGGA-C-GUGAU-UCAUC-AGGAUGAUGA-A-AGGGA-CAAAAGGGAAUA-GGGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
EF026091.1/2504-2636       UGUGUCUACGGACUG--ACACAGGCUAUCAAGG-AUGACGGCCAG---GGGACAUCGC-AGGA-C-GCGAU-UCAUC-AGGAUGAUGA-A-AGGGA-ACAAAGGGACUA-CGGAAAAAAUGUGGGCGGGUUAA---ACCGCCCCCUUUUUU-
CP000058.1/4360893-4360761 UGUGCCAACGGACAG--GCACAGGCCAUCAAGG-ACGACGGUCAA----GGACAUCGC-GGGA-U-GCGAU-UCAUC-AGGAUGAUGACC-AGGGA-AUACAGGGAUCA-GGGAUAAAAUGUGGGCGGGUCAU---ACCGCCCCUUUUUUU-
CP000949.1/4473080-4472949 UGUGCACACGGACAU--GCAGAGGCGUUC-AGG-AAGAAGGCCAA----GGACAUCGC-AAGA-C-GCGAU-UCAUC-AGGACGAUGUUU-A-GGACAAGCAGGGACUAC-GGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUC-
CP000680.1/3344431-3344299 CGUGCUCAGGGACAA--GCACAGGUCAUC-AGG-AUGAUGAUCAG----GACUGUCGC-AAGA-U-GCGAU-CCAUC-AGGACGAUGAGU-UGGGAAACAAAGGGACUAGGGAAUAAAA-GUGGGCGGCGCAA---GCCGCCCCUUUUUUU-
EF424638.1/123-1           -------AUAGACAC-------ACCCGUCAAGG-ACGAUGGGAAGG-AAGGACAUCGC-AGGA-C-GCGAU-UCAUC-AGGACGAUGAAU--AGGA-UUAAAGGGAUUA-GGGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
EU491520.1/114-1           U----ACAGGGAACACG---CAA-CCCCGAAGG-AUCGGGG-AAG----GGACGUCGCCAGGG-AGGCGAU-UCAUC-AGGAUGAUGACG-----------AGGGACU-----GAAGAGUG-GGCGGGGUAAU--ACCCCGCCCCUUUUU--
EF424630.1/123-1           -------AUAGACAC-------ACCCGUCAAGG-ACGAUGGGAAGG-AAGGACAUCGC-AGGA-C-GCGAU-UCAUC-AGGAUGAUGA-A-AAGGA-UUAAAGGGAUUA-GGGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
EF424637.1/124-1           -------AUAGACAC-------ACCCGCCAAGG-AUGACGGGAAUGGAAGGACAUCGC-AGGA-C-GCGAU-UCAUC-AGGACGAUGA-A-AAGGA-UUAAAGGGAUUA-GGGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
EF424631.1/123-1           -------AUAGACAC-------ACCCGUCAAGG-AUGAUGGGAAGG-AAGGACAUCGC-AGGA-C-GCGAU-UCAUC-AGGAUGAUGA-A-AAGGA-UUAAAGGGAUUA-GGGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
EF424640.1/124-1           -------AUAGACAC-------ACCCGUCACGG-ACGAUGGGAAAGGAAGGACAUCGC-AGGA-C-GCGAU-UCAUC-AGGACGAUGA-A-AAGGA-UUAAAGGGAUUA-GGGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
EF424632.1/124-1           -------AUAGACAC-------ACCCGUCAAGG-ACGAUGGGAAUGGAAGGACAUCGC-AGGA-C-GCGAU-UCAUC-AGGACGAUGA-A-AAGGA-UUAAAGGGAUUA-GGGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
CP000094.2/1309713-1309843 UGUGUCGACGGAUAG--ACAC-GCCCUUCAAGG-AAGAGGGGAAU----GGACAUCGC-AGGA-A-GCGAU-UCAUC-AGGACGAUGA-A-AAGGA-ACACAGGGAAUA-GGGAAAAAAUGUGGGCGGGUCAA---ACCGCCCCUUUUUUU-
#=GC SS_cons               <<<<<__________..>>>>>,<<<<<<____.__>>>>>>,,,....,,,,<<<<<.____._.>>>>>.<<<<<._____>>>>>,,.,,,,,.,,,,,,,,,,,,.,,,<<<<<<---<<<<<<<____...>>>>>>>->>>>>>:.
#=GC RF                    uGuGcacAcGGAuau..gCaCaggCccucAaGG.AugaggGcaAg....GgacaucGC.AGGA.a.GCgau.uCAUC.AGGAuGAUGauu.aagGA.auAaAGGGAcUA.gGaaaaaAgUGUGGgcGGgucAa...cCCgcCCccUuuuuU.
//
# STOCKHOLM 1.0

#=GF AC   RF00167
#=GF ID   Purine
#=GF DE   Purine riboswitch
#=GF AU   Boese B
#=GF AU   Barrick JE
#=GF AU   Breaker RR; 0000-0002-2165-536X
#=GF SE   Boese B, Barrick JE
#=GF SS   Published; PMID:12787499
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   36.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0009113; purine nucleobase biosynthetic process;
#=GF RN   [1]
#=GF RM   12787499
#=GF RT   Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis
#=GF RT   and Other Bacteria.
#=GF RA   Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR
#=GF RL   Cell 2003;113:577-586.
#=GF RN   [2]
#=GF RM   14718920
#=GF RT   Adenine riboswitches and gene activation by disruption of a transcription
#=GF RT   terminator.
#=GF RA   Mandal M, Breaker RR
#=GF RL   Nat Struct Mol Biol 2004;11:29-35.
#=GF RN   [3]
#=GF RM   15549109
#=GF RT   Structure of a natural guanine-responsive riboswitch complexed with the
#=GF RT   metabolite hypoxanthine.
#=GF RA   Batey RT, Gilbert SD, Montange RK
#=GF RL   Nature. 2004;432:411-415.
#=GF RN   [4]
#=GF RM   23842498
#=GF RT   Three-state mechanism couples ligand and temperature sensing in
#=GF RT   riboswitches.
#=GF RA   Reining A, Nozinovic S, Schlepckow K, Buhr F, Furtig B, Schwalbe H
#=GF RL   Nature. 2013;499:355-359.
#=GF CC   Riboswitches are metabolite binding domains within certain messenger RNAs
#=GF CC   that serve as precision sensors for their corresponding targets.
#=GF CC   Allosteric rearrangement of mRNA structure is mediated by ligand binding,
#=GF CC   and this results in modulation of gene expression. A class of riboswitches
#=GF CC   that selectively recognises guanine and becomes saturated at
#=GF CC   concentrations as low as 5 nM. In Bacillus subtilis, this mRNA motif is
#=GF CC   located on at least five separate transcriptional units that together
#=GF CC   encode 17 genes that are mostly involved in purine transport and purine
#=GF CC   nucleotide biosynthesis. It has also been shown that some members of this
#=GF CC   family are specific for adenine instead. Hence this family are termed
#=GF CC   purine riboswitches.
#=GF WK   Purine_riboswitch
#=GF SQ   133


X83878.1/168-267             UUACAAUAUAAUAGGAACAC-U-CAUAUAAUCGCGUGGAUAUGG-CACGCAA-GUUUCUACCGGGCA-CC--GUAAA-UGUCC---GACUAUG-GGUGAGCAAUGGAACCGC-
AF270087.1/2580-2679         ---AAAAUAAUUUAUAUGAC-U-CAUAUAAUCUAGAGAAUAUGGCUUUAGAA-GUUUCUACCGUGUCGCC--AUAAACGACAC---GACUAUG-AGUAACAAUCCAAUACAU-
AL596165.1/154156-154057     AAUCGUCUACAAUAAUAAAG-U-CGUAUAAGUUCGGUAAUAUGG-ACCGUUC-GUUUCUACCAGGCAACC--GUAAAAUGCCA---GGCUACG-AGCUAUUGUAAAAUUU---
AL596170.1/223345-223246     AUAACUUAAAACCGAAAUAC-U-UAUAUAAUAGUUGCGAU-UGG-GCGACGA-GUUUCUACCUGGUUACC--GUAAAUAACCG---GACUAUG-AGUAGUUUGUAUAAAGA--
AB008757.1/115-16            AAUGAAUCACGCUGACUCAC-U-CAUAUAAUCGCAAGAAUACGG-CUUGCGA-GUCUCUACCAGCCGACC--GUAAAUCGGCU---GACUAUG-AGUGGCAAUGUCAGGA---
U51115.1/15592-15691         ---GAAAUCAAAACACGACC-U-CAUAUAAUCUUGGGAAUAUGG-CCCAUAA-GUUUCUACCCGGCAACC--GUAAAUUGCCG---GACUAUG-CAGGGAAGUGAUCGAUAAA
AL591975.1/251119-251020     AAUCCGCUACAAUAAUAUAG-U-CGUAUAAGUUCGGUAAUAUGG-ACCGUUC-GUUUCUACCAGGCAACC--GUAAAAUGCCA---GGCUACG-AGCUAUUGUAAAAUUU---
AL591981.1/205922-205823     AUAACUUAAAACCGAAAUAC-U-UGUAUAAUAGUUGCGAU-UGG-GCGACGA-GUUUCUACCUGGUUACC--GUAAAUAACCG---GACUAUG-AGUAGUUUGUAUAAAGA--
ABDP01000013.1/128838-128739 GACAUAAUUAAAUAAUUUGC-U-CAUAUAAUUCCU-GAAUAUGG--AGGGAA-GUUUCUACCAGAUAACC--GUAAAUUGUCU---GACUAUG-AGUGGAAUCCUACUUAAU-
CP000764.1/271074-271175     AGAUAAUAUAAAACAAUCCU-U-CAUAUAUCCUCAAUAAUAUGG-UUUGAGA-GUCUCUACCGGGUUACC--GUAAACAACCU---GACUAUG-AAGGCAGUGCGUCUUAUG-
AAEQ01000019.1/51159-51260   CUUCGAAAAGAAUCACUGCC-U-CAUAUAAUCUUGGAGAUAAGG-UCCAUAA-GUUUCUACCUGGCAACC--AUGAAUUGCUA---GACUAUG-AGGGGAAAAGUGUGUAAC-
AAEK01000017.1/86437-86538   AGAUAAUAUAAAACGAUCCU-U-CAUAUAUCCUCAAAGAUAAGG-UUUGAGA-GUCUCUACCGGGUUACC--GUAAACAACCU---GACUAUG-AAGGCAGUGUGUCUUAUA-
CP000001.1/309094-309195     AAAGAAUAAUAUAUAAGACC-U-CAUAUAAUCGCGGGGAUAUGG-CCUGCAA-GUCUCUACCUAACGACC--GUUAUUCGUUA---GACUAUG-AGGGAAAGUCACUCGGUA-
CP000410.1/1642356-1642451   AAAAUUGAAUAUCGUUUUAC-U-UGUUUAUGUCGUGAAU--UGG--CACGAC-GUUUCUACAAGGUG-CC--GG-AA-CACCU---AACAAUA-AGUAAGUCAGCAGUGAGA-
AAWP01000021.1/27378-27279   GUAUAAUCGCGCCGUUUGCU-U-CGUAUAACCCCAAUGAUAUGG-UUUGGGG-GUCUCUACCAGCUC-CC--GCAAA-GUGCU---GAUUACG-AAGAGUUGAGAUCACUGU-
CP000721.1/2204674-2204778   AAAAAGUUAAUAAUAUUCAC-U-UAUAUAAAUCUGAUAAUAAGG-GUCGGAU-GUUUCUACCAAGCUACC--GUAAAUUGCUAUAGGACUAUA-AGUGUCUACUUAAAAAUU-
CP000724.1/951516-951617     CUCAGUCGAAAAUUGAAGAC-U-CAUAUAAUGUCGAUAAUAGGG-UUCGACA-GUUUCUACAGGAUCACC--GAAAAUGAUUC---UACUAUG-AGUGAAAGUGUACCUAGG-
AANE01000012.1/49153-49054   AAGUUACCGCUUAAGCCCUC-U-CGUAUAACCCCACUAAUAUGG-UUUGGGG-GUCUCUACCAGGAA-CC--GAUAA-UUUCU---GAUUACG-AAGAGUAUUGCGUUAUGC-
AE017334.2/342356-342255     UUAAUACGGACGAUGUUACC-U-CAUAUAUACUCGAUAAUAUGG-AUCGAGA-GUUUCUACCCGGCAACC--UUAAAUUGCUG---GACUAUG-GGGAAAACUAAUGAAUAU-
AAXV01000026.1/31334-31233   AUAGAUUCAUACAAUUUUAC-U-CAUAUAAUAGCGAGGAUAUGG-CUUGCAA-GUUUCUACCGAUUUACC--GUAAAUAAAUC---GACUAUG-GGUAGCAAUGCUUUUAGA-
AAWL01000019.1/26832-26933   AGACAACAUAUUGCUCCUAC-U-CGUAUAAUUUUGAGAAUAUGG-CUCAAGA-GUCUCUACCGGGCAACC--GUAAAUUGCCC---GACUACG-AGUGAAAGUGUACCUAGG-
AE016877.1/298774-298875     AGAAACAAUAAUAUAAGACC-U-CAUAUAAUCGCGGGGAUAUGG-CCUGCAA-GUCUCUACCUAACGACC--GUUAUUCGUUA---GACUAUG-AGGGAAAGUCACUCGGUA-
BA000028.3/760473-760574     CAAUUUUUAUCCAAUGCCUU-U-CGUAUAUCCUCGAUAAUAUGG-UUCGAAA-GUAUCUACCGGGUCACC--GUAAAUGAUCU---GACUAUG-AAGGCAGAAGCAGGUUCG-
CP000002.3/2295936-2295837   AAUUUGAUACAUUAUAUCAC-U-CAUAUAAUCGCGUGGAUAUGG-CACGCAA-GUUUCUACCGGGCA-CC--GUAAA-UGUCC---GACUAUG-AGUGGGCGAUAAGAAAAC-
AAEN01000023.1/16980-17081   GAAAAGUGAAUAUUAUGCCG-U-CGUAUAAUAUCGGGGAUAUGG-CCCGAAA-GUUUCUACCUAGCUACC--GUAAAUGGCUU---GACUACG-AGGCGUUUUUAUAAAGGU-
BA000043.1/272473-272574     UACGGAUAGACGAAAGCCCU-U-CAUAUAAGCGCAAGAAUAUGG-CUUGCGC-GUCUCUACCGGGCCGCC--GUAAACGGCCC---GACUAUG-AAGGCAGAAGACGCUGCU-
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CP001186.1/253132-253233     GAAAAGUGAAUAUUAU-GCCGU-CGUAUAAUAUCGGGGAUAUGG-CCCGAAA-GUUUCUACCUAGCUACC--GUAAAUGGCUU---GACUACG-AGGCGUUUGUAUAAAGAU-
D88802.1/12464-12365         AAUUAAAUAGCUAUUAUCAC-U-UGUAUAACCUCAAUAAUAUGG-UUUGAGG-GUGUCUACCAGGAA-CC--GUAAA-AUCCU---GAUUACA-AAAUUUGUUUAUGACAUU-
CP001022.1/474287-474388     GGAAGAUUGAAUAUAACACC-U-CGUAUAAUAGCAGGGAUAUGG-CUUGCAA-GUUUCUACCCGACGACC--CUAAAUCGUUG---GACUAUG-GGGUAUAUGGAUGUUCGU-
ABDT01000031.2/13681-13582   UUUAAAUUAAUAAAUGAGUU-U-CGUAUAAUUCCAAUAAUAUGG-UUUGGAA-GUCUCUACUAGGAA-CC--UAUAA-UUCCU---AAUUACG-AAGAAAAUUUUAUGCAAA-
CP001098.1/539421-539522     AUAUAUCAUUGUAUUUUGCC-U-CGUAUAAUUGUGGAGAUAUGG-UCCACGA-GUUUCUACCGGACGGCC--GUAAACUGUUC---GACUACG-GGGGAAACACCUGGGAUG-
CP003056.1/1723617-1723718   CAAUUCAAUAUGCAAUACCA-U-CGUAUAUAUUCAGGGAUAUGG-CCUGAAC-GUUUCUACCAAGCUGCC--GUAAAUAGCUU---GACUACG-AGGUAAUGAGAUAGAGUC-
AL935263.2/2968829-2968731   UUAUCAAUACAACUAAUUGC-C-UAUAUAA-UGCCAUGAUAUGG-AUGGCGA-GUUUCUACCCAGUG-CC--GUAAA-CACUG---GACUAUA-AGCGAAUUGAGUCGACGG-
CP003056.1/1737361-1737461   AUACAAAGUGAAUAUGACCC-U-CAUAUAU-AAUGGGAAUACGG-CCCAUAC-GUCUCUACCCGGUUACC--GUAAAUAAUCG---GACUAUG-AGGGAAAGCGGAAGUUGG-
#=GC SS_cons                 :::::::::::::::::(((.(.((((,,,<<<<<<<_______.>>>>>>>.,,,,,,,,<<<<<<<__.._____>>>>>>...>,,)))).))))::::::::::::::.
#=GC RF                      aaaaaauaaaaaaaauuccc.u.CgUAUAAucccgggAAUAUGG.cccggga.GUUUCUACCaggcagCC..GUAAAcugccu...GACUAcG.agggaaauuuuuuuuuuu.
//
# STOCKHOLM 1.0

#=GF AC   RF00168
#=GF ID   Lysine
#=GF DE   Lysine riboswitch
#=GF AU   Wickiser JK
#=GF AU   Barrick JE
#=GF AU   Breaker RR; 0000-0002-2165-536X
#=GF SE   Wickiser JK, Barrick JE
#=GF SS   Published; PMID:12787499
#=GF GA   30.00
#=GF TC   30.10
#=GF NC   29.70
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0009085; lysine biosynthetic process;
#=GF RN   [1]
#=GF RM   12787499
#=GF RT   Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis
#=GF RT   and Other Bacteria.
#=GF RA   Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR
#=GF RL   Cell 2003;113:577-586.
#=GF RN   [2]
#=GF RM   14523230
#=GF RT   The L box regulon: Lysine sensing by leader RNAs of bacterial lysine
#=GF RT   biosynthesis genes.
#=GF RA   Grundy FJ, Lehman SC, Henkin TM
#=GF RL   Proc Natl Acad Sci U S A 2003;100:12057-12062.
#=GF RN   [3]
#=GF RM   14597663
#=GF RT   An mRNA structure in bacteria that controls gene expression by binding
#=GF RT   lysine.
#=GF RA   Sudarsan N, Wickiser JK, Nakamura S, Ebert MS, Breaker RR
#=GF RL   Genes Dev 2003;17:2688-2697.
#=GF RN   [4]
#=GF RM   14627808
#=GF RT   Regulation of lysine biosynthesis and transport genes in bacteria: yet
#=GF RT   another RNA riboswitch?.
#=GF RA   Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS
#=GF RL   Nucleic Acids Res 2003;31:6748-6757.
#=GF CC   Riboswitches are metabolite binding domains within certain messenger RNAs
#=GF CC   that serve as precision sensors for their corresponding targets.
#=GF CC   Allosteric rearrangement of mRNA structure is mediated by ligand binding,
#=GF CC   and this results in modulation of gene expression. This family includes
#=GF CC   riboswitches that sense lysine [1] in a number of genes involved in lysine
#=GF CC   metabolism, including lysC [3].
#=GF WK   Lysine_riboswitch
#=GF SQ   47


U00006.1/98763-98567       CAGGCCAGAAGAGGC-GCGUUG-CCC-A--A--GUAA-CGGUGUUGGA---------GGAGCCAGUCCUGUG---AUAACAC-CU-GAGGGG-GUG-C-AUCGCCGAGGUGAUUGAACGGCUGGCC-A----CGUUCA-U-CAUCGGCUACA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGA--AGCGUUCGCAGUCGGGCGUUUCGC---------------------------------------AAGUGGUGG-AGCACUUCUGGGUGA
J03294.1/2297-2476         GGUGAAGAUAGAGGU-GCGAAC-UUC-AAGA--GUA--UGCCUUUGGAGA-------AAGAUGGAUUCUGUG---AAAAAGG-CU-GAAAGG-GGA-GCGUCGCCGAAGCAAAUAAAACCCCAUCG------GUAUUAUU-UGCUGGCCGUG-CAUU--GAAUAAAUGUAAGGCUGUCAAGAAA--UCA------------------------------------------------------------UUUUCUUGG-AGGGCUAUCUCGUUG
AF269536.1/680-500         AAUAGAGUUAGAGGUUGCAUUA-UUA-AUGA--CUA--ACUUAUCAGAAGUCGU---AUGGGACAUGUGUUG---A--AUAA-GU-GAAAGG-UAA-U-AAUGCCGAAAUGAUGUUAUUUC-CAUA-A----AUUAGCAU-UGUGAAGUUGG-UUGAA-CAAUAAAAACAUCACAACCACGAAU--GCU--------------------------------------------------------------UUCUUCA-AUAUUUAUUUGAAUU
AF270308.1/2156-2331       AAUAGAGUUAGAGGUUGCAUUA-UUA-AUGA--CUA--ACUUAUCAGAAGUCGU---AUGGGACAUGUGUUG---A--AUAA-GU-GAAAGG-UAA-U-AAUGCCGAAAUGAUGUUAUUUC-CAUA-A----AUUAGCAU-UGUUGGGACAA-CUUUC-GAAUAGAAGUUGUACUGUCACU-----UUA----------------------------------------------------------------UGUGA-UGUGCUACCUUAUAU
M93419.1/332-511           AGUGAAGAUAGAGGU-GCGAAC-UUC-AUCA--GUA--AAAGCUUGGAGAA------GAAUGAGCUUCAAUG---AAAAGCU-UU-GAAAGG-GAACG-UUCGCCGAAGUGAAGAAAAA---CUCAUU----UUUUUCUU-UGCUGGUCCUG-CAUU--UAAGAGAUGCCGGAUUGUCAAGGCGG-UGC-------------------------------------------------------------CGCCUUGG-AGAGCUAUCUCACUG
AF306669.1/1019-1194       AUAUUUUGAUGAGGC-GCAUCA-AUC-AUGA--GUA--AAGUUUAGAUUAC------UGUCUGCUAACAG------CUAAAU-UU-GAAAGG-GUG-C-GAUGCCGAAGC-AAUUAUAAU--AGCA-G----UUAUAAUU-UGUUGGACUUUUUGGU--UAAGAGCUGAGAGUUUGUCAUUAUU--UAA------------------------------------------------------------AAAUAAUGG-AGUGCAUCACUUGUA
X00008.1/296-492           CAGGCCAGAAGAGGC-GCGUUG-CCC-A--A--GUAA-CGGUGUUGGA---------GGAGCCAGUCCUGUG---AUAACAC-CU-GAGGGG-GUG-C-AUCGCCGAGGUGAUUGAACGGCUGGCC-A----CGUUCA-U-CAUCGGCUAAG-GGGGCUGAAU-CCC-CUGGGUUGUCACCAGA--AGCGUUCGCAGUCGGGCGUUUCGC---------------------------------------AAGUGGUGG-AGCACUUCUGGGUGA
X15196.1/270-75            GCAGCCAGAAGAGGC-GCGUUG-CCA-A-----GUAA-CGGUGUUGGA---------GGAGCCAGUCCUGUG---AUAACAC-CU-GAGGGG-GUG-C-AUCGCCGAGGUGAUUGAACGGCUGGCC-A----CGUUCA-U-CAUCGGCUACA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGA--AGCGUUCGCAGUCGGGCGUUUCGC---------------------------------------AAGUGGUGG-AGCACUUCUGGGUGA
AL591976.1/186683-186486   UGGUGAGGUAGAGGUUGCGAGA-UGC-ACUA--GUA--AUUUUUUCGAGGCGAA---ACAAAGACGCCGACG---ACAAAGA-AU-GAACAG-GUU-G-AUCGCCGAAGUGACUAUUUUCU-CUUU-GUUUAGAAAUAGU-UGUUGGGACAG-UUUCC-UAAA-GGGGCUGGACUGCUAUAAGAA-UUUGUCGAAAU----------------------------------------------------UUCUUAUAGGUGUGCUAUCUGACAA
AL596166.1/112469-112272   UGGUGAGGUAGAGGUUGCGAGA-UGC-ACUA--GUA--AUUUUUUCGAGGCGAA---ACAAAGACGCCAAUG---ACAAAAA-AC-GAACAG-GUU-A-AUCGCCGAAGUGACUAUUUUUU-CUUU-GUAUCGAAAUAGU-UGUUGGGACAG-UUUCC-UAAA-GGAGCUGGACUGCUAUAAGAA-UUUGUCGAAAU----------------------------------------------------UUCUUAUAGGUGUGCUAUCUGACAA
AAMR01000029.1/5147-5324   AUCGCACGUAGAGGC-GCAAUU-AUA-AAAA--GUA--GUUUUCGUU----------GGGGUGAUGCCAAUG---AGCGGGA-AU-GAAAGG-UCU-A-AUUGCCGAAGUAAAUUGUAU---AUCU------AAGCAAUU-UGCUGGGGUUG-UGCU--CAAUAGGUACAACACUGCCAUAGUC--UUAAUUUU-------------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
CP000002.3/2878377-2878198 GGUGAAGAUAGAGGU-GCGAAC-UUC-AAGA--GUA--GGCUUGAUGAGGA------AGAUGGAUUCCGAUG---AAGAAAG-CC-GAAAGG-GGA-GCGUCGCCGAAGCGGGGAAAAAUC-CACU-C----GUUUUUCC-UGCUGGCUUUA-CAUU--GAAUAAAUGUGAGGCUGUCAAGAAA--UCA-------------------------------------------------------------UUUCUUGG-AGAGCUAUCUCGUUG
BX950851.1/4451556-4451748 CAAGCCAGAAGAGGC-GCGUCG-CCC-AG----GUA--AGAUAUCGGAGG-------AACCGUAAUCCGCUG---AUGAUAU-CC-GAGGGG-GAG-C-GACGCCGAGAUGCGGUGAAAUU-CGGC------UUUCACCC-UAUCGACUACA-GAGGCUGAAU-CCUCUG-GGUUGUCACCGGA--UUCGUCCUGAUGGACGUCCA-------------------------------------------GCAAGGUGG-AGCGCUUCUGGGUGU
EF419299.1/175-1           AAAAGAGUUAGAGGUUGCGUCU-UUA-AUUA--GUA--ACACUUCAGAAGUUAUU--AAGGAACGUGUGUUG---A--AAGU-GU-GGAAGG-UAA-A-GAUGCCGAAAUGAAUGAUACC--CUUA-A----UUAUCAUU-UGUUGGGACAG-UUAUC-GAAUAGAAACUGUACUGUCACA-----AUU----------------------------------------------------------------UGUGA-UGUGCUACC-GACGG
CP000046.1/1759610-1759435 AAUUGAGUUAGAGGUUGCAUGU-UUA-AUUA--GUA--ACUUGUCAGAAGUAUUU--AUGGUACAUAAGUUG---A--ACAA-GU-GAAAGG-UAA-A-GAUGCCGAAAUAGAUAUAAACC-AUAA------AUUAUAUC-UAUUGGGACAG-UUUUC-GAAUAGGAACUGUACUGUCACA-----GAA----------------------------------------------------------------UGUGA-UGUGCUACCUUAUAU
BA000037.2/1373591-1373770 UAUCGACGUAGAGGC-GCAAUG-GUA-AAGA--GUA--ACUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GAAAGG-UAU-CCAUUGCCGAAGUGAAUUGCAU---AUCA------AAGCAGUU-UGCUGGGGUUG-CAUCC-GAAA-GGAACAACACUGCCAUAGUA--UUUAAUGUA------------------------------------------------------UAACUAUGG-AGCGCUACUGUAGGU
CP000647.1/4829910-4829675 AUUGCCAGAAGAGGU-GCGUUG-CCC-AG----GUAA-CCGUAUUGGA---------GGAACCAGUCCGGGG---AAGAUAC-GU-GAGGGG-GAG-C-AACGCCGAGGUGAAAGAGCGUCUGGUC-A----CGCUCC-U-CGCCGGCCACA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGA--AACGUUCGCAGUCGGGCGUUUCAUACCCGAACACCUCAGCGCCCAAAGCGGUGAGUCGGGUCUACAAGGUGG-AGCACUUCUGGGUGA
BA000004.3/1819757-1819575 AGUGAGGAUAGAGGU-GCAAAA-ACC-AAGA--GUA--CACAAUUGGAGGA------GAAUGAGAUCCGUUG---AGAAUUG-UG-GAAAGG-GGA-A-UUUGCCGAAGC---UGGAAGAAUCUCA-U----GUUCUGAA-GGCUGGUUCUG-UAUU--AAAUAAAUACAGAACUGUCAUAUAGCGGAUGUU---------------------------------------------------------GCUAUAUGG-AGGGCUAUCUCACGC
ABCF01000065.1/4547-4725   AGUGGUGAUAGAGGU-GCGGAC-UUUCAUCA--GUA--GAUGCUUCGAGGA------GUAUGGGCUCUUAUG---AAGGGUA-UC-GAAAGG-GAA-A-UUCGCCGAAGUGGAAGCAGGCU-CAUA------UCUGUUUG-CGCUGGUUCUG-UGUU--UAAGAGAUGCAGGAUUGUCAAGAUUA-ACA--------------------------------------------------------------GUCUUGG-AGAGCUAUCUCACGU
AE017143.1/992934-993104   ACAAAUUGUAGAGGU-GCAAAU-CCG-AUAA--GUA--UUUCUUCU-----------GAGUGGAAAGCGAUG---AAGGGGA-AG-GAAAGG-CGU-A-UUUGCCGAAAUCAAUUAAGC---GUCA------UCUUAGUU-GGUUGGGGUCG-UUGCC-GAAA-GGGACGACACUGUCGUAAUU--CAA-------------------------------------------------------------UAUUACGG-AGUGCUACUAUUAGG
CP000002.3/3366091-3365915 UAGUGAGGUAGAGGUUGCGCGG-AUG-AUGA--GUC--GCAUGUGUGAGG-------CUGAUGGGGCCGAUG---AUCAUAU-GC-AAAAGG-CAU-C-AGCGCCGAAGCAUAAGGAAGCC-AUUC------AUUCUUUA-UGCUGGGUCUG-CAUU--GAAUAAGUGCAGGACUGCCGCGGGU--AUU--------------------------------------------------------------CCCGCGG-AGGGCUAUCCGGAGA
CP000029.1/981298-981477   AGAUUUUGAUGAGGC-GCAUCA-AUC-AUGA--GUA--AACUUUAGAUAAU------UUGUCUGCUAACAAU---UAUAGAG-UU-AAAAGG-GUG-A-GAUGCCGAAAUGAUUCAUAAU--AGCA-G----UUAUGAAU-CGUUGGACUUAAUGGU--UAAGAGCUAUAAGUUUGUCAUUAUU--AUU------------------------------------------------------------AAAUAAUGG-AGUGCAUCACUUGUA
AAWP01000069.1/5541-5721   UAUUGCCGUAGAGGU-GCAGUC-UCG-AAGA--GUA--GCUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GGAAGG-CGA-GGAUUGCCGAAGUAGGUGGCCU---AUCG------AAGCCACU-UGCUGGGGUUG-UCUCU-GAAA-GGAACAACACUGCCAUAGUA--UAUUUACAUU-----------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
AAKK02000085.1/12844-12662 UGUUGCCGUAGAGGC-GCGGUC-UCG-AAGA--GUA--GCUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GGAAGG-CGAAG-AUUGCCGAAGUAAGUAACUC---AUCA------AAGUUACU-UGCUGGGGUUG-UAUCU-GAAA-GGAACAACACUGCCAUAGUA--UAUAUUCACAUU---------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
CP000416.1/1669940-1669758 UCGAAUAGAAGAGGC-GCGACC-AAC-AAGA--GUC--GCUUUCCGGAGA-------UGGGUCACAUUGCUG---AUGGAAG-GU-UAAAGG-GGC-G-GUCGCCGAAAUUUACGCAUUUU-GACC-G----GAUGCGUG-GGUUGGGUCCU-GGUU--GAACAAGUCAGGGACUGUCGCAGUCA-AAUAAU---------------------------------------------------------CGGCUGCGG-GGCGCUUUCAACGAU
AM263198.1/783761-783564   UGGUGAGGUAGAGGUUGCAAGA-UUC-ACAA--GUA--AUUUUUUAGAAGCGAA---ACAAAGACGCUGAUG---ACAAAGA-AU-GAACAG-GAU-G-AUUGCCGAAGUGACUAUUUUCU-CUUU-GUUUAGAAAUAGU-UGUUGGGACAG-UUUCC-UAAA-GGAGCUGGACUGCUAUAAGAA-UUUGUCGAAAU----------------------------------------------------UUCUUAUAGGUGUGCUAUCUGACAA
AP006716.1/1558409-1558233 AGAAAUUGAUGAGGC-GCAUCA-AUC-AUCA--GUA--UAUAUUAGAU---------AAACUGUCUGCAACA---GCUAAUA-UA-GAAAGG-GUG-C-GAUGCCGAAAUGAAUCAUAAU--CGCA-G----CUAUGAUU-UGUUGGACUUUGUGGU--UAAGAGCUGAAAGUUUGUCAUUAUU--AUU------------------------------------------------------------UAAUAAUGG-AGUGCAUCACUUGUA
ABDQ01000005.1/49327-49153 AACUAAGAUAGAGGU-GCGAGA-UUU-AAGA--GUA--GUAUUAUG-----------GAGUUAAGUGCUAAG---AAGUAAU-AA-GAAAGG-AAA-U-UUCGCCGAAGCUUAUAGAUAAUACUUU-A----AUGCUAUU-UGCUGGGAUUA-CAUA--AAAUAUAUGUAAGACUGUCACAAAU--AAA-------------------------------------------------------------GUUUGUGG-AGAGCUAUUAUUUUA
AE016827.1/1325416-1325239 UACACAUGUAGAGGU-GCGAAU-AUU-AUAA--GUA--UUUUUCCA-----------GAGUGGAUAACAAUG---AAGGAAA-UU-GAAAGG-AAU-A-UUUGCCGAAAUCAGUUAAGC---GUCA------UCUUAACU-GGUUGGUAACG-UCACC-GAAA-GGAACGUUACUGCCAUAGUC--AUUUUUGAU------------------------------------------------------UAACUAUGG-AGCGCUACUCGUGGG
CP000569.1/516240-516411   ACAAAUCGUAGAGGU-GCAAAU-CCG-AUAA--GUA--CUUUUUCU-----------GAGUGGAGAACGAGG---AGGAAAA-AG-GAAAGG-CGU-A-UUUGCCGAAAUCAGUUAAGC---GUCA------UCUUAAUU-GGUUGGGGUCG-UUACC-GAAA-GGGACGACACUGUCGUAAUC--CUU------------------------------------------------------------GUAUUACGG-AGUGCUACUGCUAGG
BA000031.2/1190723-1190903 UGUUGCCGUAGAGGC-GCAGUC-UCG-AAGA--GUA--GCUAUUAUU----------GGGGUGAUGCCAAUG---AAUAAUA-GU-GGAAGG-CGAAG-AUUGCCGAAGUAAGUCGUAU---AUCA------AAACGCCU-UGCUGGGGUUG-UAUCU-GAAA-GGAACAACACUGCCAUAGUA--UAUUUACAUU-----------------------------------------------------AAACUAUGG-AGCGCUACUGUAGGG
CP000425.1/2337129-2337310 CACAUCGAUAGAGGUCGCAACU-GAU-AUGA--AUC----UACGCCGAGU-------UGGAGCACAACAAAG---ACGCGUA-UUAGAGGGGGAGA-A-GUUGCCGAAAGAAUUUUGAC---GCUC-A----G-CAAAGU-UCUUGGGCUAG-UGAG--GAAAACUCACUAGACUGUCGCAAAUGGUUAAGA---------------------------------------------------------ACCAUGCGG-AGGGCUAUUCGUUCA
AASA01000017.1/10332-10501 ACAAAUUGUAGAGGU-GCGAAU-UCA-AUAA--GUA--UUUCUUCU-----------GAGUGGAAAACGAUG---AAGGGGA-AG-GAAAGG-UGA-A-UUUGCCGAAAUCAAUUAAGC---GUCA------UCUUAAUU-GGUUGGGGUCG-UUGUC-GAAA-GAAACGACACUGUCGUAGUA--AAU--------------------------------------------------------------GCUACGG-AGUGCUACUGUUAGG
AP008934.1/1400599-1400421 AGGUUUUGAUGAGGC-GCAUCA-AUC-AUUA--GUA--AAGAUUAGAAGA-------AUCUGACUGCUAGCA---GCUAAUU-UU-GAAAGG-GUG-A-GAUGCCGAAACGGUUAUAAU---AGCA-G----CUUAUAACAUGUUGGACUUUAUGGU--UAAGAGCUAAGAGUCUGUCAUUAUU--UUA------------------------------------------------------------AGAUAAUGG-AGUGCAUCACUUGUA
AAOX01000015.1/22460-22639 AGUGAAGGUAGAGGU-GCAAAC-UUC-AUCA--GUA--AAAGCUUGGAGAA------AGAUGAGUUUCCGUG---AAAAGCU-UU-GAAAGG-GAAUG-UUUGCCGAAGAAAAGGAAGUCU-CAUU------UCUUUCUU-UUCUGGUCCUG-UAUU--GAAUAAAUACUGGAUUGUCAAGACA--GCG------------------------------------------------------------CCGUCUUGG-AGAGCUAUCUCACUG
AL009126.3/3421348-3421169 CAGUGAGGUAGAGGUUGCGCGG-AUG-AUGA--GUC--ACACAUGCUA---------GGCUGACAGGGGCUGUUAAACAUGU-GU-AAAAGG-CAU-C-AGCGCCGAAGUGUGGAGAAAGCCGAUC------CUUCUCUA-UGCUGGGACUG-UAUCU-GAAUAAGUGCAGGACUGCCGCGUGC--UUU--------------------------------------------------------------UUCGCGG-AGGGCUAUCCGGAGA
AE008691.1/719320-719498   CGCAUAAAUAGAGGA-GCUGCC-AAGCAU----GUA--UUUGGCGAGGUGUUAAGGAGAAGAACCUCCAAUA---CUCGCUG-AA-GAA-GG-UUU-G-GCUGCCGAAAGGGUGAGCUUG--UUCU-U----GAGCUCAU-CCUUGGUGGUA-AAC-A-CAAA--GUUUACCACUGUCAUGGGA--CCU--------------------------------------------------------------CCCAUGA-AGCGCUAUUUAUGCA
AE004439.1/1026545-1026371 UACUUGUGUAGAGGA-GCGAUC-ACU-AUAA--GUA--UUUUUUCU-----------GAGUGGAUAACGAAG---AGGAAAA-AG-GAAAGG-AGU-G-ACCGCCGAAAUCAAUUGAAA---GUCA------UUUUGAUU-GGUUGGUGGCG-UAUUC-GAAA-GGAACGUCAUUGUCAUAGUC--UUUUUU---------------------------------------------------------AAACUAUGG-AGCGCUACUGGUUGG
CP000436.1/843556-843727   UACAUAUGUAGAGGU-GCGGCU-GUU-AUAA--GUA--AUUUUUU------------GAGUGGAUAACGAUG---A-AAAAA-AU-GAAAGG-AAU-A-GUUGCCGAAAUCAAUUAAAA---GUCA------UUUUAAUU-GGUUGGGGGCG-UAUUC-GAAA-GAAACGUCACUGUCAUAGUA--UUU-AU---------------------------------------------------------CCACUAUGG-AGCGCUACUGGUUAG
CP001186.1/1355449-1355630 CUCAAAGGUAGAGGCCGCGAUA-GGA-AAGA--GUA--AGCUAUGGGAGAU------UUAAUGGAAUCUGUG---AUCAUAGGUU-GAAAGG-GAC-U-AUUGCCGAAAUAUAAGAAUAAC-CAUC-U----UAUUCAUA-UAUUGGGACUA-CAUU--GAAUAAAUGUAGUACUGUCAUAAGA--UUU------------------------------------------------------------AUUUUAUGG-AGAGCUAUUUGGAGA
AE005176.1/2276232-2276414 CACAUCGAUAGAGGUCGCAACU-GAU-AUGAAUCUACGCCGAGUUGG----------AGCACAACAAAGACG---CGUAUUU-AG-AGGAGG-AGA-G-GUUGCCGAAAGAAUUUUGUU---GCUC------AGCAAGGU-UCUUGGGCUAG-UGAG--AAAAACUCACUAGACUGUCGCAAAUG-GUUAAUA--------------------------------------------------------ACCAUGCGG-AGGGCUAUUCGUUCA
CP000923.1/1076332-1076143 AGGUGAGGUAGAGGC-GCGGGUUAUC-AAGA--GUA--GUAUACCAGAGGU------AUUUAAGGGCCGAUG---AAGGUAU-AU-GAAAGG-GAU-G-CUCGCCGAAGC-GCGUAAAUUCCUUAA-A----GUUUACGC-AGCUGGGCCUA-UGCC--GAAUAGGUAUAGGACUGUCACUGGA--GGUUUCCCGAGC---------------------------------------------------CUUCAGUGA-AGAGCUAUCUCGCUA
AE008691.1/1930427-1930616 AGGUGAGGUAGAGGC-GCGGGU-CAUCAAGA--GUA--ACAUGCCAGAGG-------UGUUAAGGGCCGAUG---AAGGUGU-GU-GAAAGG-GGU-G-CCCGCCGAAGC-GCGUAAACUUCCUUAAG----GUUUACGC-AGCUGGGCCUA-UGCC--GAACAGGUAUAGGACUGUCACUGAAG-GCUCCCCAGGC----------------------------------------------------CUUCAGUGG-AGAGCUAUCUCGCUA
CP000826.1/4955718-4955911 CAAGCCAGAAGAGGU-GCGUCG-CCC-AG----GUA--GAGUGUCAGAGG-------AGCCGUUGUCCAAUG---ACGGCGC-UU-GAGGGG-GAG-C-GACGCCGAGGUAAGGUGAUGUG-CGGC------AUUCAUCG-UAUCGACUACA-GGGGCUGAAU-CCCCUG-AGUUGUCACCAGGG-AUUGUCCGUAGGGGCAAUCA-------------------------------------------GCAAGGUGG-GGCGCUUCUGGGUGU
AL935263.2/928916-929097   AUCGAAAGAAGAGGAUGCGGUU-AAC-AAUA--GUA--GCCGGCUGGAAGU------GGGUCACCACUUAUG---AAGGUCA-GU-GAACGG-GGC-A-ACCGCCGAAAUCGAUGGAUCAGUGACC------GAUUCAUC-CGUUGGGCCUU-GGUU--GAAUAAAUCAUGGACUGUCGCAGCUA-GAA------------------------------------------------------------UAGUUGCGG-GGCGCUAUCGACGAU
AALE02000022.1/49827-50019 UAAGCCAGAAGAGGU-GCGUCG-CCC-AG----GUA--AAGUGUCAGAGG-------AGCCGUGAUCCGCUG---AAGACAU-UC-GAGGGG-GAG-C-GACGCCGAGACACGGUGAUUUC-GGCC-------AUCAGCG-UGUCGACUGCA-GGGGCUGAAU-CCCCUG-GGUUGUCACCAGU--GCCGUUCCUUUAGGGCGGUCA------------------------------------------ACAAGGUGG-AGCGCUUCUGGGUGU
FQ670178.1/927246-927070   UACAAAAGUAGAGGC-GCAAUU-AUU-AUAA--GUA--UUUUUUCA-----------GAGUGGAUAACGAAG---AAGAAAA-AA-GAAAGG-AAU-A-GUUGCCGAAAUCAAAUAAAA---GUCG------UUUUGUUU-GGUUGGUGGCG-UGCUC-GAAA-GGGGCGACACUGUCAUAGUU--UUUCUGAU-------------------------------------------------------UAACUAUGG-AGUGCUACGGUUGUU
#=GC SS_cons               :::::((((((,,,,.<<<<<<.<<<.----..---..<<<<<<<<____......._______________..._>>>>>>.>>.------.>>>.>.>>>>>,,,<<<<<<<<<<<<__.____._....>>>>>>>>.>>>><<<<<<<.<<<<_.____.>>>>>>>>>>>,<<<<<<<_.._______........................................................__>>>>>>>.,,,,)))))):::::
#=GC RF                    aaugacgguAGAGGU.GCgucc.cuc.AugA..GUA..acuuuucuGAgg.......ggaugaaaucCgaUG...Aagaaaa.gu.GAAAGG.gag.g.gacGCCGAagugaguggaccuc.guua.a....gguccacu.cgcuGGccccg.uggcC.GAAu.gccacggggCUGuCAccgua..uuugUuc........................................................acacggUGg.AGcGCUaccggguga
//
# STOCKHOLM 1.0

#=GF AC   RF00169
#=GF ID   Bacteria_small_SRP
#=GF PI   SRP_bact_l; SRP_bact; 4.5S; 7SK; 7S; SCR
#=GF DE   Bacterial small signal recognition particle RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19838050
#=GF SS   Published; PMID:19838050
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.03 -Z 549862.597050 CM SEQDB
#=GF CL   CL00003
#=GF DR   URL; http://rnp.uthscsa.edu/rnp/SRPDB/SRPDB.html;
#=GF DR   SO; 0000590; SRP_RNA;
#=GF DR   GO; 0006617; SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition;
#=GF DR   GO; 0048501; signal recognition particle, plasma membrane targeting;
#=GF RN   [1]
#=GF RM   12520023
#=GF RT   SRPDB: Signal Recognition Particle Database.
#=GF RA   Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T
#=GF RL   Nucleic Acids Res 2003;31:363-364.
#=GF RN   [2]
#=GF RM   12140321
#=GF RT   Prediction of signal recognition particle RNA genes.
#=GF RA   Regalia M, Rosenblad MA, Samuelsson T
#=GF RL   Nucleic Acids Res 2002;30:3368-3377.
#=GF RN   [3]
#=GF RM   19838050
#=GF RT   Kinship in the SRP RNA family.
#=GF RA   Rosenblad MA, Larsen N, Samuelsson T, Zwieb C
#=GF RL   RNA Biol. 2009;6:508-516.
#=GF RN   [4]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   The signal recognition particle (SRP) is a universally conserved
#=GF CC   ribonucleoprotein involved in the co-translational targeting of proteins
#=GF CC   to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA
#=GF CC   (RFAM:RF00017) and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal
#=GF CC   SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54
#=GF CC   proteins. In most bacteria, the SRP consists of a 4.5S RNA and the Ffh
#=GF CC   protein (a homologue of the eukaryotic SRP54 protein). Some Gram-positive
#=GF CC   bacteria (e.g. Bacillus subtilis) have a longer eukaryote-like SRP RNA
#=GF CC   that includes an Alu domain [2]. The Alu domain of the longer SRP RNAs is
#=GF CC   not included in this model and therefore the reported bounds of some
#=GF CC   members are incorrect. The Signal Recognition Particle Database (SRPDB)
#=GF CC   [1] provides compilations of SRP components, with phylogenetic data and
#=GF CC   structural illustrations.
#=GF WK   Signal_recognition_particle_RNA
#=GF **   seedtax: Eukaryota; Bacteria
#=GF SQ   261


BA000034.2/177239-177336     AUAA-UAG----GCG--GAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C-UUUU---UUUUGUUGACUU----
AE000783.1/482312-482409     CCUA-GGA-C--CCG--UACU--AUCA-AGU--AUUGCUGAAU-CCCGUCAGGACU-GGAAGGUAGCAGCGGU-AAGCGAU-UUU-U-UUG-A--UG-AGU-A-CGUA---AGUCUUAGGUUUA---
CP000009.1/645655-645623     GCC-------------------------------------AAC-CCGGUCAGGUCC-GGAAGGAAGCAGCCG-------------------------------------------------------
AE009442.1/397674-397771     CUGC-CGG-U--CCC--UCGC--AACG-CUA--GAUCGAAAAC-CCCGCCAGGGCC-GGAAGGCAGCAACGGU-AUUGAUU--GA-U-GCG-G-GUG-CCG-A-GAUC---AACCGGUGGGGCC---
CP000377.1/185725-185687     ------------------------------------CGCCAAC-CUGGUCAGGUCC-GGAAGGAAGCAGCCAC-AACG-------------------------------------------------
CP000514.1/1808247-1808194   -------------------------------------GUGAAC-CCGGUCAGGCCC-GGAAGGGAGCAGCCGA-AGCGGUG-GAU-G-UGU--------------------------GUGCC-G---
AE007869.2/101545-101446     GGGA-GGU-U-GGUG--GUGG--ACGA-GCC--ACUCGCCAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AACGAGC-CAG-G-CAC-G-GGU--CG-C-CGUG--CCAGCCUCCCACCU---
CP001074.1/179393-179294     GGGA-GGU-U-GGUG--GUGG--ACGA-GCC--ACUCGCCAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AACGAGC-CCG-G-CAC-G-GGU--CA-U-CGUG--CCAGCCUCCCACCU---
CP000387.1/2183334-2183262   --------------G--GAGC--AACA-GUU--UUGCGUGAAG-CGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAAG-UAA-G-CUG-U-GUG--CU-C-U----------------------
CP001191.1/4254584-4254485   GGGA-GGU-U-GGUG--GUGG--ACGA-GCC--ACUCGCCAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AACGAGC-CCG-G-CAC-G-GGU--CA-U-CGUG--CCAGCCUCCCACCU---
AE000516.2/4160597-4160510   -GU--GGA-C--CCC--GCGC--GGCG-UCU-AUCCUGUGAAC-UCCCCCAGGGCU-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-UCG-G-GUG--CG-C-GGG-----GUCC-----------
X01074.1/170-267             UGUU-GGU-U--CUC--CCGC--AACG-CUA--CUCUGUUUAC-CAGGUCAGGUCC-GGAAGGAAGCAGCCAA-GGCAGAU--GA-C-GCG-U-GUG-CCG-G-GAUG---UAGCUGGCAGGGC---
CP000449.1/512389-512429     -----------------------------------UCGCCAAC-CCGGUCAGGUCC-GGAAGGAAGCAGCCGU-AACGA------------------------------------------------
CP001196.1/3502877-3502780   GGAG-AUU-G--GCG--GUGG--ACGA-GCC--ACUCGCCAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AACGAGGUCCG-G-AUC-G-GGU--CG-C-U-CG---UCAGUCUCCUACC---
AE016826.1/499549-499447     UGUU-AGU-A--CUCUAUAAU--ACUG-UAA-UUCUUAAGAAU-UUGGUCAGGAUU-GGAAAAUAGCAGCCAU-AUUAAGA-CAG-U-ACA-G-GUA--UU-ACGAAU--AUUACUAACAGAGA---
BA000003.2/531036-530940     UGUU-AGC-U--CCA---AAC--ACUG-CAA--UAUUGAAUAG-UUGGUCAGAUUC-GGAAGGAAGCAGCCAA-AUCAAUU--GA-U-ACA-G-GUG--UU-C-UGAU--AAAGCUAACAGAAA---
AP009256.1/217622-217709     AGC----C----UCC--GCGU--GGCG-GUA-UGUCACCCAAC-UCCCCCAGGGCA-GGAAUGCAGCAAGGGU-AAGUGGCCUCU-U-CCG-G-GUG--CG-U-GGA------G---GUUU-U----
CP000611.1/4176729-4176642   -GU--GGA-C--CCC--GCGC--GGCG-UCU-AUCCUGUGAAC-UCCCCCAGGGCU-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-UCG-G-GUG--CG-C-GGG-----GUCC-----------
AE017308.1/106146-106227     -GC----------CA--UUAG--AAUA-GCA--ACCUUGUAAC-UUGGUCAGGACA-GAAAUGAAGCAGCCACAUCGAGAA--GU-G-UUA-U-GUC--UA-A-UG-----------GUUUUU----
CP000382.1/2507739-2507704   ---------------------------------------GAAC-CCCGUCAGGUCC-GGAAGGAAGCAGCGGU-AA------------------------------------------GU-------
CP000133.1/138356-138257     GGGA-GGU-U-GGUG--GUGG--ACGA-GCC--ACUCGCCAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AACGAGC-CCG-G-CAC-G-GGU--CA-U-CGUG--CCAGCCUCCCACCU---
AM408590.1/4141851-4141764   -GU--GGA-C--CCC--GCGC--GGCG-UCU-AUCCUGUGAAC-UCCCCCAGGGCU-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-UCG-G-GUG--CG-C-GGG-----GUCC-----------
BX248354.1/219358-219448     ---G-GAC----UUC--GCAU--GGCG-CGU-AUCCCAUGAAC-UCCCCCAGGGCA-GGAAUGCAGCAAGGGUCAGUGGGC-UCU-A-GCG-G-GUG--UG-C-GGA------GUCCCCUUU-----
CP000750.2/1826545-1826597   -------------------------------------CUGAAC-CCCCCCAGGGCC-GGAAGGCAGCAAGGGU-AGGUGGG-CCC-U-GGC-G------------------------GGUG------
CP000088.1/57486-57389       UCAG-GCC-C--CUC--GUGC--GGCG-UCA--UCCUACGAAC-CUCCCCAGGGCC-GGAAGGCAGCAAGGAUAAGUAGGC-UCU-G-ACG-G-GUG--CG-C-GGG-----GGGUCCUUCGCGU--
AE017198.1/467637-467733     UUAU-AGU-U--UGU--GGGC--AAUG-UCC-GACCUCCAAAU-UGUGUCAGGACC-GGAAGGUAGCAGCACUAAGGUUGC-UUG-G-GCA-U-GUG--CC-U-UUUU--UUG---AGAAUUU----
CP000825.1/1334353-1334273   CUCG-GC-----CUU--UCGC--GGUU-UUA--ACGCCUAAAC-CUGGUCAGGACC-GGAAGGUAGCAGCCACAAGGGAUG-CUU-G-AGG-C-AGG--CG-A--------G---------------
CP000699.1/53285-53365       ---G-UCG-G-------GCGG--ACGG-UGC--CGUCGCCAAC-CCGGUCAGGUCC-GGAAGGAAGCAGCCGC-AACGAUU-UCG-U-AUC-G-GGU--CG-U--------UCCGGC----------
AP009044.1/340390-340478     ---G-GAU----CCC--GUGC--GGCG-UUU-AUCUUGUGAAC-UCCCCCAGGGCA-GGAAUGCAGCAAGGGUCAGCGAGC-UCU-G-ACG-G-GUG--CG-C-GGG------AUCCCCU-------
CP000511.1/5916848-5916790   --------------------------------------UGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGU-CAAUGGG-CUC-U-GGC-GGGUG-C------------------GCGGG-G---
X12643.1/106-207             CCCC-CGG-U--CCA--GCGC--GGCG-GGC-CAGGCGUGAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCUAAGCGCCU-CGG-U-CCG-G-GCG-CCG-C-UGGG--AAGCCGGGGGCGCU---
CP000546.1/41822-41917       GACG-GGC-C--UCC--UCGC--AUGG-UGG--GGCGGUCAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AGCCGUU-UUC-C-GCC-A-GUG-CCG-A-GGGU--CGGGCUCGUC-------
BX251412.1/198564-198476     GCC---------UCC--GCGC--GGCG-UUA-CCCGGGUGAAC-UCCCCCAGGUUA-GGAAUAAAGCAAGGGU-AGCUCGGCUCU-G-GCG-G-GUG--UG-C-GGGG----------GUCUUGC--
CP000554.1/1756425-1756329   GACU-CGG-A--CCC--AUGC--GGCC-GCG--ACGCCUAAAU-CUGGUCAGGACC-GGAAGGGAGCAGCCACACGGGAUG-CUC-G-UGA-C-AGG--CG-U-GGAC----UCCGGGUCACC----
AE017226.1/250687-250588     UCCC-GGG-G--CCU--AUGC--AAAA-AAG-GUUUUUCGAAC-CCCGUCAGAUCC-GGAAGGAAGCAGCGGU-AGAUUAA-UUC-U-UUU-U-GUG-CCG-U-AGUG---UUCCCGGGUUUUU---
U22036.1/387-479             AGAU-CGG-C--GCG--GACG--G----AGU--CCUCGCCAAC-CUGGUCAGGGCC-GAGAGGCAGCAGCCAC-AACGAGA-UCA-CCU-----CUG--GG-U-CGUC---UGCCGGUCUCCAC---
BA000021.3/607419-607516     -UUC-CAG-C--AUA--CAGC--AAUA-UUUUUAUUAGUAAAU-UCGAUCAGGUCC-GACAGGAAGCAAUCGU-AGCUACA-AAA-A-GUA-U-GUGUAUA-G-UAU-----GCUGGAAAAUU----
CP001185.1/1535072-1535040   ----------------------------------------AAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AA---------------------------------------------------
AE017263.1/790245-790165     -GC----------CG--UGAU--AAAG-AUU--ACGCCCGAAU-G-AGUCAGGACC-GGAAGGUAGCAGCUAUAAGGGAAU--GU-G-UCU-U-GUA--UC-A-CG-----------GUUUUU----
CP000151.1/2173226-2173148   CGGG-CC-----UCC--UCGC--AUGG-UGG--GGCGGUGAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AAUCGUU-UUC-C-GCC-A-GUG-CCG--------------------------
AL954747.1/470386-470485     GGCG-GGC-C--UCC--CCGC--AUUG-UGA--GGUAGUGAAU-CUGGUCAGAUCC-GGAAGGAAGCAGCCAC-AGCUAUU-UUU-C-GCA-A-GUG-CCG-G-GGGU--UCGGCUCGCCACCC---
CP000057.2/1257882-1257981   UUCU-CGG-U--CUC--UCGC--AACG-GUG--UCUGGUUUAC-UCGGUCAGGUCU-GGAAGGAAGCAGCCAA-AGUCGGA-AUU-A-CUG-U-GUG-CCG-A-GAAG--AAGCUGGGAAGGUU---
AJ011025.1/3479-3382         -GAC-UCG-G-CCUU--UCGC--GGUU-UUA--ACGCCCAAAC-CUGGUCAGGAUC-GGAAGGUAGCAGCCACAAGGGAUG-CUU-G-AGG-C-AGG--CG-A-GAUA---ACCGAGUCACUU----
AM420293.1/285535-285587     --------------------------------------UGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGU-AAGCGGG-CUC-U-GGC-G------------------------GGUGC-----
CP000083.1/3925773-3925676   UUUC-GGU-C--CCC--UCGC--AAUG-AUA--CUCUGUGAAC-UCGGCCAGGUCC-GGAAGGAAGCAACCGC-AGCAGAC--GA-C-UCA-U-GUG-CCG-A-GGUG---UGGCUGAUUGGGU---
AE014074.1/183338-183410     ----------------GGAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C------------------------
CP000114.1/418986-419062     ----------------GGAGC--AACA-UUU--ACUCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUG-CUA-A-AUG-U-GUG--CU-C--------------UUUUU-----
CP000262.1/190823-190906     CGG---------------AGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C-UUU----------UUUUGUG---
AE014073.1/412788-412885     UGUU-GGU-U--CUC--CCGC--AAUG-CUA--CUCUGUUUAC-CAGGUCAGGUCC-GGAAGGAAGCAGCCAA-GGCAGAU--GA-C-GCG-U-GUG-CCG-G-GAUG---UAGCUGGCAGGGC---
CP000448.1/35911-35941       --------------------------------------------CGUGUCAGGUCC-GGAAGGAAGCAGCACU-AA-----------------------------------------------G---
CP000444.1/3004720-3004622   CUAG-GGU-C--CCC--CCGC--AAUG-AUA--ACUUGUGAAC-UCGGCCAGGCCC-GGAAGGGAGCAACCGC-AGCAAGC--GA-C-UCG-U-GUG-CCG-G-GGUG--UCGGCUCUAGGGGA---
AE017126.1/1287985-1287888   GACU-CGG-G--CCC--AUGC--GGCU-UCG--ACGCCUAAAU-CUGGUCAGGACC-GGAAGGUAGCAGCCACAAGGGAUG-CUU-G-AAU-C-UGG--CG-U-GGAU---UCCGGGUCACCU----
AF482014.1/12-103            -GCG-GGU-C--UCC--CCGC--AUGG-CAA--AUCGGAACAC-CGGGUCAGGGGC-GGAAGCCAGCAGCCCA-CUCCGAU---G-C-GCC-A-GUG-CCG-G-GGGU--UUGGUCCGC--------
CP000431.1/4399035-4399123   ---G-GAU----CCC--GCGC--GGCGCGCA--UCCUGUGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-CCG-G-GUG--CG-C-GGG------GUCCCCU-------
CP000805.1/24333-24238       UCCG-GGG-C----C--GCCC--ACGA-AAU-AUCCCCCAAAC-CCCGCUAGGUCC-GGAAGGAAGCAACGGU-AGGGGGA--CG-C-UUC-G-GUG--CG-C-GAUC---CGCCCCGGUUUUC---
U00089.2/463960-463865       AUUU-AGA-G--CCG--UCAC--AUCA-UUA--CGGUC-GAAU-CAUGUCAGGCCA-GAAAUGGAGCAGCAUUAA-GACUA-UUU-A-AUG-A-GUG--UG-A-UGGU---UUUUUAUUGCAU----
AE016958.1/347439-347352     ---G-GAC----CCC--GCGC--GGCG-UCU-AUCCUGUGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-UCG-G-GUG--CG-C-GGG------GUCCCC--------
CP000017.1/190948-191020     ----------------GGAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C------------------------
BX294144.1/110361-110269     ---G-GCG-A--CCC--UUGC--GACU-GUG--AGUCGUGAAC-CUGGUCAGGCCU-UAACUGGAGCAGCCAUAAGCGGUG--UA-A-CUU-U-GUG--UG-A-GGGU--UGCCGCCACCG------
AE017321.1/565550-565468     ------------GGU--AUGC-AGGCA-AAA--ACUCUGUAAC-UUGGUCAGGUCA-GAAAUGAAGCAGCCACACCAGAAU-CUU-U-UUG-G-GUU-GCA-U-ACC----------UAUU------
CP000576.1/1266081-1266001   CUCG-GC-----CUU--UCGC--GGUU-UUA--ACGCCUAAAC-CUGGUCAGGACC-GGAAGGUAGCAGCCACAAGGGAUG-CUU-G-AGG-C-AGG--CG-A--------G---------------
CP000713.1/2031919-2031830   CAUU-GGU-A--GCC--UCGC--AACU-UUG--UACUACGAAC-CCCGCCAGGACC-GGAAGGUAGCAACGGU-AGUAGAU--AC-A-AGG-U-GUG-CCG-A-GGAU---GUGCU-----------
AE017143.1/1086371-1086274   UUAU-UGG-U--UUC--UCGC--AGCA-GAA--UUCAGCUUAC-UUAGUCAGGGCC-GGAAGGAAGCAGCUUG-GGUUGAA--UU-U-CUG-G-GUG-CCG-G-GAGU---CGCUGGUAAUACC---
CP000544.1/267166-267080     -----GGU-C--CCC--CCGC--GACG-AGU--CGCUGUGAAC-CCCGUCAGGCCC-GGAAGGGAGCAGCGGC-AGCAGCG-AUC-C-UCG-G-GCG-CCG-G-GGUG---UGGCU-----------
CP000259.1/197535-197632     -AUA-AUA-G--GCG--GAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C-UUUU---UUUGUUGACUUU----
D00560.1/68-144              --G---------CCG--CGAU--AAGA-AUA--ACAUCUGAAU-G-AGUUAGGACC-GGAAGGUAGCAGCUAU-AAGGAAA-AGU-G-UUC-U-GUA--UU-G-CGGU-------------------
AL111168.1/66646-66744       UUCU-UAG-A--CCU--GUGC--AAUG-CUA-UUUUUAAGCAC-CGCUUCAGGGUG-GGAACACAGCAGAGCA-CUUGAUU--UU-A-GUG-U-GUG-CCG-C-AGUU---AUCUGGGGAAGGG---
AE001273.1/286645-286544     GCUG-GGG-A-CCUC--UUAA--GAUG-AGA-GACUUCUGAAC-CGGGUCAGGAUC-GGAAGGUAGCAGCCCU-AAGGAUA-GGC-C-UUU-U-GUG-CUA-G-GAGU---UUUCUCUGGCUUAC--
CP001033.1/24808-24884       ----------------GGAGC--AACA-GUU--CUGCGUGAAG-CGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUU-UGA-A-UUG-U-GUG--CU-C--------------UUUUU-----
CP001029.1/1948777-1948745   ----------------------------------------AAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AA---------------------------------------------------
CP000025.1/65635-65733       UUCU-UAG-A--CCU--GUGC--AAUG-CUA-UUUUUAAGCAC-CGCUUCAGGGUG-GGAACACAGCAGAGCA-CUUGAUU--UU-A-GUG-U-GUG-CCG-C-AGUU---AUCUGGGGAAGGG---
AL939118.1/230082-230163     ---C-C------CUC--ACGC--GGCG-CUA-UCUGACUGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGU-AGGUCGGCUCU-G-GCG-G-GUG--CG-U-GGG--------GG----------
CP000031.1/3754765-3754862   -GAG-AGG-U-UGGC--GCGG--GCGA-GCG--CCUCGCCAAC-CUGGUCAGGUCC-GGAAGGAAGCAGCCAC-AACGAGU-CCC-G-CUU-G-GGU--CGAU-GUCC---AGCCUCUCACUU----
CP000097.1/1495241-1495145   GACU-CGG-A--CCC--AUGC--GGUU-CUG--ACGCCCAAAU-CUGGUCAGGACC-GGAAGGUAGCAGCCACACGGGAUG-CUC-A-GGA-C-AGG--CG-U-GGAC----UCCGGGUCACC----
CP000304.1/2745928-2745838   -----GGU-C--CCC--UCGC--AACG-AUC--AGCCGUGAAC-CCGGUCAGGCCC-GGAAGGGAGCAGCCGC-AGCGGUG--AC-A-UUG-U-GUG-CCG-G-GGUG---UGGCU-GGUAG-----
CP001205.1/478407-478504     CCUA-GGA-C--CCG--UACU--AUCA-AGU--AUUGCUGAAU-CCCGUCAGGACU-GGAAGGUAGCAGCGGU-AAGCGAU-UUU-U-UUG-A--UG-AGU-A-CGUA---AGUCUUAGGUUUA---
AE017285.1/878943-878860     ---G-A------GCC--GGGC--GGCG-GUA-ACGCUGCCAAC-CCCGCCAGGUCC-GAAAGGAAGCAACGGU-AACAGUU-GUU-G-CCG-G-GUG--UC-C-GGC--------UCCCU-------
AJ489606.1/805-893           AAA----A----GUG--GAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUGUCA-G-GUG-U-GUG--CU-C-UUU------U---UUUGUU----
CP000230.1/3998670-3998630   -----------------------------------UCGCCAAC-CCGGUCAGGUCC-GGAAGGAAGCAGCCGU-AACGA------------------------------------------------
CP000949.1/4005444-4005415   ----------------------------------------AAC-CUGGUCAGGCCC-GGAAGGGAGCAGCCA-------------------------------------------------------
CP000124.1/2648069-2647974   GACG-GGC-C--UCC--UCGC--AUGG-UGG--GGCGGUCAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AGCCGUU-UUC-C-GCC-A-GUG-CCG-A-GGGU--CGGGCUCGUC-------
CP001001.1/3321659-3321691   ----------------------------------------AAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AA---------------------------------------------------
AE017340.1/1992283-1992186   UGCG-GGU-C--CCC--UCGC--AACG-CUA--ACUGGUGAAC-CCGGUCAGGCCC-GGAAGGGAGCAGCCGU-AGUCAGG--GA-U-GUG-U-GUG-CCG-A-GGUG---UGGCUGGUAGAGU---
AF132127.1/653-752           AAUA-GAU-A--UCG--GAGC--AACA-GCU--UUGCGUGAAG-CGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUG-UAA-G-CUG-U-GUG--CU-C-UAUU---UUUUGUGUAAUAGU--
CP000423.1/2257654-2257576   --------------A--AGGC--AAUG-AUG-GCUUUCCGAAU-CGUGUCAGGUCC-GGAAGGAAGCAGCACUAAGGUAGG-UUC-G-UCA-U-GUG--CC-U-U------------UUGUU-----
AE000520.1/24335-24246       ---C-CGG-G--GCC--GCCC--ACGA-AAU-AUCCCCCAAAC-CCCGCUAGGUCC-GGAAGGAAGCAACGGU-AGGGGGA--CG-C-UUC-G-GUG--CG-C-GAUCC-GCCCCGG----------
AM946015.1/1687243-1687187   GGAG-CA-----------------ACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGA------------U-----------------------------------
CP000717.1/4181284-4181194   -GUG-GA----CCCC--GCGC--GGCG-UCU-AUCCUGUGAAC-UCCCCCAGGGCU-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-UCG-G-GUG--CG-C-GGGG------UCCCCU-------
CP000548.1/1119282-1119187   GACG-GGC-C--UCC--UCGC--AUGG-UGG--GGCGGUCAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AGCCGUU-UUC-C-GCC-A-GUG-CCG-A-GGGU--CGGGCUCGUC-------
CR954253.1/1408037-1407947   ----U------------GGGC--AAUG-UUC-GACCUCCGAAG-CGUGUCAGGACC-GGAAGGUAGCAGCACUAAGGUCGC-UUG-G-ACA-U-GUG--CC-C-UUUAU-UUAGCAAUUAACA----
X14404.1/127-224             UGUC-GGU-C--CCC--CCGC--AACG-AUU--ACCCGUCAAC-CUGGUCAGGUCC-GGAAGGAAGCAGCCAC-AGCGGGA--AC-A-UCG-U-GUG-CCG-G-GGUG---UGGCUGGCGGGGC---
CP000058.1/2086711-2086808   CAUC-GGU-C--CCC--CCGC--AACG-AUU--ACCCGUGAAC-CUGGUCAGAUCC-GGAAGGAAGCAGCCAC-AGCGGGA--AC-A-UUG-U-GUG-CCG-G-GGUG---UGGCUGGUGGGGG---
CP001072.2/16512-16414       UAUU-UAG-A--CCU--AUGC--AAUA-GGA-UUUUAGGGUAA-CGCUUCAGGGUA-GGAAUACAGCAGAGUC-CCCUAAU--UU-C-UUG-U-GUG-CCU-U-AGCC---AUCUGAAUAGGAG---
BX569693.1/191291-191195     -GAC-UCG-G--GCC--AUGC--GGCU-CGG--ACGCCCAAAU-CUGGUCAGGACC-GGAAGGGAGCAGCCACACGGGAUG-CUC-A-GAG-C-AGG--CG-U-GGAC---UCCGGGUCACCC----
BA000045.2/3486103-3486201   AGCC-UGG-G--CCC--GUGC--GGCU-CGG--ACGCCCGAAC-CGUGUCAGGACC-UGACGGUAGCAGCACUAAGGGAUG-CUC-U-GGG-C-AGG--CG-C-GUGG---UUCCGGGUUUUUU---
AM920689.1/3831058-3830961   CCGU-CGG-U--CCC--UCGC--GACG-CUA--GAUCGAAAAU-CCCGCCAGGGCC-GGAAGGCAGCAACGGU-AUCGAUU--GA-U-GCG-G-GCG-CCG-A-GGUC---AACCGGCGGGGAC---
BA000036.3/256434-256527     ---G-GAU----CCC--GUGC--GGCG-UUU-AUCUUGUGAAC-UCCCCCAGGGCA-GGAAUGCAGCAAGGGUCAGCGAGC-UCU-G-ACG-G-GUG--CG-C-GGG------AUCCCCUAAAAC--
BA000030.3/5095146-5095065   ---C-C------CUC--ACGU--GGCG-CUA-UCUGACUGAAC-UCCCCCAGGGCC-GGAAGUCAGCAAGGGU-AGGUUGGCUCU-G-GCG-G-GUG--CG-U-GGG--------GG----------
AE017221.1/1448447-1448346   CCCC-CGG-U--CCA--GCGC--GGCG-GGC-CAGGCGUGAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCUAAGCGCCU-CGG-U-CCG-G-GCG-CCG-C-UGGG--AAGCCGGGGGCGCU---
AP009153.1/1324702-1324799   CCCG-GGU-C--CCG--GAG---GGCG-UCA--GACCGCCAAC-UCCGUCAGGACCCCGAAGGUAGCAGCGGUACGUGGAU-CCU-G-UCG-UC--G--CU-U-CGUC---AGGCCCGGGGCAC---
AM295007.1/184037-184114     ----------------GGAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C--------------UUUUU-----
CP000282.1/1729405-1729437   ----------------------------------------AAC-CCCGCCAGGCCC-GGAAGGGAGCAACGGU-AG---------------------------------------------------
CP000437.1/1648080-1647983   ACUU-GGU-U--UCC--ACGC--AAUG-AUA--GAUUGUCAAC-CCCGCCAGGUCU-GGAAGGAAGCAACGGU-AACUUUU--GA-U-UCA-U-GUG-CCG-U-GUCA---AGGCUAAGUCAGC---
CP000107.1/1309520-1309617   CAGA-GGG-U--AAU--AUGA--GCAA-AGG--CCUUGUGAAG-UCGGUCAGGUUA-GGAAUAAAGCAGCCGU-AGCAUUG-UCC-C-UUU-G-GGU--UG-U-AUU-----GCCCAUUUUUUAUU-
AP010918.1/4139044-4138957   -GU--GGA-C--CCC--GCGC--GGCG-UCU-AUCCUGUGAAC-UCCCCCAGGGCU-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-UCG-G-GUG--CG-C-GGG-----GUCC-----------
CP000570.1/2200688-2200593   GACG-GGC-C--UCC--UCGC--AUGG-UGG--GGCGGUCAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AGCCGUU-UUC-C-GCC-A-GUG-CCG-A-GGGU--CGGGCUCGUC-------
CP000003.1/224292-224364     ----------------GGAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C------------------------
CP001298.1/2298033-2298001   ----------------------------------------AAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AA---------------------------------------------------
AP008226.1/1771741-1771640   CCCC-CGG-U--CCA--GCGC--GGCG-GGC-CAGGCGUGAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCUAAGCGCCU-CGG-U-CCG-G-GCG-CCG-C-UGGG--AAGCCGGGGGCGCU---
CP000123.1/5231-5309         -A---------GCCG--CGAU--AAGA-AUA--ACAUCUGAAU-G-AGUUAGGACC-GGAAGGUAGCAGCUAU-AAGGAAA-AGU-G-UUC-U-GUA--UU-G-CGGU---U---------------
BX897699.1/309928-309832     -GAG-GUU-G--GUG--GUGG--ACGC-ACU--GCUCGCCAAC-CGGGUCAGGUCU-GGAAAGAAGCAGCCCU-AACGAGUUCUG-G-UAC-G-GGU--CA-U-CGUA---CCAGCCUCCUAU----
BX293980.2/59916-59840       --G---------CCG--CGAU--AAGA-AUA--ACAUCUGAAC-G-AGUUAGGACC-GGAAGGUAGCAGCUAU-AAGGAAA-AGU-G-UUC-U-GUA--UU-G-CGGU-------------------
CP000010.1/1421960-1421865   GACG-GGC-C--UCC--UCGC--AUGG-UGG--GGCGGUCAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AGCCGUU-UUC-C-GCC-A-GUG-CCG-A-GGGU--CGGGCUCGUC-------
CP000284.1/1685091-1685185   GGCG-GGC-C--UCC--CCGC--AUUG-CAA--AGUAGCCAAC-CUGGUCAGGUCC-GGAAGGAAGCAGCCAC-AACUAUU--GA-A-GCA-A-GUG-CCG-G-GGGU--UGGGCUCGCC-------
AE016825.1/2560853-2560754   GGCG-GGC-C--UCC--CCGC--AUUG-CAC--GGUAGCGAAC-CUGGUCAGGUCC-GGAAGGAAGCAGCCAC-AGUUAUU-CAG-U-GCA-A-GUG-CCG-G-GGGU--CGGGCUCGCCACCC---
AL590842.1/3498558-3498461   UGUU-GGU-U--CUC--CCGC--AACA-CUA--ACUUGUGAAC-UCGGUCAGGUCC-GGAAGGAAGCAGCCGC-AGCAGGC--GA-G-GUG-U-GUG-CCG-G-GAUG---UAGCUGGCAGGGC---
CP000450.1/597363-597461     GGCG-GGC-C--UCC--CCGC--AUUG-UAA--GAUAGUGAAU-CUGGUCAGAUCC-GGAAGGAAGCAGCCAC-AGCUAUU-UUU-U-ACA-A-GUG-CCG-G-GGGU--UCGGCUCGCCACC----
CP000033.3/351328-351428     UCAU-ACU-U--GAU--GGGC--AAUG-UUU-GACCUCUGAAU-CGUGUCAGGACC-GGAAGGUAGCAGCACUAAGGUUGU-UCA-G-GCA-U-GUG--CC-U-UUUA---UUAGAAAUUAACAA--
CP000908.1/2084457-2084425   ----------------------------------------AAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AA---------------------------------------------------
CP000738.1/3636444-3636544   GGGA-GGU-U-GGUG--GUGG--ACGA-GCC--ACUCGCCAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AACGAGCCCCG-G-CAC-G-GGU--CA-C-CGUG--CCAGCCUCCCACCU---
CP000720.1/3460787-3460690   UGUU-GGU-U--CUC--CCGC--AACA-CUA--ACUUGUGAAC-UCGGUCAGGUCC-GGAAGGAAGCAGCCGC-AGCAGGC--GA-G-GUG-U-GUG-CCG-G-GAUG---UAGCUGGCAGGGC---
BX571662.1/289282-289380     CUUU-UAG-A--CCU--GUGC--AAUG-GGC-CCUUGGAGCAA-UGCUUCAGGGUG-GGAACACAGCAGAGCC-CUCCAGA--GG-U-UCA-U-GUG-CCG-C-AGGU---AUCUGAAGGGGGG---
CP000024.1/1644513-1644437   ----------------GGAGC--AACA-UCU--GUGCGUGAAG-CGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUU-UCA-G-GUG-U-GUG--CU-C--------------UUUUU-----
CP000020.2/1087907-1087810   CCCU-GGU-C--CUC--CCGC--AACA-CUA--ACUCGUGAAC-UCGGUCAGGCCC-GGAAGGGAGCAGCCGC-AGCGGGC--GA-C-GUG-U-GUG-CCG-G-GAUG---UGGCUGGGGCUUC---
AE001439.1/16900-16802       UAUU-UGG-A--CCU--AUGC--AAUA-GGA-CUUUAGGGUAA-CGCUUCAGGGUA-GGAAUACAGCAGAGUC-CCCUAAU--UU-C-UUG-U-GUG-CCU-U-AGCC---AUCUGAAUAGGAG---
FM180568.1/436931-437028     UGUU-GGU-U--CUC--CCGC--AACG-CUA--CUCUGUUUAC-CAGGUCAGGUCC-GGAAGGAAGCAGCCAA-GGCAGAU--GA-C-GCG-U-GUG-CCG-G-GAUG---UAGCUGGCAGGGC---
CP000767.1/6837-6747         UUCU-UAG-A--CCU--GUGC--AAUG-CCG-UUUAUGAGCAC-CGCUUCAGGGUG-GGAACACAGCAGAGCA-CUUGUUU--AU-G-GUG-U-GUG-CCG-C-AGUU---AUCUG-----------
BA000039.2/216057-215960     GGCU-CGG-A--AUC--AUGC--GAUC-GCA--ACGCCUCAAC-CUUGUCAGGUCC-GGAAGGAAGCAGCAAUACGGGAUG-CUU-G-CGA-U-AGG--CG-U-GAUC----UCCGGGUCACCC---
CP000241.1/18047-17949       UAUU-UAG-A--CCU--AUGC--AAUA-GGA-UUUUAGGGUAA-CGCUUCAGGGUA-GGAAUACAGCAGAGUC-CCCUAAU--UU-C-UUG-U-GUG-CCU-U-AGCC---AUCUGAAUAGGAG---
CP000552.1/1308622-1308542   CUCG-GC-----CUU--UCGC--GGUU-UUA--ACACCCAAAC-CUGGUCAGGAUC-GGAAGGUAGCAGCCACAAGGGAUG-CUU-G-AGG-C-AGG--CG-A--------G---------------
AE006914.1/1239533-1239619   ---G-CUA----GUA--GUG---GGCA-UUG-UACCUGUUUAG-UCGGUCAGGUCU-GAAAGGAAGCAGCCAG-AGUGGGA-UUC-G-AUG-GG----UCA-U-UAC------UAGCAUUA------
CP000075.1/2101610-2101707   CAUC-GGU-C--CCC--CCGC--AACG-AUU--ACCCGUGAAC-CUGGUCAGAUCC-GGAAGGAAGCAGCCAC-AGCGGGA--AC-A-UUG-U-GUG-CCG-G-GGUG---UGGCUGGUGGGGG---
CP000082.1/1173790-1173887   CAUU-GGU-A--GCC--UCGC--AACA-UUG--UUCUAUGAAU-CCCGCCAGGACC-GGAAGGUAGCAACGGU-AAUAGUU--AU-A-AUG-U-GUG-CCG-A-GGAU---GUGCUGAUGGAGU---
AE009951.2/799407-799503     CCCU-UAG-G-GGAU--AUGA--UAUA-UUA---UUGUCGAAC-CGUGUCAGAUCU-GGAAGGAAGCAGCACUAAGAUUU---AU-A-GUA-U-AUG--CA-U-GUCU---UCCUAGGGGUAUC---
AP008229.1/1053059-1052962   CCGU-CGG-U--CCC--UCGC--GACG-CUA--GAUCGAAAAU-CCCGCCAGGGCC-GGAAGGCAGCAACGGU-AUCGAUU--GA-U-GCG-G-GCG-CCG-A-GGUC---AACCGGCGGGGGC---
CP000941.1/393879-393976     CUGC-CGG-U--CCC--UCGC--AACG-CUA--GAUCGAAAAC-CCCGCCAGGGCC-GGAAGGCAGCAACGGU-AUUGAUU--GA-U-GCG-G-GUG-CCG-A-GAUC---AACCGGUGGGGCC---
AE002160.2/636783-636682     GUCG-GGG-A-CCUC--UUAA--GAUG-AGA-GACUUCUGAAC-CGGGUCAGGAUC-GGAAGAUAGCAGCCCU-AAGGAAA-GGC-C-UUU-U-GUG-CUA-A-GAGU---CUUCUCUGACUUAC--
CP000089.1/875842-875941     GGCG-GGU-C--UCC--CCGC--AUUA-CAG--UGUGGUGAAC-CUGGUCAGGUCC-GGAAGGAAGCAGCCAC-AGCCAAU-UAU-U-GUA-A-GUG-CCG-G-GGGU--UAGGCUCGCCAAUU---
CP000656.1/1332664-1332751   -GU--GGA-C--CCC--GCGC--GGCG-UCC-AUCCUGUGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-GCG-G-GUG--CG-C-GGG-----GUCC-----------
AM747720.1/2097168-2097090   CGGG-CC-----UCC--UCGC--AUGG-UGG--GGCGGUGAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AAUCGUU-UUC-C-GCC-A-GUG-CCG--------------------------
CP000380.1/860735-860813     CGGG-CC-----UCC--UCGC--AUGG-UGG--GGCGGUGAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AAUCGUU-UUC-C-GCC-A-GUG-CCG--------------------------
U00096.2/475680-475777       UGUU-GGU-U--CUC--CCGC--AACG-CUA--CUCUGUUUAC-CAGGUCAGGUCC-GGAAGGAAGCAGCCAA-GGCAGAU--GA-C-GCG-U-GUG-CCG-G-GAUG---UAGCUGGCAGGGC---
AE014184.1/822891-822803     GCC---------UCC--GCGC--GGCG-UUA-CCCGGGUGAAC-UCCCCCAGGUUA-GGAAUAAAGCAAGGGU-AGCUCGGCUCU-G-GCG-G-GUG--UG-C-GGGG----------GUCUUGC--
CU633749.1/2046219-2046315   GACG-GGC-C--UCC--UCGC--AUGG-UGG--CGCGGUCAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AGCCGUU-UUC-C-GCC-A-GUG-CCG-A-GGGU--CAGGCUCGUCC------
AE000657.1/1303771-1303861   -AU----U-A--GCC--CUGC--GGCG-GGA--CAGGGUGAAC-UCCCCCAGGCCC-GAAAGGGAGCAAGGGUAAGCCCGC-CGU-C-CCG-U-GCG--CA-G-GGUC---CUA---AAACAA----
AE016822.1/334711-334799     ---U-------CCCC--ACGU--GGCG-CCA-UCCAGGCCAAC-UCCCCCAGGGUG-GAAACGCAGCAAGGGU-AACCGGGCUCU-G-GCG-G-GUG--CG-U-GGGG---G----GUCUUUU----
CP000412.1/1420806-1420719   UGU---------AUU--GGGC--AAUG-UUC-GACCUCCGAAG-CGUGUCAGGACC-GGAAGGUAGCAGCACUAAGGUCGC-UUG-G-ACA-U-GUG--CC-C-UUU----------AUUUAGC---
CP000480.1/6352915-6352830   ------------CCC--GCGC--GGCG-UCC-AUCCUGUGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-GCG-G-GUG--CG-C-GGGG---U-----CCCCUU----
CP000454.1/596081-595992     ---G-GCC-C--CUC--AUGU--GGCG-UCA-UCCUGUUGAAC-UCCCCCAGGACC-GGAAGGUAGCAAGGGU-AAAUGGGCUCU-G-GCG-G-GUG--CA-U-GGG-----GGGUCUU--------
CP000407.1/1951132-1951055   UGG---------------AGC--AACA-UUC--GUGCGUGAAG-CGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAGG-UCG-A-GUG-U-GUG--CU----------------CUUUUU----
CP000285.1/1651769-1651815   ----------------------------------GCCGCGAAC-CCCGCCAGGCCC-GGAAGGGAGCAACGGU-AGUGGU-------------------------------------GGAU------
AM884176.1/605097-604996     GCUG-GGG-A-CCUC--UUAA--GAUG-AGA-GACUUCUGAAC-CGGGUCAGGAUC-GGAAGGUAGCAGCCCU-AAGGAUA-GGC-C-UUU-U-GUG-CUA-G-GAGU---UUUCUCUGGCUUAC--
CP001138.1/505976-506073     UGUU-GGU-U--CUC--CCGC--AACG-CUA--CUCUGUUUAC-CAGGUCAGGUCC-GGAAGGAAGCAGCCAA-GGCAGAU--GA-C-GCG-U-GUG-CCG-G-GAUG---UAGCUGGCAGGGC---
BX908798.1/871974-872075     AACC-GGG-G--ACC--UCAUGGAAUA-AAU--UAGUUCGAAC-CAGGUCAGGACA-GGAAUGUAGCAGCCUUAAGAAUCA--UA-C-UUA-U-GCC-UUG-A-GAUA--AUCUCCGGUUUUUU---
AE000513.1/2231152-2231251   UUGC-UGG-U--GCA--GCGC--AGCG-CGG--ACGCCCGAAC-CUGGUCAGAGCC-GGAAGGCAGCAGCCAUAAGGGAUG-CUU-U-GCG-G-GUG-CCG-U-UGCC---UUCCGGCAAUGCU---
AE017243.1/166222-166302     ------------CCA--CUAA--AAUA-AUA--ACCUUGUAAC-CUGGUCAGGAUA-GAAAUAUAGCAGCCAUAUCGAGAA--GU-G-UUG-U-GUU--UA-G-UGG----------UUUUU-----
CP000918.1/62477-62553       ----------------GGAGC--AACA-GUU--CUGCGUGAAG-CGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUU-UGA-A-UUG-U-GUG--CU-C--------------UUUUU-----
AE001363.1/447418-447315     GUUG-GGG-G-CCUU--UUAA-GAGAA-GGA--ACCUGCGAAU-CGGGUCAGGACU-GGAAGGUAGCAGCCCUAAGGAGAG-UUU-U-CUU-U--UG-CUA-A-AAGAAUGUUCUCCAACUUAC---
CP000924.1/2275844-2275817   ---------------------------------------------CCGUCAGGUCC-GGAAGGAAGCAGCGGU---------------------A--------------------------------
CP000850.1/277856-277919     -------------------G--------------------AAC-CUCCCCAGGGCC-GGAAGGCAGCAAGGAU-AAGCGGG-CUC-U-GGC-GGGUG--CA-C-GGGG---------GGCCUU----
CP000356.1/801540-801601     GUCG-GGC-G---------G---ACGC-AGC--CUUCGCCAAC-CCGGUCAGGUCC-GGAAGGAAGCAGCCGC-AACGAAU------------U---------------------------------
CU234118.1/808247-808343     GGAG-AUU-G--GCG--GUGG--ACGA-GCC--ACUCGCCAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AACGAGGUCCG-G-AUC-G-GGU--CG-C-U-CG---UCAGUCUCCUAC----
AE005176.1/727649-727725     ----------------GGAGC--AAUA-AGU-UUCUUACGAAG-CGUGUCAGGACC-UGACGGUAGCAGCACUAAGUAUGG--AG-C-UUA-U-GUG--CU-C--------------UUUUU-----
ACGR01000021.1/27460-27385   -----------------GGGC--AAUG-UCC-GACCUCCAAAU-UGUGUCAGGACC-GGAAGGUAGCAGCACUAAGGUUGC-UUG-G-GCA-U-GUG--CC-U--------------UUUU------
CP000408.1/1950501-1950424   UGG---------------AGC--AACA-UUC--GUGCGUGAAG-CGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAGG-UCG-A-GUG-U-GUG--CU----------------CUUUUU----
CP000422.1/1456101-1456043   AGGC-A-----------------AGGU-UGG--ACUUACGAAU-UGUGUCAGGUCC-GGAAGGAAGCAGCACUAAGUAUGC------------U---------------------------------
CP000425.1/704629-704664     --------------------------------------CGAAG-CGUGUCAGGACC-UGACGGUAGCAGCACUAAG---------------------------------------------------
ACFA01000489.1/7647-7728     ---C-C------CUC--ACGC--GGCG-CUA-UCUGACUGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGU-AGGUCGGCUCU-G-GCG-G-GUG--CG-U-GGG--------GG----------
CP001068.1/1100816-1100717   GACG-GGC-C--UCC--UCGC--AUGG-UGG--CGCGGUCAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AGCCGUU-UUC-C-GCC-A-GUG-CCG-A-GGGU--CAGGCUCGUCCCCC---
CR522870.1/1597467-1597369   UAGC-UAG-G--UCU--AUGC--AACA-GAG--AAUCACGAAC-UCCGCCAGGCCU-GGAAGGGAGCAACGGU-AGUGACA-CUC-U-CUG-U-GUG--CG-U-AGGU--UGCCUAGCUACCAU---
CP000608.1/274577-274480     ACUU-GGU-U--UCC--ACGC--AAUG-AUA--GAUUGUCAAC-CCCGCCAGGUCC-GGAAGGAAGCAACGGU-AACUUUU--GA-U-UCA-U-GUG-CCG-U-GUCA---AGGCUAAGUCAGC---
CP000510.1/2402570-2402539   ----------------------------------------AAC-CUGGUCAGAGCC-GGAAGGCAGCAGCCAU---------------------A--------------------------------
AM406671.1/1824257-1824222   --------------------------------------CGAAG-CGUGUCAGGACC-UGACGGUAGCAGCACUAAG---------------------------------------------------
CP000359.1/2311277-2311308   --------------------------------------UGAAC-CUGGUCAGGGCC-GGAAGGCAGCAGCCA-------------------------------------------------------
AE009949.1/183417-183489     ----------------GGAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C------------------------
CP001050.1/743127-743218     -GCG-GGU-C--UCC--CCGC--AUGG-CAA--AUCGGAACAC-CGGGUCAGGGGC-GGAAGCCAGCAGCCCA-CUCCGAU---G-C-GCC-A-GUG-CCG-G-GGGU--UUGGCCCGC--------
AM260522.1/1471714-1471812   UAUU-UAG-A--CCU--AUGC--AAUA-GGA-UUUUAGGGUAA-CGCUUCAGGGUA-GGAAUACAGCAGAGUC-CCCUAAU--UU-C-UUG-U-GUG-CCU-U-AGCC---AUCUGAAUAGGAG---
CP000439.1/1640051-1639954   ACUU-GGU-U--UCC--ACGC--AAUG-AUA--GAUUGUGAAC-CCCGCCAGGUCC-GGAAGGAAGCAACGGU-AACUUUU--GA-U-UCA-U-GUG-CCG-U-GUCA---AGGCUAAGUCAGC---
AE017283.1/252387-252478     ---G-UUC----CCC--GUGC--GGCG-GCA-CCUGACUGAAC-UCCCCCAGGACC-GAGAGGUAGCAAGGGU-AGGUUGGCUCU-A-CCG-G-GUG--CG-C-GGG------GAGCCCUUUU----
AP007255.1/4656404-4656445   ----------------------------------GUCGCCAAC-CCGGUCAGGUCC-GGAAGGAAGCAGCCGU-AACGA------------------------------------------------
AE002161.1/393779-393882     GUUG-GGG-G-CCUU--UUAA-GAGAA-GGA--ACCUGCGAAU-CGGGUCAGGACU-GGAAGGUAGCAGCCCUAAGGAGAG-UUU-U-CUU-U--UG-CUA-A-AAGAAUGUUCUCCAACUUAC---
CP001048.1/1157694-1157791   UGUU-GGU-U--CUC--CCGC--AACA-CUA--ACUUGUGAAC-UCGGUCAGGUCC-GGAAGGAAGCAGCCGC-AGCAGGC--GA-G-GUG-U-GUG-CCG-G-GAUG---UAGCUGGCAGGGC---
CP000116.1/544561-544656     GGCG-GGC-C--UCC--CCGC--AUGG-CUA--AGUCGUGAAU-CGGGUCAGGUCC-GGAAGGAAGCAGCCAC-AGCGAUC--CA-U-GCC-A-GUG-CCG-G-GGUU--CUGGCUCGCCA------
BA000026.2/1208314-1208396   ---G--------ACG--UCAU--AACA-UUA-GAA--GUGAAU-CGUGUCAGGAUA-GAAAUAUAGCAGCACUAAGCAAUA-UCU-U-UUG-U-GUA--UG-G-CGU---------CUUUUU-----
AL766845.1/74922-74998       ----------------GGAGC--AACA-UUU--ACUCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUG-CUA-A-AUG-U-GUG--CU-C--------------UUUUU-----
AF203881.1/14937-14897       -----------------------------------UCGCCAAC-CCGGUCAGGUCC-GGAAGGAAGCAGCCGU-AACGA------------------------------------------------
CP000249.1/312088-312037     --------------------------------------UGAAC-CCCCCCAGGGCC-GGAAGGCAGCAAGGGU-AAGCGGG-CUC-U-GGC-G------------------------GGUG------
AE004969.1/870846-870755     -GCG-GGU-C--UCC--CCGC--AUGG-CAA--AUCGGAACAC-CGGGUCAGGGGC-GGAAGCCAGCAGCCCA-CUCCGAU---G-C-GCC-A-GUG-CCG-G-GGGU--UUGGUCCGC--------
AJ237851.1/3351-3301         ---------------------------------ACGCCUAAAU-CUGGUCAGGACC-GGAAGGUAGCAGCCAC-AAGGGAU------------------------------------GCUUGA----
CP000100.1/2447996-2447899   GACU-CGG---ACCU--AUGU--GGUC-AGA--ACGCCCAAAU-CCUGUCAGGACC-GGAAGGUAGCAGCAGUACGGGAUG-CUU-U-UGA-C-AGG--CG-U-AGAC---U-CCGGGUCACUU---
CP000090.1/2325066-2325165   GACG-GGC-C--UCC--UCGC--AUGG-UGG--CGCGGUCAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAU-AGCCGUU-UUC-C-ACC-A-GUG-CCG-A-GGGC--CAGGCUCGUCCACC---
CP000887.1/40749-40653       GAGG-UUG-G--UGG--UGG---ACGA-GCC--ACUCGCCAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AACGAGCCACG-G-CAC-GG--G--CC-A-UCGU---GCCAGCCUCCCAC---
CP000479.1/372508-372610     UGGG-UGG-A-CCCC--GCGC--GGCG-UCU-AUCCUGUGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-UCG-G-GUG--CG-C-GGGGU-CCCCUACCUUCGAU---
AE013218.1/532210-532112     CUGU-UAG-U--CCU--AAAC--ACUG-UUA--AAUUGAAUAA-UUGGUCAGAUCU-GGAAAGAAGCAGCCAA-AUCAAUC--GA-U-ACA-G-GUG--UU-U-UGAUA-UAGCUAACAGAAUC---
U06833.1/215-133             G-----------CCU--UUAG--AACA-AUA--ACCUCAUAAC-CCGGUCAGGACA-GAAAUGGAGCAUCCGCAUUGAGAA--GU-G-UUG-U-GUC--UU-U-AGG----------UCUUUU----
AL157959.1/1147858-1147765   GGCG-GGU-C--UCC--CCGC--AUGG-CAA--AUCGGAACAC-CGGGUCAGGGGC-GGAAGCCAGCAGCCCA-CUCCGGU---G-C-GCC-A-GUG-CCG-G-GGGU--UUGGCCCGCC-------
AM286280.1/1762567-1762664   ACUU-GGU-U--UCC--ACGC--AAUG-AUA--GAUUGUCAAC-CCCGCCAGGUCU-GGAAGGAAGCAACGGU-AACUUUU--GA-U-UCA-U-GUG-CCG-U-GUCA---AGGCUAAGUCAGC---
BA000035.2/220057-220146     ---G-GAU----CCC--GUGC--GGCG-UUU-AUCUUGUGAAC-UCCCCCAGGGCA-GGAAUGCAGCAAGGGUCAGCGAGC-UCU-G-ACG-G-GUG--CG-C-GGG------AUCCCCUU------
AM236080.1/166490-166391     GGGA-GGU-U-GGUG--GUGG--ACGA-GCC--ACUCGCCAAC-CGGGUCAGGUCC-GGAAGGAAGCAGCCCU-AACGAGC-CCG-G-CAC-G-GGU--CA-U-CGUG--CCAGCCUCCCACCU---
AE009952.1/1179172-1179269   UGUU-GGU-U--CUC--CCGC--AACA-CUA--ACUUGUGAAC-UCGGUCAGGUCC-GGAAGGAAGCAGCCGC-AGCAGGC--GA-G-GUG-U-GUG-CCG-G-GAUG---UAGCUGGCAGGGC---
AE015925.1/446183-446284     GUUG-GGG-A-CCUU--UUAA-GAGAA-GAG--ACCUACGAAU-CGGGUCAGGACU-GGAAGGUAGCAGCCCUAAGAAGUG-UUU-U-CUU-U--UG-CUA-G-AAGU--GUUCUCCAACUUAC---
CP000440.1/1952920-1952842   CGGG-CC-----UCC--UCGC--AUGG-UGG--GGCGGUGAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AAUCGUU-UUC-U-GCC-A-GUG-CCG--------------------------
BX548175.1/365281-365377     GACU-CGG-A--CCC--AUGC--GGCC-GCG--ACGCCUAAAU-CUGGUCAGGACC-GGAAGGGAGCAGCCACACGGGAUG-CUC-G-UGA-C-AGG--CG-U-GGAC----UCCGGGUCACC----
BX548174.1/1263424-1263344   CUCG-GC-----CUU--UCGC--GGUU-UUA--ACGCCCAAAC-CUGGUCAGGAUC-GGAAGGUAGCAGCCACAAGGGAUG-CUU-G-AGG-C-AGG--CG-A--------G---------------
AE017197.1/1090177-1090275   AAUU-AUA-CUAGUA--GUG---GGCA-UUG-CUCUUGCUUAG-UUGGUCAGAUCU-GAAAAGAAGCAGCCAG-AGUAAGA-UUC-U-GUG-GG----UCA-U-UACU---AGUAUCGUUGCUU---
BX927148.1/256435-256523     ---G-GAU----CCC--GUGC--GGCG-UUU-AUCUUGUGAAC-UCCCCCAGGGCA-GGAAUGCAGCAAGGGUCAGCGAGC-UCU-G-ACG-G-GUG--CG-C-GGG------AUCCCCU-------
CP000393.1/2447402-2447475   ---C-A-----A--------C---------A-----CCUAAAC-CUUGUCAGGACC-GGAAGGUAGCAGCAACACGGGAUG-CUUGU-AGU-AGGCG----------U-------UGACUCCGGGUC
CP000413.1/387308-387396     --------------U--GGGC--AAUG-UCC-GACCUCCAAAU-UGUGUCAGGACC-GGAAGGUAGCAGCACUAAGGUUGC-UUG-G-ACA-U-GUG--CC-U-UUUU---UUGAGAAAUUAA----
CP000117.1/5535760-5535663   GACC-UGG-A--UCU--AUGC--GACU-CCA--ACGCCUAAAC-CUUGUCAGGACC-GGAAGGUAGCAGCAACACAGGAUG-CUU-G-UAG-U-AGG--CG-U-AGUC----UCCGGGUCGCCC---
CP000086.1/2494952-2495047   GACG-GGC-C--UCC--UCGC--AUGG-UGG--GGCGGUCAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AGCCGUU-UUC-C-GCC-A-GUG-CCG-A-GGGU--CGGGCUCGUC-------
AE009948.1/408906-408982     ----------------GGAGC--AACA-UUU--ACUCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUG-CUA-A-AUG-U-GUG--CU-C--------------UUUUU-----
CR848038.1/439144-439245     GUUG-GGG-A-CCUU--UUAA-GAGAA-GAG--GCCUACGAAC-CGGGUCAGGACU-GGAAGGUAGCAGCCCUAAGAAGUG-CUU-U-CUU-U--UG-CUA-G-GAGU--GUUCUCCAACUUAC---
CP000053.1/1454209-1454303   UUAU-GCU-A--GUA--GUG---GGCA-UUG-UGCCUGUUUAG-UCGGUCAGGUCU-GAAAGGAAGCAGCCAG-AAUGGGA-UUC-G-AUG-GG----UCA-U-UAC-----UAGCAUUAUUCU---
BA000022.2/1832234-1832327   GGCU-CGG-A--CUC--AUGC--GAUU-ACA--ACGCCCAAAU-CUUGUCAGGACC-GGAAGGUAGCAGCAAUAAGGGAUG-CUU-G-UGG-U-AGG--CG-U-GAAC----UCCGGGCU-------
CP000458.1/2030969-2030891   -----CGG-GCCUCC--UCGC--AUGG-UGG--GGCGGUGAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AAUCGUU-UUC-C-GCC-A-GUG-CCG--------------------------
CP000829.1/194709-194806     -AUA-AUA-G--GCG--GAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C-UUUU---UUUGUUGACUUU----
ABXF01000041.1/51954-51857   -GAG-AGG-U-UGGC--GCGG--GCAG-GCG--CCUCGCCAAC-CUGGUCAGGUCC-GGAAGGAAGCAGCCAC-AACGAGC-CCC-G-CUU-G-GGU--CGAU-GUCC---AGCCUCUCACUU----
AE004092.1/190327-190424     -AUA-AUA-G--GCG--GAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C-UUUU---UUUGUUGACUUU----
AJ235273.1/216698-216784     -GCU-A------GUA--GUG---GGCA-UUG-CUCUUGCUUAG-UUGGUCAGGUCU-GAAAAGAAGCAGCCAG-GGUAAGA-UUC-U-GUG-GG----UCA-U-UAC--------UAGUAUCA----
CP001127.1/532559-532656     UGUU-GGU-U--CUC--CCGC--AACG-CUA--CUCUGUUUAC-CAGGUCAGGUCC-GGAAGGAAGCAGCCAA-GGCAGAU--GA-C-GCG-U-GUG-CCG-G-GAUG---UAGCUGGCAGGGC---
AM233362.1/1648565-1648468   ACUU-GGU-U--UCC--ACGC--AAUG-AUA--GAUUGUCAAC-CCCGCCAGGUCU-GGAAGGAAGCAACGGU-AACUUUU--GA-U-UCA-U-GUG-CCG-U-GUCA---AGGCUAAGUCAGC---
CP000013.1/484623-484720     CCUA-GGA-C--CCG--UACU--AUCA-AGU--GUUGCUAAAC-CCCGUCAGGACU-GGAAGGUAGCAGCGGU-AAGCGAU-UUU-U-UUG-G--UG-AGU-A-CGCA---AGUCUUAGGUUGA---
CP000261.1/198467-198564     -AUA-AUA-G--GCG--GAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C-UUUU---UUUGUUGACUUU----
CP000712.1/1786696-1786793   CAUC-GGU-C--CCC--CCGC--AUUG-AUU--ACCCGUUAAC-CUGGUCAGGCCC-GGAAGGGAGCAGCCAU-AGCGGGA--AC-A-UCG-A-GUG-CCG-G-GGUG---UGGCUGGUGGGGC---
CP000076.1/2115321-2115418   CAUC-GGU-C--CCC--CCGC--AACG-AUU--ACCCGUGAAC-CUGGUCAGAGCC-GGAAGGCAGCAGCCAC-AGCGGGA--AC-A-UUG-U-GUG-CCG-G-GGUG---UGGCUGGUGGGGU---
M31831.1/60-155              ---G-G--CC--CCU--ACGU--GGUG-UCA-UCUCGCUGAACUUCCCCCAGGACC-GGAAGGUAGCAAGGGU-AGGUGGGCUCU-G-GCA-G-GUG--CG-U-GAGG---GG--UCUUCAC-GUU-
BX897700.1/281770-281674     -GAG-GUU-G--GUG--GUGG--ACGC-ACU--GCUCGCCAAC-CGGGUCAGGUCU-GGAAAGAAGCAGCCCC-AACGAGUUCUG-G-UAC-G-GGU--CA-U-CGUU---CCAGCCUCCUAU----
CT573213.2/674159-674108     --------------------------------------UGAAC-CCCCCCAGGGCC-GGAAGGCAGCAAGGGU-AAGCGGG-CUC-U-GAC-G-GGU-G----------------------------
CP001015.1/23929-24010       AUA---------GUG--GAGC--AACA-GUU--CUGCGUGAAG-CGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUU-UGA-A-UUG-U-GUG--CU-C-UUUUU------------------
CP000323.1/1769428-1769334   CAUU-GGU-A--GCC--UCGC--AACA-UUG--UUCUAUGAAU-CCCGCCAGGACC-GGAAGGUAGCAACGGU-AAUAGUU--AU-A-AUG-U-GUG-CCG-A-GGAU---GUGCUGAUGG------
AF496545.1/292-382           --------------U--GGGC--AAUG-UUC-GACCUCCGAAG-CGUGUCAGGACC-GGAAGGUAGCAGCACUAAGGUCGC-UUG-G-ACA-U-GUG--CC-C-UUUAU-UUAGCAAUUAACA----
CP000260.1/196467-196564     -AUA-AUA-G--GCG--GAGC--AACA-CUU--GUGCGUGAAG-UGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUUUUCG-G-GUG-U-GUG--CU-C-UUUU---UUUGUUGACUUU----
CP000698.1/5002851-5002906   UGGG-C------CCC--ACGC--AACG-GAA--GGUUACGAAC-UCCGUCAGGUCC-GGAAGGAAGCAGCG-----------------------G--------------------------------
ACIS01000002.1/252560-252659 GGCG-GGC-C--UCC--CCGC--AUUG-CAC--AAUAGCGAAC-CUGGUCAGGUCC-GGAAGGAAGCAGCCAC-AGUUAUU-CAG-U-GCA-A-GUG-CCG-G-GGGU--CGGGCUCGCCACCC---
CP000489.1/1806299-1806339   -----------------------------------UCGCCAAC-CCGGUCAGGUCC-GGAAGGAAGCAGCCGU-AACGA------------------------------------------------
AM286690.1/2023249-2023160   --UC-GGU-C--CCC--CCGC--AACG-AUA--AGCUGCGAAC-CCCGCCAGGCCC-GGAAGGGAGCAACGGU-AGCAGUG--GA-C-UUG-U-GUG-CCG-G-GGUG---CGGCUGG---------
CP001217.1/16624-16528       UAUU-UGG-A--CCU--AUGC--AAUA-GGA-AUUUAGGGUAA-CGCUUCAGGGUA-GGAAUACAGCAGAGUC-CCCUAAU--UU-C-UUG-U-GUG-CCU-U-AGCC---AUCUGAAUAGG-----
CP000155.1/2681699-2681772   --------------------C---------------CGUGAAC-CUGGUCAGGCCC-GGAAGGGAGCAGCCAC-AGCGGUG-GAU-C-UGU---GUG--CC-G-GGGU--GUGGCUGGUAGG-GC--
CP000050.1/3890129-3890032   CCGU-CGG-U--CCC--UCGC--GACG-CUA--GAUCGAAAAU-CCCGCCAGGGCC-GGAAGGCAGCAACGGU-AUCGAUU--GA-U-GCG-G-GCG-CCG-A-GGUC---AACCGGCGGGGAC---
CP000030.1/1132360-1132271   ---G-GGC-G--GUG--CGA---GCAG-AUU--GCGCGUGAAG-UCGGUCAGGUUA-GAAAUAAAGCAGCCGU-AGCGUCG-UCU-U-UCU-GG--G--UU-G-CGCU---UCCCAC--UGUU----
AE000511.1/16758-16660       UAUU-UAG-A--CCU--AUGC--AAUA-GGA-UUUUAGGGUAA-CGCUUCAGGGUA-GGAAUACAGCAGAGUC-CCCUAAU--UU-C-UUG-U-GUG-CCU-U-AGCC---AUCUGAAUAGGAG---
AE017196.1/1020414-1020495   ------------GGU--AUGC-AGGCA-AAA--ACUCUGUAAU-UUGGUCAGAUCA-GAAAUGAAGCAGCCAUAUCAGAAC--CU-U-UUG-G-GUU-GCA-U-ACC----------UAUU------
CP000352.1/2315225-2315324   GACG-GGC-C--UCC--UCGC--AUGG-CGG--CGCGGUCAAC-CUGGUCAGGUCG-GGAACGAAGCAGCCAC-AGCCGUU-UUC-C-ACC-A-GUG-CCG-A-GGGU--CAGGCUCGUCCCCC---
AE014295.3/1448227-1448137   ---A-GCC----UCC--ACGC--GGCG-CUA-UGUCACCCAAC-UCCCCCAGGGCA-GGAAUGCAGCAAGGGU-AAGUGGCCUCU-G-ACG-G-GUG--UG-U-GGA------GGUUUUCUU-----
CP000325.1/4792690-4792604   ---A-GGA-C--CCC--GCGC--GGCG-UCU-AUCCUGUGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGUCAAUGGGC-UCU-G-UCG-G-GUG--CG-C-GGG-----GUCC-----------
CP000671.1/1242908-1242809   UUCU-CGG-U--CUC--UCGC--AACG-GUG--UCUGGUUUAC-UCGGUCAGGUCC-GGAAGGAAGCAGCCAA-AGUCGGA-AUU-A-CUG-U-GUG-CCG-A-GAAG--AAGCUGGGAAGGUU---
CP000416.1/630383-630437     -------------------GC--AAGG-GUG-GGCUUACGAAU-CGUGUCAGGUCC-GGAAGGAAGCAGCACU----AAGU-UU----------G--------------------------------
CP000605.1/1473939-1473850   AGCC--------UCC--ACGC--GGCG-CUA-UGUCACCCAAC-UCCCCCAGGGCA-GGAAUGCAGCAAGGGU-AAGUGGCCUCU-G-ACG-G-GUG--UG-U-GGA---------GGUUUUCU---
ACFI01000013.1/131871-131958 -GU--GGA-C--CCC--GCGC--GGCG-UCU-AUCCUGUGAAC-UCCCCCAGGGCC-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-UCG-G-GUG--CG-C-GGG-----GUCC-----------
AE007317.1/24632-24708       ----------------GGAGC--AACA-GUU--CUGCGUGAAG-CGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUU-UGA-A-UUG-U-GUG--CU-C--------------UUUUU-----
CP001173.1/16513-16415       UAUU-UAG-A--CCU--AUGC--AAUA-GGA-UUUUAGGGUAA-CGCUUCAGGGUA-GGAAUACAGCAGAGUC-CCCUAAU--UU-C-UUG-U-GUG-CCU-U-AGCC---AUCUGAAUAGGAG---
CR931997.1/2353027-2352932   ---G-G----AUUCC--GCGC--GGCG-UGU-AUCUUGUGAAC-UCCCCCAGGGCA-GGAAUGCAGCAAGGGUCAACGAGC-UCU-G-ACG-G-GUG--CG-C-GGGG---U---CCCCUUUUUUAU
CP000474.1/687242-687155     ---G-GCC-C--CUC--AUGU--GGCG-UCA-UCCUGUUGAAC-UCCCCCAGGACC-GGAAGGUAGCAAGGGU-AGAUGGGCUCU-G-GCG-G-GUG--CA-U-GAG-----GGGUC----------
BA000019.2/1368751-1368654   GACC-UGG-A--UCU--AUGC--GACU-GCA--ACGCCUAAAC-CUUGUCAGGACC-GGAAGGUAGCAGCAACACAGGAUG-CUU-G-UGG-U-AGG--CG-U-AGUC----UCCGGGUCGCCC---
AP010655.1/1760060-1759988   --------------G--GAGC--AACA-GCU--UUGCGUGAAG-CGGGUCAGGGGA-GGAAUCCAGCAGCCCUAAGCGAUG-UAA-G-CUG-U-GUG--CU-C-U----------------------
CP002420.1/1285149-1285240   -GCG-GGU-C--UCC--CCGC--AUGG-CAA--AUCGGAACAC-CGGGUCAGGGGC-GGAAGCCAGCAGCCCA-CUCCAAU---G-C-GCC-A-GUG-CCG-G-GGGU--UUGGCCCGC--------
AE016795.3/3219836-3219740   CUCU-GGU-C--CUC--UCGC--AACA-AUA--GUUCGUGAAC-UCGGUCAGGUCC-GGAAGGAAGCAGCCGC-AGCGAAU--GA-C-UUG-U-GUG-CCG-G-GAUG---UGGCUGGGGUCC----
CP001872.1/468196-468276     ---G--------CCA--UUAC--AACA-AUU--AACAC-GAAC-CAUGUCAGGUCA-GAAAUGAAGCAGCAUUAA-GUAUC-UUA-A-UUG-U-GUG--UA-A-UGG---------CUUUU------
AE008692.2/868927-869021     UGGA-AG----UCGG--GCGG--ACGG-UGC--UGUCGCCAAC-CCGGUCAGGUCC-GGAAGGAAGCAGCCGU-AACGAAU-UUG-U-AUC-G-GGU--CG-U-UCCG---G--CUUCCACGUC---
JN638551.1/118-27            ---G-GAC----CCC--GCGC--GGCG-UCU-AUCCUGUGAAC-UCCCCCAGGGCU-GGAAGGCAGCAAGGGUCAACGGGC-UCU-G-UCG-G-GUG--CG-C-GGG------GUCCCCUUCA----
CP001617.1/601161-601244     ---C--------AAA--AGGC--AAGG-GUG-GAUUUACGAAU-CGUGUCAGGUCC-GGAAGGAAGCAGCACUAAGUUUGC-UUC-A-UCU-U-GUG--CC-U-UUU---------GUUUU------
#=GC SS_cons                 :::<.<<<.<..<<<..<<<<..-<<<.<<<..<<<<<<<---.<<<<<----<<<.____>>>---->>>>>.>>>>>>>.-->.>.>>>.>.>--..>>.>.>>>-...->>>>>::::::....
#=GC RF                      uaug.ggg.c..ccc..gcGc..Aacg.cca..ccccgccAAc.ccgGUCAGGgCc.GGAAgGcAGCAGCcgg.ggcgggg.uuu.g.gcg.u.gUG..Cg.c.gggu...ugccccuuuuuu....
//
# STOCKHOLM 1.0

#=GF AC   RF00170
#=GF ID   msr
#=GF DE   Retron msr RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   35.00
#=GF TC   39.10
#=GF NC   33.00
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.86 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF RN   [1]
#=GF RM   12892895
#=GF RT   msDNA-St85, a multicopy single-stranded DNA isolated from Salmonella
#=GF RT   enterica serovar Typhimurium LT2 with the genomic analysis of its retron.
#=GF RA   Ahmed AM, Shimamoto T
#=GF RL   FEMS Microbiol Lett 2003;224:291-297.
#=GF RN   [2]
#=GF RM   12459273
#=GF RT   A partial copy of msDNA from a new retron element is likely a
#=GF RT   retrotransposed DNA found in the myxobacterium Nannocystis exedens.
#=GF RA   Lampson BC, Xu C, Rice SA, Inouye S
#=GF RL   Gene 2002;299:251-261.
#=GF CC   Retron elements are found in a wide range of mainly Gram-negative
#=GF CC   bacteria. The retron encodes a reverse transcriptase that is responsible
#=GF CC   for the production of a small satellite DNA called msDNA (multi-copy
#=GF CC   single-stranded DNA). msDNA has both DNA (encoded by the retron msd gene)
#=GF CC   and RNA (encoded by the msr gene) components. The 5' end of msDNA is
#=GF CC   linked to an internal guanosine residue of the RNA strand by a 2'-5'
#=GF CC   linkage. The components of msDNA are poorly conserved in sequence between
#=GF CC   different organisms -- this family therefore represents only a subset of
#=GF CC   known msr genes. Despite considerable investigation, very little is known
#=GF CC   about the function of msDNA, the mobility of retron elements, or their
#=GF CC   effect on the host cell.
#=GF WK   Retron
#=GF SQ   9


X60206.1/2132-2205         CACCCUUAGCGAGA---GGUUUAUCAUUAA----GGUCAACCUCUGGAU-GUUGUUUCGGC-AUCCUGCAUUGAAUCUGAGUU--
X62583.1/626-698           AAACUUUUUCGAUA---GCAUUAGCUG-------GUUACAGGUCUGGCG-UGUGUUUCGCCAGGCCCAGUUGCCACGUAAU-GUG
AF261825.2/44164-44233     ACUCUUUAGCGUUA---GGCUUUG----------AUUUAUAGCCUUGUCGAGCGUUUCGCCAGACAC--UAACUUAUUGAGUACU
Z12832.1/542-622           GCUCUUUAGCGUUUUAUGGAUUUACCACCUGAUUGGUCA-AAUCUAGUUGGGCGUUGCGCA-AACUC--UAAUUUAUUGAUUACA
AB079134.1/692-757         GCUCUUUAGCUUA----GGACG------------AAUUU-CGUCUAGUCGGGUGAUUAGCCAGACUC--UAACUUAUUGAACGGG
U02551.1/12-76             ACUCUUUAGCGUU----GGAC-------------GGUUA-CGUCUAGUCGGGUGAUUAGCCAGACUC--UAACUUAUUGAACGUA
AAUT01000053.1/25963-26033 GCUCUUUAGCGAAU---GGACUACACA-------UAUUA--GUCUAGUCGGGCGUUUAGCCAGACUG--AAAUUUAUUGAACGAC
AACY022254679.1/14-79      GCUCUUUAGCUUA----GGACG------------AAAUC-CGUCUAGUCGGGUGUUUAGCCAGACUC--UAAAUUAUUGAACGAC
AALE02000035.1/1983-2051   GCUCUUUAGCGUAU---GGACGGU----------UUUUG-CGUCUAGUCGGGCGGUUAGCCAGACUC--UAACUUAUUGAGCACU
#=GC SS_cons               ::<<<<<<<-----...----------.......-----.-----<<<<-<<<<___>>>>->>>>-..------->>>>>->>:
#=GC RF                    gCucuUUAgCGuua...GGAUUauCca.......ggUua.cGUCUgGucGgGuGUUUCgCcAgaCcC..UAAcUUAuUGAaugaa
//
# STOCKHOLM 1.0

#=GF AC   RF00171
#=GF ID   Tombus_5
#=GF DE   Tombusvirus 5' UTR
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones SR
#=GF SS   Published; PMID:11162089
#=GF GA   43.00
#=GF TC   43.20
#=GF NC   39.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0039694; viral RNA genome replication;
#=GF RN   [1]
#=GF RM   11162089
#=GF RT   An RNA domain within the 5' untranslated region of the tomato bushy stunt
#=GF RT   virus genome modulates viral RNA replication.
#=GF RA   Wu B, Vanti WB, White KA
#=GF RL   J Mol Biol 2001;305:741-756.
#=GF RN   [2]
#=GF RM   13130137
#=GF RT   A second functional RNA domain in the 5' UTR of the Tomato bushy stunt
#=GF RT   virus genome: Intra- and interdomain interactions mediate viral RNA
#=GF RT   replication.
#=GF RA   Ray D, Wu B, White KA
#=GF RL   RNA 2003;9:1232-1245.
#=GF RN   [3]
#=GF RM   15367615
#=GF RT   Structural properties of a multifunctional T-shaped RNA domain that
#=GF RT   mediate efficient tomato bushy stunt virus RNA replication.
#=GF RA   Ray D, Na H, White KA
#=GF RL   J Virol 2004;78:10490-10500.
#=GF CC   Tomato bushy stunt virus is the prototype member of the Tombusviridae
#=GF CC   family. In addition to viral proteins p33 and the RNA-dependent RNA
#=GF CC   polymerase p92, and unknown host factors, RNA signals within the UTRs are
#=GF CC   necessary for genome replication. 2 RNA domains in the 5' UTR have been
#=GF CC   reported [1,2], a 5' T-shaped domain (TSD) followed by a stem-loop (SL5)
#=GF CC   and a downstream domain (DSD). These domains are combined into a single
#=GF CC   family here. Reference [2] proposes that TSD-DSD interactions are involved
#=GF CC   in the mediation of viral RNA replication. The full alignment of this
#=GF CC   family contains a number of defective interfering (DI) deletion mutants,
#=GF CC   used to study RNA virus replication.
#=GF WK   Tombusvirus_5'_UTR
#=GF SQ   9


AY163842.1/2-137 GAAAUUCUCCAGCCU-----GACC---------------AGGUGGUGAGUUGCGG----UGUUGUCUACCGUAGAGGAUUUCUCUCGU----GCCUUGUU-----------ACGGGUUUGAAGGGCGAGCCUAUCU---UC-GGA-------------GGGUAAAUUGUAACUUUCGCCAAACAGG-ACUAUG
X15511.1/2-163   GAAAUCCUCCAGGACACCUCGACC--UAGGUUGUGU---AUCCGGUGAUUUGCGU--ACUGUUGCUUUGCGUAGAGGAUUUCUCUCCU----GUUCACUAC-----AUAUCAGGGGUUUGAAGGCAGGGUCUACCUU--UCGGGG-------------GGAUAAAUUGUAACUUCCUGCAAAUAAGCAAAAUG
AJ249740.1/2-171 GAAAUUCCCCAGGAUUUCUCGACC--UAGUUCGUUGUU-AUCUGGUGACUUGCGCUAACUGUUGCUUUGCGUAGAGAAUUUCUCUCCU----UUGUUAAUUCUUUGACUU-AGGGGUUUGAAGGUUGGGUCUACCUU--UCGGGG-------------GGAUAAAUUGUAACUUCCAACAAACAAGCAACAUG
AY100482.1/2-169 GAAAUUCCUCAG-AUUUCUC--CCUGUUGACCAGGAGUUAU-CGGUGAGUUGCGC---UUUGUGCUUUGCGUAAGGGAUUUCUCUCGUACAGGUACGAUCUCGGACCAGCUACGGGUUUGAAGGGUGAGCCUAUUCU--UCGGAA-------------GGGUAAAUUGUAACUUUCACC-AAUAAGCA--AUG
M21958.1/2-168   -AAAUUCUCCAGGAUUUCUCGACC--UAGUUCGUUU---AUCUGGUGACUUGCGC-UACCGUUGCUUUGCGUAGAGAAUUUCUCUCCA----UAAUUAUUAUCUUUAGUUGUGGGGUUUGAAGGUUGGGUCUACCUU--UCGGGG-------------GGAUAAAUUGUAACUUCCAACAAACAAGCGACAUG
M25270.1/3-154   -AAAUUCUCCAGGAUUUCUCAACC--UUGGUUGUGCU--AUCUGGUGACUUGCGC---GUGUUGUC-UGCGUAGAGAAUUUCUCUCCU----UAACCAA-----------AAGGGGUUUGAAGACUGGGUCUACCGC--UUGCGG--------------GAUAAAUUGUAACUUCCAGUAAACGA-CGACAUG
X62493.1/2-182   -AAAUUCUCCAGGAUUUCUCGACC--UCGGUUGUUUU--AUCUGGUAGUUUGCGCUAAUCUUCGCUUUGCGUAGGGAAUUUCUCUCCU----UAAUACAUUUCUG-AGUUAAGGGGUUUGAAGGUUGGGUCUAUCUU--UUGAGUUUAUCUCACUAGAGGAUAAAUUGUAACUUCCAACAAAUAAGCGAUAUG
U80935.1/2-169   GAAAUUCCCCAGGAUUUCUCGACC--UAGUACGUCU---ACCUGGUGACUUGCGCUGUCUGUUGCUUUGCGUAGGGAAUUUCUCUCCA----AUAUUAUUAUCUUUAAUU-UGGGGUUUGAAGGUUGGGUCUACCCU--UCGGGG-------------GGAUAAAUUGUAACUUCCAACAAAUAAGCGACAUG
X85215.3/2-146   GAAAUAUCUCAGGAUUU---GACC---------------GUCCGGUGAGUUGCGC---UUAUCACU-UGCGUAAGGUAUUUCUCUCUUCA--UUGUUCAUAUG--------GAGGGUUUGAAGGCUGAGUCUACCACAACUGUGG-------------GGAUAAAUUGUAACUUUCAGCAAACA-GUG--AUG
#=GC SS_cons     (((((((((,,<<<<_________..__________...>>>>,,,,,,,<<<<<..___________>>>>>))))))))),<<<<<...._____________._____>>>>>,,,,,,,<<<<<-<<<-<<<_..___>>>.............>>>------------->>>>>::::::::::::::
#=GC RF          GAAAUuCccCAgGauUUCUCGACC..UaGuuuguuu...auCcGGUGAuUUgCGc..auUgUUGcUUUgCGuAggGaAUUUCUCuCcu....uuauuauuuuuuu.aauuaagGgGUUUGAAGGcuGgGuCuAcCcU..UcGgGg.............gGaUAAAUUGUAACUUcCagCAAAuAAGCaAuAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00172
#=GF ID   CAESAR
#=GF DE   ctgf/hcs24 CAESAR
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Published; PMID:11032028
#=GF GA   45.00
#=GF TC   48.80
#=GF NC   38.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   10350062
#=GF RT   Involvement of cis-acting repressive element(s) in the 3'-untranslated
#=GF RT   region of human connective tissue growth factor gene.
#=GF RA   Kubota S, Hattori T, Nakanishi T, Takigawa M
#=GF RL   FEBS Lett 1999;450:84-88.
#=GF RN   [2]
#=GF RM   11032028
#=GF RT   Identification of an RNA element that confers post-transcriptional
#=GF RT   repression of connective tissue growth factor/hypertrophic chondrocyte
#=GF RT   specific 24 (ctgf/hcs24) gene: similarities to retroviral RNA-protein
#=GF RT   interactions.
#=GF RA   Kubota S, Kondo S, Eguchi T, Hattori T, Nakanishi T, Pomerantz RJ,
#=GF RA   Takigawa M
#=GF RL   Oncogene 2000;19:4773-4786.
#=GF RN   [3]
#=GF RM   12674494
#=GF RT   Conserved repressive regulation of connective tissue growth
#=GF RT   factor/hypertrophic chondrocyte-specific gene 24 (ctgf/hcs24) enabled by
#=GF RT   different elements and factors among vertebrate species.
#=GF RA   Mukudai Y, Kubota S, Takigawa M
#=GF RL   Biol Chem 2003;384:1-9.
#=GF CC   The 3' UTR of human connective tissue growth factor/hypertrophic
#=GF CC   chondrocyte specific 24 (ctgf/hcs24) mRNA has been shown to repress ctgf
#=GF CC   gene expression [1]. Reference [2] identified a minimal RNA element,
#=GF CC   predicted to form a stable secondary structure, which acts as a
#=GF CC   post-transcriptional cis-acting element of structure-anchored repression
#=GF CC   (CAESAR), probably through direct interactions with as yet unknown nuclear
#=GF CC   factors.
#=GF WK   Ctgf/hcs24_CAESAR
#=GF SQ   9


U43523.1/3405-3479   AUGGAGACAUGGCAU---AGAGGCAGA----GAAACACACUUCAA-------AGACUUUUUCACUU-GAAAUAACUUUGCAUCUCAUUGC
U70060.1/1339-1423   CAGUAGCACAGGUUAUUUAAAGCCAGAGAGAGUGAGACCCAUGAACACUUG-AGACUGU--CACUU-GAACU-GAUUCACAUCUCAUUUU
U70060.1/1239-1321   AUGGAGACAUGGCCU---AAAGCCAGAGAGAGUGAGAC-CAUGAACACUUG-AGACUGU--CACUUUGAACUUGAUUCACAUCUCAUUUU
AF309555.1/3099-3180 AUGGAGACAUGGCCU---AAAGCCAGAGACAGUGAGACACGUGAACAUUUU-AGGCUGU--CACUU-GAAUC-GAUUCACAUCUCAUUUU
X78947.1/1179-1258   ACGGAGACAUGGCAU---GAAGCCAGAGA--GUGAGAGACAUUAACUCAUU-AGACUGG--AACUU-GAACU-GAUUCACAUCUCAUUUU
AF463517.1/1097-1169 AUGGAGACAUGGCAU---AAAGGCA------GAAGGAGACGCUAACU-----AGAUUCUC-AACUU-GAACU-GAUUUGCAUCUCAUUUU
AJ298335.1/1190-1262 AUGGAGACAUGGCAU---AAAGCCA------GAAGGAGACGCUAACU-----AGAUUCUC-AACUU-GAACU-GAUUUGCAUCUCAUUUU
M70641.1/2922-3001   ACGGAGACAUGGCGU---AAAGCCAGGAA--GUAAGGGACACGAACUCAUU-AGACUAU--AACUU-GAACU-GAGUUGCAUCUCAUUUU
AB023068.1/1240-1320 AUGGAGACAUGGCGU---AAAGCCAGGGA--GUAAGGGACACGAACUCAUUUAGACUAU--AACUU-GAACU-GAGUUACAUCUCAUUUU
#=GC SS_cons         :::((((,,<<<<__...___>>>>,,,,..<<<<________________._______.._____._____.___>>>>,)))):::::
#=GC RF              AuGGAGACAuGGCaU...AAAGCCaGAGA..GugAGAcACaugAACuCuUu.AGACUgU..aACUU.GAAcU.GAUUcaCAUCUCAUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00173
#=GF ID   Hairpin
#=GF DE   Hairpin ribozyme
#=GF AU   Ditzler M; 0000-0003-3108-4596
#=GF SE   Ditzler M
#=GF SS   Published; PMID:7966321
#=GF GA   65.00
#=GF TC   73.30
#=GF NC   38.10
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.92 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF RN   [1]
#=GF RM   7966321
#=GF RT   Structure-mapping of the hairpin ribozyme. Magnesium-dependent folding and
#=GF RT   evidence for tertiary interactions within the ribozyme-substrate complex.
#=GF RA   Butcher SE, Burke JM
#=GF RL   J Mol Biol 1994;244:52-63.
#=GF RN   [2]
#=GF RM   9207012
#=GF RT   Plant pathogenic RNAs and RNA catalysis.
#=GF RA   Symons RH
#=GF RL   Nucleic Acids Res 1997;25:2683-2689.
#=GF RN   [3]
#=GF RM   11441810
#=GF RT   Ribozyme structures and mechanisms.
#=GF RA   Doherty EA, Doudna JA
#=GF RL   Annu Rev Biophys Biomol Struct 2001;30:457-475.
#=GF RN   [4]
#=GF RM   12440983
#=GF RT   The hairpin ribozyme: from crystal structure to function.
#=GF RA   Ferre-D'amare AR, Rupert PB
#=GF RL   Biochem Soc Trans 2002;30:1105-1109.
#=GF CC   The hairpin ribozyme, like the hammerhead (RFAM:RF00008 and RFAM:RF00163),
#=GF CC   is found in RNA satellites of plant viruses. It was first identified in
#=GF CC   the minus strand of the tobacco ringspot virus (TRSV) satellite RNA where
#=GF CC   it catalyses a self-cleavage reaction to process the products of rolling
#=GF CC   circle virus replication to unit-length satellite RNA. The structure
#=GF CC   consists of 2 domains, A and B. The 3' arm of domain A, which closes
#=GF CC   helices 1 and 2, contains the cleavage site and is linked to helix 3 of
#=GF CC   domain B by a linker of variable length and sequence. This region is thus
#=GF CC   not included in this family. The hairpin ribozyme has been identified in
#=GF CC   only 3 plant satellite RNAs -- from TRSV, chicory yellow mottle virus
#=GF CC   (CYMV) and arabis mosaic virus (ARMV).
#=GF WK   Hairpin_ribozyme
#=GF SQ   5



M21212.1/157-106 CAACAGCGAAGCGGAACGGCGAAACACACCUUGUGUGGUAUAUUACCCGUUG
M14879.1/224-175 AAACAGAGAAGUCAACCAGAGAAACACACGUU--GUGGUAUAUUACCUGGUA
D00685.1/306-255 CAACAGCGAAGCGCGCCAGGGAAACACACCAUGUGUGGUAUAUUAUCUGGCA
D00721.1/306-255 CAACAGCGAAGCGCGCCAGGGAAACACACCAUGUGUGGUAUAUUAUCUGGCA
M17439.1/226-177 AAACAGAGAAGUCAACCAGAGAAACACACGUU--GUGGUAUAUUACCUGGUA
#=GC SS_cons     ::::::::::::::<<<<<-------<<<_____>>>--------->>>>>:
#=GC RF          cAACAGcGAAGcgagCCaGaGAAACACACcuUGUGUGGUAUAUUAcCuGGcA
//
# STOCKHOLM 1.0

#=GF AC   RF00174
#=GF ID   Cobalamin
#=GF DE   Cobalamin riboswitch
#=GF AU   Barrick JE
#=GF AU   Breaker RR; 0000-0002-2165-536X
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Barrick JE, Breaker RR
#=GF SS   Predicted; PFOLD
#=GF GA   30.00
#=GF TC   30.00
#=GF NC   29.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00101
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0031419; cobalamin binding;
#=GF RN   [1]
#=GF RM   12787499
#=GF RT   Riboswitches control fundamental biochemical pathways in Bacillus subtilis
#=GF RT   and other bacteria.
#=GF RA   Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR
#=GF RL   Cell 2003;113:577-586.
#=GF RN   [2]
#=GF RM   12923257
#=GF RT   Regulation of the vitamin B12 metabolism and transport in bacteria by a
#=GF RT   conserved RNA structural element.
#=GF RA   Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS
#=GF RL   RNA 2003;9:1084-1097.
#=GF RN   [3]
#=GF RM   14704351
#=GF RT   Coenzyme B12 riboswitches are widespread genetic control elements in
#=GF RT   prokaryotes.
#=GF RA   Nahvi A, Barrick JE, Breaker RR
#=GF RL   Nucleic Acids Res 2004;32:143-150.
#=GF RN   [4]
#=GF RM   28483920
#=GF RT   Cobalamin riboswitches exhibit a broad range of ability to discriminate
#=GF RT   between methylcobalamin and adenosylcobalamin.
#=GF RA   Polaski JT, Webster SM, Johnson JE Jr, Batey RT
#=GF RL   J Biol Chem. 2017;292:11650-11658.
#=GF CC   Riboswitches are metabolite binding domains within certain messenger RNAs
#=GF CC   that serve as precision sensors for their corresponding targets.
#=GF CC   Allosteric rearrangement of mRNA structure is mediated by ligand binding,
#=GF CC   and this results in modulation of gene expression [1]. This family
#=GF CC   represents a cobalamin riboswitch (B12-element) which is widely
#=GF CC   distributed in 5' UTRs of vitamin B(12)-related genes in bacteria.
#=GF CC   Cobalamin in the form of adenosylcobalamin (Ado-CBL) is known to repress
#=GF CC   expression of genes for vitamin B(12) biosynthesis and be transported by a
#=GF CC   post-transcriptional regulatory mechanism, which involves direct binding
#=GF CC   of Ado-CBL to 5' UTRs [2].
#=GF WK   Cobalamin_riboswitch
#=GF SQ   430


AF010496.1/39869-39652         GGCACCUUCGCGGCAGAUGGUU--CCCGGCCAAGCCAC---------------GCGCG----GCCGGGUG------AAAA--GGGAA-U-AC-G-G-UGUGGUGUAGGCAUCAGCCGCC------------AAAUCCGU-AACUGCCC-CC-GCAACUGUAA--GC-GG----------CGAGCACCCCCCGGCA-----------------------------ACCACUGGCCCCGACCGCG------------------------------------------------------GGG-CCGGGAAGGU---GGG--G-----AAGCCACGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAUCAGCGUCAUCAACCGC
AF010496.1/105318-105541       CCACUCAGGGCGGGCGCUGGUU--UCUGUCC----------------------UAUG------ACAGGCG------AAGA--GGGAA-U-GU-G-A-AGGGAAUUGCGACGGCUUUGCCGCGAAAC-----CCGACCGC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AGAGGGCGCCCCGAG------------------------------GCCACUGGC--ACCA------------------------------------------------------------G-CCGGGAAGGC---GGG--G-CG--ACCGUGAGGG---------------------------------------------------GACCCCCCCUCGCAUCCGC-AAGCCGGGAGACCUGCCAGCGCAUGGAUUUCGGGC
AF010496.1/116971-117194       GCUACUCCAACAGGCGAUGGU---UCCCA------------------------ACUGG----ACGGGAUU------AAUA--GGGAA-C-AC-G-G-UGAGGAUUACCCAUCAGGGGCC------------UAAUCCGU-GGCUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGACGACGGUCGAAG-----------------------------ACCACUGGCCCCCCCGAUCCACCGGGGAGAA------------------------------------------CGG-CCGGGAAGGU---GAC--C-CG--AGUUGAUCGA-----------------------------------------------------------------ACCGC-AAGUCAGGAGACCUGCCAUCGCUCUGGCGUCGCAA
AF193754.1/4343-4142           GCAAUGAGGAAGGAUUAAGGUU--CUUUGUC----------------------AUUG-----GCAAAGCU------AAGA--GGGAA-A-CU-G-G-UGCGAAAGAAUUUUC-------------------AAAGCCAG-UGCUGCCC-CC-GCAACUGUAA--AC-GG----------CGAGCAAAGAUCAAAAU----------------------------GCCACUGAUA-UUAU-----------------------------------------------------------UA-UCGGGAAGGC--UGAU--C-GG--ACGCGGUGAC------------------------------------------------------------------CCGUCAAGUCAGGAGACCUGCCUUAAACCAAGUCAUCCAC
AF193754.1/24966-24788         GGAAAUUUUUUUGCAUAGGGU---UUCCUUC----------------------GAGUG----AAGGAA--------AAUU--GGGAA-C-AA-G-G-UGC-------------------------------AAAACCUU-GGCUGCCC-CU-GCAACUGUAA--AC-AG----------UUGA--AACGCCAAAAA----------------------------GCCACUGAAU----C----------------------------------------------------------UAU-UCGGGAAGGC---GGU--U-GU--UUCGAUG---------------------------------------------------------------------CUGU-GAGCCAGGAGACCGACCCUAUGUAAUCGUUCCACG
AF263012.1/9229-9015           AGGCUGACCGGUGCAGCUGGUU--CGCCCUGUCCGC-----------------CAGGC----AGGGUGUCGC----AAGA--GGGAA-C-CC-G-G-UGG-------------------------------AAAUCCGG-GACUGC-C-CC-GCAGCGGUGA--GU-GGG---------AACGACCGCCGUCAUA-----------------------------CGCACUGGGCCCGGACG--------------------------------------------------------GGU-CUGGGAAGCG---ACG--G-CC--ACUAGGUGUC--------------------------------------------------UGCCCGGCAGACGUGCCCGC-GAGUCCGAAGACCUGCCCGCUGCCCGCACGCGACC
AF306632.1/382-181             GAUAAUCCAAGUCGUCGAGGUU--CUCCGGUUCCCA-----------------UUGAU----CCGGAGCU------AAGA--GGGAA-G-CC-G-G-UGC---------A---------------------AAUGCCGG-CGCUGC-C-CC-GCAACUGUAA--GU-GGC---------GAGCCGCUGUCCAACGAU---------------------------GUCACUGAAGCCUGCACG-------------------------------------------------------GCU-UCGGGAAGGC--CGGA--C-AG--CAGCGAUGAC------------------------------------------------------------------CAGC-AAGCCAGGAGACCGGCCCCGACAAUAUAUUGGUCC
AJ000758.1/1191-1370           UCAAACAGCAACAGUAAAGGU---GCCAA---------------------------------GAAGGCUU------AAUA--GGGAA-A-CU-G-G-UGA-------------------------------AAGACCAG-UACUGCCC-CC-GCAACUGUAA--GU-GU----------GGACGAACGAGUAUA------------------------------ACCACUGUGAAAAAA-----------------------------------------------------------UC-ACGGGAAGGU---UCU--C-AA--GUAGAAUGAU------------------------------------------------------------------ACAC-AAGUCAGGAGACCUGUCUUUAUUGUGAAGUUUCUA
AJ000758.1/1489-1668           CAUAUCGUGCAAAAAAAAGGUG--CGUAAUA----------------------UUUAC----AUUGCGUU------AAAU--GGGAA-GUCU-G-G-UGU-------------------------------GAAGCCAG-CGCGUA-C-CC-GCCACUGUGA--AG-A-----------GGAGCUGAUUGCAUUU-----------------------------GCCACUGUA------------------------------------------------------------------U-UCGGGAAGGC---GCA--A-UC--AAGUGAUGAA-------------------------------------------------------------------UCG-AAGUCAGGAAACCAGCCUUUUUCUAAUGCUAAGCU
AJ278144.1/22351-22163         CAGUAAUAUCCAGUUGUCGGU---CCUGC------------------------------------GAGUU------AAUA--GGGAA-U-CC-A-G-UGC-------------------------------AAAUCCGA-AACUGA-C-AC-GCAGCGGUAA--GG-AA----------AGGUGCGAUGAUUGCGUAAUGUG----------------------GACACGGUC--AUCC------------------------------------------------------------G-GUGGGUGGUC---AUC--U-CU--UUGUAUCUUC----------------------------------------------------------AGAUGCCCUUCU-AGGUCUGAAGACCUGUCGGUUAACGUCGCAUCUGG
AL583923.1/215513-215333       GUACUAUAUGCGACACUGUGUA--UCUGU------------------------AAAGG----CGAUGACG------AUGC--AGGAA-G-UC-G-G-UGC-------------------------------AAAGCCGG-CGCGGU-C-CC-GCCACUGUAA--UC-GG----------GGAGCGACCCUCGUAG-----------------------------GCCACGGCCA---------------------------------------------------------------UUG-GCUGGAAGGC---GAG--G-CA--AGCGGUGAU-------------------------------------------------------------------CCGA-GAGCCAGGAAACUCGCGUCAUCGCGUCCUGCUAAC
AL591978.1/19809-19999         UUAAAUAGGUCUUAUGUUGGU---GGAAUGU----------------------AUGUA----CAUUUCUG------AAAG--AGGAA-U-UC-G-G-UGC-------------------------------GAUGCCGA-AACUGCCC-CC-GCAACUGUAA--GG-UG----------GACAAGAAUCGAGAUA-----------------------------ACCACUGUACGUUUUUAG-------------------------------------------------------CGU-AUGGGAAGGU---UCG--A-UU--GUUGGAUGA-------------------------------------------------------------------AGCC-AAGUCAGGAUACUCGCCAAAUAAGACGGAAGCAAC
AL591978.1/56481-56658         GUACUAAACAACUAAAUAGGUG--AAU--------------------------------------AUAUU------AAUCC-GGGAA-A-GA-G-G-UGA-------------------------------AAAUCCUC-UACAGGCC-CUAGCUACUGUAA--UA-C-----------GGACGAAAACCAAACAUAU--------------------------GUCACUGGAA-GCAA-----------------------------------------------------------UU-CCGGGAAGAC---UGG--U-GA--GUAGGAUGAU-------------------------------------------------------------------GUU-AAGUCAGGAGACC-GCUUUUAUAUUCGAUAUCCAA
AL596167.1/167425-167616       UUAAAUAGGUCUUAUGUUGGU---GGAAUGU----------------------GUUUG----CAUUUCUG------AAAG--AGGAA-U-UC-G-G-UAU-------------------------------GAAGCCGG-AACUGCCC-CC-GCAACUGUAA--GG-UG----------GACAAGAAUUGAAAAUA----------------------------ACCACUGUGCGUUUUUGA-------------------------------------------------------CGU-AUGGGAAGGU---UCA--A-UU--GUUGAAUGA-------------------------------------------------------------------AGCC-AAGUCAGGAUACUCGCCAAAUAAGACGGAAGCAAC
AL596167.1/202425-202602       GUACUAAACAACUAAAUAGGUG--AAU--------------------------------------AUAUU------AAUCC-GGGAA-A-GA-G-G-UGG-------------------------------AAAUCCUC-UACAGGCC-CUAGCUACUGUAA--UU-C-----------GGACGAAAGCCAAACAUAU--------------------------GUCACUGGAA-GAAA-----------------------------------------------------------UU-CCGGGAAGAC---UGG--U-GA--GUAGGUUGAU-------------------------------------------------------------------GAU-AAGUCAGGAGACC-GCUAGUAUAUUCGAUAUCCAA
AL627279.1/139350-139157       CGGUAGCAUCCGUGGGCCGGU---CCUGU------------------------------------GAGUU------AAUA--GGGAA-U-CC-A-G-UGA-------------------------------AAAUCUGG-AGCUGA-C-GC-GCAGCGGUAA--GG-AA----------AGGUGAGAUGAGAGCGUAAGCA-----------------------GACACUGCC---UCC------------------------------------------------------------G-GCGGGAAGUC---AUC--A-UU--UCUGCUAUCC---------------------------------------------------AGUCAACGGAUAACCCUCC-AAGCCCGAAGACCUGCCGGCUAACGUCGCAUCUGG
AL672113.1/43141-43341         UGAUUGUGCGCAUGUCGUGGUU--CUCCGCGCGGCACUG--------------CCGUA----GCGGAGCU------AAGA--GGGAA-G-CC-G-G-UGC-------------------------------GAUGCCGG-CGCUGCCC-CC-GCAACUGUUA--GC-GG----------CGAGCCAAGCCCAUUGGU---------------------------GUCACUGAGGCGAACG---------------------------------------------------------GCC-UCGGGAAGAC---GGG--C-AG--AGGCUUUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCACGACGAACAACGUCCAC
AL939107.1/133849-134073       AGGCUGGCCCGUGCAGCUGGUU--CGCCCCGUCCGCCA---------------GGCGG----GAUGCGUCGC----AAGA--GGGAA-C-CC-G-G-UGG-------------------------------GAAUCCGG-GACUGC-C-CC-GCAGCGGUGA--GC-GGG---------AACGACCGCCGUCAUA-----------------------------CGCACUGGGCCCGACGUACCG----------------------------------------------------GGC-CCGGGAAGCG---ACG--G-CC--AGUAGGUGUC----------------------------------------------CUCCGGACAGGAGGGUGGGCCCGC-GAGUCCGAAGACCUGCCACCUGCCCGCGCGCGGAC
AL939107.1/140625-140436       -GGACGCUGAUGGGAUGAUGG---CCGGCGACAG-------------------GGCGA----CGACGGUC------C--G--AGGAA-G-CC-G-G-UGC-------------------------------GAAUCCGG-CGCGGU-C-CC-GCCACUGUGA--UC-GGU---------GAGCGGAUCCCGAAGUU----------------------------GCCACUGCCCCGGUA----------------------------------------------------------GGG-GCGGGAAGGC---CGG--G-AC--GAGCUGUGAC------------------------------------------------------------------CCGG-GAGCCAGGAAACUCACGUCGUCGCCUCCUCGACGG
AL939107.1/141879-142126       ACGCUGAUGCCCGCAGUUGGUU--CGCGCCUCCUGUCCGAUCAGGUC------UCGGC----GGCGCGACGC----AAGA--GGGAA-C-CC-G-G-UGG-------------------------------GAAUCCGG-GACUGU-C-CC-GCAGCGGUGA--GU-GGGA--------ACGAAAGCCGUCAACA------------------------------GCACUGGGCCCCAGAUGAGUUGG-------------------------------------------------AGC-CCGGGAAGC----GAC--G-GC--CGGUAGGUGC----------------------------------CCGCCGGUGAUCCGUGUCCCCGGUGAGCGCGCCCAC-GAGUCCGAAGACCUGCCACUGCGCCCGUACGCGAU
AL939107.1/147400-147583       CAGACCGUAGUAUCAGCGGGU---CAUCGCC----------------------GCG---------ACGGG------AGAC--AGGAA-G-CC-G-G-UGU-------------------------------GAAUCCGG-CACGGU-C-CC-GCCACUGUGA--CC-GG----------GGAGUGCACCCUUCGACAC--------------------------GCCACUGCGC--GCC-----------------------------------------------------------GC-GCGGGAAGGC--CAGG--G-AG--GAGCGUCGAU------------------------------------------------------------------CCGG-GAGUCAGGACACUGGCCUGUCGCGGGCCCGUUCCG
AL939125.1/243385-243171       CCUGCUUGUGCCCACCCCGGUG--GGAGCACUACUGUC---------------GCCAC----GCCUUGGU------GAAC--GGGAA-AUCC-G-G-UGU-------------------------------GAUGCCGG-UGCGGCCC-UC-GCCACUGUGAA-UC-GGG---------AAGUCCGGCUCCGGCCCUGACGGGCA-------------------GCCACUGGAUCGCUUGC--------------------------------------------------------GGU-CCGGGAAGGC---GGA--G-CA--CGGGCGGUGG---------------------------------------------------------------UACCCGU-AAGCCAGGAGACCGGCCAAGGCGCGUCGUCCAUCC
AY033236.1/563-353             GUGUAGGCUAGUAGUGCUGGUU--CGGCUGCCC--------------------CACGG----CAGUCGUCGC----AAGA--GGGAA-U-CC-G-G-UGU-------------------------------AAUUCCGG-AACUGU-C-CC-GCAGCGGUCA--AU-GG----------GAACGACACAACGUAA-----------------------------GGCACUGGGCGGCAA----------------------------------------------------------CGC-CUGGGAAGUA---GUA--G-UG--GAGGAAGUCG------------------------------------------------GGAGUGAUCUCGCAAUGCCCAU-GAGUCCGAAGACCUGCCAGCAGCGACAACAUCUGU
AY043208.1/560-782             UAUCUUUGCUCCCUGAUCGGU---UCCGAAUAGUCAUUC--------------CUCUA----UCCGGAUU------AAAA--GGGAA-U-CG-G-G-UGU-------------------------------AAAUCCCG-GACAGU-C-CC-GCUGCUGUGAA-GC-UCCGUC------UGAAUUUCCGAUAACAACUGUU-----------------------GCCACUGGGAUACCUUUUUGUAAAUAGAUAAGGA---------------------------------------GUCACCGGGAAGGC---GUC--G-GA--AACAAG----------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCGCUUAUCAAAGGCUGUUU
BX248334.1/308192-308010       CCACGCUCUGCAUGCCAAUAU---UCUUCCC----------------------GUCAGG---CGAUGACG------AUGC--AGGAA-G-CC-G-G-UGA-------------------------------GAAUCCGG-CGCGGU-C-CC-GCCACUGUCA--CC-GG----------GGAGCGACCCUCAUAA-----------------------------GCCACGGCC---ACA------------------------------------------------------------G-GCUGGAAGGC---GAG--G-CA--AGCAACGAU-------------------------------------------------------------------CCGG-GAGCCAGGAGACUCGCGUCAUCGCGUCCUGCCACC
BX248337.1/276050-275850       GGCAUCGAGCGGGGCAACGAUG--CUUCGC-----------------------------------GAG-----------A--GGGAA-C-CU-G-G-UGA-------------------------------GAAUCCGG-GACUGU-C-CC-GCAGCGGUAU--GC-AGGA--------ACGACCGCCGUCUUGGAAGUAGACA--------------------AGCACUGGUCUCAAC-----------------------------------------------------------GA-CUGGGAAGC----GAC--G-GC--CAGUAGGAGC-------------------------------------------------ACCCACCGGGUGCGAGCCUGC-GAGUCCGAAGACCUGCCAGCCGUGCCGGACGCGCC
BX248356.1/172244-172444       CUGUACAAAUCGCACCAAGGUG--UUAGUGUUG--------------------GGUGU----GUUGAAGU------GAUC--GGGAA-UGCC-A-G-UGC-------------------------------AAUUCUGGCAGCGGACC-CC-GCCACUGUAA--CC-GCAAAUUA----UGCCCAUUUCUA---------------------------------GCCACUGCAG----U----------------------------------------------------------CCU-GCGGGAAGGG---UAG--A-AA--GACACACUUU---------------------------------------------------------UUACUGGGCGCGG-UAGCCAGGAGACCGGCUUCAACAUUUUAUACGUAG
BX248357.1/28572-28772         UGUGUUACACAUUGAUUAGGU---GCAGCAU----------------------AGAAC----UGCUGC----------AU--GGGAA-U-CU-G-G-UGA-------------------------------AAAUCCAG-AGCUGA-C-GC-GCAGCGGUGA--AG-GUGCA-------AGUGAGUGCUUCAAUGUA---------------------------GCCACUGAGAGUAUAAAAA------------------------------------------------------CUC-UUGGGAAGGU---GAG--G-CA--AUUACUCUCG----------------------------------------------------------CGUAGAGCACCC-CAGUCCGAAGACCGGCCUAAUCAGAAACAUGUGCU
BX294140.1/211185-211419       UCCGAGGUGACUGAUUUGGUUU--CUGCC------------------------GAGU--------CAGUG------AACA--GGGAA-CUCC-G-G-UGA-------------------------------AAUUCCGG-GACGGU-C-CG-GCCGCUGUGU--GC-CGCCAG------AGAUCUUCCAAGUGAAGUCUCAUUGUUUGCUUUUCUAUUCA----GCCAUUGCUCGUGUUUUCGCGUUUCAACGUGAACG--------------------------------------UGA-GUGAGAAGGC---CAU--G-AG--CAAACAAAGU----------------------------------------------------------------GGUGGU-GAGUCAGAAGACCUACCUCGUACAAGACGUUUUGG
BX294144.1/76053-76292         GCAACGUUACGUGGUGCCGGU---GUUCCAA----------------------AUCUUG---GAUCACUGGG----AACA--GGGAA-CUUC-G-G-UGA-------------------------------GAUUCCGA-GACGGC-C-CG-GCCGCUGUAU--CC-GAU---------GCGAAGUUGCUGACUUGGCAACUUCCAAGCAAACAUUCCUCUUGUGCCAUUGUCGUUGAUCGGAAUUAUCCGUGA-------------------------------------------CGG-ACGAGAAGGC---GAG--C-GU--UUGCGAGUUU---------------------------------------------------------------GCAUCGG-GAGUCAGAAGACCUACCACGAAACGGACACUAUGU
BX569694.1/273573-273792       CCCCUAGGGUUUGGGUCUGGUU--UCAGCGGGGA-------------------UCAGC----CGCUGAUGGA----AACG--GGGAAAGAAC-G-G-UGC-------------------------------AAAUCCGU-CGCUGU-C-CC-GCAGCUGUAA--AG-CGUCCGGCCCCGCCGGCGUCAGUCAGAAC----------------------------G---CCCGCCAGGAGCACUAC----------------------------------------------------CGA-CGAGGAU--C---GAC--U-UU--GACCAAUCUU--------------------------------------------------CUGGCUUCUCCCCGGCCUCU-GCGCCAG----GCCGCCGUUGCCGCAUUGGCCUUG
BX571869.1/30799-30632         UUAAUACCACACCUUAAUGGU-----------------------------------------------GU------GGUU--GGGAA-G-GA-G-G-UGA-------------------------------AAGUCCUC-CGCAGCCC-CC-GCUGCUGUGA--UG-CU----------GACAACUCCGCUGAU------------------------------GCCACUGGUCGGAAA-----------------------------------------------------------GA-CUGGGAAGGU---UGC--G-GG--GAAGGGUGA-------------------------------------------------------------------CGCU-AAGCCAGAAGACCGACCUGACAGGCACGAGACAUU
BX572594.1/100625-100429       AAUACCGUGACCAGCGACGGU---UCCCG------------------------AAAG--------GGAUC------AAUA--GGGAA-C-GC-G-G-UGCGGGCUUUAGGGCUC-----------------UAUUCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCCAUUCGCCACAC-----------------------------GCCACUGGGCUUUCG-----------------------------------------------------------UC-CUGGGAAGGC---GGU--G-AA--CGGCAACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAGUCGUGGUCACACG
BX572595.1/86162-86360         GCUAGCGUGCCAAGCGAUGGU---CCUUCCG----------------------UCAG------GAAGGUG------AAAA--GGGAA-G-CC-G-G-UGGGAGGCGCGGUGCGUCUC--------------GAUCCCGG-AGCUGCCC-CC-GCAACUGUAA--GC-GA----------CGAGCCAUUGCCGAG------------------------------GCCACUGGGA----A----------------------------------------------------------UUC-CUGGGAAGGC---GGC--G-AA--UGGCGGCGAC------------------------------------------------------------------UCGC-GAGCCAGGAGACCUGCCAUCGCGUAUUGUGCUUUG
BX572595.1/100553-100338       UUUGAUCGCGCCCGUUCAGGUG--UGCCGGGA---------------------AUCGU----CCGGCA-----------CA-GGGAA-G-CC-G-G-UGCGGGCCCAAGCUUAUGGCCGCAAACCC-----AAAUCCGG-CGCUGCGC-CC-GCAACUGUGA--GC-GGU---------GAGCGAUCCUUCAAUCG----------------------------GCCACUGGGCAGCACU---------------------------------------------------------UGC-CCGGGAAGGC---GAA--G-GA--UUGCGACGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCGGCCUGAGUACGUCAUCUUCCA
BX572596.1/50556-50756         UCUGGUUUUGACGUCUUCGGUG--CCUCGCG----------------------UGCG--------AGGUG------AAACU-GGGAA-U-AC-G-G-UGCGGUGUUUUUCACC------------------UAAUCCGU-AGCUGCCC-CC-GCAACUGUAG--GC-GGA---------UCUGUCCGGAUCAUGUA----------------------------GCCACUGACGUCCUCG---------------------------------------------------------GCG-UCGGGAAGGC---GGU--C-CA--GGCGAUAU--------------------------------------------------------------------CCGU-GAGCCAGGAGACCGGCCGAAGACGGGAAGCAUCUA
BX572599.1/247113-247314       UUAACCCGAGGUUGUACCGGUG--CCUCUCG----------------------CCGA-----GAGAGGUG------AAAC--GGGAA-U-GC-G-G-UGCGGGGCGAUGCCCC------------------AAUGCCGC-AGCUGCCC-UC-GCAACUGUGG--GC-GG----------AUCGGAGCGUCCUCGCAU---------------------------GCCACUGACCAGAUC-----------------------------------------------------------GG-UCGGGAAGGC---GGA--C-GC--GCCGGAUAU-------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCGGUACAAGGUGUGCAACU
BX572599.1/256535-256331       CAAACAUCGCGCGCCGACGGUG--UCCUGUC----------------------UUCGG----ACAGGACG------AAGA--GGGAA-UAUC-G-G-AAGAUCGCUGCCUGCAGCGGU-------------CGCGCCGA-AGCUGCCC-CC-GCAACUGUAA--AC-GG----------UGAGCCGACGCAAUAC-----------------------------GCCACUGGAU--CAU-----------------------------------------------------------AU-CCGGGAAGGC---CGC--G-UC--GGCGACGAC-------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGUCGCCUGCUAUGUUGAC
BX572599.1/259196-259407       UGUGGUGCCGCUCGCUUCGGUG--CCCUUCG----------------------UUCG------AAGGGUG------AAAC--GGGAA-U-GC-G-G-UGCGGCGAGCAAUCGCC-----------------AAGUCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GGA---------UCGUCUCCGGUCACUCC----------------------------GCCACUGAGUUCGGCAUCCUAGAGC------------------------------------------------CGC-UCGGGAAGGC---GAC--C-GG--GACAAUGU--------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCGAAGUCCGCAACCAAGCC
BX572600.1/273933-274129       CAUAGUGAUCGCCGUCGAGGUU--CUUCGGGCACGA-----------------UCGUC----CCGAAGCU------AAGA--GGGAA-G-CC-G-G-UGC-------------------------------AAGGCCGG-CGCUGCCC-CC-GCAACUGUUA--GC-GGU---------GAGCCGACGUUCAGCAAA---------------------------GCCACUGGGA-GCGA-----------------------------------------------------------UC-CCGGGAAGGU--CGAA--C-AA--AGGCGAUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCUCGUCGAACGAAACGUCC
BX572608.1/190529-190732       ACUUCUAAUGGCGGUGACGGU---UCCCG------------------------AGAG--------GGAUG------AAAA--GGGAA-U-AC-G-G-UGCGGACGCAGACACUUUCGCGUUC---------UAGGCCGU-AGCUGUUC-CC-GCAACUGUAA--GC-GGA---------UCGUCUUUCGUCGGAU-----------------------------GCCACUGGGAACCUCG---------------------------------------------------------GUC-CUGGGAAGGC---GAC--G-GA--AGAUCAA---------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAUUCGUGGUCACACG
BX842572.1/309867-309685       CCACGCUCUGCAUGCCAAUAU---UCUUCCC----------------------GUCAGG---CGAUGACG------AUGC--AGGAA-G-CC-G-G-UGA-------------------------------GAAUCCGG-CGCGGU-C-CC-GCCACUGUCA--CC-GG----------GGAGCGACCCUCGUAA-----------------------------GCCACGGCC---ACA------------------------------------------------------------G-GCUGGAAGGC---GAG--G-CA--AGCAACGAU-------------------------------------------------------------------CCGG-GAGCCAGGAGACUCGCGUCAUCGCGUCCUGCCACC
L12006.1/1016-1191             CCAUAACGUAAACCAACAGGUUU-GCCACAU----------------------UUGU--------GGU-----------A--GGGAA-G-GG-G-G-UGA-------------------------------AAAUCCCC-CGCAGCCC-CC-GCUGCUGUGA--UG-C-----------UGACGACCCCGUAAAGA-----------------------------CCACUGAUC-GCAA-----------------------------------------------------------GA-UUGGGAAGG----ACG--G-GC--GAGGAGGAC--------------------------------------------------------------------GCU-AAGCCAGAAGACCUGCCUGUCGGUGAUAACCAACA
M10112.1/56-247                CUGUAGCAUCCACUUGCCGGU---CCUGU------------------------------------GAGUU------AAUA--GGGAA-U-CC-A-G-UGC-------------------------------GAAUCUGG-AGCUGA-C-GC-GCAGCGGUAA--GG-AA----------AGGUGCGAUGAUUGCGUUAUGCG----------------------GACACU--CGCCAUU-----------------------------------------------------------CG-GUGGGAAGUC---AUC--A-UC--UCUUAGUAUC--------------------------------------------------------UUAGAUACCCCUCC-AAGCCCGAAGACCUGCCGGCCAACGUCGCAUCUGG
M34485.1/360-150               UUUACACAAUUCGUAACAAGUU--AAAAGCA----------------------UUCG-------CUUU-----------A--GGGAA-A-CU-G-G-UGC-------------------------------AAAUCCAG-UGCUGCCC-CC-GCAACGGUAA--AA-AU----------GUAAACCAUAUUAAAAAAGUCAUUUAGACUUAC------------GCCACUGCAUGCAUA----------------------------------------------------------GAU-GUGGGAAGGU--GAAU--A-UG--CUUGUCUCUU-------------------------------------------------------UUUGAGAUGCCAUUU-GAGUCCGGAGACCUGCUUGUUACAUCUAUCCACUC
M57569.1/218-26                CGGUAGCAUCCGUGGGCCGGU---CCUGU------------------------------------GAGUU------AAUA--GGGAA-U-CC-A-G-UGA-------------------------------AAAUCUGG-AGCUGA-C-GC-GCAGCGGUAA--GG-AA----------AGGUGAGAUGAGAGCGUAAGCA-----------------------GACACCUGUC---------------------------------------------------------------CGG-C-GGGAAGUC---AUC--A-UU--UCUGCUAUCC---------------------------------------------------AGCCAACGGAUAACCCUCC-AAGCCCGAAGACCUGCCGGCUAACGUCGCAUCUGG
M89481.1/311-504               CGGUAGCAUCCGUGGGCCGGU---CCUGU------------------------------------GAGUU------AAUA--GGGAA-U-CC-A-G-UGA-------------------------------AAAUCUGG-AGCUGA-C-GC-GCAGCGGUAA--GG-AA----------AGGUGAGAUGAGAGCGUAAGCA-----------------------GAAACUGCC---UCC------------------------------------------------------------G-GCGGGAAGUC---AUC--A-UU--UCUGCUAUCC---------------------------------------------------AGCCAACGGAUAACCCUCC-AAGCCCGAAGACCUGCCGGCUAACGUCGCAUCUGG
U45329.1/408-194               CUAAAGUGGCAGCGUAUCGGU---UCUGCAAGUGUCAAA--------------ACGCN----CGCGGAUG------AAAA--GGGAA-U-AC-G-G-UGAGGACGACCCAAGUAAGGGCC-----------GAAACCGU-GGCUGCCC-CC-GCAACUGUGA--AC-GG----------CGAGCGAUGUCCAUCAU----------------------------GCCAUUGGCC-CCAC-----------------------------------------------------------GG-CCGAUAAGGC---GGA--C-AA--AGCCCAGAC-------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGAUAAGCAUGCGCGAAAG
Z94723.1/23034-23246           CACACGGCGCCAGUAUCGAGU---GAUGCUA----------------------GCUC-----AGCAUCGC------GAGA--GGGAA-C-CC-G-G-UGA-------------------------------GAAUCCGG-GACUGU-C-CC-GCAGCGGUAU--GC-AGG---------AACGACCGCCGUCUGGA----------------------------AGCACUGGUCUUAGAAAAAUCCG--------------------------------------------------AGA-CUGGGAAGCG---AUG--G-CC--AUUAGAAGCA--------------------------------------------------CCUAUCCAGUGCGCGCCUGC-GAGUCCGAAGACCUGCCGGCUGUGUCGGGCGCGCC
AM236080.1/2836182-2835994     GAAAUAGAUGCGCCGUCAGGUG--CCCGCCG----------------------GUAA-----GGCGGGAG------AAUC--GGGAA-U-CC-G-G-UGC-------------------------------AAGACCGG-AACGUG-C-CC-AACGCUGUAA--GG-CC----------GACGUUUGCCGCUUCAUCAC-------------------------GCCACUGGC--UUUU----------------------------------------------------------C-G-CCGGGAAGGC--UGCG--G-CA--GACGGAUGA-------------------------------------------------------------------CGCC-CAGUCAGAAGACCGGCCUGGCAAGAUAGACCGAUC
CP000283.1/2591234-2591019     CAAACAUCACGCGCCGAUGGUG--UCCCGUC----------------------UUUGG----ACGGGACG------AAAA--GGGAA-UGCC-G-G-AAGUCGCUGCCCGCAUUGAUGCGAGCAAGAC---CGAGCCGG-AGCUGCCC-CC-GCAACUGUAA--AC-GG----------CGAGCCGACGCAACAC-----------------------------GCCACUGGAU-GUUU-----------------------------------------------------------CU-CCGGGAAGGC---UGC--G-CC--UGCGACGAC-------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCAUCGCCUGCUGUGUUGAC
AE013598.1/1368227-1368452     UACCAUGCGCGCCCCUGAGGUG--ACUGUCG----------------------GCUUGCC--GGCGGUUU------AAAC--GGGAA-U-CC-G-G-UGCGCAGAUCGCCUUGGCGUGGUGC---------AAUUCCGG-AGCUGCCC-CC-GCAACGGUGG--GC-GAG---------ACAAGGGUCUGCAUGUAAC--------------------------ACCACUGUGC--GGU-----------------------------------------------------------GC-ACGGGAAGGC---GCA--G-AU--CCGGGAAGCG-------------------------------------------------------AUUGCUUCCGCUCGC-AAGCCCGGAGGCCGGCCUGAAGGGAUUGACCCGGC
AAAP01002228.1/195-394         CCUAGCGUGGCCGUCGACGGU---UCCCG------------------------AAAG--------GGAUC------AAAA--GGGAA-C-GC-G-G-UGAAGGGCCUUUGCCC------------------GAUCCCGC-GGCUGCCC-CC-GCAACUGUGA--GC-GGA---------GAGCCCUCCAUCACCAC----------------------------GUCACUGGGCGAGCCUU--------------------------------------------------------CGC-CUGGGAAGAC---GAU--G-GA--GGACAACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAGCCGUGGUCACACG
AAYH02000045.1/230200-229995   UAUCUUUGCCCGCGAAUUGGU---UCCGGAUGCAUGUUUC-------------CAUCA----UCUGGAUU------AAAA--GGGAA-U-CG-G-G-UGU-------------------------------AAAUCCCG-GACAGU-C-CC-GCUGCUGUGAA-GC-UCCGU-------UUAUAUCAUGAAAAACACCCUU-----------------------GCCACUGAUAUGCAUUGAA------------------------------------------------------AUA-UCGGGAAGGC---UUC--A-GG--AUUAG-----------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCAUUCAUUAAAGGCUGCCU
CP000283.1/2593935-2594143     CUGUUGUCGCGCAUCUUCGGUG--CCCUUCG----------------------UCGG------AAGGGUG------AAAC--GGGAA-U-GC-G-G-UGAGGCGAGUGAUCGCC-----------------CAAUCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GGA---------UUGUCUUCGGUCACAUGC---------------------------GCCACUGAGUUCGGCACCAGC----------------------------------------------------CGC-UCGGGAAGGC---GAU--C-AG--GACAACAU--------------------------------------------------------------------CCGC-AAGCCAGGAGACCGGCCGAAGACCGUAGCAACGCC
CP000463.1/3532969-3532758     UCAUAAGUUAGCCAUCGUGGUU--CUGCGGGCAAGU-----------------CGUGC----CCGGAGCU------AAGA--GGGAA-G-CC-G-G-UGCGGCGCAAGCC---------------------AAGGCCGG-AGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCCGCUGUCCAACAAU---------------------------GUCACUGGGACCGAUGAG-------------------------------------------------------GUU-UCGGGAAGGC--CGGA--C-AG--CAGCGUUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCACGAUGAAAUUCAACGUC
AAAP01003520.1/1076-875        GGCCAAGAUCAUCCCGACGGU---UCCCG------------------------CAAG--------GGAUC------AAAA--GGGAA-C-GC-G-G-UGAGGACCGUUCGGUCC-----------------GAUGCCGC-GGCUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCCUUUUCGCCACCGAC--------------------------GUCACUGGGCCACCU----------------------------------------------------------CGC-CCGGGAAGAC--GGUG--A-GA--AGGCGACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAGCCGUGGUCACACG
CP000115.1/3123579-3123785     CAUAGGAUGGGGGGUCGAGGUU--CUCCGGGACGAUU----------------CACGC----CCGGAGCU------AAGA--GGGAA-G-CC-G-G-UGUGUCUUCGGAU---------------------AAAGCCGG-CGCUGCCC-CC-GCAACUGUAA--GC-GGU---------GAGCCGUGGUCCAUCAU----------------------------GCCACUGGGU-GUUG-----------------------------------------------------------UC-CCGGGAAGGC--CGGA--C-CA--AAGCUGAGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCCCGGCAACAUAGUCGUCC
CP000463.1/3487850-3487645     UUUCGUUCGGUCAUCUUCGGUG--CCCUUGU----------------------UCGG------AAGGGUG------AAAC--GGGAA-U-GC-A-G-UGCGGCGAGCAAUCGCC-----------------AAAGCUGC-GGCUGCCC-CC-GCAACUGUAA--GC-GGA---------UUGUCCGCGAUCACUAA----------------------------GUCACUGAGGCGAGUUUCG------------------------------------------------------GCC-UUGGGAAGAC---GAU--C-GG--GACCGUAU--------------------------------------------------------------------CCGU-GAGCCAGGAGACCGGCCGAGGAUUUGUCGCAAUGC
CP000250.1/5294881-5295084     CUUUUAGUUGUAGGCGACGGU---UCCUCUC----------------------CGGA--------GGAUC------AAAA--GGGAA-U-GC-G-G-UGCGGGUGCCUUCGGAAACCC-------------AACUCCGC-AGCUGUUC-CC-GCAACUGUAA--GC-GGU---------UCGACUUUCGUCGGAAU----------------------------GCCACUGGGAAACUCG---------------------------------------------------------GUC-CUGGGAAGGC---GAC--G-GA--AGGUAACC--------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAUCCGUGGUCACACG
CP000738.1/1657203-1656988     GCCAUAUGACAGCCGUCAGGUG--CCCGC------------------------UUUUA----UGUGGGAG------AAUC--GGGAA-G-CC-G-G-UGC-------------------------------AGUUCCGG-CACGUG-C-CC-AACGCUGUGA--AG-GG----------GACGUUCUCGCCAAAAACAGGCUCUGAAUCUUUUCAGAGCUUU--GCCACUGAAUUUUAAAGU-------------------------------------------------------GAU-UUGGGAAGGC---GGC--G-GG--AGCGGAUGA-------------------------------------------------------------------UCCG-AAGUCAGAAGACCGGCCUGGCGAGAUAGACCGGCC
AM263198.1/1122851-1123040     UUAAAUAGGUCUUAAGUUGGU---GAAAUGU----------------------AUUUG----CAUUUCUG------AAAG--AGGAA-U-UC-G-G-UGC-------------------------------AAUGCCGA-AACUGCCC-CC-GCAACUGUAA--GG-UG----------GACAAGAAUUGAGAAA-----------------------------ACCACUGUGCGUUUAAU--------------------------------------------------------CGU-AUGGGAAGGU---UCA--A-UU--CUUGGAUGA-------------------------------------------------------------------AGCC-AAGUCAGGAUACUCGCCAAAUAAGACGGAAGCAAC
CP000139.1/3919800-3919587     UAUCUUUGUUCCCGAAUCGGU---UCCGAAUAGAUGUC---------------CUCUA----UCCGGAUU------AAAA--GGGAA-U-CG-G-G-UGU-------------------------------AAAUCCCG-GACAGU-C-CC-GCUGCUGUGAA-AC-UCCGAU------AAAAUUUCCGAUACGUACCUAUU----------------------GCCACUGCCUGACUCCACAUAACGAG-----------------------------------------------AAC-GCGGGAAGGC---AUC--G-GA--AAUGAG----------------------------------------------------------------------GAGC-CAGUCAGAAGACCUGCCAUUCAUCAAAGGCCGUUU
CP000481.1/1942077-1942287     AUGGUGUCGCCUGCGACUGGUU--CGACCCC----------------------UCGGG----GUCGUGCC------AACA--GGGAA-C-CC-G-G-UGU-------------------------------GAAUCCGG-GACUGC-C-CC-GCAGCGGUGA--GC-GGGA--------ACGACCGCUGUCAUCAA-----------------------------GCACUGGGCCGGAC----------------------------------------------------------GGC-CUGGGAAGC----GAC--A-GC--CAGUAGGUGA---------------------------------------------CCGGCGAUUCGCCGGUCGGGCCCGC-AAGUCCGAAGACCUGCCAGUCGCCCCGCGGACACC
CP000479.1/1283346-1283177     CAAGAAUGUCACCCGUAAGGUG-------------------------------AUGA-----------CG------AUGC--AGGAA-G-CC-G-G-UGC-------------------------------GAAUCCGG-CGCGGU-C-CC-GCCACUGUCA--UC-GG----------GGAGCGACCCUCAACG-----------------------------GCCACGGCU--GACA------------------------------------------------------------A-GCUGGAAGGC---GAG--G-CG--AGCGGCGAU-------------------------------------------------------------------CCGA-GAGCCAGGACACUCGCGUCAUCGCGUCCUGCGACC
CP000647.1/3513278-3513100     CGGCGAAACAAACCGACAGGUU--CGACACC----------------------AGU---------UUGGU------GUCA--GGGAA-G-GG-G-G-UGU-------------------------------AAAUCCCC-CGCAGCCC-CC-GCUGCUGUGA--UG-C-----------UGACGACCCCGCAAAAA-----------------------------CCACUGAUC-GAAA-----------------------------------------------------------GA-UUGGGAAGG----GCG--G-GC--GAGAACGAG--------------------------------------------------------------------GCU-AAGCCAGAAGACCUGCCUGCCGGUAACUGACCAAC
CP000133.1/3940621-3940395     ACUAUAUCUAGUGUUCAAGGUU--CCUUCGAUUCGUC----------------AGGAU----CGCGGGCG------AAGAU-GGGAA-U-AC-G-G-UGCGUUUCGCCAUGACGGCGCAAC----------AAGGCCGG-AGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAGCAACUGUCCGAUUUCAG------------------------GUCACUGAGGCAUGAU---------------------------------------------------------GCC-UCGGGAAGGCUGGGGC--A-GG--GUGCUUCGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCUUGAACUAGAUGUCCACG
CP000463.1/3491563-3491365     UUAAAGCGCUGCGUCACCGGUG--CCUCUCG----------------------CAAG------AGGGGUG------AAAC--GGGAA-U-GC-G-G-UGCGGGACGAUGUCCC------------------CAAGCCGC-AGCUGCCC-UC-GCAACUGUAA--GC-GG----------AUCACGACGUCCUUGAU----------------------------GCCACUGGCC-GAUC-----------------------------------------------------------GG-CCGGGAAGGC---GGA--C-GA--GCGAUACAU-------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCGGUGACGUUGAGCCAACU
CP000491.1/325972-326168       ACUACACGGUCGGGUGACGGU---UUCCGAU----------------------UUCG--------GAAUG------AAAA--GGGAA-C-GC-A-G-UGCGGACCAGCCGGUCC-----------------CAUGCUGC-GGCUGCCC-CC-GCAACUGUAG--GC-GG----------AUAGCCUUUGCCAACG-----------------------------GCCACUGGGU-GCGA-----------------------------------------------------------CC-CCGGGAAGGC---GGC--G-AC--AGGCGACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAGCCGUUGUCACGCG
CP000250.1/3635632-3635843     AAACAUCGCGCUGCCGACGGU---UCCUGUC----------------------UGCGG----ACGGGACG------AAGA--GGGAA-UAUC-G-G-AAGUCAUCAUCCAGACGCGGAUGAUGGC------GGUGCCGA-AGCUGCUC-CC-GCAACUGUGA--AC-GG----------CGAGCCAUCGCAACAC-----------------------------GCCACUGGGC-AGAC-----------------------------------------------------------GC-CUGGGAAGGC---UGC--G-UU--GGCCGUGAC-------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGUCGCCUGCUGAUUGACG
CP000250.1/3754381-3754174     UCUGUUUGCCAUGCCUUCGGUG--CCUCUCG----------------------AAAG------AGAGGUG------AAACA-GGGAA-U-GC-G-G-UGCGGCGAGCUUUCGCC-----------------AAUUCCGC-GGCUGCCC-CC-GCAACUGUAG--GC-GGA---------UCGUCCGCGAUCAAGCU----------------------------GCCACUGAGCGAUCGUUUUG-----------------------------------------------------CGC-UCGGGAAGGC---GAU--C-CG--GACCAUAU--------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCGCAGGCAAUCGUCCACUU
CP000230.1/1707586-1707782     UAGCCUAUGUUGUGUUACGGUU--CCCCGGACACCAC----------------AAUAU----CCGGGGCU------AAGA--GGGAA-G-CC-G-G-UGC-------------------------------GAUGCCGG-CGCUGCCC-CC-GCAACUGUCA--GC-GGC---------GAGCCUUCAUCCAUUCAU---------------------------GCCACUGGGG-AAAU-----------------------------------------------------------UC-CCGGGAAGGC---GGA--C-GA--AGGCGACGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGUGACCCUUGAAACGUCC
CP000283.1/3256000-3255793     GUGCGCGCAUCGACCUUCGGUG--CCCUUCUU---------------------GGAA--------GGGUG------AAAC--GGGAA-U-GC-G-G-UGCGGCGAGCAAUCGCC-----------------UAGUCCGC-AGCUGCCC-CC-GCAACUGUAA--GC-GGA---------UCGUCUCCGGUCAAAUGC---------------------------GCCACUGAGUUCGGCUUCAGC----------------------------------------------------CAC-UUGGGAAGGC---GAU--C-GG--GACAUUCU--------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCGAGGGUCGUUUUGGAUGC
CP000250.1/834289-834069       GCUAGCGUGGCCGGCGAUGGU---CCUUC------------------------CGCGA----GGAAGGUG------AAAA--GGGAA-U-CC-G-G-UGCGCGAACGCUCUGCAUUGAGCGAUCUC-----AAUCCCGG-UGCUGCCC-CC-GCAACUGUAA--GC-GA----------CGAGCCCGCGCCUCG------------------------------GCCACUGGGAUUCCUCUAAGGA---------------------------------------------------CUC-CUGGGAAGGC---GGC--G-AC--AAGGGCAGCG----------------------------------------------------------------ACUCGC-GAGCCAGGAGACCUGCCAUCGCGAAUUGUGCUUUG
CP000283.1/3256310-3256518     GAAGUCGCUUCAGCCUACGGUG--CCUCUCG----------------------UCGG------AGAGGUG------AAACU-GGGAA-U-GC-G-G-UGCGGCGAGAGAUCGCC-----------------AAUUCCGC-AGCUGCCC-CC-GCAACUGUGA--GC-GGAA--------UAGGUCCGGAUCAAACU----------------------------GCCACUGAGCUUCGAAGUGA-----------------------------------------------------UGC-UUGGGAAGGC---GAU--C-CG--GACAAUCU--------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCGAAGGCGUUGUUCAACUC
CP000319.1/2878648-2878845     UUCUAAAUGACCGGCGACGGU---UCUCCCU----------------------CGGG--------AGAUC------AAAA--GGGAA-C-GU-G-G-UGCGGGAUCAUCCU--------------------AACGCCAC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAAUCUGCGUCACAG-----------------------------GCCACUGGGACAUCUCG--------------------------------------------------------GCC-CCGGGAAGGC---GAC--G-CC--AGGUAACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAACCGUGGUCACACG
CP000463.1/2468338-2468530     GCUAGCGUCGCCACCGAUGGU---CCUUCCG----------------------UUUG------GAAGGUG------AAAA--GGGAA-G-CC-G-G-UGCGAGUUCGCUC---------------------CAUUCCGG-CGCUGCCC-CC-GCAACUGUAA--GC-GA----------CGAGCCAUCGCCGAG------------------------------ACCACUGGG--GCAA------------------------------------------------------------C-CUGGGAAGGC---GGC--G-AG-AGGGCGGCGAC------------------------------------------------------------------UCGC-GAGCCAGGAGACCUGCCAUCGCGGACUGUGCUUUG
CP000759.1/250860-251074       ACUAUAUAUAGUGUUCUAGGUU--CUUUCGAUUCGU-----------------UGGGU----CGAAAGCU------AAGAC-GGGAA-U-CC-G-G-UGCGUUUCAUCCAUGACGGAUGCGGC--------AAUGCCGG-AGCUGCCC-CC-GCAACUGUAA--GC-GG----------AGAGUUCUGUCCAUCAC----------------------------GUCACUGGC---UUU----------------------------------------------------------G-G-CUGGGAAGGC---GGA--C-AG--AAUGUUGAU-------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCUUGAACGAGUACGUCCAC
CP000250.1/3754538-3754747     UCUUGUCGGAUCGUCUACGGUG--CCUCU------------------------CGCGA----GAGAGGUG------AAACA-GGGAA-U-GC-G-G-UACGGCGCGAAAGCGCC-----------------AAAGCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GGA---------UCGUCGCCGAUCACAUGC---------------------------GCCACUGAGUCCGCCAAGACG----------------------------------------------------GCC-UCGGGAAGGC---GAU--C-GG--GACAACAU--------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCGUAGAUUCGUGCAAUGCC
CP000283.1/785607-785805       GAUACGGUGAACAUCGACGGU---UCCCG------------------------CAAG--------GGAUC------AAUA--GGGAA-U-GC-G-G-UGAGGAUUCUCGCGAAUCC---------------AAUUCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCCUUUCGCCAAGC-----------------------------GCCACUGGGCUUCGA-----------------------------------------------------------GC-CUGGGAAGGC---GGC--G-AA--AGGCAGCGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCGUCGUGGUCACACGC
CP000301.1/4173480-4173288     GCUAGCGUUGCGAACGAUGGU---CCUUC------------------------CACGU----GGAAGGUG------AAAA--GGGAA-G-CC-G-G-UGCGAGCGAUUUC---------------------AAACCCGG-CGCUGCCC-CC-GCAACUGUGA--GC-GA----------CGAGCCCGCGCCGAG------------------------------GCCACUGGGA--UGU-----------------------------------------------------------UC-CUGGGAAGGC---GGC--G-AG--GGGCUUUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCAUCGUGAAGAGUGCUUUG
CP000301.1/96643-96430         CUCCUAGAUGAUCGCGACGGU---UCCCCUC----------------------UGGG--------GGAUC------AAAA--GGGAA-U-GC-G-G-UGCGGGACGGCUCUCGGUUGGAGCAAGCCC----AAUGCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GGU---------UAGUCUUUCGUCUGAU-----------------------------GCCACUGGGAAACUCG---------------------------------------------------------GUC-CUGGGAAGGC---GAC--G-AA--AGGUUCCGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAAUCGUGGUCACACG
BA000040.2/5279689-5279475     CGUAGAUUGAUCGGUGACGGU---UCUCCGC----------------------ACGG--------AGAUC------AAAA--GGGAA-C-GU-G-G-UGCGAGAUUGUCCCAAUGCCGGGAUUGUCCC---AACGCCAC-GGCUGCCC-CC-GCAACUGUAA--GC-GGU---------GAAUCUUUCGUCAUAU-----------------------------GCCACUGGGAAUCUCG---------------------------------------------------------GUC-CUGGGAAGGC---GAC--G-UA--AGGUAACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAGCCGUGGUCACACG
CP000140.1/1176516-1176715     ACUUUUGUCACUGUAACAGGC---UCCGCUUAUCUCUUUUUC-----------CGGGA----GGCGGAUU------AAAA--GGGAA-C-CG-G-G-UGA-------------------------------GAAUCCCG-GACAGACC-AC-GCUGCUGUGA--AC-UUUU--------AAACAUUCGGACAAUACCUUG------------------------GCCACUGGUU-UUGU-----------------------------------------------------------AA-UCGGGAAGGC---GUC--C-UG--AAUGG-----------------------------------------------------------------------AAGU-AAGUCAGAAGACCUGCCGGUUCAUAAAUAAAUGUU
CP000739.1/543105-542876       ACAUUAACUGGGACCGACGGU---UCCCCUACCCGAGA---------------GGUGG----AGGGGAUU------AAUA--GGGAA-C-AC-G-G-UGCGGACGACCCAAAAGGGACC------------AAAACCGU-GGCUGCCC-CC-GCAACUGUAA--GC-GGA---------UCGUCGUUCAUCCUCGUGGUGCCGAGGCACCA-------------GCCACUGCGC--GAC-----------------------------------------------------------GC-GCGGGAAGGU--AGAU--G-AG--CGACUUCUGU------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGUCAAAUUCGAUCCAUCG
AATQ01000040.1/37497-37304     CUAGAUAUAGGUGCUUCAGGUGCUCGGCGGA----------------------AUCAU----CCGCCGGC------AAGA--GGGAA-G-CC-G-G-UGA-------------------------------AAAGCCGG-CACUGCCC-CC-GCAACUGUAA--GC-GG----------CGCGCGAGGCCGAUCAU----------------------------GCCACUGGGGCUGCC----------------------------------------------------------ACC-CCGGGAAGGC---CGG--U-CA--AGCGGGACCC-----------------------------------------------------------------GCCGC-GAGUCAGGAGACCUGCCGGAAGCAACAGGAUUUGA
AE015928.1/2403656-2403862     AUCUUUGCCCCCCGAAAUGGU---UCGGAGUCCGUGUCCA-------------ACGGA----CAACGAUU------AAAA--GGGAA-U-CG-G-G-UGU-------------------------------AAAUCCCG-UACAGU-C-CC-GCUGCUGUGAA-GC-UCUAUA------CAAUGUCUUAUUAAUGAACUAAUUUAUC-----------------GCCACUGAU--GUUA----------------------------------------------------------U-U-UCGGGAAGGC---ACU--A-UA--AGACAA----------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCACUUCGCGUAAAGCGUUC
CP000377.1/548354-548161       UCAAUAUCGUGUUGCUUUGGUU--CUUUCGA----------------------GGCGACU--CGCAAGCG------AAGA--GGGAA-A-CU-G-G-UGA-------------------------------AAAUCCGG-UGCUGCCC-CC-GCAACUGUAA--GC-GG----------CAAGCCCUGCCC---GU----------------------------GCCACUGACGCAUCGCU--------------------------------------------------------GCG-UUGGGAAGGC---GGG--A-GG--GGGCGUUUGA-----------------------------------------------------------------GCCGCGAAGCCAGGAGACCUGCCAGAGCACGACACACGACG
AAXE02000001.1/9613-9819       UACAUUUGCCACCGAAUCGGU---UCUGUAUUUCCCGUUC-------------GGGAA----UAUGGAUU------AAAA--GGGAA-U-CG-G-G-UGU-------------------------------AAAUCCCG-GACAGU-C-CC-GCUGCUGUGAA-GC-UCCGUUU-----UAACAUCUUGGAACUACUUUC------------------------GCCACUGACUUGUUAUAAUU-----------------------------------------------------AAG-UCGGGAAGGC---UUC--A-GG--AUGG------------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCGUUCAUUAUAAGGUUCAU
CP000664.1/92637-92429         GUCACGCCAUGCCAUGACGGU---UCCCGAGGGUCGCAC--------------GGCCC----GAGGGAUG------AAAA--GGGAA-C-AC-G-G-UGAGGGGGAAACCCC-------------------GAGUCCGC-GACUGCCC-CC-GCAACUGUGA--GC-GG----------CGAGCCGCCCCGACGGAC---------------------------ACCACUGGCC--GAU-----------------------------------------------------------GG-CCGGGAAGGU--UCGG--G-GA--CGGCCACGAC------------------------------------------------------------------CCGC-GAGUCAGGAGACCUGCCGUCGGGCGCAUCCGCGCC
AARF01000099.1/15166-14989     CUGAUAAAAAUUGAAUAGAAAA--CUGGG------------------------------------UAGAG------AUCA--GGGAA-A-GA-G-G-UGC-------------------------------GAUUCCUC-UACAGGCC-CUAGCUACUGUGA--AG-CG----------GACGAAAUCCCCUUGAU----------------------------GUCACUGGAA--CAU-----------------------------------------------------------UU-CCGGGAAGGC---GGG--A-AA--CUAGAAUGA-------------------------------------------------------------------UGCA-AAGUCAGGAGACCUCCUCUAUUCAGCCUAUGCAGC
CP000151.1/1842062-1841871     UACGGCCGUUCGUUCGCCGGU---GCCCC------------------------UCGG--------GGCCG------AAGA--GGGAA-C-AC-A-G-GGCGCGCCACGC----------------------GCCGCUGU-GGCUGCCC-CC-GCAACUGUAG--AC-AG----------CGAGCCGAUCUCCCCCUCAU-------------------------GCCACUGGU---UCC------------------------------------------------------------A-CCGGGAAGGC--CGGG--A-GC--CGGCGCCGAC------------------------------------------------------------------CUGU-CAGCCAGGAGACCUGCCGGCCUGAAAGUGCGUGCG
CP000250.1/820695-820904       CUCCUAUCGAACCGUUCAGGUG--UGCCGGGA---------------------GUCUC----CCGGCA-----------CA-GGGAA-G-CC-G-G-UCCGGGCGCCUCAGGCGGUGCCC-----------CAAGCCGG-CGCUGCGC-CC-GCAACUGUAG--GC-GGC---------GAGCGAUCCUUCAUCAU----------------------------GCCACUGCGCCGAUCG---------------------------------------------------------GGC-GCGGGAAGGC---GAG--G-GA--UUGCGACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCUGAGCCACGUCAUCUUCC
AM420293.1/5303093-5303317     GCCGAGAGCCGCGACCGCGGCG--GUC--------------------------------------GAGGC------AAGA--GGGAA-C-CC-G-G-UGC-------------------------------GAAUCCGG-GACUGC-C-CC-GCAGCGGUGA--GC-GGGA--------ACGAACGCCGUCCCCGGUCCGAGGAGACCGGGAAC----------AGCACUGGACCACAG----------------------------------------------------------CGU-CUGGGAAGC----GAC--G-GC--CAGUAGGAAC--------------------------------------ACCCGGCCACGACGAGGCCGGGAAGCGCCCGC-GAGUCCGAAGACCUGCCACCGGUGCGUGCACACCC
CP000283.1/2565817-2565609     AGAAUACUCGCCUGUCACGGU---CUUUCGAGUCGUAUGUGCACG--------CGAUC----CGAGAGCU------AAGA--GGGAA-G-CC-G-G-UGC-------------------------------AAAGCCGG-CGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCUGACGUCCGAUAGUC--------------------------GCCACUGGGCCCAUUG---------------------------------------------------------GAC-CCGGGAAGGC--AGGA--C-UG--ACGCUAAGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUACCGCGACAGUCGCAAUCGUC
CP000379.1/1074555-1074362     UUACCCUUGCGCGCUGAUGGU---UCCCGGA----------------------GACG--------GGAUC------AAAA--GGGAA-C-GC-A-GGUGAGGCAACGCCUC--------------------GAAGCUGC-GGCUGCCC-CC-GCAACUGUGA--GC-GG----------CGAAUCCGUGCCACCGCAU--------------------------GCCACUGG---GAAA--------------------------------------------------------------CCGGGAAGGC--CCGC--A-CG--GACGACGAC-------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCAUCGACCCGAGGUCCAGC
AP006841.1/2882136-2881925     UUAUCUUUGUCCCGAAUUGGUU--UCGAAUGAAGACUUU--------------CGUCA----UUCGGAUU------AAAA--GGGAA-U-CG-G-G-UGU-------------------------------AAAUCCCG-GACAGU-C-CC-GCUGCUGUGAA-GC-UUCAU-------CGAUAUCUUGAAACAAUCCUUUC----------------------GCCACUGACGUGGGGGGAAUACCU-------------------------------------------------CCG-UCGGGAAGGC---UUC--A-AG--AUUAG-----------------------------------------------------------------------AAGU-CAGUCAGAAGACCUGCCGUUCAUCAAAGGCUGUUU
CP000463.1/3487953-3488157     ACUAAAUGUUGCUGUCACGGU---CUCUCGAAUCGC-----------------UUGAU----CGAGAGCU------AAGA--GGGAA-U-CC-G-G-UGUGGCGAAAGCC---------------------GAAGCCGG-AGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCCGACGUCACCGAGU---------------------------GCCACUGGGA-GCAA-----------------------------------------------------------UC-CCGGGAAGGC---CGA--C-GA--AGGCAUUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGCGACAACGACUACGUCC
CP000716.1/1854993-1855172     AAUAACCAAUGGAAUAAAGGU---GCCUU---------------------------------AAAGGCUU------AAUA--GGGAA-G-CU-G-G-UGA-------------------------------AAAUCCAG-CGCGGC-C-CC-GCCACCGUAA--CU-GGG---------GACGAAAGUCGCAAAGU----------------------------GCCACUGGGA----U----------------------------------------------------------UUC-CUGGGAAGGU---GCG--A-CG--AGUAGGUUGA-----------------------------------------------------------------UCCAG-AAGCCGGGAGACCUGCCUUUGUUCCAAAGUGUUUC
CP000662.1/491640-491462       GUCUCAGCUACUGCGUCAGGUG--CCGCCCG----------------------CGGG--------CGGAG------AAUC--GGGAA-G-CC-G-G-UGC-------------------------------GACUCCGG-CGCGGG-C-CC-GCCGCUGUGA--CG-GG----------GAUGCUUCGGGCAGGAU----------------------------GCCACCGGUU----------------------------------------------------------------CG-CCGGGAAGGC---GCC--C-GG--GGCAGGUGA-------------------------------------------------------------------ACCG-GAGCCAGAAGACCGGCCUGACAAAGAGGUUCCUGC
BA000012.4/6749128-6749334     CUACGGUGGGUGCGUGAUGGU---CCCCGCGCCGA------------------AAGGC----AAGGGGUG------AAAA--GGGAA-C-AC-G-G-UGAGACCUCAAAAGGUC-----------------GAGACCGU-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------AGAGCAAGAUCCGACAU----------------------------GCCACUGGCCGGCAA-----------------------------------------------------------GG-CUGGGAAGGC--AGGA--U-UG--CGCUGAGAC-------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCAUCACUGAGUUGACCGGA
CP000075.1/3709306-3709505     UUUACCAUGCCGCGCGUCGGU---UUCCG------------------------AGAG--------GAACU------AACA--GGGAA-U-UC-G---CACGCCUUUCUCACCAGGCG--------------AAAAACGA-AACUGCCC-CC-GCAACUGUAG--GC-AC----------CGAGCCUGCUCCAUGACU---------------------------GCCACUGGAU--CGU----------------------------------------------------------GAU-CCGGGAAGGC--CGGA--G-CC--UGGCGAUGAC------------------------------------------------------------------GUGU-CAGUCAGGAGACCUGCCGACCCGCUUCAACCCACU
AP006841.1/3073837-3073630     UAUAUUUGUCGGCAGAUUGGU---UCGCCGAAGCUUUCCU-------------GCUUU----GGGCGAUU------AAAA--GGGAA-U-CG-G-G-UGU-------------------------------AACUCCCG-GACAGU-C-CC-GCUGCUGUGA--AG-CUUUAUUAU---AAACAUUCCGAUAGGAUACUCUUUG--------------------GCCACUGACUCGUGU-----------------------------------------------------------AG-UCGGGAAGGC--GUUC--G-GA--AUGGA-----------------------------------------------------------------------AGCU-AAGUCAGAAGACCUGCCACUCUCGCUGAUAAGUCU
CP000264.1/2259475-2259261     UGAAAUCAAACUGGUGAUGGU---GUUUCGACAUCCAAGA-------------CGAUG----UCGGACUG------AAAA--GGGAA-U-AC-G-G-UGAGGACGCGCCUUAGGGCACC------------AAAUCCGU-AACUGCCC-CC-GCAACUGUAA--GC-GG----------UAAGCGACGCCAAAUAU----------------------------GCCACUGGGA-CAGC-----------------------------------------------------------UC-CCGGGAAGGU---UGG--C-CA--AGCGUUGAU-------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAUCAGGUGUUGAAACAUU
BA000030.3/2496008-2496226     AGGCUGGGUGGUGCAGCUGGUU--CGCCCCGUCCGCCA---------------GGCGG----GAGGCGUCGU----AAGA--GGGAA-C-CC-G-G-CGG-------------------------------GAAUCCGG-GACUGC-C-CC-GCAGCGGUGA--GU-GGG---------AACGAACGCUGUCAUA-----------------------------CGCACUGGGCCCAAAA---------------------------------------------------------GGC-CCGGGAAGCG---ACG--G-CC--AGUAGGUGUC-----------------------------------------------CUCCGUACGGAGGGCGUGCUCGC-GAGUCCGAAGACCUGCCCGCUGCCCGUGCGCGACC
CP000139.1/3926628-3926422     UUAUCUUUGCCCCGAAUUGGUU--UCGGAUAGUCUAUC---------------UGCUA----UUCGGAUU------AAAA--GGGAA-U-CG-G-G-UGC-------------------------------AAAUCCCG-GACAGU-C-CC-GCUGCUGUGAA-AC-UCUGC-------UGGAAUCUUGAAAAAUACCUUU-----------------------GCCACUGAUGUGACAAUCCUC----------------------------------------------------ACA-UCGGGAAGGC---UUC--A-AG--AUAAG-----------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCAUUCAUUAAAGGCUGUUU
CP000661.1/1410118-1410316     CUAUUGAGAAACGGCUUCGGU---UCCGGCG----------------------UCAU-----GCCGGAUG------AAAA--GGGAA-C-GC-G-G-UGAGGGGUGCCCCUCC------------------AAAUCCGC-GGCUGCCC-CC-GCAACUGUAG--GC-GGC---------GAGCGACGACCGAUCAC----------------------------GCCACUGGGG----U----------------------------------------------------------UCC-CCGGGAAGGC---CGG--U-CC--GAGCGAAGAC------------------------------------------------------------------CCGC-GAGUCAGGAGACCUGCCGGAGCGAUCACCCUUUCC
AP006841.1/4035424-4035643     UAUAUUUGUCGCCGAAUUGGU---UCGGAAUCCGUGGUCA-------------ACGGA----CGAAGAUU------AAAA--GGGAA-U-CG-G-G-UGU-------------------------------AAAUCCCG-GACAGU-C-CC-GCUGCUGUGAA-AC-UCUGUA------UAGCAUCUUAUCAAUCAGCCAAUUUCGU-----------------ACCACUGACAGAAAAAGCAAACU--------------------------------------------------CUG-UCGGGAAGGUCCCGGU--A-AG--AUGUA-----------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCAUUCGUGAAUAAGAGCAU
AAMD01000084.1/10237-10455     UAUCCCCGGCCUGUCCUCGGCG--CGUCCAU----------------------GAAGUCA--UGGACGCU------CA-A--GGGAA-C-CC-G-G-UGU-------------------------------GAUUCCGG-GACUGC-C-CC-GCAGCGGUGA--AC-AGGA--------ACGACCGCCGUCCACGCA---------------------------AGCACUGGCCCCUCCCG--------------------------------------------------------GGG-CUGGGAAGC----GAC--A-GC--CAGUAGAAGG------------------------------------------AGGAUUCCCCCGAACCCUCCGCGCCUGU-GAGUCCGAAGACCUGCCGAGGUCCCGUGCCCCGCA
AE014291.4/1309296-1309068     UCGCAAUUUUCAGGAGACGGU---UCCGCCA----------------------UUGC-----GGCGGAUG------AAAA--GGGAA-C-AC-G-G-UGAAGCCAUAGGGCU-------------------GAAACCGA-GACUGCCC-CC-GCAACUGUAA--CC-GG----------AGAGCUAUCCUCCACAGGCCGCGCAAGCGGCCAAA----------GCCACUGAAAGCAGCAAUAUGCUG-------------------------------------------------CAA-UCGGGAAGGC--GGAG--G-CA--AAGCGAAGAC------------------------------------------------------------------CCGG-AAGUCAGGAGACCUGCCGUAUCCGGUCACCCAUGC
CP000489.1/2543185-2543386     GCACAGACAUGGGGCGCUGGUU--CCUGUCC----------------------UAUG------ACAGGCU------AAGA--GGGAA-U-GC-G-A-CAGGCAACCGCCU---------------------GAAA--GC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AAAGGUCGCCCCUCU------------------------------GCCACUGGC--GAAA------------------------------------------------------------G-CCGGGAAGGC---GGG--G-CG--GCCGUGGGCC-------------------------------------------------------CAGGCCCGAAUCCGC-AAGCCGGGAGACCUGCCGGUGCAGAAGGAUUGACC
CP000115.1/2411796-2412010     CCCAAACAGAUCGGCGACGGU---UCUCCCU----------------------UGGG--------AGAUC------AAAA--GGGAA-C-GU-G-G-UGCGGGAUCAUCCUAACACCGGGAUCAUUCC---AACGCCAC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAAUCUGCGUCACAC-----------------------------GCCACUGGGACAUCUCG--------------------------------------------------------GCC-CCGGGAAGGC---GAC--G-UC--AGGUAACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAACCCGUGGUCACAC
CP000489.1/2539767-2539972     GUAACAUAUGCGUGUAUCGGUG--CCCCU------------------------UUCG--------GGGCC------AAAA--GGGAA-U-GC-G-G-UGCCGUCUCCGGCGUCUUGGGGACC---------AAAUCCGC-AGCCGCCC-CC-GCGACUGUAG--GC-GGA---------GAGCGGACGCCCAUCGU----------------------------GCCACUGGCC-AUCC-----------------------------------------------------------GG-CCGGGAAGGC---GGG--C-GU--CAGCCGUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGAUGCGUGAAACCGCAAU
AAXF02000050.1/365024-364813   UAUCUUUGCCCCUGAAUUGGU---UUCAGAUAGCCAUAUC-------------AACUA----UCUGAAUU------AAAA--GGGAA-U-CG-G-G-UGU-------------------------------AAAUCCCG-GACAGU-C-CC-GCUGCUGUGAA-AC-UCUAUU------CAACUUCUUGAUAUUUACUUUU-----------------------ACCACUGACCGGGUAUAGAUAGUCA------------------------------------------------AGG-UCGGGAAGGA---AUC--A-GG--AAGG------------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCAUUCAUACCUUUAUAGCU
CP000230.1/1501900-1501675     UACCGUAUUUAGCGUUACGGUU--CCUUGGGUAUGC-----------------AAUAU----CUAGGGUG------AAGA--GGGAA-G-AC-G-G-UGCGCCCUUGAAGGGC------------------AAUGCCGG-CGCUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCCCGCGUCCAAGACU---------------------------GCCACUGGUGCGCCGGUCCUUCGGAACCG--------------------------------------------GCC-CCGGGAAGGC--CGGA--C-GG--GGGCUGUGAC------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCGUAAUGGCCGCAACGUCC
CP000283.1/727646-727425       GAUAGCGUGGCCGGCGAUGGU---CCUUCCG----------------------CCAG------GAAGGUG------AAAA--GGGAA-U-CC-G-G-UGCAAGUGAACUCUGUUCGAGUGAUCUC------AAUCCCGG-UGCUGCCC-CC-GCAACUGUAA--GC-GA----------CGAGCCCGCGCCUCG------------------------------GCCACUGGGAUUUCCUGCUUGGAA-------------------------------------------------AUU-CUGGGAAGGC---GGC--G-ACAAGGGCGAUGAC------------------------------------------------------------------UCGC-GAGCCAGGAGACCUGCCAUCAUGAAUGGUGCUUUG
CP000144.1/239679-239466       GUCACGCCGGGCUAUGACGGU---UCCCGAACGCCGCA---------------AGGUC----AAGGGAUG------AAAA--GGGAA-C-GC-G-G-UGAGGGGUGCUGACCCC-----------------AGUUCCGC-GACUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCCCGCCCCGAAGAC----------------------------GCCACUGGACCGAAAG---------------------------------------------------------GGC-CCGGGAAGGU--UCGG--G-GA--AGGCCGCGAC------------------------------------------------------------------CCGC-GAGUCAGGAGACCUGCCGUCGAGCGCGCAAGCGCC
CP000301.1/3914520-3914312     GCUACAUGUAGAUGUCACGGU---CCCUCGAAUCGC-----------------AAGAU----CGGGGGCU------AAGA--GGGAA-G-CC-G-G-UGCGGCGCGAGCC---------------------AAAGCCGG-AGCUGCCC-CC-GCAACUGUAA--GC-GGU---------GAGCCGACGUCCAGCCUUU--------------------------GUCACUGAGGCCGAAA---------------------------------------------------------GCC-UCGGGAAGAC---GGA--C-CG--AAGCGACGAU------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGCGACAACAGAACGUCUU
CP000482.1/1298216-1298027     AGUUUCAUACCGGAUCACGGU---GCCCG------------------------CAAG--------GGCUU------GAUA--GGGAA-GAUG-G-G-UGAGCUCCAAAGAGC-------------------GAUUCCCC-CGCGGA-C-CC-GCCGCUGUAA--GC-GA----------UGACGA-AGGGCACACC----------------------------GCCACUGGU--UUUU----------------------------------------------------------G-A-CUGGGAAGGC---GCC--C-----GGAGAAUGAC------------------------------------------------------------------UCGC-GAGCCAGAAAACCUGCCUGAUCCCAAACACUCGGA
CP000661.1/1554899-1555094     CACCACUGCCGCCGCGCUGGUU--CCUGUCC----------------------GCAAGC---GACAGGCG------AAGA--GGGAA-U-GC-C-----C-------------------------------CAGA-GGC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AGAGGUUGUCC----AU----------------------------GCCACUGGCC-GAAA-----------------------------------------------------------GG-CCGGGAAGGC----GG--A-CC--GCCGCGGGAC---------------------------------------------------CGCAAGGCCCCACAUCCGC-AAGCCGGGAGACCUGCCAGCGCUGAGACUUACGGG
CP000481.1/1939207-1939426     UAGGCUGAGCCCGCAGCUGGU---UCGGCCGCAGGC-----------------GAUGC----AGCCGAGCU-----AACA--GGGAA-C-CC-G-G-UGC-------------------------------GAAUCCGG-GACUGC-C-CC-GCAGCGGUGA--GU-GGGA--------ACGACCGCCGUCAACG------------------------------GCACUGGGC-GACA-----------------------------------------------------------GC-CUGGGAAGC----GAC--G-GC--CAGUAGGCAA--------------------------------------CGGUGACCGGCCGCUCCGGCGCCGCCGCCCAC-AAGUCCGAAGACCUGCCAGCUGCACACCGCCGAUG
CP000759.1/1328776-1328542     ACGUAAUAGUGUAACGACGGU---UCCCCGACCGAG-----------------AGCGA----AGGGGAUU------AAUA--GGGAA-C-AC-G-G-UGAGGACGACCCGAAAAGGGGCC-----------AAGACCGU-GGCUGCCC-CC-GCAACUGUAA--GC-GGA---------UUGCCGUUCAUCCUCGUGACGUUGAAAGCGUCAU-----------GCCACUGUGCCGGAGA---------------------------------------------------------AGC-GCGGGAAGGC--AGAU--G-AA--CAGCAGAUAU------------------------------------------------------------------UCGU-GAGCCAGGAGACCUGCCGUUUAGUGUUGUCCAUUG
ABCF01000035.1/16750-16938     UGCAAUGCCGGUAAAUAUGGU---GUCUA------------------------UAUA--------GACAA------AAUA--GGGAA-U-CU-G-G-UGA-------------------------------AAGUCCAG-AACUGUCC-CCCGCAACUGUAA--GU-GC----------UGACGAAAUAAGCGUUG----------------------------ACCACUGCCUCUGAAUAUA------------------------------------------------------GAG-GCGGGAAGGG---CUU--A-AA--GUAGGAAGAA------------------------------------------------------------------GCAC-AAGUCAGGAGACCUGCCAUAUUUAUAGCGUCUUAU
AAVM02000011.1/57485-57690     UAUCUUUGCCGCCGAAAUGGU---UCGGAAUCCGUAGCCA-------------ACGGA----CGACGAUU------AAUA--GGGAA-U-CG-G-G-UGC-------------------------------AAAUCCCG-AACAGU-C-CC-GCUGCUGUGAA-GC-UC----------AGUUCAAUGUCUUAUAAAUGAACUAAUUUGAC-------------GCCACUGAU--GUUC----------------------------------------------------------U-A-UCGGGAAGGC---AAA--U-AA--GACAA-----------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCACUUCACGUAAAACGUUC
AALV01000001.1/473478-473696   CAAUGCAGGGCGUAUGUUGGUU--CCUGUCC----------------------CAGA-------CAGGCG------AAGA--GGGAA-C-GC-G-A-UACGCAUUGAUCCAGCCUUGGGUCAGCGC-----CAAG-CGC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AGAGAGCUUUCAA---------------------------------CCACUGGCC-CGCA-----------------------------------------------------------GG-CUGGGAAGG----UGA--A-GG--UUCGCAAGGC----------------------------------------------------AAGCUGCCUUAGAUCCGC-AAGCCGGGAGACCUGCCAGCAUAGUUUGUAACGGG
AALV01000001.1/486810-487026   UGACCACCUAUUCCGGACGGUU--CCCCGUGCGCCUUCG--------------GGCAA----UCGGGGUG------AAAA--GGGAA-U-AC-G-G-UGCGGUGCCAAAGCAAAGGUGCC-----------AAAUCCGG-AACUGCCC-CC-GCACCUGUAA--GU-GA----------AGAGCAACCCGCAUU------------------------------GCCACUGGGCCACAC----------------------------------------------------------CGC-CUGGGAAGGC---GCG--G-CA--CGCAUGGAC-------------------------------------------------------------------GCACAAAGUCAGGAGACCUGCCGUCAUGGGGAUGAUCCCC
BA000040.2/3617290-3617510     AAAUGGUGGCCCGGCGUUGGUU--CCUGUCC----------------------UAUG------ACAGGCG------AAGA--GGGAA-U-GC-G-A-UAGGGUCCGAAUCGGCAAGAUUUGGGUCCA----AAAU--GC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AGAGAUGCCC----GAG----------------------------GCCACUGAUCCCUGACG--------------------------------------------------------GGA-UCGGGAAGGC-----G--G-GG--AUCGAAGGGC-------------------------------------------------------AAAACCCUGCUCCGC-AAGCCGGGAGACCUGCCAGCGCGGACGAUUUUGGA
CP000140.1/4143906-4143709     UACCUUUGCAUCCGAAUUGGU---UCCGUACGCUCGUUC--------------GGGCA----UACGGAUU------AAAA--GGGAA-U-CC-G-G-UGA-------------------------------GAAUCCGG-UACAGU-C-CC-GCUGCUGUGAA-AC-UCCUU-------UAACAUUCUAAUACUACUUUC------------------------GCCACUGGCCUAGUA-----------------------------------------------------------AG-CCGGGAAGGC---AUU--A-GA--AUGG------------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCAUUCAUUUAAGAUUCAUA
AM420293.1/6681388-6681576     UCGCCCUGUUGCGGAGAGUGUU--CGCAGCA----------------------UUCGA----GCGGCGAC------AGGUGGAGGAA-G-CC-G-G-UGC-------------------------------GAGUCCGG-CGCGGU-C-CC-GCCACUGUCA--CC-GG----------GGAGCGGACUCCAACGAC---------------------------GUCACUGCCC--UGC----------------------------------------------------------GGG-GCGGGAAGGC---GGA--G--C--GAGCGCUGAU------------------------------------------------------------------CCGG-GAGCCAGGAGACU-CCGGUCGCCGCGACCUACGAC
CP000301.1/3909916-3909716     UACAAUAUAUAGUGUUACGGUC--UCCACAUGUUAC-----------------AUCAU----GUGGGGCU------AAGA--GGGAA-G-CC-G-G-UGU-------------------------------GAAUCCGG-AGCUGCCC-CC-GCAACUGUCA--GC-GGC---------GAGCCGCCGUCCAGCGAU---------------------------AUCACUGAUGCCGCAAG--------------------------------------------------------GUG-UUGGGAAGAU--UGGA--C-GG--AAGCUGUGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGUAGCAACGUGAAACGUC
CP000283.1/714109-714317       CUUCUAUCGGCAUGUUCAGGUG--UGCCGGA----------------------GUCUU----CCGGCA-----------CA-GGGAA-G-CC-G-G-UCCGGGCGCCUUUGGCGGCGCCU-----------CAAGCCGG-CGCUGCGC-CC-GCAACUGUAG--GC-GGC---------GAGCGAUCCUUCAUCAU----------------------------GCCACUGGGCCCGUCG---------------------------------------------------------GGU-UCGGGAAGGC---GGA--G-GA--UUGCGACGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCGGCCUGAGCCACGUCAUCUUCC
AAMD01000003.1/111144-110935   AUGAGAUGUGCUUCGGCACGU---UCUUGAU----------------------GACGC----AGUAGUCUU-----AAAA--GGGAA-C-CC-G-G-UGU-------------------------------GAAUCCGG-GGCUGC-C-CC-GCAGCGGUAA--GC-GAGA--------ACGACCUCCACGACGA------------------------------GCACUGGUCCCUUCCG--------------------------------------------------------GGA-CUGGGAAGC----GGU--G-GA--CAGUAGGAAC-----------------------------------------------CCGGCGCAAGCCGGAGUGCUCGU-GAGCCCGAAGACCUGCCCGCACCUGACGUUGGAGA
AAYA01000006.1/294690-294473   CGCAUCAGCCGGAGUGCUGGUG--CCUGUGU----------------------CUAG-------CAGGUG------AAAA--GGGAA-U-GC-G-C-AGCCCCGCGUCGGGG-------------------UCAGGCGC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AAAG--GGCCCGAA-------------------------------GCCACUGGCG-ACAU-----------------------------------------------------------CG-CCGGGAAGGC---CGG--G-UU--CCGUUGGGAU-----------------------------------------CGGCAGGACUGCCUGCCGCCCAGUUCCGC-AAGCCGGGAGACCUGCCAGUGGCCGCGCCGUGGAA
AAKX01000098.1/49369-49176     UUACCCUUGCGCGCUGAUGGU---UCCCGGA----------------------GACG--------GGAUC------AAAA--GGGAA-C-GC-A-G--GCGAGGCAACGCCUC------------------GAAGCUGC-GGCUGCCC-CC-GCAACUGUGA--GC-GG----------CGAAUCCGUGCCACCGCAU--------------------------GCCACUGG---GAAA--------------------------------------------------------------CCGGGAAGGC--CCGC--A-CG--GACGACGAC-------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCAUCGACCCGAGGUCCAGC
AAKL01000016.1/79085-78906     AUCCCGCCUCACGAUGAUGGUG--CCCUU---------------------------------CCAGGGUG------AAAC--GGGAA-C-GC-G-G-UGC-------------------------------GAUGCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GA----------CGAGCCAGCGCCAACCA----------------------------GCCACCGCACCAUGA---------------------------------------------------------------CGGGAAGGC---GGC--G-CC--GGGCGAUGAU------------------------------------------------------------------GCGC-GAGCCAGGAGACCGGCCAUCUCCUUUUGUCGACGU
AE017283.1/2294565-2294765     AUAGUGACGAAUGCACGUGGUU--CCCGU------------------------GUUCG----CACGGGCC------AAGA--GGGAA-U-CC-G-G-UGU-------------------------------GAAUCCGG-AGCUGC-C-CC-GCAGCGGUAU--AU-GAG---------AACGACCGCCGUCAUGA----------------------------CGCACUGUGC--UUU----------------------------------------------------------GGC-AUGGGAAGCG---ACG--G-CU--AGUAGGAGUC----------------------------------------------------CGAUCAGGACGAGCUCAU-GAGCCCGAAGACCUGCCAGGUGUGGUCCCGCAACC
AM039952.1/3802147-3801923     UACCAUGCGCGCCCCUGAGGUG--ACUGCCG----------------------GUUGGCC--GGUGGUUU------AAAC--GGGAA-U-CC-G-G-UGCGCGCGUCGCCUUGGGCCAGGCGC--------AAUUCCGG-AGCUGCCC-CC-GCAACGGUGG--GC-GAG---------GCCAGGUGCCGCAACAU----------------------------GCCACUGUGC-AGCC-----------------------------------------------------------GC-AUGGGAAGGC---GCG--G-CA--UCGGAAGCAC--------------------------------------------------------CAGCUUCCACUCGC-GAGCCCGGAGACCGGCCUGAGGGAUUGACCCGGCA
CP000143.1/2531295-2531502     ACGGAAGGUGCGGGCGACGGUU--CCCGGAG----------------------GAAGC----UCCGGGCG------AAGA--GGGAA-U-GC-G-G-UGCGGGCCUGACAGGCCC----------------CAAGCCGC-GACUGCCC-CC-GCAACUGUAG--GC-GGC---------GAGCGCGUCCCAUCAUG----------------------------CCCACUGGCCCAGGAC---------------------------------------------------------AGG-CCGGGAAGGG---CGG--G-AC--AAGCCCAGAC------------------------------------------------------------------CCGC-GAGUCAGGAGACCUGCCGUCGACGGACCUGUAACA
CP000490.1/1566394-1566586     GCUAACUGCAACGGUCAUGGUUG-UCCCGGG----------------------GCCGACU--CGGGGAUG------AAAA--GGGAA-G-CC-G-G-UGA-------------------------------AAAGCCGG-CACUGCCC-CC-GCAGCUGUAA--GC-GGA---------GAGCGACGCCGGAUCA------------------------------CCACUGGGGCCACGC---------------------------------------------------------GCC-CCGGGAAGG----CCG--G-CC--AAGCCGAGAC------------------------------------------------------------------CCGC-AAGUCAGAAGACCUGCCAUGACGCGAAAGGACGAA
CP000441.1/778547-778740       UUACGCUUGCGCGCUGAUGGU---UCCCGGG----------------------AACG--------GGAUC------AAAA--GGGAA-C-GC-A-G-GAGAGGCAGCGCCUC-------------------GAAUCUGC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAAUCCGCGCCACCACAC--------------------------GCCACUGG---GAAA--------------------------------------------------------------CCGGGAAGGC--CGGC--G-CG--AAUAACGAC-------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCAUCGACCCGAGGUCCAAG
CP000774.1/668593-668795       UAGCAUCCGCCCCGCAAUGGU---UCCGAAGGCGAA-----------------UAGCC----GGAGGAUG------AAAA--GGGAA-C-CC-G-G-UUA-------------------------------AAUACCGG-GGCUGCCC-CC-GCAACUGUAA--GC-AGA---------GAGUUCUGCCCAACCAC----------------------------GCCACUGGCGCUCCACCUCGG----------------------------------------------------AGG-CCGGGAAGGC---UGG--G-AA--AGAACAGUGA-----------------------------------------------------------------CCUGC-GAGCCAGGAGACCUGCCAUUGCCCGUCAACGCGAA
CP000463.1/2461809-2461608     ACAUACUCUGGUGCCGAUGGU---UCCCAAA----------------------AUAU-------GGGAUG------AAAA--GGGAA-U-CC-G-G-AGCGUUGCCCGAGAUGGGCCGC------------GACACCGG-AGCUGCCC-CC-GCAACUGUGA--CC-GG----------AGAGCCGCCACCAAAU-----------------------------GCCACUGGAU--UUC----------------------------------------------------------GAU-CCGGGAAGGC---GGU--G-CC--GGCUGUGAC-------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCAUCGCCUGUGACUGACGC
CP000325.1/2461077-2460867     UUGUCGGCAUCAAGCGGCGGA---GGCUUUC----------------------GCAGC----UUCGUCGU------GAGA--GGGAA-C-CC-G-G-UGG-------------------------------GAAUCCGG-GACUGU-C-CC-GCAGCGGUAU--GC-AGGA--------ACGAACACCGUCAUCG------------------------------GCACUGGCCCCACAGCCUG-----------------------------------------------------GGA-CUGGGAAGC----GAC--G-GU--UAGUAGGAGC------------------------------------------------ACCAUCGUCGGUGCGGGCCUGC-GAGUCCGAAGACCUGCCAGUUGCGCCGGGCACGUU
CP000377.1/3101368-3101583     CCGCAUGAGAGGGGCGAUGGU---UCCCCGACGCCUAA---------------GGCCG----GUGGGAUG------AAAA--GGGAA-U-UC-G-G-UGCGGAGGAGCCAAAGGGCGCC------------AAAUCCGA-AACUGCCC-CC-GCAACUGUAA--GC-GG----------CGAGCGCCCCGUCACAG----------------------------CCCACUGAUCCUCAU----------------------------------------------------------GGA-UCGGGAAGGG---AGG--G-AC--GCGCAAUAAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAUCGCGACUUUUUAACCA
CP000494.1/3290341-3290534     CGUAUCUAACAGGAUGACGGU---UCUCCGA----------------------AAGG--------AGAGA------UUUA--GGGAA-C-AC-G-G-UGCGGGUUCUGAACCC------------------AAGGCCGU-GGCUGCCC-CC-GCAACUGUAA--UC-GGC---------GAGUGUGAGGCCAAGAC----------------------------ACCACUGG---GAAA--------------------------------------------------------------CCGGGAAGGU---GGU--U-UC--ACGCAGCGAC------------------------------------------------------------------CCGA-GAGCCAGGAGACCUGCCGUCGACAUUGCUGUUGGC
AE016958.1/2995864-2996105     AUCGAGCGAAGCAACGUUAGUA--ACGCUU-----------------------------------CGU--------AAGA--GGGAA-C-CC-G-G-UGA-------------------------------GAAUCCGG-GACUGU-C-CC-GCAACGGUAU--GC-AGGA--------ACGACCGCCGUCACCA------------------------------GCACUGGUC-GCAA-----------------------------------------------------------GA-CUGGGAAGC----GAC--G-GC--CACUAGGAACUGCCCGGCUCCUCGGCGGCCCUUCGGGACCGCAUCGUCGGCCGGGCACGCACCACCCGGUGCGCGCCUGC-GAGUCCGGAGACCUGCCAGCUGUGCCGGGCGCGCC
CP000577.1/1528291-1528485     CACCACUUCCGGCGCGCUGGUU--CCUGUCC----------------------GACCG----GACAGGCG------AAGA--GGGAA-U-GC-C-----C-------------------------------CAGA-GGC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AGAGGUUGCCC----AA----------------------------GCCACUGGCC-GCAA-----------------------------------------------------------GG-CCGGGAAGGC----GG--G-CC--GCCGCGGAGC---------------------------------------------------CGCAAGGCCCCACAUCCGC-AAGCCGGGAGACCUGCCAGCGCUGAGACUGACGGG
BA000043.1/935017-935212       AUCGUUGCGCCAAGCAAUGGU---GUCCA------------------------UCAG--------GACUU------AAUA--GGGAA-U-CC-G-G-UGU-------------------------------GAAUCCGG-AACUGCCC-CC-GCAACUGUAU--GU-GC----------GGACGAAAUGGGAUG------------------------------GCCACUGGCGGCAAGAGCCAUUCGGCGCG--------------------------------------------CCG-CUGGGAAGGC---CCC--A-AA--GUAGGACGAU------------------------------------------------------------------GCAC-GAGUCAGGAGACCUGCCUUGCUUGGAACGUUUCAU
CP000758.1/1918958-1919182     UCGCAAUUCUCAGGAAACGGU---UCCGCUG----------------------UUCA-----GGCGGAUG------AAAA--GGGAA-C-AC-G-G-UGAAGCCAUCCUGGUU------------------GAUGCCGC-GACUGCCC-CC-GCAACUGUAA--CC-GG----------AGAGCUAUCCUCCACAGCCGUGCAAGCGGUAAAA-----------GCCACUGAGAGCAGUCGAUG-----------------------------------------------------CAC-UCGGGAAGGC--GGAG--G-GA--AAGCGACGAC------------------------------------------------------------------CCGG-AAGUCAGGAGACCUGCCGUAUCCGGUCACCCAUGC
BA000012.4/1149122-1149327     CCUAAAUCCGCUCCAGACGGU---CCCUUGCCCGC------------------AACGG----CAGGGGCU------AAGA--GGGAA-U-GC-G-G-UGCGGGAUUUCGAUCUC-----------------AAAUCCGC-GGCUGUCC-CC-GCAACUGUAA--GC-GA----------AGAGCCAAGGCCGAAA-----------------------------GCCACUGGGA--CGU-----------------------------------------------------------UC-CCGGGAAGGC---GGCACC-CA--AGGCGAUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCUGCGACAAAAGAAUC
CP000301.1/4742649-4742447     UCUUUUCAGGCCGUCUUCGGUG--CCUCU------------------------GGUAA----CAGAGGUG------AAACU-GGGAA-U-GC-G-G-UGCGGCGAGAAAUCGCC-----------------AAUGCCGC-GGCUGCCC-CC-GCAACUGUAG--GC-GGA---------CUGUGCCCGAUCGAUAA----------------------------GCCACUGAUGCCGUG-----------------------------------------------------------CA-UCGGGAAGGC---GAU--C-GG--GGACCAUGU-------------------------------------------------------------------CCGU-GAGCCAGGAGACCGGCCGAAGACGCUGGUCCAACU
CP000230.1/1340533-1340749     GGCUAGCCUGCGGCUGACGGU---UCCCCCCAAGCGCA---------------AGCCG----AAGGGAUU------AAAA--GGGAA-C-AC-G-G-UGCAGGCGAAGGAUUUGUCC--------------GAAACCGU-GGCUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCCUUCCUCCGAUGAAA--------------------------ACCACUGGGGCGCGU----------------------------------------------------------GCC-UUGGGAAGGG---GGA--U-GA--AGGCGAUGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGUCCGACCCUAAUCCAUG
BA000012.4/1101095-1100897     UAUAGUCAUGCAGUCGUCGGU---UCCGU------------------------UUUG--------GAGCC------AAGA--GGGAA-U-GC-G-G-UGCGGGCGAAAUUCUUGCCC--------------AAUGCCGU-GGCUGCCC-CC-GCAACUGUGU--GC-GG-----------UAGUCCUCUCCAUAU-----------------------------GCCACUGAAGAUUCG----------------------------------------------------------UCU-UCGGGAAGGU---GGG--G-AA--GGGCGCUGAU------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGACGACGGCAAAACUGAC
AE015927.1/745345-745529       UGAAUAUGAAAAUAUUCAGGU---GCCAU------------------------UUUA--------GGUUU------AAAA--GGGAA-U-GU-G-G-UUU-------------------------------AAUUCCAC-AGCAGCCC-CC-GCUACUGUAA--UU-GA----------GGACGAAUCUUUCACAA----------------------------ACCACUCUUUCAAAAAG--------------------------------------------------------GGA-AGGGGAAGGG---AAA--G-AC--AAGGGUGAA-------------------------------------------------------------------UCAU-GAGCCAGGAGACCUGCCUGUAUAUGAAAGAUAAAC
AAXE02000001.1/18090-18297     UAAUUUUGUCUUCGGAUCGGUU--UCGUAUGAUUAAAUCA-------------GAUGA----UACGGAUU------AAAA--GGGAA-U-CG-G-G-UGA-------------------------------AAAUCCCG-GACAGU-C-CC-GCUGCUGUGAA-GC-UCCGUUU-----CAACAUCCUGAAAACUACUUUU-----------------------GCCACUGGUUUAUGGUUAU------------------------------------------------------AAA-CCGGGAAGGC---UUC--G-GG--AUGG------------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCGUUCAUUAAAGGCUAUUC
AAKV01000038.1/3066-2875       GUAGCCUUGCCGGUUCGAGGUU--CCUCGCC----------------------GGCGACG--GCGGGGCU------AAGA--GGGAA-C-GC-G-G-U-C-------------------------------GAUGCCGC-GGCUGCCC-CC-GCAACUGUGA--AC-GG----------CGAUCGUUCCCCAAU------------------------------GCCACUGCGU---------------------------------------------------------------GAC-GCGGGAAGGC---GGG--G-AA--CCGGCGGAGA-----------------------------------------------------------CGCCAGACCGU-GAGCCAGGAGACCUGCCUCGUCGAUCCCGUGGCGC
AAMD01000003.1/140975-140765   UAUAGACGCGCCUGUGCUGGU---GUCUGGGCU--------------------CACGC----CUGGACUU------AAAA--GGGAA-C-CC-G-G-UGU-------------------------------GAUUCCGG-GACUGC-C-CC-GCAGCGGUAA--GU-GAGA--------ACGAAUCUCGCCAUUG------------------------------GCACUGGCUCCUCGG---------------------------------------------------------GGG-CUGGGAAGC----GGC--G-AG--CCGUAGGAAU----------------------------------------------CCGGCCCUGGGCCGGAGCGCUCAC-GAGUCCGAAGACCUGCCCGCAUCCACCCGUGGGGA
CP000578.1/651773-651962       GCAUCGUCGGCUGGCCCUGGUU--CCCGCGG----------------------CGAUCC---CGCGGGCG------AAGA--GGGAA-G-CC-G-G-UGC-------------------------------AAGUCCGG-CGCUGCCC-CC-GCAACUGUGA--GC-GG----------CGAGCCAUCUGCCAU------------------------------GCCACUGGCCCCCAC----------------------------------------------------------GGG-CCGGGAAGGG---GCA--G-CC--GGCGUCCGAG------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGGGCCUUGACGACCAUCC
BA000040.2/3634102-3634304     AUCCUAGAUGCUCGCGACGGUU--UCCCCCG----------------------AGAG-------GGGAUG------AAAA--GGGAA-U-GC-G-G-UGCGGGGAUGUUUCCCC-----------------AAUGCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------AUAAUCCUUCGUCAGAA----------------------------GCCACUGGGUCCUCG----------------------------------------------------------GUC-CCGGGAAGGC--GACG--A-AG--UGGUGACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAGCCGUGGUCACACG
CP000362.1/3701518-3701322     GAAAAUGCAGGGCACGAUGGUU--GUUCCGGUU--------------------CAGGC----CGGGACAU------AAAA--GGGAA-C-GC-G-G-UGA-------------------------------AAUGCCGU-GGCUGCCC-CC-GCAACUGUAA--GC-GAA---------GAGUGCCUCUGUCGCAC----------------------------GCCACUGACCGAAAGAC--------------------------------------------------------GGG-UUGGGAAGGC--AAAA--G-AG--GCGCGCUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCAUCACAAACGCAACAUAA
AAMY01000011.1/25797-25600     UCCAAACAGAUCGGCGACGGU---UCUCCUU----------------------CGGG--------AGAUC------AAAA--GGGAA-C-GU-G-G-UGCGGAAUCAUCCC--------------------AACGCCAC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------UGAAUCUGCGUCAUAC-----------------------------GCCACUGGGAUAUCUCG--------------------------------------------------------GCC-CCGGGAAGGC---GAC--G-CC--AGGUAACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAAACCGUGGUCACAC
CP000490.1/155234-155429       CUACCAAGUCGCUGCAUCGGU---UUCCG------------------------CAAG--------GAAUG------AAAA--GGGAA-U-CC-A-G-CGCGCCCGAUGGGCGC------------------GAAAC-GG-AACUGCCC-CC-GCAACUGUAG--GC-GG----------CGAGCGCGAUCUGGCAG----------------------------GCCACUGGGCACGAU-----------------------------------------------------------GU-CCGGGAAGGC--AGGA--U-CC--GCGCAACGAC------------------------------------------------------------------CCGC-CAGUCAGGAGACCUGCCGGCGCGAAUUCACCAGAC
AAUW01000003.1/68358-68148     AAACCUAGAUCGUGUGAUGGUU--UCGCCCGAACAAGC---------------GUAAC----GGCGGAUG------AAAU--GGGAA-C-AC-G-G-UGAGGCGUACCCAACAGGGACC------------AAGACCGU-GGCUGCCC-CC-GCAACUGUAA--GC-GA----------AGAGCAAAGCCCUUGA-----------------------------GCCACUGGA--GCGA------------------------------------------------------------U-CCGGGAAGGC---GGG--C-UG--CGCGGAGAC-------------------------------------------------------------------UCGC-GAGCCAGGAAACCUGCCAUCCAGCGGUCCCAUUGG
AAYC01000003.1/275906-275694   CGCCUACCUGUUUUCGAUGGUU--CCUCAGGGCAGA-----------------AUGCU----GAGAGGAUGA----AAAA--GGGAA-C-AC-G-G-UGAGGUGUAGCCAACAGGCGCU------------GAAUCCGU-GACUGCCC-CC-GCAACUGUAA--GC-GG----------AUAGCGACGCCAAGCA-----------------------------CCCACUGGCC-GUAA-----------------------------------------------------------GG-CUGGGAAGGA---UGG--C-GC--AGCCAAGAC-------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAUCGUGAAUUCAACCAAG
AANB01000001.1/641586-641368   GAGCAGUGACCUAUCGAUGGU---UCCACUGAAGCCCA---------------AGGCU----UUUGGAUG------AAAA--GGGAA-U-CC-G-G-UGAGGUGUAGCCAAAAGGCGCC------------AAACCCGG-AACUGCCC-CC-GCAACUGUGA--GC-GG----------CGAGCCACUGGGAUAA-----------------------------GCCACUGAUCUGCACAGC-------------------------------------------------------AGG-UCGGGAAGGC---CCC--A-GA--CCGGCCCAGA-----------------------------------------------------------------CCCGC-AAGUCAGGAGACCUGCCCUCGUGAGUUGACCAUAG
CP000656.1/4145754-4145933     UGUAUGGCUGGUCGACCCGA----CCGGCCC----------------------CGAUG----AACAGG-----------C--AGGAA-G-CC-G-G-UGU-------------------------------GAAUCCGG-CGCGGU-C-CC-GCCACUGUGA--CC-GG----------GGAGCGAACCCCACGUCG---------------------------ACCACGGCC--GAGA------------------------------------------------------------G-GCUGGAAGGU---CGG--G-GU--GAGCGCUGAU------------------------------------------------------------------CCGG-GAGUCAGGAUACUGCUCUCGUCGGCCCUCUUGCUG
CP000781.1/3651336-3651132     UUUAGUGCCCCUGUCGAAGGU---CCCGUGG----------------------UCCCA----CACGGGCGC-----AAAA--GGGAA-U-GC-G-G-UGCGGGAGGUCUCUCCC-----------------AAUGCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------UGAGCCCCUGCCACAU-----------------------------GCCACUGUCGCCGCAAG--------------------------------------------------------GCG-CCGGGAAGGC---GGU--G-GG--GGCGCUGAU-------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCUUCGACAAGGUCCGCGCC
AM286415.1/2962117-2961936     UACUUAAAUACUGAAACAGGUA--UGUCGUG----------------------GAUA--------ACACG------AU-U--GGGAA-G-GG-G-G-UGU-------------------------------AAAUCCCC-CGCAGCCC-CC-GCUGCUGUGA--UG-CU----------GACGAACCCGCUGAG------------------------------ACCACUGAUCCAUAG-----------------------------------------------------------GA-UUGGGAAGGU---AGC--G-GG--GGAGAGUGA-------------------------------------------------------------------CGCU-AAGCCAGAAGACCAGCCAAAUCAGUAAAGAGUUUC
CU234118.1/5111792-5111599     CCGUAUCUAACAGAUGACGGU---UCUCCGA----------------------AAGG--------AGAGA------UUUA--GGGAA-C-AC-G-G-UGCGGGUCUUCGACCC------------------CAAGCCGC-GGCUGCCC-CC-GCAACUGUAA--UC-GGC---------GAGUGUGAGGCCAAGAC----------------------------ACCACUGG---GCAA--------------------------------------------------------------CCGGGAAGGU---GGU--C-UC--ACGCAGCGAC------------------------------------------------------------------CCGA-GAGCCAGGAGACCUGCCGUCGACAUUGCUGUUGGC
CR555306.1/2373817-2374002     AGUAUUUAACCGUAUCGAGGUG--CCCGC------------------------GCUCG----CGCGGGAG------AAUC--GGGAA-G-GC-G-G-UGC-------------------------------GAUUCCGC-CACGUG-C-CC-AGCGCCGUGA--UG-AG----------GAUCGUCCGGGCAGGCGUCA-------------------------GCCACUGGC--GAAA------------------------------------------------------------G-CCGGGAAGGC---GCC--C-GG--ACGAGUCGAG------------------------------------------------------------------C-CU-CAGUCGGAAGACCGGCCUCGAGACAUAUUGGCAGC
CP000781.1/4182310-4182509     UAUAGUCGUCCCGUCGUCGGUG--UUCGCUU----------------------UCGG------GCGGACC------AAGA--GGGAA-U-GC-G-G-UGCGGGAGUUUCUCCC------------------AAAGCCGC-GGCUGCCC-CC-GCAACUGUCG--GC-GGU---------GAGCGGGCCUGCAACAU----------------------------GCCACUGGA--GCAA------------------------------------------------------------U-CCGGGAAGGC---GCA--G-GC--UUCGCAAUGA-----------------------------------------------------------------CCCGC-GAGCCAGGAGACCUGCCGGCGACAUCCUGCCCGUU
CP000490.1/163550-163337       CCUAUAUGUAGGCAUCACGGUU--CUUUCGGGUCGAUC---------------CGACC----CGAAAGCG------AAGA--GGGAA-G-CC-G-G-UGCGCCUUUCGGGGC-------------------AAGGCCGG-CGCUGCCC-CC-GCAACUGUAA--GC-AGC---------GAGCCUGCGCCGGAUCAC---------------------------GCCACUGGUGCCGCACG--------------------------------------------------------GCA-UUGGGAAGGC---CGG--C-AA--GGGCAGCGAC------------------------------------------------------------------CUGC-GAGCCAGGAGACCUGCCGUGAUGAUGACGAUGAAC
CP000680.1/4136427-4136223     AGUAAGGUUGCCGCCGAUGGU---UCCGCCGCCUC------------------UGGCG----CGCGGAUG------AAAA--GGGAA-C-AG-G-G-UGCGGCGCCGCGUCGCC-----------------AAUGCCCU-GGCUGCCC-CC-GCAACUGUAA--AC-GG----------CGUACGACGCUCCCUAU----------------------------GCCACUGGCC-GCCA-----------------------------------------------------------GG-CCGGGAAGGC---GAG--C-GA--AGUGGCAAG-------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCAUCGGCAAACGGGCGUUU
CP000031.1/3058882-3059105     CCGCAUGUCCGCCCUGUUGGUG--UCCGGGC----------------------AACC--------GGAUG------AAAA--GGGAA-U-GC-G-C-CAGCGGUUCCGGGACAUGAUCCCGGGCAGCCG--UCAAGCGC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AGAGGGUGCCC----AA----------------------------GCCACUGGCC-AAAU-----------------------------------------------------------GG-CCGGGAAGGC----GG--G-AC--AUCCGCCAGA---------------------------------------------------GCAGCGCUCUGACAUCCGC-AAGCCGGGAGACCUGCCAGCACCCGAACUGCAACC
CP000390.1/3801882-3802094     UAUUCAAUGCAUGUCUGUGGUU--CUCCGGGGCGGUUUUG-------------CCGUU----CCGGAGCU------AAGA--GGGAA-G-CC-G-G-UGCGCGAUGUUGC---------------------AAAGCCGG-CGCUGCCC-CC-GCAACUGUAA--AC-GGC---------GAGCCGAAAUCCACCGGU---------------------------GUCACUGAGGUGAUAA---------------------------------------------------------GCC-UUGGGAAGAC---GGA--U-UG--AAGCGAAGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCACGGCAAGAAGAAACGUC
AAAP01003877.1/22278-22051     AUUAUAGUGCCGGGUGAUGGUU--CCCCGCGUCCGCUU---------------AGGGC----AAGGGGUG------AAAAU-GGGAA-C-GU-G-G-UGCGGCGCCCGAAAAGGGGGCC------------AAUUCCGC-GACUGCCC-CC-GCAACUGUAG--GC-GGA---------GAGGUUCCGGCCGUUAGAGAC------------------------GCCACUGGCCCUGAAAUG-------------------------------------------------------GGG-CUGGGAAGGC-UAUGC--C-GG--ACCCAACGAC------------------------------------------------------------------CCGC-GAGUCAGGAGACCUGCCAUCAUCGAGAGUCGCUUG
AE017224.1/478516-478748       CCGUAAUACCGUCAUGACGGU---UCCCCGACCGAG-----------------AGCGA----AGGGGAUU------AAUA--GGGAA-C-AC-G-G-UGAGGACGACCCAUCAAGGGGCC-----------GAGACCGU-GGCUGCCC-CC-GCAACUGUAA--GC-GGA---------UUGCCGUUCAUCCUCGUGACGCCGAAAGCGUCAU-----------GCCACUGUGC-CCAC----------------------------------------------------------GGC-ACGGGAAGGC--AGAU--G-GA--CGGCGAUUAU------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCGUCUUACGUAGUCCAUUG
CP000724.1/1570726-1570905     ACAAAAAAUAGCUUAUAAGGUG--CUCUUUC----------------------AUA---------GAGUU------AAAA--GGGAA-A-GU-G-G-UGU-------------------------------AAAUCCAC-UACAGCCC-CC-GCUACUGUAA--AU-GG----------GUAUGAAAUCCGCGAAU----------------------------GCCAUUGG---GAAA--------------------------------------------------------------CCGAGAAGGU---CGG--A-GA--GUAAGAUGAU------------------------------------------------------------------CCAU-AAGUCAGGAAACCUGCCUUAUAUUGUUAUAAAACG
CP000386.1/663892-664074       GUUAUCCUGCCCGGCGUAGGCG--GGCGA---------------------------------GAGGUC-----------C--AGGAA-G-CC-G-G-UGA-------------------------------GAGUCCGG-CACGGU-C-CC-GCCACUGUGA--CC-GGG---------GAGCGACCCCCGCACGCAGG-------------------------GCCACUGUCGCCGCGG---------------------------------------------------------GCG-AUGGGAAGGC---CGG--G-GG--AAGCGGAGAU------------------------------------------------------------------CCGG-GAGUCAGGAUACUGGCCUCUCGCCGGAGAAACCCC
AAXF02000043.1/123852-123648   AUCUUUGCCCCCCGAAAUGGU---UCAGAAUCCGUAUCCA-------------ACGGA----CGACGAUU------AAUA--GGGAA-U-CG-G-G-UGU-------------------------------AAGUCCCG-AACAGU-C-CC-GCUGCUGUGAA-GC-UC----------UGUUCAAUGUCUUAUAAUUGAACUAAUUUAAC-------------GCCACUGAU--GUUA------------------------------------------------------------A-UCGGGAAGGC---AAA--U-AA--GACAA-----------------------------------------------------------------------GAGU-CAGUCAGAAGACCUGCCAUUUUGUGUAAGACGCUC
AL646053.1/765144-764965       AUCCCGCCUCACGAUGAUGGUG--CCCUU---------------------------------CCAGGGUG------AAAC--GGGAA-C-GC-G-G-UGC-------------------------------GAUGCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GA----------CGAGUCUGCGCCAACCA----------------------------GCCACCGCACGAUGC---------------------------------------------------------------CGGGAAGGC---GGC--G-CC--AGGCGAUGAC------------------------------------------------------------------GCGC-GAGCCAGGAGACCGGCCAUCUCCUUCUGUCGACGU
AANB01000001.1/655385-655158   CGCAAGGGGGUUUUUGUUGGUU--CCUGCAA----------------------AUUG-------CAGGCG------AAGA--GGGAA-U-GU-G----ACAGGCUGAUAGGGAUUUUUGCUAUCAGCUCU-CAAG-CAC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AAAGGUCUCU----GAU----------------------------GCCACUGGCCCACCG-----------------------------------------------------------UG-CCGGGAAGGC----AA--G-AG--CACCGCAGAC-----------------------------------------------AGGCAUCGCCCGUCGAAAUCCGC-AAGCCGGGAGACCUGCCAACGCAUGAGACAACGAG
CP000738.1/523907-524111       UUAGAUGGACACACUCAAGGUG--CCGCCUG----------------------AAGGGA---GGGCGGAG------AAUU--GGGAA-G-CC-G-G-UCA-------------------------------GAUCCCGG-CGCUGCCC-CC-GCAACGGUGG--UG-GAGCG-------AACAGCCACGGCAGAAG----------------------------GCCACUGGACAGCGC-----------------------------------------------------------GU-CCGGGAAGGC---GCC--G-GG--UAGGUCCCCC-------------------------------------------------------UGCGGGACAGCUCCA-GAGCCCGGAAACCAGCCUUGAAGCAGAAACGAAUC
CP000489.1/1337566-1337356     CCAUGAGGGCCGAGCUACGGU---UCCGGCG----------------------GCGUGCC--UCCGGAUU------AAAA--GGGAA-UCCC-G-G-UGCGCCUGACCUGUUCAGGC--------------AAUGCCGG-AGCUGCCC-CC-GCAACUGUAU--GC-GGU---------GAGUGACGGUCGAUCAU----------------------------GCCACUGGCGCGAAU----------------------------------------------------------GCG-CCGGGAAGGC---CGG--C-CC--GAACGAUGAC------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCGCAGCAAUCACCCAUUUC
AAMQ01000002.1/102723-102924   CACACCGACAUACGCGACGGUU--CUCCCGC----------------------GAGG--------GAGCG------AAGA--GGGAA-CACC-G-G-UGCGACGCGCGAGCGUC-----------------UGGUCCGG-GGCUGUAC-CC-GCAACUGUGA--GC-GGC---------GAGCGAGGCGUCAACA-----------------------------GCCACUGGAUCGUCA----------------------------------------------------------GAU-CUGGGAAGGC---GGC--G-CA--UCGCAUUGAC------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCGACGCGGUCGCUCGUUCA
AAMT01000006.1/185943-186161   GCCACAAGGAUAAGGCAUGGUU--CCCGACACGGCGCAA--------------AGCGC----CAAGGGAG------AAUAU-GGGAA-U-GC-G-G-AGGGGUGAUCCAAACCGGAGCCU-----------UCAGCCGC-AGCCGCCC-CC-GCGACUGUGAC-GC-GG----------CGAGCGCCCGCCGGAU-----------------------------ACCACUGAGC--CUC----------------------------------------------------------GGC-UCGGGAAGGU---GGC--G-AA--GCGCGACGAC------------------------------------------------------------------CCGCAAAGCCAGGAGACCUGCCAUGUGAAACGAAACCCCA
AE005673.1/502948-503176       GUCUGUUGCCGUUGUCGUGGU---CUGCGGACGUU------------------CGCGU----CCGGAGCU------AAGA--GGGAA-G-UC-G-G-UGAGGGCGUGAAACCCU-----------------GAAUCCGG-CGCUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCCGCUGUCCGUUUCGU--------------------------GUCACUGACGCGCCGAAGCUGGUUCGGGGAU------------------------------------------GCG-UCGGGAAGGC-CAGGG--C-AG--GGGUGACGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCUCGACAGAUAACGUCCUC
CP000113.1/8100727-8100515     AUCCCCGCUCGCGUCCUCGGUG--UCGCCGU----------------------GGAGCCA--CGGUGACU------CA-A--GGGAA-C-CC-G-G-UGU-------------------------------GAAUCCGG-GACUGC-C-CC-GCAGCGGUGA--GC-AGGA--------ACGAACGCCGUCACGUGA---------------------------AGCACUGGCCCGAAGC---------------------------------------------------------GGG-CUGGGAAGC----GAC--G-GC--AAGUAGGUGG-----------------------------------------------GUGCUCCGUGCACCCGCGCCUGC-GAGUCCGAAAACCUGCCGAAGACCCGUGCCCUUGG
CP000712.1/3685877-3686075     UCUACCAUGCGGGCCGCCGGU---UUCCACC----------------------ACG---------GAACU------AACA--GGGAA-U-CC-C-A-GGCCUGCCAAUACGGGCC----------------AAAC--GG-AACUGCCC-CC-GCAACUGUAG--GU-GC----------CGAGCCUGCUCCAUCGAU---------------------------GCCACUGGGCCUGCC-----------------------------------------------------------GC-CCGGGAAGGC--CGGA--G-CC--GGGCCGUGAC------------------------------------------------------------------GCAC-CAGUCAGGAGACCUGCCGGCCUACAUUCACCAACC
CP000662.1/326137-325950       GCAUCGUCGCGGUGCCCUGGUU--CCCGCGG----------------------UGAUCC---CGCGGGCG------AAGA--GGGAA-G-CC-G-G-UGC-------------------------------AACUCCGG-CGCUGCCC-CC-GCAACUGUGA--GC-GG----------CGAGCCAUCUGCCAU------------------------------GCCACUGGCC--CCC----------------------------------------------------------GGG-CCGGGAAGGG---GCA--G-CC--GGCGUCCGAG------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGGGCCUUGACGACCAUCC
AL591985.1/580383-580598       CAUACCAGAUCAUGUGAUGGU---UCCGCCCGACUGA----------------AGAAC----GGCGGAUG------AAAA--GGGAA-C-AC-G-G-UGAGGACGACCCAUCAGGGGCU------------AAAACCGU-GGCUGCCC-CC-GCAACUGUGA--GC-GG----------CGAGCAAAGUCCAAGGAU---------------------------GCCAUUGGCCAUGAAU---------------------------------------------------------CGG-CUGAUAAGGC---GGA--C-AA--AGCUACGAC-------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCAUCACCUUGGGCGACACG
CP000449.1/2738434-2738239     UAGCUUUCGCGCCGCGAUGGU---UCCCU------------------------CACG--------GGAAU------AAUA--GGGAA-G-CU-G-C-UCAGGCCUUCGGGCC-------------------AAGUCCAG-CGCUGUUC-CC-GCAGCCGUAG--GC-GGC---------GAGCGGUGAGGCACAAA----------------------------GCCACUGGGG-GUGA-----------------------------------------------------------CC-CUGGGAAGGC---GCU--U-CA--UCCGCAUUGA-----------------------------------------------------------------CCCGC-AAGCCGGAAGACCUGCCGUCGCUGUCGUCUGUCCG
CP000394.1/902076-901862       CUAAGCAUGCCUGGUCGUGGUU--CUGCGGGUCCGUCAAAGAC----------GAACG----CCGGAGCC------AAGA--GGGAA-U-CC-G-G-UGCGCAUCAGC-----------------------AAAGCCGG-AGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCCUGCAUCCACCGAC---------------------------GUCACUGAGGCUUCC----------------------------------------------------------GCC-UCGGGAAGAC--AGGA--UCGC--AGGCAAUGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCACGACACCAUAAUCGUCC
CP000463.1/575538-575326       GACCUAGAUGGCCGCGACGGU---UCUUCGC----------------------AAGA--------AGAUC------AAAA--GGGAA-C-GC-G-G-UGCGGGGCCUCCCACUUGGAAUGGCCCC------UAUGCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------UUAGUCUUUCGUCUGAU----------------------------GCCACUGGGUGCUUCG---------------------------------------------------------GUC-CUGGGAAGGC--GACG--G-AA--GGUCAACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCGAUCGUGGUCACACG
CP000319.1/4032968-4032764     CCAUAGGUUGGUUGUCGAGGUU--CUCCGGGUAUU------------------CAUGC----UUGGAGCU------AAGA--GGGAA-G-CC-G-G-UGCGCUCUUGAGC---------------------AAGACCGG-CGCUGCCC-CC-GCAACUGUAA--GC-GGU---------GAGCCGUGGUCCAUCAU----------------------------GCCACUGGGU-GUUG-----------------------------------------------------------UC-CCGGGAAGGC--CGGA--C-CA--AAGCUGAGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCCCGGCAACAUAGUCGUCC
CP000480.1/6690166-6689959     GUACCGGCCAUCGAGUUCCGUG--UGCUGUC----------------------ACAGG----UGCGGAAC------GAGA--GGGAA-C-CC-G-G-UGA-------------------------------AAAUCCGG-GACUGU-C-CC-GCAGCGGUAU--GC-AGGA--------ACGACCGCCGUCAUCA------------------------------GCACUGGCCCCGCCUAG-------------------------------------------------------GGG-CUGGGAAGC----GAC--G-GC--CAGUAGGUGU--------------------------------------------------GCGUCAGCGCACGCGCCUGU-GAGUCCGAAGACCUGCCAGCCGUACCGGAUGCGCC
CP000325.1/140970-141190       AUCGCCCCACGCGGUGUCGGCA--UCGAGCGA---------------------GGCAU----CAACGAUGCGUCGUAAGA--GGGAA-U-CC-G-G-UGA-------------------------------GAAUCCGG-AACUGU-C-CC-GCAGCGGUAU--GC-AGGA--------ACGACCGCCGUCAUGAACGAAACA---------------------AGCACUGGUCCUUCA----------------------------------------------------------CGA-CUGGGAAGC----GAC--G-GC--CACUAGAAGC--------------------------------------------------ACCACCGGGUGCGCGCCUGC-GAGUCCGAAGACCUGCCAGUUGUGCCGGGCGCGCC
CP000319.1/4110955-4110750     CUUGUUUGGGAGAUCAUCGGUG--CCUCCCG----------------------CGGG--------AGGUG------AAAC--GGGAA-U-GC-G-G-UGCGGGGAUACUGCCCCC----------------AAUACCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------CCAUCCGUAUCCAUUCG----------------------------GCCACUGACCAUGCCAUGCA-----------------------------------------------------UGU-GCGGGAAGGC---GGA--U-CC--GGAUAACGG-------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCGGUGACGCAUUCUUAGGC
BA000012.4/4044596-4044395     UUAGAUCAUGUCAUCUCAGGUG--CCGCUUC----------------------GUGACGACGGGGCGGAG------AAUU--GGGAA-G-CC-G-G-UCA-------------------------------AAGUCCGG-CGCUGCCC-CC-GCAACGGUGG--UG-GAGU--------UCAAGUCGCAACGGGAG----------------------------ACCACUGGGC-AAAA-----------------------------------------------------------GC-CUGGGAAGGU---GUC--G-CG--ACCGUCCGCA-----------------------------------------------------------AGGACACUCCA-GAGCCCGGAAACCAGCCCGAGAUUUUUGAACUCGA
BA000012.4/6170874-6170694     AGGUCGCCGCCACUGCCUGGUG--CCCGCCG----------------------CAAG-------CGGGAG------AAUC--GGGAA-C-AC-G-G-UUG-------------------------------AACUCCGU-GGCGUG-C-CC-AACGCUGUAA--GG-GG----------GACCGCGCCGGUAAAU-----------------------------GCCACUGUCG---------------------------------------------------------------AUG-ACGGGAAGGC---ACC--G-GA--CGCGGGUUGA------------------------------------------------------------------UCCC-GAGCCAGAAGACCGGCCUGGCAGGCAUCGUCAUCC
CP000115.1/3122671-3122449     ACUAAAUAUAGUGGCCAAGGU---CUCUCGAGUCGC-----------------AACAC----CGAGAGCU------AAGA--GGGAA-G-CC-G-G-UGCGUCUCGGUCCGUGAUCCGGGC----------AAGGCCGG-CGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCCGAAGUCCACUUGAGU-------------------------GUCACUGGGGCUGCAAG--------------------------------------------------------GCU-CUGGGAAGAC--CGGA--C-CG--AUGCCUGGAC------------------------------------------------------------------CCGC-AAGUCAGUAGACCUGCCGUGGCAAAAAAAGAAUGU
CP000362.1/3352019-3351799     GGAAAGGGUUCUGGGGAUGGU---GUUCGGAAAGCCAAAA-------------GCAAU----CCGGGCUG------AAAA--GGGAA-U-AC-G-G-UGCGGCGUUCGUAACAGACGCC------------AAGUCCGU-GACUGCCC-CC-GCAACUGUAA--GC-GGU---------GAGCGACCCCGAUGAUC----------------------------ACCACUGGGUGCAUCCG--------------------------------------------------------CAU-CCGGGAAGGA---UCG--G-GC--AAGCUGUGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAUCAUCGAUGUAACUUCA
AAOT01000001.1/134844-135060   GCACAAAGAUCCCCGCAUGGU---UCCAGCCGGACGCGUCAC-----------GCGGC----CGAGGAUC------AAAA--GGGAA-U-GC-G-G-UGCGGGCGGAUCCAAACAGGACGCCC--------AAUGCCGC-AGCCGCCC-CC-GCGACUGUCA--GC-GGA---------GAGCGUCUCGCCAUC------------------------------GCCACUGG---GCAA--------------------------------------------------------------CCGGGAAGGC---GGC--G-CG--ACGCAGUGAC------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCAUGCACCGGCUUUUGCCG
CP000250.1/112481-112283       AGUACGGUCGCGCCCGACGGU---UCCCG------------------------CAAG--------GGAUC------AAUA--GGGAA-U-GC-G-G-UGAGGGUCGCGCGCGAUCC---------------GAUUCCGC-GGCUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCCUUUCGCCACAC-----------------------------GCCACUGGGCCUCGU-----------------------------------------------------------GC-CUGGGAAGGC---GGC--G-AA--AGGCACGGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCGUUCGUGGUCACACG
AM236080.1/4518994-4518768     ACCAUAUCUAGUGUUCGAGGUU--CCGUCGAUUCGUG----------------AGGAU----CGGCGGCU------AAGAC-GGAAA-U-UC-G-G-UGCGCGUCGCCAUCAUGGCGCGGC----------AAUGCCGG-AGCUGCCC-CC-GCAACUGUGA--GC-GG----------CGAGCAACUGUCCGAUUUCAG------------------------GUCACUGGAGCAUGAU---------------------------------------------------------GCU-CCGGGAAGGCUGGGGC--A-AA--GUGCUUUGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCUCGAAUGAAACGUCCACG
ABCL01000003.1/119153-118953   CUAGGCUGAUCCUGUCAGGGUG--CCGCCCU----------------------UUGG------GGCGGAG------AAUU--GGGAA-G-CC-G-G-UGU-------------------------------AACUCCGG-CGCUGCCC-CC-GCAACGGUAA--GG-GA----------GGGCAUUUCGGCGAUAG----------------------------GCCACUGGGCAAUUU-----------------------------------------------------------GU-CCGGGAAGGU---GCC--G-AG--AUGCGAGGGC-----------------------------------------------------CAUUUGGCCUGCCGCCC-AAGCCCGGAAACCAGCCUUGGCGGAUCGUCGAAUC
CP000133.1/2475759-2475573     GAAAUAGAUACCUCGUCAGGUG--CCCGC------------------------UUUCA----CGCGGGAG------AAUC--GGGAA-U-CC-G-G-UGC-------------------------------AAGACCGG-AACGUG-C-CC-AACGCUGUAA--GG-CC----------GACGCCCGCCGCUUCAUCAU-------------------------GCCACUGG--GUUUU----------------------------------------------------------G---CCGGGAAGGC--UGCG--G-CA--GACGGAUGA-------------------------------------------------------------------CGCC-AAGUCAGAAGACCGGCCUGGCAAGAUAGACCCAAC
CP000647.1/4660061-4660248     UUGUAGCAUUCGCCUACCGGU---CCUGU------------------------------------GAGUU------AAAA--GGGAA-C-CC-A-G-UGG-------------------------------AAAUCUGG-GGCUGA-C-GC-GCAGCGGUAA--GG-AA-----------GGUGAGAAAUGAGCGCACUCGGUGCA------------------GACACUGCGG--CUA----------------------------------------------------------GCC-GUGGGAAGUC-AUUAU--U-UC--UUGAAACAGC------------------------------------------------------------------CUCC-AAGCCCGAAGACCUGCCGGAAUACGUCGCACUGGG
CP000319.1/4033871-4034093     ACUAGAUAUGGUGGUCACGGU---CUCUCGAGUCGC-----------------AAAAU----CGAGAGCU------AAGA--GGGAA-G-CC-G-G-UGCGCCCGAGUCUUAAUGGCGGGC----------AAUGCCGG-CGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCUGAAGUCCAUUAUUGU-------------------------GUCACUGGGACCGCAAG--------------------------------------------------------GCC-CUGGGAAGAC--CGGA--C-CG--ACGCCUAGAC------------------------------------------------------------------CCGC-AAGCCAGUAGAUCUGCCGCGACAACAAAAACGUCC
AALY01000002.1/134769-134968   AGCAUUGUCGCCCCUGAUGGUU--GCCCGGG----------------------ACGAAU---CCGGGCUG------AAAA--GGGAA-C-GC-G-G-UGCGGGUCUGACCC--------------------AAUUCCGC-GGCUGCCC-UC-GCAACUGUAA--GC-GG----------CGAAUGUCUCGCACCAU----------------------------GCCACUGGCC--CUC----------------------------------------------------------GGG-CUGGGAAGGC---GCG--A-CC--CAUGAUGAC-------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCAUCCAGGGCGCUGUCCGG
CP000494.1/6303139-6303357     ACCUACUGUGAUGACGACGGU---GCCCC------------------------AUAAC----CGGGGCUC------AAAA--GGGAA-U-GC-G-G-CGCCGGACGCGUCUCGCGAGGGACAUGAUCG---AAGGGCGC-AGCUGUCC-CC-GCUCGUGCAG--GC-GG----------CAAAUGACGCGUCAUAG----------------------------GCCACUCGGAAAUCCUG--------------------------------------------------------GUC-CCGGAACGAC--GUCA--U-GG--CGGCUAUGAC------------------------------------------------------------------ACGC-GAGCCAGGGCACCCGCCGUCAGCGGUGGUCACACG
AP007255.1/306940-307165       AUUAUAGUGCCCGGCGAUGGUU--CCCCGCGACCGGCG---------------ACGGC----GCGGGGUG------AAAAU-GGGAA-C-GC-G-G-UGAGGCACCCGAAAAGGGGGCC------------GAUUCCGC-GACUGCCC-CC-GCAACUGUAG--GC-GGA---------GAGGUUCCGGCCCUGAGAGAU------------------------GCCACUGGCCCGAAAA---------------------------------------------------------GGG-CUGGGAAGGC-UAUGC--C-GG--ACCCAACGAC------------------------------------------------------------------CCGC-GAGUCAGGAGACCUGCCAUCAUCGAGAGUCGCUUG
CP000539.1/3361819-3361627     UUAUCAUCCCCGUCCUCAGGUG--CCCGCUGCCGC------------------AAGGC----AAAGGGAG------AAUC--GGGAA-G-GC-G-G-UUG-------------------------------GAGUCCGC-CGCGUG-C-CC-AACGCUGUAA--GG-AA----------GAUGACCCCCGCUCAAU----------------------------GCCACUGGCCGCCAA-----------------------------------------------------------GG-CCGGGAAGGC---GCG--G-CG--GGUCAGAUGA------------------------------------------------------------------AUCC-AAGCCAGAAGACCGGCCUGAACGUUCAUCGCGCUG
AALZ01000005.1/160175-160353   GGCCCAAUGGCCGGGUCUGGUG--UCCGCCU----------------------CGC---------GGAAG------AAUC--GGGAA-G-CU-G-G-UGA-------------------------------AACUCCGG-CACGUG-C-CC-AACGCUGUAA--UG-GG----------GAUGGUUUGCGCAUAG-----------------------------GCCACUGGAA----U----------------------------------------------------------AUU-CCGGGAAGGC---GCG--C-GG--ACCAGACGA-------------------------------------------------------------------CCCU-AAGUCAGAAGACCGGCCAGACAGUACAGCUUGCCC
CP000480.1/6704143-6703957     GGCUAUUGUUGUGGCGCUGGU---CGGCCCG----------------------ACCGGC---CCGAUGAG------UAGGU-AGGAA-G-CC-G-G-UGU-------------------------------GAAUCCGG-CAUGGU-C-CC-GCCACUGUGA--CU-GGG---------GAGCGAACCCCACAUCG----------------------------ACCACGGCU--UGAC------------------------------------------------------------G-GCUGGAAGGU---CGG--G-GU--GAGCACUGAU------------------------------------------------------------------CCAG-AAGUCAGGAUACU-GCUCUCAUUGGCCCUCUUGCU
CP000494.1/6305642-6305856     ACCUACUGUGAUGGUGACGGU---GCCCC------------------------CUGAC----CGGGGCUC------AAAA--GGGAA-U-GC-G-G-UGCCGGACGUCCUUAACGGAUCGUUCG-------AAGGCCGC-AGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAAUCUCACGUCAGAU----------------------------GCCACUGGGAAUUCUCG--------------------------------------------------------GUC-CUGGGAAGGC--GGCG--U-UG--AGGUGACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAGCCGUGGUCACACG
CP000301.1/2063662-2063445     AUGCAGUCCAUAGCCGACGGUG--CCCUGUC----------------------CUCGG----ACAGGGCG------AAGA--GGGAA-UACC-G-G--GCGCCGGGUUAAGGGAUGGUCCCUUAGGCCGGUGAAGCCGG-AGCUGCCC-CC-GCAACUGUGA--GC-GG----------ACAGCCUGCACCGAAA-----------------------------ACCACUGGGU--CUC----------------------------------------------------------GAC-CUGGGAAGGU---GGU--G-CC--GGCCAUGAC-------------------------------------------------------------------CCGC-GAGCCAGGAAACCUGCCGUCGCCUGCGAUUUCGCC
AE015928.1/1832233-1832438     UAUCUUUGUCCCCGCAUUGGU---UUGCGACUCUCAUCAC-------------GAGGG----AAGCGAUU------AAAA--GGGAA-U-CA-G-G-UGU-------------------------------AAAUCCUG-AACAGU-C-CC-GCUGCUGUAA--GU-UCCAUAGA----UAUGUUGCGAGCAAUCUACUCAAA---------------------GCCACUGGAAAGAAA----------------------------------------------------------AUU-CCGGGAAGGC---GCC--C-GC--AACAG-----------------------------------------------------------------------GAAU-AAGUCAGAAGACCUGCCAUGUAAAAUCCGUUUCAC
CP000667.1/4966842-4966623     AUGGUGUCUCCCGCAGCUGGU---UCGACCGCUCCCGCCG-------------GGAGU----GGGCGAGGC-----AAGA--GGGAA-C-CC-G-G-UGG-------------------------------GAGUCCGG-GACUGC-C-CC-GCAGCGGUGA--GU-GGG---------AACGACCGCCGUCAUCA----------------------------CGCACUGGGCUCAUCGA--------------------------------------------------------GGC-CUGGGAAGCG---ACG--G-CC--AGUAGGCGAC------------------------------------------------CGGGUCUCCCGGGCGUGCCCGC-GAGUCCGAAGACCUGCCAGCGCGCCGCACGCGUCG
CP000283.1/4855579-4855783     CAUCUAGAUGAUUGUGACGGU---UCCCCUU----------------------CCGG--------GGAUC------AAAA--GGGAA-U-GC-G-G-UGCGGACCUCUUCGGAGGACC-------------AAUGCCGC-AGCUGUUC-CC-GCAACUGUAA--GC-GGU---------UCGACUUUCGUCGGAAU----------------------------GCCACUGGGAAACUCG---------------------------------------------------------GUC-CUGGGAAGGC---GAC--G-AA--AGCUAACAC-------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAUUCGUGGUCACACG
AAYC01000005.1/205052-205266   CUCAUACAUAGCGCUGAUGGUU--UUUCCGGGGGACA----------------CUCCU----GGAAAAUG------AAAA--GGGAA-U-AC-G-G-UGAGGUGUAGCCAACAGGCGCC------------AAAUCCGU-GACUGCCC-CC-GCAACUGUGA--GC-GGA---------GAGCAUUGCUGCAACAA----------------------------GCCACUGCCC--CAA----------------------------------------------------------GGG-GUGGGAAGGC---GUA--G-CA--AGGCAUCGAC------------------------------------------------------------------CCGC-GAGUCAGGAGACCUGCCAUCUAGUAGUUCACCAAC
CP000578.1/48121-47921         GGCUACUCAAUCCUCGUCGGU---UUCCG------------------------UAAG--------GAAUU------GAAA--GGGAA-U-CC-G-C-CGCCGGACCUGUCCGG------------------CGAACCGG-AACUGCCC-CC-GCAACUGUAG--GC-GGC---------GAGGAGCUCGCGAUCAAA---------------------------GCCACUGUGGCCUCAA---------------------------------------------------------GCC-AUGGGAAGGC---CGC--G-CC--AGCCCUGUGA-----------------------------------------------------------------CCCGC-CAGUCAGGAGACCUGCCGGCGUUCGAUCUCAACGC
CP000152.1/1678463-1678270     UUACCCUUGCGCGCUGAUGGU---UCCCGGA----------------------AACG--------GGAUC------AAAA--GGGAA-C-GC-A-G-GAGAGGCAGCGCCUC-------------------GAAUCUGC-GGCUGCCC-CC-GCAACUGUGA--GC-GG----------CGAAUCCGUGCCACUGCAU--------------------------GCCACUGG---GAAA--------------------------------------------------------------CCGGGAAGGC--CGGC--A-CG--AAUCAGGAC-------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCAUCGACCCGAGGUCCAAG
CP000463.1/3539927-3539727     UACAAGAUAUGGCGUUACGGUC--CCCACAUGUCAC-----------------AUCAU----GUGGGGCU------AAGA--GGGAA-G-CC-G-G-UGU-------------------------------GAAUCCGG-CGCUGCCC-CC-GCAACUGUCA--GC-GGC---------GAGCCGCCGUCCAGCAAU---------------------------AUCACUGACGCCGCGAG--------------------------------------------------------GUG-UUGGGAAGAU--UGGA--C-GG--AAGCUGUGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGUAGCAAACGCGUAACGU
CP000031.1/3757898-3758110     CGCUACCGCUGGGUCGAUGGU---UCCCGGUCGUGC-----------------AUGCG----CCGGGAUG------AAAA--GGGAA-C-AC-G-G-UGCGGCCCUCUGGCGACAGAGGACC---------AAUGCCGA-GACUGCCC-CC-GCAACUGUAA--GC-GG----------UGAGCGAUGCCGAAAU-----------------------------GCCACUGGCC--CCC----------------------------------------------------------GGG-CCGGGAAGGC---CGG--C-AA--AGCCCGGAC-------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAUCGCAACCGUAACUCGA
CP000440.1/1742843-1742651     UACGGCCGUUCGUUCGCCGGU---GCCCU------------------------UCGG--------GGCCG------AAGA--GGGAA-C-AC-A-G-GGCGCGUAUCGC----------------------GCUGCUGU-GGCUGCCC-CC-GCAACUGUAG--AC-AG----------CGAGCCGAUCUCCCCCCUCAU------------------------GCCACUGGU---UUC------------------------------------------------------------A-CCGGGAAGGC--CGGG--A-GC--CGGCGCCGAC------------------------------------------------------------------CUGU-CAGCCAGGAGACCUGCCGGCCUGAAAGUGCGUGCG
CP000662.1/314827-314627       UUCAACGGCAGCGUCAUCGGUU--CUUCCGG----------------------CAACG----GAAGAGGA------AAGA--GGGAA-U-GC-G-G-UGAGGCCGGAUGGCC-------------------GACUCCGC-GGCUGCCC-CC-GCAACUGUGA--GC-GG----------UGAGCGAGGCCGACAU-----------------------------GCCACUGGGCGCCCU-----------------------------------------------------------GC-CCGGGAAGGC---CGG--C-CG--AAGCUGUGAU------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGCUGGCGCGCGGGGAGCG
CP000089.1/155783-155587       CCGGCCUUUAUGUCUCUCGGUG--CCCGGCCGAU-------------------UUAUC----GGCGGGAG------AAUC--GGGAA-G-GC-G-G-UGC-------------------------------AAAUCCGC-CGCGUG-C-CC-AACGCUGUAA--GG-AG----------GACGGGCGAUGCGAAAA----------------------------GCCACUGGUCAGGGAAAACC-----------------------------------------------------CGG-CCGGGAAGGC---GCA--U-CG--GCCGGGUGA-------------------------------------------------------------------AUCC-GAGUCAGAAGACCGGCCGGGAGACGAAACCGGGCU
CP000376.1/216700-216497       UACAACUCUGCCCUACGAGGUG--CUGUCCG----------------------GGCUUUCC-GGACGGAG------AAUU--GGGAA-G-CC-G-G-UGC-------------------------------GAUUCCGG-CGCUGCCC-CC-GCAACGGUCA--UG-GGAUU-------CGCGGGCGUAACAUCU-----------------------------GCCACUGGGAGGAGG-----------------------------------------------------------AC-CCGGGAAGGC---GUU--G-CG--CUCCGACCAG---------------------------------------------------------CAGGUCACCCCCA-GAGCCCGGAAACCAGCCUCGGCAGAUAUCGUCAAC
CP000283.1/3260113-3259915     UUAACCGGCCGCAGUACCGGUG--CCUCUCG----------------------AAGG------AGGGGUG------AAAC--GGGAA-U-GC-G-G-UGCGGGACGCUUGUCCC-----------------AAUGCCGC-AGCUGCCC-UC-GCAACUGUGG--GC-GG----------AUCGGAGUGUCCUUGAC----------------------------GCCACUGGCC--AAU-----------------------------------------------------------GG-CCGGGAAGGC---GGA--C-GC--UCCAAAGAU-------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCGGUACCUCUGAAAGAACU
AAYA01000008.1/50513-50733     UGCUUAACGAUCCGCGAUGGU---UCCCGGAACGCCAGCAA------------GCCAA----CCGGGAUG------AAAA--GGGAA-C-AC-G-G-UGAGGAUGUCCGCAAGGUGCC-------------GAAUCCGC-GACUGCCC-CC-GCAACUGUGA--GC-GG----------AGAGCGAUCCUGAGAAC----------------------------ACCACUGGGCCGGUAGGC-------------------------------------------------------GGC-UCGGGAAGGU---UCG--G-GA--AAGCGUUGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAUCUCCGGCGCGCUCCGC
AAYC01000002.1/248003-247819   UGAGCGGAAUCAGUUUCAGGUG--CCCUGCU----------------------CUUG------UAGGGAG------AAUC--GGGAA-G-GC-G-G-UGC-------------------------------AAAUCCGC-UGCGUG-C-CC-AACGCUGUAA--CG-GG----------GACUGGUCGACGAAUAU----------------------------GCCACUGAAG-UCAC-----------------------------------------------------------UU-UCGGGAAGGG---CGU--C-GA--CUGGGGUGA-------------------------------------------------------------------UCCG-AAGCCAGAAGACCGGCCUGGAACCCAUAUUGCCGC
CP000577.1/1097204-1097404     AUAUUGAGGAACGGCUUCGGU---UCCGGCG----------------------UGAUG----GCCGGAUG------AAAA--GGGAA-C-GC-G-G-UGCGGGGAGAUCUCCCC-----------------AACUCCGC-GGCUGCCC-CC-GCAACUGUAG--GC-GGC---------GAGCGACGACCGACGGC----------------------------GCCACUGGGA----U----------------------------------------------------------GUC-CCGGGAAGGC---CGG--U-CC--GAGCUGCGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCGGAGCGAUCACCCUUUCC
CP000301.1/4737279-4737476     UUAAACGCCGCGGUCGUCGGUG--CCUCUCG----------------------CAAG------GGAGGUG------AAAC--GGGAA-U-GC-G-G-UGCGGGACGAUGUCCC------------------AAGGCCGC-GGCUGCCC-UC-GCAACUGUAU--GC-GG----------AUCGAGACGUCCAACAU----------------------------GCCACUGGCC-GAUC-----------------------------------------------------------GG-CUGGGAAGGC---GGA--C-GA--GGAGAUAU--------------------------------------------------------------------CCGC-GAGCCAGGAGACCGGCCGGCGACGUCGAUCUUACG
AATQ01000008.1/90798-91010     CGCAUCUGGCACCACGCUGGUG--CCUGUGU----------------------AAAC--------AGGUG------AAAA--GGGAA-U-GC-G-C-CAGCCCGGGAAACCGGG-----------------UCAAGCGC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AAAGGUCCUCC---ACC----------------------------GCCACUGGC--CUUG----------------------------------------------------------C-G-CCGGGAAGGC---AGG--G-GG--GCCGCUGGAU------------------------------------------------GGCGCUGCCAUCCUGCAUCCGC-AAGCCGGGAGACCUGCCAGCGCAAGACGACACCAA
AM263198.1/1157829-1158018     CGCAUUGCCGGGUACUAAAAAA--CUAAAUA----------------------GGUGA----AUAUAUUA------AUCC--GGGAA-A-GA-G-G-UGA-------------------------------AAAUCCUC-UACAGGCC-CUAGCUACUGUAA--UA-C-----------GGACGAAAGCCAAAUAGAC--------------------------GUCACUGGAA-GAAA-----------------------------------------------------------UU-CCGGGAAGAC---UGG--U-GA--GUAGGAUGAU-------------------------------------------------------------------GUU-AAGUCAGGAGACCGCUUUUAUAUUCGAUAUCCAAA
CP000377.1/185492-185258       CGUAGCAUCCAGACAGAUGGU---UCCUGCCUCUGU-----------------UUGGG----GUGGGAUG------AAAA--GGGAA-U-AC-G-G-UGAGGCUUUGGACCAUUGGGUCCCGCC-------AAGUCCGU-GACUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGUUCCCCGGCAAAG------------------------------CCACUGACCCCAACGUCGUAACCGGCAAAAAA----------------------------------------GGG-UCGGGAAGG----GCC--G-GU--UCGCGAUGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAUCGGCAAUGUAAACCUG
CP000653.1/4368932-4368756     UUGUAGCAUUCUGUUUCCGGU---CUCAU----------------------------------GUAAGUG------AAAA--GGGAA-U-CC-A-G-UGC-------------------------------AAAUCUGG-AGCUGA-C-GC-GCAGCGGUAA--AG-AC----------UGGCGGGAUGAGAGUUGUA--------------------------GACACUGU---GAAA--------------------------------------------------------------AUGGGAAGUC---UUC--A-UC--CGUAAAACGC------------------------------------------------------------------CACU-AAGCCCGAAGACCUGCCGGAAUUACGUCGCAUCUG
CP000304.1/1397689-1397909     AACCUCCGCGUCGCCUCAGGUG--CCCCCUGGCCUUG----------------UGCCA----GACGGGUG------AAACA-GGGAA-G-CC-G-G-UCCAUUCUCACGAA--------------------GAUUCCGG-CGCUGCCC-CC-GCAACGGUAG--GC-GAG---------UCGAGAAACCGCAACG-----------------------------GCCACUGUGCAUGAC-----------------------------------------------------------GC-AUGGGAAGGC---GCG--G-UU--UCGGGAUGCC-----------------------------------------------------GCAAGGCAUACGCUCGC-AAGCCCGGAGACCGGCCUGUCGCAUUUCACUGACA
AAAP01002012.1/63-265          GCACAUCCUGGAAGUGACGGU---UCCCU------------------------UCGG--------GGAUC------AAAA--GGGAA-C-GC-G-G-UGAGGACUUUCGGGUCC-----------------GAUGCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCCUUUUCACCACCGAU--------------------------GUCACUGGAUGAGCCU---------------------------------------------------------CAU-CCGGGAAGAC--GGUG--A-GA--CGGCGACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAGCCGUGGUCACACG
AAAP01003421.1/1751-1551       GGUUAGAAGGUCAGCGACGGU---UCCCU------------------------UCGG--------GGAUC------AAAC--GGGAA-C-GC-G-G-UGAGGGUUCGCCCUC-------------------GAUGCCGC-GGCUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCCUUUUCACCACCGAU--------------------------GUCACUGGAUGGGCCU---------------------------------------------------------CAU-CCGGGAAGAC--GGUG--A-GA--GGGCGACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCAGCCGUGGUCACACG
CP000614.1/1755111-1754922     UACGGCCGUUCGUUCGCCGGU---GCCCU------------------------UCGG--------GGCCG------AAGA--GGGAA-C-AC-A-G-GGCGCGCCGCGCC---------------------G---CUGU-GGCUGCCC-CC-GCAACUGUAG--AC-AG----------CGAGCCGCGCUCCGCCACAU-------------------------GCCACUGGU---UUC------------------------------------------------------------A-CCGGGAAGGC--CGGG--A-GC--CGGCGCCGAC------------------------------------------------------------------CUGU-CAGCCAGGAGACCUGCCGGCCAGAAAGUGCGUGCG
AP006840.1/2078690-2078498     AAUACGGGCACAGCGGCAGGUG--CUCCCGGCCCCG-----------------CGCUC----CGGGAGUU------AAAA--GGGAA-G-CC-G-G-UGC-------------------------------AAGUCCGG-CACGGU-C-CC-GCCACUGUGA--CG-G-----------GGAGCCGUCCCCACGAUGC--------------------------GCCACUGGCC-GGAA-----------------------------------------------------------GG-CUGGGAAGGC---GGG--G-GA--AGGCGAUGAU-------------------------------------------------------------------CCG-AAGUCAGGAGACCUGCCUGUCGCUGCAACGUCACU
AALY01000002.1/281935-282138   CUAGGCUAAAGCUCUCAGGGUG--CCGUCCUCG--------------------CAAGG----GGCCGGAG------AAUU--GGGAA-G-CC-G-G-UGC-------------------------------AAGUCCGG-CGCUGCCC-CC-GCAACGGUAA--GG-AG----------GGGUGGUUGGGCGAUAU----------------------------GCCACUGGGCCGCGA----------------------------------------------------------GGC-CUGGGAAGGU--AGCC--C-GA--UCACAGGCCA--------------------------------------------------------GAUGGCCGUCCACC-AAGCCCGGAAACCAGCCAUGAGACAACGUCAGAAC
AL954747.1/696804-696577       UCUGCGCCCCUUGUUUGAGGUG--UCCCAGAUGCAUU----------------UGCAC----GAGGGAUG------AAAC--GGGAA-G-CC-G-G-UGCGCGCUGGAAUCAGCCAGCGC-----------AAUGCCGG-CACUGCCC-CC-GCAACGGUAA--AU-GAG---------UCAAUGAUCUGCACAC-----------------------------GCCACUGUGCUGUAU----------------------------------------------------------GGC-ACGGGAAGGC---GCA--G-AA--UCAGGAAAAC-------------------------------------------------------ACAGCUUCCGCUCAU-AAGUCCGGAGACCGGCCUGAAGCAAUAUCAUGUUA
CP000031.1/3073055-3073267     GGCUAAAUGAAGGGGUCUGGU---CCUGCCGGAG-------------------CAAUC----CGGAUGCU------AAGA--GGGAA-U-UU-G-G-UGCGACCGCCCGUCGGUU----------------CAGGCCAA-AGCCGCCC-CC-GCGACUGUAA--GC-GGU---------GAGCCUCUGUUCAACCA----------------------------GCCACUCCCGGGUUCGCCC------------------------------------------------------CCG-GGGGGAAGGC---GAA--C-AG--AGGCACUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCAGACAGGCACUGUAACAC
AM406670.1/2635166-2635365     AAACUCCCCGGCGUUGAAGGU---UCCCCGC----------------------CAGG--------GGAUU------AAAA--GGGAA-G-CC-G-G-UGCCGAGCCCAGCUCG------------------AAUUCCGG-CGCUGCCC-CC-GCAACUGUCA--UC-GGC---------GAGCGCUUCGCCACCCCAU--------------------------GCCACUGGA--UGCG----------------------------------------------------------U-U-CCGGGAAGGC--GGGC--G-AA--GCGCGACGAC------------------------------------------------------------------CCGA-GAGCCAGGAGACCUGCCCCAACGUCCAUCCUUGAA
CP000774.1/549380-549581       UACACUCCGCCCGCCUAUGGUG--CCCCGGCCG--------------------CAAAU----CCGGGGUU------AAAA--GGGAA-C-GC-C-C-GGAGCGCAUGCUCUUUC-----------------UUCGAGGC-GGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCUUUUUCCGAUUGU----------------------------GCCACUGGAU----------------------------------------------------------------GU-CCGGGAAGGC---AGG--G-AA--GGGCGAAGAC------------------------------------------------------------------CCGC-GAGCCAGGAAACCUGCCACAGGCUGUCGUCCGUCU
AATQ01000007.1/84467-84279     UUAAGCGGAGCGGGCCUCGGUU--CCGGGCC----------------------UUGU-------CCGGAG------AAUA--GGGAA-C-GC-G-G-UGC-------------------------------AAACCCGC-GACUGCCC-CC-GCAACUGUGA--GC-GGU---------GAGUGCGACCGGCAUAU----------------------------GCCACUGGGCGAAAC-----------------------------------------------------------GC-CCGGGAAGGC---CCG-CG-UC--GCGCGAUGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAAGGUGAUCACCCUCCCC
CP000158.1/1548021-1548210     ACAUCAACCCCAUCAGAUGGUG--CUCCCCU----------------------GACA------GGGAGCU------AAGA--GGGAA-G-CC-G-G-UGU-------------------------------AAAUCCGG-CGCUGUAC-CC-GCAACUGUUA--GC-CGG---------GAGCUGAUGGCCACUAU----------------------------GCCACUGGAACGCGA----------------------------------------------------------GUU-CUGGGAAGGC---GGC--C-AA--AGGCGACGAU------------------------------------------------------------------CGGU-GAGCCAGGAGACCUGCCAUCGCGUCGUUUGUCCGG
AAXE02000103.1/317216-317417   UAUUUGCCCUUUGAAACAGGU---UUCCCUGUCCUCCUUA-------------CAGGA----CAGGAAUG------AAAA--GGGAA-C-CG-G-G-UGG-------------------------------AAAUCCCG-GACAGACC-AC-GCUGCUGUGAA-AC-UUCGG-------UAACAUACCGGCAAUACUCAAU-----------------------GCCACUGAUC-GGGG-----------------------------------------------------------GA-UCGGGAAGGU---GUC--C-GG--GGAUGG----------------------------------------------------------------------AAGU-AAGUCAGAAGACCUGCCGUUUCGGUUUUGAAGAGU
CP000615.1/1891336-1891529     UUACGCUUGCGCACCGAUGGU---UCCCGGA----------------------GACG--------GGAUC------AAAA--GGGAA-C-GC-A-G-CAGAGGCCGAGCCUC-------------------CAAUCUGC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAAUCCGCGCCACCACGC--------------------------GCCACUGG---GAAA--------------------------------------------------------------CCGGGAAGGC--CGGC--G-CG--GAUGACGAC-------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCAUCGACCCGAGGUCCAGC
AAMY01000005.1/65948-65727     ACUAGAUAUGGUAGCCACGGU---CUCUCGAGUCGU-----------------CGUAC----CGAGAGCU------AAGA--GGGAA-G-CU-G-G-UGCGCCUCGGUCCAUGAUCCGGGC----------AAGGCCAG-CGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAGCCGAGUCCAAUUGAGU-------------------------GUCACUGGAACCGCAGG--------------------------------------------------------GUU-CCGGGAAGGC--CGGA--C-GG--ACGCUACGAC------------------------------------------------------------------CCGC-AAGUCAGGAGAUCUGCCGUGGCGGAAAGAACGUCC
AE005673.1/1924997-1925186     AGCUCUAGCUUCGCGUCAGGU---UCCUCGA----------------------AAGA--------GGAUG------AAAA--GGGAA-C-GA-G-G-UUG-------------------------------AAGACCUC-GGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCUUCGCGUCACAU-----------------------------GCCACUGGGCCCAAAA---------------------------------------------------------GGC-CUGGGAAGGC---GAC--G-CC--CAGAAGCAUU---------------------------------------------------------------GACCCGU-GAGCCAGGAGACCUGCCCGGCGCAGUCGUUCAUCG
CP000661.1/387171-386964       GCCGAUGGUGCGCGGGACGGUU--CCCGGGG----------------------GCAGC----CCCGGGCG------AAGA--GGGAA-U-GC-G-G-UGCGGGCCUGUUCGGCCC----------------CAAGCCGC-GACUGCCC-CC-GCAACUGUAG--GC-GGC---------GAGCGCGUCCCAUCAUG----------------------------CCCACUGGCCCCGGAC---------------------------------------------------------AGG-CCGGGAAGGG---CGG--G-AC--AAGCCGAGAC------------------------------------------------------------------CCGC-GAGUCAGGAGACCUGCCGUCAUCGGACCUGUAACA
AE016825.1/1690702-1690517     AUUCUUGCCAUUCUUGACGGUG--CCCCA---------------------------------AAAGGGUG------AAAC--GGGAA-C-GC-G-G-UGG-------------------------------AAUGCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GC----------AGAGUCCACGCCUGAC-----------------------------GCCACUGGCCCUUAGCA--------------------------------------------------------AGG-UCGGGAAGGC---GGC--G-CC--CGGACGGCGA-----------------------------------------------------------------CGCGC-GAGCCAGGAGACCGGCCGUCAAACGUGUCGACGCA
AAAP01003109.1/772-976         CAAAGGUCGUGCGGCCAAGGUU--CCUGCGGACUC------------------UUCCC----CGUGGGCU------AAGA--GGGAA-U-CC-G-G-UCGGUUCGUCC-----------------------GAUGCCGG-AGCUGCCC-CC-GCAACUGUGA--GC-GG----------CGAGCUCCCGCCGCGAGAG--------------------------GUCACUGGUGCCCCG-----------------------------------------------------------CA-CCGGGAAGGC-CGGGC--G-GG--GGCGCUGAC-------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCUCGGCACGACGAUAUUCC
ABBP01000344.1/210-416         AUACAGCGUCCGUCGACCGGC---GCCCC------------------------ACGG--------GGCCC------AAGA--GGGAA-C-GC-A-G-GGCGCGCCGCGCC---------------------G---CUGC-GGCUGCCC-CC-GCAACUGUGA--GC-AGC---------GAGUCCGCAUCCGAUCCAC--------------------------GCCACUGGCCACGCCGCCCUUUCGCGG----------------------------------------------CCG-CCGGGAAGGC--CCGC--U-GC--GGACGACGAC------------------------------------------------------------------CUGC-CAGCCAGGAGACCUGCCGGGACGUUUCGUUCGUGC
ABCL01000001.1/663982-664208   UGCAUACCGGACGUGCAAGGU---UCCUCGUUUGGGCGCAAAG----------CGCCU----CGGGGAUG------AAAU--GGGAA-U-GA-C-G-UGCCGGUGGACCCAAUUAGGGCGCC---------UAUGCGUC-AGCCGCCC-CC-GCGACUGUAA--GC-GG----------CGAGCCCCUGCCAGAU-----------------------------GCCACUGAGGUGCCUAUG-------------------------------------------------------ACC-UUGGGAAGGC---GGC--A-GA-CAGGCGACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCAGCCCUGCGUUCGUCAAUCCCG
CP000230.1/2009119-2009340     GUAAGCUUUGAGGAUCGUGGUU--CUUUGGCACCGUUUUGUC-----------GGGUG----CCGGAGCU------AAGA--GGGAA-U-CC-G-G-UGAGCCGCGUUUUGGC------------------GAUGCCGG-AGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAGCCGCUGUCAAGACGU--------------------------GCCACUGCCCCCGGCAAGG------------------------------------------------------GGG-GUGGGAAGGC-CAGAC--A-GC---GGCGACGAC------------------------------------------------------------------CCGU-AAGCCAGGAGACCUGCCGCGAUGUCAUAACCUCCC
CP000390.1/2942047-2941844     CUAAAUAUAGCCCAUCACGGU---GCUGUCGAGUCGUUC--------------GGGUC----GAGAGCUU------AAGA--GGGAA-G-CC-G-G-UGU-------------------------------GAGGCCGG-CGCUGCCC-CC-GCAACUGUAA--GC-AGC---------GAGCUUGUGUCGCGUAUU---------------------------GCCACUGGUGCUCCUAGA-------------------------------------------------------GCG-CUGGGAAGGC--CUGA--C-AG--AAGCGAUGAC------------------------------------------------------------------CUGC-AAGCCAGGAGACCUGCCGUGAUGAGCAUUGAACGU
CP000716.1/891454-891623       AUAUAAAUUGUUACUAUAGGUU--------------------------------------------------------AA--GGGAA-CUCC-G-G-UGA-------------------------------AAAUCCGG-GGCUGC-C-CA-GCAACCGUAA--CC-GGG---------GACGAAAUCCACAAAAU----------------------------GUCACUGGGAAUUUU-----------------------------------------------------------UC-CUGGGAAGGC---GUG--G-AG--AGUAGGUUGA-----------------------------------------------------------------UCCGG-GAGCCGGGAGACCUGCCUAUAGUAAGGUUAUUUCC
AAQW01000001.1/3968828-3969033 CCCAUCCGGCCCGUUCCAGGUG--CCUCCUGCCGC------------------CGCGC----AGGAGGUG------AAAC--GGGAA-G-CC-G-G-UGCGUCACUUCGGUGAU-----------------CAGUCCGG-CGCUGCCC-CC-GCAACGGUAA--GC-GA-----------GCGAAAUCCUCUUCAG----------------------------GCCACUGUGC--UCC----------------------------------------------------------GGC-AUGGGAAGGC---GAG--G-AU--UUCACGACCC------------------------------------------------------------------UCGC-AAGCCCGGAGACCGGCCUGCAACGCCCUGUUGGCA
AE016853.1/1878136-1878350     CCUUCGCGGCUUGUUUCAGGUG--CUCUGCAAUCCUC----------------GAUUG----GCAGGGUG------AAACA-GGGAA-G-CC-G-G-UGUGGAUCGACCGAUCC-----------------GAUCCCGG-CGCUGCCC-CC-GCAACGGUAA--AU-GAG---------UCAAGGCUGUGCAUCGU----------------------------GCCACUGUGU--UUC----------------------------------------------------------GAC-ACGGGAAGGC---GCG--C-AG--CCGGGGUAAC--------------------------------------------------------------CCGCUCAU-GAGCCCGGAGACCGGCCUGAACCACUCAAUGGCAU
CP000662.1/267567-267380       UCAUCACAGGGACGCUUUGGUU--CCCGCGGC---------------------AGCAC----CGCGGGCU------AAGA--GGGAA-G-CC-G-G-UGG-------------------------------GAAUCCGG-CACUGCCC-CC-GCAACUGUAA--GC-GG----------CGAGCCUUGCUUCGAA-----------------------------ACCACUGGCC--AAU-----------------------------------------------------------GG-CCGGGAAGGG---AAG--C-CG--GGCGCCCGAG------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCAGAGCCACAGAGACGACC
AM420293.1/1414592-1414388     AGUGUGUCCCGCGCUGAUGGAU--CACCACG----------------------GAAG--------GUGAGGC----AACA--GGGAA-C-CC-G-G-UGC-------------------------------GAAUCCGG-GACUGC-C-CC-GCAGCGGUGA--AC-GGG---------AACGACCGUCGUGACCGGCUCCGGCCGGUAC--------------GGCACUGGGCGCGCACG--------------------------------------------------------CGC-CCGGGAAGCC---ACG--A-CC--AGUAGGCCGC------------------------------------------------------------------CCGU-GAGUCCGAAGACCUGCCAUCGGUGCGCGCACGAGG
CP000482.1/1312853-1313047     AAUUGAAUAUCUGAUCAAGGU---GCCCG------------------------AGAG--------GGCUU------GAUA--GGGAA-GAGG-G-G-UGCCGCUCUCAGUAACGAGC--------------CAUUCCCC-CGCGGA-C-CC-GCCGCUGUAA--GC-GA----------UGACGA-AGGGCAGUAU----------------------------GCCACUGGU--GAAU----------------------------------------------------------A-A-CCGGGAAGGC---GCC--C-----GGAGGAUGAC------------------------------------------------------------------UCGC-GAGCCAGAAGACCUGCCUUUUGAUUAUUGCCACAG
CP000489.1/1328400-1328204     CGCUAUGGCGGAGUUGUCGGU---UUCCG------------------------CAAG--------GAAUU------GAAA--GGGAA-U-CC-G-C-CGGGGCAUCAGCCC--------------------CGAACCGG-AACUGCCC-CC-GCAACUGUAG--GC-GG----------CGAGCAGGGUGCGAAACA---------------------------GCCACUGUGGCCCAU----------------------------------------------------------GCC-AUGGGAAGGC--CGCA--U-CC--CUGCCGUGAC------------------------------------------------------------------CCGU-CAGUCAGGAGACCUGCCGACGCGAUGACCAACCCG
CP000271.1/1989295-1989475     AGGCAUAAUACAGCCGCCGGUU--GCCCU------------------------UCGG--------GGCCG------AAGA--GGGAA-C-AC-A-G-UGC---------------------------------CACUGU-GGCUGCCC-CC-GCAACUGUAU--GC-AGCG--------AGUCCGCCUGCGCUUCAC---------------------------GCCACUGGUU---------------------------------------------------------------CGA-CCGGGAAGGC---CGC--A-GC--GGACCAUGAC------------------------------------------------------------------CUGC-CAGCCAGGAGACCUGCCGGCGAGACUGUUCGUGCC
AAQW01000001.1/1951627-1951835 GCUGCGCGCCUUGCGACAGGUG--CCCCG------------------------CAAG--------GGGUG------AAACA-GGGAA-G-CU-G-G-UGCGUUCCGUCGGAAC------------------CAGGCCAG-CGCUGCCC-CC-GCAACGGUAG--GC-GAA---------UCAGACAGCCGCUCGAUG---------------------------ACCACUGUGC--UCC----------------------------------------------------------GGC-AUGGGAAGGC---GCG--G-CU--GGAAGCGUCC--------------------------------------------------------AGCGCUUCGCUCGC-GAGCCCGGAGACCGGCCUGACGCACCCACGGCAUC
AAYH02000045.1/230243-230451   UAUCUUUGUCCCAGUUUUGGUU--UCACCUCUCCCGGUUCUGUUG--------GAGAU----GAGUGAUGA-----AAAA--GGGAA-U-CA-G-G-UGC-------------------------------AAAUCCUG-AACAGA-C-CC-GCUGCUGUAA--GU-CCUUCCA-----AAAUCUUUGAAUAUUCUACAA------------------------GCCACUGUCCGCCCGG---------------------------------------------------------CGG-AUGGGAAGGC---AUU--C-AA--AGAG------------------------------------------------------------------------GGAU-AAGUCAGAAGACCUGCCAAGACAACAUAGUUUUAG
CP000140.1/2695629-2695426     UAUCUUUGCUACAUGCUUUGU---UCCCUUUCGGCAAUCG-------------CCGGA----UAGGGAUU------AAAA--GGGAA-U-CG-G-G-UGA-------------------------------GAAUCCCG-GACAGU-C-CC-GCUGCUGUAA--GC-UUCAUA------AACGGGUUGAGCAAUACUGUU------------------------GCCACUGUUCAUUCAAG--------------------------------------------------------UGA-AUGGGAAGGC---GCU--U-AA--GACCGG----------------------------------------------------------------------AAGU-AAGUCAGAAGACCUGCAAGGCGUGUAUAUUUUCGA
CP000698.1/4850452-4850264     UAAAUAGUUAUUCGAUCUGGUG--CGCUCAC----------------------UAACA----AGAGCGUU------AAAA--GGGAA-G-GA-G-G-UGU-------------------------------AAUUCCUC-CACUGU-C-CC-GCAACUGUGA--AC-GG----------UGAUGAAAGCCGCUGAUGU--------------------------GCCACUGAAU----A----------------------------------------------------------UAA-UCGGGAAGGC--GCGG--C-AA--GUAAAGUGAC------------------------------------------------------------------CCGU-AAGUCAGGAAACCUGCCAGGCUGAUUGCUCAAUGG
CP000383.1/1884029-1884217     ACCUUUGUUCCCGUUAAUGGU---UUAUUUCAAC-------------------GUUUG----AAAUAAUU------AAAA--GGGAA-G-CC-G-G-UGU-------------------------------AAAUCCGG-AACAGUUC-CC-GCUGCUGUAA--GC-UCAUCAU-----UACGUUAUAUUUCAUUUA---------------------------GCCACUGAAU----U----------------------------------------------------------UAU-UUGGGAAGGC---GGA--U-AU--AACA------------------------------------------------------------------------GAGU-AAGUCAGAAGACCUGCCACUAACACACUAUUCGAA
CP000382.1/2263667-2263491     AAAUUGUAUAUUAGCUUAGGUG--UCUGA------------------------UUAAU----UUCAGGUG------AAAA--GGGAA-U-AC-G-G-UGA-------------------------------AAAUCCGU-AACAGCCC-CC-GCUACUGUAA--UG-UG----------GACAAAUCU-----AAA----------------------------ACCACUGGUU--UAU-----------------------------------------------------------AA-CCGGGAAGGA--------A-GA--GGAGGAUGA-------------------------------------------------------------------AACU-AAGUCAGGAGACCUGCCUAAGCUUUGGAUAAAGAC
AARF01000375.1/31-230          UUGCAUAUUGUGGAGACAGGUG--CUUCGUCUGU-------------------AACGA----UGAAACUU------AAAA--GGGAA-GAUC-G-G-UGU-------------------------------AAAUCCGU-CGCGGU-C-CC-GCCACUGUAA--CA-GA----------GGAGCCUUGUGCCAGGCAAAC------------------------GCCACUGGUCUAAGA----------------------------------------------------------UGA-CUGGGAAGGC--GGCU--U-UA--AGGCGAUGAA------------------------------------------------------------------UCUGGAAGCCAGGAGACCUGCCUGUUCUAACGACACUGCU
AL591985.1/66246-66476         ACAUUAACUGGGACCGACGGU---UCCCCUACCCGUGA---------------GGUGG----AGGGGAUU------AAUA--GGGAA-C-AC-G-G-UGCGGACGACCCAAGAGGGACC------------AAAACCGU-GGCUGCCC-CC-GCAACUGUAA--GC-GGA---------UCGUCGUUCAUCCUUGUGGCGCCAAGGCGCCA-------------GCCACUGCGCGCGUU-----------------------------------------------------------GC-GCGGGAAGGC--AGAU--G-AG--CGACUCUGU-------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGUCAAAUCGAUCCAACGU
AAQF01000040.1/17254-17069     UUGGGCGAUUGCCGACCUGGU---CGCGG---------------------------GC----CUGGGGAG------AAUA--GGAAA-U-CG-G-G-UGU-------------------------------AAAUCCCG-AGCGGU-C-CC-GCCGCUGUGA--AC-GGG---------GAGUGAUUCCGGUAAAU----------------------------GCCACUGGCCGCCAGG---------------------------------------------------------CGG-CCGGGAAGGC---CCG--G-AA--AAACGAUGAG------------------------------------------------------------------CCGU-GAGCCAGAAGGCCUGCCCCUUGGUUAGCCGCCGCC
AASF01001990.1/2185-2411       UCCUGCGGCUCUGCUUCAGGUG--UCCCAAGGGUAUCCA--------------CCCCC----AAGGGAUG------AAAC--GGGAA-G-CC-G-G-UACGUACUGGUGAAAAUCAGAAC-----------AAUUCCGG-CGCUGCCC-CC-GCAACGGUAG--GC-GAG---------UUGCGGCGGAUCAUACA----------------------------GCCACUGCGU--UUC----------------------------------------------------------GAC-GUGGGAAGGC---GAU--C-CG--CCAGGGUCUG---------------------------------------------------------CAAGACCACUCGC-AAGCCCGGAGACCGGCCUGGAGCCCAAGGAACCUC
CP000450.1/2027042-2027265     CUCCACUCCCUUGCUUGAGGUG--UCCCAGAUGCAUU----------------UGCAC----GAGGGAUG------AAAC--GGGAA-G-CC-G-G-UGCGCACUGGAAUCAAACAAUGC-----------AAUGCCGA-CACUGCCC-CC-GCAACGGUAA--AU-GA----------GUCAAUAUUCUGCACAC----------------------------GCCACUGUGCCAUCC----------------------------------------------------------GGC-ACGGGAAGGC--GCAG--A-AU--CAGGAAAUAA------------------------------------------------------------AUCUACUCAC-AAGUCCGGAGACCGGCCUGAAGCAAUAUCAUGUUA
CR626927.1/1843997-1843789     UUAUCUUUGCAGUGCAUUGGU---UUGUAUUCUCCGUGUUC------------CGGGG----AUGCAAUU------AAAA--GGGAA-U-CA-G-G-UGC-------------------------------AAAUCCUG-AACAGU-C-CC-GCUGCUGUAA--GU-UUCACAUCAG--AUUGUUGUAAGCAACCACCACUU----------------------GCCACUGGGAAACGU----------------------------------------------------------UUC-CUGGGAAGGC---GCU--U-AU--CAACAG----------------------------------------------------------------------AAAC-GAGUCAGAAGACCUGCCUGUGCAUCUUUUUCAUUG
AAMV01000013.1/62699-62923     UGCAUACGAGAGUGGCAAGGUU--CCUCGUUUCGGUGCAAA------------GCGCC----GCGAGGAU------AAAU--GGGAA-U-GA-C-G-UGCCGGCGGACCCAAUCAGGGCGUC---------CAUGCGUC-AGCCGCCC-CC-GCGACUGUAA--GC-GG----------CGAGCCCCUGCCAGAU-----------------------------GCCACUGAGGUGUAAAA--------------------------------------------------------CCC-UUGGGAAGGC---GGC--A-GA-CAGGCGACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCAGCCCUGCGUUUGUUAAUCCCG
CP000698.1/931897-931705       AACUGAAUAUCGGAUCACGGU---GCCCG------------------------CAAG--------GGCUU------GAUA--GGGAA-GAGG-G-G-UGCCGCUCAAACCGAGC-----------------CAUUCCCC-CGCGGA-C-CC-GCCGCUGUAA--GC-GA----------GGACGA-AGGGCAUUAU----------------------------GUCACUGGUC-GAAA-----------------------------------------------------------GA-CCGGGAAGGC---GCC--C-----GGAGGAUGAA------------------------------------------------------------------UCGC-GAGCCAGAAGACCUGCCAUGAUCUUAGCACUCAAC
AAXV01000016.1/49194-49376     UCAUAUAAAACGUCGAUAAGUG--CUCGAAG----------------------AACU-------CGAGAU------AAUA--GGGAA-A-UU-G-G-UGA-------------------------------AAGUCCAA-UACAGCCC-CC-GCUACUGUAA--UA-GC----------UGAUGAAAUCGCAAU------------------------------GCCACCUGU--GCAA----------------------------------------------------------A-C-UAGGGAAGGU---GCG--A-CA--GUAAAAUGAA------------------------------------------------------------------GCUU-AAGUCAGGAAACCUGCUUAUCAGAUUGUGCAUGCA
AM406670.1/3903431-3903207     AAGGUGCGGCGCGUUUCAGGUG--CCCGAAGGCGGUCC---------------UCGCC----CCAGGGUU------AAAC--GGGAA-A-CA-G-G-UGCGCGCCUCCGGCGC------------------AAUGCCUG-UGCUGCCC-CC-GCAACGGUAA--GC-GAGU--------GCAAGGCGCAUCAACA-----------------------------GCCACUGGG--UCGU----------------------------------------------------------C-C-CCGGGAAGGC---GAU--G-CG--UCGGAGCCGG--------------------------------------------------CCACAGCCGCUCCAGCCCGC-GAGCCCGGAUACCGGCCCGAGCGCGAACUGGCGGA
AP006840.1/361924-361720       UAUAUUGGGGUUGUGACCGGU---GCACCUA----------------------UCGG-------GUGCUG------AAAA--GGGAA-C-CC-U-G-UGC-------------------------------GAAUCAGG-GACUGC-C-CC-GCAGCGGUGA--GC-AGG---------AACGACCGCCACAGCAA-----------------------------GCACUGGGC--UCC----------------------------------------------------------GGC-CUGGGAAGC----GUG--G-CC--AGUAGGACAG--------------------------------------------GCGGCAGAUGGUGCCGCCCCGCCUGC-AAGUCCGAAGACCUGCCGGUCAUCCGCUUUCAGGG
AAQG01000005.1/141632-141818   AACGGCCGCGCUGCGACAGGU---UCCCC------------------------GGCGA----CGGGGAUG------AAAAU-GGGAA----C-G-G-AUA-------------------------------ACAUCCG---GCUGCCC-CU-GCAACUGUAU--GC-GG----------UGAGUCAUCGGCCAUAU----------------------------GCCAUUGGAAGCGCAG---------------------------------------------------------CUU-CCGAGAAGGC--GACC--G-AC--CGGCGUUGAC------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCCGUCGCCGUCGUCUUUCG
CP000058.1/2582044-2581830     CCUGUACGCCUUGUUUCGGGUG--CCCCU------------------------CACG--------GGGUG------AAAC--GGGAA-A-CC-G-G-UGCGCUCACGCUGUCGAGC---------------AAGUCCGG-UGCUGCCC-CC-GCAACGGUAA--GC-GA-------------GAGAAGGUCUUA------------------------------UCCACUGUGC--UAC----------------------------------------------------------GGC-AUGGGAAGGU---GAC--C-UU--GCAGGCCUUG---------------------------------------------AACGCGCGACGUUUGAGCCCCUCGC-GAGCCCGGAGACCGGCCCGACAUCGUUGAAUGACA
ABDX01000004.1/114276-114455   UAAUAUUUUAUAUUUUUAGGU---UUGAU----------------------------------UUUAAUU------AAAA--GGGAA-A-GU-G-G-UUA-------------------------------AAGUCCAC-UACAGCCC-CC-GCUACUGUGA--UA-GG----------AUACAAGUUUCUAUUUG----------------------------ACCACUGAUUAUAUA-----------------------------------------------------------AA-UUGGGAAGGG---AGA--A-AU--GAGGAUAAG-------------------------------------------------------------------CCUU-AAGUCAGGAUACCUGCCUAAAGAUCAUGAACUAAG
CP000716.1/734867-735049       AAAUAAUAAAACAUCUAGGGU---ACCAA----------------------------------GCGGUUU------AAAA--GGGAA-CUCC-G-G-UGA-------------------------------AAGUCCGG-GGCUGC-C-CA-GCAACCGUAA--CC-GGG---------GACGAAAUCCACAAAAU----------------------------GCCACUGGGAAUUUU-----------------------------------------------------------UC-CUGGGAAGGC---GUG--G-AG--AGUAGGUUGA-----------------------------------------------------------------UCCGG-GAGCCGGGAGACCUGCCUUAGAUGUAUGGACUCCA
AP006840.1/2074430-2074237     AUAGAGCAAACAGCGGCAGGUG--CUCCCGACCCU------------------GCGGU----CGGGAGUU------AAAA--GGGAA-G-CC-G-G-UGC-------------------------------AAGUCCGG-CACGGU-C-CC-GCCACUGUGA--CG-GG----------GAGUCGCCCCUCGGGAUGU--------------------------GCCACUGGCC-CGAA-----------------------------------------------------------GG-CCGGGAAGGC--GGAG--G-GG--CGGCGAGGA-------------------------------------------------------------------UCCG-GAGUCAGGAAACCUGCCUGCCGCGCUGGCGCUGCU
CP000382.1/1272358-1272535     AAAUUAAAUAAGUCAUUAGGUG--CUCUAUU----------------------AUAA--------GAGGU------AAAA--GGGAA-A-GU-G-G-UUA-------------------------------AAAUCCAC-UGCAGCCC-CC-GCUACUGUAA--AU-GA----------GGAUGAAAUCUAAAUU-----------------------------GCCA----UCCAUAA----------------------------------------------------------GGA-----GAAGGU---UAG--A-AA--GUAAUAUGAU------------------------------------------------------------------CCAU-AAGCCAGGAAACCUGCCUAAUGUACGAUUAUUUAA
AAYC01000008.1/31758-31987     GAUAGCGCUGGAGAGGAUGGU---UCCUGCGAGACACAAACUG----------UGUGU----CCAGGAUG------AAAA--GGGAA-C-GC-G-G-UGCGGCUGGUACUGAUCAGCC-------------AAUUCCGC-GACUGCCC-CC-GCAACUGUAA--GC-GG----------UGAGCGGACCGGGUGA-----------------------------ACCACUGGCAUGGAGUUUUGCGCUCC-----------------------------------------------AGG-UUGGGAAGGA---CCG--G-UU--UCGCAGCGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAUCAUAUGAAAACUCGAA
AE016853.1/3679925-3680123     UUUACCAUGCCGGCCGUCGGU---UUCCG------------------------AGAG--------GAACU------AACA--GGGAA-U-UC-G----CCAGCUUUGUUUCAAAGGCC-------------AAAA-CGA-AACUGCCC-CC-GCAACUGUAG--GC-AU----------CGAGCCUGCUCCAAGACU---------------------------GCCACUGGAU--UCA----------------------------------------------------------GAU-CCGGGAAGGC--CGGA--G-CA--UGGUGAUGAC------------------------------------------------------------------AUGC-CAGUCAGGAGACCUGCCGACCCGAUUCAACCAACU
CP000702.1/858840-859024       AAGCCUCCCUCACCGUGCGGU---ACCCU------------------------UCGG--------GGUUC------AAAG--GGGAA-G-CC-G-G-UGG-------------------------------AAAUCCGG-CGCGGG-G-CC-GCCACCGUGA--CC-GGG---------GACGAAACCCGCAGAAC----------------------------GCCACUGGGGCGAUC----------------------------------------------------------ACC-CUGGGAAGGU---GCG--G-GG-AGUAGGAUGAU------------------------------------------------------------------CCGG-AAGCCGGGAAACCCGCCCGCGGUGAAGGGAAACCA
CP000157.1/1649862-1649676     CGGCUGCUUCACGUCACGGGUU--GCCGC------------------------GUAAC----ACCGGCCG------AAGA--GGGAA-G-GG-A-G-UGC-------------------------------GAUGCUCC-CGCUGCCC-CC-GCAACUGUGA--CC-GGG---------GAGCGACCCUGCCAAGG----------------------------GCCACUGGU---UUC----------------------------------------------------------G-A-CCGGGAAGGC--GGCG--G-GG--AAGCGACGAU------------------------------------------------------------------CCGG-GAGCCAGGAGACCUGCCCGAGACCGUCGCUUGAGC
ABDP01000007.1/7251-7432       AUUUAAUAAAAAGAUUUAGGUG--CCUUUAC----------------------AUAA-------AAGGUG------AAAA--GGGAA-U-GU-G-G-UAA--------------------------------AAGCCAC-AGCAGCCC-CC-GCUACUGUAA--UU-GA----------GGACAAAUCUUUCAUAA----------------------------ACCACUCUUU----A----------------------------------------------------------AAA-AGGGGAAGGG---AAA--G-AU--UAGGAUGAA-------------------------------------------------------------------UCAU-GAGCCAGGAGACCUGCCUAGAUUUUUAUUAGGGAA
AALV01000003.1/110855-110656   UGUCAUCGAAACCGGGUCGGU---UUCCU------------------------UCGG--------GAAAU------AAUA--GGGAA-U-UC-G-C-CAUCCGCCCUUUGGUGUGGA--------------UGAACCGG-AACUGCCC-CC-GCAACUGUAG--AC-GG----------UGAGCUACCUCCAUCAU----------------------------GCCACUGGGCCUAAA----------------------------------------------------------GGU-CCGGGAAGGC---GGG--G-AC--AGCCGCGAU-------------------------------------------------------------------CCGU-CAGUCAGGAGACCUGCCGACACUGAACCUGAAACA
AAVM02000005.1/21577-21370     CUAUCUUUGUCGCGCAUCGGU---UUGCAACUCUCACAUAC------------GAGGG----AAGCGAUU------AAAA--GGGAA-U-CA-G-G-UGU-------------------------------AAAUCCUG-AACAGU-C-CC-GCUGCUGUAA--GU-UCCACACAU---UACGUUGCGAGCAACCUACUUUUA---------------------GCCACUGGAAAGAAA----------------------------------------------------------CUU-CCGGGAAGGC---GCC--C-GC--AACAG-----------------------------------------------------------------------GAAC-AAGUCAGAAGACCUGCCGUGCAACCAAUUUCACUG
CP000158.1/1153196-1153386     ACGCCGCCUCACGCAACAGGUG--CCCGGAU----------------------CAUGG----UCCGGGUG------AAAA--GGGAA-G-CC-G-G-UGA-------------------------------GAAUCCGG-CGCUAUGC-CC-GUAACUGUGA--GC-GG----------GGAGCCGUGUGAGCCAUAC--------------------------GCCACUGG---GAAA--------------------------------------------------------------CCGGGAAGGCAGCUCU--C-UC--CGGCGAUGAU------------------------------------------------------------------CCGCGAAGUCAGGAGACCUGCCUGUUGCCGUCGUUGGCUC
CP000482.1/1280913-1280737     ACACUCAUACCGGAUCAGGGC---GCCCG------------------------ACAG--------GGCUU------GAUA--GGGAA-GAGG-G-G-UGC-------------------------------GACUCCCC-CGCGGA-C-CC-GCCGCUGUAA--GC-GA----------UGACAA-GGGGCAACG-----------------------------GCCACUGGU--UUUU----------------------------------------------------------G-A-CUGGGAAGGC---GCC--C-----GGAGGAUGAA------------------------------------------------------------------UCGC-GAGCCAGAAGACCUGCCACUGAUCCACGCCACUCA
CP000724.1/3721369-3721186     GAUGAAUUAAAUCGAAUUGGU---GCUUUAU----------------------CAA---------AGCUU------AAUA--GGGAA-A-GU-G-G-UUG-------------------------------AAAUCCAC-UACAGCCC-CC-GCUACUGUAA--GU-GA----------GGAUGAGUCCAGCAAA-----------------------------ACCACUGAUUGUGUC-----------------------------------------------------------AA-UUGGGAAGGU--GCUG--G-GU--GUCAGAAGAA------------------------------------------------------------------UCAC-AAGUCAGGAGACCUGCCAACCCUAAUUCCAAACAA
CP000036.1/1206778-1206953     UCAUAACAUACGCUGACAGGUGU-GGCACAU----------------------UUGU--------GCC-----------U--GGGAA-G-AG-A-G-UGA-------------------------------AAAUCCCU-CGCAGCCC-CC-GCUGCUGUAA--UG-C------------UGACAAACCCGAAAAU----------------------------GCCACUGAUC-GCGA-----------------------------------------------------------GA-UUGGGAAGGU---CGG--G-----AGAGGAUGAC-------------------------------------------------------------------GCU-AAGCCAGAAGACCAGCCAGUCAGUCAAUACCAACA
AE015927.1/769982-770164       UUUAAUAUUAUUUUAUUAGGUG--CUUUA-----------------------------------CAAGUU------AAAA--GGGAA-A-GU-G-G-UGA-------------------------------AAAUCCAC-UGCAGCCCACC-GUUACUGUAA--UG-CU----------GACGAAAUCUUAUAAAA----------------------------UCCACUAGAUAUAUUU---------------------------------------------------------UAU-CUGGGAAGGU---UAG--A-AA--UUAGGAAGA-------------------------------------------------------------------AGCU-AAGCCAGGAAACCUGCCUAAUAAGUGUUAAUUCUU
AE015928.1/1836296-1836502     CUAUCUUUGUCGCGCAUUGGU---UUGCAACUCUCAUGCAC------------GAGGG----AAGCAAUU------AAAA--GGGAA-U-CA-G-G-UGA-------------------------------AAGUCCUG-AACAGU-C-CC-GCUGCUGUAA--GU-UCAUUUU-----UUGGUUGCGAGCAAUCGACUUUAUA--------------------GCCACUGGAAAGCAA----------------------------------------------------------AUU-CCGGGAAGGC---GUU--C-GC--AACAG-----------------------------------------------------------------------GAAC-AAGUCAGAAGACCUACCAUGCAAACUCGUUUCACU
CP000662.1/326212-326417       AAUGACAGGCGCGUGAUCGGU---UCACCCGGGCGUCAU--------------GCGUC----CGGGGAUU------AAAA--GGGAA-C-GC-G-G-UGCGCCCCGAAGGGGC------------------AAGACCGC-GGCUGCCC-CC-GCAACUGUGA--GC-GG----------UGAGCGACGCCGAAGAU----------------------------GCCACUGGGA----G----------------------------------------------------------AUC-CCGGGAAGGC---CGG--C-CG--AGCCGAGAC-------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGCUCGCCCGCCGGCCCCC
AAUW01000004.1/197975-198192   GUUUAGGAAGAAACUGACGGU---UCCGGAGAAGGCCUUG-------------CCCGA----UCCGGAUG------AAAC--GGGAA-U-CC-G-G-UGAGGGCUUUUCAAGUCC----------------GGGUCCGG-AGCUGCCC-CC-GCAACUGUGA--GC-GG----------UGAGUGGCUGUACGAAA----------------------------ACCACUGGCGUCCUGAUG-------------------------------------------------------GGG-CCGGGAAGGG--GUAC--A-GA--CCGCGCUGAG------------------------------------------------------------------CCGC-AAGCCAGGAGACCGGCCGUCGCAUUGGCAACCCUU
AAMO01000002.1/489939-490150   GGCACAACCGAAAGGCAUGGU---UCCUCAGACGGGUCUC-------------AGGCC----CGAGGAUC------AAAU--GGGAA-U-GC-G-G-AGAGGCGACCCACAUCGGGGCCU-----------UCAGCCGC-AGCCGCCC-CC-GCGACUGUGA--GC-GG----------AGAGCAUGUGUCACGA-----------------------------GCCACUGG---GCAA--------------------------------------------------------------CCGGGAAGGC---GGC--A-CG--AUGCGACGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCAGCCCUGCGUCAAUUCUAACCG
CP000557.1/1789202-1789010     UGGCGGUAAGACAAACAAGGUG--CCUAGCCCGCU------------------UAGGG----CUUGGGUG------AAAA--GGGAA-GCUC-G-G-UGA-------------------------------AAAUCCGG-CACGGUGC-CC-GCCACUGUGA--UG-GG----------GAGCUUUGCGGCAACAA----------------------------GUCACUGAAG--GAU----------------------------------------------------------GCU-UCGGGAAGAC---GCC--G-CC--AAGCGAUGA-------------------------------------------------------------------UCCU-AAGUCAGGAGACCUGCCUUGUUUGGAUCGGACGGA
CP000076.1/5141454-5141221     CCUUCGCGACUUGUUUCAGGUG--CUCUGUGGCCCGU----------------GGCCG----ACAGAGUG------AAACA-GGGAA-G-CC-G-G-UCAGGGUCUGUUCCAGUGAUGGAGCCGACGAC--GAUUCCGG-CGCUGCCC-CC-GCAACGGUAG--AU-GAG---------UCAAGACUGCGCCUGAC----------------------------GCCACUGUGUCAAUG-----------------------------------------------------------AC-ACGGGAAGGC---GCG--C-AG--UCCGGCAGCC-----------------------------------------------------------AUGCCGCUCAU-GAGCCCGGAGACCGGCCUGAUCCAUCCAACGGCAU
CP000490.1/1574718-1574933     GCAAUGCGGGGCCGCUACGGU---UCCGGCGC---------------------GAUCU----GCCGGAUG------AAAA--GGGAA-CACC-G-G-CGCGCCCAUCGCCGCGAUGCGGACGGGC------AAGGCCGG-GGCUGCCC-CC-GCAACUGUAG--GC-GGU---------GAGCGAAGGCCGAAGGC----------------------------GCCACUGGGA-AGAU-----------------------------------------------------------CC-CCGGGAAGGC---CGG--C-CC--GAGCGAUGAU------------------------------------------------------------------CCGC-CAGCCAGGAGACCUGCCGCAGCGAUCACCCAUUUC
AAYC01000003.1/114698-114499   AAUUUUCCUAUUAAGUAAGGUG--UCGUCCC----------------------AUUG-----GGGCGGAG------AAUU--GGGAA-G-CC-G-G-UGU-------------------------------GAAUCCGG-CACUGCCC-CC-GCAACGGUAACAUC-GGG---------CAAGGGCGUAGCAAGA-----------------------------GCCACUGGGACGAGG----------------------------------------------------------ACC-CCGGGAAGGC---GCU--G-CG--GCCGGUCAUU----------------------------------------------------------UGACCCCGAUGA-AAGUCCGGAAACCAGCCUUGCCUUGAUAGUCAAAC
AE015451.1/1866934-1867155     CCUUCGCGGCGUGUUUCAGGUG--CCCUGCCAGCCCCG---------------ACUGG----GCAGGGUG------AAACU-GGGAA-G-CC-G-G-UGGGCGCCAGCAUGGCGC----------------GAUUCCGG-CGCUGCCC-CC-GCAACGGUGG--AU-GAGU--------AAAAGGCCGCGCAGG------------------------------GCCACUGGAUGCCAG----------------------------------------------------------CAU-CCGGGAAGGC---GCG--C-AG--GCCAGGGCCA----------------------------------------------------------AGGCCCACUCAC-AAGCCCGGAGACCGGCCUGAUACUGCCAACGGCAU
CP000699.1/5269738-5269503     UCCAAUGGAUGCUGUCGAGGUU--CCCUGCUCGCGAUCCGGCAACGGGUC---GCGCG----GCAGGGCU------AAGAC-GGGAA-G-CC-G-G-UGACGUCCGCGAGGACG-----------------GAGUCCGG-CGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCGGCGGUUUCAACCAU--------------------------GCCACUGGCGCCCCGCGAGGA----------------------------------------------------GCG-CCGGGAAGGC-CGGAG--C-CG--CCGUGACGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCUCCGACGCGAUAACGUUC
AAMS01000001.1/256679-256898   GGCACAACAUGACGGCACGGU---UCCCCGCACGGCGCGCA------------GCGUC----AGGGGAUC------AAAU--GGGAA-U-GU-G-G-ACGCGCCGAUCCUGUCAGGGAGGCGC--------CAAGCCAC-AGCCGCCC-CC-GCGACUGUAU--GC-GGA---------GAGUGCCUUGUUAACAU----------------------------GCCACUGGG---UCC----------------------------------------------------------G-C-CCGGGAAGGC---AAC--A-AG--GUGCAUCGAC------------------------------------------------------------------CCGC-AAGCCAGGAGACCAGCCAUGCACCGGGGAUCGCCC
CP000463.1/4804452-4804231     GUUGGUGAGCACUGCCGAGGUU--CCCUGCUGCAGGCG---------------UUUCA----GCAGGGCU------AAGAC-GGGAA-G-CC-G-A-UGGCGCUCGCGUUGAGCG----------------GAAUUCGG-CGCUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCGGCGGUUCGAUGGGU--------------------------GUCACUGGCGUUUACGAA-------------------------------------------------------GCG-CUGGGAAGGC-UAGAA--C-CG--UCGCGACGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCUUUGGCGUGAUGACGUUC
AM420293.1/6688888-6688698     GACCUCGGUCGCUCUGGAGGU---CAGGAUA----------------------CGAC-----GGCCUGCG------GCGC--AGGAA-C-CC-G-G-UGC-------------------------------GAAUCCGG-GACGGU-C-CC-GCCACUGUGA--CC-GGG---------GAGCGGACCCGACGUGCG---------------------------GCCACGGCCC-GUGA-----------------------------------------------------------GG-GCUGGAAGGC---UCG--G-GU--GACCCGCUGC---------------------------------------------------------------GAUCCGG-GAGUCAGGAGACUCGCUGCCGGCCCCGCGUCGCGC
CP000264.1/2958160-2957972     GAACAGGGUCACGGCGAUGGU---GCCCUUC----------------------UUGG------AGGGCCU------AAGA--GGGAA-C-GC-G-G-UGA-------------------------------AACCCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------UGAGCGGACCUGCGUAU----------------------------GCCACUGAGCCGACA----------------------------------------------------------AGC-UCGGGAAGGC--GCAG--G-CC--CCGCCCUGAC------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCAUCACCUGUGAAACGCAU
AP008230.1/3094247-3094065     AACAAUUUAAGGAUUUCAGGUG--CCCUUCG----------------------CCAA-----GAAGGGAG------AAUA--GGGAA-C-CG-G-G-UGC-------------------------------AAUUCCCG-GACGGA-C-CC-GCCACUGUAA--AG-AG----------GAGUCUCAGCGCUGAAU----------------------------GCCACUGGGU----------------------------------------------------------------AA-CUGGGAAGGC--AGCA--A-GG--AGACAAUGA-------------------------------------------------------------------CUCG-AAGUCAGGAGACCUGCCUGGAUCCGGGGACACAUG
AE015927.1/793516-793697       GAAUAUUAAAAUUUAUAGAGUU--ACCCAUU----------------------UUUG--------GGGUU------AAAA--GGGAA-G-GG-G-G-UUA-------------------------------GAAUCCUC-CACGGU-C-CG-GCCACUGUAA--UU-GG----------UAAGUUUAUUCCAUAA-----------------------------GCCAUUGAGA--UAU-----------------------------------------------------------UC-UCGAGAAGGU---GGA--A-AU--AAAUGAUGAA------------------------------------------------------------------CCAU-AAGUCAGGAGACCUGCUUUAUAUUUAAGAUGCAGC
AAEW02000025.1/17075-16893     UCUGCGCUGAAAGUUUCAGGU---GCUUGUU----------------------GCA---------AGCAC------AAUA--GGGAA-U-UC-C-G-UGA-------------------------------AAUUCGGG-AGUGGG-C-CC-GCCGCUGUAA--CC-AG----------GGACGAUCAACACAUUUG---------------------------GCCACUGACU--UAG-----------------------------------------------------------AG-UCGGGAAGGC--GUGU--U-GA--GACGGAAGAU------------------------------------------------------------------CUGG-AAGCCAGAAGACCUGCCUGAAACGCAAUGGUUGCA
CP000724.1/79239-79421         AGUACAUAGAAUACGUUAGGU---GUUUCAU----------------------AUGA--------AACUU------AAUU--GGGAA-A-GU-G-G-UGA-------------------------------AAACCCAC-UGCAGCCC-CC-GCUACUGUAA--GU-GC----------AGAUGAACUCGACAAAA----------------------------GCCACUAGAU----C----------------------------------------------------------AAU-CUGGGAAGGC--GUCG--A-UA--GUAAGGUGAA------------------------------------------------------------------GCAC-AAGUCAGGAGACCAGCCUAAAGUAAGAAUCAGCCU
ABCF01000001.1/214794-214982   UACAUAUUGUCGUAAACAGGU---GAUUUCAGUCG------------------AAUCU----GAAGUCUU------AAAA--GGGAA-G-UU-G-G-UGA-------------------------------AAUUCCAA-CGCGGU-C-CC-GCCACUGUAA--AU-UG----------GGAGCAAGCUGUGAUUA----------------------------ACCACUGUAC-UAAU-----------------------------------------------------------GU-AUGGGAAGGA---ACA--G-CG--AGCAAUGA--------------------------------------------------------------------CCAU-AAGCCAGGAGACCUGCCUGUUACUGCUGCACCACA
CP000076.1/4227691-4227479     GUAGCCUUGCGCUUUCGAGGUU--CUUCGGCC---------------------ACGGG----UCGAAGCU------AAGAA-GGGAA-C-GC-G-G-U-C-------------------------------GAUGCCGC-GGCUGCCC-CC-GCAACUGUGA--AG-GG----------UUCGAUUGCUGCAAG------------------------------GCCACUGCAUGGGCGUCGACGACG-------------------------------------------------CCG-GUGGGAAGGC---GCA--G-CA--AUCGCCGGUC----------------------------------------------------CGACGACUGGCAAGCCCU-CAGCCAGGAGACCUGCCUCGAUCCCAGAUUCUCAC
CP000482.1/1300492-1300303     AGUUGAAUACCGGAUCAAGGC---GCCCG------------------------AGAG--------GGCUU------GAUA--GGGAA-GAGG-G-G-UGAGCUCCGAAGAGC-------------------GAUUCCCC-CGCGGA-C-CC-GCCGCUGUAA--GC-GA----------UGACAA-AGGGCAACA-----------------------------GCCACUGGUU-UUUU-----------------------------------------------------------GA-CUGGGAAGGC---GCC--C-----GGAGGAUGAC------------------------------------------------------------------UCGC-AAGCCAGAAGACCUGCCUGAUCUCUGCACUCAAUA
AAXE02000112.1/379532-379335   UAUAUUUGUCCCAUGCAUUGU---UCCUGCUUCGCAAUCU-------------GCGGA----AAAGGAUU------AAAA--GGGAA-U-CG-G-G-UGC-------------------------------AAAUCCCG-GACAGU-C-CC-GCUGCUGUAA--GC-UUCAA-------AACGGAUUGGGCAAUUCUUUUAU----------------------GCCACUGAC--GCGA------------------------------------------------------------G-UUGGGAAGGC---GCU--C-AU--ACCGG-----------------------------------------------------------------------AAGU-AAGUCAGAAGACCUGCAACGCAUAUUUUUUCGACG
CP000578.1/1093642-1093821     GCUUUGUGGCAGGGGUCAGGUG--CCGCCUU----------------------CGGG--------CGGAG------AAUC--GGGAA-G-CC-G-G-UGG-------------------------------AAAUCCGG-CGCGGG-C-CC-GCCGCUGUGA--CG-GG----------GAUGCUUCGGGCAAGAG----------------------------GCCACCGGUU----------------------------------------------------------------CG-CCGGGAAGGC---GCC--C-GG--CGGCAGAUGA------------------------------------------------------------------ACCG-GAGCCAGAAGACCGGCCUGACGCAGAGGUUCCCGC
AAYA01000006.1/51136-50945     GCGAUCCCGUCCGUGUCAGGUG--CCUCC------------------------GUCCU----CGGGGGAG------AAUC--GGGAA-G-CC-G-G-GGC-------------------------------AGAACCGG-CGCGGG-C-CC-GCCGCUGUGA--CG-GG----------GACGGGGCGGACACAUG----------------------------GCCACUGGGCGUCAGUCAGG-----------------------------------------------------CGC-UCGGGAAGGC---GUC--C-GU--UCCGGAUGA-------------------------------------------------------------------UCCG-AAGCCAGAAGACCGGCCUGACGGCAUGGCGGCCCC
CP000724.1/86468-86650         AAAACUGAAUAUAUUUUAGGU---GUUUCAC----------------------GUGA--------AGCUU------AAUU--GGGAA-A-AU-G-G-UGA-------------------------------AAAUCCAU-CACAGCCC-CC-GCUACUGUAA--AU-GC----------AGAUGAAAUCGAUGAAG----------------------------UCCACUGGA--UUUU------------------------------------------------------------U-CUGGGAAGGA--AUCG--A-GA--GUAAAAGGAA------------------------------------------------------------------GCAU-AAGUCAGGAGACCAGCCUAAAGACCAGUAACUACC
AE015927.1/823404-823586       UUAAAUAUUUAUUUAUAAAGU---UUCUU------------------------GUAAA----AGAGAAUU------AAAA--GGGAA-G-GA-G-G-CGA-------------------------------AAAUCCUC-CACGGU-C-CG-GCCACUGUAA--UU-GG----------UGAGUUUAUUCCAUAA-----------------------------GCCAUUGAGA--UAU-----------------------------------------------------------UC-UUGAGAAGGC---GGA--A-AU--AAAUGAUGAA------------------------------------------------------------------CCAU-AAGUCAGGAGACCUGCUUUAUAAGAAUAAAUAUAC
AAMV01000014.1/59909-60128     UUAGGCUGAUCCUGUCAUGGUG--CCAUGCCGACAGCAGUCCACUGC------UCUCG----GGAUGGAG------AAUU--GGGAA-G-CC-G-G-UGC-------------------------------GAUUCCGG-CGCUGCCC-CC-GCAACGGUAA--GG-GA----------GGGCGUUUCGGCGAUAU----------------------------GCCACUGGGCGACAA----------------------------------------------------------UGC-UCGGGAAGGU---GCC--G-CG--ACGCGAGGGU-----------------------------------------------------CAUCCGGCCCGCCAUCC-AAGCCCGGAAACCAGCCUUGGCGUGACGUCGAAUC
AE015927.1/793388-793200       AAUAGUAAAUGAAAUUUAGGUG--UCCACUUUGUA------------------AAAAU----GAUGGAUG------AAAA--GGGAA-U-GU-G-G-UUC-------------------------------AAUUCCAC-AGCAGCCC-CC-GCUACUGUAA--UA-GA----------UGACAAGCCUUUAGUA-----------------------------ACCACUCUUU----A----------------------------------------------------------AAA-GGAGGAAGGU---AAA--G-GU--UAGAAUGAU-------------------------------------------------------------------UCUU-AAGCCAGGAGACCUGCCUAGAUUGUUAAAAUCCUC
CP000248.1/1228186-1228384     UGGCGCGCCGACGCCAGAGGUG--CCCGGUA----------------------ACAC--------GGGCU------AAGA--GGGAA-G-CC-G-G-UUC-------------------------------GAUUCCGG-CGCUGCCC-CC-GCAACUGUAA--CC-GGA---------UAGCGCGUCGCCCAUUCAU--------------------------GCCACUGGUGUCGGCUUCGGCCA--------------------------------------------------GCA-CCGGGAAGGC--GGGC--G-AC--GAGCCGUGAC------------------------------------------------------------------CCGG-AAGCCAGGAAACCUGCCCUUGGUUGUCGUUCCGCG
AATQ01000008.1/108753-108536   CAUCACUGACGCAUAUCCGGU---CCCGGUGCAGUC-----------------UCUGC----CCCGGGCGCA----AGAA--GGGAA-C-GC-A-G-UGCGGCACGGGCCAUUCGGUCACGGCC-------AAUUCUGC-GACUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGCAACGGCUGAUCGU----------------------------GCCACUGGA--GCAA------------------------------------------------------------U-CCGGGAAGGC---CAG--C-CC--GCGCGAUGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCGGAUACGCGCCCCUGGAA
AE015451.1/3857543-3857766     CCUUAUGCCUCGCGUUCAGGUG--CCCCU------------------------CAGG--------GGGUG------AAAC--GGGAA-A-CC-G-G-UGCGUCCCAGGCCCUUCAGCAGGGCCGGAC----AAUGCCGG-UGCUGCCC-CC-GCAACGGUAA--GC-GA------------GUGAAGCGUCUGU------------------------------ACCACUGUGCCUCGUAGUAC-----------------------------------------------------GGC-AUGGGAAGGU---GAC--G-CG--UUCCAGGAGC-------------------------------------------------------CCAGCUCUUCCUCGC-AAGCCCGGAGACCGGCCUGGCGUUCAUGAACACCC
AAOE01000043.1/7099-6915       GUUGGCGAUGUCACUGACGGUU--UAAGACA----------------------AGCUG----UACUUGUC---------U--GGGAA-U-CC-G-G-UUA-------------------------------AAUUCCGG-AGCUGCCC-CC-GCAACUGUAA--UG-GU----------CAGGACGAUGUCUGUUU----------------------------GCCACUGAAAAUUAU-----------------------------------------------------------UU-UCGGGAAGGC---GAC--A-UC--GAGCCGUA--------------------------------------------------------------------GCCA-GAGCCAGGAGACCGGCCGUCGUGCAUCUCGCAUCA
CP000076.1/2504928-2504724     AUAUGCCGCCCAGUUUCAGGUG--CCUCCUGCCGC------------------CGUGC----AGGAGGUG------AAAC--GGGAA-A-CC-G-G-UGCGCCCCUUUUCGGGC-----------------AAGUCCGG-UGCUGCCC-CC-GCAACGGUAA--GC-GA-----------GUGCUGCAUUCAACAG----------------------------GCCACUGUACCCAAG-----------------------------------------------------------GU-AUGGGAAGGC---GAA--U-GC--CGCCAGAC--------------------------------------------------------------------UCGC-AAGCCCGGAGACCGGCCUGUGACGUCUGUUUGGCA
AE015927.1/2416636-2416459     AUUUAAUAUUAGAUUUUAGGU---GUGAU------------------------CUUAU----AAUUACUU------AAAA--GAGAA-A-GU-G-G-UGA-------------------------------AAAUCCAC-UACAGCCC-CC-GCUACUGUAA--UA-G-----------UGGACGAUUCCUAUUA-----------------------------UCCACCAGUU----------------------------------------------------------------AA-CUGGGAAGGA---AGG--A-UA--AGGAAGAAA--------------------------------------------------------------------CUA-AAGUCAGGAGAACUGCCUAAAAUAUAUUACUUCGG
AAQF01000153.1/10735-10925     CCAAGUUGGGCGAUUGCCGGC---CUGGUCG----------------------CGGGC----CCGGGGAG------AAUA--GGAAA-U-CG-G-G-UGU-------------------------------AAAUCCCG-AGCGGU-C-CC-GCCGCUGUGA--AC-GGG---------GAGUGAUUCCGGUAAAU----------------------------GCCACUGGCCGCCAGG---------------------------------------------------------CGG-CCGGGAAGGC---CCG--G-AA--AAGCGAUGAG------------------------------------------------------------------CCGU-GAGCCAGAAGGCCUGCCCCCUGGUUAGCCGCCGCA
CP000139.1/5040129-5040332     GUAUCUUUGCAGUGCAUCGGU---UCAUUUAUCUCCCCUCC------------GAGGU----GAAUGAUU------AAAA--GGGAA-U-CAAG-G-UGA-------------------------------GAAUCCUG-AACAGU-C-CC-GCUGCUGUAU--GU-UUCACU------AAACGCAUAAGCAAAAUGCCAAUA---------------------ACCACUGGGA-UAAU-----------------------------------------------------------UU-CCGGGAAGGU---GCU--U-AU--AGCGG-----------------------------------------------------------------------AAAC-GAGUCAGAAGACCUGCCUGUGCAUUUAUCAAAUCU
CP000680.1/5037130-5036935     UAGCCUUCUCGCUUUCGAGGUU--CUUCCCGGCAAG-----------------CCGCC----GGGGAGCU------AAGA--GGGAA-C-AG-G-G-U-C-------------------------------GAUGCCCU-GGCUGCCC-CC-GCAACUGUAA--AC-GGU---------CGCAACUCCUUCGAUAC----------------------------ACCACUGCCU---------------------------------------------------------------CAA-GCGGGAAGGU---GAA--G-GA--CGCACAGCGU-------------------------------------------------------------GCAGACCGU-GAGCCAGGAGACCUGCCUCGAUAGACCAGCCACUU
AAYC01000005.1/102065-102276   GCGCAAGGGGGUUCAGCUGGUU--CCUGG------------------------GGAAA----CCUGGGCG------AAGA--GGGAA-U-GU-GAC-AGCUGGAAUUAUCUGGCA----------------AAAAGCAC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AUGAGACCGCC----AU----------------------------GCCACUGGG--ACAC------------------------------------------------------------C-CCGGGAAGGC---AGG--A-GG--GUCGACAGAG---------------------------------------------------CGCACGCUCUGGCAUCCGC-AAGCCGGGAGACCUGCCAGCAAGAGGAGAUUUCAA
CP000377.1/2318941-2319180     GCGCAAGGAAAUUUCGUUGGUU--CCCGAAGGUGA------------------CAGCC----UUUGGGCG------AAGA--GGGAA-U-GU-G-U-CGGGCCGGGAUCAUCCUUGCU-------------CCAAACAC-AGCCGCCC-CC-GCGACCGUGA--CC-GG----------AGAGGUCUUCC---AAC----------------------------GCCACUGGCGCGCCCCUUGUGGGC-------------------------------------------------AGG-CCGGGAAGGC---AGG--G-AG--ACCGUUCGCG---------------------------------------------CCCCACUCGGGGCGGAUCUAUCCGC-AAGCCGGGAGACCUGCCAACGCGUGAGAACCGGCG
AAQG01000024.1/17748-17526     GUUGAAGGAGCCUGUCGAGGUU--CCCCGCUUCAGGCA---------------UGACG----GCGGGGCU------AAGAC-GGGAA-G-CC-G-G-UGGUGCCCUUUGGGCA------------------GAGUCCGG-CGCUGCCC-CC-GCAACUGUAA--GC-GGC---------GAGUGGUGGCUCCAUUUUGU-------------------------GUCACUGAGCUUUUGCACGA-----------------------------------------------------GGC-UCGGGAAGGC-CGGAG--C-CA--UUGCGAUGAC------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCUUCGACGGCAUAACGUUC
CP000578.1/656987-656780       GUCACCUCAUGGCACGACGGU---UCCCGAAGGUCGCAA--------------GGCCC----GAGGGAUG------AAAA--GGGAA-C-GC-G-G-UGAGGGGAAACCC---------------------GAGGCCGC-GACUGCCC-CC-GCAACUGUGA--GC-GGC---------AAGCCGCCCCGACGGAC----------------------------ACCACUGGCC--GAU-----------------------------------------------------------GG-CUGGGAAGGU---UCG--G-GG--AUCGGCCACG----------------------------------------------------------------ACCCGC-GAGUCAGGAGACCUGCCGUCGGGCGCAUCCGCGCC
CP000301.1/3897402-3897187     UGCGAUAGUUAACAUGAUGGUG--CCUCAAUCUCGAGUCUGCGUGAGUGGAUGCGAUC----UUGAGGAU------AAUA--GGGAA-C-AC-G-G-UGC-------------------------------AAAACCGU-GACUGCCC-CC-GCAACUGUAA--GC-GG----------UUAGCCUGUCGUCCGAU----------------------------ACCACUGGGAAUUUCGU--------------------------------------------------------UUC-CUGGGAAGGU--GACG--A-UA--GGUCAGCGAG------------------------------------------------------------------CCGC-GAGCCAGGAAACCUGCCAUCGCACGAUCAAUUUCG
AAXF02000053.1/97071-97271     CUAUCUUUGUCGCGCAUUGGU---UUGCGACUCCCAUGC--------------GGGGG----AAGCAAUU------AAAA--GGGAA-U-CA-G-G-UGU-------------------------------AAAUCCUG-AACAGU-C-CC-GCUGCUGUAA--GU-UCCAUG------CAUGUUACAAGCAAUUCACUCAUU---------------------GCCACUGGAG-ACUA-----------------------------------------------------------AU-CUGGGAAGGC---GUU--U-GU--AACAG-----------------------------------------------------------------------GAAU-AAGUCAGAAGACCUACCAUGCAAUUAUGUUUCACU
CT573326.1/2524145-2524344     GUAGCCUUGCCGCUUCGAGGUU--CUCCGGC----------------------GUUGG----CCGGAGCU------AAGAC-GGGAA-C-GC-G-G-U-C-------------------------------GAUGCCGC-GGCUGCCC-CC-GCAACUGUAG--GC-AC----------UGGAACGGAUCGGCACA----------------------------GCCACUGCGC----A----------------------------------------------------------CGC-GCGGGAAGGC--GCCA--U-CC--CGCUGGCAAU------------------------------------------------------GCUGCCGGCACAGUGC-GAGCCAGGAGACCUGCCUCGUGACGUUUUCGACUU
CP000557.1/868974-869170       AUGGUGAUUGCAAGCAAUGGU---GUCCA------------------------UCAG--------GACUU------AAUA--GGGAA-U-CC-G-G-UGC-------------------------------GAAUCCGG-AACUGCCC-CC-GCAACUGUAU--GU-GC----------GGACGAAAUGGGAUG------------------------------GCCACUGGCGGUGAAAGCUUGCACGGCACG-------------------------------------------CCG-CUGGGAAGGA---CCC--A-AA--GUAGGACGAU------------------------------------------------------------------GCAC-GAGUCAGGAGACCUGCCUUGCUUGGAAGUUUCAUG
CP000377.1/2333297-2333511     GCAUUGUCGACGGCAUACGGU---GUCCCAGAGCGCAA---------------AGCGC----CGGGACUG------AAAC--GGGAA-U-GA-G-G-AACGGCGGACCCAAUCGCGGCGCC----------AAAGCCUC-AACCGCCC-CC-GCGACUGUGA--GC-GG----------UGAGCGACAUUCAGCA-----------------------------UCCACUGGCC--GCU----------------------------------------------------------GGG-CCGGGAAGGA---GAA--U-GA--UCGCCGCGAC------------------------------------------------------------------CCGC-GAGUCAGGAGACCGGCCGUAUGAAACGAGGACAGU
ABCS01000025.1/79736-79534     UAUGAGCGGAGGGCCGAUGGUC--CCGCG------------------------CGUG--------CGGGC------CCGA--GGGAA-U-CC-G-G-UGG-------------------------------AAAUCCGG-AGCUGC-C-CC-GCAGCGGUGA--GC-GGG---------AACGAAAGCUGCAUCGAA---------------------------GGCACUAGGC--CAC-----------------------------------------------------------GC-CCGGGAAGCC---GCA--G-CG--AGUAGGUCAC----------------------------------------------CGGGGUCUCGACCCCGUCGCCCGC-GAGUCCGAAGACCUGCCGUCGGUGUUGUCCGUCAC
AAEW02000019.1/41610-41805     GACGUCAUAUUGGAUCACGGU---GCCCAACGGGAGCUUAAAUG---------UCUCG----UGAGGCUU------GAUA--GGGAA-GAGG-G-G-UGC-------------------------------AACUCCCC-CGCGGA-C-CC-GCCGCUGUAA--AC-G-----------UGGACAACAGGCUCCAU----------------------------GCCACUGGU---UUC----------------------------------------------------------G-A-CCGGGAAGGC---GCC--U-GA--AGGAUGAAG--------------------------------------------------------------------CGU-AAGCCAGAAGACCUGCCUGAUCCCAACACUCAAUG
ABBE01000883.1/365-556         UACGCCCGUUCGUUCGCCGGC---GCCCC------------------------UCGG--------GGCCG------AAGA--GGGAA-C-AC-A-G-GGC-GCGUGCCGC---------------------GCCGCUGU-GGCUGCCC-CC-GCAACUGUAG--GC-AGCG--------AGCCCGCCUCCAUCUCGC---------------------------GCCACUGG---CUUG----------------------------------------------------------U---CCGGGAAGGC--CUGG--A-GC--GGGCGUCGAC------------------------------------------------------------------CUGU-CAGCCAGGAGACCUGCCGGCUUGAAAGUGCGUGCG
AAYH02000049.1/356589-356390   CUAUCUUUGUCCACGUUUUGU---UCCGCGUUCUCUAUCC-------------GGAGA----AGCGGAUG------AAAA--GGGAA-U-CG-G-G-UGA-------------------------------AAGUCCCG-AACAGU-C-CC-GCUGCUGUGA--GU-UCCAU-------GCUCGGUGUAUCAUACUUGU-------------------------GCCACUGUUCUUCGGGA--------------------------------------------------------AGA-ACGGGAAGGC---GAU--G-UA--CCGG------------------------------------------------------------------------GAAC-GAGUCAGAAGACCUGCAAAACAAAGUCGAAAAAUU
CP000058.1/3489261-3489461     UUUACCAUGCCGCCCGUCGGU---UUCCG------------------------AGAG--------GAACU------AACA--GGGAA-U-UC-G-----CACGCUUUGUCUGCACAAGGCC----------AAAA-CGA-AACUGCCC-CC-GCAACUGUAG--GC-AU----------CGAGCCUGCUCCAUGACU---------------------------GCCACUGGAU--UAA----------------------------------------------------------GCU-CCGGGAAGGC--CGGA--G-CC--UGGCGAUGAC------------------------------------------------------------------AUGC-CAGUCAGGAGACCUGCCGACCUGCUUCAACCCACU
CP000771.1/268818-268646       AUAAACCUCCCUUUGCAUGUUG-------------------------------------------------------AAA--GGGAA-GCCC-G-G-UGA-------------------------------AAAUCCGG-CGCGGG-G-CC-GCCACCGUGA--GU-GGG---------GACGAAAUUCACAAUAU----------------------------ACCACUGGCCUAAUUU---------------------------------------------------------UGG-CUGGGAAGGU---GUG--A-AG-AGUAGGAUGAU------------------------------------------------------------------CCAC-GAGUCGGGAGACCUAACAUGCAAAGGAAGGGAGCC
CP000489.1/1319736-1319936     AUUUUACCGUCAGAUCAAGGUG--CCGGG------------------------GAAAU----CUCCGGGU------AAAA--GGGAA-U-UC-G-G-UGAGGCUGUCGCC---------------------AAAUCCGA-AGCUGCCC-CC-GCAACUGUAG--GC-GG----------AGAGCCUGUCCGACAU-----------------------------GCCACUGGCGCGGAUUUC-------------------------------------------------------GCG-CCGGGAAAGC---UGG--A-CC--AGGUAAAGAU------------------------------------------------------------------CCGC-AAGUCAGGAAACCUGCCUGGAUCAAUCACCUGUUC
CP000232.1/1116483-1116660     CAAAUUUAAUAAACAACAGGUG--CCUGC-----------------------------------AGGGUU------AAAA--GGGAA-U-CA-G-G-UGU-------------------------------AAAUCCUG-AGCGGU-C-GC-GCCACUGUAA--CC-GGG---------GAGUUUUUCCUCAGAG-----------------------------GCCACUGGUG--AUC-----------------------------------------------------------UA-CUGGGAAGGC---GAG--G-AA--AAGUAAUGAG------------------------------------------------------------------CCGG-GAGCCAGGAAACCUGCCUGUUGGUUCAACCCUCGC
AAOX01000008.1/103201-103005   UAAGAAUCCGCAAGCGAUGGU---GCCCUUU----------------------UAG---------GGCAU------AAUA--GGGAA-U-CC-G-G-UUC-------------------------------AACGCCGG-AGCUGUCC-CC-GCAACUGUAA--GU-GU----------GUACGAAAUGAGCA-------------------------------UCCACUGUAUAUGAACGCUGAAUAGGCGCA-------------------------------------------UAU-AUGGGAAGGG---CUC--A-GA--GUAGGAUGAA------------------------------------------------------------------GCAC-AAGCCAGGAGACCUGCCAUGCUUGUACGAGUUUCG
CP000557.1/2323587-2323388     UUCAUAGACUCGCAGCAAGGU---GCCGC---------------------------------GAAGGCUU------AAUA--GGGAA-U-CC-G-G-UGG-------------------------------GAAUCCGG-AACUGUCC-CC-GCAACUGUCA--AU-GC----------GGACGAAAUGAAAUU------------------------------GCCACUGUGCGGCUGGAUGGCUUGCGCCGUCUCC---------------------------------------CGC-AUGGGAAGGC---UUC--A-GA--GUAGGAUGAA------------------------------------------------------------------GCAU-GAGUCAGUAGACCUGCCUUGCUUGCGCAAAAGUUU
AAYC01000003.1/148871-149085   CAUUUAGCCAAAGUGACUGGU---UCUACGAGUGCUUCAA-------------UGCGC----AGUGGAAGA-----AAUA--GGGAA-C-AC-G-G-UGCGGCGUACCCAAAAGGGACC------------AAAUCCGU-GACUGCCC-CC-GCAACUGUGA--GC-GG----------UGAGUGACGCUGAACAA----------------------------GCCACUGGGG--UUC-----------------------------------------------------------UC-CCGGGAAGGC---CAG--C-UG--AACCAAGAC-------------------------------------------------------------------CCGU-GAGUCAGGAGACCUGCCGGACACAAAGAACGAUAG
CT573326.1/1440491-1440711     CCUUCGCGGCGUGUUUCAGGUG--CCCUGUGAACCCAG---------------GUUCG----GCAGGGUG------AAACU-GGGAA-G-CC-G-G-UGGGCGCCAGCAAGGUGC----------------GAUUCCGG-CGCUGCCC-CC-GCAACGGUAG--AU-GA----------GUCGACGGCUGCGCAAG----------------------------GCCACUGGAUUUCGU----------------------------------------------------------GAU-CCGGGAAGGC---GCACGG-CC--CGGGCAUGGC-------------------------------------------------------------CCCACUCAU-GAGCCCGGAGACCGGCCUGUCACUGCCAACGGCAU
AAXE02000101.1/25986-25779     UACCUUUGCCACAGUUUUGGUU--UCACGGCUCCCAACCGCUAC---------GGGAG----GCGUGAUG------AAAA--GGGAA-U-CA-G-G-UGC-------------------------------GAAUCCUG-AACAGA-C-CC-GCUGCUGUAA--GU-UCCUCUCC----AAAUCUUUGAAUACGCUACAA------------------------GCCACUGUCCGUCAC----------------------------------------------------------CGG-AUGGGAAGGC---AUU--C-AA--AGACG-----------------------------------------------------------------------GAAC-AAGUCAGAAGACCUGCCAAAACAAACAUAGUUUUA
CP000075.1/4368222-4368008     CCUUCGCGGUUUGUUUCAGGUG--CUCUGCAAUCCUC----------------GAUUG----GCAGAGUG------AAACA-GGGAA-G-CC-G-G-UGUGGGUCGACAGAUCC-----------------GAUCCCGG-CGCUGCCC-CC-GCAACGGUAA--AU-GAG---------UCAAGGCUGUGCCUGAC----------------------------GCCACUGUGU--UUC----------------------------------------------------------GAC-AUGGGAAGGC---GCG--C-AG--CCGGGGUGAC--------------------------------------------------------------CCGCUCAU-GAGCCCGGAGACCGGCCUGAAUCACUCAAUGACAU
BA000043.1/2300644-2300445     UAAAUCAACUCGCAGCAAGGC---GCCGA---------------------------------AAAGGCUU------AAUA--GGGAA-U-CC-G-G-UGG-------------------------------GAAUCCGG-AGCUGUCC-CC-GCAACUGUCA--AU-GC----------GGACGAAAUGAAAUC------------------------------GCCACUGUACGGACGGAUGGCUUGCGCUGUUUUC---------------------------------------CGU-ACGGGAAGGC---UUC--A-GA--GUAGGAUGAA------------------------------------------------------------------GCAU-GAGCCAGUAGACCUGCCUUGCUUGCCGCAGUUUCC
CP000521.1/3325202-3325408     UGCGUUCAAAUGGAAGCAAGU---GUAAGCA----------------------AUUGA----UGCUUU-----------A--GGGAA-G-CU-G-G-UGA-------------------------------AAGUCCGG-CACUGCCC-CC-GCAACGGUAA--CA-AUG---------UAAAGCAUAUUUUUAAGUCGAAAUCGACUUAC-------------ACCACUGCA---GUA----------------------------------------------------------G-U-GUGGGAAGGU---GAA--U-AU--GUCCAUAAAU--------------------------------------------------------GAAUUAUGGCGCUG-AAGUCCGGAGACCUACUUGUUUCAUCUAUCUACCC
AAYA01000018.1/10947-10742     CAAGGAAAUCGCAUGUCCGGU---UCCGGAGUUUU------------------CACGC----UUCGGAGGA-----AAGA--GGGAA-U-GC-A-G-UGCGGCACGCGAGUGCC-----------------UACCCUGC-AGCUGCCC-CC-GCAACUGUAA--GC-GG----------CAAGCAGGGCUGAUAU-----------------------------GCCACUGGA--GAAA------------------------------------------------------------U-CCGGGAAGGC---CAG--U-CCAGAUGCGAUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGGACUGGCGCCUCAGGAA
ABCS01000001.1/110390-110179   AUAUGUUGUGCCCGCGAAGGU---GCUCGAC----------------------CCCGG----UCGGGCCC------GAGA--GGGAA-U-CC-G-G-UGA-------------------------------GAAUCCGG-AGCUGC-C-CC-GCAGCGGUAA--GC-GAG---------AACGACCGCCACAUCAGA---------------------------GGCACUGGGACGCCC----------------------------------------------------------GUC-CUGGGAAGCC---GUG--G-CC--AGUAGGUUGG---------------------------------------------ACCGACGUCGAGGUCCAGCGCUCGC-AAGUCCGAAUACCUGCCUUCGCCCGGCGCCGGGAG
AATR01000002.1/37098-37316     GCAAACAGGUUUUUGCAUGGU---UCCCCAUUAAAGUCAUAAUAA--------AUGGC----UGGGGAUC------AAAU--GGGAA-U-GU-A-G-ACAGGGACUACCCGAAUGGGGCCU----------AAAGCUGC-AACCGCCC-CC-GCGACUGUGU--GC-GG----------AGAGUGAAGCCCAAA------------------------------GCCACUGGU--GAAA------------------------------------------------------------A-CUGGGAAGGC---GGG--C-AA--AACGAUCUAU------------------------------------------------------------------CCGU-GAGUCAGGAAACCAGCCUUGCAACGGCGUUAUCGC
AM420293.1/6698575-6698393     UCUGCGACGAUGCACGGUGGU---C----------------------------CAAGC----AAGGAGUG------CGUC--AGGAA-G-CC-G-G-UGG-------------------------------GAGUCCGG-CACGGCCG-GC-GCCACUGUGA--CC-GGG---------GAGCGGACCUCCCCCGCGA--------------------------GCCACCGGG--GCGA------------------------------------------------------------C-CUGGGAAGGC--CGGA--G-GG--ACGCGGCGAG------------------------------------------------------------------CCGG-GAGUCAGGACACU-GCCACCCCUUGUUCCCACCAC
CP000699.1/3500758-3500554     AAAGCGCACGGCGCGACAGGU---UCCCGGA----------------------AACG--------GGAUC------AA-A--GGGAA-U-UC-G-G-AAGCGGGAUCGUCCCG------------------CAAGCCGA-AGCUGCCC-CC-GCAACUGUGA--UC-GG----------CGAGCGAUCGUCCAUCCCGC-------------------------GUCACUGGAUGCUCCGG--------------------------------------------------------CAU-CCGGGAAGGC-CGGAC--G-AG--ACGCGACGAC------------------------------------------------------------------CCGA-GAGCCAGGAGACCUGCCCGUCGCGGUCGUUCCAUC
AAYB01000001.1/493900-494119   GCAAACAGUACCCGUGAUGGU---UCCCAAAGCGCCGAAAA------------UGCGU----CUGGGAUG------AAAA--GGGAA-U-AC-G-G-UGAGGAAGAGCCAAAGCGCGCC------------AAAUCCGU-AACUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCGACCCCGAUGAUC----------------------------ACCACUGAGC-AAAC-----------------------------------------------------------GC-UCGGGAAGGG--AUCG--G-GC--AAGCAGCGAC------------------------------------------------------------------CCGCGAAGUCAGGAGACCUGCCAUCAAAGGGCGUCGAAAU
CP000482.1/1351280-1351088     AGCAUCAUAUCGGAUCACGGU---GCCCG------------------------CAAG--------GGCUU------GAUA--GGGAA-GAGG-G-G-UGCAACUCUUAUACGAGC----------------CAUUCCCC-CGCGGA-C-CC-GCCGCUGUAA--GC-GA----------UGACGA-AGGGCAGUAU----------------------------GCCACUGGU--GAAC----------------------------------------------------------A-A-CCGGGAAGGC---GCC--C-----GGAGGAUGAC------------------------------------------------------------------UCGC-AAGCCAGAAGACCUGCCUGAUCUUUACCACUGACU
CP000680.1/1925111-1925322     CCUGCGCGCCUUGCUUCAGGUG--CCCCGCGUCGUCUCCAUCGA---------CGGCG----CCGGGGUG------AAACA-GGGAA-G-CC-G-G-UUC---------C---------------------AAUGCCGG-CGCUGCCC-CC-GCAACGGUAG--GU-GA----------GUCAAACGCUGUUUCAG----------------------------GCCACUGUGC--AAU-----------------------------------------------------------GC-ACGGGAAGGC---GCA--G-CG--UCGAACCUUU---------------------------------------------------------CAGGUUCGCUCAC-GAGCCCGGAGACCGGCCUGUCGCAGUUCCACGGCA
AAWL01000006.1/21090-20915     CAUAUGGCAAAGGGAAUAGGU---GCCUU----------------------------------GCGGCUU------AAUA--GGGAA-GUCC-G-G-UGA-------------------------------AAAACCGG-CACGGU-C-CC-GCCACUGUAA--UG-GG----------GAGUCUGGCUGCGUUAU----------------------------GCCACUGGA--GCAA------------------------------------------------------------U-CUGGGAAGGU---GCG--G-CU--AGCAAUGA--------------------------------------------------------------------ACCA-GAGUCAGGAGACCUGCCUAUUCUAACACACACCGU
AAUW01000028.1/66358-66145     GAGCACUUAGGAAGAGAUGGU---UCCCGACUCUGAACU--------------UCGGA----GCGGGAUU------AAAA--GGGAA-C-AC-G-G-UGAGACCAGGCCGCAAGGCUUC------------AAAUCCGU-GACUGCCC-CC-GCAACUGUGA--GC-GGU---------GAGCAAACCUGAAAGC-----------------------------GCCACUGGGG--AAA-----------------------------------------------------------CC-CCGGGAAGGA---UCA--G-GC--AAGCUAUGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCAUUUCACCUUAAACCUUA
AALY01000001.1/1587847-1587653 GGGUGUCACUGCGGCGUCGGU---UUUCG------------------------AUGG--------AAACU------AAUA--GGGAA-U-CC-G-C-GGCGUCCAGCAGGGCG------------------UCAACCGG-AACUGCCC-CC-GCAACUGUAG--GC-GGC---------GAGCUGCAUCUUCAGA-----------------------------ACCACUGGGC--CGA----------------------------------------------------------GGU-CUGGGAAGGG---AAG--A-UG--ACGCCAUGAG------------------------------------------------------------------CCGU-GAGUCAGGAGACCUGCCGACGCAUAACCUGAAACC
AAYH02000040.1/99907-100108    GUAUCUUUGUCAUGCAUUGGU---UCGCUCCCCCUCUUC--------------UGGGA----AAGCGAUU------AAAA--GGGAA-U-CA-G-G-UGU-------------------------------AAAUCCUG-GACAGU-C-CC-GCUGCUGUAA--GU-UUCGUGC-----AACGUUGCAGACAAUUACUCUAU----------------------GCCACUGGAAUAUUC-----------------------------------------------------------UU-CCGGGAAGGC---GCC--U-GC--AACAG-----------------------------------------------------------------------AAAC-AAGUCAGAAGACCUGCCAUGCAUACUUUAUCAUUG
CP000771.1/1485865-1486047     AAUAUUCCAAACUGCGAAGGU---GCCGA----------------------------------AAGGCUU------AAUA--GGGAA-CUCC-G-G-UGA-------------------------------GAAUCCGG-GACGGU-C-GG-GCCACCGUGA--GU-GGG---------GACGAAAUGCUCAACUG----------------------------GCCACUGGCUUUUUU-----------------------------------------------------------AG-CUGGGAAGGC---GAG--C-AG--AGUAGGAUGA-----------------------------------------------------------------GCCAC-AAGUCGGGAGACCUGCCUUCGUAGGAUGGCAUUCC
CP000908.1/2947467-2947267     CGUAGCUUGACCGUUGACGGU---UCCCG------------------------CAAG--------GGAUC------AAAA--GGGAA-C-GC-G-G-UGGAGGGCUUUCGAGCUC----------------GAUCCCGC-GGCUGCCC-CC-GCAACUGUGA--GC-GGA---------GAGUCCUCCAUCACCAC----------------------------GUCACUGGGCAUGCCU---------------------------------------------------------CGC-CUGGGAAGAC---GAU--G-GA--GGGCGACGAC------------------------------------------------------------------CCGC-CAGCCAGGAGACCUGCCGUCAGCCGUGGUCACACG
CP000853.1/2361990-2361811     CAAAUUAAAUAGUUUUAAGGU---CUUUAGA----------------------AUAU-------AAAGUU------AAAA--GAGAA-A-GA-G-G-UUC-------------------------------AAUUCCUC-UACAGCCC-CC-GCUACUGUAA--UC-AG----------GUAUGAAAUCUUCAAA-----------------------------UCCACUGG---GAAA--------------------------------------------------------------CCGGGAAGGG---AAG--A-UA--GUAAGUCGAU------------------------------------------------------------------CUGU-AAGUCAGGAGAACUGCCUUAAAAAUAAGAAUCACA
AE007870.2/441359-441124       CUUAUGUGAGAAAGCGACGGU---UCCUACAGCCGAA----------------AGGCG----AAGGGAUU------AAUA--GGGAA-C-AU-G-G-UGCGGGCGAUCUUUUUCGUCC-------------AAUGCCUU-GGCUGCCC-CC-GCAACUGUAA--GC-GGA---------UUGUUGUUCAUCCCAGUGACGCUUGAAGGCGUCAU----------GCCACUGUUUUUUUCGG--------------------------------------------------------AAU-GCGGGAAGGC--AGAU--G-AG--GGACGCAAAU------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCGUCAAAAUGGAAACCAUC
AE008691.1/395133-395373       UGAAUAUUAAAGCCUUAUGGU---CCCAU---------------------------------GAUGGGUU------AAAA--GGGAA-GACG-G-G-UGA-------------------------------GAAUCCCG-CGCAGCCC-CC-GCUACUGUGA--GG-GA----------GGACGAAGCCCUAGUAA----------------------------GCCACUGUCCGGCACUCAACUGAGCGCGUUAGUAAGGAGAAAAGAGGGAGAGAAAUUGCGUUCAGUUGAGUGCCGG-GUGGGAAGGC---AGG--G-UG--GAGGAUGAG-------------------------------------------------------------------UCCC-GAGCCAGGAGACCUGCCAUAAGGUUUUAGAAGUUC
CP000853.1/1112785-1112962     AGUAAAUAAGAAGCAUUAGGU---UCUAA-----------------------------------AAGAUU------AAUA--GGGAA-A-UC-G-G-UUA-------------------------------AAUUCCGA-UACAGCCC-CC-GCUACUGUAA--GU-GU----------GUACGAAACCAACGGG-----------------------------UCCACUGGAU--AAU-----------------------------------------------------------AU-CUGGGAAGGU--GUUG--G-GA--GUAGGUUGAU------------------------------------------------------------------CCAC-GAGUCAGGAGACCUGCCUAAUUGCUUGUAUGAAGU
AP009385.1/1806044-1805855     UACGCGCGUUCGUUCGCCGGU---GCCCU------------------------UCGG--------GGCCG------AAGA--GGGAA-C-AC-A-G-GGCGCAUCGCGCC---------------------G---CUGU-GGCUGCCC-CC-GCAACUGUAG--AC-AG----------CGAGCCGAUCUCCCCCUCAU-------------------------GCCACUGGU---UUC------------------------------------------------------------A-CCGGGAAGGC--CGGG--A-GC--AGGCGCCGAC------------------------------------------------------------------CUGU-CAGCCAGGAGACCUGCCGGCCUGAAAGUGCGUGCG
CP000038.1/2154731-2154556     UCAUAACAUACGCUGACAGGUGU-GGCACAU----------------------UUGU--------GCC-----------U--GGGAA-G-AG-G-G-UGA-------------------------------AAAUCCCU-CGCAGCCC-CC-GCUGCUGUAA--UG-C------------UGACAAACCCGAAAAU----------------------------GCCACUGAUC-GCGA-----------------------------------------------------------GA-UUGGGAAGGU---CGG--G-UG--AGGAUGAC---------------------------------------------------------------------GCU-AAGCCAGAAGACCAGUCUGUCAGUCAAUACCAACA
CP000949.1/2158518-2158320     UCUACCAUGCGGGCCGCCGGU---UUCCACC----------------------ACG---------GAAAU------AAUA--GGGAA-U-CC-C-A-GGCCGCCCAGGCGCGCC-----------------AAAC--GG-AACUGCCC-CC-GCAACUGUAA--GU-GC----------CGAGCCCGCUCCAUCGAU---------------------------GCCACUGGAUCAGCC----------------------------------------------------------GAU-CCGGGAAGGC--UGGA--G-CC--GGGUGAUGAC------------------------------------------------------------------GCAC-CAGUCAGGAGACCUGCCGGCUUACAUUCACCAACC
AE007869.2/1640673-1640490     CCAUAGCUUCUCCGGUCAGGUG--CCCGCC-----------------------CUUGC----GGCGGGAG------AAUC--GGGAA-U-CC-G-G-UGA-------------------------------AAGACCGG-AACGUG-C-CC-AACGCUGUAA--GG-CG----------GAUGCUCUUUUUCUCAU----------------------------GCCACUGAA--GCAA------------------------------------------------------------U-UCGGGAAGGC---GAA--A-GG--GGCGGAUGA-------------------------------------------------------------------AGCU-UAGUCAGAAGACCGGCCUGGCAGGAUAGACCGAAC
CP000830.1/164274-164052       CGCAGAACAGUCAGGCAUGGU---UCCCCGUGCCCGCGCCAAG----------CGCCC----GGGGGAUC------AAAU--GGGAA-U-GU-G-G-AACGGUCCGAUCCAAACCGGAGGACC--------AAAGCCUC-AGCCGCCC-CC-GCGACUGUAU--GC-GG----------AGAGGGAGAUCGACAU-----------------------------GCCACUGGGG--CCC----------------------------------------------------------GCC-CCGGGAAGGC---CGA--U-CC-ACCCCGAUGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCAGCCAUGCGCGACACCCUUAGC
CP000853.1/1037045-1037222     UGAAUAUCAAAGUAUUAGGGUU--CUCUA------------------------CUUA--------GAGAU------AUUA--GGGAA-A-UU-G-G-UGC-------------------------------AAAGCCAA-UACAGCCC-CC-GCUACUGUAA--AC-AU----------GGACGA-GUUCUAAAA-----------------------------GCCACUGGAU--UUA-----------------------------------------------------------AU-CUGGGAAGGC---AGA--A-----GGAGGAAGAA------------------------------------------------------------------GUGU-GAGUCAGGAUACCUAACUAAUACUUGGCAUGGUUU
AARL02000087.1/606-795         UUAAAUAGGUCUUAUGUUGGU---GGAAUGU----------------------AUGUG----CAUUUCUG------AAAG--AGGAA-U-UC-G-G-UGC-------------------------------GAUGCCGA-AACUGCCC-CC-GCAACUGUAA--GG-UG----------GACAAAAAUAGAUAUA-----------------------------ACCACUGUACGUUUUAA--------------------------------------------------------UGU-AUGGGAAGGU---GCU--A-UU--GUUGGAUGA-------------------------------------------------------------------AGCC-AAGUCAGGAUACUCGCCAAAUAAGCCGGAAGCAAC
CP001025.1/1786797-1786605     UACGGCCGUUCGUUCGCCGGU---GCCCU------------------------UCGG--------GGCCG------AAGA--GGGAA-C-AC-A-G-GGCGCGCAUCGC----------------------GCCGCUGU-GGCUGCCC-CC-GCAACUGUAG--AC-AG----------CGAGCCGAUCUCCCCCCUCAU------------------------GCCACUGGU---UUC------------------------------------------------------------A-CCGGGAAGGC--CGGG--A-GC--CGGCGCCGAC------------------------------------------------------------------CUGU-CAGCCAGGAGACCUGCCGGCACUGAAAGUGCGUGC
CP000927.1/2970294-2970494     AGUGCAGCUCUCGCGACAGGU---UCCUCGA----------------------AAGA--------GGAUG------AAAA--GGGAA-CUCG-G-G-UGU-------------------------------GAAACCCG-GGCUGCCC-CC-GCAACUGUAA--GC-GGCG--------AGCCCGCGCGUCAUAA-----------------------------ACCACUGGGAGCCUCCUUCGGGAGG------------------------------------------------CCU-CUGGGAAGGC---GAC--G-CG--CACCGGCAUU---------------------------------------------------------------GACCCGC-GAGCCAGGAGACCUGCCCGUCGCGGUCGUCCUUCG
CP000873.1/297626-297839       ACCAUAUCUUGUGUUCGAGGUU--CUUUCGAUUCGA-----------------CGAGU----CGGGAGCU------AAGAC-GGGAA-U-CC-G-G-UGCGCUUGCCCAUGGUGGGCGGGC----------AAUGCCGG-AGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAGCUUUGCGCCCCAU----------------------------GCCACUGGC--GAAA------------------------------------------------------------G-CCGGGAAGGC---GGG--U-GG--AAGCGUUGAG------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCUUGAGCGUGAACGUCCAC
CP001090.1/13752-13558         CAAAAUAAAUCAAAUCACGGU---GCCCA------------------------UAGG--------GGCUU------GAUA--GGGAA-GAGG-G-G-UGCAUUUCCAUUUGGAAA----------------GAGUCCCC-CGCGGA-C-CC-GCCGCUGUAA--GC-GA----------GGACAAAGGGCAAUAAU----------------------------GUCACUGAUC-AUUA-----------------------------------------------------------GA-UUGGGAAGAC----GC--C-CG--GAGGAUGAA-------------------------------------------------------------------UCGC-AAGCCAGAAGACCUGCCGAUGAUCUCAACACUCAA
CP000958.1/1840255-1840064     UACGGCCGUUCGUUCGCCGGU---GCCCU------------------------UCGG--------GGCCG------AAGA--GGGAA-C-AC-A-G-GGC-GCCCCCCGC---------------------GCCGCUGU-GGCUGCCC-CC-GCAACUGUAG--AC-AGCG--------AGCCGAGCUCCCCCUCAU---------------------------GCCACUGGU---UUC------------------------------------------------------------A-CCGGGAAGGC--CGGG--A-GC--CGGCGCCGAC------------------------------------------------------------------CUGU-CAGCCAGGAGACCUGCCGGCCAGAAAGUGCGUGCG
AE007869.2/877627-877855       GGAUAACAUGUCCGUGAUGGUU--CCUUCCG----------------------GGCGUUCC-GGAAGGUG------AAAA--GGGAA-C-AC-G-A-UAGGGACAAAUCC---------------------UCAUUCGU-GGCUGCCC-CC-GCAACUGUGA--GC-GG----------AGAGCCUGAAACGAAAU----------------------------GCCACUGGCAAGCCAUCUCGCCUCCAUCAAGGGGGAAGGCA--------------------------------AUG-CCGGGAAGGU---GUU--U-CA--GGUUUUGAC-------------------------------------------------------------------CCGU-AAGCCAGGAGACCUGCCAUCACGGAAAUAUCCAUG
AE008922.1/3631190-3630967     UACCAUGCGCGCCCCUGAGGUG--ACUGCCG----------------------GAAUUCC--GGUGGUUU------AAAC--GGGAA-U-CC-G-G-UGCGCGCAUCGCCUUGGCGAGACGC---------AAGUCCGG-AGCUGCCC-CC-GCAACGGUGG--GC-GAG---------GUCAGGUGCCGCAACAG----------------------------GCCACUGUGC-ACAC-----------------------------------------------------------GC-AUGGGAAGGC---GCG--G-UA--CCGGAAGCGC--------------------------------------------------------AGGCUUCCACUCGC-GAGCCCGGAGACCGGCCUGAGGGAUUGACCCGGCA
CP001090.1/30663-30471         UGAAUAUGCACGAAUCACGGUG--CCCGC----------------------------------AAGGGUG------AAAA--GGGAA-GAGG-G-G-UGACGCUCUGACGAGC------------------UAUUCCCC-CGCGGA-C-CC-GCCGCUGUAA--GC-GA----------UGACGA-AGGGCAACAAC---------------------------GUCACUGAUCAUUUA-----------------------------------------------------------GA-UUGGGAAGAC---GCC--C-----GGAGGAUGAC------------------------------------------------------------------UCGC-AAGUCAGAAGACCUGCCGCUGAUUGUUGUUACUCG
CP001111.1/542487-542264       AGACUGCGCGCACUUCCAGGUG--ACCUGCGGCCAU-----------------GGCCG----GCAGGUUG------AAAC--GGGAA-G-CC-G-G-UGACGCGUGAUUCCACGC----------------CAUGCCGG-CGCUGCCC-CC-GCAACGGUAA--GCACG----------UCAGUUCCAGGCAACACC---------------------------GCCACUGUGCCGCAG-----------------------------------------------------------GC-AUGGGAAGGC---GCC--U-GG--ACGGUGGCCU------------------------------------------------------CGCGCCACCCGGCGGC-AAGCCCGGAGACCGGCCCGGAAGCCUCAGGUCGCG
CP001175.1/1515606-1515417     UUAAAUAGGUCUUAUGUUGGU---GGAAUGU----------------------AUGUG----CAUUUCUG------AAAG--AGGAA-U-UC-G-G-UGC-------------------------------GAUGCCGA-AACUGCCC-CC-GCAACUGUAA--GG-UG----------GACAAGAAUAGAUAUA-----------------------------ACCACUGUACGUUUUAA--------------------------------------------------------UGU-AUGGGAAGGU---UCU--A-UU--GUUGGAUGA-------------------------------------------------------------------AGCC-AAGUCAGGAUACUCGCCAAAUAAGCCGGAAGCAAC
AL591688.1/954760-954963       UUAGAUGAGGACACUCAAGGUG--CCGCCUC----------------------GAAGGGA--GGGCGGAG------AAUU--GGGAA-G-CC-G-G-UCA-------------------------------AAUCCCGG-CGCUGCCC-CC-GCAACGGUGG--UG-GAGCG-------AACAGCCACGGCAGAAG----------------------------GCCACUGGACACCGC-----------------------------------------------------------GU-CCGGGAAGGC---GCC--G-GG--CAGGUCCCUU---------------------------------------------------------GCGGACGGCUCCA-GAGCCCGGAAACCAGCCUUGAAGCAGAAAUAGACC
ABKL02000008.1/4023-4215       UAAAUAUAUAAUAUUAUAGGU---UCUUCAA----------------------GCA---------AGAUU------AAUA--GGGAA-A-AA-G-G-UUA-------------------------------AAUUCCUU-UACAGCCC-CC-GCUACUGUGA--UG-C-----------AGACGAAACUUUUGUUA----------------------------GCCACUAUGAUGAUAUUUUUUAUAU------------------------------------------------CUC-AUGGGAAGGA---AGA--G-GA--UUAGGAAGAA-------------------------------------------------------------------GCU-AAGUCAGGAGACCUGCCUAAAAUAUUAAAGUAAUU
CP000850.1/3174011-3173839     AUAGCCUCUCGCCGUCAAGGUG-----------------------------------------CA--------------C--GGGAA-G-CC-G-G-UGA-------------------------------AACACCGG-CGCGGCCC-UC-GCCACUGUGA--CC-GGG---------UAGCGAUCUCCGACUAC----------------------------GCCACUGGGCCCGACCG--------------------------------------------------------GGU-CUGGGAAGGC---CGG--A-GU--GAACGUCGAU------------------------------------------------------------------CCGG-AAGCCAGGAGACCGGCCUUGACAAGGAUCUCAUCC
AP008230.1/4379378-4379199     GAAUAUCAGGCGGAAUAGGGU---UGCUU------------------------AAAU--------GCAUU------AAUA--GGGAA-CUCC-G-G-UGU-------------------------------GAAGCCGG-GACAGC-C-CC-GCUACUGUAA--GA-AG----------GACGAGUCCCUUAGAGGA---------------------------UCCACUGGU--GAAA------------------------------------------------------------A-CCGGGAAGGU---AAG--G-GA--UGAGGAUGA-------------------------------------------------------------------GUUC-AAGUCAGGAUACCUGCCCCAUUCCGGAAACACAAG
CP000853.1/373263-373442       CAAAUGAAUACAUUUUAUGGUU--CUUUCUU----------------------AUGA--------AAGCU------AAGA--GGGAA-A-GA-G-G-UGA-------------------------------GAAACCUC-UGCAGCCC-CC-GCUACUGUAA--GC-A-----------GGACGAAAUUCCAAUAA----------------------------ACCACUGUGU----------------------------------------------------------------AA-AUGGGAAGGU--AGGA--A-GA--GUAGGAAGAG-------------------------------------------------------------------UGC-AAGCCAGGAGACCUGCCAUAAAACGUGAAUGAAGC
CP000943.1/944045-944239       CCUAGCCUAUCGCUCGACGGU---GCCCU------------------------CCGG--------GGCCU------AACA--GGGAA-C-GC-G-G-UGAGGGCUCGCGCCC-------------------GAAUCCGC-GGCUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCCCUCCAUCACCAC----------------------------GUCACUGGGG-UCAU-----------------------------------------------------------GC-CCGGGAAGAC---GAU--G-GG--GGGCGGCGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCUGCCGUCGACCGUGGUCACACG
CP000880.1/3464662-3464469     CGGUAGCAUCCGUGGGCCGGU---CCUGU------------------------------------GAGUU------AAUA--GGGAA-U-CC-A-G-UGA-------------------------------AAAUCUGG-AGCUGA-C-GC-GCAGCGGUAA--GG-AA----------AGGUGAGAUGAGAGCGUAAGCA-----------------------GACACUGCC---UCC------------------------------------------------------------G-GCGGGAAGUC---AUC--A-UU--UCUGCUAUCC---------------------------------------------------AGCCAACGGAUAACCCUCC-AAGCCCGAAGACCUGCCGGCUAACGUCGCAUCUGG
AE007869.2/2810186-2809969     UAAGGGUAAGGGACUGACGGU---CUUUUCCCGGC------------------AACGG----GAAAAGCU------AAGA--GGGAA-C-AC-G-G-UUCCGCCCCGAGAAAGGGU---------------CAUUCCGU-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------UAAGCCCGCACCGUAAA----------------------------GCCACUGAACCUUUAUGAUC-----------------------------------------------------GGU-UCGGGAAGGC---GGU--G-AC--AGGGUGUUGA---------------------------------------------------------------UAGCCGC-AAGCCAGGAGACCUGCCGUUUCAGGAAAAAGCGUC
CP001090.1/1002-822            GCAGAAUAUACGAUCAACGGU---GCCCA------------------------UACG--------GGCUU------GAUA--GGGAA-GUGA-G-G-UGA-------------------------------AACUCCUC-CACGGA-C-CC-GCCGCUGUAA--GC-GA----------UGACAAAGGGCAACAAU----------------------------GUCACUGAUCAAUUU-----------------------------------------------------------GA-UCGGGAAGAC----GC--C-CG--GAGGAUGAU-------------------------------------------------------------------UCGC-AAGUCAGAAGACCUGCCUUGAUCUUACAUCAUGAA
AE008691.1/396055-396295       GAAUAUAAAAAGCCUUAUGGU---CCCGU---------------------------------GAUGGGUU------AAAA--GGGAA-GACG-G-G-UGA-------------------------------GAAUCCCG-CGCAGCCC-CC-GCUACUGUGA--GG-GA----------GGACGAAGCCCUAGUAA----------------------------GCCACUGUCCGGCACUCAACUGAGCGCGUUAGUAAGGAGAAAAGAGGGAGAGAAAUUGCGUUCAGUUGAGUGCCGG-AUGGGAAGGC---AGG--G-UG--GAGGAUGAG-------------------------------------------------------------------UCCC-GAGCCAGGAGACCUGCCAUAAGGUUUUUAAAAGUU
CP001157.1/3390006-3389785     CCUGCGCGCCUCGCUUCAGGUG--CCCCAA-----------------------------------GGGUG------AAACA-GGGAA-G-CC-G-G-UGCGUGCCGCGACCAUUCGCGGCGC---------AAGGCCGG-CGCUGCCC-CC-GCAACGGUAG--AC-GAG---------UCGCGAAACCGCAAUA-----------------------------GCCACUGUGUUGCUCG---------------------------------------------------------GAC-ACGGGAAGGC---GCG--G-UU--UCGGAAGCCG--------------------------------------------------CCGCAUGGCGCUUCGCUCGU-GAGCCCGGAGACCGGCCUGUGGCGAUCCAUGGCGG
AE007870.2/921705-921914       ACAUUGGUUAGCCAUCGUGGUU--CUGCGGACG--------------------AAGGU----CCGGAGCU------AAGA--GGGAA-U-UC-G-G-UGAGGGCUUUAAUCACAGCCU-------------GAAUCCGA-AGCUGCCC-CC-GCAACUGUAA--GC-GAC---------GAGCGAAAGUCCAUCAU----------------------------GUCACUGAGG--CCG----------------------------------------------------------GCC-UCGGGAAGAC---GGA--C-CA--AAGCUAUGAC------------------------------------------------------------------CCGC-AAGCCAGGAGACCUGCCGCGAUAGAUAACGUCCAC
CP000943.1/2696265-2696461     GCUACCUUCCGCCGCGACGGUG--CCUCGGC----------------------GACG--------AGGUG------AAAA--GGGAA-C-GC-G-G-AGCGGGGCCAGCCCCG------------------GAAGCCGC-GGCUGCCC-CC-GCAACUGUGA--GC-GG----------UGCGGGCCCGCCAUCG-----------------------------GCCACUGGA--GCGA------------------------------------------------------------U-CCGGGAAGGC---GGC--G-GG--CACGGUCCAC----------------------------------------------------------------CAUCGC-GAGCCAGGAGACCUGCCGUCACCCCUUCCUCUCGA
CP000924.1/1954621-1954429     GAAUACAAAAAAUCUUAUGGU---CUUGAG-----------------------------------AAGUU------AAAA--GGGAA-A-GC-G-G-UGA-------------------------------AAAUCCGC-UGCAGCCC-CC-GCUACUGUGA--GC-GA----------GGAUGAAGCCCUAAUAA----------------------------GCCACUGCUUGGCACUCAAGAGAUGUGC---------------------------------------------CGG-GUGGGAAGGC---AGG--G-UG--GAAGAUGAA-------------------------------------------------------------------UCGC-GAGCCAGGAGACCUGCCAUAAGAUUUCGGAAGUUC
ABDO02000001.1/974410-974591   AUUUAAUAAAGAAAUUUAGGUG--CCUUU------------------------GUAGU----AAAAGGUG------AAAA--GGGAA-U-GU-G-G-UAA--------------------------------AAUCCAC-AGCAGCCC-CC-GCUACUGUAA--UU-GA----------AGACAAAUCUUUCAUAG----------------------------GCCACUCUUU---------------------------------------------------------------AAA-AGGGGAAGGG---AAA--G-AU--UAGGAUGAA-------------------------------------------------------------------UCAU-GAGCCAGGAGACCUGCCUAGAUUUUUAUUAGGAAA
AP009386.1/1277939-1278133     UUACCCUUGCGCGCUGAUGGUU--CCCGCGA----------------------GACG--------GGAUC------AAAU--GGGAA-C-GC-A-G-UGACGGCGCACGCCG-------------------GAAUCUGC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAGUCCGUGCCCUUCGC---------------------------GCCACUGG---GAGA--------------------------------------------------------------CCGGGAAGGC--GGGC--A-CC--GGGCGGCGAC------------------------------------------------------------------CCGC-GAGCCAGGAGACCAGCCAUCGACCGAGGUCCAAGC
CP000908.1/1328850-1328641     CGAAGUUGCUGCGGCCAAGGUU--CCCCCGGAUGC------------------AUGUC----CGAGGGCU------AAGA--GGGAA-U-UC-G-G-UAAGCCCGUCCGGGC-------------------GAGGCCGA-AGCUGCCC-CC-GCAACUGUGA--GC-GGC---------GAGCCACCGUCGUCGAAG---------------------------GUCACUGGUGCCCUG-----------------------------------------------------------CA-CCGGGAAGGC-CGAGA--C-GG--GGGCGCUGAC------------------------------------------------------------------CCGU-GAGCCAGGAGACCUGCCUUGGCGCGACGAUGUCCC
CP000830.1/546421-546638       AGCGAUGCUCUGAUCGAUGGU---UCCCGAAACCCGCGA--------------GGGUG----AAGGGAUG------AAAA--GGGAA-C-AC-G-G-UGAGGCGUAGCCAUCAGGCACC------------AAACCCGU-GACUGCCC-CC-GCAACUGUGA--GC-GG----------UGAGCGACCCCGUGGAC----------------------------ACCACUGGACCGAUGC---------------------------------------------------------GGU-CCGGGAAGGU---UCG--G-GG--AAGCCGUGAC------------------------------------------------------------------CCGC-GAGUCAGGAGACCUGCCAUCGAUGGUGCGCUUUCG
CP001063.1/4163721-4163911     CUGUAGCAUCCACUUGCCGGU---CCUGU------------------------------------GAGUU------AAUA--GGGAA-U-CC-A-G-UGC-------------------------------GAAUCUGG-AGCUGA-C-GC-GCAGCGGUAA--GG-AA----------AGGUGCGAUGAUUGCGUUAUGCG----------------------GACACUGCC--AUCC------------------------------------------------------------G-GUGGGAAGUC---AUC--A-UC--UCUUAGUAUC--------------------------------------------------------UUAGAUACCCCUCC-AAGCCCGAAGACCUGCCGGCCAACGUCUCAUCAUC
CP000908.1/1617572-1617372     CUAUGACCGCUCCGUGACGGUG--CCCCGGC----------------------AGCG--------GGGUG------AAAA--GGGAA-U-GC-G-G-UGAGAGGUUUUCCAGAAGCCUC------------GAUUCCGC-GGCUGCCC-CC-GCAACUGUAA--GC-GG----------CGAGUUCCUGCCACGA-----------------------------GCCACCGGGU---------------------------------------------------------------GAU-CCGGGAAGGC---GGC--A-GG--CACGAUACCA-----------------------------------------------------------------GCCGC-GAGCCAGGAGACCUGCCGUCCAGCGAAGUUUUGUU
AE007869.2/70421-70645         ACUAUAUGUGGUGUUCAAGGUU--CUUCCGAUUCGCU----------------AGGGU----UGGGAGCU------AAGAC-GGGAA-U-UC-G-G-UGCGUAACGCCAUCACGGCGGAGC----------AAGGCCGA-AACUGCCC-CC-GCAACUGUGA--GC-GG----------CGAGCAUCGUUCCGAUUUGA-------------------------GCCACUGGAGCCAAAA---------------------------------------------------------GCU-CCGGGAAGGC-UGGAA--U-AG--AUGUUGUGAC------------------------------------------------------------------CCGC-AAGUCAGGAGACCUGCCUUGAGCGCAAAUGUCCAC
AL591688.1/1999767-1999554     GGCCAUAUGCCGCCGUCAGGUG--CCCGCGA----------------------AAUG-------CGGGGG------AAUC--GGGAA-G-CC-G-G-UGC-------------------------------AGUUCCGG-CACGUG-C-CC-AACGCUGUGA--AG-GG----------GACGUUCUCGCCAAAAAGGGCUCUGAAUCUUUUCAGAGCUUU---GCCACUGAAUAUUGAAGC-------------------------------------------------------UAU-UCGGGAAGGC---GGC--G-CG--AACGGAUGA-------------------------------------------------------------------UCCG-AAGUCAGAAGACCGGCCUGGCGAGAUAGACCGGCC
CP000094.2/3552647-3552437     GUAGCCUUGCGCUUUCGAGGUU--CUUCGGC----------------------CCACG----CCGAAGCU------AAGAA-GGGAA-C-GC-G-G-UCC--------------------------------AAGCCGC-GGCUGCCC-CC-GCAACUGUGA--AC-GGU---------GCUGUUCGCUGCCAC------------------------------GCCACUGCCAACUCAAUCCAGAG--------------------------------------------------CCA-GCGGGAAGGC---GCA--G-CG--AAUACCGGGC-----------------------------------------------------CAAGGCCCGAACACCGU-CAGCCAGGAGACCUGCCUCGUCACAGAUUCUCACU
AALF02000008.1/20807-20994     UUACUGAAAUGGUUAUGUCGU---GUACGCAUUG-------------------GCACU----UAAUACAC------GACA--GGGAA-G-GG-G-G-UGA-------------------------------CAAUCCCC-CGCAGCCC-CC-GCUGCUGUGA--UG-C-----------CGACGAACCCGCUGAA-----------------------------ACCACUGAUCCAUCG-----------------------------------------------------------GA-UUGGGAAGGU---GCG--G-GG--GAGGAUGAC--------------------------------------------------------------------GCU-AAGCCAGAAGACCAGCCAAAUCGGUAAAAUAUAUU
CP002156.1/2306524-2306337     GCCAUUCAGCGAAGAGAUGGUU--CCGUG------------------------AGAGA----UCACGGCG------AAGA--GGGAA-C-CC-G-G-UGG-------------------------------CAAUCCGG-GGCUGUAC-CC-GCAACUGUGA--GC-CAG---------GAGCUGACAACCGAUAC----------------------------ACCACUGGAG-GAAA-----------------------------------------------------------CU-CCGGGAAGGG---GGU--U-GG--AAGCGAUGAU------------------------------------------------------------------CGGU-GAGCCAGGAGACCUGCCAUCGCGUCGUUCGUCCGG
AALC02000021.1/24189-24004     UUUUUUAUAUAUCGAAAUGGUC--AUGUUAU----------------------GCGCAA---AAGCAU--------AACU--GGGAA-G-GG-G-G-UGA-------------------------------CAAUCCCC-CGCAGCCC-CC-GCUGCUGUGA--UG-CU----------GACGAACCCGCUGUU------------------------------ACCACUGAUCCAUCG-----------------------------------------------------------GA-UUGGGAAGGU---UGC--G-GG--UGAGAGUGA-------------------------------------------------------------------CGCU-AAGCCAGAAGACCAGCCAGAUCGGUAAAAGAUAUU
CP003056.1/1126059-1125863     AUAUAGUAUGCGAGUAUUGGU---GGCUUUG----------------------AGAU--------GCCUG------AAAA--GGGAA-U-CC-G-G-UGG-------------------------------GAAACCGG-AGCUGCCC-CC-GCAACUGUCA--GU-GU----------GGACGAAAGAGCAAA-------------------------------CCACUGUACCGGCUGCUUUUUUUGGCGGC-------------------------------------------GGU-AUGGGAAGG----GCU--U-CA--UUAGAAUGAA------------------------------------------------------------------ACAC-AAGCCAGGAGACCUGCCAAUACUUGAAGUUUCUAU
AALE02000017.1/13768-13947     CUUCAAGAAUAAAAGGCAUGUU--AUGCACU----------------------AAAG--------CAU--------AACU--GGGAA-G-GG-G-G-UGA-------------------------------CAAUCCCC-CGCAGCCC-CC-GCUGCUGUGA--UG-C-----------UGACGAACCCGUAGAA-----------------------------ACCACUGAUCCACAA-----------------------------------------------------------GA-UUGGGAAGGU---GCG--G-GA--GAGGAUGAC--------------------------------------------------------------------GCU-AAGCCAGAAGACCAGCCCGCUCAGUAAAAGAUUUU
AALD02000002.1/89872-89688     AUUUGUAGUUACUGAUAGGGUC--AUGUUAU----------------------GCGCUA---AAGCAU--------AACU--GGGAA-G-GG-G-G-UGA-------------------------------CAAUCCCC-CGCAGCCC-CC-GCUGCUGUGA--UG-C-----------UGACGAACCCGCUGUU-----------------------------ACCACUGAUCCAUCG-----------------------------------------------------------GA-UUGGGAAGGU---GCG--G-GG--GAGAAUGAC--------------------------------------------------------------------GCU-AAGCCAGAAGACCAGCCAGAUCGGUAAAAGAUAUU
#=GC SS_cons                   :::::::::::::::[[[[[[,..<<<____......................_____....___>>>,,......,,,(..((,,,.<.<<.<.<.___...............................____>>>>.>,,<<<__.__.>>>,<<<---..<<.<<..........------<<<<<<-----............................<<<-<<<<<<_____.........................................................._>>.>>>>--->>>...>>>..>.>>..----------..................................................................>>>>.---->>>,,,,)))]]]]]]:::::::::::::::
#=GC RF                        uuaaauugaaacgaugauGGUu..ccccuuu......................aaagu....gaaggguu......AAaa..GGGAA.c.cc.G.G.UGa...............................aAaUCCgg.gGCuGcCC.CC.gCaACuGUAA..gc.Gg..........agagcaccccccAauAa............................GCCACUggcccgcaa..........................................................ggg.ccGGGAAGGC...ggg..g.gg..aaggaaugac..................................................................cCgc.gAGcCaGGAGACCuGCCaucaguuuuugaaucucc
//
# STOCKHOLM 1.0

#=GF AC   RF00175
#=GF ID   HIV-1_DIS
#=GF PI   Retroviral_psi
#=GF DE   Human immunodeficiency virus type 1 dimerisation initiation site
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Bateman A
#=GF SS   Published; PMID:8627772
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019074; viral RNA genome packaging;
#=GF RN   [1]
#=GF RM   9032337
#=GF RT   Position dependence of functional hairpins important for human
#=GF RT   immunodeficiency virus type 1 RNA encapsidation in vivo.
#=GF RA   McBride MS, Panganiban AT
#=GF RL   J Virol 1997;71:2050-2058.
#=GF RN   [2]
#=GF RM   9151848
#=GF RT   Efficient encapsidation of human immunodeficiency virus type 1 vectors and
#=GF RT   further characterization of cis elements required for encapsidation.
#=GF RA   McBride MS, Schwartz MD, Panganiban AT
#=GF RL   J Virol 1997;71:4544-4554.
#=GF RN   [3]
#=GF RM   8627772
#=GF RT   The human immunodeficiency virus type 1 encapsidation site is a
#=GF RT   multipartite RNA element composed of functional hairpin structures.
#=GF RA   McBride MS, Panganiban AT
#=GF RL   J Virol 1996;70:2963-2973.
#=GF RN   [4]
#=GF RM   12851400
#=GF RT   Rev binds specifically to a purine loop in the SL1 region of the HIV-1
#=GF RT   leader RNA.
#=GF RA   Gallego J, Greatorex J, Zhang H, Yang B, Arunachalam S, Fang J, Seamons J,
#=GF RA   Lea S, Pomerantz RJ, Lever AM
#=GF RL   J Biol Chem 2003;278:40385-40391.
#=GF RN   [5]
#=GF RM   12559920
#=GF RT   Structure of the intact stem and bulge of HIV-1 Psi-RNA stem-loop SL1.
#=GF RA   Lawrence DC, Stover CC, Noznitsky J, Wu Z, Summers MF
#=GF RL   J Mol Biol 2003;326:529-542.
#=GF RN   [6]
#=GF RM   10926523
#=GF RT   NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop SL2 of
#=GF RT   the psi-RNA packaging signal. Implications for genome recognition.
#=GF RA   Amarasinghe GK, De Guzman RN, Turner RB, Chancellor KJ, Wu ZR, Summers MF
#=GF RL   J Mol Biol 2000;301:491-511.
#=GF RN   [7]
#=GF RM   9743628
#=GF RT   Three-dimensional folding of an RNA hairpin required for packaging HIV-1.
#=GF RA   Pappalardo L, Kerwood DJ, Pelczer I, Borer PN
#=GF RL   J Mol Biol 1998;282:801-818.
#=GF RN   [8]
#=GF RM   11724565
#=GF RT   Structure of SL4 RNA from the HIV-1 packaging signal.
#=GF RA   Kerwood DJ, Cavaluzzi MJ, Borer PN
#=GF RL   Biochemistry 2001;40:14518-14529.
#=GF RN   [9]
#=GF RM   8794309
#=GF RT   Role of the DIS hairpin in replication of human immunodeficiency virus
#=GF RT   type 1.
#=GF RA   Berkhout B, van Wamel JL
#=GF RL   J Virol. 1996;70:6723-6732.
#=GF CC   This cis element is composed of four hairpins called SL1 to SL4 (SL is for
#=GF CC   Stem Loop). This element is involved in encapsidation of the retroviral
#=GF CC   RNA an essential step in replication [1-3]. It is found in HIV, SIV and
#=GF CC   CIV. It has been shown that SL1 may provide a secondary binding site for
#=GF CC   Rev [4]. SL1 [5], SL2 [6], SL3 [7] and SL4 [8] have been independently
#=GF CC   expressed and structurally characterised.
#=GF WK   Retroviral_Psi_packaging_element
#=GF SQ   70


AF042100.1/691-730 GG-ACUC-GGCUUGCU-G-AAGCGC-GCA-CGGCAAGAGGCGA-GGG
AF110973.1/184-223 GG-ACUC-GGCUUGCU-G-AAGUGC-ACU-CGGCAAGAGGCGA-GAG
AF443085.1/69-108  GG-ACUC-GGCUUGCU-G-AAGUGC-ACU-CGGCGAGAGGCGA-GAG
AF443113.1/69-108  GG-ACUC-GGCUUGCU-G-AAGUGU-ACU-CGGCAAGAGGCGA-GAG
AJ288982.1/713-752 GG-ACUC-GGCUUGCU-G-AGGUGC-ACA-CAGCAAGAGGCGA-GAG
AF197338.1/656-695 GG-ACUC-GGCUUGCU-G-AGGUGC-ACA-CAGCAAGAGGCAA-GAG
AY161888.1/12-51   GG-ACUC-GGCUUGCU-G-AAGUGC-ACA-CAGCAAGAGGCGA-GAG
AF492623.1/62-101  GG-ACUC-GGCUUGUU-G-AGGUGC-ACA-CAGCAAGAGGCGA-GAG
AY161885.1/12-51   GG-ACUC-GGCUUGCU-G-AGGUGC-ACA-CAGCAAGAGGCGA-GAA
AF193275.1/69-108  GG-ACUC-GGCUUGCU-G-AGGUGC-RCA-CAGCAAGAGGCGA-GAG
AJ291718.1/701-741 GGAACUC-GGCUUGCU-G-AGGUGC-ACA-CAGCAAGAGGCGA-AAG
AF164485.1/717-756 GG-ACUC-GGCUUGCU-G-CGGUGC-ACA-CAGCAAGAGGCGA-GAC
AF170549.1/642-681 GG-ACUCUGGCUUGCU-G-CGGUGC-ACA-CA-CAAGAGGCGA-GAG
L39106.1/237-276   GG-ACUC-GGCUUGCU-G-AGGUGC-GCA-CAGCAAGAGGCGA-GAG
AY161882.1/12-51   GG-ACUC-GGCUUGCU-G-AAGGGC-ACA-CAGCAAGAGGCGA-GAG
AY161887.1/12-50   GG-ACUC-GGCUUGCU-GAAGGUGC-ACA-CAGCAAGAGCCGA-G--
AF061640.1/97-136  GG-ACUC-GGCUUGCU-G-AGGUGC-ACG-CAGCAAGAGGCGA-GAG
AJ293865.1/46-85   GG-ACUC-GGCUUGCU---GAGUGC-ACG-CAGCAAGAGGCGAGGCG
AJ291720.1/705-745 GG-ACUC-GGCUUGCU-GAAAGUGC-ACG-CAGCAAGAGGCGA-GAG
AY180905.1/75-114  GG-ACUC-GGCUUGCU-G-AAGCGC-GCA-CAGCAAGAGGCGA-GAG
AB097873.1/63-101  GG-ACUC-GGCUUGCU-G-AAGCGC-GCA-CAGCAAGAGGCGA--GA
AB097870.1/72-112  GG-ACUC-GGCUUGCU-GAAAGCGC-GCG-CAGCAAGAGGCGA-GAG
AF077336.1/45-85   GG-ACUC-GGCUUGCU-G-AAGUGCAACA-CGGCAAGAGGCGA-GAG
AF286233.1/39-78   GG-ACUC-GGCUUGCU-A-AAGUGC-ACU-UGGCAAGAGGCGA-GAG
AF443098.1/69-108  GG-GCUC-GGCUUGCU-G-AAGUGC-ACU-CGGCAAGAGGCGA-GAG
AF110972.1/83-122  GG-ACUC-GGCUUGCU-G-AAGUGC-ACU-CGGCAAGAGGCGA-GGG
AF290027.1/703-742 GG-GCUC-GGCUUGCU-G-AAGUGC-AAU-CGGCAAGAGGCGA-GGG
AF286223.1/41-80   GG-ACUC-GGCUUGCU-G-AAGUGC-ACU-CAGCAAGAGGCGA-GGG
AF443080.1/69-110  GG-ACUC-GGCUUGCU-GAAAGUGC-ACU-CGGCAAGAGGCGAGAGG
AF110981.1/69-108  GG-ACUC-GGCUUGCU-G-AAGUGC-ACU-CGGCAGGAGGCGA-AAG
AF110974.1/184-223 GG-ACUC-GGCUUGCU-G-AAUUGC-ACU-CGGCAAGAGGCGA-AAG
AF110979.1/69-108  GG-ACUU-GGCUUGCU-G-AAGUGC-ACU-CGGCAGGAGGCGA-GAG
AF443114.1/69-108  GG-ACUC-GGCCUGCU-G-AAGUGC-ACU-CGGCAGGAGGCGA-GAG
AY074891.1/69-108  GG-ACUC-GGCUUGCU-G-AAGUGC-ACU-CGGCAGGAGGCGA-GAG
AF443089.1/69-108  GG-ACUC-GGCUUGCU-G-AAGUGC-ACU-UGGCAAGAGGCGA-GAG
AY118154.1/240-279 GG-ACUC-GGCUUGCU-G-AGGUGC-ACU-CGGCAAGAGGCGA-GAG
U86780.1/72-111    GG-ACUC-GGCUUGCU-G-AAGUGC-ACC-CGGCAAGAGGCGA-GAG
AF443084.1/69-109  GG-GAUC-GGCUUGCU-GAAAGUGC-ACU-CGGCAAGAGGCGA-GAG
AF443107.1/69-108  GG-ACUC-GGCUUGCU-G-AAGUGC-ACU-CGGCAAGAGGCGA-AAG
AF286238.1/40-80   AG-ACUC-GGCUUGCU-G-AGGUGC-ACA-CGGCAAGAGGCGAGAAG
AY161889.1/12-52   GG-ACUC-GGCUUGCU-GAAGGUGC-ACA-CGGCGAGAGGCGA-GAG
K02007.1/695-734   GG-ACUC-GGCUUGCU-G-AAGCGC-GCA-CAGCAAGAGGCGA-GGG
AF408626.1/118-157 GG-ACUC-GGCUUGCU-G-AAGCGC-GCG-CGGCAAGAGGCGA-GGG
AF286242.1/173-213 GG-ACUC-GGCUUGCU-G-AGGUGC-ACA-CGGCAAGAGGCGAGGGG
AF408632.1/261-300 GG-ACUC-GGCUUGCU-G-AAGUGC-ACA-CGGCAAGAGGCGA-GGG
AF190127.1/72-112  GG-ACUC-GGCUUGCU-G-AAGUGC-ACA-CAGCAAGAGGCGAGGGG
AF086817.1/693-733 GG-ACUC-GGCUUGCU-G-AAGUGC-GCA-CGGCAAGAGGCGAGGGG
AF385935.1/714-752 GG-ACUC-GGCUUGCU-G---AGGC-GCA-CGGCAAGAGGCGAGGAG
AF442565.1/60-101  GG-ACCC-GGCUUGCCUG-AAGCGC-GCA-CGGCAAGAGGCGGGGGG
AF442570.1/57-96   GG-ACUC-GGCUUGCU-G-AAGCGC-GCG-CAGCAAGAGGCGA-GGG
AF465242.1/767-806 GG-ACUC-GGCUUGCU-G-AAGCGC-GCA-CGGCAAGCGGCGA-GGG
AF193253.1/70-109  GG-ACUC-GGCUUGCU-G-AAGCGC-GCA-AGGCAAGAGGCGA-GGG
U88822.1/208-248   GG-ACUC-GGCUUGCU-GAAAGCGC-GCU-CGGCAAGAGGCGA-GGG
AF538305.1/694-733 AG-ACUC-GGCUUGCU-G-AAGCGC-GCA-UAGCAAGAGGCGA-GGG
AF538306.1/693-733 GG-ACUC-UGCUUGCU-G-AAGCGC-GCA-CAGCAAGAGGCGAGGGG
AF423755.1/144-183 GG-ACUC-GGCUUGCU-G-CAGCGC-GCA-CGGCAAGAGGCGA-GGG
U26546.1/74-113    GG-ACUC-AGCUUGCU-G-AAGCGC-GCA-CGGCAAGAGGCGA-GGG
AY062241.1/3-42    GG-ACUC-GGCUUGCU-G-AAGCGC-GCG-CAGCAAGAGGCGA-GUG
AY161886.1/12-51   GG-ACUC-GGCUUGCU-G-AAACGC-GUA-CGGCAAGAGGCGA-GGG
AF538304.1/695-734 GG-ACUC-GGCUUGCU-G-AAACGC-GCG-CGGCAAGAGGCGA-GGG
AB078005.1/649-688 GG-ACUC-GGCUUGSU-G-AAGCGC-GCA-CGGCAAGAGGCGA-GGG
AF042101.1/695-734 GG-ACUC-GGCUUGCU-G-UAGCGC-GCA-CGGCAAGAGGCGA-GGG
AF005495.1/41-80   GG-ACUC-GGCUUGCU-G-AAGCGC-GCA-CGGCAGGAGGCGA-GGG
AF115393.1/68-106  GG-ACUC-GGCUUGCU-G--AGUGC-ACA-CAGCGAGAGGCGA-GGC
EF394358.1/234-272 GG-ACUC-GGCUUGUG-A-CAGCGC-AA--UCACAAGAGGCGA-GGC
DQ373065.1/235-273 GG-ACUC-GGCUCGUU-G--AGUGC-ACA-CAGCGAGAGGCGA-GGC
AF382828.1/48-88   GG-ACUC-GACUUGCU-G-UAGUGC-ACAACAGCGAGAGGCGA-GGC
U42720.2/35-74     GG-ACUC-GGUCUGCU-G-CAGCGC-GCG-UAGCAGAAGGCGA-GGC
AJ271369.1/371-409 GG-ACUC-GGCUUACU-G--AGUGC-ACG-CAGUAAGAGGCGA-GGC
AY169968.1/238-276 GG-ACUC-GGCUUGUU-G--AGUGC-ACA-CAACAAGAGGCGA-GGC
#=GC SS_cons       ::.:<<<.<-<<<<<<.<.______.___.>>>>>>>--->>>.>::
#=GC RF            GG.ACUC.GGCUUGCu.G.AAGUGC.ACa.CaGCAAGAGGCGA.GgG
//
# STOCKHOLM 1.0

#=GF AC   RF00176
#=GF ID   Tombus_3_IV
#=GF DE   Tombusvirus 3' UTR region IV
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:12954222
#=GF GA   33.00
#=GF TC   33.50
#=GF NC   31.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0039694; viral RNA genome replication;
#=GF RN   [1]
#=GF RM   12954222
#=GF RT   3'-Terminal RNA secondary structures are important for accumulation of
#=GF RT   tomato bushy stunt virus DI RNAs.
#=GF RA   Fabian MR, Na H, Ray D, White KA
#=GF RL   Virology 2003;313:567-580.
#=GF RN   [2]
#=GF RM   14532132
#=GF RT   A replication silencer element in a plus-strand RNA virus.
#=GF RA   Pogany J, Fabian MR, White KA, Nagy PD
#=GF RL   EMBO J 2003;22:5602-5611.
#=GF CC   Tomato bushy stunt virus is the prototype member of the Tombusviridae
#=GF CC   family. In addition to viral proteins p33 and the RNA-dependent RNA
#=GF CC   polymerase p92, and unknown host factors, RNA signals within the UTRs are
#=GF CC   necessary for genome replication. This element contains a pseudoknot [2].
#=GF WK   Tombusvirus_3'_UTR_region_IV
#=GF SQ   18


S64508.1/531-622     UUGCCAGACACGGUUGAUCUCACCCUCCGGGGGGGCUAUAGAGAUCGCUGGAAGCACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
X62493.1/4698-4789   GAGUUAGACACGGUUGAUCUCACCCUUCGGGGGGGCUAUAGAGAUCACUGGAAGCACUACCGGACAACCGGAACAUUGCAGCAAUGCAGCCC
AF038044.1/460-550   GACCUAGACACGGUUGAUCUCACCU-UCGGGGGGGCUAUAGAGAUCGCUGGAAGCAUUACCGGACAACCGGAACAUUGCAGCAAUGCAGCCC
U16703.1/325-416     UUGCCAGACACGGUUGAUCUCACUCUCCGGGGGGGCUAUAGAGAUCGCUGGAAACACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
AF241533.1/375-463   -ACCUAGAUAUGGUUGAUCUCACCU--CGGGGGGGCUAUAGAGAUCGCUGGAAGCACUACCGGACAACCGGAACAUUGCAGCAAUGCAGCCC
M59048.1/489-578     --CCCAGACACAGUUGAUCUCACCCUUCGGGGGGGCUAUAGAGAUCGCUGGAAGCACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
M59043.1/500-591     GACCCAGACACGGUUGAUCUCACCCUUCGGGGGGGCUAUAGAGAUCGCUGGAAACACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
M21958.1/4686-4776   GACCCAGACACGGUUGAUCUCACCCUUC-GGGGGGCUAUAGAGAUCGCUGGAAGCACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
X51456.1/2110-2200   GAGUUAGACACGGUUGAUCUCACCU-UCGGGGGGGCUAUAGAGAUCACCGGAAGCACUACCGGACAACCGGAACAUUGCAGCAAUGCAGCCC
U16701.1/503-594     UUGCCAGACACGGUUGAUCUCACCCUCCGGGGGGGCUAUAGAGAUCGCUGGAAACACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
AJ249740.1/4679-4770 UGCCCAGACACGGUUGAUCUCACCCUUCGGGGGGGCUAUAGAGAUCGCUGGAAGCACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
AY100482.1/4675-4766 ACUUUGAGCACGGUUGAUCUCACCCUCCGGGGGGGCUAUAGAGAUCGCUGGAAACACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
M18056.1/306-396     GACCCAGACACGGUUGAUCUCCCCU-UCGGGGGGGCUAUAGAGAUCACUGGAAGCACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
S43932.1/386-477     AACCAAGACACGGUUGAUCUCACCCUUCGGGGGGGCUAUAGAGAUCGCUGGAAGCACUACCGGACAACCGGAACAUUGCAGCAAUGCAGCCC
M59050.1/503-592     --CCCAGACACAGUUGAUCUCACCCUUCGGGGGGGCUAUAGAGAUCGCUGGAAACACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
U80935.1/4686-4776   GACCUGGACACGGUUGAUCUCACCU-UCGGGGGGGCUAUAGAGAUCGCUGGAAGCACUACCGGACAACCGGAACAUUGCAGCAAUGCAGCCC
D00719.1/409-499     AACCAAGACACGGUUGAUCUCACCCUUC-GGGGGGCUAUAGAGAUCGCUGGAAGCACUACCGGACAACCGGAACAUUGCAGCAAUGCAGGGG
X85215.3/4673-4763   GACCCAGACACGGUUGAUCUCACCU-UCGGGGGGGCUAUAGAGAUCGCUGGAAGCACUACCGGACAACCGGAACAUUGCAGAAAUGCAGCCC
#=GC SS_cons         ::::::::::<<<<-<<<<<<-<<<____>>>AAA----->>>>>>>>>>,,,,,,,,,<<<<____>>>>,,,,<<<<<____>>>>>aaa
#=GC RF              aaccuAGACACgGcUGauCuCACCcUuCGgGGGGGCUAUAGaGauCgCcGGAAgCACUACCGGACAACCGGAACAuuGCaGaAAuGCagccc
//
# STOCKHOLM 1.0

#=GF AC   RF00177
#=GF ID   SSU_rRNA_bacteria
#=GF PI   SSU_rRNA_5
#=GF DE   Bacterial small subunit ribosomal RNA
#=GF AU   Gutell RR
#=GF AU   Nawrocki E; 0000-0002-2497-3427
#=GF SE   Published; PMID:11869452
#=GF SS   Published; PMID:11869452
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17.38 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF CL   CL00111
#=GF DR   URL; http://www.rna.ccbb.utexas.edu/;
#=GF DR   URL; http://oberon.fvms.ugent.be:8080/rRNA/ssu/index.html;
#=GF DR   URL; http://rdp.cme.msu.edu/html/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   11283358
#=GF RT   Crystal structure of the ribosome at 5.5 A resolution.
#=GF RA   Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH,
#=GF RA   Noller HF
#=GF RL   Science 2001;292:883-896.
#=GF RN   [2]
#=GF RM   11869452
#=GF RT   The comparative RNA web (CRW) site: an online database of comparative
#=GF RT   sequence and structure information for ribosomal, intron, and other RNAs.
#=GF RA   Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng
#=GF RA   B, Lin N, Madabusi LV, Muller KM, Pande N, Shang Z, Yu N, Gutell RR
#=GF RL   BMC Bioinformatics. 2002;3:2.
#=GF WK   Ribosomal_RNA
#=GF SQ   99



AY138309.1/1-1552                      UUAUUGGAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CGG--CGUG-CCUAAUACAUGCAAGUCGAGCG-AAUG---------GAUUAAGAGCU-----UGCUCU-U-AUGA---------------------------------------------------------------------------------------------------------------------------AGUU--AG-CGGCGGA-CGGGUGAGUAACACGUGGGU--AACCUGCCCAUAAGACU--GGGAUAACUCCGGGAAACCGGGGCUAAUACCGGAUAACAUUU--UGA--ACC--GCAU--GGU--U-CG-A-A-AUUGAAA-GGCG------------------------------------------------------GCUUCGG--CUGUCACUUAUGGAUGGACCCGCGUCGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCAACGAUGCGUAGCCG-ACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGAC-GAAAGUCUGACGGAGCAACGCCGCGUGAGU-GA-UGAAGGCU---UUCG--GGUCGUAAAACUCUGUUGUUAGGG-AAGAAC-AAGUGCUAGUUG--AAUAAGCUG----GCACC--UUGACGGUACCUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCG-CGCGCAGGUGGUUUCUUA-AGUCUG-AUGUGAAAGCCCA-CGGCUCAACCG-UG-GAGGGUCAUUGGAAACUGGGA-GACUU-GAGUGCAGAAGAGGAAAGUGGAAUUCCAUGUGUAGCGGUGAAAUGCGUAGAGAUAUGGAGGAACACCAG--UGGCGAAGGCGACUUUCUGGUCUGUAACUGACACUGAG-GCGCGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GAGU--GC-UAAG-UGUU-AGAGGG--U----------------------------UUCC-GCCCUUUAGUGCU-------GAA-GUUAACGCAUUAAGCACUCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCAGGUCUUGACAUC-CUCUG------------ACAACCCUAG-AGAUAGGGCUU--CUCCUU----------------------------------CGGGAG----CAGAGUGACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGAUCUUAGUUGCC-AUCA------UUWAGU--------------UG--GG-CACUCUAAGGUGACUGCCGGUGA--CAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGA-CGGU-ACAAAGAGC---UGCAAGACCGCGAGGUGGA-GCUAAUCUCAU-AAAACCGUUCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUGAAGCUGGAAUCGCUAGUAAUCGCGGAUC-AGC-AUGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUUUGU-AAC-ACCCGAAGUCGG-U-G-GGGU-AACC--UUUUU---GGAGCCA-GCCGCCUAAGGU-GGGACAGAUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAUCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
AEZG01000028.1/4341-5872               UGUUUGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CUUAACACAUGCAAGUCGAACG-GAA------------AGGUCUCUU-----CGGAGA-U-AC-------------------------------------------------------------------------------------------------------------------------------UC-GAG-UGGCGAA-CGGGUGAGUAACACGUGGGU--GAUCUGCCCUGCACUUC--GGGAUAAGCCUGGGAAACUGGGUCUAAUACCGGAUAGGACCA--CGG--GAU--GCAU--GUC--U-UG-U-G-GUGGAAA-GCG---------------------------------------------------------CUUU-----AGCGGUGUGGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUGACGGCCUACCAAGGCGACGACGGGUAGCCG-GCCUGAGAGGGUGUCCGGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGC-GCAAGCCUGAUGCAGCGACGCCGCGUGGGG-GA-UGACGGCC---UUCG--GGUUGUAAACCUCUUUCACCAUCG-ACGAAG-GUCCGGGU----------UCUCU-----CGGA--UUGACGGUAGGUGGAGAAGAAGCACCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCGAGCGUUGUCCGGAAUUACUGGGCGUAAAGAG-CUCGUAGGUGGUUUGUCG-CGUUGU-UCGUGAAAUCUCA-CGGCUUAACUG-UG-AGCGUGCGGGCGAUACGGGCA-GACUA-GAGUACUGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGGAAUGCGCAGAUAUCAGGAGGAACACCGG--UGGCGAAGGCGGGUCUCUGGGCAGUAACUGACGCUGAG-GAGCGAAA-GCG-UGGGGAGCGAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGGU-GGGU--AC-UAGG-UGUG-GGUUUC-CU----------------------------UCCU-UGGGAUCCGUGCC-------GUA-GCUAACGCAUUAAGUACCCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGCGGAGCAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUA-CCUGGGUUUGACAUGCACAGG------------ACGCGUCUAG-AGAUAGGCGUU---CCCUU----------------------------------GUGG------CCUGUGUGCAG-GUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGUCUCAUGUUGCC-AGCAC-----GUAAUG-------------GUG--GG-GACUCGUGAGAGACUGCCGGGGU--CAA-CUCG-GAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACACAUGCUACAAUGGC-CGGU-ACAAAGGGC---UGCGAUGCCGCGAGGUUAA-GCGAAUCCUUA-AAAGCCGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUC-AGCAACGCUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGUCGGU-AAC-ACCCGAAGCCAG-U-G-GCCU-AACC---CUCG---GGAGGGA-GCUGUCGAAGGU-GGGAUCGGCGAUUGGGACGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
ABKZ01000640.1/5030-3495               GAACUGAAGAGUU-UGAU-CAUGGCUCAGAUUGAACGCU-GG-CGG--CAGG-CCUAACACAUGCAAGUCGAGCG-GAU-----------GAAGGGAGCU-----UGCUCC-U-GG------------------------------------------------------------------------------------------------------------------------------AUU-CAG-CGGCGGA-CGGGUGAGUAAUGCCUAGGA---AUCUGCCUGGUAGUGG--GGGAUAACGUCCGGAAACGGGCGCUAAUACCGCAUACG-----------UCC--UGAG--GGA--------------GAAA-GUGGGGGA---------------------------------------------UCUUCGGACCU-----CACGCUAUCAGAUGAGCCUAGGUCGGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCCGUAACUG-GUCUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGC-GAAAGCCUGAUCCAGCCAUGCCGCGUGUGU-GA-AGAAGGUC---UUCG--GAUUGUAAAGCACUUUAAGUUGGG-AGGAAG-GGCAGUAAGUU----AAUACCUU----GCUGU-UUUGACGUUACCAACAGAAUAAGCACCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCG-CGCGUAGGUGGUUCAGCA-AGUUGG-AUGUGAAAUCCCC-GGGCUCAACCU-GG-GAACUGCAUCCAAAACUACUG-AGCUA-GAGUACGGUAGAGGGUGGUGGAAUUUCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGAAGGAACACCAG--UGGCGAAGGCGACCACCUGGACUGAUACUGACACUGAG-GUGCGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GUCG--AC-UAGC-CGUU-GGGAUC--C----------------------------UUGA--GAUCUUAGUGGC-------GCA-GCUAACGCGAUAAGUCGACCGCC--UGGG-GAGUAC-GGCCGCAAGGUUAAAACUCAAA-UGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCUGGCCUUGACAUG-CUGAG------------AACUUUCCAG-AGAUGGAUUGG--UGCCUU----------------------------------CGGGAA----CUCAGACACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-UAACGAGCGCAACCCUUGUCCUUAGUUACC-AGCAC------CUCGG-------------GUG--GG-CACUCUAAGGAGACUGCCGGUGA--CAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGGCCAGGGCUACACACGUGCUACAAUGGU-CGGU-ACAAAGGGU---UGCCAAGCCGCGAGGUGGA-GCUAAUCCCAU-AAAACCGAUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGAAUCGCUAGUAAUCGUGAAUC-AGA-AUGUCACGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGU-UGC-UCCAGAAGUAGC-U-A-GUCU-AACC---GCAA---GGGGGAC-GGUUACCACGGA-GUGAUUCAUGACUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUA
AAFJ01000008.1/10852-9340              ACUAUGGAGAGUU-UGAU-CCUGGCUCAGAGUGAACGCU-GG-CGG--CGUG-CCUAAUACAUGCAAGUCGAACG-AUGA---------AGCUUCUAGCU-----UGCUAG-A-AGU----------------------------------------------------------------------------------------------------------------------------GAAU-UAG-UGGCGCA-CGGGUGAGUAAGGUAUAGUU--AAUCUGCCCUACACUGG--GGGACAACACUUAGAAAUGAGUGCUAAUACCCCAUACUCCUA--CCU--AAC--AUAA--GUU--A-GG-U-A-GG-GAAA-GUU--------------------------------------------------------U---------UUCGGUGUAGGAUGAGACUAUAUAGUAUCAGCUAGUUGGUAAGGUAAAGGCUUACCAAGGCUAUGACGCUUAACUG-GUCUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUAUUGCGCAAUGGGC-GAAAGCCUGACGCAGCAACGCCGCGUGGAG-GA-UGACACUU---UUCG--GAGCGUAAACUCCUUUUCUUAGGG-AAGAAU-UC---------------------------------UGACGGUACCUAAGGAAUAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUACUCGGAAUCACUGGGCGUAAAGGG-CGCGUAGGCGGAUUAUCA-AGUCUC-UUGUGAAAUCUAA-UGGCUUAACCA-UU-AAACUGCUUGGGAAACUGAUA-GUCUA-GAGUGAGGGAGAGGCAGAUGGAAUUGGUGGUGUAGGGGUAAAAUCCGUAGAUAUCACCAAGAAUACCCA--UUGCGAAGGCGAUCUGCUGGAACUCAACUGACGCUAAG-GCGCGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCCUAAA-CGAU-GUAU--GC-UAGU-UGUU-GGGGUG--C----------------------------UAGU--CAUCUCAGUAAU-------GCA-GCUAACGCAUUAAGCAUACCGCC--UGGG-GAGUAC-GGUCGCAAGAUUAAAACUCAAA-GGAAUAGACGGGGACCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGAUACGCGAAGAACCUUA-CCUAGGCUUGAUAUC-CAACA------------AAUCCAUUAG-AGAUAGUGGAG--UGCUAGCU------------------------------UGCUAGAA----UGUUGAGACAG-GUGCUGCACGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUCGUCCUUAGUUGCU-AACAG------UUCGG-------------CUG--AG-CACUCUAAGGAGACUGCCUUCG---UAA-GGAG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGCCUAGGGCGACACACGUGCUACAAUGGC-AUAU-ACAAUGAGA---CGCAAUACCGCGAGGUGGA-GCAAAUCUAU--AAAAUAUGUCCCAGUUCGGAUUGUUCUCUGCAACUCGAGAGCAUGAAGCCGGAAUCGCUAGUAAUCGCAAAUC-AGCCAUGUUGCGGUGAAUACGU-UCCCGGGUCUUGUACUCACCGCCCGUCACACCAUGGGAGUUGAU-UUC-ACUCGAAGUGGA-A-A-UACU-AA------AUG------AGUU-AUCCCCCACAGU-GGAAUCAGCGACUGGGGUGA-AGU-CGUAACAAGGUAA-CCGUAGGAGAACCUGCGG---UU-GGAUCACCUCCUUU
GU260705.1/11747-13300                 UAACAUGAGAGUU-UGAU-CCUGGCUCAGAAUCAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCGAACG-CGA------------GGGUCCCGC-----AAGGGA-C-UA------------------------------------------------------------------------------------------------------------------------------GUA-GAG-UGGCAAA-CGGGUGAGUAACACGUGGGU--GACCUGCCUUCGAGUGG--GGGAUAACGUCCCGAAAGGGACGCUAAUACCGCAUGACAUCCUGCCG--UUG--AAAU--CGG--U-GG-A-G-AU-CAAA-GCUGGGGA---------------------------------------------UCGCAAGACCU-----AGCGCUUGAAGAGGGGCCCGCGUCCGAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCAACGAUCGGUAGCCG-GCCUGAGAGGGCGGACGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUGUUCACAAUGGGC-GCAAGCCUGAUGACGCAACGCCGCGUGGAG-GA-UGAAGAUC---UUCG--GGUCGUAAACUCCUUUCGAUCGAG-ACGAAU-GGCCCCUGGGCU--AAUCACCAG-----GGGA--GUGACGGUACCGAGAGAAGAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGGGGGGGCAAGCGUUGUUCGGAAUUACUGGGCGUAAAGGG-CUCGUAGGCGGCCAACUA-AGUCAG-ACGUGAAAUCCCU-CGGCUUAACCG-GG-GAACUGCGUCUGAUACUGGAU-GGCUU-GAGGUUGGGAGAGGGAUGCGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAGGAACACCGG--UGGCGAAGGCGGCAUCCUGGACCAAUUCUGACGCUGAG-GAGCGAAA-GCC-AGGGGAGCAAACGGG-AUUAGAUACCCCGGUAGUCCU-GGCCCUAAA-CGAU-GAAU--GC-UUGG-UGUG-GCGGGU--A----------------------------UCGA-UCCCUGCCGUGCC-------GAA-GCUAACGCAUUAAGCAUUCCGCC--UGGG-GAGUAC-GGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUCAAUUCGACGCAACGCGAAGAACCUUA-CCCAGGCUUGAACAGCGAGUG------------ACCAUUCCCG-AAAGGGAACU----UCCGC----------------------------------AAGGA-----CACUCGUAGAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGUCUGCUGUUGCC-AUCAG-----GUAAUG-------------CUG--GG-CACUCUGCAGAGACUGCCGGUGA--UAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGGCCUUUAUGUCUGGGGCUACACACGUGCUACAAUGGC-CGGU-ACAAACCGU---CGCAAAACCGUAAGGUCGA-GCUAAUCGGAG-AAAGCCGGUCUCAGUUCGGAUAGCAGGCUGCAACUCGCCUGCUUGAAGUUGGAAUCGCUAGUAAUCGCGGAUC-AGC-ACGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACAUCACGAAAGCCGGU-UGU-ACUAGAAGUCGC-U-A-CAUC-AACC--CGCAA--GGGAGAGA-GGCGCCUAAGGU-AUGGUCGGUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CUGUAGGAGAACCUGUGG---CU-GGAUCACCUCCUUU
CP001205.1/442210-440675               AUAACGAAGAGUU-UGAU-CCUGGCUUAGAACUAACGCU-GG-CAG--UGCG-UCUUAAGCAUGCAAGUCAAACG----------------GGAUGUAGC-----AAUACA-U-UC-----------------------------------------------------------------------------------------------------------------------------------AG-UGGCGAA-CGGGUGAGUAACGCGUGGAU--GAUCUACCUAUGAGAUG--GGGAUAACUAUUAGAAAUAGUAGCUAAUACCGAAUAAGGUCA--AUU--AAU--UU----GUU--A-AU-U-G-AU-GAAA-GGAAG----------------------------------------------------CCUUUAAA--GCUUCGCUUGUAGAUGAGUCUGCGUCUUAUUAGCUAGUUGGUAGGGUAAAUGCCUACCAAGGCAAUGAUAAGUAACCG-GCCUGAGAGGGUGAACGGUCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGCUAAGAAUCUUCCGCAAUGGGC-GAAAGCCUGACGGAGCGACACUGCGUGAAU-GA-AGAAGGUC---GAAA--GAUUGUAAAAUUCUUUUAUAAAUG-AGGAAU-AAGCUUUGUAGG--AAAUGACAA-----AGUG--AUGACGUUAAUUUAUGAAUAAGCCCCGGCUAAUUACGUGCCAGCAGCCGCGGUAAUACGUAAGGGGCGAGCGUUGUUCGGGAUUAUUGGGCGUAAAGGG-UGAGUAGGCGGAUAUAUA-AGUCUAUGCAUAAAAUACCA-CAGCUCAACUG-UG-GACCUAUGUUGGAAACUAUAU-GUCUA-GAGUCUGAUAGAGGAAGUUAGAAUUUCUGGUGUAAGGGUGGAAUCUGUUGAUAUCAGAAAGAAUACCGG--AGGCGAAGGCGAACUUCUGGGUCAAGACUGACGCUGAG-UCACGAAA-GCG-UAGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCUA-CGCUGUAAA-CGAU-GCAC--AC-UUGG-UGUU-AACU----------------------------------AAA----AGUUAGUACC-------GAA-GCUAACGUGUUAAGUGUGCCGCC--UGGG-GAGUAU-GCUCGCAAGAGUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUA-CCAGGGCUUGACAUAUAUAGG------------AUAUAGUUAG-AGAUAAUUAUU--CCCCGU----------------------------------UUGGGG----UCUAUAUACAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGCUGUGAGGUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGUUAUCUGUUACC-AGCAU-----GUAAUG-------------GUG--GG-GACUCAGAUAAGACUGCCGGUGA--UAA-GUCG-GAGGAAGGUGAGGAUGACGUCAAAUCAUCAUGGCCCUUAUGUCCUGGGCUACACACGUGCUACAAUGGC-CUGU-ACAAAGCGA---AGCGAAACAGUGAUGUGAA-GCAAAACGCAU-AAAGCAGGUCUCAGUCCGGAUUGAAGUCUGAAACUCGACUUCAUGAAGUUGGAAUCGCUAGUAAUCGUAUAUC-AGA-AUGAUACGGUGAAUACGU-UCUCGGGCCUUGUACACACCGCCCGUCACACCACCCGAGUUGAG-GAU-ACCCGAAGCUAU-U-A-UUCU-AACC--CGUAA--GGGAGGAA-GGUAUUUAAGGU-AUGUUUAGUGAGGGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACUGGAAAGUGCGG---CU-GGAUCACCUCCUUU
AC149043.3/15235-16757                 ACAAUGGAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-AG-CGG--CAGG-CCUAAUACAUGCAAGUCGAACG-GGC-----------UUUGGGACUU-----CGGUUC-C-AGA-----------------------------------------------------------------------------------------------------------------------------GUC--AG-UGGCGCA-CGGGUGCGUAACGCGUAUGC--AACCUACCUUCCACAGG--GGGAUAGCCCCGGGAAACCGGGAUUAAUACCGCAUGACACAG--UUG-GGUG--GCAU--CAC-CC-GA-C-U-GU-CAAA-GU----------------------------------------------------------UUCG------GCGGUGGAAGAUGGGCAUGCGUGCCAUUAGCUAGUUGGCGGGGUAGAGGCCCACCAAGGCUACGAUGGCUAGGGG-UUCUGAGAGGAUGGUCCCCCACACUGGUACUGAGACACGGACCAGACUCCUACGGGAGGCAGCAGUAGGGAAUAUUGGGCAAUGGCC-GAGAGGCUGACCCAGCCAUGCCGCGUGCAG-GA-AGAAGGCC--UUCUG--GGUUGUAAACUGCUUUUAUCUGGG-AAGAAA-ACGCCCCU----------GCGGG-----GGUA-ACUGACGGUACCAGAUGAAUAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUGUCCGGAUUUAUUGGGUUUAAAGGG-UGCGUAGGCGGCCCGUUA-AGUCAG-CGGUGAAAUCCCG-GGGCUCAACCC-CG-GAACUGCCGUUGAUACUGGCG-GGCUU-GAGUUCGGUGAAGGCGGGCGGAACUGGCGGUGUAGCGGUGAAAUGCUUAGAUACCGCCAAGAACCCCGA--UUGCGUAGGCAGCUCGCUGUGCCGAAACUGACGCUGAG-GCACGAAA-GCG-UGGGGAGCGAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GAUG--AC-UCGA-UGUU-GGCGA--------------------------------UACA---CUGUCAGCGUC-------CAA-GCGAAAGCGUUAAGUCAUCCACC--UGGG-GAGUAC-GCCCGCAAGGGUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUA-CCUAGGCUAGAAUGC-GCGUG------------ACAGGAGCAG-AGAUGCUCCCU--C-CCUU----------------------------------CGGG-G----CACAAAGCAAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUCUUCAGUUGCC-AGCAC-----AUUAUG-------------GUG--GG-GACUCUGGAGAGACUGCCUUCG---CAA-GAAGCGAGGAAGGCGGGGACGACGUCAAGUCAUCAUGGCCCUUACGCCUAGGGCUACACACGUGCUACAAUGGC-GCAU-ACAGAGGGU---AGCCAGCCAGCGAUGGUGA-GCCAAUCCCAA-AAAGUGCGUCUCAGUUCGGAUCGGAGUCUGCAACUCGACUCCGUGAAGCCGGAAUCGCUAGUAAUCGCGUAUC-AGCAACGACGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGCCAUGGAAGUCAGG-GAG-ACCUGAAGCCGG-U-G-------ACC--GUCAA--AGGA-----GCCGUCUAGGGU-AAAACUGGUAACUGGGGCUA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
EU123923.1/77-1583                     AAACUUGAGAGUU-UGAU-CCUGGCUCAGAACGAACGCU-GG-CGG--CAAG-CCUAACACAUGCAAGUCGAACG-GACAAU-----UAUUUAUAGCCUC-----U-GGCU-A-UAGGAA-----------------------------------------------------------------------------------------------------------------------AUUGUU--AG-UGGCAGA-CGGGUGAGUAAUGCGUAGGA---AUCUACCUAGUAGUAC--GGAAUAGCCAUUAGAAAUGGUGGGUAAUACUGUAUAAU-----------CCC--CGAG--GGG--------------GAAA-GA----------------------------------------------------------UUUA------UCGCUAUUAGAUGAGCCUACGUUAGAUUAGCUAGUUGGUGAGGUAAUGGCUUACCAAGGCUAUGAUCUAUAGCUG-GUCUGAGAGGACGAUCAGCCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGC-GAAAGCCUGAUCCAGCUAUGCCGCGUGAGU-GA-AGAAGGCC---UUCG--GGUUGUAAAACUCUUUCAAUAGGG-AAGAUA--A---------------------------------UGACGGUACCUAUAGAAGAAGUCCCGGCAAACUCUGUGCCAGCAGCCGCGGUAAUACGGAGGGGGCAAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGG-CACGUAGGUGGACUAGUA-AGUUAA-AAGUGAAAUACCA-AAGCUUAACUU-UG-GAGCGGCUUUUAAUACUGCUA-GACUA-GAGGUCGAAAGAGGAUAGCGGAAUUCCUAGUGUAGAGGUGAAAUUCGUAGAUAUUAGGAGGAACACCAG--UGGCGAAGGCGGCUAUCUGGUUCGAUACUGACACUGAG-GUGCGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCUGUAAA-CGAU-GAGU--GC-UAAA-UGUG-AGGA----U----------------------------UUUA----UCUUUGUAUU-------GUA-GCUAACGCGUUAAGCACUCCGCC--UGGG-GACUAC-GGUCGCAAGACUAAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCUACGCGAAAAACCUUA-CCACUUUUUGACAUG-AAGGUC----------GUAUCCCUCCU-AACAGGGGGAG--UCAGUU---------------------------------CGGCUGG----ACCUUACACAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUCAUUCUUAGUUACC-AACAG-----GUAAUG-------------CUG--GG-CACUCUAAGGAAACUGCCAGUGA--UAA-ACUG-GAGGAAGGUGGGGAUGAUGUCAAAUCAGCACGGCCCUUAUAGGGUGGGCUACACACGUGCUACAAUGGC-AACU-ACAAUAGGU---UGCGAGACCGCAAGGUUUA-GCUAAUCCAU--AAAAGUUGUCUCAGUUCGGAUUGUUCUCUGAAACUCGAGAGCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUC-AUC-ACGCCACGGUGAAUACGU-UCUCGGGUCUUGUACACACUGCCCGUCACGCCAUGGGAAUUGGC-UUA-ACUCGAAGCUGG-U-G-UGCU-AACC---GCAA---GGAAGCA-GCCAUUUAAGGU-UGGGUUAGUGACUAGGGUGA-AGU-CGUAACAAGGUAG-CUGUAGGUGAACCUGCGG---CU-GGAUUACCUCCUUU
CP001634.1/1770527-1772065             UGGAUGGAGGGUU-UGAU-CCUGGCUCAGGGUGAACGCU-GG-CGG--CGUG-CCUGACACAUGCAAGUCGUACG-GGC------------GGACCCCCU-----UCGGGG-G-GCG----------------------------------------------------------------------------------------------------------------------------AGCC--AG-UGGCGAA-CGGGUGAGUAACACGUGGGA---ACAUAUCCGCUGGUGG--GGGAUAACUACCCGAAAGGGUAGCUAAUACCGCAUAAG-----------CCC--GAAA--GGG--------------GAAA-GGUG------------------------------------------------------CAACAG----CAUCGCCAGUGGAGUGGCCCGCGGCCCAUCAGCUAGUUGGUGGGGUAAGAGCCCACCAAGGCGACGACGGGUAGCCG-GCGUGAGAGCGCGACCGGCCACAAGGACACUGAGACACGGGUCCUACUCCUACGGGAGGCAGCAGUGCGGAAUAUUGGACAAUGGGC-GAAAGCCUGAUCCAGCGACGCCGCGUGCGG-GA-CGAAGGCC---UUCG--GGUCGUAAACCGCUGUGGUAAGGG-ACGAAU-AGCCGGUGGAGU-GGAAAGCCAC-----CGGA-GGAGACGGUACCUUACUAGGAAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCGAGCGUUACCCGGAAUCACUGGGCGUAAAGGG-AGCGUAGGCGGCCCAGCA-AGUCGA-CUGUGAAAAACCG-GAGCUCAACUU-CG-GUCCUGCGGUCGAAACUGCUG-GGCUU-GAGGACAGUAGAGGGAGACGGAACUGCCGGUGUAGGGGUAAAAUCCUUAGAUAUCGGCAGGAACGCCGG--UGGCGAAGGCGGUCUCCUGGGCUGGACCUGACGCUGAG-GCUCGAAA-GCC-AGGGGAGCGAACGGG-AUUAGAUACCCCGGUAGUCCU-GGCCCUAAA-CGAU-GCUC--AC-UAGG-UGUG-GGGUGC--G----------------------------UAGA--GCACUCCGUGCU-------GAA-GCAAACGCGAUAAGUGAGCCGCC--UGGG-GAGUAC-GCCCGCAAGGGUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCGUGUGGUUUAAUUCGAUGCUAAGCGAAGGACCUUA-CCAGGGCUUGACAUG-CUGGUG----------GUACUGAACCG-AAAGGGGAAGG--ACCCACCGU----------------------------UAGGUGGGA----GCCAG-CACAG-GUGGUGCACGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCCCUAGUUGCC-AGCGG------UUAGG-------------CCG--GG-CACUCUAGGGGGACCGCCGCCGA--CGA-GGCG-GAGGAAGGGGGGGAUGACGUCAGGU-AUCGUGCCCCUUAUGUCCUGGGCGACACACGCGCUACAAUGGG-ACGG-ACAGCGGGG---AGCGAGGCAGCGAUGCUGA-GCAAAUCCCUG-AAACCGUUCCUCAGUUCGGAUUGCAGGCUGCAACCCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUC-AGCCAUGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGCCACCCGAGUUGGC-AAC-ACCUGAAGACGG-GUG-UCCC-AACC---GAAA---GGAGGGAGCCCGUUUAAGGU-GGGGCUGGCGAGGGGGGCUA-AGU-CGUAACAAGGUAG-CCCUACCGGAAGGUGGGG---CU-GGAUCACCUCCUUU
ADVG01000004.1/1323946-1322469         UGAAUGGCGAGUU-UGAU-CCUGGCUCAGGAUAAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCGAACG----------------CCCUCUCGC-----AAGAGA-G-GG-----------------------------------------------------------------------------------------------------------------------------------AG-UGGCGGA-CGGGUGAGUAACACAUGGGU---ACCUGCCCCGAGGUGA--GGAAUACCGGCGAGAAAUCGCCGACAAUACCGCAUAUG--------U--UCC--UCCG--GGA--A-----------CAAA-GCU-------------------------------------------------------CGCAAG-----GGCGCCUUGGGAUGGGCCUGUGGCCGAUUAGCUUGUUGGUGAGGUAAGAGCUCACCAAGGCCACGAUCGGUAGCUG-GUCUGAGAGGAUGGUCAGCCACACUGGGAUUGAGA-ACGGCCCAGACUCCUACGGGGGGCAGCAGUGAGGAAUUUUCGUCAAUGGGG-GCAACCCUGAACGAGCAACGCCGCGUGCAG-GA-GGACGCUU---UUCG--GAGUGUAAACUGCUUUUCUUGGGG-ACGAGU-AA---------------------------------GGACGGUACCCAAGGAAUAAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCAAGCGUUGUCCGGAGUUAUUGGGCGUAAAGCG-CACGCAGGCGGUUUCGUA-CGUCCG-GAGUGACAGUUCC-CGGCUCAACUG-GG-AAAGGUCUUCGGAAACGGCGA-GACUU-GAGGGCUUCAGAGGGACACGGAAUUCCGGGUGGAGUGGUGAAAUGCGUAGAGAUCCGGAGGAACACCAA--UGGCGAAGGCAGUGUCCUGGGAAGCAUCUGACGCUCAG-GUGCGAAA-GCU-AGGGGAGCGAACAGG-AUUAGAUACCCUGGUAGUCCU-AGCCGUAAA-CGAU-GACC--AC-UAGG-UGUG-GGAGGU--A----------------------------UCGA-CCCCUUCCGUGCC-------GUC-GCAAACGCAGUAAGUGGUCCGCC--UGGG-GAGUAC-GGUCGCAAGAUUAAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCAGCGGAGCGUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUA-CCAAGUCUUGACAUGCAGAUG------------CACCAGCGGU-AAUGCGCUGU----CCCUU----------------------------------CGGGG-----CGUUUGCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUACUGCCUAUUA-------------CAACUU------------------------CUAGGCGGAACUGCCC---U--CAC---GG-GAGGAAGGCGGGGAUGACGUCAAGUCAGCACGGCCCUUACGACUUGGGCGACACACACGCUACAAUGGC-CAGUAACAAAGGGA---UGCCAACCCGCGAGGGGGA-GCCAAGCUCAA-AAACCUGGUCUCAGUUCAGAUUGCAGGCUGAAACUCGCCUGCAUGAAGGUGGAGUUGCUAGUAACCGUAGGUC-AGC-ACACUACGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCACACCACGAAAGUCGGC-AAC-ACCUGAAGCCGC-C-A-GGCU-AACU--CUUCG--GAGAGGCA-GGCGUCGAGGGU-GGGGUUGGUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CUGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
AFPX01000069.1/35-1566                 ACAAUGGAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CUA--CAGG-CUUAACACAUGCAAGUCGUGGG-GAAACG------GCAUUAUGUGCU-----UGCACA-U-UCUGG-------------------------------------------------------------------------------------------------------------------------ACGUC-GAC-CGGCGCA-CGGGUGAGUAUCGCGUAUCC--AACCUGCCCCUUACUUG--GGGAUACCCCGUUGAAAGACGGCCUAAUACCCGAUGUGUUUC--AUU-GACG--GCAU--CCG-AU-AU-G-A-AA-CAAA-GG----------------------------------------------------------UUUU------CCGGUAAGGGAUGGGGAUGCGUCUGAUUAGCUAGUUGGCGGGGCAACGGCCCACCAAGGCGACGAUCAGUAGGGG-UUCUGAGAGGAAGGUCCCCCACAUUGGAACUGAGACACGGUCCAAACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAUGGAC-GCAAGUCUGAACCAGCCAAGUAGCGUGCAG-GA-UGACGGCC--CUAUG--GGUUGUAAACUGCUUUUAUGUGGG-AAUAAA-UUGGCGCA---------CGUGUG----CGCCA--UUGCAUGUACCUCAUGAAUAAGGACCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGAAGGUCCGGGCGUUAUCCGGAUUUAUUGGGUUUAAAGGG-AGUGUAGGCGGUCUGUUA-AGCGUG-UUGUGAAAUUUAG-GUGCUCAACAU-UU-AACUUGCAGCGCGAACUGUCA-GACUU-GAGUACACGCAGCGCAGGCGGAAUUCAUGGUGUAGCGGUGAAAUGCUUAGAUAUCAUGAGGAACUCCGA--UCGCGAAGGCAGCCUGCGGGAGUGUUACUGACGCUUAA-GCUCGAAG-GUG-CGGGUAUCGAACAGG-AUUAGAUACCCUGGUAGUCCG-CACUGUAAA-CGAU-GGAU--GC-CCGC-CGUU-GGCGC---------------------------------CCU---GCGCCUGCGGC-------CAA-GCGAAAGCAUUAAGCAUCCCACC--UGGG-GAGUAC-GCCGGCAACGGUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGAGGAACAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUA-CCCGGGCUUGAAUUGCAGUCG------------CAGCCCACAG-AGACGUGGGCU--UCCCUU----------------------------------C-GGGG----CGUCUGUGAAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGCCGUGAGGUGUCGGCUUAAGUGCCA-UAACGAGCGCAACCCCCUUUCCCAGUUGCC-AUCGG-----GUUAUG-------------CCG--GG-CACUCUGGGGACACUGCCACCG---CAA-GGUGCGAGGAAGGUGGGGAUGACGUCAAAUCAGCACGGCCCUUACGUCCGGGGCUACACACGUGUUACAAUGGC-CGGU-ACAGAGGGA---CGGUGCAAUGCAAGUUGCA-UCCAAUCUUG--AAAUCCGGUCCCAGUUCGGACUGGGGUCUGCAACCCGACCCCACGAAGCUGGAUUCGCUAGUAAUCGCGCAUC-AGCCAUGGCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGCCAUGAAAGCCGGG-GGU-GCCUGAAGUUCG-U-G-------ACC---GCGA---GGA-----GCGACCUAGGGC-AAGACCGGUGAUUGGGGCUA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAACACCUCCUUU
AF211138.2/108-1652                    UUUCUUAUGAGUU-UGAU-CAUAGCUCAGAUUGAACGCU-AG-CGA--CAAG-CCUAACACAUGCAAGUUGUGCG-AAU------------UAUUUUAUU----AAAAAAA-G-UA-------------------------------------------------------------------------------------------------------------------------------AU-UAG-CAGCGAA-CGGGUGAGUAAUGUAUAAGA---AUCUACCUUUUAGUAUUUUGAAAAGUAUAUAGAAAUGUAUAGUAAUUCAAUAUAUA-----------UCC--UAAU--GGA--------------UAAA-GUAUGA--------------------------------------------------GAUAGUCA-----UACGCUAAUAGAAGAGCUUAUAUCGAAUUAGUUAGUUGUUAAAGUAAAGGUUUAACAAGACCAUGAUUCGUAGUUG-AUCUUAGAGGAUGAACAACCACAUUGGGACUGAGACACGGCCCAAACUUUUAAGGAAGGCAGCAGUGGGGAAUAUUGGACAAUGAGC-GAAAGCUUGAUCCAGCUAUGUCGCGUGUGU-GA-AGAAGGCC---UUAG--GGUUGUAAAUCACUUUCAGCAAAGUAAGAAG-AAAAAAUUAAAU-AAUAUUUUAU----UUUUU--UUGACGUUUUUUGUAAAAGAAGCACCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAGGGGUGCAAGCGUUAAUCGGAAUUAUUGGGCGUAAAGGG-UGUGCAGGUUGUUUUUAAAAAUUAA-UUUUUAAAUAUAU-UAAAGUAAUUU-A--AUAUGGAAAUUAAUACUUAUA-AACUU-GAGUAUAAAAGAAGAAAUUAGAAUUUCAAGAGUAGCAGUGAAAUGCUUAGAUAUUUGAAAGAAUACUAG--UGGCGAAGGCGUAUUUCUAUUUUAUUACUGACACUAAU-ACACGAAA-GCA-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-UGCAGUAAA-CGAU-GUCA--AC-UAUU-UAUU-AAAUAU--CAUAAUAAUUAAUUUUAUGUAAAAAAAUUAUGU--AUUUUUAGUGAA-------AAA-GCUAACGCGUUAAGUUGACCGCC--UGGG-GAUUAC-GGCCGCAAGGUUAAAACUCAAA-UGAAUUGACGGGGGCUCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUACAACACGAAAAAUCUUA-CCUACUUUUGACAUC-CAAAG------------AAUUUAUUAG-AAAUAAUAACG--CUUUU-------------------------------------AAAG----CUUUGAGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCUA-UAACGAGCGCAACCCUUAUCUUAUUUUACU-AAAA-------UUAUC--------------UU--AG-AACUAAUAAGAAACUGCCAAUGA--UAA-AUUG-GAGGAAGGUGAGGACGACGUCAAGUCAUCAUGGCCCUUAUAAGUAGGGCUACACACGUGCUACAAUGAG-UAUA-ACAAAAAGUAUACGCUAUAUGGUAACAUAAU-GCUAAUCUUAU-AAAAAUAUUCUUAGUUUGGAUUGAAAUCUGUAACUCGAUUUCAUGAAGUUGGAAUCGCUAGUAAUCGUAAAUC-AGA-AUGUUACGGUGAAUACGU-UCUCGAGCCUUGUACACACCGCCCGUCACACCAUGGAAGUAACU-UGU-AUCAUAAGUAAU-U---------------UUAU-----------UAUUACAACGGU-AUGAUUUAUAACUGGGGUGA-AGU-CGUAACAAGGUAG-CUGUAGGGGAACCUGUGG---CU-GGAUAAAAAUAUAU
ACIN02000006.1/16266-14733             UUAUAUGAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCGAACG-GAGA---------UUACGGACGGA-----AGUUUU-C-GGAUGGAAGC--------------------------------------------------------------------------------------------------------------CUGUAAUUCUU--AG-UGGCGGA-CGGGUGAGUAACGCGUGGGC--AACCUGCCCUAUACAGG--GGGAUAGCAGCUGGAAACGGCUGGUAAGACCGCAUAAGUCGG--UUA-AAUC--GCAU--GAU-UU-GA-U-C-GG-GAAA-UGA---------------------------------------------------------GCAA-----UCAGGUAUAGGAUGGGCCCGCGUCCGAUUAGCCAGUUGGCAGGGUAAAAGCCUACCAAAGCGACGAUCGGUAGCCG-GACUGAGAGGUCGGACGGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGGAUAUUGCACAAUGGAG-GAAACUCUGAUGCAGCGACGCCGCGUGAGU-GA-AGAAGUAU---UUCG--GUAUGUAAAGCUCUAUCAGCAGGG-AAGAUG--A---------------------------------UGACGGUACCUGACUAAGAAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCAAGCGUUAUCCGGAUUUACUGGGUGUAAAGGG-AGCGCAGGCGGUUUUGCA-AGUUGA-GAGUGGAAGCAGG-GGGCUCAACCC-CC-UGACUGCUCCCAAAACUGUAA-AACUU-GAGUAUGGGAGAGGCAGGCGGAAUUCCUAGUGUAGCGGUGAAAUGCUUAGAUAUUAGGAAGAACACCGG--UGGCGAAGGCGGCCUGCUGGACCAAAACUGACGCUGAG-GCUCGAAA-GCG-UGGGUAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCUGUAAA-CGAU-GAAU--AC-UAGG-UGCU-GGGAGG-CA----------------------------UAAG--CUUUUCGGUGCC-------GUC-GCAAACGCAUUAAGUAUUCCACC--UGGG-GAGUAC-GUUCGCAAGAAUGAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCCGGUCUUGAGAUC-CUCCU-----------GAAUACUGAGU-AAUGUCAGUA---GUCCUU----------------------------------CGGGAC----AGGAGAGACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUUUUUAGUAGCC-AGCGG------UUCGG-------------CCG--GG-CACUCUAAAGAGACUGCCGAGGA--UAA-CUCG-GAGGAAGGCGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCGGGGCUACACACGUGCUACAAUGGC-AGUU-ACAGAGGGA---AGCGAAGAUGUGAAUCGGA-GCAAAUCUCAG-AAAGGCUGCCUCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGCUGGAAUCGCUAGUAAUCGCAAAUC-AGA-AUGUUGCGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGUCGGA-AAU-GCCCGAAGUCAG-U-G-GCCU-AACC---GCAA---GGGAGGA-GCUGCCGAAGGC-AGGUCUGGUGACUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAUCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
AJ965256.1/805037-803541               AGCUUGGAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-AG-CGG--CGUG-CCUUAUGCAUGCAAGUCGAACG----------------GUCUUAAGC-----AAUUAA-G-AU-----------------------------------------------------------------------------------------------------------------------------------AG-UGGCGAA-CGGGUGAGUAACGCGUAAGU--AACCUACCUCUAAGUGG--GGGAUAGCUUCGGGAAACUGAAGGUAAUACCGCAUGUGGUGG--GCC--GAC--AUAU--GUU--G-GU-U-C-AC-UAAA-GCC---------------------------------------------------------GUAA-----GGCGCUUGGUGAGGGGCUUGCGUCCGAUUAGCUAGUUGGUGGGGUAAUGGCCUACCAAGGCUUCGAUCGGUAGCUG-GUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGCAAGGAAUCUUGGGCAAUGGGC-GAAAGCCUGACCCAGCAACGCCGCGUGAGG-GA-UGAAGGCU---UUCG--GGUUGUAAACCUCUUUUCAUAGGG-AAGAAU-AA---------------------------------UGACGGUACCUGUGGAAUAAGCUUCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGAAGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGUG-AGCGUAGGUGGUCUUUCA-AGUUGG-AUGUGAAAUUUCC-CGGCUUAACCG-GG-ACGAGUCAUUCAAUACUGUUG-GACUA-GAGUACAGCAGGAGAAAACGGAAUUCCCGGUGUAGUGGUAAAAUGCGUAGAUAUCGGGAGGAACACCAG--AGGCGAAGGCGGUUUUCUAGGUUGUCACUGACACUGAG-GCUCGAAA-GCG-UGGGGAGCGAACAGA-AUUAGAUACUCUGGUAGUCCA-CGCCUUAAA-CUAU-GGAC--AC-UAGG-UAUA-GGGAGU--A----------------------------UCGA-CCCUCUCUGUGCC-------GAA-GCUAACGCUUUAAGUGUCCCGCC--UGGG-GAGUAC-GGUCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCAGCGGAGCGUGUGGUUUAAUUCGAUGCUACACGAAGAACCUUA-CCAAGAUUUGACAUGCAUGUA-----------GUAGUGAACUG-AAAGGGGAACG-ACCUGUUA--------------------------------AGUCAGG----AACUUGCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUUGGUUAAGUCCUG-CAACGAGCGCAACCCUUGUUGCUAGUUA--------------AAUUU------------------------UCUAGCGAGACUGCCCCGCG--AAA-CGGG-GAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGGCCUUUAUAUCUUGGGCUACACACACGCUACAAUGGA-CAGA-ACAAUAGGU---UGCAACAGUGCGAACUGGA-GCUAAUCCCC--AAAGCUGUCCUCAGUUCGGAUUGCAGGCUGAAACCCGCCUGCAUGAAGUUGGAGUUGCUAGUAACCGCAUAUC-AGC-AUGGUGCGGUGAAUACGU-UCUCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGCCGGU-AAC-ACUUGAAGUCGA-U-G-UGCC-AACC---GCAA---GGAGGCA-GUCGCCGAGGGU-GGGACUGGUAAUUGGGACGA-AGU-CGUAACAAGGUAG-CCGUAGCGGAAGCUGCGG---CU-GGAUCACCUCCUUU
CP002458.1/700517-699005               UUUUUCGAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CUG--UGUG-CCUAAUACAUGCAUGUCGAGCG-----------------AAGGUAGC-----AAUACC-U-U------------------------------------------------------------------------------------------------------------------------------------AG-CGGCGAA-UGGGUGAGUAACACGUGCUC--AACGUACCCUUCAGUUU--GGCAUAGCGACUGGAAACAGUCGAUAAUUUCAAAUACUCGUA--GUU--UUC--GCAU--GAA--G-AU-U-A-CGGAAAA-GAAG------------------------------------------------------CGUUUG----CUUCGCUGGAGGAGCGGGGUGCGUAACAUUAGCUAGUUGGUGAGGUAACGGCCCACCAAGGCGAUGAUGUUUAGCGG-GGUUGAGAGACUGAACCGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUAUUCCACAAUGGGC-GAAAGCCUGAUGGAGCGACACAGCGUGAAG-GA-UGAAGGUC--CUAUG--GAUUGUAAACUUCUGUGGUAAGGG-AAGAAA-AGACAGAAUAGG--AAAUGAUUU-----UGUU--UUGACGGUACCUUAUUAGAAAGCAACGGCUAACUAUGUGCCAGCAGCCGCGGUAAUACAUAGGUUGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCG-UCUGUAGGUUGUUUGUUA-AGUCUG-GCGUUAAAUUUUG-GGGCUCAACCC-CA-AAAC-GCGUUGGAUACUGGCA-GGCUA-GAGUUGUGUAGAGGUUAGCGGAAUUCCUUGUGAAGCGGUGAAAUGCGUAGAUAUAAGGAAGAACACCAAGAUGGCGAAGGCAGCUAACUGGACAUAUACUGACACUGAG-AGACGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCCUAAA-CGAU-GAUC--AU-UAGC-UGAU-GGG-----------------------------------GAA-----CUCAUCGGC-------GCA-GCUAACGCAUUAAAUGAUCCGCC--UGAG-UAGUAC-GUUCGCAAGAAUAAAACUUAAA-GGAAUUGACGGGGAUCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUUGAAGAUACGCGUAGAACCUUA-CCCACUCUUGACAUC-UUCUG-----------CAAAGCUAUGG-AGACAUAGUGG---AGGUU----------------------------------AA--------CAGAAUGACAG-AUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUUGGUUAAGUCCUG-CAACGAGCGCAACCCUUAUCCUUAGUUACU-ACCA------UUUAGU--------------UG--AG-GACUCUAAGGAGACUGCCCGAG---UAA-UCGG-GAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCUCUUACGAGUGGGGCAACACACGUGCUACAAUGGC-CGGU-ACAAAGAGA---AGCGAAGUGGUGACAUGGA-GCAAACCUCAA-AAAACCGGUCUCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUCGCUAGUAAUCGUAGAUC-AGCUACGCUACGGUGAAUACGU-UCUCGGGUCUUGUACACACCGCCCGUCAAACCAUGGGAGCUGGU-AAU-GCCCGAAGUCGG-U---------UUA---UAAA---CAA-----ACUGCCUAAGGC-AGGACUGGUGACUGGGGUUA-AGU-CGUAACAAGGUAU-CCCUACGAGAACGUGGGG---AU-GGAUCACCUCCUUU
CP001100.1/908786-907295               ACAACGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGCCAAAGG-AA-----------------AGCUU-----CGGUUA------------------------------------------------------------------------------------------------------------------------------------GU-ACU-UGGCGUA-CGGGUGAGUAAGGUAUAGGU--AAUCUGCCUCUUGGUCU--GACAUACCUUCGAGAAAUCGAAGAUAAUUUCAGAUAAUGCAG--CGG-CACC--GCAU--GGU-GA-UG-U-U-GU-UAAA-GAC--------------------------------------------------------UU--------GUUGCCAAGAGAUGAGCCUAUAUUUCAUCAGGUAGUUGGUGGGGUAAUAGCCUACCAAGCCUACGACGGAUAACUG-GUCUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGCGCAAUGGGU-GAAAGCCUGACGCAGCAACGCCGCGUGGAU-GA-UGAAGUUC---UUAG--GAAUGUAAAGUCCUUUUGUAAGGG-AAGAAA-AUCUCGC-----------UUGGU-----GAGA--CUGACGGUACCUUAUGAAUAAGCCACGGCUAACUCUGUGCCAGCAGCCGCGGUGAUACAGGGGUGGCAAGCGUUGUCCGGAUUUACUGGGUGUAAAGGG-UGCGUAGGCGGAUUGAUU-AGUCGG-GAGUUAAAGCCUC-UUGCUUAACGA-GA-GAACAGCUUCCGAUACUGUCA-GUCUA-GAGUGCCGAAGAGGAAGAUGGAAUUUCCGGUGUAGCGGUGGAAUGUGUAGAGAUCGGAAAGAACACCAG--UUGCGAAGGCAGUCUUCUGGUCGGUAACUGACGCUGAU-GUACGAAA-GCG-UGGGUAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCUGUAAA-CGAU-GGAU--GC-UAGA-UGUU-GGCUCU-------------------------------------UGGGUCAGUGUC-------GUA-GUUAACGCAUUAAGCAUCCCACC--UGGG-AAGUAC-GCUCGCAAGGGUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAUCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUA-CCUGGGCUUGACAUGCUAACU------------AAAGCCGGUG-AAAGCCGGUG----UCCGA----------------------------------AAGGG-----AGUUAGUGCAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUACAAUUAGUUGCU-AACAA-----GUAAUG-------------UUG--AG-CACUCUAAUUGGACUGCCUACG---CAA-GUAGUGAGGAAGGAGGGGAUGACGUCAAGUCCUCAUGGCCCUUACGUCCAGGGCAACACACGUGAUACAAUGGC-GACU-ACAAUGGGC---G---AAGCCGCGAGGUGAA-GAUAAUCCCAA-AAAAGUCGUCUCAGUCCAGAUCGGAGUCUGCAACUCGACUCCGUGAAGUCGGAAUCGCUAGUAAUCGCAGAUC-AGC-AUGCUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGCCAUGGAAGUCAGG-AGU-ACCCAAAGACGC-U-G----------------------------UGCGUUUAAGGU-AAGACUGGUAACUGGGGCUA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGUGG---CU-GGAUCACCUCCUUU
FQ859183.1/1179117-1180628             ACGAUGAAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-AG-CGG--CAGG-CUUAACACAUGCAAGUCGAGGG---G------------UAUAGUAGC-----AAUACU-A-GA----------------------------------------------------------------------------------------------------------------------------------GAC-CGGCGCA-CGGGUGCGUAACGCGUAUGC--AAUCUACCUUUUACAUA--GGGAUAGCCCAGAGAAAUUUGGAUUAAUACCUGAUAGUAUGU--GAU-GAUC--GCAU--GGU-UU-UC-A-C-AU-UAAA-GU----------------------------------------------------------ACCA------ACGGUAAAAGAUGAGCAUGCGUCCCAUUAGCUAGAUGGUAAGGUAACGGCUUACCAUGGCUACGAUGGGUAGGGG-UCCUGAGAGGGAGAUCCCCCACACUGGUACUGAGACACGGACCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGACAAUGGGC-GCAAGCCUGAUCCAGCCAUGCCGCGUGCAG-GA-UGACGGUC--CUAUG--GAUUGUAAACUGCUUUUGUACAGG-AAGAAA-CACUUCUAC--------GAGUAG-----AAGC--UUGACGGUACUGUAAGAAUAAGGAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUCCAAGCGUUAUCCGGAAUCAUUGGGUUUAAAGGG-UCCGUAGGCGGUUUGAUA-AGUCAG-UGGUGAAAGCCCA-UCGCUCAACGA-UG-GAACGGCCAUUGAUACUGUUA-GACUU-GAAUUAUUAGGAAGUAACUAGAAUAUGUAGUGUAGCGGUGAAAUGCUUAGAGAUUACAUGGAAUACCAA--UUGCGAAGGCAGGUUACUACUAAUGGAUUGACGCUGAU-GGACGAAA-GCG-UGGGUAGCGAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCUGUAAA-CGAU-GGAU--AC-UAGC-UGUU-GGGG---------------------------------GCAA----CUUCAGUGGC-------UAA-GCGAAAGUGAUAAGUAUCCCACC--UGGG-GAGUAC-GUUCGCAAGAAUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUA-CCAAGGCUUAAAUGUAGUUUG------------ACCGAUUUGG-AAACAGAUCUU----UCGC----------------------------------AAGA------CAAAUUACAAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGCCGUGAGGUGUCAGGUUAAGUCCUA-UAACGAGCGCAACCCCUGUUGUUAGUUGCC-AUCGA-----GUGAAG-------------UCG--GG-AACUCUAACAAGACUGCCAGUG---UAA-ACUGUGAGGAAGGUGGGGAUGACGUCAAAUCAUCACGGCCCUUACGCCUUGGGCUACACACGUGCUACAAUGGA-CGGU-ACAGAGAGC---AGCCACUACGUGAGUAGGA-GCGAAUCUAC--AAAACCGUUCUCAGUUCGGAUCGGAGUCUGCAACUCGACUCCGUGAAGCUGGAAUCGCUAGUAAUCGGAUAUC-AGCCAUGAUCCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGCCAUGGAAGCUGGG-GGU-GCCUGAAGUCGG-U-G-------ACC---GCAA---GGA-----GCUGCCUAGGGU-AAAACUGGUAACUAGGGCUA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAACACCUCCUUU
AAYP01000003.1/232298-233810           AUUUUAAAGAGUU-UGAU-CCUGGCUCAGGAUUAACGCU-GG-CGG--CAUG-CCUAAUACAUGCAAAUCGAACG-----------------AAGCCUUU-----U-AGGC-U-U------------------------------------------------------------------------------------------------------------------------------------AG-UGGUGAA-CGGGUGAGUAACACGUAUCC--AACCUACCCUUAAGUUG--GGGAUAACUAGUCGAAAGAUUAGCUAAUACCGAAUAAUAACA--UCAAUAUC--GCAU--GAG-AA-GA-U-G-UA-GAAA-GUCG------------------------------------------------------CGUUUG----CGACGCUUUUGGAUGGGGGUGCGACGUAUCAGAUAGUUGGUGAGGUAAUGGCUCACCAAGUCAAUGACGCGUAGCUG-UACUGAGAGGUAGAACAGCCACAAUGGGACUGAGACACGGCCCAUACUCCUACGGGAGGCAGCAGUAGGGAAUUUUUCACAAUGGGC-GAAAGCCUUAUGAAGCAAUGCCGCGUGAAC-GA-UGAAGGUC--UUAUA--GAUUGUAAAGUUCUUUUAUAUGGG-AAGAAA-CGCUAAGAUAGG--AAAUGAUUU-----UAGU--UUGACUGUACCAUUUGAAUAAGUAUCGGCUAACUAUGUGCCAGCAGCCGCGGUAAUACAUAGGAUGCAAGCGUUAUCCGGAUUUACUGGGCGUAAAACG-AGCGCAGGCGGGUUUGUA-AGUUUG-GUAUUAAAUCUAG-AUGCUUAACGU-CU-AGCU-GUAUCAAAAACUGUAA-ACCUA-GAGUGUAGUAGGGAGUUGGGGAACUCCAUGUGGAGCGGUAAAAUGCGUAGAUAUAUGGAAGAACACCGG--UGGCGAAGGCGCCAACUUGGACUAUCACUGACGCUUAG-GCUCGAAA-GUG-UGGGGAGCAAAUAGG-AUUAGAUACCCUAGUAGUCCA-CACCGUAAA-CGAU-CAUC--AU-UAAA-UGUC-GGCUCG---------------------------------AA--CGAGUCGGUGUU-------GUA-GCUAACGCAUUAAAUGAUGUGCC--UGGG-UAGUAC-AUUCGCAAGAAUGAAACUCAAACGGAAUUGACGGGGACCCG-CAC-AAGUGGUGGAGCAUGUUGCUUAAUUUGACAAUACACGUAGAACCUUA-CCUAGGUUUGACAUC-UAUUG-----------CGACGCUAUAG-AAAUAUAGUUG---AGGUU----------------------------------AA--------CAAUAUGACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUUUCGUUAGUUG---------------CUUU------------------------UCUAGCGAUACUGCUACCG---CAA-GGUA-GAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUAUCUAGGGCUGCAAACGUGCUACAAUGGC-UAAU-ACAAACUGC---UGCAAAAUCGUAAGAUGAA-GCGAAACAGAA-AAAGUUAGUCUCAGUUCGGAUAGAGGGCUGCAAUUCGCCCUCUUGAAGUUGGAAUCACUAGUAAUCGCGAAUC-AGACAUGUCGCGGUGAAUACGU-UCUCGGGUCUUGUACACACCGCCCGUCAAACUAUGGGAGCUGGU-AAU-AUCUAAAACCGC-A-A-AGCU-AACC---UUUU---GGAGGUA-UGCGUCUAGGGU-AGGAUCGGUGACUGGAGUUA-AGU-CGUAACAAGGUAU-CCCUACGAGAACGUGGGG---AU-GGAUCACCUCCUUU
GU567974.1/14656-16198                 CAUUUGAAGGGUU-UGAU-CCUGGCUCAGAAUGAACGUU-GG-CGG--CGUG-GAUUAGGCAUGCAAGUCGAGCG---A------------GAAUCUGUU-----GAAUGA-U-CCUUCGGGUGAAU--------------------------------------------------------------------------------------------------------GAUUCAGAGGAC----AG-CGGCAAA-CGGGGUAGUAAUGCAUAGGU---AUGUACCCUCUGGUCG--GGAAUAGCCACGGGAAACUGUGGGUAAUGCCCGAUGAU-----------CUG--GUGA--CAG--------------CAAA-GGU--------------------------------------------------------GUGAU-----UCCGCCAGAGGAGCAGCCUGUGUGGUAUUAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCUAAGAUGCCUAGGGG-GUGUGAGAGCAUGGCCCCCACCACUGGGACUGAGACACUGCCCAGACACCUGCGGGUGGCUGCAGUCGAGAAUCUUCCGCAAUGGGC-GAAAGCCUGACGGAGCGACGCCGCGUGCGG-GA-UGAAGGCC---UUCG--GGUUGUAAACCGCUGUCAGAGGGG-AUGAAA-UCGUUGGG---------GGCUAUCCCCCUUCG--UUGACAGAG-CCUCAGAGGAAGCGCGGGCUAAGUUCGUGCCAGCAGCCGCGGUAAUACGAACUGCGCGAACGUUAUUCGGAUUCACUGGGCUUAAAGGG-UGCGUAGGCGGCCUGUUA-AGUAGG-GCGUGAAAUCUGU-CGGCUCAACCG-GC-AAAUUGCGUUCUAAACUGGCA-GGCUU-GAGUGGGUCAGGGGUGUGUGGAACUUCCGGUGGAGCGGUGAAAUGUGUUGAUAUCGGAAGGAACGCCGG--UGGCGAAAGCGACACGCUGGGGCCUGUCUGACGCUGAG-GCACGAAA-GCC-AGGGUAGCGAACGGG-AUUAGAUACCCCGGUAGUCUU-GGCUGUAAA-CGAU-GAAC--AC-UAGG-UUGG-GGGGG---C----------------------------UUGU---UCCUCCCAGCC-------GUA-GCGAAAGCGUUAAGUGUUCCGCC--UGGG-GAGUAU-GGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCUCA-CAC-AAGCGGUGGAGGAUGUGGCUUAAUUCGAGGCAACGCGAAGAACCUUAUCCCGGAUUUGACAUCUACGGA-----------UUAGCUCUGUG-AAAGCAAAGUG-ACGCCUU----------------------------------CGGGUG---GAACGUAGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUCGCGUUAAGUCGCU-AAACGAGCGAAACCCUUGUCGUUAGUUGCC-AGCAC-----GUAAUG-------------GUG--GG-GACUCUAGCGAGACUGCCGGUGU--UAA-ACCG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCUUUAUGUCCGGGGCUGCACACGUCCUACAAUGGA-ACAU-ACAGACGGC---CGCGAACCCGCGAGGGUAA-GCUAAUCCGAA-AAAGUGUUCCUUAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUCGCAGGUC-AGCUAUACUGCGGUGAAUGUGU-UCCUGAGCCUUGUACACACCGCCCGUCAAGCCACGAAAGCGGGG-GGC-ACCUAAAGUCGC-C-G-GGCU-AACC---UUCG---GGAGGCA-GGUGCCUAGGGU-GAACUCCGUGAUUGGGACUA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUU
CP002525.1/485926-484416               UUUGAUGAGAGUU-UGAU-UCUGGCUCAGGAUUAAUGCU-GG-UGG--UAUG-CAUAACACAUGCAAGUCGAACG-AA-------------AAAGGCCCU-----CGGGUC-U-UU-------------------------------------------------------------------------------------------------------------------------------UU--AG-UGGCAAA-CGGGCGAGUAACGCAUACUU--AACUUACUUAUCUGAGG--AAAAUAGCAGCUCGAAAGAGCUAUUAAUAAUCCAUAGGUUUA--GGC--UAG-AGGAA--CUA--G-CU-U-A-AA-UUAA-AGGAGGCUG--------------------------------------------CCGCAAGGUGG----CCUUGCGGGUAAAUAGGAGUAUGUCCUAUUAGAUAGUUGGAGAGGUAAAGGCUCACCAAGUCGAUGAUGGGUAGCUG-GACUGAGAGGUUGAACAGCCGCAAUGGGAUUGAGAUAUGGCCCAUAUUCCUACGGGAAGCAGCAGUGAGGAAUUUUUCACAAUGGAC-GAAAGUCUGAUGGAGCAAUACCACGUGAAC-GA-UGAAGGUC---UUCU--GAUUGUAAAGUUCUUUUAUUUAGG-AAAAAA--AGCGCGACAG---GAAAUGGUC----GCGCC--CUGAUUGUACUAAUUGAAUAAGUGACAGCUAACUAUGUGCCAGCAGCUGCGGUAAAACAUAGGUCACGAGCAUUAUCCGGAUUUAUUGGGCGUAAAGGA-AGCGUAGGCUGAAGUGUG-UAUCCA-UUGUUAAAAGUAC-UUGCUUAACAA-GU-GUUC-GCGGUGGAGAUUACAC-UUCUA-GAAUUAGUUAGAGGGCACUGGAAUUCAAUGUGUAGUGGUGGAAUACGUAGAUAUAUUGAGGAACACCAG--AGGCUAAGGCGAGUGCCUGGGACAUAAUUGACGCUGAG-GCUUGAAA-GCG-UGGGUAGCAAAUGGG-AUUAGAUACCCCAGUAGUCCA-CGCCGUAAA-CGAU-GGGU--AU-UAGU-CAUU-UGAAU---------------------------------UUA---AGUUGAGUGAU-------GUA-GCUAACGCGUUAAAUACCCCGCC--UGGG-UAGUAU-AUAUGCAAAUAUGAAACUCAAA-GAAAUUGACGGGGACCUG-AAC-AAGUGGUGGAGCAUGUUGCUUAAUUCGAUCAUACACGCAAAACCUUA-CCAAGGCUUGCAAUC-UUCUG-----------CAAAGCUAUAG-AAAUAUAGUGG---AGGCU----------------------------------AU--------CAGAAUGACAG-GUGGUGCAUGGCUGUCGUCAGCUCGUGUCUUGAGAUGUUUGGUUAAGUCCCG-UAACGAGCGCAACCCUUCAUAUUAGUUG-------------UUUAGU------------------------UCUAAUAUGACUGA-AUCG---UAA-GAUC-UAGGAAGGAUGGGGCCAAGUCAAGUCAUCAUGCCCCUUAUGCCUUGGGCUGCAAACGUGCUACAAUGGU-AGAU-ACAAUGUGU---UACAAUCUAGCGAUAGUGA-GUUAAUCACCU-AAAGUCUAUCUCAGUCCGGAUAAAAGGCUGCAAUUCGCCUAUUUGAAGAUGGAAUCACUAGUAAUCCUGUGUC-AGCUAUAUCAGGGUGAAUACGU-UCCCAGGUCUUGUACACACCGCCCGUCAAACUACGAAAGAAAGU-ACU-AAUUAAAACCGU-A----------UU---UAAU-----------UACGUCUAGAUU-GGUAAUUUUGAUUGGAGUUA-AGU-CGUAACAAGGUAC-CCGUACGAGAACGUGCGG---GU-GGAUAACUUUUUAU
AFJQ01000029.1/34358-35866             AACACGGAGAGUU-UGAU-CCUGGCUCAGAACUAACGCU-GG-CGG--CGCG-UCUUAAACAUGCAAGUCAAGCG-GA-----------------GUAGC-----AAUAC-------------------------------------------------------------------------------------------------------------------------------------UC--AG-CGGCGAA-CGGGUGAGUAACACGUGGGU--AAUCUUCCUCUGAGUCU--GGGAUAACUUUCCGAAAGGGAAGCUAAUACUGGAUGGUCCCG--AGA-GAUC--AUAA--GAU-UU-UU-C-G-GG-UAAA-GA----------------------------------------------------------UUUA------UUGCUCGGAGAUGAGCCCGCGUCCGAUUAGCUAGUUGGUGAGGUAAAGGCUCACCAAGGCGACGAUCGGUAGCCG-GCCUGAGAGGGUGUUCGGCCACAAUGGAACUGAGACACGGUCCAUACUCCUACGGGAGGCAGCAGUUAAGAAUCUUGCUCAAUGGGG-GGAACCCUGAAGCAGCGACGCCGCGUGAAC-GA-UGAAGGUC---UUCG--GAUUGUAAAGUUCAGUAAGCAGGG-AAAAAU-AAGCAG--------------CAA-----UGUG--AUGAUGGUACCUGCCUA--AAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAUGGUGCAAGCGUUGUUCGGAAUCAUUGGGCGUAAAGGG-UGCGUAGGCGGACAUGUA-AGUCAG-GUGUGAAAACUGC-GGGCUCAACUC-GC-AGCCUGCACUUGAAACUAUGU-GUCUG-GAGUUUGGGAGAGGCAAGUGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAGGAACACCAG--UGGCGAAGGCGACUUGCUGGCCUAAAACUGACGCUGAG-GCACGAAA-GCG-UGGGUAGUGAACGGG-AUUAGAUACCCCGGUAAUCCA-CGCCCUAAA-CGUU-GUCU--AC-CAGU-UGUU-GGGGGU-------------------------------UUUA--ACCCUCAGUAAC-------GAA-CCUAACGGAUUAAGUAGACCGCC--UGGG-GACUAU-GCUCGCAAGAGUGAAACUCAAA-GGAAUUGACGGGGGUCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAAAAACCUCA-CCUAGGCUUGACAUGGAGUGG------------AAUCAUGUAG-AGAUACAUGAG----CCUU----------------------------------CGGG------CCGCUUCACAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUCACCUUAUGUUGCC-AUCA------UUCAGU--------------UG--GG-CACUCGUAAGGAACUGCCGGUGA--CAA-ACCG-GAGGAAGGCGGGGAUGACGUCAAAUCCUCAUGGCCUUUAUGUCUAGGGCAACACACGUGCUACAAUGGC-CGGU-ACAAAGGGU---AGCCAACUCGCGAGGGGGA-GCUAAUCUCAA-AAAUCCGGUCCCAGUUCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUC-AGC-AUGCCGCGGUGAAUACGU-UCCCGGACCUUGUACACACCGCCCGUCACACCACCUGAGUGGGG-AGC-ACCCGAAGUGGU-C-UUUGCC-AACC---GCAA---GGAAGCA-GACUACUAAGGU-GAAACUCGUGAAGGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAUCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
JF428976.1/24-1588                     AGAGAUUAGAGUU-UGAU-CCUGGCUCAGAACGAACGCU-GG-CGG--CGUG-GAUAAGACAUGCAAGUCGAACG-CUAAU--------CACGAGGUAGC-----AAUAUU-U-CGUG---------------------------------------------------------------------------------------------------------------------------GUUG-GAG-UGGCGCA-AGGGUGCGUAACGCGUGGGU--AAUCUACCGUGAAGUUU--GGGAUAACUCGCUGAAAGGCGAGCUAAUACCGGAUGUGAAAA--UAG-AGAG--GCAU--CUC-UU-UA-U-U-UU-CAGA-GCUGGGGA---------------------------------------------CCGUAAGGCCU-----GGCGCUUCACGAUGAACCCGCGACCUAUCAGCUAGUUGGUGAGGUAACGGCCCACCAAGGCUAAGACGGGUAGCUG-GUCUGAGAGGACGACCAGCCACACUGGAACUGAGACACGGUCCAGACACCUACGGGUGGCAGCAGUCGAGAAUUUUUCACAAUGGGC-GAAAGCCUGAUGGAGCGACGCCGCGUGGGG-GA-UGAAUGGC---UUCG--GCCCGUAAACCCCUGUCAUUUGCG-AACAAA-CCUUGCUAUU-----UAAAAGAUG---GCAAG--UUGAUGGUAGCGAAAGAGGAAGGGACGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGUCCCAAGCGUUGUUCGGAUUCACUGGGCGUAAAGGG-UGCGUAGGUGGCGGGGUA-AGUCGG-AUGUGAAAUCUCC-GAGCUCAACUC-GG-AAAUGGCAUUGGAAACUACCC-UGCUU-GAGGGUUGGAGGGGGGACUGGAAUACUUGGUGUAGCAGUGAAAUGCGUAGAUAUCAAGUGGAACACCAG--UGGCGAAGGCGAGUCCCUGGACAACUCGUGACACUGAG-GCACGAAA-GCU-AGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCU-AGCUGUAAA-CGGU-GCAC--GU-UUGC-UGUA-AAAGGA--A----------------------------UCGA-CCCCUUUUGUGGC-------GUA-GCCAACGCGUUAAACGUGCCGCC--UGGG-AAGUAC-GGUCGCAAGAUUAAAACUCAAA-GAAAUUGACGGGGGCCUG-CAC-AAGCGGUGGAGUAUGUGGCUCAAUUCGAUGCAACGCGAAGAACCUUA-CCUGGCCUUGACAUGCAAGUA-----------GUAGAAGGGUG-AAAGCCUGACG-AGGUAGC----------------------------------AAUACC----AGCUUGCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGUGUCCUGUUGCC-ACCCCU--ACGAGAGU------------AGGG--AG-CACUCUGGACAGACUGCCUCGCU--UAAACGAG-GAGGAAGGUGGGGAUGACGUCAAGUCAGUAUGGCCCUUACGGCCAGGGCUGCACACGUACUACAAUGCC-CGGC-ACAAAGGGA---AGCAAGACCGCGAGGUGGA-GCAAAUCCCCU-AAAACCGGGCCCAGUUCAGAUUGAAGGCUGCAACUCGCCUUCAUGAAGCUGGAAUCGCUAGUAAUGGCGCAUC-AGCUACGGCGCCGUGAAUACGU-UCCCAGGCCUUGUACACACCGCCCGUCACAUCAUGAAAGCCGUU-UGU-ACCCGAAGUCAC-C-G-UGCC-AACC---GCAA---GGGGGCA-GGUGCCGAAGGU-AUGGAUGGUGAUUGGGAUGA-AGU-CGUAACAAGGUAG-CCG----UAAAUCGUCGA---CU-GCAGGGCAUGCAAG
JN178154.1/19-1527                     CGCCCUUAGAGUU-UGAUACCUGGCUCAGGAUGAACGCU-AGUCGG--CGUGCCCUAAUGCAUGCAAGUCGAACG-AUG---------------UGCCUU-----CGGGCU-G-CU-------------------------------------------------------------------------------------------------------------------------------AU--AGCUGGCGAAGCGGGUGAGUAACACGUUUGCGUGACCUGCCCCAGAGAGG--GGGAUAACCAUUGGAAACGAUGGCUAAUACCCCGGAU-GUCU--UUA-UCGU--UAGA--GAG--U-GA-A-G-AC-UAAA-GC----------------------------------------------------------UCCG------GCGCUCUGGGAGGGGCCAGCGGCCCAUCAGCUUGUUGGUAGGGUAAUGGCCUACCAAGGCGUAAACUGGUAGGGGGGCGUGAGAGCGUGACCCCCCACACUGGUACUGACACACGGACCAGAUACCUACGGGUAGCAGCAGCAAGGAAUAUUGCGCAAUGGAC-GAAAGUCUGACGCAGCAACGCCGCGUGGAGNGA-UGAAGGCU---UUCG--GGUUGUAAACUCCUUUUCUGGGGG-AAGAGA-AA---------------------------------GGACGGUACCCCAGGAAUAAGGCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAAACGUACGGGCCGAGCGUUAUCCGGAUUUACUGGGCGUAAAGCG-CAUGC-GGCGGUUUCUUA-AGUCGG-ACGUGAAAGCUCU-CGGCUCAACUG-GG-AGAGGCCGUUCGAAACUAGGA-GACUU-GAGGAUGGUAGAGGAGAGUGGAAUUCCCGGUGUA-UGGUGAAAUGCGUA-AUUUCGGGAGGAACACCCA--UGGCNAAGGCGGCUCUCCUGGCCAUUCCUGACGCUAAN-AUGCGAAANGCUAAGGGGAGAGAACGGG-AUUAGAAACCCCGGUAUUCCUUAGCCGUAAA-CGAU-GUCA--AC-UUAGUUGUA-GGAGGU-AC----------------------------CCAA--UCCUCCUGUGCU-------GCA-GCCAACGCGUUAAGUUGACCGCC--UGGG-GACUAC-GGCCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CACAAAGCAGCGGAGCGUGUGGUUUAAUUCGAGGCUACGCGAAGAACCUUA-CCAGGGUUUGACAUG-UACGUG----------GUAGGAACGUG-AAAGCGAACCG--ACCCUU----------------------------------CGGGGA----GCGUA-CACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUAGGUUAAGUCCUG-UAACGAGCGCAACCCUCAUCGUUAGUUA-----CAU------------------------GUG--------UCUAACGAGACUGCCGGUGA--UAA-GCCG-GAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGGCCUUUAUAUCCUGGGCUACACACACGCUACAAUGGC-CAGU-ACAAUGGGU---UGCCAAGUCGCGAGACGGA-GCCAAUCCCCC-AAAGCUGGUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUCGGAGUUGCUAGUAACCGCGCGUC-AGCAACAGUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGGAAGUUGGC-AAC-GCCUGAAGUCGG-U-G-GGCUUAACC--CGCAA--GGGAGGCA-GCCGCCCAAGGC-GGGGUCGGUAACUGGGACGA-AGU-CGU-ACAAGGUAG-CUGUAGCGGAAGCUGCGG---CU-GGAUCACCUCCUUA
CU367875.1/566-1989                    UUUGUUAAGAAUU-UGAU-CCUGGUUCAGGGUGAAUGCU-AG-CGG--CGUG-CCUAAGGUAUGCAAGUCAAACU--------------------CGCGC-----AAGCG-----------------------------------------------------------------------------------------------------------------------------------------GG-UGGCGAA-CGGCUGAGUAAUACGUAGGA---AUCUACCUCUAAGUAA--GGCAUAGCCCGCCGAAAGGCGGGGUAAUUCCUUAUGUG-----------AUG--GCAA--CAU--------------CAAA-GA----------------------------------------------------------UUUA------UCGCUUAGAGAUGAGCCUACGGCCUAUCAGGUAGUUGGUUGGGUAAAUGCCUACCAAGCCUAUGACGGGUAGCUG-GUAUAAGAGUAUGACCAGCCAGAGGGGCACUGAGACACGGGCCUCACCCCUACGGGGGGCAGCAAUCGGGAAUUUUGCGCAAUGGGC-GAAAGCCUGACGCAGCGACGCCGCGUGAAG-GA-UUAAGGCC---UUCG--GGUUGUAAACUUCGUUG-------------------------------------------------------------------UAAGCACCGGCUAACUACGUGCCAGCAGCAGCGGUCAUACGUAGGGUGCAAGCAUUACCCGGUCUUAUUGGGCGUAAAGAGUUCUGUAGGCGGUUGAACA-AGUUGG-AAGUUAAAUACCU-CGGCUCAACCG-AG-GUAGGGCUUUCAAUACUGUUU-AGCUAAGAGGUGACUAGGGGAUAGCGGAACGCAUGGUGUAGCAGUGAAAUGCGUUGAUAUCAUGCGGAACACCAA--GGGGGAAGCCAGCUAUCUGGGGUUAUCCUGACGCUGAG-AGACGAAA-GCG-UGGGGAGCGAAACGG-AUUAGAUACCCGUGUAGUCCA-CGCUGUAAA-CCAU-GCCU--GC-UAGA-UGCU-CCG----------------------------------UUUU-----CGGAGUGUC-------GAA-GCUAACGCGUUAAGCAGGCCGCC--UGGG-AAGUAC-GAUCGCAAGAUUAAAACUCAAA-GGAAUUGGCGGGGACCCG-CAC-AAGCGGUGGAGCAUGCUCUUUAAUUGGCUGAUAACCCAAGAACCUUA-CCAGGGCUUGACAUG-CAUAAA----------GUAGUGAACCG-AAAGGGGAACG--ACCGGUAUC----------------------------CAGUCCGGA----GUUUG-CACAG-GUGUUGCAUGGCUGUCGUCAGUUCGUACCGUGAGGCGUACCCUUAAGUGGGU-UAACGAACGCAACCCCUACUGUCAGUUG-------------UAUCAC------------------------UCUGACGGAACUGCCUCGG---UAA-CGAG-GAGGAAGGUGGGGAUGACGUCAAGUCAGUAUUGCUCUUACGCUCUGGGCUAGAAGCAUGCUACAAUGGG-GUCG-ACAGCGCGA---AGCGAAGAGGCGACUCGGA-GCAAAUCGCU--AAACGACCUCUCAGUUCGGAUUGGAGUCUGCAAUUCGACUCCAUGAAGUUGGAAUCGCUAGUAAUCGGCGGUC-AGCUAUACGCCGGUGAAUACGU-UCUCGGGUCUUGCACACACUGCCCGUCACGUCAGCAAAGCUGGG-GCC-ACCCGAAGUCUC-A----------UU---UUGU---A-------UGGGCUCACGGU-GGAAUCAGUGAUGAGGAUGA-AGU-CGAAACAAGGUAG-CCGUAGGGGAAUCUGCGG---CU-GGAUCACCUCCUUU
CP000359.1/157581-159089               UUGAUGGAGAGUU-UGAU-CCUGGCUCAGGGUGAACGCU-GG-CGG--CGUG-CUUAAGACAUGCAAGUCGAACG-----------------AUCGUCUU-----CGGACG-G-U------------------------------------------------------------------------------------------------------------------------------------AG-UGGCGCA-CGGGUGAGUAACGCGUAACU--GACCUGCCCCCAAGACC--GGAAUAACUCCCCGAAAGGGGAGCUAAUGCGGGAUGUGCUGU--CCG--GCU--GU----GGC--C-GG-A-C-AG-UAAA-GGC---------------------------------------------------------UGAG-----GCCGCUUGGGGAUGGGGUUGCGUUCCAUCAGCUAGAUGGUGGGGUAAAGGCCUACCAUGGCGACGACGGAUAACCG-GCCUGAGAGGGUGGCCGGUCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCCCAAUGGGC-GCAAGCCUGAGGGAGCGACGCCGCGUGAGG-GA-UGAAGGUC---CUCG--GAUUGUAAACCUCUGA-ACGAGUG-ACGAAA-GGCCCC-------------GAAUG---GGGAG--AUGACGGUAGCUCGGUAA-UAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUACCCGGAAUCACUGGGCGUAAAGGG-CGUGUAGGCGGAAGGUUA-AGUCCG-ACUUUAAAGACCG-GGGCUCAACCC-CG-GGCCUGGGUUGGAGACUGGCU-UUCUG-GACCUCUGGAGAGGCAACUGGAAUUCCUGGUGUAGCGGUGGAAUGCGUAGAUACCAGGAGGAACACCGA--UGGCGAAGGCAGGUUGCUGGACAGAAGGUGACGCUGAG-GCGCGAAA-GUG-UGGGGAGCGAACCGG-AUUAGAUACCCGGGUAGUCCA-CACCCUAAA-CGAU-GCAC--GU-UGGC-CGAG-CGCGG--------------------------------GAUG---CCGUGCUGGGC-------GAA-GCCAACGCGAGAAACGUGCCGCC--UGGG-AAGUAC-GGCCGCAAGGUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCAGGUCUUGACAUG-CACCG------------AACCCUGCUG-AAAGGUGGGGG--UGCCCUU--------------------------------CGGGGAG----CGGUGACACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGCCCUUCGUUGCC-AGCAG------UUCGG-------------CUG--GG-GACUCGAGGGGGACUGCCGGUG---AAA-GCCG-GAGGAAGGCGGGGAUGACGUCUAGUCAGCAUGGUCCUUACGACCUGGGCGACACACGUGCUACAAUGAC-CAGA-ACAACGCGC---UGCGAACUUGCGAGAGUGA-GCCAAUCGCUG-AAAACUGGUCCCAGUUCAGAUCGGAGUCUGCAACUCGACUCCGUGAAGGUGGAAUCGCUAGUAAUCGCGGGUC-AGC-AUACCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGCAU-GGC-AGCUGAAACCAC-C-G-GGAG---CU---UUAC---GG---CA-GGUGUCUAGGCU-GUGGUGCAUGACUGGGGUGA-AGU-CGUAACAAGGUAA-CUGUACCGGAAGGUGCGG---UU-GGAUCACCUCCUUU
ACET01000043.1/67-1574                 CGAACGAAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GA-CAG--AAUG-CUUAACACAUGCAAGUCGACUC-GA-----------------GUCUU-----CGGAC-------------------------------------------------------------------------------------------------------------------------------------UU-GGG-UGGCGGA-CGGGUGAGUAACGCGUAAAG--AACUUGCCUCAUAGUCU--GGGACAACAUCUGGAAACGGAUGCUAAUACCGGAUAUUAUGC--UUU-CUUC--GCAU--GGA-GG-AA-G-U-AU-GAAA-GCU----------------------------------------------------------AUA-----UGCGCUAUGAGAGAGCUUUGCGUCCCAUUAGCUAGUUGGUGAGGUAACGGCCCACCAAGGCGAUGAUGGGUAGCCG-GCCUGAGAGGGUGAACGGCCACAAGGGGACUGAGACACGGCCCUUACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGACCAAAAGUCUGAUCCAGCAAUUCUGUGUGCAC-GA-UGACGUUU---UUCG--GAAUGUAAAGUGCUUUCAGUCGGG-AAGAAG-CA-------------------AG------------UGACGGUACCGACAGAAGAAGCGACGGCUAAAUACGUGCCAGCAGCCGCGGUAAUACGUAUGUCGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCG-CGUCUAGGCGGCAAGGAA-AGUCUG-AUGUGAAAAUGCG-GGGCUCAACUC-CG-UA-UUGCGUUGGAAACUGCCU-UACUA-GAGUACUGGAGAGGUAGGCGGAACUACAAGUGUAGAGGUGAAAUUCGUAGAUAUUUGUAGGAAUGCCGA--UGGGGAAGCCAGCCUACUGGACAGAUACUGACGCUAAA-GCGCGAAA-GCG-UGGGUAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCUGUAAA-CGAU-GAUU--AC-UAGG-UGUU-GGGGG--------------------------------UCAA---ACCUCAGCGCC-------CAA-GCUAACGCGAUAAGUAAUCCGCC--UGGG-GAGUAC-GUACGCAAGUAUGAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAGGAACCUUA-CCAGCGUUUGACAUC-CUACA------------AAGAGUGCAG-AGAUGCGCUUG--UGCUUCUU------------------------------CGGAAGAA----UGUAGUGACAG-GUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUCGUAUGUUACC-AGCC------UUUAGU--------------UG--GG-GACUCAUGCGAUACUGCCUGCGA--CGA-GCAG-GAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUAUACGCUGGGCUACACACGUGCUACAAUGGG-UAGU-ACAGAGAGC---GGCGAACCCGCGAGGGGGA-GCAAAUCUCAG-AAAACUAUUCUUAGUUCGGAUUGUACUCUGCAACUCGAGUACAUGAAGUUGGAAUCGCUAGUAAUCGCAAAUC-AGCAAUGUUGCGGUGAAUACGU-UCUCGGGUCUUGUACACACCGCCCGUCACACCACGAGAGUUGGU-UGC-ACCUGAAGUAGC-A-G-GCCU-AACC---GUAA---GGAAGGA-UGCUCCGAGGGU-GUGGUUAGCGAUUGGGGUGA-AGU-CGUAACAAGGUAU-CCGUACGGGAACGUGCGG---AU-GGAUCACCUCCUUU
EF173356.1/9-1570                      UUAGCGGCGCGAU-UCGC-CCUUUC--AGAUUGAACGCU-GG-CGG--UAUG-CUUAACACAUGCAAGUCGAGCG-CGA------------AAGUGGCUU-----CGGCCA-C-GA------------------------------------------------------------------------------------------------------------------------------GUA-GAG-CGGCGGA-CGGGUGCGUAACACGUGGAU--AAUCUGCCUUCAGGUCU--GGGAUAACCCUGGGAAACUAGAGCUAAUACCGGAUAAGACCA--CAG--GUU--CCAUGGAAC--C-AG-A-G-GU-AAAA-GGCG-----------------------------------------------------GCUUUCGGG-CUGUCUCCUGAAGAUGAGUCCGCGUCCCAUCAGGUAGUUGGUGAGGUAAAGGCUCACCAAGCCUAAGACGGGUAGCCG-ACCUUAGCGGGUGAUCGGCCACACGGGGACUGAGACACGGCCCCGACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGGGCAAUGGGC-GAAAGCCUGACCCAGCAAUACCGCGUGAGG-GA-UGAAGGCC---UUCG--GGUCGUAAACCUCUGUCAGCAGGA-ACGAUG-GGUUUCCGUGC---UAAUACCACG---GAGAC--UUGACGGUACCUGCAAAGGAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGGGCAAGCGUUGCUCGGAAUUACUGGGCGUAAAGGG-UCCGCAGGUGGCCUCGUA-AGUUGA-AUGUGAAAUCUCA-GGGCUUAACCC-UG-AAACUGCAUCCAAUACUGCGA-GGCUU-GAGUCCAAGAGAGGUUGGCGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCAG--UGGCGAAGGCGGCCAACUGGCUUGGAACUGACACUCAG-GGACGAAA-GCG-UGGGUAGCGAACCGG-AUUAGAUACCCGGGUAGUCCA-CGCCCUAAA-CGAU-GGAU--GC-UAGG-UGUG-GGGAU--------------------------------GAAA---AUCUCUGUGCC-------GAA-GUUAACGCAUUAAGCAUCCCGCC--UGGGGGAGUAC-GGUCGCAAGAUUGAAACUCAAA-GGAAUUGGCGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUA-CCAAGGCUUGACAUACUGGCUC----------AAGCUAAUGUG-AAAGCAUUUUG--UGUUGUAAGG-------------------------CUUGCCUUACA---UAGUCAGUACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUCCGGUUAAGUCCGG-UAACGAGCGCAACCCCUAUGUUUAGUUGCC-AGCAC-----GUAAG--------------GUG--GG-AACUCUAAAGAGACUGCCGGCGA--CAA-GCCG-GAGGAAGGCGGGGACGACGUCAAGUCAUCAUGGCCCUUAUGCUUUGGGCUACACACAUGCUACAAUGGC-GGAU-ACAAUGGGU---UGCCAAACCGUAAGGUGGA-GCCAAUCCCAUCAAAGUCCGUCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCGCUAGUAAUCGUGGAUC-AGCACUGCCACGGUGAAUACGU-UCCCGGGCCUUGCACACACCGCCCGUCACACCACGAAAGUCGGU-UCU-ACCCGAAGUGGU-U-G-AGCU-AACC--CGCAA--GGGAGGCA-GGCUCCUAAGGU-AGGGCUGGUAAUUGGGGUGAGAGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUU-
AF407729.1/1-1483                      -UCGAUUAGAGUU-UGAU-CCUGGCUCAGAAUGAACGUU-GG-CGG--CAUG-GCUAAAGCAUGCAAGUCGCACG-----------------UGCCCCGC-----AAGGGG-A-A------------------------------------------------------------------------------------------------------------------------------------AG-UGGCGGA-CGGGUCAGUAACAGGAUCGA---ACGUACCCCGAGGUGG--GGGAUAGCGGUGGGAAACUGCCGGUAAUACCUCAUGAU-----------CUC--UCCG--GAG--------------CAAA-GC----------------------------------------------------------CUCG------GCGCCUCGGGAUCGGCGAUCUUCCUAUCAGGUCGUUGGCGGGGUAAUGGCCCACCAAGCCGAAGACGGGUAGCGG-GUGUGAGAGCACGACCCGCGACAUCGGGACUGAGACACUGCCCGGACUCCUACGGGAGGCUGCAGCAACGAAUCUUCCGCAAUGGGC-GCAAGCCUGACGGAGCAAUGCCGCGUGCGG-GA-UGAAGCGU---CUUG--ACGUGUAAACCGCUGUCAGGGGGU-CGAACC-AA---------------------------------UGAU--UGCCCCCAGAGGAAGUGGCGACUAACUCUGUGCCAGCAGUCGCGGUAAUACAGAGGCCACGAACAUUAUUCGGAAUCACUGGGCUUAAAGGG-UGCGUAGGCGGGCCGCCA-AGUGUU-CUGUGAAAGCCCC-GGGCUCAACCC-GG-GAACGGCAGGGCAUACUGGCG-GUCUU-GAGGGAUCUAGGGGCAGACAGAACAGUCGGUGGAGCGGUGAAAUGCGUAGAGAUCGACUGGAAUGCCGA--UGGCGAAGGCGGUCUGCUGGGGAUCAUCUGACGCUGAG-GCACGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GCGC--AC-UAAA-UCGG-UGCCGG--U----------------------------CUGA-CCCGGUAUCGGUC-------GAC-GUGAAAACGAUAAGUGCGCCGCC--UGGG-GAGUAC-GGUCGCAAGGCUAAAACUCAAA-UGAAUUGACGGGGGCUCA-CAC-AAGCGGUGGAGCAUGUGGCUUAAUUCGAGGCAACGCGAAGAACCUUA-CCUGGGUUUGACAUG-CACGGA----------UUAACCGGUGG-AAACAUCGGCC-ACGCUCG----------------------------------CAAGAGUGGAACGUG-CACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCUGUGAAGUGUCGGGUUAAGUCCCU-UAACGAGCGCAACCCCUAUCGUUAGUUGCC-CACGG------UUCGG-------------CCG--GG-UACUCUAGCGAGACUGCCGGCGU--UAA-GCCG-GAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUACAUCCAGGGCUGCACACGUGCUACAAUGGC-GCUG-ACAGAGCGA---CGCAAUGCCGCGAGGCGGA-GCAAAUCGCAA-AAAAGGCGCCCCAGUUCGGAUUGCAGGCUGCAAUUCGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGGAGAUC-AGCUACGCUCCGGUGAAUGUGU-UCCUGAGCCUUGUACACACCGCCCGUCACGUCAUGGGAGCCGAG-GGU-GCCCGAAGCCGC-C---------ACG---AUUC---AGU-----GGUGUCCACGGC-AAGAUCGGUGACUGGGACGA-AGU-CGUAACAAGGUAG-CCGUAGGAGAACCUGCGG---CU-GGAUCACCUCCUUA
AGAG01000005.1/9780-8261               AAGGAUAAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUUGAGCG-GAGA---------UAUAUGGAGCU-----UGCUUU-A-UAUA---------------------------------------------------------------------------------------------------------------------------ACUU--AG-CAGCGAA-CGGGUGAGUAACACGUAGAU--AAUCUAUCCUAUACUGG--GGGAUAGCCCGAUGAAAGUUGGAUUAAUACCGCAUAUAGCUA--UAU-AGUU--GCAU--GAU-UA-UG-U-A-GU-GAAA-GA----------------------------------------------------------UUUA------UUGGUAUAGGAGGAGUCUGCGGCACAUUAGCUAGUAGGUGAGGUAAAGGCUUACCUAGGCGACGAUGUGUAGCCG-GUCUGAGAGGAUGAACGGCCACAAUGGAACUGAGACACGGUCCAUACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGG-GAAACCCUGAUGCAGCAACGCCGCGUGAGU-GA-AGAAGGUU---UUCG--GAUUGUAAAGCUCUGUUAGCAGGG-AAGAGG-AA---------------------------------GGACGGUACCUGCAGAGGAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUUCGGAAUAACUGGGCGUAAAGGA-UGCGUAGGCGGUUAAACA-AGUUAU-AUGUUAAAUAUAU-AGGCUUAACCU-GU-AGAAAGCAUAUAAAACUGUUU-AACUA-GAGUGCAGGAGAGGUAAGUGGAAUUCCUAGUGUAGCGGUGAAAUGCGUAGAGAUUAGGAAGAACACCAG--UGGCGAAGGCGACUUACUGGACUGUAACUGACGCUGAG-GCAUGAGA-GCA-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-UGCUGUAAA-CGAU-GGGU--AC-UAGG-UGUG-GGUUGU--G----------------------------AAUA--ACAAUUCGUGCC-------GUC-GCAAACGCAAUAAGUACCCCGCC--UGAG-GAGUAC-GAUCGCAAGAUUAAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCAGCGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCUAAACUUGACAUA-CCUUG------------AAUUACCUUGUAAUGAGGGAAG--C-UCGC----------------------------------AAGA-G----CAAGGAUACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGUUGUUAAUUGCU-AACAG-----GUUAAG-------------CUG--AG-CACUUUAGCGAGACAGCCUAGGU--UAA-CUAG-GAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUACGUUUAGGGCUACACACGUGCUACAAUGGU-GAGA-ACAGAGAGA---AGCAAGCUAGUGAUAGUGA-GCAAAACUUAU-AAAACUCAUCUCAGUUCGGAUUGCAGGCUGAAACUCGCCUGUAUGAAGAUGGAGUUGCUAGUAAUCGCGAAUC-AGA-AUGUCGCGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCACACCAUGAGAGUUGGC-AAC-ACCCGAAACCUG-U-G-GGCU-AACC--AUAUA---GGAGGCA-GCAGUCUAAGGU-GGGGUCAGUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAGGAGAACCUGCGG---CU-GGAUCACCUCCUUU
CP001055.1/1536698-1535187             UUUGCGGAGAGUU-UGAU-CCUGGCUCAGAGUUAACGCU-GG-CAU--CGUG-CAUAACACAUGCAAGUCGAACG-GGAAU-------UUUUUGUGUAGC-----AAUACA-U-GAAA--------------------------------------------------------------------------------------------------------------------------AAUUC-UAG-UGGCAGA-CGGGUGAGUAAUACAUAAGG--AAUCUACCUUGAAGUGG--GGAACAACUAGUCGAAAGAUUAGCUAAUACUCCAUAAUAUCA--CUU-AGUG--GCAU--CAC-UU-AG-U-G-AU-UAAA-GA----------------------------------------------------------UUUA------UCGCUUCAAGACGAUCUUAUGGUCUAUCAGCUAGUUGGUAGGGUAAUGGCCUACCAAGGCGACGACGGAUAGCCG-GCCUGAAAGGGCGACCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGAC-GCAAGUCUGAUCCAGCAACGAUGCGUGGAG-GA-UGAAGGUU---UUCG--GAUUGUAAACUCCUUUUGCAGGGG-AAGAAA-AA-------------------AA------------UGACGGUACUCUGCGAAUAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAGACGUAGGUGGCAAGCGUUACUCGGAAUUACUAGGCGUAAAGCG-CGCGUAGGCGGAUUGUUA-AGUCUG-UUGUGUAAUCUCU-GGGCCCAACCC-AG-AAACUGCAAUUGAAACUGGCG-AUCUU-GAGUGAGGCAGAGGAAAUCGGAAUUCCAAGUGUAGCAGUGAAAUGCGUAGAUAUUUGGAGGAACACCGG--UGGCGAAGGCGGAUUUCUGGGCCUUUACUGACGCUGAA-GUGCGAAA-GCU-AGGGGAGCAAACGGG-AUUAGAUACCCCGGUAGUCCU-AGCCGUAAA-CGAU-GAUA--AC-UAGG-UGUG-GGAGGU--A----------------------------UCGA-CCCCUUCCGUGCC-------GAC-GCUAACGCAUUAAGUUAUCCGCC--UGGG-GAGUAC-GGCCGCAAGGUUAAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGAGGUGGAUUAUGUGGUUUAAUUCGACGCUACGCGAAAAACCUUA-CCUGGGCUCGAACGA-CUGGUA---------GUAACAUUUAUG-AAAGUAGAUGU-GAUUCGC----------------------------------AAGAAA----GCCAG-CCGAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUUCUGUGUUGCC-UA--------GCAAUA------------------GG-AUCUCUCAGAAGACUGCCGCGGA--UAA-CGUG-GAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGGCCUUUAUGUCCAGGGCUACACACGUAAUACAAUGGC-AUAG-ACAGAGGGC---AGCAAUAUCGCGAGAUGGA-GCCAAUCCCU--AAACUAUGCCCCAGUUCAGAUUGCAGGCUGCAAUUCGCCUGCAUGAAGCCGGAAUCUCUAGUAAUCGCAGAUC-AGC-ACGCUGCGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCACACCACGAAAGUUAAU-UGC-AACAGAAGUGCU-C-A-GGUC------------------GUCU-GGGCCCUAAGUU-GUGAUUAGUAAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
CP002221.1/248307-246756               UUCUUGAAGAGUU-UGAU-CCUGGCUCAGCGCGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCGUGCG----------------GGGUGGCUC-----U-GCCA-C-CC-----------------------------------------------------------------------------------------------------------------------------------AG-CGGCAAA-CGGGUGAGUAACACGUGAGU--AACCUGCCCUCAGGAAG--GGGAUAACCCUCCGAAAGGGGGGCUAAUACCCUAUAAAGCCA--GGG--GUC--ACAAAGGCU--A-CC-U-G-GC-CAAA-GGGGGCCUCU------------------------------------------GCUCUGCAUGCU-----CCCGCCUGAGGAGGGGCUCGCGGCCCAUCAGGUAGUUGGUGGGGUAACGGCCUACCAAGCCUAUGACGGGUAGCCG-GCCUGAGAGGGUGGCCGGCCACAGUGGGACUGAGACACGGCCCACACCCCUACGGGGGGCAGCAGUGGGGAAUCGUGGGCAAUGGGC-GAAAGCCUGACCCCGCGACGCCGCGUGGAG-GA-AGAAGCCC---UUCG--GGGUGUAAACUCCUGUCAGGGGGG-AAGAUG-CUCACAGAGGCG-AAUAGUCUCU-----GUGG--GUGACUGUACCCCCAGAGGAAGGGACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUCCCGAGCGUUGCGCGAAUUUACUGGGCGUAAAGCG-UCCGCAGCCGGAUGGGUA-AGCGGU-UUGUCAAAGCCCA-CCGCUCAACGG-UG-GAAAGGCAUACCGAACUGCCC-AUCUU-GAGGCACGCUCAGGUAGGCGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCGG--UGGCGAAGGCGGCCUACUGGGGCUGUCCUGACGGUCAG-GGACGAAA-GCU-GGGGGAGCAAACCGG-AUUAGAUACCCGGGUAGUCCC-AGCCGUAAA-CCAU-GGGC--GC-UAGG-CGUU-GUCC---------------------------------GCAA----GGGCAGUGCC-------UCA-GCUAACGCGGUAAGCGCCCCGCC--UGGG-GAGUAC-GGGCGCAAGCCUGAAACUCAAA-GGAAUUGGCGGGGGCCCG-CAC-AACCGGUGGAGCGUCUGGUUCAAUUCGAUGCUAACCGAAAAACCUUA-CCCGGGUUUGACAUGGUGGGA------------AACCCUUGCG-AAAGCGAGGGG--UGCCGUCUU---------------------------CUGGACGGAA----UCCCACCACAG-GUGGUGCAUGGCCGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCCUUAGUUGCU-A-CUC-----UUCG---------------GAG--GG-CACUCUAAGGGGACUGCCGGCGA--UAA-GCCG-GAGGAAGGUGGGGAUGACGUCAGGUCAGUAUGCCCUUUAUGCCCGGGGCUACACAGGCGCUACAGUGGC-CGGG-ACAAUGGGA---AGCGACUCAGUAAUGAGGA-GCAAAUCCUAU-AAACCCGGUCAUGGUGCGGAUUGAGGGCUGAAACUCGCCCUCAUGAAGCCGGAAUCGGUAGUAAUGGCGGAUC-AGCUAAGCCGCCGUGAAUACGU-UCUCGGGCCUUGCACACACCGCCCGUCACGCCACGGAAGUCAGU-CUU-CCCGGAAGCCCU-C-G-GGCU-AACC--CGUAA--GGGAGGUA-GAGGACGAUGGG-AAGGCUGGCAACUGGGGCGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUU
CP000679.1/2380146-2378602             UUAAUUGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CCUAACGCAUGCAAGUCGAGCG-GAG------------AUGGUGGUU-----GAAGGU-G-AUGAGCUGGAG-------------------------------------------------------------------------------------------------------------GCUGCCAUCUU--AG-CGGCGGA-CGGGUGAGUAACACGUGAGC--AACCUACCCCCAGCACG--GGGAUAACAGCUCGAAAGGGCUGCUAAUACCCGAUGGGACCA--CGU-CAUC--GCAU--GGU-GA-UG-U-G-GU-GAAA-GGGUAGCC---------------------------------------------GGGGAGGCUAU-----ACUGGCUGGGGAUGGGCUCGCGGCCCAUCAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCG-GCCUGAGAGGGUGUACGGCCACAGUGGGACUGAGACACGGCCCACACUCCUACGGGAGGCAGCAGCGGGGAAUCUUGCGCAAUGGGC-GGAAGCCUGACGCAGCGACGCCGCGUGAGG-GA-UGAAGCCC---UUCG--GGGUGUAAACCUCUUUGGACGGGG-AGAAGA-AG--------------------G------------AGAUAGUACCCGUUUAAAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCGAGCGUUGUCCGGAAUUACUGGGCGUAAAGGG-UGCGUAGGCGGCUAUGCG-AGUUAA-GCGUGAAAGCCUU-AGGCUCAACCU-AA-GGAUUGCGCUUAAUACUGCAU-AGCUU-GAGUGCGGGAGAGGACGGCGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCAG--UGGCGAAGGCGGCCGUCUGGACCGUAACUGACGCUGAG-GCACGAAA-GCG-UGGGGAGCGAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCUGUAAA-CGAU-GGAU--GC-UAGG-UGUG-GGGGAG--A----------------------------AGGA--CUCCUCCGUGCC-------GUA-GUUAACACAAUAAGCAUCCCGCC--UGGG-GAGUAC-GGCCGCAAGGUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCAGGGCUUGACAUG-CCGGG------------GACCUGCCCG-AAAGGGUGGGG--UGCCUGACCGU------------------------AAGGUUAGGAG----CCCGGACACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCCUUAGUUGCC-AGCGG-----UUUUAG-------------CCG--GG-CACUCUAAGGGGACUGCCGUCGA--UGA-GGCG-GAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGCCCUGGGCUACACACGUGCUACAAUGGG-UGCU-ACAGAGGGC--GUGCGAAGGCGCGAGCCGGA-GCGAAUCCCAA-AAAAGCACCCCCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUC-AGC-AUGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGAGAGUCAGC-AAC-ACCUGAAGACAC-A----------GG---UUAA---GC------UGUGUUGAAGGU-GGGGCUGAUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACGGGAACGUGCGG---CU-GGAUCACCUCCUUU
HM454283.1/33305-34834                 UAAACUGAGAGUU-UGAU-CCUGGCUCAGAGCGAACGCU-GG-CGG--CGUG-CUUAACACAUGCAAGUCAUACG-GAGU---------UAUGGAGGGGU-----AACCUG-A-CAU----------------------------------------------------------------------------------------------------------------------------AACU-AAG-UGGCGGA-CGGGUGAGUAACGCGUAGGU--GACCUGCCCUUGUGACU--GGGAUAACCACUGGAAACGGUGGAUAAUACCGGAUAAGCCCA--CGA--UUA-GGUGA--UAG--U-AG-U-G-GG-AAAA-GGA---------------------------------------------------------GAAA-----UCUGCACAAGGAUGGGCCUGCGUCCUAUCAGGUAGUUGGUAAGGUAAAGGCUUACCAAGCCUAAGACGGGUAGCCG-GUCUGAGAGGAUGGACGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUGCGCAAUGGGC-GAAAGCCUGACGCAGCGACGCCGCGUGGGG-GA-UGAAGGCC---UUCG--GGUUGUAAACCCCUUUUGUAAGGG-AAGAUA--G---------------------------------UGACGGUACCUUAAGAAUAAGCCACGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGUGGCAAGCGUUGCUCGGAAUCACUGGGCUUAAAGGG-CGCGUAGGCGGUUAAUCA-AGUUUA-GGGUGGAAUGCAU-GGGCUCAACCU-AU-GAAUUGCCUUGAAAACUGGUU-GACUU-GAGUAAGCGAGGGGAUGGCGGAAUUCCUGGUGUAGCGGUGAAAUGCGUAGAUAUCAGGAGGAAGGCCGG--UGGCGAAGGCGGCCAUCUGGCGCUUAACUGACGCUGAG-GCGCGAAA-GCG-UGGGGAUCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCCUAAA-CGGU-GGGU--AC-UAGG-UGUA-GGGCUC-------------------------------UUUA--GGGUUCUGUGCC-------GAA-GGGAAACCGAUAAGUACCCCGCC--UGGG-AAGUAC-GGCCGCAAGGUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCUGGGUUUGACAUG-CAGAUG----------GUAGUGAUCCG-AAAGGUGAGCG--ACUUUCCCGU--------------------------AAGGGAGAGA----GUCUG-CACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUCCUUUGUUGCC-AUCAG-----GUUAAG-------------CUG--GG-CACUCUAAGGAAACUGCCGGCGA--UGA-GUUG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUAUAUCCAGGGCUACACACGUGCUACAAUGGU-UAUU-ACAGAGGGA---AGCAAUGCCGCGAGGUGGA-GCAAAUCCCC--AAAAAUAUUCGUAGUUGGGAUCGGAGUCUGCAACUCGACUCCGUGAACGUGGAAUCGCUAGUAAUCGCAGAUC-AGCUACGCUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACGAAAGUCUGC-UGU-ACCCGAAGAGGG-U-G-AGCU-AACC--AGCAA--UGGAGGCA-GCUCGCUAAGGU-AUGGUAGGUAAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUU
CP002054.1/854126-855678               UUUUCUGAGAAUU-UGAU-CUUGGUUCAGAUUGAACGCU-GG-CGG--CGUG-GAUGAGGCAUGCAAGUCGAACG-GAG------------CAAUUGUUU-----CGACGA-U-UG-------------------------------------------------------------------------------------------------------------------------------UU-UAG-UGGCGGA-AGGGUUAGUAAUGCAUAGAU--AAUUUGUCCUUAACUUG--GGAAUAACGGUUGGAAACGGCCGCUAAUACCGAAUGUGGCGA--UAU-UUGG--GCAU--CCG-AG-UA-A-C-GU-UAAA-GAAGGGGA---------------------------------------------UCUUAGGACCU-----UUCGGUUAAGGGAGAGUCUAUGUGAUAUCAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCUAUGACGUCUAGGCG-GAUUGAGAGAUUGGCCGCCAACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUCGCAAUGGAC-GGAAGUCUGACGAAGCGACGCCGCGUGUGU-GA-UGAAGGCU---CUAG--GGUUGUAAAGCACUUUCGCUUGGG-AAUAAG-AGAAGACGGUUA-AUACCCGCUG----GAUU----UGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGG-CGUGUAGGCGGAAAGGUA-AGUUAG-UUGUCAAAGAUCG-GGGCUCAACCC-CG-AGUCGGCAUCUAAUACUAUUU-UUCUA-GAGGAUAGAUGGAGAAAAGGGAAUUUCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAG--UGGCGAAGGCGCUUUUCUAAUUUAUACCUGACGCUAAG-GCGCGAAA-GCA-AGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCU-UGCCGUAAA-CGAU-GCAU--AC-UUGA-UGUG-GAUGGU--C----------------------------UCAA-CCCCAUCCGUGUC-------GGA-GCUAACGCGUUAAGUAUGCCGCC--UGAG-GAGUAC-ACUCGCAAGGGUGAAACUCAAA-AGAAUUGACGGGGGCCCG-CAC-AAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGGACCUUA-CCUGGGUUUGACAUGUAUAUG------------ACCGCGGCAG-AAAUGUCGUUU--U-CCGC----------------------------------AAGG-A----CAUAUACACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUAUCGUUAGUUGCC-AGCAC------UUAGG-------------GUG--GG-AACUCUAACGAGACUGCCUGGGU--UAA-CCAG-GAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGCCCAGGGCGACACACGUGCUACAAUGGC-CAGU-ACAGAAGGU---GGCAAGAUCGCGAGAUGGA-GCAAAUCCUC--AAAGCUGGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUC-AGCCAUAACGCCGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGU-UUU-ACCUUAAGUCGU-U-G-ACUC-AACC--CGCAA--GGGAGAGA-GGCGCCCAAGGU-GAGGCUGAUGACUAGGAUGA-AGU-CGUAACAAGGUAG-CCCUACCGGAAGGUGGGG---CU-GGAUCACCUCCUUU
M30790.1/1-1535                        -AUACGAAGAGUU-UGAU-CCUGGCUCAGGAUUAACGCU-GG-CGG--CGUG-CCUAAUACAUGCAAGUCGAACG-GA-------------AGUUUAAGC-----AAUUAA-A-CU-------------------------------------------------------------------------------------------------------------------------------UU--AG-UGGCGAA-CGGGUGAGUAACGCGUAAGC--AAUCUGCCCCUAAGACG--AGGAUAACAGUUGGAAACGACUGCUAAGACUGGAUAGGAGAC--AAG--AAG--GCAU--CUU--C-UU-G-U-UU-UUAA-AAGACC-------------------------------------------------UAGCAAUAG----GUAUGCUUAGGGAGGAGCUUGCGUCACAUUAGUUAGUUGGUGGGGUAAAGGCCUACCAAGACUAUGAUGUGUAGCCG-GGCUGAGAGGUUGAACGGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUAGGGAAUUUUCGGCAAUGGAG-GAAACUCUGACCGAGCAACGCCGCGUGAAC-GA-UGAAGUAU---UUCG--GUACGUAAAGUUCUUUUAUUAGGG-AAGGAA-UAAAUGAUG-------GAAAAAU----CAUUG--CUGACGGUACCUAAUGAAUAAGCCCCGGCUAACUAUGUGCCAGCAGCCGCGGUAAUACAUAGGGGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGGG-UGCGUAGGCGGUUAAAUA-AGUUUA-UGGUCUAAGUGCA-AUGCUCAACAU-UG-UGAUG-CUAUAAAAACUGUUU-AGCUA-GAGUAAGAUAGAGGCAAGCGGAAUUCCAUGUGUAGUGGUAAAAUGCGUAAAUAUAUGGAGGAACACCAG--UAGCGAAGGCGGCUUGCUGGGUCUUUACUGACGCUGAG-GCACGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GAGU--AC-UAAA-CGUU-GGG----------------------------------UAAA-----ACCAGUGUU-------GAA-GUUAACACAUUAAGUACUCCGCC--UGAG-UAGUAC-GUACGCAAGUAUGAAACUUAAA-GGAAUUGACGGGACUCCG-CAC-AAGCGGUGGAUCAUGUUGUUUAAUUCGAAGGUACCCGAAAAACCUCA-CCAGGUCUUGACAUGCUUCUG-----------CAAAGCUGUAG-AAACACAGUGG---AGGUU----------------------------------AU--------CAGUUGCACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUAUUGUUAGUUACC-AGCAC-----GUAAUG-------------GUG--GG-GACUUUAGCAAGACUGCCAGUGA--UAA-AUUG-GAGGAAGGUGGGGACGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACAAACGUGAUACAAUGGC-UGUU-ACAAAGGGU---AGCUGAAGCGCAAGUUUUUGGCGAAUCUCAA-AAAAACAGUCUCAGUUCGGAUUGAAGUCUGCAACUCGACUUCAUGAAGUUGGAAUCGCUAGUAAUCGCGAAUCCAGC-AUGUCGCGGUGAAUACGU-UCUCGGGGUUUGUACACACCGCCCGUCAAACCACGAAAGUUGGC-AAU-ACCCAAAGCCGG-U-G-GCCU-AACUU-CGCAAG-AAGAGGGA-ACCGUCUAAGGU-AGGGUCGAUGAUUGGGGUUA-AGU-CGUAACAAGGUAU-CCCUACCGGAAGGUGGGG---AU-GGAUCACCUCCUUU
ABDE02000010.1/183602-185109           UUUACGGAGAGUU-UGAU-CCUGGCUCAGAACGAACGCU-GG-CGG--CAUG-GAUUAGGCAUGCAAGUUGAACG-----------------AACUCCUU-----CGGGAG-U-G------------------------------------------------------------------------------------------------------------------------------------AG-UAGCGAA-AGGGUGAGGAACGCGUGAGU--AAUCUGCCCAUAAGUUG--GGAACAACAGUUGGAAACGACUGCUAAUACCGAAUGUGGCUA--UUG-ACCC--GCAU--GGG-UU-UU-U-G-GC-UAAA-GA----------------------------------------------------------UUUA------UCGCUUAUGGAUGAGCUCGCGUCCCAUUAGCUAGUUGGUGAGGUAACGGCCCACCAAGGCUACGAUGGGUAGCUG-GUCUGAGAGGAUGGUCAGCCACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUGGGCAAUGCGC-GAAAGCGUGACCCAGCAAUGCCGCGUGCAU-GA-UGAAGGCC---CUCG--GGUCGUAAAAUGCUGUCUCCCGUG-ACGAAU-AA---------------------------------UGACGGUAGCGGGGAAGGAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCGAGCGUUGUUCGGAUUUAUUGGGCGUAAAGGG-UCUGUAGGAGGUUUGUUA-AAUACG-AGGUGAAAUCCGG-GGGCUCAACUU-CC-GAAUUGCCUUGUAGACUGAUG-AACUA-GAGUACUGGAGAGGUAAGCGGAAUACCAGGUGUAGCGGUGGAAUGCGUAGAUAUCUGGUAGAACACCAA--UAGCGAAGGCAGCUUGCUGGACAGAAACUGACUCUGAA-AGACGAAA-GCA-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-UGCCGUAAA-CGUU-GUCA--AC-UUGA-UGUG-GGCGGA--U----------------------------UUAG-UCCUGUCCGUAUC-------GAA-GCUAACGCGAUAAGUUGACCGCC--UGGG-AACUAC-GGCCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGCUUAAUUCGAGGCAACGCGAAGAACCUUA-CCUGGGCUUGAAAUAUACCGG------------ACCGGCUGUG-AAAGCAGUCUU--CUCUUC------------------------------------GGAG----CUGGUAUACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUCGGUUAAGUCCGG-CAACGAGCGCAACCCGUGUCAUUAGUUGCC-AACAG-----GUAAUG-------------CUG--GG-GACUCUAAUGAGACUGCCUGUGU--UAA-GCAG-GAGGAAGGCGCGGAUGACGUCAAGUCAGUAUGGCCCUUACGCCCAGGGCUGCACACGUGCUACAAUGGG-GGGU-ACAAUGAGA---AGCGAAGUCGCGAGGCGGA-GCAAAUCUAC--AAAACCUCUCUUAGUUCAGAUUGCAGUCUGCAACUCGACUGCAUGAAGUUGGAAUCGCUAGUAAAUGCGUAUC-AGCUACGACGCAUUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGAU-UGC-ACCCGAAAUCGG-U-G-AUCU-AACC--UGCAA--AGGAAGAA-GCCGCCUAAGGU-GUGGUCGAUGACUGGGAUGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUU
GU565236.1/2-1524                      --CCCUUAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CUUAACACAUGCAAGUCGGACG-GUC------------AGGCUAUGA-----AGGUUC-G-CUGGAUU--------------------------------------------------------------------------------------------------------------------GGCCUGAU--AG-UGGCGGA-CGGGUGAGUAACGCGUGAGG---ACAUGGCUUCAGGAGG--GGGAUAACGUUUGGAAACGGACGCUAAGACCCCAUAUGCCGG--AAG--GUG--AAAG--UGA--U-CU-U-C-GG------------------------------------------------------------------AUCA--------GCCUGGAGAGUGACUCGCGUCCUAUCAGCUAGUUGGUGGGGUGAAGGCCUACCAAGGCGAUGACGGGUAGCCG-ACCUGAGAGGGUGGCCGGCCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGGCAAUGGGC-GCAAGCCUGACCCAGCGACGCCGCGUGGGG-GA-UGAAGUCU---UUCG--GGAUGUAAACCCUUGUUGUACGGG-ACGAAA-AC-------------------AA------------UGACGGUACCGUACGAGGAAGCCCCGGCAAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCGAGCGUUGUCCGGAAUUACUGGGCGUAAAGCG-CACGUAGGCGGGUUUUUA-AGUCGG-CCGUGAAAGGCAC-UGGCUCAACCG-GU-GCAUGUCGGUCGAUACUGGAA-GCCUU-GAGUAUGGGAGAGGGAACUGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCAG--UGGCGAAGGCGGGUUCCUGGUCCAUUACUGACGCUGAG-GUGCGAAA-GCC-GGGGGAGCGAACGGG-AUUAGAUACCCCGGUAGUCCC-GGCUGUAAA-CGAU-GGAU--GC-UAGG-UGUG-GGGGG--------------------------------GUUA---CCUUCUGUGCC-------GCA-GUUAACGCGAUAAGCAUCCCGCC--UGGG-GAGUAC-GAUCGCAAGAUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCACGUGGUUUAAUUCGAUGCAAACCGAAGAACCUUA-CCUGGGUUUGACAUG-CGCGUG----------GUACGGAGAUG-AAAGUUGAAGG--ACCCUGUAGA--------------------------GAUACAGGGA----GCGCG-CACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCAUCCAGUUGCC-AGCGA-----GUGAAG-------------UCG--GG-GACUCUGGAUGGACUGCCGGCGA--CAA-GCCG-GAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUAUGUCCAGGGCGACACACGUGCUACAAUGGC-CGGC-ACAACGGGA---AGCGAAGGGGCGACCCGGA-GCGGAUCCAAUCAAAGCCGGUCCCAGUUCGGAUUGGAGUCUGCAACCCGACUCCAUGAAGCUGGAAUCGCUAGUAAUCGCGGAUC-AGCCAAGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACCCGAGUUGGG-GGC-ACCCGAAGCCGG-A-G-GCUU-AACC--CGUAA--GGGAAGGA-UCCGUCGAAGGU-GCGUCUGGUAAGGGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUA
AF407680.1/1-1504                      -UCGAUUAGAGUU-UGAU-CCUGGCUCAAGGUGAACGCU-AG-CGG--CGGG-CCUAACACAUGCAAGUCGUGCG-----------------GAGGGGGC-----AACCCC-U-C------------------------------------------------------------------------------------------------------------------------------------AG-CGGCGGA-CGGGUGCGUAACACGUAGGU--AACCUGCCCCCAGGAGG--GGGAUAACCCUGGGAAACCAGGGCUAAUACCCCAUAAAGCAA--GGG-CACC--GCAU--GGU-GG-GC-U-U-GC-UAAA-GCC---------------------------------------------------------GAAA-----GGCGCCUGGGGAGGGGCCUGCGGCCGAUUAGCUAGUUGGUAGGGUAACGGCCUACCAAGGCGAUGAUCGGUAGCUG-GUCUGAGAGGACGGCCAGCCACAGGGACACUGAGAUACGGGUCCCACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGGCAAUGGGC-GAAAGCCUGACCCAGCCACGCCGCGUGCCG-GA-UGAAGGUC--CUAUG--GAUUGUAAACGGCUUUUCCCAGGG-AGAAAA-AGGGAGGU----------CGCCU-----CCCU--CUGAUCGUACCUGGGGAAUAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAGACGUAGGGCGCAAGCGUUACCCGGAGUUACUGGGCUUAAAGGG-UCCGUAGGCGGCUCGGCA-CGUCCU-GGGUCAAAGCCCU-CCGCUCAACGG-AG-GAACGGCUUAGGAUACGGCCG-AGCUA-GAGUCAGUCUGGGGGCGCUGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCGU--UCGCGAAGGCGGGCGCCUAAGGCUGUACUGACGCUGAG-GGACGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCCUAAA-CGAU-GCGC--AC-UAGU-CGGA-CGCCC--------------------------------GAAA---GGGUGUCUGGC-------GAA-GGGAAACCGUUAAGUGCGCCGCC--UGGG-GAGUAC-GCUCGCAAGGGUGAAACUCAAA-GGAAUUGGCGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUGGUACGCGAAGGACCUUA-CCUGGGCUUGAACGCACCACG-----------ACCGCCUGAGG-AAACUCGGGCUUUCCCCUU----------------------------------CGGGGG---ACGGGGUGCGAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCCGUAGUUGCC-CGCC--------------------------AG--GG-AACUCUACGGGGCCCGCUUCCG---CAA-GGGA-GAGGAAGGAGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGCCCAGGGCGACACACGUGCUACAAUGGGAGGGG-ACAGCGGGU---AGCAACCGGGCGACCGGAA-GCCAAUCCCUC-AAACCCCCCCUCAGUUCAGAUUGGAGUCUGCAACUCGACUCCAUGAAGGCGGAAUCGCUAGUAAUCGCGGAUC-AGCCAUGCCGCGGUGAAUACGU-UCCCGGGCCUUGCACACACCGCCCGUCACGCCAUGGGAGCCGGG-GGC-ACCCAAAGGCGC-C---------------UAAC--C--------CGCGCUCAAGGU-GAACCCGGUGACUGGGGCGA-AGU-CGUAACAAGGUAG-UCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUA
AF268004.1/16-1500                     GGCCAGUAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CGG--UAUG-CUUAACACAUGCAAGUCGAACG-GU-----------------CUCUU-----CGGAG-------------------------------------------------------------------------------------------------------------------------------------AU--AG-UGGCGGA-CGGGUGAGUAACGCGUGAGA---AUCUAGCUUCAGGUCG--GGGACAACCACGGGAAACUGUGGCUAAUACCGGAUAUG------------CC--GAGA--GGU--------------GAAA-GGC--------------------------------------------------------UU--------GCUGCCUGAAGAUGAGCUCGCGUCUGAUUAGCUAGUAGGUGUGGUAAAAGCGCACCUAGGCGACGAUCAGUAGCUG-GUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGC-GAAAGCCUGACGGAGCAAUACCGCGUGAGG-GA-GGAAGGCU---CUUG--GGUUGUAAACCUCUUUUCUCAGGG-AAGAAA-AA-------------------AA------------UGACGGUACCUGAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGGG-UCCGCAGGUGGCUAUGUA-AGUCUG-CUGUUAAAGAACC-UAGCUUAACUA-GG-UAAAAGCAGUGGAAACUACAA-GGCUA-GAGUGCGUUCGGGGUAGAGGGAAUUCCUGGUGUAGCGGUGAAAUGCGUAGAUAUCAGGAAGAACACCAG--UGGCGAAGGCGCUCUACUAGGCCGCAACUGACACUGAG-GGACGAAA-GCU-AGGGGAGCGAAUGGG-AUUAGAUACCCCAGUAGUCCU-AGCCGUAAA-CGAU-GGAU--AC-UAGG-CGUG-GCUUGU--A----------------------------UCGA-CCCGAGCCGUGCC-------GGA-GCUAACGCGUUAAGUAUCCCGCC--UGGG-GAGUAC-GCACGCAAGUGUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUA-CCAAGACUUGACAUG-UCGCG------------AAUCUCUCUG-AAAGGAGAGAG--UGCCUU----------------------------------CGGGAG----CGCGAACACAG-GUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUCGUUUUUAGUUGCC-AGCA------UUAAGU--------------UG--GG-CACUCUAGAGAGACUGCCGGUGA--CAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUACGUCUUGGGCUACACACGUACUACAAUGCU-ACGG-ACAAAGGGC---AGCUACACAGCAAUGUGAU-GCAAAUCUCACAAAACCGUAGCUCAGUUCAGAUCGCAGGCUGCAACUCGCCUGCGUGAAGUCGGAAUCGCUAGUAAUUGCAGGUC-AGC-AUACUGCAGUGAAUUCGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGU-CAC-GCCCGAAGUCGU-U-A-CCCC-AACU--GUUYG--CAGAGGGG-GAUGCCGAAGGC-AGGACUGGUGACUGGGGUGA-AGUCCGUAACAAGGUAG-C-----CGUAGGUCAUAG---CU-GUCUUCCUGCUAA-
AAXS01000094.1/4839-6350               UUUAUGGAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CGG--CGUG-CCUAAUACAUGCAAGUCGUGCG-GCAG---------CGCGAGUAGUU-----UACUAC-U-UGG----------------------------------------------------------------------------------------------------------------------------CGGC-GAG-CGGCGAA-CGGCUGAGUAACGCGUAGGA---AUGUACCCCAAAGUGA--GGGAUAAGCUCCAGAAAUGGAGUCUAAUACCGCAUAUG-----------GUC--UUCG--GAU--------------UAAA-GCU---------------------------------------------------------UUCG-----AGCGCUUUGGGAACAGCCUGCGUCCGAUUAGGUUGUUGGUGAGGUAAUGGCUCACCAAGCCGACGAUCGGUAGCUG-GUCUGAGAGGAUGACCAGCCAGACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUAAGGAAUCUUCCACAAUGGGG-GCAACCCUGAUGGAGCAACGCCGCGUGCAG-GA-CGAAGGCC---UUCG--GGUUGUAAACUGCUUUUAUGAGCG-AAGAAU--U---------------------------------UGACGGUAACUCAUGAAUAAGGGCCGGCUAACUACGUGCCAGCAGCCGCGGUCAUACGUAGGGCCCGAGCGUUAUCCGGAGUGACUGGGCGUAAAGAGUUGCGUAGGCGGUUUGUUA-AGCAGA-UAGUGAAAUCAUA-UGGCUCAACCAUUA-UGGCUAUUAUCUGAACUGGCA-AACUC-GAGAAUGGUAGAGGUAACUGGAAUUUCUAGUGUAGGAGUGAAAUCCGUAGAUAUUAGAAGGAACACCAA--UGGCGUAGGCAGGUUACUGGACCAUUUCUGACGCUAAG-GCACGAAA-GCG-UGGGGAGCGAACCGG-AUUAGAUACCCGGGUAGUCCA-CGCCGUAAA-CUAU-GGAU--GC-UAGC-UGUU-GGAGGU--A----------------------------UCGA-CCCCUUCAGUAGC-------GAA-GCUAACGCGUUAAGCAUCCCGCC--UGUG-GAGUAC-GGCCGCAAGGCUAAAACAUAAA-GGAAUUGACGGGGACCCG-CAC-AAGUAGCGGAUGAUGUUCUUUAAUUCGAUGAUAAGCGAAGAACCUUA-CCAGGGCUUGACAUC-CUGCG------------AAUUUUUCCG-AAAGGAAAAAG--UGCCCCAAGAGCACAUAAAAAGUGAUUUUGUGUGUUGUUGGGGGAA----CGCAGUGACAG-GUGCUGCAUGGCCGUCGUCAGCUCGUGUCGUGAGAUGUUUGGUUAAGUCCAU-UAACGAGCGCAACCCUUGCAAAUAGUUG-------------GAUUUU------------------------UCUAUUUGGACUGCCCCGG---CAA-CGGG-GAGGAAGGAGGGGAUGAUGUCAGGUCUUUAUUGCCCUUACGCCCUGGGCUAGAAACGUCAUACAAUGGC-CAGU-ACAAUGCGC---AGCGAAGCCGCGAGGUGAA-GCAAAUCGCAUCAAAGCUGGUCCCAGUUCGGAUAAGAGGCUGAAACUCGCCUCUUUGAAGCCGGAGUUACUAGUAAUCGCAGGUC-AGC-AUACUGCGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCAAACCAUGAAAGUCGGG-GGC-ACCCGAAGUCCU-A----------AC---UU-----GU------UAGGCCUAAGGU-GAACCAGAUGAUUGGGGUUA-AGU-CGUAACAAGGUAU-CCGUAGCGGAAGCUGCGG---AU-GGAUUACCUCCUUU
CP001364.1/780549-779064               ACAAUGUAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CCUAAUGCAUGCAAGUCGAACG----------------CAGCAGGCG-----UGCCUGGC-UG-----------------------------------------------------------------------------------------------------------------------------------CG-UGGCGAA-CGGCUGAGGAACACGUGGGU--GACCUGCCCCGGAGUGG--GGGAUACCCCGUCGAAAGACGGGACAAUCCCGCAUACG-----------CUC--GACG--GAG--------------GAAA-GCC---------------------------------------------------------GCAA-----GGCGCUCUGGGAGGGGCCUGCGGCCCAUCAGGUAGUUGGUGUGGUAACGGCGCACCAAGCCAAUGACGGGUACCCG-GUCUGAGAGGACGACCGGGCAGACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGCAAGGAAUUUUCCCCAAUGGGC-GCAAGCCUGAGGGAGCAACGCCGCGUGGAG-GA-CGACGGCC---UUCG--GGUUGUAAACUCCUUUCGGGUGGG-ACGAUG--C---------------------------------UGACGGUACCACCAGAAGCAGCCCCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGGGGCAAGCGUUGUCCGGAGUUACUGGGCGUAAAGGG-CGCGCAGGCGGUGGGCUG-CGUCGG-CGCUGAAAGCGCC-CCGCUUAACGG-GG-CGAGGCGCGCCGAUACGAGUC-CACUC-GAGGCAAGCAGAGGGUGGCGGAAUUCCGGGUGGAGCGGUGAAAUGCGUAGAGAUCCGGAGGAACGCCGG--UGGGGAAGCCGGCCACCUGGGCUUGACCUGACGCUGCG-GCGCGACA-GCG-UGGGGAGCAAACCGG-AUUAGAUACCCGGGUAGUCCA-CGCCGUAAA-CGAU-GCCG--GC-UCGG-CGUC-UGGCGCACG----------------------------UUGG-UGUGCUGGGUGCC-------UUA-GCUCACGCGGUAAGCCGGCCGCC--UGGG-GACUAC-GAGCGCAAGCUUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCAGCGGAGCGUGUGGUUUAAUUCGACGCAACACGAAGAACCUUA-CCCGGACUUGACAUGGUGCUG------------CAUCCCCUGG-AAACAGGGGCG--CCUUU-------------------------------------GAGG----GUGCACCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUCAGUCCCG-CAACGAGCGCAACCCGUGUCGGUAGUUA-------------CAGGUG------------------------UCUACCGAGACUGCCGCCGU--GACCGGCG-GAGGAAGGCGCGGAUGACGUCAAGUCAGCAUGGCCCUUACGUCCGGGGCGACACACACGCUACAAUGGC-CACG-ACAAUGCGU---UGCCAAGCCGCAAGGUGGA-GCUAAUCGCCU-AAACGUGGUCUCAGUGCAGAUCGGGGGCUGCAACUCGCCCCCGUGAAGGCGGAGUUGCUAGUAACCGCGUAUC-AGCCAUGGCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGGGAGUGGCC-AAU-GCUUGAAGUCCG-U-G-UGCU-AACCCCAGUCG--GGGAGGCA-GCGGCCGAGGGC-AGGGGCCGCGACUGGGACGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
JN178264.1/6-1519                      CGCCCUUAGAGUU-UGAU-CCUGGCUCAGAACGAACGCU-GG-CGG--CGUG-CUUAACACAUGCAAGUCGAACG-GGA-----------AAGGGGGCUU-----CGGCUC-C-UGA-----------------------------------------------------------------------------------------------------------------------------GUA-GAG-UGGCGAA-CGGGUGCGUAACACGUGAGU--AAUCUGCCUCAGACACU--GGGAUAACACUUCGAAAGGGGUGCUAAUACCGGAUAGAUCCC--UUA--GGU--GAU---GCC--G-GA-G-G-GG-GAAA-GG----------------------------------------------------------UUCG------CCGGUCUGAGAUGAGCUUGCGGCCCAUUAGCUAGUUGGCGGGGUAAUGGCCCACCAAGGCGACGAUGGGUAGCUG-GUCUGAGAGGAUGAUCAGCCACACUGGCACUGAGACACGGGCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGCGCAAUGGGC-GAAAGCCUGACGCAGCAACGCCGCGUGAAG-GA-UGAAGGCU---CUCG--AGUCGUAAACUUCUGCCUGGGGGA-AAGAUG--A---------------------------------UGACGGUACCCCCAAAGCAAGCCCCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGAAGGGGCAAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGG-CGCGU-AGCGGCUCCAUA-UGUCGG-CGGUGAAAGCAUA-CAGCUCAACUG-UA-UUGA-GCCGCGGAAACUGUGG-GGCUU-GAGGCUGGGAGGGGCUGGUGGAAUUCCCUGUGUAGCGGUGAAAUGCGUA-AGAUGGGGGAGAACACUUG--UGGCGAAGGCGGGCAGCUGGACCAGUUCUGACGCUUAG-GCGCGAA--GCG-UUGGGAGCCAACAGGAAUUAAAUACCCUGGUAGUCCA-CGCUGUAAACCGAU-GGGCCAACUUAGG-UGUC-GGCGGU--C----------------------------UUUA--GUCGUCG-UGCC-------GGC-GCUAACGCAGUAAGUGCCCCGCC--UGGG-GAGUAC-GGUCGCAAGGCUGAGACUCAAA-CGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCUAGGUUUGACAUGGACGAG------------AUGGCCGGUG-AAAGCUGGCUU--C-CCUU----------------------------------CGGG-G----CUGGUCCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCCUCUGUUGCU-ACCGG-----GUCGUG-------------CCG--GG-CACUCUGAGGGGACUGCCUCGGU--UAA-CGGG-GAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCUUUAUGCCUAGGGCUACACACGUGCUACAAUGGU-CAGG-ACAAAGGGC---UGCUACCNCCCAAGAAGAC-GCGAAUCCCAA-AAACCUGGCCCCAGUUCGGAUGGUCGGCUGCAACUCGCCGGCUUGAAGCUGGAAUCGCUAGUAAUCGGAGAUC-AGC-ACGCUCCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACGAAAGCUGCG-UGU-ACCCGAAGUCGC-U-G-AGCC-AACC--CGCAA--GGGAGCCNCGGCGCCGAAGGU-AUGCGGGGUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUU-
CP001275.1/984658-983137               GGGAUGGAGAGUU-UGAU-CCUGGCUCAGGGGGAACGCU-GG-CGG--CGUG-CCUAAUGCAUGCAAGUCGGACG-GG-------------AGCACGCUC-----UGGCGU-G-CC-------------------------------------------------------------------------------------------------------------------------------GA-CCG-UGGCGGA-CGGGUGCGUAACACGUGGGG--AACCUGCCCGGGUGCGG--GGGAUAACCCGGGGAAACUCGGGCUAAUACCCCAUACGCUUG--GCU--GGC--GGUG-GGCC--G-GC-C-A-AG-GAAA-GGCGCA-------------------------------------------------GGCGACUGU-----GCUGUGCUCGGAGGGCCCUGCGGCCUAUCAGCUAGACGGUAGGGUAACGGCCUACCGUGGCGAUGACGGGUAGCUG-GUCUGAGAGGAUGGCCAGCCACACGGGCACUGAGACACGGGCCCGACUCCUACGGGAGGCAGCAGCAGGGAAUCUUCCGCAAUGGGG-GCAACCCUGACGGAGCGACGCCGCGUGCGG-GA-GGAAGCCC---UUCG--GGGUGUAAACCGCUGUUCGGGGGG-ACGAUC-GA--------------------G------------CGACGGUACCCUCGGAGCAAGUCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAGACGUAGGGGGCGAGCGUUACCCGGAGUCACUGGGCGUAAAGGG-CGUGUAGGCGGCUGGGUA-CGCCGC-GUGUGAAAGUCCC-CGGCUCAACCG-GG-GAGGGUCGCGCGGGACGGCCU-GGCUC-GAGGGCGGGAGAGGCGGGUGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAGAUCGGGAGGAACGCCGG--UGGCGAAGGCGGCCCGCUGGCCCGUACCUGACGCUGAG-GCGCGAAG-GCG-UGGGGAGCGAACCGG-AUUAGAUACCCGGGUAGUCCA-CGCAGUAAA-CGAU-GCGG--GC-GAGG-UGUG-GGUGGU--G----------------------------UUGA-CCCCAUCCGUGCC-------GGC-GCCAACGCAGUAAGCCCGCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCAGCGGAGCGUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCAGGGCUUGACAUGCCACCG------------AACCUGGCUG-AAAGGCUGGGG--UGCCCGG-------------------------------UGAGGGAG----CGGUGGCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUCGGGGUCAGUUA-----CGC---------GG-------------GUG--------UCUGACCCGACUGCCGGGGA--AAG-CCCG-GAGGAAGGAGGGGAUGACGUCAAGUCAGCAUGGCCCUGACGCCCUGGGCGACACACACGCUACAGUGAC-CGGG-ACAGUGGGC---AGCGAAGGGGCGACCUGGA-GCCAAUCCCGC-AAACCCGGUCGUGGUGGGGAUCGCAGGCUGCAACCCGCCUGCGUGAACGCGGAGUUGCUAGUAACCGCCGGUC-AGCCAUACGGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGCUGGC-UUC-ACCUGAAGCCGG-U-G-GGCC-AACCGGCGCACGCUGGGGGCA-GCCGUCGAGGGU-GGGGCUGGUGAUUGGGACGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
CU466930.1/1801247-1799646             AUGAUGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-GAUUAGGCAUGCAAGUCGAACG-GUA------------UAAACCUUU-----CGGGGU-U-UA-------------------------------------------------------------------------------------------------------------------------------GA-GAG-UGGCGAA-CGGGUGAGUAACACGUAGGU--AAUCUACCCUCAAAACG--GGGACAACCCAGGGAAACUUGGGCUAAUACCGGAUGCG-UGC--AAG--CAA--UGUU--UUG--G-UU-G-U----UAAU-GCUAUUCACGGAAGUGAGUAGUGUUAAUGGUUGAGAGCAUUAUUUGCAUAAAAGGUGGCAUUUGC---UGCCGUUUGAGGAUGAGCCUGCGUCCUAUUAGUUAGUUGGUGAGGUAAUGGCUUACCAAGGCGAUGAUAGGUAGGCG-GCCUUAACGGGUGGUCGCCCACACUGGGAUUGAGAGACGGCCCAGACUCCUACGGGAGGCAGCAGUCGAGAAUAGUCUACAAUGGAC-GGAAGUCUGAUAGUGCGACGCCGCGUGAAC-GA-AGAAUCCC---UUCG--GGGUGUAAAGUUCUUUUAUACGUG-AGCAGU-GCCCUUUAUAUG-AAUAGUAUAG----AGGGA--GGGAUUUAAGCGUAUGAAUAAGCAACGGCUAACUCCGUGCCAGCAGCCGCGGUAACACGGGGGUUGCAAGCGUUGUCCGGAAUUACUAGGCGUAAAGUG-CAGGUAGGCGGAUAGAUA-AGUUUA-AGGUUAAAGGCUA-CGGCUUACCCG-UA-GUAAGGCGUUAGAUACUGUUU-AUCUG-GAAUGCGGUUGAGGGAGACAGAAUUCCUGGUGUAGCGGUGGAAUGCGCAGAGAUCAGGAGGAAUACCGA--AGGCGAAGGCAGUCUUCUAAGCCGAUAUUGACGCUAAA-CUGCGAAG-GUG-UGGGGAUCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CACAGUAAA-CGAU-AAUC--AC-UAGG-UGUU-GGGUUC--G----------------------------UAUA--GGACUCGGUGCC-------GGA-GCUAACGCGAUAAGUGAUUCGCC--UGGG-GAGUAC-GAUCGCAAGGUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCCGGUCUUGACAUC-UGCAG------------AAUUCUUCAG-AGAUGGAGGAG--UGCCGGCU------------------------------UGCCGGAG----CUGCAAGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCUUUCAGUUGCC-AUCA------UUAAGU--------------UG--GG-GACUCUGGAAGGACCGCUGCGGUAACAA-CGCA-GAGGAAGAUGGGGACGAGGUCAAGUCAUCAUGGUCCUUAUGACCGGGGCUACACACGUGCUACAAUGGU-AGUU-ACAGAGGGG---AGCGAAGCAGUGAUGUGGA-GCGAAUCUCAG-AAAAGCUACCCAAGUUCGGAUUGAGGUCUGCAACUCGACCUCAUGAAGCCGGAAUCGCUAGUAAUCGCGCAAC-AUC-AUGGUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGUCAGCCGAGUGGAG-UGC-ACCCGAAGGAGG-U-G-AGCU-AACC--CGUGA--GGGAAGCA-GCUUUCGAAGGU-GUGCUUUGCGAGGAGGACUA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
CP001998.1/1562911-1561358             GAUUCGGAGAGUU-UGAU-CCUGGCUCAGAGUGAACGCU-GG-CGG--CGUG-GUUAAGACAUGCAAGUCGAACG-GGAU---------UGUUUAAGUUG-----ACGCUU-C-GGUUGAUUC----------------------------------------------------------------------------------------------------------------UUAAACAUGA-GAG-UGGCAAA-CGGGUGCGUAACACGUAAGC--AACCUGCCCUAAAGUUU--GGGAUAGCUCGAGGAAACUCGAAUUAAUACCGGAUGUGGCUC--GGU--AAC--UCAU--GUU--A-CUAG-A-GC-UAAA-GCU-------------------------------------------------------UGAGAU-----GGCGCUUUAGGAGGGGCUUGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCAAAGACGGGUAGCUG-GUCUGAGAGGAUGAUCAGCCACACUGGAACUGAGACACGGUCCAGACACCUACGGGUGGCAGCAGUUUCGAAUCAUUCACAAUGGGG-GAAACCCUGAUGGUGCAACGCCGCGUGGGG-GA-UGACGGCC---UUCG--GGUUGUAAACCUCUGUCACCAAGG-AGCAAC-AAGCAGGU---------UCAUAGC---CUGCC--CUGAGUUAACUUGGAGAGGAAGCAGUGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGACUGCAAGCGUUACUCGGAUUCACUGGGCGUAAAGGG-UGCGUAGGCCGCUAAGCG-UGUCGG-GUGUGAAAUCUCG-GGGCUCAACCU-CG-AAACUGCGCCCGAAACUGUUU-AGCUA-GAGUGUCGGAGAGGUAAGCGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAGGAACACCAA--UGGCGAAGGCAGCUUACUGGACGACAACUGACGCUGAG-GCACGAAA-GCA-UGGGUAGCGAAAGGG-AUUAGAUACCCCUGUAGUCCA-UGCCGUAAA-CGUU-GUAC--AC-UAGG-UCUU-GGGGGU--U----------------------------UCGA-CCCCUUCAGGACC-------CCA-GCUAACGCGAUAAGUGUACCGCC--UGAG-GACUAC-GGCCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGCUUAAUUCGAUGCAACGCGAAGAACCUUA-CCUAGGCUUGACAUCUAUAGG-----------ACGGUUUCCAG-AGAUGGAUUCU--UCCCUU----------------------------------C-GGGG----CUUAUAGACAG-GUGCUGCAUGGCCGUCGUCAGCUCGUGUCGUGAGAUGUUUGGUUAAGUCCAG-CAACGAGCGCAACCCUCGUCCUUAGUUGCC-AGCAC-----GUAAUG-------------GUG--GG-GACUCUAAGGAGACAAACUUCUU--UCA-GAAG-UGGGAAGGUGGGGAUGACGUCAGGUCAGUAUGGCCCUUACGCCUAGGGCUGCACACGUGCUACAAUGCC-CGGU-ACAGUGGGA---CGCAAUACCGCGAGGUGGA-GCAAAUCCUC--AAAACCGGGCCCAGUUCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUGACGUAUC-AGCUACGACGUCGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGAAAGCCGGU-UCU-GCCCGAAGUACG-U-G-AGUU-AACU---UC-----GGAGACA-GCGUCCUAAGGU-AGGGCUGGUGAUUGGGAUGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUU
BX842648.2/123558-125071               AAACUGGAGAGUU-UGAU-UCUGGCUCAGAACAAACGCU-GG-CGG--CGUG-CCUAAUACAUGCAAGUCGAACG-GGG------------AAAGCUUUC-----GGGUGA-G-UA-------------------------------------------------------------------------------------------------------------------------------CU--AG-UGGCGCA-CGGGUGAGGAACGCGUGGAU--AAUCUGCCUUAGAGUGG--GGGAUAACUAGUCGAAAGAUUAGCUAAUACCGCAUAAGACCA--CAG-GAGC--UGCG--GCU-CU-AG-G-G-GU-CAAA-GG----------------------------------------------------------UUUU------UCGCUCUAAGAUGAGUCCGCGUAAGAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCGACGAUCUUUAACUG-GUCUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUAUUGCACAAUGGAG-GAAACUCUGAUGCAGCGACGCCGCGUGAGU-GA-UGAAGGCC---UUCG--GGUCGUAAAGCUCUGUCGCAGGGG-AAUAAC-AC-------------------AA------------UGAAUGUACCCUGUAAGAAAGGAUCGGCUAACUUCGUGCCAGCAGCCGCGGUAAGACGAGGGAUCCUAGCGUUGUUCGGAAUUAUUGGGCGUAAAGCG-GAUGUAGGUGGCUUUGUA-AGUCAG-AUGUGAAAGCCCA-GGGCUCAACCC-UG-GAAGUGCAUUUGAUACUGCGA-AGCUU-GAGUGUCGGAGAGGUUACUAGAAUUGUUGGUGUAGUGGUGAAAUACGUAGAUAUCAACAGGAAUACCGG--AGGCGAAGGCGGGUAACUGGCCGAACACUGACACUGAG-AUCCGAAA-GCG-UGGGGAUCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GGAU--AC-UUGU-UGUU-GGAGGU--A----------------------------UUGA-CCCCUUCAGUGAC-------GAA-GCUAACGCGUUAAGUAUCCCGCC--UGGG-GAGUAC-GGUCGCAAGAUUAAAACUCAAA-GAAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUA-CCUAGGCUUGACAUG-UACUGG----------AAGACUGGCAG-AAAUGUC-GUC--GCCCGC----------------------------------AAGGGU----CGGUA-CACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCAUUUAGUUGCC-AGCA------UUCAGU--------------UG--GG-CACUCUAGAUGGACUGCCGGUGU--UAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUGCCUAGGGCUACACACGUGCUACAAUGGU-AGUC-ACAGAGCGA---AGCUAAGCCGCGAGGUAGA-GCAAAUCGCUU-AAAAGCUAUCUAAGUUCAGAUUGAUCUCUGCAACUCGAGAUCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUC-AGA-AUGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGAAAGUUGGC-UGU-ACCAGAAGUCGC-U-G-CGCU-AACC---GCAA---GGAGGCA-GGCGCCCAAGGU-AUGGUCGAUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUU
CAEM01000062.1/13-1523                 UCAACGGAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCGAACG-AUG-----------AAACCGCCCC-----CGGGCG-G-AC-------------------------------------------------------------------------------------------------------------------------------AUGAAG-UGGCGAA-CGGGUGAGUAACACGUGACC--GACCUGCCCCCCGCCCA--GGGACAGCCCCCCGAAAGGGGGAUUAAUACCUGGUACUCCGG--GAG-CGGC--GCAU--GCC-GC-CC-C-C-GG-GAAA-GC----------------------------------------------------------UCUC------GCGGCGGGGGAUGGGGUCGCGGCCCAUCAGGUAGACGGCGGGGCAGAGGCCCACCGUGCCGACGACGGGUAGCCG-GGUUGAGAGACCGACCGGCCACAUUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGCGCAAUGGGG-GCAACCCUGACGCAGCAACGCCGCGUGCGG-GA-CGAAGGCG---UCCG--CGUCGUAAACCGCUUUCAGCGGGG-AACACC-UA--------------------A------------CGAGGGUACCCGCAGAAGAAGCCCCGGCUAAAUACGUGCCAGCAGCCGCGGUAAUACGUAUGGGGCGAGCGUUAUCCGGAUUCAUUGGGCGUAAAGCG-CGCGUAGGCGGAGCGCUA-AGCGGG-ACCUCUAACCCGA-GGGCUCAACCC-CC-GGCCG-GGUCCCGAACUGGCG-CUCUC-GAGUGCGGUAGGGGAGAGCGGAAUUCCCGGUGUAGCGGUGGAAUGCGCAGAUAUCGGGAAGAACACCGA--CGGCGAAGGCAGCUCUCUGGGCCGAAACUGACGCUGAG-GCGCGAAA-GCU-GGGGGAGCGAACAGG-AUUAGAUACCCUGGUAGUCCC-AGCCGUAAA-CGAU-GGGC--GC-UAGG-UGUG-GGGGAU--------------------------------GAG--AUCCCCCGUGCC-------GCA-GCCAACGCAUUAAGCGCCCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCAGCGGAGCAUGUGGCUUAAUUCGAAGCAACGCGAAGAACCUUA-CCAGGGCUUGACAUG-CAGGU------------GAAGCGGCGG-AGACGCCGUGG----CCGA----------------------------------GAGGA-----GCCUG-CACAG-GUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCCCGUGUUGCC-AGCA------UUCAGU--------------UG--GG-GACUCGCGGGGGACUGCCGGCGU--CAA-GCCG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGCCCUGGGCCGCACACGUGCUACAAUGGC-CGGU-ACAGAGGGU---UGCGACCCCGCGAGGGGGA-GCGGAUCCCGC-AAAGCCGGCCCCAGUUCGGAUCGGAGGCUGCAACCCGCCUCCGUGAAGCCGGAGUUGCUAGUAAUCGCGGAUC-AGC-ACGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACCCGAGUCGUC-UGC-ACCCGAAGCCGC-C-G-GCCG-AACCC-UUUCA--GGGGCGGA-GGCGUCGAAGGU-GUGGAGGGUGAGGGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
CP002175.1/779494-781044               UUUAUGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CUUAACACAUGCAAGUCGAACGGUCU------------ACCUCGACUGAUACCUUCGG-G-UUGAAGACG-----------------------------------------------------------------------------------------------------------------AGAUCUAGA-UAG-UGGCGGA-CGGGUGAGUAACACGUGAAU--AAUCUGUCCUCAAGUCU--GGGAUAACCUGGCGAAAGUCGGGCUAAUCCGAGGUAAGCUGA--GAG-UGUG--GCAU--CAC-AC-AA-U-C-AG-AAAA-GGUG------------------------------------------------------GCUCUGC---CAUCGUUUGAGGAGGAGUUCGCGGUAGAUUAGCUAGCUGGUGAGGUAAUGGCUCACCAGGGCAACAAUCUAUAGCUG-GUCUGAGAGGACGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUCUUCCACAAUGGGC-GAAAGCCUGAUGGAGCAACGCCGCGUGAGU-GA-AGAAGGUC---UUAG--GAUUGUAAAGCUCUGUCCUUAGGG-AAGAAC-CGUGGGUAUAG---UAAAUGCUA----CCCAC--CUGACGGUACCUUUGGAGGAAGCACUGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGAGUGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGG-UACGCAGGCGGAUAAUCA-AGUCAA-GCGUGAAAGGUGU-CGGCUUAACCG-AC-AGACUGCGUUUGAAACUGGUU-AUCUU-GAGUGUAACAGAGGAGAGUGGAAUUCCUAGUGUAGUGGUGAAAUACGUAGAUAUUAGGAAGAACACCAG--UGGCGAAGGCGACUCUCUGGGUUAACACUGACGCUGAG-GUACGAAA-GCU-GGGGGAGCGAACGGG-AUUAGAUACCCCGGUAGUCCC-AGCCGUAAA-CGAU-GGAU--AC-UAGG-UGUU-GGAGGU--U----------------------------CGAA--UCCUUCAGUGCC-------GGA-GUUAACGCAUUAAGUAUCCCGCC--UGGG-GAUUAC-GAUCGCAAGAUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCGAGAAUUGACAUC-CCGUG------------ACCAUCUAUG-AGAGUAGAAUU--UAGCACU-------------------------------UUGUGCUA----CACGGAGACAG-GUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUUCUUAGUUGCC-AGCGA-----GUAAUG-------------UCG--GG-GACUCUAAGAAGACUGCCGGUG---AAA-GUCG-GAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGCCCUUUAUAUCUCGGGCUACACACGUGCUACAAUGGU-UGAU-ACAGAGGGG---AGCUAAGCUGCGAAGUGGA-GCAAAUCCUUG-AAAAUCAAUCCCAGUUCGGAUUGCAGGCUGCAACUCGCCUGUAUGAAGUUGGAAUCGCUAGUAAUCGCAGGUC-AGC-AUACUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCAAUCGAGUUGGG-UGC-ACCAGAAGUCAU-C---------------UGCG-----------GAUGCCAAAGGU-GUGCCCGGCAAGAGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
AY858434.2/23-1554                     CUAGUGAUGAGUUUUGAU-CUGGGCUCAGGACGAACGCU-GG-CGG--CGUG-CUUACCACAUGCAAGUCGAACGAAGC------------UGACGAAAU-----GAUUCU-U-UCGGAAAGAAU------------------------------------------------------------------------------------------------------------UCAGAUAUGACU-GAG-UGGCGGA-CGGGUGAGUAACGCGUGAGC---ACCCUGCCCUCGGAGG--GGGAUAGUGUCUGAAACGGGACAGUAAUACCGCAUAAAGUUA--AGG-AAUG--GCAU--CAU-AC-CU-U-A-AC-CAAA-GA----------------------------------------------------------UUAU------UCGCCGAGGGAUGGGCUCGCGUCUGAUUAGAUAGUUGGUGGGGUAACGGCCUACCAAGUCGACGAUCAGUAGCCG-GACUGAGAGGUUGAUCGGCCACAUUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGG-GAAACCCUGAUGCAGCAACGCCGCGUGGAG-GA-AGACGGUU---UUCG--GAUUGUAAACUCCUGUUCUUAGGG-AAGAAG-AC-------------------AG------------UGACGGUACCUAAGGAGCAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAAUUACUGGGUGUAAAGGG-AGCGCAGGCGGGAAAGCA-AGUCAG-YYGUGAAAUCCAA-UGGCUCAACCA-UU-GAACUGCAGUUGAAACUGUUU-UUCUU-GAGUGAWGUMGAGGUUGGCGGAAUUCCGAGUGUAGCGGUGAAAUGCGUAGAUAUUCGGAGGAACACCGG--UGGCGAAGGCGGCCAACUGGGCUUUUACUGACGCUGAG-GCUCGAAA-GUG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CACUAUAAA-CGAU-GUUC--GC-UAGG-UGUG-GGGGGU--C----------------------------UGAC--CCCUUCUGUGCC-------GCA-GCAAACGCAAUAAGCGAACCACC--UGGG-GAGUAC-GAUCGCAAGAUUGAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCAGUGGAUUAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCGGCGCUUGACAUC-CUGCU------------AACGAAAUGG-AGACAUAUUAG-GUGCCCUU--------------------------------CGGGGAA----AGCAGAGACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCAUUAGUUGCU-AC---------GCAAG------------------AG-CACUCUAAUGGGACCGCUACCGA--CAA-GGUG-GAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGUGCCGGGCUACACACGUAAUACAAUGGC-CGUCAACAAAGARA---AGCAAUACCGCGAGGUGGA-GCAAAACUCC--AAAAACGGUCUCAGUUCGGACUGCAGGCUGAAACCCGCCUGCACGAAGUUGGAAUUGCUAGUAAUCGUGGAUC-AGC-AUGCCACGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGUCGGU-AAC-ACCCGAAGUCAG-U-A-GUCU-AACC---GCAA---GGAGGAC-GCUGCCGAAGGU-GGGAUCGAUGACUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAUCAGAAGGUGCGG---CU-GGAUCACCUCCUUA
CP001145.1/1133389-1131854             AUCACGGAGGGUU-UGAU-CCCGGCUCAGGACGAACGCU-GG-CGG--CGUG-CCUAAUGCAUGCAAGUCGAGCG-GGC------------UACAGUCUU-----CGGAUU-G-UA------------------------------------------------------------------------------------------------------------------------------GCU-UAG-CGGCGAA-CGGGUGAGUAACACGUAGGU--AAUCUACCCUUCAGAGG--AGGACAACCUCAGGAAACUGAGGCUAAACCUUCAUACGUUCA--CUG--GUA--GGGA--UAC--U-GG-U-G-AA-GAAAGAGUUACC------------------------------------------------GUUGAGGUA-----GCUGCUGAAGGAUGAGCCUGCGGCCCAUCAGGUAGUUGGUGAGGUAACGGCUCACCAAGCCGAAGACGGGUAACCG-GUCUGAGAGGAUGUCCGGUCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGCAGGGAAUCUUGGGCAAUGGGC-GAAAGCCUGACCCAGCGACGCCGCGUGGAG-GA-AGAAGUCC---UUCG--GGGCGUAAACUCCUGGACUGGGGG-ACGAGU-AA---------------------------------GGACGGUACCCCAGUAGAAAGGGACGGCUAACUACGUGCCAGCAGCCGCGGUAAAACGUAGGUCCCGAGCGUUGUUCGGAUUCACUGGGUGUAAAGGG-CGCGUAGGUGGUUGUCUG-UGUCUC-AUGUGAAAACUCA-GGGCUCAACUC-UG-AGAUUGCGUGGGAAACUAGGC-AGCUA-GAGGACGGUAGAGGGGAGUGGAAUUCCCGGUGUAGCGGUAAAAUGCGUAGAUAUCGGGAGGAACACCGG--UGGCGAAGGCGGCUCUCUGGGCCGAUCCUGACGCUGAG-GCGCGAAA-GCU-AGGGGAGCGAACCGG-AUUAGAUACCCGGGUAGUCCU-AGCCGUAAA-CGAU-GGGU--GC-UAGG-UGUU-GGGGGG-UA----------------------------AAGA--CCCUUCAGUGCC-------GAA-GCCAACGCGAUAAGCAUCCCACC--UGGG-GAGUAC-GGCCGCAAGGUUGAAACUCAAA-GGAAUUGGCGGGGGUCCG-CAC-AAGCGGCGGAGCAUGUGGUUUAAUUCGAUGCUGCCCGAAGAACCUUA-CCAGGGUUUGACAUG-CUGGUG----------GUAGGAACCUG-AAAGGGGGACG--ACCCAACCGU--------------------------AAGGGAGGGA----GCCAG-CACAG-GUGUUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUCGGCUUAAGUGCCG-UAACGAGCGCAACCCUCAUCCCUAAUUGCUCCUGACA---GGUAAAAG-----------GGUCAGAG-CACAAUAGGGAGACCGCUGGCGA--AGA-GCCA-GAGGAAGGGGAGGAUGACGUCAAGUCAGCAUGGCCUUUAUGCCCUGGGCUACACACAUGCUACAAUGCA-GGGU-ACAACGGGA---AGCGAAGCCGCGAGGUGGA-GCAAAUCCCCA-AAAGCCCUGCUCAGUUCGGAUCGCACGCUGCAAUUCGCGUGCGUGAAGUCGGAGUCGCUAGUAACCGUGGAUC-AGCAAAGCCGCGGUGAAUACGU-UCUCGGGCCUUGCACACACCGCCCGUCAAGCCACCCGAGUCGGG-UUC-ACCAGAAGGCCG-G------U-AACC---GAAG---AGGG----CCGGACGACGGU-GUGCCUGGUAAGGAGGGCUA-AGU-CGUAACAAGGUAG-CUGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
CP002901.1/268218-269760               GCUAUGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CGUAAUACAUGCAAGUCGAGCG-GUC-----------GACGGCUCUU-----CGGAGG-C-GUC-----------------------------------------------------------------------------------------------------------------------------GGC--AG-CGGCGGA-CGGGUGAGGAACACGUGAGU--AACCGGGCGUCCGGUGG--GGGAUAUCGGGCCGAAAGGCGCGGCAAUCCCGCAUGCGCCCC--GGG-CGGC--GCCA--GCC-GC-CG-G-G-GG-GAAA-GGC--------------------------------------------------------CUUCG----GGUCGCCGGACGGGGGGCUCGCGGCCCAUUAGCUAGUUGGGGGGGUAACGGCCUCCCAAGGCGACGAUGGGUAGCCG-GCCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCACAAUGGGC-GCAAGCCUGAUGGAGCAACGCCGCGUGAGU-GA-AGACGGCC---UUCG--GGUUGUAAAGCUCUGUCUGUCGGG-ACGAGG--ACCGCGCCG------GACGGCG-----CGGG--GGGACGGUACCGGCGGAGGAAGCCCCUGCAAACUACGUGCCAGCAGCCGCGGUAAGACGUAGGGGGCAAGCGUUGUCCGGAAUUACUGGGCGUAAAGGG-CGUGUAGGCGGUUGCGCA-CGUAGC-GGUUUUCAGCCGU-CGGCUCACCCG-AC-GGA-GGGCGGCUAAACGGCGC-AGCUC-GAGGGCAGGAGAGGUGCAUGGAAUUCCUGGUGGAGCGGUGAAAUGCGUAGAGAUCAGGAAGAACACCGG--UGGCGAAGGCGGUGCACUGGCCUGGCCCUGACGCUGAG-GCGCGACA-GCG-UGGGGAGCGAACGGG-AUUAGAUACCCCGGUAGUCCA-CGCCGUAAA-CGAU-GGAU--AC-GAGG-UGUC-GCGGGG--G----------------------------UCCA--CCCUGCGGUGCC-------GGA-GCUAACGCACUCAGUAUCCCGCC--UGGG-GAGUAC-GGCCGCAAGGUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCAGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGCAGAACCUUA-CCAGGGCUAGACGGG-ACCGU------------GAGCCGCGCG-AAAGCGCGGGG--CUGCUU----------------------------------CGGCAG---AGCGGUCGUCAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUCGUCGGCUGUUGCC-AGCGA------UUCGG-------------UCG--GG-CACUCAGCCGAGACAGCCGGGGA--CGA-CCCG-GAGGAAGGUGGGGAUGACGUCAAAUCCGCAUGGCCUUCAUGUCCUGGGCUACACACGUGCUACAAUGGC-GCCG-ACAACGGGC---CGCGACCUCGCGAGGGGGA-GCGAAUCCUUC-AAACGGCGUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCCGGAAUUGCUAGUAAUCGCGGAUC-AGC-AUGCCGCGGUGAAUCCGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUCGGC-CAC-ACCCGAAGCCGG-UCG-GUCG-AACCC-CGUCAG-GGGACGAC-CCCGUCGACGGU-GGGGCGGAUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAUCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
CP002353.1/4713330-4714852             AUCUCGAAGGGUU-UGAU-CCUGGCUCAGAAUGAACGUU-GG-CGG--CGUG-GAUUAGGCAUGCAAGUCGAACG-------------------GGCCGC-----AAGGCC----------------------------------------------------------------------------------------------------------------------------------------AG-UGGCGAA-AGGGUGAGUAAGGCGACGGC--AACCUACCCCGAGGUUG--GGCAUAGCCGGGGGAAACUCCGGGUAAUUCCCAGCGAUGUGC--GUC-UCAG--GCAU--CUG-AG-AC-G-C-AC-CAAA-GGU--------------------------------------------------------GCAAU-----UCCGCCUCGGGACGGGCCGUCGUGGUAUUAGGUAGUUGGUGGGGUCACGGCCCACCAAGCCGACGAUGCCUACCGG-GCGUGCGAGCGUGGCCCGGCACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUCGGCAAUGGGC-GCAAGCCUGACCGAGCGACGCCGCGUGGAG-GA-AGACGGCC---CUUG--GGUUGUAAACUCCUGUCGAGGGGA-AGGAAG-GGUCGGCG----------AAGAG----CCGAU-CUUGACCGC-UCCCUGGAGGAAGCACGGGCUAAGUUCGUGCCAGCAGCCGCGGUAAGACGAACCGUGCAAACGUUAUUCGGAAUCACUGGGCUUAAAGGG-CGCGUAGGCGGAAGGGCG-CGUCGG-CGUUGAAAUCCCC-CGGCUCAACCG-GG-GAAGCGGCGUCGAAACGGCCG-UUCUG-GAGGGGCGUAGAGGGACUCGGAACUUCCGGUGGAGCGGUGAUAUGCGUUGAGAUCGGAAGGAACGCCCG--UGGCGAAAGCGGAGUCCUGGACGCUUACUGACGCUGAG-GCGCGAAA-GCC-AGGGGAGCAAACGGG-AUUAGAUACCCCGGUAGUCCU-GGCUGUAAA-CGAU-GGGC--AC-UUGG-CAGU-GGGUUC--G----------------------------UCGA-UGGGUCCACUGCC-------GGA-GGGAAACCGUGAAGUGCCCCGCC--UGGG-GAGUAU-GGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCUCA-CAC-AAGCGGUGGAGCAUGUGGCUUAAUUCGAGGCUACGCGAAAAACCUUAUCCUGGGCUUGACAUG-CAGGGA----------UUAGCCGGCGG-AAACGUCGGUG-ACGCCGC----------------------------------AAGGUGG--AACCUG-CACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUCGGGUUAAGUCCCU-UAACGAGCGAAACCCCUGCGGCCAGUUGCC-AACAC-----AUCCUG-------------GUG--GG-GACUCUGGCCGGACCGCCGGCGU--GAA-GCCG-GAGGAAGGCGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUGCCCAGGGCUGCACACGUGCUACAAUGGC-GGGG-ACAAAGCGU---CGCCACGCCGUAAGGCCGA-GCCAACCGCGU-AAACCCCGCCCCAGUUCGGAUCGAGGGCUGCAACCCGCCCUCGUGAAGCCGGAAUCGCUAGUAAUCGCGGAUC-AGCAUUGCCGCGGUGAAUGUGU-UCCUGAGCCUUGUACACACCGCCCGUCAAGCCACCAAAGGGGGG-GGC-ACCCGAAGUCGC-C-GACG-----UC---UCAC---GA---CG-GGCGCCGAAGGU-GAAACUCCUGAUGGGGACUA-AGU-CGUAACAAGGUAA-CCGUAGGGGAACCUGCGG---UU-GGAUCACCUCCUUU
CP001792.1/2381215-2382713             UCAAUGAAGAGUU-UGAU-CCUGGCUCAGAACGAACGCU-GG-UGG--CGUG-UCUUAUACAUGCAAGUCGAGCG------------------AGGCAGC-----AAUGCC-G--------------------------------------------------------------------------------------------------------------------------------------AG-CGGCGAA-CGGGUGAGUAACGCGUAAGC--AAUCUGCCCCAUAUCAG--GAAAUACCCGUGCCAACGCGCGGUUAAUGUCCAGGAGAGUGG--CCU--UCC--GCAU--GGA--G-GG-U-UGAC-UAGA-GA----------------------------------------------------------UUUA------UCGGUAUGGGAUGAGCUUGCGUCCGAUUAGCUAGUUGGCGGGGCAACGGCCCACCAAGGCGACGAUCGGUAGCCG-GCCUGAGAGGGUGAUCGGCCACAUUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUAUUGCACAAUGGGG-GAAACCCUGAUGCAGCAACGCCACGUGUGG-GA-AGAAGCAU---UUCG--GUGUGUAAACCACUGUCAUGAGGG-AAUAAG--GCCCGCCU--------UCGGGC-----GGGA--UUGAAUGUACCUUGAGAGGAAGCACCGGCAAACUUCGUGCCAGCAGCCGCGGUAAUACGAGGGGUGCAAGCGUUGUUCGGAAUUACUGGGCGUAAAGGG-AGCGUAGGCGGAGAUUCA-AGCGGA-UUGUACAAUCCCG-GGGCCCAACCC-CG-GUUCUGCAGUCCGAACUGGAU-CUCUU-GGAUAGUUCAGGGGCAGGCGGAAUUCCUGGUGUAGCGGUGGAAUGCGUAGAGAUCAGGAAGAACACCGA--UGGCGAAGGCAGCCUGCUGGGGACUUAUCGACGCUGAG-GCUCGAAA-GUG-CGGGUAGCAAACAGG-AUUAGAUACCCUGGUAGUCCG-CACCGUAAA-CAAU-GCAU--AC-UGGG-UGUC-CGGGGG--G----------------------------U-----UCCCCGGGUACC-------GUA-GCCAACGCGUUAAGUAUGCCGCC--UGGG-GAGUAC-GUACGCAAGUAUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGCAGAACCUUA-CCAGGGUUUGACAUG-GGAAC-----------GCCGCGGCGAG-AGAUCGCCGUU-UUGCAGC----------------------------------AAUGCAA--CGUUCCGCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCACGUUUCCAGUUGCC-ACCC-------GCAAG--------------GG--GG-CCCUCUGGAGAGACUGCCGGGGA--CAA-CCCG-GAGGAAGGUGUGGAUGACGUCAAGUCCUCAUGGCCCUUACAUCCUGGGCUACACACGUGCUACAAUGGU-CGGU-ACAAUGGGU---CGCAACGCCGCGAGGCGGA-GCCAAUCCUC--AAAGCCGUCCUCAGUUCGGAUCGGAGUCUGCAACUCGACUCCGUGAAGCUGGAAUCGCUAGUAAUCGUGGGUC-AGC-ACACCACGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGCCAUGGGAGAAGGG-AGU-GCUCUAAGUC--------------GU---GCAA---GC---------GCCUAAAGC-AAGACCUUUGACUGGGGCUA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUUACCUCCUUU
EU686601.1/12359-13921                 UUAACGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CCUAAUACAUGCAAGUCGAACG-AGGA----------CCAGGGAGCU-----UGCUCC-C-UGU----------------------------------------------------------------------------------------------------------------------------AACC-GAG-UGGCGAA-CGGGUGAGUAACACGUGACC--AACCUGUCCUAGGGUGG--GGGACAACCUGGGGAAACCCGGGCUAAUACCGCAUGAUGCUU--CAU-CCUC--GCAU--GAG-GA-UG-A-G-AU-CAAA-GAGGGCCUC-------------------------------------------UGCUUGCAAGCU-----CUCGCCCAAGGAGGGGGUCGCGACGUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCUAUGACGCGUAGCGG-GUCUGAGAGGAUGAUCCGUCACAUUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUAUUGCGCAAUGGAC-GAAAGUCUGACGCAGCGACGCCGCGUGUGG-GA-GGAAGCCC---UUCG--GGGUGUAAACCACUGUCAGAGGGG-AAGAAC-CCCGUCGGUC------AGAAUAUGGCCGGCGG--CUGACGGUACCCUCAGAGGAAGCGCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGAGGGCGCAAGCGUUGUUCGGAAUUACUGGGCGUAAAGGG-CGGGCAGGCGGUCCGUUA-AGUCUU-CUGUGAAAAUCCG-GGGCUCAACCC-CGUGAAAUGCAGGAGAUACUGGCG-GACUA-GAGACCGGUAGAGGCUAGCGGAAUUCCUGGUGUAGCGGUGGAAUGCGUAGAUAUCAGGAAGAACACCUG--UGGCGAAGGCGGCUAGCUGGGCCGGAUCUGACGCUCAU-CCGCGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GGGC--AC-UAGG-UACC-GGGUCU--A----------------------------UAGA-CGGAUUCGGUGCC-------GCA-GCUAACGCAUUAAGUGCCCCGCC--UGGG-GAGUAC-GGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCCAGGCUUGACAUC-CUAGAG----------AAAGCUCCUGG-AAACAGGAGGC--CUCCUU----------------------------------CGGGAC----UCUAG-GACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGCCCUAUGUUGCC-AGCGG------UUCGG-------------CCG--GG-GACUCAUAGGGGACUGCCGGUGA--UAA-ACCG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGCUUGGGGCUACACACGUGCUACAAUGGC-CAGC-ACAAAGGGC---UGCCAACCUGCGAAGGUGA-GCGAAUCCCAA-AAAGCUGGUCUAAGUUCGGAUUGUAGUCUGCAACUCGACUGCAUGAAGGCGGAAUCGCUAGUAAUCGUAGAUC-AGCAACGCUACGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGAAGCCGGG-AGU-GCCCGAAGUCCG-U-G-UCCU-AACC---CUUG---GGAGGGA-GCGGCCGAAGGC-AAGCUCGGUAACUGGGGCGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUU
GU474850.1/19180-17619                 ACAAUUGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CUUGAUACAUGCAAGUCAAGGA-GAA------------CAUUAUCUU-----CGGAUA-A-UAA-----------------------------------------------------------------------------------------------------------------------------GUA-AAC-UGGCGAA-CGGGUGAGUAACGCGUAAAC--AACUUGCCUCAGAGAUU--GGGACAACAUUGGGAAACCAGUGCUAAUACCAAAUAAUGCAG--CGG-GCUC--UUCG--GAGCAC-AG-U-U-GU-UAAA-GUAG------------------------------------------------------GCUUCGG--CUUACACUUUGAGAUAGGUUUGCGUCCGAUUAGUUAGUUGGUAGGGUAAAAGCCUACCAAGACCAAGAUCGGUAGCUG-GUCUGAGAGGAUGAUCAGCCACACUGGAAUUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGUAAGGAAUUUUGCACAAUGGGC-GAAAGCCUGAUGCAGCAACGCCGCGUGAAC-GA-UGAAGUUU---UUAG--GAAUGUAAAGUUCUGUCGUAUGGG-AAGAGA-UCUUUCGAAUGUUAAUACCAUUU-----GUUA--AUGACGGUACCAUACAAGAAAGCACCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAGGGGUGCUAGCGUUGUCCGGAUUUACUGGGCGUAAAGGG-UACGUAGGCGUUUUAAUA-AGUUGU-AUGUUAAAUAUCU-UAGCUUAACUA-AG-AAAAUGCAUCCAAAACUGUUA-AAAUA-GAGUUUGAGAGAGGAACGCAGAAUUCAUGGUGGAGCGGUGACAUGCGUAGAUAUCAUGAGGAAAGUCAA--AUGCGAAGGCAGCCUUCUGGCUCAAAACUGACGCUGAG-GUACGAAA-GCG-UGGGGAGCGAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GAGU--AU-UUGG-UGCU-GGGGGA--U----------------------------UCGA-CCCUUUCAGUGCC-------GUA-GCUAACGCGAUAAAUACUCCGCC--UGGG-GACUAC-GAUCGCAAGAUUGAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCGGUGGAACAUGUGGUUUAAUUCGAUGAUACGCGAAGAACCUUA-CCUGGGUUUGACAUGUUAGUG-----------AAAGUUUUCUG-AAAAGAAUUCC--UUUUAAGAGC-------------------------UUGCUCUUAAA----CACUAUCACAG-GUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUAGGUUAAGUCCUG-CAACGAGCGCAACCCCUAUAUUUAGUUGCC-AGCAC-----AUAAUG-------------GUG--GG-GACUCUAGAUAGACUGCCCGGAA--UAA-CCGG-GAGGAAGGUGGGGAUGAUGUCAAGUCAGUAUGUCCCUUAUACCCAGGGCUACACACGUGUUACAAUGGA-UAGU-ACAAAAAGU---CGCAAUCCCGCGAGGAGGA-GCCAAUCUUU--AAAACUAUCCCCAGUUCAGAUUGAAGUCUGAAAUUCGACUUCAUGAAGCAGGAAUCGCUAGUAAUCGUAGGUC-AGC-ACACUACGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCAAGUCAUGGAAGUCUGC-AGU-ACCCGAAGAUGG-U-A-UCCU-AACC---GCAA---GGAGGGA-GCUGUUUAAGGU-AAGGCAGGUAACUGGGACUA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
CP001959.1/1912467-1913981             AGUAUGGAGAGUU-UGAU-UCUGGCUCAGAGCGAACGUU-GG-CGA--UGCG-UCUUAAGCAUGCAAGUCGAGCGGGCU------------UAUUCGGGC-----AACUGG-A-UA------------------------------------------------------------------------------------------------------------------------------AGU-UAG-CGGCGAA-CUGGUGAGUAACACGUAGGU--AAUCUGCCGUAGAGUGG--GGGAUAACCCAUGGAAACAUGGACUAAUACCGCAUAUACUCU--UGC--UAC--ACAA--GUA--G-AGUA-G-AG-GAAA-GGA---------------------------------------------------------GCGA-----UCCGCUUUACGAUGAGCCUGCGGCCUAUUAGCCUGUUGGUGGGGUAACGGCCUACCAAAGCUACGAUAGGUAGCCG-ACCUGAGAGGGUGACCGGCCACAUUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGCUGAGAAUCUUCCACAAUGGAC-GAAAGUCUGAUGGAGCGACAUCGCGUGAGG-GA-UGAAGGCC---UUCG--GGUUGUAAACCUCGGAAAUUAUCG-AAGAAU-GA--------------------G------------UGACAGUAGAUAAUG--UAAGCCUCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGAGGCAAACGUUGCUCGGAUUUACUGGGCGUAAAGGG-UGAGUAGGCGGACUUAUA-AGUCUA-AGGUGAAAGACCG-AAGCUCAACUU-CG-GGAACGCCUCGGAUACUGUGA-GUCUU-GGAUAUUGUAGGGGAUGAUGGAAUUCUCGGUGUAGCGGUGGAAUGCGCAGAUAUCGAGAGGAACACCUA--UAGCGAAGGCAGUCAUCUGGGCAUUUAUCGACGCUGAA-UCACGAAA-GCU-AGGGGAGCAAACAGG-CUUAGAUACCCUGGUAGUCCU-AGCCGUAAA-CGUU-GUAC--AC-UAGG-UGCU-UCUAU--------------------------------UUAA---AUAGGAGUGCC-------GUA-GCUAACGUCUUAAGUGUACCGCC--UGAG-GAGUAU-GCCCGCAAGGGUGAAACUCAAA-GAAAUUGACGGGUCCCCG-CAC-AAGUGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAAAAACCUUA-CCUGGGUUUGAAUUGUAAGAU-----------CAAUGAUUUAG-AGAUAAGUCAG---ACCGC----------------------------------AAGGAG----AUUUUACAUAG-GUGCUACAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUCACCCUUUGUUGCU-ACCGA-----GUAAUG-------------UCG--GG-CACUCUUAGGGGACUGCCUACGU-UCAA-GUAG-GAGGAAGGUGGGGAUGAUGUCAAGCCCUCAUGGCCCUUAUGUCCAGGGCUACACACGUGCUACAAUGGC-AAGU-ACAAAGAGA---AGCGAGACCGCGAGGUGGA-GCAAAACUCAA-AAAAGUUGCCUCAGUUCGGAUUGGAGUCUGAAACUCGACUCCAUGAAGUUGGAAUCACUAGUAAUCGUAGAUC-AGA-ACGCUACGGUGAAUACGU-UCCCGGGGAUUGUACACACCGCCCGUCACGCCAUCGGAGUUGGU-UUU-ACCUGAAGUCGU-U-A-GCCU-AACC---GCAA---GGGGGGC-GGCGCCGAAGGU-GGGACUGAUGAUGAGGGUGA-AGU-CGUAACAAGGCAG-CCGUACCGGAAGGUGUGG---CU-GGAUCACCUCCUUU
CP002903.1/662524-664069               AUGAUGGAGAGUU-UGAU-CCUGGCUCAGAACGAACGCU-GG-CGG--CGCG-UCUUAGGCAUGCAAGUCGAGCG-GUA-----------GGGUGGUGCU-----UGCACC-A-CC------------------------------------------------------------------------------------------------------------------------------UGA-GAG-CGGCGGA-CGGGUGAGUAACACGUAGGU--GACCUAUCCUCAGGUUG--GGGAUAGCCCGUGGAAACACGGGGUAAUACCGGAUGGCCUCU--UAU--GGC--UGUG--GCU--A-UA-G-G-AG-GAAA-GGCC-----------------------------------------------------CGAUAAG----GGUCGCCUGAGGAGGGGCCUGCGGCCCAUUAGCUAGUUGGUAGGGUAACGGCCUACCAAGGCGACGAUGGGUAGGGG-GUCUGAGAGGAUGGCCCCCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGCCAAGAAUCUUCCGCAAUGGGC-GAAAGCCUGACGGAGCGACGCCGCGUGGGG-GA-AGAAGGCC---GGAA--GGUUGUAAACCCCUUUUCCCAGGG-AAGAAU-AAGGGCGGG-------AGGUAAUGCCCGUCUG--AUGACGUUACCUGGGGAAUAAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCGAGCGUUGUUCGGAAUUACUGGGCGUAAAGGG-GGCGCAGGCGGUCUGGCA-AGUCUG-GUGUAAAAGGCUA-CGGCUCAACCG-UA-GU-GUGCACCGGAAACUGCUG-GGCUG-GAGUCCCGGAGGGGGAGCUGGAAUUCCCGGUGUAGGGGUGAAAUCUGUAGAUAUCGGGAGGAACGCCGG--AGGCGAAGGCGAGCUCCUGGCCGGAGACUGACGCUGAG-GCCCGAAA-GCG-UGGGGAGCGAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GUGC--AC-UAGG-CGUU-GGGCCU--------------------------------UGG--AGGCUCGGUGCC-------GAA-GCUAACGCGUUAAGUGCACCGCC--UGGG-GAGUAU-GCCGGCAACGGUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUA-CCAGGGCUUGACAUCUACCGG------------GCGGCUGCAG-AGAUGCAGCUU--CCCCGC----------------------------------GAGGGG----CUGGUAGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCGUCUGUUGCC-AUCGG-----GUGAAG-------------CCG--GG-CACUCAGGCGGGACUGCCGGUGA--CAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUGAUGCCCUGGGCUACACACGUGCUACAAUGGC-CGGU-ACAGAGGGA---GGCGAAGCCGCGAGGCGGA-GCAAAUCCCAG-AAAGCCGGUCUCAGUACGGAUUGGAGUCUGAAACCCGACUCCAUGAAGGUGGAAUCGCUAGUAAUCGCGCAUC-AGCCAUGGCGCGGUGAAUGCGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACCCGAGUCGGG-GGU-ACCCGAAGCCGG-U-A-GCCU-AACC--CGUAA--GGGAGGGC-GCCGUCGAAGGU-ACGCCUGGUGAGGGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
FP245540.1/1483-3055                   CCUUUGGAGGGUU-UGAU-CCUGGCUCAGAGUGAACGCU-GG-CGG--CGUG-GUUUAGGCAUGCAAGUCGAGCG-AUCUUGUUUCCGUUGUUGUGGGGU-----AACCUG-C-AGCAAUGG------------------------------------------------------------------------------------------------------------------UAACUUGAU--AG-CGGCAAA-CGGGUGAGCAAUACAUGGGU--AACUUGCCUCAAGGAGG--AGCAUAGUCCGUCGAAAGGCGGAGUAAUACUCCAUAACGCCU--GGA--AUC--GUAA--GGU--U-CC-C-G-GC-CAAA-GAUGGCCU---------------------------------------------CUAUUUAUAAGC---UAUCGCCAUGAGAGAGGCCCAUGUCCUAUCAGGUAGUUGGCGGGGUAACGGCCCACCAAGCCUAAGACGGGUAGCUG-GCGUCAGAGCGUGGCCAGCCACAUCGGGACUGAGACACUGCCCGGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUUCCAAUGGAC-GAAAGUCUGAGAAUGCGACGCCGCGUGAGG-GA-UGAAGGUC---UUCG--GAUUGUAAACCUAUUUUAUCGGGG-AGGAAC-CUUUUGGUGUGA--ACAAUGCCA-----AAAG--UUGACUGUACCCGGUGAAUAAGCCACGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGUGGCAAGCGUUACUCGGUUUGAUUGGGUGUAAAGGG-UCCGCAGGCGGUUACGCA-AGUGAA-AGGUGAAAUCUUU-CAGCUCAACUG-AA-AAAGUGCCUUUCAAACUGCAU-AACUU-GAGGAUGAAAGAGGAAAGUGGAACUACCGGUGUAAAGGUGAAAUUUGUGGAGAUCGGUAGGAACGCCCG--UGGAGAAGUCGGCUUUCUGGUUCAUUCCUGACGCUGAG-GGACGAAA-GCU-AGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCU-AGCUGUAAA-CGAU-GGGC--AC-UAGG-UGUU-CGUCC--------------------------------GUAA---GGAUGGGUGCC-------GCA-GCUAACGCAUUAAGUGCCCCACC--UGGG-GACUAC-GGCCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAACACGUGGUUUAAUUCGAUGCUACGCGAGGAACCUUA-CCAGGGUUUGACAUGCUGGAA-----------GUAAUCGCCUG-AAAGGGUGGGUGACCUGUAUC------------------------------CAAUCAGG----UACCAGCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUCCCUUAAGUGGGA-GAACGAGCGCAACCCCCGCCUUUAGUUGCU-ACUUUUUAGAUUUAUCU----------AGAAA--GG-CACUCUAAAGGGACUGCCCGCGU--UAA-GUGG-GAGGAAGGUGAGGACGACGUCAAGUCCGCAUGGCCCUUAUGUCCUGGGCUACACACGUGUUACAAUGCC-UGUU-ACAACGGGA---GGCUAAACCGCAAGGUGGA-GCAAAUCCCUA-AAAAGCAGGCCCAGUUCAGAUUGCAGGCUGCAAUUCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUGGCGCAUC-AGC-ACGGCGCCGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGCGCUGAAAGUGGGG-GGC-ACCUGAAGUCCC-C---------------GUAA-----------GAGGAUCACGGU-GAAUUUCAUGAUUGGCGCUA-AGU-CGUAACAAGGUAG-CCGUACGGGAACGUGCGG---CU-GGAUCACCUCCUUU
CP001708.1/643490-645015               AUUUAUGAGAGUU-UGAU-CCUGGCUCAGGAUAAACGCU-GG-CGG--CGUG-CAUAACACAUGCAAGUCGAACG-AUGAAGCU--UAAAUGAUCUCUUC-----GGAGUG-A-CCUUAA-----------------------------------------------------------------------------------------------------------------------GUGGAU-UAG-UGGCGGA-CGGGUGAGUAACGCGUGAGU--AACCUGCCUUGCACAAG--GGGAUAGCCGUUGGAAACGACGAAUAAUACCCUAUGAUAUGA--UAG-CCUC--GCAU--GAA-GC-UA-U-C-AU-CAAA-GA----------------------------------------------------------UUUA------UCGGUGUAAGAUGGACUCGCGUCUGAUUAGCUAGUUGGUGGGGUAACAGCUCACCAAGGCAACGAUCAGUAGCCG-GCUUGAGAGAGUGUACGGCCACAUUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGCACAAUGGGG-GCAACCCUGAUGCAGCGACGCCGCGUGAUU-UA--GAAGGCC---UUCG--GGUUGUAAAAAUCUUUUGUAUGGG-AAGAAA--A---------------------------------UGACAGUACCAUACGAAUAAGGACCGGCUAAUUACGUGCCAGCAGCCGCGGUAAUACGUAAGGUCCGAGCGUUGUCCGGAAUCAUUGGGCGUAAAGGG-UACGUAGGCGGAUAAGCA-AGUUAG-AAGUGAAAUCCUA-UAGCUCAACUA-UA-GUAA-GCUUUUAAAACUGCUC-AUCUU-GAGGUAUGGAAGGGAAAGUGGAAUUCCUAGUGUAGCGGUGAAAUGCGCAGAUAUUAGGAGGAAUACCAG--UGGCGAAGGCGACUUUCUGGCCAUAAACUGACGCUGAG-GUACGAAA-GCG-UGGGUAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GAGU--GU-UAGG-UGUC-UGGA---------------------------------AUAA----UCUGGGUGCC-------GCA-GCUAACGCAAUAAACACUCCGCC--UGGG-GAGUAC-GCACGCAAGUGUGAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCAGCGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCAAGUCUUGACAUAUUACGG------------CGGGGUCUAG-AGAUAGACUCUUACUUCUU----------------------------------CGGAAG---ACUGUAAUACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCA-UAACGAGCGCAACCCCUAUUGUUAGUUACC-AUCA------UUAAGU--------------UG--GG-GACUCUAGCAAUACUGCCGGUGA--CAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCUUUAUGACUUGGGCUACACACGUGCUACAAUGGC-AGGU-ACAGAGGGA---AGCGAGACUGCGAAGUUAA-GCAAAACUCAA-AAAGCCUGUCCCAGUUCGGAUUGCACUCUGCAACUCGAGUGCAUGAAGUUGGAGUUGCUAGUAAUCGCAGAUC-AGA-AUGCUGCGGUGAAUGCGU-UCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGAAGUUGGC-AAU-ACCCGAAGCCUG-U-G-AGCU-AACC---UUUA---GGGAGCA-GCAGUCGAAGGU-AGGGUCAGUAACUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAUCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
AF481102.1/22645-24192                 ACUGUAUAGAGUU-UGAU-CCUGGCUCAGAUUGAACGCU-AG-CGG--UAUG-CCUUACACAUGCAAGUCGUACG-GCA-----------GCACGGGCUU-----AGGCCU-GGUG-------------------------------------------------------------------------------------------------------------------------------GC-GAG-UGGCGAA-CGGGUGAGUAACGCCCCGGA---ACGUGCCUUGUAGUGG--GGGAUAGCCUGGCGAAAGCCAGAUUAAUACCGCAUGAA--GC--CGC--ACA--GCAU--GGC--G-CG-G-U----GAAA-GUGGG----------------------------------------------------GGAUUCAAGCCUCACGCUACUGGAUCGGCCGGGGUCUGAUUAGCUAGUUGGCGGGGUAAUGGCCCACCAAGGCUGAGAUCAGUAGCUG-GUCUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGGACAAUGGGC-GCAAGCCUGAUCCAGCAAUGCCGCGUGUGU-GA-AGAAGGCC---UUAG--GGUUGUAAAGCACUUUUGUUCGGG-AUGAAG-GAGGGCGUGCA----AACACCAUG---CCCUC--UUGACGAUACCGAAAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCGAGCGUUAAUCGGAAUCACUGGGCGUAAAGGG-UGCGCGGGUGGCUUGCCA-AGACCC-CUGUAAAAUCCUA-CGGCCCAACCG-UA-GUGCUGCGGAGGUGACUGGUA-UGCUU-GAGUAUGGCAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAGGAAUACCGA--AGGCGAAGGCAACCCCCUGGGCCAUCACUGACACUGAG-GCACGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCCUAAA-CCAU-GUCG--AC-UAGU-CGUC-GGGGGA-AG----------------------------CCCUUUUUCCUAGGUGAC-------GAA-GCUAACGCAUGAAGUCGACCGCC--UGAG-UAGUAC-GACCGCAAGGUUAAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCGGUGGAUGAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUA-CCUACUCUUGACAUG-GCGGA------------GAUUCUGCCG-AGAGGCGGAAG--UGCUCGA--------------------------------AAGAGAA----UUCGCACACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCA-UAACGAGCGCAACCCCCGUCUUUAGUUGCU-AC--------CACUGG------------------GG-CACUCUAUAGAGACUGCCGGUGA--UAA-GCCG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCUUAAUGGGUAGGGCUUCACACGUCAUACAAUGAC-UGGA-UCAAAGGGU---CGCCAACUCGAGAGAGGGA-GCUAAUCCCAU-AAACCCAGCCCCAGUUCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUC-AGC-AUGCCACGGUGAAUACGU-UCUCGGGUCUUGUACACACAGCCCGUCACACCAUGGGAGUAAGC-CGC-AUCAGAAGCAGC-A-U-CCCU-AACC--CUAUGCAGGGAAGGA-GGCUGCGAAGGU-GGGGUCUAUGACUGGGGUGA-AGU-CGUAACAAGGUAG-CAGUACCGGAAGGUGCGG---CU-GGAUUACCUCCUUA
CP002161.1/5312-6843                   AUAAAUAAGAGUU-UGAU-CCUGGCUCAGAUUGAACGCU-AG-CGG--UAUG-CUUUACACAUGCAAGUCGAACG-ACAA----------UAUUAAAGCU-----UGCUUU-A-AU-------------------------------------------------------------------------------------------------------------------------------AUAAAG-UGGCGAA-CGGGUGAGUAAUAUAUCAAA---ACGUACCUUAAAGUGG--GGGAUAACUAAUUGAAAAAUUAGAUAAUACCGCAUAUU--------A--AUC--UUAG--GAU--------------GAAA-AUAGGA-------------------------------------------------AUAAUAUCU-----UAUGCUUUUAGAUCGGUUGAUAUCUGAUUAGCUAGUUGGUAGGGUAAAUGCUUACCAAGGCAAUGAUCAGUAGCUG-GUUUUAGCGAAUGAUCAGCCACACUGGAACUGAGACACGGUCCAGACUUCUACGGAAGGCAGCAGUGGGGAAUAUUGGACAAUGGGA-GAAAUCCUGAUCCAGCAAUACCGCGUGAGU-GA-UGAAGGCC---UUAG--GGUCGUAAAACUCUUUUGUUAGGA-AAGAAA-UAAUUUUAAAUA--AUAUUUAAA-----AUUG--AUGACGGUACCUAAAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUAAUCGGAAUUAUUGGGCGUAAAGAG-UGCGUAGGCUGUUAUAUA-AGAUAG-AUGUGAAAUACUU-AAGCUUAACUU-AA-GAACUGCAUUUAUUACUGUUU-AACUA-GAGUUUAUUAGAGAGAAGUGGAAUUUUAUGUGUAGCAGUGAAAUGCGUAGAUAUAUAAAGGAAUAUCGA--UGGCGAAGGCAGCUUCUUGGAAUAAUACUGACGCUGAG-GCACGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCCUAAA-CUAU-GUCU--AC-UAGU-UAUU-AAAUUA-AA----------------------------AAUA--AAAUUUAGUAAC-------GUA-GCUAACGCAUUAAGUAGACCGCC--UGGG-GAGUAC-GAUCGCAAGAUUAAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCGGUGGAUGAUGUGGAUUAAUUCGAUGCAACACGAAAAACCUUA-CCUACUCUUGACAUG-UUUGG------------AAUUUUAAAG-AAAUUUAAAAG--UGCUUGA--------------------------------AAAAGAA----CCAAAACACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGUUAUUAUUUGCU-AA---------UAAAA------------------AG-AACUUUAAUAAGACUGCCAAUGA--CAA-AUUG-GAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUGAGUAGGGCUUCACACGUCAUACAAUGAU-AUAU-ACAAUGGGU---AGCAAAUUUGUGAAAAUGA-GCCAAUCCUU--AAAGUAUAUCUUAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUC-AGC-AUGCCGCGGUGAAUACGU-UCUCGGGUCUUGUACACACCGCCCGUCACACCAUGGAAGUGAUU-UUU-ACCAGAAAUUAU-U-U-GUUU-AACC--UUUAU--UGGAAAAA-AAUAAUUAAGGU-AGAAUUCAUGACUGGGGUGA-AGU-CGUAACAAGGUAG-CAGUAUCGGAAGGUGCGG---CU-GGAUUACAUUUUAA
AENO01000048.1/5207-3679               ACAAUGGAGAGUU-UGAC-UCUGGCUCAGGAUGAACGCU-AG-CGA--UAGG-CUUAACACAUGCAAGUCGAGGG-GCAG---------CGAGAUGUAGC-----AAUACG-U-CGU----------------------------------------------------------------------------------------------------------------------------CGGC-GAC-CGGCGAA-UGGGUGAGUAACACGUAUGC--AACUUACCUCUUAGUGG--UGAAUAACCCGAUGAAAGUCGGACUAAUACACCAUAUACUCC--UUA-GAUC--CCAU--GAG-AA-GA-G-G-AG-GAAA-GA----------------------------------------------------------UUAA------UCGCUAAGAGAUGGGCCUGCGUUCCAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCAACGAUGGAUAGGGG-GACUGAGAGGUUGACCCCCCACAUUGACACUGAGAUACGGGUCAAACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAUGGGC-GAGAGCCUGAACCAGCCAAGUCGCGUGAAG-GA-AGACUGCCC-GCAAG--GGUUGUAAACUUCUUUUGUAUGGG-AUUAAA-GUCACCUAC--------GUGUAG-----GUGU--UUGCAGUUACCAUACGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCGAGCGUUAUCCGGAAUUAUUGGGUUUAAAGGG-UGCGUAGGUUGCAAGGGA-AGUCAG-GGGUGAAAAGCUG-UAGCUCAACUA-UG-GUCUUGCCUUUGAAACUCUCU-AGCUA-GAGUGUACUGGAGGUACGUGGAACGUGUGGUGUAGCGGUGAAAUGCAUAGAUAUCACACAGAACUCCGA--UUGCGCAGGCAGCGUACUACAUUACAACUGACACUGAA-GCACGAAA-GCG-UGGGUAUCCAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCAGUAAA-CGAU-GAAU--AC-UAGA-UCUA-UGCGAU--A----------------------------UACA-----GUAUGGGUC-------UAA-GCGAAAGCGAUAAGUAUUCCACC--UGGG-GAGUAC-GCCGGCAACGGUGAAACUCAAA-GAGAUUGGCGGGGGUCCG-CAC-AAGCGGAGGAACAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUA-CCCGGGAUUGAAAUGUAGAUG------------CAUGAGGCUG-AGAGGUCUCUU--C-CCUU----------------------------------CGGG-G----CUUCUAUGUAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGCCGUGAGGUGUCGGCUUAAGUGCCA-UAACGAGCGCAACCCGCGUCGAUAGUUACU-AACGA-----GUCAAG-------------UCG--AG-GACUCUAUCGAGACAGCCGUCG---UAA-GACGUGAGGAAGGAGCGGAUGACGUCAAAUCAGCACGGCCCUUACAUCCGGGGCGACACACGUGUUACAAUGGU-AGGG-ACAGCGAGC---AGCCAUCUGGUGACAGAGA-GCUAAUCUAU--AAACCCUAUCCCAGUUCGGAUCGGAGUCUGCAACUCGACUCUGUGAAGCUGGAUUCGCUAGUAAUCGCGCAUC-AGCCAUGGCGCGGUGAAUACGU-UCCCGGACCUUGCACACACCGCCCGUCAAGCCAUGGGAGUCGGG-GGU-ACCUGAAGAGCG-U-G-------ACC--GUCAC--AGGA-----GCGCUUGAGGGU-AAAACUGGUGACUGGGGCUA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAACACCUCCUUU
GU474904.1/4693-3219                   AAACUUGAGAGUU-UGAU-CAUGGCUCAGAACGUACGCU-GG-CGG--CACG-CCUAACACAUGCAAGUCGAACG-AA-----------------GUAGC-----AAUAC-------------------------------------------------------------------------------------------------------------------------------------UU--AG-UGGCAGA-CGGGUGAGUAACAUGUGGGU---AUCUGCCCUUUGGCCU--GGAAUAACACGAGGAAACUUGUGCUAAUACUGGAUAAG-----------UCU--UUAC--GGA--------------GAAA-GCU----------------------------------------------------------UUA-----UGCACCAUUGGAUGAGCCCGCACUUGAUUAGUUUGUUGGUGGGGUAAUGGCCUACCAAGACUUUGAUCAAUAGCUG-AUUUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGCACAAUGGAG-GAAACUCUGAUGCAGCGAUGCCGCGUGAGU-GA-AGAAGGCC---CUUG--GGUUGUAAAGCUCUUUCGUCGGGG-AAGAAA--A---------------------------------UGACUGUACCCGAAUAAGAAGGUCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGACCUAGCGUAGUUCGGAAUUACUGGGCUUAAAGAG-UUCGUAGGUGGUUGAAAA-AGUUGG-UGGUGAAAUCCCA-GAGCUUAACUC-UG-GAACUGCCAUCAAAACUUUUC-AGCUA-GAGUUUGAUAGAGGAAAGCAGAAUUUCUAGUGUAGAGGUGAAAUUCGUAGAUAUUAGAAAGAAUACCAA--UUGCGAAGGCAGCUUUCUGGAUCAUUACUGACGCUGAG-GAACGAAA-GCA-UGGGUAGCGAAGAGG-AUUAGAUACCCUCGUAGUCCA-UGCCGUAAA-AGAU-GUGU--GU-UAGA-CGUU-GGAAA--------------------------------UUUA---UUUUCAGUGUC-------GCA-GCGAAAGCGAUAAACACACCGCC--UGGG-GAGUAC-GACCGCAAGGUUAAAACUCAAA-UGAAUUGACGGGGACCCG-CAC-AAGUAGUGGAGCAUGUGGUUUAAUUCGAAGAUACGCGCAGAACCUUA-CCAACACUUGACAUG-UUCGUC----------GCAACUUUAAG-AGAUUAAAGUU-UUCGGUU---------------------------------CGGCCGG----ACGAAACACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUCACUUUUAGUUGCC-AUCA------UUAAGU--------------UG--GG-CACUCUGAAAGAACUGCCAGUGA--UAA-GCUG-GAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUACGUGUUGGGCUACACACGUGCUACAAUGGU-AUCU-ACAACAGGA---AGCGAAACAGCGAUGUUAA-GCAAAUCCUU--AAAAGAUACCUCAGUUCGGAUUGCACUCUGCAACUCGAGUGCAUGAAGCUGGAAUUACUAGUAAUCGUGGAUC-AGC-GUGCCACGGUGAAUGCGU-UCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGU-UCU-ACCUUAAGGCAA-G----------GU---UUAA--UACC-----CUUGACCACGGU-AUAGUCAGCGACUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUUACCUCCUUU
DQ905772.2/52-1610                     CGCCCUUAGAGUU-UCAU-UCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CUUAACACAUGCAAGUCGAACG-AAAAG-------ACGGAAAGAGCU-----UGCUCU-U-UUCA--------------------------------------------------------------------------------------------------------------------------GAAUU-GAG-UGGCAAA-CGGGUGAGUAACACGUAAAC--AACCUGCCUUCAGGAUG--GGGACAACAGACGGAAACGACUGCUAAUACCGAAUAAGUUUC--AAG-GGUC--GCAU--GAU-CC-AU-G-G-AAGAAAA-GGUGGCCU----------------------------------------------CUACCUGUAAG--CUAUCGCCUGAAGAGGGGUUUGCGUCUGAUUAGCUGGUUGGAGGGGUAACGGCCCACCAAGGCGACGAUCAGUAGCCG-GUCUGAGAGGAUGAACGGCCACACUGGAACUGAGACACGGUCCAGACUUCUACGGGAGGCAGCAGUGGGGAAUCUUCCGCAAUGGGC-GAAAGCCUGACGGAGCAACGCCGCGUGAGU-GA-UGACGGCC---UUCG--GGUUGUAAAACUCUGUGAUCCGGG-ACGAAA-AGGCAGAGUGCG--AAGAACAAA----CUGCA--UUGACGGUACCGGAAAAGCAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGCG-CGCGCAGGCGGCUUCCCA-AGUCCC-UCUUAAAAGUGCG-GGGCUUAACCC-CG-UGA-UGGGAAGGAAACUGGGA-AGCUG-GAGUAUCGGAGAGGAAAGUGGAAUUCCUAGUGUAGCGGUGAAAUGCGUAGAGAUUAGGAAGAACACCGG--UGGCGAAGGCGACUUUCUGGACGAAAACUGACGCUGAG-GCGCGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GGAU--AC-UAGG-UGUA-GGAGGU--A----------------------------UCGA-CCCCUCCUGUGCC-------GGA-GUUAACGCAAUAAGUAUCCCGCC--UGGG-AAGUAC-GAUCGCAAGAUUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGUAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCAGGUCUUGACAUU-GAUCG------------CGAUCUGCAG-AAAUGCGGAGU--UCUUCUU--------------------------------CGGAAGA----CGAGAAAACAG-GUGGUGCACGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUCAUUUGUUGCC-AGCAC-----GUAAAG-------------GUG--GG-GACUCAAAUGAGACCGCCGCGGA--CAA-CGCG-GAGGAAGGCGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUACUACAAUGGG-UGUCAACAAAGAGA---AGCGAAACCGCGAGGAAGA-GCAAACCUCAA-AAACACACCCCCAGUUCAGAUCGCAGGCUGCAACCCGCCUGCGUGAAGCAGGAAUCGCUAGUAAUCGCGGGUC-AGC-AUACCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACUAUGAGAGUCAGA-AAC-ACCCGAAGCCGG-U-G-AGGU-AACC---GCAA---GGAGCCA-GCCGUCGAAGGC-GGAGCUGAUGAUUGGAGUGA-AGA-CGUAACAAGGUAG-CC-----GUAA-----GG---GC-GAAUUCGUUCCUUC
ABGO01000325.1/3044-1546               AACUUGAAGGGUU-UGAU-UCUGGCUCAGAACGAACGUU-GG-CGG--CAUG-GAUUAGGCAUGCAAGUCGGGGG-----------------AAUCCCGC-----AAGGGG-G-A------------------------------------------------------------------------------------------------------------------------------------AC-CGGCGUA-AGGGGCAGUAAGGCAUGGGU---ACCUACCCGGGGGUUC--GGGAUAGCCAUCAGAGAUGGUGGGUAAUACCGGAUGAC-----------CUC--GUGA--GAG--------------CAAA-GA----------------------------------------------------------UUCA------UCGCCCCCGGAGGGGCCCAUGUGAUAUUAGCUAGUUGGUGGGGUAACGGCCCACCAAGGCGAAGAUGUCUAGCGG-GUGUGAGAGCACGACCCGCGCCACUCGCACUGAGACACUGGCGAGACACCUACGGGUGGCUGCAGUCGAGGAUCUUCGGCAAUGGGG-GCAACCCUGACCGAGCGAUGCCGCGUGCGC-GA-UGAAGGCC---UUCG--GGUUGUAAAGCGCUUUAGUGGGGG-AGAAAA--GCCG----------------AG-----AGGU--GUGAUC-UAUCCCAAAAAUAAGCUCGGGCUAAGUUCGUGCCAGCAGCCGCGGUAAGACGAACCGAGCGAACGUUGUUCGGAAUCACUGGGCUUAAAGGG-CGCGUAGGCGGGCUAUCA-AGUCUG-GGGUGAAAUGCCG-CGGCUCAACCG-CG-GAACGGCCUCAGAUACUGACG-GCCUG-GAGGGAGGUAGGGGCAUGUGGAACUGUAGGUGGAGCGGUGAAAUGCGUUGAUAUCUACAGGAACUCCGG--UGGCGAAAGCGACGUGCUGGACCUCUUCUGACGCUGAG-GCGCGAAA-GCU-AGGGGAGCAAACGGG-AUUAGAUACCCCGGUAGUCCU-AGCCCUAAA-CGAU-GGGU--AC-UAGA-UAGU-AGACCA--G----------------------------AUAU--GGGUUUACUGUC-------GAA-GUUAAAAUGCUAAGUACCCCGCC--UGGG-GAGUAU-GGUCGCAAGGCUGAAACUCAAA-GAAAUUGACGGGGGCUCA-CAC-AAGCGGUGGAGCAUGUGGCUUAAUUCGAGGCUACGCGAAGAACCUUAUCCUGGACUUGACAUGUGCGAAAGCGCUCGGCAGUAGGACCCGG-AAACGGGAACGGACCCCAGCA------------------------------AUGGGGGG----ACCGAGCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUCGGGUUAAGUCCCA-UAACGAGCGAAACCCUUACCUUUAGUUGCG-ACC--------CACAA---------------G--GG-CACUCUAGAGGGACUGCCGGUGU--CAA-ACCG-GAGGAAGGCGGGGAUGACGUCAAGUCCUCAUGGCCUUUAUGUCCAGGGCUGCACACGUGCUACAAUGGU-GUAC-ACAGAGUGA---AGCGACUCUGCGAAGAGGA-GCCAAUCACAG-AAAUUACACCCCAGUUCAGAUCGCAGGCUGCAACUCGCCUGCGUGAAGCCGGAAUCGCUAGUAAUCGCGGGUC-AGCAACACCGCGGUGAAUGUGU-UCCUGAGCCUUGUACACACCGCCCGUCAAGCCACGAAAGAGAGG-GAC-GUCCGAAGCCAC-C----------UU---CACC-----------GGUGUCGAAGAC-GGACUUCUUGAUUGGGACUA-AGU-CGUAACAAGGUAA-CCGUAGGGGAACCUGCGG---UU-GGAUCACCUCCUUU
CP001226.1/93349-94879                 GAGGAUAAGAGUU-UGAU-CCUGGCUCAGAACGAAUGCU-GG-CGG--CAGG-CUUAACACAUGCAAGUCGAGCG-GGU-----------GCUCGCCACC-----AGUGGU-G-GG------------------------------------------------------------------------------------------------------------------------------CGC-UAG-CGGCGAA-CGGGUGAGUAACGCGUGAGA---AUCUGCCUUACUCUAC--GUGAUAACGCAGGGAAGCUUGCGUCAAUAACGUAUGAUUCCU--GA-----------A---------UC-A-G-GU-AAAG-AGC--------------------------------------------------------U---------GUUGGAGUAAGAUGAGCUUGCGUUAGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCUAUAGCUG-GUCUGGGAGGACGGUCAGCCACAUUGGGACUGAGACAAGGCCCAAACUUCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGC-GAAAGCCUGAUCCAGCCAUGUCGCGUGAGU-GA-AGAAGGUUUAAUAAGUGAACUGUAAAACUCUUUUGUCGGUG-ACCAUA--G---------------------------------UGAUGGUAGCUGACGAAUAAGCUCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAGACGAGGGGAGCGAGUGUUGUUCGGUUUUAUUGGGCGUAAAGGG-CGCGUAGGCGGCUUUUUA-AGUUGA-CGGCCAAAGCUUG-AAGCUCAACUU-CA-UGAC-GCUGUCAAAACUGCUA-AGCUA-GAGCUGGAUGGGGGCGAGCGGAAUUCCGAGUGUAGAGGUGAAAUUCGUAGAUAUUUGGAAGACCACCAG--AGGCGAAGGCGGCUCGCUACGUCUU-GCUGACGCUAAU-GCGCGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GAGU--GC-UAGC-AGUGGGCGCUG--CUCGCGCGUUGCGC--GUUCGUGCGCGACGCCA--CAGCGCUAUUGC-------ACA-GCUAACGCGUUAAGCACUCCGCC--UGGG-GAGUAC-GACCGCAAGGUUAAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCUACGCGUAGAACCUUA-CCAGCUCUUGACAUU-UCAGGU---------CGAAGCGGCCGU-AAAUGGGCGUU--UUCAACCAACAUU-------------------CUUGAAAGAAUGGA----CUUGA-AACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUAUGGUUAAGUCCUG-UAACGAGCGCAACCCUUGCCCUUAGUUGCUUAAAGC-----GAU----------------GCU--AG-CUCUCUAAGGGGACCGCUAAUGA--CAA-AUUA-GAGGAAGGAAAGGAUGACGUCAAGUCUUCAUGGCCUUUAUGGGCUGGGCUACACACGUGCUACAAUGGU-GGCC-ACAGAGAGU---CGCAGAGUCGCGAGGCCGA-GCUAAUCUUU--AAAAGCCAUCUCAGUCCAGAUUGCACUCUGCAACUCGAGUGCAUGAAGCAGGAAUCGCUAGUAAUCGCGGAUC-AGC-AUGCCGCGGUGAAUACGU-UCUCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGC-UUU-GCUCUAAGCCG-----------UCGC---UUUG---GCG-------CGGUCACAGU-GGAGUUAACGACUGGGGUGA-AGU-CGUAACAAGGUAG-CUGUAGGGGAACCUGUGG---CU-GAAACUUUUGAAAU
AF407694.1/1-1510                      -UCGAUUAGAGUU-UGAU-CCUGGCUCAAGGUGAACGCU-GG-CGG--CGUG-CCUAAAACAUGCAAGUCGAGUG-GG-------------CCGUGGGGU-----UUCUCA-C-GG-------------------------------------------------------------------------------------------------------------------------------UC--AG-CGGCGGA-CGGGUGAGUAACGCGUGGGU--GACCUACCCGGAAGAGG--GGGACAACCUGGGGAAACCUAGGCUAAUCCCCCAUGUGGACA--CGU--CCU--GU----GGG--G-CG-U-G-UU-UAAA-GGGU------------------------------------------------------GACGAG-----CCCGCUUCCGGAUGGGCCCGCGUCCCAUCAACUAGUUGGUGGGGUAAGAGCCCACCAA---GCACACGGGUAGCCG-GUCUGAGAGGAUGGCCGGCCACAGGGGCACUGANACAC-GGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGAC-GGAAGUCUGACGGAACGACGCCGCUUGGAG-GA-GGAAGCCC---UUCU--GGGUGUAAACUCCUGA-ACUGGGA-CAAAG----CCCUG-----------AUGAG-----GGGG--AUGACCGUACCCAGGUAA-UAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUUACUGGGCGAAAAGGG-CGUGUAGGCGGUCUGGGG-CGUCCC-AUGUGAAAGACCA-CGGCUCAACCG-UG-GGGGAGCGUGGGAUACGCUCA-GGCUA-GACGGCGGGAGGGGGUGGUGGUAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGA--UGGCGAAGGCAGCCACCUGGCUCGUUCGUGACGCUGAG-GCGCGAAA-GCG-UGGGGAGCAAACCGG-AUUAGAUACCCGGGUAGUCCA-CGCCCUAAA-CGAU-GCGC--GC-UAGG-UCUC-UGGG----------------------------------GUU----UCUGGGGGCC-------GAA-GCCAACGCGUUAAGCGCGCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCAGGCCUUGACAUGCUAGGG------------AACCUGGGUG-AAAGCCUGGGG--UGCCCGC--------------------------------GAGGGAG----CCCUAGCACAG-GUGUGGCAUGGCCGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCGUUAGUUGCC-AGCGG-----GUGAGG-------------CCG--GG-CACUCUAACGGGACUGCCUGCG---AAA-GCAG-GAGGAAGGCGGGGACGACGUCUGGUCAUCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCC-CACU-ACAGAGCGC---UGCGACCCGGUGACGGGGA-GCGAAUCGCGG-AAAGGUGGGCGUAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUC-AGCCAUGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGU-UCU-ACCCGAAGUCGC-C-G-GGAG---CC---UUGG---GG---CA-GGCGCCGAGGGU-AGGGCUCGUGACUGGGGCGA-AGU-CGUAACAAGGUAG-CUGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUA
EU262999.1/1-1529                      --UUGUUUGAGAU----C-CUUGGCUCAGAACGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCGAGCG-CGA------------AUAGGGG-C-----AACCCU-U-AG-------------------------------------------------------------------------------------------------------------------------------UA-GAG-CGGCGCA-CGGGUGCGUAACACGUGGAU--AAUCUGCCUGGAUGCCU--GGGAUAACCAGUCGAAAGAUUGGCUAAUACCGGAUAAGCCCA--CGG-UUUC--UUCG--GAG-AC-UG-A-G-GG-AAAA-GGUGGCC-----------------------------------------------UCUGUAUACAAG-CUAUCACAACCAGAUGAGUCCGCGGCCCAUCAGCUAGUUGGCGGGGUAAUGGCCCACUAAGGCGACGACGGGUAGCUG-GUCUGAGAGGACGAUCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGCGCAAUGGGC-GAAAGCCUGACGCAGCAACGCCGCGUGUGU-GA-UGAAGGUC---UUUG--GAUUGUAAAGCUCUUUCGACCGGG-ACGAAACUCGUAAAGCAU---AAUACGCUU-----UGCC--UUGACG-UACCGGGAGAAGAAGCACCGGCUAACUUGG--CCAGCAGCCGCGGUA-UACAGAGGGUGCAAGCGUUGUUCGGCAUUAUUGGGCGUAAAGCG-CGUGUAGGCGGCUUUGCA-AGUCGG-GUGUGAAAGCCCU-CAGCUCAACUG-AG-GAAGUGCGCCCGAAACUGCAG-AGCUU-GAGUGCCGGAGAGGGUGGCGGAAUUCCCCAAGUAGAGGUGAAAUUCGUAGAUAUGGGGAGGAACACCGG--UGGCGAAGGCGGCCACCUGGACGGUAACUGACGCUGAG-ACGCGAAA-GCG-UGGGUAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GAGA--AC-UAGG-UGUC-GUGGGA--G----------------------------UUGA-CCCCCGCGGUGCC-------GUA-GCUAACGCAUUAAGUUCUCCGCC--UGGG-AAGUAC-GGUCGCAAGACUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGCAGAACCUUA-CCUGGUCUUGACAUC-CUCGG------------AAUCCUUCAG-AGAUGAGGGAG--UGCCCGC--------------------------------AAGGGAA----CCGAGAGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUCGCCUUUAGUUGCC-AC--------GCAAGU------------------GG-AUCUCUAGAGGGACUGCCGGUGU--UAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCUUUAUGACCAGGGCUACACACGUGCUACAAUGGC-CGGU-ACAGAGCGC---UGCAAACCCGCGAGGGGGA-GCUAAUCGCAG-AAAACCGGUCUCAGUUCAGAUUGGAGUCUGCAACUCGACUCCAUGAAGGAGGAAUCGCUAGUAAUCGCAGAUC-AGC-ACGCUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUCGAU-UGC-UCCAGAAGUCAU-C-U--------CA---CCAA---UA------GAUGCCCAAGGA-GUGCUCGGUAACUGGGGUGA-AGU-C-UAACACGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACUCCUUCU
CP000159.1/3330048-3328509             ACUACGGAGAGUU-UGAU-CCUAGCUCAGGACGAACGCU-GG-CGG--CAGG-CUUAACACAUGCAAGUCGCACG-AGAA---------CGUUCUGGCUU-----U-GCCA-G-GACA---------------------------------------------------------------------------------------------------------------------------AGUA-CAG-UGGCGGA-CGGGUGCGUAUCGCGUAGAU--AACCUGCCCUCAGGCGC--GGGACAAUCACGGGAAACCGUGGCUAAUACCGCACGUCGUCU--GGA-UCCC--GCAU--GGG-GA-CC-A-G-AU-GAAA-GCC---------------------------------------------------------UUCG-----GGCGCCUUUGGAUGGGUCUGCGUUGGAUUAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCAACGAUCCAUAGCUG-GUCUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGCACAAUGGGG-UCACCCCUGAUGCAGCCAUGCCGCGUGGAG-GA-AGACACCC--CUAUG--GGGCGUAAACUCCUUUUCUGAAUG-AAGAAA-CCCCUGUA---------GCUUCA-----GGGC--GCGACGGUAGUUCAGGAAUAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUGUCCGGAAUCACUGGGUGUAAAGGG-UGUGCAGGCGGGGCAGCA-AGUCGG-AUGUGAAACCCCA-UGGCUUAACCA-UG-GAGGUGCAUUCGAAACUGUUG-CUCUU-GAGUCCCGGAGAGGCUGUCGGAAUUCGUGGUGUAGCGGUGAAAUGCGUAGAUAUCACGAGGAACACCAG--AGGCGAAAGCGGACAGCUGGACGGGUACUGACGCUCAG-GCACGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GAAU--GC-UCGC-CGUU-GCCUCG--------------------------------UUA--GGGGGCAGUGGC-------UAA-GCUAACGCGUUAAGCAUUCCACC--UGGG-GAGUAC-GAUCGCAAGGUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGCUCAAUUCGAUGCAACGCGAAGAACCUUA-CCUAGGCUCGAACGCUAAAGG------------ACCGCUCCUG-AAAGGGAGCUU--CCCCUU----------------------------------U-GGGG----CCUUUAGCGAG-GUACUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGUAACCCCUGUUGCUAGUUACC-AGCGG-----AUAAUG-------------CCG--GG-GACUCUAGCGAAACUGCCUGCG---CAA-GCAGUGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGUCCUUACGCCUAGGGCUGCACACGUGCUACAAUGGC-CGGU-ACAACGAGC---AGCCACCUCGCGAGAGGGA-GCGAAUCUCUG-AAAACCGGUCCCAGUUCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGCAGGAAUCGCUAGUAAUCGCGGAUC-AGCAAUGCCGCGGUGAAUCCGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGCCAUGGAAGCUGAG-AGC-ACCCGAAGUCCG-U-G-ACCC-AACC--UUUUG---GGAGGGA-GCGGCCGAAGGU-GAGCUCAGUGACUGGGGCUA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUAA
AY581819.1/1630-6                      CGGAUCCAGAGUU-UGAU-UAUGGCUCAGGAUGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCGAGCG-CGGU---------UAUUAUUCAAC-----AUUGAG-U-AUUCUAUAAAAUAUAGUUGGAAUUGACAGCGAUUUCACUUUCUGCCUUAAAAACUUAAAGAAGGAAAAGUGAAACACGCAUCAUUAAGUAACUAACUAGAAACAUAGAGUAUUGAAUGUUGAAUAAUAACU-GAG-CGGCGGA-CGGGUGAGUAACGCGUGGGU--AACCUGCCCUGUACAUA--UGGAUAACAUGCUGAAAAGCAUACUAAUACAUAAUAACGUAC--AUU-GAAG--GCAU--CUU-CG-AU-G-U-AU-CAAA-GC----------------------------------------------------------GUUA------GCGGUACAGGAUGGACCCGCGUCUGAUUAGCUAGUUGGUGGGGUAAAAGCCUACCAAGGCGACGAUCAGUAGCCG-ACCUGAGAGGGUGAUCGGCCACAUUGGAACUGAGACACGGUCCAAACUCCUACGGGAGGCAGCAGUGGGGGAUAUUGCACAAUGGGC-GAAAGC-UGAUGCAGCAACGCCGCGUGAAC-GA-UGAAGGUC---UUCG--GAUCGUAAAGUUCUGUUGCAGGGG-AAGAUA--A---------------------------------UGACGGUACCCUGUGAGGAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCUAGCGUUAUCCGGAUUUACUGGGCGUAAAGGG-UGCGUAGGUGGUCUUUCA-AGUCGG-UGGUUAAAGGCUA-CGGCUCAACCG-UA-UUA-AGCCGCCGAAACUGGAA-GACUU-GAGUGCAGGAGAGGAAAGUGGAAUUCUCAGUGUAGCGGUGAAAUGCGUAGAUAUUGGGAAGAACACCAG--UAGCGAAGGCGGCUUUCUGGACUGCAACUGACAUUGAG-GCACGAAA-GCG-UGGGUAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GAGU--AC-UAGG-UGUC-GGGG----U----------------------------UACC--CCCCUCGGUGCC-------GCA-GUUAACGCAUUAAGUACUCCGCC--UGGG-GAGUAC-ACACGCAAGUGUGAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGUAGCGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCUAAGCUUGACAUC-CCUCG-----------GACCGGUAGUU-AAUCCUACCUU----CCUU----------------------------------CGGGGC----CGAGGUGACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGUCUUUAGUUGCC-AGCA------UUUAGU--------------UG--GG-CACUCUAGAGAGACUGCCAGGGA--UAA-CCUG-GAGGAAGGCGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGCUUAGGGCUACACACGUGCUACAAUGGG-UGGU-ACAGAGGGU---UGCCAAACCGUGAGGUGGA-GCUAAUCCCUU-AAAGCCAUUUUCAGUUCGGAUUGUAGGCUGAAACUCGCCUACAUGAAGCUGGAGUUACUAGUAAUCGCAGAUC-AGA-AUGCUGCGGUGAAUGCGU-UCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGUCGGA-AAC-ACCCGAAGCCGA-U-U-AUCU-AACC---GCAA---GGAAGAA-GUCGUCGAAGGU-GGCGUCGAUAACUGGGGUGA-AGU-CGUAACAAGGUAG-CC-----GUAA------G---CU-UCACAAUCGUCGAC
FP245541.1/18860-20401                 CUAUCGGAGAGUU-UGAU-CCUGGCUCAGAACGAACGCU-GG-CGG--CGUG-GAUUAGGCAUGCAAGUCGUGCG-AGA-----------AAGAGGGCUU-----CGGCCC-U-UGA-----------------------------------------------------------------------------------------------------------------------------GUA-CAG-CGGCGAA-CUGGUGAGUAACAGGUGGGU--AACGUGCCCUGAAGUGG--GGGAUAACACCGGGAAACCGGUGCUAAUACCGCAUGUGAUCU--UUU--GGU--UCAUGGACC--G-GA-A-G-GU-UAAA-GCA---------------------------------------------------------GUAG-----UGCGCUUCAGGAUCGGCCCGCCCCCGAUUAGCUUGUUGGUGAGGUUACGGCUCACCAAGGCAUCGAUCGGUAGCUG-GUCUGAGAGGAUGGUCAGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGGGGCAGCAGUCUAGAGGCUUCGGCAAUGGGG-GCAACCCUGACCGAGCGACGCCGCGUGUGG-GAUUGAAGGCC---UUCG--GGUCGUAAACCACUGUCAUUGGGG-AAGAAU--GCCUGAAU-------GGUGAAUU---CAGGA--GGGACGGUACCCGAGAAGGAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGGGCAAGCGUUGUUCGGAUUUACUGGGCGUAAAGGG-UGUGUAGGCGGCCGCGCA-AGUCUG-GUGUGAAAUCUUCACCGCUUAACGG-GA-AGAGGGCACUGGAAACUGCGU-GGCUC-GAGUAUGGUAGAGGCAAGCGGAAUUCCUGGUGUAGCGGUGGAAUGUGUAGAUAUCAGGAAGAACACCGG--UGGCGAAGGCGGCUUGCUGGGCCAUCACUGACGCUGAG-ACACGAAA-GCG-UGGGGAGCAAACGGG-AUUAGAUACCCCGGUAGUCCA-CGCUGUAAA-CGGU-GCGC--AC-UAGU-UGUG-AGGGGU--A----------------------------UCGA-CCCCCCUUGUGAC-------GAA-GUUAACACAUUAAGUGCGCCGCC--UGGG-GAGUAC-GGCCGCAAGGUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGGAUGUUGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCUGGGCUUGAACCGCCGGUU------------AAACCUUGUG-AAAGCAGGGC---UGUGGC----------------------------------AACACG----AACCGGUAGAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGUCGCCAGUUACC-AUCA------UUCAGU--------------UG--GG-GACUCUGGCGAGACUGCCGGUGA--CAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGUCCAGGGCUACAAACGUCCUACAAUGGC-CGAG-ACAACGGGU---UGCAAGCCUGCGAAGGCAA-GCUAAUCCCUU-AAACUCGGUCUCAGUUCGGAUUGCAGUCUGCAACUCGACUGCAUGAAGUUGGAAUCGCUAGUAAUCGCAGAUC-AGC-ACGCUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACGAAAGUCAGU-UGU-UCCUGAAGGCGC-C-G-UCGG-AACC--CGCAA--GGGGCCCA-AGCGUCAACGGA-AUUACCGGUAAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAUCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
L10659.1/4-1531                        UGGAAGAAGGGUU-UGAU-CCUGGCUCAGGGUGAACGCU-GG-CGG--CGCG-CCUAACACAUGCAAGUCGAACG-GAGA----------AAGAGGAGCU-----UGCUCC-U-UGAG---------------------------------------------------------------------------------------------------------------------------UAUU--AG-UGGCGAA-CGGGUGAGUAGAACGUAGGA---ACCUGCCUAACGGACU--GGGAUAGCUACUGGAAACGGUAGGUAAUACUGGAUAAA-----------AUC--GAGA--GAU--------------AAAA-GCU---------------------------------------------------------UAGA-----AGCGCCGGGAGAGGGGUCUACGACCCAUCAGGUAGUUGGUAGGGUAAGAGCCUACCNAGCCGACGACGGGUAGCCG-AUGUGAGAGCAUGAUCGGCCACAAGGGAACUGAGACACGGUUCCUACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGCAC-GGAAGUGUGAUCCAGCGACGCCGCGUGAAG-GA-AGAAGUCC---UUCG--GGAUGUAAACUUCUGAACUUACAG-AAUAAC-AGCAUAAGG--------GGACUU-----AUGU--AUGAAGGUAAGUAAGGAA-AAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAGACGUAGGGGGCGAGCGUUGCCCGGAAUCACUGGGCGUAAAGGG-GGCGUAGGCGGUCUCAUA-AGUCAG-GUGUGAAAUGUCA-CUGCUCAACGG-UG-UCAGUGCGCAUGAAACUGUGA-GACUU-GAGGGUACCAGAGGUAGACAGAAUUACCUGAGUAGGGGUGAAAUCCGUAGAUACAGGUAAGAAUGCCAG--UGGGGAAGCCGGUCUACUGGGGUGACCCUGACGCUGAG-GCCCGAAA-GCU-AGGGUAGCAAACCGG-AUUAGAUACCCGGGUAGUCCU-AGCAGUAAA-CGAU-GCUC--AC-UAGG-UGUG-GGGC---------------------------------AAGA--AAGCUCCGUGCU-------GAA-GCAAACGCGAUAAGUGAGCCGCC--UGGG-GAGUAC-GCCCGCAAGGGUGAAACUCAAA-GGAAUUGACGGGGGUCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAAACCGAAGAACCUUA-CCAGGGCUUGACAUG-GAGAU------------AAGGCAUAAG-AAAUUAUGUCA--ACCUGUAUGU--------------------------AAAUAUAGGA----GUCUCACACAG-GUGGUGCACGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCA-CAACGAGCGCAACCCCUAUUGUUAGUUGCC-AUCA------UUAAGU--------------UG--GGCUACUCUAGCGAGACAGCCGUCGA--CGA-GACG-GAGGAAGGAGGGGAUGACGUCAGGUAAGCGUGCCCCUUAUGCUCUGGGCGACACACGUGCUACAAUGGU-GAGG-GCAAAAGGC---AGCGAAGCCGCGAGGUAGA-GCGAAUCCUAU-AAACCUCAUCGUAAUUCGGAUUGCAGGCUGAAACCCGCCUGCAUGAAACCGGAAUCGCUAGUAAUCGCAGGUC-AGCCAAACUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACGCCACCCGAGUUGGA-GAC-ACCUGAAAAGGG-AAG-AAGU-AACC---GAAA---NGGGCUAAUCUCUUCAGGGU-GGAGCUAGCGAGGGGGGCGA-AGU-CGUAACAAGGUAG-GUGUACCGGAAGGUGCGC---CU-GGAUCACCUCCUUU
EU795216.1/25258-26772                 UUGUACGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CACG-CCUAACACAUGCAAGUCGAGCG-CGA------------AAGGCACUU-----CGGUGC-C-GA------------------------------------------------------------------------------------------------------------------------------GUA-GAG-CGGCGCA-CGGGUGAGUAACGCGUGGCC--AACCCGCCCCCGGGACC--GGGACAACCCCCCGAAAGGGGGGCUAAUACCGGAUGAC-ACC--CAG--GCC--GCAG--GGC--C-GG-G-G-UU-GAAA-GC----------------------------------------------------------UCCG------GCGCCCGGGGAGGGGGCCGCGUCCCAUCAGCUGGCCGGUGAGGUGAAGGCUCACCGGGGCGACGACGGGUAGCGG-GUCUGAGAGGACGGUCCGCCACACUGGCACUGAGACACGGGCCAGACUCCUGCGGGAGGCAGCAGUGGGGAAUCUUGCGCAAUGGGC-GCAAGCCUGACGCAGCGAUGCCGCGUGGGU-GA-AGAAGGCC---CUCG--GGUCGUAAAGCCCUUUUGGCGGGG-AGGAUG--A---------------------------------UGACGUCACCCGCCGAAUAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAACACGUAGGGCGCGAGCGUUGUCCGGAAUCACUGGGCGUAAAGGG-CGCGCAGGUGGGUCCGCA-AGCGGG-GGGUGAAAGGCCG-GGGCUCAACCC-CG-GGACUGCUCACCGAACUGCGG-GCCUC-GAGGGGGUCAGGGGCCAGCGGAAUUCCGGGUGGAGAGGUGAAAUUCGUAGAGAUCCGGAGGAACGCCGG--CGGCGAAAGCGGCUGGCUGGGGCCGCCCUGACACUGAG-GCGCGAGA-GCG-UGGGGAGCGAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GGGC--AC-CGGG-CGUC-CGGGGG--G----------------------------CCGACCCCCCUGGGCGCC-------GCA-GCAAACGCGAUGAGUGCCCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAACAUGUGGUUUAAUUCGAGGCAACGCGAAGAACCUUA-CCUGGGCUUGACAUC-CCCGG------------GCCGCCCCGG-AGACGGGGCUU--CCCCUU----------------------------------CGGGGG----CCGGGUGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCCGUCCUCAGUUGCC-AGCGG------CUCGG-------------CCG--GG-CACUCUGGGGAGACUGCCGGUGA--CAA-GCCG-GAGGAAGGCGGGGACGACGUCAAGUCAUCAUGGCCCUCAUGCCCAGGGCUACACACGUGUUACAAUGGG-GGCG-ACAGCGGGC---CGCGAAGCCGCGAGGCGGA-GCGAAUCCCC--AAAAGCCCCCCCAGUUCGGAUCGCAGUCUGCAACCCGACUGCGUGAAGCCGGAAUCGCUAGUAAUCGCGGAUC-AGC-ACGCCGCGGUGAAUCCGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUCGGC-GGG-GGCGGAAGCCGC-C-G-GGCC-AACCC-CUUCGG-GGGGGGCA-GGCGUCCAAGCU-CACGUCGGCGACUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAGGAGAACCUGCGG---CU-GGACCACCUCCUUU
EU795287.1/4958-6529                   UUUUUGAAGGGUU-UGAU-CUUGGCUCAGAACGAACGCU-GG-CGG--CGUG-GAUUAGGCAUGCAAGUCGAACGAGGA------------UAUAUCCUU-----CGGGAU-A-UAA-----------------------------------------------------------------------------------------------------------------------------GCC-GAG-UGGCAUA-AGGGUGAGCAAUGCAUAGAU--UACCUACCUUUAGGAUA--AGGGCAACUUUGUGAAAACGGAGCUAAUACUUAAUAAUACAA--AAG-AAAA--UAAU--UUU--C-UU-U-U-GU-CAAA-GGGAGGGU----------------------------------------------AGCAAUACCU-----UUCGCCUAGAGAGGGGUUUAUGUCCUAUCAGCUUGUUGGUGGGGUAAUAGCCUACCAAGGCAAAGACGGGUAGCCG-GUUUAAGAGGAUGGUCGGCCACACUGGGACUGAGACACUGCCCAGACUUCUACGGAAGGCUGCAGUCGAGAAUCUUUCGCAAUGCCC-GAAAGGGUGACGAAGCGACGCCGCGUGGGU-GA-AGAAGGCC---UUCG--GGUUGUAAAGCCCUGUCAGGAGUU-AUGAAA-UGUGAGUGCGCU--AAUACUGUG----CUUAU--UUGACAAAGGCUCCAAAGGAAGUCACGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGUGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGAG-CACGUAGGUGGGUUUGCA-AGUCAG-AUGUGAAAGCCUU-CUGUUCAACGG-AA-GAAUUGCAUCUGAAACUGCUA-AUCUU-GAGUAUAGGAGGGGAGAAUGGAACUUCUGGUGGAGCGGUGAAAUGCGUAGAUAUCAGAAGGAACGCCGG--CGGCGAAAGCGAUUCUCUGGCCUAUUACUGACACUCAGUGUGCGAAA-GCU-AGGGGAGCAAACGGG-AUUAGAUACCCCGGUAGUCCU-AGCCGUAAA-CGAU-GGGC--AC-UAAG-UAGA-GGGGAU-UA----------------------------CCUA-UAUUCUCUCUGCC-------GUA-GCUAACGCAUUAAGUGCCCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUAAAACUCAAA-AGAAUUGACGGGGGCUCG-CAC-AAGCGGUGGAGCAUGUGGCUUAAUUCGAUGCAACGCGAAAAACCUUA-CCGGGGCUUGACAUG-AUAGAA----------GUAGGAACCUG-AAAGGGGGACG--AACGGUAUC----------------------------CAGUCCGUA----ACUAU-UACAG-GUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGACGUUGGGUUAAGUCCCC-UAACGAGCGAAACCCUUGUUUUUAGUUACC-AGCGG-----GUUAUG-------------CCG--GG-UACUCUAGAAAGACUGCCGUCGU--CAA-GACG-GAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUAUGCCCCGGGCUGCACACGUGCUACAAUGGU-CGGU-ACAGACGGA---AGCGAAGCCGAGAGGUGAA-GCGAAUCCUAA-AAAGCCGAUCUCAGUUCGGAUUGGAGGCUGAAAUUCGCCUCCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUC-AGCAAUGUCGCGGUGAAUAUGU-UCCCGAGCCUUGUACACACCGCCCGUCAAGCCACCCAAGCAGGA-UGC-ACCCGAAAACAU-U-AUAUCU-AACCAGGGCAACUUGGAGGAA-AAUGUUGAAGGA-GUGUUUUGUGAGGAGGACUA-AGU-CGUAACAAGGUAG-UCGUAGGAGAACCUGCGG---CU-GGAUCACCUCCUUU
EU795191.1/26193-27754                 UACACGGAGAGUU-UGAU-CCUGGCUCAGAACUAACGCU-AG-UGG--CGUG-UCUUAGUCAUGCGAGUCGAGCG-AGA-----------AAGUCUUCUU-----CGGAAG-A-CGA-----------------------------------------------------------------------------------------------------------------------------GUA-GAG-CGGCGAA-CGGGUGAGUAACGCGUGGGU--AAUCUUCCUUUGAGUUG--GGGAUAACAUUCCUAACGGAAUGCUAAUACCGAAUGUGGAGU--ACG--GCU--CUUG--GGC--C-GU-A-C-UC-UAAA-GGCGGCCUC-------------------------------------------UGCUUGCAUGCU-----GUCGCUCGAAGAUGAGCCCGCGUCCUAUUAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCAACGAUGGGUAGCCG-GCCUGAGAGGGUGAGCGGCCACACUGGCACUGAGACAAGGGCCAGUCCCCUACGGGGGCCAGCAGUCUAGAAAUUUGCACAAUCGUC-GAAAGACGGAUGCAGCGACGCCACGUGGAG-GA-UGAAGCCC---CUCG--GGGUGUAAACUCCUGUCAGGAGGG-AAGAAG-GUGCGGGUGAU----AAUACCAU----CCGUUACUUGACGGUACCUCCAGAGGAAGCUCCGGCUAACUGCGUGCCAGCAGCCGCGGUAAUACGUGGGGAGCAAGCGUUGUUCGGAUUUACUGGGCGUAAAGAG-CUCGUAGGUGGAUGUGUA-AGUCGG-AUGUGAAAUCCUC-UGGCUCAACCA-GA-GAACUGCACCCGAAACUGCAC-AUCUU-GAGUCCAGCAGAGGGAAUCGGAAUCAAGGGUGUAGCGGUGAAAUGCGUAGAGAUCCUUGAGAACACCAG--UGGCGAAGGCGGAUUCCUGGGCUGGCACUGACACUGAG-GAGCGAAA-GCG-UGGGUAGCGAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GGGU--AC-UAGG-CGUU-GGGGGA-UG----------------------------UUGA-CCCCCUCAGUGCC-------GUA-GCUAACGCAUUAAGUACCCCGCC--UGGG-GAGUAC-GGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCAGUGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUA-CCUGGGUUUGACAUC-CGGGA------------AACCCUCUAU-AAAUAGGGGGG--UGCCCUU--------------------------------CGGGGAA----UCCCGUGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGUCCUUAGUUGCC-AUCGG-----GUAAUG-------------CCG--GG-AACUCUAAGGAGACUGCCUGUGA--CAA-GCAG-GAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUACACCCAGGGCUGCACACGUGCUACAAUGGC-UGGU-ACAAACGGU---UGCAAUACCGCGAGGUGGA-GCCAAUCCGAA-AAAACCAGCCUCAGUUGGGAUUGGAGUCUGCAACUCGACUCCAUGAACGUGGAAUUGCUAGUAAUCGCGGAUC-AGC-AUGCCGCGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCAAGCUAGGAAAGCCGGA-GAU-ACCUGAAGUCGU-G-G-AUCC-AACC--CGCAA--GGGAGGAU-AGCGCCGAGGGU-AGGGCUGGCGAUUCGAGCUA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
FP245538.1/18229-19773                 UUUUUGGAGAGUU-UGAU-CCUGGCUCAGAGUGAACGCU-GG-CGG--CGUG-GAUUAGGCAUGCAAGUCGAGCG-AA-----------------CCCGC-----AAGGG-------------------------------------------------------------------------------------------------------------------------------------UU--AG-CGGCAAA-AGGGUGAGUAACACGUAAGU--AAUCUUCCCUCAAACCU--GGAAUAGCACCGUGAAAACGGUGGUAAUACCAGAUAAUUUCA--AUU-UUCC--GCAU--GGA-GA-GU-U-G-AG-CAAA-GGCGGGGA---------------------------------------------CCGAAAGGCCU-----GUCAUUUGAGGAUGAGCUUGCGUACCAUCAGCUAGUUGGUAGGGUAAAGGCCUACCAAGGCUUAGACGGUUAGCUG-GUCUGAGAGGACGACCAGCCACAUUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGGAUAUUUAGCAAUGGAC-GAAAGUCUGACUAUGCGACGCCGCGUGCAG-GA-UGAAGGUC---UUCG--GAUUGUAAACUGCUUUUGUCAGGG-GAGAAA-CCUCCGACGUU---AACACCGUC-----GGAG--CUGACGGUACCUGACGAAUAAGCCACGGCCAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGUGGCAAGCGUUACUCGGAAUUAUUGGGUGUAAAGGG-CAGGUAGGCGGCCUGGUA-AGUGAG-AGGUGAAAUCCUG-CGGUUCAAUCG-CA-GAACUGCCUUUCAAACUGUCG-GGCUU-GAGUGUGACAGAGGAAAAUGGAAUUCUCGGUGUAAGGGUGAAAUCUGUAGAUAUCGGGAAGAACACCAA--CGGCGAAGGCAAUUUUCUGGGUCACAACUGACGCUGAG-CUGCGAAA-GCU-AGGGGAGCAAACAGA-AUUAGAUACUCUGGUAGUCCU-AGCUGUAAA-CGAU-GAGU--AC-UAGG-UGUU-GGUCCC-------------------------------UUCG--GGGAUCGGUGCC-------GAA-GCUAACGCAUUAAGUACUCCACC--UGGG-GACUAC-GGUCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAACAUGUGGUUUAAUUCGAUGCUACGCGAAAAACCUCA-CCUGGGCUUGACAUG-UAUGUA----------GUAGCGAACUG-AAAGGGGAGCG--AACCGUCA------------------------------AGUCGGUU----GCAUA-CACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCAUUGCCCUAUGUUGCC-ACUCU----GGUUUGCCGAAAGGUAGAUCGGA--AG-CACUCUUAGGGGACUGCCUGGGA--CAA-CCAG-GAGGAAGGUGGAGAUGACGUCAAGUCAGUACGGCCUUUAUGCCCAGGGCGACACACGUGUUACAAUGGU-CACU-ACAAAGGGU---UGCCAACCCGCGAGGGGGA-GCUAAUCUCAA-AAAAGUGGCCUCAGUUCGGAUUGGAGUCUGCAAUUCGACUCCAUGAAGCCGGAAUCGCUAGUAAUGGUAGAUC-AGC-ACGCUACCGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGCGAUGGGAGCCGGA-AGU-ACCCGAAGUCCU-A-----------U---GUAG---A-------UAGGCCCAAGGU-AAAGCCGGUGACUGGCGCUA-AGU-CGUAACAAGGUAA-CCGUACGGGAACGUGCGG---UU-GGAUCACCUCCUUU
DQ234124.2/5-1530                      CAAGCUUAGAGUU-UGAU-CAUGGCUCAGGACGAACGCU-GG-CGG--UGCG-CCUUAUGCAUGCAAGUCGAGCG-AAGCU--------UUUCAGUAGUU-----UACUAC-A-GAAAA-------------------------------------------------------------------------------------------------------------------------UGACU-GAG-CGGCGAA-CGGGUGAGUAACGCGUGAGC--AAUCUACCUUAGUUACA--GGGAUAGCCCGAGGAAACUCGGAUUAAUACCUGAUAUUCUUU--AUU-UCUC--GCAU--GAG-AA-UA-A-A-AG-GAAA-GG----------------------------------------------------------UCAG------CCGAACUAAGAUGAGCUCGCGUUCUAUCAGCUAGUUGGUGAGGUAAAAGCUUACCAAGGCUACGACGGAUAGCUG-GUCUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCUGCAGCAGGGAAUAUUGUGCAAUGAAC-GAAAGUUUGACACAGCGACACCGCGUGUGG-GA-UGACGGAU---CUAG--GUUUGUAAACCACUUUCAGGAGGG-AAGAAA--A---------------------------------UGACGGUACCUCCACAAGAAGCCCCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCGAGCGUUGUCCGGAUUUAUUGGGCGUAAAGAG-CUCGUAGGCGGUUCAACA-AGUCGG-UCGUGAAAGUUCA-GGGCUCAACCC-UG-AAAUGUCGAUCGAUACUGUUGUGACUA-GGAUACGGUAGAGGUGAGUGGAAUUCCGAGUGUAGCGGUGAAAUGCGUAGAUAUUCGGAGGAACACCAA--UUGCGAAGGCAGCUCACUGGACCGCUAUCGACGCUGAG-GAGCGAAA-GCU-AGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCU-AGCUGUAAA-CGAU-GGAU--AC-UAGA-CGUA-GGAACUGGA----------------------------UUGA-CGGUUUCUGUGUC-------GUA-GCUAACGCGUUAAGUAUCCCGCC--UGGG-GAGUAC-GGUCGCAAGACUAAAACUCAAA-GGAAUUGACGGGACCCCG-CAC-AAGCGGCGGAGCAUGCGGCUUAAUUCGAUGAUACCCGUAGAACCUUA-CCUGGACUUGACAUAUAGGGU------------CAAGCUAUAG-AGAUAUAGUGU----GCAU----------------------------------UAGC------GCCCUAUACAG-GUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGUCCUAUGUUGCC-AGCA------UUUAGU--------------UG--GG-GACUCAUAGGAGACUGCCGGUGA--UAA-ACCG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUGCACGCAUGCUACAAUGGC-AAGU-ACAACGAGU---CGCAAUACCGCGAGGUGGA-GCAAAUCUCUU-AAAGCUUGUCUCAGUUCGGAUAGGAGUCUGCAACUCGACUCCUUGAAGUUGGAGUCGCUAGUAAUCGCAAAUC-AGCAAAGUUGCGGUGAAUACGU-UCUCGGGGUUUGUACACACCGCCCGUCAAGUCACGGAAGUCGGC-AAU-ACCCGAAGCCAG-U-G-GUCU-AACCC-UUUUA--GGGAAGAA-GCUGUCGAAGGU-AGGGUCGGUAACUGGGACUA-AGU-CGUAACAAGGUAG-CCGUACGGGAACGUGCGG---CU-GGAUCACCUCCUUA
DQ455886.1/67-1589                     GGAAUGUAGAGUU-UGAUACCUGGGUCAGGAUAAACGCU-GG-UAG--CGCA-CAUAAGACAUGCAAGUCGAACG-AACUU--------AACCAUUAGUU-----UACUAU-U-GGAG--------------------------------------------------------------------------------------------------------------------------CGGUU--AG-UGGCGGA-CUGGUGAGUAACACGUAAGC--AACCUGCCUAUCAGAGG--GGAACAACAGUUAGAAAUGACUGCUAAUACCGCAUAUGCCUU--AAU-CUUC--ACAU--GGA-GA-UA-G-A-GG-GAAA-GGA---------------------------------------------------------GCAA-----UCCGCUGAUAGAUGGGCUUGCGUCUGAUUAGCUAGUAGGUGGGGUAAAGGCUUACCUAGGCAACGAUCAGUAGCCG-GACUGAGAGGUUGGACGGCCACAUUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUCGGGAAUAUUGCGCAAUGGAG-GAAACUCUGACGCAGUGACGCCGCGUGCAG-GA-AGAAGGUU---UUCG--GAUUGUAAACUGCUUUAGACAGGG-AAGAAA-AA---------------------------------GGACAGUACCUGUAGAAUAAGCUCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGAGCAAGCGUUAUCCGGAUUUAUUGGGUGUAAAGGG-UGCGUAGACGGGAAGUCA-AGUUGG-UUGUGAAAUCCCU-CGGCUCAACUG-AG-GAACUGCAACCAAAACUAACU-UUCUU-GAGUGCUGGAGAGGAAAGUGGAAUUCCUAGUGUAGCGGUGAAAUGCGUAGAUAUUAGGAGGAACACCAG--UGGCGAAGGCGACUUUCUGGACAGUAACUGACGUUGAG-GCACGAAA-GUG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CACCGUAAA-CGAU-GGAU--AC-UAGG-UGUA-GGGGAU--G----------------------------AAUA--AUCCUCUGUGCC-------GUC-GCAAACGCAGUAAGUAUCCCACC--UGGG-GAGUAC-GGCCGCAAGGUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCAGUGGAGUAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCAAGGCUUGACAUACAGGGG------------AAUACUUAAG-AGAUUAAGUCG--CUCUUC------------------------------------GGAG----CCGCUGUACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGUGAUUAGUUGCC-AGCAC-----GUAAAG-------------GUG--GG-AACUCUAAUCAGACUGCCGGUGA--UAA-AUCG-GAGGAAGGUGGGGACGACGUCAAAUCAUCAUGCCCUAUAUGUCUUGGGCUACACACGUACUACAAUGGC-UGUA-ACAGAGGGA---AGCGAAACAGUGAUGUGGA-GCGAAACCCAA-AAAAGCAGUCUCAGUUCGGAUUGAAGGCUGAAAUUCGCCUUCAUGAAGCCGGAAUUGCUAGUAAUGGCAGGUC-AGC-AUACUGCCGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGAGAGCCGGG-GGG-ACCCGAAGUCGG-C-A-GUCU-AACC---GCAA---GGAGGAC-GCCGCCGAAGGU-AAAACUGGGGAUUGGGGGGA-AGU-CGUAACAAGGU-A-CCAUGUGUCCUCA-GCGG---UACGCCUCGCCUCCCCC
FP245539.1/21728-23295                 UUUACGGAGAGUU-UGAU-CCUGGCUCAGAACGAACGCU-GG-CGG--CGUG-GAUUAGGCAUGCAAGUCGAACG-GAU------------UUCUUAGCU----GUUUCGA-G-AA-------------------------------------------------------------------------------------------------------------------------------AU-CAG-UGGCGAA-AGGGUGAGUAACACGUGGGU--AACCUACCCAAAGGAUU--GGGACAACCAACCGAAAGGUUGGCUAAUACCGGAUAAGACCA--CGA-CUUC--GAGA--GAA-GA-UG-A-G-GU-CAAA-GAUGGGGAUCU---------------------------------------GCUUCGGCGGACCU-----AUCGCCUAUGGAGGGGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCUAUGACGGGUAGCUG-GUCUGAGAGGAUGGUCAGCCACAUCGGGACUGAGAUACUGCCCGGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUCGCAAUGGGG-GAAACCCUGACGAAGCGACGCCGCGUGCAG-GA-UUAAGGCC---UUCG--GGUUGUAAACUGCUGUCGCCUGGG-ACGAAC-AAUGUCCAGG-----UGAAUAAUCU-GGUUAU--UCGACGGUACCAGGAAAGGAAGCCACGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGUGGCAAGCGUUGUUCGGAUUCAUUGGGUGUAAAGGG-UGCGUAGGCGGCUUGGAA-AGUCAG-AUGUGAAAUACUA-CAGCUUAACUG-UA-GAACUGCAUUUGAAACUUCCA-GGCUA-GAGUGCAGGAGAGGUGAAGGGAAUUCCCGGUGUAAGGGUGAAAUCUGCAGAUAUCGGGAAGAACACCUG--UAGCGAAGGCGCUUCACUGGUCUGUUACUGACGCUGAGUGCACGAAG-GCG-UGGGGAGCGAACGGG-AUUAGAUACCCCGGUAGUCCA-CGCAGUAAA-CGAU-GUUC--AC-UAGG-UGUC-GGGCGA-GU----------------------------UUCAACUCGUUCGGUGCC-------GCA-GCUAACGCAUUAAGUGAACCACC--UGGG-GAGUAC-AGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAACGGUGGAGCAUGUGGUUUAAUACGACGAUACGCGUGGAACCUCA-CCCAGGCUUGACAUGUACUAG-----------AAAGCCUUAUG-AAAGUAGGGCC--UUCCCU----------------------------------CAAGGA----CUGGUACACAG-GUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUCCUUAGUUGCC-AGCAC-----GAAAG--------------GUG--GG-CACUCUAAGGAGACUGCUUACGA--UAA-GUAG-GAGGAAGGUGGGGAUGACGUCAAGUCAGUACGGCCCUUACGCCUGGGGCUACACACGUGCUACAAUGGU-CGGU-ACAAAGGGU---CGCCAAACCGCGAGGUGGA-GCUAAUCCCAA-AAAACCGGCCCCAGUUCAGAUCGAAGGCUGCAACUCGCCUUCGUGAAGCUGGAAUCGUUAGUAACCCCGUAUC-AGCCACGACGGGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCAAGUGAUCCGAGCUGGG-AGU-ACCCGAAGUAGU-U-U-GGUU-AACC--CGCAA--GGGAAGCC-GGCUGCGAAGGU-AAAACUAGUGAGGAGCACUA-AGU-CGUAACAAGGUAG-CCUUACCGGAAGGUGAGG---CU-GGAUCACCUCCUUU
GU180079.1/11489-13117                 AGCACGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCAUACG-GAU-----------------ACGG-----AAGUUA-G-AAAAUAGAGGUCAGAGGUUAGAAAGUAAGGAGGAAAUUAGCUCCGCUA-----------------------------------AUUUUUCCUGAUCUGACUUCUGACUUCCGACUUCUAACUUCUGUUAUC--AG-UGGCGCA-CGGGUGAGUAACGCGUGGGA---AUCUACCCGGUAGUGG--GGGAUAACCCCUCGAAAGGGGGGCUAAUACCGCAUAAG-----------UCC--UACG--GGG--------------UAAA-GAUGG---------------------------------------------------CCUCUUAGAGGCUAUCGCUUCCGGAUGAGCCCGCGUCCUAUUAGCUAGUUGGUGAGGUAAUGGCUUACCAAGGCCACGAUGGGUAGCCG-GUCUGAGAGGAUGAACGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGCGCAAUGGGG-GAAACCCUGACGCAGCAACGCCGCGUGGAU-GA-UGAAGGCC---UUCG--GGUUGUAAAGUCCUGUUCUGGGGG-AAGAAA-CGGUAGGAAGC---CAAUACCUUC---CUGCC--CUGACGGUACCCCAGCAGAAAGCUCCGGCCAAUUAUGUGCCAGCAGCCGCGGUAAUACAUAAGGAGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAG-CUCGUAGACGGUUCGGAA-AGUCAG-CUGUGAAAUCACC-AGGCUCAACCU-GG-UAGGGUCAGUUGAGACUUCCG-AACUU-GAGGGUAGAAGAGGAAAGUGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCAG--UGGCGAAGGCGGCUUUCUGGUCUACCCCUGACGUUGAG-GAGCGAAA-GCC-AGGGGAGCAAACGGG-AUUAGAUACCCCGGUAGUCCU-GGCCCUAAA-CGAU-GGAU--AC-UAGG-UGUA-GGAGGU--A----------------------------UCGA-CCCCUUCUGUGCC-------GCA-GUUAACACAUUAAGUAUCCCGCC--UGGG-GAGUAC-GGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCGGGGCUUGACAUCUUUCUG------------ACCGCCUGGG-AAACCAGGUCU--UCUUCCUU------------------------------CGGGAAGA----CAGAAAGACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCA-CAACGAGCGCAACCCUUGUCCUUAUUUGCC-AGCCU-----GUUUAC-------------AGG--UG-CACUUUAAGGAGACUGCCGUAGA--UAA-UACG-GAGGAAGGUGGGGAUGACGUCAAAUCCUCAUGCCCCUUACGUCCCGGGCUACACACGUGCUACAAUGGU-CUGU-ACAAAGGGU---GACCAAGGAGCGAUCCGGA-GUCAAUCCCAA-AAAGCAGGCCCCAGUUCGGAUUGGAGGCUGCAACUCGCCUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUC-AGC-AUGCCGCGGUGAAUCCGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACGAAAGUUGGC-GAU-ACCUGAAGUUAC-C-A-UACC-AACC--CUUCG--GGGAGGAA-GGUACCGAGGGU-AUGGUCAGCGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAUCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
CP002858.1/2251537-2249985             UGGAUGGAGAGUU-UGAU-CCUGGCUCAGAACGAACGCU-GG-CGG--CGUG-CUUAACACAUGCAAGUCAGGGG-GAA------------UCCUCCCUU-----CGGGGA-G-GUA-----------------------------------------------------------------------------------------------------------------------------GUA-CAC-CGGCGCA-CGGGUGAGUAACGCGUGAGU--GACCUACCCAUUAGACC--UGGAUAACCCGGCGAAAGUUGGGCUAAGACAGGAUGUGUUAA--UAC--ACU--UCAU--GGU--G-UA-U-U-GA-UAAAGGCAG------------------------------------------------------GUUUCGG--CUUGUGCUAAUGGAUGGGCUCGCGUCUGAUUAGCUAGUUGGUAAGGUAAAGGCUUACCAAGGCGACGAUCAUUAGGCG-GCCUGAGAGGGUGGUCGCCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGCGCAAUGGGC-GAGAGCCUGACGCAGCGACGCCGCGUGGAC-GA-GGAAGGCC---UUCG--GGUCGUAAAGUCCUUUUUUACGGG-AAGAAA-GUUAUUAACAGU--AACUGGUUA-----AUAU--UUGACGGUACCGUAAGAAUAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGGGCGAGCGUUGUUCGGAAUUACUGGGCGUAAAGCG-UACGUAGGCGGCGUGGUA-AGUCGG-AGGUUAAAGGCUA-CGGCUCAACCG-UA-GUAGGGCCUUUGAUACUAUCA-UGCUA-GAGUGUCGGAGGGGGUAGCGGAAUUCCCUGUGUAGCGGUGAAAUGCGUAGAUAUAGGGAAGAACACCAG--UAGCGAAGGCGGCUACCUGGCCGAUCACUGACGCUGAG-GUACGAGA-GCG-UGGGUAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCUGUAAA-CGAU-GGAC--GC-UAGG-UGUU-GGAGGA--A----------------------------CCGA-CCCCUUCAGUGCC-------GAA-GCCAACGCGUUAAGCGUCCCGCC--UGGG-GAGUAC-GACCGCAAGGUUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCACGUGGUUUAAUUCGAUGCUAACCGAAGAACCUUA-CCUGGUCUUGACAUC-CUCCG------------GAGGGACUAG-AGAUAGUUCUG--UGCCCGCCU---------------------------UUGGCGGGAG----CGGAGAGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUUCAUAGUUGCC-AUCGG------UAAGG-------------CCG--GG-CACUCUAUGGAUACUGCCCGUGA--UAA-ACGG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCUUUAUGACCAGGGCUACACACGUGCUACAAUGGU-ACGU-ACAGAGGGC---AGCGAAGCCGCGAGGUGUA-GCGAAUCCCUA-AAAGCGUGCCUUAGUUCGGAUUGUAGUCUGCAAUUCGACUACAUGAAGGCGGAAUCGCUAGUAAUCGCAGGUC-AGCAAAACUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACGGGAGUUGGU-UGU-ACCUGAAGCCGG-U-G-GCCC-AACU---GC-----GGAGGGA-GCCGUUUAUGGU-AUGACUGGCAACUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGUGG---CU-GGAUCACCUCCUUU
DQ767883.1/10-1557                     CCCUUGCA-------UCU-CAU-----GAAUUGAUCGCUGGG-UGGGCCGUGCCUUAACACAUGCAAGUCGAGCG-AGA-----------ACGGCCUCUU-----CGGAGG-C-UCA-----------------------------------------------------------------------------------------------------------------------------GUA-GAG-CGGCGCA-CGGGUGAGUAACGCGUGGAU--GAUCUACCUUUGAGAUU--GGGAUAACAGCUGGAAACGACUGCUAAUACCAGAUACGCUUC--AUA--UUU--AACU----U--U-AU-G-A-GG-GAAA-GAUGGCCUC-------------------------------------------UGCUUGCAAGCU-----AUCGCUCGAAGAUGAGUCCGCGUUUCAUUAGCUAGUUGGUAGGGUAAUGGCCUACCAAGGCGACGAUGAAUAGCUG-GUCUGAGAGGAUGACCAGCCACACUGGGACUGGAACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGG-GAAACCCUGACGCAGCGACGCCAUGUGAGG-GA-CGAAGGCU---CUAG--GGUCGUAAACCUCUGUCAGAAGGG-AAGAAC-CUCAUAAGAUCU-AAUAAAUCUU-----UUGA--CUGACGGUACCUUCAGAGGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCGAGCGUUAAUCGGAAUUACUGGGCGUAAAGCG-CGCGUAGGCGGCGAUGUA-AGUCAG-AUGUGAAAGCCCU-CGGCUCAACCG-GG-GAAUUGCAUUUGAUACUGCAU-UGCUU-GAGUAUCGGAGAGGGUGGCGGAAUUCCAGGUGUAGGAGUGAAAUCCGUAGAUAUCUGGAGGAACAUCAG--UGGCGAAGGCGGCCACCUGGACGAAUACUGACGCUGAG-GUGCGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GGAU--GC-UAGA-UGUC-GGGCCU-------------------------------UAAC--CGGUUCGGUAUC-------GAA-GUUAACGCGAUAAGCAUCCCGCC--UGGG-GAGUAC-GGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUA-CCUGGACUUGACAUC-CUGAG------------AAUCCUUUAG-AAAUAAGGGAG--UGCCCUU--------------------------------CGGGGAA----UUCAGUGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUUGUUAGUUGCC-AUCAC-----AUAAUG-------------GUG--GG-CACUCUAAUGAGACUGCCCGGGU--CAA-CCGG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGUCCAGGGCUACACACGUACUACAAUGGU-GGAU-ACAGAGGGU---CGCGAAGCCGCGAGGUGAA-GCCAAUCCCAG-AAAAUCCAUCCCAGUCCGGAUCGGAGUCUGCAACUCGACUCCGUGAAGUUGGAAUCGCUAGUAAUCCCGGAUC-AGC-AUGCCGGGGUGAAUACGUUUCCCGGGCUUUGUACACACCGCCCGUCACACCCCGAAAGCUGGUUUCU-GCCCAAAAUCGA-C-G-GACU-AACC---UUCG---GGAGGUA-GUCGCCUACGGU-AGGGCUGGUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCU--
FJ985790.1/19-1543                     GCAAGAUAGAGUU-UGAU-CCUGGCUCAGAUUGAACGCU-GG-CGG--AAUG-CUUUACACAUGCAAGUCGAGCG-GCA------------GCGCGGGGC-----AACCUG-G-CG-------------------------------------------------------------------------------------------------------------------------------GC-GAG-CGGCGAA-CGGGUGAGUAAUACAUCGGA---ACAUGUCCAAUCGUGG--GGGAUAGCCCGGCGAAAGCCGGAUUAAUACCGCAUGAG-----------CUC--UGAC--GAG--------------GAAA-GCGGGG--------------------------------------------------GACCUUCGGGCCUCGCGCGAUUGGGUUGGCCGAUGUCCGAUUAGCUAGUUGGUGAGGUAAAGGCUUACCAAGGCGAUGAUCGGUAGCUG-GUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGGG-GAAACCCUGAUCCAGCCAUUCCGCGUGAGU-GA-AGAAGGCC---UUCG--GGUUGUAAAGCUCUUUUGUCCGGA-GCGAAA--CGGUUACGGUG-AAUAUCCGUG-----ACUA--CUGACGGUACCGGAAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCGAGCGUUAAUCGGAAUUACUGGGCGUAAAGCG-UGCGCAGGCGGGCUUUUA-AGCCAG-ACGUGAAAUCCCC-GGGCUUAACCU-GG-GAAUGGCGUUUGGGACUGGAA-GUCUG-GAGUGCGGCAGAGGAGACUGGAAUUCCUGGUGUAGCAGUGAAAUGCGUAGAUAUCANGAGGAACACCGA--UGGCGAAAGCAGGUCUCUGGGCUGACACUGACGCUCAU-GCACGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCCUAAA-CGAUGUUCG--AC-UGGU-UGUU-GGGGGU--U----------------------------UGAC--ACUCUCAGUA---------CGA-GCU-ACGC-GUGAGUCGA-CGCCUAUGAG-AGAUUCGGGCAGCAAGGUUAAAACUCAAA-GGAAUUGGCGGGGACCCGCCAC-AAGCGGUGGAUUAUGUGGAUUAAUUCGAUGCAGCGCGAAAAACUUUA-CCUACCUUUGACAUG-UCCUG------------GAGCCCGUUG-AGAGGUGGGUG--UCCCCGA--------------------------------AAGGGAA----CGGGAACACAGUGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGGCAACGAGCGCAACCCUUUUCAUUAGUUGCC-A-CA------UUCAGU--------------UG--GG-CACUCUAAGGAGACUGCCGGUGA--CAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUGGGUAGGGCUUCACACGUAAUACAAUGGC-GCGU-ACAGAGGGC---UGCGAAGGGGUGACCUGGA-GCCAAUCCCUGAAAAGCGCGUCGUAGUCCGG-AUGCAGUCUGCAACUCGACUGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUC-AGC-AUGUCGCGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGCGGGU-UUU-ACCAGAAGUAGG-U-A-GCUU-AACC---GCAA---GGAGGGC-GCUUACCACGGU-AGGAUUCGUGACUGGGGUGA-AGU-CGUAACAAGGUA------------ACCAUCUU---CU-AGAAGAUCUCCUAC
AY858509.2/1-1537                      UCGCCCUUGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-AG-CGG--CAGG-CUUAACACAUGCAAGUCGAGGG-GCAG----------CAUUUCCAGC-----AAUGGA-A-GAU-----------------------------------------------------------------------------------------------------------------------------GGC-GAC-CGGCGCA-AGGGUGCGUCACGCGUGAGC--AACAUACCUAUCACAGG--AGGAUAAUCCAUGGAAACGUGGUCUAAUACUCCAUAGAAUUG--GUU-UCUG--GCAU--CAG-GA-AC-C-A-CU-UAAA-GC----------------------------------------------------------UACG------GUGGUGAUAGAUUGGCUCGCGUGACAUUAGCUAGAUGGAGAGGUAACGGCUCCCCAUGGCGACGAUGUCUAGGGG-UUCUGAGAGGAAGGUCCCCCACACUGGUACUGAGACACGGACCAGACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGACAAUGGGU-GGAAACCUGAUCCAGCCAUGCCGCGUGCAG-GA-AGACUGCC--CUAUG--GGUUGUAAACUGCUUUUGUAUGGG-AGCAAU-AAGCUCUAC--------GAGUAG-----GGUG--AUGAGAGUACCAUACGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCGAGCGUUAUCCGGAUUUAUUGGGUUUAAAGGG-UGCGUAGGCUGUUAUGUA-AGUCAG-CGGUGAAAUACCA-GAGCUUAACUU-UG-GGGCUGCCGUUGAUACUGCAU-AGCUG-GAAUAUGGUUGCUGUUGGCGGAAUGUGUAGUGUAGCGGUGAAAUGCAUAGAUAUUACACAGAACACCGA--UUGCGAAGGCAGCUGACAAAGCCAUCAUUGACGCUGAU-GCACGAAA-GUG-UGGGGAUCAAACAGG-AUUAGAUACCCCUGUAGUCCU-GGCAGUAAA-CGGU-GCAC--GC-UUGG-UGUG-CGGGGA--A----------------------------UCGA-CCCCCUGCGUGCC-------GGA-GCUAACGCGUUAAGCGUGCCGCC--UGGG-GAGUAC-GGUCGCAAGAUUAAAACUCAAA-GAAAUUGACGGGGACCCG-CAC-AAGCGGUGGAGUAUGUGGCUUAAUUCGAUGCAACGCGAAGAACCUUA-CCUGGGCUUGACAUGUAAUGA------------ACAACAUGUG-AAAGCAUGCGA--CUCUUC------------------------------------GGAG----GCGUUACACAG-GUGCUGCAUGGCCGUCGUCAGCUCGUGUCGUGAGAUGUUUGGUUAAGUCCAG-CAACGAGCGCAACCCCUGUUGCCAGUUACC-AGCAC-----GUGAAG-------------GUG--GG-GACUCUGGCGAGACUGCCCAGAU--CAA-CUGG-GAGGAAGGUGGGGACGACGUCAGGUCAGUAUGGCCCUUAUGCCCAGGGCUGCACACGUACUACAAUGCC-CAGU-ACAGAGGGG---GCCGAAGCCGCGAGGCGGA-GGAAAUCCUA--AAAACUGGGCCCAGUUCGGACUGUAGGCUGCAACCCGCCUACACGAAGCCGGAAUCGCUAGUAAUGGCGCAUC-AGCUACGGCGCCGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCACAUCAUGGAAGCCGGU-CGC-ACCCGAAGUAUC-U-GAAGCC-AACC---GCAA---GGAGGCA-GGGUCCUAAGGU-GAGACUGGUAACUGGGAUGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUU-
AF407718.1/1-1486                      -UCGAUUAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCGAACG--------------------GUCGC-----AAGAC-----------------------------------------------------------------------------------------------------------------------------------------AG-UGGCGCA-CGGGUGAGGAACACGUAGCU--AACCUGCCCUCAAGACC--GGGAUAACGGAUCGAAAGGUCUGCUAAUACCGGAUAAGCUCA--CGU--GAA--GUAG-AAGC--A-AG-U-G-AG-AAAA-GG----------------------------------------------------------GAUA------CCGCUUGAGGAGGGGGCUGCGGCCUAUCAGGUAGUUGGUGAGGUAAUGGCUCACCAAGCCGACGACGGGUAGGGG-GCCUGAGAGGGUGACCCCCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGGAUAUUGCACAAUGGGC-GCAAGCCUGAUGCAGCGACGCCGCGUGAGU-GA-AGAAGGCC---UUCG--AGUCGUAAAACUCUUUUGCCGAUG-ACGAGG-AA---------------------------------GGACGGUAGUCGGCGAAUAAGCCUCGGCUAACUACGUGCCAGCAGCCGCGGUAAAACGUAGGAGGCGAGCGUUAUCCGGAGUUACUGGGCGUAAAGCG-UGCGCAGGCGGUUCUGUA-AGUGGC-UUGUGAAAGCGCC-CGGCUAAACCG-GG-CGAGGACAGGUCAGACUGCAG-GGCUG-GGAUGGAACAGAGGGCUGUGGAAUUCCGGGUGUAGCGGUGAAAUGUGCAGAGAUCCGGAGGAACACCAG--AGGUGAAGACGGCGGCCUGGGUUCCAAUCGACGCUGAG-GCACGAAA-GCG-UGGGGAGCGAACGGG-AUUAGAGACCCCGGUAGUCCA-CGCCGUAAA-CGAU-GCAG--AC-UAGA-UGUU-CGUGCC-GG----------------------------GAAACCGGGAUGAGCGUC-------GCA-GCUAACGCGCUAAGUCUGCCGCC--UGGG-GAGUAC-GGUCGCAAGACUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCAGCGGAGCGUGUGGUUUAAUUCGAGGCUACACGAAGAACCUUA-CCUGGGUUUGACAUCACGGUG-----------GUAGUGAAGCG-AAAGCGGAACG---ACCUA----------------------------------CGGG------AGCCGUGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUCGGUUAAGUCCGA-AAACGAGCGCAACCCUCGGUGCCAGUUA-------------CAGGUG------------------------UCUGGCGCGACUGCCUUCGA--GAA-GGAG-GAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGGCCUUUAUAUCCAGGGCUACACACACGCUACAAUGGG-CGGC-ACAAUUGGA---AGCGAACCCGCGAGGGGGA-GCGGAUCCGUG-AAAGCCGUUCGUAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCUGGAGUUGCUAGUAACCGCAGGUC-AGCGAUACUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGGGAGCUGGU-CAC-GCCUGAAGCCGA-U-G-AGCG-AACC---GCAA---GGAAGCA-GUCGUCGAAGGC-AGGGCCGGUGACUGGGACGA-AGU-CGUAACAAGGUAG-CUGUAGCGGAAGCUGCGG---CU-GGAUCACCUCCUUA
DQ234104.2/5-1490                      CAAGCUUAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CGG--UGUG-CCUUAGGCAUGCAAGUCGAACG-AUA------------AGCUUCCUU-----CGGGAA-G-UG-------------------------------------------------------------------------------------------------------------------------------GA-CAG-UGGCAGA-CGGGUGAGUAACACGUAGGU---AUCUACCGAAGAGUGG--GGAAUAGCCAGCCGAAAGGUUGGGUAAUACCGCAUAAU-----------CCC--UCCG--GGG--------------CAAA-GUA---------------------------------------------------------UUUA-----UACGCUUUUCGAGGAGCCUGCGGGCUAUCAGUUAGUUGGUGGGGUAAUGGCCUACCAAGACUACGACGGCUAGCCG-AUGUGAGAGCAUGAUCGGCCACAAGGUUACUGAGACACGGAACCUACACCUACGGGUGGCAGCAACCGGGAAUAUUGCGCAAUGGAC-GAAAGUCUGACGCAGCGACACCGCGUGCAG-GA-AGACGCUU---UUAG--GAGUGUAAACUGCUGUGGCGAGGG-AGAAAU-UU---------------------------------UGAUAGUACCUCGCUAGAAAGCACCAGCUAACCACGUGCCAGAAGCUUCGGUAAUACGUGGGGUGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGGG-UCCGUCGGCGUCUUUAUA-AGUCGG-UUGUUUAAGACUG-AGGCUCAACUU-CA-GAGAGGCAAACGAUACUAUAA-GGAUA-GAGUCUGUUCGAGGAAACUAGAAUUCUUGGUGGAGGGGUGAAAUCCGUAGAUAUCAAGAGGAAUACCAU--GCGCGAAGGCAGGUUUCUAGGACAUGACUGACGCUCAG-GGACGAAA-GCU-UGGGUAGCAAAAGGG-AUUAGAGACCCCUGUAGUCCA-AGCCGUAAA-CGCU-CCUU--GC-UAGU-UGCU-CGAG---------------------------------UUUA----CUUGAGUGGC-------GUAAGCUAACGCGUUAAGCAAGGCGCC--UGGG-GAGUAC-GACCGCAAGGUUAAAACUCAAA-GGAAUUGACGGGGGAGCG-CAC-AACCGGUGGAGCAUGUGGUUUAAUUCGAUACAAAGCGAAAAACCUUA-CCCGGGAUUGACAUGUACCUG-----------CACGGCUAUGG-AAACAUAGCUU--UCUUC-------------------------------------GAGA----GUGGUACACAG-GUGAUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGACGUCCACUUAAGUGUGG-UAACGAGCGCAACCCUUGUUCUGUGUUA-----UAC------------------------GUG--------UCACAGAAGACUGCCCUAGUUUUAC-UAGG-GAGGAAGGAGAGGACGAUGUCAAGUCAGCAUGUCCCUUACACCUGGGGCUACACACAUCCUACAAUGGA-GCCG-ACAACAGGU---AGCGACGAGGUAACUCUGA-GCUAAUCCUCU-AAACGGCCCCUCAGUUCGGAUUGAGGGCUGCAAUUUGCCCUCAUGAAGCCGGAAUCGGUAGUAAUCGCAAAUC-AGC-AGGUUGCGGUGAAUACGU-UCUCGCUCCUUGUACACACUGCCCGUCAAGCCAGCAAAGUCAGC-AAC-GCCCGAAGCGGGUG-A-CCGU-AACUA-GUUUAC-UAGAGCGG-CCCUUCUACGGC-GAGGUUGGCGAUGAGGACUA-AGU-CGUAACAAGGUAU-CCGUACUGGAAGGUGCGG---CU-GGAUCACCUCCUUA
AY713479.1/12029-13578                 UUUUGUGAGAGUA-UGAU-ACCGGCUCAGGACGAACGCU-GG-CGG--CGUG-GAUUAGGCAUGCAAGCCGAACG-AGA-----------AGUCGGGCUU-----CGGCCC-G-AU------------------------------------------------------------------------------------------------------------------------------GGA-AAG-UGGCGAA-AGGGUGAGUAACGCGUGGGU--AAUUUACCUCUGAGAUG--GGGAUAACAAUUCGAAAGGAUUGCUAAUACCAAAUACGAUCC--GGU-UGAC--UUCG--GUC-GG-CC-G-A-AU-GAAA-GGUG------------------------------------------------------GCUUCGG--CUGCCGCUCGGAGAUGAGCCCGCGUCCUAUUAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCAACGAUGGGUAGCUG-GUCUGAGAGGAUGGUCAGCCACAUUGGGACUGAGACACUGCCCAAACUCCUACGGGAGGCUGCAGUCGAGAAUAUUUCGCAAUGGGG-GAAACCCUGACGAUGCGACGCCGCGUGGGG-GA-UGAAGGCC---UUCG--GGUUGUAAACCUCUGUGUUAUGGG-AUGAAU-UGGUCGUUGCCG--AUAAAGCAA----CGUUU--UUGACGUUACCAUAGUAGAAAGCCCCAGCUAACUACGUGCCAGCAGCUGCGGUAAUACGUAGGGGGCAAGCGUUGUCCGGAAUCACUGGGCGUAAAGCG-CGCGCAGGCGGUGGAAUA-AGUCAG-ACGUGAAAGGGUU-CGGCUCAACCG-AG-CCAUUGCGUUUGAUACUGUUU-CACUU-GAGUCUAGAAGAGGAAAGUGGAAUGUAUGGUGUAGCGGUGGAAUGCUUAGAUAUCAUAUAGAACACCCG--UGGCGAAGGCGGCUUUCUGGUCUAAGACUGACGCUCAU-GCGCGAAA-GUU-UGGGGAGCAACCGGG-AUUAGAUACCCCGCUAGUCCU-UACUGUAAA-CGAU-GGGU--AC-UAAG-UGUA-GGGGGU--G----------------------------UUGA-UUCCCUCUGUGCU-------GUA-GCUAACGCAUUAAGUACCCCGCC--UGGG-GAGUAC-GGCCGCAAGGUUAAAACUCAAG-GUAAUUGACGGGGGGCCG-CAC-AAGCGGUGGAGCAUGUCGCUUAAUUCGAAGCAACGCGAAGAACCUUAUCCAGGGCUUGACAUCGCAGUG------------ACCGCUAUAG-AAAUAUAGUUU--U-CCUU----------------------------------CGGG-A----CACUAUGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGUCUUUAGUUGCC-AUCAG-----GUAAUG-------------CUG--AG-CACUCUAAAGAGACCGCUGGUGA--CGA-GCCA-GAGGAAGGUGGGGAUGACGUCAAGUCCGCAUGGCCCUUAUGCCCUGGGCUGCACACGUGCUACAAUGGU-CGGU-ACAGAGGGA---CGCCAAACCGUGAGGUGGA-GCAAAUCCCAA-AAAGCCGACCCCAGUUCGGAUUGCAGUCUGCAACUCGACUGCAUGAAGUUGGAAUCGCUAGUAAUCGCGAAUC-AGC-AGGUCGCGGUGAAUACGU-UCCCGGCCCUUGUACACACCGCCCGUCACGCCAUGGGAGUUGGU-AGC-AUUCGAAGCGGG-U-G-ACCC-AACC---UUCG---GGAGGGA-GCUCUCUAAAAU-GAAACCGAUGACCGGGGCGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUU
AC160099.1/10055-11546                 UUUAACGAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CGG--UAUG-UCUAAGGCAUGCAAGUCUAAGG-UC-----------------UUCUU-----CGGAA-------------------------------------------------------------------------------------------------------------------------------------GG--CC-UGGCAAA-CGGGAGAGUAACACAUUGGU--AACUCACCCCUAGUUCA--AGUAUAACUCUGUGAAAACGGAGACAAUCCUUGAUAGUCCGU--UAA-UCUCCAGCAAUGGAG-UU-UA-A-C-GG-UAAA-GG----------------------------------------------------------UCCG------CCGACUAGGGAGAGGCCUAUGGCUUAUCAGCUUGUUGGUGAGGUAAAAGCUCACCAAGGCAAUGACGAGUAGCGG-GCGUAAGAGCGUGACCCGUCCCACUGGAACUGAGACACUGUCCAGACUCCUACGGGAGGCUGCAGUCAAGAAUCUUUCGCAAUGGCC-GAAAGGCUGACGGAGCAAUACCGCGUGAAG-GA-AGACACCC---CUCG--GGGCGUAAACUUCUUUUCUUAGGG-AAGAAU-UA--------------------G------------UGACGUUACCUAAGGAAUAAGCAACUGCUAACUUCGUGCCAGCAGCAGCGGUAAUACGAAGGUUGCAAGCGUUAUCCGGAAUCAUUGGGCGUAAAGCG-UCUGUAGGAUGUUUACCA-AGUCUC-AAAUUAAAACUCU-AGGCUCAACCU-AG-AGCUAGUUUGAGAAACUGAUA-AACUA-GAGACUGGGGGAGGCAAGCGGAAUGGCCGGUGUAGUACUAAUAUGCAUUGAUAUCGGCUAGAACACCAA--AUGCGAAGGCAGCUUGCUAUAACAGUCCUGACUCUGAG-AGACGAAA-GCG-UGGGUAGCGAAUGGG-AUUAGAUACCCCAGUAGUCCA-CGCCGUAAA-CUAU-GGGU--AC-UAAG-UAUU-AGGAGU--A----------------------------UCGA-UCCUCCUAGUGCUGUCGAGCUAA-GCUAACGCCUUAAGUACCCCGCC--UGGG-GAGUAC-GGUCGCAAGACUAAAACUCAAA-GGAAUUGACGGGAACCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAUGGUAAGCGGAAAACCUUA-CCAAGGCUUGACAUU-CCUGG------------AAUCUCUUGG-AAACAAGAGAG--UGCCGC----------------------------------AAGGAA----CCAGGUAACAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUCGGGUUAAGUCCUU-UAACGAGCGCAACCCUCAUCCUAAUUUA--------------UAAUU------------------------CAUUAGGAAACUGCCGAGGA--UAA-CUCG-GAGGAAGGUGAGGAUGACGUCAAAUCAGCAUGGCUCUUACGCCUUGGGCUACACACGUGCUACAAUGGC-CAGU-ACAAUGGGU---CGCUAAGUCGCAAGAUGGA-GCUAAUCCCACCAAAACUGGUCUCAGUUCAGAUUGGAGUCUGCAAUUCGACUCCAUGAAGUUGGAAUCGCUAGUAACCGCGUAUC-AGC-AUGGCGCGGUGAAUACGU-UCUCGGGUUUUGUACACACCGCCCGUCACACCAAUAGAGUUGGU-AAU-ACCCGAAGGCUC-U---------ACA---CUAA---CGU-----AGGGACGAAGGU-AGGAUCAGCGAUAAGGGUGA-AGU-CGUAACAAGGCAU-CCGUAGCGGAAGCUGUGG---AU-GGAUCACCUCCUUU
AF407728.1/1-1553                      -UCGAUUAGAGUU-UGAU-CCUGGCUCAGAACGAACGUU-GG-UGG--CGUG-GAUGAGGCAUGCAAGUCGAACG-CGA------------AA--GCCGC-----GAGGUG-A-GU-------------------------------------------------------------------------------------------------------------------------------AG--CG-UGGCGGA-CGGGCGAGUAACGCGUAAUC--AAGCUGCCUGCGAGACG--GGGAUAACCUCGGGAAACCGAGGCUAAGACCCGAUGGUCUGC--GAG-GUGC--GCAU--GCA-CU-UG-G-C-AG-UAAA-GGGCGGGAU-------------------------------------------CCUUCGGGAUCG-----CCUGCUCGCAGAGGUGAUUGCGUCCCAUCAGCUAGUUGGUAGGGUAACGGCCUACCAAGGCGACGACGGGUAGCCG-GCCUUAGAGGGUGGUCGGCCGCACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUCCGCAAUGGGC-GAAAGCCUGACGGAGCGACGCCGCGUGGAG-GA-AGAAGGCC---UUCG--GGUUGUAAACUCCUGUCACGAGUC-AAGAAG-GUGCCGUUGCG---AACAGCGAU-----GGUA-UUUGACGUAAGCUCGAGAGGAAGCACUGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGAGUGCAAACGUUGUUCGGAAUUACUGGGCUUAAAGCG-CACGUAGGCUGCGUCGUA-AGUGUC-AGGUGAAAUCCCA-CGGCUCACCCG-UG-GAACUGCCUGGCAUACUGCGA-UGCUC-GAGUGUGGUAGGGGAGAGCGGAACUCCUGGUGGAGCGGUGAAAUGCGUAGAUAUCAGGAGGAACACCGG--UGGCGAAGGCGGCUCUCUGGUCCACAACUGACGCUGAG-GUGCGAAA-GCU-AGGGGAGCAAACGGG-AUUAGAUACCCCGGUAGUCUU-AGCUGUAAA-CGAU-GGGC--AC-UAGC-UUGG-GGUCUC--C----------------------------CUGU--GUGAUCCCAGGU-------GAA-GCAAAAGUGAUAAGUGCCCCGCC--UGGG-GAGUAU-GGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCUCA-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCCAGGC-UGACAUG-CAGGG-----------GUAGGCUGGU--AAAGCCGGCUGAUUACCUU----------------------------------CGGGUGU--GACCUG-CACAG-GUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUCGGGUUAAGUCCCU-UAACGAGCGAAACCCCUACCAUUAGUUACC-AACGG-----GUAAAG-------------CCG--GG-AACUCUAGUGGGACUGCCGUUGU--CAA-AACG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGCCUGGGGCUACACACGUGCUACAAUGGC-CGGU-ACAGAGAGA---AGCAGAGCCGCGAGGCGAA-GCAGACCUCAG-AAAGCCGGCCCCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUC-AGCUACGCCGCGGUGAAUAUGU-UCCUGAGCCUUGUACACACCGCCCGUCAAGCCACGAAAGCUGAG-GGC-GCCCGAAGUCGC-U-A-GUCC-AACC---GCAA---GGAGGGC-GGCGCCGAAGGC-GAGCUCGGUGAUUGGGACUA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUA
GQ503823.1/16-1549                     CGGCCGCAGAGUU-UGAU-CAUGGCUCGGGAUGAACGCU-AG-CGA--CAGG-CUUAACACAUGCAAGUCGAGGG-GCAG----------CACAGGUAGC-----AAUACC-G-GGU-----------------------------------------------------------------------------------------------------------------------------GGC-GAC-CGGCGCA-CGGGUGAGUAACGCGUAUGC--AACUUACCUAUCAGAGG--GGGAUAACCCGGCGAAAGUCGGACUAAUACCGCAUGAAGCAG--GGG-CCCC--GCAU--GGGGAU-AU-U-U-GC-UAAA-GA----------------------------------------------------------UUCA------UCGCUGAUAGAUAGGCAUGCGUUCCAUUAGGCAGUUGGCGGGGUAACGGCCCACCAAACCGACGAUGGAUAGGGG-UUCUGAGAGGAAGGUCCCCCACAUUGGUACUGAGACACGGACCAAACUCCUACGGGAGGCAGCAGUGAGGAAUAUUGGUCAAUGGGC-GUAAGCCUGAACCAGCCAAGUCGCGUGAGG-GA-UGAAGGUU--CUAUG--GAUCGUAAACCUCUUUUAUAAGGG-AAUAAA-GUGCGGGA---------CGUGUC----CCGUU--UUGUAUGUACCUUAUGAAUAAGGAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUCCGAGCGUUAUCCGGAUUUAUUGGGUUUAAAGGG-UGCGUAGGCGGCCUUUUA-AGUCAG-CGGUGAAAGUCUG-UGGCUCAACCA-UA-GAAUUGCCGUUGAAACUGGGA-GGCUU-GAGUAUGUUUGAGGCAGGCGGAAUGCGUGGUGUAGCGGUGAAAUGCUUAGAUAUCACGCAGAACCCCGA--UUGCGAAGGCAGCCUGCCAAGCCAUGACUGACGCUGAU-GCACGAAA-GCG-UGGGGAUCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCAGUAAA-CGAU-GAUC--AC-UAGC-UGUU-UGCGAU--A----------------------------CACA-----GUAAGCGGC-------ACA-GCGAAAGCGUUAAGUGAUCCACC--UGGG-GAGUAC-GCCGGCAACGGUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGAGGAACAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUA-CCCGGGUUUGAACGCAUUCGG------------ACCGAGGUGG-AAACACCUUUU--C-UAGC----------------------------------AAUA-G----CCGUUUGCGAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGCCGUGAGGUGUCGGCUUAAGUGCCA-UAACGAGCGCAACCCUUAUCCUUUGUUGCC-AGCGG------UCCGG-------------CCG--GG-AACUCAAAGGAGACUGCCAGUGA--UAA-ACUG-GAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGC-GCAU-ACAAAGAGA---AGCGACCUCGCGAGAGCAA-GCGGACCUCAU-AAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUC-AGA-AUGCCACGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGU-UGC-AAAAGAAGUAGG-U-A-GCUU-AACC---UUCG---GGAGGGC-GCUUACCACUUU-GUGAUUCAUGACUGGGGUGA-AGU-CGUAACAAGGUAGACCGUAGCG---GCCGCGGUACCC-GGGGGAUCCCUUUU
EU939395.1/5-1542                      GGAAUUCAGAGUU-UGAU-CCUGGCUCAGGAUGAACGCU-GG-CGG--CGUG-CUUAACACAUGCAAGUCGAACG-CUUC---------CUAUCGGUGCU-----UGCACC-G-AGAA--------------------------------------------------------------------------------------------------------------------------AGAAG--AG-UGGCGGA-CGGGUGAGUAACACGUGGGU--AACCUACCUAUAAGCGG--GGGAUAACAUUCGGAAACGGAUGCUAAUACCGCAUAUAUCUU--UUC--GCC--UCCU--GGC--G-AU-U-A-GAAAAAA-GACG------------------------------------------------------GCUUCGG--CUGUCACUUAUAGAUGGACCCGCGGCGCAUUAGUUAGUUGGUGAGGUAAUGGCUCACCAAGACGAUGAUGCGUAGCCG-ACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGAC-GAAAGUCUGACGGAGCAACGCCGCGUGAGU-GA-AGAAGGUU---UUCG--GAUCGUAAAACUCUGUUGUUAGAG-AAGAAC-AAGGGUGAGAGU--AACUGUUCA-----CCCC--UUGACGGUAUCUAACCAGAAAGCCAUGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCGAGCGUUAUCCGGAUUUAUUGGGUUUAAAGGG-UGCGUAGGCGGUUGUGUA-AGUUAG-UGGUCAAAUGUCA-UGGCUCAACCU-UG-GCUUG-CCAUUAAAACUGCAC-GACUC-GAGUACAGACGAGGUAGGCGGAAUAAGUUAAGUAGCGGUGAAAUGCAUAGAUAUAACUUAGAAUUCCGA--UAGCGAAGGCAGCUUACCAGACUGUAACUGACGCUGAU-GCACGAGA-GCA-UGGGUAGCGAACAGG-AUUAGAUACCCUGGUAGUCCA-UGCCGUAAA-CGAU-GCUC--AC-UGGC-UCUG-UGCGA--------------------------------CACA---UUGUACGGGGU-------CAA-GCGAAAGUAUUAAGUGAGCCACC--UGGG-GAGUAC-GUCGGCAACGAUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGAGGAACAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUA-CCUAGGUUUAAAUGUAGUCUG------------CAUGACGUAG-AAAUAUGUCUU--U-CCUU----------------------------------CGGG-A----CCGAUUACAAG-GUGCUGCAUGGUUGUCGUCAGCUCGUGCCGUGAGGUGUCGGGUUAAGUCCCA-UAACGAGCGCAACCCUUGUCUUAUGUUGCC-AGCAC-----GUGAUG-------------GUG--GG-GACUCAUGAGAAACUGCCGGGGU--UAA-CUCG-GAGGAAGGCGGGGAUGACGUCAAAUCAGCACGGCCCUUACACCUAGGGCUACACACGUGUUACAAUGGC-CGGU-ACAGAGGGC---AGCUACUUGGUGACAAGAU-GCGAAUCUCG--AAAGCCGGUCGUAGUUCGGAUUGGAGUCUGUAACCCGACUCCAUGAAGUUGGAUUCGCUAGUAAUCGCGCAUC-AGCCAUGGCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCAAGCCAUGGAAGCCGGG-GGU-GCCUGAAGUCCG-U--------AACC---GCAA---GGA-----UCGGCCUAGGGC-AAAACUGGUGACUGGGGCUA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUG
CP001818.1/1625616-1624093             UGCUAGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CUUAACACAUGCAAGUCGGACG-GUU------------AGUAGGUGA-----AAGCUU-G-CUGGAUC--------------------------------------------------------------------------------------------------------------------CUACUGAU--AG-UGGCGGA-CGGGUGAGUAACACGUGAGA---ACCUGACCCAAGCAGG--GGGACAACUGCUGGAAACGGCAGCUAAUACCCCAUAGG-----------CGG--GAGA--CCG--U-----------UAAA-GGA---------------------------------------------------------GUGA-----UCCGGCUUGGGAGGGGCUCGCGGCCUAUCAGCUAGUAGGUGUGGUAAUGGCGCACCUAGGCGAUGACGGGUAGCCG-GCCUGAGAGGGUGUACGGCCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGGCAAUGGGG-GCAACCCUGACCCAGCGACGCCGCGUGGGG-GA-AGAAGUCC---UUCG--GGAUGUAAACCUCUGUUGUGUGGG-AAGAAG-GA-------------------UG------------UGACGGUACCACACGAGGAAGCCCCGGCAAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCGAGCGUUGUCCGGAAUUACUGGGCGUAAAGAG-CGCGUAGGCGGCUGGAUA-AGUCGG-CUGUGAAAGACGU-GGGCUCAACUC-AC-GGAUUGCGGUUGAUACUGUCU-GGCUA-GAGUGCGGGAGAGGGAAGUGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCAG--UGGCGAAGGCGGCUUCCUGGACCGCUACUGACGCUCAA-GCGCGAAA-GCU-GGGGGAGCGAACGGG-AUUAGAUACCCCGGUAGUCCC-AGCUGUAAA-CGAU-GGAU--GC-UAGG-UGUG-GGGGUC--G----------------------------UAU---GGCCUCCGUGCC-------GGA-GUUAACGCGAUAAGCAUCCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCACGUGGUUUAAUUCGAUGCAAACCGAAGCACCUCA-CCUGGGUUUGACAUG-UAGGUG----------GUAGGGAGAUG-AAAGUUGAACG--ACCCUGGGGU--------------------------AACUCAGGGA----GCCUA-CACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUAUUGCCAGUUGCU-AACGG-----GAGAG--------------CCG--AG-GACUCUGGCGAGACUGCCGUCGA--CAA-GGCG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCUUUAUGCCCAGGGCGACACACGUGCUACAAUGGC-CGGC-ACAGAGGGG---AGCGAGACCGCGAGGUGGA-GCGAAUCCCAG-AAAGCCGGUCCCAGUUCGGAUUGCAGUCUGCAACUCGACUGCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUC-AGCCAAGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACCCGAGUUGGG-UGUACCCCGAAGUCAC-C-G-GCCU-AACC--UGCGA--GGGGGGGA-GGUGCCUAAGGGGAUGCUUGGUAAGGGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCAG---CU-GGAUCACCUUCUUU
GU474881.1/32681-31122                 CAACUUGAGAGUU-UGAU-CCUGGCUCAGAAUCAACGCU-GG-CGG--CGUG-CCUCAUACAUGCAAGUCGAACG-CGA-----------AAGUAACCUU-----CGGGUU-G-CGA-----------------------------------------------------------------------------------------------------------------------------UUA-GAG-UGGCAGA-CGGGUGAGUAACGCGUGGGU--GACCUACCUUCGAGUGG--GGGACAACCCCUGUAA-UGGGGGCUAAUACCGCAUAACAUCC--UGU--UCU--UAGA--UGG--A-CA-GUG-AU-CAAA-GCUGGCCAA-------------------------------------------GCUUCGGCUUGGC---UGGUGCUUGUUGACGGACCCGCGUCCGAUUAGCUUGUUGGUGGGGUAAUGGCUCACCAAGGCUUCGAUCGGUAGCCG-GCCUGAGAGGGCGGACGGCCACACUGGGACUGAGACACGGCCCAGACUCUUACGGGAGGCAGCAGUAGGGAAUUGUUCGCAAUGGGC-GAAAGCCUGACGACGCAACGCCGCGUGGAG-GA-UGAAGAUC---UUCG--GGUUGUAAACUCCUGUCGGGAGGG-AAGAAU-AGCUUGUGGGUU-AAUACCCCAU-----AGGC--CUGACGGUACCUCUAGAGGAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGGGGGGGCGAGCGUUGUUCGGAUUUACUGGGCGUAAAGGG-CUUGUAGGCGGUGGUCUA-UGUCGG-UUGUGAAAUCCCC-AGGCUCAACCU-GG-GAACUGCAGCCGAAACUGGGU-CACUA-GAAGCCGGGAGAGGGAUGCGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAGGAACACCCG--UGGCGAAGGCGGCAUCCUGGACCGGUCUUGACGCUGAG-GAGCGAAA-GCU-AGGGUAGCAAACGGG-AUUAGAUACCCCGGUAGUCCU-AGCCCUAAA-CGAU-GAAU--GC-UUGG-UGUG-GCGGGU--A----------------------------UCGA-UCCCUGCCGUGCC-------GGA-GUUAACGCGUUAAGCAUUCCGCC--UGGG-GAGUAC-GGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCCGGGCUUGAAGCGCAAGUG------------AUCAUCGACG-AAAGUCGACU----UCCGC----------------------------------AAGGA-----CACUUGUAGAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGUCUGCUGUUGCC-AUCAG------UUCGG-------------CUG--GG-CACUCUGCGGAGACUGCCGGUGA--UAA-ACCG-GAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGGCCUUUAUGUCCGGGGCUACACACGUGCUACAAUGGC-CGGC-ACAAAGCGU---UGCGAUCCCGCGAGGGGGA-GCUAAUCGCAC-AAAGCCGGUCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUC-AGC-AUGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACAUCACGAAAGUUGGC-UGU-ACUAGAAGUCGC-C-G-AGCU-AACC--CGCUUGCGGGAGGUA-AGCGCCGAAGGU-AUGGUUGAUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CUGUAGGAGAACCUGUGG---CU-GGAUCACCUCCUUU
CP001251.1/1245769-1244222             CGGAUGGAGGGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CCUAAGGCAUGCAAGUCGAGCG-GUAGC-------UCCUAUUGGUUA-----AAGCCG-A-UAGG--------------------------------------------------------------------------------------------------------------------------AGUGA-GAG-CGGCGCA-CGGGUGAGUAACACGUAGGU--AACCUACCCCAGAGAGG--GGGAUAACACCUCGAAAGGGGUGCUAAACCCCCAUAUACUUA--CCG--AGC-GAGAU--GCU--CAGG-U-A-AG-GAAA-GGGUAUAGAGG----------------------------------------GGUAACCCUCUAU-----GCUGCUCUGGGAUGGGCCUGCGGCCUAUCAGCUAGUUGGUGGGGUAAAGGCCCACCAAGGCUAAGACGGGUAGCCG-GCCUGAGAGGGUGGUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGCCGGGAAUCUUCCGCAAUGGGG-GAAACCCUGACGGAGCGACGCCGCGUGAGG-GA-AGAAGCCC---UUCG--GGGUGUAAACCUCUUUUCUCGGGG-AAGAAG-GC--------------------A------------UGACGGUACCCGAGGAAAAAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAGACGUAGGGGGCGAGCGUUGUCCGGAUUUACUGGGCGUAAAGGG-CGUGUAGGCGGCUUAGCA-AGUCAG-AUGUGGAAGCCCC-GGGCUCAACUC-GG-GGAGGACAUCUGAUACUGCUA-AGCUA-GAGGGCAGGAGAGGAGAGCGGAACUUCCGGUGUAGCGGUGAAAUGCGUAGAUAUCGGAAGGAACGCCGG--UGGCGAAGGCGGCUCUCUGGACUGUCCCUGACGCUGAG-GCGCGAAA-GCU-AGGGGAGCGAACGGG-AUUAGAUACCCCGGUAGUCCU-AGCCGUAAA-CGAU-GGGC--AC-UAGG-UGUG-GGGAGU--------------------------------UAG--ACUCUCCGUGCU-------GCA-GCUAACGCGAUAAGUGCCCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCGCGUGGUUUAAUUCGAUGCUAAGCGAAGAACCUUA-CCAGGGCUUGACAUGCAGGCUG---------UAAGCUCACCCG-AAAGGGUGAGU-GCCAAAUAGGAGGU--------------------UUCUCCUAUUUGG----AGUCUGCACAG-GUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCCUUAGUUGCC-AGCGG-----GUAAAG-------------CCG--GG-CACUCUAAGGGGACUGCCGGCGA--AGA-GCCG-GAGGAAGGUGGGGAUGACGUCAAGUCAGUAUGCCCCUUAUGCCCUGGGCUACACACGCGCUACAAUGGG-UGGU-ACAGAGGGG---AGCGAAGCCGCGAGGCGGA-GCGAAUCCCU--AAAGCCACCCCCAGUUCAGAUCGCAGGCUGCAACUCGCCUGCGUGAAGGCGGAAUCGCUAGUAACCGCAGAUC-AGCCACGCUGCGGUGAAUACGU-UCUCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUCCGC-AAC-ACCCGAAGUCAG-G----------C----GAAG---AG------CCUGCCGAAGGU-GGGGCGGAUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
CP002432.1/2337382-2335863             UAUACGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCAAGGG-GC------------------CUUU-----CGGG--------------------------------------------------------------------------------------------------------------------------------------GC-CAC-UGGCGCA-CGGGUGAGUAACACGUGGGU--AAUCUGCCCUUUGGCCC--GGGAUAACAUCUGGAAACGGAUGCUAAUACCGGAUAAU-----------CUC--UUUU--GAG--C-----------AAAU-GGAG------------------------------------------------------CUUUCGG--GUUCCGCCGAAGGAUGAGCCCGCGCAUGAUUAGCUUGUUGGUGGGGUAACGGCCCACCAAGGCGAAGAUCAUUAGCCG-GCCUGAGAGGGUGAACGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGAC-GUAAGUCUGACGCAGCAACGCCGCGUGGAU-GA-CGAAGGCU---UUCG--GGUCGUAAAGUCCUUUAGAUGGUG-AAGAAC-CGGUACGGGAGU--AACUGCCCG-----UGCC--CUGACGGUAGCCAUAGAAUAAGCUCCGGCUAAAUCCGUGCCAGCAGCCGCGGUAAUACGGAUGGAGCAAGCGUUGUCCGGAAUCAUUGGGCGUAAAGGG-UGCGUAGGCGGUUUUUUA-AGUCUG-CAUUGUAAGUUCA-GUGCUUAACGC-UG-AAAUUGGUGCGGAAACUGGAA-GACUU-GAGUACUGUAGGGGAAAGCGGAAUGCCCUGUGUAGAGGUGAAAUUCGUAGAUAUAGGGUGGAACAUCAA--AAGCGAAGGCAGCUUUCUGGGCAGUAACUGACGCUGAG-GCACGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GGAU--GC-UAGA-UGUU-GGCGGG-AA----------------------------UCUU--CCUGUCAGUGUC-------GGA-GCUAACGCAAUAAGCAUCCCGCC--UGGG-GAGUAC-GGUCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCUGGUCUUGACAUC-CCGAU-----------GCCGUAUUCAG-AGAUGUAUAUU--UCCCUU----------------------------------CGGGGA---CAUCGGUGACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGCGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCCUGCCAUUAGUUGCC-AUCA------UUAAGU--------------UG--GG-CACUCUAGUGGGACAGCCGGAG---UAA-UCCG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUAUGACCAGGGCUACACACGUGCUACAAUGGC-AAGG-ACAACGGGA---UGCGACCUCGCGAGAGUGA-GCCAACCUCAA-AAACCUUGUCUUAGUUCGGAUUGCAGUCUGCAACUCGACUGCAUGAAGUCGGAAUCGCUAGUAAUCGCAGGUC-AGC-AUACUGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACGAAAGUCGGU-UUU-GCCAGAAGCGGG-U-G-ACCG-AAUC---UUCG---GAUAGGA-GCCUUCGAAGGC-AGGACUGGUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUAUCGGAAGGUGCGG---CU-GGAUCACCUCCUUU
AP009153.1/1882858-1884381             CUAUUGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CUUAACACAUGCAAGUCACGGG-GG-----------------CCCGC-----AAGGG-------------------------------------------------------------------------------------------------------------------------------------UA--AC-CGGCGAA-CGGGUGCGUAACACGUGAAC--AAUCUGCCUAGAUGUGG--GGGAUAGCCGGCCCAACGGCCGGGUAAUACCGCAUACGCUCU--UCG-GGUG--GCAU--CAC-UU-GA-A-G-AG-GAAA-CC----------------------------------------------------------UCCG------GGGCAUCUAGAGGAGUUCGCGGCCUAUCAGCUAGUUGGUGGGGUAACGGCCUACCAAGGCAAUGACGGGUAGCUG-GUCUGAGAGGAUGGCCAGCCACAUUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGCC-GAAAGGCUGACGCAGCGACGCCGCGUGGGG-GA-UGAAGCAU---UUCG--GUGUGUAAACCCCUGUUGCCCGGG-ACGAAC-AAGCGAUU----------UUGAU-----CGCU--CUGACGGUACCGGGUGAGGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCGAGCGUUGUCCGGAAUCACUGGGCGUAAAGGG-CGCGUAGGCGGUCUGCUA-AGCGUG-UGGUGAAAGCUCG-GGGCUCAACCC-CG-AGUCUGCCAUGCGAACUGGUG-GACUA-GAGCACUGUAGAGGCAGGUGGAAUUCCGGGUGUAGCGGUGGAAUGCGUAGAGAUCCGGAAGAACACCAG--UGGCGAAGGCGGCCUGCUGGGCAGUAGCUGACGCUGAG-GCGCGAUA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGAU-GGGG--AC-UAGG-UGCU-UGGGGG--A----------------------------GCGA-CCCCUCGAGUGCC-------GGC-GCUAACGCAUUAAGUCCCCCGCC--UGGG-GAGUAC-GACCGCAAGGUUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCCAGGCUUGACAUGUACGAG-----------AAAGCCUCUGG-AAACAGGGGCC--CCUCUU----------------------------------CGGAG-----CUCGUGCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGCCCUUAGUUACC-AGCGA-----GUAAAG-------------UCG--GG-GACUCUAGGGGGACUGCCGGUGC--CAA-ACCG-GAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGUCCUUACGUCUGGGGCUACACACGUGCUACAAUGGC-CGGU-ACAGAGGGC---UGCGAAAGAGCAAUCUGGA-GCCAAUCCCU--AAAGCCGGCCUCAGUUCGGAUUGUCGUCUGCAACUCGACGGCAUGAAGCUGGAAUCGCUAGUAAUCGCGGAUC-AGCGACGCCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGAAGCUGUG-AGC-GCCCGAAGUCGG-U-G-CAGG-AACC--CGCAA--GGGGCCAA-GCCGCCUAAGGC-GAGCGCAGUGACUGGGGCGA-AGU-CGUAACAAGGUAG-CCGUAGGGGAACCUGCGG---CU-GGAUCACCUCCUUU
AFNU01000079.1/131-1656                UAUAUGGAGAGUU-UGAU-CCUGGCUCAGGACGAACGCU-GG-CGG--CGUG-CCUAAUACAUGCAAGUCGAGCG------------------AGCACUU-----CGGUGC-U--------------------------------------------------------------------------------------------------------------------------------------AG-CGGCGAA-CGGGUGAGUAACACGUAGGC--AACCUACCCAUAAGACG--GGGAUAACUAUUGGAAACGAUAGCUAAUACCGGAUAGGAUAA--AGA--AUC--GCAU--GAC--U-CU-U-U-AUUUAAA-GAU-------------------------------------------------------GCUUCGG---CAUCACUAAUGGAUGGGCCUGCGGCGCAUUAGCUAGUUGGUGGGGUAGAAGCCUACCAAGGCAACGAUGCGUAGCCG-ACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCGGCAAUGGAC-GAAAGUCUGACCGAGCAACGCCGCGUGAGU-GA-AGAAGGUC---UUCG--GAUUGUAAAGCUCUGUUAUUAGGG-AAGAAA-AUAGGUAGCAGG--AAAUGGCUA-----AUUA--GUGACGGUACCUAAUGAGGAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGG-UUCGUAGGCGGUUUUUUA-AGUCUG-AUGUGAAAGCCCA-CGGCUUAACCG-UG-GAAGGUCAUUGGAAACUGGAA-GACUU-GAGUACAGGAGAGGAAAGUGGAAUUCCUAGUGUAGCGGUGAAAUGCGUAGAUAUUAGGAGGAACACCAG--UGGCGAAGGCGGCUUUCUGGCCUGAAACUGACGCUGAU-GAACGAAA-GCG-UGGGGAGCAAACAGG-AUUAGAUACCCUGGUAGUCCA-CGCCGUAAA-CGUU-GAGU--GC-UAAG-UGUC-GGGG---------------------------------GAGA----CCUCGGUGCU-------GAA-GUUAACGCAUUAAGCACUCCGCC--UGGG-GAGUAC-GGUCGCAAGACUGAAACUCAAA-GGAAUUGACGGGGACCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUA-CCAAGCCUUGACAUC-CCUCU-----------GACGUAUUUAG-AGAUAGAUAGU---UCCUU----------------------------------CGGGAC----AGAGGAGACAG-GUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGUCGUUAGUUGCU-AACA------UUAAGU--------------UG--AG-GACUCUAGCGAGACUGCCAGUGA--UAA-ACUG-GAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGGCUUGGGCUACACACGUGCUACAAUGGC-UAGU-ACAAAGAGA---AGCGAAGCGGUGACGUGAA-GCAAACCUCAU-AAAGCUAGUCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUGAAGUCGGAAUCGCUAGUAAUCGCGAAUC-AGC-AUGUCGCGGUGAAUACGU-UCCCGGGUCUUGUACACACCGCCCGUCACACCACGAGAGUUUGU-AAC-ACCCGAAGCCGG-U-G-GCCU-AACC---GUAA---GGAAGGA-GCCGUCUAAGGU-GGGACAGAUGAUUGGGGUGA-AGU-CGUAACAAGGUAU-CCCUACCGGAAGGUGGGG---AU-GGAUCACCUCCUUU
FP565575.1/1587658-1586098             AAUUUGGAGAGUU-UGAU-CCUGGCUCAGAACGAACGCU-GG-CGG--CGUG-CCUAACACAUGCAAGUCGAGCG-AGA-----------AAGUCCCGGC-----AACGGG-A-UGA-----------------------------------------------------------------------------------------------------------------------------GUA-AAG-CGGCAAA-CGGGUGAGUAACGCGUAGGU--AAUCUAUCCUUCGGAUC--GGGAUAACCUGCUGAAAAGUGGGAUAAUACCGGAUAACGUUC--UUG--UGG--GUAU-CCUA--U-GA-G-A-AC-CAAA-GGGGGCGA----------------------------------------------GCGUAAGCAGC---UCCCACCAAAGGAGGAGCCUGCGUCCGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCGGUAGCCG-GCCUGAGAGGGCGACCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGC-GAAAGCCUGACGCAGCGACGCCGCGUGGGU-GA-UGAAGGCC---UUCG--GGUUGUAAAGCCCUGUCUGGUGGA-ACGAAU-GGCUUAGCGGCA-AAUAACCGCU-----AGGC--GUGACGGUACCACCGAAGGAAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAGACGUAGGGGGCGAGCGUUGUUCGGAUUUACUGGGCGUAAAGCG-CGCGUAGGCGGCUAGAUA-AGUCGG-GUGUGAAAUCCCU-CGGCUUAACCG-AG-GACCCGCAUCCGAUACUGCCU-GGCUC-GAGUCUAGGAGAGGAAAGCGGAAUUCCCAGUGUAGCGGUGAAAUGCGUAGAUAUUGGGAGGAACACCGG--UGGCGAAGGCGGCUUUCCGGACUAGCACUGACGCUGAG-GCGCGAAA-GCU-AGGGGAGCGAACGGG-AUUAGAUACCCCGGUAGUCCU-AGCCGUAAA-CGAU-GGGC--AC-UAGG-UGUG-GGAGGU--A----------------------------UUGA-CCCCUUCCGCGCC-------GAA-GCUAACGCAUUAAGUGCCCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUAAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGAAGAACCUUA-CCAGGGCUUGACAUC-CCACG------------AACCUGCCUG-AAAGGGCGGGG--UGCCCGC--------------------------------AAGGGAG----CGUGGAGACAG-GUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUCACCCCUGGUUGCC-ACCGG-----AUAAAG-------------CCG--AG-CACUCGAGGGGAACUGCCAGCGU--CAA-GCUG-GAGGAAGGCGGGGAUGACGUCAAGUCAUCAUGCCCCUUACGCCCUGGGCUACACACGUGCUACAAUGGC-CGGU-ACAAAGGGA---CGCGAGACCGCGAGGUGGA-GCUAAUCCCAA-AAAACCGGUCUAAGUUCAGAUUGCAGUCUGCAACUCGACUGCAUGAAGGAGGAAUCGCUAGUAAUCGCGCAUC-AGC-ACGGCGCGGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACGAAAGCUGUC-UGU-ACUCGAAGUCGC-U-G-AGCU-AACC--CGCAA--GGGGGGCA-GGCGCCGAAGGU-AUGGUCAGUGAUUGGGGUGA-AGU-CGUAACAAGGUAG-CCGUACGGGAACGUGCGG---CU-GGAUCACCUCCUUU
CP002683.1/865959-864386               UAACGUGAGGGUU-UGAU-CCUGGCUCAGGGCGAACGCU-GG-CGG--CGCG-CCUAACACAUGCAAGUCGAGGG-GGAA----------AGGGUAGCUU-----CGGCUA-C-CCG----------------------------------------------------------------------------------------------------------------------------AGUA-CAC-CGGCAGA-CGGGUGAGUAACGCGUGGGU--AACCUACCUUGGGGUCU--GGGAUAACCACCCGAAAGGGUGGCUAAUACCGGAUACGUUCC--UGA--GGC--GCGA--GCC--G-AG-G-G-AA-GAAA-GGGUGCCACU------------------------------------------GCAUAGCAAGCA-----CCUGCCCUAAGAGGGGUCCGCGUCCCAUCAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCAACGACGGGUAGCCG-GCCUGAGAGGGUGGUCGGCCACACUGGCACUGAGACACGGGCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGGGCAAUGGCC-GAAAGGCUGACCCAGCGACGCCGCGUGGGG-GA-AGAAGGCC---UUCG--GGUCGUAAACCCCUGUCAAGGAGG-AAGAAG-CCCUUACUGGUUAAGAGCUGGUA-----GGGG--UUGACGGUACUCCUGGAGGAAGCCACGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGUGGCGAGCGUUGCCCGGAAUCACUGGGCGUAAAGGG-GGCGUAGGCGGCCGGACG-AGUCGG-ACGUGAAAGCCCG-GGGCUCAACCC-CG-GAAUUGCGUUCGAUACUGUCU-GGCUU-GAGGUCCGGAGAGGCCGGCGGAAUUCCCGGUGUAGGGGUGAAAUCCGUAGAUAUCGGGAGGAACACCGG--UGGCGAAGGCGGCCGGCUGGACGGCACCUGACGCUGAG-GCCCGAAA-GCG-UGGGGAGCAAACCGG-AUUAGAUACCCGGGUAGUCCA-CGCCGUAAA-CGAU-GGGU--GC-UAGG-UGUG-GGGGGU--------------------------------UAA--ACCUUCCGUGCC-------GAA-GCUAACGCAAUAAGCACCCCGCC--UGGG-GAGUAC-GGCCGCAAGGCUGAAACUCAAA-GGAAUUGACGGGGGCCCG-CAC-AAGCGGUGGAGCACGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUA-CCUGGGUUUGACAUGCUAGGG------------AACCCCUCAG-AGAUGAGGGGG--UGCCCGGGCU-------------------------UUGCCUGGGAG----CCCUAGCACAG-GUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCG-CAACGAGCGCAACCCUUGCCCUUAGUUGCC-AGCGG-----GUAGAG-------------CCG--GG-CACUCUAGGGGGACUGCCGGGGA--CAA-CCCG-GAGGAAGGGGGGGAUGACGUCAAGUCAUCAUGGCCCUUAUGCCCAGGGCUACACACGUGCUACAAUGGG-CGGU-ACAGAGGGA---AGCGAACCCGUAAGGGGGA-GCAAAUCCCAG-AAAGCCGCUCUCAGUACGGAUCGGGGUCUGCAACUCGACCCCGUGAAGCCGGAAUCGCUAGUAACGGCGGAUC-AGC-AUGCCGCCGUGAAUACGU-UCCCGGGCCUUGUACACACCGCCCGUCACACCACGGGAGCUGGC-UCU-GCCCGAAGUCGC-U-A-UCCC-AACCCCCGGAAGGGGGAGGGA-GGCGCCGACGGC-AGGGCUGGUGACUGGGGUGA-AGU-CGUAACAAGGUAU-CCCUACCGGAAGGUGGGG---AU-GGAUCACCUCCUUU
#=GC SS_cons                           ::::::::<<<<<.____.___>>>>>,{{{{-{{{{{{.,{.{{{..{{{{.{----{{{-{{{,,<<<--<<<.<<-............<<<<<<<__.....__>>>>.>.>>..............................................................................................................................->>.->>.>>>>,,,.,,,[[[,,,,,,((((((((..--((---(((((((,<<..<<----<<<<<<<____>>>>>>>----->>>>,,,,,<<<<..<<<..<<<..____..>>>..>.>>.>.>.>>.,,,,.<<<........................................................_____.....>>>,)))))))--))))))))))<<<--<-<<<--<<<<<<<<_______>>>>>>>>>>>----->>>>,,<<<<.<<<<____>>>>--->>>>]]],<<<<<<__________>>>>>>,<<<<____>>>>,,,}}}}}}-},,,,,<-<<<---<<<<<.____>>>>>->>>>,}}-}}}}}},,<<<<.--.----<<<<...____..>>>>----->>>>,,,<<<<<<<-.--<---.--<<<___.........______.....>>>-..---->---->>>>>>--->,,<<<<<------<<<<<-----<<____>>------->>>>>>>>>>,}}}}}}}}}},,,,,,,,,,{{{-----{,[.[[[-[-[[[,<<<<<<<-.<<<<<<.<<<<<----<<<<.<<<_____>>>.>>.>>-->>>>>>>>>-->>>>>>.>>>,,.,(((((((((--(((((((<<--<<<<<<<<---<<<______>>>------>>>>>>>>-->>,,,,<..--<<____>>>)))))))-))))))-))),,,]]]]--.]]]],,,,.<<<.<<<---<<---<<<<._________>>>>--->>>>>.>>>,,,,,,.,,,,.((((..((.,,<<.<<<<.<<<<<<.._............................____..>>>>>>>>>>>>.......,,,.<<____>>,,,,,))))))}}}}..,<<<.------.<<<<____>>>>---->>>,,,.,,,,,{{{{{-{{{{{{{.-{{.,,{{{{{{{{{{{{{{{{{,,,,<<<<________>>>>,,,,,,,,.{{{{{{{,,,,,(((.(((((............,,<<<<<<<_.___>>>>>>>,..<<<<__..................................__>>>>....)))))-))),[.[-[[[[--[[[[[[[[[,,,((((((<<<____>>>,,<<<<______>>>>.,,)))))),,,,,((((,<<<<<<<---<<.--<<<.....______.............>>>..>>.---->>>>>>>,,<<<<<<<<__..___.>>>>.>>>>,,,,,)))),,,,]]]]-]]]---]]]]]]]],,,,}}}}}}},,,}}-}}}}}}}}}},,,<<<.<<<<.-----<<<-...-<<---<<<____>>>---.>>---->>>--.--->>>>>>>,,,,,,<---<<<<<<<<________>>>>>>>>--->,,,,,}}}}},,,,,<<<<<<<<__.___.__>>>>>>>>,,,,,,}}.---}}}}}}}}}}-}},,<-<<-<<---<<<<<<<<--<<<<<<.<<<.<<<----<<<<<.<.-.<<<<.--<<...____...>>->>>>.>>>>>>--->>>.>>>>>>>>>-->>>>>>>>-.---.>>-->>-->,<<<.<<<<<<<____>>>>>>>...>>.>:::::::::::::
#=GC RF                                uuuauggAGaGuu.UGAU.CcUggCuCAGggcGaaCGCu.GG.CGG..cgcG.cuUaAcaCAuGCAAGuCGagcc.cca............cggggccuu.....aaggcc.c.cg..............................................................................................................................agg.ggg.cGgCGaA.cGGGuGAGUAAcgCGcgggc..AAccUacCcccgggugc..gGgAUAccccccgGAAAcggggggUAAUACcgcAUaaugccc..cgg..ccc..guau..ggg..c.cg.g.g.gc.uAAA.Ggc........................................................auuua.....gcCGcccgggGAugggcccgCGccccAUcAGcuAGuuGGuggGGUAAuGGCccaCCaaggCgAuGAggggUAGccG.gccuGAGAgggcGauCggCCaCAcuGGgaCUGAGAcACGgcCCagACuCCUACGGGaGGCAGCaGugggGAAUauUgcgCAAugGgc.GaAAgcCugAcgcaGCgAcgCCGCGUGggg.GA.uGAAggcc...UUcG..ggccGUAAAcccCUuUcccggGgG.AagAaa.aaccgaua.........uuuuau.....cggu..uuGAcggUAcCccgggAagAAGcccCGGCUAAcuccGUGCCAGCAGCCGCGGUAAuACggagGgggCaaGCGuugccCGGAaUuAuUGGGcGUAAAGgG.cgcGcAgGcGGcccggcA.aGucgg.gcgcgAAAucccg.cgGCUcAACcg.cg.ggaucgcgcccgaaACugccg.ggCUu.GaGuccggccGAgGggggcggAAcucccgguGUAGcgGUGAAAugCGUAGAuaucgggagGAacACCac..ugGCGAAGGCggccccCuGggccgguaCuGACgCugAg.gcgCGAAA.GCg.uGGGgAgCaAAcgGG.AUUAGAUACCCcgGUAGuCCa.cGCcgUAAA.CGAU.Gggc..gC.UAGg.cgcc.gggggg..a............................uuaa..ccccccggcgcC.......gaA.GcuAAcgCauUAAGcgccCCgCC..UGgG.GAgUAC.ggcCGCAAGgcugAAACuCAAA.GGAAUuGaCgGgGgCCCG.CaC.AAGCGguGgagcauGuGGuUUAAuuCGAuGcaAcgCGaaGAACCUUA.CCcgggcUUGAcgug.ccggg............aaccccccgG.AaAcggggggu..ccccuu..................................aagggg....cccggacacAG.GUGcugCAuGgcuGuCGUCAGCuCGuguCGUGAGauGUcgGGUUAAGUCCcg.cAaCGaGCGCAACCCccgccccuagUUgCc.Aucgg.....uuuauu.............ccg..gG.cACUcuaggggGACcgCCggcGa..uAA.gccG.GagGAAGGuggGGAuGACGuCAaguCauCauggCCCUUAugcccgGGGCuaCACaCgugcuaCAAUGgc.cggc.ACAaaggGu...aGCaAagccGcGAggcggA.GCuAAUCccau.AAAgccggcCucAGUUCGGAcuGgaGgCUGcAAcUCGcCucCagGAAGuuGGAauCGCUAGUAaucGcggcUC.AGc.AugccgCgguGAAUACGu.UCcCGGGcCuuGuACaCACCGcCCGUCAcgcCacggaAgccggc.ccc.gcCcGAAGccgc.c.g.cgcc.AAcc...uuaa...ggaggcg.ggcggCuAaGgc.ggggccggcgAccggGgcgA.AGU.CGUAaCAAGGuag.CcguaccGGAAggugcgG...cu.gGAUcAccUcCUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00178
#=GF ID   mir-24
#=GF DE   mir-24 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   47.00
#=GF TC   49.30
#=GF NC   45.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000080;
#=GF DR   MIR; MI0000081;
#=GF DR   MIR; MI0000231;
#=GF DR   MIR; MI0000572;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science 2001;294:853-858.
#=GF RN   [2]
#=GF RM   11779458
#=GF RT   microRNAs: tiny regulators with great potential.
#=GF RA   Ambros V
#=GF RL   Cell 2001;107:823-826.
#=GF CC   This family represents the microRNA (miRNA) mir-24 family. miRNAs are
#=GF CC   transcribed as ~70nt precursors (modelled here) and subsequently processed
#=GF CC   by the Dicer enzyme to give a ~22nt product. In this case the mature
#=GF CC   sequence comes from the 3' arm of the precursor. The extents of the
#=GF CC   hairpin precursors are not generally known and are estimated based on
#=GF CC   hairpin prediction. The products are thought to have regulatory roles
#=GF CC   through complementarity to mRNA. The involvement of Dicer in miRNA
#=GF CC   processing suggests a relationship with the phenomenon of RNA
#=GF CC   interference. miRNAs are numbered based on the sequence of the mature RNA.
#=GF CC   miR-24 has been identified in human and mouse [1].
#=GF WK   mir-24_microRNA_precursor_family
#=GF SQ   17


AC122794.3/95820-95755     CUCCCGUGCCUACUGAGCUGAAACA--GUUGAUUCCAG---UGCACUGGCUCAGUUCAGCAGGAACAGGAG
AF480559.1/14-81           CUCCCGUGCCUACUGAGCUGAAACACAGUUGGUUUGUG---UACACUGGCUCAGUUCAGCAGGAACAGGGG
AF480560.1/3-70            CUCCGGUGCCUACUGAGCUGAUAUCAGUUCUCAUUUUA---CACACUGGCUCAGUUCAGCAGGAACAGCAU
AAFR03027068.1/11428-11495 CUCCGGUGCCUACUGAGCUGAUAACAGUUCUGAUUUUA---CACACUGGCUCAGUUCAGCAGGAACAGGAG
AALT01392929.1/1642-1575   CUCCGGUGCCUACUGAGCUGAUAUCAGUUCUCGUUUCA---CACACUGGCUCAGUUCAGCAGGAACAGGAG
AAPN01322484.1/710-777     CUCCUGUGCCUACUGAGCUGAAACGCAGUUGCUUUGCU---UAAACUGGCUCAGUUCAGCAGGAACAGGAG
AAVX01198958.1/114-181     CUUCUGUGCCUACUGAGCUGAUAACAGUUGAUAUUGUU---UGCACUGGCUCAGUUCAGCAGGAACAGGAG
AANH01003598.1/92361-92428 CUCCCGUGCCUACUGAACUGGUAUCAGUGUUUUUUCUA---AAAACUGGCUCAGUUCAGCAGGAACAGGAG
BX664751.9/53722-53655     CUCCUGUGCCUACUGAGCUGAUAACAGUUGAUGUAUUU---AGCACUGGCUCAGUUCAGCAGGAACCGGAG
CAAE01012021.1/29337-29403 CUCCUGUGCCUACUGAGCUGAAAAC-AGUCGGAUAUCA---GACACUGGCUCAGUUCAGCAGGAACCGGAG
AANN01357153.1/1098-1031   CUCCAGUACCUACUGAACUGAAACACAGUUUUUUUCAU---GCAACUGGCUCAGUUCAGCAGGAACCGGAG
BAAF04082680.1/2546-2479   CUCCCGUGCCUACUGAACUGGUAUCAGUGUUUGACCUG---AAAACUGGCUCAGUUCAGCAGGAACAGGAG
AAQQ01011467.1/83-13       CUCCGGUGCCUACUGAGCUGAUAUCAGUUCUCAUUUUACACUACAUAGGCUCAGUUCAGCAGGAACAGGAG
AAPY01721327.1/524-457     CUCCCGCGCCUACCGAGCUGACACACACUUGGUUUGUA---CAGACUGGCUCAGUUCAGCAGGAACAGGAA
AAGU03050682.1/5446-5513   CUCCCGUGCCUACUGAGCUGAAACACAGUUGAUUUGUG---CAGACUGGCUCAGUUCAGCAGGAACAGGAG
CAAB02006053.1/17324-17391 CUCCUGUGCCUACUGAACUGGUAUCAGUGUCAUACUGG---AAAACUGGCUCAGUUCAGCAGGAACAGGAG
AAWZ02024153.1/17046-16979 CUUCCGUGCCUACUGAGCUGAUACUCAGUUGCUUUAGA---UAAACUGGCUCAGUUCAGCAGGAACAGGAG
#=GC SS_cons               <<<<----<<<-<<<<<<<<<_________________..._________>>>>>>>>>->>>---->>>>
#=GC RF                    CUCCuGUGCCUACUGAgCUGAuAucaguUuuuuUUuua...uAaACUGGCUCAGuUCAGCAGGAACAGGAG
//
# STOCKHOLM 1.0

#=GF AC   RF00179
#=GF ID   GAIT
#=GF DE   GAIT element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   See reference [1]
#=GF SS   Published; PMID:12588972
#=GF GA   37.00
#=GF TC   37.90
#=GF NC   35.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF RN   [1]
#=GF RM   12588972
#=GF RT   Transcript-selective translational silencing by gamma interferon is
#=GF RT   directed by a novel structural element in the ceruloplasmin mRNA 3'
#=GF RT   untranslated region.
#=GF RA   Sampath P, Mazumder B, Seshadri V, Fox PL
#=GF RL   Mol Cell Biol 2003;23:1509-1519.
#=GF CC   This family represents a cis-acting element in the 3'-UTR of the
#=GF CC   ceruloplasmin (Cp) gene called gamma interferon inhibitor of translation
#=GF CC   (GAIT). The GAIT element is involved in selective translational silencing
#=GF CC   of the Cp transcript. Ceruloplasmin (Cp) is a multifunctional,
#=GF CC   copper-containing glycoprotein produced by the liver and secreted into the
#=GF CC   plasma. As an acute-phase protein, its plasma concentration can double
#=GF CC   during multiple inflammatory conditions. Plasma Cp has been reported to be
#=GF CC   an independent risk factor for cardiovascular disease, including
#=GF CC   atherosclerosis, carotid restenosis after endarterectomy, and myocardial
#=GF CC   infarction. Translational silencing of Cp, and possibly other transcripts,
#=GF CC   mediated by the GAIT element may contribute to the resolution of the local
#=GF CC   inflammatory response following cytokine activation of macrophages [1].
#=GF WK   GAIT_element
#=GF SQ   8


AC131209.2/6785-6855   GUAUGUGAAAGUGUAAAAUAGAAUGUUACUUUGGAAUGACUAUAAACAUUAAAAGAAGACUGGAAGCAUAC
AC104966.4/51221-51291 GUAUGUGAAAGUGUAAAAUAGAAUGUUACUUUGGAAUGACUAUAAACAUUGAAAGAAGACUGGAAACAUAC
AK095290.1/2797-2865   GUAUGUGAAAGUGUAAAAUAGAAUGUUACUUUGGAAUGACUAUAAACAUUAAAAGAAGACUGGAAGCAU--
M13699.1/3255-3321     GUAUGUGAAAGUGUAAAAUAGAAUGUUACUUUGGAAUGACUAUAAACAUUAAAAGA-GACUGGA-GCAU--
D45045.2/8585-8655     GUAUGUGAAAGUGUAAAAUAGAAUGUUACUUUGGAAUGACUAUAAACAUUAAAAGAAGACUGGAAGCAUAC
M18058.1/1580-1650     GUAUGUGAAAGUGUAAAAUAGAAUGUUACUUUGGAAUGACUAUAAACAUUGAAAGAAGACUGGAAACAUAC
X69706.1/260-330       GUAUGUGAAAGUGUAAAAUAGAAUGUUACUUUGGAAUGACUAUAAACAUUAAAAGAAGACUGGAAGCAUAC
M13536.1/2617-2687     GUAUGUGAAAGUGUAAAAUAGAAUGUUACUUUGGAAUGACUAUAAACAUUAAAAGAAGACUGGAAGCAUAC
#=GC SS_cons           <<<<<<---<<<---------<<<<<<----<<<_____>>>-->>>>>>-------->>>---->>>>>>
#=GC RF                GuaUGuGAAaGUGUAAAAUAGaaUGUUACUUUgGAAUGACuAUAAACAuuAAAAGAAGACuGGAAgCAuaC
//
# STOCKHOLM 1.0

#=GF AC   RF00180
#=GF ID   REN-SRE
#=GF DE   Renin stability regulatory element (REN-SRE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12933794
#=GF SS   Published; PMID:12933794
#=GF GA   41.00
#=GF TC   41.00
#=GF NC   39.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0050779; RNA destabilization;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   12933794
#=GF RT   HADHB, HuR, and CP1 Bind to the Distal 3'-Untranslated Region of Human
#=GF RT   Renin mRNA and Differentially Modulate Renin Expression.
#=GF RA   Adams DJ, Beveridge DJ, Van Der Weyden L, Mangs H, Leedman PJ, Morris BJ
#=GF RL   J Biol Chem 2003;278:44894-44903.
#=GF CC   This family represents a cis-acting element in the 3'-UTR of the renin
#=GF CC   (REN) gene called renin stability regulatory element (REN-SRE) which acts
#=GF CC   to regulate renin production. REN-SRE is thought to destabilise the mRNA,
#=GF CC   promoting degradation of the sequence. It has been found that a number of
#=GF CC   proteins bind to the REN-SRE to stabilise the mRNA and promote
#=GF CC   translation. Renin is secreted by renal juxtaglomerular cells and
#=GF CC   catalyses the conversion of angiotensinogen into angiotensin I which is
#=GF CC   the rate-limiting step in the production of angiotensin II. Angiotensin II
#=GF CC   induces hypertension and REN therefore requires tight control to ensure
#=GF CC   expression appropriate to need [1].
#=GF WK   Renin_stability_regulatory_element_(REN-SRE)
#=GF SQ   13


AF193456.1/318-354   CUGCUUUGAGGACAAAGAGAAUAAAGACUUCAUGUUC
BC011157.1/1366-1401 -UGCUUUAAGGAAAAACCGAAUAAAGAUUUCAUGUUU
BC011473.1/1364-1399 -UGCUUUAAGGAAAAACCGAAUAAAGAUUUCAUGUUU
BC047752.1/1408-1444 CUGCUUUGAGGACAAAGAGAAUAAAGACUUCAUGUUC
J02941.1/1579-1615   CUGCUUUGAGGAAAAACAGAAUAAAGACUGCAUGUUU
L00073.1/390-426     CUGCUUUGAGGACAAAGAGAAUAAAGACUUCAUGUUC
L43524.1/1381-1415   -UUCUUUGAGGACCA-CAAAAUAAAGACUUCAUGUUU
M10152.1/338-374     CUGCUUUGAGGACAAAGAGAAUAAAGACUUCAUGUUC
M26901.1/338-374     CUGCUUUGAGGACAAAGAGAAUAAAGACUUCAUGUUC
M32352.1/10852-10887 -UGCUUUAAGGAAAAACCGAAUAAAGAUUUCAUGUUU
M37278.1/12220-12256 CUGCUUUAGGGAAAAACAGAAUAAAGACUGCAUGUUU
X00063.1/1061-1096   CUGCUUUGAGGACAAAGAGAAUAAAGACUUCAUGUU-
X07033.1/1395-1431   CUGCUUUGAGGAAAAACAGAAUAAAGACUGCAUGUUU
#=GC SS_cons         <<-<<<<______>>>>>>::::::::::::::::::
#=GC RF              CUGcUUUGAGGAaAAAcAGAAUAAAGACUUCAUGUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00181
#=GF ID   SNORD113
#=GF PI   sno_14q_I_II; sno_14q_I
#=GF DE   Small nucleolar RNA SNORD113/SNORD114 family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:12045206
#=GF SS   Published; PMID:12045206
#=GF GA   36.00
#=GF TC   36.00
#=GF NC   35.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF CL   CL00069
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300531;
#=GF DR   snoopy; Homo_sapiens300018;
#=GF RN   [1]
#=GF RM   12045206
#=GF RT   Identification of tandemly-repeated C/D snoRNA genes at the imprinted
#=GF RT   human 14q32 domain reminiscent of those at the Prader-Willi/Angelman
#=GF RT   syndrome region.
#=GF RA   Cavaille J, Seitz H, Paulsen M, Ferguson-Smith AC, Bachellerie JP
#=GF RL   Hum Mol Genet 2002;11:1527-1538.
#=GF CC   The imprinted human domain at 14q32 contains two clusters of tandemly
#=GF CC   repeated small nucleolar RNAs named 14q(I) and 14q(II) snoRNAs. These two
#=GF CC   clusters are named SNORD113 and SNORD114 respectively in the HGNC approved
#=GF CC   gene symbol nomenclature. The snoRNAs found in both clusters are clearly
#=GF CC   related and are represented here by a single family. These snoRNAs are
#=GF CC   intron encoded and are processed from the tissue-specific non-coding human
#=GF CC   MEG8 RNA, which lies downstream of the imprinted genes DLK1 and GTL2.
#=GF CC   snoRNAs 14q(I) and 14q(II) differ from previously identified C/D box
#=GF CC   snoRNAs in their expression profiles and lack of complementarity to rRNA
#=GF CC   and snRNA. Homologues of these snoRNAs are found in the imprinted
#=GF CC   non-coding mouse transcript Rian, and in the rat non-coding Bsr
#=GF CC   (brain-specific repetitive) RNA.
#=GF WK   Small_nucleolar_RNA_SNORD113
#=GF SQ   59


AL132709.5/185108-185034 UGGACCA-AUGAUGAGUA---------------CCAUGGGG--UAUCUG-AAACAGGAUUUUUGA-UUAAAC--------------CCAUAUGCAAUUCUGAGGUCCAU
AB014878.1/886-973       UGGAUCA-UUGAUGACCAAAAAAAAAAAAACAUCUGGGAGU--CCUCUG-AGACAUCCAUGAUGA-CCACAAC----------------AUUGGGAGUCUGAGGUCCAC
AL132709.5/152651-152577 UGGACCA-AUGAUGACAA---------------AUACCGG---CGUAUG-AGUCUUGGAUGAUGA-AUAAUAC-------------GUGUCUGGAACUCUGAGGUCCAU
AL132709.5/137723-137652 UGGAUCG-AUGAUGACUA---------------CUGGUGG---CGUAUG-AGUCAUAGACAAUGA-AUAC----------------GUGUCUGGAACUCUGAGGUCCAU
AC121784.2/82332-82403   UUGGUUG-AUGAUGACCA---------------CCGGUGG---CAUUUG-ACUCAUACAUGAUGA-CUUU----------------GAGUCUGAAACACCAAGAUCCAA
AL132709.5/145122-145048 UGGAUCA-AUGAUAAAAC---------------UUGCUGG---CAUAUG-AAUCUUGGAUAAUGG-AUGAUAC-------------GUGUGUGGAACUCUGAGGUCCAA
AL132709.5/167225-167151 UGAGCCA-GUGAUGAAAA---------------CUGGUGG---CAUAGA-AGUCAAGGAUGCUGA-AUAAUGU-------------GUGUCUAGAACUCUGAGGUUCAA
AL132709.5/158545-158469 UGAACUA-GUGGUGAUGG---------------CUUGUGG---CAUAUUUAGUCACAGAUGAUGA-AUAAAUAC------------AUGCCUGAGACUCUGAGGUUAGU
AL132709.5/146793-146719 UGGACCA-AUGAUGACAA---------------AUGGUGG---CAUUGG-AGUUAUGGACGAUGA-AUGAUAU-------------GUGUCUGAAACUCUGAGGUCCAA
AC121784.2/46958-47030   UGGAUCA-AUGAUGACCA---------------GCGGUAGC--CGUAUG-AUUCAUGGAUCAUGA-CUACA----------------GAUCUGGGAGUCUGAGUUCCAC
AC121784.2/75479-75547   AGGACCG-AUGAUGAGAU---------------CUGAUGG---UGUCUG-AGUGUUUCUCGAUGACAUGAA--------------------CAGAUAUCUGAGGUCAGG
AB014879.1/10-96         UGGAUCA-UUGAUGACCAAAAAAAAAAAACAU-CUGGGAGU--CCUCUG-AGACAUCCAUGAUGA-CCACAAC----------------AUUGGGAGUCUGAGGUCCAC
AL132709.5/138673-138602 UGGAUCG-AUGAUGACUA---------------CCGGUGG---CGUAUG-AGUCAUAUGUGAUGA-AUAC----------------GUGUUUGGAACUCUGAGGUCCAU
AL132709.5/169743-169666 GGGACCA-AUGAUAAUGA---------------CUGUUGG---GGUAUG-AGUCAGUGAGGUUGA-AUAACAGUUU----------GUAUCUGGAAAUCUGAGGUCCAA
AL132709.5/156819-156747 UUGAUGAUAUGAUGGCCA---------------CUGGUGG---CUUAUG-AGUCUUAUACAGUGA-AUACA----------------UGUUUGAAACUCUGAGGUCUGU
AB014883.1/1284-1367     UGGAUCA-UUGAUGACCAAAAAAAAUCAU----CUGGGAGU--CCUCUG-AGACAUCCAUGAUGA-CCACAAC----------------AUUGGGAGUCUGAGGUCCAC
AL132709.5/155570-155499 UGGAUCG-AUGAUGACUG---------------CUGGUGG---CGUAUG-AGUCUUACAUGAUGA-AUAC----------------GUGUCUGGAACUCUGAGGUCCAU
AL132709.5/175950-175879 UGGAUCA-AUGAUGAGUA---------------CCCUGGGG--UGUCUG-AAUCUUGGAUUUUGA-UUAAAC-----------------CCUAUAACUCUGAGGUCCAU
AL132709.5/132469-132398 UGGAUCG-AUGAUGACUG---------------CUGGUGG---CGUAUG-AGUCAUAUGCGAUGA-AUAC----------------GUGUCUAGAACUCUGAGGUCCAU
AL132709.5/148929-148858 UGGAUCG-AUGAUGACCA---------------CUGGUGG---CGUAUG-AGUCAUACAUGAUGA-AUAU----------------GUGUCUGGAACUCUGAGGUCCUU
AB014877.1/895-980       UGGAUCA-UUGAUGAACAAAAAAAAAAACAU--CUGGGAGU--CCUCUG-AGACAUCCAUGAUGA-CCACAAC----------------AUUGGGAGUCUGAGGUCCAC
AL132709.5/151720-151647 UGGACCA-GUGAUGACCA---------------CUGGUGG---CAUAUG-AGUCAUACACA-UGA-ACACCAU-------------GUUUCUAGAACUCUGAGGUCCAA
AL132709.5/166229-166160 UGGAUUG-AUGAUGACCA---------------CUGGUGG---CCUAUG-AGUCAU--ACAAUGA-AUAC----------------GUGUCUAGAACUCUGAGGUCCAU
AL132709.5/135542-135471 UGGAUCG-AUGAUGACUA---------------CUGGUGG---CGUAUG-AGUCUUUUGCGAUGA-AUAC----------------GUGUCUAGAACUCUGAGGUCCGU
AL132709.5/136822-136751 UGGAUCG-AUGGUGACUG---------------UUGAUGG---CAUAUG-ACUCACAUAUGAUGA-GUAC----------------GUAUCUGGAACUCUGAGGUCUGU
AB076245.1/1700-1771     UGGAUCU-GUGAUGACAA---------------AGGGUGG---CGUAUG-AGUUGUGGAUCAUGA-GUACA----------------UGUCUGGAAGUCUGAGAUUCAC
AL132709.5/139624-139553 UGGAUCA-AUGAUGACCA---------------CUGGUGG---CGUAUG-AGUCAUAUGUGAUGA-AUAC----------------GUGUCUGGAACUCUGAGGUCCAC
AL132709.5/134553-134482 UGGAUCG-AUGAUGAGCA---------------CUGGUGG---AGUAUG-AGUCACAUACGAUGA-AUAC----------------GUGUCUGGAACUCUGAGGUCCAU
AL132709.5/149496-149422 UGGACCA-AUGAUGACAA---------------CUGCCGG---CGUAUG-AGUGUUGGGUGAUGA-AUAAUAC-------------GUGUCUAGAACUCUGAGGUCCAA
AC121784.2/76334-76408   AGGACCA-AUGAUGAGAU---------------CUGGUGG---CGUUUG-AGUGAUACUCCAUGA-ACGCCAA-------------GUAUCCAGAAAUCUGAGGUCAAU
AL132709.5/191680-191609 UAGACCA-AUGAUGAGUA---------------UUCUGGGG--UGUCUG-AAUCAAUGAUUUUGA-UUAAAC-----------------CCUGUAACUCUGAGGUCCAU
AL132709.5/129680-129609 UGGAUCA-AUCAUGACUA---------------CUGGUAU---UGGAUG-GGUCUUCGUCAGUGA-AUGCC----------------UAUCUGGAACUCUGAGGUCCAU
AC121784.2/78528-78602   CAGAACA-AUGAUGAGAU---------------CUGGUGG---CAUCUG-AAUUUUUCUUGAUGGCAUCCA--------------UGUCAAGAGAAAUCUGAAGUCAGG
AL132709.5/180473-180397 UGGAUCA-AUGAUGAGUA---------------UGCGUGGGG-CAUCUG-AAUCAAAUAUUCUGA-UUAUACC-------------CUGUCUGUAUCUCUGAGGUCCAU
AL132709.5/183412-183335 UGGAUCA-AUGAUGAGUA---------------UUGGUGGAGGUGUCUG-AAUCAACACUUUUGA-UUAAGCC-------------CUCUGUGUAACUCUGAGAUCUGU
AL132709.5/145774-145703 UAGAUCA-GUGAUGACUA---------------CUGUUGG---UGUAUG-AGUCAUAUACGAUGA-AUACA----------------UGUCUGAAAUUCUGAGGUCCAA
AC121784.2/69447-69528   UGCAGCACCUGAUGCCCCCGGAUU---------GCUGUGG---CAUGUG-AGGCAUGUAUGUUGA-AUAUCAU-------------AUGUCUAGAACUCUGAUCUAAAA
AB076245.1/105-176       AGGGUUA-GUCUUGACCU---------------CUGGUAG---CACACA-AUUUGUGGAUGAUGG-GUACA----------------GGUCUGGAAGUCUGAAGUCUAU
AL132709.5/182043-181969 UGGACCA-GUGAUGAAUA---------------UCAUGGGG--UUUCUG-AAACAACAUUUUUGA-UUAAAC--------------CCAUCUGCAACUCUGAGGUCCAU
AL132709.5/131508-131439 UGGAUCG-AUGAUGACUA---------------CUGGUAG---C--AUG-AGUCAUAUACAGUGA-AUACA----------------UGUCUGGAACUCUGAGGUCUGU
AC121784.2/77918-77991   AGGACCG-AUGAUGAGAU---------------CUGGUGG---CGUUUG-AGUGAUACUCCAUGA-ACGCCAA-------------GUAUCCAGAAAUCUGAUG-CCUU
AL132709.5/178148-178075 UGGACCA-AUGAUGAG-A---------------UUGGAGGG--UGUCUG-AAUCAAAAAUUUUGA-UUAAAG--------------CCAUCUGUAACUCUGAGGUCCAU
AL132709.5/164433-164362 UGGAUCA-AUGAUGUCCA---------------CUGGUGG---CGUAUA-AAUCAUAUUUGGUGA-AUAUA----------------UGUCUGGAACUCUGAGGUCCAA
AL132709.5/142597-142509 UGGACUG-UUGAUGACAA---------------GUGGUGG---CUUAUGUGGUUGUACAUGCUGG-UUGUAUAUGAAGAAUAUUACAUAUCUGAAACUUUGAGGUCCAA
AL132709.5/168250-168176 UGGACCA-AUGAUGACCA---------------CUGGUGG---CGUUUG-AGUCAUGGACGAUGA-AUACUAC-------------GUGUCUGAAACUCUGAGGUCCAA
AB014881.1/925-1009      UGGAUCA-UUGAUGACCAAAAAAAAAUCAU---CUGGGAGU--CUUCUG-AGACAUCCAUGAUGA-CCACAAC----------------AUUGGGAGUCUGAGGUCCAC
AL132709.5/171766-171695 UGGACCU-AUGAUGAUGA---------------CUGGUGG---CGUAUG-AGUCAUUGACGGUGA-AUACA----------------GGUCUGGAAGUCUGAGGUCCAA
AC121784.2/77053-77127   AGGACCU-AUGAUGAGAU---------------CUGGUGG---CAUCUG-ACUGUAUCUCGAUGA-CAGCCAU-------------GAGAACAGAUGUCUGAGGUCAGG
AC121784.2/48567-48638   AGGGUUA-GUCUUGACCU---------------CUGGUAG---CACACG-AUUUGUGGAUGAUGG-GUACA----------------GGUCUGGAAGUCUGAAGUCUAU
AL132709.5/148004-147935 UGGACCA-AUUAUGACUA---------------CUG--------GUGUG-AGUCACGCAUAAUGA-ACACCAC-------------GUGUCUGGAACUCUGAGGUCCAA
AL132709.5/154547-154476 AAGAUCA-AUGAUGACUA---------------CUGUUAG---UGUAUG-AGUUACACAUGAUGA-AUACA----------------UGUCUGAAACUCUGAGGUCCAU
AB014878.1/1781-1860     -GGAUCA-UUGAUGACCAUAAAAG---------AUGUGGGAGUCGUCUG-AAACAUGCAUGAUGA-CCACAAC----------------AUUGCGAGUCUGAGGUCCAC
AL132709.5/141607-141533 UAGAACA-ACGAUAACAA---------------AUAGUAG---UGCAGG-AGUCAUAAACUAUGA-GUAAUAU-------------GUGUGUGGAACUCUGAGCAUCAA
AL132709.5/133438-133369 UGGUUCA-GUGUUGACUA---------------CUGGUGU---CGUGUG-AGUCAU--ACAAUGA-AUACA----------------UGUCUGGAACUCUGAGGCCCAU
AC121784.2/51879-51950   UGGAUCU-AUGAUGACCU---------------CUGGUGC---CGUAUG-AGUCGGGGAUCAUGA-UCACA----------------GGUCUGGGAGUCUGAGGUCCAC
AC121784.2/52659-52730   UGUAUUU-GUGAUGAUCA---------------CUGGUGC---CAGAUG-AGUUAUGCAUCAUGG-UCACA----------------GGUCUGCGAGUCCGAGGUCCAC
AL132709.5/153488-153414 UGGACCA-GUGAUGGUGA---------------CUGGUGG---UGUGUG-AGUCAUGCACAGUGA-AUAUCAU-------------GUGUCUGGAACUCUGAGGUCCAA
AL132709.5/128363-128289 UGAGCAA-GCGAUGACAG---------------CCGGUGG---UGUGUG-AGUCAUGGAGGAUGA-AUACUAA-------------GUGCCUGGAACUCUGAGGUUCAA
AL132709.5/140595-140524 UGGAUCG-AUGAUGACUA---------------CUGGUGG---CGUAUG-AGUCAUCUACAGUGA-AUAC----------------GUCUCUGGAACUCUGAGGUCUGU
#=GC SS_cons             :<<<<<_.__________..............._______...______._______________._______.............________________>>>>>::
#=GC RF                  UGGAccA.aUGAUGACcA...............CUGGUGG...CgUaUG.AGUCAUacAUGAUGA.aUAcAac.............gUGUCUGGAAcUCUGAggUCCAa
//
# STOCKHOLM 1.0

#=GF AC   RF00182
#=GF ID   Corona_package
#=GF DE   Coronavirus packaging signal
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12791173
#=GF SS   Published; PMID:12791173
#=GF GA   80.00
#=GF TC   95.20
#=GF NC   39.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019074; viral RNA genome packaging;
#=GF RN   [1]
#=GF RM   12791173
#=GF RT   Identification of probable genomic packaging signal sequence from SARS-CoV
#=GF RT   genome by bioinformatics analysis.
#=GF RA   Qin L, Xiong B, Luo C, Guo ZM, Hao P, Su J, Nan P, Feng Y, Shi YX, Yu XJ,
#=GF RA   Luo XM, Chen KX, Shen X, Shen JH, Zou JP, Zhao GP, Shi TL, He WZ, Zhong Y,
#=GF RA   Jiang HL, Li YX
#=GF RL   Acta Pharmacol Sin 2003;24:489-496.
#=GF RN   [2]
#=GF RM   11533169
#=GF RT   Cooperation of an RNA packaging signal and a viral envelope protein in
#=GF RT   coronavirus RNA packaging.
#=GF RA   Narayanan K, Makino S
#=GF RL   J Virol 2001;75:9059-9067.
#=GF CC   This family represents a predicted coronavirus packaging signal. Within a
#=GF CC   virally infected cell, viral genome and viral proteins specifically and
#=GF CC   selectively unite into progeny viruses [2]. This process is called
#=GF CC   packaging and is vital for viral replication. Viral RNA containing a
#=GF CC   packaging signal allows the sequence to be efficiently packaged into the
#=GF CC   virion [1].
#=GF WK   Coronavirus_packaging_signal
#=GF SQ   3


X51939.1/6955-7083     GACGGUGACGAUGUUAUCUUCAGCCGUACAGGGAGCCUUGAACCGAGCCAUUACCGGAGCCCACAAGGUAAUCCGGGUGGUAAUCGCGUGGGUGAUCUCAGCGGUAAUGAAGCUCUAGCGCGUGGCACU
AF208066.1/20090-20218 GACGGUGACGAUGUUAUCUUCAGCCGUACAGGGAGCCUUGAACCGAGCCAUUACCGGAGCCCACAAGGUAAUCCGGGUGGUAAUCGCGUGGGUGAUCUCAGCGGUAAUGAAGCUCUAGCACGUGGCACU
AF159126.1/64-192      GAGGGUCAGGAUGUCAUCUUCAGCCAAUUCGACAGCCUGAGAGUCAGCUCUAACCAGAGCCCACAAGGUAAUCUGGGGAGUAAUGAACCCGGUAAUGUCGGUGGUAAUGAUGCUCUGGCAACCUCCACU
#=GC SS_cons           :::::::::::<<<<<---<<--<<<---<<<<<-<<------<<<-<<<---<<<<<-<<_____>>--->>>>>->>>--->>>---->>--->>>>>->>>---->>----->>>>>:::::::::
#=GC RF                GAcGGUgAcGAuGucaUCUuCAGCCguaccGagaGCCUugaAccgaGCccUuACCgGaGCCCACAAGGUAAuCcGGGggGUAAucgagugGGUgAucuCgGcGGUAAUGaaGCUCuggCaaguggCACU
//
# STOCKHOLM 1.0

#=GF AC   RF00183
#=GF ID   G-CSF_SLDE
#=GF DE   G-CSF factor stem-loop destabilising element (SLDE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:11865046
#=GF SS   Published; PMID:11865046
#=GF GA   45.00
#=GF TC   46.60
#=GF NC   40.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0000289; nuclear-transcribed mRNA poly(A) tail shortening;
#=GF RN   [1]
#=GF RM   11865046
#=GF RT   RNA destabilization by the granulocyte colony-stimulating factor stem-loop
#=GF RT   destabilizing element involves a single stem-loop that promotes
#=GF RT   deadenylation.
#=GF RA   Putland RA, Sassinis TA, Harvey JS, Diamond P, Coles LS, Brown CY, Goodall
#=GF RA   GJ
#=GF RL   Mol Cell Biol 2002;22:1664-1673.
#=GF CC   This family represents the granulocyte colony-stimulating factor stem-loop
#=GF CC   destabilising element (G-CSF SLDE). G-CSF is secreted by fibroblasts and
#=GF CC   endothelial cells in response to the inflammatory mediators interleukin-1
#=GF CC   (IL-1) and tumour necrosis factor alpha and by activated macrophages. The
#=GF CC   synthesis of G-CSF is regulated both transcriptionally and through control
#=GF CC   of mRNA stability. In unstimulated cells G-CSF mRNA is unstable but
#=GF CC   becomes stabilised in response to IL-1 or tumour necrosis factor alpha,
#=GF CC   and also in the case of monocytes and macrophages, in response to
#=GF CC   lipopolysaccharide. It is likely that the presence of the SLDE in the
#=GF CC   G-CSF mRNA contributes to the specificity of regulation of G-CSF mRNA and
#=GF CC   enhances the rate of shortening of the poly(A) tail [1].
#=GF WK   G-CSF_factor_stem-loop_destabilising_element
#=GF SQ   16


X03655.1/931-1023            CUGAGGGU-CC-CCACCUGGGACCCUUGAGAGUAUC---AG-GUCUCCCACGUGGGAGACAAGAAAUCCCUG-UUUAAUAUUUAAACAGCAGUGUUCCCC
AAIY01407164.1/1672-1764     CUGAGGGUGCC-CACCUUGGGGCCCUUGGGAGCAGC---AG-GUCUCCCACGUGGGAGACAAGCCA-CCCUG-UUUAAUAUUUAAACGGCAGUGUUCCCU
U68481.1/913-1007            CUAAGGGU-GC-CCACCUGGGGCCUU-GGAAGCAUUGGGAA-GUCUCCCACGUGGGAGACAAGACAGCCCUG-UUUAAUAUUUAAACAGCAGUGUUCCCC
AF092533.1/899-995           CUGAGGAUGCC-CACCUCGGGGCCCUUGGAAGCAUCGGGAA-GUCUCCCAAGUGGGAGAUGAGACAGCUCUG-UUUAAUAUUUAAACAGCAGUGUUCCCC
ABDC01229622.1/2203-2298     CCGAGGAUACC-CACCAUGGGGCCCUCGGGAGA-UCAGAAG-GUCUCCCACAUGGGAGACGAGACAUCCCUG-UUUAAUAUUUAAACAGCAGUGUUCCCC
AAPY01741689.1/3185-3107     CUCUGG-----------------CCCGUGGGGCAUCAGGAG-GUCUCCCAUGUGGGAGACCAGACA--CCUG-UUUAAUAUUUAAACAGCAGUGUUCCCC
AAQQ01352634.1/1363-1267     CUGAGGUA-UC-UAACUUGGGCCCAUGGGAAGCGUCAGAAG-CUCUCUCACGUGGAAGACAAGGCCAUACCGAUGUAAUAUUUAAACAGCAGUGUUCCCC
AAKN02042390.1/41925-42015   CCCAGGUCUGU-GCCCUGCAGGGCCAGG--AGCAUC---AGGGUCUCCCGCGUGGGGGAC--GACAUCCCUG-UUUAAUAUUUAAACAGCAGUGUUCCCA
U37101.1/917-1009            CUGAGGCA-CC-UGUCUCAGGGGCCCAGGCAGCAUC---UG-GUCUCCCUUCUGGGGGACAAGACAUCCCUG-UUUAAUAUUUAAACAGCAGUGUUCCCA
AF503365.1/780-876           CUGAGGGUACC-CACCUUGGGGCCCUUGGAAGCAUCGGGAA-GUCUCCCACGUGGGAGACAAGACAGGCCUG-UUUAAUAUUUAAACAGCAGUGUUCCCC
AAEX03006469.1/26456-26361   CAAGGGUA-CC-CACCUUGAGGCCCAUGGAAGCAUCAGGAA-GUCUUCCAGGUGGGAGACAAAACAACCCUG-UUUAAUAUUUAAACAGCAGUGUUCCCC
AAGW02039696.1/153526-153614 CCGUGAGC-CC-C----CGGGGCCCUGGGGAGCACC---AG-GAGGUCCACGUGGGAGACAAGACUGCUCUG-UUUAAUAUUUAAACAGCAGUGUUCCCC
AAQR03042967.1/10930-10836   CUAGGGUA-CC-CACCAUGGG-GCCUUGGGAGGAUCAGAAG-GUCUCCCACAUUGGAGACCAGACAUCCCUG-UUUAAUAUUUAAACAGCAGUGUUCCCC
AAPE02041564.1/171341-171437 CCGAGGGCACC-CGACUUGGGGCCCUUGGAAGCAUCAGAAG-CUCUCCCACGUGGGAGACAAGACAGCCCUG-UUUAAUAUUUAAACAGCAGUGUUCGCC
AB042552.1/918-1014          CCAAGGGUACC-CACCUUGAGGCCCUCGGAAGCAUCAGGAA-GUCUCCCAAGUGGGAGACAAGACAACCCUG-UUUAAUAUUUAAACAGCAGUGUUCCCC
X05402.1/2197-2290           CUGAGGCA-CCAUCUCAGGGGGGCCCAGGCAGCAUC---UG-GUCUCCCUUCCGGGGGACAAGACAUCCCUG-UUUAAUAUUUAAACAGCAGUGUUCCCA
#=GC SS_cons                 ::<<<<<<.<<.<_____>>>>>>>>>,,,,,,,<<-----.<<<<<<<____>>>>>>>-->>-----<<<.<<<<<___>>>>>>>>:::::::::::
#=GC RF                      CucaGGgc.cc.cacCuuggggcCCugGGaAGcAuCaGaAg.GuCucCCAcgUGGgaGaCaAGaCAuccCuG.UuUAAUAUUUAaACaGCAGUGUUCCCc
//
# STOCKHOLM 1.0

#=GF AC   RF00184
#=GF ID   PVX_3
#=GF PI   PVX_cis-reg
#=GF DE   Potato virus X cis-acting regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12581634
#=GF SS   Published; PMID:12581634
#=GF GA   42.00
#=GF TC   44.00
#=GF NC   38.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   12581634
#=GF RT   Cis-acting regulatory elements in the potato virus X 3' non-translated
#=GF RT   region differentially affect minus-strand and plus-strand RNA
#=GF RT   accumulation.
#=GF RA   Pillai-Nair N, Kim KH, Hemenway C
#=GF RL   J Mol Biol 2003;326:701-720.
#=GF CC   This family represents a cis-acting regulatory element which is found in
#=GF CC   the 3' UTR of the Potato virus X genome. This element has been found to be
#=GF CC   required for minus strand RNA accumulation and is therefore essential for
#=GF CC   efficient viral replication [1].
#=GF WK   Potato_virus_X_cis-acting_regulatory_element
#=GF SQ   4


X72214.1/6355-6408   CCAUAACUACGUCCACAUAACCGACGCGUAUCCCAGUUUCAUAGUAUUUUCUGG
AF272736.2/6358-6411 CCAUAACUACGUCUACAUAACCGACGCCUACCCCAGUUUCAUAGUAUUUUCUGG
AF111193.1/6358-6411 CCAUAAUUACGUCUACAUAACCGACGCCUACCCCAGUUUCAUAGUAUUUUCUGG
AY512654.1/990-1043  CCAUAACUACGUCCACAUAACCGACGCCUACCCCAGUUUCAUAGUAUUUUCUGG
#=GC SS_cons         :::::::::<<<<_________>>>>------<<<<______________>>>>
#=GC RF              CCAUAACUACGUCuACAUAACCGACGCcUACCCCAGUUUCAUAGUAUUUUCUGG
//
# STOCKHOLM 1.0

#=GF AC   RF00185
#=GF ID   Flavi_CRE
#=GF PI   Flavi_pk3
#=GF DE   Flavivirus 3' UTR cis-acting replication element (CRE)
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Bateman A, Moxon SJ, Weinberg Z
#=GF SS   Published; PMID:9696848; Bateman A, Moxon SJ, Weinberg Z
#=GF GA   42.00
#=GF TC   42.50
#=GF NC   41.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   9696848
#=GF RT   Identification of specific nucleotide sequences within the conserved 3'-SL
#=GF RT   in the dengue type 2 virus genome required for replication.
#=GF RA   Zeng L, Falgout B, Markoff L
#=GF RL   J Virol 1998;72:7510-7522.
#=GF RN   [2]
#=GF RM   8672458
#=GF RT   Evidence for the existence of a pseudoknot structure at the 3' terminus of
#=GF RT   the flavivirus genomic RNA.
#=GF RA   Shi PY, Brinton MA, Veal JM, Zhong YY, Wilson WD
#=GF RL   Biochemistry 1996;35:4222-4230.
#=GF CC   This family represents the Flavivirus 3'-SL cis-acting replication element
#=GF CC   (CRE). The family is thought to play a crucial role in replication and is
#=GF CC   thought to be needed for the formation of a "replication complex" [1].
#=GF CC   Although evidence has been presented for an existence of a pseudoknot
#=GF CC   structure in this RNA [2], it does not appear to be well conserved across
#=GF CC   flaviviruses. Deletions of the 3' UTR of flaviviruses have been shown to
#=GF CC   be lethal for infectious clones.
#=GF WK   Flavivirus
#=GF SQ   84


AY585243.1/10869-10968 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AF306516.1/477-576     CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUAAUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AF022438.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCC-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF169684.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF069076.1/10878-10977 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGU-AAGAACACAGGAUCU
U47032.1/10877-10976   CUGG-GAAUAGACUAGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAAGAUCU
AF022439.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UUUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF217620.1/10865-10964 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AACAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AY099346.1/2415-2507   CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF204177.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAGCGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCC
M19197.1/10611-10703   CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGGACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AB074760.1/10643-10735 CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAGCGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF416457.1/10877-10976 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UACGUGGUG-GUGAGG-AAGAACACAGGAUCU
AY184212.1/10878-10978 CUGG-GAAUAGACUAGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAAGCCACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AF075723.1/10877-10976 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UGGCUGGUG-GUGAGG-AAGAACACAGGAUCU
L48961.1/10877-10976   CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUUGUG-GUGAGG-AAGAACACAGGAUCU
AF045551.2/10864-10963 CUGG-GAAUAGAGUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUAAUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
U14163.1/10877-10976   CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUA-GUGAGG-AAGAACACAGGAUCU
AF226686.1/10643-10735 CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF119661.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUC-CUGUUG-AAUC-AACAGGUUCU
U88537.1/10643-10735   CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAA--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF022440.1/10631-10723 AUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF204178.1/10631-10723 CUGG-GAA-AGACCAG---AGAU-CCUGCCG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF098737.1/10877-10976 CUGGAGAU-AGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AF306514.1/473-572     CUGG-GAAUAGAGUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-UUAAUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG-AAGAACACAGGAUCU
AF350498.1/10643-10735 CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCG
AF486638.1/10878-10977 CUGG-GAAUAUACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUUGUG-GUGAGG-AAGAACACAGGAUCU
M14933.1/102-200       CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUA-CUAGCACAGAGCGCCGA--AGUAUG-UAGCUUGUG-GUGAGG-AAGAACACAGGAUCU
AF326825.1/10557-10649 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCUG-----C-AA-CAUCA--AUC-CAGGCACAGAGCGCCGC--AAGAUG-GAU-UGGUG-UUG-UU-GAUCCAACAGGUUCU
AY145122.1/10643-10733 CUGG-GAG-AGACCAG---AGAU-CU-GCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AAC-GGAUCU
AF161266.1/10915-11014 CUGG-GAAAAGACUAGG--AGAU-CUU-CUGC-UCUAUU-----C-CAACAUCAG-UCACAAGGCACCGAGCGCCGA--ACACUG-UGACUGAUGGGGG-AG-AAGACCACAGGAUCU
AB074761.1/10643-10735 CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--AUC-CAGGCACAGAGCACCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
M84728.1/10631-10723   CUGG-GAA-AGACCAG---AAAU-ACUACUA--UCUACU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AF289029.1/10573-10665 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AA-CAUCA--AUC-CAGGCACAGAGCGCCGC--GAGAUG-GAU-UGGUG-UUG-UU-GAUCCAACAGGUUCU
AY688948.1/10964-11057 CUGG-GAU-AGACUAGG--GGAU-CUU-CUGC-UCUG-------C-AC-AACCAG-CCACACGGCACAGUGCGCCGA--UAUAGG-UGGCUGGUG-GUG-CU-AGAA-CACAGGAUCU
M12294.2/10869-10962   CUGG-GAU-AGACUAGG--GGAU-CUU-CUGC-UCUG-------C-AC-AACCAG-CCACACGGCACAGUGCGCCGA--CAUAGG-UGGCUGGUG-GUG-CU-AGAA-CACAGGAUCU
Y07863.1/10770-10871   CCUC-GAC-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
M84727.1/10631-10723   CUGG-GAC-AGACCAG---AAAU-CCAACUA--UCUACU-----C-AG-CAUCA--UUC-UAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACAGGUUCU
AY274505.1/10929-11022 CUGG-GAU-AGACUAGG--AGAU-CUU-CUGC-UCUG-------C-AC-AACCAG-CCACACGGCACAGUGCGCCGA--CAAUGG-UGGCUGGUG-GUG-CG-AGAA-CACAGGAUCU
AB185914.2/10936-11029 CUGG-GAU-AGACUAGG--AGAU-CCU-CUGC-UCUG-------C-AC-AACCAG-CCACACGGCACAGUGCGCCGA--CAAUGG-UGGCUGGUG-GUG-CG-AGAA-CACAGGAUCU
U21056.1/10762-10860   CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GAGGUC-UGU--GAGCACAGUUUGCUCA--AGAAUAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
L40361.3/10825-10927   CCCU-CAACAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
AB049391.1/623-725     CCCU-CAAUAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGAGUGACUCGGAAAAACACCCGCU
U27496.1/624-726       CCCU-CAAUAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
AB049400.1/627-729     CCCU-CAAUAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGCGUGACUCGGAAAAACACCCGCU
AB049398.1/628-730     CCCU-CAAUAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--AGAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
M76660.1/535-636       CCUC-GGU-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
AY640589.1/10762-10860 CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GGGGUC-UGU--GAGCACAGUUUGCUCA--AGAAUAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
U52417.1/345-443       CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GAGGUC-UGU--GAGCACAGUCUGCUCA--AGAAUAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
AF069066.1/10825-10927 CCCU-CAACAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGACAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
AB049396.1/620-721     CCUC-AAU-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
U52423.1/369-467       CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GGGGUC-UGC--GAGCACAGUUUGCUCU--AGAAGAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
U27494.1/1000-1101     CCUC-GGC-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGAUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
U52399.1/343-441       CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CG-GAGGUC-UGU--GAGCACAGUUUGCUCA--AGAAUAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
U17066.1/10762-10860   CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GAGGUC-UGU--GAGCACAGUUUGCUCA--AGAAUAAGCAGACCUU-UGGAUG-ACAAACACAAAACCA
U52393.1/369-467       CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GGGGUC-UGU--GAGCACAGUUUGCUCU--AGAAGAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
U54798.1/10762-10860   CAGG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GAGGUC-UGU--GAGCACAGUUUGCUCA--AGAAUAAGCAGACCUU-UGGUUG-ACAAACACAAAACCA
L06436.1/10738-10839   CCAG-G---AAACUGGGGGGGC--GGUUCUUGUUCUCCCUGAGCC-AC-CACCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUGUGUGACUCGGAAAAACACCCGCU
AB049399.1/627-729     CCCU-CAAUAGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGACAGUCUG--ACAAGG-AAG-UGAUGUGUGACUCGGAAAAACACCCGCU
U27495.1/11040-11141   CCUC-GGU-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGGUAGUCUG--ACAAGG-AGG-UGAUGUGUGACUCGGAAAAACACCCGCU
AY326413.1/368-466     CAAG-GAA-AGACCGGAG-UGGU-UCU-CUGCUUUUCCU-----C-CA-GGGGUC-UGC--GAGCACAGUUUGCUCU--AGAAGAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
AF253420.1/10842-10943 CCUC-GUC-AGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCU--AGACACAGAUAGUCUG--AAAAGG-AGG-UGAUGCGUGUCUCGGAAAAACACCCGCU
AF357219.1/530-631     CCAG-G---AAACUGGGGGGGC--GGUUCUUGUUCUCCCUGAGCC-AC-CGCCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUGAGUGACUCGGAAAAACACCCGCU
AY326415.1/368-467     CAGG-GAA-AGACCGGAG-UGG--UCU-CUGCUUUUCCU-----C-CA-AGGGUC-UGC--GAGCACAGUUUGCUU-UUAAAAGAAGCAGACCUUUUGGAUG-AAAAACACAAAACCA
AY193805.1/10685-10787 CCCU-CAUCUGAGGGGG--GGC--GGUUCUUGUUCUCCCUGAGCC-AC-CAUCA--CCC--AGACACAGGCAGUCUA--ACAAGG-AGG-UGAUGUGUGACUCGGAACAACACCCGCU
AY679147.1/10615-10703 CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUG-GAA-UGGUG-CUGUUG-AAUC-AACGGG----
AY303796.1/10878-10969 CUGG-GAAUAGACUAGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG---------AAGAACA
AY303795.1/10878-10969 CUGG-GAAUAGACUAGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG---------AGAAACA
AF254453.1/10878-10969 CUGG-GAAUAGACUGGG--AGAU-CUU-CUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGG---------AAGAACA
AY326414.1/369-467     CAGG-GAA-AGACCGGAG-UGGG-UCU-UUGCUUUUUCU-----U-CA-AGGGUC-UGC--GAGCACAGUUUGCUUU--AUAAGAAGCAGACCUU-UGGAUG-AAAAACACAAAACCA
AY303794.1/10878-10969 CUGG-GAAUAGACUGGG--AGA--UCUUCUGC-UCUAUCU----C-AA-CAUCAG-CUACUAGGCACAGAGCGCCGA--AGUAUG-UAGCUGGUG-GUGAGGAAAAACA---------
AF310149.1/353-435     CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUC-GAA-UGGUG-CUGUUGAAUC------------
AF310147.1/373-455     CUGG-GAG-AGACCAG---AGAU-CCUGCUG--UCUCUA-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--AAAAUC-GAA-UGGUG-CUGUUGAAUC------------
AF310153.1/295-377     CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCUG-----C-AA-CAUCA--AUC-CAGGCACAGAGCGCCGC--AAGAUC-GAA-UGGUG-CUGUUGAAUC------------
AY262283.1/10899-10984 CUGG-GAU-AGACUAGG--AGA--UCUUCUGC-UCUG-------C-AC-AACCAG-CCACACGGCACAGUGCGCCGA--CAAUGG-UGGCUGGUG-GUGCGAGAACA-----------
AF310926.1/379-460     CCAG-G---AAACUGGGG-GGG-CGGUUCUUGUUCUCCCUGAGCC-AC-CACCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUG--UGU------------------
AF310933.1/378-458     CCAG-G---AAACUGGGG-GGG-CGUU-CUUGUUCUCCCUGAGCC-AC-CGCCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUG--AGU------------------
AF310931.1/380-461     CCAG-G---AAACUGGGG-GGG-CGGUUCUUGUUCUCCCUGAGCU-AC-CACCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUG--UGU------------------
AF310930.1/376-457     CCCA-GGA-AGCUGGGGG-GGC--GUU-CUUGUUCUCCCUGAGCC-AC-CACCA--UCC--AGGCACAGACAGCCUG--ACAAGG-AGA-UGGUG--AGU------------------
AF310929.1/376-458     CCCA-GGA-AGCUGGGGG-GGC--GGUUCUUGUUCUCCCUGAUCC-AC-CACCA--UCC--AGGCACAGACAGCCUG--ACAAGG-AGA-UGGUG--AUU------------------
EU670438.1/10738-10819 CCAG-G---AAACUGGGG-GGG-CGGUUCUUGUUCUCCCUGAGCC-AC-CACCA--UCC--AGGCACAGAUAGCCUG--ACAAGG-AGA-UGGUG--UGU------------------
U87412.1/10631-10697   CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--A------AAA-UGGA------------------------
EF571854.1/10936-11009 CUGG-GAU-AGACUAGG--AGAU-CU-UCUGC-UCUGCA-----CAAC-CAGC---CAC-ACGGCACAGUGCGCC-G--ACAAUG-GUG--GCUG---GU------------------
FJ850060.1/10610-10676 CUGG-GAA-AGACCAG---AGAU-CCUGCUG--UCUCCU-----C-AG-CAUCA--UUC-CAGGCACAGAACGCCAG--A------AAA-UGGA------------------------
#=GC SS_cons           <<<<.___.___>>>>-..<<<-.<<<-----.------.....<.<<.<<<<<..<<<.--<<<_______>>>--..------.>>>.>>>>>.>>>---.-------->>>->>>
#=GC RF                Ccgg.GAa.AGAccgGG..gGgU.ccUuCUgc.UCUccu.....C.ag.cAcca..ccc.uAGGCACAGaucGCCug..AaAAuG.ggg.uggUg.cuGaug.AaaAAaACAggacCc
//
# STOCKHOLM 1.0

#=GF AC   RF00186
#=GF ID   SNORD101
#=GF PI   U101
#=GF DE   Small nucleolar RNA SNORD101
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14602913, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   47.00
#=GF TC   48.10
#=GF NC   41.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF CL   CL00074
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300844;
#=GF DR   snoopy; Gallus_gallus300077;
#=GF RN   [1]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res 2003;31:6543-6551.
#=GF CC   snoRNA U101 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs and guide the 2'-O-methylation of rRNA
#=GF CC   and snRNAs. The precise target of this family is unknown [1].
#=GF WK   Small_nucleolar_RNA_SNORD101
#=GF SQ   26


AB061840.1/1853-1925       GU-UUGAAUGAUGACUU---U---A-A-U----UGUCGGAUACCCCUUCACUCC-UUUUAUGAGUGAA-ACAU-A-AGAGUCUGACAAAC
AK096147.1/739-811         GU-UUGAAUGAUGACUU---U---A-A-U----UGUCGGAUACCCCUUCACUCC-UUUUAUGAGUGAA-ACAU-A-AGAGUCUGACAAAC
AL137783.12/17082-17154    GU-UUGAAUGAUGACUU---U---A-A-U----UGUCGGAUACCCCUUCACUCC-UUUUAUGAGUGAA-ACAU-A-AGAGUCUGACAAAC
ABDC01238297.1/2049-2121   GU-UUGAAUGAUGACUU---A---A-A-U----UGUCGGAUACCCCUUCACUCC-CCUUAUGAGUGAA-ACAU-A-ACAGUCUGACAAAC
AANG01372476.1/5797-5869   GU-UUGAAUGAUGACUU---A---A-G-U----UGUCGGAUACCCCUUCACUCU-UUCUGUGAGUGAA-ACCU-A-ACAGUCUGACAAAC
AAFC03068109.1/5105-5177   GU-UUGAAUGAUGACUU---A---A-G-U----UGUCGGAUACCCCUUCACUCC-UUCUAUGAGUGAA-AUCG-C-AUAGUCUGACAAAC
AAFR03001093.1/91076-91005 GU-UUGAAUGAUGACUU---G---A---U----UGUCGGAUACCCCUACACUCC-AUUUAUGAGUGAU-AAAA-A-AUGGUCUGACAAAC
AAPY01004162.1/2343-2413   GU-UUGAAUGAUGACUU---G---A-A-U----UGUCGGAUACCCCUUCACUCC-CUC--UGAGUGAA-CAAU-C-ACAGUCUGACAAAC
CAAA01055927.1/1000-927    GU-UUGCAUGAUGACUU---G---A-A-U----UGUCGGAUACCCCUUCACCCC-GUUCAUGGGUGAG-AAAC-AGCUAGUCUGACAAAC
AAIY01528082.1/1105-1176   GU-UUGAAUGAUGACUU---G---U-G-U----UGUCGGAUACCCCUUCACUC---UCCAUGAGUGAG-ACAA-AUAGAGUCUGACAAAC
AALT01050051.1/907-983     GU-UUGAAUGAUGACUUACAU---U-G-U----UGUCGGAUACCCCUUCACUCC-GUUCAUGAGUGAA-ACCUGU-AUAGUCUGACAAAC
AAQQ01497646.1/621-549     AU-UUGAAUGAUGAC-U---U---A-A-G----UGUCGGAUACCCCUUCACUCC-UUUCAUGGAUGAAAACAU-U-ACAGUCUGACAAAC
AAHX01002042.1/8818-8891   GU-UUGAGUGAUGACUU---G---U-A-U----UGUCGGAUACCCCUUCACCCC-GUUCAUGGGUGAG-AUUC-AGCUAGUCUGACAAAC
AANN01343681.1/2586-2659   GU-UUGAGUGAUGACUU---U---UUA-U----UGUCGGAUACCCCUUCACUCC-UUCC-UGAGUGAA-ACAUGC-ACAGUCUGACAAAC
AAVX01455959.1/497-568     GU-UGAAAUGAUGAAUU---A---A-U-U----UGUCGGAUACCCCUUCACUCU-CCUGAUGAGUGAG-UCAU-U-UUGUUCUGA-CAAC
BX933037.2/152-224         GU-UUGAGUGAUGACUU---CACAA-A-U----UGUCGGAUACCCCUUCACUCC-UUUUGAGUGAGAA-CUGU-G----GUCUGACAAAC
AAYZ01211852.1/1606-1677   GU-UGGGAUGAUGACUG---G---A-A-G----UGUCGGAUACCCCUUCACUCC--UGCAUGAGUGAC-AGUC-U-GCAGUCUGACGAAC
AAPN01046280.1/1549-1478   GACUUGAAUGAUGACUA---G---A---U----UGUCGGAUACCCCUACACUCCAACGUAUGAGUGAA-AAAA-A-A--GUCUGACAAUC
AAWR02015249.1/9263-9335   GU-UUGGAUGAUGACUU---A---A-A-U----UGUCGGAUACCCCUUCACUCC-CUUUAUGAGUGAA-ACUU-A-AUAGUCUGACAAAC
AAKN02045639.1/11468-11542 GU-UUGAAUGAUGACUU---A---A-AGU----UGUCGGAUACCCCUUCACUCC-UAUCAUGAGUGAA-ACAUGA-AUAGUCUGACAAAC
AAGV020900704.1/1092-1163  GU-UUGUAUGAUGAC-U---U---A-U-G----UGUCGGAUACCCCUUCACUCU-UUCAAUGAGUGAA-ACAU-U-GAAGUCUGACAAAC
AAGU03000606.1/4988-4916   GU-UUGAAUGAUGACUU---G---G-UGU----UGUCGGAUACCCCUUCACUCG-UUUUAUGAGUGAA-ACAU---ACAGUCUGACAAAC
AAGW02028778.1/12639-12568 GU-UUGAAUGAUGACUG---A---A-A-U----UGUCGGAUACCCCUUCACUCC-UUCC-UGAGUGAC-ACAC-U-GCAGUCUGACAAAC
AAQR03075875.1/6095-6023   GU-UUGAAUGAUGACUU---C---A-G-U----UGUCGGAUACCCCUUCACUCC-UUCUAUGAGUGAA-ACAU-A-ACAGUCUGACAAAC
AAEX03000181.1/84123-84196 GU-UUGAAUGAUGACUU---A---A-A-U----UGUCGGAUACCCCUUCACUCU-CUCGAUGAGUGAA-ACAUGA-ACAGUCUGACAAAC
AAWZ02013261.1/63825-63750 GU-UUGAAUGAUGAUUA---U---A-U-UAAAAUGUCGGAUACCCCUUCACUCU-AAUUAUGAGUGAG-A-AU-A-AUAGUCUGACAAAC
#=GC SS_cons               <<.<<<___________..._..._._._...._____________________._____________.____._._________>>>>>
#=GC RF                    GU.UuGAAUGAUGACUU...u...A.a.U....UGUCGGAUACCCCUUCACUCc.uUuuAUGAGUGAa.Acau.a.AuAGUCUGACaAAC
//
# STOCKHOLM 1.0

#=GF AC   RF00187
#=GF ID   SNORD102
#=GF PI   U102
#=GF DE   Small nucleolar RNA SNORD102
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:14602913, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   47.00
#=GF TC   48.40
#=GF NC   44.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300437;
#=GF DR   snoopy; Erinaceus_europaeus300410;
#=GF RN   [1]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF RN   [2]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res. 2003;31:6543-6551.
#=GF CC   snoRNA U102 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. It is found within intron 3 of the L21
#=GF CC   ribosomal protein gene. The H/ACA box snoRNA ACA27 is found in the same
#=GF CC   host gene within a different intron [1]. This family is predicted to
#=GF CC   direct a highly conserved 2'-O-methylation in 28S rRNA [2].
#=GF WK   Small_nucleolar_RNA_SNORD102
#=GF SQ   11


AB061826.1/4476-4547       AGCUUAAUGAUGACUGUUUUUUUUGAUUGC--UUGAAGCAAUGUG-AAAAACACAUUUCACCGGCUCUGAAAGCU
AL159977.10/81830-81901    AGCUUAAUGAUGACUGUUUUUUUUGAUUGC--UUGAAGCAAUGUG-AAAAACACAUUUCACCGGCUCUGAAAGCU
ABDC01168401.1/597-667     AGCUUAAUGAUGAUU-AUCUUUUUGAUUGC--UCGAAGCAAAGUG-AAAAACACAUUUCACCGGCUCUGAAAGCU
AAFC03084615.1/7250-7320   AGCUUAAUGAUGAUUGUC-UUUUUGAUUGC--UUAAAGCAACGUG-AAAAUGACAUUUCACCGGCUCUGAGAGCU
AAHX01071090.1/26625-26555 AACUUAAUGAUGAUUGUC-UAUUUGAUUGC--UUGAUGCAAUGUG-AAAACCACAUUUCACCGGCUCUGAGAGUU
AALT01314185.1/738-810     AGUUUAAUGAUGAUU-AUCUUUUUGAUUGCUUUUGAAGCAAUAUG-AAAAACACAUUUCACCGGCUCUGAAAGCU
AANN01418434.1/2417-2487   AGCUUAAUGAUGA--GUAUCUUGUUGAUGC--UUAAAGCAAUGUGAAAAAAGACAUUUCACCGGCUCUGAAAGCU
AAIY01376848.1/805-872     AGCUUGAUGAUGAUUGU-----UUGAUUGCU-UUGAAGCAACAUG-AAAAAUCCAUUUCACCGGCUCUGAGAGCU
AAGW02066083.1/70092-70162 AGCUUAAUGAUGAUUGUC-UUUUUGAUUGC--UUGAAGCAAUAUG-AAAAACACAUUUCACCGGCUCUGAAAGCU
AAPE02035995.1/47782-47852 AGCUUAAUGAUGAUUGUC-UUUUUGAUUGC--UCAAAGCAACGUG-AAAAAUGCAUUUCACCGGCUCUGAAAGCU
AAGU03053214.1/70509-70580 AGCUUGAUGAUGAUUGUCUUUUUGAUUGCU--UUGAAGCAAUGUG-AAAAACACAUUUCACCGGCUCUGAAAGCU
#=GC SS_cons               <<<<<_________________________.._____________.________________________>>>>>
#=GC RF                    AGCUuAAUGAUGAUUGUuuUUUUUGAUUGC..UUGAAGCAAuGUG.AAAAAcACAUUUCACCGGCUCUGAaAGCU
//
# STOCKHOLM 1.0

#=GF AC   RF00188
#=GF ID   SNORD103
#=GF PI   U103
#=GF DE   Small nucleolar RNA SNORD103/SNORD85
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, Daub J, INFERNAL
#=GF SS   Predicted; Moxon SJ
#=GF GA   45.00
#=GF TC   45.20
#=GF NC   43.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; HBII-251;
#=GF DR   snoRNABase; U103;
#=GF DR   snoRNABase; U103B;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF RN   [4]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res. 2003;31:6543-6551.
#=GF CC   This family includes the snoRNAs SNORD103 (U103) and SNORD85 (HBII-251) .
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. In the human genome, there
#=GF CC   are two identical copies of SNORD103 (SNORD103A and SNORD103B) which share
#=GF CC   the same host gene with SNORD85. All three snoRNAs are predicted to guide
#=GF CC   the 2'O-ribose methylation of 18S rRNA G601 [3].
#=GF WK   Small_nucleolar_RNA_SNORD103
#=GF SQ   41


AL445235.30/136607-136535    ACUGGCAAGGAUGAUACACACUUGCCCUCACUUAGACUA--UAGUUCACUGAUGAGAGCA-----------------UUGUUCUGAGCCAGU
AF357332.1/1-59              -------------AUACAUACUUGCCCUCACUUAGACCA--GAGGUCGAUGAUGAGAGCU-----------------UUGUUCUGAGCCAG-
AJ278763.1/1-66              ---UGCAGGGAUGAUACAUACUUGCCCUCACUUAGACCA--GAGGUCGAUGAUGAGAGCU-----------------UUGUUCUGAGC----
AAQQ01135135.1/1016-1088     ACUGGCAAGGAUGAUAUACACUUGCCCUCACUUAGACCA--UAGUUCGUUGAUGAGAGCA-----------------UUAUUCUGAGCCAGU
AAIY01139367.1/12870-12793   ACUGGCAAAGAUGACAUACACUUGCCCUCACUUAGACCA--UAGUUCAUUGAUGAGCGCAUCUAA------------UUGUUCUGAGCCAGU
AAPY01620768.1/2061-2133     ACUGGCAAGGAUGACAUGCACUUGCCCUCACUGAGACCA--CGGUCCAUUGCUGAGAGCG-----------------UUGUUCUGAGCCCGU
AANG01578078.1/161-238       ACUGGCAGGGAUGACAUCCACUUGCCCUCACUUAGACCA--UCGUUCGUUGAUGAGAGCACCUGA------------UUGUUCUGAGCCAGU
AAFC03057234.1/50018-49942   ACUGGCGAGGAUGACAUACACUUGACCUCACUUAGACCA--UAGUUCGUUGAUGAGAGCACCUA-------------GUAUUCUGAGCCAGU
AANN01211961.1/1598-1670     ACUGGCAAAGAUGACAUCCACUUGCCCUCACUUAGACU---CAGUUCAUUGAUGAGAGCA-----------C-----UAGUUCUGAGCCAGU
AALT01656438.1/2229-2307     AUUGGCAAGGAUGACAUCCACUUGCCCUCUCUUAGACUAUAUAGUUCAUUGAUGAGAGCACAAA-------------UUGUUCUGAGCCAAU
AL445235.30/117573-117488    UCUGGCAAUGAUGACC--CACUUGCCCUCACUGAGAACA--AAGUUCGGUAAUGAGAAUCUUUGUUAAUGGACUC--AAGUUCUGAGCCAGA
AL627104.16/25023-25105      UCUGGCGGUGAUGACC--CACUUGCCCUCACUGAGGACA--AAGUUCGAUAAUGAGAAUCUUUGUUAUGGAC-----UCGUUCUGAGCCAGA
AY349604.1/4-89              UCUGGCAAUGAUGACC--CACUUGCCCUCACUGAGAACA--AAGUUCGGUAAUGAGAAUCUUUGUUAAUGGACUC--AAGUUCUGAGCCAGC
ABDC01218124.1/4188-4104     UCUGGCAAUGAUGACU--CACUUGCCCUCACUGAGAACA--AAGUUCAAUAAUGAGAAUCUUUGUUACGGACUC---AAGUUCUGAGCCAGA
AANN01806547.1/4380-4296     UCUGGCAGUGAUGAAC--CACUUGCCCUCACUGAGAACG--AAGUUCGGUAAUGAGAAUCUUUAUUAUGGACUC---AAGUUCUGAGCCAGA
AALT01508697.1/584-668       UCUGGCAAUGAUGACC--CACUUGCCCUCACUGAGAACA--AAGUUCCGUAAUGAGAAUCUCUGUUAUGGACUC---AAGUUCUGAGCCAGA
AAYZ01079849.1/2165-2081     UCUGGCAAUGAUGACA--CACUUGCCCUCACUGAGAACG--AAGUUCGGUAAUGAGAAUCUUUGUUCUGGACUC---AAGUUCUGAGCCGGA
AANG01805514.1/9349-9433     UCUGGCAGUGAUGAGC--CACUUGCCCUCGCUGAGAACA--AAGUUCGGUAAUGAGAAUCUUUGUUAAGGACUC---AAGUUCUGAGCCAGG
AAHX01039952.1/27172-27090   UCUGGCGGUGAUGACC--CACUUGCCCUCACUGAGGACA--AAGUUCGUUGGUGAGAACCUUUGAUAUGGAC-----UCGUUCUGAGCCAGA
AAQQ01591182.1/4028-4111     UCUGGCAAUGAUGACC--CACUUGCCCUCACUGAGAACG--GAGUUCAGUAAUGAGAAUCUUUGUUACGGACU----CAAUUCUGAGCCAGA
AAPY01143135.1/1418-1499     CCUGGCAAUGAUGACC--CACUUGCCCUCACUGAGAACA--AAGUUCGGUAAUGAGAACCUUUGUUGACUC------GAGUUCUGAGCCAGG
AAFC03117268.1/2689-2605     UCUGGCAGUGAUGAGC--CACUUGCCCUCUCUGAGAACA--GAGUUCGGUAAUGACAAUCUUUACUCUGGACUC---AAGUUCUGAGCCAGA
AAFR03043953.1/8605-8519     UCUGGCAGUGAUGACA--CUCUUGCCCUCACUGAGAACA--CAGUUCGGUAAUGAGAACCUUUACUAUGUACUCAG-AAGUGCUGAGCCAGA
AAIY01667663.1/1720-1636     UCUGGCAGUGAUGACC--CACUUGCCCUCACUGAGAACA--AAGUUCGAUAAUGAGAAUCUUUGUUAUGGACUC---AAGUUCUGAGCCAGA
AANU01100659.1/10891-10807   UCUGGUAAUGAUGACC--CACUUGCCCUCACUGAGAACA--AAGUUCGGUAAUGAGAAUCUUUGUUGUGGACUC---AAGUUCUGAGCCAGA
AAVX01601717.1/213-130       UCUGGCAAUGAUGACA--CACUUGCCCUCACUGAGAACA--GCAUUCGAUGAUGAGAAUUUAAAUGUACUCAG----UAUUUCUGAGCCAGA
AAWR02028238.1/35323-35407   UCUGGCAAUGAUGAGC--CACUUGCCCUCACUGAGAACA--AGGUUCGGUAAUGAGAAUCUGUGUUAUGGACUC---AAGUUCUGAGCCAGA
AAGV020117860.1/1141-1215    ACUGGCAAGGAUGACA--CACUUGCCCUCUCUUAGACC---UAGGUCAUUGAUGAGAGCAUCUAA------------UUGUUCUGAGCCAGU
AAKN02028607.1/87211-87294   UCUGGCAGUGAUGACC--CACUUGCCCUCACUGAGGACA--GAGUUCGAUAAUGAGAACCUUUGUAUGGACUC----AAGUUCUGAGCCAGA
AAGV020117873.1/330-414      UCUGGCAAUGAUGACC--CACUUGCCCUCACUGAGAGCA--AAGCUCGAUAAUGAGAACCUUUGUUAUGGACUC---AAGUUCUGAGUCAGA
AAWR02028238.1/14115-14190   ACUGGCAAGGGUGACA--CCCUUGCCCUCACCUAGACCC--UAGUUCAUUGAUGAGAGCACCUAG------------UUGUUCUGAGCCAGU
AAGU03057587.1/7238-7154     UCUGGCAGUGAUGACC--CACUUGCCCUCACUGAGAACA--AAGUUCGGUAAUGAGAAUCUUAGUUAUGGACUC---AGGUUCUGAGCCAGA
AAGW02062736.1/56179-56263   UCUGGCAAUGAUGACC--CACUUGCCCUCACUGAGAACA--AAGUUCGGUAAUGAGAAUCUUUGUUAUGGACUC---AAGUUCUGAGCCAGA
AABR05129373.1/2173-2246     ACUGGCAGGGAUGAUCCAUACUUGCCCUCACUUAGACCA--GAGGCCAUUGAUGAGGCGCU----------------GUUUUCUGAGCCAGU
AAPE02045899.1/44596-44673   ACUGGCGAGGAUGACAUAUACUUGCCCUCACUUAGACCA--CAGUUCGUUGAUGAGAGCACCUAA------------UUGUUCUGAGCCAGU
AAPE02045899.1/66962-67046   UCUGGCAAUGAUGAGC--CACUUGCCCUCACUGAGAGCA--AAGUUCAGUGAUGAGAACCUUUGUUAUGGACUC---GAGUUCUGAGCCAGA
AAEX03001673.1/174458-174535 ACUGGCAAGGAUGACAUACACUUGCCCUCACUUAGACCA--UAGUUCGUUGAUGAGAGCACCUAA------------UUUUUCUGAGCCAGU
AAGW02062736.1/35677-35749   ACUGGCAAGGAUGAUAGAUACUUGCCCUCACUUAGACUA--UAGUUCGUUGAUGAGAGCA-----------------UUGUUCUGAGCCAGU
AAGU03057587.1/42836-42759   ACUGGCAAGGAUGACAUACACUUGCCCUCACUUAGACCU--UAGCUCACUGAUGAGAGCAUCUAA------------UUGUUCUGAGCCAGC
AAEX03001673.1/208527-208614 UCUGGCAAUGAUGAGC--CACUUGCCCUCACUGAGAACA--AAGUUCGGUAAUGAGAAUCUUUGUUAUGGACUCAAAAAGCUCUGAGCCAGA
AAQR03165843.1/666-738       GCUGGCAAGGAUGAUAAAUACUUGCCCUCACUUAGAUAA--UAGUUCAUUGAUGAGAGCA-----------------UUGUUCUGAGCCAGU
#=GC SS_cons                 <<<<<<__________.._____________________.._______________________________....._________>>>>>>
#=GC RF                      uCUGGCAAuGAUGAca..CACUUGCCCUCACUgAGAaCA..aAGUUCguUgAUGAGAaccUuUguUauggac.....uaGUUCUGAGCCAGa
//
# STOCKHOLM 1.0

#=GF AC   RF00189
#=GF ID   SNORD95
#=GF PI   U95
#=GF DE   Small nucleolar RNA SNORD95
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14602913
#=GF SS   Predicted; PFOLD
#=GF GA   55.00
#=GF TC   56.50
#=GF NC   54.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300114;
#=GF DR   snoopy; Loxodonta_africana300342;
#=GF RN   [1]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res 2003;31:6543-6551.
#=GF CC   snoRNA U95 (also referred to as Z38 ) is a member of the C/D class of
#=GF CC   snoRNA which contain the C (UGAUGA) and D (CUGA) box motifs. This family
#=GF CC   is predicted to target two neighbouring 2'-O-methylations, Cm2801 and
#=GF CC   Am2792, in 28S rRNA [1].
#=GF WK   Small_nucleolar_RNA_SNORD95
#=GF SQ   7



AC008443.10/63918-63851 GGGGCGGUGAUGACCCCAACAUGCCAUCUGAGUGUCGGUGCUGAAAUCCAGAGGCUGUUUCUGAGCUG
JN899138.1/1-68         AGGGCGGUGAUGAUUCCAACAUGCCAUCUGAGUGCCCAUGCUGAAACCCAGAGGCUGUUUCUGAGCUG
AL645849.17/60589-60655 GAG-CAAUGAUGACCCCAACAUGCCAUCUGAGUGGCUUUGCUGAAAUCCAGAGGCUGUUUCUGAGCUG
AF295529.1/6463-6530    CCAACAGUGAUGACCACAACAUGCCAUCUGAGUUGCUUUGCUGAAAUCCAGAGGCUGUUUCUGAGCUG
AJ240055.1/1-68         CCAACAGUGAUGACCACAACAUGCCAUCUGAGUUGCUUUGCUGAAAUCCAGAGGCUGUUUCUGAGCUG
AJ240056.1/1-68         CCAACAGUGAUGACCACAACAUGCCAUCUGAGUUGCUUUGCUGAAAUCCAGAGGCUGUUUCUGAGCUG
AL645849.17/62862-62929 CCAACAGUGAUGACCACAACAUGCCAUCUGAGUUGCUUUGCUGAAAUCCAGAGGCUGUUUCUGAGCUG
#=GC SS_cons            ::::<<<<________________________________________________________>>>>
#=GC RF                 ccaaCaGUGAUGACCaCAACAUGCCAUCUGAGUugCuuUGCUGAAAUCCAGAGGCUGUUUCUGAGCuG
//
# STOCKHOLM 1.0

#=GF AC   RF00190
#=GF ID   SNORA16
#=GF PI   U98
#=GF DE   Small nucleolar RNA SNORA16B/SNORA16A family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14602913
#=GF SS   Predicted; PFOLD
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00021
#=GF DR   snoRNABase; U98b;
#=GF DR   snoRNABase; ACA16;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300610;
#=GF DR   snoopy; Loxodonta_africana300204;
#=GF RN   [1]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res 2003;31:6543-6551.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the H/ACA class of snoRNAs which are
#=GF CC   predicted to guide the sites of modification of uridines to pseudouridines
#=GF CC   [2]. This family includes human snoRNAs U98b (SNORA16B) and ACA16
#=GF CC   (SNORA16A) [1,2]. There are currently no predicted targets RNAs for either
#=GF CC   of these snoRNAs [1,2].
#=GF WK   U98_small_nucleolar_RNA
#=GF SQ   29


AK092096.1/824-956         --UGGCCCUUAUCGAAGCUG--C---AGC-UGCUUC--CGCAUA--GCUGCUG--UGGUCAAAA-AGG-AGCCCAGAGUGACAGUU-UUCCUUGACGGU-----CGCCGUUCUGUUU---GUUGU-----AACUGA-UCU-GCAACA--UUUU--GGGAAAAUACAGUU
AL360091.28/68676-68810    UAUGGCCUUUAUCAAAGCUG--C---AGC-UGCUUC--CAUGUA--GCUGCUG--UGGUCAAAA-AGA-AGCCAAGAGUGACAGUU-UUCCUUGAUGGU-----CAUAGUUCUGUUU---GCUGU-----AACUGA-UCU-GCAAGA--UUUU--GGGAAAAUACCAUU
AL589681.19/171773-171905  GGCAGCCCUUAUCAAAGCUG--C---AGC-UGUUUC--CACAUA--GCUGAUG--UGGUCAAAA-AUA-AGCCUCAAGUAACAGUU-UUCCUUAACUGC-----CAUGGUUCCGUUU---ACUGU-----AACACA-UCU---AAGA--UUCU--AGGGAAAGACAGGU
AAFC03053159.1/22253-22119 GGUGGCCCUUAUCAAAGCUG--C---AGC-UGCUUC--CAUAUA--GCUGCUG--UGGUCAAAA-AGG-AGCCCAAAGUGACAGUU-UUCCUUGACGGU-----CGCAGUUCUGUUU---GCUGU-----AACUGA-UCU-GCAACA--UUUC--AGGAAAACACAGUU
AANG01797529.1/3371-3237   UGUGGCCCUUAUCGAAGCUG--C---AGC-UGCUUC--CACAUA--GCUGCUG--UGGUCAAAA-AGG-AGCCCAGAGUGACAGUU-UUCCUUGACGGU-----CGCCGUUCUGUUU---GCUGU-----AACUGA-UCU-GCAACA--UAUC--AGGAAAAGACAAUU
AANU01285292.1/1065-1199   UAUGGCCUUUAUCAAAGCUG--C---AGC-UGCUUC--CAUGUA--GCUGCUG--UGGUCAAAA-AGA-AGCCGAGAGUGACAGUU-UUCCGUGAUGGU-----CACAGUUCUGUUU---GCUGU-----AACUGA-UCU-GCAACA--UUUU--GGGAAAAUAUAGUU
AALT01584320.1/7447-7313   UGUGGCCCUUAUCGAAGCUG--C---AGC-AACUUC--CACAUA--GCUGCUG--UGGUCAAAA-AGG-AGCCCAGAGUGACAGUU-UUCCUUGACGGU-----CGCCGUUCUGUUU---GUAGU-----AACUGA-UCU-GCAACA--UUUC--GGGAAAAGACAGUU
AAQQ01591275.1/220-354     CCUGGCCCUUAUCGAAGCUG--C---AGC-UGCUUC--CACAUA--GCUUCUG--UGGUCAAAA-AGG-AGCCCAGAGCAGCAGUU-UUCCUUGACGGU-----CGCCGUUCUGUUU---GCUGU-----AACUGA-UCU-GCAACA--UUUU--GGGAAAAGACAACU
AANN01687128.1/2654-2788   AGUGGCCCUUAUCAAAGCUG--C---AGC-UGCUUC--CAUUUA--CCUGCUG--UGGUCAAAU-AGG-AGCCCAAAGUGUCAUUU-UUCCUUGAUGGU-----CGCUGUUCUGUUU---GUUAU-----AACAGU-UUU-GCAACA--UUUU--AGGAAAAGACAAUU
AAHX01040055.1/1866-2001   CGUGGCCCUUAUCGAAGCUG--C---AGC-UGCUUC--UACAUA--GCUGCUG--UGGUCAAAA-AGGUGGCCCAGAGAAACAAUU-UUCCUUGACGGU-----CGCGGUUCUGUUU---CCUAU-----AACCGA-UCU-GCAACA--UUUU--GGGAAAAGACAGCU
ABDC01121909.1/1730-1596   UGUGGACAUUAUGGAAGCUG--C---AGC-UGCUUC--CACCCA--GCUGCUG--UGGUCAAAA-AGG-AGCCCAGAGUGACAGUU-UUCCCUGAUGGU-----CAACAUUCUGGUU---UUUGU-----AACUGA-UUU-GCAACA--UUUU--GGGAAAGUACAGUU
AAYZ01160471.1/1627-1761   AGCGGCCCUUAUUGAAGCUG--C---AGC-UGCUUC--UACGUA--GCAGCUG--UGGUCAAAA-AGG-AGCCCAGAGUGACAGUU-UUCUUCGAUGGC-----CGCCAUUCUGUUU---GCUGU-----AACUGA-UCU-GCAACA--UUUC--AGGAAAAGACCCAU
AAIY01514491.1/466-334     AGUGGCUCUUAUCAAAGCUG--C---AGU-UGCUUC--CACAUA--GCUGCUG--UGGCCAAAA-AAG-AGCCCAGAGUAACU-UU-UUCCUUUAUGGU-----CACUGUUCAGUUU---GCUGU-----AACCGA-UCU-GCAACA--UUUC--AGGAAA-GACUAUU
AAPY01487909.1/569-700     CGCGGCCCUUAUCGAAGCUG--C---AGC-UGCUUC--CGCGUA--GCCGCUG--UGGUCAAAG-AGG-AGCCCAGAGUG--AGUU-UCCCC-GACAGU-----CGCCGUCCGGCCU---GCCGU-----GGCCGG-UCU-GCAACA--UUGU--GGGGAAAGACAGCC
AAFR03060642.1/27478-27342 CCAGGCCCUUAUCGAAGCUG--C---ACC-AGCUCU--UCUAUA--GCUGUUG--CAGUCAAAA-AGG-AGCCCAGAGUGACAGUU-UUCUC-GACGGU-----CGCUGUUCUAUUUAAUUCUGU-----AAUAGA-ACC-GCAACA--UUGU--GGGAAAAGACAAGC
CR385068.11/104146-104012  CAUGGCCCUGAUUGAAGCUGU-C---CAG-UUUGUC--UGU-AA--CUGGUGC--AGAUCAAAC-AGG-AGCCGAUAGCAACA-CU-UUUACUGACGGU-----CGCUGUGCAGUUA---CCUGU-----AGCUGUUUCA-GCAACA--UUUA--GGAAAAGGACAAUU
AANH01002401.1/36258-36396 ACCGGCUCCUAUCGAAGCCG--U---CCA-UGCUCU--CCAGUA---GCACUGAAUGGUCAACA-GGA-AGCCCAGAGGAAAA-CU-UCCACCGACGGU-----CGCUGUUCAGUUUAAAAAGAU-----AACUGU-UAUAGCAACA--UUAA--GGGGAAGGACAUUU
BAAE01118989.1/171-305     UGCAGGCUUCAUCGAAGCCCUUC---AUG-CUUGUC--UGU-AG--CAUCGGG--UGGUCA-UA-AGA-AGCUGAGAGAAAC--CU-UUCACCGACGGU-----CGCUGUUCAGUUUG--AAUGU-----AGCUGC-UGCAGCAACA--UUAA--GGGAAAGGACAUUU
ABAV01024688.1/25808-25672 UUCUGGCCCCGUCGAAGCUC--CC--UGU-UGUUCCU-CAUACC--ACAGGG----AGUCAAAA-GGG-AGCCAACAGUAACAGCU-UUUCU-UAUGGU-----CGCUGUUUGACUU---UGAUC-----ACCCCA-UCUUGCAGCA--UUACCCAGGAAAGCAACAUU
AAWR02035371.1/43326-43196 AAAAGGGAUUAAAGGUGCAG--C---UGC-UUUCCC--AUUUAA--GCAGCUG-----UCAAAA-AGA-G-CCCAACGUGACAGUU-UUCCUGUACGCC-----CACUGUUCUGUUG---UCUGU-----AAUUGA-UUU-AUGACA--UUUU--GGGAAAACACAGCG
AAGV020025840.1/392-526    AGUUGCUCUCAUCAAAGCUG--C---AGC-UGCUUC--CACAUA--GCUACUG--UAGUCAAAA-AGG-AGCCCAAAGUGACAGUU-UUCCUUGACCGU-----CGCCAACCCGUUC---GCUCU-----AACUGA-UCU-GCAACA--UUUU--GGGAAAAGACAGUU
AAKN02007781.1/6537-6671   GGUGGCCCUUAUCGAAGCUG--C---AGC-UGCUUG--UACAUA--GUUGCUG--CAGUCAAAA-AGG-AGCCCAGAGUAAGAAUU-UUCCUUGAUGGU-----UGCCGUUCUGUUU---GCUGU-----AACUGA-UCU-GCAACA--UUUU--GGGGAAAGACAGUU
AL732371.4/63573-63442     GGCGGCCCUUAUCACAGCUG--C---AGC-UGCUUC--CACAUA--GCUGCUG--CGGUCAAAA-AGG-AGCCCAGAGUCA---GU-UUCCUUGACCAU-----CACCAUUCUGUUU---GCUAU-----AAGUGA-UCU-GUAACA--UUUU--GCGAAAAUACAGUU
CAAB02003938.1/6916-6782   GAUGGCUCCUAUCGAAGCCG--C---CCGUGCACUC--UGUAGCAGCGGGC-----GGUCAAAC-GGA-AGCCGAGA-UGAAACCU-UUCACCGACGGU-----CGCUGUUCAGUUU---AAAGU-----AACUGC-UCCAGCAACA--UUUA--GGGGAAGGACACCU
AAWZ02034530.1/1111-1254   UCACGGCCCUCUCGAAGCUG--U---GUC-UGUCUCGUUAUGUG--GCUGAUG--CGGUCAAAA-AGG-UGCCAAAAAUAACCUUU-UCCCUUGACGGU-----CGCUGUCCAGUUG---GUUCUCCCAUAACUGU-CCA-GCAACAAUUUUU--GGGGAAAAACACGG
AAPE02042757.1/5502-5367   GAUGGCCCUUAUCAAAGCUG--C---AGU-UGCCUC--CCUGUG--CCUGCUG--CAGGCAAAAAAAA-AGCCCAGAGGGACAGUU-UUCCGUGAUGAC-----CAACACUCUGUCU---GCUGU-----AACUGA-UCU-GCAACA--UUUC--AGGAAAAUACAGUU
AADN03008189.1/30881-30739 GCCCGGCCCUAUCGAAGCUG--CGCCUGC-CG-UGC--GCUGUG--GCAGCCG--CAGUCAAAA-AGG-AGCCCAGAGCCACGCGUUUUCCUCGACGGUCGCUGCGCGGUUUGGUCU---UCUGU-----AACCGC-CCA-GCAACA--AAUG--GGGAAACUACAGGG
AAGW02023569.1/22679-22545 CGCGGCCCUUAUCGAAGCUG--C---AGC-UGCUUC--CACAUA--GCAGUUG--UGGUCAAAA-AGG-AACCCAGAGCGACAGUU-UUCCUUGACGGU-----CACCGUUCUGUUU---GCUGU-----AACCGA-UCU-GCAACA--UUUC--AGGAAAAGACAGUC
AAQR03166078.1/2516-2650   UGUGGCCCUUAUCGAAGCUG--C---AGC-UGCUUC--CAUAUA--GCUGCUG--UGGUCAAAG-AGG-AGCCUAGAGUGACAGUU-UUCCUUGACGGU-----CGCCGUUCUGUUU---GCUGU-----AACUGA-UCU-GCAACA--UUUU--GGGAAAAUACAGUU
#=GC SS_cons               :::::::<<<<<-------<..<...<<<.<<____..____>>..>>>>>--..---------.>>>.>>-------------<<.<<<<<-------.....----<<<______..._____.....>>>---.---.------..----..>>>>>>>:::::::
#=GC RF                    ugugGcCCuucuCGAAGCUg..c...agc.ugcUUC..cauaua..gcugcUG..uGGUCAAAA.aga.aGCCcAgAGuaACAguU.UuCccuGACGGU.....CGCuGuuCuGUUU...gcUgU.....aaCUGa.UCu.GCAACA..UUUu..ggGaAAagACAguU
//
# STOCKHOLM 1.0

#=GF AC   RF00191
#=GF ID   SNORA57
#=GF PI   U99
#=GF DE   Small nucleolar RNA SNORA57
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14602913
#=GF SS   Predicted; PFOLD
#=GF GA   40.00
#=GF TC   40.40
#=GF NC   38.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300815;
#=GF DR   snoopy; Homo_sapiens300553;
#=GF RN   [1]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res 2003;31:6543-6551.
#=GF CC   U99 belongs to the H/ACA class of snoRNAs which are thought to guide the
#=GF CC   sites of modification of uridines to pseudouridines, the target for this
#=GF CC   family is unknown [1].
#=GF WK   Small_nucleolar_RNA_SNORA57
#=GF SQ   26


AC073153.16/108503-108650    CCUCCUUUUCUUGGCGGGGACC-GGGCGUGCGGUCCCGCUCCCCG-UAAUGUACGGAGGUAGAAG--AAAGGG--CUCUGGCCCUCUCGGCGUUAUGUCUUCGGUGCU-U--G-CG-G-CUUCCCGUUCGCGGGUUCUAUCCUCAGACGCCGGAACACUU
AP001458.6/72689-72837       CCUCCUUUUCUUGGCGGGGAUC-GGGCUUGUGGUGCCGCUCCCCG-UAAUGUACGGAGGAAGAGGG-AAAGGG--CUCUGGCCCCCUCGGCGUCAUGUCUUCGGUGCU-G--G-CG-G-CUUCCCAUCCGCUGGUUCUAUCCUCAAACGCCGGGACACCG
BC027679.1/72-219            CCUCCUUUUCUUGGCGGGGACC-GGGCGUGCGGUCCCGCUCCCCG-UAAUGUACGGAGGUAGAAG--AAAGGG--CUCUGGCCCUCUCGGCGUUAUGUCUUCGGUGCU-U--G-CG-G-CUUCCCGUUCGCGGGUUCUAUCCUCAGACGCCGGAACACUU
AANG01067663.1/173-320       CCUCCUUUUCUUGGCGGGGGCC-GGGUGUACGGUCCCGGCCCCCG-UAAUGUACGGAGGCAGAGGG-AAAGGG--CUCUGGCCC-CUCGGCGUCAUGUCUUCGGUGCC-C--G-CG-G-CUUCCGGUCCGCGGGUUCUAUCCUCAACCGCCGGGACACCG
AAFC03050887.1/142806-142954 CCUCCUUUUCUUGGCGCGGGUC-GGGCGUGCAGUCCCGAUCCGCG-UAAUGUACGGAGGUAGAGAG-AACGGG--CUCUGGCCCCCUCGGCGUCAUGUCUUCGGUACC-G--G-CG-G-CCAGCUGUCCGCCGGUUCUAUCCUCAAGCGCCGGGACACAG
AALT01403760.1/596-448       CCUCCUUUUCUUGGCGGGUAUC-GGGCGUGCGGUCCCGAUGCCCG-UAAUGUUCGGAGGCAGAGGG-CAAGGG--CGCCUCGCCCCUCGGCGUCAUGUCUUCGGUGCC-G--G-CG-G-CUUCCCAUCCGCCGGUUCUAUCCUCAAGCGCCGGGACACGC
ABDC01087818.1/14063-13924   CCUCCUUUUCUUGGCGGGGACC-GGGCGUGUGGUCCCGCUCCCCG-UUAUGUACGGAGGCAGAGUG-AAAGGG--CUC---------CGGCGUCAUGUCUUCGGUGCC-G--G-CG-G-CUUCACAUCCGCCGGUUCUAUCCUCAAGCGCCGGGACACUG
AAYZ01093683.1/1143-1291     CCUCCUUUUCUUGGCGGGGACC-GGGCACACGAUCCCGCUCCCCG-UUAUGUACGGAGGCAGAGGA-AAAGGG--CCGUGGUCCCCUCGGCGUCAUGUCUUCGGUGCC-G--G-CU-G-CUUCCCAUGCGCCGGUUCUAUCCUCAAGCGCCGAGACAAGG
AAPY01767425.1/689-540       CCUCCUUUUCUUGGCGGGGAGU-GGGCGUGCGGUCCCGCUCCCUG-UUAUGUGUGGAGGCAGAGGGAAAGGGG--CUCCAGCCCCCUCGGCGUCAUGUCUUCGGUGCC-C--G-CG-G-CCUUCUAUCCGCUGGUUCUAUCCUCAAGCGCCGGGACACGU
AANN01717018.1/1347-1200     CCUCCUUUUCUUGGCGGGUAUC-GGG-UUGCAGUCCCGUUCCCCG-UAAUGUACGGAGGCAGAGGG-CAAGGG--CUUCGGGCCCCUCGGCGUCAUGUCUUCGGUGCC-G--G-CC-G-CUUCCAAUCCGCCGGUUCUAUCCUCAAGCACCGAGACACGG
AAPN01087141.1/2042-1894     CCUCUAUUUCUUGGCGGGGUCC-GGGUGCGCAGUCCCGCUCCCUG-UGAUGUUCGGAGGUAGAGGG-AAGGGG--CUCCGGCCUCCCCGGCGUUAUGUCUUCGGUCCC-G--G-UG-G-CUGCCCGUCCGCCGGUUCUAUCCUCACUCGCCGGGACAAGC
AAFR03068024.1/5021-5170     CCUCCAUUUCUUGGCGGAGGCC-GGGUGCUUAGUCCUGGCCCCCG-UUAUGUACGGAGGCAGAAC--AAGGGGACCCUGGGUCCCCCCGGCGUCAUGUCUUCGGUGCC-G--G-CG-G-UUCCCCAUCCGCCGGUUCUAUCCUCAAUCGCCGGGACACCG
AAIY01336208.1/650-798       CCUCCUUUUCUUGGAGGGCGCC-GGGCAUGCAGUCCAGGUCCCCG-UUAUGUACAGAGACAGAGGG-AGCGGG--CUCCGGCCCCCUCGGCGUCAUGUCUUCGGUGCC-G--G-CG-G-CUGCCCAUCCGCUGGUCCUAUCCUCAGACGCCGGGACAAGG
AANU01171861.1/23638-23492   CCUCAUUUUCUUGACAGGAACU-AGGCAUGUAGUCCUACUCCCUG-UUAUGUACAGAGGCAAAGG--GAAGAG--CUCCGGCCCCCCU--UGGCAUGUCUUUGGUGCCAU--G-CA-G-CUUCCUGUCUGCCAGUUCUAUCCUCAAGCACCAGGACACCA
BAAF04046674.1/17662-17799   CCUCCAUUUCUUGGCAUACAUGUGGUUGUUUAGUACUCAUGUGUG-UUAUGUACGGAGGAAAAUC--AAAGG---------------CAGCGCUAUGUCUUCGGUGCC-G--GUGU-GUAUUUGAAUCAUCCGGUUCUAUCCUCAAACGCUGUCACAUUG
BX323559.11/96958-97093      CCUCC-UUUCUUGGCAUGCAUGUAGUUGUUCAGUACUCAUGUGUG-UAAUGUAUGGAGGUAAAGA--GAAGC---------------CAGUGCUAUGUCUUCGGUGCC-A--G-CAUG-UUUCAUGUCUGCUGGUUCUAUCCUCAAUCAUUGGAACAAGC
AAWR02037721.1/35273-35421   CCUCCUUUUCUUGGCGGGGAUC-AGGCGUGCGGUCCCGGUCCCCG-UAAUGUACGGAGGAAGAGGG-AAAGGG--CUGCAGCCCUCUCGGCGUCAUGUCUUCGGUGCC-G--G-UG-G-CUUCCAGUCCGCCGGUUCUAUCCUCAGGCGCCGGGACACGG
AAGV020058531.1/338-190      CGUCCUUUUCUUGGCGGGGACC-GGGCAUGCGGUCCCAGACCCCGGUUAUGUAUGGAGGCAGAGA--GAGAGG--GUCCGGCCCCCGUGGCGUCAUGUCUUCGGUGCC-G--G-CG-G-CUUCCCGUCUCCCGGUCCUAUCCUCAGUCACCGGGACAGGG
AAGW02063727.1/25287-25139   CCUCCCUUUCUUGGCGGGGACC-GGGCGUACGAUCCCGCUCCCCG-UUAUGUGCGGAGGCAGAGGA-AGAGGG--CUCCGGGCCCCUCGGCGUCAUGUCUUCGGUGCC-G--G-CU-G-CUUCCCGUCCGCCGGUUCUAUCCUCAAGCGCCGAGACACGG
AAQR03147753.1/7891-7743     CCUCCUUUUCUUGGCGGGGCCC-GGGUGUGUAGUCCCGUACCCCG-UUAUGUGCGGAGGUAGAGGG-AAAGGG--CUCUGGCCCACUCGGCGUCAUGUCUUCGGUGCC-G--G-CG-G-CUUCCCGUCUGCCGGUCCUAUCCUCAAACGCCGGGACACUG
AACN010275531.1/734-586      CCUCCUGUUCUUGGCGGGGGCC-GGGUGUGCAGUCCCGGUCCCCG-UAAUGUACGGAGGCAGAAGG-AAAGGG--CUCCGGCCCCCUCGGCGUCAUGUCUUCGGUGCC-C--G-CG-G-CUUCCAGUCCGCUGGUUCUAUCCUCAAGCGCCGGGACACUG
AAPE02052749.1/14332-14184   CCUCCUUUUCUUGGCGGGGUUC-GGGCGUGCGGUCCCGGUCCCCG-UAAUGUACGGAGGCAGAGGG-AGAGGG--CUCCGGCCCCCUCGGCGUCAUGUCUUCGGUGCC-G--A-CG-G-UUGCCAGUCCGCCGGUUCUAUCCUCAAGCGCCGGGACACGG
AABR05182773.1/15508-15368   C-------AGUUGGCGGGGACC-GGGUAUGCAGGCCCGCUCCCCG-UAAUGUACGGAGGUAGAAG--AAAGGG--CUCCGGCCCUCUCGGUGUUUUGUCUUCGGGGCU-U--G-CG-G-CCUCCCGUGCGCAGGUUCUAUCCUCAGACACCGGAACACCU
AAGU03076507.1/45061-44913   CCUCCUUUUCUUGGCGGGGGCC-GGGCGUGCGGUCCCGGUCCCCG-UUAUGUACGGAGGCAGAGGG-AGAGGG--CUCCGGUCCCCUCGGCGUCAUGUCUUCGGUGCC-G--G-CG-G-CUUCCGGUCUGCUGGUUCUAUCCUCAAGCGCCGGGACAAGU
AAWZ02007517.1/22696-22836   CCUCCUUUUCUUGGCAGGCACA-GGCCUUGCCAUGCCUGGUUCUG-UAAUGACUGGAGGAAAAGG--AA----------UGCCUGCCCAGUGUUCUGUCUUCGGUGCC-A--G-CG-GUUUUGCCAUCUGCUGGUUCUAUCCUCAAGCACUGGGACAAAA
CAAB02003044.1/48413-48277   CCUCUAUUUCUUGGCAUGCAUG-AGUUGUUCAGUACUCAGGCGUG-UAAUGUACGGAGGAAAAUG--AAGUG---------------CAGUGCUAUGUCUUCGGUGCC-GGUG-CG-U-UUUCAGGUCUGCCGGUUCUAUCCUCAAUCACUGUGACAUUA
#=GC SS_cons                 <<<<<---------<<<<<<-<.<<<________>>>>->>>>>>.-------->>>>>------..------..------------<<<<<<-------------<<.<..<.<<.<.________>>>>>>>------------>>>>>>::::::::
#=GC RF                      CCUCcuUUUCUUGGCggGgacc.gGgcgUgcaGUcCcgaucCccG.UaAUGUaCgGAGGuAgAgg..AAaGGG..CUccgGcCCcCuCGGcGccAUGUCUUCGGUGCC.g..G.cg.g.cUUcccgUccgCcGGUUCUAUCCUCAAgCgCCGggACAcug
//
# STOCKHOLM 1.0

#=GF AC   RF00192
#=GF ID   BLV_package
#=GF DE   Bovine leukaemia virus RNA packaging signal
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12359429
#=GF SS   Published; PMID:12359429
#=GF GA   70.00
#=GF TC   85.40
#=GF NC   38.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019074; viral RNA genome packaging;
#=GF RN   [1]
#=GF RM   12359429
#=GF RT   The primary nucleotide sequence of the bovine leukemia virus RNA packaging
#=GF RT   signal can influence efficient RNA packaging and virus replication.
#=GF RA   Mansky LM, Gajary LC
#=GF RL   Virology 2002;301:272-280.
#=GF CC   This family represents the bovine leukaemia virus RNA encapsidation
#=GF CC   (packaging) signal which is essential for efficient viral replication [1].
#=GF WK   Bovine_leukaemia_virus_RNA_packaging_signal
#=GF SQ   5


AF033818.1/418-472 AUGGGAAAUUCCCCCUCCUAUAACCCCCCCGCUGGUAUCUCCCCCUCAGACUGGC
K02120.1/628-682   AUGGGAAAUUCCCCCUCCUAUAACCCCCCCGCUGGUAUCUCCCCCUCAGACUGGC
M10987.1/418-472   AUGGGAAAUUCCCCCUCCUAUAACCCCCCCGCUGGUAUCUCCCCCUCAGACUGGC
D00647.1/629-683   AUGGGAAACUCCCCCUCCUAUAACCCCCCCGCUGGCAUCUCCCCCUCAGACUGGC
AF257515.1/629-683 AUGGGAAAUUCCCCUUCUUAUAACCCUCCCGCUGGUAUCUCCCCCUCAGACUGGC
#=GC SS_cons       <<<<<<_________>>>>>>---------<<<<<<_____________>>>>>>
#=GC RF            AUGGGAAAUUCCCCCUCCUAUAACCCCCCCGCUGGuAUCUCCCCCUCAGaCUGGC
//
# STOCKHOLM 1.0

#=GF AC   RF00193
#=GF ID   CTV_rep_sig
#=GF DE   Citrus tristeza virus replication signal
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12202214
#=GF SS   Published; PMID:12202214
#=GF GA   100.00
#=GF TC   259.10
#=GF NC   40.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   12202214
#=GF RT   Mutational analysis of the replication signals in the 3'-nontranslated
#=GF RT   region of citrus tristeza virus.
#=GF RA   Satyanarayana T, Gowda S, Ayllon MA, Albiach-Marti MR, Dawson WO
#=GF RL   Virology 2002;300:140-152.
#=GF CC   This family represents a predicted replication signal which is highly
#=GF CC   conserved in citrus tristeza viruses. Replication signals are required for
#=GF CC   viral replication and are usually found near the 5' and 3' termini. This
#=GF CC   family is predicted to form ten stem loop structures some of which are
#=GF CC   essential for functions that provide for efficient viral replication [1].
#=GF WK   Citrus_tristeza_virus_replication_signal
#=GF SQ   9


U35120.1/2484-2755     UUGAAGUGGACGGAAUAAGUUCCUUGCGGAACUUUAUGUCGGGUUGGUAAAAACCCUU-AUGAUGGUGAUGUAUCACUAGACAAUAACC-GGAUGGGUAAAGUCUUUAAAAUGAUCGAGGGGAAAAUUAACCAUAUCCUCUCGUUGGUCUAAGCUCCCACAGAGUG-UAGUGGUCUCAAGUGAGGCUUAACGUAUGCGUGAACCAAAGAAGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACACACUGUCCCUAUGGGGGGCCAACAUAGGUCCA
AY340974.1/19024-19296 UUGAAGUGGACGGAAUAAGUUCCUCGCGGAACUUUGUGUUGGGUUGGUAAAGACCCUU-AUGAUGGUGAUAUAUCACUAGACAAUAACC-GGAUGGGUAAAGUCUUUAAAAUGAUCGAGGGGAAAAUUAACCGUAUCCUCUCGUUGGUCUAAGCUCCCACAGAGUGGUAGUGGUCUCAAGUGAGGCUUAACGUAUGCGUGAACCAAAGAAGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACGCACUGUCCCUAUGGGGGGCCAACAUAGGUCCA
AF001623.1/18977-19249 UUGAAGUGGACGGAAUAAGUUCCUCGCGGAACUAUAUGUCGGGUUGGUAAAAACCCUU-AUGAUGGUGAUAUAUCACUAGACAAUAACC-GGAUGGGUAAAGUCUUUAAAAUGAUCGAGGGGAAAAUUAACCAUAUCCUCUCGUUGGUCUAAGCUCCCACAGAGUGGUAGUGGUCUCAAGUGAGGCUUAACGUAUGCGUGAACCAAAGAAGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACACACUGUCCCUAUGGGGGGCCAACAUAGGUCCA
Y18370.1/1695-1968     UUGAAGUGGACGGAAUAAGUUCCUUGCGGAACUUUAAGUCGGGUUGGUAAAAACCCUUUAUGAUGGUGAUGUAUCACUAGACAAUAACC-GGAUGGGUAAAGUCUUUAAAAUGAUCGAGGGGAAAAUUAACCGUAUCCUCUCGUUGGUCUAAGCUCCCACAGAGUGGUAGUGGUCUCAAGUGAGGCUUAACGUAUGCGUGAACCAAAGAAGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACACACUGUCCCUAUGGGGGGCCAACAUAGGUCCA
AB046398.1/19030-19302 UUGAAGUGGACGGAAUAAGUUCCUCGCGGAACUAUAUGUCGGGUUGGUAAAAACCCUU-AUGAUGGUGAUAUAUCACUAGACAAUAACCAGGAUGGGUAAAGUCUUUAAAAUGAUCGAGGGGAAAAUUAACUGUAUCCUCUCGUUGGUCUAAGCUCCCACAGAGUGGUAGUGGUCUCAAGUGAGGCUUAACGUAUGCGUGAACCAAAGAAGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACACACUGUCCCUAUGGGGGGCCAACAUAGGUCC-
AY170468.1/19021-19293 UUGAAGUGGACGGAAUAAGUUCCUCGCGGAACUUUGUGUUGGGUUGGUAAAGACCCUU-AUGAUGGUGAUAUAUCACUAGACAAUAACC-GGAUGGGUAAAGUCUUUAAAAUGAUCGAGGGGAAAAUUAACCGUAUCCUCUCGUUGGUCUAAGCUCCCACAGAGUGGUAGUGGUCUCAAGUGAGGCUUAACGUAUGCGUGAACCAAAGAAGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACACACUGUCCCUAUGGGGGGCCAACAUAGGUCCA
Y18371.1/1831-2104     UUGAAGUGGACGGAAUAAGUUCCUUGCGGAACUUUAAGUCGGGUUGGUAAAAACCCUUUAUGAUGGUGAUGUAUCACUAGACAAUAACC-GGAUGGGUAAAGUCUUUAAAAUGAUCGAGGGGAAAAUUAACCGUAUCCUCUCGUUGGUCUAAGCUCCCACAGAGUGGUAGUGGUCUCAAGUGAGGCUUAACGUAUGCGUGAACCAAAGAAGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACACAUUGUCCCUAUGGGGGGCCAACAUAGGUCCA
U35119.1/4206-4477     UUGAAGUGGACGGAAUAAUUGCCUUGCGGAACUUUAUGUCGGGUUGGUAAAAACCCUU-AUGAUGGUGAUGUAUCACUAGACAAUAACC-GGAUGGGUAAAGUCUUUAAAAUGAUCGAGGGGAAAAUUAACCAUAUCCUCUCGUUGGUCUAAGCUCCCACAGAGUG-UAGUGGUCUCAAGUGAGGCUUAACGUAUGCGUGAACCAAAGAAGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACACACUGUCCCUAUGGGGGGCCAACAUAGGUCCA
AF260651.1/18986-19259 UUGAAGUGGACGGAAUAAGUUCCUUGCGGAACUUUAAGUCGGGUUGGUAAAAAUCCUUUAUGAUGGUGAUGUAUCACUAGACAAUAACC-GGAUGGGUAAAGUCUUUAAAAUGAUCGAGGGGAAAAUUAACCGUAUCCUCUCGUUGGUCUAAGCUCCCACAGAGUGGUAGUGGUCUCAAGUGAGGCUUAACGUAUGCGUGAACCAAAGAAGUUCUCCUUAGAGUGUGUGUUGUUUACCCAACACACUGUCCCUAUGGGGGGCCAACAUAGGUCCA
#=GC SS_cons           ::::::::<<<<----<<<<<<<____>>>>>>>-->>>><<<<<_____>>>>>,,,.,,,,,<<<<<____>>>>>,<<<----<<<._____>>>--->>>,,,,,,,,<<<<<<<<<<<____________>>>>>>>>--->>>,,,<<<-<<<<___>>>>->>><<<<<<____>>>>>>,,,,,,,,,,,,<<<<_______>>>>,<<-<<<---<<<<<<<<______>>>>>>>>----->>>->>,<<<<<______>>>>>:
#=GC RF                UUGAAGUGGaCgGAAUaaguuCCUuGCGGaacuuUacGuCGGguuGGUAAaacCCCUU.AUGAUgGuGaUaUAuCaCcAGaCAAUAaCC.GGAUGGGuAAAGuCUUUAAAAUGacCGaGgGGaAAAUUAACcgUAuCCcCuCGUUGguCUAAgCuCcCaCAGAGuGgUaGcgGcCuCAAGUGaGgCcUAACGUAUGCGUGaaCCAAAGAAGuuCUCCUuaGAGUGuGuGuuGUUUACCCaaCaCaCUGUCCCuaUGGGGGgCCAACAUAGGcCCA
//
# STOCKHOLM 1.0

#=GF AC   RF00194
#=GF ID   Rubella_3
#=GF PI   Rubella_cis_act
#=GF DE   Rubella virus 3' cis-acting element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:10074193
#=GF SS   Published; PMID:10074193
#=GF GA   35.00
#=GF TC   35.20
#=GF NC   34.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   10074193
#=GF RT   Mutagenic analysis of the 3' cis-acting elements of the rubella virus
#=GF RT   genome.
#=GF RA   Chen MH, Frey TK
#=GF RL   J Virol 1999;73:3386-3403.
#=GF CC   This family represents a cis-acting element found at the 3' UTR in the
#=GF CC   rubella virus. This family contains three conserved step loop structures.
#=GF CC   Pfam:PF00262 (CAL) which is known to bind calcium in most eukaryotic
#=GF CC   cells, is able to specifically bind to the first stem loop. CAL binding is
#=GF CC   thought to be related to viral pathogenesis and in particular arthritis
#=GF CC   which is a occurs frequently in rubella infections in adults and is
#=GF CC   independent of viral viability. All stem loop structures are thought to be
#=GF CC   important for efficient viral replication and deletion of stem loop three
#=GF CC   is known to be lethal [1].
#=GF WK   Rubella_virus_3'_cis-acting_element
#=GF SQ   25


AB080198.1/1417-1484 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGCGGGCCCCCGCGCGAAACCCGCACUAGCCCACUAGAUU
AY161373.1/1390-1443 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCC------GCAC--------
AB003353.1/1417-1484 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCAUUAGCCCACUAGAUU
AB003345.1/1417-1484 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCAUCAGCCCACUAGAUU
AB072387.1/1417-1484 UACUUGCGCGGCGCUAUUGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCAUUAGCCCACUAGAUU
AB047330.1/9674-9741 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCUGCGUGAAACCCGCACUAGCCCACUAGAUU
AB003337.1/1417-1484 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCACUAGCCCACUAGAUU
AY397695.1/1417-1484 UACUUGCGCGGCGCCAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCAUUAGCCCACUAGAUU
AY280704.1/1417-1484 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCAUUAGCCCACUGGAUU
D00156.1/2363-2430   UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCACUAGGCCACUAGAUU
AB003349.1/1417-1484 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCUGCGCGAAACCCGCAUUAGCCCACUAGAUU
AB080733.1/1417-1484 UACUUGCGCGGCGCUAUUGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCACUAGCCCACUAGAUU
D50677.1/1417-1484   UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCUGCGCGAAACCCGCACUAGCCCACUAGAUU
X05259.1/3294-3361   UACUUGCGCGGCGCUAUAGCACCGCGCUAGCGGGCCCCCGCGCGAAACCCGCACUAGCCCACUAGAUU
L19420.1/1530-1597   UACUUGCGCGGCGCUAUAGCGCCUCGCUAGUGGGCCCCCGCGYGAAACCCGCACUAGCCCACUAGAUU
AB003343.1/1417-1484 UACUUGCACGGCGCUAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCAUUAGCCCACUAGAUU
AB003355.1/1417-1484 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCAUUGGCCCACUAGAUU
AF435866.1/9655-9722 UACUUGCGCGGCGCUAUAGCGCCUCGCUAGUGGGCCCCCGCGCGAAACCCGCACUAGCCCACUAGAUU
AB080731.1/1417-1484 UACUUGCGCGGCGCUAUGGCGCCGCGCUAGUGGGCCCCUGCGCGAAACCCGCACUAGCCCACUAGAUU
AY258323.1/9674-9741 CACCUGCGCGGCGCCAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCACUAGCCCACUAGAUC
AY161374.1/1390-1443 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGCCCCCGGGCGAAACCC------GCAC--------
AY258322.1/9674-9741 UACUUGCGCGGCGCUAUAGCGCCGCGCUAGUGGGUCCCCGCGCGAAACCCGCACCAGCCCACUAGAUU
AB003341.1/1417-1484 CACCUGCGCGGCGCCAUAGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCACUAGCCCACUAGAUU
AB072383.1/1417-1484 UACUUGCGCGGCGCUAUUGCGCCGCGCUAGUGGGCCCCCGCGCGAAACCCGCAUUGGCCCACUAGAUU
M15240.2/9674-9741   UACUUGCGCGGCGCUAUAGCGCCUCGCUAGUGGGCCCCCGCGCGAAACCCGCACUAGGCCACUAGAUC
#=GC SS_cons         <<<<-<<<<<<<<<____>>>>>>>>>->>>><<<<---<<<_______>>>---->>>>::::::::
#=GC RF              uaCuUGCGcGGCGCUAUAGCGCCgCGCUaGugGGcCCCCGCGCGAAACCCGCAcUAGgCCACUAGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF00195
#=GF ID   RsmY
#=GF DE   RsmY RNA family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   57.00
#=GF TC   59.80
#=GF NC   49.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00106
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   14622422
#=GF RT   RsmY, a small regulatory RNA, is required in concert with RsmZ for
#=GF RT   GacA-dependent expression of biocontrol traits in Pseudomonas fluorescens
#=GF RT   CHA0.
#=GF RA   Valverde C, Heeb S, Keel C, Haas D
#=GF RL   Mol Microbiol 2003;50:1361-1379.
#=GF CC   The rsmY gene, like rsmZ (Rfam:RF00166), is regulated by the GacS/GacA
#=GF CC   signal transduction system in the plant-beneficial soil bacterium and
#=GF CC   biocontrol model organism Pseudomonas fluorescens CHA0. GacA/GacS target
#=GF CC   genes are translationally repressed by the small RNA binding protein RsmA.
#=GF CC   RsmY and RsmZ RNAs bind RsmA to relieve this repression and so enhance
#=GF CC   secondary metabolism and biocontrol traits [1].
#=GF WK   RsmY_RNA_family
#=GF SQ   11


AY780887.1/24-141          AUGGACGUCGCGCAGGAAGCGCAA--AGCAACAACACGGAC----AC-GUAGG--AUUCUGCCAGGACGGCG-GAGUGAAAUGGAUGU--CAGGGAAACAGUCUGC-AAAGCCCCGCUUC---GGCGGGGUUUU
CP000304.1/4177705-4177586 AGGAAUGUGGCGCAGGAAGCGCGAUCAAACAACAC-GGACC----AC-ACAGGGAGCGGUGCCAGGACGGCG-CGCGAUCAAGGAUGU--CAGGAU-UCAGUCUGC-AGAGCCCCGCUUC---GGCGGGGUUUU
D50019.1/138-18            A-GGACAUUGCGCAGGAAGCGCCA-AAGACAAUAC--GGAA----AC-UCAGGGAAUCCACCAUGGAUGGUG-GCGUAGCACGGAUGU--CAGGAUAGAGGUCUGC-AAAACCCCGCCCAAAAGGCGGGGUUUU
L12224.1/171-292           AUGGACGUAGCGCAGGACGCGCAACAAGACAUAACAGGGAC----AC-GUAGGGAAGCCUGCCAGGAUGGCG-GGGUGAAAGGGAAAU--CAGGGAAACAGUCUGG-AAAGCCCCGCUUC---GGCGGGGUUUU
CP000712.1/460861-460987   AUGGACGUUGCGCAGGAAGCGCAA-AGGACAGAUCAAGGACGACGAC-GAAGGACCACCUGCCAGGAUGGCG-GGGCGAUACGGAUGUCACAGGGAAACAGUCUGG-AAAACCCCGCUUC---GGCGGGGUUUU
CT573326.1/5427173-5427050 AUGGACGGAGCGCAGGAAGCGCAA-UGGACAGAACAGGGAC----ACCGUAGGAUUUCCUGCCAGGAUGGCG-GGGUGAAAUGGAAGUCACAGGGAAACAGUCUGG-AAAACCCCGCUUC---GGCGGGGUUUU
CP000680.1/4454083-4453965 AUGGAUUCAGCGCAGGAAGCGCCU--AGAGAAAA-AGGGAC----CC-GCUGGACAGCCACCA-GGAUGGUGUGCAGAUCAAGGAUGU--CAGGACAACAGUCUGC-AAGGCCCCGCAAU---CGCGGGGUUUU
CP000949.1/5329183-5329058 AUGGACGUUGCGCAGGAAGCGCAA-AGGACAGAACAGGGACA--AAC-GAAGGAUUUCCUGCCAGGACGGUG-GGGCGAUAGGGAUGUCACAGGGAAAAAGUCUGGGAAAACCCCGCUUC---GGCGGGGUUUU
ABEF01039908.1/238-355     AUGGACGUCGCGCAGGAAGCGCAA--AGCAACAACAGGGAC----AC-GUAGG--AUUCUGCCAGGAUGGCG-GAGUGAAAUGGAUGU--CAGGGAAACAGUCUGC-AAAGCCCCGCUUC---GGCGGGGUUUU
AACY023449337.1/803-921    AUGGAUUCAGCGCAGGAAGCGCAC---AAACGAACAGGGAC----AC-ACUGGACAGCCACCA-GGACGGUGAGCAGAUCAAGGAUGU--CAGGACAACAGUCUGC-AAGGCCCCGCAAU---CGCGGGGUUUU
AACY022429521.1/598-480    AUGGAUUCAGCGCAGGAAGCGCCU--AGACA-AACAGGGAC----AC-GCUGGACAGCCGCCA-GGAUGGUGAGCAGAUCAAGGAUGU--CAGGACUACAGUCUGC-AAGGCCCCGCAAU---CGCGGGGUUUU
#=GC SS_cons               :::::::::<<<<_____>>>>,,.,,,,,,,,,,,,,,,,....,,.,,,,,,,,,<<<<<______>>>>.>--------------..----------------.<<<<<<<<<<___..._>>>>>>>>>>
#=GC RF                    AUGGAcguaGCGCAGGAAGCGCaa.aaGAcAaaACAgGGAC....AC.guaGGaaaucCgcCcAGGAuGgcG.ggguaacAaGGAUGU..CAGGaaAAcAGUCUGc.AaaaCCCCGCuuc...gGCGGGGuuuU
//
# STOCKHOLM 1.0

#=GF AC   RF00196
#=GF ID   AMV_RNA1_SL
#=GF DE   Alfalfa mosaic virus RNA 1 5' UTR stem-loop
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14512577
#=GF SS   Published; PMID:14512577
#=GF GA   60.00
#=GF TC   62.70
#=GF NC   36.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0039689; negative stranded viral RNA replication;
#=GF RN   [1]
#=GF RM   14512577
#=GF RT   The 5' untranslated region of alfalfa mosaic virus RNA 1 is involved in
#=GF RT   negative-strand RNA synthesis.
#=GF RA   Vlot AC, Bol JF
#=GF RL   J Virol 2003;77:11284-11289.
#=GF CC   This family represents a putative stem-loop structure found in the 5' UTR
#=GF CC   in RNA 1 of alfalfa mosaic virus. RNA 1 is responsible for encoding the
#=GF CC   viral replicase protein P1. This family is required for negative strand
#=GF CC   RNA synthesis in in the alfalfa mosaic virus and may also be involved in
#=GF CC   positive strand RNA synthesis [1].
#=GF WK   Alfalfa_mosaic_virus_RNA_1_5'_UTR_stem-loop
#=GF SQ   6


X00819.1/1-35 GUUUUCAUCUUACACACGCUUGUGCAAGAUAGUUA
M35975.1/2-36 GUUUUUAUCUUACACACGCUUGUGCAAGAUAGUUA
L00163.1/1-35 GUUUUUAUCUUACACACGCUUGUGUAAGAUAGUUA
M28375.1/1-35 GUUUUUAUCUUAUACACGCUUGUGUAAGAUAGUUA
V00044.1/1-35 GUUUUUAUCUUACACACGCUUGUGUAAGAUAGUUA
M36391.1/2-36 GUUUUCAUCUUACACACGCUUGUGCAAGAUAGUUA
#=GC SS_cons  ::::<<<<<<<<<<<<____>>>>>>>>>>>>:::
#=GC RF       GUUUUUAUCUUaCACACGCUUGUGuAAGAUAGUUA
//
# STOCKHOLM 1.0

#=GF AC   RF00198
#=GF ID   SL1
#=GF DE   SL1 RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, Daub J
#=GF SS   Published; PMID:12949121; Moxon SJ
#=GF GA   75.00
#=GF TC   75.10
#=GF NC   74.10
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00020
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0000365; mRNA trans splicing, via spliceosome;
#=GF RN   [1]
#=GF RM   11376950
#=GF RT   Trans-spliced leader RNA, 5S-rRNA genes and novel variant orphan
#=GF RT   spliced-leader of the lymphatic filarial nematode Wuchereria bancrofti,
#=GF RT   and a sensitive polymerase chain reaction based detection assay.
#=GF RA   Dassanayake RS, Chandrasekharan NV, Karunanayake EH
#=GF RL   Gene 2001;269:185-193.
#=GF CC   This family represents the SL1 RNA. SL1 is commonly located in the spacer
#=GF CC   region between 5S-rRNA genes where it is involved in trans-splicing.
#=GF CC   Trans-splicing is a form of RNA processing. The acquisition of a spliced
#=GF CC   leader from a SL RNA is a intra-molecular reaction which precisely joins
#=GF CC   exons derived from separately transcribed RNAs. This mechanism of mRNA
#=GF CC   maturation has been shown to occur in a number of lower eukaryotes and is
#=GF CC   commonplace in nematodes [1].
#=GF WK   SL1_RNA
#=GF SQ   28


U31639.1/55-159      GGUUUAAUUACCCAAGUUUGAGGUAAUUGAGUGUUUCGGCCCAGAGUUUCGGCUUCUGUGGCUUGAAGAAAAAUUUUGGAACGUCCUGCUAUAUAG-CGGGACAAC
AF325545.1/133-235   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCACAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
AJ311527.1/55-157    GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCAGCCCAGAGUUUCGGCUCCUGUGGCUUGAAGUGAAAUUUUGGAACGUCCUGUA--UCGG-CGGGACAAC
AF325540.1/133-235   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCAGAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
AF297119.1/1277-1381 GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAGAGUUUAGGCUACUGUGGCUUGAAGUAAAAUUUUGGAACGUCCUGCAUGUUUG-UGGGACAAU
AF282180.1/149-252   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCAGCCCAGAGUUUCGGCUCAUGUGGCUUGAAAAUAAAUUUUGGAACGUCCUGUG--CUAAACGGGACAAA
AF282179.1/149-252   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCAGCCCAGAGUUUCGGCUCAUGUGGCUUGAAAAUAAAUUUUGGAACGUCCUGUG--CUAAACGGGACAAA
U31643.1/55-157      GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCAGAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
AF325541.1/133-235   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCAGAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
L36060.1/210-314     GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAGAGUUUAGGCUACUGUGGCUUGAAGUAAAAUUUUGGAACGUCCUGCAUAUUUG-UGGGACAAU
AF325539.1/133-235   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCAGAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
AF325542.1/116-218   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCAGAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
U09024.1/210-312     GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCAGAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
U31641.1/55-157      GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCAGAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
U31636.1/55-159      GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAGAGUUUAGGCUACUGUGGCUUGAAGUAAAAUUUUGGAACGUCCUGCAUAUUUG-UGGGACAAU
M37737.1/172-274     GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAAAGUUUCGGCUGCUGUGGCUUGAAGUAAAAUUUUGGAACGUCCUGCA--UUAG-CGGGACAAC
AJ279033.1/195-299   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAGAGUUUCAGCUACUGUGGCUUGAAGUAAAAUUUUGGAACGUCCUACAAAUUUG-UGGGACAAU
AF325547.1/161-263   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCAGAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
U31635.1/55-159      GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAGAGUUUAGGCUACUGUGGCUUGAAGUAAAAUUUUGGAACGUCCUGCAUAUUUG-UGGGACAAU
AJ250988.1/180-285   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAUAGCUUCAGCUACUGUGGCUUGAAAUAAAAUUUUGGAACGUUCUGCAAAUCUGCUGGGACAAC
U31637.1/55-157      GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCAGCCCAGAAUUAUAUCUGCUGUGGCUUGAAAUGAAAUUUUGGAAAGUCCUACA--UUAG-UGGGACAAC
M37738.1/223-325     GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCAGCCCAGAAUUAUAUCUGCUGUGGCUUGAAAUGAAAUUUUGGAAAGUCCUACA--UUAG-UGGGACAAC
U31638.1/55-159      GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAGAGUUUCGGCUACUGUGGCUUGAAGUAAAAUUUUGGAACGUCCUGCAAUUUUG-UGGGACAAC
AF325546.1/133-235   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCAGAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
U31640.1/55-159      GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAGUGUUUCAGCUACUGUGGCUUGAAGUAAAAUUUUGGAACGUCCUACAAAUUUG-UGGGACAAC
AF325543.1/133-235   GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCUGCCCAGAGUUUCGACUGCUGUGGCUUGAAGCGAAAUUUUGGAACGUCCUGCA--UGAG-CGGGACAAC
U31634.1/55-159      GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAGAGUUUAGGCUACUGUGGCUUGAAGUAAAAUUUUGGAACGUCCUGCAUAUUUG-UGGGACAAU
U31646.1/55-159      GGUUUAAUUACCCAAGUUUGAGGUAAUUGAAUGUUUCGGCCCAGAGUUUCGGCUGCUGUGGCUUGAAGUAAAAUUUUGGAACGUCCUGCUACUUAG-CGGGACAAC
#=GC SS_cons         ::<<<<<<<<<<_________>>>>>>>>>>,,<<<<-<<<__________________>>>-->>>>--------------<<<<<<<_..___>.>>>>>>:::
#=GC RF              GGuuuaauuaCCCAAGUUUGAGGuaauugaaUGcuuCuGCCCAgAGUUUcggCUacUGUGGCUUGaaguaAAAUUUUGGAAcGuCCugcA..Uuag.cgGGaCAAc
//
# STOCKHOLM 1.0

#=GF AC   RF00199
#=GF ID   SL2
#=GF DE   SL2 RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Published; PMID:10958663; Moxon SJ
#=GF GA   41.00
#=GF TC   41.00
#=GF NC   40.60
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30 -Z 549862.597050 CM SEQDB
#=GF CL   CL00020
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0000365; mRNA trans splicing, via spliceosome;
#=GF RN   [1]
#=GF RM   10958663
#=GF RT   trans splicing of polycistronic Caenorhabditis elegans pre-mRNAs: analysis
#=GF RT   of the SL2 RNA.
#=GF RA   Evans D, Blumenthal T
#=GF RL   Mol Cell Biol 2000;20:6659-6667.
#=GF RN   [2]
#=GF RM   11376950
#=GF RT   Trans-spliced leader RNA, 5S-rRNA genes and novel variant orphan
#=GF RT   spliced-leader of the lymphatic filarial nematode Wuchereria bancrofti,
#=GF RT   and a sensitive polymerase chain reaction based detection assay.
#=GF RA   Dassanayake RS, Chandrasekharan NV, Karunanayake EH
#=GF RL   Gene 2001;269:185-193.
#=GF CC   This family represents SL2 RNA. SL2 RNA is involved in trans splicing in
#=GF CC   lower eukaryotes. Trans-splicing is a form of RNA processing. The
#=GF CC   acquisition of a spliced leader from a SL RNA is a intra-molecular
#=GF CC   reaction which precisely joins exons derived from separately transcribed
#=GF CC   RNAs [2]. Approximately 25% of C. elegans genes are organised into
#=GF CC   polycistronic transcription units and the presence of SL2 on an mRNA is an
#=GF CC   indication the the gene is in an operon [1].
#=GF WK   SL2_RNA
#=GF SQ   30


M27263.1/115-224         GGUUUUAACCCA-GU--UACUCAAGGUAC-GCU-GGAGUUCUGACCUUUCG--AAA--GAAAGUGUCAAAC---GACUUU-AAUUUUUGGAAC-------CGCUCUGCUGGGGUCAUCCGGUAGAGCAAA
U29491.1/429-538         GGUUUUAACCCA-GU-UAAC-CAAGGUUA-GC-AUGUAUUCCGACCAUUCG--UAA--GAGUGUGUUGAAU---AACAAU-AAUUUUUGGAAC-------AGCUUCUUCGGGGUUAUCCGUCGAAGCAAA
U29449.1/954-848         GGUUUUAACCCA-GU-UAAC-CAAGGUUA-GCAUGGAAUU-CGAUCAUUCG--CAA--GAAUGUGUCGAA-----ACACA-AAAUUUUGGACA-------AGCUUCCUCGGGGUA-UCCGUGGGAGCAAA
AC117838.1/4385-4270     GGUUUUAACCCAAGU-UAAC-CAAGGUUA-GCAUUGAAUUUCGACCUUUCGGUAAAACGAUUGUGUUGAGA---AUCGUUCAAUUUUUGGAAC-------UGCUUCUUCGGGGUA-UCCGGGGAGGCGAA
AL034364.1/5192-5083     GGUUUUAACCCA-GU-UAAC-CAAGGUUA-GA-AUGGAUUCCGACCAUUCG--AAA--GAGUGUGUUGAAU---AACAAU-AAUUUUUGGAAC-------AGCUUAUUCAGGGUUAUCCGCAAAAGAUAA
U29449.1/1790-1898       GGUUUUAACCCAAGU-UAAC-CAAGGUUA-GCAUGGAAUU-CGAUCUUUCG--AAA--GAAUGUGUCGAAC----ACAAA-AAUUUUUGGAAC-------AGCUUCCUCGGGGUU-UCCGUGGAGGCAAA
AC117838.1/63527-63642   GGUUUUAACCCAAGU-UAAC-CAAGGUUA-GCAUUGAAUUUCGACCUGUCGGAAAAACGAUUGUGUUGAAA---AUCGCUAAAUUUUUGGAAU-------AGCUUCUUCGGGGUA-UCCGGGGAGGCGAA
AC104269.1/17469-17582   GGUUUUAACCCA-GUUUAAC-CAAGGUUA-GCU-GUCGUUUCGAUCUCUCG--AAA--GAGUGUGUCGAAUAGAAACACC-AAUUUUUGGAAC-------CGCCUCUUCGGGGAUAUCCGUUGAGGCAAA
Z82078.1/25407-25296     GGUUUUUACCCA-GU-UAAC-CAAGGUUA-GCAUUAAAUUUCGACCUUUCG--CAA--GAACGCGUUGAAAUG-CAAAUC-AAUUUUUGGAAC-------CGCUUCUUCGGGGAA-UCCGUUGAGGCAAA
U29449.1/2691-2797       GGUUUUAACCCAUAU--AAC-CAAGGUUA-GUAUGGAAUU-CGAUCAUUCG--CAA--GAGUGUGUCGAA----AACACC-AAAUUUUG-ACA-------AGCUUCUUCGGGGUA-UCCGUGGGAGCAAA
Z82078.1/25894-26004     GGUUUAUACCCA-GU-UAAC-CAAGGUUA-GCAUUAAGUUUCGACCUUUC---CAA--GAAUGUGUUGAAAUG-CAAAUU-AAUUUUUGGAAC-------CGCUUCUUCGGGGAA-UCCGUUGAAGCAAA
U29490.1/268-377         GGUUUUAACCCA-GU-UAAC-CAAGGUUA-GAAUGGA-UUCCGACCAUUCG--AAA--GAGUGUGUUGAAU---AACAAU-AAUUUUUGGAAC-------AGCUUAUUCAGGGUUAUCCGCAAAAGAUAA
Z82266.2/14265-14371     GUUUAAAACCCA-GU--UAC-CAAGGUA--AUUCGGAGUUCUGACCUUUCG--AAA--GAAAGCGUCUUUU----ACGAU-AAAUUUUGGAUU-------AGUUCAGUCGGGGUU-UCCGGCUGAACAAA
AC117838.1/61538-61644   GGUUUUAACCCAAGU-UAAC-CAAGGUUA-GCACUGAAUUUCGACGUUUCGGUAAAACGAUUGUGUUGAG------------AUUUUUGGAAC-------UGCUUCUUCGGGGUA-UCCGGGGAGGCGUA
Z82266.2/4677-4571       GUUUAAAACCCA-GU--UAC-CAAGGUA--AUUCGGAGUUCUGACCUUUCG--AAA--GAAAGCGUCUUUU----ACAAU-AAAUUUUGGAUU-------AGUUCAGUCGGGGUU-UCCGGCUGAACAAA
AF136150.1/148-257       GGUUUUAACCCA-GU-UAAC-CAAGGUUA-GA-AUGGAUUCCGACCAUUCG--AAA--GAGUGUGUUGAAU---AACAAU-AAUUUUUGGAAC-------AGCUUAUUCAGGGUUAUCCGCAAAAGAUAA
AL034364.1/7929-7820     GGUUUUAACCCA-GU-UAAC-CAAGGUUA-GC-AUGUAUUCCGACCAUUCG--UAA--GAGUGUGUUGAAU---AACAAU-AAUUUUUGGAAC-------AGCUUCUUCGGGGUUAUCCGUCGAAGCAAA
M27264.1/116-225         GGUUUUAACCCA-GU--UACUCAAGGUAC-GC-UGGAGUUCUGACCUUACG--AAA--GAGAGUGUCAAAC---AACUUU-AAUUUUUGGAAA-------AGCUCCGCUGGGGUUAUCCGGCGAACGAAA
Z93385.1/25849-25956     GGUUUUAACCCA-GU--UAC-CAAGGUAAUUC-GGAGUUU-CGAUCUUUCG--AAA--GAGAGUGUCGAUU---GUGAAC-AAUUUUUGGAAU-------AGCUCUUCCGGGGAA-UCCGGUCGGGCAAU
AF213679.2/1-109         GGUUUUAACCCA-GU-AUCU-CAAGGUACUACG-GGCGU-CUGACCUUCCACUUGU--GGUUGCGUCACA----AACCUC-AAUUUUUGGA-U-------AGCUCACUCGGGGAA-UCCGGGCGGGCAAC
AL033514.1/181360-181470 GGUUUUAACCCA-GUUUAAC-CAAGGUUA-GC-UGUCGUUUCGAUCUCUCG--AGA--GAGUGUGUCGAAUA--AAAAAU-AAUUUUUGGAAU-------CGCUUCAUCGGGGAA-UCCGUUGAAGCAAA
FO081309.1/13642-13757   GGUUUUAACCCA-GU-UAAC-UAAGGUUA-GCAUU-AAUUUCGACCUUUCG--AAA--GAUUGUGUUGAAU---AACAAU-AAUUUUUGGAAUUUUUGGAAAUAUUUUCAGGGUGA-CAGUGGAGGCAAU
FO080581.1/14164-14055   GGUUUUAACCCA-GU--UACUCAAGGUAC-GC-UGGAGUUCUGACCUUUCG--AAA--GAGAGUGUCAAAC---AACUUU-AAUUUUUGGAAC-------UGCUCUACUGGGGUUAUCCGGUAGAGCAAA
FO080148.1/38519-38413   GGUUUUAACCCA-GU-UAAC-CAAGGUUA-GCAUGGAAUU-CGAUCAUUCG--CAA--GAAUGUGUCGAA-----ACACA-AAAUUUUGGACA-------AGCUUCCUCGGGGUA-UCCGUGGGAGCAAA
FO080581.1/13489-13598   GGUUUUAACCCA-GU--UACUCAAGGUAC-GCUGGAG-UUCUGACCUUUCG--AAA--GAGAGUGUCAAAC---AACUUU-AACUUUUGGAAC-------CGCUCUGCUGGGGUUAUCCGGUAGAGCAAA
FO080275.1/6544-6435     GGUUUUAACCCA-GU-UAAU-UGAGGUUA-GCAAU-AAUUUCGACCUUUCG--AAA--GAUUGUGUUGAAU---GACAAU-AAUUUUUGGAAC-------GACUCCUUCGGGGAUAUCCGAUGAAGCAAA
FO081310.1/22496-22388   GGUUUUAAC-CA-GUUAACU--AAGGUUA-AC-AUUAAUUUCGACCAUUCG--AAA--GAUUGUGUUGAAU---AACAAU-AAUUUUUGGAAC-------AGUUUCUUCGGGGAUAUCCGAUGAAGCAAA
FO080148.1/40257-40363   GGUUUUAACCC--AUAUAAC-CAAGGUUA-GUAUGGAAUU-CGAUCAUUCG--CAA--GAGUGUGUCGAA----AACACC-AAAUUUUG-ACA-------AGCUUCUUCGGGGUA-UCCGUGGGAGCAAA
FO081574.1/35343-35452   GGUUUUAACCCA-GU--UACUCAAGGUAC-GC-UGGAGUUCUGACCUUUCG--AAA--GAGAGUGUCAAAC---AACUUU-AAUUUUUGGAAA-------AGCUUCGCUGGGGUUAUCCGGCGAAGCAAA
FO081309.1/10648-10757   GGUUUUAACCCA-GU-UAAU-UGAGGUUA-GCAAU-AAUUUCGACCUUUCG--AAA--GAUUGUGUUGAAU---AACAAU-AAUUUUUGGAAC-------AGCUUCUUCGGGGAUAUCCGAUGAAGCAAA
#=GC SS_cons             ::::::<<<<--.<<.-<<<.____>>>-.>>-->>-->>,<<<<<<<<<_..___..>>>>>->>>>---...------.------------.......---<<<<<<<<<<__._>>->>>>>>>>::
#=GC RF                  GGUUUUAAccCA.Gu.UaAC.CAAGGUuA.gCauggaaUUucgAcCucuCG..aAA..GagaGUgUcgAAu...AAcaau.AAUUUUUGGAAu.......aGCucccucggGGuu.UCCGccgagggaAA
//
# STOCKHOLM 1.0

#=GF AC   RF00200
#=GF ID   snoZ199
#=GF DE   Small nucleolar RNA Z199
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   47.00
#=GF TC   47.10
#=GF NC   46.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   snoZ199 is a C/D box small nucleolar RNA, which acts as a methylation
#=GF CC   guide RNA for sites on 18S and 25S rRNA. Rice snoZ199 is reported to be
#=GF CC   homologous to Arabidopsis snoR13.
#=GF WK   Small_nucleolar_RNA_Z199
#=GF SQ   17


AC135320.6/55492-55392  AA-UCAUGUGAUGAGAAAAUAAAAAAUAACUGCAACAAUAUGAUGGGAUUUAU--UUCCAUGAUUCC--UAUUAUUUAACUUUCUCUGAAAUUAACUUUUUUG-AUU
AF317984.1/1-78         GA-UCAGUUGAUGAGCA-------AAUA-CUGCAACAAUAUGAUGGAGAA---AUCUUUAUGAUUCU---UA-GUAUUUAAGUCUCUGA------------UG-AUC
AJ457082.1/2-76         GG-UCAAAUGAUGAGAGA------UAUAACUGCAACAAUAUGAU-----CCAUGAU---GUGAUUCU---UA-GUAUUUAAGUCUCUGA------------UG-ACC
AY112819.1/2-76         GG-UCAAAUGAUGAGA------GAUAUAACUGCAACAAUAUGAU-----CCAUGAU---GUGAUUCU---UA-GUAUUUAAGUCUCUGA------------UG-ACC
AF317983.1/5-84         AGAUCAGGUGAUGAGG-------UAAUA-CUGCAACAAUAUGAUGGAG---UAAUCUUUGUGAUUAU---UA-GUAUUUAAGUCUCUGA------------UGAUCU
AL391146.1/51064-51142  GGAUCAGUUGAUGAGC-------AAAUA-CUGCAACAAUAUGAUGGAGAA---AUCUUUAUGAUUCU---UA-GUAUUUAAGUCUCUGA------------UG-AUC
AC138464.19/50294-50216 AUAUCAUGUGAUGAGA-------AAAUAACUGCAACAAUACGAUGGA----UUCGUUCCAUGAUUCC---UA-GUAUUUAAGUCUCCGA------------UG-AUU
AC147499.5/79703-79785  GGAUCAUUUGAUGAGA-------AAAAAACUGCAACAAUAUGAUGGA----UUUGUUCCAUGAUUCCUAGUAUUUAAUUAAGUCUCUGA------------UG-AUC
AC147499.5/74223-74300  GAAUCAUGUGAUGAGA--------AAAAACUGCAACAAUAUGAUGGA----UUCGUUCCAUGAUUCU---UA-GUAUUUAAGUCUCUGA------------UG-AUC
AY220643.1/10-93        GGGUCAGGUGAUGAGG-------UUUUAACUGCAACAAUAUGAUGGGAGCUUAGCUCCUGUGAUUCC---UAUGUAUUUAAGUCUCUGA------------UG-AUC
AY220640.1/10-93        GGUUCAAGCGAUGAGG-------UUUUAACUGCAACAAUAUGAUGGGAGCUUUGCUCCUGUGAUUCC---UAUGUAUUUAAGUCUCUGA------------UG-AUC
AJ490458.1/3-86         GGUUCAAGCGAUGAGG-------UUUUAACUGCAACAAUAUGAUGGGAGCUUUGCUCCUGUGAUUCC---UAUGUAUUUAAGUCUCUGA------------UG-AUC
AJ490464.1/3-86         GGGUCAAGUGAUGAG-------GUUUAAACUGCAACAAUAUGAUGGGAGCUUAGCUCCUGUGAUUCC---UAUGUAUUUAAGUCUCUGA------------UG-AUC
AJ490460.1/1-85         GGCUCAAGUGAUGAG-------UGAAAAACUGCAACAAUAUGAUGGGAGCUAUACUCCUGUGAUUCC---UAAGUAUUUAAGUCUCUGA------------UGUACC
AY220641.1/6-90         GGCUCAAGUGAUGAG-------UGAAAAACUGCAACAAUAUGAUGGGAGCUAUACUCCUGUGAUUCC---UAAGUAUUUAAGUCUCUGA------------UGUACC
AY220642.1/9-93         GGCUCAAGUGAUGAGA-------GAAAAACUGCAACAAUAUGAUGGGAGAUAUGCUCCUGUGAUUCC---UAAGUAUUUAAGUCUCUGA------------UGUACC
AJ490466.1/1-85         GGCUCAAGUGAUGAGA-------GAAAAACUGCAACAAUAUGAUGGGAGAUAUGCUCCUGUGAUUCC---UAAGUAUUUAAGUCUCUGA------------UGUACC
#=GC SS_cons            <<-<<<----------.......---------------------<<<<<_____>>>>>--------...-------------------............>>.>>>
#=GC RF                 GgaUCAagUGAUGAGa.......aaAuAACUGCAACAAUAUGAUgGgaGuUaUaCucCcaUGAUUCc...UAugUAUUUAAGUCUCUGA............UG.AcC
//
# STOCKHOLM 1.0

#=GF AC   RF00201
#=GF ID   snoZ278
#=GF DE   Small nucleolar RNA Z278
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   36.00
#=GF TC   36.10
#=GF NC   35.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300087;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   snoZ278 is a C/D box small nucleolar RNA. Its methylation guide targets
#=GF CC   have not been reported.
#=GF WK   Small_nucleolar_RNA_Z278
#=GF SQ   7


AJ536282.1/1-115  GCCGAUGAUGAGUUGCCCAAUGUUUAGAGGGUGUAGUUGGCUCAAGUUCCUGUUUACCAGGUAGAACCUACUUGCAGCUGCUGCAUUCACGUGAUAUCAAUGGGCUUCCUGAGGU
AJ536279.1/1-115  GCCCAUGAUGAGCUGCCCAAUGAUUAGAGGGUGUAGUUGGCUCAAGUUCCUGUUCAUCAGGAAGAACCUACUUGCAGCUGCUGCAUUCACAUGUUAUCAACGGGCUUCCUGAGGU
AJ536281.1/1-115  ACCUAUGAUGAGCUGCCCAUUGUUUAGAGGAUGUAGUUGGCUCGAGUUCCUGUUUAUCAGGAAGAACCUACUUGUAGCUGCUGCAUUCACAUGUUAUCAACGGGCUACCUGAGGU
AJ536280.1/1-114  GCCCAUGAUGAGCUGCCCAAUGAUUAGAGGGUGUAGUUGGCUCAAGUUCCUGUUUAUCAGGAAGAACCUACUUGCAGCUGCUGCAUUCACAUGUUAUCAACGGGUUU-CUGAGGU
AY220683.1/11-125 GCCCAUGAUGAGCUGCCCAAUGAUUAGAGGGUGUAGUUGGCUCAAGUUCCUGUUCAUCAGGAAGAACCUACUUGCAGCUGCUGCAUUCACAUGUUAUCAACGGGCUUCCUGAGGU
AY220682.1/7-120  GCCCAUGAUGAGCUGCCCAAUGAUUAGAGGGUGUAGUUGGCUCAAGUUCCUGUUUAUCAGGAAGAACCUACUUGCAGCUGCUGCAUUCACAUGUUAUCAACGGGUUU-CUGAGGU
AY220681.1/8-122  ACCUAUGAUGAGCUGCCCAUUGUUUAGAGGAUGUAGUUGGCUCGAGUUCCUGUUUAUCAGGAAGAACCUACUUGUAGCUGCUGCAUUCACAUGUUAUCAACGGGCUACCUGAGGU
#=GC SS_cons      <<<--------------------------------------------<<<<<_____>>>>>-------------------------------------------------->>>
#=GC RF           gCCuAUGAUGAGcUGCCCAaUGaUUAGAGGgUGUAGUUGGCUCaAGUuCCuGUUuAUCaGGaAGAACCUACUUGcAGCUGCUGCAUUCACAUGUUAUCAAcGGGcUuCCUGAGGu
//
# STOCKHOLM 1.0

#=GF AC   RF00202
#=GF ID   snoR66
#=GF DE   Small nucleolar RNA R66
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   43.00
#=GF TC   43.00
#=GF NC   38.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   snoR66 is a C/D box small nucleolar RNA, which acts as a methylation guide
#=GF CC   for 18S ribosomal RNA in plants [1]. snoR66 has been alternatively named
#=GF CC   snoZ269 in rice.
#=GF WK   Small_nucleolar_RNA_R66
#=GF SQ   6


AJ532507.1/1-76 CCCCGUGAUGGCAUGGA-UCUUUGAGACCUGAGAAUUUUCUUCCUUGAUGAAA-AUCACAAGUACGAUCCCUGAGGGC
AJ532506.1/1-77 GCCCGUGAUGGCAUGAA-UCUUUGAGACCUGAGAAUUUUCUUCCUUGAUGAAAGAUCACAAGCAUUAUCCCUGAGGGC
AJ532509.1/6-77 UCCGAUGAUGGCAUGAAAUCUUUGAGACCUGACA---UUCUUG--UGAUGACA-AACAUAAGCAUAUUUCCUGAGGAC
AJ532505.1/2-77 ACCCGUGAUGGCAUGAA-UCUUUGAGACCUGAGAAUUUUCUUCCUUGAUGAAA-AUCACAAGCAUGAUCCCUGAGGGC
AJ532510.1/6-76 UCCGAUGAUGGCAUGAAAUCUUUGAGACCUGACA---UUCUUG--UGAUGACA-AACAUAAGCAUAUUUCCUGAG-AC
AJ532508.1/6-77 UCCGAUGAUGGCAUGAAAUCUUUGAGACCUGACA---UUCUUG--UGAUGACA-AACAUAAGCAUAUUUCCUGAGGAC
#=GC SS_cons    <<<--------------.-------------<<<_______>>-->-------.-------------------->>>:
#=GC RF         uCCcaUGAUGGCAUGAA.UCUUUGAGACCUGAgAAUUUUCUUcCUUGAUGAaA.AuCAuAAGCAUaaUuCCUGAGGaC
//
# STOCKHOLM 1.0

#=GF AC   RF00203
#=GF ID   snoR160
#=GF DE   Small nucleolar RNA R160
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; Griffiths-Jones SR
#=GF GA   42.00
#=GF TC   42.90
#=GF NC   41.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   snoR160 is a C/D box small nucleolar RNA, which acts as a methylation
#=GF CC   guide for 25S ribosomal RNA in plants [1]. snoR160 has been alternatively
#=GF CC   named snoZ270 in rice.
#=GF WK   Small_nucleolar_RNA_R160
#=GF SQ   9


AJ532513.1/3-77        AGCAAAAUGAGGAGGUUAUAUG-----AUCUGAAG---UAUCUAAUGUUGAUA------AUU---CAA---GGUCUUCAAAGUUCUCUGA-UUGCU
AJ532516.1/6-75        UACAA-AUGAAGAGGCUAUUUG-----UUCUGAAG--------UAUCUAAAUC-----CAUU---CAU---AGUCUUCAAAGUUCUCUGA-UUGUU
AJ532511.1/1-79        AGCGAAAUGAGGAGGAAAAAUC-----AUCCGAAG---UUUUUCUUGUGGAAA--ACACGUA---CAU---GGUCUUCAAAGUUCUCUGA-UCGCU
AJ532514.1/1-80        AGCAAAAUGAGGAGAUCAAUCG-----AUCUGAAG---UAUCUAAUGUUGAUA-UAUCCAUU---CAU---GGUCUUCAAAGUUCUCUGA-UUGCU
AC079829.6/41345-41431 AGCAUGAUGAUGAGAAAAAUGU---GCCACUGAAUUCAAAAUUCAUGUUGAUA-UAUUUAUUAUACAA-----CCUUCAAAGUUCUCUGAAUUGCU
AJ532512.1/4-84        AUCAAAAUGAGGAGGCUGUUUG-----UUCUGAAG---UAUCUAAUGUGGAUA-CAUCCAUU---CAU--GGGUCUUCAAAGUUCUCUGA-UUGCU
AP004951.1/53576-53499 AGCAAAAUGACGAGGUUUUAAU-----AUCUGAA------UAUCAUGUGGAUU-CAU-UAUU---CAAA-UUGCCUUCAAAGUUCUCUGA-UUGCU
AP004951.1/53820-53735 AGCAAAAUGAUGAAGUUGUUUU---CUGUCUGAA------UCUGGUGUGGAUUACAUAACAUAAACAUACAGGUCUUCAAAGUUCUCUGA-UUGCU
AJ532515.1/2-83        AACAA-CUGAGUGUGUUUCUCAUGAAUCUCU-AAG----CAAGAUUGUUGAUU-CAUCCAUU---CAU---GGUCUUCAAAGUUAUUUGA-UUGUU
#=GC SS_cons           <<<<<_________________.....________..._______________.________...___...___________________.>>>>>
#=GC RF                AgCAAAAUGAgGAgGuuauUuu.....aUCUGAAG...uauuUaaUGUuGAUa.cAUacAUU...CAu...GGUCUUCAAAGUUCUCUGA.UUGcU
//
# STOCKHOLM 1.0

#=GF AC   RF00204
#=GF ID   snoR12
#=GF DE   Small nucleolar RNA R12
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD, Griffiths-Jones SR
#=GF GA   39.00
#=GF TC   43.70
#=GF NC   37.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   snoR12 is a C/D box small nucleolar RNA, which acts as a methylation guide
#=GF CC   for 25S ribosomal RNA in plants [1]. snoR12 has been alternatively named
#=GF CC   snoZ44 in Arabidopsis and snoZ131 in rice.
#=GF WK   Small_nucleolar_RNA_R12
#=GF SQ   9


AJ240078.1/7-91 UAAAAGAUGACGAAAAAAAUCGUUCGGAUUCCCUUUGAAUUCCCUC-----GGGAAAGA-UGUGAUCACAA-A-CCAGCUACUUCUGAUUUUA
AJ489975.1/4-83 AUCUGGGUGAUGAAGAAAAUCAGACGGAUUCCCAUUGAAUU----------UCCAAA---UAUGAUUUUAACAACCAGCUACUUCUGACAGAU
AY220637.1/6-85 AUCUGGGUGAUGAAGAAAAUCAGACGGAUUCCCAUUGAAUU----------UCCAAA---UAUGAUUUUAACAACCAGCUACUUCUGACAGAU
AJ489976.1/4-82 AUCUGGGUGAUGAAGAAAAUCAGACGGAUUCCCAUUGGUUU----------UCCAA----UAUGAUUUUAACAACCAGCUACUUCUGACAGAU
AY112810.1/4-86 UUGGGGGUGAUGAAGAAAAUCGUUCGGAUUCCCAUUGAUUUCUAA------UCGAAA---UGUGGUCUUUA-AACCAGCUACUUCUGACUCAA
AJ532489.1/1-82 UUGGGGGUGAUGAAGAAAAUCGUUCGGAUUCCCCU-GAUUUCUAA------UCGAAA---UGUGGUCUUUA-AACCAGCUACUUCUGACUCAA
AJ532490.1/1-82 UUGAGGAUGAAGAAGAAAAUCAGACGGAUUCCCAUUGAUUUCAAA------UCGAAA---UGUGAUCUUUA-A-CCAGCUACUUCCGACUCAA
AJ240079.1/4-94 GUGAGGGUGAUGAAAAAAAUCAUUCGGAUUCCCAAUGAUUCCCUUACGUACGGGAAAUUAUGUGAUUAUUU-A-CCAGCUACUUUUGACUCAU
AJ240077.1/6-90 GUGAGGAUGACGAA-AAAAUCAUUCGGAUUCCCUUUGAAUUCCUCC-----GGGAAACA-UGUGAUUAUAU-AAUCAGCUACUUCUGACUCAU
#=GC SS_cons    <<<<<________________________________________......______...___________.________________>>>>>
#=GC RF         uugaGGgUGAuGAAgAAAAUCAuuCGGAUUCCCaUUGAuUUCcuu......ucgAAA...UgUGAUuuUaa.AACCAGCUACUUCUGACucaa
//
# STOCKHOLM 1.0

#=GF AC   RF00205
#=GF ID   snoR41
#=GF DE   Small nucleolar RNA R41
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; Griffiths-Jones SR
#=GF GA   40.00
#=GF TC   41.20
#=GF NC   39.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26 -Z 549862.597050 CM SEQDB
#=GF CL   CL00068
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   snoR41 is a C/D box small nucleolar RNA, which acts as a methylation guide
#=GF CC   for 18S and 25S ribosomal RNA in plants [1]. snoR41 has been alternatively
#=GF CC   named snoZ154 and snoZ231 in rice. The 18S methylation site is reported to
#=GF CC   be homologous to that targeted by U62 in humans (Rfam:RF00153) [1], but
#=GF CC   the snoRNA sequence similarity is not significant.
#=GF WK   Small_nucleolar_RNA_R41
#=GF SQ   7


AF317994.1/2-87 GUGAAGGCAGUGAUGAUUAAAAACU-----ACCUAUUUUAUGAGUAAUU-----C-------------UCUGAUU-AGAAAAUUUACCAAUGGAUCCUUCUGAGCCU-UCA
AJ490348.1/1-93 -----GGCUGUGAUGCGUAUUGAUA-----AGGGAUUUUCUGAGGGAUGGAGACCUAGUUUUCCUCCUCCUGAUUGAGAGAA---ACCAAUGGAUCCUUCUGAGCC-----
AY220661.1/1-96 UUGGAGGCUGUGAUGACCAAAAAA-UACCUACCUAUUUUCUGAGGGAUU-----CCAGU------CCUUCUGAUUGAUAGAA---ACCAAUGGAUCCUUCUGAGCCUGCCA
AJ490346.1/1-97 UUGGAGGCUGUGAUGACCAAAAAAAUACCUACCUAUUUUCUGAGGGAUU-----CCAGU------CCUUCUGAUUGAUAGAA---ACCAAUGGAUCCUUCUGAGCCUGCCA
AJ494936.1/1-97 UUGGAGGCUGUGAUGACCAAAAAAAUACCUACCUAUUUUCUGAGGGAUU-----CCAGU------CCUUCUGAUUGAUAGAA---ACCAAUGGAUCCUUCUGAGCCUGCCA
AJ494937.1/1-97 UUGGAGGCUGUGAUGACCAAAAAAAUACCUACCUAUUUUCUGAGGGAUU-----CCAGU------CCUUCUGAUUGAUAGAA---ACCAAUGGAUCCUUCUGAGCCUGCCA
AJ490344.1/1-97 UUGGAGGCUGUGAUGACCAAAAAAAUACCUACCUAUUUUCUGAGGGAUU-----CCAGU------CCUUCUGAUUGAUAGAA---ACCAAUGGAUCCUUCUGAGCCUGCCA
#=GC SS_cons    ::<<<<<<_________________________________________....._____......_________________...__________________>>>>->>:
#=GC RF         uUGGaGGCUGUGAUGacuAaaAAaAUACCUAccuAUUUUcUGAGGGAUu.....CcAGU......CCUUCUGAUUGAuAGAA...ACCAAUGGAUCCUUCUGAGCCuGCCA
//
# STOCKHOLM 1.0

#=GF AC   RF00206
#=GF ID   U54
#=GF PI   SNORD54; U54
#=GF DE   Small nucleolar RNA U54
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD, Griffiths-Jones SR
#=GF GA   40.00
#=GF TC   41.60
#=GF NC   39.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00008
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   U54 is a C/D box small nucleolar RNA, which acts as a methylation guide
#=GF CC   for 18S ribosomal RNA in plants [1].
#=GF WK   Small_nucleolar_RNA_SNORD54
#=GF SQ   21


AC147499.5/74526-74608   GGCUCUGUGAUAUUCUGCCUUUG-------UUGCAGUAUACGCUAUUCUGAUUCAAAUUAUGAGCAGAUAUUUUAUUAC------UAUUGAGAGCU
BT018726.1/381-464       UGCUCAAUGAUUCAGCCAUGGUAAAUCA--UGGUAAUAUACGCUAUUCUGAUCCACACAAGGAUGUCAACAACAU----------UUCUGAGAGCA
AC121328.3/104144-104228 UGCUCAAGGAUUAUAAGCCAUGUUAUGCCAUCACAAUAUACGCUAUUCUGAAUCAUAUUAAGAUGUCAUA-AACA----------UUAUGAGAGCA
BT018726.1/784-862       AGCUCAGUGAUUGUAGCCAAUUACAU----UGGCAAUAUACGCUAUGCUGACCU-CAGUUUGAUGAACAU--UUU----------UACUGAGAGCU
BT018726.1/951-1030      GGCUCAAUGAUUUCAACCAGUCAUUC----UUGAUAUAUACGCUAUUCUGAUU--GCUGCUGUUGAAAAAAAUAU----------CCAUGAGAGCA
AJ536407.1/4-86          UGCUCGAUGAUUAAUCCAUGUUAUGCCA--UGGCAAUAUACACUAUUCUGAAUCAUAUUAAGAUGCCAUA-AACA----------UUAUGAGAGCA
AL391146.1/51360-51447   GGCUCUGUGAUUGCUUCGCCUUA--U----UGGCAAUAUACGCUAUUCUGAAA--UCAGAGUAUGAAAGAUAAACAAACUGUACUUUAUGAGAGCC
AJ536403.1/3-85          UGCUCAAUGAUUAA-GCCAUGUUAAUCCA-UGGCAAUAUGCGCUAUUCUGAAUCAUAUUAAGAUGUCAUA-AACA----------UUAUGAGAGCA
AJ536410.1/1-75          AGCUUAGUGAUUGCUACCACUCACAU----UGGUUUUAUACGCUAUUCUGAUU--GGAGCUGUUGAAAAC---------------UUAUGAGAGCU
AP006480.2/37454-37375   GGCUCAAUGAUUGUUGCCAAUCACAUU---UGGUCAUAUAUGCUAUUCUGAUU--UCUAUUGGUGAAAAC-GAAU----------UUAUGAGAGCU
AJ536412.1/3-82          UGCUCAAUGAUUAA-CCCAUGCACCA----UGGCAAUACACGCUAUUCUGAAUCAUAUUAAGAUGCCAUA-AACA----------UUAUGAGAGCA
AJ536411.1/4-86          GGCUCAGUGAUUGUUGCCAAUCAUAUU---UGGUCAUAUACGCUAUUCCGAUU--UCUAUUGGUGGAAAAGAAAAAU--------UUAUGAGAGCU
AJ536404.1/4-80          AGCUCAGUGAUGCA-GCCGUUUUCAU----UGGCAAUAUACGCUAUGCUGACU----GUUUGAUGACAAAUAAGA----------AUAUGAGAGCU
AJ536408.1/2-82          AGCUCAGUGAUUCCAGCCACUUACGU----UGGCAAUAUACGCUAUACAGACCA-UAGUUUGAUGACCAAUGAGA----------AUAUGAGAGCU
AJ536409.1/2-82          AGCUCAGUGAUUCCAGCCACUUACGU----UGGCAAUAUACGCUAUACAGACCA-UAGUUUGAUGACCAAUGAGA----------AUAUGAGAGCU
AJ536406.1/4-85          GGCUCAGUGAUUGUUGCCAAUCAGAUU---UGGUCAUAUACGCUAUUCUGAUU--UCUAUUGGUGAAAAAGAAAAU---------UUAUGAGAGCU
AJ536405.1/1-81          AGCUCUGUGAUUUCAACCAAUCACAU----UGGUUUUAUACGCUAUUCUGAUU--GGAGCUGUUGAAAAAUAAGAC---------UUAUGAGAGCU
AJ536413.1/1-81          AGCUCAGUGAUUUCAACCAGUCACAU----UGGUUUUAUACGCUAUUCUGAUU--GGAGCUGUUGAAAAAUAAUAC---------UUAUGAGAGCU
AC121328.3/104676-104756 AGCUCAGUGAUUUCAACCAGUCACAU----UGGUUUUAUACGCUAUUCUGAUU--GGAGCUGUUGAAAAAUAAUAC---------UUAUGAGAGCU
AC121328.3/104500-104580 AGCUCAGUGAUUGUAGUCACUUUUGU----UGGUAAUAUACGCUAUGCUGACCA-UAGUUUGAUGAUGAAUGAGA----------AUAUGAGAGCU
AC132489.2/123921-123998 AGCUCAGUGAUUGCAGCCGUUUUCAU----UGGCAAUAUACGCUAUGCUGACU----GUUUGAUGACAAAUAAGA----------AUAUGAGAGCU
#=GC SS_cons             <<<<<_____________________....________________________.____________________..........______>>>>>
#=GC RF                  gGCUCAGUGAUUguaaCCauUuAcaU....UGGcAAUAUACGCUAUUCUGAuUc.uauuauGAUGAaAaAuAAaa..........UUAUGAGAGCc
//
# STOCKHOLM 1.0

#=GF AC   RF00207
#=GF ID   K10_TLS
#=GF DE   K10 transport/localisation element (TLS)
#=GF AU   Holmes I
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:8582290
#=GF SS   Published; PMID:8582290
#=GF GA   43.00
#=GF TC   43.90
#=GF NC   42.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0051028; mRNA transport;
#=GF DR   GO; 0008298; intracellular mRNA localization;
#=GF RN   [1]
#=GF RM   8582290
#=GF RT   A small predicted stem-loop structure mediates oocyte localization of
#=GF RT   Drosophila K10 mRNA.
#=GF RA   Serano TL, Cohen RS
#=GF RL   Development 1995;121:3809-3818.
#=GF RN   [2]
#=GF RM   11533666
#=GF RT   A nuclear lamin is required for cytoplasmic organization and egg polarity
#=GF RT   in Drosophila.
#=GF RA   Guillemin K, Williams T, Krasnow MA
#=GF RL   Nat Cell Biol 2001;3:848-851.
#=GF CC   This family represents the 44 nucleotide K10 transport/localisation
#=GF CC   element (TLS) from Drosophila melanogaster. K10 TLS is responsible for the
#=GF CC   transport and anterior localisation of K10 mRNA and acts to establish
#=GF CC   dorsoventral polarity in the oocyte [1].
#=GF WK   K10_transport/localisation_element_%28TLS%29
#=GF SQ   5


AY060415.1/2224-2267           CUUGAUUGUAUUUUUAAAUUAAUUCUUAAAAACUACAAAUUAAG
U36587.1/52-95                 CUUGAUUGUAUUUUUAAAUUAAUUCUUAAAAACUACAAAUUAAG
AC104142.6/1963-2006           CUUGAUUGUAUUUUUAAAUUAAUUCUUAAAAACUACAAAUUAAG
AABU01002762.1/8483055-8483012 CUUGAUUGUAUUUUUAAAUUAAUUCUUAAAAACUACAAAUUAAG
AC104149.6/78129-78172         CUUGAUUGUAUUUUUAAAUUAAUUCUUAAAAACUACAAAUUAAG
#=GC SS_cons                   <<<<<<<<<<<<<<<<<________>>>>>>>->>>>->>>>>>
#=GC RF                        CUUGAUUGUAUUUUUAAAUUAAUUCUUAAAAACUACAAAUUAAG
//
# STOCKHOLM 1.0

#=GF AC   RF00208
#=GF ID   snoR72
#=GF DE   Small nucleolar RNA R72
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD, Griffiths-Jones SR
#=GF GA   43.00
#=GF TC   43.00
#=GF NC   42.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300237;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   snoR72 is a C/D box small nucleolar RNA, which acts as a methylation guide
#=GF CC   for 25S ribosomal RNA in Arabidopsis [1].
#=GF WK   Small_nucleolar_RNA_R72
#=GF SQ   5


AJ429612.1/1-87        UUGCAAAUGAUGAGUUAAAUCACCAUUGAUAAAAGAAGCUCAAUUGAGCAGUGUUGGCAAUCAAAAACUUCCAUGACUCUGAUGCAA
AJ429611.1/1-87        UUGCAAAUGAUGAGUUAAAUCACCAUUGAUAAAAGAAGCUCAAUUGAGCAGUGUUGGAAAUCUAAAACUUCCAUGACUCUGAUGCAA
AJ429610.1/1-87        UUGCAAAUGAUGAGUUAAAUCACCAUUGAUAAAAGAAGCUCAAUUGAGCACUGUUGAAAAUCAAAAAUUUCCAUGACUCUGAUGCAA
AJ429609.1/1-87        UUGCAAAUGAUGAGUUAAAUCACCAUUGAUAAAAGAAGCUCAAUUGAGCAGUGUUGGAAAUCUAAAACUUCCAUGACUCUGAUGCAA
AL138652.1/55229-55315 UUGCAAAUGAUGAGUUAAAUCACCAUUGAUAAAAGAAGCUCAAUUGAGCAGUGUUGGCAAUCAAAAACUUCCAUGACUCUGAUGCAA
#=GC SS_cons           <<<<<--------------------------------<<<<____>>>>--------------------------------->>>>>
#=GC RF                uuGCaAAUGAUGAGUUAAAUCACCAUUGAUAAAAGAAGCuCAAUUGaGCAgUGUUGgaAAUCaAAAAcUUCCAUGACUCUGAuGCaa
//
# STOCKHOLM 1.0

#=GF AC   RF00209
#=GF ID   IRES_Pesti
#=GF PI   Pesti_IRES
#=GF DE   Pestivirus internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:11142379
#=GF SS   Published; PMID:11142379
#=GF GA   45.00
#=GF TC   47.20
#=GF NC   43.20
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00017
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11142379
#=GF RT   Ribosomal binding to the internal ribosomal entry site of classical swine
#=GF RT   fever virus.
#=GF RA   Kolupaeva VG, Pestova TV, Hellen CU
#=GF RL   RNA 2000;6:1791-1807.
#=GF CC   This family represents the internal ribosome entry site (IRES) of the the
#=GF CC   pestiviruses. The pestivirus IRES allows cap and end-independent
#=GF CC   translation of mRNA in the host cell. The IRES achieves this by mediating
#=GF CC   the internal initiation of translation by recruiting a ribosomal 43S
#=GF CC   pre-initiation complex directly to the initiation codon and eliminates the
#=GF CC   requirement for eIF4F [1]. The classical swine virus UTR described in [1]
#=GF CC   appears to be longer at the 5' end than other pestivirus UTRs. This family
#=GF CC   represents the conserved core.
#=GF WK   Pestivirus_internal_ribosome_entry_site_(IRES)
#=GF SQ   25


AF531433.1/108-382 AGUAGGACUAGCA-AAACGGAGGG-ACUAGCCAUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGCGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF091661.1/108-381 AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACCUUAACUCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGCGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF099102.3/107-380 AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGUGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AY072924.1/107-380 AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGGAGCC---CACCUCGAGAUGCUAUGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUGGCGGGGG-UCGCCAGGGUGAAAUCACACCA----UGUGAUGGGGGUACGACCUGAUAGGGUGCUGCAGAGGCCCA-CUAACAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF326963.1/108-381 AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUAUGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGCGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF220247.1/114-390 AGUAGGACUAGCA--AAAUAAGGGGGGUAGCAACAGUGGCGAGUUCGUUGGAUGGCUGAAGCCCUGAGUACAGGGUAGUCGUCAGUGGUUCGACGCUUUGGAGGACA---AGCCUCGAGAUGCCACGUGGACGAGGGCAUGCCCACAGCACAUCUUAACCUGGACAGGGG-UCGUUCAGGUGAAAACGGUUUAACCAACCGCUACGAAUACAGUCUGAUAGGAUGCUGCAGAGGCCCA-CUGUAUUGCUACU--GAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AY382481.1/108-382 AGUAGGACUAGCA-AAACGGAGGG-ACUAGCCAUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGCGCUGCGGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
D49532.1/108-381   AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAUAUGCUAUGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGUGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF352565.1/108-381 AGUAGGACUAGCA--AACGGAGGG-ACUAGCCAUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGGAGCC---CACCUCGAGAUGCUAUGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGCGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF407339.1/108-381 AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUAUGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGCGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
U45477.1/108-381   AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCCCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGCGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
D49533.1/108-381   AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUAUGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGUGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF091507.1/108-382 AGUAGGACUAGCA-AAACGGAGGG-ACUAGCCAUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACGCCA----CGUGAUGGGAGUACGACCUGAUAGGGCGCCGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF037405.1/106-380 AGUAGGACUAGCA--GACGGGAGG-ACUAGCCAUCGUGGUGAGAUCCCUGAGCAGUCUAAAUCCUGAGUACAGGAUAGUCGUCAGUAGUUCAACGCAGGCACGGUUC---UGCCUUGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACUUGCUUUAAUCUCGGCGGGGG-UCGCCGAGGUGAAAACACCUAA---CGGUGUUGGGGUUACAGCCUGAUAGGGUGCUGCAGAGGCCCA-CGAAUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
J04358.2/107-380   AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCACUAGCC---CACCUCGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUGGCGGGGG-UCGCUAGGGUGAAAUCACAUUA----UGUGAUGGGGGUACGACCUGAUAGGGUGCUGCAGAGGCCCA-CUAGCAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AY367767.1/108-381 AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAAUAGUUCGACGUGAGCAGGAGCC---CACCUCGAGAUGCUAAGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUGGCAGGGG-UCGCCAGGGUGAAAUCACACCA----UGUGAUGGGGGUACGACCUGAUAGGGUGCUGCAGAGGCCCA-CUAACAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AB078950.1/117-394 AGUAGGACUAGCA-UAACGAGGGG-GGUAGCAACAGUGGUGAGUUCGUUGGAUGGCUUAAGCCCUGAGUACAGGGUAGUCGUCAGUGGUUCGACGCCUCGGAAAUAGA--GGUCUCGAUAUGCCACGUGGACGAGGGCACGCCCAAAGCACAUCUUAACCUGAGCGGGGGGUCGCUCAGGUGAAAGCGGUUCAACCAACCGUUACGGAUACAGCCUGAUAGGGCGCUGCAGAGGCCCA-CUGUUUUGCUACU--AAAAAUCUCUGCU-UACAUGGCACAUGGAGUU
AY259122.1/108-381 AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGCGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF333000.1/108-381 AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUAUGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGCGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF144617.2/110-390 AGUAGGACUAGCAAAAAAUCGGGG-ACUAGCCCAGGUGGUGAGCUUCCUGGAUGACCGAAGCCCUGAGUACAGGGCAGUCGUCAACAGUUCAACACGCAGAAUAGGUUUGCGUCUUGAUAUGCUGUGUGGACGAGGGCAUGCCCACGGUACAUCUUAACCUAUCCGGGGG-UCGGAUAGGCGAAAGUCCAGUA---UUGGACUGGGAGUACAGCCUGAUAGGGUGUUGCAGAGACCCAUCUGAUAGGCUAGUAUAAAAAACUCUGCUGUACAUGGCACAUGGAGUU
AF502399.1/116-393 AGUAGGACUAGCA--AAAGUAGGGGACUAGCGGUAGCAGUGAGUUCGUUGGAUGGCCGAACCCCUGAGUACAGGGGAGUCGUCAAUGGUUCGACACUCCAUUAGUCGAGGAGUCUCGAGAUGCCAUGUGGACGAGGGCAUGCCCACGGCACAUCUUAACCCAUGCGGGGG-UUGCAUGGGUGAAAGCGCUAUU-CGUGGCGUUAUGGACACAGCCUGAUAGGGUGUAGCAGAGACCUG-CUAUUCCGCUAGU---AAAAACUCUGCUGUACAUGGCACAUGGAGUU
X96550.1/108-381   AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCCCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGUACGACCUGAUAGGGUGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
AF144618.2/106-378 AGUAGGACUAGCA--AACGGGAGG-ACUAGCUUACGUGGUGAGAUCCCUGAGUGGUCUAAGUCCCGAGUACGGGGCAGUCGUCAGUAGUUCAACGCAAUGUGGAGU----UGCCUUGAGAUGCUACGUGGACGAGGGCAUGCCCAAGACACACUUUAACCCUGGCGGGGG-UCGCCAGG-UGAACUCACCUAA---UGGUGUUGGGAUUACAGCCUGAUAGGGUGCUGCAGAGGCCCA-CGCAUAAGCUAGUAUAAAAAUCUCUGCUGUACAUGGCACAUGGAAGU
AF092448.2/108-381 AGUAGGACUAGCA--AACGGAGGG-ACUAGCCGUAGUGGCGAGCUCCCUGGGUGGUCUAAGUCCUGAGUACAGGACAGUCGUCAGUAGUUCGACGUGAGCAGAAGCC---CACCUCGAGAUGCUAUGUGGACGAGGGCAUGCCCAAGACACACCUUAACCCUAGCGGGGG-UCGCUAGGGUGAAAUCACACCA----CGUGAUGGGAGCACGACCUGAUAGGGCGCUGCAGAGGCCCA-CUAUUAGGCUAGUAUAAAAAUCUCUGCUGUUCAUGGCACAUGGAGUU
AB078952.1/118-394 AGUAGGACUAGCA-UAAUGAGGGG-GGUAGCAACAGUGGUGAGUUCGUUGGAUGGCUUAAGCCCUGAGUACAGGGUAGUCGUCAGUGGUUCGACGCCUUAGUAUAAA---GGUCUCGAGAUGCCACGUGGACGAGGGCACGCCCAAAGCACAUCUUAACCUGAGCGGGGG-UCGCUCAGGCGAAAGCAGUUUAACCAACUGUUACGAAUACAGCCUGAUAGGGUGCUGCAGAGGCCCA-CUGUACUGCUACU--AAAAAUCUCUGCUGUACAUGGCACAUGGAGUU
#=GC SS_cons       :::::::::::::..:::::::::.{{{{{{{-{{{{{{[[-[[[[[[,,((((((((,,<<<<<<____>>>>>>,,<<<<<---<<-<<<<-<<<__________...>>>->>>>---->>----->>>>><<<<__>>>>,))))-)))),,,<<<<<<<<<<___.>>>>>>>>>>,,,,<<<<<___....>>>>>,]]]]]]-]],<<<____>>>,,,,,,,,,,,,}}}.}}}---}}}}}}}------------------<<<<___>>>>:::::
#=GC RF            AGUAGGACUAGCA..AAcggaGGG.acuaGCcauaGuGGcGAgcuCccUGGguGGccuAAgcCCuGAGUACaGGgcAGuCGuCAgUgGUuCGaCgcgagcagaagcc...cgcCuCGagAUGCcAuGUGGaCGaGGGCAUGCCCAaggCACacCUUAaCCcuggCGgGGG.uCGccagGGuGAAAgCgcguuA....cgcGcUggGagcACgaCCuGAUAgGGuGcUGCAGAGgCCCa.CuauuagGCuaguAUAAAAAuCUCUGCUGUACauGGCACauGGAGUU
//
# STOCKHOLM 1.0

#=GF AC   RF00210
#=GF ID   IRES_Picorna_2
#=GF PI   Aptho_IRES; IRES_Aptho
#=GF DE   Aphthovirus internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14561883
#=GF SS   Published; PMID:14561883
#=GF GA   22.00
#=GF TC   22.20
#=GF NC   21.90
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   14561883
#=GF RT   Structural organization of a viral IRES depends on the integrity of the
#=GF RT   GNRA motif.
#=GF RA   Fernandez-Miragall O, Martinez-Salas E
#=GF RL   RNA 2003;9:1333-1344.
#=GF RN   [2]
#=GF RM   11142379
#=GF RT   Ribosomal binding to the internal ribosomal entry site of classical swine
#=GF RT   fever virus.
#=GF RA   Kolupaeva VG, Pestova TV, Hellen CU
#=GF RL   RNA 2000;6:1791-1807.
#=GF CC   This family represents the internal ribosome entry site (IRES) of the the
#=GF CC   aphthoviruses. IRES elements allow cap and end-independent translation of
#=GF CC   mRNA in the host cell. The IRES achieves this by mediating the internal
#=GF CC   initiation of translation by recruiting a ribosomal 43S pre-initiation
#=GF CC   complex directly to the initiation codon and eliminates the requirement
#=GF CC   for eIF4F [2].
#=GF WK   Aphthovirus_internal_ribosome_entry_site_(IRES)
#=GF SQ   92


L02971.1/237-705    ACCUGUAUUAUGUACAGGGU-GGCAGAUG-GCGUGC-CAUAAAUCUAUUAGUGGGAUACCACGCUUGUGGACCUUAUGCCCACACAGCCAUCCUCUAGUAAGUUUGUAAA----AUGUCUGGUGAGA--UGUGGGAACUUAUUGGAAACAA----CAAUUUGCU-UAAUAGCAUCCUAG-UGCCAGCGGAACAAC-AUCUGGUAACAGAUGCCUCUGGGGCCAAAAGCCAAGGUUUGACAGACCCAUUAGGAUUGGU----UUCAAA--ACCUGAAUUG----UUGUGGAAGAUAUU-CAGUAC--CUAUCAA----------------------UCUGGUAG-----------------------UGGUGCAAACACUAGU-------UGUAAGGCCCACGAAGGAUGCCCAGAAGGUACCCGCAGGUAACAAG-AGACAC-UGUGGAUCU-GAUCUGGGGC-CAA-CUAC---CUCUAUCAG----GUGAGUUAGUUAAAAAACGUCUAGUGGGCCAAACCCAGGGG---GG-AUCCCUGGUUUC-CUUU-UAU-UGUUAAUAUUGA
AF055846.1/245-695  UGGCA-----GAUGGCGUGC-CAUAACUC-UACUAG-UGGGAUACCACGCUUGUGGACCU-UAUGCCCACA-----CAGCCAUCCUCU-AGUAAGUUUG---UAAGACGU----CUGAUGACGUGUG--GGAAAACA----CUAGAAAUAUUAAC----UUGCUGUAAAGCAUCCUACU-G-CCAGCGGAAUCAC-AUCUGGUAACAGAUGCCUCUGGGGCCAAAAGCCAAGGUUUAGC-AGACCCUUUAGGAUUGG---UUCAAUA--CCUGAG-----UUAAUAUGGAAAG--UGCUUAGUA---CCUGCU----------------------GACUUGGU-----------------------A-GUAGU-G-CAAACACUAGUUGUAUGGCCCGC--GAAGGAUGCCCAGAAGGUACCCGUAGGUAACAAG-UGACAC-UAUGGAUCU-GAUCUGGGGC-UGG-AUAC---CUCUAUCUUG---GUGAUCCAGUUAAAAAACGUCUA--GCGGGCCAAGCCCAGGGGGGA-UCCCUGGUUUCC-CUAU-UUU-UAUUAUUAUCAC
AY593795.1/630-1091 ACGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAGCUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----UUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUAGU-GGCCGUGGGAAUCCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUAAC-GGACCCACUAUGUGUGC---AACCCCA--GCACGGCAACUUUUCUGCGAAACC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCG-AACACU-------GGUGACAGGC--UAAGGAUGCCCUCCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGGAGGGGA-CUG-GGGC---UUCUAUAAAA---GUGCCCAGUUUAAAAAGCUUCUAC-GCCUGAGUAGGCGACCGGAGG-CCGGCGCCUUUC-UUUU-AAU-UACCACUGUUUU
AY686687.1/621-1083 AAGCAAGUUUCCACAACUGA-GAAAACUC-GUGCAA-CUUGGAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GCACGGUGCU---CGACUCCA----CGCCCGGUCCACU--GGCGGGUG----UUAGUAGCAGCACUGUUGUUUCG-UAGCGGAGCAUGGU-GGCCGUGGGAACUCCCCCUUGGAGACAAGGACCCGCGGGGCCAAAAGCCACGUCCGGAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGCGAACGC--CA-CCUUAA---GGUGAC----------------------ACUGGUAC-----------------------UGGUACUCG-GUCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-GGACAC-UCGGGAUCU-GAGAAGGGGAUUUG-GGAC---UUCUCUAAAA---GUGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-UACU-ACC-CACUACUAAAUC
AF026168.2/206-666  AAGCAGGUUUCCACAACUGA-UAAAACUC-GUGCAA-CUUGAAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGCU---CGACUCCA----CGCCCGGUCCACU--GGCGGGUG----UUAGUAGCAGCACUGUUGUUUCG-UAGCGGAGCAUGGU-GGCCGUGGGAACUCCUCCUUGGUGACAAGGGCCCACGGGGCCGAAAGCCACGUCCAAAC-GGACCCAACAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGCGAACAC--CA-CCUUAA---GGUGAC----------------------ACUGGUAC-----------------------UGGUACUCG-GUCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-GGACAC-UCGGGAUCU-GAGAAGGGGA-UUG-GGAC---UUCUUUAAA----GUGCCCAGUUUAAAAAGCUUCUAC-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-CAUU-ACC-CACUACUAAAUC
AY317098.1/580-1041 AAGCAGGUUUCCACAACUGA-UAAAACUC-GUGCAU-UUUGAAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGCU---CGACUCCA----CGCUCGGUCCACU--GGCGGGUG----UUAGUAGCAGCACUGUUGCUUCG-UAGCGGAGCAUGGU-GGCCGUGGGAACUCCUCCUUGGUGACAAGGACCCACGGGGCCAAAAGCCACGUCCAGAU-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACCUUACUGCGAACAC--CA-CCUUAA---CGUGAC----------------------ACUGAUAC-----------------------UGGUACUCG-GUCACU-------GGUGACAGAC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-GGACAC-UCGGGAUCU-GAGAAGGGGA-UUG-GGAC---UUCUUUAAAA---GUGUCCAAUUUAAAAAGCUUCUAU-GUCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-CAUU-ACC-UACUACUAAAUC
AY390432.1/620-1077 AUGCAGGUUUCCACAACUGA-CACAAAUC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAUUUU-GUACUGUGCU---CGACUCCA----CGCUCGGUCCACU--AGCGGGUG----UUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGGU-GGCCGCGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUAAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGCGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCG-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAUG-UGACAC-UCGGGAUCU-GA--GGGGGA-CUG-GGAC---UUCUUUAAAA---GUGCCCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC---AU-GAA-CACAACUGAUUG
AY593791.1/697-1157 AAGCAGGUCUCCACAACUGA-CACAAACC-GUGCAA-CUUGGAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--AGCGGGUG----UGAGUAGCAGAACUGUCGCUUCG-UAGCGGAGCAUGGU-GGCCGCGGGAACCCCUCCUUGGUAACAAGGACCCGCGGGGCCGAAAGCCACGUCUUA-U-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAAUUUUUCUGUGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AUCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAC---UUCUUUAAAA---GUGCCUAGUUUAAAAAGCUUCUAC-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-UUUC-AAA-CACUACUAGACU
AY687333.1/618-1079 AUGCAGGUUUCCACAACUGA-CACACACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACACUUU-GUACUGUGAU---UGACUCCA----CGCUCGGUCCACU--GGCGGGUG----CGAGUAACAGGACUGUUGUUUCG-UAGCGGAGCAUGAU-GGCCGUGGGAUCCCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUAAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGUGAAAAA--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-UUG-GGGC---UUCUUUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-UUUU-AAC-CACUACUCAACU
AY312589.1/250-712  AUUCAGGUCCCCACAACCGA-CACAAAUC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAUUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----CUAGUAACAGCACUGCUGCUUCG-UAGCGGAGCAUGGU-GGCCGCGGGAAUUCCUCCUUGGUAACAGGGACCCGCGGGGCCGAAAGCCACGUCCUCAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGUGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AUCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCUGAGGUAACACG-CGACAC-UCGGGAUCUUGAGAAGGGGA-CUG-GGGC---UUCUUUAAAA---GCGCCUAGUUUAAAAAGCUUCUAC-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-UUUU-AAA-CAACUAUUUUUA
AY593831.1/632-1091 ACUCAGGUUCCCACAACCGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGGCAUUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----CUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGGU-GGCCGCGGGAACUCCUCCUUGGUAACAGGGACCCGCGGGGCCAAAAGCCACGUCCUCAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGUGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUUAGGUACCCUGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUUUAAAA---GCGCUUAGUUUAAAAAGCUUCUAC-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC---UU-UUA-AACAACUACUUU
AY312587.1/249-708  AUUCAGGUUCCCACAACCGA-CACAAACC-GUGCAA-CCUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAUUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----CUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGGU-GGCCGCGGGAACUCCUCCUUGGUAACAGGGACCCGCGGGGCCGAAAGCCACGUCCUCAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGUGGAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCUGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUUUAAAA---GCGCCUAGUUUAAAAAGCUUCUAC-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC---UU-UUA-AACAACUACUUU
AF377945.1/251-710  AUUCAGGUUCCCACAACCGA-CACAAACC-GUACAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAUUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----CUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGGU-GGCCGCGGGAACUCCUCCUUGGUAACAGGGACCCGCGGGGCCGAAAGCCACGUCCUUAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAGCUUUACUGUGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCUGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUUUAAAA---GCGCCUAGUUUAAAAAGCUUCUAC-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC---UU-UUA-AACAACUACUUU
Y17974.1/205-665    AUGCAGGUUUCCACGACUGA-CACAAACC-GUGCAA-CUUGAAGCUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAUUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--UGCGGGUG----UUAGUAACAGCACUGAUGCUUCG-UAGCGGAGCAUGGU-GGCCGCGGGAACUCCUCCUUGGUAACGAGGACCCGCGGGGCCGAAAGCCACGUCCUUAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGUGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-ACCACU-------GGCGACAGGC--UCCGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUUUAAAA---GUGCCCAGUUUAAAAAGCUUCUAC-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-C-UU-UUG-AACUACUACUUC
AY593799.1/634-1096 ACGCAGGUCUCCACAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--AGCGAGUG----UUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGGU-GGCCGUGGGAACCCCUCCUUGGCGACAAGGACCCACGGGGCCGAAAGCCACGUCCUUGU-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAGCUCUACUGUGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-GACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-AGAC---UUCUUUAAAA---GUGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUCUCCUU-AAC-UACCACUUCUUA
AY593766.1/632-1093 ACGCAGGUCUCCACAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--AGCGAGUG----UUAGUAGUUGUAUUGUUGCUUCG-UAGCGGAGCAUGGU-GGCCGUGGGAACCCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUGAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACCUUACGGCGAAAAC--CA-CUUUAA---AGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAUG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAC---UUCUUUAAAA---GUGCCCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUU-CACU-AAC-UGCCACUAUUUU
AY593811.1/633-1094 ACGCAGGUCUCCACAACUGA-CACAAACC-GUGCAA-UUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAUUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----CUAGUAGUAGCACUGUUGCUUCG-UAGCGGAGCAUGGU-GGCCGUGGGAACCCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUUAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGCGAAAAC--CA-CUUCAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-UUG-GGAC---UUCUUUAAAA---GUGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUU-CACA-AAC-UACUACUGUUUU
AY687334.1/618-1079 ACGUAGGUUUCCACAACUGA-CACAAACC-GUGCAA-UUUGAAGCUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--AGCGAGUG----UUAGUAGCAACACUGUUGUUUCG-UAGCGGAGCAUGAU-GGCCGUGGGAACUCCCCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUAAC-GGACCCAUCAUGUGUGC---AACCCCG--GCACGGCAACUUUGUUGUGAAAGC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACCCA-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACACCCAAGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAC---UUCUGUAAAA---GUGCCCAGUUUAAAAAGCUUCUAU-GCCUGGAUAGGCGACCGGAGG-CCGGCGCCUUUC-CUUU-ACC-UAUUACUGUUUU
AY593772.1/588-1049 ACGCAGGUUCCCGCAACUGA-CACGAACC-GUGCGA-CUUGAAGCUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACAUUUU-GUACUGUGUU---UGACUCCA----CGCUUGGUCCACU--AGCGAGUG----UUAGUAACAGCACUGUUGCUUCG-UCGCGGAGCAUGAU-GGCUGUGGGAACUCCCCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUCAC-GGACCCAUCAUGUGUGC---AACCCCA--GCACAGCAACUUUACUGUGAAAGC--CA-CUUUAA---GGUGUC----------------------ACUGAUAC-----------------------UGGUACUCA-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAUG-CGACAC-UCGGGAUCU-GAGAAGGGGG-CUG-AGGC---UUCUUUAAAA---GUGCUCAGCUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-CACU-UAC-CAAUACUGUUUU
AY593765.1/631-1092 ACGCAGGUUCCCACAACUGA-CACGAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACACUUU-GUACUGUGUU---UGACUCCA----CGCUUGGUCCACU--AGCGAGUG----UUAGUAACAGCACUGUUGCUUCG-UCGCGGAGCAUGAU-GGCUGUGGGAACUCCCCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUCAC-GGACCCAUCAUGUGUGC---AACCCCA--GCACAGCAACUUUACUGCGAAAGC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAUG-CGACAC-UCGGGAUCU-GAGAAGGGGG-CUG-AGGC---UUCUUUAAAA---GCGCUCAGCUUAAAAAGCUUCUAU-GCCUGAACAGGCGACCGGAGG-CCGGCGCCUUUC-CACU-UAC-CAAUACUGUUUU
AY593763.1/633-1094 ACGCAGGUUUCCACAACUGA-CACGAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACACUUU-GUACUGUGCU---UGACUCCA----CGCUUGGUCCACU--AGCGAGUG----UUAGUAGCAGCACUGUUGCUUCG-UCGCGGAGCAUGAU-GGCUGUGGGAACUCCCCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUCAC-GGACCCAUCAUGUGUGC---AACCCCA--GCACAGCAACUUUACUGCGAAAGC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAUG-UGACAC-UCGGGAUCU-GAGAAGGGGG-CUG-AGGC---UUCUUUAAAA---GCGCUCAGCUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-CACU-UAC-CAACACUGUUUU
AY593834.1/631-1092 AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUCGGAACUCCACCUGGUCUUUC-CAGGUCUAGA----GGGGUGACGUUUU-GUACUGUGCU---UGACUCCA----CGCUUGGCCCACU--AGCGAGUG----UUAGUAGUAGCACUGUUGCUUCG-UAACGGAGCGUGAU-GGCCGUGGGAACUCCCCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUAAC-GGACCCAUCAUGUGUGC---AACCCCA--GCACGGCAACUUUGCUGCGAAAAC--CA-CUUUAA---GGUGAC----------------------GCUGACAC-----------------------UGGUACUCA-AUCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAC---UUCUUUAAAA---GUGUCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-CCUA-AUU-ACUGCCAUUUUU
AY593823.1/635-1097 AUGCAGGUUUCCACAACUGA-CACAAACC-GUGCAA-CUUGAAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGCGACAUUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--AGCGAGUG----UUAGUAGUAGCACUGUUGCUUCG-UAGCGGAGCAUGAU-GGCCGUGGGAGCUCCCCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUACC-GGACCCAUCAUGUGUGC---AAACCCA--GCACGGCAACUUUACUGCGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AUCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUUUAAAA---GUGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUU-CACUGUUU-UACUACUGUUUU
AY359854.1/546-1007 AUGCAGGUUUCCACAACUGA-CACAAACC-GUGCAA-UCUGGAACUUCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAUUUU-GUACUGUGAU---UGACUCCA----CGCUCGGUCCACU--AGCGAGUG----UUAGUAGUAGCACUGUUGCUUCG-UAGCGGAGCAUGGU-GGCCGUGGGAACCCCACCCUGGUAACAGGGACCCACGGGGCCGAAAGCCACGUCCUAAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGCGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-ACCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCUCGAGGUAACACG-CGACAC-UCGAGAUCU-GAGAAGGUGA-CUG-GGGC---UUCUUUAAAA---GCCCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-CAUU-UAC-UACUACUGUUUU
AY593797.1/631-1092 AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGUCAUACU-GUACUGUGCU---UGACUCCA----CACUCGGUCCACU--AGCGAGUG----UUAGUAGUAGCACUGUUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACCCCUCCUUGGUAACAAGGACCCGCGGGGCCGAAAGCCACGUCCUGGC-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUAUGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGAAAC-UCGGGAUCU-GAGAAGGGGA-CCG-GGAC---UUCUAUAAAA---GUGCCCAGUUUAAAAAACUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-CUUU-AAU-UACCACUGUUUA
AY593796.1/634-1095 AUGCAGGUUUCCCCAACUGA-CACAAAAC-GUGCAA-CUUGAAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAUCUU-GUACUGUGUU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----UCAGUAAUAGCACUGUUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACCCCUCCUUGGUAACAAGGACCCGCGGGGCCGAAAGCCACGUCCUAGC-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUAUGAAAAC--CA-CUUCAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGAAAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAC---UUCUAUAAAA---GUGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUC-CUUU-AAC-UACUACUUUUAC
AY593828.1/589-1050 AUGCAGGUAUCCCCAACUGA-CACAAACC-GUGCAA-CUUGGAGCCCCGCCUGGUCUUUC-CAGGUCUAGU----GGGGCGACACUUU-GUACUGUGUU---UGACUCCA----CGCUCGGUCCACU--AGCGAGUG----UUAGUAGUAGUGUUGUUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACCCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUGUC-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGCAGCUUCAUUAUGAAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GCACCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGCGACCGGAGG-CCGGCGCCUUUU-CACU-AAU-UACCACUAUUUU
AY304994.1/590-1051 AUGCAGGUAGCCCCAACUGA-CACAAACC-GUGCAA-CUUGGAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACCUU-GUACUGUGUU---UGACUCCA----CGCUCGGUCCACU--AGCGAGUG----UUAGUAGUAGUACUGUUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAAUCCCUCCUUGGCAACAAGGACCCACGGGGCCGAAAGCCACGUCCUGAA-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGCAGCUUUAUUAUGAAACC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GUGCCCAGUUUAAAAAGCUUCUAU-GCCUGGAUAGGCGACCGGAGG-CCGGCGCCUUUC-CUUU-GAC-CACUACUGUUUA
AY593755.1/626-1086 AUGCAGGUUUCCCCAACUGA-CAUAAACC-GUGCAA-CUUGAAGCUCCACCUGGUCUUUC-CAGGUCUAGA----GGAGUGACAUUUU-GUACUGUGUU---UGACUCCA----CGCUCGGUCCACU--GGCGGGUG----UUAGUAGUAGCACUGUUGUCUCG-UAGCGGAGCAUGAU-GGCCGUGGGAACCCCUCCUUGGUAACAAGGACCCGCGGGGCCGAAAGCCACGUCCGAAC-GGACCCAUCAUGUGUGC---AACCCCA--GCACGACAACUUUACUGCGGAAAC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-UACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---CUCUUUAAG----GCGCCUGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-AAC-CAAAACUGUUUU
AY593825.1/591-1050 ACGCAGGUCUCC-CAACUGA-CACAAACC-GUGCAG-UUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAAUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUA----UCAGUAACAGCACUGAUGCUUCG-UAGCGGAGCAUGGC-GGCCGUGGGAACCCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUAAC-GGACCCGUCAUGUGUGC---AACCCCG--GCACGGCAGCUUUUCUGUGAAACU--CA-CUUUAA---CGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AACACU-------GGAGACAGGC--UAAGGAUGUCCUUCAGGUACCCCGGGGUAACACG-CGACAC-CCGAGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-C-UU-UAC-AACCACUGAUUU
M10975.1/159-619    AAGCAGGCCUCCCCAACUGA-CACAAACC-GUGCAA-UUUGGAACUCCGCCUGGUCUUUC-CUGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGCUCGGUCCACU--GGCGAGUG----UUAGUAACAGCACCGUUGCUUCG-UAGCGGAGCAUGAU-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCAAUC-GGACCCAUCAUGUGUGC---AACCCCA--GCACAGCAACUUUUCUGCGAAACU--CA-CUUCAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGUCAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GCGUCCAGGUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-C-UU-UAC-AGCCACUGACUU
AY593810.1/557-1017 AAGCAGGUUCCCCCAACUGA-CACAAACC-GUGCAA-UUUGGAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGCUCGGUCCACU--GGCGAGUG----UUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGAU-GGCUGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCAACU-GGACCUAUCAUGUGUGC---AACCCCA--GCACAGCAACUUUUCUGUGAAACU--CA-CUUCAA---GGUGGC----------------------ACUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGCCAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GCGUCCAGUUUAAAAAGCUUCUAU-GCCUGGAUAGGUGACCGGAGG-CCGGCACCUUUU-C-UU-UAU-AACCACUGACUU
AY593789.1/558-1018 AAGCAGGUCCCCCCAACUGA-CACAAAUC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----UUAGUAACGGCACUGUUGCUUCG-UAGCGGAGCAUGAC-GGCCGCGGGAAUUCCUCCUUGGUAACAAGGACCCGCGGGGCCAAAAGCCACGUCCCAAC-GGACCCGUCAUGUGUGC---AACCCCA--GCACAGCAACUUUUCUGUGAAACC--CA-CUUCAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AACACU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGCAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGG---UUCUAUAAAA---CCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-C-UU-UAU-UACCACUGAAUU
AY593829.1/633-1093 AAACAGGUUUCCCCAACUGA-CAUACACC-GUGCAA-UUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACACUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----UUAGUAACAGCACUGGUGCUUCG-UAGCGGAGCAUGGU-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUGAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUUCUGUGAAACU--CA-CUCUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUAUUCA-AGUACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUGUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGGAUAGGUGACCGGAGG-CCGGCGCCUUUC-C-AU-UAU-AACUACUGACUU
AY593793.1/633-1094 AAGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACGUU-GUACUGUGCC---UGACUCCA----CGCUCGGUCCACU--AGCGGGUG----UUAGUAACAGCACUGUUGUUUCG-UAGCGGAGCAUGAU-GGCCGCGGGAACUCCGCCUUGGUGACAAGGACCCGCGGGGCCGAAAGCCACGUCCUAAC-GGACCCAUCAUGUGUGC---AACCCCA--GCACAACAACUUUUCUGUGAAACC--CA-CCUUAA---GGUGAC----------------------ACUGACAC-----------------------UGGUACUCA-GACACU-------GGUGACAGGA--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-UGACAC-UCGGGAUCU-GAGAAGGGGA-CUA-GGGC---UUCUGUAAAA---GUGCCUAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-UAC-AACCACUGAUCA
AY593809.1/632-1093 AAGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCCACU--AGCGGGUG----UUAGUAACAGCACUGUUGUUUCG-UAGCGGAGCAUGAU-GGCCGUGGGAACUCCGCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUAAC-GGACCCAUCAUGUGUGC---AACCCCA--GCACAACAACUUUUCUGUGAAACC--UA-CCUUAA---GGUGAC----------------------GCUGAUAC-----------------------UGGUACUCA-GACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUA-GGGC---UUCUGUAAAA---GUGCCUAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CCUU-UAC-AACUACUGACUA
AY593770.1/545-1005 AAGCAGGUUUCCACAACUGA-CAUAAACC-GUGCAA-UUUGAAGCUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGCUCGAUCCACU--GGCGAGUG----UUAGUAACACCACUGCUACUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAAACCCCCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUAAC-UGACCCGUCAUGUGUGC---AACCCCA--GCACGGUAGCUUUGCUGUGAAACU--CA-CUUUAA---GGUGAC----------------------AUUGAUAC-----------------------UGGUACCCA-GACACU-------GGUGACAGGC--UAAGGAUGCCCUCCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGGAGGGGA-CUA-GGGC---CUCUAUAAAG---GCGCCUGGUUUAAAAAACUUCUAC-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-C-CC-UAU-AAUCACUGACCA
AY593767.1/631-1092 AAACAGGCUCCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCG----CGUUCGAUCCACC--GGCGAGUG----UUAGUAACACCACUGCUACUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACCCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCACAU-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGUAGCUUUGCUGUGAAACU--CA-CUUUAA---AGUGAC----------------------AUUGAUAC-----------------------CGGUACCCA-AAUACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAUG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUGUAAAA---GCGCUCAGUUUAAAAAGCUUCUAU-GUCUGGAUAGGUGACCGGAGG-CCGGCACCUUUU-CUUU-UAC-UAUUUGACUCUA
AY593771.1/631-1092 AAGCAGGUUUCUCCAACUGA-CACAAACC-GUGCAA-UUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGUUUGACCCACU--GGCGAGUG----UCAGUAACAACACUGCUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAGCUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCACAC-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGUAGCUUUGCUGUGAAACU--CA-CUUUAA---AGUGAC----------------------GUUGAUAC-----------------------UGGUACCCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGGGGUAACACG-CGACAC-CCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUGUAAAA---GCGCCCAGUUUAAAAAACUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-AAC-UAUUUUGACUUU
AY593778.1/631-1092 AAGCAGGUUUCUCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGUUCGAUCCACU--GGCGAGUG----UUAGUAACACCACUGCUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCGAAU-GGACCCGCCAUGUGUGC---AACCCCA--GCACGGUAGCUUUGUUGUGAAACC--CA-CUUUAA---AGUGAC----------------------AUUGAUAC-----------------------UGGUACCCA-AAUACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUGUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CUCU-AAC-UACUUUGACUCU
AY593780.1/631-1092 AAGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGUUCGAUCCACU--GGCGAGUG----UUAGUAACACCACUGCUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCGAAU-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGUAGCUUUGUUGUGAAACU--CA-CUUUAA---AGUGAC----------------------AUUGAUAC-----------------------UGGUACCCA-AAUACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGCAACAUG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUGUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CUCU-AAC-UACUUUGACUCU
AY593792.1/631-1092 AAGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCAUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGUUCGAUCCACU--GGCGAGUG----UUAGUAACACCACUGCUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCGGAU-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGUAGCUUUGUUGUGAAACU--CA-CUUUAA---AGUGAC----------------------AUUGAUAC-----------------------UGGUACCCA-AAUACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAUG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUGUAAAA---GCGCCCAGUUUAAAAAACUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CUUU-AAC-UACUUUGACACU
AY593760.1/588-1049 AAGCAGACUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGUUCGAUCCACU--GGCGAGUG----UUAGUAACACCACUGCUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCGAAU-GGACCCGUCAUGUGUGC---AACCCCG--GCACGGUAGCUUUGUUGUGAAACU--CA-CUUUAA---AGUGAC----------------------AUUGAUAC-----------------------UGGUACCCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGGAACAUG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUGUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CUCU-AAC-UACACUUACUCU
AY593753.1/632-1093 AAGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACACUUU-GUACUGUGUU---UGGCUCCA----CGUUCGAUCCACU--GGCGAGUG----UUAGUAACAACACUGCUACUUCG-UAGCGGAGCAUGGC-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCACAU-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGUAGCUUUGUUGUGAAACC--CA-CUUUAA---AGUGAC----------------------ACUGAUAC-----------------------UGGUACCCA-AAUACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CUUU-AAU-UACACUGAAAUU
AY593757.1/631-1092 AAGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGUUCGAUCCACU--GGCGAGUG----UUAGUAACAACACUGCUACUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCACAU-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGUAGCUUUGUUGUGAAACC--CA-CUUUAA---AGUGAC----------------------AUUGAUAC-----------------------UGGUACCCA-AAUACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CUUU-AAU-CACAUUGAAAUU
AY593794.1/627-1087 AUGCAGGUUUCCCCAACUGA-CACACACC-GUGCAA-AUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGCUCGACCCACU--GGCGAGUG----UUAGUAACACCACUGCUACUUCG-UCGCGGAGCAUGAC-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCGGAC-GGACCCGUCAUGUGUGC---AACCCCA--GCACAGUAGCUUUGUUGUGAAACC--CA-CUUUAA---AGUGAC----------------------GUUGAUAC-----------------------UGGUACCCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUCCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGGAGGGGA-CUG-GGGC---UUCUUUAAA----GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CUCU-UAC-CUACUUUGACUG
AJ251476.1/211-672  AAGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-UUUGAAACUCCGCCUGGGCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGACUCCA----CGCUCGAUCCACU--GGCGAGUG----UUAGUAACAACACUGCUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGACCCCCCCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCGAAU-GGACCCGUCAUGUGUGC---AAACCCA--GCACAGUACCUUUGUUGUGAAACU--CA-CUUUAA---AGUGAC----------------------AUUGAUAC-----------------------UGGUACUCA-AGCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-UGACAC-UCGGGAUCU-GAGAAGGGGA-CCG-GGGC---UUCUAUAAAA---GCGCCCGGUUUAAAAAGCUUCUAU-GUCUGAAUAGGUGACCGGAGG-CAGGCACCUUUC-UUUU-AAU-UACACUGGACUU
AY593788.1/630-1091 ACGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAG-CUUGGCGCUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACAUGUU-GUACUGUGUU---UGGCUCCA----CGCUCGAUCCACC--GGCGAGUA----CUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGUC-GGCCGUGGGAACUCCCCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCGCAA-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGUGAAACA--CA-CUUUAA---GGUGAC----------------------AUUGAAAC-----------------------UGGUACCCA-AUCACU-------GGUGACAGGC--UAAGGAUGCCCUCCAGGUACCCCGAGGUAACAUG-AGACAC-UCGGGAUCU-GAGGAGGGGA-CUG-AGGC---UUCUAUAAAA---GCGCUCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-UAU-AACUAUGAACUA
AY593803.1/632-1092 ACGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAG-CUUGACACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACAUGUU-GUACUGUGUU---UGGCUCCA----CGCUCGGUCCACC--GGCGAGUG----CUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACCCCCCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCACAC-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGUGAAACA--CA-CUUUAA---AGUGAC----------------------ACUGAAAC-----------------------UGGUACCCA-AUCACU-------GGUGACAGGC--UAAGGAUGCCCUCCAGGUACCCCGAGGUAACACG-AGACAC-UCGGGAUCU-GAGGAGGGGA-CUG-AGGC---UUCUAUAAAA---GCGCUCGGUUCAAAAAGCUUCUAC-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-C-UU-UAU-AAUUAUGAACUA
AJ133359.1/577-1038 AAGCAGGUUUCUCCAACUGA-CACAAAAC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACACUUU-GUACUGCGUU---UGGCUCCA----CGCUCGAUCCACU--GGCGAGUG----UUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGCCCACAC-GGGCCCGUCAUGUGUGC---AACCCCA--GCACGGCGACUUUACUGCGAAACC--CA-CUUUAA---AGUGAC----------------------AUUGAAAC-----------------------UGGUACCCA-CACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GUGCUCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-UCGGCACCUUUC-CUUU-GUA-AUUAAUGACCCU
AF274010.1/577-1038 AAGCAGGUUUCCCCAACUGA-CACAAAAC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACACUUU-GUACUGUGUU---UGGCUCCA----CGCUCGAUCCACU--GGCGAGUG----UUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGCCCACAC-GGGCCCGUCAUGUGUGC---AACCCCA--GCACGGCGACUUUACUGCGAAACC--CA-CUUUAA---AGUGAC----------------------AUUGAAAC-----------------------UGGUACCCA-CACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GCGCUCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-UCGGCACCUUUC-CUUU-ACA-AUUAAUGACCCU
AY593808.1/632-1093 ACGCAGGUUUCCCCAACUGA-CACACACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGUU---UGGCUCCA----CGCUCGAUCCACU--GGCGAGUG----UUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGCCCAAAC-GGGCCCGUCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGCGAAACC--CA-CUUUAA---AGUGAC----------------------AUUGAUAC-----------------------UGGUACCCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-ACA-AUUAAUGACCCU
AY593802.1/629-1089 AUGCAGGUUUCCCCAACCGA-CACAAACC-GUGCAA-UCUGAAGUUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGAUGACACUUU-GUACUGCACU---UGGCUCCA----CGCUCGAUCCAUC--GGCGAGUG----UUAGUAACAGCACUAUUGCUUCG-UAGCGGAGCAUGAU-GGCCGUGGGACCUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCAC-U-GGACCCAUCAUGUGUGC---AACCCCA--GCACAGCAACUUUACUGUGAAACU--CA-CUUUAA---GAUGAC----------------------AUUGAUAC-----------------------UGGUACCCA-CGUGCU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAUG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CCG-GGGU---UUCUGUAAAA---ACGCCCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAU-ACUCACUGAUUU
AJ007572.1/620-1080 AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAGCUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAUUUU-GUACUGUGCU---UGGCUCCA----CGCUCGAUCCAUC--GGCGGGUG----UUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGAA-GGCCGUGGGACCUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCAC-U-GGACCCUUCAUGCGUGC---AUUCCCA--GCACGGCAACUUUACUGUGAAAUC--CA-CUUUAA---GAUGAC----------------------AUUGAUAC-----------------------UGGUACCCA-AGUGCU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-UGACAC-UCGGAAUCU-GAGAAGGGGA-CCG-GGGU---CUCUAUAAAA---UCGCCCGGUUUAAAAAGCUUCUAC-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAU-ACCUACUGACUU
AY593756.1/544-1004 AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAGCUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGCGACACUUU-GUACUGUGUU---UGGCUCCA----CGCUUGACUCAUC--GGCGAGUG----UUAGUAGCAGCACUGUUGCUUCG-UAGCGGAGCAUGAU-GGCCGUGGGAAUUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCACAC-GGACCCAUCAUGUGUGC---AACCCCA--GCACAGCAACUUUACUGUGAAACU--CA-CUUUAA---GAUGAC----------------------GUUGAUAC-----------------------UGGUACCCA-AGCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUUUAAAA---GCGCCCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-C-UU-UAC-AACUAUUGACAU
AY593782.1/628-1086 AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-UCUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGCA---UGACUCCA----CGUUCGAUCCACU--GGCGAGUG----CUAGUAGUAGUACUGCUGUUUCG-UAGCGGAACACGAC-GGCCGUGGGACUCCCCCCUUGGUAACAAGGACCCGCGGGGCCAAAAGCCACGUCU---C-UGACCCGUCGUGUGUGC---AAACCCA--GCACAGCAGCUUUACUGCGAAAAC--CA-CUUUAA---GGUGAC----------------------AUUGAUAC-----------------------UGGUACUCA-CGCACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGCAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUGUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CCUC-UAC-UACCACUGACUC
AY593806.1/631-1092 ACGCAGGUUUCCCCAACUGA-CACAACCC-GUGCAA-CUUGAAACUCCGCUUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGUGCU---UGGCUCCA----CGCUCGAUCCACU--GGCGAGUG----UUAGUAGCAGCACUGUUGCUUCG-UAGCGGAGCAUGAC-GGCCGUGGGAAUCCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCAAAC-GGACCCGCCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGCGAAAAC--CA-CUUUAA---GGUGAC----------------------AUUGACAC-----------------------UGGUACCCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUAUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-UCUU-UAC-ACCUACUGACUU
AY593821.1/631-1092 AAGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGGCACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACCUU-GUACUGUGUU---UGACUCCA----CGCUCGAUCCACU--GGCGAGUG----UUAGUAACAGCACUGUUGCUUCG-UAGCGGAGCAUGGU-GGCCGUGGGGCUUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUAAC-GGACCCACCAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGCGAAACC--UA-CUUUAA---GGUGAC----------------------AUUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CCG-GGGC---UUCUGUAAAA---GUGCUCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-UAC-AAACUUCAACUU
D10143.1/253-713    AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACACUUU-GUACUGAGUU---UGACUCCA----CGCUCGAUCCACU--AGCGAGUG----UUAGUAGCGGUACUGCUGUCUCG-UAGCGGAGCAUGUU-GGCCGUGGGAACACCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUAAC-GGACCCAACAUGUGUGC---AACCCCA--GCACGGCAGCUUUACUGUGAAACC--CA-CUUCAA---GGUGAC----------------------AUUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAC---UCCUUUAAA----GUGCCCAGUUUAAAAAGCUUCUAU-GCCGGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-UAU-AACCACUGAAUA
AY593820.1/632-1092 AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACAUUUU-GUACUGCGUU---UGACUCCA----CGCUCGAUCCACU--AGCGAGUG----UUAGUAGCGGUACUGCUGUCUCG-UAGCGGAGCAUGUU-GGCCGUGGGAACACCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCCUAAC-GGACCCAACAUGUGUGC---AACCCCA--GCACGGCAGCUUUACUGUGAAACC--CA-CUUCAA---GGUGAC----------------------AUUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAC---UUCUUUAAA----GUGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-UAU-AACCACUGAACA
D10144.1/253-713    AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACAUUUU-GUACUGUGUU---UGACUCCA----CGCUCGAUCCACU--AGCGAGUG----UUAGUAGCGGUACUGCUGUCUCG-UAGCGGAGCAUGUU-GGCCGUGGGAACACCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCAUGUCCUAAC-GGACCCAAUAUGUGUGC---AACCCCA--GCACGGCAGCUUUACUGUGAAACC--CA-CUUCAA---GGUGAC----------------------AUUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAC---UUCUUUAAA----GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-UAU-AACCACUGAAUA
AY593817.1/632-1092 AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACAUUUU-GUACUGUGUU---UGACUCCA----CGCUCGAUCCACU--AGCGAGUG----UUAGUAGCGGUACUGCUGUCUCG-UAGCGGAGCAUGUU-GGCCGUGGGAACACCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCAUGUCCUAAC-GGACCCAACAUGUGUGC---AACCCCA--GCACGGCAACUUUACUGUGAAACC--CA-CUUCAA---GGUGAC----------------------AUUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAC---UUCUUUAAA----GUGCCCAGUUUAAAAAGCUUCUAU-GUCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-UAU-AACCACUGAGCA
AY593814.1/628-1088 AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACUCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUAACAUUUU-GUACUGUGUU---UGGCUCCA----CGCUCGAUCCACU--AGCGAGUG----UUAGUAGCGGUACUGCUGUCUCG-UAGCGGAGCAUGUU-GGCCGUGGGAACACCUCCUUGGCAACAAGGACCCACGGGGCCGCAAGCCACGUCCUAAC-GGACCCAACAUGUGUGC---AACCCCA--GCACGGCAGCUUUACUGUGAAACC--CA-CUUCAA---GGUGAC----------------------AUUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAC---UUCUUUAAA----GUGCCCAGUUUAAAAAGCUUCUAU-GUCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-UAC-AACCACUGAACA
AY593773.1/632-1093 AUGCAGGUUUCCCCAACUGA-CACAAACC-GUGCAA-CUUGAAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAUUUU-GUACCGUGCU---UGACUCCA----CGCUCGAUCCACU--GGCGAGUG----UUAGUAGCGGCACUGCUGUCUCG-UAGCGGAGCAUGUU-GGCCGUGGGAACACCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUAAC-GGACCCAACAUGUGUGC---AACCCCA--GCACGGCAGUUUUACUGUGAAACC--CA-CUUCAA---GGUGAC----------------------AUUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGG-CUG-GGGC---UUCUAUAAAA---GCGCUCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CUCU-UAC-AAAUUUUAAACU
AY593776.1/589-1047 ACGCAGGUUUCC-CAACUGA-CACUAACC-GUGCAA-CUUGAAAUCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAAUUU-GUACUGUGUU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----UUAGUAGCAGCACUGUUGUCUCG-UAGCGGAGCAUGAU-GGCCGUGGGAAUCCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCCAAU-GGACCCAUCAUGUGUGC---AACCCCA--GCACGGCAACCUUUCUGUGAAACU--CA-CUUCAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AAUACU-------GGUGGCAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-AGGC---UUCUUUAAAG---GCGCUCGGUUUAAAAAGCUUCUAU-GCCUGAACAGGUGACCGGAGG-UCGGCACCUUUC---UC-UAC-AACCACUGAUUU
AY593759.1/590-1049 ACGCAGGUUCCCCCAACUGA-CACCAACC-GUGCAA-CUUGAAAUCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAAUUU-GUACUGUGUU---UGACUCCA----CGCUCGGUUCACU--GGCGAGUG----UUAGUAGCAGCACUGUUGUCUCG-UAGCGGAGCAUGAU-GGCCGUGGGAAUUCCUCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCGCGUCCUAAC-GGACCCAUCAUGUGUGC---AGCCCCA--GCACGGCAACUUUUCUGGGAAACC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AAUACU-------GGUGGCAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CCG-AGGC---UUCUUUAAAA---GCGCUCGGUUUAAAAAGCUUCUAU-GCCUGAACAGGUGACCGGAGG-UCGGCACCUUUC---UC-UAC-AACCACUGAUUU
AY593751.1/594-1053 ACGCAGGUUUCCCCAACUGA-CACUUACC-GUGCAA-CUUGAAAUCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAAUUU-GUACUGUGGU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----CUAGUAGCAGCACUGUUGUCUCG-UAGCGGAGCAUGAU-GGCCGUGGGAAUCCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUAAC-GGACCCAUCAUGUGUGC---AACCCCA--GCACGGCGACUUUCCUGUGAAACC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AACACU-------GGUGGCAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UUGGGAUCU-GAGAAGGGGA-CUG-AGGC---UUCUUUAAAA---GCGCUCGGUUUAAAAAGCUUCUAC-GCCUGAACAGGUGACCGGAGG-CCGGCACCUUUC---UC-UAC-AAUCACUGAUAC
AY593774.1/596-1054 ACGCAGGUUUCC-CAACUGA-CACUAACC-GUGCAA-CUUGAAAUCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAAUUU-GUACUGUGUU---UGACUCCA----CGCUCGGUCCACU--GGCGAGUG----CUAGUAGCAGCACUGUCGUCUCG-UAGCGGAGCAUGAU-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUAAC-GGACCCAUCAUGUGUGC---AACCCCA--GCACGGCGACUUUUCUGUGAAACC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AAUACU-------GGCGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-AGGC---UUCUUUAAAA---GCGCUCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC---UC-UAC-AACCACCGAUUU
AY593822.1/595-1054 ACGCAGGUUUCCCCAACUGA-CACUAACC-GUGCAA-CUUGAAAUCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAAUUU-GUACUGUGUU---UGACUCCA----CGCUCGGUCCACC--GGCGAUUG----CUAGUAACAGCACUGUCGUCUCG-UAGCGGAGCAUGAU-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUAAC-GGACCCAUCAUGUGUGU---AACCCCA--ACACGGCGACUUUUCUGUGAAACC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AAUACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCAAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-AGGC---UUCUUUAAAA---GCGCUCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC---UU-UAC-AACCACUGAUUU
AY593826.1/597-1056 ACGCAGGUUUCCCCAACUGA-CACUAACC-GUGCAA-CUUGAAAUCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACAAUUU-GUACUGUGUU---UGACUCCA----CGCUCGGCCCACC--GGCGAGUG----UUAGUAGCAGCACUGUCGUCUCG-UAGCGGAGCAUGAU-GGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGUCCUAAC-GGACCCGUCAUGUGUGC---AACCCCA--GCACGGCGACUUUUCUGUGAAACC--CA-CUUUAA---GGUGAC----------------------ACUGAUAC-----------------------UGGUACUCA-AAUACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-CGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-AGGU---UUCUUUAAAA---GCGCUCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC---UU-UAC-AACCACUGAUAC
AF511039.1/582-1038 ACGCAGGUUUCCUCAACUGA-CACAACUC-GUGCAA-ACUGUAACCCCGCCUGGUCUUUC-CAGGUCUGGA----GGGGA-AGCUUUU-GUACUGUGUU---UGGCUCCA----CGUUCGGUCUACU--GGCGAGCG----CUAGUAGUGGCAAUGUUGUUUCG-UAGCGGAGCAUGUU-GGCCGUGGGAAUCCCUCCUUGGCGACAAGGACCCACGGGGCCGCAAGCCACGUCU---U-UGACCCAACAUGUGUGC---AACCCCA--GCACGGCAACCUUGCCACGAAAAC--CA-CUUCAA---GGUAAC----------------------ACUGAUAC-----------------------UGGUACUCA-AAUACU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-GGACAC-UUGGGAUCU-GAGAAGGGGA-UUG-GGAC---UUCUAUAAAA---GUGCCCAAUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-C-UC-UAC-AACUACUUUACC
AY593813.1/543-1005 AAUCAGGUUUCCUCAACUGA-CACAAACC-GUGCAA-UCUGCAGCUCCGCCUGGUCUUUC-CAGGUCUAGA----GGAGUAACAUUUU-GUACUGUGCU---UGACUCCA----CGCUCGGUCUACU--GGCGGGUG----UUAGUAGCGGCACUGUUGCUUCG-UAGCGGAGCAUGUU-GGCCGUGGGAACUCCUCCUUGGCAACAAGGACCCACGGGGCCAAAAGCCACGUCCUCAU-GGACCCAACAUGUGUGC---AACCCCA--GCACGGCAACUUUUCCGCGAAAAC--CA-CUUUAA---GGUAAC----------------------ACUGAUAC-----------------------UGGUACUCA-AACGCU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-UGACAC-UUGGGAUCU-GAGAAGGGGA-CUA-GGGC---UUCUAUAAAA---GCGCCUGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CCUU-UUCGCACUACUAAACA
AY593761.1/586-1045 ACGCAGGUC-CCUCAACUGG-UACAAACC-GUGCAA-CUUGAAACCCCGCCUGGUCUUUC-CAGGUCUAGA----GGGGUGACACUUU-GUACUGCGCA---UGACUCCA----CGUUCGGCCUACU--GGCGGGUG----CUAGUAACGGUGUUGUUGUUUCG-UAGCGGAGCAUGUU-GGCCGUGGGAACCCCCCCUUGGUAACAAGGACCCACGGGGCCGAAAGCCACGUCUUC-C-AGACCCAACAUGUGUGC---AACCCCA--GCACGGCAACUUCAUCGUGAACAC--CA-CCUUAA---GGCAAC----------------------GCUGAUAC-----------------------UGGUACUCA-GACGCU-------GGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCAAGGUAACAAG-AGACAC-UUGGGAUCU-GAGAAGGGGA-CCG-GGGC---UUCUGUAAAA---GCGCCCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-GUU-AACUCUUAACUU
AY593842.1/589-1047 ACGCAGGAAUCUUAGACCAA-C-CCGCCC-GUGCAA-CUGCAAGUUUCGCCCGGUCUUUC-CGGGUCUUGA----GAGACAAACAGAU-GUACUGAGGC---CAACUCCA----CGAUUGGUCUACU--AGCGGGUA----CUAGUAACACUCACUUUGCUUCG-UAGCGGAGCACAUG-AGCGGCGGGAACACCCCCAUGGUAACAUGGACCCGUCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGUGUGUGC---AACCCCA--GCACGGCAACUUGUUUGUGAACCA--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CCA-GAAG---UUCUAUCAAA---CUGUCUGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAC-UUAAACCCAAUU
AY593851.1/589-1048 ACGCAGGAAUCUUAGACCAA-CCCUACCC-GUGCAA-CUGCAAGUUUCGCCCGGUCUUUC-CGGGUCUAGA----GAGACAAACAGAU-GUACUGAGGC---CAACUCCA----CGAUUGGUCUACU--AGCGGGUA----CUAGUAACACUCACUUUGCUUCG-UAGCGGAGCACAUG-AGCGGCGGGAUUUCCCCCAUGGUGACAUGGACCCGCCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGUGUGUGC---AACCCCA--GCACGGCAAUUUGUCUGUGAAACA--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUCCAGGUACCCCGAGGUAACACG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CCA-GGAG---UUCUAUCAAA---CUGCCUGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAC-UACACCUUAUUU
AY593840.1/589-1048 ACGCAGGAAUCUUAGACCAA-CCCAACCC-GUGCAA-CUGCAAGUCUCGCCCGGUCUUUC-CGGGUCUUGA----GGGAUAAACAGAU-GUACUGAGAU---CAACUCCA----CGAUUGGUCUACU--AGCGGGUA----CUAGUAACACUCACUUUGCUUCG-UAGCGGAGCACAUG-AGCGGCGGGAUCUCCCCCAUGGUAACAUGGACCCGCCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGUGUGUGC---AACCCCA--GCACGGCAACUUGUUUGUGAAACA--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAUG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CCA-GGAG---UUCUAUCAAA---CUGCCUGAUUCAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UUA-UUUUACUCAAUU
AF540910.1/596-1056 ACGCAGGAAUCUUAGACCAA-CCCAACCC-GUGCAC-CUGCAAGUUUCGCCCGGUCCUUC-CGGGUCUUGA----GAGACAAACAGAU-GUACUGAGAU---CAACUCCA----CGAUUGGUCUACU--AGCGGGUA----CUAGUAACACUCACUUUGCUUCG-UAGCGGAGCACAUG-AGCGGUGGGACCUCCCCCAUGGUAACAUGGACCCACCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGUGUGUGC---AACCCCA--GCACGGCAACUUGUUUGUGAAACA--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-AUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-AGACACUUCGGGAUCU-GAGAAGGGGA-CCA-GGAG---UUCUAUCAAA---CUGCCCGGUUUAAAAAGCUUCUAU-GCCUGGAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAU-UUAAACUCACUU
AY593843.1/590-1049 ACGCAGGAAUCUCAGACCAA-CCCAACCC-GUGCAA-CUGCAAGUUUCACCCGGUCUUUC-CGGGUCUUGA----GAGACAAACAGAU-GUACUGAGAU---CAACUCCA----CGAUUGGUCUACU--AGCGGGUA----CUAGUAACACUCACUUUGCUUCG-UAGCGGAGCACAUG-AGCGGUGGGAGCUCCCCCAUGGUAACAUGGACCCACCGGGCCAAAAGCCACGCCUCACA---GCCUCAUGUGUGUGC---AACCCCA--GCACGGCAAUUUGUUUGUGAACCA--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CCA-GGAG---UUCUAUCAAA---CUGCCCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAU-CUAAACUCAAUU
AY593841.1/588-1047 ACGCAGGAAUCUUAGACCAA-CCCAACCC-GUGCAG-CUGCAAGUUUCGCCCGGUCUUUC-CGGGUCUAGA----GAGACAAACAGAU-GUACUGAGAU---CAACUCCA----CGAUUGGUCUACU--AGCGGGUA----CUAGUAACACUCACUUUGCUUCG-UAGCGGAGCACAUG-AGCGGUGGGAACUCCCCCAUGGUAACAUGGACCCACCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGUGUGUGC---AACCCCA--GCACGGCAAUUUGUUUGUGAAACA--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CCA-GGAG---UUCUAUAAAA---CUGCCUGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAC-UCAAAUUUCAUU
AY593845.1/585-1044 ACGCAGGAAUCUUAGACCAA-CCCAACCC-GUGCAA-CUGCAAGUUUCGCCCGGUCUUUC-CGGGUCUAGA----GAGACAAACAGAU-GUACUGAGAU---CAACUCCA----CGAUUGGUCUACU--AGCGGGUA----UUAGUAACACUCACUUUGCUUCG-UAGCGGAGCGCAUG-AGCGGCGGGAACUCCCCCAUGGUAACAUGGACCCGCCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGCGUGUGC---AACCCCA--GCACGGCAAUUUGUUUGUGAAACG--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-AGACAC-UCGGGAUCU-GAGAAGGGGA-UCG-GGAG---UUCUAUCAAA---CUGCCCGGUUUAAAAAGCUUCUAC-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAU-UUUAAACCUAUU
AY593853.1/545-1004 ACGCAGGAAUCUUAGACCAA-CCCAACCC-GUGCAA-CUGCAAGUUUCGCCCGGUCUUUC-CGGGUCUAGA----GAGACGAACAGAU-GUACUGAGAU---CAACGCCA----CGAUUGGUCUACU--GGCGGGUA----CUAGUAACACUCACUUUGCUUCG-UAGCGGAGCACAUG-AGCGGUGGGAACUCCCCCAUGGUAACAUGGACCCACCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGUGUGUGC---AACCCCA--GCACGGCAAUUUGUUUGUGAAACA--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGAG---UUCUAUCAAA---CUGCCCGGUUUAAAAACCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-GUU-UAAACUCAAUUU
AY593838.1/588-1047 ACGCAGGAAUCCUAGACCAA-CCCAACCC-GUGCAA-CUGCAAGUUUCGCCCGGUCUUUC-CGGGUCUAGA----GAGACGAACAGAU-GUACUGAGAU---CAACUCCA----CGAUUGGUCUACU--AGCGGGUG----UUAGUAACACUCACUUUGCUUCG-UAGCGGAGCGCAUG-AGCGGCGGGAACUCCCCCAUGGUAACAUGGACCCUCCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGCGUGUGC---AACCCCA--GCACGGCAAUUUGUUUGUGAAACA--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CCG-GGAG---UUCUAUCAAA---CUGCCCGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUA-UUU-AAACCUUGAUUU
AY593848.1/546-1005 ACGCAGGAAUCUUAGACCAA-CCCAACCC-GUGCAA-CUGCAAGUUUCGCCCGGUCUUUC-CGGGUCUUGA----GAGACAAACAGAU-GUACUGAGAC---CGACUCCA----CGAUUGGUCUACU--GGCGGAUG----CUAGUAACACUCACUUUGCUUCG-UAGCGGAGCGCAUG-AGCGGUGGGAACACCCCCAUGGUAACAUGGACCCACCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGUGUGUGC---AACCCCA--GCACGGCAACUUGUUUGUGAAACA--CA-UCUUAA---AGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CCA-GGAG---UUCUAUAAAG---CUGCCUGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUCUU-CCUU-UAC-UUGACUUAUUUU
AY593850.1/588-1048 ACGCAGGAAUCUUAGACCAA-CCCAAACCCGUGCAA-CUGCAAGUUUCGCCCGGUCUUUC-CGGGUCUAGA----GAGACAAACAGAU-GUACUGAGAC---UGACUCCA----CGACUGGUCUACU--GGCGGGUG----CUAGUAACACUCACUUUGCUUCG-UAGCGGAGCACAUG-AGCGGUGGGAACACCCCCGUGGUAACACGGACCCACCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGUGUGUGC---AACCCCA--GCACGGCAAAUUGUUUGUGAAACA--CA-UCUUAA---GGUAAC----------------------ACUGGGAC-----------------------UGGUACUUA-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GAAG---UUCUUUAAAA---CUGUCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UUA-UCCAACACAUUU
AY593846.1/546-1006 ACGCAGGAAUCUUAGACCAA-CCCAAACCCGUGCAA-CUGCAAGUUUCGCCCGGUCUUUC-CGGGUCUAGA----GAGACAAACAGGU-GUACUGAGAC---UGACUCCA----CGAUCGGUCUACU--AGCGGGUG----UUAGUAACACUCAUUUUGCUUCG-UAGCGGAGCACAUG-AGCGGUGGGACCUCCCCCAUGGUAACAUGGACUCACCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGUGUGUGC---AACCCCA--GCACGGCAACUUGUUUGUGAAACC--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACACG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CCA-GGAG---UUCUUUAAAA---CUGCCUGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAU-CAAUACUACAUU
AY593839.1/546-1005 ACGCAGGAAUCCUAGACCAACCACAACCC-GUGCAA-CUGCAAGUUUCGCCCGGUCUUUC-CGGGUCUAGA----GAGACAAACAGCU-GUACUGAGAC---UGACUCCA----CGAUCGGUCUACU--AGCGGGUG----CUAGUAACACUUACUUUGCUUCG-UAGCGGAGCACAUG-AGCGACGGGAACACCCCCAUGGUAACAUGGACCCGCCGGGCCAAAAGCCACGCCUCA---CGGCCUCAUGUGUGUGC---AACCCCA--GCACGGCGAUGUACUUGUGAACCA--CA-CCUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUCG-GUUUCU-------AGUGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-AGACAC-UUGGGAUCU-GAGAAGGGGA-CCA-GGAG---UUCUGUAAAA---CUGCCUGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAC--UCAAUUGUACU
AY593847.1/545-1003 ACGCAGGAAUCCUGGACCAA-CCACACCC-GUGCAU-UUACAAUCUUCGCCCGGUCUUUC-CGGGUCUUGA----GAGGAGACUAAGU-GUACUGAGAC---UGACUCCA----CGAUCGGUCUACU--GGCGGGUA----UUAGUAACACUCACUUUGCUUCG-UAGCGGAGCACAUG-AGCGGUGGGACCCCCCCCAUGGUGACAUGGACCCACCGGGCCAAAAGCCACGCUU---C-ACGCCUCAUGUGUGUGC---AACCCCA--GCACGGCAAUUUGCUUGUGAAACA--CA-CCUCAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUCA-AUCUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CCA-GGAG---UUCUUUAAAA---CUGCCUGGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUC-CUUU-UAC-AAACAACAAUUA
AJ251473.1/214-672  ACGCAGGUUUCCUCAACUGA-CACAA-CC-GUGCAAACAUGAAGUUUCGCCCGGUCUUUC-CGGGUCUUGA----GAGACGACAUU-U-GUACUGAGAU---CAACUCCA----CAAUUGGUCUACU--GGCGGGUG----CUAGUAAUGACUUUGUUGCUUCG-UAGCGGAGCACGCA-AGCCGCGGGAACUCCCCCUUGGUAACAAGGACCCGCGGGGCCGAAAGCCACGUUCUC-U-GAACCUUGCGUGUGUGC---AACCCCA--GCACGGUAAUACUGUCAUGAAACA--CA-CUUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-UUG-GGGC---UUCUAUCCAA---GCGCCCAAUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAG--CCGGCACCUUUU-CCUU-UAC-UCACAACUUGUU
AY593849.1/610-1068 ACGCAGGUUUCCUCAACUGA-CAUAA-CC-GUGCAA-ACUGAAGUUUCGCCCGGUCUUUC-CGGGUCUUGA----GAGACGACA-UUU-GUACUGAAAU---CAACUCCA----CAAUUGGUCUACU--GGCGGGUG----CUAGUAAUGACUUUGUUGCUUCG-UAGCGGAGCACGCA-AGCCGCGGGAACUCCCCCUUGGUAACAAGGACCCGCGGGGCCGAAAGCCACGUUCUC-U-GAACCUUGCGUGUGUGC---AACCCCA--GCACGGUAACACUGUCACGAAACA--CA-CUUUAA---GGUAAC----------------------ACCGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-CGACAC-UCGGGAUCU-GAGAAGGGGA-UUG-GGGC---UUCUAUCCAA---GCGCCCAAUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAC-CCACAACUUACU
AY593844.1/597-1056 AAGCAGGUUUCCUCAACUGA-CAU-ACCC-GUGCAA-CUUGAAGUUUCGCCUGGUCUUUC-CAGGUCUAGA----GAGACGACACUUU-GUACUGAACC---CAACUCCA----CGAUUGGUCUACU--GGCGGGUG----CUAGUAAUGGCUUUGUUGCUUCG-UAGCGGAGCAUGCA-AGCCGCGGGAACUCCCCCUUGGUGACAAGGACCCGCGGGGCCAAAAGCCACGUUCUC-U-GAACCUUGCAUGUGUGC---AACCCCA--GCACGGUGACACUGUUGUGAAACA--CA-CUUUAA---GGUAAC----------------------ACUGAGAC-----------------------UGGUACUUG-GUUUCU-------GGAGACAGGC--UAAGGAUGCCCUUCAGGUACCCCGAGGUAACAAG-AGACAC-UCGGGAUCU-GAGAAGGGGA-CUG-GGGC---UUCUUUAAAA---GCGCCCAGUUUAAAAAGCUUCUAU-GCCUGAAUAGGUGACCGGAGG-CCGGCACCUUUU-CCUU-UAU-ACAAAACCAUUU
AF361253.1/413-905  CUAGCCGUUGCGCCUUAGCG-CACAGUCC----------UGAAGGCCCCACAUCUUGUGG-AUCUUGCCGU----GGACAUGUUUC----UGGCAUGUG---UUUCUCAAGCCUGCAACCGACGACU--GAACAGAC----GUGUGAACAG--UUUGAGUGUGG-UAGCGCUGUGUGAGUUGGCGGUGGAACCCCCUCGUGGUGACACGAGCCCCCGUGGCCAAAAGCCCAGUGUUUACAGCACCUCUCACAUCCAGGGAAACCCCACCCUGGCGCUCACUCUUAGUAACACU--UC-CUAGUA---GGUAUUAGGUGGUAAGCCGAGCUCUUCCUCGGUCUU--------------------GUUCUGAAUGCA-CACA-U-------GUCUAGGGGC--UAAGGAUGUCCUACAGGUACCCGCACGUAACCUUCAGAGAG-UGUGGAUCU-GAGUAGGAGA-CUGUGGUGCGCUGCUUUACAGACGUAGCCCAGUUUAAAAAACGUCUAU-GCCCCUACAGGGUCGCGGUGGGCCGCACCCUUUC-CUUU-UAC-AAACUUGGUUUU
X96871.1/402-893    CUAGCCGUCGCGUC--UUAA-CGCGCAGC-CCUGAA-GG-----C----CCCACACCUUG-UGGAUCUUGC----CGUGGGUAUGUUU-CUGGCAUGUG---UUUCUCAAG---CCUGCAACCGAAGCCGAACAGCC----ACAUGAACAG--UUUGAGCGUGG-UAGCGCUGUGUGAGUUGGCGGUGGAUCCCCCUCGUGGUAACACGAGCCCCCGUGGCCAAAAGCCCAGUGUUUACAGCACCUCUCACAUCCAGGACGACCCCAUCCUGGCGCUCACUCUUAGU-AGUAU--GG-CUUAGUACGCAUUAG----------------------GUGGUAAGCCGAGCUCUCCCUCGGCCUUGUUCUGAAUGCA-CACA-U-------GUCUAGGGGC--UAAGGAUGUCCUACAGGUACCCGCACGUAACCUUCAGAGAG-UGCGGAUCU-GAGUAGGAGA-CCGUGGUGCACUGCUUUACAGAUGCAGCCCGGUUUAAAAAGCGUCUAU-GCCCCUACAGGGUAGCGGUGGGCCGCGCCCUUUC-CUUU-UAA-AACUACUUGUUC
#=GC SS_cons        :::::<<___>>,,,,,,,,.,,,,,,,,.<<<<<<.-------<<<<-<<<<<_____>.>>>>------....>>>>------->>.>>>>,[[[[[...[[[--[[[....---[[[[[-[[[[..----[[[[....------[[[[----[[[[[[,<<.___>>,,(((((((.((<<<<<<<-------<<<<<____>>>>>->>>>>>><<<_____>>>,,<<<<____.>>>>)))))))))<<<<..._______..>>>>]]]]]]----]]]]------..]].]]----...]]]]--......................]]]]]---.......................]]]---]]].]]]]],.......,,,,,(((((..,,,,,,,,<<<<<<<<<<---<<<<<________._____>.>>>>->>>>.>>-->>>>,<.<<<.<<<<...__________...>>->>>>>>,,,,,,,,,,,,,,,.))))),,,<<<<<-<<<<___.>>>>>>>>>:::.::::.:::.::::::::::::
#=GC RF             augcagGUuuCcucaAcuga.CaCAaacC.gugcaa.cuUgAAacccCgccuggucuUuc.caggUcUaGA....GgggugAcauuuu.guacuGuguu...uggCUCca....cgaucgguccAcc..gGcgaGug....uUAGuAaCaguauUguuGccUCg.UAGcGgagcgugag.gGcCGggGGAACuCCucCcUGGUAACAgGgaCCccCGgGGCCAAAAGCCAcGuccuaAC.ggaCCccucacguguGc...AACCCCA..gCacggCaacuUuucuGuGAAAau..ca.CuuuaA...ggUgAc......................accgauAc.......................ugGUAccca.aacaCU.......GgugAcgGGC..UAAGGAUGcCCuuCAGGUACCCcgAGGUAACAuG.aGAcAC.UcgGGAUCU.GaGaaGGgGa.ccG.gggc...UUCUuUAaAa...gcGccCgguUUAAAAAgCuUCUAU.GCCcgaAuAGGcgAccGGaGG.CCggcgCCUUUC.CuUU.UAu.uauuAuuauuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00211
#=GF ID   SNORD35
#=GF PI   U35
#=GF DE   Small nucleolar RNA SNORD35
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD, Griffiths-Jones SR
#=GF GA   36.00
#=GF TC   36.20
#=GF NC   35.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00056
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300752;
#=GF DR   snoopy; Oryzias_latipes300005;
#=GF RN   [1]
#=GF RM   8764399
#=GF RT   Intron-encoded, antisense small nucleolar RNAs: the characterization of
#=GF RT   nine novel species points to their direct role as guides for the
#=GF RT   2'-O-ribose methylation of rRNAs.
#=GF RA   Nicoloso M, Qu LH, Michot B, Bachellerie JP
#=GF RL   J Mol Biol 1996;260:178-195.
#=GF CC   U35 is a C/D box snoRNA located in intron 6 of ribosomal protein L13A and
#=GF CC   intron 3 of ribosomal protein S11 in humans [1] and at homologous
#=GF CC   positions in mouse and chicken ribosomal protein genes. U35 guides the
#=GF CC   methylation of 2'-O-ribose sites in 28S rRNA.
#=GF WK   Small_nucleolar_RNA_SNORD35
#=GF SQ   8


AB028894.1/2954-3040   GGCAAGUGAUGUCUGUU--CUCACGAUGGUCUUCAGAUGUC-CUCUAGG-----GCACUGCUGAGACAGCCAGUUGACAAAGCUGAUGCCAUAAA
AB028893.1/10920-11006 GGCAGAUGAUGUUUGUU--UUCACGAUGGUCUUCAGAUGCC-CACGUGG-----GCACUGCUGAGAAAGCCACUUGGUAAAACUGAUGCCGGAAA
AB032798.1/2193-2284   UGGUGGUGAUGUCUGAA--CUCACGAUGGUCUUCAGAGUCC-CUGUUGGUGAGGGGACUGCUGACAAUGUCAGUGGCAACUGCUGAACCAUCAGA
Z69625.1/1-89          GGCACAUGAUGUUCUUAUUCUCACGAUGGUCUUCGGAUGCCACAGUUAG----GGCAAUGCCGAUAAUGCCA-AAGGCUAAGCUGAUGCCAGGA-
X51528.1/3860-3949     GGCACAUGAUGUUCUUAUUCUCACGAUGGUCUUCGGAUGCCACAGUUAG----GGCAGUGCCGAUAAUGCCA-AAGGCUAAGCUGAUGCCAGGAG
AB028893.1/4355-4440   GGCAGAUGAUGUCCUUAU-CUCACGAUGGUCUGCGGAUGUC-CCUGUG------GGAAUGGCGACAAUGCCA-AUGGCUUAGCUGAUGCCAGGAG
X94601.1/135-219       GGCAGAUGAUGUCCUUAU-CUCACGAUGGUCUGCGGAUUG---ACUGCG-----GGAAUGGCGACAAUGCCA-AUGGCUUAGCUGAUGCCAGGAG
AB032798.1/1514-1604   UGCACAUGAUGCCAUU---CUCACGAUGGUCUUCCAAGCCU-CAUGGUGAAGGGGCUGUGACGACAACGCCACAUGGCUUUGCUGAUGCCUGGUA
#=GC SS_cons           <<<<_____________..______________________._______...._________________________________>>>>:::::
#=GC RF                gGcagAUGAUGUcuuUa..CUCACGAUGGUCUUCaGAugcC.CauuugG....GGcAaUGccGAcAAuGCCAgauGgcuaaGCUGAugCcaggaa
//
# STOCKHOLM 1.0

#=GF AC   RF00212
#=GF ID   SNORD38
#=GF PI   U38
#=GF DE   Small nucleolar RNA SNORD38
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD, Griffiths-Jones SR
#=GF GA   44.00
#=GF TC   44.40
#=GF NC   43.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300955;
#=GF DR   snoopy; Homo_sapiens300161;
#=GF RN   [1]
#=GF RM   8764399
#=GF RT   Intron-encoded, antisense small nucleolar RNAs: the characterization of
#=GF RT   nine novel species points to their direct role as guides for the
#=GF RT   2'-O-ribose methylation of rRNAs.
#=GF RA   Nicoloso M, Qu LH, Michot B, Bachellerie JP
#=GF RL   J Mol Biol 1996;260:178-195.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   U38 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U38 is located in introns 4 and 5 of ribosomal
#=GF CC   protein S8 in human and in homologous genes in mouse and cow [1]. U38
#=GF CC   guides the methylation of 2'-O-ribose residues in 28S rRNA. Mouse MBII-329
#=GF CC   snoRNA is homologous to U38 [2].
#=GF WK   Small_nucleolar_RNA_SNORD38
#=GF SQ   7


AF357365.1/1-59    ---------UGAAAAUACUGUCCAGUUCUGCUACUGA--AGGAAUGAGAUGAACA--CUUUAGUGCUGAAGA--
X97582.1/2-71      UCUC-GUGAUGAAAACUCUGUCCAGUUCUGCUACUGA-AGGGAGAGAGAUGAGAGCCUUUUAGG-CUGAGGA-A
AF270686.1/237-307 UCUCAGUGAUGAAAACUUUGUCCAGUUCUGCUACUGAUUUUCAAAGUGAUGAUAA--AGUAUAU-CUGAGGAGA
X67247.1/3039-3107 UCUCAGUGAUGAAAACUUUGUCCAGUUCUGCUACUGA--CAGUAAGUGAAGAUAA--AGUGUGU-CUGAGGAGA
X97583.1/1-69      UCUCAGUGAUGAAAACUUUGUCCAGUUCUGCUACUGA--CAGUAAGUGAAGAUAA--AGUGUGU-CUGAGGAGA
X94603.1/205-273   UCUCGGUGAUGAGAACUUUGUCCAGUUCUGCUGCUGA-UCUCUAAGUGAGGAUGA--AGU-UAU-CUGAGGAGA
X67247.1/2492-2561 UCUC-GUGAUGAAAACUCUGUCCAGUUCUGCUACUGA-AGGGAGAGAGAUGAGAGCCUUUUAGG-CUGAGGA-A
#=GC SS_cons       <<<<------------------<<<<______>>>>-.-----------------..-------.----->>>>
#=GC RF            UCUCaGUGAUGAAAACUuUGUCCAGUUCUGCUACUGA.uuggaAAGuGAuGAuaA..agUuuGu.CUGAGGAGA
//
# STOCKHOLM 1.0

#=GF AC   RF00213
#=GF ID   snoR38
#=GF DE   Small nucleolar RNA R38
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   INFERNAL
#=GF SS   Predicted; PFOLD, Griffiths-Jones SR
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   44.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300946;
#=GF DR   snoopy; Oryzias_latipes300090;
#=GF RN   [1]
#=GF RM   7667877
#=GF RT   Antisense snoRNAs: a family of nucleolar RNAs with long complementarities
#=GF RT   to rRNA.
#=GF RA   Bachellerie JP, Michot B, Nicoloso M, Balakin A, Ni J, Fournier MJ
#=GF RL   Trends Biochem Sci 1995;20:261-264.
#=GF RN   [2]
#=GF RM   11266566
#=GF RT   Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana.
#=GF RA   Qu LH, Meng Q, Zhou H, Chen YQ, Liang-Hu Q, Qing M, Hui Z, Yue-Qin C
#=GF RL   Nucleic Acids Res 2001;29:1623-1630.
#=GF RN   [3]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   snoR38 is a C/D box small nucleolar RNA conserved across yeast [1], human,
#=GF CC   Arabidopsis [2] and rice [3]. It is encoded in the intron of elongation
#=GF CC   factor-1 gamma in both pombe and cerevisiae. snoR38 guides the methylation
#=GF CC   of 2'-O-ribose sites in 28S rRNA.
#=GF WK   Small_nucleolar_RNA_R38
#=GF SQ   19


AC004288.1/11652-11734     UAUGAUG---UGAUGAACACCUUAUUUAAG--CCAAACAGUUAUCCCUGUCAUAA----------------------GAAUAAUUGAUGAUAUAU----UCAGCUGACAACAUA
AC004288.1/10223-10308     AUAUGGGCAAUGAUGAACACUUUAUUUAAG--CCAAACAGUUAUCCCUGUCAUAA----------------------GAAUAAUUGAUGAUAAAA----GUUGCUGAUUCAUAU
CR380952.1/649867-649758   UUCUAAU--AUGAUGAGAACCUUUUUACAGUAUUUUACAGUUAUCCCUGUCUGAAUGGGUUAACAAAAUGGUAAUAAACUCAUAUGUCGAUGAAU--UAUACUCUGAAUUUAGA
AL606506.11/153543-153468  GACAGCU-GAGGAUGAUUUA------------------AGUUAUCCCUGUCUGAA-AUG----------------ACACUUUUGUGAAGAGUCAU--GGUUUACUGAGGCUCGA
AJ543401.1/2-76            UUGAGCU-GAGGAUGAUUUA------------------AGUUAUCCCUGUCUGAA--AU----------------GACACUUUCUGAAGAGUCAU--GGUUUACUGAGGCUCGA
BX629359.1/12582-12513     UGUAGCC-AAUGAUGAUACA------------------AGUUAUCCCUGUCUGAA-----------------------CUGAAGUGUGGAGUUGU--GGUAACCUGAGGCUCAG
AJ543402.1/2-77            UUGAGCU-GAGGAUGAUUUA------------------AGUUAUCCCUGUCUGAA-AUG----------------ACACUUUUGUGAAGAGUCAU--GGUUUACUGAGGCUCGA
AJ276575.1/7-100           UGUUUUG-GAUGAUGAGAAACAAAAAUCA---AAAUACAGUUAUCCCUGGCUUAGGGUUUA--------------AAGCCCGU-UGCUGAGUCUUU-UGUAAUCUGACACACAU
AJ543400.1/2-75            AUAAGCC-UAUGAUGGAUUG-------------------GUUAUCCCUGUCUGAA--------------------GAUUUCAGCUGAGGGAAAAUACUCUAUUCUGAGGCUUAG
AJ543324.1/2-73            ACAAGCC-UAUGAUGGUUA--------------------GUUAUCCCUGUCUGAA--------------------AAUCUGGACUGAGGGAAAUAA-UCUAUUCUGAGGCUUAA
AJ543326.1/2-79            AUGAGCU-GAGGAUGAUUUAAA-----------------GUUAUCCCUGUCUGAAAUGG----------------UAUCUUUUGUGAGGAGGUCU--GACUUGCUGAGGCUCAG
AJ543325.1/2-85            CUGAGUC-CAUGAUGAUUUCAA-----------------GUUAUCCCUGUCUGAAGGCAAAGAA-----------AGGCCUUUCUGUGUGGAAUUU-GAAUAUCUGAAACUCAG
AK123993.1/1023-1100       CUGAGCU-GAGGAUGAUUUAAA-----------------GUUAUCCCUGUCUGAAAUGG----------------UAUCUUUUGUGAGGAGGUCU--GACUUGCUGAGGCUCAG
Z28081.1/853-955           AAACAUA--AUGAUGAAAAAAAAUUUUA----UCAAACAGUUAUCCCUGUCUGAAUGGGUAAUAAUAGGUAA---CCUCUCAUAUGUUGAUAUUU--GUAUUUCUGAUAUGUUU
AB020755.1/17565-17473     GAUUGUG-GAUGAUGAGAACAAAUAUGA----AAAAACAGUUAUCCCUGUCUGAGGAUUUU--------------AAUCCCUU-UGAUGAUUCAUU-UGUAAUCUGACACAACC
AJ490371.1/1-92            AGAUGUG-GAUGAUGAAAUCACAAGUGA----AAAUACAGUUAUCCCUGUCUGAUUCCU----------------UCAUAAGGGUGCUGAGAAUAC-UUUAAUCUGACACAGUU
AJ490356.1/2-91            CAAGGUG-AAUGAUGAAAUCACAAGU------AAAUACAGUUAUCCCUGUCUGAUUCCU----------------UUCUAAGGGUGCUGAGAAUAC-UUAAAUCUGACACAUUA
CR382136.2/1336952-1336867 UUGUUUA-CGUGAUGAGAGAUUUUUUCAUAU-UUAUACAGUUAUCCCUGUCUUAA----------------------UACAUUAUGUCGAGAAUA---UUAUUCUGA-AAAUAA
AE016817.6/964860-964758   CCCUAGU--GUGAUGAGAAAACCUUUCGA---AAAAACAGUUAUCCCUGUCUGAAUGGGCAUAAUAUCUGG----UUGCACAUGUGUCGAGAGAC--CAUACUCUGAUUUAGAG
#=GC SS_cons               <<<<<<<.____________________....___________________________................____________________..__________>>>>>>>
#=GC RF                    uuaugcc.gAUGAUGAaaaaauuuuUua....aaAuACAGUUAUCCCUGUCUGAAuggg................aaucuuaugUGauGAgaaaU..uaUauUCUGAggcauaa
//
# STOCKHOLM 1.0

#=GF AC   RF00214
#=GF ID   Retro_dr1
#=GF DE   Retrovirus direct repeat 1 (dr1)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:10438832
#=GF SS   Published; PMID:10438832
#=GF GA   42.00
#=GF TC   43.70
#=GF NC   35.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   10438832
#=GF RT   Point mutations in the avian sarcoma/leukosis virus 3' untranslated region
#=GF RT   result in a packaging defect.
#=GF RA   Aschoff JM, Foster D, Coffin JM
#=GF RL   J Virol 1999;73:7421-7429.
#=GF CC   This family represents the direct repeat 1 (dr1) element commonly found in
#=GF CC   the 3' UTR of Avian sarcoma, Rous sarcoma and Avian leukosis viruses
#=GF CC   (Alpharetroviruses and Avian type C retroviruses). dr1 is required for
#=GF CC   efficient viral replication and is thought to be involved in genomic RNA
#=GF CC   packaging although this may not be its only role [1].
#=GF WK   Retrovirus_direct_repeat_1_(dr1)
#=GF SQ   26


V01197.1/6897-6989   UGUAACGGGGCAAGGCUUGACCGAGGGGACUAUAACAUGUAUAGGCGAAAAGCGGGGUCUCGGUUGUAACGCGC-UUAGGAAGUCCCC-UCGAGG
X13818.1/316-408     UGUAACGGCGCAAGGCUUGACCGAGGGGACUAUAACAUGUAUAGGCGAAAAGCGGGGUCUCGGUUGUAACGCGC-UUAGGAAGUCCCC-UCGAGG
X03982.1/371-460     UGUAACGGGGCAAGGCUUGACCGAGGGGACUAUAACAUGUAUAGGCGUCAAGCGGGGCUUCGGUUGUA-CGCGG-AUAGGAA-UCCCC-UC-AGG
K03366.1/170-260     UGUAACGGG-CAAGGCUUGACUGAGGGGACAAUAGCAUGUUUAGGCGAAAAGCGGGGCUUCGGUUGUA-CGCGG-UUAGGA-GUCCCCCCUCAGG
M84475.1/1968-2057   UGUAACGGGGCAAGGCUUGACUGAGGGGACAAUAGCAUGUUUAGGCGAAAAGCGGGGCUUCGGUUGUA-CGCGG-UUAGGA-GUCCCC-UC-AGG
AF257656.1/1847-1936 UGUAACGGGGCAAGGCUUGACUGAGGGGACCAUAGUAUGUAUAGGCGAAAGGCGGGGCUUCGGUUGUA-CGCGG-UUAGGA-GUCCCC-UC-AGG
J02295.1/297-386     UGUAACGGGGCAAGGCUUGACUGAGGGGACUACAGUAUGUAUAGGCGAAAGGCGGGGCUUCGGUUGUA-CGCGG-UUAGGA-GUCCCC-UC-AGG
V01170.1/3359-3448   UGUCACGGGACAAGGCUUGACUGAGGGGACCAUAGCAUGUAUAGGCGAAAAGCGGGGCUUCGGUUGUA-CGCGG-UUAGGA-GUCCCC-UC-AGG
M16580.1/249-338     UGUAACGGGGCAAGGCUUGACUGAGGGGACAAUAGUAUGUUUAGGCGAAAAGCGGGGCUUCGGUUGUA-CGCGG-UUAGGA-GUCCCC-UC-AGG
AF052428.1/6961-7050 UGUAACGGGGCAUGGCUUAACUAAGGGGACUAUAGCAUGUAUAGGCGCAAAGCGGGGUUUCGGUUGUA-CGCGA-UUAGGA-GUCCCC-UU-AGG
AF257655.1/1847-1936 UGUAACGGGGCAAGGCUUGACUGAGGGGACCAUAGUAUGUAUAGGCGAAAGGCGGGGCUUCGGUUGUA-CGCGG-AUAGGA-AUCCCC-UC-AGG
K03523.1/182-271     UGUAACGGGGCAAGGCUUGACUGAGGGGACUACAGUAUGUAUAGGCGAAAGGCGGGGCUGCGGUUGUA-CGCGG-AUAGGA-AUCCCC-UC-AGG
D10652.1/6928-7017   UGUAACGGGGCAUGGCUUAACUAAGGGGACUAUGGCAUGUAUAGGCGCAAAGCGGGGUUUCGGUUGUA-CGCGA-UUAGGA-GUCCCC-UU-AGG
U41726.1/76-165      UGUAACGGGGCAUGGCUUAACUAAGGGGACUAUGGCAUGUAUAGGCGAAAAGCGGGGCUUCGGUUGUA-CGCGG-UUAGGA-GUCCCC-UC-AGG
U41729.1/76-165      UGUAACGGGGCAUGGCUUAACUAAGGGGACUAUGGCAUGUAUAGGCGCAAAGCGGGGUUUCGGUUGUA-CGCGG-UUAGGA-GUCCCC-UU-AGG
L29199.1/784-873     UGUAACGGGACAUGGCUUAACUAAGGGGACUAUGGCAUGUAUAGGCGCAAAGCGGGGUUUCGGUUGUA-CGCGA-UUAGGA-GUCCCC-UU-AGG
AF307952.1/1793-1882 UGUAACGGGGCAAGGCUUGACUGAGGGGACUGUAGCAUGUAUAGGCGUUGUGCGGGGCUUCGGUUGUA-CGCGG-AUAGGA-AUCCCC-UC-AGG
M16584.1/52-141      UGUAACGGGGCAUGGCUUAACUAAGGGGACUAUGGCAUGUAUAGGCGCAAAGCGGGGCUUCGGUUGUA-CGGGG-UUAGGA-GUCCCC-UC-AGG
J02024.1/209-298     UGUAACGGGGCAUGGCUUAACUAAGGGGACUAUGGCAUGUAUAGGCGCAAAGCGGGGCUUCGGUUGUA-CGCGG-UUAGGA-GUCCCC-UC-AGG
K00928.1/783-870     UGUAACGGGGCAUGGCUUAACUAAGGGGACUAUGGCAUGUAUAGGCGCAAAGCGGGGUUACG---GUA-CGCGACUUAGGA-GUCCCC-UU-AGG
Z46390.1/7266-7355   UGUAACGGGGCAAGGCUUGACUGAGGGGACUGCAGCAUGUAUAGGCGCUGGGCGGGGCUUCGGUUGUA-CGCGG-AUAGGA-AUCCCC-UC-AGG
AF307951.1/1793-1882 UGUAACGGGACAAGGCUUGACUGAGGGGACUGUAGCAUGUAUAGGCGCUGUGCGGGGCUUCGGUUGUA-CGCGG-AUAGGA-AUCCCC-UC-AGG
M14897.1/772-861     UAUAACGGGGCGGGGCUUGGCCGAGGGGACUGUAACAUGUAUAGGCGAAAAGCGGGGCUGCGGUUAUA-CGCGG-AUAGGA-AUCCCC-UC-AGG
AF307949.1/2012-2101 UGUAACGGGGCAAGGCUUGACUGAGGGGACUGCGGCAUGUAUAGGCGCUGGGCGAGGUUUCGGUUGUA-CGCGG-RUAGGA-AUCCCC-UC-AGG
AY027920.1/7037-7126 UGUGACGGGGCAAGGCUUGACUGAGGGGACCAUACUAUGUAUAGGCGCUGGGCGGGGCUUCGGUUGUA-CGCGG-AUAGGA-AUCCCC-UC-AGG
AF305091.1/1768-1857 UGUGACGGGGCAAGGCUUGCCUGAGGGGACCAUACUAUGUAUAGGCGCUGGGCGGGGCUUCGGUUGUA-CGCGG-AUAGGA-AUCCCC-UC-AGG
#=GC SS_cons         <<<______>>>----------<<<<<<<<<----------<<<<<<----<<<<________>>>>-.-->>>.>>>-->.>>>>>>.>>.:::
#=GC RF              uGuAACGGGgCaaGGCUUgACUgaGGGGacuAUagcAUGUAuaggCGaaAagCggGGcUUCGGuuGuA.CGCGc.cuaGGa.guCCCC.uc.AGG
//
# STOCKHOLM 1.0

#=GF AC   RF00215
#=GF ID   Tombus_3_III
#=GF DE   Tombus virus defective interfering (DI) RNA region 3
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:12477830
#=GF SS   Published; PMID:12477830
#=GF GA   35.00
#=GF TC   37.80
#=GF NC   34.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   12477830
#=GF RT   An internally located RNA hairpin enhances replication of Tomato bushy
#=GF RT   stunt virus RNAs.
#=GF RA   Ray D, White KA
#=GF RL   J Virol 2003;77:245-257.
#=GF CC   This family represents region 3 of the defective interfering (DI) RNA
#=GF CC   element of the Tombus viruses and is found in the 3' UTR. This family has
#=GF CC   been found to enhance DI RNA accumulation by approximately 10-fold as well
#=GF CC   as mediating viral replication [1].
#=GF WK   Tombus_virus_defective_interfering_(DI)_RNA_region_3
#=GF SQ   28


AJ607402.1/4365-4434 AGCGAGUAAGACAGACUCUUCAGUCUGAUGUUACGGAGAUGAGUAGAACAAAGUGA--GGGACUAUGGGUUA
S43932.1/304-370     AGCUAGUAGGACAGACUCUUCAGUCUAGGUUGGUGGAAGCAGGAGAA--CACUGC---UUGACUAGCGGAGA
D00719.1/304-372     AGCUAGUAGGACAGACUCUUCAGUCUAGGUUGGUGGAAGCAGGAGAA--CA-CUGCUUGAGGGUACAGGUUU
X15511.1/4355-4423   AGCGAGUAGGACAGACUCUUCAGUCUAGGUUGGAGGAAGCAGGAGAA--CA-CUGCUUGAGGGUACAGGUUA
AY370535.1/1734-1802 AGCGAGUAAGACAGACUCUUCAGUCUGAUACUGCCGAAGCGAGUGAA--UA-CUGUUUGAGCAUGCAGGUUA
M59042.1/351-420     ACACCUGACUCCAGACUCUUCAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
M59041.1/395-461     AGAGA-AAAGACAGACUU--CAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
AY830918.1/4354-4422 AGCGAGUAAGACAGACUCUUCAGUCUGAGUUGGUGGAUGUGAGUGU---ACUUUGUUUGAGCAUACAGGUUA
AJ288944.1/511-579   AGCGAGUAAGACAGACUCUUCAGUCUGAUUGAGUGGAAGCAAGCACU--AACCUA-GAUAGCAUGUGGGUUG
AJ288915.1/511-579   AGCGAGUAAGACAGACUCUUCUGUCUGAUUGAGUGGAAGCAAGUACU--AACCUA-GAUUGCAUGUGGGUUA
AJ288918.1/511-579   AGCGAGUAAGACAGACUCUUCUGUCUGAUUGAGUGGAAGCAAGUACU--AACCUA-GAUAGCAUGUGGGUUA
AJ288934.1/511-579   AGCGAGUAAGACAGACUCUUCAGUCUGAUUGAGUGGAAGCAAGCACU--AACCUA-GAUAGCAUGUGGGUUA
AY579432.1/4388-4457 AGCGAGUAAGACAGACUCUUCUGCCUGAGUUCGCGGAUACAAGUGUG--AAUCUAACAACGCAUACAGGUUA
AF241533.1/266-335   AGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGCGGAAACGAGUGUA--AAGCGGGCAUAGCAUACAGGUUA
AJ249740.1/4393-4462 AGCGAGUAAGACAGGCUCUUCAGUCUGAGUUCGCGGAAACGAGUGUG--AAUCUGACAACGUAUGCAGGUUA
Z68900.1/543-612     AGCGAGUAAGACAGACUCUUCAGUCUGAGUUCGCGGAUAUGAGUGUG--AAUCUGACAACGCAUACAGGUUA
Z68899.1/543-611     AGCGAGUAAGACAGACUCUUCAGUCUGAGUUCGCGGAAACGAGUGUA--AAUCUG-CAUAGCAUACAGGUUA
Z68897.1/540-609     AGCGAGUAAGACAGACUCUUCAGUCUGAGUGCGCGGAAACGAGUGUA--AAUCUGGCAACGCAUACAGGUUA
M59049.1/382-451     GGUGAGUAAGACAGACUCUUCAGUCUGAGUUUGUGAAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
X62493.1/4413-4482   AGCGAGUAGGACAGACUCUUCAGUCUGAUUCUGUGGAAAUGAGAGUA--AUUCUGACAUAGCAUACAGGUUA
AF038044.1/352-421   GGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGCGGAAACGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
M59045.1/400-469     CGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
AJ288945.1/511-580   GGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
AJ288943.1/511-580   AGCGAGUAAGACAGACUCUUCUGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
U80935.1/4399-4468   AGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGCGGAAACGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
M59043.1/392-461     AGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
M59046.1/399-468     AGCGAGUAAGACAGACUCUUCAGUCUGAGUUUGUGGAGAUGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
X85215.3/4385-4454   AGCGAGUAAGACAGACUCUUCAGUCUGAGUUCGCUGAAACGAGUGUA--AAUCUGGCAUAGCAUACAGGUUA
#=GC SS_cons         ::::::::::<<<<<<<<________>>>>>>>>-------------..<<<<<<__________>>>>>>:
#=GC RF              AGCGAGUAAGaCagACUCUUCAGUCUGAGUuuGuGGAaAcGAGUGuA..aAcCuGgcAuAGcAUACaGgUuA
//
# STOCKHOLM 1.0

#=GF AC   RF00216
#=GF ID   IRES_c-myc
#=GF PI   c-myc_IRES
#=GF DE   c-myc internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:11419940
#=GF SS   Published; PMID:11419940
#=GF GA   40.00
#=GF TC   41.40
#=GF NC   38.50
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11419940
#=GF RT   Derivation of a structural model for the c-myc IRES.
#=GF RA   Le Quesne JP, Stoneley M, Fraser GA, Willis AE
#=GF RL   J Mol Biol 2001;310:111-126.
#=GF CC   This family represents the c-myc internal ribosome entry site (IRES). The
#=GF CC   mammalian c-myc gene is a proto-oncogene which is required for cell
#=GF CC   proliferation, transformation and death. c-myc mRNA has an alternative
#=GF CC   method of translation via internal ribosome entry where ribosomes are
#=GF CC   recruited to the IRES located in the 5' UTR thus bypassing the typical
#=GF CC   eukaryotic cap-dependent translation pathway [1].
#=GF WK   c-myc_internal_ribosome_entry_site_(IRES)
#=GF SQ   23


M38057.1/1331-1632     AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUCGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
X00364.2/2502-2803     AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
M88115.1/1007-1310     AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGGUCGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUCCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCCGGCCCAGCCCUUCCGCU-GACCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCUUAUUCUGCCCAUUUGGAGACACUUCCCCGCCGC
K00559.1/358-661       AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCUUGAUCCCC-CAGGCCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCUCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
L00057.1/823-1123      AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUC-CGUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGCGGGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCC-GACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
BC000917.2/3-304       AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
S65124.1/279-580       AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGACCUCCCGCU-GAUGCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCUCUUUGC-ACUGGAACUUACAACACCCGAGUAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
M16261.1/1856-2157     AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGUGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAA-CCAGC-GGUCCGCAACCCUUGUCGCAUCCACGAAA-CUUUGUCCAUAGCAGCGGGCGGACACUUUGC-ACUGGAACUUACAACACCCGAGCAAAGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
V00568.1/162-465       AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCUUGAUCCCC-CAGGCCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
J03253.1/1772-2073     AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
M88116.1/1311-1614     AAUUUCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGGCAGGCGAGGGUGGAAGAGCCGGGCGAGCCGAGCUGCGCUCCGGGCGUCCUGGGAAGGGAGAUCCGAAGUGAAAAGGGGGCUUCGCCUCCGGUCCAGCCCUCCCGCU-GACCCCCGCAG-CCAGC-AGCCCACAACCCUCGCCGCAUCCACGAAA-CUUUGCCCUUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCUAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUCCCCAUUUGAGGACACCUCCCCGCCGC
AY232835.1/377-679     AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGGCCGGCGAGGGUGGAAGAUCCGGGCGAGCAGAGCUGCACCUCGGGCGUCGUGGGAAGGGAGAUACGGAGCGAAAAGGGGGCUUCGCCUCCGGCCCAGCCCUCCCGCU-GACCCCC-CAG-ACAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGGGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCUAGCAAGGACGCUACUCUCCCGACGCGGGGAGGCU-AUUCUGCCUAUUUGGGGACACUUCCCCGCCGC
X00196.1/545-846       AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUACGACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCC-GACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
M12026.1/524-823       AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCG--GCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUC-CGUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGCGGGUCCGCAACCCUUGCCGCAUCCACGAAAACUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCC-GACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
M20605.1/1774-2075     AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-CGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
K03015.1/568-869       AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
K02275.1/109-410       AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUGGCCUCUGUCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACAUUUCCCCGCCGC
AC103819.3/87828-88129 AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
M22633.1/506-807       AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCCGCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGCGGGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCCGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCC-GACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
AY214166.1/2047-2348   AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
M14206.1/279-580       AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
D10493.1/2500-2801     AAUUCCAGUGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGACCUCCCGCU-GAUCCCC-CAG-GCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGACACUUUGC-ACUGGAACUGACAACACCCGACCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
J04105.1/824-1125      AAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGC-CGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGUAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCU-GAUCCCC-CAG-CCAGC-GGUCCGCAACCCUUGCCGCAUCCACGAAA-CUUUGCCCAUAGCAGCGGGCGGGCACUUUGC-ACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCU-AUUCUGCCCAUUUGGGGACACUUCCCCGCCGC
#=GC SS_cons           :::::::::::::((((-((((-----((((((-((.-((((-(((-(((------((((,<<<___>>>,<<<<-<<<<--<<<<_____>>>>-->>>>->>>>,,,,,,<<<<<__AAAA__>>>>>,))))-BBBBBB.B-))))).))).))-)).-))))))--))))))))------------.------------bbbbbbb-aaaa-------.-------------------------------------------<<<<<<<<<--.------<<<____>>>---->>>>>>>>>:::
#=GC RF                AAUUcCAGCGAGAGGCaGaGGGAGCGAGCGGgCGGC.cGgCuAGGGUGGaAGAGCCGGgCGaGCAGAGCuGCGCugCGGgCGuCCuGGGAAgGGaGAuCCGGaGCGAAuAGGGGGcuUcGccUCuggCCCAGcCCUCCCGCU.GAuCCCC.CaG.cCAGC.gGcCCGCAACCCuuGCCGCAUCCACGAAA.CUUUGCCCAUAGCAGcGGGCGGGCACUUUGC.ACUGGAACUUACAACACCCgAGCAAGGACGCGACUCUCCCGACGCGGGGagGCU.AUUCUGCCCAUUUGGGGACACcuCCCCGCCGC
//
# STOCKHOLM 1.0

#=GF AC   RF00217
#=GF ID   SNORD20
#=GF PI   U20
#=GF DE   Small nucleolar RNA SNORD20
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; Griffiths-Jones SR
#=GF GA   43.00
#=GF TC   45.40
#=GF NC   42.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Gallus_gallus300108;
#=GF DR   snoopy; Loxodonta_africana300061;
#=GF RN   [1]
#=GF RM   8065311
#=GF RT   U20, a novel small nucleolar RNA, is encoded in an intron of the nucleolin
#=GF RT   gene in mammals.
#=GF RA   Nicoloso M, Caizergues-Ferrer M, Michot B, Azum MC, Bachellerie JP
#=GF RL   Mol Cell Biol 1994;14:5766-5776.
#=GF CC   U20 is a C/D box small nucleolar RNA that is encoded in intron 11 of the
#=GF CC   nucleolin gene in human, mouse and rat [1].
#=GF WK   Small_nucleolar_RNA_SNORD20
#=GF SQ   13


M55020.1/3865-3944           UGGAUAU-GAUGAC--UGAUU-ACCUGAGAAAUAACUGAUGAAAUCUCAAGAAAAUUCCUCUAGAUAGUCAAGUUCUGAUCCAG
X07699.1/9160-9239           UGGAUAU-GAUGAC--UGAUU-ACCUGAGAAAUAAUUGAUGAAAUCUCAAGAAAAUUCCUCUAGAUAGUCAAGUUCUGAUCCAG
Z34290.1/1-80                UGGAUAU-GAUGAC--UGAUU-ACCUGAGAAAUAAUUGAUGAAAUCUCAAGAAAAUUCCUCUAGAUAGUCAAGUUCUGAUCCAG
M60858.1/8893-8973           UGGAUAUCGAUGAC--UGAUU-ACCUGAGAAAUAAUUGAUGAAAUCUCAAGAAAAUUCCUCUAGAUAGUCAAGUUCUGAUCCAG
AALT01279659.1/1038-1117     UGGAAAU-GAUGAU--UGAUU-AUCUGAGAAAUAAUUGAUGAAAUAUCAAGAAAAUUCCUCUAGAUAGUCAAGUUCUGAUCCAG
AAIY01780739.1/8204-8283     UGGACAU-GAUGAC--UGCUU-AUCUGAGAAGUAACUGAUGAAAUCACAAGAAAAUUCCUCUAGAUAGUCAAGUUCUGAUCCAC
AANN01153174.1/4376-4454     UGGAUGU-GAUGAU--UGAUU-AUCUGAGUAA-AACUGAUGAAAAAUCAAGAAAAGUCCUCUAGAUAGUCAAGUUCUGAUCCAG
AAFR03061959.1/14282-14204   UGGAUAU-GAUGAC--UCAUU-AUCUGAGAAUUG-CUGAUGAAACCUCCAGAAAAUUCCUCUAGAUAGUCAAGUUCUGAUCCAG
AAPN01359272.1/1875-1798     UGGAUAU-GAUGAC--UGAUU-AUCUGAGACA-AACUGAUGAAACCAAUA-AAAAUUCCUCUAGAUAGUCAAGUUCUGAUCCAC
AAWR02034600.1/36900-36819   UGGACAU-GAUGACUAUGAUU-AUCUGAGAAAUUAUUGAUGAAAUCUCAAGAAAAUUCCUCUAGAUAGUCAAGUUCUGAUCCAG
AAGW02043063.1/1428-1350     UGGAUAU-GAUGAC--AGACG-GCCUGAGAAGGAA-UGAUGAAAUCUCGAGAGAAUUCCUCUAGAUAGUCAAGUUCUGAUCUGG
AAGU03069695.1/15515-15594   UGGACAU-GAUGAC--UGAUUUAUCUGAGAAAUAAUUGAUGAACCUCAAGAAAAUU-CCUCUAGAUAGUCAAGUUCUGACCCAG
AADN03005880.1/225882-225806 UGGAUAU-GAUGAC--UGAUU-AUCUGA---AAUGCUGAUGAAACCACUUCUAAAGUCCUCUAGAUAGUCAAGUGCUGAUCCAG
#=GC SS_cons                 <<<<___.______.._____._________________________________________________________>>>>:
#=GC RF                      UGGauAU.GAUGAC..UGAUU.AuCUGAGAAAuAAuUGAUGAAAucucaAgAAAAUUCCUCUAGAUAGUCAAGUUCUGAuCCAG
//
# STOCKHOLM 1.0

#=GF AC   RF00218
#=GF ID   SNORD46
#=GF PI   U40
#=GF DE   Small nucleolar RNA SNORD46
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; Griffiths-Jones SR
#=GF GA   40.00
#=GF TC   43.10
#=GF NC   39.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00061
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300956;
#=GF DR   snoopy; Spermophilus_tridecemlineatus300291;
#=GF RN   [1]
#=GF RM   8764399
#=GF RT   Intron-encoded, antisense small nucleolar RNAs: the characterization of
#=GF RT   nine novel species points to their direct role as guides for the
#=GF RT   2'-O-ribose methylation of rRNAs.
#=GF RA   Nicoloso M, Qu LH, Michot B, Bachellerie JP
#=GF RL   J Mol Biol 1996;260:178-195.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   U40 is a C/D box small nucleolar RNA, also known as snoZ153 in plants. The
#=GF CC   human sequence has also been annotated in the sequence databases as U46.
#=GF CC   U40 is encoded in intron 2 of the ribosomal protein S8 gene in human, and
#=GF CC   is hypothesised to guide methylation of 2'-O-ribose residues on 28S
#=GF CC   ribosomal RNA [1]. This family represents vertebrate U40.
#=GF WK   Small_nucleolar_RNA_SNORD46
#=GF SQ   5



HQ318014.1/785-888 AACUGGAGUGAUGAAAAAGUAUCCUUAGGCGUGGUUGUGGCCGUCUUGGCCACCUUUGUGCCACUUGCCA-GUGCUAGGACUUGUCAUAGUUACACUGACUGUGU
X96646.1/1-98      --GUAGGGUGAUGAAAAAGAAUCCUUAGGCGUGGUUGUGGCCGUCUUGGUCACCUGUGUGCCACUUGCCA-AUGCAAGGACUUGUCAUAGUUACACUGACU----
Z69628.1/1-100     --GUAGGGUGAUGAAAAAGAAUCCUUAGGCGUGGUUGUGGCCGUCUUGGUCACCUGUGUGCCACUUGCCA-AUGCAAGGACUUGUCAUAGUUACACUGACUGU--
X67247.1/1141-1244 AAGUAGGGUGAUGAAAAAGAAUCCUUAGGCGUGGUUGUGGCCGUCUUGGUCACCUGUGUGCCACUUGCCA-AUGCAAGGACUUGUCAUAGUUACACUGACUGUUG
X94604.1/82-186    AACUAGGGUGAUGAAAACGUAUCCUUAGGCGUGGUUAUGGCCGUCUUGGCCACCUGUACACACACUUGCCAAUGCAAGGACUUGUCAUAGUUACACUGACUGUAA
#=GC SS_cons       <<<<<<________________________________________________________________.____________________________>>>>>>
#=GC RF            aaguaGGGUGAUGAAAAaGaAUCCUUAGGCGUGGUUgUGGCCGUCUUGGuCACCUgUgUgCcacUUgcCa.AUGCAAGGACUUGUCAUAGUUACACUGACugcuu
//
# STOCKHOLM 1.0

#=GF AC   RF00220
#=GF ID   Rhino_CRE
#=GF DE   Human rhinovirus internal cis-acting regulatory element (CRE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:9848654
#=GF SS   Published; PMID:9848654
#=GF GA   45.00
#=GF TC   47.40
#=GF NC   40.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   9848654
#=GF RT   The rhinovirus type 14 genome contains an internally located RNA structure
#=GF RT   that is required for viral replication.
#=GF RA   McKnight KL, Lemon SM
#=GF RL   RNA 1998;4:1569-1584.
#=GF CC   This family represents a cis-acting regulatory element (CRE) from the
#=GF CC   human rhinoviruses. The CRE is located within the genome segment encoding
#=GF CC   the capsid proteins so is found in a protein coding region. The family has
#=GF CC   been found to be essential for efficient viral replication and it has been
#=GF CC   suggested that the CRE is required for initiation of minus-strand RNA
#=GF CC   synthesis [1].
#=GF WK   Human_rhinovirus_internal_cis-acting_regulatory_element
#=GF SQ   12


AY355264.1/1-86    GGCCUCAAUGAUGAAUUAGAGGAAGUUAUUGUCGAGAAAACGAGACAGACUUUAGCUUCCGUUGCAUCAGGACCAAAACACACCCA
AY355187.1/1-86    GGAUUGGGUGAUGAAUUAGAAGAAGUUAUUGUCGAGAAAACGAAACAGACACUAGCUUCAGUAUCAUCAGGACCAAAACACACCCA
AY355260.1/1-86    GGUCUUAAUGAUGAAUUAGAAGAGGUCAUUGUCGAGAAAACGAGACAGACAUUGGCCUCUGUUUCUUCUGGACCUAAACAUACACA
AY355273.1/1-86    GGUCUUAAUGAUGAAUUGGAGGAAGUCAUUGUUGAGAAAACGAAACAGACAUUGGCUUCUAUCACUUCUGGACCCAAACAUACUCA
AY355253.1/1-86    GGUUUGAAUGACGAGUUAGAGGAAGUCAUCGUCGAGAAAACGAAACAGACGUUGGCUUCAAUUUCAUCCGGGCCAAAAUACACUCA
AY355218.1/1-86    GGUCUGGGUGAUGAACUGGAAGAAGUUAUUGUUGAGAAAACGAAACAGACACUAGCUUCAAUAUCAUCAGGACCUAAGCAUACCCA
AY355267.1/1-86    GGGUUGGGAGAUGAACUAGAGGAAGUCAUAGUCGAAAAAACGAAACAGACGUUGGCUUCAGUUGCAACAGGUUCAAAAUAUACCCA
L05355.1/2330-2415 GGCUUAGGUGAUGAAUUAGAAGAAGUCAUCGUUGAGAAAACGAAACAGACGGUGGCCUCAAUCUCAUCUGGUCCAAAACACACACA
X01087.1/2326-2411 GGCUUAGGUGAUGAAUUAGAAGAAGUCAUCGUUGAGAAAACGAAACAGACGGUGGCCUCAAUCUCAUCUGGUCCAAAACACACACA
AY355195.1/1-86    GGCUUAGGUGAUGAAUUAGAAGAAGUCAUCGUUGAGAAAACGAAACAGACGGUGGCCUCAAUCUCAUCUGGUCCAAAACACACACA
K02121.1/2330-2415 GGCUUAGGUGAUGAAUUAGAAGAAGUCAUCGUUGAGAAAACGAAACAGACGGUGGCCUCAAUCUCAUCUGGUCCAAAACACACACA
AY355216.1/1-86    GGCUUGGGAGAAGAGCUUGAGGAAGUCAUUGUCGAGAAAACGAAACAGACAGUGGCUUCAAUUGCUUCUGGAUCUAAACACACCCA
#=GC SS_cons       <<-<<<<<<<<----------<<-<<<<<<<<<______________>>>>>>>>>->>---->>>>>>>>->>::::::::::::
#=GC RF            GGucucGauGaUGAAUUaGAaGAAGucAccGUcGAGAAAACGAAACAgACggUggCuUCaaUuuCauCgggaCCaAAAcAcACaCA
//
# STOCKHOLM 1.0

#=GF AC   RF00221
#=GF ID   SNORD43
#=GF PI   U43
#=GF DE   Small nucleolar RNA SNORD43
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; Griffiths-Jones SR
#=GF GA   45.00
#=GF TC   45.40
#=GF NC   44.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00059
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300740;
#=GF DR   snoopy; Loxodonta_africana300493;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [2]
#=GF RM   10684968
#=GF RT   The intron-containing L3 ribosomal protein gene (RPL3): sequence analysis
#=GF RT   and identification of U43 and of two novel intronic small nucleolar RNAs.
#=GF RA   Duga S, Asselta R, Malcovati M, Tenchini ML, Ronchi S, Simonic T
#=GF RL   Biochim Biophys Acta 2000;1490:225-236.
#=GF CC   U43 is a C/D box small nucleolar RNA that is encoded in intron 1 of the
#=GF CC   ribosomal protein L3 gene in human and cow [2]. Three other snoRNAs ( U82,
#=GF CC   U83a and U83b) are also encoded in the same host gene but from different
#=GF CC   introns [2]. The rice homologue is expressed from a cluster also
#=GF CC   containing snoR16 [1]. The Arabidopsis homologue is annotated as snoR41 in
#=GF CC   the sequence databases. U43 is hypothesised to guide methylation of
#=GF CC   2'-O-ribose residues on 18S ribosomal RNA [1]. This family represents
#=GF CC   mammalian U43.
#=GF WK   Small_nucleolar_RNA_SNORD43
#=GF SQ   4


AJ238853.1/1-62        CACAGAUGAUGAACUUAUUGACGGGCGGACAGAAACUGUGUGCUGAUUGUCACGUUCUGAU-U-
X96642.1/1-62          CACAGAUGAUGAACUUAUUGACGGGCGGACAGAAACUGUGUGCUGAUUGUCACGUUCUGAU-U-
AP001324.4/95881-95819 ACAG-AUGAUGAACUCAUUGACAGACAUACAGAGACUGUGUGCUGAUUGUCAUGUUCUGACUUA
AJ238851.1/484-547     CAGAAAUGAUGAACUUACUGACGGGCGGACAGAGACACUGUGCUGAUUGUCAGGUUCUGAUUUG
#=GC SS_cons           <<<<________________________________________________________>>>>
#=GC RF                caaagAUGAUGAACUUAUUGACGGGCGgACAGAgACUgUGUGCUGAUUGUCAuGUUCUGAuuug
//
# STOCKHOLM 1.0

#=GF AC   RF00222
#=GF ID   IRES_Bag1
#=GF PI   Bag1_IRES
#=GF DE   Bag-1 internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   http://ifr31w3.toulouse.inserm.fr/IRESdatabase/, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   36.90
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11494137
#=GF RT   The p36 isoform of BAG-1 is translated by internal ribosome entry
#=GF RT   following heat shock.
#=GF RA   Coldwell MJ, deSchoolmeester ML, Fraser GA, Pickering BM, Packham G,
#=GF RA   Willis AE
#=GF RL   Oncogene 2001;20:4095-4100.
#=GF CC   This family represents the bag-1 internal ribosome entry site (IRES). When
#=GF CC   expressed the BAG-1 protein is known to enhance the anti-apoptotic
#=GF CC   properties of Bcl-2. Although bag-1 translation usually occurs via a
#=GF CC   cap-dependent mechanism it has been found to contain a IRES in its 5' UTR.
#=GF CC   Translation via the IRES has been found to be common following heat shock
#=GF CC   when cap-dependent scanning is compromised [1].
#=GF WK   Bag-1_internal_ribosome_entry_site_(IRES)
#=GF SQ   15


AF022224.1/24-393          UGGGCGGUCAACAAGU-GCGGGCCUGGCUCAGCGCGGGGGGGCGCGGAGA-CCGCGAGGCGACCGGGAGCGGCUGGGUUCCCGGCUGCGCGCCCUUCGGCC-AGGCCGGGAGCCGCGCCAGUCGGAGCCCCCGGCCCAGCGUGGUCCGCCUCC-C---UCUCGGCGUCCACCUGCCCGGAGUACUGCCAGCGGGCAUGACCGACCCACCAGGGGCGCCGCCGCCGGCGCUCGCAGGCCGCGGAUG---AAGAAGAAAACCCGGCGCCGCUCGACCCGGAGCGAGGAGUU---GACCCGGAGCGAGGAGUUGACCCUGAGUGAGGAAGCGACCUGGAGUGAAGAGGCGACC------CAGAGUGAGGAGGCGACCCAGGGCGAAGAGAUG
U46917.1/26-395            UGGGCGGUCAACAAGU-GCGGGCCUGGCUCAGCGCGGGGGGGCGCGGAGA-CCGCGAGGCGACCGGGAGCGGCUGGGUUCCCGGCUGCCCCCCCUUCGCCC-AGCCCGGGAGCCGCCCCAGUCGGAGCCUCCGGCCCAGCGUGGUCCGCCUCC-C---UCUCGGCGUCCACCUGCCCGGAGUACUGCCAGCGGGCAUGACCGACCCACCAGGGGCGCCGCCGCCGGCGCUCGCAGGCCGCGGAUG---AAGAAGAAAACCCGGCGCUUCUCGACCCGGAGCAAGGAGUU---GACCCGGAGCAAGGAGUUGACCCUGAGUGAGGAAGCGACCUGGAGUGAAGAGGCGACC------CAGAGUGAGGAGGCGACCCAGGGCGAAGAGAUG
Z35491.1/44-413            UGGGCGGUCAACAAGU-GCGGGCCUGGCUCAGCGCGGGGGGGCGCGGAGA-CCGCGAGGCGACCGGGAGCGGCUGGGUUCCCGGCUGCGCGCCCUUCGGCC-AGGCCGGGAGCCGCGCCAGUCGGAGCCCCCGGCCCAGCGUGGUCCGCCUCC-C---UCUCGGCGUCCACCUGCCCGGAGUACUGCCAGCGGGCAUGACCGACCCACCAGGGGCGCCGCCGCCGGCGCUCGCAGGCCGCGGAUG---AAGAAGAAAACCCGGCGCCGCUCGACCCGGAGCGAGGAGUU---GACCCGGAGCGAGGAGUUGACCCUGAGUGAGGAAGCGACCUGGAGUGAAGAGGCGACC------CAGAGUGAGGAGGCGACCCAGGGCGAAGAGAUG
BC001936.1/27-396          UGGGCGGUCAACAAGU-GCGGGCCUGGCUCAGCGCGGGGGGGCGCGGAGA-CCGCGAGGCGACCGGGAGCGGCUGGGUUCCCGGCUGCGCGCCCUUCGGCC-AGGCCGGGAGCCGCGCCAGUCGGAGCCCCCGGCCCAGCGUGGUCCGCCUCC-C---UCUCGGCGUCCACCUGCCCGGAGUACUGCCAGCGGGCAUGACCGACCCACCAGGGGCGCCGCCGCCGGCGCUCGCAGGCCGCGGAUG---AAGAAGAAAACCCGGCGCCGCUCGACCCGGAGCGAGGAGUU---GACCCGGAGCGAGGAGUUGACCCUGAGUGAGGAAGCGACCUGGAGUGAAGAGGCGACC------CAGAGUGAGGAGGCGACCCAGGGCGAAGAGAUG
AANU01165073.1/8677-8308   UGGGCGGUCAACAAGC-GCGGGCCUGGCUCAACGCGGCGGGGCGAGGAGA-CCACGAGGCGACCGGGAGCGGCUGGGCUCUCGGCUGCGCGCCCUUCGGCC-AGGCCGGGAGCCGCGCCAGUCGGAGCCCCCGGCCCAGCGUGGCCCGCCUCC-C---UCUCGGCGUCCACCUGUCCGGGGUGCUGCCAGCGGGCAUGACCGACCCACCAGGGGCGCCGCCGCCGGCGCUCGCAGGCCGCGGAUG---AAGAAGAAGACCCGGCGCCGCUCGACCCGGAGCGAGGAAUU---GACCCGGAGCGAGGAGUUGACCCUGAGUGAGGAGGCAACGCGGAGCGAAGAGGCGACC------CAGAGUGAGGAGGCGACUCGGAGCGAAGAGAUG
AAFC03121736.1/15849-15477 UGGGCGGGCGACAAGC-GCGGGUCUGGCGGAGCGCGGGGGCGCGCGAAGACCCGCGAGGCGACCGGGAGCGGCUGGGUCCCCGGCGGCGCGCGCCUCGGCCCGGGCCGGGAGCCGCGCCAGUCGGUGCCCCCAGCCGAGCGCGGUCCGCCUCCCC---UCCCAGAAAUCUGCCGUCCGGAGCGUGACCAGAGGGCAUGCCGGAUCCACCAGAGGCGCCGCCGCCUGCGCUCGCAGGCCGCGGGUG---AAAAAGAAAGCACAGCCUCGCUCGGCCCGGAGCGAAGAGGU---GUGCCGGAGCGAAGAGAUGUCCCGGAGCGAAGAGGUGGCCCCGAGCGAAGAGGUGGUC------CCGAGCGAAGAGGUGGCCCUGAGCGAAGAGGUG
AAPY01565654.1/2644-2282   UGGGCCGUCUACAAGC-GCGG-GCUUGCGGCGCGCGGCGGCGCGCGGAGA-UCUCGAGGCAACGGGGAGCGGCUGGGCCCCCGGCGGCGCGCCCCGCGGCC-UGAACCGGAGCCGCGCCGGUCGGAG------GCCGAGCGCGGCCCGCCUCC-C---UCUCAGCGCCCAUCUGUCCGGAGUCAAGCCAGCGGUCAUGACCGACCCACCAGGGGCGCCGCCACCGGCGGUCGCAGGCCGCGGGUG---AAGAAGAAAAUCCGUACCCGCUCGGCCCGGAGCGAGGAGGU---GCCUCAGAACAAGGAGGUGCCUCAGAACAAGGAGGUGCCUCGGAGCGAGGAGGUGACC------CCGAGAACGGAGGUGGCUCGGAGCGAGGAGGCG
AAHY01035212.1/17904-18281 UGCGCUGUGAACAAAC-GC-GGCCUGGCGGGUCGCAGCGCCGCGCGGCGA-CCGCGAGGCGACCGGGAGCCGCUGGGACCCAGGCUGCGCGCCCCUCGGCC-UGCCCGGGAGCCGCGCCAGUCGGAGUCCCGGGCCGAGCGGGGCUUGCCUCC-C---UCUCAGCGUUCCUCUGUGCGCAGUGCAGCCAGCGGGCAUGACCGAUCCACCAGGGGCGCCGCCGCCGGCGCCUGCAAGCCGCGGGUG---AAGAAGAAAGUCCGGCCCCGCUCUUCUCAGAGCGAGAAGGUAGGGAGCAGCAGCAGGGAGUUGACUAGAAGUAAGAAAGUGACCCGUAGCAAGAACGUGACCGGGACCCAGGUAGAGGAGGUGACCAAGAUCGAGGAGGCG
AAIY01208106.1/11195-11564 UCGGCGGUGGAGAAAC-GCGGGCCUGGCGGAGCGCGGCAGCGCGCGGAGA-CCUCGAGGCCGCGGGGAGCGGCCGGGGCCCCGGAGGCGCGCCCUUCGGCC-AGCCCGGGAGCCGUGCCAGGUCGAGACUCCGGCC---GGUCGCAAGUCUCC-CCGGUCUCAGCGUCGGUCCGUGCGAAGCAAGACCAGCGGACAUGACCGAUCCACCAGGGGCUCCGCCGCCGGCGCUCGCAAGCCGCGGGUG---AAGAAGAAAUCACAUCCCCGCAAGGCCAGGAGCGAGGAGAU---GGCCCAGAGCAAGGAGGUGGCCCGGAGAGAGGAGAUCGCCAAGAACGAAGAGGUGGCC------CCGAAAGAGGAGGCCGCCCGGAGCGCGGAGAUG
BC159418.1/30-399          UGCUCCGUGAACAAAC-GCGGGCCUGGCGGAUCGCGGCGGCGCGCGGCGA-CCGCGAGGCGACCAGGAGCCGCUGGGACCCCGGCUGCGCGCCCCUCGGUC-GGCCCGGGAGACGCGCCAGUCGGAGUCCCGGGCCGAGCGUGGCUUGCCUCC-C---UCUCAGCGUUCAUCUGUCCGCAGUGCAGCCAGCGGGCAUGACCGAUCCACCAGGGGCGCCGCCUCCGGCGCUUGCAAGCCGCGGGUG---AAGAAGAAAGUCCGGCCCCGCUCUUCUCAGAGCGAGAAGGU---AGCUCACAGCAAGGAGUUGACUAGAAGUAAGAAGUUGACCCGCAGCAAGAAAGUGACC------GGGACCCAGGAGGCGACCCAAGUAGAGGAGGUG
AAKN02030389.1/39349-38976 UGGGCGGGUCGCCAGCCGCGGGGCUGGCUGAGCACAGUAGGGUGCCGGGA-UCGCGAGGCUACCGGGAGCGGCUGGGCCGCCGGCGGCGCGCCCCUCUGCC-CUCCCGGGUGCCACGCCGGUCAGAUCCGUCGGCCCACCAACGCCCUCCUUC-C---UCUCAGCAUCCAUUUGGCUGGACUGCAGUCAGUGGACAUGACCGAUCCACCAAGGGCGCCGCCGCCGGCGCUCGCAAGCCGCAGGUCUUAAAGAAGAAAGCCCGUUCCCACACCACCCGGAGCAAGAAGGU---GGCUCAGACCAAGAAGGUGACCCCGACCAAGAAGGCGGCCCAGACCAAGAAGGUGACC------CAGACCAAGGAGGUGGCCCAGACCAAGAAGGUG
AAGW02050218.1/3032-3378   AACAACCAAAAUUCUG-GCGGGCCUGGCGGAGCGCGGCAACGCGCAGAGA-UUGCGAGGCGACCGGGGCCAGCUG-GGCCCCAGCGGCUCGCCCCUCGGCG-GGGCCGGGAGCCGCGCCAGUCGGAGCCCCUGGCUGAGGGCGGUCAGCCAGC-U---UCUCAGCGCCCAUCCCUCCGGAGAGCAGCCGGGGGGCAUGACCGACCCACC-GGGGCGCCGCCUCCGGCGCUCGCAGGCCACGGGUG---AAGAAGAAAGUCCGUACCUGCUCGGCCCGGAGUGAGGAGGA---GCCCCCGGCAGAGGAGGUGACCCC---------------------AGACGAGGUGAUC------CAGGCGGAGGAGGUGACCGAGACUAAGGAAAUG
AAEX03007939.1/85583-85217 UGGGUGGUCAACAAGC-GCGGGUCUGGCGGAGCGCGGUGGCGCGCGGAGA-CCGCGAGGCGACCGGGAGCGGCUGGGUCCCCGGCGGCGCGCCCCUCGGCC-GGGCCGGGAGCCGCGCCAGUCGGUGCUCCCGGCCGAGCGCGGUCCGCCUCC-C---UCUCAGCGAUCGUCCGCCCGGGGUGCGGCCCGCGGGCAUGCCGGAUCCACCAGGGGCGCCGCCGCCGGCGCUCGCAGGUCGCGGGU------GAAGAAAGUGCGGCCUCGCUCGGCCCGGAGCGAAGACGU---GGCCCGGAGCCAAGAGGUGACCCGAAGUGAAGAAGUGGCCCAAAGUGAAGAGGUGACC------GAGGGCCAGGAGGUGGCCCCGAGCGAGGAAAUG
AAPE02037198.1/81159-81528 UGGGCAGGCGACAAGU-GCGGGUCUGGCGGAGCGCGGUGGCGCGCGGAGA-CCGAGAGGCGACCGCGGGCGGCAGGGCCCCCGGCGGCGCGCCACUCGGCC-GGGCCGAGAGUCGCGUCAGUCGGUGUUCCCGGCCGAGCGCGGUCCGCCUCC-C---UCUCAGCGCCCAUCCGGCCUGAGGGCGGCCAGAGGGCAUGUGGGACCCCACAAGGGCGCCACCGCCGGUGCUCGCCGGCCGCGGGUG---AAGAGGAGAGUACGGCCUCACUCAACCCAGAGCAGAGAGGU---GGCCCGGAGCGAAGAGGGGUUCCGGAGCGAAGAGGGGUUCCGGAGCGAAGAGGAGGUG------CUGAGCGAAGAGGAGAUGCUGAGCGAACAGGUG
AF116273.1/1-363           U-------CAACAAGU-GCGGGCCUGGCUCAGCGCGGGGGGGCGCGGAGA-CCGCGAGGCGACCGGGAGCGGCUGGGUUCCCGGCUGCGCGCCCUUCGGCC-AGGCCGGGAGCCGCGCCAGUCGGAGCCCCCGGCCCAGCGUGGUCCGCCUCC-C---UCUCGGCGUCCACCUGCCCGGAGUACUGCCAGCGGGCAUGACCGACCCACCAGGGGCGCCGCCGCCGGCGCUCGCAGGCCGCGGAUG---AAGAAGAAAACCCGGCGCCGCUCGACCCGGAGCGAGGAGUU---GACCCGGAGCGAGGAGUUGACCCUGAGUGAGGAAGCGACCUGGAGUGAAGAGGCGACC------CAGAGUGAGGAGGCGACCCAGGGCGAAGAGAUG
#=GC SS_cons               ::::::::::::::::.:::((((((((---------((((((<<<<___.>>>>,,,,,,,<<<<<<<<______>>>>>>>>,,,,,,))))))--))).)))))---------------------------------------(((((((.,...,,,,,,,,,,,,,,<<<<<<____________>>>>>>,,,,,,,,,,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,...,,,,,,,,,,,,,,,,,,<<<<<______>>>>>,,,,,,,...,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,......,,,,,,,,)))))))::::::::::::::::::
#=GC RF                    UGgGCgGucaAcAAgc.GCGGGcCugGCggAGCGCGGcgggGCGcGGAGA.CCgCGAGGCgACCGGGggCgGCUGGGccCCCGGCgGCGCGCcccgCGGCc.aGgCCGGGAGCCGCGCCAGUCGGAGcCcCcGGCCgAGcGuGGuccgCCuCC.C...UCUCAGCGucCauCuGcCCggAGugcaGCCAGcGGgCaUGACcGAuCCACCAGGgGCGCCGCCgCCGGCGCuCGCAgGCCGCGGgUG...AAGAAGAAAgucCGgccCcgCuCgaCCCGGaGcgAGGAGgU...GaCCCgGAgCaAGGAGuUGaCCCuGAgugAGgAgGuGaCCcggAgcGAaGAGGuGAcC......CaGAgugAGGaGGcgaCccaGAgCGAgGAGaUG
//
# STOCKHOLM 1.0

#=GF AC   RF00223
#=GF ID   IRES_Bip
#=GF PI   Bip_IRES
#=GF DE   bip internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   http://ifr31w3.toulouse.inserm.fr/IRESdatabase/, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   40.00
#=GF TC   43.20
#=GF NC   39.20
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   12237106
#=GF RT   Continuous heat shock enhances translational initiation directed by
#=GF RT   internal ribosomal entry site.
#=GF RA   Kim YK, Jang SK
#=GF RL   Biochem Biophys Res Commun 2002;297:224-231.
#=GF CC   This family represents the bip internal ribosome entry site (IRES). BiP
#=GF CC   protein expression has been found to be significantly enhanced by the heat
#=GF CC   shock response due to IRES-dependent translation. It is thought that this
#=GF CC   translational mechanism is essential for the survival of cells under
#=GF CC   stress [1].
#=GF WK   bip_internal_ribosome_entry_site_(IRES)
#=GF SQ   9


X87949.1/10-255            --CCGGCCAAGACAGCACAGACAGAUUGACCUAUUGGGGUGUUUCGCGAGUGUGAGAGGGAAGCGCCGCGGCCUGUAUUUCUAGACCUGCCCUUCGCCUGGUUCGUGGCGCCUUGUGACC--CCGGGCCCCUGCCGCCUGCAAGUCGGAAAUUGCGCUGUGCUCCUGUGCUACGGCCUGUGGCUGGACUGCCUGC---------------------------UGCUGCCCAACUGGCUGGCAAGAUGAAGCUCUCCCUGGUGGCCGCGAUGCUGCUG
M19645.1/379-625           CGCCGGCCAAGACAGCACAGACAGAUUGACCUAUUGGGGUGUUUCGCGAGUGUGAGAGGGAAGCGCCGCGGCCUGUAUUUCUAGACCUGCCCUUCGCCUGGUUCGUGGCGCCUUGUGACC--CCGGGCCCCUGCCGCCUGCAAGUCG-AAAUUGCGCUGUGCUCCUGUGCUACGGCCUGUGGCUGGACUGCCUGC---------------------------UGCUGCCCAACUGGCUGGCAAGAUGAAGCUCUCCCUGGUGGCCGCGAUGCUGCUG
X59969.1/379-626           CGCCGGCCAAGACAGCACAGACAGAUUGACCUAUUGGGGUGUUUCGCGAGUGUGAGAGGGAAGCGCCGCGGCCUGUAUUUCUAGACCUGCCCUUCGCCUGGUUCGUGGCGCCUUGUGACC--CCGGGCCCCUGCCGCCUGCAAGUCGGAAAUUGCGCUGUGCUCCUGUGCUACGGCCUGUGGCUGGACUGCCUGC---------------------------UGCUGCCCAACUGGCUGGCAAGAUGAAGCUCUCCCUGGUGGCCGCGAUGCUGCUG
BC020235.1/1-237           -----------ACAGCACAGACAGAUUGACCUAUUGGGGUGUUUCGCGAGUGUGAGAGGGAAGCGCCGCGGCCUGUAUUUCUAGACCUGCCCUUCGCCUGGUUCGUGGCGCCUUGUGACC--CCGGGCCCCUGCCGCCUGCAAGUCGGAAAUUGCGCUGUGCUCCUGUGCUACGGCCUGUGGCUGGACUGCCUGC---------------------------UGCUGCCCAACUGGCUGGCAAGAUGAAGCUCUCCCUGGUGGCCGCGAUGCUGCUG
AANU01123159.1/8527-8266   CACCGGCCGAGACAGCACAGACGGACCGACCGAUUGGGGUGUUUCGCGAGUGUGAGAGGUAAGCGCCGCGGCCUGCAUUUCCAGACCUGCCCU---CCUGGUUCGUGGCGCCUUGUGACC--CCCGGCCCCUGCCGCCUGCAAGUCGGAAACCGCGCUGCGCUCCUGUGCUGCGGCCUGUGGCUGGACUGCCUGC----------GACGCCCUGCCUGCUGCUGCUGCCGGACUGGUUGGCAAGAUGAAGCUCUCCCUGGUGGCCGCGAUGCUGCUG
AADA01225449.1/20842-20588 CGCCGGCCGAGACGGCACAGACAGACCGACCGAUUGGGGUGUUUCCUGAAUGUGAGAGGUAAGCGCCGCGGCCUGCAUUUCCAGACCUGCCCUUCGCCUGGUUCGUGGCGCCUUGUGACC--CCUG-------CCACCUGCAAGUCGGUAACCGCGCUGCGCUCCUGUGCUGUGGCCUGUGGCUGGACUGCCUGG-------------GAUGCCCUGCCUGCUGCUGCCCGACUGGCUGGCAAGAUGAAGCUCUCCCUGGUGGCCGCGAUGCUGCUG
ABDC01077565.1/377-625     CGGCGGCCAAGACAGCACGGAG---UAGACUGACUAGGGCGUUUCGGGAGGGUAAGGGGUAAACGCCGCGGCCUGCUUUUC-AGAACUCUCCCCCGCCUUGUUCGUG----------GCU--CCGGGCCCCUGCCGCCCUCACACCGGUAACCUCGCAACGCUCCCGUGCUGCGGCCUGUGGCAGGAUUGCCUGC------------GACGUCCUCCCUGCCUGGUGACCCUCUGGCCGGCAAGAUGAAGCUCUCCCUGGUGGCUGCAGUGCUGCUG
M14866.1/698-964           UACUGGCUGUGACUACACUGAC---UUGGACACUU--GGCCUUUUGCGGGUUUGAGAGGUAAGCGUCGCGGCCUGCUUCCA---GGCUACCCUGAUUUUGGUUCGUGGCUCCUCCUGACCCUGAGAACCUCUGUCGCCU-CAGAUCAGAACCGUCGUCGCGUUUCGG-GCUACAGCCUGUUGCUGGACUCUGUGAGACACCUGACCGACCGCUGAGCGACUGACUGGUCCACAGCGCCGGCAAGAUGAAGUUCACUGUGGUGGCGGCGGCGCUGCUG
AAQR03035598.1/3023-2765   CGCCGGCCAAGACAGCACAGACAG---GACUGACUUAGGUGUUUCUCGAACGUGAGAGGUGAGCGCCGCGGCCUCCUGUCCCAGACCUG-CCUUCGCCUUGUUCUUGGCUCCUUGUGACC--CCGGAGCCCUGCCGCCCUCAGACCCAUAACCUCGCUGCGCUCCUGUGCUGCGGCCUGUGGUAGGAUUGCCUAC------------GACGUCCUGCCUGCCUGGUGACCGACUCGCCGGCAAGAUGAAGCUCUCCCUGGUGGCAGCGAUGCUGCUG
#=GC SS_cons               :::((((((,,,,,<<<<<<-------------<<<<<<<----------------------<<<<<<<<<_______________________________>>>>>>>>>------>>>..>>>>-------------------------------------->>>>>>,,<<<<<___>>>>>,,,,,,,,,,............,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,)))))):::::::::::
#=GC RF                    cgCcgGCcaAGACaGCACaGACAGAUuGAccuAccgGGGugUUUCgcGAGuGUGAGAGGuAAGcGcCgCGgCCUGcaUUucuAGAcCUgCCCUucgCCUgGUuCGuGgCgCCUUgUGaCC..CcgggCCcCUGCCGCCUgCAaaUCgGaAAcuuCGCuGcGCUCCuGUGCUaCaGCcUGUgGCuGGAcUgCcUGc............aacguugugcguuucUgcUGcCCaacUgGCuGGCAAGAUGAAGCUCUCCcUGGugGCcgCGaUGCUGCUG
//
# STOCKHOLM 1.0

#=GF AC   RF00224
#=GF ID   IRES_FGF2
#=GF PI   IRES_FGF; FGF_IRES
#=GF DE   FGF-2 internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   http://ifr31w3.toulouse.inserm.fr/IRESdatabase/, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   35.00
#=GF TC   35.20
#=GF NC   34.90
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   10893274
#=GF RT   Fibroblast growth factor 2 internal ribosome entry site (IRES) activity ex
#=GF RT   vivo and in transgenic mice reveals a stringent tissue-specific
#=GF RT   regulation.
#=GF RA   Creancier L, Morello D, Mercier P, Prats AC
#=GF RL   J Cell Biol 2000;150:275-281.
#=GF RN   [2]
#=GF RM   7799942
#=GF RT   Alternative translation of human fibroblast growth factor 2 mRNA occurs by
#=GF RT   internal entry of ribosomes.
#=GF RA   Vagner S, Gensac MC, Maret A, Bayard F, Amalric F, Prats H, Prats AC
#=GF RL   Mol Cell Biol 1995;15:35-44.
#=GF CC   This family represents the fibroblast growth factor 2 (FGF-2) internal
#=GF CC   ribosome entry site (IRES). When expressed the FGF-2 protein plays a
#=GF CC   pivotal role in cell proliferation, differentiation and survival as well
#=GF CC   as being involved in wound-healing [1,2]. It has been found that FGF-2
#=GF CC   IRES activity is strictly controlled and highly tissue specific. It is
#=GF CC   thought that translational IRES dependent activation of FGF-2 plays a
#=GF CC   vital role in embryogenesis and in the adult brain [1].
#=GF WK   FGF-2_internal_ribosome_entry_site_(IRES)
#=GF SQ   6


S81809.1/991-1486          UUGUGGCCGAA-CCGCCGAACUCAGAGGCCGGCCCCAGAAAA-CCCG-AGCGAGUAGGGGGCGGCGCGCAGGA-GGGAGGAGAACUGGGGGCGCGGGAGGCUGGUGGGUGU-GGGGGGUGGAGAUGUAGAAGAUGUGACGCCGCGGCCCGGCGGGUGCCAGAUUAGCGGAC--GGUGCCCGCGGUUGCAACGGGAUCCCGGGCGCUGC-AGCUUG-GGAGGCGGCUCUCCCCAG-GCGGCGUCCGCGGAGACACCCAUCCGUGAACCCCAGGUCCCGGGCCGCCGGC-UCGCCGCGCACCAGGGGCCGGCGGACAGAAGAGCGGCCGAGCGGCUCGAGGCUGGGGGACCGCGGGCGCGGCCGCGCGCUGCCGGGCGGGAGGCUGGGGGGCCGGGGCCGGGGCCGUGCCCCGGAGCGGGUCGGAGGCCGGGGCCGGGGCCGGGGGACGGCGGCUCCCCGCGCGGCUCCAGCGGCUCGGGGAUCCCGGCCGGGCCCCGCAGGGACCAUG
X04431.1/477-973           UUGUGGCCGAAGCCGCCGAACUCAGAGGCCGGCCCCAGAAAA-CCCG-AGCGAGUAGGGGGCGGCGCGCAGGA-GGGAGGAGAACUGGGGGCGCGGGAGGCUGGUGGGUGU-GGGGGGUGGAGAUGUAGAAGAUGUGACGCCGCGGCCCGGCGGGUGCCAGAUUAGCGGACG-GCUGCCCGCGGUUGCAACGGGAUCCCGGGCGCUGC-AGCUUG-GGAGGCGGCUCUCCCCAG-GCGGCGUCCGCGGAGACACCCAUCUGUGAACCCCAGGUCCCGGGCCGCCGGC-UCGCCGCGCACCAGGGGCCGGCGGACAGAAGAGCGGCCGAGCGGCUCGAGGCUGGGGGACCGCGGGCGCGGCCGCGCGCUGCCGGGCGGGAGGCUGGGGGGCCGGGGCCGGGGCCGUG-CCCGGAGCGGGUCGGAGGCCGGGGCCGGGGCCGGGGGACGGCGGCUCCCCGCGCGGCUCCAGCGGCUCGGGGAUCCCGGCCGGGCCCCGCAGGGACCAUG
AC021205.6/16596-17093     UUGUGGCCGAA-CCGCCGAACUCAGAGGCCGGCCCCAGAAAA-CCCG-AGCGAGUAGGGGGCGGCGCGCAGGA-GGGAGGAGAACUGGGGGCGCGGGAGGCUGGUGGGUGU-GGGGGGUGGAGAUGUAGAAGAUGUGACGCCGCGGCCCGGCGGGUGCCAGAUUAGCGGACGCGGUGCCCGCGGUUGCAACGGGAUCCCGGGCGCUGC-AGCUUG-GGAGGCGGCUCUCCCCAG-GCGGCGUCCGCGGAGACACCCAUCCGUGAACCCCAGGUCCCGGGCCGCCGGC-UCGCCGCGCACCAGGGGCCGGCGGACAGAAGAGCGGCCGAGCGGCUCGAGGCUGGGGGACCGCGGGCGCGGCCGCGCGCUGCCGGGCGGGAGGCUGGGGGGCCGGGGCCGGGGCCGUGCCCCGGAGCGGGUCGGAGGCCGGGGCCGGGGCCGGGGGACGGCGGCUCCCCGCGCGGCUCCAGCGGCUCGGGGAUCCCGGCCGGGCCCCGCAGGGACCAUG
AAFC03058056.1/47679-47194 CUGCGGCCCGA-GCGCCCGACCCAGACACCCGCCCCAGAAAA-CCCGGAGCGAGUAGGGGGCGGUGCGCCGGAAGGGAGGCGGGCGGGGGGCGUGGG-GGGUCGUGGGCGUCUGGGGGUGGAGACCUAUUAGAUGUGACGCCGCGGCCCAGCGGGUAGCAGACCGGCGGACGCGGUGCCCGC---------GG-AUCCCGGGUGCUGCGGCUUAU-GGAGGCGGCCCUCCCAAGAGCGGCGGCCGCAGAGGCAUCCAGCCCUCACCCCCCGAUCCGGGACCGCCGGGCUCCCCGCGCUCUAGGG-CAGGCGGAGAGGGAAGCGGCCGAACAGCUCGAGGCUGGGGGCUCGCGGGCGCGGCCGCGUGCCGCGGGGAGGGAGGCUGGGGGGCCGGGGCCGGGGCCGCGCCGCGGAGCGCGUCGGAGGCCGGGGCCG------GGGCGCGGCGGCUCCCCGCGCGGCUCCAGGGGCUCGGGGACCCCGCCAGGGCCUUGGUGGGGCCAUG
AC157217.2/147923-147426   UUGUGGCCGAA-CCGCCGAACUCAGAGGCCGGCCCCAGAAAA-CCCG-AGCGAGUAGGGGGCGGCGCGCAGGA-GGGAGGAGAACUGGGGGCGCGGGAGGCUGGUGGGUGU-GGGGGGUGGAGAUGUAGAAGAUGUGACGCCGCGGCCCGGCGGGUGCCAGAUUAGCGGACGCGGUGCCCGCGGUUGCAACGGGAUCCCGGGCGCUGC-AGCUUG-GGAGGCGGCUCUCCCCAG-GCGGCGUCCGCGGAGACACCCAUCCGUGAACCCCAGGUCCCGGGCCGCCGGC-UCGCCGCGCACCAGAGGCCGGCGGACAAAAGAGCGGCCGAGCGGCUCGAGGCUGGGGGACCACGGGCGCGGCCGCGCGCUGCCGGGCGGGAGGCUGGGGGGCCGGGGCCGGGGCCGUGCCCCGGAGCGGGUCGGAGGCCGGGGCCGGGGCCGGGGGACGGCGGCUCCCCGCGCGGCUCCAGCGGCUCGGGGAUCCCGGCCGGGCCCCGCAGGGACCAUG
AAGV020630258.1/3728-3245  CUGCGGUCGUA-GCACCCGGUUCCGAGGCCGGCCCCUGAAAACCCCG-AGCGAGGAGGGGGCGGCGCAGAGGA-GGGAGGAGAGCUGGGGGCGCGGGAGGCCGGUGGGUGUUUGGGGGUGGAGAUGUAGAAAAUGUGACGCCGCAGCCAGGCCGGUGCCAGACCAGCGGACGCGGUGCCCGCGGUCGCAACCCGAUCCCCGACGCUGC-CGCUUGCGGAGGUGGCUCUGCCGAGAGCGGCGGCGGCGCAGCCACCCAGCC-CAAACCCCAGCUCCCG-GCCGCCGGG-UCUCCACG--------GCCGGCG--CGGAGGAGCCGCCGAGCAGCGCGAGGCUGGGGGCCCGCGGGCGCGGCCGCACGCAGCGCGGCGGGAGGCUGGGGGGCCGGGG------CCGCGCCCUGGAGCGAGUCGGAGGCCGCGGCCGGGGCCGUGGGGCGGCGGCUCCCCGCGCCGCUCCGGGGGCUCGGGUGCCCCGACAGGGCCCCGGCGGGGCCAUG
#=GC SS_cons               :::::::::::.:::::::::::::::::[[[[[[[------.-[[[.-----------[[[[[[[[[[,,,,.,,,,,,,,,,((((((-((((---------((((((,.,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<-<<<<<<<<<______________>>>>>>>>>--------->>>,,,,<<<<<<<<<<.-----<.<<<<<____>>>>>>---.>>>>>>>>>>,,,,,,))))))--))))--)))))),,,,<<<<<<<<<<<<.________________>>>>>>-------------------->>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,]]]]]]]]]]---]]]--------]]]]]]],,,,,,,,,,,,,,,<<<<___>>>>,,,,,,,,,((((((-----(((,,,,,,,,,,,,,,,,<<<<__________>>>><<<___>>>,,)))))))))::::::::::::
#=GC RF                    uUGuGGcCgaA.cCgCCgaAcuCAGAggCCGGCCCCAGAAAA.CCCg.AGCGAGuAGGGgGCgGcGCGCaGGA.GGGAGGaGAaCuGGGGGcgcGGGAGGcUgGuGGGuGU.gGGGGGUGGAGAugUAgaAgAUGUGACGCCGCgGCCcgGCGGGugcCAGAuuAGCGGACGCGgugCCCGCGGUuGCAACgGGAUCCCgGgcGCuGC.agcUug.GgaGgcGGCcCucCccAG.GCgGCgcCcGCggAGaCaCCCauCCgcgAaCCCCaGgUCCCGgGCcGCCgGc.UCgCCgCGCaCcAGgGgCcGGCGGAcAGAagAGCgGCCGAgCgGCuCGAGGCUGGGGGacCGCGGGCGCGGCCGCGCgCcGCcgGGcGGGAGGCUGGGGGGCCGGGGCCGGGGCCGuGCCccGGAGCggGUCGGAGGCCGgGGCCGGGGCCggGGgaCGGCGGCUCCCCGcGCgGCUCCAGcGGCuCGGGgAuCCCGgccGGGCCcCGcaGGGaCCAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00225
#=GF ID   IRES_Tobamo
#=GF PI   Tobamo_IRES
#=GF DE   Tobamovirus internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   http://ifr31w3.toulouse.inserm.fr/IRESdatabase/
#=GF SS   Published; PMID:9185586
#=GF GA   50.00
#=GF TC   57.10
#=GF NC   39.00
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   9185586
#=GF RT   A tobamovirus genome that contains an internal ribosome entry site
#=GF RT   functional in vitro.
#=GF RA   Ivanov PA, Karpova OV, Skulachev MV, Tomashevskaya OL, Rodionova NP,
#=GF RA   Dorokhov YuL, Atabekov JG
#=GF RL   Virology 1997;232:32-43.
#=GF RN   [2]
#=GF RM   11142379
#=GF RT   Ribosomal binding to the internal ribosomal entry site of classical swine
#=GF RT   fever virus.
#=GF RA   Kolupaeva VG, Pestova TV, Hellen CU
#=GF RL   RNA 2000;6:1791-1807.
#=GF CC   This family represents the Tobamovirus internal ribosome entry site
#=GF CC   (IRES). IRES elements allow cap and end-independent translation of mRNA in
#=GF CC   the host cell. The IRES achieves this by mediating the internal initiation
#=GF CC   of translation by recruiting a ribosomal 43S pre-initiation complex
#=GF CC   directly to the initiation codon and eliminates the requirement for eIF4F
#=GF CC   [2].
#=GF WK   Tobamovirus_internal_ribosome_entry_site_(IRES)
#=GF SQ   7


U03387.1/5455-5605   GAAUUCGUCGAUUCGGUUGCAGCAUUUAAAGCGGUUGACAAUUUCAGGAAGAGGAAAAAGAAGGUUGAAGAAAGGGAUGUAGUAAGUAA---GUAUAAAUAUAGACCGGAGAAAUACGCCGGUCCUGAUUCGUUUAAUUUAAAAGAAGAAAAUG
S68164.1/682-832     GAAUUCGUCGAUUCGGUUGCAGCAUUUAAAGCGGUUGACAACUUUAAAAGAAGGAAAAAGAAGGUUGAAGAAAAGGGUGUAGUAAGUAA---GUAUAAGUACAGACCGGAGAAGUACGCCGGUCCUGAUUCGUUUAAUUUGAAAGAAGAAAAUG
Z29370.1/5456-5606   GAAUUCGUCGAUUCGGUUGCAGCAUUUAAAGCGGUUGACAACUUUAAAAGAAGGAAAAAGAAGGUUGAAGAAAAGGGUGUAGUAAGUAA---GUAUAAGUACAGACCGGAGAAGUACGCCGGUCCUGAUUCGUUUAAUUUGAAAGAAGAAAAUG
AB017504.1/5441-5591 GAAUUCAUCGAUUCGGUUGCAGCAUUUAAAGCGGUUGACAAUUUCAGGAAAAAGAAAAAGAAGAUUGGAGGAAGGGAUGUGAUUAGUAA---GUAUAAGUAUAGACCAGAGAAGUACGCCGGUCCUGAUUCGUUACUUAAUAAAGAAGAAAAUG
AB003936.1/1522-1672 GAAUUCAUCGAUUCGGUUGCAGCAUUUAAAGCGGUUGACAAUUUCAGGAAAAAGAAAAAGAAGAUUGGAGGAAGGGAUGUGAUUAGUAA---GUAUAAGUAUAGACCAGAGAAGUACGCCGGUCCUGAUUCGUUACUUAAUAAAGAAGAAAAUG
AB017503.1/5442-5592 GAAUUCAUCGAUUCGGUUGCAGCAUUUAAAGCGGUUGACAAUUUCAGGAAAAAGAAAAGGAAGAUUGGAGGAAGGGAUGUGAUUAGUAA---GUAUAAGUAUAGACCAGAGAAGUACGCCGGUCCUGAUUCGUUACUUAAUAAAGAAGAAAAUG
D38444.1/5444-5597   GAUUUCGUCGAUUCGGUCGCAGCAUUCAAGGCGGUUGACACUUUCAGAAAGAAAAAGAAAAGGAUUGGAGGAAAGGAUGUAAAUAAUAAUAAGUUUAGAUAUAGACCGGAGAGAUACGCCGGUCAGGAUUCGUUAAAUUAUAAAGAAGAAAAUG
#=GC SS_cons         ::::::::::::::::::::::::<<<--<<--<<<___>>>>>-->>>---------------------------------(((((-(...(<<<__>>><<<<<<<<_________>>>>>>->>,))-)))))::::::::::::::::::
#=GC RF              GAAUUCgUCGAUUCGGUUGCAGCAuucAAagCGguuGACaacuucAgaaaaAaGAAAAAGAAGaUUGgAGgAAaGGaUGUaauuaguAa...guacAAguacaGaCCgGAGAAgUACGCcGGuCcugAuuCguuaaaUuauAAAGAAGAAAAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00226
#=GF ID   IRES_n-myc
#=GF PI   n-myc_IRES
#=GF DE   n-myc internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:11419940
#=GF SS   Predicted; PFOLD
#=GF GA   40.00
#=GF TC   45.00
#=GF NC   32.10
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11420678
#=GF RT   N-myc translation is initiated via an internal ribosome entry segment that
#=GF RT   displays enhanced activity in neuronal cells.
#=GF RA   Jopling CL, Willis AE
#=GF RL   Oncogene 2001;20:2664-2670.
#=GF CC   This family represents the n-myc internal ribosome entry site (IRES). The
#=GF CC   myc family of genes when expressed are known to be involved in the control
#=GF CC   of cell growth, differentiation and apoptosis. n-myc mRNA has an
#=GF CC   alternative method of translation via internal ribosome entry where
#=GF CC   ribosomes are recruited to the IRES located in the 5' UTR thus bypassing
#=GF CC   the typical eukaryotic cap-dependent translation pathway [1].
#=GF WK   n-myc_internal_ribosome_entry_site_(IRES)
#=GF SQ   6


AC010145.10/67113-67436 CACAAAAGGAGGGCGGGAGGGAGGGAGCGAGAGGCACAACUUCCUCCACCUUCGGGAGCAGUGGGCAGAGUGGGGGGCUUGGAGGGAAGAUUGGGGAACCUGGUUAGAGGGGGCGCCCAUUGCCUAUCCCCUCGGUCU-GCCCCGUUUGCCCACCCUCUCC-GGUGUGUCUGUCGGUUGCAGUGUUGGAGGUCGGCGCCGGCCCCCGCCUUCCGCGCCCCCCACGGGAAGGAAGCAC-CCCCGGUAUUAAAACGAACGGGGCGGAAAGAAGCC--CUCAGUCGCCGGCCGGGAGGCGAGCCGAUGCCGAGCUGCUCCACGUCCACCAUG
X93018.1/698-1022       CUCUGGACGCGCUGAGUGGAUGCCGGGGUCUCCUGGGAACUGGGUUGGAGCCGAACGAGCGCUAGCCAGGCGCAAGCGCUCACAGAGUGCAGCCGCCCCAGGACCCCUCCCCGCCCCCACAGACCACCCGGAGACCCCAGCGCAGAAUCGUCUCCGGAUUCCCAGCAGUCGCCUGG----AGUGUUGGAGAUUGGCUCUUGCCCCCGCCCUCCGCACACCCCAGGGAAAGGAAGCACCCCCCGGUAUUAAAAAGAGCUGAGCGGAAAGAAGGUUUCUCAGUCGCUGGCGGGCAGGCGAGCUGAUGCGGAGCUGCACCGUGUCCACCAUG
AF320053.1/5-324        GUCUGGACGCGCUGGGUGGAUGCGGGGGGCUCCUGGGAACUGUGUUGGAGCCGAGCAAGCGCUAGCCAGGCGCAAGCGCGCACAGACUG--UAGCCAUCCGAGGACACCCCCGCCCCCCCGGCCCACCCGGAGACACCCGCGCAGAAUCGCCUCCGGAUCCCCUGCAGUCGGCGGG----AGUGUUGGAGGUCGGCGCCGGCCCCCGCCUUCCGCGCCCCCCACGGGAAGGAAGCAC-CCCCGGUAUUAAAACGAACGGGGCGGAAAGAAGCC--CUCAGUCGCCGGCCGGGAGGCGAGCCGAUGCCGAGCUGCUCCACGUCCACCAUG
X53671.1/122-446        AUCUGGACGCGCUGAGUGGAUGCGGGGGUCUCCUGGGAACUGGGUUGGAGCCGAACGAGAGCUAGCUAGGCGCAAGCGCUCACAGAGUGCAGCCGCCCCAGGACCCCUCCCCGCCCCCACAGACCACCCGGAGACCCCAGCGCAGAAUCGUCUCCGGAUUCCCAGCAGUCGCCUGG----AGUGUUGGAGAUUGGCUAUUGCCCCCGCCCUCCGCACACCCUAGGGAAAGGAAGCACCCCCCGGUAUUAAAAAGAGCUGAGCGGAAAGAAGCUCUCUCAGUCGCUGGCGGGCAGGCGAGCUGAUGCGGAGCUGCACCGUGUCCACCAUG
Y00664.1/3075-3398      CACAAAAGGAGGGCGGGAGGGAGGGAGCGAGAGGCACAACUUCCUCCACCUUCGGGAGCAGUGGGCAGAGUGGGGGGCUUGGAGGGAAGAUUGGGGAACCUGGUUAGAGGGGGCGCCCAUUGCCUAUCCCCUCGGUCU-GCCCCGUUUGCCCACCCUCUCC-GGUGUGUCUGUCGGUUGCAGUGUUGGAGGUCGGCGCCGGCCCCCGCCUUCCGCGCCCCCCACGGGAAGGAAGCAC-CCCCGGUAUUAAAACGAACGGGGCGGAAAGAAGCC--CUCAGUCGCCGGCCGGGAGGCGAGCCGAUGCCGAGCUGCUCCACGUCCACCAUG
M13241.1/1329-1652      CACAAAAGGAGGGCGGGAGGGAGGGAGCGAGAGGCACAACUUCCUCCACCUUCGGGAGCAGUGGGCAGAGUGGGGGGCUUGGAGGGAAGAUUGGGGAACCUGGUUAGAGGGGGCGCCCAUUGCCUAUCCCCUCGGUCU-GCCCCGUUUGCCCACCCUCUCC-GGUGUGUCUGUCGGUUGCAGUGUUGGAGGUCGGCGCCGGCCCCCGCCUUCCGCGCCCCCCACGGGAAGGAAGCAC-CCCCGGUAUUAAAACGAACGGGGCGGAAAGAAGCC--CUCAGUCGCCGGCCGGGAGGCGAGCCGAUGCCGAGCUGCUCCACGUCCACCAUG
#=GC SS_cons            ::::::::::::::::::::::(((,,,,,,,,,,,,,,<<<<<____________________________________>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,<<<_______________>>>,,,,,,,,,,,,,,,,,,,,,,)))--------------------....-----[[[[,,,((((-((((((,,,,,,,,,,,,,,,<<____>>,,,,,,,,,<<.<___>>>,,,,,,,,,,,,,,<<<<__________..______>>>>))))))-------)))),,<<___>>,,,,,,,,,]]]]:::::
#=GC RF                 cuCuaaAcGaGcuggGuaGauagGGaGggauacugagAACugcgUugaaguugagcaagaGuuaGCaaaGuGcaaGcguUcgcaGaauGauuggGcaaCcuGguuagaccggGCcCCCAuuGcCuAuCCccagacuCuaGCgCaGaaUcgcCuCCcuaUcCCcaucaGUCuguuGG....AGUGUUGGAGgUcGGCgCcgGCCCCCGCCuUCCGCgCcCCCCAcGGgAAGGAAGCAC.CCCCGGUAUUAAAAcGAaCgGGGCGGAAAGAAGcc..CUCAGUCGCCGGCcgGgAGGCGAGCCgAUGCcGAGCUGCuCCacGUCCACCAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00227
#=GF ID   FIE3
#=GF DE   FIE3 (ftz instability element 3') element
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   PMID:8649416
#=GF SS   Predicted; stemloc, Bateman A
#=GF GA   40.00
#=GF TC   40.30
#=GF NC   39.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0061157; mRNA destabilization;
#=GF RN   [1]
#=GF RM   8649416
#=GF RT   Determinants of Drosophila fushi tarazu mRNA instability.
#=GF RA   Riedl A, Jacobs-Lorena M
#=GF RL   Mol Cell Biol 1996;16:3047-3053.
#=GF CC   The fushi tarazu gene is essential for the establishment of the Drosophila
#=GF CC   embryonic body plan. When first expressed in early embryogenesis, fushi
#=GF CC   tarazu mRNA is uniformly distributed over most of the embryo.
#=GF CC   Subsequently, fushi tarazu mRNA expression rapidly evolves into a pattern
#=GF CC   of seven stripes that encircle the embryo. The instability of fushi tarazu
#=GF CC   mRNA is probably crucial for attaining this localised pattern of
#=GF CC   expression [1]. Experiments provide evidence for at least two
#=GF CC   destabilising elements in the fushi tarazu mRNA, one located within the 5'
#=GF CC   one-third of the mRNA and the other near the 3' end (termed FIE3 for ftz
#=GF CC   instability element 3'). The FIE3 lies within a 201-nucleotide sequence
#=GF CC   just upstream of the polyadenylation signal and can act autonomously to
#=GF CC   destabilise a heterologous mRNA. Further deletion constructs identified an
#=GF CC   essential 68-nucleotide element within the FIE3 [1].
#=GF WK   FIE3_(ftz_instability_element_3')_element
#=GF SQ   5


AY190944.1/40305-40223 UGAUAAUG--------AUUCAAGAUCUUGGAGACUGACACACACACACACAUGUUUUCUUUUAAGCGAAAGUGCUUUUCUGUACAGU-AGUA
AY190954.1/18067-18131 CGAUAAUGCAACACAAGCUCAA---CUUGGAGACUGAUUA-----ACUUUUUGUUUCUA-------------------UUGUACAGUUUAUA
X79494.1/2895-2959     CGAUAAUGCAACACGAACUCAA---CUUGGAGACUGAAGA-----AUGUUUUGUUUCUA-------------------UUGUACAGCUAAUA
AY190938.1/41310-41252 UGAUAAUG--------GCCAAAAA--UUGGAGACUGAC----------ACAUGUUUUUGUACAUA-------------UAGUAGUUAAGAUC
AC095015.1/33082-33144 UGAUAAUG--------GCCAAGAGACUUGGAGACUGACAC--------ACAUGUUUUUGUACAUA-------------UAGUAGUUAAGAUA
#=GC SS_cons           ::::::::........::::::::.::<<<<<<<<<____.....____>>->>>>>>>::::::.............::::::::::::::
#=GC RF                UGAUAAUG........aCUCAAaA.CUuggAGACuGAcac.....aacaCaUGUUUcuaUuuAua.............UUGUACAGuuaAUA
//
# STOCKHOLM 1.0

#=GF AC   RF00228
#=GF ID   IRES_HepA
#=GF PI   HepA_IRES
#=GF DE   Hepatitis A virus internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   http://ifr31w3.toulouse.inserm.fr/IRESdatabase/
#=GF SS   Predicted; PFOLD
#=GF GA   55.00
#=GF TC   58.20
#=GF NC   36.80
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   8289336
#=GF RT   In vitro characterization of an internal ribosomal entry site (IRES)
#=GF RT   present within the 5' nontranslated region of hepatitis A virus RNA:
#=GF RT   comparison with the IRES of encephalomyocarditis virus.
#=GF RA   Brown EA, Zajac AJ, Lemon SM
#=GF RL   J Virol 1994;68:1066-1074.
#=GF RN   [2]
#=GF RM   11142379
#=GF RT   Ribosomal binding to the internal ribosomal entry site of classical swine
#=GF RT   fever virus.
#=GF RA   Kolupaeva VG, Pestova TV, Hellen CU
#=GF RL   RNA 2000;6:1791-1807.
#=GF CC   This family represents the internal ribosome entry site (IRES) of the the
#=GF CC   Hepatitis A virus. IRES elements allow cap and end-independent translation
#=GF CC   of mRNA in the host cell. The IRES achieves this by mediating the internal
#=GF CC   initiation of translation by recruiting a ribosomal 43S pre-initiation
#=GF CC   complex directly to the initiation codon and eliminates the requirement
#=GF CC   for eIF4F [2].
#=GF WK   Hepatitis_A_virus_internal_ribosome_entry_site_(IRES)
#=GF SQ   23


AB020568.1/165-737 CAGGGUUCUUUAAUC-UGUUUCUCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGGACGUCACCUUGCAGUGUUAACUUGGCU-CUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGAAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGAAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCCC-AGACCUCUCUGUGCUUAGGGCAAACACUCAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUGGCAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAACAAUAAUG
AB020569.1/165-736 CAGGGUUCUUUAAUC-UGUUUCUCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGGACGUCACCUUGCAGUGUUAACUUGGCU-UUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCCCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGAAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGAAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAC-UAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAAUGAUAAUG
M63025.1/74-644    CAGGGUUCUUUAAUC-UGUUUCUCUAUAAGAACACUCA-UUUUCACGCUUUCUGUCUGCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGGACGUCACCUUGCAGUAUUAACUUGGCU-CUCAUGAAGCUCUUUGAUCUUCCACAAGAGGUAGGCUACGGGUGAAACCUCUUAAGCUAGUACUUCUAUGAAGAGAUGCUUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCUUUCAACGCCGGAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGUUUGUCAGGGCUGUCUCUAGGCUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAU-UACUUGGCCUUAAAUGGGAUUCUGUGAGAGGGGAUCCC-UCCAUUGAUAGCUGGACUUUUCUUUGGGGCCUUAGGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCACUCUCAAAUAACUAUG
X70846.1/143-709   CAGGGUUCUUUAAUC-UGUUUCUCUAUAAGAACACUCAAUUU-CACGCUU-CUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGAACGUCGCCUUGCAGUGUUAACUUGGCU-CUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCUUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAG-ACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAC-CAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGAUCCC-UCCAUUUACAGCUGGACUGUACUUUGGGGCCUUAUGUGGUGUGUGCCACUGAGGUACCCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAACCAAUA--
M14114.1/144-715   CAGGGUUCUUAAAUC-UGUUUCUCUAUAAGAACACUCAUUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACACAGAUGUUUGGAACGUCACCUUGCAGUGUUAACUUGGCU-UUCAUGAAUCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGACUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGACUGUCAGGGCUGUCUUUAGGCUUAAUUCC-AGACCUCUCUGUGCUUAGGGCAAACAU-CAUUUGGCCUUAAAUGGGAUUCUGUGAGAGGGGAUCCC-UCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAAUAAUAAUG
X15464.1/82-656    CAGGGUUCUUUAAUCAUGUUUCCCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGGACGUCACCUUGCAGUGUUAACUUGGCU-CUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCUUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUCAAGACCUCUCUGUGCUUAGGGCAAACAC-CAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCCCUCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAACAAUAAUG
M63026.1/91-659    CAGGUCUCUUGAAUC-UGUUCCACUUUAUGGACACUCA--UUUCACGCUUUCUGUCUGCUUUUCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGCUGCGCCCGGCGGGGUCAACUCCAUGGUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACACAGAUGUUGGGAACGUCGCCUUGCAGUGUUAACUUGGCU-UUCAUGAAGCUUUUUGAUCUUCCACAAGAGGUAGGCUACGGGUGAAACCUCUUAAGCUAAUACUUCUAUGAAGAGAUGCUUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUU-GACAAAAACCAUUCAACGCCGGAG-ACUGGCUCUCAUCCAGUGGAUGCAUUAAGUGGAUUGUCUGUCAGGGCUGUCUCUAGGUUUAAUUCC-UGGCCUCUCUGUGCUUAGGGUAAACAA-AACUUGGCCUUAAAUGAGGUCCUGUGAGAGGGGACCUC-ACCAUUGAAUGCUGGACAUUUCUUUGGGGCCUUAUGUUUUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUCAAUAAAUAAUUAUG
M14707.1/166-737   CAGGGUUCUUAAAUC-UGUUUCUCUAUAAGAACACUCAUUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACACAGAUGUUUGGAACGUCACCUUGCAGUGUUAACUUGGCU-UUCAUGAAUCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGACUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGACUGUCAGGGCUGUCUUUAGGCUUAAUUCC-AGACCUCUCUGUGCUUAGGGCAAACAU-CAUUUGGCCUUAAAUGGGAUUCUGUGAGAGGGGAUCCC-UCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAAUAAUAAUG
X83302.1/140-708   CAGGGUUCUUUAAUC-UGUUUCUCUAUAAGAACACUCAAUUU-CACGCUU-CUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGAACGUCGCCUUGCAGUGUUAACUUGGCU-CUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAG-GCUGGCUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAC-CAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGAUCCC-UCCAUUUACAGCUGGACUGUACUUUGGGGCCUUAUGUGGUGUGUGCCACUGAGGUACCCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAACAAUAAUG
AF357222.1/165-736 CAGGGUUCUUUAAUC-UGUUUCUCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGGACGUCACCUUGCAGUGUUAACUUGGCU-CUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGAAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCCC-AGACCUCUCUGUGCUUAGGGCAAACAC-UAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUGCCAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAAUAAUAAUG
M59808.1/151-720   CAGGGUUCUUAAAUC-UGUUUCUCUAUAAGAACACUCA--UUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACACAGAUGUUUGGAACGUCACCUUGCAGUGUUAACUUGGCU-UUCAUGAAUCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGACUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGACUGUCGGGGCUGUCUUUAGGCUUAAUUCC-AGACCUCUCUGUGCUUGGGGCAAACAU-CAUUUGGCCUUAAAUGGGAUUCUGUGAGAGGGGAUCCC-UCCAUUGCCAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCGCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAAUAAUAAUG
M16632.1/162-732   CAGGGUUCUUAAAUC-UGUUUCUCUAUAAGAACACUCA-UUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACACAGAUGUUUGGAACGUCACCUUGCAGUGUUAACUUGGCU-UUCAUGAAUCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGACUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGACUGUCAGGGCUGUCUUUAGGCUUAAUUCC-AGACCUCUCUGUGCUUAGGGCAAACAU-CAUUUGGCCUUAAAUGGGAUUCUGUGAGAGGGGAUCCC-UCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAAUAAUAAUG
M59809.1/151-720   CAGGGUUCUUAAAUC-UGUUUCUCUAUAAGAACACUCA--UUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACACAGAUGUUUGGAACGUCACCUUGCAGUGUUAACUUGGCU-UUCAUGAAUCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGACUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGACUGUCGGGGCUGUCUUUAGGCUUAAUUCC-AGACCUCUCUGUGCUUGGGGCAAACAU-CAUUUGGCCUUAAAUGGGAUUCUGUGAGAGGGGAUCCC-UCCAUUGCCAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCGCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAAUAAUAAUG
X75214.1/119-690   CAGGGUUCUUUAGUC-UGUUUCUCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUAGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAAAUGUUUGAGACGUCGCCUUGCAGUGUUAACUUGGCU-CUCAUGAACCUCUCUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCUUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAC-CAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUUACAGCUGGACUGUACUUUGGGGCCUUAUGUGGUGUUUGCCGCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAACAAUAAUG
AF485328.1/165-736 CAGGGUUCUUUAAUC-UGUUUCUCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGGACGUCGCCUUGCAGUGUUAACUUGGCU-CUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGAAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAC-UAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAAUAAUAAUG
AB020564.1/165-736 CAGGGUUCUUUAAUC-UGUUUCUCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGGACGUCACCUUGCAGUGUUAACUUGGCU-UUCAUGAACCUCUUUGAUCUUUCACAAGAGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGAAGGACUGGUUCUCAUCCAGUGGAUGCAUUGAGUGAAUUGAUUGUCAAGGCUGUCUCUAGGUUUAAUCCC-AGACCUCUCUGUGCUUAGGGCAAACAC-UAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAACAAUAAUG
X75215.1/119-690   CAGGGUUCUUUAGUC-UGUUUCUCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGAGACGUCGCCUUGCAGUGUUAACUUGGCU-CUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCUUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAC-CAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUUACAGCUGGACUGUACUUUGGGGCCUUAUGUGGUGUUUGCCGCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAACAAUAAUG
M59810.1/152-721   CAGGGUUCUUAAAUC-UGUUUCUCUAUAAGAACACUCA--UUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACACAGAUGUUUGGAACGUCACCUUGCAGUGUUAACUUGGCU-UUCAUGAAUCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGACUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGACUGUCGGGGCUGUCUUUAGGCUUAAUUCC-AGACCUCUCUGUGCUUGGGGCAAACAU-CAUUUGGCCUUAAAUGGGAUUCUGUGAGAGGGGAUCCC-UCCAUUGCCAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCGCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAAUAAUAAUG
AB020565.1/165-736 CAGGGUUCUUCAAUC-UGUUUCUCUAUAAGAACACUCAAAUUUCACGCUUUCUGUCUUCUU-UCUUCCAUGGCUCUCCCCUUGCCCUAGGCACAGGGCGUCGCGCCCGGCGGGGUCAACUCCAUCAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGGACGUCACCUUGCAGUGUUAACUUGGCU-UUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCCCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAUGGUAACAGCGGCGGAUAUUGGUGAAUUGUUAAGACAAAAACCAUUCAACGCCGAAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGAAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAC-UAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUAGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCACUCUUAAACAACAAUG
X75216.1/119-690   CAGGGUUCUUUAAUC-UGUUUCUCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGAGACGUCGCCUUGCAGUGUUAACUUGGCU-CUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCUUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAC-CAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUGACAGCUGGACUGUACUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAACAAUAAUG
AB020566.1/165-737 CAGGGUCCUUUAAUC-UGUAUCUCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACACAGAUGUUUGGGACGUCUCCUUGCAGUGUUAACUUGGCUCUUCAUAAACCUCUUUGAUCUUCCACAAGAAGUACGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAAAGAUACCUUGGAUAGGGUAACACCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGAAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGUGAAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAC-UAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCACUCUUAAACAAUAAUG
AB020567.1/165-736 CAGGGUUCUUUAAUC-UGUUUCUCUAUAAGAACACUCAAUUUUCACGCUUUCUGUCUCCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACGCAGAUGUUUGGGACGUCGCCUUGCAGUGUUAACUUGGCU-UUCAUGAACCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGAAGGACUGGCUCUCAUCCAGUGGAUGCAUUGAGGGAAUUGAUUGUCAGGGCUGUCUCUAGGUUUAAUCUC-AGACCUCUCUGUGCUUAGGGCAAACAC-UAUUUGGCCUUAAAUGGGAUCCUGUGAGAGGGGGUCCC-UCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCUCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAACAAUAAUG
AF268396.1/156-727 CAGGGUUCUUAAAUC-UGUUUCUCUAUAAGAACACUCAUUUUUCACGCUUUCUGUCUUCUU-UCUUCCAGGGCUCUCCCCUUGCCCUAGGCUCUGGCCGUUGCGCCCGGCGGGGUCAACUCCAUGAUUAGCAUGGAGCUGUAGGAGUCUAAAUUGGGGACACAGAUGUUUGGAACGUCACCUUGCAGUGUUAACUUGGCU-UUCAUGAAUCUCUUUGAUCUUCCACAAGGGGUAGGCUACGGGUGAAACCUCUUAGGCUAAUACUUCUAUGAAGAGAUGCCUUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGGAGGACUGACUCUCAUCCAGUGGAUGCAUUGAGUGGAUUGACUGUCAGGGCUGUCUUUAGGCUUAAUUCC-AGACCUCUCUGUGCUUAGGGCAAACAU-CAUUUGGCCUUAAAUGGGAUUCUGUGAGAGGGGAUCCC-UCCAUUGACAGCUGGACUGUUCUUUGGGGCCUUAUGUGGUGUUUGCCGCUGAGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUCUUAAAUAAUAAUG
#=GC SS_cons       :::::::::::::::.:::<<<<_____>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,,,,,,((((((((,,<<<<<<____>>>>>>,,,,,,<<<<<<<_____>>>>>>>,,,,,)))))))),,,,,,,,,((((((-((((((((,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<______________>>>>>>,<<<<-----<<<<___>>>>---->>>>,,,,,,,,,,,,,,,<<<<<___________________________________>>>>>,,,,,,,,,,,,,<<<<<<_>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,)))).))))---))))))((((-(((((((((.(((--(((((((((,<<<<<<<<_______>>>>>>>>.,,,,,,<<<<<_____>>>>>,)))))))))----))))))))))))--)))):::::::::::::::::::::::::::::::::::::::::::::
#=GC RF            CAGGGUUCUUuAAUC.UGUuuCuCUAUAaGaaCACUCAaUUUUCACGCUUUCUGUCUuCUU.UCUUCCAGGGCUCUCCCCUUGCCCuaGgCuCcGGCCGuuGCGCCCggCGGGGUCAACuCCauGAUUAGCauGGaGCUGUAgGaGuCuaAAUUGGGGACgCaGaUGuuuGggaCGUCaCCUUGCAGUGUUAACUUGGCU.uUCAUGAAuCUCUUUGAUCUUCCACAaGgGGuAGGCUACGGGUGAAaCCcCuUagGCUAAUACuuCUAUGaaGAGAUGCcuUGGAUAGGGUAACAGCGGCGGAUAUUGGUGAGUUGUUAAGACAAAAACCAUUCAACGCCGgAGGACUGgCUCUCauCCaGuGGauGCAUUGAGUGgAUUGAuUGUCAGGGCUGUCUcUAGGuUUAAuccC.agaCCUCuCuGcGCuuaGGGCaaaCac.cacUUGGCCuuaaaUGGGaucCuGUGAGAGgGgauCCC.UCCAUUgacaGCUGGACugucCuuuggGGCCUUAUgugguGuuuGCCuCugaGGUACUCAGGGGCAUUUAGGUUUUUCCUCAUUcUUAAAuAAUAAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00229
#=GF ID   IRES_Picorna
#=GF DE   Picornavirus internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   http://ifr31w3.toulouse.inserm.fr/IRESdatabase/
#=GF SS   Predicted; PFOLD
#=GF GA   33.00
#=GF TC   33.00
#=GF NC   32.90
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   10600593
#=GF RT   Structural and functional analysis of the 5' untranslated region of
#=GF RT   coxsackievirus B3 RNA: In vivo translational and infectivity studies of
#=GF RT   full-length mutants.
#=GF RA   Liu Z, Carthy CM, Cheung P, Bohunek L, Wilson JE, McManus BM, Yang D
#=GF RL   Virology 1999;265:206-217.
#=GF RN   [2]
#=GF RM   12384597
#=GF RT   La autoantigen is required for the internal ribosome entry site-mediated
#=GF RT   translation of Coxsackievirus B3 RNA.
#=GF RA   Ray PS, Das S
#=GF RL   Nucleic Acids Res 2002;30:4500-4508.
#=GF CC   This family represents the Picornavirus internal ribosome entry site
#=GF CC   (IRES). IRES elements allow cap and end-independent translation of mRNA in
#=GF CC   the host cell. It has been found that La autoantigen (La) is required for
#=GF CC   Coxsackievirus B3 (CVB3) IRES-mediated translation, and it has been
#=GF CC   suggested that La may be required for the efficient translation of the
#=GF CC   viral RNA in the pancreas [2].
#=GF WK   Picornavirus_internal_ribosome_entry_site_(IRES)
#=GF SQ   92


L76395.1/344-595   AUGGGACGCUCUAAAACAGACACGGUGCG-AAGAGUCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCCAAUCCUAACUGCGGAGCACAU-ACUCCCAAUCCAGGGAGCAGUGUGUCGUAAUGGGUAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUCAC-AU-UGACUGCUUAUGGUGACAAUUGAAAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGUCNNCCGGUG
AY278549.1/390-640 AUAGGACG-UUAGAUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACAUAAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAGGC-GGUCGCGAACCAGUGACUGGCUUGUCGUAACGCGCAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUGUU-AUUUUUAU-CA-UGGCUGCUUAUGGUGACAAUCA-GAGA-UUGUUAUCAUAAAGCGAAUUGGAUUGGCCAUCCGGUG
AF352027.1/395-646 AUAGGACGCUCUAAUGUGGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGUGGAGCACAU-GCCUUCAAUCCAGAGGGUAGUGUGUCGUAAUGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUCUUUAC-AU-UGGCUGCUUAUGGUGACGAUUAUAGAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AJ295193.1/354-605 GUAGGACGCUCUAAUACAGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUGGUAAUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACAU-ACCCUCAAACCAGGGGGCAGUGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCAUUUU-AUUCCUAU-AC-UGGCUGCUUAUGGUGACAAUUGACAGG-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AB059820.1/266-517 AUAGGACGCUCUAAUGUGGACAUGGUGCG-AAGAGCCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACAU-GCCUUCAACCCAGAGGGUAGUGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCUUUUU-AUUCUCAU-AU-UGGCUGCUUAUGGUGACAAUUACAGAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AJ133661.1/395-646 AUGGGACGCUUCAAUACUGACAUGGUGUG-AAGAGUCUAUUGAGCUAAUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAGAU-ACCCACACGCCAGUGGGCAGUCUGUCGUAAUGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUAU-AU-UGGCUGCUUAUGGUGACAAUUAAAAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCAGUG
AY055147.1/295-546 AUGGGACGCUCUAAUUCUGACAUGGUGUG-AAGAGCCUAUUGAGCUAGCUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGUGGAGCACAU-GCUCACAAACCAGUGGGUGGUGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCCUAC-AU-UGGCUGCUUAUGGUGACAAUCA-AAGAGUUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AF177911.1/397-647 AUGGGACGCUCUAAUACAGACAUGGUGUG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACGC-ACCCUCAACCCAGGGGGUGGCGUGUCGUAAUGGGUAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCCU-U-AC-UGGCUGCUUAUGGUGACAAUUGAAAAG-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
X04468.1/392-643   CACAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUACUGAGCUACAUGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCUCAACCACGGAGCAGGU-AGUCACAAACCAGUGAUUUGCCUGUCGUAACGCGAAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUCAU-UA-UGGCUGCUUAUGGUGACAAUCC-UAGA-UUGUUAUCAUAAAGUGAGCUGGAUUGGCCAUCCGGUG
AY238473.1/393-644 CACAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACCUGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAGGC-AGUGGCAAUCCAGCGACCAGCCUGUCGUAACGCGCAAGUUCGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUUUUAC-AA-UGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAAAGCAAAUUGGAUUGGCCAUCCGGUG
X67706.1/394-645   GUAGGACGCUUCAAUACAGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACAU-ACCCUCAACCCAGGGGGCAGUGUGUCGUAACGGGUAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUCCUUAC-AU-UGGCUGCUUAUGGUGACAAUUGAAAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCAGUG
AB081359.1/266-517 AUGGGACGCUCUAAUUCUGACAUGGUGCG-AAGAGCCUAUUGAGCUAGCUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACAC-ACCCACAAACCAGUGGGCAGUGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUCCUUAU-GU-UGGCUGCUUAUGGUGACAAUCA-AAGAGUUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AJ430385.1/389-639 CAUGGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACAUAAGAAUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCUCGGAGCAGGU-GGUCACAAACCAGUGAUUGGCCUGUCGUAACGCGCAAGUCCGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUUU-AU-UG-UGGCUGCUUAUGGUGACAAUCA-CAGA-UUGUUAUCAUAAAGCGAAUUGGAUUGGCCAUCCGGUG
AF499638.1/394-645 CACAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACAAGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCAGGU-GACUUCAAGCCAGAAGUUGGCCUGUCGUAACGCGUAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCCUUU-AUUCUUAC-AA-UGGCUGCUUAUGGUGACAAUCA-UAGA-UUGUUAUCAUAAGCCGAAUUGGAUUGGCCAUCGGGUG
AY056701.1/199-450 CAUGGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACCUAAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAAGU-GCCUUCAGCCCAGAAGGUAGCUUGUCGUAACGCGCAAGUCUGUGGCGGAACCGACUACUUUGGGUGUCCCGUGUUUCCCCUU-AUUUUCAU-UG-UGGCUGCUUGCGG-GACUAUAA-UUGA-UUGCCAUCAUAAAGCGAUUUGGAUUGGCCAUCCGGAG
AF448783.1/395-646 CACAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUAAUUGAGAAUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCAGGU-GGUUACAACCCAGUAACUGGCCUGUCGUAACGCGUAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCCUAU-AA-UGGCUGCUUAUGGUGACAAUCA-CAGA-UUGUUAUCAUAAAGCGAAUUGGAUUGGCCAUCCGGUG
X89534.1/277-528   AUAGGACGCUCUAAUACAGACAUGGUGUG-AAGAGUCUAUUGAGCUAGUUGGUGGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACAC-GCUCACAAGCCAGUGAGUGGUGUGUCGUAAUGGGUAACUCCGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AACUUCAU-UU-UGGCUGCUUAUGGUGACAAUUAAGAAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
X80059.1/395-646   AUAGGACGCUCUAAUACGGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGUUAAUCCUAACUGCGGACGACAU-ACCCCUAAUCCAAGGGGCAGUGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUUUUAU-AC-UGGCUGCUUAUGGUGACAAUCUC-AGAGUUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AY186745.1/373-624 AUGGGACGCUUCAAUACUGACAUGGUGCG-AAGAGUCUACUGAGCUAGCUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAGGC-AAUCACAAUCCAGUGGGUGGCCUGUCGUAACGGGCAACUCCGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCUUUUU-AUUCUUAC-AU-UGGCUGCUUAUGGUGACAAUUACAGAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCAGUG
AF081485.1/394-644 AUGGGACGCUUCAAUACUGACAUGGUGUG-AAGAGUCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCGUGC-GCUUGCAACCCAGUGAGUAGCACGUCGUAAUGGGUAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUU--AUUCCUUG-UC-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUGCCAUAUAGCUA-UUGGAUUGGCCAUCCGGUA
AY036578.1/392-643 AUGGGACGCUUCAAUACUGACAUGGUGCG-AAGAGUCUAUUGAGCUAAUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACUGCGGAGCAGAU-GCCCGCACGCCAGCGGGUAUUCUGUCGUAAUGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUACUAC-AU-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUA
U05876.1/398-649   ACAGGACGCUCUAAUAUGGACAUGGUGCA-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACAU-ACCCUCGACCCAGGGGGCAGUGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUAU-AC-UGGCUGCUUAUGGUGACAAUUGAAAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AF311939.1/395-646 ACAGGACGCUCUAAUACAGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACAU-GCCCACAAACCAGUGGGUGGUGUGUCGUAACGGGUAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCUAUUU-AUUCCUAU-AC-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUGCCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
D90457.1/396-647   CGCAGGACGCUAGUAGUGAACAGGGUGUG-AAGAGUCUAUUGAGCUACUUAAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCAUGGAGCAGGU-AGUUGCAAUCCAGCAGCCAGCCUGUCGUAACGCGCAAGUCCGUGGCGGAACCGACUACUUUGGGUAA-CCGUGUUUCCUUUU-AUUCUUUG-UA-UGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAGAGCGACUUGGAUUGGCCAUCCGGUG
AF499639.1/393-644 CACAGGACGCUAGUUGUGAACAAGGUGCG-AAGAGCCUAUUGAGCUACAAGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCAGGU-AGUUGCAAGCCAGCAAUCGACCUGUCGUAACGCGUAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AAUUUUAA-AC-UGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAAAGCGAAUUGGAUUGGCCAUCCGGUG
X89535.1/277-527   AUGGGACGCUCCAAUACUGACAUGGUGCG-AAGAGUCCACUGAGCUAGUUGGUAUUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAGGC-ACCCACGAGCCAGUGGGCAGCCUGUCGUAAUGGGUAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCAUUU-NCUUUU-U-AU-UGGCUGCUUAUGGUGACAAUCACGGAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCAGUG
L76401.1/374-625   AUAGGACGCUCUAAUACAGACAUGGUGCG-AAGAGUCUAUUGAGCUAGCUGGUAUUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGUGGAGCACAU-GCCCCUAAUCCAAGGGGUAGUGUGUCGUAAUGAGCAAUUCCGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUCUU-AUUCUUGU-AC-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AF105342.1/394-645 AUGGGACGCUUCAAUACUGACAUGGUGCG-AAGAGUCUAUUGAGCUAAUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAGGC-ACUCGCAGACCAGCGAGCAGCUUGUCGUAAUGGGCAACUCCGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUAUU-UCCUUUAC-AC-UGGCUGCUUAUGGUGACAAUUGAGAAA-UUGUUACCAUAUAGCUA-UUGGAGUGGCCAUCCGGUG
D00820.1/392-642   CAUGGGACGCUAGUUGUGAACAAGGUGCG-AAGAGCCUAUUGAGCUACCUGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCAAAU-GCUCACAAUCCAGUGAGUGGUUUGUCGUAAUGCGCAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUUUUAU-UA-UGGCUGCUUAUGGUGACAAUCU-GAGA-UUGUUAUCAUAUAGCUA-UUGGAUUAGCCAUCCGGUG
AF268065.1/393-644 AUGGGACGCUACAAUACUGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGUGGAGCAGAU-ACCCACGCACCAGUGGGCAGUCUGUCGUAAUGGGCAACUCCGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCUUUUU-AUUCCUAC-GC-UGGCUACUUAUGGUGACAAUUGAGAGA-CUGUAACCAUAUUGCUA-UCGGGUUGGCCACCUGGUG
D00538.1/387-638   CGUGGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACUCAAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAAUC-GCUCACGACCCAGUGAGUAGGUUGUCGUAAUGCGUAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCCUUU-AUAUUCAU-AC-UGGCUGCUUAUGGUGACAAUUUACGAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCACCCAGUG
S39291.1/394-645   GCAGGACGCUCUGAUACAGACAUGGUGUG-AAGAGCCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACAC-GUUCGCAAGCCAGCGAGUGGUGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUAC-CU-UGGCUGCUUAUGGUGACAAUUGAAAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCGUCCAGUG
D00627.1/394-645   AUAGGACGCUCUAAUGCUGACAUGGUGCG-AAGAGUCUAUUGAGCUAGCUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACUGCGGAGCACGC-ACCCUCAAACCAGGGGGCAGCGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCUUUUU-AUUCCUAU-AU-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AB081369.1/266-518 AUGGGACGCUCUAAUACGGACAUGGUGUG-AAGAGUCUACUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACUGCGGAGCACACAGCUCACAAGCCAGCGAGUAGUGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-ACUCUUAU-AU-UGGCUGCUUAUGGUGACAAUUAAAGAG-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AF114383.1/394-644 AUGGGACGCUUCAAUAUGGACAUGGUGUG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACGU-GCCUCCAUUCCAGGGGGUGGCGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUC-UUUU-AAUUUUAU-AC-UGGCUGCUUAUGGUGACAAUUGAAAGA-UUGUUGCCAUAUAGCUA-UUGGAUUGGCCAUCCGGUA
U16283.1/392-643   AUGGGACGCUUCAAUACUGACAUGGUGCG-AAGAGUCUAUUGAGCUAACUAGUAGUCUUCCGGCCCCUGAAUGCGGCUAAUCUUAACUGCGGAGCAGGU-GCUCACAAUCCAGUGGGUGGCCUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUCUCUUU-GU-UGGCUGCUUAUGGUGACAAUUGAAUGA-UUGUUGCCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AF230973.1/399-650 GUAGGACGCUUCAAAGUAGACAUGGUGUG-AAGAGUCGAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAUGU-GCCCUCAAUCCAGAGGGUGGCAUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCUUUUU-AUUUCUAU-AU-UGGCUGCUUAUGGUGACAAUUGAAGGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
D16364.1/393-644   AUGGGAUGCUUCAAUACUGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAGAU-ACCCACGCACCAGUGGGCAGUCUGUCGUAAUGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUCCUUAU-AC-UGGCUACUUAUGGUGACAAUUGAGAGA-UUGUAACCAUAUUGCUA-UUGGAUUGGCCACCCGGCG
L76398.1/187-438   AUGGGACGCUUCAAUACUGACAUGGUGUG-AAGAGUCUAUUGAGCUAAUURGUAGUNMUCMGGCCCCUGAAUGCGGCUAAUCCUAACCGCGGAGCAGAU-ACCCACAUGCCAGUGGGAAGUCUGUCGUAAUGGGCAACUCUGCGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCCUUU-AUYUUUGU-AC-UGGCUGCUUAUGGUGACAAUUGAAAGA-UUGUUACCAUAUAGCYA-UUGGAUUGGCCAUCCAGUG
X79047.1/392-643   AUGGGACGCUUCAAUACUGACAUGGUGUG-AAGAGUUGACUGAGCUAGCUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGUGGAGCAAGU-GCCCACAACCCAGUGGGUGGCUUGUCGUAAUGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGA-CCGUGUUUCUCUUU-AUUCUUAU-AU-UGGCUGCUUAUGGUGACAAUCUC-AGAGUUGUUACCAUAUAGCUA-UUGGUUUGGCCAACCAGUG
L76402.1/393-643   CAUAGGACGCUAGUUGUGAACAGGGUGUG-AAGAGCCUAUUGAGCUACUAAAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCGAGU-GCUUGCAGACCAGCGAGUGGCCUGUCGUAACGCGCAAGUCCGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUCAU-UA-UGGCUGCUUAUGGUGACAAUCU-GAGA-UUGUUAUCAUAUAGCUA-UUGGAUUGGCCAUCCGGAG
L76399.1/392-643   AUAGGACGCUUCAAUAUGGACAUGGUGUG-AAGAGUCUAUUGAGCUAGUUGGUNNNNNUCCGGCCCCUGAAUGCGGCUAAUCCCAACCGCGGAGCAGGU-ACCCACAAACCAGUGGGGAGCCUGUCGUAAUGGGCAACUCUGCGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCUUNUU-AUUCUUAU-AC-UGGCUGCUUAUGGUGACAAUUGAUAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCUGGUG
L76403.1/394-645   CACAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACAUGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAGGU-GACUUCAAGCCAGAGGUUUGCCUGUCGUAACGCGCAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCCUUU-UACUUUAU-RA-UGGCUGCUUAUGGUGACAAUCA-UAGA-UUGUUAUCAUAAAGCGAAUUGGAUUGGCCAUCCGGUG
AF225473.1/351-602 AUGGGACGCUUCAAUACUGACAUGGUGCG-AAGAGUCUAUUGAGCUAAUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACUGCGGAGCACGC-GACCUCAAUCCAGAGGAUGGCGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUCUCUUU-AC-UGGCUGCUUAUGGUGACAAUUGAACAG-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AF169670.1/305-556 AUGGGACGCUCUUAUACAGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUGGUAUUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGUGGAUCAUGC-GCCCUCAAACCAGAGGGAAGCGUGUCGUAAUGGGCAACUCCGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCAUUUU-AUUCUUAC-UU-UGGCUGCUUAUGGUGACAAUUGAAAGG-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AJ295171.1/269-520 AUAGGACGCUUCAAUACGGACAUGGUGAG-AAGAGUCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCAGAGCAGAU-UCCCACACGCCAGUGGGUAGUCUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUGU-AC-UGGCUGCUUAUGGUGACAAUUGAAAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCACCCAGUG
AY167104.1/375-626 AUGGGACGCUUCAAUACUGACAUGGUGCG-AAGAGUCUAUUGAGCUAAUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAGAU-ACCCACACACCAGUGGGCAGUCUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCUCUUU-AUCCUCAU-AC-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AF499640.1/390-641 CACAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACAAGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAAGU-GCUCACGAACCAGUGAGUGGCUUGUCGUAACGAGCAAUUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-UAACUUUA-AA-UGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAAGCCGAAUUGGAUUGGCCAUCCGGUG
Y14459.1/388-637   AUAGGACGCCUCUUAGAUGACAGGGUGUG-AAGAGCCUACUGAGCUGGGUAGUAGU-CUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCGUCC-ACCAGCAAUCCAGCUGGCAGGGCGUCGUAACGGGCAACUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUUGAUCCU-AU-UU-UGGCUGCUUAUGGUGACAACGA-UAAG-UUGUUAUCAUAAAGCUC-UUGGGUUGGCCACCUGGAA
L76412.1/390-641   CAUGGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACANAAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAAGC-GGUCACGAACCAGUGAUUGGCUUGUCGUAACGCGCAAGUCCGUGGCGGAACCGACUACUUUGGGUGA-CCGUGUUUCCUGUU-AUUUUUAU-UG-CGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAAAGCGAAUUGGAUUGGCCAUCCGGUG
L76404.1/392-643   CACAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACAAGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCGGGU-GACCACAAGCCAGUGGUCCAUUCGUCGUAACGCGUAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUAU-UA-UGGCUGCUUAUGGUGACAAUCG-UUGA-UUGUUAUCAUAUAGCGAAUUGGAUUGGCCAUCCGGUG
AJ295198.1/352-602 AUAGGACGCUUCAAUAUGGACAUGGUGUG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACGU-GCUCUCAACCCAGAGGGUGGCGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCCUUU-AUCUUU-U-AC-UGGCUGCUUAUGGUGACAAUUGAAAGG-UUGUUGCCAUAUAGCUA-UUGGAUUGGCCAUCCAGUG
AF541919.1/382-632 CACGGGACGCUAGUUGUGAACAGGGUGUG-AAGAGCCUAUUGAGCUACAUGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCAUGGAGCAGGC-AGCUGCAACCCAGCAGCCAGCCUGUCGUAACGCGCAAGUCCGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUU-G-AA-UGGCUGCUUAUGGUGACAAUCA-UAGA-UUGUUAUCAUAAAGCGAGUUGGAUUGGCCAUCCAGUG
AJ295202.1/354-605 AUAGGACGCUCAAAUACAGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUAGUACUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAAGU-ACUCACAAUCCAGUGGGCAGCUUGUCGUAACGGGUAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCCUAC-AU-UGGCUGCUUAUGGUGACAAUCA-AAGAGUUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
X92886.1/392-642   AUGGGACGCUUCAAUACUGACAUGGUGUG-AAGAGUCUAUUGAGCUAAUUGGAUGU-CUCCGGCCCCUGAAUACGGCUAAUCCUAAUCGCGGAGCAGAU-ACCCACGCACCAGUGGGCAGUCUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUGU-AC-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCAGUG
AF132497.1/147-398 AUGGGACGCUUCAAUACUGACAUGGUGUG-AAGAGUCUAUUGAGCUAAUUGGUAGUCCUCCGGCCCCUGAAUGCGGAUAAUCCUAACUGCGGAGCAGAC-GCUAGCAAACCAGCGAGUAGUCUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUCAU-AC-UGGCUGCUUAUGGUGACAAUUGAAGAA-UUGUUGCCAUAUAGCUA-UUGGAUUGGCCAUCCAGUG
AJ295172.1/350-601 AUGGGACGCUUCAAUACAGACAUGGUGUG-AAGAGUCUAUUGAAAUAAUUGAUAGUUAUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAGAU-UCCCACAUGCCAGUGGGCAGUCUGUCGUAAUGGGUAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUGU-GC-UGGCUGCUAAUGGUGACAAUUGAAAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCACCCAGUG
AF328683.1/393-644 CACAGACGCUCUAAUACAGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUAGUAAUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACUGCGGAGCACAU-UCCCACAAACCAGUGGGUAGUG-GUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUUAUUUUUUAU-AU-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AJ293918.1/392-644 CAUGGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACCCAAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAAGU-GUCCUCAACCCAGGGGAUGGCUUGUCGUAACGCGAAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUUUUAUGUA-UGGCUGCUUAUGGUGACAAUCA-AAGG-UUGUUACCAUAAAGCAAUUUGGAUUGGCCAUCCGGUG
AF499641.1/391-641 CAUGGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACUCAAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCGAGU-GCUCACAAUCCAGUGAGUGGCUUGUCGUAACGCGCAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUUUUAC-UA-UGGCUGCUUAUGGUGACAAUCU-AGGA-UUGUUAUCAUAUAGCUU-UUGGAUUGGCCAUCCGGUG
L76413.1/391-642   CAUGGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACUUAGGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCUUAACCACGGAUCAAGU-GCCUUCAAACCAGGAGGUGGCUUGUCGUAAUGCGCAAGUCCGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-NUUUCNUN-UG-UGGCUGCUUAUGGUGACAAUCA-UAGA-UUGUUAUCAUAAAGCGAAUUGGAUUGGCCAUCCGGUG
L76405.1/393-644   CACAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACAAGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCAGGU-AGUUGCAAACCAGCAACUGGCCUGUCGUAAUGCGCAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUUUUAC-AA-UGGCUGCUUAUGGUGACAAUCA-UAGA-UUGUUAUCAUAAAGCGAUUUGGAUUGGCCAUCCGGUG
U77070.1/391-641   AUGGGACGCUUCAAUACUGACAUGGUGCG-AAGAGUCCAUUGAGCUAAUUGGUAGU-CUCCGGCCCCUGAAUGCGGCUAAUCCCAACUGCGGAGCAGAC-ACCCACAAGCCAGUGGGCAGUCUGUCGUAACGGGUAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUAU-AC-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCACCCGGUG
AY278553.1/392-643 CACAGGACGCUAGAUGUGAACAAGGUGUG-AAGAGCCCACUGAGCUACAAGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCAGGU-AGUUGCAAACCAGCAGCCGGCCUGUCGUAACGCGCAAGUCUGUGGCGGAACCGACUACUUUGGGUGA-CCGUGUUUCCUUUU-AUCUUUUC-AA-UGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAAAGCGACUUGGAUUGGCCAUCCGGUG
X84981.1/391-641   AUAGGACGCUCUAAUACGGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUAGU-GUUCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGUGGAGCACAU-GCCCCUAAUCCAAGGGGUAGUGUGUCGUAACGGGCAACUCCGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUAC-AU-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUGCCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
U22521.1/394-645   AUAGGACGCUCUAAUACGGACAUGGCGUG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACAU-ACCCUUAAUCCAAAGGGCAGUGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCUUUUU-AUUCUUGU-AU-UGGCUGCUUAUGGUGACAAUUAAAGAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCAGUG
AY055151.1/298-550 AUAGGACGCUCUAAUGCGGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUAGUGGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACAU-GCCUUCAAUCCAGAGGGUAGUGUGUCGUAAUGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGG-CCGGGUUUCCUUUUAUUCCUUAU-AU-UGGCUGCUUAUGGGGACAAUUACAGAA-UUGUUACCAUAUAGCUA-UUGGAUCGCCCAUCCGGUG
AY167106.1/374-624 AUGGGACGCUUCAAUGUGGACAUGGUGCG-AAGAGUCUAUUGAGCUGGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACGC-GCCCUCACUCCAGAGGGUAGCGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUAUUU-U-AU-UGGCUGCUUAUGGUGACAAUCAAAGAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AF499642.1/390-641 CAUAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACUUGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCAUGGAGCAGGC-GGUCACAGACCAGUGACUAGCUUGUCGUAAUGCGCAAGUCUAUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUUUUAU-UA-UGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAAAGCGAAUUGGAUUGGCCAUCCGGUG
AF317694.1/391-642 AUGGGACGCUCUAAUAUGGACAUGGUGUG-AAGAGUCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAUGU-ACCUCCAAUCCAGGAGGUGGCGUGUCGUAAUGGGCAACUCUGCAGCGGAACCGACUACUUUGGGAGU-CCGUGUUUCCUUUU-AUUCUUAC-AC-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
L76406.1/393-645   CACAGGACGCUAGUUGUGAACAGGGUGUG-AAGAGCCUAUUGAGCUACAUGAGAAUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCAAGU-GAUCGCAAACCAGUGAUUAGCUUGUCGUAACGCGCAAGUCUGUGGCGGAACCGACUACUUUGGGUGA-CCGUGUUUCCUUUU-AUUUUUNU-UCNUGGCUGCUUAUGGUGACAAUCA-UAGA-UUGUUAUCAUAAAGCGAAUUGGAUUGGCCAUCCGGUG
AF363454.1/426-676 AUAGGACGCCAUUUCAGUGACAGGGUGUG-AAGAGCCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCGUCC-ACCAGCAAACCAGCUGACAGGGCGUCGUAACGGGUAACUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUUGAUCCU-AU-UU-UGGCUGCUUAUGGUGACAACGA-UAAG-UUGUUAUCAUAAAGCUU-UUGGGUUGGCCACCUGGAA
X90722.2/392-643   AUAGGACGCUCUAAUACAGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGAUAAUCCUAACUGUGGAGCAGAU-ACCCACGAACCAGUGGGCAGUCUGUCGUAACGGGCAACUCCGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCCAAA-UC-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUGCCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AF169665.1/311-562 ACAGGACGCUCUAAUACAGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAUGC-ACCCACAAGCCAGUGGGUAGCGUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGA-CCGUGUUUCUUUUU-AUUCUCUC-AU-UGGCUGCUUAUGGUGACAAUUGAGGAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AJ295190.1/353-605 CACAGGACGCUAGUUGUGAACAAGGUGUGGAAGAGCCUAUUCAGCUACAUGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAGGC-GAUCGCAAACCAGCAAUUAGCCUGUCGUAACGCGAAAGUCUGUGGCGGAACCGACUACUUUGGGUGA-CCGUGUUUC-UCUU-AUUUUUAU-UCAUGGCUGCUUAUGGUGACAAUCA-UAGA-UUGUUAUCAUAAAGCGAGUUGGAUUGGCCAUCCGGUA
AY167107.1/373-624 GUGGGACGCUUCAAUACUGACAUGGUGCG-AAGAGCCUAUUGAGCUAAUUGGUAUUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACUGCGGAGCAGAU-ACCCACACACCAGUGGGCAGUCUGUCGUAACGGGCGACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCAUUU-AC-UGGCUGCUUAUGGUGACAAUUGAGAAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AF499643.1/390-640 CAUGGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACUUGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAAGU-GCUCUCAAACCAGAGAGUGGCUUGUCGUAACGCGUAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUUUUAU-CA-UGGCUGCUUAUGGUGACAAUCU-AAGA-UUGUUAUCAUAUAGCUU-UUGGAUUGGCCAUCCGGUU
AF499635.1/390-640 CAUGGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACUUGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCAUGGAGCAAGU-GCCCACAAGCCAGUGGGUGGCUUGUCGUAAUGCGCAAGUCUAUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUAU-UA-UGGCUGCUUAUGGUGACAACCU-AAGA-UUGUUGUCAUAUAGCUU-UUGGAUUGGCCAUCCGGUG
AY062273.1/288-534 AUGAGACGCU-AGACAUGAACAAGGUGUG-AAGAGUUUAUUGAGCUACUAUAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCAUGGAGCAAGU-GCUCACAAACCAGUGGGUUGCUUGUCGUAACGCGCAAGUCCGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCACUUU-UUACUU-U-UA-UGACUGCUAAUGGUGACAAUUU-AAUA-UUGUUACCAUUUGGCUUGUCAAAUUG---AUCACAUA
AJ288062.2/207-458 CAUAGGACGCUAGAUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACACGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAAGC-GGUCACGAACCAGUGGCUGGCUUGUCGUAACGCGCAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUGUU-AUUUUUAU-CA-UGGCUGCUUAUGGUGACAAUCU-GUGA-UUGUUAUCAUAAAGCGAUUUGGAUUGGCCAUCCGGUG
AF225477.1/351-602 AUGGGACGCUUCAAUAUGGACAUGGUGUG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGUGGAGCAUGC-GCCCCCAUUCCAGAGGGUAGCGUGUCGUAACGGGUAACUCCGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-ACCUCUAU-AU-UGGCUGCUUAUGGUGACAAUUGAAAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCACCCGGUG
AF504533.1/308-559 AUGGGACGCUCUAAGAUGGACAUGGUGCG-AAGAGCCUAUUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACUGCGGAGCAUGU-GUCUUCACUCCAGAAGAUAGCAUGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCCUAC-AC-UGGCUGCUUAUGGUGACAAUUCAAGAA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
L76393.1/393-644   CACAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACANGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCACGGAGCAGGU-GGUUGCAACCCAGCAACCGGCCUGUCGUAACGCGCAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUUUAAAUU-NU-UG-UGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAAAGCGAUUUGGAUUGGCCAUCCGGUG
X90723.2/393-644   AUAGGACGCUUCAAUGUGGACAUGGUGUG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAAUCUCGGAGCAGGC-ACCCACAAACCAGUGGGCAACCUGUCGUAAUGGGUAACUCUGCGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCCUUU-AUUCUUGU-AU-UGGCUGCUUAUGGUGACAAUUAGGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AJ295191.1/358-608 AUGGGACGCUCUAAUAUGGACAUGGUGUG-AAGAGUCUAUUGAGCUAGUUAGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCACGU-GUCCCCAACCCAGGGGAUAGCGUGUCGUAACGGGUGACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUU--AUUCUUAU-CC-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGUUAUCCGGUG
X89532.1/277-528   AUGGGACGCUUCAAUACUGACAUGGUGCG-AACAGUCUACUGAGCUAGUUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAGGU-ACCCACGAGCCAGUGGGCAGCCUGUCGUAAUGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCAUUU-ACUCUUAU-AC-UGGCUGCUUAUGGUGACAAUCAC-GGAAUUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCAGUG
L76408.1/391-642   CACAGGACGCUAGUUGUGAACAAGGUGCG-AAGAGCCUACUGAGCUACUAGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCGGGU-GCUCACAAGCCAGUGAGUUGCCUGUCGUAAGGCGUAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCUAUUU-AUCUC-AU-AUAUGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAAAGCGAGUUGGAUUGGCCAUCCGGUG
L76394.1/391-643   CACAGGACGCUAGAUUUGAACAAGGUGCG-AAGAGUCUAUUGAGCUACCAAAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCCAACCACGGAGCAGGC-GCUCACAAUCCAGUGAAUAGCCUGUCGUAACGCGUAAGUCUGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCAUUU-UCUCUCUUGUA-UGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAAAGCGAACUGGAUUGGCCACCCGGAG
X90724.2/394-645   AUGAGACGCUUCAAUACUGACAUGGUGCG-AAGAGUCUAUUGAGCUAACUGGUAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCAGGC-GCUCGCAAACCAGUGAGUAGCCUGUCGUAACGGGUAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUUCUUAU-AU-UGGCUGCUUAUGGUGACAAUUGAGAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUG
AJ295192.1/353-604 AUAGGACGCUCUAAUACGGACAUGGUGCG-AAGAGUCUAUUGAGCUAGUUGGUAGUAGUCCGGCCCCUGAAUGCGGCUAAUCCUAACUGCGGAGCGCGC-GCCCCCAUUCCAGGAGGUAGCGCGUCGUAACGGGCAACUCUGCAGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-AUCUUUAU-UC-UGGCUGCUUAUGGUGACAAUUGACAGA-UUGUUACCAUAUAGCUA-UUGGAUUGGCCAUCCGGUC
AF499637.1/391-642 CAUAGGACGCUAGUUGUGAACAAGGUGUG-AAGAGCCUAUUGAGCUACACAAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCAUGGAGCAAGU-GAUCACAAUCCAGUGAUAUUCUUGUCGUAACGCGCAAGUCCGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCCUUUU-ACUUUUAU-CA-UGGCUGCUUAUGGUGACAAUCA-UUGA-UUGUUAUCAUAAAGCGAAUUGGAUUGGCCAUCCGGUG
AY062275.1/288-534 AUG-AGACGCUAGACAUGAACAAGGUGUG-AAGAGUCUAUUGAGCUGCUAUAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCAUGGAGCAAGU-GCUCACAAACCAGUGAGUUACUUGUCGUAACGCGCAAGUCCGUGGCGGAACCGACUACUUUGGGUGU-CCGUGUUUCACUUU-UUACUUUU-AU--GACUGCUAAUGGUGACAAUUU-AAUA-UUGUUACCAUUUGGCUUGUCGAAUUG---AUCACAUA
#=GC SS_cons       :::<<<___>>>,,,,,,,<<___>>,,,.,,,,((------(((((---((--------(((-(((------(((----(((---(((((((,<<<<<.<<<<<<______>>>>>>>->>>><<<<_>>>>,,,,,)))))))-)))-)))--------)))---.)))-----------.--))----.--.)))))))-<<<<<<<<<<<<<____>>.>>>>>>>>>>>::::::.:::::::::::::::::::
#=GC RF            auagggcgccccaaUauggaCAuGGuGuG.AAGAGcCUAUUGaGCuaguugguAGUCCUCCGGCCCCUGAAUGCGGCUAAuCCUAACcgcgGaGCaggc.gcccgCAaaCCAGcgggcgGccuGcCGuAaCGgGcAAcuCcgcgGCGGaACCGACUACUUUGGGUGU.CCGUGUUUCcuUUU.AUccUUau.au.ugGCugCUuauGGugaCaaucaaaaga.uuGuuaCCauauAGCuA.UUGGAUUGGCCAUCcgGUG
//
# STOCKHOLM 1.0

#=GF AC   RF00230
#=GF ID   T-box
#=GF DE   T-box leader
#=GF AU   Barrick JE
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Vitreschak AG
#=GF AU   Gelfand MS
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Barrick JE, predicted; Vitreschak A, PMID:12770710
#=GF SS   Published; PMID:12770710
#=GF GA   93.00
#=GF TC   93.00
#=GF NC   92.90
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.50 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000140; attenuator;
#=GF DR   GO; 0000049; tRNA binding;
#=GF RN   [1]
#=GF RM   8045882
#=GF RT   Interaction between the acceptor end of tRNA and the T box stimulates
#=GF RT   antitermination in the Bacillus subtilis tyrS gene: a new role for the
#=GF RT   discriminator base.
#=GF RA   Grundy FJ, Rollins SM, Henkin TM
#=GF RL   J Bacteriol 1994;176:4518-4526.
#=GF RN   [2]
#=GF RM   10943892
#=GF RT   tRNA determinants for transcription antitermination of the Bacillus
#=GF RT   subtilis tyrS gene.
#=GF RA   Grundy FJ, Collins JA, Rollins SM, Henkin TM
#=GF RL   RNA 2000;6:1131-1141.
#=GF RN   [3]
#=GF RM   11497434
#=GF RT   The GA motif: an RNA element common to bacterial antitermination systems,
#=GF RT   rRNA, and eukaryotic RNAs.
#=GF RA   Winkler WC, Grundy FJ, Murphy BA, Henkin TM
#=GF RL   RNA 2001;7:1165-1172.
#=GF RN   [4]
#=GF RM   12547201
#=GF RT   Solution structure of the Bacillus subtilis T-box antiterminator RNA:
#=GF RT   seven nucleotide bulge characterized by stacking and flexibility.
#=GF RA   Gerdeman MS, Henkin TM, Hines JV
#=GF RL   J Mol Biol 2003;326:189-201.
#=GF CC   Uncharged tRNA acts as the effector for transcription antitermination of
#=GF CC   genes in the T-box leader family [1-3]. T-boxes are found upstream of many
#=GF CC   aminoacyl-tRNA synthetase genes and some amino acid biosynthetic genes
#=GF CC   usually in Gram-positive bacteria. The anticodon of a specific tRNA base
#=GF CC   pairs to a specifier sequence within the T-box motif, and the NCCA
#=GF CC   acceptor tail of the tRNA base pairs to a conserved bulge in the T-box
#=GF CC   antiterminator hairpin [4].
#=GF WK   T-box_leader
#=GF SQ   48


AE017335.3/64645-64865     AUUCGAGCAUU-GA-ACGGA--CAAAGUAGUG-UCUAUU-UCCCUA-UUU--------------------------CAGAGA--GCUGAUGGUU---GGUGUGA--AUCAGU---AUAAAG-AUAUGAC-AUGAAA--UUCA-UCCU-GGAGCA----------UCUUUCAUGAC--GAAUUA-----------------UUACUUGUGAUGAA-AGACGGUAGUUUA----UACCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------ACAAAUAGAGU-GGUGAAGU------------------------------------------------------------------------------------UUCUUCAC---AAC--UAGGGUGGUACCGCGAUC-----AUUU-----AUCGUCCCUACA
AE017355.1/4358542-4358291 UGAAAGACGAU-GA-UAAGG--AAAAGUAGUA-UAUAC--UAUAAU-CCA--------------------------AAGCGA--GUCAGGGAC----GGUGAGA-GCCUGAU---GAGGCG--GUAUAU-GUGAAG--AACA-CCUU-GGAGUU----------GCUAACCGAAA--UUGAAUCUUGUAU----------UCAAGAGUAGACUU-AGACGGGAAUCCG----GCCUGUUACAAACCGGGAAGUA---------------------------------------------------------------------------------------------------------------------------------------UGUAUUACAUACGA-GUUAAAGU----------------------------------------------------------------------------------UGGUCUUUAUGACAAA--UUGGGUGGUACCGCGAAGU----UUAA--CCUUUCGUCCCUUUA
AE017355.1/1226056-1226300 AUGAAAUCGUUUAA-GUAAG--AAGAGUACGU-AUAUUG-GAGACG-UUA--------------------------CAGAGA--GCCGGGGAUA---GGUGGGA-GCCCGGU---GCGGUG-CUAUAUA-CGGAA---UGGG-CUUA-CGAGA-----------GGUAUGCUGAA--CAAUUA-----------------UUUUCAGUAGGCA--ACCCGGGUUC-------CGCCGUUACAAGGAUAAGGUAUAUAUUUUG-------------------------------------------------------------------------------------------------------------------------------UACCUGAAUAAAGC-GGGAUGCU-----------------------------------------------------------------------------------UUUGCGUCC---AACA-UGAGGUGGUACCACGGUA-----AAUU----UAUCGUCCUCUAC
AE017334.2/1340126-1340353 AAGAAAGCGUU-GA-GAGGG--AGGAGUAGUU-GAUUGU-GAAGCC-UCA--------------------------CAGAGA--GUCGGUGGUU---GCUGGAA--ACCGAU----GGUUC--ACGUCG-ACGAAC--AUCG-CCCU-UGAGU-----------GCUAAGCUGAAG-C----------------------GUUUGUCUAGGCUU-AGACGGUAG--------CUCCGUUAUUAGCUAGACUCAU---------------------------------------------------------------------------------------------------------------------------------------UUAUGGGUCACUGA-GGCAAGAG-----------------------------------------------------------------------------------UAUUCUUGC---AAAG-AAGGGUGGUACCGCGAA------AUCU-----UUCGUCCCUUCA
AE017355.1/1391715-1391963 AUGAAAUCGAU-GA-GCAAG--AAGAGUAUGU-AUAUUU-GAUACG-UU---------------------------CAGAGA--GCUGGGGGAA---GGUGUGA-GCCCGGU---ACGAUA-AAAUAUA-CAGAA---UGGG-CUUG-CGAGA-----------GGUAUGUUGAA--C----------------------AUUGUAGUAGGCA--ACCCGGGUUC-------CGCCGUUAAAAGGAUAGAGUAUCGGAGUUUUUCCU--------------------------------------------------------------------------------------------------------------------------GUACUUGAACAAGU-GGGAUUUA-------------------------------------------------------------------------------------UCAAUCC---AAU--UGAGGUGGUACCACGGUAUUAACAUUACAUAUAUCGUCCUCUAC
AE017334.2/1382910-1382652 AAAAAUUCAUU-GA-CGAGA--ACGAGUACGU-UAUAGA-ACUGUC-CCC--------------------------CAGAGA--GUUGGCGAUUU--GCUGAAA--GCCAAC---GUUCAG-UGCGUAG-CCGAAA--AUCA-UCUC-CGAGAA----------GUAGAACCGAA--U----------------------GUUGCAGUAAGUUCUUACCGGCUGUC------CCCCGUUACAAGGAACACGUAUCAUGUU---------------------------------------------------------------------------------------------------------------------------------GUACGUUGCAGAGCCGUAUACAUAUAGACUCAUU---------------------------------------------------------------------UCUACAUGUAUA---AAU--UAGGGUGGUAUCGCGGGUAAAU-AUAA-----CUCGUCCCUUUC
AE017334.2/2727398-2727177 AUAUAUGCGCU-GA-AGAGGA-AACAGUAGUG-CUUAUC-UCACUG-UUA--------------------------AAGAGA--GCUGAUGGUA---GGUGUGA--AUCAGU---ACAAAG--AUAAGC-AUGAAU--UACAGCCUU-GGAGCA----------UCUUUUCCGCC--A----------------------ACUUUUGGAGGGAA-AGACGGUCAAAU-----GAUCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------AAGAAGAAGAGA-GGUAGACAGG------------------------------------------------------------------------------UAUUUAGUCUAC---AAC--UAGGGUGGUACCGCGAU------AAAU-----AUCGUCCCUACU
AE017355.1/2768289-2768053 AUGCAUGCGUU-GA-AAGGAAAAGCAGUAGUU-GUUGUU-UCCCUG-UAA--------------------------CAGAGA--GCUGGUGGUC---GGUGUGA--ACCAGU---ACAAAA--ACAAGA-GCGAAU--UACAGUCCU-AGAGCA----------UCUUUUUCGUA--GUAAAGAUAGUAUUUAU------CUUUAUGAAGGGAA-AGACGGUCAGAU-----GAUCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------ACAAUGAAGAGA-GGUAGACG--------------------------------------------------------------------------------AAAGAAGUCUAC---AAC--UAGGGUGGUACCGCGAU------AAAU-----AUCGUCCCUACU
AE017334.2/2761487-2761277 CGAAAAUCGUU-GA-AGGGA--AAUAGUACAU-AUGUCUUCUUGCG-AAA--------------------------GAGAGU--GGAAUUCACCG--GCUGAAA--GAUUCC---UCGUAUAGAAUAUA-UCGAA---CCUA-UCCC-UGAGU------------CUUAAAUGAA---------------------------------AGUUUA-GG-CGUUCGC-------CUGCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------UAGGCACCAAGU-GGAUAUCU-----------------------------------------------------------------------------------AUGUAUAUC---AAU--UAAGGUGGUACCGCGGAACA---AUGA-CCGUUUCGUCCUUUUU
AE017334.2/3964823-3965043 GAAUCGGCGUU-GA-UAGGA--UUUAGUAGUA-UUUCGA-UUUCUGAUUU--------------------------CAGAGA--GCUGGCGGUC---GGUGCGA--ACCAGU---ACAGAA--CGAAUU-AUGAAU--UACC-CCCU-GGAGCU----------UCUUUUGCGAAACG----------------------UAAGAAGUAGUGAA-AGACGGUUAUA------GACCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------UGUCUAAAGAGU-GGUGAAACG-------------------------------------------------------------------------------AAACUGUUUCAC---AAUU-UAGGGUGGUACCGCGAA-------AUU-----UUCGUCCCUGCA
AE017334.2/4166233-4166461 AUAUCGGCUUU-GA-AGGAAU-ACCAGUAGCGACUUAUA-UCCCUG-UCU--------------------------CAGAGA--ACUGAUGGUU---GGUGCAA--AUCAGU---ACAUAU--ACAAGC-GUGAAU--UACAAUUCU-GGAGCU----------UCUUUCCCGUA--AUGCUUUUU--------------AUGCAUGAAGAGAA-AGACGGAUCU-------UUCCGUUA------------------------------------------------------------------------------------------------------------------------------------------------------UCUUAAAGUGAGU-GGUAAACAA-------------------------------------------------------------------------------UUACUUGUUUAC---AAA--UAGGGUGGUACCGCGAU------UUUU-----AUCGUCCCUAUC
AE017334.2/4266551-4266319 AUAAAUGCCUU-GA-AGGGG--AAGAGUAUAA-CAAGAA-ACGUCU-UCA--------------------------GAGAGG--AGAAUCAUUA---GCUGGGA--GAUUCU-CUAGAUAG--UUAUGU-UAGAAG--GUAG-CCCU-GGAGCA----------UCUUUUCUGAAC-GGAAUAG----------------UUCUCAUUAGGAAA-AGACGGAUUU-------GUCCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------UCAAGUUAAGA-GUAUAAGCAAAUUCCUG-----------------------------------------------------------------------GAUUUGUUUGUA---AAU--AAAGGUGGUACCGCGAU------GUCC-----CUCGUCCUUUUU
AE017334.2/4211066-4210836 AUAUAACCGUU-GA-UAGAG--AAGAGUAAAU-GAGAU--ACACAU-GGA--------------------------AAGAGA--AGAAAUGUCUUAGGCUGAAAACAUUUCU--ACAUGGU--GACUGA-UUGAAU--GACA-CUCU-AGAGGU----------UUCAACUUGAAC-GGCAUAUA---------------CGCUUAGUAGGGAU-GAACGCACAUUU-----AAGCGUUA---------------------------------------------------------------------------------------------------------------------------------------------------------UUAAAAAAGU-GGAAGCAU-----------------------------------------------------------------------------------ACGUGCUUC---AAU--UAGGGUGGCACCACGGGU-----AUAA-UACUCUCGUCCCUACU
AF188935.1/65116-65336     AUUCGAGCAUU-GA-ACGGA--CAAAGUAGUG-UCUAUU-UCCCUA-UUU--------------------------CAGAGA--GCUGAUGGUU---GGUGUGA--AUCAGU---AUAAAG-AUAUGAC-AUGAAA--UUCA-UCCU-GGAGCA----------UCUUUCAUGAC--GAAUUA-----------------UUACUUGUGAUGAA-AGACGGUAGUUUA----UACCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------ACAAAUAGAGU-GGUGAAGU------------------------------------------------------------------------------------UUCUUCAC---AAC--UAGGGUGGUACCGCGAUC-----AUUU-----AUCGUCCUACAU
AL591980.1/26617-26392     AUGAAAACAUC-AA-ACAAG--AAUAGUACUU-UUUCAU-CGAUUU-UUA--------------------------AAGAGA--GUUAGCGGUU---GGUGGGA--GCUAAU---AAAUAG-AUGAUUC-AGGAAU--GGGC-CUUG-UGCGU-----------GAUACCUUGAA--------------------------AUCAAGUAGGGGU-GAACGGGUGC-------UCCCGUUAUAGAGCAGCUGCAAAUA------------------------------------------------------------------------------------------------------------------------------------UUGCAGCACGGAGA--UAGGGUU------------------------------------------------------------------------------------UAUCCCUA---AAA--UGAGGUGGCACCGCGA-------UAAC------UCGUCCUCUGA
AL591980.1/26907-26666     AUGAUAGCAUU-GA-AGAAGA-GUAAGUAGCA-UGAUG---AAAGU-UUU--------------------------UAGAGA--GCUGACGGUU---GGUGAAA--GUCAGU---AGCGGA--CAUGAU-GUGAA---UGGA-CUUC-UGAGCU----------CUG-AUCUGAA--AGGAUU-----------------UUCUUAGUAGGAUA-CAGCGAUUAGGCCU---UAUCGUUACACAAGGCGCCCAUUCGAAAUU-------------------------------------------------------------------------------------------------------------------------------UGGAUGGAUUAAGU-GAACUGUU-----------------------------------------------------------------------------------UUUACAGUU---AAU--CAAGGUGGUACCACGGG-------UCU-----CUCGUCCUUGUC
AL591980.1/61543-61342     GAAAUAGCGAU-GA-AUUGG--AGUAGUAAUC-UGCAUAUUUUGAU-GUG--------------------------AAGAGA--GCUGACGGUU---GGUGCAA--GUCAGU---CACAAA--AUCUGG-AUGAA---CUUA-CCAU-GGAGCU----------UGGGUG-----------------------------------------UAU-CCCCGUUUU--------CCGCGUUA-----------------------------------------------------------------------------------------------------------------------------------------------------AGGAAUUGAUAAGUUGAGUGGUC-------------------------------------------------------------------------------------AAACACU---AAU--GUGGGUGGUACCGCGGGAGA---AGCA--UCUCUCGUCCCAUGG
AL596169.1/7643-7416       UUAAAACUAGC-GA-CAGAG--AAAAGUAAGA-AAAUC--CAUGCU-AUA--------------------------CAGAGAAUUUAUCCCAUUUG-GCUGAAA--GGAUAAAGAUAGUCA--UAUUUU-CCGAAA-AGACA-CUCU-CGAGGU----------UUCUUGUUGAA---------------------------AACAGUAAACAA-GAACGUAUUC-------AGGCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------ACUGACUUAAGU-GAGGACUU--------------------------------------------------------------------------------AUUAAUAGUUCU---AAU--UAGGGUGGUACCACGGGUGUAA-AUAA--ACUCUCGUCCCUUGU
AL596169.1/42600-42374     CUAAAUGCGAU-GA-AGAGG--AAGAGUAGGU-CAUUU---AUUUU-UCU--------------------------AAGAGA--GAAAGCGGUC---GGUGUAA--GCUUUC---AAAAAU---AAUGU-CUGAAG--GUAG-CCUU-GGAGCA----------GUUUUCCUGAA-------------------------AUAAUAGUAGGGAAUAACCGGUAGAUCUCGUCUAUCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------ACACAAUGAAGU-GCCUACAUU-------------------------------------------------------------------------------UCUUAUUGUAGG---UAA--AAAGGUGGUACCGCGAAU-----AAUACUCUUUUCGUCCUUUUA
AL596169.1/50920-50690     AACAAAGUGAU-GA-AAAGG--ACAACCAAUU-UAACG---GAAAA-UUA--------------------------UAGAGA--GGAAGGGCUA---GCUGGGA-ACCUUCU---AUUGGA--ACUUAA-AUUUGG--ACCA-CCUU-GGAACU----------UCUAUUAGGAAC-GUUUU------------------UUACUAGUAAUAAU-AGACGGAUCG-------CUCCGUUA-----------------------------------------------------------------------------------------------------------------------------------------------------CAGGCGACAAGAGU-GAAGUAGUUAA-----------------------------------------------------------------------------UUUUAGCUAUUUCUGAAUC-UUGGGUGGAACCACGAGC-----AUAA----ACUCGUCCCUUGA
AL596169.1/99989-99781     AAAAUGACUAU-GA-ACGGA--CGAAGUAGUU-GCUUAU-UCUUAU-UCC--------------------------UAGAGA--GCUAGUGGUU---GGUGGAA--ACUAGU---AGAGAU--AAGUAG-ACGAAU--UACA-UCCC-GGAGUCAC--------GCUGCACAGGA------------------------------UAAUGGUGC-GGCCGGUGUUG------AGCCGUUA----------------------------------------------------------------------------------------------------------------------------------------------------------UUUUUUGAA-GUAGGAUU------------------------------------------------------------------------------------UUUUCCUA---AAAG-UAGGGUGGUACCACGUUA-----AUUA----AUACGUCCCUUCG
AL596169.1/133792-133568   ACGAAAACAUG-AA-ACAAG--AAUAGUACUU-UUCAU--CGAUUU-UCA--------------------------AAGAGA--GUUAGCGUUU---GGUGCGA--GCUAAU---AAAUAG--AUGAAAUAGGAAU--GGGC-CUUG-UGCGU-----------GAUACCUUGAA--------------------------CUGAAGUAGGGGU-GAACGGGAGC-------UCCCGUUAUAGAGCAGCUGCAAAA-------------------------------------------------------------------------------------------------------------------------------------AAGCAGCACUGAGA-UAGGGGGA-------------------------------------------------------------------------------------UUCCCCU---AAAA-UGAGGUGGCACCGCGA-------UAAC------UCGUCCUCUGA
AL596169.1/134084-133841   AUGAUAGCUUU-GA-UGAAGA-GUAAGUAGCA-UGAUG---AAAGU-UUU--------------------------UAGAGA--GCUGACGGUU---GGUGAAA--GUCAGU---AGCGGA--CAUGAU-GUGAA---UGGA-CUUC-UGAGCU----------CUG-GUUUGAA--AAGGAAUU---------------UCCUUAGUAGGAUG-CAGCGAUUAGGCCU---UAUCGUUACACAAGGCGCCCAUUCGGAAUU-------------------------------------------------------------------------------------------------------------------------------UGGAUGGAUUAAGU-GAACUGUU-----------------------------------------------------------------------------------UUUGCAGUU---AAU--CAAGGUGGUACCACGGG-------UCU-----CUCGUCCUUGUC
AE017180.1/2085740-2085459 AAACAGGCCGU-GA-AGAGG--AGUAGUAGUC-CGACCC-CUUAUC-UUUGUCGGUAGCAGCGAAAAUGCCGACGCCAGAGA--GCCGGUGCUU---GGUGCAA--ACCGGU---AUAAGG--AA--GG-ACGAA---CUCG-CCUC-GGAGCC----------GCCCCCGCGAA--AUCGGUCGUUGUCGAUUGACGAUCCGCAGGUAGUUGG-GGCCGUAUC--------CCGCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AGGGAAAAUGA-GGUUCUUGUGUCGCCGUUUAUCGGC---------------------------------------------------------------GCAUGCGAGGACGA-AAA--AAGGGUGGUACCGCGAGC-----GCAA--GCCUUCGCCCCUUUA
BX571857.1/386293-385924   GUAAACACAAU-AA-AGAGG---AAAGUAAAA-CACACC-CUGCUU-AUA--------------------------CAGAGA--GUCUUUAGUA---GCUGAGA--GAAGAU---UUUGAA-AGCGUGU-UUGAAA--AUGG-CCUU-GGAGUG----------UUGAUGCCAAU------------------------------AUGAGGUGU-CUACGGGUUC-------GCCCGUUAUAGCGAUACAGUAUUAACAUUGAUGUUAAAUGGCGUACUGGAUUCUUUACGCACGAUUUUUUGUUAAUAAGUAUGGGAUAGCACAUUACUAUAUCCUUACUUACUGACUUUAAUUGUGAUAAUUGUUCAGUAAGCAUAUUUACUUUUAAUGCGUACUGAAUAA-GGUUAUUUCAG-----------------------------------------------------------------------------CGAUGGAAUAAC---AAAU-AAAGGUGGUACCGCGAAAC----AUAA--GCUUUCGUCCUUUUU
BX571857.1/1715591-1715290 UUUAAUAUAGG-AU-UUGGG--AAGAGUAAGU-UCAAA---UUAUU-UUA--------------------------AAGAGA--GCAUAUGAUUU--GGUGUGA--GUAUGU---AAAUGA--UUUUUA-CUGAAG--GUAG-CCCACAGAGUA----------UCUUAGCUGAAC-GUGA-------------------UUAAUAGUAGGCUA-AGACGUGUUU-------GAGCGUUAA----------------------------------------------------------------------------------------------------------------------------------------------------UCAUAAUCUAGAGU-GCUUGAAGAGAUGAAGCAUUUCAAAUUUCACGAUGAUAGUAUUGGUAUGAUUAUUCCAAUUAUGUUAAAAGAGUGAAUUUGAUAUUAAACAUCCUUCUUG---AAU--AUAGGUGGUACCACGGA-------AUA-----UCCGUCCUAUUU
BX571857.1/12485-12696     CAUUGUUCG-------UAGG--ACAAGUAAUA-UAUAGU-GUUCGA-UAU--------------------------CAGAGA--GCUUGUGGUU---AGUGUGA--ACAAGA---AUCAAC--AUAUAU-AUGAA---UCUA-CCUA-----------------CUUAAUUUAAA----------------------------------AGAAC-AAUCGGUGAU-------AACCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------UUUUAGUGAAGU-GCAAUUUAGGUUUAGUGUAUCUUUA---------------------------------------------------------------UAACUUAAAUUGUU-AAA--UAGGGUGGCAACGCGUA-------GAC-----CACGUCCCUUGU
BX571857.1/1674695-1674518 AUUCGUAU--------AAAG--AUGAGUAGUU-AAUGA--UUUGUU-UAU--------------------------CAGAGA--UGUACUGGUU---GGUGAAA--AGUACA---ACAAA----CAUUA-GUGAAC--GCUA-CUUU----AUG----------C-----------------------------------ACAACUGUA----------------------------UAG-------------------------------------------------------------------------------------------------------------------------------------------------------UCGAUUUAAAGU-GAUAAAUGUGUUG---------------------------------------------------------------------------AAUUGCAUUUAU---AAC--UAGGGUGGUACCGCGAU------AACG-----UUCGUCCCUUUU
BX571856.1/12478-12693     UAAGACAUUGU-UC-GUAGG--ACAAGUAAUA-UAUAGU-GUUCGA-UAU--------------------------CAGAGA--GCUUGUGGUU---AGUGUGA--ACAAGA---AUCAAC--AUAUAU-AUGAA---UCUA-CCUA-CUUAUU----------U------------A----------------------AAAGAACAA--------UCGGUGAU-------AACCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------UUUUAGUGAAGU-GCAAUUUAGGUUUAGUGUAUCUUUA---------------------------------------------------------------UAACUUAAAUUGUU-AAA--UAGGGUGGCAACGCGUA-------GAC-----CACGUCCCUUGU
AM180355.1/917359-917569   ACAAAUCCAAU-GA-UAGAG---AAAGUAGCA-UAUA----UGGAU-UUA--------------------------CAGCGA--GUUAGGGGUU---GGUGUAA-GCCUAGC---AAUGAA--GUCUAU-GUGAAG--AGAG-CUCU-GGAGGA----------GAUUAUCAGAA-------------------------ACUUUAGUAUGAUA-AUUGGUUUAC-------CCGCCUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AGGGAUUGAGA-GGAUAAGU---------------------------------------------------------------------------------ACUUACUUAUC---AAA--AAGAGUGGUAACGCGGAU-----AUAA-----UUCGUCUCUUAG
AM180355.1/17621-17826     UAAAAAGCUGU-GA-AGGAA--AAUAGUAAAA-AACAG---AUUGU-AUU--------------------------CAGAGA--AUGAGUGGAU---GGUGAAA--ACUCAU---UACAAU---GGUUU-UUGAA---UCUA-CUCU-AGAGCU----------UCUAGUU-------------------------------------AAAGCU-AGACGUUUAC-------CUACGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------UAGGUCUGAGA-GGAUUAUACAU-----------------------------------------------------------------------------UUUAGUAUAGUC---AAU--UAGGGUGGCAACGCGGAUAA---AAGA---UUUUCGUCCCUUUU
AM180355.1/2066647-2066854 UUAAAUCCUGU-GA-GAAAG---AGAGUAACU-UCUAU---GUGUU-UUA--------------------------UAGAGA--GCUGAGGAU----GGUGGAA-GCUUGGC---AAAUAA--GUAUUA-GUGAAA--AGAA-CUUU-GGAGGA----------UACUAAUUGAA---------------------------UUUAGUAUGUUA-GUAGGUAAUC-------UCGCCUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AGAGAAAGAGU-GGAUAAGU----------------------------------------------------------------------------------UUAUCUUAUC---AAU--UAGAGUGGUAACGCGGAU-----AUAU-----UUCGUCUCUUGG
AM180355.1/1762876-1763128 AUAAAUGCUAU-GA-AGAGA--AGAAGUAGGG-CUAGAU-UUUAUU-UAA--------------------------CAGAGA--GUUCCAGUUU---GGUGAAA--UGGAAU---AAAUUG-AUUUAGU-UUGAA---UACA-UCUC-AGAGCA----------CUAUCUCUGAA--AGAUAA-----------------CAACCAUUAAGAGA-UAUCGGAUUAGU-----ACACGUUAUAGUACACGAGUAUAUGUA----------------------------------------------------------------------------------------------------------------------------------AUUGUACUCUAAGA-GAUUAAUAUCG-----------------------------------------------------------------------------UGAGAUAUUGAUG--AAC--UAAGGUGGUAACACGUAA-----GCAA-UGCUUUCGUCCUUUUA
AM180355.1/1488475-1488713 ACAAAUACAGU-GA-UAAGG--AAUAGUAAAA-UAUUU--GAUGUC-UUA--------------------------CAGAGA--GAGGGAAAU----GCUGGAA--GCCCUU---AGAAUA--UGAUAU-UUGAA---GCAG-CCUU-UUAGUA----------GCAAUCUUGAA--CAAUUUAUCUUUUAUAAAGAAG-AUUUAAGUAGAGAU-UGACGGUAG--------UUACGUUAUAGCUA-----------------------------------------------------------------------------------------------------------------------------------------------AGGUUUUCCGAAGA-UAUCAUAC----------------------------------------------------------------------------------UUUGUAUGAU---AAU--UAGGGUGGUACCGCGAU------UGUC-----CUCGCCCCUAUA
AM180355.1/73005-73213     AAAUUAGCUAU-GAUAAAGA--AAUAGUAAAA-UGAUG--AAAUCU-UCA--------------------------CAGAGA--GAAAACGGU----GGUGAGA--GUUUUC---AAGAGG--AAGUCU-UUGAA---CCUG-UCUU-UUAGCU----------UAAAGGUAUAA---------------------------------AAAUCU-UUACGGUAGG-------AACCGUUA------------------------------------------------------------------------------------------------------------------------------------------------------UAUUCCCAAAAGA-GAGCUAUU-----------------------------------------------------------------------------------CAUAUAGCU---AAC--UAGAGUGGUACCGCGGAA-----AUUAAACCUUUCGUCUCUAUA
AM180355.1/1152611-1152857 AAAAAAGUGAU-GA-AUAGA--AGUAGUAAGA-ACAAU---GAAAC-UUU--------------------------CAGAGA--GCUAAAGGAU---GGUGUGA--UUUAGU---AGUUGA---UAGUU-CUGAA---CUUG-UCUA-GGAGCU----------GUUUUCUAAGA-------------------------UUUAAAUCUUAGAAUAAUCGGAGUAAUU----CCACGUUAUAGGAAAUAUAGUCAUUAUAAUUAUUGUAUU----------------------------------------------------------------------------------------------------------------------GGCUAUUACUAAGG-GAGCUUUU-----------------------------------------------------------------------------------UAGAAAGCU---AAA--UAGAGUGGUACCGCGAGC-----AAAA----CCUCGUCUCUAAU
AM180355.1/1830935-1831175 AAAAAGGCGAU-GA-AUAGG--AAGAGUAAAU-CUAAUU-CGAUUA-CCA--------------------------GAGAGA--AGAGUCCGUUG--GCUGGAA--GACUUU---UUAAAUUAGAGGGA-UUGAAA--ACUA-CCUA-GGAGCU----------ACU-UUCUGAA--GUCAUCUGCAUUAGUAG------AUUUUAGUAAGAAU-AGUCGUUAG--------CUGCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AAGUGUAAAGU-GAGUUUUCAUGA----------------------------------------------------------------------------CAUAUGAAAACU---AAA--UUAGGUGGAACCGCGGGA-----AUAA-UACUCUCGUCCUUAUG
AM180355.1/849427-849661   GUAAAUGCAAU-GA-AAGAG--GAAAGUAUUU-UGAUUA-AACUUA-GUA--------------------------AAGAGAU-AAACACCUAG---GCUGGGA--GUGUUU--UCUAAGA--GGUCAU-GAGAAG--UUCC-CUCU-GGAGUA----------ACAGAGCUGAAA-U----------------------UUUACAGUAGGCUU-UGACGUCAAAA------ACGCGUUA-----------------------------------------------------------------------------------------------------------------------------------------------------AGUUUGUUAGAGGU-GGUUUGAUGAUUUUU-------------------------------------------------------------------------AAAUUGUUAAAC---UAC--UAGGGUGGUACCGCGAAACU---AUAG--CCUUUCGUCCCUAGA
AM180355.1/1831241-1831476 AUAAAAGCGAU-GA-AUAGG--AAGAGUAAAU-UUAAU---UCGAC-UAU--------------------------CAGAGA--GGAAAGUUCACAGGCUGAAAGACUUUCU--AAGUUUG---AGAAA-UUGAAA--ACUA-CCUA-GGAGC-----------UGUGGUCUGAA--GUUACUUUAAAAA----------GUUUUAGUAAGACU-AACCGUUAA--------CUGCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AAGUGUAAAGU-GGAUUUUAUCAAUA--------------------------------------------------------------------------AAUGAUAAAAUC---AAA--UUGGGUGGAACCGCGAGU-----AUGG----ACUCGUCCCUUUA
AM180355.1/2451314-2451545 UGAAAGGCAUU-GA-UUAGG--AAGAGUAAAU-CUGAA---UCGAU-UAC--------------------------CAGAGAA-GGAAACUACUA--GCUGAAA-UGUUUCC-CUAAUUAG---AAGGA-UUGAAA--ACUA-CCUA-GGAGCU----------UCUAU-CCGAA--GUUAUCUUAAUG-----------AUUUUAGUAGGAAU-AGACGUUUUUAUUAC--UUGCGUUA--------------------------------------------------------------------------------------------------------------------------------------------------------AAGUAUCAAGU-GGAUUUUU-------------------------------------------------------------------------------------UAAAAUC---AAU--UUGGGUGGAACCGCGGGA-----AACA-GAUUCUCGUCCCUUUU
AM180355.1/683160-683398   AUCAUAGUGUU-GA-AGAGG--AAGAGUAGAG-UAGAA---ACCAU-UCU--------------------------CAGAGA--AUUUGGGUCUAUGGCUGAGAGCCCAUGU---AAUAGG---UCUAU-UUGAAA--ACUA-CCUU-GGAGC-----------UGAGCUUAUUA--GCAGUAUUUGUAUUUAUACU---AUACGUGAAAGUGC-UC-GGGUGAC-------GACC-UUA-----------------------------------------------------------------------------------------------------------------------------------------------------UAGUCAUCAAGAGG-GUUGUAUAU-------------------------------------------------------------------------------ACUUGUAUACGCC--AAC--UUGGGUGGAACCGCGAA------UUAA----UAUCGUCCCAAAC
CP000232.1/18501-18733     GCCAAAGCGAU-GA-AGGGG-----AGUGCCG-GCGGCCCACUCCG-GUAGGC-----------------------GAGAGA--GCUGGUGGUU---GGUGGGA--ACCAGC---CCGGAG--GCUGUC-GGGA----GGCA-CCCC-UGAGU-----------ACCCGGCGAGA--AAUCCUGUU--------------AAGGAAUUAAGCCG-GGGCGGUCAU-------GUCCGUUA-------------------------------------------------------------------------------------------------------------------------------------------------------CGCAUGUCGAGG-GGGUCAGGUUUGGCAU------------------------------------------------------------------------AAUAACCUGGCC---AAG--CAGGGUGGCACCGCGGGU-----AAAA---CUCUCGUCCCUUUU
CP000918.1/1745988-1745765 UCAACAAA--------UCAG--AAAAGUAACU-AUUU----UUGAU-CUU--------------------------CAGGGA--GCCUGUGGUG---AUUGUGA--AUAGGU---GGUUGG---AAGUA-GUGAAA-GUGGG-CUGA----UUUUGAAAA----UGAAUUUGAAA-----------------------------CAAUGAAAAU-UC-GGUGCGC-------ACACCUUACAGUGCAGCUUGUUGUU------------------------------------------------------------------------------------------------------------------------------------AAACAAGGCAGAGAUGUAAAGGG--------------------------------------------------------------------------------AUAGUCCCUUUAU--AAU--UGAGGUGGCACCGCGUU-------ACC-----AACGCCCUCACA
AE005176.1/68627-68394     AAAUUUAA-AA-CA-ACAAG---AAAGUAACU-UUGAUUUUGAAAU-CUU--------------------------UAGGAA--GUUGGUGGU----UGUGCAA--ACCAAC---GUUUUC--AGCAAA-GUGAA---UGGG-CUUG-UGAUUAACUAAUAAAUUUGAUUUAAAA----------------------------AAAUAAAGAAU-CA-CGGCCGC-------UUCCGUUACAGAGCAACUUGUUUU-------------------------------------------------------------------------------------------------------------------------------------UUGACAAGUUCUAA-GAAAAUCA-----------------------------------------------------------------------------------UUUGAUUUU---AAAUUUACGGUGGCACCGCGCU-------CAA-----AGCGCCCGUAGG
AE005176.1/1228400-1228613 ACGAGAGA--------UGAA--AAGAGUAGUC-UUAGG---UAUCA-GUU--------------------------GAGAGA--GCCUU--GUU---GCUGAGA--AAAGGU---CUGAUA---UUGGG-AUGAAC--CACA-CUCA----UCGCUAUCUU---ACUCACAUUAU---------------------------------UAUGUG-AG-CGUUAG--------CUGCGUUAAUGCUAAGUUG------------------------------------------------------------------------------------------------------------------------------------------UUAUAACUUACCGA-GGUCACUUUUG-----------------------------------------------------------------------------UGAAAAAGUGAU---AAAU-UAAGGUGGAACCACGAU-------UAA-----ACCGUCCUUUAA
CP001033.1/1194722-1194505 UUAACCAU--------UCAG--AAAAGUAAUC-AUAC----AAACU-UUU--------------------------UAGAGA--GUCUGUGGUA---GCUGAAA--ACAGAU---AAGUGG---CAAUG-AUGAAAAUUGGG-CUGA----AUG----------CUA-UUUAGAA--U----------------------UUGAAAUUAUAAAAAUUCGGUAAGC-------ACACCUUACAGUGCAUCUCGUUA--------------------------------------------------------------------------------------------------------------------------------------UUGCGAGACUGAGC-GAUAGGGA----------------------------------------------------------------------------------AAUUCCCUAU---AAU--UGAGGUGGUACCGCGC-------AUCG------ACGUCCUCACA
AP008230.1/2186652-2186888 CGAACAACGAU-GA-AAGAG-----AGCAUCU-GUUAGC-CCAGAC-CUU--------------------------CAGGGA--ACUAAAGUCGGAGACUGAAAGCUUUAGU---GGUUGCUGGUAACA-GAGA----UUCA-CUCU-GGAGUU----------GCAUUCCUGAA-------------------------CUCAAAGUAGGGAA-UGCCGGCCGC-------UUCCGUUAAGAGCCUUGAUUCAUUCC-----------------------------------------------------------------------------------------------------------------------------------AGGAUCAUGUGAGU-GGCUGUUG----------------------------------------------------------------------------------UACAUACAGC---AAA--AAGGGUGGUACCGCGUGA-----CUUA----ACUCGUCCCUUAU
AE005176.1/2251117-2250951 AACAAGUU--------GACG--AGGAGUAAUA-AAGC----AAGAC-UUA--------------------------UAGAGA--GAACACGGUU---GGUGAAA--GUGUUC---AGUCAA---ACUUU-AUGAAG--GUUG-CGUC----AUU----------U--------------------------------------CAAGAA-----------------------AA---UUAU----------------------------------------------------------------------------------------------------------------------------------------------------GGCAUAAAAUGAGU-GUCGUCAA-------------------------------------------------------------------------------------UUGACGA---AAA--UCAGGUGGUACCGUGC-------GGAA------GCACCCUGGAG
#=GC SS_cons               ::::::<<---.--.-<<<<..-------<<<.<<<---.----<<.<--..........................------..<<<<<<____..._______..>>>>>>...>>>---..-->>>>.>>----..----.>>>>.--->>,..........,<<<<<<<___.._......................_________>>>>>.>>,<<<____.......__>>>,,,,....................................................................................................................................................,,,,,,,,,,,,,,.,<<<<<<<___............................................................................._____>>>>>>>...,,,..,<<<<-------<<<<<_.....____...._>>>>>>>>>:::
#=GC RF                    auaAAagCaaU.gA.aggGG..AAaAGUAauu.cacauc.cuuauu.uUa..........................cAGAGA..gccggcGgUu...GgUGaGA..gccggu...aaauaa..auguga.auGAAa..auug.CCcc.gGAGca..........ucuuucccGAA..g......................uuaauAgUAgggaa.agaCGguuuc.......gccCGUUAu....................................................................................................................................................UgauuauauaaAGa.Gguuguuguaa.............................................................................aaAUucaacaac...AAa..uagGGUGGUACCgCGaga.....AuaA....UcuCGuCCcuUuu
//
# STOCKHOLM 1.0

#=GF AC   RF00231
#=GF ID   SCARNA13
#=GF PI   U93
#=GF DE   Small Cajal body specific RNA 13
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:12409454, INFERNAL
#=GF SS   Published; PMID:12409454
#=GF GA   49.00
#=GF TC   49.20
#=GF NC   41.60
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   12409454
#=GF RT   A Cajal body-specific pseudouridylation guide RNA is composed of two box
#=GF RT   H/ACA snoRNA-like domains.
#=GF RA   Kiss AM, Jady BE, Darzacq X, Verheggen C, Bertrand E, Kiss T
#=GF RL   Nucleic Acids Res 2002;30:4643-4649.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. U93 is composed of two
#=GF CC   tandemly arranged box H/ACA RNA motifs and belongs to the H/ACA class of
#=GF CC   guide RNAs. U93 is predicted to guide pseudouridylation of the U2
#=GF CC   spliceosomal snRNA [2].
#=GF WK   Small_Cajal_body_specific_RNA_13
#=GF SQ   24


AL672023.7/41296-41569       AUAUCUGCA--GUAUUGAACCCACACUGGGUUG--CUGGAACCCUAGAACACACAGGACUUGAAGAAAAAGCAUGCUCCAGAGG-AA-GCUGACACAUCCCUACU-UAAAAGCC--AGUGGCUCCAUGUACAAUU-UU-CCUCUGCUAGGCU-CUGGG-UACUGUUUCCAUGGUGAUAACAG-C-UGUGCCA--UGUCAUU-AUCGAUCCACUAACAGUAAAAAAAGCCUU--GCAGUCAGGAUAAUGUUUAGCAGACAGCAUGGUUUCUGUUGGACACU--A-AGUUCUGCUACAA--
BC036576.2/999-1273          A-AUCUGUA--GUCUUGGAGCCGCACAGGGUUG--GUGGUACCCUCGAGCACACCAGACUUGCAGAAAAAGCAUACUCCAGAGG-AA-GCUGAGGCAUGCCUGCU-CGAGAGCC--AGCUGUUCCAUGUGCAAUU-UU-CCUCUGAUAGUUU-CUGGU-CACUGUUGCCACGGUGAUAAUGA-C-UGGGCUA--UGUCAUU-AUCUAUCCGCCAACAGUAAGAGAAGCUUU--GCAGUCGAGAUAUUGUUUAGCAGAUGGAGUGUUUUCUGUUGAACACU--A-AGUACUGCCACAAGU
AF492209.1/1-275             A-AUCUGUA--GUCUUGGAGCCGCACAGGGUUG--GUGGUACCCUCGAGCACACCAGACUUGCAGAAAAAGCAUACUCCAGAGG-AA-GCUGAGGCAUGCCUGCU-CGAGAGCC--AGCUGUUCCAUGUGCAAUU-UU-CCUCUGAUAGUUU-CUGGU-CACUGUUGCCACGGUGAUAAUGA-C-UGGGCUA--UGUCAUU-AUCUAUCCGCCAACAGUAAGAGAAGCUUU--GCAGUCGAGAUAUUGUUUAGCAGAUGGAGUGUUUUCUGUUGAACACU--A-AGUACUGCCACAAGU
ABDC01193434.1/6179-5903     A-AUCUGUA--GUCUUGGAGCCGCACAGGGUUG--GUGCUACCCUGGAGCACACCAGACUUGCAGAAAAAGCAUACCCCAGAGG-AA-GCUGAGGCAUGCCUGCU-CAAGAACC--AGCGGUUCCAUGUGCAAUU-UU-CCUCUGAUAAUUC-CUAGA-UACUGUUGCCACGGUGAUGAUGA-C-UGUGCCA--UGUCAUU-AUCUAUUCACCAACAGUAAGAGAAGCUUG--GCAGUCGAGAUAUUGUUUAGCAGAUGGAGUGGUUUCUGUUGGACACUUUA-AGUACUGCUACAAAU
AAPY01739836.1/11143-10869   G-UUCUGUA--GUCUUGGGGUCGCGCUGGGUUG--GUGGUACCCUAGAGCACACCAGACUUGCAGAGACAGCAUACCCCAGAGG-AA-GCUGAGGCAUGCCUGCU-CGAGAGCC--AGCGGUUCCAUGUGCAAUG-UU-CCUCUGAUAGUUC-CUGGG-UACUGUUGCCACGGCGAUAAUGG-C-UGUGCCG--UGUCAUU-AUCUAUCCACCAACAGUAAGAGAAGCCUU--GCAGUCGAGAUAUUGUUUAGCAGAUGGAGUGGUUUCUGUGUGACACU--A-AGUACUGCAACAAAU
AANG01131950.1/278-4         G-AUCUGUA--GUCUUGGAGCCGCCCUGGGUUG--GUGGUACCCUAGAGCACACCAGACUUGCAGAAAAAGCAUACUCCAGAGG-AA-GCUGAGGCAUGACUGCU-CAAGAGCC--AGCCGUUCUAUGUGCAAUU-UU-ACUCUGAUAGUUC-CUGGG-UGCUGUUGCCACGGUGAUAAUGA-C-CGCGCCG--UGUCAUU-AUCUAUCGACGGACAGCAAGAGAAGCCUU--GCAGUCGAGAUAUUGUUUAACAGACAGAGUGGCUUCUGUUGGACACU--G-AGUACUGCUACAUUA
CT867964.5/1060-785          G-AUCUGUA--GUCUUGGAGCCGCCCAGGGUUG--GUGGUACCCUAGAGCACACCAGACUUGCAGAGAAAGCAGACU-CAGAGG-AA-GCUGAGGCAUAACUGCU-CAAGAGCC--AGCAGUACGAUGUGCAAUU-UU-CCUCUGAUAGUUC-CUGGG-UACUGUUGCCACGGUGAUAAUGG-C-UGUGCCAG-UGCCGUU-AUCUAUCAACCGACAGUAAGAGCAGCUUUUUGCAGUC-AGAUAUUGUUUAACAGAUGGAGUGGUUUCUGUUGGACACU--A-AGUACUGCUACAAGU
AAFC03077033.1/54767-55040   G-AUCUGUA--GUCUCGGCGUCGCACUGGGUUG--AUGGUACCCUGGAGCAUCCCAGACUUGCAGAGAAAGCAUCCUCCAGAGG-AA-GCUGAGGCAUGACUGCU-CGAGGGCC--GGCAGUGCCAUGUGCAAUU-UU-CCUCUGAUAGUUC-CCAGU-G-CUGUUGCCACGGCGAUGGUGG-C-UGUGCCA--UGCCAUU-GUCUAUCAACCGACAGGAAGAGAAAACUG--GCAGUC-AGAUAUUGUUUAACAGACGAAGUGGUUUCUGUUGGACACU-UA-AGUACUGCUAACAAA
AAFR03013275.1/137818-137545 U-GUCUGCA--GUCUUGGAAU-GCUCUGGGUUA--UUUGUGCCCCUGAGUACACCUGACUUGCAGAAAGAACAUAUUCCAGAGG-AA-GCUGAGGCAUGGCUGUU-AAAGGACG--AACAGCAUUAUGUGCAAUA-UU-CCUCUGACACCAG-CUGAA-UACUGUUGCCACGGUGAUGGUGA-C-UUCUCUG--UGUCAUU-AUCUAUCAACCAACAGUAAGAGAAGCUUU--GCAGUCAAGAUAUUGUUUAGCAAAUGGAGAAAUUUUUGCUAAACACU--A-AAAACUGCUAUAAAA
AAQQ01349496.1/2307-2033     G-GUCUGCG--GUCUUGGGCCCGCGCUGGGUUG--GUUGCCUUCAAGAGCCCACCACACUUGCAGAAUAAGCAUACUCCGGAGGAAA-GCUGA-GCAUGGCUGCU-CCAGAGCC--AGCGUUUCCAUGUGCAAUU-UUCCCUCGGAUAGCUC-CCGGAAUACUGUUGCCACGGUGAUAAUGA-C---CUCCG--UGUCAUU-AUCUAUCCACCAACAGUAAGAGAAGCUUU--GCAGUCGCGAUAUUGUUUGGCAGACAGAGUGGUUUCUGUUGGACACU--A-AGUACUGCUACAAAU
AAIY01333890.1/2440-2162     G-AUCUGCGGAGUCUCGGCCACGUCCAGGGUUG--GCAGUACUCCUCGGCACACUAGACUCGCAGGAAAAGCAUAUCCUGGAGG-UAAGCUGAGGCAUGCCUGCU-CGAGAGCC--GGCAGUGCCAUGUGCCAAUGUU-CCUCGGAUACCGC-CUGGU--ACUGUUGCCACGGUGAUAAUGG-C-UGUGCCCG-UGUCAUU-AUCUAUCCACCAACAGUCAGAGCAGCUUC--GCAGUCGAGAUAUUGCUCAGCAGACAGAGCGGCCUCUGCUGGGCACU--A-AAAACUGCUACACGU
AAPN01136094.1/2217-2493     C-AUCUGCA--GCCUCGGAGGUGCUCUGGGUUG--UUAGUACCCU-GGGCGGAUGGGGCUCGCAGAGAGAACAUAGCCCAGAGG-AA-GCUGAGGCAUGACUGUU-AAAGGGGC--AGCAGCGCCAUGUGCAAUA-UU-CCUCUGACACCAAACCAGA-UACUGUUGUCACGGCGAUGAUGA-CCUCUCUCG--UGUCAUCUGUCUAUCUAUCAACAGUUAGAGCAGCGUC--GCAGUCAAGAUAUGGUUCGGCAAAGGGAGUGGUUUCUGCCGAACACU--G-AGAACUGCUAUAAGC
AAYZ01080882.1/1624-1347     ACAUCUGCA--GUCCUGGCCCCGCGCUGGGUCG--GACGUGCCCCUGCGCCUACCAGACUUGCAGGAACAACAUGGUGCGGAGG-AA-GCCGAGGCAUGGCCGCCCCCAGGGCC--AGCGGCUGCAUGUGCAAUG-UU-CCUCGGACAGAUC-CCGAG--GCUGUGGCCACGGGGAUGGCGG-CCCGGGCCC--UGCCGUC-AUCCAUCCGCCAGUAGCCAGAGCAGCUCU--GCAGUCCAGAUAUUGUUCGGCAGACUGAGUGGUUUCUGUUGGACACU--UCAGUACUGCGACACGU
AALT01655515.1/714-452       A-ACGUGCA---------AGCCACACAGAAUUG--GUGGUACCGUAGAGCAUACCAGACUUGCGC-AAAAGCAUCCUUUGGAAG-AA-GCUGAGGCAUGAGUGCC-CGAUCUCC--AGCAAUU-UAUGUGCAAUU-UU-CUUCUGACAGUUU-CUGGG-CAUAGUUGCCAUGGCAAUAAUGA-C-UCGGCAG--UGUCAUU-AUCGAUCU-CUAACAGUAAGAGAUGCUCU--GCAGUUGGGAUAUUGUUUAACAAACAG--UGGUUUCUGUUGGACACU--A-AGUAGUGCUACAAAU
AAGV020398416.1/1545-1273    G-GUCUGUA--GUCUUGGAGCCGCUCUGGGUUG--GUGGUGCCCUCGAGCUCACCAGACUAGCAGAAAAAGCAUACUCCAGAGG-AA-GCUGAGGCAUGACUGCU--GAAGGUC--AGCAGUUUCAUGUGCAAUU-UU-CCUCUGAUAGAUC-CUGGG-UACUGUUGCCACGGUGAUGAUGA-C-CUUGCCA--UGUCGUU-AUCUAUCAAACAACAGUAAGAGAAGCUUU--GCAGUCGAGAUAUUGUUUAGCAGA-UGAGUGGUUUCUGUUGGACACU--A-AGUACUGCUACAAGU
AAWR02019953.1/14414-14140   -GAUCUGUA--GUCUUGGAGCUGCGCUGGGUUG--GUGGUACCCUAGAGCACACCAGACUUGCAGAAAAAGCAUACUGCAGAGG-AA-GCUGAGGCAUGACUGCU-CAAGAGCC--AGCAGUGCCAUGUGCAAUU-UU-CCUCUGAUAGUCA-CUGGG-UACUGUUGCCACGGUGAUGAUGA-C-UGUGCCG--UGUCCUU-AUCUAUCCGCCAACAGUAAGAGAAACCUU--GCAGUCGAGAUAUUGUUUAACAGAUGGAGUGGUUUCUGUUGGACACU--A-AGUACUGCUACAAAU
AAKN02053416.1/131306-131577 G-AUCUGUA--GUCUUGGCUCCGCGCGGGGUUG--GUGGUACCCUAGAGCACACCAGACUUGCAGAGAUAGCGUACUCCGGAGG-AA-GCUGAGGCAUGCCUGCU-CGAGAGCC--AGCGGGUCCAUGUGCAAUG-UU-CCUCUGAUAGUUU-CCAGU--ACUGUUGCCACGGUGAUAAUGG-C-UGUGCUG--UGUCAUU-AUCGAUCCACCAACAGUAAGAGAAGCUUU--GCAGUCAAGAUAUUGUUUAGCAGACAUAGUGA--UCUGUUGGACACU--A-AGUACUGCUACAAAC
AABR05139205.1/38021-37747   A-AUCUGUA--GUCUUGGACCUGCGCUGGGUUG--GUGGUACCCUCGAGCACACCAGACUUGCAGAAAAAGCAUACUCCAGAGG-AA-GCUGAGGCAUGCCUGCU-CGAGAGCC--AGCGGUUCCAUGUGCAAUU-UU-CCUCUGAUAAAUC-CUGGG-UACUGUUGCCACGGUGAUAAUGA-C-UGUGCCG--UGUCAUU-GUCGAUCCACCAACAGUCAGAGAAGCUUU--GCAGUCAAGAUAUUGUUUAGCAGACGGAGCGGUUUCUGUUGGACACU--A-AGUGCUGCUACAAGA
AADN03004563.1/97214-96942   C-CUCUGUA--GUCGAAGAGAUGCCCUUGGUUG--GUGGUACUCU-GGGCGUACCAGGCUUGCAGAGAGAGCACCGGUGUGAGG-AA-GCCGAGGCAUGCCUGUU-AGAGCAGC--AGCAGCAACAUGCGCAAUA-UU-CCUCUAACAGUUA-CA--A-UCCUGUUGCCACGGAGAUAAUGA-CUUAUCCCA--UGUCAUU-AUUGAUCUAUCAACAGUAAGAGCAAUUUU--GCAGUC-UGAUAUUGUUUAGCAAAUAGAGUAAUGUCUGCUGAACACU-UA-AAAACUGCUAUAAAU
AAPE02007236.1/4734-4994     -GGCCUGCA--GUCUUGGAGCCGCGCUGGGUUG--GCGGUACCCGAGGGCACACCAGACUUGCAGGAAAAGCAAACCCCGGAGG-AA-GCUGAGGCAUGACUGCU-CGAGAGCC--AGC-CUGCCAUGUGCAAUG-U-------GAAAUUCC--------ACUGUUGCCACGGCGAUAGUGA-C-UGU-CUG--UGUCAUU-AUCUAUCCACCAACAGUGAGAGAAGCUUU--GCAGUCGAGAUAUUGUUUAACAGAUGGAGUGCUUUCUGUUGGACACU--A-AGUACUGCUACAAAG
AAGW02050031.1/56650-56923   -CACCUGCA--GCCUGGGCGCCUCGCAGGGUCG--GAGGU-CCCCAGCGCUCACCAGACUUGCAGACACAACAUACUCCAGAGG-GA-GCUGAGGCAUGGCUGCC-CCAGAGCU--GAGGGCUCCAUGUGCAAUU-UU-CCUCUGAUAGCUC-CUGGC-UGCUAUUGCCAUGGAGAUGAUGG-C-UAUGCCC--UGUCAUU-AUCGAUCCACCAACAAGAAGAGAAGCUUU--GCAGUCGAGAUACUGUUUGGCAGAUGGAGUGGUUUCUGUUGGACACU--A-AGUACUGCUACAAAU
AAWZ02001014.1/31750-32022   -CAUCUGCA--GCUUUCAACCUGCCCUUAGUUGUCUCUGUACUAU-GGGCAUGUUAGCUUUGCAGAAAGAGCAUUUGAUUGAGG-AA-GCCGAGGCAGGACUGU--AAAAAGUAACAGCAGCUCCAUGUGCAAUG-UU-CCUC--UGACACA-AAUAC-UACUGUUGCUACGGAGAUAAUGAUC-AUCCCAA--UGUCAUU-AUCCAUCUAUCAACAGUGAGAAUAAAUUU--GCUAU-GAGAUAUUGUUUAGCAAAUUGAGUAU--UUUGCUGAACACU--A-GAAACAGCUACAUUU
AAGU03025845.1/18436-18163   G-AUCUGUA--GUCUUGGAGGCGCACUGGGUUG--GCGGUACCCUC-AGCACACCAGACUUGCAGAAAAAGCAUACUCCAGAGG-AA-GCUGAGGCAUGGCUGCU-CUAGGGCC--AGCAGUUCCAUGUGCAAUU-UU-CCUCUGAUAACGC-CUGGG-UACUGUUGCCACGGUGAUAAUGG-C-UGUGCCG--UGUCAUU-AUCUAUCAACCAACAGUAAGAGAAGCUUU--GCGGUCGAGAUAUUGUUUAGCAGAUGGAGUGCUUUCUGUUGGACACU--A-AGUACUGCUACAAAU
AAEX03005960.1/16321-16045   G-GUCUGCA--GUCCUGGCGCGGCGCUGGGUGG--CUGGUACCCGGGGGCACACCAGACUCGCAGAAAGAGCAUCCUCCGGAGG-AA-GCUGAGGCAUGGCCGCC-CCAAGGCC--AGCGGCUCUAUGUGCAAUG-UU-CCUCCGAUAGCUA-CCGGG-UGCUGUUGCCACGGUGAUGAUGA-C-UGUGCGCAGUGUCGUU-AUCUAUCGACCAACAGGAAGAGAAGCUCU--GCAGGCAAGAUAUUGUUCAACAGACGGAGCGCUUUCUGUUGGACACU--A-AGCACUGCUACAAGU
#=GC SS_cons                 :.:<<<<<<..<<<<-----------<<<<<__.._____>>>>>---------->>>>->>>>>>,,,,,,,,,,,,<<<<<<.<<.------<<<<<---<<<.________..>>>----->>>>>------.>>.>>>>>>,,,,,,,.,,,,,.,<<<<<<<-------<<<<<<<<.<._______.._>>>>>>.>>>------->>>>>>>,,,,,,,,,,,,..<<<<<---------<<<<<<<<<<__________>>>>>>>>>>---..-.--->>>>>:::::::
#=GC RF                      a.auCUGca..GucuuGGagccGCaCcgGGuUG..gugGUaCCcgaGaGCacACcagaCUugCAGaaAaAGCAUacuccaGAGG.aA.GCUGAGgCAUgaCUGcu.caAgaGcc..agCaGuuccAUGuGCAAUu.Uu.CCUCugAuAguuc.CugGa.UaCuGUugCCACGGuGAuaauGa.C.UgugCca..UGuCauu.aUCuAUCuAccaACaGuaAGAGaAGcUUU..GCaGUCgAGAUAUUGuucagCAGAuaGAGUGgUUUCUGcuggaCACU..A.AGuACuGCUAcAAau
//
# STOCKHOLM 1.0

#=GF AC   RF00232
#=GF ID   Spi-1
#=GF DE   Spi-1 (PU.1) 5' UTR regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:9207037
#=GF SS   Published; PMID:9207037
#=GF GA   40.00
#=GF TC   61.00
#=GF NC   37.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   9207037
#=GF RT   The conserved 5'-untranslated leader of Spi-1 (PU.1) mRNA is highly
#=GF RT   structured and potently inhibits translation in vitro but not in vivo.
#=GF RA   Hensold JO, Stratton CA, Barth D
#=GF RL   Nucleic Acids Res 1997;25:2869-2876.
#=GF CC   Spi-1 regulates myeloid gene expression during haemopoietic development.
#=GF CC   This family represents a regulatory element found in the 5' UTR of Spi-1
#=GF CC   mRNA which is able to inhibit the translation Spi-1 transcripts by 8-fold.
#=GF CC   Mutations in this regulatory region of the 5' UTR can lead to
#=GF CC   overexpression of Spi-1 which has been linked to erythroleukemic
#=GF CC   transformation [1].
#=GF WK   Spi-1_(PU.1)_5'_UTR_regulatory_element
#=GF SQ   5


AC090559.7/2975-2808   CUCACCCAGGGCUCCUGUAGCUCAGGGGGCAGGCCUGAGCCCUGCACCCGCCCCACGACCGUCCAGCCCCU-GACGGGGCACCCCAUCCUGA-GGGGCUCUGCAUUGGCCCCCACCGAGGCAGGGGAUCUGACCGACUCGGAGCCCGGCUGGAUGUUACAGGCGUGCAAA
X17463.1/689-858       CUCACCCAGGGCUCCUGUAGCUCAGGGGGCAGGCCUGAGCCCUGCGUCUGACCCACGACCGUCCAGUCCCCCGACGGGGCACCUGGUCCUGAGGGGGAUCCGCCUUGAUCCCCACCGAAGCAGGGGAUCUGACCAACCUGGAGCUCAGCUGGAUGUUACAGGCGUGCAAA
U34046.1/345-511       CUCACCCAGGGCUCCUGUAGCUCAGGGGGCAGGCCUGAGCCCUGCACCCGCCCCACGACCGUCCAGCCCCU-GACGGGC-ACCCCAUCCUGA-GGGGCUCUGCAUUGGCCCCCACCGAGGCAGGGGAUCUGACCGACUCGGAGCCCGGCUGGAUGUUACAGGCGUGCAAA
AC090582.9/66882-66715 CUCACCCAGGGCUCCUGUAGCUCAAGGGGCAGGCCUGAGCCCUGCACCCGCCCCACGACCGUCCAGCCCCU-GACGGGGCACCCCAUCCUGA-GGGGCUCUGCAUUGGCCCCCACCGAGGCAGGGGAUCUGACCGACUCGGAGCCCGGCUGGAUGUUACAGGCGUGCAAA
M32370.1/1-150         CU----CAGGGGGC---------AGG-------CCUGAGCCCUGCGUCUGACCCACGACCGUCCAGUCCCCCGACGGGGCACCUGGUCCUGAGGGGGAUCCGCCUUGAUCCCCACCGAAGCAGGGGAUCUGACCAACCUGGAGCUCAGCUGGAUGUUACAGGCGUGCAAA
#=GC SS_cons           :::::::<<<<<<<--<<-<<<<___>>>>-->>-->>>>>>>(((((((---------((((((,<<<<<.--<<<<<<_____>>>>>>-.>>>>><<<<--<<<<<<<<<_________>>>>>>>->>------>>>><<<_>>>))))))---))))))):::::
#=GC RF                CUcAccCaGGGcuCcUGcAGcccAgGgggCAGgCCUGagCCCugCgcCcGaCCCACGACCguCCaGcCCCc.GACgGGgcACCucgcCCcGA.gGGGguCcgCaucGgcCCCCACCGAaGCAGGGGgcCUgaCCaACucgGaGCcCgGCuGGacGUUACgGgcGcGCAAA
//
# STOCKHOLM 1.0

#=GF AC   RF00233
#=GF ID   Tymo_tRNA-like
#=GF DE   Tymovirus/Pomovirus/Furovirus tRNA-like 3' UTR element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15033563
#=GF SS   Published; PMID:15033563
#=GF GA   40.00
#=GF TC   41.40
#=GF NC   38.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   15033563
#=GF RT   The tRNA-like structure of Turnip yellow mosaic virus RNA is a
#=GF RT   3'-translational enhancer.
#=GF RA   Matsuda D, Dreher TW
#=GF RL   Virology 2004;321:36-46.
#=GF CC   This family represents a tRNA-like structure found in the 3' UTR of
#=GF CC   Tymoviruses, Pomoviruses and Furovirus. This family (in conjunction with
#=GF CC   Rfam:RF00390 and a 5'-cap) are known to enhance translation [1].
#=GF WK   pomovirus_tRNA-like_3'_UTR_element
#=GF SQ   28


M58314.1/2-79        GAA--C--UACAGU--UC-CGCUCCUCUAGCACACAGAGGUC-AAU-UG-GGUGCGAC-CCCC-C-CCUCUCCCGUG-GGUCAACGGGAACC
U88847.1/591-676     UUAG-CUCGCCAGUUAGCGAGGUCUGUCCCCACACGACAGAU-AAU-CG-GGUGCAACUCCCGCC-CCUUUUCCGAG-GGUCAUCGGAACCA
J04375.1/6130-6211   AAAU-AUGACCGGU--GUCAUAGCCUCUAGCACACAGAGGUC-GCG-UG-GGUUCAACUCCCC-C-CCUUUUCCGAG-GGU-AUCGGAAACC
AF035201.1/605-688   CCAG-GUCGCCAGU--GCGACACCCGUUCCCACACAACGGGC-ACU-GG-GGUGCAACUCCCCCG-UCUAUCCUGGA-CGUCACCAGGACCA
V01418.1/610-695     UUAG-CUCGCCAGUUAGCGAGGUCUGUCCCCACACGACAGAU-AAU-CG-GGUGCAACUCCCGCC-CCUCUUCCGAG-GGUCAUCGGAACCA
M54918.1/75-159      UUAG-CUCGCCAGUUAGCGAGGUCUGUCCCCACAGGACAGAU-AAU-CG-GGUGCAACUCCCGCC-CCUCUUCCGAG-GGUCAUCGGAACC-
M24799.1/120-196     UCAG-CUCGCCAGUUAGCGAGGUCUGUCCCCACACGACAGAU-AAU-CG-GGUGCAACUCCCGCC-CCUUUUCCGAG-GG---UC--A----
M58313.1/1-81        -AAU-GAAGGCAGU--CCUUCUCCCUUUAGCACACAAAGGUC-AAU--G-GGUGCGACUCCC-CC-CCUUUUCCGAG-GGUCAUCGGAAACC
J04374.1/6247-6330   UAAUUGCGGACAGU--UCCGCUCCCUCUAGCACACAGAGGUC-CAUUUG-GGUGCGACUCCCCCC-CC--UCCCGUG-GGUCAACGGGAACC
AF035200.1/578-659   UCAG--UCGCCAGU--GCGAGGCCCAUUCUCUCUCAAUGGGU--AU-UG-GGUGCAACCCCCCCG-UCCAUCUCGAA-CGUCAUCGAGACCA
Y16104.1/6590-6672   UAAUUGAGGACAGU--UCCUCUCCCUCUAGCACACAGAGGUC-AAACUG-GGUGCAACUCCCCCC-CC--UUCCGUG-GGU-AACGGAAACC
AF035633.1/1296-1379 UAAUUGAGUCCAGU--GACUCUCCCUCUAGCACACAGAGGUC-AAACCG-GGUGCAAC-CCC-CC-CUCCCCCCGUA-GGUUAACGGGACCA
AJ277556.1/2880-2963 GAAGAGCGGCCAGUU-GCUGCUGCGAUCAAGACACGAUCGUUCAAA-AG-GGUGCAACUCCCCCC-CC--CUUGGAG-GGU-AUCCAAGACC
AF035199.1/569-652   CCAG-GUCGCCAGU--GCGACACCCGUUCCCACACAACGGGC-AUU-GG-GGUGCAACUCCCCCG-UCUAUCCUGGA-CGUCACCAGGACCA
M24802.1/87-163      UUAG-CUCGCCAGUUAGCGAGGUCUGUCCCCACACGACAGAU-AAU-CG-GGUGCAACUCCCGCC-CCUUCUCCGAG-GG---UC--A----
D00637.1/6279-6362   UCAG-GUCGCCAGU--GCGACACCCGUUCCCACACAACGGGC-AUU-GG-GGUGCAACUCCCCCG-UCCAUCCUGGA-CGUCACCAGGACCA
Z66493.2/2920-3005   GGAU-GAGACGAGUUAGUCUCGACCAUUUUCACACAAUGGUU-CUGAGG-GGUGCAACUCCCCCC-CUUAACUAGAG-GGAAAUCUAG-CCC
M15284.1/14-96       YAAU-GAAGGCAGU--CCUUCUCCCUUUAGCACACAAAGGUC-AAA-UG-GGUGCGACUCCCC-C-CCUUUUCCGAG-GGUCAUCGGAAACC
X54354.1/598-681     UUAG-CUCGCCAGU--GCGAGGCUCGUUCCCACACAACAAGU-AAU-GGUGGUGCAACUCCCCCG-UCC-UCCCGAA-CGUCAUCGGGACCA
M24797.1/93-169      UUAG-CUCGCCAGUUAGCGAAGUCUGUCCCCACACGACAGAU-AAU-CG-GGUGCAACUCCCGCC-CCUUUUCCGAG-GG---UC--A----
M58311.1/2-83        UUCU-CUCG--AGU--GCGAGGCCCAUUCACACACAAUGGGU--AU-UG-GGUGCAACCCCCCCG-UCCAUCUCGAACGGUCAUCGAGACCA
AF035636.1/614-699   UCAG-CUCGCCAGUUAGCGAGGCCUGUUCCCACACAACAGGU-AAU-CG-GGUGCAACUCCCGCC-CCUACUCCGAG-GGUCAUCGGAACCA
AF035198.1/571-654   UCAG-GUCGCCAGU--GCGACACCCGUUCCCACACAACGGGC-AUU-GG-GGUGCAACUCCCCCG-UCUAUCCUGAA-CGUCAUCAGGACCA
M24801.1/102-178     UCAG-CUCGCCAGUUAGCGAAGUCUGUCCCCACACGACAGAU-AAU-CG-GGUGCAACUCCCGCC-CCUUUUCCGAG-GG---UC--A----
AF035202.1/598-681   GUAG-UCGGCCAGU--GCCGAGGCCCUUCACACACAAGGGUU-AAU-GG-GGUGCAACUCCCCCG-CCCAUCUCGAG-CGUCAUCGAGACCA
M58310.1/2-84        UUA--GUUGCCAGU--GCGACACCCGUUCCCACACAACGGGC-A---UG-GGUGCAACUCCCCCGUCCCACUCUGGACGGUCACCAGGACCA
U91413.1/613-696     UUAG-CUCGCCAGU--GCGAGGCCUCUUCCUACACAAGAGGU-AUU-GG-GGUGCGACUCCCCCG-UCUAUCCUGAA-CGUCAUCAGGACCA
AF035402.1/1622-1704 UAAUUGUGGACAGU--UCCACUCCCUUUAGCACACAAAGGUCCAAU-CG-GGUGCGACUCCCCCC-CC--UCCUGUG-GG-CUACAGGAACC
#=GC SS_cons         ::::.<<<<<____..>>>>>,<<<<<<_______>>>>>>,.,,,.<<.<<_______>>>>AA.A,,,,<<<<<a.aa___>>>>>::::
#=GC RF              uuAg.gucGcCAGU..gCgacgcCcguuccCACACaacgGgu.Aau.gG.GGUGCAACUCCCcCc.CCuaUcccGag.GGUCAuCgggAcCa
//
# STOCKHOLM 1.0

#=GF AC   RF00234
#=GF ID   glmS
#=GF DE   glmS glucosamine-6-phosphate activated ribozyme
#=GF AU   Winkler WC
#=GF AU   Nahvi A
#=GF AU   Roth A
#=GF AU   Collins JA
#=GF AU   Barrick JE
#=GF AU   Breaker RR; 0000-0002-2165-536X
#=GF SE   Barrick JE, Breaker RR
#=GF SS   Published; PMID:15029187
#=GF GA   37.00
#=GF TC   38.50
#=GF NC   35.60
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0003824; catalytic activity;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   15029187
#=GF RT   Control of gene expression by a natural metabolite-responsive ribozyme.
#=GF RA   Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR
#=GF RL   Nature 2004;428:281-286.
#=GF RN   [2]
#=GF RM   16699515
#=GF RT   Backbone and nucleobase contacts to glucosamine-6-phosphate in the glmS
#=GF RT   ribozyme.
#=GF RA   Jansen JA, McCarthy TJ, Soukup GA, Soukup JK
#=GF RL   Nat Struct Mol Biol. 2006;13:517-523.
#=GF RN   [3]
#=GF RM   16784238
#=GF RT   Evidence for preorganization of the glmS ribozyme ligand binding pocket.
#=GF RA   Hampel KJ, Tinsley MM
#=GF RL   Biochemistry. 2006;45:7861-7871.
#=GF CC   This entry contains a glucosamine-6-phosphate activated ribozyme that is
#=GF CC   found in the mRNA for GlmS. GlmS is an enzyme that uses
#=GF CC   fructose-6-phosphate and glutamine to generate glucosamine-6-phosphate.
#=GF CC   The ribozyme catalyses self cleavage of the glmS mRNA that is thought to
#=GF CC   regulate GlmS activity [1].
#=GF WK   glmS_glucosamine-6-phosphate_activated_ribozyme
#=GF SQ   18


AF270378.1/2268-2051       UUAAUAAUUAAAGCGCCUGUGCAAAAUACCUAAAUAGUUAUCAAGUAUUAAAAGUUAAAAUAGUAGAACUU----UUAUAGAUAACGAUUUGG--AUUUUGUAGACGAGGA-GGAUAGUGAUCGA-AUCAGAUCGGCGGAUGCUAUCCCGGAUG---UGGCA-----CAUUCGUUAG-CUUAUUAAGUAAAUCAUUAAGGUGACUUAGUGGACAAAG-UUAAUAAGAUCGCCAAAC
AB006424.1/2989-3156       CCUAUAAUUAUAGCGCCCGAACUAAGCGCC-----------------------CGGAAAA------------------------------AG---GCUUAGUUGACGAGGAUGGAGG-UUAUCGA-AUU---UCG-CGGAU--CCUCCCGGCUGAGUGUGCAGAUCACAGCCGUAAG-AAUUUCU-UCAAACCAAGGGGGUGACUCCUUGAACAAAG--AGAAAUCACAUGAUCUU
AC078934.3/32621-32405     AGUACAGUUAAAGCGCCUGUGCAAAUAAAUAUUUGUAUU----UGAAGAUUAAAGGUUAAUAUAUGAGUGGCCUUUAUAGAGUGCAAUAUAUG--UAUUUGUAGACGAGGA-GGAUAGUGAUCGAAUAGA--UCGGCGGAUGCUAUCCCGGAUG---UGGCU-----CAUUCGUUAG-CUUAUUAAGUAAAACAUUAGGGUGACUUAAUGGACAAAG-UUAAUAAGAUCGCCAGAA
AL596166.1/50734-50929     AACUGAAUAGAAGCGCCAGAACUGAUUGGG-----------------------ACGAAAAUGCUUAAAGGUG--AAAUUCCUGGAAAGUAAAC--AAUCAGUUGACGAGGA-GGAGAUUAAUCGA-AAUU--UCGGCGGGAG-UCUCCCGGCUG---UGCAUG----CAGUCGUUAAGUCUUACUUACAAAUCAUUUGGGUGACCAAGUGGACAGAG-UAGUAAUGAAACAUGUGC
CP000557.1/163698-163870   GACGACAAAAAAGCGCCUGGACUAAGCGCG-----------------------GGAACG---------------------------GACGCGC--GCUUAGUUGACGAGGA-GGAGGUUUAUCGAGGUUU--UCGGCGGAUG-CCUCCCGGCUGG-AGCGAUG---ACAGCCGCAA--GUCCUCUCUUAAAACAAAGGGGUGACCCUUUGGACAAAG-GGGAGGAUGUCAUCGCAC
AE016830.1/2055460-2055313 CAAUAUCGGAUAGCGCCAGACCUGAAC--------------------------------------------------------------------GUUCAGGUGACGAGGAGAGAGC-UUAUCGA-AGAU--UCGGCGGGUG-GCUCUAGGG-----ACUGCA------CUCUACA--GAUAACAAAGAAAAACUAAUUGUGAAGUUAG-AACAAAG-CGGUUAUCACGCAGGUAG
AE001437.1/179915-180075   AUUAUAGUUAAAGCGCCCGAACUUGAGUGA-----------------------UAUAGU-------------------------------UCA--UUUAAGUUGACGAGGA-UGGGGAGAAUCGA-AUCU--UCGGCGGAUG-CCCCACGGUA----CCGCA-----CUACCGUUAG-CGGUUG--GUAAAAGCAGAAAGUGAUUUCUGUCACAAAG-C-CAAUCUGGUGUUAAAA
AE017333.1/183152-183325   UUUAUAGUUAUAGCGCCCGGACUAAGCGUA-----------------------CGGAUGA-----------------------------AACA--GCUUAGUUGACGAGGAUGGAGGUUUAUCGA-AUUU--UCGGCGGAUG-CCUCCCGGCUGACCUCAAAGAUCACAGCCGCAAG-GAUUUCC-UCAAACCAAAGAGGCGACUCUUUGAACAAAG--GGAAAUUGCAUGAUCUU
AM263198.1/720655-720850   AAUUAAAUAGAAGCGCCAGAACUGAUUGGG-----------------------ACGAAAAUACUUGAAGGUG--AAAUUCCUGAAAAGUAAC---GGUCAGUUGACGAGGA-GGAGAUUAAUCGA-AAGU--UCGGCGGGAG-UCUCCCGGCUG--UAGCAUG----CAGUCGUUAAGUCUUACUUACAAAACAUUUGGGUGACCAAAUGGACAGAG-UAGUAAUGAAAUAUGUGU
BA000043.1/166978-167147   GACGAGACAAAAGCGCCUGGACUAAGCGUUG--------------------GACGGAAGA-------------------------------AC--GCUUAGUUGACGAGGA-GGAGGUUUAUCGAGGUUU--UCGGCGGAUG-CCUCCCGGCUGG-AGCGAUG---ACAGCCGCAAGUCCUCUC--UUAAAACAAAGGGGUGACCCUUUGCACAAAG---GGGAGGAUGUCAUCGC
AP008934.1/759374-759589   AGUUCAAUUAAAGCGCCUGUACAAGUGAAGAGGUUAUGUG--UUUGUAAUUUAAGGUUUAUAACAGAAAUC----UUAAUAGACACGAUAAUCGAAGUUUGUAGACGAGGA-GGGUAGUUAUCGA-ACCA--UCGGCGGAUGCUAUCCCGGAUG---UGGCU-----CAUUCGUUAA-CUUAUUAAGGAAAACAUUAGGGUAACCUGGUGCACAAAG-UUAAUAAGAUAGCCAAAA
AP006716.1/888948-889158   AUAAAUUAUAAAGCGCCAGGGCAAAAU-AUAAGUGUACC----UAUAAUCAAAAGUUAAAUAUGAGAGCUU----UUGUAGGGCAAUUUAUU---UCUUUGCAGACGAGGA-GAAUAGUCAUCGAAAAUA--UCGGCGGAUGCUAUUCCGGAUG---AGGCU-----CAUUCGUUAG-CUUAUUAUUUAAAACAUUUAGGUAACUAAAUGCACAAAA-AUAAUAAGAAUGCCUAAA
AE017262.2/770944-771139   AAUUAAAUAGAAGCGCCAGAACUGAUUGGG-----------------------ACGAAAAUACUUGAAGGUG--AAAUCCCUGAAAAGUAAAC--AGUCAGUUGACGAGGA-GGAGAUUAAUCGA-AGUU--UCGGCGGGAG-UCUCCCGGCUG---UGCAUG----CAGUCGUUAAGUCUUACUUACAAAUCACUUGGGUGACCAAGUGGACAGAG-UAGUAAUGAAACAUGUUU
CP000924.1/498335-498489   AAAAUUUAAAAAGCGCCUGGGCUUAAAGUG--------------------------UAU--------------------------------AC--UUUAAGCUGACGAGGA-CAGGGUUUAUCGA-GUUA--UCGGCGGGUG-CCCUGCGGUU-----UCCUG----CGACCGAUAAAGGACUG--GUAAAA-CCACAGGCGACUGUGG-CAUAGAG---CAGUCUGGGCAGGGAG
AE008691.1/2101605-2101448 UUUAAUUUAGAAGCGCCUGGACUUAAAGCC--------------------------UUAA------------------------------GGC--UUUAAGUUGACGAGGG-CAGGGUUUAUCGA-GACA--UCGGCGGGUG-CCCUGCGGUC----UUCCUG----CGACCGUUAGAGGACUG--GUAAAA-CCACAGGCGACUGUGG-CAUAGAG---CAGUCCGGGCAGGAAA
AARQ02000011.1/391-585     AAUUGAAUAGAAGCGCCAGAACUGAUUGGG-----------------------ACGAAAAUGCUUGAAGGU---GAAAUCCCUGAAAAGUAUC--GAUCAGUUGACGAGGA-GGAGAUUAAUCGA-AGUU--UCGGCGGGAG-UCUCCCGGCUG---UGCAUG----CAGUCGUUAAGUCUUACUUACAAAUCAUUUGGGUGACCAAGUGGACAGAG-UAGUAAUGAAACAUGCUU
CP001617.1/730337-730488   UAAAGCGGAAUAGCGCCAGGACUUUAG-----------------------------AAU------------------------------------CUAAAGUUGACGAGGAUGACGU-UUAUCGA-UAA---UCGACGGGUG-ACGUCAGGG-----ACUGCA------CUCUACA--GGUCAAUUACAAAAACCGACUGUGAGGUUGGUGACAGAUAUAUUGACCACGCAGCUAG
FJ935779.1/2022-2192       CCUAUAAUUAUAGCGCCCGAACUAAGCGCC-----------------------CGAAAAA-------------------------------AG--GCUUAGUUGACGAGGAUGGAGG-UUAUCGA-AUUU--UCGGCGGAUG-CCUCCCGGCUGAUUAUGCAGAUCACAGCCGUAAG-GAUUUCU-UCAAACCAAGGGGGUAACUCCUUGAACAAAG--AGAAAUCACAUGAUCUU
#=GC SS_cons               :::::::::::::::::::<<<<<<<<-<_......................._______.........................._____>-..>>>>>>>>,,,,,,,,.<<<<<----<<<<.____..>>>>------.>>>>><<<<<<...______....>>>>>>,,,,.<<<<<<<-------<<<<<<<____>>>>>>>-------.->>>>>>>::::::::::
#=GC RF                    aauaaaauuAAAGCGCCuGaaCugagcgcu.......................aggaaaA..........................aauaagc..gcucaGuuGACGAGGA.gGagguUuAuCGA.auuu..UCGgCGGaUG.ccuCcCGgcuG...uggcuG....CagcCGuuAg.cuucucuuauAAAacacggggGUGAccccguggACAAAG.uagagaagAuauauaaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00235
#=GF ID   Plasmid_RNAIII
#=GF DE   Plasmid RNAIII
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Pubmed:14583190
#=GF SS   Predicted; ILM
#=GF GA   60.00
#=GF TC   143.70
#=GF NC   48.80
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF RN   [1]
#=GF RM   14583190
#=GF RT   Antisense-RNA mediated transcriptional attenuation: importance of a U-turn
#=GF RT   loop structure in the target RNA of plasmid pIP501 for efficient
#=GF RT   inhibition by the antisense RNA.
#=GF RA   Heidrich N, Brantl S
#=GF RL   J Mol Biol 2003;333:917-929.
#=GF CC   This RNA is found in bacterial plasmids including pIP501. RNAIII acts by
#=GF CC   transcriptional attenuation of the essential repR-mRNA. RNAIII is composed
#=GF CC   of four stem loops with loops L3 and L4 that interact with the RNA target
#=GF CC   [1].
#=GF WK   Plasmid_RNAIII
#=GF SQ   7


X72021.1/463-336       ACAGAUAUUUAAGUAUCUGAUUAAUAAAGUAAUUAAAUACUUUACCAAAUUUUGGGUCUCGACUUCUUUAAUUGAUUGGUGGUAAUCAAUUAAGGCUCGC-AGUUAAAAUUUCU-CAGGCUUUAACU-GGU
U83488.1/6284-6157     ACAGAUAUUUAAGUAUCUGAUUAAUAAAGUAAUUAAAUACUUUACCAAAUUUUGGGUCUCGACUUCUUUAAUUGAUUGGUGGUAAUCAAUUAAGGCUCGC-AGUUAAAAUUUCU-CAGGCUUUAACU-GGU
X17655.1/463-336       ACAGAUAUUUAAGUAUCUGAUUAAUAAAGUAAUUAAAUACUUUACCAAAUUUUGGGUCUCGACUUCUUUAAUUGAUUGGUGGUAAUCAAUUAAGGCUCGC-AGUUAAAAUUUCU-CAGGCUUUAACU-GGU
X66468.1/479-349       ACAGAUAUUUAAGUAUCUGAUUAAUAAAGUAAUUAAAUACUUUACCAAAUUUUGGGUCUCGACUUCUUUAAUUGAUUGGUGGUAAUCAAUUAAGGCUCGCAACUUAUUUUCUUGGCGGAAAAUAAGUUGGU
X64695.1/344-214       ACAGAUAUUUAAGUAUCUGAUUAAUAAAGUAAUUAAAUACUUUACCAAAUUUUGGGUCUCGACUUCUUUAAUUGAUUGGUGGUAAUCAAUUAAGGCUCGCAACUUAUUUUCUUGGCGGAAAAUAAGUUGGU
AE016833.1/45764-45634 ACAGAUAUUUAAGUAUCUGAUUAAUAAAGUAAUUAAAUACUUUACCAAAUUUCGGGUCUCGACUUCUUUAAUUGAUUGGUGGUAAUCAAUUAAGGCUCGCAACUUAUUUUCUUGGCGGAAAAUAAGUUGGU
X92945.2/35048-34918   ACAGAUAUUUAAGUAUCUGAUUAAUAAAGUAAUUAAAUACUUUACCAAAUUUUGGGUCUCGACUUCUUUAAUUGAUUGGUGGUAAUCAAUUAAGGCUCGCAACUUAUUUUCUUGGCGGAAAAUAAGUUGGU
#=GC SS_cons           :<<<<<<<____>>>>>>>,,,,,<<<<<<<______>>>>>>>,,,,,,,,<<<<---------<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>,,,<<<<<<<<<<____>>>>>>>>>>:::::
#=GC RF                ACaGauauUUAAguauCuGAUUAAuaaaGuaAUUAAAuaCuuuaCCAAAUUUcGgGUCUCGACUUCuuuaauuGauugGUGGuaauCaauuaagGCuCgCAAcuuauuguccuugCggacaauaagUUGGU
//
# STOCKHOLM 1.0

#=GF AC   RF00236
#=GF ID   ctRNA_pGA1
#=GF DE   ctRNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   PMID:12670963
#=GF SS   Published; PMID:12670963
#=GF GA   45.00
#=GF TC   45.20
#=GF NC   42.30
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   12670963
#=GF RT   Control of rep gene expression in plasmid pGA1 from Corynebacterium
#=GF RT   glutamicum.
#=GF RA   Venkova-Canova T, Patek M, Nesvera J
#=GF RL   J Bacteriol 2003;185:2402-2409.
#=GF CC   Rolling circle replication plasmids contain a number of mechanisms to
#=GF CC   maintain a low copy number. One of these methods is to transcribe a small
#=GF CC   RNA called ctRNA (for counter-transcribed RNA) than is transcribed on the
#=GF CC   opposite strand to RepB the replication initiation protein. ctRNA binds to
#=GF CC   the mRNA of repB and causes translational inhibition.
#=GF WK   ctRNA
#=GF SQ   15


AP005225.1/19073-19000 GCUUUCUCC--GGUGGUCGAAGACC-GGGGUAAAGCGGAGCGUC-UAACAGUG--UCUGCUGUUA-GGCGCUCAAC-UAUUU------
AB003157.1/651-573     GCUUUCUCCCAGGUUUG----GACUGGGGG-UUAGC-CGACGCCCUGUGAGUU--ACCGCUCACGGGGCGUUCAACAUUUUUCAG-GU
X90817.2/2232-2155     GCUUUCUCCCAGCUGAU----GACUGGGGG-UUAGC-CGACGCCCUGUGAGUU--CCCGCUCACGGGGCGUUCAAC-UUUUUCAG-GU
AF164956.1/9389-9312   GCUUUCCCCCAGGUUGU----GACUGGGUGAUAAGC-GAACACCUUACGAGCUUGGACCCUCGUAGGGUGUUC----UUUUUUGU-GU
AF486522.1/174-97      GCUUUCUCCCAGAUUGC----GCCUGGGUGAUAAGC-GAGCGUCGAACUGGUU--GCAGCCGGUUCGGCGCUCAU--UUUUUCGU-UU
AF401314.1/174-98      GCUUUCUCCCAGGUG-G----GACUGGGGGUAAAGC-GAGCGUCGAACUGGUA--GCCGCCGGUUCGGCGCUCAU--UUUUUCGU-UU
AY266269.1/177-99      GCUUUCUCCCAGGUAGU----GGCUGGGUGUAAAGC-GAGCGUCGAACUGGUU--GCAGCCGGUUCGGCGCUCAUU-UUUUUCGU-UU
AB084384.1/4361-4283   GCUUUCUCCCAGCUGAU----GACUGGGGG-UUAGC-CGACGCCUCGACAGUU--ACAGCUGUCGGGGCGUUCAACAUUUUUCAA-GU
AY263990.1/177-99      GCUUUCUCCCAGGUUGG----GACUGGGUGUAAAGC-GAGCGUCGAACUGGUU--GCAGCCGGUUCGGCGCUCAUU-UUUUUCGU-UU
AY061891.1/2640-2718   GCUUUCUCCCAGGUGUG----UGCUGGGUGAUAAGC-GAAAGUC-AUCGGGUU--GCCGCCCGGU-GGCUUUCUUCGUUUUUCAUUGU
AF024666.2/33919-33990 GCUUUCUCCCAGAUUGU----GGCUGGGUGAUAAGC-GAGCGUCGAUCCGGUU--GCCGCCGG-UCGGCGCUCAU--UUUUU------
AF121000.1/7510-7587   GCUUUCCCCCAGGUUGU----GACUGGGCGAUAAGC-GAACACCUUACGAGAUUGGACCCUCGUAGGGUGUUC----UUUUUUGU-GU
AF492560.1/11730-11652 GAUUUCUCCCAGGUGUG----UGCUGGGUGAUAAGC-GAAAGUC-AUCGGGUU--GCCGCCCGGU-GGCUUUCUUCGUUUUUCAUUGU
AF364477.1/176-98      GCUUUCUCCCAGGUUGG----GACUGGGUGUAAAGC-GAGCGUCGAACUGGUU--GCCGCCGGUUCGGCGCUCAUU-UUUUUCGU-UU
AY048596.1/176-99      GCUUUCUCCCAGGUUGG----GACUGGGUGUAAAGC-GAGCGUCGAACUGGUU--GCCGCCGGUUCGACGCUCAU--UUUUUCGU-UU
#=GC SS_cons           <<<--<<<<<<<_____....__>>>>>>>--->>>.-<<<<<<<<<<<<<<_..___>>>>>>>>>>>>>>::::.::::::::.::
#=GC RF                GCUUUCcCCCAGgUugu....GACUGGGgGauAAGC.GagCGcCgcgcggGuU..gCcgCccgcgcGgCGcuCAuc.UUUUUCgu.gU
//
# STOCKHOLM 1.0

#=GF AC   RF00237
#=GF ID   mir-9
#=GF DE   mir-9/mir-79 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   44.00
#=GF TC   44.00
#=GF NC   43.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000050;
#=GF DR   MIR; MI0000129;
#=GF DR   MIR; MI0000157;
#=GF DR   MIR; MI0000374;
#=GF DR   MIR; MI0000466;
#=GF DR   MIR; MI0000467;
#=GF DR   MIR; MI0000468;
#=GF DR   MIR; MI0000720;
#=GF DR   MIR; MI0000721;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science 2001;294:853-858.
#=GF RN   [2]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol 2002;12:735-739.
#=GF RN   [3]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science 2001;294:858-862.
#=GF RN   [4]
#=GF RM   12812784
#=GF RT   Temporal regulation of microRNA expression in Drosophila melanogaster
#=GF RT   mediated by hormonal signals and broad-Complex gene activity.
#=GF RA   Sempere LF, Sokol NS, Dubrovsky EB, Berger EM, Ambros V
#=GF RL   Dev Biol 2003;259:9-18.
#=GF CC   miR-9 has been identified in Drosophila (MIR:MI0000129) [1], mouse
#=GF CC   (MIR:MI0000720) and human (MIR:MI0000466) [2], and the related miR-79 in
#=GF CC   C. elegans (MIR:MI0000050) [3] and worm (MIR:MI0000374) [4]. The mature
#=GF CC   ~21nt miRNAs are processed from hairpin precursor sequences represented
#=GF CC   here. miR-9 is processed from the 5' arm of its precursor, and miR-79 from
#=GF CC   the 3' arm. The bounds of the precursors are predicted based on
#=GF CC   conservation and base pairing and are not generally known.
#=GF WK   Mir-9/mir-79_microRNA_precursor_family
#=GF SQ   43


Z81467.1/13319-13384           AUCUUUGGUGAUUCAGCUUCAAUGAUUGGCUACAGGU-UUCUUUCAUAAAGCUAGGUUACCAAAGCU
AC005316.1/63325-63386         CUCUUUGGUUAUCUAGCUGUA-UGAGUGC-CACAGA--GCCGU-CAUAAAGCUAGAUAACCGAAAGU
AF155142.1/45725-45784         AUCUUUGGUUAUCUAGCUGUA-UGAGUGU-AUUGG----UCUU-CAUAAAGCUAGAUAACCGAAAGU
AC116051.4/129891-129952       AUCUUUGGUUAUCUAGCUGUA-UGAGUGG-UGUGGA--GUCUU-CAUAAAGCUAGAUAACCGAAAGU
AASV01010872.1/688-628         GUCUUUGGUUAUCUAGCUGUA-UGAGUGA-UAAAU---AACGU-CAUAAAGCUAGCUUACCGAAGUU
BAAB01140220.1/33-92           AUCUUUGGUUAUCUAGCUGUA-UGAGUAU-UACUG----ACGU-CAUAAAGCUAGGUUACCGGAGUU
CAAE01015022.1/86446-86507     AUCUUUGGUUAUCUAGCUGUA-UGAGUGA-CGUACA--AUCUU-CAUAAAGCUAGAUAACCGAAAGU
AAFR03045064.1/82617-82556     CUCUUUGGUUAUCUAGCUGUA-UGAGUGU-UAUUGA--GCUAU-CAUAAAGCUAGAUAACCGAAAGU
BAAF04029497.1/530-469         GUCUUUGGUUAUCUAGCUGUA-UGAGUGU-GAUUUA--CCCAU-CAUAAAGCUAGAUAACCGAAAGU
AAGE02019539.1/116880-116941   CUCUUUGGUUAUCUAGCUGUA-UGAGUGA-AUUUAG--AACAU-CAUAAAGCUAGCAUACCGAAGUU
AL954314.8/15829-15770         CUCUUUGGUUAUCUAGCUGUA-UGAGUUA-UAACA----CUGU-CAUAAAGCUAGAUAACCGAAAGU
AAAB01008960.1/1144939-1144878 CUCUUUGGUUAUCUAGCUGUA-UGAGUGU-AUUUUA--AACGU-CAUAAAGCUAGCAUACCGAAGUU
BAAE01170633.1/457-398         AUCUUUGGUUAUCUAGCUGUA-UGAGUGU-UCUGC----UCGU-CAUAAAGCUAGAUAACCGAAAGU
BAAF04047241.1/1745-1804       AUCUUUGGUUAUCUAGCUGUA-UGAGUUG-GUGUA----AUAU-CAUAAAGCUAGAGAACCGAAUGU
BAAF04134102.1/794-855         AUCUUUGGUUAUCUAGCUGUA-UGAGUGC-CGUAUU--UUCUU-CAUAAAGCUAGAUAACCGAAAGU
AAVX01083387.1/420-360         CUCUUUGGUUUUCUAGCUGUA-UGAGUGU-GUUAU---ACCUU-CAUAAAGCUAGACAACCGAAUGU
AANH01005485.1/10565-10509     GUCUUUGGUUAUCUAGCUGUA-UGAGUUU-UAAUU-------U-CAUAAAGCUAGAGAACCGAAAGU
CAAE01014654.1/3052-3111       AUCUUUGGUUAUCUAGCUGUA-UGA--GU-UUAUGU--AAUAU-CAUAAAGCUAGAGAACCGAAUGU
BX465834.20/130413-130472      AUCUUUGGUUAUCUAGCUGUA-UGAGUAU-UUUGC----ACUU-CAUAAAGCUAGAUAACCGAAAGU
BX664610.10/157221-157162      CUCUUUGGUUAUCUAGCUGUA-UGAGUUU-AUGUG----AUAU-CAUAAAGCUAGAGAACCGAAUGU
AANH01000350.1/78292-78353     GUCUUUGGUUAUCUAGCUGUA-UGAGUGU-UAAUCA--UCCAU-CAUAAAGCUAGAUAACCGAAAGU
AAVX01065791.1/2124-2183       GUCUUUGGUUAUCUAGCUGUA-UGAGUUU-AUUCA----CCGU-CAUAAAGCUAAAUAACCGAAAGU
AANU01176011.1/665-604         CUCUUUGGUUAUCUAGCUGUA-UGAGUGC-CACAGA--GCCGC-UCUCAAGCUAGAUAACCGAAAGU
AAZX01012164.1/4457-4517       UUCUUUGGUUAUCUAGCUGUA-UGAGUUU-GGUUG---UACAU-CAUAAAGCUAGGUUACCGGAGUU
AAJJ01000398.1/19121-19058     UUCUUUGGUUAUCUAGCUGUA-UGAGUAU-UGUUUAAUAACAU-CAUAAAGCUAGGUUACCGGAGUU
CR848047.6/7022-7083           AUCUUUGGUUAUCUAGCUGUA-UGAGUGU-UAUUCA--UUCUU-CAUAAAGCUAGAUAACCGAAAGU
AAQA01000025.1/15457-15396     UACUUUGGUUAUCUAGCUGUA-UGAGUAA-GUUACU--GGCUU-CAUAAAGCUAGGUUACCAAAGCU
AAKO01001629.1/14298-14360     UGCUUUGGCGCUUUAGCUGUA-UGAUAGA-UUUAAAC-UACUU-CAUAAAGCUAGAUUACCAAAGCA
AAZO01004437.1/24877-24818     UUCUUUGGUUAUCUAGCUGUA-UGGAUAU-UUUGA----ACUU-CAUAAAGCUACAUUACCGAAGGU
AAGE02024640.1/55219-55280     UGCUUUGGCGCUUUAGCUGUA-UGAUAGA-AUUUAA--UAUUU-CAUAAAGCUAGAUUACCAAAGCA
AAST01027169.1/135-76          UCUUUUGGUUAUCUAGCUGUA-UGAGUGA-UAAUA----ACGU-CAUAAAGCUAGCCUACCGAAGUU
AAZO01004036.1/9217-9278       UUCUUUGGUGAUCUAGCUGUA-UGGAUAA-UAAUUU--UAUUC-CAUAAAGCUAUUUUACCGAUGUC
AAFR03052350.1/15878-15820     AUCUUUGGUUUCCUAGCUGUG-UGAGUGU-CUCUG-----AAU-CAUAAAGCUGGAGAACCGAAUGU
AAPN01432088.1/257-198         GUCUUUGGUUAUCUAGCUGUA-UGAGUGU-AUGUG----AUGU-CAUAAAGCUAGAGAACCGAAUGU
AAJJ01003219.1/11147-11088     UUCUUUGGUGAUCUAGUUGUA-UGAGUGU-UUUAU----AUAU-CAUAAAGCUGGUUCAGCAAAGCA
AAGV020387958.1/714-775        AUCUUUGGUUAUCUAGCUGUA-UGAGUGG-UGUGGA--GUCUU-CAUAAAGCUAGAUAACAAAAAAG
CAAK05014843.1/1888-1946       CUCUUUGGUUAUCUAGCUGUA-UGAGUUA-UGAAA-----UAU-CAUAAAGCUAGAGAACCGAAAGU
CU467822.7/141255-141194       AUCUUUGGUUAUCUAGCUGUA-UGAGUGU-UUAUCU--GCCUU-CAUAAAGCUAGAUAACCGAAAGU
CU462873.19/8896-8955          AUCUUUGGUUAUCUAGCUGUA-UGAGUGU-GCUGG----CCGU-CAUAAAGCUAGAUAACCGAAAGU
AEKZ01008225.1/40713-40773     UUCUUUGGUUAUCUAGCUGUA-UGAGUAU-UAUUC---GACAU-CAUAAAGCUAGGUUACCGGAGUU
AADG06003322.1/33812-33872     UACUUUGGUAAUAUAGCUCUA-UGAUUUU-AAUUA---AGGAU-CAUAAAGCUAGAUUACCAAAGCA
AGKD01013711.1/6608-6669       GUCUUUGGUUAUCUAGCUGUA-UGAGUGU-UAAAUA--CCUGU-CAUAAAGCUAGAUAACCGAAAGU
AAGJ04054934.1/20471-20532     CUCUUUGGUUAUCUAGCUGUA-UGAGUGA-UGUCAA--UGCAU-CAUAAAGCUAGGUUACCAAAGAU
#=GC SS_cons                   :::<<<<<<<<<<<<<<<--<.<<<____.______..____>.>>>-->>>>>>>>>>>>>>>:::
#=GC RF                        uUCUUuGGUuaucUAGCUGUA.UGAGUGu.uauuaa..uacuU.CAUAAAGCUAgauaACCgAAggU
//
# STOCKHOLM 1.0

#=GF AC   RF00238
#=GF ID   ctRNA_pND324
#=GF DE   ctRNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   PMID:9682491
#=GF SS   Predicted; ILM
#=GF GA   45.00
#=GF TC   46.50
#=GF NC   44.70
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0060908; plasmid copy number maintenance;
#=GF RN   [1]
#=GF RM   9682491
#=GF RT   Involvement of antisense RNA in replication control of the lactococcal
#=GF RT   plasmid pND324.
#=GF RA   Duan K, Liu CQ, Supple S, Dunn NW
#=GF RL   FEMS Microbiol Lett 1998;164:419-426.
#=GF CC   Rolling circle replication plasmids contain a number of mechanisms to
#=GF CC   maintain a low copy number. One of these methods is to transcribe a small
#=GF CC   RNA called ctRNA (for counter-transcribed RNA) than is transcribed on the
#=GF CC   opposite strand to RepB the replication initiation protein. ctRNA binds to
#=GF CC   the mRNA of repB and causes translational inhibition.
#=GF WK   ctRNA
#=GF SQ   48


AF179847.1/3382-3298   UG--AGAACUACUCCUUUUAUGGGUGG-UUUG--GC-UAAGCAUGAAGAAAUUCCGUGCAAAGAA--UUUUUCUUCAUG-CUU-UUAUUAUAUCA
U35629.2/270-185       UA--GUAAUUGCUCC-UUUGUGAGUGAUUUUG--GU-UAAGCAUGAAGAAAUGCUCUGCAAAAAGU-UUUUUCUUCAUG-CUU-UUAUUAUAUCA
U79032.1/443-358       UA--GUAAUUGCUCC-UUUGUGAGUAAUUUUG--GU-UAAGCAUGAAGAAAUGCUCUGCAAAAGGU-UUUUUCUUCAUG-CUU-UUAUUAUAUCA
AF036485.2/32199-32115 UAA-AGAUACGCUCC---UCUGCGUGUUCAUA--AG-UAAGUAUGAAGAAAUUCUCGUUCAAAAGU-UUGUUCUUCAUA-CUU-UUAUUAUAUCA
AF142640.1/277-192     UAG-AAAACUGCUCC-UUUGUGAGUGAGUUUA--GA-UAAGCAUGAAGAAACACUUUUCGUAGAG--AGAUUCUUCAUG-CUU-UUAUUAUAUCA
AF179848.1/8272-8187   UAG-AAAACUGCUCC-UUUGUGAGUGAGUUUA--GA-UAAGCAUGAAGAAACACUUUUCGUAGAG--AGAUUCUUCAUG-CUU-UUAUUAUAUCA
AF153414.1/503-418     UAG-AAAACUGCUCC-UUUGUGAGUGAGUUUA--GA-UAAGCAUGAAGAAACACUUUUCGUAGAG--AGAUUCUUCAUG-CUU-UUAUUAUAUCA
AB079380.1/1237-1152   UAG-AAAACUGCUCC-UUUGUGAGUGAGUUUA--GA-UAAGCAUGAAGAAACACUUUUCGUAGAG--AGAUUCUUCAUG-CUU-UUAUUAUAUCA
AF207855.1/225-140     UAG-AAAACUGCUCC-UUUGUGAGUGAGUUUA--GA-UAAGCAUGAAGAAACACUUUUCGUAGAG--AGAUUCUUCAUG-CUU-UUAUUAUAUCA
AL592102.1/21892-21975 UAG-AAAACUGCUCC-UUU--GAGUGUUUUUA--GA-UACGCAUGAAGAUUCUCUCGACGAAAAG--UGUUUCUUCAUG-CUU-UUAUUAUACCA
AB079381.2/1234-1150   UGA-GAAGUUGCUCC--UUAUGAGUAAUUUUG--GC-UAAGCAUAGAGAAG-UCAUUUCGUCGUGA-AUUUUCUCUAUG-CUU-UUAUUAUAUCA
X96950.1/294-210       UGA-GAAGUUGCUCC--UUAUGAGUAAUUUUG--GC-UAAGCAUAGAGAAG-UCAUUUCGUCGUGA-AUUUUCUCUAUG-CUU-UUAUUAUAUCA
AJ550510.1/1776-1692   UGA-GAAGCCGCUCC--UUAUGAGUAAUUUUG--GC-UAAGCAUAGAGAAG-UCAUUUCGUCGUGA-AUUUUCUCUAUG-CUU-UUAUUAUAUCA
AF242367.1/9673-9756   UGA-GAAGUUGCUCC--UUAUGAGUAAUUUUG--GU-CUAGCAUAGAGAAGAAACUUUAGCGAG---AUUUUCUCUAUG-CUU-UUAUUAUAUCA
AF243383.1/12152-12069 UGA-GAAGUUGCUCC--UUAUGAGUAAUUUUG--GU-CUAGCAUAGAGAAGAAACUUUAGCGAG---AUUUUCUCUAUG-CUU-UUAUUAUAUCA
U90222.1/593-510       UGA-GAAGUUGCUCC--UUAUGAGUAAUUUUG--GU-CUAGCAUAGAGAAGAAACUUUAGCGAG---AUUUUCUCUAUG-CUU-UUAUUAUAUCA
U26550.1/472-389       UGA-GAAGUUGCUCC--UUAUGAGUAAUUUUG--GU-CUAGCAUAGAGAAGAAACUUUAGCGAG---AUUUUCUCUAUG-CUU-UUAUUAUAUCA
X85168.1/446-362       UGA-UAAGUUGCUCC--UUAUGAGUAAUUUUA--GU-UAAGCAUAGAGAAG-UCAUUUAGCGGUGU-ACUUUCUCUAUG-CUU-UUAUUAUAUCA
U16027.2/271-187       UGA-GAAGUUGCUCC--UUAUGAGUAAUUUUA--GU-UAAGCAUAGAGAAG-UCAUUUAGCGGUGU-ACUUUCUCUAUG-CUU-UUAUUAUAUCA
AF001314.2/271-188     UGU-AAAUACGCUCC-----UUUGCGUGUUUUA-GU-CUGGCAUAGAGAAAGUCAUUUAGCGGUGU-AUUUUCUCUAUG-UUU-UUAUUAUAUCA
AF036485.2/36706-36789 UAG-AAAUACGCUCC-----UUUGCGUGUUUUA-GU-CUGGCAUAGAGAAAUUCAUUUAGACGUGU-GAUUUCUCUAUG-CUU-UUAUUAUAUCA
X96948.1/291-208       UAG-AAAUACGCUCC-----UUUGCGUGUUUUA-GU-CUGGCAUAGAGAAAUUCAUUUAGACGUGU-GAUUUCUCUAUG-CUU-UUAUUAUAUCA
X96949.1/273-190       UAG-AAAUACGCUCC-----UUUGCGUGUUUUA-GU-CUGGCAUAGAGAAAUUCAUUUAGACGUGU-GAUUUCUCUAUG-CUU-UUAUUAUAUCA
Z25476.1/322-245       -------UACGCUCC-----UUUGCGUGUUUUA-GU-CUGGCAUAGAGAAAUUCAUUUAGACGUGU-GAUUUCUCUAUG-CUU-UUAUUAUAUCA
AF013595.1/382-299     UGU--AAA-UACUCC-UUUGUGAGUGAUUUUA--GA-UAGGCAUAGAGAAAAAUCUUUAGCGAGUC-AAUUUCUCUAUG-CUU-UUAUUAUA-CA
AJ132009.2/384-301     UGU-AAA--UACUCC-UUUGUGAGUGAUUUUA--GA-UAGGCAUAGAGAAAAAUCUUUAGCGAGUC-AAUUUCUCUAUG-CUU-UUAUUAUA-CA
AF097472.2/1273-1189   UAG-UAA--UACUCC-UUUGUGAGUGUUUUUA--AA-UAGGCAUAGAGAAAAAUCUUUAGCGGGUC-AAUUUCUCUAUG-UUU-UUAUUAUAUCA
Z22704.1/624-539       UAG-UAA--UACUCC-UUUGUGAGUGUUUUUA--AA-UAGGCAUAGAGAAAAAUCUUUAGCGAGUC-AAUUUCUCUAUGCUUU-UUAUUAUAUCA
L02920.1/726-641       UAG-AAAGUUACUCC-UUUGUGAGUGAUUUUA--AG-UAGGCAUAGAGAAACUGAUUUCGCUGUC--GAUUUCUCUAUG-CUU-UUAUUGUAUCA
X60454.1/788-706       UGG-AAA--UACUCC-UUUGUGAGUGAUUUUA--CA-UAGGCAUAGAGAAACUGAUUUUGCGGUC--GUAUUCUCUAUG-CUU-UCA-UAUACCA
AF178424.1/2150-2063   UAG-AAAGUUACUCC-UUUGUGAGUGAUUUUA--AG-GUGGCAUAGAGAAAGUGAUUUUGCGGUCAUAAUUUCUCUAUG-CUU-UUAUUAUACCA
AF097471.1/6633-6719   UAG-UAAGUUGCUCC-UUUGUGAGUGAUUUUA--AG-UAGGCAUAGAGAAAGUCAUUUCGCGGUGA-AUUUUUUCUAUG-CUU-UUAUUAUAACA
AF036485.2/2903-2986   UAG-AAA--UACUCC-UUUGUGAGUG-UUUAAG-AA-UAAGCAUAGAGAAAGUUUUCUUAGCGGGA-AAUUUCUCUAUG-CUA-UUAUUAUACC-
X92946.1/4236-4153     UAG-AAA--UACUCC-UUUGUGAGUG-UUUAAG-AA-UAAGCAUAGAGAAAGUUUUCUUAGCGGGA-AAUUUCUCUAUG-CUA-UUAUUAUACC-
AE001272.1/57810-57723 UAG-AAAGUAACUCC-UUUGUGAGUGAUUUUAG-AA-UUAGCAUAGAGAAAACAUUUUUGCGAGUG-AAUUUCUCUAUG-CUU-UUAUUAUAUCA
Z25477.1/365-281       UAG-AAA--UACUCC-UUUGUGAGUGUUUUGUG-AU-UAAGCAUAGAGAAG-UGAUUUAGACGUCA-AUUUUCUCUAUG-CUU-UCAUUAUACAA
Y12736.2/294-210       UAUAAAAUACGCUCC-----UUUGCGUGUUUGA-AA-UAGGCAUAGAGAAAGUCAUUUUGCCGUGA-AUUUUCUCUAUG-CUU-UUAUUAUAUCA
X96951.1/294-210       UAUAAAAUACGCUCC-----UUUGCGUGUUUGA-AA-UAGGCAUAGAGAAAGUCAUUUUGCCGUGA-AUUUUCUCUAUG-CUU-UUAUUAUAUCA
X96952.1/270-186       UAUAAAAUACGCUCC-----UUUGCGUGUUUGA-AA-UAGGCAUAGAGAAAGUCAUUUUGCCGUGA-AUUUUCUCUAUG-CUU-UUAUUAUAUCA
AJ550509.1/1767-1683   UAUAAAAUACGCUCC-----UUUGUGUGUUUGA-AA-UAGGCAUAGAGAAAGUCAUUUUGCCGUGA-AUUUUCUCUAUG-CUU-UUAUUAUAUCA
Z25475.1/578-494       UGU-AAAUACGCUCC-----UUUGCGUGUUAUAAAG-UGGACAUAGAGAAAGAUUCUUUGCGGGA--UAGUUCUCUAUG-UCUUUUAUUGUACCA
U44843.1/716-628       UGU-AAAUACGCUCC-UUUGUGAGUGUUUUUGA-AU-UAGGUAUAGAGAAACUGAUUUUGCCGUCAUGAUUUCUCUAUG-CUU-UUAUUAUACCA
AF116286.2/3521-3437   UAU-AAAUACGCUCC-----UUUGUGUGUUUUAGUA-GUAGCAUAGAGAAAGUCAUUUCGUAGUGA-GUUUUCUCUAUG-CUU-UUAUUAUACUA
AF247159.1/562-478     UAU-AAAUACGCUCC-----UUUGUGUGUUUUAGUA-GUAGCAUAGAGAAAGUCAUUUCGUAGUGA-GUUUUCUCUAUG-CUU-UUAUUAUACUA
AF409136.1/6689-6605   UAU-AAAUACGCUCC-----UUUGCGUGUUUUAGUA-GUAGCAUAGAGAAAGUCAUUUCAUAGUGA-GUUUUCUCUAUG-CUU-UUAUUAUACUA
D63820.1/954-870       UAU-AAAUACGCUCC-----UUUGCGUGUUUUAGUA-GUAGCAUAGAGAAAGUCAUUUCAUAGUGA-GUUUUCUCUAUG-CUU-UUAUUAUACUA
X56550.1/964-880       UAU-AAAUACGCUCC-----UUUGCGUGUUUUAGUA-GUAGCAUAGAGAAAGUCAUUUCAUAGUGA-GUUUUCUCUAUG-CUU-UUAUUAUACUA
AJ493278.1/8242-8159   UAU-AAAUACGCUCC-----UUUGCGU-UUUGUGUAAUAAGCAUAAAGAAAAACUUUUGGUCGGG--AAUUUCUUUAUG-CUU-UUAUUGUACCA
#=GC SS_cons           :::.<<<<<<<<<<_..____>>>>>>>>>>-..--.-<<<<<<<<<<<<<_______________.__>>>>>>>>>>.>>>.:::::::::::
#=GC RF                UAu.aAAcccgCucC..UUgUgaGcgggUUua..aa.UaaGCAUaGAGAAaaucaUUUuGuaGuga.auuUUCUCuAUG.Cuu.UUAUUAUAuCA
//
# STOCKHOLM 1.0

#=GF AC   RF00239
#=GF ID   mir-124
#=GF DE   mir-124 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12844358
#=GF RT   Computational identification of Drosophila microRNA genes.
#=GF RA   Lai EC, Tomancak P, Williams RW, Rubin GM
#=GF RL   Genome Biol 2003;4:R42.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol 2002;12:735-739.
#=GF CC   miR-124 has been identified in Drosophila (MIR:MI0000373) [1], C. elegans
#=GF CC   (MIR:MI0000302) [2], mouse (MIR:MI0000150) and human (MIR:MI0000443) [3].
#=GF CC   The mature ~21nt miRNAs are processed from hairpin precursor sequences
#=GF CC   represented here, in this case originating from the 3' arm. The bounds of
#=GF CC   the precursors are predicted based on conservation and base pairing and
#=GF CC   are not generally known.
#=GF WK   mir-124_microRNA_precursor_family
#=GF SQ   56


AC021518.12/83108-83029          GCUCUGCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGAGCC
AC055869.13/127592-127511        GCCUCUCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA-AUGUCCAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-AUGGGGCU
AL096828.29/88058-88137          GGCCC-CUCUGCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUCUAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGGCGCC
BX511178.6/169755-169675         -UGCUUUUCUUCGUGU----UCACAGCGG---ACCU-UGAUUUAA-AUGUCCAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGAUGGC
AANH01005777.1/13142-13063       UUGUGUCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-UUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAUUACCC
AAVX01290765.1/186-107           UUCUCGCUCUCAGUGU----UCAUGGCGG---AUCU-UGAUUUAA--UGUG-GUACAAUUAAGGCACACGGUGAAUGCUAAGG-GAGGGGCC
CR381647.10/84956-85035          UCUCG-CUCUGCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUCCAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAAGAAUC
BAAF04094312.1/9605-9526         UUUCCUCUCUCAGUGU----UCACAGUGG---ACCU-UGAUUUCA---AAACAGUCAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGAAUCC
AAPN01339562.1/220-301           GCCUGUCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA-AUUUGUACACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCCCAGCC
AANH01002585.1/13981-13901       UUGCCACUCCUCGUGU----UCACGGCGG---ACCU-UGAUUUAU--UAGCAAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGGAAUC
BX324109.8/64997-64917           CCGCCACUCUGCGUGU----UCACGGCGG---ACCU-UGAUUUAA--UAUCCAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGGGGUC
AAZO01006175.1/169136-169059     UGCCUGCUCCUCGUGU----UCACUGUUG---GCCU-UG----AU-GUUUUAAUGAUCAUAAGGCACGCGGUGAAUGCCAAGA-GCUAGCUC
BAAE01194669.1/2121-2201         UUUCCACUCCUCGUGU----UCACAGCGG---ACUU-UAAUUGAU--UAAGCGCACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGGAAUC
BX248497.11/64645-64566          CUCUCGCUGUACGUGU----UCACAGUGG---ACCU-UGAUUUAU--UGUA-UUUCAAUUAAGGCACGCGGUGAAUGCCAACA-GCACAGCC
BAAF04002878.1/3181-3101         UUGUCACUCUGCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUCCAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGGAAUC
BAAF04105842.1/7834-7753         UUUUCUCUCCUCGUGU----UCACAGCGG---ACCU-UGAUUUAA-AUGUCCAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGCGACC
AANH01005533.1/39962-40041       CUUCCUCUCUCAGUGU----UCACAGUGG---ACCU-UGAUUUAA--AAUC-AUUCAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGAAGCC
AAVX01073976.1/511-432           CUCGUUCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCCGGGCC
AAVX01582238.1/229-149           CUCCUGCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUUUAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAAGUGCC
AAVX01233922.1/370-449           CCCCCACUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUU-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAAGGGCC
AABS01000310.1/18792-18714       CGCUUAUGAGUCGUGU----UUACUGUGG---ACCU-UG-CUGUG--UGACGUCACA-AUAAGGCACGCGGUGAAUGCCAAUC-AAAAGUCG
AASU01002643.1/1016-1092         GUUUUUCUCCUGGUAU----CCACUGUAG---GCCU-AUAUGUAU--UUCC---ACCAUA-AGGCACGCGGUGAAUGCCAAGA-GCGAACGC
AC189672.3/51235-51156           UCGACACGCUUCGUGU----UCACUGUCU---GUCU-UGAUCUUU--UAUU-CGAGAAUUAAGGCACGCGGUGAAUGCCAAGC-GUGGGACG
AAJJ01000069.1/11639-11717       GUCAUUCUCCUAGUGU----UCACUGUUG---GCCUGUAUGUUUU--UGUA---ACGCAUAAGGCACGCGGUGAAUGCCAAGA-GCAGACUU
AACN010875145.1/527-607          ACUCUGCCCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAUUAGCGGAGCC
AAGE02000531.1/21424-21342       GUUUUUCUCCUGGUAU----CCACUGCCG---GCCUAUAUGUCCU-AUUUCGGUACUCAUAAGGCACGCGGUGAAUGCCAAGA-GCGAACGC
AAAB01008984.1/10212826-10212908 GUUUUUCUCCUGGUGU----UCACUGUAG---GCCUGUAUGUUCU-AUUGCGGAUUUCAUAAGGCACGCGGUGAAUGCCAAGA-GCGAACGA
AABS01000310.1/18932-18854       CUAUGUUCGGUAGUAU----UUAUUGUGG---ACCU-UG-CUGUG--UGACGUCACA-AUAAGGCACGCGGUGAAUGCCAACG-AAUUUUUG
AADK01010415.1/6990-7072         GUCCACCUCCUCGCGU----UCACUGCCGGAGCCGU-UAUGUAUA--UUUA-AAAUUCAUAAGGCACGCGGUGAAUGCCAAGA-GCGGACUC
AAWT01063851.1/2130-2054         CCAUGAAAAUUUGCAU----UUACAACGU---GUCU-UUAGUUCA--UGUG---ACACU-AAGGCACGCGGUGAAUGCUGAAU-UAAAUGGU
BX323067.11/106925-107004        CUCUGGCUUUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-UUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGAGCC
AAQB01006734.1/278415-278339     GUUUUUCUCCUGGUAU----CCACUGCAG---GCCU-AUAUGUUA--UUUG---ACCAUA-AGGCACGCGGUGAAUGCCAAGA-GCGAACGA
AANI01016269.1/7414-7490         GUUUUUCUCCUGGUAU----CCACUGUAG---GCCU-CUAUGAAU--UUUG---ACCAUA-AGGCACGCGGUGAAUGCCAAGA-GCGAACGA
AAWU01000987.1/43993-44075       GUUUUUCUCCUGGUGU----UCACUGCCG---GCCUGUAUGUCCU-AUUGAGGUUUUCAUAAGGCACGCGGUGAAUGCCAAGA-GCGGACGA
AAQQ01613377.1/480-556           AGGCCCCUCUGCGUGU----CCACAGCGG---ACCU-GA-UUUUA--UGUCUAUACA-UUUAGGCACGCGGUG-AUGC-AAGA-GAGCGCUC
AACT01004897.1/11101-11179       UGCGCUUCAUCCGCGU----UUGCUGCGG---ACCU-UC-UUGUG--UGACAUCACA-AUAAGGCACGCGGUGAAUGCCAAUG-AAACGUCA
AACT01007791.1/10034-10112       CCAAGUUCGAUCGUGU----UUAUUGUGG---ACCU-UGC-CGUG--UGACGUCACA-GUAAGGCACGCGGUGAAUGCCAACG-AACUCGCG
FP017274.3/18078-18158           UUUUUGCUCUUUGUGU----UCACAGUGG---ACCU-UGAUUUAA--UUUCAAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGAAGCC
AAWZ02009650.1/4800-4719         GCCCCUCUCUGCGUGU----UCACAGCGG---ACCU-UGAUUUAA-AUGUCCAUACAAUUAAGGCACGCGGUGAAUGCUAAGA-ACGAGGCU
CAAB02005961.1/37252-37171       UGGUCUCUCCUCGUGU----UCACAGCGG---ACCU-UGAUUUAA-AUGUCCAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGCAGCU
CAAB02009061.1/535-451           UAAACUUUCCACGAAUUCGAUCACGGCGG---ACCU-UAAUUUAU--CUGCCCAUCAAUUCAGGCACGCGGAGAAUGCCAAGA-GAGGAAUC
AEVX01011340.1/56538-56623       UCUGUGCUCCUUGCGU----UCACUGCGGGCUUCCA-UGUGCCAACUUUUCAAAAUUCAUAAGGCACGCGGUGAAUGCCAAGA-GCGGACCA
AAWZ02034331.1/1530-1450         GCUUGGCCCUUCGUGU----UCACAGUGG---ACCU-UGAUUUCA--UGUGGACACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCCCAGCC
AAWZ02008050.1/15223-15144       CGCUGCCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGGGCU
AAWZ02006431.1/94608-94528       GCCCUUCUCUGCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUCCAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGCGGCU
AADN03007879.1/154-234           GCCUCUCUCUGCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUCCAUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GAGGAGCC
AADN03008224.1/1979-2058         CCCCAGCGUUUUGUGU----UCACUGCAG---ACCU-UGAUUUAA--UGUC-ACACGAUUAAGGCACGCAGUGAAUGCCAAAG-UUUGGGGC
AADN03002517.1/215257-215336     CUCUGCCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGAUCC
AAGJ04089024.1/54216-54298       AUCCCGUUCUUAGUGU----UCACUGUGA---UCCU-UGAUUUAU-AUUCUAAAACAAUUAAGGCACGCGGUGAAUGCCAAGGCUCGAGGGU
AY866112.1/445-524               GCUCUGCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGAGCC
AY866113.1/459-538               GCUCUGCCCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGAGCC
AY866116.1/445-524               GCUCUGCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGAGCC
AY866115.1/445-524               GCUCUGCCCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGAGCC
AY866117.1/414-493               GCUCUGCCCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGAGCC
AY866118.1/431-510               GCUCUGCCCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGAGCC
AY866114.1/342-421               GCUCUGCUCUCCGUGU----UCACAGCGG---ACCU-UGAUUUAA--UGUC-AUACAAUUAAGGCACGCGGUGAAUGCCAAGA-GCGGAGCC
#=GC SS_cons                     ::<<<<<<<---<<<<....-<<<-----...-<<<.<<<<____..__________>>>>>>>------>>>->>>>--->>.>>>>>:::
#=GC RF                          uuuccucucuucGuGU....UCACuGCGG...aCCU.UgauUUaa..UgucaauACAauuAAGGCACGCGGUGAAUgCCAAga.gaggagcc
//
# STOCKHOLM 1.0

#=GF AC   RF00240
#=GF ID   RNA-OUT
#=GF DE   RNA-OUT
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   PMID:2482367, INFERNAL
#=GF SS   Predicted; Pfold
#=GF GA   41.00
#=GF TC   41.50
#=GF NC   40.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   2482367
#=GF RT   Insertion sequence IS10 anti-sense pairing initiates by an interaction
#=GF RT   between the 5' end of the target RNA and a loop in the anti-sense RNA.
#=GF RA   Kittle JD, Simons RW, Lee J, Kleckner N
#=GF RL   J Mol Biol 1989;210:561-572.
#=GF CC   Transposition of insertion sequence IS10 is regulated by an anti-sense RNA
#=GF CC   which inhibits transposase expression when IS10 is present in multiple
#=GF CC   copies per cell. The anti-sense RNA (RNA-OUT) consists of a stem domain
#=GF CC   topped by a flexibly paired loop; the 5' end of the target molecule,
#=GF CC   RNA-IN, is complementary to the top of the loop, and complementarity
#=GF CC   extends for 35 base-pairs down one side of RNA-OUT [1]. This bacterial RNA
#=GF CC   is also found in the genomic sequence of eukaryotic organisms. This is
#=GF CC   probably due to vector contamination.
#=GF WK   RNA-OUT
#=GF SQ   16


AF078527.1/2546-2614         UCGCGCAUCUUGUUGUCCAAGUGU-------AGUUUUU-GGCGAAACCAUUUGAUCAUGCAACAAGAUGCGCUUCCA
AF133699.1/3533-3601         UCGCGCAUCUUGUUGUCCAAGUGU-------AGUUUUU-GGAGAAACCAUUUGAUCAUGCAACAAGAUGCGCUUCCA
AF162223.1/9033-9102         UCGCACAUCUUGUUGUCUGAUUAU-------UGAUUUUUCGCGAAACCAUUUGAUCAUAUGACAAGAUGUGUAUCCA
AF248639.1/3345-3414         UCGCACAUCUUGUUGUCUGAUUAU-------UCAUUUUUCGCGAAACCAUUUGAUCAUAUGACAAGAUGUGUAUCCA
EF158106.1/10782-10851       UCGCACAUCUUGUUGUMUGAUUAU-------UGAUUUUUCGCGAAACCAUUUGAUCAUAUGACAAGAUGUGUAUCCA
AE017220.1/3200649-3200718   UCGCACAUCUUGUUGUCUGAUUAU-------UGAUUUUUCGCGAAACCAUUUGAUCAUAUGACAAGAUGUGUAUCCA
AAWQ01000001.1/205744-205675 UCGCACAUCUUGUUGUUUGGUUGU-------UGUUUUUUGGCGAAAUCAUUUGAUCACAUGACAAGAUGUGCAUCUA
AY691910.1/4002-4071         UCGCACAUUUUGUUGUCUGAUUAU-------UGAUUUUUGGCGAAACCAUUUGAUCAUAUGACAAGAUGUGUAUCUA
AJ627386.1/14727-14658       UCGCACAUUUUGUUGUCUGAUUAU-------UGAUUUUUGGCGAAACCAUUUGAUCAUAUGACAAGAUGUGUAUCCA
AB262965.1/7478-7547         UCGCACAUCUUGUUGUCUGGUUAU-------UGAUUUUUCGCAGAACCAUUUGAUCACAUGACAAGAUGUGCAUCUA
BA000032.2/1400255-1400186   UCGUACAUCUUGUUGUUUGGUUGU-------UGUUUUUUGGCGAAAUCAUUUGAUCACAUGACAAGAUGUGCAUCUA
AASA01000102.1/10006-9937    UCGCACAUUUUGUUGUCUGAUUAU-------UGAUUUUUGGCGAAACCAUUUGAUCAUAUGACAAGAUGUGUAUCUC
AY236073.2/2048-2116         UCGCGCAUCUUGUUGUCCAAGUGU-------AGUUUUU-AGCGAAACCAUUUGAUCAUGCAACAAGAUGCGCUUCCA
AAZW01000016.1/47862-47938   UCACACAUCUUGUUGUUUGAUUAUUGAUUAUUGAUUUUUGGCGAAACCAUUUGAUCACAUGACAAGAUGUGUUUCUA
ABJT01000108.1/2744-2813     UCGCACAUCUUGUUGUCUGAUUAU-------UGAUUUUUCGCGAAACCAUUUGAUCAUAUGACAAGAUGUGUAUCUA
HM015773.1/4447-4379         UCGCGCAUCUUGUUGUCCAAGUGU-------AGUUUUU-GGCGAAACCAUUUGAUCAUGCAACAAGAUGCGCUUCCA
#=GC SS_cons                 ::<<<<<<<<<<<<<<-<<-----.......----------<<<<____>>>>-->>->>>>>>>>>>>>>>:::::
#=GC RF                      UCgCaCAUCUUGUugucuGAuUaU.......UGaUUUUUgGCgAAACCAUUuGAUCaUacgACAAGAUGuGcaUCuA
//
# STOCKHOLM 1.0

#=GF AC   RF00241
#=GF ID   mir-8
#=GF DE   mir-8/mir-141/mir-200 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   36.00
#=GF TC   36.00
#=GF NC   35.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000128;
#=GF DR   MIR; MI0000166;
#=GF DR   MIR; MI0000243;
#=GF DR   MIR; MI0000342;
#=GF DR   MIR; MI0000457;
#=GF DR   MIPF; MIPF0000019;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science 2001;294:853-858.
#=GF RN   [2]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA 2003;9:175-179.
#=GF CC   miR-8 from Drosophila [1] (MIR:MI0000128) and human and mouse mir-141
#=GF CC   (MIR:MI0000166, MIR:MI0000457), mir-429 (MIR:MI0001642) and mir-200
#=GF CC   (MIR:MI0000243, MIR:MI0000342) [2] are expressed from the 3' arm of
#=GF CC   related precursor hairpins (represented here). Members of this precursor
#=GF CC   family have now been predicted or experimentally confirmed in a wide range
#=GF CC   of species (MIPF:MIPF0000019). The bounds of the precursors are predicted
#=GF CC   based on conservation and base pairing and are not generally known.
#=GF WK   Mir-8/mir-141/mir-200_microRNA_precursor_family
#=GF SQ   13


U47924.1/176113-176193     CCCUGGGUCCAUCUU-CCAGUACAGUGUUGGAUGGUCUAAUUGUGAAGCUCCUAACACUGUCUGGUAAAGAUGGCUCCCGGG
AC002397.1/179832-179912   CUCUGGGUCCAUCUU-CCAGUGCAGUGUUGGAUGGUUGAAGUAUGAAGCUCCUAACACUGUCUGGUAAAGAUGGCCCCCGGG
AL627204.7/130619-130543   CUCUGUGGGCAUCUU-ACCGGACAGUGCUGGAUUUCUUGGC----UUGACUCUAACACUGUCUGGUAACGAUGUUCAAAGGU
AL390719.47/106960-107036  CCCUGUGAGCAUCUU-ACCGGACAGUGCUGGAUUUCCCAGC----UUGACUCUAACACUGUCUGGUAACGAUGUUCAAAGGU
U47924.1/175703-175780     GGGGGCCCUCGUCUU-ACCCAGCAGUGUUUGGGUGCGGUUG---GGAGUCUCUAAUACUGCCGGGUAAUGAUGGAGGCCCCU
AC002397.1/179426-179504   AGGGGCCCUCGUCUU-ACCCAGCAGUGUUUGGGUGCUGGUUG--GGAGUCUCUAAUACUGCCGGGUAAUGAUGGAGGCCCCU
AC099021.1/85263-85337     AUCUGUUCACAUCUU-ACCGGGCAGCAUUAGAUCCUUUUU-----AUAACUCUAAUACUGUCAGGUAAAGAUGU-CGUCCGU
AL627204.7/131391-131318   AGCCGUGGCCAUCUU-ACUGGGCAGCAUUGGAUAGUGUC------UGAUCUCUAAUACUGCCUGGUAAUGAUGA-CGGCGGA
AL390719.47/106206-106279  AGCCGUGGCCAUCUU-ACUGGGCAGCAUUGGAUGGAGUC------AGGUCUCUAAUACUGCCUGGUAAUGAUGA-CGGCGGA
AACT01021688.1/8974-9043   GUCGGUC-GCAUCUUCAUCACGCGGUGUUCU----AGAACU----CAUUCU--AACACUGUCUGGUAAAGAUGC-GAUCGGC
AABS01001272.1/8701-8771   CCCUGGU-GUAUCUUGGUCAUAUAGUGUUGU----AGAUUC---AUGAUCU--AACACUGUCUGGUAAAGAUGC-AUUCGAC
AACT01017089.1/11024-10956 CACUGAA-GCAUC-A-ACCCGGUAGUACGAUAUGUG---------AACUGUAUAAUACUGCCUGGUAAUGAUGA-UUCAGUG
AABS01001272.1/8339-8408   AACCGAA-UCACC-A-ACCACGUAGUAUCGGAGCAU----U----GUGUGUCUAAUACUGCCUGGUAAUGGUGA-UUGGGUG
#=GC SS_cons               :::::<<-<<<<<<<.<<---<<<<<<<<<<__________....______>>>>>>>>>>--->>>>->>>>>.>>:::::
#=GC RF                    auCuGcgucCAUCUU.ACCgggCAGUgUUgGAUuguuuauu....aagUcUCuAAcACUGcCUGGUAAuGAUGg.cgccGgu
//
# STOCKHOLM 1.0

#=GF AC   RF00242
#=GF ID   ctRNA_pT181
#=GF DE   ctRNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   PMID:2478296
#=GF SS   Published; PMID:2478296
#=GF GA   56.00
#=GF TC   58.90
#=GF NC   52.30
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0060908; plasmid copy number maintenance;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   2478296
#=GF RT   pT181 plasmid replication is regulated by a countertranscript-driven
#=GF RT   transcriptional attenuator.
#=GF RA   Novick RP, Iordanescu S, Projan SJ, Kornblum J, Edelman I
#=GF RL   Cell 1989;59:395-404.
#=GF CC   Rolling circle replication plasmids contain a number of mechanisms to
#=GF CC   maintain a low copy number. One of these methods is to transcribe a small
#=GF CC   RNA called ctRNA (for counter-transcribed RNA) than is transcribed on the
#=GF CC   opposite strand to RepB the replication initiation protein. ctRNA binds to
#=GF CC   the mRNA of repB and causes translational inhibition.
#=GF WK   ctRNA
#=GF SQ   16


AE015931.1/1673-1576   AUACAAAAA----CAUAAAAACAUC-----GACUGUUUUAUAUUUUGG---CUAGUCGU--UCACGUAAACUUUGGUCGGUUUGGGGUGG-ACGACUUCUU--UUUUAUUUUGCU
AE016832.1/3301-3217   AUACAAU-------UAAGAAACAAAC----AUCGACUGUU--UAUU---------UUGC--UCAC--AAACUUUGGUCGG---GGAGUGA-GCGACUUCUUAUUUUUAUUUUGUU
X07371.1/1034-1130     AUACAAAUUA-AGAACAAAAACAUC-----AACUGUUUUU--CUUUAAG-GUAAGUCGCUAUCAC--AAACUUUGGCGAG---GGAGUGA-GCGACUUCUU---UUUACUUUGUU
X02529.1/1113-1011     AUACAAAAA---UUAAUAAAACAUAACUCUUUAUAUUUUA---UUUAGG--AUUGUCGU--UCACGAAAACUUUGGUCGGUUUGGGGUGA-ACGACUUCUU-UUUUUAUUUGUGU
X02166.1/1113-1011     AUACAAAAA---UUAAUAAAACAUAACUCUUUAUAUUUUA---UUUAGG--AUUGUCGU--UCACGAAAACUUUGGUCGGUUUGGGGUGA-ACGACUUCUU-UUUUUAUUUGUGU
J03323.1/109-11        AUACAAAAA---UUAAUAAAACAUAACUCUUUAUAUUUUA---UUUAGG--UAAGUCGCAUUCAC-AAAACUUUGGUAGG---GGCGUGA-GCGACUUCUU---UUUAUUUGUUU
X06627.1/3281-3182     AUACAAAAAUUAAGAAAAAAACACC-----AACUGUUUUU-CUUUAAGG--UAAGUCGCAUUCAC--AAACUUUGGUCAG---GGAGUGA-GCGACUUCUU-UUUUUGUUUUUUU
U74623.1/124-27        AUACAAAAU---AUAAAAAAACAA----CUUAGUGUUUUU--UCUUUGG-GUAAGUCGCAUUCAC--AAACUUUGGUCAG---GGCGUGA-GCGACUUCUU-UUUUUAUUUUGUU
AE015930.1/3274-3180   AUACAAGAU----UAUAAAAACAA----CUCAGUGUUUUU-UUCUUUGAAUGAUGUCGU--UCAC--AAACUUUGGUCAA---GGCGUGA-GCGACUCCUU---UUUAUUUUGUU
U38428.1/3559-3465     AUACAAGAU----UAUAAAAACAA----CUCAGUGUUUUU-UUCUUUGAAUGAUGUCGU--UCAC--AAACUUUGGUCAA---GGCGUGA-GCGACUCCUU---UUUAUUUUGUU
U38656.1/3674-3580     AUACAAGAU----UAUAAAAACAA----CUCAGUGUUUUU-UUCUUUGAAUGAUGUCGU--UCAC--AAACUUUGGUCAA---GGCGUGA-GCGACUCCUU---UUUAUUUUGUU
AB037671.1/30845-30939 AUACAAGAU----UAUAAAAACAA----CUCAGUGUUUUU-UUCUUUGAAUGAUGUCGU--UCAC--AAACUUUGGUCAG---GGCGUGA-GCGACUCCUU---UUUAUUUUGUU
M26321.1/106-200       AUACAAGAU----UAUAAAAACAA----CUCAGUGUUUUU-UUCUUUGAAUGAUGUCGU--UCAC--AAACUUUGGUCAG---GGCGUGA-GCGACUCCUU---UUUAUUUUGUU
U36910.1/5169-5075     AUACAAGAU----UAUAAAAACAA----CUCAGUGUUUUU-UUCUUUGAAUGAUGUCGU--UCAC--AAACUUUGGUCAG---GGCGUGA-GCGACUCCUU---UUUAUUUUGUU
U35036.1/3779-3686     AUACAAGAU---AUAAAAAAACAA----CUUAGUGUUUUU--UCUAGGUAA---GUCGCUAUCAC--AAACUUUGGCGAG---GGAGUGA-GCGACUUCUU---UUUAUUUUGUU
U38429.1/4117-4026     AUACAAAAA----UUAAAAAACACAU---GACACAUCUUUUCUUUAGG---UAAGUCGU--UUAC--AAACUUUGGCGA----GGAGUAACACG--UUCUU---UUUAUUUGUUU
#=GC SS_cons           ::::<<<<-....---<<<<<<<__..._____>>>>>>>.->>>>---..---<<<<<..<<<<.._____________...___>>>>.>>>>>:::::...:::::::::::
#=GC RF                AUACaAgau....uAaaaAaacaaa...CuuaauguuUuu.uucUuaGg..uaaGUCGc..uCAC..AAACUUUGGUcaG...GGaGUGa.gCGACUUCUU...UUUAUUUuguU
//
# STOCKHOLM 1.0

#=GF AC   RF00243
#=GF ID   traJ_5
#=GF DE   traJ 5' UTR
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   PMID:14633993
#=GF SS   Predicted; ILM
#=GF GA   50.00
#=GF TC   51.40
#=GF NC   47.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF CL   CL00016
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0003676; nucleic acid binding;
#=GF RN   [1]
#=GF RM   14633993
#=GF RT   FinO is an RNA chaperone that facilitates sense-antisense RNA
#=GF RT   interactions.
#=GF RA   Arthur DC, Ghetu AF, Gubbins MJ, Edwards RA, Frost LS, Glover JN
#=GF RL   EMBO J 2003;22:6346-6355.
#=GF CC   The FinOP system regulates the transfer of F-like plasmids. FinP
#=GF CC   Rfam:RF00107 encodes an antisense RNA product that is complementary to
#=GF CC   part of the 5' UTR of the traJ mRNA. The traJ gene encodes a protein
#=GF CC   required for transcription from the major transfer promoter, pY. The FinO
#=GF CC   protein is essential for effective repression, acting by binding to FinP
#=GF CC   and protecting it from RNase E degradation.
#=GF WK   traJ_5'_UTR
#=GF SQ   6


AE006471.1/61487-61592 UUGUAGUUAACGCUACGUUAAAAAAACAA-GUUAAA-UCGCCGAUACAGGGAGCUG-UCACUCCCUGCAUCGACUGUCCAUAGAAUCCUUUG--AGGAGGUUCCUAUGUGU
AF389529.1/1005-1112   UUGUAGUUAACACUACGUUAAAAAAUGAACGUUAAA-UCGCCGAUGCAGGGAGUUGGUCCCUCCCUGCAUCGACUACCCAUAGAAUCCUUUG--AGGAGGCUCCUGUGUAU
AF550679.1/2929-3039   ACGUGGUUAAUGCCACGUUAAAAUUUGAAAUUGAAAAUCGCCGAUGCAGGGAGACGUGAACUCCCUGCAUCGACUGUCCAUAGAAUCCUUUGUGAGGAGGUUCCUAUGUAU
M20941.1/109-216       AUGUGGU-AAUGCCACGUUAAAACA-GAUAUUAAAAAUCGCCGAUGCAGGGAGA-GCGACCUCCCCGCAUCGACUGUCCAUAGAAUCCUUUGAGAGGAGGUUCCUAUGUAU
AF237697.1/390-500     ACGUGGUUAAUGCCACGUUAAAAUUUGAAUUUGAAAAUCGCCGAUGCAGGGAGUUCUCUCCUCCCUGCAUCGACUGUCCAUAGAAUCCUUUGUGAGGAGGUUCCUAUGUAU
X55896.1/933-1040      ACGUGGUUAAUGCCACGUUAAAAUGUGAACUUGAAAAUCGCCGAUGCAGGGAGCUUGUCCCUCCCUGCAUCGACUGUC-AUAGAAUCCUUUG--AGGAGGUUCCUAUGUGU
#=GC SS_cons           :<<<<<<____>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<<<<<___>>>>>>>>>>>>>>--<<<---<<<<____>>>>..----------->>>:::
#=GC RF                acGugGcUAAugCcaCgUUAAAAuaugAAauUuAAAAUCGCCGauGCaGGGaGccguuggCuCCCuGCauCGACuguCCAuagaAUCCuuug..AGGAGGUUCCUaugUaU
//
# STOCKHOLM 1.0

#=GF AC   RF00244
#=GF ID   mir-26
#=GF DE   mir-26 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   39.00
#=GF TC   39.00
#=GF NC   38.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000083;
#=GF DR   MIR; MI0000084;
#=GF DR   MIR; MI0000573;
#=GF DR   MIR; MI0000575;
#=GF DR   MIR; MI0000706;
#=GF DR   MIR; MI0000750;
#=GF DR   MIPF; MIPF0000043;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science 2001;294:853-858.
#=GF RN   [2]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol 2002;12:735-739.
#=GF CC   miR-26 is processed from multiple predicted precursor hairpins in both
#=GF CC   mouse (MIR:MI0000573, MIR:MI0000575, MIR:MI0000706) and human
#=GF CC   (MIR:MI0000083, MIR:MI0000084, and MIR:MI0000750) [1,2]. miR-26 appears to
#=GF CC   be a vertebrate specific miRNA and has now been predicted or
#=GF CC   experimentally validated in many vertebrate species (MIPF:MIPF0000043).
#=GF CC   The hairpin precursors (represented here) are predicted based on base
#=GF CC   pairing and cross-species conservation -- their extents are not known. In
#=GF CC   this case the mature sequence is excised from the 5' arm of the hairpin.
#=GF WK   mir-26_microRNA_precursor_family
#=GF SQ   5


AC121759.9/5238-5311     UGGCUGGAUUCAAGUAAUCCAGGAUAGGCUGUU-UCCAUCUGUGAGGCCUAUUCUUGAUUACUUGUUUCU-GGAGG
AC055818.9/198196-198123 UGGCCUCGUUCAAGUAAUCCAGGAUAGGCUGUGCAGGUCCCAAGGGGCCUAUUCUUGGUUACUUG-CACG-GGGAC
AC099740.2/37721-37649   CAACCGGGUUCAAGUAAUCCAGGAUAGGCUCUGUAUCUGUCUU--GGCCUAUGCUUGAUUACUUG-CUCUUGGAGG
AF229163.1/26516-26586   GGACCCAGUUCAAGUAAUUCAGGAUAGGUUGUG-UGCUGUCCA---GCCUGUUCUCCAUUACUUGGCUCG-GGGAC
AP000497.1/44360-44431   UGGCCUCGUUCAAGUAAUCCAGGAUAGGCUGUGCAGGUCCCAAUG-GCCUAU-CUUGGUUACUUG-CACG-GGGAC
#=GC SS_cons             ::::::::::<<<<<<<<<-<<<<<<<<<_________________>>>>>>>>>->>>>>>>>>.::::.:::::
#=GC RF                  uGgCCugGUUCAAGUAAucCAGgAuAGGCUGUGcagcUucCaaggGGCCUaUuCUUgaUUACUUG.CuCg.GGgac
//
# STOCKHOLM 1.0

#=GF AC   RF00245
#=GF ID   mir-19
#=GF DE   mir-19 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   52.10
#=GF NC   49.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00110
#=GF DR   MIR; MI0000073;
#=GF DR   MIR; MI0000074;
#=GF DR   MIR; MI0000075;
#=GF DR   MIR; MI0000546;
#=GF DR   MIR; MI0000688;
#=GF DR   MIR; MI0000718;
#=GF DR   MIPF; MIPF0000011;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science 2001;294:853-858.
#=GF RN   [2]
#=GF RM   11914277
#=GF RT   miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.
#=GF RA   Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L,
#=GF RA   Rappsilber J, Mann M, Dreyfuss G
#=GF RL   Genes Dev 2002;16:720-728.
#=GF RN   [3]
#=GF RM   12919684
#=GF RT   Embryonic stem cell-specific MicroRNAs.
#=GF RA   Houbaviy HB, Murray MF, Sharp PA
#=GF RL   Dev Cell 2003;5:351-358.
#=GF CC   miR-19 is processed from multiple predicted precursor hairpins in both
#=GF CC   mouse (MIR:MI0000546, MIR:MI0000688, MIR:MI0000718) and human
#=GF CC   (MIR:MI0000073, MIR:MI0000074, and MIR:MI000075) [1,2,3]. miR-19 has now
#=GF CC   been predicted or experimentally confirmed in a wide range of vertebrate
#=GF CC   species (MIPF:MIPF0000011). The hairpin precursors (represented here) are
#=GF CC   predicted based on base pairing and cross-species conservation -- their
#=GF CC   extents are not known. In this case the mature sequence is excised from
#=GF CC   the 3' arm of the hairpin.
#=GF WK   mir-19_microRNA_precursor_family
#=GF SQ   46


AF480555.1/4-78                UAUGGUUAGUUUUGCAGGUUUGCA-UCCAGC-------UGUGUG-AUAUUCUGCUGUGCAAAUCCAUGCAAAACUGACUGUGGU
AF480556.1/2-81                UACAAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUGUAUAUGUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AF480554.1/6-77                CUCUGUUAGUUUUGCAUAGUUGCACUACAAG----------AAG--AAUGUAGUUGUGCAAAUCUAUGCAAAACUGAUGGUGGC
AAFR03020267.1/47295-47221     UAUGGUUAGUUUUGCAGGUUUGCA-UCCAGC-------UGUAUG-AUAUUCUGCUGUGCAAAUCCAUGCAAAACUGACUGUGGU
AY866364.1/1068-1147           UACAAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUGUAUAUGUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AY866317.1/799-873             UAUGGUUAGUUUUGCAGGUUUGCA-UCCAGC-------UGUGUG-AUAUUCUGCUGUGCAAAUCCAUGCAAAACUGACUGUGGU
AAHX01085677.1/2212-2286       UAUGGUUAGUUUUGCAGGUUUGCA-UCCAGC-------UGUAUA-AUAUUCUGCUGUGCAAAUCCAUGCAAAACUGACUGUGGU
AY866360.1/1064-1143           UACAAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUACAUGUAUAUAUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AY866310.1/774-848             UAUGGUUAGUUUUGCAGGUUUGCA-UCCAGC-------UGUGUA-AUAUUCUGCUGUGCAAAUCCAUGCAAAACUGACUGUGGU
AAYZ01184872.1/1043-1117       UAUGGUUAGUUUUGCAGGUUUGCA-UCCAGC-------UGUGUG-AUAGUCUGCUGUGCAAAUCCAUGCAAAACUGACUGUGGU
AY866366.1/713-792             UACAGUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUACAUGUAUAUAUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AAPN01226808.1/924-995         CUCUGUUAGUUUUGCAUAGUUGCACUACAAG----------AAG--AAUGUAGUUGUGCAAAUCUAUGCAAAACUGACGGUGGC
AAPY01386199.1/1137-1058       UACAGUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUGUGUAUAUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AAQQ01373887.1/2650-2573       UACGAUUAGUUUUGCAGGUUUGCAUUUCAGC------AUAUAUGUAUACAUAGCUGUGCAAAUCCAUGCAAAACUGACCGUGAU
ABDC01275774.1/2263-2184       CACGAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUGUAUAUAGGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AAFC03125572.1/1362-1437       UACAGUUAGUUUUGCUGGUUUGCAUUUCAGC-------GUGUGG-AUAUAUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AAHY01210291.1/5583-5504       UACGAUUAGUUUUGCAGAUUUGCAGUUCAGCG----UAUAUGUGAAUAUAUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGGG
AANG01459906.1/2349-2270       UACGGUUAGUUUUGCAGGUUUGCAUUUCAGCG----GAUAUAUGUAUGUAUAGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AY875971.1/257-328             CUCUGUUAGUUUUGCAUAGUUGCACUACAAG----------AAG--AAUGUAGUUGUGCAAAUCUAUGCAAAACUGAUGGUGGC
AY866318.1/761-832             CUCUGUUAGUUUUGCAUAGUUGCACUACAGG----------AAG--AAUGUAGUUGUGCAAAUCUAUGCAAAACUGAUGGUGGC
AALT01065661.1/586-507         CCCAGUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAAAUCUACAGGGCUGUGCAAAUCCAUGCAAAACUGACUGUGAU
AAIY01238597.1/3252-3175       UACGGUGAGUUUUGCAGGUUUGCAUUUCAGC------AUGUAUGUAUCUAUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAG
CAAE01014781.1/2073487-2073558 CUCUGUCAGUUUUGCAUGGUUGCGCUGCAAG----------AAG--AAAUAAGUUGUGCAAAUCUAUGCAAAACUGACAGCGGU
BAAF04019480.1/13763-13692     CUCUGUUAGUUUUGCAUAGUUGCACUGCAAG----------AAG-AGAUGCG-UUGUGCAAAUCUAUGCAAAGCUGAUAGUGGC
AANH01005312.1/95619-95548     CUCCGUUAGUUUUGCAUAGUUGCGCUCCAAG----------AAG-AAAUGCG-UUGUGCAAAUCUAUGCAAAGCUAACGGUGGC
AADA01312424.1/2142-2221       AGGAAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUAAAGGGGUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
CAAK05051440.1/16032-15961     CUCUGCUAGUUUUGCAUAGUUGCACUACAAG-----------AA-AUAUUGAGUUGUGCAAAUCUAUGCAAAACUGAUGGUGGC
AAKN02053349.1/40109-40028     UACAAUUAGUUUUGCAGGUUUGCAUUUCAGCGUAUAGAUAUAUC--UACAUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AAWR02034046.1/17116-17037     UACGAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUGUAUAUAUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AAEX03026925.1/968921-968842   UCCGGUUAGUUUUGCAGGUUUGCAUUUCAGCG----UACUUGUGCAUAUAGGGCUGUGCAAAUCCAUGCAAAACUGACCGUGAU
AAGW02046787.1/21646-21567     CACAAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUACCUGUAUACAUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
CAAB02000121.1/15413-15484     CUCUGCUAGUUUUGCAUAGUUGCACUACAAG-------AAUAGA-----GGAGUUGUGCAAAUCUAUGCAAAACUGAUGGUGGC
AAWZ02030636.1/2841-2915       UCUGGUUAGUUUUGCAGGUUUGCA-UCCAGC-------UGUAUA-AUGUGUUGCUGUGCAAAUCCAUGCAAAACUGACUGUGGC
AAGU03084137.1/1014-941        UACAGUUAGUUUUGCAGGUUUGCAUUGCAGU--------AUAUG--UAUAUGGCUGUGCAAAUCCAUGCAAAACUGACGGUGAU
CR390304.1/227-301             UCUGGUUAGUUUUGCAGGUUUGCA-UCCAGC-------UGUAUG-AUACUCUGCUGUGCAAAUCCAUGCAAAACUGACUGUGGC
AAQR03131415.1/5488-5410       CACGAUUAGUUUUGCAGGUUUGCAUUUCAGCG-----UAUUGUGUAUAUCAGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AY866368.1/1071-1150           UACAAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUGUAUAUGUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AY866363.1/1070-1149           UACAAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUGUAUAUGUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AY866361.1/1037-1116           UACAAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUGUAUAUGUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AY866362.1/494-567             CACGAUUAGUUUUGCAGGUUUGCAUUUCAGC------G----UAUACAUAAGGCUGUGCAAAUCCAUGCAAAACUGAUCGUGAU
AY866311.1/1045-1119           UAUGGUUAGUUUUGCAGGUUUGCA-UCCAGC-------UGUGUG-AUAUUCUGCUGUGCAAAUCCAUGCAAAACUGACUGUGGU
AY866311.1/740-811             CUCUGUUAGUUUUGCAUAGUUGCACUACAAG----------AAG--CAUGUAGUUGUGCAAAUCUAUGCAAAACUGAUGGUGGC
AY866316.1/1028-1102           UAUGGUUAGUUUUGCAGGUUUGCA-UCCAGC-------UGUGUG-AUAUUCUGCUGUGCAAAUCCAUGCAAAACUGACUGUGGU
AY866316.1/722-793             CUCUGUUAGUUUUGCAUAGUUGCACUACAAG----------AAG--AAUGUAGUUGUGCAAAUCUAUGCAAAACUGAUGGUGGC
AY866365.1/1025-1104           UACAAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUGUAUAUGUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
AY866359.1/1067-1146           UACAAUUAGUUUUGCAGGUUUGCAUUUCAGCG----UAUAUAUGUAUAUGUGGCUGUGCAAAUCCAUGCAAAACUGAUUGUGAU
#=GC SS_cons                   ::<<<<<<<<<<<<<<---<<<<<---<<<_.......______.________>>>>>>>>----->>>>>>>>>>>>>>::::
#=GC RF                        uacggUuAGUUUUGCAgGuUUGCAuUuCAGc.......UaUAug.AuAUaugGCUGUGCAAAUCcAUGCAAAACUgAccgUGau
//
# STOCKHOLM 1.0

#=GF AC   RF00246
#=GF ID   mir-135
#=GF DE   mir-135 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   47.00
#=GF TC   49.60
#=GF NC   46.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000161;
#=GF DR   MIR; MI0000452;
#=GF DR   MIR; MI0000453;
#=GF DR   MIR; MI0000645;
#=GF DR   MIR; MI0000646;
#=GF DR   MIR; MI0000715;
#=GF DR   MIPF; MIPF0000028;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol 2002;12:735-739.
#=GF RN   [2]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A 2004;101:360-365.
#=GF CC   miR-135 has been shown to be expressed in human (MIR:MI0000452,
#=GF CC   MIR:MI0000453), mouse (MIR:MI0000161, MIR:MI0000646, MIR:MI0000715) and
#=GF CC   rat (MIR:MI0000645) [1,2]. miR-135 has now been predicted or
#=GF CC   experimentally confirmed in a wide range of vertebrate species
#=GF CC   (MIPF:MIPF0000028). The hairpin precursors (represented here) are
#=GF CC   predicted based on base pairing and cross-species conservation -- their
#=GF CC   extents are not known. In this case the mature sequence is excised from
#=GF CC   the 5' arm of the hairpin.
#=GF WK   mir-135_microRNA_precursor_family
#=GF SQ   32


BC025935.1/2921-2832           AGGCCUCACUGUUCUCUAUGGCUUUUUAUUCCUAUGUGAUU--CUAUUGCUCGCUCAUAUAGGGAUUGGAGCCGUGGCGUACGGUGAGGAUA
AC018659.35/133427-133338      AUUCACUCUAGUGCUUUAUGGCUUUUUAUUCCUAUGUGAUA--GUAAUAAAGUCUCAUGUAGGGAUGGAAGCCAUGAAAUACAUUGUGAAAA
AC094021.2/73294-73205         AGGCCUCGCUGUUCUCUAUGGCUUUUUAUUCCUAUGUGAUU--CUACUGCUCACUCAUAUAGGGAUUGGAGCCGUGGCGCACGGCGGGGACA
AC098936.2/102185-102095       CCACUCUGCUGUGGCCUAUGGCUUUUCAUUCCUAUGUGAUUG-CUGUCCCAAACUCAUGUAGGGCUAAAAGCCAUGGGCUACAGUGAGGGGC
AC125204.4/96061-95972         AUUCACUCUAGUGCUUUAUGGCUUUUUAUUCCUAUGUGAUC--GUAAUAAAGUCUCAUGUAGGGAUGGAAGCCAUGAAAUACAUUGUGAAAA
AY865879.1/478-567             AUUCACUCUAGUGCUUUAUGGCUUUUUAUUCCUAUGUGAUA--GUAAUAAAGUCUCAUGUAGGGAUGGAAGCCAUGAAAUACAUUGUGAAAA
AY865876.1/338-427             AGGCCUCGCUGUUCUCUAUGGCUUUUUAUUCCUAUGUGAUU--CUACUGCUCACUCAUAUAGGGAUUGGAGCCGUGGCGCACGGCGGGGACA
AY865877.1/420-509             AGGCCUCGCUGUUCUCUAUGGCUUUUUAUUCCUAUGUGAUU--CUACUGCUCACUCAUAUAGGGAUUGGAGCCGUGGCGCACGGCGGGGACG
AY865882.1/491-580             AUUCACUCUAGUGCUUUAUGGCUUUUUAUUCCUAUGUGAUA--GUAAUAAAGUCUCAUGUAGGGAUGGAAGCCAUGCACCACAUAAUGUAAA
BX855597.6/51414-51323         AAACACUACUGUGCUUUAUGGCUUUCUAUUCCUAUGUGAUUUUGAUAUGAUGUAUCAUGUAGGGUUCAAAGCCAUUAGGUACAGAGUGGCUU
AY865878.1/475-564             AUUCACUCUAGUGCUUUAUGGCUUUUUAUUCCUAUGUGAUA--GUAAUAAAGUCUCAUGUAGGGAUGGAAGCCAUGAAAUACAUUGUGAAAA
AY865880.1/464-553             AUUCACUCUAGUGCUUUAUGGCUUUUUAUUCCUAUGUGAUA--GUAAUAAAGUCUCAUGUAGGGAUGGAAGCCAUGAAAUACAUUGUGAAAA
AY865881.1/510-599             AUUCACUCUAGUGCUUUAUGGCUUUUUAUUCCUAUGUGAUA--GUAAUAAAGUCUCAUGUAGGGAUGGAAGCCAUGAAAUACAUUGUGAAAA
AAPN01269426.1/3344-3254       GCUCUCUGCUGUGGCCUAUGGCUUUUUAUUCCUAUGUGAUUG-CUGCUUUGAACUCAUGUAGGGCUGAAAGCCAUGGGCUACAGAGAGGGGA
AAFR03023061.1/3870-3780       GCUCUCUGCUGUGGCCUAUGGCUUUUCAUUCCUAUGUGAUUG-CUGUUCCCAACUCAUGUAGGGCUAAAAGCCAUGGGCUACAGGGAGGGGA
AAVX01101128.1/378-289         ACUCGCUCCUGUGCUUUAUGGCUUUUUAUUCCUAUGUGAUU--GUGACAUGAUCUCAUGUAGGGAGAGAAGCCAUGAAAUACACAGUGAGAA
AAIY01255743.1/1211-1301       CGGCUCCGCUGCGGCCUAUGGCUUUUCAUUCCUAUGUGAUUG-AUGUUCCAAACUCAUGUAGGGCUAAAAGCCAUGGGCUACAGUGAGGGGC
AAPY01288096.1/117-27          CAGCUCUGCUGUGGCCUAUGGCUUUUCAUUCCUAUGUGAUUG-CUGUUCCAAACUCAUGUAGGGCUAAAAGCCAUGGGCUACAGUGACCCAA
AANH01002554.1/13894-13804     AGCCACAUUUGUGUCUUAUGGCUUUCUAUUCCUAUGUGAGUU-GGUUUGGCAUGUCAUGUAGGGUCUAAAGCCAUUAGAUACUCAGUGGACA
AANG01260705.1/5894-5806       AGGCCUCGCUGUUCUCUAUGGCUUU-UAUUCCUAUGUGAUU--CUACUGCUCACUCAUAUAGGGAUUGGAGCCGUGGCGCACGGGCGGGGGC
CAAE01014729.1/2152458-2152549 AACCACGAUUGUGUCUUAUGGCUUUCUAUUCCUAUGUGAGUUAUUUACAGCAGGUCAUGUAGGGUUUAAAGCCAUUGGACACGCGGUGGGCA
BAAF04047621.1/18500-18411     GUGCACCAUUGUGUAUUAUGGCUUUUUAUUCCUAUGUGAUG--GUGAAAAAUGUUCAUGUAGGAACAGAAGCCAUUUUACACGUGGCGAUAC
AAGV020089264.1/878-968        AUUCACUCUAGUGCUUUAUGGCUUUUUAUUCCUAUGUGAUAG-UAAUAAAAGUCUCAUGUAGGGAUGGAAGCCAUGAAAUACAUUGUGAAAA
AAPE02029537.1/1917-1828       CAGCUCUGCUGUGGCCUAUGGCUUUUCAUUCCUAUGUGAUU--GCCGUUGGAACUCAUGUAGGGCUAAAAGCCAUGGGCUACAGUGAGGGGC
CAAB02007023.1/26915-27005     ACUCGCUGCUGUGUUUUAUGGCUUUCUAUUCCUAUGUGAUUU-UCUCUAGCAUGUCACAUAGGGUCUAAAGCCAUUGGGUACAGAGUGGGAG
AAGW02025372.1/952-862         CAGCUCUGCUGUGGCCUAUGGCUUUUCAUUCCUAUGUGAUUG-CUCCUCCAAACUCAUGUAGGGCUAAAAGCCAUGGGCUACAGUGAGGGGC
AAGU03032128.1/66433-66343     CAUCUCUGCUGCGGCCUAUGGCUUUUCAUUCCUAUGUGAUUG-CUGUUCCCAACUCAUGUAGGGCUAAAAGCCAUGGGCUACAGUGAGGGGC
AAWZ02020739.1/53045-52955     GCCCUCUGCUGUGGUCUAUGGCUUUUUAUUCCUAUGUGAUUG-CUUUUCAUAACUCAUGUAGGGCUAAAAGCCAUGGGCUACACAGAGGAAU
AAEX03018256.1/46864-46774     CAGCUCUGCUGUGGCCUAUGGCUUUUCAUUCCUAUGUGAUUG-CUGUUUCUAAUUCAUGUAGGGCUAAAAGCCAUGGGCUACAGUGAGGGGC
ADDD01008157.1/1751-1661       GCCCUCUGCUGUGGUCUAUGGCUUUUUAUUCCUAUGUGAUUG-CUUUUCCUAACUCAUGUAGGGCGAAAAGCCAUGGGCUACUCAGGGGAGG
AB513653.1/330-419             AUUCACUGUGGUGUUUUAUGGCUUUUUAUUCCUAUGUGAUA--GUAAUAAUGUCUCAUGUAGGGAUGGAAGCCAUGAAAUACAUUGUGAAAA
AB513654.1/278-367             AUUCACUGUGGUGUUUUAUGGCUUUUUAUUCCUAUGUGAUA--GUAAUAAUGUCUCAUGUAGGGAUGGAAGCCAUGAAAUACAUUGUGAAAA
#=GC SS_cons                   :::<<<----<<<<<<<<<<<<<<<----<<<<<<<<<<__..___________>>>>>>>>>>--->>>>>>>>>>>>>>>--->>>::::
#=GC RF                        auuCccugcuGUgcccuAuGGCUuuUUAUuCCUAugUGAUu..gUaaUaauaacUCAugUAGGgaUaaaAGCCaUggggcACauuggGgaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00247
#=GF ID   mir-160
#=GF DE   mir-160 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   48.00
#=GF TC   48.00
#=GF NC   47.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000032;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12202040
#=GF RT   Prediction of plant microRNA targets.
#=GF RA   Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP
#=GF RL   Cell 2002;110:513-520.
#=GF CC   miR-160 has been predicted or experimentally confirmed in a range of plant
#=GF CC   species including Arabidopsis and rice (MIPF:MIPF0000032). miR-160 is
#=GF CC   predicted to bind complementary sites in the untranslated regions of auxin
#=GF CC   response factor genes to regulate their expression [1].The hairpin
#=GF CC   precursors (represented here) are predicted based on base pairing and
#=GF CC   cross-species conservation -- their extents are not known. In this case
#=GF CC   the mature sequence is excised from the 5' arm of the hairpin.
#=GF WK   mir-160_microRNA_precursor_family
#=GF SQ   7


AL161547.2/49332-49418    UCGUGCCUGGCUCCCUGUAUGCCACAAGAAAACAUCGAUUUAGUUUC--------------------------------------------------AAAAUCGAUCACUAGUGGCGUACAGAGUAGUCAAGCAUGA
AC004697.3/97809-97725    GUAUGCCUGGCUCCCUGUAUGCCAUAUGCUGAGCCCAUCGAGUAUCGAUGA---------------------------------------------------CCUCCGUGGAUGGCGUAUG-AGGAGCCAUGCAUAU
AC084320.10/152194-152329 AUAUGCCUGGCUCCCUGUAUGCCACUCGCGUAGCUGCCAAACUCAGUUGAAACAACUGCCUUCUCCCGGCGAGAUUCAGGCAUUGUGUUCGUACGUUUGGCUCUACUGCGGAUGGCGUGCG-AGGAGCCAAGCAUGA
AP004591.3/100727-100819  AUGUGCCUGGCUCCCUGUAUGCCACUCAUCUAGAGCAACAAACUUCUGCGAGAG-------------------------------------------GUUGCCUAUGAUGGAUGGCGUGCA-CGGAGCCAAGCAUAU
AB022221.1/11161-11075    UUAUGCCUGGCUCCCUGUAUGCCACGAGUGGAUACCGAUUUUGGUUUU-------------------------------------------------AAAAUCGGCUGCCGGUGGCGUACA-AGGAGUCAAGCAUGA
AK101881.1/424-511        GUGUGCCUGGCUCCCUGUAUGCCACACAUGUAGACCAACCCAUGGUGUCUG----------------------------------------------GUUGCCUACUG--GGUGGCGUGCA-AGGAGCCAAGCAUGC
AK071620.1/251-338        GCGUGCCUGGCUCCCUGUAUGCCACUCAUGUAGCCCAAUCCAUGGUGUGUU------------------------------------------------UGGAUGCUGUGGGUGGCGUGCA-AGGAGCCAAGCAUGC
#=GC SS_cons              <<<<<<-<<<<<<<-<<<<<<<<<--<<<______________________..............................................__________>>>-->>>>>>>>>.->>>>>>>->>>>>>
#=GC RF                   gcaUGCCUGGCUCCCuGuAUGCCACucgcguAgaucaauaaauuuuuugaa..............................................uauauCuaCugcgGaUGGCGUgCa.AGGAGCCAAGCAugc
//
# STOCKHOLM 1.0

#=GF AC   RF00248
#=GF ID   mir-148
#=GF DE   mir-148/mir-152 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   49.00
#=GF TC   49.60
#=GF NC   48.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000174;
#=GF DR   MIR; MI0000253;
#=GF DR   MIR; MI0000462;
#=GF DR   MIR; MI0000550;
#=GF DR   MIR; MI0000616;
#=GF DR   MIR; MI0000617;
#=GF DR   MIR; MI0002015;
#=GF DR   MIR; MI0001189;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol 2002;12:735-739.
#=GF RN   [2]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A 2004;101:360-365.
#=GF RN   [3]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF CC   The expression of miR-148 has been demonstrated in human (MIR:MI0000253),
#=GF CC   mouse (MIR:MI0000550), rat (MIR:MI0000616) and zebrafish (MIR:MI0002015)
#=GF CC   [1,2,3]. miR-148 has also been predicted in chicken (MIR:MI0001189). These
#=GF CC   predicted hairpin precursor sequence are related to those of mir-152,
#=GF CC   which has been expressed in mouse (MIR:MI0000174) and is predicted in
#=GF CC   human (MIR:MI0000462) [1]. The hairpin precursors (represented here) are
#=GF CC   predicted based on base pairing and cross-species conservation -- their
#=GF CC   extents are not known. In this case the mature sequence is excised from
#=GF CC   the 3' arm of the hairpin.
#=GF WK   Mir-148/mir-152_microRNA_precursor_family
#=GF SQ   5


AL596384.17/69144-69229 UGUUCCCCG-GGCCUAGGUUCUGUGAUACACUCCGACUCGGGCUCUG-GAGCAGUCAGUGCAUGACAGAACUUGGGCCCGGUAGGACC
AC004477.2/81383-81297  UGUCCCCCCCGGCCCAGGUUCUGUGAUACACUCCGACUCGGGCUCUG-GAGCAGUCAGUGCAUGACAGAACUUGGGCCCGGAAGGACC
AC078778.34/32602-32516 UUAGCAUUUGAGGUGAAGUUCUGUUAUACACUCAGGCUGUGGCUCUCUGA-AAGUCAGUGCAUCACAGAACUUUGUCUCGAAAGCUUU
AC010719.4/30463-30378  UGGUCUUUUGAGGCAAAGUUCUG--AGACACUCCGACUCUGAGUAUGAUAGAAGUCAGUGCACUACAGAACUUUGUCUCUAGAGGCUG
AL953901.15/62198-62283 UGUUCACCU-GGCUCAAGUUCUGUGAUACACUCAGACUUUGAAUCAG-UGGUAGUCAGUGCAUGACAGAACUUUGGCCCGGACGGACC
#=GC SS_cons            :<<<<-----<<<<<<<<<<<<<<----<<<<--<<<<_________.____>>>>>>>>---->>>>>>>>>>>>>>----->>>>:
#=GC RF                 UggcCauuuggGcccAaGUUCUGugAuACACUCaGaCUcuGgcUcUg.gAGaAGuCAGUGCAUgaCAGAACuUgggCcCggaAGgccc
//
# STOCKHOLM 1.0

#=GF AC   RF00249
#=GF ID   mir-46
#=GF DE   mir-46/mir-47/mir-281 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   54.50
#=GF NC   48.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.88 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000017;
#=GF DR   MIR; MI0000018;
#=GF DR   MIR; MI0000366;
#=GF DR   MIR; MI0000370;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science 2001;294:858-862.
#=GF RN   [2]
#=GF RM   12844358
#=GF RT   Computational identification of Drosophila microRNA genes.
#=GF RA   Lai EC, Tomancak P, Williams RW, Rubin GM
#=GF RL   Genome Biol 2003;4:R42.
#=GF RN   [3]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell 2003;5:337-350.
#=GF CC   miR-46 (MIR:MI0000017) and miR-47 (MIR:MI0000018) are expressed in C.
#=GF CC   elegans from related hairpin precursor sequences [1]. The predicted
#=GF CC   hairpin precursor sequences for Drosophila miR-281 (MIR:MI0000366,
#=GF CC   MIR:MI0000370) [2,3] are also related and so are also present in this
#=GF CC   family. The hairpin precursors (represented here) are predicted based on
#=GF CC   base pairing and cross-species conservation -- their extents are not
#=GF CC   known. In this case the mature sequences are expressed from the 3' arms of
#=GF CC   the hairpin precursors.
#=GF WK   Mir-46/mir-47/mir-281_microRNA_precursor_family
#=GF SQ   11


Z69663.1/519-592               AACUGA-AGAGAGCAGUCUAUUGACAGUCGGUUAC---UCGAAAUCUUU-ACUGUCAUGGAGGCGCUCUCU-UCAGAUGA
Z82094.1/4737-4814             AGCUGA-AGAGAGCCGUCUAUUGACAGUUCAAGACCACGAGUCGUUGUGUGCUGUCAUGGAGUCGCUCUCU-UCAGAUGA
AAGD02001364.1/45012-44939     AGCUGA-AGAGAGCCGUCUAUUGACAGUUCGUUUC----UAUACUUAUGUACUGUCAUGGAGUCGCUCUCU-UCAGAUGA
AAGD02008041.1/22073-22144     GACUGA-AGAGAGCAUUCUGUUGACAGUUCGAUUC------CGAACUCCUACUGUCAUGGAGGCGCUCUCU-UCAGGUGA
CAAC02000474.1/2327234-2327305 GACUGA-AGGGAGCUUUCUUUUGACAGUUCGAUUU------CGAACUCUUACUGUCAUGGAGGCGCUCUCU-UCAGGUGA
CAAC02000548.1/1087471-1087541 AGCUGA-AGAGAGCCGUCUAUUGACAGUUCGCUUG-------UUUCAUGUGCUGUCAUGGAGUCGCUCUCU-UCAGAUGA
ABEG02000765.1/32563-32488     AGCUGA-AGAGAGCCGUCUAUUGACAGUUCGUCUCU--GUUCAGUCAGGUACUGUCAUGGAGUCGCUCUCU-UCAGAUGA
EU047595.1/860-934             GAAUAA-AGAGAGCUGUCCGUCGACAGUCCAGAAA---CUAUUUAAUAUCACUGUCAUGGAAUUGCUCUCU-UUGUAUAA
ACKM01001453.1/97066-97131     GGCUGA-AGAGAGCAGUCUGUUGACAGUUAGAAUG------------GACACUGUCAUGGAGUCGCUCUCU-UCAGAAAC
CADV01004502.1/1105-1177       GGCCUA-AGAGAGCCACCUGUUGACAGUUGGAGCC----AG-AUUUAGAUACUGUCAUGGAGUUGCUCUCU-UAAGGCAA
ABJB010980769.1/513-586        -CCCGAAAGAGAGCAAUCCGUGGACAGUGUGUAUG----UCCGAAAUGGAACUGUCAUGGAGUCGCUCUCUUUCGGGCG-
#=GC SS_cons                   ::<<<<.<<<<<<<--<<<<<-<<<<<<_______....___________>>>>>>>>>>>--->>>>>>>.>>>>::::
#=GC RF                        agCuGA.AGAGAGCagUCuaUUGACAGUucGauuc....uauaauuuuguACUGUCAugGAGUCGCUCUCU.UCaGaUGA
//
# STOCKHOLM 1.0

#=GF AC   RF00250
#=GF ID   mir-TAR
#=GF PI   TAR
#=GF DE   Trans-activation response element (TAR)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12882959
#=GF SS   Published; PMID:12882959
#=GF GA   40.00
#=GF TC   40.20
#=GF NC   39.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0007073;
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12882959
#=GF RT   The apical loop of the HIV-1 TAR RNA hairpin is stabilized by a cross-loop
#=GF RT   base pair.
#=GF RA   Kulinski T, Olejniczak M, Huthoff H, Bielecki L, Pachulska-Wieczorek K,
#=GF RA   Das AT, Berkhout B, Adamiak RW
#=GF RL   J Biol Chem 2003;278:38892-38901.
#=GF RN   [2]
#=GF RM   18299284
#=GF RT   Identification of functional microRNAs released through asymmetrical
#=GF RT   processing of HIV-1 TAR element.
#=GF RA   Ouellet DL, Plante I, Landry P, Barat C, Janelle ME, Flamand L, Tremblay
#=GF RA   MJ, Provost P
#=GF RL   Nucleic Acids Res. 2008;36:2353-2365.
#=GF RN   [3]
#=GF RM   19220914
#=GF RT   HIV-1 TAR miRNA protects against apoptosis by altering cellular gene
#=GF RT   expression.
#=GF RA   Klase Z, Winograd R, Davis J, Carpio L, Hildreth R, Heydarian M, Fu S,
#=GF RA   McCaffrey T, Meiri E, Ayash-Rashkovsky M, Gilad S, Bentwich Z, Kashanchi F
#=GF RL   Retrovirology. 2009;6:18.
#=GF CC   This family represents the HIV trans-activation response (TAR) element
#=GF CC   which is known to be required for the trans-activation of the viral
#=GF CC   promoter and for virus replication. The TAR hairpin acts as a binding site
#=GF CC   for the Tat protein and this interaction stimulates the activity of the
#=GF CC   long terminal repeat promoter [1]. Further experiments have shown that TAR
#=GF CC   acts as a miRNA that protects against apoptosis [2,3].
#=GF WK   Trans-activation_response_element_(TAR)
#=GF SQ   45


U24479.1/327-387     GGGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCCAC
AF254724.1/392-452   GGGUCUCUCUUGUUAGACCAGAUUUGAGCCUGAGAGCUCUCUGGCUAGCUAGAGAACCCAC
U51296.1/362-421     GGGUCUCUCUUGUUAGACCAGGUC-GAGCCCGGGAGCUCUCUGGCUAGCAAGGGAACCCAC
AF286239.1/8968-9027 GGGUCUCUCUUGUUGGACCAGAU-AGAGCCUGGGAGCUCUCUGGCUAGCAGGGGAACCCAC
AF102206.1/384-443   GGGUCUCUCUUGCUAGACCAGAU-UGAGCCUGGGAGCUCUCUGACUAGCAGAGGAACCCAC
L28878.1/358-418     RGGUCUCUCURGUUAGACCAGAUCUGAGCCURRGAGCUCUCURGCUAACUARGGAACCHAC
AF457076.1/8775-8834 AAGUCUCUCUUGUUAGACCAGAUC-GAGCCUAGGAGCUCUCUGACCAGCGAAGGAACCCAC
AF254695.1/392-452   GGGUCUCUCUAGGUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCCUUCUAGAGAACCCAC
AF457068.1/8753-8812 GGGUCUCUCUUGUUAGACCAGAU-AGAGUCUGAGAACUCUCUGGCUAGCGAGGGAACCCAC
AY037273.1/8734-8794 AGGUCUCUCUAAGUAGACCAGAUCUGAGCCUAGGAGCUCUCUGGCUAACUAAGGAACCCAC
AF411965.1/9548-9608 GGGUCUCUCUAGGCAGACCAGAUUUGAGCCCGGGAGCUCUCUGGCUAUCUAGGGAACCCAC
AF254726.1/391-451   GGGUCUCUCUAGGUGGACCAGAUCUGAGCCUGGGCGCUCUCUGGCUACCUAGGGAACCCAC
AF096779.1/454-514   GGGUCUCUCUAGGUAGACCAGAUCUGAGCCUGGGAGCUCUAUGGCUAUUUGGGGAACCCAA
AF063164.1/454-514   GGGCUCCUCUGGUUAGACCAAAUCUGAGGCUGGGAGCUCUCUGGCUAGCUAGGGAACCCAC
AF457086.1/8766-8825 GGGUCUCUCUUGGUAGACCAGAUC-GAGCCUGGGAGCUCUCUGGUUGACAAGGGAACCCAC
AF190128.1/8856-8916 GGGUCUCUUUGGUUAGACCAGAUCUGAGCCUGGGAGUUCUCUGGCUGGCCAAGGAACCCAC
U72138.1/316-376     GGGUCUCUCUAGUUAGACCAGAUCUAAGCCUAAGAGCUCUCUGGCUGACUAGGGAACCCAC
AF442567.1/8145-8205 AGGUCUCUCUUGCUAGACCAGAUCUGAGCCUAGGAGCUCUCUGGCUAGUUAAGGAACCCAC
AF457071.1/8730-8789 AAGUCUCUCUUGUUAGACCAGAUC-GAGCCUAGGAGCUCUUUAGCUAGCAAAGGAACCCAC
AF063176.1/456-516   GGCUCUCUCUAGUUGGACCAGAUCUGAGCCUAGAAGCUCUCUGGCUAACUAGGGAACCCAC
AF321523.1/455-515   GGGUCUCUCUAGGUAGGCCAGAUCUGAGCCCGGGAGCUCUCUGGCUAUAUGGGGAACCCAC
AF443094.1/8913-8973 GGGUCGCCUUAGGUAGACCAGAUCUGAGCCCGGGAGCUCUCUGGCUAUCUAGGGAACCCAC
AF119820.1/463-523   GGGUCUCUCUGGUUAGGCCAGGUCUGAGCCUGGGAGCUCUCUGGCUAGCUUAGGAACCCAU
AF063151.1/456-516   GGGUCUUUCUGGUUAGACCGAAUCUGAGCCUGGGAGCUCUCUGGCUAGCUAGGGAAUCCAC
AF254684.1/394-453   GGGUCUCUCUAGGUAGACCAGGUCCAAGCCCGGGAGCUC-CUGGCUAUCUAGGAAACCCAC
AF457057.1/8730-8789 AGGUCUCUCUUAGUAGACCAGAUC-GAGCCUAGGAGCUCUCUAGCUAGCAAAAGAACCCAC
AF103818.1/9605-9663 GGGUCUCUUCG-CUAGACCAGAUAAGAGCCCGGGAGCUCUCUGGCUAG-UGUAGAACCCAC
AF484484.1/8728-8787 AGGUCUCUCUUGUUAGACCAGAUC-GAGCCUAGGAGCUCUCUAGCUAGCAGGGAAACCCAC
U72094.1/327-387     GGGUCUCUCUAGUUAGACCAGAUCUAAGCCUAGGAGCUCUCUAGCUAGCUAAAGAACCCAC
AF196736.1/484-544   GGGUCUCUCUAGUUAGACCAGAUUCGAGCCUGGGAGCUCUCUGGCUAGUGGAGGAACCCAC
L28844.1/328-388     AGGUCUCUCUUGUUAGACCAGAUCCGAGCCUAGGAACUCUCUGGCUAACUAAGGAACCCAC
AF196762.1/466-526   GUGUCUCUCUAGUUAUACCAUAUCUGAUCCUGGGAGCUCUCUGGCUAGCUAGGGAACCCAC
AF457060.1/8743-8802 AGGUCUCUCUUGUUGGACCAGAU-AGAGCCUAGGAGCUCUCUGGCUAGCAAAAGAACCCAC
AF457079.1/8708-8767 GGGUCUCUCUUAGUAGACCAGAU-AGAGCCUGGGAGCUCUCUGGCUAGUAAGGGAACCCAU
AF484519.1/8748-8808 GGGUCUCUCUUGUCAGACCAGAUUUGAGCCUGAGAGCUCUCUGGCCGACUAGGGAACCCAC
AF286233.1/8890-8950 GGGUCUCUCUAGGUAGACCAGAUCUGAGCCCGAGUGCUCUCUGGCUAUCCAGGGAACCCAC
AY074891.1/8871-8931 GGGUCUCUCUAGGUAGAUCAGAUCAGAGCCUGGGAGCUCUCUGGCUAUCUGGGGAACCCAC
AF063150.1/456-516   GGGUCUCUCUGGUUAGACACAAUCUGAGCCUGGGAGCUCUCUGACUAGCUAGGGAACCCAC
U72122.1/306-366     UGGUCUCUCUUGUUAGACCAGAUCAGGGCCUGAGAGCUCUCUGGCUAACUAGGGAACCCAC
AF443095.1/8922-8982 GGGUCUCUCUAGGUAGACCAGAUAUGAGCCUGGGAGCUCUCUGGCUGCUUAGGGAACCCAC
X52154.1/9632-9691   GGGUCUCUUUCACUGGACCAGAUUUGAGCCUGGGAGCUCUCUACC-AGUGAAGGAACCCAC
AF115393.1/8994-9054 GGGUCUCUCUUGCUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGUCAGGUAGAGAACCCAC
AF063179.1/457-517   GGGUCUCUCUAGUCAGACCAGAUCUGAGCCUGAAAGCUCUCUAGCUAGCUAGGGAACCCAC
AF465242.1/9763-9822 GGGUCUCUCUAGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAGCU-GAGAACCCAC
DQ373065.1/9036-9095 GGGUCUCUCUUGUUAGACCAGAUUAGAGCCUGGGAGCUCUCUGGCUAGCAAG-GAACCCAC
#=GC SS_cons         <<<<-<<<<<<<<<<<-<<<<<---<<<<______>>>>>>>>>>>>>>>>>>>>>>>>::
#=GC RF              GGGUCUCucuagcuaGACCAGAUCUGAGCCUGGGAGCUCUCUGGCuagcuaggGAACCCAC
//
# STOCKHOLM 1.0

#=GF AC   RF00251
#=GF ID   mir-219
#=GF DE   mir-219 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000044;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12624257
#=GF RT   Vertebrate microRNA genes.
#=GF RA   Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP
#=GF RL   Science 2003;299:1540.
#=GF RN   [2]
#=GF RM   12844358
#=GF RT   Computational identification of Drosophila microRNA genes.
#=GF RA   Lai EC, Tomancak P, Williams RW, Rubin GM
#=GF RL   Genome Biol 2003;4:R42.
#=GF CC   miR-219 was predicted in vertebrates by conservation between human, mouse
#=GF CC   and Fugu and cloned in Fugu [1], and later predicted and experimentally
#=GF CC   confirmed in Drosophila [2]. miR-219 homologs have since been predicted or
#=GF CC   experimentally confirmed in a wide range of species which include the
#=GF CC   platyhelminth Schmidtea mediterranea, several arthropod species and a wide
#=GF CC   range of vertebrates (MIPF:MIPF0000044). The hairpin precursors
#=GF CC   (represented here) are predicted based on base pairing and cross-species
#=GF CC   conservation -- their extents are not known. In this case the mature
#=GF CC   sequence is excised from the 5' arm of the hairpin.
#=GF WK   mir-219_microRNA_precursor_family
#=GF SQ   13


AF100956.1/111730-111659     GCUCCUGAUUGUCCAAACGCAAUUCU----CGAGUCUCUGGCUCCGGCCGAGAGUUGCGUCUGGACGUCCCGAGCC
D84401.1/35519-35448         GCUCCUGAUUGUCCAAACGCAAUUCU----CGAGUCUAUGGCUCCGGCCGAGAGUUGAGUCUGGACGUCCCGAGCC
AL359091.10/91897-91825      GCCACUGAUUGUCCAAACGCAAUUCUUGUACGAGUCUGCGGC--CAACCGAGAAUUGUGGCUGGACAUCU-GUGGC
AY152826.1/42824-42753       GCUCUUGAUUGUCCAAACGCAAUUCU----CGAGUCUAUGGCUCCGGCCGAGAGUUGAGUCUGGACGUCCCGAGCC
AL928926.9/24183-24111       GCCACUGAUUGUCCAAACGCAAUUCUUGUACGAGUCUGCGGC--CAACCGAGAAUUGUGGCUGGACAUCU-GUGGU
AJ421778.1/62949-62878       GCUCCUGAUUGUCCAAACGCAAUUCU----CGAGUCUAUGGCUCUGGCCGAGAGUUGAGUCUGGACGUCCCGAGCC
AAPN01125568.1/829-757       GCCGCUGAUUGUCCAAACGCAAUUCUUGUGCGAGUUUGCGGC--CAACCGAGAAUUGUGACUGGACAUCU-GUGGC
AAFR03043752.1/856-788       GCUCCUGAUUGUCCAAACGCAAUUCU----CGUGGCUCCGGCCCU---CGAGAGUUGGGUCUGGACAUCCCGAGCC
AE014296.4/17308119-17308189 AGCUAUGAUUGUCCAAACGCAAUUCU----UGUUGAUAUUCA-AUAUUCAAGGGUUGCGACUGGGCAUCGCGGCUC
AAWZ02035889.1/954-887       GGUCCUGAUUGUCCAAACGCAAUUCU----UG--UCUCCGCU--CCACCGAGAGUUGAGUCUGGACAUCAGGAGCC
AY866244.1/138-209           GCUCCUGAUUGUCCAAACGCAAUUCU----CGAGUCUAUGGCUCCGGCCGAGAGUUGAGUCUGGACGUCCCGAGCC
AY866245.1/430-501           GCUCCUGAUUGUCCAAACGCAAUUCU----CGAGUCUAUGGCCCCGGCCGAGAGUUGAGUCUGGACGUCCCGAGCC
AY866243.1/430-501           GCUCCUGAUUGUCCAAACGCAAUUCU----CGAGUCUAUGGCUCUGGCCGAGAGUUGAGUCUGGACGUCCCGAGCC
#=GC SS_cons                 :::::::::<<<<<<--<<<<<<<<<....<<__________._____>>>>>>>>>>>-->>>>>>:::::::::
#=GC RF                      GcucCUGAUuGUCCAAACgCAAuUCU....CGAGUcUauGGc.ccaaCCGAGAgUUGcGuCUGGACaUCcCGaGcC
//
# STOCKHOLM 1.0

#=GF AC   RF00252
#=GF ID   Alfamo_CPB
#=GF DE   Alfalfa mosaic virus coat protein binding (CPB) RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14718638
#=GF SS   Published; PMID:14718638
#=GF GA   70.00
#=GF TC   72.00
#=GF NC   68.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0045727; positive regulation of translation;
#=GF RN   [1]
#=GF RM   14718638
#=GF RT   Efficient translation of alfamovirus RNAs requires the binding of coat
#=GF RT   protein dimers to the 3' termini of the viral RNAs.
#=GF RA   Neeleman L, Linthorst HJ, Bol JF
#=GF RL   J Gen Virol 2004;85:231-240.
#=GF CC   This family represents the Alfalfa mosaic virus (AMV) coat protein (CP)
#=GF CC   binding RNA which is found in the 3' UTR. AMV CP can stimulate the
#=GF CC   translation of AMV RNA by between 50 and 100-fold. This family contains at
#=GF CC   least two CP binding sites which are thought to be essential for efficient
#=GF CC   RNA translation [1].
#=GF WK   Alfalfa_mosaic_virus_coat_protein_binding_(CPB)_RNA
#=GF SQ   18


U12510.1/700-876     UGAUGUACCCCAUUAUUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAACGACUUCAUAUUGCUUAUA-UGUGUGCUGAUGCACACAUAUAAAUGCUCAUGCGAAACU-GCAUGAAUGCCCCUAAGG-----
V00048.1/700-881     UGAUUUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
K03542.1/1961-2142   UGAUUUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
V00049.1/42-226      GGAGCUAUAAUACUAAUUUCUGAAUUAGUCAUUGGUAAUUCAA--UGCCAACCUCCACAGGGUGGACUAAGGUUGAGGUAUAGAAUCCUAUUCGCUCCUGGUAGGAGAAAUUCUAUAUUGCUUAUA-UACGUGCUUGUGCACGUAUAUAAAUGCUCAUGCAAAAUU-GCAUGAAUGCCCCUAAGGGA-GC
M59241.1/2007-2188   UGAUGUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGAAACAACUUCAUAUUGCUUAUA-UAUGUGCUAGUGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
X01572.1/2408-2593   CAAGGGCACGCCGAGCUUGAUGUUUUCUUGACA--UAAGUCAAAUUGCCAACCUCCACUGGGUGGGUCAAGGUUGAGGUAUAGAAUCCUAUUCGCUCCUGAUAGGAGAAAUUCUAUAUUGCUUAUA-UAUGUGCUUACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
AF015716.1/1857-2038 UGAUGUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGAGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAACGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
L00162.1/783-964     UGAUUUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
V00050.1/43-228      CAAGGGCACGACGAGCUUGAUGUUUUCUUGACA--UAAGUCAAAUUGCCAACCUCCACUGGGUGGAUUAAGGUUGAGGUAUAGAAUCCUAUUCGCUCCUGAUAGGAGAAAUUCUAUAUUGCUUAUA-UAUGUGCUUAUGCACAUAUAUAAAUGCUCAUGCAAAACUUGCAUGAAUGCCCCUAAGGGA-GC
AF015717.1/1857-2038 UGAUGUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAACGACUUCAUAUUGCUUAUA-UAUGUGCUAGCGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
L00163.1/3459-3644   GGAGCUAUAAUCAUAAUUUCUGAAUUAGUCAUUGGUAAUUCAA--UGCCAACCUCCACUGGGUGGGUUAAGGUUGAGGUAUAGAAUCCUAUUCGCUCCUGAUAGGAGAAAUUCUAUAUUGCUUAUA-UACGUGCUUAUGCACGUAUAUAAAUGCUCAUGCUAAAUU-GCAUGAAUGCCCCUAAGGGAUGC
AF332998.3/2078-2257 UGAUUUACCCCAUUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUACUAUG---UAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
V00051.1/50-230      UGAUGUACCCCAUUAAUUUGGGA--UGCCAAAG--UCAUUUGA--UGCUCACCUCCACUGGGUGGAUCAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAGC-
X00819.1/1874-2055   UGAUGUACCCCAAUAAUUUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAACGACUUCAUAUUGCUUAUA-UAUGUGCUGGUGCACACAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
U12509.1/700-876     UGAUGUACCCCAUUAAUCUGGGA--UGCUAAAG--UCAUUUAA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAACGACUUCAUAUUGCUUAUA-UAUGUGCUAACGAACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGG-----
AF294432.1/721-902   UGAUGUACCCCAUUAAUUUGGGA--UGCCAAAG--UCAUUUGA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
K02703.1/1856-2037   UGAUGUACCCCAUUAAUUUGGGA--UGCCAAAG--UCAUUUGA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGUCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
AF294433.1/721-902   UGAUGUACCCCAUUAAUUUGGGA--UGCCAAAG--UCAUUUGA--UGCUGACCUCCACUGGGUGGAUUAAGGUCAAGGUAUGAAGCCCUAUUCGCUCCUGAUAGGAUCGACUUCAUAUUGCUUAUA-UAUGUGCUAACGCACAUAUAUAAAUGCUCAUGCAAAACU-GCAUGAAUGCCCCUAAGGGAUGC
#=GC SS_cons         ::::::::<<<<______>>>>,..,,,<<<<_..___>>>>,..,,,<<<<<<<<<<___>>>>---->>>>>>,<<<<<<<<<<<<<<<<_______>>>>>>---->>>>>>>>>>,,<<<<<.<<<<<<<____>>>>>>>>>>>>,,,,<<<<<<<____>.>>>>>>,,,,<<<___>>>::::
#=GC RF              ugAuguAccccauuAaUUugggA..Ugcugaag..UcAuucaA..UGCcgaCCuCCaCUGGGuGGAUUAaGGucgAgguauggaguCCuauuCGCUCCUgauaGGAucgacuccauauuGCuuaua.uauGuGCUaAuGCaCauauauaaAUGCuCauGCaAAAcu.GCauGaAUGCCCCUAAGGGAuGC
//
# STOCKHOLM 1.0

#=GF AC   RF00253
#=GF ID   mir-101
#=GF DE   mir-101 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   60.00
#=GF TC   82.80
#=GF NC   57.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000103;
#=GF DR   MIR; MI0000148;
#=GF DR   MIR; MI0000739;
#=GF DR   MIPF; MIPF0000046;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11914277
#=GF RT   miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.
#=GF RA   Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L,
#=GF RA   Rappsilber J, Mann M, Dreyfuss G
#=GF RL   Genes Dev 2002;16:720-728.
#=GF RN   [2]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol 2002;12:735-739.
#=GF CC   Expression of miR-101 has been validated in both human (MIR:MI0000103,
#=GF CC   MIR:MI0000739) [1] and mouse (MIR:MI0000148) [2].This mirna appears to be
#=GF CC   specific to the vertebrates and has now been predicted or confirmed in a
#=GF CC   wide range of vertebrate species (MIPF:MIPF0000046). The hairpin
#=GF CC   precursors (represented here) are predicted based on base pairing and
#=GF CC   cross-species conservation -- their extents are not known. In this case
#=GF CC   the mature sequence is excised from the 3' arm of the hairpin. This family
#=GF CC   also contains a predicted homologue of mir-101 from Tetraodon fluviatilis.
#=GF WK   mir-101_microRNA_precursor_family
#=GF SQ   24


AF480539.1/1-75              UGCCCUGGCUCAGUUAUCACAGUGCUGAUGCUGUCUAUUCUAAAGGUACAGUACUGUGAUAACUGAAGGAUGGCA
U53213.1/1397-1471           UGCCCUGGUUCAGUUAUCACAGUGCUGAUGCUGUCCCCAUCGAAGGUACAGUACUGUGAUAACUGAAGGAUGGCU
AL645668.15/99743-99669      UGCCCUGGCUCAGUUAUCACAGUGCUGAUGCUGUCCAUUCUAAAGGUACAGUACUGUGAUAACUGAAGGAUGGCA
AF480540.1/1-75              UGUCCUUUUUCGGUUAUCAUGGUACCGAUGCUGUAUAUCUGAAAGGUACAGUACUGUGAUAACUGAAGAAUGGUG
CR626910.5/33110-33184       UGCCCUGGUUCAGUUAUCACAGUGCUGAUGCUGUCCAUCUUAAAGGUACAGUACUGUGAUAACUGAAGGAUGGCU
BAAE01143575.1/1513-1587     UGUCCAUUUUCAGUUAUCAUGGUACCGGUGCUGUCUGCCUAUCAAGUACAGUACUAUGAUAACUGAAGAUUGGCA
AANH01004612.1/58976-58902   UGUCCAUUUUCAGUUAUCAUGGUACCGGUGCUGUGUCUGUCUCGAGUACAGUACUAUGAUAACUGAAGAUUGGCA
AY866070.1/479-553           UGCCCUGGCUCAGUUAUCACAGUGCUGAUGCUGUCUAUUCUAAAGGUACAGUACUGUGAUAACUGAAGGAUGGCA
AAPY01713944.1/4864-4938     UGCCCUGGCUCAGUUAUCACAGUGCUGAUGCUGUCCAUUCUAAAGGUACAGUACUGUGAUAACUGAAGGAUGGCA
AANN01682059.1/2057-1983     UGCCCUGGCUCAGUUAUCACAGUGCUGAUGCUGUCCAUUCGAAAGGUACAGUACUGUGAUAACUGAAGGAUGGCA
AAPN01060708.1/3293-3219     UGUCCUUUUUCGGUUAUCACGGUACCGAUGCUGUAUAUGUGAAAGGUACAGUACUGUGAUAACUGAAGAAUGGUG
AAFR03042358.1/11128-11202   UGCCCUGGCUCAGUUAUCACAGUGCUGAUGCUGUCCGUUCUCAAGGUACAGUACUGUGAUAACUGAAGGAUGGCA
CAAE01015039.1/966600-966526 UGCCCUGGUUCAGUUAUCACAGUGCUGAUGCUGUCCCCAUCGAAGGUACAGUACUGUGAUAACUGAAGGAUGGCU
ABDC01196822.1/2747-2821     UGUCCUUUUUCGGUUAUCAUGGUACCGAUGCUGUAUAUCUGAAAGGUACAGUACUGUGAUAACUGAAGAAUGGUG
AALT01200793.1/110-184       UGCCCUGGCUCAGUUAUCACAGUGCUGCUGCUGUCCGUUCUGAAGGUACAGUACUGUGAUAACUGAAGGAUGGCA
AANG01427088.1/756-830       UGUCCUUUUUCGGUUAUCAUGGUACCGAUGCUGUAUGUCUGAAAGGUACAGUACUGUGAUAACUGAAGAAUGAUG
AAKN02026025.1/30348-30274   UGUCCUUUUUCGGUUAUCAUGGUACCGAUGCUGUAUGUCUGAAAGGUACAGUACUGUGAUAACUGAAGAAUGGUG
AAWR02017667.1/7804-7878     UGCCCUGGCUCAGUUAUCACAGUGCUGAUGCUGUCAGUUCUAAAGGUACAGUACUGUGAUAACUGAAGGAUGGCA
AAPE02028098.1/10759-10833   UGUCCUUUUUCGGUUAUCAUGGUACCGAUGCUGUAUAUCUGGAAGGUACAGUACUGUGAUAACUGAAGAAUGGUG
AAWZ02009138.1/146482-146408 UGCCCUGGCUCAGUUAUCACUGUGCUGAUGCUGUCUAUACUAAAGGUACAGUACUGUGAUAACUGAAGGAUGGCA
AAQR03024419.1/1909-1983     CGCCCUGGCUCAGUUAUCACAGUGCUGAUGCUGUCCGCUCUGAAGGUACAGUACUGUGAUAACUGAAGGAUGGCG
AC190246.4/74028-73954       UAUCCUUUUUCGGUUAUCAUGGUACCGGUGCUGUAUACGUGAAAGGUACAGUACUGUGAUAACUGAAGAAUGGUG
AABR05015983.1/64520-64594   UGUCCUUUUUCGGUUAUCAUGGUACCGAUGCUGUAGAUCUGAAAGGUACAGUACUGUGAUAGCUGAAGAAUGGUG
CAAB02012226.1/22873-22799   UGUCCAUUUUCAGUUAUCAUGGUACCGCUGCUGUGUCCCUCUCAAGUACAGUACUAUGAUAACUGAAGAUUGGCA
#=GC SS_cons                 :::<<<<-<<<<<<<<<<<<<<<<<<<_____________________>>>>>>>>>>>>>>>>>>->>>->>::
#=GC RF                      UGuCCuuucUCaGUUAUCAcaGUaCuGAUGCUGUauaUuuuaAAGGUACaGuACugUGAUAACuGAAgaaUGGca
//
# STOCKHOLM 1.0

#=GF AC   RF00254
#=GF ID   mir-16
#=GF DE   mir-16 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   44.00
#=GF TC   44.10
#=GF NC   43.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00085
#=GF DR   MIPF; MIPF0000006;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12434020
#=GF RT   Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16
#=GF RT   at 13q14 in chronic lymphocytic leukemia.
#=GF RA   Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan
#=GF RA   S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce CM
#=GF RL   Proc Natl Acad Sci U S A 2002;99:15524-15529.
#=GF CC   miR-16, miR-15, mir-195 and miR-457 are related miRNA precursor sequences
#=GF CC   (MIPF:MIPF000006). This miRNA family appears to be vertebrate specific and
#=GF CC   members of this family have been predicted or experimentally validated in
#=GF CC   a wide range of vertebrate species (MIPF:MIPF0000006). miR-16 and miR-15a
#=GF CC   are clustered within 0.5 kb at 13q14 in human, a region shown to be
#=GF CC   deleted or down-regulated in more than half of B cell chronic lymphocytic
#=GF CC   leukaemias (CLL) [1]. The hairpin precursors (represented here) are
#=GF CC   predicted based on base pairing and cross-species conservation -- their
#=GF CC   extents are not known. In this case the mature sequence is excised from
#=GF CC   the 5' arm of the hairpin.
#=GF WK   mir-16_microRNA_precursor_family
#=GF SQ   12


AL669869.10/100495-100571 UCCUGGCUCUAGCAGCACAGAAAUAUUGGCAUGGGGAAGUGAGUCUG-----CCAAUAUUGGCUGUGCUGCUCCAGGCAGGG
AY865955.1/411-487        CCUGGGCUCUAGCAGCACAGAAAUAUUGGCACAGGGAAGCGAGUCUG-----CCAAUAUUGGCUGUGCUGCUCCAGGCAGGG
AL606727.3/61372-61292    GCCUGGCUGUAGCAGCACGUAAAUAUUGGAGUCAAAGCACUUGCGAAUC-CUCCAGUAUUGACCGUGCUGCUGGAGUUAGGC
CR478286.10/109802-109722 UCCUCGCUUUAGCAGCACGUAAAUAUUGGUGUGUUAUAGUCAAGGCCAA-CCCCAAUAUUAUGUGUGCUGCUUCAGUAAGGC
AC154660.2/77731-77651    GCGGUGCCUUAGCAGCACGUAAAUAUUGGCGUUAAGAUUCUGAAAUUAC-CUCCAGUAUUGACUGUGCUGCUGAAGUAAGGU
AY866308.1/534-614        GCAGUGCCUUAGCAGCACGUAAAUAUUGGCGCUAAGAUUCUAAAAUUAU-CUCCAGUAUUAACUGUGCUGCUGAAGUAAGGU
AF480551.1/1-81           GCAGUGCCUUAGCAGCACGUAAAUAUUGGCGUUAAGAUUCUAAAAUUAU-CUCCAGUAUUAACUGUGCUGCUGAAGUAAGGU
AY865836.1/531-611        GUUCCACUCUAGCAGCACGUAAAUAUUGGCGUAGUGAAAUAUGUAUUAAACACCAAUAUU-ACUGUGCUGCUUCAGUGUGAC
AY865833.1/553-633        GUUCCACUCUAGCAGCACGUAAAUAUUGGCGUAGUGAAAUAUAUGUUAAACACCAAUAUU-ACUGUGCUGCUUUAGUGUGAC
AY865835.1/569-649        GUUCCACUCUAGCAGCACGUAAAUAUUGGCGUAGUGAUAUAUAUAUUAAACACCAAUAUU-ACUGUGCUGCUUUAGUGUGAC
AF480552.1/1-81           GUUCCACUCUAGCAGCACGUAAAUAUUGGCGUAGUGAAAUAUAUAUUAAACACCAAUAUU-ACUGUGCUGCUUUAGUGUGAC
AC119847.12/19552-19632   GUUCCACUCUAGCAGCACGUAAAUAUUGGCGUAGUGAAAUAAAUAUUAAACACCAAUAUU-AUUGUGCUGCUUUAGUGUGAC
#=GC SS_cons              ::::<<<---<<<<<<<<---<<<<<<<<____________________.__>>>>>>>>---->>>>>>>>--->>>::::
#=GC RF                   gcuucaCUcUAGCAGCACGUAAAUAuUGGcGUaguGAaauuaauaUuAa.CuCCAaUAUUgaCUGUGCUGCUuuAGugaGgc
//
# STOCKHOLM 1.0

#=GF AC   RF00255
#=GF ID   mir-218
#=GF DE   mir-218 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   54.00
#=GF TC   54.50
#=GF NC   53.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000026;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF CC   miR-218 appears to be a vertebrate specific microRNA and has now been been
#=GF CC   predicted and experimentally confirmed in a wide range of vertebrate
#=GF CC   species (MIR:MIPF0000026). The extents of the hairpin precursors are not
#=GF CC   known. In this case the mature sequence in excised from the 5'arm of the
#=GF CC   hairpin.
#=GF WK   MiR-218_microRNA_precursor_family
#=GF SQ   18


AC021118.6/58844-58939       UGUAGCGAGAUUUUCUGUUGUGCUUGAUCUAACCAUGUGGUUGCGAGG----UAU---GA---GUAAAACAUGGUUCCGUCAAGCACCAUGGAACG-UC-ACGCAGCU
AC011365.5/25751-25846       CGCUGCGGGGCUUUCCUUUGUGCUUGAUCUAACCAUGUGGUGGAACGA----UGG---AA---ACGGAACAUGGUUCUGUCAAGCACCGCGGAAAG-CA-CCGUGCUC
AL732401.6/60812-60907       UGCCGCGGGGCUUUCCUUUGUGCUUGAUCUAACCAUGUGGUGGAACGA----UGG---AA---ACGGAACAUGGUUCUGUCAAGCACCGCGGAAAG-CA-UCGCUCUC
AAFR03012608.1/12590-12685   GGCCACGGGGCUUUCCUUUGUGCUUGAUCUAACCAUGUGGUGGAACGA----UAG---AA---ACAGAACAUGGUUCUGUCAAGCACCGCGGAAAG-CU-CCGUGCUU
AAPN01020455.1/68716-68811   GGCCAUGGGGCUUUCCUUUGUGCUUGAUCUAACCAUGUGGUGGAACAA----UAU---AA---ACAGAACAUGGUUCUGUCAAGCACCACGGAAGG-CU-CCGUGUUU
AAVX01277185.1/1303-1208     CUCAGCGGGAUUUUUCGUUGUGCUUGAUCUAACCAUGUGGUUGCAAGG----UAC---GA---AUAAAACAUGGUUCUGUCAAGCACCAUGGAACG-UC-ACGUAGCC
AANH01008177.1/992-1091      GUCAGCAGGGUGUUCCUUUGUGCUUGAUCUAACCAUGUGUCUGAACGG----UUCCUAUA---GUAAAACAUGGUUCUGUCAAGCACCAUGGAACGGCC-CUGCCAAA
BAAE01009772.1/4377-4476     GUCAGCAGGUUGUUCCUUUGUGCUUGAUCUAACCAUGUGGCUGCCAGGUUCCUAA---AA---GUGGAACAUGGUUCUGUCAAGCACCAUGGAACG-GC-CCGGCAAA
CAAE01010875.1/62872-62773   GUCAGCAGGUUGUUCCUUUGUGCUUGAUCUAACCAUGUGGCUGCCAGG----UUC---UUAUCGUGGAACAUGGUUCUGUCAAGCACCAUGGAACG-GCCCUGCGAAA
CU550699.5/12753-12848       UUCAGCGGGGUUUUCCUUUGUGCUUGAUCUAACCAUGUGGUUGCAGAC----UCA---GA---CUAAUACAUGGUUCUGUCAAGCACCAUGGAAGG-UC-UUGCAGCA
AAWZ02010025.1/32266-32171   GUUAAUGGGAUUUUCCUUUGUGCUUGAUCUAACCAUGUGGUAGAACAA----UAC---AA---AUUGAACAUGGUUCUGUCAAGCACCAUGGAAGG-CU-CCAUGCUU
CAAB02009890.1/123547-123448 GUCAGCAGGUUGUUCCUUUGUGCUUGAUCUAACCAUGUGGCUGCCGGG----UUCUUAUA---GUGGAACAUGGUUCUGUCAAGCACCAUGGAACG-GCCCUGCCAAA
ADDD01069768.1/7727-7822     GUCCAUGGGGUUUUCCUUUGUGCUUGAUCUAACCAUGUGGUAGAACAA----UAC---AA---AUUGAACAUGGUUCUGUCAAGCACCAUGGAAGG-CU-GCAUACUC
AAPE02044145.1/10965-10870   GUCCGUGGGGCUUUCCUUUGUGCUUGAUCUAACCAUGUGGUGGAACGA----UGG---AA---ACGGAACAUGGUUCUGUCAAGCACCGCGGAAGG-CC-CCGCGCUC
AY866240.1/451-546           CGCUGCGGAGCUUUCCUUUGUGCUUGAUCUAACCAUGUGGUGGAACGA----UGG---AA---ACGGAACAUGGUUCUGUCAAGCACCGCGGAAAG-CA-CCGUGCUC
AY866232.1/539-634           UGUAGCGAGAUUUUCUGUUGUGCUUGAUCUAACCAUGUGGUUGCGAGG----UAU---GA---GUAAAACAUGGUUCCGUCAAGCACCAUGGAACG-UC-ACGCAGCU
AY866236.1/393-488           CGCUGCGGGGCUUUCCUUUGUGCUUGAUCUAACCAUGUGGUGGAACGA----UGG---AA---ACGGAACAUGGUUCUGUCAAGCACCGCGGAAAG-CA-CCGUGCUC
AY866230.1/165-260           UGUAGCGAGAUUUUCUGUUGUGCUUGAUCUAACCAUGUGGUUGCCAGG----UAU---GA---GUAAAACAUGGUUCCGUCAAGCACCAUGGAACG-UC-ACGCAGCU
#=GC SS_cons                 ::::<<<<<<<<<<<<---<<<<<<<<---<<<<<<<<__________....___...__..._____>>>>>>>>--->>>>>>>>--->>>>>>.>>.>>>>::::
#=GC RF                      gucagcggggcgUUCCuUUGUGCUUGaUCUaaCCaUGUGGuuGaaaGa....Uau...aA...auagAACAuGGuuCUGuCAAGCACCAuGGAAcg.cc.ccgcaauu
//
# STOCKHOLM 1.0

#=GF AC   RF00256
#=GF ID   mir-196
#=GF DE   mir-196 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR
#=GF SS   Predicted; PFOLD
#=GF GA   58.00
#=GF TC   58.50
#=GF NC   56.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000238;
#=GF DR   MIR; MI0000279;
#=GF DR   MIR; MI0000552;
#=GF DR   MIR; MI0000553;
#=GF DR   MIPF; MIPF0000031;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA 2003;9:175-179.
#=GF RN   [2]
#=GF RM   12624257
#=GF RT   Vertebrate microRNA genes.
#=GF RA   Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP
#=GF RL   Science 2003;299:1540.
#=GF CC   miR-196 has been shown to be expressed in human (MIR:MI0000238,
#=GF CC   MIR:MI0000279) and mouse (MI0000552, MI0000553) [1,2]. miR-196 appears to
#=GF CC   be a vertebrate specific microRNA and has now been predicted or
#=GF CC   experimentally confirmed in a wide range of vertebrate species
#=GF CC   (MIPF:MIPF0000031). In many species the miRNA appears to be expressed from
#=GF CC   intergenic regions in HOX gene clusters. The hairpin precursors
#=GF CC   (represented here) are predicted based on base pairing and cross-species
#=GF CC   conservation -- their extents are not known. In this case the mature
#=GF CC   sequence is excised from the 5' arm of the hairpin.
#=GF WK   mir-196_microRNA_precursor_family
#=GF SQ   14


AC116662.1/14702-14792    UCUGAACUGGUCGGUGAUUUAGGUAGUUUCCUGUUGUUGGGAUCCACCUU-U-CU-CUCGACAGCACGACACUGCCUUCAUUAC--UUCAGUUGAA
AC012531.11/129347-129438 GCUCAGCUGAUCUGUGGCUUAGGUAGUUUCAUGUUGUUGGGAUUGAGUUU-UGAA-CUCGGCAACAAGAAACUGCCUGAGUUAC--AUCAGUCGGU
AC116664.1/86748-86839    UGGAA-CUGCUGAGUGAAUUAGGUAGUUUCAUGUUGUUGGGCCUGGGUUUCUGAA-CACAACAACAUUAAACCACCCGAUUCAC--GGCAGUUACU
AC011194.15/60947-61038   CGGGA-CUGUUGAGUGAAGUAGGUAGUUUCAUGUUGUUGGGCCUGGCUUUCUGAA-CACAACGACAUCAAACCACCUGAUUCAU--GGCAGUUACU
AF224262.1/4259-4347      UAGAA-CUGGCGUGUGAUUUAGGUAGUUUCAUGUUGUUGGGGCUCAAGUC-U-AU-CUCUACAACACGAAACUGCCUGAAUUAC--UGCAGUUA-U
AF089743.1/3391-3478      UCG-A-CUGUCGUGUGGUUUAGGUAGUUUCAUGUUGUUGGGGUCCA-UUUCU-AA-CUCUGCAACAUGAAACUGUCUUAAUUGC--CCCAGUUAC-
AL645795.3/72052-71960    GACAA-CUGCUAAGUGAUUUAGGUAGUUUUAUGUUGUUGGGCUCUAUUUUAU-AU-CCCCGCAACACGAAACUGUCUUAAUUGCCUCGCAGUGAGA
AC132195.4/6836-6926      UAAGA-CUGCA-UGUGAUUUAGGUAGUUUCAUGUUGUUGGGGCUCCAUUU-UCAAUCCCUACAACACGAAAGUGCCUUAAUUGC--UCCAGUUAAA
U92573.1/5950-6038        ACCGA-CUGUCGAGUGGUUUAGGUAGUUUCAUGUUGUUGGGGUCCA-UUU-CAAA-CUCUGCAACAUGAAAC-GUCUUAAUUGC--CCCAGUUACA
BX005254.9/126100-126009  GCGCGGCUGGUGCGUGGUUUAGGUAGUUUCAUGUUGUUGGGAUUGGCUUCCUGG--CUCGACAACAAGAAACUGCCUUGAUUAC--GUCAGUUCGU
AC129959.6/149884-149793  UGGAA-CUGCUGAGUGAAUUAGGUAGUUUCAUGUUGUUGGGCCUGGAUUUCUGAA-CACAACGACAUUAAACCACCCGACUCAC--GGCAGUUACU
AC004080.2/42937-42848    CAGAA-CUGGUCGGUGAUUUAGGUAGUUUCCUGUUGUUGGGAUCCACCUU-U-CU-CUCGACAGCACGACACUGCCUUCAUUAC--UUCAGUUGAA
AF533976.1/31698-31785    UCG-A-CUGUCGAGUGGUUUAGGUAGUUUCAUGUUGUUGGGGUCCA-UUUCU-AA-CUCUGCAACAUGAAACUGUCUUAAUUGC--CCCAGUUAC-
AC107365.2/86856-86767    CCAGA-CUGUCGAGUGGUUUAGGUAGUUUCAUGUUGUUGGGAUU-ACAUU-CAAA-CUCUGCAACGUGAAACUGUCUUAAUUGC--CCCAGUUUCA
#=GC SS_cons              ::::<.<<<----<<<<<---<<<<<<<<--<<<<<<<<<<______________.>>>>>>>>>>-->>>>>>>>--->>>>>..-->>>>::::
#=GC RF                   uagaA.CUGuugaGugauUUAGGuaGUuUCAUGuuGucGgGauucaauUUcUgAa.CcCgaCaaCAugAaACugCCUuAauuaC..uuCAGUUaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00257
#=GF ID   mir-194
#=GF DE   mir-194 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   55.00
#=GF TC   55.20
#=GF NC   54.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000236;
#=GF DR   MIR; MI0000488;
#=GF DR   MIR; MI0000732;
#=GF DR   MIR; MI0000733;
#=GF DR   MIPF; MIPF0000055;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA 2003;9:175-179.
#=GF RN   [2]
#=GF RM   14573789
#=GF RT   Reduced accumulation of specific microRNAs in colorectal neoplasia.
#=GF RA   Michael MZ, O' Connor SM, van Holst Pellekaan NG, Young GP, James RJ
#=GF RL   Mol Cancer Res 2003;1:882-891.
#=GF CC   Expression of miR-194 has been verified in mouse (MIR:MI0000236,
#=GF CC   MIR:MI0000733) [1] and human (MIR:MI0000488, MIR:MI0000732) [2]. miR-194
#=GF CC   appears to be a vertebrate specific miRNA and has now been predicted or
#=GF CC   experimentally confirmed in a range of vertebrate species
#=GF CC   (MIPF:MIPF0000055). The hairpin precursors (represented here) are
#=GF CC   predicted based on base pairing and cross-species conservation -- their
#=GF CC   extents are not known. In this case the mature sequence is excised from
#=GF CC   the 5' arm of the hairpin.
#=GF WK   mir-194_microRNA_precursor_family
#=GF SQ   29


AC127556.4/107032-107116     UGGCUC--CCA-CCCUCUGUAACAGCAACUCCAUGUGGA-AG-UGCCCACUGGU-U-CCAG-UGGGGCUGCUGUUAUCUGGGG-UGGC-GGCUAG
AC000159.6/81267-81351       UGGUUC--CCG-CCCCCUGUAACAGCAACUCCAUGUGGA-AG-UGCCCACUGGU-U-CCAG-UGGGGCUGCUGUUAUCUGGGG-CGAG-GGCCAG
AC103590.2/171205-171121     AUGGUG--UUA-UCAAGUGUAACAGCAACUCCAUGUGGA-C--UGUGUACCAAU-UUCCAG-UGGAGAUGCUGUUACUUUUGA-UGGU-UACCAA
AC129195.3/65540-65457       AUGGAG--UCA-UCGGGUGUAACAGCAACUCCAUGUGGA-C--UGUGCUCGGAU-U-CCAG-UGGAGCUGCUGUUACUUCUGA-UGGC-CUCCAA
ABDC01135093.1/234-150       UGGCUC--CCA-CCCCCUGUAACAGCAACUCCAUGUGGA-AG-UGCCCACUGGU-U-CCAG-UGGGGCUGCUGUUAUCUGGGG-UGGG-GACCUG
AAFC03085979.1/1394-1478     ACGGCG--UCA-UCGAUUGUAACAGCAACUCCAUGUGGA-CU-GUGCGUCAAUU-U-CCAG-UGGAGAUGCUGUUACUUUUGA-UGGC-UGCCAA
AANN01206173.1/2762-2845     AAGGGA--UUA-UCAAGUGUAACAGCAACUCCAUGUGGA-C--UGUGUACAAUU-U-CCAG-UGGAGAUGCUGUUAUUUUUGA-UGAU-UGCCAA
AAIY01704218.1/1026-942      GGGUUC--CCG-UCCCCUGUAACAGCAACUCCAUGUGGA-GG-UGCUCGCUGGU-U-CCAG-UGGAGUUGCUGUUGCCUGGGG-CGAG-GGCCAC
AANG01032370.1/407-323       CUGGGG--UUA-UCAAGUGUAACAGCAACUCCAUGUGGA-CU-GUGUACCAAUG-U-CCAG-UGGAGAUGCUGUUACUUUUGA-UGAU-UACCAA
AAYZ01125558.1/495-410       UUAGCU-CCCA-CCCCCUGUAACAGCAACUCCAUGUGGA-AU-GCUCAGCUCUU-U-CCAG-UGGGGCUGCUGUUAUCUGGGG-UGGG-AGCUGG
AAPN01023116.1/334-252       UGGAGC--CCA-CCCCUUGUAACAGCAACUCCAUGUGGA-AG-GGUCUCCUGGU-U-CCAG-UGGAGCUGCUGUUAUCUUGGG-UG---GGUCAU
AAPY01700927.1/1388-1304     AUGGAG--UUA-UCAAGUGUAACAGCAACUCCACGUGGA-CU-GAAUACCGAUU-U-CCAG-UGGAGAUGGUGUUACUUCUGA-UGAU-UACCAA
AANH01000564.1/249696-249610 GUGGUG-UUCG-CUGGAUGUAACAGCAACUCCAUGUGGA-AG-CUGCGUCCAGU-U-CCAG-UGGAGGUGCUGUUACCUGCAG-AGGACCACCCA
AALT01482191.1/6150-6232     CUGGGG--UGG-CCGAGUGUAACAGCAACUCCAUGUGGA-C---CGUGUCCAAG-C-CCAG-UGGAGAUGCUGUUACUCUCGG-CGGC-UUCCAG
BX248510.4/109392-109307     UUGGUG--CUGACUGCUUGUAACAGCAACUCCAUGUGGA-A--GGUUUGUGUCU-U-CCAG-UGGAGCUGCUGUUGCGUGCAGAUAGU-CACCAU
BAAE01291848.1/854-770       CUGGUG-UUUG-CUGGAUGUAACAGCAACUCCAUGUGGA-A--GCUGUGUCUGU-U-CCAG-UGGAGGUGCUGUUACCUGCAG-AGAC-CACCGA
CAAE01014650.1/773482-773569 CUGGUG-CGCG-CUGGAUGUAACAGCAACUCCAUGUGGA-AGCUGUAUGUGUGU-U-CCAG-UGGAAGUGCUGUUACCUGCAG-AGAUCCACCGG
AY866324.1/252-166           GUUGGUAACCA-UCAAAAGUAACAGCAUCUCCA-CUGGA-AA-UUGGUACACAG-U-CCACAUGGAGUUGCUGUUACACUUGA-UAAC-ACCAUU
AAGV020435009.1/201-286      UCGGCC-GCCG-CCCCCUGUAACAGCAACUCCAUGUGGA-AG-UGCCCGCUGGU-U-CCAG-UGGGGCUGCUGUUAUCCGGGG-CGGG-GGCCAG
AAWR02033463.1/86616-86532   AUGGGG--UCA-UCAAGUGUAACAGCAACUCCAUGUGGA-CU-GGGUACCAAUU-U-CCAG-UGGAGAUGCUGUUACUUUUGA-UGGU-UACCAA
AAKN02038532.1/88369-88285   GGGCUC--CCU-CCCCCUGUAACAGCAACUCCAUGUGGA-AG-UGCCCACUGGU-U-CCAG-UGGGGCUGCUGUUAUCUGGGG-CGGG-GGCCCG
AABR05040650.1/15390-15473   AUGGAG--UCA-UCACGUGUAACAGCAACUCCAUGUGGA-C--UGUGCACAGAU-C-CCAG-UGGAGCUGCUGUUACUUUUGA-UGGC-CUCCAG
AAGU03077813.1/8996-8912     AUGGAG--UUA-UCAAAUGUAACAGCAACUCCAUGUGGA-CC-AGGUACCGACU-U-CCAG-UGGGGAUGCUGUUACUUUUGA-UGGC-UACCAA
AAEX03018351.1/31475-31391   UGGGAG--UCA-UCAAGUGUAACAGCAACUCCAUGUGGA-UU-GUGUGCCAAUU-U-CCAG-UGGAGAUGCUGUUACUUUUGA-UGGU-UACCAA
CAAB02008127.1/35388-35472   UGGGUC--UCA-CCAGCUGUAACAGCAUCUCCAUAUGGAAAA-AACCCUCUGGUUU-CCAG-UGGAGCUGCUGUUAUCUAUGG-AG---GGCCAC
AAQR03078873.1/635-551       AUGGAG--UCA-UCAAGUGUAACAGCAACUCCAUAUGGA-CU-AUGUGCCAAUU-U-CCAG-UGGAGAUGCUGUUACUUUUGA-UGGU-UACCAA
AAWZ02006025.1/14998-14915   UACAGU-GUCG-UCAAGUGUAACAGCAACUCCAUGUGGA-A---UAAGUAGAUU-U-CCAG-UGGAGGUGCUGUUACUUUUGA-AGCU-ACUGAC
AADN03003271.1/76146-76064   CUGGUG--CUC-UCAUAUGUAACAGCAACUCCAUGUGGA-C---UACACUGACU-U-CCAG-UGGAGAUGCUGUUACUUUUGA-UAGC-GGCUCA
AY866321.1/214-298           AUGGUG--UUA-UCAAGUGUAACAGCAACUCCAUGUGGA-CU-GUGUACCAAUU-U-CCAG-UGGAGAUGUUGUUACUUUUGA-UGGU-UACCAA
#=GC SS_cons                 ::<<<<..-<<.<<<<--<<<<<<<<<-<<<<<--<<<<.__.___________.>.>>>-.>>>>>->>>>>>>>>-->>>>.>>--.>>>>::
#=GC RF                      uuggug..uca.cCgcaUGUAACAGCAACuCCAUGUGGA.au.uuuuuacuauU.U.CCAG.UGGaGaUGCUGUUACuUgcGg.uggu.caccaa
//
# STOCKHOLM 1.0

#=GF AC   RF00258
#=GF ID   mir-130
#=GF DE   mir-130 microRNA precursor family
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones SR, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   55.00
#=GF TC   55.30
#=GF NC   54.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000156;
#=GF DR   MIR; MI0000408;
#=GF DR   MIR; MI0000448;
#=GF DR   MIR; MI0000748;
#=GF DR   MIPF; MIPF0000034;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol 2002;12:735-739.
#=GF RN   [2]
#=GF RM   12919684
#=GF RT   Embryonic stem cell-specific MicroRNAs.
#=GF RA   Houbaviy HB, Murray MF, Sharp PA
#=GF RL   Dev Cell 2003;5:351-358.
#=GF CC   miR-130 has been identified in mouse (MIR:MI0000156, MIR:MI0000408) [1],
#=GF CC   and in human (MIR:MI0000448, MIR:MI0000748) [2]. miR-130 appears to be
#=GF CC   vertebrate specific miRNA and has now been predicted or experimentally
#=GF CC   confrimed in a range of vertebrate species (MIPF:MIPF0000034). The hairpin
#=GF CC   precursors (represented here) are predicted based on base pairing and
#=GF CC   cross-species conservation -- their extents are not known. In this case
#=GF CC   the mature sequence is excised from the 3' arm of the hairpin.
#=GF WK   mir-130_microRNA_precursor_family
#=GF SQ   9


AP000662.4/36681-36763      UGCUGGCCAGAGCUCUUUUCACAUUGUGCUACUGUCUGCACCUGUCACUAGCAGUGCAAUGUUA-AAAGGGCAUUGGCCGUGUA
AL928914.15/23540-23459     UGCUGGCCGGAGCUCUUUUCACAUUGUGCUACUGUCUA-ACGUGUACCGAGCAGUGCAAUGUUA-AAAGGGCAUCGGCCUUGUA
AAFC03029349.1/944-1026     UGCGGGCCGGAGCUCUUUUCACAUUGUGCUACUGUCUGCGCCUGUCACUAGCAGUGCAAUGUUA-AAAGGGCAUUGGCUGUGCA
AAFR03038969.1/302-384      UCCUGGCCAGAGCUCUUUUCACAUUGUGCUACUGUCUGCACCUAUCACUAGCAGUGCAAUGUAA-AAAGGGCAUUGGCUGGGCA
AAPN01026753.1/160-77       UCCCGGCCGGAGCUCUUUUCACAUUGUGCUACUGUCUGCGCCCGUCACUAGCAGUGCAAUGUAAUAAGGGGCUUCGGCGGGGCA
AAWR02041426.1/16299-16217  UGCGGGCCGGAGCUCUUUUCACAUUGUGCUACUGUCUGCACCUACCACUAGCAGUGCAAUGUUA-AAAGGGCAUUGGCCAUGUA
AAGW02038159.1/34457-34539  UGCUGGCCAGAGCUCUUUUCACAUUGUGCUACUGUCUGCGCCUAUCACGAGCAGUGCAAUGUCA-AAAGGGCAUUGGCCAUGUA
AAWZ02011385.1/100027-99945 CCCUGUCCAAGGCUCUUUUCACAUUGUGCUUCUGUCUGUGCCCGACCCAAGCAGUGCAAUGUUA-AAAGGGCAUUGGGUGGGUG
AY865862.1/358-440          UGCUGGCCAGAGCUCUUUUCACAUUGUGCUACUGUCUGCACCUGUCACUAGCAGUGCAAUGUUA-AAAGGGCAUUGGCCCCCCA
#=GC SS_cons                <<<-<<<<<<-<<<<<<<<--<<<<<<<<<______________________>>>>>>>>>-->.>>>>>>>->>>>>>-->>>
#=GC RF                     ugCuggCCggAGCuCuUUUCACAUUGugCUACUGUCUGcaCcugucaCuAGCAGugCAAUGUuA.AAaGgGCAucGGccguGca
//
# STOCKHOLM 1.0

#=GF AC   RF00259
#=GF ID   IFN_gamma
#=GF DE   Interferon gamma 5' UTR regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:11832212
#=GF SS   Published; PMID:11832212
#=GF GA   40.00
#=GF TC   41.60
#=GF NC   39.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0045727; positive regulation of translation;
#=GF RN   [1]
#=GF RM   11832212
#=GF RT   Human interferon-gamma mRNA autoregulates its translation through a
#=GF RT   pseudoknot that activates the interferon-inducible protein kinase PKR.
#=GF RA   Ben-Asouli Y, Banai Y, Pel-Or Y, Shir A, Kaempfer R
#=GF RL   Cell 2002;108:221-232.
#=GF CC   This family represents a pseudoknot containing stem-loop structure found
#=GF CC   in the 5' UTR of interferon (IFN) gamma mRNA. This structure is thought to
#=GF CC   be involved in translational regulation and the pseudoknot has been found
#=GF CC   to activate PKR which is known to be a translational inhibitor. Mutations
#=GF CC   in the pseudoknot structure have been found to reduce PKR activation and
#=GF CC   increase the translation of IFN-gamma [1].
#=GF WK   Interferon_gamma_5'_UTR_regulatory_element
#=GF SQ   5


J00219.1/351-519     CAUUGUUCUGAUCAUCUGAAGAUCAGCUAUUAGAAGAGAAAGAUCAGUUAAGUCCUUUGGACCUGAUCAGCUUGAUACAAGAACUACUGAUUUCAACUUCUUUGGCUUAAUUCUCUCGGAAACGAUGAAAUAUACAAGUUAUAUCUUGGCUUUUCAGCUCUGCAUCGUU
X01992.1/3-171       CAUUGUUCUGAUCAUCUGAAGAUCAGCUAUUAGAAGAGAAAGAUCAGUUAAGUCCUUUGGACCUGAUCAGCUUGAUACAAGAACUACUGAUUUCAACUUCUUUGGCUUAAUUCUCUCGGAAACGAUGAAAUAUACAAGUUAUAUCUUGGCUUUUCAGCUCUGCAUCGUU
AF375790.2/1570-1738 CAUUGUUCUGAUCAUCUGAAGAUCAGCUAUUAGAAGAGAAAGAUCAGUUAAGUCCUUUGGACCUGAUCAGCUUGAUACAAGAACUACUGAUUUCAACUUCUUUGGCUUAAUUCUCUCGGAAACGAUGAAAUAUACAAGUUAUAUCUUGGCUUUUCAGCUCUGCAUCGUU
X64659.1/2643-2811   CAUUUUUCUGAUCAUCUGAAGAUCAGCUAUUGGAAGAGAAAGAUCAGCCAAGUCCUUUGGACCUGAUCAACUUGAUACGAGAACUACUGAUUUCAACUUCUUUGGCUGAGCUCUCUCCGAAACAAUGAAAUAUACAAGUUAUAUCUUGGCUUUUCAGCUCUGCGUCGUU
Z54144.2/2620-2785   CAUUCUUCUGAUCAUCUGCAGAUCAGCAAUUAGAAAAGAAAGAUCAGCUACCUCCUUGGGACCUGAUCA---UAACACAGGAGCUACCGAUUUCAACUACUCCGGCCUAACUCUCUCCUAAACAAUGAAAUAUACAAGCUAUUUCUUAGCUUUACUGCUCUGUGGGCUU
#=GC SS_cons         :::::::AAAAAAA<<<<<<<<--<<<<<--<<<<<----<<<<<<<<--<<<--<<<<____aaaaaaa_______>>>>->>>>>>>>>>>--->>>>>->>>>>---->>>->>>>>(((((((,,<<<<<_____>>>>>,,,<<<<____>>>>,,,)))))))
#=GC RF              CAUUgUUCUGAUCAuccGaaGaUCaGCcaUUaGaaGAGAAagauCaGuuAaguCCuuuGGACCUGAUCAgCUUgAuACaagAacuaCuGauuuCAACuuCuuugGCuuAAuuCuCuCggaaacgauGAAauauaCAAGuuauauCUUgGCuUUuCaGCcCUGCaucguu
//
# STOCKHOLM 1.0

#=GF AC   RF00260
#=GF ID   HepC_CRE
#=GF DE   Hepatitis C virus (HCV) cis-acting replication element (CRE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14722290
#=GF SS   Published; PMID:14722290
#=GF GA   35.00
#=GF TC   35.10
#=GF NC   34.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   14722290
#=GF RT   A cis-acting replication element in the sequence encoding the NS5B
#=GF RT   RNA-dependent RNA polymerase is required for hepatitis C virus RNA
#=GF RT   replication.
#=GF RA   You S, Stump DD, Branch AD, Rice CM
#=GF RL   J Virol 2004;78:1352-1366.
#=GF CC   This family represents the Hepatitis C virus (HCV) cis-acting replication
#=GF CC   element (CRE) which is found in the coding region of the RNA-dependent RNA
#=GF CC   polymerase NS5B. Mutations in this family have been found to cause a
#=GF CC   blockage in RNA replication and it is thought that both the primary
#=GF CC   sequence and the structure of this element are crucial for HCV RNA
#=GF CC   replication [1].
#=GF WK   Hepatitis_C_virus_cis-acting_replication_element
#=GF SQ   52


AB047641.1/9329-9379 GCCGGCGGGGGCGACAUUUAUCACAGCGUGUCGCGUGCCCGACCCCGCUUA
AB049100.1/9230-9280 UACAGCGGGGGAGACAUAUAUCACAGCCUGUCUCGUGCCCGACCCCGCUGG
AB031322.1/1663-1713 UACAGCGGGGGAGACAUAUAUCACAGCCUGUCUCGCGCCCGACCCCGCUGG
AF207760.1/9249-9299 UACAGCGGGGGAGACAUAUAUCACAGCGUGUCUCGUGCCCGGCCCCGCUGG
AF207752.1/9249-9299 UACAACGGGGGAGACAUAUAUCACAGCCUGUCUCGUGCCCGACCCCGUUGG
D50481.1/9249-9299   UACAGCGGGGGAGACAUAUAUCACAGCGUGUCUCGUGCCCGACCCCGCUGG
M84754.1/9261-9311   UACGGCGGGGGAGACAUAUAUCACAGCCUGUCUCGUGCCCGACCCCGCUGG
Y11604.1/9193-9243   GCCGGCGGGGGAGACAUUUAUCACAGCAUGUCUCAUGCCCGACCCCGCUAU
D49775.1/983-1033    GCCGGCGGGGGCGACAUAUAUCACAGCGUGUCGCGAGCCCGACCCCGCAUC
AF165061.1/9249-9299 UACAGCGGGGGAGACAUUUAUCACAGCCUGUCUCGUGCCCGACCCCGUUGG
AB057682.1/1663-1713 UACAGCGGGGGAGACAUAUAUCACAGCUUGUCUCGUGCCCGACCCCGCUGG
AF207768.1/9249-9299 UACAGCGGGGGAGACAUAUAUCACAGCCUGUCUCACGCCCGACCCCGCUGG
AF359413.1/808-858   UACAGCGGGGGAGACAUAUAUCACAGCCUGUCUCGUGCCCGACCCCGUUGG
D86537.1/983-1033    GCCGGCGGGGGGGACAUUUAUCACAGCGUGUCCCGUGCCCGACCCCGCUAC
D16192.1/986-1036    UACAACGGGGGAGACAUUUAUCACAGCGUGUCUCGUGUCCGGCCCCGUUGG
D14484.1/9261-9311   UACAGUGGGGGAGACAUAUAUCACAGCCUGUCUCGUGCCCGACCCCGCUGG
AF054260.1/326-376   UACAGCGGGGGAGACAUAUAUCACAGCCUGUCUCGUGCCCGGCCCCGCUGG
AF207763.1/9249-9299 UACAGCGGGGGAGACAUUUAUCACAGCGUGUCUCGUGCCCGACCCCGCUGG
AF009606.1/9264-9314 UACAGCGGGGGAGACAUUUAUCACAGCGUGUCUCAUGCCCGGCCCCGCUGG
D63822.1/9294-9344   UACAGCGGGGGGGACAUAUUUCACAGCGUGUCCCAUGCCCGACCCCGCGUA
AJ132996.1/9266-9316 UACAGCGGGGGAGACAUAUAUCACAGCCUGUCUCCUGCCCGACCCCGCUGG
AB057685.1/1663-1713 UACAGCGGGGGAGACAUAUAUCACAGCCUGUCUCAUGCCCGACCCCGCUGG
AB057608.1/1663-1713 UACAGCGGGGGAGACAUAUAUCACAGCCUGUCUCAUGCCCGACCCCGUUGG
AF511949.1/9265-9315 UACAGCGGGGGAGACAUUUAUCACAGCGUGUCUCGUGCCCGGCCCCGCUGG
D16190.1/986-1036    UACAGCGGGGGAGACAUUUAUCACAGCGUGUCUCAUGUCCGGCCCCGUUGG
AB049092.1/9230-9280 UACAGCGGGGGAGACAUAUAUCACAGCGUGUCUCGCGCCCGACCCCGCUGG
D86530.1/983-1033    GCCGGCGGGGGCGACAUAUAUCACAGCGUGUCGCGAGCCCGACCCCGCCUU
D63857.1/9168-9218   UAUAGCGGGGGAGACAUAUAUCACAGCCUGUCUCAUGCCCGACCCCGCUGG
D10076.1/986-1036    GCCGGCGGGGGCGACAUUUAUCACAGCGUGUCGCGUGCCCGACCCCGCCUA
AF176573.1/9261-9311 UACGGCGGGGGAGACAUAUAUCACAGCCUGUCUCGCGCCCGACCCCGCUGG
D14853.1/9264-9314   UACAGCGGGGGAGACAUUUAUCACAGCGUGUCUCAUGUCCGGCCCCGCUGG
D86541.1/983-1033    GCUGGCGGGGGAGACAUUUAUCACAGCAUGUCUCGUGCCCGACCCCGCUAU
D86533.1/983-1033    GCUGGCGGGGGAGACAUUUAUCACAGCAUGUCUCAUGCCCGACCCCGCUAU
D49779.1/983-1033    UACAGCGGGGGGGACAUAUUUCACAGCGUGUCCCGUGCCCGACCCCGCGUA
Y13184.1/9211-9261   GCUGGCGGGGGGGACAUUUAUCACAGCAUGUCCCGUGCCCGACCCCGCAAC
D50480.1/9249-9299   UACAGCGGGGGAGACGUGUAUCACAGCCUGUCUCGUGCCCGACCCCGCUGG
AF064490.1/9178-9228 GCCGGCGGGGGGGACAUUUAUCACAGCAUGUCCCGUGCCCGACCCCGCUGC
AJ238800.1/8920-8970 UACAGCGGGGGAGACACAUAUCGCAGCCUGUCUCGUGCCCGACCCCGCUGG
AY051292.1/9264-9314 UACAGCGGGGGAGACAUUUAUCACAGCGUGUCUCAUGCCCGGCCCCGUUUG
AF054264.1/326-376   UACGGCGGGGGAGGCAUAUAUCACAGCCUGUCUCGUGCCCGACCCCGCUGG
D86536.1/983-1033    GCCGGCGGGGGAGACAUUUAUCACAGCAUGUCUCGUGCCCGACCCCGCUAU
AB047643.1/9326-9376 GCUGGCGGGGGCGACAUUUAUCACAGCGUGUCGCGUGCCCGACCCCGCUUA
D86539.1/983-1033    UCCGGCGGGGGAGACAUCUAUCACAGCGUGUCUCAUGCCCGACCCCGCUAU
AB057615.1/1663-1713 UACAGCGGGGGAGACAUAUAUCACAGCCUGUCUCACGCCCGGCCCCGCUGG
AB049096.1/9230-9280 UACGGCGGGGGAGACAUAUAUCACAGCCUGUCUCGUGCCCGACCUCGCUGG
AF165050.1/9249-9299 UAUAGCGGGGGAGACAUAUAUCACAGCCUGUCUCGUGCCCGACCCCGCUGG
U01214.1/9262-9312   UACAGCGGGGGAGACAUAUAUCACAGCGUGUCUCAUGCCCGACCCCGCUGG
D86542.1/983-1033    GCCGGCGGGGGAGACAUUUAUCACAGCAUGUCUUAUGCCCGACCCCGCUAC
D86534.1/983-1033    UCCGGCGGGGGAGACAUCUAUCACAGCGUGUCUUAUGCCCGACCCCGCUAU
D45194.1/983-1033    GCCGGCGGGGGAGACAUUUAUCACAGCGUGUCUCAUGCCCGACCCCGCUAU
AF238481.1/9295-9345 GCCGGCGGGGGCGACAUUUAUCACAGCGUGUCGCGUGCCCGACCCCGCUUG
AB001040.1/156-206   UACAGCGGGGGAGACAUAUAUCACAGCCUGUCUCGCGCCCGACCCUGCUGG
#=GC SS_cons         ::<<<<<<<<<<<<<<____________>>>>>>-------->>>>>>>>:
#=GC RF              UAcaGCGGGGGaGACAUaUAUCACAGCgUGUCuCGUGCCCGACCCCGCugg
//
# STOCKHOLM 1.0

#=GF AC   RF00261
#=GF ID   IRES_L-myc
#=GF DE   L-myc internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14730027, INFERNAL
#=GF SS   Published; PMID:14730027
#=GF GA   60.00
#=GF TC   61.40
#=GF NC   52.70
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.13 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   14730027
#=GF RT   L-Myc protein synthesis is initiated by internal ribosome entry.
#=GF RA   Jopling CL, Spriggs KA, Mitchell SA, Stoneley M, Willis AE
#=GF RL   RNA 2004;10:287-298.
#=GF CC   This family represents the L-myc internal ribosome entry site (IRES). The
#=GF CC   myc family of genes when expressed are known to be involved in the control
#=GF CC   of cell growth, differentiation and apoptosis. L-myc undergoes translation
#=GF CC   via internal ribosome entry and bypasses the typical eukaryotic
#=GF CC   cap-dependent translation pathway [1].
#=GF WK   L-myc_internal_ribosome_entry_site_(IRES)
#=GF SQ   11


M19720.1/224-444           AAUGCGC-CUGCAGCUCGCGCUCCCGCGCCGAUCCCGAGAGCGUCCGGGC--CGCCGUGCGCGAGCGAGG----GAGGGCGCGCGCGCGGGGGGGGCGCGCUCGUGAGUGC-GGGCCGCGCUCUCGGCGGCGCGCAUGUGCGUGUGUGCUGGCUGCCG--------GGCUGCCCCGAGCCGGCGGGGAGCCGGUCCGCUCCAGGUGGCGGGCGGCUGGAGCGAGGUGAGGCUGCGGG
X07262.1/108-322           AAUGCGC-CUGCAGCUCGCGCUCCCGCGCCGAUCCCGAGAGCGUCCGGGC--CGCCGUGCGCGAGCGAGG----GAGGGCGCGCG-GCGGGGGGG-CGCGCU-GUGAGUGC-GGGCCGCGCUCUCGGCGG---NCAUGUGCGUGUGUGCUGGCUGCCG--------GGCUGCCCCGAGCCGGCGGGGAGCCGGUCCGCUCCAGGUGGCGGGCGGCUGGAGCGAGGUGAGGCUGCGGG
X13945.1/710-931           AAUGCGC-CUGCAGAUCGCGCUCCCGCGUCGAUCCCGGGAGCGUCCUGGC--UGCCGUGUGCGAGCGAGG----CGGGGGGCGCGCGCACGGGGGGCGCGCUCGUGAGUGCGGGGCCGCGCGCUCGGUGGCGCGCAUGUGUGUGUGUGCGGGCUGCCG--------GGCUUCCCCGAGCCGGCGGGGAGCCGCUCCGCUCCAGGUGGCGGGCGGCGGGAGCGAGGUGAGGCUGCGGG
ABDC01243145.1/6436-6216   AAUGCGC-CUGCAGCUCGCGCUCCCGCGCCGAUCCCGGGAGCGUCCGGGC--UGUCGUGCGCGAGCGAGG----GAGGGGGCGCGCGCGGAAGGGGCGCGCUCGUGAGUGC-GGGCCGCGCGCUCGGUGGCGCGCAUGUGCGUGUGUGCGGGCUGCCU--------GGCUGCCCCGAGCGGGCCGGGAGCCGGUACGCUCCAGGUGGCGGGCGGCGGGCGCGAGGUGAGGCUGCGGG
AAYZ01189975.1/961-737     AAUGCGC-CUGUAGCUCGCGCUCCCGCGCCGAUCCCGGGAGCGUCCGGGC--CGCCGUGCGCGAGCGGGGAGCGGGGGGCGCGCGCGCUCGGGGGGAGCGCUCGGGAGUGA-GGGCCGCGCGCUCGGUGGCGCGCAUGUGCGUGUGUGCGGGCUGCCG--------GGCUGCCCCGAGCCGGCGGGGAGCCGCUCCGCUCCAGGUGGCGGGAGGCGGGAGCGUGGUGAGGCUGCGGG
CR956650.4/44739-44511     AAUGCGC-CUGCAUCUCGCGCUCCCGCGCCGCUCCCGGGAGCGUCCCGGC--AGCCGUGCGCGAGUGAAG----GCGGGAGCGCGCGCGCGGGGGGCGAGCUCCUGAAUGC-GGGCCGCGCGCUCGGUGGCGCGCAUGUGCAUGUGUGCGGGCUGCCGGGCUGCCGGGCUGCCCCGAGCCGGCGGGGAGCCGGUCCGCUCCAGGUGGCCGGCAGCGGGAGCGAGGUGAGGCUGCGGG
AAFC03027628.1/37586-37805 AAUGCGC-CUGCAUCUCGCGCUCCCGCGCCGCUCUCGGGAGCGUCCGGGC--CGCCGUGCGCGAGCGGGG----GCGGGAGCGCGCGCUGGGGG-GCUAACGCCUGUGUGC-GGGCCUCGCACUCGGUGGCGCGCAUGUGCAAGUGUGCGGGCUGCUU--------CGCUGCCCCGAGCGGGCGGGGAGCCGGUCCGCUCCAGGUGGCCGGUGGCGGGAGCGAGGUGAGGCUGCGGG
AAGV020059830.1/1662-1879  AAUGCUC-CGGGAGCUCGCGCUCCCGCGCAGAUCACGGGAGCGCACGGGC--UGCCGUGCGCGAGCGAGG----GUGAGCGCGCGCGCUCUCGAGGCGUGCUCUUGAGUGC-GGGCCGCGCGCUCAGUGGCGCGCAUGUGUAUGUCUGCGGGCUGCCG--------GGCUACCCGCAGCCGGCGGCGAGCCGGUCCGCGCCAGGUGGC---UGGCCGGAGCGAGGUGAGGCUGCGGG
AAEX03009567.1/79923-80142 AAUGCGC-CUGCAUCUCGCGCUCCCGCGCCGAUCCCGGGAGCGUCCGGGC--CGCGGUGCGCGGGCGAGG----GCGGGGGCGCGCGC-GGGGGGGCGCGCUCUAGGGUGC-GGGCCGCGCGCUCGGGGGCGCGCAUGUGCCUGUGUGCGGGCUGCCG--------GGCUGCCCCGAGCCGGCGGGGAGCCGGUCCGCUCCAGGUGGCGGGCGGCGGGAGCGAGGUGAGGCGACGGG
AACZ03006050.1/697-478     AAUGCGC-CUGCAGCUCGCGCUCCCGCGCCGAUCCCGAGAGCGUCCGGGC--CUCCGUGCNCGAGCGAGG----GAGGGCGCGCGCGCGGGGGG-GCGCGCUCGUGAGUGC-UGGCCGCGCUCUCGGCGGCGCGCAUGUGCGUGUGUGCUGGCUGCCG--------GGCUGCCCCGAGCCGGCGGGGAGCCGGUCCGCUCCAGGUGGCGGGCGGCUGGAGCGAGGUGAGGCUGCGGG
AAPE02035639.1/13935-13716 AAUGCGCCU-GCAUCUCGCGCUCCCGCGCCUAUCCCGGUAGCGUC-UGGGGGCUUCGUGCACGAGCGAGG----GA--GAGCGGGCGCGCGUGGGGCGCGCUCUUGGAUGC-GGGUCGCGCGCUCGGUGGCGCGCAUGUGCUUGUGUGCGGGCUGCCG--------GGCUGCCCCGAGCCGGCCCCGAGCGGGUCCGCUCCCGGUGGCGGGCGGCCGGAGCGAGGUGAGACUAGGGG
#=GC SS_cons               ::::::<.<-<--<<<<<<<<____>>>>---AAAA-->>>>-->->>,<..<-<<<<<<<<<-<<__aa....aa__>>->>>>>>>>>>>,<-<<<<<<<<<<____>>.>>>->>>>>->,<<<<<<<<<<<<<<____>>>>>>>-->>>>>>>........,,(((((((,,<<<<<<_____>>>>>>,<<<<<<-<-<<_____>>->->>>>>>,))-)-----)))):
#=GC RF                    AAUGCGC.cugcAgCucGCGCUCCCGCGCcGaUCcCGggaGcGUcCgGGc..cgccGuGCgCGAgcGAGG....gaGGgcGCGcGCgCggggGGGGCgcGCccgcGagUgc.ggGcCgcGCgCUcGGcgGCGCgCaugUGcacguGcGCgGGCugCCg........gGCugCCCCgAgCCgGCgggGAGCcGGucCGCuCCAGGcgGCgGGcgGCuGGaGCGAGGUGAGGCuGcgGG
//
# STOCKHOLM 1.0

#=GF AC   RF00262
#=GF ID   sar
#=GF DE   sar RNA
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Pubmed:9042942, INFERNAL
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   43.00
#=GF TC   44.80
#=GF NC   40.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   9042942
#=GF RT   Antisense RNA control of gene expression in bacteriophage P22. I.
#=GF RT   Structures of sar RNA and its target, ant mRNA.
#=GF RA   Schaefer KL, McClure WR
#=GF RL   RNA 1997;3:141-156.
#=GF CC   Sar RNA is an antisense RNA that is partly responsible for the negative
#=GF CC   regulation of antirepressor synthesis during development of bacteriophage
#=GF CC   P22 [1].
#=GF WK   sar_RNA
#=GF SQ   4


AF527608.1/15090-15023 GUUGGUUUUUCUCCAAGGAUUUACUGACAACCGAAGCCCUGACUGUUACCGCGGUUGGGGCUUCAACU
X01916.1/599-532       GUUGGUUUUUCUCCAAGGAUUUACUGACAACCGAAGCCCUGACUGUUACCGCAGUUGGGGCUUCAACU
AY121861.1/1816-1749   GUUGGUUUUUCUCCAAGGAUUUACUGACAACCGAAGCCCUGACUGUUACCGCAGUUGGGGCUUCAACU
CP000711.1/6497-6564   UCGUUAAUUCCUAUGCGUGGUUUUACGAUACCGAAGCCCUGACUGUUCCCGCAGUUGGGGCUUCAACU
#=GC SS_cons           <<<<<<________________>>>>>>----<<<<<<<<<<<<<<____>>>>>>>>>>>>>>::::
#=GC RF                guggguuUUuCUccAaGgAuUUacucacaACCGAAGCCCUGACuGUUaCCGCaGUUGGGGCUUCAACU
//
# STOCKHOLM 1.0

#=GF AC   RF00263
#=GF ID   SNORA68
#=GF PI   U68
#=GF DE   Small nucleolar RNA SNORA68
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   43.00
#=GF TC   43.30
#=GF NC   42.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.5 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300869;
#=GF DR   snoopy; Loxodonta_africana300439;
#=GF RN   [1]
#=GF RM   9106664
#=GF RT   The family of box ACA small nucleolar RNAs is defined by an evolutionarily
#=GF RT   conserved secondary structure and ubiquitous sequence elements essential
#=GF RT   for RNA accumulation.
#=GF RA   Ganot P, Caizergues-Ferrer M, Kiss T
#=GF RL   Genes Dev 1997;11:941-956.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   U68 is a member of the H/ACA class of small nucleolar RNAs (snoRNAs) which
#=GF CC   act as guides in the the modification of uridines to pseudouridines [2].
#=GF WK   Small_nucleolar_RNA_SNORA68
#=GF SQ   26


Y11162.1/1-133               AUUGCAC-CU---AAACCCAA--GAAUCACUGUU-UCUUAU-AGCGGUGGUUUAAACAGAGGUGCAAACAGC-A-AGCG-GAUCUUGUCGCCUUUGGGGGGCUG-UG-GCCGUGCCCCUCAAAGUGAAUUUGGAGG-UUCCACAACU
AC008474.9/113719-113587     UUCUCAC-CU---AAACCCAA--GAAUCACUGUU-UCUUAU-AGCGGUGGUUUAAACAGAGGUGCAAACAGC-A-AGUG-AAUCUCGUCGCCUUUGCGGGGCUG-UG-GCCAUGCCCCUCAAAGGAAAUUUGGAGG-CUCUACAGCC
AANU01234533.1/2567-2699     CUCUCAC-CU---AAAGCCAA--GAAUCAUUGUU-UCUUGU-AGCGGUGGUUUAAACAGAGUUAUAAACAGC-A-AGUG-AAUCUCGUCGCCUUUGUGGGGCUG-UG-GCCAUGCCCCUCAAAGUGAAUUUAGAGG-CUCUACAGCC
AAQQ01143976.1/1834-1702     CCUGCAC-CU---CAACCCAA--GAAUUGCUGUU-UCUCGU-AGCAGUGGUUUAAACAGAGGUGCUCACAGC-A-AGUG-GAUCUCGUCGCCUUUGAGAGGCUG-UG-GCUGUGCCCCUCAAAGUGAAUUUGGAGG-UUCUACACUC
AANG01185971.1/1373-1505     GAAGCAC-CU---CAACCCAA--GAACUGCUGUU-UCUUGU-AAUAGCGGUUUAAACAGAGGUGCUGACAGC-A-AGUU-GAUCUCGUCGCCUUUGGGGGGCUG-UG-GCCGUGCUCCUCAAAGUGAAUUGAGAGG-UUCUACAGCC
AAPY01778033.1/934-1066      CUCGCAC-CU---AAACCCAA--GGGCCGCGGUU-UGCCGU-AGCUGCGACUUAAACAGGGGUGCGGACAGC-A-AGCG-GACCUCGUCGCCUUUGGGGAGCUG-UG-GCCAUGCCCCUCAAAGUGAAUCUGGAGG-UCCCACACCU
AAFC03006887.1/54868-55001   CAAGCAC-CU---AAACCCAA--GAACUGCUGUU-UCUUGU-AGCAGUGGUUUAAACAGAGGUGCUAACAGC-A-AAUGUUACCUCGUCGCCUUUGUGGGGCUG-CA-GCCGUGCCCCUCAAAGUGAAUUUGGAGG-UUCUACACAC
AAKM01002076.1/56-186        GUUGCAC-CU---AAACCCAA-AGAAUCACUGUU-UCUUGA-AGUGGUGGUUUAAAC--AGGUGCAAACAGC-A-AGCG-AACCUCAUCACCUUUG-GUGGCUG-UG-GCAGUGCCCCUCAAAGUGAACUUAGAAG-CUCUACAUCC
AANN01612551.1/710-579       UUAGCAC-CU---AAACCCAA--CGGCCACUAUU-UAUUAU-AAUAGUGGCUCAAACACAGGUGCUAACAGCAA-AGGG-UACCUCGUCGCCUUUGGAGGAC---UU-GCUGUGCCCUUCAAAGUGAACUUAGAGG-UUCUACACAC
AAIY01069146.1/1428-1297     CUUGCAC-CC---AAACCCAA--GGACUGUGGCU-UCUCGU-AGCAGCAGUUUAAAGAGUGGUGCGCACAGA-A-AGUG-GGCCUUGUCGCCUUUGAGGGGCUG-UG--CAGUGCCCCUCAGAGUGAAUGUGAAGG-UUCGACAAGC
AALT01055144.1/1338-1206     CAAGCAC-CU---AAACCCAA--GAGCUGUUACU-UCUUAU-AGUACCAGCUUAAAUAGAGGUACUGACAGG-A-AACA-CACCUCCUCACCUUUAGGGAGGCU-UG-CCUGUGGCCCUCAAAGUGAAUUUAGAGG-UUUUACAACC
AC019302.14/153716-153846    CUGGCAC-CC----AACCCAA--GAACUGUCGCU-GCCUGU-AGCGGCUGUUUAAAUAGUGGUGCACACAGC-A-AAGG-GGCUUCGUCGCCUUUGGGGGGCUG-UG--CAGUGCCCCCCAGAGUGAAUCAGUAGG-CUCUACAGAA
AAFR03031274.1/75999-76135   CUUGCAC-CC---AAACCCCAAAAGAUCUUUGUU-UUUCCUUAACAAUGAUCUUUUCUUGGGUGCAAACAUC-A-AAAG-AACCUUGUCGCCUUUCUGGAGCUGAUA-AAAGUGCCCCAGAAAGUGAAAUAGUGGG-UUCUACAUUC
AB005653.1/1285-1413         UUGGCAC-CC----AACCCAA--GAACUGCCGCU-AC-UAU-AGCGGCUGUUUAAACAGUGGUGCACACAGC-A-AA-G-UGCUUCGUCGCCUUUGGGGGGCUG-UG--CAGUGCCCUCCAGAGUGAAUCAGGAGG-UUCUACAGUU
AADA01170112.1/362-489       GUCGCAC-UU---AAACUUAA--GACUCUU--UU-UCUUGC-AGCAGUGGUUUAAACAGAGGAACAAACAGG-A-A----GAUCUUGUCGCCUUUGAGGGGCUG-UG-GUUGGGCCCCUCAAAGUGACUUUGGAGG-UUCUACGCCA
AAPN01184835.1/1500-1362     ACUGCAC-CCCCAAGCCCCAA--AGAUCAUUGUUUCCUUCUUCACAAUGAUCUUAUCUGGGGUGCUGACAUC-A-AUUG-UACCUCGUCGCCUUUCAAGAGCUG-UUCGAAGUGCUCCUGAAAGUGAAAUGGAAGG-UUCAACAUAU
AAKN02046884.1/23494-23626   CUUGCAC-CU---CAACCCAA--GAACCGCCACU-UCCCGU-AGUGACGGUUUAAACAGGGGUGCACAUAGU-A-AGUG-GAUCUCGUCGCCUUUGGAGGGCUG-UG-GCUGUGCCCACCAAAGUGAAUUUGGAGG-UUCCACACCC
AAGV020559111.1/2197-2066    CCCGCGC-CC---AAACCCAA--GAGCCGCCGUU-UGCGGU-AACGGCGGCUCAAGCAGCGGCGCGGACAGC-A-CGCG-AGCCUCGUCGCCUUUGGGGGGCUG-UG--CCGUGCCCCCCGGAGUGAAUGUGGAGG-UUCGACAGGC
AADN03001201.1/163886-163755 AAUGCAC-ACA-AAAACCCAA--AGAAUGUUGUU-CCUCGU-AAUGACGUUCUUGUCGUGUGUGCAGAUAUU-A-UAUG-UAUCUUGUCGCCUUUCCAGAGCUG-AG-GU---GCUCUUGAAAGUGAAACUUGAGG-UUCUACAUGA
AAWZ02000196.1/23785-23656   ACUGCAU-AC---AAACCCAA--AGAGCAUUGUU-UAUAAA-UAAAAUGUUCUUGUCAUGUGUGCAGAUAUG-A-AAUG-UACCUUGUCGCCUUUCAAGAGCUG-AA-GU---GUUUUUGAAAGUGAAAUUGAAGG-UCCUACAAUU
AAEX03012289.1/62549-62416   CCAGCAC-CU---CAACCCAA--GAACUGCUGUU-UCUCAU-AGCAGCGGUUUAAACAGAGGUGCUAACAGC-AAAGUG-GAUCUCGUCGCCUUUGGGGGGCUG-UG-GCUGUGCUCCUCAAAGUGAAUUUGGAGG-UUCUACACCC
AAQR03004723.1/28297-28425   UUUGCAC-CU---AAACUCCA--AAAUUGCUGUU--AAUAU-AGCAGUGAUUUAAACAGAUGUGCAGACA-----AGUG-GAUCUCAUCACCUUUGGAGGGCUG-UG-ACUAUGCCCCUCAAAGUGAAUGUGGAG-GUUCUAUAUCC
AAPE02055521.1/11137-11266   CAAGCAC-CU---AAACCCAA--GAACUGCUGUU-UGCUGU-AGCUGCAGUUGAAAC--AGGUGCUAACAGC-A-AGUG-GAUCUUGUCGCCUUUG-GGGGCUG-UG-ACUGUGCCCCUCAAAGUGAAUUGGAAGG-UUCUACACUC
AAGU03050420.1/23208-23077   CUUGCAC-CC---AAACCCAA--GAACCGCAGUU-UCUCGU-AGCGGCGGUUUAAACAGUGGUGCACACAGC-A-AAUG-GACCUUGUCGCCUUUGGGGAGCUG-U--CCCAUGCCCCCCAGAGUGAAUAUGGAGG-UUCUACACCC
AAGW02002827.1/10798-10927   UGCCCAUACU---AAACCCAA--GAAUCACAGUU---GUGU-AGCAGUGAUUUAAACACAGGUGUGCACAGC-A-AGUG-GAUCUCAUCGCCUUU--GGGGCUG-AG-GCUGUGCCACUGGAAGUGAAUCUGGAAG-UCUUACACCC
FM165404.1/1-130             UGCACAC-AA---AAACCCAA--AGAAUGUUGUU-CCUCGU-AAUGACGUUCUUGUCGUGUGUGCAGAUAUU-A-UAUG-UAUCUUGUCGCCUUUCCAGAGCUG-AG-GU---GCUCUUGAAAGUGAAACUUGAGG-UUCUACAUGA
#=GC SS_cons                 :<<<<<<.<<...--------..-<<<<<<<<<<.______.>>>>>>>>>>------->>>>>>>>-----.-.---<.<<<<<<-----<<<<<<<<<<<__.__._____>>>>>>>>>>>-------->>>>.>>>:::::::
#=GC RF                      uccgCAC.cu...AAACCCAA..ggaccgcugcU.UcUugU.AgcagcggucUAAaCAgagGUGcggACAgc.A.AguG.gacCUcGUCGCCUuUgggggGCUG.Ug.gcuGUGCcccccAaAGUGAAuuuggAGg.ucCUACAuuc
//
# STOCKHOLM 1.0

#=GF AC   RF00264
#=GF ID   SNORA64
#=GF PI   U64
#=GF DE   Small nucleolar RNA SNORA64/SNORA10 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:10487763, Daub J
#=GF SS   Published; PMID:10487763
#=GF GA   35.00
#=GF TC   35.30
#=GF NC   34.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF CL   CL00041
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300780;
#=GF DR   snoopy; Echinops_telfairi300096;
#=GF RN   [1]
#=GF RM   10487763
#=GF RT   Nucleolar localization signals of box H/ACA small nucleolar RNAs.
#=GF RA   Narayanan A, Lukowiak A, Jady BE, Dragon F, Kiss T, Terns RM, Terns MP
#=GF RL   EMBO J 1999;18:5120-5130.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   This family belongs to the H/ACA class of small nucleolar RNAs (snoRNAs)
#=GF CC   which act as guides in the the modification of uridines to pseudouridines
#=GF CC   [2]. This family includes the human snoRNAs U64 and ACA10 and mouse
#=GF CC   MBI-29.
#=GF WK   Small_nucleolar_RNA_SNORA64/SNORA10_family
#=GF SQ   9


AJ609432.1/1-133         GGUCUCUCAGCUCCGCUUAACCACAC---GGGUCCAGUGUGUGCUUGGCGUGUUUUCAGGGAGGCAGAGAAAGGCUCUCCUAAUGCACGACAGACCCGCCCAGAA-UGGCCUCUCUGUUCCU-AGGAGUGCGACAAUU
AB007147.1/104-236       GGUCUCUCAGCUCCGCUUAACCACAC---GGGUCCAGUGUGUGCUUGGCGUGUUUUCAGGGAGGCAGAGAAAGGCUCUCCUAAUGNACGACAGACCCGCCCAGAA-UGGCCUCUCUGUUCCU-AGGAGUGCGACAAUU
AC016907.6/186868-187000 GGUCUCUCAGCUCUGCUUAACCACAC---GGGUCCAGUGUGUGCUUGGCGUGUUUUCAGGGAGGCAGAGAAAGGCUCUCCUAAUGCACGACAGACCCGCCCAGAA-UGGCCUCUCUGUUCCU-AGGAGUGUGACAAUU
AC026222.5/26043-25912   GGCCUCUCAGUUCCGCUUAAUCACAC---AGGUCCAGUGUGUGCUUGGUGUCUUUUCUGGGAGGCAGAGGAAGGCUCUCCUAAU-CACAACAGACCUGCCCAGAA-GGGCCUCUCUAUUUCU-AGGAGUAUGAUAGCU
AC008083.23/27997-28128  GGCCUCUCAGUGCCGCUUAAUCACAC---AGGUCCAGUGUGUGCUUGGUGUCUUUUCUGGGAGGCAGAGGAAGGCUCUCCUAAU-CACAACAGACCUGCCCAGAA-GGGCCUCUCUAUUUCU-AGGAGUAUGAUAGCU
AC011891.3/54747-54616   ACACUCUCAGCUAUGUAUAGUUACACCUGGCUUCACUUGUGUGACUUUUGCAA---UGGGAAGAGAGAGAGAAGGUCCCCUUGGU-ACCUCAGCUCGGCCUUAUGGUGGCC--UCUUUCCUUGAAGGGUGCAACAAAA
AC099331.2/140721-140854 AGACUCCCAGCUCUGCCCAGUUACACUAGGCUUCGCCUGUGUGGCUUCUGUAA---UGGGGAGGGAGAGAAAGGAUCUCCCCAGG-ACCUCAGAUUGGCUUUACUGUGGCAUCUCUUUCCUUGAGGGACACAAUAGGU
Y11158.1/1-134           ACUCUCUCGGCUCUGCAUAGUUGCACUUGGCUUCACCCGUGUGACUUUCGUAA---CGGGGAGAGAGAGAAAAGAUCUCCUCAGG-ACCUCGGAUGGGCCUUACUGUGGCCUCUCUUUCCUUGAGGGGUGCAACAGGC
BC063011.1/424-557       ACUCUCUCGGCUCUGCAUAGUUGCACUUGGCUUCACCCGUGUGACUUUCGUAA---CGGGGAGAGAGAGAAAAGAUCUCCUCAGG-ACCUCGGAUGGGCCUUACUGUGGCCUCUCUUUCCUUGAGGGGUGCAACAGGC
#=GC SS_cons             :<<<<<<<--<<<<<---<<<<<<<<____________>>>>>>>>-------...>>>>>->>>>>>>-------<<<<<<<<<.-----<<<-<<<<<_______>>>>>->>>--->>>>>>>>>::::::::::
#=GC RF                  acuCUccCAGcuCcGCuUAgucaCACuuGGguUCaagUGUGugacUuuuGUau...CgGggAGggAGagAAAgGaUCuCCucagg.ACauCaGaucgGCCuuaaaGUGGCcgCuCuuUuccugaGGaGUgcaAcAguu
//
# STOCKHOLM 1.0

#=GF AC   RF00265
#=GF ID   SNORA69
#=GF PI   U69
#=GF DE   Small nucleolar RNA SNORA69
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   http://ribosome.miyazaki-med.ac.jp/, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   47.00
#=GF TC   48.20
#=GF NC   44.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300829;
#=GF DR   snoopy; Danio_rerio300125;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   U69 is a member of the H/ACA class of small nucleolar RNAs (snoRNAs) which
#=GF CC   act as guides in the the modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA69
#=GF SQ   16


Y11163.1/1-132             AAAGCAGGUUGCAAUUACAGUGCUUCAUUUU-GUG------GAAGUACUGCCAUUAUCCUGCUGAAAGAA-AAGC-CGUGUU-AAUCA-UUUUUGAUUUUGCCUU-UA-UGAGGGU-AAAAUCAUGACAGAUUGACAUGGACAAUU
AL451076.14/9592-9462      AAAGCAGGUAGCAAUUACAGUGCUUCAUUUU-GUG------GGAGUACUGCCAUUAUCCUGCUGAAAGAA-AAGC-CAUGUU-GGUUG-UUUCUGAUUUUUGCUU-U--UGGGGUA-AAAAUCGUGACACCUUGACAUGAACAGUU
AF357420.1/1-122           ---------AGCAAUUACAGUGCUUCAUUUU-GUG------GGAGUACUGCCAUUAUCCUGCUGAAAGAA-AAGC-CAUGUU-GGUUG-UUUCUGAUUUUUGCUU-U--UGGGGUA-AAAAUCGUGACACCUUGACAUGAACAGUU
AAQQ01738740.1/317-187     AGAGCAGGUUGCAAUUACAGUGCUUCAUUUU-GUG------GAAGUACUGCCAUUAUCCUGCUGAAAGAA-AAGC-UAUGUU-GAUCA-UUUUUGAUUUUGCCUU-C--UGGGGGU-AAAAUCAUGACAGAUUGACAUGGACAAUU
AAPY01384073.1/257-126     AAAGCAGGUUGCAAUUACAGUGCUUCAUUUU-GUG------GAAGUACUGCCAUUAUCCUGCUGAAAGAA-AAGC-UGUGUU-GAUCG-UUAUUGAUUUUGCCCA-UA-UGGGGGU-AAAAUCAGGACAGAUUGGCAUGGACAAUU
AANG01458023.1/2010-1879   AAAGCAGGUUGCAAUUACAGUGCUUCGUUUU-GUG------GAAGUACUGACAUUAUCCUGCUGAAAGAA-AAAC-AGUGUU-GAUCA-UUUUUGAUUUUGCCUC-UC-UGAGGGU-AAAAUCAGGACAGAUUGACAUGGACAAUU
AAFC03106839.1/13057-12924 AAAGCAGGUUGCAAUUACAGUGCUUUCUUUU-GUG------GAAGUAUUGACAUUAUCCUGCUGAAAGAA-AAUC-UGUGUU-GAUCGUUUUUUGAUUUUGCCAU-UUAUGGGGGU-AAAAUCAUGACAGAUUGACAUGAACAGUU
ABDC01119942.1/12639-12507 UACGCAGGUUGUAAUUACAGUGCUUUGUUUU-GGG------GAAGUACUGCUGUUAUCCUGCUGAAAGAC-AAGC-UGUGUU-AGUCA-UUUUUGAUUUUGCCUU-UA-UGAGGGUAAAAAUCAUGACAGAUUGGCAUGGACAAUU
AANU01204711.1/10197-10060 AAAGCAAGCUGCAAUUACAGUGCUUCAUUUU-GUGAAAUACUAAAUACUGCCAUUAUCCUGCUGAAAGAA-AAGC-UGUGUU-AAUGA-UUUUUGAUUUUGUCUU-UG-UGAGAGU-AAAAUCAUGACAGAUUGACAUGGACAAUU
AAIY01660259.1/2985-3115   AAAGCAGGCUGCAAUUACAGUACUUCAGUUU-GUG------GAAGUACUGCCAUUAUCCUGCUGAGAGAAAAAGC-CAUGUU-GGCCG-GCUCUGGUUUUGCCUC-U--U-CAGGU-GAGAUCAUGACCGGUUAGCAUGUACAAUU
AALT01504839.1/3774-3641   UGAGCAGGUUGCAGUUCCAGUCCUUUGUUUUCGUG------GGAGUGCUGGCAUAACCCUGCUGAAAACA-AAUA-UGUGCC-AAUCA-UUUUUUAUUUUACCUCAUU-CGGAGGU-AAAAUGAUCACUGAUUAGCACAGACAGUU
AAWR02033858.1/20008-19876 UAAGCAGGUUGCAAUUACAGUGCUUCAUUUU-GUG------GAAGUACUGACAUUAUCCUGCUGAAAGAA-AAUCUUGUGUG-GAUCA-UUUUUGAUUUUGCCUU-UG-UGAGGGU-AAAAUCAUGACAGAUUGACAUGGACAAUU
AAQR03131765.1/1482-1350   AAAGCAGGUUGCAAUUACAGUACUUCAUUCU-GUG------GAAGUAUUGCCAUUAUCCUGCUGAAAGAA-AAGC-CGUGUUUAAUCA-UUUCCGGGUUUGCCUG-UA-UGGGGGU-AAAAUCCUAACAGAUUGACACGGACAAUU
AAEX03026831.1/32223-32092 AAAGCAGGUUGCAAUUACAGUGCUUCAUUUU-GUG------GAAGUACUGACAUUACCCUGCUGAAAGAA-AAUG-UGUGUC-GAUCA-UUUUUGAUUUUGCCUU-UA-UGAGGGU-AAAAUCAUGACAGAUUGAUAUGGACAAUU
AC198461.3/169981-169844   AAAGCAAGCUGGAAUUGCAGUGCUUCAUUUU-GUGAAAUACUAAAUACCAUCAUUAUGCUGCUGAAAGAA-AAGC-UGUUUU-AAUGA-UUUUUGAUUUUGUCUU-UG-UGAGAGU-AAAAUCACGACAGAUUGACAUGGACAAUU
AAGW02041626.1/24583-24452 AAAGCAGGUUGCAAUUACAGUGCUUUAUUUU-GUG------AAAGUACUGUCAUUAUCCUGCUGAAAGAA-AAGC-UGUGUU-GGUCC-UUUUUGAUUUUGCCAC-UG-UGCUGGU-AAAAUCAUGACAGACUGACAUCGACAAUU
#=GC SS_cons               ::<<<<<<---------<<<<<<<<<_____.___......>>>>>>>>>------->>>>>>-------.---<.<<<<<<.<<<<-.----<<<<<<<<<<<<.__.__>>>>>.>>>>>>>----->>>>>>>>>>>::::::
#=GC RF                    aAaGCaGGuUGcAAUUACaGugCuucaUUUU.GUG......gaaGcaCuGcCAUUAUCCuGCuGAAAGAA.AAgc.cguGuc.aauca.UUUuugauuuugcCcc.Ua.UGggGgc.aaaaucaugACagauugaCacggACAaUU
//
# STOCKHOLM 1.0

#=GF AC   RF00266
#=GF ID   snoZ17
#=GF DE   Small nucleolar RNA Z17
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   http://ribosome.miyazaki-med.ac.jp/, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   44.00
#=GF TC   44.70
#=GF NC   42.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF CL   CL00053
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300938;
#=GF DR   snoopy; Loxodonta_africana300514;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   Z17 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z17
#=GF SQ   26


AJ224024.1/1-72            GGUGCAGAUGAUGAC-ACUGUAAAGCGACCAAAGUCUGAACAAAG-UGAUUGGU-ACCUCGUUGUCUGA-UGCACC
AF001689.1/2296-2367       GGUGCAGAUGAUGAC-ACUGUAAAGCGACCAAAGUCUGAACAAAG-UGAUUGGU-ACCUCGUUGUCUGA-UGCACC
AF001689.1/3399-3470       GGUGCAAAUGAUGCA-UAUGUUA-GCGACCAAAGCCUGAUCUUUGCUGAUUAGU--CAUAAUUAACUGACUGCACC
AJ224025.1/2-73            GGUGCAAAUGAUGCA-UAUGUUA-GCGACCAAAGCCUGAUCUUUGCUGAUUAGU--CAUAAUUAACUGACUGCACC
ABDC01347295.1/8749-8820   GGUGCAAAUGAUGAC-ACUGUAAAGCGACCAAAGUCUGACCAAAA-UGAUUUCU-ACCUCAUUAUCUGA-UGCACC
AANN01481002.1/718-646     GGUGCAAAUGAUGAU-UCUGUAUAGCGACCAAAGUCUGAGAAAGGCUGAUUUCU-AUCUCAUUGUCUGA-UGCACC
AANU01205354.1/3441-3512   GGUGCAGGUGAUGAC-ACUGUAAAACGACCAAAGUCUGAACAAAA-UGAUUGGU-ACCUCGUUGUCUGA-UGCCCU
AAYZ01187588.1/1075-1145   GGUGCACAUGAUGAC-AUUAUUUAGCGACCAAAGUCUGAUGAAGA-UGAUUGCA--CCUCAUUGUCUGA-UGCACC
AAPY01743681.1/8244-8314   GGUGCAAAUGAUGAC-AUUAUUCAGCGACCAAAGUCUGACAGAAA-UGAUUGCU--UCUCAAUGUCUGA-UGCACC
AALT01536072.1/657-587     GGUGCAAAUGAUGAC-ACUAUUAAGCGACCAAAGUCUGACAAAAG-UGAUUGCU--ACUCAGUGUCUGA-UGCAAC
AAQQ01709973.1/1321-1391   GGUGCAGCUGAUGAC-AGCAUUUAGCGACCAAAGUCUGAUGAAAC-UGAUUGCU--ACUUAUUGUCUGA-UGCACC
AAHY01094589.1/16207-16137 GGUGCAUGUGAUGAC-AUUAUUUAGCGACCAAAGUCUGAUAAAGA-UGAUUGUG--AUCUAUUGUCUGA-UGCACC
AAFR03044819.1/3240-3311   GGUGCAGAUGAUGAU-AUCUAUA-GCGACCAAAGUCUGAGUAAAA-UGAUAGGCAACUUCAGUGUCUGA-UGCACC
AAPN01416195.1/1477-1545   GGUGCAGAUGAUGAC-AUCACA--GCGACCAAAGCCUGAGUAAA--UGAUUGCA-ACCUCACUGGCUGA-UGCACC
AAIY01565342.1/752-821     GGUGCAAAUGAUGACAUCUAUUCAGCGACCAAAGUCUGAUCAAAA-UGAUUGCU-AUUUAGU---CUGA-UGCACU
AAGV020173148.1/4127-4193  GGUGCAAAUGCUGCA-CC-GUUA-GUGACCAAAGCCUGACUUUAGAUGAUUAGU------CUUAACUGACUGCACC
AAKN02033341.1/2087-2018   GGUGCAAAUGAUGAA-UCUGUUA-GCGACCAAAGCCUGACUUC--CUGAUUAGU--CACAACUGACUGACUGCACC
AAWR02013172.1/62940-63011 GGUGCAAAUGAUGUG-UAUGUUA-GCGACCAAAGCCUGACCUUUGCUGAUUAGG--CCUAACUGACUGACUGUACC
AAHX01064981.1/3059-2989   GGUGCAUAUGAUGAC-AUUAUUUAGCGACCAAAGUCUGAUGCAGA-UGAUUGCA--GUCUAUUGUCUGA-UGCACC
AAPE02030647.1/4780-4852   GGUGCAAAUGAUGUG-UCUUAUUAGCGACCAAAGCCUGACUUUUGCUGAUUAGU--CUUAACUGACUGACUGCACC
AAGU03065331.1/66667-66738 GGUGCAGAUGAUGCC-UCUGUUA-GUGACCAAAGCCUGAUGUUUGGUGAUGAGU--CUUAACUGACUGACUGCACC
AAEX03006669.1/8655-8726   GGUGCAGAUGAUGAC-ACUGUUUAGCGACCAAAGUCUGACAAAAA-UGAUUGCU-ACUUCAUUGUCUGA-UGCACC
AAGW02049846.1/3359-3288   GGUGCACGUGAUGAC-AUUGUUAAGCGACCAAAGUCUGAUAAAGA-UGAUUGCU-ACCUCAUGGUCUGA-UGCACC
AJ010678.1/1-71            GGUGCAUGUGAUGAC-AUUAUUUAGCGACCAAAGUCUGAUAAAGA-UGAUUGUG--AUCUAUUGUCUGA-UGCACC
EU094074.1/4-72            GGUGCAGAUGAUGAC-AUCAC--AGCGACCAAAGCCUGAGUAAA--UGAUUGCA-ACCUCACUGGCUGA-UGCACC
EU094073.1/3-71            GAUGCAAAUGAUGAA-CC---GUAGUGACCAAAGCCUGAACCUUGGUGAUGAAG--CUUGACCACGUGA-UGCAUC
#=GC SS_cons               <<<<<<_________._____________________________.________.._____________.>>>>>>
#=GC RF                    GGUGCAaAUGAUGAc.acUgUUaAGCGACCAAAGuCUGAuuaaaa.UGAUUggu..cuUcAuUGuCUGA.UGCACC
//
# STOCKHOLM 1.0

#=GF AC   RF00267
#=GF ID   snoR64
#=GF DE   Small nucleolar RNA R64/Z200 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   45.00
#=GF TC   45.90
#=GF NC   43.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol 2002;12:2002-2013.
#=GF CC   This family of plant small nucleolar RNAs belong to the C/D class of
#=GF CC   snoRNA which contain the C (UGAUGA) and D (CUGA) box motifs. This family
#=GF CC   includes Arabidopsis thaliana snoRNA R64 and Oryza sativa snoRNAs Z200 and
#=GF CC   J16. Most of the members of the box C/D family function in directing
#=GF CC   site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_R64/Z200_family
#=GF SQ   14


AP004752.3/112622-112715   AAAAAGCAAUUAGGAAUCAUGAAA---ACGUUCGCAUGUCAGACUUCAGAGAUGCCAUGG-------CAUUAAUGAGAAGAU-GUUUUCAUUUU-CUGAGCUUAUA
AJ490459.1/2-95            AAAAAGCAAUGAGGAAUCAUGAAA---ACUUUCGCAUGUCAGACUUCAGAGAUGCCAUGG-------CAUUAAUGAGAAGAU-GUUUUCAUUUU-CUGAGCUUAUA
AP004591.3/13337-13431     AAAAAUGCUAUGAGGAAUCAUGAAA--ACUUUCGCAUGUCAGACUUCAGAGAUGCCAUGG-------CAUCAAUGAGAAGAU-GUUUUCAUUUU-CUGAGCUUAUA
AJ490465.1/2-92            AAAAUGCUAUGAGGAAUCAUGAAA---ACUUUCGCAUGUCAGACUUCAGAGAUGCCAUGG-------CAUCAAUGAGAAGAU-GUUUUCAUUUU-CUGAGC---UU
AJ457082.1/314-407         UUGUUGCGAGGAUGAAUUAUGAACA--AACUUCGCAUGUCAGACUUCGGAGAUG-CUUCA----AAGCAUCCAUGAGAAGAC-AUGUCAUACGA-CUGAGCAA---
AC147499.5/74642-74736     GUAUUGCUGUGAUGAAUUAAGAAA---AAUUUCACAUGUCAGACUUCAGAGAUU-UUUAU-------AAUCAAUGAGAAUGACAAUUCUUAAUUUCUGAGCUGGAU
AF317988.1/2-96            CUUCUGCUGUGAUGAUCUUUUGAAUA-AAAUUCACAUGUCAGACUUCAGAGAUC-UUU-U-------GAUCUAUGAGAAAAAACAUUCAUAAUU-CUGAGCAGAAG
AF317987.1/2-93            CUUCUGCGGUGAUGAUUUUAUGAG---AAAUUCACAUGUCAGACUUCAGAGAUU-CUUGU-------AAUCUAUGAGAAUAA--AUUCAUAUAU-CUGAGCAGAAG
AC138464.19/31802-31707    UUUUUGUGGUGAUAAUUAUAGAAGA--AAAUUCACAUCUCAGACUUUAGAGAUU-UUCAU-------GAUCAAUGAGAAUGUCAAUUCUUAUUCGCAAAGCAAAAA
AC138464.19/49742-49649    UUUCUGCAGUGAAGAAUGAAGAAGA--AAAUUCACAUGUUAGACUCUAGAGAUU-UUUAU-------GAUCAAUGAGAAUGG-CAACUUAUUCA-CUAAGCAGAAA
AASG02003290.1/4244-4338   CUUCUGCGGUGAUGAAUUUAUGAAAACCAAUUCACAUGUCAGACUUCAGAGAUU-CUU-C-------AAUCAAUGAGAAGAA-AUUUCAUACUU-CUGAGCAGAAG
AC189232.1/54652-54754     CUUGUGCUAUGAUGAUCUUUUGAAUA-AAAUUCACAUGUCAGACUUCAGAGAUU-CUUCUAAUUAAGAAUCCAUGAGAAUAAAUAUUCAUAAUU-CUGAGCACAAG
AARH01002391.1/42426-42331 CUUCUGCAGUGAUGAAGUCAUGGAGUAAGAUCCACAUGUCAGACUUCAGAGAUU-UUU---------AAUCGAUGAGAAGAGACUUCCAUAACUUCUGAGCAGAAU
AM479394.1/455-360         CUUCUGCGAUGAUGAAGUAUGAAAA--CAAUUCACAUGUCAGACUUCAGAGAUU-UUUAA------AAAUCUAUGAGAAGAA-AAUUCAUAUUUUCUGAGCAGAAG
#=GC SS_cons               <<<<<<<------------------..-----------------------<<<<._____.......>>>>-----------.-----------.---->>>>>>>
#=GC RF                    cuucuGCaaUGAuGAauuaagaAAa..AaaUUCACAUGUCAGACUUCAGAGAUu.cUUau.......aAUCaAUGAGAAgAa.auUUcauauuU.CUGAGCagaag
//
# STOCKHOLM 1.0

#=GF AC   RF00268
#=GF ID   snoZ7
#=GF PI   snoR77
#=GF DE   Small nucleolar RNA snoZ7/snoR77
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
#=GF SS   Predicted; PFOLD
#=GF GA   43.00
#=GF TC   43.40
#=GF NC   42.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.81 -Z 549862.597050 CM SEQDB
#=GF CL   CL00057
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300111;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol 2002;12:2002-2013.
#=GF CC   snoZ7 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_snoZ7/snoR77
#=GF SQ   5



AC235267.1/40198-40265 CCGAUGAGGAUUAGAUUUAAAU--UGGAAUUACCGUCUGA------U-CUUUGAUGAGAA--UUUCUGGCUGACUGAGG
AC007233.7/16999-17076 CCGAUGAUGAUUAUUGCUAAACUAUGGAAUUACCGUCUGAGUUUAUU-CUUUGACGAGAAAAACGCUGGCUUACUGAGG
AJ010674.1/1-79        CCGAUGAUGAUUAUUGCGAAAAUAUGGAAUUACCGUCUGAGUUAAUUUCUUUGAUGUUAAAAACGCUGGCUAACUGAGG
DQ108823.1/555-632     CCGAUGAUGAUUAUUGCUAAACUAUGGAAUUACCGUCUGAGUUUAUU-CUUUGACGAGAAAAACGCUGGCUUACUGAGG
AK117712.1/558-635     CCGAUGAUGAUUAUUGCUAAACUAUGGAAUUACCGUCUGAGUUUAUU-CUUUGACGAGAAAAACGCUGGCUUACUGAGG
#=GC SS_cons           <<_____________________________________________._____________________________>>
#=GC RF                CCGAUGAuGAUUAuUgcuAAAcUAUGGAAUUACCGUCUGAGUUuAUU.CUUUGAuGAGAAAAAcgCUGGCUuACUGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF00270
#=GF ID   SNORD61
#=GF PI   U61
#=GF DE   Small nucleolar RNA SNORD61
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   43.00
#=GF TC   43.20
#=GF NC   42.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00067
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300832;
#=GF DR   snoopy; Danio_rerio300124;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   U61 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD61
#=GF SQ   36


X96661.1/1-73                GCUAUGAUGAAUU--UGAUUG------C-AUUGAUCGUCU-GACAUGAU-AAUGUAUU---UUUGUCCUCUAAGAAGUUCUGA-GCUU
AF266720.1/161-233           GCUAUGAUGAAUU--UGAUUG------C-AUUGAUCGUCU-GACAUGAU-AAUGUAUU---UUUGUCCUCUAAGAAGUUCUGA-GCUU
AL672106.9/106229-106159     GCUGUGAUGAAUU--UGAAUC------C-ACUGAUCUUCC-GACAUGAUAAAUGCAUU------GUCCUCUAAGAAGUUCUGA-GCUU
AAPY01386508.1/870-799       GCUGUGAUGAAUU--UGAUUA------C-ACUGAUCAUCU-GACAUGAU-AAUGUAUU----UUGUCCUCUAAGAAGUUCUGA-GCUU
ABDC01371259.1/3997-3928     GCUAUGAUGAAUU--UGAUUG------C-ACUGAUCAUAU-GAUAUGAU-AACGUAUU------GUCCUCUAAGAAGUUCUGA-GCUU
AAFC03028609.1/18530-18459   GCUAUGAUGACUU--UGAUUG------C-AUUGAUCACAU-GAAAUGAU-AAUGUGCU----UUGUCCUCUAAGAAGUUCUGA-GCUU
AANG01460325.1/234-166       GCUGUGAUGAAUU--UGAUUA------C-GUUGAUCGUCU-GACGUGAU-A---CAUU----UUGUCCUCUAAGAAGUUCUGA-GCUU
AAPN01018488.1/457-529       UCCAUGAUGAAUU--UCACGG------C-GUUGAUCGUCC-GAAGUGAU-GAUGCAUC---CUUGUCCUCUAAGAAGUUCUGA-GAUC
BAAF04075663.1/1933-1863     GCUGUGAUGAUCU--UUAUGG------U-UUUGAUGA-AG-GAUGAAAU-AAACAAAC----CGUUCCUCUAAGAAGUUCUGA-GCUC
BAAE01189781.1/4141-4075     GCUGUGAUGAUCU--UUAUGG------U-UUUGAUGA-------AGGAU-GAAAUAAA---CCGUUCCUCUAAGAAGUUCUGA-GCUC
BAAF04075663.1/4458-4383     GCCAUGAUGAACU--UGUGUGUUUGAUC-AGUGAUGAACU-GAAACAAC-A--CAACU----CAUUCCUCUAAGAAGUUCUGA-GCUC
AACT01002366.1/14510-14440   GCUGUGAUGACUUCCUUACUC------A-UCUGAAUAU-U-GUGAUGAG-CACAAAUU------GUCCUCUAAGAAGUACUGA-GCUU
AAVX01084559.1/715-787       GCAAUGAUGACUU--CACUGG------C-ACUGACACUUU-GAACUGAU-UUUGCCUU---AUUUUCCUCUAAGAAGUUCUGA-GCUU
AANN01374732.1/407-342       GCUGUGAUGAAUU--UAAUUA------A-AUUGAUCAUCU-GAUUUUA-------CUG----UUGUCCUCUAAGAAGUUCUGA-GCUU
AL929434.3/99848-99772       GCUGUGAUGAAUU-CUUGUGG------U-GGUGAUCUACUUGAACUGAU-CUAGUCCAC-AAUUGUCCUCUAAGAAGUUCUGA-GCUU
AANH01012428.1/2998-2926     GCGAUGAUGAUGU--UUUUUG------G-UUU--UGAGCA-GCACUGAA-AAAGAACUA-CCAAUUCCUCUAAGAAGUUCUGA-GCUC
AL929434.3/101169-101092     GCUGUGAUGUUUU--UUUUUGU---GGC-AGUGAUCUACUUGAGCUGAU-CUAGUCCAC--AAUUUCCUCUAAGAAGUUCUGA-GCUU
AAFR03051555.1/28725-28801   GCGAUGAUGAAUG--UCAAUU------CUAUUGAACUUAU-GAAGUGAU-GAUGUAUUUGUUGUUUACUCUAAGAAGUUCUGA-GCUG
CAAE01007262.1/14447-14519   GCAAUGAUGACCU--UCA-GC------U-UUUGAGCAAGG-GAUGAAAA-UAACCUCAG--CAAUUCCUCUAAGAAGUUCUGA-GCUC
AABS01000002.1/837566-837501 GCUGUGAUGACUU--UCUUAC-------------UCAUCU-GAAUUCUU-GAUGAGAA----AAUUCCUCUAAGAAGUGCUGA-GCUU
ABAV01033144.1/1175-1105     GGAAGGAUGAACC-AUAAUCG------C-UACAAUGAUCA-AGAGUGAU-UAUACACU------UUCCUCUAAGAAGUUCUGA-CCAG
AANU01279689.1/53293-53222   GUAGGGAUUAUUG--AAAAUU------U-AAGUAGCAUAA-UCAAUGUA-AUAUUAUU----UUGUCCUCUAAGAAGUACUGC-ACAU
AAKN02048065.1/14805-14877   GCUGUGAUGAAUU--UGAUUG------A-AUUGAUAAUCU-GACAUGAU-AAUGUAUU---UUUGUCCUCUAAGAAGUUCUGA-GCUU
AAGV020470516.1/1302-1237    GCUGUGAUGAGUU--UGAUUG------C-AUUGAUCAUCG-GAGAUG--------AUU---UUUGUCCUCUAAGAAGUCCUGA-GCUU
AAWR02034100.1/59888-59817   GCUAUGAUGAAUU--UGAUUG------C-AUUGAUUAUCC-AAAAUGAU-AAUAUAUU----UUGUCCUCUAAGAAGUUCUGA-GCUU
AAHX01115259.1/3006-3078     GCUGUGAUGAAUU--UGAAUC------C-ACUGAUCAUCU-GACAUGAUAAAUGCAUU----UUGUCCUCUAAGAAGUUCUGA-GCUU
AASC02022674.1/25005-25080   CCGAUGAUGAAUG--UUUUGG------A-UUCCUAUUUUU-GCAAUGAC-GAUGUUAAA-AAAUUACCUCUAAGAAGUUCUGAUGGGA
AAEX03026954.1/222007-221936 GCUGUGAUGUAUU--UAAUUG------C-GUUGAUUGUCU-GAAAUGAU-ACAUUAUU----UUGUCCUCUAAGAAGUUCUGA-GCUU
AADN03004067.1/192021-191957 GCUAUGAUGACUC--CUAUAA------U-GUUGAUCUUAC-GACAUG--------AUC----AUGUUCUCUAAGAAGUUCUGA-GCUU
AAGU03081857.1/11034-11105   GCUGUGAUGAAUU--UUAUUG------C-AUUGAUCUUCU-GAAAUGAU-AAUGUAUU----UUGUCCUCUAAGAAGUUCUGA-GCUU
AAPE02002133.1/21923-21994   GCUAUGAUGAAUU--UAAUUG------C-AAUGAUCAUCU-GAAAUGAU-AAUGUAUU----UUGUCCUCUAAGAAGUUCUGA-GCUU
AAWZ02030293.1/20807-20735   GCUGUGAUGAAUG--UAACAG------C-UUUGAUCAGCU-GAGAUGAU-AGGGCUCA---UGUGUCCUCUAAGAAGUUCUGA-GCAG
AAGW02046882.1/17835-17764   GCUAUGAUGAAUU--UAAUUG------C-AUUGAUCAUUU-GACAUGAU-UAAUUAUU----UUGUCCUCUAAGAAGUUCUGA-GCUU
CAAB02005182.1/14862-14934   GCAAUGAUGACCU--UCA-GG------U-UUUGAGGAAGU-GAUGAAAA-AACCUCCAG--CUAUUCCUCUAAGAAGUUCUGA-GCUC
AAGJ04131028.1/11885-11813   GUUAGGAUGACUU--UCUUUU------G-ACUGAUAUUAU-UUAUGAGG-AAUAUUUG---AAAUACCUCUAAGAAGUUCUGA-AUGU
JN899124.1/4-75              GCUAUGAUGAUUU--CGAUUG------C-AUUGAUCAUAU-GAAAUGAU-AAUGUACU----UUGUCCUCUAAGAAGUUCUGA-GCUU
#=GC SS_cons                 <<___________..______......_.___________.________.________...._____________________.>>::
#=GC RF                      GCuAUGAUGAaUU..UuAUUG......c.auUGAUcaUcU.GAaaUGAu.aAuguAuu....uUuUCCUCUAAGAAGUUCUGA.GCUu
//
# STOCKHOLM 1.0

#=GF AC   RF00271
#=GF ID   SNORD60
#=GF PI   U60
#=GF DE   Small nucleolar RNA SNORD60
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   42.00
#=GF TC   42.50
#=GF NC   41.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00066
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300357;
#=GF DR   snoopy; Gasterosteus_aculeatus300119;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF CC   U60 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD60
#=GF SQ   22


X96660.1/1-83                AGUCUGUGAUGAAUUGCUU----UGACUUCUGACACCUCGUAUGAAAA--CUGC----AC-GUGCAG--U---CUGAUUAUU-UAGCAA-GACUGAGG--CUU
AL512272.15/46660-46588      AGGUUGUGAUGAAUUGCUU----UAAUUUCUGACACCUCAUAUGAAAG--CUGC----AC-UUGCAG--U---C---------UUGCAA-GAC--AGG--CUU
AC132367.3/116009-115932     AGCCCGUGAUGAAUUAAU---------UUCUGACACCUCGUAUGAAAA--CUGC----AU-GCGUAG--U---CUGAUUACA-UUAUAA-GACUGAGG--CUU
AAFC03060159.1/22148-22230   GGCCUGUGAUGAAUUGCUU----UAAUUUCUGACACCUCGUAUGAAAA--CUGC----AC-GUGCAG--U---CUGAUUAUA-UUGCAA-GACUGAGG--CUU
AC145332.48/70876-70794      AGCCUGUGAUGAAUUGCUU----UCGUUUCUGACACCUCGUAUGAAAA--CUGC----AU-GUGCAG--U---CUGAUUAUU-UUGCAA-GUCUGAGG--CUU
AAPY01326808.1/1948-2030     AGCCUGUGAUGAUUUGCUU----UGACUUCUGACACCUCGUAUGAACU--CUGC----AC-ACGCAG--U---CUGAUUAUU-UUGCAA-GACUGAGG--CUU
AANN01253908.1/1232-1152     AGCCUGUGAUGAGU--CUU----UCAUUUCUGACACCUCGUAUGAGAA--CUGC----AC-GUGCAG--U---CUGAUUAAU-UUGCAA-GACUGAGG--CUU
AAFR03030919.1/82988-83070   AGCCAGUGAUGAGACAUUU----CCAUUUCUGACACCUCGUAUGAAAU--CUGC----AU-GUGCAG--U---UUGAUUAUA-UAGCAA-CCCUGAGG--CUC
AANU01195072.1/25007-24933   AGGAUGUGAUAAAUUGCUU----UAAUUUCUGACACCUCGUAUGAAAG--CUGC----AC-UUGUAG--U---C---------UUGCAA-GACUGAGG--CUU
AAHX01062900.1/21442-21360   AGCCUGUGAUGAAUUCAA--------UUUCUGACACCUCGUAUGAAAA--CUGCAUACAU-GUGCAG--U---CUGAUUACA-CUAUAA-AACUGAGG--CUG
AAYZ01471651.1/4075-4154     AGCCUGUGAUGAGUCGCU-------CUUUCUGACACCUCGUAUGACAG--CUGC----UC-CUGCAG--C---CUGAUUACG-CCGCGA-AGCUGAGG--CUU
AAPN01242684.1/1464-1546     AGCCGAUGAAGACACUUUG----CGAUUUCUGACACCUCGUAUGAGAG--CUGC----AU-CUGCAG--C---CUGAUUCUA-ACACUG-GACUGAGG--CUC
AAIY01574892.1/1744-1657     AGCUAGUGAUGAAUUGCG-----UAAUUUCUGACACCUCGUAUGAGAA--CUGCACGCAC-GUGCGG--U---CUGAUUAGC-UUGCAA-GACUGAAGGCCUC
AANH01003292.1/103517-103600 AGCCAGUGAUGACAAACAA----ACUUUUCUGACACCUCGUAUGAGAG--CUGC----AC-U-GCGG--C-UCCUGAUUCUA-ACGCUG-AUCUGAGG--CUC
AAVX01247128.1/765-678       AGUCUAUGAUGAGCCUCUU----UACUUUCUGACACCUCAUAUGAAAGUGUUGC----UU-UAGCAACGC---UUGAUUACA-UUUCUGUGUCUGAGG--CUU
CR855320.18/32836-32749      AGCCGCUGAUGACUUCCAUUAA-CUUUUUCUGACACCUCGUAUGAAAG--CUGU----AU-UU-CAG--C-AUCUGAUUAUAAACUUAA-GUCUGAGG--CUC
AAWR02040069.1/846-928       AGCCUGUGAUGAAUUGCUU----UAGUUUCUGACACCUCGUAUGAAAA--CUGC----GC-GCGCAG--U---CUGAUUAUU-UUGCAA-GACUGAGG--CUU
AAKN02007402.1/75658-75575   AGCCAAUGAUGAAUUGCUC----UAAAUUCUGACACCUCGUAUGAGAA--CUGC----AUAGUGCAG--U---CUGAUUAUA-UUGCGA-AACUGAGG--CUU
AAGV020834868.1/1462-1380    AGCCUAUGAUGAAUUGCUC----UAAUUUCUGACACCUCGUAUGAAAA--CUGC----AC-GUGCAG--U---CUGAUUAUU-UUGCAA-AGCUGAGG--CUU
AAWZ02041114.1/5323-5234     AGCCCGUGAUGAGCUCUUCCAUUUAUUUUCUGACACCUCGUCUGAACA--CUGC----GC-UUGCAG--UGAACUGAUUAUG-AACAUG-AGCUGAGG--CUU
AAEX03004625.1/20005-20088   AGCCUGUGAUGAGUCGCUUU---UUACUUCUGACACCUCGUAUGAAAA--CUGC----AC-GUGCAG--U---CUGAUUAUU-UUGCAA-AACUGAGG--CUU
AAQR03078024.1/8848-8766     AGCCUAUGAUGAAUUGCUG----UAAUUUCUGACACCUCGUAUGAAAG--CUGC----AC-GUGCAG--C---CUGAUUAUU-UUGCAA-CACUGAGG--CUU
#=GC SS_cons                 <<<<---------------....------------------------<..<<<<....__.__>>>>..>...---------.------.------>>..>>:
#=GC RF                      AGcCugUGAUGAauugcuu....UaaUUUCUGACACCUCGUAUGAAAg..CUGC....Ac.uUGCAG..c...CUGAUUAua.uugcaA.gaCUGAGg..CUu
//
# STOCKHOLM 1.0

#=GF AC   RF00272
#=GF ID   SNORA67
#=GF PI   U67
#=GF DE   Small nucleolar RNA SNORA67
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   45.00
#=GF TC   46.50
#=GF NC   44.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300411;
#=GF DR   snoopy; Homo_sapiens300113;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   U67 belongs to the H/ACA class of snoRNAs which are thought to guide the
#=GF CC   sites of modification of uridines to pseudouridines.
#=GF WK   Small_nucleolar_RNA_SNORA67
#=GF SQ   12


Y11161.1/1-137            AUCCAAGGUGAUUCCCUCUCCAAGGGGA-CAUC--AGUGCC--UC-UCAGGAAAGUAGCAGCUUGGAAUAGAAUCUGGCAUGCCUAAGGCCUUUGGGGAACUG-GGA--------UGCUUAUUUCCUCUGCCUUCCU-UGGCUGCCCACAUGG
AC002069.2/21330-21191    AUCCAAGGCGAUUCCCUCUCCAAGGGGA-CAUCU-AGUGCCCCUC-UCAGGAAAGUAGCAACUUGGAAUAGAAUCUGGCAUGCCUAAGGUCUUUGAGGAACAG-GGA--------UGCUUAUUUCCUCUGCCUUCCU-UGGCUGCCUACAUAG
AL512326.25/75899-76039   AUCCAAGGUGAUUCCCUCUCCAAGGGGAACAUCC-AGUGCCCCUC-UCAGGAAAGUAGCAACCUGGAACAGAAUCUGGCAUGCCUAAGGCAUUUGGGGAACAG-GGC--------UGGUUAUUUCCUCUGCCUUCCU-UGGCUGCCUACAUGG
AC012119.8/92875-93023    AUCCAAGGGGAUUCCCUCUCCAAGGGAA-CAUGC-AGUGCCCCUC-UCAGGAAAGUAACAACCUGGAAUAGAAUCUGGCAUGCCUAAGGUCUUUGAGGAAUAGAGGAAUAGAGGAUGCUUGUUUCCUCUGCCUUCCU-UGGCUGCCUACAUGG
AL022724.2/112300-112159  AUCCAAGGUGAGUCUCUCUCCAAGGGGCUGA-CU-AGUGCCUCUC-UUAGGACAGUAGCAAGUUGGAAUAAAAUCUGGCAUGCCUAAGGUCUUUAAGGAACAGGGGA--------UGCUUACUUCUUUUGCGUUCCUCUGGCGGCCUACAUAG
AL627097.6/104835-104975  GUCCAAGGUGAUUCCCUCUCCAAAGGGCUGA-CUGUGUGCCACUU-UCAGGAA--CAGCAAUUUGGAAGAAAGCCAGGCAUGCCUGAGGUCUUUGAUGAACAAGGAA--------UACUUGUUUCCUUUGCCCUCCUCUGGCUGCCUACAUGU
AL603707.5/47205-47063    GUCCAAGGUGAUUCCCUCUCCAAAGGGCUGA-CUGUGUGCCCUUU-UCAGGAACGUAGCAACUUGGAAGAAAACCAGGCGUGCCUGAGGUCUCUGGUGGACAAGAAA--------CUCUUGUUUCCUUUGCCCUCCUCUGGCUGCCUACAUGU
AB011595.1/4785-4927      GUCCAAGGUGAUUCCCUCUCCAAAGGGCUGA-CUGUGUGCCCUUU-UCAGGAACGUAGCAACUUGGAAGAAAACCAGGCGUGCCUGAGGUAAAUGGUGGACAAGAAA--------CUCUUGUUUCCUUUGCCCUCCUCUGGCUGCCUACAUGU
AL691512.11/142138-142006 GUCCAUGGUGAUUCCCUCUCCAAAGGACUGAUUG-UGUGCCCUUU-UCAGAAACGUAGCAACUUGGAAGACAGCCAGGCAUGCCCAAAGUCUCUGGUGAACAA-GGA--------A------UUCUUGU---UUCCUUUGGCUGCCUACAUAU
AL808133.17/112145-112003 GUCCAAGGUGAUUCCCUCUCCAAUGGUCUGAGUA-UGUGCCUUUU-UCAGGAAUGUAGCAAGUUGGAAGAAAACCAGGCAUGUCUGAGGUCUCUGCUGAUCAAGGAA--------CACUUGUUUCCUUAGCCCUCCUCUGGCUGCCUACAUGU
AC104314.8/112253-112111  GUCCAAGGUGAUUCCCUCUCCAAAGGGCUGACUG-UGUGCCCUUU-UCAGGGACGUAGCAACUUGGAAGAAAGCCAGGCAUGCCCAAGGUCUCUGGUGAACAGGGAA--------UACUUGUUUCCUUUGCCUUCCUUUGGCUGCCCACAUAU
CU914279.16/177477-177336 AUCCAAGGUGAUUCCCUCUCCAAGGGGC-CUGCU-UGUGCCCCUCUUCUGGAAAGUAGCAGCUUGGAAUAACAUCUGGCAGGCCUGAGG-CUCUGGCGGCGAGGGGC--------UGUAAACAUCCUCUGCCUGCCUUGGGCUGCCCACACAC
#=GC SS_cons              :<<<<<<-<<--------<<<<<<<<<<______.___>>>>>>>.--->>>------>>->>>>>>--------<<<<-<<<--<<<-----<<-<<<________........______>>>->>------>>>-->>>>>>>::::::::
#=GC RF                   aUCCAaGGuGAUUCCCUCUCCaAggGgcUgAucu.uGUgcCccUu.UCAGGAAaGUAGCaACuUGGAAuAaAAuCgggcAugcCUgagGUCUuuGggggAcAgGGgA........ugcUUacucCCuuUGCCUuccUugggcugcCUACAUgu
//
# STOCKHOLM 1.0

#=GF AC   RF00273
#=GF ID   SNORD59
#=GF PI   U59
#=GF DE   Small nucleolar RNA SNORD59
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; ILM; Moxon SJ, Daub J
#=GF GA   45.00
#=GF TC   45.40
#=GF NC   43.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00065
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Oryzias_latipes300062;
#=GF DR   snoopy; Oryzias_latipes300061;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   U59 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD59
#=GF SQ   24


X96659.1/1-75                  CCUU-CUAUGAUGAUUUUA--UCAAAAUGAC-UUUCGUUCUUCUGAGUUUGC----UGAAGCC-ACA-UUUAGG-UACUGAGAAGG
M19482.1/4348-4418             CCU--CACUGAUGAGU-----ACGUUCUGAC-UUUCGUUCUUCUGAGUUUGC----UGAAGCC-AGA-UGCAAU-UUCUGAGAAGG
AANG01089171.1/891-821         CCU--CACUGAUGAGU-----AGCUUCUGAC-UUUCGUUCUUCUGAGUUUGC----UGAAGCC-AGA-UGCCAU-UCCUGAGAAGG
AAPY01020387.1/1161-1091       CCU--UGCUGAUGAGU-----AGCUUCUGAC-UUUCGUUCUUCUGAGUUUGC----UGAAGCC-AGA-UGACAU-UUCUGAGAAGG
AAHX01047139.1/3474-3403       CCUU-CCUUGAUGAUU-----AGCUUCUGAC-UUUCGUUCUUCUGAAUUUGC----UGAAGCC-AGA-UGCCAU-UCCUGAGAAGG
AANU01226211.1/10321-10251     ACU--CACUGAUGAGU-----AGCUUCUAAC-UUUCAUUCUUCUGAGUUUGC----UGAACCC-AGA-UGCCAU-UCCUGGGAAGG
AAFR03065551.1/12698-12626     CCUU-CACUGAUGAGUA----GCUUUCUGAC-UUUCGUUCUUCUGAUUUUGC----UGAAGCC-AGA-UGCCAC-UUCUGAGAAGG
AANN01165367.1/1556-1630       CCUU-CUAUGAUGAUUCUA--UCCAAAUGAC-UUUCGUUCUUCUGAGUUUGC----UGAAGCC-AUA-UUUAGG-CUCUGAGAAGG
AAQQ01535324.1/1585-1510       CCUUUCUGUGAUGAUUUUA--CCAAAAUGAC-UUUCGUUCUUCUGAGUUUGC----UGAAGCC-AAA-UUCAGA-UACUGAGAAGG
AAPN01043377.1/629-701         CCUU-CGCUGAUGAGUG----ACUCUUUGAC-UUUCGUUCUUCUGAGUCUGC----UGAAGCC-AUU-UGUCUA-UUCUGAGAAGG
AAYZ01238767.1/3030-2956       CCUU-CAUUGAUGAGU-----AGCUUCUGAC-UUUCGUUCUUCUGAGAUUGUGAA-UGAAGCC-AGA-UGCCAU-UCCUGAGAUGG
AAHY01090049.1/33733-33661     AUU--CUGUGAUGACUUU---ACCAAAUGAC-UUUCGUUCUUCUGAGUUUGC----UGAAGCC-ACA-CUCAGG-UGCUGAGAGGG
BAAF04010654.1/2506-2432       UCUU-CAGUGAUGAUUUA---AUACAGUGAC-UUUCGUUCUUCUGAGAUUAC----UGAAGCCAACA-UUUCUG-UCCUGAGAAGA
AANH01010881.1/31953-31884     UCUU-CAGUGAUGAUU-----AACAA---AC-UUUCGUUCUUCUGAGUUUAC----UGAAGCCAAUA-UUUCUG-UCCUGAGAAGA
AALT01341217.1/2987-3064       CCUU-CUGUGAUGAUUUUAUCCAAAAUUGAC-UUUCGUUCUUCUGAGCUUGC----UGAAGCC-AUAAUAGAGA-AACUGAGAAGG
CAAE01014729.1/2855051-2855123 UCUU-CUGUGAUGAUCA----ACACAUUGAC-UUUCGUUCUUCUGAGUCUAC----UGAAGCC-ACC-UCGUUG-UCCUGAGAUGA
AAGV020309194.1/1079-1009      CCU--CAUUGAUGAUU-----AACUUCUGAC-UUUCGUUCUUCUGAGUUUGC----UGAAGCC-AGA-UCCAAU-UCCUGAGAAGG
AAKN02044480.1/12363-12294     CCU--CCCUGAUGA-------AGUUUCUGACUUUUCGAUCUUCUGAGUUUGC----UGAAGCC-AGA-UGCCAU-GCCAGAGAAGA
CR381647.10/175042-175113      UCU--UGAUGAUGAUUUG---ACAAUUUGAC-UUUCGUUCUUCUGAGUCUGA----UGAAGCC-AAA-UUUUGU-CCUGAAAGAG-
AAWZ02009713.1/7683-7753       CCU--UGAUGAUCCAU-----AAAAUAUGAC-UUUCGUUCUUCUGAGCUUGC----UGAAGCC-AUG-UUUUUG-AUCUGAGAAGG
CAAB02009821.1/3541-3613       UCUU-CUGUGAUGAUCA----ACACAUUGAC-UUUCGUUCUUCUGAGUGUAC----UGAAGCC-AUC-UUUUUG-UCCUGAGAAGA
AAGW02059157.1/79047-78972     CCUU-CACUGAUGAGU-----AGCUUCUGAC-UUUCGUUCUUCUGAGUUUGUCGAGUGAAGCC-AGA-UGCUGU-UCCUGAGAUGG
AAEX03006929.1/8524-8449       CCUU-CAAUGACGAUUAUA--UCAAAAUGAC-UUUCGUUCUUCUGAGUUUGC----UGAAGCU-ACA-UUUCAGGUACUGAGAAGG
AADN03009150.1/1764-1692       CCUU-CGCUGAUGAGUA----ACCUUUUGAC-UUUCGUUCUACUGAGCUUGC----UGAAGCA-ACG-UUCAUU-ACCUGAGGAGG
#=GC SS_cons                   <<<-.<___________....__________.____________________...._______.___.______.______>->>>
#=GC RF                        cCUU.CaaUGAUGAuUu....AcauuuUGAC.UUUCGUUCUUCUGAGUUUGC....UGAAGCC.AuA.Uuucau.UcCUGAGAAGg
//
# STOCKHOLM 1.0

#=GF AC   RF00274
#=GF ID   SNORD57
#=GF PI   U57
#=GF DE   Small nucleolar RNA SNORD57
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   47.00
#=GF TC   47.10
#=GF NC   46.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00058
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300983;
#=GF DR   snoopy; Oryzias_latipes300063;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   U57 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD57
#=GF SQ   23


X96656.1/1-72              UGGAGGUGAUGAACUGUC-U----G---AGCCUGACCUU-GUAGAAUGGAGGC---AAAA----AA-----A-CUGAUUUAAUGAGCCUGAUCC
AF357378.1/1-59            ----------GAACGAAC-U----U---GGCCUGACCUU-CAGAAAUGGAGGC----AAU----AC-----AACUGAUUUAAUGAGCCUGA---
AL833804.16/188215-188286  UGGAAAGGAUGAACGAAC-U----U---GGCCUGACCUU-CAGAAAUGGAGGC----AAU----AC-----AACUGAUUUAAUGAGCCUGAUCC
AAHX01025040.1/7727-7798   UGGAGAUGAUGAACUGAC-U----C---AGCCUGACCUU-CAGAAAUGGAGGU----GAU----AA-----AACUGAUUUAAUGAGCCUGAUCC
AANG01691521.1/1173-1244   UGGAGGUGAUGAACUGGC-U----A---AGCCUGACUUU-GUAGAGUGGAGGC----AAA----AA-----AACUGAUUUAAUGAGCCUGAUCC
AAFC03071760.1/12715-12786 UGGAGGUGAUGAACUGUC-U----U---ACCCUGACCAU-GAAGUGUGGAGGC----AAA----AA-----AACUGAUUUAAUGAGCCUGAUCC
AANN01172229.1/602-674     UGGAGGUGAUGAACUAUUAU----U---AGCCUGACUUU-GUAGACUGGAGGC----AAA----AA-----AACUGAUUUAAUGAGCCUGAUCC
AAPY01643549.1/7403-7333   UGGACAUGAUGAAUUGUU-C----U---AACCUGACCUC-GUAG-AUGGAGGC----AAA----AA-----AACUGAUUUAAUGAGCCUGAUCC
AAQQ01611468.1/8008-7929   UGGAGAUGAUGAACCAUC-UUGCUU---GGCCUGACCUU-GUGAAGUGGAGGC----AAAAACAAA-----AACUGAUUUAAUGAGCCUGAUCC
AALT01117771.1/41-117      UGGAGAUGAUGAACUCUC-U---UG---GGCCUGACCUU-GUUGAGUGGAGGGGCAAAAA----AU-----AAUUGAUUUAAUGAGCCUGAUCC
AAFR03017399.1/22236-22303 UGGAGGUGAUGAGCAUCC-U----U---ACCCUGAC--U-CCAGAGUGGAGGC----A------AA-----AACUGAUUUAAUGAGCCUGAUCC
AAYZ01171747.1/3910-3989   UGGAGAUGAUGAGCCACC-U----UACUACCCUGACCUU-GUGGAGUGGAGGC----AAA----ACAAAAUAACUGAUUUAAUGAGCCUGAUCC
BAAE01007813.1/2619-2686   UGUAAAUGAUGAAAGGUC-U----U---UCCCUGAUGUC-ACAGUGAGGGUG------------AA-----AACUGAUUUAAUGAGCCUGAUGC
CT027620.13/109696-109762  UGUGAGUGAUGA-CUCUU-U----C---CUCCUGAC--U-CCUACGUGGAGGC----G------AA-----AACUGAUUUAAUGAGCCUGACAC
ABAV01009160.1/9312-9384   GCCAAGUGAUGAUGGUUU-U---UC---AGCCUGACCCU-CAAAACAUGGAGG----UUC----UA-----AUCUGAUUUAAUGAGCCUGAUGG
AAWR02026420.1/23526-23456 UGGAGGUGAUGAGCUGUC-U----U---AGCCUGACCUG-GUAGAGUGGAGGC----AA-----AA-----AACUGAUUUAAUGAGCCUGAUCC
AAGV020356674.1/814-883    UGGAGGUGAGGAGCUGUC-U----U---AGCCUGACCUU-GAAAGUAG--GGG----CAA----AA-----AACUGGUUUAAUGAGCCUAAUCC
AAQR03054002.1/15844-15771 UGGAGGUGAUGAACUGCC-U----U---AGCCUGACCUUAGUCGAGUGGAGGC---AAAA----AA-----AACUGAUUUAAUGAGCCUGAUCC
AAGW02062549.1/32452-32522 UGGAAGUAAUGAGCUG-C-U----U---AGCCUGACCUU-CUAGAGUGGAGGC----AAA----AA-----AACUGAUUUAAUGAGCCUGAUCC
AAGU03041322.1/19624-19554 UGGAAGUGAUGAACUGUC-U----U---AGCCUGACUUU-GUAAAGUGGAGGC----AA-----AA-----AACUGAUUUAAUGAGCCUGAUCC
AADN03010123.1/8885-8818   CGGAUGUGAUGUGAAGCG-C----C---CACCUGACCCC-CC---GUGGAGGC----AA-----AA-----AGCUGAUUUAAUGAGGCUGAUCC
CAAB02005786.1/32403-32339 UGUAGAUGAUGA-CAGGC-U----U---UCCCUGAUGUC-ACUGAG----GGC----A------AU-----AACUGAUUUAAUGAGCCUGAUGC
EU094146.1/4-71            UGGAGAUGAUGAGCCACU-U----G---GUCCUGAACCU---AGCGUGAGGGC----A------AA-----AGCUGAUUUAAUGAGCCUGAUCC
#=GC SS_cons               :<<<______________._...._...___________._____________....___....__.....____________________>>>
#=GC RF                    UGgAgaUGAUGAaCuauc.U....u...agCCUGACCUU.guagAgUGGAGGC....AAA....AA.....AACUGAUUUAAUGAGCCUGAUcC
//
# STOCKHOLM 1.0

#=GF AC   RF00275
#=GF ID   SNORD56
#=GF PI   U56
#=GF DE   Small nucleolar RNA SNORD56
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   36.00
#=GF TC   36.30
#=GF NC   35.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300478;
#=GF DR   snoopy; Echinops_telfairi300041;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   U56 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD56
#=GF SQ   7


X96655.1/1-71             CCACAAUGAUGGCAAUAUUUUUCGUCAACAGCAGUU-CACCUAGUGAGUGUUGAGACUCUGGGUCUGAGUGA
AL833804.16/187896-187965 CUACAAUGAUGGUAAUAUUUUUCGUCAACAG-AGUU-CACCUAGUGAGUGUUGACACCUUGGGUCUGAGUGA
AP000827.6/86976-87046    CUACAAUGAUGGCAAUAUGUUUCAUCGACAGCAGUU-CACCCAUUGAGUGUUGAUACCGUGGGUCUGAGUGA
AL049759.10/111034-110967 CCGCAGUGACAGCAAUAUUUUUCAUCCACAG---UU-CACCUCAUGAAUGUUGUCACUUUGGGUCUGAGUGA
AC012501.7/86967-86897    CUAUUAGGAUGACAAUAUUUUUUGUCAGCAGCAGCU-UACCUAAUGAGUGUUGAUGCUUUGGGUCUGAGUGA
AC004130.1/61046-61116    CUACAAAGAUAGCAACACUUUUCAUCAACAGCAGUU-CACCUAGAGAGAGUCGACACUUUUUGUCUGAGUGA
AL135844.9/13971-13900    CUAAAACAAUGUCAAUAGUUUUCAUCAACAGCAGUUGAACCUAGUAAGUGUCGAUACUUUGGGUCUGAGUGG
#=GC SS_cons              :<<<---<<<<___________>>>>----------.------------------------------->>>:
#=GC RF                   CuAcAAuGAuggCAAUAuUUUUcaUCAACAGCAGUU.cACCUAgUGAGUGUUGAuACUUUGGGUCUGAgUgA
//
# STOCKHOLM 1.0

#=GF AC   RF00276
#=GF ID   SNORD52
#=GF PI   U52
#=GF DE   Small nucleolar RNA SNORD52
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   45.00
#=GF TC   46.30
#=GF NC   44.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00063
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300615;
#=GF DR   snoopy; Takifugu_rubripes300021;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF CC   U52 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD52
#=GF SQ   20


X96651.1/1-66              GGGAAUGAUGAUU-UCACAGACUAGAGUCUCCGAUGC-UGGUCAUGAUGUCA-AAACU--AAGUUCUGA-UC
AL773527.8/126615-126549   GGGAAUGAUGAUU-UCUCAGACUAGAGUCUCUGAUGC-UGGUCCUGAUGUCA-AAAUU--AAUUUCUGACUC
X77209.1/655-590           GAGAAUGAUGAUU-UCACAGACUAGAGUCUCUGACUC-UGCCCUUGAUGUCA-ACUAU--AAAU-CUGACUC
AF109906.1/100346-100281   GAGAGUGAUGAUU-UCACAGACUAGAGUCUCUGACGC-UGUCCUUGAUGUCA-GCUAU--AAAU-CUGACUC
AAQQ01546498.1/489-555     GAGAAUGAUGAAU-UUACAGACUAGAGUCUCUGAGGC-UGGUCCUGAUGUCA-AAAGU--AAGUUCUGACUC
AAFC03050905.1/46533-46467 GGGAAUGAUGAUU-UCUCAGACUAGAGUCUCUGAUAC-UGGUUUUGAUGUCA-AAAUU--GAUUUCUGACUC
AAYZ01082793.1/2695-2761   GGGAAUGAUGAUC-UCACAGACUAGAGUCUCUGACAC-UGGUUCUGAUGUCA-AACUU--AAGUUCUGACUC
AALT01488983.1/2001-2067   GGGAAUGAUGAUU-UCACAGACUAGAGUCUCUGACAC-UAGGCCUGAUGUCA-AAUUU--ACAUUCUGACUC
ABDC01612123.1/549-482     GGGAAUGAUGAUU-UCACAGACUAGAGUCUCUGACACAUGGUCAUGAUGUCA-AAACU--AAGUUCUGACUC
AANG01354597.1/381-449     GGGAAUGAUGAUUGUCUCAGACUAGAGUCUCUGAUGC-UGGACUUGAUGUCAAAAAUU--AAGUUCUGACUC
AANN01754372.1/2219-2152   GGGAAUGAUGAUU-CUUAAGACUAGAGUCUCUGACGC-UGGUUCUGAUGGCAGAAAUU--AGUUUCUGAUUC
AAIY01395239.1/353-290     GGGAAUGAUGAUU-UCUCAGACUAGAGUCUCUGA--C-UGGUCUUGAUGUCU-UUUUG--UUGU-CUGACUC
BX511233.10/65902-65968    UGCAGUGAUGAUU-CCAUAGACUAGAGUCUCUGAUAA-CAACAUGAAGAUCU-ACACA--UUUCUCUGAGCA
AAKN02021588.1/41753-41687 GGGAAUGAUGAUU-UCACAGACUAGAGUCUCUGACAC-UGGUUCUGAUGUCA-AAAAU--AAUGUCUGACUC
AAWR02009906.1/28300-28367 GGGAAUGAUGAUU-UCUCAGACUAGAGUCUCUGAUGC-UGGUUCUGAUGUCA-AAACUU-AAGUUCUGACUC
AAPE02062606.1/1142-1204   GGGAAUGAUGAGU-UCUCAGACUAUAGUCGCUGAUGU-UGGUUCUGAAGUGA-A------AAGUUCUGACUC
AAEX03008219.1/36845-36912 GGGAAUGAUGAUU-UCUCAGACUAGAGUCUCUGACAC-UGGUCUUGAUGUCAAAAAUU--ACGUUCUGACUC
AAPE02050090.1/12489-12422 GGGAAUGAUGAUU-UCUCAGACUAGAGUCUCUGACGC-UGGCUCUGAAGUGAAAAAUU--AAGUUCUGACUC
CAAB02010444.1/29772-29704 UGGAAUGAUGAUU-UUGCAGACUAGAGUCUCUGAAAA-UCCUGAAGUAGCUU-UCUUUUAUUGCACUGACCA
AAGW02070280.1/41124-41190 GGGGAUGAUGAUU-UCACAGACUAGAGUCUCUGACCC-UGGUCCUGAUGUCA-AAAAU--GAGUUCUGACUC
#=GC SS_cons               <<<__________._______________________.______________._____.._________>>>
#=GC RF                    GgGAAUGAUGAUU.UCaCAGACUAGAGUCUCUGAuac.UGgUcuUGAuGUCA.AaauU..aagUUCUGACuC
//
# STOCKHOLM 1.0

#=GF AC   RF00277
#=GF ID   SNORD49
#=GF PI   U49
#=GF DE   Small nucleolar RNA SNORD49
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   37.00
#=GF TC   37.10
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00062
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300079;
#=GF DR   snoopy; Oryzias_latipes300028;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF CC   U49 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD49
#=GF SQ   28


AAYZ01665444.1/416-340         UGCUCUGAUGACACAGGUAGCAAAUAGGAAGUGCCGUCAGA-GCGAGAACUGACGAUC-CUGGAGAC-GCGUGUCUGAGC
CR524332.1/704-776             UG--AUGAUGAUACCCCAGA---AUAGGAAGUGCCGUCAGAUGCGAGAACUGACGAUA-ACCUUCUU-AUUUAUCUGAAA
CAAE01015001.1/1084295-1084363 GUCAAUGAUGAAA--ACUAA----UAGGAAGUGCCGUCUGAUGCGAUAACUGACGAUG-UUUAAUA----UUCACCGUUC
AAFR03054690.1/25422-25495     GUUCAUGAUGAUACCACUCA---AUAGGAAGUGCCGUCAGAUGCGAUAACUGACGAUG-AACUUGAU--CAUGUCUGACA
AL596181.10/71072-71001        UG--AUGAUGAAACUAGAAAA-AAAAGGAAGUGCCGUCCGAUGCGACAACUGACGACA-UCCCUAG----UUAGCUGACU
AAVX01157372.1/479-550         UUUGAUGAUGAAAACUUGAA----UAGGAAGUGCCGUCAGAUGCGAGAACUGACGAUAAUCUAUUU----AAUUCUGACU
AANN01832263.1/7047-7114       UGCUCUGAUGAAAUCACUCA----UAGGAAGUGCCGUCAGAUGCGACAGCUGACGAGA----AUUC----CUGGCUGAUG
AALT01061078.1/652-582         UGCUCUGAUGACACGGCUAA----UAGGAAGUGCCGUCAGAAUCGAUAACUGACGACG-AGAAGCC----UGGGCUGACU
AAFC03040867.1/17266-17197     UGCUCUGAUGAGAUCACUAA----UAGGAAGUGCCGUCAGAAGCGAUAACUGACGAUA-G-UUUUC----CCGACUGACU
AL596181.10/70701-70630        UGCUGUGAUGAGAUGACUAA---GUAGGAAGUGCCGUCAGAGUCGAUAACUGACGAUA-ACUGCUC----CUGGCUGACU
AC093484.2/160294-160365       UGUCCUGAUGAUACUUGUAA----UAGGAAGUGCCGUCAGAAGCGAUAACUGACGACG-UCUAAUG---UCUAUCUGACC
ABDC01454908.1/743-813         UGUCCUGAUGAUACUGGAAA----UAGGAAGUGCCGUCAGAGACGAUAACUGACGACG-UUUAUGC----UUGUCUGACC
AAIY01670945.1/1259-1329       UGGCCUGAUGAUAUUGGUAA----UAGGAAGUGCCGUCAGACGCGAUAACUGACGAUG-UCUGUAC----CUGCCUGACC
AAQQ01674205.1/1071-998        UGCUCUGAUGAAACCAUUAAU-AAUAGGAAGUGCCGUCAGAAGCGAUAACUGACGAUA-ACUAUUC----CUGGCUGACU
AAPY01312558.1/77-7            UGCUCUGAUGAAAUCACUAA----UAGGAAGUGCCGUCAGAAGCGAUAACUGACGAUA-ACUACUC----CUGGCUGAUG
X96649.1/1-71                  UGCUCUGAUGAAAUCACUAA----UAGGAAGUGCCGUCAGAAGCGAUAACUGACGAAG-ACUACUC----CUGUCUGAUU
AAKN02044274.1/36691-36762     UGCUCUGAUGAUACCACUUA---AUAGGAAGUGCCGUCAGAAUCGAUAACUGACGAUA-ACUAUUC----CUGGCUGACC
AAWR02013550.1/46999-46929     UGCUCUGAUGAAAUCACUAA----UAGGAAGUGCCGUCAGAAGCGAUAACUGACGAUA-ACAAUUC----CUGGCUGACU
AAGV020452875.1/3182-3112      UGCUCUGAUGAAAACCAUAA----UAGGAAGUGCCGUCAGAAGCGAUAACUGACGAUA-ACUAUUC----UUGGCUGACU
AAHX01064314.1/33324-33394     UGCACUGAUGAAACUAGAAA----UAGGAAGUGCCGUCCGAAACGACAACUGACGACA-UCUCUAU----UUAGCUGACU
CAAB02009479.1/1273-1347       GUCAAUGAUGAAAUCCUGGA---AUAGGAAGUGCCGUCAGAUGCGACAACUGACGAUU-UCUCAUCC-ACUUUUCUGAGG
AAPE02032623.1/1099-1032       UGCUCUGAUGAAAUCACCAA----UAGGAAGUGCCGUCAGAAGCGGUAACUGACGAUA----AUUC----CUGGCUGACU
AAWZ02037281.1/5205-5276       CGGGGUGAUGAUGCC-GAGA----UAGGAAGUGCCGUCAGAUGCGAGAACUGACGAGA-CGCUCAUC--UCCGUCUGACC
AAQR03080114.1/3135-3205       UGCUCUGAUGAAAUCGCUAA----UAGGAAGUGCCGUCAGAAGCGAUAACUGACGAUA-ACUAUUA----CUGUCUGACU
AAGW02049334.1/39269-39339     UGACCUGAUGAUACCAGUAA----UAGGAAGUGCCGUCAGAGGCGAUAACUGACGAUG-CCCGUAG----CCGUCUGAGC
AAGU03082540.1/21976-21906     UGUCCUGAUGAGAUUGGUAA----UAGGAAGUGCCGUCAGAAGCGAUAACUGACGAUA-UCUGCGU----UUGUCUGACU
EU094177.1/4-81                UGCAAUGAUGAUAACAUGGAA-UAUAGGAAGUGCCGUCAGAUGCGAUAACUGACGAUA-AUCUCUGUACCUAAUCUGACC
JN899114.1/1-71                UGCUCUGAUGAAAUCACUAA----UAGGAAGUGCCGUCAGAAGCGAUAACUGACGAUA-AUAACUC----CUGGCUGACU
#=GC SS_cons                   ::::::::::::::::::::....::::::::::::::::::::::::::::::::::.:::::::....::::::::::
#=GC RF                        UGcucUGAUGAaAccacuaA....UAGGAAGUGCCGUCAGAuGCGAuAACUGACGAua.acuauuc....uUGuCUGAcu
//
# STOCKHOLM 1.0

#=GF AC   RF00278
#=GF ID   SNORD50
#=GF PI   U50
#=GF DE   Small nucleolar RNA SNORD50
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Moxon SJ
#=GF GA   42.00
#=GF TC   42.30
#=GF NC   41.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300234;
#=GF DR   snoopy; Gallus_gallus300002;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF RN   [3]
#=GF RM   10792466
#=GF RT   Intronic U50 small-nucleolar-RNA (snoRNA) host gene of no protein-coding
#=GF RT   potential is mapped at the chromosome breakpoint t(3;6)(q27;q15) of human
#=GF RT   B-cell lymphoma.
#=GF RA   Tanaka R, Satoh H, Moriyama M, Satoh K, Morishita Y, Yoshida S, Watanabe
#=GF RA   T, Nakamura Y, Mori S
#=GF RL   Genes Cells 2000;5:277-287.
#=GF CC   U50 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1]. U50 is an
#=GF CC   intronic snoRNA gene located on chromosome 6q15, at the breakpoint of
#=GF CC   chromosomal translocation t(3;6)(q27;q15). The U50HG gene is composed of
#=GF CC   six exons, whose spliced transcripts have little potential for coding a
#=GF CC   protein, and its introns produce both U50 and U50-like (U50') snoRNAs that
#=GF CC   are localised in nucleoli [3].
#=GF WK   Small_nucleolar_RNA_SNORD50
#=GF SQ   26


AB017710.1/1702-1771         AAUCAAUGAUGAAACCUAUCCCGAAGCUGAUAA--CCUGAAG--AAAA---AUAAGUA-CGGAUUCGGCUUCUGAGAU
X96662.1/1-74                UAUCUGUGAUGAU-CUUAUCCCGAACCUGAACU--UCUGUUGAAAAAAAAAACUUUUA-CGGAUCUGGCUUCUGAGAU
AB116374.1/1155-1226         AGUCUAUGAUGAU-CCUAUCCCGAACCUGAAUU--CCUGUUG--AAAGACCAUACUUA-CGGAUCUGGCUUCUGAGAU
AB116376.1/1-69              --UCUAUGAUGAU-CCUAUCCCGAACCUGAAUU--CCUGUUG--AAAAACCAUAAUUA-CGGAUCUGGCUUCUGAGA-
AB116375.1/1406-1477         AGUCUAUGAUGAU-CCUAUCCCGAACCUGAAUU--CCUGUUG--AAAAACCAUAAUUA-CGGAUCUGGCUUCUGAGAU
AAHX01056136.1/8975-9046     GAUCUAUGAUGAU-CCUAUCCCGAAUCUGAAUU--CCUGUUG--AAAAAAUAUAAUUA-CGGAUCUGGCUUCUGAGAU
AAPY01434504.1/371-300       UACCUAUGAUGAU-CCUAUCCCGAACCUGAAUU--UCUGUUG--AAAAAAAUAAAAUA-CGGAUCUGGCUUCUGAGAU
AAYZ01287241.1/3299-3227     UAUCUAUGAUGAU-CCUAUCCCGAACCUGAAUU--CCUGUUG-AAAAAAGUAAACUUA-CGGAUCUGGCUUCUGAGAU
AAPN01320559.1/1525-1596     UGUCUGUGAUGAU-UCUAUCCCGAACCUGAACU--CCUGUUG--AAAAAAAACACAAA-CGGAUCUGGCUUCUGAGAU
AAFR03001945.1/112320-112391 UAUUAAUGAUGAU-UCUAUCCCGAACCUGAAUU--CCUGUUG--AAAAACUACAUAUA-CGGAUCUGGCUUCUGAGAU
AANG01363621.1/1518-1449     AAUCCAUGAUGAU-CUUAUCCCGAACCUGAAUA--UCUGUUG--AGAAAACU--UAUA-CGGAUCUGGCUUCUGAGAU
AADA01151228.1/5736-5663     UAUCUGUGAUGAU-CUUAUCCCGAACCUGAACU--UCUGUUG-AAAAAAAAACUUUUACCGGAUCUGGCUUCUGAGAU
AANN01311246.1/7650-7717     UAUCUAUGAUGAU-CUUAUCCCGAACCUGAAUU--UCUGUUG--AGAAAACG----UA-CGGAUCUGGCUUCUGAGAU
AACN010584535.1/696-627      AAUCUAUGAUGAU-CUUAUCCCGAACCUGAAUA--CAUGUUG--AGAAAACC--AAUA-CGGAUCUGGCUUCUGAGAU
AALT01262864.1/410-482       GAUCAAUGAUGAAACCUAUCCCGAAACUGAUCA--CCUGAAG--AAAAAAACAUGUUA-CGGAUUCGGCUUCUGAGAU
AAIY01165594.1/1456-1528     UAUCUAUGAUGAU-CCUAUCCCAAACCUGAACA-AACUGUUG--AAAAAAAGUUUAUA-UGGAUCUGGCUUCUGAGUU
AAFC03092119.1/22465-22534   GAUCAAUGAUGAACCCUAUCCCGAAGCUGAUAA--CCUG-----AAGAAAAGCAUGUA-CGGAUUCGGCUUCUGAGAC
AAVX01032274.1/1256-1323     AAUCAGUGAUGAAAACAAUCCAAAACCUGAAUU--UCUGAUG--AAAAUCUA-----A-CGGAUCUGACUGCUGAGAU
AAWR02014676.1/39190-39121   AAUUCAUGAUGAAACCUAUCCCGAAGCUGAUUA--CCUG-----AAGAAAAGCAUGUG-CGGAUUCGGCUUCUGAGAU
AAGV020235195.1/2881-2950    UAUCUGUGAUGAU-CCUAUCCCGAACCUGAAUU--UCUGUUG--AAAAAAGUU--AUA-CGGAUCUGGCUUCUGAGAU
AAWZ02018256.1/5249-5322     AAUCAUUGAUGAG-ACUAUCCCGAACCUGAUUU-CUUUGAUG-AAAAAACUGCCAAUA-UGGAUCCGGCUUCUGAGGU
AAGW02019269.1/19649-19576   UAUCUAUGAUGAU-CUUAUCCCGAACCUGAAUUUU-CUGUUG-AAAAAAAACGCUAUA-CGGAUCUGGCUUCUGAGAU
AADN03003200.1/14425-14355   CAUCUAUGAUGAU-CCUAUCCCGAACCUGAAUU-CUUUGCUG--AAAAA--CCUACUA-CGGAUCCGGCAUCUGAGAU
AAGU03001878.1/19290-19359   UAUCUAUGAUGAU-CCUAUCCCGAAACUGAAUU--UCUGUUG--AAAAAACU--UAUA-CGGAUCUGGCUUCUGAGAU
EU094096.1/1-71              A-UCAGUGAUGAG-CAUAUCCCGAACCUGACUU--CUUGAUG--AAAACACUAUUAUA-CGGAUCUGGCAUCUGAGAA
JN899117.1/2-75              GAUCAAUGAUGAAACCUAUCCCGAAGCUGAUUA--CCUGAAG-AAAAAAAAGCACAUA-CGGAUUCGGCUUCUGAGAU
#=GC SS_cons                 :<<<_________.___________________.._______..______________.________________>>>
#=GC RF                      uAUCuAUGAUGAu.CcUAUCCCGAAcCUGAaUu..uCUGuUG..AAAAAAaauauaUA.CGGAUCUGGCUUCUGAGAU
//
# STOCKHOLM 1.0

#=GF AC   RF00279
#=GF ID   SNORD45
#=GF PI   U45
#=GF DE   Small nucleolar RNA SNORD45
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   42.00
#=GF TC   42.80
#=GF NC   41.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300909;
#=GF DR   snoopy; Homo_sapiens300006;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF CC   U45 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD45
#=GF SQ   11


AF357369.1/1-61         ---------------GGCAUGUAUU--CUGAAUCUAAAGUUGAUUAUAAA--CCACUUUAGCUCUAGAAUUACUCUGAGA----
AL357314.11/74156-74234 GGUCAAUGAUGAGUUGGCAUGUAUU--CUGAAUCUAAAGUUGAUUAUUA---CUACUUUAGCUCUAGAAUUACUCUGAGACCUG
X96645.1/1-71           GGUCAAUGAUGUAAUGGCAUGUAUUAGCUGAAUCUAAAGUUGAUG------------UGAGUUCUAGAAUUACACUGAGACCU-
AL357314.11/76561-76632 GGUCAAUGAUGUAAUGGCAUGUAUUAGCUGAAUCUAAAGUUGAUG------------UGAGUUCUAAAAUUACACUGAGACCUU
X96644.1/1-84           GGUCAAUGAUGUGUUGGCAUGUAUUAUCUGAAUCUAUUGCUGAUGUGUAAUAACACUUUAGCUCUAGAAUUACUCUGAGACCUU
AL627443.6/42094-42164  GGUCAAUGAUGUCGUGGCAUGUAUCAGCUGAAUCCAAAGUUGAUG------------UGAGUUCCAAAAUUAUACUGAGACUU-
AL033518.14/62151-62081 GGUCAAUGAUGUAAUGGCAUGUAUUAGCUGAAUCCAGAGUUGAUA------------UGAGUUCUAAAAUUACACUGAAGCUG-
AL590229.3/91513-91584  GGUCAAUGAUGUAAUGGCAUGUAUUAGCUGAAUCCAAAGUUGAAG------------UGAAUUCUAAAAUUACACCAAGACCUU
AC087184.7/97885-97805  GGUCAAUGAUGUGUUGGCAUGUAUUAUCUGAAUUCGCUGAUG-UGUCAUA--ACACUUUAGCUCUAGAAUUACGCUGAGACCUU
AC087184.7/96828-96758  GGUCAGUGAUGUCAUGGCAUGUAUUAGCUGAAUGCUAACCUGAUG------------CAAGUUACAAA-UUACACUGAGACCUU
AL499609.9/76028-75947  GGUCAAA-AUGUGUUGACAUGUAUUACCUGAAUUUAUUGCUGAUGUAUAAUAACACUUCAACUCUAAAAUAAUAUAGCUUUUG-
#=GC SS_cons            <<<<_____________________________________________...__________________________>>>>::
#=GC RF                 GGucAAUGAUGUauUGGCAUGUAUUAgCUGAAUcuAaaGuUGAUGuuuA...acACUUuAGuUCUAaAAUUACaCUGAgaCCUu
//
# STOCKHOLM 1.0

#=GF AC   RF00280
#=GF ID   SNORD51
#=GF PI   U51
#=GF DE   Small nucleolar RNA SNORD51
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   49.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00054
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300725;
#=GF DR   snoopy; Loxodonta_africana300446;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF CC   U51 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD51
#=GF SQ   14


AL049840.8/49457-49533     AUUGUUACAU--UGA-UAAAAUCAAAUCACCAUCUUUUAGCUAAGCUUGUGCUGGAUUUGCUUUUUUUCUGAUAAAGAUG
AL645950.13/73701-73778    CUGGGUACAUGAUGAAUAAAAUCAAAUCACCUUCUUUCGGCUGAGCUCCUGAUGGAUUUGCUUUUU--CUGAUAAAUCUG
X96650.1/1-70              ---GUUGCAUGAUGAAUAAAAUCAAAUCACCAUCUUUCGGCUGAGUUCGUGAUGGAUUUGCUUUUUU-CUGAUU------
AAPY01284286.1/1238-1315   CUGGUUACAUGAUGAAUAAAAUCAAAUCACCAUCUUUCGGCUGAGGUCCUGAUGGAUUUGCUUUUU--CUGAUAAAGCUG
AAYZ01152970.1/1365-1442   CCAGUUACAUGAUGAAUAAAAUCAAAUCACCAUCUUUCGGCUGAGCUCGUGAUGGAUUUGCUUUUU--CUGAUGAAACUG
AALT01001762.1/215-139     CUGGUUGUGUGAUGAAUAAAAUCAAAUCACCAUCUUUCGGCUGAGUUCCUGAUGGAUUUGCUUUUUU-CUGAUAA--CAG
AAFR03041977.1/28195-28118 CUGGCUACAUGAUGAAUAAAAUCUAAUCACCAUCUUUCGGCUGAGUUCGUGAUGGAAUUGCUUUUUU-CUGAUU-GGCUG
AANG01689589.1/2853-2930   ACUUAAAAAUGAUGAGUAAAACCAAAUCACCAUCUUUCGGCUGAGCUCGUGAUGGAUUUGCUUUUUU-CUGAU-GAGACU
AAWR02007092.1/1049-1127   CCUGUUACAUGAUGAAUAAAAUCAAAUCACCAUCUUUCGGCUGAGCUCCUGAUGGAUUUGCUUUUUU-CUGAUACAGUUG
AAQR03032350.1/10236-10158 CUGGUUCCAUGAUGAAUAAAAUCAAAUCACCAUCUUUCGGCUGAGCUGGUGAUGGAUUUGCUUUUUU-CUGAUAAAGCUG
AABR05162547.1/29642-29719 CUGGGUACAUGAUGAAUAAAAUCGAAUCACCAUCUUUCGGCUGAGCUCCUGAUGGAUUUGCUUUUUU-CUGAUGUC-CAG
AAGU03009554.1/92752-92675 CUGCUUAUGUGAUGAAUCAAAUCA-AUCACCAUCUUUCGGCUGAGCUUGUGAUGGAUUUGUUUUUUU-CUGAUAAAGCUG
AAWZ02015247.1/62710-62633 UUGGUGACAUGAUGAACAAAACCAAAUCACCAUCUUUCGGCUGAAAUUGUGAU-GAUUUGUUUUUUU-CUGAAUGAUCUA
EU094134.1/5-68            -------CAUGAUGAAUCAAAUCAAAUCACCAUCUUUCGGCUGAGAUCGUGAUGGAUCUGCUUUAUU-CUGA--------
#=GC SS_cons               <-<--<<____________________________________________________________.____>>--->->
#=GC RF                    cUgGuuacAUGAUGAAUAAAAUCAAAUCACCAUCUUUCGGCUGAGcUcgUGAUGGAUUUGCUUUUUU.CUGAuaaAgcug
//
# STOCKHOLM 1.0

#=GF AC   RF00281
#=GF ID   SNORD47
#=GF PI   U47
#=GF DE   Small nucleolar RNA SNORD47
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; ILM; Moxon SJ, Daub J
#=GF GA   50.00
#=GF TC   50.30
#=GF NC   49.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300641;
#=GF DR   snoopy; Oryzias_latipes300022;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF RN   [3]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   U47 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD47
#=GF SQ   20


X96647.1/1-77                AACCAAUGAUG-UAAUGAUUCUGCCAAAUGAAAUA-UAAUGAUAUCA-CU-G-UAAAACCGUUCCAUUUUGA-UUCUGAGGUU
X67268.1/1927-2003           AACCAGUGAUG-UGAUGAUUCUGCCAAAUGAUACA-AAGUGAUAUCA-CC-U-UUAAACCGUUCCAUUUUAU-UUCUGAGGUU
AF357371.1/1-65              ----------G-UGAUGAUUCUGCCAAAUGAUACA-AAGUGAUAUCA-CC-U-UUAAACCGUUCCAUUUUAU-UUCUGAGG--
AAIY01534871.1/691-615       AACCAAUGAUG-UAAUGAUUCUGCCAAAUGAAACA-UCAUGAUAUUA-CU-C-AAUAACCGUUCCAUUUUAA-UUCUGAGGUU
ABDC01278790.1/3577-3652     AACCAAUGAUG-UAAUGAUUCUGCCAAAUGAAAUA-GAAUGAUAUCA-CU-U-AAAAACCGUUCCAUUUUG--UUCUGAGGUU
AAPY01728088.1/9117-9195     AACCAAUGAUGUUAAUGAUUCUGCCAAAUGAAAUA-GAAUGAUAUCA-CU-UAUAAAACCGUUCCAUUUUGA-UACUGAGGUU
AAYZ01154866.1/3685-3609     AGCCAGUGAUG-CAAUGAUUCUGCCAAAUGAAAAA-GAAUGAUAUCA-CC-U-GCAAACCGUUCCAUCUAAA-CACUGAGGCU
AAFC03120161.1/30696-30772   AACCAGUGAUG-UGAUGAUUCUGCCAAAUGA-AUA-GAAUGAUAUCAACC-A-AAAAACCGUUCCAUUUUGA-UUCUGAGGUU
AAPN01008930.1/64475-64398   AACCAAUGAUG-AUAAGAUUCUGCCAAAUGAAAGA-GACUGAUUUCA-CC-U-AUAAAACGUUCCUUUUUUUAUUCUGAGGUU
AAFR03026464.1/108949-108871 AACCAGUGAUGUUAAUGAUUCUGCCAAAUGAAAUGGCAAUGAUUUCA-CC-C-AUAUACCGUUCCACUUUUA-UUCUGAGGUU
BAAE01161714.1/315-390       AACCGAUGAUG-AAACGAUUUUGCCAAAUGACUCC-UGCUGAUUAUA-AC-C-CUUUACCGUUCCAUUUUU--UUUUGAGGUU
BAAF04088084.1/9612-9687     AACCGAUGAUG-AAACGAUUCUGCCAAAUGACUGC-UGCUGAUUAUA-AC-C-CUUUACCGUUCCAUUUUU--GUCUGAGGUU
CR759968.6/155156-155227     AACCUGUGAUG-AAAUGAUUCUGCCAAAUGAAUCC-UAAUGAUUAUA-CC-C---CAACCGUUCCAUAU----UUCUGAGGUU
CR759968.6/155415-155485     AACCUGUGACG-ACAUGAUUCUGCCAAAUGA-AUC-UAAUGAUUAUA-CC-C---CAACCGUUCCAUAU----UUCUGAGGUU
AAGV020619277.1/2224-2299    AACCAGUGAUG-UAAUGAUUCUGCCAAAUGAAGUA-GAAUGAUAUCA-CU-C--AAAACCGUUCCAUAUUGU-UUCUGAGGUU
AAWR02036950.1/19475-19398   AACCAGUGAUG-UGAUGAUUCUGCCAAAUGAAAUA-GAAUGAUAUCA-CU-UAUAAAACCGUUCCAUUUUGA-UUCUGAGGUU
AAPE02018271.1/28457-28381   AACCAGUGAUG-UAGUGAUUCUGCCAAAUGAAAUA-GGAUGAUAUCA-CU-C-AUUUACCGUUCCAUUUUUA-UUCUGAGGUU
AAGU03036956.1/69957-70033   AACCAGUGAUG-UAAUGAUUCUGCCAAAUGAAAUA-GAAUGAUAUCA-CU-C-AAAAACCGUUCCAUUUUAA-UUCUGAGGUU
AAQR03057788.1/30947-31024   GAUCAAUGGUG-UAAUGAUUCUGCCCAAUGAGAUA-GAAUGAUAUCA-UUUG-UAAAACUAUUCCAUUUUGA-UUCUGAGGUU
JN899112.1/1-75              AACCAGUGAUG-UGAUGAUUCUGCCAAAUGA-AUA-AGAUGAUAUCA-CC-C-AUAAACCGUUCCAUUUUGA-UUCUGAGG-U
#=GC SS_cons                 <<<<_______._______________________.___________.__._.___________________.______>>>>
#=GC RF                      AACCAgUGAUG.uaAUGAUUCUGCCAAAUGAaAuA.gAAUGAUaUCA.Cc.u.auaAACCGUUCCAUUUUuA.UUCUGAGGUU
//
# STOCKHOLM 1.0

#=GF AC   RF00282
#=GF ID   SNORD48
#=GF PI   U48
#=GF DE   Small nucleolar RNA SNORD48
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   36.00
#=GF TC   36.20
#=GF NC   34.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300616;
#=GF DR   snoopy; Loxodonta_africana300453;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF CC   U48 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD48
#=GF SQ   8


AF109906.1/101404-101342   AGUAAUGAUGAUUUCUGGUGAUUCUGAGUGUC-UCGCUGACGCCAUCACCGCAGCGCGCUGACC
AL773527.8/127279-127217   GGUAAUGAUGACCCCAGGUGAUUCUGAGUGUC-UCGCUGACGCCAUCACCGCAGCGCGCUGAUC
X96648.1/1-63              AGUGAUGAUGACCCCAGGUAACUCUGAGUGUG-UCGCUGAUGCCAUCACCGCAGCGCUCUGACC
AALT01488983.1/1433-1494   GGUGAUGAUGACC-CAGGUGACUCUGAGUGUC-UCGCUGACGCCAUCACCGCAGCGCGCUGACC
AAYZ01082793.1/1567-1630   GGUAAUGAUGACCUUAGGUGAUUCUGAGUGCCAUCGCUGACGCCAUCACCGCAGCGCGCUGACC
AAGU03088573.1/8929-8868   UG-AUUGAUGACCCCAGGUGAUUCUGAGUGUC-UCGCUGACGCCAUCACCGCAGCGCGCUGACA
AAGW02070280.1/39680-39741 GUUGAUGAUGACCCCAGGUGACUCUGAGUGUC-UCGCUGACGCCAGCACCGCAGCGCGCUG-AC
JN899113.1/2-64            GGUAAUGAUGACCCCAGGUGAUUCUGAGUGUC-UCGCUGACGCCAUCACCGCAGCGCGCUGAUC
#=GC SS_cons               <<______________________________._____________________________>>
#=GC RF                    ggUaAUGAUGACCcCAGGUGAuUCUGAGUGUC.UCGCUGACGCCAUCACCGCAGCGCGCUGAcc
//
# STOCKHOLM 1.0

#=GF AC   RF00283
#=GF ID   SCARNA18
#=GF PI   U91
#=GF DE   small Cajal body-specific RNA 18
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:12032087, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   40.00
#=GF TC   42.10
#=GF NC   38.70
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [3]
#=GF RM   15556860
#=GF RT   Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for
#=GF RT   modification of snRNAs in metazoa.
#=GF RA   Tycowski KT, Aab A, Steitz JA
#=GF RL   Curr Biol. 2004;14:1985-1995.
#=GF RN   [4]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. This C/D box domain U91
#=GF CC   (also known as U4-8) was identified by Darzacq and is predicted to guide
#=GF CC   the 2'O-ribose methylation of U4 snRNA C8 [1]. This C/D domain was later
#=GF CC   found associated in tandem with another C/D box domain U12-22
#=GF CC   (RFAM:RF00492). Both the doublet (U12-22/U4-8) and singlet (U4-8) forms of
#=GF CC   this snRNA have been purified from Hela cells [1]. The doublet form
#=GF CC   U12-22/U4-8 has been shown to localise to the nucleoplasm and is proposed
#=GF CC   to reside in the Cajal bodies whereas the U4-8 single domain appears to
#=GF CC   accumulate in the nucleolus [3]. In humans the genomic location of
#=GF CC   U12-88/U4-8 is intergenic and the purified transcript has been shown to
#=GF CC   possess a methylated guanosine cap suggesting it is independently
#=GF CC   transcribed by RNA pol II [3].
#=GF WK   Small_Cajal_body_specific_RNA_18
#=GF SQ   20


AF357342.1/1-62            --------------AU-GACCACU-GCGCAAUCUGAGUUCUGGGAACCAGGUGAUGGAGUGUG--CUGAGAACA--CUGAGG---
AY077741.1/1-83            UGGCCGAUGAUGACGA-GACCACU-GCGCAAUCUGAGUUCUGGGAACCAGGUGAUGGAGUAUGUUCUGAGAACAGACUGAGGCCG
AC090227.10/15359-15277    UGGCCGAUGAUGACGA-GACCACU-GCGCAAUCUGAGUUCUGGGAACCAGGUGAUGGAGUAUGUUCUGAGAACAGACUGAGGCCG
AL592064.14/82927-83010    UGGCCAGUGAUGAAGU-CACCAUUAGUGCAGUCUGAGUUCUGGGAACCAGGUGAUGGAGUGUGUUCCAAGAAUGGACUGAGGGCC
AANU01101212.1/1480-1562   UGACCAGUGAUGAAGU-CACCAUU-GUGCAGUCUGAGUUCUGGGAACCAGGUGAUGGAGUGUGUUCUAAGAACUGACUGAGGGCC
ABDC01297764.1/1645-1727   UUGCCGAUGAUGACGU-GACCACU-GCGCAAUCUGAGUUCUGGGAACCAGGUGAUGGAGUGUGUUCUGAGAACGGACUGAGGCUG
AAYZ01094280.1/2675-2757   UGGCCAAUGAUGACCA-GACCACU-GCGCAAUCUGAGUUCUGGGAACCAGGUGAUGGAGUGUGCUCUGAGCACGGACUGAGGCCG
AAFC03053505.1/66323-66241 UGGUCGAUGAUGACGU-GACCACU-GCGCAAUCUGAGUUCUGGGAACUAGGUGAUGGAGCGUGUUCUGAGAACGGACUGAGACCG
AAPY01347300.1/1993-1911   UGGCCGAUGAUGACGU-GACCACU-GCGCAAUCUGAGUUCUGGGAACCACCUGAUGGAGCGUGUUCUGAGAACCGACUGAGGCCG
AAIY01249536.1/1104-1186   CGGUCGGUGAUGACGU-GACCACU-GCGCAAUCUGAGUUUUGGAAACCAGAUGAUGGAGUGUGAGCUAAGCACGGACUGAGGCCG
AANN01109527.1/812-730     UGGUCGAUGAUGACCUAGACCACU-GCGCAAUCUGAGUUCUGGGAACCAGGUGAUGGAGUGUGUCCUGAGGACAG-CUGAGACCG
AANG01025936.1/3125-3205   UGGUCAAUGAUGACGU-GACCACU-GCGCAAUCUGAGUUCUAGGAACCUGGUGAUGGAAUGUG--CUCAGAGCGGACUGAGACCG
AAHX01095967.1/17609-17687 CUGCCGAUGAUGACAU-GACCACU-GCGCAAUCUGAGUUCUGGGAACCAGGUGAUGGAUUGUG--CUGCGAACA--CUGAGGCCA
AAKN02020097.1/24241-24159 UGGCCAAUGAUGACUA-GACCACU-GCGCAAUCUGAGUUCUGGGAACCAGGUGAUGGAGUGUGCUGUAACAGCAGACUGAGGCCG
AAGV020429307.1/439-358    UGGUCGGUGAUGACGU-GACCACU-GCUCAAUCUGAGUUCUUAGAACCAGGUGAUGGAGUGUGG-CUGAGAAUGGACUGAGACCG
AAGU03013210.1/58113-58031 UGGUCGGUGAUGACGU-GACCACU-GCGCAAUCUGAGUUCUGGGAACCAGAUGAUGGAGCCUGUGCUGAGCACGGACUGAGACAG
AAGW02032389.1/3932-4014   UGGCCAAUGAUGACCA-GACCACU-GCGCAAUCUGAGUCCUGGGCACCAGGUGAUGGAGUGUGUUCUGAGAACAGACUGAGGCCG
AAEX03017760.1/16604-16686 GGGUCGAUGAUGACGU-GACCACU-GCGCAAUCUGAGUUCUAGGAACCAGGUGAUGGAGUGGAUGCUGAGAGCGGACUGAGACCU
AAPE02017035.1/34119-34194 UGGUCAAUGAUGACAA-GACCACU-GCGCAAUCUGAGUUCUGGAAACCAGAUGAUGGAGUGUGUUCGGA-------CUGAGACCG
AAQR03077543.1/26098-26180 UCGCCGAUGAUGACAG-GACCACU-GCGCAGUCUGAGAUCUGGGAACCAGGUGAUGGAGUGUGUUCUCAGAACGGACUGAGGCUG
#=GC SS_cons               :<<<<-----------.-------.--------------<<<<___>>>>------------------------------>>>>:
#=GC RF                    UggcCgAUGAUGACgu.GACCACU.GCGCAAUCUGAGUUCUgGGAACcAGGUGAUGGAGUGUGuuCUgAGAACgGACUGAGgccg
//
# STOCKHOLM 1.0

#=GF AC   RF00284
#=GF ID   SNORD74
#=GF PI   snoZ18; Z18
#=GF DE   Small nucleolar RNA SNORD74
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   41.00
#=GF TC   41.70
#=GF NC   40.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00069
#=GF DR   snoRNABase; U74;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300795;
#=GF DR   snoopy; Homo_sapiens300096;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   9819378
#=GF RT   Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene
#=GF RT   and a member of the 5'-terminal oligopyrimidine gene family reveals common
#=GF RT   features of snoRNA host genes.
#=GF RA   Smith CM, Steitz JA
#=GF RL   Mol Cell Biol. 1998;18:6897-6909.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   Z18 also identified as U74 (SNORD74) belongs to the C/D class of snoRNA
#=GF CC   which contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members
#=GF CC   of the box C/D family function in directing site-specific 2'-O-methylation
#=GF CC   of substrate RNAs [1]. U74 is predicted to guide the 2'O-ribose
#=GF CC   methylation of 28S rRNA residue C3820 [3]. In humans U74 shares the same
#=GF CC   non-protein coding host gene (gas5) with 9 other snoRNAs (U44, U47, U75,
#=GF CC   U76, U77, U78, U79, U80 and U81)[2].
#=GF WK   Z18_small_nucleolar_RNA
#=GF SQ   22


AF141346.1/240-319           GUG-CCCUGCCUCUGAUGAAGCCU-G-UGUUGGUAGGGACAUCUGACAGUAA-UGAUGAAUGCCAACCGCUCUGAUGGUGGCAC
AL591203.15/7971-8050        GUG-CCCUGCCUCUGAUGAAGCCU-G-UGUUGGUAGGGACAUCUGAGAGUAA-UGAUGAAUGCCAACCGCUCUGAUGGUGGCAC
AJ224026.1/1-80              GUG-CCCUGCCUCUGAUGAAGCCU-G-UNUUGGUAGGGACAUCUGAGAGUAA-UGAUGAAUGCCAACCGCUCUGAUGGUGGCAC
AC107390.4/33836-33915       UUG-AUCUACCUCUGAUGAAACCU-G-UGUUGGUGGGGACAUCUGAGAGUGU-UGAUGAAUGCCAGUGACUCUGAUAGAAAAAA
ABDC01278790.1/451-530       GUU-CCCUGCCUCUGAUGAAGCCU-G-UGUUGGUAGGGACAUCUGAGAAUGU-UGAUGAAUGCCAACUGCUCUGAUGGCCGAAC
AAFC03120161.1/27739-27818   UUG-CUCUGCCUCUGAUGAAGCCU-G-UGUUGGUAGGGACAUCUGAGAUUGU-UGAUGAAUGCCAACGGCUCUGAUGGCGGCGU
AACN010363118.1/4-83         GCU-UCCUGCCUGUGAUGAAGCCU-G-UGUUGGUAGGGACAUCUGAGACUGU-UGAUGAAUGCCAACGGCUCUGAUGGCGGCGC
AAPY01728088.1/6170-6246     UUC-CCCUGCCUCUGAUGAAGCCU-G-UGUUGGUAGGGACAUCUGAGAAAAC-UGAUGAAUGCCAACGGCUCUGAU---GGCAG
AAHY01000621.1/5079-5000     GUG-UUCAUGCUAUGAUGAAGGCU-A-UGUUGGUAGGGACAACUGAGCUUGU-UGAUGAAUACCAACGAUUCUGAUGGCAGAGC
AAIY01534871.1/2905-2829     GUG-GCGUGCCUGUGAUGAAGCUC-G-UGUUGGUAGGGACAUCUGAGACU---UGAUGAAUGCCAACUGCUCUGAUGGCG-CAU
AAQQ01622741.1/4914-4988     AUG-CC-----UGGGAUGAAGCCU-G-UGUUGGUAGGGACAUCUGAAAGUGC-UGAUGAAUGCCAGUGGCUCUGAUGGUGGUGU
AAFR03026464.1/112950-112873 CCU-UGCUGUGUGUGAUGAAAGUA-A-CGUUGGUAGGGACAUCUGAGAUUGC-UGAUGAAUGCCAACGUCUCUGAUG--CGGGG
AAPN01008930.1/68818-68738   UGC-CCCUACCUGUGAUGAAAACAAG-UGUUGGUAGGGACAUCUGAGAAAGC-UGAUGAAUGCCAACACAGCUGAGUCGGGGCU
AAWR02036950.1/22598-22519   GUG-UCCUGCCUCUGAUGAAGCCU-G-UGUUGGUAGGGACAUCUGAGACUGU-UGAUGAAUGCCAACGGUUCUGAUGGCGGUGC
AAGV020273689.1/518-597      GUG-CCCUGCCUCUGAUGAAACCA-A-UGUUGGUAGGGACAUCUGACGAUGU-UGAUGAAUGCCAACAGCUCUGAUGGUGGCGC
AAHX01076292.1/16150-16070   GUGACUCUUGCAAUGAUGAAGGUU-A-UGUUGGUAGGGACAACUGACCUUGU-UGAUGAAUACCAACAAUUCUGAUGGCAGAGC
CU467861.6/34076-34156       UGU-UUACUUGUAUGAUGAAGAAU-A-UGUUGGUAGGGACAUCUGAGAAAAUCUGAUGAAUGCCAACAUUUCUGACAUGUAGCA
AAGU03036956.1/66981-67058   GUG-CCCUUCCUGUGAUGAAACCU-G-UGUUGGUAGGGACAUCUGAGACU---UGAUGAAUGCCAACUUCUCUGAUGGCAGUGC
AAWZ02013556.1/133203-133124 CUC-CCCUGCACAUGAUGAUAAAU-GAUGUUGGUAGGGACAUCUGAGAAU-A-UGAUGAAUACCAACAUCUCUGAGCCAGGGGU
AAPE02018271.1/31457-31378   GUG-CCCUGCCUCUGAUGAAGCUU-A-UGUUGGUAGGGACAUCUGAGACUGU-UGAUGAAUGCCAACAGCUCUGAUGGCGGCGC
AADN03005691.1/156359-156282 GUG-CCC-GCACAUGAUGAAAACU-A-UGUUGGUAGGGACAUCUGAGAG-GC-UGAUGAGUACCAACAUAUCUGAGCUGGGCAU
AAQR03038677.1/7923-8000     GUG-CCCUGCCUCUGAUGAAGCCC-A-UGUUGGUAGGGACAUCUGAGAGU---UGAUGAAUGCCAACUGCUCUGAUGGUGGAGC
#=GC SS_cons                 <<<.<<__________________._._________________________.__________________________>>>>>
#=GC RF                      gcg.ccCUgccUaUGAUGAAgccU.g.UGUUGGUAGGGACAUCUGAGAaUGu.UGAUGAAUGCCAACagcUCUGAUgguggcgc
//
# STOCKHOLM 1.0

#=GF AC   RF00285
#=GF ID   snoZ6
#=GF PI   Z6
#=GF DE   Z6 small nucleolar RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   35.00
#=GF TC   35.10
#=GF NC   34.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   Z6 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Z6_small_nucleolar_RNA
#=GF SQ   7


BC041570.1/378-468   UGCUGGUGGUGAAGCUCCCUCUCUCCGAGCACUGGGCCCUGCCUGGGGGCUCCCGGGAGCCAGGGGAGAUGCUACCUCGGAAGCUGAAGCG
AJ010679.1/1-91      UGCUGGUGGUGAAGCUCCCUCUCUCCGAGCACUGGGCCCUGCCUGGGGGCUCCCGGGAGCCAGGGGAGAUGCUACCUCGGAAGCUGAAGCG
AJ344343.1/4557-4647 UGCUAGUGAUGAAGCUGCCUCGCUCUGAGCACUGGGCCUUGCCUGGGGGCUCUAGGGAGCCAGGGGAGAUGCUACCACGGAAGCUGAAACG
AY749166.1/4115-4205 UGCUGGUCAUGAAGUUGCCUCAAUCCGAGCACUGGGCCUUGCCUGGGGGCUCUCGGGAGCCAGGGAAGAUGCUACCACGGAAGCUGAAACA
AB017549.1/452-542   UGCUGGUGGUGAAGCUCCCUCUCUCCGAGCACUGGGCCCUGCCUGGGGGCUCCCGGGAGCCAGGGGAGAUGCUACCUCGGAAGCUGAAGCG
AB166747.1/4408-4498 UGCUAGUGAUGAAGCUGCCUCGCUCUGAGCACUGGGCCUUGCCUGGGGGCUCUAGGGAGCCAGGGGAGAUGCUACCACGGAAGCUGAAACG
AB193179.1/4143-4233 UGCUGGUCAUGAAGUUGCCUCAAUCCGAGCACUGGGCCUUGCCUGGGGGCUCUCGGGAGCCAGGGAAGAUGCUACCACGGAAGCUGAAACA
#=GC SS_cons         <<<<___________________________________________________________________________________>>>>
#=GC RF              uGcUgGUgaUGAAGcUgCCUCucUCcGAGCACUGGGCCuUGCCUGGGGGCUCucGGGAGCCAGGGgAGAUGCUACCaCGGAAGCUGAAgCg
//
# STOCKHOLM 1.0

#=GF AC   RF00286
#=GF ID   SCARNA8
#=GF PI   U92
#=GF DE   Small Cajal body specific RNA 8
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Published; PMID:12032087
#=GF GA   53.00
#=GF TC   54.10
#=GF NC   52.90
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. U92 belong to the H/ACA box
#=GF CC   class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail
#=GF CC   structure, conserved H/ACA-box motifs and is found associated with GAR1
#=GF CC   [1]. Its is predicted to guide the pseudouridylation of residues U44 in U2
#=GF CC   snRNA [1]. This family also includes the mouse H/ACA box snoRNA MBI-57
#=GF CC   identified in [2].
#=GF WK   Small_Cajal_body_specific_RNA_8
#=GF SQ   22


AY077742.1/1-131             UGGGAGGCUGAUACACAAAUUGGGCUGAA--AUACUGCUCUACUUGUCACCAUGCCUCCCUAGAAUAA---A-C-UGCCUUUUGAUGACCGGGACGAAUUGAGUGAAAUCGUAACGGACAGAUACGGGGCAGACAGAU
AF357402.1/1-118             -------------CGCAACUUGGGCAGAA--GUACUGCUCCAGUUGUCACUGGACCUCCCCAGAGUAA---A-C-UGCCUUUUGAUGACCAGGGCGAAUUGAGUGAAAUCGUCAUGGACAGAUACGGGGCAGACAAUU
AL824707.7/136518-136388     CGGGAGAGUGAUACGCAACUUGGGCAGAA--GUACUGCUCCAGUUGUCACUGGACCUCCCCAGAGUAA---A-C-UGCCUUUUGAUGACCAGGGCGAAUUGAGUGAAAUCGUCAUGGACAGAUACGGGGCAGACAAUU
AAYZ01536223.1/357-487       UGGGAGGCUGAUACACAAAUUGGGCUAGA--GUACUGCCCUAAUUGUCACAGUGCCUCCCUAGAGUAA---A-C-UGCCUUUUGAUGACCGGGACGAAUUGAGUGAAAUCGUAACGGACAGAUACGGGGCAGACAGUU
AANG01621014.1/2846-2976     UGGGAGGCUGAUACACAAAUGGGGCUGAA--GUACUGCUCUGAUUGUCACUGUACCUCCCUAGAAUAA---A-C-UGCCUUUUGAUGACCGGGACGAAUUGAGGGAAAUCGUAACGGACAGAUACGGGGCAGACAGUU
AALT01563465.1/3655-3785     UGGGAGGCUGAUACACAAAUUGGGCUGAA--GUAGUGCUCUGAUUGUCACCAUACCUCCCCAAAACAA---A-C-UGCCUUUUGAUGACCGGGACGAAUUGAGUGAAAUCGUAACGGACAGAUACGGGGCAGACAGUU
AAFC03023002.1/28553-28420   UGGGAGGCUGAUACACAAAUUGGGCUGAA--GUACUGCUCUAAUUGUCACUAUACCUCCCUAGAAUAAUACA-C-UGCCUUUUGAUGACCGGGACGAAUUGAGAGAAAUCGUAACGGACAGAUACGGGGCAGACAGUU
AANN01823665.1/3599-3469     UGGGAGGCUGAUACACAAGUUGGGCUGAA--GUACUGCUCUGUUUGUCACUACACCUCCCUAGAACAA---A-C-UGCUCUUCGAUGACCGGGACGAAUUGAGAGAAAUCGUAACGGACAGAUACGGGGCAGACAGUU
AAPN01422918.1/1235-1366     UGGGAGACUGAUACACAGAUAGGGCUGAA--GUACUGCUCUAAAUGUCACAAUGCCUCCCUAGAAUAA---AAC-UGCCUUUUGAUGACCGGAACGAAUUGAGUGAAAUCGUAACGGACAGAUACGGGGCAGAUAACU
AAIY01287712.1/1130-1262     UGGGAGGCUGAUACACAAAUUGAGCUGAAGUGUGCUGCUCUAAUUGUCACCAAACCUCCCUAGAAUAA---A-C-UGCCUUUUGAUGACUGGGACGAACUGAGUUAAAUCGUCACGGACAGAUACGGGGCAGACAGUU
BX005437.5/116336-116466     UGGGAAACUGAUACAAGGGCAGUGU-UAA--GCAGUACUCUACCCUUCACAAGUUUUCCCUAUAUCAA---ACC-UGCUCUCUGAUGACCGGUGCGAGUUGAGAGAAAUCGCCACGGACAGAUACGGGGCAGACAUAC
BAAF04014862.1/7646-7516     UGGGAGGCAGAUACCUGGACAGUCCAGAA--GUGU-GCGCUGUCUGUCACUGGUCCUCCCUAGAGAAU---C-CUUGCUCUCUGAUGACCGCGGCGAAUUGAGAGAAAUCGCCACGGACAGAUACGGAGCAGACACUG
AANH01007175.1/10629-10499   UGGGAGGCAGAUACCUGGGCAGUCCUGA---GUAGUGCUCUGUCCGUCACUAGUCCUCCCUACAGCAU---CCC-UGCUCUCUGAUGACCGAGGCGAACUGAGAGAAAUUGCCACGGACAGAUACGGAGCAGACACUU
CAAE01003771.1/1780-1650     UGGGAGGCAGAUACCUGGGCAGGCCUG-A--GCGCCGGCCUGUCCGCCACGCGUCCUCCCGACAGCAU---CGC-UGCUCUCUGAUGACCGCGGCGAGUUGAGGGAAAUCGCCGCGGACAGAUACGGAGCAGACAGGC
AAKN02033215.1/216587-216460 UGGAAGGCAAACACACAAAUUGGGCUGAC--AUGCUACUCUAAUUGCCCCCAGGCCUCCCUAGACUAC---A-U-UGCUUUUUGAUGACCAAGACA--UUAAAUGAAA-UGCAACGGACAGAUGUGGGGCAGUCAAUU
AAGW02032988.1/3004-2874     UGGGAGGCUGAUACACAAAUUGAGCUGAG--GUGCUGCUCUGAUUGUCACGAUGCCUCCCUAGAAUAA---A-C-UGCCUUUUGAUGACCGGAACGAAUUGAGAGAAAUCGUAACGGACAGAUACGGGGCAGACAGUU
AAGU03018929.1/83475-83605   UGGGAGGCUGAUACACAAAUUGGGCUGAA--GUACUGCUCUAAUUGUCACCAUACCUCCCUAGAAUAA---A-C-UGCCUUUUGAUGACUGGGAUGAAUUGAGUGAAAUCAUAACGGACAGAUACGGGGCAGACAGUU
AAPE02029438.1/84827-84957   UGGGAGGCAGAUACACAAAUUGAGCUGCA--GUACUGCUCUAAUUGUCACCAUACCUCCGUAGAAUAA---A-C-UGCCUUUUGAUGACCGGGACGAAUUGAGAGAAAUCGUAACGGACAGAUACGGGGCAGACAGUU
CAAB02006631.1/18904-19033   UGGGGGGCAGAUACCUGGGCAGGCCUGA---GCACUGGCCUGUCCGUCAC-GCGUCUCCCGACAGAAU---UCC-UGCUCUCUGAUGACCGCGGCGAGUUGAGGGAAAUCGCCGCGGACAGAUACGGAGCAGACACUC
AABR05027791.1/11759-11629   CGGGAGAGUGAUACACAAGUUGGGCAGAA--GUGCUGCUCCAAUUGUCACUAGAUCUCCCCACAGUAA---A-C-UGCCUUUUGAUGACCAGGGCGAAUUGAGUGAAAUCGUCAUGGACAGAUACGGGGCAGACAAUU
AAWZ02018546.1/20024-20154   UGGGAGGCUGAUACUCAAUGAGAG-AAAA--GCCAUGCUCUCCUUGUCACAAGCUCUCCCUAUAACAA---G-GAUGCCUUUCGAUGACCGGAACGAACUGAGGGAAAUCGUAACGGACAGAUACGGGGCACACAAUU
EU240326.1/2-131             UGGGAGGCUGAUACACAAAUAGGGCUAAA--U--CUGCUCUAGUUGUCACAUGUUCUCCCUAUAGUAA---AAU-UGCCUUCUGAUGACCGGGACGAAUUGAGGGAAAUCGUAACGGACAGAUACGGGGCACACAAGU
#=GC SS_cons                 :<<<<<<-------<<<<---<<<<____.._____>>>>--->>>>------->>>>>>--------...-.<.<<<<<<-------<<<--<<<<___________>>>>-->>>-------->>>>>>>::::::
#=GC RF                      UGGGaGgCuGAUACacagauuGggCugAA..GUacUGccCUaacuguCACuauacCuCCCuAgAauAa...a.c.UGCccuuUGAUGACCGgggCGaAUUGAGuGAAAuCGcaACGGACAGAUACgggGCAgACAauu
//
# STOCKHOLM 1.0

#=GF AC   RF00287
#=GF ID   SNORD44
#=GF PI   U44
#=GF DE   Small nucleolar RNA SNORD44
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; Moxon SJ, Daub J
#=GF GA   40.00
#=GF TC   40.70
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00060
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Rattus_norvegicus300167;
#=GF DR   snoopy; Macaca_mulatta300477;
#=GF RN   [1]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF RN   [2]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   U44 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1,2].
#=GF WK   Small_nucleolar_RNA_SNORD44
#=GF SQ   12


AF141346.1/1960-2019         CCUGGAUGAUGAUA--GCAAAUG-CUGACUGAAC-AUGAAGGUCUUAAUUAGCUCUAACUGA-CU
X96643.1/1-60                CCUGGAUGAUGAUA--GCAAAUG-CUGACUGAAC-AUGAAGGUCUUAAUUAGCUCUAACUGA-CU
AL138691.15/31428-31368      CCUGGGUGAUGAUAA-GCAAAUG-AUGCCUGAAU-GUGAAGGUCAUACUCGGCUUUAGCUGA-UU
AAPY01728088.1/7700-7760     CCUGGAUGAUGAUAA-GCAAAUA-CUGACUGAAU-AUGAAGGUCUUAAUUAGCUCUAACUGA-UU
AANU01094999.1/4541-4481     CCUGGGUGAUGACAA-GCAAAUG-GUGCCUGAAU-GUGAAGGUCAUAUUUGGCUUUAACUGA-UU
AAIY01534871.1/1638-1579     CCUGUGUGAUGAUAA-GCAAAUG-CGGACUAAAG-AUGAAGGUCUUAAUUAGCUCUAGCUG--AU
AAQQ01328837.1/491-552       CCUGGAUGAUGAUAA-GAAGAUAACUGAUUGAAC-GUGAAGUUUUUAAUUAGCUCUAACUGA-UU
AAHX01076292.1/14842-14782   CCUACAUGAUGACAA-ACAAAUG-CUGACU-AAU-GUGAAGAUCUUAAUUAGCUCUAUCUGAUGU
AALT01136474.1/317-257       CCUGCAUGAUGAUAA-GCAAAGA-CUGACUCAAA-GUGAAGGUCUUA-UUAGCUCUACCUGACGC
AAKN02017778.1/47429-47490   CCUGGAUGAUGAUAA-GCAAAUA-CUGACUGAACUAUGAAGGUCUCAAUUAGCUCUAACUGA-UC
AAEX03005203.1/130747-130808 CCUGUAUGAUGAUAA-GCAAAUA-CUGACUGAAC-AUGAAGGUCUUAAUUAGCUCUACCUGACAU
AAQR03038677.1/9231-9291     CCUGGAUGAUGAUAAAGCAAGUA-CAGACUGAAA-GUGAA-GUCUUAAUUAGCUCUAACUGA-UU
#=GC SS_cons                 :::<<__________._______.__________.___________________________.>>
#=GC RF                      CCUggAUGAUGAUAA.GCAAAUa.CUGACUGAAu.gUGAAGGUCUUAAUUAGCUCUAaCUGA.cu
//
# STOCKHOLM 1.0

#=GF AC   RF00288
#=GF ID   snoZ30
#=GF PI   Z30
#=GF DE   Z30 small nucleolar RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   50.00
#=GF TC   52.60
#=GF NC   43.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300317;
#=GF DR   snoopy; Oryzias_latipes300067;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   Z30 belongs to the C/D class of snoRNA which contain the C (UGAUGA) and D
#=GF CC   (CUGA) box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Z30_small_nucleolar_RNA
#=GF SQ   20


AJ007734.1/1-97              AUGCAAUGAUGAGCG-AAGU-AUAGUCUGACCUGGUAUUGCCA-UUGCU-UU---GGCGC---UGGCUCUGACCAGGGUGUGAC--CC----C---UUAAUCUUCUCUCUGAGCUG
AL713883.1/98037-98133       AUGCAAUGAUGAGCG-AAGU-AUAGUCUGAUCUGGUAUUGCCA-UUGCU-UU---GGCGC---UGGCUCUGACCAGGGUGUGAC--CC----C---UUAAUCUUCUCUCUGAGCUG
AC118772.5/60281-60186       AUGCAAUGAUGAGUG-AAGU-ACAGUCUGACCUGGUAUUGCCA-UUGCU-UU---GCUA----UGGCUCUGACCAGGGUGUGAC--CC----C---UUAAUCUUCUCUCUGAGCUG
AJ007733.1/1-97              AUGCGAUGAUGAGUG-AAGU-AGAGCCUGACCUGGUAUUGCCA-UUGCU-UC---ACUGU---UGGCUUUGACCAGGGUAUGAU--CU----C---UUAAUCUUCUCUCUGAGCUG
AAQQ01699669.1/3347-3251     AUGCAAUGAUGAGCG-AAGU-AUAGACUGACCUGGUAUUGCCA-UUGCU-UU---AAUGU---UGGCUUUGACCAGGGUAUGAU--CC----C---UUAAUCUUCUCUCUGAGCUG
AAFC03037354.1/64880-64784   AUGCGAUGAUGAGUG-AAGC-AUAGUCUGACCUGGUAUUGCCA-UUGCU-UC---AGUGU---UGGCUUUGACCAGGGUAUGAC--CC----C---UUAAUCUUCUCUCUGAGCUG
AAYZ01014283.1/739-834       AUGCGAUGAUGAGUG-AAGU-AUAGUCUGACCUGGUAUUGCCA-GUG-U-UC---AAAGU---UGGCUUUGACCAGGGUAUGAC--CU----C---UUAAUCUUCUCUCUGAGCUG
AANN01181702.1/2299-2398     AUGCGAUGAUGAGUG-AAGU-AUAGUCUGACCUGGUAUUGCCA-UUGCU-GCAGAGUUGU---UGGCUUUGACCAGGGUAUGAU--CC----U---UUAAUCUUCUCUCUGAGCUG
AAFR03044613.1/158609-158513 ACGCAAUGAUGAGUG-AAGU-AUAGUCUGACCUGGUAUUGCCU-UGGCU-UC---UGUUU---UGGCUCUGACCAGGGCAUGAU--CA----C---UUAAUCUUCUCUCUGAGCUA
AAIY01778340.1/527-623       AUGCGAUGAUGAGUG-AAGU-CUAGUCGGACCUGGUAUUGCCA-UUGUG-UU---AGCUC---UGUCUCUGACCAGGGCAUGAC--CC----C---UUAAUCUUCUCUCUGAGCUC
AAPN01133377.1/2345-2444     ACGCAGUGAUGAGCGGAAGU-AUAGUUUGACCUGGUAUGGCCC-AGGCU-UC---CCGGC-UUGGGCCCUGACCAGGACAUGAU--CA----C---UUAAUCUUCUCUCUGAGCUG
AANH01004197.1/54667-54769   CUGCAGUGAUGAGCC--UUA-AGUGACUGAUCUGGUAUUGCUUUUUCCU-UU---CUUGGGGAGAGCUCUGACCAGGGAAUGAU--CU----CGACUUAAUCUUCUCUCUGAGCAG
AACN010227604.1/1368-1272    AUGCGAUGAUGAGUG-AAGU-AUCGUCUGACCUGGUAUUGCCA-UUGCU-UC---AGUGU---UGGCUUUGACCAGGGUAUGAU--UC----C---AUAAUCUUCUCUCUGAGCUG
AAQR03122085.1/8443-8347     AUGCGAUGAUGAGUG-AAGU-AGAGUCUGACCUGGUACUGCCA-CUGCU-UC---AGUGU---UGGCUUUGACCAGGGUAUGAU--CC----C---UUAAUCUUCUCUCUGAGCUG
CAAB02000194.1/112100-112004 CUGCAAGGAUGAUUG-UUGA-UGUGACUGACUUGGCACUGCUG---GCC-UC---CGGGU---CAGCUUUGGCCAGGAAAUGACAGCU----G---UUAAUCUUCUCUCUGAGCAG
AADN03007661.1/114214-114117 AAGCAAUGAUGAGUG-AAGU-AUUCUCUGAACUGGUAUUGCUG-AGACUCUU---UGUCU---UUGCUCUGACCAGGGCAUGAU--CA----C---GUAAUCUUCUCUCUGAGCUU
AAGU03054608.1/8430-8526     AGGCAAUGAUGAGUG-AAGU-GUAGGCUGACCUGGUAUGGCCA-UUGCU-UU---AGUCU---UGGCUUUGACCAGGGUAUGAU--CC----C---UCAAUCUUCUCUCUGAGCUG
AAPE02043924.1/52845-52749   AUGCGAUGAUGAGUG-AAGU-AUAGUCUGACCUGGUAUUGCCA-UUGCU-UC---AGUGU---UGGCUCUGACCAGGGUGUGAU--CA----C---UUAAUCUUCUCUCUGAGCUG
AAGW02039188.1/30086-30182   ACGCAAUGAUGAGUG-AAGU-AUAGUCUGACCUGGUAUUGCCA-CUGUU-UC---AAAGU---UGGCUUUGACCAGGGUAUGAU--CC----C---UUAAUCUUCUCUCUGAGCUG
AAGJ04141122.1/20295-20391   A-GCGAUGAUGAUUG-AAGUCAAUGCCUGACCUGAUAUGGCUU-GUGU--------CUAU---AAGCUUUGAUCAGUAGAUGAC--UCAUUAU---UUAAUCUUCUCUCUGAGCUG
#=GC SS_cons                 <-<<-----------.----.------------------<<<<._____.__..._____...>>>>-----------------..--....-...---------------->>>:
#=GC RF                      auGCaAUGAUGAGUG.AAGU.AuaGuCUGAcCUGGUAUUGCcg.uUGCU.Uu...agugu...cgGCUuUGACCAGGGuAUGAu..Cc....c...UUAAUCUUCUCUCUGAGCuG
//
# STOCKHOLM 1.0

#=GF AC   RF00289
#=GF ID   SNORND104
#=GF PI   snoZ12; Z12
#=GF DE   Small nucleolar RNA SNORD104
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   40.00
#=GF TC   42.70
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.43 -Z 549862.597050 CM SEQDB
#=GF CL   CL00077
#=GF DR   snoRNABase; U104;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300032;
#=GF DR   snoopy; Echinops_telfairi300001;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res. 2003;31:6543-6551.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. U104 (SNORD104) also known as Z12 is predicted to
#=GF CC   guide the 2'O-ribose methylation of C1327 of 28S rRNA [3].
#=GF WK   Z12_small_nucleolar_RNA
#=GF SQ   18


AC025362.12/104594-104663    GCUGUGAUGACAUUCCAAUU-AAA-GCACGUGUUAGACUGCUGACGCGGGUGAUGCGAACUGGAGUCUGAGC
AJ010676.1/1-70              GCUGUGAUGACAUUCCAAUU-AAA-GCACGUGUUAGACUUCUGACGCGGGUGAUGCGAACUGGAGUCUGAGC
AJ010677.1/3-72              GCGAUGAUGACACUCCAUAC-AUA-GCACGCGUUAGACUGCUGAUCCGGGUGAUGCGAAUCGUAAUCUGAGC
AAHX01066269.1/69687-69618   GCCAUGAUGACACUCCAUAC-AAA-GCACGCGUUAGACUGCUGAUCCGGGUGAUGCGAAUCGGAGUCUGAGC
AAQQ01697664.1/746-677       GCAGUGAUGACAUUCCAAAU-AAA-GCACGUGUUAGACUGCUGACGCUGGUGAUGCGAACUGUAGUCUGAGC
AALT01505651.1/668-599       GCCGUGAUGACAUUCCAAUC-AAA-GCACGUGUUAGACUGCUGAUGCUGGUGAUGCGAACAGAAGUCUGAGC
AAFC03045555.1/64581-64650   GCGGUGAUGACAUCCCAAAU-AAA-GCACGUGUUAGACUGCUGACGCGGGUGAUGCGAACUGGAGUCUGAGU
AC191241.1/59001-59070       GCCGUGAUGACUUUCCAAUU-AAA-GCACGUGUUAGACUGCUGACACGGGUGAUGAGAACUGGAGUCUGAGC
AANG01166973.1/2480-2549     GCAGUGAUGACAUGCCAAAA-AAA-GCACGUGUUAGACUGCUGACGCGGGUGAUGCGAACUACAGUCUGAGC
AAPY01361107.1/2082-2012     GCGGUGAUGACCUCCCAAAUGAAA-GCACGUGUUAGACUGCUGAUGCGGGUGAUGCGAACUGAAGUCUGAGC
AAYZ01032340.1/3354-3422     GCGGUGAUGACAG-CCAAUU-CAA-GCACGUGUUAGACUGCUGAAGCGGGUGAUGCGAACUCCACACUGAGC
AANN01815579.1/1524-1590     GCAGUGAUGACUGCC---UU-CGA-GCAUGUGUUAGACUGCUGACCAGGGUGAUGCCACUCGGAGUCUGAGC
AAPN01068259.1/172-237       GCUGUGAUGACUUCCCUUGA-A-----ACGUGUUAGACUGCUGAUGCGAAUGAUGCCACUUCCAAUCUGAGC
AAWR02012489.1/59279-59210   GCGGUGAUGACAUCCCAAUC-AAA-GCACGUGUUAGACUGCUGACGCGGGUGAUGCGAACUGGAAUCUGAGC
AAQR03042176.1/42626-42557   GCCGUGAUGACUUUCUAAUU-AAA-GCACGUGUUAGACUGCUGACGCGGGUGAUGCGAACUAGAGUCUGAGC
AAPE02024657.1/45472-45403   GCGGUGAUGACAUACCAAUC-AAA-GCACGUGUUAGACUGCUGACAAGGGUGAUGCGAACUAGAGUCUGAGC
AACN010464480.1/1023-1093    GCAGUGAUGACAUUCCAGAA-AAAUGCACGUGUUAGACUGCUGACGCGGGUGAUGCGAACUACAGUCUGAGU
AAGW02039970.1/177673-177742 GCGGUGAUGACAUCCAAAUU-AAA-GCACGUGUUAGACUGCUGAUGCGGGUGAUGCGAACUGGAGUCUGAGC
#=GC SS_cons                 <<__________________.___._____________________________________________>>
#=GC RF                      GCaGUGAUGACaUuCCAauu.AAA.GCACGUGUUAGACUGCUGAcgCGGGUGAUGCGAACUggAgUCUGAGC
//
# STOCKHOLM 1.0

#=GF AC   RF00290
#=GF ID   BaMV_CRE
#=GF DE   Bamboo mosaic potexvirus (BaMV) cis-regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14585345
#=GF SS   Published; PMID:14585345
#=GF GA   100.00
#=GF TC   181.30
#=GF NC   35.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0039689; negative stranded viral RNA replication;
#=GF RN   [1]
#=GF RM   14585345
#=GF RT   Functional analysis of the cloverleaf-like structure in the 3'
#=GF RT   untranslated region of bamboo mosaic potexvirus RNA revealed dual roles in
#=GF RT   viral RNA replication and long distance movement.
#=GF RA   Chen IH, Meng M, Hsu YH, Tsai CH
#=GF RL   Virology 2003;315:415-424.
#=GF CC   This family represents a cloverleaf-like cis-regulatory element found in
#=GF CC   the 3' UTR of the bamboo mosaic potexvirus. This family is thought to play
#=GF CC   an important role in the initiation of minus-strand RNA synthesis and may
#=GF CC   also be involved in the regulation of viral replication [1].
#=GF WK   Bamboo_mosaic_potexvirus_(BaMV)_cis-regulatory_element
#=GF SQ   5


L77962.1/6225-6364   AACGUUGCAUGAUCGUAAAACAUGCCCGGCUUACCGUGAGCCGCCUUUGAAAGAAAGGUUUACACGGACUCUGUUGCGUUACGCACGUACCUAACUUGUGCCGGCAGAAUAAAGACCUUUUGGUUUCUACAGUUUUUUCC
AF047977.1/876-1015  AACGUUGCAUGAUCGUAAAACAUGCCCGGCUUACCGUGAGCCGCCUUUGAAAGAAAGGUUUACACGGACUCUGUUGCGUUACGCACGUACCUAACCCGUGCCAGCAGAAUAAAGACCUUUUGGUUUCUACAGUUUUUUCC
AF077362.1/600-739   AACGUUGCAUGAUCGUAAAACAUGCCCGGCUUACCGUGAGCCGCCUUUGAAAGAAAGGUUUACACGGACUCUGUUGCGUUACGCACGUACCUAACCCGUGCCAGCAGAAUAAAGACCUUUUGGUUUCUACAGUUUUUUCC
D26017.1/6226-6365   AACGUUGCAUGAUCGUAAAACAUGCCCGGCUUACCGUGAGCCGCCUUUGAAAGAAAGGUUUACACGGACUCUGUUGCGUUACGCACGUACCUAACCCGUGCCAGCAGAAUAAAGACCUUUUGGUUUCUACAGUUUUUUCC
AF077359.1/1060-1199 AACGUUGCAUGAUCGUAAAACAUGCCCGGCUUACCGUGAGCCGCCUUUGAAAGAAAGGUUUACACGGACUCUGUUGCGUUACGCACGUACCUAACCCGUGCCAGCAGAAUAAAGACCUUUUGGUUUCUACAGUUUUUUCC
#=GC SS_cons         ::::::<<<<<_________>>>>>,<<<<<<_____>>>>>><<<<<_____>>>>>-------<<--<<<<<<<------<<<<<_________>>>>>>>>>>>>------->>:::::::::::::::::::::::
#=GC RF              AACGUUGCauGAUCGUAAAACauGCCCGGCuuACCGUgaGCCGCCuuuGAAAGaaaGGUUUACACGGACuCuGuuGCGUUACGCaCGUACCUAACcCGuGCCagCaGaAUAAAGACCUUUUGGUUUCUACAGUUUUUUCC
//
# STOCKHOLM 1.0

#=GF AC   RF00291
#=GF ID   snoR639
#=GF DE   Small nucleolar RNA snoR639/H1
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   42.00
#=GF TC   43.50
#=GF NC   41.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Drosophila_melanogaster300199;
#=GF RN   [1]
#=GF RM   10087258
#=GF RT   minifly, a Drosophila gene required for ribosome biogenesis.
#=GF RA   Giordano E, Peluso I, Senger S, Furia M
#=GF RL   J Cell Biol 1999;144:1123-1133.
#=GF RN   [2]
#=GF RM   12736298
#=GF RT   RNomics in Drosophila melanogaster: identification of 66 candidates for
#=GF RT   novel non-messenger RNAs.
#=GF RA   Yuan G, Klambt C, Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Nucleic Acids Res 2003;31:2495-2507.
#=GF CC   snoR639 or snoH1 belongs to the H/ACA class of snoRNAs which are thought
#=GF CC   to guide the sites of modification of uridines to pseudouridines. snoH1 is
#=GF CC   found in an intron of the mfl gene in Drosophila [1].
#=GF WK   H1
#=GF SQ   9


AANI01014830.1/134411-134552 ACCCCAUGAUAUUAAGCCGGCAGACGCAUGUAUUUUAACC--AGCU--GCGUCUGUGACUAUGACUGGGAACAGUAACGCUGCUGAUGUGUGUAUGUUGGA-GUUGCG---CCUUGCUUGUGUA-UCCGACAAAGUUAUUUUCAGACCACA
AAQB01006286.1/232569-232425 ACCCCAUGAUAUUAAGCCGGCAGUUGCUCGAAAUUUAACCAAG--A--GCAGCUGUGACUAUGACUGGGAACAUUAAAGUCGCUGAUGUGUGUAUGUUAAA-CAGCGUAUUCUUUACCCUGCGCGUUCGACAAAGU-AAUUUCAGACCACA
AAPT01021461.1/4272-4413     ACCCCAUGAUAUUAAGCCGGCAGACGCUUGUAAUUUAACC--A--GCGGCGUCUGUGACUAUGACUGGGAACAGUAAAGCCGCUGAUGUGUGUAUGUUGGAAUUGCGC-----UUUAUCUGCGCAUCUGACAAAGAUUUAUUCAGACUACA
AAPP01018787.1/102387-102251 ACCCCAUGAUAUUAAGCCGGCAGAUGCUCG-AAUCUCCAC--G--C--GCAUUUGUGACUAUGAUUGGGAACAGUAAUGCUCCUGAUGUGUGUAUGUUGUU-GCAACUC--CUCAAUACUGCUU---CAACAAAGA-AUUUUCAGUCGACA
AADE01000218.1/100180-100042 ACCCCAUGAUAUUAAGCCGGCAGACGCCCGUAUACCCCAU--A--A--GCGUCUGUGACUUUGAUUGGGAACAGUAAAGGUGCUGAUGUGUGUAUGUUGGG-CAGCGC---UCUU-UCCUGCGCACUCGACAAAGA-AAUUUCAGACUACA
AAEU02000398.1/3912-4051     ACCCCAUGAUAUUAAGCCGGCAGGUGCUUGCAAUCCCCAC--G--G--GCACCUGUGACUAUGAUUGGGAACAACAAAGCUGCUGAUGUGUGUAUGUUGGG-CAGCGC---UGUGAUCUUGCGCGCUUGACAAAGA-UUUUUCGGUCGACA
AJ544019.1/1-128             ------------UAAGCCGGCAGGUGCCUGCAAUCCCCAC--G--G--GCACCUGUGACUAUGAUUGGGAACAGCAAAGCUGCUGAUGUGUGUAUGUUGGG-CAGCGC---UCUUAUCCUGCGCGCUCGACAAAGA-AUAUUCGGUCGACA
AF089836.1/1-140             ACCCCAUGAUAUUAAGCCGGCAGGUGCCUGCAAUCCCCAC--G--G--GCACCUGUGACUAUGAUUGGGAACAGCAAAGCUGCUGAUGUGUGUAUGUUGGG-CAGCGC---UCUUAUCCUGCGCGCUCGACAAAGA-AUAUUCGGUCGACA
AF097634.1/1819-1958         ACCCCAUGAUAUUAAGCCGGCAGGUGCCUGCAAUCCCCAC--G--G--GCACCUGUGACUAUGAUUGGGAACAGCAAAGCUGCUGAUGUGUGUAUGUUGGG-CAGCGC---UCUUAUCCUGCGCGCUCGACAAAGA-AUAUUCGGUCGACA
#=GC SS_cons                 :::::::::::::::::::<<<<<<<<_____________.._.._..>>>>>>>>--------------------------<<<<--------<<<<<<<.--<<<<..._________>>>>->>>>>>>----.---->>>>::::::
#=GC RF                      ACCCCAUGAUAUUAAGCCGgCAGgcGCuuGuAaUcuaaaC..g..a..GCgcCUGuGACUAUGAuUGGGAACAguAAaGcuGCuGAUGUGUGUAUGUuggg.cagcgc...uuUuauccUgcgcgcccgACAAAGa.AuuUUCaGaCuACA
//
# STOCKHOLM 1.0

#=GF AC   RF00292
#=GF ID   snoTBR5
#=GF DE   Small nucleolar RNA TBR5
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   44.00
#=GF TC   44.40
#=GF NC   36.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   10747997
#=GF RT   Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei.
#=GF RT   Sequence conservation and implications for 2'-O-ribose methylation of
#=GF RT   rRNA.
#=GF RA   Dunbar DA, Wormsley S, Lowe TM, Baserga SJ
#=GF RL   J Biol Chem 2000;275:14767-14776.
#=GF CC   TBR5 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_TBR5
#=GF SQ   6


AF016399.1/719-808       GACAUGAUCGACACCUUGGCUGAUGUAAAGCCGUCGCAGAUGGACGUUGAGUGGCGCACGCCGUGAAACCAACCC------CCGCCUCGUCUGAUC
AF016400.1/574-664       GAUGUGAUCGACAACCAGGCCGAUGUGAAGCCGUCGCAGAUGGACGU----UGACACA-GCAAUGAAAACAGCGUUAUUUCACGCCCCGUCUGAUC
AF168732.1/1-90          GAAGUGAUUGACACCUAGGCCGAUGUAAAGCCGUCGCAGAUGGACGUUGA-UAUCUU-----GUGAAAACAGUACUAUUUUAUGCCCUGACUGAUC
Z50171.1/562-651         GAAGUGAUUGACACCUAGGCCGAUGUAAAGCCGUCGCAGAUGGACGUUGA-UAUCUU-----GUGAAAACAGUACUAUUUUAUGCCCUGACUGAUC
FR798979.1/436127-436215 GACAUGAUCGACACCUAGGUUGAUGUAAAGCCGUCGCAGAUGGACAUUGAGUGGCGCACGCCGUGAAACCGACCC-------CGCCUCGUCUGAUC
FR796401.1/451285-451373 GACAUGAUCGACACCUAGGCUGAUGUAAAGCCGUCGCAGAUGGACGUUGAGUGGCGCACGCCGUGAAACCAACCC-------CGCCUCGUCUGAUC
#=GC SS_cons             <<________________________________________________._______.___________________________________>>
#=GC RF                  GAaaUGAUcGACAcCUAGGCuGAUGUAAAGCCGUCGCAGAUGGACGUUGA.UguCucA.GCcGUGAAAaCAacaCUAUUUuacGCCucGuCUGAUC
//
# STOCKHOLM 1.0

#=GF AC   RF00293
#=GF ID   snoM1
#=GF DE   Small nucleolar RNA snoM1
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; ILM: Moxon SJ
#=GF GA   40.00
#=GF TC   41.20
#=GF NC   37.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Drosophila_melanogaster300117;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   M1 is a member of the H/ACA class of snoRNAs which are thought to guide
#=GF CC   the sites of modification of uridines to pseudouridines. snoM1 seems to be
#=GF CC   found exclusively in Drosophila species.
#=GF WK   Small_nucleolar_RNA_snoM1
#=GF SQ   7


AF375471.1/1-99            AAUUCAAUGAUUUCAACUUCACUGCUGACCAGCCACGCCUCAACGCCUCGGAGUGUUUGC----CCCCAGUCUCUGAUAGAUACACCAUAUUCUAAUA-CACAC
AB032438.1/918-1016        AAUUCAAUGAUUUCAACUUCACUGCUGACAAGCCACGCCUCACCGCCUCGGAGGGAUUGC----CCCUAUUCCCUAACAAAUAGAGCAUAUUCUAAUU-AACAC
AB032439.1/767-865         AAUUCAAUGAUUUCAACUUCACUGCUGACCUGCCACGCCUCACCGCCUCGAAGGGAUUGG----CCCUAUUCCCUAACAAAUAGAGCAUAUUCUAAUU-AACAC
DQ185017.1/645-748         AAUUCAAUGAUUUCAACUUCACUGCUGACCAGCCACGCCUCACCGCCUCGGAGGGAUUGCCUUUCCCCAUUUCCUGACAAAUCGAGCAUAUUCUAAUUCAACAC
AAKO01002130.1/31671-31576 AAUUCAAUGAUUUCAACUUCACUGCUGACCAGCCACGCCUCAACGCCUCGGAGUGAUUGU----CC-CAGUCUCUGAUAG--ACAGCAUAUUCUAAUA-CACUU
AB032437.1/932-1035        AAUUCAAUGAUUUCAACUUCACUGCUGACCAGCCACGCCUCACUGCCUCGGAGGGAUUGCCUUUCCCCAUCCCCUGACAAAUCGAGCAUAUUCUAAUUCAACAC
AAGH01015529.1/6334-6429   AAUUCAAUGAUUUCAACUUCACUGCUGACCAGCCACGCCUCAACGCCUCGGAGUGAUUGU----CC-CAGUCUCUGAUAG--ACAGCAUAUUCUAAUA-CACGA
#=GC SS_cons               (((--((((<<<<---<<<<_____________________________>>>>>>>>,,,....,,,<<<___>>>,,,,,,,,,,,,))))---))).:::::
#=GC RF                    aauUCaaugauucCAACuuCACUGCUGACcAGCCACGCCUCAacGCCUCGgaGggauUGc....CCCcagUCucugAuAaAUagAgCAuauuCUAauu.aACac
//
# STOCKHOLM 1.0

#=GF AC   RF00294
#=GF ID   snoTBR17
#=GF DE   Small nucleolar RNA TBR17
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   40.00
#=GF TC   72.30
#=GF NC   30.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.79 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10747997
#=GF RT   Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei.
#=GF RT   Sequence conservation and implications for 2'-O-ribose methylation of
#=GF RT   rRNA.
#=GF RA   Dunbar DA, Wormsley S, Lowe TM, Baserga SJ
#=GF RL   J Biol Chem 2000;275:14767-14776.
#=GF RN   [2]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF CC   TBR17 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_TBR17
#=GF SQ   6



AF168728.1/150-269         UGCGCUC----AGUGGACAUGAUGCUCCGCCGC---CCAUAUAUCCCGCUAUGUAUAUCCUGUGUGCGCUCUAGUUCCG-UUGGGACCCUGAAGAG------UAAGCACACUAAACCAUGCAUUAUACAUGACC
Z50171.1/84-208            UGCUCUC----AGUGGACAUGAUGCUCCGCCGC---CCAUAUAUCCCGUUAUGUAUAUCCUGUGUGCGCUCUAGUUCCG-UUGGGACCCUGAAGAGUAAGAGUAAGCACACUA-ACCGUGCAUUAUACAUGACC
HE575324.1/2850286-2850408 UGCUCUCUACAAGGGCACAUGAUGCUCCGCCGC---CACGUUAUCCCACUAUGCAUAUCCUUAGUGCGCCCUAGCUCCCUUUGGCGCUCUGAUGGG------UCAGUACA--AAACCAUGCAUCAUACAUUCAG
FR796401.1/453114-453234   UGCUGCU----CGCGCGCCUGACGCACCGCCGCGCGCCGCGGUUCCCGUUACGCAUAUCCUGUGUGCGCUCCAGCCCCG-UCGGGGCCAUGACGAG------UUCGCAA--CCAACCAUGCGUUACACAUUGCC
FR799592.1/451263-451380   UGCGCG-------CGCGCCUGACGCACCGCCGCGCGCCGCGGUUCCCGUUACGCAUAUCCUGUGUGCGCUCCAGCCCCG-UCGGGGCCAUGACGAG------UCCGCAA--CCAACCAUGCGUUACACAUUGCC
FR798979.1/436434-436554   UGCCUCG----CGCGCGCCUGACGCACCGCCACGCGCCGCGGUUCCCGUUACGCAUAUCCUGUGUGCGCUCCAGCCCCG-UCGGGGCCAUGACGAG------UCCGCAA--CCAACCAUGCGUUACACAUUGCC
#=GC SS_cons               :::::::....:::<<_________________...___________________________________________.________________......________._____________________>>
#=GC RF                    UGCucuc....aGuGgaCaUGAuGCuCCGCCGC...CcauauaUCCCGuUAuGcAUAUCCUGUGUGCGCUCuAGcuCCg.UuGGggCCaUGAaGAG......UcaGCAaA.uaAACCAUGCaUUAuACAUuacC
//
# STOCKHOLM 1.0

#=GF AC   RF00295
#=GF ID   snoTBR7
#=GF DE   Small nucleolar RNA TBR7
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   45.00
#=GF TC   47.60
#=GF NC   34.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.87 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   10747997
#=GF RT   Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei.
#=GF RT   Sequence conservation and implications for 2'-O-ribose methylation of
#=GF RT   rRNA.
#=GF RA   Dunbar DA, Wormsley S, Lowe TM, Baserga SJ
#=GF RL   J Biol Chem 2000;275:14767-14776.
#=GF CC   TBR7 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_TBR7
#=GF SQ   10


AF545070.1/587-661       GAUAUGAUGAUUGA-CG--UAACAUCACAGACUUUGACGAACCCGUGAGCAAGAAACACUGUCGC--CCCAGUCUGACCG
AF545069.1/568-642       GAUAUGAUGAUUGA-CG--UAACAUCACAGACUUUGACGAGCCCGUGAGCAAGAAACACUGUCGC--CCCAGUCUGACCG
AF545068.1/590-664       GAUAUGAUGAUUGA-CG--UAACAUCACAGGCUUUGACGAACCCGUGAGCAAGAGACACUGUCGC--CCCAGUCUGACCG
AF016400.1/448-527       GAUAUGAUGAUUGAACGGUAAACAUCACAGACUUUGACGAACCCGUGAGAAAGAAACACUGUCGGUAACCAGUCUGACAG
AF168734.1/1-75          UGAAUGAUGACUGA-CA--AAACAUCACAGACUUUGAUGACCCCAUGAACAAGAAAAAUUGUUGC--CCCAGACUGAAUU
Z50171.1/339-410         UGCA-GAUGACUGA-CA--AAACAUCACAGACUUUGAUGACCCCAUGAACAAGAAAAAUUGUG----CCCAGACUGAUUU
AF016399.1/550-622       CACAUGAUGAUUGA-CU-GUAACAUCACAGACUUUGAGU---CGCGAUGAUAGCAACCAUGUCGC--CCCAGUCUGACGU
FR799592.1/450183-450255 CAGAUGAUGAUUGA-CU-GUAACAUCACAGACUUUGAGU---CGCGAUGAUAGCAACCAUGUCGC--CCCAGUCUGACGU
FR798993.1/731492-731564 CAGAUGAUGAUUGA-CU-GUAACAUCACAGACUUUGAGUCGC-GAUGAG--AGCAGCCAUGUCGC--UCCAGUCUGACGU
FR799572.1/645195-645267 CAGAUGAUGAUUGA-CU-GUAACAUCACAGACUUUGAGU---CGCGAUGAUAGCAACCAUGUCGC--CCCAGUCUGAUGU
#=GC SS_cons             ::::::::::::::.::.::::::::::::::::::<<<____>>>:::::::::::::::::::..:::::::::::::
#=GC RF                  uAuAUGAUGAUUGA.Cu.guAACAUCACAGACUUUGacgAaCCcguGAGaaAGaAACaaUGUcGC..cCCAGUCUGAcuu
//
# STOCKHOLM 1.0

#=GF AC   RF00296
#=GF ID   snoR16
#=GF DE   Small nucleolar RNA R16
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   45.00
#=GF TC   45.90
#=GF NC   42.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300027;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol 2002;12:2002-2013.
#=GF CC   snoR16 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_R16
#=GF SQ   18


AY559178.1/865-955         GACGGCAAGCGAUGUGC---AAAACUUUAUCCUA-CACACUUAAUGGAAUUACUGCCAUGUGUGGACUAAU---CUCCGCUUAUUAUCUGAUGCUUUU
AY559178.1/1040-1124       UGUGGCAAGUGAUGCAGAAGUUAAUAUUAUGCUA-UACAC----UGAAACU-------UUUGUGGACAAAAA-ACUCCGCUUAUUAUCUGAUGCCACA
AJ532540.1/1-88            GGUGGCAAAUGAUGUGAAA-ACAAUCUUAUCCUA-CACAC----UGAAUCUUUG---AUGUGUGGACAAACA-UCUCCGCUUAUUAUCUGAUGCCACU
AC025814.7/54017-53931     AUUGGCAAAUGAAGAAUUGAUUAAUUUAUGCUUA-ACCAC----UG-AUGAACA---GUG-UUGACAAAACA-UCUCCGCUUAUUAUCUGAUGCCAUA
AC025808.8/30370-30454     AUUGGCAAAUGAUGAGU---AGAAUCUUAUCCUA-CACAC----AG-AUGUAUC---A-GUGUUGACUACCAAUCUCUGCUUAUUAUCUGAUGCCAUA
AF317964.1/1-81            --UGGCAAAUGAUGAGU---AGAAUCUUAUCCUA-CACAC----AG-AUGUAUC---A-GUGUUGACUACCAAUCUCUGCUUAUUAUCUGAUGCCA--
AC116426.1/42034-42121     GGUGGCAAAUGAUUUGAAA-ACAAUCUUAUCCUA-CACAC----UGAAUCUUUG---AUGUGUGGACAAACA-UCUCCGCUUAUUAUCUGAUGCCACU
AC116426.1/41850-41940     GUCGGCAAGUGAUGUGA---ACAUUUAUAUGCUAUCACUCAA--UGGAAAUUUCC--AUGUGUGGACCAAUAAUCUCCGCUUAUUAUCUGAUGCCUUC
AJ536402.1/1-77            --UGGCAUGUGAUGC-----ACAAUCUUAUCCUA-CACAC----UGAAUGCA-----AUGUGUGGACAAAUA--CUCUGCUUAUUAUCUGAUGCCA--
AJ532541.1/1-85            ---GGCAAGUGAUGUGA---ACAUUUAUAUGCUAUCACUCAA--UGGAAAUUUCC--AUGUGUGGACCAAUAAUCUCCGCUUAUUAUCUGAUGCC---
DQ108830.1/335-421         AUUGGCAAAUGAAGAAUUGAUUAAUUUAUGCUUA-ACCAC----UG-AUGAACA---GUG-UUGACAAAACA-UCUCCGCUUAUUAUCUGAUGCCAUA
AC115687.1/128847-128934   GGUGGCAAAUGAUUUGAAA-ACAAUCUUAUCCUA-CACAC----UGAAUCUUUG---AUGUGUGGACAAACA-UCUCCGCUUAUUAUCUGAUGCCACU
AC115687.1/128663-128753   GUCGGCAAGUGAUGUGA---ACAUUUAUAUGCUAUCACUCAA--UGGAAAUUUCC--AUGUGUGGACCAAUAAUCUCCGCUUAUUAUCUGAUGCCUUC
AARH01006167.1/50772-50855 GAAGGCAAAUGAUGGAAAA-AAAUUCUUAUCCUA-CACAC----UGAAUUAA-------AUGUGGACCAAAA-ACUCCGCUUAUUAUCUGAUGCCUUU
AASG02000069.1/78455-78538 AGUGGCAUGUGAUGAAU---AAGUUCUUAUCCUA-CACAC----UGAAUUUG-----UUGUGUUGACUACUU-ACUCCGCUUAUUAUCUGAUGCCGUU
AM460165.1/26075-25995     GAAGGCAAAUGAUGAAA---AUAGUCUUAUCCUA-CACUC----UGAAGUUA-------AUGUAGACUAUAA--CUCCGCUUAUUAUCUGAUGCCUUC
CU459062.7/46553-46628     UUUGGCAAAUGACGA----------UUCACUGUA-AAUAC----UG-AAUAAUC---AUG--UCGAUUAUCA-ACUCCGCUUAUUAUCUGAUGCCUUU
AC189493.2/8156-8242       UAUGGCAGAUGAUGAAUUG-AUUACUUGUGCUUAAAUCAC----AGAAUAAU------AGUGUUGACAAACAAUCUCCGCUUAUUAUCUGAUGCCAUG
#=GC SS_cons               ::<<<<<__________...______________._____....__________..._______________.__________________>>>>>::
#=GC RF                    guuGGCAAaUGAUGaau...AuAaUuUUAUccUA.cACAC....UGaAuuuauu...AUGUGUgGACuAAuA.uCUCCGCUUAUUAUCUGAUGCCaUu
//
# STOCKHOLM 1.0

#=GF AC   RF00300
#=GF ID   snoZ221_snoR21b
#=GF PI   snoZ221
#=GF DE   Small nucleolar RNA Z221/R21b
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Wilkison A
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, Wilkison A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   44.00
#=GF NC   43.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z221 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z221
#=GF SQ   12


AJ242536.1/1-83            A---G-GC-UGUGAUG----A-----UUGAGAAUGUCAUGCACCACUCUGAU--UU----------------------UU--UGUGCUGAUAAUCA-----UCUCUAACCCAUAUUUUAUCUGA----GCC---U
AC132565.30/9192-9106      A---G-GC-UAUGAUGAAUCA-----UAGAGAUAGUCAUGCACCACUUUGAU--UU----------------------CC--UGUGCUGAUAACUU-----UCUUAUACCCAUUAUUUUUCAGA----GCC---U
AASG02003325.1/11570-11485 A---GUGA-UGAGAUG----A-----UUGAGAAAGUCAUGCACCACUCUGAU--UU----------------------UUUCUGUGCUGAUAAGUU-----UCUCAUACCCAUUACACAUCUGA----GCC---U
AARH01002823.1/33127-33215 G---G-GC-AGUGAUG----ACGAUUUUGAGAAAGUCAUGCACCACUCUGAUAUUA----------------------UC--UGUGCUGAUAAAUC-----UCUCAUACCCAUAUGUU-UCUGA----GCC---C
AM468648.2/6775-6684       G---G-GC-AGUGAUG----AG--AUUGAAGAAAGUCAUGCACCACUCUGAU--UGAUC----------------AAAUC--UGUGCUGAUAAAUC-----UUUCUUACCCAUUUUUUUUCUGA----GCC---C
AC189380.2/32952-32873     U---G-GC-AGUGAUG----A-----UUGAGAAUGUCAUGCACCACUCUGA----U----------------------UU--CGUGCUGAUAACUA-----UCUCUA-CCCAUAUUAUAUCUGA----GCC---U
AJ494916.1/1-115           G---A-GAUGGCGAUG----AU---GAGGAACUAGUCAUGCACCACUCUGAA--CUCGGGAGAGUU--AUCUCUCCUGUU--CUUGCUGACGACAAACAGACUUGCUACCCAUUAUCAAUCUGAGCCUACU---C
AJ494917.1/1-112           GAUUG-GC-GAUGAUG----A------GGAACUAGUCAUGCACCACUCUGAA--CUCGGGAGAGUUCUCUCUCUCCUGUU--CUUGAUGACAAACAG---ACUUACUACCCAUUAUCAAUCUGA----GCCUACU
AP002968.2/137677-137788   G---A-GAUGGCGAUG----AU---GAGGAACUAGUCAUGCACCACUCUGAA--CUCGGGAGAGUU--CUCUCUCCUGUU--CUGGCUGACAAACAG---ACUUGCUACCCAUUAUCAAUCUGAGCCUACU---C
AACV01004671.1/38461-38572 G---A-GAUGGCGAUG----AU---GAGGAACUAGUCAUGCACCACUCUGAA--CUCGGGAGAGAU--CUCUCUCCUGUU--CUUGCUGACAAGCAG---ACUUACUACCCAUUAUCAAUCUGAGCCUGUU---C
AP004359.4/6869-6980       G---A-GAUGGCGAUG----AU---GAGGAACUAGUCAUGCACCACUCUGAA--CUCGGGAGAGUU--CUCUCUCCUGUU--CUGGCUGACAAACAG---ACUUGCUACCCAUUAUCAAUCUGAGCCUACU---C
AAAA02006659.1/6971-7083   G---A-UU-GGCGAUG----AU---GAGGAACUAGUCAUGCACCACUCUGAA--CUCGGGAGAGUUCUCUCUCUCCUGUU--CUUGAUGACAAACAG---ACUUACUACCCAUUAUCAAUCUGAGCCUACU---C
#=GC SS_cons               <...<.<<._______....__...___________________________.._____................_____..______________....._______________________....>>>...>
#=GC RF                    g...G.Gc.gGuGAUG....Au...gugGAaauAGUCAUGCACCACUCUGAa..uUcGg................cUGUU..uuUGCUGAuAAaua.....uuUacUACCCAUUaUuaAUCUGA....gCC...c
//
# STOCKHOLM 1.0

#=GF AC   RF00301
#=GF ID   snoZ256
#=GF DE   Small nucleolar RNA Z256
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Moxon SJ
#=GF GA   50.00
#=GF TC   54.60
#=GF NC   43.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z256 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z256
#=GF SQ   5


AL731594.5/115272-115179 AUUUGCCGGUCAUGUUGACUAUAGCAACCCGAGCAUGGCUGAUAGGACUCCUGAAGUACACCAUUAACAGCUGGUCCGAAUUGAAGGCCUAGUU
AJ494969.1/1-90          --CUGCUAGUCAUGCUGACCACAGCCGCCCAGGCAUGGUUGACGGGGCUACCGAGGUACACCAUCAACAGUUGGUCCGAACUGAAGUGGCAG--
AP005930.3/106994-106901 GCCUGCUAGUCAUGCUGACCACAGCCGCCCAGGCAUGGGUGACGGGGCUACCGAGGUACACCAUCAACAGUUGGUUCGAACUGAAGGGGCAGUU
AJ494970.1/1-94          ACCUGCUGGUCAUGCUGACCACCGCCGCCCGAGCAUGGCUGACAGGGCUACCAAGGUACACCAUCAACAGCUGGGCCGAGAUGAAGGGACAGUU
AJ494971.1/1-94          ACCUGCCGGUCAUGCUGACCACCGUCGCCCGAGCAUGGCUGACAGGGCUACCAAGGUACACCAUCAACAGCUGGGCCGAGCUGAAGGGACAGUU
#=GC SS_cons             ::<<<<<_______________________________________________________________________________>>->>>::
#=GC RF                  AccUGCcgGUCAUGcUGACcAcaGCcGCCCgaGCAUGGcUGAcaGGGCUACcgAGGUACACCAUcAACAGcUGGucCGAacUGAAGgGaCAgUU
//
# STOCKHOLM 1.0

#=GF AC   RF00302
#=GF ID   SNORA65
#=GF PI   U65
#=GF DE   Small nucleolar RNA SNORA65
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   70.10
#=GF NC   69.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00042
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300367;
#=GF DR   snoopy; Oryzias_latipes300066;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   U65 belongs to the H/ACA class of snoRNAs which are thought to guide the
#=GF CC   sites of modification of uridines to pseudouridines [1,2].
#=GF WK   Small_nucleolar_RNA_SNORA65
#=GF SQ   14



EU240328.1/8-136         CCCGCCACUGUACCUGUCUUG-UAAUGCAGUGAC-UU-GUAUAGUCCAGAGGUGGGCUGAGAGAAAAUGCCAUCCU--AGGAAACAGGGUUAUUCUUCU-U-GUGGGUAACUCUGUGCCGAAGGC-UGGGAACAGCA
BT056663.1/385-510       CCCGCCACUUUGCCAGUCU-G-UCU-GCGUGACU-GA-GUGUAGUCCAGUGGAG-GCUAAGAUGGACCCA-GCUCU--AGGAAACAUGGCUGCCCAGGC-G-GUGGGCAACUUUGUGCCGAAAGGCCUGGAACAAUU
BX324171.9/130678-130552 CCCGCCACUGUGCUAGUCUUU-UAA--AGUGACU-CU-GUACAAUCCAGUGGAG-GCUCAGAGUGACCCA-G-C-UCUAGGAAGCAGGGCGGCCCAAAC-UGAUGGGCAGCUCUGUGCCGAAAGACCUGGAACAAAC
BX324171.9/129405-129279 CCCGCCACUGUGCUUGUC-UG-UAA--GAGUGACCGU-GUACUGUCCAGAGG-AAGCUCAGAGUGACCCA-GCUCU--AGGAAGCAGGACUGGUCAAUUCA-GUGACUAGCCCUGUGCCAAAAGGCCUGGAACAUGG
BX324171.9/130123-129997 CCCGCCACUGUGCUUGU-CUG-UAA--GAGUGAC-UGUGUACUGUCCAGAGGAG-GCUCAGAGUGACCCA-GCUCU--AGGAAGCAGAACUGCCCAGUU-UAAUGGGUAACUCUGUGCCGAAAGGUCUGGGACAUGU
HQ318051.1/2569-2697     CCCGCCACUGCACCCGGUCAG-UUU-CUGUCGGC-UG-GUGCAAUCCAGUGGUGAGCUGAUAGUAAACCCCAGCUU--AGGAAACAGGGUUGUUCUUCA-U-GUGGAUGACUCUGUGCCGAAAGCAUGGGAACAGCC
AF357418.1/1-118         ----------CACCUGACCAG-UAU--UGUUGGC-UG-GUGCAAUCCAGUGGUGAGCCGACAGUGAGCCCCAGCUUUUAGGAAACAGGGCUGUCCUACA-U-GUGGAUGGCUCUGUGCCGAAAGCAUGGGAACAG--
AC156290.10/22658-22538  CCCACCACUG-ACCUGACCAG-UAU--GGUUGGC-UG-GUACAAUAUAGUAGUGAACUGACAGUGAGCCCCAGCUUUCAGGGAAUGGGGCUGUCCUACA-U-AUGAAU--------GUUGAAAGCAUGGGAACACCC
Y11159.1/8-137           CCCGCCACUGCACCUGACCAGGUCU-CUGUUGGC-UG-GUGCAAUCCAGUGGUGAGCUGAUAGUAAACCCCAGCUU--AGGAAACAGGGUUGUUCUUCA-U-GUGGAUGACUCUGUGCCGAAAGCAUGGGAACAGCU
AL445222.9/104424-104295 CCCGCCACUGCACCUGACCAGGUCU-CUGUUGGC-UG-GUGCAAUCCAGUGGUGAGCUGAUAGUAAACCCCAGCUU--AGGAAACAGGGUUGUUCUUCA-U-GUGGAUGACUCUGUGCCGAAAGCAUGGGAACAGCC
AL662817.11/27635-27507  AAAGCCACUGCACCUGACCAG-UAU--UGUUGGC-UG-GUGCAACACAGUGGUGAGCUGACAAUAAGCCC-AGCUUUUAGGAAACAGGGCUGUCCUACA-U-GUGGAUGGCUCUGUGCCGAAAGCAUGGAAACAGCC
AC130841.4/21411-21298   CUGAAUACUGUAACGGUCCCCUUUA-AAAGAACG-AG-GA----CUCAGUGCUGAGCUGACAGGAAGCCC--------------CAGGGUUGUCCUACA-U-GUGGGUGACUCUGUGCUGAAAGCAUGGGAACAGCC
AC154504.2/92187-92059   CCCGCCACUGCACCUGACCAG-UAU--UGUUGGC-UG-GUGCAAUCCAGUGGUGAGCUGACAGUGAGCCC-AGCUUUUAGGAAACAGGGCUGUCCUACA-U-GUGGAUGGCUCUGUGCCGAAAGCGUGGGAACAGCC
BC075731.1/796-925       CCCGCCACUGCACCUGACCAG-UAU--UGUUGGC-UG-GUGCAAUCCAGUGGUGAGCUGACAGUGAGCCCCAGCUUUUAGGAAACAGGGCUGUCCUACA-U-GUGGAUGGCUCUGUGCCGAAAGCAUGGGAACAGCC
#=GC SS_cons             ::::<<<<<<------<<<<<.<<_..___>>->.>>.>>------>>>>>>---------------<<<.<<<<<..-<<---<<<<<<--<<<____._.__>>>-->>>>>>-->>-->>>>->>>>:::::::
#=GC RF                  CccGcCaCUGuaCcuGaCcag.uau..uguugac.ug.GuaCAaUcCAGuGguGAGCUgAgAGugAaCCc.ggcuU..AGGAAACAggGcUGccCuaca.U.GUGggUagCucUGUGCCGAAagcacgGGAACAgcc
//
# STOCKHOLM 1.0

#=GF AC   RF00303
#=GF ID   snoR86
#=GF DE   Small nucleolar RNA snoR86
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   40.00
#=GF TC   40.20
#=GF NC   37.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300124;
#=GF DR   snoopy; Arabidopsis_thaliana300207;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol 2002;12:2002-2013.
#=GF CC   snoR86 is a member of the H/ACA class of small nucleolar RNAs (snoRNAs)
#=GF CC   which act as guides in the the modification of uridines to pseudouridines
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_snoR86
#=GF SQ   11


AL138659.1/77819-77696       GAGCAAUGACGUCAAAAU---AA----AAAUGGC-GUAAGUUGCCUUGAAGGUUGGCAACAACAAAUA--------GCGAUUCUCCGUGCCUAUCAAGUUUUCUAAUCUUGAUUGUU----GGCCUCGAACAAGUCGCUACAUU
AJ505659.1/1-124             GAGCAAUGACGUCAAAAU---AA----AAAUGGC-GUAAGUUGCCUUGAAGGUUGGCAACAACAAAUA--------GCGAUUCUCCGUGCCUAUCAAGUUUUCUAAUCUUGAUUGUU----GGCCUCGAACAAGUCGCUACAUU
AARH01007754.1/2159-2040     GAGCAAGGGUGUC--------GA----AAAUGGC-ACAACUUGCAUUGAAGGUUGGCAA-UACUAAUA--------GCAAUUCUCCGUGCCUAUCAAAUCUUGAUUUCAUUUUGAUU--AUGGCCUCGAACAAGUUGCUACAUU
AASG02009944.1/1753-1868     GAGCAAAUGCGUC--------GA----AAAUGGC-GAAAUUUGCAUUGAAGGUUGGCAAUAUCAA-UA--------GCAAUUCUCCGUGCCUAUUAAAUCGAUCAUUUUGA--UUAU----GGCCUCGAACAAGUUGCAACAGU
AACV01024246.1/8981-8858     GAGCAAAGGGGCC--AGA---UG----CAGUGGC-UAUCUUUGCAUUGAAGGUUGGCGACAACGAACAAAC-----GCAGUUCUCCGUGCCGCUCAGAUUUUCUCUGUUUUGUG-AC----GGCCUCGAACAAGCUGCUACAUC
AARH01010162.1/241821-241954 GAGCAAGGACGUCAAGAA---AAAAG-AGAUGGC-GUGAUUUGCAUUGAAGGUUGGCUAUAUCAAUGAUAAAAUUGGCGAUUCUCCGUGCCUGUCAAAUCUGUUCAUUUUGAUC-AU----GGCCUCGAACAAGUCGCUACAAA
AL731740.4/7530-7650         GAGCAAAGGGGCC--UGA---UA----AAGUGGC-GAUCUUUGGAUUGAAGGUUGGCGACAACGA-UU--------GCAGUUCUCCGUGCCGCUCAGAUUUUCCUCUCUUUUGUGAC----GGCCUCGAACAAGCUGCUACAUC
AC007767.3/47035-47162       GAGCAAGGGCGUC-UAGU---UU----AAAUGAC-GUGAGUUGCCUUGAAGGUUGGCGAUAACAAGUUUU------GCGAUUCUCCGUGCCUAUCAAAUUUUGUUUUUCGUAUUGAU-AAUGGCCUCGAACAAGUCGCUACAUU
AASG02009944.1/2138-2259     GAGCAAGAGUGUC--------UA----AAAUGACUACAACUUGCAUUGAAGGU-GGCCA-UAUCAAUA--------GCAAUUCUCCGUGCCUAUCAAAUCUCUUAAUUUCAUUUUGAUUAUGGCCUCGAACAAGUUGCUACAUU
AM448130.2/819-690           GAGCAAAGGCGUCGAAUA---AAAGAGAAAUGAC-GCAAUUUGCCUUGAAGGUUGGCGAUAAGGAAAAAUG-----GCGAUUCUCCGUGCCUGUCAAUCAUUUUUAUUUUGAUC-AU----GGCCUCGAACAAGUCGCUACAUU
AC189297.2/132599-132725     GAGCAAUGACGUCAAAAUAUAAA----AAAUGGC-GUGAGUUGCCUUGAAGGUUGGCAAUAACAAUAA--------GCGAUUCUCCGUGCCUAUCAAGUUUUCUUUAUACUGAUUGC----GGCCUCGAACAAGUCGCUACAUU
#=GC SS_cons                 ::::::::<<<<<.____...__....____>>>.>>,,,<<<<<_________>>>>>---------........<<<<<<------<<<__________________________....>>>-------->>>>>>::::::
#=GC RF                      GAGCAAaGgcGcC.Aaaa...aA....AAAUGgC.gcaAuUuGCcUUGAAGGUUgGCaAuAAcaAauA........GCgauUCUCCGUGCCUaUCAAaUuUuuuuuUuuuuauuuau....GGCCUCGAACAAgucGCUACAuu
//
# STOCKHOLM 1.0

#=GF AC   RF00304
#=GF ID   snoZ279_R105_R108
#=GF PI   snoZ279
#=GF DE   Small nucleolar RNA Z279/snoR105/snoR108
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, Daub J, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   54.00
#=GF TC   55.30
#=GF NC   49.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00081
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF CC   This family includes the plant snoRNAs known as Z279, snoR105 and snoR108.
#=GF CC   All three are members of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1].
#=GF WK   Small_nucleolar_RNA_Z279
#=GF SQ   20


AL713946.3/150758-150869     GGG-AGAUGAGGAGUGG-UA--ACAUCUCGCAACUUU-UACUGCGAGAGGGG-UG-CCCGCCCCAACCCAAGCCU-GUUACGACA-AC-AGGGGC-A-UCCCCAUCAUUU-UACCA-UCUGAUCCC
AJ536284.1/1-112             GGG-AGAUGAGGAGUGG-CA--ACAUCUCGCAACUUU-UACUGCGAGAGGGG-UG-CCCGCCCCAACCCAAGCCU-GUUACGACA-AC-AGGGGC-A-UCCCCAUCAUUU-UACCA-UCUGAUCCC
AJ536283.1/1-110             GGG-AGAUGAUGAGUGG-UA--ACAUCUCGCUAAUUAAUGUUGCGAGAGGGG-UG-UCUGCCCCAACCAA-GCCU-GUUACGACA-AC-AGGG-C-A--CUCCAAUAUUU-UACCA-UCUGAUCCC
AC021043.4/111618-111721     GGG-AUAUGAUGAAUGG-UA--AAAACUCGC---UUA-UAUUGCGAGAAGAG-CG-UUCCGCCCA---AA-GCCU-GUUACGACU-AU-UGGG-C-G--CUCUCUUUUUUACACAA-UCUGAUCCC
AC189264.1/14531-14636       GGG-AAAUGAGGAGUGGUUA--UUUUCUCGC-UUUUA-UUAUGCGAGAAGAGCGU-UUCGCUCC-------GCCU-GUUACGACA-AU-UGAGCG-C-UCUCCUUUGUCU-UACCA-UCUGAUCCC
AB006707.1/79618-79722       GGG-AAAUGAGGAAUGGUUA--UAAUCUCGC----UU-UAAUGCGUGAUGAG-CG-CUCCGCUCAAAGCCUG-----UUACGACU-AA-UUGGGC-G-CUCCAAUUUUUA-UACAA-UCUGAUCCC
AC010852.7/39511-39410       GGG-AAAUGAGGAGUGG-UUAUUAAACUCGC-----U-UAAUGCGAGAAGAG-UG-UUUCGCUC----A--GCCU-GUUACGACU-AU-UGAG-C-A--CUCUCCUUCUUUUAUCA-UCUGAUCCC
AASG02000449.1/1977-1873     GGG-AUAUGAUGAGUGG-UC--AAUGCUCGCUAAUUG-CUAUGCGAGAUGGG-UG-UCCGCCCCUUGCCA------GUUACGACA-AU-AUGGGC-A--CUCUCAUCUGU--ACCA-UCUGAUCCC
AC193778.1/61498-61393       GGG-AUGUGAUGAGUGG-UC--AAUACUCGCAUUAAA-AUAUGUGAGAAGGG-UG-UC-----CAGGCUUAGCCU-UUUACGACA-AU-UUGGGC-G--CUCU-CAAUUU-UACCAAUCUGAUCCC
AARH01001039.1/573251-573357 GGG-AUAUGAUGAGUGG-UC--AGUACUCGCAAUUAA-ACAUGCGAUAUGGG-UG-UCCAACCCACUC----CCUGGUUACGACA-AC-AGGG-C-A-CUCCCAUC--UU-CACCAAUCUGAUCCC
CU024896.7/59229-59332       GGG-AUAUGAUGAGAGG-UU--GAGUCUCGCACAUAA-UAU-GCGAGUUGGG-UG-UUCGCCCCAAGC----CUG-GUUACGACA-AU-UGGG-C-ACUCUCGUUUAAUC-A---A-UCUGAUCCC
AC137065.26/13599-13701      GGG-AAAUGAGGAGUGG-UU--GGAUCUCACCAAUUU-U---GUGAGUUGAG-UGUUCCGCCCACAGC----CUG-GUUACGACA-AU-UGGG-C-A--CUCUCCCAAUU---CCAAUCUGAUCCC
CT868736.5/110822-110719     GGG-AUAUGAUGAGUGG-UU--GAGUCUCGCACAUAA-UAU-GCGAGUUGGG-UG-UUCGCCCCAAGC----CUG-GUUACGACA-AU-UGGG-C-A--CUCU--CAUUU-AAUCAAUCUGAUCCC
AARH01002873.1/98519-98413   GGG-AUAUGAUGAGUGG-UC--AAUGCUCGCAUAUAA-ACAUGCGAGAUGGG-UG-UCCAGCCCACUC----CCUGGUUACGACA-AC-AGGG-C-A--CUCCCAUCUUC-ACCUA-UCUGAUCCC
AJ505633.1/2-106             GGG-AUAUGAUGAAUGG-UA--AAAACUCGC---UUA-UAUUGCGAGAAGAG-CG-UUCCGCCCAAAG----CCU-GUUACGACU-AU-UGGG-CAG--CUCUCUUUUUUACACAA-UCUGAUCCC
AJ505636.1/8-110             GGGGAAAUGAGGAAUGG-UUA-UAAUCUCGC----UU-UAAUGCGUGAUGAG-CG-CUCCGCUCAAAG----CCU-GUUACGACUAAU-UGGG-C-G--CUCCAAUUUUUAUACAA-UCUGAU---
AC193778.1/21092-20986       AGG-AUAUGAUGAGUGG-UCA-AAUGCUCAC-AAUAA-UUUUGUGAGAAGGA-UG-CCUAAGCUCAGC----CUG-GUUACGACA-AUUUAGG-C-C--UUCUCAAUUUU-AUCAA-UUUGAUCCU
AL928750.3/55751-55862       GGG-AGAUGAGGAGUGG-UA--ACAUCUCGCAACUUU-UACUGCGAGAGGGG-UG-CCCGCCCCAACCCAAGCCU-GUUACGACA-AC-AGGGGC-A-UCCCCAUCAUUU-UACCA-UCUGAUCCC
AC123520.2/27158-27049       GGG-AGAUGAUGAGUGG-UA--ACAUCUCGCUAAUUAAUGUUGCGAGAGGGG-UG-UCUGCCCCAACCAA-GCCU-GUUACGACA-AC-AGGG-C-A--CUCCAAUAUUU-UACCA-UCUGAUCCC
FN595227.1/11340260-11340157 GGG-AUAUGAUGAGUGG-UC--AACGUUCGCAACAAA-UAU-GCGAGAUGGG-UG-UCCGCCCUAGCC-----UG-GUUACGACA-AU-UGGG-C-A--CUCUCAUCUUU--ACCAAUCUGAUCCC
#=GC SS_cons                 (((.(---------(((.((..,,,,<<<<<______.____>>>>>,<<<<.<<.<<----------....-<<.<<_______.>>.>>>>.>.>..>>>>,,,,,,,.))))).-----))))
#=GC RF                      GGG.AuAUGAuGAGugG.uc..aaauCuCGCaaaUua.UaaUGCGaGAgGgG.uG.cccgccCcAaac....Ccu.gUUACGACa.Ac.aggg.C.a..CcCcauuaUUU.gaCca.UCUGAUCCC
//
# STOCKHOLM 1.0

#=GF AC   RF00305
#=GF ID   snoZ248
#=GF DE   Small nucleolar RNA Z248
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   120.00
#=GF TC   150.80
#=GF NC   115.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z248 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z248
#=GF SQ   5


AJ494961.1/1-137           GCAGCGCCGUGAUGACCUUGUGGAACGACGCCGGCGAGAGGGCCGCGAGCUCCGCCGUCCACCAGUCGGGCGGCGACCUCGUCGGGAACAGCACCUCGUUGCAGAUCCUGAGCGCGAUAGCGUCAGCUGAUCGCUGC
AK060741.1/737-601         GCAGCGCCGUGAUGACCUUGUGGAACGACGCCGGCGAGAGGGCCGCGAGCUCCGCCGUCCACCACUCGGGCGGCGACCUCGUCGGGAACAGCACCUCGUUACAGAUCCUGAGCGCGAUAGCGUCAGCUGAUCGCUGC
AK064985.1/714-578         GCAGCGCCGUGAUGACCUUGUGGAACGACGCCGGCGAGAGGGCGGCGAGCUCCGCCGUCCACCACUCGGGCGGCGACCUCGUCGGGAACAGCACCUCGUUGCAGAUCCUGAGCGCGAUAGCAUCAGCUGAUCGCUGC
AAAA02033424.1/23901-23765 GCAGCGCCGUGAUGACCUUGUGGAACGACGCCGGCGAGAGGGCCGCGAGCUCCGCCGUCCACCAGUCGGGCGGCGACCUCGUCGGGAACAGCACCUCGUUGCAGAUCCUGAGCGCGAUAGCGUCAGCUGAUCGCUGC
AK119514.1/713-577         GCAGCGCCGUGAUGACCUUGUGGAACGACGCCGGCGAGAGGGCGGCGAGCUCCGUCGUCCACCACUCGGGCGGCGACCUCGUCGGGAACAGCACCUCGUUGCAGAUCCUGAGCGCGAUAGCAUCAGCUGAUCGCUGC
#=GC SS_cons               ((((((------------------------((((((((,<<<<_____>>>><<<<<<<<_______>>>>>>>>,,))))))))----------------------------------------------))))))
#=GC RF                    GCaGCGCCGUGAUGACCUUGUGGAACGACGCCGgCGaGAGgGCcGCGAGCuCCGcCGuCCACCAcUCGGgCGgCGACCuCGuCGGGAACAGCACCUCGUUgCAGAUCCUGAGCGCGAUAGCgUCAGCUGAUCGCuGC
//
# STOCKHOLM 1.0

#=GF AC   RF00306
#=GF ID   snoZ178
#=GF DE   Small nucleolar RNA Z178
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   100.00
#=GF TC   195.30
#=GF NC   45.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z178 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z178
#=GF SQ   5


AJ490412.1/1-152         GGAGGAGACUGAUGAUGGAACCGUCUGACACGCCGGCCCCCGCCGGCGCCGACGGUGCCUCCAAGGUCGACCCUCCAGCUCGUCUCUCCCCGUCGUCACCUACCUCUCUCUGUCACUCGCUCGCUCACUCACUCUUGCGCCUGAUUUGCUUC
AJ490410.1/1-152         GGAGGAGACUGAUGAUGGAACCGUCUGACACGCCGGCCCCCGCCGGCGCCGACGGUGCCUCCAAGGUCGACCCUCCAGCUCGUCUCUCCCCGUCGUCACCUACCUCUCUCUGUCACUCGCUCGCUCACUCACUCUUGCGCCUGAUUUGCUUC
AJ490411.1/1-152         GGAGGAGACUGAUGAUGGAACCGUCUGACACGCCGGCCCCCGCCGGCGCCGACGGUGCCUCCAAGGUCGACCCUCCAGCUCGUCUCUCCCCGUCGUCACCUACCUCUCUCUGUCACUCGCUCGCUCACUCACUCUUGCGCCUGAUUUGCUUC
AJ490409.1/1-152         GGAGGAGACUGAUGAUGGAACCGUCUGACACGCCGCCCCCCGCCGGCGCCGACGGUGCCUCCAAGGUCGACCCUCCAGCUCGUCUCUCCCCGUCGUCACCUACCUCUCUCUGUCACUCGCUCGCUCACUCACUCUUGCGCCUGAUUUGCUUC
AAAA02010461.1/4116-4267 GGAGGAGACUGAUGAUGGAACCGUCUGACACGCCGGCCCCCGCCGGCGCCGACGGUGCCUCCAAGGUCGACCCUCCAGCUCGUCUCUCCCCGUCGUCACCUACCUCUCUCUGUCACUCGCUCGCUCACUCACUCUUGCGCCUGAUUUGCUUC
#=GC SS_cons             <<<<------<<<<<<<<-<<<<<<-----<<<<<<<____>>>>>>>-->>>>>>--------------------------------->>>>>>>>--------------------------------------------------->>>>
#=GC RF                  GgaGGAGACUGauGauGGAaCCGuCUGACACGCCGgCCCCCGcCGGCGCCGaCGGuGCCUCCAAGGUCGACCCUCCAGCUCGUCUCUCCCCguCguCACCUACCUCUCUCUGUCACUCGCUCGCUCACUCACUCUUGCGCCUGAUUUGCuuC
//
# STOCKHOLM 1.0

#=GF AC   RF00307
#=GF ID   snoR98
#=GF DE   Small nucleolar RNA snoR98
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Griffiths-Jones S
#=GF GA   44.00
#=GF TC   44.90
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00038
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300139;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol 2002;12:2002-2013.
#=GF CC   snoR98 belongs to the H/ACA class of snoRNAs which are thought to guide
#=GF CC   the sites of modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_snoR98
#=GF SQ   4


AJ505675.1/1-117       GUUUAAUAGAU-AACCAUAUGUGCCUUUAUACAUUUUCUCCGCACAUCAUCUGAGGCAGAUAUUAAUGCUUGUUUUCCUCUCUUUAUGGA-CUUCGAGUUUGGCUUUCUUGUCACAUUU
AJ298137.1/1505-1621   GUUUAAUAGAU-AACCAUAUGUGCCUUUAUACAUUUUCUCCGCACAUCAUCUGAGGCAGAUAUUAAUGCUUGUUUUCCUCUCUUUAUGGA-CUUCGAGUUUGGCUUUCUUGUCACAUUU
AC005287.4/31785-31897 GAUAAUUGGAUGAACCAUAU-UUCC--UAUA---UCUCUCCUGACAUCGAAUAAUUCAGAUAUUAAUGCUUGUGUUCCUCUCUAUAUGGAACUUCAAGUUUGGCUAUUCUGUUACAUUC
AJ505653.1/1-88        ---------------------------UAUA---UCUCUCCUGACAUCGAAUAAUUCAGAUAUUAAUGCUUGUGUUCCUCUCUAUAUGGAACUUCAAGUUUGGCUAUUCUGUUACAUU-
#=GC SS_cons           <<<<--<<<<<.------<<<<<<_________________>>>>>>->>>>>>>>>----------<<<<<-<-<<<_________>>>.>-->>>>>::::::::::::::::::::
#=GC RF                GccuAacagau.AACCAUauGugcCUUUAUAcAUUuUCUCCgcaCauCaucugaggCAGAUAUUAAUgCuuGUgUuCCUCUCUuUAUGGa.cUUCaaGuUUGGCUuUuuUGUuACAUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00309
#=GF ID   snosnR60_Z15
#=GF PI   snoZ193
#=GF DE   Small nucleolar RNA snR60/Z15/Z230/Z193/J17
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones S
#=GF SS   Predicted; Griffiths-Jones S
#=GF GA   41.00
#=GF TC   41.00
#=GF NC   40.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00070
#=GF DR   snoRNABase; U80;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Oryzias_latipes300023;
#=GF DR   snoopy; Gasterosteus_aculeatus300081;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell. 2002;109:145-148.
#=GF RN   [2]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science 1999;283:1168-1171.
#=GF RN   [3]
#=GF RM   15556860
#=GF RT   Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for
#=GF RT   modification of snRNAs in metazoa.
#=GF RA   Tycowski KT, Aab A, Steitz JA
#=GF RL   Curr Biol. 2004;14:1985-1995.
#=GF RN   [4]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [5]
#=GF RM   11266566
#=GF RT   Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana.
#=GF RA   Qu LH, Meng Q, Zhou H, Chen YQ
#=GF RL   Nucleic Acids Res. 2001;29:1623-1630.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. The family includes the yeast snoRNA snR60 (also known
#=GF CC   as Z15) and the corresponding human guide snoRNA U80 (SNORD80) [2,3]. This
#=GF CC   family also includes the Arabidopsis orthologue of Z15 and a large number
#=GF CC   of related plant snoRNAs Z230, Z193 and J17 [4,5].
#=GF WK   J17
#=GF SQ   23


AJ617329.1/1-83          -------UUCUUUGAUGAUUCC----AAA-AAAGCAUAGUUCA-ACUGAGCAUCGU-------AUGCUGAAACUUU---UU-CCAUC------UGAUUUGCACGUCAGUCUGA-----------
AY220644.1/1-79          ----GA-----GUGAUGAG-------CAAAAAUGCAUAGUUCA-GAUGAUCAAACCCUA----GUGGUUAUGAUUACUUUG---AAU--AAAUAGUCUUUCGCUC-------------------
AJ223844.1/4-101         AAAGGAUUUCUUUGAUGAUUCC----AAA-AAAGCAUAGUUCA-ACUGAGCAUCGU-------AUGCUGAAACUUU---UU-CCAUC------UGAUUUGCACGUCAGUCUGA---GAUUUCUC
AJ224029.1/1-77          --GAUACC---AUGAUGAU--------AA-----CAUAGUUCA-GCAGACUUA----------ACUCUGAUGAACA--------AUC-----AUGUCUUUCGCUCCUAUCUGA---UGUAUC--
X67268.1/1446-1526       CCGAUACC---AUGAUGAU--------AA-----CAUAGUUCA-GCAGACUUA----------ACUCUGAUGAACA--------AUC-----AUGUCUUUCGCUCCUAUCUGA---UGUAUCUG
CR759968.6/154278-154362 GUGAUGCAG--AUGAUGAC-------------UGCAUAGUUCA-GCAGAAAC-----------UCCAUGUAGAACA-------CAGA--GCAAUGUCUUUCGCUCCUAGCUGA---UGCAUCAC
AL807371.1/51971-51865   CUUGGGCUUCCGUGAUGAUUUA--CAAUCAUAAGCAUAGUUCA-UCUGAAUUA----------UUCAUGAAGACAACUACG--UAUU--UUAUAGUCUUUCGCUCCCAUCUGAUUUUGCCCUUU
CR759968.6/154064-154148 GUGAUGCAA--AUGAUGAC-------------UGCAUAGUUCA-GCAGAAUU-----------UCCAUGUAGAACA-------CAGA--GCAAUGUCUUUCGCUCCUAGCUGA---UGCAUCAC
CR382126.1/190306-190191 UAUAUCUUA--AUGAUGAUACAUUUCCUUCAGUGCAUAGUUCA-ACUGAUAAGGAUAACUUCCUAUAUGAAGAUAAAAAUU--CAUCGAAUUUAGUCUUUCGCUCCUAUCUGA---AAUCUCUG
AF141346.1/3076-3157     CCGAUACA---AUGAUGAU--------AA-----CAUAGUUCA-GCAGACUA--------------ACGCUGAUGA------GCAAU--AUUAAGUCUUUCGCUCCUAUCUGA---UGUAUCUG
CR382127.1/78421-78330   CCGCAA-----AUGAUGAUUAA----GAA-UUCGCAUAGUUCA-UCUGACUA-----------UCAAUGAAGAAUUAAUCU--UAGC-----AUGUCUUUCGCUCCUAUCUGA---UUUUUAUC
AF064272.1/1-104         ---UGUUA---AUGAUGAUAACC---AAA-GAUGCAUAGUUCA-ACUGAUUGAACAUACUAUCGAAAUGAAGAUAAAAAUUUCCAUCGAAAUUAGUCUUUCGCUCCUAUCUGA-----AC----
AJ223035.1/1-105         ---UGUUA---AUGAUGAUAACC---AAA-GAUGCAUAGUUCA-ACUGAUUGAACAUACUAUCGAAAUGAAGAUAAAAAUUUCCAUCGAAAUUAGUCUUUCGCUCCUAUCUGA-----ACA---
Y18560.1/2007-1909       AAGAAGCC---CUGAUGAC------CAACCAAUGCAUAGUUCACACUGAAUGCAA--------UUUGUGAAGAUA-------CCAACGAUUUUAGUCUUUCGCUCCUAUCUGA-CUGGCUUUCU
BT017923.1/629-724       UGAGGUCGG--GUGAUGAG------------UUGCAUAGUUCA-GAUGAUCAACCCUC-----GUGGUUCUGAUUACAUUG---AGU--AAUUAGUCUUUCGCUCCUAUCUGA---CGACCUUA
AJ240074.1/1-88          -----UCAA--GUGAUGAU-------UGAUAACGCAUAGUUCA-GAUGAUAAAU---------UCUAUUAUGAUUAACAUCUUCAGC----AUAGUCUUUCGCUCCUAUCUGA---UGA-----
AF317944.1/1-91          -AGGGUCAA--GUGAUGAU-------UAAUAAUGCAUAGUUCA-AAUGAUC---------------UCCAUGAUUACUAUU-CAGUA--GCACAGUCUUUCGCUCCUAUCUGA---UGGCCCU-
AJ490437.1/1-100         -AAGGUCGA--GUGAUGAG-------CAAAAAUGCAUAGUUCA-GAUGAUCAAACCCUA----GUGGUUAUGAUUACUUUG---AAU--AAAUAGUCUUUCGCUCCUAACUGA---CGGCCUU-
AJ494935.1/1-96          UGAGGUCGG--AUGAUGAG-------CAA--UUGCAUAGUUCA-AAUGAUUACA---------UUUGUAACUAUUAUGGUU-ACAUC---UAAAGUCUUUCGCUCCUAACUGA---CGACUUUA
AJ490439.1/1-96          UGAGGUCGG--AUGAUGAG-------CAA--UUGCAUAGUUCA-AAUGAUUACA---------UUUGUAACUAUUAUGGUU-ACAUC---UAAAGUCUUUCGCUCCUAACUGA---CGACUUUA
AP004460.2/66056-66151   UGAGGUCGG--AUGAUGAG-------CAA--UUGCAUAGUUCA-AAUGAUUACA---------UUUGUAACUACUAUGAUU-ACAUC---UAAAGUCUUUCGCUCCUAACUGA---CGACUUUA
AJ810173.1/437-337       GCAGUGAA---AUGAUGAUGAAAAUAUUA-AUUGCAUAGUUCA-ACUGAUAUAU------------AUGAAGAUAAAAAUA-CCAUC--AAAUAGUCUUUCACCCCUAUCUGA---UUCACAAU
AB020746.1/70534-70437   AGGGAUCAA--GUGAUGAU-------UGAUAACGCAUAGUUCA-GAUGAUAAAU---------UCUAUUAUGAUUAACAUCUUCAGC----AUAGUCUUUCGCUCCUAUCUGA---UGACCCUU
#=GC SS_cons             :::<<<<<_..________.......___._____________.__________.........__________________._____..________________________...>>>>>:::
#=GC RF                  uaagggcga..aUGAUGAu.......aAA.aauGCAUAGUUCA.acUGAuuaaa.........uuuaUgAaGAUuAaaaUu.cCAuc..auauAGUCUUUCGCUCCUAUCUGA...cgcccuUu
//
# STOCKHOLM 1.0

#=GF AC   RF00310
#=GF ID   snoZ165
#=GF DE   Small nucleolar RNA Z165
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Moxon SJ
#=GF GA   90.00
#=GF TC   103.20
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z165 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z165
#=GF SQ   5


AJ490381.1/1-92            ACCAUUCUAUGAUGAAUUGUCCUUAGCGGAUUCCGAUGAACCUGAUGUUAAUUUGGUUCUCUGAGAACAUGCUAUGACAUGUCUGAAAUAAU
AJ490390.1/1-83            -----UCUAUGAUGAAUUGUCCUUAGUGGAUUCUGAUGAACCUGAUGUCAUUUUGGUUCAAUGAGAACAUGCUAUGACAUGUCUGAGA----
AC078839.4/85064-85155     ACCAUUCUAUGAUGAAUUGUCCUUAGUGGAUUCUGAUGAACCUGAUGUCAUUUUGGUUCAAUGAGAACAUGCUAUGACAUGUCUGAGACAAU
AACV01021447.1/27566-27475 ACCAUUCUAUGAUGAAUUGUCCUUAGUGGAUUCUGAUGAACCUGAUGUCAUUUUGGUUCAAUGAGAACAUGCUAUGACAUGUCUGAGACAAU
AC078839.4/63426-63517     ACCAUUCUAUGAUGAAUUGUCCUUAGCGGAUUCCGAUGAACCUGAUGUUAAUUUGGUUCUCUGAGAACAUGCUAUGACAUGUCUGAAAUAAU
#=GC SS_cons               :::<<<___________________________________________________________________________________>>>
#=GC RF                    ACCauuCUAUGAUGAAUUGUCCUUAGuGGAUUCuGAUGAACCUGAUGUuAuUUUGGUUCaaUGAGAACAUGCUAUGACAUGUCUGAgAuaau
//
# STOCKHOLM 1.0

#=GF AC   RF00311
#=GF ID   snoZ188
#=GF DE   Small nucleolar RNA Z188
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   51.30
#=GF NC   41.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z188 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z188
#=GF SQ   21


AACV01021456.1/15260-15139 GCGUGCUAGUGAUGAUUAAAGAAGUU--AAAAAUGGUGAAUCCUGGAUUAAUG-UGCUCGCGUGCCGCUGUGUGCGCGCGCGGCUGGAGAUUUUUUUUUUCU---CUCUGUUCUUCUGUGAGUUCUUC
AACV01021456.1/14245-14131 UCGUGCUGGUGAUGAUUAAAGAGCU---AGCAAUGGUGAAUUC--GAUGAAUU-UGUUCGCGUGCCGCUGGGUGCGC-----AGCAGUGGUGAUAUGCAUUCUUACGCAGUUCAU--CUGAGGCACGC
AACV01021456.1/14512-14398 UCGUGCUGGUGAUGAUUAAAGAGCU---AGCAAUGGUGAAUUC--GAUGAAUU-UGUUCGCGUGCUGCUGGGUGCGC-----AGCAGUGGUGAUAUGCAUCCUUACGCAGUUCAU--AUGAGGCACGC
AAAA02029410.1/24575-24698 GCGUGCCAGUGAUGAUUACAGAGAUA--AAAAAUGGUGAAUUCUGGAUGAGCGGUGCUCGCGUGUCGCUGCGUGCGCGCGCGCUCGGCCGUGGUGAUAUCCCUUGCUCAGUUCAU--CUGAGGCACGC
AJ490432.1/1-121           GCGUGCUAGUGAUGAUUAAAGAAGUU--AAAAAUGGUGAAUCCUGGAUUAAUG-UGCUCGCGUGCCGCUGUGUGCGCGCGCGGCUGGAGAUUUUUUUUUUCU---CUCUGUUCUUCUGUGAGUUCUU-
AACV01021454.1/21881-22004 GCGUGCCAGUGAUGAUUACAGAGAUA--AAAAAUGGUGAAUUCUGGAUGAGCGGUGCUCGCGUGUCGCUGCGUGCGCGCGCGCUCGGCCGUGGUGAAAUCCCUUGCUCAGUUCAU--CUGAGGCACGC
AK242639.1/2352-2231       GCGUGCUAGUGAUGAUUAAAGAAGUU--AAAAAUGGUGAAUCCUGGAUUAAUG-UGCUCGCGUGCCGCUGUGUGCGCGCGCGGCUGGAGAUUUUUUUUUUCU---CUCUGUUCUUCUGUGAGUUCUUC
AK242639.1/1337-1223       UCGUGCUGGUGAUGAUUAAAGAGCU---AGCAAUGGUGAAUUC--GAUGAAUU-UGUUCGCGUGCCGCUGGGUGCGC-----AGCAGUGGUGAUAUGCAUUCUUACGCAGUUCAU--CUGAGGCACGC
AK242639.1/1604-1490       UCGUGCUGGUGAUGAUUAAAGAGCU---AGCAAUGGUGAAUUC--GAUGAAUU-UGUUCGCGUGCUGCUGGGUGCGC-----AGCAGUGGUGAUAUGCAUCCUUACGCAGUUCAU--AUGAGGCACGC
AAAA02029414.1/5475-5600   GCGUGCUAGUGAUGAUUAAAGAAGUAGCAAAAAUGGUGAAUCCUGGAUGAAUG-UGCUCGCGUGCCGCUGUGUGCGCGCGCGGCCGGAGAUUUUUUCUCUCUCU-CUCUGUUCUUCUGUGAGUUCUUC
AAAA02029414.1/6498-6612   UCGUGCUGGUGAUGAUUAAAGAGCU---AGCAAUGGUGAAUUC--GAUGAAUU-UGUUCGCGUGCCGCUGGGUGCGC-----AGCAGUGGUGAUAUGCAUUCUUACGCAGUUCAU--CUGAGGCACGC
AAAA02029414.1/6231-6345   UCGUGCUGGUGAUGAUUAAAGAGC-A--AGCAAUGGUGAAUUC--GAUGAAUU-UGUUCGCGUGCCGCUGGGUGCGC-----AGCAGUGGUGAUAUGCAUUCUUACGCAGUUCAU--CUGAGGCACGC
AC079936.7/138143-138022   GCGUGCUAGUGAUGAUUAAAGAAGUU--AAAAAUGGUGAAUCCUGGAUUAAUG-UGCUCGCGUGCCGCUGUGUGCGCGCGCGGCUGGAGAUUUUUUUUUUCU---CUCUGUUCUUCUGUGAGUUCUUC
AC079936.7/137128-137014   UCGUGCUGGUGAUGAUUAAAGAGCU---AGCAAUGGUGAAUUC--GAUGAAUU-UGUUCGCGUGCCGCUGGGUGCGC-----AGCAGUGGUGAUAUGCAUUCUUACGCAGUUCAU--CUGAGGCACGC
AC079936.7/137395-137281   UCGUGCUGGUGAUGAUUAAAGAGCU---AGCAAUGGUGAAUUC--GAUGAAUU-UGUUCGCGUGCUGCUGGGUGCGC-----AGCAGUGGUGAUAUGCAUCCUUACGCAGUUCAU--AUGAGGCACGC
AM237454.1/4239-4126       GCGUGCCAAUGAUGAUCGAAAAGCGU-------CGGUGAAUUCUGGAUGAAUG-CGCUUGUGCACCGACCAGU----GUGCAGCUAUGCAUGGUGAUAUCACCUGCGUAAUACAU--CUGAGGCACGC
AC078839.4/159694-159817   GCGUGCCAGUGAUGAUUACAGAGAUA--AAAAAUGGUGAAUUCUGGAUGAGCGGUGCUCGCGUGUCGCUGCGUGCGCGCGCGCUCGGCCGUGGUGAUAUCCCUUGCUCAGUUCAU--CUGAGGCACGC
AC078839.4/165188-165309   GCGUGCUAGUGAUGAUUAAAGAAGUU--AAAAAUGGUGAAUCCUGGAUUAAUG-UGCUCGCGUGCCGCUGUGUGCGCGCGCGGCUGGAGAUUUUUUUUUUCU---CUCUGUUCUUCUGUGAGUUCUUC
AC078839.4/166203-166317   UCGUGCUGGUGAUGAUUAAAGAGCU---AGCAAUGGUGAAUUC--GAUGAAUU-UGUUCGCGUGCCGCUGGGUGCGC-----AGCAGUGGUGAUAUGCAUUCUUACGCAGUUCAU--CUGAGGCACGC
AC078839.4/165936-166050   UCGUGCUGGUGAUGAUUAAAGAGCU---AGCAAUGGUGAAUUC--GAUGAAUU-UGUUCGCGUGCUGCUGGGUGCGC-----AGCAGUGGUGAUAUGCAUCCUUACGCAGUUCAU--AUGAGGCACGC
AJ490431.1/1-124           GCGUGCCAGUGAUGAUUACAGAGAUA--AAAAAUGGUGAAUUCUGGAUGAGCGGUGCUCGCGUGUCGCUGCGUGCGCGCGCGCUCGGCCGUGGUGAUAUCCCUUGCUCAGUUCAU--CUGAGGCACGC
#=GC SS_cons               :<<<<<<___________________.._________________________._____________________________________________________________..____>>>>>>:
#=GC RF                    gcGuGccaGUGAUGAUUAAAGAgcUu..AaaAAUGGUGAAUUCUGGAUGAAUg.UGcUCGCGUGCCGCUGuGUGCGCGcGCGaucaGuggUgaUauuuuUccUUaCuCaGUUCaU..cUGAggCaCgC
//
# STOCKHOLM 1.0

#=GF AC   RF00312
#=GF ID   snoZ206
#=GF DE   Small nucleolar RNA Z206
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   50.00
#=GF TC   58.10
#=GF NC   39.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z206 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z206
#=GF SQ   6


AJ490472.1/1-132           GCAGC-C-GGAUGAUGAGGUCAAGGUGAACGUGACGGUGCGCCGGUCGACGGCGCUGCUGGGCGGCACCGGUGCAGUAGUGCAAGAAGGUGGGCCUCAGGUGGUCGACGGGGUGAUGUGGUUCUGACCGGCGGC-
AK070157.1/3551-3683       GCAGC-C-GGAUGAUGAGGUCAAGGUGAACGUGACGGUGCGCCGGUCGACGGCGCUGCUAGGCGGCACCGGUGCAGUAGUGCAAGAAGGUGGGCCUCAGGAGGUCGACGGGGUGAUGUGGUUUCGACCGGCGGCG
AJ490476.1/1-128           GCAGC-C-GGAUGAUGAGGUCAAGGUGAACGUGACGGUGCGCCGGUCGACGGCGCUGCUGGGCGGCACCUACGCGGU---GCGAGGAAGCGG-CCUCAGAUGGUCGACGGGGUGAUGUGGUUCCGACCGGCGGC-
AAAA02025462.1/36027-36156 GCAGCGU-GAACAAUGAGGUCAAGGUGAGCGUGACGGUGCGCCGGUCGACGGCGCUGCUGGGCGGCGCCGGCGCGGU---GCAAGGAGGCGCACCUCAGGUGUUCGACGGGGUGAUGUGGUUCCUGCCGGCGGC-
AP005158.3/97518-97390     GCCGC-C-GG---AUGAGAUCAAGGUGAACGUGACAGUGCGCCGGUCGACGGCGCUGCUGGGCGGCACCGGUGCAGUAGUGCAAGAAGGUGGGCCUCAGGUGGUCGAUGGGGUGAUGUGGUUCCGACCGGCGGC-
AP005158.3/85114-84985     GCAGC-AAGGACAAUGAGGUUGAGGUGAGCGCGACGGUGCGCCGGUCGACGGCGCUGCUGGGCGGCACCGACGCGGU---GCGAGGAGGCGGGCCUCAGAUGGUCGACGGGGUGAUGUGGUUCCGACCGGCGGC-
#=GC SS_cons               :::<<.<.<<___________________________________________________________________...______________________________________________>>>>>:::.
#=GC RF                    GCAGC.c.GGAugAUGAGGUcAAGGUGAaCGUGACGGUGCGCCGGUCGACGGCGCUGCUGGGCGGCACCGguGCaGU...GCaAGaAGGuGggCCUCAGgUGgUCGAcGGGGUGAUGUGGUUccgACCgGCGGC.
//
# STOCKHOLM 1.0

#=GF AC   RF00313
#=GF ID   snoZ173
#=GF DE   Small nucleolar RNA Z173
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   70.00
#=GF TC   73.10
#=GF NC   65.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z173 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z173
#=GF SQ   4


AC078839.4/76753-76859     GCAGCGCCGAUGAUGAGUUCACAAAUGUACUAGGUUGAAUUCUGAUCGAAGAACCUCUCUUGGUUCGAACGAUGGCCACCUGUGUUCCUCUCGAUCUGAGGCGCUGC
AJ490403.1/1-105           -CAGCGCCGAUGAUGAGUUCACAAAUGUACUAGGUUGAAUUCUGAUCGAAGAACCUCUCUUGGUUCGAACGAUGGCCACCUGUGUUCCUCUCGAUCUGAGGCGCUG-
AJ490392.1/1-107           GCAGCGCCGAUGAUGAGUUCACAAAUGUACUAGGUUGAAUUCUGAUCGAAGAACCUCUCUUGGUUCGAACGAUGACCACCUGUGUUCCUCUCGAUCUGAGGCGCUGC
AAAA02029403.1/13648-13542 GCAGCGCCGAUGAUGAGUUCACAAAUGUACUAGGUUGAAUUCUGAUCGAAGAACCUCUCUUGGUUCGAACGAUGACCACCUGUGUUCCUCUCGAUCUGAGGCGCUGC
#=GC SS_cons               :<<<<<<<___________________________________________________________________________________________>>>>>>>:
#=GC RF                    GCaGCGCCGAUGAUGAGUUCACAAAUGUACUAGGUUGAAUUCUGAUCGAAGAACCUCUCUUGGUUCGAACGAUGaCCACCUGUGUUCCUCUCGAUCUGAGGCGCuGC
//
# STOCKHOLM 1.0

#=GF AC   RF00314
#=GF ID   snoZ182
#=GF DE   Small nucleolar RNA Z182
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Moxon SJ
#=GF GA   80.00
#=GF TC   86.20
#=GF NC   39.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z182 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z182
#=GF SQ   6


AJ490427.1/1-92            AGUGUGCCUAUGAUGAAAUGUUUCGACCUGUGUCAGGAUUUGAACCACUGGGCAUGUAAAUCUCAGUAGGUUUUUUUUUGCUGAGGCAUAUU
AJ490423.1/1-86            ACUGUGCCUAUGAUGAA-UGUUGA-ACCUGUGUCAGGAUUUGAACCACUGGGCAUGUAAAUCUCACUAGGUUUUUU----CUGAGGCAUGUU
AJ490421.1/1-86            ACUGUGCCUAUGAUGAA-UGUUGA-ACCUGUGUCAGGAUUUGAACCACUGGGCAUGUAAAUCUCACUAGGUUUUUU----CUGAGGCAUGUU
AACV01021454.1/9963-10048  ACUGUGCCUAUGAUGAA-UGUUGA-ACCUGUGUCAGGAUUUGAACCACUGGGCAUGUAAAUCUCACUAGGUUUUUU----CUGAGGCAUGUU
AAAA02029410.1/14014-14105 AGUGUGCCUAUGAUGAAAUGUUUCGACCUGUGUCAGGAUUUGAACCACUGGGCAUGUAAAUCUCAGUAGGUUUUUUUUUGCUGAGGCAUAUU
AC078839.4/149128-149219   AGUGUGCCUAUGAUGAAAUGUUUCGACCUGUGUCAGGAUUUGAACAACUGGGCAUGUAAAUCUCAGUAGGUUUUUUUUUGCUGAGGCAUAUU
#=GC SS_cons               ::<<<<<<____________________________________________________________________________>>>>>>::
#=GC RF                    AguguGCCUAUGAUGAAAUGUUuaGACCUGUGUCAGGAUUUGAACcACUGGGCAUGUAAAUCUCAgUAGGUUUUUUUUUGCUGAGGCauaUU
//
# STOCKHOLM 1.0

#=GF AC   RF00315
#=GF ID   snoJ33
#=GF DE   Small nucleolar RNA J33
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; Moxon SJ
#=GF GA   45.00
#=GF TC   45.40
#=GF NC   44.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   J33 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_J33
#=GF SQ   5


AF071527.1/15699-15624 UCGU----GGGAUGAUGUACUACUACCGGGCUCUUAAGAUGCUCGCUUUUCUUGACUCUGCGUCUGAAAUGGAC-AUUCGG
AK120402.1/2723-2803   CUGUGAGGGGAAUGAUGUACUACUACAGGGCUCUCAAGAUGCUUGCUUUUCUUGAUAAUGCAUCUGAAGUAGAAAUUACAG
AY220665.1/1-80        CUGUGAGGGGAAUGAUGUACUACUAUGAAGCUCUCAAGAUGCUGACAUUUCUUGAUUCUGCAUCUGAACAUGAC-UUACGG
AARH01010162.1/358-438 CUGUGAGGGGAAUGAUGUAUUAUUACCGUGCUCUUAAGAUGCUGGCUUUUCUUGAUUCUGCCUCGGAGAUGGACAUUAAAG
AM450233.2/10563-10483 CUGUAAGGGGAAUGAUGUAUUAUUAUCGAGCUCUCAAGAUGCUGGCCUAUCUCGAUUCUGCAUCAGAAAAGGACAUUGAAG
#=GC SS_cons           <<<<<<_____________________________________________________________________>>>>>>
#=GC RF                CugugAGGGGAAUGAUGUAcUAcUAccGaGCUCUcAAGAUGCUgGCuUUUCUUGAUUcUGCaUCuGAAaugGAcAUuacaG
//
# STOCKHOLM 1.0

#=GF AC   RF00316
#=GF ID   snoR43
#=GF DE   Small nucleolar RNA R43
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; ILM; Moxon SJ
#=GF GA   50.00
#=GF TC   56.10
#=GF NC   43.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300243;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF CC   R43 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_R43
#=GF SQ   16


AB016878.1/77210-77138   AGC-UGAUGAUGAUUCUAUACUUGAUGUUACUGACCAGAUUGUAUCUGAGUAUAAUCGCCUGCUUCCUGAGUCU
AF317967.1/1-73          AGA-UCAUGAUGAUUCUAUAUUUGAUAUUACAGACCAGUUACUAGUUGAAGACAAUCGCAUGCUACCUGAGUCU
AC007170.6/43858-43786   AGA-UCAUGAUGAUUCUAUAUUUGAUAUUACAGACCAGUUACUAGUUGAAGACAAUCGCAUGCUACCUGAGUCU
AF147262.1/111265-111337 AGA-UGAUGAUGAUUCUAUAUUUGAUAUCAUAGACCAGUUACUAGCUGAAGACAAUCGCAUGCUACAUGAGUCU
AJ429605.1/1-73          AGA-UGAUGAUGAUUCUAUAUUUGAUAUCAUAGACCAGUUACUAGCUGAAGACAAUCGCAUGCUACAUGAGUCU
AL161505.2/174357-174429 AGA-UGAUGAUGAUUCUAUAUUUGAUAUCAUAGACCAGUUACUAGCUGAAGACAAUCGCAUGCUACAUGAGUCU
AB028614.1/60467-60394   AGACUAAUGAUGAUUCUAUACUUAAUGUUACUGACCAGUGGGUAGCUGAAGAUACUAGCAUGUUGCAUGAGUCU
AL161514.2/105918-105846 AGC-UGAUGAUGAUUCUAUACUUGAUGUUACUGACUAGUGGGUAGCUGAAGAUAAUCGCCUGCUGCCUGAGUCU
AJ429606.1/1-68          ------AUGAUGAUUCUAUACUUGAUGUUACUGACUAGUGGGUAGCUGAAGAUAAUCGCCUGCUGCCUGAGUCU
AJ429607.1/1-68          ------AUGAUGAUUCUAUGUUUGAUAUUACAGACCAGUUACUAGCUGAAGACAAUCGCAUACUGCCUGAGUCU
AJ429608.1/1-68          ------AUGAUGAUUCUAUACUUGAUAUUACUGACUAGUGGGUAGCUGAAGAUAAUCGCCUGCUACCUGAGUCU
AB046440.1/51762-51691   -GA-CAAUGAUGAUUCUAUGUUUGAUAUUACAGACCAGUUACUAGCUGAAGACAAUCGCAUACUGCCUGAGUCU
AB017069.1/54572-54644   AGC-UGAUGAUGAUUCUAUACUUGAUAUUACUGACUAGUGGGUAGCUGAAGAUAAUCGCCUGCUACCUGAGUCU
AC069553.6/42430-42359   -GA-CAAUGAUGAUUCUAUGUUUGAUAUUACAGACCAGUUACUAGCUGAAGACAAUCGCAUACUGCCUGAGUCU
AL117386.1/38647-38575   AGC-UGAUGAUGAUUCUAUACUUGAUGUUACUGACUAGUGGGUAGCUGAAGAUAAUCGCCUGCUGCCUGAGUCU
AB073153.1/87384-87456   AGC-UGAUGAUGAUUCUAUACUUGAUGUUACUGACCAGUGGUUAGCUAAAGAUAAUCGCCUGCUGCCUGAGUCU
#=GC SS_cons             <<<.--------------------------------------<<<<_______________>>>>------>>>
#=GC RF                  AGa.UgAUGAUGAUUCUAUAuUUGAUaUUACuGACcAGUuaguAGcUGAAGAuAAUCGCaUgCUaCcUGAGuCU
//
# STOCKHOLM 1.0

#=GF AC   RF00317
#=GF ID   snoZ163
#=GF DE   Small nucleolar RNA Z163/Z177 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones S
#=GF SS   Predicted; Griffiths-Jones S
#=GF GA   39.00
#=GF TC   39.30
#=GF NC   37.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   This family of plant snoRNAs belong to the C/D class of snoRNA which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. This family includes rice
#=GF CC   snoRNA Z163 and Z177. Most of the members of the box C/D family function
#=GF CC   in directing site-specific 2'-O-methylation of substrate RNAs [1].
#=GF WK   Small_nucleolar_RNA_Z163/Z177_family
#=GF SQ   7


AC078839.4/60990-61073 UGGCCAGUGAUGAGAUGAAACGUGAGUUGUGCAGACACUCCACUGAUA-CCAAAUGAAGCGCAGGGA-----------UUAGUCCUUCUGAGGCCA
AJ490408.1/1-91        UGGCAGGUGAUG-GAUGAAACCUGAGUUGUACAGACACUCUUAAGUGAGUUGAAUGAAGUGCACUGAAACACAC----AUUGCGACUCUGAGGCCA
AJ490405.1/1-95        UGGCCGGUGAUG-GAUGAAACCUGAGUUGUACAGACACUCUUAAGUGAGUUGAAUGAAGUGCACUGACACACACUCACAUUGCGUCUCUGAGGCCA
AJ490407.1/1-94        UGGCCGGUGAUG-GAUGAAACCAGAGUUGUACAGACACUCUUAGUGAG-UUGAAUGAAGUGCAAUGACACACACUCACAUUGCAUCUCUGAGGCCA
AJ490398.1/1-94        UGGCCGGUGAUG-GAUGAAACCAGAGUUGUACAGACACUCUUAGUGAG-UUGAAUGAAGUGCAAUGACACACACUCACAUUGCAUCUCUGAGGCCA
AJ490378.1/1-83        UGGCCAGUGAUUAGAUGAAACGUGAGUUGUGCAGACACUCCACUGAAA-UUAAAUGAAGCGCAGUGA-----------UUAGUC-UUCUGAGGCCA
AJ490379.1/1-84        UGGCCAGUGAUGAGAUGAAACGUGAGUUGUGCAGCCACUCCACUGAAA-CCAAAUGAAGCGCAGGGA-----------UUAGUCCUUCUGAGGCCA
#=GC SS_cons           <<<<<_______.___________________________________._________________________...._____________>>>>>
#=GC RF                UGGCCgGUGAUG.GAUGAAACcuGAGUUGUaCAGACACUCuuaugaaA.UUgAAUGAAGuGCAauGAcACACAC....aUuGcaucUCUGAGGCCA
//
# STOCKHOLM 1.0

#=GF AC   RF00318
#=GF ID   snoZ175
#=GF DE   Small nucleolar RNA Z175
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   43.00
#=GF TC   49.40
#=GF NC   39.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z175 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z175
#=GF SQ   6


AJ490406.1/1-81            GCGGCAAUGAUGAGAAUGCAAUUCUAUGAUGUACUUUGAUUUUUCUAUGAUGUACUUUAAUUCUAUGAUACUCUGAGCCAU
AC078839.4/78433-78513     GCGGCAAUGAUGAGAAUGCAAUUCUAUGAUGUACUUUGAUUUUUCUAUGAUGUACUUUAAUUCUAUGAUACUCUGAGCCAU
AJ490399.1/1-81            GUGGCAAUGAUGAGAAUGCAAUUCUAUGAUGUACUUUGAUUUUUCUAUGAUGUACUUUAAUUCUAUGAUACUCUGAGCCAU
AAAA02029403.1/10313-10233 GUGGCAAUGAUGAGAAUGCAAUUCUAUGAUGUACUUUGAUUUUUCUAUGAUGUACUUUAAUUCUAUGAUACUCUGAGCCAU
AACV01021447.1/34197-34117 GCGGCAAUGAUGAGAAUGCAAUUCUAUGAUGUACUUUGAUUUUUCUAUGAUGUACUUUAAUUCUAUGAUACUCUGAGCCAU
AJ490396.1/1-46            GUGGCAAUGAUGAGA-----------------ACUUUGAUUUUUCUAUGAUG------------------CUCUGAGCCAU
#=GC SS_cons               ::<<<_______________________________________________________________________>>>::
#=GC RF                    GuGGCAAUGAUGAGAAUGCAAUUCUAUGAUGUACUUUGAUUUUUCUAUGAUGUACUUUAAUUCUAUGAUACUCUGAGCCAU
//
# STOCKHOLM 1.0

#=GF AC   RF00319
#=GF ID   SNORA23
#=GF PI   snoMBI-1
#=GF DE   Small nucleolar RNA SNORA23
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAalifold; Griffiths-Jones S
#=GF GA   45.00
#=GF TC   46.50
#=GF NC   43.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.11 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; ACA23;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300764;
#=GF DR   snoopy; Danio_rerio300118;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [4]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the H/ACA class of snoRNAs which are
#=GF CC   thought to guide the sites of modification of uridines to pseudouridines
#=GF CC   [1]. This family includes human snoRNA ACA23 (SNORA23) and mouse snoMBI-1
#=GF CC   [2,3]. ACA23 is predicted to guide the pseudouridylation of residue U3737
#=GF CC   and U4331 of 28S rRNA [4].
#=GF WK   Small_nucleolar_RNA_MBI-1
#=GF SQ   9



FJ915959.1/8-189         GCCGUAAUGUGUGCAUAGGU-UUCAUCUGUGUCUGGUAGCAGUGUCUGUCUGUGUUUUGCAUUCAG-AUCUUGCUAUCCACAC-AAACGUCAUGCAGCCAAAGAGUAACUUGGGAUCAUAGUACUGGUCUAGUGUUGUCUCUG---GACACAUCUACCACUGGCCAGCCUCCAAAUUCCCACACACAG
AC192839.3/174952-175133 GCUGUAAUGUGUGCAUAGGU-UUCAUCUGUGUCUGGUAGCAGUGUCUGUCUGUGUUUUGCUUUCAG-AUCUUGCUAUCCACAC-AAAUAUCAUGCGGCCAAAGAGUAACUUGGGAUCAUAGUACUGGUCUAGUGUUGUCUCUG---GACACAUCUACCACUGGCCAGCCUCCAAAUUCCCACACACAG
CU658147.9/6051-6229     U--GAAUGGUGUGCGUAGUG-UCCGUCUGCGUUUAGUGCCGUCUCCGGUCUGUGUCUUACAGGCUGUGGGACGGUUCUCACACCGCACUC---ACGGCCACAGAGCCACCGGAGAUCAUAGUACUGGCCUAGUGUUG--UCUAAAUGAC-CAUCCACCACUGACCAGCCUCCAUAGUCUCCAACAAAA
EU240259.1/3-184         GCAGUACUGUGUGCAUAGUUGUUCAUCUGUGUCUGGUGGUAUAGUCUAUUUGUGUUCUACAUUUAG-ACUGUACUACUCACAC-AAAACC--UGUGGCCAAAGAUGAACUUGAGAUCAUAGUACUGGUCUAGUGAC--GUCUGAAUGACAUGCCUCCCACUGGCCAGCCUCCAUACUCUCAAACAUCU
AJ295844.1/31324-31502   ---GUAAUGUGUGCAUAGGU-UUCAUCUGUGUCUGGUAGCAGUGUCUGUCUGUGUUUUGCAUUCAG-AUCUUGCUAUCCACAC-AAACAUCAUGCGGCCAAAGAGUAACUUGGGAUCAUAGUACUGGUCUAGUGUUGUCUCUGG---ACACAUCUACCACUGGCCAGCCUCCAAAUUCCCACACACAG
AC121995.2/104161-104344 UGAGUCCUGUGUGCAUAGUU-UUCAUCUAUGUCUGGUAGCAGUAUCUGUCUGCGUUUUGCAUUCAG-AUCUUGCUAUCCACAC-AAACGA-AUGCAGCCAAAGAAUAAGUUGGGAUCAUAGUACUGGCCUAGUGUUGUGUUUUUUUAACACAUCUCCCACUGGCCAGCCUCCAAAUUCCCAGACACAA
AC132192.3/71954-71776   ---GUAAUGUGUGCAUAGGU-UUCAUCUGUGUCUGGUAGCAGUGUCUGUCUGUGUUUUUCAUUCAG-AUCUUGCUAUCCACAC-AAACAUCAUGCGGCCAAAGAGUAACUUGGGAUCAUAGUACUGGUCUAGUGUUGUCUCUGG---ACACAUCUACCACUGGCCAGCCUCCAAAUUCCCACACACAG
AJ278435.1/32194-32377   UGAGUCCUGUGUGCAUAGUU-UUCAUCUAUGUCUGGUAGCAGUAUCUGUCUGCGUUUUGCAUUCAG-AUCUUGCUAUCCACAC-AAACGA-AUGCAGCCAAAGAAUAAGUUGGGAUCAUAGUACUGGCCUAGUGUUGUGUUUUUUUAACACAUCUCCCACUGGCCAGCCUCCAAAUUCCCAGACACAA
AF357383.1/1-184         UGAGUCCUGUGUGCAUAGUU-UUCAUCUAUGUCUGGUAGCAGUAUCUGUCUGCGUUUUGCAUUCAN-AUCUUGCUAUCCACAC-AAACNA-AUGCAGCCAAAGAAUAAGUUGGGAUCAUAGUACUGGCCUAGUGUUGUGUUUUUUUAACACAUCUCCCACUGGCCAGCCUCCAAAUUCCCANACACAA
#=GC SS_cons             ::::::::::::<<<<----.--------<<<-<<<<<<<<<-<<<<<--<<<_____>>>-->>>.>>->>>>>>->>>->>.>-----.>>>>---------------<<<<<--------<<<<<<-<<<<-<<<<<<_____>>>>>>----->>>>>>>>>>--------->>>>>:::::::
#=GC RF                  ucaGuaauGUGUGCauAGuu.UUCAUCUguGucuGGuagcaguguCuGUcuGcGUUUUgCauuCaG.acccugcuauCCaCaC.aAAcau.auGCgGCCAAAGAguAAcUuGgGaUCAUAGUACuGGcCUaGuGUuGugucUgaaUgacaCaUCUaCCaCuGgCCaGCCUCCAaAuuCcCaaACAcAa
//
# STOCKHOLM 1.0

#=GF AC   RF00320
#=GF ID   snoZ185
#=GF DE   Small nucleolar RNA Z185
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   50.00
#=GF TC   57.40
#=GF NC   39.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z185 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z185
#=GF SQ   5


AJ490429.1/1-84            UGGUCACAUGAUGUUUGUAUCACCACCCAUCUGAAGCAGGCUGAAUGUCAGUCUGCAUGUGCAGAAAUGUGAU--UCUGAUGGCUA
AJ490425.1/1-86            UGGCCACAUGAUGUUUGUAUCACCACCCAUCUGAAGCAGUCUGAAUGUCAGUCUGCAUGUGCAGAAAUGUGAUAUUCUGAUGGCUA
AC078839.4/148113-148196   GAGCUA--UGCAGAAACUAUCACCACCCAUCUGAAGCAGUCUGAAUGUCAGUCUGCAUGUGCAGAAAUGUGAUAUUCUGAUGGCUA
AC078839.4/149971-150054   UGGUCACAUGAUGUUUGUAUCACCACCCAUCUGAAGCAGGCUGAAUGUCAGUCUGCAUGUGCAGAAAUGUGAU--UCUGAUGGCUA
AAAA02029410.1/12994-13079 UGGCCACAUGAUGUUUGUAUCACCACCCAUCUGAAGCAGUCUGAAUGUCAGUCUGCAUGUGCAGAAAUGUGAUAUUCUGAUGGCUA
#=GC SS_cons               <<<<<<__________________________________________________________________________>>>>>>
#=GC RF                    ugGccACAUGAuGuuugUAUCACCACCCAUCUGAAGCAGuCUGAAUGUCAGUCUGCAUGUGCAGAAAUGUGAUAUUCUGAUggCua
//
# STOCKHOLM 1.0

#=GF AC   RF00321
#=GF ID   snoZ247
#=GF DE   Small nucleolar RNA Z247
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z247 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z247
#=GF SQ   8


AC136222.2/290-162       CCCAUUGA--UGAUGAUGAUCUGAUCAGCUAUAUCAUUGCUGGUCUUGAUGAAGAAUAUGUGC-CGGUAAUCUCGUCCAUUGUUGGGCGAC-CAGAUCAGGUGACCGUCAGUGAG--------GCCUUUGCUUAG--UUGAUA
AJ494955.1/1-137         ---CUGGAAAUGAUGAUGAUCUGAUCUCCCAUAUCCUUGCUGGUUUGGAUUUUGAUUAUAAUC-CUGUUGUGUCCUCGAUUAC-GGGACGCACUGAGUCUGUUUCCUUUGGUGAAGUCUAUGCGCAACUGCUGAGUUUCGAG-
AJ494959.1/1-139         GCCCUUGA--UGAUGAUGAUCUGAUCUCCCAUAUCCUUGCUGGUUUGGAUUUUGAUUAUAAUC-CUGUUGUGUCCUCGAUUAC-GGGAUGCACCGAGUCUGUUUCCUUUGGUGAAGUCUAUGCGCAGCUGCUGAGUUUCGAGC
AP004158.3/94593-94731   GCCCUUGA--UGAUGAUGAUCUGAUCUCCCAUAUCCUUGCUGAUUUGGAUUUUGAUUAUAAUC-CUGUUGUGUCCUCGAUUAC-GGGACGCACUGAGUCUGUUUCCUUUGGUGAAGUCUAUGCGCAACUGCUGAGUUUCGAGC
AJ494956.1/1-139         GCCCUUGA--UGAUGAUGAUCUGAUCUCCCAUAUCCUUGCUGGUUUGGAUUUUGAUUAUAAUC-CUGUUGUGUCCUCGAUUAC-GGGACGCACUGAGUCUGUUUCCUUUGGUGAAGUCUAUGCGCAACUGCUGAGUUUCGAGC
AJ494957.1/1-139         GCCCUUGA--UGAUGAUGAUCUGAUCUCCCAUAUCCUUGCUGGUUUGGAUUUUGAUUAUAAUC-CUGUUGUGUCCUCGAUUAC-GGGACGCACUGAGUUUGUUUCCUUUGGUGAAGUCUAUGCGCAGCUGCUGAGUUUCGAGC
AJ494958.1/1-139         GCCCUUGA--UGAUGAUGAUCUGAUCUCCCAUAUCCUUGCUGGUUUGGAUUUUGAUUAUAAUC-CUGUUGUGUCCUCGAUUAC-GGGACGCACCGAGUUUGUUUCCUUUGGUGAAGUCUAUGCGCAGCUGCUGAGUUUCGAGC
AP006237.3/140787-140661 CAUCUUGA--CGAUGACGAUCUGAUCUCAUACAUCCUCACAGGCCUUGACUUCG-UGGUGUCCUCUGUUGCUGCAC--------GUGUAGAGCCCAU-----GACAGUGGGUGAUCUGUAUGCGCAACUGCUGAGCUUUGAGC
#=GC SS_cons             :::<<<<<..-----------------------------------------------------.-------------------.-------<<<<<<_________>>>>>>------------------------->>>>>:
#=GC RF                  gcccUuGA..UGAUGAUGAUCUGAUCUcccAUAUCcUUGCUGGUuUgGAUUUuGAUUAUaauC.CUGUUGUgUCcUCgAUUAc.GGGacGcaCcgAgUuuGUuuCcuUcgGuGAagUcUAUGCGCAaCUGCUGAGUUUCgAgc
//
# STOCKHOLM 1.0

#=GF AC   RF00322
#=GF ID   SNORA31
#=GF PI   snoMBI-161
#=GF DE   Small nucleolar RNA SNORA31
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Griffiths-Jones S
#=GF SS   Predicted; RNAalifold
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; ACA31;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300391;
#=GF DR   snoopy; Gallus_gallus300029;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [4]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   ACA31 (SNORA31) belongs to the H/ACA class of snoRNAs which are thought to
#=GF CC   guide the sites of modification of uridines to pseudouridines [1]. ACA31
#=GF CC   is predicted to guide the pseudouridylation of U3713 in 28S rRNA and U218
#=GF CC   in 18S rRNA [4]. This family includes the mouse homologue snoMBI-161 [3].
#=GF WK   Small_nucleolar_RNA_MBI-161
#=GF SQ   5


AF357400.1/1-112       ------------------CUCGAACAGUUUGUGGUUGUUCUUCUGGUUUGCACUAGGAUGCAAAAGGAAACUCUCCCUGCGCUUCCUGCCUGCCUUUGUGGCAGUUCAGAUUGAAUUAGGGAGUACAUCU
AL845471.7/44715-44842 UUGCAUGCAUUGACAGCCCUUGACCAGUUUGUGGUUGUUCUUCUGGUCUGUACUAGGAUGCAAAAGAAAAG-CUCCCUGAGUGUUCUGCCUGCCUCUGUGGC-GUUUAGAUUGAAUUGGGAUAUACAUCU
AJ609441.1/1-130       CUGCAUCCACUGAUAGACCUUGAACAAUUUACUGUUGUUCUUUUGGUUUGCACUAGGAUGCAAAAGAAAGAAAUCCCUGCGCUUUCUGUCUGUCUUUGUGGCGGCCCAGAUUGAAUUGGGGAAUACAUCU
AJ225898.1/4306-4432   CUGCAUCCACUGAUAGACCUUGAACAGUCUGCUGUUGUUCUUUUGGUUUGCAAUAGGAUGCCAAAGGAAAA--UCCCUGCG-UUUCUGUCUGUCUUUGUGGCAGCCCAGAUUGAAUUGGGGGAUACAUUU
AY186881.1/3825-3954   CUGCAUCCACUGAUAGACCUCGAACAGUUUGUGGUUGUUCUUCUGGUUUGCACUAGGAUGCAAAAGGAAACUCUCCCUGCGCUUCCUGCCUGCCUUUGUGGCAGUUCAGAUUGAAUUAGGGAGUACAUCU
#=GC SS_cons           :<<<<<<<--<<-<<<<<<--<<<<<<<_____>>>>>>>---->>>>>>>>--->>>>>>>-----------<<<<<<--<--<<<<-<<<<<_____>>>>>-->>>>-->--->>>>>>::::::::
#=GC RF                cuGCaucCAcuGAcagaCCUuGaaCaguUUgugguuGuuCUUuUGGucugCacUAGgauGCaAAAGaAAAaucuCCCcgcGcuUuCuGuCuGcCUuUGUGgCaGuuCaGaUUgAAUugGGGaaUACAUcU
//
# STOCKHOLM 1.0

#=GF AC   RF00323
#=GF ID   snoR79
#=GF DE   Small nucleolar RNA R79
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   80.00
#=GF TC   93.10
#=GF NC   55.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol 2002;12:2002-2013.
#=GF CC   R79 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_R79
#=GF SQ   5


AJ429614.1/1-63        --AGGUGAUGAUGAUAAAGAUGAACGCUUGGGAACUUCGACUGACAGUGAGAACACUGAACUUUC
AJ429613.1/1-65        GAAGGUGAUGAUGAUAAAGAUGAACGCUUGGGAACUUCGACUGACAGUGAGAACACUGAACUUUC
AF318009.1/1-65        GAAGGUGAUGAUGAUAAAGAUGAACGCUUGGGAACUUCGACUGACAGUGAGAACACUGAACUUUC
AF262038.1/28916-28852 GUAGGUGAUGAUGAUAAAGAUGAACGCUUGGGAACUUCGACUGACAGUGAGAACACUGAACUUUC
AK221296.1/1548-1612   GUAGGUGAUGAUGAUAAAGAUGAACGCUUGGGAACUUCGACUGACAGUGAGAACACUGAACUUUC
#=GC SS_cons           <<<<<_______________________________________________________>>>>>
#=GC RF                GaAgGUGAUGAUGAUAAAGAUGAACGCUUGGGAACUUCGACUGACAGUGAGAACACUGAACuUuC
//
# STOCKHOLM 1.0

#=GF AC   RF00324
#=GF ID   snoMBII-202
#=GF DE   Small nucleolar RNA MBII-202
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   40.00
#=GF TC   40.30
#=GF NC   39.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300816;
#=GF DR   snoopy; Gallus_gallus300046;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   MBII-202 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1].
#=GF WK   Small_nucleolar_RNA_MBII-202
#=GF SQ   30


ABDC01407961.1/461-543         UGAUGA---CAGUC-UCCGGAAUCGCUGCACUGCUU-U-GAUGAAAGCCCAUUUGAACCCUUUUCCAU-----CUGAUGA--CUGAGC--------GUUU---UCG-C
AANU01214492.1/21213-21296     UGAUGA---CAUUC-UCCGGAAUCGCUGGACGGCCU-U-GAUGAAAGCACGUUUGAACCCUUUUCCAU-----CUGAUCG--CUGGGC--------CUCU---CCAUC
AK026501.1/773-856             UGAUGA---CAUUC-UCCGGAAUCGCUGUACGGCCU-U-GAUGAAAGCACAUUUGAACCCUUUUCCAU-----CUGAUUG--CUGAGG--------CUUU---UCAUC
AC010538.9/180240-180157       UGAUGA---CAUUC-UCCGGAAUCGCUGUACGGCCU-U-GAUGAAAGCACAUUUGAACCCUUUUCCAU-----CUGAUUG--CUGAGG--------CUUU---UCAUC
X65514.1/66-149                UGAUGA---CAUUC-UCCGGAAUCGCUGUACGGCCU-U-GAUGAAAGCACAUUUGAACCCUUUUCCAU-----CUGAUUG--CUGAGG--------CUUU---UCAUC
AC092123.4/24307-24224         UGAUGA---CAUUC-UCCGGAAUCGCUGUACGGCCU-U-GAUGAAAGCACAUUUGAACCCUUUUCCAU-----CUGAUUG--CUGAGG--------CUUU---UCAUC
AAQQ01676157.1/1791-1710       UGAUGA---CAUUC-UCCGGAAUCGCUGUACUGCCG-U-GAUGAAAGUACACUUGAACCCUUUUCCAU-----CUGACGG--CUGAGC--------GU-----UUGUU
BC086577.1/368-450             UGAUGA---CAUUC-UCCGGAAUCGCUGUACUGUCU-U-GAUGAAAGUACUUUUGAACCCUUUUCCAU-----CUGACU---ACGAGC--------UUUC---UCGGC
AAFR03032402.1/14057-13969     UGAUGAC-AUAUUC-UCCGGAAUCUCUGUACUGCCUCU-GAUGAAAGUACAUUUGAACCCUUUUCCAU-----CUGAUGA--CUGUUG--------UGAUC-UUUCUC
AANN01735692.1/3277-3192       UGAUGA--CAAUUC-UCCGGAAUCGCUGCGUCUCUG-U-GAUGAAAGCUUGCUCGAACCCUUUUCCAU-----CUGACGG--CUGAGC--------UCUC--GUCCUC
BAAF04006228.1/568-488         UGUGAUGACACAUC-UCCGGAAUCUCUGUAGUUCUU-U-GAUGAAA---AACUUGAACCUUUUU---------CUGAUGA--CUGCUC--------UGAA--AAUCUC
AANH01000366.1/110501-110419   GAUGAUGACAAAAC-UCCGGAAUCUCUGUAUUUCUU-U-GAUGAAA---CACUUGAACCCUUUU--UU-----CUGAUGA--CUGCUC--------UGAA--AAAUAU
AAIY01379030.1/710-782         CAUGAU---GACGC-UCCGGAAUCGCUGCACUGCCG-U-GAUGAAAGAUCAUUUGAACCCUUUGCCGG-----CUGAUG------------------------ACCGU
CAAA01068197.1/6898-6983       UGAUGA---CAUUC-UCCGGAAUCGCUGUACUGACU-U-GAUGAAAGUACUUUUGAACCCUUUUCCAU-----CUGAUGACACCGAGU--------UUUC---UCGGC
AAPN01209129.1/3789-3700       UGAUGAC-ACAUUC-UCCGGAAUCUCUGUACUGCCUCU-GAUGAAAGUAUAAUUGAACCCUUUUCCAU-----CUGAUGA--CUGCGG--------CUGCCGCUCAGU
CAAE01014581.1/1544680-1544604 UGAUGA--CAAAUC-UCCGGAAUCUCUGUAUUGACU-U-GAUGA----AUACUUGAACCCAUUA--AU-----CUGAUAC--UGGCUG--------CA-----UCGAU
CU683900.5/6328-6410           UGAUGACGGCUUUC-UCCGGAAUCUCUGCACAUCCU-U-GAUGA-----CUUUUGAACCCUUUUCUGG-----CUGAUGA--CUGCAG--------UUUA--UUCAGC
AAWR02022017.1/114386-114456   UGAUGA---CAGUC-UCCGGAAUCACUGUUACGCUU-U-GAUGA---------AGACCCCUUUACGUGCUUGGCUGA---------GG--------AG-----UCAAU
AAGV020441936.1/257-166        UGAUGA---CAUUC-UCCGGAAUCACUGUACUGCUU-U-GAUGAAAGUACCUUUGAACCCUUUUCCAU-----CUGAUGA--CUGUGGGGAGAAAAAAAG---UUAUU
AAGU03070663.1/24581-24506     UGAUGA---CAUUC-UCCGGAAUCGCUGUACUGCUU-UUGAUGAAA----------AGUCUUUUCCAC-----CUGAUGA--UCGUGG-------ACUUU---UUAUU
AAPE02031289.1/8534-8451       UGAUGA---CAUUC-UCCGGAAUCGCUGUACUGCCU-U-GAUGAAAGUACACUUGAACCCUUUUCCAU-----CUGACGA--CUGAGC--------CCUU---CCAUU
AADN03006363.1/16912-16832     GAUGAG---AAGUC-UCCGGAAUCGCUGUACUGCAU-U-GAUGA---UUCCCUCGAACCCUAGUCUGU-----CUGAUGG--CUGCGG--------CAGC---UCUGU
AADA01095166.1/802-876         UUCUUA---CA---------AAUCUAAAUG-UGCUU-U-GAUGCAAGUAUAUUUGAACCCCUUUCCAU-----CUGAUAA--CUGAGC--------AAAA---UAAUA
AAQR03058651.1/3800-3716       UUUUAU---AAUUCAUUAAGGAGUACUUGGCUGCUU-U-GAUGGAAGUACCUUUGAACCCUUUUCCAU-----CUGAAAA--CUGAUG--------ACCA---AAAAA
AAWZ02028909.1/3308-3386       UGAUGA--AAAUUC-UCCGGAAUCUCUGUACUCCAU-U-GAUGA----UCCCUUGAACCCAUAUCUG------CUGAUGG--CUGUGG--------UA----AUGGUU
CAAB02001292.1/999-1084        UGAUGA--CAAAUC-UCCGGAAUCUCUGUAUUUACU-U-GAUGA----AUACUUGAACCCAUUAAUCUGA-UACUGACUG--CAUAUU--------UCCU--GUCAUC
AC163617.5/148762-148677       UGAUGA---CAUUC-UCCGGAAUCGCUGUACUGACU-U-GAUGAAAGUACUUUUGAACCCUUUUCCAU-----CUGAUGACACCGAGU--------UUUC---UCGGC
JN899128.1/5-71                UGAUGA---CAUUC-UCCGGAAUCGCUGCAUCGCUG-U-GAUGAAAGCACAUUUGAACCCUUUUCCAU-----CUGA------------------------------C
EU240331.1/7-70                GAUGAG---AAGUC-UCCGGAAUCGCUGUACUGCAU-U-GAUGA---UUCCCUCGAACCCUAGU---------CUGU--------------------------CUGAU
EU094058.1/8-77                AUGACA---CAUUC-UCCGGAAUCUCUGUACUGCCUCU-GAUGAAAGUAUAAUUGAACCCUUUUCCAU-----CUGA--------------------------UG--A
#=GC SS_cons                   :<<<<<..._____._____________________._._____________________________....._______..______........____...>>>>>
#=GC RF                        Ugauga...cAuUC.UCCGGAAUCuCUGUAcUGCuU.U.GAUGAAAGUAcauUUGAACCCUUUUCCaU.....CUGAUga..CUGagg........uuuu...ucauc
//
# STOCKHOLM 1.0

#=GF AC   RF00325
#=GF ID   SNORD53_SNORD92
#=GF PI   SNORD53; U53
#=GF DE   Small nucleolar RNA SNORD53/SNORD92
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; Moxon SJ
#=GF GA   46.00
#=GF TC   46.50
#=GF NC   45.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.47 -Z 549862.597050 CM SEQDB
#=GF CL   CL00063
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300920;
#=GF DR   snoopy; Gallus_gallus300073;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell 1996;85:1077-1088.
#=GF RN   [3]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [4]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   U53 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].This family includes mouse MBII-316 identified in [3]. The human
#=GF CC   orthologue HBII-316 (SNORD92) is predicted to guide the 2'O-ribose
#=GF CC   methylation of 28S rRNA A3846 [4].
#=GF WK   Small_nucleolar_RNA_SNORD53
#=GF SQ   37



FM245454.1/1310-1382         --U-UCCAGUGAUGAUACCC-----AAAA--GGUUUCGCA--UGUAU--CCGA-UU-------AAGAUGAC--GA-UA-A-AC-CUUGGCUG--UCUGAGCG-A--
X96652.1/1-78                --A-UGCUAUGAUGACAUCC-----AUAU--GGUUUCGCU--GCUGG--CUGA-GU-UU-C-AGAGAUGAC--AC-CU-U-UCUCUUGGCUG--UCUGAGCC-U--
AF357377.1/1-68              -------------GAUAUCC-----UCAU--GGUUUCGCG--UCUGU--CUGA-GU-CU-C-AGAGAUGAC--AC-CU-U-UCUCUUGGCUG--UCUGAGCA-U--
AC097720.5/99784-99861       --A-UGCUAUGAUGACAUCC-----AUAU--GGUUUCGCU--GCUGG--CUGA-GU-UU-C-AGAGAUGAC--AC-CU-U-UCUCUUGGCUG--UCUGAGCA-U--
AAQQ01098685.1/966-1043      --A-UGCUAUGAUGACAACC-----ACAU--GGUUUCGCU--UCUGG--CUGA-GU-UU-C-AGAGAUGAC--AC-UU-U-UCUCUUGGCUG--UCUGAGCA-U--
AAHX01042265.1/61060-60983   --C-UGCUGUGAUGAUAUCC-----ACAC--GGUUUCGCG--UCUGG--CUGA-GU-UU-C-AGAGAUGAC--AC-CU-U-UCUCUUGGCUG--UCUGAGCA-U--
AALT01651459.1/2446-2369     --G-UGCAGUGAUGAUGUCC-----AUAU--GGUUUCGCU--UCUGG--CUGA-GU-CU-C-AGAGAUGAC--AC-UU-U-UCUCUUGGCUG--UCUGAGCA-U--
AANN01688271.1/7800-7879     --C-UGCUAUGAUGACACCC-----ACAUAUGGUUUCGCU--UCUGG--CUGA-GC-UU-C-AGAGAUGAC--AC-CU-U-UCUCUUGGCUG--UCUGAGCA-U--
AAPN01065335.1/8282-8359     --A-UGCCGUGAUGAUUACC-----AUCU--GGUUUCGCU--UUUGG--CUGA-GU-UU-C-CGUGGUGAC--AC-CU-U-UCUCUUGGCUG--UCUGAGCU-U--
AAFR03004750.1/49698-49621   --C-UGCUGUGAUGACUUCC-----AUUU--GGUUUCGCU--UGUGA--CUGA-GU-UU-C-AGAGCUGAU--GC-UU-C-UCUCUUGGCUG--UCUGAGUG-G--
AAPY01599111.1/9463-9540     --U-UGCUGUGAUGACUUCC-----AUUG--GGUUUCGCA--UGUUG--CUGA-GU-UC-C-AGUGAUGCC--UC-UU-U-UCUCUUGGCUG--UCUGAGCA-G--
AANU01293451.1/11576-11500   --U-UGCUGUGAUGACUAUC-----AU-U--GGUUUCGCA--UGUUG--CUGA-GU-UU-C-AGUGAUGCC--UC-UU-U-UCUCUUGGCUG--UCUGAGCA-A--
AANG01194723.1/519-594       --U-UGCUGUGAUGAUUUCC-----AUUG--GGUUUCGCA--UGUUG--CUGA-GU-UC-C-AGUGAUG----CC-UU-U-UCUCUUGGCUG--UCUGAGCA-G--
AAIY01696762.1/705-780       --U-UGCCAUGAUGACUUCC-----AGUG--GGUUUCGCA--UAUUG--CUGA-GC-UC-C-AAUGAUGAC--UC----U-UCUCUUGGCUG--UCUGAGCA-G--
AAYZ01232906.1/8001-8075     --U-UGCUGUGAUGACUU-C-----AUUG--GGUUUCGCA--AGUUG--CUGA-CC-CU-C-AGUGAUGCG--UC----C-UCUCUUGGCUG--UCUGAGCA-G--
AAVX01115814.1/1001-927      --G-UGCUAUGAUGACUUA------AUAA--GGUUUCGCU-AUGUUU--CUGA-GA-AA-A-UCGGAUGAC--AC-UU-C----CUUGGCUG--UCUGAGCA-U--
CAAE01007089.1/118765-118841 --C-GGG-AUGAUGACCCAC-----AG-U--GGUUUCGCU--CAUUGGCCUGA-GC-CC-C-AGUGAUGUC--AC--U-U-CCUCUUGGCUG--UCUGACCU-G--
AAWR02004239.1/65672-65597   --U-UGCUGUGAUGAUUUUC-----AUUG--GGUUUCGCA--UGUUG--CUGA-CU-UC-C-GAUGAUGCC--UC----U-UCUCUUGGCUG--UCUGAGCA-A--
AAKN02023481.1/87762-87838   --U-UGCUGUGAUGACUUUC-----AUUG--UGUUUCGCA--UGUUU--CUGA-GU-UC-C-AGUGAUACC--UC--U-U-UCUCUUGGCUG--UCUGAGCA-A--
CU076099.7/5812-5731         --C-AAACAUGAUGAUACCAG---AGAAU--GGUUUCGCUAACUUGA--CUGA-UG-UC-A-UGUGAUGUU--AC-AC-U-UCUCUUGGCUG--UCUGAUUU-A--
AC154569.2/160868-160781     UGG-UGCUGUGAUGAUGCCUUAAAAUUGU--GGUUUCGA----CUCA--CUGA-GAGUA-A-CGUGAGGACCUAC-AG-U-UC-CUUGGCUGUGUCUGAGCA-CC-
AC154469.3/43246-43159       UGG-UGCUGUGAUGAUGCCUUAAAAUUGU--GGUUUCGA----CUCA--CUGA-GAGUA-A-CGUGAGGACCUAC-AG-U-UC-CUUGGCUGUGUCUGAGCA-CC-
AC097720.5/86379-86467       UGG-UGCUGUGAUGAUGCCUUAAUAUUGU--GGUUUCGA----CUCA--CUGA-GAGUA-A-AAUGAGGACCUAC-AA-U-UC-CUUGGCUGUGUCUGAGCA-CCC
AALT01647276.1/1156-1069     UGG-UGCUGUGAUGAUGCCUUAAAAUUGU--GGUUUCGAC----UCU--CUGA-GU-AUAA-AAUGAAGACCUAC-AA-U-U-CCUUGGCUGUGUCUGAGCA-CU-
AAIY01667790.1/737-651       CGG-UGCUGUGAUGAUGCCUUAAAAUUGU--GGUUUC--A--ACUCA--CUGA-GA-GU-A-AAUGAAGAC--UU-ACAA-UUCCUUGGCUGUGUCUGAGCA-CC-
AANN01688271.1/1154-1240     UGG-UGCAGUGAUGAUGCCUUAAGAUUGU--GGUUU--CU--ACUCA--CUGA-GA-GU-A-AAUGAAGACCUAC-AA-U-UC-CUUGGCUGUGUCUGAGCA-CU-
AAHX01042265.1/70325-70234   UGG-UGCUGUGAUGACGUCUUAAAACUGU--GGUUCUGACUCACUCA--CUGA-GA-GG-AGUGUGAGGACCUAC-AA-U-UC-CUUGGCUGUGUCUGAGCA-CC-
AAKN02023481.1/68656-68743   UGG-UGCUGUGAUGAUGCUGUAAAAUUGU--GGUUUUGA----CUCA--CUGA-GAGUA-A-AAUGAAGACCUAC-AA-U-U-CCUUGGCUGUGUCUGAGCA-CC-
AAWZ02013075.1/17230-17147   ---AUGCUGUGAUGAUACCUGG-AAAUGU--GGUUUC--A--ACUAU--CUGACGG-UU-G-AGUGAGGAC--AU-AA-AAUUCCUUGGCUGUGUCUGAGCAC---
AADN03003632.1/13778-13856   --A-UGCAGUGAUGAUCUCC----AUCUU--GGUUUCGCU--UUUUG--CUGA-GU-UC-C-AGUGAAGAC--UC-AU-U-UCUCUUGGCUG--UCUGAGCA-U--
AAQR03049513.1/5995-6071     --A-UGCUGUGAUGACAUCC-----AAAU--GGUUUCGCU--ACUGG--CUGA-GU-UU-C-AGAGAUGAC--AC-C--U-UCUCUUGGCUG--UCUGAGCA-U--
AAEX03010810.1/27108-27187   --A-UGCUAUGAUGACAUCCA---UAUAU--GGUUUCGCU--UCUGG--CUGA-GU-UC-C-AGAGAUGAC--AC-CU-U-UCUCUUGGCUG--UCUGAGCA-U--
AAGU03043080.1/2957-3032     --A-UGCUGUGAUGACAUCC-----ACGU--GGUUUCGCU--UCUGG--CUGA-GU-UU-C-AGUGAUGAC--AC----U-UCUCUUGGCUG--UCUGAGCA-U--
EU240227.1/1-84              --A-UGCAGUGAUGAUCUCUUA-AGUAGU--GGUUUC--A--AUUCA--CUGA-UUGUU-G-AAUGAAGAC--CUGAA-U-UUCCUUGGCUGUGUCUGAGCG-U--
AAPE02028454.1/93072-93147   --U-UGCUGUGAUGAUUUUC-----AUUG--GGUUUCGCA--UGUUG--CUGA-GU-UC-C-AGUGAUGCC--UC----U-UCUCUUGGCUG--UCUGAGCA-U--
AAWZ02013075.1/18442-18365   --C-UGCUGUGAUGAUGUCC-----ACGU--GGUUUCGCU--CACUU--CUGA-UA-UG-U-GGUGAGGAC--AG-UU-U-CCUCUUGGCUG--UCUGAGCA-G--
AAGW02005748.1/19167-19242   --U-UGCCGUGAUGACUUCC-----GUUG--GGUUUCGCA--UGUUG--CUGA-GC-CC-C-AGUGAUGCG--UC----C-UCUCUUGGCUG--UCUGAGCA-G--
#=GC SS_cons                 ..<.<<<_____________.....____.._________.._____..____.__.__._._________..__.__._.___________.._____>>>.>..
#=GC RF                      ..c.uGCUGUGAUGAuauCc.....augU..GGUUUCGCu..ucUua..CUGA.Gu.uu.a.AGUGAuGAC..aC.au.U.UCUCUUGGCUG..UCUGAGCa.g..
//
# STOCKHOLM 1.0

#=GF AC   RF00326
#=GF ID   snoZ155
#=GF DE   Small nucleolar RNA Z155
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Griffiths-Jones S
#=GF SS   Predicted; Griffiths-Jones S
#=GF GA   43.00
#=GF TC   43.20
#=GF NC   42.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z155 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z155
#=GF SQ   8


AF318010.1/1-76          ---UGGAAUGAUGAUAACGAUUUUUCGGAUAUAUUAAUUUAUUCUGUCGACC-AAAACUCAGACUACAAUUAUCUGACUA---
AY707468.1/1-82          GGGUGGAAUGAUGAUAACGAUUUUUCGGAUAUAUUAAUUUAUUCUGUCGACC-AAAACUCAGACUACAAUUAUCUGACUAAUU
AY664413.1/185186-185259 UGUUGAAGGGAUGAUAAG-CCUUG-CAGCAACUCG-----A-GUGUUAACAA-AAAAUUUAGCCUACAAUUAUCUGAUCAACU
AJ490349.1/1-78          --UUGAUGUGAGGAUAAAACUUUCACAGAAACUCUUUUG-AUGUGUUGACCCUAAAAUUCAGACUACAAUUAUCUGAUCAG--
AC104707.2/85787-85706   AGUUGAUGUGAGGAUAAAACUUUCACAGAAACUCUUUUG-AUGUGUUGACCCUAAAAUUCAGACUACAAUUAUCUGAUCAGCU
AJ490347.1/1-76          AGUUGAUGGGAUGAUAAC-CUUUCACAGAAACUGU-----AUGUGUUGACCC-AAAAUUCAGACUACAAUUAUCUGAUCAACU
AJ490345.1/1-76          AGUUGAUGGGAUGAUAAC-CUUUCACAGAAACUGU-----AUGUGUUGACCC-AAAAUUCAGACUACAAUUAUCUGAUCAACU
AY220660.1/1-76          AGUUGAUGGGAUGAUAAC-CUUUCACAGAAACUGU-----AUGUGUUGACCC-AAAAUUCAGACUACAAUUAUCUGAUCAACU
#=GC SS_cons             <<<<<<_________________________________.____________.________________________>>>>>>
#=GC RF                  aGuUGauguGAUGAUAAcgcUUUcaCAGAaAcuuUaaUu.AUgUguUgAcCC.AAAAUUCAGACUACAAUUAUCUGAuCAaCu
//
# STOCKHOLM 1.0

#=GF AC   RF00327
#=GF ID   snoZ194
#=GF DE   Small nucleolar RNA Z194
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   50.00
#=GF TC   59.30
#=GF NC   39.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z194 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z194
#=GF SQ   5


AK099797.1/502-609       AGCAGAUUGAUGAUGAAACAAUUUCUCCAAGCGUUUGUUACGCUGACAUCCAUAUAUGAUGGAGGGCUAUGUUACCAUAGCCUUCAUAGUUUUCAAUCUGAACCAUCU
AJ490440.1/1-108         AGCAGAUUGAUGAUGAAACAAUUUCUCCAAGCGUUUGUUACGCUGACAUCCAUAUAUGAUGGAGGGCUAUGUUACCAUAGCCUUCAUAGUUUUCAAUCUGAACCAUCU
AL731784.3/24013-23910   AGCAGAUUGAUGAUGAAACAAUUUCUCCAAGCGUUUGUUACGCUGA--UCCAUA--UGAUGGAGGGCUAUGGUAACAUAGCCUUCAUAGUUUUCAAUCUGAACCAUCU
AAAA02035057.1/4449-4556 AGCAGAUUGAUGAUGAAACAAUUUCUCCAAGCGUUUGUUACGCUGACAUCCAUAUAUGAUGGAGGGCUAUGUUACCAUAGCCUUCAUAGUUUUCAAUCUGAACCAUCU
AAAA02035057.1/6282-6385 AGCAGAUUGAUGAUGAAACAAUUUCUCCAAGCGUUUGUUACGCUGA--UCCAUA--UGAUGGAGGGCUAUGGUAACAUAGCCUUCAUAGUUUUCAAUCUGAACCAUCU
#=GC SS_cons             :::((((,,,,,,,,,,,,,,,,,,,,,,<<<<<_____>>>>>,,,,,,,,,,,,,,,,,<<<<<<<<<<____>>>>>>>>>>,,,,,,,,,,,,,,,,,,,))))
#=GC RF                  AGCaGauUGAUGAUGAAACAAUUUCUCCAaGCGuUUGUUaCGCuGAcAUCCAUAUAUGAUGGagGGCuauGuUAaCauaGCCuuCAUAGUUUUCAAUCUGAACCauCu
//
# STOCKHOLM 1.0

#=GF AC   RF00328
#=GF ID   snoZ161_228
#=GF PI   snoZ161
#=GF DE   Small nucleolar RNA Z161/Z228
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Wilkinson AC; 0000-0001-7406-0151
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   45.00
#=GF TC   47.60
#=GF NC   43.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00056
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z161 and Z228 are members of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1,2].
#=GF WK   Small_nucleolar_RNA_Z161/Z228
#=GF SQ   11


AJ494930.1/3-84              GGGCCUAAUGAUGAGAAUAUGUAAUUUA-U-CUCACAACGGUCUGCUGA--GAAUUC---UUU-----GAUGU----GACAUAU-AU---UCUCUGAAGCCC
AJ490373.1/3-94              GGGCCAUGUGAUAAGAAUCCAUAUGCAA-UACUCACGACGGUCAUCUGAUACACUUA---GUGUG--UCAUGUUGCAGUCAUAU-AU---UCUCUGAUGCCC
AJ494931.1/3-84              GGGCCUAAUGAUGAGAAUAUGUAAAUUA-U-CUCAAAACGGUCUGCUGA--GAAUUC---CUU-----GAUGU----GAGAAAU-AU---UCUCUGAAGCCC
AJ494932.1/3-84              GAGCCUACUUACGAGAAUAUGUAAAUUA-U-CUCACAACGGUCUGCUGA--GAAUUC---UUU-----GAUGU----GACAAAA-AU---UCUCUGAAGCCC
AJ490374.1/3-95              GGGCCAUGUGAUGAGAAUCCAUAUGCAA-UACUCACGACGGUCGUCUGAUACACUUA---GUGUG--UCAUGUUGCAGUCAUAUUAU---UCUCUGAUGCCC
AJ494933.1/3-84              GGGCCUAAUGAUGAGAAUAUGUAAAUUA-U-CUCACAACGGUCUACUGA--GAAUUC---UUU-----CAUGU----GACAAAU-AU---UCUCUGAAGCCC
AJ490376.1/2-91              GGGUCAUGUGAUGAGAAACAAUAUGCA---ACUCACGACGGUCAUCUGAGACACUUA---GUGUG--UAAUGGUGCAGUCAUAUUAU----CUCUGAUGCCC
AARH01001039.1/627146-627050 AAAUCAAGUGAUGAAUCUGGAUUGUAAAUUUCUCACGACGGUCGUCUGAGACACUU---CGUGUCAACACUGAUGUAAAGAUCCAAU--GUUUCUGAUGAUU
AASG02002047.1/5666-5571     AAAUCAAGUGAUGAAAUUGGAUUUAAAU-UUCUCACGACGGUCGUCUGAGGCACCUCAAAGUGUC--GAAUUGAUGAGUGAUCCAAU---CAUCUGAUGAUU
AM423845.2/409-506           AAACCAGGUGAUGAGUUUGGAUUAAAUU-UUCUCACGACGGUCGUCUGAGACACAAU---GUGUCGCCUUUGAUGCAUCGAUCCAAUACUUCUCUGAUGGUU
AC193778.1/40189-40094       AAGCCGCUUGAUGAUUUUUGGAUAAUAU-U-CUCACGACGGUCGUCUGAGGUACAUUUAUGUGCC--UAACUGAUGAUAGAUCCAAU--UUUUCUGAUGGUU
#=GC SS_cons                 <<<<------------------------.----------------------<<<___...>>>--..--------------------...-------->>>>
#=GC RF                      gggCCaagUGAUGAgaaUauaUaaauaa.UuCUCACGACGGUCguCUGAGAcAcuUc...gUgUc..uaAUGuugcAgagAUauAAU...UcUCUGAUGccc
//
# STOCKHOLM 1.0

#=GF AC   RF00329
#=GF ID   snoZ162
#=GF DE   Small nucleolar RNA Z162
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   45.00
#=GF TC   46.30
#=GF NC   44.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z162 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z162
#=GF SQ   9



ABXC01001605.1/118086-117999 UUGGGCACAAUGAGGAGUUAAUUUUGCUAAUGUAUCUCCGAGGCCAGAAGGUCAAUGAUUCUUA-----UGUCCUUUUCAUUCUGAGUGCCCU
ABXC01001605.1/104054-103967 UUGGGCACAAUGAGGAGUUAAUUUUGCUAAUGUAUCUCCGAGGCCAGAAGGUCAAUGAUUCUUA-----UGUCCUUUUCAUUCUGAGUGCCCU
AECO01021519.1/799-886       GGUGGCACAGUGAGGAACUAAUUUUGCUAAUGUAUCUAUGAGGUCAAAAGGCCAGUGAAUCAAA-----UGUCCUUUUCAUUCUGAGUGCCAA
ACYM01075370.1/27425-27333   AGAGGCACAAUGAGGAGAAAUUAUAGUAGUGGUAUUUAUGAGAUUCAUAAAUCAAUGACUAAAAAUUUUAGUCCUUUUCAUUCUGAGUGCCUU
AJ490377.1/1-87              U--GGCACAAUGAGGAACUAACUUUGCUAAUGUAUCUAUGAGGCCAUUAGGCUAAUGACUCAAA----AUGUCCUUUUCAUUCUGAGUGCCAC
AP004260.2/16932-16845       UUUGGCACAAUGAGGAGGUAAUUUAGCUAAUGUAUCUCUGAGGUCUGAAGGCCAAUGACUCCUA-----UGUCCUUUUCAUUCUGAGUGCCUU
AJ490375.1/1-88              UUUGGCACAAUGAGGAGGUAAUUUAGCUAAUGUAUCUCUGAGGUCUGAAGGCCAAUGACUCCUA-----UGUCCUUUUCAUUCUGAGUGCCUU
AP004306.3/60382-60295       UUUGGCACAAUGAGGAGGUAAUUUAGCUAAUGUAUCUCUGAGGUCUGAAGGCCAAUGACUCCUA-----UGUCCUUUUCAUUCUGAGUGCCUU
AC084762.8/87156-87068       GGUGGCACAAUGAGGAACUAACUUUGCUAAUGUAUCUAUGAGGCCAUUAGGCUAAUGACUCAAA----AUGUCCUUUUCAUUCUGAGUGCCAC
#=GC SS_cons                 :::<<<<<-<<<<<----------------------------<<<____>>>------------.....------->>>>>----->>>>>::
#=GC RF                      uuuGGCACAaUGAgGAguUAAUUUuGcUAAuGUAUcUaUGAGgccaaaAggccAAUGAcUcaaA.....UGUCCUUuUCAuUCUGAGUGCCuu
//
# STOCKHOLM 1.0

#=GF AC   RF00330
#=GF ID   snoZ43
#=GF DE   Small nucleolar RNA Z43
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   43.00
#=GF TC   44.50
#=GF NC   42.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300061;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z43 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z43
#=GF SQ   7


AJ429604.1/1-103           GGACAGUGACGAUUGAUAUUUAAGGUCUCGUUCGUCGUAAAAACGGCCGUAAAAAGCCUAU---UUGCCGACCAUUCUGUUAUAUCACCACCCAUAUUCUGAGUCC
AJ240080.1/1-102           GGACAGUGACGAUUGAUAUU-AAGGUCUCGUUCGUCGUAAAAACGGCCGUAAAAAGCCUAU---UUGCCGACCAUUCUGUUAUAUCACCACCCAUAUUCUGAGUCC
AC122722.7/4040-4136       GGACAUUGAUGAAUACUGUGAUAGGUCUCGUUCGUCGU---AAUGG---UAAAUU---UUUACCUUGCCGACCAUUCUGUUAUAUCACCACCCAUAUUCUGAGUCC
AC122722.7/22593-22688     G-ACACUGAUGAAUACUGUGACAGGUCUCGUUCGUCGU---AAUGG---UAAAUU---UUUACCUUGCCGACCAUUCUGUUAUAUCACCACCCAUAUUCUGAGUCU
AC108499.3/94134-94034     GGACGGUGAAGAUCGUAUCUAUUGGUCUCGUUCGUCGU--AACUGG---CAAAUUGUUUUUGCCUUGCCGACCAUCCUGAUAUAUCACCACCCAUAUUCCGAGUCC
AASG02001268.1/27383-27482 GGACUGUGACGAUUGAUAUCAUUGGUCUCGUUCGGCAU---AAUGG---CAUGCUAUGCUUGCCUUGAUGACCAUCCUGAUAUAUCACCACCCAUAUUCUGAGUCC
AM447919.2/1765-1671       GGACUGUGACGAGUUGUGUGAAAGGUCUCGUUCGUCGU---AAUGG---CAAAUU-----UGCCUUGCCGACCAUCCUGAUAUAUCACCACCCAUAUUCCGAGUCC
#=GC SS_cons               <<<<----------------------------------...-----...-<<<_______>--->>------------------------------------>>>>
#=GC RF                    GGACagUGAcGAuUgaUaUuAuaGGUCUCGUUCGUCGU...AAuGG...uAaauuguuUuugCCuUGcCGACCAUuCUGuUAUAUCACCACCCAUAUUCuGAGUCC
//
# STOCKHOLM 1.0

#=GF AC   RF00331
#=GF ID   snoZ169
#=GF DE   Small nucleolar RNA Z169
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   55.00
#=GF TC   59.30
#=GF NC   38.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.60 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z169 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z169
#=GF SQ   3


AJ490386.1/1-69        GUGGCUAUGAUGAGGAAAA-GAUUCAAUGAUGUAUUAUGAUUA-CUCACACAUCGCAAUGCUCUGAGCCAC
AC078839.4/82266-82334 GUGGCUAUGAUGAGGAAAA-GAUUCAAUGAUGUAUUAUGAUUA-CUCACACAUUGCAAUGCUCUGAGCCAC
AC078839.4/80262-80332 UUUGCAAUGAUGACAAAAACGAUUGGAUGAUGUACUUUGAUUAACUCAUAAAUCGCAAUGCUCUGAGCGAC
#=GC SS_cons           <<<<<<_____________._______________________._____________________>>>>>>
#=GC RF                gUgGCuAUGAUGAggAAAA.GAUUcaAUGAUGUAuUaUGAUUA.CUCAcAcAUcGCAAUGCUCUGaGCcAc
//
# STOCKHOLM 1.0

#=GF AC   RF00332
#=GF ID   snoZ266
#=GF DE   Small nucleolar RNA Z266
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, Daub J
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   43.00
#=GF TC   44.20
#=GF NC   42.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z266 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z266
#=GF SQ   11


AJ532495.1/1-89              GAUUGGCAGGAAUGAUGAAUCAAUUAGAUGUGCGAA--------GUCUCCUUG--------UGAGCUUAA-CUUUUGA---GGCAUACAUU-CUGUCUGACCUGCCAAUC
AJ532493.1/1-82              ---UGGCAGUAGUGAUGAAUCAAU-AGAUGUGUGAA--------GUGACCUUA--------UGAACUUAA-CUUUUGA---GGCAUACAUU-CUGUCUGAACUGCCA---
AJ532496.1/2-91              GAUUGGCUGGGAUGAUGAAUCAAUUAGAUGUGUGAA--------CUCACCUUA--------UGAUCUAAAACUUUUGA---GGCAUAAUUA-CUUUCUGACCUGCCAAUC
AJ532494.1/1-86              -AUUGGCAGGAAUGAUGAAUCAAUUAGAUGUACGAG--------GUUACCUUA--------UGAGCUAAA-AUUUUGA---GGCAUACAAU--UGUCUGACUUGCCAAU-
AAAA02028020.1/10150-10062   GAUUGGCAGGAAUGAUGAAUCAAUUAGAUGUGCGAA--------GUCUCCUUG--------UGAGCUUAA-CUUUUGA---GGCAUACAUU-CUGUCUGACCUGCCAAUC
AP005546.3/28934-29023       GAUUGGCUGGGAUGAUGAAUCAAUUAGAUGUGUGAA--------CUCACCUUA--------UGAUCUAAAACUUUUGA---GGCAUAAUUA-CUUUCUGACCUGCCAAUC
AARH01006732.1/230193-230291 AAUUGGCAAGUAUGAUGAUUCAAUUAGAUGUGUGAA--------UGGAAAUUAAUCCAUAUUGAACUCAACAUUUUGA---GGCAUUUUUAAUUGUCUGACUUGCGUGUU
CU024877.11/2234-2325        AAUAUGCAAGUAUGAUGAUUCAAUUAGAUGUAUGAAAGGAGA--AAUCCUUGC--------UGAACUCUAUUUUUUGA---GGCA----AA-CUGUCUGACUUGCUUAUU
AC008153.5/70761-70668       AACGGCGAGGGAUGAUGAUUCAAUUAGAUGUGCGAAUG------GUUUCAUCA--------UGAGCUCAAAAACUUUAUUUGGCAUUUUAU--AAUCUGACUUCGCCGUC
AC189547.2/72063-71971       AGCGGCGAGG-AUGAUGAUUCAAUUAGAUGUGCGAAUG------GUUUCAUUA--------UGAGCUUACAAACUUAAUUUGGCAAUUAUU--AAUCUGACUUCGCCGUC
AM469974.2/11715-11812       UGGCGGCAAGAGUGAUGAUUCAAUUAGAUGUGUGAAAGGAGAUUUCUUCUUUC--------UGAACUCAAAUCAUUGA---GGCAUAUUAA-UUUCCUGACUUGCCACCC
#=GC SS_cons                 <<<<<<<<<<__________________________........_________........_________________...__________.________>>>>>>>>>>
#=GC RF                      gacugGcAgGaAUGAUGAuUCAAUUAGAUGUGuGAA........uuuuCaUUa........UGAaCUuAAaauuUUGA...GGCAUauuua.cUgUCUGACcUgCcaguc
//
# STOCKHOLM 1.0

#=GF AC   RF00333
#=GF ID   snoZ157
#=GF DE   Small nucleolar RNA Z157/R69/R10
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   55.00
#=GF TC   55.50
#=GF NC   54.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00063
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300069;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z157, R69 and R10 are members of the C/D class of snoRNA which contain the
#=GF CC   C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1].
#=GF WK   R10
#=GF SQ   10


AF317993.1/1-96          ---UUUAUGGUGAUGA-AACGAAUAUUU-CGUGGACUAGAGUUUCAGAUCUGGG-CUCUUCACCCAGAAUUUGAAGAAACAACCCUU-GGCUGUCUGAGUAAA---
AF317936.1/1-96          ---AAUAUGGUGAUGA-UA-CAAGAGUAUUGUGGACUAGAGUUUCAGAUCUGGGAUUCUUCUCCCAGAAGUUGAAGAUU-AACCCUU-GGCUGUCUGAGUAUU---
AF317937.1/1-96          ---AAUAUGGUGAUGA-UA-CAAGAGUAUUGUGGACUAGAGUUUCAGAUCUGGGAUUCUUCUCCCAGAAGUUGAAGAUU-AACCCUU-GGCUGUCUGAGUAUU---
AJ505638.1/15-116        UUGAAUAUGGUGAUGA-UA-CAAGAGUAUUGUGGACUAGAGUUUCAGAUCUGGGAUUCUUCUCCCAGAAGUUGAAGAUU-AACCCUU-GGCUGUCUGAGUAUUAAU
AJ490368.1/1-90          ---GGAGCGGUGAUGA-G--CAAUUUUU-UGUGGACUAGAGUUUCUGAUACUAC-UUUU---GUAGU-AUUUGAAGACCAAACCCUU-GGCUGUCUGAGCUCC---
AJ490353.1/1-97          GAACAUGUGGUGAUGA-G--CAACUUCUUUGUGGACUAGGGUUUCUGAUAACAC-UACGCA-GUGUU----UGAUGACCAAACCCUUUGGUUGUCUGAGCUCCUCU
AJ490354.1/3-101         AUGGGAG---UGAUGAAGAACAAUUUUUAUUUGGACUAGAGUUUCUGAUACUGC-UACUUU-GUGGU-AGUUGAAGACUAAACCCUU-GGCUGUCUGAACUUCCAU
AC135559.4/53404-53306   AUGGGAG---UGAUGAAGAACAAUUUUUAUUUGGACUAGAGUUUCUGAUACUGC-UACUUU-GUGGU-AGUUGAAGACUAAACCCUU-GGCUGUCUGAACUUCCAU
AP004797.3/108010-108108 UUGGUAGCGGUGAUGA-G--CAAUUUUUAUUUGGACUAGAGUUUCUGAUACUGC-UACUUU-GUGGU-AGUUGAAGACCAAACCCUU-GGCUGUCUGAGCUUCCAG
AJ490369.1/1-99          UUGGUAGUGGUGAUGA-G--CAAUUUUUAUUUGGACUAGAGUUUCUGAUACUGC-UACUUU-GUGGU-AGUUGAAGACCAAACCCUU-GGCUGUCUGAGCUUCCAG
#=GC SS_cons             <<<<<<<<--------.--.---------------------<<<<---<<<<<<.______.>>>>>.>--->>>>-----------.---------->>>>>>>>
#=GC RF                  gugggugcGGUGAUGA.gA.cAAuuuUuuUgUGGACUAGAGuuUCuGAuccggc.UuCUUu.gccgg.agUUGAagAcuAAACCCUU.GGCUGUCUGAgcacccac
//
# STOCKHOLM 1.0

#=GF AC   RF00334
#=GF ID   SNORA3
#=GF PI   snoMBI-28
#=GF DE   Small nucleolar RNA SNORA3/SNORA45 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   51.00
#=GF TC   51.20
#=GF NC   50.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00022
#=GF DR   snoRNABase; ACA3;
#=GF DR   snoRNABase; ACA3-2;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300761;
#=GF DR   snoopy; Homo_sapiens300363;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16361266
#=GF RT   A novel experimental approach for systematic identification of box H/ACA
#=GF RT   snoRNAs from eukaryotes.
#=GF RA   Gu AD, Zhou H, Yu CH, Qu LH
#=GF RL   Nucleic Acids Res. 2005;33:e194.
#=GF RN   [4]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the H/ACA class of snoRNAs which are
#=GF CC   thought to guide the sites of modification of uridines to pseudouridines
#=GF CC   [1]. This family includes mouse snoMBI-28 and human homologues ACA3
#=GF CC   (SNORA3) and ACA3-2 (SNORA45). Both ACA3 and ACA3-2 share the same host
#=GF CC   gene [3]. MBI-28, ACA3 and ACA3-2 are all predicted to guide the
#=GF CC   pseudouridylation of residues in 28S rRNA [1,2,3].
#=GF WK   Small_nucleolar_RNA_MBI-28
#=GF SQ   6


AJ609428.1/1-130       AUCGAGGCUAGAGUCACGCUUGGGUAUCGGCUAUUGCCUGAGUGUGCUAGAGUCCUCGAAGAGUAACUGCUGACCUU-AUUCACUGGCUGUG-GGCCUUAUG-GCACAGUCAGUCACCAGGUUAGAGACAUGC
AB020236.1/2404-2533   AUCGAGGCUAGAGUCACGCUUGGGUAUCGGCUAUUGCCUGAGUGUGCUAGAGUCCUCGAAGAGUAACUGCUGACCUU-AUUCACUGGCUGUG-GGCCUUAUG-GCACAGUCAGUCACCAGGUUAGAGACAUGC
AB020237.1/3193-3322   GCCGAGGCUAGAGUCACAUCCUGACA-UGGUGCUUGUCCUGGUGUGCUACAGUUCUCGGAGAGAAUCG-CUGGUCUUGAUUCAUUGGUAGGG-GCCUUCAGUGUCCCUUCUAGUGCCCAGAUCAGAAACAUGG
AB020236.1/3615-3745   GCCGAGACUAGAGUCACAUCCUGACA-CAACUCUUGUCCUGGUGUGCUAGAGUACUCGAAGAGAAUCUACUGGUCUUGAUUCACUGGUGGGG-GCAGUCGGUGCCCCCGUUAGUGCCCAGAUCAGAAACAUAC
AC104360.8/62127-61997 GCCGAGACUAGAGUCACAUCCUGACA-CAACUCUUGUCCUGGUGUGCUAGAGUACUCGAAGAGAAUCUACUGGUCUUGAUUCACUGGUGGGG-GCAGUCGGUGCCCCCGUUAGUGCCCAGAUCAGAAACAUAC
AF357390.1/1-120       ------------GUCACGCUCAGGUAUUGCUUGUUGCCUUAGUGUGCUUAAGUCCUCGAAGAAUAACUGCUGACCUU-AUUCACUGGCUGUGUGGACUUUCUGGCACAGUCAGUCACCAGGUUAGUGACAUAU
#=GC SS_cons           :<<<<<<<<--<<-<<<<<<--<<<<._______>>>>-->>>>>>>>-->>>->>>>>----------<<<<<<<-<---<<<<<<-<<<<.<<_______>>>>>>->>>>>>->->>>>>>>::::::::
#=GC RF                gcCGaGgCuAGaGUCaCacccuGgca.cgacuaUugcCuugguGuGCuAgaGcaCuCGgAGAGaAuCugCugacCuUGAUUcacuggugGgG.gcauUuauugcCcCcgccagugaCCaGgucaGAaACAUac
//
# STOCKHOLM 1.0

#=GF AC   RF00335
#=GF ID   snoZ13_snr52
#=GF DE   Small nucleolar RNA Z13/snr52
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   47.00
#=GF TC   51.00
#=GF NC   41.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.72 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Z13 or snr52 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1].
#=GF WK   Small_nucleolar_RNA_Z13/snr52
#=GF SQ   42


AJ223843.1/1-95                AUUUU-GAAAAUGAUGAAAAU-AA-CGCGGAUGAAAU----AUAU-------------------------GU-CCGAGA-GCGCAA--A---A---A-AU-GUGUGGAUAU-U-UCCG--UUGCCUUCCUUCUGAU-UCA----AAAU
AJ251862.1/1-95                AUUUU-GAAAAUGAUGAAAAU-AA-CGCGGAUGAAAU----AUAU-------------------------GU-CCGAGA-GCGCAA--A---A---A-AU-GUGUGGAUAU-U-UCCG--UUGCCUUCCUUCUGAU-UCA----AAAU
AL683874.1/62362-62458         GUUGA-UCAGGUGAUGAAAUA-UU--UCGGAUGUAAA----CUCACA-----GACC-------------UGU-UCUGAAUGCGCAA--A---A---C-C--GUGUAGAGAU-U-UCCG--UUGCCUUCCUUCUGAU---------GAU
BX284747.1/26398-26296         GCCCA-CACCCUGAUGAAAUA-UU-CUCGGAUGUAAA----AUUUUA-----CUUU-------------UGU-CUGAAAAGCGCAA--A---A---A-CA-AUGUUGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-CUG----UGGU
AACD01000034.1/68640-68741     CAUGA-UCAAAUGAUGAAAUA-UU-UUCGGAUGUAAA----CUCACA-----GACC-------------UGU-UCUGAAUGCGCAA--A---A---C-C--AUGUGGAUAU-U-UCCG--UUGCCUUCCUUCUGAU-UGA----UCAU
AAKD03000001.1/1486904-1486804 GUUGA-UCAGGUGAUGAAAUA-UU-UUCGGAUGUAAA----CUCACA-----GACC-------------UGU-UCUGAAUGCGCAA--A---A---C-C--GUGUAGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-GA-----UCAA
AAJN01000011.1/21289-21391     CAAGG-UCACAUGAUGAAAUA-UA-UUCGGAUGUAAA----CUCACA-----GACC-------------UGU-UCUGAAUGCGCAA--A---A---A-CC-AUGUGGAUAU-U-UCCG--UUGCCUUCCUUCUGAU-UGA----UCGU
AAKE03000002.1/1685042-1684943 GUUGA-UCAGGUGAUGAAAUA-UU--UCGGAUGUAAA----CUCACA-----GACC-------------UGU-UCUGAAUGCGCAA--A---A---C-C--GUGUAGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-GA-----UCAA
AAIM02000151.1/53716-53817     UGCUC-CCAUAUGAUGAAAUA-UU--UCGGAUGUAAA----ACAUUG-----UCAU-------------UGU-CGGAAA-GCGCAA--A---A---A-AUAAUGUCGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-UGG----GAUU
AAIH02000423.1/19672-19773     GAUGA-UCUUAUGAUGAACUA-UU--UCGGAUGUAAA----CACAGA-----CCUG-------------U-U-CCGAACAGCGCAA--A---A---A-CC-GUGUGGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-CAG---AUCAU
AACM02000388.1/98906-98806     UAUUC-CCAUAUGAUGAACUA-UU--UCGGAUGUAAA----AACA-------UUUA-------------UUC-UCGGAAAGCGCAA--A---A---A-AUAAUGUCGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-CGA----GAAA
AAFU01000751.1/18088-18187     GCCCU---UCAUGAUGAACUA-UU--UCGGAUGUAAA----ACUU-------UACU-------------UGU-CUGAAAAGCGCAAACA---A---A-CA-AUGUUGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-CAA----UGGC
AAID01000569.1/6977-7076       UUUCU-UUUAGUGAUGAAAUA-UU--CCGGAUGUUAA----AUCAUA-----UUGU--------------CU-CCGAGA-GCGCAA--A---A---C-C--GUGUGGAGAU-UUUCCG--UUGCCUUCCUUCUGAU-UCU----AGAC
ABAS01000005.1/1119542-1119442 CUUGAAUCUUAGGAUGAAACA-UU--UCGGAUGUAA-----AUCACA-----GACC-------------UGU-UCUGAAAGCGCAA--A---G---C-C--GUGUGGAUAU-U-UCCG--UUGCCUUCCUUCUGAU-CAU----UGAU
AAGT01000278.1/24504-24604     AUUAUUCAAUAUGAUGAAAUA-UU--CCGGAUGUUAA----ACAC-A-----UUAU-------------ACU-CCGAGA-GCGCAA--A---A---C-CC-AUGUGGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-UGU----CUAU
AM270168.1/143221-143326       CUCGA-UCAAAUGAUGAAAUA-UU--UCGGAUGUAAA----CUCACA-----GACC-------------UGUUCCGAAUUGCGCAAACA---A---U-UC-AUGUGGAUAU-UUUCCG--UUGCCUUCCUUCUGAA-UGA----UCGA
ABAR01000036.1/11171-11270     GCCCU-UUCCAUGAUGAAGUA-UU--UCGGAUGUAAA----CACA-------GACC-------------UGU-UCCAAGAGCGCAA--A---A---C-C--GUGUGGAUAU-U-UCCG--UUGCCUUCCUUCUGAUAUUC----AAGC
AAIW01000409.1/2518-2420       GUUGU--CAUCUGAUGAAAUA-CU--ACGGAUGUAA-----AUCACA-----GACC-------------UGU-UCUGAA-GCGCAA--U---A---C-G--AUGUGGAUAU-UUUCCG--UUGCCUUCCUUCUGAU-UUG----ACAU
AATM01000018.1/440-526         UUUGA---AAAUGAUGAAACA-UU-UACGGAUGAUAC----AU---------------------------GU-CCGAGA-GCGCAA--A---A---C-C--GUGUGGAUAA-U-GCCG--UUGCCUUCCUUCUGAU--------UCAU
AARE01000390.1/11618-11521     GAUUG----UAUGAUGAAUCA-UU-UACGGAUGUAA-----AUCACA-----GACC-------------UGA-UCCGAAUGCGCAA--A---A---C-C--GUGUGGAUCU-UUUCCG--UUGCCUUCCUUCUGAU-CA-----CAAU
AASO01001135.1/6085-6180       AUCG-----CAUGAUGAAAUA-UU--ACGGAUGUAA-----AUCACA-----GACC-------------UGU-UCCGAA-GCGCAA--U---A---C-G--AUGUGGAUAU-UUUCCG--UUGCCUUCCUUCUGAC-CUA----ACGU
AC198241.1/2819-2721           AGCUC-GCAA--GAUGAAAUA-UU-UUUGGAUGAAAA----ACAA--------AUA-------------CCA-CCGAUG-GCGCAA--A---A---A-CC-AUGUGGAAAU-C-UCCAUGUUGCCUUCCUUCUGAU-CAA----GAGC
AAFP01000131.1/3122-3220       CCUUU-UAUGAUGAAGUAUUU-UU---CGGAUGUAAA----UUGCCUUCGGGCACA-------------UGU-CCGAGA-GCGCAA--A---A---A-CC-AUGUGGACAU-C-UCCG--UUGCCUUCCUUCUGA-----------AU
AAXI01000183.1/9324-9229       UCCCU-UUCGAUGAUGUAAAA-UU-UUCGGAUGUAAA----UCAUUU-----AAAC--------------CA-CCGAGA-GCGCAA--A---A---C-C--GUGUGGAUAUCU-UCCG--UUGCCUUCCUUCUGA----------GUC
AACO02000090.1/37646-37744     CCUUU-UAUGAUGAAGUAUUU-UU---CGGAUGUAAA----CUGCCUUCGGGCACA-------------UGU-CCGAGA-GCGCAA--A---A---A-CC-AAGUGGACAU-C-UCCG--UUGCCUUCCUUCUGA-----------AU
AACP01000201.1/16770-16660     GGCGU-CAACGUGAUGAACUA-UU-UACGGAUGUAAA----ACUGUC-----CUUCGCGACUUGUCAUUUGU-CCGAGA-GCGCAA--A---A---C-C--GUGUGGAUGU-U-UCCG--UUGCCUUCCUACUGAU--------CUGU
CR382130.1/1714839-1714745     UCAAC-CACAAUGAUGAAGCA-UU---AGGAUGUAAA----UUAU---------UU-------------CAC-CCGAGA-GCGCAA--A---A---AACC-GUGCGGAUAU-U-UCCU----GCCUUCCUUCUGAU-UUU----GUGU
AAGI01000024.1/22361-22462     CACUG-UCCGAUGAUGUAAUACUU-UUCGGAUGUAAA----CCCAUU-----AAAC--------------CA-CCGAGA-GCGCAA--A---A---C-C--GUGUGGAUAU-UUUCCG--UUGCCUUCCUUCUGAG-ACC----CAAC
AADS01000253.1/14674-14780     CCUAU-CCGCAAGAUGAAGCC-AA-CACGGAUGUAAAUGAGCUCUGC-----UCGC-------------UGU-CCGAGA-GCGCAA--A---A---C-CUCGUGUGGAUUG-U-UCCG--UUGCCUUCCUUCUGAC-CAU----ACGU
FQ790281.1/409136-409037       UUUCU-UUUAGUGAUGAAAUA-UU--CCGGAUGUUAA----AUCAUA-----UUG--------------UCU-CCGAGA-GCGCAA--A---A---C-C--GUGUGGAGAU-UUUCCG--UUGCCUUCCUUCUGAU-UCU----AGAC
BN001307.1/2992419-2992520     CAUGA-UCAAAUGAUGAAAUA-UU-UUCGGAUGUAAA----CUCACA-----GACC-------------UGU-UCUGAAUGCGCAA--A---A---C-C--AUGUGGAUAU-U-UCCG--UUGCCUUCCUUCUGAU-UGA----UCAU
AE017348.1/118868-118973       CACCC-UUUUAUGAUGAAGUA-UUUUUCGGAUGUAAA----CUGCCUUCGGGCACA-------------UGU-CCGAGA-GCGCAA--A---A---A-CC-AAGUGGACAU-C-UCCG--UUGCCUUCCUUCUGAA-UCA------UU
AP007154.1/588668-588567       GAUGA-UCUUAUGAUGAACUA-UU--UCGGAUGUAAA----CACAGA-----CCUG-------------UUC-CGAAC-AGCGCAA--A---A---A-CC-GUGUGGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-CAG---AUCAU
AM921928.1/6-91                -----------UGAUGAAAUA-UU--UCGGAUGUAAA----CUCACA-----GACC-------------UGU-UCUGAAUGCGCAA--A---A---C-C--GUGUAGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-GA---------
AJ617322.1/3-83                A-------AAAUGAUGAAAAU-AA-CGCGGAUGAAAU----AUAU-------------------------GU-CCGAGA-GCGCAA--A---A---A-AU-GUGUGGAUAU-U-UCCG--UUGCCUUCCUUCUGA-------------
EU780965.1/2-92                AC-------CCUGAUGAAAUA-UU-CUCGGAUGUAAA----AUUUUA-----CUUU-------------UGU-CUGAAAAGCGCAA--A---A---A-CA-AUGUUGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-----------C
AAIL02000049.1/272250-272155   CCUUC----CAUGAUGAAAUA-UU--GCGGAUGUAAA----UCUAUU-----GUCA-------------CGU-CUGAAU-GCGCAA--A---C---C-C---UGUAGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-CUG----GAAA
ABDF02000002.1/2241332-2241428 CCUUU----CAUGAUGAAAUA-UU--GCGGAUGUAAA----CUUUUU-----GUCA-------------CGU-CGGAAA-GCGCAA--A---A---C-C--AUGUCGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-UGC----AAAG
AACS02000002.1/532175-532276   UUUGG-CUCUGUGAUGAAGCA-CU--ACGGAUGUAAA----AUCA-------UUUC-------------UGU-CCGAGAUGCGCAU--A---ACUCC-CC-GUGUGGAUAC-U-UCCG--UUGCCUUCCUUCUGAG-GC-----CCAU
AACU03000016.1/199430-199331   UUGGC-UAUCAUGAUGAAAUA-UU--CCGGAUGUAAA----AACA-------------------------GU-CUGAAAUGCGCAA--ACAUA---A-CC-CCCUGUUGAU-U-UCCG--UUGCCUUCCUUCUGAU-UAUA--UGCCU
AFQF01003682.1/38231-38332     UUCUC-CCAUAUGAUGAAAUA-UU--UCGGAUGUAAA----ACAUUG-----UCAU-------------UGU-CGGAAA-GCGCAA--A---A---A-AUAAUGUCGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-UGG----GAUU
ABDG02000024.1/2501358-2501460 UCCCC-UUUCAUGAUGAAAUA-UA--CCGGAUGUAAA----CUUU-U-----GUCA-------------CGU-CGGAAA-GCGCAA--A---A---C-C--AUGUCGAGAU-U-UCCG--UUGCCUUCCUUCUGAU-UUAUCAAGGGG
#=GC SS_cons                   ::<<<.---------------.--..-<<<<______....______.....____.............___.______.______.._..._..._.__.__________._.>>>>..----------------.---....>>>:
#=GC RF                        uucgc.uaauAUGAUGAAaUA.UU..uCGGAUGUAAA....aucaua.....uauc.............UGU.CcGAaA.GCGCAA..A...A...a.Cc.gUGUGGAuAU.U.UCCG..UUGCCUUCCUUCUGAU.uaa....gcgu
//
# STOCKHOLM 1.0

#=GF AC   RF00336
#=GF ID   snoJ26
#=GF DE   Small nucleolar RNA J26
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; ILM; Moxon SJ, Daub J
#=GF GA   50.00
#=GF TC   62.00
#=GF NC   43.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   J26 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_J26
#=GF SQ   5


AY220656.1/1-147       UGGAAAAAAACAACACAGUGGGUAAGUUAGGAGAAGGUGACUUUUUCUCUUUUUCUGAA-----GGUUGGAGCUCUGCCCAUUAUAUUAAGAAGUUGGUUUCAGACUACAAUUCAAGGAUAUUACAUGGAACAAAAAGCAACUGAGCUUUCA-
AY220657.1/1-148       UGGAAAAAAACAACACAGUGGGUAAGUUAGGAGAAGGUGACUUUUUCUCUUUUUCUGAA-----GGUUGGAGCUCUGCCCAUUAUAUUAAGAAGUUGGUUUCAGACUACAAUUCAAGGAUAUUACAUGGAACAAAAAGCAACUGAGCUUUCAC
AC137998.2/5577-5723   UGGAAAAAA-CAACACAGUAGGUAAAUUAGGAGAAGGUGACUUUUUCUCUUUUUCUGAA-----GGUUGGAGCUCUGCCCAUUAUAUUAAGAAGUUGGUUUCAGACUACAAUUCAAGGAUAAUACAUGGAACAAAAAGCAACUGAGCUUUCAC
AP003861.2/88090-88241 UGGAAAAAA-CAACACAGUGGGUAAGUUAGGAGAAGGUGACUUUUUCUCUUUUUCUGAAGUAAAGGUUGGAGCUUUGCUCAUUAUAUUAAGAAGUUGGUUUCAGACUAUAAUUCGAGGAUAUUACAUAGAACAAAAAGCAACUGAACUUUCAC
AK068808.1/2266-2115   UGGAAAAAA-CAACAAAGCGAGUAAGUUAGGAGAAGGUGACCUUUUCUCUUUUUCUGAAGUAAAGGUUGGAGCUCUGCCCAUUAUAUUAAGAAGUUGGUUUCGGAAUACAAUUCGAGGAUAUUACAUGGAACAAAAAGCAACUGAACUUUCCC
#=GC SS_cons           ::<<<<---.-------------------------------------------------.....-------------------<<<<<----<<<<<___________>>>>>---->>>>>------------------------->>>>::
#=GC RF                UGGaaaAAA.CAACAcAGUggGUAAgUUAGGAGAAGGUGACUUUUUCUCUUUUUCUGAA.....GGUUGGAGCUcUGCcCAUUauauuAAGAaguuGGUUUCAGAcUACaauuCaAGgauauUACAUgGAACAAAAAGCAACUGAgCuuuCaC
//
# STOCKHOLM 1.0

#=GF AC   RF00337
#=GF ID   snoZ112
#=GF DE   Small nucleolar RNA Z112
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF CL   CL00062
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12136108
#=GF RT   A novel gene organization: intronic snoRNA gene clusters from Oryza
#=GF RT   sativa.
#=GF RA   Liang D, Zhou H, Zhang P, Chen YQ, Chen X, Chen CL, Qu LH
#=GF RL   Nucleic Acids Res 2002;30:3262-3272.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Z112 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_Z112
#=GF SQ   6


AJ489963.1/1-178           GUCCCGGUGAGGAAUCUAAGACC-----AUAGGAAGUGCCG------ACUUUAAACAGCAGCUGCUGGUCUCCUUUGCAAGUG-UCCAUCCUUCGACCAUAACCUUUGUGGUUUGGUCUUGGAUGGAGUACCCAUUUGCAAUUGGUUUAAUUCGGGUGU-GUGUGUGAUUUUAAACGGGUCUCU-GAGGGAC
AJ489964.1/1-182           GUCCCGGUGAGGAAUCUAAGACC-----AUAGGAAGUGCCGUAUGACACUUUAAACAGCAGCUGCUUUUCUCCUUUGCAAGUG-UCCAUCCUUCGACCAUAACCUUUGUGGUUUGGUCUUGGAUGGAGUACCCAUUUGCAAUUGGUUUAAUUCGGGUGU-GUGUG--AUUUUAAACGGGUCUCU-GAGGGAU
AJ320263.1/3-186           GUCCCAGUGAGGAUUCUAUGACC-----AUAGGAAGUGCCGUAUGACACUUUAAACAGCAGCUGCUUUUCUCAUUUGCAAGUG-UCCAUCCUUCGACCAUAACCUUUGUGGUUUGGUCUGGGAUGGAGUACCCAUUUGCAAUUGGUU-AAUUCAGCUGU-GUGUGUGAUUUUAAACGGGUCUCUUGAGGGAU
AY013245.2/64928-65111     GUCCCGGUGAGGAAUCUAAGACC-----AUAGGAAGUGCCGUAUGACACUUUAAACAGCAGCUGCUUUUCUCCUUUGCAAGUG-UCCAUCCUUCGACCAUAACCUUUGUGGUUUGGUCUUGGAUGGAGUACCCAUUUGCAAUUGGUUUAAUUCGGGUGU-GUGUGUGAUUUUAAACGGGUCUCU-GAGGGAU
AAAA02011059.1/20354-20171 GUCCCGGUGAGGAAUCUAAGACC-----AUAGGAAGUGCCGUAUGACACUUUAAACAGCAGCUGCUUUUCUCCUUUGCAAGUG-UCCAUCCUUCGACCAUAACCUUUGUGGUUUGGUCUGGGAUGGAGUACCCAUUUGCAAUUGGUUUAAUUCGACUGU-GUGUGUGAUUUUAAACGGGUCUCU-GAGGGAC
Y11048.1/873-1061          GUCCCAGUGAAGAUCCCAAGACCUACCGAUAGGAAGUGCCGUUUGACACUGCAAACAGCAGCUGCCUCUCUCAGCUGCAGGUGUUCCAUCCUUUGACCAUAACCUUUGUGGUUUGGUC-AGGCUGGAGCUCCCAUCUGCAGCUGUUU-GUUUCAGCUGUGGUGUGUGAUUUUAAUCGGGUCUCU-GAGGGAC
#=GC SS_cons               <<<<<------------------.....----------------------------------------------<<<<<<<<<.<<<<<<<---<<<<<-<<<<_____>>>>>>>>>-->>>>>>>----->>>>>>>>>------------------.------------------------.-->>>>>
#=GC RF                    guCCCgGUGAgGAauCuAAGACC.....AUAGGAAGUGCCGUaUGACACUuuAAACAGCAGCUGCuuuUCUCauuuGCaaguG.uCCauCCUUcGaCCaUaaCCUUUGUGGuuuGGuCUuGGauGGaGuaCCCauuuGCaauUGgUUUAaUUCgGcUGU.GUGUGUGAUUUUAAaCGGGUCUCU.GAGGGac
//
# STOCKHOLM 1.0

#=GF AC   RF00338
#=GF ID   snoR53
#=GF PI   snR53
#=GF DE   Small nucleolar RNA snR53
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Daub J
#=GF GA   70.00
#=GF TC   97.20
#=GF NC   39.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00080
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science 1999;283:1168-1171.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snR53 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_snR53
#=GF SQ   5


AF064265.1/1-91            UUUGAUGAUGAUUA-CACUCCAUGCUAAUCAUGAACGUGUUCGA---UGUAAAU-UUGAAUACGAUGAUUAAAAUUGUUGUUUACGCUUUCUGAAA
AF270839.1/1-87            --------UGAUUAACACUCCAUGCUAAUCAUGAAUGUGUUCAAAUAUAUAUAU-UUGAAUACGAUGAUUAAAAUUGUUGUUUACGCUUUCUGAAA
U18779.1/8673-8763         UUUGAUGAUGAUUA-CACUCCAUGCUAAUCAUGAACGUGUUCGA---UGUAAAU-UUGAAUACGAUGAUUAAAAUUGUUGUUUACGCUUUCUGAAA
AACG02000007.1/85209-85116 UUUGAUGAUGAUUAACACUCCAUGCUAAUCAUGAAUGUGUUCAAUA-UAUAUAU-UUGAAUACGAUGAUUAAAAUUGUUGUUUACGCUUUCUGAAA
AACI02000122.1/13726-13635 UUUAAUGAUGAUUA-CACUCCAUGCUAAUCAUGAAUGUGUUCAA---UGUAAAUUUUGGAUGCGAUGAUUAAAAUUGUUGUUUACGUUUUCUGAAA
#=GC SS_cons               <<------------.--------------------<<<<<<<<<..._______.>>>>>>>>>------------------------------>>
#=GC RF                    uuUgAUGAUGAUUA.CACUCCAUGCUAAUCAUGAAcGuguuCaa...UgUAaAU.uuGaauaCgAUGAUUAAAAUUGUUGUUUACGcUUUCUGAaa
//
# STOCKHOLM 1.0

#=GF AC   RF00339
#=GF ID   snoR60
#=GF DE   Small nucleolar RNA snoR60
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ; Daub J
#=GF GA   40.00
#=GF TC   41.00
#=GF NC   39.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00074
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300214;
#=GF DR   snoopy; Arabidopsis_thaliana300192;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   10829025
#=GF RT   Fibrillarin genes encode both a conserved nucleolar protein and a novel
#=GF RT   small nucleolar RNA involved in ribosomal RNA methylation in Arabidopsis
#=GF RT   thaliana.
#=GF RA   Barneche F, Steinmetz F, Echeverria M
#=GF RL   J Biol Chem 2000;275:27212-27220.
#=GF CC   snoR60 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_snoR60
#=GF SQ   10


AF228365.1/1-73              UUGCAAAUGAUGAU-CUUACUUGGAUUCCCCUUCAGAUCAUU-A--UGGGUGAUGCAAUCUCCAAGUUUCUGAUGUA
AF228364.1/1-74              CGGCAGAUGAUGAU-UUUACUUGGAUUCCCCUUCAGAACAUUUA--UGGGUGUUGCAAACUCCAAGCUUCUGAUGCU
AJ532536.1/2-76              CUGCAAAUGAUGAG-CUUACUCGGAUUCCCCUUCAGGACAUCAAAUUGGAUGAUGCAAA-UUCGAGUUCCUGAUGCG
AAAA02007626.1/8599-8673     CUGCAAAUGAUGAG-CUUACUCGGAUUCCCCUUCAGGACAUCAAAUUGGAUGAUGCAAA-UUCGAGUUCCUGAUGCG
AC144738.2/12152-12226       CUGCAAAUGAUGAG-CUUACUCGGAUUCCCCUUCAGGACAUCAAAUUGGAUGAUGCAGA-UUCGAGUUUCUGAUGCA
AARH01006572.1/460504-460575 AUGCAUAUGAUGAA-UUAACUCGGAUUCCCCUUCAAGACAUA-U--UGGGUGAUGUAAA-AUCGAGUUUCUGAUGCA
AASG02000600.1/49849-49777   AGGCAUAUGAUGAGAUUUACUCGGAUUCCCCUUCAGGACUUC-A--UGGGUGAUGUAAA-CUCGAGUUUCUGAUGCA
AC151823.11/74710-74640      AUGCAUGUGAUGAG--UUACUCGGAUUCCCCUUCAGGACUUC-U--UGGAUGAUGUAGA-CCCGAGAUUCUGAUGCA
AM436404.1/12550-12480       AUGCAAAUGACGAG--UUACUCGGAUUCCCCUUCAAGACAUU-A--UGGGUGAUGCAAA-CUCGAGUUUCUGAUGCA
AC189309.2/31643-31571       UUGCAAAUGAUGAU-CUUACUUGGAUUCCCCUUCAGAUCAUU-A--UGGGUGAUGCAAACUCCAAGUUUCUGAUGCU
#=GC SS_cons                 :<<<<_________.___________________________._.._____________._____________>>>>
#=GC RF                      auGCAaAUGAUGAg.cUUACUcGGAUUCCCCUUCAGgACAUu.A..UGGgUGAUGcAAA.uuCgAGUUUCUGAUGCa
//
# STOCKHOLM 1.0

#=GF AC   RF00340
#=GF ID   SNORA36
#=GF PI   snoMBI-87
#=GF DE   Small nucleolar RNA SNORA36 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   43.00
#=GF TC   43.50
#=GF NC   41.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00035
#=GF DR   snoRNABase; ACA36;
#=GF DR   snoRNABase; ACA36B;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300708;
#=GF DR   snoopy; Homo_sapiens300432;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [4]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   ACA36 (SNORA36A) belongs to the H/ACA class of snoRNAs which are predicted
#=GF CC   to guide the sites of modification of uridines to pseudouridines [1].
#=GF CC   ACA36 is predicted to guide the pseudouridylation of residue U105 and
#=GF CC   U1244 of 18S rRNA [4]. This family includes the mouse homologue snoMBI-87
#=GF CC   [3] and also identifies the human paralog ACA36B (SNORA36B) [2].
#=GF WK   Small_nucleolar_RNA_snoMBI-87
#=GF SQ   6


AC129195.3/135944-135814 UUCCAAAGUGUUGAGUUCAGCCCAGGGUCCCCUCCCUGCUCUGCUAAUUAGACUUUGGAACAUUGAAGCUGGCUGGGGAAAAUGACUGGAUAGAAAACAUUAUUCUAUUCAUUUACUCCCCAGCCUACACA-
AF357412.1/1-113         -------------------GCCCAGGGUCCCCUCCCUGCUCUGCUAAUUAGACUUUGGAACAUUGAAGCUGGCUGGGGAAAAUGACUGGAUAGAAAACAUUAUUCUAUUCAUUUACUCCCCAGCCUACACAU
AL445435.11/96511-96381  UUCCAAAGUGUUAAGUUCAGUUCAGGGUAGCUUCCCUGCUCUGUUAAUUAAACUUUGGAACAUUGAAACUGGCUAGGGAAAAUGAUUGGAUAGAAACUAUUAUUCUAUUCAUUUA-UCCCCAGCCUACAAAA
AC079121.5/42943-42813   UUCCAAAGUGUUGAGUUCAGUCCAGGGCAGCUUCCCUGUUCUGUUAAUUAAACUUUGGGACAUUGAAAUGGGCUAGGGGAGAUGAUUGGGUAGAAAGCAUUAUUUUAUUCAUUUGCCUCCCAGCCUACAAA-
AC122390.4/99926-99796   GUCCAAAGUGUUGAGUUCAGUUCAGGGCAGCUUCCUUGUUCUGUUAAUUAAACUUUGGGACAUUGAAAUUGGCUGAGAAAAAUGACUGAAUAGAGAGUAUUACUCUAUUCAUAUACUUCU-AGCCUACACAA
AF067016.1/546-676       UUCCAAAGUGUUGAGUUCAGUCCAGGGCAGCUUCCCUGUUCUGUUAAUUAAACUUUGGGACAUUAAAAUGGGCUAAGGGAGAUGAUUGGGUAGAAAGUAUUAUUCUAUUCAUUUGCCUCCCAGCCUACAAA-
#=GC SS_cons             <<<<<<<<<--------<<<--<<<<<______>>>>>-->>>-------->>>>>>>>>----------<<<<-<<<<-------<<<<<<<<<_______>>>>>>>>>----->>>>->>>>:::::::
#=GC RF                  ucCCaaaGuGUUgAGUUCaGucCaGGGuagCuUCCCuGuUCuGuUAAUUAaaCuuuGGgaCAUUGAAauuGGCuagGggAaAUGAuuGgauaGaaAauAUUAuuCuauuCaUuUaCccCcCaGCCUACAaAa
//
# STOCKHOLM 1.0

#=GF AC   RF00341
#=GF ID   snoZ39
#=GF DE   Small nucleolar RNA Z39
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   39.00
#=GF TC   39.90
#=GF NC   36.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300353;
#=GF DR   snoopy; Cavia_porcellus300166;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z39 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z39
#=GF SQ   5


AJ240058.1/1-60        GUACAUGUGAUGA-AGCAAAUCAGUAUGAAUAAA---AUGAUACUGUAAACGCUUUCUGAUGUA
AJ240057.1/1-60        GUACAUGUGAUGA-AGCAAAUCAGUAUGAAUAAA---AUGAUACUGUAAACGCUUUCUGAUGUA
AC010361.3/23932-23994 GUGCAUGUGAUGA-AGCAAAUCAGUAUGAAUGAAUUCAUGAUACUGUAAACGCUUUCUGAUGUA
U58655.1/2127-2188     -UGCAUAUGAUGA-AGCAAAUCAGUAUGAGUAAAAUCAUGAUACUGUAAACGCUUUCUGAUGCA
BX932341.1/250-311     GCAUAUAUGAUGUGAACGAAACAGUAUGAG--AAUCUGUGAUACUGUAAACGCUUUCUGAUGUG
#=GC SS_cons           :<<<<------<<.<<<----<<<<<<_____________>>>>>>----->>>>>---->>>>
#=GC RF                GuaCAUgUGAUGa.AGCAAAUCAGUAUGAaUAAAuucAUGAUACUGUAAACGCUuUCUGAUGua
//
# STOCKHOLM 1.0

#=GF AC   RF00342
#=GF ID   snoZ40
#=GF DE   Small nucleolar RNA Z40
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   50.00
#=GF TC   51.70
#=GF NC   44.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Gasterosteus_aculeatus300091;
#=GF DR   snoopy; Danio_rerio300057;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z40 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z40
#=GF SQ   5


AK057183.1/1267-1339 CGAUGUUAUGAUGAUGGGCGAAAUGUUCAACUGCUCUGAAGGGGCUGAAUGAAAAUGGCCUUUCUGAACAUCC
AJ236935.1/696-624   UGAUGUUAUGAUGAUGGGCAACAUGUUCAACUGCUCUGAAUGGGCUGAAUGAAAAUAGCCUUUCUGAACAUCA
AP001273.4/3902-3830 CGAUGUUAUGAUGAUGGGCGAAAUGUUCAACUGCUCUGAAGGGGCUGAAUGAAAAUGGCCUUUCUGAACAUCC
AJ240060.1/1-73      UGAUGUUAUGAUGAUGGGCAACAUGUUCAACUGCUCUGAAUGGGCUGAAUGAAAAUAGCCUUUCUGAACAUCA
AJ240059.1/1-70      -GAUGUUGUGAUGA-GGGCAAAAUGUUCAACUGCUCUGAAUGGGCUGAAUGAAAGUAGCCUUUCUGAACAUC-
#=GC SS_cons         :<<<<<_____________________________________________________________>>>>>:
#=GC RF              uGAUGUUAUGAUGAUGGGCaAaAUGUUCAACUGCUCUGAAuGGGCUGAAUGAAAAUaGCCUUUCUGAACAUCa
//
# STOCKHOLM 1.0

#=GF AC   RF00343
#=GF ID   snoZ122
#=GF DE   Small nucleolar RNA Z122
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   38.00
#=GF TC   39.30
#=GF NC   37.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300100;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [3]
#=GF RM   9891049
#=GF RT   Seven novel methylation guide small nucleolar RNAs are processed from a
#=GF RT   common polycistronic transcript by Rat1p and RNase III in yeast.
#=GF RA   Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y,
#=GF RA   Caizergues-Ferrer M, Bachellerie JP
#=GF RL   Mol Cell Biol. 1999;19:1144-1158.
#=GF CC   Z122 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z122
#=GF SQ   23


AJ458935.1/853-941           UUUGGGAAAUGAUGAACAAUUCAUCUCAG----------------AUAUCCUUUAUGG---AUUUAUUUUCA----GAAUGAUGAAAAUUUGCACGUCAGUCUGAUCCCAAA
AJ490491.1/1-89              UUUGGGAAAUGAUGAACAAUUCAUCUCAG----------------AUAUCCUUUAUGG---AUUUAUUUUCA----GAAUGAUGAAAAUUUGCACGUCAGUCUGAUCCCAAA
AJ010669.1/1-82              --UGGGAUAUGAUGA-CAA---AAAUACG----------------AUAUCUCUAAGGC--UAAUUGCUGUGC----GGAUGAAAUGUAUUUGCACGUCAGUCUGAUCCCA--
AK069030.1/2288-2376         UUUGGGAAAUGAUGAACAAUUCAUCUCAG----------------AUAUCCUUUAUGG---AUUUAUUUUCA----GAAUGAUGAAAAUUUGCACGUCAGUCUGAUCCCAAA
AP009338.1/8469-8551         UUUGGGAUAUGAUGCUAAAGAUUUUUAAC----------------AGAGGCUUUAG---------CUUUGCU----GAAUUAUUGAUAUUUGCACGUCAGUCUGAUCCCAAA
AC161107.24/105444-105363    UUUGGGAUAUGAUGAUAAU---AAUGCUG----------------ACA-----GAGGC---ACUAGCUGUUC---UGAAACAAAAAUAUUUGCACGUCAGUCUGAUCCUAAA
AASG02005749.1/15149-15064   GUUGGGAAAUGAUGA-GAAGUUAUCUCA-----------------AGUUAUCAAAGGC---ACUAGCUGUGC----UGAAUGUCU-UAUUUGCACGUCAGUCUGAUCCCAAA
AARH01006106.1/238770-238847 UUUGGGAGAUGAUGAGAAA--------------------------AUUAAUCAGAGGC---ACCAGCUCUGC----UGAA-AUUCUAUUUUGCACGUCAGUCUGAUCCCAGA
AABZ01000605.1/1778-1877     UUUGUGAUGUGAUGA-CAAUUCCUUGAGCUAUAUAU--UUUCUUGAGAUCCUCAAUGA---AGAAAACGUCU----CAUUAAAU--GAUUUGCACGUCAGUCUGAUCACAAA
AARH01029632.1/973-1050      UUUGGGAGAUGAUGAGAAA--------------------------AUUAAUCAGAAGC---ACAAGCUCUGC----UGAA-AUUCUAUUUUGCACGUCAGUCUGAUCCCAGA
AC004450.3/12297-12384       UUUGGGAAGUGAUGA-UAAGAUAUAUCA-----------------AUAUAUCAUAGGC---ACAUGCAAUGC---UGAACGAUAUAUAUUUGCACGUCAGUCUGAUCCCUUU
AACI02000031.1/8678-8777     UUUGUGAUGUGAUGACAACUUCU-UGAGCUAUAUAU--UUUCUUGAGAUCCUCAAUGA---AGAAAACGUCU----CAUUAAAU--GAUUUGCACGUCAGUCUGAUCACAAU
Z49211.1/837-936             AUUGUGAUGUGAUGACAACUUCUUGAGC-UAUAUAU--UUUCUUGAGAACAUCAAUGA---AGAAAACGUCU----CAUC--AAAUGAUUUGCACGUCAGUCUGAUCACAAG
AC156827.4/71471-71551       UUUGGGAAAUGAUGAUAAU---AAUGCUG----------------ACA-----GAAGC---ACUAGCUCUGC----UGAAUUAUAUUAUUUGCACGUCAGUCUGAUCCUAAA
ABPO01000513.1/3275-3174     AUCGUGAUGUGAUGACAACUUCUUGAGC-UAUAUAUUUUCUUCCGAGAUUUUCAAUGA---AGAAAACAUCU----CAUCAAAU--GAUUUGCACGUCAGUCUGAUCACAAU
ABXC01000771.1/16884-16982   UUUGGGAAGUGACGAAUAACUAAAUUCAGAUAUC-----CAUCCU-----AUUAUGGA---UUUAUGUGUGUACUGAUAUGAUGAAAAUUUGCACGUCAGUCUGAUCCCAUA
FN596494.1/6033321-6033414   UUUGGGAAAUGAUGAGAGAUUCAAACAGGUU-----------AGCAUAGGCUUAAUGG---UUUUUUUGGCA----UGCUGAAUAUUUUUUGCACGUCAGUCUGAUCCCAAA
AJ010795.1/1-94              ---GUGAUGUGAUGACAACUUCUUGAGC-UAUAUAU--UUUCUUGAGAACAUCAAUGA---AGAAAACGUCU----CAUCAAAU--GAUUUGCACGUCAGUCUGAUCAC---
AJ010670.1/1-82              ---GGGAAGUGAUGA-UAAGAUAUAUCA-----------------AUAUAUCAUAGGC---ACAUGCAAUGC---UGAACGAUAUAUAUUUGCACGUCAGUCUGAUCCC---
AJ010671.1/1-82              ---GGGAAGUGAUGA-UAAGAUAUAUCA-----------------AUAUGUCAUAGGC---ACUUGCAAUGC---UGAACAAUAUAUAUUUGCACGUCAGUCUGAUCCC---
AJ010673.1/1-83              -CUGGGAAAUGAUGAUAAG---UAUAUCG----------------AUAUUUCAGAGGC---GUAUGCAAUGC---UGAACGAAC--UAUUUGCACGUCAGUCUGAUUCCAG-
AJ458935.1/455-549           UUAGGGAUAUGACGAAAAACUUAUUCCAGAG-----------GUU--GUUUCUGAGGGUAGAUCUCUUCU--G--CCUGUGAUUAAACCUUGCACGUCAGUCCGAUCCCAUU
FN595232.1/1755304-1755211   UUUGGGAAAUGAUGAGAGAUUCAAACAGGUU-----------AGCAUAUGCUUAAUGG---UUUUUUUGUCA----UGUUGAAUAUUUUUUGCACGUCAAUCUGAUCCCAAA
#=GC SS_cons                 <<<<<<<________________________...........________________...___________...._____________________________>>>>>>>
#=GC RF                      uuuGGGAaaUGAUGAaaAAuUcauuucaGua...........uuuAuAUuuuuaAgGa...AuuaauugUgu....uaaugAuuaauAUUUGCACGUCAGUCUGAUCCCaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00344
#=GF ID   snoZ267
#=GF DE   Small nucleolar RNA Z267
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   43.00
#=GF TC   43.00
#=GF NC   42.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z267 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z267
#=GF SQ   5


AY069871.1/80-155      UUGAUGCCUGUGAUGGUGUUAAAUAUACUUUGAGAGAUGCGUCUCUACGAAAAAAAAAUCAACUCUGAGGCAUUUU
AC011809.2/63495-63570 UUGAUGCCUGUGAUGGUGUUAAAUAUACUUUGAGAGAUGCGUCUCUACGAAAAAAAAAUCAACUCUGAGGCAUUUU
AY220696.1/1-73        AAAUUGCCUAUGAUGGUGUUAAAUAUACUUUGAGCAGCUCG---CUGUGAAAAAUACUUACAAUCUGAGGCCAUUU
AJ532499.1/1-73        AAAUUGCCUAUGAUGGUGUUAAAUAUACUUUGAGCAGCUCG---CUGUGAAAAAUACUUACAAUCUGAGGCCAUUU
AJ532500.1/1-65        ----UGCCUGUGAUGGUGUUAAAUAUAUUUUGAGCUUUCAG---CUAUGAAAAAUCAUUUUAAUCUGAGGCA----
#=GC SS_cons           ::<<<<<<_________________________________...________________________>>>>>>::
#=GC RF                uuauuGCCUgUGAUGGUGUUAAAUAUACUUUGAGcaauucG...CUauGAAAAAuAauUaaAaUCUGAGGCaauUU
//
# STOCKHOLM 1.0

#=GF AC   RF00345
#=GF ID   snoR1
#=GF DE   Small nucleolar RNA snoR1
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Wilkinson AC; 0000-0001-7406-0151
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   49.00
#=GF TC   49.80
#=GF NC   47.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00066
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snoR1 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_snoR1
#=GF SQ   13


AJ532543.1/5-99            UGCCGUGAUGAU---UGCUCGCUUAUUUCUGACACCUCUUGUAUGAGAAGUUGUUC---UUUC-------CUCUUCCUUGGGGAUGAG-GAGGAGCACUUCGCUGAGCA
AJ300656.1/3-95            GGCGAUGAUGAUCAAUGCU---UAAUUUCUGACACCUCUUGUAUGAGAAGAGCUUGA--UAAC-------CUCUUCUUUGAGCACAUU-AUGCAAUACU---CUGAGCC
AAAA02005023.1/6403-6489   UGCUGUGAUGAGCAUUUGC---UUACUUCUGACACCUCUUGUAUGAGAAGGGCCU---------------CCCUUCCUUGAGCAGAUU-UAGCAACCCU---CUGAGCU
Y11048.1/29-119            AGCUGUGAUGUGCA---CUGC-UUUCUUCUGACACCUCUUGUAUGAGCAGGGACUU---UGUU-------CCCUCCGUUGAGCAGAUU-CAGCAACUCU---CUGAGCU
AARH01007419.1/62347-62252 GGCCGUGAUGAAGAGUGCUAC-AUAAUUCUGACACCUCUUGUAUGAGAGGAGCUUUUC-GGAG-------CUCUUCUUUGAGCACAUA-CAGCAACUCU---CUGAGCC
AM460458.2/2484-2388       GGCAAAGAUGAAGAGUGCUUU-AUAUUUCUGACACCUCUUGUAUGAGAAGAGCUCUCAAAAAG-------CUCUUCUUUGAGCACAUA-CAGCUACUCU---CUGAGCC
AASG02003803.1/17082-16987 GGCAAAGAUGAAGAGUGCUU--CUAAUUCUGACACCUCUUGUAUGAGAAUCUCUUUCUAAGAG-------CUCUUCUUUGAGCACAGA-UAGCAACUCU---CUGAGCC
CT961056.6/118556-118462   GGCGAGGAUGAAGAGUGCUAUUUAUAUUCUGACACCUCUUGUAUGAGAUGAAUCAG---AGGA-------UUCAUCUAUGAGCACAUA-AAGCAACUCU---CUGAGUC
AK069055.1/771-869         AGCUGUGAUGAGCAU---UGC-UUUCUUCUGACACCUCUUGUAUGAGAAGUGCUUC---UCCCAGAGAAGCUCUUCGUUGAGCAGAGUAUAGCAAUUGU---CUGAGCU
CP000590.1/67608-67522     GGCGAUGAUGAUCA---CC---ACA-UUCUGACACCUCUUGUACGAG-ACUUUGUG---GCCA-------UUGUUCGAUGAACUCAUU-AUGCAUAAGA---CUGAGCC
AJ532544.1/4-90            UGCUGUGAUGAGCAUUUGC---UUACUUCUGACACCUCUUGUAUGAGAAGGGCCU---------------CCCUUCCUUGAGCAGAUU-UAGCAACCCU---CUGAGCU
AJ532545.1/6-104           AGCUGUGAUGAGCAUUGCU----UUCUUCUGACACCUCUUGUAUGAGAAGUGCUUC---UCCCAGAGAAGCUCUUCGUUGAGCAGAGUAUAGCAAUUGU---CUGAGCU
AC189633.2/51934-52027     GGCAAGGAUGAUUACUGCU---UAAUUUCUGACACCUCUUGUAUGAGAAGAGCUUGA--UAAA-------CUCUUCCUUGAGCACAUU-AUGCAAAUACU--CUGAGCC
#=GC SS_cons               <<__________________..__________________________________...____.......__________________.__________..._____>>
#=GC RF                    gGCuguGAUGAucAuUGCUu..uuauUUCUGACACCUCUUGUAUGAGAAGugcuUu...uaaa.......CUCUUCuUUGAGCAcAuu.uAGCAAcucU...CUGAGCc
//
# STOCKHOLM 1.0

#=GF AC   RF00348
#=GF ID   snoR9_plant
#=GF DE   Small nucleolar RNA snoR9
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   43.00
#=GF TC   44.60
#=GF NC   40.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snoR9 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2]. This family is not related to Rfam:RF00065.
#=GF WK   Small_nucleolar_RNA_snoR9
#=GF SQ   7


AB016878.1/364-492      AUGUAUGAGAAGAUGAAUGAAGAAAAGAAAGUUCCGGUGAUGUUGUAACGUUCAGGCGGUGAACAUAGUCUGGGAAAACGAGUUAAAGAAGCAAGGGACGUUUCGUAUUUCCGUCGAGGAUGCUGACAU
AL161507.2/7333-7461    AUGUAUGAGAAGAUGAAUGAAGACAAGAAAGUUCCGGUGAUGUUGUAACGUUCAGGCGGUGAACACAGUCUGGGAAAACGAGUUAAAGAAGCAAGGGACGUUUCGUAUUUCCGUCGAGGAUGCUGACAU
AC007288.13/16248-16120 AUGUAUGAGAAGAUGAAUGAAGAAAAGAAAGUUCCGGUAAUGUUGUAACGUUCAGGCGGUGAACACAGUCUGGGAAAACGAUUUAAAGAAGCAAGGGACGUUUCGUAUUUCCGUCGAGGAUGCUGACAU
AB028614.1/46886-46758  AUGAACGAAGAAAAAGAUGAUUAGAUAGAAGUUUCGGUGAUGUUCCAACGCUCAGGCGUUAAACACAGACCGGAAAGACGAGAUAAAGAAGCAAGGGACGUUUCGUAUUUCCAUUGAUGAUGCUGACAU
AF318014.1/1-129        AUGAAUGAUGAAAACGAUGAUUAGAUAGAAGUUUCGGCGAUGUUGUUACACUCAGGCAUAAAACUCAGUCAGAGAUGACGAGUUUAAAAAGCUAGGGACGUUUCGUAUUUCCAUUGAUGAUGCUGACAU
AF318015.1/2-130        AUGAAUGAUGAAAACGAUGAUUAGAUAGAAGUUUCGGCGAUGUUGUUACACUCAGGCAUAAAACUCAGUUAGAGAUGACGAGUUUAAAAAGCUAGGGACGUUUCGUAUUUCCAUUGAUGAUGCUGACAU
AF318013.1/1-129        AUGAAUGAUGAAAACGAUGAUUAGAUAGAAGUUUCGGCGAUGUUGUUACACUCAGGCAUAAAACUCAGUUAGAGAUGACGAGUUUAAAAAGCAAGGGACAUUUCGUAUUUCCAUUGAUGAUGCUGACAU
#=GC SS_cons            <<<___________________________________________________________________________________________________________________________>>>
#=GC RF                 AUGaAUGAugAaAaggAUGAuuAgAuagAAGUUuCGGuGAUGUUGUaACguUCAGGCguuaAACaCAGUcuGgGAagACGAGUUaAAgAAGCaAGGGACGUUUCGUAUUUCCaUuGAuGAUGCUGACAU
//
# STOCKHOLM 1.0

#=GF AC   RF00349
#=GF ID   snoR11
#=GF DE   Small nucleolar RNA R11/Z151
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   50.00
#=GF TC   52.00
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300039;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snoR11/Z151 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1,2].
#=GF WK   Small_nucleolar_RNA_R11/Z151
#=GF SQ   5


AF326225.1/1-89  AAGCUGAUGAUGAUAAAAA-C---AAUUAUCUUAGCGGAUUUCAGUGAGGUUUUUG---AAUCAAUGAAC--UGAAU-UUGUUACACACACUGAAGCUU
AF317938.1/3-92  GAGCUGAUGAUGAAAAAAAAC---AAUUAUCUUAGCGGAUUUCAGUGAGGUUUUUG---AAUCAAUGAAC--UGAAU-UUGUUACACACACUGAAGCUU
AJ490337.1/6-104 GGGCUUGUGAUGAUUCAGGUCCGAAAGGAUCUUAGCGGAUUUCUGUGAGGCGAUUCUGUCGUCGUUGAUCGCUUAAUGUUGUUACACACACUGAAGCCU
AF317939.1/1-90  AAGCUUAUGAUGAUAGAAAAC---AAUUAUCUUAGCGGAUUUCAGUGAGGUUUUUC---AAUCAAUGAUC--UGAAU-UUGUUACACACACUGAGGCUU
AF317940.1/1-87  --GCCUAUGAUGAUAAAAA-C---AAUUAUCUUAGCGGAUUUCAGUGAGGUUUUUUUAAAAUCAAUGAUC--UGAAU-U-GUUACACACACUGAGGC--
#=GC SS_cons     <<<<<________________...________________________________...___________.._____.________________>>>>>
#=GC RF          agGCuuAUGAUGAUaaAAAaC...AAuuAUCUUAGCGGAUUUCaGUGAGGuuuUUu...aAUCAaUGAuC..UgAAU.UUGUUACACACACUGAaGCcu
//
# STOCKHOLM 1.0

#=GF AC   RF00350
#=GF ID   snoZ152
#=GF DE   Small nucleolar RNA Z152/R70/R12/
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   50.00
#=GF TC   51.90
#=GF NC   43.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300044;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Z152 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2]. This family also contains snos R70 and R12 from Arabidopsis
#=GF CC   thaliana.
#=GF WK   R12
#=GF SQ   9


AF317995.1/1-111         ----UGCGAUGAUGAUAAAAUAGCACG--AAG-GUGCGUGAAGGGCAGUGGACAAAGCAAUGAAAAUUUG---------UUUUGCCGUGAGCUCUCUUU--AAUAAACGACUUCUCCUUCCACUGAGCA----
AF317941.1/1-96          --GAUGCAAUGAUGAGAUAAAAGCACG--AAGAGUGUGAGAAGAGCAGUGGG---------------------------UU-UACCGUGAGCUCUCCUU--UA-AAACGACUUCUCCUUCCACUGAGCAUU--
AJ490338.1/1-98          GCAAUGCAAUGAUGAUUUUA---------AUGGGUUUUAGCAGUGGCGGCGUCA--------------------------GUCGCCGUGAGCUUUCAAUCCAAAAAACGACUUCUCUUUCCACUGAGCAUUGC
AF317942.1/1-96          --GAUGCAAUGAUGAGAUGAAAGCACG--AAGAGUGUGAGAAGAGCAGUGGG----------------------------UUUACCGUGAGCUCUCCUU--UA-AAACGACUUCUCCUUCCACUGAGCAUU--
AACV01003559.1/6732-6639 --AAUGCAAUGAUGAUUUUA---------AUGGGUUUUAGCAGUGGCGGCGUCA--------------------------GUCGCCGUGAGCUUUCAAUCCAAAAAACGACUUCUCUUUCCACUGAGCAUU--
AC189511.1/15393-15269   --GAUGCUAUGAUGUGAUAAAAGCACG--AAGAGUGUAAGAAGAGCAGUGGACAAUUACAAAUUCUGAAAAGGGUUUGUUCUUGCCGUGAGCUUUCCUA--AUUAAACGACUUCUCCUUCCACUGAGCAUA--
AP006087.1/71580-71475   --GGUGCAAUGAUGAGAUAA---AACA--CUCUAUGUGUAUUGGGCAGUGGACGUUACCAUCAGG--------------UUUCGCCGUGAGCCUAAUAU--UA--AACGACUUCUCCUUCCACUGAGCACU--
AASG02005717.1/6918-6795 --GAAGCAAUGAUGAGGUGA-AGCACUGAAACAGUGUUGAAAGGGUAGUGGACAGGUACCCAGUUGAUAACUGAGG---GCUUGCCGUGAACUCUAUCUA-AUUAAACGACUUCUCCUUCCACUGAGCUCC--
AM467034.1/3213-3321     --UGUGCUGUGAUGAGACGA--GACAC--AUUGGUGUUCAUAGGGCAGUGGACGGGCCCAAUGG---------------GUCUGCCGUGAGCCUAUUGAA-UUCAAACGACUUCUCCUUCCACUGAGCACA--
#=GC SS_cons             ..<<<<<_____________.______..___________________________________...............____________________.._________________________>>>>>..
#=GC RF                  ..gguGCaAUGAUGAgaUaA.AGcACg..AagaGUGUuagaAGgGcAGUGGaCAauuacAuaau...............uuUUGCCGUGAGCUuUcuuU..aauAAACGACUUCUCCUUCCACUGAGCacc..
//
# STOCKHOLM 1.0

#=GF AC   RF00351
#=GF ID   snoR20
#=GF DE   Small nucleolar RNA R20
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   43.00
#=GF TC   43.20
#=GF NC   40.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snoR20 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_R20
#=GF SQ   4


AL161547.2/22249-22338 AAGGAUGAU----GAAUACAAUUG----GUACAUAAAUUUAGUUGUGA--AACUCACAUGUUGAAAAAAGUAGAAUAC--CGAUGAAUAUCAAAGCUGACUU
AF317945.1/1-90        AAGGAUGAU----GAAUACAAUUG----GUACAUAAAUUUAGUUGUGA--AACUCACAUGUUGAAAAAAGUAGAAUAC--CGAUGAAUAUCAAAGCUGACUU
AC006413.4/30276-30369 AAGGAUGAAUAUGGAAUACAAUUG----GAACAUAAAAUUUGUCUUGA--AACUCACACGUUGAAAGUAGUAGAACAC--CAAUGAAUAUCUUAGCUGAUUU
AC183492.1/43523-43620 GAGGAAGAU----GAAGAUAACUGAGAAGUAGAAAAUAUUAGUUUUGUUUAACUCACAUGUUGAAACAAGUAGAAUAUAGCUAUGACUAUCAAAGUUGGUUU
#=GC SS_cons           <<<______....___________....____________________..____________________________..___________________>>>
#=GC RF                aAgGAuGAu....GAAuAcAAuUG....GuAcAuAAaaUUaGUUuUGa..AACUCACAUGUUGAAAaaAGUAGAAUAc..CaAUGAaUAUCaaAGcUGacUu
//
# STOCKHOLM 1.0

#=GF AC   RF00352
#=GF ID   snoR21
#=GF DE   Small nucleolar RNA R21
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   45.00
#=GF TC   45.20
#=GF NC   44.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   snoR21 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_R21
#=GF SQ   6


AF317946.1/1-83            AAUCCCAAUGAUGACUUAUUAAGAUUAAAAAUGUUAAAAGUAGUGA-CUGAU-AUCUUUUGAUGAAAUUU---UAGCUCUGAGGGAUU
AL021636.3/72356-72274     AAUCCCAAUGAUGACUUAUUAAGAUUAAAAAUGUUAAAAGUAGUGA-CUGAU-AUCUUUUGAUGAAAUUU---UAGCUCUGAGGGAUU
AF326226.1/1-81            -AUCCCAAUGAUGAAUGAU-AUGAA-AAAAAUGUUAAAAGUAGUGA-CUGAUUAUACCUUGAUUACUAGU---CAAUUCUGAGGGAUU
AL021636.3/72154-72074     -AUCCCAAUGAUGAAUGAU-AUGAA-AAAAAUGUUAAAAGUAGUGA-CUGAUUAUACCUUGAUUACUAGU---CAAUUCUGAGGGAUU
AASG02005532.1/7775-7857   CUUCCCUAUGAAGAAUGAU-AUUUGUAUGUUAAAUAAAAGUAGUGGGCUGAU-CUCCAUUGAUGACUGAC---CAAUUCUGAGGGAUG
AARH01000785.1/12491-12575 UAUCCCUAUGAAGAAUGAA-CUGAU-AUUUCAAUUAAAAGUAGUGGGCUGAU-CUCCAUUGAUGAUCACUAACCAAUUCUGAGGGAUG
#=GC SS_cons               <<<<<<_____________.__________________________._____._________________..._________>>>>>>
#=GC RF                    caUCCCaAUGAuGAaUgAU.AuGAuUAaaaaugUUAAAAGUAGUGa.CUGAU.aUccaUUGAUgAcuauU...cAAUUCUGAGGGAug
//
# STOCKHOLM 1.0

#=GF AC   RF00353
#=GF ID   snoR31_Z110_Z27
#=GF DE   Small nucleolar RNA snoR31/Z110/Z27
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   45.00
#=GF TC   45.30
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300003;
#=GF DR   snoopy; Arabidopsis_thaliana300004;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [3]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   This family contains several related snoRNAs including R31, Z27 and Z110.
#=GF CC   Family members belong to the C/D class of snoRNAs which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1,2,3].
#=GF WK   Z27
#=GF SQ   8


AJ489960.1/1-96 AGUAUCAGAG--GAUGA-AACCUUAUAACAA---UCUUAGGACACCUUCUGACACAGUGCA-AUCACACUGUGAAUGAGAAGG-CUUUUCUUU-CUGAUGAUGCU
AJ010687.1/1-99 -GCAUGAGAG--GAUGA-AAGCUUGAAACAAUCUUAGGACACCUUCUGACACAGCGCGUUACAUCACGUUGUGAAUGAGAAGG-CAAUUCUUUUCUGAUGAUGC-
AJ240070.1/1-95 -UGGAGAAAUAUGAUGAUAAUAAUCAGUAAAU-AUCUUAGGACACCUUCUGACACAGUUUA-------CUGUGUAUGAGAAUGACUUGUUAAU-CUGAUUCUCCA
AF317952.1/1-90 CUGGAGAAAU--GAUGAGAA--AUCAGAUAA--AUCUUAGGACACCUUCUGACACAGAUU--------CUGUGUAUGAGAAUGACAUCAUAUU-CUGAUCUUCAG
AF317953.1/1-90 CUGGAGAAAU--GAUGAGAA--AUCAGAUAA--AUCUUAGGACACCUUCUGACACAGAUU--------CUGUGUAUGAGAAUGACAUCAUAUU-CUGAUCUUCAG
AJ307931.1/1-96 AGUAUCAGAG--GAUGA-AACCUUAUAACAAUCUUAGGACACCUUCUGACACAGUGCU----AUAACACUGUGAAUGAGAAGG-CUUUUCUUU-CUGAUGAUGCU
AJ489959.1/1-96 AGUAUCAGAG--GAUGA-AACCUUAUAACAAUCUUAGGACACCUUCUGACACAGUGCA----AUCACACUGUGAAUGAGAAGG-CUUUUCUUU-CUGAUGAUGCU
AJ010675.1/1-90 CUGGAGAAAU--GAUGAGAA--AUCAGAUAA--AUCUUAGGACACCUUCUGACACAGAUU--------CUGUGUAUGAGAAUGACAUCAUAUU-CUGAUCUUCAG
#=GC SS_cons    <<<<<<<---..-----.--------------.----------------<<___>>----..---------------------.---------.---->>>>>>>
#=GC RF         cggaugAaAu..GAUGA.AAccuUaaaAcAAU.aUcuuAggaCacCUuccgacacggaUU..AUcACaCUGUGaAUGAGAAuG.CuUuuuuUU.CUGAUcauccg
//
# STOCKHOLM 1.0

#=GF AC   RF00355
#=GF ID   snoR28
#=GF DE   Small nucleolar RNA snoR28
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   45.00
#=GF TC   48.00
#=GF NC   39.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   R28 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_snoR28
#=GF SQ   9


AF317949.1/1-74              GAU---GGUGAUGAUGUGUUCUUGUGUGAGUAUGAGUAUGAUGUUCAUUGGCGUAGCUUUAAGCGUUUGGCUGA-AUU
BT004309.1/805-878           GAU---GGUGAUGAUGUGUUCUUGUGUGAGUAUGAGUAUGAUGUUCAUUGGCGUAGCUUUAAGCGUUUGGCUGA-AUU
AF317950.1/1-74              GAU---GGUGAUGAUGUGUUUUUGUGUGAGUAUGAGUAUGAUGUUCAUUGGGGUAGCUUUAAGCGUGUGGCUGA-AUU
AJ421410.1/955-1028          GAU---GGUGAUGAUGUGUUUUUGUGUGAGUAUGAGUAUGAUGUUCAUUGGGGUAGCUUUAAGCGUGUGGCUGA-AUU
AAAA02018380.1/82969-82892   GAUCAAGGAGAUGACGUAUUCUACUGUGAAUAUGAAUAUGAUAUACACUGGCAUAAUUUUAAGCGUCUGGCAGACAUC
AARH01003843.1/468937-468860 GAUGAAGGAGAUGACAUUUUCAUGUGCGAAUAUGAAUAUGACAUACAUUGGCACAGUUUCAAGCGUUUAGCUGAUAUU
AF417481.1/986-1063          GAUGGAGGAGAUGAUGUAUUUUACUGUGAAUAUGAGUAUGAUAUUCAUUGGCAUAAUUUUAAGCGUUUGGCAGAUAUU
AASG02003017.1/11736-11659   AAUGAAGGAGAUGAUAUUUUCUUAUGCGAGUAUGAGUAUGACAUCAUCUGGCAUUCUUUCAAGCGUCUAGCUGAGAUU
AB037135.2/1029-1106         GAUCAAGGAGAUGACGUAUUCUACUGUGAAUAUGAAUAUGACAUACACUGGCAUAAUUUUAAGCGUCUGGCAGACAUC
#=GC SS_cons                 <<<________________________________________________________________________>>>
#=GC RF                      gAUgAAGGaGAUGAuGUaUUcUugUGUGAgUAUGAgUAUGAuaUuCAuUGGCaUAguUUUAAGCGUuUGGCuGAuAUc
//
# STOCKHOLM 1.0

#=GF AC   RF00356
#=GF ID   snoR32_R81
#=GF DE   Small nucleolar RNA R32/R81/Z41
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   45.00
#=GF TC   46.40
#=GF NC   40.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300130;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   This family contains the related snoRNAs R32, R81 and Z41 which are
#=GF CC   members of the C/D class of snoRNA containing the C (UGAUGA) and D (CUGA)
#=GF CC   box motifs. Most of the members of the box C/D family function in
#=GF CC   directing site-specific 2'-O-methylation of substrate RNAs [1,2].
#=GF WK   Small_nucleolar_RNA_R32/R81/Z41
#=GF SQ   6


AY707463.1/3-93        ---GGAAUAUGAUGAAAG------UUGUA---UAUCGGUGAUGGU-------CUUUUGAUUCAUAUGAUCGACAAAAAUUUCAACUCGCUACGUUCUUUCUGAUUCUUUU
AF317954.1/1-88        ---AGAAUAUGAUGAAAG------UUGUA---UAUCGGUGAUGGU-------CUUUUGAUUCAUAUGAUCGACAAAAAUUUCAACUCGCUACGUUCUUUCUGAUUCU---
AJ240071.1/6-99        UGUAGAAUAUGAUGAAAG------UUGUA---UAUCGGUGAUGGU-------CUUUUGAUUCAUAUGAUCGACAAAAAUUUCAACUCGCUACGUUCUUUCUGAUUCUUAC
AF323461.1/1-98        UGAAGAAUGUGAUGAAAG------UUGUCGAUUAUGUGUGAUGAU------UCUUUAGAUUCAAUUGAUCGAUAAAAACUUCAAUUCGCUACGUUCUUUCUGAUUCUUCA
AJ240072.1/1-98        UGAAGAAUGUGAUGAAAG------UUGUCGAUUAUGUGUGAUGAU------UCUUUAGAUUCAAUUGAUCGAUAAAAACUUCAAUUCGCUACGUUCUUUCUGAUUCUUCA
AP009676.1/64521-64418 AGACGAACAUGAUGAAAGCAAAAAUUAAAAAGAAUGCGUGAUCAUCAAACAUUAUGUGUUUGAUAUGAUCG------AACUUGUCAUGCUACGUUCUUUCUGAUUCGUCU
#=GC SS_cons           :::<<<<___________......_____________________......____________________________________________________>>>>:::
#=GC RF                uGAaGAAUAUGAUGAAAG......UUguaaAuuAUguGUGAUgaU......UcuUuuGaUUcAuaUGAUCGAuAAAAAuUUcAacucGCUACGUUCUUUCUGAUUCuUcu
//
# STOCKHOLM 1.0

#=GF AC   RF00357
#=GF ID   snoR44_J54
#=GF DE   Small nucleolar RNA R44/J54/Z268 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   48.00
#=GF TC   48.70
#=GF NC   46.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00069
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300077;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   R44, J54 and Z268 are members of the C/D class of snoRNA which contain the
#=GF CC   C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1].
#=GF WK   Small_nucleolar_RNA_R44/J54/Z268_family
#=GF SQ   29


AY220692.1/2-94            GGUGCAGGUGAUGAGAAGCAAGACAGGGACAUCAG-AUCUCCUUCC-------------GUGGG--GAGUGAUC--GACUAAAGUCUC-AAUGGGAAUCUCUCUGAUGCAUU
AP005757.2/6127-6035       GGUGCAGGUGAUGAGAAGCAAGACAGGGACAUCAG-AUCUCCUUCC-------------GUGGG--GAGUGAUC--GACUAAAGUCUC-AAUGGGAAUCUCUCUGAUGCAUU
AY220693.1/1-99            -AUGCAUAUGAUGAGAAGCAAGACAGGGACAUCAGCACCCCCUUUCUGU------GAAGGUGGG--GAGUGAUC--GACUAAAGUCUC-AAUGGGAAUCUCUCUGAUGCAU-
AP005757.2/5906-5806       GAUGCAUAUGAUGAGAAGCAAGACAGGGACAUCAGCACCCCCUUUCUGU------GAAGGUGGG--GAGUGAUC--GACUAAAGUCUC-AAUGGGAAUCUCUCUGAUGCAUA
AJ532497.1/1-103           GAAGCAGGUGAUGA-AAGCCAGACAGG-ACAUCAGCACCCUCUUCUCUUUU--GAGAGAGAUGG--GAAUGAUC--GACUAA-GUCUAUAAUGGGAAUCUCUCUGAUGCUUU
AY220694.1/1-104           GAAGCAGGUGAUGA-AAGCAAGACAGGGACAUCAGCACCCUCUUCUCUUUU--GAGAGAGAUGG--GAAUGAUC--GACUAA-GUCUAUAAUGGGAAUCUCUCUGAUGCUUU
AF317960.1/1-80            --UGCAAGUGACGA-UGAAUAGACAGGGACAUCAG-AAGUUCUAUA----------------------AUGAU---GACUAAUGUCUA-GAUGGGAAUCUCUCUGAUGCA--
AY069871.1/443-526         AGUGCAAGUGACGA-UGAAUAGACAGGGACAUCAG-AAGUUCUAUA----------------------AUGAU---GACUAAUGUCUA-GAUGGGAAUCUCUCUGAUGCACA
AY090970.1/294-388         UGUGCAAGUGAUGA-UAAAAAGACAGGGACAUCAGAUUCUCCUUUG--------GGAGAAGUA---UAAUGAU---GAUUAA-GUCUA-GAUGGGAAUCUCUCUGAUGCACC
AF317959.1/1-97            UAUGCAAGUGAUGA-UGAAAAGACAGGGACAUCAGAAUCUCCUUGU---U---AGGAGAUGA----GAAUGAU---GACUAAUGUCUA-GAUGGGAAUCUCUCUGAUGCAUA
AC135465.23/42922-43010    CUUGCAAGUGACGAUAAAUUAGACAGGGACAUCAG-AUCUCCUAAU-------UAGAGAACA-------UGAU---GAUUUGUCGA-----UGGGAAUCUCUCUGAUGCAUA
AC135465.23/42234-42322    GUUGCAAAUGAUGACAAACUAGACAGGGACAUCAG-AUCUCCUAAU-------UAGAGAAAA-------UGCU---GAUUU--GUCUG---UGGGAAUCUCUCUGAUGCACA
AB010073.1/79857-79773     UUUGCAAGUGACGA-UUAACAGACAGGGACAUCAG-AAAAUAUUCUG----------------------UGUU---GACUAUAGUCUAUAAUGGGAAUCUCUCUGAUGCAUA
AJ532503.1/1-102           -UAGCAUAUGAUGAGAAGCAAGACAAGAACAUCUGCAGUGCAUCUGAAUCAAAUCAAGAUGCAGCAACAGGAU---GACUCAUGUCUA---GGGGAA--UCUCUGAUGCUA-
AJ532502.1/1-104           UUGGCAUAUGAUGAGAAGCAGGACAAGAUCACCUGCCGCAUUCCU-GAUCCAAAUCAGGGACG-CAAUAGCAUGAUGACUC-UGUCUA---GGGGAA--UCUCUGAUGCUAA
AJ532504.1/1-104           UUAGCAGAUGACGAGAAUCGAGACAAGGUGUC-UGCAGCGUGCUCGAUCCAAGUCGGGGAGCG-CGAUAGCAUGAUGACUC-CGUAUA---GAGGAA--UCUCUGAUGCAAG
AJ532501.1/1-105           UUAGCAGAUGACGAGAAUCGAGACAAGGUGUC-UGCAGCGCCCCUCGAUCCGAGUCGGGGAGCGCGAUAGCAUGAUGACUC-CGUCUA---GGGGAA--UCUCUGAUGCAAG
AP003509.3/126406-126509   UUAGCAUAUGAUGAGAAGCAAGACAAGAACAUCUGCAGUGCAUCUGAAUCAAAUCAAGAUGCAGCAACAGGAU---GACUCAUGUCUA---GGGGAA--UCUCUGAUGCUAU
AAAA02025515.1/16604-16696 GGUGCAGGUGAUGAGAAGCAAGACAGGGACAUCAG-AUCUCCUUCC---------GAGGGGAG------UGAUC--GACUAAAGUCUC-AAUGGGAAUCUCUCUGAUGCAUA
AASG02005935.1/3152-3240   AAUGCAAGUGAUGAUAAACUAGACAGGGACAUCAGUUACUCCUUCG----------------GA--GGAUGAU---GACUA-AGUCUA-AAUGGGAAUCUCUCUGAUGCUUG
AARH01007574.1/77646-77552 UGUGCAAAUGAUGAUAAAAUAGACAGGGACAUCAGCUACUCCUUUU--------UUAGGGAGG-----AUGAU---GACUA-AGUCUAAAAUGGGAAUCUCUCUGAUGCAUU
AC135465.23/42434-42519    UGCGCAGAUGAUGACAAGAUAGACAGGGACUC-AGCACUCCGAAGG----------------GA--GAAUGUU---GAUUU--GUCUA--AUGGGAAAAUCUCUGAUGCGUU
AARH01007574.1/77488-77393 UGUGCAAAUGAUGAUAAAACAGACAGGGACAUCAGCCACUCCAAUU---------GAAAUUGGA--GAAUGUU---GACUA-UGUCUA-AAUGGGAAUCUCUCUGAUGCAAA
AARH01010384.1/53441-53347 UGUGCAGAUGAUGAUAGAACAGACAGGGACAUCAGCCACUCCAAUU---------GAAAUUGGA--GAAUGUU---GACUU--GUCUA-AAUGGGAAUCUCUCUGAUGCACA
AARH01010384.1/53588-53494 AAGGCAGGUGAUGAUAAAAUAGACAGGGACAUCAGUUACUCUCUUU--------UUAGGGAGG-----AUGAU---GACCA-AGUCUAAAAUGGGAAUCUCUCUGAUGCCUU
AM468060.2/3268-3351       UGUGCAAGUGACGA--UAUCAGACAGGGACAUCAGCACCUCCAAUG----------------GA--GAAUGAU---GAUUU--GUCUU---UGGGAAUCUCUCUGAUGCACA
AASG02005935.1/3531-3613   UGUGCAAAUGACGA-UAAGAAGACAGGGACAUCAGUACUCCACCGG----------------------AGCAU---GAUGAUUGUCUU---UGGGAAUCUCUCUGAUGCCUG
AC189574.2/21504-21599     UGUGCAAGUGACGA-UAAAAAGACAGGGACAUCAGAUUCUCCUUAG--------GGAGAAGUA---GAAUGAU---GAUUAUUGUCUA-AAUGGGAAUCUCUCUGAUGCACU
FN594950.1/6204764-6204680 CAUGCAAGUGAUGUUAAAGCAGACAGGGACAUCUGCACUCUUUAGG------------------A-GAUUGAU---GACUU--GUUCU---UGGGAAUCUCUCUGAUGCAUU
#=GC SS_cons               :<<<<<________________________________________........_________..._______...____________._________________>>>>>:
#=GC RF                    uguGCAaaUGAUGAgAAaaaAGACAGGGACAUCaGcAucuccuuuu........ugAGagaug...gaAuGAU...GACUaauGUCUa.AAUGGGAAUCUCUCUGAUGCaca
//
# STOCKHOLM 1.0

#=GF AC   RF00358
#=GF ID   snoZ101
#=GF DE   Small nucleolar RNA Z101
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   44.00
#=GF TC   44.80
#=GF NC   41.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00057
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Z101 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_Z101
#=GF SQ   13


AJ489945.1/1-100             GUGAUGCAGAUGAGGAGACGCA---AGAUUUAA-UGGGUAAUUUGCGUCUGAG-GCAUCUCUGUGAUGUCACACCCUUUUUCACCUUGAAGAUCUGAUGCAUCUA
AJ307914.1/1-96              --GAUGCAGAUGAGGAGGCACA---AGAUUUAA-UGGGUAAUUUGCGUCUGAG-GCAUCUCUGUGAUGUCACACCCUUUUUCACCUUGGAGAUCUGAUGCAUC--
AAAA02019713.1/24827-24926   GUGAUGCAGAUGAGGAGACGCA---AGAUUUAA-UGGGUAAUUUGCGUCUGAG-GCAUCUCUGUGAUGUCACACCCUUUUUCACCUUGAAGAUCUGAUGCAUCUA
AASG02003152.1/15228-15137   AUUGGGCAGAGGAUGAAUCUCA---UAUUUUAA-UGGGUAAUUUGCGGCUGAA-U-AUUUCAUUGAUG-------CUAUAUCACCUUGGAGACCUGAUGCCCUUG
AC007767.3/46842-46937       GUGGGGCAGAUGAUGAUUAUCA--UAAAACAAA-UGGGUAAUUUGCGACUGAUAAUAUUACAUUGAUGU------GUUUUUCACCUUGGAGAACUGAUGUCCCCA
AP006141.1/89791-89880       AAUGGGCAUAUGAUGAAACUUA---UUAUGUAAAUGGGUAAUUUGCGUCUG----AAUUUCAUUGAUGCUAA--A------CACCUUGGAGAACUGAUGCCCAUA
AC146791.12/24938-24845      AAUGGGUACGUGAUGAAUCUAAGUUUGUGUAAA-UGGGUAAUUUGCAUCUGAA--UAUCAUU--GAUGUUA------UUAUCACCUUGGAGAACUGAUACCCAUA
AARH01009456.1/205048-205138 UUGGGGCGUAUGAUGAAUCUCA---UGUUUUAA-UGGGUAAUUUGCGUCUGAA-U--UUUUGUUGAUG-------CUCUAUCACCUUGGAGACCUGAUGCCCUUU
AARH01008371.1/236837-236748 UUGGGGCAUAUGAUGAAUCUCA---UGUUUUAA-UGGGUAAUUUGCGUCUGAA-U--UUUUCUUGAUG-------CUAUA-CACCUUGGAGACCUGAUGCCUUUC
AC146791.12/24424-24331      AAUGGGCAUAUGAUGAAUCUAAAUUUGUGUAAA-UGGGUAAUUUGCAUCUGAA--UAUUAUU--GAUGUUA------AAAUCACCUUGGAGAACUGAUGCUCAAU
AM480118.2/5735-5827         UUGGGGCAAGUGAUGAAUCUCA---UAAACUUA-UGGGUAAUUUGCGUCUGAA-UUUUUUCAUUGAUG-------CUAUAUCACCUUGGAGACCUGAUGCCGCUU
FN596247.1/5692346-5692438   CAGGGGCAAGUGAUGAAUCUCA---UGAAGUAA-UGGGUAAUUUGCGUCUGAA-UUUUUCCAUUGAUG-------CUAUUUCACCUUGGAGAACUGAUGCCCCCU
AJ309195.1/691-592           AUGAUGCAGAUGAGGAGGCACA---AGAUUUAA-UGGGUAAUUUGCGUCUGAG-GCAUCUCUGUGAUGUCACACCCUUUUUCACCUUGGAGAUCUGAUGCAUCUA
#=GC SS_cons                 ::<<<<<<--------------...--------.-------------------.-<<<<_____>>>>---....---------------------->>>>>>::
#=GC RF                      augggGCAuAUGAuGAauCucA...ugauuuAA.UGGGUAAUUUGCGUCUGAa.ucaUcucuuUgAugUuA....cUuUuUCACCUUGGAGAaCUGAUGCcccua
//
# STOCKHOLM 1.0

#=GF AC   RF00359
#=GF ID   snoZ102_R77
#=GF DE   Small nucleolar RNA Z102/R77
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   40.00
#=GF TC   41.30
#=GF NC   39.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00060
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [3]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF CC   Z102 and R77 and are members of the C/D class of snoRNA which contain the
#=GF CC   C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1,2,3].
#=GF WK   R77
#=GF SQ   9


AF318005.1/1-85            AGA-GAUAUGAUGAUG-GAAUUAGAUUUCCCUAUUGGUUUGA--UCGCCGUUAUGAUGGCAUCUUA--CGUAUUAGCUCUAUCUGAUC-UCU
AJ307915.1/1-86            -GAUGAUAUGAUGAUC-AAAUUUGAU-UCCCUAUUGGUUUGAU-UGGCCGCCAUGAUGGCCUCAAAU-UGUAUUAGCUCUAUCUGAUCAUC-
AF318006.1/6-89            GAAUGAAGUGAUGAUUGAACUUUGUU-UCCCUAUUGGUUUGAU--CGCCGAUAUGAUGGCAUAC-----GUAUUAGCUCUAUCUGAUCAUUC
AJ489946.1/1-87            GGAUGAUAUGAUGAUC-AAAUU-GUU-UCCCUAUUGGUUUGAU-UGGCCGCUAUGAUGGCCUCAAAU-UGUAUUAGCUCUAUCUGAUCAUCU
AM440351.2/20146-20060     GAAUGAUAUGAUGAAU-GAAUUUGUU-UCCCUAUUGGUUUGAU--CGCCGGGAUGAUGGCGACAAAU-AGUAUUAGCUCUAUCUGAUCAUUC
AASG02011106.1/5923-6010   GAAUGAUAUGAUGAUU-UAUUUUGUU-UUCCUAUUGGUUUGAU--UGCCGUGAUGAUGGCAUCAAUUGUGUAUUAGCUCUAUCUGAUCAUUC
AARH01002859.1/41059-41142 GAAUGAAAUGAUGAUU-A---UUGUU-UCCCUAUUGGUUUGAUCUUGCCGCAAUGAUGGCAUCAUU---GUAUUAGCUCUAUCUGAUCAUUC
AAAA02000994.1/12691-12604 UGAUGAUAUGAUGAUC-AAAUUUGAU-UCCCUAUUGGUUUGAU-UGGCCGCCAUGAUGGCCUCAAAU-UGUAUUAGCUCUAUCUGAUCAUCU
AACV01014226.1/37896-37982 GGAUGAUAUGAUGAUC-AAAUU-GUU-UCCCUAUUGGUUUGAU-UGGCCGCUAUGAUGGCCUCAAAU-UGUAUUAGCUCUAUCUGAUCAUCU
#=GC SS_cons               :<<<<-----------.---------.-------------<--.-<<<<________>>>>->----.------------------->>>>:
#=GC RF                    ggAuGAuAUGAUGAUu.aAaUUUGuU.UCCCUAUUGGUUUGAU.UcGCCGuuAUGAUGGCgUCaaaU.uGUAUUAGCUCUAUCUGAUCaUcu
//
# STOCKHOLM 1.0

#=GF AC   RF00360
#=GF ID   snoZ107_R87
#=GF DE   Small nucleolar RNA Z107/R87
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAfold; Moxon SJ, Daub J, Gardner PP
#=GF GA   50.00
#=GF TC   50.20
#=GF NC   49.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300058;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [3]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z107 and R87 are members of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNA
#=GF WK   Small_nucleolar_RNA_Z107/R87
#=GF SQ   9


AJ298135.1/1-115        GAGAAAUCGUGGUGAUGACUUGGAAAUAUU-CAAGCUCAACAGACCGUAAUGUAGGAUUU--U--------------UCCUAGUGGAAAGUCUUGCGUGUGUCGAUAAUCCCGCUGAACUGAGCGAUUUCUC
AY013245.2/61987-62105  ----GAUGGCAGUGACGACUUGGUAAUAUU-CAAGCUCAACAGACCAAAUCACAGGUCUUCCUCUCUGGAUCCAC--UCCUCUGGGAUUGAUUUG--UAUGCCGAUUUUCCCGCUGAACCGAGCCAUC----
AY013245.2/57789-57907  ----GAUGGCAGUGACGACUUGGUAAUAUU-CAAGCUCAACAGACCAAAUCACAGGUCUU--UCUCUCUGGAUCCACUCCUCUGGGAUUGAUUUG--UAUGCCGAUUUUCCCGCUGAACCGAGCCAUC----
AJ489952.1/1-119        ----GAUGGCAGUGACGACUUGGUAAUAUU-CAAGCUCAACAGACCAAAUCACAGGUCUUCCUCUCUGGAUCUAC--UCCUCUGGGAUUGAUUUG--UAUGCCGAUUUUCCCGCUGAACCGAGCCAUC----
AJ307928.1/3-121        ----GAUGGCAGUGACGACCUGGUAAUAUU-CAAGCUCAACAGACCAAAUCACAGGUCUU--UCUCUCUGGAUCUACUCCUCAGGGAUUGAUUUG--UAUGCCGAUUUUUCCGCUGAACCGAGCCAUC----
AJ307662.1/4013-4128    ----GAUGGCAGUGACGACCUGGUAAUAUU-CAAGCUCAACAGACCAAAUCACAGGUCUU--UCUCUCUGGAUC---UACUCAGGGAUUGAUUUG--UAUGCCGAUUUUUCCGCUGAACCGAGCCAUC----
AC135465.23/41412-41522 ----GAUCACGAUGAUGACUCCAUAAAAUU-CAAGCUCAACAGACCGCAGUGCAGUGCUU--UCUU-CU--CU-----UUCGAGAGAUUGCUUUG-CGUGUC-GAUAACCCCGCUGAACUGAGUGAUC----
AJ489954.1/1-104        ------UGGCUGUGACGACUAGGUGAAAUU-CAAGCUCAACAGACCAAAUCACAGGUCUC--UCUCCAAGGCCUU-UGGAGAUGGGAUCUGUAUGCCGA-----GU--UUCCGCUC-----AGCCG------
AF318011.1/1-106        -------GGCAGUGAUGACUCGG--AAAUUUCAAGCUCAACAGACCGGAAUUAGGCGUUU--CUUCCAA----UU-UAUUGGUUGAGUCGUUUCUG-UGU--CGAUAACCCCGCUGAUCUGAGCC-------
#=GC SS_cons            ....<<<<<<____________________._____________________________.._____________..__________________.._________________________>>>>>>....
#=GC RF                 ....GAugGCaGUGAuGACUuGGUAAuAUU.CAAGCUCAACAGACCaaAuuacAGgucUU..UCUCuauggcuuu..uccuaugGGAUuGaUUUG..UaUGcCGAUaaUcCCGCUGAACuGAGCcaUC....
//
# STOCKHOLM 1.0

#=GF AC   RF00361
#=GF ID   snoZ119
#=GF DE   Small nucleolar RNA Z119
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   70.00
#=GF TC   77.20
#=GF NC   39.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Z119 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z119
#=GF SQ   6


AJ490487.1/1-97        UUUUGGAGAUGAUGAUUUGUAUCAGAGGCUGUUUCUGAGGACGGGCCAAUGGCUCUCCCAGUGCUGCAAA-GAACUGAUUUGCCGUUCUGAUCCAAAA
AJ490488.1/1-94        --UUGGAGAUGAUGAUUUAUAUCAGAGGCUGUUUCUGAGGAUGAGCCUUGAGCUCACCCAGUGCUGCAAAAGAACUGAUUUGCCGUUCUGAUCCAA--
AJ458935.1/1-97        UUUUGGAGAUGAUGAUUUGUAUCAGAGGCUGUUUCUGAGGACGGGCCAAUGGCUCUCCCAGUGCUGCAAA-GAACUGAUUUGCCGUUCUGAUCCAAAA
AP003537.3/57284-57187 UUUUGGAGAUGAUGAUUUAUAUCAGAGGCUGUUUCUGAGGAUGAGCCUUGAGCUCACCCAGUGCUGCAAAAGAACUGAUUUGCCGUUCUGAUCCAAUU
AK065940.1/429-526     UUUUGGAGAUGAUGAUUUAUAUCAGAGGCUGUUUCUGAGGAUGAGCCUUGAGCUCACCCAGUGCUGCAAAAGAACUGAUUUGCCGUUCUGAUCCAAUU
AK065940.1/211-307     UUUUGGAGAUGAUGAUUUGUAUCAGAGGCUGUUUCUGAGGACGGGCCAAUGGCUCUCCCAGUGCUGCAAA-GAACUGAUUUGCCGUUCUGAUCCAAAA
#=GC SS_cons           ::(((((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<_____>>>>>,,,,,,,,,<<<<<________>>>>>,,,,,,,,)))))::
#=GC RF                UUuuGGaGAUGAUGAUUUaUAUCAGAGGCUGUUUCUGAGGAuGaGCCuuuaGCuCaCCCAGUGCUGCaaaAGAACUGAuuuGCCGUUCUGAuCCaaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00362
#=GF ID   Pospi_RY
#=GF DE   Pospiviroid RY motif stem loop
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14500815
#=GF SS   Published; PMID:14500815
#=GF GA   40.00
#=GF TC   42.50
#=GF NC   37.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   14500815
#=GF RT   Characterization of the RNA motif responsible for the specific interaction
#=GF RT   of potato spindle tuber viroid RNA (PSTVd) and the tomato protein Virp1.
#=GF RA   Gozmanova M, Denti MA, Minkov IN, Tsagris M, Tabler M
#=GF RL   Nucleic Acids Res 2003;31:5534-5543.
#=GF CC   This family consists of several Pospiviroid sequences which are related to
#=GF CC   the potato spindle tuber viroid (PSTVd) RY motif stem-loop. The RY motif
#=GF CC   (5'-ACAGG and CUCUUCC-5') in PSTVd, is thought to bind with the tomato
#=GF CC   protein Virp1. The exact function of this motif and the significance of
#=GF CC   Virp1 binding is unknown. It is however thought that RY motifs are
#=GF CC   essential for establishing a viroid infection [1].
#=GF WK   Pospiviroid_RY_motif_stem_loop
#=GF SQ   16


AF458995.1/144-222 GGCC-GACAGGAGUAAUUCCCGCCGAAACAGGGUUUUCACCCUUCCUUUCUUCGGGUGUCCUUCCUC-GCGCCCGCAGGAC
Y09886.1/145-223   GGCC-GACAGGAGUAAUUCCCGCCGAAACAGGGUUUUCACCCCUCCUUUCUUCGGGUGUCCUUCCUC-GCGCCCGCAGGAC
Z34272.1/136-214   GGCC-GACAGGAGUAAUUCCCGCCGAAACAGGGUUUUCACCCUUCCUUUCUUCGGGUGUCCUUCCUC-GCGCCCGCAGGUC
AY492077.1/144-222 GGCC-GACAGGAGUAAUUCCUGCCGAAACAGGGUUUUCACCCUUCCUUUCUUCAGGUGUCCUUCCUC-GCGCCCGCAGGAC
AY492080.1/145-223 GGCC-GACAGGAGUAAUUCCUGCCGAAACAGGGUUUUCACCCUUCCUUUCUUCGGGUGUCCUUCCUC-GCGCCCGCAGGAC
X15663.1/149-228   GUUCAGACAGGAGUAAUCCCAGCUGAAACAGGGUUUUCACCCUUCCUUUCUUCUGGUUUCCUUCCUCUGCUUCAGC-GGCC
U51895.1/143-221   GGCC-GACAGGAGUAAUUCCUGCUGAAACAGGGUUUUCACCCUUCCUUUCUUCAGGUUUCCUUCCUC-GCGCCCGCAGGAU
Y09887.1/145-223   GGCC-GACAGGAGUAAUUCCCGCCGAAACAGGGUUUUCACCCUCCCUUUCUUCGGGUGUCCUUCCUC-GCGCCCGCAGGAC
AY492083.2/145-223 AGCC-GACAGGAGUAAUUCCCGCCGAAACAGGGUUUUCACCCUUCCUUUCUUCGGGUGUCCUUCCUC-GCGCCCGCAGGAC
AF536193.1/30-108  GGCC-GACAGGAGUAAUUCCCGCCGAAACAGGGUUUUCACCCUUCCUUUCUUCGGGUUUCCUUCCUC-GCGCCCGCAGGAC
AY493559.1/145-223 GGCC-GACAGGAGUAAUUCCCGCCGAAACGGGGUUUUCACCCUUCCUUUCUUCGGGUGUCCUUCCUC-GCGCCCGCAGGAC
X95293.1/144-221   UUGA-GACAGGUGUAA-CCCAGCUGAAACAGGGUUUUCACCCUUCCUUUCUUCUGGUUUCCAUCCUC-UCGCCGGAAGGUC
AY492076.1/144-222 GGCC-GACAGGAGUAAUUCCUGCUGAAACAGGGUUUUCACCCUUCCUUUCUUCGGGUGUCCUUCCUC-GCGCCCGCAGGAC
K00818.1/146-224   UUGA-GACAGGAGUAAUCCCAGCUGAAACAGGGUUUUCACCCUUCCUUUCUUCUGGUUUCCUUCCUC-UCGCCGGAAGGUC
X17268.1/143-221   GGCC-GACAGGAGUAAUUCCUGCUGAAACAGGGUUUUCACCCUUCCUUUCUUCGGGUUUCCUUCCUC-GCGCCCGCAGGAU
AY492079.1/144-222 GGCC-GACAGGAGUAAUUCCCGCCGAAACAGGGUUUUCACCCUUCCUUUCUUCAGGUGUCCUUCCUC-GCGCCCGCAGGAC
#=GC SS_cons       <<<<.<<-<<<<------<<<<--<<<<-<<<<<____>>>>>--->>>>-->>>>-->>>>--->>.>->>>::::::::
#=GC RF            ggcc.GaCaGGaGUAAUuCCcGCuGaaaCaGGGuUUUCaCCCuUCCuuuCUUCgGGUguCCuUCCuC.gCgcccGcAGGaC
//
# STOCKHOLM 1.0

#=GF AC   RF00363
#=GF ID   mir-BART1
#=GF DE   mir-BART1 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15118162
#=GF SS   Published; PMID:15118162
#=GF GA   85.00
#=GF TC   92.20
#=GF NC   42.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF CL   CL00097
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   15118162
#=GF RT   Identification of Virus-Encoded MicroRNAs.
#=GF RA   Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright
#=GF RA   AJ, Marks D, Sander C, Tuschl T
#=GF RL   Science 2004;304:734-736.
#=GF CC   This family represents the mir-BART1 microRNA precursor found in Human
#=GF CC   herpesvirus 4 (Epstein-Barr virus) and Cercopithicine herpesvirus 15.
#=GF CC   mir-BART1 is found in all stages of infection but expression is
#=GF CC   significantly elevated in the lytic stage. In Epstein-Barr virus mir-BART1
#=GF CC   is found in the intronic regions of the BART (Bam HI-A region rightward
#=GF CC   transcript) gene whose function is unknown. The mature sequence is excised
#=GF CC   from the 5' arm of the hairpin [1].
#=GF WK   mir-BART1_microRNA_precursor_family
#=GF SQ   5


M80517.1/151635-151704   GGGGGUCUUAGUGGAAGUGACGUGCUGUGAAUACAGGUCCAUAGCACCGCUAUCCACUAUGUCUCGCCCG
AJ507799.2/139346-139415 GGGGGUCUUAGUGGAAGUGACGUGCUGUGAAUACAGGUCCAUAGCACCGCUAUCCACUAUGUCUCGCCCG
AY037858.1/133690-133759 GUGGGUUUUAGUGGAAGUGACGUGCUGUGAUUAGGUACCCAUAGCACCGCUAUCCACUAUGUCUCACCAG
DQ279927.1/140174-140243 GGGGGUCUUAGUGGAAGUGACGUGCUGUGAAUACAGGUCCAUAGCACCGCUAUCCACUAUGUCUCGCCCG
AY961628.3/139265-139334 GGGGGUCUUAGUGGAAGUGACGUGCUGUGAAUACAGGUCCAUAGCACCGCUAUCCACUAUGUCUCGCCCG
#=GC SS_cons             ::<<<---<<<<<<<<<<<--<<<<<<<<-<<____>>->>>>>>>>>>>>->>>>>>>--->>>:::::
#=GC RF                  GgGgGUcUUAGUGGAAGuGACGUGCUgUGAauAcAgguCCAuAGCACCgCUAUCCACUAUGUCuCgCCcG
//
# STOCKHOLM 1.0

#=GF AC   RF00364
#=GF ID   mir-BART2
#=GF DE   mir-BART2 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15118162
#=GF SS   Published; PMID:15118162
#=GF GA   60.00
#=GF TC   62.80
#=GF NC   38.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   15118162
#=GF RT   Identification of Virus-Encoded MicroRNAs.
#=GF RA   Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright
#=GF RA   AJ, Marks D, Sander C, Tuschl T
#=GF RL   Science 2004;304:734-736.
#=GF CC   This family represents the mir-BART2 microRNA precursor found in Human
#=GF CC   herpesvirus 4 (Epstein-Barr virus) and Cercopithicine herpesvirus 15.
#=GF CC   mir-BART2 is expressed in all stages of infection but expression is
#=GF CC   significantly elevated in the lytic stage. In Epstein-Barr virus mir-BART2
#=GF CC   is found in the intronic regions of the BART (Bam HI-A region rightward
#=GF CC   transcript) gene whose function is unknown. mir-BART2 is thought to target
#=GF CC   the virally encoded polymerase BALF5 for degradation. The mature sequence
#=GF CC   is excised from the 5' arm of the hairpin [1].
#=GF WK   mir-BART2_microRNA_precursor_family
#=GF SQ   8


L06830.1/499-438         UUUAAAAAAUUUAUUCGCCCUUGCGUGUCCAUUGUUGCAAGGAGCGAUUUGGAGAAAAUAAA
AJ507799.2/152745-152806 ACUAUUUUCUGCAUUCGCCCUUGCGUGUCCAUUGUUGCAAGGAGCGAUUUGGAGAAAAUAAA
L06834.1/497-438         --AAAUAUUUUUAUUCGCCCUUGCGUGUCCAUUGUUGCAAGGAGCGAUUUGGAGAAAAUAAA
L06836.1/496-438         --AAAUUUUU-UAUUCGCCCUUGCGUGUCCAUUGUUGCAAGGAGCGAUUUGGAGAAAAUAAA
L06828.1/499-438         AAUUAAAUUUUUAUUCGCCCUUGCGUGUCCAUUGUUGCAAGGAGCGAUUUGGAGAAAAUAAA
L06831.1/499-438         UUUUAAAUUUUUAUUCGCCCUUGCGUGUCCAUUGUUGCAAGGAGCGAUUUGGAGAAAAUAAA
L06835.1/497-438         --AUAUUUUUUUAUUCGCCCUUGCGUGUCCAUUGUUGCAAGGAGCGAUUUGGAGAAAAUAAA
L06829.1/499-438         ACUUUUUUUUUUAUUCGCCCUUGCGUGUCCAUUGUUGCAAGGAGCGAUUUGGAGAAAAUAAA
#=GC SS_cons             ::<<<<<<<<-<<-<<<<<<<<<<<__________>>>>>>>->>>>-->>->>>>>>>>::
#=GC RF                  auuaauuuuUUuAUUCGCCCUUGCGUGUCCAUUGUUGCAAGGAGCGAUUUgGAgaaaauaAA
//
# STOCKHOLM 1.0

#=GF AC   RF00365
#=GF ID   mir-BHRF1-1
#=GF DE   mir-BHRF1-1 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15118162
#=GF SS   Published; PMID:15118162
#=GF GA   70.00
#=GF TC   74.80
#=GF NC   37.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   15118162
#=GF RT   Identification of Virus-Encoded MicroRNAs.
#=GF RA   Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright
#=GF RA   AJ, Marks D, Sander C, Tuschl T
#=GF RL   Science 2004;304:734-736.
#=GF CC   This family represents the mir-BHRF1-1 microRNA precursor found in Human
#=GF CC   herpesvirus 4 (Epstein-Barr virus) and Cercopithicine herpesvirus 15. In
#=GF CC   Epstein-Barr virus mir-BHRF1-1 is found in the 5' UTR of the BHRF1 (Bam HI
#=GF CC   fragment H rightward open reading frame 1) gene which is known to encode a
#=GF CC   distant Bcl-2 homologue. The mature sequence is excised from the 5' arm of
#=GF CC   the hairpin [1].
#=GF WK   mir-BHRF1-1_microRNA_precursor_family
#=GF SQ   5



AF200364.1/20287-20352 UAUUAACCUCUCCUGGCACCCGAGUUGACAGUUUUGCC-CCAACCCGGUUCCAGCAGAGGUUAGCAA
K03329.1/1798-1863     UAUUAACCUGAUCAG-CCCCGGAGUUGCCUGUUUCAUCACUAACCCCGGGCCUGAAGAGGUUGACAA
AY037858.1/35320-35385 UAUUAACCUGAUCAG-CCCCGGGGUUGCCUGUCUUAGCACUAACUCCGGGCCUGAAGAGGUUGACAA
M17293.1/957-1022      UAUUAACCUGAUCAG-CCCCGGAGUUGCCUGUUUCAUCACUAACCCCGGGCCUGAAGAGGUUGACAA
V01555.2/53759-53824   UAUUAACCUGAUCAG-CCCCGGAGUUGCCUGUUUCAUCACUAACCCCGGGCCUGAAGAGGUUGACAA
#=GC SS_cons           ::<<<<<<<--<<<<.-<<<<<-<<<<--<<______>>->>>>->>>>>->>>>-->>>>>>>:::
#=GC RF                UAuuAACCUgauCaG.CccCgGAGUUgcCUGUUUuAuCACcAACCCcGggCCuGaAGAGGUUgaCAA
//
# STOCKHOLM 1.0

#=GF AC   RF00366
#=GF ID   mir-BHRF1-2
#=GF DE   mir-BHRF1-2 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15118162
#=GF SS   Published; PMID:15118162
#=GF GA   80.00
#=GF TC   82.40
#=GF NC   51.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   15118162
#=GF RT   Identification of Virus-Encoded MicroRNAs.
#=GF RA   Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright
#=GF RA   AJ, Marks D, Sander C, Tuschl T
#=GF RL   Science 2004;304:734-736.
#=GF CC   This family represents the mir-BHRF1-2 microRNA precursor found in human
#=GF CC   herpesvirus 4 (Epstein-Barr virus), cercopithicine herpesvirus 15 and
#=GF CC   herpesvirus papio. In Epstein-Barr virus mir-BHRF1-2 is found in the 3'
#=GF CC   UTR of the BHRF1 (Bam HI fragment H rightward open reading frame 1) gene
#=GF CC   which is known to encode a distant Bcl-2 homologue. The mature sequence is
#=GF CC   excised from the 3' arm of the hairpin [1].
#=GF WK   mir-BHRF1-2_microRNA_precursor_family
#=GF SQ   5


AJ507799.2/42848-42912 CUUUUAAAUUCUGUUGCAGCAGAUAGCUGAUACCCAAUGUUAUCUUUUGCGGCAGAAAUUGAAAG
AF231984.1/771-835     CUUCCAAAUUCUGCCGCAGCAGAUAGCUGAUACUCCGUGUUAUCUUUUGCGGCAGGAUUUUAAAG
AY037858.1/36669-36733 CUUUUAAAUUCUGCCACAGAAGAUAGCUGAUACUCGAUGUUAUCUUUUGCGGGGGAAUUUCCAAG
AF231983.1/56-120      CUUUUAAAUUUUGCCGUAGCAGAUAGUUGAUACUUAAUGCUAUCUUUUGCGGUGAAAUUUGAAAG
DQ279927.1/42964-43028 CUUUUAAAUUCUGUUGCAGCAGAUAGCUGAUACCCAAUGUUAUCUUUUGCGGCAGAAAUUGAAAG
#=GC SS_cons           <<<<<<<-<<<<<<<<<<<-<<<<<<<___________>>>>>>>->>>>>>>>>>>->>>>>>>
#=GC RF                CUUucAAAUuCugccGCAGcAGAUAgCUGAUACuCaAUGuUAUCUUUUGCggcaGaAuUUgaAAG
//
# STOCKHOLM 1.0

#=GF AC   RF00367
#=GF ID   mir-BHRF1-3
#=GF DE   mir-BHRF1-3 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15118162
#=GF SS   Published; PMID:15118162
#=GF GA   80.00
#=GF TC   93.70
#=GF NC   35.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   15118162
#=GF RT   Identification of Virus-Encoded MicroRNAs.
#=GF RA   Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright
#=GF RA   AJ, Marks D, Sander C, Tuschl T
#=GF RL   Science 2004;304:734-736.
#=GF CC   This family represents the mir-BHRF1-3 microRNA precursor found in Human
#=GF CC   herpesvirus 4 (Epstein-Barr virus). In Epstein-Barr virus mir-BHRF1-3 is
#=GF CC   found in the 3' UTR of the BHRF1 (Bam HI fragment H rightward open reading
#=GF CC   frame 1) gene which is known to encode a distant Bcl-2 homologue. The
#=GF CC   mature sequence is excised from the 5' arm of the hairpin [1].
#=GF WK   mir-BHRF1-3_microRNA_precursor_family
#=GF SQ   4


V01555.2/55254-55318 UCUAACGGGAAGUGUGUAAGCACACACGUAAUUUGCAAGCGGUGCUUCACGCUCUUCGUUAAAAU
M17416.1/1451-1515   UCUAACGGGAAGUGUGUAAGCACACACGUAAUUUGCAAGCGGUGCUUCACGCUCUUCGUUAAAAU
M11923.1/401-465     UCUAACGGGAAGUGUGUAAGCACACACGUAAUUUGCAAGCGGUGCUUCACGCUCUUCGUUAAAAU
M80517.1/55254-55318 UCUAACGGGAAGUGUGUAAGCACACACGUAAUUUGCAAGCGGUGCUUCACGCUCUUCGUUAAAAU
#=GC SS_cons         ::<<<<<<<-<<<<<<-<<<<<<---<<<_________>>>>>>>>>>>>>>>->>>>>>>::::
#=GC RF              UCUAACGggAAGuGUGUAAGCACACACGuAAUUUGCAAgCGGUGCUUCACgCUCuuCGUUAAAAU
//
# STOCKHOLM 1.0

#=GF AC   RF00368
#=GF ID   sroB
#=GF DE   sroB RNA
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Storz, G; LocARNA; Infernal
#=GF SS   Predicted; LocARNA
#=GF GA   44.00
#=GF TC   44.80
#=GF NC   43.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   14602901
#=GF RT   RNomics in Escherichia coli detects new sRNA species and indicates
#=GF RT   parallel transcriptional output in bacteria.
#=GF RA   Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A,
#=GF RA   Wagner EG
#=GF RL   Nucleic Acids Res 2003;31:6435-6443.
#=GF RN   [2]
#=GF RM   19682266
#=GF RT   Switching off small RNA regulation with trap-mRNA.
#=GF RA   Overgaard M, Johansen J, MÃ¸ller-Jensen J, Valentin-Hansen P
#=GF RL   Mol Microbiol 2009;73:790-800.
#=GF WK   sroB_RNA
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   16


U00096.2/506428-506511       ACA---CCGUCGCU-UAAAGUGACGGCAUAAUAAUAAAAAAAUGAAA--UUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU
BAAY01013502.1/811-892       ACA---CCGAUGCU-UUAAGCAUUGGGAUCAUAAU--AAUGAUGAAA--UUCCUCUUUGACGGGCCAAUAGAAAUAUUGGCCAUUUUUUU
CP000880.1/2358967-2358886   AGA---UCCGAAGCGAAAGCGUCGGG-AUAAUAAU--AACGAUGAAA--UUCCUCUUUGACGGGCCAAUAGCGAUAUUGGCCAUUUUUUU
CP000822.1/2470165-2470084   UAA---CCAGGGCG-CUACGUCCUGGCAUAAUAAU--AACGAUGAAA--UUCCUCUUUGACGGGCCAAUAGAAAUAUUGGCCAUUUUUUU
CP000783.1/2728614-2728530   CAA---CCGUCCGCUAAGGCGCACGGCAUAACGAC--AAUAACGAAAAGUUCCUCUUUGACGGGCCAGUAGCGAUACUGGCCUUCUUUUU
CP000826.1/1266711-1266787   -------ACAGGGUUACAAUGCGU-AUAACUACA---AUACAAGAAA--UUCCUCUUUGACUGGCCAGUAGCGAUAUUGGCCACUUUUUU
AM942759.1/2356448-2356369   UAA---GAGGGCGGAGUGAUGACUCUCUUGUAUA---AUGA--AAAA--UUCCUCUUUGACUGGCCGAUAGCAAUAUCGGCUUUUUUUUA
CU468135.1/2762296-2762217   CGG---CUAAAUGCAGGAACGAUAACUAAAAUCAU--AAUGAUG-----UCCUUAUUUGACGGGUCGAUAGCAAUAUCGGCCCUUUUUUU
CP000964.1/4251888-4251807   CGA---UCCGGGAUGCAAAUCCCGGG-AUAAUAAU--AAUGAUGAAA--UUCCUCUUUGACGGGCCAAUAGCAAUAUUGGCCAUUUUUUU
CP000720.1/3409810-3409729   CCG---CAAGGAAUGUGAGUGCUUAAUAACUAAA---AUAAUGAAAA--UUCCUCUUUGACUGGCCGGUAGUGAUAUCGGCCAUUUUUUA
AM286415.1/3329579-3329500   GUA---AGGAGUGU--GAGAGCUAAAUAACUAAA---AUAAUGAAAA--UUCCUCUUUGACUAGCCGAUAGCGAUAUCGGCUAUUUUUUU
AALE02000006.1/213519-213600 ---CCGCAAGGAAUAUGAGAGCUUAAUAACUAAA---AUAAUGAAAA--UUCCUCUUUGACUGGCCGAUAGCGAUAUCGGCCAUUUUUUU
AALD02000001.1/65988-65910   ------CAAGGAGUGAGAGCGCUUAAUAACUAAA---AUAAUGAAAA--UUCCUCUUUGACUGGCCGAUAGCGAUAUCGGCCAUUUUUUU
AALC02000044.1/32691-32612   GCA---AGGAGUGU--GGGCGCUAACUAACUAAA---AUAAUGAAAA--UUCCUCUUUGACUGGCCGAUAGUGAUAUCGGCCAUUUUUUU
ABWL02000008.1/254866-254785 ACA---CCGAUGCA-UUAAGCGUCGGCAUAAUAAU--AAUGAUGAAA--UUCCUCUUUGACGGGCCAAUAGAAAUAUUGGCCAUUUUUUU
ABWM02000018.1/15892-15971   CAA---CCGAAGGU---CUCCUUCGGCAUAAUAAA--AACGAUGAAA--UUCCUCUUUGACGGGCCAAUAGAGAUAUUGGCCAUUUUUUU
#=GC SS_cons                 :::...:::<<<<<____>>>>>,,,,,,,<<___.._>>-------..------------<<<<<<<<<____>>>>>>>>>:::::::
#=GC RF                      aaA...cagggcgcauaAgcgccuaguAuauuaAu..AaaaaugAAA..UUCCUCUUUGACuGGCCgaUAGcgAUAucGGCCaUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00369
#=GF ID   sroC
#=GF DE   sroC RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14602901
#=GF SS   Predicted; PFOLD
#=GF GA   45.00
#=GF TC   46.90
#=GF NC   44.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0000498; base pairing with RNA;
#=GF DR   GO; 0043487; regulation of RNA stability;
#=GF RN   [1]
#=GF RM   14602901
#=GF RT   RNomics in Escherichia coli detects new sRNA species and indicates
#=GF RT   parallel transcriptional output in bacteria.
#=GF RA   Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A,
#=GF RA   Wagner EG
#=GF RL   Nucleic Acids Res 2003;31:6435-6443.
#=GF RN   [2]
#=GF RM   25630703
#=GF RT   Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge
#=GF RT   of the  GcvB small RNA.
#=GF RA   Miyakoshi M, Chao Y, Vogel J
#=GF RL   EMBO J. 2015;34:1478-1492.
#=GF CC   This family consists of a number of bacterial sroC RNA genes of around 160
#=GF CC   bases in length. sroC is found in several Enterobacterial species [1]. It
#=GF CC   base-pairs with GcvB. This interaction triggers the degradation of GcvB by
#=GF CC   RNase E, alleviating the GcvB-mediated mRNA repression of other amino
#=GF CC   acid-related transport and metabolic genes [2].
#=GF WK   sroC_RNA
#=GF SQ   6


AL627267.1/186594-186434   ACUAACUAAAACUAAAUGGGACGGGA-CUCCUGUCCUCUCGAUUGUCGC-UCAGCACGGACAGACUAUAAGCCUGAUGGUCGUUCCCCAUCGGGCCUGAAA-CCGCAGAUCGCCGGGCAACAAUCUUCGAGGGUAGCGCUGCUACCCUUUUUUUUCGGAGUAGA
U10981.1/183-345           ACUAAUUACAAGAACCAGGGGCGGAAAUUCCAGCCCUCUCGAUUGUUAC-GUAGCACGGACAGACUAUACGCCUGAUGGUCGUUCCCCAUCGGGCCUGAAAACCGCAAUACGCUGGGUAACAAUCUUCGAGGGUAGCAGUUAACGCUGCUACCCUCUUUUUUCU
CP000653.1/1296938-1296786 ACUAAUUAGAACCAUAG-GGGCGGGAUCUCCUGCCCUCUCGAUUGUCGG-GAAGCGUGGACAGACUAUACGCUGAGUGGUCGUUCCCCACUCAGCGCGAAA-----AUUGAGCUUCUCACCAAUCUUCGAGGGUAGCGCUGCUACCCUUUUUUUUC----UGGA
AACY022982399.1/683-842    ACUAACUAAAAUA--AAUGGGAGGCU-UCCCCUCCCUCUCGAUUGCUAC-UCGGCACGGACAGACUAUAAGCCUGAUGGUCGUUCCCCAUCAGGCCUGAAAACCGCAAAACGCCGAAUAACAAUCUUCGAGGGUAGCGCUGCUACCCUUUUUUUUCUGGAGUAG
CP000647.1/770129-769968   ACUAAUUAUAACAACCAGGGGCGGGAUAUCCUGCCCUCCCGAUGAUUGUCACAGCACGGACAGACUAUACGGCGGCUGGUCGUUCCCCAGCCGCCGCGAAUACCGAAACAAGCUGGACAACCGUCUUCGAGGGUAGCACUGGCUACCCUUUUUUUUCCAG--GA
AM933173.1/719229-719069   ACUAACUAAAACUAAAUGGGACGGGA-CUCCUGUCCUCUCGAUUGUCGC-UCAGCACGGACAGACUAUAAGCCUGAUGGUCGUUCCCCAUCGGGCCUGAAG-CCGCAAAUCGCCGGGCAACAAUCUUCGAGGGUAGCGCUGCUACCCUUUUUUUUCGGAGUAGA
#=GC SS_cons               :::::::::::(((,,,,<<<<<<_____>>->>>><<<<<<<<<<-<<.------<<<-<<<-------<<<<<<<<<_______>>>>>>>>>>>>---->>>----------->>->>>>>--->>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,))):
#=GC RF                    ACUAAuUAaAAccaaaagGGGcGGgAuuUCCugCCCuCuCGauuGuugc.ucAGCACGGACagACUAUAaGccgGgUGGUCGUUCCCCAcCcggCcuGAAaACCGcAaaacGCuGggcAaCaauCUUCGaGgGUAGCgcUgcuacCcuUUUUUUUcuuagugga
//
# STOCKHOLM 1.0

#=GF AC   RF00370
#=GF ID   sroD
#=GF DE   sroD RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14602901
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   51.40
#=GF NC   44.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   14602901
#=GF RT   RNomics in Escherichia coli detects new sRNA species and indicates
#=GF RT   parallel transcriptional output in bacteria.
#=GF RA   Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A,
#=GF RA   Wagner EG
#=GF RL   Nucleic Acids Res 2003;31:6435-6443.
#=GF CC   This family consists of a number of bacterial sroD RNA genes of around 90
#=GF CC   bases in length. sroD is found in several Enterobacterial species but its
#=GF CC   function is unknown [1].
#=GF WK   sroD_RNA
#=GF SQ   5


X07055.1/58-143              UUACGUGACGAAGCGCGCGGCAAAGUGGACAAUAAAGCCUGAGCGUUAAGUCAGU---CGUC---AGACGCCGGUUAAUCCGGCGUUUUUUU
L02649.1/1951-2034           UUACGUGACGAAGCGC--GGCAAAGUGGACAAUAAAGCCUGAGCGUUAAGUCAGU---CGUC---AGACGCCGGUUAAUCCGGCGUUUUUUU
ABEJ01000013.1/114065-113977 CUGCGUGACGAAGCCCGUGGCAAAGUAGACAAUAAAGCCUGAGCGUUAAGUCAGCUAACGAG---AGACGCCGGUUAAGCCGGCGUUUUUUU
CP000653.1/2564343-2564255   UUACGUGACGAAGCGCGCGCCAAAGUGGACAAUAAAGCCUAAGCUUCGAGUAAGU---CGCCAUGAGACGCCGGUUUAGCCGGCGUUUUUUA
CP000647.1/2543344-2543259   CUGCGUGACGAAGCGCGCGCUAAAGUGGACAAUAAAGGCUAAGUAACGAAUGAGU---CGCC---UGACGCCGGCUACGCCGGCGUUUUUUA
#=GC SS_cons                 ::::::::::::::<<<-<<<_______________>>>----------------...>>->...-<<<<<<<<_____>>>>>>>>:::::
#=GC RF                      uUaCGUGACGAAGCgCGcGgcAAAGUGGACAAUAAAgcCUgAGcguuaAGUcAGU...CGuc...AgaCGCCGGUUAAgCCGGCGuuUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00371
#=GF ID   sroE
#=GF DE   sroE RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14602901
#=GF SS   Predicted; PFOLD
#=GF GA   51.00
#=GF TC   52.10
#=GF NC   49.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   14602901
#=GF RT   RNomics in Escherichia coli detects new sRNA species and indicates
#=GF RT   parallel transcriptional output in bacteria.
#=GF RA   Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A,
#=GF RA   Wagner EG
#=GF RL   Nucleic Acids Res 2003;31:6435-6443.
#=GF CC   This family consists of a number of bacterial sroE RNA genes of around 90
#=GF CC   bases in length. sroE is found in several Enterobacterial species but its
#=GF CC   function is unknown [1].
#=GF WK   sroE_RNA
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   4


M11843.1/93-184            AUAACGUGAUGGGAAGCGCCUCGCUUCCCGUGUAUGAUUGAACCCGCAUGGCUCCCGAAACAUUGAGGGAAGCGUUGAGGGUUCAUUUUUAU
AACY020347183.1/418-327    AUAACGUGAUGGGAAGCGGCGUGCUUCCCGUGUAUGAUUGAACCCGCAUGGCUCCCGUAUCGCUCGGGGAAGCGCUGAGGGUUCAUUUUUAU
CP000647.1/3122897-3122822 AUAACGUGUUGGGAAGCGAUACGCUUCCCGUGUAUGAUUGAACCUG-------CGGGCGCGAGGCGCCG---------GGGUUCAUUUUUGU
FM200053.1/390269-390360   AGAACGUGAUGGGAAGCGGCGCGCUUCCCGUGUAUGAUUGAACCCGCAUGGCUCCCGGUUCGUUCGGGGAAGCGCUGAGGGUUCAUUUUUAU
#=GC SS_cons               :::::::::<<<<<<<<<___>>>>>>>>>--------<<<<<<<--------<<<__________>>>--------->>>>>>>:::::::
#=GC RF                    AuAACGUGauGGGaaGCGacaCGCuuCCCgUGUAUGAUuGaaCCcGCAUGGCUCccGuaucauucgggGAAGCGcUGAgGGuuCaUUUUUaU
//
# STOCKHOLM 1.0

#=GF AC   RF00372
#=GF ID   sroH
#=GF DE   sroH RNA
#=GF AU   Barquist L; 0000-0003-4732-2667
#=GF SE   PMID:14602901, INFERNAL
#=GF SS   Predicted; Barquist L
#=GF GA   80.00
#=GF TC   88.70
#=GF NC   72.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   14602901
#=GF RT   RNomics in Escherichia coli detects new sRNA species and indicates
#=GF RT   parallel transcriptional output in bacteria.
#=GF RA   Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jager JG, Huttenhofer A,
#=GF RA   Wagner EG
#=GF RL   Nucleic Acids Res 2003;31:6435-6443.
#=GF CC   This family consists of a number of bacterial sroH RNA genes of around 160
#=GF CC   bases in length. The function of this family is unknown [1].
#=GF WK   sroH_RNA
#=GF SQ   2


U00096.2/4188510-4188350   GAAAAUAAGAACACAUGUUCUCAUCUUCCAGGAUGCAGCAGACUGAAGAAAUUCAGACAUCCCGCAACCUGCGAUUAUCGCAAGGUCAAGGCAAAGUCCGGUAAUGGCGUUCUGAAUACCAGAGAUAAUUCUCUGGCGAAACCCACCUUAAGGUGGGUUUU
AAJV02000038.1/11464-11616 AUACACAUGCGGUCAUGAUAAUGCAGUUAAGGAUGCAGCAGACUGAUU-AAUCCAGACAUCCCGCUACAAGCGUA---CGC-UGGUC-AGGCCUGGUCCGGUAAAGGUGCUCUGAAUACCAGAGAUAUU--UCUGGCGAAACCCACCUCAAGGUGGGUUUU
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<<<____>>>>>>::::
#=GC RF                    aaAaAuAaGaagaCAUGuUauuauauUuaAGGAUGCAGCAGACUGAauAAAUuCAGACAUCCCGCaACauGCGauUAUCGCAaGGUCAAGGCaaaGUCCGGUAAuGGuGuUCUGAAUACCAGAGAUAaUUCUCUGGCGAAACCCACCUuAAGGUGGGUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00373
#=GF ID   RNaseP_arch
#=GF DE   Archaeal RNase P
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Brown JW, The Ribonuclease P Database, PMID:9847214
#=GF SS   Published; PMID:9847214
#=GF GA   84.00
#=GF TC   84.20
#=GF NC   83.80
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00002
#=GF DR   URL; http://jwbrown.mbio.ncsu.edu/RNaseP/home.html;
#=GF DR   SO; 0000386; RNase_P_RNA;
#=GF DR   GO; 0008033; tRNA processing;
#=GF DR   GO; 0004526; ribonuclease P activity;
#=GF DR   GO; 0030681; multimeric ribonuclease P complex;
#=GF RN   [1]
#=GF RM   9759486
#=GF RT   Ribonuclease P: unity and diversity in a tRNA processing ribozyme.
#=GF RA   Frank DN, Pace NR
#=GF RL   Annu Rev Biochem 1998;67:153-180.
#=GF RN   [2]
#=GF RM   9847214
#=GF RT   The Ribonuclease P Database.
#=GF RA   Brown JW
#=GF RL   Nucleic Acids Res 1999;27:314.
#=GF CC   Ribonuclease P (RNase P) is a ubiquitous endoribonuclease, found in
#=GF CC   archaea, bacteria and eukarya as well as chloroplasts and mitochondria.
#=GF CC   Its best characterised activity is the generation of mature 5'-ends of
#=GF CC   tRNAs by cleaving the 5'-leader elements of precursor-tRNAs. Cellular
#=GF CC   RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its
#=GF CC   catalytic activity in the absence of the protein subunit, i.e. it is a
#=GF CC   ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown
#=GF CC   to retain its catalytic function, but is still essential for the catalytic
#=GF CC   activity of the holoenzyme. Although the archaeal and eukaryotic
#=GF CC   holoenzymes have a much greater protein content than the bacterial ones,
#=GF CC   the RNA cores from all the three lineages are homologous -- helices
#=GF CC   corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular
#=GF CC   RNase P RNAs. Yet, there is considerable sequence variation, particularly
#=GF CC   among the eukaryotic RNAs.
#=GF WK   Ribonuclease_P
#=GF SQ   70


AF192349.1/1-262           ---------------------------------------------------------------------------------------GAGGAAAGUCCCGCCUCCAGAUCA---AGGGAAGUCCC-GCGA--GGGAC-AAGGG-UAGUACCCUU--GG-CAA-CUGC-ACAGAAAACU-UACCC--CUAAAUAUUC-AAU--GAGGAU-------UUGAUUCGAC---------------------------------------------------------------------------------------------------------------------UCU--UACCUUG--GCGA--CAAGGUA------AGAUAGAUGAAGAG--------------------------------------------------------AAUAUU-U-AG--GGGUUGAAAC--GCAG----UCCUUCCC--GGAGCAAGU--AGG----------GGGGUC---AAUGAGAA-UGAUCUGAA------------------------------------------------GAC-CUC--CCUUG--ACGCAUAGUCGAAUCCCCCA----------------------------------------------------------AA--UACAGAAGCGGGCUUA--------------------
AF192350.1/1-267           ---------------------------------------------------------------------------------------GAGGAAAGUCCCGCCUCCUGGCCU---AAAGGAGUCUC-UAUA--GAGAC-AAGGGCAACA-CCCUU--GG-CAA-CUAU-ACAGAAACAAGUACCU--UGAAAGCUA--CAU--GUGAAAA------UGAUUGUGCC---------------------------------------------------------------------------------------------------------------------CCU--UCCUCUG--GUAA--CGGAGGA------AGAAACAUGAGAGU---------------------------------------------------------AGCUU-U-CA--AGGAUGAAAAG-AUAG----ACCUCCUA--GGAGCAAGU--AGA----------GGGAAA---GAUGAGAC-UAGGCCCGA------------------------------------------------UUU-CCC-UCUAGG--ACGCAUAGCCAAAUCCCCCA-------------------------------------------------------ACCAU--UACAAAAGCGGGCUUA--------------------
AF192362.1/1-260           ---------------------------------------------------------------------------------------GAGGAAAGUCCAGCCUCCAACCCUU--ACAAGAACCCC-GUAA--GGGGU-AGGGA-UAGAAUCCCU--GG-CUA-CUAC-ACAGAAACGA--AGCC--CUAAUACUA--GAUA-GAUGAU-------UGG----------------------------------------------------------------------------------------------------------------------------ACCU-ACUAGCAA-GUAA-UUGCUAGU---------AGUACGAUAAU---------------------------------------------------GAUGAAAGUAU-U-AG--GGCUUGAAACG-GUAG----ACCUCUUG--GGAGCAAGU--UGA----------AGGGG----GAUGAGCA-AAGGGUUGA-------------------------------------------------CU-CCU-UAUAGU--ACGCUUAGUCGAAUCCCCUC----------------------------------------------------------AG--UACAAAAGCUGGCUUA--------------------
AF192363.1/1-259           ---------------------------------------------------------------------------------------GAGGAAACUGCAGCCUCCAACCCUU--ACAAGAACCCC-GUAA--GGGGU-AGGGA-UAGAAUCCCU--GG-CUA-CUAC-ACAGAAACGA--AGCC--CUAAUACUA--GAUA-GAUGAU-------UGG----------------------------------------------------------------------------------------------------------------------------ACC--UACUAGCAAGUAAUUGCUAGUA--------GUACAUGAUAGA-----------------------------------------------------UGAAAGUAU-U-AG--GACUUGAAACG-GUAG----ACCUCUUG--GGAGCAAGU--UGA----------AGGGG----GAUGAGCA-AAGGGUUAG-------------------------------------------------CU-CCA--UAUGU--ACGCUUAGUCGAAUCCCCUC----------------------------------------------------------AG--UACAAAAGCUGGCUUA--------------------
L13597.1/422-736           UAGGGGAGCCUAACAGGGGGUUA-CGGGA----------------------------------------AUA-----------UCCUGAGGAAACUCCAGCCUCCAAGCCUC--AUGGGAGCAGU-UAGA--UCUGC-AGGGU-UAGU-GCUCU--GG-CUA-CUGC-ACAGAAACGU-AACCGGUAUAAUAGGA--UAU--GAAAAUGAGUUU-AUA----------------------------------------------------------------------------------------------------------------------------UGU--AGUCUAG--GUAA--CUAGGCU---------ACAUAAAUGAG--------------------------------------------------------ACCUAU-U-AUACCGGCUGAAACG-GCAG----UCCUCCCA--GGAGCAAGU--AAG----------GAGGG----GAUGAGUU-GAGGUUCAA-------------------------------------------------CC-CUC-CUAAGG--ACGCUUAGUAGAAUCCCCCU---------------------------------------------------------AAA--UACAAAAGCUGGGUUAUUGU-UAGGCUCCC-CUUAU
AF121773.1/1-303           UAGGGGAGCCUAACAGGGGGCCA-CGG------------------------------------------GAAA------------CUGGGGAAACUCCAGCCUC-UCGCCCA--GGGGGAGUCCC-GCGA--GGGAC-GGGGU-UAGGUGCUCC--GA-CAA-CUGC-ACAGAAACGA-GACCU--GCGGUGGG---CCA--GAUGAAAAUGAU-CAU----------------------------------------------------------------------------------------------------------------------------UUACCCCAUCUG--GCGA--CGGAUGG------GAGGGUGUGAGAGA---------------------------------------------------------CCUAU-C-GU--GGGUUGAAACG-GCAG----AUCUCCCC-UUGAGCAAGU---AG----------GGGAG----GAU--AGG-GCAAAAUGA-------------------------------------------------CU-CCC--CUGAU--ACGCAGAGCCUAAUCCCCCA----------------------------------------------------------AG--UACAGAAGCUGGGUUAUUGU-UAGGCUCCC-----C
AJ248283.1/174477-174806   UUGGCGAGGGGGCUGGGGGCUGU-CGGGC----------------------------------------UCGU----------ACCCGAGGAAGUUCCGCCCACCGCACCGGG-GCCGCGGUGCC-GCAA--GGCAC-CUCCC-GAGA-GGGAG--GG-CAA-CGGC-ACAGAAACGA-CACGU--CCCUCGGGG--GAU--GUGGAUGAAAGCGGUG----------------------------------------------------------------------------------------------------------------------------AAG--GCUCCCG--GCGA--CGGGAGC--------CGAGCUAACCCG-------------------------------------------------CAGACAAUCCCGA-G-GGGAUCGGUGAAACG-GCCG----UCCCGCGG--GGUGCAAGGCCGAGUUA-------GGGCC----GAUGAGUUCCCGGUGUGA-------------------------------------------------GG-CCC-GUGGUAGGCCGCUUAGUCGAAUGCCCCC---------------------------------------------------------GUA-GUACAGAAGGCGGGCUA-UAG-CCCCCUCGC---CCA
BA000001.2/168172-168500   UAGGCGAGGGGGCUGGGGGCCCU-CGGGG----------------------------------------UGC-----------UCCCGAGGAAGUUCCGCCCACCGCACCGGG-GCCGCGGUGCC-GCAA--GGCAC-CUCCC-GAGA-GGGAG--GG-CAA-CGGC-ACAGAAACGA-CACGC--CCCUCGGGG--GAU--GUGGAUGAAAG--CGGUG--------------------------------------------------------------------------------------------------------------------------AAG--GCUCCUG--GUGA--CGGGGGC-----------CGAGUUAAC----------------------------------------------CCGCAGACGAUCCCGA-G-GGGAUCGGUGAAACG-GCCG----UCCCGCGG--GGUGCAAGGCCGAGUUA-------GGGCC----GAUGAGUUCCCGGUGUGA-------------------------------------------------GG-CCC-GUGGUAGGCCGCUUAGUCGAAUGCCCCC---------------------------------------------------------GUA-GUACAGAAGGCGGGCUA-UAG-CCCCCUCGC---CUA
AF192358.1/1-331           UAGGCGAGGGGGCUGGGGGCUGC-CGGGCU---------------------------------------UUAU----------GCCCGAGGAAGUUCCGCCCACCGCACCGGG-GCCGCGGUGCC-GUAA--GGCAC-CUCCC-GAGA-GGGAG--GG-CAA-CGGC-GCAGAAACGA-CACGU--CCUCCGAGG--GAU--GGGAAUGAAAGCGGUG----------------------------------------------------------------------------------------------------------------------------AAG--GGGGCUG--GUGA--CAGCUCC--------CGAGCUAACCCG-------------------------------------------------CAGACGACCUCGG-G-GGGAUCGGUGAAACG-GCCG----UCCCGCGG--GGUGCAAGGCCGAAAGA-------GGGAC----GAUGAGUUCCCGGUGUGA-------------------------------------------------GU-CCC-GUGGUUGGCCGCUUAGUCGAAUGCUCCC--------------------------------------------------------UUAA--UACAGAAGGCGGGCUA-UAG-CCCCCUCGC---CUA
AF192364.1/1-331           UAGGCGAGGGGGCUGGGGGCUGU-CGGGC----------------------------------------UCGU----------ACCCGAGGAAGUUCCGCCCACCGCACCGGG-GCCGCGGUGCC-GCAA--GGCAC-CUCCC-GAGA-GGGAG--GG-CAA-CGGC-ACAGAAACGA-CACGU--CCCUCGGGG--GAU--GUGGAUGAAAG--CGGAG--------------------------------------------------------------------------------------------------------------------------AAG--GCUCCUG--GCGA--CAGGAGC-----------CGAGCUAAC----------------------------------------------CCGCAGACAAUCCCGA-G-GGGAGCGGUGAAACG-GCCG----UCCCGCGG--GGUGCAAGGCCGAGUUA-------GGGCC----AAUGAGUUCCCGGUGUGA-------------------------------------------------GG-CCC-GUGGUAGGCCGCUUAGUCGAAUGCCCCC---------------------------------------------------------GCAGGUACAGAAGGCGGGCUA-UAG-CCCCCUCGC---CUA
U42988.1/1-279             ---------------------------------------------------------------------------------------GAGGAAAGUCCAGCCACCGCACCGGG-GCCGCGGUGCC-GCAA--GGCAC-CUCCC-GAGA-GGGAG--GG-CAA-CGGC-GCAGAAACGA-CACGU--CCCGGCGGA--UAU--GGGGAUGAAAG--CGGUG--------------------------------------------------------------------------------------------------------------------------AAG--GGCCCCG--GCGA--CGGUGCC-----------CGAGAUAAC----------------------------------------------CCGCAGACGACCCGUC-G-GGGACCGGUGAAACG-GCCG----UCCCGCGG--GGUGCAAGGCCGAGGAA-------GGGGC----GAUGAGUUCCCGGUGGGA-------------------------------------------------GU-CCC-GUGUUAGGCCGCUCAGUCGAAUGUCCCC--------------------------------------------------------UUGA--UACAGAAGGGGGCUUA--------------------
AF192365.1/1-317           -------GGGGGCU-GGGGCCCU-CGGGUA---------------------------------------UUUG----------ACCCGAGGAAGUUCCGCCCACCGCACCGGG-GCCGCGGUGCC-GCAA--GGCAC-CUCCC-GGAA-GGGAG--GG-CAA-CGGC-GCAGAAACGA-CACGU--CCCUCGGGA--AAU--GUGGAUGAAAGCGGUG----------------------------------------------------------------------------------------------------------------------------AAG--GCUCCCG--GCGA--CGGGAGCUGAGUUAACCCGCAGACAAU---------------------------------------------------------CCCGA-G-GGGAGCGGUGAAACG-GCCG----UCCCGCGG--GGUGCAAGGCCGAGAUA-------GGGGC----UAUGAGUUCCCGGUGUGA-------------------------------------------------GC-CCC-GUGGUAGGCCGCUCAGUCGAAUGCCCCA--------------------------------------------------------UUAA--UACAGAAGGCGGGCUA-UAG-CCCCCU---------
U42986.1/1-293             ------AGCCGAAGGGCAGCUGA-CGGUCCC--------------------------------------UCAA--------GGGGCUGAGGAAACUCCACCCAUCAUACAGA--ACCGUGGUGCC-GUGA--GGCAU-CAGCU-GAGA-GGCUG--GA-CCC-UGGA-GCAGAAACGA-CACGU--CUCCUGAUG--GAU--GAUAAU--------------------------------------------------------------------------------------------------------------------------------------GAA--GCUUCAC--CCUC--AAGGAGC-------------AGACUGA--------------------------------------------------------CACCAG-G-AGGACCGGUGAAACG-GCCA----UUCCACGG--GAUGCAAGGACAAAUG--------CUGCC----GGUGAUUA--CUGUAGGA-------------------------------------------------GG-CAG--AGGUAGUCCGCCCAGAUGAAUGCUGCC----------------------------------------------------------GA--AACAGAAGGUGGGUUA--CUCUCGGCA---------
AF295979.1/1-293           ------AGCCGAAGGGCAGCUGA-CGGUCCC--------------------------------------UCAA--------GGGGCUGAGGAAACUCCACCCAUCAUACAGA--ACCGUGGUGCC-GUGA--GGCAU-CAGCU-GAGA-GGCUG--GA-CCC-UGGA-GCAAAAACGA-CACGU--UUCCUGAUG--GAU--GAUAAU--------------------------------------------------------------------------------------------------------------------------------------GAA--GCUUCAC--CCUC--AAGGAGC-------------AGACUGA--------------------------------------------------------CAUCAG-G-AGGACCGGUGAAACG-GUCA----UUCCACGG--GAUGCAAGGACAAAUG--------CUGCC----GGUGAUUA--CUGUAGGA-------------------------------------------------GG-UAG--AGGUAGUUCGCCCAGAUGAAUGCUGCC----------------------------------------------------------GA--AACAGAAGGUGGGUUA--CUCUCGGCA---------
AF192356.1/9-302           ------AGCCGAAGGGCAGCUGA-CGGCCCAU-------------------------------------UUUU---------GGGCUGAGGAAACUCCACCCAUCAUACAGA--ACCGCGGUGCC-GUGA--GGCAU-CAGCU-GAGA-GGCUG--GA-CCC-UGGA-GCAGAAACGA-CACGU--CUUCUGGUG--GAU--GAUAAUGAA----GCU----------------------------------------------------------------------------------------------------------------------------UCA------CCC--UUAA--AGGA--------------GCAGACUGA--------------------------------------------------------CACCAG-G-AGGACCGGUGAAACG-GCCA----UUCCGCGG--GAUGCAAGGACAAAUA--------CUGCC----UGUGAUUA--CUGUAGGA-------------------------------------------------GG-CAG--AGGUAGUCCGCCGAGAUGAAUGCUGCC----------------------------------------------------------GA--AACAGAAGGUGGGUUA--CUCUCGGCA---------
AF121774.1/9-309           ------AGCCGAAGGGCAGCUAC-CGGUUUCUAUAGAUUUAAUGUCUGUA-------------------GUUA----------AACUGAGGAAACUCCACCCAUCGUACAGA--ACCGUGAUGUC-CUAA--GACAU-CUGCU-GAGA-AGCAG--GA-CUC-UGGA-GCAGAAACGA-CACGU--CUUCUGGUG--GAU--GAACAU-------GAA----------------------------------------------------------------------------------------------------------------------------GAU------------CCG--------------------UCUGAUUGA--------------------------------------------------------CACCAG-G-AGGAACGGUGAAACG-GCCA----AUCCACGG--GAUGCAAGGGUAAACA--------CUGCC----AGUGAAUC--CUGUAUGA-------------------------------------------------GG-CAG--AGGUAACUCGCAUAGAUGAAUGCUGCC---------------------------------------------------------ACC--AACAGAAGGUGGGUUA--CUCUCGGCA---------
U42987.1/1-244             ---------------------------------------------------------------------------------------GAGGAAAGUCCAGCCAUCACCCUAA--ACCCCGGUGCC-GCAA--GGCAU-CGGCC-GAGA-GGCCG--GA-CCC-UGGC-GCAGAAACGA-CACGU--CUCCCGAUG--GAU--GAUAAU--------------------------------------------------------------------------------------------------------------------------------------GAG----GCCCCAAUUAA-AGGGGU---------------UGAUUGA--------------------------------------------------------CAUCGG-G-AGGAUCGGUGAAACG-GCCA----AUCCGGGG--GAUGCAAGGGUGAAAAU-------CUGCC----AAUGAUAU--------GA-------------------------------------------------GG-CAG--AGAUUGCCCGCUUAGAUGAAUGCUGCC----------------------------------------------------------UA--AACAGAAGGUGGCUUA--------------------
AL445066.1/122037-121735   CGGGAAAGCGCGAGGGCAGCUGA-CGCCC----------------------------------------UUG-----------AGGUGAGGAAAGUCCCCCCUCCUCGGCGG--UAUCCGGCUGGCGCAA-GCCAGC-AUCCU-GAGA-GGGAU--GG-UAA-AGGC-AAAAGAAAUA-AACGG--UCUCCGGUA--AAG--CAUGAU-------UCC----------------------------------------------------------------------------------------------------------------------------GAA-------------GG--------------------GAUGACGUU---------------------------------------------------------UCCGG-A-GGAUCCGAUGGAAA--GCCU----CCCCGGAU--GGAGAAAGUCUAAACG--------GAUCC----UGUGAGGC--CGCCGUGA-------------------------------------------------GG-AUC--GGGUAAGACGAACAGUCGAAUGCUGCC-----------------------------------------------AGCCCAUUGGGUG--AACAGAAGGGGGCUUA--CUCCGCGGAUUCCCGCCA
BA000011.4/537155-537457   UGAGAAAGCACGAGGGCAACUGA-CGCC-----------------------------------------GUAA-----------GGUGAGGAAAGUCCCCCCUCCUCGGCAG--GGCCCAGUUGGCGCAA-GCCAGU-GUUCC-GAGA-GGAAU--GG-UAA-AGGC-AAAAGAAAUC-AACGG--UUCCCAGUA--AAG--GAUGAA-------CUC----------------------------------------------------------------------------------------------------------------------------GAA-------------GG--------------------GGAGACGUU---------------------------------------------------------UCUGG-G-AGAUCCGAUGGGAA--GCCU----UCCUGGGU--GGAGAAAGUCUAAAAU--------GGCCC----UGUGAAGC--UGCCGUUA-------------------------------------------------GG-GCC--GGGUGAGACGACUAGUCGAAUGUUGCC----------------------------------------------AGCCCGAAAGGGUG--AACAGAAGGGGGCUUA--CUCCGUGGAUUCUCAUCU
U42984.1/3-369             UGCGAGAGAGGCUGGACGGCUGA-CGGGCC---------------------------------------UUCG---------GGUCUGAGGAAAGUCUCCCCACCGCUCCGGAUACACGAACAUCUGUAAAGGAUGU-CGGGC-GAGA-GCCCG--GG-CCC-UGGC-ACAGAAACGAUAACCA--UCCUCUGAA--AAUGCGAUGAU-------GCG----------------------------------------------------------------------------------------------------------------------------GAA-----------------------------------GCUGAGAUC---------------------------------------------------------UCAGG-G-UAAAUGGAUGAAACG-GCGA---ACCCUCGUG--GGUGCAAGU--UGG----------AAAUCGGG-GAGAAGAG-AAUUCCGGA--------------------------------------CUCUCCCGGUUGU-UUU--UGGAA--ACGCAUAGCCGAAUGCCGUC-ACUGCAAGAGUCCUCAGGACCAUUUCCUCCACUGAUGGGUGAUAGGAAAUCUUUGCAGG--AACAGAAGGGAGCUUA--CGUGCCUCACUCGCAUAA
U42983.1/1-375             ---GGCAGAGGGAGCCCGGCUGCCCGUGCC---------------------------------------GUGA---------GGCAUGAGGAAAGUCCCCCCACCCGUUCGGGCACGCGGCCGGACACAC-GUCCGG-GGCGG-GAGA-CCGCC--GG-CAC-UGGA-ACAGACACGA-CACGU--CCCUCCCAC--ACC--GAUGAG-------GCGCGC-------------------------------------------------------------------------------------------------------------------------GAC--CCACCCC--GAAA--GGGACGG---------CAGUUAACCCG----CCGAGGGCGUGGCCGCCACACCGGCGGCCACGGACCGGUGAUCGACACCCCAAUGGGA-G-GGGAGCGAUGGAACG-GCCA---ACCCCCGCC--GGUGCAAGUCC-------------ACGCGCG--CAUGGUAG-CCCGAACCA-------------------------------------CCCGAAAGGGGCCG-CGU-------GGACGCUCAGCCGAAUGCCGGG---------------------------------------------------------CCG--AACAGAAGGGGGCUUA--CUCCCCUCAGCU--CGUA
M61003.1/281-714           ---GGCAGAGAGAGCCCAGUUCC-CGUGCCC--------------------------------------GAGA-------CGGGCAUGAGGAAAGUCCCCCCACCGUCCGAAC-GGGUGACCGGGCGCAA-GCCCGG-AGUCG-GAGA-CGGCU--GG-CGC-UGGA-ACAGAAACGA-GACCG--CUCGACCCG--ACC--GAUGAU-------GCGCGCGCGACGGCUCCGCCGUCGCCGGCGCGGCCGUCACGGCCGCGUGC-----------------------------------------------------------------------------GAA--CCGACCC--GUAA--GGGAAGG---------GAGCUAACCCG--------------------------CAGAGGGAUGAGGUGGCGUCGCCAUCUCCGACGGUC-G-AGAACGGAUGGAACG-GCGA---AUCCUCACC--GGUGCAAGUCC-------------GCGCC----GCGAAGGG-UAGUUCGGACGGCGCGUCGGGUUCGCCCGUCGCGCCCUCGGGGGGCUCGCCCCGAGAAGGACGC-------GGACGCUGAGCCGAAUGCUGGG---------------------------------------------------------ACG--AACAGAAGGGGGCUUA--CUCCUCUCAGCC--GCUU
U42982.1/1-358             ---GGCAGAGAGAGCCCGGCCAC-CGCGGCGUGCCAGCAGCACGCAGCU--------------------GCCAGCGGGCACGCACGCGAGGAAAGUCCCCCCACCGCCGGGC--AGGUGACCGGG-GAAA-CCCCGG-GACGG-GAGA-CCGUC--GG-CGC-UGGA-ACAGCAACGA-GACCG--CUCCCCCGC--GAGUGGAUGAC-------GUGGCGC------------------------------------------------------------------------------------------------------------------------GAA--CCGACCC--GCGA--GGGAAGG---------GAGCUAACCCA---------------------------------------------CAGAACGCAGACCGGGG-G-AGAACGGAUGGAACG-GCGA---ACCCUCACC--GGUGCAAGUCC-------------ACGCCACGCGGCGCGAG-CCGCACGGU---------------------------------------AGCCCGGCAGGGACGU-------GGACGCUCAGCCGAAUGCCGGG---------------------------------------------------------ACG--AACAGAAGGGGGCUUA--CUCCUCUCAGCC------
U42981.1/1-475             ---GGCAGAGAGAGCCCGGCCAC-CGCGGCGUACCGACAGGCACACACGU-------------------GCCAGCGGGUACGCACGCGAGGAAAGUCCCCCCACCGCCGGGC--AGGUGACCGGG-GAAA-CCCCGG-GACGG-GAGA-CCGUC--GG-CGC-UGGA-ACAGCAACGA-GACCC--CUCCACCCG--ACC--GAUGA--------GGCGCGGGCGGUGGCAUCGCCACCGUCUCGGCGCGAGCGGCACGGGGUGCAUCGUGCGCCCCGAAGCGAGCGGGCACCGCCCG--------------------------------------------CGA--CGCAGCC--GCGA--GCGUGCG---------AACCCGACGCA-----AAACGGCCACUGGUCGGACAAAGCAACGGGGAGCUAACCCGCCGAGGGAUGAGGGUG-G-AGAACGGAUGGAACG-GCGA---AUCCUCACC--GGUGCAAGUCC-------------ACGCCAC--GCGGAUCG-GCCGCACGG--------------------------------------UAGCCCGGCAGGGACGU-------GGACGCUCAGCCGAAUGCCGGG---------------------------------------------------------GCG--AACAGAAGGGGGCUUA--CUCCUCUCAGCC--AUGU
U42980.1/1-474             ---GGGAGAGAGAGCCCGGCUGC-CGCGGGCGUCGU---------------------------------GCGA-------CGCGCGCGAGGAAAGUCCCCCCACCUGUUCGGGCAGGUGACCAGACGCAA-GUCCGG-GGCGG-GAGA-CCGCU--GG-CUC-UGGA-ACAGAAACGA-CACGU--CUCGGCCCG--ACC--GAUGA--------UGCGUGCGAACCCGACCGCGAGGAAGGGGAGUUGACCCGCAGAGGGAGUGUGGUCGGUAUCCCGUGGUUCGAAUCCACGGAUUGCGAGCGCGGUUCGACGCGUCUCUGACGCGGGACCCGCGACCGAGUG--CGACGGC--ACGA--GCCGUCG---------AACACGCACGG-------------------------------------CGCGAUUGACCACACUGAGACGGCC-G-AGGAGCGAUGGAACG-GCGA---ACCCUCACC--GGUGCAAGUCC-------------GUGCCG---UGGUAGCC-CGAACAUCU-------------------------------CGCGGCUCCGCCGCGAACGG-CGC-------GGACGCUUAGCCGAAUGCUGGG---------------------------------------------------------ACG--AACAGAAGGGGGCUUA--CUCCUCUCACCC--GUUU
AF192355.1/6-239           ------AGGGGGCUGGUGACUAU--CCAA------------------------------------------------------UUGGGAGGAAGCUCCGCCCACCCAUUAU----GUGCA-------ACA--------AUCCC-GAGA-GGGAUU-GA-AUG-GGGC-AUAGAAACGA-CACGG--CCUUAAAACA-GAU--GACGAUG------AUA----------------------------------------------------------------------------------------------------------------------------UCC-----------GAAA--------------------AUUGAGGAG---------------------------------------------------------UUUUA-A-GGAAUCGGUGAAACG-GCCC--CAUUCUGCAC-GGGUGCAAGC--------------------------------------AUUA----------------------------------------------------------------GCGUUUAGCUGAAUGUCGCC---------------------------------------------------------GAAAUUACAGAAGGCGGGCUA-UAG-CCCCCA---------
AF192354.1/6-238           ------AGGGGGCUGGUGACUAU-CC-------------------------------------------ACUG-------------GGAGGAAGCUCUGCCCACC----CAA--UUGUGU-------AGA--------UUUCCUGAGAAGGAAU--GA-AUA-GGGU-AUAGAAACGA-CACGG--UUCUAAGAAA-UAU--GACUAUGAU----AUU----------------------------------------------------------------------------------------------------------------------------UUC------------AAA--------------------AUUGAGGAU---------------------------------------------------------UCUUA-G-AAAAUCGAUGAAACG-ACCU-UAUUUUACACG--GGUGCAAGCAU------------------------------------------------------------------------------------------------------AUGUGCUAAGCUGAAUGUCACC---------------------------------------------------------GAAAUUACAGAAGGCAGGCUA-UAG-CCCCCA---------
AF192357.1/6-239           ------AGGGGGCUGGUGACUAU----CC----------------------------------------AACU----------GG--GAGGAAGCUCUGCCCACU----CAA--UUACGU-------AGA--------UUUCCUGAGAAGGAAU--AA-ACA-AAGU-AUAGAAACGA-CACGG--UUCCAAAAAA-UAU--GACUAUG------AUA----------------------------------------------------------------------------------------------------------------------------UUU-----------UAAA--------------------AUUGAGGAU---------------------------------------------------------UUUUG-G-AAAAUCGAUGAAACG-ACUU-UGUUUUGCGUG--AGUGCAAGCAU---------------------------------------U--------------------------------------------------------------AUGCGCUAAGCUGAAUGUCACC---------------------------------------------------------GAAAUUACAGAAGGCAGGCUA-UAG-CCCCCA---------
AP006878.1/1601575-1601254 ---GCGAGGGGGUCGGGGGCUCU-CGGGG----------------------------------------UAC-----------UCCCGAGGAAGUUCCGCCCACCGCACCGGG-GCCGCGGUGCC-GCAA--GGCAC-CGGCC-GAGA-GGCCG--GG-CAA-CGGC-GCAGAAACGA-CACGG--CCCCCCGGA--UAU--GGGGAUGAAAG--CGG----------------------------------------------------------------------------------------------------------------------------UGAA-GGGCCCG--GCGA--CGGUGCC-----------CGAGCUAAC----------------------------------------------CCGCAGACGACCCGGG-G-GGAUGCGGUGAAACG-GCCG----UCCCGCGG--GGUGCAAGGCCGAGGGA-------GGGGC----GAUGAGUUCCCGGUGUGA-------------------------------------------------GC-CCC-GUGGUAGGCCGCUCAGUCGAAUGCCCCC---------------------------------------------------------UUG-AUACAGAAGGCGGGCUA-CGG-CCCCCUCGC------
AE017261.1/818125-818417   ---AAAAGCCCGAGGGCAACCGA-CGCCG----------------------------------------CAA-----------AGGUGAGGAAAGUCCCCCCUCCUGGAUGG--AAUGCGUCCGUCGAAA-GGCGGA-GUCCC-GAGA-GGGAU--GG-UAA-AGAG-AAAAGAAAUA-AACGG--UCCGGGUAA--AAG--CAUGAU-------UCG----------------------------------------------------------------------------------------------------------------------------AAA--------------A--------------------GAUGACGU----------------------------------------------------------UCCCC-G-GCAGCCGAUGAGAA--CUCU----CCCCGCAU--GGAGCAAGUCUAAGAU--------GGGCC----CGUGAACA-CCAUCCCGA-------------------------------------------------GG-CCC--AGGUAAGACGCAUAGUCGAAUGUUGCC-----------------------------------------------AGCCUUAAAGGUG--AACAGAAGGGGGCUUA--CUCCGGGCAUUU------
BA000002.3/445647-445322   ---CGGCGCCGGCCGGCGGCCCA-CGGCCCCCCA-----------------------------------GCCA------GGGGGGCUGAGGAAACUCCGCCCUCCCCGCGGC--GGCCGGGCCCC-GCAA--GGGGC-ACGGGUGAAA-CCCGU--GG-CAA-CGGC-ACAGAAACGA-CACGG--CCCCGGGGC--GUGUCGAGGAC-------GCGGCUA------------------------------------------------------------------------------------------------------------------------GGC--CGCCCUG--GCAA--CAGGGCG-----------GCAGCAAAC-----------------------------------------------CGCAGAGGAACCCCG-G-GGAUGCGGUGAAACG-GCCG----CCCCCGGC--GGAGCAAGGCC-CC----------CGGGC----GGUGAGGG-CCGCGCGAA-------------------------------------------------GC-CCG-GGGGGAGACCGCUUAGCCCAAUGCCGCC---------------------------------------------------------GAA-GUACAGAAGGCGGGUUA-UGG-CCGGCGCCG------
BA000023.2/326017-326320   ---GGGAGCCCUAGAUUGGGCUA-CGG------------------------------------------GUUG------------CUGAGGAAACACCGGCCUCCAGGUCCC--AGGGAGACCCC-GUUA-AGGGGU-AGGGG-UAGCACCCCU--AG-CAA-CUAC-ACAGAAACGA-GACUG--GCAUGAUAGCAGAU--GAAGAUGAU----UUG----------------------------------------------------------------------------------------------------------------------------AUG--GUAACCCAAGUAAUUGGGUUAC--------CUAAAUGAGAGC---------------------------------------------------------UAUCA-U-GC--CAGUUGAAACG-GUAG----UCUCUCCU--GGAGCAAGU--GGG----------GAAAA----GAUGAGAA-GGGACCCGA-------------------------------------------------UU-UUC-CCCGAG--ACGCUAAGUCAAAUCCCAAA----------------------------------------------------------AA--UACAGAAGCCGGGUUAUGCU-AGGGCUCCC------
CP000099.1/1976649-1976349 ---GAGAGAGGCUGGACGGCUGA-CGGGCC---------------------------------------UUUG---------GGUCUGAGGAAAGUCUCCCCACCGCUCCGGAUACACGAACAUCUGUAAAGGAUGU-CGGGC-GAGA-GCCCG--GG-CCC-UGGC-ACAGAAACGAGAACCA--UCCCCUGAA--AAUGCGAUGAU-------GCG----------------------------------------------------------------------------------------------------------------------------GAA-----------------------------------GCUGAGGUC---------------------------------------------------------UCAGG-G-AAAAUGGAUGAAACG-GCGA---AUCCUCGUG--GGUGCAAGU--UGG----------AAAUCGGG-AAGAAGAG-AAUUCCGGA--------------------------------------CUCUCCCGGUUGU-CUU--UGAAA--ACGCAUAGCCGAAUGCCGUC---------------------------------------------------------ACU--GCAAGAGUCAUCAUGA-CCA---UUUUCUC-----C
AADL01001374.1/1146-855    ---AAAAGCCCGAGGGCAACUGA-CGCC-----------------------------------------GAAA-----------GGUGAGGAAAGUCCCCCCUCCACAGCUG--GCUGCAACCGGUGAAA-GCCGGU-AUGCC-GAGA-GGCAU--GG-UUA-AGAG-ACAAGAAAUA-AACGG--UUCCAUGUG--AAG--GAUGAU-------UUG----------------------------------------------------------------------------------------------------------------------------AAA--------------A--------------------AAUGACGUU---------------------------------------------------------UCAUG-G-AGUGCUGAUGAGAA--CUCU----CCCUGCAG--GGAGCAAGUCUAAAUU--------GAAUC----GUUGACUA-CAGCUGCUA-------------------------------------------------GA-UUC--AGGUAAGACGCAUAGUCGAAUGUUGCC------------------------------------------------AACCGAAAGGCU--AACAGAAGGAGGCUUA--CUCCGGGCAUUU------
AF192352.1/6-318           ---GCAAGCCGAAGGGCAGCUAC-CGGUUUCUAUAGAUUUAAUGUCUGUA-------------------GUUA----------AACUGAGGAAACUCCACCCAUCAUGCAGA--GCCGUGGUGCC-GU----AGCAU-CAGCU-GAGA-GGCUG--GA-CCC-UGGA-GCAGAAACGA-CACGU--CUCCUGGUG--GAU--GAUAAUGAA----GCU----------------------------------------------------------------------------------------------------------------------------UCA------CCC--UCAA--GGA---------------GCAGACUGA--------------------------------------------------------CAUCAG-G-AGGACCGGUGAAACG-GCCA----UUCCACGG--GAUGCAAGGACAAAUG--------CUGCC----UGUGAUUA--CUGUAGGA-------------------------------------------------GG-CAG--AGGUAGUCCGCCCAGAUGAAUGCUGCC-----------------------------------------------------------G--AACAGAAGGUGGGUUA--CUCUCGGCAUGC------
AADL01001899.1/2026-1711   ---GAAAGCUCGAGGGCAGCUUA-CGCUCC---------------------------------------AGUG----------GAGUGAGGAAAGUCUCCCCUCCUGGGUGG--GUAUCAGCCUG-CAAU-GCAGGU-AUUCC-GAGA-GGAAU--GG-CAA-CGAC-AAAAGAAAGA-AACAU--UUCCAGGUA--AAG--AAUGAU-------UCC----------------------------------------------------------------------------------------------------------------------------CUG-------------AG--------------------GAUGACAUU---------------------------------------------------------UCCUG-G-AUCGAUGAUGGAACA-GUCG----ACCUGAUU--GGAGAAAGUCCAAA----------GAGACCC--CGUGAGAC-CACUCUGAG-----------------------------GGUCGGGUAGGACGCAGCGUGC-CUU-----AUGGCC--AUAGUCGAAUGCUGCC-------------------------------------------AGCCUGAUUUACAGGGG--AACAGAAGGGAGCUUA--CUCCGGGCAUUC------
CP000493.1/2947-3271       ---GGGCCCCGGCUGGCCGCUGA-CGGGCCG--------------------------------------UUCA---------GGCCCGAGGAAACUCCGCCCUCCCCGCGGC--ACCGGGGCCCC-GAGA-GGGGGC-GCGGGUAACA-CCCGC--GG-CAA-CGGC-ACAGAAACGG-CACGC--CCACCCGCGG-GAG--GACGAU-------GAGGCGGCGA---------------------------------------------------------------------------------------------------------------------GGG--CUCCCCG--GCGA--CGGGGAG-----------CCAGUAACC-----------------------------------------------CGCUGAGGACCCGGG-U-GGGUGCGUUGAAACG-GCCG----UCCCCCGG--GGAGCAAGG-CGGC----------GCGCC----GAUGAGGGCCGCGCGAUU-------------------------------------------------GG-CGC-GCCGGCGUCCGCUUAGUCGGAUGCGGCC---------------------------------------------------------GUAGGUACAGAAGGCGGGUUA-UAG-CCGGGGCCC------
DQ314494.1/27634-28030     ---GGCAGAGAGAGCUCAGCUCC-CGUGGUCGAUACAAUGGUGAAUGAUGUAUUGACACAUCAACUGCCGUAU------CGGCAAACGAGGAAAGUCCCCCCACCGUCUGGAC-AGGUGACCGAGCACAA-GCUUGG-AGUUG-GAGA-CAGCU--GG-CAC-UGGA-ACAGAAACGA-UACCA--CUCAGCCUG--ACC--AAUGAG-------ACGUGC-------------------------------------------------------------------------------------------------------------------------GAA--CCACCCC--GUAA--GGGACGG---------CAGUUAACCCG------UCGAGGGAGCGGCUAUGUGACGUGUCGAUAACGGAAUAAAACCGCAUUAGAUGGGU-G-AGAAUGGAUGGAACG-GCGA---AUCCUCACC--GGUGCAAGUCC-------------ACGCCAG--AAAGGUAG-UCCGGACAG-------------------------------------------------GG-CGU-------GGACGCUUAGCCGAAUGCUGAG---------------------------------------------------------UUG--AACAGAAGGGGGCUUA--CUCCUCUCAGCC------
AACY020432185.1/1212-1503  ---GGGAGUAGGAGGGUCGCUGA-CAGUGC---------------------------------------CAGA----------CACUGAGGAAAGUCCCCUCUCCAAGAUGC--AAGCGGUCCGGUGCAA-GCCGGA-GGUCC-GGGA-GGGUC--GG-CUC-UGCA-AUAGAAACGU-C-CCG--CGCCAGGCG--CAC--GAUGAU-------CCC----------------------------------------------------------------------------------------------------------------------------GAA-------------AG--------------------GGUGAGGUU---------------------------------------------------------UCCUG-A-CCG-CGGCUGGAACG-AGCA----ACCCCGCU--GGAGCAAGUCCAAGCA--------GGCCC----AUAGUGCA-UCGACA----------------------------------------------------GG-GCC--GGGUAGGAUGCAUAGUUGAAUGCGACC------------------------------------------------AGCUGAAAGGUG--AACAGAAAGGGGCUUA--CUCCCUACACCC------
CP000678.1/1099369-1099089 ---GCAAGUUAAAG-ACAGCUGU-UGGUU----------------------------------------UUUU----------AACUAAGGAAACUCCGCCCAUCGUUACAG--ACUAUGGCGUU-GAAA--AACGU-AUACU-GAGA-GGUAU--GA-CUC-UGGA-GCAGAAACGA-CACGU--CUUUUAAUG--GUU--GACUAUG------AUA----------------------------------------------------------------------------------------------------------------------------UUU--------------A--------------------AUUGAGGAC---------------------------------------------------------AUUGA-A-AGAAUCGGUGAAACG-GCCA----UUCCAUAG--GAUGCAAGAACAAAAA--------AUGCU----GAUGACUA--CUGUAAGA-------------------------------------------------GG-CAA--AAGUAGUUCGCUAAGAUGAAUGCUGU-----------------------------------------------------------UA--AACAGAAGGUGGGUUA--CUCUUAACAUGC------
AE010299.1/809829-809468   ---GAGAGAGGCUGGACGGUUGC-CGGACC---------------------------------------UACU---------GGUCUGAGGAAAGUCUCCCCACCGUUCCGGACACACGAACAUCUGUAAAGGAUGU-CGGGC-GAGA-GCCCG--GG-CUC-UGGC-ACAGAAACGAUAACCA--UCCCCUGGA--AAUGCGAUGAU-------GUC----------------------------------------------------------------------------------------------------------------------------AUA--------------A--------------------GCUGAGGUC---------------------------------------------------------ACAGG-G-AGAGUGGAUGAAACG-GCGA---AUCCUCGUG--GGUGCAAGU--UGG----------AAAUCG---GGAAAGCA-CGAGCAGUC---------------------------------UGGACUCAUCCCGGUUGU-UUU--UGGUA--ACGCUUAGCCGAAUGCCGUC-GAUGCAAGAGUCCCCAGGGACCGUUCCUCCCACUGAUGGGUGGCAGGAAUAUUUGCAUG--AACAGAAGGGAGCUUA--CGUGCCUCACUC------
AACY023684782.1/313-604    ---GGGAGCAGGAGGGUCGCUGA-CAGUGC---------------------------------------UAGA----------CACUGAGGAAAGUCCCCUCUCCAUGAUGC--AAGCGGUUCGGCGCAA-GCCGAG-GGCCC-GGGA-GGGUC--GG-CUC-UGCA-ACAGAAACGA--ACUG--UGCCGGGAG--CAC--GGUGAA-------CCC----------------------------------------------------------------------------------------------------------------------------GAA--------------A--------------------GGGGGAGGU--------------------------------------------------------UUCCCG-A--ACGCAGCUGGAACG-AGCA----ACCCCGCU--GGAGCAAGUCCAAGCA--------GGCCC----GUAUGGCA-UCGACA----------------------------------------------------GG-GCC--GGGUAGGAUGCAUAGUUGAAUGCGGCC------------------------------------------------AACCGAAAGGUG--AACAGAAAGGGGCUUA--CUCCCUGCACCC------
L77117.1/643504-643761     ---GUAAGGGGGCUGGUGACUUU-CCCCUCU--------------------------------------UUAA---------GAGGGGAGGAAGUUCCGCCCACCCCAUUUA--UGGGCAGC-------------GU-CCCCU-GAGA-AGGGGCGGG-AGA-UGCA-GCAGAAACGA-CACGG--CUCCGGAAGA-GAU--GACGAUG------AUA----------------------------------------------------------------------------------------------------------------------------GUG------------AAA--------------------GUUGAGGAC---------------------------------------------------------UUCCG-G-AGAACCGGUGAAACG-GGCAUCUCCCCUGCCCGGGGUGCAAGCCG------------------------------------GUUU--------------------------------------------------------------CGGCGCUUAGCCGAAUGUCACC---------------------------------------------------------GAAAUUACAGAAGGCGGGCUA-UAG-CCCCCAUAC------
CR936257.1/554292-554662   ---GGCAGAGGAAGCCCGGUCCC-CGUGGGCGCGCU---------------------------------UUGU------GCGCCCAUGAGGAAAGUCCCCCCACCCUCCGGGC-AGGUGACCGGACGCAA-GUCCGG-AGCGG-GAGA-CCGCU--GG-CAC-UGGA-ACAGAAACGA-GACCC--CUUCCGCCG--AGC--AAUGAG-------GCGUGC-------------------------------------------------------------------------------------------------------------------------GAC--CCGACCC--GCGA--GGGAAGG---------AAGCUAACCCGCCGAGCGCGCGUCGCCGUACGGCGACGCCCGGGCGAGCGGCAUCAGCCGCGAGCCGACGCGG-A-AGAAGGGAUGGAACG-GCGA---AUCCUCACC--GGUGCAAGCCC-------------GUCGCAA--CAUGGUAG-CCCGGAGAC-------------------------------------------------GC-GAC-------GGGCGCUCAGCCGAAUGCCGGG---------------------------------------------------------UCA-AAACAGAAGGGGGCUUA--CUCUCCUCAGCC------
CP000575.1/936394-936051   ---AGGGGCGGGUCAGCUGCUCA-CGCCCCCUACUCUAG------------------------------GAGA--------GGGGGUGAGGAAACUCCGCACACCCCGCGGC--UCCACGGCCCC-GAAA-CGGGGC-GCGGC-GAGUAGCCGC--GG-CUC-CGGC-ACAGAAACGA-CACGG--CCACCGCUCG-GAU--GGCGAU-------GAAGCGGUGA---------------------------------------------------------------------------------------------------------------------GGA--GCCCCCG--GCAA--CGGGGGC-----------UCAGCAACC-----------------------------------------------CGUUGAGGACGGCGG-U-GGAUGCGUUGAAACG-GCCG---GUCCCGUGG--GGUGCAAGGCCCCCCUAAUUAUUAGGGGG----GAUGAGGUGGCCGCGCAA-------------------------------------------------CC-CCCUGUUGGGGGCCGCAUAGUCUAAUGCAGCU----------------------------------------------------------UG--UACAGAAUGCGGGUUA-UGG-CCCGCCCCU------
CP000300.1/2570177-2569824 ---GAGAGAGGAAGGACGAUUGC-CGGGUA---------------------------------------UUUG----------ACCUGAGGAAAGUCUCCCCAUCAUCCAGAU-ACACGAACACCUGUGAAGGGUGU-CGGGU-GAGA-ACCCG--GG-CUC-UGGC-ACAGAAACGA-UACCA--CACCAUAUC--AAUGCUAUGAU-------ACC----------------------------------------------------------------------------------------------------------------------------GAA-------------AG--------------------GUUGAGGUC---------------------------------------------------------GUAUG-G-AACGUGGAUGGAACG-GCGA---AACCUCGUG--GAUGCAAGUUGGAG----------UAGGGA---UCAAGCAG-GUUUCUGGA---------------------------------------------CUGCCC-CGA-AUUUAUUAACGCAUAGCCGAAUAUCGUCAAUGCAAGUGUCCACAAGGACCAUUCCCAAAUCAGCCCUGCUGAUGGGAAGCUUUGCAUC--AACAGAAGGGAGCUUA--CUCUCCUCACUC------
AE008384.1/2201586-2201226 ---GAGAGAGGCUGGACGGCUGC-CGGACC---------------------------------------UUCA---------GGUCUGAGGAAAGUCUCCCCACCGCUCCGGACACACGAACAUCUGUAAAGGAUGU-CGGGC-GAGA-GCCCG--GG-CCC-UGGC-ACAGAAACGAUAACCA--UCCCCUGCA--AAUGCGAUGAU-------GCC----------------------------------------------------------------------------------------------------------------------------AUA--------------A--------------------GCUGAGGUC---------------------------------------------------------GCAGG-G-AGAGUGGAUGAAACG-GCGA---AUCCUCGUG--GGUGCAAGUUGGAA----------AUCGGGA--AGUACGAG-CAGUCCGGA---------------------------------------AUCGUCCCGGUU-GGU--UUUGGUAACGCUUAGCCGAAUGCCGUC-GCUGCAAGAGUCCUCAGGGACCGUUUCUUACACUGCUGGGUGCAAGAAAGCUUUGCAGU--AACAGAAGGGAGCUUA--CACGCCUCACUC------
AACY023355499.1/390-686    ---GGGAGUAGGAGGAUCGCUGA-CAGAGU---------------------------------------UCGA----------CUCUGAGGAAAGUCCCCUCUCCACAGUGC--AGACGGCUUAC-AGAA--GUAAG-AGAACAGAAAUGGUCA--GGUCAA-UGCA-GCAGAAACGA--ACGA--UGCAAGGUGUGUAC--AAUGAU-------GUU----------------------------------------------------------------------------------------------------------------------------GAA-------------AG--------------------ACGGAGAUU---------------------------------------------------------GCCUU-G-UGG-UCGAUGAGACG-AGCA----ACCCCGUU--GGAGCAAGUCCAAACA--------GUCCC----GCCGAAGCGGCACGCCGA-------------------------------------------------GG-GAC--AGGUAGGAUGCUAAGUUGAAUGCGGUC--------------------------------------------------ACCGAAAGGG--AACAGAAAGGGGCUUA--CUCCCUACUCCC------
AACY020193628.1/2120-1823  ---GGGAGCAGGAGGGUUGCUGA-CAGUGU---------------------------------------UCGA----------CACUGAGGAAAGUCCCCUCUCCAAGAUGC--GAGCGGCCUGGUUAAC-GCCAGG-GACCC-GGGA-GGGUC--GG-CUC-UGGA-ACAGAAACGA--ACCG--UGUGGCGAGUUAAC--GGUGAA-------UCC----------------------------------------------------------------------------------------------------------------------------CGA--------------A--------------------GGAGGAGGU--------------------------------------------------------UUCGCC-A--ACAUGGAUGAAACG-GCCA----CCCCCGCU--GGAGCAAGUCCAAGCA--------GGCCC----GUCAAGCAGCAUCUGCUA-------------------------------------------------GG-GCC--GGGUAGGAUGCUAAGUUGAAUGCAACC------------------------------------------------AGCCGUAAGGUG--AACAGAAAGGGGCUUA--CUCCCUGCACCC------
AACY020130475.1/1982-2269  ---AGGAGGUGGAGGGCGACCGA-CGGUC-----------------------------------------UUA----------GGCUGAGGAAAGUCCCCUCUCCAUGAGCA--AGGCAG---CC-GCAA--GG----AAUCC-GAGA-GGAUU--GG-CAA-UGCA-ACAGAAACGA-CACAG--CC-UCACAAU-GGG--AAUGAU-------CGU----------------------------------------------------------------------------------------------------------------------------CUA------------GGA--------------------CGUGACGUC---------------------------------------------------------UGUGA-A-GGAUUUGGUGAAACG-AGCA----CCUCUGCC--GGAGCAAUUCCAAGUA--------UCCGC----GUAGACCU--GCUCGGGA-------------------------------------------------GC-GGU--AGGUAGGAAGCAUAGCUAAAUGUCGCC-----------------------------------------------GGCCAUUUUGGUU--AACAGAAAGGGGCUUA--CUCCCACCACCU------
AACY020076567.1/923-627    ---GGAUGCAGGAGGACUGCUGA-CAGACU---------------------------------------UCGA----------GUCUGAGGAAAGUCCCCUCUCCAUAGUGC--AGGCGGUCGAC-ACAA--GUCGA-GACACAGAAAUGGGUC--GGUCAA-UGGU-GCAGAAACGA--ACGA--UGAGUGGUGUGUAC--GAUGAA-------UCC----------------------------------------------------------------------------------------------------------------------------GGA-------------AG--------------------GACGAGAUU---------------------------------------------------------GCCAU-A-UUG-UCGAUGAGACG-AGCA----ACCCCGCU--GGAGCAAGUCCAAACA--------GUCCC----GUUAAUGUUGCACGCACA-------------------------------------------------GG-GAC--AGGUAGGAUGCUAAGUUGAAUGCAGUC--------------------------------------------------ACCGAAAGGU--AACAGAAAGGGGCUUA--CUCCCUGCAUUC------
AACY020084850.1/1118-1414  ---GGGAUUAGGAGGACCACUGA-CAGUGU---------------------------------------ACGA----------CACUGAGGAAAGUCCCCUCUGCACAGGUGC-AGGUGGCCCGUCGCAA-GGCGGG-UGUCC-GGGA-GGGCA--GG-CUC-UGUA-GAAGAAACGA--AUCG--GCUCGGGCG--CAC--GAUGAA-------UCC----------------------------------------------------------------------------------------------------------------------------GAA--------------A--------------------GGAGGAGAU--------------------------------------------------------UUCCCG-AUGC--UGACUGAGACG-AACA----ACCCCACC--GCAGCAAGUCCAAACA--------GUUCU----GUUGAUGG--CACCGAUA-------------------------------------------------GG-AAC--GGGUAGGAUGCAAAGUUGAAUGUGGUC----------------------------------------------AACCAGCAAUGGUG--AACAGAAAGGGGCUUA--CUCCCUAAUCCC------
AACY020124386.1/1460-1169  ---GGGAGCAGGAGGGUCGCUGA-CAGUGU---------------------------------------ACGA----------CACUGAGGAAAGUCCCCUCUCCGUGAUGC--GAGUGGCUCGACGCAA-GUCGGG-GGUCC-GGGA-GGGCC--GG-CUC-UGCA-ACAGAAACGA--ACUG--CCCCGGGAG--UAC--GAUGAA-------UCC----------------------------------------------------------------------------------------------------------------------------GCG--------------A--------------------GGAGGAGGU--------------------------------------------------------UUCCCG-A-CGG-UGGCUGGAACG-AGCA----ACCCCGCU--GGAGCAAGUCCAAGCA--------GGCCC----GUAGUGCA-UCAGCA----------------------------------------------------GG-GCC--GGGUAGGAUGCAUAGUUGAAUGCGACC------------------------------------------------AGCCGAAAGGUG--AACAGAAAGGGGCUUA--UUCCCUGCACCC------
AACY020236668.1/2417-2713  ---GGGAGUAGGAGGACCGCUGA-CAGAGU---------------------------------------UCGA----------CUCUGAGGAAAGUCCCCUCUCCAAAGUGC--AGGCGGCUACC-AAAA--GGAAG-CAAACAGAAAUGGUUG--GGUUCA-GGCU-GCAGAAACGA--ACGA--UGCAAGGUGUGUAC--AAUGAC-------GUU----------------------------------------------------------------------------------------------------------------------------GAA-------------AG--------------------ACCGAGGUU---------------------------------------------------------GCCUU-G-UUG-UCGAUGAGACG-AGCC----ACCCCGCC--GGAGCAAGUCCAAACC--------GUCCC----GUUGACUCGGCACGACGA-------------------------------------------------GG-GAC--AGGUAGGAUGCACAGUUGAAUGCGGUC--------------------------------------------------ACCGAAAGGG--AACAGAAAGGGGCUUA--CUCCCUACUCCC------
AACY020067856.1/2661-2954  ---GGGAGCAGGAGGGUCACUGA-CAGUGU---------------------------------------ACGA----------CACUGAGGAAAGUCCCCUCUCCAAGAUGC--AAGCGGUCCGAUUAAC-GUCGGA-GAUCU-GGGA-AGGUC--GG-CUC-UGUA-AUAGAAACGA--ACUA--CAUCAGUCGAGUAC--AGUGAU-------UCC----------------------------------------------------------------------------------------------------------------------------GGA-------------AG--------------------GAAGAGGUU---------------------------------------------------------GUCUG-AAUG--UAGAUGGAACG-AGCA----ACCCCGCU--GGAGCAAGUCCAAGCA--------GUCCC----GUAUGGCA-UCAACA----------------------------------------------------GG-GAC--AGGUAGGAUGCUAAGUUGAAUGUGACC------------------------------------------------AGCUGAAAAGUG--AACAGAAAGGGGCUUA--CUCCCUGCACCC------
AACY021439066.1/482-185    ---GGGAGCAGGAGGGUUGCUGA-CAGUGU---------------------------------------ACGA----------CACUGAGGAAAGUCCUCUCUCCACGAUGC--AAGCGGCCCGGUUGAC-GCCGGG-GGCUC-GAGA-GGGCC--GG-CUC-UGGA-ACAGAAACGA--ACCG--UGCUGCGCGAGUAC--GAUGAA-------UCC----------------------------------------------------------------------------------------------------------------------------GAA-------------AG--------------------GACGAGAUU---------------------------------------------------------GCGCA-A--ACCCGGAUGAAACG-GCCA----UCCCCGCU--GGAGCAAGUCCAAGCA--------GGCCU----GUUAAGUUGCAUCGGCAA-------------------------------------------------GG-GCC--GGGUAGGAUGCAAAGUUGAAUGCAACC------------------------------------------------AGCCGCAAGGUG--AACAGAAAGGGGCUUA--CUCCCUGCACCC------
AACY022209960.1/390-94     ---GGGAGUAGGAGGGCUGCUGA-CAGAGU---------------------------------------UAGA----------CUCUGAGGAAAGUCCCCUCUCCAUAGCGC--AUGUGCCUCAC-AGAA--GAGAG-AAGUCAGAGAUGGUUA--GGUUAA-UGCA-AUAGAAACGA--ACGA--UAUAGGGGUAGUAC--AAUGAU-------GUU----------------------------------------------------------------------------------------------------------------------------GAA-------------AG--------------------ACAGAGGUU---------------------------------------------------------UCCCU-A-UUG-UCGAUGAAACG-AGCA----ACCGCACA--GGAGCAAGUCCAAGCA--------GUUCC----AUUGAGAUUGCGCGUCUA-------------------------------------------------GG-AAC--AGGUAGGAUGCUUAGUUGAAUGCAGCC--------------------------------------------------ACCGCAAGGU--AACAGAAAGGGGCUUA--CUCCCUACUCCC------
AACY020323814.1/1431-1135  ---GGGAGUAGGAGGGCUGCUGA-CAGAGU---------------------------------------UCGA----------CUCUGAGGAAAGUCCCCUCUCCGUAGCGC--AUGUGCCUCAC-AGAA--GAGAG-AAAUCAGAGAUGGUUU--GG-UUAGUGCA-AUAGAAACGA--ACGA--UAUAGGGGUUGUAC--AAUGAA-------GUU----------------------------------------------------------------------------------------------------------------------------GAA-------------AG--------------------ACAGAGAUU---------------------------------------------------------UCCUU-A-UUG-UCGGUGAAACG-AGCA----UCCGCACA--GGAGCAAGUCCAAGCA--------GUUCCA---GCCAGGUU-GCGCGCCUA-------------------------------------------------GG-AAC--AGGUAGGAUGCUAAGUUGAAUGCAGCC--------------------------------------------------GCCGAAAGGU--AACAGAAAGGGGCUUA--CUCCCUACUCCC------
AACY023059622.1/732-434    ---GGGUGCAGGAGGACUGCUGA-CAGACU---------------------------------------UCGA----------GUCUGAGGAAAGUCCCCUCUCCACAGUGC--AGGUGGUCGAC-ACAA--GUCGA-GGUUCAGAGAUGAGUC--GGUCAA-UGGU-GCAGAAACGA--ACGA--UAUGUGGUGUGUAC--AAUGAA-------UCU----------------------------------------------------------------------------------------------------------------------------GAA-------------AA--------------------GACGAGGUU---------------------------------------------------------GCCAC-A--AUGUCGAUGAGACG-AGCA----ACCACACU--GGAGCAAGUCCAAACA--------GUCCC----UUUGAGGCGGCACGUCUA-------------------------------------------------GG-GAC--AGGUAGGAUGCUUAGUUGAAUGCAGUC------------------------------------------------ACCGGUAACGGG--AACAGAAAGGGGCUUA--CUCCCUGCACCC------
AACY020123929.1/7087-6796  ---GGGAGCAGGAGGGUCGCUGA-CAGUGU---------------------------------------UAGA----------CACUGAGGAAAGUCCCCUCUCCGCGAUGC--AGGCGUCUCGUCACAA-GACGGG-GGUCC-GGGA-GGGCC--GG-CUC-UGCA-GCAGAAACGA--ACCA--UGCCAGGAG--UAC--GGUGAA-------CCC----------------------------------------------------------------------------------------------------------------------------GCG--------------A--------------------GGGGGAGGU--------------------------------------------------------UUCCUGAG-UG--UGGCUGGAACG-GGCA----ACCACGCC--GGAGCAAGUCCAAGCA--------GGUCC----GAAUGGCA-UCGACA----------------------------------------------------GG-ACC--GGGUAGGAUGCAUAGUUGAAUGCGACC------------------------------------------------AGCCGAAAGGUG--AACAGAAAGGGGCUUA--CUCCCUGCACCC------
AACY022737222.1/362-65     ---GGGAGCAGGAGGGUUGCUGA-CAGUGC---------------------------------------AAGA----------CACUGAGGAAAGUCCCCUCUCCACGACGC--AAGUGGCUCGGUUUAC-GCCGAG-GAUCC-GAGA-GGGUC--GG-CCA-UGUA-GAAGAAACGA--ACCG--UGGCAGGUG--UGUGCUAUGAA-------UCC----------------------------------------------------------------------------------------------------------------------------GAA--------------A--------------------GGAGGAGGU--------------------------------------------------------CGCCUG-U-UUA-CGGAUGGAACG-AACA----ACCCCACU--GGAGCAAGUCCAAACA--------GUCCC----GUCGACGAGCGUCGCCGA-------------------------------------------------GG-GAC--GGGUCGGAUGCUAAGUUGAAUGCAACC------------------------------------------------AGCCUAAUGGUG--AACAAAAAGGGGCUUA--CUCCCUGCACCC------
AACY022727466.1/349-648    ---GGGAGUGGGAGGACCGCUGA-CAGAGC---------------------------------------CAGA----------CUCUGAGGAAAGUCCCCUCUCCACGGUGC--ACAUGGGCCGC-ACAA--GCGGCAGGUCG-GAAA-CGAUCA-GGUCAA-UGCA-GCAGAAACGA--ACGA--CGCGUGGGUUGAAC--GAUGAU-------GUC----------------------------------------------------------------------------------------------------------------------------GAA-------------AG--------------------ACGGAGGUU---------------------------------------------------------UCCAC-G-UGG-UCGAUGAGACG-AGCA----ACCCCAUG--GGAGCAAGCCCAGACA--------GCCCU----GACGACGCGGCACGCCGA-------------------------------------------------GG-GGC--GGGUAGGGUGCACAGUUGAAUGCGGUC-----------------------------------------------ACCGUUUUUCGGG--AACAGAAAGGGGCUUA--CUCCCCACUCCC------
AACY021710726.1/634-929    ---GGGAGCAGGAGGACUGCUGA-CAGGGU---------------------------------------UCGA----------CCCUGAGGAAAGUCCCCUCUCCAUAGUGC--AGGUGUCCGAA-AGAA--UUCGG-UGGACAGAAAUGGCCA--GGUCAA-UGAA-GAAGAAACGA--ACAA--AAUCAGGUGUGUAC--AAUGAA-------UCG----------------------------------------------------------------------------------------------------------------------------GAA-------------AC--------------------GACGAGAUU---------------------------------------------------------GCUUG-A-AUU-UUGAUGGAACG-AUCA----ACCACACU--GGAGCAAGUCCAAAUC--------GUCUC----ACUGAUGC-UGCACGUUA-------------------------------------------------GA-GAC--AGGUAGGAUGCUAAGUUGAAUGCAGUC--------------------------------------------------ACCGAAAGGG--AACAGAAAGGGGCUUA--CUCCCUGCUCCC------
AACY023860274.1/1463-1166  ---GGGAGUGAGAGGACCGCUGA-CAGAGU---------------------------------------UCGA----------CUCUGAGGAAAGUCCCCUCUCCAUAGUGC--AGGUGGUUCAC-AGAA--GUGAA-AGAUCAGAGAUGGUCA--GGUCAA-UGCC-ACAGAAACGA-UACGA--UACCAGGUGUGUAC--AAUGAU-------GUU----------------------------------------------------------------------------------------------------------------------------GAA-------------AA--------------------ACGGAGGUU---------------------------------------------------------GCCUGAG-UG--UUGAUGGAACG-AGCA----ACCCCACU--GGAGCAAGUCCAAAUC--------GUCCU----GUUGAAGCGGCACGCAGA-------------------------------------------------GG-GAC--AGGUAGGAUGCUGAGUUGAAUGCGGUC--------------------------------------------------ACCGAAAGGC--AACAAAAAGGGGCUUA--CUCCUCACUCCC------
AACY023878832.1/921-1218   ---GGGAGUGAGAGGACCGCUGA-CAGAGU---------------------------------------UCGA----------CUCUGAGGAAAGUCCCCUCUCCAUAGCGC--AGGUGGUUCAC-AGAA--GUGAA-AGAUCAGAGAUGGUCA--GGUCAA-UGCC-ACAGAAACGA-UACGA--UACCAGGUGUGUAC--AAUGAU-------GUU----------------------------------------------------------------------------------------------------------------------------GAA-------------AG--------------------ACGGAGGUU---------------------------------------------------------GCCUG-A--AUGUCGAUGGAACG-AGCA----ACCCCACU--GGAGCAAGUCCAAAUC--------GUCCC----GCUUAUGUUGCACGCACA-------------------------------------------------GG-GAC--AGGUAGGAUGCUAAGUUGAAUGCGGUC--------------------------------------------------GCCGAAAGGU--AACAAAAAGGGGCUUA--CUCCUCACUCCC------
AACY021957214.1/341-628    ---AGGAGAUGGAGGGCGACCGA-CGGCC-----------------------------------------UUG----------GGCUGAGGAAAGUCCCCUCUCCAAGAGCA--AGGCAG---CC-GUAA--GG----AAUCC-GAGA-GGAUU--GG-CAA-UGCA-ACAGAAACGA-CACAG--CC-CCACUA--UAGG-AAUGAU-------CGU----------------------------------------------------------------------------------------------------------------------------CAA------------GGA--------------------CGUGACGUC---------------------------------------------------------AGUGG-A-GGAUUUGAUGAAACG-AGUA----CCCCUGCC--GGAGCAAUUCCAAGUA--------ACCGC----UUAGACCU--GCUCGGGA-------------------------------------------------GC-GGU--AGGUAGGAUGCGAAGCUAAAUGUCGCC-----------------------------------------------AACCUUUUAGGUU--AACAGAAAGGGGCUUA--CUCCCAUCACCU------
ABEF01053878.1/2997-3288   ---GGGAGCAGGAGGGUCGCUGA-CAGUGU---------------------------------------ACGA----------CACUGAGGAAAGUCCCCUCUCCGCGAUGC--AGGUGGUCCGACGUAA-GUCGGA-GGUCC-GGGA-GGGCC--GG-CUC-UGCA-ACAGAAACGA--ACCG--CGCCAGGCG--CAC--UGUGAA-------CCC----------------------------------------------------------------------------------------------------------------------------GAA--------------A--------------------GGGGGAGGU--------------------------------------------------------UUCCUG-A-CCG-UGGCUGGAACG-AGCA----CCCCCGCC--GGAGCAAGUCCAAGCA--------GGUCC----GCAUGGCA-UCGACA----------------------------------------------------GG-ACC--GGGUAGGAUGCACAGUUGAAUGCGACC------------------------------------------------AGCCGCAAGGUG--AACAGAAAGGGGCUUA--CUCCCUGCACCC------
AE009439.1/40217-40574     ---GGCCGUGG---GGCCGCUAA-----------------------------------------------GGG--------------GAGGAAGCUCCGCCCCCGGGCCCGGG-CCCGCCGCCCC-GAGA-GGGGGC-CGGCC-GAGA-GGCCG--GG-GAC-CGGCCACAGAAACGA-CACGU--CCGUCGGCG--GAU--GGCGAUGA-----CGCGGCUGAGGCCCGCCGUGGGCGGGCCGAG------------------------------------------------------------------------------------------------AAG--GGCCCCG--GCGA--CGGGGCC-----------CGAGCUAAC----------------------------------------------CCGCAGAGGACGCCGG-C-GGGAUCGGUGAAACGGGCCG----CCCGGCGG--GGGGCGAGGCCGAAUG--------AGCCC----GAUGAUAC-GAGGGUGAU-----------------------GCCCCCGAUGAGUUCCCGGGCCGGAGGG-GGA--UGGUAGGCCGCUGAGGUGAAUGCCGCC---------------------------------------------------GUCUAAGGC--UACAGAAGGCGGG---------CUAUAGCC------
AE006641.1/225037-224732   ---GGGAUCCCUAGCGGGGGUAA-CGGGG----------------------------------------CAAA----------CCCUGAGGAAACUCCGGCCUCCAACCCUU--ACAAGAACCCC-GUAA--GGGGU-AGGGA-UAGAAUCCCU--GG-CUA-CUAC-ACAGAAACGA--AGCC--CUAAUACUA--GAUA-GAUGAU-------UGG----------------------------------------------------------------------------------------------------------------------------ACC--UACUAGCAAGUAAUUGCUAGUA--------GUACAUGAUAGA-----------------------------------------------------UGAAAGUAU-U-AG--GGCUUGAAACG-GUAG----ACCUCUUG--GGAGCAAGU--UGA----------AGGGG----GAUGAGCA-AAGGGUUGA-------------------------------------------------CU-CCU-UAUAGU--ACGCUUAGUCGAAUCCCCUC----------------------------------------------------------AG--UACAGAAGCCGGGUUAUGCU-AGGGAUCCC------
CP001365.1/2448394-2448035 ---GACAGAGGGAGCCCGACUCC-CGUGCC---------------------------------------UCUG----------GCAUGAGGAAAGUCCCCCCACCGGCCGGAC-AGGCGACCGGGCACAC-GCCCGG-AGUCG-GAGA-CGGCU--GG-CUC-UGGA-ACAGCAACGA-CACCC--CCCACCCCG--ACC--CGUGAU-------UCGCGCGAUCGCUUCGGCGAUCGCGGCGGCCGCGGGAUCACCCGCGACCGCGC--------------------------------------------------------------------------GAA--CCGACCC--GCAA--GGGAAGG-----------GAGUUAACC--------------------------------------------CGAUGAGGAUCGACGGGU-G-GGAACGGAUGGAACG-GCGA---AUCCUCGCC--GGUGCAAGUCC-------------GCGCCA---CAAGGUAG-UCCGGCCAC-------------------------------------------------GG-CGC-------GGACGCUUAGCCGAAUGUCGGG---------------------------------------------------------AUG--AACCGAAGGGGGCUUA--CUCCCCUCAGUC------
#=GC SS_cons               ...[[[-[[[[[[[[[[[[[,,,.<<<<<_.......................................____..........>>>>>,,,,AAA,AAAAA((((-BBBBBB..-(((((<<<<<.____._>>>>>.<<<<<.____.>>>>>..<<.---.<<<<.----------.--<<<..<<<<<<<<-..---..------.......<<-............................................................................................................................---..<<--<<<..____..>>>-->>...........>>-------........................................................->>>>>.>.>>-->>>--------.>>>>...-->>)))))..)))),,,<<<<---..........<<<<<....________.bbbbbb___.................................................>>.>>>..----->>>>,,,,,,,,,,,,]]]]]].........................................................---..-------aaaaaaaa-..]]-]]]]]-]]]......
#=GC RF                    ...GggAGcggGaGggcgGCUga.Cgggcc.......................................uuga..........gcccGAGGAAAgUCCcCCCaCCauuccga..AggcggcCggc.GcAA.GgccGg.ggcgc.GAGA.gcgcc..GG.Cac.uggc.ACAGAAACGA.cACcc..cucccggcg..aau..GAUGAu.......gcg............................................................................................................................gaa..ccacccc..GcaA..gggaagg...........gcuGAaauu........................................................agccgg.g.agaaggGaUGaAACG.gcca...AuCCccgcc..GGuGCAAGuccaaa..........gcgcc....gaugAgag.ucagcauga.................................................gg.cgc..ugguaggaCGCUuAGcCGAAUGCcgcc.........................................................aug..AACAGAAGGgGGcUUA..CuCCccgCAccC......
//
# STOCKHOLM 1.0

#=GF AC   RF00374
#=GF ID   Gammaretro_CES
#=GF DE   Gammaretrovirus core encapsidation signal
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:15003457
#=GF SS   Published; PMID:15003457
#=GF GA   51.00
#=GF TC   51.00
#=GF NC   50.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.50 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019072; viral genome packaging;
#=GF RN   [1]
#=GF RM   15003457
#=GF RT   NMR structure of the 101-nucleotide core encapsidation signal of the
#=GF RT   Moloney Murine Leukemia Virus.
#=GF RA   D'Souza V, Dey A, Habib D, Summers MF
#=GF RL   J Mol Biol 2004;337:427-442.
#=GF RN   [2]
#=GF RM   15457265
#=GF RT   Structural basis for packaging the dimeric genome of Moloney murine
#=GF RT   leukaemia virus.
#=GF RA   D'Souza V, Summers MF
#=GF RL   Nature. 2004;431:586-590.
#=GF CC   This family represents the Gammaretrovirus (mammalian type C retrovirus)
#=GF CC   core encapsidation signal and related sequences. The Moloney murine
#=GF CC   leukaemia virus (MMLV) core encapsidation signal is know to be essential
#=GF CC   for stable dimerisation and efficient genome packaging during virus
#=GF CC   assembly [1]. Dimerisation of the viral RNA genomes is proposed to act as
#=GF CC   an RNA conformational switch which exposes conserved UCUG elements and
#=GF CC   enables efficient genome encapsidation [2].
#=GF WK   Gammaretrovirus_core_encapsidation_signal
#=GF SQ   22


X14576.1/670-769   GUCUGUACUAGUUAGCUAACUAGAUCUGUAUCUGGCGGUUCCGUGGAAGAACUGACGAGUUCGG-AUUCCCGACCGCAGCC-CUGAGAGACGUCUCAG-GGGC
K02712.2/736-835   AUCUGUACUAGUUAGCUAACUAGAUCUGUAUCUGGCGGUUCCGUGAAAGAACUGACGAGUUCG-UAUUCCCGGCCGCAGCC-CUGGGAGACGUCUCAGAGG-C
AF033811.1/12-112  GUCGGUACUAGUUAGCUAACUAGCUCUGUAUCUGGCGGACCCGUGGUGGAACUGACGAGUUCGGAACACCCGGCCGCAACC-CUGGGAGACGUCCCAG-GGAC
K03363.1/295-394   UUCUGUACUAGUUAGCUAACUAGGUCUGUAUCUGGCGGCUCCGUGGAAGAACUGACGAGUUCG-UAUUCCCGACCGCAGCC-CUGGGAGACGUCUCAG-GGGC
M12275.1/344-445   GUCUGUACUAGUUGGCUAACUAGAUCUGUAUCUGGCGGUCCCGCGGAAGAACUGACGAGUUCG-UAUUCCCGGCCGCAGCCCCUAGGAGACGUCCCAGCGGCC
S80082.1/697-796   GUCUGUACUAGUUAGCUAACUAGAUCUGUAUCUGGCGGUUCUGCGGAAGAACUGACGAGUUCG-UAUUCCCGGCCGCAGCC-CUGGGAGACGUCCCAGCGG-C
U00220.1/894-994   GUCUGUACUAGUUAGCUAACUAGCUCUGUAUCUGGCGGACCCGUGGUGGAACUGACGAGUUCUGAACACCCGGCCGCAACC-CUGGGAGACGUCCCAG-GGAC
M64095.1/673-772   AUCUGUACUAGUUAGCUAACUAGAUCUGUAUCUGGCGGUUCCGUGGAAGAACUGACGUGUUC-AUAUUCCCGACCGCAGCC-CUGGGAGACGUCUCAGAGG-C
Z11128.1/274-374   GUCUGUACUAGUUGGCCGACUAGAUUGGUAUCUGGCGGAUCCGUGGUGGAACUGACGAGUUCGAGACACCCGGCCGCAACC-CUGGGAGACGUCCCAG-GGAC
AF411814.1/275-375 GUCUGUACUAGUUGGCCGACUAGCUCUGUAUCUGGCGGACCCGUGGUGGAGCUGACGAGUUCGGAACACCCGGCCGCAACC-CUGGGAGACGUCCCAG-GGAC
U13766.1/293-392   AUCUGUACUAGUUAGCUAACUAGAUCUGUAUCUGGCGGUUCCGUGGAAGAACUGACGAGUUCG-UAUUCCCGACCGCAGCC-CUGGGAGACGUCUCAGAGG-C
AF169256.1/297-396 UUCUGUACUAGUUAGCUAACUAGAUCUGUAUCUGGCGGCUCCGUGGAAGAACUGACGAGUUCG-UAUUCCCGACCGCAGCC-CUGGGAGACGUCUCAGAGG-C
AF462057.1/276-376 GUCGGUACUAGUUAGCUAACUAGCUCUGUAUCUGGCGGACCCGUGGUGGAACUGACGAGUUCGGAACACCCGGCCGCGACC-CUGGGAGACGUCCCAG-GGAC
K02729.1/786-886   GUCUGUACUAGUUGGCCGACUAGCUCUGUAUCUGGCGGACCCGUGGUGGAACUGACGAGUUCGGAACACCCGGCCGCAACC-CUGGGAGACGUCCCGG-GGAC
J02266.1/718-818   GUCUGUACUAGUUAGCUAACUAGCUCUGUAUCUGGCGGACCCGUGGUGGAACUGACGAGUUCUGAACACCCGGCCGCAACC-CAGGGAGACGUCCCAG-GGAC
M93134.1/274-374   GUCUGUACUAGUUGGCCGACUAGCUCUGUAUCUGGCGGACCCGUGGUAGAACUGACGAGUUCGGGAUACCCGGCCGCAACC-CUGGGAGACGUCCCAG-GGAC
M96854.1/729-829   GUCUGUACUAGUUAGCUAACUAGCUCUGUAUCUGGCGGACCCGUGGUGGAACUGACGAGUUCUGAACACCCGGCCGCGACC-CUGGGAGACGUCCCAG-GGAC
AF019230.1/276-376 GUCUGUACUAGUUGGCCGACUAGCUCUGUACCUGGCGGACCCGUGGUGGAACUGACGAGUUCGGAACACCCGGCCGCAACC-CUGGGAGACGUCCCGG-GGAC
AJ583798.1/721-821 GUUUGUACUAGUUGGCCGACUAGCUCUGUACCUGGCGGACCCGUGGUGGAACUGACGGGUUCGAGACACCCGGCCGCAACC-CUGGGAGACGUCCCAA-GGAC
M26526.1/655-755   GCCUGUACUAGUUGGCUGACUAGACCUGUAUCUGGCGGUUCCGUGGAAGAACUGACGAGUUCGGAGUUCCCGGCCGCAACC-CUGGGAGACGUCCCGG-GGAC
U94692.1/274-374   GUCUGAACUAGUUGGCCGACUAGCUCUGUAUCUGGCGGACCCGUGGUGGAACUGACGAGUUCGAGACACCCGGCCGCAACC-CUGGGAGACGUCCCAG-GGAC
V01185.1/721-821   GUCUGUACUAGUUAGCUAACAUGCUCUGUAUCUGGCGGACCCGUGGUGGAACUGACGAGUUCUGAACACCCGGCCGCAACC-CUGGGAGACGUCCCAG-GGAC
#=GC SS_cons       ::<-<--<<<<<<____>>>>>>-->->,,,,,,<<<<--<<<-<<<<<<<<<____>>>>>---->>>>>>>>>>>,,<<.<<<<<<____>>>>>>.>>::
#=GC RF            gUcuGUACuaGuuaGCuaaCuaGaUCugUAUCUGGCGGaucCGUGGugGaaCuGACGaGuuCggaAcaCCCGgCCGCAaCC.CuGgGaGACGuCcCaG.GGaC
//
# STOCKHOLM 1.0

#=GF AC   RF00375
#=GF ID   HIV_PBS
#=GF DE   HIV primer binding site (PBS)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14757051
#=GF SS   Predicted; PFOLD
#=GF GA   38.00
#=GF TC   38.10
#=GF NC   37.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.99 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0000946; base pairing with tRNA;
#=GF RN   [1]
#=GF RM   14757051
#=GF RT   RNA interactions in the 5' region of the HIV-1 genome.
#=GF RA   Damgaard CK, Andersen ES, Knudsen B, Gorodkin J, Kjems J
#=GF RL   J Mol Biol 2004;336:369-379.
#=GF RN   [2]
#=GF RM   11384976
#=GF RT   Initiation of HIV-1 reverse transcription is regulated by a primer
#=GF RT   activation signal.
#=GF RA   Beerens N, Groot F, Berkhout B
#=GF RL   J Biol Chem 2001;276:31247-31256.
#=GF CC   This family consists of several, structured HIV primer binding sites
#=GF CC   (PBSs). tRNA(3)(Lys) binds to the PBS to initiate reverse transcription
#=GF CC   [2].
#=GF WK   Primer_binding_site
#=GF SQ   130


U24479.1/452-550    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGGGAAACCAGAG
AF004394.1/579-677  CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGUGAAAGUAGAACCAGAG
L28915.1/462-560    CUCUGGUAACUAGAGAUCCCUCAGACCCCUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCCGAAAGCGAAAGUAGAACCAGAG
AF096645.1/525-623  CUCUGGUAACUAGAGAUCCCUCAGACCUCAUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
AF254716.1/529-627  CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUUGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAGACCAGAG
AF196751.1/580-678  CUCUGGUAACUAGAGAUCCCUCAGAUCUCUUUCGUCCGGGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUCGAAAACGAAAGUAGAACCAGAG
AF254708.1/507-605  CUCUGGUAACUAGAGAUCCCUCAGACCUCUUUGGUCGGUGUGA--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
AF196727.1/580-678  CUCUGGUAACUAGAGAUCCCUCAGACCCCUUUAGUCAGAGUGA--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
AF196719.1/577-675  CUCUGGUAACUAGAGAUCCCUCAGACUUCUUUAGUCNGUGUAG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
AF239651.1/517-615  CUCUGGUAACUAGAGAUCCCUCAGACCUUUUGUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAGACCGGAG
AF239643.1/539-637  CUCUGGUAACUAGAGAUCCCUCAGACCACCUUAGUCUGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
AF239627.1/518-616  CUCUGGUAACUAGAGAUCCCUCAGACCUUUAGUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAAGACCAGAG
AF254678.1/508-606  CUCUAGUAACUAGAGAUCCCUCAGACCUCUCUAGUCAGUGUAG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
AF408632.1/146-244  CUCUGGUAACUAGAGAUCCCUCAGACAAUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAGAACCAGAG
U80517.1/412-510    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCGGAAAGAGAAAGAGAAACCAGAG
U80509.1/411-509    CUCUGGUAGCUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGA--AAAAUCUCUAGCAGUGGCGCCUGAACAGGGACCUGAAAGCGAAAGGGAAACCAGAG
L28851.1/453-551    CUCUGGUAGCUAGAGAUCCCUUAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGRGAAACCAGAG
L28843.1/453-551    CUUUGGUAGCUAGAGAAYCCUUAGACCCUUUAAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGRACAGGGACUUGAAAGCGAAAAGAGAACCAGAG
U81466.1/410-508    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGA--AAAAUCUCUAGCAGUGGCGCCCAACGUGGGGCCGGAAAGCGAAAGAGAAACCGGAG
AF110973.1/69-167   CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUUGGUAUUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAAGGCCAGAG
U81458.1/412-510    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAACGAAAGUAGAACCGGAG
AF110965.1/68-166   CUCUGGUAACUAGAGAUCCCUCAGACCCUUCGUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACGCGAAAGUGAAAGUAAGACCAGAG
AF096646.1/517-615  CUCUGGUAACUAGAGAUCCCUCAGACACCUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
AF254725.1/519-617  CUCUGGUAACUAGAGAUCCCUCAGACCUUUUUAGUCCGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGUGAAAGUAAAACCGGAG
AF196752.1/594-692  CUCUGGUAACUAGAGAUCCCUCAGACCCAUUGUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAACGAAAGUAAGACCAGAG
AF254709.1/516-614  CUCUGGUAACUAGAGAUCCCUCAGACACCUGUAGUCCGGGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACGUGAAAGCGAAAGUAAAGCCAGAG
AY463218.1/1-99     CUCUGGUAACUAGAGAUCCCUCAGACCUAUUUUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACGUGAAAGCGAAAGUAAGACCAGAG
AF196728.1/602-700  CUCUGGUAACUAGAGAUCCCUCAGACCAUUCUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
L02317.1/126-224    CUCUGGUAGCUAGAGAUCCCUCAUACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCGGAAAGCGAAAGAGAAACCAGAG
M17449.1/578-676    CUCUGGUAGCUAGAGAUCCCUCAGAUCCUUUUAGGCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGAAAAACCAGAG
AF239644.1/517-615  CUCUGGUAACUAGAGAUCCCUCAGACACUUGUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAGACCAGAG
U89858.1/452-550    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGCGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAGAGCGAAAGAGAAACCAGAG
L28860.1/453-551    CUCUGGUAGCUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAGCAGGGACUUGAAAGCGAAAGAGAAACCAGAG
U81467.1/412-510    CUCUGGUAACUAGAGAUCCCUCAGACCAUUUUAGUCCGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGGAAAACCAGAG
U81459.1/412-510    CUCUGGUAACUAGAGAUCCCUCAGACCUCUGUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACGCGAAAGCGAAAGUAGAACCAGAG
AF256206.1/579-677  CUCUGGUAACUAGAGAUCCCUCAGACCCAUUUAGUCAGUGUGA--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCCGAAAGCGAAAGAGAAACCAGAG
AF385934.1/620-718  CUCUGGUAACUAGAGAUCCCUCAGACUAUUUUAGUCAGUGUGA--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUAGAAAGCGAAAGUAGAACCAGAG
AF254734.1/517-615  CUCUGGUAACUAGAGAUCCCUCAGACCUUUAUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAGAACCAGAG
AF096639.1/552-650  CUCUGGUAGCUAGAGAUCCCUCAGACCACUUUUGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAGACCAGAG
AF254718.1/545-643  CUCUGGUAACUAGAGAUCCCUCAGACCAUUUUUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCAGAAAGCGAAAGUAAGACCAGAG
AY463227.1/28-126   CUCUGGUAACUAGAGAUCCCUCAGACCCUUGUUGGUAUUGUGG--CAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAACGAAAGUAGAACCAGAG
AF003887.1/579-677  CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAAGCCAGAG
AF196737.1/563-661  CUCUGGUAACUAGAGAUCCCUCAGACCAAAUUAGUCAGUGAGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
L28887.1/483-581    CUCUGGUAGCUAGAGAUCCCUCAGAUCCUUUUAGUCAGUGUGG--AAAUUCUCUAGCAGUGGCGCCCGAACAGGGACCGGAAAGUGAAAGAGAAACCAGAG
AF408626.1/3-101    CUCUGGUAACUAGAGAUCCCUCAGACCAUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCCGAAAGCGAAAGUARAACCAGAG
AF254700.1/513-611  CUCUGGUAACUAGAGAUCCCUCAGACCCUUGUUGGUUGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAGACCAGAG
AF196711.1/597-695  CUCUGGUAACUAGAGAUCCCUCAGACACUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACGGGAAAGCGAAAGAGAAACCAGAG
L28853.1/451-549    CUCUGGUAGCUAGAGAACCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGUGAAAAGRAAACCAGAG
L28845.1/453-551    CUYUGGUAGCUAGAGAUCCCUUAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGUGAAAGGGRAACCAGAG
U73092.1/235-333    GUCUUGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAAGAGGGACCUGAAAGCGAAAGGGAAACCAGAG
AF096648.1/517-615  CUCUGGUAACUAGAGAUCCCUCAGACCCAUUUAGUCUGUGUAG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
AF254727.1/518-616  CUCUGGUAACUAGAGAUCCCUCAGACCUUUGUUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCCGAAAGCGAAAGUAAGACCAGAG
AY463236.1/28-126   CUCUGGUAACUAGAGAUCCCUCAGACCAUUCGUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGUGAAAGUAAGACCAGAG
AF239638.1/518-616  CUCUGGUAACUAGAGAUCCCUCAGACCCUUUGUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCAGAAAGUGAAAGUAAGACCAGAG
AF075719.1/581-679  CUCUGGUAACUAGAGAUCCCUCAGAUCCUUUUAGGCAAUGUAG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCAAAAGAGAAACCAGAG
U80536.1/411-509    CUCUGGUAGCUAGAAAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUUUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAAACCGGAG
U80528.1/410-508    CUCUGGUAACUAGAGAUCCCUCAGACCAUUUUAGUCAGUGUGA--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCGGAAAGCGAAAGAGAAACCAGAG
L28862.1/453-551    CUCUGGUAGCUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGA--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUAAAAGCGAAAGAGAAACCAGAG
AF133821.1/905-1003 CUCUGGUAACUAGAGAUCCCUCAGACCUCUUUAGUCAGUGUAA--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
L28846.1/453-551    CCCUGGUAGCUAGAGAUUCCUUAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGRACAGGGACUUGAAAGUGAAAGGGGAACCAGAG
AF538302.1/601-699  CUCUGGUAGCUAGAGAUCCCUCAGACCCUUUAAUUCCGUGUAG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGAGAAACCAGAG
AY463237.1/28-126   CUCUGGUAGCUAGAGAUCCCUCAGACCCUUUGUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUAAAAGCGAAAGUAAGACCAGAG
AF239655.1/541-639  CUCUGGUAACUAGAGAUCCCUCAGACUUCCUUAGUUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
L28889.1/483-581    CUCUGGUAGCUAGAGAUCCCUCAGAUCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGUGAAAGAGAAACCAGAG
AF254698.1/516-614  CUCUGGUAACUAGAGAUCCCUCAGACCUCUUUAGUCAGUGUGG--AAAAUCACUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAGAACCAGAG
AF254710.1/518-616  CUCUGGUAACUAGAGAUCCCUCAGACACCUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAAGACCAGAG
AF254702.1/533-631  CUCUGGUAACUAGAGAUCCCUCAGACCUCUUUAGUCCGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUCGAAAGCGAAAGUAGAACCAGAG
U80529.1/412-510    CUCUGGUAACUAGAGAUCCCUCAGACCCAAUUAGCCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGAGAAACCAGAG
AF196713.1/612-710  CUCUGGUAACUAGAGAUCCCUCAGACCCUUUAAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGAGAAACCAGAG
L28855.1/453-551    CCCUGGUAGCUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGAGAAACCAGAA
U81478.1/411-509    CUCUGGUAACUAGAGAUCCCUCAGACUCUUGUAGUCAGUGUAG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCCUAAAGCGAAAGAGAAACCAGAG
U21135.1/579-677    CUCUGGUAACUAGAGAUCCCUCAGACCAUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCCGAAAGCGAAAGGGAAACCAGAG
U34604.1/580-678    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGAGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACGCGAAAGCGAAAGAGAAACCAGAG
AF538303.1/599-697  CUCUGGUAGCUAGAGAUCCCUCAGACCCUUUUACCCAGUGUAG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGGGAAACCAGAG
AF254737.1/526-624  CUCUGGUAACUAGAGAUCCCUCAGACACUUUAUAGCUGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAGACCAGAG
M27323.1/123-221    CUCUGGUAACUAGAGAUCCCUCAGAUCCGUUUAGUCCGAGUGA--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAGAACCAGAG
AF239648.1/539-637  CUCUGGUAACUAGAGAUCCCUCAGACCACUUUAGUUUGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCAGAAAGCGAAAGUAGAACCAGAG
U88822.1/93-191     CUCUGGUAACUAGAGAUCCCUCAGACAGCUUUAGUCCGGGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAGAACCAGAG
U80538.1/412-510    CUCUGGUAACUAGAGAUCCCUCAGACACUUUUAGUCAGUGUAG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGAGAAACCAGAG
U69589.1/125-223    CUCUGGUAACUAGAGAUCCCUCAGACCAUUUUAGUCAGUGAGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGAGAAACCAGAG
AY463220.1/28-126   CUCUGGUAACUAGAGAUCCCUCAGACCCUUGUUGGUAGUGCGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAAGACCAGAG
AF196722.1/580-678  CUCUGGUAACUAGAGAUCCCUCAGACCUCUUUAGUCAACGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAACGAAAGUAGAACCAGAG
U51291.1/488-586    CUCUGGUAACUAGAGAUCCCUCAGACCCUCUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAGAACCAGAG
AF042106.1/381-479  CUCUGGUAUCUAGAGAUCCCUCAGACCCUUUUAGUCCGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGGGAAACCAGAG
AY423382.1/202-300  CUCUGGUAACUAGAGAUCCCUCAGACCAAUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAAACCAGAG
L28880.1/453-551    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUAAAAGCGAAAGAAAAACCAGAG
U43141.1/49-147     CUCUGGUAGCUAGAGAUCCCUCAGAUCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
AF254681.1/513-611  CUCUGGUAACUAGAGAUCCCUCAGACCUCUUUAGUCCGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGUGAAAGUAGAACCGGAG
U80512.1/438-536    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUAGGA--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGAGAAAGAGAAACCAGAG
AF086817.1/578-676  CUCUGGUAACUAGAGAUCCCUCAGACCAUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCAAAAGAGAAACCAGAG
AF254712.1/538-636  CUCUGGUAACUAGAGAUCCCUCAGACACCUUUUGUCAGUGUGG--AAAGUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAGACCAGAG
AF196731.1/579-677  CUCUGGUAACUAGAGAUCCCUCAGACAUCUGUUGUCCGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUGAGACCAGAG
U80513.1/411-509    CUCUGGUAACUAGAGAUCCCUUAGACCCUUAUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGGAAAACCAGAG
AF538305.1/579-677  CUCUGGUAUCUAGAGAUCCCUCAGACCAAUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCGGAAAGCGAAAGAAAAACCAGAG
U73100.1/465-563    GUGUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGAGAAACCAGAG
M26727.1/125-223    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUUAAAGUGAAAGUGGAACCAGAG
AF196732.1/580-678  CUCUGGUAGCUAGAGAUCCCUCAGAUCCUUUUUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAGACCAGAG
AF196724.1/579-677  CUCUGGUAACUAGAGAUCCCUCAGACUCAUUUUGUCAGAGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGUGAAAGUAGAACCAGAG
AF239640.1/518-616  CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCCGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGGACCAGAG
L28866.1/453-551    CUCUAGUAGCUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUAG--AAAAUCUCUAGCAGUGGCGCCCAACGUGGGGCUCGAAAGCGAAAGAGAAACCAGAG
L28858.1/453-551    CUCUGGUAGCUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGACGCCCGAACAGGGACUUGAAAGCGAAAGAGAAGCCAGAG
AF286236.1/77-175   CUCUGGUAUCUAGAGAUCCCUCAGACCACUUUAGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCGGAAAGCGAAAGUAAAACCAGAG
AY167123.1/95-193   CUCUGGUAGCUAGAGAUCCCUCAGACCUUGUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
AF405202.1/210-308  CUCUGGUAACUAGAGAUCCCUCAGACCCUUCGUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAGGCCAGAG
U81463.1/412-510    CUCUGGUAACUAGAGAUCCCUCAGACUCUUGUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGAGAAAGAGAAACCAGAG
AF196767.1/578-676  CUCUGGUAUCUAGAGAUCCCUCAGACCAUUUAAGUCCGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAUGACCAGAG
AY162224.1/589-687  CUCUGGUAACUAGAGAUCCCUCAGACCCUUUGUGGUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUGAGACCAGAG
L28905.1/463-561    CUCUGGUAACUAGAGAUCCCUAAGACCCCUUUAGUCAGUGUGA--AAAAUCUCUAGAAGUGGCGCCCGAACAGGGACCCGAAAGCGAAAGUAGAACCAGAG
AF196741.1/577-675  CUCUGGCAGCUAGAGAUCCCUCAGACCUCAUUUGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAGGCCAGAG
AY463223.1/28-126   CUCUGGUAACUAGAGAUCCCUCAGACUCUUUGUGGUAGUGCGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCUGAAAGCGAAAGUAAGACCAGAG
AF196717.1/578-676  CUCUGGUAACUAGAGAUCCCUCAGACACCUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACGCUAAAGUGAAAGUAGAACCGGAG
L28867.1/453-551    CUCUGGUAGCUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGACGCCCGAACAAGGACUUGAAGGCGAAAGAGAAACCAGAG
AF254676.1/517-615  CUCUGGUAACUAGAGAUCCCUCAGACCUCUUUAGUCUGUGGGG--AAAAUCUCUAGCAGUGGCGCCCAACGUGGGGCACGAAAGCGAAAGUAAGACCAGAG
U39362.2/578-676    CUCUGGUAGCUAGAGAUCCCUCAGACCAUCCUAGUUAGUGUAG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCGGAAAGCGAAAGAGAAACCAGAG
U80531.1/410-508    CUCUGGUAACUAGAGAUCCCUCAGACCUGUGUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGAGAAACCAGAG
L28841.1/453-551    CUUUGGUAGCUARAGAUCCCUUAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAAGGAAACCAGAG
AY118157.1/126-224  CUCUGGUAACUAGAGAUCCCUCAGACUACUUUUGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCCGAAAGCGAAAGUAAGACCAGAG
K03458.1/5030-5128  CUCUGGUAACUAGAGAUCCCUCAGAUACCUUUAGUCAGAGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGUCCUGAAAGCGAAAGUAGAACCAGAG
L28914.1/463-561    CUCUGGUAACUAGAGAUCCCUCAGACCCAUUUAGUCAGUGUAA--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCCGAAAGCGAAAGUAGAACCAGAG
AF096644.1/518-615  CUCUGGUAACUAGAGAUCCCUCAGACC-AUUUUGGUAGCGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCCGAAAACGAAAGUAAGACCAGAG
AF254707.1/516-614  CUCUGGUAACUAGAGAUCCCUCAGAUCUCUUUGGUCUGCGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAGAACCAGAG
L28876.1/483-581    CUCUGGUAACUAGAGAUCCCUCAGACCAUUUUAGUCAGUGUGG--AAAAUCUCUAGMAGUGSCGCCCGAACAGGGACUUGAAAGCGAAAGGGAAACCAGAG
AY352275.1/580-677  CUCUGGUAUCUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGUGAAAGUUAA-CCAGAG
U80508.1/412-510    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAACGAAAGUGAGACCAGAG
L28850.1/453-551    CUYUGGUAGCUAGAGAUCCCUUAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGUGAAARGRGAACCAGAG
U81465.1/411-509    CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUUAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAACGAAAGAGAAACCAGAG
AJ271445.1/577-675  CUCUGGUAGCUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUAG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGUGAAAGUUGAACCAGAG
AY517299.1/14-112   CUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGGGAAACCAGAG
AF465242.1/652-750  CUCUGGUAACUAGAGAUCCCUCAGACCAUUUUAGUCAGUGUGG--AAAAUCUCUAGCAGUGGCGCCCGAACAGGGACCGGAAAGCGAAAGAGAAACCAGAG
DQ373063.1/124-224  CUCUGGUAUCUAGAGAUCCCUCAGAUAACUGUAGUCUGUGCGGCCAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAACGAAAGUAAGACCAGAG
#=GC SS_cons        (((((((,,<<<<<<<<__________________________..___>>>>>>>>,,,,,,,,<<<_____>>>,,,,,,,,,,,,,,,,,,,)))))))
#=GC RF             CuCuGGuAaCuaGaGauCCCUCAGACccuUuUaGucaGUGUGG..AAAauCuCuaGCAGUGGCGCCCGAACAGGGACuuGAAAGcGAAAGuaaAaCCaGaG
//
# STOCKHOLM 1.0

#=GF AC   RF00376
#=GF ID   HIV_GSL3
#=GF DE   HIV gag stem loop 3 (GSL3)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14757051
#=GF SS   Predicted; PFOLD
#=GF GA   42.00
#=GF TC   42.00
#=GF NC   41.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019074; viral RNA genome packaging;
#=GF RN   [1]
#=GF RM   14757051
#=GF RT   RNA interactions in the 5' region of the HIV-1 genome.
#=GF RA   Damgaard CK, Andersen ES, Knudsen B, Gorodkin J, Kjems J
#=GF RL   J Mol Biol 2004;336:369-379.
#=GF RN   [2]
#=GF RM   14517075
#=GF RT   Deletion of stem-loop 3 is compensated by second-site mutations within the
#=GF RT   Gag protein of human immunodeficiency virus type 1.
#=GF RA   Rong L, Russell RS, Hu J, Laughrea M, Wainberg MA, Liang C
#=GF RL   Virology 2003;314:221-228.
#=GF CC   This family consists of several HIV gag stem loop 3 (GSL3) sequences. GSL3
#=GF CC   is known to direct specific packaging of HIV-1 genomic RNA. Deletion of
#=GF CC   GSL3 leads to decreases in both viral RNA packaging and dimerisation [2].
#=GF WK   HIV_gag_stem_loop_3_(GSL3)
#=GF SQ   72


Z97095.1/19-102     GGCCAGGGGGAAA-GAAAAAAUAUAGAUUAAAGCUUCUAGUAUGGCCAAGCAGGGGACUAGGCCGAUUCGCAGUUAAUCUUGCCU
AF017874.1/1-83     GCCCGGGGGA-AA-GAAAAAUUUUAAUUUAAAACAUAUAGUAUGGGCNAGCACGGAGUUAGAANGAUUCGCAGUCAAUCCUGGCC
AY169804.1/341-424  AGCCAGGAUCUAA-AAAGAAAUAUAGGCUAAAACAUUUAAUAUGGGCAAGCAAAGAGCUGGAAAGAUUCGAAUGUAAUCCUGGUC
AY161884.1/173-253  GGCCAGGGGG-AA-GAAAA--UUUAGAAUGAAACAUUUAGUAUGGGCAAGCAGGGAGCUGGACAGAUUUGCACUCAACCCUGACC
AB034898.1/65-148   GGCCGGGGGGAAA-GAACUUAUAUAGGAUGAACCAUUUAGUAUGGGCAAGCAGAGAGUUAGAAAGAUUCGCACUUAACCCUGAAC
U56340.1/68-151     GGCCAGGAGGAAA-GAAACACUAUAUGCUAAAACACCUAGUAUGGGCAAGCAGGGGGCUGGAAAAAUUUGCACCUUACCCUUGCC
L11796.1/65-148     GACCGGGGGG-AAGGAAAAAAUACAAAAUGAAGCAUCUAAUAUGGGCAAGCAGGGAAUUAGAAAGAUUUGCACUUGAUCCUGGCC
AY128253.1/71-154   AGCCAGGGGG-AAGGAAACGUUAUAUGAUGAAACACCUAGUCUGGGCAAGCAGGGAGCUGGAAAGAUUUGCACUUGACCCUGGCC
AF480722.1/11-94    GGCC-GGAGGAAAAGAAAAAAUAUAGAAUGAAGCAUCUAAUAUGGGCAAGCAGGGAGCUAGAACAAUUUGCAAUUAAUCCAGGCC
U88826.1/220-303    GGCCAGGGGG-AAGGAAAAAGUAUAAACUAAAACAUAUAGUAUGGGCAAGCAGGGAACUGGGGAGAUUUGCACUUAACCGUGACC
AF110972.1/244-327  GGCCAGGGGGAAA-AAAGCGCUAUAUGAUGAAACAUUUAGUAUGGGCAAGCAGGGAGCUGGAAAAUUUUGCACUUAACCCUGCCC
AY128257.1/65-148   GGCCAGGGGGAAA-GAAAUGCUACAUGAUGAAACACCUAAAAUGGGCAAGCAGGGAGCUGGAAAGAUUUUCACUUAACCCUGACC
AY169814.1/328-411  GGUCAGGAUCAAA-AAAGAAAUAUCAACUAAAACAUUUAGUAUGGGCAAGCAAGGAGCUAGAAAGAUUUGCAUGUAAUCCUGAUC
AY093605.1/65-148   AGCCAGGGGGAAA-GAAAAAAUAUAGAAUGAAGCAUCUAGUAUGGGCAAGCAGGGAGUUGGAAAGAUUCGCAGUUGAUCCUAGCC
AY161888.1/169-252  GGCCGGGGGGAAA-GAAAAAAUAUAGAAUGAAACAUCUCAUGUGGGCAAGCAGGGAACUAGAGCGAUUUGCACUUGAUCCUGGCC
AF073400.1/1-82     GGCCAGGGG--AA-GAAAAAAUAUAGACUAAAACAUCUGGUAUGGGCAAGCAGGGAGCUAGAACGAUUCGCAGUUAAUCCCGGCC
AY371170.1/59-142   GGCCAGGGGG-ACGCAAAAGGUAUAAGCUAAAACAUAUAAUAUGGGCAAGCAGGGAGCUAGAACGAUUUGCACUUAAUCCUGGUC
Z97075.1/19-102     GGCCGGGGGGAAA-GAAAAAAUAUAGAUUAAAACAUCUAGUAUGGCCAAGCAGGGAACUAGAACAAUUCGCAGUUAAUUCUGGCU
M17451.1/368-451    GGCCAAGGGGAAA-GAAAAGAUAUAAGUUAAAACAUAUAGUAUGGGCAAGCAGGGAGCUAGAACGAUUUGCUGUCAAUCCUAGCC
AY451105.1/148-231  GACCAGGGAGAAA-CAAAAAGUAUAAAUUAAAACAUAUAGUAUGGGCAGGCAGGGAGCUAGAACGAUUCGCAAUUGAUCCUGGCC
AF443086.1/231-314  GGCCAGGGGGGAA-AAACCAUUAUAUGUUAAAACACUUAGUAUGGGCAAGCAGGGAGCUGGAAAGAUUUGCACUUAACCCUGCCC
L11795.1/65-148     GGCCAGGAGGAAA-GAAACAAUAUAGACUGAAACAUUUAGUGUAGGCAAGCAAGGAGCUAGAAAGAUUCGCACUUAACCCUAGCC
AY038239.1/65-148   GGCCAGAGGGAAA-AAAGAAAUAUCAAUUAAAACAUAUAGUAUGGGCAAGCAGGGAACUAGAACGAUUAGCGGUUAAUCCUGGCC
AY463237.1/304-387  GGCCAGGGGGAAA-GAAAAGCUAUAUGAUAUAGCACUUAAUAUGGGCAAGCAGGGAGCUGGAAAGAUUUGCACUCAACUCUGGCC
AF457064.1/59-142   GGCCAGGGGGAAGGGAAAAA-UAUCGACUGAAACAUUUAGUAUGGGCAAGCAGGGAGCUGGAUAGAUUCACACUUAACCCUAGCC
AY451228.1/148-231  AGCCAGGGAGCAA-GAAAAGAUAUCGAUUAAAACAUAUAGUACGGGCAAGCAGGGAGCUAGAACGAUUCGCAGUCAACCCUGGCC
AB074078.1/95-178   GGCCAGAGGGAAA-GAAAAAAUAUCACUUAAAACAUAUAGUAUAGGCAAGCAGAGAGCUGGAACGACUCGCAGUUAAUCCUGGCC
AF457057.1/59-142   GGCCAGGAAGAAA-GAAAAAAUAUAAAUUAAAACAUCUAGUAUAGGCAAGCAAAGAGCUGGACAGAUUUGCACUUAACCCUAGCC
AF386038.1/65-148   GGCCAGGGGG-AAGCAAAAAAUAUAAAUUAAAACAUAUAAUAUGGGCAAGCAAGGAGCUAGAACGAUUUGCGAUUAAUCCUGACC
AJ437045.1/65-148   CGCCAGGGGGAAA-GAAAAAAUAUAAAUUAAAGCACAUAGUCUGGGCAAGCAGGGAGCUAGAACGAUUCGCAGUUAACCCUAGCC
AF286233.1/200-283  GACCAGGAGGAAA-GAAACGCUAUAUGCUAAAACACAUAGUAUGGGCAAGCAGGGAGCUGGACAGAUUUGCACUUAACCCUGGUC
L04602.1/65-148     GGCCAGGGGGAAA-GAAGAAGUACAAGCUAAAGCACAUCGUAUGGGCAAGCAGGGAGCUAGAACGAUUCGCAGUUAAUCCUGGCC
U43172.1/65-148     GGCCGGGGGGAAA-GAAAAAGUAUCAGAUAAAACAUAUAGUGUGGGCAAGCAGGAAGCUGGAGAAAUUUGCACUUAACCCCGGUC
AJ271370.1/413-496  GGCCAGGGGGAAA-GAAAAAAUACAGAUUGAAACAUUUAGUAUGGGCAAGCAGGGAGCUGGAAAGAUUCGCUUGUAACCCAGGUC
AY451097.1/148-231  GGCCAGGGGG-AAGUAAAAGAUAUAAGCUAAAACAUAUAGUAUGGGCAGGCAGGGAACUAGAACGAUUCGCGGUUAAUCCUGGCC
L11761.1/65-148     GGCCAGGGGG-AAGAAAAAAAUAUAGGCUGAAACAUUUAGUAUGGGCAAGCAGAGAGUUAGAAAGAUUCGCACUUAACCCUAGCU
AB081748.1/65-148   GCCCAGGGGGAAA-GAAAAAAUAUAGAAUAAAACACCUAGUAUGGGCAAGCAGGGAGUUGGAAAGAUUCGCGUUUAACCCUAGCC
AY371169.1/59-142   GGCCGGGGGG-ACGGAAAAGAUAUAGAUUAAAACAUUUAGUAUGGGCAAGCAGAGAGCUGGAAAGAUUCGCACUUAACCCUAGCC
AF491241.1/65-148   GGCCAGGGGGAAA-GGAACACUAUAUGCUAAAACAUUUAAUAUGGGCAAGCAGGGAGCUGGAAAAAUUUGCACUUAACCCAGGCC
AB081226.1/65-148   GGCCAGGGGGAAA-GAAAAGAUAUAUGCUAAAACACCUAAUAUGGGCAAGCAGGGAGCUGGACAGAUAUGCACUUAACCCUGACC
AF543950.1/38-121   GGCCAGGAGGAAA-GAAACAUUAUAUGCUAAAACACCUAAUAUGGGCAAGCAAAGAGCUGGAAAGAUUUGCACUUAACCCUGGCC
AF103818.1/896-979  GACCUGGGGGAAA-GAAAAAGUAUAUGAUGAAACAUUUAGUUUGGGCAAGCAGGGAGCUGGAAAGAUUUGCUUGUAACCCAGGUC
AY371159.1/59-142   GACCAGGGGGAAA-GAAACAAUAUAGAAUGAAACAUUUAGUAUGGGCAAGCAGAGAGUUAGACAGAUUCGCACUUGACCCUGGCC
AF061641.1/256-339  CGCCAGGGGGAAA-GAAAAAAUACAGACUGAAACAUCUAGUAUGGGCAAGCAGAGAGAUGGAGAGAUUUGCACUUAACCCUGGCC
AF084742.1/65-148   GGCCAGGAGGAAA-GAAACAGUAUAGAUUAAAACAUAUAGUAUGGGCAAGCAGGGAACUAGAACGAUUCGCAGUUAACCCUGACC
AJ252872.1/65-148   GGCCAGGGAA-AGACAAAAGAUAUAAACUAAAACAUAUAGUAUGGGCAAGCAGGGAGCUAGAACGAUUUGCAUUAAAUCCUGGCC
AY134921.1/65-148   GGCCAGGAGGAAAAGAGAAA-UAUCAAUUGAAGCAUAUAGUAUGGGCAAGCAGGGAGCUAGAACGAUUCGCAGUUAAUCCUGGCC
AY206649.1/65-148   GGCCAGGGGGGAA-GAAAAAAUAUCAGUUAAAACAUAUAGUAUGGGCAAGCAGGGAGCUAGACCGAUUCGCACUUAAUCCUGGUC
AF484492.1/59-142   GGCCAGGGGGAAA-GAAACGAUAUAAAUUGAAACAUCUAGUAUGGGCAAGCAGGGAGCUGGAAAGAUUUGCACUUAACCCCAGCC
AF516184.1/262-345  GGCCAGGAGGAAA-GAAAAAGUAUAAACUAAAACAUCUAGUAUGGGCAAGCAGAGAGUUGGAAAGAUUCGCAAUUAACCCUAGCC
AJ249235.1/65-148   GGCCAGGGGGAAA-GAAAAAAUACAGGCUAAAACAUCUAGUAUGGGCAAGCAGGGAGCUAGAACGAUUUGCACUUAACCCUAACC
AF286236.1/352-435  GGCCAGGGGG-ACGCAAAAAAUAUAGACUAAAACAUCUAGUAUGGGCAAGCAGGGAGCUGGAAAAAUUCGCAAUUAACCCUGGUC
AF484517.1/59-142   GGCCAGGAGGAAA-GAGAAAAUAUAGGCUGAAACAUCUAGUAUGGGCAAGCAGGGAGCUGGAAAGAUUCGCACUUGACCCUGGCC
AF484506.1/59-142   GGCCAGGGGG-AAGCAAAAGAUAUAGACUAAAACAUAUAGUAUGGGCAAGCAGAGAACUAGAACGAUAUGCACUUAAUCCUGGCC
AF069673.1/59-142   GGCCAGGGGGAAA-GAAAAAAUAUAAACUGAAACAUAUGGUAUGGGCAAGAAGGGAGCUGGAAAAAUCCGCACUUAACCCUAGCC
AF418330.1/65-148   GGCCAGGGGGAAA-AAAGUGUUAUAAAUUAAAACAUAUAAUAUAGGCAAGCAAGGAGCUAGAACGAUUCGCAGUUAACCCUGGCC
L32865.1/729-812    GGCCAGGGGGAAA-GACACUAUAUAAACUAAAACAUAUAAUAUGGGCAAGCAGGGAGCUAGAGCGAUUCGCAGUUAAUCCUGGCC
U11549.1/65-148     GGCCAGGAGGAAA-GAAAAAAUAUGCACUAAAACAUUUGAUAUGGGCAAGCAGGGAGCUAGAACGAUUUAAACUUAAUCCUGGCC
AF281696.1/65-148   GGCCAGGGGGAAA-GAAAAUGUAUAAACUAAAACAUAUAGUAUGGGCAAGCAGGGAACUAGAAAGAUUCGCACUUAACCCCGGUC
AJ249237.1/66-149   GGCCGGGGGGGAA-GAAAAAAUAUAGGCUGAAACAUAUAGUAUGGGCAAGCAGGGAGCUAAAACGAUUUGCACUUAAUCCUGGCC
AJ276595.1/171-254  GGCCAGCGGGAAA-GAAAAAAUAUAGAAUGAAACUUCUAGUAUGGGCAAGCAGGGAGUUGGAAAGAUUUGCAAUUAACCCUGGCC
AF075703.1/195-278  GGCCGGGGGGAAA-GAAACAAUAUAGAAUAAAACAUCUAGUAUGGGCAAGCAGGGAGCUAGAACGAUUUGCAAUAGAUCCUGGCC
AF443105.1/231-314  GGCCAGGGGG-AAGGAAAAAAUAUAGGCUAAAACACUUAGUAUGGGCAAGCAGGGAGCUGGAAAAUUUUGCACUCAACCCUGGCC
AY371160.1/59-142   GGCCAGGGGGAAA-GAAACAAUAUAGACUAAAACAUCUAGUAUGGGCAAGCAGGGAGCUGGACAGGUUCGCGCUUAACCCUGGCC
AF286242.1/334-417  GGCCAGGGGGAAA-GAAAAAAUAUAGACUAAAGCAUUUGGUAUGGGCAAGCAGAGAGCUGGAAAAAUUUUCAAUUAACCCUGGCC
AB081212.1/65-148   GGCCAGGGGGAAA-GAAAUGCUAUAUGUUAAAACAUUUAAUAUGGGCAAGCAGAGAGCUGGAACGAUUUGCAGUUAACCCUGGCC
AF443089.1/230-313  GGCCAGGGGGAAA-GAAACACUAUAUGUUAAAGCAUCUAGUAUGGGCAAGCAGGGAGCUGGAAAGAUUCGCACUCAACCCUGGCC
AB115516.1/65-148   GGCCAGGGGG-AAGCAAAAAGUAUAAGAUGAAACAUAUAGUAUGGGCAAGCAGGGAGUUGGAAAGAUUCGCACUUAACCCUGGCC
AF017892.1/29-112   GGCCAGGGAGUAA-AAAAAGCUAUAAAUUAAAACAUAUAGUAUGGGCAAGCAGGGAGCUAGAACGAUUCGCACUUAACCCUGGCC
AJ437049.1/65-148   GGCCAGGGGGAAA-GAAAAAGUAUAAAUUAAAACAUGUUGUAUGGGCAAGCAGGGAGUUAGAACGAUUCGCAGUCAACCCUGGCC
AY288840.1/65-148   GGCCAGGGGGAAA-GAAAAAAUAUAGAUUAAAACAUCUAGUAUGGGCAAGCAGGGAACUAGAGAGAUUUGCAGUCAACCCUGGCC
AF465242.1/927-1010 GGCCAGGAGGAAA-GAAAAAAUAUAGACUAAAACAUCUAGUAUGGGCAAGCAGGGAGCUAGAACGAUUUGCACUUAAUCCUGGCC
#=GC SS_cons        <<<<<<<<_____._______________________________________________________________>>>>>>>>
#=GC RF             GgCCaGGgGGAAA.GAAAAAaUAUAaauUAAAACAUaUAGUAUGGGCAAGCAGGGAGCUaGAAaGAUUuGCAcUUAAcCCuGGcC
//
# STOCKHOLM 1.0

#=GF AC   RF00377
#=GF ID   snoU6-53
#=GF DE   Small nucleolar RNA U6-53/MBII-28
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   36.00
#=GF TC   36.40
#=GF NC   35.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.39 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300792;
#=GF DR   snoopy; Loxodonta_africana300522;
#=GF RN   [1]
#=GF RM   10490628
#=GF RT   Nucleolar factors direct the 2'-O-ribose methylation and pseudouridylation
#=GF RT   of U6 spliceosomal RNA.
#=GF RA   Ganot P, Jady BE, Bortolin ML, Darzacq X, Kiss T
#=GF RL   Mol Cell Biol 1999;19:6906-6917.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   U6-53 or MBII-28 is a member of the C/D class of snoRNA which contain the
#=GF CC   C (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1]. This family possesses sequence complementarity to U6
#=GF CC   spliceosomal RNA and is likely to direct its 2'-O-methylation [1].
#=GF WK   Small_nucleolar_RNA_U6-53/MBII-28
#=GF SQ   25


AF357382.1/1-99              ----------GA-GC-U-GCCAUGCUAAUACUGAGUCACCAGGCAGGGCAGUAUUGUCCUGGUUUGGGUGCCAGUGAGUUUAACAAAACUUCUCAUGUGGAG------ACCUGAGGGA-
AL161747.5/13638-13529       UCCCAAUGAUGA-GU-U-GCCAUGCUAAUACUGAGCCACCAGGUAGGGCAGUGUUGCCCUGGUUUGGGUGCCAGUGAGUUUAACAAAACUUCUCACAUGAAG------AUCUGAGGGGC
AJ243222.1/1-109             UCCCAAUGAUGA-GU-U-GCCAUGCUAAUACUGAGCCACCAGGUAGGGCAGUGUU-GCCUGGUUUGGGUGCCAGUGAGUUUAACAAAACUUCUCACAUGAAG------AUCUGAGGGGU
AL161747.5/8490-8387         CCCCUGUGAUGA-GU-U-GCCAUGCUAAUACGGAGACACCAGGUAGGG-AGUUUUACCCUAACUUGGGUGUU-----GUUGAAAUAAACUCUUUCUCGUAAA------UGCUGAGGGGC
AAYZ01083119.1/8039-7930     CCCCAGUGAUGA-GU-U-GCCAUGCUAAUACUGAGCCACCAGGUAGGGCAGUGUUGCCCUGGCUUGGGUGCCAGUGAGUUAAACAAAACUUCUCACAUGAAA------ACCUGAGGGGC
AAXN01021992.1/297-188       UCCCGAUGAUGA-GU-U-GCCAUGCUAAUACUGAGUCACCAGGCAGGGCAGUGUUGCCCUGGUUUGGGUGCCAGUGAGUUUAACAAAACUUCUCAUGUGGAG------ACCUGAGGGAC
AANN01811685.1/1535-1644     CCUCAGUGAUGA-GU-U-GCCAUGCUAAUACUGAGCCACCAGGCAGGGCAGUGUUGCCCUGGUUUGGGUGUCGGUGAGUUUAACAAAACUUCUCAUGUGGAG------ACCUGAGAGGC
AAQQ01611284.1/1397-1506     UCCCAAUGAUGA-GU-U-GCCAUGCUAAUACUGAGCCACCAGAUAGGGCAGUAUUGCCCUGGUUUGGGUGCCAGUGAGUUUAACAAAACUUCUCAAAUGGAA------ACCUGAGGGAC
AAIY01506494.1/329-438       CCCUCAUGAUGA-GU-U-GCCAUGCUAAUACUGAGCCACCAGGUAGGGCAUUAUUGCCCUGGUUUGGGUGCCAGUGAGUUUAACAAAACUUCUCAUGUGGAG------ACCUGAAGGGC
AAFR03022260.1/171021-171130 CCCCCAUGAUGA-GU-U-GCCAUGCUAAUACUGAGUCACCAGGCAGGGUAGUAUUACUCUGAGCUGGGUGCCAGUGAGUGGAAGAACACUUCUCACAUGGAG------ACCUGAGGGGC
ABDC01344386.1/3970-3862     CCCCUGUGAUGA-GU-U-GCCAUGCUAAUACUGAGACACUAGGUAGGG-AGUUUUACCCUGCAUUGGGUGUUGUUGAGAUAAACUCUACUUCUCCUAAAUCU------ACCUGAGGGGC
AAFC03096048.1/21922-22030   CCCCUGUGAUGA-GU-U-GCCAUGCUAAUUCUGAGACACCAGGUAGGGGAUUUUU-CCCUGCAUUGGGUGUUACUGAGAUAAAUUCUACUUCUCUUAAAUCA------GACUGAGGGGC
AAPY01471620.1/5219-5113     CCCCUGUGAUGA-GU-U-GCCAUGCUAAUACUGAGACACCAGGUAGGG---ACUUACCCUAUGUUGGGUGUUGUUGAGAUAAUCUUUACUUCUCAUGAAUCU------AUCUGAGGGGC
AALT01565313.1/2336-2233     CCCCUGUGAUGA-AU-U-GCCAUGCUAAUACUGAGACAUCAGGUAGGG--GUUUUACCCUGCAUUGGAUGUU-----GUUGAUAUAAAUUCUUUCUUACAUG-----CAUCUGAGGGGC
AAPN01299515.1/98-1          CCCCCGUGACGA-GU-U-GCCAUGCUAAUACCGAGGCAUCAGUCGGAGCAGUGACGCUCUGGGCUGGGUGCCGGUGAGUCAGACCACGCCUCUCACCCGGG------------------
CR388231.17/5989-5875        UUCCAAUGAUGA-GCCU-GCCAUGCUAAUACUGAUGCACCAGAGUUUG-ACUGUGUCUCAC-ACUGGGUGUAAGUGUGUUCAACUAAACUUCUCACACUUGCAGUGUGCUCUGAGGAAA
AANH01002636.1/14075-13974   CUCCGAUGAUGAUCC-C-GCCAUGCUAAUACCGAUACACCAGGCGGAUGCUUGUU-GUCCG-UCUGGGUGUAAGUGAGUUCUACUCACCUUCUCAUG-------------CUGAUGCUA
AAGV020202921.1/5918-5810    CCCCUGUGAUGA-AU-U-GCCAUGCUAAUACUGAGACACCAGGUAGGG-AGUAUUACCCUGCAUUGGGUGUUGUUGAGAUAAACUCUUCUUCUGUUAAAACU------ACCUGAGGGGC
AAWR02001648.1/103235-103130 CCCCUGUGAUGA-GU-U-GCCAUGCUAAUACUGAGAUAUCAGGAGAGG-UGUUUUACCUUGCACUGGGUGUU---GAGAUAAAUUCUGCUUCUCUUAAAUCU------ACCUGAGGGGC
CAAB02005034.1/43076-42979   CUCCAAUGACGA-UC-CAGCCAUGCUAAUACUGAUGCACCAGGUAGGC-----UUUGCCUA-GCUGGGUGCACGUGAGUUCAUCUCACCUUCUCACG-------------CUGACGUUU
AAWZ02028508.1/42509-42401   CACCCAUGAUGA-CU-A-GCCAUGCUAAUACCGAGCCACCGAGUGGAGCUGUCUGCUUUGAACUCGGGUGUCAGUGAGUUAAGCUU-GCUUCUCACAGGAAG------ACCUGAGGUGU
AAQR03183072.1/13926-14035   UCCCAGUGAUGA-GU-U-GCCAUGCUAAUACUGAGACACCAGGUAGGGCAGUAUUGCCCUAGUUUGGGUGCCAGUGAGUUUAAAAAAACUUCUCACAUGGAG------ACCUGAGGGGC
AAEX03009852.1/211746-211637 CCUCAAUGAUGA-GU-U-GCCAUGCUAAUACUGAGUCACCAGGUAGGGCAGUGUUGCCCUAGUUUGGGUGCCAGUGAGUUUAACAAAACUUCUCACGUGGAG------ACCUGAGGGGC
AAGW02024211.1/69094-69202   CCCCUGUGAUGA-GU-U-GCCAUGCUAAUACUGAGACACCAGGACGGG-AGUUUUACCCUGCACUGGGUGUUAUUGAAGUAAACUAUACUUCUCGUCAAUCU------ACCUGAGGGGC
AAPE02015088.1/26433-26541   CCUCGAUGAUGA-AU-U-GCCAUGCUAAUACUGAGCCAUCAGGUGGGGCAGUGUUGCCCUA-CUUGGGUGCCAGUGAGUUGAACAAAACUUCUCAUGUGGAG------ACCUGAGGGGC
#=GC SS_cons                 <<<<--------.--.-.-------------------------<<<<<________>>>>>-----------------------------------------......------>>>>:
#=GC RF                      ccCcaaUGAUGA.gU.U.GCCAUGCUAAUACUGAGaCACCAGGcaGggcAgUuUUaccCuggauUGGGUGuuAgUGAGUUaAAcuaaaCUUCUCauaugaag......AcCUGAgGggc
//
# STOCKHOLM 1.0

#=GF AC   RF00378
#=GF ID   Qrr
#=GF DE   Qrr RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15242645
#=GF SS   Published; PMID:15242645; Moxon SJ
#=GF GA   50.00
#=GF TC   59.20
#=GF NC   42.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.99 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0009372; quorum sensing;
#=GF RN   [1]
#=GF RM   15242645
#=GF RT   The Small RNA Chaperone Hfq and Multiple Small RNAs Control Quorum Sensing
#=GF RT   in Vibrio harveyi and Vibrio cholerae.
#=GF RA   Lenz DH, Mok KC, Lilley BN, Kulkarni RV, Wingreen NS, Bassler BL
#=GF RL   Cell 2004;118:69-82.
#=GF RN   [2]
#=GF RM   25579683
#=GF RT   A qrr noncoding RNA deploys four different regulatory mechanisms to
#=GF RT   optimize quorum-sensing dynamics.
#=GF RA   Feng L, Rutherford ST, Papenfort K, Bagert JD, van Kessel JC, Tirrell DA,
#=GF RA   Wingreen NS, Bassler BL
#=GF RL   Cell. 2015;160:228-240.
#=GF RN   [3]
#=GF RM   17234887
#=GF RT   Multiple small RNAs act additively to integrate sensory information and
#=GF RT   control quorum sensing in Vibrio harveyi.
#=GF RA   Tu KC, Bassler BL
#=GF RL   Genes Dev. 2007;21:221-233.
#=GF CC   This family represents a set of small RNAs (the Qrr RNAs) that are thought
#=GF CC   to be involved in the regulation of quorum sensing in Vibrio species. It
#=GF CC   is believed that these RNAs, guided by a protein, Hfq, can mediate the
#=GF CC   destabilisation of the quorum-sensing master regulators LuxR/HapR mRNAs
#=GF CC   [1].
#=GF WK   Qrr_RNA
#=GF SQ   30


AF228519.1/623-518           UGACCC-UU--U-AAGCCAAAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAAU----UUA---C--UUUCACAUGAACAAUA-A-AGCCAACCG-G---G-A--UA--UU--G-CGGUUGGCUUCUUUUUU
AAOU01000009.1/38611-38505   AUGACU-CU--U-AAGUUAAGAGUCAA-CCUAGCCAACUGACGUUGUUUGUGGAUU----UUU-------UUCACUAAAACAAUG-A-CGCCAACCG-A--AC-C--UU--UUUAU-CGGUUGGCUUUUUUUUA
AAZW01000001.1/225809-225699 UGACCC-UUC-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACCUAUGUUU---U--GUUCACAAAUAU-AUA-G-AGCCAAUCG-C---G-A-UUA--UU--G-CGGUUGGCUAUUUUUUU
AAPS01000011.1/74129-74021   UGACCC-UU--UCUAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACC---AUCU---U--GUUCACAAAUAU-AUA-C-AGCCAAUCA-C---G-A--CUCCUU--G-UGGUUGGCUUUUUUUUA
CP000626.1/316725-316831     UGACCC-UU--C-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACA----CCA--UU--GUUCACACUUAUAG-A-C-GGCCAAUCA-C--AC-U--UC--UU--G-UGGUUGGCCUUUUUUUU
BA000038.2/627093-627201     UGACCCUUU--U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACC----UGA--UU--GUUCACAAAUAU-AUA-C-AGCCAAUCA-CC-UC-G--UA--UU--G-UGAUUGGCUUUUUUUUU
AY525157.1/427-333           UGACCC-UU--A-G-------GGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUA----AAG---U--GUUCACA-----AAUA-ACAGCCAAUAG-A---C-C--UU--UU--U-CUAUUGGCUAUUUUUUU
BA000038.2/77804-77914       CGACCC-UUA-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUA---CACA--UU--GUUCACAUCAUACAUA-A--GCCAAUCG-CACUC-A--UU--UU--G-CGGUUGGUUUUUUUUUU
AAMR01000015.1/54374-54266   UGACCC-UUC-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACC----UUU---GUUGUUCACGAUAUAUAUA-G--GCCAAUUG-C---G-A-AUA--UU--G-CGAUUGGCCAUUUUUUU
AAPS01000004.1/297770-297662 UGACCC-UUA-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUA----CAA-AUU--GUUCACAAGUAU-AUA-C-CGCCAAUCA-C---GUU--UA--UU--G-UGAUUGGCGUUUUUUCU
BA000037.2/1211555-1211462   CGACCC-CU--C---------GGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACC----UAG---U--GUUCACA--AUUGAUA-G---CCAAUAG-U---G-A--AA--UG--A-CUGUUGGCUUUUUUUUG
CR378666.1/200201-200099     UGACUC-UU--A-AUGUA---GAGUCAACCUAGCCAACUGACGUUGUUUGUGGAAU----GAA-------UUCACUAAAACAAUG-A-UGCCAACCG-A---A-A-CUA--UU--C-CGGUUGGUUUUUUUUUA
AAWP01000010.1/13378-13270   UGACCC-UUC-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACU----CGAAUUU--GUUCAC---AAAUAUAUA-AGCCAAUCG-C--AC-A--AA--UU--G-CGGUUGGCUAUUUUUUU
ABCH01000003.1/97606-97713   CGACCC-UC--U-GAUUUAA-GGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACAC--CUCU---U--GUUCACACG--UUAUA-U-AGCCAAUCG-CCUUG-U--UU--UC--G-CGAUUGGCUUUUUUCUU
AAZW01000005.1/104630-104523 UGACCC-UUC-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACC---UUUA--UU--GUUCACACAAAAUAUA-U-GACCAAUCA-C-----A--CG--UU--G-UGAUUGGUUUUUUUUGC
AAZW01000005.1/96839-96948   UGACCC-UUC-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACCU--AUUC--UU--GUUCACAAAAUAUAUA-A--GCCAAUCG-C---G-A-UUA--UU--G-CGGUUGGCUAUUUUUUU
BA000038.2/524169-524277     UGACCC-UUA-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUA---AUGA-CUU--GUUCACAC-AUAAAUA-C-GGCCAAACA-C---C-U--GA--UU--G-UAUUUGGCCUUUUUUUU
CP001235.1/1112212-1112117   UGACCC-GC----------AAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUA---AUCA--AU--GUUCACA-----AAUA-ACAGCCAAUAG-A---C-U--CA--U---U-CUAUUGGCUAUUUUUUU
CP002470.1/1347248-1347355   UGACCC-UUA-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACU----UGA-UUU--GUUCACAUGUAU-AUA-A--GCCAAUCG-C--AC-C--UU--UU--G-CGGUUGGCUCUUUUUUU
CP002470.1/512141-512249     UGACCC-UUA-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUA---AUGA-CUU--GUUCACACAUAU-AUA-C-GGCCAAACA-C---C-U--GA--UU--G-UGUUUGGCCUUUUUUUA
FM954973.2/366376-366484     UGACCC-UUC-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACC---CAUA--UU--GUUCACACAAAAUAUA-U-GACCAAUCA-C---C-C--UU--UU--G-UGAUUGGUUUUUUUUUG
CP001486.1/573576-573467     UGACCC-UUAAU-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUG----AAA--UU--GUUCACAUUUGUUUUA-UCAGCCAAUCA-C---C-C--UU--UU--G-UGAUUGGCUUUUUUCUU
BA000032.2/782753-782860     UGACCC-UUU-C-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACC----CAA--UU--GUUCACAAGUAU-AUA-C-AGCCAAUCA-C--AC-A--CC--UU--G-UGGUUGGCUUUUUUUUU
CP000626.1/104277-104170     UGACCC-UUG-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUA----GUA--UU--GUUCACAUCAUAUAUA-A--GCCAAUCG-C--GG-U--UC--UU--G-CGAUUGGCUAUUUUUUU
CP000790.1/111193-111301     CGACCC-UUC-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUA---CACA--UU--GUUCACAAAAUACAUA-A--GCCAAUCG-C--CC-U--AA--UU--G-CGGUUGGCUAUUUUUUU
AE016796.2/1358360-1358470   CGACCC-UUA-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUA---CACA--UU--GUUCACAUCAUACAUA-A--GCCAAUCG-CACUU-A--UU--UU--G-CGGUUGGUUUUUUUUUG
BA000031.2/2207453-2207547   CGACCC-CUC-----------GGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACG----AUA---U--GUUCACAA----AACA-A--GCCAAUAGA---CC-C--GA--CU-G-CCUAUUGGCUUCUUUUUU
CP001806.1/296943-296835     UGACCC-UUU-C-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACC----ACU--UU--GUUCACAAAUAU-AUA-C-AGCCAAUCA-C--G--AAUCC--UU--G-UGGUUGGCUUUUUUUAU
CP001806.1/664518-664626     CGACCC-UUC-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAACUU--GAUU--UU--GUUCACAUGUAU-AUA-A--GCCAAUCG-C--AC-U--CU--UU--G-CGGUUGGCUAUUUUUUU
BA000032.2/200580-200688     UGACCC-UUA-U-UAAGCCGAGGGUCA-CCUAGCCAACUGACGUUGUUAGUGAAUA---CACA--UU--GUUCACAAGUAU-AUA-C-CGCCAAUCA-C--CU-U--UC--UU--G-UGAUUGGCGUUUUUUCU
#=GC SS_cons                 <<<<<<.___._.________>>>>>>.,,,,,,,,,,,,,,,<<<<--<<<<<<<....___.._>..>>>>>>------->>>.>.,,<<<<<<<.<..._._..__..__..>.>>>>>>>::::::::::
#=GC RF                      uGaCCC.UUa.u.uAagccgAGGGuCa.CCUAGCCAACUGACGuugUUAGUGaAca....uua..Uu..gUuCACAaaaauaAua.a.aGCCAAccG.c...c.a..ua..UU..g.CggUUGGCUuUUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00379
#=GF ID   ydaO-yuaA
#=GF DE   ydaO/yuaA leader
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Barrick JE, Breaker RR
#=GF SS   Predicted; Barrick JE, Breaker RR
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   36.20
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   15096624
#=GF RT   New RNA motifs suggest an expanded scope for riboswitches in bacterial
#=GF RT   genetic control.
#=GF RA   Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M,
#=GF RA   Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR
#=GF RL   Proc Natl Acad Sci U S A 2004;101:6421-6426.
#=GF CC   This family represents a conserved RNA structure found upstream of the
#=GF CC   ydaO and yuaA genes in Bacillus subtilis and related genes in other
#=GF CC   bacteria. The ydaO/yuaA element is thought to act as a genetic "off"
#=GF CC   switch for the ydaO and yuaA genes in its native state. It is believed
#=GF CC   that the element may be triggered during osmotic shock leading to
#=GF CC   activation of ydaO, a predicted amino acid transporter gene, and members
#=GF CC   of the yuaA-yubG operon which code for KtrA and KtrB K+ transporters [1].
#=GF WK   YdaO/yuaA_leader
#=GF SQ   106


AL939120.1/174742-174619     CCAGGUAAGUCGCC-G-C--ACCG---------------GUCA----------------------------CC-ACCGGAG-----CG-------------------------------------GCU---------CGGGGU-GAA-GCCGUACCC---------------------------------------------------------GUCAGGG------------------------CACGGCCGGGC--------ACCUCCC---C------------GCCCGAACCCGACAGCUCACCUCGCA-GGCG-U----AAGGAGAGGGA
AL939118.1/280215-280371     CGUGCGCACGCGCC-G-A--AUCCC--------------GCAA---------------------------GGG-AACCGGGGA-ACCA------------------------------------CCACA-------UUGGGGU-GAA-UCGGGCG------------------------------------------------------------UAUGCCGCCGUGGGAACACGGUCGGCAGGCACCCGUAGGAG--------ACCUUCCU--G------------CUCCGAACCCGUCAGCUAACCCGGUA-GGCG---AAAGGAAGGAAAGG
AL939121.1/140405-140238     AGUCCGGCCUGCCC-G-C--A-CG---------------GCAC----------------------------CGGAGCCGGGGA-CCCAACCGA-------------------------------GAACU-------UUGGGGU-GAA-UCGGCCUCACCGCCCUCGACGCGAGGACG-------------------------------------GUCC----------------------------GCCGUAGGGCAA------ACCUUCCGC-G-----CCACACCGCCCGAACCCGACAGCUAACCCGGUA-GGCGGAGCACUGGAAGGAGUC
AL939115.1/44787-44621       UCGCGUCAAGCGCC-G-A--AGGC------------------A----------------------------GG-AGCGGGGGA-CCCAAGGUAAGUGCCGCACCGGGCAGUUGAGCCGGAGCGGCUAGGG------GUGGAGCCGAG-UUCCGCGA----------------------------------------------------------GGAAC--------------------------CCGGC-CGGGCA-------ACUCAACC--G------------GCCCGAACCCGACAGCUCACCUCGCA-GGCG-U-CGGUGAGGGGAUCA
AF299117.1/4182-4326         UGUAGUCAAG-GCU-G-A--AUUUCCC------------AAAAAG-------------------------GAA-AACGGGGGA-ACCA-------------------------------------UAAU--------GGGGGU-GAA-UCACUUUUUAGGAG----------------------------------------------------UUAAACUUCUUG-------------------AAGUGACGGAAA-------GGUAUCA----------------UUCCGAACCCGGCAGCUAACCUCGUA-AGCG----UGUGAACCGUUUU
BX927150.1/172169-172001     CAUUCAUGUGGGCCAU-A--UUGCA--------------GACA---------------------------GGG-A-CGGGGAA-ACCACCCACCAUCUUUUCACAAAAGAAGGCAUGGAGGC--CAACUCC-----UUGGGGU-GAA-GCCAG-------------------------------------------------------------ACAUCC-------------------------ACUGGCAGAGCA-------ACUCCUC---C------------GCUCUAACCCGACAGCUAACCUCG-ACGGCG-ACAAAUGAGAGGAAAA
AL939125.1/103160-103305     AGUCCCCGUACGGC-GCG--AGCC---------------AGG-----------------------------GG-AGCCGGGGA-CCCAUC----------------------------------GCAGUCC-----CUGGGGU-GAA-UCGGACGCCCGCG-----------------------------------------------------CGCACCGCGAGGGG-----------------GUCCGUAGGAG--------ACCUUCCA--C------------CUCCGAACCCGUCAGCUAACCCGGUA-GGCG------AGAGGGAAGGA
AAES01000021.1/15273-15418   AACCUAAAAUCGCU-GAG--UUCCA--------------GAAA---------------------------UGG-AGCGGGGGA-ACCAAUUUUGUGCAUC------------------------GUCAC-------UUGGGGU-GAA-UCUUUCA-----------------------------------------------------------GUUUU--------------------------GAAAGUAGGGCU-------ACUCUUUA--G------------GCCCGAAUCCGACAGCUAACCUCGUA-AGCG---UUUAGAGAGGAGGU
BA000043.1/224415-224554     GAAUAUUUAGCGCU-G-A--AUCCG--------------UCAU----------------------------GG-AGCGGGGGA-CCCACUUGUUGCAACGCUC---------------------GUUGC-------UAGGGGU-GAA-UCC---------------------------------------------------------------GAAA------------------------------GGACGGGCA-------UCUCUCCA--A------------GCCCGAACCCGACAGCUAACCUCGCA-AGCG-C-UUUGGGGAGGGACG
AE017225.1/3137586-3137727   UAAAACCUUUUGCU-G-A--GUCCA--------------AAUUU--------------------------UGG-AGCGGGGGA-ACCACUUUUGUAGCUAUG----------------------CUACU--------UGGGGC-GAA-UCUU--------------------------------------------------------------UUUU-----------------------------AAGUAGGGA--------ACUCUCAC--U------------UCCCGAGUCCGACAGCUAACCUCGUA-AGCG-UAAUGGGAGAGGAAGG
AAEK01000002.1/18140-18287   UUUUGUAAUACGCU-G-A--GUCCA--------------AUUAUA-------------------------UGG-AGCGGGGGA-ACCAAUUUGUGCAUU-------------------------GUCAC-------UUGGGGU-GAA-UCUUU-------------------------------------------------------------CAAUUUU------------------------GAAAGUAGGGCU-------ACUCUCAA--A------------GUCCGAAUCCGACAGCUAACUUCGUA-AGCG-UCUUGAGAGAGGACGG
CP000764.1/713115-713260     AACCUUAUAUCGCU-G-A--GUCCA--------------AUGAUU-------------------------UGG-AGCGGGGGA-ACCAAUUUUGUGCAUU------------------------GUCAC-------UUGGGGU-GAA-UCUUUCA-----------------------------------------------------------UGAU---------------------------GAAAGUAGGGCU-------ACUCUUUA--G------------GCCCGAAUCCGACAGCUAACUUCGUA-AGCG---UUUGGAGAGGAGGU
CP000478.1/2207806-2207671   CCGGAGUAAUCGCC-G-A--GUCCU--------------GCAUGGGC-----------------------AGG-AGCGGGGGA-ACCG------------------------------------AGUUU-------UUGGGGC-GUA-UCGCCGA-----------------------------------------------------------UCAU----------------------------GGCGAAGGGCA-------AGCUCUUC--G------------GCCCGAGCCCGUCAGCUAACCUCGCA-GGCG-U-CGAAGGGUAGAGCC
AAOX01000019.1/14342-14479   UCGAAAGAUGCGCU-U-A--AUCUU--------------UUAA----------------------------AG-AGCGGGGGA-UCCAACCGGCAUACAC------------------------AUGCC-------UCGGGGU-GAA-UCCU--------------------------------------------------------------UUAC-----------------------------AGGUAGGGC--------ACUCUCAA--A------------GCCCGAAUCCGACAGCUAACCUCGUA-AGCG-U-UAUUGAGAGGACAA
AE017333.1/525158-525301     AAUCCAAAAUCGCU-U-A--AUCUA--------------AAAA----------------------------AG-AGCGGGGGA-ACCAUUUAGAGGCGUAC-----------------------AGCCU-------CCGGGGU-GAA-UCCUU--------------------------------------------------------------UUA----------------------------AAGGUAGGGCAA------ACUCUCGU--G-----------AGCCCGAAUCCGUCAGCUAACCUCGUA-AGCG-UUAAGAGAGAGGGAGA
CP000726.1/1414382-1414259   AAACAAAUCAUGCC-G-A--AUCUUCUUU----------AUGA----------------------------AG-UACCGGGGA-UACU----------------------------------------C-------UUGGGGU-GAA-UCUCU-----------------------------------------------------------------U--------------------------AGGAAUAGGGU--------ACCUCUA----------------ACCCGAACCCGUCAACUAACCUGGGA-GGCA-A-UAUGGAGGGAUUUA
AAFX01048773.1/685-551       ACAACUAAAACGCU-C-A--AUUCCCG------------AGAAG--------------------------GGG-AGCGGGGGA-CCCA------------------------------------AUCCG-------UUGGGGC-GAA-UGGUCCG-----------------------------------------------------------CUUG----------------------------GACCUAGGGCAA------GCUCUUCA--U------------GCCCGAGCCCGACAGCUAACCCCGUA-AGCG---UGGCGAGAAGAGCU
CP000764.1/2226760-2226900   UAAAACCUUUUGCU-G-A--AUCCA--------------CUAUG--------------------------UGG-AGCGGGGGA-CCCAUUUUUGUAGCAUUUG---------------------CUACU--------UGGGGC-GAA-UCUUU--------------------------------------------------------------------------------------------UUAAGUAGGGAA-------ACUCUCAC--U------------UCCCGAGUCCGACAGCUAACCUCGUA-AGCG---UAAUGGGAGAGGGA
AAEK01000002.1/19276-19421   AACCUAAAAUCGCU-G-A--GUUCU--------------AGAAA--------------------------UGG-AGCGGGGGA-ACCAAUUUUGUGCAUU------------------------GUCAC-------UUGGGGU-GAA-UCUUUCA-----------------------------------------------------------UUUUU--------------------------GAAAGUAGGGCU-------ACUCUUUA--G------------GCCCGAAUCCGACAGCUAACCUCGUA-AGCG---UUUAGAGAGGAGGU
AAXV01000026.1/33590-33441   AUUUCUAAAUCGCU-G-A--AGCAA--------------ACUA----------------------------GA-CGCGGGGGA-CCCAUUUUAGACGGAGUGCAUAAG----------------CAAUCC------UUGGGGU-GAA-UCUCU-------------------------------------------------------------UCUUUUG------------------------AAGGGUAGGGCU-------ACUCAG-----------------GCCCGAAUCCGACAGCUAACCUCGUA-AGCG---UUAAGAGCAGAUAA
AP008230.1/891859-892004     UGCAGUCAAG-GCU-G-A--AUUUCCCA-----------AAAAG--------------------------GAA-AACGGGGGA-ACCA-------------------------------------UAUU--------GGGGGU-GAA-UCAUUGUUAAGGAGAGCAAA----------------------------------------------CUCCUUA------------------------AAAUGACGGAAA-------GGUAUCA----------------UUCCGAACCCGGCAGCUAACCUCGUA-AGCG----UGUGAACCGUUUU
CP000252.1/1919119-1919252   UAAUGCAUGGCGCU-U-A--AUCCUCGAUUC--------AAGA----------------------------GG-AGCGGGGGA-CCCG------------------------------------UUCUC-------CUGGGGC-GUA-UCGCC-------------------------------------------------------------AUUU----------------------------GGCGUAGGGCA-------CCUCUUC---G------------GCCCGAGCCCGUCAGCUAACCUCGCA-GGCA-U-CGAUGAGGGGACUC
CP000612.1/2967251-2967121   UAUUAAAAAACGCC-U-A--AUUUC--------------UAUU---------------------------GAA-AGCGGGGGA-ACCAG-----------------------------------UUAUU-------AUGGGGU-GAA--CUACCA-----------------------------------------------------------GUGU----------------------------GUAG-CGGGCU-------AACUUUC---U------------GUCCGAACCCGUCAGCUAACUCCGUA-GGCG-UAGAAAGUGGGGAAAU
BA000030.3/4374746-4374567   GUCGCGUAAGCGCC-G-C--AGGC------------------A----------------------------GG-AGCGGGGGA-CCCAAGGUAGGCGCCGGGCCCAGCACUUGAGGCUGGU---CCGGC-------UAGGGGU-GAA-GUCGCGCGCC--------------------------------------------------------GGAAUCGGCAGAGGAAGGCG-----------CGCGGCCGGGCA-------ACUCAACC--G------------GCCCGAACCCGACAGCUCACCUCGUA-GGCG-U-CGGUGAGGGGAUCA
AAWL01000001.1/57092-56953   AACAAAGCAAAGCC-G-A--AUUCC--------------GUAU---------------------------GGA-AGCGGAGGA-CCCA------------------------------------CCUUU-------UUGGGGU-GAA-UUCUGCC-----------------------------------------------------------ACAA---------------------------GCAGAAAGGAUGUUU----ACCUCUCU--U---------GCCAUCCUAACCCGACAGCUAACUUCGUA-GGCU-AAAGCAAAGAGGUCGA
CP000141.1/2221513-2221384   AUUAACCAAACGCU-G-A--AUUCCC-------------GUUACG-------------------------GGA-AGCGGGGGA-ACCA------------------------------------CUUUU--------UGGGGU-GAA-UCCU--------------------------------------------------------------UUUC-----------------------------AGGUAGGGCG-------ACUCCUUC--C------------GCCCGAACCCGUCAGCUAACCUCGUA-AGCG-U-CGAAGGGGGAGCAA
CP000382.1/667370-667242     AUCUGAACAAUGCC-G-A--AUCUC--------------CAUUUG-------------------------GAG-UACGGGGGA-UAUA---------------------------------------UU-------UUGGGGU-GAA-ACUUA-------------------------------------------------------------UUUUUAU------------------------AUAAGUAGGGU-----------UCCUC--A------------AUCCUAACCCGUCAACUAACCUCGGA-GGCA-A-AACGAGGAGGAAAU
CP000568.1/1397353-1397223   AGAUUUUAAGCGCU-U-A--AUCA---------------GUUU----------------------------UG-AGCGGGGGA-ACCA-------------------------------------UUUU-------UUGGGGU-GAA-UCUUG-------------------------------------------------------------GUUUUUG------------------------CCAGGUAGGGUUA------ACUCUUUC--G------------ACCCGAACCCGUCAGCUAACCUCGUA-GGCG---UUGAUAGAGGAGUA
CP000612.1/87012-87130       AUGGGAACAAUGCC-G-A--AUCCC--------------AAAG----------------------------GG-UACGGAGGA-ACCG------------------------------------UUUA---------UGGGGU-GAA-UCC---------------------------------------------------------------UUUU------------------------------GGUAGGGAU-------AUCCUU-----------------GCCCGAACCCGUCAGCUAACUCCGGA-GGCA---AAAGGAAAGGAGAA
CP000448.1/1297836-1297702   AUUAGAUUCAUGCC-G-A--AUCCAGUUAA---------AUAAC--------------------------UGG-AACGGGGGA-ACCA--------------------------------------AUU-------UUGGGGU-GAA-UCCGGCU-----------------------------------------------------------UUUG----------------------------CUGGUAGGGCA-------AUCCCCU---U------------GCCCGAAUCCGUCAGCUAACCUCGCA-GGCU-U-UUGGGGGAGGGUAU
CP000721.1/1710119-1709985   AUAUAUGUAACGCU-U-A--AUCA----------------CUU----------------------------UG-AACGGGAGA-ACCA-------------------------------------UUUU-------UUGGGGU-GAA-UCUUA-------------------------------------------------------------UUACACGAUA---------------------AUAAGUAGGGUU-------AAUUUUCU--U----------CAAUCCGAAUCCGUCAGCUAAUCUCGUA-AGCG-U-AGAAGAGAAGUUUU
CP000764.1/711905-712051     GUUUUUGUAACGCU-G-A--GUCCA--------------AUGAUU-------------------------UGG-AGCGGAGGA-ACCAAAUGGUGCAUG-------------------------GUCAC-------UAGGGGU-GAA-UCUUUCA-----------------------------------------------------------UGAU---------------------------GAAAGUAGGGCU-------ACUCUCAA--A------------GUCCGAAUCCGACAGCUAACUUCGUA-AGCG-UUUUGAGAGAGGGUGG
AAOX01000003.1/202929-203071 AGCACUGAAACGCU-G-A--AUCU----------------UAU----------------------------UG-AGCGGGGGA-ACCAACUUUUGACUGCAUGCUG------------------CAGUC-------UUGGGGU-GAA-GCCAU-----------------------------------------------------------------G--------------------------AAUGGCAGGGAG-------ACUCUUAC--C------------UUCCUAAUCCGACAGCUAACUCCGUA-AGCG-U-UGUUUAAGAGAGUG
CP000721.1/3440152-3440282   AUAAUUAUAACGCU-G-A--AUCU----------------UUU----------------------------UG-AACGGGAGA-ACCA-------------------------------------UUUU-------UUGGGGU-GAA-UCUUA-------------------------------------------------------------UUUUAGG------------------------AUAAGUAGGGUU-------AUUUUCUUC-A------------AUCCGAAUCCGUCAGCUAAUCUCGUA-AGCG-U-UGAAGAGAAGUUUU
BA000043.1/3286126-3285968   CCCUAAAGAUCGCU-G-A--AUCCG--------------AAUA----------------------------GG-AGCGGGGGA-ACCAACCGUGGCUUUGUGCG--------------------CCACA--------UGGGGU-GAA-UCCUGUUCAGGACGCCU-------------------------------------------------GUUCUGA------------------------ACGGGUAGGGUG-------ACUCUCAU--C------------ACCCGAAUCCGUCAGCUAACCUCGUA-AGCG---UGUUGAGAGAAGGG
CP000232.1/459162-459290     AAUAAGCGAGCGCU-G-A--AUCCC--------------UGAAUA-------------------------GGG-AACGGGGGA-ACCA------------------------------------CUUCU--------UGGGGU-GAA-UCCU--------------------------------------------------------------UUUU---------------------------C-AGGUAGGGUU-------AACUUUC---G------------ACCCGAACCCGGCAGCUAACUUCGUA-AGCG-U-AGAAAGGUGAGGUG
AAWL01000006.1/97044-96924   AGCUAUAUAAAGCC-U-A--AUCCA--------------GCUC---------------------------AGG-AGCGGGGGA-ACCA------------------------------------UUAC---------UGGGGU-GAA-ACUCU--------------------------------------------------------------UUA----------------------------GGAGUGGGGU--------GCCUUCA----------------ACCCUAACCCGUCAGCUAACCUCGUC-GGCU-U----AGAGAGGAGAA
CP000612.1/3033561-3033714   UAUUAAAACAGGCC-G-A--AUCUCCG------------GAAAUUCCG----------------------GAG-UACGGGGGA-CAAA------------------------------------AAUUA-------AUGGGGU-GAA-UCCGUAACUUUUUCGGAGGUGC--------------------------------------------AAAAAAG------------------------UACGGUAGGGU--------GCCCUCA----------------ACCCGAACCCGUCAGCUAACCUCGAA-GGCC---AGAGGAGGGUAAAA
BA000030.3/5051634-5051477   CGUGCGCGUGUGCC-G-A--AUCCU--------------GCAA---------------------------GGG-AACCGGGGA-ACCA------------------------------------UCAAC-------UUGGGGU-GAA-UCACGCGGAUGCCGCCGUGGCAACACGGCA------------------------------------GGUAUAC------------------------GCGCGUAGGAG--------ACCUUCCU--G------------CUCCGAACCCGUCAGCUAACCCGGUA-GGCC-A-GAAGGAAGGAAAGG
CP000481.1/1069182-1069310   CGAUCGCCCGCGCC-G-A--AUCC---------------ACCA----------------------------GG-AGCCGGGGA-CCCA------------------------------------CCUUCCC-----CAGGGGU-GAA-UCCGC-------------------------------------------------------------GUCC----------------------------GCGGUAGGGCG-------ACUCUUCC--C------------GCCCGAACCCGUCAGCUAACCCGGUA-GGCG---CUGAGGAAGAACAG
AAWL01000002.1/117860-117729 AUACUAAACGUGCC-G-A--AGUUCCUU-----------CAAAG--------------------------GAA-CACGGAGGA-ACCA------------------------------------UUAC---------UGGGGU-GAA-UCCGC-------------------------------------------------------------ACAU----------------------------GCGGUAGGGA--------UUUCCCUU--A------------UCCCGAACCCGUCAGCUAACUUCGUA-GGCA-GAGAAAGGGAGUGGUU
CP000667.1/1922123-1922257   CGUGCCGACCCGCU-C-A--AUCACC-------------GAAAG--------------------------GUG-AACCGGGGA-CCCG------------------------------------UUCUAU------CUGGGGU-GAA-UCCGCGA-----------------------------------------------------------GUCU---------------------------CGCGGUAGGGCG-------UACUUCC---C------------GUCCGAAUCCGUCAGCUAACCCGGUC-AGCG-G-UAUCGGAAGGAGUC
CP000612.1/2353812-2353671   UGUAAAUAAUAGCU-U-A--AUCCU--------------GUAAAUAUAU---------------------GGG-AACGGAGGA-CCCG-------------------------------------ACUU-------UUGGGGU-GAG-UCCGGUU------------------------------------------------------------UUUAAC------------------------GCCGGUAGGGUUUU-----AACCUUUC--G------------GCCCGAACCCGUCAGCUAACUUCGUA-GGCU-U-UAAAGAAAGGGGAG
AAJM01000133.1/9684-9540     AACCUUAAAUCGCU-GAG--UUCCA--------------GAAA---------------------------UGG-AGCGGGGGA-ACCAAUUUUGUGCAU-------------------------CGUCA-------CUUGGGU-GAA-UCUUUCA-----------------------------------------------------------GUUUU--------------------------GAAAGUAGGGCU-------ACUCUUUA--G------------GCCCGAAUCCGACAGCUAACCUCGUA-AGCG---UUUAGAGAGGAGGU
BA000004.3/632283-632434     CACCUUUAAUCGCU-G-A--AUCUC--------------UAUU---------------------------GAG-AGCGGGGGA-ACCAUACCUGACAGAGUUGUUU------------------CUGUC-------UUGGGGU-GAA-UCUUAUG------------------------------------------------------------UUUUUU------------------------AUAAGAAGGGAU-------ACUCUCC---A------------UCCCUAAUCCGACAGCUAACCUCGUA-AGCG-U-UGAUUCGAGAGAGG
AE017194.1/3159877-3160019   UAAAACCUUUUGCU-G-A--GUCCA--------------AAAUU--------------------------UGG-AGCGGGGGA-ACCAUUUUUGUAGCUUUG----------------------CUACU--------UGGGGC-GAA-UCUUAUU-------------------------------------------------------------------------------------------UAAGUAGGGAA-------ACUCUCAC--U------------UCCCGAGUCCGACAGCUAACCUCGUA-AGCG-UAAUGGGAGAGGAAGG
BA000030.3/2949709-2949550   GGACAGUCAUCGCC-G-A--GUCCCC-------------GUAUGGCGCGAGCCAG---------------GGG-AGCCGGGGA-CCCA------------------------------------UCGCAGUCC---CUGGGGU-GAA-UCGGGCACCCUCUCC---------------------------------------------------UGAGGGA------------------------GCCCGUAGGAG--------ACCUUCCU--G------------CUCCGAACCCGUCAGCUAACCCGGUA-GGCG-A-GAAGGAAGGAAAGG
AP008230.1/1719300-1719165   UUAUAAUAAACGCC-U-A--AUCUGGGGU----------AUCC---------------------------UAG-AGCGGGGGA--CUA------------------------------------AAUUU-------CUGGGGU-GAA-UCGCACC-----------------------------------------------------------UCCU---------------------------GUGCGUAGGGCU-------UACACUUU--C------------GCCCGAAUCCGUCAACUAACCCCGUA-GGCU-A-AGAAAGGUGUCUGA
CP000481.1/2373007-2372860   ACGUCGGAGCCGCC-G-A--ACCUG--------------CCUCG--------------------------CAG-GACCGGGGA-CCCAGCACCGGCGCACA-----------------------GCGCC-------CAGGGGU-GAA-UCCGGUG-----------------------------------------------------------UUCGC--------------------------ACCGGUAGGGCG-------AUCUUCCC--C------------GCCCGAACCCGUCAGCUAACCCGGUA-GGCG-G-UCAAGGGAGAGAGG
AE001437.1/1374236-1374371   UCCUUAAGAGUGCC-G-A--AUCUU--------------AAUAAUAUUU---------------------AAG-UACGGGGGA-ACAC---------------------------------------AU-------UGUGGGU-GAA-UCUUACG-----------------------------------------------------------ACUAUUC------------------------GUAAGUAGGGU--------GCCUUCA----------------ACCCGAAUCCGUAAGCUAACCUCGGA-GGCA-A-AAUUGAUAAAGGAA
AP008230.1/5140258-5140118   AAUUAAGUGAAGCU-G-A--AUCUGAGGUACAAA-----GCCU---------------------------CAG-AACGGGGGA-AACG------------------------------------UCACG--------UGGGGU-GAA-UCGCAGG-----------------------------------------------------------AUAU----------------------------UGCGUAGGGCAU------ACACCUUU--U------------GCCCGAAUCCGUCAACUAACCUCGUA-AGCA-G-GAAAGGUGGUCAAA
AP006840.1/606473-606333     CGUCCACAAACGCU-G-A--AUUCCC-------------ACCA---------------------------GGA-AACGGGGGA-CCCA------------------------------------GAAUCCAC----CAGGGGC-CAAGCGCAGUG-----------------------------------------------------------GCUUC--------------------------ACUGCCCGGGCG-------ACACUCCU--G----------CCGUCCGCGCCCGUCAGCUAACCCCGUA-AGCG-U-CGCAGGGGGAGACC
CP000679.1/237778-237930     CCUUUUGAAAAGCU-G-A--AUUCCCAGGG---------GUAAAGCCCUG--------------------GGA-UACGGGGGA-CCCA------------------------------------ACCUUU------UUGGGGU-GAA-UCAGAAG-----------------------------------------------------------CAAAAAAGC----------------------UUCUGUAGGGCUA------ACCCUUUC--G------------GCCCGAACCCGUCAGCUAACCUCGGA-AGCU-UUGAAAGGGAGGCAAA
CP000232.1/1412184-1412326   UAUCCUGGAACGCU-G-A--AUUGC--------------GGUGUGCAGCC--------------------GUA-AGCGGGGGA-CCCA------------------------------------AUUUC-------CCGGGGU-GAA-UCUUGCC-----------------------------------------------------------GGUUAUACCG---------------------GUGGGUAGGGCU-------AGACGUG----------------GCCCGAAUCCGUCAGCUAACUUCGUA-AGCG---UGAAGGGAAUACCG
BA000028.3/1706087-1706245   CCUUUUUAGUCGCU-G-A--AACUGUUGCUUUA------GUAUUGUG-----------------------CAG-UGCGGGGGA-CCCAUUUUUGGCAAUAAAACAU------------------UUGUC-------UUGGGGU-GAA-UCUAA-------------------------------------------------------------AUAU----------------------------UUAGAAGGGAU-------ACUUUAU---G------------UCCCUAAUCCGACAGCUAACCUCGUA-AGCG-U-CAUAGGGAGAAAAG
AE015927.1/2209149-2209011   AUACGUACUAUGCU-G-A--AUCCUAUUUAAAA------AAAU---------------------------AGG-UACGGAGGA-ACCA------------------------------------AGAAA-------UAGGGGU-UAA-UCUUUAA-----------------------------------------------------------AUGUU--------------------------UAAAGAAGGGAA-------AACCUUG---A--------------CCUAACCCGUCAGCUAACUUCGGA-AGCA-A-GAAAGGUGGAAAAA
AAOX01000003.1/202757-202896 UGACCUGAUCCGCU-G-A--AUCC----------------AUA---------------------------CAG-AACGGAGGA-CCCAACUGAUUAUUCCAGAA--------------------UAAUU-------AUGGGGU-GAA-GCC---------------------------------------------------------------GAAA------------------------------GGCCGGGGG-------ACUUCUGC--C------------UUCCGAACCCGUCAGCUAACUUCGUA-AGCG-U-UGCAGGAGAGAGGA
CP000728.1/3775383-3775509   UACUAUUAUUAGCC-U-A--AGUUU--------------UUUA---------------------------AAA-CACGGGGAA-ACCA-------------------------------------AAUU-------UUGGGGU-GAA-UCGUA-------------------------------------------------------------AAAU----------------------------UACGUAGGUU--------AUACCUUU--U--------------CCGAACCCGUCAGCUAACCCCGUA-GGCA-AAAGGAGUGAGAAAAU
CP000673.1/279064-278931     CAAUAUCAUUAGCC-U-A--AGUUUUA------------UAAA---------------------------AAA-CACGGGGAA-ACCAGUA---------------------------------CUAUU-------UUGGGGU-GAA-UCGUAAU-----------------------------------------------------------UUAU----------------------------UACGUAGGUU--------AUGCCUUU--U--------------CCGAACCCGUCAGCUAACCCCGUC-GGUA-A-UAAGGAGGAUAUAU
BA000035.2/944145-943971     AAACCACACACGCU-U-C--UACCUUGUAGAAGACUUGCAGAC---------------------------AGG-GACGGGGAA-CCCACCUGCCCACCGCGGGCACCGGAGGUA----------ACUCC-------UUGGGGU-GAA-GCCGAAG-----------------------------------------------------------UUCUCC-------------------------UUCGGCAGGGC--------ACAUCCUC--C------------GCCCUAACCCGACAGCUAACCUCGAC-GGCG-ACAGAUGAGAGGACAU
AAOX01000002.1/156408-156546 AAAAUGAAUCGGCU-U-A--AUCUC--------------AUAUU--------------------------GAG-AGCGGAGGA-ACCA------------------------------------AUUUU--------UGGGGC-UAA-UCCUGCA-----------------------------------------------------------GGAA---------------------------GCAGGAGGGAUGAGAAUGAUCUUUCGC--C------------AUCC-UGCCCGUCAGCUAACUUCGUC-GGCU-A-AAGCGAGUGAGGUC
CP000673.1/658090-657951     CUAUAAAACAAGCC-U-A--AACUU--------------CCAAAACUGGAAUC-----------------AAG-UGCGGGGGAUAACA------------------------------------AUAUU--------UGAGGU-GAA-UCUUUUU-----------------------------------------------------------AUUA---------------------------AAAAGUAGGACA-------AUCCCU-----------------CUCCGAACCUGUCAACUAACCUCGUA-GGCU-A-AUUAGGGAGGAUAU
AE015927.1/2711017-2711139   AAUAACAUAA-GCC-U-A--AGUU----------------UAA----------------------------AA-CGCGGGGGA-ACCA------------------------------------UUAAU--------UGGGGU-GAA-UCACAUU-----------------------------------------------------------UAUU---------------------------UUGUGUAGGUU--------AGCCUU-----------------UACCGAACCCGUCAGCUAACCCCGUU-GGUA---AAAGGAGUGAAUAA
CP000232.1/2197504-2197633   UAUUUUUUAGCACC-G-A--AUUCCCG------------GGUAGGCG-----------------------GGA-AACGGGGGA---UA------------------------------------UUUU---------UGGGGU-GAA-GAGCC--------------------------------------------------------------AAA----------------------------GGCUCCGGGCU-------AACUCUC---G------------GUCCGAACCCGUCAACUAACCUCGUA-GGUG-U-GCGAGAGUGGAGGU
CP000667.1/3890461-3890591   GCGGGGCCACCGCC-U-A--AUCACCU------------GCCAGG-------------------------GUG-AGCCGGGGA-ACCA------------------------------------GGUAC-------CUGGGGU-GCA-UCCGC-------------------------------------------------------------GUCA----------------------------GCGGUAGGGA----------UCUUCC--G------------UCCCGAACCCGUCAGCUAACCCGGUC-GGUG-G-UUGACGGAAGGACA
AAXV01000025.1/10441-10579   AUUUAAUAAUGGCC-A-A--AUCUC--------------AAACAUU------------------------GAG-AACGGAGGA-CCCA------------------------------------AUAUA-------UUGGGGU-UAA-UUCUG--------------------------------------------------------------AAAU--------------------------ACAGAAAGGAUGAGAA---ACUCUUUC--G----------CCAUCC-UACCCGUCAGCUAACUUCGUC-GGCU-A-AAGCGAAGGAGGUC
AE017180.1/2728254-2728393   ACAUUCAUGCAGCC-G-A--GAUCCGUUCGCGA------GAAC---------------------------GGG-UGCGGGGGA-CCCA------------------------------------CUUC---------GGGGGC-GUA-UUCCGGC-----------------------------------------------------------AAUGGCG------------------------CCGGAUAGAGG--------ACUUUCA---G------------CCUCGAGCCCGUCAGCUAACCUCGUA-GGCA-U-CUGGAAGGGCACGA
AP009389.1/2311724-2311891   CUGUAUGCAUCGCU-G-A--AUUCC--------------GAAA---------------------------GGA-AGCGGGGGA-CCCA------------------------------------ACCAU--------UGGGGU-GAA-UCCCGUUCAGCUGCCGGCAACCCUGCGGACACCAACCGGCA-------------------------GCUA---------------------------ACGGGUAGGGCUA------AUUCCUUC--G------------GCCCGAAUCCGUCAGCUAACCUCGCA-AGCG-UUGAAAGGAAGGAUAA
AE001437.1/3232090-3232211   UAUCAUUAGC--CU-A-A--AUUU------------------U---------------------------AAA-AACGGGGAA-ACCA------------------------------------AUUUU--------UGGGGU-GAA-UCGCAUA-----------------------------------------------------------AUAU---------------------------AUGCGUAGGUUU-------GUGCCUU----------------UACCGAAUCCGUCAGCUAACCUCGU--AGAA---UAAAAGGAGGAAGA
CP000002.3/542499-542640     UAGCGCCACACGUU-U-A--AUCCU--------------UUAGU--------------------------AGG-AGUGGGGGA-CCCG------------------------------------AUCAU-------UUGGGGU-GAA-UUUUUCU-----------------------------------------------------------GUUCCCGUGCGAACC----------------GAAAGACGGACA-------UCUCUUC----------------GUCCGAACCCGUCAGCUAACCUCAUC-AACG---UGAAGAGAGUCAUG
BA000030.3/5911883-5911718   AUCAAUCCACCACU-C-A--CUCAC--------------GCACGGC------------------------AGG-AGCGGGGAA-ACCAGGUAAGUCGCCGUCCGGUCACCACGCCGGA------GCGGC-------UCGGGGU-GAA-GCCGCGU-----------------------------------------------------------CCUCGGA------------------------CGCGGCCGGGC--------AUCUCCA----------------GCCCGAACCCGACAGCUCACCUCGCA-GGCG-C-CGGAGAGGAAAUUC
CP000473.1/5838272-5838399   AAUAUGAAGUCGCC-G-A--GCUCC--------------ACCU---------------------------GGA-GACGGGGGA-CCCAAG----------------------------------UUUUU-------UUGGGGC-GCA-GUCC--------------------------------------------------------------GCAA-----------------------------GGACGGAGU--------ACUUUCA---A------------GCUCUAGCCCGACAGCUAACCCCGUA-GGCG-G-AUUUGAGAGUCACC
CP000679.1/819128-818978     AUAUCAAAAAAGCU-G-A--AUUCCUGUGUAAAGAG---CACA---------------------------GGA-UAGGGGGGA-CCCA------------------------------------CUUUU-------UCGGGGU-GAA-UCAAGGC-----------------------------------------------------------AUCUUG-------------------------CCUUGUAGGGCAAAUA---UCCCUUUC--U------------GCCCGAACCCGUCAGCUAACCCCCGA-AGCU-UUGAAAGGGAGGUUUG
BA000030.3/4296121-4296312   GCGCGGCCUCCGCC-G-A--GUCCG--------------GCGUGCCGCCCGUGGCAGC------------UGG-AGCCGGGGA-CCCAAC----------------------------------CGACC-------UCGGGGU-GAA-UCGGCUCAGCCGCCUUGAAGGGCUUCAACCGCCUUGAAGG--------------------------GCAAC--------------------------GACCGUAGGGCA-------AACCUUCC--G----AAGCACGCGCCCGAACCCGACAGCUAACUCGGUA-GGCG-G-AACACGGAAGGAGA
BA000030.3/2009780-2009620   CCCGCACACUCACC-C-G--UGCCC--------------GGCA----------------------------GG-AGCGGGGGA-CCCACAGGCAACAACGCCUGUUCCGGUCUCCGGAA-----CAGGC-------UAGGGGU-CAA-GUCGCGC-----------------------------------------------------------GCAAG--------------------------CGCGGCCGGGC--------AUCUCCA----------------GCUCGCACCCGACAGCUCACCUCGCA-GGCA-U-CGGAGAGGAAUGCA
AL939129.1/64567-64726       ACUCAUCGACCACC-C-G--UACAC--------------GGCA----------------------------GG-AGCGGGGGA-CCCACAGGUAGAACUGCCUGUUCCGGUUCCCGGA------ACGGC-------UUGGGGU-AAA-GCCGCGC-----------------------------------------------------------UCCGG--------------------------CGCGGCCGGGC--------AUCUCCA----------------GCCCGCACCCGACAGCUCACCUCGCA-GGCG-C-CGGAGAGGAAUUCA
AE000516.2/965771-965549     GCCGAUAGCACGCC-G-A--ACUCC--------------AUCCAGUGGGCGAGGGAUUCCGACCGCGGAUGGA-GGCGGGGGA-CCCACCAGGUCCGCCGAGAUCGGACCGGAGCCGCAUACG-GCUCC-------UUGGGGU-GAA-GCCAACGUCGUUCGCCGAUGU---------------------------------------------ACGAC--------------------------CGCGGCCGGGUG-------AUCCUCUC--CACGGCGAAUCCAACCCGAACCCGACAGCUGACCUCGUA-GGCG-UGUACCGAGAGGAAUU
CP000454.1/860269-860482     UCACGGUACGAAUC---A--CCUCC--------------UGGC---------------------------AGA-GGCGGGGGA-ACCACAACCGGCCGUUGCAAGA------------------CGGCC-------UUGGGGU-GAA-GUCCGUCAGCGGCAAAGCACCUCCGACGAAGGAUUCCUUUGGGAUACCCCUGUGUCGGAUGCCUUGCAUUG--------------------------GCGGACCGGGUCUUUG---AUCUCUCU--G------------ACCCGAAUCCGACAGCUAACUCCGCA-GGCU-U-CCCAGAGAGGAUAA
CP000001.1/1793577-1793723   UUUUCUAAAUCGCU-G-A--AACC---------------GCAU----------------------------GG-UGCGGGGGA-CCCGUUCUUAUGGAUUAGUUC-------------------UUAAUCCA----AUGGGGU-GAA-UCCUU-------------------------------------------------------------GAAA----------------------------AAGGUAGGGCU-------ACUCAUA---G------------GCCCGAAUCCGACAGCUAACCUCGUA-AGCG-U-UAUAUUGAGAAGGA
CP001124.1/643212-643081     GGAAUUUAGCAGCC-G-A--GAUCC--------------GUCACCGAC----------------------GGA-UGCGGGGGA-CCCA------------------------------------CUUA---------AGGGGC-GUA-UUCCA--------------------------------------------------------------GACA--------------------------AUGGAUAGGGC--------ACUUCCA---A------------GCCCGAGCCCGUCAGCUAACCUCGUA-GGCA-U-UUGGGAGAGCAUGG
CP001348.1/597732-597876     AAUAAUUUAUCGCU-G-A--AUUAUGGCAGUUUGACU--GCUA----------------------------UA-AGCGGGGGA-ACCA------------------------------------UUCAA-------AUGGGGU-GAA-UCCUGUG-----------------------------------------------------------UUAU----------------------------CAGGUAGGGUU-------AGUCUCUUACA------------ACCCGAAUCCGGCAGCUAACUUCGUA-AGCG-U-UGGGGAGAAAGUGA
CP001348.1/2317685-2317544   AAAUUAAAAA-GCU-G-A--AUCCUC-------------GAAAG--------------------------AGG-UACGGAGGA-ACCA------------------------------------AGAUU--------UGGGGU-UAA-UCCAUUC-----------------------------------------------------------UUUAUUCUUUUAUUG----------------AAUGGUAGGGAG-------GUCCUAUU--G-------------CCCGAGCCCGUCAGCUAACUUCGGA-AGCG---CUACUAUAGGAGGG
CP001022.1/2525926-2525774   UCUCAAAGUACGCC-G-A--GUUCA--------------UGAU---------------------------UGA-AGCGGGGGA-CCCAACCGUCACGACAC-----------------------GUGAC-------ACGGGGU-GAA-UCUUCUC-----------------------------------------------------------AGACAAG------------------------AGAAGUAGGGCA-------AAAUCCUA--G--------GUAUGCCCGAAUCCGACAGCUAACCUCGCA-GGCG-U-UUUAGGAGGGAACG
ABDA02000001.1/440841-440988 UUUUUGUAAACGCU-G-A--GUCCA--------------AUUAUA-------------------------UGG-AGCGGAGGA-ACCAAUUUGUGCGUAG------------------------GCACU--------AGGGGU-GAA-UCUUUCA-----------------------------------------------------------AGUUU--------------------------GAAAGUAGGGCU-------ACUCUCAA--A------------GUCCGAAUCCGACAGCUAACUUCGUA-AGCG-UCUUGAGAGAGGACGG
CP001348.1/872452-872592     GUACAAAAUAUGCU-G-A--AUCCUUGUGAUUUAUG---ACGA----------------------------GG-UACGGAGGA-ACCA------------------------------------AGAAA-------AGGGGGU-UAA-UCCAU-------------------------------------------------------------UUUA---------------------------UAUGGUAGGGUG-------AUCCUAU---U------------ACCCGAACCCGGCAGCUAACUUCGGA-AGCA-CAGUAUAGGAGGAAUA
AE008691.1/1020677-1020802   AGUUAAAACAUGCC-G-A--AUCCCCG------------AUAAG--------------------------GGG-UACGGGGGA-UGUA-------------------------------------AAUU--------UGGGGU-GAA-UCCAC-------------------------------------------------------------GUAU---------------------------UGUGGUAGGGUG-------GCCCUC-----------------ACCCGAACCCGUCAACUAACCUCGGA-GGCA-----AAGGGGGUAAAU
CP000885.1/2073734-2073865   GAUGAAACAAAUCC-G-A--AUAUC--------------UUUAU--------------------------GGU-AGUGGGGGA-ACCA------------------------------------AUUUC--------AGGGGU-GAA-UCUUAGU-----------------------------------------------------------AUUU----------------------------UAAGAGGGGC--------AGCUUGGG--A------------GCCCUAAUCCGUCAGCUAAUCCCAUA-GGAG-AAUACCAAGCGAAUGA
CP000853.1/56237-56106       AUAUACAUAGCGCU-G-A--AUUCU--------------UUUA---------------------------AGA-AGCGGGGGA-ACCA------------------------------------UUAUU-------UUGGGGU-GAA-UCUCAUA-----------------------------------------------------------UCUA----------------------------UGAGACGGGUCA------ACUCUUUC--G------------AUCCGAAUCCGUCAGCUAACCUCGUA-AGCG---UUGAAAGGGGAGAC
CP000850.1/603238-603111     GCGGUACCACCGCC-C-A--AUCGC--------------CGCGGG-------------------------GCG-GGCCAGGGA-ACCA------------------------------------GGCAC-------AUGGGGU-GAA-UCCGC-------------------------------------------------------------AUCA----------------------------GCGG--AGACC-------ACUUCCG----------------GCCCGGACCUGUCAGCUAACCCGGUC-GGCG-G-UCAACGGAAGGGAU
CP001336.1/3262209-3262073   AAGAAAUGUGGGCU-G-A--AUCCG--------------GACCGUGUGUC--------------------UGG-AACGGGGGA---UA------------------------------------AUCUU-------UUGGGGU-GAA-UCGCA-------------------------------------------------------------GUCA----------------------------UGCGUAGGGCUUG-----CACCUUUU--U------------GCCCGAAUCCGUCAACUAACCUCGUA-AGCG-A-CGAAAGGUGGAAAA
CP000850.1/1933321-1933455   CGUGCCGACCCGCU-C-A--AUCGCC-------------GUAAG--------------------------GCG-AACCGGGGA-CCCG------------------------------------UUCCAC------CUGGGGU-GAA-UCCGCGA-----------------------------------------------------------GCUU---------------------------CGCGGUAGGGCG-------UACUUCC---C------------GUCCGAAUCCGUCAGCUAACCCGGUC-GGCG-G-UAUCGGAAGGAGUC
AE008691.1/1853404-1853270   UAAUCGUUAUCGCU-G-A--ACCCG--------------AAAA----------------------------GG-GGCGGGGGA-CCCA------------------------------------CACUU-------UUGGGGC-GAA-UCUCU-------------------------------------------------------------UCCUACGGG----------------------AAGAGUAGGGUU-------ACUCCUUC--G------------ACCCGAGCCCGUCAGCUAACCUCGCA-AGCG-U-GGGAAGGAGAAAUA
AB001488.1/19151-19294       GAAAACAAAUCGCU-U-A--AUCUG--------------AAAU---------------------------CAG-AGCGGGGGA-CCCAAUAGAACGGC--------------------------UUUUUGCCG---UUGGGGU-GAA-UCCU--------------------------------------------------------------UUUU-----------------------------AGGUAGGGCUA------ACUCUCAUA-U------------GCCCGAAUCCGUCAGCUAACCUCGUA-AGCG-U-UCGUGAGAGGAGAU
ACMD01000040.1/12378-12525   UUUUGUAAUACGCU-G-A--GUCCAAAU-----------GUAU----------------------------GG-AGCGGAGGA-ACCAAUUUGUGCGUC-------------------------GUCAC-------UAGGGGU-GAA-UCUUU-------------------------------------------------------------CAAUGUU------------------------GAAAGUAGGGCU-------ACUCUCAA--A------------GUCCGAAUCCGACAGCUAACUUCGUA-AGCG-UCUUGAGAGAGGACGG
CP000924.1/1503502-1503372   UAUGCAAUCUUGCC-G-A--AUCC---------------GAAA----------------------------GG-UACGGAGGA-ACCG------------------------------------CUUUU--------UGGGGU-UAA-UCUGCAG-----------------------------------------------------------UGAAGC-------------------------UGCAGUAGGGAU-------ACCUUCU---G------------UCCCGCACCCGACAGCUAACUCCGGA-GGCA-A-UAAAGGAAGGAGAU
CP000923.1/2119184-2119053   AAAUGCUAAACGCU-G-A--AUUCG--------------UAAA----------------------------GA-AGCGGGGGA-ACCA------------------------------------CUUU---------GGGGGU-GAA-UCCAUCUU----------------------------------------------------------UUGAUAA------------------------GAUGGUAGGGUU-------AUCUUUC---G------------ACCCGAACCCGUCAGCUAACCUCGUA-AGCG---UUGAAAGAGGAGGA
AL009126.3/3188193-3188341   UCUCUUUUACCGCU-U-A--AUCA---------------AACA----------------------------CG-AACGGGGGA-ACCAACGAUUGGCUGUU-----------------------UUAUUAACAGCCUUGGGGU-GAA-UCUUA-------------------------------------------------------------CUAA---------------------------GUAAG-AGGGGGU------ACUCUGAA--U------------CCCU-AAUCCGACAGCUAACCUCGUA-GGCG-UAUACAGAGAGGAGGU
CP000820.1/6974887-6974725   UGACUCCCUCCGAC-G-AGCAUCUG--------------AGGC---------------------------AGG-AACGGGGGA-CCCAUGUUUCUCUGGGCGUCGCCUCCUCGG----------CGCCC-------UUGGGGC-GAA-GCCGGAC-----------------------------------------------------------ACGCAUGAGGCG-------------------UUCGGCCGGGC------------UCCC--A------------GCCCGAACCCGACAGCUCACCUCGCA-GGCG---UAGGGGAAGGACCA
AE008691.1/927258-927390     ACAUGCUAAACGCU-G-A--AUUCG--------------UUAA----------------------------GA-AGCGGGGGA-CCCA------------------------------------CUCUU-------UUGGGGU-GAA-UCCAUCU-----------------------------------------------------------UUUAAAA------------------------GAUGGUAGGGUU-------AUCUUUC---G------------ACCCGAACCCGUCAGCUAACCCCGUA-AGCG---UUGAAAGAGAAGGA
CP000903.1/3134671-3134815   UACAACCUUUUGCU-G-A--GUCCA--------------AAUUU--------------------------UGG-AGCGGGGGA-ACCAAUUAUGUAGCUUUUUG--------------------CUACU--------UGGGGC-GAA-UCUU--------------------------------------------------------------UUUU-----------------------------AAGUAGGGAA-------ACUCUCAC--U------------UCCCGAGUCCGACAGCUAACCUCGUA-AGCG-UAAUGGGAGAGGAAGG
AE008691.1/890816-890945     UUUGCAAUCUUGCC-G-A--AUCC---------------GAAA----------------------------GG-UACGGAGGA-ACCG------------------------------------CUUUU--------UGGGGU-UAA-UCUGC-------------------------------------------------------------GGAUUCC------------------------CGCAGUAGGGAU-------GCCUUCU---G------------UCCCGCACCCGACAGCUAACUCCGGA-GGCA-U-UAAAGGAAGGAGAU
CP001186.1/738417-738564     UUUUUGUAAACGCU-G-A--GUCCA--------------AUUAUA-------------------------UGG-AGCGGAGGA-ACCAAUUUGUGCGUC-------------------------UGCAC-------UAGGGGU-GAA-UCUUU-------------------------------------------------------------CAAAUUU------------------------GAAAGUAGGGCU-------ACUCUCAA--A------------GUCCGAAUCCGACAGCUAACUUCGUA-AGCG-UCUUGAGAGAGGACGG
CP000850.1/4190713-4190844   GCGUGGCCGCCGCC-U-A--AUCGCCU------------GCCAGG-------------------------GCG-AGCCGGGGA-ACCA------------------------------------GGUAC-------CUGGGGU-GCA-UCCGC-------------------------------------------------------------GUCA----------------------------GCGGUAGGGA----------UCUUCC--G------------UCCCGAACCCGUCAGCUAACCCGACC-GGCG-GUUGACGGAAGGACAU
AP008230.1/4597555-4597682   ACUUAAUAUGGGCU-U-A--AUUUC--------------CCAAGGG------------------------GAA-AACGGGGGA-ACCA--------------------------------------AUU-------UAGGGGU-GAA-UCGUU--------------------------------------------------------------UUA----------------------------AACGUAGAGCA-------UGUUUCA----------------GCUCGAACCCGUCAGCUAACCUCGUA-AGCA-U-UGAAGCACAUGAGG
CP001176.1/769318-769465     UUUUUGUAAACGCU-G-A--GUCCA--------------AUUAUA-------------------------UGG-AGCGGAGGA-ACCAAUUUGUGCAGU-------------------------GUCAC-------UAGGGGU-GAA-UCUUUCA-----------------------------------------------------------AGUUU--------------------------GAAAGUAGGGCU-------ACUCUCAA--A------------GUCCGAAUCCGACAGCUAACUUCGUA-AGCG-UCUUGAGAGAGGACGG
CP001083.1/1451441-1451318   AAACAAAUAAUGCC-G-A--AUCUU--------------CUUUACG------------------------AAG-UACCGAGGA-UACU----------------------------------------C-------UUGGGGU-GAA-UCUCU-----------------------------------------------------------------U--------------------------AGGAAUAGGGU--------ACCUCUA----------------ACCCAAACCCGUCAACUAACCUGGAA-GGCG-A-UAUGGAUGGAUUUA
#=GC SS_cons                 ::::::::::{{{{.,.,..,<<<_..............____..........................._>>.>[[[[[[,,.,,<<__.................................._____......._>>(((,.,,,.,<<<<__..........................................................._____.........................._>>>>,,<<<<_.......________.._............>>>>,,,))),,,,,,,,,]]]]]],.}}}}.:.::::::::::::::
#=GC RF                      uauuauaaaacGCc.G.A..Auccc..............auaa...........................ggg.agCGgGGGA.aCCaau..................................cuauu.......UuGGGGU.GAA.Uccgguu...........................................................auauu..........................accgguAGGGca.......AcccUccu..g............gCCCGAACCCGaCAGCUAACCuCGcA.gGCg.u.uaaaGAGaGgAaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00380
#=GF ID   ykoK
#=GF DE   ykoK leader
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Barrick JE, Breaker RR
#=GF SS   Predicted; Barrick JE, Breaker RR
#=GF GA   60.00
#=GF TC   60.90
#=GF NC   59.60
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0032026; response to magnesium ion;
#=GF RN   [1]
#=GF RM   15096624
#=GF RT   New RNA motifs suggest an expanded scope for riboswitches in bacterial
#=GF RT   genetic control.
#=GF RA   Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M,
#=GF RA   Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR
#=GF RL   Proc Natl Acad Sci U S A 2004;101:6421-6426.
#=GF RN   [2]
#=GF RM   21315082
#=GF RT   Insights into metalloregulation by M-box riboswitch RNAs via structural
#=GF RT   analysis  of manganese-bound complexes.
#=GF RA   Ramesh A, Wakeman CA, Winkler WC
#=GF RL   J Mol Biol. 2011;407:556-570.
#=GF CC   This family represents a conserved RNA structure found upstream of the B.
#=GF CC   subtilis ykoK gene and genes with related functions in other bacteria. The
#=GF CC   regulatory role of this RNA element is unknown although it has been
#=GF CC   suggested that it may serve as a genetic "off" switch in response to a
#=GF CC   cellular compound that requires a metal ligand as seen in the Rfam:RF00174
#=GF CC   family [1].
#=GF WK   ykoK_leader
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   157


BX571871.1/238808-238637       GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGUUGCUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-AU-U-AGGACA-GGAUAU-AUCGAA---CCAAGGU--A-U-AUCCCCAUGUAACU-UUCU------------------------GAUAAUU---CAGGA-----UACGUUGUAUA-G-UGCUAAAACCGAG-ACGUA---GAGAUAGUCG
AY129558.1/14501-14670         GCAACAUCU-C-GUUA-GG-C-GAGGCU-CCUGUA-U-AA-AC----------A-----------------------------AAGGCCACUGAUCUCACGACG-UCGAGAGA-CGCCCA-----AG-CU-C-AGGACA-GUUUUC-AUCGGA---UUAAGGU---GU-AAACCCAAGUGGCU-UCCG-------------------------GCAUG----CCGGA-----UACGUUAUACA-G-UGCUAAAGCUGGU-ACGUG---GGGAUGAUGA
BX842577.1/4252-4421           UAAGCACCU-C-GUUA-GG-U-GAGGCG-GCUACA-C-GA-AC----------A-----------------------------UAGGCCACUGACCC-CGAACG-UCGAGAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCUU-CCCGGC---UUAAGGG---UU-GAGCCCAGGUGGCU-UCCG------------------------GCUUAC-----CGGA-----CACGUCGUGUG-G-UGCCGAAGCUCUG-ACGAGA--GGGGUGCGGA
X90691.1/1632-1461             GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------AAGGUUGCUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-AU-U-AGGACA-GGUUAU-AUCGAA--CAGAAGGU--A-U-AACCCGAAGUAACU-UCCCGC---------------------AGUCUGC-----GGGA-----UACGUUGUAUA-G-UGCUAAACCGA-G-ACGU----GAGAUAGCCU
AL596173.1/245334-245167       AGUUUUGCC-U-GUUA-GG-U-GAGGCU-CCUAUG-C-AA-AC----------A-----------------------------CAGGCCACUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGGAUU-GUCGGA---UUAAGGC---UU-UCCAUAAUGUGGCU-AAGA-------------------------GUAAU-----UCUU-----UACGUUGUAUA-G-UGCCAAAACUUUA-GCGAG---GGGAGUCUGU
AL035300.1/11215-11044         CAAGCACCU-C-GGUA-GG-U-GAGGCU-UCUGCA-U-GG-AU----------A-----------------------------UAGGCCACCGAUCC-CGGACG-UCGAGAGA-UGCAUC-----GG-GU-C-AAGACA-ACU---CCCAGGG---UU--GGG---UCCAAGUCCAAGUGGUU-UCUGG----------------------ACGUUGGU---CCAGA-----UAUGCUGUGCA-G-UGCCUAAGCUCCG-GCGAUG-AGGGGAUGCGU
AL591984.1/47104-46938         AGUUUUGCC-U-GUUA-GG-U-GAGGCU-CCUAUG-C-AA-AC----------A-----------------------------CAGGCCACUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGGAUU-GUCGGA---UUAAGGC---UU-UCCAUAAUGUGGCU-AAGA-------------------------GUAU------UCUU-----UACGUUGCAUA-G-UGCCAAAACUUUA-GCGAG---GGGAGUCUGU
AJ250603.1/195-363             UAAUAACCU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUAUUGCCCA-GAAACG-UCGAAAGU-CGCCAA-----UG-GG-U-AAAACA-GAAACU-GUCGGA---UUAAGGC---UU-UUUCCAA--UAGCU-AAGA-------------------------AUGUU----UUCUU-----UACGUUGUAUA-G-UGCUAAAACUCGG-ACGAUG-AGAUGAUGCUA
AB089921.1/2048-2202           AUGGAAAAU-C-GGUA-GG-U-GAGGCUUACCAUA-A-GG-AU----------A-----------------------------CGGAUGACUACCGC-AAAGCAGUGGAGACACUACUCG-----UU-GG-U--CAACA-GUCCU-GAUCG-----CCAAGGU---CA-AGACUAUGCUCAUU------------------------------UCA-----------------UUGCCUUAUG-G-AGUUAAAGCUUGA-ACG-----GUAAAUACUU
AL583922.1/170727-170556       CAAGUGCCU-C-GUUA-GG-U-GAGGGU-UCUGCA-C-GG-AU----------A-----------------------------UAGGCCACUG--------ACG-UCGAACGA-UGCCCA-----GG-AG-C-AGGACA-GUUCCU-CCCAGA---UUAAGGAG-UUU-GAGCCUAAAUUGUU-UCCGGCU-------------------CUCAUUGAG---CUGUA-----CAUGUCGUUUG-G-UGCCAAAGCUCUG-ACGAUA--GGGAGGCCGU
AF031552.1/1396-1226           ACAGCAUCU-C-GUUA-GG-C-GAGGCU-CCUGUA-C-AA-AC----------A-----------------------------UAGGCCACUGAUCUCACGACA-UCCAGAGA-UGCCCA-----AG-AU-C-AGGACA-GUUUUC-AUCGGA---UUAAGGU---GU-UAACCCAAGUGGCU-UUCG------------------------CGUGAG-----CGAA-----UACGUUGUGCA-G-UGCUGAAGCUGGG-ACUCGG--GGAAUGAAGU
AF117609.1/346-514             UAAUAACCU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUGUUGCCCA-GAAACG-UCGAAAGU-CGCCAA-----UG-GG-U-AAAACA-GAAACU-GUCGGA---UUAAGGC---UU-UUUCCAA--UAGCU-AAGA-------------------------AUGUU----UUCUU-----UACGUUGUAUA-G-UGCUAAAACUCGG-ACGAUG-AGAUGAUGCUA
AAFX01011285.1/689-521         AAUAAAGCU-U-GUUA-GG-U-GAGGUU-ACUGGU-U-GA-AC----------A-----------------------------GAGGCUGCUGCCCG-GAAAUG-UCGAAAGA-CACCAA-----UG-GG-U-AGAGCA-GGCGUA-GUCGGA---UUAAGGC---UU-CGCAUAAGGCAGCU-UUCC-------------------------GGAAUC---CGGAA-----UAAGUCAACCU-G-AACUAAAACUC-U-ACGAG---GAGCUUCAUG
AE017194.1/1660591-1660756     AUAAGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AAUGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAUG-AUCGAA---UUAAGGU---UU-UUCUUAACGUAGCU-GGUA-------------------------AUGU-------ACC-----UAUGCUAUACA-G-UGCUAAAACUC-G-GCGAGG-GAGAGGUCCGU
CP000717.1/2055847-2056021     CAAGCACCU-C-GCUA-GG-U-GAGGCG-UCUGCG-C-GG-AU----------A-----------------------------UAGGCCACUGACCU-CGAACG-UCGAAAGA-CGCCCA-----GG-GU-C-AGGACA-GCUCUU-CCCGGC---UUAAGGG---UU-GAGCCCAAGUGGCU-UCCGGCU-------------------GGACCGGC-----CGGA-----UACGCCGUGUG-G-UGCCAAAGCUCUG-ACGAGA--GGGGUGCCGA
CP000412.1/281461-281624       CAAAUGAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------CACGCUAUCGCCCA-GAAACA-UCCAGAGA-UGCCAA-----CG-GG-U-UAAAUA-GAAAUU-GUCGAA---AUAAGGC---AC-UUUC-CAGGUAGCU-AGCA-------------------------UGU--------GCU-----UACGUCACGUA-G-UGUUAAAGCUG-A-GCGAUU--AGUCAAUAGC
AE016822.1/2178766-2178596     AGAGCACUU-C-GUUA-GG-U-GAGGCU-CCUGCG-U-GA-AC----------A-----------------------------CAGGCCACUGAUCUGACGACG-UCGAGAGA-UGCCCA-----AG-AU-C-AGGACA-GGUCUC-CCCGGC---CUAAGGG---GU-GACCCCAGGUGGCU-UCCCG-----------------------CCCGGC-----GGGA-----CACGUCGCGCA-G-UGCCGAAACUCUU-ACGUG---GAAGUGCCGA
CP000416.1/2122885-2122722     AUAAAUUGC-A-AUUA-GG-U-GAGGUU-ACUUUA-A-GA-AC----------A-----------------------------UAGGUUGUUGCCCA-GAAAUG-UCGAGAGA-CAGGAA-----UG-AG-U-AAAGCA-GAAACU-GCCGAA---UUAAGGC---UU-UUUC-AAAACAACU-AGAC-------------------------UAGU-------UCU-----UACGUCUUAAA-G-UGCUAAAACUC-A-AUGAA---UGCGUCGAUA
CP000728.1/236297-236462       UAAUAAUGUAC-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------UACGCUACUGCCCG-GAAACA-UCGAGAGA-UGCCAA-----UG-GG-U--CACCA-GGUAUU-ACCGAA---GUAAGGU---UU-UACUUAAUGUAGCU-GGCU-------------------------GUGG-------UCC-----AAAGCUAUAUA-G-UGCUAAAACUC-A-ACGAUU--GAUGUUAAAG
AASN01000027.1/80343-80511     UAAGCACCU-C-GUUA-GG-U-GAGGCG-GCUACA-C-GA-AC----------A-----------------------------UAGGCCACUGACCC-CGAACG-UCGAGAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCUU-CCCGGC---UUAAGGG---UU-GAGCCCAGGUGGCU-UCCG-------------------------GCUUA----CCGGA-----CAGGUCGUGUG-G-UGCGAAAGCCU-G-ACAGAA--GGGGUCGGUU
AE016830.1/3116366-3116533     AAAUAACCU-U-GUUA-GG-U-GAGGCU-CCUAUC-C-AA-AC----------A-----------------------------UAGGCUAUUGCGCA-GAAAUG-UCGAAAGA-CACCAA-----UG-UG-U-AAAACA-GGAAUG-GUCGAA---UUAAGGC---UC-UUCUAAAAAUAGCU-AAGA-------------------------GAAA------UCUU-----UACGUUGGAUA-G-UGCUAAAGCUCAG-ACGAUG--AGAACCGAUU
CP000482.1/1208117-1207951     GUCGUUCCU-C-GUUA-GAAU-GAGGCG-UUUGCA-C-AA-AC----------A-----------------------------CAGGCUGCUACCCA-GAAACG-UCGAAAGA-CGCCAA-----UG-CG-G-UCAACA-GGUUCU-GCCGGA---UUAAGGC---UU-AACCUAAUGCAGCU-GGCC-------------------------CCAG-------GCC-----UACGUUGUGCU-C-UGCCAAAAUCC-A-ACCAGA--GGGGAAUUGG
ABDV01000005.1/84537-84695     AAUAUUAAU-C-GGUA-GG-U-GAGGUU-ACCACC-G-GG-AU----------A-----------------------------CGGAUUGCUGCCGC-AAAAUAGUGGAGACACUAUGAG-----AA-GG-U--UAGCA-GGCUAU-GUCGAGA-AACAAGGC---AU-AAUCUAAUGCAAUU----------------------------------U-----C--------AUUGCCCAGUG-A-AGCUAAAACUUGA-ACGA----UAUUAUACUU
AARF01000169.1/465-629         GCUAGUCUC-C-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AAUGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAUG-GUCGAA--AAGAAGGC---CC-CUCUUAAUGUAGCU-GGUU-------------------------UUAA-------ACC-----UAUGCUGUACA-G-UGCUAAAACUC-A-ACGAA---GGAGAGGUUA
BA000004.3/3341002-3340838     AGUUGUCUU-C-GUUA-GG-U-GAGGCU-CCUGUG-CUGG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAACG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAC---AUAAGGU---GA-UUUUUAAUGUAGCU-GGAU-------------------------GAU--------UCC-----UAUGCCGCACA-G-UGCUAAAGCUC-U-ACGAAU--GGGGGACAGU
CP000673.1/3641499-3641330     UUUUUGUUA-U-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------UAUGCUACUGCCCG-GAAACA-UCGAGAGA-UGCCAA-----UG-GG-U--CAACA-GGUAUU-ACCGAA---UUAAGGU---UU-UACUUAAUGUAGCU-GGACA----------------------AAAUUUA-----GUCU-----AAAGCUAUAUA-G-UGCUAAAACUCAG-ACGAU---UUAAAAGUUU
AAAK03000021.1/12650-12476     AAUAAGAUU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUACUGCCCA-AAAACG-UCGAGAGA-CGCCAA-----UG-GG-U-AGAACA-GGAAUU-GUCGAG---AUAAGGC---UU-UUCAUAAGGUAGCU-AAAAGCA------------------GGUAUCUGC-----UUUU-----UACGUUGUACA-G-UGUCAAAACUC-A-ACGAUG--AGAUCUGAGA
ABDQ01000001.1/467807-467647   UAAGUACCU-C-GGUA-GG-U-GAGGUU-ACUACA-A-GG-AU----------A-----------------------------CGGGUUGCUACCGUGAAAGAG-UGGAAACA-UUCUAA-----AC-AG-G-UUAGCA-GGUUUU-GCCGAACAAAGAAGGC---UU-AAUCUAAUGCAACU----------------------------------A-----C--------AUUGCCUUGCA-G-AGCCAAAACUUGA-ACGAG---AAAGUAUAGA
BA000004.3/2041941-2042105     AAUCAUCCU-C-GUUA-GG-U-GAGGCU-CCUGUG-CUGG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAACG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAACC-AUCGAC---AUAAGGU---GG-UUUUUAACGUAGCU-GGCU-------------------------UCG--------UCC-----UAUGCCGCACA-G-UGCUAAAGCUC-U-ACGAAU--GGAGGAGUUU
AAWL01000016.1/43438-43265     GUACUUCCU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-AA-AC----------A-----------------------------UAGGCCACUGCCCG-GAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U-AGAACA-GGUAUU-ACCGGC---AUAAGGU---UU-UACUUAAGGUGGCU-GAGCAU--------------------UUUGUUUG-----ACUC-----UACGUUAUACA-G-UGCCAAAGCUCAA-ACGAGU--GGGGAGGUUA
CP000480.1/5735476-5735649     ACCGCGCUU-C-GUUA-GG-U-GAGGCU-CCUACA-C-GA-AC----------A-----------------------------CAGGCCACUGAUCCGACGACG-UCGAGAGA-CGCCCA-----GG-GU-U-AGGACA-GAUCUU-CCCGGC---CUAAGGG---AU-GAUCCGAAGUGGCU-UCCCAC--------------------CUCAAGGU-----GGGA-----CACGUCGUGCA-G-UGCCAAAGCUCUG-AUGAG---GAAGUGCUCG
AP009389.1/428061-428228       UAUGUUCUU-C-GUUA-GG-U-GAGGCU-UCUACA-C-AG-AC----------A-----------------------------UAUGCCACUGCCCG-GAAAUG-UCGAGAGA-CGCCUA-----CG-GG-U--UAACA-GGUACU-GCCGGA---UUAAGGU---UU-UACUUAAUGUGGCU-GGGA-------------------------UCUUU-----UCCC------UAGCUGUGUAUG-UGUCAAAGCUUUG-ACGAGU--GGAGAAGGUU
CP000679.1/1386114-1386270     GAAAUAUCU-C-GGUA-GG-C-GAGGCU-CCUACA-G-GG-AU----------A-----------------------------UAGGCUGCUGCCGCGAAAGAU-UGGAGACA-AUCUGA-----GC-UG-G-UAAACA-GGUUUU-GCCGAA--UCCAAGGC---AU-AACCUAAUGCAGCU------------------------------UUU----------------UAUGCCGUGUA-G-UGCCAAAGCUUGU-AC------GAGGUAGCUA
AE016958.1/3916507-3916677     CAAGCACCU-C-GGUA-GG-U-GAGGCG-UCUGCA-U-GG-AU----------A-----------------------------CAGGCCACUGACCC-CGAACG-UCGAGAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCUU-CCCGGA--CCCAAGGG---UU-GAGCCCAAGUGGCU-UCCG-------------------------GAGCC----CCGGA-----UACGCCGUGCA-G-UGCCGAAGCUCCG-ACGAGA--GGGGUGCGAC
CP000647.1/4212343-4212524     UAACGAUCU-C-GUUAUGG-C-GAGGCU-CCUGCA-U-AA-AU----------A-----------------------------CAAGUUACCGCCCUGUUGGUA-UCGAGAGA-GACCACU---CAG-GG-A-AAUACA-GGCUUCCAUCGAA---UCAAGGU---GU-UGCC-AAGGUAACU-UCUGGCGGU---------------CAUGACCGUU-----CAGA-----UACGUUAUGCA-G-UGCUAAAACCAGG-ACGUA---GGGAUCUGCC
CP000568.1/2645160-2644994     GAAUAUUUU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AG-AA----------A-----------------------------GACGCUGCUGCCCG-GAAACG-UCGAAAGA-CGCCAA-----UG-GG-U--AAACA-GGCACU-ACCGGA---UUAAGGU---UU-UGCUUAAUGCAGCU-GGU--------------------------GUUGC-----AGCC-----UAAGCUGUAUA-G-UGCCAAAGCUC-A-ACGAGG-GAAAGAUAUAA
AE017198.1/1073421-1073588     CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-AA-AU----------A-----------------------------UAUGCUGAUGCCCA-GGAACA-UCCAGAGA-UGCCAA-----CG-GG-U-CAAACA-GGAACU-GUCGAG---UUAAGUC---UU-UUCC-CAGUCAGCU-AGUU-------------------------GAAAA-----AACU----UUACGUUACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUUAAAU
CP000413.1/234944-235115       CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------UAUGCUGUCGCCCA-GCAACA-UCCAGAGA-UGCCAA-----CG-GG-U-CAAACA-GGGAUC-GUCGAU---AUAAGGC---CC-UCCC-CAGCCAGCU-AGUU-------------------------AUUUUUAAUAACCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUAAAAA
AE016958.1/1663674-1663849     CAAGCACCU-C-GCUA-GG-U-GAGGCG-UCUGCA-C-GG-AC----------A-----------------------------CAGGCCACUGACCU-CGAACG-UCGAAAGA-CGCCCA-----GG-GU-C-AGGACA-GCUCCU-CCCGGA---UUAAGGG---UU-GAGCCCAAGUGGCU-UCCGGCU------------------UUUGACGGC-----CGGA-----UACGCCGUGUG-G-UGCCGAAGCUCUG-ACGAGA--GGGGUGCCGC
CP000325.1/5326076-5325906     CAAGCACCU-C-GGUA-GG-C-GAGGCG-UCUGCA-U-GG-AU----------A-----------------------------CAGGCCACUGACCC-CGAACG-UCGAGAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCUU-CCCGGC---CUAAGGG---UU-GAGCCCAAGUGGCU-UCCG-------------------------GAUAGU---CCGGA-----UACGCCGUGCA-G-UGCCGAAGCUCCC-ACGAGA--GGGGUGCGUU
AE016830.1/1024864-1024697     UUUGUAAUA-A-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUAUUGCUCA-GAAAUG-UCGAGAGA-CACCAA-----UG-AG-U-AGAACA-AGACUG-GUCGAG--GAGAAGGC---UU-UUCUCAAAAUAGCU-AAGA-------------------------GUGA------UCUU-----UACGUUGUAUA-G-UGCUAAAGCUC-A-ACGUUC--AUGUUGAUGU
CP000724.1/3301490-3301319     AAAAUAACU-U-GUUA-GG-A-GAGGCU-CCUAAA-U-GA-AC----------A-----------------------------CAGGCUAUUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U-AGAACA-GGCAUG-AUCGGA---UUAAGGU----C-UGCUUAAGAUAGCU-GAUUCA--------------------AUUACUUG-----AAUC-----UACGUCAUUUA-G-UGCUAAAACCAGU-ACGAG---GAGUUAAUAG
AP006627.1/810916-810751       UAUAUUCCU-C-GUUA-GG-U-GAGGCU-CCUGUG-CAGG-AG----------A-----------------------------UACGCUGCUACCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAACC-AUCGAC---AUAAGGU---GG-UUUUUAAUGUAGCU-GGCA-------------------------AUA--------GCC-----UAUGCCGCACA-G-UGCUAAAGCUC-U-ACGAAU-GGAGGCUAUUU
CP000423.1/1285762-1285925     GGUGCUUUC-C-GUUA-GG-U-GAGGCU-CCUAUA-C-G--AA----------C-----------------------------AAUGCUGCUGCUCA-GAAACA-UCGAGAGA-UGCCAA----UUG-AG-U--CAACU-GCGUCU-GCCC-A---UUAAGGC---UU-ACGCUAAUGCAGCU-GAAG-------------------------CUCG------CUUC-----UAGG-CGUAUA-G-UGCUAAAACUA-A-ACGAUU--GGGAUGCUUU
CP000544.1/1425650-1425831     AGCGAGUCC-C-GUUA-GG-U-GAGGCU-CCUGUG-C-CG-AC----------A-----------------------------AGGUGUGCUGCCCA-GAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U-UGAACA-GGCCCU-GCCGAA---CGAAGGC---UU-GGUCUAAUGCACAC-CGCGGCCC----------------GCGCCCUGCG-----CGCGGCCUUUGAGUCGCACA-G-UGCCGAAGCUC-U-ACGAAG--GGGACUUGGU
CP000141.1/329676-329842       UAUUUUCUU-C-GUUA-GG-U-GAGGCU-ACUUCC-U-GG-AU----------A-----------------------------UAGGCUACUGCCCG-GAAAUG-UCGAGAGA-CACCAA-----CG-GG-U--AAACA-GGUAUU-ACCGGC---UUAAGGU---UU-UACCUAAUGUAGCU-GAGG-------------------------GUUU------CCUC-----UAAGCCAGGUU-G-AGCUAAAGCUUUG-ACGAGU--GGAGAAGGUU
CP000413.1/962812-962978       CAAAUGAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-AA-AU----------A-----------------------------UACGCUGAUGCCCA-GCAACA-UCUAGAGA-UGCCAA-----CG-GG-U-UAAACA-GGAAUU-GUCAAC---UUAAGGC---UU-UUCC-CAGUCAGCU-AGUU-------------------------AAAAA-----ACUU-----CACGUUACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUAAAUC
AE017198.1/231904-232076       CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------CAUGCUGUCGCCCA-GCAACA-UCCAGAGA-UGCCAA-----CG-GG-U-CAAACA-GGGAUC-GUCGAU---AUAAGGC---CC-UCCC-CAGCCAGCU-AGUUAUA-------------------UUUUUAUA-----ACCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUAAAAA
AAXV01000059.1/1758-1594       GACUCCCUU-C-GUUA-GG-U-GAGGCU-CCUAUG-U-GG-AG----------A-----------------------------UACGCUACUACCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAA---AUAAGGU---GU-UUUUUAACGUAGCU-GGAU-------------------------AAUU-------UCC-----UAUGCCGCAUA-G-UGCUAAAACUC-A-ACGUUU--GAAGGUAACA
CR936503.1/1082354-1082189     UCGCUUUUC-C-GUUA-GG-U-GAGGCU-CCUAUA-U-GA-AC----------A-----------------------------UACGCUGCUACUCA-GAAACA-UCGAGAGA-UGCCAA----UUG-AG-U--CAACA-AAAACU-GCC-AA---UGAAGGC---UU-UUUCUAACGUAGCU-GAAC-------------------------AUGG------UUUC-----UACGUCAUAUA-G-UGCUAAAACUG-A-ACGAUU--GGGAACGCCA
CP000232.1/409831-409996       GCAAACCUU-C-GUUA-GG-U-GAGGCU-UCUGCA-U-AG-AC----------A-----------------------------GACGCCACUGCCCG-GAAACG-UCGAAAGA-CGCCAA-----UG-GG-U--CAACA-GGUAUU-ACCGGC---UUAAGGU---UU-UACCUAAUGUGGCU-GAGA-------------------------AAAU------UCUC------UAGCUAUGCACG-UGCCAAAGCUC-A-ACGAGU--GGGGGUUAAU
BA000004.3/3340549-3340386     CAACCACUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UAUGCUGCUGCCCA-AAAACG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAC---AUAAGGU---GA-UUUUUAAUGUAGCU-GGCA-------------------------AUG--------UCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAAU--GAAGGGAAUC
AE001437.1/789407-789580       AAAAGUUUU-A-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------UACGCUACUGCCCA-GAAACA-UCGAGAGA-UGCCAAA---UUG-GG-U--CAGCA-GAUAUU-ACCGAA---UCAAGGU---UC-UAUCUAAUGUAGCUGGAUUUA---------------------UAGUUUU-----AAUC-----UAAGCUAUAUA-G-UGCUAAAGCUC-U-ACUGUC--UAAUUUCGUA
CP000479.1/3338383-3338199     UAAGCACCU-C-GUUA-GG-U-GAGGCG-UCUACA-C-GA-AU----------A-----------------------------CAGGCCACUGACCC-CGAACG-UCGAAAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCCU-CCCGGC---UUAAGGG---UU-GAGCCCAGGUGGCU-UCCGGCUCGGA-----------UUGUCGUUCGGGC---CAGGA-----CACGUCGUGUG-G-UGUCAAAGCUCUG-ACGAGA--GGGGUGCGGA
AE001437.1/3501846-3501683     AUAAUGUAU-U-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------UAUGCUACUGCCCA-AAAAUA-UCGAAAGA-UGCCAA-----UG-GG-U--UAACA-GGUACU-ACCGAA---UUAAGGU---UU-UACUUAAUGUAGCU-GGGA-------------------------UUA--------CCC-----AAAGCUAUAUA-G-UGCUAAAGCUC-A-ACGAAA--GAUAGUGUAU
AAJM01000138.1/1999-1823       UGCUGAACC-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGCUAUUGCCCA-AAAAUG-UCGAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGAAUU-GUCGGG---UUAAGGC---UC-UUCUUAAGAUAGCU-AAGUGAUG----------------AAUUUUCAUU-----ACUU-----UACGUUGUAUA-G-UGCCAAAGCUC-U-ACUAGG--GGGAAAAGCC
AE016830.1/1027779-1027612     AUAGAAUCA-U-AUUA-GG-U-GAGGUU-ACUCUGAA-GA-AC----------A-----------------------------CAGGUUAUCGCUCG-GAAAUG-UCGAGAGA-CAGUAA-----CG-AG-U-AAAGCA-GGGAUU-GUCGAA---UUAAGGC----U-UUCCUAAGAUAACU-AGAA-------------------------UUUUU-----UUCU-----UACGUCUCAGA-A-AGCCAAAGCUC-A-AUUAUU--GUGAUUACCC
AE016830.1/1323290-1323457     CUGAAUAAU-U-GUUA-GG-U-GAGGCU-CCUAUU-U-GG-AC----------A-----------------------------AAUGCUGCUGCCGC-GAAAGGAUCGAGAGACCCUUAG-----UU-GG-U-UGAACA-GGAAUA-AUCG-----UGAAGGU---UA-UUCAUAAUGUAGCU-GAUA-------------------------CAUGU-----UAUC-----UACGCCCUAUA-G-UGCUAAAGCUC-A-ACGAUA--GAGAAUCUUA
CP000325.1/3411572-3411396     CAAGCACUU-C-GCUA-GG-U-GAGGCG-UCUGGA-C-GG-AU----------A-----------------------------CAGGCCACUGACCU-CGAACG-UCGAAAGA-CGCCAC----CGG-GU-C-AGGACA-GCUCUU-CCCGGC---UUAAGGG---UU-GAGCCCAAGUGGCU-UCCGGCU------------------UGAAAGCGU-----CGGA-----UACGCCGUGUG-G-UGCCAAAGCUCUG-ACGAGA--GGGGUGCCGC
CP000721.1/3911114-3911286     UAAAAACUU-U-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------CAUGCUGCUGCCCG-GAAACG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGUAUU-GCCGGA---UUAAGGU---UC-UACUUAAUGUAGCC-GAAAAC--------------------CAUAUGGU-----UUUC-----UAUGCUCUAUA-G-UGCUAAAACUC-A-ACGAGU-GAAGGUUAAUA
AE017333.1/1420164-1420328     ACAGCUCUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAU---CUAAGGU---GA-UUUUUAAUGCAGCU-GGCA-------------------------UGCU-------GCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAUG--GAAGGCGUUA
CP000698.1/2388949-2388777     GUAAUUCCU-C-GUUA-GG-AAGAGGCG-UUUGCA-C-AA-AC----------A-----------------------------AAAGCUACUGCCCA-GAAACG-UCGAAAGA-CGCCAA-----UGCGG-U-AGACCA-GGUUUA-GUCGGA---UUAAGGC---UU-UAUCUAAUGUAGCU-GGUUGU---------------------CAUUUUC-----GACC-----UACGUUGUGCA-C-UGCUGAAACUCAA-ACCA----GGGGAAAGUC
CP000686.1/5712317-5712483     GUUGCUCCC-U-GGUA-GG-C-GCGGCU-U-CACA-C-AA-AC----------A-----------------------------CAGGUUACUGCUCC-GGCCCG-UCGAAAGA-CGCUCA-----GG-GG-C--GCACA-GCAGG--CUCGGC---UUAAGGG---CU-UUGCCAAGGUAACU-ACGG-------------------------UUCAA-----CCGU-----UACGUUGUGUG-AAAGCUUAAGAUCAA-CCGGAG--GGGGAGCGUU
CP000416.1/93409-93243         AAUAGAAGC-U-GUUA-GG-U-GAGGCU-CCUAUG-C-GG-A-----------A-----------------------------AAUGCUACUGCUCA-GAAACG-UCGAGAAA-CGCCAA-----UG-AG-U--CAGCU-GUUCAG-GUCAAU---CGAAGGC---CU-GAUCUAACGUAGCU-GUUA------------------------AGUGAU-----UAAC-----UACGCCGUAUA-G-UGCUAAAACUC-A-ACGACU--AGCUAGACAC
CP000612.1/2523319-2523491     CAUUUUCUU-C-GUUA-GG-U-GAGGCU-UCUACA-U-AG-AC----------A-----------------------------GAUGCCACUGCCCG-GAAAUG-UCGAGAGA-CUCUAA-----CG-GG-U--UAACA-GGUAUU-ACCGGA---UUAAGGU---UU-UACCUAAUGUGGCU-GGGACA--------------------UUCCCAAU-----GCCC------UAGCUAUGUAUG-UGCUAAAGCUUGU-ACGAGU--GGGGAGGCCA
CP000478.1/2034435-2034257     UCGAUCCUC-A-GGUA-GG-U-GAGGCU-CCCGUG-UGAC-AC----------A-----------------------------CAGGCCGCUGCCCA-GAAGUA-UCCAAAGA-UACGGCGCAACAG-GG-U-AGAACA-GGCACU-CCCGGA---UUAAGGG---UU-UGCCUAAGGCGGCU-GAGGC-----------------------GAUAAGC---GUCUC----UUACGGUGCACG-G-UGCUGAAGCUUGA-ACGAG---UGGGGGAAUC
CP000478.1/2956592-2956762     AAAAUUCCU-C-GUUA-GC-AUGAGGCG-UUUGCA-C-AA-AC----------A-----------------------------CAGGCUGCUGCCCA-GAAAUG-UCGAAAGA-CGCCAA-----UG-GG-U-AGACAA-GGUAUG-GUCGGC---AUAAGGC---UU-UACCCGAGGUAGCU-GGUUC-----------------------UUCGAA-----AACC-----UACGUUGUGCA-C-UGCCGAAAGUC-U-ACGAGU--GGGGAAAUGA
AACY022501423.1/463-646        UACCGAUCU-C-GUUAUGG-C-GAGGCU-CCUGUA-C-AA-AU----------A-----------------------------CAAGUUACCGCCCUGCUGGUA-UCGAGAGA-GACCACU---CAG-GG-A-AAUACA-GGCAUCCAUCGAA---UCAAGGU---GU-UGCC-AAGGUAACU-UCUGACGAUU-------------UCACCAUCGGA-----CAGA-----UACGUUGUUCA-G-UGCUAAAACCAGG-ACGUA---GGGAUCUGCC
AP008232.1/1074084-1073916     GCAGUAUCU-C-GUUU-GG-C-GAGGCU-CCUAUA-C-AA-AU----------A-----------------------------CAGGUUACUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-GU-U-AGGACA-GGCUUU-AUCGGA---UUAAGGU---UU-AGCCCAAAGUAACU-UCUG-------------------------UUGUA-----CAGA-----UACGUUGUAUA-G-UGCCAAAACCGUG-ACGUG---GAGAUAGGCU
AB271060.1/1350-1503           AUGAAAAAU-C-GGUA-GG-U-GAGGCU-ACCAUA-G-GG-AU----------A-----------------------------CGGAUGACUACCGCAAAGUAG-UGGAGACA-CUAUGC-----GC-UG-G-UUAGCA-GUUGAG-AUCG-----CUAAGGU---UU-UGACUAAUGUCAUU----------------------------------U-----C--------ACUGCCCUACG-G-AGUUAAAGCUUGA-ACG-----GAACACAAGA
AE016825.1/3525127-3525291     GCAGUGUCU-C-GUUC-GG-C-GAGGCU-CCUAUG-C-AA-AC----------A-----------------------------CAGGUCACUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-GU-U-AGGACA-GGCUUU-AUCGGA---UUAAGGU---UU-AGCCCAAAGUGACU-UCCA-------------------------AC---------GGA-----UACGUUGCAUA-G-UGCCAAAACCUAG-ACGCG---GAGAUCGCUU
AE016830.1/1268265-1268435     AAUAAGAUU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U-AGAACA-GGAACU-GUCGAA---UGAAGGC---UU-UUCUUAAGGUAGCU-AAAA-------------------------GCAAUC--GCUUUU-----UACGUUGUAUA-G-UGCUAAAGCUC-A-ACGAUA--AGAACGAUUA
AAJM01000138.1/2313-2480       AAUAAUCUU-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AACGCUGCUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAACG-GUCGGA---UUAAGGC---CC-UUCUUAAUGUAGCU-GGUU-------------------------AUAAA-----AACC-----UAUGCUAUACA-G-UGCUAAAACUC-A-ACGAGG-GAGUGGUAUAC
AARF01000550.1/280-107         AGAUAUCCU-C-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------AAAGCCACUGCCCG-GAAAUA-UCGAGAGA-UACCUA-----CG-GG-U-AGAACA-GAAAUU-GUCGGA---UUAAGGC---UU-UUUCUAAGGUGGCU-AAGAGAU-------------------GCUUCUAC-----UCUU-----UACGUUGUAUA-G-UGCUAAAAC-CAG-ACCAGG--GGGAACGGAC
CP000804.1/127786-127952       GUUGCUCCC-U-GGUA-GG-C-GCGGCU-U-CACG-C-AA-AC----------A-----------------------------CAGGUUACUGCUCC-GGCCCG-UCGAAAGA-CGCUCA-----GG-GG-C--GCACA-GCAGG--CUCGGC---UUAAGGG---CU-UUGCCAAAGUAACU-GCGG-------------------------CGCUG-----CCGC-----UACGUUGUGUG-ACAGCUUAAGCUCAA-CCGGAG--GGGGAGUGUU
AE008691.1/2398115-2397950     UUAAUACCU-C-GUUA-GG-U-GAGGCU-CCUAUA-C-AG-AU----------A-----------------------------CAGGCUGCUGCCCG-GAAACA-UCGAGAGA-UGGUAA-----CG-GG-U--GAACA-GGCAUU-ACCGAA---UCAAGGU---UU-UGCCUAAUGCAGCU-GGAG-------------------------UUUU------CUCC-----AAAGCUGUAUA-G-UGCCAAAGCUC-A-ACGAAG--GAAAUUGGAU
AJ002571.1/47742-47907         UAGGAACUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAC---AUAAGGU---GA-UUUUUAAUGCAGCU-GGAU-------------------------GCUU------GUCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAUU--GAAGGCGCCC
CP001175.1/2843327-2843491     AGUUUUGCC-U-GUUA-GG-U-GAGGCU-CCUAUG-C-AA-AC----------A-----------------------------CAGGCCACUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGGAUU-GUCGGA---UUAAGGC---UU-UCCAUAAUGUGGCU-AAGA-------------------------GUAU------UCUU-----UACGUUGCAUA-G-UGCCAAAACUUUA-GCGAG---GGGAG-UCU-
CP001124.1/3732610-3732441     ACUGUUCCU-C-GUUA-GC-AUGAGGCG-UUUGCA-C-AA-AC----------A-----------------------------GAGGCUACUGCCCA-AAAACG-UCGAAAGA-CGCCAA-----UG-GG-U-AGACCA-GGGCUU-GCCGGA---UUAAGGC---UU-GACCUAAGGUAGCU-GGUU-------------------------CUUCC----UGACC-----UACGUUGUGCA-C-UGCUGAAAACC-U-ACGAGU--GGGGAACCAC
AE005176.1/1288920-1288763     -CAUAGCCG-UCGGUA-GG-U-GAGGCU-ACCGCA-G-GG-AU----------A-----------------------------CGGGUUGCUGCCGC-AGAGUCGUGGAGACACGAUGAG-----AG-GG-C--CAACA-GUUCAC-GUCGAAA-AACAAGGC---GU-GAAAUAGUGCAACA------------------------------ACA-----------------UCGCCCUGCG-G-AGCUAAAGCUUGA-ACG-----AUAGCUUGUA
CP000962.1/3124853-3124692     AAUAAACCU-C-GGUA-GG-U-GAGGUU-ACUACA-A-GG-AU----------A-----------------------------CGGGUUGUUGCCGUAAAAGAA-UGGAAACA-UUCUUA-----AC-UG-G-UUAGCA-GGUUUU-GCCGAACAAAGAAGGC---AU-AAUCUAAUACAGCU----------------------------------U-----C--------AUUGCCUUGCA-G-AGCCAAAACUUGA-ACGAGA--AAGUGUUGUU
CP001186.1/4113904-4114071     UAUGGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AACGCUGCUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAAG-GUCGGA--AUGAAGGC---CU-UUUUUAACGUAGCU-GGUU-------------------------UCAG------UACC-----UAUGCUAUACA-G-UGCUAAAACUC-A-ACGAGG-GAGAGGUGCAU
ACOM01000001.1/624108-624271   AAAUAAAUU-U-GUUA-GG-U-GAGGCU-CCUAUA-A-AG-AU----------A-----------------------------UAUGCCGCUACCCA-GAAAAA-UCGAGAGA-UUCCAA-----CG-GG-U--UAACA-GAAAUU-AUCG-----CAAAGGU---AA-UUUUUAAUGUGGCU-GACU-------------------------AGAA------AGUC-----AAAGCUCUAUA-G-UGCUAAAGCUC-U-ACAACU--AAGUAAUUAU
CP001390.1/3327040-3327209     GAAAUUCCU-C-GUUA-GG-AAGAGGCG-UUAGCA-C-AA-AC----------A-----------------------------GAAGCUACUGCCCA-GAAACG-UCGAAAGA-CGCCAA-----UGCGG-U-AGACCA-GAUUCA-GUCGGA---UUAAGGC---UU-UAUCUAAGGUAGCU-GGUG-------------------------GUGGU----UCACC-----UACGUUGUGCU-C-UGCUAAAACUCAA-ACCA----GGGGAAAAUG
AE005176.1/907250-907410       CUAAC-CAU-C-GGUA-GG-U-GAGGCU-ACCACA-G-GG-AU----------A-----------------------------CGGGUUGCUGCCGC-AGAGUCGUGGAGACACGAUGAG-----AG-GG-C--CAACA-GUUCAC-GUCGAAAAAAGAAGGC---GU-GAAAUAGUGCAACA------------------------------ACA-----------------UCGCCCUGCG-G-AGCUAAAGCUUGA-ACGAUA-CUGGGUACUU-
CP001124.1/511763-511594       CGGGUUCCU-C-GUUA-CG-AUGAGGCG-UUUGCU-C-AA-AC----------A-----------------------------CAGGCUACUGCCCG-GAAACG-UCGAAAGA-CGCCAA-----CG-GG-U-AGACCA-GGUCUU-GCCGGC---UUAAGGC---UU-GACCCAAGGUAGCU-GGUC------------------------CCCCGG-----GACC-----UACGUUGCGCA-C-UGCCGAAAACC-U-ACGAGA--GGGGAAUCCG
CP001348.1/2365884-2365715     CUAAAUAUU-C-GUUA-GG-U-GAGGUU-CCUAUA-C-AG-AU----------A-----------------------------AAUGCUGCUGCCCG-GAAACA-UCGAGAGA-UGCCAA-----UG-GG-U--CAACA-GGUAUU-ACCGAA---AUAAGGU---UU-UACUUAAUGUAGCU-GGAG-------------------------AUAAAG--UGGUCC-----AAAGCUGUAUA-G-UGCUAAAACUC-A-ACGAGU--GAAGGGUUUU
CP000885.1/3684636-3684463     AUUAAACUU-C-GGUA-GG-U-GAGGCU-ACCGCA-G-GG-AU----------A-----------------------------UGGAUUGCUACCGC-GAAAUAAUGGAGACACUAUUAG-----UU-GG-U--UAGCA-GGUUGU-GUCGAA---UCAAGGC---AU-AACCUAAUGCAAUU-UCAAGGC------------------GUCAAAUGU-----ACGC-----CAUGCCCUGCG-A-UGCUAAAGCUUGA-ACG-----GUUAAUUGCU
CP001176.1/2412253-2412418     AAUAAACUU-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AACGCUGCUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAACG-GUCGGA---UUAAGGC---CC-UUCUUAAUGUAGCU-GGUU-------------------------AUAAA-----AACC-----UAUGCUAUACA-G-UGCUAAAACUC-A-ACGAG---GGAGUGGUAU
CP000924.1/241045-241209       UUAAUACAA-UCGUUA-GG-U-GAGGCU-CCUAUA-C-AG-AU----------A-----------------------------CACGCUGCUGCCCG-GAAACA-UCGAGAGA-UGCUAA-----CG-GG-U--CAACA-AGUAUU-ACCGAA---UUAAGGU---UU-UACUUAAUGCAGCU-GGAG-------------------------GAUG------CUCC-----AAAGCUGUAUA-G-UGCCAAAGCUC-A-ACGA----AUUGAAAUGU
CP000033.3/206473-206636       UAUAAAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------CACGCUAUCGCCCA-GAAACA-UCCAGAGA-UGCCAA-----CG-GG-U-UAAAUA-GGUGUC-GUCGAC---UUAAGGC---GA-GAUC-CAGAUAGCU-AGCA-------------------------UGU--------GCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUAACGG
ACMS01000077.1/22055-22218     AUAAGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AAUGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAUG-AUCGAA---UUAAGGU---UU-UUCUUAACGUAGCU-GGUA-------------------------AUGA-------ACC-----UAUGCUAUACA-G-UGCUAAAACUC-G-ACGAG---GGAGAGGUCU
ACAO01000024.1/41200-41025     AUAUAACCU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAAGCUAUUGCGCA-GAAACG-UCGAAAGA-CGCCAA-----UG-UG-U-AAAACA-GGAAUU-GUCGGA---UUAAGGC---UU-UUCAUAAAAUAGCU-AAGAGAGC-----------------AAAUGACUU-----UCUU-----UACGUUGUAUA-G-UGCUAAAACUCGG-ACGAU---GAGAUUGCUG
ACLX01000114.1/2858-3034       UUUAUAACC-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGCUAUUGCCCA-AAAAUA-UCGAAAGA-UGCCAA-----UG-GG-U-AGAACA-GGAAUU-GUCGGA---UUAAGGC---UC-UUCUUAAGAUAGCU-AAGUGAUG----------------AAUGAUUCAU-----CCUU-----UACGUUGUAUA-G-UGCCAAAACUC-A-ACUAGG--GGGGAAUGAG
CP000813.1/1287638-1287801     AUGAGACUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAC---AUAAGGU---GA-UUUUUAAUGCAGCU-GGAU-------------------------UUU--------UCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAUU--GAAGGAGCAA
ABDP01000004.1/121407-121244   AAUAGUGUA-C-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------UAUGCUACUGCCCG-GAAACA-UCGAGAGA-UGCCAA-----UG-GG-U--CACCA-GGUAUU-ACCGAA---GUAAGGU---UU-UACUUAAUGUAGCU-GGCU-------------------------GUAG-------UCC-----AAAGCUAUAUA-G-UGCUAAAACUC-A-ACGAUU--G-AUGUUAAA
CP000560.1/1275022-1275187     UAAGAACUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GGAAUC-AUCGAC---AUAAGGU---GA-UUCUUAACGCAGCU-GGAU-------------------------GGCU------GUCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAUU--GGAGGCCCCG
ACMP01000214.1/1800-1624       UGCUAAACC-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGCUAUUGCCCA-AAAAUG-UCGAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGAAUU-GUCGGA---UUAAGGC---UC-UUCUUAAGAUAGCU-AAGUAAUC----------------AAUUUCCAUU-----ACUU-----UACGUUGUAUA-G-UGCCAAAGCUC-U-ACUAGG--GGGAGGAAAG
ACAJ01000014.1/157903-157714   GGAUAACCU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAAGCUAUUGCGCA-GAAACG-UCGAAAGA-CGCCAA-----UG-UG-U-AAAACA-GGAAUU-GUCGGA---UUAAGGC---UC-UUCAUAAAAUAGCU-AAGAAGAAAUAAAUA---CUACUAAUUUGCUUCU-----UCUU-----UACGUUGUAUA-G-UGCCAAAACUCGG-ACGAU---GAGAUUGCUU
ACND01000068.1/9860-9684       UGCUUAACC-U-GUUA-GG-U-GAGGCU-CCUAUG-C-AA-AC----------A-----------------------------CAGGCUAUUGCCCA-AAAAUG-UCGAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGAAUU-GUCGGA---UUAAGGC---UC-UUCUUAAGAUAGCU-AAGUAAUG----------------AAUUUUCAUU-----ACUU-----UACGUUGUAUA-G-UGCCAAAGCUC-U-ACUAGG--GGGGAAAAGC
ACMV01000122.1/63091-63256     AUAUGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------GACGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAAG-GUCGGA--AUGAAGGU---CU-UUUUUAACGUAGCU-GGUU-------------------------UGA--------ACC-----UAUGCUAUACA-G-UGCUAAAGCUC-A-ACGAGG-GAGAGGUACGA
ACNO01000010.1/64597-64770     GCAGUACCU-C-GUUA-GG-U-GAGGCU-UCUGCA-C-GA-AC----------A-----------------------------CAGGCCACUGAUCUCACGACG-UCGAGAGA-CGCCCA-----AG-GU-U-AGGACA-GAUCUC-CCCGGC---UUAAGGG---GU-GAUCCAAAGUGGCU-UCCCGG--------------------UCUUGAUC-----GGGA-----CACGUCGUGCA-G-UGCCAAAACUCGG-ACGUG---GAGGUGUUUU
ACBV01000002.1/67696-67865     UAAGCACCU-C-GUUA-GG-U-GAGGCG-GCUACA-C-GA-AC----------A-----------------------------CAGGCCACUGACCC-CGAACG-UCGAAAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCCU-CCCGGC---UUAAGGG---UU-GAGCCCAGGUGGCU-UCCG------------------------GAUUAC-----CGGA-----CACGUCGUGUG-G-UGCCAAAGCUCUG-ACGAGA--GGGGUGCGGG
CP001034.1/3063723-3063914     UUAUAAACU-C-GUUA-GG-U-GAGGCU-CCUGGG-U-GG-AU----------A-----------------------------UAAGCUGCUGCCCA-AAAACG-UCGAGAGA-CGCCAA-----UG-GG-U-AUAACA-GACAGU-GUCGGC---UUAAGGC----C-UGUCUAAUGCAGCU-GGUCCUCUUCUACCUUAUUAGAUAUUAAAUUUCG-----GAUC-----UACGUCACCCA-G-UGCCAAAGCUAAG-ACGAG---GAGUGCGUAA
ABJD02000101.1/1953821-1953650 GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGUUACUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-AU-C-AGGACA-GGAUAU-AUCGAA---CGAAGGU---AU-AUCCCCAUGUAACU-UCCAA----------------------UGUAAGU-----UGGA-----UACGUUGUAUA-G-UGCUAAAACCGAG-ACGUA---GAGAUAGCCA
CP000826.1/2785644-2785471     GCAGUAUCU-C-GUUU-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGUUACUGAUCUGACGACA-UCGAGAGA-UGCCCA-----AG-GU-U-AAGACA-GGCUUU-AUCGGA---UUAAGGU---UC-AGCCCAAGGUAACU-UCUGAU--------------------GAAUACAU-----CAGA-----UACGUUGUAUA-G-UGCUAAAACCUGG-ACGCG---GAGAUAGGCU
CU458896.1/4831187-4831017     UCAGCACCU-C-GCUA-GG-C-GAGGCU-CCUGCA-C-GA-AC----------A-----------------------------CAGGCCACUGAUCCGACGACG-UCGAGAGA-CGCCCA-----GG-GU-U-AGGACA-GAUCUC-CCCGGC---UUAAGGG---GU-GAUCCGAGGUGGCU-UCCC-------------------------GUCCA-----GGGA----UUACGUCGUGCA-G-UGCCGAAGCUCUG-ACGAGA--GAGGUGGUCG
ACGH01000107.1/2043-1878       AAUAGAAGC-U-GUUA-GG-U-GAGGCU-CCUAUG-U-GA-A-----------A-----------------------------AAUGCUACUGCUCA-GAAACG-UCGAAAAA-CGCCAA-----UG-AG-U--CAGCU-GUUCUA-GUCAAA---GUAAGGC---UU-GAACUAACGUAGCU-GUUA-------------------------UUGAA-----UAAC-----UACAUCACAUA-G-UGCUAAAGCUC-A-ACGACU--GGCUAAAGCU
ABIN01000151.1/583-766         UAAGCACCU-C-GUUA-GG-U-GAGGCG-UCUACA-C-GA-AU----------A-----------------------------CAGGCCACUGACCC-CGAACG-UCGAAAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCCU-CCCGGC---UUAAGGG---UU-GAGCCCAGGUGGCU-UCCGGUUUGGA----------UUUUUUCCAGGCC-----AGGA-----CACGUCGUGUG-G-UGCCGAAGCUCUG-ACGAGA--GGGGUGCGGA
ACGU01000110.1/97211-97378     CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-AA-AU----------A-----------------------------UACGCUGACGCCCA-GCAACA-UCCAGAGA-UGCCAA-----CG-GG-U-UAAACG-GGAACU-GUCGAA---UUAAGGC---UU-UUCC-CAGUCAGCU-AGUU-------------------------AAACA-----GACU----UCACGUUACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAAAAUCG
ABVP01000024.1/147149-146978   GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGUUACUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-AU-U-AGGACA-GGAUAU-AUCGAC---CGAAGGU---AU-AUCCCCAUGUAACU-UCCAG----------------------UAUUCAU-----CGGA-----UACGUUGUAUA-G-UGCUAAAACCGAG-ACGUG---UAGAUAGCUU
ACLM01000103.1/132-299         CAAAUGAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-AA-AU----------A-----------------------------UACGCUGACGCCCA-GCAACA-UCCAGAGA-UGCCGA-----UG-GG-U-UAAACA-GGAACU-GUCGAA---UUAAGGC---UU-UGCC-CAGUCAGCU-AGUU-------------------------GAACA-----GACU----UCACGUUACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAGAAAUC
ACEC01000025.1/21421-21256     AAAGAACAC-C-GUUA-GG-U-GAGGUU-ACUUUA-C-GG-AU----------A-----------------------------U-GGCUAUUGCCCG-GAAAUG-UCGAGAGA-CGCCAA-----CG-GG-U--CAGUU-GACACU-AUCGAA---UCAAGGU---UU-UGUCUAAUAUAGCU-GACA-------------------------GUUC------UGUC-----UAUGCCGUAGA-G-AGCCAAAGCUC-G-ACGAAC-AGGGGUGUGGC
BABE01005974.1/721-547         AAUAAGAUU-U-GUUA-GG-U-GAGCUU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUACUGCCCA-AAAACG-UCGAGAGA-CGCCAU-----NN-GG-U-AGA-CAGGGAAUN-GUCGAG---AUAAGGC---UU-UUCAUAAGGUAGCU-AAAAGCA------------------GGUAUCUGC-----UUUU-----UACGUUGUACA-G-UGUCAAAACUC-A-ACGAUG--AGAUCUGAGA
ACLN01000004.1/169541-169717   AAUUUGAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AA----------A-----------------------------UAUGCUGUUGCCCA-GCAACA-UCCAGAGA-UGCCAA-----CG-GG-U-UAAACA-GGGAUC-GUCGAU---UUAAGGC---CC-UCCC-CAGACAGCU-GGUUACUA----------------ACUUUGUAGU-----AACG----UUACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUGAAUUAA
CP000517.1/232404-232566       AAGUAAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------CACGCUAUCGCCCA-GAAACA-UCUAGAGA-UGCCAA-----CG-GG-U-UAAAUA-GGUGUC-GUCGAC---UUAAGGC---GA-GAUC-CAGAUAGCU-AGCA-------------------------U---------UGCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUGACAA
ACKR01000005.1/5717-5880       CAAAUAAAC-U-GUUA-GG-U-GAGGCU-CCUACG-U-GA-AC----------A-----------------------------CAAGCUAUCGCCCG-GAAACA-UCCAGAGA-UGCCAA-----CG-AG-U-AAAAUA-GUUCUU-GUCGAG---AUAAGGC---GA-GAUC-CAGAUAGCU-AGCC-------------------------UGU--------GCU-----UACGUCACGUA-G-UGUCAAAACUG-A-ACGACG--AGGAAACAUC
CP001364.1/587050-586882       UUCGCUCCU-U-GGUA-GG-C-GCGGUC-UGCAUA-C-AA-AC----------A-----------------------------CAGGUUGCUGCUCC-GACCCG-UCGAAAGA-CGCUUA-----GG-GG-U--AUACA-GUAUAG-CUCGGC---UUAAGGG---UU-AUGCUAAAGCAACU-GUAG-------------------------CGCUG-----CUAC-----UACGUUGUAUG-CGGGCUUAAGCUCAA-CCGAAG--AGGGAGCAAA
CP001393.1/739372-739528       AAGAUAUCU-C-GGUA-GG-C-GAGGCU-CCUACA-G-GG-AU----------A-----------------------------UAGGCUGCUGCCGCGAAAGAU-UGGAGACA-AUCUGA-----GC-UG-G-UGAACA-GGUUUU-GCCGAA--ACCAAGGC---AU-AACCUAAUGCAGCU---------------------------------UU-----U--------UAUGCCGUGUA-G-UGCCAAAGCUU-GUAC------GAGGUAGCUU
CP000910.1/746842-747026       GCAGCACCU-C-GUUA-GG-C-GAGGCU-CCUGCG-C-GA-AC----------A-----------------------------CAGGCCACUGAUCUGACGACA-UCGAGAGA-UGCCCA-----AG-AU-C-AGGACA-GGCCGC-CUCGGC---UUAAGGG---GC-GGUCCCAAGUGGCU-UCCGGUGCCAGU--------AAAUAUUGCCAGCC-----CAGA-----UACGUCGCGCA-G-CGCCGAAGCUC-U-ACGUG---GGGGUGACUC
AB385841.1/13217-13047         CACGCACCU-C-GUUC-GG-U-GAGGCG-UCGUCA-C-GG-AC----------A-----------------------------CAGGCCACUGAUCC-CACCCG-UCGAGAGA-CGCUCC-----GG-AU-C-AGGACA-GGUCUC-CCCGGC---CCAAGGG---GU-GACUCCAAGUGGCU-GCCC------------------------CACCCG-----GGGC-----UACGCCGUGAC-G-UGCCAAAGCUCUG-ACGAGU-GGGGGUGAGCC
ACNB01000463.1/4534-4369       AUAUGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AACGCUGCUACCCA-AAAAUG-UCGAGAUA-CGCCAA-----UC-GG-U--CAACA-GGAACG-GUCCAA---UUAAGGCCCUUC-UUCUUAAUGUAGAU-GGUU-------------------------UUAA-------ACC-----UAUACUGUACA-G-UGCUAAAACUC-A-AUGA----GGGGGCUUUU
ABQP01000004.1/146576-146420   UGAGAGCGU-C-GGUA-GG-C-GAGGCU-ACCGCA-G-GG-AU----------A-----------------------------UGGGUUGCUGCCGC-UAACAG-UGGAGACA-CUGCAC-----GC-AG-G-UCAGCA-GUUCUU-GUCGGA---UUAAGGC---AU-GAACUAACGCAACU----------------------------------C-----C--------ACCGCCCUGCG-A-UGCUGAAGCUUGA-ACGAU---GACACGACCA
CP001095.1/485733-485576       UGGGAGCGU-C-GGUA-GG-C-GAGGCU-ACCGCA-G-GG-AU----------A-----------------------------UGGGUUGCUGCCGC-UAACAG-UGGAGACA-CUGCAC-----GC-AG-G-UCAGCA-GUUCUU-GUCGGA---UCAAGGC---AU-GAACUAACGCAAUU----------------------------------C-----C--------ACCGCCCUGCG-A-UGCUGAAGCUUGA-ACGAUG--GCCGAAUCGG
CP001078.1/1435636-1435795     UAAUAUUCU-C-GGUA-GG-U-GAGGUU-ACCAUA-G-GG-AU----------A-----------------------------CGGAUUGCUGCCGC-AAAAUAAUGGAGACAUUAUUAG-----UU-GG-U--UAGCA-GGAUAC-GUCGAAA-AAUAAGGC---GU-AUCUUAAUGCAAUU----------------------------------U-----C--------AUUGCCCUACG-A-AGCUGAAGCUUGA-ACGAG---GAGAUAGUAA
ACDH01000013.1/27326-27487     AAAUAGAUC-C-GGUA-GG-U-AAGGCU-ACUACA-G-GG-AU----------A-----------------------------UGGGUUGCUGCCGC-AAAAUAGUGGAGACACUAUGCG-----UU-GGUU-UGAACA-GGCGAU-AUCGAA--ACCAAGGU---AU-CAUCUAAUGCAACU----------------------------------U-----C--------ACCGCCCUGUA-G-AGUUAAAGCUCAA-ACGGUG--GCGUAAAUCA
ACDK01000064.1/73825-73664     UUAAUAUUU-C-GGUA-GG-U-GAGGUU-ACCACA-A-GG-AU----------A-----------------------------AGGGUUGCUGCCGCAAAAUAG-UGGAGACA-CUAUGA----GAA-GG-U--UAGCA-GUCUAU-GUCGAA--GCCAAGGC---AU-AGACUAAUGCAAUU----------------------------------U-----C--------AUCGCCUUGUG-A-AGCUGAAGCUUGU-ACGAUGAUGAAGCAGUUU
CP001056.1/1473093-1473254     UAAUAUUCU-C-GGUA-GG-U-GAGGUU-ACCAUA-G-GG-AU----------A-----------------------------CGGAUUGCUGCCGC-AAAAUAAUGGAGACAUUAUUAG-----UU-GG-U--UAGCA-GGAUAC-GUCGAAA-AAUAAGGC---GU-AUUUUAAUGCAAUU----------------------------------U-----C--------AUUGCCCUACG-A-AGCUGAAGCUUGA-ACGAGC-AGAUAAUAAGA
ABWO01000186.1/16693-16863     AAUAAGAUU-C-GGUA-GG-U-GAGGCU-ACCACA-G-GG-AU----------UUGGAU------------------UUUCCUAAGAUUGCUGCCGCAACAACG-UGGAGACA-CGAUUC-----GC-UG-G-UUAGCA-GGAUAU-GUCGCA--GAUAAGGC---AU-AUCUUAAUGCAAUU----------------------------------U-----A--------UAUGCCCUGUG-A-UGCUAAAGCUUGA-ACGAUG--UUGUCACGGA
ACIL02000005.1/103424-103269   GGUGCAAUU-C-GGUA-GG-U-GAGACU-ACCAUA-G-GG-AU----------A-----------------------------CGGAUGACUACCGCAAAGAAG-UGGAGACA-CUUCGC----GUU-GG-U--UAGCA-GUUGCU-GUCG-----AGAAGGC---GG-CGACUAACGUCAUU----------------------------------U-----C--------AUCGCCCUAUG-A-UGUUAAAGCUUGG-ACGAU---GAAUGAGAAA
ACKZ01000007.1/32791-32946     AUAGUAAAU-C-GGUA-GG-U-GAGACU-ACCAUG-G-AG-AU----------A-----------------------------CGGAUGACUACCGC-AAAAUAGUGGAGACACUAUUCG-----UU-GG-U--CAGCA-GCCUCU-GUCG-----UGAAGGC---AG-AGACUAAUGUCAUU----------------------------------U-----C--------AUCGCUCCAUG-A-UGUUAAAGCUUGG-ACGAG---AAUAUAAGAA
ABFX02000002.1/189276-189122   UAAAAGAAU-C-GGUA-GG-U-GAGACU-ACCAUA-G-GG-AU----------A-----------------------------CGGGUUGCUACCGCAAAGCA-GUGGAGACAC-UGUGC-----GC-UG-G-UCAACA-GUUCUU-GUCG-----UGAAGGC---AA-AAACUAAUGCAAUU----------------------------------A-----C--------AUGGCCCUAUG-A-UGUUGAAGCUUGA-ACGA----GAUAAAGUUA
AAVL02000037.1/263157-262991   CUACUUUAU-C-GGUA-GG-U-GAGGUU-ACCAUA-G-GG-AUUCGG--UUUA-AU------------------------CCUAAGAUUGCUGCCGCGAGAUUG-UGGAGACA-CAAUUA-----GU-UG-G-UUAGCA-GGAUGU-GUCG-----UUAAGGC---AU-AACCUAAUGCAAUU--------------------------------AAU-----A--------UACGCCCUAUG-A-UGCUAAAGCUUGA-AC------GGUGAUUUUA
ABYT01000060.1/16817-16983     AAAGAUAUA-C-GGUA-GG-U-GAGGUU-ACCGCA-G-GG-AU----------UUGGAU-------------------UUCCUAAGAUUACUGCCGCAAAGUUG-UGGAGACA-CGACUC----GUU-GG-U--CAGCA-GGCAAA-GUCG-----CAAAGGC---UU-GGCUUAAUGUAAUU----------------------------------U-----A--------UAUGCCCUGUG-A-UACUAAAGCUUGA-ACGGUG--AUACUAGAUU
CP000764.1/1422391-1422554     UAAAGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AAUGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAUG-AUCGAA---UUAAGGU---UU-UUCUUAAUGUAGCU-GGUA-------------------------AUGU-------ACC-----UAUGCUAUACA-G-UGCUAAAGCUC-G-GCGAG---GGAGAGGUUC
CP000822.1/4527413-4527596     UAUCGAUCU-C-GUUAUGG-C-GAGGCU-CCUGCA-C-AA-AU----------A-----------------------------UAAGUUACCGCCCUGCUGGUA-UCGAGAGA-GACCACU---CAG-GG-A-AAUACA-GGCAUCCAUCGAA---UCAAGGU---GU-UGCC-AAGGUAACU-UCUGACGAUA-------------UCACUAUCGGG-----CAGA-----UACGUUGUGCA-G-UGCUAAAACCAGG-ACGUA---GGGAUCUGCC
ABOU02000050.1/75054-74870     ACAUCAUUU-C-GGUA-GG-U-GAGGUU-ACCACA-G-GG-AU----------UGGAUGAUUCGGCUUAUGUCGUUAAAUCCGAAGAUUGCUACCGCGGAAUUG-UGGAGACA-CGAUGA-----GC-UG-G-UUAGCA-GGCUGC-GUCG-----CGAAGGC---GC-AACUUAAUGCAAUU----------------------------------U-----A--------UAUGCCCUGUG-A-UGCUAAAGCUUGA-ACGGU---GCUAUUAUUU
CP001727.1/2253817-2253654     UGCGUUCCU-C-GUUA-GG-C-GAGGCU-ACUAUA-C-GA-AC----------A-----------------------------CAAGCCACUGCCCG-GAAACG-UGGAGACA-CGCCAA-----UG-GG-U-AGAACA-GGUAUG-GCCGGC---UUAAGGC---UU-UACCUAACGUGGCU-GGGU-------------------------UUU--------CCC-----UACGUCGUAUA-G-UGCCAAAGCUC-A-ACCAG---GGGGAUGUGC
ACCI02000061.1/145679-145508   GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGUUACUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-AU-U-AGGACA-GGAUAU-AUCGAC---CGAAGGU---AU-AUCCCCAUGUAACU-UCCUG----------------------CUAAGUC-----AGGA-----UACGUUGUAUA-G-UGCUAAAACCGAG-ACGAA---GAGAUAGCUU
ABYU02000030.1/155655-155490   GAGAAAAAU-C-GGUA-GG-U-GAGGUU-ACCACA-G-GG-AUUUGGGAGACCU-----------------------------AAGAUUGCUGCCGCAGAUUUG-UGGAGACA-CAAUGC-----GC-UG-G-UUAGCA-GGCUAU-GUCG-U---GGAAGGC---AU-AACCUAAUGCAAUU----------------------------------U-----A--------UAUGCCCUGUG-A-UACUAAAGCUUGU-ACGU----GGCACUCAGA
CP001700.1/1972480-1972312     AGGACACCU-C-GUUC-GG-U-GAGGCG-UCUUCA-C-GG-AC----------A-----------------------------AAGGCCACUGAUCC-CAUCGG-UCGAGAGA-CCCUCC-----GG-AU-C-AGGACA-GAUCUC-CUCGGC---UUAAGGG---GU-GAUCCCAAGUGGCU-GCGC-------------------------AGCUG-----ACGC-----UACGCCGUGAA-G-UGCCGAAGCUCUG-ACGAGA--GAGGUGGCCG
CP002743.1/503463-503307       UGGGAGCGU-C-GGUA-GG-C-GAGGCU-ACCGCA-G-GG-AU----------A-----------------------------UGGGUUGCUGCCGC-UAACAG-UGGAGACA-CUGCAU-----GC-UG-G-UCAACA-GUUCUU-GUCGGA---UCAAGGC---AU-GAACUAAUGCAAUU----------------------------------C-----C--------ACCGCCCUGCG-A-UGCUGAAGCUUGA-ACGAU---GGCUCGAAUC
ACDB02000044.1/535177-535016   UAAUAGUUC-C-GGUA-AG-U-AAGGCU-ACUAUA-G-GG-AU----------A-----------------------------UGGGUUACUGCCGCAAAAUAG-UGGAGACA-CUAUGC----GCU-GGUU-UGAACA-GGCAAC-AUCGAA--ACCAAGGU---GU-UAUCUAAUGUAACU----------------------------------U-----C--------ACCGCCCUACA-G-AGUUAAAGCUCAA-ACGGUG--GUAAAAAAUA
ABWM02000004.1/570492-570323   CAACGAUCU-C-GUUAUGG-C-GAGGCU-CCUGUA-C-AA-AU----------A-----------------------------CACGUUAUCGCUCUGGUGGGU-UCGAGAGA-ACCGGCA---CAG-GG-U-AAAACA-GGCACU-GUCGAA---UCAAGGC---UU-UGUC-AGUAUAACU-UCCC-------------------------UUGC------GGGA-----UACGGUGUACA-G-UGCUGAACCCAGG-ACGUG---GGGAUCUCUU
CP001720.1/1833967-1834136     AUAAUUCCU-C-GUUA-GG-U-GAGGCU-UCUGCA-U-AGAAC----------A-----------------------------UAUGCCACUGCCCG-GAUAGG-UCGAAAGA-CCGUAA-----CG-GG-U--UAACA-GGUAUU-ACCGGA---UUAAGGU---UU-UAUCUAAUGUGGCU-GAGA-------------------------UUUAU----GUCUC-----U-AGCUGUGCAUG-UGCCAAAACUCGU-ACGAGU--GGGGAAUGGG
AL935263.2/1874649-1874486     AUCAGUUGC-A-AUUA-GG-U-GAGGUU-ACUUUA-A-GA-AU----------A-----------------------------UAGGUUAUCGCCCA-GAAAUG-UCGAGAGA-CAGGAA-----UG-AG-U-AAAGCA-GAAUUU-GCCGAA---UUAAGGC---UC-UUUC-AAGAUAACU-AGA--------------------------CUAG------UUCU-----UACGUCUUAAA-G-UGCUAAAACUC-A-AUGAA---UGCGUCGAUG
CP001706.1/2088420-2088246     UAGGUGUCU-C-GUUA-GG-U-GAGGCU-CCAUCG-C-GA-AC----------A-----------------------------UAGGCCACUCAUCUGACGACA-UCGAGAGA-UGCCCA-----AG-AU-G-AGGACA-AAUCCU-CCCGGC---UUAAGGG---UU-GAUUCCAAGUGGCU-UCCUACG-------------------UUUGGCGU-----AGGA-----CACGUCGCGGU-G-UGUCAAAGCUCUU-ACGUG---GACGCGCCAC
ACCD01000002.1/42362-42531     GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGUUACUGAUCUGACGACG-UCCAGAGA-CGCCCA-----AG-GU-U-AGGACA-GGUUAU-AUCGGA---UUAAGGU---AU-AACCCAAAGUAACU-UCUG-------------------------AGAAA----UCAGA-----UACGUUGUAUA-G-UGCUAAAACUUAG-ACACG---GAGAUAGCCA
CP001739.1/2726594-2726752     GAGAAAAAU-C-GGUA-GG-U-GAGGCU-AACAUA-A-GG-AU----------A-----------------------------AGGAUUGCUGCCGCGAAAAGA-UGGAGACA-UUUUUA-----GCAGG-UCUGAACA-GUCUGG-GUCG-A---AUAAGGC---UC-AGAAUAAUGCAAUU----------------------------------U-----C--------AUUGCCUUAUG-A-AGUUAAAACUUGA-ACGAU---GAUUACAUUU
ABXV02000030.1/100107-99935    GCAGUAACU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGUUACUGAUCUGACGACG-UCUAGAGA-CGCCCA-----AG-AU-C-AGGACA-GGAUAU-AUCGAC---CGAAGGU---AU-AUCCCCAUGUAACU-UCCUGC---------------------UUUAUUC-----AGGA-----UACGUUGUAUA-G-UGCUAAAACCGAG-ACGAA---GAGAUAGCGA
CP001834.1/1924075-1923906     AACUAAUCA-U-AUUA-GG-U-GAGGUU-ACUCUG-AAGA-AC----------A-----------------------------UAGGUUAUCGCUCA-AAACUG-UCGAGAGA-CAAUAA-----UG-GG-U-AAAGCA-GGACUA-GUCGAA---UCAAGGC---UU-UUCC-AAGAUAACU-AGAAA-----------------------UAUCAU-----UUCU-----UACGUCUCAGA-A-AGCCAAAACUCAA-AUGUC---GUGAUUAAAU
ABWG02000004.1/102839-102676   CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------CACGCUAUCGCCCA-GGAACA-UCCAGAGA-UGCCAA-----CG-GG-U-UAAACA-GGUAUU-GUCGAG---UUAAGGC---AC-UAUC-CAGAUAGCU-AGCA-------------------------UGU--------GCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGAUU--GGUUAUAACG
CP001966.1/2592315-2592145     UCAGUACCU-C-GCUA-GG-U-GAGGCU-CCUGCG-C-GA-AC----------A-----------------------------CAGGCCACUGAUCCGACGACG-UCGAGAGA-CGCCCA-----GG-GU-U-AGGACA-GAUCCU-CCCGGA---UUAAGGG---UU-GAUCCGAAGUGGCU-UCCC------------------------GGACAC-----GGGA----UCACGUCGCGCA-G-UGCCGAAGCCC-G-ACGAGA--GGGGUGCGAG
ACGO02000002.1/246026-245855   CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------UAUGCUGUCGCCCA-GCAACA-UCCAGAGA-UGCCAA-----CG-GG-U-CAAACA-GGGAUC-GUCGAU---AUAAGGC---CC-UCCC-CAGCCAGCU-AGUUAU--------------------GUUAAAUA-----ACCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUAAAAA
CP001791.1/527842-527676       UGAAUCCCU-C-GUUA-GG-U-GAGGCU-CCUGCA-GUGG-AG----------A-----------------------------CAUGCUGAUGCCCA-ACAACG-UCCAAAGA-CGCCAA-----UG-GG-U-UGAACA-GGAACC-AUCGAC---AUAAGGU---GG-UUUUUAACGCAGCU-GAGC-------------------------GCCG-------CUC-----UAUGCCCUGCA-G-UGCUAAAGCUC-A-ACGAAU--GGAGGAAAAA
CP002104.1/1491224-1491064     GAGCACGGU-C-GGUA-GG-U-AAGGCU-ACCACG-G-GG-AU----------A-----------------------------CGGGUUGCUGCCGCAACACA-GUGGAGACAC-UGCAA----GUU-GG-U--CAACA-GUCGUU-GUCGAU--UUCAAGGC---UU-CGACUAAUGCAACA----------------------------------C-----C--------ACCGCCCUGCG-A-AGCUGAAGCUUGA-ACGACA-AGAUUAAGGUU
ACFX02000041.1/21421-21266     AAGAACAUU-C-GGUA-GG-U-GAGGCU-ACCACA-G-GG-AU----------A-----------------------------AGGGUUACUGCCGGUUAAAGG-UGGAGACA-CCUCUAA---UCA-GG-U--CAGCA-GUCUGU-GUCGCU---GUAAGGC---GC-AGAAUAAUGUAAUU----------------------------------------U--------CACGCCCUGUG-A-AGCUAAAGCUUGA-ACG-----GAUUGGAUAC
#=GC SS_cons                   ::::[[[[[.[.[[--.--.[.[[[[[-.-[[[[[.[.[[.,,..........,.............................,,,(((((<<<<<<.----<<.<<____>>.>>----.....>>.>>.-.---->>.<<<<--.<<<___...____>>>...--.>>>>,,,,))))),.<<<_........................._____....._>>>.....,,,,]]]]]]].].-]]-----]]]-].]]----..]]]]]]::::
#=GC RF                        aaaauaccc.c.GuUA.GG.u.gAGGCU.ccugcg.c.Gg.Au..........A.............................uAgGcugcUGCccc.aAAacg.UcGAGAgA.cgccaA.....gg.gG.u.auAACA.Ggccuu.guCGaa...uuAAGgc...uU.ggcCUAAugcagCU.ggcu.........................uuuau.....agcc.....UAcGcCgcgca.g.UGCUAAAgCUcga.aCGAug..gggguaauuu
//
# STOCKHOLM 1.0

#=GF AC   RF00381
#=GF ID   Antizyme_FSE
#=GF DE   Antizyme RNA frameshifting stimulation element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15147837
#=GF SS   Published; PMID:15147837
#=GF GA   40.00
#=GF TC   42.10
#=GF NC   39.20
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0006452; translational frameshifting;
#=GF RN   [1]
#=GF RM   15147837
#=GF RT   Identification of a new antizyme mRNA +1 frameshifting stimulatory
#=GF RT   pseudoknot in a subset of diverse invertebrates and its apparent absence
#=GF RT   in intermediate species.
#=GF RA   Ivanov IP, Anderson CB, Gesteland RF, Atkins JF
#=GF RL   J Mol Biol 2004;339:495-504.
#=GF CC   This family represents a structural element which is found in antizyme
#=GF CC   mRNA and is known to promote frameshifting. Antizyme genes have have two
#=GF CC   partially overlapping open reading frames, the second, which encodes the
#=GF CC   functional protein requires +1 translational frameshifting. This
#=GF CC   frameshift is stimulated by a pseudoknot present 3' of the frameshift site
#=GF CC   in the antizyme mRNA. The frameshifting efficiency is dependent on the
#=GF CC   level of polyamines in the cell, when the polyamine concentration is high
#=GF CC   frameshifting is more likely to occur which leads to an increase in the
#=GF CC   quantity of functional antizyme produced. The functional antizyme acts to
#=GF CC   reduce ornithine decarboxylase (ODC) activity which leads to a drop in
#=GF CC   polyamines present in the cell. Therefore, this family can be thought of
#=GF CC   as a biosensor for intracellular free polyamines [1].
#=GF WK   Antizyme_RNA_frameshifting_stimulation_element
#=GF SQ   13


BC056833.1/241-299       UGAUGCCCCUCACCCACCUCUGAAGAUCCCAGGUGGGCGAGGGAACGGAGCACGGGAUC
AF242520.1/225-280       UGAUGCCCCUCACCCACUGUCGAAGAUCCCCGGUGGGCGAGGGGGCGGC---AGGGAUC
AF258463.1/230-288       UGAUGUCCCUCACCCACCCCUGAAGAUCCCAGGUGGGCGAGGGAAUAGUCAGAGGGAUC
D10706.1/256-314         UGAUGUCCCUCACCCACCCCUGAAGAUCCCAGGUGGGCGAGGGAACAGUCAGCGGGAUC
AC004152.1/16641-16699   UGAUGCCCCUCACCCACCCCUGAAGAUCCCAGGUGGGCGAGGGAAUAGUCAGAGGGAUC
AF291576.1/215-270       UGAUGCCCCUCACCCAUCAGUGAAGAUCCCGGGUGGGCGAGGGAACGG---AAGGGAUC
D11373.1/473-530         UGAUGUCCCUCACCCAGCCCUGAAGAGCCCAGGUGGGCGAGGGAACAGUCAGC-GGAUC
BC054690.1/204-259       UGAUGCCCCUCUCCCACUAACGAAGAUCCCGGGUGGGCGAGGG-ACGGGCA--GGGAUC
AB017117.1/228-286       UGAUGUCCCUCUCCCACCCCUGAAGAUCCCAGGUGGGCGAGGGAAUGAUCAGCGGGAUC
AF196332.1/69-127        UGAUGUCCCUCACCCACCCCUGAAGAUCCCAGGUGGGCGAGGGAAUAGUCAGAGGGACC
AF293339.1/257-315       UGAUGUCCCUCACCCACCCCUGAAGAUCCCAGGUGGGCGAGGGGAUAGCCAGAGGGAUC
AC127562.3/159570-159515 UGAUGCCCCUCACCCACUGUCGAAGAUCCCCGGAGGGCAAGGGGGCGGC---AGGGAUU
AC145407.3/104311-104366 UGAUGCCCCUCACCCACUGUUGAAGACCCUCAGUGGGUGAGGGGGCGGC---AAGGAUC
#=GC SS_cons             :::::<<<<<<-<<<<<<______AAAAAA_>>>>>>->>>>>>:::::::::aaaaaa
#=GC RF                  UGAUGcCCCUCACCCACcccUGAAGAUCCCagGUGGGCGAGGGgAcgGuCAGAGGGAUC
//
# STOCKHOLM 1.0

#=GF AC   RF00382
#=GF ID   DnaX
#=GF DE   DnaX ribosomal frameshifting element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:9300054
#=GF SS   Published; PMID:9300054
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0006452; translational frameshifting;
#=GF RN   [1]
#=GF RM   9300054
#=GF RT   Structural probing and mutagenic analysis of the stem-loop required for
#=GF RT   Escherichia coli dnaX ribosomal frameshifting: programmed efficiency of
#=GF RT   50%.
#=GF RA   Larsen B, Gesteland RF, Atkins JF
#=GF RL   J Mol Biol 1997;271:47-60.
#=GF RN   [2]
#=GF RM   9209069
#=GF RT   Conservation of the Escherichia coli dnaX programmed ribosomal frameshift
#=GF RT   signal in Salmonella typhimurium.
#=GF RA   Blinkova A, Burkart MF, Owens TD, Walker JR
#=GF RL   J Bacteriol 1997;179:4438-4442.
#=GF CC   This family represents a ribosomal frameshifting element found in the mRNA
#=GF CC   of the dnaX gene in E. coli. The dnaX gene has two encoded products tau
#=GF CC   and gamma which are produced in a 1:1 ratio. The gamma protein is
#=GF CC   synthesised due to programmed frameshifting and is shorter than tau. The
#=GF CC   two products of the dnaX gene are DNA polymerase III subunits [1,2].
#=GF WK   DnaX_ribosomal_frameshifting_element
#=GF SQ   5


X04487.1/1830-1894         UGCAGGGAGCAACCAAAGCAAAAAAGAGUGAACCGGCAGCCGCUACCCGCGCGCGGCCGGUGAAU
U66040.1/1434-1498         CGCAGGGAGUAACCAAAACAAAAAAGAGUGAACCGGCAGCCGCAUCCCGCGCGCGGCCGGUGAAU
CP000036.1/386666-386730   UGCAGGGAGCAACCAAAGCAAAAAAGAGUGAACCGGCAGCCGCUACCCGCGCGCGUCCGGUGCCA
CP000647.1/497602-497666   GUCAGGGAGCAACCACCCCAAAAAAGAGUGAACCGGCAGCCGCUUCCCGCGCGCGGCCGGUGAAU
CP000653.1/1056799-1056863 CGCAGGGAGCAACCAAGCCAAAAAAGAGUGAACCGGCAGCGCCAGGAAGAGCGCGGCCGGUUAAU
#=GC SS_cons               :::::::::::::::::::::::::::::::<<<<<<-<<<<<_____>>>->>->>>>>>::::
#=GC RF                    uGCAGGGAGCAACCAAaaCAAAAAAGAGUGAACCGGcAGCCgCuacccGcGCGCGgCCGGUGAAU
//
# STOCKHOLM 1.0

#=GF AC   RF00383
#=GF ID   IS1222_FSE
#=GF DE   Insertion sequence IS1222 ribosomal frameshifting element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15126494
#=GF SS   Published; PMID:15126494
#=GF GA   45.00
#=GF TC   45.30
#=GF NC   39.00
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0006452; translational frameshifting;
#=GF RN   [1]
#=GF RM   15126494
#=GF RT   -1 frameshifting at a CGA AAG hexanucleotide site is required for
#=GF RT   transposition of insertion sequence IS1222.
#=GF RA   Mejlhede N, Licznar P, Prere MF, Wills NM, Gesteland RF, Atkins JF, Fayet
#=GF RA   O
#=GF RL   J Bacteriol 2004;186:3274-3277.
#=GF CC   This family represents the insertion sequence IS1222 ribosomal
#=GF CC   frameshifting element. The element stimulates frameshifting which is known
#=GF CC   to be required for transposition [1].
#=GF WK   Insertion_sequence_IS1222_ribosomal_frameshifting_element
#=GF SQ   5


X78052.1/454-571         GGCGCUUCAGGUGGCUCUUGGGCGAAAGUACUGACGACAGACCAGAAGCGGGAAGCCGUGAUGUUGAUAUGUGAUGCGACCGGUCUGUCGCAACGUCGUGCCUGCAGGCUCACAGGUU
AY378100.1/192650-192767 GGCACUUCAGGUGGCUCUGGGGCGAAAGUACUGACGACAGACCAGAAGCGGGAAGCCGUUGAGUUUAUGUGUGAUGCGACCGGUCUGUCGCAACGUCGUGCCUGCAGGCUUACAGGUU
AF324174.1/302-419       GGCGCUUCAGGUGGCUCUGGGUCGAAAGUUCUGACGACAGACCAGAAGCGGGAAGCCGUGGACGUCAUGUGUGAGGUCGCCGGUCUGUCGCAACGUCGUGCCUGCAGGCUGGCAGGUC
AY528232.1/302-419       GGCGCUUCAGGUGGCUCUGGGGCGAAAGUACUGACGACAGACCAGAAGCGGGAAGCCGUGAUGUUGAUGUGUGAUGCGACCGGUCUGUCGCAACGUCGUGCCUGCAGGCUUACAGGUU
AJ414030.1/131-14        GGCGCUUCAGGUGGCUCUUGGGCGAAAGUACUGACGACAGACCAGAAGCGGGAAGCCGUGAUGUUGAUGUGUGAUGCGACCGGUCUGUCGCAACGUCGUGCCUGCAGGCUAACAGGUU
#=GC SS_cons             ::::::::::::::::::::::::::::::::::(((((((((,,,,<<<<____>>>>,,,<<<<__________>>>>,)))))))))::::::::::::::::::::::::::::
#=GC RF                  GGCgCUUCAGGUGGCUCUgGGgCGAAAGUaCUGACGaCaGaCCAGAAgCGGGAAGCCGugauGucgAUgUGUGAuGcgaCCGGuCuGuCGCAACGUCGUGCCUGCAGGCUuACAGGUu
//
# STOCKHOLM 1.0

#=GF AC   RF00384
#=GF ID   Pox_AX_element
#=GF DE   Poxvirus AX element late mRNA cis-regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:10049834
#=GF SS   Published; PMID:10049834
#=GF GA   60.00
#=GF TC   62.60
#=GF NC   41.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.52 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0031123; RNA 3'-end processing;
#=GF RN   [1]
#=GF RM   10049834
#=GF RT   A 43-nucleotide RNA cis-acting element governs the site-specific formation
#=GF RT   of the 3' end of a poxvirus late mRNA.
#=GF RA   Howard ST, Ray CA, Patel DD, Antczak JB, Pickup DJ
#=GF RL   Virology 1999;255:190-204.
#=GF CC   This family represents a cis-regulatory element present at the 3' ends of
#=GF CC   poxvirus late mRNAs and is known as the AX element.The AX element is
#=GF CC   involved in directing the efficient production and orientation-dependent
#=GF CC   formation of of late RNAs [1].
#=GF WK   Poxvirus_AX_element_late_mRNA_cis-regulatory_element
#=GF SQ   10


AF012825.2/142988-142927 GAAUCUUUUCACAAAAGACUUUAUCCGACAAUUCAUCAUCUGUCAAUUGUGGAUUUGAAUGC
Y16780.1/125961-125900   GAAUCUUUUCACAAAAGAUUUUAUCCGAUAAUUCUUUCUCGGUCAAUUUCGGAUUUGAAUGC
AY243312.1/134177-134116 GAAUCUUUUCACAAAAGAUUUUAUCCGAUAAUUCUUCAUCGGACAAUUUCGGAUUUGAAUGC
AF482758.2/151000-150939 GAAUCUUUUCACAAAAGAUUUUAUCCGAUAAUUCUUCAUCAGACAAUUUCGGAUUUGAAUGC
L22579.1/125586-125525   GAAUCUUUUCACAAAAGAUUUUAUCCGAUAAUUCUUUCUCGGUCAAUUUCGGAUUUAAAUGC
AF380138.1/134189-134128 GAAUCUUUUCACAAAAGAUUUUAUCCGAUAAUUCUUCCUCGGACAAUUUCGGAUUUGAAUAC
AY009089.1/135275-135214 GAAUCUUUUCACAAAAGAUUUUAUCCGAUAAUUCUUCCUCGGACAAUUUCGGAUUUGAAUGC
DQ066533.1/2983-2922     GAAUCUUUUCACAAAAGAUUUUAUCCGACAAUUCUUCAUCGGACAAUUUCGGAUUUGAAUGC
DQ441437.1/126423-126362 GAAUCUUUUCACAAAAGAUUUUAUCCGAUAAUUCUUUCUCGGUCAAUUUUGGAUUUGAAUGC
DQ439815.1/139301-139240 GAAUCUUUUCACAAAAGAUUUUAUCCGACAAUUCUUCAUCGGACAAUUUCGAAUUUAAAUGC
#=GC SS_cons             :<<<<<<<<___>>>>>>>><<<<<<<<-<<<<<<_____>>-->>>>>>>>>>-->>::::
#=GC RF                  GAaUCUUUUCACAAAAGAuUUuAUCCGAUAAUUCuUcaUCgGaCAAUUUCGGAUUUgAAUGC
//
# STOCKHOLM 1.0

#=GF AC   RF00385
#=GF ID   IBV_D-RNA
#=GF DE   Infectious bronchitis virus D-RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:11119581
#=GF SS   Published; PMID:11119581
#=GF GA   35.00
#=GF TC   40.90
#=GF NC   34.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019079; viral genome replication;
#=GF DR   GO; 0019072; viral genome packaging;
#=GF RN   [1]
#=GF RM   11119581
#=GF RT   cis-acting sequences required for coronavirus infectious bronchitis virus
#=GF RT   defective-RNA replication and packaging.
#=GF RA   Dalton K, Casais R, Shaw K, Stirrups K, Evans S, Britton P, Brown TD,
#=GF RA   Cavanagh D
#=GF RL   J Virol 2001;75:125-133.
#=GF CC   This family represents a cis-regulatory element known as defective RNA or
#=GF CC   D-RNA. This region is thought to be essential for viral replication and
#=GF CC   efficient packaging [1].
#=GF WK   Infectious_bronchitis_virus_D-RNA
#=GF SQ   10


U52601.1/1238-1278     GGUAGAUAGGCAUGUAGCUU-AGCACCUACAUGUCUAUCGCC
AF111995.1/1438-1478   GGAAGAUAGGCAUGUAGCUU-AGCACCUACAUGUCUAUCGCC
AY319651.1/27421-27462 GGAAGAUAGGCAUGUAGCUUGAUUACCUACAUGUCUAUCGCC
AJ278334.1/215-256     GGAAGAUAGGCAUGUAGUUUGAUUACCUACAUGUCUAUCGCC
U52594.1/1381-1422     GGCAGAUAGGCAUGUAGCUUGAUUACCUACAUGUCUAUCGCC
L06251.1/212-253       GGGAGAUAGGCAUGUAGCUUGAUUACCUACAUGUCUAUCGCC
U52596.1/1422-1463     GAAAGAUAGGCAUGUAGCUUGAUUACCUAUAUGUCUAUCGCC
M28565.1/1541-1582     GGAAGAUAGGCAUGUAGCUUGAUUACCUACAUGUGUAUCGCC
U52598.1/1424-1465     GGAAGAUAGGCAUGUAGCUUAAUUACCUACAUGUCUAUCGCC
AF111996.1/1438-1478   GGCAGAUAGGCAUGUAGCUU-AGCACCUACAUGUCUAUCGCC
#=GC SS_cons           <<--<<<<<<<<<<<<<_________>>>>>>>>>>>>>->>
#=GC RF                GGaAGAUAGGCAUGUAGCUUGAUUACCUACAUGUCUAUCGCC
//
# STOCKHOLM 1.0

#=GF AC   RF00386
#=GF ID   Entero_5_CRE
#=GF DE   Enterovirus 5' cloverleaf cis-acting replication element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:11250909
#=GF SS   Published; PMID:11250909
#=GF GA   46.00
#=GF TC   46.00
#=GF NC   45.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0039689; negative stranded viral RNA replication;
#=GF RN   [1]
#=GF RM   11250909
#=GF RT   5' cloverleaf in poliovirus RNA is a cis-acting replication element
#=GF RT   required for negative-strand synthesis.
#=GF RA   Barton DJ, O'Donnell BJ, Flanegan JB
#=GF RL   EMBO J 2001;20:1439-1448.
#=GF CC   This family represents a cis-regulatory element found at the 5' end of
#=GF CC   Enterovirus genomes. The element has a cloverleaf like secondary structure
#=GF CC   and is known to be a multifunctional cis-acting replication element (CRE),
#=GF CC   required for the initiation of negative strand RNA synthesis [1].
#=GF WK   Enterovirus_5'_cloverleaf_cis-acting_replication_element
#=GF SQ   160


AY302558.1/1-90  UUAAAACAGCCUGUGGGUUGCC-CCCACCCGCAGGGCCCAUUGGGC-GCUAGCACACUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-CC
AJ132961.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACUCUGGUA----------------UCACGG----------------UACCUUUGUACGCCUGUUUUAU-AC
D00214.1/1-90    UUAAAACAGCCUGGGGGUUGUA-CCCACCCCUGGGGCCCACGUGGC-GCUAGUACUCUGGUU----------------CGUUAG----------------AACCUUUGUACGCCUGUUUUCC-CC
AF541919.1/1-81  U--------C--UGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACACUGGUA----------------UCACGG----------------UACCUUUGUACGCCUGUUUUAU-AC
AY508696.1/2-91  UUAAAACAGCCUGGGGGUUGUA-CCCACCCCUGGGGCCCACGCGGC-GCUAGUACUCUGGUA----------------CGUUAG----------------UACCUUUGUACGCCUGUUUUCC-CC
D00627.1/2-91    UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGCGCCACCGGGC-GUUAGCACACUGGUA----------------UCACGG----------------UACCCUUGUGCGCCUGUUUUAU-AA
AF029859.2/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GUUAGCACACUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AF114383.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCGCAGGGCCCACUGGGC-GCCAGCACUCUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAA-AA
V01148.1/1-91    UUAAAACAGCUCUGGGGUUGUA-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UUGCGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AY278549.1/1-91  UUAAAACAGCUCUGGGGUUGUA-CCCACCCCAGAGGCCCACGUGGCGGCUAGCACUCCGGUA----------------UUACGG----------------UACCCUUGUGCGCCUGUUUUAU-AC
X92886.1/1-90    UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCAUUGGGC-GCUAGCACACUGGUA----------------UCACGG----------------UACCCUUGUGCGCCUGUUUUAU-CC
AF352027.1/1-89  UUAAAACAGC-UGUGGGUUGUA-CCCACUCACAGGGCCCACGUGGC-GCUAGCACUCUGGUU----------------CUGCGG----------------AACCUUUGUGCGCCUGUUUUAC-GC
AY560657.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACACCGGUA----------------CCACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AJ577590.1/1-90  UUAAAACAGCCUGUGGGUUGCU-CCCAUCCACAGGGCCCACUGGGC-GCCAGCACUCUGGUA----------------UUGCGG----------------UACUUUAGUGCGCCUGUUUUAU-AU
AY302553.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCCAGCACUCUGGUA----------------UUACGG----------------UACCCUUGUGCGCCUGUUUUAU-AU
AY302545.1/1-90  UUAAAACAGCCUGUGGGUUGAU-CCCACCCACAGGGCCCAUUGGGC-GCUAGCACUCUGGUA----------------UUACGG----------------UACCCUUGUGCGCCUGUUUUAC-AC
AY421765.1/2-91  UUAAAACAGCCUGUGGGUUGUC-CCCACCCACAGGGCCCACUGGGC-GUUAGCACUCUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUUAU-AA
AJ133661.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCCAGCACACUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-CC
AF499643.1/1-90  UUAAAACAGC-CUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACUCUGGUA----------------UUACGG----------------UACCUUUGUACGCCUGUUUUAU-AU
AF499635.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACUCUGGUA----------------UUGCGG----------------UACCUUUGUACGCCUGUUUUAU-AU
S76772.1/1-90    UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GUUAGCACACUGGUA----------------UCCCGG----------------UACCUUUGUGCGCCUGUUUUAU-AU
M21949.1/1-89    UUAAAACAGCCUGUGGGUUGAU-CCCACCCACAGGGCCCAUUGGG--GCUAGCACUCUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AF311938.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCCAGCACACUGGUA----------------UCGUGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AF230973.1/2-91  UUAAAACAGCCUGUGGGUUGAU-CCCACCCGCAGGGCCCACUGGGC-GCCAGCACACUGGUA----------------UCAAGG----------------UACCUUUGUGCGCCUGUUUUAU-AA
AF177911.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCUAGCACACUGAUU----------------CUGCGG----------------GAUCUUUGUGCGCCUGUUUUAU-AA
AF465516.1/1-90  UUAAAACAGCCUGUGGGUUGAU-CCCACCCACAGGGCCCAUUGGGC-GUCAGCACCCUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AU
AY302540.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACAGGGC-GCAAGCACACUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-CU
X04468.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACACUGGUA----------------UCACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AY238473.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACACUGGUA----------------UUGCGG----------------UACCUUUGUACGCCUGUUUUAU-AC
AY421760.1/1-90  UUAAAACAGCCUGUGGGUUGCA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACUCUGGUA----------------UCACGA----------------UACCUUUGUGCGCCUGUUUUAU-AU
D16364.1/1-90    UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCUAGCACACUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUGAC-UU
L76407.1/1-91    NNAAAACAGCUCUGGGGUUGCU-CCCACCCCAGANNNCCACGUGGCGGCNAGUACUCUGGUA----------------UUGCGG----------------UACCUUUGUACGCCUGUUUUAU-AC
AF119795.2/2-88  U-AAAACAGC-UGUGGGUUGCA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACUCUGGUA----------------CUGAGG----------------UACCUUUGUGCGCCUGUUUU-U-AC
AF083069.1/1-90  UUAAAACAGCCUGUGGGUUGCA-CCCACCCACAGGGCCCACUGGGC-GCUGGUACACUGGUA----------------UUAAGG----------------UACCCUUGUACGCCUGUUUUAU-AU
AF328683.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GUUAGCACACUGGUA----------------UCCCGG----------------UACCUUUGUGCGCCUGUUUUAU-GU
AF524867.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCAUGGGGC-GCAAGCACACUGGUA----------------UUGCGG----------------UACCUUUGUGCGCCUGUUUUAU-CC
AF111981.2/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACUCUGGUA----------------CUACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AF538840.1/1-91  UUAAAACAGCUCUGGGGUUGCA-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UUGCGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AY426531.1/1-90  UUAAAACAGCUCUGGGGUUGUU-CCCACUCAAG-GGCCCACGUGGCGGCUAGUACUCUGGUA----------------UCUCGG----------------UACCUUUGUACGCCUGUUUUAA-UU
X67706.1/1-90    UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACUCUGGUA----------------CCGCGG----------------UACCUUUGUGCGCCUGUUUUAU-AU
AF302996.1/1-90  UUAAAACAGC-UGUGGGUUGUCACCCACCCACAGGGUCCACUGGGC-GCUAGCACUCUGGUA----------------CCUCGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AF465511.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACUCCGGUA----------------UUACGG----------------UACCCUUGUACGCCUGUUUUAU-AU
L24917.1/1-89    UUAAAACUGGAUCUGGGUUGUU-CCCACCCAGAUCACCUACAUGGU-GUU-GUACACUAUUA----------------UUACGG----------------UAAUCUUGUACGCCAGUUUUAU-AC
L76410.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UCACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
X79047.1/1-90    UUAAAACAGCCUGUGGGUUGUC-CCCACCCACAGGGCCCACUGGGC-GCUAGCACACUGGUA----------------UCCCGG----------------UACCUUUGUGCGCCUGUUUUAU-AU
AF363455.1/1-122 CUAAAACAGCCUGCGGGUUGUA-CCCGCCCGCAGGGCCCACUGGGC-GCUAGUACUCUGGUACGCUAGUACACUAGCACGUUAGUGCUUUUGUACGCCAGUACCUUUGUACGCCUGUUUUAU-UU
L76402.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCUGGUA----------------UCGCGG----------------UACCUUUGUACGCCUGUUUUAU-AC
AJ577593.1/1-78  GU------------GGGUUGUA-CCCAUCCACAGGGCCCACUGGGC-GCCAGCACUCUGGUA----------------UUGCGG----------------UACCUUAGUGCGCCUGUUUUAU-AU
L76393.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCUGGUA----------------CCACGG----------------UACCCUUGUACGCCUGUUUUAA-AC
AJ293918.1/1-91  UUAAAACAGCUCUGGGGUUGCU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACUCUGGUA----------------UUGCGG----------------UACCUUUGUACGCCUGUUUUAU-AC
AY302556.1/1-90  UUAAAACAGCCUGUGGGUUGAU-CCCACCCACAGGGCCCAUUGGGC-GCUAGCACUCUGGUA----------------UCACGG----------------UACCCUUGUGCGCCUGUUUUAU-GU
AF123433.1/1-91  UUAAAACAGCCUGGGGGUUGUA-CCCACCCCCGGGGCCCACGUGGC-GCCAGUACUCUGGUU----------------CGCUUAA---------------AACCUUUGUACGCCUGUUUUCC-CC
AY302548.1/1-91  UUAAAACAGCCUGUGGGUUGCA-CCCACCCACAGGGCCCACAGGGC-GCUAGCACUCUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAUUAC
X90723.2/1-90    UUAAAACAGCCUGUGGGUUGUU-CCCAUCCACAGGGCCCACUGGGC-GCUUGCACUCUGGUA----------------UCACGG----------------UACCAUUGUGCGCCUGUUUUAU-AU
D00625.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACACUGGUA----------------UCGCGG----------------UACCUUUGUACGCCUGUUUUAU-AC
AY421768.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACUCUGGUA----------------CUACGG----------------UACCUUUGUGUGCCUGUUUUAA-GC
AF499638.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACACCGGUA----------------UUACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AF448783.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACACCGGUA----------------UUACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AY302551.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCUACAGGGCCCACUGGGC-GUCAGCACACUGGUA----------------UCCCGG----------------UACCUUUGUGCGCCUGUUUUAU-AU
AY302543.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCAUUGGGC-GCUAGCACUCUGGUA----------------UUGCGG----------------UACCUUUGUGCGCCUGUUUUAU-AU
AY421763.1/1-90  UUAAAACAGCCUGUGGGUUGCA-CCCACCCACAGGGCCCACUGGGC-GCCAGCACUCUGGUA----------------UCGCGG----------------UACCUUUGUGCGCCUGUUUUAU-GA
X80059.1/1-90    UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACACUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
M24196.1/2-84    U-AAAACAGCUCUGGGGUUGUA-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UUGCGG----------------UACCUUUGUACGCCUGU--------
AF499641.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCUGGUA----------------UUACGG----------------UACCUUUGUACGCCUGUUUUAC-AC
X79369.2/2-91    UUAAAACAGCCUGGGGGUUGUU-CCCACCCCUGGGGCCCACGUGGC-GCUAGUACUCUGGUA----------------CGCUAG----------------UACCUUUGUACGCCUGUUUUUC-CC
AF447485.1/1-70  UUCCCAC--C---------------C-A---UAGGGCCCACGGGGC-GCCAGCACUCUGGUA----------------UCACGG----------------UACCCUUGUGCGCCUGUUUUAU-AA
AY421739.1/3-73  UUCCCAC--CCC----A---------------GAGGCCCACGUGGCGGCUAGUACUCUGGUA----------------UCACGG----------------UACCUUUGUACGCCUGUUUUAU-AC
AF111984.2/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACUCUGGUA----------------CCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AF465514.1/1-91  UUAAAACAGCCUGUGGGUUGUA-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UUACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
L76413.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCUGGUA----------------UCACGG----------------UACCUUUGUACGCCUGUUUUAC-AC
AJ493062.2/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCAUUGGGC-GCUAGCACACUGGUA----------------UUCCGG----------------UACCCUUGUGCGCCUGUUUUAU-CU
L76405.1/1-91    NNAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACACUGGUA----------------UCACGG----------------UACCCUUGUACGCCUGUUUUAU-GC
AY302559.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCAUUGGGC-GUCAGCACCCUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AU
AY508697.1/2-91  UUAAAAGAGUCAGGGGGUUGUA-CCCACCCCUGGGGCCCACGUGGC-GCUAGUACUCUGGUA----------------CGCCAG----------------UACCUUUGUACGCCUGUUUUCC-CC
U77070.1/1-90    UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GUCAGCACACUGGUA----------------UUGCGG----------------UACCCUUGUGCGCCUGUUUUAU-CU
AF081485.1/1-90  UUAAAACAGCCUGUGGGUUGAU-CCCACCCACAGGGCCCACUGGGC-GCUAGCACACUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUUAU-CU
AF114384.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACUCUGGUA----------------UUGCGG----------------UACCUUUGUGCGCCUGUUUUAC-CC
AF363453.1/1-120 UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCUAGUACACUGGUA-UGCCUUACCUCGGUAUUACGGUACCGAUGUAUAUAG-UACCUUUGUACGCCUGUUUUAU-AU
AF085363.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCUAGCACACUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUUAU-CU
AJ544513.1/1-91  UUAAAACAGCUCUGGGGAUGUA-CCCACCCCAGAGGCCCACGUGGCGGCUAGCACUCCGGUA----------------UCACGG----------------UACCCUUGUGCGCCUGUUUUAU-AC
AF162711.1/1-90  UUAAAACAGCCUGUGGGUUGAU-CCCACCCACAGGGCCCACUGGGC-GCCAGCACACUGGUA----------------UCGUGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AJ577591.1/1-78  GU------------GGGUUGUU-CCCAUCCACAGGGCCCACUGGGC-GCCAGCACUCUGGUA----------------UUGCGG----------------UACCUUAGUGCGCCUGUUUUAU-AU
AY302554.1/1-89  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCAUG-GGC-GCUAGCACACUGGUA----------------UCGUGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AY302546.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCAUUGGGC-GCUAGCACUCUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUUAU-GU
D00435.1/1-90    UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCUAGUACACUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUGAC-UU
AY421766.1/1-90  UUAAAACAGCCUGUGGGUUGCA-CCCACCCACAGGGCCCAAUGGGC-GUCAGCACUCUGGUA----------------CCGAGG----------------UACCUUUGUGCGCCUGUUUUAU-UU
L05355.1/1-85    UUAAAACAGCGGAUGG---GUAUCCC-ACCAUUCGACCCAUUGGGU-G-UAGUACUCUGGUA-----------------CUAUG----------------UACCUUUGUACGCCUGUUUCUC-CC
D00239.1/1-88    UUAAAACUGGGUGUGGGUUGUU-CCCACUCACACCACCCAAUGGGU-GUU-GUACUCUGUUA----------------UUCCGG----------------UAACUUUGUACGCC-AUUUUCC-CU
X02316.1/1-89    UUAAAACUGGAUCCAGGUUGUU-CCCACCUGGAUUUCCCACAGGGA-G-UGGUACUCUGUUA----------------UUACGG----------------UAACUUUGUACGCCAGUUUUAU-CU
AJ133662.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCCAGCACACUGGUA----------------UCACGG----------------UACUUUUGUGCGCCUGUUUUAU-CU
AF546702.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCUGGUA----------------UUACGG----------------UACCUUUGUACGCCUGUUUUGU-AU
AF499636.1/1-91  UUAAAACAGCUGUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UCACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AY036578.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCCAGCACACUGGUA----------------UCUUGG----------------UACCUUUGUGCGCCUGUUUUAU-CC
AY278553.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCGGAGGCCCACGUGGCGGCUAGUACUCUGGUA----------------UCACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
U05876.1/1-90    UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACUCUGAUU----------------CUACGG----------------AAUCCUUGUGCGCCUGUUUUAU-GU
AY302541.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACUCUGGUA----------------UUACGG----------------UACCCUUGUGCGCCUGUUUUAU-AU
AY421761.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACACUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
X84981.1/1-90    UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCCAGCACUCUGGUA----------------UCGCGG----------------UACCUUUGUGCGCCUGUUUUGU-UU
L76399.1/1-90    NNAAAACAGCCUGUGGGUURUU-CCCACNCACAGGGUCCACUGGGC-GCUAGCACACUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUNUUUUAU-AC
AF119796.3/2-88  U-AAAACAGC-UGUGGGUUGCA-CCCACCCAC-CGGGCCACUGGGCCGCUAGCACUCUGGUA----------------CUGAGG----------------UACCUUUGUGCGCCUGUUUU-U-AC
U22521.1/1-90    UUAAAACAGC-UGUGGGUUGUCACCCACCCACAGGGUCCACUGGGC-GCUAGUACACUGGUA----------------UCUCGG----------------UACCUUUGUACGCCUGUUUUAU-AC
AF447483.1/2-68  U--------CCC---------A-CCC-A---CGGGGCCCAAUGGGC-GCUAGCACUCCGGUA----------------UUACGG----------------UACCCUUGUGCGCC--UGUUUU-AU
AF111982.2/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACUCUGGUA----------------CUACGG----------------UACCUUUGUACGCCUGUUUUAU-AC
L76411.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UCACGG----------------UACCCUUGUACGCCUGUUUUAC-AC
L76403.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCUGGUA----------------YUACGG----------------UACCCUUGUACGCCUGUUUUAU-AU
AJ577594.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCAUCCACAGGGCCCACUGGGC-GCCAGCACUCUGGUA----------------UUGCGG----------------UACCUUAGUGCGCCUGUUUUAU-AU
L76394.1/1-91    NNAAAACAGCUCUGGGGUUGCU-CCCACCCCAGAGGCCCAAGUGGCGGCUAGUACUCUGGUA----------------UCGCGG----------------UACCUUUGUACGCCUGUUUUAU-AC
AY302557.1/1-90  UUAAAACAGCCUGUGGGUUGCA-CCCACCCACAGGGCCCAUUGGGC-GCUAGCACCCUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AY302549.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACUCUGGUA----------------CUACGG----------------UACCUUUGUGUGCCUGUUUUAU-AC
AY421769.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACACUGAUU----------------CUGCGG----------------GAUCUUUGUGCGCCUGUUUUAU-AU
D90457.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACACUGGUA----------------UCACGG----------------UACCUUUGUACGCCUGUUUUAA-AC
AF499639.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UUGCGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AY167106.1/1-68  C----AC--CC----------A-CCC-A---UAGGGCCCACCGGGC-GCCAGCACUCUGGUA----------------UCAUGG----------------UACCUUUGUGCGCCUGU--UUU-AU
M16248.1/1-89    UUAAAACUGGGAGUGGGUUGUU-CCCACUCACUCCACCCAUGCGGU-GUU-GUACUCUGUUA----------------UUACGG----------------UAACUUUGUACGCCAGUUUUUC-CC
AY302552.1/1-90  UUAAAACAGCCUGUGGGUUGAU-CCCACCCACAGGGCCCACUGGGC-GCUAGCACUCUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AY302544.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCAAUGGGC-GCUAGCACUCCGGUA----------------UUACGG----------------UACCCUUGUGCGCCUGUUUUAU-UU
AY421764.1/1-90  UUAAAACAGCCUGUGGGUUGCA-CCCACUCACAGGGCCCACUGGGC-GCUAGCACACUGAUU----------------UCCCGG----------------AAUCCUUGUGCGCCUGUUUUAU-AU
AF136379.1/2-89  U-AAAACAGCCUGUGGGUUGCA-CCCACCCACAGGGCCCAUUGGGC-GCUAGCACUCUGGUA----------------CUGAGG----------------UACCUUUGUGCGCCUGUUUU-U-AC
AF499642.1/1-91  UUAAAACAGCUCUGGGGUUGUA-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UUACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
V01150.1/1-91    UUAAAACAGCUCUGGGGUUGCA-CCCGCCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UUGCGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AF447486.1/1-70  UU-------CCC---------A-CCC-A---CGGGGCCCACGGGGC-GCUAGCACUCUGGUA----------------UCACGG----------------UACCCUUGUGCGCCUGUUUUAU-AA
AF201894.1/1-72  G------AG--UGU---UCCCA-CCCA---ACAG-GCCCACUGGGU-GUU-GUACUCUGGUA----------------UUACGG----------------UACCUUUGUACGCCU-A-UUUU-AU
AJ416942.1/1-91  UUAAAACAGCUCUGGGGUUGUA-CCCACCCCAGAGGCCCACGCGGCGGCUAGUACUCCGGUA----------------UUGCGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AF465515.1/1-91  UUAAAACAGCCUGUGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCUGGUA----------------UUACGG----------------UACCUUUGUACGCCUGUUUUGU-AU
AF317694.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCUAGCACUCUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUUAC-AU
L76406.1/1-91    NNAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------UUACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
L76397.1/1-73    G--------------GGUUGUU-CCCACCA-CAGGGCCUACUGGGC-GCCAGCACACUGGUA----------------UCACGG----------------UACUUUUGUGCGCC--UNUUUU-AU
X05690.1/1-90    UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCAAUGGGC-GCUAGCACACUGGUA----------------UUCCGG----------------UACCUUUGUGCGCCUGUUUUAU-AA
AF447481.1/1-68  U--ACCCACCCA-------------C------AGGGCCCACUGGGC-GUUAGCACACUGGUA----------------UCGCGG----------------UACCUUUGUGCGCCUGUUU--U-AU
AF363454.1/1-120 UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCUAGUACACUGGUA-UGCCUUACCUCGGUAUUACGGUACCGGUGUAUAUAG-UACCCUUGUACGCCUGUUUUAU-AU
AY465356.1/1-89  UUAAAACAGC-UGUGGGUUGCA-CCCACUCACAGGGCCCACUGGGC-GCAAGCACUCUGGUA----------------CCUCGG----------------UACCUUUGUGCGCCUGUUUUGU-AC
AJ577592.1/1-76  ------------GUGGGUUGUU-CCCAUCCACAGGGCCCACUGGGC-GCCAGCACUCUGGUA----------------UUGCGG----------------UACCUUAGUGCGCC--UGUUUU-AC
AY302555.1/1-79  U-----------GUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCUAGUACACUGGUA----------------CCAAGG----------------UACCUUUGUACGCCUGUUUUAU-AC
AY724745.1/2-91  UUAAAAGAGUCAGGGGGUUGUA-CCCACCCCUGGGGCCCACGUGGC-GCCAGUACACUGGUG----------------UGCUAG----------------CACCUUUGUACGCCUGUUUUUC-CC
D00820.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCCGGUA----------------CCCCGG----------------UACCCUUGUACGCCUGUUUUAU-AC
AF123432.1/1-90  UUAAAACAGCCUGGGGGUUGUA-CCCACCCCUGGGGCCCACGCGGC-GCCAGUACUCUGGUA----------------CGCUAG----------------UACCUUUGUACGCCUGUUUUCC-CC
AY302547.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACCGGGC-GCUAGCACACUGGUA----------------UCGCGG----------------UACCUUUGUGCGCCUGUUUUAU-UU
AF241359.1/2-91  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACGGGGC-GCUAGCACACUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AU
AY302539.1/1-90  UUAAAACAGCCUGUGGGUUGUA-CCCACCCACAGGGCCCACUGGGC-GCCAGCACACUGGUA----------------UCACGG----------------UACCCUUGUGCGCCUGUUUUAU-CC
AY421767.1/1-90  UUAAAACAGCCUGUGGGUUGCA-CCCACUCACAGGGCCCACUGGGC-GCUAGCACUCUGGUA----------------CCGUGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AF268065.1/1-90  UUAAAACAGCUUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCUAGUACACUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUGAC-CC
AY036579.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCAUUGGGC-GUCAGCACCCUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AU
AF499637.1/1-91  UUAAAACAGCUCUCGGGUUGUU-CCCCCCCCAGAGGCCCACGUGGCGGCCAGUACUCCGGUA----------------UUACGG----------------UACCCUUGUACGCCUGUUUUGU-AU
AF448782.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACACUGGUA----------------UUACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
U57056.1/1-90    UUAAAACAGCCUGUGGGUUGAU-CCCACCCACAGGGCCUAUUGGGC-GCUAGCACUCUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AU
D00538.1/1-90    UUAAAACAGCUCUGGGGUUGCU-CCCACCCCAGAGGCCCACGUGGCGGCUAGUAAUCUGGUA-----------------UCAGG----------------UACCUUUGUACGCCUGUUUUAU-AU
AY302550.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCUAGCACACCGGUA----------------UCACGG----------------UACCCUUGUGCGCCUGUUUUAU-CC
AY302542.1/1-90  UUAAAACAGCCUGUGGGUUGUU-CCCACCCACAGGGCCCACUGGGC-GCAAGCACACUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUUAC-AU
AY421762.1/2-91  UUAAAACAGCCUGUGGGUUGCU-CCCACCCACAGGGCCCACUGGGC-GCUAGCACACUGAUU----------------UUACGG----------------AAUCUUUGUGCGCCUGUUUUAU-AU
L76409.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGCGGCGGCUAGUACUCCGGUA----------------UUACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
M16560.1/1-89    UUAAAACAGCCUGUGGGUUGUU-CCCACCCACA-GGCCCAUUGGGC-GCUAGCACUCUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAC-AU
AF499640.1/1-91  UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACUCCGGUA----------------UUGCGG----------------UACCCUUGUACGCCUGUUUUAC-AC
X79368.1/2-91    UUAAAAGAGUCAGGGGGUUGUA-CCCACCCCUAGGGCCCACGUGGC-GCCAGUACUCUGGUA----------------CAUUAG----------------UACCUUUGUACGCCUGUUUUCC-CC
U22522.1/1-89    UUAAAACAGC-UGUGGGUUGUU-CCCACUCACAGGGCCCACUGGGC-GCUAGCACUCUGAUU----------------UUACGA----------------AAUCCUUGUGCGCCUGUUUUAU-AU
AF447484.1/2-70  UCCCACCAAC------A----------------GGGCCCACGGGGC-GCCAGCACUCUGGUA----------------UCACGG----------------UACCCUUGUGCGCCUGUUUUAU-AA
AJ276224.1/1-90  UUAAAACAGGGUGUGGGUUAUU-CCCACCCACAGGGCCCACCGGGC-GCUAGCACACUGGUA----------------UCACGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
X00595.1/1-91    UUAAAACAGCUCUGGGGUUGUA-CCCACUCCAGAGGCCCACGUGGCGGCUAGCACUCCGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUUAU-AC
AF465513.1/1-91  UUAAAACAGCCUGUGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCCAGUACUCCGGUA----------------UUGCGG----------------UACCCUUGUACGCCUGUUUUAC-AC
L76412.1/1-91    UUAAAACAGCUCUGGGGUUGUA-CCCACCCCAGAGGCCCACGUGGCGGCUAGUACUCUGGUA----------------UUACGG----------------UACCCUUGUACGCCUGUUUUAU-AC
L76404.1/1-91    UUAAAACAGCUCUGGGGUUGUU-CCCACCCCAGAGGCCCACGUGGCGGCUAGCACCCUGGUA----------------UUACGG----------------UACCUUUGUGCGCCUGUUUUAA-AA
#=GC SS_cons     :(((((((,<<<<<<<<<____.___>>>>>>>>><<<_____>>>.<<--<<<<---<<<<................______................>>>>--->>>>>>,))))))):.::
#=GC RF          UuaaaaCaGcccgcGGGuUGUu.CCCaCCCgcgggGCCCAcugGGC.GCuAGcaCuCUGGua................uuacGG................uaCCuUUGugCGCCuGuuuuaU.au
//
# STOCKHOLM 1.0

#=GF AC   RF00387
#=GF ID   IRES_FGF1
#=GF DE   FGF-1 internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15314170
#=GF SS   Published; PMID:15314170
#=GF GA   38.00
#=GF TC   39.10
#=GF NC   36.20
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   15314170
#=GF RT   Internal Ribosome Entry Site Structural Motifs Conserved among Mammalian
#=GF RT   Fibroblast Growth Factor 1 Alternatively Spliced mRNAs.
#=GF RA   Martineau Y, Le Bec C, Monbrun L, Allo V, Chiu IM, Danos O, Moine H, Prats
#=GF RA   H, Prats AC
#=GF RL   Mol Cell Biol 2004;24:7622-7635.
#=GF CC   This family represents the FGF-1 internal ribosome entry site (IRES). The
#=GF CC   FGF-1 IRES is present in the 5' UTR of the mRNA and allows cap-independent
#=GF CC   translation. It is thought that FGF-1 IRES activity is strictly controlled
#=GF CC   and highly tissue specific [1].
#=GF WK   FGF-1_internal_ribosome_entry_site_(IRES)
#=GF SQ   6


M60515.1/145-312        CGCUCCAGGGGAAUCAGGGCAUCGC----CUCCUUUUCUGGGAGGACACUCCCUUCUGAUGGUGAAUGGGAACUCCCUUCCUCCUGCAGCAGCCUGCCUGCAGCUG-UCCUGGUAGAACAGUGUGGACAUUGCAGAAGCUGUCACUGCCCCAGAAAGAAAGCACCCCAGAGCC
Z14149.1/354-521        CGCUCCAGGGGAAUCAGGGCAUCGC----CUCCUUUUCUGGGAGGACACUCCCUUCUGAUGGUGAAUGGGAACUCCCUUCCUCCUGCAGCAGCCUGCCUGCAGCUG-UCCUGGUAGAACAGUGUGGACAUUGCAGAAGCUGUCACUGCCCCAGAAAGAAAGCACCCCAGAGCC
X59612.1/146-313        CGCUCCAGGGGAAUCAGGGCAUCGC----CUCCUUUUCUGGGAGGACACUCCCUUCUGAUGGUGAAUGGGAACUCCCUUCCUCCUGCAGCAGCCUGCCUGCAGCUG-UCCUGGUAGAACAGUGUGGACAUUGCAGAAGCUGUCACUGCCCCAGAAAGAAAGCACCCCAGAGCC
AC120558.12/85564-85725 GGCUCUAGGGG--UAAGGGCAUUGCCUGACGACUUUUCUGGAUGGACACUCCCUCCUAAUGGUGAAUGGAAACUCCCUUUCUC----AGUAGCCUCCUUGUAGUUCAUCCCGGUAGCCCAGUGUG---AUUGCAGCCGCUGCCACCACCC-AGACAGGAAGCCUCCCAGAGC-
AC110730.10/34981-34820 GGCUCUAGGGG--UAAGGGCAUUGCCUGACGACUUUUCUGGAUGGACACUCCCUCCUAAUGGUGAAUGGAAACUCCCUUUCUC----AGUAGCCUCCUUGUAGUUCAUCCCGGUAGCCCAGUGUG---AUUGCAGCCGCUGCCACCACCC-AGACAGGAAGCCUCCCAGAGC-
AF067191.1/1071-1232    GGCUCUAGGGGG-UAAGGGCAUUGC-UGACGACUUUUCUGGAUGGACACUCCCUCCUAAUGGUGAAUGGAAACUCCCUUUCUC----AGUAGCCUCCUUGUAGUUCAUCCCGGUAGCCCAGUGUG---AUUGCAGCCGCUGCCACCACCC-AGACAGGAAGCCUCCCAGAGC-
#=GC SS_cons            :[[[[--[[[[--[[<<<<-----<....<<<<<_____>>>>>>----->>>>((((,,<<-<<<-<<<____>>>>>>-->>,<<<<<<<<----<<<<<<-<<.<<<______________>>>>>>>>>>>-->>>>--->>>>,,)))),,]]-----]]]]-]]]]:
#=GC RF                 gGCuCuAGGGgaAucaGGGCAUuGC....CgcCuUUUCUgGgcGGACACUCCCucCugAUgGUgaaUGGgAACUcCCuucCUCcugcgGcaGCCUgCcuGcaguug.ucCuGGUAGaaCAGUGUGgacauugCagaaGCuguCACcgcCCcaGgaAgaAAGCacCCCAGaGCc
//
# STOCKHOLM 1.0

#=GF AC   RF00388
#=GF ID   Anti-Q_RNA
#=GF PI   QaRNA
#=GF DE   Anti-Q RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14651627
#=GF SS   Published; PMID:14651627
#=GF GA   45.00
#=GF TC   46.30
#=GF NC   35.60
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   14651627
#=GF RT   Characterization of cis-acting prgQ mutants: evidence for two distinct
#=GF RT   repression mechanisms by Qa RNA and PrgX protein in pheromone-inducible
#=GF RT   enterococcal plasmid pCF10.
#=GF RA   Bae T, Kozlowicz BK, Dunny GM
#=GF RL   Mol Microbiol 2004;51:271-281.
#=GF RN   [2]
#=GF RM   20097859
#=GF RT   Direct evidence for control of the pheromone-inducible prgQ operon of
#=GF RT   Enterococcus faecalis plasmid pCF10 by a countertranscript-driven
#=GF RT   attenuation mechanism.
#=GF RA   Johnson CM, Manias DA, Haemig HA, Shokeen S, Weaver KE, Henkin TM, Dunny
#=GF RA   GM
#=GF RL   J Bacteriol. 2010;192:1634-1642.
#=GF RN   [3]
#=GF RM   20332003
#=GF RT   Structural analysis of the Anti-Q-Qs interaction: RNA-mediated regulation
#=GF RT   of E. faecalis plasmid pCF10 conjugation.
#=GF RA   Shokeen S, Johnson CM, Greenfield TJ, Manias DA, Dunny GM, Weaver KE
#=GF RL   Plasmid. 2010;63:0-0.
#=GF CC   Qa RNA is a cis-regulatory element from Enterococcus faecalis which is
#=GF CC   known to negatively regulate prgQ transcription via an antisense mechanism
#=GF CC   [1].
#=GF WK   Anti-Q_RNA
#=GF SQ   6


AE016833.1/44522-44622 GUUGUAACUAAUGUUGCAACAAACGA---------GAACCGAGUAUAGUUCAUGGGGUUCUGUUGCAAAGUUUUAAAUAAAGAAUAAAAUCCC-UUACGGUAUC-UAUGAUU-
AE016831.1/5476-5375   GUUGUAACUAAUGUUGCAACAAACGA---------GAACCGAGUAUAGUUCAUGCUGU-AUCAUGAAUUGUUUAACUGUCCUCUAGGAUUCCC-GUCCUAUGACAGUCGGUUC
AE002565.1/35056-35157 GUUGUAACUUAUGUUGCAACAAACGA---------GAACCGAUUAUAGUUCAUGGUGU-CUCAUGAAUUAUUUAACUGUCCUCUGGGAUUCCC-GUCCCAUGGCAGUCGGUUC
D78016.1/6410-6307     GUUGUAACUUAUGUUGCAGUGUUCGA---------GAACCGAGUAUAGUUCAUGGGAUCAGCAUGAAUUAUUUAACUAUCCUCUUGGGUUGGUAGCCCAAAGAUAGUCGGUUC
AE016833.1/5415-5306   AUUCUACCUUAUUUGAUAGUAGAUUUAAAACUUUGCAACAGAACC--GUUCAUGGGUAUAGCAUGAAUUGUUUAACUGUCCUCUAGGAUUCCC-GUCCUAUGGCAGUCGGUUC
AY855841.2/8399-8298   GUUGUAACUAAUGUUGCAACAAACGA---------GAACCGAGUAGAGUUCAUGUCAU-ACCAUGAAUUGUUUAACUGCCCCCUAGGAUUGCC-GUCCUAUGGCAGUCGGUUC
#=GC SS_cons           <<<<<<<<____>>>>>>>>------.........(((((((,,,,<<<<<<<<_______>>>>>>>>,,,,,,<<<<<---<<<<<<____.>>>>>>->>>>>)))))))
#=GC RF                guUguaacUuAUguugcAacAaAcgA.........GAACcGagUAuagUuCAuGggauuauCaUGaAuugUUUAAcUgcccucugGgauUccC.gucCcaUggcAguCgGUUC
//
# STOCKHOLM 1.0

#=GF AC   RF00389
#=GF ID   satBaMV_CRE
#=GF DE   Bamboo mosaic virus satellite RNA cis-regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12832220
#=GF SS   Published; PMID:12832220
#=GF GA   100.00
#=GF TC   127.70
#=GF NC   24.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0039703; RNA replication;
#=GF RN   [1]
#=GF RM   12832220
#=GF RT   Structural and mutational analyses of cis-acting sequences in the
#=GF RT   5'-untranslated region of satellite RNA of bamboo mosaic potexvirus.
#=GF RA   Annamalai P, Hsu YH, Liu YP, Tsai CH, Lin NS
#=GF RL   Virology 2003;311:229-239.
#=GF CC   This family represents a cis-regulatory element found in the 5' UTR of
#=GF CC   bamboo mosaic virus satellite RNA (satBaMV). The family is thought to be
#=GF CC   essential for efficient replication [1].
#=GF WK   Bamboo_mosaic_virus_satellite_RNA_cis-regulatory_element
#=GF SQ   42


AY205187.1/1-157 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGUU-CCCUAUAGUCCGCGUUGGCGGUGCUGCA-ACCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUAAAUACGACGCUUACCAAGAC
AY205179.1/1-159 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCCAUAGUCCGCUUUGGCGGUGCAGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205224.1/1-157 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAACACUAGACCACGAGAGUCCCCCUAUAGUCC-CGUUAGGG-UGCGGCAGGCUCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205216.1/1-154 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAACACUAGACCACGAGGGCACCCCUACAACCC---AAGG-G-UGCGGCAGGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205170.1/1-159 GAAAACUCACCGCAACGAAACGAAAAUAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCUAUAGUCCGCUUUGGCGGUGCGGCACUCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205208.1/1-159 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAAUACUUGACCACGAGGGGCCCCCUAUAGUCUGCUUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205162.1/1-159 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCUAUAGUCCGCUUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205199.1/1-157 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAGUACUUGACCACGAGGGUU-CCUUAUAGUCCGCGUUGGCGGUGCUGCA-GCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUAAAUACGACGCUUACCAAGAC
AY205228.1/1-158 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAACACUAGACCAUGAGGGCUCUCCUAUAGUCC-CGCUGAGGGUGCGGCAGGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205182.1/1-159 GAAAACUCACCGCAAGGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCUAUAGUCCGCUUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205174.1/1-159 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCUAUAGUCCGCUUUGGCGGUGCAGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205166.1/1-159 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGCCCCCUACUAUCUGCGUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACCGCGGUAUUCCCCGCACUCCGUCGAGCGGUAAAUACGACGCUUACCAAGAC
AY205211.1/1-159 UAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAAUACUUGACCACGAGGGCUCCCCUAUAGUCUGCUUUGGCGGUGCGGCAGGCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205203.1/1-159 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGCCCCCUACUAUCUGCGUUGGCGGUGCGGCAGCCCCCGUGCGACAGGCUAACCGCGGUAUUCCCCGCACUCCGUCGAGCGGUAAAUACGACGCUUACCAAGAC
AY205186.1/1-159 GAAAACUCACCGCAACGAAACGAAAAUAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCUAUAGUCUGCUUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205231.1/1-158 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAAUACUAGACCACGAGGGCCCCCCUAUAGUAC-CGUUGAGGUUGCGGCAGGCCCCGUGCGAUAGGCUAACUGUGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205223.1/1-159 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAAUACUUGACCACGAGGGGCCCCCUAUAGUCUGCUUUGAGGGUGUGGUAGGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205215.1/1-159 GAAAACUCACCGCAACGGAACGAAACAAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCUAUAGUCUGCUUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205227.1/1-158 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAACACUAGACCACGAGGGCCCCCCUAUAGUCC-CGCUGAGGGUGUGGCAGGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205219.1/1-152 GAAAACUCACCGCAACGAAACAAA-----UCGUUCAGAAACACUUGACCACGAGGGGUCCUCUAUAGUAC-CG-UCAGGUUGCGGCAGCCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUAUUAAGAC
AY205165.1/1-159 GAAAACUCACCGCAACGAAACGAAAAGAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCUAUAGUCCGCUUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205210.1/1-159 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAAUACUUGACCACGAGGGGCCCCCUAUAGUCUGCUUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACUGAGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205202.1/1-159 GAAAACUCACCGAAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGCCCCCUACUAUCUGCGUUGGCGGUGCGGCAGCCCCCGUGCGACAGGCUAACCGCGGUAUUCCCCGCACUCCGUCGAGCGGUAAAUACGACGCUUACCAAGAC
AY205193.1/1-157 GAAAACUCACCGAAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGUU-CCCUAUAGUCCGCGUUGGCGGUGCUGCA-ACCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUAAAUACGACGCUUACCAAGAC
AY205230.1/1-158 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAAUACUAGACCACGAGGGCCCCCCUACAGCCC-CGCUGAGGGUGCGGCAGGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205169.1/1-159 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCUAUAGUCUGCUUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205222.1/1-157 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAACACUAGACCACGAGGGCCCCCCUACAG-CC-CGCUGAGGGUGCGGCAGGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205214.1/1-159 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCUAUAGUCUGCUUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205197.1/1-157 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGUU-CCCUAUAGUCCGCGUUGGCGGUGCUGCA-ACCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUAAAUACGACGCUUACCAAGGC
AY205226.1/1-158 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAACACUAGACCAUGAGGGCCCCCCUAUAGUAC-CGUUGAGGUUGCGGCAGGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205218.1/1-157 GAAAACUCACCGC-ACGAAACGAAACAAAUCGUUCAGAAACACUAGACCACGAGGGCCCCCCUAUAGUCC-CGCUGAGGGUGCGGCAGGUCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205172.1/1-159 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGAUCCCCUAUAGUCCGCUUUGGCGGUGCGGCACCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205164.1/1-159 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGCCCCCUAUUAUCUGCGUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACCGCGGUAUUCCCCGCACUCCGUCGAGCGGUAAAUACGACGCUUACCAAGAC
AY205201.1/1-159 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGCCCCCUACAAUCUGCGUUGGCGGUGCGGCAGCCCCCGUGCGACAGGCUAACCGCGGUAUUCCCCGCACUCCGUCGAGCGGUAAAUACGACGCUUACCAAGAC
AY205184.1/1-159 GAAAACUCACCGCAACGAAACGAAAAUAAUCGUUCAGAAAUACUUGACCAUGAGGGGUCCCCUAUAGUCUGCUUUGGCGGUGCGGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205176.1/1-159 GAAAACUCACCGCAACGAAACGAAAACAAUCGUUCAGAAAUACUUGACCACGAGGGGUCCCCCAUAGUCCGCUUUGGCGGUGCAGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUAAAUACGACGCUUACCAAGAC
AY205221.1/1-157 GAAAACUCACCGCAACGAAACGAAACAGAUCGUUCAGAAACACUAGACCAUGAGGGCUCCCCUAUAGUCC-CGCUGAGGGUGCGGCAGGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCC-GCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205213.1/1-156 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAAUACUUGACCACGAGGGCCCCCCUAUAGUCC-AGUUUUGG-UGCGGC-GGCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205217.1/1-158 GAAAACUCACCGCAACGAAACGAAACAAGUCGUUCAGAAACACUAGACCACGAGGGCCCCCCUAUAGUCC-UGUUGAAGGUGCGGCAGGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205209.1/1-157 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAAUACUUGACCACGAGGGGU-CCCUAUAGUCCGCGUUGGCG-UGCGGCAGCCCCCGUGCGAUAGGCUAACUGCGGUAUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205229.1/1-157 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAACACUAGACCAUGAGGGCCCCCCUAUAGUCC-CGCUGAGG-UGCUGCAGGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
AY205220.1/1-157 GAAAACUCACCGCAACGAAACGAAACAAAUCGUUCAGAAACACUAGACCAUGAGGGUUCCCCUAUAGUCC-CGCUGAGGGUGCGGU-GGCCCCGUGCGAUAGGCUAACUGUGGUGUUCCCCGCACUCCGUCGAGCGGUUAAUACGACGCUUACCAAGAC
#=GC SS_cons     ::::::::(((((-(((,<<<<<______>>>>><<<-----<<<---<<<<-<<<<<--<<------<<-<_____>>>--->>-->>>>>>>>>--->>>----->>>,<<<<<_____>>>>>,)))---))))):::::::::::::::::::::
#=GC RF          GAAAACUCaCCGCAaCGAaaCGaAAaaAAuCGuuCaGAAAuACugGACCacGAGGGgcCCCcUAUAGUccGcguUGggggUGCgGCAgcCCCCguGCGAcaGGCUAACuGugGuguUCCCCgcaCuCCGuCGAGCGGuuAAUACGACGCUUACCAAGAC
//
# STOCKHOLM 1.0

#=GF AC   RF00390
#=GF ID   UPSK
#=GF DE   UPSK RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:9223489, INFERNAL
#=GF SS   Published; PMID:9223489
#=GF GA   38.00
#=GF TC   38.60
#=GF NC   37.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   9223489
#=GF RT   The role of the pseudoknot at the 3' end of turnip yellow mosaic virus RNA
#=GF RT   in minus-strand synthesis by the viral RNA-dependent RNA polymerase.
#=GF RA   Deiman BA, Kortlever RM, Pleij CW
#=GF RL   J Virol 1997;71:5990-5996.
#=GF RN   [2]
#=GF RM   15033563
#=GF RT   The tRNA-like structure of Turnip yellow mosaic virus RNA is a
#=GF RT   3'-translational enhancer.
#=GF RA   Matsuda D, Dreher TW
#=GF RL   Virology 2004;321:36-46.
#=GF CC   This family represents a pseudoknot structure from turnip yellow mosaic
#=GF CC   virus which is thought to be needed for efficient transcription as
#=GF CC   disruption of the pseudoknot structure gives rise to a 50% drop in
#=GF CC   transcription efficiency [1]. This family acts in conjunction with
#=GF CC   Rfam:RF00233 to enhance translation [2].
#=GF WK   UPSK_RNA
#=GF SQ   6


J04373.1/6212-6234 UAAGUUCUCGAUCUUUAAAAUCG
M24803.1/1-23      UAAGUUCUCGAUCUCUAAAAUCG
AF035635.1/619-641 UGAGUUCUCGAUCUCUAAAAUCG
M24804.1/82-104    UGAGUUCUCUAUCUCUAAAAUCG
M24801.1/79-101    UAAGUUCUCGAUCUUUAAAAUCG
M24805.1/67-89     UGAGUUCUCGAUCUCUAAAAUCG
#=GC SS_cons       :AAA::::<<<<aaa____>>>>
#=GC RF            UaAGUUCUCGAUCUCUAAAAUCG
//
# STOCKHOLM 1.0

#=GF AC   RF00391
#=GF ID   RtT
#=GF DE   RtT RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   PMID:1840671
#=GF SS   Published; PMID:1840671; Moxon SJ
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   44.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0034198; cellular response to amino acid starvation;
#=GF RN   [1]
#=GF RM   1840671
#=GF RT   A novel RNA product of the tyrT operon of Escherichia coli.
#=GF RA   Bosl M, Kersten H
#=GF RL   Nucleic Acids Res 1991;19:5863-5870.
#=GF CC   This family represents a bacterial cis-regulatory element known as RtT
#=GF CC   RNA. The exact function of RtT is unknown although it is thought that it
#=GF CC   may be involved in changing the cellular response in relation to amino
#=GF CC   acid starvation [1].
#=GF WK   RtT_RNA
#=GF **   6 seqs of Photorhabdus luminescens currently overlap with tRNA family
#=GF **   RF00005 (Daub J)
#=GF SQ   57


K01197.1/984-1115              AUUCUGCCCAUG-CGGGG---AAGGAUGAG----AA--------GCU-UCG---ACC-----AAGGUUCGACUCG-AGCGCC-AG---CGAGAGAGCG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUAAUCCU-UCCCCCACCACCA
K01197.1/1340-1471             AUUCUGCCCAAG-CGGGG---AAGGAUGAG----AA--------GCU-UCG---ACC-----AAGGUUCGACUUG-AGCGCC-AG---CGAGAGAGCG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUAAUCCU-UCCCCCACCACCA
K01197.1/1162-1293             AUUCUGCCCAUG-CGGGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGGCUCG-AGCGUC-AG---CGAGAGAGCG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUAAUCCU-UCCCCCACCACCA
K01197.1/689-818               UUUGCACUCAU--CGGGG---AAGGGUGAG----AA--------CCU-UCG---ACU-----AAGGUUCGAUUCG-AGCGAA-AG---CGAGAGAGCG---UUGCCACAGGCAACGGCCC-GAAG--GUGA--GGAGCGA-AGCGACGAAUAAUCCU-UCCCCCACCACCA
AL627269.1/199748-199617       AUUCUACCCAUG-UGGGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGAUUCG-AGCGAA-AG---CGAGAGAACG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--AACGCGC-AGCGCUGAGUCAUCCU-UCCCCCACCACCA
AL627269.1/199937-199799       --AGCGGCCAAA-GGGAG---CAGACUGUA----AAUCUGCCG-UCA-UCG---ACUUCG--AAGGUUCGAUUCG-AGCGC--AG---CGAGAAAGCG---UUGCCGUAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUCAUCCU-UCCCCCACCACCA
BA000007.2/1732540-1732408     AGUUUGCACUCAUCGGGG---AAGGGUGAG----AA--------CCU-UCG---ACU-----AAGGUUCGACUCG-AGCGAA-AG---CGAGAGAACG---UUUUCACAGGCAACGGCCC-GAAG-GGUGA--GGAGCGA-AGCGACGAAUAAUCCU-UUCCCCACCGCCA
CP000653.1/2490772-2490901     AUUCUGCCCAUG-C-GGG---AAGGAUGAG----AA--------GCU-UCG---ACC-----AAGGUUCGAUUCG-AGCGC--AG---CGAGAAAGCG---UUGCCGCAGGCAACGACCC-GAAG-GGUGA--AGCGCAA-CGCGCUGAGUAAUCCU-UCCCCCACCACCA
ABEJ01000013.1/51349-51479     UAUCUCUCCGUA-CGGGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGAUUCG-AGCGC--AG---CGAGAAAGCG---UUGCCGUAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUAAUCCU-UCCCCCGUCAUCC
CP000647.1/2417762-2417892     AUUCUGCCCCA--CGGGG---AAGGAUGAG----AA--------GCU-UCG---ACC-----AAGGUUCGACUCG-AGCGA--AA---CGAGAGAACG---UUGCCGCAGGCAACGGCCC-GAAG-GGCGA--GGCGCUUUAGCGCCGAGUAAUCCU-UCCCCCACCACCA
ABEJ01000013.1/51173-51304     UAUCUCUCCGUA-CGGGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGAUUCG-AGCGAA-AG---CGAGAAAGCG---UUGCCAACGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUAAUCCU-UCCCCCACCACCA
AACY022990324.1/906-777        AUCCAUCCCAUG-C-GGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGAUUCG-AGCGG--AG---CGAGAAAGCG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--GGCGCAA-CGCGCCGAGUAAUCCU-UCCCCCACCACCA
CP000647.1/2417286-2417418     UGUUUGCACUUA-GCGGG---AAGGGUAAG----AA--------CCU-UCG---ACU-----AAGGUUCGACUCG-AGCGCC-AG---CGAGAGAACG---UUGCCGCAGGCAACGGCCC-GAAG-GGCGA--GGAGAGAUAGCGACGAGUUAUCCU-UCCCCCACCACCA
ABCD01000001.1/1209721-1209847 AGUUCUCAUAUC-UGGGG---AAGG-UAAG----AA--------CCU-UCG---A-C-----AAGGUUCGCGCCG-AGCGU--AG---CGAGACAACG---ACGCAAA--GCGGCGGCCC-GAAG-GGUGA--GGAACGC-AGUGACGAAUAAUCCU-UCCCCCACCACUA
CP000653.1/2490477-2490606     AGUUUGCACUUA-UCGGG---AAGGGUGAG----AA--------CCU-UCG---U-U-----AAGGUUCGACUCU-UGCGA--AG---CAAGAGAACG---UUGCCUCUGGCAACGGCCC-GCAG-GGUGA--GGAGCGA-AGCGACGAAUAAUCCU-UCCCCCACCACCC
AM286415.1/2461012-2461139     AUAGCACCCAUC-AGGGG---AAGG-UAAG----AA--------CCU-UCG---ACC-----AAGGUUCGCGCCG-AGCAU--AG---CGAGACAACG---ACGCGCA--GCGGCGGCCC-GAAG-GGCGA--GGAACAA-CGUGACGAGUAAUCCU-UCCCCCACCACCA
CP000026.1/1188633-1188503     UAUCUCUCUGUA-CGGGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGAUUCG-AGCGC--AG---CGAGAAAGCG---UUGCCGUAGGCAACGGCCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUCAUCCU-UCCCCCACCACCA
CP000668.1/2358364-2358239     AUACUACACAUG-UCGUG---UGGG-UGAG----AU--------CCU-GCG---UUC------AGGUUCGAGCCG-AGCGA--AG---CGAGACAGCA---ACGCGUCA-GCGUUGACCC-GAAG-GGCG---AGGCCAG-AG-GCCGAGUCAUCCC-GCACGGCCCACCA
AACY022966564.1/505-633        CUGAUGCCCACA-GAGGG---AGGG-UGAG----AA--------CCC-UCG----CC------GGGUUCGAGCAG-AGCAGCUUG---CUGCGAUGAA---CGGCCGCAGGCCG--CCCC-GAAGGGGUGA--GCCACGC-AGUGGCGAAUCAUCCC-UCCCUCACCGCCA
AM286415.1/1356898-1357023     UACUACACAAUA-UCGUG---UGGG-UGAG----AC--------CCU-GCG---UUC------AGGUUCGAGCCG-AGCGA--AG---CGAGACAGCA---ACGCGCCA-GCGUUGACCC-GAAG-GGCG---AGGCCAG-AG-GCCGAGUCAUCCC-GCACGACCCACCA
AP008232.1/2265591-2265464     CCUGAGCUUCGC-GGGGG---AAGG-UGAG----AA--------CCU-UCG---ACC-----CAGGUUCGCGUCG-AGCCU--CG---CGAAACAACG---AUGUGCA--GUAUCGGCCC-GCAG-GGUGA--GGCGCAA-CGCUCCGAAUCAUUCU-UCAUCCCCCCCUU
BX950851.1/2643863-2643992     CAAAUUCCCAUU-AGGGG---AAGG-UGAG----AA--------CCU-UCG---ACC-----AAGGUUCGACAAA-ACCGGUACG---GUUUUGAGCA---ACGCUUA--GCGUUGACCC-GCAG-GGUGA--GGUGCGA-AGCGCCGAAUUAUCCU-UCCCCCACCACCA
CP000647.1/2417587-2417717     AUUCUGCCCUAC-A-GGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGACUCG-AGCGA--AG---CGAGAGAACG---UUGCCGCAGGCAACGGCCC-GAAG-GGCGA--GGCGCUUUAGCGCCGAGUAAUCCU-UCCCCCACCACCA
AAPI01000014.1/20293-20165     GUAGUCAGUGUG-UGGAG---GUGGAUUAG----AG--------CCA--------CC-----UUGGUACGACAAGUAGCUUU-AGCUGCUUGAA--CG---UCACGACA-GUGACGGCCC-GGAG-GGUGA--GGCUCGC-AGAGCCGAAUAAUCCA-CCUCCCGCCACCA
BX571864.1/9913-10045          UAGCUCAGUCGG-UAGCG---CAGU-UGACUUUUAA--------UCAAUUG---GUCG----CAGGUUCGAGCCG-AGCGA--AG---CGAGACAACA---GCGCGUAA-GCGCUGGCCC-GAAG-GGCGA---GGCCGU-AG-GCCGAGUCAUCCU-GCACGACCCACCA
AE014613.1/4007497-4007613     UAUCUGAAGCCU-GAC-----GAGGAUGAG----AACCU-----CCG-GGG---GCAA----GAGGUUCGACUCG-AGCGA--AG---CGAGAGAACG---UUGCGUCA-GCAACGGCCC-GCAG-UG------GCA-----------AGUCAUCCU-CU-GUCACCGGCA
AE017220.1/3771152-3771036     UAUCUGAAGCCU-GAC-----GAGGAUGAG----AACCU-----CCG-GGG---GCAA----GAGGUUCGACUCG-AGCGA--AG---CGAGAGAACG---UUGCGUCA-GCAACGGCCC-GCAG-UG------GCA-----------AGGCAUCCU-CU-GUCACCGGCA
CP000647.1/839192-839329       UUGGCCCGCAGG-GCGAGUCUCAGGAUGAG----ACGAGUU---UCU-CUG---CAG-----CAGGUUCGGGUCG-AACGU--AG---UGAGACAACGGAGCCGCUUGCGGCGACGGCCC-GCAG-GGCGA--GGCGAA-----GCCGAGUCAUCCU-GCACGACCCACCA
CP000653.1/205263-205397       GCAUUCUGCGAG-CUGAA---AAGGAUGAG----AA--------CCU-CCG---GGGAAA--GAGGUUCGACUCC-AGCGG--AG---CGAGAGAACG---UUGCGUGA-GCAACGGUCC-GAAG-UCCGACAGGACGGC-CUCCAUCAUCAAAUUU-UUACACCCGCGAA
BX936398.1/3198195-3198071     CGAGUAUCAGGA-UGAUA---CGAG-U-AA----AA--------UCU-GCG---UUC------AGGUUCGAGCCG-AGCGA--AG---CGAGACAGCA---ACGCGUCA-GCGUUGACCC-GAAG-GGCG---AGGCCAG-AG-GCCGAGUCAUCCC-GCACGACCCACCA
CP000720.1/3235413-3235281     UAGCUCAGUUGG-UAGAG---CAGU-UGACUUUUAA--------UCAAUUG---GUCG----CAGGUUCGAGCCG-AGCAG--AG---CGAGACAACA---ACGCGCCA-GCGUUGACCC-GAAG-GGCGA---GUCCAG-AG-GACGAGUCAUCCC-GCACGACCCACCA
CP000038.1/4038671-4038804     UGCAUUUGAAGC-CCAU----GAGGAUGAG----AA--------CCU-CCGGGGGCGGG---GAGGUUCGACUCG-AGCGA--AG---CGAGAGAACG---UUGCGCCA-GCAACGGCCC-GCAG-GGCGA--GCCACGA-AGUGGCGAGUAAUCCU-CUAUCACCGACCA
CP000668.1/1094373-1094498     UUCUCAUAUCUG-GGGA-----AGG-UAAG----AA--------CCU-UCG---A-C-----AAGGUUCGCGCCG-AGCGU--AG---CGAGACAACG---ACGCAAA--GCGGCGGCCC-GAAG-GGUGA--GGAACGC-AGUGACGAAUAAUCCUGAGACUGUAAACAA
CP000886.1/1268729-1268599     AUAUCUCUCUGU-ACGGG---AAGGAUGAG----AA--------GCU-UCG---ACC-----AAGGUUCGAUUCG-AGCGC--AG---CGAGAAAGCG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUCAUCCU-UCCCCCACCACCA
AE009952.1/3361562-3361433     CUCAGUUGGCAG-AACAG---UUGACUUUU----AA--------UCAAUGG---GUCG----CAGGUUCGAGCCG-AGCAG--AG---CGAGACAACA---ACGCGCCA-GCGUUGACCC-GAAG-GGCGA---GUCCAG-AG-GACGAGUCAUCCC-GCACGACCCACCG
CP001144.1/1516028-1515888     CGAGCGAUCAUA-AGGGA---GCUGACUAC----AAAUCUGCCGUCA-UCG---ACUUC---AAGGUUCGACUCG-AGCAAU-AG---UGAGAGAACG---UUGCCGCAGGCAACGGCCC-GAAG-GGUGA--GGAGCUUUAGCUCCGAAUAAUC---CUUCCCGCUAUAG
CP001113.1/1849039-1849170     -GUUUGCACUUGUCGGGG---AAGGGUGAG----AA--------CCU-UCG---AUU-----AAGGUUCGACUCG-AGCGAA-AG---CGAGAGAACG---UUGCCAACGGCAACGGCCC-GUAG-GGUGA--GGAGCGA-AGCGACGAAUAAUCCU-UCCCCUACCACCA
CP000826.1/2990919-2991045     UGUCACUCCCAA-GCGGG---AAGGAUGAG----AA--------GCU-UCG---A-C-----AAGGUUCGAGUCU-CACGC--AG---UGAGACAACG---CGCUUC---AGCGCGGCCC-GAAG-GGUGA--GUCGCAC-AGCGACGAAUAAUCCU-UCCCCCACCACCA
CP001120.1/1900502-1900627     -GUUUGCACUUGUCGGGG---AAGGGUGAG----AA--------CCU-UCG---AUU-----AAGGUUCGACUCG--------AG---CGAAAGAACG---UUGCCAACGGUAACGGCCC-GUAG-GGUGA--GGAGUGA-AGCGACGAAUAAUCCU-UCCUCCACCACCA
CP001113.1/1849514-1849644     AUUCUACCCAUG-CGGGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGAUUCG-AGCGC--AG---CGAGAAAGCG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-UGCGCUGAGUCAUCCU-UCCCCCACCACCA
AM933173.1/1427571-1427440     AUAUCUCUCUGU-ACGGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGAUUCG-AGCGUC-AG---CGAGAAAGCG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUCAUCCU-UCCCCCACCACCA
CP001113.1/3794911-3794793     GUAUCUGAAGUC-UGAC----GAGGAUGAG----AACCU-----CCG-GGG---GCAA----GAGGUUCGACCCG-AGCGA--AG---CGAGAGAACG---UUGCGCCA-GCAACGGCCC-GCAG-UG------GCA-----------AGUCAUCCU-CUGUCACCGGCAG
CP001113.1/1849688-1849818     AUAUCUCUCUUA-C-GGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGAUUCG-AGCGAA-AG---CGAGAAAGCG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUCAUCCU-UCCCCCACCACCA
AE006468.1/1852986-1853116     AUAUCUCUCUGU-ACGGG---AAGGAUGAG----AA--------GCU-UCU---ACC-----AGGGUUCGAUUCG-AGCGC--AG---CGAGAAAGCG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUCAUCCU-UCCCCCACCACCA
CP000826.1/307799-307914       UUAAAUUGCGGA-AGGGG---AAGG-CGAA----AG--------UCU-UCA---G-C-----AAGGUUCGAGUUG--------UG---CAGCGCAUCG-------CGCAG---CCGGCCC-GAAG-GGUGA---GAGUUA-AGCGACGAACAAUCCU-UCUCCCACCUAAA
CP000946.1/186073-186206       UGCAUCUGCAGC-UCAU----GAGGAUGAG----AA--------CCU-CCG---GGGGCAGGGAGGUUCGACUCG-AGCGA--AG---CGAGAGAACG---UUGCGCCA-GCAACGGCCC-GCAG-GGCGA--GCCACGA-AGUGGCGAGUAAUCCU-CUAUCACCGACCA
AAMJ02000054.1/693-825         UAGCUCAGUUGG-UAGAG---CAAU-UGACUUUUAA--------UCAAUUG---GUCG----CAGGUUCGAGUUG-AGCGC--AG---CGAAACAACGGAGCCGCUCGCGGCGACGGCCC-GAAG-GGCGA---GCGA------AGCGAGUCAUCCU-GCACGACCCACCA
CP001120.1/1900964-1901094     AUAUCUCUCCGU-ACGGG---AAGGAUGAG----AA--------GCU-UCG---ACU-----AAGGUUCGAUUCG-AGCGC--AG---CGAGAACGCG---UUGCCGCAGGCAACGACCC-GAAG-GGCGA--AGCGCGC-AGCGCUGAGUCAUCCU-UCCCCCACCACCA
AALF02000043.1/29063-28936     AUGAGCCACUUG-AGGGG---AAGG-UGAA----AA--------CCU-UCG---ACG-----AAGGUUCGAGCCG-AGCGU--AG---CGAGUCAACG---ACGCGCA--GCGGCGGCCC-GAAG-GGUGA--GGAAUGA-AGUGACGAAUAAUCCU-UCCCCCACCACCA
AALF02000004.1/134256-134139   UAUCAAAAUGAU-ACGAG--------U-------AA--------CCU-GCG---UUC------AGGUUCGAGCCG-AGCGA--AG---CGAGACAGCA---ACGCGCA--GCGUUGACCC-GAAG-GGCG---AGGCCAG-AG-GCCGAGUAAUCCC-GCUCGACCCACCA
AALC02000051.1/43-169          GAUGAGCACUCA-AGGGG---AAGG-UGAA----AA--------CCU-UCG---A-U-----AAGGUUCGAGCCG-AGCGU--AG---CGAGACAGCG---ACGCAAC--GCGGCGACCC-GAAG-GGUGA--GGAACGA-AGUGACGAAUAAUCCU-UCCCCCACCACCA
AALD02000016.1/32339-32465     AAUAAUACUCAU-CGGGG---AAGG-UGAG----AA--------CCU-UCG---A-C-----AAGGUUCGCGCCG-AGCGC--AG---CGAGACAACA---ACGCAUC--GCGUUGGCCC-GAAG-GGCGA--GGAACGA-AGUGACGAGUCAUCCU-UCCCCCACCACCA
AALD02000054.1/22952-22823     CUCAAUUGGUAA-AGCAG---UUGGCUUUU----AA--------UCAAUUG---GUCG----CAGGUUCGAGCCG-AGCGA--AG---CGAGACAGCA---ACGCGUUA-GCGUUG-ACCCGAAG-GGCGA---GUCCGC-AG-GACGAGUCAUCCC-GCACGACCCACCA
AALE02000009.1/54864-54978     AUAACAGCUAUU-CGGGG---AAGG-UAAG----AA--------CCU-UCA---ACC------AGGUUCGCACCG-AGCGC--AG---UGAGACAACG---ACGCAAA--GCGGCGGCCC-GCAG-GGUGA--GC------------GAAUAAUCCU-UCCCC-AUCACUA
AALD02000068.1/10127-10252     AACAACCCAGAA-UCGUG---UGGG-UGAG----AC--------CCU-GCG---UGC------AGGUUCGAGCCG-AGCGA--AG---CGAGACAGCA---ACGCGUCA-GCGUUGACCC-GAAG-GGCG---AGGCCAG-AG-GCCGAGUCAUCCC-GCACGGCCCACCA
AALD02000042.1/4463-4589       AAUGAGCACUUA-AGGGG---AAGG-UGAA----AA--------CCU-UCG---A-U-----AAGGUUCGAGCCG-AGCGU--AG---CGAGACAACG---ACGCAAA--GCGUCGGCCC-GAAG-GGUGA--GGAACGA-AGUGACGAAUAAUCCU-UCCCCCACCACCC
AALD02000068.1/9847-9979       UAGCUCAGUUGG-UAGAG---CAGU-UGACUUUUAA--------UCAAUUG---GUUA----AAGGUUCGAGCCG-AGCGA--AG---CGAGACAGCA---ACGCGUCA-GCGUUGACCC-GAAG-GGCGA---AUCCGC-AG-GAUGAGUAAUCCC-GCACGAUAAGCAC
#=GC SS_cons                   ::::::::::::.::(((...((((-(---....--........---.-((...-((.....----((((,,,<<._____..__...>>,,,,,,<<...<<<<____.>>>>>>,,,).)))-.))))-..-------.-----------)-))).)))):::::::::
#=GC RF                        uuauuuugcaua.ugGgG...gaGGAUGAg....AA........cCu.UCG...acc.....aAGGUuCGAgucg.AGCGa..AG...cgAGAaAaCG...ucGCgucA.GCgaCGgCCC.GaAG.ggCGA..GGcgCga.AGcGaCGAgUaAUCCu.cCcCccaCCACCA
//
# STOCKHOLM 1.0

#=GF AC   RF00392
#=GF ID   SNORA5
#=GF PI   snoACA5
#=GF DE   Small nucleolar RNA SNORA5
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   30.00
#=GF TC   30.10
#=GF NC   29.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF CL   CL00024
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300928;
#=GF DR   snoopy; Oryzias_latipes300079;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA5 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA5
#=GF SQ   6


AJ609453.1/1-134        UG-CAGCCGUGUCAAAUUCAGUACCUGUC-CUAUGCAUGGUAGGCACUGGCCCAGAAGGCUGCCACAG-AAACA-CUGUGACUCAUGGGCC-C-UGUUCCUGUGUCCCAGGCUCA-G-GGAUAAAUUUGGUUACAGACAUCA
AC013416.4/54383-54515  UGGCAGCCAUGUCAAAUUCAGUGCCUGCC-CUGUCUAUGGUAGGCACUGGCCCAGAAGACUGCCACAG-AAACA---GUGACUCACAGGCC-C-UGUUACUGUGUCCCAGGCUCA-G-GGAUAAAUUUGGUUACAGACACCA
AC020634.16/18995-18865 UG-CAGCUGUGUCAAAUUUGGUGCCUGCC-CUGCCUGUG-UAGGCACUGACCCAGAAGGCUGCCACAG-AAACA-C--UGACUCAUGGGCC-C-UGUUCCUGUGUCUCGGGCUCA-G-GGAUAAAUUUGGUUACAGAUACCA
AL603787.8/33357-33225  UG-CAGCUGUGUCAAAUUCAGUGCCUCUC-CUAAUGAUGGCAAGCACUGGCCCAGAAGGCUGCCAUAG-AAACU-CUGUGACUCCUGAGCU-C-UGUUCCCCA-UGCUAGGUUCA-G-GGAUAAAUGGAGUCACAGACAUCA
AC112261.4/56192-56327  UG-CAGUCAAGUCAAAUUCAGUCCCUGCC-CUGUC-AUGGUGGGAACUGGCCUAGAUGGCUGCCACAA-CAAGUUCUGCUGCUCAUGGGCCCC-GGGUCUCCUGUCCUGGAACCU-GGGGAUAAGUUUGGCUGCAGACACUA
AC013416.4/55441-55577  UG-CAGUCAAGUCAAAUUCAGUGCCCGUUUCUGUC-AUAGCGGGGGCUGGCCCAGAUGGCUGCCACAGCAAGCU-CCACAGCUCAUGGGCC-CUGGGUCACCUACCCUGGGACCUGG-GGAUAAGUUUGGCUGUGGACAGUG
#=GC SS_cons            :<.<<<------------<<<<<<<<<<<.________>>>>>>>>>>>---------->>>>-----.-----.--<<<<<<------<<.<.<<_________________>>.>.>>-------->>>>>>::::::::
#=GC RF                 UG.CAGccauGUCAAAUUCaGugCCugcc.CUgucuAUggcaGGcaCuGGCCcAGAaGGCUGCCACAG.AAAcu.CuGcggCuCAUGGGCC.C.uGuUccucUgUcCuaGGauCa.G.GGAUAAaUUUgGccgCAGACAucA
//
# STOCKHOLM 1.0

#=GF AC   RF00393
#=GF ID   SNORA8
#=GF PI   snoACA8
#=GF DE   Small nucleolar RNA SNORA8
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF CL   CL00026
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300972;
#=GF DR   snoopy; Homo_sapiens300373;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA8 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA8
#=GF SQ   5


AJ609454.1/1-139          UGCACUGC-AUGGUAUCUGCACUCAGCAGUUUACACCUGCUAGGGUGUUCAAAGGUCAGUGCUAUAGAAAUUCAGUAUCUGGCAUCGUUGGUUUUCUUGGCUUUGUGCUUGUUAA-ACCUGGUAUUUCUACUGAUACAGUA
AC007448.14/61996-61858   UGCACUGC-AUGGCAUCUGCACCCAGCAGUUUACUCUUGCUAAGGUGUUCAAAGGUCAGUGCUAUAGAAAUUCAGUAUCUGGCAUCAUUGGUUUUCUUGACUUUGUGCUUGUUAA-ACCUAGUAUUUCUAUUGAUACAGUA
Z77249.2/39964-40102      UGCACUGC-GUGGUAUCUGCACUCAGCAGUUUACUCCUGCUAGGGUGUUCAAAGGUCAGUGCCAUAGAAAUCCAGUAUCUGGUUUCAUUGGUUUUCUUGGCUUUGUGCUUGUUAA-ACCUGGUAUUUCUAUUGAUACAGCA
AJ236935.1/1495-1357      UGCACUGC-AUGGUAUCUGCAUUCAGCAGUUUGUUCCUGCU-GGGUGUUCAAAGAACAGUGCAAUAUAAAUUCAGUAUCUGGCAUCGUUGGUUUUCUUGGCUUUGUGCAAGUUAAGACCUGGUAUUUCUACUGAUACAGUA
AL365205.35/103138-103277 UGCAUUGCCAUGGUAUCUGCACUCAGUAGUUUAUUCCUGCU-GGGUGUCCAAAGAUCAGUGCCAUAGAAAUUCAGUAUCUAGCAUCACUGAUUUUCUUGGCUUUGUGCUUGUUAAAACUUGGUAUUUCUAUUGACACAGUA
#=GC SS_cons              :<<<<<<-.-----<<<<<<<<<<<<<<<_______>>>>>->>>>>>---->>>>>>>>>>--<<<<<<<<<<<-----<<<<<___________________>>>>>------.-->>>>->>>>>>>:::::::::::
#=GC RF                   UGCacuGC.AUGGuacCugCaccCaGcaGUUUAuuCCugCuAGgguGuuCAAaGguCaguGCuAuagaaaucCaGUAUCUgGcauCauUGgUUUUCUUGgCUUUgugCcuGUUAA.ACCuGgUauuucuauUGAuACAGuA
//
# STOCKHOLM 1.0

#=GF AC   RF00394
#=GF ID   SNORA4
#=GF PI   snoACA4
#=GF DE   Small nucleolar RNA SNORA4
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   56.00
#=GF TC   56.20
#=GF NC   55.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00023
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300370;
#=GF DR   snoopy; Loxodonta_africana300459;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA4 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA4
#=GF SQ   7


AJ609452.1/1-137         -UACCAAAAGUUAGCUUUU-UGGGGGGCAGGUUU---UUAAGUAACCUUUGCCAACUUGGGCUAUUUGGAAGAGUAAA----AGACCACACUCCACAGUGGGCUAUACCACUUA-----GUAUAGUUCGCUACUAUUUUGUGGCCUACAUG
AC010746.8/140334-140470 CUACCAAAAGUUAAUUUUU-UAUGGGGAAGGCUUU--CUAAAUAACCUUUACCAAUUUGGGCUAUUUGGGAGAGUAAAGGAAAGACCACACUCCACAGCGGGCUAUACCA-----------AUAGUUCACUACUAUUUUGUGGUCUACAUU
X56953.1/4645-4782       -UACCAAAAGCUAGAUUUG-UGG--GGAAGGUUUA--UUAAAUAACCUUAACCAAUUCAGGCUAUUUGGUAGAAUAAGU--AAGACCACACUCCACAGUGGGCUAUACCACUUA-----GUAUGGUUCAUUACUAUAUUGUGGCCUACAUU
AC098709.3/37074-36935   CUACCAGAAGCUAUAUUUG-UGG--GGAAGGUUUUA-UUAAAUUACCUUAACCAAUGCAGGCUAUUUGGUAGAAUGAGU--AAGACCACACUCUGCAGUGGGAUAUACCACUUA-----GUAUGGUUCAUUACUAUAUUGUGGCCUACAUU
AC004830.1/58886-58743   CUAUCAAAAGUUACUUUUUGUGGGGUGGAAGUUUU--UAAAAUAACCUUUACCUACGUGGGCUGUUUUGGAAAAUAAAGAAAAGACCACACUCAGCAGAGGGCUAUACCCCUUA-----GUAUAGUUCACCACUAUUUUGCAGCUUAUAUU
AL109931.18/1398-1543    -UACCAAAAGUUAAUGUUU-UCA-GAGAAUGCUUUGGUUAAAAAGCCUUUACCAACUUGGGCUGUUUGGGAUAAUAAUG--UUGGCCACUUUCCACAGUGGGUUAUAACAUUAAUAUAUAUAUAAGUCACUAUUAGUUUGUAAUCUACAUU
AC145474.2/49871-49731   CAAACAAAUAAAAACCUAA-UAAUAUAAAGGUCUU--GCUAAUAACCUUAACCAAUUCAUGCUAUUUGGCAGAAUGAGU--AAGACCACACUCCACAGUGGACUAUACCACUUA-----CUAUGGUUCAUUACUAUAUUGUGGCCUACAUU
#=GC SS_cons             :::<<<<<---<<<<<<--.-<<--<<<<<<<<__..______>>>>-->>>>-->>->>>>>>>>>>>----------..-<<-<<<<<------<<<<<<<<<<<<______.....>>>>>>>>>>>>------->>>>>->>:::::
#=GC RF                  CUAccAaAAGuuAgccuUu.UaggGgGcagGuuUU..uuAAAUaaCcUUugCcAAcuuaggcUaUuUgguAgAAUAAau..AaGACcaCaCUCcACaGuGggcuAUAcCAcUuA.....gUAUaguuCaCuACUAUuUuGugGcCuACAUU
//
# STOCKHOLM 1.0

#=GF AC   RF00396
#=GF ID   SNORA13
#=GF PI   snoACA13
#=GF DE   Small nucleolar RNA SNORA13
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15199136, INFERNAL
#=GF SS   Predicted; CMfinder
#=GF GA   53.00
#=GF TC   53.30
#=GF NC   52.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF CL   CL00028
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300763;
#=GF DR   snoopy; Loxodonta_africana300511;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA13 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA13
#=GF SQ   50


AJ609455.1/1-133             AGCCUUU--GUGUUGCCCAUUCACUUU-GGAAACUAGUGAAUGUGGUGU-CAA--AAAAGGCGUAAAUUAAAC--G-CUUU---GCAGCCUU--UUCCUGCCC-UUAAAUUUGA-------UACC-UUUGGUGUAGGA-------GCUGCAU---AAGUAACAGUU
AJ278435.1/9043-9175         AGCCUUU--GUGUUGCCCAUUCACUUUUGGUCACUAGUGAAUGUGGUGU-CAA--AAAAGGCAUAAAUAAAU---G-CUUU---GCGGCCUU--UCCUGUCCC-UGGAGUUUGG-------UAUC-UUGGGUGUACGA-------GCUGCAU---AAGUAACAGUA
AC132358.3/106983-106852     AGCCUUU--GUGUUGCCCGUUCACUUU-GGUCGCUAGUGAAUGUGGUGU-CAG--AAAAGGCAUAAAUAAAU---G-CUUU---GCGGCCUU--UGCUUGCCC-UGGAGUUCGG-------UAUC-UCGGGUGUAGGA-------GCUGCAU---AAGUUACAGAA
AAHX01070284.1/5211-5345     AGCCUUU--GUGUUGCCUGUUCACUUUUGGUCACUAGAGAAUAUGGUGU-CAAAGAAAAGGCAUAAAUUAAU---G-CUUU---GUAGCCUU--UCCUUUCCC-UGGAGUUUGG-------UAUC-UUGGGUGUAGGA-------GCUGCAU---AAGUAACAAAG
AAIY01236626.1/2232-2365     GGCCUUU--GUGUUGCCCAUUCACUUUCGGAAACUUGUGAAUGUGGUGU-CAA--AAAAGGCAUAAAUCAAAU--U-CUUU--UGCAGCCAU--U-ACUGCCC-UUGAAUUUGG-------UUUC-UUUGGCGUAGGC-------GUUGCAU---AAGGAACAGUU
AANN01152062.1/693-825       AGCCUUU--GUGUUGCCCAUUCACUUU-GGAAACUAGUGGAUGUGGUGU-CAA--AAAAGGCUCAAAUCGAAC--A-CUUA---UCAGGCUU--UUCCUGCCU-UUGAUUUUGA-------UGUC-UUAGGCAUAGGA-------ACUGCAU---AAGUAACAGCA
AAFC03010584.1/35356-35492   CGCCUUU--GUGUUGCCCAUUCACUUUUGGAAACUAGUGGAUGUGGUGU-CAA--AAAAGGCGAACACAAAAC--A-CUUU--CGCAGCUUUUUUUCCUGCCC-UUGUAUUUGA-------UGUC-UUUGGUGUAGGA-------GCUGCGU---AAGUAACAUAC
AAYZ01369655.1/1722-1589     GGCCUUC--GUGUUGCCCAUUCGCCUUUGGAAACUGGCGAACGUGGUGU-CAA--GGAGGGCGUACAUUGACU--G-CUUG---GCAGGCUU--UUCCAGCCC-UGAGAUUCCA-------UAUC-UCUGGUGCAGGA-------UCUGCAC---AAGUGACAGUU
AAQQ01663945.1/749-611       AGCCUUU--AUGUUACCCGUUCACUUUUGGAAGCUCGUGAAUGUUGUAU-UAA--AAGAGGCAUAAAU-ACAU--G-CUUU---GUGGC-UU--UUUGUGCCC-UAAAAUUUAG-------UAUA-UUUGGUGUAGAAGGUAGAAGCUGUAU---AAGUAACAGUU
AALT01498951.1/5420-5288     CGCCUUU--GUGUUGCCCAUUUACUUU-GGAAGCUAGUGAAUGUGGUGU-CAA--GAAAGGCGUAAAGUAAGC--C-CUUG---GCAGGGUU--UUCCUGCUU-GUGACCCUGC-------UGUC-UCAGGCACAGGA-------ACUGCAC---AAGGAAUAGGA
ABDC01143981.1/2282-2160     UAGCUUU--CUGUUGCCUGUUUACUUU-CAAAACUAGUGAAUGUGGUGU-CAA--AAAUG-UGUAAAUUAAAC--A-CUUA---UCAGCAUU--UUCCUGUUC-UU----------------AAA-UUUGGUGUAGGA-------GCUGCGU---AAGUAACAGUU
AAPN01395207.1/14997-14866   GCCUUUU--GUGUUGCCCGUUCAUUUUUGGUUACUGAUGAAUGUGGUGU-CAA--AAAAGGCGCAAAUGAAAC--U-CUUG---GCAGCUCU--GUUUCACCC-UAGGUUUCCG-------UUCC-UUUGGUGCUUUU-------GCUGCG-----AGGAACAUAU
AAYZ01027169.1/3596-3726     GGCCUUU--GUGUUACCUGUUUGCCUUUGGAAACUAGUGAAUGU---GU-CAG--GAAAGGCAGGCAUGGACU--G-CUUU---GCAGCCUU--CUCCCACUA-UUAGAUUUGG-------UAUC-UCCAGUGCAGGA-------CCUGCAC---AGGCGACAGUU
AAPN01382943.1/7088-7218     GCCUUUU--GUGUUGCCCGUUCACUUUUGGCUGCUAGUGAAUGUGGUGU-CAA--AAAAGGCGCAAAUCAAAU--C-CGUG---GCAGCCCU--A--UUUUCA-CUGGAUUCUA-------UUCC-UGUGGUGUACUU-------GCUGCAC---A-GGAACAUGG
AAQQ01631284.1/2257-2125     AGCCUUU--GUGUUGCCCGUUCACUUUUGUAAACUAGUGAAUGUGGUGU-CAA--AAAAGGCACAAAUAAAU---A-CUUU---GCAGCCUU--UUCCUGCCC-UUAAAUUUUA-------UAUU-UUUGGUGUAGGA-------ACUGCAU---AAGUGACAGUU
AAIY01459118.1/1378-1516     GGCCUUU--GUGUUGCCCAUUCACGUACGGAAACUAGUGAGCGUGGUGU-CAA--GAAAGGUGCAAGUUAAACACC-CUCACUCACAGCCAC--GUUAUGCUU-UUGAAUUUGG-------UUUC-UUUGGCAUAGGA-------GCUGCCU---AAGGAACAGUU
AAHX01094447.1/1947-2080     AGCCUUU--GUGUUGCCCGUUCACUUUUGGUCACUAGUGAAUGUGGUGU-CAA--AAAAGGCAUAAAUUAAU---G-CUUU---GCGGCCUU--UCCUCUCCC-UGGAGUUUGG-------UAUC-UUGGGUUUCAGG------AGCUGCAU---AAGUAACAGAA
AAYZ01143594.1/1053-920      CGCCUUC--GUGUUGCCCGUUCGCCUUUACCCGCUGGCGGCCGUGGUGU-CAA--GCAAGGCGGACAUGGAGC--G-CUUG---GCAGCCUU--UUCCGGCCC-GGAGGUUGGA-------UAUC-UCCGACGCAGGA-------CCUGCUC---AAGCGACAGGC
AAYZ01065793.1/7267-7135     GGCCUUC--GUGUUGCCCAUUCGCCUU-GGAAAGUGGCGAGUGUGGUGU-CAA--GGAAGGCGUACAUUGACU--G-CUCG---GCAGCCUU--UUCCAGCCC-UGAGAUUCGG-------UGUC-UCCGGUGCAGGA-------UCUGCAC---AAGUGACAGUU
AAIY01587028.1/1262-1395     GGCCUUU--GUGUUGCCC-UUCGCUUUUGGAAACUAGUGAACGUGGUGU-CAG--AAAAGGUACAAAUUAAAC-AC-CCUG---UCAGCCAU--GUUCUGCUU-UUGAAUUCGG-------UUUC-UUUGGCGUCGGA-------GCUGCAU---AAGGAACAGUU
AAFC03054459.1/44220-44087   AGCCUUU--GUGCUGCCUGUUCACUUUUGGAAAUCGGUGACUGUGGUGU-CAA--AAAAGGCAUAAACCAAAC--A-CUUU--UGCAGCCUU--U-UCUGCCC-UUCUAUUUGA-------AAUC-UUUGGUGUAGGA-------GCUGCAU---AAGUAAUAGAU
AAIY01240193.1/210-343       GGCCUUU--GUGUUGCCCAUUCACUUUCGGAAACUUGGGAAAGUGGUGU-CAA--AAAAG-CAUAAAUUACAU--G-CUUU--UGCAGCCAU--UUUUGCCCU-UGAAUUUUGG-------UUUC-UUUGGCGGAGGC-------ACUGCAU---AAGAAACAGUU
AAIY01312099.1/1361-1495     GGCCUUU--GUGUUGCCCGUUCGCUUUCGGAAACUAGUGAACGUGGUGU-CAA--AAAAGGCGCAAAUGAAAC-AC-CCUG---GCAGCCAC--GUCCUGCCU-UUGAAUUCGG-------UUUC-UUUGGCGUCGGA-------GCUGCGU---AAGGAACAGUU
AAFR03047480.1/154809-154678 GCCUUUU--GUGUUGCCCGUUCACUUU-GGCCACUGGUGCACGAGGUGU-CAA--AAAAGGCGCAAAGGAAG---A-CUUU---GCAGCCUC--CUCUCGG-C-AGGCAUCUGC-------GUGC-CUUG-GCCGAGUG-----UGCUGGCA---AAGUGACAGUC
AANN01537351.1/11651-11518   AGCCUUU--GUGUUGCCCAUUCACUUUCGGAAACUAGUGAAUGUGGUGU-CAA--AAAAGGCAUACAUUAAC---A-CUUA---GCAGGCUU-UUUCCUGCCU-UUGAACUUGA-------UGUC-AUGGGCUUAGGA-------ACUGCCU---AAGUAACAAUA
AANG01334021.1/1063-1197     AGCCUUU--GUGUUGCCAAUUCACUUUUGGAAACUAGUGAAUGUGGUGU-CAA--AAACGGUGGAA---------G-CUUU---GCAGCCUU--UUCCUGCCC-UUGAAUUUUAAUUUGAAUAUU-GUUGGUGUAGGA-------GCUGGAU--AAAGUAAGAGUU
AC197853.3/96197-96328       UGCCUUU--GUGUUGCCCAUUCAUUGCCUUCUAA-AAUGAAUGUGGUGU-CAA--AAAAGGCAAACAAGAAUU--C-UUGC---UCAAGCUG--UGUAAGGGG-CUGGCUAUCU-------GCCUUUCUCCUCCCUGU------UUUUG------CAAGGACAGAA
AAVX01611070.1/153-282       UGCCUUU--GUGUUUCCCACUUUCUUUGCUAUAGAUG--AGUGCGGUGU-CAA--AAAAGGCACAAAGUAACU--U-C--A---GCUGUUAC--AGGUGUCCU-GGCAGUCUUU-------AUUU-UUCAG-GAUUUGUU---AUACAGCU------GAAAUACCA
AANH01001171.1/28395-28527   UGCCUUUAUGUGUUGCCCUUUCAUUGUUCCCUU--AGUGAUCGGGGUGU-CAA--AUAAGGCAUACAAUGACA--C-UUGU--GGCUGUUUG--GUAA--AAU-UGGUUUCACG-------UGAC-UUCUUUUCAUUA-------ACAGCUG---CAAGGACAUUU
BAAF04129670.1/2372-2236     UGCCUUCAGGUGUUGCCCUUUCAUUGC-CCCCCUUGAUGAAAGAGGCGU-CAG--CAAAGGCAAACAUCAAGU--C-UUGG---GGGUCGGC--CUCUGACCG-GUUCCUCAAU-------GGUG-ACCUG-GUCAGA-------AGCUCCAUACCAAGAACAGAG
CAAE01015022.1/693816-693681 UGCCUUCUCGUGUUGCCCGUUUGCUGUCUCCUAC-AGCGAAUGCGGUGU-CGA--UAAAGGCAAACAUCAAUG-UU-UUGG---AUUGGCCU--AAGCAAGGU-UCUACCCCAG-------UAGC-CUUGUCUUAAGU-------UCUAUAC---CAAGAACACUU
AAKN02038152.1/35114-35246   AGCCUUU--GUGUUGCCCAUUCACCUUGGAAAGCUAGUGAAUGUGGUGU-CAA--AAAAGGCAUAAAUAAA----AGCUUU---GCAGCUUU--UUCCUGCCC-UUAUAUUUGG-------UAUA-UUUGGUGUAGGA-------GCUGCAC---AAGUAACAGUU
AAKN02047320.1/113234-113102 AGCCUUU--GUGGUGCCCAUUCACUUUUGAAAGCUAGUGAAUGUGGUGU-CAA--AAAAGGCAUAAAUAAAA---G-CUUU---GUAGCUUU--UUCCUGCCC-UUAUAUUUGG-------UAUA-UUUGGUGUAGGA-------GCUACAC---AAGUAACAGUU
AAKN02028174.1/24073-23943   AGUCUUU--GUAUUGCCCAUUUACUUUUAAAAACUAGUAAAUACGGUGU-CAA--AACAGGCAUAAAUAAAUG--U-CUUA---AU--UAUU--UUCCUGACC-UUAUAUUGGA-------UAUA-UUUGGUGCAGGA-------ACAGCAU----AGUAACAACU
AAKN02038796.1/146603-146736 AGCCUUU--GUGUUGCUCAUUCACUUUUGAAAGCUAGUGAAUGUGGUGUCCAA--AAAAAGCAUUGAUAAAA---G-CUUU---GCAGCUUU--UCCCUGCCC-AUGUAUUUGG-------UAUA-GUUGGUGUAGGA-------GCUGCAC---AAGCAACAGUU
AAWR02002782.1/37431-37299   AGCCUUU--GUGUUGCCCAUUCACUUU-UGAAACUAGUGAAUGUGGUGU-CAA--AAAAGGCGCAAACUAAAC--A-CUUG---GCAGCUUU--UUCCUGCCC-UUGAAUUUGA-------UAUC-UUUGGUGUAGAA-------GCUGCAU---AAGUAACAGUU
CU638697.5/2356-2485         UGCCUUU--GUGUUGCCCAUUCAUUUCCUAUUA--GAUGAAUGUGGUGU-CAA--CUAAGGCACACAUUAAAC--C-UUGA--AAUAGCCAA--AGAGAGGAC-CGGC---CAC-------UCGU-UCUCUUGCUUGU-------GCUGUAA---CAAGAACAACA
AAPE02051502.1/26404-26271   AGCCUUU--GUGUUGCCCAUUCACUUUUGGAAACUAGUGAAUGUGGUGU-CAA--AAAAGGCAUAAACUACAC--A-CUUU---GCAACCCU--UUCCUGCCC-UUGAAUUUGA-------UGUC-UUUGGUGGAGGA-------GCUGUGU---AAGUAACAGUU
AAGU03068299.1/14881-14750   GACCUGU--GGGUUGCCCAUUCGCUUGCAGAAACCAGUGAAUGUGGUGU-CA----AAAGGCAUCAAUUAAAU--U-CUUU---GCAGCCAU--UUCCGGCCC-UUGAACUUGA-------UAUC-UUUGAUGUAGGA-------ACUGCAU---GAGUUACAGUU
AAGU03003788.1/610-743       AGCCUUU--GUGUUGCCCGUUCACUUUCGGAAACUAGUGAAUGUGGUGU-CAA--AAAAGGCGUAAAUUAAAC--C-CUUU---GCAGCCAU--UUUCUGCCC-UUGAAUUUGA-------UUUC-UUUGGUGUAGGA-------GCUGCGU---AAGUUACAGUU
AAEX03001958.1/1667-1540     GGCCUUU--GUGUUGCCCGUUCACCUUCCGAAACUGGUGAACGCGGUGU-CAG--AAAAGGCGGAAAGCAAGG--C-CCUG---GCGGCGCU--U-CCUGCCC---GGACCGUG-------GGUC-U--GGGGCGCGC-------GCCGCC----GGGUCACAGUU
AAQR03059578.1/10876-10744   AGCCUUU--GUGUUGCCCAUUCACUUU-GGAAACUAGUGGAUGUGGUGU-CAA--AAAAGGCGUACAUUAAAU--G-CUUU---GCGGCCUU--UUCCUGCCC-UUAAAUCUGG-------UAUU-UUUGGUGUAGGA-------GCUGCAU---AAGUAACAGUU
AAWZ02001624.1/9399-9527     UGCCUUU--GUGUUGCCCGUUCAUUAUUUUCUAC-AAUGAAUGUGGUGU-CAG--ACAAGGCAUAUAUUAAGU--C-U--A---GUUGGCAU--GUGUUUUAGAGUGGGUCAUA-------CACC-CUUCUCUUCAUU-------UCAGCU------AGAACAUAC
AAGW02013420.1/6727-6594     AGCAUUU--GUAUUGCCUGUUCGCUUUUGGAAAUGAGUGAAUGUGGUGU-CAA--GAAAGGCAAACAGGGAAU--A-CUUU---GCAGCCUU--UUCUGGCCC-UUAGGUUUGG-------UAUC-UUCCGUGCAGGA-------ACUGUAC---AAGUAACAGUU
AACN010045790.1/472-346      UGCCUUU--GUGUUGCCCAUUCUUUUUUGGAAACUUGCGAAUGUGGUGU-CAA--AAAAAGCAGAAUCUAAAC--A-CUUU---GCAGCCUU--UUCCUGUCC-UUGAA--------------UU-UUUGGUGUAGGA-------GCUGUAU---AAGUAACAGUU
AAGW02056444.1/12630-12497   GGCCUUU--GUGUUGCCCCUUCGCUCAUGGAAACUAGUGAAUGUGGGGU-CAA--AAAAGGCAUACAGGGAAU--G-CUUU---GCAACCUU--UUCCUGCCC-UUAGACUGUG-------UAUC-UUCCGGGCAGGA-------CUCCCAC---AAGUAACUGUU
CAAB02008485.1/16154-16285   UGCCUUUAUGUGUUGCUCUGUCAUUGUUGCCAU--AAUGAUCAGGGUGU-CAA--ACAAGGCAUACAGUGACA--C-AUGU--GGCUGC------CUGUUGAAGGAGUUUCACC-------UGAC-UCUUUUAAGCGG-------CCGGCUG---CAUGAACAAAC
EU094022.1/3-134             UGCCUUU-UGUGUUGCCCGUUCACUUUUGGCUGCUAGUGAAUGUGGUGU-CAA--AAAAGGCGCAAAUCAAAU--C-CGUG---GCAGCCCU--A--UUUUCA-CUGGAUUCUA-------UUCC-UGUGGUGUACUU-------GCUGCAC---A-GGAACAUGG
EU094031.1/3-135             UGCCUUU-UGUGUUGCCCGUUCAUUUUUGGUUACUGAUGAAUGUGGUGU-CAA--AAAAGGCGCAAAUGAAAC--U-CUUG---GCAGCUCU--GUUUCACCC-UAGGUUUCCG-------UUCC-UUUGGUGCUUUU-------GCUGCG-----AGGAACAUAU
FJ915951.1/3-135             AGCCUUU--GUGUUGCCCAUUCACUUU-GGAAACUAGUGAAUGUGGUGU-CAA--AAAAGACGUAAAUUAAAC--G-CUUU---GCAGCCUU--UUCCUGCCC-UUGAAUUUGG-------UAUC-UUUGGUGUAGGA-------GCUGCAU---AAGUAACAGUU
#=GC SS_cons                 :<<<<<<..-<<-<<<<<<<<<<<<__________>>>>>>>>->>>>-.>>-..->>>>>>-----------..<.<<<<...<<<<<---..-<<<<<<<<.--<<______.......__>>.--->>->>>>>>.......>>>>>>-...>>>>:::::::
#=GC RF                      aGCCUUu..GUGUUgCCCauUCaCuUUuggaaACUaGuGAauGUGGuGU.CAA..AaAAGGCAuAaAuuAAau..c.CUuu...gcaGccuU..uuccugccc.uugaaUUugg.......Uauc.UUUggUgcagga.......gCugcau...aAGgAACAguu
//
# STOCKHOLM 1.0

#=GF AC   RF00397
#=GF ID   SNORA14
#=GF PI   snoACA14
#=GF DE   Small nucleolar RNA SNORA14
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15199136, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   36.00
#=GF TC   36.50
#=GF NC   35.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Echinops_telfairi300708;
#=GF DR   snoopy; Echinops_telfairi300620;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA14 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA14
#=GF SQ   18


AJ609457.1/1-135             CUGCAUUC-UUAAACCCUCUUGGUAGCUUCGUUCUAAGUGCUUCCAAGAUA-UGAGUGAAUGCUAUAGA-AAUUGCAGGGGAGUCCAAAGGGCUGCGC-UU--C-UCCC-GUGGCUCAGUCUUAUUUCAUA--CCUGCGACA----UCU
AC093126.2/112985-113119     UUGCAUUC-UUAAACCCUCUUGGUGGCUUUCCUCUAAAUGCUUCCAAGAUA-UGAGCAAAUGCUAUAGA-AAUUGCAGGGAAGUCCAAAGGGCUGCGC-UU--C-UCCU-GUGGCUCAGUCUUAUUUCAUA--CCUGUGACA----UCU
AJ609456.1/1-134             -UGCAUUC-UUAAACCCUCUUGGUGGCUUCCCUGUAAAUGCUUCCAAGAUA-UGAGCGAAUGCUAUAGA-AAUUGCAGGAAAGUCCAAAGGGCUGCGC-GU--C-UCCU-GUGGCUCAGUCUUAUUUCAUA--CCUGCAACA----UCU
AAFC03054517.1/102386-102252 GUGCAUUC-UUAAACCCUCUUGGUAGCUCCACUGUAAAGGCUUCCAAGAUA-UGAGUGAAUGCUAUAGA-AAUCGCAGGGGCGUCCAAAAGGCUGCAC-GU--U-UCCU-GUGGCUCAGCCUUAUUUCAUA--CCUGCGACA----UCU
AAQQ01663584.1/95-227        UUGCAUUC-UUAAACCCUCUUGGCGGCUUCGCCU--AGUGCUUCCAAGAUA-UGAGUGAAUGCUAGAGA-AAUUGCGGGGGAGUCCAAAGGGCUGCGC-CU--C-UCUC-GUGGCUCAGCCUCAUUUCAUA--CCUGCGACA----UCU
AANN01009758.1/1394-1528     GUGCAUUC-UUCAUUUCUCUUGGUAGCUAUACUCUAAAUGCUUCCAAGAUA-UGAAUGAAUGCUAUAUA-AACUGUAGGGACAUCCAAAGGGCUGUGA-UU--C-UCCU-AUGUCUCAGUCUUAUUUCAUA--CCUGCAACA----UGU
AAIY01388714.1/1569-1701     CAGCAUUC-UUAAACCCUCUUGGUAGCUUCCUUU---GUACUUCCAAGAUAAUGAAUGAAUGCUACAGA-AAUGGCAGGAGAGUCCAAAAGGCUGAGC-CU--C-ACCU-GUGGCUCACUCUUAUUUCAUA--CCUGCGACA----UUU
AALT01309783.1/1217-1084     GCGCAUUC-UUAAACCCUCUUGGCGGC---GCUCCGAUCGCCCCCAGGAUA-UGAGUGAAUGCGAUAGA-AACCGCAGGGGAGUCCAAAGGGCUGCGC-CC--CCUCCCCGUGGCGCGGCCUUAUUUCAUA--CCUGCGACA----UCA
AAFR03023742.1/28176-28310   CCGCAUUC-UUAAACCCUCUUGGUAGCCUUGCUCUAA--GCUUCCAAGAUA-UGAGUGAAUGCCACAGAAAAUUGCAGAUGAAUCCAAAAUGCUAGGUAUU--U-UCCU-CUGACUUGGCAUUAUUUCAGA--UCUGUGACA----ACU
ABDC01185435.1/3618-3742     UUGCAUGCAUUA-----------GAGCUUUGUUCUAAAUGCUUCCAAGAAA-UGAGUGAAUGCUAUAGA-AAUUGCAGAGGAGUCCAAAGGGCUGCGC-UU--C-CCCU-GUGGCUCAGUCUUAUUUCAUA--CCUGUGACA----UCU
AAYZ01007503.1/2164-2029     UGGCAUUG-CUCCACCUUCUUGG-GGUCGCGCUGUGUCCGCCUCCAGGAUA-GGAGCGAAUGCUACAGA-AACGGCAGGGGAGUCCAAAGGGCUGCGC-UC--C-UCCC-GUGGCUCAGCCUUAUUUCAGA--CCUGCGACAA--AUUU
AAPN01185969.1/875-1012      CUGCAUUC-UUAAACCCUCUUGGUAGCGUCGCCAGAA--GCUGCCAAGAUA-CGAGUGAAUGCGACAGGAAACUGCAGAUCAAUCCAGAAUGCCGGGC-UUGGC-UUCU-GUGGCCUGGCAUUCUUUCACUAAUCUGAAACA----GCU
AAPE02049895.1/70920-71049   UUGCAUUC-UUAAACCCUCUUGGUGGC--UGCUCUCGGUGCCUCCAGGAUA-UGAGUGGAUGCGACAGG-AACCGCAGG--AGUCCAAAGGGCUGCGC-CU--C--CCG-GUGGCUCAGCCUUAUUUCAGA--CCUGCGACA----UCU
AAQR03108143.1/1932-1801     AUGCAUUC-UUAAAUUUCCUUGGUAGCUUUACUCU--GUGCUUCCAUGAUA-UGAGUGAAUGCAUA-GA-AAUUGCAGAGGAAUCCAAAGGACUGUGC-UU--C-ACCU-AUGGCUCAGUGUUAUUUUAUA--CCUGUGACA----UCA
AAGW02026299.1/175784-175650 UUGCAUUC-CUAAACCUUCUUGGUAGCUUCGCUGAAAACGCUUCCAAGAUA-UCAGUGAAUGCUAUAGA-AAUCGCAGGGGAGUCCAAAAGGCUGCCC-UU--C-UCCU-GUGGAUCAGUCUUAUUUCAUA--CCUGCGACA----UAU
AAWZ02004746.1/40093-39953   AAGCAUUC-UCAAACCCUCCUGGUACUGUUGCCAUUAUAACUUCCAGGAUA-AGAAUGAAUGCUAAAUAAAAAUGUAGAGUUAUCCAAAAUGCAGAACAUU--C-UGUU-GUAGUUUUGCAUUAUUUCACC--UCUUCAACAAAAAUAU
FJ915952.1/1-132             CUGCAUUC-UUAAACCCUCUUGGUAGCUUCGUUCUAAGUGCUUCCAAGAUA-UGAGUGAAUGCUAUAGA-AAUUGCAGGGGAGUCCAAAGGGCUGCGC-UU--C-UCCC-GUGGCUCAGUCUUAUUUCAUA--CCUGCGACA-------
EU094000.1/2-139             CUGCAUUC-UUAAACCCUCUUGGUAGCGUCGCCAGAA--GCUGCCAAGAUA-CGAGUGAAUGCGACAGGAAACUGCAGAUCAAUCCAGAAUGCCGGGC-UUGGC-UCCU-GUGGCCUGGCAUUCUUUCACUAAUCUGAAACA----GCU
#=GC SS_cons                 ::<<<<-<.<<<-----<<<<<<-<<<____________>>>->>>>>>--.>>>>--->>>>---<<<.--<<<<<<<---------<<<<<<<-<<.--..<.____.>-->>->>>>>>>--------..>>>>>>>--....>>>
#=GC RF                      uuGCAUUC.ucaAACCcuCuUGGUaGcuuugCuauaAaugCuUCCAaGaUA.ugaGUGAAUGCuAuaga.AAucgcAGgggAgUCCAAaaggCuGcgC.uU..c.UcCu.gUGGcUCaGccuuAUUUCAua..cCUgcgaCA....ucu
//
# STOCKHOLM 1.0

#=GF AC   RF00398
#=GF ID   SNORA15
#=GF PI   snoACA15
#=GF DE   Small nucleolar RNA SNORA15
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15199136, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   47.00
#=GF TC   47.00
#=GF NC   46.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300508;
#=GF DR   snoopy; Loxodonta_africana300467;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   ACA15 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1]. This family also includes
#=GF CC   the mouse MBI-79 sequence as described in [2].
#=GF WK   Small_nucleolar_RNA_SNORA15
#=GF SQ   22


AJ609458.1/1-133             GCAUGGCCGAAUACUGUGU----U-UUUAUCAGUAGUUUACACAGCCAGACACCAUGCAAAAGCA--GUC--UUCCCUUUAGAAUGAC--UGAUGGUAUGCUA-AGG-UUUUUCA--U-AGCAUAUCA-UUAUUAAAGGUGAAUACAAAU
AC073210.8/134490-134624     GCAUGGCUGAAUACUGUGUUC--U-UUUAUCAGUAGUUUACACAGCCAGACACCAUGCAAAAGCA--GUC--UUCCCUUUAGAAUGAC--UGAUGGUAUGCUA-AGG-UUUUUCA--U-AGCAUAUCA-UUAUUAAAGGUGAAUACAAAU
AF357410.1/1-116             ---------------GUGUUC--U-UUAGUCAGUAAUUUACACAGCCAGACACCAUGCAAAAGUAAAGUC--UUCCUUUUAAGAUGGC-----UGAUAUGCUG-----UAUUUUA--U-GGUAUAUCA-UUAUUAGAAGUGAGUACAAAU
AF000144.1/1681-1555         GCAUGGCUGAAUACUGUGUUC--U-UUAGUCAGUAAUUUACAUAGCCAGACACCAUGCAAGAGUAAAGUC--UUCCUUU-AAGAUGGC-----UGCUAUGCUG-----UAUUUUA--U-GGUAUAUCA----UUAAAAGUGAGUACAAGU
ABDC01385519.1/2665-2531     GCAUGGCUGAAUACUGUGUUC--U-UUUAUCAAUAGUUUACACAGCCAGACACCAUGCAAAAGCA--GUC--UUCCCUUUAAAAUGAC--UGAUGAUAUGCUA-AGU-UUUUCCA--U-AGCAUAUCA-UUAUUAAAGGUGAAUACAAAU
AANU01195128.1/4636-4770     GCAUGGCUGAAUACUGUGUUG--U-UUUAUCAGUAGUUUACACAGCCAGACACCAUGCAAAAGCA--GUC--UUCCCUUUAGAAUGAC--UGAUGGUAUGCUA-AGG-UUUUUCA--U-AGCGUAUCA-UUAUUAAAGGUGAAUACAAAU
AAQQ01678318.1/233-368       GCAUGGCUGAAUACUGUGUAC--U-UUAGUCAGUAUUUUACACAGCCAGACACCAUGCAAAAGUAAAGUC--UUCCUUUUAUAAUAAC---UGUGGUAUGCUA-AGG-UUUUUCA--U-AGUGUGCCC-CUAUUAAAAGUGAAUACAGAC
AAYZ01395334.1/4311-4446     GCAUGGCUGAAUACUGUGUUC--C-UUCAUCAGUAGUCUACACAGCCAGACACCAUGCAAAAGUAAAGUC--UUCCUUU-AGAAAUUA--UUUUGAUAUGCCG-AGU-UUUUCCU--U-AGCAUAUCA-UCAUUGAAAGUGAAUACACGU
AALT01601228.1/818-951       GCAUGGCUGAAUACUGUGUUC-UU-UUUAUCAAUAUUUUACACAGCCAGACACCAUGCAAAAGUAAAGUU--UUCCCUU-GAAAAGGC--UUUUGAUAUGUUG-----CUUUUUG--U-GGCAUAUCA-UUAUUAAAAGUGGCUACAAAU
AANN01763690.1/116-252       GCAUGGCUGAAUACUGUGUUC-UU-UUGAUCAGUAGUUUACACAGCCAGACACCAUGCAAAAGUAAAGUU--UUCUCUCUGCAGUGAC--UU-UGGUAUGCUA-AGA-UUUGUG---U-GGCAUGUCAUCUGUUAGAAGUAGAUACAAAU
AAFR03053799.1/41865-41724   GCAUGGAUGAAUACUGUGUUU--UCUUUGUCGGUAGUUAACACAGCCAGACACCAUGCAAAAGUACAUUCUCCUCCUUUGAAAUGGUC-UUAAUGGUAUGCUA-AGA-AUUGCCA--UCAGCAUGCUA-UUACUCAAGGGGAUCACAAGC
AAIY01631212.1/1096-961      GCAUGGCCGAAUACUGUGUUU--U-UUUAUCCGUAAUCUACACAGCCAGACACCAUGCCAUAGUA-UCAU--UUCCCUUUA-ACGUAC--UUCCGGUGUGCUG-UGUCUUCUUCG--U-GGCAUAUCA-UCUGUAAAGGUGAACACAGAG
AAKN02045360.1/39269-39402   GCAUGGCUGAAUACUGUGUUC--U-UUAAUCAGUAGUUUACACAGCCAGACACCAUGCAAAAGUAAAAAC--UUCCUUUUAAAAUGAC---AAUGAUAUGCUG---U-UUUUUCA--U-GGUGUAUCA-UUAUUAAAAGUGAUUACAAAU
AAWR02041249.1/36934-36798   GCAUGGCUGAAUACUGUGUUU--U-UUUAUCAGUAGUUUACACAGCCAGACACCAUGCAAAAGUAAAGUC--UUCUUUU-AAAAUAACUAUGAUGUUAUGCUA--UG-UUUUUUA--U-AGCAUAUCA-UUAUUAAAAGUGGAUACAAAU
AAGV020608540.1/193-54       GCAUAGCCGAAUACUGUGUUC--U-UUUAUCAGUAGUUUACACAGCCAGACACCAUGCAAAAAUGUAGUC--UUCCCUUUAAAAUUGUUAUGAUGGUAUGCUA-AGUCUUCUUCA--U-AGCAUAUCG-UUAUUAAAGGUGAAUACAAAU
AAPE02016524.1/26587-26724   GCAUGGCUGAAUACUGUGUUC-UU-UUUGUCAGUAGCUUACACAGCCAGACACCAUGCAAAAGUA--GUC--UUCCCUUUAAAAUGGCUAUGAUGGUAUGCCA-AGU-UUUUUCA--U-AGCAUAUCA-UUACUAAAAGUGGAUACAAAU
AAQR03075567.1/62922-63056   GCAUGGCUGAAUACUGUGUUC--U-UUCAUCAGUAGUUUACACAGCCAGACACCAUGCAAAAGCA--GUC--CUCCCUUUUAAAUGAC--UGAUGAUAUGCUA-AGU-UAUUUCA--U-AGCAUAUCA-CUGUUAAAGGUGAACACAAAC
AAGW02070483.1/7410-7276     GCAUGGCUGAAUACUGUGUUC--U-UUUGUCAGUAGUUUACACAGCCAGACACCAUGCAAAAGUAAAAGC--UUCCCUUGGAAAUCA---UUUUGGUAUGCUG-AGU-UUUUCU---U-AGCAUAUCA-UUAUUGAAAGUGAAUACAAAU
AAGU03064421.1/26028-26167   GCAUGGCUGAAUACUGUGUUC-UU-UUUAUCAGUAAUUUGCACAGCCAGACACCAUGCAAAAGUAUCAUC--UUCCCUUUAAAAUGUUUAUGAU-GUAUGCUA-ACUUUUUCUCA--U-GGCAUAUCA-UUAUUAAAGGUGAAUACAAAU
AAEX03004179.1/101824-101963 GCAUGGCUGAAUACUGUGUUC-UU-UUUAUCAGUAGUUUACACAGCCAGACACCAUGCAAAAGUAAAGUG--UUCCCUUUAAAAUGCCUCUAAUGGUGUGCUA-AGC-UUUUUCA--U-AGCAUAUCA-UUUUUAAAAGUGAAUACAAGU
FJ915953.1/4-138             GCAUGGCCGAAUACUGUGUUC--U-UUUAUCAGUAGUUUACACAGCCAGACACCAUGCAAAAGCA--GUC--UUCCCUUUGGAAUGAC--CAAUGGUAUGCUA-AGG-UUUUUCA--U-AGCAUAUCA-UUAUUAAAGGUGAAUACAGAU
EU240272.1/3-134             GCAUGGACGAAUUCUGCUAUAGCU-UUCUUCAGUAGCUAUUGCAGUCAGACACUAUGCCAGAUUCAAUUC-----CCGUUUU---ACA--CUCUGGCAUGCUUUUUA-UAUGUGAGUG-GGCAUGCCC-UUGGAAGUGG----GAUACAA
#=GC SS_cons                 <<<<<<-------<<<<<<__.._.______________>>>>>>------->>>>>>------------..<<<<<<<<<<------..<<<<<<<<<<<<<.___._______..>.>>>>>>>>>.>>>>>>>>>>->>>:::::::
#=GC RF                      GCAUGGcuGAAUACUGuguUc..U.UUuaUCAGUAgUUuacaCAGCCAGACACCAUGCAAAAGUAaAgUc..uuCCcuuuaaAaugac..ugauGguauGCua.agu.UuUuUcA..u.aGCauacCa.ucauuaaagGUGaauACAaAu
//
# STOCKHOLM 1.0

#=GF AC   RF00399
#=GF ID   SNORA24
#=GF PI   snoACA24
#=GF DE   Small nucleolar RNA SNORA24
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15199136
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   40.00
#=GF TC   41.30
#=GF NC   39.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300500;
#=GF DR   snoopy; Gallus_gallus300008;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA24 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA24
#=GF SQ   5


AL662805.13/69144-69017 CUCUAUUUAACUUUGGGACCUGUCGGCUGUGUCAUGCUUCCUUUGUAGCCAUGGAAGAGC-------UUCUUAUUUAUUGGAAAAGCUGUUAUCUUUUGUAUAGUAUCAGAGUCUGACUUGCACAAGUAACAUUC
AJ609460.1/1-131        CUCCAUGUAUCUUUGGGACCUGUCAGCCGUGGCAGUCUCCCUUCCUAGCCAUGGAAGAGCA----UAUCCUUGUUUAUUGGCAAAGCUGUCACCAUUUAAUUGGUAUCAGAUUCUGACUUGCACAAGUAACAUUC
AJ609478.1/1-124        CUCCAUGUAUCUUUGGGACCUGUCAGCCGUGGCAGUCUCCCUUCCUAGCCAUGGAAGAGCA----UAUCCUUGUUUAUUGGCAAAGCUGUCACCAUUUAAUUGGUAUCAGAUUCUGACUUGCACAAGU-------
AC079945.21/34878-35012 CUCCAUGUGUCUUUGGAACCUGUCAGCUGUGGCAGUUGCCCUUCCUAGCCAUGGAAGAGUAAGUAUAUUCUUGUUUAUUGGCAAAGCUGUCACCAUUUCAUUGGUAUCAGAUUCUGACUUGCACAAGUAACAUUC
AC068213.7/10987-11117  CUCCAUGUAUCUUUGGGACCUGUCAAGUGUGGCAGUCUCCCUUCCUUGCCAUGGAAGAGCA----UAUUCUUGUUUACCAGCAAAGCUGUCACCAUUUAAUUGGUAUCAGAUUCUGACUUGCACAAGUAACAUUC
#=GC SS_cons            :<<<<<<-------<<<<-<<<<<______>>>>>-->>>>-------->>>>>>------....------<<<<--<<<<<<<--<<<--<<<<______>>>>-->>>-------->>>>->>>-->>>>:::
#=GC RF                 CuCcaugUAuCUUUGGgaCcuGcCAgcuGUGgCagucucCCUUccUAGCcaugGaAGAGcA....UAUuCUuguuUAuuGGcaaAGCuGUcacCaUUUaauuGguAUCaGAuUCUGACuugCACaaGUaacaUUC
//
# STOCKHOLM 1.0

#=GF AC   RF00400
#=GF ID   SNORA28
#=GF PI   snoACA28
#=GF DE   Small nucleolar RNA SNORA28
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15199136, INFERNAL
#=GF SS   Predicted; RNAFOLD
#=GF GA   65.00
#=GF TC   66.90
#=GF NC   64.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00033
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300926;
#=GF DR   snoopy; Gallus_gallus300092;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   ACA28 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA28
#=GF SQ   26


AJ609462.1/1-126             AAGCAACACUCUGUGGCAGAUG-AUCAAAAC--UGUCUGACACAAUUU-GAGCUUGC-UAUA-GCAA------G-A-AAGUCUAACCUAUUCCGGU--GUUCUCUCUCCC-AUGAGACAA-GCC--GUUAUAUAGACUUAAACAGU
AL138976.5/150375-150500     AAGCAACACUCUGUGGCAGAUG-AUCAAAAC--UGUCUGACACAAUUU-GAGCUUGC-UAUA-GCAA------G-A-AAGUCUAACCUAUUCCGGU--GUUCUCUCUCCC-AUGAGACAA-GCC--GUUAUAUAGACUUAAACAGU
AF357387.1/1-122             -----ACACUCUGUGGCAGAUG-AACAAAAC--CGUCUGACACAAUUU-GAGCUUGC-UAUA-GCAA------G-A-AAGUCUAACCUAUUCCGGU--GUUCUCUUUCCCCAUGAGACAA-GCC--GUUAUAUAGGCUCUAACAAA
AAQQ01697208.1/1311-1436     AAGCAACACUCUGUGGCAGAUU-AUUGAAAC--UGUCUGACACAAUUU-GAGCUUGC-UAUA-GCAA------G-A-AAGUCUAACCUAUUCCGGU--GUUCUCUUUUCU-GUGAGACAA-GCC--GUUAUAUGGGCUUAAACAGU
AAFC03040565.1/7340-7215     AAGCAACACUCUGUGGCAGAUA-ACCAAAAU--UGUCUGACACAAUUU-GAGCUUGC-UAUA-ACAA------G-A-AAGUCUAACCUAUUCCGGU--GUUCUCUUUUCU-GUGAGACUA-GCC--GUUAUAUAGACUUAAACACU
ABDC01252812.1/2076-2201     AAGCAACACUCUGUGGCAGAUA-AUCAAAAC--UGUCUCUCAGAAUUU-GAGCUUGC-UAUA-GCAA------G-A-AAGUCUAACCUAUUCCGGU--GUUCUCCCUUCC-GUGAGACAA-GCC--GUUAUAUGGACUUACACAGU
AAIY01676530.1/1418-1544     AAGCAACACUCUGUGGCAGAUG-AUCAAAAC--CGUCUGUCACAAUUU-GCGCUUGC-CACA-GCAA------A-AAAAGUCUAACCUAUUCCGGU--GUUCUCUCCUCA-GUGAGACUA-GCC--GUUAUAUGGACUUGAACAAU
AANN01302642.1/2007-2132     AAGCAACACUCUGUGGCAGAUA-AUCGAAAG--UGUCUGUCACAAUUU-GAGCUUGC-UAGA-GCAA------U-U-AAGUCUAACCUAUUCCGGU--AUUCUCUUCUCU-GUGAGAUAU-GCC--GUUAUAUAGACGUAAACAUU
AANG01201912.1/1981-1858     UUGUGACACUCUGUGUCAGAUG-AUUGAAGU--UGUCUGAUGCAAUUU-GAGCUUGC-UAUA-GCAA------G-A-AAGUCUAACCUAUUCCAGU--GU--UCCCCUCC-AUGAGACCA-ACU--GUUAUACAGACUUAAACAUU
AAYZ01548677.1/59-182        AAGCAACACUCUGUGGCAGACU-GUCAAUCA----UCUGACACAAUUU-GCGCUUGC-UAUA-GCAA------G-G-AAGUCUAACCUAUUCCGGU--GUGCACUCUGCU-GUGAGGCCG-ACU--GUUAUUCAGCCUUAAACAGU
AAFR03013521.1/163747-163871 AAGUAACACUCUGUGGCAGACA-AAAAGU----UGUUUGACACAAUUU-AAACUUGCAGACA-AUAA------G-U-AAGUCUAACCUAUUCCAGU--GGUCUCUCUUAA-AUGAGACCA-UCU--GUUAUAUAGGCUCAAACAAU
AALT01500620.1/4999-4881     AGUCCACACUCAGUAGCAGAUG-AUCCAAAG--UGUCUGGU--------GCAUUUGC-AACA-GCAA------G-G-CAGUCUAACCUAUUCCGGU--GCUCUCUUCUCC-AUGAGACAA-GCU--GUUAUAUAGACUUCAACAGC
AADA01103542.1/59-191        AAGACACUGUUGGGG-CAGGAUGAUUAAAAACUGUUUUGACGCCAAUUGGAGCUUGC-UAUACGCAA------G-A-AAGUCUAGCCUAUUUCGGGUGUUUUUUUUCUCC-AUGAGACAAGGCG--GUUAUAUAGACUUGAACAGG
AAWR02020121.1/2826-2951     AAGCAACACUCUGUGGCAGAUG-AUUGAAAA--UGUCUGACACAAUUU-GAGCUUGC-UAUA-GCAA------G-A-AAGUCUAACCUAUUCCGGU--GUUCUCUUCUCC-GUGAGACGA-GCC--GUUAUAUAGACUCAAACAGU
AAHX01046683.1/4367-4242     AAGCAACACUCUGUGGCAGAUG-AACAAAAC--UGUCUGACACAAUUU-GAGCUUGC-UAUA-GCAA------A-U-AAGUCUAACCUAUUCCGGU--GUUCUCUUCUCU-GUGAGACAA-GCC--GUUAUAUAGGCUCAAACAAA
AAKN02051986.1/295375-295500 AAGCAACACUCUGUGACAGAUU-AUCAAAAU--AGUCUGUCACAAUUU-GAGCUUGC-UAUA-GCAA------G-A-AAGUCUAACCUAUUCCGGC--ACUCUCCUUUCU-GUGAGACAA-GCC--GUUACAUAGACUGAAACAAG
AAGV020876670.1/1062-936     AAGCAAUGCUCUGUG-CAGAUG-AUUAAAAC--CAUCUGGCACAAUUU-CUGCUUGC-UAUA-ACAA------G-A-AAGUCUGACCUAUUCUGGU--GUUCUCUCUUUG-ACGAGACAA-GCCCCAUUAUAUAGACUACACCAGC
EU240313.1/5-128             AAGCAACACUCUGUAGUAAGCA-UUUGGU----UGCCUGCUGCAAUUU-AAGCUUGC-UAAA-UCAG------A-A-AAGUCUAACCUAUUCCAGG--GAUCUCUGCUUU-GUGAGGUCG-CUU--GUUAUAUAGACUUGUACAGC
EU094016.1/6-130             AAGUAACACUCUGUGGCAGACA-AUGU------UGUCUGACUCAAUUUUGAGCUUGC-UAUA-GUAAA----AG-A-AAGGCUAACCUAUUCCAGC--GGUCGCUUUCAA-GUGAGACUG-UCU--GUUAUAUAGACUUUGACAGG
EU094010.1/6-134             AAGUAACACUCUGUGGCAGACA-CCGU------UGUCUGACUCAAUUUUGAGCUUGC-UAUA-AUAAAAAAAAA-A-AAGCCUAACCUAUUCCAGU--GGUCUCUUUUAA-AUGAGACCA-UCU--GUUAUAUAGACUGUGACAGU
AAEX03006046.1/2366-2489     AAGCAACACUCUGUGGCAGAUG-AUGGGAGU--UGUCUGACACAAUUU-GAGCUUGC-UAUA-GCAA------G-A-AAGUCUAACCUAUUCCAGU--GU--UCUCCUCA-AUGAGACCA-ACU--GUUAUAUAGACUUAAACAAC
AAPE02053647.1/19333-19210   AAGCAACACUCUGUGGCAGAUG-AUCGACAC--UGUCUGACACAAUUU-GAGCUUGC-UACA-GCAA------C-A-AAGUCUAACCUAUUCCGGU--G--CUCUCCUCU-AUGAGACAA-GCC--GUUAUAUAGACUUAGACAGU
AAGW02034578.1/37770-37895   AAGCUACACUCUAAGGCAGACU-GUCAAAAC--UGUCUGACACAAUUU-GAACUUGC-CAUA-GCAA------G-G-AAGUCUAACCUAUUCCAGU--AUUCUUUCUUCU-GUGAAACAA-ACU--GUUAUAGAGACUUAAACAGU
AAWZ02020991.1/19647-19524   AAGCAACACUCUGUGGUAGAUA-UCUCAU----UGUCUGCUUCAAUUU-AAGCUUGC-UAUA-AUAA------ACA-UAGUCUAACCUAUUCCAGA--GG--UCUCUGUAGGUGAGGUCA-UCU--GUUAUAUGGGCUCUAACAUC
AAQR03042191.1/4692-4567     AAGCAACGCUCUGUGGUAGAUG-AUCAAAAC--UGUCUGACACAAUUU-GAGCUUGC-UAUA-GCAA------G-A-AAGUCUAACCUAUUCCGGU--GUUCUCCCUUCU-GUGAGACGA-GCC--GUUACAUAGACUUAAACAGU
AAGU03026170.1/2730-2856     AAGCAACACUCUGUGGCAGAUG-AGCAAAAC--UGUCUGACACAAUUU-GCGCUUGC-UAUA-GUAA------G-A-AAGUCUAACCUAUUCCGGU--GUUUUCUUCCUCAGUGGGACAA-GCC--GUUAUAUAGACUUAAACAUU
#=GC SS_cons                 ::::::::<<<<<<<-<<<<<<.________..>>>>>>->>>>----.>>>-----.----.----......-.-.<<<<<<<---<<<--<<<<..----<<<<____.__>>>>---.>>>..>-->>>>>>>>>>:::::::
#=GC RF                      AAGcaACACucuGuGGCAGacg.auuaAaAu..cguCUGaCaCaAUUU.gaGCUUGC.UAUA.gcAA......g.A.aAGuCuaACCUAUUCCgGc..guUCuCucuUcu.aUgaGaCaA.gCc..GUUAUAuaGaCUuaAACAgu
//
# STOCKHOLM 1.0

#=GF AC   RF00401
#=GF ID   SNORA20
#=GF PI   snoACA20
#=GF DE   Small nucleolar RNA SNORA20
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15199136
#=GF SS   Predicted; ILM; Moxon SJ
#=GF GA   60.00
#=GF TC   62.00
#=GF NC   59.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00030
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300675;
#=GF DR   snoopy; Homo_sapiens300149;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA20 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA20
#=GF SQ   17


AJ609459.1/1-132         CUUCCCAUUUAUUUGCUGCUUGUAGUCUCACAGUGAUACGAGCAGUUAUACGCAUGGGAUAAAAUAACAUUGGGCCACUGUAAAUUGAGAUGAAGUAACCAUUUUCAUCUCUUCUGCA-GGGACUAGACAUUG
AC092174.5/156814-156683 CUUCCCAUUUAUUUGCUGCUUAUAGUCUCACUGUGAUAUGAGCAAUUAUACACAUGGGAUAAAAUAAUAUUGAGCCACUGUAAAUUGAGAUGAAGUAACCGUUUUCAUAUCUUCUGCA-UGGACUAGACAUUG
AC034114.17/7622-7492    CUUCCCAUUUAUUUGCUGCUA-UAGUCUCAUAAUGAUACAAGCAGUUAUAUGCAUGGGAUAAAAUAAUAUUGGGACAUUGUAAAUUGAAAUGAAGUAACCAUUUUCAUCUUUUCUGCA-UGGACAAGACAUUG
AY057819.1/673-800       UUUCCCAUUAAUUUGCUGCUC-UAGUCUGUCAGUGAUAGGAGCGGUUAUACGCAUGGGAUAAAACAAUAUUGGGCCACUGUACAUGGAGAUGAAAU--GUGUUUU-GUCUCUCGUACA-UGGUCUAGACAUUG
AC011749.2/64633-64502   CUUCCCAUUUAUUUGCUGGUA-UAAUGAUACAAUGAUAUGAGCAGUUAUACUCUUUGGAAAAAAUAAUAUUGGGCCAUUGUAAAUUGACAUGAAGUAAGUAUUUUCAUAUCAUCUGCAAUGGACUAGAUGUUG
AC095353.9/75194-75323   CUUCCCAUUUAUUUGCUGGUA-UAGUCUCACAAUGAUAUGGCCAGUUAUACUUAUGGGAAAAAAUAAUAUUGGGCCAUCGUAUAUUGACAUGA-GUAACUAUUUUCACCUCUUCUGCA-UGGACUAUCUAUAU
X61220.1/665-792         UUUCCCAUUAAUUUGCUGCUC-UAGUCUGUCAGUGAUAGGAGCGGUUAUACGCAUGGGAUAAAACAAUAUUGGGCCAUUGUACAUGGAGAUGAAAU--GUGUUUU-GUCUCUCGUACA-UGGUCUAGACAUUG
AY057823.1/668-796       UUUCCCAUUAAUUUGCUGCUC-UAGUCUUUCAGUGAUAGGAGCAGUUAUACGCAUGGGAUAAAACAAUAUUGGGCCAUUGUACAUGGAGAUGAAAA-UGUGUUUG-GUCUCUUGUACA-UGGUCUAGACAUUG
X61222.1/667-794         UUUCCCAUUAAUUUGCUGCUC-UAGUCUGUCAGUGAUAGGAGCGGUUAUACGCAUGGGAUAAAACAAUAUUGGGCCAUUGUACAUGGAGAUGAGAU--GUGUUUU-GUCUCUCGUACA-UGGUCUAGACAUUG
X61217.1/665-792         UUUCCCAUUAAUUUGCUGCUC-UAGUCUGUCAGUGAUAGGAGCGGUUAUACGCAUGGGAUAAAACAAUAUUGGGUCAUUGUACAUGGAGAUGAAAU--GUGUUUU-GUCUCUCGUACA-UGGUCUAGACAUUG
X61218.1/665-792         UUUCUCAUUAAUUUGCUGCUC-UAGUCUGUCAGUGAUAGGAGCGGUUAUACGCAUGGGAUAAAACAAUAUUGGGCCAUUGUACAUGGAGAUGAAAU--GUGUUUU-GUCUCUCGUACA-UGGUCUAGACAUUG
X61211.1/665-792         UUUCCCAUUAAUUUGCUGCUC-UAGUCUGUCAGUGAUAGGAGCGGUUAUACGCAUGGGAUAAAACAAUAUUGGGCCAUUGUACAUGGAGAUGAAAG--GUGUUUU-GUCUCUCGUACA-UGGUCUAGACAUUG
AY057822.1/675-802       UUUCCCAUUAAUUUGCUGCCC-UAGUCUGUCAGUGAUAGGAGCGGUUAUACGCAUGGGAUAAAACAAUAUUGGGCCAUUGUACAUGGAGAUGAAAU--GUGUUUU-GUCUCUCGUACA-UGGUCUAGACAUUA
AY057821.1/669-796       UUUCCCAUUAAUUUGCUGCUC-UAGUCUGUCAGUGAUAGGAGUGGUUAUACGCAUGGGAUAAAACAAUAUUGGGCCAUUGUACAUGGAGAUGAAAU--GUGUUUU-GUUUCUUGUACG-UGGUCUAGACAUUG
AY057744.1/16-142        UUUCCCAUUAAUUUGCUGCUC-UAGUCUGUCAGUGAUAGGAGCGGUUAUACGCAUGGGAUAAAACAAUAUUGGGCCAU-GUACAUGGAGAUGAAAU--GUGUUUU-GUCUCUCGUAUG-UGGUCUAGACAUUG
X61221.1/661-790         UUUCCCAUUAAUUUGCUGCUC-UAGUCUGUCAGUGAUAGGAGCAGUUAUACGCAUAGGAUAAAACAAUAUUGGACCAUUUUACGUGAAGAUGAAGU--GUGUUUUUGUCUCUUGUAGAAUGGUCUAGACAUUG
AY057824.1/664-791       UUUCCCAUUAAUUUGCUGCUC-UAGUCUGUCAGUGAUAGGAGCGGUUAUACGCAUGGGAUAAAACAAUAUUGGGCCAUUAUACAUGGAGGUGAAAU--GUGUUUU-GUCUCUCGUAUG-UGGUCUAGACAUUG
#=GC SS_cons             ::<<<<<<------<<<<<<<.<<-<<_______>>>>->>>>>>>------->>>>>>----------<<<<<<<<-<<<<----<<<<<<<<<<..__>>>>>.>>>>>--->>>>.>>>>>>>>::::::
#=GC RF                  uUuCCcauUaAUUUgCuGcuc.uaGuCUguCAgUGauaggagCaGuUAUACgCaugGGauAAAAuAAUAuugGgCCaUuguacAUgGagaugaaac..gUguuuu.aucuCUuguaca.uGGcCuagAcAUUG
//
# STOCKHOLM 1.0

#=GF AC   RF00402
#=GF ID   SNORA25
#=GF PI   snoACA25
#=GF DE   Small nucleolar RNA SNORA25
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15199136, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   85.00
#=GF TC   85.20
#=GF NC   84.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300866;
#=GF DR   snoopy; Echinops_telfairi300348;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA25 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA25
#=GF SQ   30


AJ609461.1/1-133             GGGUCAUUUCAAAGAGGGCUUAUGAGGCUGUGAAACCCAGAGCUCUUAACGCUGUGACCAAAGAUGGAAGUUCUCUAUAGGAAGCC--AUA-G-CACUC---CUAAUGUUUGGUG--C-UAUGUUUUCCUGA---GGAGAUAUAA-A
AC094019.2/47367-47494       AGGUCAUUUCAAAGAGGUCUUGUGAGGCUGUGAAACCAAGAGCUCUUAACACUGCGACCAAAGAUGGAAGUUCUCUAUAGGAUGCC--AUG-G-CAUU-----UGAU----GGUG--C-UAUGUUUUCUUGA---GGAGAUAUAAGA
AC012291.11/20685-20802      AGGUCAUUUCAAAGA----------GGCUGCAAAACCAAGAGCUCUUAACGCUGUGAGCAAAGAUGGAAGUUCUCUCUAGGAUGCC--AUG-G-CACU-----CGAU----GGUG--G-UAUGUUUUCCUGG---GGAGAUAUAAGA
AC084794.3/215294-215169     AGAUCAUUUCAAAGAGGGCUCGUGGGGCUAUGAAACCAUGAGCUCUUAAUGCUAUGACCAAAGACUGAAGUUCUCUAUAGGACGCC--AUA-G-CACU-----CAAU----GGUG--C-UGU--UUUCCUGA---GGAGACAUAAGA
AC076966.25/56587-56462      AGGUCACUUCAAAGAGGGCUUGUGGGGCUGUGAAACCAAGAGGUCUUAACAGUAUGACCAAAAACUGAAGUUCUCUAUAGGAUGCU--GUA-G-CACU-----CAAU----GGUG--C-UAUGUUUUCCUCA---GGAGAUAU--GA
AC092590.2/35181-35054       AGGCCAUUUUAAAGAGGGCUCAUGGGACUAUGAAACCAAGAGCUCUUAAUGCUGUGACCAAAGAUUGAAGUUCUCUAUAGGU-UGCCAAAG---CACU-----CAGU----GGUG--C-UGUGUUUUCCUGA---GGAGAUAUAAGA
BX640788.1/449-324           AGGUCACUUCAAAGAGGGCUUGUGGGGCUGUGAAACCAAGGGGUCUUAACAGUAUGACCAAAAACUGAAGUUCUCUAUAGGAUGCU--GUA-G-CACU-----CAAU----GGUG--C-UAUGUUUUCCUCA---GGAGAUAU--GA
AL137139.9/16415-16289       AGGUUAUUUCAAAGAGGGCUCAUGAGGCUAUGAAACCAAGAACUCUUAAUGCUAUGACCAAAGAUUGAAGUUCUCUAUAGAAUGCC--AUA-G-CACU-----CAAU----AAUG--U-UAUGUUUUCUUGA--GGCAUAUAA--GA
AC124254.5/29323-29197       AGGACAUUUCAAUGCGGGCUCAUGGGGCUGUGAAGCCAAGAGCUAUUAACACUAUGACCAAGGAUUGAAAUUCUCUAUAGGAU-CC--GUA-G-CACU-----GAAU----AGUG--C-UAUAUUUUCCGGA---GGAAGUAUAAGA
AANU01213134.1/11922-11797   AGAUCAUUUCAAAGAGGGCUCACAGGGCUGUGAAACCAUGAGCUCUUAACGCUAUGACCAAAGACUGAAGUUCUCUAUAGGAUGCC--AUA-G-CACU-----CAAU----GGUG--C-UGU--UUUCCUGA---AGAGAUAUAAGG
ABDC01626488.1/422-549       UGGUCAUUUCAAAGAGGGCUCAUGGAGUUGUGAAACCAAGAGCUCUUAACGCUGUGACCAAAUAUUGAAGUUCUCUGCAGGAUGCU--GUA-A-CACU-----AAAU----AGUG--C-UAUGUUUUCCUGA---GGAGAGGUACAA
AANG01072513.1/826-700       AGGUCAUUUCAAAGAGGGCUUGUGGGGCUA--AAACCAAGAGCCCUUAACGCUGUGACCAGAUAUCGAAGUUCUCCAUAGGAUAUA--AUA-G-UUAC----UCAGU----GUUG--C-UAUGUUUUCCUGA---GGAGAUACAAGA
AAQQ01146348.1/614-742       UGGUCAUUUCAAAGAGGGCUUUUGGGGCUGUGAAACCAGGAGCCCUUAACGCAGUGACCACAGAUUGAUGUUCUCCACAGGACCCC--AUA-GUCACU-----CAGU----AGUG--C-UGUAUAUUCCUGA---GGAGAUAACAUU
AAPY01155118.1/4341-4471     GGGUCAUUUCAAAGAGGGCUCCUGAGGCUAUAAAACCAGGAGCUCUU-ACGCAGUGACCGAAGACUGAAGUUCUCUAUAGGAUGCC--AUA-GUUGCUC--AGUAAU----AGCA--C-UAUGUUUUCCUGG---GGAGAUACAAGA
AAFC03036620.1/30928-30802   AGGUCAUUUCAAAGAGGGCUUAUGAGACCA--AAACCGGGAGCUCUUAAUGCUGUGACCAAAGAUUGAAGUUCUCCAUAGAAUAUU--ACG-GUCACU-----CAAA----AGUG--C-UAUGUUUUCCUAA---GGAGAUAAGAUU
AADA01361275.1/23869-23742   AGAUAACUUCAAAGAGGGCUUGCGGAGCUGCAAAACCAAGAGCUUUUAAUG-UAUUACUGAAUAUUGAAGUUCUCCAUAGGAUGCC--AUA-GUCACU-----CAGU----AGUG--C-UAUAUCUUCCUAA---GCAGAUAUAAGA
AAIY01239345.1/6572-6446     AGCUCAUUUCAAAGAGGGCUUGU--GGAACUGAGACCAAGAGCUCUUAAGGCUGUGACCAAAGAUUGAGAUUUGCCAUAGAAUGCC--ACA-GUCACU-----CCCU----AGUG--C-UGUUUUCUCCUGU---GGAGAUACAAGA
AAFR03025134.1/22649-22782   AGGUCAUUUCAAAGAGGGCUUGCAUGGCUAUAAAACCAGAAGCUCUUAACGCUGUGACCUAAGAGGAAAAGUCUCUAUAGGAUGCC--AUG-AUUAAUU---GAUAU----AUUA--U-CAUGGUCUCUUACUAAUGAGAUACAAGU
AANN01814642.1/7765-7889     AGGUCAUUUCAAAGAGAGCUUUUU-GG--AUUAAACCAGGAGCUCUUAACGCUGUGACCAAAGAU-GAAGUUCUCCCUGAGAUGUG-AUCA-G-CACU-----GAGU----AGUG--C-UGUGUAUUCUUGG---GAUGAGACAAGA
AAKN02033025.1/13015-13143   AGGUCAUUUCAAAGAGGGCUUGUGGGAAUGUGAAACCAAGAGCUCUUAACACAGUGACCACAGAAUGAAGUUCUCCACAGUAUGUC--AUA-GUCACU-----CAGU----AGUG--C-UAUGUUUUCCUGA---GGAGAAAAACAU
AAHX01053335.1/102384-102512 AGGUCAUUUCAAAGAGGGCUUG-GUGGCUGUAAAACCAAAAGCUCUUAACGCUGUGACCAAAGAUUGAUGUUCUUCACAGAGCAGA--CCAUG-CACUU--UGUGAU----AGUG--C-UGU--UUUUCUGA---GAAGAUAACAUG
AAWR02017934.1/97230-97356   AGGUCAUCUCAAAGAGGGCUUGUGGGACCA--AAACCAGGAGCUCUUAACGCUGUGACCAAAGAUUGAAGUUCUCCAUAGGAUAUA--AUA-GUCACU-----CAGU----AGUG--C-UAUGUUUUCCUGA---GGAGAUACAUCC
AC155259.1/217782-217650     AGGUCAUUUCAAAGAGGGCUUUUUGGGCUAUAAAACCCACAGCUCUUAACGCUGUGACCAAAGAUUGAUGUUCUUCACAGAGAAAA-UCCU-G-CACUGU-UUUGAU----AGUG--C-UGUGUUUUUCUGA---GAAGAUAACAUA
EU094029.1/4-132             AGGUCAUUUCAAAGAGGGUUCGUAUGGCUGUAAAACCAGCAGCCCUUAACGCGAUGACCUAAUA--GGAACUCUCUACAGGUUACC--ACUC-UCACU-----AAGU----AGUGCA-CUGUGGUUUCCUCC---UGAGACACAGUG
JN899076.1/1-127             AGGUCAUUUCAAGGAGGGCUGAUGGGA--CCAAAUCCAGGAGCUCUUAACGCUGUGACCAAAGAUUGAA-UUCUCCAUAGGAUGUA--AUA-GUCACU-----UGAU----AGUG--C-UAUGUUUUCCUGA--UGGAGAUACAGAA
FJ915961.1/2-133             AGGUCAUUUCAAAGAGGGCUCAUGAGGCUGUGAAACCCAGAGCUCUUAACGCUGUGACCAAAGAUGGAAGUUCUCUAUAGGAUGCC--AUA-G-CACUCCUAUGUUU----GGUG--C-UAUGUUUUCCUGA---GGAGAUAUAA-A
AAQR03000416.1/3548-3675     UGGUCAUUUCAAAGAGGGCUUGUGGAGUUGUGAAACCAAGAGCUCUUAACGCUGUGACCAUAUAUUGAUGUUCUCUGUAGGAUGCU--AUA-A-CACU-----AAAU----AGUG--C-UAUGUUUUCCUAA---GGAGAAGACAUA
AAEX03003661.1/33709-33581   AGGUCAUUUCAAAGAGGGAAUUUGGGGGGCUGAAGCCAAGAGCUCUUAACACUGUGACCAAAUAUUGAAAUUCUCUAUAGGAUGUA--AUG-GUCACU-----CAAU----AGUG--C-UGUGGUUUCCUGA---GGAGAUAUGAGA
AAPE02025112.1/56872-56745   GGGUCAUUUCAAAGAGAGCUUAUGGGACUA--AAACCAGGAGCUCUUAACGCUGUGACCGAAAAUUGAAGUUCUCCAUAGGAUGUA--AUAAA-CACU-----CAAU----AGUG--UCUAUUUUGUCCUGA---AGAGAUAUAUGA
AAGW02065927.1/9728-9856     AGGUCAUUUCAAAGAGGGCUUGUGGAGCUGUGAAACCAAGAGCUCUCAAUGCUGUGACUAAAGACUGAUGUUCUCCAUGGGAUGUU--GUA-GUCACU-----CAAU----AGUG--C-UGUGUUUUCCUGU---GGAGGUAUAAGA
#=GC SS_cons                 :<<<<<<------<<<<<<<<-<--<<________>>->>>>>>>>>------>>>>>>------------<<<<<--<<<<----..<<<.<.<<<<.....____....>>>>..>.>>>---->>>>--...>>>>>:::::::
#=GC RF                      AGguCAuUUCAAAgAGgGCUcauggGGcUaUgAAACCAagAGCuCUuAAcGCUgUGacCAAAgAuuGAAGUUCUCcAUaGGaUgcc..aua.g.CAcu.....caaU....agUG..c.uauGUUUuCCuga...gGAGAUAuAAga
//
# STOCKHOLM 1.0

#=GF AC   RF00403
#=GF ID   SNORA41
#=GF PI   snoACA41
#=GF DE   Small nucleolar RNA SNORA41
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15199136, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   80.00
#=GF TC   85.00
#=GF NC   76.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300178;
#=GF DR   snoopy; Loxodonta_africana300445;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   ACA41 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1]. The family also includes
#=GF CC   the mouse sequence MBI-83 described in [2].
#=GF WK   Small_nucleolar_RNA_SNORA41
#=GF SQ   31


AF357411.1/1-113           -------------------CAGCUGUCUUUA-UGGUAGCAGUUGUAGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-ACACAA--UUUAAU-GCCU-CUUUCUUAGCCACACAGGAGG-AGG---AUUAUGUGUGACAGACACAA
AL645950.13/74028-74159    UUCCACAGCUACUGGUCUACAGCUGUCUUUA-UGGUAGCAGUUGUAGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-ACACAA--UUUAAU-GCCU-CUUUCUUAGCCACACAGGAGG-AGG---AUUAUGUGUGACAGACACAA
AC121963.3/78058-77927     UUCCACAGCUACUGGUCUACAGCUGUUUUUA-UGGUAGCAGUUGUAGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-ACACAA--UUUAAU-GCCU-CUUUCUUAGCCACACAGAAGG-AGG---AUUACGUGUGACAGACACAA
AC007383.4/101218-101349   UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UGGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUUAACACA------AAC-ACCU-CUUUCUUAGCAAAACAGAAAGUGGGU-AUAUAUGUGUGACAGACACAA
AC090527.3/17174-17301     UUCCACCACUAUUGGUCUGCAGCUCUUCUUA-UGGUAGCAGUUGUUGCAUUUC-UCUGUGGGAAAGAAA-------AGAGGA--UUAAAC-ACCU-CUUUCUUAGCAAAACAGAGAGUAGG---CAUAUGUGUGACAGACACAA
AJ609464.1/1-132           UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UGGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUUAACACA------AAC-ACCU-CUUUCUUAGCAAAACAGAAAGUGGGU-AUAUAUGUGUGACAGACACAA
AAQQ01276679.1/221-355     UUCCACAGCUACUGGUCUGCAGCUGUUCUAA-UGGUAGCAGUUGUAGCAUUCC-UCUGUGGGAAAUAAA-CUGUU-AUACAA--UUAUAU-GCCU-CUUUCUUAGCCAAAGAGAAAGUGGGC-ACAUGUGUGUGACAGACACAU
AAFC03055400.1/29161-29294 UUCCACAGCUACUGGUCUGCAGCUGUUCUUAAAGGUAGCAGCUGUGGCAUUCC-ACUGUGGGAAAGAAA-CUGUC-ACACAA--CUCAAC-ACCU-CUUUCUCAGCACAACAGAAAGUGGG---CAUGUGUGUGACAAACACAA
AAIY01152799.1/3962-4099   UUCCACAGCUACUGGUCUGCAGCUGUUUUUA-UGGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-GUGUU-ACCCAAUGUGACAU-CCCU-CUUUCCCAGCAAAAUGGAAAGUUGGGCAUAUGUGUGUGACAGACACAG
AANG01689589.1/3219-3352   UUCCACAGCUACUGGUCUGCAGCCGCUCUUA-UGGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGGAAACUGUC-ACACAA--UUAAAU-ACCU-CUUUCUUAGCACGACAGAAAGUGGG---CAUGUGAGUGACAAACAGAU
AAYZ01152970.1/1639-1769   UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UGGUAGCGGUUGUGGCAUUCC-ACUGUGGGAAAGCAA-CUGUC-ACAAU----UAAAC-ACCU-CUUUCUUGGCAAACCAGAAAGGGGG---CAUAUUUGUGACAGACAGGA
AAPY01235580.1/6370-6239   UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-CAGUAGCACUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-A-ACGG--UUAAAU-ACCU-CUUUCUUAGUAAAAUAGAAAGUAGU---CAUGUGUGUUUCAGACAAAA
ABDC01218542.1/3016-3147   UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UG-UAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUCAUGACACAG--UCAUAC-ACCU-CUUUCUUAGCAAA-CGGAAAGUGGG---UAUCAGGGUGACAGACACAA
AANN01478268.1/1238-1104   UUCCACAGCUAGUGAUAUGCAACUGUUCUUA-AGGUAGCAGUUGUGACAUUCU-UCUGUGAGAAAGAAA-UAAUG-ACACAAAUUUAAAU-ACCU-CUUGCCUAGCAAAACAGAAAGUUGG---CAUAUGUGUGACAAAUAAGA
AAFR03041977.1/27839-27705 UUCCACAGCUACUGGUCUGCAACUGUUCUCAUCUAUAGCAGUUGUUGUAUUCC-ACUGUGGGAAAGGAA-CUGUU-ACACUG--UUAAAUAACCU-CUUUCU-AAUAUAACAGAAAGUGGG--UUCUUUGUGUGACAGACACCU
AALT01533432.1/8901-8769   UUCCAUAGCAGCAGGUCUGCAAUUGCUCUUC-CUGUAGCAAUUGUGGCAGUCA-UCUGUGAGGAAGAAA-UUGUU-A-CUUG--GUUAAC-ACUG-CUUUCUUAGCAAAAUAGACAGUAAU--AGUGUAAUUUGUCAGGCUAGA
AAVX01259799.1/576-710     UUCCACAGAUACUGGUCUGGAAUUGCUUGCU-UGGUAGUAGUUUCAGUAUUCCUUCUGUGGAAUAAUAA-UUGUU-GCACUC--AGUUAU-CAGCUCUUUAUAAAUCACUAUCAAAGUGCU---UUAUGGUGUGACACACAUUU
AAKN02019509.1/9665-9798   GUCCACAGCUACUGGUCUGCAGCUGCUGUCAAUCGUAGCAGCUGUGGCAUUCC-ACUGUGGGAAAGGAA-GUGUU-ACACAG--UUAAAU-ACCU-CUUUCUUAUCCAAGAAGAAAGUGGG---CAUGUGUGUGACAGACAGUG
AAHX01054375.1/23514-23383 UUCCACAGCUACUGGUCUGCAGCUGUCCUUA-UGGUAGCAGUUGUAGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-ACACAA--UUUAAU-GCCU-CUUUCUUAGCCACAUAGAAAG-AGG---AAUAUGCGUGACAGACACAA
AAWR02007092.1/1413-1544   CCCCACAGCUCCUGGGCCGCAGCUGUUCUCA-CGGCAGCAGCUGUGGCAUUCC-UCUGUGGGAGAGAAA-CUGUU-ACACGA--UUGAAA--CCG-CUUUCUUAGCAAAACAGAAAGCGGG---CAUGUGUGUGACAAACACAG
AAGV020028150.1/1950-2082  CUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UGGUGGCAAUUGUGGCAUUCC-UCUGUGGUAAAGAAU-CUGUU-ACAUAA--UUAAAU-ACUU-CUUUCUUAGCAAAACAGAAAGUGGG---CAUGUGUGUGACAAAGUUAA
EU094007.1/3-137           UUCCACAGCUACUGGUCUGCAGCUGUUGUGCUCUGUAGCAGUUGCAGUAUUCCAUCUGUGGGAAAGAAACUUGUUGACACUG--UUCGUU-ACCC-CUUUCUCGGCAAC--AGAAUGGGGU---UUUCUGUGCGACAGACAAAU
EU240316.1/2-135           GUCCACAGUUACUGGUCUGAAACUGUUCAGGACUGUAGCAGUUGCAGUAUUCCCUCUGUGGAAGAUAAA-CUGUU-ACGUAG--UAUUAA-GCUC-CUUCUCAGAUCUUCUAAGAAG-GAC---UUUCUAUGUAACAAACAACG
FJ915969.1/1-130           UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UGGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUUAACACA------AAC-ACCU-CUUUCUUAGCAAAACAGAAAGUGGG---CAUAUGUGUGACAGACAUAA
AAWZ02015247.1/62201-62072 UUCCACAGCUACUGGCCUGCAACUGUUCAGUAUUGUAGCAAUUGCAGUAUUCCAGCUGUGGGAGAUUAG-CAGUU-ACACC------UAU-AUGA-UUCUCCUUUCAAA-UGGGGAGAUAA---UUGACGUGUAACGGACAAGA
AAPE02003230.1/9283-9415   UUCCACAGCUACUGGUCUGCAGCUGUUCUCA-UGGUGGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-UUGUU-ACACGA--UUAAAC-ACCU-CUUUCUUAGCAAAACAGAAAGGGGG---CAUAUGUGUGACAAACAUGA
AACN011054043.1/216-348    UUCCACAGCUACUGGUCUGCAGCUGUUCUUA-CAGUAGCAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-AUGCAA--UUAAAC-ACCU-CUUUCUUAGCACAACGGAAAGUGGG---CAUAUGAGUAACAAACAUAA
AAQR03032350.1/9868-9736   AUCCACAGCUACUGGUCUGCAGCUGUUCUUA-UG-UAACAGUUGUGGCAUUCC-UCUGUGGGAAAGAAA-CUGUUAACACAG--UUAAAU-ACCU-CUUUCUUAGCAAAACAGAAAGUGGG---UAUACGUGUGACAGACAGAA
AADN03005226.1/24909-25042 GUCCACAGUUACUGGUCUGAAACUGUUCAGGACUGUAGCAGUUGCAGUAUUCCCUCUGUGGAAGAUAAA-CUGUU-ACGUAG--UAUUAA-GCUC-CUUCUCAGAUCUUCUAAGAAG-GAC---UUUCUAUGUAACAAACAAUG
AAGW02037058.1/8662-8794   UUCCGCAACUACUGGUCUGCAGCUGUUCUUA-UGGUAGCAGUUGUGGCAUUCC-ACCGUGGGAAAGAAA-CUGUU-AUACAA--UUAAAU-ACCU-CUGUCUUAGCAAAACAGAAAGUGGG---UAUAUGUGUGACACACAUGA
AAGU03009554.1/92378-92246 UUCCACAGCUACUGGUCUGCAACUGUCUUCA-UGGUAGCAGUUGCGGCAUUCC-UCUGUGGGAAAGAAA-CUGUU-ACGUGA--UUAAAC-ACCU-CUUUCUUAGCAAAACAGAAAGUGGG---CAUAUGUGUGACAGACAAGA
#=GC SS_cons               ::<<<<----------<<<<<<<<<______.______>>>>>>>>>------.--->>>>--------.-----.<<<<<-..------.-<<<.<<<<<<_________>>>>>>->>>...---->>>>>:::::::::::
#=GC RF                    UUCCACAGCUACUGGUCugcAacUGUUcUua.ugGUAGCAguUgcaGcAUUCC.UCUGUGGGAAAGaAA.cUGUU.ACacaa..UuaaAu.accc.CUuucuUAgCAAaacagaaAGUggg...uaUauguGUGACAgACAaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00404
#=GF ID   SNORA46
#=GF PI   snoACA46
#=GF DE   Small nucleolar RNA SNORA46
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   80.00
#=GF TC   81.20
#=GF NC   76.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300809;
#=GF DR   snoopy; Gallus_gallus300044;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA46 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA46
#=GF SQ   22


AJ609467.1/1-135             AGCACUAUA-UUUAAACCUGUGGAUGGGAAU-AUUCCCCAUUCUUGGUUACGCUGUAGUGCAAAA-GAAUU-CCU--GGCUC--U---CUG--U-----UGCACAGCUGAC-U-U-G-UGCCAUUCUGCUGUUGCUG-UAUAGAGUUAAGGAACAUGG
AC127300.3/152460-152595     AGCACUAUA-UUUAAACCUAUGUAUGGGAAA-UUUCCCCAUUCUUGGUUACGCUGUAGUGCAAAAAGAAUU-CCU--GGCUC--C---UUG--U-----AGCACAGCUGAC-U-G-A-UGCCAUUUUGCUGUUGCUU-UAUGGAGUUAAGGGACAUGA
BX005181.5/33577-33708       CAGAAGUUG-GGUAAGCC-AUGAAUGGGAAA-UUUCCUCAUUCUUGGUUACACUAUAGUUCGAAAAGAAUU-CCU--GGCUU--C---UUG--U-----UGCACAGCUGAC-U-C-A-UGCCAUUUUGCUG---CUU-CAUGGAGUUAAGGAACAUGA
AAPY01141093.1/1066-1200     AGCACUAUA-UUUAAGCCGAUGGAUGGGAAC-UUUCCCCAUUCUUGGUUACGCUGUAGUGCAAAA-GAAUU-CCU--GACUC--U---UUG--A-----UGCAUAGCUGAC-U-U-G-CACCAUUCUGCUGUUGCAU-UAUGGAGUUAAGGAACAUAU
AAFC03050240.1/112749-112887 AGCACUAUA-UUUAAACCUGUGAAUAGGAAU-UUUCCCUAUUCUUGGUUACGCUGUAGUGCAAAA-GAAUU-CCU--GGCUC--CUUUCUA--U-----UGCACAGCUGAC-U-UUG-UGCCAUUCUGCUGUUGCUG-UAUGGAGUUAAGGAACAUAA
AAQQ01133141.1/584-719       AGCACUAUA-UUUAAACCUGUGGAUGGGAAU-UUUCCCCAUUCUUGGUUACGCUGUAGUGCGAAA-UAAUU-CCU--GUCUC--U--UCUG--U-----UGCACAGCUGAC-U-U-G-UAUAAUUCUGCUGUUGCUU-UAUGGAGUUAAGGAACAUGA
AALT01542231.1/3490-3624     AGCACUAUA-UUUAAACCAAUGGAUGGGACU-CUUCCCCAUUCUUGGUUACGCUGUAGUGCAAAA-GAAUU-CCU--GGCUC--U---UCA--U------GCACAGCUGAC-U-U-UCUGCCAUUCUGCUGUUGCAA-UAUUGAGUUAAGGAACAUGU
AAYZ01235350.1/6405-6270     AGCACUAUA-UUUAAGCCUAUGGAUGAGAAU-UGUCCUCAUCAUUGGUUACGCUGUAGUGCAAGA-GAAUU-CCU--GGCUC--C---AUCUGC-----UGCACAGCUGAC-U-U-G-UGCAAUUCUGCUGUUGCUU--GUGGAGUUAAGGAACAUUG
AANG01072522.1/3049-3184     UGCACUAUUCUUUAAACCUGUGGAUGGGAAU-UUUCCCCAUUCUUGGUUACGCUGUAGUGCAAAA-GAAUU-CCU--GGCUC--U---UUCUCU-----UGCACAGCUGAC-C-----UGCCAUUCUGCUGUUGCUA-UGUAGAGUUAAGGAACAUAA
AANN01537316.1/4990-4853     CGCACUAUA-UUUAAACU-GUGGAUGGGAAU-CUUUACCAUUCUUAGUUACGCUGUAGUGCAAAAUAAUUU-CUUGAGGUUU--C---UUGUGU-----UGCACAGCUGAC-U-U---UGCCAAUCUGCUGUUGCUA-UAUGAAGUUAAGGAACAUAU
AAIY01027614.1/1771-1908     AGCACUAUA-UUUAAACCAAUGGAUGGACAU-UUUCCCCAUUCUCGGUUACGCUGUAGUGCUAAAGAAUUC-CCU--GGCUC--U---UCU--UCCCCAGGCACAGCUGAC-U------GCCAUUUGGCUGUUGCUU-UGUGGAGUGAAGGAACACAG
ABDC01219465.1/275-141       AGCACUAUA-UUUAAACCUGUGGAUGGGAAU-UUUCCCCAUUCUUGGU-ACGCUGUAGUGCAAAA-GAAUU-CCU--GGCUC--UA-UCUC--U-----UGCAAAGCUUAC-U-U-A-UACUAUACUGCUGUGGCUA-UAUGGAGUAAAGGA-CAUGA
AAPN01252044.1/34964-35098   AGCACUAUU-UUUAAACCUAUUGAUGGAAAA-CCUCACCAUCCUAGGUUACGCUAUGGUGCAAAAUAAUUU-CUU--GGCUC--U----CC--U-----AGCACAGCUGAC-U-G-U-U-CCUUUAUACUGAUGCUGUGGUGGAGUUAAAGAAACAUU
AAWR02027097.1/29868-29731   AGCACUAUG-UUUAAGCCUGUGGAUGGGAAU-UUUCCCCAUUCUUGGUUACGCUGUAGUGCAAAA-GAAUU-CCU--GGCUC--UU-UCUG--U-----UGCACAGCUGAC-U-UUG-UGCCAGUCUGCUGGUGCUG-UAUGGAGUUAAGGAACAUAA
AAKN02026933.1/5603-5736     AGCACUAUA-UUUAAACU-AUGGAUGGGAAU-UUUCCCCAUUCUUGGUUACGCUGUAGUGCAAAA-GAAUU-CCU--GGCUC--U---AUC--U-----UAAACAGCUGAC-U-U-G-UCUCAUUCUGCUGUUGCUU-UGUGGAGUUAAGGUACAGAA
AAHX01097108.1/12094-12228   AGCACUAUA-UUUAAACCUAUGGAUGGGAAA-UGUCCCCAUUCUAGGUUACGCUGUAGUGCGAGAAGAAUU-CCU--GGCGC--C---UCA--U-----UGCACAGCUGAC-U-C-G-CGCCGUUUGGCUGUUGCUC-UGUGA-GCUAAGGGACAUGA
AAGV020190570.1/2240-2378    AGCACUAUA-UUUAAACCUAUGGAUGGGAAU-UUUCCCCAUUCUUGGUUACGCUGUAGUGCAAAA-GAAUU-CCU-UGGCUC--UU-UCCA--U-----UGCACAGCUGAC-UAU-G-UGCCAUUCUGCUGUUGCUC-UUUGGAGUUAAGGAACACAA
EU240289.1/2-137             AGCACUAUU-UUUAAACCUGUUGGUGGAUUUUCCUGGCCAUCAUGGGUUACGCUGUAGUGCAAAA-GAAUCUCCU--GGCUC--U---UCA--G-----AGUAUAGUUGGC-C-----UUCUGUUUGGCUGAUGCUGCUCUGAAGCUAAGGGACAGAG
AAEX03001554.1/86031-86168   AGCACUAUA-UUUAAACCUGUGGAUGGGAAU-UUUCCCCAUUCUUGGUUACGCUGUAGUGCAAAA-GAAUU-CCU--GGCUC--U---UUA--UG---CUGCACAGCUGACAU-U-G-UGCCAUUCUGCUGUUGCUG-AAUAGAGUUAAGGAACAUAA
AAGW02052877.1/31618-31482   AGCACUAUA-UUUAAACCUAUGGAUGAGAAU-UUUCCUCAUUCUUGGUUACGCUGUAGUGCAAAA-GAAAA-CCU--GGCUC--CA-UCUG--U-----UGCACAGCUUAC-U-U-G-UACCAUUCUGCUGUUGCUU-AAUGGAGUUAAGGAACAUUG
AAQR03000194.1/7481-7350     AGCACUAUA-UUUAAGCCUAUGGACAGGAAU-CUUCCCCAUUCUUGGUUACACUGUGAAGCAAAA-GAAUU-CCU--GGUUU--U---CUC--U-----UGCACAGCUGAC-U-U-G-UACCAUUCUGGUG---UUC-AAUGGAGUUAAGGAGCUUUA
AAGU03065931.1/25350-25212   AGCACUAUA-UUUAAACCAAUGAAUGGAAAU-UUUCCCCGUUCUUGGUUACGCUGUAGUGCUAAA-GAAUU-CCU-UGGCUCUUC---CUC--U-----UGCACAGCUGAC-U-CUG-UGCCAUUCUGCUGUUGCUG-UAUGGAGUUAAGGAACAUAA
#=GC SS_cons                 :<<<<<<<<.----<<<<---<<<<<<<___.____>>>>>>>-->>>>---->>>>>>>>----.---<<.<<<..<<<<<..<...-<<..-.....-<<<<<<<-<<_._._._.______>>->>>>->>>--.>>->>>>>>->>>>>:::::
#=GC RF                      AGCaCuaua.UUUAAaCCuaUggauGGgAAu.uuUccCCauccUuGGuUACGCuguaGuGCaAAA.gAAuu.CCU..ggCUc..c...uuc..U.....uGcacAGCUgaC.U.u.g.UgCcAUucuGCUguugCUu.gaUggAGuuAAGGaaCAuaa
//
# STOCKHOLM 1.0

#=GF AC   RF00405
#=GF ID   SNORA44
#=GF PI   snoACA44
#=GF DE   Small nucleolar RNA SNORA44
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   55.00
#=GF TC   56.20
#=GF NC   52.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00036
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300045;
#=GF DR   snoopy; Echinops_telfairi300333;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   ACA44 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1]. The family also contains
#=GF CC   the mouse snoRNA sequence MBI-64 described in [2].
#=GF WK   Small_nucleolar_RNA_SNORA44
#=GF SQ   27


AF357394.1/1-116           ---------------AAGGGCUGUGGCU-GCCUGUAG---CCAUGGGAUCUCCAACUGCAUGCCAGAGUAA--UGGAGAGACUUUGACAGCUCAGGUCAGCACAGUGC----CUGCA-GCUGCCACUCAUCUUUCCUAUAUA-
AL929577.9/131453-131576   UAGCA-UAUU---CCAGGGGCUGUGGCU-GCUUGUAG---CCAUGGGAUCUCCAAGCGCCUGCCAGAGCAA--UGGAGAGACU--GGCAGCCCAGGUCAGCACAGGGC----CUGCA-GCGGCCACUCAGCUUUCCUAUAG--
AC140395.2/70817-70690     AAGCA-UGUU--UCCAAGGGCUGUGGCU-GCUUGUAG---CCAAGGGAUCUUCAAAUGCAUGCCAGAGUAA--UGGAGAGACUUUGACAGUGCAGGUCAGCACAAAGC----CUGCA-GCUACCACUCAGCUUUCCUGUAUA-
AL606832.4/24041-23913     CAGCG-UGUU--UCCAAGGGCCUUGGCU-GGCUGUGG---CCAUGGGAUCUCCAGCUGUAGACCAGAGUAAC-UGGAGA-ACUUGGACAGCCCAGGUCAGCACAGUGC----CUGCA-GCUGCCACUUAGCUUUCCUAUAAUG
AL844536.13/202595-202468  GGGGGGUGUU--UCCAGGGGCGGUGGCU-GCUUGUAG---CCAUGGGAUCUCCAACUGCAUGCCAGAGUAA--UGGGGAGGCUUUGACAGCCCAGGUCAUCACAGUGC----CUGCA-GCUGCCACUCAGCUU--CUGUAUAG
AJ609466.1/1-132           CAGCA-UGUU--UCCAAGGGCUGUGGCU-GGUCAUAG---CCAUGGGAUCUCCAACUGCAUGCAAGAGCAACCUGGAAAGACUUUGACAGCGCAGGUCAGUACAAUAC----CUGCAAGCUGCCACUCAGCUUUCCUAUAAUG
AAQQ01591275.1/780-909     CAGCA-UGUU--UCCAAGGGCUGUGGCU-GGUUGUGG---CCAUGGGAUCUCCAACUGCAUGCAAGAACAAC-UGGAGAGACUUUGACAGCUCAGGUCAGCACAAUAC----CUGCA-GCUGCCACUCACCUUUCCUAUAAAG
AANG01797529.1/2747-2617   CAGCA-UGUU--UCCAAGGGCUGUGGCC-GGUUGUGG---CCAUGGGAUCUCCAACUGCAUGCGAGAGCAACCUGGAGAGACUUUGACAGCACAGGUCAACAUAAUAC----CUGCA-GCUGCCACUCGCCUUUCCUAUAAAC
AAFC03094460.1/588-718     CAGCA-UGUU--UCCAAGGGCUGUGGCU-UGUUGUGG---CCAUGGGAUCUCCAACUGCAUGCGAGAGCAACGUGGAGAGACUUUGACAGCACAGGUCAGCGUAAUAC----CUGCA-GCUGCCACUCGCCUUUCCUAUAAUU
AANN01350357.1/608-478     CAGCA-UGUU--CCCAAGGUUUAUGGCU-GGUGGUAG---CCAUGGGAUCUCCAACUGCAUGCAAGAAUAACCUGGAGAGACUUUGACAGCACAGGUCAGCAUAAUAC----CUGUA-GCUGCCACUCAACUUUCCUAUAUUU
AAYZ01245008.1/3131-3002   CAGCA-UGUU--UCCAAGGGCUGUGGCU-GGCUGUAG---CCAUGGGAUCUCCAACUGCAUGCGAGAGCAACCUGGAGGGCCUUUGACAGCGCAGGCCAGCCC-GUGC----CUGCA-GCUGCCACUCAGCUUUCCGAUAGUU
ABDC01345381.1/612-482     CAGCA-UGUU--CCCAAGGCCUGUGGCU-GGUUGUGG---CCACGGGGUCUCCAACUGCAUGCGAGAACAACCUGGAGAGACUUUGACAGCUCGGGUCAGCACAAUAC----CUGCA-GCUGCCACUCGCCUUUCCUAUAAUC
AALT01584320.1/6707-6579   AAGCA-UGUU--UCCAAGGUCUGUGGCU-GAUAGUGU---CCACGGUAUCUCCAACUGCAUGCGAGAGCAACCUGGAGAGACUUUGACAGCACAGGUCAC--CAGUAC----CUGCA-GCUGCCACUCGACUUUCCUAUAAAC
AAPY01100952.1/1824-1953   CAGCA-UGUU--UCCAAGGGCUGUGGUU-GCUGGUGG---CCACGAGUUCUCCAACUGCAUGCGAGAGCAACGUGGAGGGACUUUGACAGCCCGGGUCACACC-GCAC----CUGCA-GCUGCCACUCGCCUUUCCUAUAAAC
AAIY01102179.1/767-638     GAGCA-UGUU--CCCAAGGUCCGUGGCU-UG-UGUGG---CCAUCUGAUCUCCAACUGCACGCAAGAGCAACUUGGGGAGACUGUGACAGCUCAGGUCAGCAAAGGCU----CUGCA-GCUGCUACUCACCUUCCCUAUAAAA
AAFR03060642.1/26562-26433 CAGCA-UGGC--UUCAAGGGCUGUGGCU-UGAAGUAG---CUACAGGGUCUCCAACUACAUGCGAGAACAUGCUGGAAAGACUUUGACAGCUCUGGUCACCUC-GUAU----CUGAA-GCUGCCACUCAACUUUCCUAUAUUC
AAPN01440676.1/3439-3306   CGGCA-UGUU-CUUCAAGGGCCGAGGCU-GGACGCAGUAGCCUCGGCGUCUCCAACUGCAUGCCACAACAGCCUGGAGAGACUUUGACAGCGCAGAGCCUGCC-GUGC----CUGGU-GCUGCCACUCGGCUCUCCCACAGUU
AAWR02028293.1/8543-8673   CAGCA-UGUU--UCCAAGGGCUGUGGCU-GGUUGUAG---CCAUGGGAUCUCCAACUGCAUGCAAGAACAACCUGGAGAGACUUUGACAGCUCAGGUCACCAUAAUAC----CUGCA-GCUGCCACUCGCCUUUCCUAUAACA
AAHX01064261.1/8700-8828   AAGCA-UGUU--UCCAAGGGCUGUGGCU-GCUCAUAG---CCAUGGGAUCUCCAACUGCAUGCCAGAGUAA--CGGAGAGACUUUGACAGCCCAGGUUAUCACAGUGC----CUGCU-GUUGCCACUCAGCUCUCCUAUAUGU
AAGV020164015.1/236-106    CAGCA-UGUU--CCCAAGAUCUCUGGUU-GCUUGUGG---CCAAGGGAUCUCCAACUGCAUGCGAGAGCAACCUGGAGAGACUUUAACAGCUCAGGUCAGCGGAGUAC----CUGCA-GCUGCCACUCAACUUUCCUAUAAUG
AAKN02028628.1/53104-53233 CAGCA-UGUU--UCCAAGGGCUGUGGCU-GG-UGUAG---CCAUGGGAUCUCCAACUGCAUGCGAGAGCAACCUGGAGAGACUUUGACAGCUCAGGUCAACCCAAUAC----CUGUG-GCUGCCACUCACCUUUCCUAUAAGG
EU240303.1/1-129           CUGCA-UGUUAAUCCAAGAGCUGUGGCUCUGACGUAG---CUGCAGG-UCUCCAACAACAUGCAAGAGCAAC-GGGAAGGUCUUUGACUGCUC-GGCCUCUU--CUGC----CUGUU-GCUGUCACUCACCCCUCCUAUAUAU
FQ217911.1/370-498         AAGCA-UGUU--UCCAAGGGCUGUGGCU-GCUCAUAG---CCAUGGGAUCUCCAACUGCAUGCCAGAGUAA--CGGAGAGACUUUGACAGCCCAGGUUAUCACAGUGC----CUGCU-GUUGCCACUCAGCUCUCCUAUAUGU
AAGW02062791.1/16032-16162 CAGCA-UGUU--UCCAAGGGCUGUGGCU-GGCUGUGG---CCAUGGGAUCUCCAACUGCAUGCGAGAGCAACCUGGAGAGACUUUGACAGCUCAGGUCAGCACCGUAC----CUGCA-GCUGCCACUCAACUUUCCGAUAAUU
AAQR03114580.1/3775-3904   CAGCA-UUCU--UCCACGAGCUGUGGCU-GCCUGCAG---CUACGGGAUCUCCAUCUGCAUG-GAGAGCAAUCGGGGGACACUUCCACAGCUCAAGUCAGCACAAAGC----CUGCA-GCUGCCAUUCGCCUUUCCUAUAACG
AAPE02033931.1/62499-62628 CAGCA-UGUU--CCCAAGGGCUGUGGCU-GG-UGUAG---CCAUGGGCUCUCCAACUGCAUGCGAGAGCAACCUGGAGAGACUUUGACAGCUCAGGUCAGCAUAGUAC----CUGCA-GCUGCCACUCGCCUUUCCUAUAUCU
AAEX03008401.1/10114-10247 CAGCA-UAUU--UCCAAGGGCUAUGGCC-AGCUGUGG---CCAUGGGAUCUCCAACUGCAUGCGAGAGCAACCCAAAGACACUUUGACAGCACA-GAUAGCAUAAAGCCUACGUGCA-GCUGCCACGCACCUUUCCUAGAACU
#=GC SS_cons               :::::.::::..:<<---<<<<<<<___.___>>>>>...>>-->>----------------------------<<<<<<---------<<-<<<<___________>....>>>--.--->>------->>>>>>:::::::
#=GC RF                    cAGCA.UGUU..UcCAAGGGCugugGCU.ggucgcaG...CCAuGgGAUCUCCAACUGCAUGCaAGAGcAAccuGGagaGACUUUGACAGCuCaGGuCAgcacAgugC....CuGcA.GCUGCCACUCAaCucuCCUAUAauu
//
# STOCKHOLM 1.0

#=GF AC   RF00406
#=GF ID   SNORA42
#=GF PI   snoACA42
#=GF DE   Small nucleolar RNA SNORA42/SNORA80 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:1637349
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   70.00
#=GF NC   69.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; ACA42;
#=GF DR   snoRNABase; ACA67;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300467;
#=GF DR   snoopy; Homo_sapiens300588;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   16373490
#=GF RT   A computational screen for mammalian pseudouridylation guide H/ACA RNAs.
#=GF RA   Schattner P, Barberan-Soler S, Lowe TM
#=GF RL   RNA. 2006;12:15-25.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the H/ACA class of snoRNAs that guide
#=GF CC   the sites of modification of uridines to pseudouridines [1]. Human ACA42
#=GF CC   (SNORA42) was cloned from HeLa cells by immunoprecipitation with anti-GAR1
#=GF CC   antibody [1]. Its is predicted to guide the pseudouridylation of residues
#=GF CC   U109 and U572 of 18S rRNA [3]. ACA42 shares the same host gene with ACA26,
#=GF CC   ACA46, ACA50 [1]. This family also includes mammalian snoRNA ACA67
#=GF CC   (SNORA80) which was identified by computational screening and its
#=GF CC   expression in mouse experimentally verified by Northern blot and primer
#=GF CC   extension analysis [2]. ACA67 is proposed to guide the pseudouridylation
#=GF CC   of the same 18S rRNA residues as ACA42 [3].
#=GF WK   Small_nucleolar_RNA_SNORA42
#=GF SQ   21


AC005995.3/26676-26542    GCAUGGGUUUGGA-UUAUGACAGGC--CCAUCCCCCUGGACCUCUCAUAGU-GCCCCAUGCCAGAGCAAACUGUGGCCCCGAACCAUUGCCUGGCUUCUGUACCCGUGGGCCACUGGCACUGAAGAGGGUUACACAGUG
AC101774.6/57905-57781    GCAUGGAUUUGGAUUUAUGGCAGGC--UCAUCUCCCUGGGCCUCUCAUAGU-GUCCCAUGCUAGAGCAAAUUGUGGCUCCUAACCAUUGCCC------AGCCUCCGU-----GCUGGCACUGAAAUGGGUCACACUGUG
AC107774.8/124931-124798  GCAUUAGUUUGGAUUUAUGGCAGGC--CCCUUUCCCUGGGCCUCUCAUAGU-GUUCUGUGCUAGAGCAGCUCUUGGCUCUGAACCAUUGCCUGGCCUG--UGUCUGUAGGCUGCUGGCACUGAAGUGGGUCACACAAUA
AC110037.13/145188-145321 GCAUGGGUUUGGAUUUAUGGCAGGC--CCGUUCCCCUGGGUCUGUCAUAGU-GUCCCGUGCUAGAGCAACCCGUGGCCCCGAACCAUUGCCUGGCCUC--UGCCUGUAGGCUGCUGGCACUGAAGUGGGUCGCACAGAA
AC116348.3/101703-101837  GCAUGGGUUUGGAUUUAUGAUGGGC--UGGAUUCCCUAGGCCUCUCAUAGU-ACCCCAUGCCAGAGCAAACUGUAGCCCC-AACCAUUGCCGGGCCUCUAUGCCUGUAGGCUGCUGGCACUGAAGUGGGUUGCACAGUA
AC116478.14/139669-139534 GCAUGGAUUUGGAUUUAUGGCAGGC--UAGUCCCCAUGGGCCUCUCAUAGU-GUCCCAUGCUAGAGCAAACUGUGGCUCCUAACCAUUGCCCAGCCUCCAUGCCUAUAGGCUACAGGCACUGAAGUACGUCACACAGUG
AC117251.3/19321-19187    GCAUAGAUUUGGA-CUAUGGCAGGC--UCCUCCCCAUGGGCUUCUCAUAGU-GUCUCAUGCUAGAGCAAACUGUUGCUCCUAACCAUUGUCCAGCCUCAGUCCCUGUAGGCUGCUGGCCCUGAAGUGGGUCACACAGUA
AC124097.6/136688-136555  GCAUGGGUUUGGAUUUAUGACAGGC--CCGUUCCCCUGGGCCUCUCAUAGU-GUCCCAUGCUAGAGCAAUCCAUGGCCCCAAACCAUUGCCUGGCCUG--UGUCUGUAGGCUGCUGACAGUGAAGUGGGCCACAAAGUU
AC137644.3/51929-52064    GGAUUAACCACGAUAAACGAGGGACAACUGUACCCCUGGGUCUCUACUAGU-GUCCCAUGCCAGAGCAGACUGUGGCCUUGAACCAUUGCCUGGUCUC--UGCCUGUAGGCUGCAGGCACUGAAGUGAGUUGUACAGUG
AC150887.4/108298-108162  GCAUGGUAAUGAAUUUAUGGCAGGU--CCUCCUCUGUGGGCCUCUCAUAGUGUACCCAUGCCAGAGUAAAUUGCAGCCUCGAACCAUUACCCAGCCUCCUUACUUGUGGGCUGUGAGCACUGAAGGGGGUUGUACAAUG
AC157481.2/3500-3365      GCAUGGGUUUGGAUUUAUGAUGGGC--CCGUCCCCCUGGACCUCUCAUAGU-ACCCCAUGCCAGAGCAAACUGUAGCCCGGAACCAUUGCCUGGCCUCUGUGCCCGUAGGCUGCUGGCACUGAAGUGGGUUGCACAAUA
AC158518.2/47302-47437    GUAAGUCAUUGGAUUGAUGGCAGGC--UCGUCCCCCUGGGCCUCUCAUAGU-GUCCCAUGCUAGAGCAAAUUGUGGCUCCUAACCAUGACCUGGCCUCCGUGCCUGUAGGUGGCUGGCACUGAAGUGGGUCACACAGUG
AC163651.2/112415-112550  GCAUGGAUUUGGAUUUAUGGCAGGC--UCUUCCCCGUGGGCCUCUCAUAGU-GUCCCAUGCUAGAGCAAAUUGUGGCUCCUAACCAUUGCCCAGCCUCCGUGCCUGUAGGCUGCAGGCACUGAAGUGGGUCACACAACG
AJ609465.1/1-134          ---UGGUAAUGGAUUUAUGGUGGGU--CCUUCUCUGUGGGCCUCUCAUAGUGUACCCAUGCCAUAGCAAAUGGCAGCCUCGAACCAUUGCCCAGUCCCCUUACCUGUGGGCUGUGAGCACUGAAGGGGGUUGCACAGUG
AL592436.7/80211-80078    GCAUGGUAGUGGGUUCAUUGGGGGC--CCUUCUCUGUGGGCCUC--AUAGCGUACCCAUGCCAGUGUAAACUUGAGCCUUGAACCAUUGCCCAGCCUC-CUUCCCAUGGGCUGUGUGUAGCGAAGGGGGUUGCACAGUG
AL954208.1/3730-3595      GCAUGGGUUUGGAUUUAUGAUGGGC--CCGUCCCCCUGGACCUCUCAUAGU-ACCCCAUGCCAGAGCAAACUGUAGCCCCGAACCAUUGCCUGGCCUCUGUGCCCGUAGGCUGCUGGCACUGAAGUGGGUUGCACAAUA
AP000033.1/31795-31930    GCAUGGGUUUGGAUUUAUGAUGGGC--CCGUCCCCCUGGACCUCUCAUAGU-ACCCCAUGCCAGAGCAAACUGUAGCCCUGAACCAUUGCCUGGCCUCUGUUCCCGUAGGCUGCUGGCACUGAAGUGGGUUGCACAAUA
AY841870.1/3444-3579      GCAUGGGUUUGGAUUUAUGACAGGC--CCGUCACCCUGGGCCUGUCAUAGU-ACCCCAUGCCAGAGCAAACUGUGUCCCCGAACCAUUGCCUGGCCUCUGUGCCCGUAGGCUGCUGGCACUGAAGUGGGUUGCACAGUG
J03733.1/1705-1840        GCAUGGAUUUGGAUUUAUGGCAGGC--UCUUCCCCGUGGGCCUCUCAUAGU-GUCCCAUGCUAGAGCAAAUUGUGGCUCCUAACCAUUGCCCAGCCUCCGUGCCUGUAGGCUGCAGGCACUGAAGUGGGUCACACAAUG
U36394.1/2953-3082        GCAUGGGUUUGGAUUUAUGGCAGGC--UCGUCCCCCUGGGCCUCUCAUAGU-GUCCCAUGCCAGAGUAAAUC-CGGCCC-GAACCAUUGC-CUGCCUC--UGGCAGUAGGCUGCA-GGACUGAAGUGGGUUGCAGAGUG
X07944.1/2336-2468        GCAUGGAUUUGGAUUUAUGACAGGC--UCAUCCCCGUGG-CCUCUCAUAGU-GUCCCGUGCUAGAGCAAAC--UGGCUCCUAACCAUUGCCCAGCCUUGGUGCAUGUAGGCUGCUGGCACUGAAGUGGGUCACACAAUG
#=GC SS_cons              <<<<<<<<------<<<<<<-<<<<..<_________>>->>>->>>>>>-.>>>>->>>>------------<<<<<<-----<<---<<<<<<<<__________>>>>>>-->>--->>---->>>>>>:::::::
#=GC RF                   GCAuGggcuUGGAUuuAuGacaGGC..ccgUccCCcUgGGCCuCuCaUagU.gccCCaUGCuAGAGCAAAcugcggCcccgAACCaUUGCccgGCCucugUgcCuGUaGGCcgCugGCACuGAAGuggGucgCACAgUg
//
# STOCKHOLM 1.0

#=GF AC   RF00407
#=GF ID   SNORA50
#=GF PI   snoACA50
#=GF DE   Small nucleolar RNA SNORA50
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   90.00
#=GF TC   90.20
#=GF NC   89.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00034
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Gallus_gallus300045;
#=GF DR   snoopy; Rattus_norvegicus300977;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA50 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA50
#=GF SQ   14


AC010287.9/54576-54441       AAGCACUGCCUUUGAACC--UGAUGUGUCUUGUUUGUAGCUUCACGGGCCAAGCAACAGUGCUAGAGCAUAA---CGACUUGUU-AUAACUGGGGCUCUUCAG--CUCUCAA-CUGAACUGCUCUUUUAAAAACAAGGUACAUUU
AJ609468.1/1-136             AAGCACUGCCUUUGAACC--UGAUGUGUCUUGUUUGUAGCUUCACGGGCCAAGCAACAGUGCUAGAGCAUAA---CGACUUGUU-AUAACUGGGGCUCUUCAG--CUCUCAA-CUGAACUGCUCUUUUAAAAACAAGGUACAUUU
AC127300.3/141571-141705     AAGCACUGCCUUUGAAUC--UGAUGUGUCUUGUUUGUAGCUUCACGGGCCAAGCAACAGUACUAGAGCAUAA---GGACUUGUU-AUAACUGGG-CUCUUCAG--CUCGCAA-CUGAACUGCUCUUUUAAAAACAAGGUACAUUU
AAIY01789533.1/679-813       AAGCACUGCCUUUGAACC--UGAUGUGUCUAGUUUGUAGCUUUACAGGCCGAGCAACAUUGCUAGAGCAUAA---GGACUUGUU-AUAACUGGG-CUCUUCAG--CUCCCAA-CUGAACUGCUCUUGUAAAAACAAGGUACAUUU
AAFR03049113.1/29769-29632   AAGCACUGCCUUUGAACC--UGAUAUGUCUUGUUUGUAGCUUCUCAGGCCAAGCAACAGUGCUAGACCAUAUU-UGGACUUGUU-AUAACUGGGGCUCUUCAG--GUUCAAA-CUGAAUUGUUCCUUUAAAAACAAGGUACAUUG
BAAF04042401.1/3300-3437     CUGCACUGUCUUUGAACC--UCGUUGGUCUUGUCUGUGACCAUUUUGGCCAAGCAACAGUGCUAAAUCAAAC---UGCUUGUUC-AUAACUGGAGCUUCUUAGAAAAAACAG-CUAAGUUGCUCUUUUAAAAGCAAGUUACAACU
CAAE01015006.1/194471-194610 CAGCACUGUCUUUGAACC--UGACUGGUCCCAUCAGUGACCUCUCAGGCCAAGCUACAGUGCUAAAUGAAACU-UGGACUUGUUCAUAACUGGGGCAACCUGG-CAACAAUC-CCAAGUUGCUCUUUUAAAAGCAAGUCAUAGCU
AANH01005120.1/104420-104557 CUGCACAGCUUUUAAACC--UUGUUGGUCUCGCCUGUGACCUCUUAGGCCAAGCUACGUUGCUAAAGCAUUG--CAGCCUUGUUCAUAACUGGAGCCUCCUGG--AAACCCC-CCAGUUAGCUCUUUUAAAUGCAAGUCACAGUU
CR392029.12/79956-80090      AAGCACUGUCUUUGAACC--UGUGUAGCC-CAUCCAUGGCUCAGCGGGCCAAGCAACAGUGCAACAGUAAA-----GGGUUGUU-AUAACUGGAGCCCCUUGG-CUUUUCUUCCCAAGUUGCUCUUUUAAAAGCAACCUACAAAU
AAHX01097108.1/1222-1342     GAGCGCUGCCUUUGAAUC--UGAU--GUCUUACUUGUAGCUCAAG-GGCCAGGCAACAGUGCUAGAGGAAAG---------------AACUGGG-CUCUUCAG--CGCUCAG-CUGAGCUGCUCUUUUACAAACAAGGUCCAUUU
AAGV020190566.1/334-468      AAGCACUGCCUUUGAAUC--UAAUAUGUCUUGUUUGUAGCUUCUC-AGCCAAGCAACAGUACUAGAGCAUAA---GGACUUGUU-AUAACUGGGGCUCCUCAG--CUCUCAG-CUGAACUGCAGUUUUAAAAAUGAGGUGCAUUU
FJ915991.1/1-135             ACGCGCUGUCUUUGAGCCCCCGCCGAGCCU-CCUCGUGGCGCCGGGGGUCAAUCUGCAGCGCUAGAGCAUGU---G--CUUGCGCAUAACUGGGGCCGCUUGG---CCCCCC-GCGGGCGGCCCUUUUAACCGCGAGCGACAAUU
AAWZ02035002.1/26495-26631   CAGCACUGUCUUUGAACC--UGACGUGUCU--UCUGUAGCUUCUCGGGCCAAGCCACAGUGCUAGAUUACGACCAGUCCUUGUU-AUAGCUGGGGAACUUCAG--UUCUGAA-CUGAAAUGCUCCUUUAAAAACAAGGCACAUCU
CAAB02001937.1/405569-405708 CUGCACUGUCUUUGAACC--UGACCGGUCCUGUCGGUGACCUCUUAGGCCAAGCGACAGUGCUACAUGAAAUC-CAAACUUGUUCAUAACUGGGGCAACCUGA-CAACAAUC-UCAUGUUGCUCUUUUAAAAGCAAGUCACAUCU
#=GC SS_cons                 :<<<<<<<__________..____________________________________>>>>>>>---------...---<<<<<<.------<<<-<--<<<<<.._______.>>>>>-->->>>------>>>>>>::::::::
#=GC RF                      aaGCaCUGuCUUUGAACC..UgauuuGUCUugUuuGUagCuucucaGGCCAAGCaACAGuGCuAgAgcAuaa...gGacUuGuu.AUAACUgGgGCuccucgG..aucucaa.CcgaguUGCcCuUUUAAAaaCaAguuACAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF00408
#=GF ID   SNORA1
#=GF PI   snoACA1
#=GF DE   Small nucleolar RNA SNORA1
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   70.00
#=GF TC   70.10
#=GF NC   69.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300098;
#=GF DR   snoopy; Homo_sapiens300007;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA1 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA1
#=GF SQ   29


AJ609425.1/1-130           UGCCUCAUUCUAGA--------GAAUGGGCACUGUUG-A---UCAUG-GUGUC-CA-AAAAUAGUUAAUGUGGCUAAAUUGAG---ACAGGUUAUGCUUCCAU-CACAGUA-UGCAUA--UUGCAGUGGUGACAAUGAGACCUGUAACAUUU
AC018607.12/34735-34867    AGCCUCAUGCUAGA-----UGAGAAUGGGCACUGUUG-A---UCAAG-GUGUC-CA-AAAAUAGUUAAUGUGGCUAAAUUGAG---AUAGGUUAUGCUUCCAU-CACAGUA-UGCAUA--UUGCAGUGGUGACAAUGAGACCUGUAACAUUU
AC023271.11/39009-38876    AGCCUCAUUCUAGA-----UGAGAAUGGGUACUGCUG-A---UCAUG-GUGUC-CA-AAAAAC-UUUAUGUGGCUAAAUUGAGAC-ACAGGCUAUGCUUCCAU-CACAGUA-CACAUA--UUGCAGUGGUGACAAUGAAACCUGUAACAUUU
AC004125.1/88446-88314     AGCCUCUUUCUAGA-----UGAGAAUGGGCACUGUCG-A---UCAUG-GUGUC-UG-AAAAU--UGUAAGUGGCUAAAUUGAAAC-ACAGGUUAUGCUUCCAU-AAGAGUA-UAUGUA--UUGCAGUGGUGACAAUGAGACCUGUAACACUU
AJ236935.1/1104-969        AGCCUCAUUCUAGA-----UGAAAGUGGGCACUGUUG-U---CUGUG-GUGUC-CA-AAAAUCAUUAAUGUGGCUACAUUGAGAAUACAGGUUUUGCUUCCAU-CACAGUA-AUCUUA--UUACAGUGGUGACAAUGACACCUGUGACAUUU
AC023950.6/158570-158435   UGCCCCAUUCUCAA-----AGAGAAUAGGCACUGUUG-A---UCAUG-CGAUC-CA-GAGAUUGUUAAUGGGGCUGCAUUGAGAA-ACAAGCUAUGUUUCCAUUCACAGCA-AACACA--UCGCAGUGGUGACAAUGAGACCUGUAACAUUU
AANU01130859.1/10090-10225 UGCCUCAUUCUAGA-----UGAGAAUGGGCACUGCUG-AUCAUCAUG-GUGUC-CA-AAAAUAGUUAAUGUGGCUAAAUUGAG---ACAGGUUAUGCUUCCAU-CACAGUA-UGCAUA--UUGCAGUGGUGACAAUGAGACCUGUAACAUUU
AACN010072016.1/1597-1463  AGCCUCAUUCUAGA-----UGGUAAUGGGCACUGUCC-U---UCAUG-GUGUC-CA-GAAAUUGUUAAUGUGGCUACAUUGAGAC-ACAGGUUAUGCUUCCAU-CACAGUA-AGUUUA--UUGCUGUGGUGACAAUGAGGCCUGUAACAUUU
ABDC01191151.1/2216-2086   AGCCUCAUUCUAGA-----UGAGAAUGGACAC--UUG-A---UCAUA-GUGUC-CA-AAAAUUGUUGAUGUGGCUAAAUUGAC---ACAGGUUAUGCUUCCAU-CACAGUA-CAUGUA--UUACAGUGGUGACAAUGAGACCUGUAACAUUU
AAPY01155118.1/1908-2039   AGCCUCAUUCUAGU-----UUCAAUUGGACACUGUGG-A---UCA---GUGUC-CA--AAAUUGUUAAUGUGGCUAAAUUGAGAC-ACAGGCUAUGCUUCCAU-CACAGUA-AACGUA--UUACAGUGGUGACAAUGAGACCUGUAACAUUU
AC154296.2/158134-158266   AGCCUCAUUGUACA-----UAAGAAUGGGCAUUGUUG-G---UCA---UUGUC-CA-GAACUGGUCGAUGUGGCUAAAUUGAGAU-ACAGGUCAUGCUUCCAU-CACAGCA-GAUACA--UUACAGUGGUGACAAUGAGACCUGUAACAUUU
AAFC03070145.1/76783-76650 AGCCUCAUUCUAC------UGAAAAUGGGCAC--UUG-U---UCAUG-GUGUC-CAUAAAACUGUUAAUGUGGCUACAUUGAGAACACAGGUUUUGCUUCCAU-CACUGUA-AUUUUA--UUGCAGUGGUGACAAUGAGACCUGUAACAUUU
AAQQ01510166.1/907-1037    ACCCUCAUUCUAGA-----UGAGAAUAGGCACUGUGG-A---UUA---GUGUC-UA-AAAUUGGUCAGUGUGGCUAAAUUGAC---ACAGUUUAUGCUUCUAU-CACAGUA-UAUGUA--UUGCAGUGGUGACAAUGAGACCUGUAACAUUU
AANG01161430.1/3973-4107   AGCCUCAUUCUAGA-----UGGAAAUAAGUACUACCA-U---UCAUG-GUGUC-CA-GAAAUUGUUAACGUGGCUACAAUAAGAC-ACAGGUUAUGCUUCCAU-UGCAGCA-AGUUGA--UUGCAGUGGUGACAUUGAGAACUGUAACAUUU
AANN01814642.1/5758-5885   AGCCUCAUUCUAGA-----UAAAAAUGGGCACUGUUG-A---UUUAG-GUGUU-CA-GAAA---UAGAUGUGGCUACAUUGAU---ACAGGUUAAGCUUCCAC-CACAGCA-UC--UA--UUGCAUUGGUGACAAUGAGGCCUGCAACAUGU
AAIY01662003.1/6599-6729   AGCCUCAGUCUG-------UGAAAGUGGGCACAGCUG-A---UCACG-GUGUC-CA-GACAAG-CAGUUGUGGCUGAAAGGAU-G-ACAGGUUUUGCUUCCAC-CACUGUG-GGUUAA--UUUCAGUGGUGACAAUGAGACCUGUAACACUU
AAFR03025134.1/20790-20920 UGCCAUAUUUCUAA-----UGAUCAUGAGCACACUUGGA---AGUUU-GUGUU-CA-GAAU---AUAAUGUGGCUAUAAUAAAAG-ACAGGUUUUGCUUCCAU-CAC--UA-AAGUUU--UGUUAGUGGUGACAAUGAGACCUGUAACAAUC
AAPN01307029.1/38316-38181 UGCCCCAUUCCAAA-----UAUUCAUGGACACAGUUC-A---UGUUU-GUGUCACA-UGGA---ACAAUGUGGCUACAGUGAAAGCACAGGUUUUGCUUCCAU-CACAGUA-AAAAUAAGUUACUCUGGUGACAAUGAGACCUGUAACAGGA
AAYZ01116994.1/4345-4471   AGUGGCGU------------GAGAAUGAACGCUGCGA-A---UCAUG-GUGUC-CA--ACAUAGCCAGUGUGGCUGAAUGGAGCU-GCAGGAUAUGCGUCCAU-CACAGUA-AAUGAA--UGGCAGUGGUGACAAUGAGGCCUGUAGCAUUU
AALT01217367.1/895-1025    GGCCUCAUUCCAUG-----UGCAUGUGGGCCCAGCUG-A---CCCUG-GUGUC-CA-GAGG---GAAAUGUGACCACAUUGAC-C-ACAGGUCAUGCUUCCAU-CAUAGCA-GGCUCG--UUGCUGUGGUGACAAUGGGACCUGUGACAGGU
AAKN02056731.1/45032-45162 UGCCUCAUUCUAGA-----UUAGAAUGGGCACUGUUG-A---U--UG-GUGUC-CA-AAACUGGUCAAUGUGGCUGAAAUUGU-C-ACAGGUCAUGCUUCCAU-CACAGUA-AAUGU---UUACAGUAGUGACAAAGAGACCUGUAACAUCU
AAGV020161067.1/1151-1281  AGCCUCAUUCCU-------UGAGCAUGGGCACAGUUU-A---UCAUG-GUGUC-CA-AAAUUGAUAAAUGUGGCUAAAUUGAG---ACAGGUUAUGCUUCCAU-CACAGUA-AAUUUA--UUGCAGUGGUGACAAUGAGACCUGUAACAUUU
AAWR02017934.1/95430-95564 GGCCUCAUUUUAGA-----UGAAAAUGGGCACUCUUA-U---UCAUG-GUGUC-CA-GAAAUUGUUAAUGUGGCUAUAUUGAGAC-ACAGGUUAUGCUUCCAU-CACAGUA-CGUGUA--UUACAGUGGUGACAAUGAGACCUGUAACAUUA
EU240223.1/2-133           UGCCUUGUUAUUCA-----GCAGGUAGACACAACUC-------CAUG-UGUGU-CU-CAAUUGAACAACGGGGCUAGAA-GAGCA-ACAGGUUGUGCUUUCCU-CACUGUAACACCCA--UUGCAGUGGUGACAAUGAGACCUGUGACAGGU
AADN03001015.1/68879-68748 CGCCUUGUUAUUCA-----GCAGGUAGACACAACUC-------CAUG-UGUGU-CU-CAAUUGAAGAACGGGGCUAGAA-GAGCA-ACAGGUUGUGCUUUCCU-CACUGUAACACCCA--UUGCAGUGGUGACAAUGAGACCUGUGACAGGU
AAHX01113924.1/736-872     AGACUCAUUGUACA-----UAAGAAUGGGCAUUGUUG-U---UGGUCAAUGUC-CA-GAACUGGUCAAUGUGGCUAAAUUGAGAU-ACAGGUCAUGCUUCCAU-UACAGCAGAUUAAA--UUACAGUGGUUACAAUGAGACCUGCAACAUUU
AAGW02008739.1/14826-14692 GGCCUCAUUGUAGA-----UGAGAAUGGGCACUGUUA-A---ACAUG-GUGUC-CA-AAAACUGUUAAUGUGGCUAAAUUGAGAU-ACAGGUUAUGCUUCCAU-CACAGCA-AAUGAA--UUGCAGUGGUGACAAUGAGACCUGUAACAAUU
AAQR03000416.1/2199-2338   AGCCUCAUUCUAAAUAAAAUAAGAGUGGGCACUGUUG-A---UAAUA-GUGUU-CA-AAAAUUGUUAAUGUGGCUAAAUUGAGAC-ACAGGUUAUGCUUCCAU-CACAGUA-UAUGUA--UUACAGUGGUGACAAUGAGACCUGUGACAUUU
AAPE02001978.1/26329-26464 AGCCUCAUUCUAGA-----UGAAAAUGGACACUGUUG-C---UCAUG-GUGUC-CA-GAAAUUGUUAAUGUGGCUGCAUUGAGAACACAGGUUAUAUUUCCAU-CACAGUA-ACUUUA--UUGUAGUGGUGACAAUGAGAUCUGUAACAUAA
#=GC SS_cons               :<<<-<<<------.....------<<<<<<<_____._..._____.>>>>>.>>.---------->>>->>>-----------.<<<<<---------<<<.<<<____.______.._____>>>>>>--------->>>>>:::::::
#=GC RF                    aGCCUCauUcUagA.....UgAgaauGGgcacuGUug.a...UcaUg.guguC.Ca.aAAaUuGuuAauGUGGCUAaAuUGAgAa.aCAGGUUaUGCUUCCAu.CACAGUA.aauuuA..UUgCAGUGgUGACAAUGAGACCUGuAACAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF00409
#=GF ID   SNORA7
#=GF PI   snoACA7
#=GF DE   Small nucleolar RNA SNORA7
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   100.00
#=GF TC   100.00
#=GF NC   99.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF CL   CL00025
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300743;
#=GF DR   snoopy; Homo_sapiens300732;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   ACA7 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1]. The family also contains
#=GF CC   the mouse sequence MBI-141 as mentioned in [2].
#=GF WK   Small_nucleolar_RNA_SNORA7
#=GF SQ   31


AC109169.13/56788-56927      GACCUCUUGGGAUCGCGUCUGGAGAGUAGCUAGUAUUCUUCCAGCUUCGGAAGCAAGAGGGAGA---GCAAGCCU-------AGCAGAGG--UACCCAUUCCAUUCCCAGUUUGCU---C-GGUAGCUGGUGAUUGGAAGACACUCUGCAACAUUA
K02060.1/2116-2255           GACCUCUUGGGAUCGCGUCUGGAGAGUAGCUAGUAUUCUUCGAGCUUCGGAAGCAAGAGGGAGA---GCAAGCCU-------AGCAGAGG--UACCCAUUUCAUUUCCAGUUUGCU---C-GGUAGCUGGUGAUUGGAAGACACUCUGCAACAUUA
AJ609430.1/1-139             GACCUCCUGGGAUCGCAUCUGGAGAGUGCCUAGUAUUCUGCCAGCUUCGGAAAG-GGAGGGAAA---GCAAGCCU-------GGCAGAGG--CACCCAUUCCAUUCCCAGCUUGCU---CCGU-AGCUGGCGAUUGGAAGACACUCUGCGACAGUG
AL449212.1/17376-17238       GACCUCCUGGGAUCGCAUCUGGAGACUGCCUAGUAUUCUGCCAGCUUCGGAAAG-GGAGGGAAA---GCAAGCCU-------GGCAGAGG--CACCCAUUCCAUUCCCAGCUUGCU---CCGU-AGCUGGUGAUUGGAAGACACUCUGCGACAGUG
AC112497.4/53262-53124       UACCUCCCAGGAUGGCAUCUGGA-AGUGGAUAGUAUUCUGCCAGCUUUGGAAACUGGAUGAAAA---GCAAAUCU-------GGCAGAGG--UACCCAUUUCAUUCCCAGCUUGCU---CAGU-AGCUGGUGAUUGGAAGAAACUCUGCAACAGUG
AP000577.5/69612-69474       GAGCUUCCAGGAUCACCCCUGCAGAGUGGCUAAUAUUCUGCCAGCUUCGGAAAG-GGAGGGGAA---GCAAGCCU-------GGCAGAGG--CACCCAUUCCAUUCCCAGCUUGCU---UAGU-AGCUGGCCAUGGGAAGACACUGUGCAACACUG
AC020553.4/138195-138051     AAUCUCCUGGGAUUGUGUCUGGCGAGUGCCCAGUAUUCUGCCACCUUCAGAAG--GAAGGGAAA---GCAAACCUUCAUGAAAGCAGAGG--CAUUCAUUCCAUUCCCAGCUUGCU---CCAG-AUCUGGCAGUUGGAAGACAUUCUGCAACAAUG
AANG01579022.1/6110-6249     GACCUCCCAGGAUCGCGUCUGGAGAGUGGUUCGUAUUCUGCCAGCUUCGGAAACGGGAGGGAAA---GCAAGCCU-------GGCAGAGG--UACCCAUUCCAUUCCCAGUUUGCU---CAGU-AGCUGGAGAUUGGAAGACACUCUGCAACAAUG
AAPY01753143.1/3789-3650     GACCUCCUGGGAUCGCGUCUGGAGAAUGGCUAGUAUUCUGCCAGCUUCGGAAAUGGGAGGGAGA---GCAAAGCC-------GGCAGAGG--UACCCAUUCCAUUCCCAGCUUACA---CAAU-AGCUGGUGAUUGGAAGAUGCUCUGCAACAGUG
AAFC03075477.1/41178-41039   AACCUCCCAGGAUCGCAUCUGGAGAAUGGCUUGUAUUCUGCCAGCUUCGGAGUCGGGAGGGAAA---GCAAGCCU-------GGCAGAGG--UACCCAUUCCAUUCCCAGUUUGCU---CAGU-AUCUGGUGAUUGGAAGACACUCUGCAACAAGA
AANU01236502.1/19416-19555   UACCUCCAAGGAUGGCAUCUGGAGAGUGGAUAGUAUUCUGCCAGCUUUGGAAACUGGAUGAAAA---GCAAAUCU-------GGCAGAGG--UACCCAUUCCAUUUCCAGCUUGCU---CAAU-AGUUGGUGAUUGGAAGAAACUCUGCAACAAUG
AAIY01681131.1/1960-2097     GACCUCCCAGGAUCGCAUCUGGAGAAUAGCUAGUAUUCUGCCAGCUUCGGAGACGGGAGGGAAA---ACAAGCCU-------AUCAGAG----ACCCAUUCCAUUCCCAGUUUGCU---CAGU-AACUGGUGAUUGGAAGACACUCUGUGACAGUG
AALT01598265.1/3312-3449     GACCUCCCAGGAUCGCGUCUGGAGAAUUGCUAGUCUUCUGCCAGCUUCGGAGAUGGGAGGGAAA---GCAAACCA-------GGCAGAGC--UACCAAUUCCAUUCCCAGCUUGCC---CCGU-AGCUGGUGAUCGGAAG--ACUCUGCAACAUUG
ABDC01216570.1/6285-6143     GACCUCCUGGGAUGGCAUCUGGAGAGUGGCUAGUAUUCUACCAGCUUCGGAAACAGGCGGGAAAUUCGCAAGCCU-------AGCAGAGG--UACCCAUUCCAUUCCCAGCUUGCU---CGGU-AGCUGGUGAUUGGAAGACACUCCACAACAAGU
AAYZ01254110.1/12199-12337   GACCUCCCUGGAUCGCGUCUGGAGAGUCCCCAGUGCUCUGCCAGCUUCGGAAGCGGGAGGGAGA---GCAAAGCC--------GCAGAGC--UGCCCAUUCCAGUCCCAGCUUGCC---CGGU-GGCUGGUGCCUGGAAGAUACUCUGCAACAGAG
AAPN01131271.1/1272-1409     UCCCUCUUGGGAUCACAUCUGGAGAGUUUCCAGGACUCUUCCAGUCUUGGCUAUGGGAGGGAAA---G----UCA-------GGCAGAGGGCUACCCAUUCCAUUCCUAGCUUGGG---CUGU-GGCUAGCGAGUGGAAGGCAGUCUGCUACAAAG
AAWR02032515.1/19329-19468   AACCUCCCAGGAUCGCGUCUGGAGAGUGGCUAGUAUUCUGCCAGCUUCGGAGACGGGAGGGAAA---GCAAGCCU-------GGCAGAGG--CACCCAUUCCAUUCCUAGCUUGCU---CAGU-AGCUGGUGAUUGGAAGACACUCUGCAACAAUG
AAGV020426044.1/1495-1634    GACCUCCCAUGAUCAUGUCUGGAGAAUGGCUAGUAUUCUACCAGCUUUGGAGAUAGAAGGGACA---GCAAGCCC-------AGCAGAGA--UGCCCACUCCAUUCCCAGUUUACU---CAGU-AGCUGGUGAUUGGAAGAUACUCUGCAACAGUG
AC118412.6/119226-119087     GACCUCUUGGGAUCGCGUCUGGAGAGUGGCUAGUAUUCUGCCAGCUUCGGAAGCAGGAGGGAGA---ACAAGUCU-------AGCAGAGG--UACCCAUUCCAUUCCCAGUUUGCU---CAGU-AGCUGGUGAUUGGAAGACACUCUGCAACAUCA
EU094039.1/1-138             CCCCCCUCAGCUUCGCACCUGGAGAGUUUCCAGUACUCUACCAGUCUCGGCUAGGGGAGGGAGA---G----UGA-------AGCAGAGGCCUACCCAUUCCAUUCCCAGCUUGGU--CCAGU-GGCUGGCGAGUG-AAGACAAUCUGCUACAGGU
EU094046.1/3-140             CCCCUCUCAGCGUCUCACCUGGAGAGUUUCCAGUCCUCUACCAGUUAUGACUACAGGAGGGAGA---G----UCA-------AGCAGAGGCCUGUCCAUUCCAUUCCUAGCUUGGC---CAGU-GGCUAGUUAGUGGAAGACAAUCUGCUACAAGU
EU094042.1/3-143             CCCCUCUCAGGAUCUCACCUGGAGAGUUCCCAGUACUCUACCAGUCUCGACUACAGGAGGGAAA---G----UCA-------GGCAGAGUCAUAUCCAUUCCAUUCCUAGCUUGGGCGGCAGU-GGCUAGCGAGUGGAAGGCAAUCUGCUACAAGU
FJ915984.1/1-139             AACCUCCUGGGAUCGCGUCUGGAGAGUGCCUAGUAUUCUGCCAGCUUCGGAAAG-GGAGGGAAA---GCAAGACU-------GGCAGAGG--CACCCAUUCCAUUCCCAGCUUGCU---CCGU-AGCUGGCGAUUGGAAGACACUCUGCGACAGUG
EU094050.1/1-138             CCCCCCUCAGCUUCGCACCUGGAGAGUUUCCAGUACUCUACCAGUCUCGGCCAGGGGAGGGAGA---G----UGA-------AGCAGAGGCCUACCCAUUCCAUUCCCAGCUUGGC---CAGU-GGCUGGCGAGUGGAAGACAAUCUGCUACAGGU
EU094047.1/2-139             AACCUCUCAGGGUCGCACCUGGAGGGUUUCCAGUACCCUACCAGUCUCGGCUAUGGGAGGGAGA---G----UUA-------AGCAGAGGAAUACCCCUUCCAUUUCUAGCUUGGC---CAGU-GGCUAGCAAGUGGAAGACAAUCUGCUACAAGU
AAWZ02022840.1/49086-49224   GACCUCCCAGGAUCGCAUCUGGAGAGUUUUCCAUACUCUUCCGGCCUCGGACAUGGGAGGAAGA---GC---GGU-------GGCAGAAAAGUACCCAUUCCAUUGCUGGCUGUAA---AGUA-GGCUAGUAAAUGGAAGUUACUCUGCAACAUUU
AAPE02040183.1/92865-93004   CACCUCGCAGGAUCAUGUCUGGAGAGUGGCUAAUAUUCUGCCAGCUUCGGAGACAGGAGGGAAA---GCAAGCCU-------GGCAGAGG--UACCCAUUACAUUCCCUGCUUGCU---UAGU-AGCUGGUGACUGGAAGACACUCUGCAACAAUG
AAGU03069309.1/25109-25246   GACCUCCCAGGACCUUGUCUGAAGAGUGGCUAAAAUUCCAUCAGCUUCAGAGAUGAGAGGGAAA---GCAAGCCU-------GUCAGAGG----CCCGUUUCAUUCCCAGCUUGCU---CAGU-AGGUGGUGACUGGAAGAUGCACUGUGACAAUG
AAGW02010966.1/45971-45833   GACCUCCUGGGAUCGUGUCUGGAGAGUGGCCCGUCUUCUGCCAGCUUCAGAAGCGGGAGGGAAA---GCAAGGCU--------GCAGAGG--CACCCAUUCCAUUCCCAGCUUGUU---CAGU-AGCUGGUGAUUGGAAGACCCUCUGCACCAGGA
AAQR03059591.1/40323-40462   GACCUUCUGGGAUAGCAUCUGGAGAGUCCCUGGUAUUCUGCCAGCUUCAGAAGCAGGAGGGAAA---GCAAGCCU-------AGCAGAGG--UACCCAUUCCAUUCCCAGCUUAUU---CUGU-AGCUGGUGAUUGGAAGACACUCUGCUACAAGU
AAEX03012060.1/196899-197038 GACCUCCCAGGAUCGCGUCUGGAGAGUGGUUGGUAUUCUGCCAGCUUCGGAGGCGGGAGGGACA---GCAAGCCU-------GGCAGAGG--UACCCAUUCCAUUCCCAGUUGGCU---CAGU-AGCUGGUGAUUGGAAGACACUCUGCAACAGCA
#=GC SS_cons                 ::<<<<<-----<<<---<<<<<<<<<<_____>>>>>>->>>>--->>>----->>>>>----...--------.......-<<<<<<-..------<<<<<-<<<<<<<<____...____.>>>>>>->>->>>>>---->>>>>>:::::::
#=GC RF                      gACCuCccaGGAucgcaUCUGGaGAgucgCuAGgacUCugCCAGCUUcggAaAuggGaGGGAaA...GCAAgucu.......agCAGAgg..UACCCAUUCCAUucCcAGcuUGcu...CaGU.agCUgGugauUGGAAGAcAcUCUGcaACAaug
//
# STOCKHOLM 1.0

#=GF AC   RF00410
#=GF ID   SNORA2
#=GF PI   snoACA2
#=GF DE   Small nucleolar RNA SNORA2/SNORA34 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   70.00
#=GF TC   70.00
#=GF NC   69.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00021
#=GF DR   snoRNABase; ACA2a;
#=GF DR   snoRNABase; ACA2b;
#=GF DR   snoRNABase; ACA34;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300623;
#=GF DR   snoopy; Homo_sapiens300764;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the H/ACA class of snoRNAs which are
#=GF CC   predicted to guide the sites of modification of uridines to pseudouridines
#=GF CC   [1]. This family includes human snoRNAs ACA2a (SNORA2A), ACA2b (SNORA2B)
#=GF CC   and ACA34 (SNORA34). ACA2a and ACA2a are predicted to guide
#=GF CC   pseudouridylation of U4263 and U4282 in 28S rRNA and ACA34 is predicted to
#=GF CC   guide the pseudouridylation of residue U4269 and U4282 of 28S rRNA [2]. In
#=GF CC   humans all three of these snoRNAs share the same host gene [2].
#=GF WK   Small_nucleolar_RNA_SNORA2
#=GF SQ   18


AC079951.35/117550-117416 UAGGCCCUGAAUC-AAGAC---CAAUGGUUUGC---UGUAGCUGUUGGUUUCAAACAGGAGCUAAGAGUGAUGUCUUCCUUGUGGUCUGUUGGCUAUU-CAGU-AUUCCAGU-GCGAAUUGCCAAUUCAGUUGGAAGAAACAUAG
AC113292.6/67439-67304    UUGACCCUUAAUC-AAGGCC--AGCAGUU-UGC---UGAAGCUGUUGGUUUCAAGCAGGCAACUAAAUAAAUGUCUUUCU--AGGUCUGUUGGCCAUUUCAGAAAUUUAAAAAUGUAAUGGUCAUUGGGUGUGGUGGCACAUACC
AC122035.2/34589-34724    UUGGCCCUGAAUC-AAGGC---UACAGUU-UAC---UGAAGCUGUUGGUUUCAAGCAGGAGCCUAAAGAAAUAUCUUUCU-AUGGUCUGUUGGCCAUUGCAGAAAUUUGUAAGUCUAAUGGCCAAUUCAUUAGAAAGAAACAUCU
AL078581.11/71236-71370   UAGGCCCUGAAUC-AAGAAACGUGAUGGUUUGCCAUUGUAGCUAUUGGUUUCAAACAAGAGCCAAGAUUGAUGUCUUUCUUAUGGUCUGUUGGCUA--------AUCCCAGU-AUGAAUGGCCAGUUCAGCUAGAAGAAACAAAC
AJ609443.1/1-137          GUGGCCCUGACUG-AAGACC--AGCAGUUGUAC---UGUGGCUGUUGGUUUCAAGCAGAGGCCUAAAGGACUGUCUUCCU-GUGGUCUGUUGGCUGUU-CUGGGACCUCAGUAGGGAAUGGCUAUUUCAUUUGGAAGAAACAACC
AC094784.13/200042-200174 AAGACUCAGAAUUCAAGACC--AGCAGUUGUAC---UGUAGCUGUUGGUUUCAAGCAGGCGCCUAAAGAGCUGUCCUCCU-GUGGUUUAUUGGCUCUU-CUGG-ACUUCAAUA---GAGUGAC-UUCCCUCUGGAAGAAACAACC
AC007240.2/22839-22705    UAGGCCCUGAAUC-AAGAC---UAGUGUUUUGC---UGUAGCUGUUGGUUUCAAACAGGAUCCGAGAGUGAUGUCUUCCUUGUGGUCUGUUCACUGCU-CAGU-AUCCCAGU-GUCAGUGGCCAAUUCAGUUGGAAGCAACAUGG
AC142113.2/112130-111996  AUGGCCCUGAAUC-AAGGC---UGCAGUU-UAC---UGAAGCUGUUGGUUUCAAGCAGGAGCCUAAAGAAAUAUCUUUCU-GUGGUCUGUUGGCCAUUGCAGAAAUU-GUAAGUCUUAUGGUCAAUUCAUUAGAAAGAAACAUCU
AJ609427.1/1-137          UUGGCCCUGAAUC-AAGGC---CAGCAGUUUGC---UGAAGCUGUUGGUUUCAAGCAGGAGCCUAAAGAAUUGUCUUUCU-AUGGUCUGUUGGCCAUUUCAUAACUUUGGAAAUGUAAUGGUCAAUUCAUUAGAAAGAAACAUGA
AL840639.3/24683-24819    UUGGCCCUGAAUC-CAGGCC--AGCAGUU-GGC---UGAAGCUGUUGGUUUCAAGCAGGUGCCUAAAUAAAUGUCUUUCU-ACCGUCUGUUGGCCAUUUCCGAAAUUUGAAAAUGUAACAGUCAAUUCAUUAGAGAGAAACAUCU
AL929067.8/86732-86868    AUGGCCCUGAAUC-GAGGC---CAGCAGUUUAC---UGAAGCUGUUGGUUUCCAGCAGGAGCCUAAAGAAAUGUCUUUCU-AUGGUCUGUUAGCCAUUUUGUGAAUUUGUAAACCUAAUGGUCAACUCAUUAGAAAGAAACAUCU
AC126547.4/57251-57386    UUGGCCCUGAAUC-AAGGC---CGCAGUU-UAC---UGAAGCUGUUGGUUUCAAGCAGGAGCCUAAAGAAAUAUCUUUCU-AUGGUCUGUUGGCCAUUGCAGAAAUUUGUAAGUCUAAUGGUCAAUUCAUUAGAAAGAAACACCU
AJ609426.1/1-135          UAGGCCCUGAAUC-AAGAC---CAAUGGUUUGC---UGUAGCUGUUGGUUUCAAACAGGAGCUAAGAGUGAUGUCUUCCUUGUGGUCUGUUGGCUAUU-CAGU-AUUCCAGU-GCGAAUUGCCAAUUCAGUUGGAAGAAACAUAG
AL731670.13/807-943       AUGGCCCUGAAUC-GAGGC---CAGCAGUUUAC---UGAAGCUGUUGGUUUCCAGCAGGAGCCUAAAGAAAUGUCUUUCU-AUGGUCUGUUAGCCAUUUUGUGAAUUUGUAAACCUAAUGGUCAACUCAUUAGAAAGAAACAUCU
AL359273.11/19405-19541   UUGGUCCUGAUUC-AAGGC---CAGCAGUUUGC---UGAAGCUGUUGGUUUCAAGCAGGAGACUAAAUAAUUGUCUUUUC-AUGGUCUGUUGGCCAUCUUAUAACUUUGGAAAUGUAAUGUCCAAUUCAUUAGAAAUAAACAUCU
AC079951.35/115286-115150 GUGGCCCUGACUG-AAGACC--AGCAGUUGUAC---UGUGGCUGUUGGUUUCAAGCAGAGGCCUAAAGGACUGUCUUCCU-GUGGUCUGUUGGCUGUU-CUGGGACCUCAGUAGGGAAUGGCUAUUUCAUUUGGAAGAAACAACC
AY214596.1/495-630        UUGGCCCUGAAUC-AAGGC---CAGCAGUUUGC---UGAAGCUGUUGGUUUCAAACAGGAGCCUAAAGAAGUCUCUUUCU-AUGGUCUGUUGGCCAUUUCGGAUCUU-GGAAAUGUAAUGGUCAAUUCAUUAGAAAGAAACAUCU
AC079951.35/128361-128226 UUGGCCCUGAAUC-AAGGC---CAGCAGUUUGC---UGAAGCUGUUGGUUUCAAGCAGGAGCCUAAAGAAUUGUCUUUCU-AUGGUCUGUUGGCCAUUUCAUAACUUUGGAAAUGUAAUGGUCAAUUCAUUAGAAAGAAACAUG-
#=GC SS_cons              ::<<<--------.-----...-----------...-----<<<<<-<___>->>>>>-->>>----------<<<<<<-.---------<<<<<<<<__________________>>>>>>>>-------->>>>>>:::::::
#=GC RF                   uuGgcCCUGAAUc.AAGaC...uaaaGuUuUgC...UGaAGCUGuUGGUUUCAAgCAGGagcCuAAAgaaaUGuCuUcCU.aUGGUCUGUUGgCcauuuCagaAAUUUgaaaAuguaaugGcCAaUUCAuUuGgAaGaAACAucu
//
# STOCKHOLM 1.0

#=GF AC   RF00411
#=GF ID   SNORA9
#=GF PI   snoACA9
#=GF DE   Small nucleolar RNA SNORA9
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   85.00
#=GF TC   85.60
#=GF NC   84.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00027
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300578;
#=GF DR   snoopy; Loxodonta_africana300060;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA9 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA9
#=GF SQ   36


AJ609431.1/1-133           UAGCAAG-C-CU--CCAGCGUGCUUGGGUCUGCGGUGACCCUAU-GCAUUCCUUCAGUGCUUGCUAGAA-CAGUUUUGAAAC-GGUUUGAGGCCUUGCCCUG-CUCC--AUC--C--AGAGCAAGGUUAUAG--AAAUUUCAGACAAUG
Z78021.1/341-473           UAGCAAG-C-CU--CCAGCAUGCUUAGGUCUGCAGUGACCCUAU-GCAUCCCUACAGUGCUUGCCAGAA-CAGUUUUGAAAC-GGUUUGAGGCCUUGCCCUG-CUCC--AUC--C--AGAGCAAGGGUAUAG--AAAUUUCAGACAAUU
AL646047.9/33135-33004     UAGCAAG-C-CU--CCAGCGUGCUUGGGUCUGCAGUGACCCUGU-GCAUUCCUACAGUGCUUGCCAGAA-CAAUUUUGAAGU-GGUUUGAGGCCUUGCCCUG-CCCU--CUC--C--AGAGCAAGGUUAUAG--AAAUUUCAGACAAU-
AC117503.8/209801-209669   UAGCAAG-C-CU--CCAGCGUGCUUGGGUCUGCAGUGACCCCGU-GGAUUCCUACAGGGCUUGCCAGAA-CAGUUUUGAAAU-GGUUUGAGGCCUUGCCGUG-CUCC--AUG--U--AGAGCAAGGUUAUAG--AAAUUUCAGACAAUG
AC114006.3/20483-20615     UAGCAAG-C-CA--CCAGCAUGCUUGGGUCUGCAGUGACCCUGU-GCAUCCCUAAAGUGCUUGCCAGAA-CAAUUUUGAAGUUGGUUUGAGGCCUUGCCCUG-GUCU--UUC--C--AGGGCAAGGUUAUAG--AAAUUUCAGACAAU-
AL356754.18/44935-45063    --GCAAG-C-CU--CCAGCGUGCGUGGGUCUGUGGUGAUG-UGU-GCAUUCCUACACUGCUUGCCAGAA-CAGUAUUGAAAU--AGUGGAGCGUUUGUCCUG-CUCC--AUC--C--AGAGCAAGGUUAUAG--AAAUUUCAGACAAUU
ABDC01193986.1/19178-19046 UAGCAAG-C-CU--CCAGCGUGCCUGGGUCUGCGGUGACCCUGU-GCAUUCCUACAGCGCUUGCCAGAA-CAGCUUUGAAAC-GGUUUGAGGCCUUGCCCUG-CUCC--AUC--C--AGAGCAAGGUUAUAG--AAAUUUCAGACAAUU
AAPY01834891.1/809-677     UAGCAAG-C-CU--CCAGCGUGCUUGGGUCUGUGGUGACCCUUU-GCAUUCCUACAGUGCUUGCCAAAG-CAGUUUUGAAAU-GGUUUGAGGCCUUGCCCUG-CUCU--UUC--C--AGAGCAAGGUUAUAG--AAAUUUCAGACAAUU
AAFC03011982.1/5679-5548   CCGCAAG-C-CU--CCAGCGUGCUUGGGUCUGCAGUGACCCUGU-GCAUUCCUACAGUGCUUGCAAGAA--AAUUUUGAAAC-GGUUUGAGGCCUUGCCCUG-CUCC--AUC--C--AGAGCAAGGUUAUAG--AAAUUUCAGACAGUU
AALT01657895.1/6423-6292   UGGCAAG-C-CU--CCAGCGUGCUGGGGUCUGGAGUGACCCUGU-GCAUUCCUACAGUGCUUGCAAGAA-CAUUA-UGAAAU-GGUUUGAAGCCUUGCCCUG-CUCC--AUU--C--AGAGCAAGGUUAUAG--AAAUUUCAGACAAAU
AANU01297689.1/7632-7502   UAGCAAG-C-CU--CCAGCAUGCUUGGGUCUGUGGUGACCCUAU-GCAUUCCUUCAGUGCUUGCUAGAA-CAGUUUUGAAAC-GGUUUGAGACCUUGCCCU---UCU--AUC--C--AGAGCAAGGUUAUAA--AAAUUUCAGACAAUG
AAQQ01086791.1/629-498     UAGCAAG-C-CU--CCAGCGUGCUUGGGUCUGCAGUGACCCUAUUGCAUUCCUACAGUGCUUGCCAGAA-UACU--UGAAAU-GGUUUGAGGCCUUGCCCUG-CCCU--AUC--C--AGAGCAAGGUUAUAG--AAAUUUCAGACAACU
AAIY01636053.1/324-190     CUGCAAG-C-CU--CCAGCGUGUCUGGGUCUGGAGUGACCCUGU-GCAUUCCUACAGUGCUUGCAAGAA-CAGUUUUGAAAC-GGUUUGAGGCCUUUCUCUG-CACC--AUCUCC--AGAGCAAGGUUAUAG--AAAUUUCAGACAAAC
AANG01386371.1/4823-4692   CGGCAAG-C-CU--CCAGCGUGCCUGGGUCUGGGGUGGCCCCGU-GCAUUCCUUUAGUGCUUGCAAGAA-CAUUGG-GAAAC-GGUUUGAGGCCUUGCCCUG-CUCC--AUC--C--AGAGCAAGGUUAUAG--ACAUUUCGAACAGAU
AANN01742351.1/3375-3244   CUGCAAG-C-CU--CCAGCGUGCCUGGGCCUGUGGUGACCCAGU-GCAUUCCUAUAGUGCUUGCUAGAA-CAAUU-UGGAAC-GGUUUGAGGCCUUGCUCUG-CUCC--ACC--U--GGAACAAGGUUAUAG--AAAUUUCAGACAGUC
AAYZ01463456.1/133-4       CAGCAAG-C-CU--CCAGCGUGCUGGGGCCUGUCGUG-CCCUAU-GUAUUCCUGCAGUGCUUGCCAGAG-CAAUU-CGGAAC-GGUUUGAGGCCUCGCCCUG-CUUC--AUC--C--AGAGCGAGGUUAUAG--AC-UUUCGGACAGUC
DQ096896.1/840-971         GAGCAAG-U-UU--CCAGCAUGGUUGGGUUUGCCGUAGCCCUGC-CCAUUCCUGUAGAACUUGCCAGAU-CAGCACUGAGAC-GGUUUGAGGCCUCCUGUUG--UCC--CUC--C--AGCAGAAGGUUAUAG--AACUCUCGGACACUU
AAPN01421147.1/3278-3144   UCGCAAG-C-CU-ACCAGCAUGUCUCGGCCUGACGUGGCCCUGG-GUAUUCCUUUGGUGCUUGCCAGAG-CAGCCUUGGGGU-GGUUUGAGGCUUCUCCCUGCCCCC--UUC--C--AGGGAGAGGUUAUAG--AAAUCUCAGACAAUC
AAFR03030408.1/28070-27936 GUGCAAG-CUUU--CCAGCAUGUCGGUGUCCUCUAUGACCCCAG-ACAUUCCUAAAGA-CUUGCUAGAG-UAAUCCUGAGAU-GGUUUGAGGCCUCACUCUG-CUCUGACUU--C--GGAGUAAGGUUAUAG--AAAUCUCAGAUAUUG
BX927310.10/40710-40579    CUGCAGG-CUGU--UCAGCGAGGCUGAGUCUCCUGUGACUCUGU-CCUUUCCUUUA-UGUCUGCUAGA--UAGACAUGGAGU-GGUUUGAGACCCUGUUGUC-UACU--AAA--U--ACAGCGUGGUUAUAG--AAACUCCAGAUAAAC
BAAF04001882.1/2703-2572   GUGCAGA-UCAU--CCAGCGAGGCUAGGCCUGCAGUGGCUCCGC-CCUCUCCUGUUGG-UCUGCUAUAG-UAAU--GGAGGU-GGUUUGAGGCCCUGUUGUG-GUUC--UG---C--ACAGCUGGGUUAUAGGUAAACCUCCGACAUGU
AAKN02012258.1/37785-37653 UAGUAAG-C-CU--CCAGCGUGCUUGGAUCUGGUGUGAACCUGU-GCAUUCCUAAAGCGCUUGCUAGAG-CAGCUUUGAAAU-GGUUUGAGGCCUUGCCCUG-CUCU--AUC--C--AGAGCAAGGUAAUAG--AAAUUUCAGACAGUU
AAWR02031803.1/48538-48407 CUGCAAG-C-CU--CCAGCGUGCUUGGGUCUGGGGUGACCCUGU-GCAUUCCUACAGUGCUUGCGAGAA-CA-UUUUGAAAC-GGUUUGAGGCCUUGCCCUG-CUCC--AUC--C--AGAGCAAGGUUAUAG--AAAUUUCAGACAAUC
AAGV020805534.1/1441-1307  UUGCAAG-U-CU--CCAGCGUGCUUGGGUCUGCAGUGACCCUGU-GCAUUCCUACAGUGCUUGCAAGAA-CAGUUUUGAAAU-GGUUUGAGGCCUUGCUCUG-CUCC--GUCUAC--GGGGCAAGGUUAUAG--AAAUUUCAGACAGUU
AC146547.2/206598-206732   GUGCAGA-C-CUUUCCAGCGAGGCUCAGCCUGCCGUGGCUCUGU-CCUUUCCUGUAGUGUCUGCUAGA--GAGACGUGAGGC-UGUUUGAGGCCCUGCUGUG-GCCC--CU---C--GCUGCAGGGUUAUAGGAAAACCUCAGACACGU
AC193899.3/92761-92893     UAGCAAG-C-CU--CCAGCGUGCUUGGGUCUGCAGUGACCCCGU-GGAUUCCUACAGGGCUUGCCAGAA-CAGUUUUGAAAU-GGUUUGAGGCCUUGCCCUG-CUCC--AUG--U--AGAGCAAGGUUAUAG--AAAUUUCAGACAAUG
AAGW02072219.1/36838-36971 UUGCACG-C-UU-CCCAGCAUGCUUGGGUUUAGAGUAACUCAGU-GCAUUCCUGCGGUGCUU-CUAGA--GUGUUCUGAGAU-GGUUUGAGGCCUCGCCCUG-UUGC--UACCUC--AGCGCAUGGUCGUAG--GCACUUCAGACAGUU
AAGW02061831.1/5386-5518   CCGCAAG-C-CU--CCAGCGUGCCUGGGCCUGCCGUGACCCUGU-GCAUUCCUGCGGUGCUUGCCAGAG-CAGUGUCGAAAC-GGUUUGAGGCCUUGCCCUG-CCCC--AUC--C--GGAGCAAGGUUAUAG--AACUUUCAGACAGCU
AAQR03037650.1/725-856     UAGCAAG-C-CU--CCAGCACGCUUGGGUCUGUGGUGACC-UGU-GUAUUCCUACAGCGCUGGCUAGAA-CAGCUCUGAAGC-AGUUUGAGGCCUUGCCCUG-CCCU--ACC--C--AGAGCAAGGUUAUAG--AAAUUUCUGACAAUC
AAPE02017365.1/47665-47535 CUGCAAG-C-CU--CCAGUGUGCUUGGGUCUGGGGUGAUCCUAU-GCAUCCCUACAGUACUUGCGAGAA-CAGUUG-GAAAC-AGUUUGAGGCCUUGCC-UG-CUGC--AUC--C--GGAGCAAGGUAAUAG--AAGUUUCAGAAAGUU
AAGU03080655.1/91528-91662 UGGCAAG-C-CU-UCCAGCAUGUUUGGAUCUGGGGUGACUCCUG-GUAUUCCUGCAGUGCUUGCCAGA--GUGUUCUGAAGU-GGUUUGAGACCUGGCUCCG-UCCC--UUGUUU--AGAGCACAGCCACAG--GCAUUUCAGACAGUU
AADN03002823.1/17586-17455 CCGCAAGGC-UU--CCAGCAUGGUGGGGCCUGCCGUGGCCCCAU-CCAUUCCUGCAGCGCUUGCCAGAG-CAGCCCUGGGGU-GGUUUGAGGCCUCUUUCUG-UCUC--U----C--AGGGGGAGGCUAUAG--AAACCCCAUACACGC
AAEX03023460.1/11510-11379 CGGCAAG-C-GU--CCAGCGUGCUGGGGUCUGCGGUGACCCUGU-GCAUUCCUGCACCGCUUGCCACAG-CA-UCCUGAGAC-GGUUUGAGGCCUUGCCCUG-CUCC--AUC--C--AGAGCGAGGUUAUAG--AAAUUUCAGACAGGC
AAGU03017566.1/42172-42037 UUGCAAG-C-CU--CCAGCAUGCUUGGGUCUGGAGUGGCCCUGU-GCAUUCCUCCAGUGCUUGCAAAAAACAGUUUUGAAAC-GGUUUGAGGCCUCGCUCUA-CACC--AUC--UACAGAGCAAGGUUAUAG--AAAUUUCAGACAGUU
AAGW02015855.1/60923-61055 UAGCAAG-C-CU--CCAGCACAUGUGGGCUAGCUGUGACUCUGU-GCAUUCCUACAGUGUGUGCUGGAA-CAUUCUCCAAAC-GGUUUGAGGCAUUGCCCUG-CUCC--AUC--C--AGAGCAAGGUUAUUG--AACUUUUCAGAACAU
AAGW02059454.1/3977-4109   CAGCAAG-C-CU--CCAGCAUGCUUGGGUCUGCUGUGACCCUGU-GCAUUCCUGCAGUGCUUGCCAGAA-CAGUUUUGAAAC-GGUUUGAGGCCUUGCCCUG-CUCC--AUC--C--AGUGUAAGGUUAUAG--AACUUUCGGACAAUU
#=GC SS_cons               ::<<<<<.<.--..------<<<--<<<<<______>>>>>---.>>>---------->>>>>>-----.------<<<<<-.---------<<<<<<-<<<.____..___..>..>>->>>>>>------..--->>>>>:::::::
#=GC RF                    uuGCAaG.C.cU..CCAGCguGcuUGgGuCUGcaGUGaCcCugU.gCaUUCCUacAGuGCuUGCuAGAa.cAgUuuuGaggu.GGUUUGAGGCCuugcccug.cucC..aUc..c..agagcaaGGUUAUAG..AAAccuCaGACAauu
//
# STOCKHOLM 1.0

#=GF AC   RF00412
#=GF ID   SNORA21
#=GF PI   snoACA21
#=GF DE   Small nucleolar RNA SNORA21
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   80.00
#=GF TC   80.20
#=GF NC   78.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00031
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Echinops_telfairi300410;
#=GF DR   snoopy; Echinops_telfairi300073;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   ACA21 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1]. This family also contains
#=GF CC   the mouse sequence MBI-3 as shown in [2].
#=GF WK   Small_nucleolar_RNA_SNORA21
#=GF SQ   5


AJ609436.1/1-133       CCCCCUUUUAAAAGCACUCAAUGGGCCUGUGGCUAAUGACCUAUUGAGCCGUCAAGAAAGGGGAGAGUGAAAA-CAUCGCUUUUGGGUGAAGUGGCAACAUGU---GUUGUUU-GCUUCAAUCGGUGGUGUGACAAGG
AK095288.1/748-880     CCCCCUUUUAAAAGCACUCAAUGGGCCUGUGGCUAAUGACCUAUUGAGCCGUCAAGAAAGGGGAGAGUGAAAA-CAUCGCUUUUGGGUGAAGUGGCAACAUGU---GUUGUUU-GCUUCAAUCGGUGGUGUGACAAGG
AF357384.1/1-128       ----------AAAGCACUCAGUGAGCCUUUUGCUAGUGACCCACUGAGCCGUCAAGAAGGGGCAGAGUGAAAAACACCACUUUUGGGUGAAGUGGCAACGUGUUGUGUUGUUUAACUUCAAUCGGUGUUGUGACAAGA
AC145397.1/50734-50599 CCCC-UUUUAAAAGCGCUCAGCGGGCCUUUUGCUGAUGACCCACUGAGCUGUCAAGAAGGGGCAGAGAGAAAA-CACCACUUCCGGGUGAAGUGGCAACAUAAUUUGUUGUUUAACUUCAAUCCGUGUUGUGACAAGA
AC145398.2/90981-90846 CCCC-UUUUAAAAGCGCUCAGCGGGCCUUUUGCUGAUGACCCACUGAGCUGUCAAGAAGGGGCAGAGAGAAAA-CACCACUUCCGGGUGAAGUGGCAACAUAAUUUGUUGUUUAACUUCAAUCCGUGUUGUGACAAGA
#=GC SS_cons           :<<<.<<<--------<<<<<<<<<______________>>>>>>>>>-------->>>>>>-----------.--------------<<<<<--<<<<_______>>>>---->>>>>:::::::::::::::::::
#=GC RF                CCCC.uuuUAAAAGCaCuCagugGGCCUuUuGCUaAUGACCcacuGaGCuGUCAAGaaaGGGcAGAGuGAAAA.CAuCaCUUuuGGGUGaaGuGGCaaCAUguUuUGuuGUUUAaCuuCAAUCgGUGuUGUGACAAGa
//
# STOCKHOLM 1.0

#=GF AC   RF00413
#=GF ID   SNORA19
#=GF PI   snoACA19
#=GF DE   Small nucleolar RNA SNORA19
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   80.00
#=GF TC   80.80
#=GF NC   79.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300364;
#=GF DR   snoopy; Gallus_gallus300094;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   ACA19 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1]. The family also includes
#=GF CC   the mouse sequence MBI-51 as shown in [2].
#=GF WK   Small_nucleolar_RNA_SNORA19
#=GF SQ   34


AJ609435.1/1-128           GUGCACAUUUCAUUGACCUGCUUUCUUUU-----AUGUGAGUAGUGUUAUUUCUUAUGUGCUAUACAAAUAAUUGAAGGCUAAUUAGCAGUAUAACUAUAAA-UAGU-AA-U-GCUGCCAGUCUCCUU-CAGACAAAA
AL355598.26/27295-27168    GUGCACAUUUCAUUGACCUGCUUUCUUUU-----AUGUGAGUAGUGUUAUUUCUUAUGUGCUAUACAAAUAAUUGAAGGCUAAUUAGCAGUAUAACUAUAAA-UAGU-AA-U-GCUGCCAGUCUCCUU-CAGACAAAA
AC123930.4/14152-14283     UUGCACAUUUCAUUGACCUGCUUUCUUUUGAA-AAUGUGAGCAGUGUUAUUUCUUAUGUGCUAUACAAAUAGUUGAAGGUUAAUUAGCAGAGUAACUGAAUA-UAGU-AA-U-UCUGCCAGUCUCCUU-CAGACAAAA
AANG01055650.1/1827-1698   AUGCACAUUUCAUUGACCUGCUUUCUUUUGUA-UAUGUGAGCAGUGUUAUUUCUUAUGUGCUAUACAAAUAGUUGAAGGCUAAUUAGCAGUAUAACU--AAA-UAGU-AA-U-GCUGCCAGUCUCCUU-CAGACAAAU
AAPY01661099.1/194-62      GUGCACAUUUCAUUGACCUGCUUCCUAUUGUAUAAUGUAAGCAGUGUUAUUUCUUAUGUGCUAUACAGAUUGUUGAAGGUUAAUUAGCAGUAUAACUAUAAA-UAGU-AA-U-GCUGCCAGUCUCCUU-CAGACAUAA
AAQQ01207541.1/1015-883    AUGCACAUUUCAUUGACCUGCUUUCCUUUGUA-UAUGUGAGCAGUGUUAUUUCUUAUGUGCUACACAAAUAGUUGAAGGUUAAUUAGCAGAAUAACUAUAAA-UAGU-AA-U-GCUGCCAGUCUCCUUUCAGACAAAA
AAFC03067696.1/23786-23915 GUGCACAUGUCAUUGACCUGCUUUCUCUCUUG-UAUGUGAGCAGUGUUAUUUCUUCUGUGCUAUACAAAUAAUUGAAGGCUAAUUAGCAGUAUAACU--AAA-UAGU-AA-U-ACUGCCAGUCUCCUU-CAGACAAAC
AAIY01362900.1/842-713     GUGCACAUUUCAUUGACCUGCUUCCAUUUAU---AUGUGAGCAGUGUUAUUUCUUAUGUGCUAAACAAGUAGCUGAAGGUUAAUUAGCAGUUUAACUGAACG-UAGU-AA-U-GCUGCCAGUCUCCUU-CACACAAAA
AAFR03024732.1/49382-49512 GUGCACGUUUCAUUGACCUGCUUUCAUUGUUC--ACGAAAGCAGUGUUAUUUCUGACGUGCUAUACAAUUUAUAGAAGGUUAAUUAGCAGUAUAACUUGGUA-UAGU-AA-U-GCUGCCAGUCUCCUU-CAAACACAC
AANN01771774.1/1296-1167   GUGCACAUUUCAUUGACCUGCUUUCUUCUGCU-GGUGUUAGCAGUGUUAUUUCUGAUGUGCUAUAGAAAUAGCUGAAGGUUAAUUAGCAGUGUAACU--AAA-UAGU-CG-C-GCUGCCAGUCUCCUU-CAGACAGUU
AAPN01114340.1/2052-2183   GUGCACAUUUCAUUGACCUGCUUUCAUUGCAU--UGUGGAGCAGUGUUAUUUCUGAUGUGCUAUAUAAACUGUUGAAGGUUAAUUAGCAGCACAACUCUAUA-UAGUAAA-U-GCUGCCAGUCCCCUU-CAGACAGAU
AALT01468171.1/15879-16007 GUGCACAUUUCAUUGACCUGCUUUCUAAUGUU-CUUGUGAGCAGUGUUAUUUCUCAUGUGCUACAU-UAUAAUUGAAGGCUAAUUAGCAGUAUGACU--AAA-UAGU-AA-U-ACUGCCAGUCUCCUU-CAGACAGUU
ABDC01496715.1/1084-953    GUGCACAUUCCAUUGACCUGCUUUCAUUUGUA-UAUGUGAGCAGUACUUUUUCUGAUGUGUUAUACAAAUAGUUCAAGGUAAGUUAGCAGUAUAGCUAUAAA-GAGU-AA-U-GUUGCCAGUCUCCUU-CGUAUAAAA
AAYZ01427784.1/652-522     CUGCACAUUUCAUUGACCUGCUUUCCUUUCUA-CAUGUGAGCAGUGUUAUUUCUGAUGUGCUAUACAAA--ACUGAAGGCUAAUUAGCAGCCUGACUGUUCAGUAGU-AA-U-GCUGCCAGUCUCCUU-CAGACAUGA
BAAF04038905.1/7117-6989   UUGCACAUUUCAUUGUCCUGCUCUUUACUU----UUAAGAGUUGUGAUAUUUCUGCUGUGCUAGAAAAA-AACUGGAGGUAAAUUAGCAGAGUGACUAUUUG-GUGU-CAUC-UUUGCCAGUCCCCUU-CAUACAUGU
CAAE01007485.1/50050-50178 GGGCACAGUUCAUUGUCCGGCUCCGCUGUCC---GUCGGGGCUGCGAUAUUUCUGAUGUGCUAGAACGA--GCUGGAGGUUAAUUAGCAGAGCGGCUGCUGG-GUGC-CU-CGUCUGCCAGUCCCCUU-CACACACUG
AANH01001477.1/15797-15670 AUGCACAAAUCAUUGUCAUGCUCUUAGUCUU---UUGAAAGCUGUGAUAUUUCUGUUGUGCUAGAAAAU--UCUGGAGGUAAAUUAACAGGGUGGCUACUUG-UGCC-AC-U-UCUGCCAGUCCCCUU-CAUACAAUU
AAWR02007429.1/15588-15717 GUGCACAUUUCAUUGACCUGCUUUCUCUCGUA-UAUGUGAGCAGUGUUAUUUCUUAUGUGCUAUAUAAACAGUUGAAGGUUAAUUAGCAGUAUAACU--AAA-UAGU-CA-U-GCUGCCAGUCUCCUU-CAGACAGUU
AAKN02003058.1/62071-62199 GUGCACAUUUCAUUGUCUUUUUUCAUCUAUA---UUGAGAGAAAAGAUAUUUCUGAUGUGCUAGACAACC-UUUGAAGGUAAAUUAGCAGCAUGACUAACUU-AGCC-AU-U-GCUGUCAGUCACCUU-CAGACAAGA
AAGV020558147.1/1261-1136  UAGCACAUUUCAUUGACUUGCUUUCUUUU-----GUGUGAGCAGUGUUAUUUCUUAUGUACUAUUCAAAUAGUUGAAGGGUAAUUAGCAGUAUCACU--AAA-UAGU-AA-U-GCUGCCAGUCGUCUU-CAAACAAAA
AAHX01066731.1/33946-33815 CUGCACAUUUCAUUGACCUGCUUUCCUUUGAC-UGUGUGAGCAGUGUUAAUUCUUAUGUGCUAUACUAAUAGUUGAAGGUUCAUUAGCAGAGUAACUGCAUA-UAGU-AA-U-UCUGCCAGUCCCCUU-CAGACAAAA
FJ915956.1/1-132           GUGCACAUGUCAUUGACCUGCUUUCUUCUGUA-UAUGUGAGCAGUGUUAUUUCUUAUGUGCUAUACAAAUAAUUGAAGGCUAAUUAGCAGUAUAACUAUAAA-AAGU-AA-U-GCUGCCAGUCUCCUU-CAGACAAAA
CR387241.1/112-244         AUGCACAUUUCAUUGACCUGCUUUCAUUGCAA-GUGAUGAGCAGUGUUAUUUCUGGUGUGCUAAAGAAAUAUUUGAAGGCUAAUUAGCAGCUUAGCUGUACG-UAGU-UACU-GCUGCCAGUCUCCUU-CAUACAAAG
CU855499.13/114122-114251  GUGCACAUUUCAUUGACCUGCCUUCUCUUGUA-UAUGUGAGCACUGUUAUUUCUUAUGUGCUAUACAAAUAAUUAAAGGUUCACUAGCAGUAUAACU--AUA-UAGU-AA-U-GCUGCCAGUCCCCUU-CAGACAAAU
EU240338.1/1-124           AAGCACUUCACAUUCUU----UUUCUUUAAUA--GUGGGAAC--AAAGAUAUUUGAAGUGCUAAAAAGA-ACUUGAAGGUAAAUUAGCAGUGUGGUUAAUGU-UGCC-AG-U-ACUGUCAGUCACCUU-CAUACAAAA
EU240314.1/1-133           ACGCACAUUUCAUUGACCUGCUUUCAUUGCAA-GUGAUGAGCAGUGUUAUUUCUGGUGUGCUAAAGAAAUAUUUGAAGGCUAAUUAGCAGCUUAGCUGUACG-UAGU-UACU-GCUGCCAGUCUCCUU-CAUACAAAG
FQ227960.1/40-171          UUGCACAUCUUAUUGACCUGCUUUCUUUGGAA-UAUGUGAGCAGUGUUAUUUCUUACGUGCUAUACACAUAGUUGAAGGUUAAUUAGCAGAGUAACUGCAUA-UAGU-AA-U-UCUGCCAGUCCCCUU-CAGACAAAA
AACZ03071819.1/3779-3907   GUGCACAUUUCAUUGUCUUUUUUCUUUAUU----UCAAGAGAAAAGAUAUAUCUGAUGUGCUAAACAAACCUUUGGAGGUUAAUUAGCAGCAUGACU-AAUU-UAGC-CA-UUGCUGCCAGUCACCUU-CAAACAAGU
AAWZ02027052.1/39211-39081 AUGCACAUAUCAUUGACCUGCUUCCUUUGCAU--UGGCAAGCAGUGUUAUUUCUGAUGUGCUAAAGGAAUGUCUGAAGGCUAAUUAGCAGCUUCGUUUCAUU-UAGU-GU-U-GCUGCCAGUCUCCUU-CGUACAAGC
AAGW02051107.1/19524-19655 CUGCACAUUUCAUUGGCCUGCUUUCUUUAUAU--GUGUGAGCAGUGUUAUUUCUUAUGUGCUACACAAAUAGUUGAAGGUUAAUUAGCAGUAUAACUAUCAAGUAGU-AA-U-GCUGCCAGUCUCCUU-CAGACACAA
AAQR03046717.1/1758-1886   GUGCACAUUUCAUUGACCUGCUUUCUUUAU----AUGUGAGCAGUGUUAUUUCUCAUGUGCUAUACAGAUAGUUGAAGGUUAAUUAGCAGUAUAACUAUAAA-UAGU-AA-U-GCUGCCAGUCUCCUU-CAGACAAGA
AAEX03015577.1/23253-23125 GUGCACAUUUCAUUGACCUGCUUUUCUUGUAU--AUGUGAGCAGUGUUAUUUCUUACGUGCUAUACAAAUAGUUGAAGGUUAAUUAGCAGUAUAACU--AAA-UGGU-AA-U-GCUGCCAGUCUCCUU-CAGACACAU
AAPE02042235.1/16420-16547 GCGCACAUUUCAUUGACCUGCUUUCUUGUAU---AUGGGAGUAGCGUUAUUUCUCAUGUGCUAUACAAAUAGUUGAAGGCUAAUUAGCAGUAUAACU--AAG-UAGU-AA-U-GCUGCCAGUCUCCUU-CAGACAAAC
AAGU03026370.1/19843-19972 GUGCACAUUUCACUGACCUGCUUUCUUUUAUA-UUUGUGAGCAGUGUUAUUUCUUUUGUGCUAUACAAAUAGUUGAAGGUUAAUUAGCAGUAUAACU--AAG-UAGU-AA-U-GCUGCCAGUCUCCUU-CAGACAAAC
#=GC SS_cons               ::<<<<<----------<<<<<__________.._____>>>>>------------>>>>>------------<<<<<<-------<<<<<<<-<<<_____._>>>.->.>.>>>>>------>>>>.>>:::::::
#=GC RF                    gUGCACaUUUCAUUGaCcuGCUUUcuuUuuua..aUguGAGCagUGuUAUUUCUuAuGUGCUAuAcAAAUAgUuGaAGGuUAAUUAGCAGcguagcuauaaa.Uagc.aa.c.gCUGCCAGUCuCCUu.CagACAaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00414
#=GF ID   SNORA22
#=GF PI   snoACA22
#=GF DE   Small nucleolar RNA SNORA22
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   80.00
#=GF TC   80.00
#=GF NC   79.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300777;
#=GF DR   snoopy; Loxodonta_africana300466;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA22 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA22
#=GF SQ   31


AJ609437.1/1-134             UUGCACAGUGAACACCCAAGUGUGCU-UUAUAGUU-C-C----CUUGGCUU--UGACCCUGUGCUAGAGCAUUG----CCUGCUCUUCUCCUCUG-CAUUAAAAGGAAUAUU--UAUCCUUUUAAAUGUAUUCAGAAAGCCAGCACAUUA
AC073210.8/129951-130084     UUGCACAGUGAACACCCAAGUGUGCU-UUAUAGUU-C-C----CUUGGCUU--UGACCCUGUGCUAGAGCAUUG----CCUGCUCUUCUCCUCUG-CAUUGAAAGGAAUAUU--UAUCCCUUUAAAUGUAUUCAGAAAGCCAGCACAUUA
AC092579.3/114744-114881     UUGCACAGUGAACACCCAAGUGUGCU-UUAUAGUU-C-C----CUUGGCUU--UGACCCUGUGCUAGAGCAUUCAUUACCUGUUCAUCUGCUCUG-CAUUGAAAGGAAUAUU--UGUCCUUUUAAAUGUAUUCAGAAAGCCAGCACAUUA
AC121336.3/155535-155667     UUGGGCAGUGAACACCCAAGUGUGCU-UUAUAGUU-C-C----UUUGGCUU--UGACUUUGUGCUAGAGCAAUG----UCUGUUAUUUUUCUCUG-CAUUGAAAGGAGCAUU--UAUCCUUUUAAAUGUAUUCAGAAAGCCAGUACAUU-
AB022159.1/10119-10254       UUGCACAGUGAACACCCAAGUGUGCU-CUGUAGUU-C-C----CUUGGCCU--UGACUCUGUGCUAGAGUAAAG----UCUGUUCUUUUCCUCUGACAUUAAAAGGAAUACU-GUGUCCUUUUCAAUGUAUUCAGAAAGUCAGCACACCA
AAFC03070778.1/3796-3663     UUGCACAGUGAACACCCAAGUGUGCU-UUGUAGUU-C-C----CUUGGCUU--UGACUCUGUGCUAGAGUAAUG----UCUGUUCUUUUCCUCUG-CAUUGAAAGGACUAUU--UAUCCUUUUAAAUGUAUUCAGAAAGUCAGCACAUUA
AANN01150672.1/731-865       UUGCACAGUGAACACCCAAGUGUGCU-UUAUAGUU-C-C----CUUGGCUU--UGACCCUGUGCUAGAGCAAUG----UCUGUUCUUUUCCUCUG-CGUUGAAAGGGCUACU-UUAUCCCUUUAAAUGUAUUCAGAAAAGCAGCACAUUA
AAPY01320644.1/537-670       UUGCACAGUGAACACCCAAGUGUGCU-UGAUAGUU-C-C----CUUGGCUU--CGACUCUGUGCUAGAGCAAUG----UCUGGUCUUUUCCUCUG-CGUUGGAAGGACUAUU--UAUCCUUUUAAAUGUAUUCAGAAAACCAGCACAUAA
AALT01504546.1/1608-1479     UUGCACAGUGAACACCCAAGUGUUCU-UUAUAGUU-C-C----CUUGGUUU--UAACUCUGUGCUAGAGCAAUG----UCUGUUCUUUUCCUCUG-CACUGAAAGGACUA------UCCUUUUAAGUGUAUUCAGAAAGUCAGCACAUUA
AAIY01105610.1/1801-1934     UCGCACAGUGAACACCCGAGUGUGCU-UCGUAGUU-C-C----CUUGGCCU--UGACACUGUGCUAGAGCAAUG----UCUGGUCUUUUCCUUUG-CAUUGAGAGGCACAUU--CAUCCUUUCAAAUGUAUUCAAAAGGCCAGCACAUCU
ABDC01507313.1/680-547       UUGUACAAUGAACACCCAAGAGAGCU-UUAUAGUU-C-C----CUGGACUU--UGACACUGUGCUGGAGCAAUG----ACUGUUCUUUUCCUCUG-CAUUGAAAGGAGUAUU--UAUCCUUUUAGAUGUAUUCAGAAAGCCAGCAAGCAC
AAFR03053799.1/48700-48567   CUGCACAGAGAACACCCAAGCUUACU-UUGUAGUU-C-C----CUUGGCUC--AUAGUCUGUGCUAGAGUAAUA----GCUGCUCUUUUCCUCUG-CAUUGGAAGGAAUAUC--UAUCCUUUUAUAUGUAUUCAGAAGGGCUGCACAUUU
AAHX01095956.1/6269-6143     CUGCACAGUGAACACCCAAGUGUGCU-CUGUAGUU-C-C----CUUGGCCU--UGACUUUGUGCU-----AAAG----UCUUUUCUUUUCCUCUG-CAUUGAAAGUA--CUG--UGUCCUUUUAAAUGUAUUCAGAAAAUCAGCACACCA
AAPN01399938.1/10516-10383   UCGCACAGCGAACACCCAAGUGUGCU-CUCUAGUU-C-U----CUUGGUCU--AAAUUCUGUGCUAAAGCAAAC----GUUGUUCUUUUCCUCUG-CAAUGAAAGGAGUCCU--UUUCCUUUUAUAUGUAUUCAGAAGGACAGCACACGG
AC188585.3/120174-120042     UUCCACAGUGAAUA-CCAAGUUUGCU-UUAUAGUU-C-C----CAUGGCUU--UGACUGUAUGCUAGAGCAAUG----UCUGUGGUUUCCCUCUG-CAUUGAAAGGAGCAUU--UAUCCUUUUAAAUGUAUUCAGAAAGCCAGCACAUUU
AAYZ01395334.1/11-145        UUGCACAGUGAACACCCA--AGUGUGCUUGCCACU-U-GGGGGGGUGGCUU--UGAUUCUGUGCUACAGCAACG----UCUGUCCUUUUCCUCUA-CAUUGAAAGGCGCUUU----GUCCUUUGAAUGUAUUCAGAAAGUCAGCACAUGA
CAAE01015001.1/644943-644807 GUGCACAGCGAACACCCAAGGAUGCUAACAUGGCU-CCC----CCUGGUCUCCUGAAUCUGUGCUAAAGUA-AA----UCUGAUUUGUACCUCUG-CAUUUGGAGAGCUGCU--UUCUCUUUUAAAUGUAUUCAGCAGAUCAGAAUAAAU
AANH01000630.1/47101-47237   AAGCACAGAGAACACCCAAGGGUGCUAACGUAGCU-CCC----CCUGGUCUCUUGUAUCUGUGCUACAGUA-AA----UCUGAUCUGUACCUCUG-CAUUUGGGGAGUCCCU--UUCUCUCCUACAUGUAUUCAGCGGAUCAGAAUAAAC
BAAE01260308.1/33-169        GUGCACAGUGAACACCCAAGGAUGCUGCUGUGGCUCU-C----CCUGGUCUCCUCUAUCUGUGCUACAGUA-AC----UCUGAUCUGUACCUCUG-CAUUGGGACAGUCUCC--UCCUCUCCUACAUGUAUUCAACAGAUCAGAAUAAUC
AAKN02045360.1/34070-34205   UUGCACAGUGAACACCCAAGUGUGCU-UUGUAGUU-C------CUUGGCUU--UGACUCUGUGCUAGAGUAAUG---UCCUGUUCUUUCCCUCUG-CAUUGAAAGGACUAUUUUUUUCCUUUUAAAUGUAUUCAGAAAGGCAGCACAUAC
AAWR02041249.1/41666-41533   UUGCACAGUGAACACCCAAGUGUGCU-UUAUAGUU-C-C----CUUGGUUU--UGAAUCUGUGCUAGAGCAAUG----UCUGUUCUUUUCCUCUG-CGUUGAAAGGACUAUU--UAUCCUUUUAAAUGUAUUCAGAAAGUCAGCACAUAU
AAGV020756141.1/682-811      UUGCACGGUGAACACCCAAGUGUACU-UUAUAGUU-C-C----CUUGGCUU--UGACUCUGUGCGAGAGCAAUA----UCUGUUCUUCUCCUCUG-CAUUGAAAGGAAUA------UCCUUUUAAAUGUAUUCAGAAGUUCAGCACAUUU
EU240266.1/1-132             UUGCACAGUGAACACCCAAGUGUGCU-UCAUAGUU-C-C----CUUGGUUU--UAAUUCUGUGCUAGAAUA--A----CCUGUGCUUUUCCUCUG-CAUUGGAAGGAUUGGC--AUUCCUUUUAUAUGUAUUCAGAAGGACAGUACAUUU
AC210185.5/49852-49719       UUGCACAGGGAAUACCCAAGUGUGCU-UUAUAGUU-U-C----CUUGGCUU--UGACCCUGUGCUAGAGCAUUA----CCUGUUCUUCUCCUCUG-CAUUGAAAGGAAUAUU--UAUCCUUUUAAAUGUAUUCUGAAAGCCAGCACAUUA
AC183835.2/139954-139821     UUGCACAGUGAACACCCAAGUGUGCU-UUAUAGUU-C-C----CUUGGCUU--UGACCCUGUGCUAGAGCAUUG----CCUGCUCUUCUCCUCUG-CAUUGAAAGGAAUAUU--UAUCCUUUUAAAUGUAUUCAGAAAGCCAGCACAUUA
AAPE02029714.1/60660-60793   UUGCACAGUGAACACCCAAGUGUUCU-UUAUAGUU-C-C----CUUGGCUU--UGACUCUGUGCUAGAGCAAUG----UCUGUUCUUUUCCUCUG-CAUUGAAAGGACUGUU--UAACCUUUUAAAUGUAUUCAUAAAGUUAGCACAUUA
CAAB02004364.1/67803-67667   GUGCACGGUGAACACCCAAGGGUGCUAACAUGGCU-CCC----CCUGGUCUCUUCUACCUGUGCUAUAGUA-AA----CCUGAUUUGUACCUCUG-CAUUUGGGGAGCUGUC--UCCUCUCUUAAAUGUAUUCAGCAGAUCAGAAUAACU
AAGW02070483.1/11846-11713   UUGCACAGUGAACACCCAAGUGUGCU-UGAUAGUU-C-C----CUUGGCUU--UAACUCUGUGCUACAGCAAUG----UCUGUUCUUUUCCUCUG-CAUUGAAAGGAGUUUU--UAUCCUUUCAAAUGUAUUCAGAAAGUCAGCACAUUA
AAQR03103689.1/10688-10559   UGGCACAGUGAACUCCCAUGGU-GCU-UUACGCUU-G-C----CUUGGCUU--UGACUCUGUGCUGGAGCAAUG----UCUGAUC-UUUCCUCUU-CAUUAAAAAGA--AUU--UAUCCUUCUAAAUGUAUUCAAAGAGCUGGAACCUUU
AAEX03015256.1/99943-100074  ACACUUAG--AACAGUUAGAUGGCUU-UAAUGGUU-C-C----CUUGGCUU--UGACACUGGGAUAGAGCAAUG----UGUGUUUUUUACCUCUG-CAUUGAAUAGACUGUU--UAUCCUUUUGAAUGCAUUCAGAAAGUCAACACAUUA
AAGU03064421.1/22012-22145   UUGCACAGUGAACACCCAAGUGUGCU-UUAUAGUU-C-C----CUUGGCCU--UGACUCUGUGCUAGAGCAACA----UCUGUUCUUUUCCUCUG-CAUUGGAAGGAGUAUU--UAUCCUUUUAAAUGUAUUCAAAAGGUCAGCACAUUU
#=GC SS_cons                 ::<<<<<<-<--<<-<<<<<-<-<<<.____>>>-.>.-....>>>>>---..>>-->>>>>>>,<<<<<<___....__>>>>>>,,,,,<<<<.<<<<<<<<<<<_____..__>>>>>>>->>>>---->>>>::::::::::::::
#=GC RF                      uUgCaCAGUgAAcaCCCAaGugUgcu.uuaUagcU.c.C....CuUGGcUU..ugAccCUGuGcUagagcAAug....uCUgcucuUUuCCuCUG.CAuugaaaGggaUaUU..UaccCuuuuAaaUGUAUUCAGaAaguCAGcAcAuua
//
# STOCKHOLM 1.0

#=GF AC   RF00415
#=GF ID   SNORA30
#=GF PI   snoACA30
#=GF DE   Small nucleolar RNA SNORA30/SNORA37 family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   90.00
#=GF TC   91.20
#=GF NC   89.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; ACA30;
#=GF DR   snoRNABase; ACA37;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Takifugu_rubripes300026;
#=GF DR   snoopy; Danio_rerio300064;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the H/ACA class of snoRNAs that guide
#=GF CC   the sites of modification of uridines to pseudouridines [1]. This family
#=GF CC   includes human ACA30 (SNORA30), ACA37 (SNORA37) and the mouse homolog
#=GF CC   MBI-26 [1,2]. Both ACA37 and ACA30 are predicted to guide the
#=GF CC   pseudouridylation of residue U4643 of 28S rRNA [3].
#=GF WK   Small_nucleolar_RNA_SNORA30
#=GF SQ   11


AC061992.11/62174-62302   UGGGCCCUUU-CACAGGCCCU-CCCCUCGGCAGUGGGGCCAGGAUUGGGUUGCUGGUGCUGAGAGAAAGCCC-UUGAUUGCAU--CCUUGCUCUGGGACU----GUACCAG-UGGCAGCUGUCACUUAGUGGGACAGAG
AJ609440.1/1-129          CUGGCACUUU-CACAGUUCCU-UCCCCAGGCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAACCC-UUGAUUGUAU--UCUUGCCCUGGGAUU----AUACCAG-UGGCAACUGUCACUCAAUGGGACAGUG
AL929469.10/31415-31550   UGAGCACUUU-AACAGGUCCUGGUCUCUGUGUGGUAGACCAUGAUUUGGUAGCUGGUGCUGAAAUUAAAUCUGUCUCUCAUGA--AAAACCCCAGAUUUUCGCUCUGUCUGCUGGGUGCAUUUGAGAGAGAGGACACUU
AL929469.10/26637-26772   UAAGCACUUUUAACAGGUCGUGGUCUCAGUGCAGUAGGCCAUGAUUUGGUAGCUGGUGCUGAUAUGAAAGCU-CUCUUUGAAGAAAAUCCAGCGGCUCUUCGU-AUGGCUG-UUUGGAUUAUCAGGGAGAGACACACAG
AL929469.10/25756-25891   UAAGCACUUUUAACAGGUCGUGGUCUCAGUGCAGUAGGCCAUGAUUUGGUAGCUGGUGCUGAUAUGAAAGCU-CUCUAUGAAGAAAAUCCAGCGGCUCUUCGU-AUAGUUG-UUUGGAUUAUCGGAGAGAGACACACAG
AF357389.1/1-107          ------------------------CUUUGUCAGUGGGGUCAGGAUUUGGUAGCUGGUGCUGAGAUAAAACCC-UUGAUUACAU--CCUUGCCCUGAUACU----GUACCAG-UGGCAGCUGUUACUCAAGGGAACAGUG
AC122417.4/78415-78544    CUAGCACUUUUCACAGGUCCU-UCCUUUGUCAGUGGGGUCAGGAUUUGGUAGCUGGUGCUGAGAUAAAACCC-UUGAUUACAU--CCUUGCCCUGAUACU----GUACCAG-UGGCAGCUGUUACUCAAGGGAACAGUG
AC124482.3/139847-139976  CUAGCACUUUUCACAGGUCCU-UCCUUUGUCAGUGGGGUCAGGAUUUGGUAGCUGGUGCUGAGAUGAAACCC-UUGAUUACAU--UCUUGCCCUGAUACU----GUACCAG-UGGCAGCUGUUACUCAAGGGAACAGUG
AJ609444.1/1-129          UGAGCACUUU-CACAGGUCCU-CCCUCAGGCUGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAACCU-UUGUUGGCAU--CCUUGCCCUGGGACU----GUGCCAG-UGGCAGCUGUCAUUCAAUGGGACAAUU
AC093462.11/145947-146075 UGAGCACUUU-CACAGGUCCU-CCCUCAGGCUGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAACCU-UUGUUGGCAU--CCUUGCCCUGGGACU----GUGCCAG-UGGCAGCUGUCAUUCAAUGGGACAAUU
AL445624.3/80903-80775    CUAGCAUUUU-CACAGGUCCU-CCCUCAGGCUAUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAACGC-UUGAUUGCAU--CCUUGCCCUGGGACU----GUGCCAG-UGGCAGCUGUCACUCAAUGGGACAAUU
#=GC SS_cons              ::<<<<<<--.--<<<-<<<<.-<<<<_______>>>>-->>>>->>>------>>>>>>---------<<<.<<<<-<<-<<..--<<<<<<<<<____....___>>>>.->>>>>-->>>>->>>>->>>::::::
#=GC RF                   uaaGCaCuUU.aACagGuCcU.ucCccaGucuguggGgcCAgGaUuuGGUAGCUgGuGCuGAgAuaAAAccc.uugcUugcac..aauugccCuGguauU....aUacCaG.UggcaacUgucaugcaaugggACAaug
//
# STOCKHOLM 1.0

#=GF AC   RF00416
#=GF ID   SNORA43
#=GF PI   snoACA43
#=GF DE   Small nucleolar RNA SNORA43
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   80.00
#=GF TC   80.40
#=GF NC   79.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00029
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300091;
#=GF DR   snoopy; Homo_sapiens300456;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA43 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA43
#=GF SQ   21


AJ609446.1/1-136           CG-UGUCCUGGACCUG------UUGGCACCACAGA--CAGUUGCUCUGCUGUGCCUGUGGCC--UCGG-GGCAAAGAGAAAGUGGCGAUUUCUACACUCAGUGCUCGGGAACCAGUGGGCACUGAGAAUGGUUUAUGGCCUGACAUUA
AK090585.1/1147-1282       GC-UGUCCUGGACCUG------UUGGCACCACAGA--CAGUUGCUCUGCUGUGCCUGUGGCC--UCGG-GGCAAAGAGAAAGUGGCGAUUUCUACACUCAGUGCUCGGGAACCAGUGGGCACUGAGAAUGGUUUAUGGCCUGACAUUA
AC096587.1/25864-25727     GC-UAUCCUGGACUUG------CCAGCCCCAUAGACACAGUUGCUGUGCUGUGCCUGUACUA--UUGG-AGCAAAGAAAAAGUGGCUAUUUCUAUGCUCAGUGUUCACAAACCAGUGAGCACUAAGAAUGGUUUAUAGCCUGACAUUU
AC026161.4/89260-89123     GC-UGUCCUGGACCUG------CCAGCUGCACAGAUGCAGAUGCUCUGCUAUGCCUGUAACA--UCGG-GGCGAAGUGAAAGUGGCUAUUUCUACACUCAGUUUUCAGAAAACAGUGAACAACAAGAAUGGAUAAUAGCCUGACAUUU
AC034186.5/119166-119029   GC-UGUCCUGGACCUG------CCAGCUGCACAGAUGCAGAUGCUCUGCUAUGCCUGUAACA--UCGG-GGCGAAGUGAAAGUGGCUAUUUCUACACUCAGUGUUCAGAAAACACUGAACAACAAGAAUGGAUAAUAGCCUGACAUUU
AL732311.13/48731-48593    GC-UGUCCUAGAUCAGC----ACCACAGGCAUGGCA-CAGCUGCUCAGCUGAGCCUGUGACA--UUGG-GGCAAAGAGCAAGUGGCUGUUUCUACGCUCAGUGCUCAGAAGCCCGUGAGCACUAAGAAUGGUUUGUAGCCUGACAUUU
AC136926.4/4433-4305       AAAAUCUGAGAACA-------ACCACAGGCAUGGC------U---CAGCUUUGCCUGUGACA--UCGG-GGAAAAGAGCAAGUGGCUAUUUCUACACUCAGUGUUCAGAAGCCAGUGAGCACUAAGAAUGGUUUGUAGCCUGACAUUU
ABDC01507407.1/1127-990    GC-UGCACUGGUCCUG------CCAGCACCACAGGUGUGGCUGCUCUGCUGCACCUGUGACA--UCGG-GGCAAAGAGAAAGUGGCUAUUUCUACGCUCAGUGUUCCGAAACCAGUGAACACUAAGAAUGGUUUGUAGCCUGACAUUU
AANU01102204.1/7007-7140   GC-UGUCCUGGACCUG------UCGGCA--CCAGA--CAGUUGCUCUGCCGUGCCUGUGACC--UCGG-GGCAAAGAGGAAGUGGCGAUUUCUACACUCAGUGCCCGGGAACCAGUGGGCACUGAGAAUGGUUUAUGGCCUGACAUGA
AANG01778266.1/91-226      CA-GACGCCGGGCCUC------CCGGCACCACAGACACAGCUGCUCUGCUGCACCUGUGACG--UUGG-GGCAAAGAGGAAGCGGCUAUUUCUACGCUCAGUGCUCAGAA--CCGUGGGCACUAAGAAUGGUUUGUAGCCGAACAUGC
AAFC03061596.1/7185-7318   GA-UGCC--GGAUUUG------CCGGCACCACGGGUGCGGCCGCCCUGCUGCGCCUGUGCCG--UUGG-GGCAGAGAGAAAGCGGCUAUUUCUACGCUCAGUGCUCAGAACCA--UGGGCACUAAGAAUGGUUUGUAGCCAAACAUCA
AALT01661828.1/1748-1607   AG-UGCCCUGCGGAUGCUGAGCUGAGCGCCUCAGACAUGGCUGCCCGGAUGCAUCUGUGACA--ACAG-GGCACACAGUAAGUGGCUAUUUCUACGCUCAGUGUCCAGA--CCCAUGGGCACUAAGAAUGGUUUGUAGCCUCACAUUG
AAWR02025983.1/2331-2464   GA-UG--CUGGACCUG------CCAGCACCACAGACGCAGCUGCUCUGCUGCACCUGUGACG--UCAG-GGCAAAGAGCAAGUGGCUAUUUCUACGCUCAGUGCUCAGAA--CAGUGAGCACUAAGAAUGGUUUGUAGCCUGACAUUU
FJ915971.1/1-134           GC-UGUCCUGGACCUG------UCGGCA--CCAGA--CAGUUGCUCUGCCGUGCCUGUGACC--UCGG-GGCAAAAAGGAAGUGGCGAUUUCUACACUCAGUGCCCGGGAACCAGUGGGCACUGAGAAUGGUUUAUGGCCUGACAUGA
JN899077.1/13-146          GA-UGCC--GGACCUG------CCGGCACCAUGGCUGCAGCUGCUCUGCUGCACCUGUGACC--UUGG-GGCAAAGAGGAAGCGGCUAUUUCUACGCUUAGUGCCCAGAA--CAGUGGGCACUAAGAAUGGUUUGUAGCCGGACAUUG
EU094030.1/2-136           GG-UGCCCCUC-----------GAGGCGUUGCAGAUGUGGCUGCGGUGCCCCAUUUGUGUCA-UGAGGUGGCAGAGAGGAUAAGGCUAUGUCUACGCUCCGUGUUCAAAAAUUUGUGAGCACGCAGAAUGAUUAAUAGCCUGACAGUU
EU094034.1/4-136           UA-UGCCCCUA------------GAGGCGUACAGAUGGGGCUGCUGUGCCUCAUUUGUGUCAUAUGGU-GGCAUAGAGCAAAAGGCUAUGUCUACGCUCGGUGUUCUCAG-UCCAUGAACACUCAGAAUGAUUAGUAGCCUGACAAUG
AAPE02038825.1/6643-6777   CG-GGUGCUGGACCUG-------CGGCACCACAGACGCGGCUGCCGUGCUGCACCUGUGACG--CCAG-GGCACAGAGGAAGUGGCUAUUUCUACGCUCAGUGCUCAGAA--CAGUGGGCACUAAGAAUGGUUUGUAGCCUGACAUUC
AAQR03116487.1/1257-1120   AC-UGUACUGGACCUG------CCAGCACCACAGGUGUGGCUGUGCUGCUGUGCCUGUAACA--UCAG-GGCAAAGAGAAAGUGGCUAUUUCUACGCUCAGUGUUCAGAAACCAGUGAGCACUAAGAAUGGUUUAUAGCCUGACAUUU
AACN010843946.1/504-369    CA-GGUGCUGGACCUA------CUAGCACCACAGAUACAGCUGCUUUGCUGCACCUGGGAUG--UCAG-GGCAAAGAGGAAGUGGCUAUUUCUACGCUCAGUGCUCAGAA--CAGUGGGCACUAAGAAUGGUUUGUAGCCAAACAUGC
AACZ03027090.1/32836-32712 GC-UGUCCUGGACCUG--------------CCAGG-----AUGCUCUGCUAUGCCUGUAACA--UCGG-GGCGAAGUGAAAGUGGCUAUGUCUACACUCAGUGUUCAGAAAACAGUGAACAACAAGAAUGGAUAAUAGCCUGACAUUU
#=GC SS_cons               ::.<<<<<<<<-----......--------<<<<____________________>>>>----..>>>>.>>>>----------<<<-----<<<--<<---<<<<<<________>>>>>>--->>-->>>------>>>::::::::
#=GC RF                    ga.uGccccggAccUG......ccaGcacCaCaGaugcaGcUGCucUGCUguacCuGuGaCa..ccgg.ggCaaAGAGaAAGuGGCUAUUUCUACgCUCAGUGcuCaGAAacCaGuGagCACUaAGAAUGGUUugUAGCCUGACAUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00417
#=GF ID   SNORA56
#=GF PI   snoACA56
#=GF DE   Small nucleolar RNA SNORA56
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   80.00
#=GF TC   92.50
#=GF NC   77.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00039
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Macaca_mulatta300700;
#=GF DR   snoopy; Tupaia_belangeri300420;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA56 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA56
#=GF SQ   17


AJ609449.1/1-129             CGGCAGACAGUUAUCCC-UUUCUAGUCUGGCUCGUGGGA-CUCUAGA-GGGAGUCAGUCUGCAACA-GUAAG---UGG-UGAG---UUCU---UCUGUCCAGCGUCA--GUAUUUUGAUGG-UGGCUUUAGA-CUUGCCAGAUAACA
AF067021.1/482-610           CGGCAGACAGUUAUCCC-UUUCUAGUCUGGCUCGUGGGA-CUCUAGA-GGGAGUCAGUCUGCAACA-GUAAG---UGG-UGAG---UUCU---UCUGUCCAGCGUCA--GUAUUUUGAUGG-UGGCUUUAGA-CUUGCCAGAUAACA
AJ010396.1/584-712           CGGCAGACAGUUAUCCC-UUUCUAGUCUGGCUCGUGGGA-CUCUAGA-GGGAGUCAGUCUGCAACA-GUAAG---UGG-UGAG---UUCU---UCUGUCCAGCGUCA--GUAUUUUGAUGG-UGGCUUUAGA-CUUGCCAGAUAACA
AF067020.1/980-1114          CGGCAAACAGUUAUCCCCUUUCUAGUCUGGCUCCUGGGAACUCUAGAAGGGAAUCAGUCUGCCACAAGUAAG---UGGGUGAA---UUCU---UCUGUCCA-CGUCA--GUAUUUUGAUGGGUNGCUUNAAAACUUGCCAGAUAACC
AAPY01755613.1/4896-5019     UGGCAG----UUAUCCU-UUUCUAGUCUGGCUCCUGGGA-CUCUAGA-AGGAGUCAGUCUGCAACA-AUAAG---UGG-UGAG---UUCU---UCUGUCCAGUGUCA--GUGU-UUGAUGG-UGGCUGUAGA-CCUGCCAGAUAUCA
AALT01522843.1/1298-1170     CCGCAGAUGGUUAUCCC-UUUCUUGUCUGGCAUGGGGGA-CUCUAGA-GGGAGUCAAUCUGCAAAA-ACAAG---UGG-UAAG---UUCUGCUUCUGCCUAGCUUGU--GCCUAU---UGG-UGGCUUUAGA-CUUGCCAAACAUGG
AAFC03026691.1/25084-25212   AAGCAGC-AGUUAUCCC-UUUCCAGUCUGGCUUGUGAGA-CUCUAUA-GGGAGUCAAUCUGCAAUAGUUAAG---UGG-UUAG---UUCU---UCUGUCUAGGAUCA--GUGUUUUCAUGG-UGACUUUGGA-GUUGCCAUAUGUUA
AAFR03063568.1/11670-11804   AAGCAGACAGUUAUCCC-UUUCUGGUCUUCCUCUCGUGA-CCUUAGA-GGGAGUCAGUCUGCAACA-UGAAGUGAUGG-CAAG--CUGUU---UCUGGCCAGCAUCACAGUGUGUUGAUGG-UGGUUUCAGC-CUUGCCAGACACCC
AAWR02040681.1/192386-192517 CAGCAGACAGUUAUCCC-UUUCUAGUCUGGGUCAUGGGA-CUCUAGA-GGGAGUCAGUCUGCAACA-GCAAG---UGG-UGAGUUCUUCU---UCUGUCCAGCGUCA--GUAUUUUGAUGG-UGGCUUUAGA-CUUGCCGGAUAGCA
AAGV020334157.1/3542-3670    UAGCAGACAGUUAUCCC-UUUCUAGUCUGGCUCACGGGA-CUCUAGA-GGGAGUCAGUCUGCAACA-UUAAG---UGG-UGAG---UUUU---UCUGUCCAGCGUCA--GUAUUUUGAUGG-UGGCUUUAGA-CUUACCAGAUAUCA
AC186067.22/167381-167255    CAGCAGACAGUUGCCCU-UUUCUAGUCUGGCUCGAGGGA-CUCUAGA-GGGAGUCCGUCUGCGACA-GUAAG---UGG-UGAG-----CU---CGUGUCUGUCAUCA--GUAUUUUGACGA-UGGCCGUAGA-CUUGCCAGAUAGCG
AC202044.3/84019-83894       CGGCAGACAGUUAUCCC-UUUCUAGUCUGGCUCGUGGGA-CUGUAGA-GGGAGUCAGUCUGUAACA-GUAAG---UGG-UGAG---UUCU------GUCCAGCGUCA--GUAUUUUGAUGG-UGGCUUUAGA-CUUGCCAGAUAACA
AC157529.2/35836-35708       CGGCAGACAGUUAUCCC-UUUCUAGUCUGGCUCGUGGGA-CUCUAGA-GGGAGUCAGUCUGCAACA-GUAAG---UGG-UGAG---UUCU---UCUGUCAAGCGUCA--GUAUUUUGAUGG-UGGCUUUAGA-CUUGCCAGAUAACA
EU094018.1/2-134             AAGCAGGCGGUUAUCCC-UCUCUAGCCUG-AUCGGGUGG-CUCUAGA-GGGAGUCAGUCUGCAAAA-UCAAA---UGG-AAGG---CCCUGUUUCUGUCCAGCACCACAGUGCUUUGGUGG-UGGUUGCAGA-CCUGCCAUAUAUGG
EU094011.1/2-131             AGGCAGAUGGUUAUCCC-UCUCUAGUCUG-AUCCAGUGU-CUCUAGA-GGGAGUCAGUCUGCAAAA-UCAAC---UGG--GGG---CCCUGUUUCCGUCCAGCAUCAUGGUUCUUUGAUGA-UGGUUUCAGA-CCUGCCAUAC--AU
AAGU03086851.1/17075-16948   GUGCAGACAGUUACCCC-UUUCUAGUCUGGCUCCUGGGA-CUCUAGA-GGGAGUCAGUCUGAAAUA-UUAAG---UAG-UGAA---CUCG---UCUGUCCAGUGUCA--GUGUUC--AUUGGCAACUUUAGA-CUUGCCAAGUAUCA
AAPE02031702.1/77896-77768   CAGCAGACAGUUAUCCC-UUUCUAGUCUGGCAUGUGGGA-CUUUAGA-GGGAGUCAGUCUGCAACA-GUAAG---UGG-UGAG---UUGC---UUUGUCCAGCGUCA--GUAUUUUGAUGG-UGGCUUUAGA-CUUGCCAGAUAACU
#=GC SS_cons                 ::<<<<<<---------.--<<<<<<<<________>>>.-->>>>>.-------->>>>>>----.-----...<<<.<<<<...-<<<...---<<<---<<<<<..<____>>>>>>-.->>>--->>>.>>>>>>>:::::::
#=GC RF                      aaGCAGacAGUUAUCCC.UUUCuaGuCcGGcUcguGgGa.CUCuaGA.GGGAGUCAguCUGCAAcA.uuAAG...uGG.cgag...Uucu...UcUGcCcAGcguCa..gUaUuuuGacgG.UGgCUuuaga.cuugCCagAUAuca
//
# STOCKHOLM 1.0

#=GF AC   RF00418
#=GF ID   SNORA58
#=GF PI   snoACA58
#=GF DE   Small nucleolar RNA SNORA58
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD
#=GF GA   75.00
#=GF TC   75.00
#=GF NC   73.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00036
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300089;
#=GF DR   snoopy; Homo_sapiens300665;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   ACA52 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1]. This family also includes
#=GF CC   the mouse sequence MBI-12 as reported in [2].
#=GF WK   Small_nucleolar_RNA_SNORA58
#=GF SQ   20


AJ609450.1/1-137             GGGCAUACUCGUAGACCUUGCCUGACUGUGCUCA-UGUCCAGGCAGGGGGGACAGU-GUAUGCAAGAAU-AAUUUGGAG-UUCCUGCCAGC-UCUAACCAGCUU-----CAUCAGUGGCUGGAUAAAUUGCAGGACUCUAAACAUUU
AL049745.9/70858-70993       GGGCAUACCCGUAGACCUUGCCUGACUGUGCUCA-UGUCCAGGCAGGGGGGACAUU-GUAUUCGAGAUU-AAUUUGAAG-UUCCUGCCAGC-UUUAUCCAGCUU-----AAUCAGUGGCUGGAUAAAUAGCAGGACUGUAA-CAUUC
AL590431.11/107122-107257    GGGCAUACCCGUAGACCUUGUCUGACUGUGCUCA-UGGCCAGGCAGGGGGGACAGU-GUAUGCAAGAGU-AAUGUGGAG-UUUGUGCUAAC-UCUAGCCAGCUU-----AAUUAGUGACUGGAUAAAUUGCACAACUCUCA-CAUUC
AF357386.1/1-126             ---------CGUAGACCUUGCUUGACUCUUGUCUGUGGCCAAGCAAGGGGGACAGA-GUAUGCGAGAGU-AAUU-GGAG-UUCAUGCAAGU-UCUAACCAGCUU-----ACUCAGUAGCUGGGUGAAUUGCAGUACUCCAA-CAUU-
ABDC01240840.1/7748-7883     UGGCAUACCCGUAGACCUUGUCUGACUAGGCUAA-UGGUCAGGCAGGGGGGACAGU-GUAUGCAAGAGU-AAUUUGGAG-UUCAUGCCAGC-UCUAGCCAGCUU-----AAUCAGUGGCUGGAUAAAUUGCAGUACUCUAA-CAUUC
AAYZ01244227.1/6985-6849     AGGCAUACCAGUAGACCUUGUCUGACUGUGUUCA-UAGCCAGGCAGGGGGGACAGU-GUAUGCAAGAGUUAAUUUGGAG-UUCUUGCCAGC-UGUAGCCAGCUG-----AAUCAGUAGCUGGGUAAAUUGCUGCACUCCAA-CAUGA
AAQQ01789110.1/2055-1919     AGGCAUAUCCGUAGACCUUGCUUGGCUCUGCUUA-UGGCCAGGCAGGGGGGACAGU-GUAUGCAAGAAU-AAUCCGGAG-UUUAUGCAAAC-UCAAACCAGCUU-----CUUCGGUAGCUGGAUAAAUUGCAGUACUCCCUACAUUU
AAFC03027776.1/78849-78983   GGGCAUACUUGUAGACCUUGCCUGACUAUCCCUG-UGGCCAGGCAGGGGGGACAGU-GUAUGCAAGAGU-AAUAUGGAG-UUUGUGCUAGC-UCUUGCCAGC-U-----CAUUAAUGGCUGGAUGAACUGCAGUUCUCCAA-CAUUC
AALT01368588.1/10575-10440   AGGCAUAACAGUAGACCUUACCUGACCCUGCCCA-UGGUCAGGCAGGGGGGACAGU-GUAUGCAAGAGU-GAUGUGGAG-UUCAUGCCAUC-UCUAGUCAGCUU-----CAUAAGUGGCUGAAUAAUUUGCGGUACUCCUA-CAUUC
AANG01021210.1/2924-3059     GGGCACACCCGUAGACCUCGCCUGACUCUGCCCG-UGGCCGGGCGAGGGGGACAGU-GUGUGCAAGAGU-CACGGGGAG-UUCUUACCAGC-UCCAGCCAGCUC-----GCUCGCCGGCUGGAUAAAU-GCAGUGCUCCCAACAUUC
AAFR03052180.1/39136-39003   UGGCACACCAGUAGACCUUGUGUAACU--GCCUG-UAGUCACACAAGGGGGACAGU-GUGUGCCAGAGG-AAGC-AGAG-CUGCUGUGAGCCUAUGGCCAGCAC-----UAUCAGUGGUUGGCUGUAUCACAUUACUCUGA-CAUCU
AAIY01556911.1/2337-2197     GGGCAGACUCGUAGACCUUGCUUAACAGUGCUCA-UAGCCAGGCGAGGGGGACAGUUGUGUGCAAGAGU-GCUGUGAAU-UUAA-GCCAGC-UCUAGCCACUGAUUAAACAUCAGUGGUUGGAUAAAUUGUAGUACUCUAA-CAUUC
AAGV020286123.1/3444-3308    UAGCAUACAAGUAGACCUUGCCUGGCUUUGUUUA-UAGCCAUGCAAGGGGGACAAU-GUAUGCAACAGU-AAUUUGGAAGUUUGUGCCAGC-UCUAGCCAGCUU-----AAUUAAUGGCUGGAUAAAUUGCAGUAUUCCAA-CAUUC
AAWR02038694.1/28998-28863   GGGCAUACCCGUAGACCUUGCCUGACUAUGCUCA-UGGCCAGGCAGGGGGGACAGU-GUAUGCAAGAGU-AAUUUGGAG-UUCGUGCCGGC-UCUCGCCAGCUU-----AAUCAGUGGCUGGAUAAACUGCAGUACUCCAA-CAUUC
FJ915977.1/1-136             GGGCAUACCCGUAGACCUUGCCUGACUGUGCUCA-UGGCCAGGCAAGGGGGACAGU-GUAUGCAAGAGU-AAUGUGGAG-UUUGUGCUAAC-UCUAGCCAGCUU-----AAUUAAUGACUGGAUAAAUUGCACAACUCUCA-CAUUC
AAQR03004710.1/116908-117043 AGGCAUACCAGUAGACCUUGCCUGACUCAGCUCG-UGGCCAGGCAGGGGGGACAGU-GUAUGCAAGAAU-AAUUUGGAG-UUUGUGCCAGC-UCUAGCCAGCUU-----AAUCAGUGGCUGGGUAAACUGCAGUACUCCAA-CAUUC
AAHX01045690.1/49714-49848   AGGCAUAUCCGUAGACCUUGCUUGACUCUGCCUG-UGGCCAAGCAAGGGGGACAGC-GUAUGCAAGAGU-AAUU-GGAG-UUCAUGCAAGU-UCUAACCAGUUU-----AACCAGUAGCUGGGUGAAUUGCAGUACUCCAA-CAUUC
AAEX03005350.1/129693-129557 GAGCAUACCCGUAGACCUCGUCUGACUGUGCUUG-UGGCCAGGCGAGGGGGACAGU-GUAUGCAAGAGU-AACUUGGAG-UUUGUGCCAGG-UCUAGCCAGCUA-----AAUCAGUAGCUGGAUAAAUUGCAGCACUCCCAACAUUC
AAGU03056415.1/42942-43077   GGGCAUACUCGUAGACCUUGCUUGACUGUGCUCA-UGGCCAGGCAGGGGGGACAGU-GUAUGCAAGAGU-AAUUUGGAG-UUUAUGCCAGC-UCUGGCCAGCUU-----CAUCAGUGGCUGGAUAAAUUGCAGUACUCCGA-CAUUC
AAPE02038631.1/120933-121068 GGGCAUACCCGUAGACCUUGCCUGACUGUGCUCA-UGGCUAGGCAGGGGGGACAGU-GUAUGCAAGAGU-AAUUUGGAG-UUUGUGCCAGU-UCUAGCCAGCCU-----ACUCAGUGGCUGGAUAAGUUGCAUUACUUCAA-CAUUU
#=GC SS_cons                 ::<<<<<<-------<<<<<<<<<__________.____>>>>>>>>>--------.>>>>>>------.-----<<<<.-<--<<<----.-----<<<<<__.....________>>>>>------->>>-->>>>>::.:::::
#=GC RF                      gGGCAuAcccGUAGACCuuGccUGACUgUGcuca.UgGCCAggCaaGGGGGACAGU.gUaUGCAAGAGU.AAUuUggAG.UuuauGCcAGc.UcUAgCCAgcuu.....aAUcAgUGgcUGGaUAAAUUGCaguaCUccaA.CAUUc
//
# STOCKHOLM 1.0

#=GF AC   RF00419
#=GF ID   SNORA52
#=GF PI   snoACA52
#=GF DE   Small nucleolar RNA SNORA52
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   71.00
#=GF TC   71.20
#=GF NC   67.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF CL   CL00038
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300768;
#=GF DR   snoopy; Echinops_telfairi300683;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA52 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA52
#=GF SQ   21


AJ609448.1/1-134             UGGUCCAU-CCUAAUCCCUGCCGG-UCCAUCUGU-GG--C--CUGCCAGGUUUCGCUUGUGGACCAGAGCACCCUAGAAG-CCUCAC-C-C-GAG--GAGUGAG-CAG-GGCUCCAGUGGGCUCACGUCAUGG-GCA--CUUCUAGACACUC
AB061837.1/2430-2563         UGGUCCAU-CCUAAUCCCUGCCGG-UCCAUCUGU-GG--C--CUGCCAGGUUUCGCUUGUGGACCAGAGCACCCUAGAAG-CCUCAC-C-C-GAG--GAGUGAG-CAG-GGCUCCAGUGGGCUCACGUCAUGG-GCA--CUUCUAGACACUC
AC109542.6/197354-197221     UGGUCCAU-CCUAAUCCCUGCUGG-UCAGCC--CGUG-AU--CUGCCAGGCUUCGCUUGUGGACCAGAGCAUCCUAGAAA-CCCUGC-C-A-GAG--UUGUGCG-AGG-CCUUUUUGUGUGCUUGUGCCGGCA-GCG--CUUCUGAACACGC
X55153.1/1676-1809           UGGUCCAU-CCUAAUCCCUGCUGG-UCAGCC--CGUG-AU--CUGCCAGGCUUCGCUUGUGGACCAGAGCAUCCUAGAAA-CCCUGC-C-A-GAG--UUGUGCG-AGG-CCUUUUUGUGUGCUUGUGCCGGCA-GCG--CUUCUGAACACGC
AAFC03097110.1/4392-4258     CGGUCCAU-UCUAAUCCCUGCCGG-UCAGCC--UGUG-GC--CUGCCAGGCUUCGCUUGUGGACCAGAGCACCCUAGAAG-CCUUAC-C-CAGAG--GAGUGAG-CAG-GGUCUCCGUGGGCUCAUGCUAUGG-GCG--CUUCUAGACAACC
AANG01640232.1/288-421       UGGUCCAU-CCUAAUCCCUGCCGG-UCAGCC--UGUG-GC--CUGCCAGGUUUCGCUUGUGGACCAGAGCACUCGAGAAG-CCUCAC-C-CAGAG--AAGUGAG-CAG--GCUUCAGUGGGCUUGUGCCGGGG-AUG--CUUCUAGACAUUC
ABDC01529339.1/1-132         ---UCCAUCCCUAAUCCCUGCUGG-CCCCCU--GUGG-AC--CUGCCAGGUUUCGCUUGUGGACUAGAGCACCCUAGAAG-CUUCAC-C-C-AGA--GAGUGAG-CAG-AGCUUCAGCUAGCUCAUGUCACGG-AUG--CUUCUAGACAUUA
AAQQ01384200.1/1380-1248     U-GUCCAU-CCUAAUUCCUGCUGG-UCAAC---UAUG-GC--CUGCCAGGUUUCGCUUGUGGACUACAGCACUGUAGAAG-CCUGAC-C-U-GAG-UGGGUGAG-CAA-GGCCUUCAAGGGCUCAUGCCGGGG-AUG--CUUCUGGACACUG
AAIY01543731.1/3884-4020     CAGUCCAU-CCUAAUCCCUGCUGG-CCAGGC--CGUG-GC--CCACCAGGGUUCGCUUGUGGACCAGAUCACCCUAGGAGCCUUGCC-C-A-GCG--GAUCGGU-CAG-ACUUUUGGUGGCCUCACUCCAUGG-GCAUGCUCCCAGGACAGC
AANN01790302.1/1491-1617     GGGUCCAU-CCUAAUCCCUGCUGG-CCGGC---CAUG--G--CCUCCGGGGUUCGCUCGUGGACCAGAGCACCGUGGAAG-UCCCAC-C-CACCA--GCGAGGG-------UCUCUGUGG-CCCUUUGCAUGG-GUG--CUUCUAAACACCC
AALT01232683.1/1888-1759     AGGUCCAU-CCUAAUCCCUGCUGG-CUAGCC--AGUG-GC--CUGG-AGGGUUCACUUGUGGACCAGAGCACCCUGAACG-CCCUCC-C-AGGAA--GACCGGG-CUA-CUGUGUCCUG-GCCUGGGGCUGGG-UUU--C---UGGACAUUC
AAFR03066205.1/4239-4369     CUGUCCAU-CCUAAUUCCUGCUGG-UCGCUC--C-UGUAC--CUGCCAGGCUUCGCUGGUGGACCAGAGUAUCUCGGAGA-CUCUCC-C-G-G------UGCCG-CGC-CGCCGCAGUGGCCGGCAGCCAGCCAGGG--UCUCUAAACACUC
AAGV020943529.1/1465-1332    GGGUCCAU-UCUAAUCCCUGCUGG-CCAGCC--UGUG-GC--CUGCCAGGCUUCGCUUGUGGACCAGAGCACCCUAGAAG-CCUGCC-UUA-GAG--GAGUGAG-CUG--GCUGCAGUGGGCUCACACUGCGG-GUG--CUUCUAGACAUGC
AAWR02047868.1/1151-1285     CAGUCCAU-CCUAAUUCCUGCCGG-UCAGCC--UGUG-GC--CUGCCAGGUUUCGCUUGUGGACCAGAGCACCCUAGGAG-CCUCAC-C-CAGAG--GAGCUGG-CAG-GGCUUCAGUAGGCUCAUGCCACGG-GCG--CUUCUAGACAUUC
AAKN02056355.1/137040-136905 UGGUCCAU-UCUAAUUCCUGCUGG-UCAGGC--UGUG-GC--CUGCCAGGUUUCGCUUGUGGACCACAGCACUCUGGAAG-CUUGACUC-A-AAA--GAAUGAG-CACAGGCCCUCAUGGGCUUAUGUUGGAG-GCA--CUUCUGGACACUU
AC102547.8/25951-25815       UGGUCCAU-CCUAAUACCUGCUGG-UCAGCC--AGUG-AU--CUGCCAGGCUUCGCUUGUGGACCAGAGCAUCCUAGAAA-CACUGC-C-A-GAGUUGUGCAAGGCCU-UUUCAUUUUAGGCUUGUGCCUGCA-GCG--CUUCAGAACACCC
HQ318037.1/679-812           GGGUCCAU-CCUAAUCCCUGCUGG-UCAGCC--UGUG-GC--CUGCCAGGUUUCGCUUGUGGACCAGAGCACUCUAGAAG-CCUCAC-C-CAGAG--AAGUGGG-CAG--GCUUCAGUGGGCUUGUGCCAGGG-GCG--CUUCUAGACAGUC
AC190029.3/119190-119057     UGGUCCAU-CCUAAUCCCUGCUGG-UCCGUC--UGUG-GC--CUGCCAGGUUUCGCUUGUGGACCAGAGCACCCUAGAAG-CCUCAC-C-U-GAG--GAGUGAG-CAG-GGCUCCAGUGGGCUCAUGUCAUGG-GCG--CUUCUAGACACUC
AADN03004446.1/121593-121461 AGGUCCAU-UCUAAUUCCUAGCAGGUUGGUG--C-CA-GUACCUGUGGGGUUUCGCUUGUGGACCACAUUAUACUGGAAG-ACUUAA-A-U-GUG--U-AUGAG-CUU-ACUGGUAGUUUGCUCAUGACAUAG-U----UUUCUGGACAUAC
AAEX03003503.1/61797-61663   UGGUCCAU-CCUAAUCCCUGCCAG-UCGGCC--UGUG-GC--CUGCCAGGUUUCAUUUGUGGCCCAGAAUAUUCUAGAAG-CCUUAC-CUA-GAG--GAGUGAG-CAA-GGCUUCAGUGGGCUUGUACCAGAG-GUG--CUUCUAGACACUC
AAQR03181100.1/17910-17779   UGGUCCAU-CCUAAUUCCUGCUGG-CCCCCA--GUGG--C--UUGCCAGGUUUCGCUUGUGGACUAGAGCAUCCUAGAAG-CUUCAC-C-C-AAA--GAGUGAG-CAG-GGAUUCAGUUGGCUCAUGUCAUU--GUG--CUUCUAGACACUC
#=GC SS_cons                 <<<<<<<<.-------<<<<-<<<.-<<<__..>->>.--..>>>->>>>-------->>>>>>>>-------<<<<<<<.------.-.-.---..--<<<<<.<__.___________>>>>>>-------.---..>>>>>>>::::::
#=GC RF                      ugGUCCAU.CCUAAUcCCUGCcgG.UCggcc..cgcG.gc..CugCCAGGuUUCGCUUGUGGACcaGAGCAcccuaGAAG.CcUuaC.C.a.GaG..gagugaG.Cag.aguuuuaGUgGGCucacGcCaugG.gug..CUUCuagACAcuC
//
# STOCKHOLM 1.0

#=GF AC   RF00420
#=GF ID   SNORA61
#=GF PI   snoACA61
#=GF DE   Small nucleolar RNA SNORA61
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   74.00
#=GF TC   74.00
#=GF NC   73.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300287;
#=GF DR   snoopy; Loxodonta_africana300174;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA61 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA61
#=GF SQ   25


AJ609451.1/1-130           AUCCUCCUGAU-CCCUUUCCCAUCGGAUCUGAACACUGGUCUUGGUGGUCGUAAA-AGGAGG-----AAAAGUAAUAG---UGAAGCUG-GCCUAAAUG-U---UGU---AAUCUGGUAUAUGGCAUGUGGGCUAGUUUCAGACAGGU
AL670276.13/34787-34916    ACCCUCCGGUUUCCCUUUCCCAUCGGAUCUUGACGCUGGUCUUGGUGGUCGUUAA--GGAGG-----AAGAGCACCC----UGAAGCUG-GCCUCACAG-CG-AUGC---AGUCUGCUGUAGAGCA-GCAGGCCAGACUCAGACAUGC
AL807234.6/143918-143791   ACCCUCCAGUUUCCCUUUCC-AUCAGAUCUUGACACUGGUCUUGGUGGUCGUAAA--AGAGG-----AAGAGUGGCC----UGACACUG-GCCUCACAG-CG-AUGC---AGUU-GCUGUAGAGCA-GCAGGCCAAACUCAGACAUGC
AL929545.8/89263-89392     ACCCUGCGGUUUCCCUUUCCCAUCAGAUCUUGACACUGGUCUUGGUGGUCAUAAA--GGUGG-----AAAAGCAGCC----UGAAGCUG-GUCACACAG-CA-AUGC---AGUUUGCUGUAGAGCA-ACAGUCCAGACUCAGACAUGC
ABDC01019451.1/1606-1737   GCCCUCCAGUU-CCCUUUCCCAUCUGAUCUGAACACUGGUCUUGGUGGUCGUAAA-AGGAGG-----AAAAGUAAUAC---UGAAGCUG-GCCACGCAG-UG-UUGU---AGUUUGUUAUAUGGCACGUGGGCUAGUUUCAAACAAAG
AACN010799948.1/292-160    ACCCUCCGGUU-CCCUUUCCCAUCGGAUCUGAACGCUGGUCUUGGUGGUCGUAAA-AGGAGG-----AAAAGGAAAAG---UGAAUCUG-GCCCUGCAG-UGCUUAU---AGUCUGGUAUAUAGCUUGUGGGCUAGUUUCAAACAAGG
AANG01671212.1/157-289     ACCCUCCGGUU-CCCUUUCCCAUCAAAUCUGAACACUGGUUUUGGUGGUCAUAAG-AGGAGG-----AAGAGAAACAC---UGAAGCUG-GCCUCACAG-UGCUUAU---GGUCUGGUAUAUAACCCAUGGGCUAGUUUCAAACAAGG
AALT01584320.1/6370-6236   ACCCUCCUGUU-CCCUUUCCCAUCGGAUCUGAACACUGGUCUUGGUGGUCGUAAA-GGGAGG-----GAUAGUAACAC---UGAAGCUG-GCCUCACAG-GG-CUCCUUGGUUCUGCCAUGUAGCACAUGGGCUAGUUUCAAACAAAC
AANN01000642.1/789-921     GCCCUCUGGUU-CCCUUUCCCAUCAGAUCUGAAUAUUGGUCUUGGUGGUCGUAAA-AGGAGG-----GAUAGCAAUAC---UGAAGCUG-GCUUCAUAGGCU-CUGU---AGUCUGCCAUUUAAUAUGUGGGCUAGUUUCAAACAAAU
AAFC03087627.1/39513-39638 ACCCUCCAGUU-CCCUUUCCCAUCGGAUCUAAACCCUGGUCUUGGUGGUCAUAAA-AGGAGG-----AAUAGUAGUAC---UGAAACUGUGCUCG---------UGG---UGUGUGCUGUACAGCACGUGGGCUAGUUUCAGACAAGG
AAIY01614200.1/1964-2085   ACCCUCCAGUU-CCCUUUCCCAUCGGAUCAUAAUACUGGUCUGGGUGGUCGUAAA-AGGAGG-----AAAAGAAACAC---UGAAGCUG-GCCC------UC-AGUG---CUCUUGGAG----CCC-UUGGGCUAGUUUCAAACAGGG
AAYZ01245008.1/2835-2707   ACCCUCCAGCU-CCCUUUCCCAUCGGAUCUGAACACUGGUCUUGGUGGUCGUUCA-AGGAGG-----AAGAGUGAACC---UGGAGCUG-GCCUGGCGC-UG-GCGC---ACCU-GCUGCACAGC--ACGGCCCGGUUUCAGACAGGG
AAQQ01371992.1/3282-3151   AACCU-CUCAUUCCCUUUCUCAUCAGCUCUGAACACUGGUCUUGGUGUUGGCAAA-AGAAGG-----ACAAAUUAUAC---UGAAGUUG-ACCUCAAAG-UU-UUGC---AGUUUGGUACAUAGUAUGUGAGCUAAUUUCAAGCAGGG
AAPY01601113.1/9600-9737   ACCCUCUGACU-UCCUUCCCCUUUGGAACUGAACACUGGUCUUGGUGGUAGUUAAAACGAGGUAGUAAAAAGUAAUAC---UGAAGCUG-GCCAUAUGG-UG-GUGU---AGCCUGGUAUACAACAUGUGGGCUGGUUUUGAACAGGC
AANU01284457.1/990-1119    AUCCUCUGGUU-CCUUUUCCCAUUGGAUCUGAAUGCUGGUCUUGGUGGUUGUAAA-AGGAGG-----AAAAGUAACAC---UGAAGGUG-GCUUCGCAG-UC-UUGU---AGUCUGGCAUA--UCGUUUCCACAAUGGUUUGAAAUAA
CR389043.1/365-482         UCCCUCCAGAU-CCCUUUCCCAUCAGAUCUGAAUACCGAUCUUG-UGGUCGAAAA-AGGAGG-----AAAAGCAGCAU---UCAGACUG-GCCU-------U-GGCC---UCUUUGCU-----GGC-ACAGCCCUG-CUCUGAGCGGG
AC106169.5/11615-11486     ACCCUCCUGUUUCCCUUUCCCAUCGGAUCUUGACACUGAUCUUGGUGGUCCUUAA--CGAGG-----AAGAGUACAC----UGAAGCUG-GCCUCACAG-CG-AUGC---AGCUUGGUGUAGAGCA-UCAGGCCAGAUUCGAACAUGC
AAGV020994835.1/913-793    -AUCUUCUGGUUUCCUUUCCCAUCUUAUCUGAACCCUGGUCUGGGUGGUCAUAAA-AGGAGG-----AAAAGUAACU----UUAAACUG-ACCUCACAG-GG-C--------UUUGUAGCAUG-----UUGGUUAGUUUCAAUCAGGU
AAWR02028293.1/8900-9032   CCCCUCCGGUU-CCCUUUCCCAUCGGAUCUGAACUCUGGUCUUGGUGGUCGUAAA-AGGAGG-----AAAAGUAAUGC---UGAAGCUG-GCCUCACGG-CGCUUGU---AGUCUGCUAUAGAGCAUGUGGGCUAGUUUCACACAAGG
AAKN02003745.1/41666-41800 ACCCUCCAGUU-CCCUUUCCCAUCGGAUCUAAACACUGGUCUUGGUGGUCGUUAA-AGGAGG-----GAAAGGAGGAAUGCUGAAGCUG-GCCCCAACG-CC-UUAU---AGUCUGGUAUACUGCAGAUGGGCUAGUUUCAAACAGGG
FJ915978.1/2-131           AUCCUCCUGUU-CCCUUUCCCAUCGGAUCUGAACACCGGUCUUGGUGGUCGUAAA-AGGAGG-----AAAAGUAAUAG---UGAAGCUG-GCCUGAAU---G-UUGU---AAUCUGGUAUAUGGCAUGUGGGCUAGUUUCAGACAGGU
EU094023.1/3-130           ACCCUCUGGAU-CCCUUUCCCAUCAGGUCUGCACACCGACCUGGGUGGUCGUAAA-UGGAGG-----GAAAGGAACU----GGAUGCGG-GCCCGAGUG----UCUG----GUGUGGAGACAGCGGACCAGGCCCGGUCCUCACAAUC
AAPE02052949.1/58030-58149 ACCCUCCAGUU-CCCUUUCCCAUCGGAUCUGAACACCGAUCUUGGUGGUCGUAGA--GGAGG-----AAAAGUAAUAA---UGAAGCUG-GCCUCACAG-UG-C---------UUACAGUCUG-----UGGGCUAGUUUCAAACAAGG
AAGW02062791.1/16318-16446 ACCCUCCGGUU-CCCUUUCCCAUCGGAUCAGAACACUGGUCUUGGUGGUCGUACA-AGGAGG-----AAAAGUGAUAC---UGAAGCUG-GCCUCACCG-UG-UUGU---AGUCUGAUAUA--GCA-CUGGGCCAGCGUCAGACAGGG
AAQR03047486.1/5415-5549   AUCCUCCCGAUUCCCUUUCUUAUCAGAUCUGAAUACUGGUCUUGGUGGUUGUAAA-AGGAAG-----AAAAGUAAUACA-CUGAAGCUG-ACCUCACAU-UG-UUGU---AGUGUGGUAUAUAUCAUGUGGGCUAGUUUCAAACAAAG
#=GC SS_cons               ::<<<<<----.-------<<<<<-<<<<________>>>>-->>>>>-------.->>>>>.....-----------...-----<<<.<<<<-----.--.-<<<..._____________>>>--->>>>>>>::::::::::::
#=GC RF                    AcCCUCcaGuU.CCCUUUCCCAUCgGAuCUGAACACUGgUCUUGGUGGUcGUAAA.AgGAGG.....AAAAGuAAuac...UGAAGCug.GCcccAcaG.ug.uugc...AgUuUGguaUAuagcaugUggGCcaGuUUCaaACAaGg
//
# STOCKHOLM 1.0

#=GF AC   RF00421
#=GF ID   SNORA32
#=GF PI   snoACA32
#=GF DE   Small nucleolar RNA SNORA32
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   60.00
#=GF TC   60.30
#=GF NC   59.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300602;
#=GF DR   snoopy; Homo_sapiens300366;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA32 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA32
#=GF SQ   9


AJ609442.1/1-121          UGGUCAUUACCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAAAAA--UUUCCCAGUAGGUUUUCUA-UCUGCUACUUUGCUAGCAAUCAGCUUAUUGGGAACAGUU
AK128061.1/3770-3890      UGGUCAUUACCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAAAAA--UUUCCCAGUAGGUUUUCUA-UCUGCUACUUUGCUAGCAAUCAGCUUAUGGGGAACAGUU
AK027016.1/1395-1517      UGGUCAUUACCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAAAAAAAUUUCCCAGUAGGUUUUCUA-UCUGCUACGUUGCUAGCAAUCAGCUUAUUGGGAACAGUU
AL589699.4/106209-106088  UGGUCAUUACCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAGAAAA-AUUCCCAUGAGGUUUUUCA-UAUGCUACUUGACUAGCAGUUAACCUGUUGGGAACAUUU
AL591067.35/160576-160455 UGGUCAUUACCAAGGCUUUUAGAAUGCAGUUUCUCAUUUGCUGUGGACAUGACCAUAAAGAAAA-AUUCCAAUGAGGUUUUUCA-UAUGCUACUUGACUAGCAGUUAACCUGUUGGGAACACGU
AC133505.3/6863-6742      UGGUCAUUACCAAGGCUUUUAGAAUGCAGUUUCUCACUUGCUGUGGACAUGAACAUAAAGAAAA-AUUCCCAUGAGGUUUUUCA-UAUGCUACUUGACUAGCAUUUAACCUGUUGGGAACAUGU
AC021733.12/63797-63917   -GGUAAUUACCAAGAUUUUUAGAAUGCAGUUUCUCAUUUGCCAGGGAAAUGACCAUAAAAUAA--UUUCCCACUAGAUUUUUUUAUCUGUUACCUUGCUAGCAAGCAGUCUAUUGGGAACAUUU
AP001741.1/8721-8841      UGGUUGUUACCAAGGCAUUUAGCAUGCAAUUUCUCAUUUGCUGUGGACACGACGAGAAGAGAA--UUCCUCACUCGGUUUUCUG-UCUGCCACCUUGCUAGCGAUCAGCCCACUGGGAACAUUU
AL954241.1/199482-199602  UGGUUGUUACCAAGGCAUUUAGCAUGCAAUUUCUCAUUUGCUGUGGACACGACGAGAAGAGAA--UUCCUCACUUGGUUUUCUG-UCUGCCACCUUGCUAGCGAUCAGCCCACUGGGAACAUUU
#=GC SS_cons              ::<<<<<--<<<-------------<<<<________>>>>-->>>-->>>>>----------..---<<<<---<<<<-----.--<<<__________>>>--->>>>--->>>>:::::::
#=GC RF                   UGGucauUACCaAGGCuUUUAGaAUGCagUUUCUCAUuuGCUGuGGAcaugaCcAuAAAaaAA..uUUCcCauuaGGcuUUuua.UcuGCUACuUugCUAGCaaUcagCCUaUuGgGAACAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF00422
#=GF ID   SCARNA24
#=GF PI   snoACA12
#=GF DE   Small Cajal body specific RNA 24
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   70.00
#=GF TC   73.60
#=GF NC   68.50
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00018
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300788;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. ACA12 belongs to the H/ACA
#=GF CC   box class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail
#=GF CC   structure,the conserved H/ACA-box motifs and is found associated with GAR1
#=GF CC   [2]. ACA12 is predicted to guide the pseudouridylation of residue U40 of
#=GF CC   the spliceosomal U6 snRNA [2].
#=GF WK   Small_Cajal_body_specific_RNA_24
#=GF SQ   23


AJ609482.1/1-130             UGGACAUUUAU--UUUUAUUCAGUUUCUUCUCAAGGUGAAGAUA-ACU-CUUUGUAAAUGUCCUACAGA-------AAUAUAGUAGCUUUCUGUUCUUCCUUUGCAAG-UAA-AAAG-GGUGGGUCGUUCCACUACUGACAUUU
AL645729.14/35264-35393      UGGACAUUUAU--UUUUAUUCAGUUUUUUCUCAAGGUGAAGGUA-ACU-GUUUGUAGAUGUCCUAGAGA-------AAUAUUGUAGCUUUCUGUUCACCCUUUGCAAC-UAA-AAAG-CAUGGACUGUUCCACUACUGAGAUUU
AC011120.11/127524-127388    CAGACAUUCAU--UUUUAUCCAGUUUCUUCUCAAAGUGAAGAUA-ACU-UUUUGUAAAUGUCCUAAAGUCAUGUAGAAUGUAGUAGCUUUCUGUUCACACUGUACAAA-UAA-AAAG-GAUGGAUCAUUCUACAACUGACAUUA
AAFC03040928.1/6763-6892     UGGACAUUUAC--UUCUAUUCAGUUUCUUCUGAAGGUGAAGAUA-ACU-CUUUGUAAAUGUCCUAAAGA-------AAUACAGUAGCUUUCUGUUCACCCUUUGCUAG-UAA-AAAG-GGUGGAUCGUUCCACUACUGACAUUU
AAIY01149578.1/1023-1152     UGGACAUUUAU--UCUUAUUCAGUUUCUUCUUAAGGUGAAGAUA-ACU-CUUUAUAAAUGUCCUAGAGA-------AAUAUGGUAGCUUUCUGUUCACCCUUUGCAAG-UAA-AAAG-GGUGGAUUGUUCCACUACUGACACUU
ABDC01430031.1/3467-3596     UGGACAUUUAU--UUUUAUUCAGUUUCUUCUCAAGGUGAAGAUA-ACU-CUUUUUAAAUGUCCUAGAGA-------AAUAUAGUAGGUUUCUAUUCAACCUUUGUAAG-UAA-AAAG-GGUGGAUCGUUCUACUACUGACAAUU
AANU01100835.1/3577-3448     UGGACAUUUAU--UUUUAUUCAGUUUCUUCUCAAGGUGAAGGUA-ACU-GUUUGUAAAUGUCCUAGAGA-------AAUAUGGUAGCUUUCUGUUCACCCUUUGCAAG-UAA-AAAG-CGUGGAUUAUUCCACCGCUGACAUUU
AAQQ01362516.1/1193-1322     UGGACAUUUAU--UUUUAUUCAGUUUCUUCUCAAAGUGAAGGAA-ACU-CUUUGUAAAUGUCCUAGAGA-------AAUAUAGUAGCUUUCUGUUCACCUCUUGUAAG-CAA-AAAG-GGUGGAUCGUUCCACUACUGACAUUC
AAPY01747800.1/1383-1513     UGGACAUUGAC--UUUUAUUCAGUUUCUUCUCAAAGUGAAGAUA-ACU-CUUUAUAAAUGUCCUAGAGA-------AAUAUAUUAGCUUUCUGUUCACCCUUUGCAAG-UAA-AAAGGGGUGGAUCGUUCCACUACUGACAUUU
AAYZ01705947.1/614-742       UGGACAUUUAU---UGUAUUCAGUUUCUUCGCAAGGUGAAGAUA-ACU-CUUUGUAAAUGUCCUAGAAU-------AAAAUAGUAGCUUUCUGUUCACCUUUUGCAAG-UGA-AAAA-GGUGGAUCGUUCCACUGCUGACAUUU
BX649240.1/16244-16375       UGGACAUUGAU--CUUAUUUCAGUUUCUCCUUCAUGUGGAGAUA-ACU-GAUCCUCAGUGUCCCACAUA-------AACAUAGAAGCUAUCUGUUCACUCUUGGAAAG-UAAACAAGGGUUGGAUCGUUCCACUUCUGACAAAU
AAFR03045911.1/103810-103679 UGGACAUUAGU--UUUAUUUCAGUUUCUCCUUCAUGUGGAGAUU-ACU-GAUCCCAAGUGUCCUAUAUA-------AAUACAGAAGCUAUCUGUUCACUCUUGGAAAG-UAAACAAGAGUUGGAUCGUUCCACUUCUGACAAAU
AALT01160167.1/12030-11901   UGGACAUUUAU--UUUCAAGCAAUUUCUUCUUACAGCGAAGAUA-ACA-ACUACUGAAUAUCCUAGAGA-------AAAUCAGUAGUUCUCUGUGUAUCCUAUGCAAG-UAA-AAUG-GGUGUAUCACCCCACUACUGACAUUU
AAHX01111234.1/19885-20006   UGGACAUUUAU--AUUGUCAAA--UUCUUCAGCAAGUGAAGAUAAUGUCAUUUAUGAAUGUCC---------------UGUAGUAGCUUUCUGUUCAUCCUUUUCGAG-AAG-AGAG-GGUGGAUGGUACCUCUACUGACAUUC
AAKN02043886.1/64417-64546   UGGACAUUUAU--UUUUAUUCAGUUUCUUCUCAAGGUGAAGAUA-ACA-CUUUAUAAAUGUCCUAGAGA-------AAUAUAGUAGCUUUCUGUUCACCCUUUGCAAG-UUA-AAAG-GGUGUAUCGUUCCACUACUGACAUUU
AAGV020289204.1/1435-1564    CGGACAUUUAU--UUUUAUUUGGUUUCUUCUCAAGAUGAAGAUA-ACU-CUUUGUAAAUGUCCUAGAGA-------AAUAUAGUAGCUUUCUGUUCACCCUUUGCAAG-GAA-AAAG-GGUGGAUCGUUCCACUACUGACAUUU
CT485675.4/156870-156741     UGGACAUUUAU--UUUUAUUCAGUUUCUUCUCAAGGUGAAGAUA-ACU-CUUUGUAAAUGUCCUACAGA-------AAUAUAGUAGCUUUCUGUUCAUCCUUUGCAAG-UAA-AAAG-GGUGGGUCGUUCCACUACUGACAUUU
CU570746.9/23443-23572       UGGACAUUUAU--UUUUAUUCAGUUUCUUCUCAAGUUGAAGAUA-ACU-CUUUGUAAAUGUCCUAGAGA-------AAUAUAGUAGCUUUCUGUUCACCCUUUGCAAG-UAA-AAAG-GGUGGAUCGUUCCACUACUGACAUUU
AAPE02002209.1/33830-33958   UGGACAUUUAC---UUUAUUCAGUUUCUUCUUAAGGUGAAGAAA-ACU-CUUUGUAAAUGUCCUAGAGA-------AAUAUAGUAGCUUUCUGUUCACACUUUGCAAG-UAA-AAAG-GGUGGAUCGUUCCACUACUGACAUAU
AAEX03026211.1/313679-313807 UGGACAUUUAU--UUUUGUUCAGUUUCUUCUUAAGGUGAAGA-U-ACU-CUUUGUAAAUGUCCUAGAGA-------AACAUAGUAGCUUUCUGUUCACUCUUUGCAAG-UAA-AAAG-GGUGGAUCGUUCCACUGCUGACACAC
AAGW02040860.1/7455-7326     UGGACAUUUAC--UUUUGUUUGGUUUCUUCUCAAAGUGAAGAUA-ACU-CAUUGUGAAUGUCCUAGAAC-------AAUAUAGUAGCUUUCUGUUCACCUUUUGCAAG-UGA-AAAA-GGUGAAUCGUUCCACUGCUGACAUUU
AADN03000452.1/149076-148946 UGGACACGUAAGUUUUCUUUCAGUUUCUCCUCUAUGUGGGGAAA-GCU-GUAC-UA-GUGUCCUAUAGU-------AACACAGAAGCUAUCUGUUCAACUCUGAUGAGUUAA-UAGA-GUUGGAUCGUUCCACUUCUGACAGCU
AAQR03091953.1/1258-1387     UGGACAUUUAC--UUUUAUUCAGUGUCUUCUCAAGGUGAAGACA-ACU-CAUUGUAAAUGUCCUAGAGA-------AAUACAGUAGCUUUCUGUUCACCCUCUGCAAG-UAA-GAAG-GGUGGGUCGUUCCACUACUGACAUUU
#=GC SS_cons                 :<<<<<<<<<<..--------<<<<<<<<<_______>>>>>->.>>>.---->>>>>>>>>>------.......----<<<<<<-------------<<<<_____.___.>>>>.-------------->>>>>>::::::
#=GC RF                      UGGACAuUuac..UUUuaUuCaGuuuCuuCUcaAaGUGaaGaUa.aCu.cuUuguaAaUGUCCUAgAga.......AAuAcaGuaGCUuUCUGUUCAccCuuugcAAG.UAA.aaaG.GgUGGAUcGUUCCACuaCugACAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF00423
#=GF ID   SCARNA4
#=GF PI   snoACA26
#=GF DE   Small Cajal body specific RNA 4
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   60.00
#=GF TC   61.20
#=GF NC   57.00
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00019
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300780;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. ACA26 belongs to the H/ACA
#=GF CC   box class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail
#=GF CC   structure, conserved H/ACA-box motifs and is found associated with GAR1
#=GF CC   [2]. Its is predicted to guide the pseudouridylation of residues U39 and
#=GF CC   U41 in U2 snRNA [2].
#=GF WK   Small_Cajal_body_specific_RNA_4
#=GF SQ   24


AJ609483.1/1-129           ACUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGUAAGACUUUGCUGAUACAUUCCUCCUAGAAAA-AA-GGGUUGGAGAGAGCAGCCUUCACUGA-----AGAGUA-UCAC-AGGG-CUGACUGUACUACCCAACACUC
AY270787.1/135-13          ACUGGAGGACUAA-GGAGGCUGGG-UCUGAUGAGGCAAGAUUUUGCUGAUACAUUGCUCCUAGAAAA-AA-GGGUUGGCAAGAGCAGCC----CUGG-----AGAC---UCAC-ACGG-CUGACUGUUCUACCCAACACUC
AL645803.19/80160-80034    -CUGGAGGAUCAA-GGAGGCUGAG-UCUGAUGAAGCAAGACUUUGUUGAUACACUCCUCCUAGACAA-AA-GGGU-GGGGAGAGCAGCCCGUACUGG-----AGAAAG-CCAC-AGGG-CUCACUGUGCUACCCAACAUUU
AAPY01340777.1/683-811     ACUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGCAAGACUUUGCUGAUACCCUCCUCCUAGAGAA-AA-GGGUUGAAGAGAGCAGCCGUCAUUGG-----AGAAUG-UCGC-AGGG-CUGACUGUACCACCCAACAUUG
AAIY01148998.1/131-258     ACUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGCAAGGCUCUGCUGAUACACUCCUCCUAGACAA-AA-GGGGUGGAGAGAGCAGCCCUUA-UGG-----AGAACA-UCAC-AGGG-CUGACUUUACUACCCAACAUUU
AANG01021475.1/9614-9486   GCUGGAGGACUAA-GAAGGCUGAG-UCUGGUGAAGCAAGACUCUGCUGAUACAAUCCUCCUAGAGAA-CA-GGGUGGGCGAGAGCAGCCCUCACUGG-----AGGACA-CCAC-GGGG-CUGACUGCACGACCCGACACGC
AANN01670216.1/501-630     GGUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGCAAGACUCUGCUGAUACAAUCCUCCUAGAGAA-AA-GGGUUUGAGAGAGCAGCUCUUACCGG----GAGAAAG-UCAC-AGGG-CUGACUGUAGUACCCAACAUUC
AALT01070738.1/638-766     UCUGGAGGAUCAA-GAAGGCGGAG-UCUGAUGAAGCAAGACUCGGCUGAUACAAUCCUCCUAGAGAA-AG-GGGUCAGAGAGAGCAGCCCUGCCUGG-----AGCACU-GCAC-AGGG-CUGACUGCACCACCCGACAUUC
AAFR03052106.1/48119-48247 GCUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGCUAGACUCUGCUGAUACAAUCCUCCUACAGAA-AA-GGGUUGGAGAGAGCAGUCCCACUUCG-----AGAAUA-GUAA-AGGA-CUGACUGUACUACCCAACAUUA
AAYZ01608759.1/256-126     CCUGGAGGACUAA-GAAGGCCAAG-UCUGAUGAAGCAAGCCUUGGCUGAUACACUCCUCCUAGAAAA-AAAGGGUUGGAGAGAGCAGCCCUUCAUGG-----AGAAGGUCCCA-GGGG-CUGACUGUACUACCCAACAUUC
AAFC03006841.1/13718-13584 ACUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGCAAGACUCUGCUGAUACAAUCCUCCUAGAAAA-AAAGGGUUGGAGAGAGCAGCCCUCCGUGUGUUAUAGAAUA-UCAC-AGGG-UUGACUGUAUGACCCGACAUUC
AANU01114943.1/32839-32967 ACUGGAGGACUAA-GGAGGCCAGA-UCUGAUAAGGCAAGAUUUUG-UAAUACGUUGCUCCUAGAAAA-AA-GGGUUGGCAAGAGCAGCCCUCACUGG-----AGACUA-UCAC-AGGGACUGACUGUUCAACCCGACACUC
AAWR02038660.1/76508-76636 GCUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGCAAGACUCGGCUGAUACAAUCCUCCUAGAAAA-AG-GGGUUGGAGAGAGCAGCCCUUAUUGG-----AGAGUA-UCAC-AGGG-CUGACUGUACUACCCAACACUC
AAKN02015658.1/41428-41300 ACUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGCAAGACUUUGCUGAUACAUUCCUCCUAAAAAA-AG-GGGUUGGAGAGAGCAGCCCAAAUUGG-----AGAACG-UCAC-AGGG-CUGACUGUACUACCCAACAUUC
AAGV020375682.1/3325-3454  ACUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGUAAGACUCUGCUGAUACAUUCCUCCUAGAAAAUAA-GGGUUGGAGAGAGUAGCCCUUAUUGG-----AGAAUA-UCAC-AGGG-CUGACUGUACUACCCAACAUUU
FJ915949.1/1-128           -CUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGCAAGACUUUGCUGAUACAUUCCUCCUAGAAAA-AA-GGGUUGGAGAGAGCAGCCUUCACUGA-----AGAGUA-UCAC-AGGG-CUGACUGUACUACCCAACACUC
AABR05089070.1/21288-21415 ACUGGAGGACCAA-GAAGGCGGAG-UCUGAUGAAGCAAGACUUUGCUGAUACACUCCUCCUAGACAA-AG-GGGU-GGAGAGAGCAGCCCUUAUUGG-----AGAAAA-CCAC-AGGG-CUCACUGUACUACCCAACAUUU
AAPE02017312.1/35937-35810 GCUGGAGGACU-AAGAAGGCUGAGU-CUGAUGAAGCAAGACUCUGCUGAUACAAUCCUCCUAAAAUA-AA-GGGU-GGAGAGAGCAGCCCUUAUUGG-----AGAAUA-UCAC-AGGG-UUGACUGUACUACCCAACAUUU
AAWZ02029584.1/19863-19736 CAUAGAGGAUUAA-GAAGGCAGAG-CCUGUUGA-GCAGGGCUCUGCUGAUACCAUCCUCUUAGAGAA-AU-GGGGUGGAGAGAGGGGUCCCACUUGC-----AGAGAU-GCAA-AGAC-CUCACUGUUCUAUCCAACAAAA
AAQR03049276.1/452-580     CCUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGUAAGAUUUGGCUGAUACAUUCCUCGUAGAGAA-AA-GGGUUGGAGAGAGAAGCCCUUACUGG-----AGAGUG-UCAC-AGGG-CUGACUGUACUACCCAACACAU
AAEX03005332.1/11482-11610 GCUGGAGGACUAA-GAAGGCGGAG-UCUGGUGAAGUAAGACUCUGCUGAUACAAUCCUCCUAGAAAA-CA-GGGUGGGAGAGAGCAGCCCUCGGUGG-----AGAACA-GCAC-AGGG-CUGACUGUACGACCCAACAUGC
AADN03008350.1/25310-25182 ACUGGAGGACUAA-UCAGACUGAG-UCUGAAGA-GUGGGACUCAGUUGACAGUGAUCUCCUAGAAGA-AAAGGGAUGGAGAGAGCAGUCCUAUGUAG-----AAGAAA-GCAA-AGGG-CCCACUGUGCCAUCCAACAGUG
AAGU03010363.1/30003-30129 UCUGGAUGACCAA-GAAGGCAGAA-UCUGAUGAAGCAAGA--CUGCUUAUACAAUUCUCUUAGAAAA-AA-GGAUUGGAGAGAGCAGCCCUUACUGG-----AAAAUA-UCAC-AGGG-UUGCCUGUACUAUCCAAUAUUG
AAGW02000423.1/11522-11651 GCUGGAGGACUAA-GAAGGCUGAG-UCUGAUGAAGCAAGACUCGGCUGAUACACUCCUCCUAGAAAA-AA-GGGUUGGAGAGAGCAGCUCUCCUUGG-----AGAAGA-UCACGGGGG-CUGACUGUACUACCCGACAUUC
#=GC SS_cons               :<<<<<<<<----.---<<<-<<<.<<<_________>>>>>>->>>------->>>>>>->>----.--.<<<<-------<<<<<<<<<---<<<.....______.>>>-.>>>>.>>>->>----->>>>:::::::
#=GC RF                    aCuGGaGgaCUAA.GAAgGCugaG.uCuGAUGAAGcAaGaCucuGCuGAUACaaucCuCCUaGAaAA.AA.GGGuUGGAGAGaGcaGcCCuuauugg.....AGAaua.ccac.aGGg.CugACuGUacuaCCCAACAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00424
#=GF ID   SCARNA16
#=GF PI   snoACA47
#=GF DE   Small Cajal body specific RNA 16
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   65.00
#=GF TC   66.10
#=GF NC   63.90
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. ACA47 belongs to the H/ACA
#=GF CC   box class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail
#=GF CC   structure, the conserved H/ACA-box motifs and is found associated with
#=GF CC   GAR1 [2]. ACA47 is predicted to guide the pseudouridylation of residue U5
#=GF CC   of the U1 spliceosomal snRNA [2].
#=GF WK   Small_Cajal_body_specific_RNA_16
#=GF SQ   37


AJ609486.1/1-187             ACGGUC-UGGGGAAAGGCUCC-UGUGUU-GUUGAGCCUGCCAA-GUUGUGGGUGCAGCAUGG-U-ACCAGGCAGCC-CAA--CCCUGACCUAAAGUAAAU----UCCC--GGAAG-AAG-------UC-UUUCC-UGGGUUUUGAA-UUUGCAGUAAC-AGGUGUGAGCAUUCUAGC-AGCAGUUUGAUGAUCAUGUAUGAUACUGCAAACAGGA
AL158048.35/50425-50242      AUGGUC-UGGGGAAAGGCUCC-UAUGUU-UUUGAACCUGCCCA-GUUGUGGGUGCAAUCUUG-C-ACCAGGCAGCC-CAA--CCCUGACCUAAAGUAAAU----UCCC-----AG-AAG-------UC-UUUCC-UGGGUUUUGAA-UUUGCAGUAAC-AGCUGUGGGCAUUCUAGC-AGCAGUUCGAUGAUCAUGUAUGGUACUGCAAACAGGA
AC093157.2/150637-150823     AUGGUC-UUGGGAAAGGCUCC-UGUGUU-GUUGAACCUGCUCA-GUUGUGGGUGCAGCCUUG-U-ACCAGGCAGCC-CAA--CCCUGACCUAAAGUAAAU----UCCC--AGGAA-AAG-------UC-UUUCC-UAGGUUGUGAA-UUUGCAGUAAU-AGGUGUGUGCAUCCUAGC-AGCAGUUUGAUGAUCAUGUAUGAAACUGCAAACAGGA
AC069157.8/65923-65741       AUGGUC-UGGGGAAAGGCUCC-UGUGUG-GCUGAACCUGCCCA-GCUGUGGGUGCAGCCUUG-U-ACCAGGCACCC-CAA--CCCUGACCUAAAGUAAAU----UCCC--AGGAG-AAG-------UC-UUUCC-UGGGAUUUGAA-UUUGCAGUAAC-AGGUGUGAACAUUCUAGC--GCAGUUUGAU---CAUAUAUGAUACUAUAAACAGGA
AC068544.7/102252-102068     AUAGUC-UGUGGAAAGGCUAC-UGUGUU-GUUGAACUUGCCCA-GCUGUGGGUGCAGCCAUG-U-ACCAGGCAGCC-CAA--GCCUGACAUAAAGUAAAU----UCCC--AGGAG-AAG-------UC-UUUCC-UGGGUUUUGAA-UUUGCAGUAAC-AGGUGUAAGCAUUCCAGC-AGCAGUUUGUUGAUCAUG--UGAUAUCAGAAAUGCAA
AL627205.12/140769-140961    ACGGUC-UGGGAAAAGGCUCC-UGUGUG-GCUGUACCCGCCC--GAGGUGGGUGCAGCCCCG-U-ACCAGACAGCC-CGA--CCUUGACCUAAAGUAAAA----UCCC--AGAGG-AGGAGGAACCUC-UUCCC-UGGGGUUAGAA-UUUGCAGUAAC-AGGUGUGGACAUCCUAGC-AGCAGUUUGGUGGUCAUGUAUGAUACUGCAAACAGGA
ABDC01227248.1/65-248        AUGGUC-UGGGGAAAGGCUCC-UGUGUU-GUUGAACCCGCCCA-GUUGUGGGUGCAGCCUUG-U-ACCAGGCAGCC-CAA--CCCUGACCUAAAGAAAAU----UCCC--AGAAG-----------UC-UUUCC-UGGGAUUUGAA-UUUGCAGUAAC-AGGUGUGAGCAUUCUAGC-AGCAGUUUGAUGAUCAUGUAUGAUACUGCAAACAGGA
AANU01180104.1/11905-11720   AUGGUC-UCGGGAAAGGCUCC-UGUGUU-GUUGAACCUGCCA--AUUGUGGGUGCAGCGUUG-U-ACCAGGCAGCC-CAA--CCCUGACCUACAGUAAAU----UCCC--GGGAG-AAG-------GC-UUUCC-UGGGUUUUGAA-UUUGCAGUAAC-AGGUGUGAGCAUUCUAGC-AGCAGUUUGGUGAUCAUGUAUGAUACUGCAAACAGGA
AAFC03022382.1/31783-31596   GUGGUC-UGGGGAGAGGCUCC-UGUGUU-GUUGAACCUGCCCA-GUUGUGGGUGCAACCUUG-U-ACCAGGCAGCC-CGA--CCCUGACCUAAAGUAAAU----UCCU--AGGAG-AAC------UGU-UUUCC-UGGGUUUUGAA-UUUGCAGUAAC-AGGUGUGAACAUUCUAGC-AGCAGUUUGAUGAUCAUGUAUGAUACUGCAAACAGAA
AANG01169155.1/5677-5865     AUGGUC-UGGGGAGAGGCUCC-UGUGUU-GCUGAACCUGCCGG-CUUGCGGGUGCAGCCUUG-UAACCAGACAGCC-CGA--CCCUGACCUAAAGUAAAU----UCCC--GGGAGCAAG-------UU-UUUCC-UGGGGUUUGAA-UUUGCAGUAAC-AGGUGUGAACAUUCUAGC-AGCAGUUUGAUGAUCAUGUAUGAUACUGCAAACAGGA
AAHX01066807.1/71589-71772   ACGGUC-UGGGGAAAGGCUCC-UGUGUG-GUUGACCCUGCCC--UAGGUGGGUGCAGCCCUG-U-ACCAGACAGCC-CGA--CCUUGACCUAAAGUAAAU----UCCC--GGAGG-AGC------AUC-CUCCC-CGGGGUUUGAA-UUUGCAGUAAC-AGGUGUGAGCAUCUUAGC----AGUUUGGUGGUCAUGUAUGAUACUGCAAACAGGA
AANN01153286.1/1817-2003     AUGGUC-UGGAGAAAGGCUCC-UGUGUU-GUUGGACCUGCCCA-GA-GUGGGUGCAGCCUUG-U-ACCAGGCAGCC-CGA--CCCUGACCUAGAGUAAGU----GCCU-GGGGAC-AAG-------UU-CUCCC-UGGGCUUGGAA-CUUGCAGUAAC-AGGUGUGAACAUUCUAGC-AGUAGUUUGAUGAUCAUGUAUGAUACUGCAAACAGGG
AAIY01323550.1/4949-5132     UCGGUC-UGGGGAACGGCUUC-UGUGUG-GCUGGACCCGCCCA-GCAGUGGGUGCAGCCUGG-U-ACCAGACAGCC-CCA--CCCUGACCUAGAGCAAAU----GCUC--GGGGC-----------GC-UCCCC-UGGGCUUGAAA-CUUGCAGUAAC-AGGUGUGAACAUUCUAGU-AGUAGUUUGAUGAUCAUGUAUGCUACUGCAAACAGGA
AAFR03028999.1/47437-47616   AUGGUC-UGAAAAAAGGCUAC-UGUGUG-GUUGAACC-CCAGA-AACCUGGGUGCAGCCCUG-U-ACCAGUUAGCC-UGA--CUUUGACCUAGAGUAAAU----UCCC--------AGG-------AA---AAA-UGGGAUUUUAAUUUUGCAGUAAC-AGGUGUGAGCAUUCUAGC-AGCAGUUUGAUGAUCAUGUAUAAUACUGCAAACAAUA
AAPN01024575.1/1029-1216     GUGGUC-AGGAGAAAGGCUGC-UGAGUG-GUUGAGCCCGGUCA-GCCG--GGCACGGCCUUG-U-AGCAGUUGGCC-UUGAUCCCCGACCUAGAGUAAAC----CCCC--AGGAA-AGC-------UC-CUUUC-UGGGAUUUGAACUUUGCAGUAGC-AGGUGUGAGCAUUCUAGC-AGCAGUUUGAUGAUCAUGUAUGAUACUGCAAACAAGA
AAYZ01114058.1/190-377       AUGGUC-UGGGAACCGGCUCC-UGUGUC-GUUGCACCUGCCG--GCGGUGGGCGCAGCACCGAU-ACCAGGCAGCC-CGA--CCCUGACCUAAAGUGAAG----GCCC--AGGGCGACG-------ACAGCCCC-AGGGUU--GAC-UUUGCAGUAAACAGGUGUGAGCAUUCUAGC-AGCCGCUUGAUGGUCAUGUAUUAUACUGCAAACAGGC
AAQQ01109564.1/635-815       GUGGUC-CGGGGAACGGCGCC-UGUGUU-GUCGCACCUGCCCA-GUGGCCUGUGCAGCC-CG-U-ACCAGGCAGCC-CCA--CCCUGACCUAGAGUAAGU----CC----CGGGG-AGC-------CC-UCCCG----GGUCGGAA-UCUGCAGUAAC-AGGUGUGAGCACUCUGGG-CAGCCGCUUGUGGUCAUGUAUGAUACUGCAAACAGGC
AALT01483174.1/2240-2058     CUGGUC-UGGCGAAAGGCUCC-CGUGUG-UC---GCCUCGCA---GUGUGGGUGCGGCCUCG-U-ACCGGGCAGCG-UGA--CCCUGACCUACAGCAAAC----GCCC--CAGAG-CCCAA---GGGC-CUCCC-GGGGC---GCG-UCUGCAGUAAC-AGGUGUGAGCAUCCUAGC-AGCAGUUUGAUGAUCAUGUAUGAUACUGCACACAGAA
AAIY01113267.1/1143-960      UAUGAU-UGGGGAACAGCUCC-UAUGCG-GCUUAACCCACCCA-GCAUUGGGUGCAGCCUGG-U-ACCAGACAGCC-CCA--CCCUGACCUAGAGCAAAU----GCUU--GGGGC-----------GC-UCCCC-UGGGCUUAGAA-CUUGCACUAAC-AGGUGUGAACAUUCUAGU-AGUAGUUUGAUGAUCAUAUAUGCUACUGCAAACAGGA
AANU01249114.1/1748-1929     AUGGUC-UGUGGAAAGGCUCC-UGUGUU-GUUGAACUUGCCCA-GUUGUGGGUGCAGCUAUG-U-ACCAGGCAGCC-CAA--GGCCGACAUAAAGUAAAU----UCCC--AGAAG-----------UC-UUCCC-UAGGUUUUGAA-UUUGCAGUAAC-AGGUGUGAGCAUUCCAGC-AGCAGUUUGGUGAUCAGAAAUGAAA--GCUAAAGGAG
AANN01194312.1/1217-1403     AUGGUC-UGUAGAAAGGCUCC-UGUGUU-GCUGAACUUCUCCA-GC-AUAGGUGCAGCCUUG-U-ACUAGGCAGCU-CAA--CCCUGACCUAGAGU---G----UGCC--AGGGA-CUUCA---GGUU-GCCCU-AGGGCUUUGAA-CUUACAAUAAC-AGGUGUGAACAUUCUAGC-AGCAAUUUGAUGAUAAUGUAUGAUACUGCAAACAAAC
AAIY01696549.1/687-872       CAGAAU-GAAGAAAUGAAUAC-UGUAUGAUUUGAAUUCAAGAAAAGUGUGAGUGCAGCCUGG-U-ACCAGACAGCC-CCA--CCAUGACCUACAGCAAGU----GCUC--GGGGC-----------GC-UCCCU-UGGGCUUGAAA-UUUGCAGUAAC-AGAUGUGAACAUUCUAGU-AGUAGUUUGGUGAUCGUGUAUACUACUGCAAACAGGA
AAIY01302780.1/1279-1446     ACGGUC-UGGGGAC-GGCUCC-UGCAUG-GCUGGACCCGCCCA-GCAGUGGGUGCAGUCC-------CA-------------CCCUGACCUAGAGCAAAU----G-CU--GGGGU-----------GC-UCCCC-UGGGCUUGAAA-CUUGCAGUAAC-AGGUGUGAACAUUCUAGUAAGUAGUUUGAUGAUCAUGUAUGCUACUGCAAACAGGG
AANU01292006.1/9352-9170     AUGGUC-UGGGGAAAGGCUCC-UGUGUG-GUUGAACCUGCCCA-GUUGUGGGUACAGCCUUG-U-A-CUGGCAGCC-CAA--CCCUGACCUAAAGUAAAU----UCCC--AGGAG-AAG-------UC-UUUCC-UGGGAUUUGAA-UUUGCAGCAAC-AGAUGUGAACAUUCUAGU-GGCAGUUU---GAUCAUGUAUGAUACUAUAAAUAGGA
AANU01219929.1/5530-5716     AUGGCC-UUGGGAAAGGCUCC-UGUGUU-GUUGAACCUGCUCA-GUUGUGGGUGCAGCCUUG-C-ACCAGGCAGCC-CAA--CCCUGCCCUAAAGUAAAU----UUCC--AGGAA-AAG-------UC-UUUCC-UGGGUUGUGAA-UCUGCAGUAAC-AGGUGUGCACAUCCUAGC-AGCAGUUUGAUGAUCAUGGAUGAAACUGCAAACAGGA
AALT01276097.1/1207-1031     CUGGUC-UGGGGAAAGGCUCC-CGUGU--GCUG-GCCCGCAG----UGCGGGUGCGGCCUUG-U-ACCGGGCAGCA-CAA--CCUUGACCUACAGCAAGC----GCCA--GGGAGCAGU-------GU-CUCCC-AGCGC-----A-UCUGCAGUAAC-AGGUGAGACCAUCCUAGC-AGCAGAUUGAUGAUC-AAAAUGAUACUGCACACAGAA
AANU01215616.1/4941-5112     UUGAUC-ACAGGACCCCCUUA-AA-CUC-AUAAAUAAA------------UUAUUGAUGCAC-C-AG---ACAGCC-UGA--CCCUGACCCAAAGUAAAU----UCCC--AGGAG-UCG-------UC-UUUCC-UGGGUUUUGAA-UUUGCCGUAAC-AGGCGUAAACAUUCUAGC-AGCAGUUUGGUGAUCAUGUAUGAUACUGCAAACAGGA
AANN01729317.1/397-213       AUGGUC-UGGAGAAAGGCUCC-UGUGUU-GUUGGACCUGCCCA-GC-AUGAGUGCAGCCUUG-U-ACCAGGCAGUC-AGA--CCUUGACCUAGAGUAAGU-----GCC--UGAAC-AAG-------UU-CUCAU-GGGUCUUGGAA-CUUUCAGUAAC-AGGUGUGAGUAUUCUAGC-AGCAGUUUGGUGAUUAUGUAUGAUACUGCAAACAGGA
ABDC01168306.1/9156-8969     AUGGUC-UGGGGAAAGGCUUC-UGUGUU-GUUGAACCUGCCCA-GUUGUGGGUGCAGCCUUG-U-ACCAGGCAGCC-UGA--CCCUGACCUAAAGUAAAU----UCUC-AGGAGA-AAG-------UC-UUACC-UGGGUUUUAAA-UUUGCAGUAAC-AGGUGUGAGCAUUCUAGC-AGCAGUUUGAUGAUCAUGUAUGAUACUGCAAACAGGA
EU240229.1/1-168             GAGGGC-CUGGGGAUGGCUGC-UG-GCG-GCUGU-------------GUC---UCAGCCUGG-U-GCCUGCUGGCC-UUA-CCCGUGCCCCAGAUCAACC----U-CC--AGAGG-UCC-------CC-CUGCU--GGGUUCCUCC-UAUGCAGUAAC-AGGUGUGAGCAUCCAUGC-AGCAUUCUGAUGGUCAUGUAUGAUACUGCACACA--A
CU655873.22/179924-180111    AUGGUCUUGGGGAGAGGCUCC-UGUGUU-GUUGAGCCUGCCCC-GUUGUGGGUGCAACCUUG-U-ACCAGGUAGCC-CGA--CCCUGACCUAAAGUAAAU----UCCC--AGGAG-AGU-------UG-AUUCC-UGGGUUUUGAA-UUUGCAGUAAC-AGGUGUGAACAUUCUAGC-AGCAGUUUGAUGAUCAUGUAUGAUACUGCAAACAAAA
AAHX01039931.1/4243-4430     AUGGUC-UGGGGAAAGGCUCCUUGUGUG-GUUGACCCUGCCC--GAGGUGGGUGCAGCCCUG-U-ACCAGAUAGCC-CGA--CCUUGACCUAAAGUAAAU----UCCC--AGAGG-CGC-------AU-CCUCCCUGGGGUUAGAA-UUUGCAGUAAC-AGGUGUGAACCUCUCGGU-GGCAGUUCAGUGGUCAUGUAUGAUACUGCAAACAGGA
AAWZ02009180.1/36450-36265   GUGGGC-UGGGAAAUGGUUAC-UGUGUA-GCUG-----GACUU-CCUGAGACC-CAGCCUUA-U-ACCUGCUAACCUGAA--CCUUGCCCUAGAUAAAAAAGAAAACU--GGCAC-ACU-------CC-UUCCU-GGGGUCUGCCC-UAUGCAGUAGC-AGGUGUGAACAUUCUACC-AGUAUUUUGAUGAUCAUGUAUGAUACUGCAUACACGU
AAEX03000900.1/9081-9262     AUGAUC-UGAGGAAAGGCUCC-UGUGUU-GCUGAACCUGGCCU-GUAGUGGGCGCAGCCUUG-U-ACCAGGCAGCC-AGA--GCCUGACCUA-AGUCAAU----UCCC--AGGAU-A------------GUUCU-UGGAGUUUGAA-UUUGCAAUAAC-AGGUGUAAACAUUGUAGC-AGCAGUUUGAUGAUCAUAUGUGUUAUUGCAAAUAGGA
AADN03007535.1/130190-130358 AGGGCC-UGGGGAU-GGCUGC-UG-GCG-GCUGU-------------GUC---UCAGCCUGG-U-GCCUGCUGGCC-UUA--CCCGUGCCCCAGAUCAAC----CUCC--AGAGG-UCC-------CC-CUGCU--GGGUUCCUCC-UAUGCAGUAAC-AGGUGUGAGCAUCCAUGC-AGCAUUCUGAUGGUCAUGUAUGAUACUGCACACAACG
AAQR03091190.1/6640-6463     ACAGUC-UGGGGCAAGGCUCC-UGAGUU-GCUGCAUCUGCCCA-GCUGCAGGUUCAGCUUUG-U-ACCAGGAAGCC-CAA--CGUUAACAUAAAUU---------CCC--AGAAG-----------UC-UUUCC-UGC-AUCAGAA-UCUGCAGUAAC-AGGUGUGAGCAUUCUAGC-AGCAGAUUGAUGAUCAUGUAUUAUACCGUACACAGGA
AACN011006597.1/519-327      AUGGUC-UGCGGAAAGGCUCC-UGUGUG-GCCGCACCUGCCCG-GGUGUGGGUGCAGCCUUG-U-ACCAGGCAGCC-CGA--GCCUGACCUAGAGUAAAA----UCCCCCGGGGG-GGCCC---AGUU-CCCCC-CGGGGUUUGGA-UUUGCAGUAAC-AGGUGUGAACAUUCUAGC-AGCAGUUUGAUGAUCAUGUAUGAUACUGCAAACAGGA
#=GC SS_cons                 ::<<<<.-<<<----<<<<<<.<<-<<<.<<<<-<<<______.______>>>->>>>>---.-.>>>>>>->>>>.---..>>>->>>>,,,,,,,,,,....,<<<..<<<<<.___.......__.>>>>>.->>>,,,,,,,.<<<<<<<<<-<.<----<<<-<<<<--<<<.____>>>->>>>->>>---->>->>>>>>>>>:::::
#=GC RF                      augGuC.UgggGAAagGCucC.uGUGug.gcuGaaccuGccca.guuGUGgguGCagccUuG.U.aCCaGgcaGCc.caA..cccUGaCcUAaAGUAAAu....ucCc..gGggg.aag.......uc.cccCc.ugGguUUugAA.uuUGCAGUAAc.AGGUGUGAaCAucCUagc.AGcAguuUgaUGAUCAUGUAUgAUACUGCAaaCAgga
//
# STOCKHOLM 1.0

#=GF AC   RF00425
#=GF ID   SNORA18
#=GF PI   snoACA18
#=GF DE   Small nucleolar RNA SNORA18
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   70.00
#=GF TC   70.10
#=GF NC   69.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.04 -Z 549862.597050 CM SEQDB
#=GF CL   CL00038
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300096;
#=GF DR   snoopy; Gasterosteus_aculeatus300089;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA18 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA18
#=GF SQ   29


AJ609471.1/1-132             GUUGAGGUCUAUCCCGAUGGGGCUUUUCCUGU-AGCCUGCACAUCGUUGGAAACGCCUCAUAGAGU-AACUCUGUGGUUUUACUUUACUCACAGGACUAUU----GUUAGAUCU-GUGGG-AA-GGA-AUUACAAGACAGUU
AC026355.13/69334-69207      UUUGAGGUCUUUCCCGAUGGGACUUUUC-UGU-AGGCUGCACAUCAUUGGAAACGCCUCAUAGAGUUAACUCUGUGGUUUUACUUUACUCACAGGACUCUU----GUUAGAUCU-GUGGG-AA------CUACAAGACAGUU
AC079969.5/116696-116565     GUUGAGGUCUAUCCCGAUAGGUCUUUUCCUGU-AGCCUGCACGUUGUUGGAAAUGCCUCAUAGAGU-AACUCUGUGAUUUUACUUUACUUACAGGACUAUU----GUUACAUCU-GUGGG-AA-GGA-ACCACAAGACAGUU
BC021677.1/1965-1834         GUGGAGGUCUAUUCCAAUGGGGCUUUUCCUGU-AG-CUGCAUGUUGUUGGAAACUCCUCAUAGACU-AACUCUGUGGUUUUGCUUUACUCACAGGACUAUUA---GUUAGGUCU-GUGGG-AA-GGA-ACUACAAGACAGUU
BC056964.1/2999-3129         UUUGAGGUCUAUCCCGACGGGGCUUCCCUAGU-AGCCAG-ACGUCGUUGGAAACGCCUCAUACAGU-AACU-UGUGGUUUUACUUGACUCACAGGACUGACU---GUUAGGUCU-GUGGG-AA-GGA-ACUACAAGACAGCU
AANU01299933.1/8068-8200     UUUGAGGUCUAUCCCGAUGGGACUUUUCCUGG-AGGCUGCACGUUGUUGGAAAUGCCUCAUAGAGUUAACUCUGUGGUUUUACUUUCUUCACAGGACUCUU----GUUAGAUCU-GUGGG-AA-GGA-ACUACAAGACAGUU
ABDC01191151.1/3590-3459     GUUGAGGUCUAUCCCGGUGGGGCUUUUUCUGU-AGCCAU-ACAUCGUUGGAAACGCCUCAUAGAGU-AACAUUGUGGUUUUGCUUUCCUCACAGGACUAUUU---GUUAGAUCU-GUGGG-AA-GAA-ACUACCAGACAGUU
AAXO01012431.1/766-636       UUUGAGGUCUAUCCCGAUGGGGCUUCGUUAGU-AGCCAC-ACAUCGUUGGAAACGCCUCAUAUAGU-AACU-UGUGGUUUUGCUUGACUCGCAGGACUGUUU---GUUAGGUCU-GUGGG-AA-GGA-ACUACAAGACAGCU
AAPY01155118.1/406-536       GUUGAGGUCUAUCCCGAUGUGGCUUUUCCUGU-AG-CUGCACAUCGUUGGAAACGCCUCAUAGAGU-AACAGUGUGG-UUUGCUUUACUCACAGGACUAUUU---GUUAAUUCU-GUGAG-AA-AGA-ACUACAUUACAGAA
AAIY01662003.1/5107-5240     GUUGAGGUCUAUCCCGAUGGGGCCUUGUCUGU-AGACCC-ACAUCGUUGGAAACGCCUCACAGAGU-AACUCUGUGG-UUUGCUUUACUCGCAGAACUGCUAUUGGUUGGAUCU-GUGAG-GA-AGA-ACUACAAGACAAAU
AAFC03094524.1/37240-37110   AUUGAGGUCUAUCCCGAUGGGGCUUUUUCUAU-AAACCU-ACAUCGUUGGAAACGCCUCAUAGAGU-AACUAUGUAGUUUCC-UUUACUCAUAGAACUACCU---GUUAGAUCU-GUGGG-AA-AAA-ACUACAAGACAAAG
AAYZ01083577.1/19006-18875   CUUGAGGUCUAUCCCGAUGGGGCUUUUUCGAU-AGCCAC-UCAUCGUUGGAAACGCCUCGUAAAGC-AACUCUGUGGUUCUGCUUUACUCCCAGGACCUUUU---CUUAGGUCU-GUGGG-AA-GAA-ACUACAAGACAGUU
AANN01814642.1/4430-4559     AUUGAGGUCUAUCCCGAUGGGGCUCUGCUGUG-AACCCU--UGUCGUUGGAAACGCCUCAUAGAGU-AA-UCAUGUAGUCUGCUUUACUCACAGAACUGCUG---GUUAGAUCU-GUGAG-AA-AGA-ACUGCAAGACAGCU
AAQQ01183542.1/2603-2474     GUGGAGGUCCAUCCUGAUAGGGCCUUUCCUAU-AGCCAC-ACAUUGCUGUAAAUACCUGAUAGAGU-AAC--UAUGGUUUUACUUUACUCACAGAACUAUUU---GUUAGAUCU-AUGAG-AA-AGA-ACUAAAGGAUAGUU
AANH01012026.1/44195-44062   GCUGAGGUCUAUCCCGACGGGCCUUUCACUGU-AGGGCC-AUGUCGUUGGAAAUACCUCACACAGU-AACUCUGUAGUAUCGCUUUACCCACAUGUUCACUG--CCAUGAGCAUAGUGAG-AU-AUA-ACUGCAGAACACGA
AALT01051090.1/1328-1453     GUUGAGGUCUAUCCCGAUGGGGCUUUUCUGUG-AGCCU--AUGUCGUUGGAAACGCCUCAUAGAGG-AU---UGCGG-UUUGCUUGAUUCUCAGGACUGCCU---GUUAGACCU-GAGAG-AA-AGC--UACCCCGACAGCU
CR936321.10/45587-45453      UCUGAGGUCUAUCCCGACUGGCCCCUCUCAGUAGGGCUU--AGUCGUUGGAAAUGCCUCAAAGAUA-AAGUCUGUAGUAUCGCUUUACCCAUGUUGCUAAUUU-CAUUAGCUUU-GUGGG-AA-AAACACUGCAGUACAUUC
AAFR03025134.1/19268-19400   UUUGAGGUCUAUCCUGAUGGGUCCUUUUCAGUAGGUCCU--UAUCCUUGGAAACGCCUCAGAAAGC-AAAUGUGUAGUUACGCUUUACCCAUUGAUCUCCAU---ACCAGGUCU-AUGGG-GAUAAA-ACUACAAAACAAUU
AAGV020161067.1/44-172       GCUGAGGUCUAUCCCGAUGGGGUCUCUGUA---GACCC--ACAUCGUUGGAAACGCCUCACAGAGG-AAUGUUGUGGUUCAGCUUUACUCACAGAACUAUUU---AUUAGAUCU-GUGAG-AA-GGA-ACUACAAGACAGAU
AAWR02017934.1/94002-94132   GUUGAGGUCUAUCCCGAUGGGGCUUUUUCUGU-AGACCC-ACAUCGUUGGAAACGCCUCAUAGAGU-AAUUAUGUGGUUUC-CUUUACUCACAGAACUGUGU---GUUAGAUCU-GUGGG-AA-AGA-ACUACAAGACAGCU
AAKN02037651.1/18519-18645   CUUGAGGUCUAUCCCGAUGGAGCU---UCUGU-AGCUAC-ACAUCGCUGGAAACGCCUCAUAGAGU-AACAUU--GGUUUUGCUCUACUCACAGGUCUGCUU---CUUAGGCCU-GUGAU-AA-AGC-ACUACAAGACAGCA
EU094025.1/5-135             UUUGAGGUCUAUCCCGAUGGGACCUCUCAU-A-GGUCC--ACGUCGUUGGAAACGCCUCAGAGAAA-AAAGUUGUGGUCUCGCUUUACCUACCGAACUGUGU---GUUGGAUCG-GUGGGGGA-AAA-GCCACAAGACAGUU
FJ915955.1/2-133             GUUGAGGUCUAUCCCGAUGGGGCUUUUCCUGU-AGCCUGCACGUCGUUGGAAACGCCUCAUAGAGU-AACUCUGUGGUUUUACUUUACUCACAGGACUAUU----GUUAGGUCU-GUGGG-AA-GGA-ACUACAAGACAGUU
EU240261.1/1-132             GUUGAGGUCUAUCCCGAUAGGAUCUCUUCUGUAGGUUC--AUGUCGUUGGAAACGCCUCACAGAAC-AAACUUGUGGUUUAGUUUUACCCUUGGAGCUACCU---GUUAGCUCU-GUGGG-AU-AGA-ACUACAAGACAAAU
AAGW02008739.1/16239-16108   GUUGAGGUCUAUCCCGAUGGGGCUUUCCCUAU-AGCCAU-UCAUCGUUGGAAACGCCUCAUAGAGC-AACUCUGUGGUUUUGCUUUGCUCACAGGACUUAUU---CUUGGGUCU-GUGGG-AA-GGA-ACUACAAGACAGUU
AAWZ02006558.1/132579-132448 AUUGAGGUCUAUCCCGAUGGGACUUUGCUGUA-UGUUCU--UGUCGUUGGAAAUGCCUCAUAGAAA-AAACUUGCGGAUUCGCUUUACUCAUUAAGCUGUGU--UGUCAGCUUA-GCGGG-AU-AAA-ACUGCAAGACAGUU
AAQR03025299.1/27972-27841   GUUGAGGUCUAUCCCGAUGGGGCUUUUUCUGU-AGCCAC-ACAUUGUUGGAAACACCUCAUAGAGU-AACACUGUGGUUCUGCUUUACUCGCAGGUCUAUUU---GUUAGGUCU-GUGGG-AA-AGA-ACUACAAGACAAUU
AAPE02025112.1/59901-59771   AUUGAGGUCUAUCCCGAUGGGUCUUUUUCUGU-AGACUU-ACAUCGUUGGAAACGCCUCAUAGAAU-AAAUAUGUUGUUUC-CUUUAUUCACAGAACUGCGU---GUUAGAUCU-GUGGG-AA-GGA-AUUACAAGACAGCU
AAEX03012728.1/176173-176303 UUUGAGGUCUAUCCCGAUGGGGCUUUUUCUGU-AGACCU-ACAUCGUUGGAAACGCCUCAUAGAGU-AUAUGUGUGGUUUC-CUUUAUUCACAGAACUAUAU---GUUAGAUCU-GUGGG-AA-AGA-ACUACAAGACAUCU
#=GC SS_cons                 ::<<<<<<---<<<<<<<<<<<<<________.>>>>>-.->>>>>-->>>--->>>>>>------.---------------<<<<-<<<<<<<<-<<<___...__>>>->>>.>>>>>.>>.>>:.::::::::::::::
#=GC RF                      gUuGAGGuCUAUCCCGAuggGgCuUUuucugU.aGcCcu.AcaUCGUUGGAAAcgCCUCauAgAgu.AAcuuUGUgGUUUugcuuuAccCacaggaCuauuU...gUuaGaccu.guGgg.aa.agA.ACUACAAGACAguU
//
# STOCKHOLM 1.0

#=GF AC   RF00426
#=GF ID   SCARNA15
#=GF PI   snoACA45
#=GF DE   Small Cajal body specific RNA 15
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   65.00
#=GF TC   65.40
#=GF NC   64.20
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00019
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300779;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. ACA45 belongs to the H/ACA
#=GF CC   box class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail
#=GF CC   structure, the conserved H/ACA-box motifs and is found associated with
#=GF CC   GAR1 [2]. ACA45 is predicted to guide the pseudouridylation of residue U37
#=GF CC   of the U2 spliceosomal snRNA [2].
#=GF WK   Small_Cajal_body_specific_RNA_15
#=GF SQ   22


AJ609485.1/1-127           CUGGAGAC--UAAGAA--AAUAGAGUCCUUG-AAAUCAAGCUGACUCUGCUUUUA---GCCUCCUAAAUGAAAA-GGUAGAUAGAACAGGUCUUGUUUGCAAAAUAAAUUCAAGACCUACU--UA-UCUACCAACAGCA
AL355802.13/56900-57026    CUGAAGAC--UAAGAA--AAUAGAGUCCUUA-AAGUCAAGCUGAGUCUGCUGUUA---GCCUCCUAAAUGAAAG-GAUAGACAGAACAGGUCUUGUUUGCAAAAUAAAUUCAAGACCUACU--UA-UCUACCGACAGCA
AL021395.16/134332-134456  CUGGAGAC--UAAGAA--ACC--AGUCCUUG-AAGUCAAGCUGACUCUGCUUUUA---GCCUCCUAAAUUAAAA-GAUAGAUAGAAUAGGUCUUGUUUGCAAAAUAAAUUCAAGAUCUACU--CA-UCUAUCAAUAGCA
AANU01259224.1/203-329     CUGGAGAC--UAAGAA--AACAGAGUCCUUG-AAGUCAAGCUGACUCUGAUUUUG---GCCUCCUAAAUGAAAA-GAUAAAUAGAACAGGUCUUGUUUACAAAAUAAAUUCAAGACCUACU--UA-UCUAUCAACAGCA
AAYZ01043390.1/7481-7607   CUGGAGAC--UAAGAA--AACAGAGUCCUUG-AAGUCAAGCUGACUCUGCCUUUA---GCCUCCUAAAUGAAAA-GGUAGAUAGAACAGGUCUUGUUGGCAAAGUGAUUUCAAGACCUACU--UA-UCUACCAACAGCC
AAIY01626672.1/2150-2024   CUGGAGAC--UAAGAA--AAGAGAGUCCUUG-AAGUCAAGCUGGCUCUGCUUCUA---GUCUCCAAAAUGAAAA-GGUAGAUAGAACAGGUCUUGUGAACGAAAUAUAUUCAAGACUUACA--UA-UCUACCAACAGCA
AAFC03086362.1/45749-45627 CU----GC--UAAGAA--AAUAGAGUCCUUG-AAGUCAAGCUGACUCUGCUUUUA---GCCUCCUGAAUGAAAA-GGUAGAUAGAACAGGUCUUGUUUGCAAAAUGAAUUCAUGACCUACA--UA-UCUACCAACAGCA
AANN01624857.1/5804-5929   CUGGAGAC--UAAGGA--AGUAGAGUCCUUG-AAAUCAAGCUGACUCUGCCCUUA---GCCUCCUAUGUGACAA-GGUAGAUAGAACAGGUCUUG-GUGCGAGAUAAAUUCAAGACCUACU--UC-UCUGCCAACAGCA
AALT01503069.1/3751-3878   CUGGAGAC--GGAGCA--AAAGGAGUCCUUG-AAGUCAAGCCGACUCUGCUCUGA---GCCUCCGAAAUGAAACAGGUAGAAAGAACAGGUCUUGUGUGCACAGUGAACGCAAGGCCUACG--UA-UCUACCAACACGG
ABDC01323625.1/886-758     AUGAAAAA--CAAGAAAGAUUAGUAUUAAGA-AUAAACUCCCGACUCUGCCUUUA---GCCUCCUAAAUGAAAA-GGUAGAUAGAACAGGUCUUGUUUGCAAAAUAAAUUCAAGACCUACU--UA-UCUACCAACAGUA
AAFR03044917.1/37293-37424 CUGGAGGC-CUAAGAA--AGUGGAGUCAUUG-AAGUCAUACUGACUCUUCUGAUACUAGCCUCCUAAAUGAAAA-GGUCGUUGGAACAGGCCCUGUCUUCAAGAUGAAUUCAGGUCCUACU-UCA-UCAACCAACAGUG
AAPN01158836.1/1882-2014   UUGGAGGA-UUAAGAA--AGUCGAGUCAUUG-CAGUCCAGCAGGUUCGACUGAUACGCUCCUCCUACAUGAAAA-AGGUAGAGGAACAGGCCCUGGGUGCCAGGUCGACUCUGGGCCUACUUACU-CUACCUACAGUGA
AAKN02016015.1/49545-49419 UCGGAGAC--UGAGAA--AACAGAGUCCUUG-AAGUCAAGCUGACUCUGCAUUUA---GCCUCCUAAAUGAAAA-GGUAGAUAGAACAGGUCUUGUUUGCAAAAGAAACCCAAGACCUACU--UA-UCUACCAACAGCA
FJ915947.1/1-127           CUGGAGAC--UAAGAA--AAUAGAGUCCUUG-AAAUCAAGCUGACUCUGCUUUUA---GCCUCCUAAAUGAAAA-GGUAGAUAGAACAGGUCUUGUUUGCAAAAUAAACUCAAGGCCUACU--UA-UCUACCAACAGCA
FJ915949.1/1-128           CUGGAGGA-CUAAGAA--GGCUGAGUCUGAU---GAAGCAA-GACUUUGCUGAUACAUUCCUCCUAGAAAAAAG-GGUUGGAGAGAGCAGCCUUCACUGAAGAGU-AUCACAGGGCUGACU-GUA-CUACCCAACACUC
EU240270.1/2-132           CCGGAGGA-CUAAGAA--AGUGGAGUCGGUG-CCUUCAUGCCCACCCCGCUGAUACUAUCCUCCAAAAGGAAAU-GGUGGAAGAACAAGG-CCUGCCCGCGAGGUAAGGGCAGGGCCUGCU-UCC-UCCGCCUACAGGG
AJ609483.1/2-129           CUGGAGGA-CUAAGAA--GGCUGAGUCUGAUGAAGU----AAGACUUUGCUGAUACAUUCCUCCUAGAAAAAAG-GGUUGGAGAGAGCAGCCUUCACUGAAGAGU-AUCACAGGGCUGACU-GUA-CUACCCAACACUC
AAEX03002348.1/36459-36586 CUGGAGAC--UAAGAA--AACAGAGUCCUUG-AAGUCAAGCCAACUCUGCUAUUA---GCCUCCUAAAGGAAAA-GGUAGAUAGAACAGGUCUUGUUAGCAAAAUAAAUUCAAGACCUACU--UAAUCUACCAACAGCA
AAGW02066462.1/16854-16728 CUGGAGAC--UAAGAA--AUGAGAGUCCUUG-AAGUCAAGCCGACUCUGCCUUUA---GCCUCCUAAAUGAAAA-GGUAGAUAGAACAGGUCUUGUUCGCAAAGGAAGUUCAAGACCUACU--UA-UCUACCAACAGCA
AAWZ02015194.1/77450-77581 UUGGAGGA-CCAAGAA--AGUAGAACCAGUG-AAGUCAUUU-GGCUCUACUGAUACUAUCCUCCUAAAUUAAAU-GGUAGAUGAACAAGGUCCUGUCUAUGACAUAUAGCAUAGCCUUACUACUA-UCUGCCAACAAUA
AAPE02001963.1/29490-29617 GGGAGGGCAUUAUGCC--AAUAAUUGCUUUG--AGAUAUAUGAAAGCUGCUUUUA---GCCUUCUAAAUUAAAA-GGUGGAUAGAACAGGUCUUGUUUGCAAAAUAAAUUCAAGACCUACU--UA-UCUUCCAACAGAA
AADN03005910.1/96596-96466 CCGGAGGA-CUAAGAA--AGUGGAGUCGGUG-CCUUCAUGCCCACCCCGCUGAUACUAUCCUCCAAAAGGAAAU-GGUGGAAGAACAAGG-CCUGCCCGCGAGGUAAGGGCAGGGCCUGCU-UCC-UCCACCUACAGGG
#=GC SS_cons               ::<<<<<<.-<<<---..--<<<<<<<<<<<.____>>>>-->>>>>>>--->>>...>>>>>>----------.<<<<<<<<----<<<<<<<<_______________>>>>>>>>---..>>.>>>>>>:::::::
#=GC RF                    cUGGAGGc.cuAaGAA..AacgGaguCcuug.AAGUcaagcuGacuCcgCUuuUa...gCCUCCUAAAugAAAa.GGuaGaugGAAcaGGuCuUGuuUGCaAaaUAAauuCAaGaCCuACU..ca.uCuaCCAACAgua
//
# STOCKHOLM 1.0

#=GF AC   RF00427
#=GF ID   SCARNA23
#=GF PI   snoACA11
#=GF DE   Small Cajal body specific RNA 23
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   60.00
#=GF TC   61.60
#=GF NC   58.60
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. ACA11 belongs to the H/ACA
#=GF CC   box class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail
#=GF CC   structure,the conserved H/ACA-box motifs and is found associated with GAR1
#=GF CC   [2]. H/ACA snRNAs are predicted to guide the modification of uridines to
#=GF CC   pseudouridines in substrate RNAs however, no target RNA has been
#=GF CC   identified for scaRNA ACA11.
#=GF WK   Small_Cajal_body_specific_RNA_23
#=GF SQ   18


AJ609470.1/1-125             GCGCUCACUAAGGCUCGGUCCUCUCC---ACGUGGUCCUGACCUGUC----CUCUGUGAGCAAGAG-AAACAG--GACUGG-UUUGGGGGUGUCCUGUCUCAGUGGACA-CAGGACACCACGGUUUUCAGUACAACA
Z68164.1/2183-2059           GCGCUCACUAAGGCUCGGUCCUCUCC---ACGUGGUCCUGACCUGUC----CUCUGUGAGCAAGAG-AAACAG--GACUGG-UUUGGGGGUGUCCUGUCUCAGUGGACA-CAGGACACCACGGUUUUCAGUACAACA
AC122438.2/85050-85178       CUGCUCAUUAGGGCUCAGUCUUCCUC---UUGUGGUCCUGACCUGCCUGCCCUCCAUGAGCAAGAG-AAUCUG--GACUGG-UU-GGGGGUGUCCUGUCCAAGUGGACAACAGGACUCCACGGUUUUCAGUACAACA
AAPY01235787.1/509-385       GUGCUCACUGGGGCUCAGUCUGUUCC---AUGUGGUCCUGACCUACC----UUCUGUGAGCAAGAG-AAACAG--GACUGG-UCUGGGGGUAUCCUGUCUGAGUGGACA-UGGGAUACCACAGUUUUCAGUACAACA
AAHX01078308.1/69079-68953   CUGCUCACCAGGGCUCAGUCCUCCUCCUCUUGUGGUCCUGACCUGCC----CUCUGUGAGCAAGAG-AAUCUG--GACUGG-UU-GGGGGUGUCCUGUCCAAGUGGACA-CAGGACUCCACGGUUUUCAGUACAACA
AANG01286776.1/1625-1751     GGACUCGCUGGGGCUUGGUCCUCGCC---ACGUGGUCCUGACCUGCC----CUCCGUGAGUGAGAG-AAACAGAGAACUGG-UUUGGGGGCGUCCUGUCCCAGUGGACA-CAGGAGACCACGGUUUCCAGUACCACA
AALT01468052.1/1151-1026     AUGCUCACCAGGGCUUGGUCUUCUCC---GUGUGGUCCUGACCUGCC----CUCCAUGAGCAAGAG-AGACUG--AACUGGUUUUGGGGGUACCCUGUCUGAGUGGACA-UGGGAGACCACGGUUUUCAGUACAACA
AAYZ01525352.1/651-527       GCGCUCGCUGGGGCGCGGUCCUCUCC---GUGUGGUCCCGACCUGCC----UUCCGUGAGCAAGAG-AAGCAG--AACUGG-UUUGGGGGUGUCCUGUCCGAGUGGGUG-CAGGUCACCACGGUUCCCAGGACGACA
AAIY01099169.1/807-930       GUGCUCACCAAGGCUUGGUCCUUACU---ACAUGGUUCCGGCCUGCC-----UGCGUGAGCAAGAG-AAGGAG--GGCUGG-UUUGGGGGUGUCCUGUCCAAGUGGCCC-CAGGACUCCAUGGUUUCCAGGCCAACA
AANN01334949.1/1075-951      GCGCUCAUUGGGGCUUGGUCUCUUCC---UUGUGGUCCUGACCUGCC----UUCCCUGAGCGAGAG-CAACAG--AACUGGUUUUGGGGGUCUCCUGUCUGAGUAGACU--GGGAGACCAUGGUUUUCAGUGCGACA
AAFC03027510.1/8884-9007     UCGCUCACCAGCGCUCGGUC-UCUCC---UCGUGGUGCUGGCCUGCC----CUCCGUGAGCCAGAG-AAACAG--GACUGG-UUUGGGGGUCUCCCAUCCGAACAGCCA-CGGGAGACCACGGUUUCCAGUGCGACA
AAFR03017244.1/99072-98947   GUGCUCACUAAAACUUUGUCCCUUCC---AUGUGGUUGUGACA-GUU---AAUAAGUGAGCUAGAUUAAUUAG--UAUUGA-AUUGGGGGUGUCAUAUACCAGCUCAUA-UGAUACACCACAGUUUUCAAUACAACA
AAKN02019878.1/4426-4302     GUGCUCACU-GGGCUUGGUCUUCUCC---AUGUGGUCCUGACCUGCC---CACUUGUGAGCAAGAG-AAUUGG--AACUGG-UUUGGGGGUGUCCUGUCUGAGUGAACA-UUGGACACCACAGUUUUCAGUACAACA
AAWR02005861.1/34308-34184   GUGCUCACCAGGGCUCGGUCCUUUCC---AGGUGGACCUGACCUGCC----CUCCAUGAGCGAGAG-AAACAG--UACUGG-UUUGGGGGUCUCCUGUCCGAGUGGACA-CGGGAGACCAUGGUUUUCAGUACAACA
AAGU03039173.1/4338-4214     GUGCUCAUCGUGGCUCGGUCCUUUCC---AUGUGGUCCCGACCUGCC----CUCAGUGAGCAAGAG-AAAGAG--GACUGG-UUUGGGGGCGUCCCGUCCAAGUGGUCA-UGGGAUACCAUGGUUUUCAGUACAACA
AAEX03002459.1/49396-49272   ACACUCGCUGGGGCCUGGUCCUCUCC---AUGUGGUCCUGACCUACC----CCCCGUGAGGGAGAG-AAACAG--GGCUGG-UUUGGGGGUGUCCCACCCCAGUGGACA-UGGGAGACCACGGUUUCCAGCACAACA
AAQR03085685.1/5553-5429     GCGCUCAUGAGGGCAUGGUCCUGUCC---AUGUGGUCUGGACCUACC----CUCCACGAGCAAGAA-AAACAG--AACUGG-UUUGGGGGUGUCCCAUCUGUGUGGACA-UGGGACACCAUGGUUUUCAGUACAACA
AAGW02050083.1/150058-150182 GCGCUCACCAGGACUCGGUCAUCUCC---UUGUGGUCCUGACCUGUC----CUCUGUGAGCAAGAG-AGACAG--GACUGG-UUUGGGGGUGCCCUGUCUGAGUGGACA-CGGGACACCACGGUUUUCAGUACAACA
#=GC SS_cons                 ::<<<<<<---<<<--<<<<----<<...____>>---->>>>->>>....---->>>>>>-----.-----<..-<<<<<.-<<<--<<<<<<<<<<<<____>>>>-.->>>>>>>>->>>--->>>>>->::::
#=GC RF                      gugCUCacuagGGCuugGuCcuuuCC...auGUGGUccuGaCcUGCC....cUccguGAGcaAGAG.AAacaG..aaCUGg.UucGGGGGugucccguccaAGUggacA.ugggacaCCACggUUUcCAGuACAACA
//
# STOCKHOLM 1.0

#=GF AC   RF00428
#=GF ID   SNORA38
#=GF PI   snoACA38
#=GF DE   Small nucleolar RNA SNORA38
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   60.00
#=GF TC   60.00
#=GF NC   58.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300501;
#=GF DR   snoopy; Echinops_telfairi300125;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA38 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA38
#=GF SQ   25


AJ609474.1/1-132             UCCUCCUACAAAGGCGUGUCUGUGGUUCCCUGUCUUUGGACACGUAAGAAUUGGAGGAAAAUAAAUG---UGGAUUUGGGAAAC-UUUGAGGCCAGCUUGCU----UCUUGCAGGCUCAUGAUCAACCAAUCUCACAUAA
Z15025.1/12945-12815         UCCUCCUACAAAGGCGUGUCUGUGGUUCCCUGUCUUUGGACAUGUAAGAAUUGGAG-AAAAUAAAUG---UGGAUUUGGGAAAC-UUUGAGGCCAGCUUGCU----UCUUGCAGGCUCAUGAUCAACCAAUCUCACAUAA
BX548169.4/36965-36835       CCCUCCUACAAAGGCGUGUCUGUGGUUUCCUGUCUUUGGACACGUAAGAAUUGGAGGCAAAGAAAUA---UGGACUUGGAGACG-UCUGGGGCCAGCUUGCU----CCCUGCAGGCUCUAGUUCAACCA-UCCUACAUAG
AC006534.10/104122-104252    CCCUCCUACAAAGGCAUGUCUAUAGUUCCUUGUCUUUGGACAUGUAAGAAUUGGAGGCAAAGAAAUG---UGGACUUGGAGAAA-UCUGGGGCCAGCUUGCU----CUCCGCAGGCUCAAGAUCAACCA-UCCCACAUAG
AC087863.10/61455-61585      CCCUCCUACAAAGGCAUGUCUAUAAUUCCUUGUCUUUGGACAUGUAAGAAUUGGAGGGACAGAAAUG---UGGACUUGGAGAAA-UCUGGGGCCAGCUUUCU----CAUCACAGGCUCAACAUCAACCA-UGCCACAUAG
AACN010548547.1/927-797      CCCUCCUACAAAGGCAUGUCUGUAGUUCCUUGUCUUUGGACAUGUAAGAAUUGGAGGCAAAGAAAUG---UGGACUUGGAGAAG-UCUGGGGCCAGCUUGCU----CCCUGCAGGCUCAAGAUGAACCA-UCCAACAGAG
AANG01354549.1/1896-2026     CCCUCCUACAAAGGCGUGUCUGUAGUUCCCUGUCUUUGGACACGUAAGAAUCGGAGGAAGAGAAACG---UGGAUUUGGAGAAG-UCUGGGGCCAGCUUGCU----UCCUGCAGGCUCAAGAUCAACCA-UCCAACAGAG
AAPY01568187.1/4887-5017     CCCUCCUACAAAGGCGUGUCUGUGGUUGCCUGUCUUUGGACACGUAAGAAUUGGAGGCAGAGAAAUG---UGGAUUUGGAGGAA-UCUGGAGCCUGCUUGCU----CCCCGCAGGCUCAAGAUCACCCA-UCCCAUAUAG
AC148688.1/58172-58303       CCCUCCUACAAAGGCGUGUCUGUGGUUCCCUGUCUUUGGACACGUAAGAAUUGGAGGCAAAGAAAUG---UGGAUUUGGGAAAC-UUUAAGGCCAACUUGCU----CCUUGCAGGCUUAUGAUCAACCAAUCUCACAUAA
AALT01655667.1/7474-7604     ACCUCCUACAAAGGCGUGUCUAUGGUUCCCUGUCUUUGGAUACGUAAGAACCGGAGGUAAAGAAAUG---UGGACCUGAAGAAA-UUUGGGGCCAGCUUGCU----CCUCGCUGGCUCAAGAUCAGCAG-UCCCACAUGG
AAIY01447792.1/2011-1881     UCCUCCUACAAAGGCGUGUCUGUGGUUCCCUGUCCUUGGACACGUAAGAAUUGGAGGCAAAGAAAUG---UGGAUUUGGAGAAG-UUUGGGGCCAGCUUGCU----CCUCGCAGGCUCCAGCGCCCCCA-UCCCACACUG
AAQQ01042623.1/1589-1718     CCCUCCUACAAAGGCGUGUCUUUGGUUCCCUGUCUUUGGACACGUAAGAACUGGAGGAAAAGAAUUG---UGGAUUUGGGGAAG-UCUGGGGCCAGCUUGCU----CCUCGCGGGCUCA-GAUCAGUCA-UCCCACAUAG
ABDC01075727.1/1626-1755     CCCUCCUACAAAGGCAUGUCUGUGGUUCCUCAUCUUUGGACAUGUAAGAGUCGGAGGCAAAGAAACG---UGGAAUUGGAGAAG-UCUG-GGCCAGCUUGCU----CCCCGCAGGCUCAAGAUCAACCA-UCCCACAUGC
AAYZ01252661.1/56-187        UCCUCCUACAAAGGCGUGUCUAUGGUACCCUGUCUUUGGACACGUAAGAAUUGGAGGCAAAGAAAUG---UGGACUUGGGGAAGUUCUGGAGCCAGCUUGCU----CCCCGCAGGUUCAAGACCAACCC-UCCCACAUUG
AANN01115406.1/393-523       UCCUCCUCCAAAGGCGUGUCUUUAGUUCCUUAUCUCUGGACAUGUAAGAAUUGGAGGUAAAGCAAUG---CGGAUUUGGAGAAG-UCUUGGACCAGCUUGCU----CCCUGAAGGUUCAAGAUCAACCU-UCCCACAAAG
AAFR03043823.1/141570-141436 ACCUCCCACAAAGGCGUGUCUGUGGCUUCCCAUCCAUAGAUACGUAAGAACUGGAGGCAAAGAAAUG---AGGAUUAGGAAAAG-UUCAAGACUGGCUUACUCAACCCUUGCUGGUCUAGGACUUCCUG-UCCAACAAUA
AAGV020109420.1/154-285      CCCUCCUACAAAGGCGUGUCUGUGAUCUCCUGUCCUUGGACACGUAAGAAUUGGAGGCAUAGAGAUG---UGGACUUGGAGAAG-UCUGGAGCCAGCUUGCU----CCCUGCAGGCUCAAGAACACCCUUUCCCACACAG
AAKN02013806.1/104003-104133 CCCUCCUACAAAGGCGUGUCCUUUGCUCCCUGUCUUUGGAUGCGUAAGAACUGGAGGCAAAGAAAUG---AGGAUUUGGAGAGA-UCUCGGGCCGGCUUGCU----CCCCGCAGGCUCAAGAUCACCUG-UCCCACAAUA
FQ482107.2/120780-120650     UCCUCCUACAAAGGCGUGUCUGUGGUUUCCUGUCUUUGGACACGUAAGAAUUGGAGGCAAAGAAAUG---UGGACUUGGAGAAG-UCUAGGGCCAGCUUGCU----CCUUGCAGGCUCAAGAUCAACCA-UCCCACAUAG
AC147634.3/91724-91591       UCCUCCUACAAAGGCGUGUUUUUGGUUCCCUGUCCUUGGACACGUAAGAAUCGGAGGCAAAGAAACGUGGUGGAUUUGGAAAGG-UCUGGGACCAGCUUGCC----CCCUGCAGGCUCAGAAUCAACCA-UCCCACAGAA
BX883046.1/13397-13264       UCCUCCUACAAAGGCGUGUUUUGGGUUCCCUGUCCUUGGACACGUAAGAAUCGGAGGCAAAGAAAUGUGGUGGGUUUGGAAAGG-UCUGGGACCAGCUUGCC----CGCCGCAGGCUCAGGAUCAACCA-UCCCACAGAG
AAPE02050101.1/50498-50368   CCCUCCUACAAAGGCGUGUCUGUGGUUCCCUGUCUUUGGACACGUAAGAACUGGAGGCAAAGCAAUG---UGGACUUGGAGAAG-UCUGGAGCCAGCUUGCU----CCCUGCAGGCUCAAGAUCAACCA-UCCCACAUAG
AAGU03088578.1/49087-48957   UCCUCCUACAAAGGCGUGUCUGUGGUUCCCUGUCCUUGUACACGUAAGAAUUGGAGGCAAAGAAAUG---UGGACUUGGAGAAG-GCUGGGGCCAGCUCGCU----ACUUGCAGGCUCAAGCUCAUCCA-UCCCACAUCG
AAGW02056726.1/17812-17943   CCCUCCUACAAAGGCGUGUCUGUGACUCCCUGUGUUUGGACACGUAAGAAUUGGAGGCAAAGAAAUG---UGGACUUGGGGAAGUUCUGGGACCAGCUUGUU----CCGUGCAGGCUCAGGAUCAACCA-UCCCACAGAG
AAQR03044078.1/1913-1783     UCCUCCUACAAAGGCGUGUCUAUGGUUCCCCAUCUUUGGACGCGUAAGAACUGGAGGCAAAGAAAUG---UGGAUUUGGAGAAG-UCUGGGGCUAGCUUAUU----CCCCACAGGCUCAAGAUCAACCA-UCCCACAUAA
#=GC SS_cons                 :<<<<<--------<<<<<<<--<<___>>------->>>>>>>-------->>>>>----------...-<<<-<--------.---------<<<<<<<_....____>>>>>>>----------->.>>>:::::::
#=GC RF                      uCCUCCUACAAAGGCGuGUcugUgGUUcCcUGUCuUUggACaCGUAAGAAuUGGAGGcAAAGAAAUG...UGGauuUGGAgAAg.UcUgGGgCCaGCuugCU....ccuuGcagGCuCAaGAuCAaCca.uCCcACAuag
//
# STOCKHOLM 1.0

#=GF AC   RF00429
#=GF ID   SNORA29
#=GF PI   snoACA29
#=GF DE   Small nucleolar RNA SNORA29
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00030
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300912;
#=GF DR   snoopy; Echinops_telfairi300599;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   ACA29 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1]. The family also contains
#=GF CC   the mouse sequence MBI-39 as described in [2].
#=GF WK   Small_nucleolar_RNA_SNORA29
#=GF SQ   26


AF357392.1/1-124             ------------CUACCACAUUUUCUACUGAUAAUAGAUUUUGGUGGCUAUGCUUAUGGGAUAGA-UUAAA--GUUGCCAUGAUCUGAAGAGAGAGGGCUUUGC---AGUGUCCUCCCU-C--UAUAUGAAA-UGGCUGGACAGUA-----
AJ609472.1/1-140             UUUCUCAUUUGACUACCACAUUUUCUCCUAAUAAUAGAUUUUAGUGGCUAUGCUUAUGGGAUAGA-UUAAA--CUUGCCAUGAUCUGAAGAGGGAGGGUUUUUU---CAUGUCCUCCUC-C--UAUAUGAAA-UGGCUGAACGG-AUAUUA
S46763.1/4187-4324           UUUCCCAUUUGACUACCACAUUUUU--CUCCUAAUAGAGUUUAGUGGCUAUGCUUAUGGGAUAGA-UGAAA--GGUGCCAUGAUCUGAAGAGGGGGAGCUGUCC---UGUGUCUUUCCU-C--UAUAUGAAA-UGGCUGAACAG-AAACCA
AAQQ01007810.1/1923-1784     UUUCCCAUAUGACUACCACAUUUUCUUCUAAUAAUAGACUUUAGUGGCUAUGCUUAUGGGAUAGA-UUAAA--GUUGCCAUGAUCUGAAGAGGGAGGAUUUUCA---AGUGUUCUCCUU-C--UAUAUGAAA-UGGCUGAACAA-AAAGUC
AAHX01002920.1/48724-48860   CUUCCCAUUUGACUACCACAUUUUC---UCCUAAUAGAGUUUAGUGGCUAUGCUUAUGGGAUAGA-UGAAA--AGUGCCAUGAUCUGAAGAGGGGGAGCUGUUC---CGUGUCUUUCCU-C--UAUAUGAAA-UGGCUGAACAG-AAAACC
ABDC01266374.1/2723-2584     UUUCCCAUUUGACUACCACAUUUUCUCCUAAUGAUAGAUUUUAGUGGCUAUGCUUAUGGGAUAGA-UUAAA--AUUGCCAUGAUCUGAAGAGGGAUGAUCUUUU---GGUGUCUUCCUU-C--UAUAUGAAA-UGGCUGAACAG-AAAGUU
AAPY01008775.1/1164-1026     CUUCCCGUUUGACUACCACAUUUUCUCCUUGUAAUAGAUUUUAGUGGCUAUGCUUACGGGAUAGA-UUAAA--AUCGCCAUGAUCUGAAGAGGGAGGG-UUUUU---GGUGUCCUCCUC-C--UAUAUGAAA-UGGCUGAACAG-AACAUG
AALT01080871.1/2191-2329     UUUCCCAUUUGACUACCACAUUUUCUCCUACUAAUAGACUUUGGUGGCUAUGCUUGUGGGAUAGA-GUAAA--AUUGCCAUGAUCUGAAG-GGGAGGAUUUCUU---UGUGUCCUCUUC-C--UAUAUGAAA-UGGCUGAACAG-CAAAAA
AAYZ01400907.1/6753-6614     UUUCCCAUUUGACUACCACAUUUUCUUCAAUUAAUAGAUUUUAGUGGUAAUGUGUGUGGGAUAGA-UUAAA--GUUGCCAUGAUCUGAAAGGGGAGGCGUUUUU---GGUACCCUCCUU-C--UAUAUGAAA-UGGCUGAACAG-AAAAAG
AAFC03124996.1/5463-5599     UUUCCCAUUUGACUACCACAUUAUC---UCCUGAUAGAUUUUAGUGGCUAUGCUUGUGGGAUAGA-UAAGA--ACUGCCGUGAUCUGAAGAGGGGGGAUUUGCU---CGUGUCCUCCUC-C--UAUAUGAAA-UGGCUGAACAG-AGCAUU
AAIY01629999.1/5581-5443     GUUCCCAUGUGACUACCACUUCAACUCUUAAUAAUAGAUUGUAGUGGCUAUGCUUGUGGGAUAGAGUGAUU--UUUGCCAUGAUCUGAAGAGGGAGG--UUUAU---UGUGUCCUCCUC-C--UAUAUGAAA-UGGCUGUACAG-AAAAUG
AANN01210070.1/913-1051      UUUCCCAUUUGACUACCACAUUUUCUUCUCUUACUGGAAUUUCGUGGCUAUGCUUGUGGGAUAGA-GUAAU--GCCGCCGUGAUCUGAAGGAGGAGGG-UUUCC---UGUGUCCUCCUC-C--UAUAUGAAA-UGGCCGGACAG-AGCGGU
AAFR03000650.1/148260-148397 CUUCCCAUUUGACUACCACUUUUUC---ACUUAAUAGA-UUUAGUGGCUAUGCUUAUGGGAUAAA-AUAUA--GCUGCCAUGGUCUGAUG-GAGAAAAAGUGUC---UGGGUCUUUUUU-UCCUAUAUGAAA-UGGCAGAACAAUCUAGCU
AAKN02044242.1/65927-66065   UUUCCCAUUUGACUACCACAUUUUCUCCUG-UGAUAGAUUUUAGUGGCUAUGCUUAUGGGAGAGA-UGAAA--GUUGCCAUGAUCUGAAGAGGGAGGGCUUUUC---AGUGCCCUCCUC-C--UAUAUGGAA-UGGCUGAACAG-AAGACC
AAGV020744449.1/910-768      UUUCCCAUUUGACUACCACUUUUUCUCUUAAUAAUGGAUUUUAGUGGCUAUGCUUAUGGGAUAAA-UGAAA--AUUGCCAAAACCUGAAGAGGGAGGAUUUUGUGUGUGUGUCCUCCUC-C--UAUAUGAAA-UGGGUGGUUAG-AAAACU
AAWR02039337.1/17742-17605   UUUCCCAGUUGACUACCACAUUUUCUCCUA--AAUAGAUUUUAGUGGCUAUGCUUAUGGGAUAGA-CUAAA--AUUGCCAUGAUCUGAAGAGGGAGGAUUUGUU---UGUGUCCUCCUC-C--UAUAUGAAA-UGGCUGGACAA-AGUUGG
CU582830.1/48886-48751       CUUCCCAUUUGACUACCACUUUUUU---GAAUCACAGA-UUGAGUGGUUAUGCUUAUGGGAUAGA-CAAAA-AGCUGCCAUGGUCUGAAGGAGAAGAUGUUUGA---UAUCUUUUUC-C-C--UAUAUGAAA-UGGCAGAACAA-AACCAG
EU240306.1/1-133             AUUCCCAUUAUACUACCACUUUUUCAAUCUCCAGAGGA----AGUGGCUAUGCUUGUGGGAUAGA-GGAAAAUGUUGCCACGGUCUGAAGGAAAAGG--UUGAU---UGUAUCUUUUUC-C--UACAUGAAGUUGGCAGGACAU-----CA
FQ225819.1/1-137             CUUCCCAUUUGACUACCACAUUUUC---UCCUAAUAGAGUUUAGUGGCUAUGCUUAUGGGAUAGA-UGAAA--AGUGCCAUGAUCUGAAGAGGGGGAGCUGUUC---CGUGUCUUUCCU-C--UAUAUGAAA-UGGCUGAACAG-AAUUUU
CU855864.8/193197-193336     CUUCCCAUUUGACUACCACAUUAUCUCCUAAUAAUAGAUUUUAGUGGCUAUGCUUGUGGGAAAGA-UUAAA--AUUGCCAUGAUCUGAAGAGGGAGGGUUGAUU---UGUGUCCUCCUC-C--UAUAUGAAA-UGGCUGAACAG-GAAAUG
AAQR03090220.1/5891-6030     UUUCCCAUUUGACUACCACAUUUUCUCCUAAUGGUAGAUUUUAGUGGCUAUGCUUAUGGGAUAGA-UUAAA--GUUGCCGUGAUCUGAAGGAGGAGGGUUUUUC---AGUGUCCUCCUU-C--UAUAUGAAA-UGGCUGAACAU-AAAGUU
AAPE02028062.1/47474-47613   CUUCCCAUUUGACUACCACAUUUUGUCCUAAUAAUAGAUUUUAGUGGCUAUGCUUAUGGGAUAGA-UUAAA--AUUGCCAUGAUCUGAAGAGGGAGGAUUUAUU---UGUGUCCUCCUCC---UAUAUGAAA-UGGCUGAACAG-AAAAAA
AAGW02053227.1/1550-1688     UUUCCCAUUUGACUACCACGUUUUCUCCAAUUAGUAGAUUUCAGUGGCUAUGCUUAUGGGAUAGA-UGAAA--ACUGCCAUGAUCUGAAGAGGGAGAG-GAUUU---GGUACCCUCCUU-C--UAUAUGAAA-UGGCUGGACAG-AAGAUG
AAWZ02008955.1/20993-21127   CUUCCCAUUUGACUGCUACUUGUUUGCACUUCAAAAUA----AGUAGCUAUGCUUGUGGGAUAUA-GAAGU-AUCUGCCAUAGUUUUAAG-GAGAAGA-CUGAU---AGUAUCUUCUUC-C--UAUAUUUAA-UGGCAAAACAU-AUUAAA
AADN03002983.1/20761-20625   AUUCCCAUUAUACUACCACUUUUUCAAUCUCCAGAGGA----AGUGGCUAUGCUUGUGGGAUAGA-GGAAAAUGUUGCCACGGUCUGAAGGAAAAGG--UUGAU---UGUAUCUUUUUC-C--UACAUGAAGUUGGCAGGACAU-CAUCUG
AACN010004284.1/5469-5330    UUUCCCAUUUGACUACCACAUUUUCUCCCAAUAAUAGAUUUUGGUGGCUAUGCUUAUGGGAUAGA-UUAAA--AUUGCCAUGAUCUGAAGAGGGAGGAUUUAUU---UGUGUCCUCCUC-C--UAUAUGAAA-UGGCCAAACAG-AAAAUU
#=GC SS_cons                 :::<<<<--------<<<<________________________>>>>--------->>>>-----.-----..---<<<<--------------<<<<______...__________>>.>..>--------.>>>>:::::::.::::::
#=GC RF                      uUUCCCAUUUGACUACCACaUUUUCuccuaaUAAUAGAuUUUAGUGGCUAUGCUUaUGGGAUAGA.uuAAA..auUGCCAUGAUCUGAAGaGGGAGgguUUuuu...uGUgUCcUcccc.C..UAUAUGAAA.UGGCuGaACAg.Aaaauu
//
# STOCKHOLM 1.0

#=GF AC   RF00430
#=GF ID   SNORA54
#=GF PI   snoACA54
#=GF DE   Small nucleolar RNA SNORA54
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   60.00
#=GF TC   60.10
#=GF NC   59.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00034
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Danio_rerio300102;
#=GF DR   snoopy; Gallus_gallus300090;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA54 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA54
#=GF SQ   5


BX901883.5/169709-169573 GUGCACUGUUCGUAACCUGUUUCAGCCUACCAGUCUGAGAUUUGGGUUCCAUUCCAGUGCAAGAUUAAUAAACUCAGUGAGGCAGGGGAGU--GGUGCCUCAUUUGU-GCUUUCUCCCUGUUCACUCUCUGAUGACAUUC
BX640401.2/48470-48342   AUGCACUGUUCGUAACCUGUUAGCAGUGUAAUUCUGUUAAC--GGGUUCCAUUCCGGUGCUACAUGAUA--ACCCC--AAG--AUAACAGA-AGGCUGGCUGUUUGUUUGCCUGUUCCC-UUUA-UUUUGGGGGACAUAA
BX640401.2/45102-44982   UCGCACUGCUCGUAACCUUUUGACAGCAUAUUCCUGUGAAU--AGGUUCCAUUCCAGUGCUACAACAA---AUCCAGUAAU--GGAAGGCUGACAGAC-----UCCA-UGUCCCUUCCGUAUU------UGGAGACAUUC
AJ609479.1/1-123         GAGCACUGUUCGUAACCCGUUAGCCUGGCUGUA--GCUAAU--GGGUUCCAUUCCGGUGCAAUAGCAU---UUCCAGCGACACAUGACUGACUGACUGG----UGGC-UUUCAGUUUCAGGUCU-----UGGAGACAAAU
AP001294.1/48463-48589   CAGCACUGUUCGUAACCUGUCAGCCUUGCUGUG--GCUGGU--GGGUUCCAUUCCAGUGCUACAGGAU---UUCCAGUGACACAUGACUGACUGGCUGGCUAGUGGC-UUUCAGUUUCAGGUCU-----UGGAGACACAC
#=GC SS_cons             ::<<<<<<---<-<<<<<<<<<<<<_________>>>>>>>..>>>>>->---->>>>>>--------...-<<<<--<<<----<<<<<_________________.___>>>>>---->>>-.....>>>>:::::::
#=GC RF                  uuGCACuGUUCGUAACCcguuagcguuguuuUuccgcuaac..gGGUUCCAUUCCaGUGCuAcAuuAu...aucCaGUgAcaCAugagggacaGgcugguuauUuGu.uuUcccuccCaggUca.....uGgaGACAuac
//
# STOCKHOLM 1.0

#=GF AC   RF00431
#=GF ID   SNORA55
#=GF PI   snoACA55
#=GF DE   Small nucleolar RNA SNORA55
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   45.00
#=GF TC   47.20
#=GF NC   44.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300862;
#=GF DR   snoopy; Loxodonta_africana300470;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA55 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA55
#=GF SQ   29


AJ609480.1/1-137             GAGCACCUGAAUCUUUCCCAUUCCUU-GCUGCCUCGUGCCGGUGUGGGGACAGAUGGUGCUACAGAAUGAGCAGAGGAAAUCCAGACAGGUUGUUU-UCCA-UUUGUCU-UGGGGCCUGUCUCUACAGC-UCUGCCACAUUU
AC124598.5/176959-176830     --GCACU-AAAUCUUUCCCAGGCCU--GCUGCUUGGUGCCGGUCUGGGGACAGACAGUGCUAUACUA-GAGCAGAGGAAAUCCAGACAGGUCGUUU--CCA-UCUGCC--UGGGGCCUGUCUCUACAAC-UCUGCCACACUC
AL606917.12/4887-5017        --GCACU-AAAUCUUUCCCAGGCCU--GCUGCCCGGUGCCGGUCUGGGGACAGACAGUGCUAUACUA-CAGCAGAGGAAAUCCAGACGGGUCGUUU--CCA-UCCGCCC-UGGGGCCUGUCUCUACAAC-UCUGCCACACUU
AALT01049511.1/846-979       --GCACCUAAAUCUUUCCCAUUCCUU-GCUGCUUCGUGCUGGCAUGGGGACAGAUGGUGCUAUAGUACAAGCAGAGGAAAUCCAGAUGGGUUGUUU--CCA-CUUGUCU-UGGGACCUGUCUCUACAAC-UCUGCCACACUU
AAQQ01076179.1/4047-4179     --GCACC-CGAUCUUUCCCAUUCCU--GCUGCUUCGUGCUGGUCUGGGGACAGAUGGUGCUACACUAUGAGCAGAGGAUAUCCAGACGGGUUGUUU-UCCA-UUUGUCU-UGGGACCUGUCUCUACAAC-UCUGCCACAUUU
AANN01707595.1/2020-1886     --GCACCUGAAUCUUUCCCAUUCCUU-GCUGUUUCGUGCAGGCAUGGGGACAGAUGGUGCUACAGUAUGAGCAGAGGAAAUCCAGACAGGUUCUUU-UCCA-UUUGUCU-UGGGACCUGUCUCUACAAC-UCUGCCACAUUA
AAFC03075293.1/7961-7827     --GCACCUGAAUCUUUCCCAUUCUCU-GCUGCUUCGUGCUGGUGUGGGGACAGAUGGUGCUACAGUAUGAGCAGAGGAAAUCCAGACAGGCUGUUA-GCCA-UUUGUCU-UGGGGCCUGUCUCUACAAC-UCUGCCACACUU
AAIY01667802.1/1413-1280     --GCACCUGAAUCUUUCCCAUUCCGG-ACUGCCUCGUGCUGGUGUGGGGACAGAUGGUGCUACAGCAUGAGCAGAGGGAAUCCAGACGGGUGGUUU--CCA-UUUGUCU-UGGGGCCUGUCUCUACAAC-UCUGCCACACUC
CR956427.7/772-638           --GCACCUGAAUCUUUCCCAUUCUUU-GCUGCUUCGUGCUGGUGUGGGGACAGAUGGUGCCACAGUAUGAGCAGAGGAAAUCCAGACGGGUUGUUU-CCUG-UUUGUCU-UGGGACCUGUCUCUACACC-UCUGCCACACUU
AAPY01081364.1/1206-1337     --GCACCGGAAUCUUUCCCGCUCCUU-GCUGCCUCGUGCUGGUGUGGGGACAGGUGGUGCCACAGUGUGAGCAGAGGAUAUCCAGACGGGCCGU----CCA-UUUGCCU-UGGGGCCUGUCCCUACAAC-UCUGCCACAUUU
AAYZ01448689.1/2842-2708     --GCACCUGAAUCUUUCCCAUUUCCU-GCUGUUCUGUGCUGGUGUGGGGACGCACGGUGCCAUAGUGUGAGCAGAGUAAAUCCAGACAGGUUGUUU-UCCA-UUCAUCU-UGGAACCUGUCCCUACAAC-UCUGCGACAUUU
AAFR03044173.1/22529-22663   --GCACCUGCAUCUUUCCCAUUCUUG-GCUGCUUUGUGCCUGUCUGGGGACAGGUGGUGCUACAGUACAAGCAGAGGAAAUCCAGACAGGUUAUCU-UCUG-UUUACUU-UGGGGCUUGUCUCUACAAC-UCUGCCACACUU
AAPN01168550.1/12156-12290   --GCACCUGAAUCUUUCCCAUGCCUU-GCUGGGCAGUGUGGGUUUGGGGACAGAUGGUGCUACACUAGCUGCAGAGGAAAUCCAGGCAGGUUACUU-UCCA-UUUACAU-UGCAACUUGCCUCUACAAC-UCUGCCACAUUU
ABDC01046829.1/2784-2918     --GUACCUAAAUCUUACCCAUUUCUU-GCUGCUUCGUGCUGCUGUGGAGACAGAUGGUUCUACGGUAUGAGCAGAGGAAAUCCAGAAAGGUUGCUU-UUCA-UUUAUCU-UGGAGCCUGUCUCUACAGC-UCUGCCACAUUU
AAWR02028016.1/7959-8093     --GCACCUGAAUCUUUCCCAUUCUUU-GCUGCUUUGUGCUGGUGUGGGGACAGAUGGUGCUACAGUAUGAGCAGAGGAAAUCCAGACGGGUUGUUU-UCCA-UUUGUCU-UGGGGCCUGUCUCUACAAC-UCUGCCACACUC
AC114512.5/186766-186635     --GCACUCAAAUCUUUCCCAGGCCU--GCUGCUUGGUGCCGGUCUGGGGACAGGCAGUGCAAUAGUA-GAGCAGAGGAAAUCCAGACGGGUUGUUU--CCA-UCUGUCC-UGGGGCCUGUCUCUACAAC-UCUGCCACACUC
AAKN02054322.1/26905-26773   --GCACC-CAAUCUUUCCCAUUCCU--GCUGCUUUGUGCUGGCCUGGGGACAGUGGGUGCUACAACAUGAGCAGAGGAUAUCCAGACGGGUUGCUU-UCCA-UUUGUCU-UGGGGCCUGUCUCUACAAC-UCUGCCACAUUG
AAGV020174727.1/1112-1246    --GCACCUGAAUCUUUCCCAUUCCCU-GCUGCUUUGUGCUGGUGUGGGGACAGAUGGUGCUACAGUAUGAGCAGAGGAAAUCCAGACAGGUUGUUU-UCCA-UUUGCCU-UGAGGCCUGUCUCUACAAC-UCUGCCACAGUU
EU240224.1/3-135             --GCACCUGAAUCUUUCCUAUUCCUU-GCUGUGCAGUGCAGGUCUGGGGACAGUUGGUGCUACAGCA-CAGCAGCAGAAAUCCAGAUGGGUUACUU-UCCA-CUCGC-U-UGGAACUCAUCUCUACAGC-UCUGCAACAUUU
EU240304.1/3-130             --GCACC-UAAUCUUUCCCAUUCCUU-GCUGUGCAGUGUGAGCCUGGGGACGCAUGGUGCUGACAGAAAAGCAGAGUAAAUCCAGACAAGUGGUUC--UUC-AUUGACU-----AAUUGUCUCUACACC-UCUGCAACAGU-
EU094001.1/4-138             --GCACCUGAAUCUUUCCCGUGCCUU-GCUGGGCAGUGUGGGUUUGGGGACAGAUGGUGCUACACUAGCUGCAGAGGAAAUCCAGGCAGGUUACUU-UCCA-UUUACAU-UGCAACUUGCCUCUACAAC-UCUGCCACAUUU
EU094013.1/4-137             --GCACCUAAAUCUUUCCCACUCCU--GUGACCCCGUGCGGGAGUGGUGACAAAUGGUGCUACAGAA-UGGCAGAGGAAAUCCAGACAGGUCGCUACACCA-AUCAUCC-AGGCACCUGUCCCUACAAC-UCUGCAACAUGU
AAGU03057908.1/19655-19522   --GCACCUGAAUCUUUCCCAUUCUCU-GCUGCCUCGUGCUGGUGUGGGGACAGACGGUGCUACAACACGAGCAGAGGAAAUCCAGACGGGUUGUUC--GCA-UUUGUCU-UGGGGCCUGUCUCUACAAC-UCUGCCACACUC
AAGW02003126.1/53074-53208   --GCACCUGAGUCUUUCCCAUUCCCU-GCUGCUCUGUGCUGGUGUGGGGACGGAUGGUGCCACAGCGUGGGCAGAGGAAAUCCAGACGGGCUGUUU-UCCA-UUCACCU-UGGAGCCUGUCUCUACAGC-UCUGCUACAUUU
AAPE02037968.1/8613-8746     --GCACCUGAAUCUUUCCCAUUCUUU-GCUGCUUCGUGCUAGUGUGGGGACAGAUGGUGCCACAGUA-AAGCAGAGGAAAUCCAGACGGGUUGUUU-UUCA-UUUGUCU-UGCGGCCUGUCUCUACAGC-UCUGCCACACUU
AAQR03149923.1/18746-18877   --GCACCUAUAUCUUUCCCAUUCCUU-GCUGAUUCGUGCUGGUGUGGGGACAGAUGGUGCUAUAGCAUCAGCAGAGGAAAUCCAGACAGGU--UUU--CCA-UUUGUCU-UGGGGCCUGUCUCUACAAC-UCUGCCACAUUU
AAWZ02028783.1/6715-6851     --GCACCUGAAUCUUUCCCAGGCCUCGCAAAACAAGUGGGGGUCUGGGGACAAGGGGUGCUAAAGCA-AAGCAGAGGAAAUCCAGAUGGGCCGCCU--CUUAUCUGCAGUGAGGGCCUGUCUCUACACCUUCUGCUACACUG
AADN03008187.1/23656-23526   --GCAUCUGAAUCUUUCCCACUCCUU-GCGAUGUAGUGCCGGACUGGGGACACAUGAUGCAACAGGA-AAGCAGAGGAAAUCCAGACAGGCUCUUU--C---ACUGUAU-UGGGGUUUGUCUCUACACC-UUUGCAACAUUU
AAEX03009572.1/102239-102373 --GCACCUGAAUCUUUCCCAUUCUUU-GCUGCUCUGUGCUGGUGUGGGGACAGACGGUGCAACAGUACAAGCAGAGGAAAUCCAGACAGGUUGUUU-UCCA-UUUGUCU-UGGGGCCUGUCUCUACGAC-UCUGCCACACCU
#=GC SS_cons                 ..<<<<<-------<<<<<<<-<<__._____________>>->>>>>>>----->>>>>----------<<<<<<-------<<<<<<<<-----.-<<<._______.>>>->>>>>>>>------>.>>>>>:::::::
#=GC RF                      ..GCACCUgAAUCUUuCCCacuCcUu.GcUGcuuaGUGcugGuguGGGgACAgauGGUGCuAcAguAuaAGCAGAGGAAAUCCaGacaGGcuguUU.ucCa.uUUgucU.uGgggCCuguCuCUACAaC.UCUGCcACAuUu
//
# STOCKHOLM 1.0

#=GF AC   RF00432
#=GF ID   SNORA51
#=GF PI   snoACA51
#=GF DE   Small nucleolar RNA SNORA51
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   50.00
#=GF TC   50.20
#=GF NC   49.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300016;
#=GF DR   snoopy; Homo_sapiens300046;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA51 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA51
#=GF SQ   9


AJ609477.1/1-132          GGCCUCCUGGUGCUUACCA-CAGGCUGUGUUCUUACACUGACUGUAUAGAAAGAG-GAGGUAGAGUAAACCUACCCCAUAUACACCUCAGCUCAGGCCC-UGUGCCUGGUCUGUAUUGUGAAU-GGGGGAACAUAG
AC007240.2/163812-163679  GGCCUCCUGGUACUUACCCACAGGCUGCGUUCUUACACUGGCUGUACAGAAAGAG-GAGCUAGAGUAAACCUACCUAAUAUACACCUCAGCCCAGGCCC-UGUGCCUGGUCUGUAUUGUGAAUGGGGGGGACAUAG
AL833804.16/186436-186568 GGCCUCCUUGUGCUUACCA-CAGGCUGUGUUCCUACACUGACUGUAUAGAAAGAG-GAGGCAGAAUAAACCUACCCCAUGUACACCUCAGCCUAGGCCACUGUGCCUGGUCUGUAUUGUGAAU-GGGGAGACACGG
AC020918.6/165518-165651  GGCCUCCUGGUGCUUACAAGCAG-CUGUGUGCUUGCAUUGACUGUACAGAAAAAAAGAGAUAGAGUAAACACACCCCGUAUACAACUCAGCCCAGGUCC-UGUGCCUUGUCUAUAUUGUGAAUAGGGGGGACAUAG
AL844850.9/118508-118640  GGCCUCCUUGUGCUUACCA-CAGGCUGUGUCCCUACACUGACUGUAUAGAAAGAG-GAGUCAGAAUAAACCUACCCCAGGUACACUUUAGCCUAGGCCACUGUACCUGGUCUGUAUUGUGAAU-GGGGAGACAUGU
AC116183.6/44055-44187    AGCCUCCUUGUGCUUAGCA-CAGGCUGUGUUCCUACACUGACUGUAUAGAAAGAG-GAAGGAGAAUAAAACUACCCUGUGUACACCUCAGCCUAGGCCACUGUGCCUGGUCUGUAUUGUGAAU-GAGUAGACAUGG
AL591429.9/1550-1680      -GCCUCCUA-UGCUUACCA-CAGGCUGUGUUCCUACACUGACCAUAUAGAAAGAG-GAGGCAGAAUAAACCUAUCCUAUGUACACUUCAGCCUAGGCCACUGUGUCUGGUCUGUCUUGUAAAU-GGGGAGACAUGU
AC009967.8/26053-26184    GGCUUCCUAGUACUUACCA-UGGUCUGUGUUCUUACGCUGACUGUAUAGAAACAG-GAGGCAGAGUAAACCGACCCCACAUAUACCUCAGCCCAGGCCC-UGUGCUGCGUCUGUAUUGUGAAU-CAGGAGACAUGG
AL583883.12/106543-106671 GGAGUCCUG---CUUACCA-CACACUGUAUUCUUAUGCUGACGGUAUAUGGAGAG-GAGGCAGAGCAAACCGACUCCCUGUACAGCUUAUCCCAGGUCAUUGUGCCUGAUCUGUAUUGUGAAU-GGGGAGACAUG-
#=GC SS_cons              :<<<<<<<-----------.<<<---<<<<____>>>>--->>>--------->>.>>>>>------------<<<<<<--------<<<-<<<<<<______>>>>>>->>>-------->>.>>>>::::::::
#=GC RF                   GgccUCCUgGUgCUUAccA.caGgCUGuGuuCuUaCaCUGACugUAUAGAAAgAG.GAggcAGAgUAAACcuAcCccauaUACAccUcAGCccaGGcCacUGUgCCuggUCUgUAUUGUGAau.ggGgaGACAUgg
//
# STOCKHOLM 1.0

#=GF AC   RF00433
#=GF ID   Hsp90_CRE
#=GF DE   Hsp90 cis-regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15347681, INFERNAL
#=GF SS   Published; PMID:15347681
#=GF GA   50.00
#=GF TC   61.50
#=GF NC   47.30
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   15347681
#=GF RT   Translational regulation of Hsp90 mRNA. AUG-proximal 5'-untranslated
#=GF RT   region elements essential for preferential heat shock translation.
#=GF RA   Ahmed R, Duncan RF
#=GF RL   J Biol Chem 2004;279:49919-49930.
#=GF CC   The hsp90 gene product is involved in the Drosophila heat shock response
#=GF CC   and translation of the hsp90 mRNA is very inefficient under normal growth
#=GF CC   temperatures. When heat shock occurs translation becomes more efficient.
#=GF CC   This family represents a section of the Drosophila hsp90 mRNA 5' UTR that
#=GF CC   is required for increased translational efficiency during the heat shock
#=GF CC   response. The exact mechanism of action unknown [1].
#=GF WK   Hsp90_cis-regulatory_element
#=GF SQ   6


X03810.1/877-1028            AGUCUUGAAAAAAAUUUCGUACGGUGUGCGUCGUAACAACAAGCAGCGUCUGAAAAGUUUUGUGAAUUUCCAAUUCUAUACAAAGCAAAGUGAAAAUAUCUGUAUUUUUACCUUUAUUCUGUGAAUAGAACGAAAAACAUACAUACAAGGUG
AY122080.1/193-344           AGUCUUGAAAAAAAUUUCGUACGGUGUGCGUCGUAACAACAAGCAGCGUCUGAAAAGUUUUGUGAAUUUCCAAUUCUAUACAAAGCAAAGUGAAAAUAUCUGUAUUUUUACCUUUAUUCUGUGAAUAGAACGAAAAACAUACAUACAAGAUG
X03811.1/879-1030            AGUCUUGAAAAAAAUUUCGUGCGGUGUGCGUCGUUACAGCAAACAGCGUCUGAAAAGUUUUGUGAAUUUCCACUUCUACACAAAGCAAAGAGAAAAUAUCUGUAUUUUUACCUUUAUUCUGUGAAUAGAACGAAAAACAUAAAUACAAGGUG
J01106.1/161-312             AGUCUUGAAAAAAAUUUCGUACGGUGUGCGUCGUAACAACAAACAGCGUCUGAAAAGUUUUGUGAAUUUCCAAUUCUAUACAAAGCAAAGUGAAAAUAUCUGUAUUUUUACCUUUAUUCUGUGAAUAGAACGAAAAACAUACAUACAAGGUG
AAEU02000132.1/310682-310830 AGUCUUAAAAAAAU-UUCGUGAGGUGUGCGUCGUUACAGCAAGCAGCGUCUGA--AGUUUUGUGAAUUUCCAAUUCUAUACAAAGCAAAGUGAAAAUAUCUGUAUUUUUACCUUUAUUCUGUGAAUAGAACGAAAAACAUACAUACAAGGUG
AAPQ01006550.1/448359-448507 AGUCUUGAAAAAAU-UUCGUGCAGUGCGCGUCGUAGCAGCAAAUAGCGUCUGA--AGUUUUGUGAAUUUCCAAUUCUAUACAAAGCAAAGUGAAAAUAUCUGUAUUUUUACCUUUAUUCUGUGAAUAGAACGAAAAACAUACAUACAAGGUG
#=GC SS_cons                 :((((((,,,,,,,<<<<<-<<<-<<<--<<_______>>-->>>->>>->>>>>,,,,,<<<<--<<<<---<<<<<<-<<-<<-<<<<<<<<<<<<____>>>>>>>>->>>>--->>->>->>>>>>->>>>-->>>>,,,,)))))):
#=GC RF                      AgcCuuGAAAAAAauuuCgUgcGGuGcGCGcCGUaACAgCAAgCaGCgcCcGaaaAGUUUuguGAAuuuCCAauuCuauACaAaGCaaaGugaaaauaUCUGuauuuucaCCuuuAUUCuGuGAauaGaaCGaaaAACacacAUACaaGgcG
//
# STOCKHOLM 1.0

#=GF AC   RF00434
#=GF ID   BTE
#=GF DE   Luteovirus cap-independent translation element (BTE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15351207
#=GF SS   Published; PMID:15351207
#=GF GA   45.00
#=GF TC   46.70
#=GF NC   32.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0031369; translation initiation factor binding;
#=GF DR   GO; 0006413; translational initiation;
#=GF RN   [1]
#=GF RM   15351207
#=GF RT   Subgenomic RNA as a riboregulator: negative regulation of RNA replication
#=GF RT   by Barley yellow dwarf virus subgenomic RNA 2.
#=GF RA   Shen R, Miller WA
#=GF RL   Virology 2004;327:196-205.
#=GF CC   This family represents the Luteovirus cap-independent translation element
#=GF CC   (BTE) as found in barley yellow dwarf virus (BYDV), bean leafroll virus
#=GF CC   and soybean dwarf virus. This family mediates translation of genomic
#=GF CC   (gRNA) and subgenomic RNA1 (sgRNA1) [1].
#=GF WK   Luteovirus_cap-independent_translation_element
#=GF SQ   17


AB076046.1/1867-1967 -UGGUGAGUUGCUGUUG--UGGGAUCCUGGGAAACAGGUUCGGUGAACA-AAAGCCGGUAAUCUCG-----------GG-CGUUUGUCAG-----------ACG-CCGCCGAAUCA-ACACAGUAUGCAU
AY220739.1/4842-4940 ACACC-ACUCGCAAA--UUC-GGAUCCUGGGAAACAGGCA-GAACUUCG---GUUCG-UAAGCUCG-----------GGUAAACUAGUCC-----------UUUACCGUCGUAUCGUACUUUGUGUGGCC
AF235167.1/4816-4915 ACACC-ACUAGCACA-AAUC-GGAUCCUGGGAAACAGGCA-GAACUACG---GUUCA-UAAGCUCG-----------GGUAGGCCGUCAA-----------CCUACCGCCGUAUCGUAUUGUGUUUGGCC
AB076047.1/1872-1973 -UGGUGAGUUGCUGUCG--UGGGAUCCUGGGAAACAGGUUCGGUGAACAAAAAGCCGGUAAUCUCG-----------GG-CGUUCGUCAG-----------ACG-CCGUCGUAUCA-ACACAGUAUGCAU
AB076048.1/1871-1967 ---GUGAGUUGCUGUCG--UGGGAUCCUGGGAAACAGGUUCGGUGAACAAAAAGCCGGUAAUCUCG-----------GG-CGUUUGUCAG-----------ACG-CCGUCGUAUCA-ACACAGUAUG---
D11032.1/4816-4915   ACACC-ACUAGCACA-AAUC-GGAUCCUGGGAAACAGGCA-GAACUACG---GUUCG-UAAGCUCG-----------GGUAGGCCGUCAA-----------CCUACCGCCGUAUCGUAUUGUGUUUGGCC
AF441393.1/5292-5389 GCGCC-ACUAGUGCA-U--C-GAAUCCUGGGAAACAGGCACGGAGAACA-AAAUCCGGUAAGCUCG-----------GG-AAGCCGUCAA-----------CUU-CCGCCGUAUUG--AUGAAAACAACU
D85783.1/4816-4915   ACACC-ACUAGCACA-AA-UCGGAUCCUGGGAAACAGGCA-GAACUACG---GUUCA-UAAGCUCG-----------GGUAGGCUGUCAA-----------CCUACCGCCGUAUCGUAUUGUGUUUGGCC
X07653.1/4819-4918   ACACC-ACUAGCACA-AA-UCGGAUCCUGGGAAACAGGCA-GAACUUCG---GUUCG-UAAGCUCG-----------GGUAGGCCGUCAA-----------CCUACCGCCGUAUCGUAUUGUGUUUGGCC
AB076042.1/1877-1973 ---GUGAGUUGCUGUCG--UGGGAUCCUGGGAAACAGGUUCGGUGAAUAAAAAGCCGGUAAUCUCG-----------GG-CGUUCGUCAG-----------ACG-CCGUCGUAUCA-ACACAGUAUG---
AF218798.2/4817-4938 ACACC-ACUAACACA-AGCC-GAAUCCUGGGAAACAGGCA-GAACUUAG---GUUCG-UAAGCUCGGGUAAUUGGAAGGUGGGCUGUCAACCCACCACCAUCUUACCGCCGCAUUGCCUUGUGUUUGGCC
X80050.1/6-105       ACACC-ACUAGCACA-AAUC-GGAUCCUGGGAAACAGGCA-GAACUACG---GUUCA-UAAGCUCG-----------GGUAGGCUGUCAA-----------CCUACCGCCGCAUCGUAUUGUGUUUGGCC
AJ007491.1/1974-2073 ACACC-ACUAGCACA-AUCC-GGAUCCUGGGAAACAGGCA-GAACCUCG---GUUCA-UAAGCUCG-----------GGUAGGCCGUCAA-----------UCUACCGCCGUAUCGUUUUGUGUUUGGCC
D11028.1/4805-4903   ACACC-ACUCGCAAA--UAC-GGAUCCUGGGAAACAGGCA-GAACUUCG---GUUCG-UAAGCUCG-----------GGUAAACUAGUCC-----------UUUACCGCCGUAUCGUACUUUGUGUGGCC
AB076043.1/1872-1973 -UGGUGAGUUGCUGUCG--UGGGAUCCUGGGAAACAGGUACGGUGAACAAAAAGCCGGUAAUCUCG-----------GG-CGUUCGUCAG-----------ACG-CCGUCGUAUCA-ACACAGUAUGCAU
AJ007492.1/1972-2071 ACACC-AGUAGCACA-AAUC-GGAUCCUGGGAAACAGGCA-GAACUACG---GUUCA-UAAGCUCG-----------GGUAGGCCGUCAA-----------CCUACCGUCGUAUCGUAUUGUGUUUGGCC
L24049.1/5262-5363   -UGGUGAGUUGCUGUCG--UGGGAUCCUGGGAAACAGGUUCGGUGAACAAAAAGCCGGUAAUCUCG-----------GG-CGUUUGUCAG-----------ACG-CCGUCGCAUCA-ACACAGUAUGCAU
#=GC SS_cons         :::((.(--((((((.(--(.((,,<<<<_____>>>>,,.<<<<____...>>>>,.,,,<<---...........<<<<<<_______...........>>>>>>--->>,)))--))))))))))::
#=GC RF              Acacc.acUcgCaca.gauc.GgAUCCuGGGAAACaGGca.Ggacuacg...gucCG.UAAgCUCG...........GGucggcuGUCAa...........ccgaCCGcCGcAuCguacuguGcguggcc
//
# STOCKHOLM 1.0

#=GF AC   RF00435
#=GF ID   ROSE
#=GF DE   Repression of heat shock gene expression (ROSE) element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   PMID:11726689
#=GF SS   Published; PMID:11726689; Griffiths-Jones S
#=GF GA   45.00
#=GF TC   46.00
#=GF NC   44.20
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   11726689
#=GF RT   A mRNA-based thermosensor controls expression of rhizobial heat shock
#=GF RT   genes.
#=GF RA   Nocker A, Hausherr T, Balsiger S, Krstulovic NP, Hennecke H, Narberhaus F
#=GF RL   Nucleic Acids Res 2001;29:4800-4807.
#=GF RN   [2]
#=GF RM   15466035
#=GF RT   Replicon-specific regulation of small heat shock genes in Agrobacterium
#=GF RT   tumefaciens.
#=GF RA   Balsiger S, Ragaz C, Baron C, Narberhaus F
#=GF RL   J Bacteriol 2004;186:6824-6829.
#=GF CC   This family represents a 5' UTR cis-regulatory element found in heat shock
#=GF CC   mRNAs and is known as the ROSE (repression of heat shock gene expression)
#=GF CC   element. The ROSE element is a negative regulator of heat shock gene
#=GF CC   expression. The secondary structure is thought to be regulated by
#=GF CC   temperature. This regulation blocks access to the ribosome binding site
#=GF CC   under normal conditions. During heat shock however, the structure changes
#=GF CC   freeing the ribosome binding site and allowing expression to occur [1,2].
#=GF WK   Repression_of_heat_shock_gene_expression_(ROSE)_element
#=GF SQ   13


CP000009.1/1450710-1450627 ---------------------CCGGCCGCC--AAA--GGGGUCGGCA----------AACAGAACU----AUC----AGUUUUGAU----CUUGUG-UCCAUGUUGCUCAAAGGAGGAUAUGGCUAUGAGAG
AY316747.1/256783-256687   ---------------------CCGACCGCCA-AAA-UGGCGUCAGCCUG---GUCAGGGAGCGCCGAG--CUU--CUUGGCGCUCC----CUCAUA-UCUAUGUUGCUCUACGGACGAUGUAGCUAUGAGAA
BA000012.4/1943819-1943723 ---------------------UCGGUCGCC-GCAUAAGGGGCCGAUGU----GUCAGGGAGCGCCAUG--CUU--CUUGGCGUUCC----CUCGUA-UCUAUGUUGCUCCAAGGAGGAUGUAGUUAUGAGAA
AY316747.1/197909-198003   ---------------------GCCGAUGCC--AAUU-GGGUCGGCAUG----GUCAGGGAGCGCCACG--CUU--CUUGGCGCUUC----CUCGUA-UCUAUGUUGCUCUACGGAGGAUGUAGCUAUGAGAA
AP003017.1/94542-94451     ---------------------UCGGG-GC---UUCG--G-CCCGACA------GAUUGGGCGUCGCAG-AGACG-CUGCGACGCUG----CUUGUAACCCAUGUUGCUUUACGGAGGAUAUGGCUAUGAGAA
AL591985.1/872145-872052   ---------------------AGAGCCGCCU-GUA-AGGGGCUCGCA----------GUCGAGGAG--CUCCGUU--CUCUUCGGCGCUCCUCAUCGUCCAUGUUGCUC-AAGGAGGAUAUGGCUAUGAGAA
U55047.1/3106-3215         CGCCGC-GACAAGCGGU----CCGGGCGCC--CUAG-GGGCCCGGCG------GAGACGGGCGCCGGA--GGUG-UCCGACGCCUG----CUCGUA-CCCAUCUUGCUCCUUGGAGGAUUUGGCUAUGAGGA
U55047.1/5180-5291         UGCCGC-GACAAGCGGU----CCGGGCGCCC-UUCGGGGGCCCGGCG------GAGACGGGCGCCGGA--GGUG-UCCGACGCCUG----CUCGUA-CCCAUCUUGCUCAGUGGAGGAUUUGGCUAUGAGGA
AJ003064.1/2430-2312       CGCCGCCGCAGGGCGGCUCU-CCGGGCGCC--UGAC-GGGCUCGGCGAAUCCAGAGACGGGCACCGG--UCGUGU-CCGGUGCC-G----CUCGUA-ACCAUUUUGCUCCGUGGAGGAUCUGGCUAUGCGCA
AJ010144.1/622-738         GCCGCC-GA-GAGGUGGCGUCCCCGACGCC--UCAU-GGGUCGGGAACGAC-UGAGACGGGCACCGG--UCGUGU-CCGGUGCC-G----CUCGUA-UCCAUUUUGCUCCUUGGAGGAUUUGGCUAUGCGCA
AJ003064.1/2697-2806       GCCACGCGGGAGCGUGGCG--CCGGAUGCC--UCUC-GGGUCCGG--------CAGACG-CCAUCGGG-CAGAA-UCCGAUGU-UG----CUCCUA-UCCAUAUUGCUCAGAGGAGGAUGUGGUUAUGAGAA
AE007872.2/51225-51317     ---------------------CCAGCCGCUG-ACGACGGGGCUGGACU----UGCUGGGAGCGCCG---CCUUU---CGGCGCUUC------CGUA-CCCAUGUUGCUUCAAGGAGGAUAUGGCUAUGGCAA
AE007872.2/441983-442075   ---------------------CCAGCCGCUGAGGUCAGGGGCUGGCC----------UUGUUGGACG---CGC---CGUCUUUCAGCGCU-CCGUA-CCCAUGUUGCUUCAAGGAGGAUAUGGCUAUGGCAA
#=GC SS_cons               .....................<<<<<<-<<..____.>>>>>>>>,,......,,,,<<<<<<<<<<.._____..>>>>>>>>>>....<<<<<<.-<<<<<<<-<<<____>>>>>>>>>>->>>>>>::
#=GC RF                    .....................ccgGccGCC..uuau.GGggCcggca......gagacgggcgccgg..ucuug..ccggcgcccg....CuCgUa.uCCAugUuGCUCcaaGGAGgAcaUGGCuAuGaGaA
//
# STOCKHOLM 1.0

#=GF AC   RF00436
#=GF ID   UnaL2
#=GF DE   UnaL2 LINE 3' element
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:15273327
#=GF GA   55.00
#=GF TC   55.00
#=GF NC   54.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0032197; transposition, RNA-mediated;
#=GF RN   [1]
#=GF RM   15273327
#=GF RT   Solution structure of an RNA stem-loop derived from the 3' conserved
#=GF RT   region of eel LINE UnaL2.
#=GF RA   Baba S, Kajikawa M, Okada N, Kawai G
#=GF RL   RNA 2004;10:1380-1387.
#=GF CC   The eel long interspersed element (LINE) UnaL2 and its partner short
#=GF CC   interspersed element (SINE) share a conserved 3' tail containing a
#=GF CC   stem-loop that is critical for their retrotransposition. Presumably, the
#=GF CC   first step of retrotransposition is the recognition of their 3' tails by
#=GF CC   UnaL2-encoded reverse transcriptase. The solution structure of a
#=GF CC   17-nucleotide RNA derived from the 3' tail of UnaL2 was determined by NMR
#=GF CC   [1].
#=GF WK   UnaL2_LINE_3'_element
#=GF **   40 sequences (zebrafish) currently have an 4bp overlap with tRNA
#=GF **   predictions (RF00005) on the opposite strand (Daub J)
#=GF SQ   30


AB001839.1/75-130    UGUAUGCACGCAUGACUA-AGUCGCUUUGGAUAAAAGCGUCUGCUAAAUGGCAUUUU
AB179624.1/3561-3614 GAUAUGCACUUUUG--UA-CGUCGCUUUGGAUAAAAGCGUCUGCGAAAUAAAUGUAA
AB012888.1/161-214   AACUUUCCAAUUUG--UA-AGUCGCUCUGGAUAAGAGCGUCUGCUAAAUGACUUAAA
AB012889.1/249-302   AACUUUCCAAUUUG--UA-AGUCGCUCUGGAUAAGAGCGUCUGCUAAAUGACUUAAA
AB012890.1/215-268   AACUUUCCAAUUUG--UA-AGUCGCUCUGGAUAAGAGCGUCUGCUAAAUGACUUAAA
AB012891.1/247-300   AACUUUCCAAUUUG--UA-AGUCGCUCUGGAUAAGAGCGUCUGCUAAAUGACUUAAA
AY543891.1/989-936   AAUGCACCAAUUUG--UA-AGUCNGUCUGGAUAAGAGCGUCUGCUAAAUGACGUAAA
AB012893.1/257-310   AACUUUCCAAUUUG--UA-AGUCGCUCUGGAUAAGAGUGUCUGCUAAAUGACUUAAA
AB012892.1/155-208   AACUUUCCAAUUUG--UA-AGUCGCUCUGGAUAAGAGCGUCUGCUAAAUGACUUAAA
AB179625.1/214-267   UGUAAAAAGUUGUG--UA-AGUCGCUCUGGAUAAGAGCGUCUGCUAAAUGCCUGUAA
AB179627.1/188-241   UGUAAAAAGUUGUG--UA-AGUCGCUCUGGAUAAGAGCGUCUGCUAAAUGCCUGUAA
AB179631.1/212-266   GUGUAAAAGUUGUG--UAAAGUCGCUCUGGAUAAGAGCGUCUGCUAAAUGCCUGUAA
AB179629.1/214-267   AUGUAAAAGUUGUG--UA-AGUCGGUCUGGAUAAGAGCGUCUGCUAAAUGCCUGUAA
AB179628.1/210-263   AUGUAAAAGUUGUG--UA-AGUCGCUCUGGGUAAGAGCGUCUGCUAAAUGCCUGUAA
AB179626.1/214-267   AUGUAAAAGUUGUG--UA-AGUCGCUCUGGAUAAGAGCAUCUGCUAAAUUCCUGUAA
AB001842.1/98-151    UGUGCACAGGACUG--UA-AGUCGCUUUGGAUAAAAGCGUCUGCUAAAUGGCAUAUU
AB001843.1/100-153   UGCACACAUGACUG--UA-AGUCGCUUUGGAUAAAACCGUCUGCUAAAUGGCAUAUU
AB001852.1/99-152    UGCGCACAUGACUG--UA-AGUCGCUUUGGAUAAAAGCGUCUGCUAAAUGGCAUAUU
AB001841.1/106-159   UGCACGCAUGACUG--UA-AGUCGCUUUGGAUAAAAGUGUCUGCUAAAUGGCAUAUG
AB001849.1/107-160   UGCACACAUGACUG--UA-AGUCGCUUUGGAUAAAAGCGUCUGCUAAAUGGCAUAUU
AB001861.1/126-179   GGCACGUAUGACUG--UA-AGUCGCUUUGGAUAAAAGCAUCUGCUAAAUGGCAUAUG
AB001969.1/103-156   UGCACACAUGACUG--UA-AGUCGCUUUGGAUAAAAGCGUCUGCUAAAUGGCAUAUA
AB001962.1/107-160   UGCACACAUGACUG--UA-AGACGCUUUGGAUAAAAGCGUCUGCUAAAUGGCAUAUA
AB001963.1/111-164   UGCACACAUGAAUG--UA-AGUCGCUUUGGAUAAAAGCGUCUGCUAAAUGGCAUAUA
AB001846.1/106-159   UGCGCACAUGACUG--UA-AAUCGCUUUGGAUAAAAGCGUCUGCUAAAUGGCAUAUU
AB001847.1/99-152    AAAAACAACAACUG--UA-AGUCGCUUUGGAUAAAAGCGUCUGCUAAAUGGCAUAUU
AB001853.1/99-152    UGCACGCAUGACUG--UA-AGUCGCUUUGGAUAAAAGCGUCUGCUAAAUGGCUUAUU
AB001864.1/79-132    UGCACGCAUGACUG--UA-AGUCGCUUUGGAUAAAAGCAUCUGCCAAAUGGCAUAUU
AB001966.1/108-161   UGCACACAUGACUG--UA-UGUCGCUUUGGAUAAAAGCGUCUGCGAAAUGGCAUAUA
AB001863.1/91-144    UCCACACUUGAAUG--UA-AGUCGCUUUGGAUAAAAGCAUCUGCUAAAUGGCUGUGU
#=GC SS_cons         ::::::::::::<<..<<.---<<<<<<_____>>>>>>-->>>->:::::::::::
#=GC RF              ugcacaCAuguuUG..UA.AGUCGCUuUGGAUAAaAGCGUCUGCUAAAUGgCuUAua
//
# STOCKHOLM 1.0

#=GF AC   RF00437
#=GF ID   HLE
#=GF DE   Hairy RNA localisation element (HLE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12743042
#=GF SS   Published; PMID:12743042
#=GF GA   60.00
#=GF TC   69.20
#=GF NC   55.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0006403; RNA localization;
#=GF RN   [1]
#=GF RM   12743042
#=GF RT   The Drosophila hairy RNA localization signal modulates the kinetics of
#=GF RT   cytoplasmic mRNA transport.
#=GF RA   Bullock SL, Zicha D, Ish-Horowicz D
#=GF RL   EMBO J 2003;22:2484-2494.
#=GF CC   This family represents the hairy localisation element (HLE) found in
#=GF CC   Drosophila species. HLE is located in the 3'-UTR of the hairy gene and
#=GF CC   contains two stem-loops. HLE is essential for the mediation of apical
#=GF CC   localisation and the two stem-loop structures act to allow the recognition
#=GF CC   of hairy mRNA by the localisation machinery [1].
#=GF WK   Hairy_RNA_localisation_element_(HLE)
#=GF SQ   5


AY055841.1/7634-7765       GUAGACAUUUCACAUCAUU-CGCCGGGAUUGCGCAAAUGUUGCUUUGAAGUG-UUGCAAACAUGCGAAUCCUAAAACUCGGUUCACGGCUUCGUUGGCUUAGUUUCCUGGCUUAUAUCCUGGAAACCCGUCGGC
AY055833.1/7586-7717       GUAGACAUUUCACAUCAUU-CGCCGGGAUUGCGCAAAUGUUGCUUUGAAGUG-UUGCAAACAUGCGAAUCCUAAAACUCGGUUCACGGCUUCGUUGGCUUAGUUUCCUGGCUUAUAUCCUGGAAACCCGUCGAC
AY055843.1/7514-7643       GUAGACAUUUCACAUCAUU-CGCCGGGAUUGCGCAAAUGUUGCUUUGAAGUG-UUGCAAACAUGCGAAUCCUAAA--UCGGUUCACGGCUUCGUUGGCUUAGUUUCCUCGCUUAUAUCCUGGAAACCCGCCGGC
AY262008.1/1-124           AGAGACAUUUCACAUCAUUUCGCCAGGAUAACGCAAAUGUUGCUUUGAAGUGCUUUAAAACAUGCGAAUUCCUUC--AUGGUCCAAAACACUUCGCUGUGAGUUU---ACCUCAACC-----AACUUUCAGUGA
AAPQ01006549.1/31239-31110 GUUGACAUUUCACAUCAUU-CGCCGGGAUUGCGCAAAUGUUGCCUUGAAGUG-UUGCAAACAUGCGAGUCCUAAC--UCGGUCCACGGCUUCGUCGGCUUAGUUUCCUGGCUUACAUCCGGGAAACCCGCCGGC
#=GC SS_cons               :::::<<<<<<----<<<<.<<<_______>>>-->>>>------->>>>>>.----------------------..---------------<<<<<<---<<<<<<-<<_______>>->>>>>>-->>>>>>
#=GC RF                    guAGACauuuCACAUCauu.CGcCgGGAUugCGCAaauGUUGCUUUGaaguG.UUgcAAACAUGCGAAUcCuaaa..ucGGUuCAcggCuucgccggcUuAGuuuCCUgGCUuAuauCcuGGaaaCccgccggc
//
# STOCKHOLM 1.0

#=GF AC   RF00438
#=GF ID   SNORA33
#=GF PI   snoACA33
#=GF DE   Small nucleolar RNA SNORA33
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   74.00
#=GF TC   74.40
#=GF NC   73.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300167;
#=GF DR   snoopy; Echinops_telfairi300782;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA33 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA33
#=GF SQ   28


AK096147.1/2648-2777         AAGCCAG-CCAAUG--AAUCUGC-UUAC--CUGAUUGUGU-UUGUGCAGA-CAUAC-UUU-----AAAAA----CUGGCAAUA---GUAAAGCCAUGUUACGAGCCUUAAGGACAU-----UGAAGUCGUUAAGGUCCCUGAGAAUGGCUAUAACA
AB061840.1/3761-3890         AAGCCAG-CCAAUG--AAUCUGC-UUAC--CUGAUUGUGU-UUGUGCAGA-CAUAC-UUU-----AAAAA----CUGGCAAUA---GUAAAGCCAUGUUACGAGCCUUAAGGACAU-----UGAAGUCGUUAAGGUCCCUGAGAAUGGCUAUAACA
AJ609473.1/1-130             AAGCCAG-CCAAUG--AAUCUGC-UUAC--CUGAUUGUGU-UUGUGCAGA-CAUAC-UUU-----AAAAA----CUGGCAAUA---GUAAAGCCAUGUUACGAGCCUUAAGGACAU-----UGAAGUCGUUAAGGUCCCUGAGAAUGGCUAUAACA
AC116119.12/257476-257604    AAGUCAG-CCAAUU--AAUCUGC-UUAU--CUCAAUGU---UUCUGCAGA-AAUUU-AGA-----AAGGG----CUGGAAAUG---AUAGUGUCAUGAUAUGAAUCUUAAGGGCAG----CUGAAGCCUUUAAGGUCCCUGAAAGUGGCUACAGUA
AF357393.1/1-105             ------------------------------CUCAAUGU---UUCUGCAGA-AAUUU-AGA-----AAGGG----CUGGCAAUA---UUAAUGCCAUGGUACGAGCCUUAGGGGCAG----CUGAAGCCUUUAAGGUCCCUGAAAGUGGCUACAGUA
AAFC03034720.1/9191-9320     AAGCCAG-CCAAAG--AAUCUGC-UUAC--CUGAAUGUGU-UUCUGCAGA-AAUUU-AGA-----AAAUG----CUGGCAAUA---GGAAAGCCAUGUUACGAGCCUUAAAGACAU-----UGAAGUCAUUAAGGUCCCUGAAAAUGGCUACAAGG
AANG01372476.1/7418-7547     AAGCCGG-CCAAUG--AAUCUGC-UUAG--CUGAAUGUGU-UUCUGCAGA-AAUUU-AAA-----AAACG----CUGGCAAUA---GGAACGCCAUGUUACGAGCCUUAAAGACAU-----UGAAGUCAUUAAGGUCCCUGAAAAUGGCUACAAGA
ABDC01238297.1/3668-3797     AAGCCAG-UCAAUU--AAUCUGC-UUAC--CUGAAUGUGU-UUUUGCAGA-AAUUU-UAA-----CAAAG----CUGGCAAUA---GUAAAGCCAUGGUACGAGCCUUACGGACAU-----UGAAGUCGUUAAGGUCCCUAAAAAUGGCUAUAACA
AAQQ01527784.1/1402-1532     AAGCCAG-CUAGUG--AAUCUGC-UUAC--CUGCAAAUGU-UUCUGCAGA-AAUUUUAGA-----AAAAG----CUGGCAAUA---AUAAUGCCAUCUUACGAGCCUUAAAGACAC-----UGAAGUCCUUAAGGUCCCUGAAAAUGGCUACAAUA
AAIY01528082.1/2502-2635     AAGCCAG-CCAUUG--AUUCUGC-UUAC--UUGAUUGUGU-UUCUGCAGA-AAUUU-AGA-----AAAAG----CUGGCAAUAACAGUAAAGCCAUGUUACGAGCCUUAAGGAUAA----UUGAGAUCAUUAAGGUCCCUGAAAAUGGCUACAUUA
AANN01343682.1/479-607       AAGCCAG-UCAAUG--AAUCUGC-UUAC--CUGAUUGUGU-UUCUGCAGA-AAUUU-UUU-----A-UAA----CUGGCGAUA---GCAAUGCCAUGUUACGAGCCUUAAUGACAU-----UAGGGUCUUUAAGGUCCCUGAAAGUGGCUAUAUAA
AADA01174885.1/16896-16763   AAGCUAG-CCAAUG--AAUCUGC-UUAC--CUAAACAUGU-UUCUGCAGA-AAUUU-UUAUUUUAAAAAG----CUAGUAAUA---GCAAAGCCAU-UUAUGAGCCUUAAGUUUAC-----UGAAGUUGUUAAGAUCCCUGAAAAUGGCUAUAACA
AAFR03001093.1/89171-89045   AAGCCAGUACAUUA--CAUCUGAUUUAC--CUGAAUGUGU-UUUU-CAGA-AGU-----A-----AAAUA----UUGGCAAUA---GUACAGCCAUGGUACGAGCCUUAAAAACUG-----UGAGGUCUUUAAGGUCCCUGAGAAUGGCUACAGUA
AALT01431502.1/1908-1782     CAGCCAG-UAAAUA--AAUCUGC-UUAG--UUGAAUGU---GUUGGCAGA--AUUU-AGA-----AAUAG----CUGGCAAUA---GUAAAACCAUGUUAUGAGCCUUUAUGGCAU-----UGAGGUUGUUAAGGUCCCUUAAAGUAACUACAGAA
AANU01245430.1/36044-36172   AAGCUAG-CCAAUG--AAUCUGC-UUAC--CUAAACAUGU-UUCUGCAGA-AAUUU-UUAUUUUAAAAAG----CUGGUAAUA---GCACAGUCAU-UUAUGAGCCUUAAG----------UAAAGUUGUUAAGGUCUCUGAAAAUGGCUAUAACA
CR407384.1/558-422           ACACCAGUUAAUAA--UCUCUGC-UCAA--CUUGAAAGUG-UUUUGCAGGGCAUGU-UUU-----AAAACACUACUGGUAA-A---GUAAAGCCACAGUACGAGCCUUGAAGAAAAU---UUCUUGUCUUUGAGGUCCCAAGAGAUGGCUACAUCU
AAWR02015249.1/10940-11069   AAGCCAG-CCAAUG--AAUCUGC-UUAC--CUGAAUGUGU-UUUGGCAGA-AAUUU-AGA-----GCAAG----CUGGCAAUA---GUAAAGCCAUGUUACGAGCCUUAACGACGU-----UGAAGUCGUUAAGGUCCCUGAAAGUGGCCACAAGA
AAKN02047732.1/6077-5944     AAGCCAG--CGAUG--AAUUUGC-UUAU--CUGUAUGUGU-UUGUGCAGA-AAUGU-ACC-----AAAAG----CUGGAGAUA---AUAAUGCCAUGUUACAAGCCUUAAAGACAUGUCAUUGAAGUCAUUAAGGUCCCUGAAAAUGGCUACAUUU
AAGV020962123.1/393-264      AAGCCAG-CCAAUG--UCUCUGC-UUAC--CUGAACGUGU-UUCUGCAGA-AAUUU-UGA-----AAAGG----CUGGCAAUA---GUAAAGCCAUGCUACGAGCCUUAAGGACAC-----UGAAGUCAUUAAGGUCCCUGAAAAUGGCAACAGCG
AAHX01095683.1/9294-9422     AAGCCAG-CCAUCU--AGUCUGC-UUAG--CUCUGUGU---UUCUGCAGA-AAUGU-AGA-----AAAGG----CUGGCAAUA---GUAAUGCCAUGUUACGAGCCUUAAGGACAG----CUGAAGUUUUUAAGGUCCCUGAAAAUGGCUACAGUG
EU093995.1/2-135             AAGCCAGUAUACUU--CAUCUGC-UUAA--CUGAACGUG--UUUUGCAGA-AGGGA-UGUGU-GAAUAU----GCUGGCAAUA---GCAUAGCCUGGGUACGAGCCUUGAAGACUC-----UGUAGUCAUUAAGGUCCCUGAAAUUGGCAACAUCU
EU240307.1/1-136             C-ACCAGUUAAUAA--UCUCUGC-UCAA--CUUGAAAGUG-UUUUGCAGGGCAUGU-UUU-----AAAACACUACUGGUAA-A---CUAAAGCCACAGUACGAGCCUUGAAGAAAAU---UUCUUGUCUUUGAGGUCCCAAGAGAUGGCUACAUCU
EU093997.1/2-135             AAGCCAGUAUACUU--CAUCUGC-UUAA--CUGAACGUG--UUUUGCAGA-AGGGA-UGUGU-GAAUAU----GCUGGCAAUA---UCAUAGCCUGGGUACGAGCCUUGAAGACUC-----UGUAGUCAUUAAGGUCCCUGAAAUUGGCAACAUCU
AAEX03000181.1/85726-85855   AAGCCAG-CCAAUG--AAUCUGC-UUAC--CUGAAUAUGU-UUCUGCAGA-AAUUU-AAA-----AAUUG----CUGGCAAUA---GUAAUGCCAUGUUACGAGCCUUAAAGACAC-----UGAAGUCCUUAAGGUCCCUGAAAAUGGCUAUAAGA
AAGW02028778.1/11257-11126   AAGCCAG-CCAAUG--AAUCUGC-UUACUACCUAUUGUGU-UUCUGCAGA-AAUCU-AGA-----AAAAG----CUGGCAAUA---GUAGUGCCAUGUUACGAGCCUUAAAGACAU-----UGAAGUCUUUCAGGUCCCUGAAAAUGGCUACAACA
AAWZ02013261.1/62537-62408   CUGCCAG-UAGAAUGAAGUCUGC-UUAA--CCUUUUAAAUGUUCUGCGGA-GAUCU---------AAAUG----CUGGCAACA---GUAAAGCCAGGGUACGAGCCUUGAAGACUU-----AGUAGUCAUCGAGGUCCCAAUAAAUGGCUACACUU
AAPE02007475.1/211799-211671 AAGCCAG-CCAAUA--AGUCUGC-UUAC--CUGAAUGU-G-UUCUGCAGA-AAUUU-AGA-----GAAAG----CUGGCAAUA---GUAAAGCCAUGUUACGAGCCUUAAAGACAU-----UGAAGUCCUUAAGGUCCCUGAAAAUGGCUAUAAGA
AAQR03075875.1/4507-4378     AAGCCAG-CCAAAU--AAUCUGC-UUAC--CUGAAUGUGU-UUCUGCAGA-AAGUU-UUU-----AAAAU----CUGGCAAUA---GUAAAGCCAUGUUACGAGCCUUACGGACAU-----CCAAGUCGUUAAGGUCCCUGAAAAUGGCUAUAACA
#=GC SS_cons                 ::<<<<<.------..--<<<<<.____..__________.____>>>>>.-----.---.....-----....>>>>>----...-----<<<<--------<<<<<<<-<<<__.....____>>>->>>>>>>--------->>>>:::::::
#=GC RF                      AAgCCAG.ccAaug..aauCUGC.UUAc..CUgaaugUgU.UUuUGCAGa.aAUuU.uua.....AAAag....CUGGcAAUA...gUAAaGCCAuGuUACGAgCCUuaAagacAu.....UgaagucaUuaAGGuCCCUgAAAAUGGCUAcAaua
//
# STOCKHOLM 1.0

#=GF AC   RF00439
#=GF ID   SNORD87
#=GF PI   U87
#=GF DE   Small nucleolar RNA SNORD87
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   50.00
#=GF TC   51.10
#=GF NC   49.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300380;
#=GF DR   snoopy; Echinops_telfairi300138;
#=GF RN   [1]
#=GF RM   12119114
#=GF RT   U87 RNA, a novel C/D box small nucleolar RNA from mammalian cells.
#=GF RA   Gogolevskaya IK, Makarova JA, Gause LN, Kulichkova VA, Konstantinova IM,
#=GF RA   Kramerov DA
#=GF RL   Gene 2002;292:199-204.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [3]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   U87 (HBII-276) is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1].
#=GF WK   Small_nucleolar_RNA_SNORD87
#=GF SQ   10


AF396686.1/578-664         GCUGGCACAAUGAUGAC--UUA----AGUUUUUGCCGUUUACCCAGCUGAGUGUUUCUUUGAAGAGAGAAUCUUAAAAGACUGAGAUGCCAGC
AF357333.1/1-64            ----------------C--UUA----AGUUUUUGCCGUUUACCCAGCUGAGUGUUUCUUUGAAGAGAGAAUCUUAAAAGACUGAGA-------
AF272707.1/1-72            ------ACAAUGAUGAC--UUA----UGUUUUUGCCGUUUACCCAGCUGAGGGUUUCUUUGAAGAGAGAAUCUUAA--GACUGAGC-------
AF396685.1/1899-1983       GCUGGCACAAUGAUGAC--UUA----UGUUUUUGCCGUUUACCCAGCUGAGGGUUUCUUUGAAGAGAGAAUCUUAA--GACUGAGCUGCCAGC
AAFC03063700.1/26102-26016 ACUGGCACAGUGAUGACAAGUU----ACUUUUUGCCGUUUACCCAGCUGAGGGUAUCUUUGAAGAAAUAACUUUAA--GACUGAGAUGCCAGU
AAYZ01273769.1/1560-1476   GCUGGCACAAUGAUGAC--UUG----AAUUUUUGCCGUUUACCCAGCUGAGGGUUUCUUUGAUGAAAUUACAUCAA--AACUGAGAUGCCAGU
AAKN02001154.1/7148-7232   GCUGGCACAAUGAUGAC--AUA----AAUUUUUGCCGUUUACCCAGCAGAGGGUUUCUUUGAAGAAAUCAUUUUAA--GACUGAGAUGCCAGU
AC011031.12/168663-168575  GCUGGCACAAUGAUGAC--UUAAAUUACUUUUUGCCGUUUACCCAGCUGAGGUUGUCUUUGAAGAAAUAAUUUUAA--GACUGAGAUGCCAGU
AAQR03133797.1/20592-20508 GCUGGCACAAUGAUGAC--UUA----AAUUUUUGCCGUUUACCCAGCUGAGGGUAUCUUUGAAGAAAUAAUUUUAA--GACUGAGAUGCCAGU
AADA01186893.1/3589-3677   GCUGGCACAAUGAUGAC--UUAAAUUACUUUUUGCCGUUUACCCAGCUGAGGGUGUCUUUGAAGAAAUAAUUUUAA--GACUGAGAUGCCAGU
#=GC SS_cons               <<<<<<<__________..___....__________________________________________________..________>>>>>>>
#=GC RF                    gCuGGCaCAAUGAUGAC..uUA....AaUUUUUGCCGUUUACCCAGCUGAGGGUuUCUUUGAAGAaAuAAUuUUAA..GACUGAGAuGCCaGc
//
# STOCKHOLM 1.0

#=GF AC   RF00440
#=GF ID   SNORD37
#=GF PI   U37
#=GF DE   Small nucleolar RNA SNORD37
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Moxon SJ
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   44.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Danio_rerio300156;
#=GF DR   snoopy; Loxodonta_africana300513;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   8764399
#=GF RT   Intron-encoded, antisense small nucleolar RNAs: the characterization of
#=GF RT   nine novel species points to their direct role as guides for the
#=GF RT   2'-O-ribose methylation of rRNAs.
#=GF RA   Nicoloso M, Qu LH, Michot B, Bachellerie JP
#=GF RL   J Mol Biol 1996;260:178-195.
#=GF RN   [3]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF CC   U37 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_SNORD37
#=GF SQ   6


BX293565.25/6224-6291    AUUGAUGAUGAUUUAAACAUUCUUCACUUUGACCUGAAUAUCUUGUGAUGAGAAUUUUCAAUCUGAUA
AL359396.5/115844-115908 GUUCAUGAUAAGUAA-CAUUUCUUCAAUUUGACCUG-AUGUGUAUUGAAGA-AAACCAGCAUCUGAGG
AC155932.6/138556-138619 CACCAUGAUGACGGA--AAUUCUUCACUUUGACCUG-AUGUCUGUUGAAGA-AACUCAGUGUCUGAGA
X94606.1/1-64            ACACAUGAUGACUGA--AAUUCUUCACUUUGACCUG-AUGUCUGUUGAAGA-AACUCUGUGUCUGAGC
J03200.1/2682-2745       ACACAUGAUGACUGA--AAUUCUUCACUUUGACCUG-AUGUCUGUUGAAGA-AACUCUGUGUCUGAGC
X94602.1/153-218         AUUCGUGAUGACUGAUCAUUUCUUCACUUUGACCAG-AUGUCUACUGAAGA-AAGCCUGCGUCUGAGG
#=GC SS_cons             <<_____________.____________________.______________.______________>>
#=GC RF                  ccuCAUGAUGAcUgA.cAaUUCUUCACUUUGACCUG.AUGUCUauUGAAGA.AAuUCUGugUCUGAgg
//
# STOCKHOLM 1.0

#=GF AC   RF00441
#=GF ID   snoZ242
#=GF DE   Small nucleolar RNA Z242
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   90.00
#=GF TC   100.30
#=GF NC   33.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res 2003;31:2601-2613.
#=GF CC   Z242 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_Z242
#=GF SQ   5


AJ494948.1/1-194           --GGACCAGGAUGAUGACUGGCCAAAUCCAGCUGGUGAUGGAGCCGGAGGCGCGCGGUGACCGGAGGCGGUGGCCUGUCGUGCUGGCAGAAAUUGCGGAGCAUGGUGGCCGGUCCGCAAUGAUAAUCUCAUCACAACAGCAGGUCGAUCUUCAGUGUAGACCUGAACAUGAAAAUACUAAAACUCUGAACUGAUUU--
AP005501.3/23358-23161     AGGGACCAGGAUGAUGGCUGGCCAAAUCCAGCUGGUCAUGGAGCCGGAGGCACGCGGUGACCGGACGCGGUGGCCUGUCGUGCCGGCAGAAACUGCGGAGCAUGGUGACCGGUACACAAUGAUAAUCUCAUCACAGCAACAGGUCGAUCUUCUGUGUAGACCUGAACAUGAAAAUCCUAAAACUCUGAACUAAUUUCA
AJ494949.1/1-198           AGGGACCAGGAUGAUGGCUGACCAAAUCCAGCUGGUGAUGAAGCCGGAGGUGCACGGCGGCCAGAGGCGGUGGCAUGUCGUGCCGGCAGAAACUGCAGAGCAAGGUGGCCGGUACUCAGUGAUAAUCUCAUCACAGCAGCAGGUCGAAGUGCAGUGCGGACCUACACAUGAAAAAUCUAAAAAUCUGAAUUGGUUUCU
AP004560.3/126987-126790   AGGGACCAAGAUGAUGGCUGACCAAAUCCAGCUGGUGAUGGAGCCGGAGGCGCAUGGCGGCCAGAGGCGGUGUCAUGUUGUGCUGGCAGAAACAGCAUAGCAAGGUGGUCGGUACUCAGUGAUAAUCUCAUCACAGCAGCAGGUCGAAGUGCAGUGCAGACCUACACAUGAAAAAUCUAAAAAUCUGAAUUGGUUUCU
AAAA02023133.1/34236-34039 AGGGACCAGGAUGAUGACUGGCCAAAUCCAGCUGGUGAUGGAGCCGGAGGCGCGCGGUGACCGGAGGCGGUGGCCUGUCGUGCUGGCAGAAAUUGCGGAGCAUGGUGGCCGGUCCGCAAUGAUAAUCUCAUCACAACAGCAGGUCGAUCUUCAGUGUAGACCUGAACAUGAAAAUACUAAAACUCUGAACUGAUUUCA
#=GC SS_cons               :<<<<<<<<----------------------------------------------------------------------<<<<<<<<------<<<___>>>----->>>>>>>>-------------------------------------------------------------------------->>>>>>>>:
#=GC RF                    AGggacCagGAUGAUGgCUGgCCAAAUCCAGCUGGUgAUGGAGCCGGAGGcGCgcGGuGaCCgGAgGCGGUGgCaUGUcGugCcGGCAGAAAcuGCggAGCauGGUGGCCgGuaCuCAaUGAUAAUCUCAUCACAgCAGCAGGUCGAucUuCAGUGuAGACCUgaACAUGAAAAuuCUAAAAaUCUGAAcuGguuuCu
//
# STOCKHOLM 1.0

#=GF AC   RF00442
#=GF ID   ykkC-yxkD
#=GF DE   Guanidine-I riboswitch
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Barrick JE, Breaker RR
#=GF SS   Predicted; Barrick JE, Breaker RR
#=GF GA   71.00
#=GF TC   72.20
#=GF NC   70.30
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   15096624
#=GF RT   New RNA motifs suggest an expanded scope for riboswitches in bacterial
#=GF RT   genetic control.
#=GF RA   Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M,
#=GF RA   Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR
#=GF RL   Proc Natl Acad Sci U S A 2004;101:6421-6426.
#=GF RN   [2]
#=GF RM   27989440
#=GF RT   Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread
#=GF RT   Riboswitch  Class.
#=GF RA   Nelson JW, Atilho RM, Sherlock ME, Stockbridge RB, Breaker RR
#=GF RL   Mol Cell. 2017;65:220-230.
#=GF RN   [3]
#=GF RM   28096518
#=GF RT   Structural basis for guanidine sensing by the ykkC family of riboswitches.
#=GF RA   Battaglia RA, Price IR, Ke A
#=GF RL   RNA. 2017;23:578-585.
#=GF RN   [4]
#=GF RM   28017522
#=GF RT   Structural Basis for Ligand Binding to the Guanidine-I Riboswitch.
#=GF RA   Reiss CW, Xiong Y, Strobel SA
#=GF RL   Structure. 2017;25:195-202.
#=GF CC   This family represents a conserved RNA structure found upstream of the
#=GF CC   ykkC and yxkD genes in Bacillus subtilis and related genes in other
#=GF CC   bacteria. The function of this family is unclear although it has been
#=GF CC   suggested that it may function to switch on efflux pumps and
#=GF CC   detoxification systems in response to harmful environmental molecules [1].
#=GF CC   The Thermoanaerobacter tengcongensis sequence EMBL:AE013027 overlaps with
#=GF CC   Rfam:RF00167 suggesting that the two riboswitches may work in conjunction
#=GF CC   to regulate the the upstream gene which codes for Swiss:Q8RC62, a member
#=GF CC   of Pfam:PF00860 (Moxon SJ, pers. obs.). Nelson [2] showed that this
#=GF CC   riboswitch senses and responds to guanidine and it was renamed Guanidine-I
#=GF CC   riboswitch. Furthermore, they demonstrated that bacteria are capable of
#=GF CC   endogenously producing guanidine and the riboswitch controls genes whose
#=GF CC   products are involved in modification or pumping out guanidine as a toxic
#=GF CC   compound from bacteria. Crystal structures of the riboswitch bound to the
#=GF CC   ligand have also been determined.[4][5]
#=GF WK   YkkC-yxkD_leader
#=GF SQ   97


AY316747.1/71407-71301        GCAGAUG-UUUCUAGGGUUCCGAUGC--C-GUCA--------------------G-G--GCAUGUCUG-GACCGAGAGAA-A-C-CUCCGGUGG--------------------GGAGACA---------------UCCA--C-CGGG-UCCACGGCGGGAUAAAAGCCCGGGAGGC
BX569692.1/338223-338321      GGCGGAGAAACCUAGGGUUCCGAUCC--C-GUCA----------------------G--GGAUGCCUG-GUCCGAGAGGU-UUC-GGUCGG-------------------------UUCU-----------------G----C-CGGC-UGCACGGAGGGACAAAAGCCCGGGAGAC
D78189.1/4535-4646            UGUAAAGUUUUCUAGGGUUCCGCAUG--UCAAUU---------------------GA--CAUGGACUG-GUCCGAGAGAA-AAC-ACAUACGCG--------------------UAAAUAGA-------------AGCGC--G-UAUG-CACACGGAGGGAAAAAAGCCCGGGAGAG
AB016894.1/3319-3421          AGAAAGGUUUUCUAGGGUUCCGCGGC--UGCUUU--------------------GUG--GCCGGCCUGUGACCGAGAGAA-AAC-GCGCG-G------------------------CAUU-------------------C--U-CGCG-UACACGGAGGGACAAAAGCCCGGGAGGA
BX571660.1/22706-22807        CGAACAGAUGGCUAGGGUUCCGAUGA--UCGCUU---------------------GA--UCAUG-CUG-GUCCGAGAGCU-AUC-GGCCUCU-----------------------UGAGU-------------------A--G-AGGU-UACACGGAGGGAUAAAAGCCCGGGAGGU
BX572597.1/165163-165059      AGAGUUGGUGGCUAGGGUUCCGGCCU--G--UUU----------------------C--AGGCG-CUG-GUCCGAGAGCU-GCC-CCCCGAAGG--------------------GAGAAA----------------UCCU--U-CGGA-CGCACGGCGGGACAAAAGCCCGGGAGAC
AF116356.1/182-293            UGAGUUGGUGGCUAGGGUUCCGGCGU--UUUUCU--------------------GAA--GCGCGACUG-GUCCGAGAGCC-ACC--ACCGGCGG--------------------AGGAGAAA-------------ACCCG--U-CGGG-UGCACGGCGGGACAAAAGCCCGGGAGAC
AE017333.1/1406463-1406565    GUUAAAGUUUUCUAGGGUUCCGCACA--U-UCGU----------------------A--UGUGGCCUG-GUCCGAGAGAA-AAC-ACAUAUGA----------------------UUUGU------------------UC--A-UAUG-CACACGGAGGGAUAAAAGCCCGGGAGUA
BA000045.2/1020511-1020399    AAAACUGGCUUCUAGGGUUCCGGUCC--CGCUCCUG----------------UGGUG--GGACGGCUG-GUCCGAGAGAA-GCA--GCCGGUCC--------------------GACAGC----------------AGGG--C-CGGU-CACACGGCGGGAGAAAAGCCCGGGAGAG
CP000091.1/18427-18312        CCGAAGGGUAGCUAGGGUUCCGGUCG--UGCCAUG------------------CGCG--CGAUGGCUG-GUCCGAGAGCG-ACC-GGCCACCGG--------------------CACCUGAU------------CCGCCG--G-CGGC-UCCACGGCGGGACAAAAGCCCGGGAGGU
CR543861.1/1073618-1073719    CAUAAGGUGAUCUAGGGUUCCGAUGC--UGUUUAC-----------------UAACA--GGAUGGCUG-GUCCGAGAGAU-UAC-GGUUC--------------------------GUAA------------------------GAAC-UACACGGAGGGAUAAAAGCCCAGGAGGU
AP008934.1/2424072-2423973    AAUAAAGCUUUCUAGGGUUCCGCAAG--GUGAUU---------------------AC--UUUGGUCUG-GUCCGAGAGAA-AGC--CACAUA------------------------UUUU-------------------U--A-UGUG--ACACGGAAGGAUAAAAGCCUGGGAGAU
CP000075.1/4719777-4719879    GCAAUAGCCGACUAGGGUUCCGGCUU--GCCGCC-------------------AGGC--AAGUGGCUG-GUCCGAGAGUU-GGC-GACCUC-------------------------CAGU-----------------A----G-AGGU-UACACGGCGGGACAAAAGCCCGGGAGAC
AP006627.1/4004674-4004578    CACAAAUGCGCCUAGGGUUCCGCUUC--AUUUGU--------------------------AAGGGCUG-GUCCGAGAGGU-GCA--CACGGC------------------------GUCU-------------------G--C-CGUG--ACACGGAGGGAUAAAAGCCCGGGAGAC
BA000004.3/741978-741875      CCAAAUGUUUUCUAGGGUUCCGCUUG--C--AAG----------------------G--CAAGGCCUG-GUCCGAGAGAA-AAC-GCAAAAAAG---------------------AUUG-----------------UCUU--U-UUUG-UCCACGGAGGGAGAAAAGCCCGGGAGAU
BX950851.1/2166770-2166871    UGAAUAGCUGGCUAGGGUUCCGAUCC--AUGCAA--------------------UAU--GGAUGUCUG-GUCCGAGAGCU-GGC-GACCUC-------------------------CAGU-----------------U----G-AGGU-UACACGGCGGGACAAAAGCCCGGGAGAC
BA000043.1/632114-632216      GGGAAUGUUUUCUAGGGUUCCGCGGC--UGCUUU--------------------GCG--GCCGGCCUGCGACCGAGAGAA-AAC-GCGCGGC-------------------------AUC-------------------G--C-CGCG-UGCACGGAGGGACAAAAGCCCGGGAGGA
AE017333.1/3988916-3988810    AAGGUGGUUUUCUAGGGUUCCGCAGU--GCCCUC-------------------CCGC--GCUGGUCUG-GUCCGAGAGAA-AAC-ACAUAGCGA---------------------AGUAU------------------CG--U-UAUG--ACACGGUGGGAUAAAAGCCCAGGAGUU
AP006840.1/808978-808865      GAUCAGGUUUUCUAGGGUUCCGCGGC--GUCACG---------------------GC--GCCGGUCCG-GUCCGAGAGAA-AAC-GCACAACCGGC----------------GGGAGAGCG---------------CCGG--C-UGUG-UACACGGCGGGACAAAAGCCCGGGAGGA
BA000028.3/3401735-3401639    GUAAAUACUUUCUAGGGUUCCGCC------UUAU--------------------U------GGGUCUG-GUCCGAGAGAA-AGU-GCAAAGAA-----------------------UUUU------------------UU--C-UUUG-UCCACGGAGGGAUAAAAGCCCGGGAGAU
BA000022.2/801401-801280      GGAUAUUGUUUCUAGGGUUCCGAUUC--CUGGUGAU----------------GUGGG--GAAUGGCUG-GUCCGAGAGAA-ACA-GGCUAGGC----------------------UUUGUAAAG--------AUUUUUGCCAC-UAGC-UACACGGCGGGACAAAAGCCCGGGAGAC
CP000091.1/1611056-1610941    CCGAAGGGUCGCUAGGGUUCCGGUCG--CGCUGC--------------------GCG--CGAUGUCUG-GUCCAAGAGCA-ACC-GGCCUCAGGC------------------GCGCUCGAC------------CGCGUC--C-AGGC-UCCACGGCGGGACAAAAGCCCGGGAGGU
CP000089.1/86805-86928        UUAAUGGGCGGCUAGGGUUCCGGUUU--C--GUC--------------------G-G--AAAUGUCUG-GUCCAAGAGCU-GCC-GGUUCUGUCUGCCGUGGG--UGAUUGCCGCGGUGU-----------------GUC--A-GAGC-UCCACGGAGGGAUAAAAGCCCGGGAGGA
CP000304.1/2184496-2184399    GAAAUAGCCGACUAGGGUUCCGACUC--GCUC-----------------------GC--GAGUGGCUG-GUCCGAGAGUU-GGC-GACCUC-------------------------CAGU----------------------G-AGGU-UACACGGCGGGAUAAAAGCCCGGGAGAA
ABDW01000004.1/105268-105170  UAUAAAGUUUUCUAGGGUUCCGUAAC--U--UUU--------------------U-A--GUUAGUCUG-GUCCAAGAGAA-AAC-GCACAG-------------------------AAAG-----------------A----C-UGUG-AACACGGAAGGAUAAAAGCCUGGGAGAU
AACY020487820.1/810-909       GAAAUGGAUGACUAGGGUUCCGAUCC--GCCCAG---------------------GC--GGGUGACUG-GUCCGAGAGUC-AUC-GACCUC-------------------------CGAU----------------------G-AGGU-UACACGGCGGGAUAAAAGCCCGGGAGAA
AP008230.1/4836847-4836749    AAAAAUGUUUUCUAGGGUUCCGCAAC--A-CGCU--------------------U-U--GUUGGUCUG-GUCCGAGAGAA-AAC-UCACAGCC----------------------U----------------------GG--C-UGUG--UCACGGAGGGAUAAAAGCCUGGGAGAG
CP000301.1/5067771-5067660    GGAGUUGGCUGCUAGGGUUCCGGCCU--UGCGUGA------------------UGCA--GGGUG-CUG-GUCCGAGAGCG-GCC-GCUUGCGGG---------------------GGAGACA-------------UCCUC--G-CAGG--ACACGGCGGGACAAAAGCCCGGGAGAC
AACY022570280.1/322-224       CCAAUAGCUGGCUAGGGUUCCGGUUC--ACGCAG---------------------GU--GAAUGUCUG-GUCCGAGAGCU-GGC-GACCU--------------------------CUGC-----------------G------AGGU-UACACGGCGGGACAAAAGCCCGGGAGAC
CP000110.1/1021660-1021560    GCGGAUGAAAUCUAGGGUUCCGAUCU--CUUCAC---------------------GG--GGAUGCCUG-GUCCAAGAGGU-UUC-CACCGG-------------------------CCUU-----------------G----C-CGGU-UGCACGGAGGGACAAAAGCCCGGGAGAC
AM180355.1/2762349-2762255    AAUUUAGUUUUCUAGGGUUCCGCAUU-----UUA--------------------U----AAUGGUCAG-GUCCAAGAGAA-AAC-GCACAA-------------------------UUG-----------------------U-UGUG-UACACGGAAGGAUAAAAGCCUGGGAGAU
CP000460.1/60769-60638        CUUCAGGAUCGCUAGGGUUCCGGUCG--UGCGGCGUG-------------UGCCGCG--CGAUGCCUG-GUCCGAGAGCA-AUCCGGUCUUGCCUUCGCCUC-----GACGAGAGGAAAC-----------------GGC--G-AGGC-UCCACGGAGGGAUAAAAGCCCGGGAGGU
AACY020561157.1/192449-192570 UCUUAGGGGUGCUAGGGUUCCGGUUC-----AUC-------------------------GAACGUCUG-GUCCGAGAGCAGCCC-GGUGCGGGUUCGUCCGAU--CGCGAGACCGGACGC-----------------ACA--C-GCGC-UACACGGCGGGACAAAAGCCCGGGAGAU
CP000304.1/2174098-2173996    UUCAAGGAGAACUAGGGUUCCGGCUC--ACAGGG--------------------AGU--GGGCG-CUG-GUCCGAGAGUU-CUC-CGGUCCC-----------------------AGGGA-----------------C-G--G-GACU--ACACGGAGGGAUAAAAGCCCGGGAGAC
CP000542.1/4178508-4178625    CAGAAGGGUCGCUAGGGUUCCGGUCG--CACACAU-----------------CGAUG--CGGCG-CUG-GUCCGAGAGCA-ACC-GGCCUCAGGCGCG-------------CACGACCGC-----------------GCC--C-AGGC-UCCACGGCGGGACAAAAGCCCGGGAGAU
CP000450.1/2598462-2598562    GCUUUACGAAACUAGGGUUCCGGCUU--UCCAAG---------------------GG--AAGUGACUG-GUCCAAGGGUU-UCG-GGCCCUUU----------------------C----------------------AA--G-GGGU-UCCACGGAGGGAUAAAAGCCCGGGAGGU
CP000529.1/42882-42765        ACAAAUGACAGCUAGGGUUCCGGCCA--CUUGUUC-----------------GCAAG--CGGUGUCUG-GUCCGAGAGCA-GUC-GGCCAGCAG---------------------CGGCCCAC----------ACCACUG--C-AGGU-UCCACGGCGGGACAAAAGCCCGGGAGGU
CP000394.1/1970354-1970241    AACGUAUGCGACUAGGGUUCCGGCUG--C-CUGU----------------------G--CAGUGACUG-GUCCGAGAGUC-GCA-AUCCGGUACCUCC------------UUUCAGGAAA-----------------GGG--C-UGGA-CACACGGCGGGAUAAAAGCCCGGGAGGU
CP000511.1/851507-851616      GUGGGGCGCGCCUAGGGUUCCGCCGG--C-AGGC--------------------A-G--CCGGGUCUG-GUCCGAGAGGC-GCA-GGCGGCCGGCA-----------------CCGGAGC-----------------CCG--G-CCGU-UCCACGGCGGGACAAAAGCCCGGGAGAC
AACY022304416.1/191-289       GGCGGAGAAACCUAGGGUUCCGAUCC--C-GUCA----------------------G--GGAUGCCUG-GUCCGAGAGGU-UUC-GGUCGG-------------------------CACA-----------------A----C-CGGC-UGCACUGAGGGACAAAAGCCCGGGAGAC
CP000616.1/127215-127094      UCUUAGGGUCGCUAGGGUUCCGGUUC-----AUC-------------------------GAACGUCUG-GUCCGAGAGCA-GCC-CGGCGCGCGGGCGUCCGAUCACGAAAACGGACGCC-----------------CGC--G-CGCU--ACACGGCGGGACAAAAGCCCGGGAGAU
AACY020944359.1/616-715       CAAAUAGAGCGCUAGGGUUCCGGCCG--CUGU-----------------------AG--CGGUGACUG-GUCCGAGAGCA-CUC-GACCUU------------------------UCAGA-----------------C----A-AGGU-UACACGGCGGGAUAAAAGCCCGGGAGAC
CP000521.1/1496368-1496463    UCAAAAGUGAUCUAGGGUUCCGAUAC--U--UAC----------------------A--GUAUGUCUG-GACCGAGAGUU-CAC-GGUUC--------------------------CUAG-----------------C------GAAC-UACACGGAGGGAUAAAAGCCCGGGAGGA
AACY023003357.1/203-105       GAAAUGGACGGCUAGGGUUCCGGCCU--GCUUCA--------------------AGC--AGGUG-CUG-GUCCGAGAGCU-GUC-GACCU--------------------------CGGU-----------------G------AGGU-UACACGGCGGGAUAAAAGCCCGGGAGAG
CP000721.1/3993909-3993812    AUUUAAGUUUUCUAGGGUUCCGCAGU--U--UGU----------------------A--ACUGG-CAG-GUCCGAGAGAA-AAC-GCAUAGU------------------------UUAU-------------------A--C-UAUG-UUCACGGAAGGAUAAAAGCCUGGGAGAU
CP000774.1/2046573-2046691    GUUGGCAGCGGCUAGGGUUCCGGCUU--CGCGUGUAGU-----------UGUUUGCG--AAGUG-CUG-GUCCGAGAGCC-GCA-CCCUGUCCG---------------------GUGAAC--------------AGCGG--G-CAGG-UACACGGCGGGACAAAAGCCCGGGAGAC
CP000271.1/1848426-1848294    CUUCAGGAUCGCUAGGGUUCCGGUCGGACGCUUUC-----------------AUGCGCACGAUGCCUG-GUCCGAGAGCA-AUCCGGUCUUGCC---------------------GUUCACCUUCUUUCAAGGCGCCGGC--G-AGGC-UCCACGGAGGGAUAAAAGCCCGGGAGGU
AANE01000002.1/189556-189666  CAAUGGUAUAGCUAGGGUUCCGACUU--U--GAA--------------------A-A--AAGUGUCUG-GUCCGAGAGCU-AUC-GACCUCACC---------------------UGACAUU------------CUCAGU--GAAGGU-UACACGGAGGGAUAAAAGCCCGGGAGAA
ABDX01000001.1/159014-159112  UAUAUGGUUUUCUAGGGUUCCGUAGC--U--UUU--------------------U-A--GUUAGUCUG-GUCCAAGAGAA-AAC-GCACAG-------------------------AUAA-----------------A----C-UGUG-AACACGGAAGGAUAAAAGCCUGGGAGAU
AACY020686856.1/831-737       GCGGAUGAAAUCUAGGGUUCCGGUC-----UACG--------------------G-----GACGACUG-GUCCAAGAGAU-UUC-AGCCGG-------------------------CUCU-----------------G----C-CGGC--ACACGGAGGGAUAAAAGCCCGGGAGAC
CP000544.1/2583259-2583363    GCAAUAGGCGUCUAGGGUUCCGUCCG--CAGGCA---------------------UG--CGGAGCCUG-GUCCGAGAGUC-GCC-GACCUCUC-----------------------CCAG-----------------AGG--G-GGGU-UACACGGAGGGACAAAAGCCCGGGAGAU
CP000781.1/1413287-1413177    CGAGUUGGUGGCUAGGGUUCCGGCAU--CCCGCG---------------------GG--AUGUG-CUG-GUCCGAGAGCU-GCC-ACUGCUCCG---------------------GGAGACA-------------UCCGG--G-GCGGGUGCACGGCGGGAUAAAAGCCCGGGAGAC
AAMT01000009.1/114932-114823  GUGCAGGACGCUUAGGGUUCCGCCGC--GCCAAA---------------------GC--GCGGGUCUG-GUCCGAGAAGC-GUC-ACCCAUCCG---------------------GCAAAU--------------UCCGG--C-AGGG-CACACGGCGGGCCAAAAUCCCGGGAGAC
AACY022971551.1/806-690       ACAAUGGCCGACUAGGGUUCCGGCUC--GUCCGA-------------------UGAC--GAGUGGCUG-GUCCGAGAGUG-GGC-GACCUCAUCAGCG-------------GCGGGGAGC-----------------CGC--G-AGGU-UACACGGCGGGACAAAAGCCCGGGAGAA
AACY021185329.1/257-381       AGAAUAGCUGACUAGGGUUCCGGCGC---CAAAU--------------------GGC--GCGCGACUG-GUCCGAGAGUC-AGC-GACCUCGAUCGACGCGAC---GAAAAAGAUUGCGU-----------------UUG--C-AGGU-UACACGGCGGGACAAAAGCCCGGGAGAU
CP000463.1/1370978-1371085    AGAGUUGGUGGCUAGGGUUCCGAUCU--UGCGUG---------------------CA--AGGUG-CUG-GUCCAAGAGCC-GCC-CCCCGAAGGG-------------------AGAAAU-----------------CCU--U-CGGA-UGCACGGCGGGACAAAAGCCCGGGAGGC
CP000282.1/1455387-1455513    CCAAUGGAUGGCUAGGGUUCCGGCUG--UAAAUA---------------------AA--CAGUGACUG-GUCCGAGAGCC-AUC-GACCUUCUAAGUGGUAGCC-AAUUUGCAUAUUGGU-----------------AAG--A-GGGU-UACACGGCGGGAUAAAAGCCCGGGAGGA
CP000283.1/2437685-2437791    AGAGUUGGUAGCUAGGGUUCCGGCCU--U-GUCU--------------------G-A--AGGCG-CUG-GUCCGAGAGCU-GCC-CCCCGAAGGG-------------------AGAAAU-----------------CCU--U-CGGA-CGCACGGCGGGACAAAAGCCCGGGAGGC
AAXV01000003.1/157177-157083  UGUAAAGUUUUCUAGGGUUCCGUAGC-----UGA--------------------U----GCUAGUCUG-GUCCGAGAGAA-AAC--CACAA-------------------------UUUU-----------------U----U-UGUG--ACACGGAGGGAUAAAAGCCUGGGAGAU
CP000680.1/1531681-1531564    GAAAUGGCCGACUAGGGUUCCGGCCC--ACCCGCA-----------------CGGGU--GGGUGACUG-GUCCGAGAGUG-GGC-GACCUCGGAGCG--------------GCGGGAAGC-----------------CGC--G-GGGU-UACACGGCGGGAUAAAAGCCCGGGAGAA
AAFY01010653.1/807-706        CAAAUAGAGCGCUAGGGUUCCGGCUG--A-GCUG--------------------U-U--CAGUGACUG-GUCCAAGAGCA-CUC-GACCUNU------------------------CAGA-----------------C-A--A-AGGU-UACACGGCGGGACAAAAGCCCGGGAGAC
AAYA01000003.1/309765-309872  GGGCAGGGCGUUUAGGGUUCCACCGC--C--AUA--------------------C-G--GCGGGUUCG-GUCCGAGAAAU-GCC-ACCCGGCGG---------------------GCAAAC--------------UCCCG--C-AGGG-CACACGGCGGGGCAAAAUCCCGGGAGAC
CP000460.1/61202-61326        UCUUAGGGGUGCUAGGGUUCCGGUUC--A--UCA--------------------U-C--GAACGUCUG-GUCCAAGAGCAGCCC-GGCGCGAGUUCGUCCGGU--CGCAAGACCGGAUGC-----------------ACG--C-GUGC-UACACGGCGGGACAAAAGCCCGGGAGAU
AACY022815670.1/204-110       GCGGAAGAGAUCUAGGGUUCCGGUCC-----UUC--------------------G----GGACGACUG-GUCCAAGAGGU-UUC-AGCCGGC---------------------------U-----------------C-G--C-CGGC--GCACGGAGGGAUAAAAGCCCGGGAGAC
CU234118.1/7058767-7058665    AGAGUUGGCAGCUAGGGUUCCGGUUC--UCAUCG--------------------CGA--GAACG-CUG-GUCCGAGAGCA-GCC-GCCAGGG------------------------GAGA-----------------G-C--C-CUGG-UGCACGGCGGGAUAAAAACCCGGGAGAC
CP000656.1/84923-84804        GUGGGGCGCGUCUAGGGUUCCGCCGG--CGGCAUUCGU-----------CGAACAGG--CCGGGUCUG-GUCCGAGAGAC-GCA-GGCGGCCGGC------------------ACCGACG-----------------CAG--A-CCGU-UCCACGGCGGGAGAAAAGCCCGGGAGAC
CP000414.1/1882072-1882171    UCUAUAGUUUUCUAGGGUUCCGCUAU-----AAU--------------------A----AUAGGUCUG-GUCCAAGAGAA-AAC-AUACAAUG-----------------------AUUA------------------CA--U-UGUA-CACACGGACGGAUAAAAGCCUAGGAGAU
CP000697.1/2994092-2993982    GCAAAGCCGAGCUAGGGUUCCGGCCG--GAUCAAA------------------AAUC--CGGCG-CUG-GUCCGAGAGCU-UCA-GCCGCGCGGG-------------------AGACAU-----------------CCG--C-GCGG-UCCACGGCGGGACAAAAGCCCGGGAGAG
AACY022488354.1/229-332       GCAAUGGCCGACUAGGGUUCCGGCUC--GCUUGAA------------------AAGC--GAGUGGCUG-GUCCGAGAGUU-GGC-GACCUC-------------------------CAGU-----------------U----G-AGGU-UACACGGCGGGAUAAAAGCCCGGGAGAC
AANO01000003.1/316950-317071  GGAAGCAGCUUCUAGGGUUCCGGUUC--GCGUCAGUUCGCUUCAGCGAGCCCGAUGC--G-GCGUCUG-GUCCGAGAGAA-GCU-CACCGGG------------------------GUCA-------------------C--C-CGGU-UGCACGGAGGGAUAAAAGCCCGGGAGAC
AACY020631184.1/852-757       GGA---GAAACCUAGGGUUCCGGUUC--C-GUCA----------------------G--GGAUGACUG-GUCCGAGAGGU-UUC-GGUCGG-------------------------UUCU-----------------G----C-CGAC-UGCACGGAGGGACAAAAGCCCGGGAGAC
AM236083.1/312516-312624      AGAGUUGGUGGCUAGGGUUCCGGCGU--C-GCAA----------------------G--ACGUGGCUG-GUCCGAGAGCU-GCC--ACCGGCAGGG----------------GAGACAUC-----------------CUG--C-CGGG-UGCACGGCGGGACAAAAGCCCGGGAGAC
AAKY01000210.1/24279-24412    CUUCAGGAUCGCUAGGGUUCCGGUCG--CACGGCGUCAC----------ACGCCGAG--CGACGUCUG-GUCCGAGAGCA-AUCCGGUCUUGCCGCCUGCC------UUUGCGAGGCCCC-----------------GGC--G-AGGC-UCCACGGAGGGACAAAAGCCCGGGAGGU
AACY023278747.1/300-199       CAAAUAGAUCGCUAGGGUUCCGGCGU--UAUAGA---------------------CA--ACGUGACUG-GUCCGAGAGCA-AUC-GACCUUC-------------------------AUU-----------------C-G--G-AGGU-UACACGGCGGGAUAAAAGCCCGGGAGGU
AAFY01015288.1/310-411        CUAAUAGAUAACUAGGGUUCCGGUGA--A-UUUA--------------------C-U--UCACGUCUG-GUCCGAGAGUU-GUC-AACCUC--A---------------------UGAGU-----------------A----G-AGGU-CACACGGAGGGAUAAAAACCCGGGAGGU
CP000673.1/2546156-2546053    UUUAAAGUUUUAUAGGGUUCCGCAGU--UUGAAAU-----------------UGAUA--AUUGGUCUG-GUCCAAGAUAA-AAC-GCACAG--------------------------UUU-----------------G----C-UGUG-UUCACGGAAGGAUAAAAGCCUGGGAGAU
AL954747.1/2634203-2634101    GUUUCACGAAACUAGGGUUCCGGCUU--UCCCAG--------------------GGA--AAGUGACUG-GUCCGAGAGUU-UCG-GGCCCUGCC---------------------A----------------------GC--A-GGGU-UCCACGGAGGGAUAAAAGCCCGGGAGGU
CP000450.1/2598249-2598146    AUUACUUUGGGCUAGGGUUCCGGCUU--UCCAAG---------------------GG--AAGUGACUG-GUCCGAGGGCC-CGA-GGCUUC-------------------------UCCAU--------------AAC----G-AAGC-GCCACGGAGGGAUAAAAGCCCGGGAGAU
CP000616.1/127702-127837      CUUCAGGAUCGCUAGGGUUCCGGUCG--UGUGGCGCAGG---------CGCGCCGCG--CGAUGUCUG-GUCCGAGAGCA-AUCCGGUCUUGCCUUCGCCUC-----GACGAGAGGAAAC-----------------GGC--G-AGGC-UCCACGGAGGGAUAAAAGCCCGGGAGGU
AACY020561157.1/192016-191883 CUUCAGGAUCGCUAGGGUUCCGGUCG--UGCGGCGUUC-----------GCGCCGCG--CGAUGGCUG-GUCCGAGAGCA-AUCCGGUCUUGUCUUCUCCUC-----GCUUCGAGGAAAC-----------------GGC--G-AGGC-UCCACGGAGGGAUAAAAGCCCGGGAGGU
AAFY01000234.1/1647-1549      ACUAAAGGUAGCUAGGGUUCCGACUU--A--UUU--------------------A-U--AAGUGUCUG-GUCCGAGAGCA-ACC-GACUCU-------------------------UAAA-----------------U----A-GAGU-UACACGGAGGGAUAAAAGCCCGGGAGGU
CP000103.1/1087459-1087562    GUAGCGCGAAACUAGGGUUCCGGCUU--CUUUUU---------------------CG--AAGUGUCUG-GUCCGAGAGUU-UCC-GGCUUCGU-----------------------CAUG------------------AC--G-AGGC-UCCACGGAGGGAUAAAAGCCCGGGAGAU
AAFX01006062.1/502-399        GUAAAGCGAAACUAGGGUUCCGGCUU--UCUGCU---------------------GA--AAGUGUCUG-GUCCGAGAGUU-UCC-GGCUUCGU------------------------CGU-----------------GAC--G-AGGC-UCCACGGAGGGAUAAAAGCCCGGGAGAU
AL954747.1/2634421-2634524    AUUACUUCAGGCUAGGGUUCCGGCUU--UCCCAG--------------------GGA--AAGUGACUG-GUCCGAGAGCU-UGA-GGCUUCG------------------------UCAU-----------------A-C--G-AAGC-UCCACGGAGGGAUAAAAGCCCGGGAGGU
CP001348.1/2951117-2951220    CAUAUAGUUUUAUAGGGUUCCGCAGU--UUAAUUU-----------------AAACA--ACUGGUCUG-GUCCGAGAUAA-AAC-GCACA--------------------------GUUU----------------AA------UGUG-UUCACGGAAGGAUAAAAGCCUGGGAGAU
CP000908.1/4131856-4131747    CGAGUUGAUCGCUAGGGUUCCAGCAU--C-UCUU--------------------U-G--AUGUGUUCG-GUCCGAGAGCG-GUU-GCCGCGGCG---------------------GGAGACA-------------UCCGC--C-CGGA-UGCACGGCGGGAUAAAAGCCCGGGAGAC
CP001053.1/1408226-1408092    CUUCAGGAUCGCUAGGGUUCCGGUUG--UGCGCAGAUC-----------AAUGCGCA--CGAUGUCUG-GUCCGAGAGCA-AUCCGGUCUUGCC---------------------GUUCACCUUCUUUCAAGGCGCCGGC--G-AGGC-UCCACGGAGGGAUAAAAGCCCGGGAGGU
ABDT01000102.2/4407-4311      AGAUAAGUUUUCUAGGGUUCCGCAGU--U--UAU----------------------A--GCUGGUCAG-GUCCAAGAGAA-AAC-GCACA--------------------------GUAA----------------AA------UGUG-UUCACGGAAGGAUAAAAGCCUGGGAGAU
CP000960.1/472628-472749      UCUUAGGGUUGCUAGGGUUCCGGUUC-----AUC-------------------------GAACGUCUG-GUCCGAGAGCA-GCCCGGCACGGGUUCACCCGAU--CGCGAGACCGGAUGC-----------------GCA--C-GUGC-UACACGGCGGGACAAAAGCCCGGGAGAU
AL009126.3/3988942-3988840    ACAGUGGUUUUCUAGGGUUCCGCAAU----GCAA-------------------------AUUGGACUGUGACCGAGAGAA-AAC-ACAUAGCAG---------------------CUUG-----------------GCUG--U-UAUG--ACACGGUGGGAUAAAAGCCCAGGAGUU
CP000853.1/1397256-1397351    AUUUAAGUUUUCUAGGGUUCCGCAGC--U--UAU----------------------A--ACUGG-CAG-GUCCGAGAGAA-AAC-ACACAG-------------------------CUAA----------------------U-UGUG-UACACGGAAGGAUAAAAGCCUGGGAGAU
CP001083.1/2486240-2486145    AUUUAAGUUUUCUAGGGUUCCGCAGC--U--UGU----------------------A--GAUGG-CAG-GUCCGAGAGAA-AAC-ACACAGUU---------------------------------------------GA--C-UGUG-UACACGGAAGGAUAAAAGCCUGGGAGAU
CP002620.1/1522002-1521902    CCAAUAGCCGGCUAGGGUUCCGGCUC--GCCACA--------------------GGC--GAGCGACUG-GUCCGAGAGCU-AGC-GACCUC-------------------------CAGC----------------------G-AGGU-UACACGGCGGGACAAAAGCCCGGGAGAA
FN668941.1/529411-529517      AAUAGAGUUUUAUAGGGUUUUGCAAU--UAUUAA---------------------UG--AUUGGCCUG-GUCCGAGAUAA-AAC-CCACAACAU---------------------AGUUU-----------------UUG--U-UGUG-AACACGGAAGGACAAAAACCUGGGAGAU
CP003056.1/927248-927350      AAAACUGUUUUCUAGGGUUCCGCGGA--A--GAA--------------------A-U--UCCGGCCUG-GUCCGAGAGAA-AAC-ACACAGUC----------------------GUAUU-----------------AUG--C-UGUG--ACACGGAAGGAUAAAAGCCUGGGAGAU
CP003056.1/927033-926937      ACAUUAGUUUUCUAGGGUUCCGCAG------UAC--------------------G-----CUGGUCAG-GUCCAAGAGAA-AAC-ACACAGUU-----------------------GGA-------------------AA--C-UGUG-CACACGGAGGGAUAAAAGCCCGGGAGAU
CP000094.2/1520387-1520287    GCAAUGGCUGACUAGGGUUCCGGCUC--GCAUCU---------------------GC--GAGUGGCUG-GUCCGAGAGUU-GGC-GACCUC-------------------------CAGU-----------------U----G-AGGU-UACACGGCGGGACAAAAGCCCGGGAGAC
#=GC SS_cons                  ::::::<<<<<<<---------<<<<..<<____...................._>>..>>>>-----.------->>>>.>>>.-<<<<<<<_....................._____................._>>..>.>>>>.::::::::::::::::::::::::::::
#=GC RF                       auaaaaggcugCUAGGGUUCCGgccc..cguuua....................gcg..gggcGuCUG.GUCCGAGAGca.gcc.ggccgggcu.....................guuaa.................agc..c.cggc.UaCACGGaGGGAuAAAAGCCCGGGAGau
//
# STOCKHOLM 1.0

#=GF AC   RF00443
#=GF ID   SNORA27
#=GF PI   snoACA27
#=GF DE   Small nucleolar RNA SNORA27
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   64.00
#=GF TC   65.10
#=GF NC   63.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00032
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300779;
#=GF DR   snoopy; Homo_sapiens300181;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   ACA27 is a member of the H/ACA class of snoRNA that guide the sites of
#=GF CC   modification of uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_SNORA27
#=GF SQ   24


AJ609439.1/1-126           UACCCCCUUUUCACUUUGC-CAGUUGGAC----UUA-----UGUCUUUAUUGGUCAUUCAAGUGGGGCAAAGGAAA-UA-UC-CUUUU-AAAACUCAGGCAAAC-UGGGU-GUUUG-UCU-G------UAUCCUGUCAGAG-GAAACAAAU
AC092324.3/97410-97533     AACCCCCUUUUCACUUUGC-CAAUUGGAC----UUA-----UGUCUUUAUUGAUCAUUCAAGU-GAGCAAAGGAAA-UA--CGCUUUA-AAAACUCAGGCAAAC---GGU-GUUUG-UCUUG------UAUCCCGUCAGAG-GAAACAAAU
AL121933.15/171786-171653  UACCCUCUUUCCACUUUGC-CAACUGGAU----GUA-----UGUCUUUACUGGUCAUUCCAGUGGGGCAAACGAAA-UA-UC-CUUUUUAAAACUCAGGCAAAC-UGGGU-GUUUG-UCAUGGUCAUGUAUCCUGUCAGAG-AAAACAAAC
AAIY01376848.1/1110-1236   CACCCCCUUUUCACUUUGC-CAAUUGGAC----UUA-----UGUCUUUAUUGGUCAUUCAAGUGGGGCAAAAGAAA-UA-UC-CUUUU-AAAACUCAGGCAAAC-UGGGU-GUUUG-UCUUG------GAUCCUGUCAGAG-GAAACAGGU
ABDC01394715.1/4253-4128   AAACCCCUUUUCACUUUGC-CAAUCGGAC----UUA-----UGUCUUUAUUGGUCAUUCAAGUGGGGCAAAGGAAA-UA-UC-CUUUU-AAAACUCAGGCAAAC--UGGU-GUUUG-UCUUG------UAUCCUGUCAACG-GAAACAAAU
AAFC03084615.1/7567-7693   ACACCCCCUUUCACUUUGC-CAAUUGGAC----UUA-----UGUCUUUAUUGGUCAUUCAAGUGGGGCAAAGGAAA-UA-AC-CUUUU-AAAACUCAGGCAAAC-UGGGU-GUUUG-UCUUG------UAACCUGUCAGAG-GAAACAUUG
AANU01212081.1/6652-6777   AACCCCCUAUUCACUUUGC-CAAUUGGAC----UUA-----UGUCUUUAUUGAUCAUUCAAGU-GGGCAAAGGAAA-UA-UG-CUUCA-AAAACUCAGGCAAAC-UGGGU-GUUUG-UCUUG------UAUCCUGUCAGAG-GAAGCAAAU
AAPY01625859.1/1783-1909   CACCCCCUUUUCUCUUUGC-CAGUUGGAC----UUA-----UGUCUUUAUUGGCCAUUCAAAUGGGGCAAAGGAAA-UG-UC-CUUUU-AAAACUCAAGCAAAC-CAGGU-GUUUG-UCUUG------UAUCCUGUCAAAG-GAAACAAAU
AANN01406612.1/485-609     UUUUCCCCUUUCACUUUGC-CAAUUGGAC----U-------UGUCUUUAUUGGUCAUUCAAGUGAGGCAAAGGAAA-UA-CC-CUUUU-AAAACUCAGGCAAAC-UGGGU-GUUUG-UCUUG------UAUCCUGUCAGAG-GAAACAAAA
AC124828.14/64217-64345    ACCCCCCCUUUCACUUUGC-CAAUUGGAC----UUA----AUGUCUUCAUUGGCCAUUCAAGUGGGGCAAAGGAAA-UA-AC-CUUUU-AAAACUCAGGCAAACUUAAGU-GUUUG-UCUUG------UAACCUGUCAGGG-GAAACAUUA
AAFR03025660.1/72910-73039 CUCCCCUCUUUCACUUUAC-CAAUUAGACA-CAUCA-----UGUCUUUAUUGGUCAUUCAAGUGGGGUAGAAGAAA-UA-UC-CUUUU-AAAACUCAAGCAAAC-UGGUU-GUUUG-UCUUG------CAUCCUGUCAGAG-GAAACAAUC
AALT01465822.1/498-624     UGCCCCUGUCUCACUUUCC-CAAUUGGAU----UUA-----UGUCUUUAUUGGUCAUUCAAGUGGGGCAAAGGAAG-UG-UC-CUUUU-AAAACUCAAGCAAAC-UGGGA-AUUUG-UCUUA------CAUCUAGUCAGAG-GAAACAAUA
CR352531.1/338-470         CACCCUCCUUUCACUUUGC-CAGUUAGACACUUUUU-----UGUCUUGAUUGGUCAUUCAAGGUGGGUAAAGUAUA-CA-UC-CUUUU-AAAACCCAAGCAAAUGGUGGUCAUUUG-UCUUG------GAUCCUGUCAGAG-GAAACAGGU
AAQQ01358889.1/291-161     UGUCUCUCUUUCACUUUGCUCAAAUGGAC----UGA-----UGUCUUUAUUGGUCAUUCAAGUGGGGCAAAGGAAA-UG-UUCUUCUU-AAAACUCAGGCAGAU-GAAGU-GUUUGCUCACG------UAACCUGUCAGAUUGAAGUAGAU
AAPN01100359.1/2880-3011   UCCCCCCCUUUCACUUUGC-CAGUUAGAC----AUUUCUCUUGUCUUUAUUGGUCAUUCAAAUGGGGUAAAUUAAU-UU--C-CUUUU-AAAACUCAAGCAAACAAAUUU-GUUUG-UCUUG------UAUCCUAUCAGGG-GAGACAUUU
AAYZ01151931.1/8532-8405   UAACCCUUAUUCACUUUGU-CAAUUGGGCU--UUUA-----UGUUUUCUGUGGUCAUGUGAUUGGGGCAAACUAAC-UA-UC-CUUUC-UAAAUUCA-GGAAAC-UGAGU-AUUUG-UAUUA------UAAUCUGUCAGAG-GAAAGAAAC
AAWR02035292.1/38650-38777 UACCCCCUUUUCACUUUGC-CAAUUGGAC----UUA-----UGUCUUUAUUGGUCAUUCAGGUGGGGGAAAGGAAAAGA-UC-CUUUU-AAAACUCAAGCAAAC-UGAGU-GUUUG-UCUUG------UAUCCUGUCAGAG-GAAACAAAU
AAKN02010429.1/3339-3465   AAAGCCCCUUUCACUUUGC-CAGUGGGAC----UUA----AUGUCUUCAUUGGUCAUUCAAGUGGGGCAAAGGAAA-UA-UC-CUUUU-AAAACUCUGGCAAAC--UAGU-GUUUG-UCCUG------UAACCUGUCAGAG-GGAACAGUC
FJ915962.1/1-128           UACCCCCUUUUCACUUUGC-CAAUUGGAC----UUA-----UGUCUUUAUUGGUCAUUCAAGUGGGGCAAAGGAAA-UAAUC-CUUUU-AAAACUCAGGCAAAC-UGAGU-GUUUG-UCUUG------UAUCCUGUCAGAG-UAAACAAAU
EU093991.1/1-131           CC-CCCCCUUUCACUUUGC-CAGUUAGACAUUU---CU-CUUGUCUUUAUUGGUCAUUCAAAUGGGGUAAAUUAAU--U-UC-CUUUU-AAAACUCAAGCAAACAAAUUU-GUUUG-UCUUG------UAUCCUAUCAGGG-GAGACAUUU
AC005214.1/14143-14018     AAACCCCUGUUCACUUUGC-CAAAUGGAU----UUG-----UGUCUUUAUUGCUCAU-UAAUUGGGGCAAAGGAAA-UA-UC-CUUUU-AAAACUCAGGCAAAC-UGAGU-GUUUG-UCUUG------UAUCCUGUCAGAG-GAAAGAAAU
AAGW02066083.1/70455-70583 CGCCCCCUUUUCACUUUGC-CAAUUUGAC----UUUU---UUGUCUUUAUUGGUCAUUCAAGUGGGGCAAAGGAAC-UA-UC-CUUUU-AAAACUCAAGCAAGC-UGAGU-GUUUG-UCUUG------UAACCUGUCAGAG-GAAACAAAC
AAPE02035995.1/48107-48232 CACCCCCUUUUCACUUUGU-CAAUUGGAC----UUA-----UGUC-UUAUUGGUCAUUCAAGUGGGGCAAAGGAAA-UG-UC-CUUUU-AAAACUCAGGCAAAC-GGGGU-GUUUG-UUUUG------UAUCCUGUCAGAG-GAAACAAAA
AAQR03131808.1/6552-6427   GCCCCCCUUUUCACUUUGC-CAGUUGGAC----UUA-----UGUCUUUAUUGGUCAUUCAAGUGGGGCAAAGAAAA-UA-UC-CUUUU-AAAACUCAGGCAAAC--UGGU-GUUUG-UCUUG------UAUCCUAUCAAAG-GAAAAAAAU
#=GC SS_cons               :::::::::::::::::::.:::::::::....:::.....<<<<<---<<<<____>>>>--->>>>>-------.--.<<.<<<<-.------<<<<<<<<<._____.>>>>>.>>>->......--------->>>>.>>:::::::
#=GC RF                    uacCCCcuUUUCACUUUGC.CAAUUgGAC....UUA.....UGuCuUUAuuGgUCAUuCaagUGgGgCAAAggAAa.Ua.uc.CuuUU.AAAACUCaggCAAAc.uggGU.gUUUG.ucuUG......UAuCCUGUCAgaG.gaAAcAaau
//
# STOCKHOLM 1.0

#=GF AC   RF00444
#=GF ID   PrrF
#=GF DE   PrrF RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15210934
#=GF SS   Published; PMID:15210934
#=GF GA   80.00
#=GF TC   81.10
#=GF NC   79.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF RN   [1]
#=GF RM   15210934
#=GF RT   Identification of tandem duplicate regulatory small RNAs in Pseudomonas
#=GF RT   aeruginosa involved in iron homeostasis.
#=GF RA   Wilderman PJ, Sowa NA, FitzGerald DJ, FitzGerald PC, Gottesman S, Ochsner
#=GF RA   UA, Vasil ML
#=GF RL   Proc Natl Acad Sci U S A 2004;101:9792-9797.
#=GF RN   [2]
#=GF RM   29507088
#=GF RT   The Pseudomonas aeruginosa PrrF1 and PrrF2 small regulatory RNAs (sRNAs)
#=GF RT   promote  2-alkyl-4-quinolone production through redundant regulation of
#=GF RT   the antR mRNA.
#=GF RA   Djapgne L, Panja S, Brewer L, Gans J, Kane MA, Woodson SA,
#=GF RA   Oglesby-Sherrouse AG
#=GF RL   J Bacteriol. 2018; [Epub ahead of print]
#=GF CC   PrrF RNA is a small RNA involved in iron homeostasis and is found
#=GF CC   exclusively in Pseudomonas species. PrrF sequences are the functional
#=GF CC   homologues of Rfam:RF00057 and are found in tandem. Their expression is
#=GF CC   induced under iron limitation by the ferric uptake regulator (Fur) and
#=GF CC   they act to negatively regulate several genes including sodB and sdh. Both
#=GF CC   homologues inhibit translation of antR mRNA, which affects quorum sensing
#=GF CC   and virulence factor production.[2]
#=GF WK   PrrF_RNA
#=GF SQ   18


AF055999.1/130-281         UUGACAUGGAAAUGAGAAUCAUUAUUACGUCACUCAACUGGUCGCGAGAUCAGCCGG-UAAGCUG-AGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGCACUUU-GCCGGGUCUUUUUUUG
CP000076.1/6028153-6028301 UUGACUUCGAAAUGAGAAUCGUUAUGAU-UAUCACAACUGGUCGCGAGAUCAGUCGA-UAACCUG-GAAGAC-CAGUGGUUCGGACU-CUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUAUUUGACCCGGCUCUU--GCCGGGUCUUUUUUUG
CP000712.1/5089139-5089287 UUGACGGCUAAAUGAGAAUUGUUAUGAU-UAUCACAACUGGUCGCGAGACUGGUUGGAUAAGCUA-AGAGCCCCUGGU--UCGGACUCU-CAGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-AUUGACCCGGCAAUUU-GCCGGGUCUUUUUUUG
CT573326.1/3656603-3656753 UUGACUGGCAAAUGAUAACGAUUAUUAUUGCACUCAGCAGGUCGCGAGACCCGCUGGAUAACCUGCAACGUCCUCAG--GUCGGACGCU-CAGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGCUUUUU-GCCGGGUCUUUUUUUU
CP000712.1/2024547-2024401 UUGACUGGCAAAUGAUAACGAUUAUUAUUGCACUCAGCUGAUCGCGAGAUCCGCUGGAUAACCUG-AAAG-CUUAG---GUCG--CUCU-CAGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGCUUUUUUGCCGGGUCUUUUUUUU
AE016853.1/3549457-3549603 UUGAUUUUCAAAUGAUAAUGAUUAUUAUUGC-GUCAGCGGUUCGCGAGAACCGCUGG-AUAACCU-GGAAGUCUUAG--GUCGGCUUCC--GGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGAUUUUU-UCCGGGUCUUUUUUUU
CP000075.1/3620503-3620649 UUGACUUGCAAAUGAUAAUGAUUAUUAUUGCA-UCAGCGGGUCGCGAGACUCGCUGG-AUAACCC-GGAAGUCUUAG--GUCGGCUUCCA--GAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGCUUUUU-GCCGGGUCUUUUUUUG
CP000058.1/1035702-1035556 UUGACUUAGAAAUGAGAAUCGUUAUGAU-UAUCGCAUCCGGUCGCGAGACUGGACGG-UAA-CUG-AAAGACCUUGGU--UCGGACUUU-CAGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGCUCUUU-GCCGGGUCUUUUUUUG
CT573326.1/5016966-5017115 UUGACUACGUAAUGAGAAUCGUUAUGAU-UAUCACAGCUGGUCGCGAGACUGGUUGGGUAACCUG-AAAG-CUCCCUGGUUCGGACUCU-CAGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-AUUGACCCGGCAACUU-GCCGGGUCUUUUUUUG
CP000058.1/2575317-2575171 UUGACUUGCAAAUGAUAAUGAUUAUUAUUUCA-UCAGCGGGUCGCGAGAUCCGCUGGAUAAUCUG-GAAGUCUUAG---GUCGG-CUUC-CUGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGCUUUUU-GCCGGGUCUUUUUUUG
CP000076.1/4555423-4555571 UUGACUUGCAAAUGAUAAUGAUUAUUAUUGCAAGCAACUGGUCGCGAGAUCAGUCGA-UAGCCCA-AAGGACCUUAG--GUCGGACCUU-UGGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGCUUUUU-GCCGGGUCUUUUUUUU
CP000304.1/3533667-3533811 UUGACGCAGAAAUGAGAAUUGUUAUUAU-UAUCGCAACUGAUCGCGAGGUCAGCCGA-UA-GCUG-AAGG-CUCAGGCAGUCGAUCCUU-CAGGUUAUCUCCUCAUCAGGCUAAUCACGGUU-UU-GACCCGGCUCU---GCCGGGUCUUUUUUUG
CP000680.1/1126779-1126630 UUGACUAUGAAAUGAGAAUUGUUAUUAUUAC-CUCAACUGGUCGCGAGAUCAGCCGA-UAAGCUAAAGAGAC-CAUUCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-AUUGACCCGGCUCUU--GCCGGGUCUUUUUUUG
CP000949.1/2010463-2010319 UUGACUGCCAAAUGAUAACGAUUAUUAUUGCACUCAGCUGAUCGCGAGAUCUGCUGGAUAACCUG-GAGC-----UUAGGUC---GCUCUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGCUUUUU-GCCGGGUCUUUUUUUU
CP000094.2/5412550-5412698 UUGACUUGGUAAUGAGAAUCGCUAUGAU-UAUCACAACUGAUCGCGAGAUCAGUCGA-UAUUCUGAAAAGCC-CUUGG-UUCGGACUCU-CAGAUUAUCUCCUCAUCAGGCUAAUCACGGUUAUUUGACCCGGUUUUU--ACCGGGUCUUUUUUUG
CP000094.2/4145111-4145258 UUGACUUGCAAAUGAUAAUGAUUAUUAUUGCAAGCAACUGGUCGCGAGAUCAGUCGA-UGGACCA-G-AGACCUUAG--GUCGGUCUUC-UGGACUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGCUUUUU-GCCGGGUCUUUUUUUU
BK005486.1/1-148           UUGACCUGAUAAUGAGAAUAGUUAUUAUUACAC-CAACUGGUCGCGAGGCCAGCAGG-UAAGCUG-AGAGACCAAGCA-GUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UC-GACCCGGCACUUU-GCCGGGUCUUUUUUU-
BK005485.1/1-151           UUGACAUGGAAAUGAGAAUCAUUAUUAUGUCACUCAACUGGUCGCGAGAUCAGCCGG-UAAGCUG-AGAGACCCACGCAGUCGGACUCUUCAGAUUAUCUCCUCAUCAGGCUAAUCACGGUU-UUUGACCCGGCACUUU-GCCGGGUCUUU-UUUU
#=GC SS_cons               ::::::::::::::::::::::::::::::::::<<<<<<<<<____>>>>>>>>>,.,,,,<<<.<<<<-<______.___>-->>>>.>>>,,,,,,,<<<____>>>,,,,,,,,,,,,.,,,<<<<<<<<_____.>>>>>>>>::::::::
#=GC RF                    UUGACuuggAAAUGAuAAUuaUUAUuAUuucacuCggCuGguCGCGAGacCaGccGg.UAAaCuG.ggaGaCcuuagu.gUCGGaCucc.CaGAUUAUCUCCUCAUCAGGCUAAUCACGGUU.UUUGaCCCGGcuuUUU.gCCGGGuCUUUUUUUg
//
# STOCKHOLM 1.0

#=GF AC   RF00445
#=GF ID   mir-399
#=GF DE   mir-399 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   57.00
#=GF TC   57.00
#=GF NC   56.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0001020;
#=GF DR   MIR; MI0001021;
#=GF DR   MIR; MI0001022;
#=GF DR   MIR; MI0001023;
#=GF DR   MIR; MI0001024;
#=GF DR   MIR; MI0001025;
#=GF DR   MIR; MI0001053;
#=GF DR   MIR; MI0001054;
#=GF DR   MIR; MI0001055;
#=GF DR   MIR; MI0001056;
#=GF DR   MIR; MI0001057;
#=GF DR   MIR; MI0001058;
#=GF DR   MIR; MI0001059;
#=GF DR   MIR; MI0001060;
#=GF DR   MIR; MI0001061;
#=GF DR   MIR; MI0001062;
#=GF DR   MIR; MI0001063;
#=GF DR   MIR; MI0001064;
#=GF DR   MIR; MI0001065;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   15200956
#=GF RT   Computational Identification of Plant MicroRNAs and Their Targets,
#=GF RT   Including a Stress-Induced miRNA.
#=GF RA   Jones-Rhoades MW, Bartel DP
#=GF RL   Mol Cell 2004;14:787-799.
#=GF CC   mir-399 was identified in both Arabidopsis thaliana and Oryza sativa
#=GF CC   computationally and was later experimentally verified. mir-399 is thought
#=GF CC   to target mRNAs coding for a phosphatase transporter [1]. The mature
#=GF CC   sequence is excised from the 3' arm of the hairpin.
#=GF WK   mir-399_microRNA_precursor_family
#=GF SQ   13


AC021043.4/36317-36195   AAAUGCAUUACAGGGUAAGAUCUCUAUUGGCAGGAAAC-CAUUACU---------UAGAUCUUUGCAUCUCUU-----UAUGCAUU--GCUUUUAAUUAGUGAG------------UUAUCUGCCAAAGGAGAUUUGCCCUGUAAUUCUUCU
AC004481.3/15484-15601   AUAUGCAUUACAGGGCAAGAUCACCAUUGGCAGAGAUC-UAUUACU---------UCAUUCUU-GCAUCA--------UAUGCAUA--AAUGUUUGUGG-UGAG------------CUCUCUGCCAAAGGAGAUUUGCCCGGUAAUUCUCUU
AC004481.3/13564-13465   GGUUGGAUUACUGGGCGAAUACUCCUAUGGCAGA---------------------UCGCAUUGGCUAGAU---------AUGCAAG--UAAAAUGCUU--------------------CUCUGCCAAAGGAGAUUUGCCCCGCAAUUCAUCC
AC004481.3/13991-14099   GAAAGCAUUACAGGGCGAAUCCUCUAUUGGCAGUGG---AAGUUGA---------UGACCCUUAUAUGUU---------AU---UU--UCUCAUCAUU------U-----------UCCUCUGCCAAAGGAGAUUUGCCUCGCAAUGCUUCA
AP003142.2/99250-99133   ACAUGCAUUACCGGGUGAGU-CUUCCUUGGCAGUGUUC-GAAUCGG---------CAGUACCGGUCUGCAA-------GUGAUCGG--UCAAUCACCA--GUUC------------ACCGCUGCCAAAGGAGAUUUGCCCAGCAAUGCAACU
AP003142.2/100157-100305 CUGUGAAUUACAGGGC-AGUUCACCUUUGGCACAAGGGCAAGCAGUAGAAACCAUGCGUGCUUGCUAGAGCUGGAAAUGAUGCUGGU-AGCAUUGCAUG-GUUCAGGGAUCACAGAUCUCGUGCCAAAGGAGAAUUGCCCUGCGAUUUUGUC
AK108715.1/1199-1094     AGCUGCAUUGCUGGGCAAGUUGUCCUUUGGCAGAUGU------------------UGCAGUUCAUCAUCG---------AUGCCUG--GGGGUUACCA----GA------------CUA-CUGCCAAAGGAAAUUUGCCCCGGAAUUCAUUC
AC111015.2/21804-21909   AGCUGCAUUGCUGGGCAAGUUGUCCUUUGGCAGAUGU------------------UGCAGUUCAUCAUCG---------AUGCCUG--GGGGUUACCA----GA------------CUA-CUGCCAAAGGAAAUUUGCCCCGGAAUUCAUCU
AC111015.2/16598-16489   CGGCGAAUUACAGGGCGGUUUCUCCUUUGGCACGUACGGAGGCAAG---------GCAUGCGGUGAAA----------AAUCUCUA--------GCUA--GCCA-------------UGCGUGCCAAAGGAGAAUUGCCCUGCGAUUCACCA
AC111015.2/18487-18585   CCAUGCAUUACUGGGC-AGGUCUCCCUUGGCAGUGG------CCGA---------UCGAGCUGAUCA-----------AACCAC----GCAAAAG----------------------CCACUGCCAAAGGAGACUUGCCCAGCAAUGCAGAU
AP004030.2/66544-66659   GUGAGAAUCACAGUGCAGUU-CUCCUCUGGCAUGGA---GGGCAAG---------AGGAGCUGAAUAGCU--------AAUGGAUGA-UAAACUGCUA--GCCU------------UUCCCUGCCAAAGGAGAGCUGCCCUGCCAUUCAGUG
AP004030.2/91144-91262   AUGUGCAUUGCAGGGCAACUACUCCAUUGGCAGAGGGAUGGAUUGG---------AUAUGGAUAUGGCUG---------AUGCUUCCAUUUGAUCCCA--UCCC-------------UAUCUGCCAAAGGAGAUUUGCCCAGCGAUUCACUC
AP004030.2/79982-79886   GUGAGAAUCACAGUGCGAUU-CUCCUCUGGCAUGGC-------AUG---------AGAGGCCUAAAAAAGA-------GACGCACU-------------------------------GCCGUGCCAAAGGAGAAUUGCCCUGCCAUUCAGAA
#=GC SS_cons             ::::<<<<<-<<<<<<<<<--<<<<--<<<<<<<<<__._______........._______________........________..__________..____............_>>>>>>>>>-->>>>->>>>>>>>>->>>>>::::
#=GC RF                  augUGcAUuACaGGGCaAuUUCuCCuUUGGCAggggug.aAguagu.........ucgugCUuauuAgag........gAUGcaug..uauauUgcua..guuc............uccccUGCCAAAGGaGAaUuGCCCuGCaAUgCauuu
//
# STOCKHOLM 1.0

#=GF AC   RF00446
#=GF ID   mir-133
#=GF DE   mir-133 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   42.00
#=GF TC   43.20
#=GF NC   41.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000159;
#=GF DR   MIR; MI0000362;
#=GF DR   MIR; MI0001206;
#=GF DR   MIR; MI0000450;
#=GF DR   MIR; MI0001248;
#=GF DR   MIR; MI0000451;
#=GF DR   MIR; MI0001255;
#=GF DR   MIR; MI0000820;
#=GF DR   MIR; MI0001325;
#=GF DR   MIR; MI0000821;
#=GF DR   MIR; MI0000822;
#=GF DR   MIR; MI0000906;
#=GF DR   MIR; MI0001195;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol 2002;12:735-739.
#=GF CC   mir-133 was first experimentally characterised in mouse [1] and homologues
#=GF CC   have since been discovered in several other species. The mature sequence
#=GF CC   is excised from the 3' arm of the hairpin.
#=GF WK   mir-133_microRNA_precursor_family
#=GF SQ   46


AL929326.9/103254-103340     AAUGCUUUGCU----AAAGCUGGU-AAAAUGGAACCAAAUC----ACCUCUUCAA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUAUGCUUUGAU
AL672157.5/51527-51613       AAUGCUUUGCU----GAAGCUGGU-AAAAUGGAACCAAAUC----AGCUGUUGGA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUGCGCAUUGAU
AL449263.6/10756-10670       AAUGCUUUGCU----AGAGCUGGU-AAAAUGGAACCAAAUC----GACUGUCCAA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUGUGCAUUGAU
AL391221.15/84070-84157      UGCCCCCUGCU----CUGGCUGGU-CAAACGGAACCAAGUC---CGUCU-UCCUGAGA----G-GUUU--GGUCCCCUUCAACCAGCUACAGCAGGGCUGGCAA
BX276101.6/114604-114519     -ACGCCUUGCU----GUGGCUGGU-CAAAUGGAACCAAGUC---AGGUGUUUCUGCGA----G-GUUU--GGUCCCCUUCAACCAGCUACUGC--GUCGUGAAU
AC105947.11/187380-187294    AAUGCUUUGCU----AAAGCUGGU-AAAAUGGAACCAAAUC----GCCUCUUCAA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUAUGCAUUGAU
AAVX01266048.1/613-699       GAUGUUUUGCU----GAAGCUGGU-AAAAGAGAACCAGAUC----GAUUGUUACA-CG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUGUGCAUUCAU
AAPN01261137.1/7422-7509     UGAACCCUGCU----CUGGCUGGU-CAAACGGAACCAAGUC---CGUCUGCCUGA-GA----G-GUUU--GGUCCCCUUCAACCAGCUACAGCGGGGCCGACAU
CAAE01015003.1/756593-756507 CACGCCUUGCU----GUGGCUGGU-CAAACGGAACCAAGUC---AGGUGUUUCUGUGA----G-GUUU--GGUCCCCUUCAACCAGCUACUGC--GUCGGCACA
AC147912.2/162581-162667     AAUGCUUUGCU----AAAGCUGGU-AAAAUGGAACCAAAUC----ACCUCUUCAA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGGAUUGCAUUGAG
AALT01338720.1/1443-1531     UGCCCCUUGCU----CUGGCUGGU-CAAACGGAACCAAGUC---CGUCUUCCUCA-GA----G-GUUUUGGGUCCCCUUC-ACCAGCUACAGCAGGGCUGGGCC
AAIY01559715.1/853-939       GAUGCUUUGCU----AGAGCUGGU-AAAAUGGAACCAGAUC----GGCCGUAUGA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUGCGCAUUGAG
AAYZ01364872.1/887-973       AAUGCUUUGCU----AAAGCUGGU-AAAAUGGAACCAAAUC----GACUCUGCAA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUGCGCAUUGAC
AAPN01136163.1/2110-2024     GGCCAGCUGCU----GGGGCUGGU-CAAAAGGAACCAGAUC----GCCUCUCCAC-CU----G-AUUU--GGUCCCCUUCAACCGGCUGCAGCGGGUUGCCGGC
AAVX01020289.1/2798-2712     AAUGCUUUGCU----AAAGCUGGU-AAAAUGGAACCAAAUC----AACUAUUCUA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUGCGCAUUGAU
AAFR03005395.1/22086-22172   AAUGCUUUGCU----AAAGCUGGU-AAAAAGGAACCAAAUC----ACCUGUGCGA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUGUGCAUUAAU
AAQQ01431588.1/1752-1838     AAUGCUUUGCU----GAAGCUGGU-CAAAUGGAACCAAAUC----GGCUGCUCAC-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUGCGCAUUGAC
CAAE01007044.1/175-261       AAUGCUUUGCU----GCAGCUGGU-CAAAUGGAACCAGAUC----UCCUUCUGUC-UG----G-AUUU--GGUCCCCUUCAACCAGUUGCAGCAUUGACGUCCU
AAFR03002451.1/32623-32536   UGCACCUUGCU----CUGGCUGGU-CAAACGGAACCAAGUC---CGUCUGACUGA-GA----G-GUUU--GGUCCCCUUCAACCAGCUACAGCAGGGCUGACAU
AAIZ01001189.1/55294-55207   AACGGCUGUAU----GUAGCUGGUUGACAUCGGGUCAGAUC----UAUUUUAUCA-AG----U-AUUU--GGUCCCCUUCAACCAGCUGUAUCAGUGGUUGAUU
AASW01052175.1/117-202       AACGCUGUG-U----GUAGCUGGUUGACAUCGGGUCAGAUC----UGUUUUUUAA-GC------AUUU--GGUCCCCUUCAACCAGCUGUAGCCAGUGGUUGCU
AAZX01000650.1/47832-47922   AAUGUUAAGCU-----UAGCUGGUUGAACACGGGUCAAAUAUAACGCACGAUUGA-CG----C-AUUU--GGUCCCCUUCAACCAGCUGUAGUUGACAUUAGUC
AAPT01020977.1/40328-40419   UUUACAACGCUGUAUGUAGCUGGUUGACAUCGGGUCAGAUC----UAUUUAUUCG-AG----U-AUUU--GGUCCCCUUCAACCAGCUGUAGCAGUGGUUGAUG
AANI01016239.1/47521-47435   AACGCUGUG-U----GUAGUUGGUUGACAUCGGGUCAGAUC----UAUUUCUGAA-AG----C-AUUU--GGUCCCCUUCAACCAGCUGUAGCAGUGGUUGAAG
AAZO01007144.1/88847-88936   AAUGCUCUUCU----UUAGCUGGUUGACGCCGGGCCAAGUUU--AGCCGAUUCGA-GU----C-AUUU--GGUCCCCUUCAACCAGCUGUAGUUGGCAUUUAGA
AADK01000091.1/43441-43353   CGUUGUUCGCU----UUAGCUGGUUGACUUCGGGUCAAAUU----GUCAUUUUCAUAU----C-AUUU--GGUCCCCUUCAACCAGCUGUAGUUAACAUCUGCU
AAPU01010689.1/170290-170375 AACGCUGUG-U----GUAGUUGGUUGACAUCGGGUCAGAUC----UGUUUUUCGA-GA------AUUU--GGUCCCCUUCAACCAGCUGUAGCAGUGGUUGAUG
AAQB01006401.1/332784-332872 CAACACUGAAU----GUAGCUGGUUGACAUCGGGUCAGAUC----UAUUUAUUUG-AA----GCAUUU--GGUCCCCUUCAACCAGCUGUAGCAGUGGUUGAUC
AACT01005834.1/3375-3295     CUUGUGACGGU------UGUUGGU--AAAGAGGAUCGAACC----UGAA-AAAUG-AU----G-GUUU--GGUCCCCUUCAACCAGCU--ACCGAUGCAACGCA
AAJJ01000046.1/77209-77292   AAUGUGCAGCU----UUAGCUGGUUGAAUCCGGGUCAAAU--------UGUAAAU-GC----U-AUUU--GGUCCCCUUCAACCAGCUGUGGUUGACAUUGCGA
AANH01006842.1/37352-37440   CACGCCUUGCC----GUGGCUGGU-CAAACGGAACCAAGUC---AGGUGUUUCUG-UG---AG-GUUU--GGUCCCCUUCAACCAGCUACUGCGCCGUGAAUUC
AABS01000844.1/21320-21411   UGCGGGUGUCG----GUCGUUGGU-AAAGUGGAAUCAAACC---UUACGGUUUUA-GUCCAUG-GUUU--GGUCCCCUUCAACCAGCUGCUGCUACCACGCACA
AAPP01015693.1/86515-86606   UCUGCAACGCUGUAUGUAGCUGGUUGACAUCGGGUCAGAUC----UAUCUUUUCA-AG----C-AUUU--GGUCCCCUUCAACCAGCUGUAGCAGUGGUUGAUG
AAEU02000272.1/43410-43324   AACGCUGUG-U----GUAGCUGGUUGACAUCGGGUCAGAUC----UGUUUUUCCA-AG----C-AUUU--GGUCCCCUUCAACCAGCUGUAGCCAGUGGUUGAU
BAAF04047944.1/3038-2950     CUCGCCUUGCU----GUGGCUGGU-CAAACGGAACCAAGUCA--GGUGUUUCAGA-GA----G-GUUU--GGUCCCCUUCAACCAGCUACUGCGUCGUGAAUCA
CAAK05040482.1/11317-11401   CACGGCUUAGU------UGCUGGU-AAAACGGAACCAAGUC---GGGUGUUUGCGAGA----G-GUUU--GGUCCCUUUCAACCAGCU--ACUGCGCCGUGAAU
AY865868.1/428-514           AAUGCUUUGCU----AGAGCUGGU-AAAAUGGAACCAAAUC----GCCUCUUCAA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUAUGCAUUGAU
FJ469647.1/6244-6331         GGCCCCCUGCU----CUGGCUGGU-CAAACGGAACCAAGUC---CGUCUUCCUGA-GA----G-GUUU--GGUCCCCUUCAACCAGCUACAGCAGGGCUGGCAA
AY865870.1/382-467           AAUGCUUUGCU----AGAGCUGGU-AAAAUGGAACCAAAUC----GCCUCUUCAA-UG----G-AUUU--G-UCCCCUUCAACCAGCUGUAGCUAUGCAUUGAU
AY865873.1/326-412           AAUGCUUUGCU----AGAGCUGGU-AAAAUGGAACCAAAUC----GCCUCUUCAA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUAUGCAUUGAC
AADN03008235.1/118737-118822 GGUGCCUUCCU----GGGGCUGGU-AAAAAGGAACCAGAUC----AACU-ACAAC-UG----G-AUUU--GGUCCCCUUCAACCAGCUGCAGUGGGGCACGAGG
AAGJ04155436.1/18887-18799   AAUGUAGCGCU----UUAGCUGGU-AAACGGGAACCAAAUCG--UGAAGUAAAUG-CG----G-AUUU--GGUCCCCUUCAACCAGCCGUAGCACUGCAUUCUA
AAWZ02017015.1/25332-25245   UGAGUCCUGCU----CUGGCUGGU-CAAAGGGAACCACGGC---UGUCUUCCUUG-AA----G-GUUU--GGUCCCCUUUAACCAGCUACAGCAGUCCUGAUAU
AAWZ02024324.1/1942-2028     UAUGUGUCCCU----AGGGCUGGU-AAAAAGGAACCAGAUC----GACUGGCAAC-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUGGUGGCACGUGAAA
AAWZ02009612.1/61633-61719   GAUGCUUUGCU----AAAGCUGGU-AAAAUGGAACCAAAUC----ACCUGUUAAA-UG----G-AUUU--GGUCCCCUUCAACCAGCUGUAGCUAUGUAUUGAU
AADN03003607.1/197879-197966 UAUGCUCUGCU----CUGGCUGGU-CAAACGGAACCAAGCC---CGUCUUCUUCG-GA----G-GUUU--GGUCCCCUUCAACCAGCUAUAGCAGUGUUGAAAA
#=GC SS_cons                 ::::::::<<<....--<<<<<<<.------<<<<<<<<<<....__________.__....>.>>>>..>>>----->>->>>>>>>-->>>:::::::::::
#=GC RF                      aauGcuuugCu....guaGCUGGU.aAAAugGAACCAaAuc....gacuuuuuua.ug....g.aUuU..GGUCCCCUUCAACCAGCuGUaGcugugcuuuaau
//
# STOCKHOLM 1.0

#=GF AC   RF00447
#=GF ID   IRES_Kv1_4
#=GF PI   IRES_Kv1.4
#=GF DE   Voltage-gated potassium-channel Kv1.4 IRES
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Published; PMID:15339906
#=GF SS   Predicted; RNAalifold
#=GF GA   100.00
#=GF TC   121.30
#=GF NC   99.80
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   15339906
#=GF RT   Structurally distinct elements mediate internal ribosome entry within the
#=GF RT   5'-noncoding region of a voltage-gated potassium channel mRNA.
#=GF RA   Jang GM, Leong LE, Hoang LT, Wang PH, Gutman GA, Semler BL
#=GF RL   J Biol Chem 2004;279:47419-47430.
#=GF CC   This family represents the Kv1.4 voltage-gated potassium-channel internal
#=GF CC   ribosome entry site (IRES). This region has been shown to mediate internal
#=GF CC   ribosome entry in cells derived from brain, heart, and skeletal muscle,
#=GF CC   tissues known to express Kv1.4 mRNA species [1].
#=GF WK   Voltage-gated_potassium-channel_Kv1.4_IRES
#=GF SQ   6


U03723.1/645-902         UAAGUUUGAGGAACACUAGGC-GUUGUCUAGACGAGGCAAGCUCUGGAAAGCAACGCCGAGUCUCUGAGAAGAGGGAG-CAUGGGGUGUGCUGAUUUAAAAACAGAAAAUGCAAAGUUGGA-CUGAAAA-UAUCCCACGUCUUCUAAGCAAUCUGCUUAAGGCUUCCAAACUUACCUUAAUUUGGUAAGAAAAUAAGCUGCCCUAUUUUUCUUUCUUCUUCUCUUACAACUGGAACCAGGCAUUUCCA-AAACCACCACCAUG
BX293548.5/121402-121143 UAUGUUUGAGGAACACUAGGCUGUUGUCUAGACGAGGCAAGCUCUGGAAAGCAACGCCGAGUCUCUGAGAAGAGGGAG-CAUAGGCUGUGCUGAUUUAAAAACAGAAAAUGCAAAGUUGGA-CUGAAAA-UAUCCCACGUCUUCUAAGCAAUCUGCUUAAGGCUUCCAAACUUACCUUAAUUUGGUAAGAAAAUAAGCUGCCCUAUUUUUCUUUCUUCUUCUCUUACAACUGGAAGCAGCCAUUUCCCCAAACCACCACCAUG
U06156.1/48-307          UGGGCUUGAGAGUGCUAGGUUGUUUAUCUAGACCAGCCAAGCUCUGGAGAGCAAUGUUGAAUCCCUGGGAACAGAGAG-CAUGGGGCGUACUGAUUUAAAAACAGAAAAUGCAAAGUUGGA-CUGAAAA-UAUCCUUAGUCUUCCAAGCAAUCUGCUUAAGGGUUCCAAACUUACCUUAAUUUGGUGAGAAAAGAAGCUGCCCUAUUUUUCUUUCUUCUUCUUCUACAACUGGAACCAGCCAUUUCCAAAAACCACCACCAUG
X16002.1/236-494         AUGUUUGAGGAGCACUAGGCU-GUUGUCUAGACUAAGCAAGCUCUGGAAAGCAAUGCUGAGUCUCUGAGAAGAGGGAG-CAUGGGGUGUGCUGAUUUAAAAACAGAAAAUGCAAAGUUGGA-CUGAAAA-UAUCCCAAGUCUUCUAAGCAAUCUGCUUAAGGCUUCCAAACUUACCUUAAUUUGGUAAGAAAAUAAGCUGCCCUAUUUUUCUUUCUUCUUCUCUUACAACUGGAACCAGCCAUUUCCCCAAACUACCACCAUG
M55514.1/896-1157        UAGUCUUGAGAGUGCCAGGCUAUUUAUCUCGACCAGCCAAGCUCUGGAGAGCAAUGUUGAAUCCCUGAGAAGAGAGAGGCAUGGGGCGUGCUGAUUUAAAAACAGAAAAUGCAAAGUUGGAGCUGAAAA-UAUCCUUAGUCUUCCAAGCAAUCUGCUUAAGGGUUCCAAACUUACCUUAAUUUGGUGAGAAAAGAAGCUGCCCUAUUUUUCUUUCUUCUUCUUCUACAACUGGAACCAGCCAUUUCCGAAAACCACCACCAUG
X57033.1/213-453         UUUACUUGA-AGUGCCAGGC----CAUCU------------CUCUGGAGAGCAACGUUGAAUCCCUGAGAAGAGAGAG-CAUGGGGCGUGCUGAUUUAAAAACAGAAAAUGCAAAGUUGGA-CUGAAAAAUAUCCUUCAUCUUCCAAGCAAUCUGCUUAAGGGUUCCAAACUUACCUUAAUUUGGUGAGAAAAGAAUCUGCCCUAUUUUUCUUUCUUCUUCUC---CAACUGGAACCAGCCAUUUCCCCAAACCGCCACCAUG
#=GC SS_cons             :::::::::::::::::::::::::::::::::::::::::::::(((((----------------((((((((((((.-((((((((-(((--(((,,,,,<<<<---<<<----<<<<<.--<<___._________>>->>>>>>>>->>>>,,,,,,,,,,,,,,,<<<<<<_______>>>>>>,)))--)))))))))))--))))))))))))----------------------)))))::::::::::::::::
#=GC RF                  uauuuUuGAGagugccagGuuagUUaUCUaGACuAggCAAGCUCUGGaaaGCAAuGuuGAaUCuCUgaGaaGagaGag.CaugGGGcgUGcuGAuuuAAAAACaGaAAAuGCAAAGuugGa.CUGaAAA.UAUCCuuaGuCUuCcaaGCaAuCuGCUUAAGGgUUCCAAACuuaCCUUAAUUUGGuaaGAaaauAagCugCCCuauUUuuCuuuCuuCuuCUcuUACAACUGGAAcCAGcCAuuuCCaaAAACcACCACCAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00448
#=GF ID   IRES_EBNA
#=GF DE   Epstein-Barr virus nuclear antigen (EBNA) IRES
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Published; 12555070
#=GF SS   Predicted; PFOLD
#=GF GA   100.00
#=GF TC   220.30
#=GF NC   32.00
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   12555070
#=GF RT   Epstein-Barr virus U leader exon contains an internal ribosome entry site.
#=GF RA   Isaksson A, Berggren M, Ricksten A
#=GF RL   Oncogene 2003;22:572-581.
#=GF CC   This family represents an Epstein-Barr virus internal ribosome entry site
#=GF CC   (IRES) which is found in the U leader exon in the 5' UTR of the
#=GF CC   Epstein-Barr nuclear antigen 1 (EBNA1) gene. The EBNA IRES allows EBNA1
#=GF CC   translation to occur under situations where initiation from the 5' cap
#=GF CC   structure and ribosome scanning is reduced. It is thought that the EBNA
#=GF CC   IRES is necessary for the regulation of latent gene expression [1].
#=GF WK   Epsteinâ€“Barr_virus_nuclear-antigen_internal_ribosomal_entry_site
#=GF SQ   6


AY037858.1/48958-49174 ----UCAGCUGAUCGUUGUUGUCAUUCUUCAAUUUUUGCAGGUAACUCAGAAAGCGUUUCUUGAGCUUCCCGGGGAUGAGCGUCUGGGAGAGCUGAUUCUGCAGACCGGCUAGGAGCCGCAGGGCGUUCUCCGGGGCGCGGCCCGAGACCGUCGCGUCGUAGACAGCCAGGAGACCCGGGAGCAGAUUCACCGCAGCGGCCGUCUCCCUCAAGGUGCUGUG
AF448220.1/5364-5580   ----UGAGCUGAUCGUUGUUGUUAUUCUUCAAUUUCUGCAGGUAACUUAGGAAGCGUUUCUUGAGCUUCCCUGGGAUGAGCGUUUGGGAGAGCUGAUUCUGCAGCCCAGAGAGUAGUCUCAGGGCAUCCUCUGGAGCCUGACCUGUGAYCGUCGCAUCAUAGACCGCCAGUAGACCUGGGAGCAGAUUCACCGCCGCGGCCGUCUCCUUUAAGGUGCUGUG
M12553.1/318-517       ----AGAGGAUGAAGACUAAGUCACAGGCUUA----GCCAGGUAACUUAGGAAGCGUUUCUUGAGCUUCCC-------------UGGGAGAGCUGAUUCUGCAGCCCAGAGAGUAGUCUCAGGGCAUCCUCUGGAGCCUGACCUGUGAUCGUCGCAUCAUAGACCGCCAGUAGACCUGGGAGCAGAUUCACCGCCGCGGCCGUCUCCUUUAAGACCCCACC
S45894.1/393-608       AAAAGGCGCGGGAUAGCGUGCGCUACCGGAUG-----GCGGGUAACUUAGGAAGCGUUUCUUGAGCUUCCCUGGGAUGAGCGUUUGGGAGAGCUGAUUCUGCAGCCCAGAGAGUAGUCUCAGGGCAUCCUCUGGAGCCUGACCUGUGAUCGUCGCAUCAUAGACCGCCAGUAGACCUGGGAGCAGAUUCACCGCCGCGGCCGUCUCCUUUAAGUGUGAAUC
M23028.1/471-674       ----GGG-------------CCCCCCGGUAUCGGGCCAGAGGUAACUUAGGAAGCGUUUCUUGAGCUUCCCUGGGAUGAGCGUUUGGGAGAGCUGAUUCUGCAGCCCAGAGAGUAGUCUCAGGGCAUCCUCUGGAGCCUGACCUGUGAUCGUCGCAUCAUAGACCGCCAGUAGACCUGGGAGCAGAUUCACCGCCGCGGCCGUCUCCUUUAAGACCCACCA
M13941.1/141-357       ----GUGGUGUAAAGUUUUGCCUGAACCUGUGGUUGGGCAGGUAACUUAGGAAGCGUUUCUUGAGCUUCCCUGGGAUGAGCGUUUGGGAGAGCUGAUUCUGCAGCCCAGAGAGUAGUCUCAGGGCAUCCUCUGGAGCCUGACCUGUGAUCGUCGCAUCAUAGACCGCCAGUAGACCUGGGAGCAGAUUCACCGCCGCGGCCGUCUCCUUUAAGUGUGAAUC
#=GC SS_cons           ....<<<______________>>>-----------------------------[[[,,,,,,(((,,<<<<______________>>>>,,,,,<<----<<---<<______________>>>>->>))),((---(((,,<<<<<<<______>>>>>>>,,,,<<<<_____>>>>,,,)))-----)),,]]]::::::::::::::::::::::::
#=GC RF                ....gggGcugaaaguuguugcccuucuuauauuuuugcAGGUAACUUAGGAAGCgUUUCUUGaGCUuCCCuGGGAUGAGCGUuUGGGaGAGCUGaUUCUGCAGcCCAGAgAGuAGUCuCAGGGCAuCCuCUGGAGCCuGACCuguGauCGUCGCauCauaGACcGCCaGuAGACCuGGGAGCaGAUUCACCGCcGCGGCCGUCUCCUUUAAGauucaaua
//
# STOCKHOLM 1.0

#=GF AC   RF00449
#=GF ID   IRES_HIF1
#=GF DE   HIF-1 alpha IRES
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   http://ifr31w3.toulouse.inserm.fr/IRESdatabase/, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   110.00
#=GF TC   121.40
#=GF NC   105.10
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   12006670
#=GF RT   Hypoxia-inducible factor-1alpha mRNA contains an internal ribosome entry
#=GF RT   site that allows efficient translation during normoxia and hypoxia.
#=GF RA   Lang KJ, Kappel A, Goodall GJ
#=GF RL   Mol Biol Cell 2002;13:1792-1801.
#=GF CC   This family represents the hypoxia-inducible factor 1-alpha internal
#=GF CC   ribosome entry site. HIF-1a is a subunit of the HIF-1 transcription
#=GF CC   factor, which induces transcription of several genes involved in the
#=GF CC   cellular response to hypoxia. The HIF-1a IRES allows translation to be
#=GF CC   maintained under hypoxic cell conditions that inhibit cap-dependent
#=GF CC   translation [1].
#=GF WK   HIF-1_alpha_IRES
#=GF SQ   17


AF003695.1/1-260           ---------------CGCG-AGG-ACUGUCCU---CGCCGCCGUCGCGGGCAGUGUCUA--GCCAGGCCUUGACAAGCUAGCCGGAG-G---A--GCGCC---UAG---GAACCC-GAGCCGGAGCUCAGCGAGC-----GCAGCCUGCA-CGCCCGCCUCGC--GUCCCG-GGGG-G---GUCCCGC-CUCCCACCCCG--CCUCUGGACUUGUCUCU---UUCCCCGC----------------GCGCGCGGACAGAGCCGGCGUUUAGGCCC-GAGCGAGCCC--GGGGGCCGCCGGCCG-GGAAGACAACGCGGGCACCGAUUCGCCAUG
AC124712.5/89561-89837     CUCGGCUG-AGGGGACGCG-AGG-ACUGUCCU---CGCCGCCGUCGCGGGCAGUGUCUA--GCCAGGCCUUGACAAGCUAGCCGGAG-G---A--GCGCC---UAG---GAACCC-GAGCCGGAGCUCAGCGAGC-----GCAGCCUGCAGCUCCCGCCUCGC-CGUCCCG-GGGG-G--CGUCCCGC-CUCCCACCCCG--CCUCUGGACUUGUCUCU---UUCUCCGC----------------GCGCGCGGACAGAGCCGGCGUUUAGGCCC-GAGCGAGCCC--GGGGGCCGCCGGCCG-GGAAGACAACGCGGGCACCGAUUCGCCAUG
U29165.1/1-267             ---------------CACG-AGGCAGCACUCU---CUUCGUCGCUUCGGCCAGUGUGUCGGGCUGGGCCCUGACAAGCCA-CCUGAG-G---A--GAGGC---UCG---GAGCCG-GGCCCGGACCCCGGCGAUU-----GCCGCCCGCUUCUCUCUAGUC-----UCACG-AGGG-G--UUUCCCGC-CUCGCACCCCC-ACCUCUGGACUUGCCUUUC-CUUCUCUUCUC-------------CGCGUGUGGAGGGAGCCAGCGCUUAGGCCG-GAGCGAGCCU--GGGGGCCGCCCGCCG-UGAAGACAUCGCGGGGACCGAUUCACCAUG
AL137129.4/84771-85050     CUCGUCUG-AGGGGACAGG-AGG-AUCACCCU---CUUCGUCGCUUCGGCCAGUGUGUCGGGCUGGGCCCUGACAAGCCA-CCUGAG-G---A--GAGGC---UCG---GAGCCG-GGCCCGGACCCCGGCGAUU-----GCCGCCCGCUUCUCUCUAGUC-----UCACG-AGGG-G--UUUCCCGC-CUCGCACCCCC-ACCUCUGGACUUGCCUUUC-CUUCUCUUCUC-------------CGCGUGUGGAGGGAGCCAGCGCUUAGGCCG-GAGCGAGCCU--GGGGGCCGCCCGCCG-UGAAGACAUCGCGGGGACCGAUUCACCAUG
BC026139.1/3-278           CGCGUCC--GGGGGACGCG-AGG-ACUGUCCU---CGCCGCCGUCGCGGGCAGUGUCUA--GCCAGGCCUUGACAAGCUAGCCGGAG-G---A--GCGCC---UAG---GAACCC-GAGCCGGAGCUCAGCGAGC-----GCAGCCUGCAGCUCCCGCCUCGC-CGUCCCG-GGGG-G--CGUCCCGC-CUCCCACCCCG--CCUCUGGACUUGUCUCU---UUCUCCGC----------------GCGCGCGGACACAGCCGGCGCUUAGGCCC-GAGCGAGCCC--GGGGGCCGCCGGCCG-GGAAGACAACGCGGGCACCGAUUCGCCAUG
BX648795.1/1-268           -------------GACAGG-AGG-AUCACCCU---CUUAGUCGCUUCGGCCAGUGUGUCGGGCUGGGCCCUGACAAGCCA-CCUGAG-G---A--GAGGC---UCG---GAGCCG-GGCCCGGACCCCGGCGAUU-----GCCGCCCGCUUCUCUCUAGUC-----UCACG-AGGG-G--UUUCCCGC-CUCGCACCCCC-ACCUCUGGACUUGCCUUUC-CUUCUCUUCUC-------------CGCGUGUGGAGGGAGCCAGCGCUUAGGCCG-GAGCGAGCCU--GGGGGCCGCCCGCCG-UGAAGACAUCGCGGGGACCGAUUCACCAUG
Y13656.1/1406-1682         CUCGGCUG-AGGGGACGCG-AGG-ACUGUCCU---CGCCGCCGUCGCGGGCAGUGUCUA--GCCAGGCCUUGACAAGCUAGCCGGAG-G---A--GCGCC---UAG---GAACCC-GAGCCGGAGCUCAGCGAGC-----GCAGCCUGCAGCUCCCGCCUCGC-CGUCCCG-GGGG-G--CGUCCCGC-CUCCCACCCCG--CCUCUGGACUUGUCUCU---UUCUCCGC----------------GCGCGCGGACAGAGCGGGCGCUUAGGCCC-GAGCGAGCCC--GGGGGCCGCCGGCCG-GGAAGACAACGCGGGCACCGAUUCGCCAUG
AAHX01045099.1/3401-3678   CUCGUCUG-AGGGGACGCG-AGG-ACUGUCCU---CGCUACCGUCGCGAGCAGUGUCUG--GCCAGGCCUUGACAAGCCAGCCGGAG-G---A--GCAAC---UAG---GAACCC-GAACCAGAGCCCGGCGAGC-----GCAGCCUGCAGCUCCCGCCUCGC-CGUCCCG-GGGG-G-GUGUCCCGC-CUCACACCCCG--CCUCUGGACUUGCCCCU---UUCUCUGC----------------GCGUGAGGACAGAGCCGGCGCUUAGGCCG-GAGCGAGCCC--AGGGGCUGCCGGCCG-GGAAGACACCGCGGGCACCGAUUCGCCAUG
AANU01200208.1/36718-36435 CUCGUCUG-AGGGGACAAG-AGG-AUCACCCU---CGCCGUCGCUUCGGCCAGUGCGUCGGGCUGGGCCCUGACAAGCCA-CCUGAG-G---A--GAGGU---UCG---GAGCCG-GGCCCGGACCCCGGCGAUU-----GCCGCCCGCUUCUCCUGCUUCUG--GUCUCA-CGAG-GUGUUUCCCGC-CUCGCACCCCC-ACCUCUGGACUUGCCUUGC-CUUCUCUCUCC--------------GCGUGUGGAGGGAGCCAGCGCUUAGGCCG-GAGCGAGCCU--GGGGGCCGCCCGGCG-UGAAGGCAUCGCGGGGACCGAUUCACCAUG
AAPY01808891.1/325-590     CUUGUCU--GAGGG-CAC--GGG-AGGAUCUU---AUUAGUC---------AGUGUGUCA-GCUGGGCCCUGACAAGCAG-CCCGAG--------GAGGC---UCU---GAACCG-AGCCUGGAGCUCCACGACU-----GCCGCUUGCACCUCCUGCGCCUGGUUUUGCG-AGGG-G--UUUCCCGC-CUCGCACCCCU-ACCUCUGGACUUGCCUCU---CCUCGCUCC---------------ACGUGUGCAGGGAGCCAGCACUUAGGCCA-GAGCGAGCCU--GGGAGCCGCCAGCCG-UGAAGGCAUCAUGGAGACCGAUUCGCAUGG
AANN01688922.1/883-596     CUCGGCUG-AGGGGACGCG-AGG-AUUCCGGU---CGCCAGUGCUUCGGGCCCGGCCCG--GACG---CUUAGCAAGCUA-CCUGAG-G---AGCGGCUC--UUCG---GAGCCG-AACCUGGAUCCCCGGGACUGAACUGCAGCCUGCUCUUCCUGCCUCUGUUCUCACG-AGGG-G--GCUCCCGU-CUCGCACCCCA--CCUCUGGACGUGCCUCCC--UUUCCCUCUCU-----------CCGCGUGCGGAGGGAGCCAGCGCAUAGGCCG-GAGCGAGCCU--GGGGGCCGCCGGCCG-CGAAGGCUUCGCGGGCACCCGUUCGCCAUG
AALT01574306.1/1321-1607   CCUAGCGUGAGGGGACGCG-AGG-AUCGAGC----CGCCGCCGCUUCUGCCGGUGCGUC--G---GGCCCUGACAAGCAGCCGCGAGAG---A--GGCUC--UUCG---GAGGCG-GCCCUGCAGCCCAGCGAUU-----GUCGCCUGGG-GUCUC----------ACGAG-GGAUUG--GCCGCCGCGCACCCCAGCCC--UGUCUGGACGUGCCUCCCCUUUCUCUCUCCCUCUCGCUCUCCCCUUGUGCGGAGGCAGCCAGCGGCUUUGGAC-GGGCGAGCCU--GGGGGCCGCCGGCCA-CGAAGGCUUCGCCGGGACCCAUUCACCAUG
AAGV020185138.1/939-1224   UUGUUUG--AGGGAACCGG-AGG-GUCGCCCU---CGGCGCCGCUUGGGCCAGUGUUUCGGGGCCGGCCCUGACAAGCAG-CCCGAG-G---A--GGGCC---UCGAACGACUCA-AACCUGGACUUCUGCGAUU-----GUCGCUUCCUUUUCCUGCCUCUG--AGCUCG-GGAG-GGGUUUCCCGC-CUCGCAGCCCCCGCCCCUGGACUUGCUUCUC-CUCCUCCCUCU--------------GCGUGUGGAGGGAGCCAACGCUUAGGCCG-GAGCGAGCCU--AGGGGCCGCCGGCCG-UGAGG-CCGCUCGGGGGCCUGUUCGCCAUG
AB169332.1/16-299          CUCGUCUG-AGGGGACAAG-AGG-AUCACCCU---CGCCGUCGCUUCGGCCAGUGCGUCGGGCUGGGCCCUGACAAGCCA-CCUGAG-G---A--GAGGU---UCG---GAGCCG-GGCCCGGACCCCGGCGAUU-----GCCGCCCGCUUCUCCUGCUUCUG--GUCUCA-CGAG-GUGUUUCCCGC-CUCGCACCCCC-GCUUCUGGACUUGCCUUGC-CUUCUCUCUCC--------------GCGUGUGGAGGGAGCCAGCGCUUAGGCCG-GAGCGAGCCU--GGGGGCCGCCCGGCG-UGAAGGCAUCGCGGGGACCGAUUCACCAUG
HM125970.1/11-290          CUCGUAUG-AGGGGACGGG-AGG-ACUGUCCU---UGCUGCCGUGGUGGGCAGUGGCUG--GCCAGGCCCCGACAAACGAGCCCGAG-G---A--GCUCC---UGG---GAGCCC-GAGCCGGAGCCGGGCGAGC-----GCAGCUUGCAGCUCCCGCCUCGC-CGUCCCG-GGGG-G-GCGUCUCGC-CUCGCACCCCG--CCUCUGGACUUGCCCCU---UUCUCUGG----------------GCGUGCGGACCGAGCCAGCGCUUAGGCCGUGAGCGAGCCC--GGGGGCCGCCGGCGGGGGAAGGCACCGCGGGCACUGAUUCGCCAUG
AAEX03005770.1/1176-1468   CUCGUCUG-AGGGGACGCG-AGG-AUCGGCCUGGUCGCCGCCGCUUGGGCCAGCGCGUCGGCUCGGGCCUUGACAAGCCG-CCCGAG-G---G--GAGGCUCUCCG---GAGCCUAGAGCUGGACCCUAGCGAUC-----GCCGCCCGCC-CUUCCUGCCCGC--GUUCUGCGAGGGG--UUUCCCGC-CUUGCACCUCCCACCUCGGGACGUGCCUCCG--CUCCCCUCGU-------------CGCGUGCGGAGGGAGCCAGCGCUUAGGCCG-GAGCGAGCCUGGGGGGGCUACCGGCCG-GGAAGGCUUCGCGGGGACCGAUUCGCCAUG
AAPE02031378.1/50562-50292 CUCGUCCG-AGGGGACGCGGAGC-AUCGCC-U---CGUCGCCGCUGCAGUCAGUCGCCCG-GCCGGGCCUUGACAAGCUG-CCGGAG-GGGAG--GCUCC---UCU---GAGCCC-GUCCCGGAGUCCCGCGGCU-----GCCGCCGGUUCCUCCAGCGUCUG--GUCUCA-CGAG-G--GGCUGCG-----------CA--CCGCUGGACGCGCCUCUC-CUUCUCUCCCC--------------GCGCGCGGAGAGAG-CG-AGCUUAGGCCG-CAGCGAGCCU--GGGGGGCGCCGGCCG-UGAAGGCAUCGCGGCGACCGAUUCGCCAUG
#=GC SS_cons               <<<_____.__>>>,,<<<.<<<._____>>>...>>>,<<<__________________.____>>>,,,,,,,,,,,,.,,,,,,.,...,..<<<-<...---...------.-------------------.....-----------<<<<<_______.._____>.>>>>.>..>>>,,,,,.,,,,,,,,,,,..,,,,,,,,,<<<-<<<<-..---<<<____..............______>>>->>>>->>>,,,,,,,,,<<.<-<<<_____..______>>>>>>:::.::::::::::::::::::::::::::::::
#=GC RF                    CucguCuG.AGggGACgcG.AGg.AucgucCU...CgccGcCGcuucGGcCAGUGugUcG.GccgGgCCuUGACAAGCua.CCuGAG.G...A..ggguC...UcG...GAgcCg.GacCuGGAgCcCaGCGAuu.....GCcGCCuGcuucuCccGccUCug..gUCucg.gGag.G..ccucCCGC.CUCgCAcCCCc..CCUCUGGACcuGCCUccc..UUCuCcuccc..............GCGUGcgGagggAGCCagCGcUUAGGCCc.GAGCGAGCCU..GGGGGCCGCCgGCCG.uGAAGgCauCGCGGGgACCgAUUCgCCAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00451
#=GF ID   mir-395
#=GF DE   mir-395 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   56.00
#=GF TC   56.00
#=GF NC   55.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0001007;
#=GF DR   MIR; MI0001008;
#=GF DR   MIR; MI0001009;
#=GF DR   MIR; MI0001010;
#=GF DR   MIR; MI0001011;
#=GF DR   MIR; MI0001012;
#=GF DR   MIR; MI0001028;
#=GF DR   MIR; MI0001029;
#=GF DR   MIR; MI0001030;
#=GF DR   MIR; MI0001031;
#=GF DR   MIR; MI0001032;
#=GF DR   MIR; MI0001033;
#=GF DR   MIR; MI0001034;
#=GF DR   MIR; MI0001035;
#=GF DR   MIR; MI0001036;
#=GF DR   MIR; MI0001037;
#=GF DR   MIR; MI0001038;
#=GF DR   MIR; MI0001039;
#=GF DR   MIR; MI0001040;
#=GF DR   MIR; MI0001041;
#=GF DR   MIR; MI0001042;
#=GF DR   MIR; MI0001043;
#=GF DR   MIR; MI0001044;
#=GF DR   MIR; MI0001045;
#=GF DR   MIR; MI0001053;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   15200956
#=GF RT   Computational Identification of Plant MicroRNAs and Their Targets,
#=GF RT   Including a Stress-Induced miRNA.
#=GF RA   Jones-Rhoades MW, Bartel DP
#=GF RL   Mol Cell 2004;14:787-799.
#=GF CC   mir-395 was identified in both Arabidopsis thaliana and Oryza sativa
#=GF CC   computationally and was later experimentally verified. mir-395 is thought
#=GF CC   to target mRNAs coding for ATP sulphurylases [1]. The mature sequence is
#=GF CC   excised from the 3' arm of the hairpin.
#=GF WK   mir-395_microRNA_precursor_family
#=GF SQ   25


AL606669.4/12205-12120 GAGUCCCUAGGAGUUCCUUUCAAG-CACUUUACGACACACUG----UAUU-GAGAGU-------------------------------------------------------UGUCGUGAAGUGUUUGGGGGAACUCUUAGUGUCGC
AP004460.2/70702-70813 GUGUUCCCAAGAGUUCCUUGCAAG-CACUUCACAUAGAACUUC---UGUUACUCUCAUGUAACAUUGGGAA-------------------------------CUUGAGAAGCUACUGUGAAGUGUUUGGGGGAACUCUAGGUGGCAC
AL606669.4/11928-11841 GUAUUGUCGUGAGUUCCCUUCAAG-CACUUCACGUGGCACU-----AUCU-CAAUGCCUA----------------------------------------------------CUAUGUGAAGUGUUUGGGGGAACUCUCGAUAUCAC
AL606669.4/11785-11698 GUAUUAUCGAGAGUUCCCUUCAAC-CACUUCACGUGGCACU-----GUUU-CAAGGCCUA----------------------------------------------------UUGUGUGAAGUGUUUGGGGGAACUCUCGAUAUCAC
AP004460.2/70542-70640 GUUUUACCGGGAGUUCUCUUCAAG-CACUUCACGUAGAGCUUU--CUAUUGACAUGGAGCUUUA---------------------------------------------GAACAAUGUGAAGUGUUUGGGGGAACUCUUGGUACCAA
DQ063654.1/98-192      AUGUUUUCUAGAGUUCCUCUGAG--CACUUCAUUGGAGAUACAA-UUUUU-UAUAAAAUAGUUU------------------------------------------------UCUACUGAAGUGUUUGGGGGAACUCCCGGGCUGAU
AC000348.2/5930-6029   AUGUCCCCAUGAGUUCCCUUUAA--CGCUUCAUUGUUAAAUA------CU-CAAAGCCACAUUGGUU--------------------------------------UGUAUACAACACUGAAGUGUUUGGGGGGACUCUUGGUGUCAU
DQ063653.1/31-130      AUGUCCACAUGAGUUCCCUUUAA--CGCUUCAUUGUUGAAUA------CU-CAAAGCCACAUUGGUU--------------------------------------UGUAUAUAACACUGAAGUGUUUGGGGGGACUCUUGGUGUCAU
AC010675.6/79489-79378 AUGUCCCCUUGAGUUCCCUU-AAA-CGCUUCAUUGUUCAUACU---UUGU-UAUCAUCUAUCGAUCGAUCAA-----------------------------UCAAUCUGAUGAACACUGAAGUGUUUGGGGGGACUCUAGGUGACAU
AC149601.3/18879-18765 UUGUCUCUUAGAGUUCCUUUGAA--CGCUUCAUGCAUGAGAAU---AUCU-AUUUGGUCUAAAAUCCAUUAGA--------------------------AAAAUAGUUCUUCUUAAAUGAAGUGUUUGGGGGAACUCUUGGGUUCAA
AC149601.3/13054-12939 UUGUUUCUUAGAGUUCCUUUGAA--CGCUUCAUGCAUGAGAAU---AUGU-AUUUGGUCUAAUAUCCAUUAGAA-------------------------AAGAUAGUUCUUCAUCAAUGAAGUGUUUGGGGGAACUCUUGGGUUCAA
AL606669.4/12067-11979 GUAUUAUCAAGAGUUCUCUUUAAG-CACUUCAUACGACACCAU---UAUU-UAUAGGGU-----------------------------------------------------UGUUGUGAAGUGUUUGGAGGAACUCUCGGUGUCAU
AL606669.4/12421-12280 UUGUCCACUGGAGUUCUCCUCAAUCCACUUCAGUAGAUAGCU----AUGG-CUAGGCCUCAUUGCAUUGCACUGUUACAUAACUGUGAUCAUGGGGCCAAAAGCUAGCUAUGUAUAGUGAAGUGCUUGGGGGAACUCCAGUUGACAC
AP004460.2/70367-70478 UUGUUACCUGGAGUUUCCUCAACA-CACUUCACAUCUGCUAGGCCCUAUUACAAUUGCGCAAUGUGGAG----------------------------------UCUGCAAUUGGUAGUGAAGUGUUUGGGGGAACUCUAGGUGGCAC
GQ419501.1/9-151       UUAUCCACUGGAGUUCUCCUCAAACCACUUCAGCAGAUAGCUAG-CUAGG-CCUCAUUGCAUUGCACCACUGUUGCAUAACUAUG--AGCAUGGGGCCAAAAGUUAGCUGCUUAUAGUGAAGUGUUUGGGGAAACUCCGGUUGGCAA
GQ419446.1/211-322     GUGUUCCCAAGAGUUCCUUGCAAG-CACUUCACAUAGAACUUC---UGUUACUCUCAUGUAACAUUGGGAA-------------------------------CUUGAGAAGCUACUGUGAAGUGUUUGGGGGAACUCUAGGUGGCAC
GQ419429.1/16-114      GUUUUACCGGGAGUUCUCUUCAAG-CACUUCACGUAGAGCUUU--CUAUUGACAUGGAGCUUUA---------------------------------------------GAACAAUGUGAAGUGUUUGGGGGAACUCUUGGUACCAA
FM164126.1/264-375     AUGUCCCCUUGAGUUCCCUU-AAA-CGCUUCAUUGUUCAUACU---UUGU-UAUCAUCUAUCGAUCGAUCAA-----------------------------UCAAUCUGAUGAACACUGAAGUGUUUGGGGGGACUCUAGGUGACAU
GQ419404.1/235-322     GUAUUAUCGAGAGUUCCCUUCAAC-CACUUCACGUGGCACU-----GUUU-CAAGGCCUA----------------------------------------------------UUGUGUGAAGUGUUUGGGGGAACUCUCGAUAUCAC
FM164068.1/196-295     AUGUCCCCAUGAGUUCCCUUUAA--CGCUUCAUUGUUAAAUA------CU-CAAAGCCACAUUGGUU--------------------------------------UGUAUACAACACUGAAGUGUUUGGGGGGACUCUUGGUGUCAU
FM164019.1/258-166     AUGUCUCCUAGAGUUCCUCUGAG--CACUUCAUUGGGGAUACA---AUUU-UUCUAAAUGAUUA------------------------------------------------UCCACUGAAGUGUUUGGGGGAACUCCCGGACCCAU
GQ419410.1/92-179      GUAUUGUCGUGAGUUCCCUUCAAG-CACUUCACGUGGCACU-----AUCU-CAAUGCCUA----------------------------------------------------CUAUGUGAAGUGUUUGGGGGAACUCUCGAUAUCAC
GQ419459.1/384-482     GUUUUAUCGGGAGUUUCCUUCAAG-CACUUCACGUAGAGCUUU--CUAUUGAUAUGGAGCUUUG---------------------------------------------GAACAAUGUGAAGUGUUUGGGGGAACUCUUGAUACCAA
GQ419467.1/723-808     GUAUCACCGUGAGUUCCCUUCAAG-CACUUCACGUGGCACU-----AUUU-CAAUGCC------------------------------------------------------UAUUGUGAAGUGUUUGGGGGAACUCUCGAUGUUCC
GQ419408.1/92-179      GUAUUGUCGUGAGUUCCCUUCAAG-CACUUCACGUGGCACU-----AUCU-CAAUGCCUA----------------------------------------------------CUAUGUGAAGUGUUUGAGGGAACUCUCGGUAUCAC
#=GC SS_cons           ::::<<<<<-<<<<<<<<<<-<<<.<<<<<<<<<<<<______...____.__________________.................................._________>>>>>>>>>>>>>>>>>>>>>>>>>->>>>>::::
#=GC RF                uUgUcccCuaGAGUUCCCuucAAa.CACUUCAcuacguAuuuu...uuuU.caaugucucAuUguauag..................................uuaguuauucguagUGAAGUGuUUggGGGAACUCUaGggguCAc
//
# STOCKHOLM 1.0

#=GF AC   RF00452
#=GF ID   mir-172
#=GF DE   mir-172 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   70.00
#=GF TC   70.00
#=GF NC   69.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000215;
#=GF DR   MIR; MI0001139;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   15200956
#=GF RT   Computational Identification of Plant MicroRNAs and Their Targets,
#=GF RT   Including a Stress-Induced miRNA.
#=GF RA   Jones-Rhoades MW, Bartel DP
#=GF RL   Mol Cell 2004;14:787-799.
#=GF RN   [2]
#=GF RM   12225663
#=GF RT   CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in
#=GF RT   microRNA metabolism in Arabidopsis thaliana.
#=GF RA   Park W, Li J, Song R, Messing J, Chen X
#=GF RL   Curr Biol 2002;12:1484-1495.
#=GF RN   [3]
#=GF RM   12226481
#=GF RT   Short RNAs can identify new candidate transposable element families in
#=GF RT   Arabidopsis.
#=GF RA   Mette MF, van der Winden J, Matzke M, Matzke AJ
#=GF RL   Plant Physiol 2002;130:6-9.
#=GF CC   mir-172 has been experimentally verified in Arabidopsis thaliana [2,3].
#=GF CC   This family is thought to target mRNAs coding for APETALA2-like
#=GF CC   transcription factors [1]. The mature sequence is excised from the 3' arm
#=GF CC   of the hairpin.
#=GF WK   mir-172_microRNA_precursor_family
#=GF SQ   11


AP006162.2/95640-95748   GUGUUUGCGGG---CGUGGCAUCAUCAAGAUUCACA------------------------------------------------------------UC-CAUGCAUAUAUCACAAGAC-GCAC-----AUA----UACAUC-CGAUUUGGC---UGAGAAUCUUGAUGAUGCUGCAUCCGCAGACAA
AY498859.1/608-716       UUGUUUGUAGG---CGCAGCACCAUUAAGAUUCACA---------------------------------------------------------------UGGAAAUUGAUAAAUACC---CUAAAUUAGG------GUUUUGAUAUGUAUA---UGAGAAUCUUGAUGAUGCUGCAUCAACAAUCGA
AC005851.3/82204-82319   UUGUUGGCUGC---UGUGGCAUCAUCAAGAUUCACA------------------------------------------------------------UC-UGUUGAUGGACGGUGGUGAUUCACUCUCCACA----AAGUUCUCUAUGAAAA---UGAGAAUCUUGAUGAUGCUGCAUCGGCAAUCAA
AL132975.1/70385-70497   UUGUUUGCUAU---UGCAACAUCUUCAAGAUUCAGA------------------------------------------------------------AA-UCAGAUUCUCUUAUGGGU--UUUCUUUUGAGCC---UUUAUU--UUUUGGUU---UGAGAAUCUUGAUGAUGCUGCAGCGGCAAUUAA
AP005247.3/132313-132203 CUUGUUGCGGG---UGCAGCGUCAUCAAGAUUCAC--------------------------------------------------------------G-UGUGCCGCACGGCACACG--UAUCGGUUUUCA----AGUGUAG-UCAUCGUG---CGUGAAUCUUGAUGAUGCUGCACCAGCAAAGAG
AC008153.5/42438-42316   CUGUUCGCUGU---UGGAGCAUCAUCAAGAUUCACAAAUCA-------------------------------------------------------UC-AAGUAUUCGUGUAAAUAA--ACCCAUUUAUGAUUAGAUUUUUGAUGUAUGUA---UGAGAAUCUUGAUGAUGCUGCAGCUGCAAUCAG
AP004048.3/57506-57395   GUGCUUGCAGG---UGCAGCACCAUCAAGAUUCACA------------------------------------------------------------UCGAGUUCAUCCCUAAACGAGA-UCGAGGUUGGC------UGACU-AUAUGUGA----UGAGAAUCUUGAUGAUGCUGCAUCAGCAAACGC
AY728438.1/4-122         ---------GA---UGCGGCAGCAUCAAGAUUCACAAACUUUAAGGCUUGAGU-------------------------------------------UG-GGGUGGUACACGGUCACC--UCCUUUACUCGA----AAGGUUCCUUAAUUUCUGAUGGGAAUCUUGAUGAUGCUGCAUCGGC------
AY728434.1/1-161         GCG------GA---UGCGGCAUCAUCAAGAUUCACAAGCUUUAAGGCUUGAGUGAGAGGGGUGGCAUACGGUCACCUCCUUUAAGGCUUGAGUGAGAG-GGGUGGCAUACGGUCACC--UCCUUUAGUCCA----AAGGGU-CCUUUUUUA---UGGGAAUCUUGAUGAUGCUGCAUCGGC------
AY728436.1/1-132         ---------GCCUAUGGAGCAUCAUCAAGAUUCACAAGCUUUAUUAGGGCUAGUGUGUGGUGAU--------------------------------GA-UGGUGGCUUUUGGUGGUC--CCUUUUUUUCAAU---CCAAUAGCCCUUUGAA--UUGGGAAUCUUGAUGAUGCUGCAGCGGC------
AY728437.1/1-132         ------GCCGA---UGGAGCACCAUCAAGAUUCACAAACUUUAUUAGGGCUAAUAAGUGGUGAUG-------------------------------AU-GGUGGCUUUUGGUGGUCC--CUUCGUUUCAAC----CCAAUAGCCAUUUGAA--UUGGGAAUCUUGAUGAUGCUGCAGCGGC------
#=GC SS_cons             :::::::::<<...<<<<<<<<<<<<<<<<<<<-<<_____.......................................................__.__________________..____________....________________...>>->>>>>>>>>>>>>>>>>>>>>:::::::::
#=GC RF                  uUGuUuGCuGc...UGcaGCAuCAUCAAGAUUCACAAaCUU.......................................................ug.uGgugauauaugaucacc..uCuuuuuuuacA....aauaUugcuuUuUgua...UGaGAAUCUUGAUGaUGCugCAgCgGCAAucAa
//
# STOCKHOLM 1.0

#=GF AC   RF00453
#=GF ID   Cardiovirus_CRE
#=GF DE   Cardiovirus cis-acting replication element (CRE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:10500216
#=GF SS   Published; PMID:10500216
#=GF GA   37.00
#=GF TC   37.30
#=GF NC   36.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   10500216
#=GF RT   A coding RNA sequence acts as a replication signal in cardioviruses.
#=GF RA   Lobert PE, Escriou N, Ruelle J, Michiels T
#=GF RL   Proc Natl Acad Sci U S A 1999;96:11560-11565.
#=GF CC   This family represents a Cardiovirus cis-acting replication element (CRE)
#=GF CC   which is located within the region encoding the capsid protein VP2 and is
#=GF CC   required for viral replication [1].
#=GF WK   Cardiovirus_cis-acting_replication_element
#=GF SQ   4


AB090161.1/1485-1517 UCGGCCGUAAACACCCAAUCAUCAGUAGGCCGA
M94868.1/505-537     UCGGCCACAAACACUCAAUCCUCCGUUGGCCGG
U32924.1/505-537     UCGGCCACAAACACACAGUCUACUGUUGGCCGG
U20288.1/324-356     UCGGCCACAAACACGCAGUCUACUGUUGGCCGA
#=GC SS_cons         <<<<<<<---<<<__________>>>>>>>>>>
#=GC RF              uCGGCCACAAACaCuCAaUCuuCuGUUGGCCGa
//
# STOCKHOLM 1.0

#=GF AC   RF00454
#=GF ID   p27_CRE
#=GF DE   p27 cis-regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12837699, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   42.00
#=GF TC   42.70
#=GF NC   35.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   12837699
#=GF RT   Cell cycle-dependent translation of p27 involves a responsive element in
#=GF RT   its 5'-UTR that overlaps with a uORF.
#=GF RA   Gopfert U, Kullmann M, Hengst L
#=GF RL   Hum Mol Genet 2003;12:1767-1779.
#=GF CC   This family represents a structured G/C rich element located in the 5' UTR
#=GF CC   of p27 mRNA. This element contributes to cell-cycle regulated translation
#=GF CC   and when deleted leads to a 50% drop in regulation. The element is thought
#=GF CC   to be able to form several different structures with similar free energy.
#=GF CC   It has been suggested that proteins may only bind to a specific structure
#=GF CC   thus conformational changes could regulate translation [1].
#=GF WK   p27_cis-regulatory_element
#=GF SQ   12


AF480891.2/120-178         CCACCUUAAG-GCCGCGCUCGCCAGCCUCGGCGGGGCGGCUCCCGCCGCCGCAACCAAUG
AB003688.1/2994-3052       CCACCUUAAG-GCCGCGCUCGCCAGCCUCGGCGGGGCGGCUCCCGCCGCCGCAACCAAUG
U77915.1/677-735           CCACCUUAAGAGC-GCGCUCGCCAGCCUGGGCGGAGCGGCUCCCGGCGCCGAGACCAAUG
U51681.1/1648-1700         CCACCUUAAGAGC-GCG-UCGC-AGCCU---GGGGA-GGCUCCCGGCACCGAGACCAAUG
AAYZ01005918.1/1-57        --ACCUUAAG-GCCGCGCUCGCCAGCCUCGGUGGGGCGGCUCCCGGCGCCGCGACCAAUG
AAQQ01623836.1/404-347     CCACCUUAAGACC-GCGCUUGCCAGCCUCGGCUGGGCGGCUCCCGGCGC-GCGACCAAUG
AAKN02030905.1/9746-9804   CCACCUUAAGAGC-GCGCUCGCCAGCCUCGGCUGGGCGGCUCCCGGCGCCGCGACCAAUG
AB083336.1/647-705         CCACCUUAAG-GCCCAGCUCGCCAGUCUCGGCUGGGCGGCUCCCGGCGCCGCGACCAAUG
AAGW02044714.1/46655-46713 CCACCUUAAG-GCCGCGCUCGCCAGCCUCGGCGGGGCGGCUCCCGGCGCCGCGACCAAUG
AEHL01096286.1/215-273     CCACCUUAAG-GCCGCGCUCGCCAGCCUCGGCGGGGCGGCUCCCGGCGCCGCAACCAAUG
AB005590.1/2427-2485       CCACCUUAAG-GCCGCGCUCGCCAGCCUCGGCGGGGCGGCUCCCGCCGCCGCAACCAAUG
AAQR03139182.1/4493-4551   CCACCUUAAG-GCCGCGCUCGCCAGCCUCGGUGGGGCGGCUCCCGGCGCUGCAACCAAUG
#=GC SS_cons               ::::::::<<.<<-<<____>>-->>>>--<<<<<-<<<___>>>->->>>>::::::::
#=GC RF                    CCACCUUAAG.GCCGCGCUCGCCAGCCUCGGcgGGGCGGCUCCCGGCGCcgCgACCAAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00455
#=GF ID   mir-15
#=GF DE   mir-15 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD
#=GF GA   58.00
#=GF TC   58.00
#=GF NC   57.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00085
#=GF DR   MIR; MI0000069;
#=GF DR   MIR; MI0000438;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science 2001;294:853-858.
#=GF RN   [2]
#=GF RM   12434020
#=GF RT   Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16
#=GF RT   at 13q14 in chronic lymphocytic leukemia.
#=GF RA   Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan
#=GF RA   S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce CM
#=GF RL   Proc Natl Acad Sci U S A 2002;99:15524-15529.
#=GF CC   This family represents the related mir-15a and mir-15b sequences. In
#=GF CC   humans miR-15a and miR-16 are clustered within 0.5 kb at 13q14. This
#=GF CC   region has been shown to be deleted in more than half of B cell chronic
#=GF CC   lymphocytic leukaemias (CLL). Both miR-15a and miR-16 are deleted or
#=GF CC   down-regulated in more than two thirds of CLL cases [2]. The mature
#=GF CC   sequence is excised from the 5' arm of the hairpin.
#=GF WK   mir-15_microRNA_precursor_family
#=GF SQ   17


AC119847.12/19404-19489      ACCUUAAAGUACUGUAGCAGCACAUCAUGGUUUACA-UACUACAGUCAAGA--UGCGAAUCAUUAUUUGCUGCUCUAGAAAUUUAAGGA
AL606727.3/61589-61504       GCCUGUCGGUACUGUAGCAGCACAGAAUGGUUUGUG-AGUUAUAACGGGGG--UGCAGGCCGUACUGUGCUGCGGCAACAACGACAGGA
AAYZ01325292.1/263-348       GCCUUAAAGUACUGUAGCAGCACAUCAUGGUUUACA-UAAUAUAGUCAAUA--UGCGAAUCAUAAUUUGCUGCUCUAGAAAUUUAAGGA
AAPN01007038.1/19411-19492   ACCUUGGGGUAAAGUAGCAGCACAUAAUGGUUUGUG-AGUUUUGAAA------UACAGGCCAUAUUGUGCUGCCUCAAAAAUACAAGGA
CAAE01014537.1/473298-473386 CCCUUAGACUGCUUUAGCAGCGCAUCAUGGUUUGUAAUGAUGUGGAAAAAAGGUGCAAACCAUAAUUUGCUGCUUUAGAAUUUUAAGGA
AANH01002998.1/16865-16950   CCCUUAGACUGCUAUAGCAGCGCAUCAUGGUUUGAA-ACAAUGUGGAAAGG--UGCGAACCAUUAUUUGCUGCUUUAGAAUUUUAAGGA
BAAF04019869.1/1029-1115     ACCUUAGAAUGCUGUAGCAGCGCAUCAUGGUUUGAAACAGUCAGAAAAAAG--UGCGAACCAUUAUUUGCUGCUUUAGAAUUUUAAGGA
AAVX01075355.1/1195-1112     ACUUUGUGGUGAUGUAGCAGCACAUAAUGGUUUGUG-AGUUGUAUGG-AGA--UACAGGCCAUGUUGUGCUGCCAUAUGAACACAA-GA
ABDC01320645.1/1722-1804     GCCUUAAAGUACUGUAGCAGCACAUCAUG-UUUACA-UACUACAGUC-AGA--UGCGAU-CAUUAUUUGCUGCUUUAGAAAUUUAGGGA
AY865833.1/401-486           GCCUUAAAGUACUGUAGCAGCACAUCAUGGUUUACA-UGCUACAGUCAAGA--UGCGAAUCAUUAUUUGCUGCUCUAGAAAUUUAAGGA
AY866300.1/461-545           ACCUUGGAGUAAAGUAGCAGCACAUAAUGGUUUGUG-GA-UUUUGAAAAGG--UGCAGGCCAUAUUGUGCUGCCUCAAAAAUACAAGGA
AY865835.1/417-502           GCCUUAAAGUACUGUAGCAGCACAUCAUGGUUUACA-UACUACAGUCAAGA--UGCGAAUCAUUAUUUGCUGCUCUAGAAAUUUAAGGA
EF042973.1/240-157           CCCUUGGAGUAAAGUAGCAGCACAUAAUGGUUUGUG-GA-UGUUGAAAAGG--UGCAGGCCAUACUGUGCUGCCUCAA-AAUACAAGGA
GQ903793.1/262-345           ACCUUGGAGUAAAGUAGCAGCACAUAAUGGUUUGUG-GA-UUUUGAAAAGG--UGCAGGCCAUAUUGUGCUGCCUCAA-AAUACAAGGA
AAWZ02004563.1/7975-8060     GCUUUAAAGUACUCUAGCAGCACAUCAUGAUUUGUA-UGUCAUAGUAAAUA--UGCAAGUCAUUAUUUGCUGCUUUAGAAUUUUAAAGA
CAAB02000842.1/95609-95522   CCCUUAGACUGCUAUAGCAGCGCAUCAUGGUUUGUAACGAUGUAGAAAAGG-GUGCAAGCCAUAAUCUGCUGCUUUAGAAUUUUAAGGA
ADDD01069202.1/34766-34681   GCCUUAAAGUACUCUAGCAGCACAUCAUGGUUUGCA-UGCUGUAGUGAAGA--UGCGAAUCAUUAUUUGCUGCUUUAGAAAUUUAAGGA
#=GC SS_cons                 :<<<<<----------<<<<<<-<--<<<<<<<<<<.______________..>>>>>>>>>>-->->>>>>>---------->>>>>:
#=GC RF                      aCCUugaAgUAcUgUAGCAGCaCAUcAUGGuuuGca.uauUauagaaAAga..ugCaaaCCAUaaUuuGCUGCuuUAgAAaUucaAGGA
//
# STOCKHOLM 1.0

#=GF AC   RF00456
#=GF ID   mir-34
#=GF DE   mir-34 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   INFERNAL; Griffiths-Jones S
#=GF SS   Predicted; PFOLD
#=GF GA   53.00
#=GF TC   53.10
#=GF NC   52.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00087
#=GF DR   MIR; MI0000584;
#=GF DR   MIR; MI0000268;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12624257
#=GF RT   Vertebrate microRNA genes.
#=GF RA   Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP
#=GF RL   Science 2003;299:1540.
#=GF RN   [2]
#=GF RM   12554860
#=GF RT   Numerous microRNPs in neuronal cells containing novel microRNAs.
#=GF RA   Dostie J, Mourelatos Z, Yang M, Sharma A, Dreyfuss G
#=GF RL   RNA 2003;9:180-186.
#=GF RN   [3]
#=GF RM   12919684
#=GF RT   Embryonic stem cell-specific MicroRNAs.
#=GF RA   Houbaviy HB, Murray MF, Sharp PA
#=GF RL   Dev Cell 2003;5:351-358.
#=GF CC   Human mir-34a was discovered computationally [1] and later experimentally
#=GF CC   verified [2]. The mature sequence is excised from the 5' arm of the
#=GF CC   hairpin.
#=GF WK   mir-34_microRNA_precursor_family
#=GF SQ   18


AY866161.1/514-604       GUGAGUGUUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGAGCAAUAGUGAAGGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCAC
AY866162.1/471-561       GUGAGUGUUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGAGCAAUAGUGAAGGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCAC
AY866156.1/471-561       GUGAGUGUUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGUGCAAUAGUGAAGGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCAC
AC119831.6/97933-97854   GAGUCUAGUUACUAGGCAGUGUAGUUAGCUGAUUGCUA---AUAGUAC---------CAAUCACUAACCACACAGCCAGGUAAAAAGACUGA
AP002008.5/124682-124761 GAGUCUAGUUACUAGGCAGUGUAGUUAGCUGAUUGCUA---AUAGUAC---------CAAUCACUAACCACACGGCCAGGUAAAAAGAUUUG
BX950179.6/113794-113711 GGGGUUGGUCUGUAGGCAGUGUUGUUAGCUGAUUGUUUC--AUAUGAACUA------UAAUCACUAACCAUACUGCCAACACAACAACCUAC
BX119985.7/114097-114014 GGGGUUGGUCUGUAGGCAGUGUUGUUAGCUGAUUGUUUC--AUAUAAACUA------UAAUCACUAACCAUACUGCCAACACAACAACCUAC
AC119831.6/98467-98384   GUGCUCGGUUUGUAGGCAGUGUAAUUAGCUGAUUGUAGU--GCGGUGCUGA------CAAUCACUAACUCCACUGCCAUCAAAACAAGGCAC
AP002008.5/124182-124265 GUGCUCGGUUUGUAGGCAGUGUCAUUAGCUGAUUGUACU--GUGGUGGUUA------CAAUCACUAACUCCACUGCCAUCAAAACAAGGCAC
BX548008.7/163918-164007 GUGAGUGGUUCUCUGGCAGUGUCUUAGC-UGGUUGUUGUGUGGAGUGAGAA-CGAAGCAAUCAGCAAGUAUACUGCCGCAGAAACUCGUCAC
AL606914.9/21743-21653   GUGAGUAAUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGAGUAUUAGCUAAGGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCAC
AY866155.1/449-538       GUGAGUGUUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGAGCAAUAGUAA-GGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCAC
AY866157.1/430-519       GUGAGUGUUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGAGCAAUAGUAA-GGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCAC
AY866158.1/164-253       GUGAGUGUUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGAGCAAUAGUAA-GGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCAC
AY866159.1/449-538       GUGAGUGUUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGAGCAAUAGUAA-GGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCAC
AL591166.12/20647-20558  GUGAGUGUUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGAGCAAUAGUAA-GGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUGCAC
AY866163.1/462-551       GUGAGUGUUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGAGCAAUAGUAA-GGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUACAC
AY866160.1/436-525       GUGAGUGUUUCUUUGGCAGUGUCUUAGC-UGGUUGUUGUGAGCAAUAGUAA-GGAAGCAAUCAGCAAGUAUACUGCCCUAGAAGUGCUACAC
#=GC SS_cons             <<-<<<<-<<<<<-<<<<<<<<-<<<<<.<<<<<<________________._____>>>>>>>>>>>->>>>>>>>->>>>>->>>>>>::
#=GC RF                  GgGgguggUucucuGGCaGUgucgUugg.UGaUUGUUgUGaguAaUAguaA.gGAAGCAAuCAccaAcuacACuGCCagagaAacacccCAc
//
# STOCKHOLM 1.0

#=GF AC   RF00457
#=GF ID   IRES_mnt
#=GF DE   Mnt IRES
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Published; 11314024, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   100.00
#=GF TC   118.30
#=GF NC   90.10
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11314024
#=GF RT   An internal ribosome entry segment in the 5' untranslated region of the
#=GF RT   mnt gene.
#=GF RA   Stoneley M, Spencer JP, Wright SC
#=GF RL   Oncogene 2001;20:893-897.
#=GF CC   This family represents the Mnt internal ribosome entry site (IRES). Mnt is
#=GF CC   a transcriptional repressor related to the Myc/Mad family of transcription
#=GF CC   factors. It is thought that this family allows efficient Mnt synthesis
#=GF CC   when cap-dependent translation initiation is reduced [1].
#=GF WK   Mnt_IRES
#=GF SQ   21


Y07609.1/151-354             UUUUAUUUUGCAAAUAUUUUGGGAGACAUUGAUUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUUUCUGAGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCGGCCCGCCAGCCUGACCUGUGCUUGGCUCCGCGGGCCGCAGCCUCGGCCCCGGCGCGCCCCCGGCUGCUCUC--GCCGCGAUG
Y13440.1/13-215              UUAUAUUUUGCAAAUAUUUUGAGAGACAUUGAUUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUCCCUGCGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGGCUC-GCGGGCCGCAGCCUCGGCCCCGGCGCGCCCCCGGCAGCUCUC--GGCGCGAUG
X96401.1/13-215              UUAUAUUUUGCAAAUAUUUUGAGAGACAUUGAUUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUCCCUGCGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGGCUC-GCGGGCCGCAGCCUCGGCCCCGGCGCGCCCCCGGCAGCUCUC--GGCGCGAUG
AAFC03038179.1/9139-9341     UUACAUUUUGCAAAUAUCUGGGGAAACAUUGAUUUUUCUU-----C-CUGUGCUC-CCCCGUUCUUCCCUGCGGAGUGCGCUGCGCCG-CCCAGUCCUGACGCCCCC-C-GGAGCUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGGCUC-GCGGGCCGCAGUCUCGGCCCCGGCGCGCCCCCGGCAGCUCUC--GGCGCGAUG
AANN01706250.1/1170-967      AUCUAUUUUGUAAAUAUUUGGGGAGAUGUUAAAUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUCCCUGCGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCCCC-GGAGGUGAUC-CCUCCCUCCUGCCUCCCCGCCAGCCUGACCUGUGCCUGGCUC-GCGGGCCGCAGUCUCGGCCCCGGCGCGCCCCUGGCAGCUCUC--GGCGCGAUG
AAIY01803948.1/595-391       UUAUAUUUUGCAAAUAUUUGGGGAGACACUGACUUUUCUC-----C-CCGUGCUC-UCCCAUUCCUCUCUGCGGAGUGCGCUGCGCCA-CCCAGCCCUGUCGCUUCC-CAGGAGGUGAUCACUUGCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGGCUC-GCGGGCCGCAGCCUCGGCUCCGGCGCACCCCCGGCAGCUCUC--AGCGCGAUG
AAPY01744069.1/3642-3440     UUGUAUUUUGCAA--AUUUUGGGAGACAUUGAUUUUCCUC-----C-CUGUGCUC-C-CCGUUCUUCCCUGCGGAGUGCGCUGCGCCGGCCCAGCCCUGUCGCCCCC-A-GGAGGUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCUGGCUC-GCGGGCCGCAGCCUUGGCCCCGGCGCGCCCCCGGCAGCUUCUCGGGCGCGAUG
AANG01158687.1/155-1         UUAUAUUUUGCAAAUAUUUUGGGAAACAUUAAUUUUUGUU-----U-CCGUGCUC-UCCCGUUCUUCCCUGCGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUG----------GGUG----------CCCGCCA-------CCCUGACCUGUGCCCGGCUCGC------------------------G
AADA01120667.1/7779-7577     UUAUAUUUUGCAAAUAUUUUGAGAGACAUUGAUUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUCCCUGCGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGGCUC-GCGGGCCGCAGCCUCGGCCCCGGCGCGCCCCCGGCAGCUCUC--GGCGCGAUG
ABDC01240867.1/1414-1212     UUAUAUUUUGCAAAUAUUUUGGGAGACAUUGAUUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUCCCUGCGGAGUGCGCUGCGCCG-CCCAACCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGGCUC-GCGGGCCGCAGCCUCGGCCCCGGCGCGCCCCCGGCAGCUCUC--GGCGCGAUG
AALT01384160.1/2852-3054     UUAUAUUUUGCAAAUAUUUUGGGAGACAUUGAUUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUCCCUGCGGAGUGAGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCUCGGCUU-GCGGGCCGCAGUCUCGGCCCCGGCGCGCCCCCGGCUGCUCUC--GGCGCGAUG
AAGV020135489.1/2590-2392    UUUACAUUUGCAAACUUUGGGAGACAUGUUUUUUUUUUUUUAUUUC-CCGUGCUC----CCUGUUCUCCUGA-GAGUCCGCUGCGCCG-CCCAGCC-UGUCGCCCCC---GGAGGUGAGC-CCUCCCUCCUGCCUG-CUGCCAGCU-GACCUGUGCCCGGCUC-GCGGGCAGCAGCCUCUGCC-CGGCGAGCCCCCGGCAGCUGUC--GGCGCGAUG
AAWR02013275.1/6588-6386     UUCUAUCUUGCAAAUAUUUUGGGAAACAUUGAUUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUCCCUGCGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGGCUC-GCUGGCCGCAGUCUCGGCUCCGGCGCGCCCCCGGCAGCUCUC--GGCGCGAUG
AAKN02033263.1/168240-168443 UUAUAUUUUGCAAAUAUUUUGGGAGACAUUGAUUUUCCUG-----C-CCGUGCUCUCCCCGUUCUUUCCUGUGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCCGCCCGCCAGCCUGACCUGUGCCUGGCUC-GCGGGCCGCAUCUUCGGCCCCGGCGCGCCCCCGGCCGCUCUC--GGCGCGAUG
AC212181.4/122863-122661     UUAUAUUUUGCAAAUAUUUUGAGAGACAUUGAUUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUCCCUGCGGAGUGCACUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGGCUC-GCGGGCCGCAGCCUCGGCCCCGGCGCGCCCCCGGCAGCUCUC--GGCGCGAUG
AL604066.9/47692-47894       UUUUAUUUUGCAAAUAUUUUGGGAGACAUUGAUUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUUUCUGAGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCGGCCCGCCAGCCUGACCUGUGCUUGGCUC-GCGGGCCGCAGCCUCGGCCCCGGCGCGCCCCCGGCUGCUCUC--GCCGCGAUG
AABR05020750.1/57609-57810   UUUUAUUUUGCAAAUAUUUUG-GAGACAUUGAUUUUUCUC-----C-CCGUGCUC-CCCCGUUCUUUCCUGAGGAGUGCGCUGCUCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCGGCCCGCCAGCCUGACCUGUGCUUGGCUC-GCGGGCCGCAGCCUUGGCCCCGGCGCGCCCCCGGCUGCUCUC--GGCGCGAUG
AAQR03150339.1/8569-8771     UUAUGUUUUGCAAAUAUUUUGGGAGACAUUGAUUUUUCUC-----C-CUGUGCUC-CCCCGUUCUUCCCUGUGGAGUGCGCUGCUCUG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGACUU-GCGGGCCGCAGCCUCGGCCCCGGCGCGCCCCCGGCAGCUCUC--GGCGCGAUG
AAGW02049729.1/535-737       UUCUAUUUUGCAAAUAUUUUGGGAGACAUUGAUUUUUCCA-----C-CCGUGCUC-CCCGGUUCUCGCUCGCGGAGUGCGCCGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAGC-CCUCGCUCCCGCCUGCCCGCCAGCCUGACCGGUGCCUGGCUC-GCGGGCCGCAGCCUCGGCCCCGGCGCGCCCCCGGCCGCUCUC--GGCGCGAUG
AACN010747261.1/282-485      UUCUAUUUUGCAAAUAUUUUGGAAAACAUUAAUUUUUUCU-----CUCCGCGCUC-UCCCGUUCUUCCCUGCGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCGCCCUCCUGCCUGCCCGCCAGCCUGACCUGUGCCCGGCUC-GCGGGCCGCAGUCUCGGCCCCGGCGCGCCCCCGGCGGCUCUC--GGCGCGAUG
AAPE02038088.1/22553-22755   UUAUAUUUUGCAAAUAUUUUGGGAGACAUUGAUUUUCCUG-----C-CCGUGCUC-CCCCGUUCUUGCCUGCGGAGUGCGCUGCGCCG-CCCAGCCCUGUCGCCCCC-C-GGAGGUGAUC-CCUCCCUCCUGCCUGCCCGCCAGCCUGUCCUGUGCCUGGCUC-GCGGGCCGCAGUCUCGGCCCCGGCGCGCCCCCGGCAGCUCUC--AGCGCGAUG
#=GC SS_cons                 ::::::::::::::::::::::<<<<__________>>>>.....,.,<<<<<<<.<_______________>>>>>>>>--((((((.,,,,,,,,,,,,,,,,,,.,.<<<<<_____.>>>>>,,,,,,,,,<<<<<<-<<<<____________>>>>-.>>>>>>,,,,,,,,,,,,,,))))))::::::::::::::::..:::::::::
#=GC RF                      UUaUAUUUUGCAAAUAUUUuGggagaCAUUgAUUUUucuc.....C.CcGcgCUC.cCCCgUUCUUcCCUGcgGAGugCgCUGCGCCG.CCCAGCCCUGUCGCCCCC.C.GGaGGUGAUC.CCuCCCUCCUGCCuGCCcGCCaGCcUGACCUGUGCCcgGCuc.GCgGGCCGCAGcCUcGGCCCCGGCGCGCCCCCGGCaGCUcUC..GGCGCGAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00458
#=GF ID   IRES_Cripavirus
#=GF DE   Cripavirus internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Published; 11233983
#=GF SS   Published; PMID:11233983
#=GF GA   80.00
#=GF TC   97.60
#=GF NC   52.90
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11233983
#=GF RT   A tertiary structure model of the internal ribosome entry site (IRES) for
#=GF RT   methionine-independent initiation of translation.
#=GF RA   Kanamori Y, Nakashima N
#=GF RL   RNA 2001;7:266-274.
#=GF CC   This family represents a Cripavirus internal ribosome entry site (IRES)
#=GF CC   which is required for the production of capsid proteins through
#=GF CC   IRES-mediated translation [1].
#=GF WK   Cripavirus_internal_ribosome_entry_site_(IRES)
#=GF SQ   7


AF178440.1/5925-6123 UUGACUAUGUGAUCUUGCUUUCG----UAAUAAAAUUCUGUACAUAAAAGUCGAAAGUAUUGCUAUAGUUAAGGUUGCGCUUGCCUAUUUAGGCAUACUUCUCAGGAUGGCGCG-UUGCAGUCCAA-CAAG-AUCCAGGGACUGUACAGAAUUUUCC-UAUACCUCGAGUCGGGUUU-GGAA--UCUAAGGUUGACUCGCUGUAAAUAAU
AB017037.1/6286-6484 GAAAAUGUGUGAUCUGAUUAGAAG--UAAGAAAAUUCCUAG-UUAUAAUAUUUUUAAUACUGCUACAUUUUU-AAGACCCUUAGUUAUUUAGCUUUACCGCCCAGGAUGGGGUG-CAGCGUUCCUG-CAA-UAUCCAGGGCAC--CUAGGUGCAGCCUUGUAGUUUUAGUGGACUUUAGGCU--AAAGAAUUUCACUAGCAAAUAAUAAU
AF014388.1/6078-6278 GUUAAGAUGUGAUCUUGCUUCCUU--AUACAAUUUUGAGAGGUUAAUAAGAAGGAAGUAGUGCUAUCUUAAU-AAUUAGGUUAACUAUUUAGUUUUACUGUUCAGGAUGCCUAU-UGGCAGCCCCA-UAA-UAUCCAGGACAC-CCUCUCUGCUUCUUAUAUGAUUAGGUUGUCAUUUAGAA--UAAGAAAAUAACCUGCUAACUUUCAA
AF218039.1/6028-6228 GCAAAAAUGUGAUCUUGCUUGUAA--AUACAAUUUUGAGAGGUUAAUAAAUUACAAGUAGUGCUAUUUUUGU-AUUUAGGUUAGCUAUUUAGCUUUACGUUCCAGGAUGCCUAG-UGGCAGCCCCA-CAA-UAUCCAGGAAGC-CCUCUCUGCGGUUUUUCAGAUUAGGUAGUCGAAAAACC--UAAGAAAUUUACCUGCUACAUUUCAA
AF183905.1/5647-5848 CCAACAAUGUGAUCUUGCUUGCGGA-GGCAAAAUUUGCACAGUAUAAAAUCUGCAAGUAGUGCUAUUGUUGG-AAUCACCGUACCUAUUUAGGUUUACGCUCCAAGAUCGGUGGAUAGCAGCCCUAUCAA-UAUCUAGGAGAA-CUGUGCU-AUGUUUAGAAGAUUAGGUAGUCUCUAAACA---GAACAAUUUACCUGCUGAACAAAUU
AB006531.1/6003-6204 CUGACUAUGUGAUCUUAUUAAAAUUAGGUUAAAUUUCGAGGUUAAAAAUAGUUUUAAUAUUGCUAUAGUCUU-AGAGGUCUUGUAUAUUUAUACUUACCACACAAGAUGGACCG-GAGCAGCCCUC-CAA-UAUCUAGUGUAC--CCUCGUGCUCGCUCAAACAUUAAGUGGUGUUGUGCGA--AAAGAAUCUCACUUCAAGAAAAAGAA
AF022937.1/6935-7121 AGUGUUGUGUGAUCUUGCGCGAU-------AAAUGCUGACG---UGAAAACGUUGCGUAUUGCUACAACACU-----UGGUUAGCUAUUUAGCUUUACUAAUCAAGACGCCGUC-GUGCAGCCCAC-AAAA-GUCUAGAUA----CGUCACAGGAGAGCAUACGCUAGGUCGCGUUGACUAUCCUUAUAUAU-GACCUGCAAAUAUAAAC
#=GC SS_cons         <<<<<<<<<------<<<<<<<<<..__________AAAAAAA_______>>>>>>>>>---->>>>>>>>>.,,,BBBB,,<<<<____>>>>,,,,,<<<<-<<<<<bbbb<.<<<_____>>>.>--.>>>>>->>>>,a.aaaaaa,,,<<<<<---<<<<_CCCCC>>>>-->>>>>..:::::::::ccccc::::::::::::
#=GC RF              ccgAcuaUGUGAUCUUgCuugcgg..auaaAAAUuUuaaaggUaaaAAAaccgcaaGuAuUGCUAuagUcgg.AauuagcUUagcUAUUUAgcuUUACugccCAgGAuggcuug.ugGCAGCCCca.cAA.uaUCcAGggcac.ccuuuaugcugccuuauagguUAgGUagccuUuaggca..uaAgAaaUUuACcUGCuaAaaauaAu
//
# STOCKHOLM 1.0

#=GF AC   RF00459
#=GF ID   MPMV_package
#=GF DE   Mason-Pfizer monkey virus packaging signal
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14687944, INFERNAL
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   54.00
#=GF TC   54.00
#=GF NC   53.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019072; viral genome packaging;
#=GF RN   [1]
#=GF RM   14687944
#=GF RT   Mutational analysis of the predicted secondary RNA structure of the
#=GF RT   Mason-Pfizer monkey virus packaging signal.
#=GF RA   Mustafa F, Lew KA, Schmidt RD, Browning MT, Rizvi TA
#=GF RL   Virus Res 2004;99:35-46.
#=GF RN   [2]
#=GF RM   7884866
#=GF RT   Secondary structure model of the Mason-Pfizer monkey virus 5' leader
#=GF RT   sequence: identification of a structural motif common to a variety of
#=GF RT   retroviruses.
#=GF RA   Harrison GP, Hunter E, Lever AM
#=GF RL   J Virol 1995;69:2175-2186.
#=GF CC   This family represents a group of sequences that are related to the
#=GF CC   Mason-Pfizer monkey virus (MPMV) packaging signal. The packaging signal is
#=GF CC   located in the 5' UTR and is required for specific RNA encapsidation [1].
#=GF WK   Mason-Pfizer_monkey_virus_packaging_signal
#=GF **   seedtax: Eukaryota; Viruses
#=GF SQ   9


AF126467.1/349-623       UGGCGCC-C-AACGUG---GGGC-U-GGAUACGA--GGGAAUC-CUGUGAGGAA---GAG----AGCGCG-UAACACGGCCGGCAGUCA-AAGUGAAAG------AAAAACC---UUCCA--GCUGCCGCGGGAACCUGCCGCGUC--GG-CAAUAAAGGUAAGCGUUGCG-UUCGAAUAUGGGACAAGAAUUAAGCCAACAUGAACUUUAUGUAGAACAGUUAAAAAAGGCUCUAAAGACACGGGGAGUAAAGGUUAAGGGUAAUGAUUUACUCAAAUUCUUUGAUUUUGUAAAGGAUACCUGCCCUU
M11841.1/351-632         UGGCGCC-C-AACGUG---GCGU-U-GGAUACGA--GGGAAUU-UCGUGAGGAA---GAC----GACGCGGUUUGCCGGCCCG--GAUUAAAAGAGAAACGAAA-GUAAACU---UUCUUCGGCCGCCGCGGGAGCCUGCCGCGUA--GGACCUGAA-AGUAAGUGGUGCG-CUCGGAUAUGGGGCAGGAAUUAAGCCAGCACGAACGUUAUGUGGAACAAUUAAAACAGGCUUUAAAGACACGGGGAGUAAAGGUUAAAUAUGCUGAUCUCUUAAAGUUUUUUGAUUUUGUAAAGGAUACUUGUCCUU
M16605.1/349-623         UGGCGCC-C-AACGUG---GGGC-U-GGAUACGA--GGGAAUC-CUGUGAGGAA---GAG----AGCGCG-UAACACGGCCGGCAGUCA-AAGUGAAAG------AAAAACC---UUCCA--GCUGCCGCGGGAGCCUGCCGCGUC--GG-CAAUAAAGGUAAGCGUUGCG-CUCAAAUAUGGGACAAGAAUUAAGCCAACAUGAACUCUAUGUAGAACAAUUAAAAAAGGCUCUAAAGACACGGGGAGUAAAGGUUAAGGGUAAUGAUUUGCUCAAAUUCUUUGAUUUUGUAAAGGAUACCUGCCCUU
AF033815.1/123-398       UGGCGCC-C-AACGUG---GGGC-U-GGAUACGA--GGGAAUU-UCGUGAGGAA---GAC----GACGCG-UUCGCCGGCCGGC-GAUUAAAAGUGAAAG------UAAACUC--UCUU--GGCCGCCGCGGGAACCUGCCGCGUU--GGACCU-GAAAGUAAGUGUUGCG-CUCGGAUAUGGGGCAAGAAUUAAGCCAGCAUGAACGUUAUGUAGAACAAUUGAAGCAGGCUUUAAAGACACGGGGAGUAAAGGUUAAAUAUGCUGAUCUUUUGAAAUUUUUUGAUUUUGUGAAGGAUACUUGUCCUU
AANU01253468.1/8032-8307 UGGCGCCUC-AACGUG---GAGCCU-GGAAACGA--GGGAUUC--CGUGAGGAA---GAG----GACGCG-AAAGAACGGUCGACCUUCAAGGUGAAACU-----AAACUCC---UCCGA--UC-ACCGCGGGAACCUGCCGCGUC--AG-AAUUGAAGGUAAGUGACGUG-UCCG-AAAUGGGACAAGAAUUAAGUCAACAUCAAAUCUAUGUAGGACAAUUAAAAGAGGCUUUAAAGAUACGAGGAGUAAAGGUUAAAUGUAAUGAUUUGUUUAAAUUUUUUGAUUUUGUAAAAGACACUUGCCCUU
AC113268.8/165062-164780 UGGCGCC-UGAACAGG---GACC-U-GGA---AACGAGGGACU-CCGUGAGGAA---GAG----GACGCCAAAGGACGGUCGACCGCUAACCCAGACAAAAGGAGUAAAACUC--UUCCG-AUCA-CCGCGGGAACCUGCUGCGUC--UGAAUCGAA-GGUAAGUGGCGCG-UCCG-AAAUGGGACAAGAAUUAAGUCAGCAUCAGAUCUAUGUAGGACAAUUAAAAGAGGCUUUAAAGAUACGAGGAGUAAAGGUUAAAGGUAAUGAUUUGUUUAAGUUUUUUGAUUUUGUAAAAGAUACUUGCCCUU
AAIY01568405.1/1114-839  UGGCACC-C-AAUGCG---GGGC-CCGGAUACGA--GGG-AUA-CCGUGAGGAA---GAA----GGCGC--AAAGGAGGCCGGC-GAGUAAAAGUGAGAG-----AAAAUUC---CUUC--GGCCACCGCAGGAGCCUGCUGCGCUGAGGCUGAAGGUGAGUAAAA--GAG-CCUGAAAAUGGGACAAGAAUUAAGCCACCAUCAGAUUUAUGUGAGACAAUUGAAAGAGGCUUUAAAGGCACGAGGAGUAAAGGUGAAUAGUGAGGAUUUAUUCAAAUUUUUUGGCUUUAUAAAAGAUAUGUGUCGUU
AAHX01057948.1/6286-6014 UGGUGCC-C-ACUGUGUGGGGCC-U-GUAUACAG--GGGCUUUAUCUUGAGGAA---GAA----GAC----UCAGGUGGCUGGCUUUGUAUACAGAAAU----------UCC---UUUGA-AU--GUCGAGGGAGCCUGCCGUGGC--UGAAACGAAGGGGAGUGAUAGAA-UCUGAAUAUGGGACAAGCAUUAAGCUAACAUGAGGUCUUUGUGAAACAAUUAAAAGAGGCAUUAAAGGUUCGAGGAGUAAAGGUAAAAACCAACGAUCUGUUUACAUUUUUUGAUUUUGUUAAGGAUCUUUGUCCUU
ABDC01313292.1/5294-5577 UGGCGCC-C-AACGUG---GGGC-UCGGAUACGA--GGGAUGC-A-GUGAGGACAUGGACGUGUGUCGCC-AAAGCUCGUAGGGACCGAGCAGCUUAAAG-----UGAAAGUGCCUUCGA--CCA-UUGCGGGAGCCUGCCUCGCU--UGAGUA-AAAGUUGA---AUGCGUCUGCAAAAAUGGGCAGGAACUUAGCCAACAUCAAUUGUAUGUAACACAAUUGAGGGAAGUGUUAAAUACACGAAGAGUAAAGGUUGCAAAAGCAGAUUUGUUUAGAUUCUUUGAUUUUAUAAAGGAUGUGUGCCCCU
#=GC SS_cons             :::::<<.<.---<<<...____._.___>>>--..>>>,,,,.<<<<______..._>>....>>,,,,.,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.....,,,,<<<...<<---.-<<<--<<<<<_______>>>>>--..>>->--->>->>>,,,,,<<<<-.<<<<____>>>>>>>>,,,,<<<<<<_______________________________>>>->>>,,,,,,<<<<<<<<--<<<<<<_______>>>>>>------>>>>>>>>,,,,,,,,<<<<<<____>>>>>>
#=GC RF                  UGGCGCC.C.AAcGug...GggC.U.GGAuaCGA..GGGaauu.ccgUGAGGAA...GAc....ggCGCg.uaaGaugGccGGcaguuuAaAaugaAAag.....aaAAacc...uucua.agCcgcCGcGGGAgCCUGCCgCGuu..gGAcaauaaagguaAguguuGcG.cccgAAuAuggggCaaGAAUUaaGCcAaCAUgAaaUuUAUGUagaACAAUUaAAAgAgGCuuuAAAGAcACGaggAGuAAAgGUcaAaaauaaugAUcUgUUuAaaUUcuuUGAUUUUgUAAagGauacuUguCcuU
//
# STOCKHOLM 1.0

#=GF AC   RF00460
#=GF ID   U1A_PIE
#=GF DE   U1A polyadenylation inhibition element (PIE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   PMID:15491147
#=GF SS   Published; PMID:15491147
#=GF GA   50.00
#=GF TC   53.30
#=GF NC   47.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1900363; regulation of mRNA polyadenylation;
#=GF RN   [1]
#=GF RM   15491147
#=GF RT   Global and Local Dynamics of the U1A Polyadenylation Inhibition Element
#=GF RT   (PIE) RNA and PIE RNA-U1A Complexes.
#=GF RA   Clerte C, Hall KB
#=GF RL   Biochemistry 2004;43:13404-13415.
#=GF RN   [2]
#=GF RM   10742179
#=GF RT   The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the
#=GF RT   basis of cooperativity in regulation of polyadenylation by human U1A
#=GF RT   protein.
#=GF RA   Varani L, Gunderson SI, Mattaj IW, Kay LE, Neuhaus D, Varani G
#=GF RL   Nat Struct Biol 2000;7:329-335.
#=GF CC   This family represents the U1A polyadenylation inhibition element (PIE).
#=GF CC   PIE is a regulatory RNA which is responsible for the regulation of the
#=GF CC   length of the polyA tail of the U1A pre-mRNA. The PIE is located in the
#=GF CC   U1A mRNA 3' UTR. PIE adopts a U-shaped structure, with binding sites for a
#=GF CC   single U1A protein at each bend and when complexed with the two proteins
#=GF CC   it blocks activity of poly(A) polymerase (PAP), and inhibits its activity
#=GF CC   [1,2].
#=GF WK   U1A_polyadenylation_inhibition_element_(PIE)
#=GF SQ   39


BC000405.2/1511-1584         CCAC-ACAGCAUUGUACCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGCGCUGUUAGGCCGGA---AUUAAAGUGGCUU
AC129561.13/165007-165080    CCAC-ACAGCAUCGUACCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGUGCUGUUAGGUUGUG---AUUAAAGUGAGUU
L15447.1/1070-1143           CCAC-ACAGCAUUGUACCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGCGCUGUUAGAUUGUG---AUUAAAGUGAGUU
AC138288.13/11165-11238      CCAC-ACAGCAUUGUACCCAGAGUCUG--UCCC-CAGAAAUUGCACCUGGCGCUGUUAGGUUGUG---AUUAAAGUGAGUU
AC079644.9/92689-92762       CCAC-ACAGCAUUUUACCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGGGCUGUUAAAUUGUG---AUUAAAGUGAGUU
BC064308.1/1203-1278         CUUCAAAAGCAUUGCACCCAGAGUCUG-GUCUG-CAGACACUGAACCUGGAGCUUUGUUGUUUUU---AUUAAAGCAUGUU
BC044979.1/1100-1174         UGUU-UCAGCAUUGCACCCAGAGUCUG-CAACU-CGGACAUUGUACCUGGAGCUUGUGUUGUUGU---AAUAAACAUGAUU
AY387676.1/1047-1119         CCAC-ACAGCAUUGUACCCAGAGUCUG---CUC-CAGACAUUGCACCUGGCGCUGUCAGGCUGGA---AUUAAAGUGGGUU
CAAE01014537.1/748648-748723 UCAC-AAAGCAUUGCACCCAGAAUCUGGUUUAC-CAGACAUUGUACCUGGAGCUUUUUCUUUUAC---AUUAAAACCUUAU
AANN01507962.1/6383-6456     UCAC-ACAGCAUUGUACCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGCGCUGUUAGGCUGGA---AUUAAAGCGAUUU
AAFR03060702.1/3323-3397     CGCC-UCAGCAUUGUACCCAGAGUCUG-CCCUA-CAGACAUUGCACCUGGAGCUGUGGGGCGAAA---AUAAAAUGUUGGA
BC090598.1/1354-1428         CUUU-UAAGCAUUGCACCCAGAGUCUG-CAAGU-CAGGCAUUGUACCUGGAGCUUUUUUCUUUUC---UUUGCAAUAAACU
AALT01441576.1/1383-1456     UCAC-ACAGCAUUGUACCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGCGCUGUUAGGCCGGA---AUUAAAGUUGACG
AAPY01018805.1/111-40        CCAC-ACAGCAUUGUACCCAGAGUCUG--UCC--CAGACAUUGCACCUGGUGCUGUUAGG-UGCA---AUUAAAGUAGUUU
AANH01003005.1/83662-83740   UCAU-GAAGCAUUGCACCCAGCGUCUG-GUCUGCCAGACAUUGUACCUGGAGCUUUUUUGUUUUUCUAAUUAAAAUGGGUU
AANN01587824.1/1524-1451     UCAC-ACAGCACUGUACACAGAGUCUG--UCCC-CAAACAUUAUAUGUGGUGUUGUUUGGCUGGA---AUUAAAGUAGUUU
CT030175.7/147966-147893     CCAC-ACAGCAUUGUAUCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGGGUGCUACGCUCUCU---GGUCGAGUCAACU
AAHX01084618.1/3005-3076     CCAC-ACAGCCCUGUACCCAGAGUCU---CCCC--AGACAAUGCACCUGGCGCUGUUGGCGAGUG---AUUAUAGUGAGUU
AAFR03003560.1/26480-26406   UACC-UCAACAUUGUACCCAGAGUCUG-CCCUA-CAGUCGUUGCACCUGGAGCUGCAGGGAGAAA---AAAAAUGUUUGAU
BAAF04019938.1/6725-6800     UUUG-AAAGCAUUGCACCCAGUGUCUGACUUGU-CAGACAUUGUACCUGGAGCUUGGUAUUUGUU---GUUUUGUAUUAAA
AAGV020568098.1/7219-7146    CCAC-ACAGCAUUGUACCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGCGCUGUUAGGUUGGA---AUUAAAGUAAUUU
AAKN02012888.1/69498-69426   CCAC-AUGGCAUUGGAUCCAGAGUGUG--UCCC-CAGACAUUGUACCUGGCGCUGUUA-GCUGGA---AUUAAAGUACGUU
AAGV020154154.1/268-341      CUAC-ACAGCACUGCACCCAGAGUCUG--CCCC-CAUAUAGCACACCUGGCGGUGUUCAGCCAAA---AUCAAAGUGGUUU
AC211878.4/9394-9321         CCAC-ACAGCAUUGUAUCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGGGCUGUUAGACUGUG---AUUUAAGUGAGUU
BT081526.1/1226-1293         UUUG-AAAGCAUUGCACCCAGAGUCUG-CUUGG-CAGACAUUGUACCUGGAGCUUGU-------G---AAUAAAGCAUUUU
X57953.1/1102-1176           UGUU-UCAGCAUUGCACCCAGAGUCUG-CAACU-CGGACAUUGUACCUGGAGCUUGUGUUGUUGU---AAUAAACAUGAGA
AB171239.1/879-952           CCAC-ACAGCAUUGUACCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGCGCUGUUAGGCCGGA---AUUAAAGUGGUUU
BC112544.1/1059-1132         CCAC-ACAGCAUUGUACCCAGAGUCUG--UCAC-CAGACAUUGCACCUGGCGCUGUUAGGCUGGA---AUUAAAGUGUUUU
BC086331.1/1057-1128         CCAC-ACAGCAUUGUACCCAGGGUCU---UCCC--AGACAUUGCACCUGGCGCUGUUGGGUUGUG---AUUAAAGUGAGUU
BT048863.1/1366-1442         UUAU-AAAGCAUUGCACCCAGGGUCUGUUUCACCCAGACAUUGUACCUGGAGCUUUUCUGUUUGA---UUAAAACUUGCCA
AAGU03061722.1/129981-130053 ACAC-ACAGCAUCGUACCUAGAGUCUG--UCCC-CAGACAUUGUACCUGGAGCUGUUAGGCCAGA---AUUAAA-GUGUUU
AAQR03177285.1/3309-3236     CCAC-ACAGCAUUGUACCCAGAGUCUG--UCCC-CAGACAUUGCACCUGGUGCUGUUAGGGUGGA---AUUAAAGUGUUUU
AAGU03049942.1/11746-11673   CCAC-ACAGCAUAGUACCCAAAGUCUU--UCCC-CAGACAUUACACCUGGUGCUGUUAGGCCCGA---AUUAAAGUGGUUU
AAWZ02015054.1/7690-7764     AAAA-AAAGCAUUGCACCCAGGGUCUG-ACAGC-CAGACAUUGCACCUGGAGCUUUUCUGUUUUG---GAAUAAAAAUGUG
AABR05094928.1/39570-39641   CAAC-ACAGCAUUGUACCCAGGGUCU---UCCC--AGACAUUGCACCUGGCGCUGUUGGGUUGUG---AUUAAAGUGAGUU
CAAB02000844.1/137735-137810 UCAC-AAAGCAUUGCACCCAGAAUCUGGUUUGC-CAGACAUUGUACCUGGAGCUUUUUCUCUUUA---UAUUAAAACGUUA
AAQR03163399.1/5995-6068     CCAC-ACAGCACUGUACCCAGAGUCUG--UGCC-CAGACAUUGCACCUGGCACUGUUAGUCUGGA---AUUAAUGUGGUUU
AAEX03005528.1/39396-39323   CCAC-ACAGCAUUGUACCCAGAGUCUG--UCCC-CAGACAUUGCACCGGGUGCUGUUAGGCCAGA---AUUAAAGUGUUUU
AAQR03099725.1/15807-15734   CCAC-ACAGCAUUGUACCCAGAGUCUG--UCCC-CAGACAUUGCACCUAGUGCUGUUAGGGUGGA---AUUCAAGUGGUUU
#=GC SS_cons                 ::::.<<<<<-------<<<<-<<<<<..____.>>>>>------->>>>->>>>>:::::::::...:::::::::::::
#=GC RF                      ccAC.acAGCAUUGuACCCAGAGUCUG..UCcc.CAGACAUUGcACCUGGaGCUguUagguUuua...AUUAAAgUgguUU
//
# STOCKHOLM 1.0

#=GF AC   RF00461
#=GF ID   IRES_VEGF_A
#=GF DE   Vascular endothelial growth factor (VEGF) IRES A
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Published; PMID:9774635
#=GF SS   Published; PMID:9774635
#=GF GA   160.00
#=GF TC   162.00
#=GF NC   158.50
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   9774635
#=GF RT   Two independent internal ribosome entry sites are involved in translation
#=GF RT   initiation of vascular endothelial growth factor mRNA.
#=GF RA   Huez I, Creancier L, Audigier S, Gensac MC, Prats AC, Prats H
#=GF RL   Mol Cell Biol 1998;18:6178-6190.
#=GF CC   This family represents the vascular endothelial growth factor (VEGF)
#=GF CC   internal ribosome entry site (IRES) A. VEGF is an endothelial cell mitogen
#=GF CC   with many crucial functions such as embryogenic development and wound
#=GF CC   healing. The 5' UTR of VEGF mRNA contains two IRES elements which are able
#=GF CC   to promote efficient translation at the AUG start codon [1], this family
#=GF CC   represents IRES A.
#=GF WK   Vascular_endothelial_growth_factor_(VEGF)_IRES_A
#=GF SQ   7


BC061468.1/104-409   GCUAGCUCGGGCCUGGAGAAGCCGGGGCCCGAGAAGAGAGGGGAGGAAGA----GAAGGAAGAGGAGAGGGGGCCGCAGUGGGC-GCUCGGCUCUCAGGAGCCGAGCUCAUGGACGGGUGAGGCGGCCGUGUGCGCAGACAGUGCUCCAGCCGCGCGCGCGCCCCAGGCCCCGGCCCGGGCCUCGGUUCCAGAAGGGAGAGGAGCCCGCCAAGGCGCGCAAGAGAG--CGGGCUGCCUCGCAGUCCG-AGCCGGAGAG--GGAGCGCGAGCCGCGCCGGCCCCGGACGGGCCUCCGAAACCAUGAACUUUCUGCUC
U22373.1/1690-1983   GCUAGCUCGGGCCUGGAGAAGCCGGGGCCCGAGAAGAGAGGGGAGAA---AG-AGAAGGAAGAGGAGAGGGGGCCGCAGUGGGC-GCUCGGCUCUCGGGAGCCGGGCUCAUGGACGGGUGAGGCGGCGGUGUGCGCAGACAGUGCUCCAGCCGCGCGCG--CCCCAGGCCCCGGCCCGGGCCUCGGUUCCAGAAGGGAGAGGAGCCCGCCAAGG--CCGGCAAGAGAGCGG-CUGCCUCGCAGUCCG-AGCCGGAGAG--GGAGCGCGACGCGCGC-GGCCCCGGACGG-CCUCUGAAACCAUGAACUU-------
AF022375.1/415-716   GCUAGCUCGGGCCGGGAGGAGCCGCAGCCGGAGGAGGGGGAGGAGGAAGAAGA-GAAGGAAGAGGAGAGGGGGCCGCAGUGG-CGACUCGGCGCUCGGAAGCCGGGCUCAUGGACGGGUGAGGCGGCGGUGUGCGCAGACAGUGCUCCAGC-GCGCGCGCUCCCCAG-CCCUGGCCCG-GCCUCGGG-CCGGGAGGAAGAGUAGCUCGCCGAGGCGCCGAGGAGAG--CGGGCCGCCCCACAGCCCG-AGCCGGAGAG--GGA-CGCGAGCCGCGC--GCCCCGGUCGGGCCUCCGAAACCAUGAACUUUCUGCUG
AJ544164.1/1765-2070 GCUAGCUCGGGCCUGGAGAAGCCGGGGCCGGAGCAGAGGGAGGAGGAAGA----GAAGGAAAAGGAGAGGGGGUCGCAGUGGGC-GCUCGGCUCUCGGGAGCCGGGCUCAUGGACGGGUGAGGCGGCCGUGUGCGCAGACAGUGCUCCAGCCGCGCGCGCGCCCCAGGCCCUGGCCCGGGCCUCGGUUCCAGAAGGAAGAGCAGCCCGCCAAGGCGCGGAGGAGAG--CGGGCUGCCUCGCAGUCCG-AGCCGGAGAG--GGGGCACGAGCCGCGCCGGCCCCGGCCGGGCCUCCGAAACCAUGAACUUUCUGCUC
M63971.1/3107-3415   GCUAGCUCGGGCCGGGAGGAGCCGCAGCCGGAGGAGGGGGAGGAGGAAGAAGA-GAAGGAAGAGGAGAGGGGGCCGCAGUGG-CGACUCGGCGCUCGGAAGCCGGGCUCAUGGACGGGUGAGGCGGCGGUGUGCGCAGACAGUGCUCCAGCCGCGCGCGCUCCCCAGGCCCUGGCCCGGGCCUCGGGCCGGGGAGGAAGAGUAGCUCGCCGAGGCGCCGAGGAGAG--CGGGCCGCCCCACAGCCCG-AGCCGGAGAG--GGAGCGCGAGCCGCGCCGGCCCCGGUCGGGCCUCCGAAACCAUGAACUUUCUGCUG
U41383.1/1944-2240   GCUAGCUCGGCCCUGGAGAGGCCGGGGCCCGAGAAGAGAGGGGAG---------GAAGGAAGAGGAGAGGGGGCCACAGUGGGC-GCUCGGCUCUCAGGAGCCGAGCUCAUGGACGGGUGAGGCGGCCGUGUGCGCAGACAGUGCUCCAGCCGCGCGCGCGCCCCAGGCCCCGGCCCGGGCCUCGGUUCCAGAAGGGAGAGGAGCCCGCCAAGGCGCGCAAGAGAG--CGGGCUGCCUCGCAGUCCGGAGCCGGAGAGAGGGAGCGCGAGCCGCCGCGGCCCCGGACGG-CCUCCGAAACCAUGAACUUU------
M32976.1/252-560     GCUCGCUCGGGCCGGGAGGAGCCGCAGUCGGAGGAGGGGGAGGAGGAAGAAGA-GAAGGAAGAGGAGAAGGGGCCGCGGUGG-CGACUCGGCUCUCGGAAGCCGGGCUCAUGGACGGGUGAGGCAGCUGUGUGCACAGACAGUGCUCCAGCCGCGCGCGCGCCCCAGGCCCUGGCCCGGGCCUCGGCUCCGAGAGGAAGAGGAGCCCGCCUGGGCGCCGAGGAGAG--CGGGCCGCCCCGCAGCCCG-AGCCGGAGAG--GGAGCGCGAGCCGCGCCGGCCCCGGCCAGGCCUCCGAAACCAUGAACUUUCUGCUC
#=GC SS_cons         :<<--<<<-<<<<<<______>>>-->>>->>>->>-----------((-((..((-((--((((----((((((((-((((-(.-----((((((----((((((((--(((,,<<<-<<<<<<<<<<<<-<<<<_____>>>>-->>->>>>->>>->>>>>>,<<<---<<<<<<--<<<<<<<<<-<<<<<_________>>>->>-->>>->>>>>>----..>>>>>>>>>)))-)))))).))--------..-))))))--)))))))-))))))-------))))-----))------))-))-)):
#=GC RF              GCuaGCuCGGgCCgGGAGaAGCcGgaGcCgGaGaaGaGaGaGGAGgAaGAgg..gaAGGAAGaGGAGAgGGGGccgcAGcGggc.aCUCGGcgcuCgGaAccCGggCuCAcGgACGGGUGgGGCGGCgGuGUGCgCAGACAGcGCUCCaGCcGCGCGCGCcCCCCAGGCCCugGcCCGGGccucgGgcCcgGggGGaAGAGuAGCccGCcaAGgcGCcgaggAGAG..CGGgCcGCCcCgCaGccCG.ggCCGGAGAG..GGagcgCGAgcCgCgccggCCCCGGaCgGGCCuCcGAAACCAUGAACucUccGCuc
//
# STOCKHOLM 1.0

#=GF AC   RF00462
#=GF ID   IRES_APC
#=GF DE   APC internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Published; 12034871
#=GF SS   Published; PMID:12034871
#=GF GA   50.00
#=GF TC   59.90
#=GF NC   40.30
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   12034871
#=GF RT   Attenuated APC alleles produce functional protein from internal
#=GF RT   translation initiation.
#=GF RA   Heppner Goss K, Trzepacz C, Tuohy TM, Groden J
#=GF RL   Proc Natl Acad Sci U S A 2002;99:8161-8166.
#=GF CC   This family represents an APC internal ribosome entry site (IRES) which is
#=GF CC   located in the coding sequence of the gene. APC is a tumour suppressor
#=GF CC   gene which is associated with the inherited disease adenomatous polyposis
#=GF CC   coli (APC).It is thought that IRES-mediated translation of APC is
#=GF CC   important for an apoptotic cascade [1].
#=GF WK   APC_internal_ribosome_entry_site_(IRES)
#=GF SQ   6


BX934229.1/489-541 AGUCUCCACCUUACUGAAAAUUUCUCCUUGCAAACAGAUAUGACCAGAAGGCA
BX932893.1/573-625 AGCCUCCCCCUUACUGAAAAUUUCUCCUUGCAAACAGAUAUGACCAGAAGGCA
M74088.1/529-581   AGUCUUCCUUUAACUGAAAAUUUUUCCUUACAAACAGAUAUGACCAGAAGGCA
M73548.1/549-601   AGUCUUCCUUUAACUGAAAAUUUUUCCUUACAAACAGAUUUGACCAGAAGGCA
U64442.1/511-563   AGCCUUCCUCUUACAGAAAAUUUUUCCAUGCAGACUGAUAUGACCAGAAGACA
M88127.1/505-557   AGCCUGCCUUUAACUGAAAAUUUUUCCUUACAGACAGACAUGACAAGACGGCA
#=GC SS_cons       :<<<<<<----<<<<<__________________>>>->>------>>>>>>:
#=GC RF            AGcCuuCCUuUuACuGAAAAUUUUUCCUUaCAAACaGAUaUGACCAGaaGgCA
//
# STOCKHOLM 1.0

#=GF AC   RF00463
#=GF ID   ApoB_5_CRE
#=GF DE   Apolipoprotein B (apoB) 5' UTR cis-regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15157107
#=GF SS   Published; PMID:15157107
#=GF GA   55.00
#=GF TC   68.10
#=GF NC   51.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0045727; positive regulation of translation;
#=GF RN   [1]
#=GF RM   15157107
#=GF RT   Translational control of apolipoprotein B mRNA: regulation via cis
#=GF RT   elements in the 5' and 3' untranslated regions.
#=GF RA   Pontrelli L, Sidiropoulos KG, Adeli K
#=GF RL   Biochemistry 2004;43:6734-6744.
#=GF CC   This family represents an apolipoprotein B (apoB) cis regulatory element
#=GF CC   located in the 5' UTR of apoB mRNA. The element is important for optimal
#=GF CC   translation [1].
#=GF WK   Apolipoprotein_B_(apoB)_5'_UTR_cis-regulatory_element
#=GF SQ   5


AJ331299.1/203-76          AUUCCCCCCGAUAGAUACGGGGUUUAGUGCCCUUAUCGGUUCCGGCCGAUCAGCAGACCGGGCUUCCAGACAGGGCCGGGUGGCAGAGGCCAGGCCGCACGCCCUGGAGCCGCGCCACCGCAGCUGGU
X04714.1/1-127             AUUCCCACCGGGACCUGCGGGGCUGAGUGCCCUUCUCGGUUGCUGCCGCUGAGGAGCCCGCCCAGCCAGCCAGGGCCGCGAGGCCGAGGCCAGGCCGCA-GCCCAGGAGCCGCCCCACCGCAGCUGGC
X16152.1/899-1020          AUUCCCACCGGGACCUGCGGGGCUGAGUGCCCUUCUCGGUUGCUGCCGCUGAGGAGCCCGCCCAGCCAGCCAGGGCCGCGAGGCCGAGGCCAGGCCGCA-GCCCAGGAGCCGCCCCACCGCA---G--
ABBA01045079.1/69176-69050 AUUCCCACCGGGACCUGCGGGGCUGAGUGCCCUUCUCGGUUGCUGCCGCUGAGGAGCCCGCCCAGCCAGCCAGGGCCGCGAGGCCGAGGCCAGGCCGCA-GCCCAGGAGCCGCCCCACCGCAGCUGGC
AANU01117284.1/2465-2339   AUUCCCACCGGGACCUGCGGGGCUGAGUGCCCUUCUCGGUUGCUGUCGCUGAAGAGCCCGCCCAGCCAGCCAGGGCCGCGAGGCCGAGGCCAGGCCGCA-GCCCAGGAGCCGCCCCACCGCAGCCGGC
#=GC SS_cons               ::<<<<___>>>>,,(((((<<<<<-<<<--<<<<<<<<<_______>>>>>>>>>-->>>->>>>>,<<<--<<<<____>>>>-->>>,,,,))))).<<<----<<<-<<______>>->>>>>>
#=GC RF                    AUuccCaCCGggaccugCGGGGcugAguGCCCuccucgguUgCuGcCgcugaggaGcCCgcccagCCAGcCAGgGCCGcGaGGCcGAGgCCAGGCCGca.gCCCaGGgGCCGCcCCACCGCAGCcGGc
//
# STOCKHOLM 1.0

#=GF AC   RF00464
#=GF ID   mir-92
#=GF DE   mir-92 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   47.00
#=GF TC   47.30
#=GF NC   46.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000093;
#=GF DR   MIR; MI0000094;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   11914277
#=GF RT   miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.
#=GF RA   Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L,
#=GF RA   Rappsilber J, Mann M, Dreyfuss G
#=GF RL   Genes Dev 2002;16:720-728.
#=GF RN   [2]
#=GF RM   12919684
#=GF RT   Embryonic stem cell-specific MicroRNAs.
#=GF RA   Houbaviy HB, Murray MF, Sharp PA
#=GF RL   Dev Cell 2003;5:351-358.
#=GF CC   This family represents the microRNA precursor mir-92. Human miR-92 has two
#=GF CC   predicted hairpin precursor sequences: mir-92-1 on chromosome 13 and
#=GF CC   mir-92-2 on chromosome X. miR-92 has also been cloned from mouse embryonic
#=GF CC   stem cells [2]. The mature sequence is excised from the 3' arm of the
#=GF CC   hairpin.
#=GF WK   mir-92_microRNA_precursor_family
#=GF SQ   23


AF480564.1/1-75                --UCAUCCCUGGGUGGGGAUUUGUUGCAUUACUUGUGU-UCUAUA-UAAAGUAUUGCACUUGUCCCGGCCUGUGGAAGA---
AY866364.1/1209-1288           AUUCAUCCCUGGGUGGGGAUUUGUUGCAUUACUUGUGU-UCUAUA-UAAAGUAUUGCACUUGUCCCGGCCUGUGGAAGAAAG
AY866362.1/627-706             GUUCAUCCGUGGGUGGGGAUUUGUUGCAUUACUUGUGU-UAUAUG-UAAAGUAUUGCACUUGUCCCGGCCUGUGGAAGAAAA
AY866313.1/1180-1257           CUUUCUACACAGGUUGGGAUCGGUUGCAAUGCUG--UG-UUUCUG-UAUGGUAUUGCACUUGUCCCGGCCUGUUGAGUUUGG
AAFC03125572.1/1510-1589       AUUCAUUCAUGGGUGGGGAUUUGUUGCACUGCUUGUGU-UAUAUA-UAAAGUAUUGCACUUGUCCCGGCCUGUGGAAGAAAU
AAPY01386199.1/998-919         GUUCAUCUGUGGGUGGGGAUUUGUUGCAUUACUUGUGU-UAUAGA-AAAAGUAUUGCACUUGUCCCGGCCUGUGGAAGAAAG
AAFR03020267.1/47179-47102     CUUUCUACACAGGUUGGGAUCAGUUGCAAUGCUG--UG-UCUGUC-UGUAGUAUUGCACUUGUCCCGGCCUGUUGAGUUUGG
AALT01065661.1/430-350         AUUCAUCCAUGGGUGGGGAUUUGUUGCAUUACUUAUGUACAUGUA-UAAAGUAUUGCACUUGUCCCGGCCUGUGGAAGAAAC
AAIY01238597.1/3124-3045       AUUCAUCCCUGGGUGGGGAUUGGGUGCAUUACUUGUGU-CCUGUG-UGAAGUAUUGCACUUGUCCCGGCCUGUGGAAGAAAG
AANH01000396.1/150776-150700   CUUCCUGUGCAGGUGGGGAUUAGUAGCAAUGCUG--UG-UACCAG-AA-GGUAUUGCACUUGUCCCGGCCUGUAUAGGAAAA
CAAE01014781.1/2073848-2073925 UUUCCUGUACAGGUUGGGAGAGGUAGCAAUGCUCGGAG-UUCAUG---UGGUAUUGCACUUGUCCCGGCCUGUGGAGGAAGA
BAAF04006740.1/9737-9661       UGUCCUGUGCAGGUGGGGAUUAGUAGCAAUGCU---GU-UCUCCA-CGAGGUAUUGCACUUGUCCCGGCCUGUAAAGGAACG
AAGV020363925.1/1340-1417      CUUUCUACACAGGUUGGGAUCAGUUGCAAUGCUG--UG-UUUACA-UUUGGUAUUGCACUUGUCCCGGCCUGUUGAGUUUGG
CAAK05029381.1/12544-12621     CUUUCUGCGCAGGUUGGGAUUGGUAGCAAUGCUG--UG-UGUUUU-GAAGGUAUUGCACUUGUCCCGGCCUGUAAAGGAUUG
AAKN02053349.1/39968-39889     AUUCAUCCAUGGGUGGGGAUUUGUUGCAUUACUUGUAU-UAUAUG-UAAAGUAUUGCACUUGUCCCGGCCUGUGGAAGAAAG
BX571778.7/42340-42261         AUUCAUCCACAGGUGGGGAUUGGUGGCAUUACUUGUGU-UAGAUA-UAAAGUAUUGCACUUGUCCCGGCCUGAGGAAGAAAG
CR390304.1/341-418             CUUUCUACACAGGUUGGGAUCAGUUGCAAUGCUG--UG-CGUUUC-UGUGGUAUUGCACUUGUCCCGGCCUGUUGAGGUUGG
AAEX03026925.1/968784-968705   AUUCAUCCGCGGGUGGGGAUUUGUGGCAUUACUUGUGU-UCCAUA-UAAAGUAUUGCACUUGUCCCGGCCUGUGGAAGAAAG
AAGU03084137.1/881-802         GUUCAUCCAUGGGUGGGGAUUGAGUGCAUUGCUUGUGU-UAUGUA-UAAAGUAUUGCACUUGUCCCGGCCUAUGGAAGAAAG
AAGW02046787.1/21509-21429     AUUCAUCCGCUGGUGGGGAUUUGUCGCAUUACUUGUGU-UCUAUGGUAAAGUAUUGCACUUGUCCCGGCCUGUGGAGGAAAG
AAWZ02030636.1/2951-3030       CUUUCUACACAGGUUGGGAUUGGUUGCAAUGCUGUCUA-UGUGUA-UGUGGUAUUGCACUUGUCCCGGCCUGUUGAGGUUGG
CAAB02005283.1/88710-88787     UUUCCUGUGCAGGUUGGGAGAGGUAGCAAUGCUC--AG-AGAUUA-UGCGGUAUUGCACUUGUCCCGGCCUGUGGAGGAAGG
AABR05054502.1/20428-20505     CUUUCUACACAGGUUGGGAUUUGUCGCAAUGCUG--UG-UUUCUG-UAUAGUAUUGCACUUGUCCCGGCCUGUUGAGUUUGG
#=GC SS_cons                   :::<<<--<<<<<<-<<<<<-<<<-<<<<<<<<<____.______.__>>>>>>>>>>>>->>>>>->>>>>>-->>>::::
#=GC RF                        aUUccUaCacaGGUgGGGAuUaGUuGCAaUgCuuGUgu.UaUaUa.UaaaGuAuUGCACuUgUCCCGGCCugugGAggAaag
//
# STOCKHOLM 1.0

#=GF AC   RF00465
#=GF ID   JEV_hairpin
#=GF DE   Japanese encephalitis virus (JEV) hairpin structure
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15113895
#=GF SS   Published; PMID:15113895
#=GF GA   45.00
#=GF TC   45.90
#=GF NC   44.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0032774; RNA biosynthetic process;
#=GF RN   [1]
#=GF RM   15113895
#=GF RT   Accumulation of a 3'-terminal genome fragment in Japanese encephalitis
#=GF RT   virus-infected mammalian and mosquito cells.
#=GF RA   Lin KC, Chang HL, Chang RY
#=GF RL   J Virol 2004;78:5133-5138.
#=GF CC   This family represents a small hairpin structure found in the 5' UTR of
#=GF CC   Japanese encephalitis and related viruses. This element is significantly
#=GF CC   over-represented upon host cell infection and it has been suggested that
#=GF CC   the family may play a role in regulating RNA synthesis [1].
#=GF WK   Flavivirus
#=GF SQ   20


AY303798.1/10454-10512 AUGGAGUCAGGCCAG--CAAAA-GCUGCCACCGGAUACUGGGUAGACGGUGCUGCCUGCGUC
L54071.1/246-304       AUGGAGUCAGGCCAG--CAAAC-GCUGCCACCGGAUACUGGGUAGACGGUGCUGCCUGCGUC
AY277251.1/10451-10508 UGU-AGUCAGGCCGG--CAAA-CGCCGCCACCGGAAGUUGGGUAUACGGUGCUGCCUGUGAC
AF196543.1/291-350     AGAGAGUCAGGCCAGACUAGAG--CUGCCACCGGAAGUUGAGUAGACGGUGCUGCCUGCAAC
AF458353.1/265-324     AGGAAGUCAGGCCGGAGCAUUU--CCGCCACCGGAUGCUGAGUAGACUGUGCUGCCUGCGUC
L48966.1/292-348       -GUGAGUCAGGCCAG--UGAAA-ACUGCCACCGGAUGUUGG-UAGACGGUGCUGCCUGCGAC
L78128.1/10429-10487   ACGGAGUCAGGCCAG--CAAAA-GCUGCCACCGGAUACUGGGUAGACGGUGCUGCCUGCGCC
L54067.1/246-304       AUGGAGUCAGGCCAG--CAAAC-GCUGCCACCGGAAACUGGGUAGACGGUGCUGCCUGCGUC
AF306516.1/54-112      AUGGAGUCAGGCCAG--CAAAA-GCUGCCACCGGAUAAUGGGUAGACGGUGCUGCCUGCGUU
AY278556.1/147-205     GUGGAGUCAGGCCAG--CAAAA-GCUGCCACCGGAUACUGAGUAGACGGUGCUGCCUGCGUC
AF458352.1/265-324     AGGAAGUCAGGCCGGAGCAUUU--CCGCCACCGGAUGUUGAGUAGACGGUGCUGCCUGCGUC
AF306515.1/54-112      AUGGAGUCAGGCCAG--CAAAA-GCUGCCACCGGAUAAUGGGUAGACGGUGCUGCCUGGGUU
AF098736.1/10454-10512 AUGGAGUCAGGCCAG--CAAAA-GCUGCCACCGGAUACUGGGCAGACGGUGCUGCCUGCGUC
L48980.1/304-362       AUGGAGUCAGGCCAG-GUAACA--CUGCCACCGGAAGUUGGGUAUACGGUGCUGCCUGUACC
AY184212.1/10454-10512 AUGGAGUCAGGCCAG--CGUUA-GCUGCCACCGGAUACUGGGUAGACGGUGCUGCCUGCAAC
AY316157.1/10440-10498 GUGGAGUCAGGCCAG--CAAAA-GCUGCCACCGAAUACUGAGUAGACGGUGCUGCCUGCCUC
AF306514.1/49-107      GUGGAGUCAGGCCAG--CAAAA-GCUGCCACCGGAUACUGAGUAGACGGUGCUGCCUGGGUU
AF458346.1/310-369     UGGAAGUCAGGCCAG-ACAAAU-GCUGCCACCGGAAGUUGAGUAGACGGUGCUGCCUGCGAC
M18370.1/10454-10512   AUGGAGUCAGGCCAG--CAAAA-GCUGCCACCGGAUACUGGGUAGACGGUGCUGUCUGCGUC
AF306517.1/63-121      AUGGAGUCAGGCCAG--CAAAA-GCUGCCACCGGAUACUGGGUAAACGGUGCUGCCUGCGUC
#=GC SS_cons           :::::<-<<<<<-<<..<<---.-<<<<<--<<<___>>>>>>>>---->>>>>>>>>>:::
#=GC RF                AuGGAGUCAGGCCAG..CAAAa.GCuGCcACCGgAUacUGgGUaGACGGUGCUGCCUGCGuC
//
# STOCKHOLM 1.0

#=GF AC   RF00467
#=GF ID   RSV_PBS
#=GF DE   Rous sarcoma virus (RSV) primer binding site (PBS)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15153244
#=GF SS   Published; PMID:15153244
#=GF GA   47.00
#=GF TC   47.30
#=GF NC   46.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 1900268; regulation of reverse transcription;
#=GF RN   [1]
#=GF RM   15153244
#=GF RT   Selection of functional mutations in the U5-IR stem and loop regions of
#=GF RT   the Rous sarcoma virus genome.
#=GF RA   Johnson M, Morris S, Chen A, Stavnezer E, Leis J
#=GF RL   BMC Biol 2004;2:8.
#=GF CC   This family represents a structured region around the Rous sarcoma virus
#=GF CC   primer binding site (PBS). This region is known to be required for the
#=GF CC   efficient initiation of reverse transcription [1].
#=GF WK   Rous_sarcoma_virus_(RSV)_primer_binding_site_(PBS)
#=GF SQ   22


X03980.1/56-130    AUUCCCUGACGACUACGAGCACAUGCAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
D10652.1/56-130    AGUCCCUAACGGUUGCGAACACCUGGAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUAGUUAGGGAAU
X06197.1/56-130    AGUCCCUAACGAUUGCGAACACCUGAAUGAAGCGGAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
AY013304.1/231-305 AGUCCCUAACGAUUGCGAACACCUGAAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
L29198.1/285-359   AUUCCCUGACGACUACGAGCACCUGCAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUAGUUAGGGAAU
AF033808.1/56-130  AUUCCCUAACGAUUGCGAACACCUGAAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUAGUUAGGGAAU
L10923.1/347-421   AUUCCCUGACGACUACGAGCACCUGCAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
X51496.1/44-118    AUUCCCUGACGACUGCGAACACCUGAAUGAAGCUGAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
V01170.1/56-130    AUUCCCUGACGACUACGAGCACCUGAAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
X68524.1/56-130    AUUCCCUAACGAUUGCGAACACCUGAAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
M21526.1/290-364   AGUCCCUAACGAUUGCGAACACCUGAAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUGGUUAGGGAAU
M10455.1/56-130    AUUCCCUGACGACUACGAACACCUAAAUGAAGCGGAAGGCUUCAUUUGGUGACCCCGACGUGAUAGUUAGGGAAU
M31387.1/56-130    AUUCCCUGACGACUACGAGCACAUGCAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGAUGUGAGGGUUAGGGAAU
Z46390.1/280-354   AUUCCCUGACAACUACGAGCACCUGCAUGAAGCGGAUGGCUUCAUUUGGUGACCCCGAUGUGAUAGUUAGGGAAU
AY350569.1/56-130  AUUCCCUGACGACUACGAGCACAUGCAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUCAUUAGGGAAU
J02339.1/57-131    AUUCCCUGACGACUACGAGCACAUGCAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUUGUUAGGGAAU
V01174.1/383-457   AGUCCCUAACGAUUACGCGAACCUGAAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
M11786.1/56-130    AUUCCCUAACGACUACGAGCACCUGCAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
X51863.1/290-364   AUUCCCUAACGAUUGCGAACACCUGAAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUGGUUAGGGAAU
AY027920.1/280-354 AUUCCCUGACGACUACGAGCACCUGAAUGAACCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
Y00302.1/56-130    AGUCCCUAACGAUUGCGAACACCUGCAUGAAGCGAAAGGCUUCAUUUGGUGACCCCGACGUGAUCGUUAGGGAAU
L21974.1/290-364   AGUCCCUAACGAUUGCGAACACCUGAAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUAGUUAGGGAAU
#=GC SS_cons       ::<<<<<<<<----------------<<<<<<<_____>>>>>>>-------------------->>>>>>>>::
#=GC RF            AuUCCCUaACGAuUaCGAaCACcUGaAUGAAGCAGAAGGCUUCAUUUGGUGACCCCGACGUGAUaGUuAGGGAAU
//
# STOCKHOLM 1.0

#=GF AC   RF00468
#=GF ID   HCV_SLVII
#=GF DE   Hepatitis C virus stem-loop VII
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Griffiths-Jones S; 0000-0001-6043-807X
#=GF SE   PMID:15452207
#=GF SS   Predicted; RNAalifold; Griffiths-Jones S
#=GF GA   45.00
#=GF TC   45.60
#=GF NC   43.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF RN   [1]
#=GF RM   15452207
#=GF RT   Cis-acting RNA signals in the NS5B C-terminal coding sequence of the
#=GF RT   hepatitis C virus genome.
#=GF RA   Lee H, Shin H, Wimmer E, Paul AV
#=GF RL   J Virol 2004;78:10865-10877.
#=GF CC   This family represents the Hepatitis C stem-loop VII structure found in
#=GF CC   the coding region of the RNA-dependent RNA polymerase gene, NS5B. The
#=GF CC   structure is important (but not essential) for colony formation, though
#=GF CC   its exact function and mechanism are unknown [1].
#=GF WK   Hepatitis_C_virus_stem-loop_VII
#=GF SQ   110


AB154194.1/9114-9179 AAGCUCCUGUCCCAGGGGGGGAGGGCUGCCAACUGUGGCAAAUACCUCUUCAACUGGGCAGUAAGG
AB080299.1/9126-9191 AAGUUACUGUCCCAGGGGGGGAGGGCCGCCACUUGUGGCAAGUACCUCUUCAACUGGGCAGUAAAG
AF177036.1/9195-9259 CCCUCAUCUCCC-GUGGGGGGAGAGCGGCCGUUUGCGGUCGAUAUCUCUUCAAUUGGGCGGUGAAG
AY682766.1/1540-1605 AAGCUUCUGUCCAGAGGAGGCAGGGCUGCCAUAUGUGGCAAGUACCUCUUCAAUUGGGCAGUAAGA
D49766.1/849-913     AGCUUAUCGCCC-AGGGUGGGAAAGCCGCUAUAUGCGGCACGUACCUCUUUAACUGGGCCGUAAAA
AB189095.1/1528-1593 AAGCUACUGUCCCAGGGGGGGAGGGCCGCCACUUGCGGUAAAUACCUCUUCAACUGGGCAGUAAGG
AY232731.1/9159-9223 CGCUCAUCGCCC-AAGGAGGGAGAGCGGCCAUUUGCGGCCGCUACCUCUUCAACUGGGCGGUGAAG
D86536.1/849-913     AGCUUAUCGCCC-AGGGAGGUAGAGCCAAAAUCUGUGGCAUAUACCUCUUUAACUGGGCGGUAAAA
D87362.1/849-913     AACUCAUCGCCC-AAGGGGGGAAAGCGGCUAUAUGCGGUAAGUACCUCUUCAAUUGGGCGGUGAAG
AB031663.1/9196-9260 CACUCAUCUCCC-AGGGAGGGAGAGCGGCCACUUGUGGCUUCUAUCUCUUCAACUGGGCGGUGAGG
AF054263.1/191-256   AAGCUACUGUCCCAGGGGGGGAGGGCCGCCACUUGUGGCAGAUACCUCUUUAACUGGGCAGUAAGG
M58335.1/9117-9182   AGGCUACUGUCCCAGGGAGGGAGGGCCGCCACUUGUGGCAAAUACCUCUUCAACUGGGCAGUAAAA
AB189089.1/1528-1593 AAGCUGCUGUCCCAGGGGGGGAGGGCUGCUACUUGUGGCAAAUACCUCUUCAACUGGGCAGUAAGG
AB189101.1/1528-1593 AAGCUACUGUCCCAGGGGGGGAGGGCUGCCACAUGUGGCAGAUACCUGUUCAACUGGGCAGUAAGG
AY973861.1/1514-1578 AGCUUAUCGCCC-AGGGAGGGAAGGCCAAAAUAUGUGGCCUUUAUCUCUUCAAUUGGGCGGUACGC
D87356.1/849-913     AACUCAUUGCCC-AGGGGGGGAAAGCUGCUAUAUGCGGCAAGUACCUCUUUAACUGGGCGGUGAAG
AY682786.1/1540-1605 AGGCUUCUGUCCAGGGGAGGCAGGGCUGCCAUAUGUGGCAAAUACCUCUUCAACUGGGCAGUAAGA
D84262.2/9155-9219   AACUCAUUGCCC-AAGGUGGGAAAGCAGCGAUAUGCGGCAAGUACCUCUUUAACUGGGCAGUGAAG
AF238482.1/9161-9225 CCCUCAUCUCCC-AUGGAGGGAGGGCGGCCGUUUGCGGUCGGUAUCUCUUCAACUGGGCGGUGAAG
AY682753.1/1540-1605 AGGCUUCUGUCCAGAGGAGGCAGGGCUGCCAUUUGUGGCAGGUACCUCUUCAACUGGGCAGUAAGG
AB047645.1/9192-9256 CCCUCAUCUCCC-GCGGGGGGAGAGCGGCCGUUUGCGGUCGGUAUCUCUUCAACUGGGCGGUGAGG
AB049095.1/9095-9160 AAGCUACUGUCCCAAGGAGGGAGGGCCGCCACUUGUGGCAAGUACCUCUUCAACUGGGCAGUAAGG
AB057681.1/1528-1593 AAGCUACUGUCCCAAGGGGGGAGGGCCGCCACUUGUGGCAGGUACCUGUUCAACUGGGCGGUAAGG
D63821.1/9152-9216   AGCUCAUUUCCC-AGGGAGGGAAGGCCAAAAUCUGUGGCCUUUACCUCUUCAACUGGGCAGUGCGC
AY232745.1/9159-9223 CACUCAUCGCCC-AGGGAGGGAGGGCGGCCAUUUGCGGUCGCUACCUCUUUAACUGGGCGGUGAAG
AY973849.1/1498-1563 AGGCUCCUGUCCAGAGGAGGGAGGGCUGCCAUAUGUGGCAAGUACCUCUUCAACUGGGCAGUAAGA
AB057616.1/1528-1593 AAGUUACUGUCCCAGGGGGGGAGGGCCGCUAAUUGCGGCAAAUACCUCUUCAACUGGGCAGUAAGG
D49374.1/9164-9228   AACUCAUUGCCC-AAGGAGGAAAGGCCAGAAUAUGCGGUCUAUACCUCUUUAACUGGGCAGUGCGC
AY232739.1/9159-9223 CACUCAUCGCCC-AAGGGGGGAGGGCGGCCAUCUGUGGCCGCUACCUCUUCAACUGGGCGGUGAAG
AB189115.1/430-495   AAGCUACUGUCCCAGGGGGGGAGGGCUGCCACGUGUGGCAAGUACCUCUUCAACUGGGCAGUAAGG
D86543.1/849-913     AGCUCAUCGCCC-AGGGAGGGAGAGCCAAGAUCUGUGGCAUAUAUCUCUUCAACUGGGCGGUGAGA
U16362.1/9127-9192   AAGCUACUGUCCCAGGGGGGGAGGGCCGCCACUUGUGGCAAGUACCUCUUCAACUGGGCGGUGAGG
D49767.1/849-913     AGCUCAUUUCCC-AAGGAGGGAAGGCCAAAAUCUGCGGCCUGUACCUCUUUAACUGGGCAGUGCGC
AY232732.1/9159-9223 CACUCAUCGCCC-AAGGAGGGAAGGCAGCCAUUUGUGGCCGCUACCUCUUCAACUGGGCGGUGAAG
D86537.1/849-913     AGCUCAUCGCUC-AGGGGGGCAAGGCCAGAAUCUGUGGCAUAUACCUCUUCAACUGGGCGGUGAAA
AJ000009.1/9109-9174 AAGCUACUGUCCCAGGGGGGAAGGGCUGCCACUUGUGGCCGCUACCUCUUCAACUGGGCAGUAAAG
D37862.1/849-913     AGCUUAUCACCC-GAGGGGGGAAAGCUGCUAUAUGCGGCAAGUACCUCUUCAACUGGGCGGUAAAA
D87357.1/849-913     AACUCAUUGCCC-AGGGAGGUGCAGCAGCAAUAUGCGGCAAGUACCUCUUUAACUGGGCGGUGAGG
D84263.2/9133-9197   AGCUCAUCGCCCAAGGGGGGAAACAC-GCUAUAUGCGGUAAGUACCUCUUCAAUUGGGCCGUGAGA
D16617.1/849-913     AGCUCAUUGUCC-AGGGGGGAAAGGCCAGAAUAUGUGGUCUAUACCUCUUUAACUGGGCAGUGCGC
D49760.1/849-913     CCCUCAUUGUCC-AAGGAGGGAAGGCGGCUAUAUGCGGCCGCUAUCUCUUCAAUUGGGCAGUGAAG
D86530.1/849-913     CCCUCAUUGCCC-GGGGAGGGAGGGCGGCCAUAUGUGGCCGCUACCUCUUUAACUGGGCAGUGAGA
D14853.1/9129-9194   ACACUCCUAUCCCAGGGGGGGAGAGCCGCUAUAUGCGGUAAGUAUCUCUUCAACUGGGCGGUGAAA
AB049096.1/9095-9160 AAGCUACUGUCCCAAGGGGGGAGGGCUGCCACCUGUGGCAAAUACCUCUUCAAUUGGGCUGUAAGG
AY232746.1/9159-9223 CACUCAUUGCCC-AGGGAGGGAGAGCGGCCAUUUGUGGACGCUACCUCUUCAACUGGGCGGUGAAG
D30797.1/849-913     AGCUCAUUGCUC-AGGGGGGGAAAGCCGCUAUUUGCGGCAAGUACCUCUUCAACUGGGCGGUGAAG
AF064490.1/9044-9108 AGCUCAUCGCUC-AGGGAGGUAAGGCCGCCAUCUGCGGCAUCUAUCUCUUCAACUGGGCGGUGAAA
D49780.1/849-913     CCCUCAUUGUCC-AAGGAGGAAGAGCGGCCACAUGUGGCCGCUACCCCUUCAAUUGGGCAGUGAAG
M84754.1/9126-9191   AAGCUACUGUCUCAGGGGGGGAGGGCUGCCACUUGUGGCCGGUACCUCUUCAACUGGGCGGUAAAG
AF207758.1/9114-9179 AAGCUGCUGUCCCGGGGGGGGAGGGCAGCCACUUGUGGCAAAUACCUCUUCAACUGGGCAGUGAGG
D49774.1/849-913     AGCUCAUUUCCC-AGGGAGGGAAGGCUAAAGUCUGCGGCCUUUACCUCUUUAACUGGGCAGUGCGC
AB057598.1/1528-1593 AGGCUACUGUCCCGGGGGGGGAGGGCUGCCACUUGUGGCAAAUACCUCUUCAACUGGGCAGUAAAG
AB186421.1/842-907   AAGCUGCUGUCCCAGGGGGGGAGGGCCGCCACUUGUGGCAGGUACCUCUUCAACUGGGCGGUAAAA
D87364.1/849-913     AGCUCAUCGCCC-AGGGGGGGAAAGCCGCUAUCUGCGGUAAGUACCUCUUCAACUGGGCGGUGAAG
S62220.1/9137-9202   AAACUACUGUCCCAGGGGGGGAGGGCGGCCACUUGCGGCAAAUACCUCUUCAACUGGGCAGUAAAG
U45476.1/9126-9191   AAGCUACUGUCCCCGGGGGGGGAGGGCUCCACUUGUGGCAAAUACCUCUUCAACUGGGCAGUAAGG
D37863.1/849-913     AGCUGAUCAGCC-GGGGGGGGAAAGCCGCAAUAUGCGGCAAGUACCUCUUCAAUUGGGCGGUAAAA
AY682761.1/1540-1605 AGGCUUCUGUCCAGAGGAGGCAGAGCUGCCAUAUGUGGCCAGUACCUCUUCAACUGGGCAGUAAGA
D84264.2/9142-9206   AGCUUAUUGCCC-AAGGGGGAGGCGCUGCAAUUUGCGGCAAGUACCUCUUCAACUGGGCAGUAAAG
D86531.1/848-913     AAGUUGCUGUCCCAGGGGGGGAGGGCUGCCAUCUGCGGUAAGUACCUCUUCAACUGGGCAGUAAGG
D37857.1/849-913     AGCUCAUUGCUC-AGGGGGGGAAAGCCGCUAUUUGCGGCAGAUACCUCUUCAAUUGGGCCGUGAGA
AB057683.1/1528-1593 AAGCUGCUGUCUCAGGGGGGGAGGGCCGCCAUUUGUGGCAAAUACCUCUUCAACUGGGCAGUAAGG
AY682775.1/1540-1605 AGGCUACUGUCCAGGGGAGGUAGGGCUGCCAUAUGUGGCAAGUACCUCUUCAACUGGGCUGUAAAG
D49775.1/849-913     CCCUCAUUGCCC-AGGGAGGGAGAGCGGCCAUAUGUGGCCGCUAUCUCUUUAAUUGGGCUGUGAGG
D49769.1/849-913     CUCUCAUCGUCC-GGGGGGGGAGGGCGGCCACCUGUGGCCGCUACCUCUUUAACUGGGCGGUGAAG
AY232734.1/9159-9223 CACUCAUCGCCC-AGGGAGGGAGAGCGGCCACUUGUGGCCGCUACCUCUUCAACUGGGCGGUGAGG
D86539.1/849-913     AGCUCAUCGCCC-AGGGAGGGAAAGCCAAAAUCUGUGGCGUGUACCUCUUCAACUGGGCGGUGAAA
D84265.2/9139-9203   AGCUUAUUGCCC-AAGGAGGGAAAGCCGCAGUAUGUGGCAAGUACCUCUUCAAUUGGGCGAUAAAG
D16619.1/849-913     AGCUUAUCGCCC-AAGGAGGAAAGGCCAAGAUUUGUGGCCUCUACCUUUUCAAUUGGGCGGUACGC
AB057690.1/1528-1593 AGGCUACUGUCCCAGGGGGGGAGGGCCGCCACUUGUGGCAAAUACCUCUUCAAUUGGGCAGUAAGG
D37858.1/849-913     AACUCAUCGCCC-AGGGGGGGAAAGCCGCAAUAUGUGGUCGGUACCUCUUUAACUGGGCUGUGAGA
AB049098.1/9095-9160 AAACUACUGUCCCAGGGGGGGAGGGCCGCCACCUGUGGCAAAUACCUCUUCAACUGGGCAGUGAAG
U89019.1/9109-9171   AAGCUACUGUCCCAAGGGGGGAGGGCUGCCACUUGU---GAAUACCUCUUCAAUUGGGCGGUAAAG
AY878650.1/9125-9189 AGCUUAUCGCCC-AGGGAGGGAACGCAGCGAUUUGCGGCAAGUACCUCUUUAAUUGGGCGGUAAGG
D10988.1/9196-9260   CACUCAUCGCCC-AAGGAGCGAGGGCGGCCAUUUGUGGCCGCUACCUCUUCAACUGGGCGGUGAAA
M67463.1/9129-9194   AGGCUUCUGGCCAGAGGAGGCAAGGCUGCCAUAUGUGGCAAGUACCUCUUCAACUGGGCAGUAAGA
AB189118.1/430-495   AAGCUGCUGUCCCAGGGAGGGAGGGCUGCCACUUGUGGCAAGUACCUCUUUAACUGGGCAGUAAGG
D49776.1/849-913     CCCUCAUUGCCC-AAGGGGGAAAAGCGGCCACGUGUGGCCGCUACCUCUUCAAUUGGGCGGUGAGG
AB057612.1/1528-1593 AGGCUACUGUCUCAGGGGGGGAAGGCUGCCACUUGUGGCAAAUACCUCUUCAACUGGGCGGUAAGG
AB189099.1/1528-1593 AGACUGCUGUCCCAGGGGGGGAGGGCUGCCACUUGUGGCAAAUACCUGUUCAACUGGGCAGUGAAG
AY973865.1/1529-1593 AACUCAUUGCCC-AAGGGGGGAAAGCGGCCAUAUGCGGUAAGUACCUCUUUAACUGGGCAGUGAAG
D00828.1/852-916     CACUCAUCGCCC-AGGGAGGGAGAGCGGCCAUCUGUGGCCGUUACCUCUUCAACUGGGCGGUGAAG
D87353.1/849-913     AGCUUAUUGCCC-AAGGAGGGAAGGCUGCAAUAUGUGGCAAGUACCUCUUUAAUUGGGCGAUAAAG
D16613.1/849-913     AGCUCAUCGCUC-AAGGAGGAAAGGCCAAAAUUUGUGGUCUUUACCUCUUCAAUUGGGCGGUACGC
AB057679.1/1528-1593 AAGCUACUGUCCCAGGGGGGGAGAGCUGCCACUUGUGGCAGAUAUCUGUUCAACUGGGCGGUAAGG
AY232742.1/9159-9223 CACUCAUCGCCC-AGGGAGGGAGGGCGGCCAUUUGUGGCCGAUACCUCUUCAACUGGGCUGUGAAG
D50467.1/849-913     AGCUCAUCGCUC-AGGGAGGUAGGGCCGCCAUCUGCGGCACCUAUCUCUUUAACUGGGCGGUGAGA
D84398.1/850-913     CCUCAUCAGCCG--GGGGGGGAGGGCGGCCACGUGCGGUCGCUACCUCUUCAACUGGGCUGUGAAG
AB057692.1/1528-1593 AAGUUGCUGUCCCAGAGGGGGAGGGCCGCCAUUUGUGGCAAGUACCUCUUCAACUGGGCAGUAAAA
AF511948.1/9130-9195 AGACUUCUGUCCAGAGGAGGCAGGGCUGCCAUAUGUGGCAAGUACCUCUUCAACUGGGCAGUAAAA
D87360.1/849-913     AACUCAUUGCCC-AAGGAGGGAGAGCAGCUAUAUGCGGCAGAUACCUCUUUAACUGGGCGGUGAAG
AB030907.1/9196-9260 CACUCAUCAUCC-AGGGAGGGAGGGCGGCCACUUGUGGACGCUACCUCUUCAACUGGGCGGUGAAG
AB057600.1/1528-1593 AAGCUGCUGUCCCAGGGGGGGAGAGCUGCCACUUGUGGCAAGUACCUCUUCAACUGGGCAGUAAAA
AY682758.1/1540-1605 AGGCUCCUGUCCAGGGGAGGCAGAGCUGCCAUAUGUGGCAAGUACCUCUUCAAUUGGGCAGUAAGA
D31973.1/853-916     CCUCAUCAGCCG--AGGUGGGAGGGCGGCCACAUGUGGCCGUUACCUCUUCAACUGGGCUGUGAAG
D37853.1/849-913     AACUCAUUGUCC-AGGGAGGAAGGGCCAGAAUAUGUGGCCUAUACCUCUUUAACUGGGCAGUGCGU
D50480.1/9114-9179   AAGCUACUGUCCCAGGGGGGGAGGGCCGCCACCUGUGGGAGGUACCUCUUCAACUGGGCAGUAAAG
D49778.1/849-913     CCCUCAUUGUCC-AAGGAGGAAAAGCGGCCAUAUGCGGCCGCUACCUCUUUAAUUGGGCAGUGAAG
AB057614.1/1528-1593 AAGCUACUGUCCCAGGGAGGAAGGGCCGCCAUCUGUGGCAAAUACCUCUUCAAUUGGGCAGUAAGG
D50409.1/9208-9271   CCUCAUCAGCCG--AGGGGGGAGCGCGGCCACAUGUGGCCGCUACCUCUUCAACUGGGCUGUGAGG
AY460204.1/9129-9194 AAGCUACUGUCCCGGGGGGGGAGGGCUGCCAUUUGCGGCACGUACCUCUUCAACUGGGCAGUAAAG
D16621.1/849-913     AGCUUAUAGCUC-AGGGGGGAAAGGCCAAAAUCUGUGGCCUUUACCUCUUUAACUGGGCUGUACGC
D86529.1/849-913     CGCUCAUCUCCC-GGGGUGGGAGGGCGGCCAUUUGUGGCCGUUACCUCUUCAACUGGGCGGUGAAA
D16615.1/849-913     AGCUCAUCGCCC-AAGGAGGGAAGGCCAGAAUAUGUGGCUUGUACCUCUUCAACUGGGCAGUACGC
AF238481.1/9161-9225 CCCUCAUCUCCC-AUGGGGGGAGAGCGGCCAUUUGCGGUCGGUAUCUCUUCAACUGGGCGGUGAAA
AB047644.1/9195-9259 CCCUCAUCUCCC-GAGGGGGGAGAGCGGCCAUUUGUGGCCGGUAUCUCUUCAACUGGGCGGUGAAG
AY682779.1/1540-1605 AAGUUGCUGUCCCAGGGGGGGAGGGCCGCCAUCUGUGGCAGGUACCUCUUCAACUGGGCAGUAAGG
AB057680.1/1528-1593 AAGCUGCUGUCCCAGGGGGGGAGGGCCGCCACGUGUGGCAAGUAUCUCUUCAACUGGGCGGUAAGG
D49772.1/849-913     CCUUAAUUGUCC-AAGGAGGAAGAGCGGCCAUAUGUGGCCGCUACCUCUUCAACUGGGCAGUUAAG
D86542.1/849-913     AGCUUAUCGCCC-AGGGAGGUAAAGCCAAGAUAUGUGGCAUAUACCUCUUCAACUGGGCGGUAAAA
#=GC SS_cons         ::::::<<<<<<.-<<<<<<----<<<<<_____>>>>>----->>>>>>----->>>>>>:::::
#=GC RF              AacUuAcuGcCC.AgGGaGGGAggGCcgCcAUuUGcgGCaagUACCuCUuCAACUGGgCagUaAag
//
# STOCKHOLM 1.0

#=GF AC   RF00469
#=GF ID   HCV_SLIV
#=GF DE   Hepatitis C stem-loop IV
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15452207
#=GF SS   Predicted; ILM; Moxon SJ
#=GF GA   45.00
#=GF TC   45.10
#=GF NC   44.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF RN   [1]
#=GF RM   15452207
#=GF RT   cis-acting RNA signals in the NS5B C-terminal coding sequence of the
#=GF RT   hepatitis C virus genome.
#=GF RA   Lee H, Shin H, Wimmer E, Paul AV
#=GF RL   J Virol 2004;78:10865-10877.
#=GF CC   This family represents the Hepatitis C stem-loop IV structure found in the
#=GF CC   NS5B coding region. The family, along with Rfam:RF00468, is important (but
#=GF CC   not essential) for colony formation, though its exact function and
#=GF CC   mechanism are unknown [1].
#=GF WK   Hepatitis_C_stem-loop_IV
#=GF SQ   110


D87352.1/1040-1076   CUGUGCCUACUCCUACUGUCCGUAGGGGUAGGCAUCU
AY045702.1/9320-9356 UUGUGCCUACUCCUACUUUCAGUAGGGGUAGGCAUCU
AB080299.1/9318-9354 UGGUGCCUACUCCUACUUUCCGUAGGGGUAGGCAUCU
AF177036.1/9387-9422 UUG-GCCUACUCCUACUUUUUGUAGGGGUAGGCCUUU
AY232748.1/9350-9386 CUCUGCCUACUCCUACUUAGCGUAGGGGUAGGCAUCU
AF207766.1/9306-9342 UUGUGCCUACUCCUACUUUCUGUGGGGGUAGGCAUCU
D10988.1/9387-9423   CUUUGCCUACUCCUACUUAGCGUAGGAGUAGGCAUCU
D49766.1/1040-1076   CUGUGCCUACUCCUACUUACAGUAGGGGUAGGCAUCU
AY232731.1/9350-9386 CUUUGCCUACUCCUACUUAGCGUAGGGGUAGGCAUCU
D86536.1/1040-1076   CUGUGCCUACUCCUACUCUCAGUAGGGGUAGGCAUCU
D14312.1/1043-1079   CUUUGCCUACUCCUACUAACGGUAGGGGUAGGCAUCU
D87362.1/1041-1076   UUG-GCCUACUCCUACUCACCGUAGGGGUAGGCAUCU
AB057602.1/1720-1756 UUGUGCCUACUCCUACUUUCCGUAGGGGUAGGCAUUU
M67463.1/9321-9357   UUUUGCCUACUCCUGCUUGCUGCAGGGGUAGGCAUCU
AB049091.1/9236-9272 UUGUGCCUACUCCUACUUUCCGUAGGGGUAGGCAUCU
AB016785.1/9328-9364 UGGUGCCUACUCCUACUCUCUGUAGGGGUAGGCAUCU
AB031663.1/9387-9423 CUUUGCCUACUCCUACUCAGCGUAGGGGUAGGCAUCU
AF054263.1/383-419   UUGUGCCUACUCCUACUUUCUGUAGGGGUAGGCAUUU
AB057688.1/1720-1756 UUCUGCCUACUCCUACUUUCUGUAGGGGUAGGCAUCU
D49776.1/1041-1076   UUG-GCCUACUCCUGCUUAGUGUAGGGGUAGGCAUCU
M58335.1/9309-9345   CUGUGCCUACUCCUACUUUCUGUAGGGGUAGGCAUCU
AF169002.1/9387-9422 UUG-GCCUACUCCUACUUUUCGUAGGGGUAGGCCUCU
D14306.1/1043-1079   CUUUGCCUACUCCUACUAACAGUAGGGGUAGGCAUCU
D84262.2/9347-9382   UUG-GCCUACUCCUACUCACUGUAGGGGUAGGCAUCU
AY044867.1/5094-5130 UGGUGCCUACUCCUACUCUCCGUAGGGGUAGGCAUCU
AF165053.1/9306-9342 UGGUGCCUACUCCUACUUUCUGUAGGGGUAGGCAUCU
AB057606.1/1720-1756 UGGUGCCUACUCCUACUUUCUGUAGGGGUAGGCAUUU
AF176573.1/9318-9354 UUGUGCCUACUCCUACUCUUCGUAGGGGUAGGCAUCU
AF009070.1/31-67     UUUUGCCUACUCCUGCUCACUGCAGGGGUAGGUAUCU
D63821.1/9344-9379   UUG-GCCUACUCCUACUUACGGUAGGGGUAGGCAUCU
AF290978.1/9309-9345 UUUUGCCUACUCCUGCUCGCUGCAGGGGUAGGCAUCU
AB057616.1/1720-1756 UUGUGCCUGCUCCUACUAUCUGUAGGGGUAGGCGUUU
AB047639.1/9386-9422 UUCGGCCUACUCCUACUUUUCGUAGGGGUAGGCCUCU
AB049101.1/9287-9323 UUGUGCCUACUCCUACUUUCUGUAGGGGUAGGCAUCU
D49374.1/9355-9391   CUUUGCCUACUCCUACUUACCGUAGGGGUAGGCAUUU
D86533.1/1040-1076   CUGUGCCUACUCCUACUCUCCGUAGGGGUAGGCAUCU
AY232739.1/9350-9386 CUUUGCCUACUCCUACUCAGCGUAGGAGUAGGCAUCU
AF483269.1/9283-9319 UUGUGCCUCUUCCUACUUUCCGUAGGGGUAGGCAUCU
D37859.1/1040-1076   CUGUGCCUACUCCUGCUUGCGGUGGGAGUAGGCAUCU
AB049099.1/9321-9357 UUGUGCCUACUCCUACUUUCCGUAGGAGUAGGCGUCU
AF054260.1/383-419   UUGUGCCUACUCCUACUUUUUGUAGGGGUAGGCAUUU
D49773.1/1041-1076   UUG-GCCUACUCCUACUUGCGGUAGGAGUAGGCAUCU
D86543.1/1040-1076   CUGUGCCUACUCCUACUAUCCGUAGGGGUAGGCAUCU
U16362.1/9319-9355   UUGUGCCUACUCCUACUUUCCGUGGGGGUAGGCAUCU
Y13184.1/9268-9304   CUGUGCCUACUCCUACUUAGCGUAGGGGUAGGCAUCU
X76918.1/9308-9344   CUUUGCCUACUCCUACUAACGGUGGGGGUAGGCAUCU
D49767.1/1041-1076   UUG-GCCUACUCCUACUCAUGGUAGGAGUAGGCAUCU
Y12083.1/9285-9320   UUG-GCCUACUCCUACUUACCGUAGGGGUAGGCAUCU
AY232732.1/9350-9386 CUUUGCCUACUCCUACUCAGUGUAGGAGUAGGCAUCU
AB047642.1/9386-9422 CUUAGCCUACUCCUACUUUCUGUAGGGGUAGGCCUCU
AF208024.1/9300-9336 UUGUGCCUACUCCUGCUUUCUGUGGGGGUAGGCAUCU
D49777.1/1041-1076   UUG-GCCUACUCCUACUCAGCGUAGGGGUAGGCCUCU
AF356827.1/9318-9354 UUGUGCCUACCCCUACUCUCUGUAGGGGUAGGCAUCA
D37862.1/1040-1076   CUGUGCCUACUCCUACUUUCUGUAGGGGUAAGCAUCU
AF207760.1/9306-9342 UGGUGCCUACUCCUACUGUCUGUAGGGGUAGGCAUCU
D87357.1/1040-1076   CUGUGCCUACUCCUACUUUCCGUAGGGGUAGGCAUCU
D84263.2/9324-9360   CUGUGCCUACUCCUACUCACCGUAGGGGUAGGCAUCU
D16617.1/1040-1076   CUUUGCCUACUCCUACUCACCGUAGGGGUAGGCGUUU
D49760.1/1041-1076   UUG-GCCUACUCCUACUCAGCGUAGGAGUAGGCCUCU
D86530.1/1041-1076   UUA-GCCUACUCCUACUCAUUGUGGGGGUAGGCAUCU
D14853.1/9321-9357   UGGUGCCUACUCCUACUUUCAGUGGGGGUAGGCAUUU
AF238483.1/9353-9388 UUG-GCCUACUCCUACUUUCUGUAGGGGUAGGCCUCU
D00825.1/1043-1079   UUCUGCCUACUCCUGCUUGCUGCAGGGGUAGGCAUCU
AF207754.1/9306-9342 UUGUGCCUACUCCUACUUUCUGUGGGGGUAGGCAUUU
D50483.1/9306-9342   CUUUGCCUACUCCUACUCUCCGUAGGGGUAGGCAUCU
AB057682.1/1720-1756 UGGUGCCUACUCCUACUUACUGUAGGGGUAGGCAUCU
D49770.1/1041-1076   UUG-GCCUACUCCUACUUACGGUGGGGGUAGGCAUCU
D86540.1/1040-1076   CUGUGCCUACUCCUACUUUCAGUAGGGGUAGGCAUCU
AJ278830.1/9321-9357 UUUUGCCUACUCCUGCUUGCUGCAGGGGUAUGCAUCU
AF064490.1/9235-9271 CUGUGCCUACUCCUACUUACCGUGGGGGUAGGCAUCU
D84398.1/1041-1076   UUG-GCCUACUCCUACUUUGCGUAGGGGUAGGCAUCU
AB057692.1/1720-1756 UGGUGCCUACUCCUACUCUCUGUAGGGGUAGGCAUUU
AF511948.1/9323-9358 UUA-GCCUACUCCUGCUCGCUGCAGGGGUAGGCAUCU
D14310.1/1043-1079   CUUUGCCUACUCCUACUAACAGUGGGGGUAGGCAUCU
D16192.1/1043-1079   UGGUGCCUACUCCUACUCUCAGUGGGGGUAGGCAUCU
D14484.1/9318-9354   UUAUGCCUACUCCUACUUUCUGUAGGGGUAGGCGUCU
D49774.1/1041-1076   UUG-GCCUACUCCUACUCACGGUAGGGGUAGGCAUCU
D31973.1/1044-1079   UUA-GCCUACUCCUACUUAGCGUAGGGGUAGGCAUCU
Y11604.1/9250-9286   CUGUGCCUACUCAUACUUACAGUAGGGGUAGGCAUCU
D49768.1/1041-1076   UUG-GCCUACUCCUACUUACGAUAGGGGUAGGCAUCU
D37853.1/1040-1076   CUUUGCCUACUCCUACUCACCGUAGGGGUAGGCAUUU
AB057604.1/1720-1756 UGGUGCCUACUCCUACUGUCUGUGGGAGUAGGCAUCU
AB047643.1/9384-9419 UUA-GCCUACCCCUACUUUGUGUAGGGGUAGGCAUCU
AF165045.1/9306-9342 UGGUGCCUACUCCUACUUUCUGUGGGAGUAGGCAUCU
D37863.1/1040-1076   CUAUGCCUACUCCUACUCACAGUAGGGGUAGGCAUCU
AF207761.1/9306-9342 UGGUGCCUACUCCUACUUUCUGUGGGAGUAGGCAUUU
D50409.1/9399-9434   UUG-GCCUACUCCUGCUUUGCGUAGGGGUAGGCAUCU
D37857.1/1040-1076   CUGUGCCUACUCCUACUUACGGUAGGGGUAGGCAUCU
D49771.1/1041-1076   UUG-GCCUACUCCUACUCACAGUAGGGGUAGGCAUCU
AY651061.1/9321-9357 UGGUGCCUACUCCUACUCUCAGUAGGGGUAGGCAUCU
AF511949.1/9322-9358 UUUUGCCUACUCCUGCUUGCCGCAGGGGUAGGCAUCU
D16621.1/1040-1076   CUUUGCCUACUCCUACUCACAGUAGGGGUAGGCAUCU
D49759.1/1041-1076   UUG-GCCUACUCCUACUUACAGUAGGGGUAGGCAUCU
D38079.1/1040-1076   CUGUGCCUACUCCUACUUGCGGUGGGAGUAGGCAUUU
D37860.1/1040-1076   CUGUGCCUACUCCUACUUGCAGUGGGAGUAGGCAUCU
D16615.1/1040-1076   CUUUGCCUACUCCUACUCACCGUAGGGGUAGGCAUCU
AB049094.1/9322-9358 UGGUGCCUACUCCUGCUUUCUGUAGGGGUAGGCAUCU
D49779.1/1040-1076   CUGUGCCUACUCCUACUUACUGUAGGGGUAGGCAUCU
D37864.1/1040-1076   CUGUGCCUACUCCUACUUACGGUGGGGGUAGGCAUCU
AB049088.1/9318-9354 UUAUGCCUACUCCUACUUUCYGUAGGGGUAGGCAUCU
AB049100.1/9287-9323 UGGUGCCUACUCCUACUCUCUGUGGGGGUAGGCAUCU
D16619.1/1040-1076   CUGUGCCUACUCCUACUAACAGUAGGGGUAGGCAUCU
AB057690.1/1720-1756 UGGUGCCUACUCCUACUUUCCGUAGGGGUAGGCGUCU
D16190.1/1043-1079   UGGUGCCUACUCCUACUUUCAGUGGGGGUAGGCAUCU
D37858.1/1040-1076   CUAUGCCUACUCCUACUUGCGGUGGGAGUAGGCAUCU
AF238485.1/9353-9388 UUG-GCCUACUCCUACUUUCCGUAGGGGUAGGCCUCU
AF207756.1/9306-9342 UUGUGCCUACUCCUACUUUCUGUAGGAGUAGGCAUCU
AY051292.1/9321-9357 UGGUGCCUACUCCUACUUUCAGUAGGGGUAGGCAUCU
AB057684.1/1720-1756 UGGUGCCUACUCCUACUCUCCGUAGGGGUAGGCAUUU
D49772.1/1040-1076   CUAGGCCUACUCCUGCUCAGCGUGGGAGUAGGCCUCU
#=GC SS_cons         :<<<<<<<<<<<<<<<_____>>>>>>>>>>>>>>>:
#=GC RF              UUGUGCCUACUCCUACUUuCuGUAGGGGUAGGCAUCU
//
# STOCKHOLM 1.0

#=GF AC   RF00470
#=GF ID   Toga_5_CRE
#=GF DE   Togavirus 5' plus strand cis-regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:11720292
#=GF SS   Predicted; PFOLD
#=GF GA   120.00
#=GF TC   140.60
#=GF NC   115.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0016032; viral process;
#=GF DR   GO; 0032774; RNA biosynthetic process;
#=GF RN   [1]
#=GF RM   11720292
#=GF RT   Cis-acting RNA elements at the 5' end of Sindbis virus genome RNA regulate
#=GF RT   minus- and plus-strand RNA synthesis.
#=GF RA   Frolov I, Hardy R, Rice CM
#=GF RL   RNA 2001;7:1638-1651.
#=GF RN   [2]
#=GF RM   24482115
#=GF RT   A viral RNA structural element alters host recognition of nonself RNA.
#=GF RA   Hyde JL, Gardner CL, Kimura T, White JP, Liu G, Trobaugh DW, Huang C,
#=GF RA   Tonelli M, Paessler S, Takeda K, Klimstra WB, Amarasinghe GK, Diamond MS
#=GF RL   Science. 2014;343:783-787.
#=GF CC   This family represents a Togavirus virus 5' plus strand cis-regulatory
#=GF CC   element which is thought to be essential for both plus and minus strand
#=GF CC   RNA synthesis [1].Genus Alphaviruse belongs to the Togaviridae family.
#=GF CC   Alpha viruses contain secondary structural motifs in the 5' UTR that allow
#=GF CC   them to avoid detection by IFIT1[2].
#=GF WK   Togavirus_5'_plus_strand_cis-regulatory_element
#=GF SQ   33


L01442.2/1-259   AUGGGCGGCG-------C------AU--GAGAGAAGC-------CCAGA--C--C-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAGCG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAAUGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
AF004459.2/1-259 AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCA--CACC-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAACGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
AF103734.1/1-280 AUUGGCGGCGUAGUACAC--ACUAUU--GAAUUAAACA------GCCGA--C--C-----AAUUGC-ACUACCAUC-ACAAUGGAGAAGCCAGUAGUU-AACGUAGACGUAGACCCUCAGAGUCCGUUUGUC-GU-GCAACUGCAAAA--GA-GCUUCCCGCAAUUUGAGGUAGUAGCACAGCAGGUCACUCCAAAUGACCAUGCUAAUGCCAGAGCAUUUUCGCAUCUGGCCAGUAAACUAAUCGAGCUGGAGGUUCCUACCA-CAGCGACGAUUUUGGACAUAGGCAGCGCACCGGCUCGUAGAAU
AF069903.1/1-259 AUGGGCGGCG-------C------AU--GAGAGAAGC-------CCAGA--C--C-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAGCG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAAUGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
L00930.1/1-259   AUGGGCGGCG-------C------AU--GAGAGAAGC-------CCAGA--C--C-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAACGCCAGAGCGUUCUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
AF126284.1/4-298 GCGGACGGACUAGUACUUGUACUACA--GAAUUAACUGCCGUGUGCCGC--C--CGCUAAACUAGCCCCAAUCAUCGAAAAUGGAGAAACCGACAGUG-CACGUUGACGUAGACCCCCAAAGUCCGUUUGUG-CU-ACAACUGCAGAA--GA-GUUUCCCACAAUUCGAGAUUGUGGCUCAGCAGGUCACUCCGAAUGACCAUGCUAAUGCCAGAGCUUUUUCGCAUCUGGCUAGUAAACUGAUCGAACAUGAGAUCCCCACCU-CAGUUACGAUCUUGGACAUAGGAAGCGCACCAGCUCGUAGAAU
J04332.1/1-259   AUGGGCGGCG-------C------AU--GAGAGAAGC-------CCAGA--C--C-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAGCG--GA-CGUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAAUGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
U34999.1/1-258   AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCAAAC--C-----AAUA---ACUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAU------AGUCCCUUCCUC-AG-AGCAUUACAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACAGAUAAUGACCAUGCUAACGCCAGAGCGUUUUCGCAUUUGGCAUCGAAAUUGAUCGAGACGGAGGUGGAACCAU-CCGAUACGAUCCUAGACAUUGGAAGUGCGCCUGCCCGCAGAAU
AF075257.1/1-265 AUGGGCGGCGCAUGA-----GAGAUU--AGCCCAA---------UACCA-----------AAUCAU-ACUACCCAA-AU-AUGGAGAAAGUUCACGUU-GACAUCGAGG-AGG-----AUAGCCCCUUCCUC-AG---AGCUUUACAACGGA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACCGAUAACGACCAUGCUAAUGCUAGAGCCUUUUCGCAUCUAGCUUCUAAGUUGAUCGAAACGGAGGUAGACCCAU-CCGAUACGAUCCUAGACAUAGGCAGUGCACCUGCCCGUAGAAU
AF075258.1/1-259 AUGGGCGGCG-----CAU------UA--GAGAGUA---------GCCCA--A--------AACUAA-ACUACC--C-AACAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGUCCGUUCCUC-AG---AGCUUUACAACGGA-GUUUUCCACAGUUUGAGGUAGAAGCCAAGCAGGUCACAGACAACGACCAUGCUAAUGCUAGAGCGUUUUCGCAUCUAGCUUCCAAAUUAAUCGAAACGGAGGUUGACCCAU-CCGAUACGAUUUUAGACAUAGGCAGUGCGCCUGCCCGCAGAAU
AF075255.1/1-258 AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCA--A--G-----AAUAAA-ACUACC--C-AUCAUGGAGAAGGUUCACGUU-GAUAUCGAGGAAGAC------AGCCCCUUCCU---C-AGAGCUUUACAACGGA-GCUUCCCCCAGUUUGAGGUAGAAGCCAAGCAGGUUACAGACAACGACCAUGCUAACGCUAGAGCGUUUUCGCAUCUAGCAUCUAAACUGAUCGAGACGGAGGUGGAACCAU-CCGAUACGAUCUUAGACAUUGGAAGUGCGCCCGCUCGCAGAAU
AF448536.1/1-258 AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCAAAC--C-----AAUA---ACUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAU------AGUCCCUUCCUC-AG-AGCAUUACAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACAGAUAAUGACCAUGCUAACGCCAGAGCGUUUUCGCAUUUGGCAUCGAAAUUGAUCGAGACGGAGGUGGAACCAU-CCGAUACGAUCCUAGACAUUGGAAGUGCGCCUGCCCGCAGAAU
AF448539.1/1-258 AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCA--AAUC-----AAUA---ACUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAU------AGUCCCUUCCUC-AG-AGCAUUACAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACAGAUAAUGACCAUGCUAACGCCAGAGCGUUUUCGCAUUUGGCAUCGAAAUUGAUCGAGACGGAGGUGGAACCAU-CCGAUACGAUCCUAGACAUUGGAAGUGCGCCUGCCCGCAGAAU
U55360.2/1-259   AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCA--CACC-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAACGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
U38304.1/1-280   NUUGNCGGCGUAGUAUAC--ACUAUU--GAAUCAAACA------GCCGA--C--C-----AAUUGC-ACUACCAUC-ACAAUGGAGAAGCCAGUAGUU-AACGUAGACGUAGACCCGCAGAGUCCGUUUGUC-GU-GCAACUGCAAAA--GA-GCUUCCCGCAAUUUGAGGUAGUAGCACAGCAGGUCACUCCAAAUGACCAUGCUAAUGCCAGAGCAUUUUCGCAUCUGGCCAGUAAACUAAUCGAGCUGGAGGUUCCUACCA-CAGCGACGAUUUUGGACAUAGGCAGCGCACCGGCUCGUAGAAU
AF448538.1/1-258 AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCAAAC--C-----AAUA---ACUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAU------AGUCCCUUCCUC-AG-AGCAUUACAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACAGAUAAUGACCAUGCUAACGCCAGAGCGUUUUCGCAUUUGGCAUCGAAAUUGAUCGAGACGGAGGUGGAACCAU-CCGAUACGAUCCUAGACAUUGGAAGUGCGCCUGCCCGCAGAAU
J02368.1/38-316  ACCGGGGUUCGGUUCCCC--GACGGG--GAGCCAAACA------GCCGA--C--C-----AAUUGC-ACUACCAUC-ACAAUGGAGAAGCCAGUAGUA-AACGUAGACGUAGACCCCCAGAGUCCGUUUGUC-GU-GCAACUGCAAAA---A-GCUUCCCGCAAUUUGAGGUAGUAGCACAGCAGGUCACUCCAAAUGACCAUGCUAAUGCCAGAGCAUUUUCGCAUCUGGCCAGUAAACUAAUCGAGCUGGAGGUUCCUACCA-CAGCGACGAUCUUGGACAUAGGCAGCGCACCGGCUCGUAGCAU
L04653.1/1-259   AUGGGCGGCG-------C------AA--GAGAGAA---------GCCCAAAC--C-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG---AGCUUUACAACGGA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAAUGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
AF448537.1/1-258 AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCAAAC--C-----AAUA---ACUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAU------AGUCCCUUCCUC-AG-AGCAUUACAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACAGAUAAUGACCAUGCUAACGCCAGAGCGUUUUCGCAUUUGGCAUCGAAAUUGAUCGAGACGGAGGUGGAACCAU-CCGAUACGAUCCUAGACAUUGGAAGUGCGCCUGCCCGCAGAAU
U55362.2/1-259   AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCA--CACC-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAAUGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCUCGCAGAAU
AF004472.2/1-259 AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCA--CACC-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAAUGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
U38305.1/1-280   AUUGGCGGCGUAGUACAC--ACUAUU--GAAUCAAACA------GCCGA--C--C-----AAUUGC-ACUACCAUC-ACAAUGGAGAAGCCAGUAGUU-AACGUAGACGUAGACCCUCAGAGUCCGUUUGUC-GU-GCAACUGCAAAA--GA-GCUUCCCGCAAUUUGAGGUAGUAGCACAGCAGGUCACUCCAAAUGACCAUGCUAAUGCCAGAGCAUUUUCGCAUCUGGCCAGUAAACUAAUCGAGCUGGAGGUUCCUACCA-CAGCGACGAUUUUGGACAUAGGCAGCGCACCGGCUCGUAGAAU
L01443.1/1-259   AUAGGCGGCG-------C------AU--GAGAGAAGC-------CCAGA--C--C-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAGCG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAAUGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
M69205.1/1-280   AUUGGCGGCGUAGUACAC--ACUAUU--GAAUCAAACA------GCCGA--C--C-----AAUUGC-ACUACCAUC-ACAAUGGAGAAGCCAGUAGUU-AACGUAGACGUAGACCCUCAGAGUCCGUUUGUC-GU-GCAACUGCAAAA--GA-GCUUCCCGCAAUUUGAGGUAGUAGCACAGCAGGCCACUCCAAAUGACCAUGCUAAUGCCAGAGCAUUUUCGCAUCUGGCCAGUAAACUAAUCGAGCUGGAGGUUCCUACCA-CAGCGACGAUUUUGGACAUAGGCAGCGCACCGGCUCGUAGAAU
AF429428.1/1-279 AUUGACGGCGUAGUAGAC--ACUAUU--AUAAGAAAUA------GCCGA--C--C-----AAUAGC-ACU-CCAUC-ACAAUGGAGAAACCUGUAGUU-AACGUGGACGUAGACCCCCAGAGUCCGUUUGUC-GC-UCAGCUGCAGAA--GA-GUUUCCCGCAAUUUGAGGUAGUAGCACAGCAGGCCACUCCAAAUGACCAUGCUAACGCCAGAGCAUUUUCGCAUCUGGCCAGUAAACUAAUCGAGCUGGAGAUUCCGAUCA-CAGCGACGAUUUUGGACAUUGGCAGCGCACCAGCUCGUAGAAU
AF103728.1/1-280 AUUGACGGCGUAGUACAC--ACUAUU--GAAUCAAACA------GCCGA--C--C-----AACAGC-ACUACCAUC-AUAAUGGAGAAGCCUGUAGUU-AACGUAGACGUAGACCCCCAGAGUCCGUUUGUC-GC-UCAACUGCAAAA--GA-GCUUCCCGCAAUUCGAGGUAGUAGCACAGCAGGCCACACCAAAUGACCAUGCUAAUGCCAGAGCAUUUUCGCAUCUGGCUAGUAAAUUAAUCGAGCUGGAGGUUCCUACCA-CAGCGACGAUUUUGGACAUAGGCAGCGCACCGGCUCGUAGAAU
AF075259.1/1-263 AUGGGCAAUACGUAAGAG--UAGCCC--AAA--AA----------CUG------------AAUACA-CCUACC--C-AUCAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGACAGCCC--GUUCCUUCG-A-GC-UUUAC---AGCG--GA-GCUUCCCACAGUUUGAGGUAGAAGCCAAGCAGGUCACCGAUAAUGACCAUGCUAAUGCCAGAGCGUUUUCGCAUCUGGCCUCCAAAUUGAUCGAGACGGAGGUAGAACCAU-CCGAUACGAUCCUAGACAUAGGCAGUGCACCGGCACGCCGAAU
AF100566.1/1-260 AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCA--CACC-----AAUUAC--CUACCCAA-A-AAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAAUGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
AF492770.1/1-279 AUUGGCGGCGUAGUACAC--ACUAUAAAGAAUCAA---------GCCGA--C--C-----AAUUGC-ACUACCAUC-AUCAUGGAGAAACCUGUAGUU-AACGUUGACGUAGACCCUCAGAGUCCGUUCAUU-AC-GCAACUGCAGAA--GA-GUUUCCCGCAGUUUGAGGUAGUAGCACAGCAGGCCACACCAAAUGACCAUGCAAAUGCCAGAGCUUUUUCGCAUCUGGCCAGCAAACUGAUCGAGCUGGAGGUCCCGACCA-CAGCGACGAUCUUGGACAUCGGCAGCGCACCUGCUCGUAGAAU
M20162.1/25-292  UUCGCCUUUCUUGGAUCC---CUUGU--UACUCCA-CC------GCAG---------------UGA-GAGAUAAAC-A--ACCCAGAA---UGAAGGUCACUGUAGAUGUUGAGGCUGACAGCCCAUUUUUG-AAGGC-CCUUCAGAA---AGCAUUCCCGGCUUUUGAGGUUGAAUCACAGCAGGUCACACCUAAUGACCAUGCUAAUGCCAGAGCUUUUUCGCAUCUGGCCACAAAGUUAAUUGAACAAGAGGUUCCAGCCAACAUC-ACCAUCCUGGACGUGGGCAGUGCGCCCGCAAGGAGGUU
AF004458.2/1-259 AUGGGCGGCG-------C------AU--GAGAGAA---------GCCCA--CACC-----AAUUAC--CUACC--C-AAAAUGGAGAAAGUUCACGUU-GACAUCGAGGAAGAC------AGCCCAUUCCUC-AG-AGCUUUGCAACG--GA-GCUUCCCGCAGUUUGAGGUAGAAGCCAAGCAGGUCACUGAUAAUGACCAUGCUAAUGCCAGAGCGUUUUCGCAUCUGGCUUCAAAACUGAUCGAAACGGAGGUGGACCCAU-CCGACACGAUCCUUGACAUUGGAAGUGCGCCCGCCCGCAGAAU
AF075253.1/1-257 AUGGGCGGCGU------------AU---GAGAGUA---------GCCCA--A--------AUUAAA-ACUACC--C-AUUAUGGAGAA---AGUUC----ACGUUGAUAUCGAGGAGGAUAGCCCCUUCCUCAGA-GC-UUUGCAACG--GA-GCUUCCCCCAGUUUGAGGUAGAAGCCAAGCAGGUCACAGACAAUGACCAUGCUAAUGCUAGAGCGUUUUCGCAUCUAGCUUCCAAACUGAUCGAAACGGAGGUAGAACCAU-CCGACACGAUCCUAGACAUUGGAAGUGCGCCCGCCCGCAGAAU
J02363.1/1-280   AUUGACGGCGUAGUACAC--ACUAUU--GAAUCAAACA------GCCGA--C--C-----AAUUGC-ACUACCAUC-ACAAUGGAGAAGCCAGUAGUA-AACGUAGACGUAGACCCCCAGAGUCCGUUUGUC-GU-GCAACUGCAAAA--AA-GCUUCCCGCAAUUUGAGGUAGUAGCACAGCAGGUCACUCCAAAUGACCAUGCUAAUGCCAGAGCAUUUUCGCAUCUGGCCAGUAAACUAAUCGAGCUGGAGGUUCCUACCA-CAGCGACGAUCUUGGACAUAGGCAGCGCACCGGCUCGUAGAAU
#=GC SS_cons     ::::((((,,,,,,,,,,...,,,,,..,,,,,,,.,.......,,,,,..,..,.....,,,,,,.,<<<<<--<.----<<<-<<<----------.---------------------<<<------<__.__._>->>>------..--.-->>>>>>------>->>>>>,,,,,,<<<<<<<<<_______>>>>>->>>>,,,<<<<<<<<______>>->>>>>>,,,,,,,,,<<<<<__________________.______>>>>>,,,,,,,,,,,,,,,,,,,,,,,)))):::::
#=GC RF          AUgGgCGgcguaguAcac...cuaau..GAaagAA.c.......GCcgA..c..C.....AAUuac.aCuACCAuC.AaAAcGGAGAAAguucaaGUU.gACaUcGAgGuAGAcccucAaAGuCCaUUcgUc.au.acaaCUgCAaaa..GA.GcUUCCCgCAgUUUGAGGUaGaAGCcaAGCAGGuCaCugauAAuGaCCAUGCUAAUGCCAGAGCgUUUUCGCAUCUGGCuucuAAAcUgAUCGAaacGGAGGUugaaaCau.CaGauACGAUccUaGACAUuGGaAGuGCgCCuGCcCGcAGAAU
//
# STOCKHOLM 1.0

#=GF AC   RF00471
#=GF ID   snosnR48
#=GF DE   Small nucleolar RNA snR48
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; ILM
#=GF GA   60.00
#=GF TC   67.20
#=GF NC   57.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 36.46 -Z 549862.597050 CM SEQDB
#=GF CL   CL00066
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science 1999;283:1168-1171.
#=GF CC   snR48 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_snR48
#=GF SQ   6


DQ115391.1/34856-34969     UCAUA-AUGAUGAU-UUCACUUAUACCUAUAUGUUUUUUUCUGGCAUCUCUAAUGUUAGGAUG-CGAAGUUUAAGUACUCUC-CAUUCAAUGAAUACAA-UUUUUGAC---AAUAUCUGAUU
AF064261.1/1-113           UCAUA-AUGAUGAU-UUCACUUAUACCUAUAUGUUU-UUUCUGGCAUCUCUAAUGUUAGGAUG-UGAAGUUUAAGUACUCUC-CAUUCAAUGAAUACAA-UUUUUGAC---AAUAUCUGAUU
CR382122.1/717566-717458   UUUCA-AUGAUGAC-UACAUCU--------AGGUACAUUUCUGGCAUCUCUAAUGUUAGGGUG-G-GCGUUUAAGUACUUCU-CACUCGAUGAAUAGAAACCUUUAACCAUAAUAACUGAAA
CR382128.1/1675383-1675296 UUACA-AUGAUGAU-CCAAAUU--------GCAUUU-UUUCUGGCAUCUCUAAUGUUAGCGUC-CUCCG-----------G--GACCCGAUGAAUAUAA-UUUUU-AC-------UCUGAAA
CR380957.2/423517-423635   CUACA-AUGAUGACACUCAUAUUUUGUUACCUAUUU-UUUCUGGCAUCUCUAAUGCUAGAGCAGCGACGUUUAAGUACUUUCCUGCUCGAUGAAUAUAAACAAAUGAC-UACAAGACUGACA
AE016819.5/1469639-1469744 UUUCACAUGAUGAU-CUAUUCU--------AGCUUU-UUUCUGGCAUCUCUAAUGUUAGGAUG-AGAAGUUUAAGUACUCUC-CAUUCGAUGAAUACAA-CCUAUGAC---UAUAUCUGAAC
#=GC SS_cons               :::::.::::::::.:::::::::::::::::::::.::::::::::::::::::::::<<<<.__________________.>>>>::::::::::::.::::::::...:::::::::::
#=GC RF                    UUacA.AUGAUGAu.uucAuuUaUacuUAuauaUUU.UUUCUGGCAUCUCUAAUGUUAGggug.cGaaGUUUAAGUACUuuc.caccCgAUGAAUAuAA.uuUuUGAC...aAuAuCUGAaa
//
# STOCKHOLM 1.0

#=GF AC   RF00472
#=GF ID   snosnR55
#=GF DE   Small nucleolar RNA snR55/Z10
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Griffiths-Jones S
#=GF GA   50.00
#=GF TC   51.60
#=GF NC   48.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00054
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science 1999;283:1168-1171.
#=GF CC   snR55 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1]. This family does not appear to have the C/D box snoRNA terminal stem
#=GF CC   structure.
#=GF WK   Z10
#=GF SQ   6


AF064267.1/1-98            UUAUUUGAUGAAUAGACACCACAAUCGUCUUUUUUUUAUCCGGCGAUGAUUCCUUUGGAA-UAUGUGCCAUGGAUUACAUCAUGCAUCACCAUCUGAUU
AJ002157.1/1-98            UUAUUUGAUGAAUAGACACCACAAUCGUCUUUUUUUUAUCCGGCGAUGAUUCCUUUGGAA-UAUGUGCCAUGGAUUACAUCAUGCAUCACCAUCUGAUU
CR380953.1/76850-76759     UCAAAUGAUGAAUAGACAUUCC----GUCUUUUAACUAUCCGGCGAUGAUUCAUU--GAA-UAUGUGCCUCGGAUAAAAACAUGCAUCACCAUCUGAUU
CR382122.1/550960-551053   GUACUUGAUGAACG--CUUUCCA--CAGCUUUUUAAGAUCCGGCGAUGAUUUCUUCGGAAAUAUGUGCCU-GGAUAACAUCAUGCAUCACCAUCUGAUA
AJ575660.1/49019-49094     UCAACUGAUGAAAU----UUUCA--CA-CACU---UUUGCAGGUGAAAACG------------UGAUCCA-AGCAAAAAACAUGCAUCACCAUCUGACA
CR382138.2/1137390-1137465 UUAUAUGAUGAUUG----UUACA--CAACAUU---CAAUCCGGUGAACCC-------------UGAGCCAUGGAU-AAAACAUGCAUCACCAUCUGACC
#=GC SS_cons               ::::::::::::::..:::::::..::::::::::::::::::::::::::::::..:::.::::::::::::::::::::::::::::::::::::::
#=GC RF                    UuAuuUGAUGAAua..CaUUaCA..CguCuUUUuuuuAUCCGGcGAugAuuccUU..GAA.UAUGuGCCauGGAUaAaAuCAUGCAUCACCAUCUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF00473
#=GF ID   snosnR54
#=GF DE   Small nucleolar RNA snR54
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Griffiths-Jones S
#=GF GA   50.00
#=GF TC   61.80
#=GF NC   46.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.20 -Z 549862.597050 CM SEQDB
#=GF CL   CL00065
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science 1999;283:1168-1171.
#=GF CC   snR54 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_snR54
#=GF SQ   8


AY864855.1/568-672         UACUCUGAUGAUUAUUCUUUAAAAUUUAUUAACUUUCGUUCUACCGAAUAAAAACUAUGUUUUUUUACAUCAAACGAUGUUGGGGAAAA--CUUUAUUAAUCUGAUU
U85049.2/1114-1200         UACUCUGAUGAUU--CUUUA-AAAUUUAUUAACUUUCGUUCUACCGA-UA----------------CCAUCAAACGAUGUUGGGGAAAAAACUUUAUUAAUCUGAUU
CR382122.1/491586-491502   UA-UAUGAUGAUUAACUUUACUAUUAUAAUAACUUUCGUUCUACUGA-UU----------------UGAUCAAACGAUCGGGUAGAAGA--CAAU--AUAUCUGACU
AF064266.1/1-86            UAAGAUGAUGAUCAACUUUU-UAUAUCAAUAACUUUCGUUCUACUGACUG----------------UGAUCAAACGAUCUUGUAGAGAA--CUUU--UACUCUGAAU
Z46729.1/12595-12510       UAAGAUGAUGAUCAACUUUU-UAUAUCAAUAACUUUCGUUCUACUGACUG----------------UGAUCAAACGAUCUUGUAGAGAA--CUUU--UACUCUGAAU
CR382138.2/158404-158487   UACCAUGAUGAUCAACU----CAAAUUAAUAACUUUCGUUCUACCGAUUU----------------ACAUCAAACGAUGUUGUGGAGAA--AUUG-AUUCACUGACC
CR380957.2/1050569-1050656 UGAAAUGAUGAUUAAACUUU-UAAUAUUAUAACUUUCGUUCUACUGACUG----------------CGAUCAAACGAUCUUGUAGAAAA--CUUUUAUUUGCUGAUU
AE016818.2/861218-861297   UGGGAUGAUGAUCA-------UAAAUCAAUAACUUUCGUUCUACUGACUG----------------CGAUCAAACGAUCGUGUAGACAC--CUUU--UACUCUGACC
#=GC SS_cons               ::::::::::::::::::::.:::::::::::::::::::::::::::::................:::::::::::::::::::::::..::::.:::::::::::
#=GC RF                    UAcuaUGAUGAUuAacuUUu.uAauUUAaUAACUUUCGUUCUACuGAcUg................ugAUCAAACGAUcUUGugGAaAA..CUUU.uUaauCUGAuU
//
# STOCKHOLM 1.0

#=GF AC   RF00474
#=GF ID   snosnR57
#=GF DE   Small nucleolar RNA snR57
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Griffiths-Jones S
#=GF GA   50.00
#=GF TC   52.80
#=GF NC   46.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science 1999;283:1168-1171.
#=GF CC   snR57 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_snR57
#=GF SQ   5


CR382122.1/550657-550747   UUCU--AAAUGAUUAUAAAAA---CAAAAUAUUUAUAACUGAGGAAGUAUAUGCAGGACAUAUUGUUAUUUAGGAAUUCUUCGUUUAUGAUC----AGGA
AJ575660.1/48834-48920     GGCA--AAAUGAUUAGGAACA--------UAUUUUCUACUGAGGAUGUAAAUGCAGGACAAAUCGUUA---AGGAAUUCUUCGUUUAUGAUCUUAGUGCA
AF064269.1/1-88            ----AAGCGUGAUUAUAAAAAAUGAUUUAAAUAUUUUUCUGAGGAAGUAUAUGCAGGACAUAUUGUGAAUUAGGAAUUCUUCGUUUAUGAUC--------
U19028.1/2512-2416         GGUUAAGCGUGAUUAUAAAAAAUGAUUUAAAUAUUUUUCUGAGGAAGUAUAUGCAGGACAUAUUGUGAAUUAGGAAUUCUUCGUUUAUGAUCU---GGCC
CR382138.2/1137204-1137296 UUAU---CAUGAUUAAACCCAAUGAUAU-AACAAAUGACUGAGGAUGCAUAUGCAAGACAAAAAUAAAUUUAGGAAUUCUUCGUUUAUGAUUU---AUAC
#=GC SS_cons               <<<<.._______________________________________________________________________________________...>>>>
#=GC RF                    ggcu..acaUGAUUAuAAAaAAUGauauAaAUaUuUuaCUGAGGAaGUAUAUGCAGGACAuAUuGUuAuUUAGGAAUUCUUCGUUUAUGAUcU...agcc
//
# STOCKHOLM 1.0

#=GF AC   RF00475
#=GF ID   snosnR69
#=GF DE   Small nucleolar RNA snR69
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300036;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science 1999;283:1168-1171.
#=GF CC   snR69 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_snR69
#=GF SQ   6


AJ617339.1/1-89            UACCAUGAUGAACACGAGCCAGAAG--GCUCAAU--AUUCUAUUAAACCCAGCUCUUUGAA-CCAAUAGUUGUGA-------AACGAGAAACAAGUU-----------------CUGA--
CR382128.1/364100-364187   UGGAGUGAUGAUAACGAGCCAGAAG--GCUCUAU------UUAUAAACCCAGCUCGUCGAUAUUAUUUGAAAUGA-------GAAAAAAAGUUUAUG-----------------CUGAUU
BX842623.1/49237-49145     UUGAAUGAUGAUAAAAGGCCCAAGG--CCUGAAU-------UAUAAACCCAGCUCUUCGAU-UCCUCUAUGAGGAUCCAUGAGACAAAAACUUUAUC-----------------CUGACA
CR382126.1/2373959-2374052 UUUAAUGAUGAGAAAAUGUCCUUAG--UGACAAU-----GCUAUAAACCCAGCUCUUCGA--UCAUUAGAAAUGA-------GAAGAGAUACCUGUCAAA----------CGCUCUGAUA
AF064281.1/1-101           GUUUAUGAUGAGACCACGUCCUUAG--UGACAAU-----GCUAUAAACCCAGCUCUUCGAU-UCGUUUUUAAUGA-AAGGGAGAAGAUUUUUUUGUCAAA----------CGCUCUGAGU
CR380958.2/218391-218508   GUUUAUGAUGAUAACGUCAUCAAAAGAUGACAAUUUAUUGCUAUAAACCCAGCUCUUCGAU-UCGUUUCAUCUCU-UCAGGAGAAGUAACAGACAUGAGACCAAUAGUUUAUAUCUGAUA
#=GC SS_cons               :::::::::::::::::::::::::..:::::::.....::::::::::::::::::::::.<<<<_____>>>>.::::::::::::::::::::::::..........::::::::::
#=GC RF                    uuuuAUGAUGAuAAcguGcCcaAAG..ugaCAAU.....gcUAUAAACCCAGCUCUUCGAU.ucauUUgaaauga.ucAgGAGAAGAaAaauuuaUcAaA..........auaUCUGAua
//
# STOCKHOLM 1.0

#=GF AC   RF00476
#=GF ID   snosnR61
#=GF DE   Small nucleolar RNA snR61/Z1/Z11
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ
#=GF SS   Predicted; Daub J
#=GF GA   45.00
#=GF TC   45.10
#=GF NC   44.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   12736298
#=GF RT   RNomics in Drosophila melanogaster: identification of 66 candidates for
#=GF RT   novel non-messenger RNAs.
#=GF RA   Yuan G, Klambt C, Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2003;31:2495-2507.
#=GF CC   This family of small nucleolar RNAs belongs to the C/D class of snoRNA
#=GF CC   which contain the C (UGAUGA) and D (CUGA) box motifs. This family includes
#=GF CC   Schizosaccharomyces pombe snR61, Drosophila melanogaster Z1 and
#=GF CC   Saccharomyces cerevisiae snR61 and Z11 snoRNAs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1].
#=GF WK   Z11
#=GF SQ   56


AF085227.1/271-347             AUUCAAUGAUGAUAUU------CAUCCCAGUUCUGC-UACUGAAC----AUCAACAUGUAGAC--A-CA-AA----UAUACCAAUUA---------AACUGAUUG
BX897674.1/14234-14316         UGUCCAUGAUGAAACAA--AAUAUUUUCAGUUCUGC-UUCUGAAU-----AAUAAUGAGCGAU--AACC-AA---UUAUACCAAAACC--------UUCUGAUAU
CR380953.1/76656-76565         UUUUCAUGAUGAAAAAC-UUUACUUUUCAGUUCUGC-UUCUGAACCA-AAUACACAGGAAGAU--AACC-AA----UAUACCAAAGCUCAAA---AAUCUGAAUU
U19028.1/2059-1969             CUACAAUGAUGAUAAAA-UUUACUAUUCAGUUCUGC-UUCUGAACCA-AAAUAAUAGGAAGAU--AACC-AA---UUUUACCAAAGCUCAA-----AUCUGAUUU
AF064273.1/1-90                CUACAAUGAUGAUAAAA-UUUACUAUUCAGUUCUGC-UUCUGAACCA-AAAUAAUAGGAAGAU--AACC-AA---UUUUACCAAAGCUCAA-----AUCUGAUU-
AJ002158.1/1-89                -UACAAUGAUGAUAAAA-UUUACUAUUCAGUUCUGC-UUCUGAACCA-AAAUAAUAGGAAGAU--AACC-AA---UUUUACCAAAGCUCAA-----AUCUGAUU-
CR382122.1/551225-551315       UUAUUGUGAUGAAUCC---UAAAUUAUCAGUUCUGC-UUCUGAACCAAAAAUUACAGGAAGAU--AACU-AA----UUUACCAAGCUCAAUA---AAUCUGAAAU
AJ575660.1/49220-49297         CUAUAAUGAUGACAAA----AAAUUUUCAGUUCUGC-UUCUGAAA------GAGAAUGAAGAU--AACA-AA----AUUACCAAAAC---------CUCUGACAU
AC007474.5/10843-10917         UUAACAUGAUGAUGAU-------UUUUCAGUUCUGC-UACUGAAG------ACAGUUGACGAA--AGCA-AA----AAUACCAAAAU---------CACUGAAAC
X06869.1/1619-1694             UUAACAUGAUGAUGAU-------UUUUCAGUUCUGC-UACUGAAG-----AGAGUUGACAGAA--AGCA-AA----AAUACCAAAAU---------CACUGAAAC
U46015.1/1-74                  -UAACAUGAUGAUGAU-------UUUUCAGUUCUGC-UACUGAAG-----AGAGUUGACAGAA--AGCA-AA----AAUACCAAAAU---------CACUGAAA-
AAPP01018767.1/34107-34180     UUUCCAUGAUGAUUAC-------CUUUCAGUUCUGC-UACUGAAG------AUUUUUGACGAU--AGCA-AA----AAUACCAAACC----------ACUGAAAA
AAPT01021521.1/180950-181024   UUUAUAUGAUGAUAUC-------UAUUCAGUUCUGC-UACUGAAG------AAUUUUGACGAA--AGCA-AA----AAUACCAAAAU---------CACUGAAAA
AACH01000029.1/4630-4718       UUAUAAUGAUGAUAAC---UUAUUUUUCAGUUCUGC-UUCUGAACCA-AAAUAAUAGGAAGAU--AACC-AA---CUUUACCAAAGCUCAA-----AUCUGAUUU
AADE01001199.1/2659-2731       UUACCAUGAUGAUUAU--------UUUCAGUUCUGC-UACUGAAG------AACUUUGACGAU--AGCA-UA----AAUACCAAACC----------ACUGAAAA
AATX01000008.1/32508-32423     UUUUCAUGAUGAGAAUC-UAUUUUUUUCAGUUCUGC-UUCUGCAA-----CAUCAUUGAAGAA--AACA--A----AAUACCAAAGUAACG----AUCCUGAUAU
ABAR01000022.1/339555-339640   AUUUCAUGAUGAAACA---AAUAUUUUCAGUUCUGC-UUCUGCAA-----AUCUCUUGAAGAU--AACA-AAU-ACCUUACCAAAACGUU------UCCUGAUAU
AAAB01008846.1/4047077-4047157 UUUACAUGAUGAUACAA--CAUUUAAUCAGUUCUGC-UUCUGAAC----CAAUGUGAUAGGAU--AACA-------CAUACCAAAAUA--------AUCUGAAAU
AAGT01000385.1/121420-121500   UUUAUAUGAUGAAAAAA--AUAAUUAUCAGUUCUGC-UUCUGAAC------AUUCAUGUUGAU--AACC-AA----AAUACCAAACUU--------UUCUGAUCU
AACI02000091.1/12317-12226     UUACAAUGAUGAUAAAA-CUUACUUUUCAGUUCUGC-UUCUGAACCA-AAAUAAUAGGAAGAU--AACC-AAC--UUUUACCAAAGCUCAA-----AUCUGAUUU
AAPO01000062.1/266420-266510   AUUGAAUGAUGAGAAAC--CAAAAAUUCAGUUCUGC-UUCUGAACCA-AAAUAAUCUGAAGAU--AACU-AA----UUUACCAAGCUUACUA---AUUCUGAUUC
AAKD03000003.1/768205-768121   CUUUCAUGAUGAGAAA---CAUUUUUUCAGUUCUGC-UUCUGCAA-----AAACCUUGAAGAA--AACC-AAAUACCUUACCAAAAAC--------UCCUGAUCC
AAJN01000068.1/1567-1651       UUUCCAUGAUGAGAAAC--AUUUUUUACAGUUCUGC-UUCUGCAA-----ACUCAUUGAAGAA--AACC-AAAUACCUUACCAAAUC---------UACUGAUAU
AAXI01000415.1/357945-357865   CUCAUAUGAUGAACGU----AUUUUUUCAGUUCUGC-UACUGAAC------UUCAUUGAAGAA--AACA-------UAUACCGCUUACCUU----UGUCUGAUCA
AAIH02000042.1/42191-42275     CUUUCAUGAUGUAAAAAAGUUUUUAUUCAGUUCUGC-UUCUGCAA-----AUACAUUGAAGAA--AACU-AAA--CCAUACCAAACC---------UUCUGAUAC
AAKE03000036.1/33730-33645     UCUUCGUGAUGAGAGAC--AUUUUUUUCAGUUCUGC-UUCUGCAA-----AAACCUUGAAGAA--AACA-AAAUACCUUACCAAAAAC--------UCCUGAUCA
AAJI01002134.1/176-262         UUUCUAUGAUGAGAAAC--CUUCUAUUCAGUUCUGC-UUCUGCAA-----ACUCAUUGAAGAA--ACCC-CA----UUUACCAAAAAUAACG---AUCCUGAUCC
AAZN01000219.1/53824-53738     UUUAAAUGAUGAUAAAACUUUAUUUUUCAGUUCUGC-UUCUGAAC------AUACAGGAAGAU--AACC-AU----UUUACCAAGCUCAUA----UUUCUGACAU
CP000500.1/1136409-1136497     UUAGUAUGAUGAAAAAC--CUAAUUUUCAGUUCUGC-UUCUGAACCAAAAAUAACGUGAAGAU--AACA------CCAUACCAAAGCUCAU-----AUCUGAUUU
ABAS01000002.1/2104142-2104228 GUUUCAUGAUGAAACA---AAUAUUUUCAGUUCUGC-UUCUGCAA-----AUUCCUUGAAGAU--AACA-AAU-ACCUUACCAAAAACGUU-----UCCUGAUAC
AAFU01000870.1/46021-45941     CUUCCAUGAUGAGAAUC--UUUCAAUUCAGUUCUGC-UUCUGAAC------AAGAAUGAAGAU--ACCC-------CAUACCAAAAUAAU------CUCUGAUAU
AAFP01000402.1/19830-19914     CUUCUGUGAUGAACAC---AAUUAUUUCAGUUCUGC-UACCGAGU-----GCUCGUGAGCGAC--AACCCAA----UAUACCAAAAAUUUU-----AUCUGAACU
AAIW01000022.1/32140-32055     UUAUCAUGAUGAGAUCC-UAUUUUUUUCAGUUCUGC-UUCUGCAA-----UCACAUUGAAGAA--AACA--A----AAUACCAAAGUAACG----AUCCUGAUAU
AAFM01000024.1/161660-161745   AAUUUAUGAUGAAAAACUUUUUUUUUUCAGUUCUGC-UUCUGAAC-------CUUAUGAAGAC--AAAA-CC----UAUACCAAAGCUCAA----UAUCUGAGAU
AADM01000299.1/152108-152023   UUAGCAUGAUGAUAAA---CUAUACAUCAGUUCUGC-UUCUGAAA------AUACAGGAAGAU--AACC-AA---CUUUACCAAAGCUCAAA---AAUCUGAUAU
AACT01000546.1/15183-15107     AUACAAUGAUGAUAUUG--UAACUUGCCAGUUCUGC-UUCUGAUU------UGAAGUGAUGAU--AAAC-AU---UACAACCA-------------UUCUGAGAA
AAPU01010056.1/21880-21956     UUUAUAUGAUGAUAAA-----UUGCCUAAGUUCUGC-UACUGAAU------AAUAAUGAGGAU--AGCA-AA----AAUACCAAAUU---------CACUGACAA
AB312541.1/53-127              UUAACAUGAUGAUGAU-------AUUUCAGGUCUGC-UACUGAAG------ACAGUUGACCAC--AGCA-AA----AAUACCAAAAU---------CACUGAAAC
AAEU02000430.1/19692-19766     UUGACAUGAUGAUGAU-------UUUUCAGUUCUGC-UACUGAAG------ACAGUUGACGAU--AGCA-AA----AAUACCAAAAU---------CACUGAACA
AARE01003809.1/2651-2738       CUGCAAUGAUGAAACAA-UUUUUCAUUCAGUUCUGC-UUCUGCAA-----ACUCCUUGAAGAU--AACCUAA----AAUACCAAAACGAUA----CACCUGAUGC
AAFT01000065.1/221747-221834   UUUUUAUGAUGAAAAA---CUAAAUUUCAGUUCUGC-UUCUGAACCA-AAAAAUUCUGAAGAU--AACC------CAUUACCAAAGCUCAA----UUUCUGACAA
AM270348.1/9466-9381           AUCCAAUGAUGAGAAAC--AAUUUUUUCAGUUCUGC-UUCUGCAA-----AAACCUUGAAGAA--AACA-AAAUACCUUACCAAAAAC--------UCCUGAUCC
CR382138.2/1137569-1137658     UUUUUAUGAUGAUAAAC-UUUACUUUUCAGUUCUGC-UUCUGAACCA-AAAAUACCUGAAGAU--AACC-------CUUACCAAAGCUCAAA---UAUCUGACAU
AACE03000007.1/337574-337487   UUCAAAUGAUGAUACA-----AAAUAUCAGUUCUGC-UUCUGAAC----CACGGAAGGAAGAC--AACC-UA----UUUACCAAAGCUCAAUUAGUUUCUGACAA
AE017352.1/388389-388473       CUUCUGUGAUGAACAC----AAUUAUUCAGUUCUGC-UACCGAGU-----GCUCGUGAGCGAC--AACCCAA----UAUACCAAAAACAUU----UAUCUGAACU
BN001307.1/2991666-2991751     CUUGCAUGAUGAGACAA--AUUUUUUUCAGUUCUGC-UUCUGCAA-----ACUUCUUGAAGAA--AAAC--A----AAUACCAUACCAAAAA---CUCCUGAUGC
GQ282317.1/1-68                AUGAAAUGAUGAAACA--------AAACAGUUCUGC-UUCUGAAU-----UUAUUUUGAUGAU--AACU--------AUGCCC-------------AACUGAUCU
FQ790341.1/265922-266010       UUUGUAUGAUGACAAAA-CCUUCCAUUAAGAACGGCCUUCUGAAU------AACCAUGUCGAUUCAAUC-AA----UAUAUCAAGCUCAAC----AGUCUGACUC
AE016815.5/457615-457529       UCUAGAUGAUGAUAAAA-CUUUUUAUUCAGUUCUGC-UUCUGAAC------AUCUAGGAAGAU--AACU-CU----AUUACCAAAGCUCAAA---ACUCUGACAG
FQ790340.1/218306-218386       UUUAUAUGAUGAAAAA---AAAUUAAUCAGUUCUGC-UUCUGAAC------UUUCAUGUUGAU--AACC-AA----UAUACCAAAACUU-------UUCUGAUCC
HE576761.1/127319-127235       UUUAAAUGAUGAUAAAA--CUUACUUUCAGUUCUGC-UUCUGAAC------AUACAGGAAGAU--AACC-CA---UUUUACCAAAAAUUAU-----AUCUGAAAC
AACU03000079.1/125743-125826   GUCUCAUGAUGACAACA--CUUUUUUUCAGUUCUGC-UACUGAAA------GCAAUUGAUGAC--AAAC-CU----UAUACCAAAAACAAC-----CUCUGAAUG
AAIL02000010.1/512354-512271   UGUCGAUGAUGAAAAA---CCUUUAUUCAGUUCUGC-UUCUGAUC------AUCUUUGAUGAC--UCCU-AA----AUUACCAAACCAAGA----UCUCUGAUAU
ABDF02000091.1/18546-18629     CGUUGAUGAUGAGAAAC--CUUUUUUUCAGUUCUGC-UUCUGAAC-------ACCCUGAUGAC--UCCU-AA----AUUACCAAACCAAGA----UCUCUGAUGC
AAFN02000011.1/299910-299816   UUAGAAUGAUGAAAAAU-AAAUGUUAUCAGUUCUGC-UUCUGAACCA-AAAUAAUCUGAAGAU--AUCA-AC----UUUACCAAGCUCUAGAAUUACACUGAUUU
ABDG02000022.1/57658-57742     ACUUUAUGAUGAAAAUC--CUUUUUUCCAGUUCUGC-UACUGAAC------AUUAUUGAUGAC--UCCU-AA----AUUACCAUACCAAGA----UCUCUGAUGU
#=GC SS_cons                   :::::::::::::::::..:::::::::::::::::.::::::::.....:::::::::::::..::::.::....:::::::::::::::.....:::::::::
#=GC RF                        uUuuuAUGAUGAuAaaa..uuUuUUUUCAGUUCUGC.UUCUGAAc.....aaaauuUGAaGAu..AACc.AA....uaUACCAAAacuaaa.....uuCUGAuau
//
# STOCKHOLM 1.0

#=GF AC   RF00477
#=GF ID   snosnR66
#=GF DE   Small nucleolar RNA snR66
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Griffiths-Jones S
#=GF GA   65.00
#=GF TC   69.10
#=GF NC   63.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Macaca_mulatta300410;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science 1999;283:1168-1171.
#=GF CC   snR66 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_snR66
#=GF SQ   4


AF064278.1/1-86          -------AUCAAAUGAUGAAAUACCAAUGCAACA--GAGUCAAGCUCUGAGUU-U-CAAAAAGAAA------CAUGGACGAGA-UUGCUUUUUUAUUA-----CUGACC--------
CR382125.1/739697-739799 AGGAUUUUUAACGUGAUGAAAUAACAAUGCAACAUAGAGUCAAGCUCUGAGCU-U--AUAUAG---------CAUGGACGAGACUUGC-UUUUUACAAACGUACUGAUCA-AAUUUC
AJ223036.1/7-107         AUAAUUCAUCAAAUGAUGAAAUACCAAUGCAACA--GAGUCAAGCUCUGAGUU-U-CAAAAAGAAA------CAUGGACGAGA-UUGCUUUUUUAUUA-----CUGACCAUGAUUAU
CR380959.2/701281-701392 UUUUUUUUUAAUAUGAUGAAAUACCAAUGCAACAUAGAGUCAAGCUCUGAGCUAUACAAAUAGAUAGAAUAGCACGGAAGAGACUUGC-UACUUAUUAU----CUGAUCCCAUAAAA
#=GC SS_cons             <<<<<<_______________________________________________._.__________......________________.__________....________>>>>>>
#=GC RF                  gugauuuuUaAaAUGAUGAAAUAcCAAUGCAACAUAGAGUCAAGCUCUGAGuU.U.CAaAuAGAaA......CAuGGAcGAGACUUGC.UuuUUAUuAu....CUGAuCauaaucac
//
# STOCKHOLM 1.0

#=GF AC   RF00478
#=GF ID   SCARNA6
#=GF PI   U88
#=GF DE   Small Cajal body specific RNA 6
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Marantidis E
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ, Daub J, INFERNAL
#=GF SS   Published; PMID:12032087, Daub J
#=GF GA   68.00
#=GF TC   68.00
#=GF NC   67.70
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   U88 is small Cajal body specific RNA (scaRNA). scaRNAs are a novel class
#=GF CC   of small nuclear RNAs which localise to the Cajal bodies [1]. U88 is found
#=GF CC   associated with both fibrillarin and Gar1p and co-localises with coilin in
#=GF CC   Cajal bodies [1]. U88 scaRNA is composed of both an H/ACA box and a C/D
#=GF CC   box conserved domains domains and is predicted to guide 2'-O-methylation
#=GF CC   of residue U41 of the U5 snRNA [1]. This family also includes human scaRNA
#=GF CC   U87 and a mouse homologue MBI-46 described in [2]. In humans both U88 and
#=GF CC   U87 scaRNAs share the same host gene and both are predicted to guide
#=GF CC   modification of the same residue (U41 of U5 snRNA)[1,3].
#=GF WK   Small_Cajal_body_specific_RNA_6
#=GF SQ   17


AC013726.7/131686-131422     GGUCAAUGAUGAAUGGUAAAAGGUCUGAGU---CCUCAGAUC-CC--CUCCCGGC-AUCCCAGUUAUCCCCAGCUGC-------CUCUCCUCCAUCGCACUUCAGAAGUGCUGCGAUGGGCAGAAGG-GCAGCUGACACUCCGUGAUGUC--CCUCAUUCUGUGUUCCUCCGUGAGCUCAGGG-AAGACACUG--GUU-----GGCAUCCAACAGC-UUAGUCACAAAGGGA-UUUGAUU-----GUUGGGAGUGCUGGUAUCUGUGGCUAU-GAUCUGCCUUGUUCAAGCUGAGACC
AC102630.6/82156-82420       GGUCAGUGAUGAAUAGUAAAAGGUCUGACU---UCCGAGGUC-GC--CUCCCAGC-AGCCUAC--AUCCCCAGCUGCUUAC---CUCUCUCCCAUCAUGCUCUAGUAGUGCUAUCAUGGGCAAACACAGUAGCUGACAUGCAGUGAUGUC--UC-CAUUCUGUCUUCCCUGACAAGUCCAGAG-AAGGCACUG--GUU-----GGCAUCCAACAGC-UUGGUCACAA-GGGA-UUUGGUU-----GUUGGGAGUGCUGGCGUCCUUGGCUAU-GAUCUGACAUUUU-AAGCUGAGACC
AY077738.1/1-265             GGUCAAUGAUGAAUGGUAAAAGGUCUGAGU---CCUCAGAUC-CC--CUCCCGGC-AUCCCAGUUAUCCCCAGCUGC-------CUCUCCUCCAUCGCACUUCAGAAGUGCUGCGAUGGGCAGAAGG-GCAGCUGACACUCCGUGAUGUC--CCUCAUUCUGUGUUCCUCCGUGAGCUCAGGG-AAGACACUG--GUU-----GGCAUCCAACAGC-UUAGUCACAAAGGGA-UUUGAUU-----GUUGGGAGUGCUGGUAUCUGUGGCUAU-GAUCUGCCUUGUUCAAGCUGAGACC
AF357345.1/1-249             ---------------GUAAAAGGUCUGACU---UCCGAGGUC-GC--CUCCCAGC-AGCCUAC--AUCCCCAGCUGCUUAC---CUCUCUCCCAUCAUGCUCUAGUAGUGCUAUCAUGGGCAAACACAGUAGCUGACAUGCAGUGAUGUC--UC-CAUUCUGUCUUCCCUGACAAGUCCAGAG-AAGGCACUG-GGUU-----GGCAUCCAACAGC-UUGGUCACAA-GGGA-UUUGGUU-----GUUGGGAGUGCUGGCGUCCUUGGCUAU-GAUCUGACAUUUU-AAGCUGAGA--
AAHX01061348.1/17112-16850   GGUCAAUGAUGAAUAGUAAAAGGUCUGACU---UCCGAGGUC-GC--CUCCCAGC-AGCCUAC--AUCCCCAGCUGCUUAC---CUGUCUCCCAUCAUGCUCUAGUGGUGCUGUCAUGGGCAGAAACAGUAGCUGACAUGCAGUGAUGUC--UC-CUUUCUGUCUUCCCUAAC-AGCCCAGAG-AGGACACUG--GUU-----GGCAUCCGACAGC-UCAGUCACAA-GGGA-GUA-AUU-----GUUGGGAGCGCUGGCGUCCUCGGAUAU-GAUCUGACAUUUU-AAGCUGAGACC
ABDC01309289.1/542-806       GGUCAAUGAUGAAUAGUAAAAGGUCUGACU---CC-CAGAUG-CC--CUCCCUGC-AUCCCAACAGUCCCCAGCCAC-------CUCUCUUCUGUCAGGGCCCGGGAGUGCUGUGAUGGGCAGAAGG-GCAGCUGACACUCUGUGAUGUC--CC-UGUUCUGUGUUCCUUGGUGAGCCCAGGG-AGGACUCCAUGGUU-----GGCAGCCAACAGC-CCAGUCACAAAGGGA-UUUGCUU-----CCUGGGAGUGCGGGUAUCUGUGGCUAU-GAUCUGACCUUUUCAAGCUGAGACC
AAQQ01187293.1/120-389       GGUCGAUGAUGAGUAGUAAAAGGUCUGACU---GCCCAGGUC-CC--CUCCCAGC-AUCCUGAAUGUCCCCAGCUGC-------CUCAAUCCCAUCAGGCUCCAGUGGUGCCACAAUGGGCCAGAGA-GCAGCUGACAGGCAGGGAUGGC--UU-GAGUCUGUGUUCCCUGGUGAGCCAAGGG-AAGACACGGUGGUU-----G-CAUCCAACAGC-UUAGCCACGAAGGGC-AAGGGACUUUUGGUUGGGAGAGCUGGUAUCUGUGGCUGU-GAUCUGACGUUUUCAAGCUGAGACC
AAIY01463479.1/2054-1800     GGCCCAUGAUGACUGGUAAAAGGUCUGACA---CCCCAGGCC-CGUGUGCCCUGC-C--------GUCCCCAGCUGC-------CCCUCCCCUGUCAGGCUGCAGCCAUGCCAUGCUGGGCAC-AGG-GCAGCUGACACCUUGUGGUGCC--CC-CACCCCGUGUC-CCUGACGAGCCCAGGU-GCCACUGUG--GUU-----GGUGCCCAACAGC-UGCAUGACCAAGGGA-CCUGGAG-----GCAGAGCACACCGGGGUCUGGGGGCU--GAUCUGACGUUGCCAAGCUGAGGCC
AAPN01081849.1/10135-9862    GGUCAGUGAUGAAUAGUAAAAGGUCUGACUGG-CCAGAGACU-GCG-CUUUCAUC-ACCAUCCUGAUUCCCUGCAGCC------UCUUUUUCCAUCAGACCCCAGUAGUGCUCUGAUUGGCGGAGGA-ACUGCUGAAAUUGUGCGAUGUCUUCU-ACUUUUGUGUUCGCCGGAGUUCCGGGCG-A-CACAGCA--GUUGGGUAGGCGUCCAACAGGAGCAGUCGUAAAGGAG-UUUCGGU-----GGUGGAAGU-UUGGAGGUCUUGGUUGU-GAUCUGAAGUUUUCAAGCUGAGACC
AANU01247013.1/1478-1742     GGUCAAUGAUGAAUGGUAAAAGGUCUGAGU---CCUCAGAUC-CC--CUCCCAGC-AUCCCAGUUAUCCCCAGCUGC-------CUCUCCUCCAUCGCGCUUCAGAAGUGCUGUGAUGGGCAGAAGG-GCAGCCGACACUCCGUGAUGUC--CCUCAUUCUGUGUUCCUCCGUGAGCUCAGGG-AAGACACUG--GUU-----GGCAUCCAACAGC-UUAGUCACAAAGGGA-UUUGAUU-----GUUGGGAGUGCUGAUAUCUGUGGCUAU-GAUCAGACUUGUUCAAGCUGAGACC
AY077737.1/2-276             GGUC-GUGAUGAUUGGUAAAAGGUCUGAUUGCACUGAAUGUCACA--GUCCCUUUGUUGCCCUCAACUCCCAGCAGCCCAUUUUUUCCCUCCCGUCACAUUUAAGUCAUG-UGU-AUGGGAUCAUGGAGCAGCUGAUAAUUUGGGAUUCU--GU-CAGUGUGUGUUUC--UGAGAGUGAUCGA-CUCACAGCU-GACG-----AGUAUCCAACAAAACCAGUUACACAGGAG-ACUGACG-----AGUGGCAGUCAUGGGUGUGAUGGUGCAUGAUCUCAAGUUUUCAAUCUGAGACC
AAWR02034636.1/226-487       GGUCAGUGAUGAGUAGUAAAAAGGCUGACU---CCCCAGGUC-CC--CUCCUUGC-GUCUUCAUCAUCCCCAGAUGC-------CUCUC-UCCAUCCGGCUCCAGUGAUGCUCUGAUGGGCAAAGGG-GCAGCUGACACUCCGUGAGGUC--CC--AGUUCUGUGUUCUUGGCAAGCCCAGGG-CCGAUGGCGUAGUU-----GGCGUCCCACAGC-UU-GUCACGAAGGGA-UUUGAUU-----GUUGGCAGUGCUGGUAUCUGUGGUUGU-GAUCGGAAGGUUC-AAGCUGAGGCC
AAGV020120383.1/2816-3082    GGUCAGUGAUGAAUAGUAAAAGGUCUGAGU---CCCCAGGUC-CC--UUCCCUGU-AUCCAGAUGGUCCCCAGCUGC-------UUCUCCUCCAUCAGGCUCCAGUAGUGCCAUGAUGGGCCAAAGG-GCAGCUGACAGUUGGAGAUGUC--CC-UUUCUGGUGUUUCUUGGUGAGCCCAGGG-AAGACGCUGUGGUC-----GGCAUCCAACAGC-UUUGUUACAAAGGGACUUUGGUC-----GGUGGGAGUGCUGGGAUCUGGGGUUUU-GAUCUGACGUUUUCAAGCUGAGACC
AAGW02066331.1/13022-13277   GGUCAAUGAUGAACAGUAAAAGGUCUGAUU---GCCCAGGU--GC----CCCUGC-UUCCCAGCAGUCCCCAGCCGC-------CUCUCUCCCACAG-GCUCCAGGUGUGCUGUUGUGGGCCAGAGG-GCUGCUGACACUGUGUGAUGUC--CC-CAUCCCGCCUUCCCUGAUGAGCCUGGGU-GAGGCACGU-GGUC-----GGCAUCCAACAGC-AUAGUCACUGAGGGG-UCUGGU------GUUGGG--UGCAGGCGUCUGCGGUGUG--AUCUGCCCUUUG-CAGCUGAGACC
AAGU03069623.1/10650-10392   GGCCCGUGAUGACUGGUAAAAGGUCUGACC---ACCCAGAUC-CC-----CCGGC-ACCCUGCCGGUCCCCAGCUGC-------CCCUCUCCCGUCAGGCUCCAGUCGUGCCGUGAUGGCCAC-AGG-GCAGCUGACACCCGGUGGUGCC--CC--GUCCUGUGU-CCCUGGCGAGCUUGGGGAGACGCCGUG--GUU-----GGCACCCAACAGC-ACAGUGACAAAGGAA-UUUGGAC-----CCUGGGAGUGCCGGGGCCUGAGGUGAU-GAUCUGACGUUUCCAAGCUGAGGCC
AACZ03020699.1/4729-4993     GGUCAAUGAUGAAUGGUAAAAGGUCUGAGU---CCUCAGAUC-CC--UUCCCGGC-AUCCCAGUUAUCCCCAGCUGC-------CUCUCCUCCAUCGCACUUCAGAAGUGCUGCGAUGGGCAGAAGG-GCAGCUGACACUCCGUGAUGUC--CCUCAUUCUGUGUUCCUCCGUGAGCUCAGGG-AAGACACUG--GUU-----GGCAUCCAACAGC-UUAGUCACAAAGGGA-UUUGAUU-----GUUGGGAGUGCUGAUAUCUGUGGCUAU-GAUCUGCCUUGUUCAAGCUGAGACC
AAPE02003619.1/134393-134653 GGUCAAUGAUGACUAGUAAAAGGGCUGACU---CCCCAGGUC-CC--CUCCCUGC-AUCCUCACCAUCCCCAGCCGC-------CUUGCUCCCAUCAGGCUCCAGUAGUGCUUUGAUGGGUAAAAGG-GCAGCUGACACUCUGUGAUGUC--CC-AGGUCUGUGUUCCUUGGCGAGCCCAGGG-AGGACACGU-GGUU-----GGCAUCCCACAGC-C-AGUCUCGAAGGGA-UGUGAUU-----ACUGGGAGUG-UGGUACCUGUGGUUCU-GAUCUGAC--UUUCAAGCUGAGACC
#=GC SS_cons                 ((((--------------------------...---((((((.--..((((((((.----------((((<<<<<<<.......------<<<<<<<<<<_________>->>>>>>>>>-------.>>>>>>>,,,,,,,<-<<<<<<..--.-----<<<<<<<<<<<_______>>>>>.>>>>>>---.----.....>>>>>>>,,,,,,.,,,,,,,,,,,)))).-------.....))))))))-------------------.))))))---------------))))
#=GC RF                      GGuCAaUGAUGAaUaGUAAAAGGUCUGAcU...cCccAGguC.cc..cucCCagc.auCCuaauaaucCCCaGCuGC.......cUCUCUcCcaucacgCUccAGuaGUGCcgugaugGgCaaAaGg.GCaGCuGAcAcucuGuGauguC..cc.cauUcuGuguucccugGuGAGCccaggg.aacaCacug.GGUU.....GgcauCCAACAGc.uuAGUcACaAAGGga.uuUGauu.....gcuGGgagUgcUGGuauCuguGGuuaU.GauCUgAcgUUUUCAAGCUGAGaCC
//
# STOCKHOLM 1.0

#=GF AC   RF00479
#=GF ID   snosnR71
#=GF DE   Small nucleolar RNA snR71
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; Moxon SJ
#=GF GA   60.00
#=GF TC   60.00
#=GF NC   59.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF RN   [2]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science 1999;283:1168-1171.
#=GF CC   snR71 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_snR71
#=GF SQ   7


CR382130.1/3357485-3357571 UUUG--AUGAUGAAACACU-UA-CUCAGCUCACUCAGA-GC-UCUGCAAUGCU-GAUAA------CCUUCCUAACAACGCAACAAUAACCUGACCCUUAC
AF064283.1/1-90            -GUUAUAUGAUGAUAACCU-U--CUCAGCUCACUCAGA-UCUUUUGAUAUGAUUGAUAAAAAUUUCCUAUCCAACAUUCAUCAAUUUAUCUGACC-----
CR382123.1/242557-242465   AUUUACGUGAUGAUAACCU-UA-CUCAGCUCACUCAGA-UUAUCCG---UGAUCGA-AAGCAUUUCCUAUCCAACAUUCAUCAAAAUAUCUGAUCAAAAU
U10397.1/27874-27969       UGUUAUAUGAUGAUAACCU-U--CUCAGCUCACUCAGA-UCUUUUGAUAUGAUUGAUAAAAAUUUCCUAUCCAACAUUCAUCAAUUUAUCUGACCAAACA
CR380956.2/779063-779158   GUGUUUAUGAUGACAAACUAUAUCUCAGCUCACUCAGA-UCACCCG---UGAUUGAUAAUAUAUUCCUAUCCAACAUUCAUCAAUUUACCUGACUUUUAU
CR382137.2/1877647-1877739 UGUU--AUGAUGAUAACCU-AA-CUCAGCUCACUCUUAGUCAAUGACGAUGCU-GAUAACCUUUU--UUUCCAACAUUCAUCAAUUUAUCUGAUUCAAUA
AE016819.5/1629456-1629547 UCUUACAUGAUGAUAACUU-A--CUCAGCUCACUCAGA-AAUACA----UGAUUGAGAACUUUUCCUAAUCCAACAUUCAUCAAUAUAUCUGACUAGAAG
#=GC SS_cons               <<<<_______________.__._______________._________________________________________________________>>>>
#=GC RF                    uuuuAuAUGAUGAuAAcCU.uA.CUCAGCUCACUCAGA.ucaucuGauAUGaUUGAUAAaauUUUCCUaUCCAACAUUCAUCAAuuUAuCUGAcuaaaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00480
#=GF ID   HIV_FE
#=GF DE   HIV Ribosomal frameshift signal
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14747573
#=GF SS   Published; PMID:14747573
#=GF GA   42.00
#=GF TC   42.00
#=GF NC   41.90
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   14747573
#=GF RT   The human immunodeficiency virus type 1 ribosomal frameshifting site is an
#=GF RT   invariant sequence determinant and an important target for antiviral
#=GF RT   therapy.
#=GF RA   Biswas P, Jiang X, Pacchia AL, Dougherty JP, Peltz SW
#=GF RL   J Virol 2004;78:2082-2087.
#=GF CC   This family represents the HIV Ribosomal frameshift signal. HIV uses a
#=GF CC   system called -1 ribosomal frameshifting to produce the required ratio of
#=GF CC   Gag and Gag-Pol polyproteins. The stem-loop structure of the frameshift
#=GF CC   signal is thought to impede the ribosome and cause slippage in the 5'
#=GF CC   direction, this causes the -1 frameshift and translation then continues in
#=GF CC   the new frame [1].
#=GF WK   HIV_ribosomal_frameshift_signal
#=GF SQ   145


AF067154.1/1449-1500 UUUUUUAGGGAAAAUUUGGCCUUCCCACAAGGGGAGGCCAGGGAAUUUCCUU
AF349363.1/33-84     UUUUUUAGGGAAGAUCUGGCCUUCCCACAAGGGGAGGCCAGGGAAUUUUCUC
AF156820.1/43-94     UUUUUUAGGGAAGAUCUGGCCUUCCUACAAGGGAAGGCCAGGGAAUUUUUUU
AY090761.1/678-729   UUUUUUAGGGAAAAUCUGGCCUUCCCACAAGGGAAGGCCAGGGAACUUCUUU
AJ488926.1/1306-1357 UUUUUUAGGGAAAAUUUGGCCUUCCAGCAAGGGAAGGCCGGGAAAUUUUCUU
AF286239.1/1448-1499 UUUUUUAGGGAAAAUUUGGCCUUCCCACAGCGGGAGGCCAGGGAAUUUUCCU
AJ249236.1/1281-1332 UUUUUUAGGGAAAAUUUGGCCUUCCAACAGGGGGAGGCCAGGAAAUUUUCUU
AY563170.1/1281-1332 UUUUUUAGGGAAAAUUUGGCCUUCCAACAAGGGAAGGCCAGGAAAUUUYCUC
AF484493.1/1290-1341 UUUUUUAGGGAAAAUUUGGCCUUCCCACAAGGGGAGGCCAGGAAAUUUUCCC
AY206650.1/1302-1353 UUUUUUAGGGAAAAUCUGGCCUUCCCACAAAGGAAGGCCAGGGAAUUUUCUU
AY535721.1/171-222   UUUUUUAGGGAAAAUCUGGCCUUCCAACAAGGGGAGGCCAGGGAACUUUCUU
AJ286137.1/52-103    UUUUUUAGGGAGAAUUUGGCCUUCCAGCAAGGGGAGGCCAGGAAAUUUCCCU
AY181067.1/27-78     UUUUUUAGGGAAAAUUUGGCCUUCCAGCAAAGGGAGGCCAGGAAACUUUCCC
AY140131.1/1170-1221 UUUUUUAGGGAAAAUUUUGCCUUCCCACAAGGGGAGGCCCGGAAACUUCUCC
L11789.1/1281-1332   UUUUUUAGGGAAAAUUUGGCCUUCCAACAAAGGGAAGCCAGGGAAUUUUCUC
AJ535032.1/23-74     UUUUUUAAGGAAAAUUUGGCCUUCCAACAAGAGGAGGCCAGGGAAUUUUCUC
AY165215.1/142-193   UUUUUUAGGGAGACUUUGGCCUUCCCACAAGGGGAGGCCAGGGAAUUUUCCU
AY519079.1/46-97     UUUUUUAGGGAAAAUYUGGCCUUCCCACAAGGGRAGGCCAGGRAACUUUCCU
AY037273.1/1284-1335 UUUUUUAAAGAAAAUUUUGCCUUCCCACAAGGGGAGGCCUAGAAAUUUCCUU
AY682547.1/1576-1627 UUUUUUARRGAAGAUCUGGCCUUCCCACAAGGGAAGGCCAGGGAAUUUCCUU
AY093603.1/1290-1341 UUUUUUAGGGAAGAUUUGGCCUUCCCACAAGGGGAGGCCAGGGAACUUUCCU
AY358059.1/1284-1335 UUUUUUAGGGAAAAUUUGGCCUUCCAACAAGGGAAGGCCAGGGAAUUUUCCU
AF442571.1/584-635   UUUUUUAGGGAGAAUUUGGCCUUCCAACAAGGGAAGGCCAGGAAACUUCCUU
AY519118.1/46-97     UUUUUUAGGGAAGAUCUGGYCUUCYCACAAGGGAAGGCCAGGGAAUUUURUU
AY455779.1/1536-1587 UUUUUUAGGGAAAAUUUGGCCUUCCCACAAGGAAAGGCCCGGGAAUUUCCCU
L11756.1/1299-1350   UUUUAUAGGGAAAAUCUGGCCUUCCAGCAAGGGGAGGCCAGGAAAUUUUCCU
AF408627.1/1519-1570 UUUUUUAAGGAAAAUUUGGCCUUCCAACAAGGGGAGGCCGGGAAAUUUCCUU
AY140557.1/891-942   UUUUUUAAGGAAAAUUUGGCCUUCCAACAAGGGAAGGCCAGAAAAUUUUCUU
AY519101.1/46-97     UUUUUUAGGGAAAAUCUGGCCUUCCCACAAGGGGAGGCCAGGRAAYUUYCUR
AY255816.1/1280-1331 UUUUUUAGGGAAAWWWWGGCCUUCCCACAAGGGGAGGCCAGGGAAUUUCCUU
AY484783.1/10-61     GUUUUUAGGGAAAAUCUGGCCUUCCCACAAGGGGAGGCCAGGGAAUUUUCAU
AY492778.1/819-870   UUUUUUAGGGAAAAUUUGGCCUUCCAACAAAGGAAGGCCGGGGAAUUUCCUU
AF156840.1/71-122    UUUUUUAGGGAAGAUCUGGCCUUCUUCCAGGGGAAGGCCAGGGAAUUUUCUU
AF247519.1/1233-1284 UUUUUUAGGGAAAAUUUGGCCUUCCCACAAGGGAAGGCCGGGGAACUUUCUC
AF119819.1/2102-2153 UUCUUUAGGGAGAAUGUGGCCUUCCAGCAAGGGGAGGCCAGGAAAUUUUCUU
U21135.1/2084-2135   UUUUUUAGGGAAGAUCUGGUCUUCCCAAAAGGGAAGGCCAGGGAAUUUUCCU
AB074055.1/1347-1398 UUUUUUAGGAAAGAUCCGGCCUUCCCACAAGGAGAGGCCAAGGAAUUUUCUU
AY371167.1/1284-1335 UUUUUUAGGGAGAAUUUGGCCUUCCAACAGAGGGAGGCCCGGAAAUUUUCCU
AF024053.1/108-159   UUUUUUAGGGAAAGUCCGGCCUUCCUCCAAGGGAAGGCCAGGGAAUUUUCUU
AY331287.1/1296-1347 UUUUUUAGGGAAGCUCUGGCCUUCUCAGAAGGGAAGGCCAGGGAAUUUUCUU
AY484777.1/1-50      UUUU--AGGGAAAAUCUGGCCUUCCCACAAGGGGAGGCCAGGAAAUUUUCUU
AY492788.1/854-904   UUUUUUACGGAAAUUUUGGCCUUCCCACAAGGGAAGGCCAGGG-ACUUCCUU
AJ405961.1/1-52      UUUUUUAGGGAAAGUUUGGCCUUGGAGCAAGGGAAGGCCAGGGCAUUUCCUU
AY322191.1/1547-1598 UUUUUUAGGGAGAAUUUGGCCUCCCAACAAGGGGAGGCCAGGAAACUUUCCU
AY519082.1/46-97     UUUUUUAGGGAAGAUCUGGCCUUCCCACAGGGGGAGGCCAGGAAAUUUCCUU
AY518946.1/46-97     UUUUUUAGGGAAAAUCUGGCCUUCCCACARGGGGRGGCCAGGGAAUUUUCUU
AY304893.1/1283-1334 UUUUUUAGGGAGAAUGUGGCCUUCCAGCAAGGGGAGGCCAGGGAACUUCAUU
AY165261.1/239-290   UUUUUUAGGGAAAAUCUGGCCUGUCCACAAGGACAGGCCAGGGAAUUUUUGU
AY165229.1/242-293   UUUUUUAGGGAAGAUCUGGCCUUCCUCCAARGGAAGGCCAGGGAAUUUUCUC
AY253307.1/1299-1350 UUUUUUAGGAAGACUCUGGCCUUCCCACAAGGGGAGGCCAGGAAAUUUCCUU
AF282967.1/1-52      UUUUUUAGGGAAAAUCUGGCCUUCCCACAAGGAAAGGCCAGGGAAUUUUUUA
AB078714.1/1275-1326 UUUUUUAGGCAAGCUCUGGCCUUCCCACAAGGGAAGGCCAGGGAAUUUUACU
AF005494.1/1413-1464 UUUUUUAGGGAAAAUUUGGCCUUCCAACAAGGGGAGGCCCGGAAACUUCAUC
AY519017.1/46-97     UUUUUUAGGGAAAGUCUGGCCUUUCCACAAGGAAAGGCCAGGGAACUUUCAC
AJ583741.1/51-102    UUUUUUAGGGAAAAUUUGGCCUUCCAACAAAGGGAGGCCGGGAAACUUUCUU
AY371144.1/1284-1335 UUUUUUAAGGAAAAUUUAGCCUUCCAGCAAAGGGAGGCCAAGGAAUUUUCCU
AF457057.1/1284-1335 UUUUUUAAAGAGAAUUUAGCCUUCCAGCAAGAAGAGGCCAGGAAAUUUUCCU
AF293420.1/1-52      UUUUUUAGGGAAAAUCUGGCCUCCCUGCAAGGGAAGGCCAGGAAAUUUUCUU
AY519076.1/46-97     UUUUUUAGGAAAGAUCUGGCCUUCCCACAAGGGAAGGCCAGGGAACUUCCUG
AB074075.1/1326-1377 UUUUUUAAGGAAGAUCUGGCCUUCCCACAAGGGAAGGCCAAAGAAUUUCCUU
AF024243.1/90-141    UUUUUUAGGGAAGAUCUGGCCUUCCCACAAGGGGGGGCCAAGGAAUUUCCUU
AJ006022.1/1658-1709 UUUUUUAGGGAAGAGCUGGUCUCCCUUCAAAGGGAGACCAGGAAACUUCCCC
AY371154.1/1293-1344 UUUUUUAGGGAAGAUCUGGCCUUCCAGCAGUGGGAGGCCAGGGAAUUUUCUU
AY518966.1/46-97     UUUUUUAGGGAAAAUCUGGCCUUCCUCCAGGGGGAGGCCAGGGAACUUUCUG
AB097866.1/1400-1451 UUUUUUAGGGAAAAUCUGGCCUUCCCACGAGGGGAGGCCAGGGAACUUCCUC
AJ291719.1/2082-2133 UUUUUUAGGGAAAAUCUGGCCUUCCAGCAAGGGAAGGCCAGGGAAUUUUAUC
AY140149.1/1173-1221 UUUUUUAGGGAGAAUGUGGCCUUCCAGCAAGGGGAGGCCGGGAA---UUCCU
AJ313391.1/51-102    UUUUUUAGGGAAAAUUUUGCCUCCCAGCAAGGGGAGGCCAGGAAAUUUUCCU
AF411964.1/2087-2138 UUUUUUAGGGAAAAUUUGGCCUUCCCGCAACGGGAGGCCAGGAAACUUUCUU
AF024423.1/123-174   UUUUUUAGGAAAAAUCUGGCCUUCCCACGAGGGGAGGCCAAGGAAUUUCCUU
AY322189.1/1554-1605 UUUUUUAGGGAAAAUCUGGCCUUCCAACAAAGGAAGGCCAGGGAACUUCCCU
AY561244.1/1200-1251 UUUUUUAGGGAAGAUCUGGCCUUCCUCCAAGGGAAGGCCAGGGAACUUCCUU
AY492785.1/846-897   AUUUUUAGGGAAAAUUUGGCCUUCCAACAAUGGGAGGCCAGGGAAUUUUCUU
AJ437033.1/1299-1350 UUUUUUAGGGAGAAUCUGGCCUUCCCACAAGGAAAGGCCAGGGAAUUUUCCU
U29410.1/1299-1350   UUUUUCAGGGAAGACCUGGUCUUCCCACAAGGGAAGGCCAGGGAACUUUCUU
AY518943.1/46-97     UUUUUUAGGGAAAAUCUGGCCUUCCCACAARGGRAGGCCAGGGAAUUUYCUG
U26546.1/1464-1515   UUUUUUAGGGAAWAUCCGGCCUUCCCACAUKGGAAGGCCAGGGRAUUUCCUU
AY561238.1/1290-1341 UUUUUUARGGAAAAUCUGGCCUUCCCACAAGGGGAGGCCAGGAAAUUUCCUC
AY140558.1/888-939   UUUUUUAGGGAAAAUUUGGCCUCCCAGCAAGGGGAGGCCAGGGAAUUUUCUC
AY484784.1/1-48      UU----AGGGAAGGUCUGGCCUUCCCACAAGGGGAGGCCAGGGAACUUUCUU
U53656.1/165-216     UUUUUUAAAGAAGAUCUGGCCUUCCUACAAGGGGAGGCCAGAGAAUUUUCUU
AY536235.1/1541-1592 UUUYYUAGGGAGAAUUUGGCCUUCCAACAAGGGGAGGCCAGGAAAUUUCCUU
AY165197.1/238-289   UUUUUUAGGGAAGAUCUGGYCUUCCCGGAAGGGAAGGCCAGGGAAUUUUCUU
AY535742.1/171-222   UUUUUUAGGAAAAAUCUGGCCYUCCUACAAGGRGAGGCCAGGGAACUUYCUU
AF443114.1/1446-1497 UUUUUUAGGGAGAUUUUGGCCUUCCCAGAAGGGGAGGCCUGGGAAUUUCCUU
U29404.1/1299-1350   UUUUUUAGGGAAAACCUGGCCUUCCCUCAAGGGAAGGCCAGGGAACUUUCUU
AF484510.1/1293-1344 UUUUUUAGGAAAAAUUUGGCCUUCCCGCAACGGAAGGCCAGGGAACUUCCUU
AY358053.1/1284-1335 UUUUUUAAGGAAAUUUUGGCCUUCCAACAAGGGAAGGCCGAGGAAUUUUCCU
AY535670.1/171-222   UUUUUUAAGAAAAAUCUGGCCUUCCUACAAAAGGAGGCCAAGGAACUUUCUU
AY358063.1/1284-1335 UUUUUUAGGAAAGCUUUGGCCUUCCAACAAGGGAAGGCCGGGGAAUUUUCCU
AY492772.1/840-891   UUUUUUAGGGAAAUUCUGGCCUUCCCACAGUGGGAGGCCAGGGAAUUUUCUU
X52154.1/2152-2203   UUUUUUAGGGAAAGGUUGGCCUUCCCGCAGCGGGAGGCCAGGCAACUUUGUG
AY181081.1/46-97     UUUUUUAGGGARRAUYUGGCCUUCCAGCAAGGGGAGGCCAGGGAAUUUCCUU
AY519093.1/46-97     UUUUUUAGGGAAAAUCUGGCCUUCCCACUCRGGRAGGCCAGGGAAUUUUCUU
AY561241.1/1290-1341 UUUUUUAAAGAAAAUCUGGCCUUCCUCCAAGGGAAGGCCAAGAAAUUUUCUU
AB074076.1/1320-1371 UUUUUUAAAGAAGAUCUGGCCUUCCCACAGUGGAAGGCCAAAGAAUUUUUUU
AY535690.1/171-222   UUUUUUAGGAARAAUCUGGCCUUCCUACAAGGGGAGGCCARGGAACUUUCUU
AF323226.1/65-116    UUUUUUAGGGAAAWUCUGGCCUUCCCNCAAGGGCAGGCCAGGGAAUUUUYUU
AF484485.1/1293-1344 UUUUUUAGGGAAAAUUUGGCCUUCCCACAGAGGAAGGCCAGGGAACUUCCUU
AJ313421.1/50-101    UUUUUUAGGGAAAAUUUGGCCUCUCAACAAAGGGAGGCCAGGGAACUUUCCU
AY181075.1/46-97     UUUUUUAGGGARAAUUUGGCCUUCCMACARGGGGRGGCCAGGGAAUUUYCUU
AB097867.1/1478-1529 UUUUUUAGGGAAGCUAUGGCCUUCCGACAGAGGAAGGCCGGGGAAUUUUCCU
AY484781.1/1-50      UUUU--AGAGAAAAUCUGGCCUUCCCACAAGGGAAGGCCAGGGAAUUUCGUU
AF024385.1/93-144    UUUUUUAGGGAAAAUCUGGCCUCCCCUUGUGGGGAGGCCAGGGAACUUCCUU
AJ313415.1/51-102    UUUUUUAGGGAGAAUCUGGCCUUCCAGCAAAGGGAGGCCAGGGAACUUUCUC
AF457051.1/1293-1344 UUUUUUAGGGAAAAUUUGGCCUUCCUCCAAGGGGAGGCCGGGGAACUUUCUU
AF286240.1/914-965   UUUUUUAGGGAAAAUUUGGCCUCCCAACAGAGGGAGGCCAGGAAAUUUUCCC
AY304963.1/1283-1334 UUUUUUAAAGAAAAUUUGGCCUUCCCACAAAAGGAGGCCAAAGAAUUUCCUU
AF042105.1/1440-1491 UUUUUUAGGAAAAAUCUGGCCUUCCCACAAGGGGAGGCAAGAGAACUUUCUU
AF457088.1/1278-1329 UUUUUUAGGGAAGAUUUGGCCUUCCAACAAAGGGAGGCCAGGAAAUUUUCCU
AY037269.1/1290-1341 UUUUUUAGGGAAAAUAUGGCCUUCCAACAGCGGAAGGCCAGGGAAUUUCCUU
AF442567.1/1455-1506 UUUUUUAAAGAAAAUUUGGCCUUCCAACAAGGGAAGGCCAAGGAACUUCCUU
AY519015.1/46-97     UUUUUUAGGGAAGAUCUGGCCUUCCCACAAGGGAAGGCCAGGAAACUUUCUU
AF457071.1/1281-1332 UUUUUUAAGAAGAAUUUGGCCUUCCAGCAAGAGGAGGCCAGGAAAUUUUCCU
AY441922.1/80-131    UUUUUUAGGGAAAAUCUGGCCUUCCCACAAGGGRAGGCCAGGRAAUUUUSUC
AY140137.1/1034-1085 UUUUNUACGGAGAAUUUGGCCAUCCANCAAGGGGCCGUCCGNCAAUUUCAUU
AY253315.1/1287-1338 UUUUUUGGGGAAAAUCUGGCCUUCCCACAAAGGGAGGCCAGGAAAUUUCCUU
AY255828.1/1281-1332 UUUUUUAGAGAAAAUUUAGCCUUCCAACAAGGGGAGGCCAAAGAAUUUCCUU
AF119820.1/2110-2161 UUUUUUAGGGAGAAUGUGGCCUUCCAGCAAAGGAAGGCCGGGGAAUUUUCUU
AF443109.1/1467-1518 UUUUUUAGGGAAGAUUUGGCCUUCCCGCGGAGGAAGGCCAGGGAAUUUCCUU
AF076998.1/1440-1491 UUUUUUAGGGAGAGUUUGGCUUUCCCACAAGGGAAGGCCAGGGAAUUUCCUC
AY455784.1/1548-1599 UUUUUUAGGGAAAAUUUGGCCUUCCCCCCAGGGGAGGCCCGGCAAUUUCCUU
AJ249235.1/1281-1332 UUUUUUAGGGAAGUUCUGGCCUCUCAACAAAGAGAGGCCAGGAAAUUUUCUU
AF457059.1/1287-1338 UUUUUUAGGGAGACUUUGGUCUUCCCACAAGGGAAGGCCAGGGAACUUCCUC
AF442570.1/1448-1499 UUUUUUAGGGAAAAUCUGGCCUUUCCGCAGGGACAGGCCAGGGAACUUCCUU
L11771.1/1296-1347   UUUUUUAGGGAGACUUUGGCCUUCCCGCAAGGGAGGGCCUGGAAACUUCCUU
L11798.1/1290-1341   UUUUUUAAAGAAAAUUUGGCCUUCCAGCAAGGGGAGGCCAAGGAACUUUCCU
AF408626.1/1506-1557 UUUUUUAGGGAAAAUUUGGCCUUUCCACAAGGGGAGGCCCGGGAAUUUUAUU
AY037266.1/1278-1329 UUUUUUAGGGAAAAUUUGGCCUUCCAACAGUGGGAGGCCCGGGAAUUUCCUU
AY165283.1/224-275   UUUUUUAGGGAAACUUUGGCCUUCCAGCAAAGGGAGGCCAGGGAAUUUUCCU
AY535669.1/171-222   UUUUUUAGGAAAAAUCUGGCCUUCCUACAAAAGGAGGCCAGGAAAUUUUCUU
U53654.1/165-216     UUUUUUAAGGAAGAUCUGGCCUUCCUACAAAAAGAGGCCAAGGAAUUUUCUU
AF484496.1/1275-1326 UUUUUUAGGGAAAAUCUGGCCUUCCCACAAGGGGAGGCCGGGAAACUUUCCA
AB074070.1/1350-1401 UUUUUUAAGGAAAAUCUGGCCUUCCCACAAGGGGAGGCCAAGGAAUUUUCUU
AY140134.1/1158-1206 UUUUUUAGGGAAAAUCUGGCCUUCUCACAAGGGAAGGCCAGGAA---UUGUU
AF484519.1/1293-1344 UUUUUUAGGGAGAGCUUGGCCUUCCCUCAAGGGAAGGCCGGGGAACUUCCUC
AY518978.1/46-97     UUUUUUAGGGAAAAUCUGGUCUUCCCACAAGGGAAGGCCAGGGAAUUUCCUG
AY206647.1/1296-1347 UUUUUUAGGGAAAAUCUGGCCUUCCCAGAAGGGAAGGCCGGGGAAUUUCCUU
AF442568.1/1448-1499 UUUUUUAGGGAAAAUUUGGCCUUCCAGCAAGAGGAGGCCAGAGAAUUUUCCU
AY165211.1/236-287   UUUUUUAGGGAAAAUUUGGCCUUCCCGUGGGGGGAGGCCAGGGAAUUUCCUU
AY358055.1/1284-1335 UUUUUUAAGGAAGAUUUGGCCUUCCAACAAAGGAAGGCCAAAGAAUUUUCCU
AY518998.1/46-97     UUUUUUAGGGAAGAUCUGGCCUUCCYACAAGGGGAGGCCAGGRAAUUUYCUU
AB078707.1/1299-1350 UUUUUUAGGGAGGCUCUGGCCUUCCCACAAGGGAAGGCCAGGGAAUUUCCUC
AF484483.1/1292-1343 AUUUUUAGGGAGAUUUUGGCCUUCCCACAAGGGAAGGCCAGGGAAUUUCCUU
AY140164.1/1155-1204 UUUUUUAGGGAAAAUUUGGCCUUCCAGCAAGGGGAGGCCAGGAA--UUCCUC
#=GC SS_cons         :::::::::::::::<<<<<<<<<<______>>>>>>>>>>:::::::::::
#=GC RF              UUUUUUAGGGAAAAUcuGGCCUuCCcACAAGGGaAGGCCagGGAAUUUUCUU
//
# STOCKHOLM 1.0

#=GF AC   RF00481
#=GF ID   HCV_X3
#=GF DE   Hepatitis C virus 3'X element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15452207
#=GF SS   Published; PMID:15452207
#=GF GA   73.00
#=GF TC   76.50
#=GF NC   60.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0039694; viral RNA genome replication;
#=GF RN   [1]
#=GF RM   15452207
#=GF RT   cis-acting RNA signals in the NS5B C-terminal coding sequence of the
#=GF RT   hepatitis C virus genome.
#=GF RA   Lee H, Shin H, Wimmer E, Paul AV
#=GF RL   J Virol 2004;78:10865-10877.
#=GF RN   [2]
#=GF RM   12610131
#=GF RT   3' nontranslated RNA signals required for replication of hepatitis C virus
#=GF RT   RNA.
#=GF RA   Yi M, Lemon SM
#=GF RL   J Virol 2003;77:3557-3568.
#=GF RN   [3]
#=GF RM   12592007
#=GF RT   Structure-function analysis of the 3' stem-loop of hepatitis C virus
#=GF RT   genomic RNA and its role in viral RNA replication.
#=GF RA   Yi M, Lemon SM
#=GF RL   RNA 2003;9:331-345.
#=GF CC   This family represents the Hepatitis C virus 3'X element which contains
#=GF CC   three stemloop structures that are essential for replication [2].
#=GF WK   Hepatitis_C_virus_3'X_element
#=GF SQ   22


AB047641.1/9561-9659 -UGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAUUGCCGUAACUGGUAUCUCUGCAGAUCAUGU
AF009071.1/259-356   --GGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCGGCAUGACUGCAGAGAGUGCUGAUACUGGCCUCUCCGCAGAUCAUGU
AB049091.1/9448-9547 UUGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGGUCAUGU
AB016785.1/9439-9538 UUGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAUGU
AF139594.2/9517-9616 AUGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAUGU
AB047645.1/9585-9683 -UGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCCGUAACUGGUCUCUCUGCAGAUCAUGU
AF009075.1/228-327   UAGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCUUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAAGU
AB049095.1/9486-9585 CUGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAUGU
AJ278830.1/9512-9610 C-GGUGGCUGGCUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAUGU
AB047640.1/9576-9674 -UGGUGGCUCCAUCUUAGCCCUGGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCCGUAACUGGUCUCUCUGCAGAUCAUGU
D85019.1/111-210     UUGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGGGAGUGCUGAUACUGGCCUCUCUGCAGAUCAUGU
AJ132997.1/9434-9533 UUGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCGGUGAGCCGCAUGACCGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAUGU
AF169005.1/9602-9700 -UGGUGGCUCCAUCUUAGCCCUAGUCACGGCUACCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCCGUAACUGGUCUCUCUGCAGAUCAUGU
AF009074.1/195-294   UUGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCUGAAACUGGCCUCUCUGCAGAUCAUGU
D85026.1/113-211     -AGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCUUGACUGCAGAGAGUGCUGUAACUGGCCUCUCUGCAGAUCAAGU
AB119282.1/9554-9653 AUGGUGGCUCCGUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAUGU
D85021.1/137-236     UUGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCUGAUACUGGCCCCUCUGCAGAUCAUGU
D85516.1/9436-9535   UUGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACCGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAUGU
D85025.1/114-212     -AGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAUGU
AF169003.1/9595-9693 -UGGUGGCCCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCAUGACUGCAGAGAGUGCCGUAACUGGUCUCUCUGCAGAUCAUGU
AF009072.1/224-321   --GGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCGGCAUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCUGAUCAUGU
S82227.1/259-356     --GGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCUGCAUGACUGCAGAGAGUGCUGAUACUGGCCUCUCCGCAGAUCAUGU
#=GC SS_cons         :<<<-<<<<_______>>>>>>>,<<<<<<---<<<______>>>>>>>>>---<<<<<<<<<<<<<<<<-<<<<____>>>>>>>>>>>>>>->>>>>>
#=GC RF              uugGUGGCuccAUcUUaGCCCcaGuCaCgGcUAgCcGUGAAAgGcCcGuGaGccgCauGaCuGCaGaGaGUgCcgauAccgGcCuCuCuGCaGAuCauGc
//
# STOCKHOLM 1.0

#=GF AC   RF00482
#=GF ID   snoF1_F2
#=GF DE   Small nucleolar RNA F1/F2/snoR5a
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   60.00
#=GF TC   60.00
#=GF NC   59.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   This family contains F1, F2 and snoR5a sequences, all of which are members
#=GF CC   of the the H/ACA class of snoRNA that guide the sites of modification of
#=GF CC   uridines to pseudouridines [1].
#=GF WK   Small_nucleolar_RNA_F1/F2/snoR5a
#=GF SQ   8


Z96806.1/1-140         -AAUGGCCAUUUGGUAUCUGACACAUGGUCUGCUCUUGUGACUAUUAGUCUCGAAAUAUGGCAUAAAACAAGGGGGAACGGAUCUUGCGACAUUGGUGGUUCCUCUAUGAUCCUCCAAUUACUAUAUAGCCGUUUACAAUU
AK099797.1/1076-1214   UUAUG-CCAUUUGGUAUCUGACACAUAAUC-AUUUCUCUGAUUAUGUGUCUCGAAACAUGGCAGAAAGUGAGGGGGAACGGUCCUUGCGACACUGGUUGCUACUAUAUGAGCUUCUAGUUACUAUAUACCCGUUUACAUUU
AL731784.3/25271-25133 UUAUG-CCAUUUGGUAUCUGACACAUAAUC-AUUUCUCUGAUUAUGUGUCUCGAAACAUGGCAGAAAGUGAGGGGGAACGGUCCUUGCGACACUGGUUGCUACUAUAUGAGCUUCUAGUUACUAUAUACCCGUUUACAUUU
Z96808.1/1-140         UUAUG-CCAUUUGGUAUCUGACUCAUUGUCUACUUUUGUGACUAUGUGUCUUGAAAUAUGGCAUAUAAUAAGGGGGAACGGAUCUUGCGACAUUGAUGGCUCCUGUAUGAGCCUCCAAUUACUAUAUAGCCGUUUACAUGU
AL731784.3/23367-23229 UCAUG-CCAUUUGGUAUCUGACACAUAAUC-AUUUAUCUGAUUAUGCGUCUCGAAACAUGGCAGAAAGCGAGGGGGAACGGUCCUUGCGACACUGGUUGCUGCUAUAUGAGCUUCUAGUUACUAUAUACCCGUUUACAUAU
X67711.2/1771-1910     UUAUG-CCAUUUGGUAUCUGACUCAUUGUCUACUUUUGUGACUAUGUGUCUUGAAAUAUGGCAUAUAAUAAGGGGGAACGGAUCUUGCGACAUUGAUGGCUCCUGUAUGAGCCUCCAAUUACUAUAUAGCCGUUUACAUGU
AJ532548.1/1-139       UUAUG-CCAUUUGGUAUCUGACACAUAAUC-AUUUCUCUGAUUAUGUGUCUCGAAACAUGGCAGAAAGUGAGGGGGAACGGUCCUUGCGACACUGGUUGCUACUAUAUGAGCUUCUAGUUACUAUAUACCCGUUUACAUUU
X67711.2/2553-2693     UAAUGGCCAUUUGGUAUCUGACACAUGGUCUGCUCUUGUGACUAUUAGUCUCGAAAUAUGGCAUAAAACAAGGGGGAACGGAUCUUGCGACAUUGGUGGUUCCUCUAUGAUCCUCCAAUUACUAUAUAGCCGUUUACAAUU
#=GC SS_cons           :::<<.<<<<---------<<<<<<<<<<<-<______>>>>>>>>>>>>------->>>>>>-------------<<<<<----------<<<<<-<<<<________>>>>->>>>>---------->>>>>:::::::
#=GC RF                UuAuG.CCauUUGGUAUCUGaCgcauaguCUauUuuUguGacuaugcGuCUcGAAAuauGGCauAaAauaAGGGGGaaCGGauCUUGCGACacugGUgGcuaCUaUAUGagCcUCcaguUACUAUAUAgCCGuuUACAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF00483
#=GF ID   IRES_IGF2
#=GF DE   Insulin-like growth factor II IRES
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Published; PMID:11903044
#=GF GA   70.00
#=GF TC   80.40
#=GF NC   48.70
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11903044
#=GF RT   Human insulin-like growth factor II leader 2 mediates internal initiation
#=GF RT   of translation.
#=GF RA   Pedersen SK, Christiansen J, Hansen TO, Larsen MR, Nielsen FC
#=GF RL   Biochem J 2002;363:37-44.
#=GF CC   This family represents the insulin-like growth factor II (IGF-II) internal
#=GF CC   ribosome entry site (IRES) which is found in the 5' UTR of IGF-II leader 2
#=GF CC   mRNA. This family allows cap-independent translation of the mRNA and it is
#=GF CC   thought that this family may facilitate a continuous IGF-II production in
#=GF CC   rapidly dividing cells during development [1].
#=GF WK   Insulin-like_growth_factor_II_IRES
#=GF SQ   9


AC132217.15/106569-106689 GCGACCGGGCAUUGCCCCCAGUCUCCCCCAAAUUUGGGCAUUGUCCCCGGGUCUUCCAACGGACUGGGCGUUGCUCCCGG-ACACUGAGGACUGGCCCCGGGGUCUCGCUCACCUUCAGCAG
X03562.1/168-288          GCGACCGGGCAUUGCCCCCAGUCUCCCCCAAAUUUGGGCAUUGUCCCCGGGUCUUCCAACGGACUGGGCGNNGCUCCCGG-ACACUGAGGACUGGCCCCGGGGUCUCGCUCACCUUCAGCAG
AY242112.1/19400-19519    ACGACUGGGCAUUGCCCCCAGUUUCCCCCAAAUUUGGGCAUUGUCCCUGGGUCUUCCAACGGACUGGGCGUUGCCCCCGG-ACACUGCGGACUGCCCCCGGGGUCUCGCUCACCUUCAGC-G
AF020598.1/561-681        ACGACUGGGCAUUGCCCCCAGUUUCCCCCAAAUUUGGGCAUUGUCCCUGGGUCUUCUAACGGACUGGGCGUUGCCCCGGG-ACAUUGGGGACUGCCCCCGGGGUCUUGCUCACCUUCAGCAG
AY242109.1/19270-19389    ACGACUGGGCAUUGCCCCCAGUUUCCCCCAAAUUUGGGCAUUGUCCCUGGGUCUUCCAACGUACUGGGCGUUGCCCCCGG-ACACUGCGGACUGCCCCCGGGGUCUCGCUCACCUUCAGC-G
U00664.1/1237-1354        ACGACUGGGCAUUGCCCCCAGUUUCCCCCAAAUUUGGGCAUUGUCCCCGGGUCUUCCAACGGACUGGGCGUUGCCCC-GG-ACGCUGGGGACUGCCCC-GGGGUCUCGCUCACCUUCAGC-G
AC013548.13/54281-54401   ACGACUGGGCAUUGCCCCCAGUUUCCCCCAAAUUUGGGCAUUGUCCCCGGGUCUUCCAACGGACUGGGCGUUG-CCCCGGUUCACUGGGGACUGCCCUUGGGGUCUCGCUCACCUUCAGCAG
M36329.1/1311-1429        ACGACUGG-CAUUGCCCCCAGUUUCCCCCAAAUUUGGGCAUUGUCCCCGGGUCUUCCAACGGACUGG-CGUUG-CCCCGGUUCACUGGGGACUGCCCUUGGGGUCUCGCUCACCUUCAGCAC
AC098563.6/58764-58884    ACCACUGGGCAUUGCCCCCAGUUUCCCCCAAAUUUGGGCAUUGUCCCCGGGUCUUCCAACGGACUGGGCGUUG-CCCCGGGACACUGGGGACUGCCUUUGGGGUCUCGCUCACCUUCAGCAA
#=GC SS_cons              ::<<<-<<<<___>>>>--->>>,,,<<<<____>>>>,,,,<<<<--<<<___>>>--->>>><<<<------<<<<<<.________________>>>>>>->>>>::::::::::::::
#=GC RF                   ACgaCuGGGCAUUGCCCCCAGucUCCCCCaAAUUuGGGCAUUGucCCcGGgUCUuCCAACGgaCuGgGCGUUGccCCCgg.aCAcUGgGGACUGcCcccGGGgUCuCgCUCACCUUCAGCAg
//
# STOCKHOLM 1.0

#=GF AC   RF00484
#=GF ID   IRES_Cx32
#=GF DE   Connexin-32 internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Published; PMID:10931843
#=GF GA   80.00
#=GF TC   83.30
#=GF NC   34.70
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   10931843
#=GF RT   Analysis of a Charcot-Marie-Tooth disease mutation reveals an essential
#=GF RT   internal ribosome entry site element in the connexin-32 gene.
#=GF RA   Hudder A, Werner R
#=GF RL   J Biol Chem 2000;275:34586-34591.
#=GF CC   This family represents the connexin-32 internal ribosome entry site (IRES)
#=GF CC   which allows cap independent translation during conditions such as heat
#=GF CC   shock and stress [1].
#=GF WK   GJB1
#=GF SQ   6


L47127.1/400-550          AUAUGACUCCCCAGCACCGGGCGGUGAUGAAUUGGGACGCAGGCGCGGAGCC-CAGGGACCACUCCCCCUGCACAGACAUGAGACCAUAGGGGACCUGUCUGGGUGGCCUCAGGGAUAGGCGCUCCCCA-AGGUAAGAGGGCUUUGUUGAGUU
M23565.1/710-859          AUAUGACUCUCCAGCACCGGGAGGCGAUGAAUUGGGACGCAGGCGCG-A-CCACAGGGACCACUCCCCCUACACAGACAUGAGACCAUAGGGGAGCUGUCUGGGUGGCCUCAAGGAUAGGCGCUCCCCCGAGGUAACCGGGCUAUCU-GGGUU
AY303808.1/346-495        AUAUGACUCCCCAGCACCGGGCGGCGAUGAAUUGGGACGCAGGCGCGGA-CC-CAGGGACCACUCCCCCUGCACAGACAUGAGACCAUAGGGGACCUGUCUGGGUGGCCUCAGGGAUAGGCGCUCCCCA-AGGUAAUGGGGCUUUGUUGGGUU
AL683892.12/123280-123428 AUAUGACUCUCUAGCACCGGGAGGCGAUGAAUUGGGACGCAGGCGCG-A-CCACAGGGACCACUCCCCCUACACAGACAUGAGACCAUAGGGGAGCUGUCUGGGUGGCCUCAAGGAUAGGCGCUCCCCG-AGGUAACCGGGCUAUCU-GGGUU
BC022426.1/1-118          --------------------GCGGUGAUGAAUUGGGACGCAGGCGCGGAGCC-CAGGGACCACUCCCCCUGCACAGACAUGAGACCAUAGGGGACCUGUCUGGGUGGCCUCAGGGAUAGGCGCUCC------CCAAGG------UGU-GAAU-
S83323.1/50-200           AUAUGACUCCCCAGCACCGGGCGGUGAUGAAUUGGGACGCAGGUGCGGAGCC-CAGGGACCACUCCCCCUGCACAGACAUGAGACCAUAGGGGACCUGUCUGGGUGGCCUCAGGGAUAGGCGCUCCCCA-AGGUAAGAGGGCUUUGUUGAGUU
#=GC SS_cons              ::::::::(((----((((((--(((-----(((((,<<<____>>>,,.<<.<--<<<<---<<<<<_____________________>>>>>--->>>>-->->>,)))))-------)))--)))-.-)))----)))::::::.:::::
#=GC RF                   AUAUGACUCcCcAGCaCCGGGcGGcGAUGAAcuGgGACGCAGGcGCGGA.CC.CAGgGaCCACuCCCCCUgCACAGACAUGAGACCAUAGGGGacCUGuCuGGGUGGCCuCagGGAUAGGCgCUCCCCa.AGGuAAuaGgGCUuUgU.GagUU
//
# STOCKHOLM 1.0

#=GF AC   RF00485
#=GF ID   K_chan_RES
#=GF DE   Potassium channel RNA editing signal
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15361858
#=GF SS   Published; PMID:15361858; Moxon SJ
#=GF GA   51.00
#=GF TC   51.00
#=GF NC   50.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0006382; adenosine to inosine editing;
#=GF RN   [1]
#=GF RM   15361858
#=GF RT   Control of human potassium channel inactivation by editing of a small mRNA
#=GF RT   hairpin.
#=GF RA   Bhalla T, Rosenthal JJ, Holmgren M, Reenan R
#=GF RL   Nat Struct Mol Biol 2004;11:950-956.
#=GF CC   This family represents a group of sequences related to the human potassium
#=GF CC   channel Kv1.1 hairpin element which directs the efficient modification of
#=GF CC   an adenosine to inosine by an adenosine deaminase acting on RNA (ADAR).
#=GF CC   The ADAR modification causes an isoleucine/valine recoding event which
#=GF CC   lies in the ion-conducting pore of the potassium channel. It is thought
#=GF CC   that this editing event targets the process of fast inactivation and
#=GF CC   allows a more rapid recovery from inactivation at negative potentials [1].
#=GF WK   Potassium_channel_RNA_editing_signal
#=GF SQ   85


U06156.1/1880-1993   GUGGGCUAUGGGGACAUGAAGC-CCAUCACUGUGGGGGGCAAGAUCGUGGGGUCCC-UGUGUGCCAUUGCAGGUGUGUUAACCAUUGCUUUGCCAGUGCCAGUGAUUGUCUCUAAC
M95914.1/1261-1374   GUGGGCUACGGAGACAUGCGGC-CGAUCGGGGUGUGGGGCAAGCUGGUUGGCUCUC-UGUGCGCCAUCGCUGGCGUGCUCACGAUCGCGCUUCCUGUCCCUGUCAUUGUGUCUAAU
AY329366.1/1456-1569 GUGGGCUAUGGGGACAUGC-ACCCCAUCACCAUCGGGGGCAAGAUCGUGGGGUCUC-UGUGUGCCAUCGCGGGGGUGCUGACCAUCGCUCUGCCCGUGCCCGUCAUAGUCUCCAAU
AF075160.1/1209-1322 CUGGGGUAUGGUGACAUGGUGC-CGAAGACAAUAGCUGGCAAGAUUUUUGGUUCAA-UAUGCUCCUUGAGUGGAGUCUUAGUGAUUGCUCUGCCAGUUCCUGUAAUUGUCUCCAAC
M38217.1/1195-1308   GUGGGUUACGGCGAUAUGC-ACCCAGUGACCAUAGGGGGCAAGAUUGUGGGAUCUC-UCUGUGCCAUCGCCGGUGUCUUGACCAUCGCAUUGCCAGUUCCCGUGAUUGUUUCCAAC
AF166008.1/340-453   CUCAGGUAUGGUGACAUGGUGC-CAAAAACCAUAGCAGGGAAGAUUUUUGGUUCUA-UCUGUUCGCUGAGUGGGGUCUUGGUCAUUGCUCUACCUGUUCCGGUGAUUGUAUCCAAC
L48691.1/1171-1284   GUUGGUUAUGGGGAUAUGGCAC-CCAAGACUUAUGUGGGUAUGUUUGUUGGUGCCC-UGUGUGCCCUUGCUGGUGUGUUGACAAUUGCGCUACCAGUACCAGUCAUUGUGUCCAAC
AY329361.1/1209-1322 GUUGGCUACGGAGACAUG-GUCCCCACCACCAUCGGGGGGAAAAUCGUGGGGUCUC-UGUGUGCCAUCGCUGGCGUAUUAACCAUUGCCUUACCCGUGCCCGUCAUAGUGUCUAAC
AF508735.1/1111-1224 CUGGGGUAUGGUGAUAUGGUAC-CAAAAACCAUAGCAGGGAAGAUUUUUGGUUCCA-UCUGUUCGCUGAGUGGUGUCUUGGUCAUUGCUCUACCUGUUCCAGUUAUUGUAUCCAAC
U20342.1/1144-1257   GUUGGCUAUGGGGACAUAU-AUCCUAAGACAUUGCUGGGUAAAAUUAUUGGGGGCC-UUUGUUGCAUUGCUGGUGUGUUAGUUAUAGCAUUGCCUAUACCAAUUAUAGUGAAUAAC
M35664.1/1146-1259   GUAGGCUAUGGAGACAUGG-UCCCUACAACAAUAGGUGGCAAAAUAGUAGGCUCUC-UGUGUGCAAUUGCAGGCGUAUUAACCAUUGCCUUACCUGUCCCUGUUAUAGUAUCCAAU
AF166003.1/1167-1280 CUUGGCUACGGAGACAUGGUGC-CCAGCACCAUUGCUGGCAAGAUUUUCGGGUCCA-UCUGCUCACUCAGUGGCGUCUUGGUCAUUGCCCUGCCUGUGCCAGUCAUUGUGUCCAAC
Y07588.1/172-285     CUGGGCUAUGGUGAUAUGU-ACCCCAAGACCUGGUCGGGCAUGGUGGUGGGGGCUC-UGUGUGCGCUGGCCGGGGUGCUCACCAUCGUCAUGCCCGUGCCCGUCAUUGUCAAUAAC
U89873.1/663-775     CUUGGGUAUGGCGACAUGGUGC-CUAGCAC-AUCGCAGGCAAAAUUUUUGGGUCCA-UCUGCUCACUUAGUGGUGUCUUGGUCAUUGCCUUGCCUGUACCAGUCAUUGUGUCUAAC
AF454388.1/1126-1239 CUGGGAUAUGGAGAUAUGGUGC-CCAAAACAAUUGCAGGGAAAAUUUUUGGCUCCA-UCUGUUCCCUGAGUGGCGUCUUGGUCAUUGCCCUGCCGGUCCCUGUGAUUGUUUCCAAC
X60797.1/1180-1293   CUGGGCUAUGGAGACAUGU-AUCCCAAGACGUGGUCUGGGAUGCUGGUUGGGGGAC-UGUGUGCCCUGGCUGGUGUGCUGACCAUUGCCAUGCCCGUGCCUGUCAUUGUCAACAAC
X12589.1/1364-1477   GUGGGAUACGGUGACAUGU-ACCCUGUGACAAUUGGAGGCAAGAUCGUGGGCUCCU-UGUGUGCCAUCGCUGGUGUGCUGACAAUUGCCCUGCCCGUACCUGUCAUUGUGUCCAAU
X16001.1/1190-1303   GUCGGUUAUGGUGAUAUGC-ACCCAGUGACCAUAGGAGGCAAGAUUGUGGGCUCUC-UUUGUGCCAUCGCAGGUGUCUUGACCAUUGCAUUGCCGGUUCCUGUGAUUGUUUCCAAC
AB084422.1/1249-1362 CUAGGAUAUGGUGAUAUGGUGC-CUAAAACAAUUGCCGGAAAAAUCUUCGGAAGCA-UUUGUUCCUUGAGCGGAGUCCUGGUCAUCGCUCUCCCGGUACCGGUCAUCGUUUCUAAU
M30312.1/1217-1330   GUCGGUUAUGGUGAUAUGC-ACCCAGUGACCAUAGGAGGCAAGAUUGUGGGCUCUC-UUUGUGCCAUCGCAGGUGUCUUGACCAUUGCAUUGCCGGUUCCUGUGAUUCUUUCCAAC
AF319664.1/1334-1447 GUUGGGUAUGGAGAUAUCU-AUCCACAGACUCUGCUUGGUAAAAUAGUCGGUGGGC-UUUGCUGCAUCGCAGGCGUGUUGGUGAUCGCUUUACCAAUUCCCAUCAUCGUCAACAAC
AF032099.1/1303-1416 GUUGGCUAUGGGGACAUGGCAC-CCGUCACCGUGGGUGGCAAGAUCGUGGGCUCUC-UGUGUGCCAUUGCAGGUGUGCUCACCAUCUCUCUGCCUGUGCCUGUCAUUGUCUCUAAC
AY179603.1/1735-1848 CUGGGCUAUGGUGACAUGU-ACCCCAAGACAUGGUCUGGGAUGCUGGUCGGGGCAC-UGUGUGCCCUGGCUGGUGUGCUGACCAUUGCCAUGCCGGUGCCCGUCAUUGUCAACAAC
L02751.1/1573-1686   GUGGGCUAUGGGGACAUGAAGC-CCAUCACUGUAGGGGGCAAGAUUGUCGGGUCCC-UGUGUGCCAUUGCGGGUGUCUUAACCAUUGCUUUGCCAGUGCCAGUGAUUGUCUCUAAC
U42975.1/1160-1273   CUGGGGUAUGGAGACAUGGUGC-CUAAGACAAUUGCUGGGAAGAUAUUUGGCUCCA-UCUGCUCCCUAAGCGGCGUCCUGGUCAUUGCUCUGCCAGUCCCCGUCAUAGUCACCAAC
M68880.1/2362-2475   CUGGGCUAUGGAGACAUGU-AUCCUCAGACGUGGUCUGGGAUGUUGGUGGGAGCAC-UGUGCGCCCUGGCUGGUGUGCUGACCAUUGCCAUGCCGGUGCCCGUCAUCGUGAACAAU
M55514.1/2727-2840   GUGGGCUAUGGGGACAUGAAGC-CCAUCACUGUAGGGGGCAAGAUUGUCGGGGUCC-UGUGUGCCAUUGCGGGUGUCUUAACCAUUGCUUUGCCAGUGCCAGUGAUUGUCUCUAAC
AF375605.1/1111-1224 UUAGGAUACGGCGACAUGG-UUCCCCACACGCCCACGGGUAAGAUUGUGGGUGGCG-UGUGUUCGCUAUCCGGUGUGUUGGUUAUCGCGCUCCCUGUACCUGUUAUCGUCUCCAAC
AF107781.1/1102-1215 CUGGGAUAUGGAGACAUGGUGC-CUAAGACAAUCGCAGGGAAGAUAUUUGGCUCCA-UCUGCUCCCUCAGCGGUGUCCUGGUCAUUGCCCUGCCGGUCCCUGUGAUAGUCUCCAAC
AF017129.1/1373-1486 GUGGGCUAUGGAGAUAUGACGC-CCGUGGGUGUGUGGGGCAAGAUCGUUGGGUCCC-UGUGUGCCAUCGCUGGUGUCCUUACCAUCGCUCUUCCUGUUCCCGUUAUCGUGUCAAAC
AF048712.1/1102-1215 CUGGGGUACGGAGACAUGGUGC-UUAAGACGAUUGCAGGGAAGAUCUUCGGCUCCA-UCUGCUCCUUGAGUGGCGUCCUGGUCAUUGCCCUGCCAGUCCCUGUGAUUGUUUCCAAC
U78642.1/1141-1254   UUAGGGUAUGGCGAUAUGGUGC-CAAAAACAAUCCCUGGUAAACUAGUUGGUAGUA-UUUGCUCAUUAAGUGGGGUAUUAGUGAUAGCUCUACCCGUACCUGUUAUAGUAUCGAAC
X66185.1/1123-1236   GUAGGCUAUGGAGACAUGG-UUCCGACUACCAUUGGGGGAAAGAUCGUGGGUUCCC-UAUGUGCAAUUGCAGGUGUUUUAACCAUUGCCUUACCGGUCCCUGUCAUAGUGUCCAAU
U03723.1/2475-2588   GUGGGCUAUGGGGACAUGAAGC-CCAUCACAGUCGGGGGAAAGAUUGUGGGGUCCC-UGUGUGCCAUUGCGGGUGUCUUAACCAUUGCUUUGCCUGUGCCGGUGAUUGUGUCUAAC
AF252301.1/1598-1711 GUAGGGUAUGGUGACAUGG-UCCCGACCACCAUUGGUGGCAAGAUUGUGGGCUCCC-UCUGUGCCAUUGCAGGUGUGCUGACAAUUGCCUUGCCCGUGCCUGUCAUUGUUUCCAAC
U75448.1/1122-1235   CUGGGGUAUGGAGACAUGGUGC-CUAAGACAAUUGCUGGGAAGAUAUUUGGCUCCA-UCUGCUCCCUAAGCGGCGUCCUGGUCAUUGCUCUGCCAGUCCCCGUCAUAGUCUCCAAC
U96110.1/1273-1386   GUAGGCUAUGGGGACAUGU-GCCCGACCACCCCAGGGGGGAAGAUUGUGGGCACUC-UGUGUGCCAUUGCAGGGGUCCUCACCAUUGCCCUCCCUGUGCCUGUCAUUGUCUCCAAC
AY232553.1/1231-1344 GUGGGGUACGGAGACAUGC-GUCCCGUGGGAGUGUGGGGUAAGAUUGUGGGCUCAU-UAUGUGCUAUCGCAGGCGUGCUAACAAUAGCGCUUCCGGUUCCAGUGAUAGUUUCUAAU
U38182.1/1906-2019   GUGGGCUAUGGUGACAUGU-GCCCAAUCACCCCAGGGGGAAAGAUCGUGGGCACUC-UGUGUGCCAUUGCAGGGGUCCUCACCAUUGCACUCCCUGUGCCCGUCAUUGUCUCCAAC
AY329362.1/1365-1478 GUUGGCUAUGGAGAUAUGU-GUCCCACCACCCUGGGUGGGAAGAUCGUGGGGACUC-UGUGUGCUAUUGCAGGAGUGCUGACCAUCGCUCUGCCCGUCCCCGUCAUCGUCUCAAAC
Y07589.1/82-195      CUGGGCUACGGAGACAUGU-AUCCUCAGACUUGGUCAGGCAUGCUGGUGGGGGCCC-UCUGCGCUCUUGCCGGCGUGCUGACCAUUGCCAUGCCUGUCCCUGUCAUUGUGAACAAU
M17211.1/1733-1846   GUUGGAUAUGGUGACAUGACGC-CCGUCGGCUUCUGGGGCAAAAUUGUCGGCUCUU-UGUGCGUGGUCGCUGGUGUGCUGACAAUCGCACUGCCGGUACCGGUUAUCGUCAGUAAU
AF132853.1/1195-1308 UUGGGAUAUGGGGACAUGU-ACCCAAUGACUUGGUCUGGCAUGUUGGUGGGUGCUC-UUUGUGCUUUGGCAGGUGUGCUAACUAUUGCUAUGCCAGUCCCUGUUAUUGUCAACAAU
AF284420.1/1334-1447 GUAGGCUAUGGAGACAUGG-UUCCAACCACCAUUGGGGGAAAGAUAGUGGGCUCUC-UGUGCGCCAUCGCAGGUGUGUUAACCAUUGCCUUACCGGUCCCAGUCAUAGUGUCCAAU
AY147192.1/1892-2005 CUGGGGUAUGGUGACAUGG-UACCAAAAACCAUAGCAGGGAAGAUUUUUGGUUCCA-UCUGUUCGCUGAGUGGGGUCUUGGUCAUUGCUCUACCUGUUCCAGUGAUCGUCUCUAAC
M74449.1/1173-1286   GUAGGCUAUGGAGACAUGG-UUCCAACUACCAUUGGGGGAAAGAUAGUGGGUUCUC-UGUGUGCAAUUGCAGGUGUGUUAACCAUUGCCUUACCAGUCCCUGUCAUAGUGUUCAAU
M55515.1/1302-1415   GUGGGUUACGGCGAUAUGC-ACCCAGUGACCAUAGGGGGGAAGAUUGUGGGAUCUC-UCUGUGCCAUCGCCGGUGUCUUGUCCAUCGCAUUGCCAGUUCCCGUGAUUGUUUCCAAC
BC054804.1/1537-1650 GUAGGUUAUGGGGACAUGU-ACCCCAUGACGGUAGGGGGCAAGAUUGUGGGCUCAC-UGUGCGCCAUUGCUGGGGUCCUCACCAUUGCAUUACCGGUACCGGUCAUUGUCUCCAAU
AF223409.1/1162-1275 CUUGGCUAUGGAGACAUGU-ACCCUCAGACAUGGUCUGGCAUGCUGGUGGGAGCGC-UGUGUGCUCUGGCUGGUGUGCUGACUAUCGCCAUGCCAGUGCCUGUUAUUGUCAAUAAC
AF493544.1/1545-1658 GUGGGCUAUGGGGACAUGAAGC-CCAUCACCGUGGGGGGCAAGAUCGUGGGGUCCC-UGUGUGCCAUUGCUGGUGUCUUAACCACUGCUUUGCCAGUGCCAGUGAUUGUCUCUAAC
M59980.1/1343-1456   CUGGGGUAUGGCGACAUGGUAC-CAAAAACCAUAGCAGGGAAGAUUUUCGGGUCUA-UCUGCUCACUGAGCGGAGUCUUGGUCAUCGCGCUACCCGUGCCUGUGAUCGUGUCUAAC
M64226.1/1117-1230   CUUGGGUAUGGAGAUAUGGUAC-CUAGCACCAUUGCAGGCAAAAUUUUUGGGUCCA-UCUGCUCACUUAGCGGUGUCUUGGUCAUUGCCUUGCCUGUGCCAGUCAUUGUAUCCAAC
M96747.1/472-585     CUGGGCUAUGGAGACAUGU-ACCCGCAGACGUGGUCCGGCAUGCUGGUGGGGGCUC-UGUGUGCGCUGGCGGGCGUGCUCACCAUCGCCAUGCCCGUGCCCGUCAUCGUGAACAAU
AF323751.1/1477-1590 GUAGGUUAUGGAGAUAUGUCAC-CUGAAACAGUAGGUGGGAAACUGGUUGGGUCUC-UUUGUGCCAUUGCCGGUGUGCUGACCAUCUCCUUGCCAGUGCCAGUCAUUGUAUCCAAU
M32660.1/1111-1224   CUGGGAUAUGGCGACAUGGUGC-CAGAGACAAUAGCUGGCAAAAUUGUGGGCGGCG-UCUGCUCGCUUAGCGGUGUGCUGGUCAUCGCCUUACCUGUACCUGUUAUCGUAUCGAAC
L22218.1/1705-1818   GUAGGCUACGGGGACAUGAGGC-CCAUCACUGUAGGGGGCAAGAUUGUGGGCUCAC-UGUGCGCCAUAGCUGGGGUCCUCACCAUUGCUCUGCCUGUGCCCGUCAUCGUCUCCAAU
AY138839.1/1562-1675 CUGGGCUACGGGGACAUGU-ACCCCAAGACCUGGUCGGGGAUGCUGGUCGGGGCGC-UGUGCGCCCUGGCCGGGGUGCUCACCAUCGCCAUGCCUGUGCCCGUGAUCGUCAACAAC
M59211.1/1348-1461   UUAGGCUAUGGGGAUAUGU-ACCCCCAAACAUGGUCAGGGAUGUUGGUGGGGGCCU-UGUGUGCUCUGGCUGGAGUGCUGACCAUAGCUAUGCCUGUGCCCGUCAUUGUCAACAAU
X16003.1/1685-1798   GUAGGCUAUGGAGACAUGG-UUCCAACUACCAUUGGGGGAAAGAUAGUGGGUUCUC-UGUGUGCAAUUGCAGGUGUGUUAACCAUUGCCUUACCAGUCCCUGUCAUAGUGUCUAAU
M59313.1/33-146      UUAGGCUAUGGGGAUAUGU-ACCCCCAAACAUGGUCAGGGAUGUUGGUGGGGGCCU-UGUGUGCUCUGGCUGGAGUGCUGACCAUAGCUAUGCCUGUGCCCGUCAUUGCCAACAAU
AF205856.1/1102-1215 CUGGGAUACGGAGACAUGGUGC-CUAAGACGAUUGCAGGGAAGAUCUUCGGCUCCA-UCUGCUCCUUGAGUGGCGUCCUGGUCAUUGCCCUGCCAGUCCCUGUGAUUGUUUCCAAC
AF395810.1/1102-1215 GUAGGAUACGGCGACAUGC-AUCCGGUCACCAUUGGGGGGAAGAUCGUGGGUUCCC-UGUGCGCCAUCGCCGGGGUGUUAACCAUAGCCCUGCCAGUUCCUGUCAUAGUGUCCAAC
U32923.1/1090-1203   GUAGGUUAUGGCGAUUUAU-UCCCCUCUACGUAUUUCGGAAAAAUGGUUGGUGCAC-UUUGUGCGAUAUCCGGUGUGCUUGUGAUAGCACUUCCUGUACCUGUUAUAGUUAGUAAU
L19740.1/1135-1248   GUAGGCUAUGGAGACAUGG-UUCCAACUACCAUUGGGGGAAAGAUCGUGGGUUCCC-UGUGUGCAAUUGCAGGUGUGUUAACCAUUGCCUUACCGGUCCCCGUCAUAGUGUCCAAC
X62841.1/1711-1824   CUUGGCUAUGGGGACAUGU-AUCCUAAGACAUGGUCAGGAAUGCUGGUGGGUGCGC-UGUGUGCACUGGCUGGUGUGCUAACCAUUGCCAUGCCUGUGCCUGUCAUCGUCAAUAAC
AF149787.1/1406-1519 GUGGGCUACGGGGACAUGAGGCCC-AUCACAGUGGGGGGCAAGAUCGUGGGCUCCC-UGUGCGCCAUCGCCGGGGUCCUCACCAUCGCCCUGCCAGUGCCCGUCAUCGUCUCCAAC
AF026006.1/1132-1245 GUUGGGUAUGGAGACAUCU-AUCCCAAGACUCUCCUGGGGAAAAUUGUGGGGGGUC-UCUGCUGCAUCGCAGGGGUCCUGGUGAUUGCUCUUCCCAUCCCCAUCAUUGUCAAUAAC
AY494950.1/597-710   CUGGGCUACGGAGACAUGU-AUCCUCAGACUUGGUCAGGCAUGCUGGUGGGGGCCC-UCUGUGCUCUCGCUGGUGUGCUGACCAUUGCCAUGCCUGUCCCUGUCAUUGUGAACAAU
AF323749.1/1123-1236 GUAGGCUAUGGAGACAUGG-UCCCUACAACAAUAGGUGGCAAAAUAGUAGGCUCUC-UGUGUGCAAUUGCAGGCGUAUUAACCAUUGCCUUACCUGUCCCUGUUAUAGUAUCCAAC
AF493545.1/787-900   CUGGGCUACGGGGACAUGU-ACCCCAAGACGUGGUCGGGCAUGCUGGUGGGGGCGC-UGUGUGCGCUGGCCGGCGUGCUCACCAUCGCCAUGCCGGUGCCUGUCAUCGUCAACAAC
AB018545.1/1858-1971 GUCGGAUAUGGAGAUAUAU-AUCCAAAGACAGUGCUUGGCAAACUUGUUGGUGCAA-CUUGCUGCAUUACUGGUGUUCUGGUCAUUGCCCUCCCCAUUCCCAUCAUUGUAAACAAC
L26968.1/1511-1624   GUUGGUUAUGGAGAUAUGCGAC-CGGUUACUGUAUGGGGUAAAUUAAUUGGUUCAU-UAUGUGCUAUCGCUGGUGUACUAACUAUUGCACUUCCUGUUCCUGUGAUUGUAUCAAAC
AF308934.1/1774-1887 CUGGGCUAUGGCGACAUGU-ACCCGGAGACGUGGUCGGGCAUGCUGGUGGGCGCAC-UGUGCGCUUUGGCGGGUGUGCUGACCAUUGCCAUGCCCGUGCCCGUCAUUGUCAACAAC
M74898.1/595-708     CUGGGGUAUGGAGACAUGGUGC-CUAAGACAAUUGCUGGGAAGAUAUUUGGCUCCA-UCUGCUCCCUAAGCGGCGUCCUGGUCAUUGCUCUGCCAGUCCCCGUCAUAGUCUCCCCA
X17621.1/1700-1813   GUAGGUUAUGGGGACAUGU-ACCCCAUGACGGUGGGAGGCAAGAUUGUGGGCUCAC-UGUGUGCCAUUGCUGGGGUCCUCACCAUUGCAUUACCGGUACCGGUCAUUGUCUCCAAU
M32661.1/1132-1245   GUCGGCUACGGCGACAUGG-CCCCCAAAACCUACAUUGGCAUGUUCGUGGGUGCCC-UCUGCGCCCUGGCCGGCGUACUAACCAUCGCACUGCCAGUGCCCGUCAUCGUCAGCAAC
AF069526.1/1261-1374 GUGGGCUACGGCGACAUGGCGC-CAAAGACGUACGUGGGCAUGUUUGUGGGCGCUC-UGUGUGCUCUAGCGGGCGUGUUGUGCAUCGCUCUGCCCGUGCCCGUCAUCGUGUCCAAC
BX537638.1/3883-3996 CUGGGCUACGGAGACAUGU-ACCCCAAGACGUGGUCAGGCAUGCUGGUAGGGGCAC-UGUGUGCACUGGCUGGCGUGCUCACCAUCGCCAUGCCGGUGCCUGUCAUCGUCAACAAC
X07132.1/1560-1673   GUUGGAUAUGGUGACAUGACAC-CCGUCGGCGUUUGGGGCAAGAUUGUGGGAUCAC-UUUGUGCCAUUGCUGGCGUGCUGACCAUCGCACUGCCGGUGCCGGUCAUCGUCAGCAAU
U52223.1/8-121       UUAGGCUAUGGGGAUAUGU-ACCCCCAAACAUGGUCAGGGAUGUUGGUGGGGGCCU-UGUGUGCCCUGGCCGGAGUGCUGACAAUAGCCAUGCCUGUGCCUGUCAUUGUCAACAAU
U45979.1/1659-1772   GUAGGCUAUGGGGACAUGA-GACCCGUCACUGUGGGGGGCAAGAUCGUGGGCUCGC-UGUGUGCCAUCGCUGGGGUCCUCACCAUCGCCCUGCCUGUGCCCGUCAUUGUCUCCAAC
X17622.1/2129-2242   GUAGGUUACGGGGACAUGU-ACCCCAUGACUGUGGGGGGAAAGAUCGUGGGCUCGC-UGUGUGCCAUCGCUGGGGUCCUCACCAUUGCCCUGCCUGUGCCCGUCAUCGUCUCCAAC
M27158.1/2168-2281   GUAGGCUAUGGAGACAUGAGACCC-AUCACUGUAGGGGGCAAGAUCGUGGGUUCAC-UGUGCGCCAUAGCUGGGGUCCUCACCAUUGCCCUGCCUGUCCCCGUCAUCGUCUCCAAC
M94258.1/1101-1214   GUGGGCUAUGGUGACAUGU-ACCCUGUGACAAUUGGAGGCAAAAUCGUGGGCUC-CUUGUGUGCCAUCGCUGGUGUGCUGACAAUUGCCCUGCCUGUACCUGUCAUCGUGUCCAAC
U38240.1/1156-1269   GUCGGCUACGGCGAUAUGC-ACCCUGUGACCAUAGGGGGCAAGAUUGUGGGCUCUC-UGUGUGCCAUCGCCGGGGUUUUGACCAUUGCAUUGCCCGUUCCUGUGAUUGUUUCCAAC
#=GC SS_cons         <<-<<-<<<<<-<<<<-<<.<<---------------<<<<--------<<<____._____>>>---------->>>>---------------->>>>->>>>->>>>>->>->>
#=GC RF              gUgggccAugGagAcaUGc.acCCuaagACaaUugggGGcAAGaUuGUggGcuCuc.UgUGUgCcaUuGCuGGuGUgCUgaccAUuGCucUgCCugugCCugUcAUcgUguccAAc
//
# STOCKHOLM 1.0

#=GF AC   RF00486
#=GF ID   mir-129
#=GF DE   mir-129 microRNA precursor family
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD
#=GF GA   50.00
#=GF TC   60.40
#=GF NC   49.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   MIR; MI0000252;
#=GF DR   MIR; MI0000222;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF RN   [1]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol 2002;12:735-739.
#=GF RN   [2]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA 2003;9:175-179.
#=GF CC   mir-129 was first experimentally characterised in mouse [1] and homologues
#=GF CC   have since been discovered in several other species. The mature sequence
#=GF CC   is excised from the 5' arm of the hairpin.
#=GF WK   mir-129_microRNA_precursor_family
#=GF SQ   6


AC072048.4/151314-151401 UCUCCUU--UGGAUCUUUUUGCGGUCUGGGCUUGCUGUUC-UCUCGACAGUAGUCAGGAAGCCCUUACCCCAAAAAGUAUCUACGGGAGGC-
AL683878.9/67086-66997   UGCCUUUCGCGAAUCUUUUUGCGGUCUGGGCUUGCUGUACAUAACU-CAAUAGCC-GGAAGCCCUUACCCCAAAAAGCAUUCGCGGAGGGCG
BX649263.6/91330-91421   UGUCCUUUUCAGGUCUUUUUGCGGUCUGGGCUUGCUGUUCCUUGAACCAGUAGCCAGGAAGCCCUUACCCCAAAAAGUAUCUGCAGAGGACC
BX927136.11/83051-82960  UGUCCUUCACGGCUCUUUUUGCGGUCUGGGCUUGCUGUUCCUUAAAUCACCAGUCAGGAAGCCCUUACCCCAAAAAGUAUCUGUGUGGGAUC
AC068205.25/6866-6955    UGCCCUUCGCGAAUCUUUUUGCGGUCUGGGCUUGCUGUACAUAACU-CAAUAGCC-GGAAGCCCUUACCCCAAAAAGCAUUUGCGGAGGGCG
AC018662.3/139956-140044 UCUCCUU--UGGAUCUUUUUGCGGUCUGGGCUUGCUGUUCCUCUCAACAGUAGUCAGGAAGCCCUUACCCCAAAAAGUAUCUGCGGGAGGC-
#=GC SS_cons             :::::::::<<<<<<<<<<<<<<<<--<<<<<<-<<<_________________>>>->>>>>>-->>>>>>>>>>>->>>>>:::::::::
#=GC RF                  UguCcUUcacggauCuuuuuGcGGuCUGGGCuuGCuGUuCaUuacaaCAaUAGuCaGGaaGCCCUUaCCcCaaaaaGuauccgcGgagGgcc
//
# STOCKHOLM 1.0

#=GF AC   RF00487
#=GF ID   IRES_Cx43
#=GF DE   Connexin-43 internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Published; PMID:10618489
#=GF GA   70.00
#=GF TC   70.30
#=GF NC   65.40
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   10618489
#=GF RT   Connexin43 mRNA contains a functional internal ribosome entry site.
#=GF RA   Schiavi A, Hudder A, Werner R
#=GF RL   FEBS Lett 1999;464:118-122.
#=GF CC   This family represents the connexin-43 internal ribosome entry site (IRES)
#=GF CC   which allows cap independent translation during conditions such as heat
#=GF CC   shock and stress [1].
#=GF WK   GJA1
#=GF SQ   14


AC010228.8/17300-17506    GUAGCAGCUUUUACGAGGUAUCAGCACUUUUCUUUCAUUGGGGG-AAGGUGUGAGGAAAGUAACAAACAGCAGCGGAGUUUUAAACUUUAAAUAGACAGGUCUGAGUGCCUGAAUUUGCCUUUU-CAUUUUACUUCAUCCUCCAAGGAGUUCAAUCA--CCUGGCGUGA---CUUCACUUCUUUUAA---GCAAAAGAGUGGUGCCCAGGCAACAUG
AC011421.2/104487-104693  GUAGCAGCUUUUACGAGGUAUCAGCACUUUUCUUUCAUUGGGGG-AAGGCGUGAGGAAAGUAACAAACAGCAGCGGAGUUUUAAACUUUAAAUAGACAGGUCUGAGUGCCUGAAUUUGCCUUUU-CAUUUUACUUCAUCCUCCAAGGAGUUCAAUCA--CCUGGCGUGA---CUUCACUUCUUUUAA---GCAAAAGAGUGGUGCCCAGGCAACAUG
AL139098.15/101802-102009 AAAAAAGCUUUUACGAGGUAUCAGCACUUUUCUUUCAUUAGGGGGAAGGCGUGAGGAAAGUACCAAACAGCAGCGGAGUUUUAAACUUUAAAUAGACAGGUCUGAGUGCCUGAACUUGCCUUUU-CAUUUUACUUCAUCCUCCAAGGAGUUCAAUCA--CUUGGCGUGA---CUUCACUACUUUUAA---GCAAAAGAGUAAGUUUUUAAAAAAUGA
M65189.1/48-254           GUAGCAGCUUUUACGAGGUAUCAGCACUUUUCUUUCAUUGGGGG-AAGGCGUGAGGAAAGUAACAAACAGCAGCGGAGUUUUAAACUUUAAAUACACAGGUCUGAGUGCCUGAAUUUGCCUUUU-CAUUUUACUUCAUCCUCCAAGGAGUUCAAUCA--CCUGGCGUGA---CUUCACUUCUUUUAA---GCAAAAGAGUGGUGCCCAGGCAACAUG
M65188.1/1-168            ---------------------------------------GGCUUUUAG-CGUGAGGAAAGUACCAAACAGCAGCGGAGUUUUAAACUUUAAAUAGACAGGUCUGAGUGCCUGAACUUGCCUUUU-CAUUUUACUUCAUCCUCCAAGGAGUUCAAUCA--CUUGGCGUGA---CUUCACUACUUUUAA---GCAAAAGAGUGGUGCCCAGGCAACAUG
AY427560.1/1-203          ------GCUUUUACGAGGUAUCAGCACUUUUCUUUCAUUGGGGGAAAGGCGUGAGGGAAGUACCCAACAGCAGCAGACUUUGAAACUUUAAACAGACAGGUCUGAGAGCCCGAACUCUCCUUUU-CCUUUGACUUCAGCCUCCAAGGAGUUCCACCA-CUUUGGCGUGCCGGCUUCACUUUCAUUAA---GUGAAAGAACAGGGUCU-CUC-UGUA-
AY427555.1/54-262         AAAAACGCUUUUACGAGGUAUCAGCACUUUUCUUUCAUUGGGGGAAAGGCGUGAGGGAAGUACCCAACAGCAGCAGACUUUGAAACUUUAAACAGACAGGUCUGAGAGCCCGAACUCUCCUUUU-CCUUUGACUUCAGCCUCCAAGGAGUUCCACCA-CUUUGGCGUGCCGGCUUCACUUUCAUUAA---GUGAAAGAGAGGUGCCCAGACAUG---
M63801.1/15-223           AAAAACNCUUUUACGAGGUAUCAGCACUUUUCUUUCAUUGGGGGAAAGGCGUGAGGGAAGUACCCAACAGCAGCAGACUUUGAAACUUUAAACAGACAGGUCUGAGAGCCCGAACUCUCCUUUU-CUUUUGACUUCAGCCUCCAAGGAGUUCCACCA-CUUUGGCGUGCCGGCUUCACUUUCAUUAA---GUGAAAGAGAGGUGCCCAGACAUG---
BC055375.1/1-158          ---------------------------------------------------AAGAGGUAAUCCCCAACAGCAGCAGACUUUGAAACUUUAAACAGACAGGUCUGAGAGCCCGAACUCUCCUUUU-CCUUUGACUUCAGCCUCCAAGGAGUUCCACCA-CUUUGGCGUGCCGGCUUCACUUUCAUUAA---GUGAAAGAGAGGUGCCCAGACAUG---
X06656.1/1-204            -----GGCUUUUACGAGGUAUCAGCACUUUUCUUUCAUUGGGGGGAAGGCGUGAGGAAAGUACCAAACAGCAGCAGACUUUUAAACUUUAAACAGACAGGUCUGAGAGCCUGAACUCUCAUUUUUCCUUUGACUUCAGCCUCCAAGGAGUUCCACCAACUUUGGCG--GCGGCUUCACUUUCAUUAA---GUGAAAGAGAGGUGCCCAGACAUG---
AY206455.1/1-196          --------------GAGGUAUCAGCACUUUUCUUUCAUUGGGGG-AAGGCGUGAGGAAAGUACCAAACAGCAGCAGACUUUUAAACUUUAAAUAGACAGGUCUGCGAGCCUGAGCCCUCCUUUU-C-UUUGACUUCAGCCUCCAAGGAGCCUCAUCA-CUUUGGCGCGCCGGCUUCGCUUUCAUUAAAUAGCGAAAGAGAGGUGCCCAGACAUG---
AY324140.1/1-199          ------------ACGAGGUAUCAGCACUUUUCUUUCAUUGGGGGAAAGGCGUGAGGAAAGUACCAAACAGCAGCAGACUUUUAAACUUUAAACAGACAGGUCUGAGAGCCUGAACUCUCAUUUUUCCUUUGACUUCAGCCUCCAAGGAGUUCCACCAACUUUGGCGCGCCGGCUUCACUUUCAUUAA---GUGAAAGAGAGGUGCCCAGACAUG---
AY555737.1/22-232         AAAAACGCUUUUACGAGGUAUCAGCACUUUUCUUUCAUUGGGGGGAAGGCGUGAGGAAAGUACCAAACAGCAGCAGACUUUUAAACUUUAAACAGACAGGUCUGAGAGCCUGAACUCUCAUUUUUCCUUUGACUUCAGCCUCCAAGGAGUUCCACCAACUUUGGCGCGCCGGCUUCACUUUCAUUAA---GUGAAAGAGAGGUGCCCAGACAUG---
AY206456.1/1-193          --------------GAGGUAUCAGCACUUUUCUUUCAUUGGGGG-AAGGCGUGAGGAAAGUACCAAACAGCAGCAGACUUUUAAACUUUAAAUAGACAGGUCUGGGAGCCUGAGCCCUCCUUUU-C-UUUGACUUCAGCCUCCAAGGAGCCUCACCG-CUUUGGCGCGCCGGCUUCGCUUUCAUUAA---GCGAAAGAGAAGUGCCCAGACAUG---
#=GC SS_cons              .....:<<<--<<<___>>>-->>>,,,,,,,,(((-(((((((((((----((((-(((,,,,,,,,,,,,,,<<<<<<_________________>>>>>><<<<<______>>>>>,,))).))))---))))--)))))))-)))--------.-<<<<<-<<<<<--<<<<<<<<_____>>...>>>->>>--->>>>>>>>>>::::...
#=GC RF                   .....agCuUUuaCGAGGuaUCaGcACUUUUCUuuCAuuGGgGGgaaGGCGUgagGaaagUAcCaAACAGCAGCaGacuuUuAAACUUUAAAuAGACagguCuGagaGCCuGAACucuCcUuuu.CcuuUgACuucAgCCuCCaaGGagUUccAuCA.CccuGGCGcgccGGCuucgCuuucaUUaa...GcgAaaGAGaggcgCCCaggcAug...
//
# STOCKHOLM 1.0

#=GF AC   RF00488
#=GF ID   U1_yeast
#=GF DE   Yeast U1 spliceosomal RNA
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Zwieb C, The uRNA database, PMID:9016512
#=GF SS   Published; PMID:2405391
#=GF GA   80.00
#=GF TC   87.60
#=GF NC   70.70
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00005
#=GF DR   SO; 0000391; U1_snRNA;
#=GF DR   GO; 0000395; mRNA 5'-splice site recognition;
#=GF DR   GO; 0030627; pre-mRNA 5'-splice site binding;
#=GF DR   GO; 0005685; U1 snRNP;
#=GF RN   [1]
#=GF RM   9016512
#=GF RT   The uRNA database.
#=GF RA   Zwieb C
#=GF RL   Nucleic Acids Res 1997;25:102-103.
#=GF RN   [2]
#=GF RM   2405391
#=GF RT   Saccharomyces cerevisiae U1 small nuclear RNA secondary structure contains
#=GF RT   both universal and yeast-specific domains.
#=GF RA   Kretzner L, Krol A, Rosbash M
#=GF RL   Proc Natl Acad Sci U S A 1990;87:851-855.
#=GF CC   U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved
#=GF CC   in pre-mRNA splicing). Its 5' end forms complementary base pairs with the
#=GF CC   5' splice junction, thus defining the 5' donor site of an intron. There
#=GF CC   are significant differences in sequence and secondary structure between
#=GF CC   metazoan and yeast U1 snRNAs, the latter being much longer (568
#=GF CC   nucleotides as compared to 164 nucleotides in human). Nevertheless,
#=GF CC   secondary structure predictions suggest that all U1 snRNAs share a 'common
#=GF CC   core' consisting of helices I, II, the proximal region of III, and IV [1].
#=GF CC   This family represents the larger yeast sequences. Family Rfam:RF00003
#=GF CC   contains the metazoan U1 sequences.
#=GF WK   Yeast_U1_spliceosomal_RNA
#=GF SQ   5


M17205.1/245-812         AUACUUACCUUAAGAUAUCAGAGGAGAUCAAGAAGUCCUACUGAUCAAACAUGC--GCUUCCAAUAGUAGAA-GGACGUUAAGCAUUUAUCAUUGAACUAU-AAUUGUUCAU-UGAAGUCAUUG---AUGCAAACUCC--------------------------UUGGUCACACACACAUACGGCGCGGAAGGCGUGUUUGCUGACGUUUCCAUUCCCUUGUUUCAAUCA-UUGGUUAA-UCCCUUGAUUCCU-UUG-----GGGAUUUUUGGGUUAAACUGAUUUUUGGGGCCCUUUGUUUCUUCUGCCUGGAGAAGUUUGACACCCAA--AUUCAAAUUGGUGUUAGGGGAGCUGGGGCCUUUCAAAAGAGAGCUUUGUAGAGGCAUUCUUUUUGACUACUUU-UCUCUAGCGUGCCAUUUUAGUUUUU-GACGGA-GAUUCGAAUGAACUU-AAGUUUAUGAUGAAGGUAUGGCUGUUGAGAUUAUUUGGUCGGGAUU----GUAG-UUUGAAGAUGUGCUCUUUUGAGCAGUCU-CAACUUU-GCUCGUUCCCGUU-AUGGGAAAAAUUUUGGAAGGUCU-UGGUAGGAACGGGUGGAUCUUAUAAUUUUUGAUUUAUUUU
M17411.1/141-708         AUACUUACCUUAAGAUAUCAGAGGAGAUCAAGAAGUCCUACUGAUCAAACAUGC--GCUUCCAAUAGUAGAA-GGACGUUAAGCAUUUAUCAUUGAACUAU-AAUUGUUCAU-UGAAGUCAUUG---AUGCAAACUCC--------------------------UUGGUCACACACACAUACGGCGCGGAAGGCGUGUUUGCUGACGUUUCCAUUCCCUUGUUUCAAUCA-UUGGUUAA-UCCCUUGAUUCCU-UUG-----GGGAUUUUUGGGUUAAACUGAUUUUUGGGGCCCUUUGUUUCUUCUGCCUGGAGAAGUUUGACACC-AA--AUUCAAAUUGGUGUUAGGGGAGCUGGGGCCUUUCAAAAGAGAGCUUUGUAGAGGCAUUCUUUUUGACUACUUU-UCUCUAGCGUGCCAUUUUAGUUUUU-GACGGCAGAUUCGAAUGAACUU-AAGUUUAUGAUGAAGGUAUGGCUGUUGAGAUUAUUUGGUCGGGAUU----GUAG-UUUGAAGAUGUGCUCUUUUGAGCAGUCU-CAACUUU-GCUCGUUCCCGUU-AUGGGAAAAAUUUUGGAAGGUCU-UGGUAGGAACGGGUGGAUCUUAUAAUUUUUGAUUUAUUUU
U03475.1/1-528           AUACUUACCUUAAGAUGUCAACAGAGAUCAUGAAGUUUG-UUGACCGGGUAUGA--GGUUUUCAAGGAAAUACCGGAAUGGUAUUGUUUUCUCGGAGAUGAUACUUACAGCUUUUACAUUUACA---UUUUAUCUGUACGGUUUUC------------------CUG-CAAUCCACACAUAUUUGGCAAACCUGGUACCUGCUGACAUUUCG-UUCUCCCGUUACUUUUU-UGGAGGCC--------UUGGU--UUA-----ACC---------UCGACUCCACUAGAGUAGCCCUUUUUUCCUUCUGCCUGGAGAAGAAUGGUACU-GA--UUACAAGUCAGUGCUGGGAGAGUCAUCGC--UGUGGCCAGUUUAGUUUCAUUUUAAUGAUCUGGGCUCAAGGA-AUGUCAUGAAAGGCUGACUUACUAGUCUCUGAUCUAUUC-AUUAACUU--GUUUACAGGUUU-----------AUGGGUGAGAGGU----------------------AGAAACUUUGAGUCAGAAAUUCUG-UCAUUUC-UCCGGUUCAGGAA-ACUUGUUCAGAAAGGCUGCAUCCGUGGUAGAAAUGGGUGGAUCUUAUAAUUUUUGAGUA-UUUC
U03476.1/1-572           AUACUUACCUUAAGAUAUCAGAGGAGAUCAAGAAGUCCUACUGAUCAAACAUGC--GCUUCCAAUGGUAGAA-GGAUGUUAAGCAUUUAUCUCUGAAUUAUUAAUAAUUCUC-UGAAAUAAUUG---AUGCAAACUCC--------------------------UUGGUCACUUACACAUACAUUGCGGAAGGCGUGUUUGCUGACGUUCCG-UUCCCUUGUUUCAAUCA-UCGAUUAU-CCCUGUGGUUUCU-UUG-----GAAAUCGCGGGGUUCAAUUGAUUUUUGAGGCCCUUUGUUUCUUCUGCCUGGAGAAGUUUGACACC-AA--AUUCAAAUUGGUGUUAGGGGAGUUGGGGCCUUUUAGAAGAGAGUGUUGUUGAGGUAUUCUUAUAGUGUACUUU-CCUCUAGCGCACCGUUCAAUCUUUUAGAUGGCUGAUUCUCAUGGACUUUUAGUUCAUGAUGAAGGUAUAGCCGUUGGGGUUGGCCGGUCAGGACU----GUAUAUUUGAGGAUGCGUUCUUUUGAGCAAUCU-CGGUUUC-ACUCGUUGUCAUUUAUGAGAAAAAUUCUGGAAGGUCU-UGGUAGGAACGGGUGGAUCUUAUAAUUUUUGAUUUAUUUU
CR380957.2/492841-493435 AUACUUACCUUAAGAUGUCAGAGGAGAUCAAGAAGUCCUUCUGACCAGGCAUCGUUUUUUUCCAAUUUAGAG-GGAAGUUAUGCAUUU---CCUGCAUUGG-AA--GUUCUC-UGAUCUUUUGGGAUAAGAAAACUUCUUUUUGCUCCAAUUGAUGUAAACUCCCUGGUCACUUGCACAUACUU-GCGGAAAAGGUGUCUGCUGACGUUUCG-UUCCCCAAUUCCAAUAAGUGGGUUAAUUUCUUUGUUUUUUCUUAAUUGCAAAAGCUUGGAUUUUUAUCUACUUUUGGAGUCCUGUGUUCAUUCUGCCUGGAGAAUUAUGGCACC-AGGUAUUAUAACUGGUGCUUGGGGAGCUGGUUAC-UGUAUGGUAUUCAGAUUCGAGGGCAU--UUUGUCCUAAUUGGGAUUCCAGUUUAAGUAAUCAUAGUUG-CUUUGAGGAAGCC-AAGGUGUU--A-UGACUGGUUC--UUCUUAACAUUGGGUGAUGACUAUUGCUCUUUUGAGUAG-UAUGAAAUUAUCUGAAGUGGAGGUUCUGGUAAUAGCAUAAAGAUGCUG---AUAGUCCUUAUUACCCAAUAUUC-UCAUGGAGGCCACUGAUUCU--AGGUUUU-CAAUC-UAUG
#=GC SS_cons             :::::::::{{{{{{,<<<<<<<<<__________>>>>->>>>><<<<<<<<<..-<<<<<----------.---<<<______________________.__________.___________...___________________..................________________>>>---->>>>>>>>>>>>>>,,,,[[[[[[,.,((((((<<<<<<<---.<<<<<---.------<<<<<<_.___.....>>>>>>---------->>>>>--->>>>>>>,,,,,,,,,<<<<<______>>>>>,,,,<<<<<.<<.._______>>>>>>>,)))))),,,,,,,,,.,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,,,,.,,,,,,,,..,,,,,,,,,,,,..,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,....,,,,.,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,.,,,,,,,<<<<__._>>>>,,,,,,,,,,,,,,,,,,.,,,,,]]]]]],,,,,,}}}--}}}::::::::::.::::
#=GC RF                  AUACUUACCuuaAGAUgUCAGaGGAGAUCAAGAAGUCCuaCUGAcCaggCAUgc..GcuUcCaAaaGUAGAA.GGAcGUUAuGCAUUUaUCucUGAAuUau.AAUUgUUcuu.UGAaaUuuUuG...AUGcAAACUucuuuUUuuu..................uUGGUcACucACACAUACguuGCGgAaggcGUGccuGCUGACGuuuCg.UUCCCccGUucCaaUcA.UgGguUAa.UcCuuUGaUuccU.UUa.....ggaAuCuUgGggUUaAacCcAuUUuuGgaGCCCUUUGUUucUUCUGCCUGGAGAAgUaUGgCACC.aa..AUUcAAAuuGGUGcUggGGGAGcUGGgGcC.UuUAaaagAuugagUUuuagaGGcAUucUUUuuGcuuAcUuu.auUCuAGuguAagaUuucAuauUUu.gucuGAuGAaUCc.AUGaAcUU..AgUUaaUGaUua..gUaUugccgUUGGGuuaaguuugUcGggaUU....GUAG.UuUGAaaAUgUgUuauUUuGAGauuuuu.uaAUUUc.ucuaGUUcccguu.AcgggaaaAAUUauGgAAgaUCu.UGGUAGaaaCGGGUGGAUCUUAuaaUUUUUGAuUu.UUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00489
#=GF ID   ctRNA_p42d
#=GF DE   ctRNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15554980
#=GF SS   Published; PMID:15554980
#=GF GA   50.00
#=GF TC   50.90
#=GF NC   49.70
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   15554980
#=GF RT   Two discrete elements are required for the replication of a repABC
#=GF RT   plasmid: an antisense RNA and a stem-loop structure.
#=GF RA   Venkova-Canova T, Soberon NE, Ramirez-Romero MA, Cevallos MA
#=GF RL   Mol Microbiol 2004;54:1431-1444.
#=GF CC   This family represents a group of ctRNAs (or counter-transcribed RNAs)
#=GF CC   from p42d and related plasmids. ctRNAs are small, highly structured,
#=GF CC   antisense sequences which are involved in negative regulation. Members of
#=GF CC   this family are known to bind to the mRNA of repC causing translational
#=GF CC   repression [1]. This model contains the predicted stem-loop structure
#=GF CC   followed by a U-rich tract which is proposed to act as a Rho-independent
#=GF CC   transcriptional terminator.
#=GF WK   ctRNA
#=GF SQ   10


AP002086.1/162393-162352   AG--AGGCUUCCACGACGGCGA--CGUUU-GGGGGCCU--UUCUUUUGC
AL591985.1/56504-56550     AGAAGGGUUUCCGCAGCG-CUAGUCGUUC-GGAAGCCUUUUUCUUUUGC
AY177731.1/758-804         AGAGAGGCUUCCACGACGGCAA--CGUUUGGGGGGCCUUUUUCUUUUGC
AP003017.1/123644-123689   AGAAGGGCUUCCGCGACGGCGA--CGUUC-GGGGGCCUUUUUCUUUUGC
AF313446.1/3043-3000       AGAGG-GCUUCCGCGACGGCAA--CGUUC-GGGGGC-CUUUUCUUUUGC
AF283811.2/2623-2577       AGAAGGGCUUCCAUGACGGCAA--CGUUUCGGGGGCCUUUUUCUUUUGC
U80928.5/369940-369894     AGAAGGGCUUCCACGACGGCGA--CGUUGAGGGAGCUCUUUUCUUUUGC
AE008918.1/92070-92115     AGAAGGGCUUCCACGACGGCAA--CGUUU-GGGGGCCUUUUUCUUUUGC
AE006469.1/1351314-1351358 AGGAAGGCUUCCACGGCU-UGU-UCGUU--GGGGGCCUUUUUCUUUUGC
AE007870.2/1024273-1024317 AGAAAGGCUUCCGUG-CGGCAA--CGUUC-GGGGGCUUUUUUCUUUUGU
#=GC SS_cons               ::::<<<<<<<<--<<<<____..>>>>-.>>>>>>>>:::::::::::
#=GC RF                    AGAAaGGCUUCCACGACGGCaA..CGUUu.GGGGGCCuUUUUCUUUUGC
//
# STOCKHOLM 1.0

#=GF AC   RF00490
#=GF ID   S-element
#=GF DE   S-element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15554980
#=GF SS   Published; PMID:15554980
#=GF GA   47.00
#=GF TC   47.40
#=GF NC   45.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0045182; translation regulator activity;
#=GF DR   GO; 0009299; mRNA transcription;
#=GF RN   [1]
#=GF RM   15554980
#=GF RT   Two discrete elements are required for the replication of a repABC
#=GF RT   plasmid: an antisense RNA and a stem-loop structure.
#=GF RA   Venkova-Canova T, Soberon NE, Ramirez-Romero MA, Cevallos MA
#=GF RL   Mol Microbiol 2004;54:1431-1444.
#=GF CC   This family represents a group of S-elements from p42d and related
#=GF CC   plasmids. The S-element has multiple functions and is believed to act as a
#=GF CC   negative regulator of repC transcription, be required for efficient
#=GF CC   replication and act as a translational enhancer of repC [1].
#=GF WK   S-element
#=GF SQ   29


AP002086.1/162438-162505   AGUCAAGAGUCUUUGGCACCG---U--UUUUGGUGA-GCAGAUUUCUUUUGCCUA--U-U-GAAGGGUG-AA-AGAC-AUG
X04833.1/2648-2715         CGUCAAGAGUUUUUAGCGCCG---U--UUU-GGUGA-GCUGAUUUCCUUUGCCUG--C-U-GAAAGGUG-AA-AGAUGAUG
AF528525.1/25033-25100     CGUCAAGAGUCUUUGGCAUCG---U--UUU-GGUGG-GCGUUUUUCUGUUGCCU---U-UAGAAAGGUA-GA-GGAAAAUG
AY177731.1/717-649         AGUCAAGAGUCUUUGGCACCG---UAAUUU-GGUGA-GCAGGUUUCUUUUGCCUU--U-U-UGAAGGUG-A--AGAAGAUG
AP003017.1/123604-123538   UGUCAAGAGUC-GUGGCGCCA---U--UUC-GGCGA-GCAGGUUUCUUUUGCCUU--CGU-GAAAGGUG-AG-GGAA-AUG
U80928.5/369981-370048     CGUCAAGAGUCUUUGGCGCCG---U--UUU-GGUGA-GCGAAUUUCCUUUGCCUG--C-U-GAAAGGUG-AG-AGACAAUG
AF283811.2/2664-2730       AGUCAAGAGUCUUUGGCAUCG---U--UUU-GGUGA-GCGUGAAUCUUUUGCCUU--U-UUGAAAGGCG-A--GGAC-AUG
AF313446.1/3084-3151       AGUCAAGAGUCUUUGGCACCGA--A--UUU-GGUGAGGCGUGA-UCUUUUGCCUU--G-AAGAA-GGCG-AA-GAAA-AUG
CP000137.1/504055-504122   UGUCAAGCAUCUUCGGCAUCC---U--UUU-GGGUG-GUAGAUUUCUUUUGCCUU--G-AAAAAAGGUG-AG-GGAC-AUG
AM236081.1/2394-2461       CGUCAAGAGUCUUUGGAACCG---A--UCU-GGUGA-GCAAAUUUCUUUUGCCUG--C-U-GAAAGGUA-AG-AGACGAUG
CP000741.1/184582-184649   CGUCAAGAGUCUUUGGCACCG---U--UUU-GGUGA-GGGGAUUUCUUUUGCCUG--C-U-GAAAGGUG-AA-AGACGAUG
AM236081.1/79147-79212     AGUCAAGAGUC-UUGGCACCG---A--UUU-GGUGA-GCGGAUUUCUUUUGCCUG--A-A-GAAAGGUG-AG-AGAA-AAA
AL591985.1/56464-56398     UGUCAAGCAUUUUUGACGUCG---U--UUC-GGCGA-ACGGAUUUCUUUUGCCUU--G-G-AAAAGGUG-AA-GAAA-AUG
CP000759.1/1892129-1892062 UGUCAAGUGUAAUUAGCGUCA---U--UUC-GGCGG-GUGGAUUUCUUUUGCCUU--G-U-GGAAGGUG-AA-AGAAAAUG
CP000136.1/249581-249646   UGUCAAGAGCUUUUGGCGCCG---U--UUU-GGCGA-GCGGAUUUCUUUUGCCU---C-A-GUGAGGUG-GA-AGAG-AUG
CP000761.1/27-94           CGUCAAGAGUUUUCGGCGCCA---U--UUU-GGCGA-ACAAAUUUCUUUUGCCUG--U-U-GACAGGUA-GA-AAACGAUG
AM040265.1/90-157          UGUCAAGUGUAUUUAACGUCA---A--UUU-GGCGG-GUGGAUUUCUUUUGCCUU--G-U-GGAAGGUG-AA-AGAAAAUG
CP000762.1/70689-70623     UGUCAAGCGUU-UUGACGUCGU--U--UGC-GGCGA-ACGGAUCUCUUUUGCCUU--C-A-GUUAGGUG-AG-AGAA-AUG
CP000391.1/110125-110191   UGUCAAGAGUCCU-GGCGUCG---U--UUC-GGCGA-GCAGAUUUCUUUUGCCUG--A-G-AGAGGGUGAAA-GGAA-AUG
CP000760.1/70833-70900     UGUCAAGAGUCGUAAGCGUCU---U--UUU-GGCGG-GUGGAUUUCUUUUGCCUU--U-U-GAAAGGUG-AG-AGGGAAUG
AM236084.1/2341-2406       UGUCAAGAGUUUUUGGCGCCG---U--UUU-GGUGA-GCGGAUUUCUUUUGCCU---C-G-UUGAGGUA-GA-CGAU-AUG
EF066650.1/2360-2426       AGUCAAGAGUCUUUGGCACCG---A--UUU-GGUGA-GCGGAUUUCUUUUGCCCG--A-C-GAAAGGUG-AA-AGAA-ACA
AM236086.1/2290-2355       AGUCAAGCGUCUUAGGCACCAA--A--UUG-GUGGA--UGGUUUUCUUUUGCCUG--A-A-CGAAGGUG--A-AGGC-AAA
AM236083.1/2343-2411       AGUCAAGA-GUCUUGGCGCCGCU-U--UUU-GGUGA-GCAGAAUUCUUUUGCCUAAAC-U-GA--GGUA-AA-GGCAAAUG
BA000013.4/308946-308880   UGUCAAGAGUCUA-GGCGUCGA--U--UCG-GC-GA-GCAGAUUUCUUUUGCCUA--A-U-CGAGGGUG-AA-AGAAAAUG
CP000762.1/37633-37699     UGUCAAGAGUC-AUAGCGUCA---U--UUU-GGCGG-GUGGAUUUCUUUUGCCUU--U-C-GAAAGGUA-AGAGGAA-AUG
AE007870.2/1024232-1024163 AGUCAAGAGUCUU-GGCAUCGAAUU--UUUCGGUGA-GCGAUUUUCUUUUGCCU---UGU-GAAAGGUG-AA-AGAC-AUG
U00090.2/2450-2518         AGUCAAGAGUCUUUGGCACCG---G--AACGGGUGA-GCGGACGUCUUUUGCCUG--A-G-GAUAGGUG-AA-AGAAGAUG
AE006469.1/1351271-1351204 AGUCAAGAGUCCUUGGCACCG---U--UUUUGGUGA-GCUGCUUUCUUUUGCCU---UAU-CGAAGGUG-AA-GGAA-AUG
#=GC SS_cons               ::::::::<<<<<<--<<<<-...<..<<<.<<-<-.<<<<<_____>>>>>->-..>.>.>>>>>>>>.>>.>>>>.:::
#=GC RF                    aGUCAAGAgUcuuuGGCgCCG...u..uuc.gguGA.GCgGaUUUCUuUuGCCUu..c.u.gaaaGGuG.aa.agAc.AUG
//
# STOCKHOLM 1.0

#=GF AC   RF00492
#=GF ID   SCARNA17
#=GF PI   snoU12-22
#=GF DE   small Cajal body-specific RNA 17
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Moxon SJ
#=GF SS   Published;PMID:15556860
#=GF GA   75.00
#=GF TC   76.30
#=GF NC   74.70
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15556860
#=GF RT   Guide RNAs with 5' Caps and Novel Box C/D snoRNA-like Domains for
#=GF RT   Modification of snRNAs in Metazoa.
#=GF RA   Tycowski KT, Aab A, Steitz JA
#=GF RL   Curr Biol 2004;14:1985-1995.
#=GF RN   [2]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. The complete human
#=GF CC   U12-22/U4-8 scaRNA is composed of two tandem C/D box domains (termed
#=GF CC   U12-22 and U4-8). The 5' and 3' C/D domains are predicted to guide the
#=GF CC   2'O-ribose methylation of residue U22 in U12 (RFAM:RF00007) and residue C8
#=GF CC   in U4 (RFAM:RF00015) snRNAs respectively [1]. This family only includes
#=GF CC   only the 5' C/D box domain (U12-22) as the 3' C/D box is represented by
#=GF CC   RFAM:RF00283. The 3' C/D domain (U4-8) was also cloned previously by
#=GF CC   Darzacq [2] and called U91. Both the doublet (U12-22/U4-8) and singlet
#=GF CC   (U4-8) forms of this snRNA have been purified from Hela cells [1]. The
#=GF CC   doublet form U12-22/U4-8 has been shown to localise to the nucleoplasm and
#=GF CC   is proposed to reside in the Cajal bodies whereas the U4-8 single domain
#=GF CC   appears to accumulate in the nucleolus [1]. In humans the genomic location
#=GF CC   of U12-88/U4-8 is intergenic and the purified transcript has been shown to
#=GF CC   possess a methylated guanosine cap suggesting it is independently
#=GF CC   transcribed by RNA pol II [1].
#=GF WK   Small_Cajal_body_specific_RNA_17
#=GF SQ   6


AC090227.10/15587-15444   CUUUCGGGUCCCCAUUGCAGCCCCCGGAUGAGCCCGCAGUAUUUUCCUUAUAUGAUCAGGUCCCAUUGCGGGCG-GCGCCGCUUGCCCGGAGCCUGAGAGGAUUAUGAAAACGUGGCGAGCGAAAUGGGGCCAGGGGACCUGGAG
AC129097.27/183442-183585 UUCUCAGGUCCCCAGUGCAGCCCCCAGAUAAGACUGCAGUAUUUUCCUUAUAUGAUCUGGUCCCACCGUGGGCA-GCACUGCAUGCCCAGAGCCUGAGAGGAUUAUGAAAACAUGGCAAGGGAAGUGAGGCCAGGGAACCCAGCA
AC018751.30/166114-165972 UUCUCAGGUCCCCAGUGCAGCCCCAAGAUGAGCCUGCAGUAUUUUCCUUACAUGAUCUGGUCCUACUGUGGGCA-GCGCUGC-UGCCCAGAGCCUGAGAGGAUUAUGAAAACAUGGCAACGGAAGUGAGGCCAGGGGACACAGCA
AC125020.7/181527-181661  CGCAUGGGUCCCCGAGGCAG-CCCUGAGUGAGCCCCGUGUAUUUUCCUUAUGUGAUCAGGC-CUCUCAU-AGUG-GGGCUGCUGGUUUGGAGCCUGAGAGGAUUAUGAAAAUGGGGCAG------UGUUACCAGCUGUUCUUGAC
AC127289.4/19294-19156    CACCUGGGUCCCCGAGGC-AUCCCGGAGUGAGCCCGGUGUAUUUUCCUUAUAUGAUUAGGC-CUCUCAU-A-CAGGCGCUGCUGGUUUGGAGCCUGAGAGGAUUAUGAAAACGUGGCAGGUGA--UGGAGUCAGGGGACCUGGAG
AC023490.5/121842-121984  UUCUCAGGUCGCCAGUGCAGCCCCAAGAUGAGCCUGCAGUAUUUUCCUUACAUGAUCUGGUCCUACUGUGGGCA-GCGCUGC-UGCCCAGAGCCUGAGAGGAUUAUGAAAACAUGGCAACGGAAGUGAGGCCAGGGGACACAGCA
#=GC SS_cons              <<<-<<<<<<<<<------<<<<<-------------------------------<<<<<<-<<---<<<<<<<.____>>>>>>>-->>->>>>>>----------------------------->>>>>-->>>>>>>>>>>>
#=GC RF                   ccCucggGuCcCCaauGCAGcccCaagaUGAGcCugcaGUAUUUUCCUUAuAUGAUcaGGcCCcauugugaGca.GcGCugCuugcccgGAgCCugAGAGGAUUAUGAAAAcauGGCAaggGAAgUGgggCCAGGgGaCccgGgg
//
# STOCKHOLM 1.0

#=GF AC   RF00493
#=GF ID   snoU2-30
#=GF DE   Small nucleolar RNA U2-30
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Published;PMID:15556860
#=GF GA   60.00
#=GF TC   60.70
#=GF NC   57.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300884;
#=GF DR   snoopy; Gallus_gallus300000;
#=GF RN   [1]
#=GF RM   15556860
#=GF RT   Guide RNAs with 5' Caps and Novel Box C/D snoRNA-like Domains for
#=GF RT   Modification of snRNAs in Metazoa.
#=GF RA   Tycowski KT, Aab A, Steitz JA
#=GF RL   Curr Biol 2004;14:1985-1995.
#=GF CC   U2-30 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. This family directs the 2'-O-methylation of A30
#=GF CC   in Rfam:RF00004 [1].
#=GF WK   Small_nucleolar_RNA_U2-30
#=GF SQ   21


AC149132.1/66733-66664       GGGCAAUGAUGUAAAGG-UUU-UACGA--CUGACCUUU-GUAACUAUGAAGGUUUCUACACUUGACCUGAGCUCA
AL732366.7/162427-162358     GGGCAAUGAUGUAAAGG-UUU-UACGA--CUGACCUUU-GUAACUAUGAAGUUUUCUACACUUGACCUGAGCUCA
AAFC03051600.1/63240-63171   GAGCAAUGAUUAAAAGG-UUU-UACUA--CAGACCUUU-AUAACUAUGAAGGUUUCUACACUUGAUCUGAGCUCA
AAQQ01146349.1/2027-1958     GAGCAAUGAUGAAAAAA-UUU-UACUG--CUGACCUUU-GUAACUAUGAAGGUUUCUACACUUGACCUGAGCUCA
AAHX01053335.1/109150-109081 GAGCAAUGAUGAAAAGG-UUU-UAGUA--CUGAAUUUU-GUCACUAUGAAGGUUUCUACACUUGAUCUGAGCUCA
AANG01702163.1/610-541       GAGCAAUGAUGGAAAGA-UUU-UACUA--CUGACAUUU-ACAACUAUGAAUGUUUCUACACUUGAUCUGAGCUCA
AC155259.1/208125-208194     GAGCAAUGAUGAAAAGG-UUU-UAGUA--CUGAAUUUU-GUCACUGUGAAGGCUCCUACACUUGACCUGAGCUCA
AAPY01627812.1/1189-1120     GAGCGAUGAUGAUAAGG-UUU-UCCUA--CUGACCUCU-GUAACUCUGAAGGUUUUUACACUUGAUCUGAGCUCA
ABDC01012712.1/996-1066      GAGCGAUGAUGAAAAGGCUUU-UACUA--UGGACCUUU-AUAACUAUGAAAGUUUCUACACUUGACCUAAGUUCA
AANU01130858.1/4485-4416     GGGCAAUGAUGAAAAGG-UUU-UACUA--CUGAUCUUU-GUAACUAUGAAGGUUUCUACACUUGACCUGAGCUCA
AAYZ01278320.1/134-203       GAGCAAUGAUGAAAUGG-UUU-UACAA--CUGACCUUU-AUAACUAUGAAGUUUUCUACACUUGACCUGAGCUCA
AALT01537168.1/1957-1890     GAGUUCUGAUUAAAAUA-UUU-AAUUAAUCUGACCUUU-----UUCUAAGGGUUUCUACACUUGAUCUGAGCUCA
AAWR02013196.1/69723-69654   GAGCAAUGAUGGAAAGA-UUU-UACUA--CUGAUCUUU-AUAUCUGUGAAGGUUUCUACACUUAAUCUAAGCUCA
AAKN02037651.1/28929-28860   GAGCAAUGAUGAAAAGU-UUU-UACUA--CUGACCUUU-AUAACUAUGAAGGUUUCUACACUUGACCUGAGCUCA
AAGV020161069.1/1572-1503    GAGC-AUGAUGAGAAGG-UUU-CAUGA--CUGACCUUUUAUAAUUAUGAAGGCUUCUACACUUGACCUGAGCUCA
BK005567.1/284-353           GGGCAAUGAUGAAAAGG-UUU-UACUA--CUGAUCUUU-GUAACUAUGAUGGUUUCUACACUUGACCUGAGCUCA
AAPE02001620.1/89567-89498   GAGCAAUGAUGAAAAGG-UUU-GACUA--CUGACCUUU-GUAAUUAUGAAGGUUUCUACACUUGACCUGAGCUCA
AAEX03002086.1/292189-292120 GAGCAAUGAUGAAAAGG-UUU-UACUA--CUGAUCUUU-ACAACUAUGAAGGUUUCUACACUUGAUCUGAGCUCA
AAGU03058301.1/54057-54125   GAGCAAUGAUGAAAAAG-UU--UGCUA--CUGACCUUU-GGAACUAUGAAGGUGUCUACACUUGACCUGAGCUCA
AAGW02008739.1/1722-1791     GAGCAAUGAUGAAAAGG-UUU-UACAA--CUGACCUUU-AUAACUAUGAGGUUUUCUACACUUGACCUGAGCUCA
AAQR03000416.1/11747-11678   GAGCAAUGAUGAAAAGG-UUUCUACUA--CUGAUCUUU--UAACUAUGAAGGUUUCUACACUUGACCUGAGCUCA
#=GC SS_cons                 <<<<--------<<<<<.<<_._____..__>>>>>>>.------------------------------->>>>:
#=GC RF                      GAGCAAUGAUGAAAAgg.UUU.UAcUA..CUGAccUUU.aUAACUAUGAAGGUUUCUACACUUGAcCUGAGCUCA
//
# STOCKHOLM 1.0

#=GF AC   RF00494
#=GF ID   snoU2_19
#=GF DE   Small nucleolar RNA U2-19
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Published;PMID:15556860
#=GF GA   39.00
#=GF TC   39.10
#=GF NC   38.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.62 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300350;
#=GF DR   snoopy; Loxodonta_africana300303;
#=GF RN   [1]
#=GF RM   15556860
#=GF RT   Guide RNAs with 5' Caps and Novel Box C/D snoRNA-like Domains for
#=GF RT   Modification of snRNAs in Metazoa.
#=GF RA   Tycowski KT, Aab A, Steitz JA
#=GF RL   Curr Biol 2004;14:1985-1995.
#=GF CC   U2-19 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. This family directs the 2'-O-methylation of G19
#=GF CC   in Rfam:RF00004 [1].
#=GF WK   Small_nucleolar_RNA_U2-19
#=GF SQ   29


AL732366.7/162677-162598     GAUCAAUGAUGAA-ACUAGCCAAAUCUGAGCAUCAGAAGGCU-UUCCGGUCU-ACCUGAUGC-AUGAUCUCUACAG--UUCUGAGA
AC149132.1/66984-66905       GAUCAAUGAUGAA-ACUAGCCAAAUCUGAGCAUCAGAAGGCU-UUCCAGUCU-ACCUGAUGC-AUGAUCUCUACAG--UUCUGAGA
AC093872.3/45198-45119       GAUCAAGGAUGAA-AAUACCCAAAUUUGAGUAUCAGAAGACC-UUCCAGUCU-ACUUGAUGC-AUGAGCUCUACAG--UUUUAAGA
AC069285.8/146535-146456     GAUCGAUGAUGAA-AAUAAGCAAGUUUGAGCAUCAGAAGACC-UUCCAGUCU-ACUUGAUGC-AUGAGCUCUACAG--UUUUAAGA
AANU01145590.1/4072-4151     AUUCAAGGAAGAA-AAUAAUGAAAUUUGAGCAUCAGAAGACC-UUCCAGUCU-ACUUGAUGC-AUGAGCUCUACAG--UUUUAAGA
ABDC01012712.1/719-798       GAUCAGUGAUGAC-AAUAGCCAAAUCUGAGCAUCAGAAGACA-UUCCAGUCU-ACCUGAUGC-AUGAUCUCUACAG--UUCUGAGA
AAFC03026370.1/26588-26509   GAUCAGUGAUGAA-AGUAGCCAAAUCUGAGCAUCAGAAGACC-ACCCAGUGU-ACCUGAUGC-AUGAUCUCUAUAG--UUCUGAGA
AAIY01511656.1/2745-2666     GAUCAAUGAUGAA-AAUAGCCAAAUCUGAGCACCAGAGGACC-AUCCGGUCU-AUCUGAUGC-AUGAUCUUCAUCA--UUCUGGGA
AB215689.1/207-132           ----AAUGAUGAA-AAUAGCCAAAUCUGAGCAUCAGAAGACC-UUUCAGUCU-ACCUGAUGC-AUGAUCUCUGUAG--UUCUGAGA
AAHX01002682.1/29606-29527   GAUCAAUGAUGAA-AAUAGCCAAAUCUGAGCAUCAGAAGGCC-UUUUGGUCG-GCUGGGUGC-AUGAUCUCUAUAG--UUCUGAGA
AANN01460207.1/3110-3034     GAUCAAUGAUGAA-AAUAGCCAAAUCUGAGCAUCAGAAGAUC-UUU-AGUCU-ACCUGGUGC-AUGAUCUCU--AG--UUCUGAGA
AANG01702163.1/853-774       AAUCAAUGAUGAA-AAUAGACAAUUCUGAGCAUCAGAAGACC-UUCUAAUUU-GCCUGAUGC-AUGAUCCCUAUAG--UUCUGAAA
AAPY01140828.1/233-155       GAUCAAUGAUGAA-ACUAGCCAAAUCUGAGCAUCGGAAGACC-UUCCAGUCU-ACCUUACGC-AUGAUCUCU-UAG--CUCUGAGA
AAPN01307029.1/30865-30944   GAUCAGUGAUGAAAAAUAGCCAAAUCUGAGCAUCAG-AGGCC-AUCUGGUCU-ACAUGGUGC-AUGAUCACUAUAG--UUCUGGGA
AAFR03025138.1/100392-100310 GAUCAAUGAUGAAAAAUAGCCAAAUAUGAGCAUCAGGAGACC-UUCUGGUCU-UUGUGGUGC-AUGAUUUGUAUGUGUUUCUGAGA
AALT01064673.1/9295-9374     GAUCAAUGAUGAA-AAUAGCCAAGUCUAAGCAUCAGGAGGCC-AUGCAGGCU-GCCUGAUGC-GUCAUCUAGUUCU--UUUUUAUA
AY679122.1/12-93             GGUCUGUGAUGAGAAAUAGCCAAAUCUGACCACCAGGAGAUA-AAAUCAUCU-UCCAGGUGUAAUGAUUUGUACAG--UUCUGAGA
AAVX01218124.1/520-438       GGUCAAUGAUGAAAAAUAGCCAAAUCUGAGCACCAGUAGAUC-AGUUGAUCU-AAUUGGUGA-AUGAUUGGUGUACAGACCAGAGA
AAYZ01117356.1/2844-2924     GAUUGAGGACAAA-AAGAGCCAAACCCAAGCAUCACAAGAUC-CUGUAGUCUUACCUGAUAC-AUGAGCUCCAAAG--UUCCGAAA
AF339756.1/216-132           GGUCUGUGAUGAGAAAUAGCCAAAUCUGACCACCAGAAGAUAAAAACAAUCU-UCCAGGUGUCAUGAUUUAUAUGUAGUUCUGAGA
AAKN02037651.1/29205-29126   GAUCAAUGAUGAA-AAUAGCCAAAUCUGAGCAUCAGAAGACU-UUGCGGUCU-CCCUGAUUC-AUGAUCUCUAUAG--UUCUGGGA
AC155259.1/207919-207994     GAUCAGUGAUGAA-AAUAGCCAAAUCUGAGCAUCAGAAGGCC-UUUUGGU-----CUGGGGC-AUGAUCUCUCUAG--UUCUGAGA
BK005567.1/29-108            GAUCAAUGAUGAA-ACUAGCCAAAUCUGAGCAUCAGAAGUCU-UUCCAGUCU-ACCUGAUGC-AUGAUCUCUACAG--UUCUGAGA
AAQR03039365.1/18972-19051   GAUCAAUGAUGAA-AAUAGCCAAAUUUGAAUAUCAGAAGACA-UUCCAAUCU-ACCUGAUGC-AUGAUCUCUACAG--UUCUGAGA
AEYP01059655.1/3157-3078     GAUCAAUGAUGAA-AAUAGCCAAAUCUGAGCAUCAGAAGACC-UUCCAGUCU-ACCUGAUGC-AUGAUCUCUCUAG--UUCUGAGA
AADN03001253.1/127222-127301 AGUCUGGGAUGAGAAACAGCCAAAUCUGAACACCAGAAGAUA-AAACUAUCU-UCCAGGUAU-AGCAG-UAUGCAG--UUCUGAGA
AAPE02066189.1/3426-3505     GGUCAAUAAUGAA-AAUAGCCAAAUCUGAGCAUCAAAAGACC-UUCCAGUCU-ACCUGAUGU-AUGAUCUCUAUAG--UUCUGAGA
AAGW02008739.1/1444-1524     GAUCAAUGAUGAA-AAUAGCCAAAUCUGAGCAUCAGAAGACC-UUCUAGUCUUACCUGAUGC-AUGAUCUCCAUUG--UUCUGAGA
AAGU03058301.1/53826-53905   GAUCAGUGAUGAA-AAUAGCCAAAUCUGAGCAUCAGAAGACC-UUCUAGUCU-ACCUGAUGC-AUGAUCUCUAUAG--UUCUGGGA
#=GC SS_cons                 :::::::::::::.:::::::::::::::<<<<<---<<<<_._____>>>>.---->>>>>.:::::::::::::..::::::::
#=GC RF                      GAUCAAUGAUGAA.AAUAGCCAAAUCUGAgCAuCAGAAGacc.uUccaguCU.aCcUGaUGc.AUGAUCUcUAuAG..UUCUGAGA
//
# STOCKHOLM 1.0

#=GF AC   RF00495
#=GF ID   IRES_Hsp70
#=GF DE   Heat shock protein 70 (Hsp70) internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Published
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   80.00
#=GF TC   91.80
#=GF NC   70.60
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   12682055
#=GF RT   Distinctive properties of the 5'-untranslated region of human hsp70 mRNA.
#=GF RA   Rubtsova MP, Sizova DV, Dmitriev SE, Ivanov DS, Prassolov VS, Shatsky IN
#=GF RL   J Biol Chem 2003;278:22350-22356.
#=GF CC   This family represents heat shock protein 70 (Hsp70) internal ribosome
#=GF CC   entry site (IRES) which allows cap independent translation during
#=GF CC   conditions such as heat shock and stress.
#=GF WK   Heat_shock_protein_70_(Hsp70)_internal_ribosome_entry_site_(IRES)
#=GF SQ   14


S52686.1/274-488        AUAACGGCUAGCCUGAGG--AGCUGCUGCGACAGUCCACUACCUUUUUCGAGAGUGACUCCCGUUGUCCCAAGGCU-U-CCCAGAGCGAACC-UGUGCGGCUGCAGGCACCGGCGC-GUCGAGUUYCCGGCGUCCGGAA-GGACCGAGCUCUU-CUCGCGGAUCCAGUGUUCCGUUUCCAGCCCCCAA-----UCUCAGAGCCGAGCCGACAGAGAGCA-GGGAACCGC----
AC148662.1/79642-79858  AAAACGGCCAGCCUCAGG--AGCUGCUGCGACAAUCGGCUUUCUUUUCUGAGAGUGACUCCCUGGGUCCCAAGGCU-UUCCCAGAGCGAACG-UGUGCGGCUGCAGGCAUCAGCGC-GUUGAGUUUCCGGCGUUCCGAA-GGAGUGAGCUCUU-GUCGCGGGUCCCGUCCGCCGUUUCCAGUCCCGAA-----UCUCGGAGCGGAGCAGACAGCAGGG----CACCGGCAUGG
AC148662.1/67681-67897  AAAACGGCCAGCCUCAGG--AGCUGCUGCGAGAAAUCGCUGCGUUUCCAGAGCGUGGCUCCCGUUGUCCCGAGGCU-U-CCCAGAGCGAACC-UGUGCGGCUGCAGGCACCAGCGCCGUUGAGUUUCCGGCGUUCCGGA-GGAGUGAGCUCUU-GUCGCGGGUCCCGUCCGCCGUUUCCAGUCCCGAA-----UCUCGGAGCGGAGCAGACAGCAGGG----CACCGGCAUGG
AL671762.10/35585-35802 AAAACGGCCAGCCUGAGG--AGCUGCUGCGAGGGUCCGCUUCGUCUUUCGAGAGUGACUCCCGCGGUCCCAAGGCU-U-UCCAGAGCGAACC-UGUGCGGCUGCAGGCACCGGCGU-GUUGAGUUUCCGGCGUUCCGAA-GGACUGAGCUCUU-GUCGCGGAUCCCGUCCGCCGUUUCCAGCCCCCAG-----UCUCAGAGCGGAGCCCACAGAGCAG--GGCACCGGCAUGG
AL671762.10/23389-23608 AUAACGGCUAGCCUGAGG--AGCUGCUGCGACAGUCCACUACCUUUUUCGAGAGUGACUCCCGUUGUCCCAAGGCU-U-CCCAGAGCGAACC-UGUGCGGCUGCAGGCACCGGCGC-GUCGAGUUUCCGGCGUCCGGAA-GGACCGAGCUCUU-CUCGCGGAUCCAGUGUUCCGUUUCCAGCCCCCAA-----UCUCAGAGCGGAGCCGACAGAGAGCAGGGAACCGGCAUGG
BC063507.1/1-202        -----GGA--GC-----------UGCUGCGAGGGUCCGCUUCGUCUUUCGAGAGUGACUCCCGCGGUCCCAAGGCU-U-UCCAGAGCGAACC-UGUGCGGCUGCAGGCACCGGCGU-GUUGAGUUUCCGGCGUUCCGAA-GGACUGAGCUCUU-GUCGCGGAUCCCGUCCGCCGUUUCCAGCCCCCAG-----UCUCAGAGCGGAGCCCACAGAGCAG--GGCACCGGCAUGG
X70684.1/2-184          --AA----U-UCC-----------G------------------UUUCUAGAGCGUGGCUCCCGUUGUCCCGAGGCU-U-CCCAGAGCGAACC-UGUGCGGCUGCAGGCACCAGCGCCGUUGAGUUUCCGGCGUUCCGGA-GGACUGAGCUCUU-GUCACGGGUCCCGUCCGCCGUUUCCAGUCCCGAA-----UCUCGGAGCGGACGAGACAGCAGGG----CACCGGCAUGG
AY149618.1/12219-12431  AGAAACAGCAGCCUGGAGAGAGCUGAUAAAACUUACGGCUUAGUCCG-UGAGAGCAGCUUCCGCAGACCC---GCUAU-CUCCAAG--GACCGCCCCG---AGG-GGCACCAGAGC-GUUCAGUUUUCGG-GUUCCGAAAAGCCCGAGCUUCUCGUCGCAGAUCCUCUUCACCGAUUUCAGGUUUGAAGCUUAUCUCGGAGCCGAAAAG---GCAGGG----CACCGGCAUGG
X04676.1/269-487        AUAACGGCUAGCCUGAGG--AGCUGCUGCGACAGUCCACUACCUUUUUCGAGAGUGACUCCCGUUGUCCCAAGGCU-U-CCCAGAGCGAACC-UGUGCGGCUGCAGGCACCGGCGC-GUCGAGUUUCCGGCGUCCGGAA-GGACCGAGCUCUU-CUCGCGGAUCCAGUGUUCCGUUUCCAGCCCCCAA-----UCUCAGAGCGGAGCCGACAGAGAGCA-GGGAACCGCAUGG
AL662834.8/79426-79645  AUAACGGCUAGCCUGAGG--AGCUGCUGCGACAGUCCACUACCUUUUUCGAGAGUGACUCCCGUUGUCCCAAGGCU-U-CCCAGAGCGAACC-UGUGCGGCUGCAGGCACCGGCGC-GUCGAGUUUCCGGCGUCCGGAA-GGACCGAGCUCUU-CUCGCGGAUCCAGUGUUCCGUUUCCAGCCCCCAA-----UCUCAGAGCCGAGCCGACAGAGAGCAGGGAACCGGCAUGG
BC057397.1/1-196        ------GCU-GC--GAG-------GGUCCGU--------UUCGUCUUUCGAGAGUGACUCCCGCGGUCCCAAGGCU-U-UCCAGAGCGAACC-UGUGCGGCUGCAGGCACCGGCGU-GUUGAGUUUCCGGCGUUCCGAA-GGACUGAGCUCUU-GUCGCGGAUCCCGUCCGCCGUUUCCAGCCCCCAG-----UCUCAGAGCGGAGCCCACAGAGCAG--GGCACCGGCAUGG
M98823.1/1024-1235      AGAAACAGCAGCCUGGAGAGAGCUGAUAAAACUUACGGCUUAGUCCG-UGAGAGCAGCUUCCGCAGACCC--G-CUAUCUCCA-AG-GACCG-CCCG-----AGGGGCACCAGAGC-GUUCAGUUUUCGGGUUCCGAAA-AGCCCGAGCUUCUCGUCGCAGAUCCUCUUCACCGAUUUCAGGUUUGAAGCUUAUUUCGGAGCCG---GAAAAGCAGGG----CACCGGCAUGG
M11717.1/274-492        AUAACGGCUAGCCUGAGG--AGCUGCUGCGACAGUCCACUACCUUUUUCGAGAGUGACUCCCGUUGUCCCAAGGCU-U-CCCAGAGCGAACC-UGUGCGGCUGCAGGCACCGGCGC-GUCGAGUUUCCGGCGUCCGGAA-GGACCGAGCUCUU-CUCGCGGAUCCAGUGUUCCGUUUCCAGCCCCCAA-----UCUCAGAGCCGAGCCGACAGAGAGCA-GGGAACCGCAUGG
AB018045.1/2322-2530    AUAACGGCUAGCCUGAGG--AGCUGCUGCGACAGUCCACUACCUUUU-CGAGAGUGACUCCCGUUGUCCCAAGGCU-U-CCCAGAGCGAACC-UGUGCGGCUGCAGGCACCGGCGC-GUCGAGUUUCCGGCGUCCGGAA-GGACCGAGCUCUU-CUCGCGGAUCCAGUGUUCCGUUUCCAGCCCCCAA-----UCUCAG--CGGA-CACCGAGCGGCU----CAUCGG---GG
#=GC SS_cons            ::::(((((-((((((((..----((((-((-------------(((-((((---(((((-----((((,,,,<<<.<.____>>>>,,,<<.<<<______>>>>>,,<<<<-<<.<<<<______>>>>>>>>>>,,.))))-)))-))--.))))-)))--------------))))))------.....))))))-))-)-)))):::::::::....:::::::::::
#=GC RF                 AuAAccgccAGCCuGagg..AGCUgcUgcGacaguCcgCUucgUuccucGAgAGUGaCUcCCGuuGuCCCAAGGCU.u.cCCAgAGCGAACC.ugcGcGGCUgcaGGCACcggcgc.GucGAGUUUcCggCguccgGAA.GGaCcgAGCuCUU.cUCgCggaUCCugUucuCCGuUuCcAgcccccAA.....ucuCaGAGCggAgcggAcAGaaggg....cAcCgGCAUGG
//
# STOCKHOLM 1.0

#=GF AC   RF00496
#=GF ID   Corona_SL-III
#=GF DE   Coronavirus SL-III cis-acting replication element (CRE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12767992
#=GF SS   Published; PMID:12767992
#=GF GA   65.00
#=GF TC   67.60
#=GF NC   34.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0039703; RNA replication;
#=GF RN   [1]
#=GF RM   12767992
#=GF RT   Stem-loop III in the 5' untranslated region is a cis-acting element in
#=GF RT   bovine coronavirus defective interfering RNA replication.
#=GF RA   Raman S, Bouma P, Williams GD, Brian DA
#=GF RL   J Virol 2003;77:6720-6730.
#=GF CC   This family represents a coronavirus cis-acting replication element (CRE).
#=GF CC   Members of this family are related to Bovine coronavirus stem-loop III and
#=GF CC   function as cis-acting elements for defective interfering (DI) RNA
#=GF CC   replication [1].
#=GF WK   Coronavirus_SL-III_cis-acting_replication_element
#=GF SQ   5


AF523846.1/84-125 CACUCCCUGUAAUCUAUGCUUGCGAGCUUAGACUUUUCAUAG
AF220295.1/85-126 CACUCCCUGUAUUCUAUGCUUGUGGGCGUAGAUUUUUCAUAG
AF391542.1/85-126 CACUCCCUGUAGUCUAUGCCUGUGGGCGUAGAUUUUUCAUAG
AY585228.1/84-125 CACUCCCUGUAAUCUAUGCUUGUGGGCGUAGAUUUUUCAUAG
AF523845.1/85-126 CACUCCCUGUAGUCUAUGCUUGUGGGCGUAGAUUUUUCAUAG
#=GC SS_cons      ::::::::::::<<<<<<<<____>>>>>>>>::::::::::
#=GC RF           CACUCCCUGUAaUCUAuGCuUGUGgGCgUAGAUUUUUCAUAG
//
# STOCKHOLM 1.0

#=GF AC   RF00498
#=GF ID   EAV_LTH
#=GF DE   Equine arteritis virus leader TRS hairpin (LTH)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:14970388
#=GF SS   Published; PMID:14970388
#=GF GA   70.00
#=GF TC   76.90
#=GF NC   40.40
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   14970388
#=GF RT   Secondary structure and function of the 5'-proximal region of the equine
#=GF RT   arteritis virus RNA genome.
#=GF RA   Van Den Born E, Gultyaev AP, Snijder EJ
#=GF RL   RNA 2004;10:424-437.
#=GF CC   This family represents the equine arteritis virus leader
#=GF CC   transcription-regulating sequence hairpin (LTH). The LTH is thought to be
#=GF CC   a key structural element in discontinuous subgenomic RNA synthesis and is
#=GF CC   critical for leader TRS function [1].
#=GF WK   Equine_arteritis_virus_leader_TRS_hairpin_(LTH)
#=GF SQ   6


AJ488295.1/169-213 UGCCAUCGUCGUCGAUCUCUAUCAACUACCCUUGCGACUAUGGCA
AJ488296.1/170-214 UGCCAUCGUCGUCGAUCUCUAUCAACUACCCUUGCGACUAUGGCA
AJ488294.1/169-213 UGCCAUCGUCGUCGAUCUCUAUCAACUAUCCUUGCGACUAUGGCA
AJ488298.1/170-214 UGCCAUCGUCGUCGAUCUCUAUCAACUACCCCUGCGACUAUGGCA
AJ488297.1/169-213 UGCCAUCGUCGUCGAUCUCUAUCAACUAUCCUUGCGACUAUGGCA
AJ488299.1/170-214 UGCCAUCGUCGUCGAUCUCUAUCAACUACCCUUGCGACUAUGGCA
#=GC SS_cons       <<<<<<-<<<<<_____________________>>>>>->>>>>>
#=GC RF            UGCCAUCGUCGUCGAUCUCUAUCAACUAcCCUUGCGACUAUGGCA
//
# STOCKHOLM 1.0

#=GF AC   RF00499
#=GF ID   Parecho_CRE
#=GF DE   Human parechovirus 1 (HPeV1) cis regulatory element (CRE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:12438643
#=GF SS   Published; PMID:12438643
#=GF GA   55.00
#=GF TC   59.90
#=GF NC   52.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019079; viral genome replication;
#=GF DR   GO; 0040007; growth;
#=GF RN   [1]
#=GF RM   12438643
#=GF RT   Terminal RNA replication elements in human parechovirus 1.
#=GF RA   Nateri AS, Hughes PJ, Stanway G
#=GF RL   J Virol 2002;76:13116-13122.
#=GF CC   This family represents a Parechovirus cis regulatory element which is
#=GF CC   located in the 5'-terminal 112 nucleotides of the genome of human
#=GF CC   parechovirus 1 (HPeV1). The family consists of two stem-loop structures
#=GF CC   (SL-A and SL-B) together with a pseudoknot. Disruption of any of these
#=GF CC   elements impairs both viral replication and growth [1].
#=GF WK   Human_parechovirus_1_(HPeV1)_cis_regulatory_element_(CRE)
#=GF SQ   5


AF055846.1/1-102 -------------UCCUAGAGAGCUUGGCCGUCGGGCCUUAUA-CCCGACUUGCUGAGUUUCUCUAGGAGAGU-CCCUUUCCCAGCCCUGAGGCGGCUGGUCAAUAAAAGCCUCAAA
AJ005695.1/1-113 UUUGAAAGGGGUCUCCUAGAGAGCUUGGCCGUCGGGCCUUACACCCCGACUUGCUGAGUUUCUCUAGGAGAGU-CCCUUUCCCAGCCA-GAGGUGGCUGGUCAAACAAUACCA--AA
L02971.1/1-115   UUUGAAAGGGGUCUCCUAGAGAGCUUGCC--UAGGGCCUUAUAACCCGACUUGCUGAGCUUCUAUAGGAAAAAACCCUUUCCCAGCCUUGGGGUGGCUGGUCAAUAAAAACCCCCAU
AB084913.1/1-113 UUUGAAAGGGGUCUCCUAGAGAGCUUGGCCGUCGGGCCUUAUACCCCGACUUGCUGAGCUUCUCUAGAAGAGU-CCUUUUCCCAGCCA-GAGGUGGCUGGUUAAAUAAUACCU--AC
S45208.1/1-115   UUUGAAAGGGGUCUCCUAGAGAGCUUGCC--UAGGGCCUUAUAACCCGACUUGCUGAGCUUCUAUAGGAAAAAACCCUUUCCCAGCCUUGGGGUGGCUGGUCAAUAAAAACCCCCAU
#=GC SS_cons     :::<<<<<<<<<<<<<<<<<<<<<<<<<<-<<<<<<________>>>>>>-->>>>>>>>>->>>>>>>>>->.>>>>>>><<<<<<__AAAAA>>>>>>:::::::::aaaaa:::
#=GC RF          UUUGaaagGGgucucCuagagagCuuggCcGucGGGCCUUAuAaCCCgaCUUGcugaGcuuCucuaGgagagc.CCcuuuCCCaGCCuUGaGGuGGCuGGUcAAuaAAaACCucaAu
//
# STOCKHOLM 1.0

#=GF AC   RF00500
#=GF ID   TCV_H5
#=GF DE   Turnip crinkle virus (TCV) repressor of minus strand synthesis H5
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15220455
#=GF SS   Published; PMID:15220455
#=GF GA   70.00
#=GF TC   72.90
#=GF NC   37.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 1902679; negative regulation of RNA biosynthetic process;
#=GF RN   [1]
#=GF RM   15220455
#=GF RT   Biased hypermutagenesis associated with mutations in an untranslated
#=GF RT   hairpin of an RNA virus.
#=GF RA   McCormack JC, Simon AE
#=GF RL   J Virol 2004;78:7813-7817.
#=GF RN   [2]
#=GF RM   15220437
#=GF RT   Repression and derepression of minus-strand synthesis in a plus-strand RNA
#=GF RT   virus replicon.
#=GF RA   Zhang G, Zhang J, Simon AE
#=GF RL   J Virol 2004;78:7619-7633.
#=GF CC   This family represents the turnip crinkle virus (TCV) hairpin 5 (H5) which
#=GF CC   contains a large symmetrical internal loop (LSL). H5 can repress
#=GF CC   minus-strand synthesis when the 3' side of the LSL pairs with the
#=GF CC   3'-terminal 4 bases of the RNA(GCCC-OH) [1,2].
#=GF WK   Turnip_crinkle_virus_(TCV)_repressor_of_minus_strand_synthesis_H5
#=GF SQ   5


X05193.1/1360-1404   GGGUAACCACUAAAAUCCCGAAAGGGUGGGCU-GUGGUGACCUUCC
M29290.1/257-302     GGGUAACCACUAAAAUCCCGAAAGGGUGGGCUAGUGGCGACCCUCC
X12750.1/269-313     GGGUAACCACUAAAAUCCCGAAAGGGUGGGCU-GUGGGGACCCUCC
AY312063.1/3963-4007 GGGUAACCACUAAAAUCCCGAAAGGGUGGGCU-GUGGUGACCUUCC
M22445.2/3960-4004   GGGUAACCACUAAAAUCCCGAAAGGGUGGGCU-GUGGUGACCUUCC
#=GC SS_cons         <<<<-<<<<<------<<<____>>>------.>>>>>->>>>:::
#=GC RF              gGGUAaCCACUAAAAUCCCGAAAGGGUGGGCU.GUGGuGACCcUCC
//
# STOCKHOLM 1.0

#=GF AC   RF00501
#=GF ID   Rota_CRE
#=GF DE   Rotavirus cis-acting replication element (CRE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:
#=GF SS   Predicted; Pfold; Moxon SJ
#=GF GA   40.00
#=GF TC   40.20
#=GF NC   39.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0039703; RNA replication;
#=GF DR   GO; 1902680; positive regulation of RNA biosynthetic process;
#=GF RN   [1]
#=GF RM   11289804
#=GF RT   Features of the 3'-consensus sequence of rotavirus mRNAs critical to minus
#=GF RT   strand synthesis.
#=GF RA   Chen D, Barros M, Spencer E, Patton JT
#=GF RL   Virology 2001;282:221-229.
#=GF CC   This family represents a Rotavirus cis-acting replication element (CRE)
#=GF CC   found at the 3'-end of rotavirus mRNAs. The family is thought to promote
#=GF CC   the synthesis of minus strand RNA to form viral dsRNA [1].
#=GF WK   Rotavirus_cis-acting_replication_element
#=GF SQ   14


AF506293.1/992-1056 GGAAUUUAAUUCGCUU-CGAUUCAAGAAUGA-GAU-ACGAAGCAAGAAUAGAAAGCGCUUAUGUGACC
X57944.1/992-1059   GGAAUUUAAUUCGCUUUCGGUUCAAAAAUGAUGAUGACGAAGCAAGAAUAGAUAGCGCUUAUGUGACC
J02353.1/992-1059   GGAAUUUAAUUCGUUAUCGAUUUGAGAAUGGGUAUGACAAAGUAAGAAUAGAAAGCGCUUAUGUGACC
AB022770.1/991-1058 GGAAUUUAAUUCGCUUUCGAUUUGAGAAUGAUGAUGACGGAGCAAGAAUAGAAAGCGCUUAUGUGACC
J02420.1/992-1059   GGAAUUUAAUUCGUUAUCGGUUUGAAGGUGGGUAUGGCAGAGCAAGAAUAGAAAGCGCUUAUGUGACC
L04534.1/991-1058   GGAAUUUAAUUCACUUUCGAUUCGAGAAUGAUGAUGACGAAGCAAGAAUAGAAAGCGCUUAUGUGACC
AF506018.1/992-1059 GGAAUCUAAUUCGUUAUCUGUUUGAAGGUGGGUAUGGCAGAGUAAGAAUAGAAAGCGCUUAUGUGACC
L04530.1/992-1059   GGAAUUUAAUUCGCUAUCGAUUUGAGAAUGGGUAUGGCAAAGUAAGAAUAGAAAGCGCUUAUGUGACC
L20901.2/990-1057   GGCGUUUAAUUCGCUAUCAAUUUGAGGAUGAUGAUGGCUUAGCAAGAAUAGAAAGCGCUUAUGUGACC
L04531.1/992-1059   GGCGUUUAAUUCGCUAUCAAUUUGAGGAUGAUGAUGGCUUAGCAAGAAUAGAAAGCGCUUAUGUGACC
Z21640.1/992-1059   GGAAUUUAAUUCGCUAUCGAUUUGAGAAUGGGUAUGGCAAAGUAAGAAUAGAAAGCGCUUAUGUGACC
L04532.1/991-1058   GGCGUUUAAUUCGCUAUCAAUUUGAGGAUGAUGAUGGCUUAGCAAGAAUAGAAAGCGCUUAUGUGACC
L04529.1/992-1059   GGAAUUUAAUUCGUUAUCGAUUCAAGAAUGGGUAUAACGAAGUAAGAAUAGAAAGCGCUUAUGUGACC
X06722.1/992-1059   GGAAUUUAAUUCGCUUUCGAUUCAAGGAUGAUGAUGACGGAGCAAGAAUAGAAAGCGCUUAUGUGACC
#=GC SS_cons        <<-<<-<<<--<<<<-<<-<<<<______________________>>>>->>->>>>->>>->>-->>
#=GC RF             GGAaUUUAAUUCGcUaUCgaUUcGAGaAUGaugAUGaCaaAGcAAgAAuAGAAAgCGCUUAUGuGACC
//
# STOCKHOLM 1.0

#=GF AC   RF00502
#=GF ID   TCV_Pr
#=GF DE   Turnip crinkle virus (TCV) core promoter hairpin (Pr)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15220455
#=GF SS   Published; PMID:15220455
#=GF GA   40.00
#=GF TC   46.30
#=GF NC   37.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 1902680; positive regulation of RNA biosynthetic process;
#=GF RN   [1]
#=GF RM   15220455
#=GF RT   Biased hypermutagenesis associated with mutations in an untranslated
#=GF RT   hairpin of an RNA virus.
#=GF RA   McCormack JC, Simon AE
#=GF RL   J Virol 2004;78:7813-7817.
#=GF CC   This family represents the turnip crinkle virus (TCV) core promoter
#=GF CC   hairpin (Pr). Pr is located in the 3' UTR and is required for minus strand
#=GF CC   RNA synthesis [1].
#=GF WK   Turnip_crinkle_virus_(TCV)_core_promoter_hairpin_(Pr)
#=GF SQ   4


X12750.1/324-353     ACAGCCUCCCUCCUCG----GACGGGGGGCCUGC
X05193.1/1415-1448   AUAGCCUCCCUCCUCGCGCGGGGGGGGGGCCUGC
M22445.2/4015-4048   AUAGCCUCCCUCCUCGCGCGGGGGGGGGGCCUGC
AY312063.1/4018-4051 AUAGCCUCUCCCCUCGCGCGGGGGGGGGGCCUGC
#=GC SS_cons         ::::<<<<<<<<________>>->>>>>>:::::
#=GC RF              AUAGCCUCCCcCCUCGCGCGGgGGGGGGGCCUGC
//
# STOCKHOLM 1.0

#=GF AC   RF00503
#=GF ID   RNAIII
#=GF DE   RNAIII
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Gardner P
#=GF SS   Published; PMID:26504242
#=GF GA   47.00
#=GF TC   47.60
#=GF NC   34.60
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   10836788
#=GF RT   Probing the structure of RNAIII, the Staphylococcus aureus agr regulatory
#=GF RT   RNA, and identification of the RNA domain involved in repression of
#=GF RT   protein A expression.
#=GF RA   Benito Y, Kolb FA, Romby P, Lina G, Etienne J, Vandenesch F
#=GF RL   RNA 2000;6:668-679.
#=GF RN   [2]
#=GF RM   26504242
#=GF RT   RNAIII of the Staphylococcus aureus agr system activates global regulator
#=GF RT   MgrA by stabilizing mRNA.
#=GF RA   Gupta RK, Luong TT, Lee CY
#=GF RL   Proc Natl Acad Sci U S A. 2015;112:14036-14041.
#=GF CC   This family represents RNAIII which is known to regulate the expression of
#=GF CC   many Staphylococcus aureus genes encoding exoproteins and cell wall
#=GF CC   associated proteins. In S.aureus, RNAIII acts as the effector of the agr
#=GF CC   system and is transcribed from the P3 operon. The RNAIII transcript also
#=GF CC   contains the 26 amino acid delta-haemolysin gene (hld) [1].
#=GF WK   RNAIII
#=GF SQ   10


X52543.1/1570-1057         AGAUCACAGAGAUG-UGAUGGAAA-AUAGUUG--AUGA--GUUGUUUAAUUUUAAGAAUUUUUA----------------------------UCUUAAUUAAGGAAGGAGUGAUU--UC---AAUGGCACAAGAUAUCAUUUCAACAAUCGGUGACUUAGUAAAAUGGAUUAUCGACACAGUGAACAAA-UUCACUAAAAAAUAAGAUGAAUAAUU-AAUUAC--UUUCAUUGUAAAUUUGUUAUCUUCGUAUAGUACUAAAAGUA----UGAGUUAUUAAGCCAUCCCAACUUAAUAACCAUGUAAAAUUAGC-----AAGUGAGU-AA-CAUUUGCUAGUA-GA--GUUAGUUUCCUUGGACUCAGUGCUAUGUAUUUUUCUUAAUUAUCAUUA--CA---------GAUAAUUAU---UUCUAGCAUGUAAGCUAUCGUAAAC-AACAUC--GAUUUAUCA---UUAUU--UGAUAAAUA----AAAUUUUUUUCAUAAUUAAUAACAUCCCCAA--AAAUAGAUUGAAAAAAUAA-CUGUAA-AACAUUCCCUUAAUAAU--AAGU-----AUGGUCGUGAGCCCCUCCCAAGCUCGCGGCCUU
X17301.1/911-398           AGAUCACAGAGAUG-UGAUGGAAA-AUAGUUG--AUGA--GUUGUUUAAUUUUAAGAAUUUUUA----------------------------UCUUAAUUAAGGAAGGAGUGAUU--UC---AAUGGCACAAGAUAUCAUUUCAACAAUCGGUGACUUAGUAAAAUGGAUUAUCGACACAGUGAACAAA-UUCACUAAAAAAUAAGAUGAAUAAUU-AAUUAC--UUUCAUUGUAAAUUUGUUAUCUUCGUAUAGUACUAAAAGUA----UGAGUUAUUAAGCCAUCCCAACUUAAUAACCAUGUAAAAUUAGC-----AAGUGAGU-AA-CAUUUGCUAGUA-GA--GUUAGUUUCCUUGGACUCAGUGCUAUGUAUUUUUCUUAAUUAUCAUUA--CA---------GAUAAUUAU---UUCUAGCAUGUAAGCUAUCGUAAAC-AACAUC--GAUUUAUCA---UUAUU--UGAUAAAUA----AAAUUUUUUUCAUAAUUAAUAACAUCCCCAA--AAAUAGAUUGAAAAAAUAA-CUGUAA-AACAUUCCCUUAAUAAU--AAGU-----AUGGUCGUGAGCCCCUCCCAAGCUCGCGGCCUU
AENR01000015.1/29267-29826 AUAUCACAGAGAUG-UGAUUGAAAGAUAGUUG--AAAA-AUUUGCUUAAUCUAGUC--GAGUGAAUGUUAAAUUCAUUCGUAUCCAUUACCU----UAAUUCGAAAGGAGUGAAG--UUA-UAAUGGCAGCAGAUAUCAUUUCUACAAUCGGUGAUUUAGUAAAAUGGAUUAUCGAUACAGUUAAUAAA-UUCAAAAAAUAAUUU-UUGAAUGAGUCUAUUGU--AACUUUUGUAACUUUGUUUUCUUC--GUAUAAUUAAUACUAUUAGUGAGUUGUUGAGCCAUCCCAACUUAAUAAUUUACUAAUAUAAACUAAGCAAGUGAGA-AG-CAUUUGCUAGUA-GC--UGUAGUUUCCUUGGACUCAGUGUUACGUAUUAUUUUUAGCUACCUUAA--UA---------GGUAAUUAU---UUCUAGCAUGUAAGCUAUCGUAAAC-AACAUU-CAAUUUAUCAUGUUAAAU--AGAUAAAUUCACUAAAAUUUUUUCAUAAUUAAUAACAUCCCCAA-AAAAUAGAUUGAAAAAAUAA-CUGUAAAAACAUUCCCUUAAUAAU--AAGUU--AUCAAGCCGUGAGUCUCUCCCAAGCUCACGGCUUU
ACPZ01000045.1/1378-1885   CCAAAAAU---AAU-UUUUUCAAG-UUAGUUAAGAUGA--GU-AUUUAGGAUUUACAAUAAU----------------------------------UCAAAUGGAAGGAGUGAUU--UC---AAUGACUGCAGAUAUCAUUUCAACAAUUGGUGAUUUUGUAAAAUGGAUUUUAGAUACAGUAAAAAAA-UUCACUAAAUAAUA-GUAGA--AA------------UUCAUUGUAACUUUGUUUUCUUC--GUA----UAAUAGG-----UGAGUUAUUAAGCCAUCCCAACUUAAUAACUU-ACAACAUUAGU-----AGGUGACCAAA-CAUUUACUAAUAUGACUGUAGUUUUCCUUGGACUCAGUGUUACGUAUUAUUCUUAGCUACCUUUAACUA---------GGUA--UUU---UUCUAACAUGUAAGCUAUCGUAAAACAACAUU-CAAUUUAUCAUUAUAAAAAGAGAUAAAUUCACUAAAAUUUUUUCAUAAUUAAUAACAUCCCCAA-AAAAUAGAUUGAAAAAAUAA-CUGUAAAAACAUUCCCUUAAUAAU--AAGUUAUCAAAAGCCGUGAGCCCCUCCCAAGCUCACGGCUUA
AJ223776.1/254-759         CCAAAAAU---AAU-UUUUUCUAG-UUAGUUAAGAUGA--GU-AUUUAGGAUUUACAAUAAU----------------------------------UCAAAUGGAAGGAGUGAUU--UC---AAUGACUGCAGAUAUCAUUUCAACAAUUGGUGAUUUUGUAAAAUGGAUUUUAGAUACAGUAAAAAAA-UUCACUAAAUAAUA-GUAGA--AA------------UUCAUUGUAACUUUGUUUUCUUC--GUA----UAAAAGG-----UGAGUUAUUAAGCCAUCCCAACUUAAUAACUU-GCAACAUUAGU-----AGGUGACCAAA-CAUUUACUAAUAUGACUGUAGUUUUCCUUGGACUCAGUGUUACGUAUUAUUCUUAGCUACCUUUAAUUA---------GGUA--UUU---UUCUAACAUGUAAGCUAUCGUAAAACAACAUU-CAAUUUAUCAUUAUAAAAAGAGAUAAAUUCACUAAAAUUUUUUCAUAAUUAAUAACAUCCCCAAAAAAAUAGAUUGAAAAAAUAA-CUGUAAAAACAUUCCCUUAAUAAU--AAGUUAUCAAAAGCCGUGAGCCCCUCCCAAGCUCACGGU---
AM295250.1/1561872-1561408 GGAAUGCAUUGUUGAUAUUC-----UUCGUUA--AAAAAUAAUG--CAUUAAACUGACUGAUCA----------------------------UCCAUAUUAUUGUAAAGGAGGUA--UGUAACAUGGCAGGCGAUAUCGUAGGUACAAUCGGUGACUUCGUUAAAUUAAUCAUCGAAACUGUAAACAAA-UUCACUAACAAAUAAUCCCUUUGUUU-UAUUGUCCUUUGAGUAUAAGCACUAA---AUUGU----------------------------------------------------UUAAUCCUU------------UUC-AGG--------AGG--AA--AUGUUUGUCCUUGCAUUUCCUUCUGGUCCUUAUUAUUUGUACGCCGGA--UAGAAAAUUUGGUGUACAUA---UUAGAAUA-AUAAAUUAUCGUGAGC-AUCAUUAAAAUUUAUCA---AAUAU--CGGUAAAUUC-ACUAAAAUUUUUCAUAAUUAAUAACAUCCCCAA--AAAUAGAUAGAAAAA-UAA-CUGUAA--ACAUUCCCUUAAUAAU--AAGUU-UAAUAGCCCGUGAGUUCCUCCCAAACUCACGGGCAU
FR870271.1/1078161-1078576 AUAUCACAGAGAUG-UGAUAGAUA-----UUG--AUAA--A-------GCUUUUUGAAAACUAA----------------------------UUGGAUUGUAGCUA-----------CG---AUGAGCUUUUCA---------AUUUUCCAACAAU-GAUUGUAGUAAGUUGUUGGAGCUGUA----UA---UUCUCAAUAAUA---GAAGUUA------------UUCAUU----CUUAACUA--UGUUUUCUUCGUUAAAUUGAU-UAAUUAUUGUUAAGCCAUCCCAACUUAAUGAUAAUUGAUGAAU-----------UG-CU-AA-CA--------UU-GA--GUUG----UGUAGGGCUCAAUGUAGAUAAUUACGCUUAG------CUA--CU---------------UAA---CUGUAGAAGGUAA----UU----------AUU--AUACUAGUG---UUA----CUCUAGUCA----GAA-GAUUUUCAUAAUUAAUAACAUCCCCAA--AUUAUUAUUGAAAA--UAACUGUAAA-AACAUUCCCUUAAUAAGCG-A-----AAAAAGUCGUGAGUCACUCCCAAACUCACGACUUU
CP002439.1/1771321-1770954 AGCUUACA-UGA-C-UAAGGGAG-------CA--ACAA--UCUAUUGGAGUCUUUGAUUUUAUU----------------------------UAUAAUUUAAGGA---GGUGCUC--AC---UAUGGCAGCAGAUAUCAUUAGCACAAUCGUUGAAUUUGUUAAACUUAUCGCAGAAACAGUAGAAAAA-UUUAUCAAAAAAUAAGAU------UU-GAUAAA--AGUAUUUGUUAGA-----AUCUUUUU-------------------------------CCUUACUUA----------------GACU-----------------AA---------AGUA-AA--AUCA---------GGUUU--------CGAUAUUGA----------------A-----------------G---CCAUUGUA-----GCAAUAUUUAAU-A--AUC--GGUA---------AAUU-------CACU----AAAU-UUUUUCAUAAUUAAUAACAUCCCCAA----UUAAAUAGAAUAACUGU-AAAUAA-AACAUUCCCUUAAUAUG--AAGA-------ACAGGCGAGUCCCUCCCAAGCUCGUCUGUUC
AP008934.1/875378-875797   UCUUCGUAUAGUUG-UUAUAGUUA-CACAAUU--AGUA--CUCGUUUUUUCAAUUAA-----------------------------------UUGAUUACAAACAAGAGGAGGCUGAUG--UAGUGACAAACCAUUUCUCAGCAGUAAUUAGUGAUUUCGUAAAAUAAUACUUUCAGGUA-----CACAACGCGCUUAAGCAAA----------------------UUAAGC-----------AAUCCCUAAUUUGAAU-----------------------------------------------------------------------------------U-UG-UAGAACAUUCCCAGUCUCAAUUCAAAUAUCAUUUUAACAUUGUCUAUAA--CA--------GAGACAAUUAAAGUUUUAACAUGUAAGCUAUCGUAAAC-AUCAUU-CAAUUUAUCAUUUUAAAU--CGGUAAAUUC-ACUAAAUUUUUUCAUAAUUAAUAACAUCCCCAA--AAAUAGAUAGAGAAAUAAC-UGUAAA-AACAUUCCCUUAAUAAU--AAGUU-ACAAAAACCGUGAGUCCCUCCCAAGCUCACGGUUUU
AP006716.1/1005297-1005707 UUGAGUUAA--AUA-AUUUUGUUU-GUAGUUG--CGAA----------AUUAUUGACACCUUUA-----------------------------CC---AUAUGUUGUAAGUGUUA--UU---AAUGGUU-AUGAAACCAUUGCAAU-AGUAGUAAUGU---CCCAUUGGUUAUUAUUACUAAAGUG----ACUUCUUGUUUAUAUGAAGU----------UUC--UUACUUUG--------UUUUCUUCGUGUAGUUAAAAGAGU------UAAUUAAUAAGCCAUCCCAACUUAUUAAUUA-ACAAAGUAAA--------GUUACU-GA-AGUUUAAACUCA-GU--GGAAAGUGU----UUAACUUAGCUAU----------UGUAAGAUAUAG--AA---------GUUAAAUAU---UUUCAGGAUGUAAGCUAUAG--------------U--------------------------A----AAAUU---UUCAUAAUUAAUAACAUCCCCAA--A---AGAUUGAA---AUAA-CUGUAAAAACAUUCCCUUAAUAUG--AA---------AGUCGCGAGUUCCUCCCAAGCUCGUGACUUU
#=GC SS_cons               ::<<<<<<____>>.>>>>,,,,,.{{{{{{{..,,[[..[[[[[[[[,,,<<<<<<_______............................>>>>>>,,,,,,,,<<<<<<<<-..<<...__________>>->>>>>>>>,,,,,<<<<<<<<<_________>>->>>>>>>,,,,<<<<<____.>>>>>,,,,,,,,,,<<<-<<<<<......<<<.._______>>>--->>>>>>>>,,,,,((((((((,,,,,,.....,,,<<<<<<<<<_________>>>>>>>>>,,.,,,,,<<<--........-<<___.__.>>------>>>,.<<..<<<__________>>>>>)))))))),,,,,,,,,,<<<<<<<<____..__.........>>>>>>>>,...,,,<<<<______>>>>,,,]]]]].]]]-]].,,<<<<<<<<..._____..>>>>>>>>,,.,,,,,,<<<<<<<<--<<<-<<___________..__>>->>>>>>>>>>>}}}.}}}}--.-----------------..-----..----<<<<<<<<<<_________>>>>>>>>>>::
#=GC RF                    auaucacagaGAug.ugauuGaaa.cuaGuUa..AugA..guuguUuaauuuuuggAauauUuA............................UccaaaauAaGgaAggaguGauu..uc...AAUGGCagaagaUauCauuucaAcAAucggugAccUaGUaAAAUggaUcaucgauACagugaaaAaA.uucacUaAAuAAUAaGaugagcga......uac..uUUcaUUguaAcuucgcuauCUUcuUguagcacuAAaAgu.....ugAgUuauUaAGCCAUCCCAACUuAauaAcua.uuAAuacuAa........GuGAcu.AA.CaUUUacuaguA.ga..gucauuUUCCUuGgacucagugcuacuuAUUaUUaUuaguuaccaUuA..uA.........gguaacuau...UUuuagcAUGUAAgcuaUcGuaAac.aacAUc.caauuUAucg...UAAaU..cgaUAaauuC.auaAAauUUUUUCaUAAUuAauAACAUCCCCAA..AAauAgAUuGAAAAAauAa.CuggAA.AACAUUCCCUUAAUAAu..AAGUU..aAaAagcCGuGAGcCcCUCCCAAgCUCaCGgcuUU
//
# STOCKHOLM 1.0

#=GF AC   RF00504
#=GF ID   Glycine
#=GF PI   gcvT
#=GF DE   Glycine riboswitch
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Barrick JE, Breaker RR
#=GF SS   Predicted; Barrick JE, Breaker RR
#=GF GA   32.00
#=GF TC   32.00
#=GF NC   31.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0006545; glycine biosynthetic process;
#=GF RN   [1]
#=GF RM   15472076
#=GF RT   A glycine-dependent riboswitch that uses cooperative binding to control
#=GF RT   gene expression.
#=GF RA   Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR
#=GF RL   Science 2004;306:275-279.
#=GF RN   [2]
#=GF RM   29089431
#=GF RT   In Vivo Behavior of the Tandem Glycine Riboswitch in Bacillus subtilis.
#=GF RA   Babina AM, Lea NE, Meyer MM
#=GF RL   MBio. 2017; [Epub ahead of print]
#=GF CC   This family represents the bacterial glycine riboswitch. Glycine
#=GF CC   riboswitches usually consist of two metabolite-binding aptamers domains
#=GF CC   with similar structures in tandem. The aptamers cooperatively bind glycine
#=GF CC   to regulate the expression of downstream genes. In Bacillus subtilis, this
#=GF CC   riboswitch is found upstream of the gcvT operon which controls glycine
#=GF CC   degradation. It is thought that when glycine is in excess it will bind to
#=GF CC   both aptamers to activate these genes and facilitate glycine degradation
#=GF CC   [1].Â In vivo experiments demonstrated that glycine does not need to bind
#=GF CC   both aptamers for regulation. Mutation to the first aptamer caused
#=GF CC   greatest reduction in downstream gene expression, while mutation to the
#=GF CC   second one had varying effects. Glycine-induced expression of the gcvT
#=GF CC   operon is needed for B. subtilise growth, swarming motility and biofilm
#=GF CC   formation (in high glycine enviroment).[2]
#=GF WK   Glycine_riboswitch
#=GF SQ   44


AL766849.1/65640-65772     AGACGGACUU-CUGGAGAGACCUA----------------UAAGUAGCAACAUCUUUGUAUUGACACCAAGAUGUGCUCUAGG-CGCCGAAGGGGCAA-GAAGAGUAAAACAA----------------------CUCC-------------------------UCCAAUCUCUCAGGC---------------AAAAG-GACAGAAGCUAAAAG
AL766849.1/65560-65639     UGACGUCAUU-CAGGAGAAGAAAG----------------UUAGA----------------------------------CUUU-CGCCGAAGGAAUUA----------------------------------------------------------------------CACUCUCAGGU--------GUCUUAAGACAG-GACUGAUUGAC----
CR522870.1/1448610-1448703 AUGAACAUAG-CAGGAGAGAUUUU----------------UCCCAUGGCAGUACGGAUGG-----------------GGAAGG-CACCGAAGAAGUAA----------------------------------------------------------------------AUCUUUCAGGU---------------CAAAG-GACUGCUAUGGGACG
CR522870.1/1448704-1448793 -----AGCCU-CUGGAGAGUCUC-----------------AUUAU-----------------------------------GGG-CACCGAAGGAGCAA-GCCAGCGUGUA-------------------------GCUG-------------------------GUGAACCUCUCAGGU---------------ACAAGGGACAGAGUGUAGCAG
BX842577.1/344356-344453   CGCUCUAGUG-CGGGAGAGUUCUGUGGCUG----------CCAGC--------------------------------UACGGA-CGCCGAAGGAGCAAUACCUC-------------------------------UCC--------------------------GUCAACCUCUCAGGC---------------ACCCG-GACCGCGCGAGACUA
BX842577.1/344457-344587   -----UGCCU-CUGGAAAGCGGUGGC--------------GACCCCUGGCGGUC-----------------------CUCACC-CGCCGAUGGGGAAA-GGCGAUU-----------------------------CACC-------UGACGGUGGACAGAGUCGCCGAAUCUCUCAGGCGCCUGGCGUGCAGGU--GAA-GACAGAGGGAGAGGG
AL939108.1/255539-255444   UGACCCCGCG-CGGGAGAGUCCUCCGGAC-----------AUCAC--------------------------------CGGAGG-CGCCGAAGGAGCAA-AUCCU-------------------------------CCCC-------------------------GG-AAUCUCUCAGGC---------------UCACG-UACCGCACGGACGAG
AL939108.1/255442-255325   -----UCACU-CUGGAAAGCAGGGCGGGU-----------GUCGACGGCUUC-------------------------CGCUCU-CACCGACGGUGAAA-GCCGGGCAGAGC------------------------UCCA--------------GGGCUCGCCCGGUGAAGCUCUCAGGU--------------UGAGAU-GACAGAGGGGGAGGC
AE000516.2/79275-79185     UGACGCGAUG-UGGGAGAA-CCUCC---------------AUGUC----------------------------------GAGG-CGCCGUAGGAGCAA-UCUCCU------------------------------CCCC-------------------------GAGAAUCUCUCAGGC---------------CCAAG-CACCACACCGCCGAG
AE017355.1/2242861-2242742 GGACGAAUCU-CUGGAGAGACUCCCUCUCGCU--------UUAAAUAGCGUAGAGGAA-------------------AACGAG-CACCGAAGGAGCAAAUCCGC-------------------------------UACU-------------------AUAGCGGAUAAUCUCUCAGGU---------------AAAAG-GACAGAGACAAGCGA
AE017355.1/2242962-2242862 AUGAACCAUU-CAGGAGAA-GGUC----------------UAUU-----------------------------------GAUC-UACCGACGGGGCAA-AAAGUUGUUAACC-----------------------GACU-------------------------UUGAAACUCUCAGGU--------CUUGUUUACAAG-UA--GAACUGCAUGG
AL596168.1/161626-161717   GUGAAUGUAA-ACAGAGAGACUG-----------------UGAAA--------------------------------AG-CAG-CGCCGACGGGGAAA-GCAUAAG-----------------------------UUAU-------------------------GUGAAACUCUCAGGC---------------AAAAG-GAUGUUUACGGGACG
BX640445.1/160210-160126   ACGUGCAGUU-CGGGAGAGACCGU----------------CCAGC--------------------------------GGACGG-CGCCGACGGAGCAA-CCA---------------------------------CCCC-------------------------GG-AAACUCUCAGGC---------------AAAAG-GACCGACCUGC----
BX640445.1/160122-160016   -----AACAU-CUGGAGAGUGGCGCGCG------------GUAC---------------------------------GGCGCC-CACCGAAGGGGAU--CCCUG-------------------------------GCGC-------GUUUGCAGCGGCGCACGGGUGAAGCUCUCAGGU---------------AAAUG-GACAGAUGGGGUUGC
D84432.1/169999-170100     AUGACAGCAA-GGGGAGAGACCUGACC-------------GAAAACCUCGGGA------------------------UACAGG-CGCCGAAGGAGCAA-ACU---------------------------------GCGG------------------------AGUGAAUCUCUCAGGC---------------AAAAG-AACUCUUGCUCGACG
BX640439.1/206443-206535   ACGCAUGUCG-CGGGAGAGAGCGGCCG-------------AUUGC--------------------------------GGCUGC-CGCCGAAGGCGCAA-UUC---------------------------------GCCC-------------------------GG-AAUCGCUCAGGU--------------AACCCA-UACCGCGACUGCAUC
AL591978.1/212840-212931   GUGAAUGUAA-GCAGAGAGACUGC----------------GAAAA----------------------------------GCAG-CGCCGACGGGGAAA-GCAUA-------------------------------UAUU-----------------------AUGUGAAACUCUCAGGC---------------AAAAG-GAUGUUUACGGGACG
CR543861.1/1990167-1990077 AUGAUUAUUG-CAGGAGAGAUAUUCU--------------UGCAA--------------------------------AGGAUA-CGCCGAAGGAGCAA-CG----------------------------------ACCC-------------------------CGGAAACUCUCAGGC---------------AGAAG-GACUGUAAUAAUCGA
CR543861.1/1990073-1989965 -----AUAAU-CUGGAGAGAAGUAUU--------------UCAAA--------------------------------AAUACU-CACCGAAGGGGAUG-GUACG-------------------------------UAGA-----UUUAUGGAAAUCUAUAGCUACCGAAGCUCUCAGGU---------------ACCCU-GACAGAUGGGGCAAC
CR378670.1/15794-15904     -----AGCCU-CUGGAGAGACCCG----------------UUAAA---------------------------------UCGGG-CGCCGAAGGAGCAA-GCUUU-------------------------------CCUUUUUGCUGUUUUAACAUGCAUGGAAAGUGAAACUCUCAGGC---------------AAAAG-GACAGAGGAGAUAAG
AJ312125.1/453-315         AGACGAUACU-CUGGAGAGACCA-----------------UAUA------------------------------------AGG-CACCGAAGGAGCAA-AUUUAAUUGAGAUCUUUAUAUAAAUAAAAAAGCUCAUCCC----UUUUUUAGAUCAAGCGAUUAAAUGAAUCUCUCAGGU---------------AAAAG-GACAGAGAACUGAAU
AJ312125.1/523-454         AUGAAGGUGG-CAGGAGAGACCC------------------AUGA---------------------------------G-GGG-CGCCGAAGAAGUAA----------------------------------------------------------------------AGCUUUCAGGC--------------U--UAG-GACUGUCAUCA----
AL939123.1/278145-278052   UGAAUCCGCG-CGGGAGAGUCCCCGG---------------CCGCG-------------------------------CCGGGG-CGCCGAAGGAGCAA-GUCCC-------------------------------UCCC-------------------------UUGAAUCUCUCAGGC---------------ACCGU-UACCGCGCGGGCGAG
AL939123.1/278050-277936   -----CACAU-CUGAAAAGCGGACCGCC------------CCCGACGG-----------------------------CGGUCC-CACCCAAGGUGCAA-GCCCUGA-----------------------------UCGC-------CGUACUCCGGUGGCCGUGGCGAACCUCUCAGGU--------------UCCGAU-GACAGAUGGGGAGGA
AJ301559.2/6878-7012       UUCGACAACU-CUGGAAAGUGGUGGGA-------------GCACC----------------------------------CACC-CGCCCAAGGGGAAA-GGUGCCGGU---------------------------GCGC--GCAUGUCAGCGCGCCGUGUUCUACCGAAUCUCUCAGGCGCACGCGUCAGCGAGCACAC-GACAGAGGGGGAGGA
AJ301559.2/6784-6876       CGCCUGCGCG---GGAGAGUUCCGAGGC------------AUCCAGU------------------------------CUCGGA-CGCCGAAGGAGCAAUACCUC-------------------------------CCC--------------------------GUCAAUCUCUCAGGC---------------ACACG-GAC---GCGUGUGGG
BX572605.1/160670-160756   CUAAGUCGCGUCGGGAGAGAUCGGCC--------------GCAA---------------------------------GGCCGG-CGCCGAAGGAGCAA-CCG---------------------------------CCCC-------------------------GG-AAACUCUCAGGC---------------AAACG-GACCGCGCGGC----
BX572605.1/160757-160849   CGACUGACAU-CUGGAAAGAGACCCUGCCGGGC-------GAUCCCGGGA---------------------------CGGGUC-CGCCGACGGGAUAA----------------------------------------------------------------------UGCUCUCAGGC---------------ACAGC-GACAGAUGGGGCUCG
AE016822.1/1714518-1714420 GAGGCCGAUG-CGGGAGAGCUGCGGG--------------GGAGAACCCG---------------------------CCCGCGGCACCGAAGGAGCAA-UCCUC-------------------------------CCC--------------------------GACAAUCUCUCAGGU---------------ACGCG-UACCGCAUCGGACUG
BX897699.1/1435970-1435876 -----UUUUG-CGGGAGAGUGCAGGC--------------UGCAAGUUUUUGG------------------------GUCUGC-CGCCGAAGGGGAAA-AUA---------------------------------GCCC-------------------------GU-AAUCUCUCAGGC------------UCU--AAG-GACCGUAAAAGAAGA
BX897699.1/1435871-1435783 -----CAGAU-CUGGAAAGUCGG-----------------GAGG---------------------------------GG-CCG-CGCCGAAGGUGUAA-GCGAA-------------------------------AACU-------------------UUUUUCGCGAGUCUCUCAGGU--------------U--UGU-AACAGAGGGGUGCAG
BX950851.1/2645129-2645034 UUGAAGCCAA-CUGGAGAGAGGUUGC--------------GAUGC----------------------------------AACC-CACCGAAGGGGCAA-GCAGC-------------------------------UCUG---------------------CUGCGU-AAACUCUCAGGU--------------AAAGCG-GACAGAGGGAGUGGC
BX950851.1/2645260-2645133 CCGCUCCUCG-CAGGAGAGAGGGCGUGUACUCCAGCAUACUUCAAGCUACAUGUACGUUGGCAUAAAGUAUA-----ACGCUC-CGCCGAAGGCGCAA-AC----------------------------------UCCC-------------------------AU-AAUCGCUCAGGC--------------UACCCU-AACUGCGAAUU----
AE008691.1/313165-313055   AUGAAGAUAG-CGAGAGAUUAUCUUCC-------------AUAAAUG------------------------------GAAGAU-AGCCGAAGGGGAAA-UACAAAG-----------------------------GCCC-------------GCCAAGCCUUUGUAGAAGCUCUCAGGC---------------GGCAG-GAUCGCUAUCGGAUA
AE008691.1/1826306-1826220 -----AUAUC-CCGGAAAG-CCUC----------------UAAA-----------------------------------GAGG-CACCGAAGGAGCAA-UUCUUCUAU---------------------------AAAG-------------------------AAGAAUCUCUCAGGU---------------AAACA-GACGGGGGAAUAAAA
AE008923.1/1392465-1392356 -----CAACU-CUGGAGAGACCGGCC--------------GAUG-----------------------------------CCGG-CGCCGAAGGGGCAC-GAAACGCAGGCAG-----------------------GCCA---------CGCGCCAGGCCGCGUUUUUAAACUCUCAGGC---------------AAAAG-GACAGAGGGGCGCGA
AL591688.1/1674990-1674906 CGACCUCGUU--GGGAGAAACCGG----------------UUCGA---------------------------------UCCGG-UGCCGAAGGAGCAA-CCG---------------------------------CCCC-------------------------GG-AAACUCUCAGGC---------------CAAAG-GACC-AGCAAGGUG-
AE014292.2/713320-713218   UAAGACAACU-CUGGAAAGUCGGGGG---------------CAAC----------------------------------UCCG-CGCCGAAGGUGUAA-GUAUGGCUUUAUAUAUA-------------------GCCA------------------------UGCGAGUCUCUCAGGC--------------C--UGA-GACAGAGGGGCACGA
AE004439.1/116056-116172   -----AACCC-UUGGAGAGAGCCG----------------UUAUAUUAAAAAGAGAUAA------------------AACGGC-CGCCGAAGGCGCAA-AAAGA-------------------------------GCGG---------UUAAUUUUUCCGUUUUUUCAAACGCUCAGGC---------------AAAAG-GACAGGGGCAACAAG
AE008691.1/1826408-1826312 AUGAAGAAUG-CGGGAGAGACCC-----------------UAACC-----------------------------------GGG-CGCCGAAGGAGCAA-GCGGGUAUAUGGCCUGUAU-----------------ACUC-------------------------GUGAAACUCUCAGGC---------------AAAAG-GACCGCAUUC-----
BX842572.1/79202-79095     -----CAACU-CUGGAGACAGGGACG--------------GUCGCACCGACC-------------------------GUGCCU-GACCGAAGGUGUAGAGCGGC-------------------------------GCCA-------------UGAUGCGACGCCGC-AGACUCUCAGGU---------------UUCAG-GACAGAGCGGGGAGG
AE008922.1/1299977-1299896 GUAACACGGU--GGGAGAA-GCGGC---------------ACUG-----------------------------------CCGC-UGCCGAAGGCGCAA-CA----------------------------------GCCC--------------------------GUAAUCGCUCAGGC--------------C--CGA-UACC-AUCUUCAACA
CP000919.1/381215-381303   GGACGGAACU-CUGGAGAGACC------------------GUAAA------------------------------------GG-CACCGAAGGGGCAA-GGCAG-------------------------------GCAA----------------------CUGCUCAAACUCUCAGGU---------------AAAAG-GACAGAGCUAGGAUA
CP000262.1/1070832-1070913 UGAUGUCAUG-CAGGAGA--AGAA----------------UUUA-----------------------------------UUUU-CGCCGAAGGAGUUA----------------------------------------------------------------------UACUCUCAGGU---GUUCAGUUUUUGAACGG-GACUGUUUGAU----
#=GC SS_cons               :::::(((((.(((,,,,,,<<<<__.............._____................................__>>>>.,<<<<<--<<<---.<<___...............................____.........................>>---->>>>>->>>...............,,,,,.,,)))))))):::::
#=GC RF                    auacaccccu.CuGGAGAGacccggu..............uuaaa................................aucggg.CGCCGAAGGaGcAA.gcaua...............................uCcc.........................gcgAAuCuCUCAGGC...............AaaAg.GACaGagggggaaag
//
# STOCKHOLM 1.0

#=GF AC   RF00505
#=GF ID   RydC
#=GF DE   RydC RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15618228
#=GF SS   Published; PMID:15618228
#=GF GA   45.00
#=GF TC   45.80
#=GF NC   30.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   15618228
#=GF RT   A small bacterial RNA regulates a putative ABC transporter.
#=GF RA   Antal M, Bordeau V, Douchin V, Felden B
#=GF RL   J Biol Chem. 2005;280:7901-7908.
#=GF CC   This family represents a bacterial non-coding RNA called RydC. RydC is
#=GF CC   thought to regulate an mRNA, yejABEF which encodes an ABC transporter
#=GF CC   protein. RydC is known to bind the protein Hfq which causes a
#=GF CC   conformational change in the RNA molecule. The Hfq/RydC complex is then
#=GF CC   thought to bind to the target mRNA and induce its degradation [1].
#=GF WK   RydC_RNA
#=GF SQ   5


U00096.2/1489530-1489467   CUUCCGAUGUAGACCCGU-AUUCUUCGCCUGUACCACGGGUC-GGUUUUAGUACAGGCGUUUUCUU
AL627270.1/77020-76955     CUUCCGAUGUAGACCCGUCCUCCUUCGCCUGCGUCACGGGUCCUGGUUAGACGCAGGCGUUUUCUG
CP000038.1/1826318-1826381 CUUCCGAUGUAGACCCGU-AUUCUUCGCCUGUACCACGGGUC-GGUUUUAGUACAGGCAUUUUCUU
CU928161.2/1508420-1508357 CUUCCGAUGUAGGCCCGU-AUUCUUCGCCUGUACCACGGGUC-GGUUUUAGUACAGGCGUUUUCUU
CP001113.1/1726026-1726091 CUUCCGAUGUAGACCCGUCCUCCUUCGCCUGCGUCACGGGUCUUGGUUAGACGCAGGCGUUUUCUG
#=GC SS_cons               :::::::::::<<<<<<<.______AAAAAAAAA_>>>>>>>.:::::::aaaaaaaaa:::::::
#=GC RF                    CUUCCGAUGUAGaCCCGU.aUuCUUCGCCUGuacCACGGGuC.gGuUUuaguaCAGGCGUUUUCUu
//
# STOCKHOLM 1.0

#=GF AC   RF00506
#=GF ID   Thr_leader
#=GF DE   Threonine operon leader
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:6186194
#=GF GA   55.00
#=GF TC   56.50
#=GF NC   54.80
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0009088; threonine biosynthetic process;
#=GF RN   [1]
#=GF RM   6186194
#=GF RT   Attenuation in amino acid biosynthetic operons.
#=GF RA   Kolter R, Yanofsky C
#=GF RL   Annu Rev Genet 1982;16:113-134.
#=GF CC   At least 6 amino acid operons are known to be regulated by attenuation
#=GF CC   [1]. In each a leader sequence of 150-200 bp is found upstream of the
#=GF CC   first gene in the operon. This leader sequence can assume two different
#=GF CC   secondary structures known as the terminator and the anti-terminator
#=GF CC   structure. In each case the leader also codes for very short peptide
#=GF CC   sequence that is rich in the end product amino acid of the operon. The
#=GF CC   terminator structure is recognised as a termination signal for RNA
#=GF CC   polymerase and the operon is not transcribed. This structure forms when
#=GF CC   the cell has an excess of the regulatory amino acid and ribosome movement
#=GF CC   over the leader transcript is not impeded [1]. When there is a deficiency
#=GF CC   of the charged tRNA of the regulatory amino acid the ribosome translating
#=GF CC   the leader peptide stalls and the antiterminator structure can form. This
#=GF CC   allows RNA polymerase to transcribe the operon [1]. In the Rfam alignment
#=GF CC   the consensus structure is of the terminator. The alternative consensus
#=GF CC   structure is the antiterminator structure.
#=GF WK   Threonine_operon_leader
#=GF SQ   25


M10393.1/122-16              -CACC-------ACCAUUACCACCA---CCAUCACCAU------UACC------ACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGCAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
CR378664.1/249363-249488     UUAUC-------AGCACAACCACAA---CCACAACCAUUAUUAUUACUGGCACGAUUAUUCGUGUUGGUG-CGGGCUGAUACGCA-UAAGAUUC--UAAA-AAAAAGCCCGCA-CUUCUUAUUAGAUGCGGGCUUUUUUUUU
BX950851.1/4357430-4357315   CUAUC-------AGCCUAAUCACCACGAUUAUUACCAU------CACCGAUACAACC---AGUAACGGUG-CGGGCUGACGCAUA-CAAAGAUU-CCAG--AAAAAGCCCGCA-CCGA-A--CAG-UGCGGGCUUUUUUUUU
BX571860.1/286462-286580     UUAUC-------AGCCUGAAAACCACAAUGAUUACCAC------CACCGGGACCACA---GGUUGCGGGG-CGGGCUGACGCAUA-UAUAAAAC-AGAGA-AAAAAGCCCGCA-UCCAAAU-CAGAUGCGGGCUUUUUUUU-
U00096.2/184-310             ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
U14003.1/332669-332795       ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
V00360.1/26-152              ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
J01706.1/44-170              ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
AF487900.1/184-310           ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
M28570.1/169-295             ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
X68872.1/167-293             ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
X60821.1/811-927             AUAUC-------AGCCUGACUACCACAAUUAUUACCAC------CACCGAUACCACA---GGUAACGGGG-CGGGCUGACGCGCA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUAAU--CAG-UGCGGGCUUUUUUUU-
D10387.1/811-927             AUAUC-------AGCCUGACUACCACAAUUAUUACCAC------CACCGAUACCACA---GGUAACGGGG-CGGGCUGACGCGCA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUAAU--CAG-UGCGGGCUUUUUUUU-
D10386.1/76-192              AUAUC-------AGCCUGACUACCACAAUUAUUACCAC------CACCGAUACCACA---GGUAACGGGG-CGGGCUGACGCGCA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUAAU--CAG-UGCGGGCUUUUUUUU-
D10385.1/76-192              AUAUC-------AGCCUGACUACCACAAUUAUUACCAC------CACCGAUACCACA---GGUAACGGGG-CGGGCUGACGCGCA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUAAU--CAG-UGCGGGCUUUUUUUU-
AAYV01000002.1/459724-459606 ACAUC-------AGCCUGAACACAA---CGAUUAUUACCAC---CACCGAAACCACA---GGUUACGGGG-CGGGCUGACGCGUA-CAGGAAACAAUAGA-AAAAAGCCCGCA-CCUAGA--CAG-UGCGGGCUUUUUUUUU
AE005174.2/215-328           CCACC-------ACCAUCACCACCA---CCAUCACCAU------UACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUC
CP000653.1/632784-632902     GCGUU-------AGCACCACCACCA---UUACAACAACCAU---CAUCAUUACCACA---GGUAACGAUG-CGGGCUGACGCGUAACAGGAAAA-ACAGA-AAAAAGCCCGCA-CCUAAA--CAG-UGCGGGCUUUUUUUUC
AP008232.1/715571-715690     GCUUC-------AGCCACAGCACCA---UUAUUACCACCAC---CACCGAUACCACCACGGGUAGCGGCG-CGGGCUGACGCAUA-CAGGAAUC--CAGA-AAAAAGCCCGCA-CCUUGA--UAA-UGCGGGCUUUUUUUUA
CP000627.1/2075691-2075573   GCCUA-------AUCGUAAUGACCA---CCAUUAUUACCAU---UACCGACACGUCG---CAUGUUGGGG-CAGGCUGCUGAGCG-CAAAAUUU-CACAA-AAAAGGCCUGUA-UCCCAAC-CGA-UACAGGCCUUUUUUUA
CP000302.1/3285222-3285104   CUCAG-------AGUAUUACUCUUA---UCACCAUUACAAC---CACCACAAUCAAU---AUUGUGGGGG-CGGGCUAGCGCACC-UAAAAGAU-UUACAAAAAAAGCCCGCU-UCCCAC--UGA-AGCGGGCUUUUUUGUU
CP000746.1/858744-858862     CCGAC-------CGCACUUUUACCA---UGAUGACGAUUAC---CACCAUUAUGAC----CUUUAUAAUGGCGGGGUAGUGCGAA-CGAAAGAU-AUUCA-AUUAAGCCCGCAACCUGAA--AAG-UGCGGGCUUUUUUGCA
AAMK02000025.1/34036-34149   UGAAA-------CGCAUUAGCACCA---CCAUUACCAU------CACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
CP000826.1/750669-750787     AUAUC-------AGCCUGAACACAA---CAAUUAUUACCAC---CACCGAUACCACA---GGUAACGGGG-CGGGCUGACGCGUA-CAGGAAACAAAAGA-AAAAAGCCCGCA-CCUA-AC-CAG-UGCGGGCUUUUUUUUC
CP001235.1/2607111-2606993   GCCUA-------AUCGUAAUGACCA---CCAUUAUUACCAU---UACCGACACGUCG---CAUGUUGGGG-CAGGCUGCUGAGCG-CAAAAUUU-CACAA-AAAAGGCCUGUA-UCCCAAC-CGA-UACAGGCCUUUUUUUA
#=GC SS_cons                 :::<<.......<<<-<<<<<--<<...<<-<<<<<_____..._____________...>>>>>->>>>.--->>>>>->>>--.--->>---.--<<<.<<<<<<<<<<<<.<_____..__>.>>>>>>>>>>>>>>>:
#=GC RF                      acauc.......cGCaucAgcACca...ccAuuAccAccAc...CACCauuACcACa...ggUaacggug.CGGgcUgacGCguA.CAggaaAc.acagA.AAAAAGCCCGCa.cCUaaa..cAg.uGCGGGCUUUUUUuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00507
#=GF ID   Corona_FSE
#=GF DE   Coronavirus frameshifting stimulation element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15680415
#=GF SS   Published; PMID:15680415
#=GF GA   38.00
#=GF TC   38.60
#=GF NC   35.70
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   15680415
#=GF RT   Programmed ribosomal frameshifting in decoding the SARS-CoV genome.
#=GF RA   Baranov PV, Henderson CM, Anderson CB, Gesteland RF, Atkins JF, Howard MT
#=GF RL   Virology 2005;332:498-510.
#=GF CC   This family represents a conserved stem-loop found in Coronaviruses which
#=GF CC   can promote ribosomal frameshifting. This family interacts with a
#=GF CC   downstream region to form a pseudoknot structure, the region varies
#=GF CC   according to the virus but pseudoknot formation is known to stimulate
#=GF CC   frameshifting. In the classical situation a sequence 32nt downstream of
#=GF CC   the stem is complementary to part of the loop. In other Coronaviruses
#=GF CC   however, there is another stem loop structure around 150nt downstream that
#=GF CC   can interact with this family to form kissing stem loops and stimulate
#=GF CC   frameshifting [1].
#=GF WK   Coronavirus_frameshifting_stimulation_element
#=GF SQ   23


M22458.1/6906-6992     UGCAUCGAAGUUCCAGACC-CAACCGGGUCUGGAGCUUGGUUCUGCUAUUGGAUGUGAUCCUGAUGU-UCACUGGACCGC-UUUUGGUGU
AY700211.1/13603-13687 GGAUUCGGGGUACAAGUGUAAAUGCCCGUCUUGUACCCUG---UGCCAGUGGCUUGGACACUGAUGU-UCAAUUAAGGGC-AUUUGACAU
AF029248.1/13602-13686 GGGUUCGGGGUACAAGUGUAAAUGCCCGUCUUGUACCCUG---UGCCAGUGGCUUGGACACUGAUGU-UCAAUUAAGGGC-AUUUGACAU
M55148.1/13661-13745   GGGUUCGGGGUACAAGUGUAAAUGCCCGUCUUGUACCCUG---UGCCAGUGGCUUGGACACUGAUGU-UCAAUUAAGGGC-AUUUGAUAU
AY903459.1/13342-13426 GGGUUCGGGGUGCGAGUGUAGAUGCCCGUCUCGUACCCUG---CGCCAGUGGUUUAUCUACUGAUGU-ACAAUUAAGGGC-AUUUGAUAU
AY585229.1/13341-13425 GGGUUCGGGGUACGAGUGUAGAUGCCCGUCUCGUACCCUG---CGCCAGUGGUUUAUCUACUGAUGU-ACAAUUAAGGGC-AUUUGAUAU
AF391541.1/13342-13426 GGGUUCGGGGUACGAGUGUAGAUGCCCGUCUCGUACCCUG---UGCCAGUGGUUUAUCUACUGAUGU-ACAAUUAAGGGC-AUUUGAUAU
AY597011.2/13601-13685 GGGUUCGGGGUACUAGUGUGAAUGCCCGGCUAGUACCCUG---UGCUAGUGGUUUAUCUACUGAUGU-UCAAUUAAGGGC-AUUUGACAU
AY297028.1/13388-13471 GGGUUUGCGGUGUAAGU---GCAGCCCGUCUUACACCGUG---CGGCACAGGCACUAGUACUGAUGUCUGUCUACAGGGCAUUUUGAUAU
AY313906.1/13399-13480 GGGUUUGCGGUGUAAGU---GCAGCCCGUCUUACACCGUG---CGGCACAGGCACUAGUACUGAUGU-CGUCUACAGGAC-UUUUGAUAU
AY394996.1/13384-13465 GGGUUUGCGGUGUAAGU---GCAGCCCGUCUUACACCGUG---CGGCACAGGCACUAGUACUGAUGU-CGUCUACAGGGC-UUUUGAUAU
AY567487.2/12440-12518 GAGCAAGGGGUUCUAGU---GCAGCUCGACUAGAACCCUG------CAAUGGCACGGACAUCGAUAA-GUGUGUUCGUGC-UUUUGACAU
AY518894.1/12426-12504 GAGCAAGGGGUUCUAGU---GCAGCUCGACUAGAACCCUG------UAAUGGCACGGACAUCGAUAA-GUGUGUUCGUGC-UUUUGACAU
X69721.1/12521-12599   GAGUCCGGGGCUCUAGU---GCCGCUCGACUAGAGCCCUG------UAAUGGUACAGACAUAGAUUA-CUGUGUCCGUGC-AUUUGACGU
AJ011482.1/2289-2367   GAGUGCGGGGUUCUAGU---GCAGCUCGACUAGAACCCUG------CAAUGGUACUGAUCCAGACCA-UGUUAGUAGAGC-UUUUGACAU
DQ010921.1/12180-12258 GAGUGCGGGGUUCUAGU---GCAGCUCGACUAGAACCCUG------UAAUGGUACUGAUCCAGACCA-UGUUAGUAGAGC-UUUUGACAU
AF353511.1/12621-12699 GAGUACGGGGCUCUAGU---GCAGCUCGACUAGAGCCCUG------UAAUGGUACUGAUACACAACA-UGUGUAUCGUGC-UUUUGACAU
AY851295.1/12361-12442 GGGUACGGGGUAGCAGU---GAGGCUCGGCUGAUACCCCU---AGCUAAUGGAUGUGACCCCGAUGU-UGUAAAGCGAGC-CUUUGAUGU
AY641576.1/12298-12379 GGGUACGGGGUAGCAGU---GAGGCUCGGCUGAUACCCCU---UGCUAAUGGAUGUGACCCCGAUGU-UGUAAAGCGAGC-CUUUGAUGU
AY514485.1/12359-12440 GGGUACGGGGUAGCAGU---GAGGCUCGGCUGAUACCCCU---UGCUAAUGGAUGUGAUCCUGAUGU-UGUAAAGCGAGC-CUUUGAUGU
DQ001339.1/12352-12433 GGGUACGGGGUAGCAGU---GAGGCUCGGCUGAUACCCCU---UGCUAGUGGAUGUGAUCCUGAUGU-UGUAAAGCGAGC-CUUUGAUGU
AY646283.1/12211-12292 GGGUACGGGGUAGCAGU---GAGGCUCGGCUGAUACCCCU---UGCUAAUGGCUGUGAGCCUGAUGU-UGUUAAGCGAGC-CUUUGAUGU
AY319651.1/12392-12473 GGGUACGGGGUAACAGU---GAGGCUCGGCUGAUACCCCU---UGUUAAUGGUUGUGAACCUGAUGU-UGUAAAGCGAGC-CUUUGAUGU
#=GC SS_cons           ::::::<<<<<<<<<<<...AAAAAAAA>>>>>>>>>>>:...::::::::::::::::::::::::.:::::::aaaaa.aaa::::::
#=GC RF                GGGUuCgGGGUaccAGu...GaaGCuCGaCUgguACCCuG...UGcuAaUGGuucuGAuaCUGAUGU.UguauaaAGaGC.uUUUGAUAU
//
# STOCKHOLM 1.0

#=GF AC   RF00509
#=GF ID   snosnR64
#=GF DE   Small nucleolar RNA snR64
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   38.00
#=GF TC   43.20
#=GF NC   37.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00069
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science 1999;283:1168-1171.
#=GF CC   snR64 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1].
#=GF WK   Small_nucleolar_RNA_snR64
#=GF SQ   10


AF064276.1/1-101             UUG-UAUGAUGAGGAACCAGAUAGGGACAACAGAU--------UCUCAAGUGACGAGGAACAUCU-UUU-AAA-GCCCAGUUUUUAGUAGAGCUUAGGGCGCCUUUACUGACU
CR382122.1/1258384-1258281   UUUAGAUGAUGAGUAACCAGAUAGGGACAACAGAUAUUC----GUUUAAGUGACGAGGAAAGUCU-UUU-AAUUGCCCAGUUUUUAGUAGAGCUU-GGGCGCACU--CUGAUU
AAZN01000105.1/58834-58734   AUAUAAUGAUGAGGAACUAGAUAGGGACAACAGAAACUC----AGUUUAGUGACGAGGAAAGUCU-UUU-AAG-CCC--GUUUUUAGUAGAACUU-GGGCAUCUU--CUGAUU
AACI02000800.1/1219-1117     UUUGUAUGAUGAGUAACCAGAUAGGGACAACAGAU---U----UUUUAAUUGACGAGAAACAUCU-UUU-AAA-GCCCAGUUUUUAGUAGAGCUUAGGGCGCUUUUACUGACU
AACG02000104.1/23599-23701   UUUGAAUGAUGAGGAACCUGAUAGGGACAACAGAU--UC----UCGAAUGUGACGAGAAACA-UC-UUU-AUA-GCCCAGUUUUUAGUAGAGCUUAGGGCGCCUUUACUGACU
AACF01000028.1/29283-29178   UUUAUAUGAUGAGUAACCAGAUAGGGACAACAGAUCUCA----AUUGAAGUGACGAGGAAAGUCU-UAU-AAA-GUCCAGUUUUUAGUAGAGCUUCGGACGCCAAUUCUGAUA
AADM01000212.1/117541-117439 CUAAAGUGAUGAGGAACCAGAUAGGGACAACAGAC--UU----GUUUGAAUGACGAGGAAAGUCU-UUU-ACA-GCCCAGUUUUUAGUAGAGCUU-GGGCGCCAUACCUGAUA
AACE03000009.1/904058-903953 UUAGCAUGAUGAGUAACUAGAUAGGGACAACAGAUAUC-----CUUUAAGUGACGAGGAAAGUCUAUUU-AAAUGCCCAGUUUUUAGUAGAGCUU-GGGCGCAAAACCUGAUC
CR380957.2/32801-32910       UUUACAUGAUGAGGAACCAGAUAGGGACAACAGACCUCGAUUUUUUGGAAUGACGAGGAAAGUCU-UUUCAAU-GCCAAGUUUUUAGUAGAGCUUUUGGCGAUUU-CCUGAAC
AE016819.5/1223900-1223801   UCGAAAUGACGAGGAACCAGAUAGGGACAACAGAG--------GUCUCAGUGACGAGGAACAUCU-UUA-AAU-GCCCAGUUUUUAGUAGAGCUU-GGGCGCCUA-ACUGAUC
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::....::::::::::::::::::::::.:::.:::.:::::::::::::::::::::::::::::::::::::::
#=GC RF                      uUuaaAUGAUGAGgAACCAGAUAGGGACAACAGAuauuu....uuuuaAgUGACGAGGAAagUCU.UUU.Aaa.GCCCAGUUUUUAGUAGAGCUUaGGGCGccuuuaCUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF00510
#=GF ID   Tombus_IRE
#=GF DE   Tombusvirus internal replication element (IRE)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15795270
#=GF SS   Predicted; PFOLD
#=GF GA   45.00
#=GF TC   64.80
#=GF NC   33.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   15795270
#=GF RT   The p92 Polymerase Coding Region Contains an Internal RNA Element Required
#=GF RT   at an Early Step in Tombusvirus Genome Replication.
#=GF RA   Monkewich S, Lin HX, Fabian MR, Xu W, Na H, Ray D, Chernysheva OA, Nagy
#=GF RA   PD, White KA
#=GF RL   J Virol 2005;79:4848-4858.
#=GF CC   This family represents the Tombusvirus internal replication element (IRE)
#=GF CC   which is located within the region coding for p92 polymerase. The element
#=GF CC   is essential for viral replication and is thought to be required at an
#=GF CC   early stage of this process such as template recruitment and/or replicase
#=GF CC   complex assembly [1].
#=GF WK   Tombusvirus_internal_replication_element_(IRE)
#=GF **   This family overlaps with Rfam:RF00215 in the sequence M18056.1
#=GF SQ   23


AF266518.2/1229-1322 GGUAGUGGAAGAGGUCGGAACUGCCCACCGCCUUGGUUAUGACGGGUUUCUGUCAUACUAUAGCGGCGCGAAGUUGCGUACUUAUUCGAAUGCC
U16701.1/157-229     GGUCUCCGAGGAGGUCGGGGUUGCCCACCGUUUGAUC---------------------UACAACGGUGCGAAGCUCCGUACUUACACGCGGGCU
U16701.1/335-408     GGUCUCCGAGGAGGUCGGGGUUGCCCACCGUUUGAU--------------------ACUACAACGGUGCGAAGCUCCGUACUUACACGCAGGCU
M59043.1/235-328     GGUUUGUGAGGAGGUUGGAGUAGCCCACCGACUUGGGUAUGAUGGGUUUCUGUCAUACUACAGCGGUGCGAAACUCCGUACUUACACACGAGCC
AJ249740.1/1362-1455 AGUUUGUGAGAAGGUUGGGGUGGCCCACCGAUAUGGGUAUGAUGGUUUCCUGUCAUACUACAGUGGUGCGAAACUCCGUACUUACACACGAGCU
D00719.1/148-241     AGUUUGUGAGAAGGUUGGGGUGGCCCAUCGCUUAGGGUAUGACGGGUUCCUGUCAUACUACAGUGGUGCGAAACUCCGUACUUACACGCGAGCU
AF241533.1/150-240   GGUUUGUGAGAAGGUUGGGGUAG-CCACCGAUU-GGGUAUGAUGGGAUC-UGUCAUACUACAACGGUGCGAAACUCCGUACUUACACACGAGCC
U16705.1/328-414     GGUCUCCGAGGAGGUCGGGGUUGCCCACCG-UUUGGGUAUGAUG------UAUCAUACUACAACGGUGCGAAGCUCCGUACUUACACGCGGGCU
U16705.1/156-229     GGUCUCCGAGGAGGUCGGGGUUGCCCACCGUUUGAU--------------------ACUACAACGGUGCGAAGCUCCGUACUUACACGCGGGCU
M59047.1/249-342     GGUUUGUGAGAAGGUUGGGGUAGCCCACCGACUUGGGUAUGAUGGGUUUCUGUCAUACUACAGCGGUGCGAAACUCCGUACUUACACACGAGCC
U80935.1/1360-1453   GGUUUGUGAGAAGGUUGGGGUAGCCCACCGACUUGGGUAUGAUGGGUUUCUGUCAUACUACGACGGUGCGAAACUCCGUACUUACACACGAGCC
S64508.1/180-267     GGUCUGCGAGAAGGUCGGGGUUGCCCACCGUUUAGGGUAUGA----UUUA--UCAUACUACAGUGGUGCGAAGCUCUGUACUUACACGCGGGCU
U16698.1/157-246     GGUCUCCGAGGAGGUCGGGGUUGCCCACCG-UUUGGGUAUGAUGGAU--CUAUCAUACUACAC-GGUGCGAAGCUCCGUACUUACACGCGGGCU
AY100482.1/1360-1453 GGUUUGUGAGAAGGUCGGAGUUGCCCACCGUUUUGGGUAUGAUGGGUUUCUAUCAUACUACAACGGUGCGAAGCUGCGUACUUACACGCGAGCC
M59050.1/253-345     GGUUUGUGAGGAGGUUGGGGUAGCCCACCGACUUGGGUAUGAUGGGUUUCUGUCAUACUACA-CGGUGCGAAACUCCGUACUUACACACGAGCC
X62493.1/1373-1466   GGUUUGUGAGAAGGUUGGAGUUGCCCACCGGUUGGGGUAUGACGGUUUCCUGUCAUACUACAGCGGCGCGAAGCUCCGUACUUACACACGAGCU
M25270.1/1345-1438   GGUCUGCGAGAAGGUCGGGGUUGCCCACCGUUUGGGGUAUGAUGGAUUUCUAUCAUACUACAGUGGUGCGAAGCUCCGUACUUACACGCGGGCU
AJ607402.1/1372-1465 AGUCUGUGAGAAGGUUGGGGUGGCCCACCGACUUGGGUAUGAUGGAUUUCUGUCAUACUACAGCGGUGCGAAACUCCGUACUUACACACGGGCU
M18056.1/145-217     GGUUUGUGAGAAGGUUGGGGUAGCCCACCGACUGUCA---------------------UACAGCGGUGCGAAACUCCGUACUUACACACGAGCC
U16706.1/157-228     GGUCUCCGAGGAGGUCGGGGUUGCCCACCGUUUGAC----------------------UGCAACGGUGCGAAGCUCCGUACUUACACGCGGGCU
AY163842.1/1244-1337 UGUCUGUGAGAAGGUCGGAGUUUCCCAACGCUUGGGGUAUGACGGAUUUCUGUCAUACUACAGUGGGGCGAAAUUGCGCACUUACUCGCGGGCG
X85215.3/1373-1466   AGUUUGUGAGAAGGUUGGGGUCGCCCACCGACUUGGGUAUGAUGGAUUUCUGUCAUACUACAACGGUGCGAAACUCCGUACUUACACACGGGCU
GQ259478.1/1335-1428 AGUUUGUGAGAAGGUUGGAGUUGCCCACCGACUUGGGUAUGAUGGAUUUCUGUCAUACUACAACGGUGCGAAGCUCCGUACUUACACACGAGCU
#=GC SS_cons         <<<<<<<<--------<<<<<----<<<<<------<<<<<<<<<____>>>>>>>>>----->>>>>---->>>>>--------->>>>>>>>
#=GC RF              gGuccgcGAGaAGGUuGgaGcuGCCCaCCGauUuggguauGacgGaUUuCuguCauacUACAaCGGuGCGAAgCucCGUACUUACACgcgggCc
//
# STOCKHOLM 1.0

#=GF AC   RF00511
#=GF ID   IRES_KSHV
#=GF DE   Kaposi's sarcoma-associated herpesvirus internal ribosome entry site
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Published; 11160685, INFERNAL
#=GF SS   Published; PMID:11160685
#=GF GA   100.00
#=GF TC   317.10
#=GF NC   30.10
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11160685
#=GF RT   Kaposi's sarcoma-associated herpesvirus vCyclin open reading frame
#=GF RT   contains an internal ribosome entry site.
#=GF RA   Bieleski L, Talbot SJ
#=GF RL   J Virol 2001;75:1864-1869.
#=GF RN   [2]
#=GF RM   14993645
#=GF RT   A polypyrimidine tract facilitates the expression of Kaposi's
#=GF RT   sarcoma-associated herpesvirus vFLIP through an internal ribosome entry
#=GF RT   site.
#=GF RA   Bieleski L, Hindley C, Talbot SJ
#=GF RL   J Gen Virol 2004;85:615-620.
#=GF CC   This family represents the Kaposi's sarcoma-associated herpesvirus (KSHV)
#=GF CC   internal ribosome entry site (IRES) present in the vCyclin gene. The
#=GF CC   vCyclin and vFLIP coding sequences are present on a bicistronic transcript
#=GF CC   and it is thought the IRES may initiate translation of vFLIP from this
#=GF CC   bicistronic transcript [1,2].
#=GF WK   Kaposi's_sarcoma-associated_herpesvirus_internal_ribosome_entry_site_/
#=GF WK   (IRES)
#=GF SQ   5


AF148805.2/123462-123215 UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG
U40667.1/2005-2252       UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGGUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGGUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG
U79416.1/354-601         UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCGACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG
U93872.2/123729-123482   UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUAACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG
U75698.1/123214-122967   UUGCUAUGCCGCGGCAGACUCCUUUUCCCGCCAAGAACUUAUAGACCAGGAGAAAGAACUCCUUGAGAAGUUGGCGUGGCGAACAGAGGCAGUCUUAGCGACGGACGUCACUUCCUUCUUGUUACUUAAAUUGCUGGGGGGCUCCCAACACCUGGACUUUUGGCACCACGAGGUCAACACCCUGAUUACAAAAGCCUUAGUUGACCCAAAGACUGGCUCAUUGCCCGCCUCUAUUAUCAGCGCUGCAG
#=GC SS_cons             :::::::::<<<---<<<<<<<<<<---<<<<<--<<<<<-------<<<<<______>>>>>---->>>>>---->>>>>--->>>>>->>>>>-->>>,,<<<_______>>>-----------------((((((((((,,,<<<<----<<-<<<<<<------<<-<<<____>>>->>---->>>>>>>>--->>>>,,,,,,,,,,,<<<_____>>>,))))))-----)))):::::::
#=GC RF                  UUGCUAUGCCGCGGCaGaCuCCucuUCCCGCCaAGaaCuuAUAGACCaGGaGAAAGAACuCCuUGAGaaGuuGGCGuGGCGAACagaGGCaGuCuUAGCGACGGaCGUaACUuCCUUCUUGUUACUUAAAUUGcuGgGgGGCUCCCaaCACCUGGACuuuuGGCACCACgAGGuCaACaCCCcGAUUACaaaaGCCUUAGuuGACCCAAAGACUGGcUCAUUgCCCGCCcCcAUUAUCagCGCUGCAG
//
# STOCKHOLM 1.0

#=GF AC   RF00512
#=GF ID   Leu_leader
#=GF DE   Leucine operon leader
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:6186194
#=GF GA   50.00
#=GF TC   51.20
#=GF NC   47.40
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0009098; leucine biosynthetic process;
#=GF RN   [1]
#=GF RM   6186194
#=GF RT   Attenuation in amino acid biosynthetic operons.
#=GF RA   Kolter R, Yanofsky C
#=GF RL   Annu Rev Genet 1982;16:113-134.
#=GF CC   At least 6 amino acid operons are known to be regulated by attenuation
#=GF CC   [1]. In each a leader sequence of 150-200 bp is found upstream of the
#=GF CC   first gene in the operon. This leader sequence can assume two different
#=GF CC   secondary structures known as the terminator and the anti-terminator
#=GF CC   structure. In each case the leader also codes for very short peptide
#=GF CC   sequence that is rich in the end product amino acid of the operon. The
#=GF CC   terminator structure is recognised as a termination signal for RNA
#=GF CC   polymerase and the operon is not transcribed. This structure forms when
#=GF CC   the cell has an excess of the regulatory amino acid and ribosome movement
#=GF CC   over the leader transcript is not impeded [1]. When there is a deficiency
#=GF CC   of the charged tRNA of the regulatory amino acid the ribosome translating
#=GF CC   the leader peptide stalls and the antiterminator structure can form. This
#=GF CC   allows RNA polymerase to transcribe the operon [1]. In the Rfam alignment
#=GF CC   the consensus structure is of the terminator. The alternative consensus
#=GF CC   structure is the antiterminator structure.
#=GF WK   Leucine_operon_leader
#=GF SQ   6


M64039.1/2-149             CUGGAGCUGA--AUUA-AUGU---CACAUAUCGUUCGUUUCACUGGGCUACUACUACUCAACGCAUUUAUUGUGCGCGGUAGACCGGUGGGCGGCAUUCA--ACA-UUAAGUCAGCUCGAAGUCAAAC--AAAACCCGCGC--CGUUGCGCGGGUUUUUUU
CP000653.1/704557-704410   CUGGAGCAUG--AUUC-AUGA---UUCGUACCGUUCGUUCUCUCAGCCUACUACUACUAAACGCAUCUCUUUUGCGCGGUAGGCUGGCGAACGAAAUUCA--ACGUUGAAUCGU-CUCCAGUAAACAA--GAAACCCGCGC--CAUUGCGCGGGUUUUUUU
BX950851.1/4281970-4282116 CGAGACACGA--CACU-AUGUUCAAGUUUACUGUCC------UACUAAGCCUACUACUAAACGCAUCCUUCUUGCGCGGUAGGUUUGUGGGCAGACUUCAGAACU-AAGUUUCUCGCCACACGAUACA--AAAACCCGCGC--UGAUGCGCGGGUUUUUUU
AP008232.1/768795-768654   CAUAACUUAU--GUUC-A--A---GUCUAUCCGUCUACUAAGC-------CUACUACUACACGUAGAAUUGAUGCGCGGCAGGCUGGUGCACGGUAUUCA--GAACUGAAUUCGGGCCACUCCAGAUU--AAAACCCGCGCACUACUGCGCGGGUUUUUUU
AE009952.1/4041329-4041474 GAGAAGCUGAAAUUUAUGUUCUA-CUCAACCCGUCUACUAAGC-------CUACUACUUAACGCAUCUCUCUUGCGCGGUAUGUUGGUGGACGGAAAUCA--GAA-CUGAUUCAGCCAUCAAGAUUAA--CAAGCCCGCGC--AAAUGCGCGGUUUUUUUU
J01642.1/51-200            CUGGAGCUGA--UUUA-AUGA---CUCACAUCGUUCGCUUUAUCGGUCUACUACUACUAAACGCAUCUUCUUUGCGCGGUAGACGAGUGAGCGGCAUCCA--GCA-UUAAGCCAGCACGCAGUCAAACAAAAAACCCGCGC--CAUUGCGCGGGUUUUUUU
#=GC SS_cons               :::<-<<<<<..-<<<.<<<<...------<<<<<<<<<<-------------<<<<<---<<<<_______>>>>->>>>>-->>>>>>>>>>------..>>>.>>>>->>>>>->----------..<<<<<<<<<<<..____>>>>>>>>>>>:::
#=GC RF                    CuggAgcugg..uuuc.augc...cuCauacCGuccgcuaaauuagacuaCUAcUaCuaAACGCAUcuuUuuUGCGCgGuAggcuggcggaCGgaAUUCA..gca.ugaauccagcccacauuAaaaa..aAAacCCGCGC..uauUGCGCGGguUUuUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00513
#=GF ID   Trp_leader
#=GF DE   Tryptophan operon leader
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:6186194
#=GF GA   41.00
#=GF TC   41.40
#=GF NC   40.80
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0031556; transcriptional attenuation by ribosome;
#=GF DR   GO; 0000162; tryptophan biosynthetic process;
#=GF RN   [1]
#=GF RM   6186194
#=GF RT   Attenuation in amino acid biosynthetic operons.
#=GF RA   Kolter R, Yanofsky C
#=GF RL   Annu Rev Genet 1982;16:113-134.
#=GF CC   At least 6 amino acid operons are known to be regulated by attenuation
#=GF CC   [1]. In each a leader sequence of 150-200 bp is found upstream of the
#=GF CC   first gene in the operon. This leader sequence can assume two different
#=GF CC   secondary structures known as the terminator and the anti-terminator
#=GF CC   structure. In each case the leader also codes for very short peptide
#=GF CC   sequence that is rich in the end product amino acid of the operon. The
#=GF CC   terminator structure is recognised as a termination signal for RNA
#=GF CC   polymerase and the operon is not transcribed. This structure forms when
#=GF CC   the cell has an excess of the regulatory amino acid and ribosome movement
#=GF CC   over the leader transcript is not impeded [1]. When there is a deficiency
#=GF CC   of the charged tRNA of the regulatory amino acid the ribosome translating
#=GF CC   the leader peptide stalls and the antiterminator structure can form. This
#=GF CC   allows RNA polymerase to transcribe the operon [1]. In the Rfam alignment
#=GF CC   the consensus structure is of the terminator structure.
#=GF WK   Tryptophan_operon_leader
#=GF SQ   22


J01557.1/117-211           CACGGUUGGUGG-CGCACUUCCUGAUUU-CGGGCAGUGUC--UUAC-------------------GUCCGCAAUAUG--CAACCAGAUA----CC--CGGCCCGCCAAA-UGAGCGGGCUUUUUUUU
BX950851.1/2602822-2602926 CAUGGUUGGUGG-CGCUCUUCCCUCUCG-CGGGUGGACUAA-UCACGCAU---------------CGCUGUUAUCACA-CAUGCAGAUAUUC-CC--AGGCCCGCUUAACUAAGCGGGCUUUUUAUU
M24960.1/62-157            CACGGUUGGUGG-CGCACUUCCUGAUAG-CGGGCGGUGUAU-GAAC-------------------AGCUGUAAUCAG--CCAAACGAUA----CC--CGGCCCGCCUGU-UAAGCGUGCGUUUUUUG
J01739.1/99-194            CACAGCUGGUGG-CGCACCUCCUGACGA-CGGGCGGCGUGA-UCGCGU------------------UUUGCAUUCAG--CAUACAGAUA----CC--CGGCCCGCCAA--UGAGCGGGCUUUUUAUU
X17149.1/292-395           CUUGCUUGGUGG-CGCACUUGGACAAG--UUCUUGGUGG-G-CUAACGUGUACUUCUA-------GUUUAGAAAAAC--AAACGUCAUA--------AAGCCCGCUACU-CAAGCGGGCUUUUUAUU
BX571867.1/113873-113973   AUCCGUUGGUGG-CAUAACUUCCCAGUA-AGGGCGGUAUGG-UCACGCAC---------------AUAAAUCAACAG--UGCCAAAUUA----CCA-AAACCCGCCUAA-UCAGCGGGUUUUUUUAU
M60741.1/37-130            AAAGGUUGGUGG-CGCACUUCCUGAAA--CGGGCAGUGUAU-UCACCA--------------------UGCGUAAAG--CAAUCAGAGA----CC--CAGCCCGCCUAA-UGAGCGGGCUUUUUUUU
M60742.1/36-129            AAAGGUUGGUGG-CGCACUUCCUGAAUU-CGGGCAGUGUAU-UCACCA--------------------UGCGA-GAG--UAGGGAACUG----CC--AGGAUCAAAGAU-AAAACGAAAGGCUCAGU
CP000720.1/2235898-2235999 CUGCGUUGGUGG-CAUAUCUCCCUCUCU-CGGGCGAUGUAA-UCACGCAU---------------AUCCGUCAUCAGACAGUGCAGAUU----GCUUCAGCCCGCUAA---UAGCGGGUUUUUUUAU
AAMR01000069.1/10988-11102 CUUAAUUGGUGG-CGCACUUGGACAAG--UUCUUGGUGGGC-UAACGUGUACUUCUAGUUAAACAGUUUGUUUAUAAA-AAAGUUAUCA----CU--AAGCCCGCUUUA-AUAGCGGGCUUUUUAAU
CP000653.1/2394233-2394327 CACGGUUGGUGG-CGCACUUCCUGAAUAUCGGGCAGUG----UCAUUC-----------------GUGUGCGUUACG--AAAACAGAUA----CC--UGGCCCGCGACU-AU-GCGGGCUUUUUUAU
AAPS01000055.1/16549-16446 CUUGCUUGGUGG-CGCACUUGGACUAG--UUCUUGGUGGGC-AAACGUAUACUUCUA--------GUUUAUAGAACC--AAACGUUGUA--------AAGCCCGCUACU-UAAGCGGGCUUUUUUGU
AM286415.1/2419797-2419898 CUGCGUUGGUGG-CACAUCUCCCUCUUC-CGGGCGGUGUAA-UCGCGCAU---------------AUCAGUCAUCAGACAGUGCAGAUU----GCUUCAGCCCGCUAA---UAGCGGGUUUUUUUAU
AAWP01000078.1/5392-5495   CUUGCUUGGUGG-CGCACUUGGACAAG--UUCUUGGUGGGC-AAACGUGUACUUC----------UAGUUUAGAGAA--UUAAAUGUCA----CA--AAGCCCGCUACC-UCAGCGGGCUUUUUGUU
AY027546.1/150-252         CACGGUUGGUGG-CGUACCUCCCUCUUG-CGGGCGGUGUAA-UCGCGCAU---------------AGCUGUCAUCUG--ACAAUGCAGAUUU-CC--UGGCCCGCACCU-GAUGCGGGCUUUUUUAU
AAOJ01000014.1/31576-31482 AAUAAUUGGUGGUGGCACU-CCUACUUA-CGGGCGGUGUGAAUAGCUG---------------------UAACUCAG--CAAAAUUGCA----AC--GAGCCCGCCAUC-AAUGCGGGCUUUUUUAU
CP000826.1/2936614-2936717 CUUCGUUGGUGG-CGUCACUCCCUUUUU-CGGGCGGAGUAA-UCACGCAU---------------ACCUGUCAUCUG--ACACUGCAGAUUCCCU--AAGCCCGCUGGU-AACGCGGGCUUUUUUAU
CP001233.1/1206524-1206422 CUGGCUUGGUGG-CGCACUUGGACAAG--UUCUUGGUGGGC-UCACGUGUAU-------------UUCUAAGUUUAGA-UACUCACACA----CC--UAGCCCGCCAACUUGAGCGGGCUUUUUAUU
FM200053.1/1217752-1217657 CACGGUUGGUGG-CGCACUUCCUGAUAG-CGGGCGGUGUAU-GAAC-------------------AGCUGUAAUCAG--CCAAACGAUA----CC--CGGCCCGCCUGU-UAAGCGGGCUUUUUUUU
BA000037.2/1235781-1235679 CUCGCUUGGUGG-CGCACUUGGACAAG--UUCUUGGUGGGC-UAACGUGUACUUUU---------AAUAAAGAAAAU--GAAUCACACA--------AAGCCCGCUAAC-CAUGCGGGCUUUUUAUU
AALF02000036.1/7566-7465   CUGCGUUGGUGG-CACAUCUCCCUCUCU-CGGGCGGUGUAA-UCACGCAU---------------AUCAGUCACCAGACAAUGCAGAUU----GCUUCAGCCCGCUAA---UAGCGGGCUUUUUUAU
AALD02000034.1/37477-37578 CUGCGUUGGUGG-CACAUCUCCCUCACU-CGGGCGGUGUAA-UCGCGCAUUCCA-----------GUCAUCAGACAG--UGCAGAUUGC----UU--CAGCCCGCGAA---UAGCGGGUUUUUUUAU
#=GC SS_cons               ::::::::<<<<.-<<<<<-<<<<____.>>>>->>>>>--.>>>>----...............------------..----------....--..-<<<<<<<<___._>->>>>>>>:::::::
#=GC RF                    CuuggUUGGUGg.CgCACcUcccgaauu.cgggCgGUGuaa.uCACGuaU...............aucUguaaucAG..aaaacagauA....CC..aaGCCCGCuaau.uaAGCGGGCuUUUUuaU
//
# STOCKHOLM 1.0

#=GF AC   RF00514
#=GF ID   His_leader
#=GF DE   Histidine operon leader
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:6186194
#=GF GA   49.00
#=GF TC   49.10
#=GF NC   48.90
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0000105; histidine biosynthetic process;
#=GF RN   [1]
#=GF RM   6186194
#=GF RT   Attenuation in amino acid biosynthetic operons.
#=GF RA   Kolter R, Yanofsky C
#=GF RL   Annu Rev Genet 1982;16:113-134.
#=GF CC   At least 6 amino acid operons are known to be regulated by attenuation
#=GF CC   [1]. In each a leader sequence of 150-200 bp is found upstream of the
#=GF CC   first gene in the operon. This leader sequence can assume two different
#=GF CC   secondary structures known as the terminator and the anti-terminator
#=GF CC   structure. In each case the leader also codes for very short peptide
#=GF CC   sequence that is rich in the end product amino acid of the operon. The
#=GF CC   terminator structure is recognised as a termination signal for RNA
#=GF CC   polymerase and the operon is not transcribed. This structure forms when
#=GF CC   the cell has an excess of the regulatory amino acid and ribosome movement
#=GF CC   over the leader transcript is not impeded [1]. When there is a deficiency
#=GF CC   of the charged tRNA of the regulatory amino acid the ribosome translating
#=GF CC   the leader peptide stalls and the antiterminator structure can form. This
#=GF CC   allows RNA polymerase to transcribe the operon [1]. In the Rfam alignment
#=GF CC   the consensus structure is of the terminator structure.
#=GF WK   Histidine_operon_leader
#=GF SQ   33


AF353562.1/601-464           UCAUCACCAU-CAUCACCCAGC-CUAG-UCUUUCGGGA--GAUGU-ACGCAUAC-CC---GGGAGAUAGGAA------ACUCCCGGAGGUGAAAA-----UCAAAGUGAAAACAGAUU---UU---AAACCCUCGGGAGACCAACAUCUCUCGAGGGUUUUU-UAG
V00285.1/27-149              CCAUCAUCAC-CAUCAUCCUGA-CUAG-UCUUUCAGGC--GAUGU-----GUGC-U----GGAAGACGUUCA----GAUCUUCCAG--------------UGG-UGCAUGAACGCAUG--AGA---AAGCCCCCGGAAGAUC---ACCUUCCGGGGGCUUUAU-AU
V00284.1/504-627             CCAUCAUCAC-CAUCAUCCUGA-CUAG-UCUUUCAGGC--GAUGU-----GUGC-U----GGAAGACAUUCA----GAUCUUCCAG--------------UGG-UGCAUGAACGCAUG--AGA---AAGCCCCCGGAAGAUC---ACCUUCCGGGGGCUUUUUAUU
AL627273.1/55225-55348       UAAACAUCAC-CAUCAUCCUGA-CUAG-UCUUUCAGGC--GAUGU-----GUGC-U----GGAAGACAUUCA----GAUCUUCCAG--------------UGG-UGCAUGAACGCAUG--AGA---AAGCCCCCGGAAGAUC---AUCUUCCGGGGGCUUUUUUUU
J01804.1/733-856             CCAUCAUCAC-CAUCAUCCUGA-CUAG-UCUUUCAGGC--GAUGU-----GUGC-U----GGAAGACAUUCA----GAUCUUCCAG--------------UGG-UGCAUGAACGCAUG--AGA---AAGCCCCCGGAAGAUC---AUCUUCCGGGGGCUUUUUUUU
K01997.1/133-253             CCAUCAUCAC-CAUCAUCCUGA-CUAG-UCUUUCAGGG--CAUGU-----GUGC-U----GGAAGACGUUUG----GAUCUUCCAG--------------UGG-UGCAUGAACGC-----AAA---GAGCCCCCGGAAGAUU---CGCUUCCGGGGGCUUUUUUUU
BX950851.1/2916213-2916334   CCAUCAUCAC-CAUCAUCCUGA-UUAG-UCUUUCGGAC-GGUUG------GUGC-U----GGAAGACGUUCA----GAUCUUCCAG--------------UGG-CGCA-GAACACAA---AGA---GAGCCCUCGGAAGAUC---AUCUUCCGAGGGUUUUUUUAU
BX571864.1/137183-137060     UUACCACCAU-CAUCAUCCUGA-UUAG-UCUUUCAGGC-GGUUGU-----GUGC-U----GGAAGACGUUUAACG-GGUCUUCCGG--------------UGG---CAUGAAUGCGAU--AAA---AACCCCCGGAAGGAUC-----CUUCCGGGGGUUUUUUUAU
CR378666.1/168502-168367     ACAUCACCAU-CAUCAUCCUGA-CUAG-UCUUUCGGGA-GGAUACGCCUCACUC-U----GGAAGACAACCAAAA-ACUCUUCCAGUGUU----------UGA-UAAAAUAAAGAAU----UC---AAACCCUCGGA-GAGCAA-CACUUCCGAGGGUUUUUUGCG
M10633.1/9-136               CCAUCAUCAC-CAUCAUCCUGA-CUAG-UCUUUCAGGC--GAUGU-----GUGC-U----GGAAGACAUUCA----GA---UCCAGUAAUGACCUCAGAACUC-CAUCUGGAUUUGUU---CA---GAACGCUCGGUUG--------CCGCCGGGCGUUUUU-UAU
ABCD01000002.1/201134-201005 CCAUCACCAC-CAUCAUCCUGA-CUAG-UCUUACAGGC-CGAUGU-----GUGC-U----GGAAGACGGUUAACG-AAUCUUCCAGGU------------GGC-GUAGAGAACGCAGU--AGA---GAGCCCUCGGAAGAUA---AUCUUCCGAGGGCUUUUUUAU
CP000627.1/725692-725825     UCAUCACCAU-CAUCAUCCCUAAGGUG-UCUUUCGGGA--GAUGU-ACGCAUAC-CC---GGGGGACAGGAA------UCUCCCGGAGUUGAAAUC----AGA-GCCAUAAAAAGAUU----C---UAACCCUCGGGAGACCAA-ACCUCCCGAGGGUU----UUU
AAPS01000015.1/61126-60990   UCAUCACCAU-CAUCACCCAAU-CUAG-UCUUUCGGGC--GAUGU-ACGCAUAC-CC---GGGAGGCAGGAA------ACUCCCGGAGGUAAAAU-----CAA-AGUAAAAGCAGAUU---UU---AAACCCUCGGGAGACUUCAAUCUCCCGAGGGUUUUU-UAG
AM286415.1/3001521-3001651   CCAUCAUCAC-CAUCAUCCUGA-CUAG-UCUUGCAGGC-CGAUGU-----GUGC-U----GGAAGACGGUUAACG-AAUCUUCCAGG-------------UGG-CGGUAGAACGCAAUAGAGA---AAGCCCUCGGAAGAUU---AUCUUCCGAGGGCUUUUUUGU
AAOJ01000004.1/310327-310192 UCAUAUUCAU-CAUCAUCCUGA-CUAG-UCUUUCGGGA-GGAUACGCCUCACCC-U----GGAAGACAACAU----UAUCUUCCAG--------------UGGUCACAAGGAAUAAUC--AAAUUCAGACCCUCGGAAGAUACA-AGCUUCCGAGGGUUUUUUAAU
ABCH01000038.1/25070-25203   UCAUCACCAU-CAUCACCCAGC-UUAA-UCUUUCGGGA--GAUGA-ACGCAUAC-CC---GAGAGAUAGGUA----AAACUCUCGGAGGUUCGAU-----UUA-AGAUUUAAAGAAUU--------AAACCCUCGGGAGACCAA-AGCUCCCGAGGGUUU---UUU
AAWQ01000036.1/24955-25092   UCAUCACCAU-CAUCACCCAGC-CUAG-UCUUUCGGGA--GAUGU-ACGCAUAC-CC---GGGAGGCAGGAA------ACUCCCGGAGGUGAAAAU----CAA-AGUAAGAACAGAUU---UU---AAACCCUCGGGAGACGCCAAUCUCUCGAGGGUUUUU-UAG
AP008232.1/1873732-1873609   CCAUCAUCGC-CAUCAUCCUGA-CUAG-UCUUUCAGGU--GAUGA-----GUGC-U----GGAAGACGCUUU----AAUCUUCCAG--------------UGG-CGCAAGAAUGUUCAG-AGA---GAGCCCUCGGAAGAUU----UCUUCCGAGGGCUUUUUGGC
AAPH01000008.1/132138-132003 ACAUCACCAU-CAUCAUCCUGA-CUAG-UCUUUCGGGA-GGAUACGCCUCACUC-U----GGAAGACAGCCAAAA-AAUCUUCCAGUGUU----------UGA-UAAAAUAAAGAAU----UC---AAACCCUCGGA-GAACAU-CACUUCCGAGGGUUUUUGCGU
AAZG01000003.1/177933-177812 CCAUCAUCAC-CAUUCAACUGA-AUAA-UCUUUCAGGU-UUUUGG----UGUGC-U----UGGAAGAUUU--------CUUCCGAGC-------------UGA-CAGGAUAAUAAAAA--UCU---UACCCCUCGGAAG-GC---AACUUUCGAGGGGUUUUGUUU
AASA01000085.1/5327-5205     UCACCACCACACUUUAACCUGA---UA-UCUUUCGGGCAUUUGGU-----GUGUGC----GGAAGAUAAC--------UCUUCCGAGC------------AAG-UGUAGCAAAUCAAU--AAA---GAUCUCUCGGAAG-GC---AACUUUCGAGAGAUUUUUUUA
AAMR01000029.1/7219-7354     UCAUCACCAU-CAUCACCCUAU-CUAG-UCUUUCGGGG-AGAUUU-ACGUAUAC-C----CGGGAGCAAGAA----UUCUCCCGGAGGUU----------AAG-UCAAAGAAUUUAGA--UUU---AAACCCUCGGGACGACAAAGUCUUCCGAGGGUUUUUUAGU
AAZE01000002.1/78509-78373   CCAUCAUCAC-CAC--ACCUGA-UUA--UCUUUCAGGC---GUGA-UUGUAUGU-UU---GGAAGAUAAUAAAA--UAUCUUCCGAGUGUAAUAAAA---AUC-AGUGUAAAAGCAAU--AAA---UACCCCUCGGAAG-GC---AAUUUUCGAGGGGUUUUCUUU
AAZW01000066.1/7603-7739     UCAUCACCAU-CAUCACCCUAU-CUAG-UCUUUCGGGG-AGAUUU-ACGUAUAC-C----CGGGAGCAAGAU----UACUCCCGGAGGUUA---------AGU-CAAAAGAAUUUAGA--UUU---AAACCCUCGGGAUGACAGAGUCUUCCGAGGGUUUUUUAGU
AAPG01000014.1/25546-25666   ACACCACCAU-CAUCAU-AUGA-CGUGAUCUUUCA--G--GAUCU----UGUUC-U----GGAAGAGUGUGA-----UUCUUCCAG--------------UGG-UUAUACAUCUAUCU--AAA---AAACCCCGGAAGGCAU----CCCUUCCGGGGUUUUUUUUA
ABCQ01000049.1/7613-7494     GCAUCACCAU-CAUCAUAUUUG-AUUA-GCUUUCAGGC-UGUUGA-----CUGG-A----GG--UGUAUGCA----CGCAAGCUUC-------------------CGGAACUCAUUUA--GAA---AAACCCUCGGAAGAUUU--AUCUUUCGGGGGUUUUUUCGU
CP000388.1/3492162-3492275   AAAACAUCAC-CAUCAUAUAGC-AUAA-CCUUUC---A--GGUUG-----GUGC-U----GGAAGGUCUAUUGA--UUCCUUCCUG--------------CGG-CGUAACGAUUAACU---------AGCCCUCGGAAG-GA---AACUUCCGGGGGUU----UUU
L42023.1/490465-490601       CCAUCAUCAC-CAC--ACCUGA-UUA--UCUUUCAGGC---GUGA-UUGUAUGU-UU---GGAAGAUAAUAAAA--UAUCUUCCGAGUGUAAUAAAA---AUC-AGUGUAAAAGCAAU--AAA---UACCCCUCGGAAG-GC---AAUUUUCGAGGGGUUUUCUUU
CP000510.1/2015450-2015329   AUCACUGCAC-CAUCAUAUUAU-CUAA-UCUUUCA--G--GAUCU----UAUUC-UU---GGGAGAAUUUUUGC--GUUCUUCCAG-------------------AGGUUACCAAUAA--AAU---AAACCCCCGGAAGUCC---GCCUCCCGAGGGUUUUUUAGU
CP001139.1/1153054-1153176   UCAUCACCAC-CAUCAUCCUGA-UUAG-UCUUUCGGGA-GGAUAC-----GUAU-UAUCCGGAAGGCAAUUUGAAUUUCCUUCCGA--------------UGA----AUAAAAAUUCU---------AACCCUCGGAAGGUCA--AACUUCUGAGGGUU----UUU
AE004439.1/1390138-1390265   --AUCACCAU-C--UACCCUGA-UUA--UCUUUCGGGU--AUUUU--GUGAUGC-U----UGGAAGAUAACAA---AUCUUCCGAGUGUG----------CGA-UAAAAUGACGAACA--AUA---UAAACCUCUCGGAAGCC--AUUUCGAGAGGUUUUUUUAUC
CP000826.1/1771603-1771477   CCAUCAUCAC-CAUCACCCUGA-CUAG-UCUUUCAGGC--GAUGU-----GUGC-U----GGAAGACGGUUUUUU-AAUCUUCCAG--------------UGGCGCGCAGAAUGCAAG--AGA---GAGCCCUCGGAAGAUU----UCUUCCGAGGGUUUUUUUUU
BA000037.2/1375659-1375794   UCAUCACCAU-CAUCACCCAGU-CUAG-UCUUUCGGGA--GAUGU-ACGCAUAC-CC---GGGAGAUAGGAA------ACUCCCGGAGGUGAAA------AUC-AUCAAAUUCAGAUU---UU---AAACCCUCGGGAGACCAACAUCUCUCGAGGGUUUUU-UAG
#=GC SS_cons                 :::::::<<<.<<<<--<<<<<.____.____>>>>>-..>>>>-....->>><.<....<<<<<<______....__>>>>>>>>--............---.--------------..<<<...<<<<<<<<<<<<<___...__>>>>>>>>>>>>>>>>:::
#=GC RF                      uCAUCAccAc.cAucAuCCuGa.cUAG.UCUUuCaGGa..gaUgu....ugUgc.u....GGaAGgcaauuA....uacCUuCCagag............uga.uauaaaAAcaaAuu..aaa...aAaCCCuCGGgaGAuc...AuCucCCGaGGGuUuuuuuuU
//
# STOCKHOLM 1.0

#=GF AC   RF00515
#=GF ID   PyrR
#=GF DE   PyrR binding site
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:11726695
#=GF GA   54.00
#=GF TC   54.00
#=GF NC   53.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.78 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0015855; pyrimidine nucleobase transport;
#=GF DR   GO; 0019856; pyrimidine nucleobase biosynthetic process;
#=GF RN   [1]
#=GF RM   11726695
#=GF RT   Molecular recognition of pyr mRNA by the Bacillus subtilis attenuation
#=GF RT   regulatory protein PyrR.
#=GF RA   Bonner ER, D'Elia JN, Billips BK, Switzer RL
#=GF RL   Nucleic Acids Res 2001;29:4851-4865.
#=GF CC   This family represents the PyrR binding site and terminator structure.
#=GF CC   This RNA structure is found upstream of a variety of genes involved in
#=GF CC   pyrimidine biosynthesis and transport. The alignment also includes a
#=GF CC   portion of the antiterminator structure.
#=GF WK   PyrR_binding_site
#=GF SQ   41


M59757.2/2712-2828           AAAACCUUU-UAAUG-AAAGUCCAGAGAGGCUUG--GAAGGGU-------------------------------------------UAUGAAGAGAAGGAAGCUUCA-----AUGCUGCCCUCUAUUUAA-------------------------------------------CCAUACCCCGAGUCUAUCU------------UAGACCGGGGUUUUUUUUCA
M59757.2/547-663             AGAUUCUUU--AAA--ACAGUCCAGAGAGGCUGA--GAAGGAUAACG--------------------------------------GAUAGACGGGAUGCGUGUAU-------AGGCGCGCACCUUGUCCU-------------------------------------------AAAACCCCUCUAUGCUCU-------------GGCAGGAGGGGUUUUUUCUU
M59757.2/1239-1357           AUCACCUUUUUAAGG-GCAAUCCAGAGAGGUUGCAAAGAGGUGC--------------------------------------------ACAACAAAGGCCCAAAAAG-----UAUUCGGCAGGUCUUU---------------------------------------------GUAUGCCUCU-UUGCGUAAAAA---------AGCAAAGAGGUUUUUUUAUA
X73308.1/235-367             AGCACCUUU-UAAU--UAAGUCCCGCGAGGCUUA-AAAAGGUGUGAA--------------------------------------AACAGGCGCAUCCAGGGCCGGAG----UGCACCUUCUUCGGCUCUGCCAUGCGCCGAUCG----------------------------UCACACCUUGCCUGG-----------------CCGGCAAGGUGUUUUUUUU
X84262.1/148-332             AUGACCUUU-AAAU--UUAGUCCCGUGAGGCUAA--GAAGGCAGCUCAAAAUCCAUAUAUAA-----------------------ACAAGAAAUUCUUGGCAAACAUUCG--AAUUGACAGGAAGACCGGGGAGGAAGCUUUUCGGACAGUUUAAGCAGACUUUG--------AGAGACCAUU-UUAGACACGGAGACUGAGUGUAUAAAAUGGUCUUUUUGCU
AE017355.1/3732753-3732639   AAGCCCUUU-UAAAU-GUAGUCCUGUGAGGCUGC-CAAAGGGU------------------------------------------CUUGGCUUUCAUAUGUCAAA-------UUUGGCAUACGAAAGUGU-------------------------------------------AGGACUCUUU-GUGCACA-------------GGCACAAAGAGUUUUUUUAU
AJ000109.1/697-884           AAAACUUU--UAAU--CUAGUCCAGAGAGGCUAG--CAAGGUUGUGAACAGGAAAUAUUAUGCUUAAAAGUUACUGACAAAAGAGCGGUGUA-GCUU-GGUCCAU-------AAGUACCAAAGCGGACAGGGCUAGUUCUGUCAGUAAACUGUCAGGGCAUAUUAG-------GACACAUCUG-CUAGGUU-------------UCUGGCAGAUGUUUUUGCUU
AF068902.1/6383-6487         AAAACCUU--UAAA--GCAGUCCAGAGAGGCAGC--UAAGGUU--------------------------------------------AGACGGUGAAAGGGUGGAG------ACUACCCAUUUUU-------------------------------------------------CGUGGAACCUUGCUGUU--------------GGCAGGUUCCUUUUUUCGU
AL766848.1/172483-172364     AUAUCCUU--UAAGGUAUUGUCCAGAGAGGCAAA--CAAGGAAUUGCGU------------------------------------UAACAAAUAGUAAGUUAGUUCCCU---AUCUAGCUUACUAUUUUG-------------------------------------------CAGAGCCUCC-UUGU-----------------UUUAGGAGGCUUUUUUCUA
AJ132624.1/224-346           CUAACCUU--UAAG--AUUGUCCAGAGAGGCAGG--CAAGGUC---------------------------------------------AGAAAUUAAUAAUGUAA-------UAAUAUGAUGGAUACUGUCCAUUUUCUGAU-------------------------------ACCUACCUGC-AUUCUCUUU-----------GGAAUGCAGCUUUUUUGUAU
AE017334.2/3710686-3710572   AAGCCCUUU-UAAAU-GUAGUCCUGUGAGGCUGC-CAAAGGGU------------------------------------------CUUGGCUUUCAUAUGUCAAA-------UUUGGCAUACGAAAGUGU-------------------------------------------AGGACUCUUU-GUGCACA-------------GGCACAAAGAGUUUUUUUAU
AL596170.1/181975-181872     AACACUUUUUUAAAA-GCAGUCCUGUGAGGCUGA--CAAAGAG-------------------------------------------------UGAUUAAUUUCUA-------UAGGGGAUUAUU-------------------------------------------------CUAUACUCUU-UGUCGACCG-----------AGGCAAGGGGUAUUUUUUAU
U48870.1/2609-2725           AGAUUCUUU--AAA--ACAGUCCAGAGAGGCUGA--GAAGGAUAACG--------------------------------------GAUAGACGGGAUGCGUGUAU-------AGGCGCGCACCUUGUCCU-------------------------------------------AAAACCCCUCUAUGCUCU-------------GGCAGGAGGGGUUUUUUCUU
X74207.1/3091-3251           AAAACCUU--UAAC--UAAGUCCAGAGAGGCUUG--CAAGGAUACGGAAAAUUUAUCUUG-------------------------GAUUACUGACAAACUAAGGAUG-----AACUUCUUUUUUAGCGUAUUUGUCUGUCAGUAAAUGACCAAUUUUU---------------UAGUACACUU-GUAAGUUCU-----------CUUACAAGUGUUUUUUUAUU
AL591981.1/164574-164471     AACACUUUUUUAAAA-GCAGUCCUGUGAGGCUGA--CAAAGAG-------------------------------------------------UGAUUAAUUUCUA-------UAGGGGAUUAUU-------------------------------------------------CUAUACUCUU-UGUCGACAC-----------AGACAAGGGGUAUUUUUUAU
AE017225.1/3711254-3711140   AAGCCCUUU-UAAAU-GUAGUCCUGUGAGGCUGC-CAAAGGGU------------------------------------------CUUGGCUUUCAUAUGUCAAA-------UUUGGCAUACGAAAGUGU-------------------------------------------AGGACUCUUU-GUGCACA-------------GGCACAAAGAGUUUUUUUAU
X76083.1/647-773             GGAACCUUU--AAGU-UCAGUCCUGUGAGGCUGA--AAAGGGGUCG---------------------------------------GAAUGACAAAGAAGGGCGAUG------UAUGCCCAUCUUGUUUGGUGAUAAGCG----------------------------------CGCCAUCCCC-CGCUUCAC------------AGGCGGGGGAUUUUUUGUGC
X76083.1/2797-2929           AGCACCUUU-UAAU--UAAGUCCCGCGAGGCUUA-AAAAGGUGUGAA--------------------------------------AACAGGCGCAUCCAGGGCCGGAG----UGCACCUUCUUCGGCUCUGCCAUGCGCCGAUCG----------------------------UCACACCUUGCCUGG-----------------CCGGCAAGGUGUUUUUUUU
X76083.1/1336-1438           CGACCCUUU-UAAGC-GCAGUCCCGUGAGGCUGC-AAAAGGGG---------------------------------------------------CGGAAUCGUUU-------CGGCUGUUUCU--------------------------------------------------GCACCCUCUU-UGCGUCUUCGC---------GGGCAAAGAGGGAUUUUUUU
AJ012720.1/1924-2038         AGUUCCUUU--AAA--UUAGCUCAGAGAGGCUGA--AAAGGAU------------------------------------------GAACGGACGUAC-GCUUUCA-------AGGAAGCCGUGCGUAAUUUC-----------------------------------------GGACAGCCUAGCCGCUUUG------------AGUGGUGGGCUGUCUUUUCU
AF044978.1/176-335           GUAACCUUU--AAGU-UUAGUCCCGUGAGGCUAA--GAAGGAAUC----------------------------------------AUGCAAAAGAACACUAGGUG-------CGCUUAGUUAGUAAGUUGUGUGGGCUACAUGGUACCCUUGUACCUUUUUAAACUGUAACCAACAUCCUCCU-AUCCUCAUA-----------CGGGUAGGAGGAUUUUUUGU
AM263198.1/1891529-1891421   ACACUUUUU-UAAAA-GCAGUCCUGUGAGGCUGA-CAAAGAGU-----------------------------------------------GAUUAAUUUCUAUAU-------AUUUAGGGGAUUAUU----------------------------------------------CUAUACUCUU-UGUCGACAC-----------AGACAAGGGGUAUUUUUUAU
CP000023.1/493796-493904     AAGUCCUU--UAAUU-ACUGUCCAGAGAGGCAGG--CAAGGAG------------------------------------------CUAUGAGAAGUGCGCAGGUG-------AA-CUGUGCCAUGUUUUU-------------------------------------------GUGUAUCUCC-UUGU----------------UUCAAGGGGAUUUUUUGUAU
CP000002.3/1724430-1724551   AUCCUUUUU-UAAAU-GCAUUCCAGUGAGUUUGC--AAAGAGGGAUGG-------------------------------------AACGAAAGAAAGCCGCCUUA-------CCGUGCGGCGGUCUUU---------------------------------------------GUCUGCCUCU-UUGCGCAAUUUA--------AGCAAAGAGGCUUUUUUAAU
BA000043.1/1165375-1165499   GGAACCUUU--AAGU-UCAGUCCUGUGAGGCUGA--AAAGGGGUCG---------------------------------------GAAUGACAAAGAAGGGCGAUG------UAUGCCCAUCUUGUUUGGUGAUAAGCGCG--------------------------------CCAUCCCCCG-CUUC----------------ACAGGCGGGGGGUUUUUUGU
AE017333.1/1725773-1725889   AAAACCUUU-UAAAU-GAAGUCCAGAGAGGCUUG--AAAGGGU------------------------------------------UGCGGAGAGAGAAGUGCAAAAA-----AGCGCAUUCUCUGAUUCA-------------------------------------------CUGUACCCCA-AGCCGUUA------------UGGCCUGGGGUUUUUUUACG
AL009126.3/1620329-1620445   AAAACCUUU-UAAUG-AAAGUCCAGAGAGGCUUG--GAAGGGU-------------------------------------------UAUGAAGAGAAGGAAGCUUCA-----AUGCUGCCCUCUAUUUAA-------------------------------------------CCAUACCCCGAGUCUAUCU------------UAGACCGGGGUUUUUUUUCA
CP000919.1/624651-624755     AAAACCUU--UAAA--GCAGUCCAGAGAGGCAGC--UAAGGUU--------------------------------------------AGACGGUGAAAGGGUGGAG------ACUACCCAUUUUU-------------------------------------------------CGUGGAACCUUGCUGUU--------------GGCAGGUUCCUUUUUUCGU
AE005176.1/1080400-1080547   AUAACUUU--UAAA--CUAGUCCAGAGAGGCUAG--CAAGGUUGAAAUCAGGAAAAAUUGAU-----------------------UCUAUUUUUACUGACAGGAU-------UUUCUGUCAGUAAAAGUGAAUUUGUUUUGAUACUU--------------------------UUUACACUUG-CUAGGAUU------------CUUGGCAAGUGUUUUUUAU-
AE009948.1/1054718-1054599   AUAUCCUU--UAAGGUAUUGUCCAGAGAGGCAAA--CAAGGAAUUGCGU------------------------------------UAACAAAUAGUAAGUUAGUUCCCU---AUCUAGCUUACUAUUUUG-------------------------------------------CAGAGCCUCC-UUGU-----------------UUUAGGAGGCUUUUUUCUA
AL009126.3/1618161-1618277   AGAUUCUUU--AAA--ACAGUCCAGAGAGGCUGA--GAAGGAUAACG--------------------------------------GAUAGACGGGAUGCGUGUAU-------AGGCGCGCACCUUGUCCU-------------------------------------------AAAACCCCUCUAUGCUCU-------------GGCAGGAGGGGUUUUUUCUU
CP001033.1/1229356-1229224   UAUUCCUU--UAAA--CCUGUCCCGUGAGGCAGG--CAAGGAGC-----------------------------------------GCGAUAAAGUAGAAGGGUGA-------AGUCUAUACUGUGUGCAGUAGGGCUCGCUUGGCUAUAAAU---------------------UUCAAGUCUC-CUUGUU---------------UAAGGAGACUUUUCUUUUU
AE005176.1/1401723-1401583   AAAACUUU--UAAU--CUAGUCCAGAGAGGCUAG--CAAGGUUGUGAACAAGAAAUAUUAU------------------------CCUUAAAAGUUACUGACAGA-------ACUGUCAGUAAGUUGCUAAGGCAUUUUAG--------------------------------GACACAUCUG-CUAGGUU-------------UCUGGCAGAUGUUUUUGCUU
ABQL01000005.1/599722-599838 AUCACCUUU-UUAA--GCAAUCCAGAGAGGUUGC--AAAGAGGUGC------------------------------------------ACAACAAAGGCCCAAAAAG-----UAUUCGGCAGGUCUUU---------------------------------------------GUAUGCCUCU-UUGCGUAAAAA---------AGCAAAGAGGUUUUUUUAUA
AE009949.1/721177-721294     UAUUCCUU--UAAA--ACAGUCCUGUGAGGCUGU--CAAGGAGACGGAUU-----------------------------------AAAAACAUGCACCAUGAUACU------UAAUUGUGCUAUAUUUUG-------------------------------------------CUGAAUCUCC-UUGUUU---------------CCAAGGAGAUCUUUUUAUU
CP000259.1/744106-744214     GACACCUU--UAAG--UGAGUCCAGAGAGGCAAA--CAAGGUA------------------------------------------UACAAGAUAAAAAAAGGGAA-------UUCCCUUUUAGUUUGCUG--------------------------------------------UAGCCUCGC-UUCUUU---------------GGUAGCGAGGCUUUUUGGU
AE005176.1/1385029-1384872   AAAACCUU--UAAC--UAAGUCCAGAGAGGCUUG--CAAGGAUACGGAAAAUUUAAUUUGGUUU---------------------ACUGACAGCUUAAAGAUGAACUUUUUUAGCGCAUUUAUUCUGUCAGUAAAUUACCAGUUUUUU-------------------------AGUACACUUG-UAAGUUC-------------UCUUACAAGUGUUUUUUUGU
CP000259.1/678792-678909     UAUUCCUU--UAAA--ACAGUCCUGUGAGGCUGU--CAAGGAGACGG--------------------------------------AUUAAAAACAUGCACCAUGAUACU---UAAUUGUGCUAUAUUUUG-------------------------------------------CUGAAUCUCC-UUGUUU---------------CCAAGGAGAUCUUUUUAUU
AGLY01000019.1/86907-87018   UAUUCCUU--UAAC--ACUGUCCCGUGAGGCAGG--CAAGGAGCG----------------------------------------ACAAAGAAAAAAGUGCAGGAAC-----AACUGUACUUAUAUUUUG-------------------------------------------UGAAAUCUCC-UUGU-----------------AUGAGGAGAUUUUUUCUUA
AL935263.2/2407973-2407881   AGCACCUU--UAAC--UUAGUCCUGUGAGGCUAA--CAAGGGG--------------------------------------------------------AACGGU-------CAUGU--------------------------------------------------------AGGGUCUCCCACGCUUUUCGCAGGA------AAACAGGGUGACUCUUUUUU
AL935263.2/2142423-2142309   AGUUCCUUU--AAA--UUAGCUCAGAGAGGCUGA--AAAGGAU---------------------------------------------GAACGGACGUGCGCUUUCAAGG--AAGCUGUGCGUAAUUU--C------------------------------------------GGACAGCCUAGCCGCUUUG------------AGUGGUGGGCUGUCUUUUCU
#=GC SS_cons                 ::<<<<<<<.----..<<<<<<______>>>>>>..>>>>>>>,,,.......................................,,,,<<<<<<<<<<<<<<__.......__>>>>>>>>>>>>>>-----------..................................<<<<<<<<<<.<<<<____............_>>>>>>>>>>>>>>:::::
#=GC RF                      AaaaCCUUu.UAAa..ucAGUCCaGaGAGGCUga..aAAGGuugcg.......................................aaaagaauacuaagguagaa.......aacuaccuuaguauucugggauaguuc..................................aaaaccccuu.uugcuuuu............ugcaaaagggguuuuUUuuU
//
# STOCKHOLM 1.0

#=GF AC   RF00516
#=GF ID   ylbH
#=GF DE   ylbH leader
#=GF AU   Barrick JE
#=GF AU   Breaker RR; 0000-0002-2165-536X
#=GF SE   Barrick JE
#=GF SS   Predicted; Barrick JE
#=GF GA   50.00
#=GF TC   55.00
#=GF NC   49.40
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   15096624
#=GF RT   New RNA motifs suggest an expanded scope for riboswitches in bacterial
#=GF RT   genetic control.
#=GF RA   Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M,
#=GF RA   Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:6421-6426.
#=GF CC   This family is a putative regulatory RNA structure that is found upstream
#=GF CC   of the ylbH gene in B. subtilis and related low GC Gram-positive bacteria.
#=GF WK   ylbH_leader
#=GF SQ   3


AE017355.1/3773586-3773470 AGAAAAAAAACCCUGC---AAA----GCAGGG---------------CUCUUCUUAUACUAGCAUGUACUAGUAAGAAGGCAAAGGGAGAGGAGAAACCGGAGGAAGAACUUAUGGGGAAACGUAAGUCUUCUCCGCGG
AE008691.1/1456779-1456662 AUAA------GGGAGGCCUAAAAAGGCUUCCCUUUUUAAAUUUUUAAUCCAG----GCAGG-AGUUCG-CCUGC--CUGGA-CUGGGAGAGGAGAAAUUGAAGGAAGAA-UU--GGGGAAAU--UUCUAUUC-CCGUUA
AL009126.3/1569199-1569319 AUAAAAAAAUCCCCGCAGGCA--UCUGCGGGG---------------UCCUUCUAUUCCUUAAUAUGUUAAGGA-GAAGGCAAAGGGAGAGGAGAAACCGGAGGAAGAACUUAUGGGGAAACGUAAGUCUUCUCCGCGG
#=GC SS_cons               ::::::::::<<<<<<<<<___.>>>>>>>>>...............<<<<<----<<<<<<______>>>>>>.------->>>>>-----------<<<<-<<<<-<<<<<__________>>>>>>>>>>>>>:::
#=GC RF                    AuAAAAAAAaccccgcccuaAA.agggcgggg...............ccCugCUaagccgggaauuuacccggc.GaaGGaAcaGggAGAGGAGAAAucGgaGGaagAaCuuaUGGGGAAAuGuaaGucuuCucCgugg
//
# STOCKHOLM 1.0

#=GF AC   RF00517
#=GF ID   serC
#=GF DE   serC leader
#=GF AU   Barrick JE
#=GF SE   Barrick JE
#=GF SS   Predicted; Barrick JE
#=GF GA   35.00
#=GF TC   35.90
#=GF NC   34.40
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   16086852
#=GF RT   Evidence for a second class of S-adenosylmethionine riboswitches and other
#=GF RT   regulatory RNA motifs in alpha-proteobacteria.
#=GF RA   Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M,
#=GF RA   Rudnick ND, Breaker RR
#=GF RL   Genome Biol. 2005;6:R70.
#=GF CC   This family is a putative regulatory RNA structure that is found upstream
#=GF CC   of the serC-serA operon in some alpha-proteobacteria. The final stem of
#=GF CC   the structure overlaps the ribosome binding site of the serC reading
#=GF CC   frame.
#=GF WK   serC_leader
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   70


BX572606.1/323831-323780     CAGCGGGAAACCUCUC-CCCACCGAG-AGGCAG-CUAUCUGGAAGGAUAGACUAU
AACY024111847.1/1129-1078    UGGUGGGACACCCCUC-CCCAACGAG-GGGCAU-AUAUCUGUAAGGGUAAAAUAA
AACY020298717.1/1738-1789    CGGCGGGACACCCCUC-CCCAACGAG-GGGCGC-AUAUCUGAAAGGGUAUCAGAC
AAGA01005882.1/680-629       CAGUGGGACACCCUUC-CCCAACGAA-GGGCAU-UUAUCUGUAAGGAUAGCAUCA
CP000377.1/3187372-3187423   CGGUGGGACACCCCUC-CCCAACGAG-GGGCGC-UUAUCUGGAAGGGUAGCAUUU
AAOT01000027.1/33635-33584   CGGCGGGACACCUCUC-CCCAACGAG-AGGCGC-AUAUCUGUGAGGGUAUCAGAC
AACY022833952.1/803-752      CAGUGGGUCACGCCUC-CCCAACGAG-GCGCAA-CUAUCUGAGAGGGUAGAGACA
ABEF01032305.1/896-845       ACGUGGGACACCCUUC-CCCAACGAA-GGGCGC-UUAUCUGAAAGGGUAGCUACA
AACY023803751.1/1051-1102    CGGUGGGACACCCCUC-CCCAACGAG-GGGCGA-UUAUCUGGAAGGAUACCACCA
AAMS01000001.1/302336-302387 CGGUGGGACACCCUUC-CCCAACGAA-GGGCGA-UUAUCUGAGAGGAUACCAGAA
AACY020046202.1/1708-1759    CAGUGGGACACCCCUC-CCCAACGAG-GGGCGA-UUAUCUGAAAGGGUAGCAUUA
AAYA01000021.1/26312-26261   CGGCGGGACACCUCUC-CCCAACGAG-AGGCAU-CUAUCUGGAAGGUUAGCAGAU
AACY020421993.1/1563-1512    ACGUGGGACACCUCUC-CCCAACGAG-AGGCAA-UUAUCUGGAAGGGUAACAGAC
CP000362.1/192256-192307     AAGUGGGACACCCUUC-CCCAACGAA-GGGCGA-UUAUCUGGAAGGAUAGCAUCA
ABCR01000001.1/310139-310190 CGGCGGGACACCCCUC-CCCAACGAG-GGGCGC-UUAUCUGGAAGGAUAGCAUCA
AM236080.1/4187938-4187886   CGGCGGGACACCCUUC-CCCAACGAA-GGGCUUUCUAUCUGAGAGGAUAGCAUCA
AACY020312862.1/2647-2698    AAGUGGGUUACGUCCC-CCCACCGGG-ACGCAC-CUAUCUGGAAGGAUAGGAGGA
AAPJ01000002.1/467103-467154 UCGCGGGACACGCCUC-CCCAACGAG-GCGCUU-CUAUCUGUGAGGGUAGCUUAG
CP000143.1/3121070-3121121   CAGCGGGACACCUCUC-CCCAACGAG-AGGCAU-CUAUCUGGAAGGAUACCAUGU
AAUW01000002.1/189511-189460 AGGUGGGCCACCUCUC-CCCAACGAG-AGGCAA-CUAUCUGCGAGGGUAGACAGA
CU234118.1/6173717-6173665   CGGCGGGACACCUCCC-CCCAACGGG-AGGCUUACUAUCUGGAAGGAUAGACGAU
CP000283.1/4347138-4347086   CGGCGGGACACCUCCC-CCCAACGGG-AGGCUAGCUAUCUGGAAGGAUAGAACAU
AAMY01000008.1/65545-65493   CGGCGGGACACCUCCC-CCCAACGGG-AGGCUUGCUAUCUGGAAGGAUAGAUUAU
BA000040.2/8141408-8141356   CGGCGGGACACCUCCC-CCCAACGGG-AGGCUUACUAUCUGGAAGGGUAGAAUAU
AATQ01000012.1/64952-65003   CGGCGGGACACCCCUC-CCCAACGAG-GGGCAU-CUAUCUGGAAGGUUAGGCAGA
AANB01000011.1/126080-126029 CGGCGGGACACCCUUC-CCCAACGAA-GGGCAG-AUAUCUGUAAGGAUAGCAUCA
AAMV01000009.1/49920-49869   CAGUGGGACACCCCUC-CCCAACGAG-GGGCGC-UUAUCUGAGAGGGUAGCUAAA
AACY021366942.1/533-584      CGGUGGGCUACCUCUC-CCCAACGAG-AGGCAU-UUAUCUGGAAGGAUAGGAUAA
CP000390.1/3433409-3433357   CAGCGGGCUACCCCUC-CCCACCGAG-GGGCGAGCUAUCUGGAAGGAUAGGAACA
AACY022082869.1/122-173      AAGUGGGUUACCCCUC-CCCAACGGG-GGGCAA-CUAUCUGGAAGGAUAGAGUAA
AAFX01106401.1/35-87         CGGCGGGACACCUCUC-CCCAACGAG-AGGCUUUCUAUCUGGAAGGAUAGGCCGC
AATP01000001.1/657956-657905 CAGUGGGACACGCCUC-CCCAACGAG-GCGCGC-CUAUCUGAAAGGGUAGUCAAG
AACY021335122.1/749-800      CCAUGGGACACCUCUC-CCCAACGAG-AGGCAA-UUAUCUGUAAGGGUAACAGAC
AAFZ01000432.1/94-43         CGGCGGGACACCCUUC-CCCAACGAA-GGGCAU-AUAUCUGAGAGGAUACCAGCA
AALY01000003.1/267437-267386 CCGCGGGACACCCUUC-CCCAACGAA-GGGCGC-UUAUCUGGAAGGAUAGCAUCA
AACY022945176.1/11-62        AGUUGGGACACCUCUC-CCCAACGAG-AGGCAA-UUAUCUGGAAGGGUAAAAGAC
CP000774.1/2318876-2318927   CGGCGGGACACCCCUC-CCCACCGAG-GGGCAG-CUAUCUGAGAGGAUAGGUUGC
AACY022909959.1/213-162      CCGUGGGACACCCCUC-CCCAACGAG-GGGCGC-AUAUCUGAAAGGGUAUCAGUG
AACY020146350.1/2180-2129    AAAUGGGACAGCUCUC-CCCAACGAG-AGUCAA-CUAUCUGGAAGGGUAGAGAAC
CP000463.1/4658994-4658943   CGGCGGGAAACCUCUC-CCCACCGAG-AGGCUG-CUAUCUGGAAGGAUAGAAUAU
CP000250.1/1496443-1496494   CGGCGGGAAACCUCUC-CCCACCGAG-AGGCAG-CUAUCUGGAAGGAUAGAUGAU
AACY020272957.1/165-114      CCUUGGGACACUCCUC-CCCAACGAG-GAGCAA-CUAUCUGUAAGGAUAGAAGAC
BA000012.4/3114180-3114129   CCGUGGGCCACCCCUC-CCCAACGAG-GGGCCA-CUAUCUGGAAGGAUAGACCAC
AAFZ01020518.1/795-744       GAGGUGGACACCUCUC-CCCAACGAG-AGGCUA-CUAUCUGAAAGGGUAGACAAU
ABEF01013353.1/245-296       CCGUGGGACACCCCUC-CCCAACGAG-GGGCGG-CUAUCUGAGAGGGUAGAGCCA
AACY020303882.1/1109-1160    CCGUGGGACACCUCUC-CCCAACGAG-AGGCGC-UUAUCUGGAAGGGUAGCAUCA
AACY023835866.1/1375-1426    CGGUGGGACACCCCUC-CCCAACGAG-GGGCGA-AUAUCUGGAAGGAUACCAUGU
AACY023232832.1/291-240      AGGUGGGACACCCCUC-CCCAACGAG-GGGCAG-AUAUCUGUAAGGAUACCAUAA
AAYC01000004.1/254435-254384 GCGUGGGACACCUCUC-CCCAACGAG-AGGCAU-AUAUCUGUAAGGAUAGCAUUG
AACY021195471.1/681-732      AGUUGGGACACCUCUC-CCCAACGAG-AGGCGA-AUAUCUGGAAGGGUAACAGAC
AACY023805332.1/358-305      AGGUGGGCCACGCCUC-CCCACCGAGUGCGCGACCUAUCUGGAAGGAUAGGAGGA
AAXZ01000001.1/499271-499322 CGGUGGGACACCCUUC-CCCAACGAA-GGGCAU-AUAUCUGUGAGGAUAACAUUU
AAMO01000011.1/44897-44846   CGGCGGGACACCCCUC-CCCAACGAG-GGGCGC-UUGACUGGAAGGUUACCAUCA
AACY022458901.1/374-425      GAGCGGGACACCCCUC-CCCAACGAG-GGGCGC-UUAUCUGGAAGGGUACUGUCG
AACY020528169.1/50-101       CGGCGGGACACCCCUC-CCCAACGAG-GGGAUA-UGUUCAUCAGAGAAUUCCCUU
AACY022227135.1/192-243      UCGUGGGACACCCCUC-CCCAACGAG-GGGCGC-AUAUCUGAAAGGGUAGCAUUG
AACY020487674.1/254-203      ACGUGGGACACCUCUC-CCCAACGAG-AGGCGA-AUAUCUGGAAGGGUAACAGAG
AACY023239986.1/99-150       CCGUGGGACAUCCUUC-CCCAACGAA-GGGCGC-AUAUCUGAGAGGAUAGCAUUG
AACY023242384.1/866-814      UGGUGGGACACCCCUCCCCCAACGAG-GGGCAG-AUAUCUGUAAGGAUAACAUAA
AACY021062570.1/418-367      UGAUGGGACACCCCUC-CCCAACGAG-GGGCAG-AUAUCUGUAAGGAUAACAUUA
AAFZ01014317.1/444-392       CGGUGGGCCACAUCUC-CCCAACGAG-AUGCGACCUUUCUGUGAGGAAAGGAGAC
AACY021164314.1/775-826      ACGUGGGCCACCUCUC-CCCAACGAG-AGGCGA-AUAUCUGAAAGGGUAACAGUU
CP000264.1/260954-261005     CGGUGGGACACCCUUC-CCCAACGAA-GGGCGC-AUAUCUGUGAGGAUACCAUUA
AACY020461845.1/7739-7790    AGAUGGGACACCCUUC-CCCAACGAA-GGGCGC-AUAUCUGAGAGGAUAGCAUUG
AACY020036858.1/1232-1181    UUCUGGGACACCCUUC-CCCACCGAA-GGGCAA-CUAUCUGAGAGGGUAGCGAUA
AACY022912780.1/892-942      UAGUGGGCCACGCCUC-CCCACCGAGUGCGCGACCUAUCUGGAAGGAUAG---GA
CP000943.1/7027720-7027669   CGGCGGGACACCUCUC-CCCACCGAG-AGGCGC-CCAUCUGGAAGGAUGGACACC
AE007870.2/788262-788211     CGGCAGGACACCUCUC-CCUAACGAG-AGGCGC-CUAUCUGAAAGGGUAGUCAAA
AL591688.1/2938131-2938080   CGGCGGGACACCCCUC-CCCAACGAG-GGGCUU-CUAUCUGAGAGGAUAGCAUAU
AE008917.1/358098-358150     AAGUGGGCCACGUCUC-CCCAACGAG-ACGCGUGCUAUCUGAGAGGAUAGAAACA
#=GC SS_cons                 ::::::::::<<<<<<.______>>>.>>>---.<<<<<<____>>>>>>:::::
#=GC RF                      cgGuGGGACACCCCUC.CCCAACGAG.GGGCga.cUAuCUGgAAGGaUAgcauaa
//
# STOCKHOLM 1.0

#=GF AC   RF00518
#=GF ID   speF
#=GF DE   speF leader
#=GF AU   Barrick JE
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   37.00
#=GF TC   37.80
#=GF NC   33.60
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   16086852
#=GF RT   Evidence for a second class of S-adenosylmethionine riboswitches and other
#=GF RT   regulatory RNA motifs in alpha-proteobacteria.
#=GF RA   Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M,
#=GF RA   Rudnick ND, Breaker RR
#=GF RL   Genome Biol. 2005;6:R70.
#=GF RN   [2]
#=GF RM   22418845
#=GF RT   A survey of sRNA families in alpha-proteobacteria.
#=GF RA   del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N,
#=GF RA   Jimenez-Zurdo JI
#=GF RL   RNA Biol. 2012;9:119-129.
#=GF CC   This family is a putative regulatory RNA structure that is found upstream
#=GF CC   of the speF gene encoding ornithine decarboxylase in Agrobacterium
#=GF CC   tumefaciens and other alpha-proteobacteria.
#=GF WK   speF_leader
#=GF SQ   6


BX897699.1/1421859-1421707 UUCCAGCUGUCCAAAUGCUGGGAUA---ACUAUAGAGGCACA-CCU-CAUUGCCUUCAGUGCGGAAGUG--GUUUUCUCAACUCCAAUCAAAAAGGCAGAAAAAGUAAAGCAACG-CGAUUUUCGCGCUGUUUUUUCGCUGCAUGCAAUGCUGCUUUCUUC
CP001852.1/97256-97407     UUUCGGCUGUCCAAAAGUCGAAAUU---ACUGAAGAGGCACA-CCUUCAUUGCCAGAAGUGCGGAUGCG--GUUCUC-CAAUUCCAAGCCAA--GGCAGACAAAGCGGAGUAACGCUUAGUUUAGCGUUGUUCCAUCGCCGCAUAAAGUUUUCGCGUGACA
AE007870.2/205625-205477   UGCCGGCUUUCCAUCAGCCGGGGU----ACUGAAGAGGCACA-CCAUCAUUGCCUGAAGUGCGGUCGGGUCAUUCCCUCCAAUCGAUGGCAGACAAAGCCGAAUGAU-GCUCUGGCAGGGCAUCGU-UCACAUUCGCGCCUUG-AGCGUAUGC-UAUC---
CP001096.1/997826-997671   UGCCGGCUUUCCAUCAGCCGGCGCGAAUACCGAAGAGGCUUGUCCUUCAUUGCCAGU-GAGCGGGCGGG--AUCCUUCCCAACCAAUCCAAGGCAGCACUGCUCGUCCGAGCUGAUCGCUCGUCGCGCCUCCAUCGCGCGACG-GCGCUGAAGCCGUCGG-
BX897700.1/1185164-1185013 UUCCAGCUGUCAAAAUGCUGGGGUA---ACUAUAGAGGCACA-CCU-CAUUGCCUUCAGUGCGGAAGUG--GUUUUCUCAACUCCAAUCAAAAAGGCAGAAAAAGUAGAGCAACG-UGGUUUUCACGCUGUUUUU-CGCUGCAUGCAAUGUUGCUUUCUUC
CP002781.1/2962253-2962101 UGCCGGCUCUCCAACAGCCGGGGUU---ACUGAAGAGGCACA-CCUUCAUUGCCGGAAGUGCGGUUGGGUUAUUCCCUCCAAUCCAUGGCAGACAAAGCCGAAUCCUAGCCUUUGCGGGCUUUGAU-UCAAAUUCGCGCAUCG-AGCGCAUGCAUGGUU--
#=GC SS_cons               <<<<<<<<_______>>>>>>>>,,...,,,,,,,,<<<<__._______>>>>------(((,,,,,,..,,,,,,,,,,,,,,,,<<_________>>,,,,,,,<<<<<_____>>>>>,,,,,,,,,,,,,,)))::::.::::::::::::::::.
#=GC RF                    ucCCGGCuuUCCAaaaGCCGGggUu...ACUGAAGAGGCaCA.CCUUCAUuGCCuGaAGUGCGGauGgG..aUUCUCUCaAaUCcAugcaAgAcaGcAgcgAAaGuuagcccucGcugggcuUcGcGuuguuuUcgCGCugCg.acagUguugcugUcuu.
//
# STOCKHOLM 1.0

#=GF AC   RF00519
#=GF ID   suhB
#=GF DE   Makes More Granules Regulator RNA (mmgR)
#=GF AU   Barrick JE
#=GF SE   Barrick JE
#=GF SS   Predicted; Barrick JE
#=GF GA   41.00
#=GF TC   41.00
#=GF NC   40.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00108
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0006353; DNA-templated transcription, termination;
#=GF DR   GO; 0005515; protein binding;
#=GF DR   GO; 1901698; response to nitrogen compound;
#=GF RN   [1]
#=GF RM   16086852
#=GF RT   Evidence for a second class of S-adenosylmethionine riboswitches and other
#=GF RT   regulatory RNA motifs in alpha-proteobacteria.
#=GF RA   Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M,
#=GF RA   Rudnick ND, Breaker RR
#=GF RL   Genome Biol. 2005;6:R70.
#=GF RN   [2]
#=GF RM   18793445
#=GF RT   Prediction of Sinorhizobium meliloti sRNA genes and experimental detection
#=GF RT   in strain 2011.
#=GF RA   Valverde C, Livny J, Schluter JP, Reinkensmeier J, Becker A, Parisi G
#=GF RL   BMC Genomics. 2008;9:416.
#=GF RN   [3]
#=GF RM   20398411
#=GF RT   A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing
#=GF RT   alpha-proteobacterium Sinorhizobium meliloti.
#=GF RA   Schluter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen
#=GF RA   S, Janicke S, Becker JD, Giegerich R, Becker A
#=GF RL   BMC Genomics. 2010;11:245.
#=GF RN   [4]
#=GF RM   28167519
#=GF RT   Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti
#=GF RT   by the Trans-Encoded Small RNA MmgR.
#=GF RA   Lagares A Jr, Ceizel Borella G, Linne U, Becker A, Valverde C
#=GF RL   J Bacteriol. 2017; [Epub ahead of print]
#=GF RN   [5]
#=GF RM   27033949
#=GF RT   Phylogenetic distribution and evolutionary pattern of an
#=GF RT   alpha-proteobacterial small RNA gene that controls polyhydroxybutyrate
#=GF RT   accumulation in Sinorhizobium meliloti.
#=GF RA   Lagares A Jr, Roux I, Valverde C
#=GF RL   Mol Phylogenet Evol. 2016;99:182-193.
#=GF RN   [6]
#=GF RM   24786641
#=GF RT   Genome-wide profiling of Hfq-binding RNAs uncovers extensive
#=GF RT   post-transcriptional rewiring of major stress response and symbiotic
#=GF RT   regulons in Sinorhizobium meliloti.
#=GF RA   Torres-Quesada O, Reinkensmeier J, Schluter JP, Robledo M, Peregrina A,
#=GF RA   Giegerich R, Toro N, Becker A, Jimenez-Zurdo JI
#=GF RL   RNA Biol. 2014;11:563-579.
#=GF RN   [7]
#=GF RM   21484295
#=GF RT   Evidences of autoregulation of hfq expression in Sinorhizobium meliloti
#=GF RT   strain 2011.
#=GF RA   Sobrero P, Valverde C
#=GF RL   Arch Microbiol. 2011;193:629-639.
#=GF RN   [8]
#=GF RM   27010014
#=GF RT   Expression of the Sinorhizobium meliloti small RNA gene mmgR is controlled
#=GF RT   by the nitrogen source.
#=GF RA   Ceizel Borella G, Lagares A Jr, Valverde C
#=GF RL   FEMS Microbiol Lett. 2016; [Epub ahead of print]
#=GF RN   [9]
#=GF RM   29214973
#=GF RT   Expression of the small regulatory RNA gene mmgR is regulated negatively
#=GF RT   by AniA  and positively by NtrC in Sinorhizobium meliloti 2011.
#=GF RA   Ceizel Borella G, Lagares A Jr, Valverde C
#=GF RL   Microbiology. 2018;164:88-98.
#=GF CC   SuhB later renamed mmgR (makes more granules regulator) was a putative
#=GF CC   non-coding RNA found multiple times in the Agrobacterium tumefaciens
#=GF CC   genome and related alpha-proteobacteria. [1] Other non-coding RNAs
#=GF CC   uncovered in the same analysis include: speF, ybhL, metA, and serC.
#=GF CC   [1]Several studies inSinorhizobium meliloti showed that suhB element is
#=GF CC   indeed a non-coding RNA:firstly it was detected on Northern blot and
#=GF CC   called Sm8RNA[2], secondly in an RNAseq study referred to as
#=GF CC   SmelC689.[3]The mutant phenotype's (strain lacking the small RNA)
#=GF CC   cytoplasm contains higher content of polyhydroxybutyrate (PBH)storage
#=GF CC   granules than wild type strain. The sRNA is required to limit the PBH
#=GF CC   intracellular accumulation when the nitrogen-fixing Sinorhizobium meliloti
#=GF CC   is under condition of surplus carbon in relation to nitrogen. It has been
#=GF CC   renamed to mmgR. Further study confirmed that mmgR fine-tunes the
#=GF CC   regulation of PBH storage.[4]Northern blot confirmed the expression of the
#=GF CC   sRNA in other rhizobia species. MmgR homologues were found in most
#=GF CC   alpha-proteobacteria. The Rho-independent terminator and a single stranded
#=GF CC   region 10-mer (UUUCCUCCCU)are completely conserved. Hence, it was proposed
#=GF CC   to define a new family of alpha-proteobacterial sRNA: alpha-r8 of which
#=GF CC   mmgR is a member.[5] RNA binding protein Hfq is binding and stabilising
#=GF CC   mmgR.[6][7] Expression of the mmgR gene was shown to be controlled by
#=GF CC   nitrogen (N).[8] Further study[9] has shown that the regulatory proteins
#=GF CC   NtrC may be required for expression of mmgR gene upon N limitation. Under
#=GF CC   carbon (C) limitation, mmgR transcription is repressed by AntiA.[9]
#=GF WK   suhB
#=GF SQ   87


BX572599.1/15450-15533       UCGCGGUCCCCUUCCUUGGGGCGUUUC--CUCCCU---AGACUUG----GGCCCG-GGCGCCGAAU---GGCGA-C-C-GGGCCUCUUUAUUUGUCCUUC
AF322012.1/25589-25659       CCCAGAGGCCC-UCAU--GGGCGUUUC--CUCCCU----GACUAA----GGCCAC-CC----UUCG-------G-G-G-UGGCUCUUUU-UUUCGGCUAU
BX572595.1/309155-309232     UAUCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUU-----GGGCCG-CUUG--CCAU---CGCAA-G-C-GGCCCUUUUU-UCUUUUCGGA
AF079317.1/78771-78848       CAGGCUUGCCU-UUC---AGGCAUCCU--CUCCCA---AGACUUUCAC-GGGGCC-GGCA--GCAA-----UGC-U-G-GCCCCAUUUU-UUUGUUCAUG
AF389112.1/19268-19192       AGCUGUUCCCC-UCU---GGAGG-UUC--AUACCUUC-AAACUCAC---GGGCCG-CGGU--UUUU-----CCG-G-C-GGCCCUUUUU-UCUUCCGCGC
CP000463.1/1921343-1921272   UAUCGUUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUU-----GGCCGC-CA----GCAA-------U-G-G-CGGCCUUUUU-CUUGGGCGCG
CP000133.1/3768823-3768896   UGUAAAUACCCUCCUU--GGGUGUUUC--CUCCCU---AGACUU-----AGCCGC-GCUG--ACA-------AG-C-G-CGGUUCUUUU-UUGGCCCUUG
AM236084.1/138840-138918     AGCUGUUCCCC-UCU---GGAGGUUUU--UGACCUUC-ACACUUCAU--GGGCCU-CGGU--UCUU------CC-G-ACGGCCCAUUUU-UUUGUUCCCA
AAUW01000002.1/264596-264521 UCGUACCGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUCG----GGCCGC-CUCU--UUU-------GA-GAG-CGGCCUUUUU-UUUGUCCUGA
CU234118.1/6450641-6450565   UAUCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUU-----GGGCCG-CUUG--UCAU----UCAA-G-C-GGCCCUUUUU-UUUGCGCCAA
CP000356.1/3133980-3134053   CACCCUUGCCU-UUU---AGGCAUCCU--CUCCCA---AAACUUUCAC-GGGCCG-CC----UUUG-------G-G-C-GGCCCUUUUU-UUGUCCGUUU
AAQG01000001.1/67741-67816   CGACCCUGCCU-UUC---AGGCAUCCU--CUCCUA---AAACUUUCAC-GGGCUG-AUCU--UCG-------GA-U-C-GGCCCUUUUU-UUCAAGAAUU
AAAP01003214.1/450-371       GUCCGAUGCCCAUGGC--GGGCGUUUC--CUCCCU---UGACUUCG---GCCCCG-CGCG--ACGA----CCGCUG-C-GGGGCCUUUU-UUUCGGCUCC
AB270530.1/160225-160149     GGAGGGUGCCU-UUC---AGGCAUCCU--CUCCCA---AAACUUUCCAAGGGGCU-GGC---UCAC------GC-U-G-GCCCCAUUUU-UUUGCCCGCC
CP000248.1/3382782-3382708   AGAGGGGGCCU-UUC---AGGCAUCCU--CUCCCA---AACUUUUCA--AGGCUG-GCCU--UCG-------GG-C-C-GGCCUUUCUU-UUUGCGCAAC
AAQG01000005.1/130678-130604 CAAAGGUGCCU-UUC---AGGCAUCCU--CUCCUAA--AAACUUUC---GGGCUG-GUCA--UUC-------GA-C-C-GGCCCUUUUU-UUUGCGGCAC
CP000248.1/619116-619192     AGAUUCUGCCU-UUC---AGGCAUCCU--CUCCCA---AAACUUUCC--GACCCG-GCGG--GCAA-----CUG-C-C-GGGUCUUUUU-UUUGUUCGCG
CP000115.1/3182654-3182579   UAUCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUCG----GGUCGC-UUGU--UCGA------CG-G-G-CGGCCCUUUU-UCUUUGCGGG
CP000738.1/2832254-2832324   UGCAAAUACCCUCCUU--GGGUGUUUC--CUCCCU---AGACUUGA---CCGCGC-C-------AU-----U---G-G-CGCGGUUCUU-UUUGAGCACG
CP000319.1/1293380-1293456   UAUCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUUG----GGCCGC-UUGU--UUUG-----ACG-A-G-CGGCCCUUUU-UCUUUUCCGU
DQ304716.1/15695-15767       CCCAGAGGCCCCACAC--GGGCGUUUC--CUCCCU----GACUU-----GGGCCA-CCCU--UCG-------GG-G-U-GGCUUUUUUU-UUGGCUCUAU
CP000301.1/4505920-4505991   UGCUGAGGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUU-----GGCCGC-CA----GCAA-------U-G-G-CGGCCUUUUU-CUUGGCCGCC
AM236080.1/4327667-4327738   UGUAAAUACCCUCCUU--GGGUGUUUC--CUCCCU---AGACUUAG---CCGCGC-U-----CACA---------A-G-CGCGGUUUUU-UUUGGCCGGG
CP000250.1/4004467-4004386   UCGUGGUCCCCUUCCUUGGGGCGUUUC--CUCCCU---AGACUU-----GGCCCG-GGCG--CCGA-UCGGCGA-C-C-GGGCCUUUUU-AUUGUUUAUG
CP000699.1/270155-270231     GGAGCGGGCCU-UUC---AGGCAUCCU--CUCCUAA--UGACUUAC---GGGCUG-GUUC--UUCG-----GAG-C-C-GGCCCUUUUU-UUUGUCGGCG
AAAP01002228.1/46-117        GCCCGUAGCCCUUCU---GGGCG-UUU--CUCCCU---AGACUUCG---GGCCGU-CC----UUCG-------G-G-G-CGGCUUUUUC-UUUCAAAGGC
BA000012.4/2445831-2445909   UGUCCAUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUUC----GACCGU-AUCG--UGCA---AACGA-U-G-CGGUCUUUUU-UUACACCUGC
CP000248.1/1748107-1748030   GGGACGGGCCU-UUC---AGGCAUCCU--CUCCCA---AACUUUUCA--GGGCCG-CCCG--GCAA----CGGU-G-C-GGCCCAUUUU-UUUGCGCUUC
CP000781.1/3139571-3139493   UGCCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUU-----GGACCG-CUCC--GGCA--ACGUGA-G-C-GGUCCCUUUC-UUUUUGGGCC
BA000040.2/8474773-8474695   UACCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUUGG---GCCGCU-UGCG--UCAU----UCGC-G-A-GCGGCCCUUU-UUUCUUUGGG
CP000774.1/2181288-2181361   UGCCGCAGCCCUUCCU--GGGCGUUUC--CUCCCU---AAACUU-----GGGCCC-UGGU--UCG-------CC-A-G-GGCCCCUUUU-UUUGUCCAAA
CP000699.1/3265832-3265756   AGAACGGGCCU-UUC---AGGCAUCCU--CUCCUA---AAACUUUCAA-GGCCGG-UCCC--CUCG------GG-A-U-CGGCCCUUUU-UUUGUUUUGG
AE005673.1/1676248-1676323   AGCCUCUGCCCUUCCU-GGGGCGUUUC--CUCCCUAC-UUAUUUCA---GCCCGG-C-----UUUU-----C---G-C-CGGGCUUUUC-UUUUGGCGGU
AE005673.1/2357606-2357528   CGCCUCUGCCCUUCCU--GGGCGUUUC--CUCCCUA--UGACUUUGU--AGCCCG-GUCU--UCAU------GG-C-C-GGGCUUUCUU-UUUGCGCGAU
CP000283.1/2195859-2195939   UCGCGGUCCCCUUCCUUGGGGCGUUUC--CUCCCU---UGACUUG----GCCCGGGCGCC--GAUU-----GGC-GAC-CGGGCCUUUU-UAUGUGCUGG
CP000781.1/3139027-3138951   UGUCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUUG----GGCCGU-UCGC--UCAC-----GCG-G-A-CGGCCCCUUU-CUUUUUGGGC
CP000741.1/40124-40047       AACUGUUCCCC-UCU---GGAGG-UUC--AUACCUUCAAAACUAAU---GGGCCG-CGG---UUUU-----CCG-A-C-GGCCCUUUUUUUCUCUUCCGA
CP000301.1/865315-865392     UAUCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUU-----GGGCCG-CUUG--CCAA---CGCAA-G-C-GGCCCUUUUU-UCUUGUGCGG
CP000463.1/785292-785369     UAUCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUU-----GGGCCG-CUUG--CUUU---UGCAA-G-C-GGCCCUUUUU-UCUAUUUGGG
Y13942.1/606-684             AGCUGUUCCCC-UCU---GGAGGUUUU--GACCUUC--AAACUUAUCA-GGCCGC-GGGA--AAUA-----UCC-A-G-CGGCCUUUUU-UUUGCCGAUG
U80928.5/172832-172754       AGCUGUUCCCC-UCU---GGAGGUUAU--UGACCUUC-ACACCUUAAA-GGGCCC-UGGU--UUU-------CC-A-GCGGCCCUAUUU-UUCUGCAUAG
BA000040.2/2983919-2983843   UCGGAUUGCUUUGCUC--GGGCGUUUC--CUCCCU---AGACUUGG---GCCGCU-UGUC--ACAA------AC-A-A-GCGGCUCUUC-UUUUUUGUGC
AAMY01000008.1/38850-38774   AUCGCUUGCCCUCCUU--GGGCGUUUC--CUCCCUA--UAACUUG----GGUCGC-UUGU--UCGA------CG-A-G-CGGCCCUUUU-UCUUUGCAAC
AM236080.1/3605533-3605611   GGCUGUUCCCC-UCU---GGAGGUUUU--UGACCUUC-ACACUUAUAA-GGGCCC-UGGU--UUU-------CC-A-GUGGCCCUCUUU-UUUUGCCUUU
CP000134.1/157338-157415     AGCUGUUCCCC-UCUG--GAGGUUUAU--UGACCUUC-ACACUUCAU--GGGCCG-CGGU--UU--------CC-G-CUGGCCCAUUUU-UUUAUCUCCC
AAQG01000006.1/124997-125072 AGAAUGAGCCU-UUC---AGGCAUCCU--CUCCUA---AAACUUUAC--GGGCUG-GCUC--AUUG------AG-C-U-GGCCCUUUUU-UUGUUCUUUC
AP002086.1/116758-116838     AGCUGUUCCCC-UCU---GGAGGUUUAAAUUACCU---UCACAUCUAA-AGGGCC-CGAG--UUUU-----CUC-GUG-GCCCUCUUUU-UUUGUCCUGA
AM236080.1/3605756-3605835   AGCUGUUCCCC-UCUG--GAGGUUUUU--UGACCUUC-ACAAUUAUAA-GGGCCC-UGGU--UUUC------CG-G-U-GGCCCUCUUU-UUUUGCCCAA
CP000157.1/2875608-2875687   CGGGCAGGCCU-UUC---AGGCAUCCU--CUCCCA---AACUUUUCC--GGCCCG-GUUG--GCUC--GUCCAG-C-C-GGGCCUUUUU-CUUGUCCGCG
AAQG01000002.1/80572-80645   GGGCUGUGCCU-UUC---AGGCAUCCU--CUCCUAA--AAACUUAU---CGGCUG-AUCU--UCG-------GA-U-C-AGCC-UUUUU-UUUGUCAUCG
AM236085.1/567123-567047     AGCUGUUCCCC-UCU---GGAGGUUUA--UACCUUC--ACAAUUAAU--GGGCCA-CGGU--UCU-------CC-G-UCGGCCCUUUUU-UUUCGCGAAA
AAMW01000002.1/352244-352171 UGAUCCUGCCU-UUU---AGGCAUCCU--CUCCCA---AACUUUCA---CAGCCC-GGCC--CCGU------GC-C-G-GGCU-UUUUU-UGUCUGCGCU
CP000494.1/6214814-6214732   AGAUUUAGCCCUUCUU-GGGGCGUUUC--CUCCCU---GGACUUG----GGCCGC-CUGU--ACGUCCUGUGCA-G-G-CGGCUUCUUU-CUUUGUCAGU
CU234118.1/5701624-5701545   GAAUUCAGCCCUUCUU-GGGGCGUUUC--CUCCCU---GGACUUGGGC-CGCCUG-CACG--CUAC------GU-G-C-GGGCGGCUUC-UUUCUGUGGA
CP000133.1/3117932-3118010   AGCUGUUCCCC-UCU---GGAGGUUAU--UGACCUUC-ACAAUUCAAA-GGGCCC-UGGU--UUUC------CG-G-U-GGCCCUCUUU-UUUUGCCCAA
CP000759.1/1718870-1718948   UGUCGAUGCCUUUCG---GGGCAUUUC--CUCCCU---AGUCUUUGA--CCGCGC-UCGU--AUCG----UUCG-G-G-CGCGGUUCUU-UUUAUCUGCG
CP000738.1/1337287-1337206   AGCUGUUCCCC-UCU---GGAGGUUUAAAUUACCUUCACAACUAUAA--GGGCCC-AAGU--UCUU------CU-U-GUGGCCCUCUUU-UUUUCCUUGU
AATP01000009.1/136895-136971 AGCUGUCGCCUCACG---GGGCGUUUC--CUCCCU---AGACUUUG---ACCGCG-UUGG--UUUU-----CCG-U-C-GCGGUUUCUU-UUUGCCUUCU
CP000250.1/5104508-5104432   UAUCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUUG----GGCCGC-UUGC--CAUC-----GCA-A-G-CGGCCCUUUU-UUCUUUUGGC
ABCG01000003.1/80914-80992   UCUACCUGCCU-UUC---AGGCAUCCU--CUCCCA---AGACUUUUCCAGCCCGG-UUGG--UUCG-----CCA-G-C-CGGGCUUUUU-UUCUUGCGCC
CP000738.1/1337083-1337005   AGCUGUUCCCC-UCU---GGAGGUUUG--AAACCUUCACAACUGAAA--GGGCCC-AAGU--UUU-------CU-U-GUGGCCCUCUUU-UUUUGCACGU
CP000390.1/2995403-2995481   UGUCCAUGCCCAUCUU--GGGCGUUUC--CUCCCU---AGACUUU----GACCGU-GUCG--UGAA---AACGA-U-A-CGGUCUCUUU-UUAAAUGCCU
CP000761.1/22250-22326       AGCUGUUCCCC-UCU---GGAGGUUCA--AGAUCUCC-ACACUUCAU--GGGCCG-CGGU--UUC-------CG-A-C-GGCCCAUUUU-UUUAUCUUUC
AE007869.2/2163483-2163561   AGCUGUUCCCC-UCU---GGAGGUUUU--GACCUUC--AAACUUGUC--AGGCCG-CGGA--GCAA----UCCA-G-C-GGCCUUCUUU-UUUGGAGCCG
CP000943.1/838723-838796     UCGUGCAGCCCUUGAU--GGGCGUUUC--CUCCCU---ACACUUC----GGGCCG-CCCC--UC--------GG-G-C-GGCCCUUUUU-CUUGACGGCC
AL591688.1/1698688-1698611   AGCUGUUCCCC-UCU---GGAGGUUUG--AAACCUUCACAACUGAA---AGGGCC-CAAG--UUUC------UU-GUG-GCCCUCUUUU-UUUGUCGGC-
CP000943.1/6874211-6874286   CCCCGCUGCCCUCGAU--GGGCGUUUC--CUCCCU---AGACUUC----GGGCCG-CUCC--UCGU------GG-G-C-GGCCUCUUUU-UUGGGCCGUC
CP000943.1/2086262-2086190   UUUCGCAGCCC-UCAU--GGCCGUUUC--CUCCCU---AGACUUCU---GGCCGC-UG----CUGA-------A-A-G-CGGCCCUCUU-UUUAGCUUAU
AL591688.1/1698892-1698811   AGCUGUUCCCC-UCU---GGAGGUUUUAAUUACCUUCACAACUACAA--GGGCCC-AAGU--UUUU------CU-U-GUGGCCCUCUUU-UUUUGCCUGG
AL591688.1/3046725-3046795   UGCAAAUACCCUCCUU--GGGUGUUUC--CUCCCU---AGACUUGA---CCGCGC-C-----GCU----------G-G-CGCGGUUCUU-UUUGAGCAGC
CP000943.1/2055180-2055106   GGCGAUUGCCCUCUUG--GGGCGUUUC--CUCCCU---AGACUUC----GGGCCG-CUC---GCGA------GG-G-C-GGCCUUUUUU-UCUGCCUUGG
CP000943.1/2021225-2021152   UCUCGCAGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUUCG---GGCCGU-UC----GCGA-------G-A-G-CGGCCUUUUU-UUUGGCCCGC
AE007870.2/979666-979597     UGUAAAUACCCUCCUU--GGGUGUUUC--CUCCCU---AGACUUGA---CCGCGC-------UCAG-----------G-CGCGGUUUUU-UUUGCCCGGC
CP000943.1/6991028-6990955   UCCCGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUUG----GGCCGC-AC----CUCG-----U-G-U-G-CGGCCUUUUU-UCUGCGCCGU
CP000943.1/6131628-6131701   UGUGAGUGCCCUCCUU--GGCCGUUUC--CUUCCU---AGACUUC----GGGCCG-CUC---CCGA------GA-G-C-GGCCUUCUCU-UCAUGCGCG-
CP000908.1/2841623-2841696   UCCCGCUGCCCUCUUU--GGGCGUUUC--CUCCCU---AGACUUCG---GGCCGC-CC----UUAG-------G-G-G-CGGCUUUUUU-UUGUUCUAGA
AE006469.1/552915-552990     --AACUGUUCCUCUCU--GGAGGUUCA--UACCUUC--AAACUCAU---GGGUCG-CGGU--UUUC------CG-A-C-GGCCCUUUUC-UUUUUUCUCU
CP000943.1/1103572-1103496   GAGGAUUGCCCUUCGU--GGGCGUUUC--CUCCCU---AGACUUC----GGGCCG-CUCU--UACC-----AGG-G-C-GGCCUCUUUC-UUUGGGCGGC
AE007869.2/2163297-2163376   AGCUGUUCCCC-UCU---GGAGGUUUU--UGACCUUC-ACACUUAAA--GGGCCC-UGGA--UCUA-----UCC-G-GCGGCCCUCUUU-UUUUACCCGC
CP000943.1/3832827-3832900   CCGUGCUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUUCG---GGCCGC-UC----GCGA-------G-G-G-CGGCCUUUCU-UUUGUCCAGG
CP000943.1/4905110-4905036   UUCUGCUGCCCUCUUU--GGGCGUUUC--CUCCCU---AGACUU-----GGGCCA-CACC--GCGC------GU-G-U-GGCCUUUUUU-CUUUGGGGGU
CP000908.1/3636727-3636801   UCCCGCAGCCCUUCUU--GGGCGUUUC--CUCCCU---AGACUUC----GGGCCG-UCCU--UCG-------GG-G-C-GGCCUUUUUU-UGUCCGCGGU
CP000943.1/3212905-3212831   CGGGUGUGCCCUCCUU--GGGCGUUUC--CUCCCU---AGACUUC----GGGCCG-CUC---GCGA------GG-G-C-GGCCUUUUUC-UUUUCUGAGC
CP000943.1/7427588-7427663   CCUCGCAGCCCUCCAU--GGGCGUUUC--CUCCCU---AGACUUC----AGGCCG-CCCU--AUGU------GG-G-C-GGCCUCUUUU-CUAGAACACC
CP000943.1/3548552-3548478   CCACGCCGCCC-CUGU--GGGCGUUUC--CUCCCU---AGACUUC----GGGCCG-UUCC--GCAA------GG-G-C-GGCCUUUUUU-GUUGCUGCGC
CP001298.1/3007465-3007392   UCCUGCAGCCCUUCUU--GGGCGUUUC--CUCCCU---AGACUUCG---GGCCGU-CC----UUCG-------G-G-G-CGGCCUUUUU-UCUUUUUGGC
CP001722.1/602904-602833     AGAAAGUGCCU-UUC---AGGCAUCCU--CUCCUA---AUACUAC----GGUCGG-UC-G--UUAA-------G-A-C-CGACCUUUUU-UUUAUUCUGA
#=GC SS_cons                 :::::::<<<<_____..>>>>-----..------...--------...<<<<<<.<<<_..____......>>.>.>.>>>>>:::::.::::::::::
#=GC RF                      uGcuGuUGCCCUUCUU..GGGCGUUUc..CUCCCU...AgACUUua...GGgCCg.cccu..ucuu......gg.g.c.GGcCCUUUUU.UUUguccugc
//
# STOCKHOLM 1.0

#=GF AC   RF00520
#=GF ID   ybhL
#=GF DE   ybhL leader
#=GF AU   Barrick JE
#=GF SE   Barrick JE
#=GF SS   Predicted; Barrick JE
#=GF GA   50.00
#=GF TC   52.00
#=GF NC   35.30
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   16086852
#=GF RT   Evidence for a second class of S-adenosylmethionine riboswitches and other
#=GF RT   regulatory RNA motifs in alpha-proteobacteria.
#=GF RA   Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M,
#=GF RA   Rudnick ND, Breaker RR
#=GF RL   Genome Biol. 2005;6:R70.
#=GF CC   This family is a putative regulatory RNA structure that is found upstream
#=GF CC   of an uncharacterized membrane protein in alpha-proteobacteria.
#=GF WK   ybhL_leader
#=GF SQ   6


CP000758.1/105606-105684   CAGGCAUGCUGGGGUCCCGCCAGCGGCGCCUGGCGGC-----GGCUCGACCUUUUGAGCGCCCCCGACACCGGA--------CGGGACAUGG
BA000012.4/3454186-3454120 CAGGCAUGCUGGAGCCCCGCCAGCGGCGCCUGGGUCCGUAA----------------GA-GGCCCGACACCGGA--------CGGGGCAGAA
CP000133.1/4169049-4169118 CAGGCAUGCUGGAGCUCCG-CAGCGGCGCCCGG--------------GUCGAGAACC------CCGACACCGUAUCUCC-UUCGGAGCUUGU
AM236080.1/4812613-4812682 CAGGCAUGCUGGAGCUCCG-CAGCGGCGCCCGGG--UCGAAA---------------AC---CCCGACACCGUA-UUUCCAUCGGAGCUUGU
AL591688.1/3506025-3506114 CAGGCAUGCUGGAGCCCCG-CAGCGGCGCCUGGGCGCGCAAAGGAACGACAAGGUUCGC-CGCCCGACACCGUAACUUCAACCGGGGCUUAA
AE007869.2/2665549-2665616 UAGGCUUGCUGAAGCUCCG-CAGCGGCGCCCGGG-----------------AGGUAU-----CCCGACACCGUAGCAAUCA-CGGAGCUCAA
#=GC SS_cons               :::::::::::<<<<<<<<.---<<<----<<<<<<<..........__________>-.>>>>>>--->>>--.----.-.>>>>>>>>::
#=GC RF                    CAGGCAUGCUGgaGCcCCG.CAGCGGCGCCcGGGcgc..........GaCaagguuugc.cgCCCgACACCGuA.cuuc.a.CGGgGCuuaa
//
# STOCKHOLM 1.0

#=GF AC   RF00521
#=GF ID   SAM_alpha
#=GF DE   SAM riboswitch (alpha-proteobacteria)
#=GF AU   Barrick JE
#=GF AU   Corbino KA
#=GF AU   Breaker RR; 0000-0002-2165-536X
#=GF SE   Barrick JE
#=GF SS   Predicted; Barrick JE
#=GF GA   36.00
#=GF TC   36.00
#=GF NC   35.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0045814; negative regulation of gene expression, epigenetic;
#=GF RN   [1]
#=GF RM   16086852
#=GF RT   Evidence for a second class of S-adenosylmethionine riboswitches and other
#=GF RT   regulatory RNA motifs in alpha-proteobacteria.
#=GF RA   Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M,
#=GF RA   Rudnick ND, Breaker RR
#=GF RL   Genome Biol. 2005;6:R70.
#=GF CC   This family is a riboswitch found predominantly in alpha-proteobacteria
#=GF CC   that binds S-adenosyl methionine (SAM). Its structure and sequence appear
#=GF CC   to be unrelated to the SAM riboswitch Rfam:RF00162 found in Gram-positive
#=GF CC   bacteria. This SAM riboswitch is located upstream of the metA and metC
#=GF CC   genes in Agrobacterium tumefaciens, and other methionine and SAM
#=GF CC   biosynthesis genes in other alpha-proteobacteria. Like the other SAM
#=GF CC   riboswitch, it probably functions to turn off expression of these genes in
#=GF CC   response to elevated SAM levels.
#=GF WK   SAM-II_riboswitch
#=GF SQ   40


AJ012295.1/100-178           GAAUUAUCCCGUGGUG-AUUUGGCC-GGUCGGCUUGCA-GCCACGUUAAACAAGU-GGCUAAAA-AGACCGGG-UUGAAACCGGU
BX572608.1/148770-148849     GACUUAUCCCGUGGUG-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAACAAGU-CGCUAAAC-AGGCCGGG-GACGUUGUGGU
BX572607.1/122628-122549     ACCAGAACUCGUGGUC-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAACAACU-CGCUAAAC-AGGCCGGG-GACAGUUCCGA
CP000301.1/5473167-5473246   GACUUAUCCCGUGGUG-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAAUAAAU-CGCUAAAC-AGGCCGGG-GACAGUGUGAU
CP000115.1/164818-164739     UACGUCUCCCGUGGUG-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAACAAGU-CGCUAAAC-AGGCCGGG-GACAAUGUGAU
CP000494.1/790440-790361     CACUUAUCCCGUGGUG-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAAUAAGU-CGCUAAAC-AGGCCGGG-GACGAAUGUGA
CP000319.1/239336-239415     GACCUGUCCCGUGGUG-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAAUAAGU-UGCUAAAC-AGGCCGGG-GACAAUGUGAU
CP000463.1/5459740-5459819   AACUUAUCCCGUGGUG-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAAUAAAU-CGCUAAAC-AGGCCGGG-GAUAUGUGUCC
AAMY01000002.1/143789-143710 GACGCGCUCCGUGGUG-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAACAAGU-CGCUAAAC-AGGCCGGG-GACAGCGCGAU
CP000390.1/128049-128127     CUUUAUCCCCGUGGUG-AUUUGGCC-GGUCGGCUUGCA-GCCACGUUAAAGAAGU-CGCUAAAA-AGGCCGUG-CUCGAAGCUCG
CP000738.1/3178367-3178444   CAAACAAUCCGUGGUG-AUUUGGCC-GGCCGGCUUGCA-GCCACGUUAAAGAAGU-CGCUAAAG--GGCCGAG-GGAACGAUAGA
CP000774.1/443091-443012     GCCCGAACUCGUGGUG-AUUUGAGCCGACCGGCUUGCG-GCCACGUUAAAUAAUU-CGCUAAAA-AGGUCGGG-ACGCGAGCCCC
AAUW01000005.1/136978-137057 GGCGCACUUCGUGGUG-AUUUGGGCCGGCCGGCUUGCA-GCCACGUUAAACAAGU-UGCUAAAA-AGGCCGGA-GGUGAGAACCC
BA000040.2/1515209-1515288   UGCCUGUUCCGUGGUC-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAAAAACU-CGCUAAAC-AGGCCGGG-GACGCUUCCGA
CP000158.1/3446494-3446417   AUCCUCGUCCGUGGUG-AUUUGGCC-GGCCGGCUUGCA-GCCACGUUAAACAAGU-CGCUAAAG--GGCCGAG-AUGCAGGAAAC
CP000133.1/4272024-4272101   AAGGCACUCCGUGGUG-AUUUGGCC-GGCCGGCUUGCA-GCCACGUUAAAAAAGU-CGCUAAAG--GGCCGCG-UGCGGACCGGU
CP000250.1/4839177-4839098   GCCAGAUCCCGUGGUC-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAACAACU-CGCUAAAC-AGGCCGGG-GACAGUUUCUG
AM236080.1/4895428-4895351   UAAGGCCUCCGUGGUG-AUUUGGCC-GGCCGGCUUGCA-GCCACGUUAAAAAAGU-CGCUAAAG--GGCCGCG-UGCGGACCGGU
CP000283.1/4563959-4563880   CCGCGAUCCCGUGGUC-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAACAAUU-CGCUAAAC-AGGCCGGG-GAUAGUUUCGA
BA000012.4/2853663-2853740   CAACAGUUCCGUGGUG-AUUUGGCC-GGUCGGCUUGCA-GCCACGUUAAACAAUU-CGCUAAAG--GGCCGUU-UGCGUGACGUA
CP000758.1/425473-425394     AAUGUGUUCCGUGGUG-AUUUGGCC-GGCCGGCUUGCA-GCCACGUUAAAGAAUU-CGCUAAAAAAGGCCGCG-GUUCGUUACCG
AAAP01003864.1/43186-43108   GUCUUGGUCCGUGGUG-AUUUGUCC-GACCGGAUUGCG-GCCACGUUAAACAUCC-CGCUAAAG-AGGUCCGA-GCGCUCCGCUA
CP000230.1/3707118-3707042   CCCCAGAUUCGUGGGG-AUUUGAG---ACCGGCUUGCG-CCCACGUUAAACAAAC-AGCUAAAA-GGGUCGUG-UGACGAAAGUC
AP007255.1/4636275-4636197   GACUCGAAGCGUGGUG-AUUUGUCC-GACCGGAUUGCG-GCCACGUAAAACAUCC-CGCUAAAG-AGGUCCGA-GCGCUCCGCCA
AATP01000002.1/342466-342543 GCAAAGGACAGUGGUG-AUUUGGCC-GGCCGGCUUGCA-GCCACGUUAAACAACU-CGCUAAAG--GGCCGAU-CCGAUCGUGGA
AAPJ01000002.1/433486-433409 CAAAGCAGAAGUGGUG-AUUUGGCC-GGCCGGCUUGCA-GCCACGUUAAAGAAGU-CGCUAAAG--GGCCGUU-CUGACGAUAUG
CP000394.1/99101-99022       AGUCCUCUCCCUCGCG-AUUUGUCC-GGCCAGCUUGCG-GCGAGGUUAAAUAAUCGCGCUAAAG-AGGCCUGG-GGAGCGUUGUU
ABCL01000002.1/530718-530642 AGUCGCAACCGUGGCG-AUUUGUU---ACCGGAUUGCGGGCCACGUUAAACAAAC-CGCUAAAA--GGUCAGG-AUGAAAGGCCC
CP000781.1/516361-516281     CCGCUCACUCGUGGUGAAUUUGAGCCGGCCCGCUUGCA-GCCACGUUAAACAACCUUGCUAAAA--GGCCGGG-GACGAACAGAC
CP000009.1/1829616-1829537   GUGCCUGACCCUCGUG-AUUUGAGC-GGCCGGCUUGCG-GCGAGGCUAAAGAACUGCGCUAAAG-AGGCCCUG-CGUCGUUAUCG
AAMT01000001.1/270050-270128 CGCGAUUGCCGUGGCG-AUUUGUC--UUCCGGAUUGCGGGCCACGUUAAUCACUC-CGCUAAAG-AGGUCUGG-GACGAUGAACG
CP000577.1/522526-522602     GGCAAAUGCCGUGGUG-CUUUGU----GCCGGAUUGCGGGCCACGUUAAAGAAAC-CGCUAAAG-AGGCGAGG-GCCCGCCGCCC
AAMV01000014.1/88367-88291   AUGCGCGACUGUGGCG-AUUUGUU---ACCGGAUUGCGGGCCACGUUAAACAAAC-CGCUAAAA--GGUCAGG-AUGAAAGGCCC
CP000661.1/637462-637539     GCCGGGCCUCGUGGUG-CUUUGUU---GCCGGAUUGCGGGCCACGUUAAAGAAGC-CGCUAAAG-AGGCGAGG-GCGCACAGCCC
CU234118.1/6715248-6715169   UGCCCGUUCCGUGGUC-AUUUGAGCCGGCCGGCUUGCA-GCCACGUUAAAAAACU-CGCUAAAC-AGGCCGGG-GACGUUAUCGA
AE007869.2/429434-429356     AGCUUAUCCCGUGGUG-AUUUGGCC-GGUCGGCUUGCA-GCCACGUUAAACAAGU-GGCUAAAA-AGACCGGG-UGCUAGGAACC
CP000830.1/2546702-2546778   CCGCGACACCGUGGUG-AUUUGGU---GCCGGAUUGCAGGCCACGUAAAACACGC-UGCUAAAA--GGACGCG-GAACCCCCGAG
CP001389.1/177149-177071     GCUUUAUCCCGUGGUG-AUUUGGCC-GGUCGGCUUGCA-GCCACGUUAAACAAGU-AGCUAAAA-AGGCCGGGUGUCAAACCGG-
AE007869.2/2703451-2703527   AAACGCCUCAGUGGUG-AUUUGCC--GACCGGCUUGCA-GCCACUUUAAAGAAGU-CGCUAAAG--GGUCGAG-GAAAAGGGCAA
AL591688.1/3461766-3461843   CAAAUGAUCCGUGGUG-AUUUGGCC-GGCCGGCUUGCA-GCCACGUUAAAGAAGU-CGCUAAAG--GGCCGAG-GGAACAAUGGA
#=GC SS_cons                 :::::::::<<<<<<_.________.____________.>>>>>>::::::::::.::::::::.::::::::.:::::::::::
#=GC RF                      aacuuauuCCGUGGuG.AUUUGacC.GGCCGGCUUGCA.gCCACGUUAAAcAAgU.CGCUAAAa.AGGCCggG.gacaaauugua
//
# STOCKHOLM 1.0

#=GF AC   RF00522
#=GF ID   PreQ1
#=GF DE   PreQ1 riboswitch
#=GF AU   Barrick JE
#=GF AU   Breaker RR; 0000-0002-2165-536X
#=GF SE   Barrick JE
#=GF SS   Predicted; Barrick JE
#=GF GA   39.00
#=GF TC   39.30
#=GF NC   38.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.41 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0008616; queuosine biosynthetic process;
#=GF RN   [1]
#=GF RM   14660578
#=GF RT   Identification of four genes necessary for biosynthesis of the modified
#=GF RT   nucleoside queuosine.
#=GF RA   Reader JS, Metzgar D, Schimmel P, de Crecy-Lagard V
#=GF RL   J Biol Chem 2004;279:6280-6285.
#=GF CC   This family is a bacterial riboswitch that binds to the metabolite preQ1,
#=GF CC   an intermediate in the biosynthesis of the modified nucleoside queuosine
#=GF CC   from GTP. One example of this riboswitch is located in the leader of the
#=GF CC   Bacillus subtilis ykvJKLM (queCDEF) operon which encodes four genes
#=GF CC   necessary for queuosine production [1]. PreQ1 binding to the riboswitch
#=GF CC   aptamer is thought to induce premature transcription termination within
#=GF CC   the leader to down-regulate expression of these genes.
#=GF WK   PreQ1_riboswitch
#=GF SQ   35


AE017355.1/1568663-1568707   AAUAACGUGGUUCGAA---ACC-AUCCCACG---------------------UAAAAAAACUAAGGAGAU
AE017355.1/1321429-1321472   ACGGGAGAGGUUCGCGA--AC---UCCCUCU---------------------AUAAAAAACUAUGGAAAC
AL766846.1/39196-39152       CUCGGACUGGUUCGAAA--ACU--UCCCAGA---------------------AUAAAAAACUAAGUGACU
AL596166.1/191853-191900     CCACACGUGGUUCAUUCAUACC-AUCCCACG---------------------UAAAAAAACUAGGAGGAA
X99978.2/10136-10181         CAAUACGUGGUUCGUA---ACC-AUCCCACG--------------------UUAAAAAAACUAGGAGGAA
AE016827.1/1848390-1848434   UAAUUCGUGGUUCGAAA--ACC--UCCCACG---------------------CAAAAAAACUAAGGAAAA
AASA01000045.1/1296-1252     UUAUUUGUGGUUCGUAA--ACC--UCCCACA---------------------CAAAAAAACUAAGGACAC
CP000746.1/2223340-2223384   UUCAUCGUGGUUCGCAA--ACC--UCCCACG---------------------CAAAAAAACUAAGGAAAU
AAXV01000007.1/14855-14899   AGCACCGUGGUUCGUAA--CCA--UCCCACG---------------------AAAAAAAACUAAGGAGAA
AAXB02000001.1/142227-142271 CUUGAACUGGUUCGAAA--ACC--UCCCAGU---------------------AUAAAAAACUAGGCAAAG
CP000513.1/859945-859989     CCGCUUGUGGUUCGAAA--ACU--UCCCACA---------------------CUAAAAAACUAGGAAAAA
AARF01000079.1/5363-5319     AUGGGAGAGGUUCGAGA--UCU--UCCCUCU---------------------AUAAAAAACUAAGGAGCU
CP000233.1/1599957-1600001   CUUGGACUGGUUCGUAA--ACU--UCCCAGU---------------------AUAAAAAACCAAGAAUCU
BA000028.3/467676-467632     AUCACCGUGGUUCGUAA--CCA--UCCCACG---------------------CAAAAAAACUAGGAAGGA
AE017333.1/1501710-1501754   GCGGGAGAGGUUCUAGC--AAA--ACCCUCU---------------------AUAAAAAACUAAGGAAAG
CR936503.1/1598027-1597983   AAAAACGUGGUUCGUAA--CCA--UCCCACG---------------------CUAAAAAACUAGGAGGAU
ABDX01000003.1/184506-184550 UUGGUAGAGGUUCGUAA--CCA--UCCCUCU---------------------AUAAAAAACUAAGGGCUG
CP000414.1/1235047-1235002   AUAAUAGCGGUUCAUCA--ACC-AUCCCGCU---------------------UAAAAAAACUAGGAGAUA
AAYG02000018.1/120313-120357 UCUGGACUGGUUCGUGA--ACU--UCCCAGU---------------------AUAAAAAACCAAGUAUCU
ABCF01000001.1/139145-139189 GCAGGAGAGGUUCUAGC--UUA--ACCCUCU---------------------AUAAAAAACUAAGGAAAC
AE002098.2/329220-329176     CCGCCCGUGGUUCGAAA--ACC--UCCCACA---------------------UUAAAAAACUAAGGAAAC
AAAK03000099.1/1629-1673     CUUGGACUGGUUCGGAA--ACU--UCCCAGA---------------------AUAAAAAACUAAGUAUCU
CP000764.1/1180651-1180694   AUGGGAGAGGUUCGCGA--AC---UCCCUCU---------------------AUAAAAAACUAUGAGAAC
AAOX01000006.1/21305-21347   ACGGUAGAGGUUCUAG----CU--ACCCUCU---------------------CAAAAAAACUAAGGAAAA
BA000004.3/2373342-2373299   GUGAGAGAGGUUCGCGA--AC---UCCCUCU---------------------AUAAAAAACUAAGGCAAG
AP006627.1/2249570-2249527   AAAGAAGAGGUUCGCGA--AC---UCCCUCU---------------------AUAAAAAACUAACCAAUU
AM421808.1/1884627-1884671   CGCCCCGUGGUUCGAAA--ACC--UCCCACA---------------------CUAAAAAACUAAGGAAAC
AAVO02000002.1/275638-275594 UCAUAACUGGUUCGAAA--CCC--UCCCAGU---------------------AUAAAAAACUAGGUCAUG
CP000029.1/370924-370878     AUAACAGAGGUUCCUAG--CCGAAACCCUCU---------------------AUAAAAAACUAGACAUGA
AP006716.1/2221258-2221304   UCAAAAGAGGUUCCUAG--CUGAAACCCUCU---------------------AUAAAAAACUAGACAAUA
AP008934.1/2076124-2076170   UAUAAAGAGGUUCCUAG--CUGAUACCCUCU---------------------AUAAAAAACUAGACACAU
AARM02000383.1/1741-1694     CCACACGUGGUUCAUUCAUACC-AUCCCACG---------------------UAAAAAAACUAAGGAGGA
AL009126.3/1439274-1439318   GCGGGAGAGGUUCUAGC--UAC--ACCCUCU---------------------AUAAAAAACUAAGGACGA
AE004439.1/209165-209100     UUCAUAGUGGUUCGUA---ACC-CUCCCACUUGAACAACCAACAAUUGUUCGAAACAAAACUAGGAAAAU
AL935263.2/2519559-2519515   GCUGGCCUGGUUCGUAA--ACU--UCCCAGG---------------------AUAAAAAACCAAGAACUU
#=GC SS_cons                 :::::<<<<<_______..___..__>>>>>.....................::::::::::::::::::
#=GC RF                      uuaauAGUGGUUCGUAA..ACC..UCCCACU.....................AaAAAAAACUAGGaAAAu
//
# STOCKHOLM 1.0

#=GF AC   RF00523
#=GF ID   Prion_pknot
#=GF DE   Prion pseudoknot
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:11160898
#=GF SS   Published; PMID:11160898
#=GF GA   39.00
#=GF TC   39.00
#=GF NC   38.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0006412; translation;
#=GF RN   [1]
#=GF RM   11160898
#=GF RT   Pseudoknots in prion protein mRNAs confirmed by comparative sequence
#=GF RT   analysis and pattern searching.
#=GF RA   Barrette I, Poisson G, Gendron P, Major F
#=GF RL   Nucleic Acids Res 2001;29:753-758.
#=GF CC   This family represents a predicted pseudoknot structure found in prion
#=GF CC   protein mRNA. It has been suggested that the family has a possible effect
#=GF CC   in prion protein translation [1].
#=GF WK   Prion_pseudoknot
#=GF SQ   148


AY350268.1/189-228       CCAUGG--AGG---UGG---CUGGGG---CCAACCUCAUGG---AGGUGGCUGG
AY350268.1/237-279       CCAUGG--UGG---UGG---CUGGGG---ACAGCCACAUGGUGGUGGAGGCUGG
S80743.1/84-123          CCAUGG--UGG---UGG---CUGGGG---ACAGCCUCAUGG---UGGUGGCUGG
S80743.1/36-75           GGGCGG--UGG---UGG---CUGGGG---GCAGCCUCAUGG---UGGUGGCUGG
AF009181.2/237-279       CCAUGG--UGG---UGG---CUGGGG---GCAGCCACAUGGUGGUGGAGGCUGG
U08299.1/180-219         UCAUGG--UGG---UGG---CUGGGG---GCAGCCUCAUGG---UGGUGGCUGG
U08299.1/228-267         CCAUGG--UGG---UGG---CUGGGG---ACAGCCUCAUGG---CGGUGGCUGG
U08311.1/204-243         CCAUGG--UGG---CGG---CUGGGG---ACAGCCUCAUGG---UGGCGGCUGG
AY320375.1/93-132        CCAUGG--AGG---UGG---CUGGGG---CCAGCCUCAUGG---AGGUGGCUGG
AY320375.1/141-180       UCAUGG--AGG---UGG---CUGGGG---UCAGCUCCAUGG---UGGUGGCUGG
AY320375.1/189-231       ACAUGG--UGG---UGG---CUGGGG---ACAGCCACAUGGUGGUGGAGGCUGG
U08305.1/228-267         CCAUGG--UGG---UGG---CUGGGG---GCAGCCUCAUGG---UGGUGGCUGG
AY320369.1/123-162       UCAUGG--AGG---UGG---CUGGGG---CCAGCCUCAUGG---AGGUGGCUGG
AY320369.1/72-114        UCAGGG--AGGGGGUGG---CUGGGG---UCAGCCCCAUGG---AGGUGGCUGG
AY133042.1/273-312       CGGUGG--UGG---AGG---CUGGGG---ACAGCCCCACGG---UGGAGGCUGG
AY133042.1/219-261       CGGCGG--UGG---AGG---CUGGGG---ACAGCCCCAUGGUGGUGGCGGCUGG
AY133042.1/165-207       GGGUGG--UGG---CGG---CUGGGG---UCAGCCCCACGGCGGUGGAGGCUGG
AY133036.1/109-148       CCAUGG--CGG---UGG---CUGGGG---UCAGCCCCACGG---UGGUGGCUGG
AY133036.1/157-196       UCACGG--UGG---CGG---CUGGGG---UCAGCCCCAUGG---UGGCGGCUGG
AF139166.1/150-189       UCAUGG--UGG---UGG---CUGGGG---CCAGCCCCAUGG---UGGUAGCUGG
AF139166.1/99-141        CCACAG--CGG---GGGGACCUGGGG---UCAGCCCCAUGG---AGGUAGCUGG
AF139166.1/198-231       UCAUGG--UGG---UGG---CUGGGG---------CCAUGG---AGGUGGCUCG
U08312.1/159-198         UCAUGG--UGG---CGG---CUGGGG---GCAGCCCCAUGG---UGGUGGCUGG
AY133043.1/142-190       CCAUGG--AGG---UGGAGGCUGGGGUCAGCAGCCCCAUGGAGGUGGAGGCUGG
AY133037.1/237-276       UGGUGG--UGG---UGG---CUGGGG---ACAACCCCACGG---UGGUGGCUGG
AY133037.1/183-225       UCAUGG--UGG---UGG---CUGGGG---GCAACCCCAUGGUGGCGGAGGUUGG
AF113940.1/126-165       CCACGG--AGG---CGG---CUGGGG---CCAGCCCCAUGG---UGGAGGCUGG
AF113940.1/78-117        CCACGG--AGG---AGG---CUGGGG---UCAGCCCCACGG---AGGCGGCUGG
U75389.1/207-246         UCAUGG--UGG---UGG---CUGGGG---ACAGCCUCAUGG---UGGUGGCUGG
U75389.1/159-198         UCAUGG--UGG---UGG---CUGGGG---UCAGCCUCAUGG---UGGCGGCUGG
AY133050.1/213-252       CCAUGG--UGG---CGG---UUGGGG---GCAACCCCAUGG---UGGCAGCUGG
AY133050.1/165-204       GGGUGG--UGG---UGG---CUGGGG---GCAGCCCCAUGG---UGGCAGCUGG
AY133050.1/261-300       UCAUGG--UGG---CGG---CUGGGG---GCAACCCCAUGG---UGGUGGCACC
AY133044.1/136-181       CCAUGG--UGG---UGGAGGCUGGGG---UCAGCCCCAUGGUGGUGGAGGCUGG
AY133044.1/190-235       CCAUGG--UGG---UGGAGGAUGGGG---UCAGCCUCAUGGUGGUGGCGGUUGG
AJ132392.1/146-185       UCAUGG--AGG---UGG---CUGGGG---UCAGCCCCAUGG---UGGUGGCUGG
AY133051.1/210-249       CCAUGG--UGG---UGG---CUGGGG---UCAGCCGCAUGG---UGGUGGUUGG
AY133051.1/162-201       GGGCGG--UGG---CGG---CUGGGG---UCAACCCCAUGG---UGGUGGUUGG
AY133045.1/139-184       CCAUGG--CGG---CGGAGGCUGGGG---UCAGCCCCACGGGGGUGGAGGCUGG
AY133045.1/85-130        CCAGGG--AGG---CGGAGGCUGGGG---UCAGCCCCAUGGGGGUGGAGGCUGG
AY133039.1/103-142       UCAUGG--UGG---UAG---CUGGGG---CCAGCCCCAUGG---UGGUAGCUGG
AY133039.1/151-184       CCAUGG--CGG---UGG---CUGGGG---------CCAUGG---AGGUGGCUCG
AF113942.1/192-234       CCAUGG--UGG---UGG---UUGGGG---ACAGCCACAUGGUGGUGGAGGCUGG
AF113942.1/93-135        UCAGGG--AGGGGGUGG---CUGGGG---UCAGCCCCAUGG---UGGUGGCUGG
U08309.1/180-219         CCAUGG--UGG---CGG---CUGGGG---ACAGCCUCAUGG---UGGUGGCUGG
U08309.1/132-171         CCAGGG--UGG---UGG---CUGGGG---GCAACCCCAUGG---UGGCGGCUGG
AY133052.1/237-279       CCAUGG--UGG---UGG---CUGGGG---ACAGCCCCAUGGUGGUGGAGGCUGG
AY133052.1/189-228       CCAUGG--CGG---UGG---CUGGGG---UCAGCCCCACGG---CGGCGGCUGG
AY133046.1/348-387       CCAUGG--UGG---AGG---CUGGGG---UCAGCCCCAUGG---UGGUGGCUGG
AY133046.1/300-339       GGGUGG--UGG---UGG---CUGGGG---CCAGCCCCACGG---UGGAGGCUGG
AF090852.1/93-135        CCAGGG--AGGGGGUGG---CUGGGG---UCAGCCCCAUGG---AGGUGGCUGG
AF113943.1/69-108        CCACGG--AGG---CGG---CUGGGG---UCAGCCCCACGG---AGGAGGCUGG
AF113943.1/18-60         CCAGGG--AGGGGGCGG---CUGGGG---UCAGCCCCACGG---AGGAGGCUGG
AF113937.1/90-129        CCAUGG--UGG---CGG---CUGGGG---UCAGCCCCACGG---UGGUGGCUGG
AY133053.1/112-151       CCACGG--AGG---UGG---CUGGGG---UCAGCCCCACGG---AGGUGGUUGG
AY133053.1/160-202       CCACGG--UGG---UGG---CUGGGG---ACAGCCCCAUGGUGGCGGAGGCUGG
AF015603.1/183-222       CCAUGG--CGG---CGG---CUGGGG---GCAGCCUCACGG---UGGUGGCUGG
AF015603.1/231-270       CCACGG--CGG---UGG---CUGGGG---GCAGCCCCACGG---UGGUGGCUGG
AF113938.1/90-129        UCAUGG--UGG---CGG---CUGGGG---UCAGCCCCACGG---UGGUGGCUGG
AY133054.1/213-252       CCAUGG--UGG---UGG---CUGGGG---UCAGCCCCACGG---UGGUGGCUGG
AY133054.1/162-204       CCAGGG--AGGGGGAGG---CUGGGG---CCAGCCCCACGG---UGGUGGCUGG
AY133054.1/261-303       CCAUGG--UGG---UGGAGGCUGGGG---UCAGCCCCAUGG---UGGUGGCACC
AY133048.1/133-178       CCAUGG--UGG---UGGCGGCUGGGG---UCAGCCCCAUGGUGGUGGCGGCUGG
AY133061.1/85-127        CCAAGG--AGG---UGGAGGCUGGGG---ACAGCCUCAUGG---AGGUGGCUGG
AY133061.1/136-178       CCAUGG--UGG---CGGUGGCUGGGG---ACAACCCCAUGG---UGGUGGUGGC
AY133055.1/609-651       CCACGG--UGG---UGG---CUGGGG---ACAGCCCCAUGGUGGUGGUGGCUGG
AY133055.1/558-600       UCACAG--UGG---CGG---CUGGGG---ACAGCCCCAUGGUGGUGGCGGCUGG
AY133049.1/112-151       CCACGG--UGG---CGG---CUGGGG---UCAGCCCCACGG---UGGCGGCUGG
AY133049.1/208-247       CCAUGG--UGG---CGGAGGCUGGGG---ACAGCCCUAUGG------UGGCAAG
U29185.1/25677-25716     UCAUGG--UGG---UGG---CUGGGG---GCAGCCCCAUGG---UGGUGGCUGG
AY133056.1/213-255       UCAUGG--UGG---UGG---CUGGGG---ACAGCCCCAUGGUGGCGGUGGCUGG
AY133056.1/264-306       CCACGG--UGG---UGG---CUGGGG---ACAGCCCCAUGGUGGCGGUGGCUGG
AF117310.1/156-198       CCAUGG--AGG---UGG---CUGGGG---ACAGCCACAUGGUGGUGGAGGCUGG
U15164.1/177-216         UCAUGG--UGG---UGG---CUGGGG---GCAACCCCAUGG---UGGCGGCUGG
U29186.1/28866-28905     CCACGG--UGG---UGG---CUGGGG---ACAACCCCAUGG---GGGCAGCUGG
U29186.1/28914-28953     UCAUGG--UGG---UAG---UUGGGG---UCAGCCCCAUGG---CGGUGGAUGG
AY133057.1/112-151       UCAUGG--UGG---CGG---CUGGGG---ACAGCCCCACGG---UGGUGGUUGG
AY133057.1/160-202       ACAUGG--UGG---UGG---CUGGGG---ACAGCCCCAUGGCGGCGGUGGCUGG
AF117311.1/48-87         CCACGG--UGG---UGG---CUGGGG---ACAGCCCCACGG---UGGUGGCUGG
AF117311.1/96-138        CCACGG--UGG---UGG---CUGGGG---ACAGCCCCAUGGUGGUGGAGGCUGG
U15165.1/153-192         CCAGGG--UGG---UGG---CUGGGG---GCAGCCUCAUGG---UGGUGGCUGG
U15165.1/201-240         CCAUGG--UGG---CGG---CUGGGG---ACAGCCCCAUGG---UGGCGGAUGG
AY133058.1/240-282       CCACGG--UGG---UGG---CUGGGG---ACAGCCCCAUGGUGGGGGUGGCUGG
AY133058.1/189-231       UCACGG--UGG---UGG---CUGGGG---ACAGCCCCACGGUGGUGGUGGCUGG
S69654.1/204-243         CCAUGG--UGG---UGG---CUGGGG---ACAACCUCAUGG---UGGUGGCUGG
S69654.1/252-291         UCAUGG--UGG---UGG---CUGGGG---UCAGCCCCAUGG---CGGGGGCUGG
AY327450.1/213-252       UCAUGG--AGG---UGG---CUGGGG---CCAACCUCAUGG---AGGUGGCUGG
AY327450.1/261-303       CCAUGG--UGG---UGG---CUGGGG---ACAGCCACAUGGUGGCGGAGGCUGG
AY208166.1/147-186       CCAUGG--GGG---CGG---CUGGGG---ACAGCCCCACGG---GGGUGGCUGG
AF117313.1/123-162       UCAUGG--AGG---UGG---CUGGGG---UCAGCCCCAUGG---AGGUGGCUGG
AY371694.1/611-650       CCAUGA--AGG---UGG---CUGGGG---CCAACCUCAUGG---AGGUGGCUGG
S80539.1/54-93           UCAUGG--CGG---UGG---CUGGGG---GCAGCCCCAUGG---UGGUGGCUGG
AY639093.1/189-228       CCAUGG--GGG---UGG---CUGGGG---CCAACCUCAUGG---AGGUGGCUGG
AF117314.1/177-216       CCAUGG--UGG---UGG---CUGGGG---GCAGCCCCAUGG---UGGGGGCUGG
AF117314.1/225-264       UCAUGG--CGG---GGG---CUGGGG---UCAGCCUCAUGG---CGGUGGCUGG
AY367643.1/296-338       CCAUGG--UGG---UGG---CUGGGG---ACGGCCACAUGGUGGUGGAGGCUGG
AF117321.1/165-204       UCAUGG--AGG---UGG---CUGGGG---UCAGCCCCAUGG---UGGUGGUUGG
U08952.1/213-252         CCACGG--GGG---UGG---CUGGGG---ACAGCCCCACGG---GGGUGGCUGG
U08952.1/165-204         GGGUGG--UGG---CGG---CUGGGG---CCAGCCCCACGG---GGGUGGCUGG
S46825.1/253-292         CCACGG--GGG---UGG---CUGGGG---UCAGCCCCACGG---GGGUGGCUGG
AY367639.1/202-244       UCAGGG--AGGGGGUGG---CCGGGG---UCAGCCCCAUGG---AGGUGGCUGG
L07623.1/162-204         CCAGGG--AGGGGGUGG---CUGGGG---ACAGCCCCACGG---AGGUGGCUGG
AY639096.1/189-228       CCAUGG--AGG---UGG---CUGGGG---CCAACCUCAUGG---AGGAGGCUGG
AF117323.1/108-147       CCAUGG--AGG---UGG---CUGGGG---ACAGCCACAUGG---AGGUGGCUGG
AL163932.5/150210-150250 CCAAGAUGUGG---AGG---CUGGGG---UCAGCC-CUUGG---UGGAGGUUGC
AF117324.1/204-243       UCAUGG--UGG---UGG---CUGGGG---GCAGCCCCAUGG---UGGUGGUUGG
AF117324.1/153-195       UCAGGG--UGG---CGGCACCUGGGG---GCAGCCCCAUGG---UGGUGGCUGG
AY360091.1/199-238       CCAUGR--AGG---UGG---CUGGGG---CCAACCUCAUGG---AGGUGGCUGG
AY360091.1/247-289       CCAUGG--WGG---UGG---CUGGGG---GCAGCCACAUGGUGGUGGAGGCUGG
AF134232.1/172-130       GCAUGG--UGG---UGG---UUGGGG---ACAGCCCCAUGGUGGUGGAGGCUGG
M33958.1/354-393         UCAUGG--UGG---UGG---UUGGGG---UCAGCCCCAUGG---UGGUGGCUGG
M33958.1/306-345         CCAUGG--UGG---UGG---AUGGGG---ACAGCCCCAUGG---UGGUGGCUGG
AF367623.1/228-267       UCAUGG--UGG---UGG---CUGGGG---UCAGCCCCAUGG---CGGUGGCUGG
AF367623.1/180-219       CCAUGG--UGG---UGG---CUGGGG---ACAACCCCAUGG---CGGUGGCUGG
X74771.1/213-252         CCAUGG--AGG---CGG---CUGGGG---CCAGCCUCAUGG---AGGUGGCUGG
X74759.1/189-228         CCAUGG--AGG---UGG---CUGGGG---CCAGCCUCAUGU---AGGUGGCUGG
X74759.1/237-276         CCAUGG--UGG---UGG---CUGGGG---ACAGCCACAUGG---UGGUGGAGGG
AF367624.1/180-219       CCAUGG--CGG---UGG---CUGGGG---ACAGCCUCACGG---UGGUGGUUGG
AF367625.1/156-195       CCAUGG--UGG---UGG---CUGGGG---ACAGCCCCAUGG---CGGUGGCUGG
AF367625.1/204-243       UCACGG--UGG---UGG---UUGGGG---UCAGCCCCAUGG---CGGCGGCUGG
AY585239.1/168-210       GCAUGG--UGG---UGG---CUGGGG---ACAGCCGCAUGGUGGUGGAGGCUGG
AF117329.1/135-174       CCAUGG--UGG---UGG---CUGGGG---UCAGCCGCACGG---UGGUGGUUGG
U08293.1/180-219         CCAUGG--UGG---CGG---CUGGGG---ACAGCCCCAUGG---CGGUGGCUGG
U08293.1/132-171         CCAGAG--CGG---UGG---CUGGGG---GCAGCCUCAUGG---UGGUGGCUGG
AF177293.1/3-42          CCAGGG--CGG---CGG---CUGGGG---ACAACCCCAUGG---GGGUGGCUGG
U08295.1/201-240         CCAUGG--UGG---CGG---CUGGGG---ACAGCCCCAUGG---UGGCAGCUGG
AK090575.1/288-327       CCAUGG--UGG---UGG---CUGGGG---ACAGCCUCAUGG---UGGCAGCUGG
AY723286.1/271-313       GCAUGG--AGG---UGG---CUGGGG---ACAGCCACAUGGUGGUGGAGGCUGG
U08302.1/228-267         UCAUGG--UGG---CGG---CUGGGG---ACAGCCUCAUGG---UGGUGGCUGG
U08302.1/180-219         UCAUGG--UGG---UGG---CUGGGG---GCAGCCUCAUGG---UGGCGGCUGG
AY168450.1/109-148       CCAUGG--UGG---UAG---UUGGGG---ACAGCCCCACGG---UGGUGGCUGG
AY168450.1/58-100        CCACAG--UGG---GGGCAACUGGGG---CCAGCCCCAUGG---UGGUGGUUGG
U08297.1/180-219         UCAUGG--UGG---UGG---CUGGGG---GCAACCUCAUGG---UGGUGGCUGG
U75385.1/135-174         GGGUGG--CGG---UGG---CUGGGG---GCAGCCUCAUGG---UGGUGGCUGG
AY133040.1/166-208       UGGUGG--UGG---UGG---CUGGGG---ACAGCCCCAUGGUGGUGGUGGCUGG
AY133034.1/180-219       UCACGG--UGG---CGG---CUGGGG---GCAGCCCCAUGG---UGGUGGCUGG
U08310.1/249-288         CCAUGG--UGG---UGG---CUGGGG---ACAGCCUCAUGG---UGGCGGCUGG
U08310.1/201-240         CCAUGG--UGG---CGG---CUGGGG---ACAGCCCCAUGG---UGGCGGCUGG
U08304.1/177-216         UCAUGG--UGG---UGG---CUGGGG---GCAACCUCAUGG---UGGCGGCUGG
AY320368.1/171-213       CCAUGG--UGG---UGG---CUGGGG---ACAGCCACGUGGUGGUGGAGGCUGG
AY133041.1/82-127        GCAGGG--UGG---CGGCACCUGGGG---GCAGCCUCAUGGUGGUGGUGGCUGG
AY133035.1/207-249       UCAUGG--UGG---CGG---CUGGGGGCAGCAGCCUCAUGG---UGGUGGCUGG
AY133035.1/258-297       CCAUGG--UGG---CAG---CUGGGG---ACAGCCCCAUGG---UGGUGGUAGC
AAPY01183835.1/229-187   CCAGGG--CGG---UGGCACCUGGGG---GCAGCCUCAUGG---UGGUGGCUGG
FJ796962.1/153-192       CCAGGG--UGG---UGG---CUGGGG---GCAGCCUCAUGG---UGGUGGCUGG
U75383.1/135-174         GGGUGG--UGG---UGG---CUGGGG---GCAGCCUCAUGG---UGGUGGCUGG
EU341507.1/224-263       GGGCGG--UGG---UGG---CUGGGG---UCAGCCCCAUGG---UGGCGGCUGG
AY133038.2/321-360       AGGUGG--UGG---UGG---CUGGGG---ACAACCCCACGG---UGGUGGCUGG
#=GC SS_cons             <<<<<<..___...___...______...______>>>>>>...::::::::::
#=GC RF                  CCAuGG..UGG...UGG...CUGGGG...aCAGCCCCaUGG...UGGUGGCUGG
//
# STOCKHOLM 1.0

#=GF AC   RF00524
#=GF ID   R2_retro_el
#=GF DE   R2 RNA element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15146081
#=GF SS   Published; PMID:15146081
#=GF GA   38.00
#=GF TC   38.10
#=GF NC   37.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 1900268; regulation of reverse transcription;
#=GF RN   [1]
#=GF RM   15146081
#=GF RT   Secondary structure models of the 3' untranslated regions of diverse R2
#=GF RT   RNAs.
#=GF RA   Ruschak AM, Mathews DH, Bibillo A, Spinelli SL, Childs JL, Eickbush TH,
#=GF RA   Turner DH
#=GF RL   RNA 2004;10:978-987.
#=GF RN   [2]
#=GF RM   7679954
#=GF RT   Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal
#=GF RT   target site: a mechanism for non-LTR retrotransposition.
#=GF RA   Luan DD, Korman MH, Jakubczak JL, Eickbush TH
#=GF RL   Cell 1993;72:595-605.
#=GF CC   This family represents the 3' UTR region of the R2 retrotransposable
#=GF CC   element. This family is known to interact with the R2-encoded reverse
#=GF CC   transcriptase in a reaction known as target primed reverse transcription
#=GF CC   (TPRT) [1,2].
#=GF WK   R2_RNA_element
#=GF SQ   15


U13033.1/1423-1658   ACUUAGCU-AAAACGUUUGGUUC--AA----AACAUU---UGCUUGCUGUCUUGGCAUAACAUCAAUA-AAGGCAUAAACAUCGCAAAACAAUGGUUAUAUAUAAAUGGCU-AUGAGGAUGG--UUUUAGUACG-UAGGCGUUGC---GGAAC-UUCG----------GU-UCAGAUAGAGCAAUGAAUCGUGCAUGCUAG-GAAAACUGACCACACGC--AGU--UGGCAGCCCUAGUAUCUUUCGAUAGAUUU---CCAUACCUCCGCGAUC
U81812.1/515-708     ACUUAGCC-UAUACACUAUGUUGG-AG----AGAGAC----GCUUGCUACCUAGGCAUAAUGUGAA-U-UAGGUAUAAACAUCGUGGU--------------U--GUAAAC-UUGAG-UGGG--UUUUAGUACGGUAUGCGUG-----AUUAC-UUC-----------GU-AAU--------CAUGAAUCGUGCAUGCUAG-UGGGGU---------------UUG-GCCUCCACUAGUAUCUUU-GA-AGAUUU---UCCUUCCUCAGCGAUC
U13034.1/1423-1648   ACGUAGCU-UAAACGUUUGGUUCA-CA----UACAUC---UGCCUGCUGCCUUGGCAUAAUAUCAA-A-AAGGCAUAAACAUCGCACAAUAAUGGU------UAAUACGGCUAUGAGGAUGG--UUUUAGUACG-UAGGCGUUGC---GGAAC-UUCG----------GU-UCAGAUAGAGCAAUGAAUCGUGCAUGCUAG--GAAACUGACCA-------AAUGGUGGCAGCCCUAGUAUCUUUCGA-AGAUUU---CCAUACCUUUGCGAUC
U81813.1/515-708     ACUUAGCC-UAUACACUAUGUUGG-AG----AGAGAC----GCUUGCUACCUAGGCAUAAUGUGAA-U-UAGGUAUAAACAUCGUGGU--------------U--GUAAAC-UUGAG-UGGG--UUUUAGUACGGUAUGCGUG-----AUUAC-UUC-----------GU-AAU--------CAUGAAUCGUGCAUGCUAG-UGGGGU--------------UUGGCCUCU--ACUAGUAUCUUU-GA-AGAUUU---CCCUUCCUCAGCGAUC
U13035.1/1423-1647   ACGUAGCUUAAAACGUUUGGUUCA-CA----UACAUC---UGCCUGCUGCCUUGGCACAAUAUCAA-A-AAGGCAUAAACAUCGCACAUAAUGGUUAU----U--UACGGCUAUGAGGAUGG--UUUUAGUACG-UAGGCGUUGC---GGAAC-UUCG----------GU-UCGGAUAGAGCAAUGAAUCGUGCAUGCUAG---GAACUGACC--------AAAUAACGCAGCCCUAGUAUCUUUCGA-AGAUUU---CCAUACCUUUGCGAUC
U81814.1/504-719     GCUUGAUC-UCUGUAUUUGUUUCU-AUUUUGAACAUU---UGCCUGCUACCUUGGCAUAACAUCAA-U-AAGGUACAAACAUCGCAAA---------------AAGUCAUC-AUAAGGUGGG--UUUUAGUACG-UAGGCGCUGU---AGAAC-UUAA--------UUGU-UCUGAUAGAGCAGCGAGUCGUGCAUGCUAG-UCUAAC-------------AUUUCUUGCU-ACCUAGUAUCUUUAGA-AGAUUU---CCCUCCCUUAGCGGUC
U81815.1/525-734     AUGUACUA-ACCUCUAGCUUUUCUUAU----ACCUUU---UGCCUGCUACCUUGGCAUUACAUCUAAA-AAGGUACAAACAUCGCAUU-----------------GUCAUA-AAGAGG-UGG--UUUUAGUACG-UAGGCGCUGU---GGGAC-UUCA--------UUGU-CCCGGUGAUGCAGUGAAUCGUGACUACGAGAUUGUCC-------------AGUAGUUGGU--GCUCGUAUCUUUAGA-AGAUUU---CCUU-CCUCGGCGAUC
U81985.1/508-709     ACCUAGCC-GAAACACUAUGUUGG-AA----AGAAGA---CGCUUGCUACCUAGGCAUAAUGUAAAAU-UAGGUAUAAACAUCGCAGU--------------U--GUAAAC-UUGAGG-UGG---UUUAGUACG-UAGGCGUGAU---GAUGA-CUUG----------UU-GAAG-UGAAACCACGAAUCGUGCUCGCUAU---UA-C--------------GUUGGCCCUUA-AUAGUAUCUAU-GA-AGAUUU--CCCAU-CCUCAGCGGUC
X51967.1/3349-3585   ACUUAGCU-AAAUCGUUUGGUUC--AA----AACAUU---UGCUUGCUGUCUUGGCAUAACAUCAAUA-AAGGCAUAAACAUCGCAAAAUAAUGGUUAUAAUUAAAUGGCU-AUGAGGAUGG--UUUUAGUACG-UAGGCGUUGC---GGAAC-UUCG----------GU-UCAUAUAGAGCAAUGAAUCGUGCAUGCUAG-GAAAACUGACCACACAC--AGUGUUGGCAGACCUAGUAUCUUUCGA-AGAUUU---CCAUACCUCCGCGAUC
U81809.1/517-738     ACUUAAUC-A-UGCACCACGAAC--AU----AUUGAUGAAAGCUUGCUGCCGUAGCAUAACACCUAAAAACGGCAUAAAAUUCGCAU---------------------AAA-ACGAGGCGGU--UUUUAGUACG-UAGGCAUCUCUGGGGGGA-GGAU----------AU-CCACCCCAA-UGAUGAAUCGUGCAUGCACACUCACAUAGGCCAAACAAGAACUACCGGCCGAGUGUGUAUCUUUUGA--GAUUU---UACGACCUUAGCGA-C
AF015819.1/3308-3490 AAAUCGCA-U-UGGGAUAGGAUG--AU----AGCG------------CACCUGGUCAUCGUCUCUC-U-CAGCUGCUCA-CUUGCUGUUC----------UAAGUGAUAAUACCGUUG---UUUUUUUAGUGGG-UAUUCUUUU-----ACGC-UUUC----------GUAG---------GAGCGAGUCCCACACUCU-U--GGAGC-------------AAUCCGGG-----GUAGUGCCUAA--A-CGCAUU---UCUU-CAAC-GUAAAA
U13031.1/1423-1644   ACUUAGCU-AAAUCGUUUGGUUC--AA----AACAUU---UGCUUGCUGUCUUGGCAUAACAUCAAUA-AAGGCAUAAACAUCGCAAAUAAUGGUAAUAUA-UAAAUGGCU-AUGAGGAUGG--UUUUAGUACG-UAGGCGUUGC---GGAAC-UUCG----------GU-UCA------GCAAUGAAUCGUGCAUGCUAG--GAAACUGA----------AGUGUUGACAGACCUAGUAUCUUUCGAUAGAUUU---CCAUACCUCCGCGAUC
U81810.1/484-703     ACUUAAUC-A-UGCAUCACGUUC--AU----AUUAAA---AGCUUGCUGCCGUAGCAUAACAUCUAAAAACGGCAUAAAAUUCGCUUA--------------------AAA-ACGAGGCCUU--UUUUAGUACG-UAGGCGUCUUCU-GGGUC-GUAU----------GA-ACCCACA---AGAUGAAUCGUGCAUGCACACUCUUAUUGGCUAAAUAAC-AUCAUAACCUGAGUGUGUAUCUUUUGA-AGAUUUUUACGAU-CCUUAGCGAAC
U13032.1/1423-1651   ACUUAGCU-AAAACGUUUGGUUC--AA----AACAUU---UGCUUGCUGUCUUGGCAUAACAUCAAUA-AAGGCAUAAACAUCGCAAAUAAUGGUAAUAUA-UAAAUUGGCUAUGAGGAUGG--UUUUAGUACG-UAGGCGUUGC---GGAAC-UUCG----------GU-UCAGAUAGAGCAAUGAAUCGCGCAUGCUAG--GAAACUGA----------AGUGUUGACAGACCUAGUAUCUUUCGAUAGAUUU---CCAUACCUCCGCGAUC
U81811.1/530-751     ACGUAGCUGAGCGCGUUUGAUAUA-GU----GAUAAA---UGCCUGCUGCCUGGGCUCAACAUCAAAUGCAGGCAUAAACAUCGCAAC--------------UAGCA-ACA-AGGAGGAUGGU-UUUUAGUACG-UAGGCAUUGC---GGAACCCUCAACGUGAAGAAGU-UCAGAUAGAGCAAUGAAUCGUGCAUGCUAG-AGUCAU---------------UGGUUCGA--CCUAGUAUCUUUCGA-AGAUUU---CCAUUCCUUCGCGAUC
#=GC SS_cons         ::::::::.::::::::::::::..::....::::::...:::::::<<<<<<_______________.>>>>>>-----(((((---..............---------.-(((((-(((..,,,,,<<<<<.----<<<<<<...<<<<<.____..........>>.>>>------>>>>>>--->>>>>,<<<<<<.______............._____________>>>>>>,,,,,,,,.,,,,,,...)))--)))))))))):
#=GC RF              ACuUAgcu.aaugCguUagGUUc..Au....Aacauu...uGCuUGCUGcCuuGGCAUAAcAUCaAaa.aaGgCAUAAACaUCGCaaa..............UAaguuAau.auGaGGaugg..UUUUAGuaCG.UAGGCguugc...ggaac.uUca..........gu.uccgAUagAgcaacGAAUCGugCAugCuag.ugaaac.............AaUauuggCugaccuaGuaUCUUUcGA.AGAUUU...ccaUaCCuCaGCGAuC
//
# STOCKHOLM 1.0

#=GF AC   RF00525
#=GF ID   Flavivirus_DB
#=GF PI   Flavivirus_DB1
#=GF DE   Flavivirus DB element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15956576
#=GF SS   Published; PMID:15956576
#=GF GA   36.00
#=GF TC   36.20
#=GF NC   35.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0006412; translation;
#=GF RN   [1]
#=GF RM   15956576
#=GF RT   Control of translation by the 5'- and 3'-terminal regions of the dengue
#=GF RT   virus genome.
#=GF RA   Chiu WW, Kinney RM, Dreher TW
#=GF RL   J Virol 2005;79:8303-8315.
#=GF CC   This family represents the flavivirus 3' UTR elements DB1 and DB2. These
#=GF CC   DB elements are thought to be required for efficient translation [1].
#=GF WK   Flavivirus
#=GF SQ   111


AF169684.1/10540-10612 UGGGGGCC--CAA--GGCGAGAUGAAGCUG---UAGU-CUCGC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCGAAACA
AF169684.1/10454-10525 -GGAGGCC-ACAA--ACCAUG--GAAGCUG---UACG-CAUGG--CGUAGUGGACUAGCGGUUAGAGGAGACCCCUCCCUCACA
AF226686.1/10552-10623 -CGGGGCC--CAAC-ACCAGG-GGAAGCUG---UAC--CUUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCCCCCGCACAAC
AF226686.1/10468-10539 -GGAGGCU-GCAA--CCCAUG--GAAGCUG---UACG-CAUGG-GGU-AGCAGACUAGUGGUUAGAGGAGACCCCUCCCAAGAC
AF017254.2/1303-1372   -CACGGCC--CAG--CCUGAC-UGAAGCUG---UAG--GUCAG-GGG-AA-GGACUAGAGGUUAGUGGAGACCCCGUGCCACAA
AF017254.2/1225-1298   ACGCGGCC--CUAG-CCCUGG-UAAUGGUGU--UAA--CCAGG-GCGAAA-GGACUAGAGGUUAGAGGAGACCCCGCGGUUUAA
AY590190.1/314-383     -CACGGCC--CAG---CCUGGCUGAAGCUG---UAGG-UCAGG--GG-AA-GGACUAGAGGUUAGUGGAGACCCCGUGCCACAA
AY590190.1/236-309     ACGCGGCC--CUAG-CCCCGG-UAAUGGUGU--UAA--CCAGG-GCGAAA-GGACUAGAGGUUAGAGGAGACCCCGCGGUUUAA
AF119661.1/10540-10612 CGGGGGCC--CAA--GGUGAGAUGAAGCUG---UAGU-CUCAC-UGG-AA-GGACUAGAGGUUAGAUUAGACCCCCCCAAAACA
AF119661.1/10454-10525 -GGAGGCC-ACAA--ACCAUG--GAAGCUG---UACG-CAUGG--CGUAGGGGACUAGCGGUUAGAGGAGACCCCUCCCUUACA
AF310146.1/282-353     -CGGGGCC--CAAC-ACCAUG-GGAAGCUG---UAC--CUUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCCCCCGCACAAC
AF310146.1/198-269     -GGAGGCU-GCAA--CCCAUG--GAAGCUG---UACG-CAUGG-GGU-AGCAGACUAGUGGUUAGAGGAGACCCCUCCCUAGAC
AY278442.1/10759-10832 ACGCGGCC--CUAG-CCCUGG-UAAUGGUGU--UAA--CCAGG-GCGAAA-GGACUAGAGGUUAGAGGAGACCCCGCGGUUUGA
AF100467.1/10518-10590 UGGGGGCC--CAA--GGUGAGAUGAAGCUG---UAGU-CUCAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAAAAAA
AF100467.1/10432-10503 -GGAGGCC-ACAA--ACCAUG--GAAGCUG---UACG-CAUGG--CGUAGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUACA
AY099345.1/2325-2397   -CGGGGCC-CGAGC-ACUGAG-GGAAGCUG---UAC--CUCCU-UGCAAA-GGACUAGAGGUUAGAGGAGACCCCCCGCAAAUA
AY099345.1/2241-2312   -GGAGGCU-GCAA--ACUGUG--GAAGCUG---UACG-CACGG-UGU-AGCAGACUAGCGGUUAGAGGAGACCCCUCCCAUGAC
AF022439.1/10540-10612 UGGGGGCC--CAA--GGCGAGAUGAAGCUG---UAGU-CUCGC-UGG-AA-GGAAUAGAGGUUAGAGGAGACCCCCCCGAAACA
AF080251.1/10786-10858 AUGCGGCC--CAA--GCCCCCUCGAAGCUG---UAGA-GGAGG-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCGCAUUUGCA
AF080251.1/10705-10780 CCACGGCC--CAA--GCCUUGUCUAGGAUGCAAUAGA-CGAGG-UGU-AA-GGACUAGAGGUUAGAGGAGACCCCGUGGAAACA
M29095.1/10540-10612   UGGGGGCC--CAA--GGUGAGAUGAAGCUG---UAGU-CUCAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAAAACA
AY152231.1/334-407     AGGGGGCC-CGAA--GCCAGGAGGAAGCUG---UACU-CCUGG-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAACACA
AY152231.1/245-316     -GGAGGCC---AU--GCGCCACGGAAGCUG---UACG-CGUGG-CAU-AUUGGACUAGCGGUUAGAGGAGACCCCUCCCAUCAC
U47032.1/10785-10857   AUGCGGCC--CAA--GCCCCCUCGAAGCUG---UAGA-GGAGG-UGG-AG-GGACUAGAGGUUAGAGGAGACCCCGCAUUUGCA
U47032.1/10704-10779   CCACGGCC--CAA--GCCUCGUCUAGGAUGCAAUAGA-CGAGG-UGU-AA-GGACUAGAGGUUAGAGGAGACCCCGUGGAAACA
U88535.1/10552-10623   -CGGGGCC--CAAC-ACCAGG-GGAAGCUG---UAC--CCUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCCCCCGCACAAC
U88535.1/10468-10539   -GGAGGCU-GCAA--ACCAUG--GAAGCUG---UACG-CAUGG--GGUAGCAGACUAGUGGUUAGAGGAGACCCCUCCCAAGAC
AB122020.1/10540-10612 CGGGGGCC--CAA--GGUGAGAUGAAGCUG---UAGU-CUCAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAAAACA
AY326412.1/250-314     -CACGGCC--CAA--GCCUCGUCUAGGAUGCAAUAGA-CGAGG-UAG-AG-GGACUAGAGGUUAGAGGAGACCC----------
AF309961.1/267-339     UGGGGGCC--CAA--GGUGUGGUGAAGCUG---UAGC-CACAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCACAAAU
AF309961.1/182-253     -GGAGGCC-ACAA--GCCAUG--GAAGCUG---UACG-CAUGG-UGU-AGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUAAG
AF309953.1/271-343     UGGGGGCC--CAA--GGUGUGUUGAAGCUG---UAGC-CACAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAGACAA
AF309953.1/185-256     -GGAGGCC-ACAA--ACCAUG--GAAGGUG---UACG-CGUGG-UGU-AGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUAAG
AF359579.1/10540-10612 UGGGGGCC--CAA--GGUGAGAUGAAGCUG---UAGU-CUCAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCGAAAUA
AF359579.1/10454-10525 -GGAGGCC-ACAA--ACCAUG--GAAGCUG---UACG-CAUGG--CGUAGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUGCA
AF217620.1/10773-10845 AUGCGGCC--CAA--GCUUCCUCGAAGCUG---UAGA-GGAAG-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCGCAUUUGCA
AF217620.1/10692-10767 CCACGGCC--CAA--GCCUCGUCUAGGAUGCAAUAGG-CGAGG-UGU-AA-GGACUAGAGGUUAGAGGAGACCCCGUGGAAACA
AF098735.1/10785-10857 AUGCGGCC--CAA--GCCUCCUCGAAGCUG---UAGA-GGAGG-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCGCAUUUGCA
AF098735.1/10704-10779 CCACGGCC--CAA--GCCUCGUCUAGGGUGCAAUAGA-CGAGG-UGU-AA-GGACUAGAGGUUAGAGGAGACCCCGUGGAAACA
AF310147.1/282-353     -CGGGGCC-CAAC--ACCAGG-GGAAGCUG---UAC--CCUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCCCCCGCAUAAC
AF310147.1/198-269     -GGAGGCU-GCAA--CCCAUG--GAAGCUG---UACG-CAUGG-GGU-AGCAGACUAGUGGUUAGAGGAGACCCCUCCCAAAAC
AY152355.1/245-316     -GGAGGCC---AU--GCGCCACGGAAGCUG---UACG-CGUGG-UAU-AUUGGACUAGCGGUUAGAGGAGACCCCUCCCAUCAC
AY289214.1/10759-10832 ACGCGGCC--CAAG-CCCCGG-UAAUGGUGU--UAA--CCAGG-GCGAAA-GGACUAGAGGUUAGAGGAGACCCCGCGGUUUAA
AF309954.1/185-257     -GGAGGCC-ACAA--ACCAUG--GAAGCUG---UAACGCAUGG-UGU-AGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUAAG
AY590206.1/236-309     ACGCGGCC--CUAG-CCCCGG-UGAUGGUGU--UAA--CCAGG-GCGAAA-GGACUAGAGGUUAGAGGAGACCCCGCGGUUUAA
AF100469.1/10519-10591 UGGGGGCC--CAU--GGUGAGAUGAAGCUG---UAGU-CUCAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAAAACA
AF100469.1/10433-10504 -GGAGGCC-ACAA--ACCAUG--GAAGCUG---UACG-CAUGG--CGUAGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUUCA
AF404756.1/10759-10832 ACGCGGCC--CUAG-CCCCGGUAAUGGC-G---UUAA-CCAGG-GCGAAA-GGACUAGAGGUUAGAGGAGACCCCGCGGUUUAA
AF309955.1/269-341     UUGGGGCC--CAA--GGUGUGUUGAAGCUG---UAGC-CACAC-UGG-AA-GGACCAGAGGUUAGAGGAGACCCCCCCAGACAA
AF309955.1/184-255     -GGAGGCC-ACAA--ACCAUG--GAAGGUG---UACG-CAUGG-UGU-AGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUAAG
AY590207.1/314-383     -CACGGCC--UAG---CCUGGCUGAAGCUG---UAGG-UCAGG--GG-AA-GGACUAGAGGUUAGUGGAGACCCCGUGCCACAA
AY145121.1/10552-10623 -CGGGGCC--CAA--GCCAGGAGGAAGCUG---UACU-CCUGG-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCGCACAAC
AF169679.1/10540-10612 UGGGGGCC--CAA--AGUGAGAUGAAGCUG---UAGU-CUCAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCGAAACA
AF100151.1/258-330     UGGGGGCC--CAA--GGUGAGAUGAAGCUG---UAGU-CUCAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAAGACA
AF310149.1/179-250     -GGAGGCU-GCAA--ACCGUG--GAAGCUG---UACG-CACGG-UGU-AGCAGACUAGCGGUUAGAGGAGACCCCUCCCAUGAC
AY326407.1/282-342     -----GCC--UGGA-ACCAAUACAGAUCAC---UGGU-CUUGGGUGUUAA-GGACUAGAGGUUAGAGGAGACCC----------
AF309956.1/269-341     UGGGGGCC--CAA--GGUGUGUUGAAGCUG---UAGC-CACAC-UGG-AA-GGACCAGAGGUUAGAGGAGACCCCCCCAGACAA
AF309956.1/184-255     -GGAGGCC-ACAA--ACCAUU--GAAGCUG---UACG-CAUGG-UGU-AGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUAAG
AY688948.1/10867-10936 -CACGGCC--CAA---CUUAGCUGAAGCUG---UAAG-CUAAG--GG-AA-GGACUAGAGGUUAGAGGAGACCCCGUGCCAAAA
AY688948.1/10790-10863 ACGCGGCC-ACAA--CCCUGGCUA-UGGUGU--UAA--CCAGG-GAG-AAGGGACUAGAGGUUAGAGGAGACCCCGCGUUAAAA
AF514883.2/10552-10623 -CGGGGCC--CAAC-ACCAUG-GGAAGCUG---UAC--CUUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCCCCCGCAUAAC
AF311958.1/10552-10623 -CGGGGCC--CAAC-ACCAUG-GGAAGCUG---UAC--CUUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCCCCCGCUCAAC
AY648961.1/10525-10597 -CGGGGCC-CGAGC-UCUGAG-GGAAGCUG---UAC--CUCCU-UGCAAA-GGACUAGAGGUUAGAGGAGACCCCCCGCAAAUA
AF254452.1/10705-10780 CCACGGCC--CAA--UCCUCGUCUAGGAUGCAAUAGA-CGAGG-UGU-AA-GGACUAGAGGUUAGAGGAGACCCCGUGGAAACA
M35172.1/447-517       -AGUGGCC--CAA--GCUCGCC-GAAGCUG---UAAG-GCGGG-UGG-AC-GGACUAGAGGUUAGAGGAGACCCCACUCUCAAA
AF208017.1/800-873     ACGCGGCC-AUAA--CCCUGG-CUAUGGUGU--UAA--CCAGG-GAG-AAGGGACUAGUGGUUAGAGGAGACCCCACGUUAAAA
AY490240.2/10837-10906 -CACGGCC--CAG--CCUGAC-UGAAGCUG---UAG--GUCAG-GGG-AA-GGACUAGAGGUUAGUGGAGACCCCGUGCCACAG
AF100145.1/268-340     CGGGGGCC--CAA--GGUGAGAUGAAGCUG---UAGU-CUCAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAAAAUA
AB074761.1/10552-10623 -CGGGGCC--CAAC-ACCAGG-GAAAGCUG---UAC--CCUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCCCCCGCAUAAU
AB074761.1/10468-10539 -GGAGGCU-GCAA--ACCAUG-GA-AGCUG---UACG-CAUGG-GGUUGC-AGACUAGUGGUUAGAGGAGACCCCUCCCAAGAC
S73076.1/496-553       -----GCCUGCAA--CCCAUG-GA-AGCUG---UAC--CCUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCC----------
M93130.1/10430-10501   -GGAGGCU-GCAA--ACCGUG-GA-AGCUG---UACG-CACGG-UGU-AGCAGACUAGUGGUUAGAGGAGACCCCUCCCAUGAC
AY326409.1/179-238     -----GCC-UGAA--GGCAAAUC--AGUUCAC-UGGA-UUUGC-UGUUAA-GGACUAGAGGUUAGAAGGGACCC----------
L24512.1/435-504       -CACGGCC--CAG---CCUGGCUGAAGCUG---UAGG-UCAGG--GG-AA-GGACUAGAGGUUAGUGGAGACCCCGUGCCGCAA
L24512.1/357-430       ACGCGGCC--CUA--GCUCUGGCAAUGGUGU--UAAC-CAGAG-UGA-AA-GGACUAGAGGUUAGAGGAGACCCCGCGUUCUGA
AY152083.1/245-316     -GGAGGCC---AUGCGCCACG-GA-AGCUG---UACG-CGUGG-CAU-AUUGGACUAGCGGUUAGAGGAGACCCCUCCCACCAC
AY152287.1/245-316     -GGAGGCC---AUGCGCCACG-GA-AGCUG---UACG-CGUGG-CAU-AUUGGACUAGCGGUUAGAGGAGACCCCUCCCAUGAC
AF100146.1/269-341     UGGGGGCC--CAA--GGCGAGAUGAAGCUG---UAGU-CUCGC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCGAAGCA
M12294.2/10772-10841   -CACGGCC--CAA---CUUGGCUGAAGCUG---UAAG-CCAAG--GG-AA-GGACUAGAGGUUAGAGGAGACCCCGUGCCAAAA
M12294.2/10694-10767   ACGCGGCC-AUAA--CCCUGG-CUAUGGUGU--UAA--CCAGG-GAG-AAGGGACUAGAGGUUAGAGGAGACCCCGCGUAAAAA
AB178040.1/10468-10539 -GGAGGCU-GCAA--CCCAUG--GAAGCUG---UACG-CAUGG-GGU-AGCAGACUAGUGGUUAGAGGAGACCCCUCCCGAAAC
AF169680.1/10540-10612 UGGGGGCC--CAA--GGCGAGAUGAAGCUG---UAGU-CUCGC-UUG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCGAAACA
AF310150.1/133-204     -GGAGGCC---AU--GCGCCACGGAAGCUG---UACG-CGUGG-CAU-AUUGGACUAGUGGUUAGAGGAGACCCCUCCCAUUAU
AF180817.1/10552-10623 -CGGGGCC--CAAC-ACCAGG-GGAAGCUG---UAC--CCUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCCCCCGCGUAAC
AF289029.1/10391-10462 -GGAGGCC---AU--GCGCCACGGAAGCUG---UGCG-CGUGG-CAU-AUUGGACUAGCGGUUAGAGGAGACCCCUCCCAUCAC
AY152199.1/334-407     AGGGGGCC-CGAA--GCCAGGAGGAAGCUG---UACU-CCUGG-UGG-AA-GGACUAGAGGUUAUAGGAGACCCCCCCAACACA
AF309959.1/257-329     UGGGGGCC--CAA--GGUGUGGUGAAGCUG---UAGC-CACAU-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAGACAA
AF309959.1/171-242     -GGAGGCC-ACAA--ACCAUG--GAAGCUG---UACG-CAUGG-UGU-AGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUAAA
AY184212.1/10786-10858 AUGCGGCC--CAA--GCCCCUUCGAAGCUG---UAGA-AGAGG-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCGCAUCUGCA
AY184212.1/10705-10780 CCACGGCC--CAA--GUCUCGUCCAGGAUGCAAUGGA-CGAGA-UGU-AA-GGACUAGAGGUUAGAGGAGACCCCGUGGAAACA
AY316157.1/10771-10840 AUGCGGCC--CAA--GCCCCCUCGAAGCUG---UAGA-GGAGG-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCGCAAUU---
AY316157.1/10690-10765 CCACGGCC--CAA--GCCUCGUCUAAGAUGCAAUAGA-CUAGG-UGU-AA-GGACUAGAGGUUAGAGGAGACCCCGUGGAAACA
AF306514.1/380-449     AUGCGGCC--CAA--GCCCCCUCGAAGCUG---UAGA-GGAGG-UGU-AA-GGAAUAGAGGUUAGAGGAGACCCCGCAAUU---
AF306514.1/299-374     CCACGGCC--CAA--GCCUCGUCUAAGAUGCAAUAGA-UUAGG-UGU-AA-GGACUAGAGGUUAGAGGAGACCCCGUGGAAACA
AJ242984.1/10359-10430 -CCGGGCC--CAA--CCCAGCUAGGGAUAG---CCUU-UCUGG-GGU-AA-GGACUAGAGGUUAGUGGAGACCCCCGGCUUUUG
AF309641.1/10454-10525 -GGAGGCU-GCAA--CCCAUG--GAAGCUG---UAGC-GAUGG-GGU-AGCAGACUAGUGGUUAGAGGAGACCCCUCCCGAAAC
AF100464.1/10530-10602 UGGGGGCC--CAA--GGCAAGAUGAAGCUG---UAGU-CUCGC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCGAAACA
AF100148.1/172-243     -GGAGGCC-ACAA--ACCAUG--GAAGCUG---UACG-CAUGG-UGU-AGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUUCA
AY152247.1/245-316     -GGAGGCC---AU--GCGCCACGGAAGCUG---UACG-CGUGG-CAU-AUUGGACUAGUGGUUAGAGGAGACCCCUCCCAUCAC
M87512.1/10534-10605   -CGGGGCC--CAAC-ACCAGG-GGAAGCUG---UAU--CCUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCCCCGGCAUAAC
AB051292.1/10773-10845 AUGCGGCC--CAA--GCCCCCUCGAAGCUG---UGGA-GGAGG-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCGCAUUUGCA
AY277665.1/10552-10623 -CGGGGCC--CAAC-ACCAUG-GGAAGCUG---UAC--CUUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCGCCCGCAUAAC
AF309951.1/271-343     CGGGGGCC--CAA--GGUGAGAUAAAGCUG---UAGU-CUCAC-CGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAAAACA
AF100149.1/258-330     UGGGGGCC--CAA--GGUGAGAUGAAGCUG---UAGC-CUCAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAAAACA
AF298808.1/10538-10609 -CGGGGCC--CAAC-ACUAGG-GGAUGCUG---UAC--CCUGG-UGGUAA-GGACUAGAGGUUAGAGGAGACCCCCCGCAUAAC
AF306516.1/385-457     AUGCGGCC--CAA--GCCCCCUCGAAGCUG---UAGA-GGGGG-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCGCAUUUGCA
AY278441.1/10759-10832 ACGCGGCC--CUAG-CCCUGG-UGAUGGUGU--UAA--CCAGG-GCGAAA-GGACUAGAGGUUAGAGGAGACCCCGCGGUUUGA
AF100458.1/258-330     UGGGGGCC--CAA--GGUGAGAUGAAGCUG---UAGU-CUCAC-UGG-AA-GGACUAGAGGUUAGAGGAGACCCCCCCAAAAAC
AF075723.1/10704-10779 CCACGGCC--CAA--GCCUCGUCUAGGAUGCAAUAGA-CGAGG-UGU-AA-GGACUAGAGGUUAGAGGAGACCCCGUGGAAAUA
AY037116.1/10540-10612 UGGGGGCC--CAA--GGUGAGAUGAAGCUG---UAGU-CUCAC-UGA-AA-GGACUAGAGGUUAGAGGAGACCCCCCCGAAAUA
EF629368.1/10525-10597 -CGGGGCC-CGAGC-ACUGAGGGA-AGCUG---UAC--CUCCU-UGCAAA-GGACUAGAGGUUAGAGGAGACCCCCCGCAAACA
#=GC SS_cons           .(((((<<..---..<<<<<<<<_______...__>>.>>>>>.>--.--.>>,,,,,,<<<<______>>>>)))))::::::
#=GC RF                .gGgGGCC..CAA..gccacgccgAAGcUG...UAgg.cgugg.cGg.AA.GGACUAGAGGUUAGAGGAGACCCCcCccauaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00526
#=GF ID   snoMe28S-U3344
#=GF PI   snoMe28S-U3344a; sno28S-U3344a
#=GF DE   Small nucleolar RNA Me28S-U3344
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   50.00
#=GF TC   51.60
#=GF NC   38.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me28S-Um3344 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   28S U-3344 [1].
#=GF WK   Small_nucleolar_RNA_Me28S-U3344
#=GF SQ   8


AC104631.2/33035-32954       A-U-CUUAAUGAUGACUACAUUGUAAAUUCUUGAUAGGAAGAGUAUGAAACAUAAUGAGUACUAAAACAACCAAGCUGA----CAAAA--
AC104631.2/34419-34338       AUC-UGUUGUGAUGAAUACAUUUUAAAUUCUUGAUAGGAAGAGUAUGAAACAUAAUGAGUACCAAAAA--CCUAGCUGA-----AUUGGU
AANI01016544.1/160806-160723 AUUGCCAAAUGAUGAUUACUUUUGUAAUUCUUGAUAGGAAGAGUAUGAAACAUAAUGAGUACUAUAAAAAAAUA-CUGA-----UGCAGC
AAFS01000767.1/35932-35850   AUC-AAAUGUGAUGAUUACUUUUGUAAUUCUUGAUAGGAAGAGUAUGAAACAUAAUGAGUACGAACAA-ACCAAACUGA-----UUUGAU
AAPU01009887.1/3433-3515     CGC-CAAUAUGAUGAAUACUUAUGUAAUUCUUGAUAGGAAGAGUAUGAAACAUAAUGAGUACUAUAUA--CUAAUCUGA----UUUAGAA
AAPT01021393.1/13048-13134   UUG-CUUAAUGAUGAUUACCUUUGUAAUUCUUGAUAGGAAGAGUAUGACACAUAAUGAGUACUAUAAA--AUUAACUGAUUCGCAAUCUU
AAPP01019164.1/31009-31090   CUU-UGUGGUGAUGACUACUUUGUAAAUUCUUGAUAGGAAGAGUAUGAAACAUAAUGAGUACUAAACA---AAUGUUCU----GAUUAAC
AAPQ01006057.1/398007-397924 AUC--UUUAUGAUGACUACAUUGUAAAUUCUUGAUAGGAAGAGUAUGAAACAUAAUGAGUACUAAAACAACCAAGCUGA----CAAAGAC
#=GC SS_cons                 ::<.-<<_____________________________________________________________.._________...._>>->::
#=GC RF                      aUc.ccuuaUGAUGAuUACuUUuuuAAUUCUUGAUAGGAAGAGUAUGAAACAUAAUGAGUACUAaAaA..cuaAgCUGA....cagugau
//
# STOCKHOLM 1.0

#=GF AC   RF00527
#=GF ID   snoMe28S-G3255
#=GF PI   snoMe28S-G3255a
#=GF DE   Small nucleolar RNA Me28S-Gm3255
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   44.00
#=GF TC   44.60
#=GF NC   43.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00066
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Drosophila_melanogaster300032;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me28S-Gm3255 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   28S G-3255 [1].
#=GF WK   Small_nucleolar_RNA_Me28S-Gm3255
#=GF SQ   10


AC008186.5/23701-23785         AGUUAUCUGAUGAU-UUAUAAUUCUAUUUUCUGACAUCUCUUAUGAACCGUUGUGAUUCAAAUCAGUUAUAA-CUAAUU--CUGACACA
AC008186.5/24468-24549         AUGUAAAUGAUGCUUUUAA------AAUUUCUGACAUCUCUAAUGAACCGUUGUGAUUCAAAUUUUUC-UAAUAUAAUUAACUGAUCAU
AAPP01018724.1/106634-106550   GAUUCUAUGAUGAU-UUAUUAAAUUCUUUUCUGACAUCUCUAAUGAACCGUUGUGAUUCAAAUCAGUU-UAAUAAAUUU--CUGAAGUU
AAEU02000094.1/193595-193512   AAUUAUCUGAUGAUUUGUU--UUCUAUUUUCUGACAUCUCUUAUGAACCGUUGUGAUUCAAAUCAGUUAUAA-CAAAUU--CUGACACU
AAFS01000046.1/161956-162039   AAUAUUCUGAUGAAUAUCU----UUAUUUUCUGACAUCUCUUAUGAACCGUUGUGAUUCAAUACAAUU-AAUUAUUAUCUACUGAAGCU
AAGH01023660.1/5285-5360       AUG------AUGCUUUUAA------AUUUUCUGACAUCUCUAAUGAACCGUUGUGAUUCAAAUUUUUG-UAAUAUAAUUAACUGAUCAU
AAPQ01007360.1/2428596-2428511 AUUAAUAUGUUGAUGCUUUAAAAUU--UUUGUGACAUCUGUAAUGAAGC-UUGUGAUUCAAAAUUUUUCUAUUAUAAUUAACUGAUGAC
AASS01036184.1/1711-1633       AU---AAUGAUGCUUUUAA------AUUUUCUGACAUCUCUAAUGAACCGUUGUGAUUCAAAUUUUUG-UAAUAUAAUUAACUGAUCAU
AAKO01000502.1/98060-98140     AGGU-UAUGAUGCUUUUAA------AUUUUCUGACAUCUCUAAUGAACCGUUGUGAUUAAAAUUUUUG-UAAUAUAAUUAACUGAUCAU
AAEU02000094.1/192782-192704   GUU---AUGAUGCUUUAAA------AUUUUCUGACAUCUCUAAUGAACUGUUGUGAUUCCAAGUAUUUCUUU-AUAAUUAACUGAUAAU
#=GC SS_cons                   <<<----------------....-------------------<<<<____>>>>--------------.----------------->>>
#=GC RF                        auuuaUaUGAUGaUUUUau....uUAUUUUCUGACAUCUCUaAUGAACCGUUGUGAUUCAAAuuauUu.UAaUAUAAUUAACUGAuaau
//
# STOCKHOLM 1.0

#=GF AC   RF00528
#=GF ID   snoMe28S-Gm1083
#=GF PI   snoMe28S-Gm1083a
#=GF DE   Small nucleolar RNA Me28S-Gm1083
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805, INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   48.00
#=GF TC   67.40
#=GF NC   37.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me28S-Gm1083 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   28S G-1083 [1].
#=GF WK   Small_nucleolar_RNA_Me28S-Gm1083
#=GF SQ   11


AY060937.1/627-715           CGUUA--UC-UGAUGAGCAAU-AACUUUCGCCCCUAGCUGAAAAA-----UGAUACUUCUCAUGUUGAAUGCGAGAUUGGUCUUACUGAAAAUAACGG
AY060937.1/872-959           UAUUAGUUC-UGAUGAGCAUU-AACUUUCGCCCCUAUCUGAAAU------UGAAACUUCUCUUGUUGAAUGCGAGAUUGGUCUUACUGAAAA--ACUA
AY060937.1/1109-1197         UAUUA--UCAUGAUGAGCAUU-AACUUUCGCCCCUAUCUGAAAU------UGAAACUUCUCAUGUUGAAUGCGAGAUUGGUCUUACUGAAAAGAAUUU
AY060937.1/1349-1435         UUUUA--AG-UGAUGAGCUUU-AACUUUCGCCCCUAUCUGAAAU------UGAAACUUCUCCUGUUGAAUGCGAGAUUGGUCUUACUGAAAUG-ACUC
AAEU02000398.1/5097-5184     CGUUA--UC-UGAUGAGCAUU-AACUUUCGCCCCUAUCUGAAAU------UGAAACUUCUCAUGUUGAAUGCGAGAUUGGUCUUACUGAAAAUAACGC
AAPQ01007082.1/155445-155533 CCUUC--UUAUGAUGAGCAUU-AACUUUCGCCCCUAUCUGAAAU------UGAAACUUCUCAUGUUGAAUGCGAGAUUGGUCUUACUGAAAAGAAUUC
AAQB01006286.1/230801-230713 UUUUA--ACCUGAUGAGCAUU-AACUUUCGCCCCUAUCUGAAAAU-----UGAAACUUCUCUUGUUGAAUGCGAGAUUGGUCUUACUGAAAAA-ACAA
AAPP01018787.1/99846-99759   UUUGA--UA-UGAUGAGUACU-AACUUUCGCCCCUAUCUGAAAUU-----UGAAACUUCUCCUGUUGAAUGCGAGAUUGGUCUUACUGAAUAA-AUUA
AAST01027501.1/303-215       CGUUA--UC-UGAUGAGCAAU-AACUUUCGCCCCUAGACGAAAAA-----UGAAACUUCUCAUGUUGAAUGAGAGAUGGGUAUUAAAGAAAAUAACGC
AAPT01021461.1/5798-5892     UAUUU--UG-UGAUGAGAAUUUAACUUUCGCCCCUAUCUGAACACAAAUGUGAAACUUCUCAUGUUGAAUGCGAUAUUGGUCUUGCUGAUAAUAAAAC
AAPU01010270.1/4322-4412     AUAU------UGAUGAGCUUCAAGCUUUCGCCCCUAUCUGAAAACUAAG-AGAAACUUCCAAUGUUGAAUGCGUGAUUGGUCUUACUGAAAUGAAACU
#=GC SS_cons                 <<<<_..__.___________._______________________.....________________________________________>>>->:::
#=GC RF                      ucuua..Uc.UGAUGAGcAuU.AACUUUCGCCCCUAUCUGAAAau.....UGAAACUUCUCaUGUUGAAUGCGAGAUUGGUCUUACUGAAaagAacuu
//
# STOCKHOLM 1.0

#=GF AC   RF00529
#=GF ID   snoMe28S-Am2589
#=GF PI   snoMe28S-Am2589a
#=GF DE   Small nucleolar RNA Me28S-Am2589
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   37.00
#=GF TC   37.40
#=GF NC   36.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me28S-Am2589 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   28S A-2589 [1].
#=GF WK   Small_nucleolar_RNA_Me28S-Am2589
#=GF SQ   16


AAQB01006145.1/99907-100016  UCCAUAAUGAUGUCAAUUACCUAACUGAUUACUAUUUUCGAUCUAUUUUUGAGAGAUUU-UUG-GUUACUUUAAAGAUGUGCUCGAUUGCGAGGCAUUUGUCUGAAUGAAAG
AAPQ01007048.1/171637-171746 UUGAAAUUGAUGAUAAAUU-GUCACUGAUAGUUGGACUUAAUCUAUUUUUGAGAGAGUCGUAAACUUUUCCAA-GGAUGUUCGCACUUGCGAGGCAUUUGUCUGAUUCGCUC
AAGH01006567.1/583-474       UUGAAAAUGAUGUUAAACU-GUCACUGAUAGUUGGACUUAAUCUAUUUUGGAGAGAGUCGUAAACUUUUCCUA-GGAUGUUCGCAUUUGCGAGGCAUUUGUCUGAUUCGCUU
AAFS01000198.1/37463-37357   CAGCAUAUGAUGAUAAAAUACAAACUGAAACGUUGUCGUGGUCUAUUUUUGAACACUUC-GAU-GU-UACCCUGGGAUGGUCGCAUUUGCGAGGCAUUUGCCUGAUGC--UU
AAPP01018740.1/144360-144468 AGCCAAAUGAUGUUACAAU-CAUACUGAGUGCCGCUAUCGAUCUAUUUUUGAUUGAUUC-UGG-CGUAUAAAAGGGAUGUUCGCAGCUGCGAGGCAUUUGUCUGAUGGAAGC
AE013599.4/17215769-17215875 GAGCACUUGAUGAUAAACUACAAACUGAAACGUUGUUGUGGUCUAUUUUUGAACACUUC-GAU-GU-UACCUUGGGAUGGUCGCACUUGCGAGGCAUUUGCCUGAUGC--UU
AAPP01018740.1/151124-151233 CCGAAACUGAUGAUAACCU-GUCACUGAUAGUUGGGCUCAAUCUAUUUUGGAGCGAGUCGUAAACUUUUCCCA-GGAUGUUCGCUUUUGCGAGGCAUUUGUCUGAUUCGUUU
AAEU02000410.1/178718-178826 UUGAAAAUGAUGUUAAAUU-GUCACUGAUAGUUGGACUUAAUCUAUUCUGGAGAGAGUCGUAA-ACUUUUUUA-GGAUGUUCGCUUUUGCGAGGCAUUUGUCUGAUUCGCUC
AANI01014934.1/203066-202959 AAGCACAUGAUGAGACACU-UGAACUGAAACGUUGUUGUGGUCUAUUUUUGAACACUUC-GAU-GU-UAACAAGGGAUGGUCGCAUUUGCGAGGCAUUUGUCUGAUGCAUUU
AAPQ01007048.1/168316-168424 GAGCACUUGAUGAUAAACUACAACCUGAAACGUUGUUGUGGUCUAUUCUUGAACACGUC-GAU-GU-UACCAUGGGAUGGUCGCACUUGCGAGGCAUUUGCCUGAUGCUAAU
AAFS01000198.1/41703-41596   AGCCAAGUGAUGUUACAAU-UCAACUGAGCGCCGUUAUCGGUCUAUUUUUGAUUGAUUU-UGG-CUGUUAAAA-GGAUGUUCGCAGUUGCGAGGCAUUUGUCUGAUGGAAUA
AAIZ01002207.1/59451-59342   UUGAAAAUGAUGUUAAACU-GUCACUGAAAGUUGGGCUCAAUCUGUUUUGGAGCGAGUCGUAAACUUGUCCCA-GGAUGUUCGCAUUUGCGAGGCAUUUGUCUGAUUCAAUC
AAQB01006145.1/107012-107119 GAAGAGAUGAUGAUAAAUU-GUCACUGAUAGUUGGACUAAAUCUAUUUUUGAUCGAGUCGUAA-ACUUUUUUAAGGAUGUUCGGUUUGCCGAGGCAUUUGUCUGAUUU--UU
AAPU01010147.1/89010-88903   UUGCACAUGAUGAGACACU-UAGACUGAAACGUUGUUGUGGUCUAUUCUUGAACACUCC-GAU-GU-UAUUAAGGGAUGGUCGCAUUCGCGAGGCAUUUGUCUGAUGCAUUA
AAPT01021484.1/868237-868130 AAGCACCUGAUGAGACUUU-CAUACUGAAACGUUGUUUUGGUCUAUUUUUGAACACUAC-GAU-GU-UAAUAAGGGAUGGUCGCAUUUGCGAGGCAUUUGUCUGAUGCGCUA
AAPP01018740.1/147210-147318 UUGCAUUUGAUGAUAAACUCCACGCUGAUACGUUGUUGUGGUCUAUUUUUGAACACUUC-GAU-GU-UACCUUGGGAUGGUCGCAUUUGCGAGGCAUUUGCCUGAUGCUCUC
#=GC SS_cons                 ::<<<______________._______________________________________.___._________________________________________>>>::::
#=GC RF                      uugcaaaUGAUGaUAAAuU.cuaACUGAuAguUgguuuugaUCUAUUUUUGAacgauUC.uAa.gUUUuuuuAgGGAUGuUCGCauUUGCGAGGCAUUUGUCUGAugcaaUu
//
# STOCKHOLM 1.0

#=GF AC   RF00530
#=GF ID   snoMe28S-Cm2645
#=GF PI   snoMe28S-Cm2645a
#=GF DE   Small nucleolar RNA Me28S-Cm2645
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; PFOLD; Moxon SJ, Daub J
#=GF GA   48.00
#=GF TC   48.60
#=GF NC   46.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00069
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Drosophila_melanogaster300075;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me28S-Cm2645 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   28S C-2645 [1].
#=GF WK   Small_nucleolar_RNA_Me28S-Cm2645
#=GF SQ   20


AC093047.1/47159-47233       ACAACCAUGAUGAAAUCGUUAGAUGGGGACAACUGAUUACUGUGACUGAUUCAUC----U----CGAUAGUAGA-UCUGA-UUUU
AY069135.1/400-474           UUUUUUGUGAUGAAAUCGUUAGAUAGGGACGUCUGAUAUCUGUGACUGAUUUAUC----U----CGAUAGUAGA-UCUGA-UUUU
AC002443.1/58722-58796       ACAACCAUGAUGAAAUCGUUAGAUGGGGACAACUGAUUACUGUGACUGAUUCAUC----U----CGAUAGUAGA-UCUGA-UUUU
AC002443.1/59187-59261       UUUUUUGUGAUGAAAUCGUUAGAUAGGGACGUCUGAUAUCUGUGACUGAUUUAUC----U----CGAUAGUAGA-UCUGA-UUUU
AASR01036123.1/538-612       ACAACCAUGAUGAAAUCGUUAGAUAGGGACUUCUGAUGUCUGUGACUGAUUUAUC----U----CGAUAGUAGA-UCUGA-UUUU
AAQB01006396.1/408007-407928 UAUGAUAUGAUGAAUACUAUAGAUAGGGACAACUGAUGUCUAUGACUGAUUUAUCUAAUU----UGAUAGUAGA-UCUGAACAUA
AAPP01015693.1/123430-123504 AUUUUAAUGAUGAUAACUUAUGAUAGGGACAUCUGAUGUCUAUGACUGAUUUAUC----A----UGAUAGUAGA-ACUGA-AAUU
AAEU02000272.1/17586-17517   ACAAUUAUGAU-----CGUUAGAUGGGAUCAACUGAUGCCUAUGCCUGAUUCAUC----U----UGAUCGUAGA-UCUGA-UUUU
AAQB01006396.1/408545-408468 AUGUGUAUGAUGAAUAACUUAGAUAGGGACAACUGAUGUCUAUGACUGAUUUAUC----UAACUUGAUAGUAGA-GCUGA--CUU
AAFS01000334.1/41859-41931   CUUUUUGUGAUGAUA-CCUUUGAUAGGGACAUCUGAUGUCUAUGAUUGAUUUAUC----A----UGAUAGUAGA-ACUGA--UUG
AADE01000239.1/56445-56373   CUCUCUCUGAUGAUA-CCUUUGAUAGGGACAUCUGAUGUCCAUGAUUGAUUUAUC----A----UGAUAGUAGA-ACUGA--UUG
AAGH01010549.1/523-450       UAUUUUGUGAUGAAAUCGUUAGAUAGGGACUUCUGAUGUCUGUGACUGAUUUAUC----U----CGAUAGUAGA-UCUGA--UUA
AADE01000239.1/55756-55682   CUUUUUCUGAUGAUAAACUAUGAUAGGGACAUCUGAUGUCUAUGACUGAUUUAUCU---U----UGAUAGUAGA-ACUGA--UUG
AAQB01006396.1/408254-408175 UUAUGUAUGAUGAAUAAUUUAGAUAGGGACAACUGAUGUCUAUGACUGAUUUAUCUAAUU----UGAUAGUAGA-UCUGACGCUA
AAFS01000334.1/42558-42629   AUGGUGAUGAU----ACCUUUGAUAGGGACAUCUGAUGUCUAUGACUGAUCUAUC----A----UGGUUUAACAUUCUGA-AUAU
AAPP01015693.1/122736-122810 GUUAACUUGAUGAUAACUUAUGAUAGGGACAUCUGAUGUCUAUGACUGAUUUAUC----A----UGAUAGUAGA-ACUGA-UUAU
AAIZ01001189.1/17671-17596   UUUGAUGUGAUGAUAAACUAUGAUAGGGACAUCUGAUGUCCAUGACUGAUUUAUC----U----UGAUAGUAGA-ACUGAUUACU
AAPQ01007039.1/284260-284186 UAAAUUGUGAUGAAAUUGAUAGAUAGGGACUACUGAUGUCUGUGACUGAUAUAUC----U----UGAUAGUAGA-UCUGA-UUUU
AAPP01015693.1/123201-123276 UUUUUUAUGAUGAUAACUUAUGAUAGGGACAUCUGAUGUCUAUGACUGAUUUAUC----A----UGAUAGUAGA-ACUGAUUAUA
AANI01016231.1/123573-123497 ACUUUAAUGAUGAAAGCUUU-GAUAGGGACAUCUGAUGUCUAUGAUUGAUUUAUCACU-U----UUUAUAUAGA-ACUGA-ACUU
#=GC SS_cons                 <-<<___________________________________________________...._....__________._____.>>->
#=GC RF                      auuauuaUGAUGAaAacuUUaGAUAGGGACAuCUGAUGUCUAUGACUGAUUUAUC....U....UGAUAGUAGA.uCUGA.uaUu
//
# STOCKHOLM 1.0

#=GF AC   RF00531
#=GF ID   snoMe28S-Gm3113
#=GF DE   Small nucleolar RNA Me28S-Gm3113
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; ILM; Moxon SJ, Daub J
#=GF GA   70.00
#=GF TC   72.50
#=GF NC   38.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me28S-Gm3113 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   28S G-3113 [1].
#=GF WK   Small_nucleolar_RNA_Me28S-Gm3113
#=GF SQ   15


AC010057.7/174297-174216     GGU-UUU--UGUGAUGACAUAGCUAUUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGCGUAAA--CGUCAAU-AUCUGAUAAAU
AC010057.7/174076-173991     UUG-UUUUCAAUGAUGAUUUUCGAGUUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGUGUAAAGUUAUGUUU-UUCUGAUAACA
AAPP01019316.1/65510-65432   UUU-UGU-----GAUGAUAUAGCUAUUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUUGUGUAAA--UUUGUUU-AACUGAUUAGA
AAPT01020539.1/126869-126954 AUU-AACGUAAUGAUGAGCUACGU-UUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGUGUAAAUUUAUUAUCGCUGAAAUUUAA
AAPP01019316.1/65235-65151   AUU-UUUAAAAUGAUGAUUUACGA-UUUUACCUUGGGACACCUAUGAA--AGAU-CU-UGAUUAGUGUAAAGUUAUGUUU-UUCUGAUAAAA
AAIZ01007899.1/13931-14016   AUU-AUUUCCAGGAUGAUUUACGA-UUUUACCUUGGGACACCUAUGAA--AGAC-CUGUGAUUAGUGUAAAGUUAUAUUU-AGCUGAUAAAA
AADE01000021.1/111219-111300 UUGCGUUUUUGUGAUGAGAUAGCAA--UUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGUGUAAA--UUUUAAC-AACUGA-ACCA
AANI01017365.1/197782-197862 AAU-UACAUUGUGAUGAGCUAAGU-UUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGUGUAAA----UUGAU-AAUUGCUGAAU
AAPU01011522.1/238759-238676 AAU-UGCUCUGUGAUGAGCUAAGC-UUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGUGUAAUGUUAUAAAU-G-CUGAUAAAU
AJ784351.1/2-80              UUU-U----GGUGAUGACAUAGCUAUUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGCGUAAA--CGUCAAU-AUCUGAU-AAA
AAQB01006228.1/175045-174959 GAU-UUGAAUGUGAUGAUAUAACGUAAUUACCUUGGGACACCUAUGAA--AAGUUUU-UGAUUAGUGUAACAGCUUACUG-AUUAACUCAAU
AAPT01020539.1/126632-126714 UGC-UUU-CUAUGAUGAUAUAUAUAUAUUACCUUGGGACACCUAUGAAAUAUGC-CU-UGAUUAGUGUAAA----UUUUA-AACUGACAAAC
AAPQ01006530.1/557034-556953 GCU-UUU--UGUGAUGACAUGUGAAUUUUACCUUGGGACACCUAUGAA--AUGC-CU-UGAUUAGCGUAAA--CUAUAGU-AUCUGAUAAAU
AAEU02002336.1/12406-12487   GGU-UCU--UGUGAUGACAUAGCAACAUUACCUUGGGACACCUAUGAU--AUAC-CU-UGAUUAGUGUAAA--UUUCAAU-AUCUGAUAAAU
AANI01017365.1/197544-197625 AUG-UUA--UCUGAUGAUAUAGUAAU--UACCUUGGGACACCUAUGAAAUAUGC-CU-UGAUUAGUGUAAA-UUUUAUGA-AACUGA-AACU
#=GC SS_cons                 :<<.<<__________________________________________..____.__._____________.________._______>>>>
#=GC RF                      auu.uuuuuugUGAUGAuaUAagaaUuUUACCUUGGGACACCUAUGAA..AUGC.CU.UGAUUAGUGUAAA.uUuUuauu.AucUGAUaaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00532
#=GF ID   snoMe18S-Um1356
#=GF DE   Small nucleolar RNA Me18S-Um1356
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; ILM; Moxon SJ
#=GF GA   50.00
#=GF TC   53.50
#=GF NC   46.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.74 -Z 549862.597050 CM SEQDB
#=GF CL   CL00054
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me18S-Um1356 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   18S U-1356 [1].
#=GF WK   Small_nucleolar_RNA_Me18S-Um1356
#=GF SQ   21


AASS01027918.1/1012-1092     UU-G--------AUUGAUGACAACUUCAUACUC--AAAUCAGAGAA-AUUAUGUUGAAAUC---CUUUUAACAUGCAUCACCAUCUGAAUAA-----CAAA
AE014296.4/20447343-20447428 AC-UCCUU--A-AUUGAUGACAACUUCAUACUC--AAAUCAGAGAA-AUUAUGUUGAAAUC---CUUUUAACAUGCAUCACCAUCUGAAUCA-----AGUA
AJ784844.1/652-737           AU-UCCCA--A-AUUGAUGACAACUUCAUACCC--AAAUCAGAGAA-AUAAUGUUGAAAUC---UUUUUAACAUGCAUCACCAUCUGAAUAA-----AAUA
AAPP01019315.1/203189-203276 AU-UAUUA--G-AGUGAUGACAACUUCAUACCC--AAUGCAGAGAA-AUUAUGUUGAAAAA---UACUUAACAUGCAUCACCAUCUGAUUAC---UUAGUU
AAIZ01025242.1/736-657       AU-CCCCA--U-AAUGAUGACAACUUCAUACCA--AUCUCAGAGCA-AUUAUGUUGAAAUC---CUAUUAACAUGCAUCACCAUCU-----------GAUA
AAPP01019315.1/203428-203513 AU-AAAUA--A-AGUGAUGAUAACUUCAUACCC--AACUCUGAGAAAAUAAUGUUGAAAUC---UAUUUAACAUGCAUCACCAUCUGAAUU------UGUA
AAPT01020666.1/53928-53843   UA-AUUUU--A-AAUGAUGAAAACUUCAUACAC--UACUCAGAUCA-AUUAUGUUGAAAUC---UUUUUAACAUGCAUCACCAUCUGAUUAG-----UUAC
AAPT01020666.1/54166-54077   AU-ACCUU--UCAAUGAUGAUAAAUUCAUAUCU--UCCUCAGACAA-AUUAUGUUGAAAUC---UAUUUAACAUGCAUCACCAUCUGAUUAC--UCAUAUA
AAIZ01025242.1/267-182       AU-UCCCA--U-AAUGAUGAAAACUUCAUACGA--AUCUCAGAGCA-AUUAUGUUGAAAUC---CUAUUAACAUGCAUCACCAUCUGAAAUA-----GAUC
AAPU01011573.1/516306-516391 AU-AUUUUC-U-AAUGAUGAUAACUACAUA-GC--AAAUCAGAGCA-AUAAUGUUGAAAUU---UACAGACAAUGCACUACCAUCUGAUUGC-----UAUA
AAQB01008020.1/35862-35772   CA-AACUC--A-AAUGAUGAUAAUUACAUACACCAAUAUCAGAGAA-AUUAUGUUGAAAUCA--UUUUUAGCAUGCAUCACCAUCUGAUUGA---GAUUGC
AAKO01002293.1/4228-4315     AA-UCCUU--U-CUUGAUGACAACUUCAUACCA--AACUCAGAGAA-ACUAUGUUGAAAUC---UUUUUAACAUGCAUCACCAUCUGAUUAA---AAAUUU
AADK01043615.1/939-1025      UA-AAAUU--A-CAUGAUGACA-UUUCACACCA--AAUUCUGAAAA-UUAUGAUUGA---U---UUUUUAACAUGCAUCACCAACUGAUUAUCACAAUUAU
AAPU01011573.1/516056-516142 UU-AUAUU--U-UCUGAUGAUAUCUUCAUA-CU--AACUCAGAACC-AUUAUGUUGAUAUUGAUUGCACGCCAUGCACUACCAUCUGAUUA------UAAU
AAEU02004640.1/1356-1270     UACUCCUU--A-AUUGAUGACAACUUCAUACCC--AACACAGAGAA-AUGAUGUUGAAAUC---UUUUUAACAUGCAUCACCAUCUGAACAU-----AUAA
AAFS01000276.1/52025-51939   UA-UUCCCA-U-AAUGAUGACAACUUCAUACCA--AUCUCAGAGCA-AUUAUGUUGAAAUC---CUAUUAACAUGCAUCACCAUCUGAUCAC-----AUAC
AAPP01019315.1/203914-204000 AU-UCCCCUAA-AUUGAUGAUAACUUCAUACCC--AACUCAGAACA-CUUAUGUUGAAAUC---UUUUUAACAUGCAUCACCAUCUGAAUA------AAUC
AANI01017434.1/331723-331633 AC-AACUC--G-AAUGAUGAUAGAUUCAUAACCC-AAACCAGAGAA-AUUAUGUUGAAAUC---UAUUUAACAUGCAUCACCAUCUGACAAC-GAGUUGUU
AAPT01020666.1/53686-53600   AA-ACCUU--UCAAUGAUGACAAUUUCAUACCC--UACUCAGAGCA-AUUAUGUUGAAAUC---UAUUUAACAUGCAUCACCAUCUGACUAA-----UUUC
AADK01043615.1/551-633       CU-UUUGC--A-AAUGAUGAUAUUUUAAACACCA-AACACUGAAAU-AUUGUGAU----UG---AUUUGAACAUGCAUCACCAACUGAAGCC-----AAAA
BAAB01138996.1/627-707       CU-UUUGC--A-AAUGAUGAUAUUUUAAACACCA-AACACUGAAAU-AUUGUGAU----UG---AUUUGAACAUGCAUCACCAACUGAAGCC-----AA--
#=GC SS_cons                 <<.<____.._._____________________..___________.______________...____________________________.....>>>:
#=GC RF                      uu.uucUu..a.AaUGAUGAuAAcUUCAUAccc..AAcUCAGAgaA.AUUAUGUUGAAAUc...UuUUUAACAUGCAUCACCAUCUGAuuaa.....aaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00533
#=GF ID   snoMe18S-Gm1358
#=GF DE   Small nucleolar RNA Me18S-Gm1358
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; Daub J
#=GF GA   50.00
#=GF TC   50.50
#=GF NC   44.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me18S-Gm1358 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   18S G-1358 [1].
#=GF WK   Small_nucleolar_RNA_Me18S-Gm1358
#=GF SQ   12


AC008234.9/100346-100423     UAUUUCAAA-----UGAUGAUA-U-UUCCAUGCACCACUCUGAAGCUUUUAUUAGCAUCGUGCAGAUUAUGGAU-UUCUGAA-AAUU
AC008234.9/101391-101468     UUUUUCAAA-----UGAUGAUA-C-UUCCAUGCACCACUCUGAAGCUUUUAUUAGCAUUGUGCAGAUUAUGGAU-UUCUGAAUAAU-
AAKO01000332.1/5610-5532     UUUUUCACA-----UGAUGAUA-C-UUCCAUGCACCACUCUGAAGCUUUUAUUAGCACCGUGCAGAUUAUGGAU-UUCUGAAUAUUG
AAPQ01006469.1/479113-479035 UUUUUCAAA-----UGAUGAUA-U-UUCCAUGCACCACUCUUAAGCUUUAAUUAGCACUGUGCAGAUUAUGGAU-UUCUGAAUAUUG
AAPP01016852.1/3402-3327     AUUUUAUUG-----UGAUGAUA-U-UUCCAUGCACCACUCAUAAGCUAGAAAUAGC---UUGCUGAAUAUGGAA-UUCUGAAAAAUG
AJ784368.2/1-75              U--UUCAAA-----UGAUGAUA-C-UUCCAUGCACCACUCUGAAGCUUUUAUUAGCAUUGUGCAGAUUAUGGAU-UUCUGAAUAA--
AAPT01019411.1/21008-20926   UAUUCCAAACAUACUGAUGAUA-C-UUCCAUGCACCACUCUGAUGCUUUU-UAAGCAACGUGCAGAUUAUGGAUAUUCUGAA-AAAU
AAPQ01006469.1/480031-479954 UAUUUCAAA-----UGAUGAUA-U-UUCCAUGCACCACUCUGAAGCUUUCAAUAGCGUCGUGCUGAUUAUGGAU-UUCUGAA-CAUU
AASU01043497.1/1692-1619     UCUUUUAAGUUAUAUGAUGAUA-UUUUCCAUGCACCACUCUGA-----------GUUCAGUGUAGAUUAUGGAU-AUCUGACCGAUG
AAEU02001014.1/25106-25176   UAUUGGUCAUA---UGAUGAUAAU-UUCCGUGCACCACUCUGA-----------GUUUAGUGUUGAUUAUGGUU-AUCUGAUGCAUU
AASW01007106.1/796-863       AAUCCUAUA-----UGAUGAUA-UUUUCCAUGCACCACUCUGAA--UUCA---------GUGUAGAUUAUGGAU-AUCUGAC-GGAU
AAKO01003964.1/3835-3768     AAGUUUAUA-----UGAUGAUA-UUUUCCAUGCACCACUCUGA-----------GUUCAGUGUAGAUUAUGGAU-AUCUGAC-GGAU
#=GC SS_cons                 :<-<<____.....________._._________________________________________________.________>>->
#=GC RF                      UaUuucAaA.....UGAUGAUA.U.UUCCAUGCACCACUCUGAAGCUUuuAuUAGcauaGUGcAGAUUAUGGAU.uUCUGAauaauu
//
# STOCKHOLM 1.0

#=GF AC   RF00534
#=GF ID   SgrS
#=GF DE   SgrS RNA
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published;PMID:17383224
#=GF SS   Predicted; RNAalifold
#=GF GA   37.00
#=GF TC   38.40
#=GF NC   36.80
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0032057; negative regulation of translational initiation in response to stress;
#=GF DR   GO; 0043488; regulation of mRNA stability;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   17209026
#=GF RT   The novel transcription factor SgrR coordinates the response to
#=GF RT   glucose-phosphate stress.
#=GF RA   Vanderpool CK, Gottesman S
#=GF RL   J Bacteriol. 2007;189:2238-2248.
#=GF RN   [2]
#=GF RM   17383224
#=GF RT   Physiological consequences of small RNA-mediated regulation of
#=GF RT   glucose-phosphate stress.
#=GF RA   Vanderpool CK
#=GF RL   Curr Opin Microbiol. 2007;10:146-151.
#=GF RN   [3]
#=GF RM   17383928
#=GF RT   Mechanism of RNA silencing by Hfq-binding small RNAs.
#=GF RA   Aiba H
#=GF RL   Curr Opin Microbiol. 2007;10:134-139.
#=GF CC   In sugar transport-related sRNA (SgrS) is induced under conditions of
#=GF CC   glucose phosphate stress in E.coli. This small RNA acts to negatively
#=GF CC   regulate the translation and stability of the ptsG mRNA, which encodes the
#=GF CC   major glucose transporter in E. coli [2]. SgrS forms a specific
#=GF CC   ribonucleoprotein complex with RNAse E and the chaperone Hfq and acts by
#=GF CC   base pairing with the ptsG mRNA. The crucial base-pairs for action of SgrS
#=GF CC   are confined to the 6 nt region overlapping the Shine-Dalgarno sequence of
#=GF CC   the ptsG mRNA [3].
#=GF WK   SgrS_RNA
#=GF SQ   8


AL627265.1/129989-130226   GAUGAAGCAAGAGGAA----------GAGGU-CACUAUGCGCCAGUUCUGGUUGAGAUAUUUUGCCGCGACGGAAAAAACGUCCUGGCUGGCUUGCCUGAGCGCGCCGCAGCGCUUAAAAAUGCUCGC-GGAACUGAUGCAGUGGGAGGCGACC---------GAUU---GAAGCC-AAUUGCAGACAUCAUGUGU--------------GACUGAGUAUUGGUGUAGGCGAUAGCCUA-----AAAUCACCCGCCAGCAGAUAAUAUC--UGCUGGCUUUUUU-
AY653237.1/1-227           GAUGAAGCAAG---------------GGGGUGCCCCAUGCGUCAGUUUUAUCAGCACUAUUUUACCGCGACAGCGAAGUUGUGCUGGUUGCGUUGGUUAAGCGUCCCACAACGAUUAACCAUGCUUGA-AGGACUGAUGCAGUGGGAUGACCGC---------AAUUCUGAAAGUUGACUUGCCUGCAUCAUGUGU--------------GACUGAGUAUUGGUGUA-----------------AAAUCACCCGCCAGCAGAUUAUACC--UGCUGGUUUUUUUU
AE014075.1/81708-81934     GAUGAAGCAAG---------------GAGGUGCCCCAUGCGUCAGUUUUAUCAGCACUAUUUUACCGCGACAGCGAAGUUGUGCUGGUUGCGUUGGUUAAGCGUCCCACAACGAUUAACCAUGCUUGA-AGAGCUGAUGCAGUGGGAGGGGAGU---------CAUUCUGACUACUGAUUUGCGGACAUCAUGUGU--------------GACUGAGUAUUGGUGUU-----------------AAUCGCCACGCCAGCAGUGAUUAUC--UGCUGGCUUUUUUG
CP000647.1/81039-81262     GAUGAAGCGAGGAGGUGAAUAUGAU-GAGGUCUACCGCAAAAUCGUUCUACCAACGCUACUUUUCUGCGACGCAGGAAGCGUCCUGGCUGGCCCGCCUGAUGGCAGGAC-GACAGCAGGAAAUUCUGGGGGAACUGAUGCAGUGGGGAGUGACGUCAACG---ACCUCUGAUCAUUGACUUGCAGACAUCAUGUGU--------------GACUGAGUAUUGGUGUU-----------------AUACUCGUC-------------------------GUUUUUC
BX950851.1/4292548-4292300 GGAG--GUGGCUCAUG----------ACAAUUUCCCGUUUGUC-CCAGUUCUAUCGAACCUACUUAUCGACCUGUAAAGCGAAGUGGUUGCGAUGGAUAUCUACCCAACAGCGCGU-UGCAUUAUUGCAGCAGGCGACGCAGUGGCACCUGAACGAAAUGUCCGACGACGAAUACC--GUCAUUGGCUCUAGGUGGUGCGAGGAAAAGUAUUCUGAGUAAUGGUGAU-----------------AUUUCACCAACCAGCGAGUUUUC-U--CGCUGGUUUUUUUU
CP000462.1/540605-540390   CAUGAGCCAUGCCAAC----------CCCAUCAAAC-CGAACCGGAUCCAGCA--GAUCCUGCGC------CGUUACUUCAAGCG-------GAUCCUGCCCAGGCCG--CUGACCCUGAUC----GA-GGAUCCCAU--------GAGCCAGC---------UCAACCGCCUGAUGCAGUGG-GAUAUGAACCAG--------------AUCGACGAUCGGGAGUAUCGCCGCCGCCUC----UGAGCCCCUCUCGCCCGGAUCGCGCAAGGGAGAACGCAGUU
CP000644.1/4002404-4002190 CAUGAAC----CAGCA----------AAGCGCCCCCA-----AACCGAACCGGAUCCAGCAAACCCUGCGUCGUUACUUCAAGCGGAUCCUGCCUCGC---CCGCUGACCCUGA--UCGAGGAUCCCA--------------UGAGCCAGCUCA---------ACCGCCUGAUGCAGU----GGGACAUGCACCAG--------------AUCGAUGACAAGGAGUAUCGUCGCCGCCUCUGAGUGCAGCCCCGGUUGCUCAAAG---G--CGAGGCCCAUCGCC
CP000653.1/698137-698383   GAUGAAGCAAGGGAGUGAACGAUGAAGAGGUCAACCGCACGUCAGUUUUAUCAGCAGUACUUUUUAGCGACAAAAGGAGUGUCCUGGCUGGCCCGCCAGUGCGCCGAGCAGCGGCUGAAAAUGCUGGA-AGAAUUGAUGCAGUGGGAGGUUACGCAAACG---ACUUCUGAACGCUGACUUGCCUCGAUCAUGUGU--------------GACUGAGUAUUGGUGCU------------------UAUCACCCGCCAGCAAAAUGUUUU--UGCUGGCUUUUUUC
#=GC SS_cons               [[[[--[[[[[,,,,,..........,,,,,,,((((((((((((((((-((((((,,,,,,,,,,,<<<<<<<<______>>>>->>>>,,,<<<<<<<-<<<______>>>->>>>>>>)))-))).))))))))))))-)))),,,,,,,,.........,,,<<________>>]]]]]---]]]]------..............-----------------.................---------<<<<<<<<_______>..>>>>>>>:::::::
#=GC RF                    gAUGAAgCaagcaaaa..........gaGgUcccCCaugcguCaGuucuaucagcgaUaCUuuuCcgCGaCcgcuAaauCGagcgGGuUGcGcugccugagCgcccaACAgcGAucaggcacgcUuga.ggaaCuGaugcaGuGGgaaGugAcc.........accuCcGaAuGCuGacuuGcaGACAUcAuGUGg..............guCUGAGUAuUGGUGUa.................AuaucaCCCgcCagCggaauuUcuc..cGcuGgcuUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00535
#=GF ID   snoMe28S-Am982
#=GF DE   Small nucleolar RNA Me28S-Am982
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; Daub J
#=GF GA   49.00
#=GF TC   49.10
#=GF NC   47.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00054
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me28S-Am982 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   28S A-982 [1].
#=GF WK   Small_nucleolar_RNA_Me28S-Am982
#=GF SQ   13


AC006074.1/17650-17571         GUGUUGUGAUGA-AUGAAACUU---ACACCAUCUUUCGACUGA-AAAAUGUUAUGAAGCUAUACGAGUUUUUA--CUGAAACCCCUU
AC006074.1/17919-17840         AUUUCGUGAUGA-AUGACCCUA---UCAUCAUCUUUCGACUGA-AAAUCAUUUUGAUGCUAUACUAGUUUUCA--CUGAAUUUUAAA
AASR01002759.1/1062-983        GUGUUGUGAUGA-AUGAAACUU---ACACCAUCUUUCGACUGA-AAAAUCUUAUGAUGCUAUACAAGUUUUCA--CUGAAACCCCCU
AANI01016540.1/23340-23260     UGUUUAUGAUGA-ACCAAACUUA--UCACCAUCUUUCGACUGAGCACAAACGUUGAUGCUAUACAAGUUU-CA--CUGAUUCAUUUG
AAPQ01007360.1/2428822-2428744 AUUUCGUGAUGA-AUGACUUUU---AUACCAUCUUUCGACUGA-AAAACACUUUGAUG-UAUACAAGUUUUCA--CUGAAUUUUAAA
AAPQ01007360.1/2429115-2429037 AUUUCGUGAUGA-AUGACCAUU---ACAUCAUCUUUCGACUGA-AAAACACUUUGAUG-UAUACUAGUUUUCA--CUGAAUUUUAAA
AJ784270.1/2-76                GUGUUGUGAUGA-AUGAAACUU---ACACCAUCUUUCGACUGA-AAAAUGUUAUGAAGCUAUACGAGUUUUUA--CUGA-----AAC
AAEU02000094.1/193360-193284   AUUUCGUGAUGA-AUGACACUU---AAACCAUCUUUCGACUGA-A---CAUUUUGAUGCUAUACAAGUUUUUA--CUGAAUUUUAAA
AAQB01008772.1/57096-57174     GUUUCAUGAUGAGCUAAAACUU---UCACCAUCUUUCGACUGA-UAAAUAU--UGAUGCUAUAUAAGUUUUUACCCUGA--UUACAU
AJ784269.1/2-76                AUUUCGUGAUGA-AUGACCCUA---UCAUCAUCUUUCGACUGA-AAAUCAUUUUGAUGCUAUACUAGUUUUCA--CUGA-----AUU
AAEU02000094.1/193073-192994   GUGUUGUGAUGA-AUGAAACUU---ACACCAUCUUUCGACUGA-AAAAUGUUAUGAUGCUAUACAAGUUUUCA--CUGAAAUAUCUU
AAGE02029551.1/878-798         AUAUCGUGAUGA-AUAAACUUA---UCACCAUCUUUCGACUGA-UCACAUCGUGACUGUUAUAUAGUUCCUUAA-CUGAUGCCGGUU
AADG06000500.1/4125-4199       AUUAUAUGAUGA-UUCAAAUAAUAAUCACCAUCUUUCGACUGA-G---AACUGUGAUG-----GUAAUUUUUA--CUGAAAGCAAUU
#=GC SS_cons                   <<<_________._________...__________________._____________________________.._________>>>
#=GC RF                        guuUuGUGAUGA.AUgAAacUu...uCACCAUCUUUCGACUGA.aAAauauUuUGAUGCUAUAcaAGUUUUuA..CUGAauuuuaac
//
# STOCKHOLM 1.0

#=GF AC   RF00536
#=GF ID   snoMe28S-Cm3227
#=GF DE   Small nucleolar RNA Me28S-Cm3227
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805; INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   43.00
#=GF TC   43.30
#=GF NC   42.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me28S-Cm3227 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   28S C-3227 [1].
#=GF WK   Small_nucleolar_RNA_Me28S-Cm3227
#=GF SQ   13


AC007580.6/21024-21105       GUUUUUCUGAUGAUAAGUUCAAUCUGAACAAAGUGCUGUUGAUUUACAACUUAAAAUUAAACCAAAAGGAUUCUGAUA------AAAU
AC007580.6/21266-21347       UUGUACCUGAUGAUAAGUUUAAUCUGAACAAAGUGCUGUUGAUUCACAACUUAAAAUUAAACCAAAAGGAUUCUGAAA------UCAA
AC008306.3/141140-141221     GUUUUUCUGAUGAUAAGUUCAAUCUGAACAAAGUGCUGUUGAUUUACAACUUAAAAUUAAACCAAAAGGAUUCUGAUA------AAAU
AC008306.3/141382-141463     UUGUACCUGAUGAUAAGUUUAAUCUGAACAAAGUGCUGUUGAUUCACAACUUAAAAUUAAACCAAAAGGAUUCUGAAA------UCAA
AAPQ01007059.1/552187-552107 AUUUUUCUGAUGAUAAGUUCAAUCUGAACAAAGUGCUGUUGAUUUAUAACUUAAAACUAAACCAAAAGGAUUCUGAG-------AAAU
AAGH01008909.1/291-204       AUUUUCCUGAUGAUAAGUUUAAUCUGAACAAAGUGCUGUUGAUUCACAACUUAAAAUUAAACCAAAAGGAUUCUGAAACCCAUUAAAU
AANI01014857.1/48922-49003   UUUCUUAUGAUGAUAAGUUCAAUCUGAACAAAGUGCUGUUGAUCAACAACUUAAAACUAAACCAAAAGGAUUCUGAUA------AACA
AAIZ01001490.1/1530-1610     UGUAU-CUGAUGAUAAGUUCAAUCUGAACAAAGUGCUGUUGAUUUUCAACUUAAAACUAAACCAAAAGGAUUCUGAAA------AACA
AAEU02000421.1/59673-59591   UUUU-CCUGAUGAUAAGUUCAAUCUGAACAAAGUGCUGUUGAUUCACAACUUAAAAUUAAACCAAAAGGAUUCUGAAA----CGCAAA
AAQB01006254.1/94312-94393   AUUUACAUGAUGAUAAGUUCAAUCUGAACAAAGUGCUGUUGAUUCAUAACUUAAAAAUUAACCAAAAGGAUUCUGAAG------AAAU
AAKO01000641.1/32745-32823   AUUUUCCUGAUGAUAAGUUUAAUCUGAAAAAAGUGCUGUUGAUUCACAACUUAAAAUUAAACCAAAAGGAUUCUGA---------AAC
AAPP01018790.1/49649-49570   GUUUAGCUGAUGAUAAGUUCAAUCUGAACAAAGUGCUGUUGAUUCACAACUUAAAAUUA-ACCAAAAGGAUUCUGAAA-------AAU
AADE01001829.1/1491-1567     UGU-----GAUGAUAAGUUCAAUCUGAACAAAGUGCUGUUGAUCCACAACUUACAAUUAAACCAAAAGGAUUCUGAAA------AACG
#=GC SS_cons                 <<<-<_________________________________________________________________________......>>>>
#=GC RF                      guuUuucUGAUGAUAAGUUcAAUCUGAACAAAGUGCUGUUGAUUcACAACUUAAAAuUAAACCAAAAGGAUUCUGAaA......aaac
//
# STOCKHOLM 1.0

#=GF AC   RF00537
#=GF ID   snoMe28S-Am2634
#=GF DE   Small nucleolar RNA Me28S-Am2634
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; ILM; Daub J
#=GF GA   50.00
#=GF TC   58.10
#=GF NC   41.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me28S-Am2634 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   28S A-2634 [1].
#=GF WK   Small_nucleolar_RNA_Me28S-Am2634
#=GF SQ   18


AC093192.2/140443-140346     AACUUC-----UUUAUUGUGAUGAUAUUU-U-GAGUAGGAAUCUCAUUGAGCCUCAGUCAUUCGUUGCUUUGAAAUUAAUUUUG-UCUCUCACUG-AUUGCAAGCAU
AC093192.2/140665-140574     UGUAAU-----CUGCUC-UGAUGAUAUUU-C-GAGUAGGAAUCUCAUUGAGC-----UACCU-GUAGCUAUGAAAUCAAUUUUAAUCUCCCACUG-AUCAAAUCAUU
AC093192.2/140885-140801     UAUAACA----CUUAGC-UGAUGAUAUUA-C-GAGUAGGAAUCUCAUUGAAA-----UAACC-------AUGAAAUCAAUUUUA-UCUCC-ACUG-AUAGCAUUAUG
AC105264.3/54702-54605       AACUUC-----UUUAUUGUGAUGAUAUUU-U-GAGUAGGAAUCUCAUUGAGCCUCAGUCAUUCGUUGCUUUGAAAUUAAUUUUG-UCUCUCACUG-AUUGCAAGCAU
AC105264.3/54924-54833       UGUAAU-----CUGCUC-UGAUGAUAUUU-C-GAGUAGGAAUCUCAUUGAGC-----UACCU-GUAGCUAUGAAAUCAAUUUUAAUCUCCCACUG-AUCAAAUCAUU
AC105264.3/55144-55060       UAUAACA----CUUAGC-UGAUGAUAUUA-C-GAGUAGGAAUCUCAUUGAAA-----UAACC-------AUGAAAUCAAUUUUA-UCUCC-ACUG-AUAGCAUUAUG
AAPU01011424.1/25535-25628   AUAAAU-----AUAUUU-UGAUGAUACUU-U-GAGUAGGAAUCUCAUUGAGCUUCAGUCAUUCGUUGCAUUGAAAUUAACUUUC-UCA---ACUG-AAUAAAUUUGU
AAPU01011093.1/111411-111507 AAUAUU-----CUUAGUUUGAUGAUAUUUGU-GAGUAGGAAUCUCAAUGAGCUGUAAUCAUUCGUUGCAGUGAAAUUAAAUUU---CUACUAGUA-ACCGUAAUGCA
AAPQ01006533.1/457851-457759 UUUGAUAU---UUGCUC-UGAUGAUAUUU-C-GAGUAGGAAUCUCAUUGAGC-----UACCG--UAGCUAUGAAAUCAAUUUUAAUCUCUCACUG-AUCAAAUUAUU
AADE01000764.1/1329-1424     AUUAGU-----AUAUUG-UGAUGAUUUUU-U-GAGUAGGAAUCUCAUUGAGCUUCAGUCAUUCGUUGCUUUGAAAU-AAGUUUG-UCUCUUACUG-AUAUGUUUAGU
AANI01017292.1/82823-82729   UCUAUU-----UCUAUA-UGAUGAUUUUUUC-AAGUAGGAAUCUCAUUGAGCUUCAGUCAUUCGUUGCCAUGAAAUCAACUUCU-UUUCC---UG-AACAUAAUAUC
AADE01000764.1/871-966       UAUAUUU----UUUUUC-UGAUGAUUUUU-C---GUAGGAAUCUCACUGAGCUUCAGUCAUUCGUUGCUUUGAAAUCAAUUUAU-CUUUCUGAUU-AUACCAAUAGU
AAPT01002824.1/1781-1684     UUUUUAA----UAAAUUCUGAUGAUAUUU-UAGAGUAGGAAUCUCAUUGAGCUUCAGUCAUUCGUUGCCAUGAAAUCAA--ACA-UCUCUCACUG-AACAAUGAACU
AAPT01002824.1/1325-1230     UACAUA-----UUAUUA-UGAUGAUAUUA-UAGAGUAGGAAUCUCAUUGAGCUUCAGUCAUUCGUUGCCAUGAAAUUAA--ACA-UCUCUAACUG-AUAAAAGUGCU
AAPT01002824.1/1557-1461     UGUUAU-----UUAUAA-UGAUGAUAUUU-UAGAGUAGGAAUCUCAUUGAGCUUCAGUCAUUCGUUGCCAUGAAAUUAA--ACA-UCUCUAACUGAACUUUAUAAAU
AASR01028110.1/560-654       ACUAUC-----UUCAUUCUGAUGAUAUUU-U-GAGUAGGAAUCUCAUUGAGCCUCAGUCAUUCGUUGCUUUGAAAUUAAUUUUG-UCUCUCACUG-AUU---GUGCA
AASS01010574.1/756-844       AAUGUAUAACACUUAGC-UGAUGAUAUUU-C-GAGUAGGAAUCUCAUUGAAA------------UAACCAUGAAAUCAAUAUUU-UCUCA-ACUG-AUAAUAACAUU
AAQB01006165.1/155968-155874 AAUUUC-----GAAUGA-UGAA-ACACUU-U-ACGUAGGAAUCUCAUUGAGCUUCAGUCAUUCGUUGCCUUGAAAACAA-UAAU-CCUCUGACUA-CUAGAAAGACA
#=GC SS_cons                 ::<<<_.....______.___________._.____________________________________________________.__________.______>>>::
#=GC RF                      uauguu.....uUuauu.UGAUGAUAUUU.u.GAGUAGGAAUCUCAUUGAGCUUCAGUcAUUCGUUGCuaUGAAAUcAAuUUua.UCUCuuACUG.AuaaaAacauu
//
# STOCKHOLM 1.0

#=GF AC   RF00538
#=GF ID   snoCD11
#=GF DE   Small nucleolar RNA CD11
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; ILM; Daub J
#=GF GA   60.00
#=GF TC   67.60
#=GF NC   38.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   CD11 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. Most of the members of the box C/D family
#=GF CC   function in directing site-specific 2'-O-methylation of substrate RNAs
#=GF CC   [1,2].
#=GF WK   Small_nucleolar_RNA_CD11
#=GF SQ   26


AC097725.2/165119-165045     UUGUGGCUUA--AUGAGGAUUGA-UU-U-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAAACUGA---AAUACCUU
AC097725.2/165332-165259     UUUUGUCUUA--AUGAGGAUUGA-UU-U-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAAACUGA----AAACGUU
AC097725.2/165542-165471     UUAAUUCUG----UGAUGAAUGA-UU-G-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAGACUGA-AUAUAAC---
AAQB01006225.1/108648-108570 AAAAUUUUUC--GUGAUGAUUGAAUG-G-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAGGCUGAUAAAUUUCAAU
AADE01001557.1/13023-12949   UAUCCCUUUC--GUGAUGAAUGA-UU-U-AA-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAUUCUGA---AGUGAUUC
AASW01038929.1/1995-1923     UUAAUUCUG----UGAUGAAUGA-UU-G-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAGACUGA---AUAUAUCU
AAPQ01006550.1/477143-477069 AAUUGUCUUA--AUGAGGAUUGA-UU-U-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAAACUGA---AAUACCUU
AADE01001557.1/13238-13165   UCAAUUCCA----UGAUGAAUGA-UU-U-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAUCCUGA--AAUUAUUCA
AAEU02000133.1/6713-6639     UUUUAUUUUA--AUGAGGAUUGA-UU-U-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAAACUGA---AAUACCCU
AASR01018550.1/9-82          AUUCGAAUUC--CACAGGAUUGA-UU-U-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAAACUGA---AAA-CAUA
AAPU01011489.1/8452-8525     UUUAUUCCA----UAAUGAAUGA-AU-U-GG-CGGAAGAGUUCUUUAAAGACAAUAUUCGUGACCCAAGACUGA---CGAAUCCU
AAPT01020493.1/36714-36641   UGAUGACCA----ACCUGUUUUA-UG-U-CG-CGGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAGGCUGA--AUUUAAGAC
AAPT01020493.1/36957-36881   AAUUGUAAAA--AUGAUGAAUGA-UU-U-UGGCUGAAGAGUUC-UUGAUGACCAUAUUCAUCACCCAAGACUGA--UAAAUAUUA
AAQB01006225.1/108201-108126 GUUAGUUUCC--AUGAUGAUUGA-UCGG-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAUGCUGA---UAUUUGUU
AAIZ01010159.1/6147-6224     AGUAAUCAUACCAUGAUGAAUGA-UU-U-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAUCCUGA--UCACUCAAU
AAPT01020493.1/37189-37113   CUGAAAAAUU--AUGAUGAUUGA-UU-U-UGGCGGAAGAGUUC-UUGAAGACUAAAUUCAUCACCCAAGACUGA--CUUUGAAAU
AANI01013986.1/36103-36176   AGUUUCUUAA--GUGAUGAACGA-UU-U-GA-CGGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAGACUGA----CUUCAUA
AAPQ01006550.1/477349-477276 UAUAUUCUA----UGAUGAAUGA-UU-G-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAGACUGA--AUAUAACUA
AAIZ01010159.1/5718-5791     UCUCAAUUCC--AUGAUGAAUGA-UU-U-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAUCCUGA----AGUUAUU
AAPP01019299.1/29302-29230   UGGCUACUA----UGAUGAACGA-AU-G-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAGACUGA---CACAGCCA
AANI01013986.1/36317-36391   AUUGAAAAAU--CUGAUGAAUGA-UU-U-GG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAGACUGA---AUAUGUAG
AAEU02000133.1/6925-6852     UAUUCAUUCU--AUGAUGAAUGA-UU-G-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAGACUGA----AUAUAUC
AAPP01019299.1/29526-29453   UUUCUCUACC--AUGAUGAAUGA-AU-G-AG-CGGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAGACUGA----AAAUAUA
AADE01001557.1/12809-12736   UAAUCAUGCC--AUGAUGAAUGA-UU-U-AG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAUCCUGA----UCACUCA
AAPU01011489.1/8684-8762     AGUAACUACA--GUGAUGAACGA-UG-C-AA-CGGAAGAGUUCCUUGAAGACUAUAUUCAUCACCCAAGACUGAUGCCACUAAUU
AAQB01006225.1/108418-108345 UUU--UCCG----UGAUGAUUGA-UU-GGAG-CAGAAGAGUUC-UUGAAGACUAUAUUCAUCACCCAAUGCUGA-ACAAAACUAU
#=GC SS_cons                 <<<-------..-----------.--.-.--.--<<<___>>>.------------------------------...->>>::::
#=GC RF                      uuuauuuuua..aUGAUGAaUGA.UU.u.aG.CaGAAGAGUUC.UUGAAGACUAUAUUCAUCACCCAAgaCUGA...aaaaaauu
//
# STOCKHOLM 1.0

#=GF AC   RF00539
#=GF ID   snoMe28S-Cm788
#=GF DE   Small nucleolar RNA Me28S-Cm788
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15987805
#=GF SS   Predicted; ILM; Daub J
#=GF GA   45.00
#=GF TC   46.00
#=GF NC   39.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Drosophila_melanogaster300078;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF RN   [2]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell 2002;109:145-148.
#=GF CC   Me28S-Cm788 is a member of the C/D class of snoRNA which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. This family directs 2'-O-methylation of
#=GF CC   28S C-788 [1].
#=GF WK   Small_nucleolar_RNA_Me28S-Cm788
#=GF SQ   5


AC010057.7/173600-173526     AUAAGCUCUAUGAUGUUAUUUUACAUAUGUUAGACUAAUGAAAUGAUUUGAUUGUAAUUUAGUAACUGAGCUUAU
AC010057.7/173837-173765     UUAAA--CAAUGAUGUUAUUUUACAUAUGUUAGACUAAUGAAAUGAUUUGAUUGUAAAUUAGUAACUGAGAAUGU
AAPQ01006530.1/556557-556485 AUUAA-ACAAUGAUGUUA-UUUACAUAUGUUAGACUAAUGAAAUGAUUUGAUUGUAAAUUAGUAACUGAGAAAGU
AAQB01006228.1/174760-174688 ACAAU-ACUAUGAUGUU-UUUUACAUAUGUUAGACUAAUGAAAUAAUUUGAUUGUAAAUUACGUACUGAGUUUGU
AJ784353.1/4-72              ACAAU------GAUGUUAUUUUACAUAUGUUAGACUAAUGAAAUGAUUUGAUUGUAAAUUAGUAACUGAGAAUGU
#=GC SS_cons                 <<<__.__________________________________________________________________>>>
#=GC RF                      acaAa.aCuAUGAUGUUAUUUUACAUAUGUUAGACUAAUGAAAUGAUUUGAUUGUAAAUUAgUAACUGAGaaugu
//
# STOCKHOLM 1.0

#=GF AC   RF00540
#=GF ID   snopsi18S-1854
#=GF DE   Small nucleolar RNA psi18S-1854
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; ILM; Moxon SJ
#=GF GA   40.00
#=GF TC   43.00
#=GF NC   36.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   psi18S-1854 is a member of the H/ACA class of snoRNA. This family is
#=GF CC   responsible for guiding the modification of uridines 1854 and 1937 to
#=GF CC   pseudouridine in Drosophila 18S rRNA [1].
#=GF WK   Small_nucleolar_RNA_psi18S-1854
#=GF SQ   16


AC012160.7/77294-77140     UCAUUAUCCGUCCAAAACUAAAACUGCAGCGUUG--A-UCCCUA----------CAGCGUUGUGGUAUUC-AAUUGGACCACAAUAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGCCUCAAAAAUGCAA-CCUUAAUAAAGC-AAUAAAUCAACAGCAAAAAUUC
AC012160.7/77640-77489     UCAUUAUCCGUCCAAAACUAAAACUGCAGCGUUG--A-UCCUUA----------CAGGGUUGUGGUAUUC-AACUGGACCAUAAUAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGCCUCAAAAAUGCAA-CCUUAAUAAAG--CAUAAAUCAACA--AAAACCUA
AC012160.7/77986-77835     UCAGUGUCCGUCCAAAACUAAAACUGCAGCGUUG--A-UCUCUG----------CAGCGUUGUGGCAUUC-AAUUGGACCACAGGAAAUCCCAUGGUUAGCUAUUCCUCUUAAGGGCAUGGCCUCAAAAAUGCAA-UCUUAAUAAAG--CAUAAAUCAACA--AAAUCCUA
AF426408.1/1766-1920       UCGAUUUAUGUCCAAAACUAAAACCGCAUCAGUG--A-UUUACA----------CGCUGGCGUGGUAUUC-AAUUGGACUACAUAAAAGCCCAUGAUUAACUAUUCCUCUUAAGGGCAUUUGCUCGAAGAUGCAAACCUUAAUAAAGU-CA-AAAUCAACAGCAGAAGCUC
AF426408.1/186-341         UUUUUUUACGUCCAUAACUAAAACCGCAGCAGUG--A-ACGAAA----------CGUUGUUGUGGUAUUC-AAAUGGACUAUAUUAUACGCCAUGAUUUACUAUUCCUCUUAAGGGUAUCGGCUUGAAGAUAUUAACCUUAAUAAAGU-CAAAAAUCAACAGCAAAUACAC
AF426408.1/1418-1573       UCGAUUUAUGUCCAAAACUAAAACCACAUCAGUG--C-UUCGCA----------CGCUGGCGUGGUAUUC-AACUGGACUACAUCGAAAUCCAUGGCUAACUAUUCCUCUUAAGGGCAUUGGCUCGUAGAUGCAAACCUUAAUAAAGU-CAAAAAUCAACAGCAUCUUUGC
AAPQ01006005.1/4302-4148   UCAAUAUCCGUCCAAAACUAAAACUGCAGCGUUG--A-UCUCUA----------CAGCGUUGUGGUAUUC-AAUUGGACUACAACAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGGCUCAAAAAUGCAA-CCUUAAUAAAGC-AAUAAAUCAACAACACCAGCAA
AAPT01018955.1/16423-16577 UCGAAGUAUGUCCAAAACUAAAACCGCAUCAGUG--A-UUCACA----------CGCUGAUGUGGUAUUC-AAUUGGACUACAUCAAAGCCCAUGAUUUACUAUUCCUCUUAAGGGCAUUGGCUAAAAGAUGCGAACCUUAAUAAAGU-CA-AAAUCAACAGUUAUCAAUA
AAGH01016719.1/1323-1477   UCAUUAUCCGUCCAAAACUAAAACUGCAGCGUUG--A-UCUCUA----------CAGCGUUGUGGUAUUC-AACUGGACCACAAUAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUAGCCUCAAAAAUGAAA-CCUUAAUAAAGC-AAUAAAUCAACAAAACCAGCAA
AAKO01002760.1/34912-34758 UUAGUAUCCGUCCAAAACUAAAACUGCAGCGUUG--A-UCUCUA----------CAGCGUUGUGGUAUUC-AAUUGGACCACAGGAAACCCCAUGGUUAGCUAUUCCUCUUAAGGGCAUGGCCUCAAAAAUGCAA-CCUUAAUAAAGC-AAUAAAUCAACAAAACCAGCAA
AAPP01018319.1/47168-47014 ACGAUAUCCGUCCAAAACUAAAACUGCAGCGUUG--A-UCCUCA----------CAGCGUUGUGGUAUUC-AAUUGGACCAAAAUGAACCCCAUGGUUAACUAUUCCUCUUAAGGGCAUUGCCUCAAAAAUGCGAACCUUAAUAAAGU-CU-AAAUCAACAAUAAAAUACA
AAEU02000718.1/22448-22294 UCAUUAUCCGUCCAAAACUAAAACUGCAGCGCUG--A-UUCCCA----------CAGCGUUGUGGUAUUC-AACUGGACUACAACAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGGCUCAAAAGUGCAA-CCUUAAUAAAGC-AAUAAAUCAACAAAACCUCCCC
AAPU01009646.1/39739-39893 UUGGCUUAUGUCCACAACUAAAACCGCAUCAGUG--A-CCCACA----------CGCUGGUGUGGUAUUC-AAUUGGACUACAUUGAACCCCAUGGUUAACUAUUCCUCUUAAGGGCAUUGGCUAAAAGAUGCAUUCCUUAAUAAAGU-CA-AAAUCAACAUUAGCAAUUU
AAIZ01005601.1/28268-28424 UCCUCCUCCGUCCUAAACUAAAACUGCAGCGAUG--AUUCCACA----------CGUCGUUGUGGUAUUC-AAUAGGACCAAACCAAAGCCCAUGAUUUGCUAUUCCUCUUAAGGGCAUUGGCUUGAAUAUGCGAACCUUAAUAAAGU-UUAAAAUCAACAAUCAUACAUA
AAFS01000909.1/11343-11498 UUCCUGCACGUCCUAAACUAAAACUAUAGCGAUG--A-UUUUGA----------AGUCGCUGUGGUAUUC-AAUUGGACCAAAGUAACAUCCAUGGUUAACUAUUCCUCUUAAGGAUAUCGCCUUGAAGAUAUUUACCUUAAUAAAGU-CACAAAUCAACAACAACAACAG
AAQB01006339.1/42170-42334 AUUGAUUACGUCCAUCACUAAAACUAUAGCAAUGAGA-UUUUCAUAAAUCAAUAAAUUGUUGUAGUAUUCUAAAUGGACUACAACAAAC----UGAUAAACUACUCCUCUUAAGGAUAUCGUCUCGAAGAUAUAA-CCUUAAUAAAGUUCAAAAAUCAACAAAAUCAUCAU
#=GC SS_cons               :::::::::<<<<<<-------<<<<<<<<<<<<.._.______..........>>>>>>>>>>>>----.-->>>>>>---------------<<<<-----------<<<<<<-<<<__________>>>---->>>>>>------.---->>>>::::::::::::::
#=GC RF                    UcauuuUacGUCCaaAACUAAAaCcgcagCgguG..A.UuuuuA..........CaccGcugugGuAUUC.AAuuGGACuAcAauAAAccCCAUGauuAaCUAUUCCUCUUAAGGGcAUuGgCUcaAAaAUgcaAACCUUAAUAAAGu.cAuAaauCAACAauAacaacua
//
# STOCKHOLM 1.0

#=GF AC   RF00541
#=GF ID   snopsi28S-2876
#=GF DE   Small nucleolar RNA psi28S-2876
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; PFOLD; Moxon SJ
#=GF GA   100.00
#=GF TC   127.80
#=GF NC   38.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   psi28S-2876 is a member of the H/ACA class of snoRNA. This family is
#=GF CC   responsible for guiding the modification of uridines 2876 and 2956 to
#=GF CC   pseudouridine in Drosophila 28S rRNA [1].
#=GF WK   Small_nucleolar_RNA_psi28S-2876
#=GF SQ   8


U35631.2/189-333           ACGGUG-GCCGGUAGCAAUGGCUUGUGGUUCGU--UU----------AG-AG----ACUGCUUGCUUAUAACACUUGGCCAGAACGAAAAUCUAUCUAAUAUCCGUAGCGUCAUAAUGUGUAGUAUA-GCCGACAUUUGGCGUAUGAAACGAAGAGACAUUAUC
AF426408.1/2331-2471       CAUUUG-GCCAGCAACGAUGGCACGCAGUUCGA--AC----------CG-CG----ACUGCGUUCUUAUAACGCUUGGCUAUAAUAAACAUCUAUCU---AUCCGUAGCGUCACAAUGUGUAAU-UA-GCCGACAUUUGGCGUAUGAACUGAAGAGACAUCACA
AASV01043460.1/657-805     ACGGUG-GCCGGUAGCAAUGGCUUGUGGUCCCA--UU----------AG-AGACUGACUGCUUGCUUAUAACACUUGGCCAGAACGAAAAUCUAUCUUAUAUCCGUAGCGUCAUAAUGUGUAGUAUA-GCCGACAUUUGGCGUAUGAAACGAAGAGACAUUAUC
AAPT01018955.1/17011-17152 CAAUUG-GCCAGCAACGAUGGUGCGCAGUUCGA--GC----------AG-CG----ACUGUGUUCUUAUAACGCUUGGCUAUAAUAAACAUCUAUCC--UAUCCGUAGCGUCACAAUGUGUAAU-UG-GCCGACAUUUGGCGUAUGAACUGAAGAAACAUUUCA
AAQB01006339.1/43171-43326 CCUAUGCGCCAGCAGCAAUGGCUUGUGGUUCCA--AUUCAACUUGAAAG-AG----ACUGCUUGCUUAUAAAGCUUGGCUAGAAUAAAAUUCUAUCGUAUAUCCGUAGCGUUUUAAAUGUGUACAUA-ACCGACAUUUGGCGUAUGAACUGAAGAGACAAAUCU
AAFS01000909.1/13514-13657 CAUGCA-GCCAGCAGCAAUGGCUUGUGGUUCGA--UU----------GG-CG----ACUGCUUGCUUAUAAUGUUUGGCCAGAACAUUCUUCUAUCU--UAUCCGUAGCGUCACAAUGUGUAAUAUAAUCCGACAUUUGGCGUAUGACCUGAAGAGACAUCUUA
AAPU01009646.1/40294-40435 GUUUUG-GCCAGCAACGAUGGCGCGCAGUUCGAGCAC----------AG-AG----AUUGCGUUCUUAUAACGU-UGGCUAUAAUAAACAUCUAUCU---AUCCGUAGCGUCACAAUGUGUAAU-UA-ACCGACAUUUGGCGUAUGAACCGAAGAGACAUUUAC
AAPP01018319.1/46616-46473 GCAAAG-GCCGGUAGCAAUGGCUUGUGGUUCGA--UU----------UGGAG----ACUGCUUGCUUAUAACACUUGGCCAGAACGAAAUUCUAUCU--UAUCCGUAGCGUCACAAUGUGUAUUUUA-GCCGGCAUUUGGCGUAUGAACUGAAGAGACAUUUCA
#=GC SS_cons               ::::<<.<<<<<<-----------<<<<<____..__..........__.__....>>>>>----------->>->>>>>>----------------..----------<<<----<<<---<<<<-.<<<<<___>>>>>>>>>--->>>---->>>::::::
#=GC RF                    acuaug.GCCaGcAgCaAUGGCuuGcgGUUCgA..uu..........aG.aG....ACugCuUgCUUAUAAcgCUuGGCcagAAuaAAaaUCUAUCu..UAUCCGUAGCGUcAuAAcggGuAauauA.gCCgaCAUuuGGcguauGAAccgAAGAgACAUuuua
//
# STOCKHOLM 1.0

#=GF AC   RF00542
#=GF ID   snopsi28S-1192
#=GF DE   Small nucleolar RNA psi28S-1192
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; ILM; Moxon SJ
#=GF GA   44.00
#=GF TC   44.50
#=GF NC   41.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   psi28S-1192 is a member of the H/ACA class of snoRNA. This family is
#=GF CC   responsible for guiding the modification of uridine 1192 to pseudouridine
#=GF CC   in Drosophila 28S rRNA [1].
#=GF WK   Small_nucleolar_RNA_psi28S-1192
#=GF SQ   15


AC012160.7/76008-75871     AAUAGGUCCAAUCUAAUUCUGCAUGGUG------GUUUAAUUAUGUAGUCUCGCUUUUGGACCAGAUUAAUUUCCA--UCCUUUAUUAUCCUUGUGCU-UGUAAU--AUUGCUUAGUUCAAUGCACAUGAGAAACGUAAAGGAACACUA
AC012160.7/76359-76220     ACUAG-UCCAAUCUAAUUCUGCAUCAUG------GUUUAUUUAUGUAGUCUCGCUUUUGGACCAGAUCAAACUCCAAAUCUCUUAUUAUCCUUGUGCU-AGUGACC-ACUUAACUGUCCUAUGCACACGAGAAACGUAAAAGAACACUU
AC012160.7/76180-76044     CGGGGGUCCAAUCUAAUUCUGCAUAGUG------GUUUAAUUAUGUAGUCUCGCUUUUGGACCAGAACAAUCACCA--UCCUUUAUUAUCCUUGUGCU-UGUGAC--AAUA-UCAGUCUAAUGCACACGAGAAACGUAAAAGAACAUUA
AF426408.1/2971-3114       AGUAGGUCCAGUCUAAUUCUGCAUCAUGUCACUUGGAUAUUGUUGCAGACUCGCUUUUGGACAAGAGCAAUGUAUG--UCUUUUAUUAUCCUUGUGCU-UGUGGC--AACACUCAGCUCAAUGCACACGAGAAACGUAGAAGAACAAUU
AF426408.1/2797-2940       AGUAUGUCCAGUCUAAUUCUGCAUCAUGUCACUUGGAUAUUGUUGCAGACUCGCUUUUGGACAAGAGCAAUGUUUG--UCUUUUAUUAUCCUUGUGCU-UGUGGC--AACACUCAGCUCAAUGCACACGAGAAACGUAGAAGAACAAUC
AASS01035502.1/1208-1344   AAUAGGUCCAAUCUAAUUCUGCAUCGUG------GUUUAAUUAUGUAGUCUCGCUUUUGGACCAGAUUAAAUCACA--UCCUUUAUUAUCCUUGUGCU-UGUGAC--AAUA-UCAGUUCAAUGCACACGAGAAACGUAAAAGAACAUUA
AAPQ01006005.1/2997-2860   CGGGGGUCCAAUCUAAUUCUGCAUAAUG------GUUUAUUUAUGUAGUCUCGCUUUUGGACCAGAACAAUCACCA--UCCUUUAUUAUCCUUGUGCU-UGUAAU--AUCAUUUAGUUCAAUGCACACGAGAAACGUAAAAGAACACUC
AAEU02000718.1/21003-20866 AAUAGGUCCAGUCUAAUUCUGCAUCAUG------GUUUAAUUAUGUAGUCUCGCUUUUGGACCAGAUUAAUUCCCA--UCCUUUAUUAUCCUUGUGCU-UGCAAU--AUCAUUCAGUUCAAUGCACACGAGAAACGUAAAAGAACACUA
AAPP01018319.1/45936-45799 UUUAGGUCCAAUCUAAUUCUGCAUCAUG------GCUUAUUUAUGUAGUCUCGCUUUUGGACCAGAAAAAUCCCCA--UUUUUUAUUAUCCUUGUGCU-UGUAAC--ACACUCCAGUUCAAUGCACACGAGAAACGUAAAAGAACACUA
AAKO01002760.1/33606-33469 AAUAGGUCCAAUCUAAUUCUGCAUCGUG------GUUUAAUUAUGUAGUCUCGCUUUUGGACCAGAUUAAUUCAAA--UCCUUUAUUAUCCUUGUGCU-UGUAAU--AUUACUUAGUUCAAUGCACACGCGAAACGUAAAUGAACACUA
AAFS01000909.1/14435-14576 AUUCGGUCCAAUCUAAUUCUGCAUCAUG------GUUUAUUUAUGUAGUCUCGCUUUUGGACAAAACUAAUCCACAAAUCUUUUAUUAUCCUUGUGCU-UGUGGCACUAUCCCCUGUCCAAUGCACACGAGAAACGUAGAAGAACAUUA
AAPT01018955.1/17384-17525 AUUAUGUCCAGUCUAAUUCUGCAUCAUGUCACUGGGAUAUUGAUGCAGACUCGCUUUUGGACAAUAACAAAG------UCUUUUAUUAUCCUUGUGCU-UGUGGCAACAUUAUCAGCUCAAUGCACACGAGAAACGUAGAAGAACAACU
AAIZ01005601.1/29360-29501 GAUAGGUCCAAUCUAAUUCUGCAUCAUG------GUUUAUUUAUGUAGUCUCGCUUUUGGACAAAACUAACCCACAGAUCUUUUAUUAUCCUUGUGCU-UGUGGCAUUAUCCCCUGUCCAAUGCACACGAGAAACGUAGAAGAACAGAU
AAPU01009646.1/41004-41148 ACUACGUCCAGUCUAAUUCUGCAUCAGGUCAUUUGGAUACUGUUGGAGACUCGCUUUUGGACAAGAUCAAUAUUAUG-UCUCCUAUUAUCCUUGUGCU-UGUGGC--AACACCCAGCUCAAUGCACACGAGAAACGUAGAAGAACAACU
AAQB01006339.1/44074-44218 UUCGAGUCCAAUCUAAUUCUAUCUUAUGAUCAUUGCCUAAUAAGAUAGACUCGCUUUUGGACUAGAUAAAUUUUCU--UCUUUUAUUAUCCUUGUGCUUUGUGUC--CUUUUAUCUGACAAGGCACACGAGAAACGUAAAUGAACAAAA
#=GC SS_cons               ::::<<<<<<--------<<<<<<<<<<......___>>->>>>>>>>--------->>>>>>-------------..<<<<<<<<----<<<<<<__.______..__________________>>>>>>---->>>>>>>>::::::
#=GC RF                    auuagGUCCAaUCUAAUUCUgCaucaug......GuuuauugauGcAGuCUCGCUUUUGGACcAgAuuAAuuuuca..UCuuuUAuUAUCCuuGUGCU.UGUgac..aauauucaGuuCAAUGCACACgaGAAACgUAaaaGAACAaua
//
# STOCKHOLM 1.0

#=GF AC   RF00543
#=GF ID   snopsi18S-1377
#=GF DE   Small nucleolar RNA psi18S-1377
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   48.00
#=GF TC   48.10
#=GF NC   44.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Drosophila_melanogaster300244;
#=GF DR   snoopy; Drosophila_melanogaster300246;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   psi18S-1377 is a member of the H/ACA class of snoRNA. This family is
#=GF CC   responsible for guiding the modification of uridines 1377 and 1279 to
#=GF CC   pseudouridine in Drosophila 18S rRNA [1].
#=GF WK   Small_nucleolar_RNA_psi18S-1377
#=GF SQ   15


AC009733.5/161685-161548     UCGUUUUUGUGUUAUUUGCUGGAAGUUACAUCCAAAG-CCAGUGAUUGUCAAACAGAACGUAAAUU------AA-----UGC----GGCUAUCACUCCACAAUGUUGAGCCGGCUUU---CCAGGGCUACUGCAUUACUUUUCG--GCUCGCCACACUC
AC009733.5/161938-161801     UCGUUCUUGUGUUUUUCGCUGGCUGU-CCUUCCAAAG-CCAGUGAUUGUCAAACAGAACGUACAUU------AA-----UGGCA--GCUUAUCACUCCACAAUGUUGAGCCGAGUUU---UCACGGUUACUGCAUUACUUUCCG--GCUCGCCACA-UC
AC009733.5/161346-161211     CCGUUCUUGUGUUAUUCGCU-A-AGCGAUUACCUAAGCUCAGCGAUUGUCAAACAGAACGUAGAUU------AA----CUGCC---GCUAAUCACUCCACAAUGUUGAGCCGACUCU---CAACGGCUACUGCAUUACUAUAUG-----CGCCACAUUC
AC009733.5/161167-161032     CCGUUCUUGUGUUAUUUUCUGGACGUUGUU--CAAGU-CCAGCGAUCGUCAAACAGAACGCAAAGU------AA-----UGCA---ACGAAUCACUCCACAAUGUUGGGUCUACUUUG--CCAGGACAGCAUCAUUACU-UAAG--GAUUGCAACA-GC
AC009733.5/161513-161377     CCGUUCUUGUGUUAUUCGCUAGAUCUU-UU--CAUGGCCUAGCGAGCGUCAAACAGAACGCAAACU------GA-----AGCA---ACGAAUCACUCCACAAUGGUGGGUCUACUUUA--CCAGGACUGCAUCAUUACU-AAAG--GAUUGCUACAGUU
AASV01031167.1/4034-3895     UCGUUUUUGUGUUAUUCGCUGGAAGUUACAUCCAAAG-CCAGUGAUUGUCAAACAGAACGUACAUU------AA-----UGGCA--GCUUAUCACUCCACAAUGUUGAGCCGGCUUU---CCAGGGCUACUGCAUUACUUUCCG--GCUCGCCACAGUU
AAPQ01006793.1/3548-3686     UCGUUUUUGUGUUAUUUGCUGGAAGUUAUAUCCAAAG-CCAGUGAUUGUCAAACAGAACGUAAAUC------AA-----UGGC---AGCUAUCACUCCACAAUGUUGAGCCUUCCUC---CCACGGCUACUGCAUUACUUUCCG--GCUCGCCACACUU
AAEU02000258.1/5736-5598     CCGUUCUUGUGUUUUUCGCUGGUUGU-CCUACCAAAA-CCAGGGAUUGUCAAACAGAACGCAAAUU------AA-----UGGCA--GCUUUUCACUCCACAAUGUUGAGCCCACUUA---CCUCGGCUACUGCAUUACUUUCCG--GCUCGCCACAUUA
AAPP01019605.1/52369-52229   CCGUUCUUGUGUUAUUCACUGGAUGUUAUUGUCAAAU-CCAGUGAUUGUCAAACAGAACGAAGAUC------AA-----AGCAA--ACUAAUCACUCCAUAAUGAUGGGCCGACUUAAC-CCUGGGCCACUUCAUUACUAAAUG---AUUGCGACAUUU
AAQB01009417.1/147577-147440 CCGUUCUUGUGUUAUUCGCUGAACUCAUUUACCUAGU-UCAGCGAUUGUCAAACAGAACGCAGAAU------AA-----AGC--------AUUACUCCACGAUGUUAAGCUCAUUACUG-CCAGAGCUCUUACAUUACUACAAAUUCCUUGCGACAAAA
AADE01000059.1/83917-83774   CCGUUCUUGUGUUAUUCGCUAGACUU-ACCUUCUAGU-CCAGCGAUUGUCAAACAGAACGUACACU------AAUCCCAGGCA---ACUACUCACUCCACAAUGAUUAGCCGACAAUAG-ACAAGGCUUCAUCAUUACUAAAUG---UUUGCCACAUUU
AAIZ01003265.1/29460-29604   CCGUUCUUGUGUUAUUCACUGGACUCACCU--UAUAGUCCUGUGAUUGUCAAACAGAACGUACAGUAAACUCAA-----AGCA---ACUACUCACUCCACAAUGAAAAGUCGACUAUAA-CCAAGGCUUCAUCAUUACUAAAUG---UUUGCUACAGAG
AAPT01019341.1/28626-28488   CCGUUCUUGUGUUAUUUGCUGAAUUU-AGAUACUCGU-UCAGUGAUUGUCAAACAGAACGCACAUU------AA------GUA---CCACCUUACUCCAUAAUGUUGAGCUGACUCUGGUCUAUAGCUUUUACAUUACU-AAAA--GCUGGUUACAUGC
AANI01014608.1/264424-264282 CCGUUCUUGUGUUAUUCGCUGAAUCUGUUAAUCUCGU-UCAGCGAUUGUCAAACAGAACGCAAAGC------GA----ACUCCAGGCCAGUUUACUCCACAUUGCAGAGCCUUGAAUG--CCUCGGCUUCUACAUAACU-ACCC--GCUCGCCACAUUU
AAPU01011021.1/13919-14061   CCGUUCUUGUGUUAUUCGCUGAAUUUG-UACUCCCAU-UCAGCGAUUGUCAAACAGAACGCACAGA------AA----AUUCCAAGUCAGCGGAAUCCACAUUGUUGAGCCUAUAUACA-ACAAGGCUUCUACAUUACU-AAUU--CCUGGCCACAUUC
#=GC SS_cons                 :<<<<<<--<<----<<<<<<<_______________.>>>>>>>---->>--->>>>>>------......--.....----...--------------<<<<<--<<<<_______..____>>>>--->>>>>::::::::..:::::::::::::
#=GC RF                      CCGUUCUUGUGUUAUUCgCUGGAuuUuauuuuCaaau.CCAGcGAUUGUCAAACAGAACGuAaAuU......AA.....uGca...aCuaaUcACUCCACaaUGcUgaGcCuAcuuua..cCAaGgCuuCugCAuuACUaaaug..gcUuGCcACAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00544
#=GF ID   snopsi28S-3327
#=GF DE   Small nucleolar RNA psi28S-3327
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ, INFERNAL
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   70.00
#=GF TC   78.80
#=GF NC   48.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00021
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   psi28S-3327 is a member of the H/ACA class of snoRNA. This family is
#=GF CC   responsible for guiding the modification of uridine 3327 in Drosophila 28S
#=GF CC   and U1920 in Drosophila 18S rRNA to pseudouridine [1].
#=GF WK   Small_nucleolar_RNA_psi28S-3327
#=GF SQ   14


AJ629276.1/1-140             ---UUGGCUGGUUCGAAGACCACAAAACGCUCC--UC------GAAAGUUGC----GUGGUUCAAAAACAAU-AAGCCAAAAGCAAUUUUUGUCACGACGGUCUCUGAU-GCG-GCA-U-UCCA-AAGUCGCUUCAGUAACUUUUACGUGCAAUGACAGUC
AJ629274.1/1-140             ---AGGGCUUUGUCGAAGACCGUUUUGCGUGUA--GA------AUAGUGCGCCG-AUUGGUUCAAAA---CG-AAGCCCAAAGCAAUUUUUGAUACGACGGUCUCUGAU-UCG-ACA-A-AUCC-CAGUUGAUUCAGUAACUUUUACGUGCAAUUACAAAA
AC093546.2/141131-141273     CUGUGGGCUACGUCGAAGACCGAUUUCCGCUUG--UU------GCCAUGUGUCU-AUUGGUUCAAAU---CG-AAGCCCAAAGCAAUUUUUGAUACGACGGUCUCUGAU-UCG-GCA-U-UCCA-CAGUCGUCUGAGUAACUUUUACGUGCAAUUACAAUG
AC093546.2/140954-141096     GAAAGGGCUUUGUCGAAGACCGUUUUGCGUGUA--GA------AUAGUGCGCCG-AUUGGUUCAAAA---CG-AAGCCCAAAGCAAUUUUUGAUACGACGGUCUCUGAU-UCG-ACA-A-AUCC-CAGUUGAUUCAGUAACUUUUACGUGCAAUUACAAAA
AC093546.2/141558-141700     UCAUUGGCUGGUUCGAAGACCACAAAACGCUCC--UC------GAAAGUUGC----GUGGUUCAAAAACAAU-AAGCCAAAAGCAAUUUUUGUCACGACGGUCUCUGAU-GCG-GCA-U-UCCA-AAGUCGCUUCAGUAACUUUUACGUGCAAUGACAGUC
AJ629275.1/1-140             ---UGGGCUACGUCGAAGACCGAUUUCCGCUUG--UU------GCCAUGUGUCU-AUUGGUUCAAAU---CG-AAGCCCAAAGCAAUUUUUGAUACGACGGUCUCUGAU-UCG-GCA-U-UCCA-CAGUCGUCUGAGUAACUUUUACGUGCAAUUACAAUG
AAEU02000204.1/528924-528781 UUGUGGGCUUCGUCGAAGACCGAUUUGCGCCUG--UU------GCCAUGUGUUU-AUUGGUUCAAAU---CG-AAGCCCAAAGCAAUUUUUGAUACGACGGUCUCUGAU-UCG-GCAUU-UCCA-CAGUCGUCUUAGUAACUUUUACGUGCAAUUACAAAG
AAPP01019317.1/508640-508498 UAGUGGGCUUUGUCGAAGACCGAUCUACGCUCA--UA------ACAAUGUGUUU-UUUGGUUCAAAA---CG-AGGCCCAAAGCAAAUUUUGAUACGACGGUCUCUGAU-CUG-GCA-U-UCCA-CAGCCAUUUUAGUAACUUUUACGUGCAAUUACAAAC
AAIZ01003890.1/4966-5109     UGUCUGGCUUUAUCGAAGACCGAUCUAUGUCAU--UU------GCAAUACGUUC-AUUGGUUCAAAA---UG-AAGCCCAAAGCAAUUUUUGUUACGACGGUCACUGAU-CUGUGCA-U-UCCG-CAGCCAUUUCAGUAACUUUUACGUGCAAUUACAUUC
AAPU01011600.1/223057-222915 AGAUGGGCUACAUCGAAGACCAUUUAGUGUUUC--UC--------CAUACGCCA-AUUGGUUCAAAA---UG-AAGCCCAAAGCAAUCUUUGAUACGACGGUCUCUGAUCUUGAGCA-U-UCUC-CAGCCGUUUCAGUAACUUUUACGUGCAAUUACAAAU
AAQB01006207.1/233840-233991 UUGUGGGCUUUAUCGAAGACCGAUUUAUGUUUU--UUUUUAAAGUGAUACAUUACAUUGGUUCAAAA---UG-AAGCCCAAAGCAAUUUUUGUUACGACGGUCACUGAUCUUG-GCA-UAUUCA-CAGCCAUUUCAGUAACUUUUACGUGCAAUUACAAUU
AANI01017400.1/61684-61826   CGUCGGGCUUCAUCGAAGACCGUUUAGCGU--U--UU------CCAGUACGCCA-AUUGGUUCAAAA---UG-AAGCCCAUAGCAAUUUUUGAUACGACGGUCUCUGAA-CUGUGCA-UAUUGC-CAGCCGUUUCAGUAACUUUUACGUGCAAUUACAAAU
AAPT01020713.1/90899-91044   UUCUUGGCUGGUUCGAAGACCACAAAACGCAUU--CA------AAUUCAAGUUG-CGUGGUUCAAAA---ACAAAGCCCAAAGCAAUUUUUGAUACGACGGUCUCUGAU-UUGUGCA-U-UUUAUCAGCCAUUUCAGUAACUUUUACGUGCAAUUACAUUU
AADE01000247.1/76084-76226   UCCCUGGCUGGUUCGAAGACCACAAAGCGCUAAAAUU------CCAAGUUGC----GUGGUUCAAAU---ACUAAGCCAAAAGCAAUUUUUGUCACGACGGUCUCUGAU-CUGAGCA-U-UCCA-CAGCCGUUUCAGUAACU-UUACGUGCAAUUACAACU
#=GC SS_cons                 :::<<<<<<-<<-----<<<<<<<---<<<___..__......_____>>>---.>>>>>>>-----...>>.->>>>>>---------<<<-<<<<--<<<--<<-<-.-<<.<<_._.____.__>>>>-->->>-->>>---->>>>>>>::::::::
#=GC RF                      uuaugGGCuucgUCGAAgaCCacuuuacgcuuu..uu......auaaugcguuu.aguGGuuCAAAa...cg.AaGCCcaAAGCAAUUUuuGacaCGACgGuCUCuGaU.ucG.gCA.U.Ucca.cAGcCguUucaGUAaCuUUUACGugCaaUUACAauu
//
# STOCKHOLM 1.0

#=GF AC   RF00545
#=GF ID   snopsi18S-841
#=GF DE   Small nucleolar RNA psi18S-841/snoR66
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   50.00
#=GF TC   54.70
#=GF NC   41.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF CL   CL00033
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Drosophila_melanogaster300187;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   psi18S-841 is a member of the H/ACA class of snoRNA. This family is
#=GF CC   responsible for guiding the modification of uridine 841 in Drosophila 18S
#=GF CC   rRNA to pseudouridine [1].
#=GF WK   Small_nucleolar_RNA_psi18S-841/snoR66
#=GF SQ   24


AJ544010.1/1-140             -----GCGCACUCUGUGUCACAU-C-GAUAUAUC----CAGCCUCAUGUGAUGACAAUUUGUAAGCUU-GCUAGAAUAA-G--GGGG---A--GCU--UCG-CUUAUCCAUGCGGCAACUAUCUUCAGCCC-----AG-AU-GCCGCAUUGAAUUCGGGC--CUCACA----UGCU
AC007175.1/70408-70552       GGCAAGCGCACUCUGUGUCACAU-C-GAUAUAUC----CAGCCUCAUGUGAUGACAAUUUGUAAGCUU-GCUAGAAUAA-G--GGGG---A--GCU--UCG-CUUAUCCAUGCGGCAACUAUCUUCAGCCC-----AG-AU-GCCGCAUUGAAUUCGGGC--CUCACA----UUAA
AC007175.1/73628-73766       UGCAAAUGCACUCUGUGUCACAU-U-G---AAUU----UACCUACAUGUGAAGACAAUUUGUUAGUUU-GCUAUAUGAA-A--GAGA---U--GUG--AC---UUAUCCAUGCAAUUAGUGCCGUAAAAG------GU-UG-AUUGCAUUGAAAUCGCAU--UUUACA----CUAU
AAKO01001995.1/15226-15363   UGCAAAUGCACUCUGUGUCACAU-----UAAAAC----UAGCUUCGUGUGAUGACAAUUUGUUAGUUU-GCCAGAUCA------AGG---A--GAU--GCGUCUUAUCCAUGUGG-CUAAGUUCUUACCAA-----UU-UG-UUCACAUUGAAAACGCCC--CUAACA-----UGA
AAPP01018740.1/149264-149399 GGCAGAUGCACUCUGUGACACAC-A-G------A----AAUCCACUUGUGAUUACAAUUUGUUAGUUU-GCCAGAGCAA-----GGG---G--AUG--CGG-UUUAUCCAUGUAGU--CUAAGCCCUGCCU-----GG-GGGAUUGCAUUGAAAACGUAU--CUUACA----CUAU
AADE01000570.1/47469-47613   GGCAAAUGCACUCUGUGUCACAU-U-GAAACA------CAGCCUCAUGUGAUGACAAUUUGUUAGUUU-GCUAGAUCAA-G--UGGG---AACGGG--GCGUCUUAUCCAUGUGGUUGGU-CUAUGACCAA-----GC-UA-AUCACAUUGAAAACGCUC--CUUACA----CGAC
AE013599.4/17218411-17218548 UGCAAAUGCACUCUGUGUCACAU-----UAAAAC----UAGCUUCGUGUGAUGACAAUUUGUUAGUUU-GCCAGAUCA------AGG---A--GAU--GCGUCUUAUCCAUGUGGCUGAGUUCUU-ACCAA-----UU-UA-UUCACAUUGAAAACGCCC--CUAACA-----UGA
AANI01014934.1/204797-204661 UGCAAGUGCACUCUGUGUCACAU-U-GAUUU---------GCCACAUGUGAUGACAAUUUGUUAACUU-GCCAGAUCAA-A--CCAA---A--GCU--GCG-UUUAUCCAUGUGAUUGUGUCCUUAAGACU---------A-GUUGCAUUGAAAACGCGC--CUUACA----CUCC
AAQB01006145.1/106064-106201 AGCAAGCGCACUCUGUGUCACAU-U-GAUUGACC---------UCAUGUGAAUACAAUUUGUAAGUUU-GCCAGAGUAA-G--GUGU---A----G--CUU-CUUAUCCAUGUGAUUGG--ACUCCAACUU-----GC-UA-AUCACUUUGACGAAGUCU--ACGACA--GCUUAA
AAPQ01007048.1/170987-171123 GGCAAAUGCACUCUGUGUCACAU-----UAAAAC----UAGCUUCGUGUGAUGACAAUUUGUUAGUUU-GCCAGAUCA------AGG---A--GAU--GCGUCUUAUCCAUGUGGUCAUGUUCUUCCAAUU--------UG-UUCACAUUGAAUACGCCC--CUAACA-----UGA
AAQB01006145.1/105410-105549 CGCAAGCGCACUCUGUGUCGCAUUC-GA----------AAACCUCAUGUGAUUACAAUUUGUAAGUUU-GCCAGAGUAA-G--GUGU------------AG-CUUCUUAUCCAUAUGAUUAGAUUCCUAACAUGAUAA-UC-AUUUUGACGAAGUCUACG--ACAACU----UUAU
AAEU02000410.1/178067-178205 UGCAAAUGCACUCUGUGUCACAU-----UAGAAC----UAGCUUCGUGUGAUGACAAUUUGUUAGUUU-GC-CAAAUCA-A--C--G---A--GAU--UCGUCUUAUCCAUGUGGUCAUGUUCUU-ACCAA-----UU-UG-CUCACAUUGAAAACGACC--CUAACA----UGAG
AADE01000570.1/43651-43795   GGCAAAUGCACUCUGUGUCACAU-U-GAAACA------CAGCCUCAUGUGAUGACAAUUUGUUAGUUU-GCUAGAUCAA-G--UGGG---A--ACGGGGCGUCUUAUCCAUGUGGUUGGU-CUAUAACCAA-----GC-UG-AUCACAUUGAAAACGCAU--CGUACA----UCCU
AANI01014934.1/200613-200477 UGCAAGUGCACUCUGUGUCACAU-U-GAUUU---------GCCACAUGUGAUGACAAUUUGUUAACUU-GCCAGAUCAA-A--CCAA---A--GCU--GCG-UUUAUCCAUGUGAUU-GUGUCCUUAAA-------AC-UA-AUUGCAUUGAAAACGCGC--CUUACA----CUCC
AAPT01021484.1/865760-865621 UGCAAGCGCACUCUGUGUCACAU-U-GA-----------AUCCUCAUGUGAAGACAAUUUGUAAACUU-GCUAAACUAA-A--CUAA---A--GCU--GCGACUUAUCCAUGUGUUCAUGCAAUAAAAUCA-----AAUUG-AUCACAUUGAAUACGGGC--UUUACA----CUCG
AAPT01021484.1/865591-865439 UGCAAGUGCACUCUGUGUCACAU-U-GAUUUUCAAUAACAACCACAUGUGAUGACAAUUUGUUAACUU-GCUAAACUAAAU--CUAA---A--GCU--GCGACUUAUCCAUGUGAUC-GUGUCCUUUCAAA-----AU--U-AUCACAUUGAAUACGCGC--UUUACACUCCUUAU
AAPQ01007048.1/167136-167278 GGCAAGCGCACUCUGUGUCACAU-C-G--ACAUC----CAGCCCCAUGUGAUGACAAUUUGUAAGCUU-GCUAGAAUAA-G--GGGG---U--GCU--UCG-CUUAUCCAUGUGGCAACUAUCUUCAGCCC-----AG-GU-GCCGCAUUGAAUUCGGGC--CUCACA----UUAG
AAEU02000410.1/177487-177625 UGCAAAUGCACUCUGUGUCACAU-U-G---AAAC----AAACUACAUGUGAAUACAAUUUGUUAGUUU-GCUAUAAUAA-A--GAGA---U--GCG--U---CUUAUCCAUGCAAUUAGUGCCGAAAAAG------GU-UG-AUUGCAAUGAAAU--CGCAUUUUACA----CUAU
AANI01014934.1/200366-200224 UGCAAGAGCACUCUGUAUCACAU-AAAAUUUUUA----UAACCUCAUGUGA-GACAAUUUAAUACCUU-GCUAGAUUAA-A--UUAA---A--GCU--GCGACUUAUCCAUGUGUUC-GUGUCCUUAUA-------AC-UG-AUCACAUUGAAUACGCGC--UAUACA----CUAG
AAPQ01007048.1/170360-170498 UGCAAAUGCACUCUGUGUCACAU-U-G--AAAUU----AACUA-CAUGUGAAGACAAUUUGUUAGUUU-GCUAUAUUAA-A--GAGA---U--GCG--U---CUUAUCCACGCAAUUA-CUUCCGUAUCAG-----GA-UG-AUUGCGUUGAAAU--CGCAUUUUACA----CUAU
AAEU02000410.1/174266-174410 AGCAAGCGCACUCUGUGUCACAU-C-G--AUAUC----CAGCCCCAUGUGAUGACAAUUUGUAAGCUU-GCUAGAACAA-GGAGGGG---G--GCU--UCG-CUUAUCCAUGUGGCAACUAUCUUUAGCCC-----AG-UU-GCCGCAUUGAAUUCGGGC--CUCACA----UUAA
AAPP01018740.1/146006-146141 GGCAAGCGCACUCUGUGUCACAC-A-G------A----CAGCCACUUGUGAUUACAAUUUGUAAGUUU-GCCAGAUCAA-----GGG---G--AUG--CGU-CUUAUCCAUGUGGUC-CAUUCCCCCAAAG-----GG-UG-ACUGCAUUGAAAACACAU--CUUACA----UCAC
AAKO01001995.1/14897-15030   GGCAAAUGCACUCUGUGUCACAU-U-G---AACU----UAACUACAUGUGAAGACAAUUUGUUAGUUU-GCAAUAUUAA-A--GAGU---U--GCG--U---AUUAUCCAUGUAUUUA-AAGCCGUAUCAG-----GG-UG-AUUACAUUGAAAU--CGC--AUU-------UUAC
AAPU01010147.1/86455-86314   UGCAGGCGCACUCUGUGUCACAU-U-GAAUUAUC---------UCAUGUGAUGACAAUUUGUUACCCUUGCUAGAGUAA-G--UUGAUGAA--GCU--GCGACUUAUCCAUGUGAUUGAGUUUUUCCAGCU---------G-AUUGCAUUGAAUGCGCGC--UUUACA----UUAC
#=GC SS_cons                 :<<<<<<--<<--<<<<<<<<<<.-.<<______...._____>>>>>>>>>->>>---->>-->>>>.>>-----<<<.-..-<<<...-..<<<..-<<.----<<-<<<<<<<<-<<___________.....>>.->.>>>>>>>->>--->>>>>..>>>---....>>>:
#=GC RF                      uGCAagcGCACUCUGUgUCACAu.u.GauauAuc....uAaCcuCaUGUGAugACAAUUUGUuAgcuU.GCuAgAuuaa.a..gcgg...a..Gcg..ucG.CUUAUCCaugcggucaguaucuuuaaaaa.....ac.Ug.accgcauUGAAaaCgcgC..ccgACA....uuau
//
# STOCKHOLM 1.0

#=GF AC   RF00546
#=GF ID   snopsi28S-3316
#=GF DE   Small nucleolar RNA psi28S-3316
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Moxon SJ
#=GF SS   Predicted; RNAFOLD; Moxon SJ
#=GF GA   65.00
#=GF TC   67.30
#=GF NC   48.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol 2004;24:5797-5807.
#=GF CC   psi28S-3316 is a member of the H/ACA class of snoRNA. This family is
#=GF CC   responsible for guiding the modification of uridine 3316 in Drosophila 28S
#=GF CC   rRNA to pseudouridine [1].
#=GF WK   Small_nucleolar_RNA_psi28S-3316
#=GF SQ   33


AJ629213.1/2-130             CGCACCUAAA-AGCGUUUUCUCGUC-GGCUCGUU----AAAUGCUCUUGAAAAUCGUAGAU-GUGUGCCAGAGC-G---A---AGC-----UCAGUUGC-AAGUGAUAC--GGCCA--U-UUUUUG-----UG-----GCAGAUAUCCAUA--ACG-CUGACUACAA--
AJ629256.1/2-132             UGCACCUAAA-AGCGUUUCCUUGCA-AGCCCGUU----AACUGCUCUUGGAAAUCGUAGAU-GUGUGCAAAAUC-A---A---UCC---UCACAAUAGC-AAGUGAUUU--UAGUU--C-CUCU-------AA-----CUCA-AAUCCAUUU-ACA-UUGUGAACAUAC
AJ629215.1/2-133             AGCACCUAAA-AGCGUUUUCUUAUC-AGCUUGAU----AAAUGCUCUUGAAAAUCGUAGAU-GUGUGCAAUAGC-A---A---UAU---CUACAAUAGC-UUGGGAUUC---AGUU--U-CUAUAU-----AA-----CUUC-AAUCCGUUC-AGA-UUGUAAACAUCC
AJ629214.1/2-135             CGCACCUAAA-AGCGUUUUCUUGCC-AGCCCGUU----AAGUGCUCUCGAAAAUCGUAGAU-GUGUGCCAGAGC-A---A---UCG---UCGCAGUUGC-AAGUGAUCU--AGAUC--C-GUGACA-----GA-----AUCA-GAUCCAAUU-AAAGCUGGGCUCAUUU
AJ629257.1/2-132             UGCACCUAAA-AGCGUUUUCUUGUC-AGCCUGAU----AAAUGCUCUUGAAAAUCGUAGAU-GUGUGCAAAAUC-A---A---UCC---UCACAAUAGC-AAGUGAUUU--UAGUU--C-CCUU-------AA-----CUCU-AAUCCGUUU-ACA-UUGUGAACAGUC
AAQB01006145.1/106227-106364 GGCACCUAAAAAGCGUUUUCCUGUU-GG-UAGAA----AAGUGCUCUGGAAAAUCGUAGUU-GUGUGCUAUAGCGA---A---UUC---UUUCCAUAGC-AAAACGACU--UGACU--U-AUUUUU-----AGAGAGUUCUU-GUCUAUUA--AAU-UGGUAAACAGAU
AAEU02000410.1/177646-177776 UGCACCUAAA-AGCGUUUUCUUGCA-AGCUUGUU----AAAUGCUCUUGAAAAUCGUAGAU-GUGUGCAAAAUC-A---A---UCA---UUACAAUAGC-AAGUGAUUU--UUGUU--C-CUCU-------AA-----CUCA-AAUCCAUUU-ACA-UUGUGAACAUAC
AAKO01001995.1/14441-14572   AGCACCUAAA-AGCGUUUUCUUGUU-AGCCUGAU----AAAUGCUCUUGAAAAUCGUAGAU-GUGUGCAAUAGC-A---A---UCU---CUACAAUAGU-UUGGGAUUC---AGUU--U-CUAUAU-----AA-----CUUC-AUUUCGUUC-AGA-UUGUAAACAUCC
AAPP01018740.1/149100-149230 UGCACCUAAA-AGCGUUUUCUUGCC-GGCCUGUU----ACCUGCUCUUGAAAAUCGUAGAU-GUGUGCCAGAAC-A---A---GCU---UCCCAACAGC-AAGUGACAA--GAGUU--C-UUAU-------AA-----CUCU-UAUCCGUUU-ACG-UUGUGAAUAAUU
AADE01000570.1/43470-43610   AGCACCUAAA-AGCGUUUUCUUGCC-AGCCCAAU----AAAUGCUCUUGAAAAUCGUUGAU-GUGUGCCAGACA-A---AAC-UUC---UCGCAACAGCAAAGUGAUCG--GAGUU--C-CAUUCAUUGAUGA-----CUCU-GGUCCGUUU-ACG-UUGUGAACACCA
AAIZ01002209.1/800-668       AGCACCUAAA-AGCGUUUUCUUGCC-AGCCCAAU----AAAUGCUCUCGAAAAUCGUAGAU-GUGUGCCAUAGC-A---A---GGC-----UCAGUUGC-AAGUGAUUC--UGCCC--C-AUCAAU-----GG---CAGCAG-GAUCACCAU-AAG-CUGGCUACAGAU
AAPT01021484.1/866249-866118 GGCACCUAAA-AGCGUUUUCUUGUA-GGUCAACU----UAAUGCUCUUGAAAAUCGUAGCU-GUGUGCCAGAUU-A---A---A-----UCUAAGUUGC-AAGUGACUUUUUGAGU--U-UUUAAU-----AU-----UGAA-AGUCCAUA--ACG-CUGGGAACAGAA
AAPU01010147.1/86824-86691   GGCACCUAAA-AGCGUUUUCUUGAU-UGCUUUUU----AAACGCGCCUGAAAAUCGUAGCU-GUGUGCCAGAGC-A---A---UUG---CUGCGGUUGC-AAGUGAAUU--GAUGU--C-AAUUAG----UGC-----AACA-AUUCCAUUU-ACA-CCACGCACAUGU
AANI01014934.1/204965-204832 AGCACCUAAA-AGCGUUUUCUUGAU-UGCUUUUU----AAACGCGCCUGAAAAUCGUAGCU-GUGUGCUAGAGC-A---A---UUG---CUGCGGUUGC-AAGUGUCUU--GAUGC--CAGUUAAU-----GC-----AUCA-ACUACAUUA-ACA-CCUCGCACAAGC
AAQB01006145.1/105133-105272 AGCACCUUAA-AGCGUUUUCUUGUC-GGCCAAAUUAUAAAAUGCUCUGGAAAAUCGUACAAAGUGUGCAAAACU-A---A---AGUAAAAAACAGUUGC-AAGUGAUUC--CAAUA--A-ACACAU-----UG-----UUGG-AAUCCAUU--ACG-CUGAUUACACGC
AAPU01010147.1/86995-86867   AGCACCUAAA-AGCGUUUUCUUGCA-CGCCAAUU----AAAUGCGCUUGAAAAUCGUACAU-GUGUGCUAGAUC-A---A---AGC-----UAAGUUGC-AAGUGACUC---UUUG--A-AGUAUU-----UA-----GAAG-AGUCCAUA--ACG-CUGAGUACAUUU
AAEU02000410.1/174095-174228 CGCACCUAAA-AGCGUUUUCUUGCC-AGCCCCUU----AAGUGCUCUCGAAAAUCGUAGAU-GUGUGCCAGAGC-A---A---UCG---UCGCAGUUGC-AAGUGAUCU--GAAUC--C-AUGACA-----GA-----AUCU-GGUCCAUUUUAAA-CUGGGCUCAUUU
AAPQ01007048.1/170212-170343 AGCACCUCAA-AGCGUUUUCUUGCC-AGCCUAAU----AAAUGCUCUUGAAAAUCGUAGUU-GUGUGCAAUAGC-A---A---UCU---UUACAAUAGC-AAGUGAUUC---AGUU--U-CGUUAU-----AA-----CUUC-GAUCCGUUU-ACG-UUGUGAACAUUC
AAPP01018740.1/149471-149601 AGCACCUAAA-AGCGUUUUCUUGCC-AGCCCGUU----AACUGCUCUUGAAAAUCGUAGAU-GUGUGCCAGAGC-A---A---GCU---UCCCAACAGC-AAGUGACAA--GAGUU--C-UAAU-------GA-----CUCU-UGUCCGUUU-ACG-UUGUGAAUAAGU
AAQB01006145.1/101702-101836 UGCACCUAAA-AGCGUUUUCUUGUCCGCCUUAAA----AAAUGCGCUUGAAAAUCGUAGAU-GUGUGCUAGAAU-AUAUA---UAU---AGACAGUUGC-AAGUGAUUC--CAAUU--G-AUUUAC-----AG-----U-GG-AAUCCAUG--ACG-CUGACUACAGAU
AAEU02000410.1/177902-178032 UGCACCUAAA-AGCGUUUUCUUGCA-AGCUUGUU----AAAUGCUCUUGAAAAUCGUAGAU-GUGUGCAAAAUC-A---A---ACA---UUACAAUAGC-AAGUGAUUU--UAGUU--U-CUUU-------AA-----CUCU-AAUCCGUUU-ACA-UUGUAAACAUUC
AADE01000570.1/43319-43453   CGCACCUAAA-AGCGUUUUCUUGAU-AGUCUCUUUG--AAAUGCUCUUGAAAAUCGUAGAU-GUGUGCCAUAGC-A---A---GGC-----UCAGUUGC-AAGUGAUUC--UGCCC--C-AUCGAU-----GG---CAGCAG-AAUCAUAAU-AAG-CUGGCUACAGAU
AANI01014934.1/200945-200817 AGCACCUAAA-AGCGUUUUCUUGUA-CGCCAACU----CAAUGCGCUUGAAAAUCGUAGCU-GUGUGCUAGAGC-A---A---AGC-----UUAGUUGC-AGGUGACUU--UUUGU--A-CUUCAA-----AU-----AA-G-AGUCCAUA--ACG-CUGAGUACAUUU
AAPT01021484.1/865929-865796 AGCACCUAAA-AGCGUUUUCUCGAU-AGCUUUUU----AAACGCUCCUGAAAAUCGUAGCU-GUGUGCUAGAAC-A---A---AUG---CUGAGGUUGC-AAAUGAAUU--GAUGC--C-AAUUAA----UGC-----AUUA-UUUCUAUUU-ACA-UCUCGCACAAGC
AAQB01006145.1/105578-105716 UGCACCUAAAAAGCGUUUUCCUGUU-GG-UAGAA----AAGUGCUCUGGAAAAUCGUAGUU-GUGUGCUAAAGC-A---AAAUUUC---UUUCCAUUGC-AAGUGACUU--GAUUCAUC-CUAAGA-----GA-----GUCUUUGUCCAUUU-AUU-UGGUGAACAGUU
AAPQ01007048.1/166965-167098 CGCACCUAAA-AGCGUUUUCUUGAC-AGCCUGUU----AAGUGCUCUUGAAAAUCGUAGAU-GUGUGCCAGAGC-A---A---UCG---UCGCAGUUGC-AAGUGAUCU--GGAUC--C-AUGACA-----GA-----AUCA-GGUCCAUUU-UAAGCUGGGCUCAUUU
AAPQ01007048.1/170822-170950 UGCACCUAAA-AGCGUUUUCUUGCC-AGCUCAUU----A--UGCUCUUGAAAAUCGUAGAU-GUGUGCAAAAUC-A---A---UCC---UCACAAUAGC-AAGUGAUUU--UAGUU--C-CUUC-------AA-----CUCU-AAUCCGUUU-ACA-UUGUGAAUAGUC
AAPP01018740.1/145856-145988 CGCACCUAAA-AGCGUUUUCUUGCC-AGCCCGUU----AACUGCUCUUGAAAAUCGUAGAU-GUGUGCCAGAGC-A---A---CCU---UUGCAACAGC-AAGUGAUCU--GGGUU--C-UCCUGU-----AA-----CUUU-UAUCCGUUG-ACG-UUGUAAACAUUU
AAEU02000410.1/177350-177470 AGCACCGAAA-AGCGUUUUCUUGCC-AGCCUGAU----AAAUGCUCAUGAAAAUCGUAGAU-GUGUGCCAUAGC-A---A---UUU---UUACAAUAGC-AAGUGAUAC---AG------------------------CUUC-GAUCCGUUU-ACA-UUGUAAACAUCC
AAPQ01007048.1/170519-170649 UGCACCUAAA-AGCGUUUUCUUGCA-AGCCCUUU----AAAUGCUCCUGAAAAUCGUAGAU-GUGUGCGAUAAC-A---A---UCC---ACACAAUAGC-AAGUGAUUU--UUGUU--C-CUCU-------AA-----CUCA-AAUCCAUUU-ACA-UUGUGAACAUAU
AAPT01021484.1/870042-869913 AGCACCUAAA-AGCGUUUUCUUGUA-GGCCAAUU----CAAUGCUCUUGAAAAUCGUAGCU-GUGUGCCAGAUU-A---A---AUC-----UAAGUUGC-AAGUGACUU--UUUGU--A-UUUCUA-----AA-----UAAA-AGUCCAUA--ACG-CUGAGUACAUUU
AAPQ01007048.1/166822-166952 CGCACCUAAA-AGCGUUUUCUCGUC-GGCUUGUU----AAAUGCUCUUGAAAAUCGUAGAU-GUGUGCUAGAGG-G---A---UGC-----UCAGUUGC-AAGUGAUUC--GGCCU--U-UCUUCG-----UG-----GCAGAUAUACAUA--ACG-CUGACUACAAGU
AAPT01021484.1/869884-869751 AGCACCUAAA-AGCGUUUUCUUGAU-AGCUUUUU----AAACGCUCCUGAAAAUCGUAGCU-GUGUGCUAGAAU-A---A---AUG---CUGCGGUUGC-AAAUGAAUU--GAUGC--CAAUUAUU-----GC-----AUUA-UUUCUAUUU-ACA-CCACGCACAAUC
#=GC SS_cons                 <<<<<<----.-<<<<<<<<--<<-.<_______....___>>>---->>>>>->>>----.>->>>>>-----.-...-...---...<<<<<<<---.<<<<<<<<<..-<<<<.._.______.....>>.....>>->.>>>->>>>>.-->.>>>>>>::::::
#=GC RF                      cGCACCUAAA.AGCGUUUUCUUGcc.gGCcuauU....AAacgCUCUuGAAAAUCGUAGaU.GUGUGCgAgAgc.A...A...uuu...ucccagcuGC.aagugaccc..uggcc..c.auuuau.....gg.....ccug.gguCcauuu.Acg.cugggaACAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00547
#=GF ID   IRES_TrkB
#=GF DE   TrkB IRES
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15908588; INFERNAL
#=GF SS   Predicted; RNAFOLD
#=GF GA   40.00
#=GF TC   43.60
#=GF NC   38.20
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   15908588
#=GF RT   Internal initiation of translation of the TrkB mRNA is mediated by
#=GF RT   multiple regions within the 5' leader.
#=GF RA   Dobson T, Minic A, Nielsen K, Amiott E, Krushel L
#=GF RL   Nucleic Acids Res 2005;33:2929-2941.
#=GF CC   This family represents the TrkB internal ribosome entry site (IRES) which
#=GF CC   is present in the 5' leader sequence of the mRNA. TrkB is a neurotrophin
#=GF CC   receptor which is essential for the development and maintenance of the
#=GF CC   nervous system. The IRES element allows cap-independent translation of
#=GF CC   TrkB which may be needed for efficient translation in neuronal dendrites
#=GF CC   [1].
#=GF WK   TrkB_IRES
#=GF SQ   16


AF410902.1/3685-4037         CCCCCAUUCGCAUCUAACAAGGAA-UCUGCGCCCCAGAGAGUCCCGG-GAGCGCCGCCGGUCGGUGCCCGGCGCGCCGGGCCAUGCAGCGACGGCCGCCGCGGAGCUCCGAGCAGCGGUAGCGCCCCCCUGUAAAGCGGUUCGCUAUGCCG-GGGC-CACUGUGAACCCUGCCGCCUGCCGGAACACUCUUCG--CUCCGGACCAGCUCAGCCUCUGAUAAGCUGGACUCGGCA--CGCCC--GCAACAA----GCACCGAGGAG-UUAAGA--GAGCCGCAA---GCGCAGGGAAGGCCUCCCCGCACGGGUGGGGG---AAAGCG-GCCGGUGCAGC---GCGGGGACAGGCACUCGG------GCUGGCACUGGCUGCUAGGG
BC031835.1/57-409            CCCCCAUUCGCAUCUAACAAGGAA-UCUGCGCCCCAGAGAGUCCCGG-GAGCGCCGCCGGUCGGUGCCCGGCGCGCCGGGCCAUGCAGCGACGGCCGCCGCGGAGCUCCGAGCAGCGGUAGCGCCCCCCUGUAAAGCGGUUCGCUAUGCCG-GGGC-CACUGUGAACCCUGCCGCCUGCCGGAACACUCUUCG--CUCCGGACCAGCUCAGCCUCUGAUAAGCUGGACUCGGCA--CGCCC--GCAACAA----GCACCGAGGAG-UUAAGA--GAGCCGCAA---GCGCAGGGAAGGCCUCCCGGCACGGGUGGGGG---AAAGCG-GCCGGUGCAGC---GCGGGGACAGGCACUCGG------GCUGGCACUGGCUGCUAGGG
AF410900.1/132-482           CCCCCAUUCGCAUCUAACAAGGAA-UCUGCGCCCCAGAGAGUCCCGG---ACGCCGCCGGUCGGUGCCCGGCGCGCCGGGCCAUGCAGCGACGGCCGCCGCGGAGCUCCGAGCAGCGGUAGCGCCCCCCUGUAAAGCGGUUCGCUAUGCCG-GGAC-CACUGUGAACCCUGCCGCCUGCCGGAACACUCUUCG--CUCCGGACCAGCUCAGCCUCUGAUAAGCUGGACUCGGCA--CGCCC--GCAACAA----GCACCGAGGAG-UUAAGA--GAGCCGCAA---GCGCAGGGAAGGCCUCCCCGCACGGGUGGGGG---AAAGCG-GCCGGUGCAGC---GCGGGGACAGGCACUCGG------GCUGGCACUGGCUGCUAGGG
AB066522.1/601-957           CCCCCAUUCGCGUCUAAUAAGGAG-CCUGCACCCCAGAGAGUCCCGG-GAGCGCCGCCGGUCGGUGCCCGGCGCCCCGGGCCAUGCAGCAACGGCCGCGGCGGAGCUCCGAGCGGCGGUAGCACCCCCCUGUAAAGCGGUUCACGAUGCCG-GGGC-CACUGUGAACCCUGCCGCCUGCCGGAAUACGCUCCG--CUCCGGACCAGCUCAGCCUGUGAUACGCUGGACUCCGCG--CGCCC--GCAGCAAGCAAGCACCGAGGAG-UCAAGA--GGGCCGCAA---GCGCGGGGAAGGCCUCCCCGCACAGGUCGGGG---AAACCG-GCCGGUGCAGC---GUGGGGACACUCACUCGG------GCUGGCACUGGCUGCUAGGG
AAFC03008207.1/17938-17606   UCGCAGCGCGCGUCUAGCCAGAAG-CCUGAGCCCCAGAGCAUCCCGG-GAGCGCCGCGGGCCGGUGCUCGGCUCGUUGGGCCAUGCAGCGGCGGCCGCCGCGGAGCUGCGAGCGGCGGUAGCGCC-CCCUGUGAGAAGGCCCGAGAUGCCC-CUGC-CACUGUGAACGGUGCCGCC----CGACAG--------------GACACGCUCAGCCCCUGACACGCUCGGCUCUGCG--CGCCU--GAGACCA----GCACCGAGAG----GAGA--CAGCGGUGA---GCGCGGCAAAGGCCACUCGGCGCGGGCAGGGG---AGACCG-GCCGGGACAGC---UCAGCGACACGCACUCAG------GCUGACUCGGGCUGGCACUG
AACN010092991.1/2691-2361    UCCCAGUGCGCGUCUAGCAGGAG--CCUGCGUCCCCGGGG-UGCCGG-CAGCGCCGCCGGCCGGUGCUGGGUGCGCCGGGCCAUGCAGCGGCGGCCGCGGCGGAGCUCCGAGCGGCGGUAGCGCC-CCCUGUGAGGCGACCAGAGAUGCCC-CGGC-CACUGUGAACCGCGCCGCCCGCCAGGACACGCUCAG--CC-----CGGGA-----------CACGCUCGGCUCUGCG--CGCCC--GCGACAG----GCACCGG--GG-C-GAGG--GAGCGACCA---GCGCGGCGCAGGCCGCCCAGCGGGGGCGGGGG---AGGCCG-GCCGGUGCGGC---GCGGGGCCACCUACUCGC------UCUGACUCCGGCUGGCACUG
ABDC01308569.1/339-680       UCCCUGUGCGCCUCUAGCCAGAAG-CCUGCGCCUCGGAGAGUCCCGG-----------GCAGCG--CCCGGCGCGCCGGGCCAUGCAGCGACGGCCGCGGCGGAGCUCGCAGCGGCGGUAGCGCC-CCCUGUGAGGCGGCCCGCGAUGCCC-CGGC-CGCUGUGAACUGUGCAGCCCGCCCGAACGCGCGCCG--C-CCGGGCCGGCUCAGCCUUGGGCACUCUGGACUGCGAG--CGGCC--GCGACGA----GCAGCCAGGAG-UCGAUA--GAGCUGCAG---GCGCGGGGAAGGCCUGCCCGCACAGGUGGGGG---AAGCCG-GCCGGUGCAGCAGCGCGGGGACAGACACUCGG------GCUGGCGCUGGCGGCGAGGG
AAPY01539916.1/1689-1339     UCCCCGUGCGCUUCUAGCAAGCAG-CCUGCGCCCCAGAGAGUACC-G-GAGCGCCGCGGGUCGGUCCCCGGCGCACCGGGCCAUGCAGUGGAGGCCGCGGCGGAGCUCCGAGCGGCGGUAGCGCC-CCCUGUGAAUUGGCCCGCGAUGCCC-CGGC-CACUGUGAACGGUGCUGACGGCGGGAAUACGCUGAA--ACCAGGACAAGCUGAGCCUCGGACACAGUCGACUCAGCG--CGCCC--GCAGCAA----GCUCAGAGGAC-UCGGGA--GAGCGGCGA---GCGCGGGGAAGGCCUCCCCGCACCGGCUGGGG---AAGCCG-GCCGGUGCCUC---GCGGGGACAGGCGCUCGA------GCUGGCACUGGCGGCCAGGG
AL390777.13/31208-31560      CCCCCAUUCGCAUCUAACAAGGAA-UCUGCGCCCCAGAGAGUCCCGG-GAGCGCCGCCGGUCGGUGCCCGGCGCGCCGGGCCAUGCAGCGACGGCCGCCGCGGAGCUCCGAGCAGCGGUAGCGCCCCCCUGUAAAGCGGUUCGCUAUGCCG-GGGC-CACUGUGAACCCUGCCGCCUGCCGGAACACUCUUCG--CUCCGGACCAGCUCAGCCUCUGAUAAGCUGGACUCGGCA--CGCCC--GCAACAA----GCACCGAGGAG-UUAAGA--GAGCCGCAA---GCGCAGGGAAGGCCUCCCCGCACGGGUGGGGG---AAAGCG-GCCGGUGCAGC---GCGGGGACAGGCACUCGG------GCUGGCACUGGCUGCUAGGG
U12140.1/1-351               CCCCCAUUCGCAUCUAACAAGGAA-UCUGCGCCCCAGAGAGUCCCGG---ACGCCGCCGGUCGGUGCCCGGCGCGCCGGGCCAUGCAGCGACGGCCGCCGCGGAGCUCCGAGCAGCGGUAGCGCCCCCCUGUAAAGCGGUUCGCUAUGCCG-GGAC-CACUGUGAACCCUGCCGCCUGCCGGAACACUCUUCG--CUCCGGACCAGCUCAGCCUCUGAUAAGCUGGACUCGGCA--CGCCC--GCAACAA----GCACCGAGGAG-UUAAGA--GAGCCGCAA---GCGCAGGGAAGGCCUCCCCGCACGGGUGGGGG---AAAGCG-GCCGGUGCAGC---GCGGGGACAGGCACUCGG------GCUGGCACUGGCUGCUAGGG
AAIY01406106.1/1742-1417     UCCCGGAGCGCCUUUUGCCAGGAG-CCUGCACCCCAGUGAACCCCGGAGAGCGCCGCCGGCGGGUGCUCCCAGAGCCAGGCCAUGCAGCGGUGGCCACGACAGAGCUUGGAGCGGCGGUAGCGCC-UCCUGUGUGGCGGUCCACGAUGCCC-CAGC-CACUGUGAACAGUGCC-CUACCCAG----CCCUGGA-------GACG--------CU----------UGCCUCUGCU--UGCCCGUGUGACCA----GCACCAAGGAA-UCCAGG--GACCCAGGA---GCGCAGCGAAGGCCGCCCAACGCGUGCAGAGG---AGGCCG-ACCCGCACAGC---GCAGGG-CACAUACUCAG------GCUGACUGGAGCUGGCACUG
AAKN02016624.1/72414-72067   AUCCCGCUAGC------CA-GGAG-UCUGCGCCCUAGAGCGUCCC---CAGCGCCGAGGGCCGGUGCCCGGCGUGCUA-ACCAUGCGUCUGCGGCCAAGGCCGAGCUCCGAGCGGCGUUAGCGCC-CUCUGCGAAGCGCCCUGCGAUGCCC-CAGC-CACUGUGAACCUUUCUGCCUGCCCAGAUACACUCAA--CCCAGGACGAAAUCAGCCUUGGACACCCUGCACUCUGCGCACGCAC--GCAACAA----ACAGAGAAGAG-UCCAGUCCGGAGGGCAGAAAGCG-CAGGAGGGCCUCCCCGCGCCGGCAGGAG---AAGCCG-GCGGGUGCAAG---GAGGCGACACUCAUCCGG------GCUGGCACUGGCGACUAGGG
AAWR02015439.1/103996-103665 UCCCAGUGUACGUCUAGCAAGGAG-GCUGCGCCCCAGAGAGUCCGGG-GAGCGCCGCCGGCUGGUGCCCGGCGCGCCAGGCCAUGCAACGGCGGCAGCGGCGGAGCUCAGAACGGCGGUAGCGCC-CCCUGUGAGGCGGCCAGAGAUGCCC-CGGC-CGCUGUAAACGGUGCCGCCCGCCAGGACACGCUCAG--C---CCU-----GGACACGCUCU--------GCUCUGCG--CGCCC--GCGACGA----GCACCGA---G-UAGAGA--GAGCGGCGA---GCGCUGUGAAGGCUACCUAGCC----CUGGGAGAGGAGGCCAGCCGGUGCAGCGCAGGGACACUACUCAGUCUGACUCCGGCUGGCACUG----------
AAGU03017127.1/98438-98102   UCCCCGUGCGCAUUUAACCAGGAG-CCUGCGCGGGAGCCAGUCCCGG-GAGCGCCGCCGGCCGGUGCCCACCGCGCCAGGCCAUGCAGCGGCGGCCGCGGCGGAGAUCUGAGCGGCGGUAGCGCC-CCCUGUGAGGUUGCCCUCAAUGCCC-CAGG-CACUGUGAACCGUGCCGUCAGCCGGGACACACUCAGCCCCGGAGACG--------CU----------CGGCUCUGCA--CGCCG--GCGACCA----GCACCGACUAGUCCGAAG--GACCGGCGA---GCGCGGGGAAGGCCGCUCGGCGCGGGCAGAGG---AAGCCG-ACCGGUGCAGC---GCGAGGACACGCACUUGG------GCUGACUCGGGCUGGCACUG
AAQR03015300.1/149616-149955 UCCCUGUGCGCUUGUAGUAAGGAG-CCUGUGCCCCAGAGAGUCCCGG-GUG-------GC-----ACCCGGCGCUCCAGGCCAUGCAGCCACGGCCACCACGUAGCUCGCAGCGGCGGUAGCGCC-CCCUGUGAAGCGGCCCGCGAUGCCC-CUAC-CGCUGUGAACUCUGCAGCCCGCCCGAACACUCUCCG--CCCGGGACCGGCUGUACUUCGGACACGCUCGACUCUGAG--CGCCA--GCGACAA----GCGACGAGGAG-UCCAGA--GAGCUGCAA---GCUCGGAGAAGGCCUCCCCGCACAGGUGGGGG---AAGCCG-GCCGGUGCAGC---GCGGGGACAGACACUCGG------GCUGGCGCUGGCGGCUAGGC
AY265419.1/124-431           UCCGUGCCGGUU------UAGCGGUUCUGCGACCCAAAGAGUCCAGG-GAGAGCCACCGAGUGGCGCCUGGCGUAUAGGACCAUGCAG---C---CGCCUUGUGGCUUGGAGCAGCG---GCCCG-UGAUGUU-CCAGCCACUGUGAACCAUUUGGUCAGCGCCAACCU---GCUCAGCCCCAGCA------------CCGACAGGCUCAGCCUCUGGUACGCUCCUCUCGGCG---GGAG--GCCAUCA----GCACCAAGC----A-GCA--AGAGGGCUC---AG----GGAAGGCCUCCCCCCUCCGGCGGGGG---ACGCCU-G---GCUCAGC---GUAGGGACACGCACUCUG------ACUGA------CUGGCACUG
#=GC SS_cons                 {{{{{{{{{{,,,,,,,,,,<<<-.<<<<_____>>>>--->>>,[[.[[[-[[[,,,<-<<<<--<<<<<<<-<<<<-<<______>>-->>>>>>>>>->>---->>>>->,<<<<<-<-<<<.<---<<<-<<<<___>>>>->>>->.->>>.>>>>>>,,,((((((-((-(((-((----(((((-(..((((,,,<<<<<<<<<___>>>>--->>>>>,,<<<<--..-<<__.._______....>>->>>>)))).)-))))..)--)))))-...)))))))),,]]]]]]]],,,,}}}}}}}}}}...--<<<<.<<<<<<<<<<<...-<<<<________>>>>-......>>>->>>>>>>>>>>>::::
#=GC RF                      cCCCcGcccGCaUcUAgCaAGgaG.uCuGCGcCCCaGaGAGucCcGG.GaGCGCCGCcGgucgGUGcccggcgcgCCgGGcCAUGCAgCggcGGccgccgCggAGCUCcgaGCggCgGuAGCgCc.ccCUGugAcgcggcccgcgAugCCg.cgGc.CaCuGugAACcccGCcGcCuGCCcgaAcACccucag..ccccgGACcagcucagcCUcugauAcgcugGaCUcggCg..CGCcc..GCaACaA....GCAccgAgggg.ccgagg..GAgcgGCaa...gCGCgggGAAGGCCuCCCcgCaCgggCgGGGg...AagcCg.GCCgGuGcaGc...GcGggGACAcgCAcuCgG......gCuGgCaCcGGCcGgcAggG
//
# STOCKHOLM 1.0

#=GF AC   RF00548
#=GF ID   U11
#=GF DE   U11 spliceosomal RNA
#=GF AU   Griffiths-Jones S; 0000-0001-6043-807X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Marz M; 0000-0003-4783-8823
#=GF SE   Griffiths-Jones S; PMID:18390578
#=GF SS   Published; PMID:15210936
#=GF GA   39.00
#=GF TC   39.10
#=GF NC   38.90
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00005
#=GF DR   SO; 0000398; U11_snRNA;
#=GF DR   GO; 0000395; mRNA 5'-splice site recognition;
#=GF DR   GO; 0030627; pre-mRNA 5'-splice site binding;
#=GF DR   GO; 0005692; U11 snRNP;
#=GF RN   [1]
#=GF RM   2973606
#=GF RT   Additional low-abundance human small nuclear ribonucleoproteins: U11, U12,
#=GF RT   etc.
#=GF RA   Montzka KA, Steitz JA
#=GF RL   Proc Natl Acad Sci U S A 1988;85:8885-8889.
#=GF RN   [2]
#=GF RM   15210936
#=GF RT   Identification of an evolutionarily divergent U11 small nuclear
#=GF RT   ribonucleoprotein particle in Drosophila.
#=GF RA   Schneider C, Will CL, Brosius J, Frilander MJ, Luhrmann R
#=GF RL   Proc Natl Acad Sci U S A 2004;101:9584-9589.
#=GF RN   [3]
#=GF RM   19030770
#=GF RT   Evolution of spliceosomal snRNA genes in metazoan animals.
#=GF RA   Marz M, Kirsten T, Stadler PF
#=GF RL   J Mol Evol. 2008;67:594-607.
#=GF CC   The U11 small nuclear (snRNA), together with U4atac/U6atac, U5, and U12
#=GF CC   snRNAs and associated proteins, forms a spliceosome that cleaves a
#=GF CC   divergent class of low-abundance pre-mRNA introns.
#=GF WK   U11_spliceosomal_RNA
#=GF SQ   72


AALT01584327.1/366-499         AAAAAGGGCUUC-UGCCG----------------------------UGAG--UGGCACACGU----AG-GG-CAA-----------------------------------------------------------------------------------------------------------------AUCGC-UUGC----U-CU-ACGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUG--CACCGCAG-GGCA---GCUAG-UGAUC-------------------------------------------GUU-G--GUC--CUGG-CGCCCCG
ABBA01035051.1/9337-9470       AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----AG-GG-CAA-----------------------------------------------------------------------------------------------------------------CUCGA-UUGC----U-CU-GCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUAUUUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCUU
AANU01100842.1/307-440         AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----AG-GG-CAA-----------------------------------------------------------------------------------------------------------------CUCGA-UUGC----U-CU-UCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GACAUUCG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCUU
AAHX01087747.1/21614-21481     AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGC----AG-GG-CAA-----------------------------------------------------------------------------------------------------------------CUUGA-UUGC----U-CU-GCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUACUUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCAG-CGCCUGC
AANN01366666.1/1503-1371       AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGACACACGU----AG-GG-CAG-----------------------------------------------------------------------------------------------------------------CUCGU-UUGC----U-CU-ACGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUU---GUUGUUAG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCUG
AAHY01040494.1/2284-2417       AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGC----AG-GG-CAA-----------------------------------------------------------------------------------------------------------------CUCGA-UUGC----U-GU-GCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUAAUUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCUU
AACN010249771.1/1049-1182      AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----AG-GG-CAG-----------------------------------------------------------------------------------------------------------------CUCCA-UUGC----U-CU-UCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUACCUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCCU
AAFC03093783.1/14151-14019     AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----AG-GG-CAG-----------------------------------------------------------------------------------------------------------------CUCGU-UUGC----U-CU-ACGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUU---GGUAAUAG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CUGG-CGCCCCC
AAPY01441723.1/669-536         AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGC----CG-GG-CGG-----------------------------------------------------------------------------------------------------------------CUCGU-UCGC----U-CU-GCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUACUCG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCUG
ABDC01471663.1/1847-1980       AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----GG-GG-CAA-----------------------------------------------------------------------------------------------------------------CUCGA-CUGC----U-CU-UCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GAUAUUCG-GGCU---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCUU
AAYZ01217881.1/672-806         AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGC----AG-AG-CGG----------------------------------------------------------------------------------------------------------------CUCUGU-UUGC----U-CU-GCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUUUGUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CUAG-CGCCCUU
CAAE01008611.1/5075-5208       AAAAAGGGCUUC-UGCUG----------------------------UGUG--UAGCACAGGA----GG-GG-UGG----------------------------------------------------------------------------------------------------------------UGUUUA-CCAC----U-CC-UCCUGCGGAAUCGCC--AUCAAGA-GAUUUCGGAAGCACAAUUUUU---AUAACUGG-GGCU---GCUGG-UGAUC-------------------------------------------ACU-C--GUC--CUGG-CGCCCCG
AAIY01590504.1/4258-4391       AAAAAGGGCUUC-UGUCG----------------------------UUAA-GUGGCACACGU----AG-GG-CAU-----------------------------------------------------------------------------------------------------------------CUCUA-UUGC----U-CU-ACGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCGUAAUUUUU---GUUACCUG-GGCU---GCUAG-UGAUC-------------------------------------------GUU-G--GUC--CUGG-CGCCCUG
CR385068.11/137382-137517      AAAAAGGGCAUC-UGCUG----------------------------UGAG--UAGCAUAGCU----GU-GG-AAG-----------------------------------------------------------------------------------------------------------------GGAUU-CUCUG--AC-AC-AGUUACGGAAUCGCU--AUCAAGA-GAUUUCGGAUGCAUAAUUUUUA--UGACACGG-GGCU---GCUAA-UGAUC-------------------------------------------GUU-G--GUC--UUGG-CGCCCCA
AANH01002401.1/29976-29843     AAAAAGGGCUUC-UGCCA----------------------------UGUU--UGGUACAGGA----GG-AGUGGG-----------------------------------------------------------------------------------------------------------------GAUGA-CCCC----U-CC-UUUUGCGGAAUCGCC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUU---AACACAGG-GGCU---GCUAG-UGAUC-------------------------------------------ACU-U--GUC--CUGG-CGCCCCG
BAAF04001666.1/1184-1319       AAAAAGGGCUUC-UGCCG----------------------------UGAA--UGGUACAGGG----GA-GG-GGAG---------------------------------------------------------------------------------------------------------------UGAUCC-UCUU----C-UC-CCUUGCGGAAUCGCU--AUCAAGA-GAUUUCGGAAGCACAAUUUUUG--CUACUUGA-GGCU---GCUGG-UGCUC-------------------------------------------ACU-G--GUC--CCGG-CGCCUCC
AAFR03060642.1/81119-81261     AAAAAGGGCUUC-UGUCG----------------------------UGCA--UGGCACACGU----CG-AG-CGGCGGGG-------------------------------------------------------------------------------------------------------GUAUCCUCAG-CCGU----U-UU-UCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCACAAUUUUU---GUUAACUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CUAG-CGCCCUU
AAJJ01001715.1/9129-9258       AAAAAGGGUGCU-UGCUA----------------------------CUUU-AUAGCACAUGA----GG------C-----------------------------------------------------------------------------------------------------------------UAACC-G---------CC-UCGUGGGGUAUGGCA--AUCAAGA-CAUACCCAGCACAUAAUUUUUG-GCCACGUGG-AGCU---GUUUC-UUGGC-------------------------------------------AUU-GUUCCA--GAGG-CGCUCCC
AAVX01045818.1/2085-1950       UAAAAGGGUUUC-UGCCG----------------------------UGAG--UGGCACACGG----AG-GA-GGCA---------------------------------------------------------------------------------------------------------------CCACGU-GCUC----U-AU-CCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUG--GCGACCGG-GGCA---GCCGG-UGAUC-------------------------------------------ACG-U--UAC--CUGG-CGCUCCC
AACT01041795.1/13567-13430     UAAAAGGGCUUC-CGUCG----------------------------UGAC--UGGCGCAUGU----AU-UG-GGCU--------------------------------------------------------------------------------------------------------------UUAACUA-GUUC----G-GU-AUGUGUGGAAUCGCA--AUCAAUA-GAUUCCGGAAGCACAAUUUUUA--CAACAUAGUGGAU---GUUGG-UUGCC-------------------------------------------GCU-U--GCA--CCGA-CGCCCGU
AABS01000278.1/4728-4592       UAAAAGGGCUUC-CGUCG----------------------------UGAC--UGGCGCGUGU---UAC-GG-GUU-----------------------------------------------------------------------------------------------------------------UUAAC-AGCC----U-GUUUCUCGUGGAAUCGCA--AUCAAUA-GAUUCCGGAAGCAUCAUUUUUG--UAAGUUUGUGGUU---GUUGG-UUGCC-------------------------------------------GCU-U--GCA--CCGA-CGCCCGU
AAZX01001930.1/10834-10698     AAAAAGGGUACU-CGCUA----------------------------CUUCGAUAGCGCGUCG----AU-CC-GCA------------------------------------------------------------------------------------------------------------------AUAU-UGUG----G-AG-CGGCGGGGUAUGGCC--AUCAAGA-CAUACCCAGUAUGUAAUUUUUGUAACCGAGGA-GGCU---GUGGG-CUGCC-------------------------------------------AAA-U--GCA--CUAA-CGCCUCC
AAZO01007178.1/21512-21382     UAAAAGGGUGCU-UGCUG----------------------------CUUAGAUAGCACAUAG----GU-CC----------------------------------------------------------------------------------------------------------------------AAAC----G----G-GC-CUGUGGGGUAUGGUU--AUCAAGA-CAUAUCCAGCACGUAAUUUUUG-UACCUGUAG-GGCU---GUUGA-CUGCC-------------------------------------------AAUAU--GCA--UCGA-CGCCCUC
AAWT01063690.1/26739-26607     UAAAAGGGCCUC-UGCUG----------------------------UGCG--UAGCACAGAA----UC-AG-ACA----------------------------------------------------------------------------------------------------------------UAAUUA-UGUU----C-GA-UUCUGCGGAAUGGUU--AUCAAGA-CAUUUCGGAGGAAUAAUGUUU---AGAAAUCG-AGCU---GCUAU-GUUUC-------------------------------------------AUA-U--AA---CUGG-CGCUCCU
ABAV01020362.1/5206-5079       UAAAAGGGCCUU-UGCAG----------------------------UCAC--UUGCACGUGG----GC-CU-GU----------------------------------------------------------------------------------------------------------------------C--ACG----G-GC-CUGCGCGGAAUCGCC--AUCAAGA-GAUUUCGGAGGCAUAAUCUUUG--GACUCUUU-GGCA---GUUGG--CGCC-------------------------------------------ACU-G-UUCG--CCGA-CGCCCUA
AAGE02014423.1/39375-39225     UAAAAGGGUGCU-UGCUCUAC----------------------GUUUAUA--UGGCACACCU----AA-UU-GUACUUC---------------------------------------------------------------------------------------------------------CAAUGGAAG-UUCG----G-UU-GGGUGAGGUAUGGUU--AUCAAGA-CAUACCUAGCACAUAAUUUUU---AAUUAGAA-GACA---GUUGA-CCGCUGC---------------------------------------UUGCA-U--GCG--UCGA-CGUCUUC
AANG01616273.1/2533-2400       AAAAAGAGCUUC-UGUUG----------------------------UGAG--UGGCACACGU----AG-GG-CAG-----------------------------------------------------------------------------------------------------------------CUCCA-UUGC----U-CU-UCGUACAGAAUAGAC--AUCAAGA-GAUUUCAGAAGCAAAAUUUUUU--GGUACCCA-GGCA---GCGGG-UGAUC-------------------------------------------AUU-G--GUC--CCGG-UGCCCCA
AAPN01131876.1/439-572         AAAAAGGGCUUC-UGCCG----------------------------UGCG--UGGCACACGG----GA-AG-CGGCGGG--------------------------------------------------------------------------------------------------------GUCCCCUCAG-CCGU----U-UC-UCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCACAAUUUUU---GUCCCCGG-GGC-------CG-CUGGU-------------------------------------------GAU---------CGCU-UGUCCUG
BAAB01132489.1/1656-1782       CAAAAGGGUGUU-UGCCG----------------------------CUUGGAUGGCACGCGG----CC-CC------------------------------------------------------------------------------------------------------------------------UC----G----G-GG-UCGUGGGGUAUGGUU--AUCAAGA-CAUACUCAACACAUAAUUUUUG-UCGAGAGGA-AGCA---GUUGG-CUACC--------------------------------------------UG-C--GUA--CCGG-CGCUUCC
AAWU01003184.1/54824-54673     CAAAAGGGUGCU-UGCUCUAC----------------------GUUUAUA--UGGCACACUU----GG-CA-GAGUU------------------------------------------------------------------------------------------------------------UUAACAGA-CUUG----G-CC-UGGUGAGGUAUGGUU--AUCAAGA-CAUACCUAGCACAUAAUUUUUA-ACAACAGAA-AGCU---GUUGA-CUGCGAAU-------------------------------------CCUUGU-U--CCG--UCGG-CGCUUUC
AAAB01008915.1/2021-2191       UAAAAGGGUGCU-UGCUUUUCUA-----------------CGCUUUUGUA--UGGCACAUCU----GU-GC-GGCGCCGAGCUCGG------------------------------------------------------------------------------------------UUGAGUCCGGCCAGGUG-UCCG----U-AC-CGGUGGGGUAUGGCU--AUCAAGA-CAUAUCCAGCACGUAAUUUUUG-ACCCCGGAA-GGCA---GUUGA-CUCGCU----------------------------------------CCUCU-G--CG---UCGA-CGCCUUC
AACW02000090.1/428771-428920   AAAAAGGGCGCG-UCACAAAGUCGGUCU--------UUAGACCUGACCAA--UGUGUCAAAA----GU-----UU-----------------------------------------------------------------------------------------------------------------UUAUU-GA--------AC-UUUUGCGGUAUGGAU--AUCAAGA-CAUAUCGAGCGCAUAAUUUUUU-GAUUAUAUU-GGAA---GCUCG-CUGUA-------------------------------------------CUU-U--ACU-UUUGG-CUUCGCU
AATU01001667.1/7717-7852       AAAAAGGGCAGG-CCUUG----------------------------CC----UAAGGCACAG---UAC-GG-GCG-----------------------------------------------------------------------------------------------------------------GCACA-UGCC---UC-CU-UUGUGGUGAAUCGCG--AUCAAGA-GAUUUGCCCUGCAUAAUUUCUG--AGCGGCCG-CGUU---GGAAUGGGUCU-------------------------------------------GUG-A--GGCUAAUUC-CAC-CGG
AASG02007614.1/6497-6368       UAAAAGGGUCGGUUGGCU----------------------------AAUU-AUGCCACACUC----AU-----CC-----------------------------------------------------------------------------------------------------------------UUGUU-CG--------GU-GAGUGCCGUAUGGCA--AUCAAGA-CAUAUGGCCGACAUAAUUUGUG--GAGCCUUA-AUA----GGGUU-GGCCC-------------------------------------------GCUUG--GUC--GACC-CUCUUGU
AAAA02007290.1/27897-28021     AAAAAGGGUCGGUUGGCU----------------------------AUGU-AUGCCACAUCC----AU------------------------------------------------------------------------------------------------------------------------CCAUCC----------AU-GGGUGCUGUAUGGCU--AUCAAGA-CAUAUGGCCGGCAUAAUUUGUG-GAAAUAGAU-AGG----GUUGG-CUCGC-------------------------------------------U---A--CGG--CCGA-CCCUCCA
AARH01003793.1/16313-16186     UAAAAGGGUCGGUUGGCU----------------------------AAAU-AUGCCACACUC----GC-----CC-----------------------------------------------------------------------------------------------------------------UAGUC-UG--------GU-GAGUGCCGUAUGGCU--AUCAAGA-CAUAUGGCUGACAUAAUUUGUG--GGACAGCA-CAG----GGUUG--GCUC-------------------------------------------GCC-U--GGC--CGAC-CCUCCGU
AM423809.2/2725-2853           UAAAAGGGUCGGUUGGCU----------------------------AAAU-AUGCCACUCUC----AC-----CC-----------------------------------------------------------------------------------------------------------------UCGUC-UG--------GU-GAGUGCUGUAUGGCU--AUCAAGA-CAUAUGGCCGACAUAAUUUAUG--GAAACCUU-AUAG---GGUUG--GCUC-------------------------------------------CUC-U--GGC--CGAC-CCUUCAU
AAQQ01061209.1/4064-4200       AAAAAAGGCUUC-UGUCA----------------------------UGAU--UGGUACAU-------G-UA-GGG-----------------------------------------------------------------------------------------------------------------CAACU-CUCU----U-CC-UUAUGCAAAAUCCAC--AUCAAGA-GAUUUUGGAAGCAUAAUAUUUU--GGUAGGUG-AGCA---GCUGG-UGAUUGUU------------------------------------GAUUAAA-A--AUU--UUA--UGCUUAU
AB025638.1/90124-90258         AAAAAGGGUCGGAUGGCU----------------------------AUUU-AUGCCACGCUC----AG-CC-UAA-----------------------------------------------------------------------------------------------------------------GAUAA---GG----G-GU-GAGUGCUGUAUGGCAAAAUCAAGA-CAUAUGGCCGACAUUAUUUCUG--GAACAACC-CAUG---GGUUG--GCUC-------------------------------------------GCU-C--GGC--CGAC-CCUCCAA
AAQX01000552.1/67979-67843     AAAAAGGGCAGG-CCUUG----------------------------CC----UAAGGCACAGUAUGGG-GC-GGC------------------------------------------------------------------------------------------------------------------UCCG-GCCG----U-CC-UUGUGGUGAAUCGCG--AUCAGGA-GAUUUGCCCUGCAUAAUUUCUG--AGCAGCCG-CGCU---GGAAUGGACCU-------------------------------------------CAC-G--GGCUAAUUC-CAC-CGG
AC161863.21/36376-36251        AAAAAAGGUCGGUUGGUU----------------------------AAAU-AUGCCACACUC----AU------U-----------------------------------------------------------------------------------------------------------------AGAAU-G---------GC-GAGUGCUGUAUGGCU--AUCAAGA-UAUAUGACUGACAUAAUUUUUG--UGAAUCAA-UAG----GGUUG--GCUC-------------------------------------------GUU-A--AGU--CGAC-CCUCUUU
AASW01036016.1/5510-5240       AAAAAGGGUGCU-CGUCCUGGCACGUUUCCG--AUCACGAAACUGAAGUG-CGGACGCAUUG----CG-CC-GCAAGAGCGUCUCCUUCGCUCCGCCCCUGGACUUCCGGGG--------------------------------------GUGGGCGGGGGCGAGCGUUCUAUUGCCGCCUUCGACGCCUCCU-UGCG---CG-CC-CAGUGGGGUAUGGCU--UUG-----CAUAUCCAGUGCGUAAUUUUU---GUAUUUGG-GGCC---GCGGC-UGCACAUUGUGGAUUGCUCGGGGA----UUCCCGGAUCUCCCUGCGUGCCA-G--UGC--GCUG-CGCCCCG
AANI01017315.1/47163-47421     AAAAAGGGCGCU-CGUCUUAGCACGUUCCAA-UGUUAGGAGCUUGAUUGC--AGACGCAUUG----CG-CC-GUUGGCUCAUCCAUACGCUCUUCGUGGGUGGG-------------------------------------------------------GGCGUGCGCUACAUUGCCGCCUUUGAUGGGUUCU-GGCG---UG-CU-CAGUGGGGUAUGGCU--UUG-----CAUAUCCAGUGCGUAAUUUUUG--UAUUUAGG-GGCA--GGCGGC-UGCACUUUGGUGACAACCGAAUUGCG-GAUUUGUCUGCGUGUCGGUGGUCC-G--UGC--GCUG-CGCCCCC
AABU01002767.1/1211444-1211716 AAAAAGGGUGCU-CGUCCUGGCACGUUUCCG--AUCACGAAACUCAAGUG-CGGACGCAUUG----CG-CC-GCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUUCUCCGGG------------------------------------GAUAGGCGGGGGCGAGCGUUCCAUUGCCGCCUUCGACGCCUCCU-UGCG---CG-CC-CAGUGGGGUAUGGCU--UUG-----CAUAUCCAGUGCGUAAUUUUU---GUAUUUGG-GGCC---GCGGC-UGCACAUUGUGGAUUGCUCGGGGA----UUCCCGGAUCUCCCUGCGUGCCA-G--UGC--GCUG-CGCCCCG
AAPQ01006553.1/254812-254542   UAAAAGGGCGCU-CGUCCUGGCACGUUCCCG--AUCACGGAACUCAAGUG-CAGACGCAUUG----CG-CC-GCAGGAGCGUCUCCUUCGCUCCGCCCCCGGACCUCCGGUG--------------------------------------GUGGGCGGGGGCGAGCGUUCCAUUGCCGCCUUCGACGCCUCCU-UGCG---CG-CC-CAGUGGGGUAUGGCU--UUG-----CAUAUCCAGUGCGUAAUUUUU---GUAUUUGG-GGCC---GCGGC-UGCACAUUGUGGAUUGCUCGGGGA----UUCCUGAAUCUCCCUGCGUGCCA-G--UGC--GCUG-CGCCCCG
AAEU02000135.1/1824-1552       UAAAAGGGCGCU-CGUCCUGGCACGUUCCCG--AUCACGGAACUCAAGUG-CAGACGCAUUG----CG-CC-GCAGGAGCGUCUCCUUCGCUCCGCUCCUGGAUUUCCAGUG--------------------------------------GUGGGCGGGGGCGAGCGUUCCAUUGCCGCCUUCGACGCCUCCU-UGCG---CG-CC-CAGUGGGGUAUGGCU--UUG-----CAUAUCCAGUGCGUAAUUUUUU--GCUUCUGG-GGCC---GCGGC-UGCACAUUGCGGAUUGCUCGGGGAU---UCCCCGAAUCUCCUUGCGUGCCC-G--UGC--GCUG-CGCCCCG
AAPP01015607.1/39970-39770     AAAAAGGGUGCU-CGUCUUCGCGCGUUCGA----UCGCUGAACAAAAGUG-CAGACGCAUUG----CG-CC-GCAGGACCAUCUCAUUUUUUGGUGUG-------------------------------------------------------------------CGUCUAAUUGCCGCCUUCGAUGGUUCCU-UGCG---UG-CC-CAGUGGGGUAUGGCU--UUG-----CAUAUCCAGUGCAUAAUUUUU----GUAAUGG-GGCU---GGCGG-CUGCA-------------------------------------------CCU-C--GAA--CCGUUCGCACUG
AATT01000197.1/1408-1220       AAAAAGGUCGGG-UCCAA----------------------------CCUC-AUUGGACAGGA----A---U-AAGCAAGCGGAUGGUUCAUUGCGAUCAGAGC---------------------------------------------------------CAAUGCAUAUUGACUUUGCUUUGCAGUACCUCA-CUUG----A-CU-CCCUGCGAUUUGGCAGCAUCAAUAACAAACCGCCCGAGUAAUUUUUA--AUAUAGGA-GGU----GUUCU-AACGG-------------------------------------------C---C--UGU--AUUG-UAUCUGC
AAPT01020584.1/16528-16265     AAAAAGGGUGCU-CGUCCUGGCAUGUUCCCG-UAUUAGGAACUUAAAUGC--AGACGCAUUG----CG-UC-AUUGGCCCAAUCCUACGUUCCUUGAAUGGGGCG----------------------------------------------------GGGGCGUGCGCUGAAUUGCCGCCUUUGUUGGGAUCC-AAUG---UG-CC-CAGUGGGGUAUGGCU--UUG-----CAUAUCCAGUGCGUAAUUUUUG--UAUUUCGG-GGCA--GGCGGC-UGCACGCUUUCUGAGCAGCUGGAUAGCAGAUACUUCUGCGUGCCAGCAGCUCG--UGC--GCUG-CGCCCCA
AAKO01000845.1/101970-101700   AAAAAGGGUGCU-CGUCCUGGCACGUUUCCG--AUCACGAAACUGAAGUG-CGGACGCAUUG----CG-CC-GCAGGAGCGUCUCCUUCGCUCCGCCCCUGGACUACCGGGG--------------------------------------GUGGGCGGGGGCGAGCGUUCCAUUGCCGCCUUCGACGCCUCCU-UGCG---CG-CC-CAGUGGGGUAUGGCU--UUG-----CAUAUCCAGUGCGCAAUUUUU---GUAUUUGG-GGCC---UCGGC-UGCACAUUGUGGAUUGCUCGGGGA----UUCCCGGAUCUCCCUGCGUGCCA-G--UGC--GCUG-CGCCCCG
AAQB01007749.1/152453-152180   GAAAAGGGUGCU-CGUCCUGGCACAUUUCCU--AUCCUGGAAUAUUAGUG-CAGACGCAUUG----CA-CU-GUUUGGCCCAUCCGUACGCCGCUUCUCCCCUCUCCUCACGGUUGGGGGCUGGAGUGGUGGGGGGCGUGCGUGAAAUUGCCGCCCUUUGGAUCACUUUUCUGUGCGGGGCUUUUCUCAACAA-AACA----G-UC-CAGUGGGGUAUGGCU--UUG-----CAUAUCCAGUGCAUAAUUUUUG--UUCUUGGG-GCUC---GCGGC-UGUACCU---------------------------------------AGUUG-G--UAC--GCCU-UGGAUUG
AAPU01011491.1/523623-523884   AAAAAGGGUGCU-CGUCUUUGGCGCUUUCCGUAUUUUACGAGAAACAGUG-CGGACGCAUUG----UG-CC-GUUUGCCCAUUCCUACGCUCUUCGUGGGCGGG-------------------------------------------------------GGCGCGCGUCGAAUUGCCGUCUUCGAUGGGUGCA-AACG---CG-CA-UAGUGGGGUAUGGCU--UUG-----CAUAUCCAGUGCGUAAUUUUU---GUGUUAGG-GGCAUAGGUAGC-UGUACGUUUGGGACGGCCGGAUAGCG-GAGUUCUCUGCGUGCCGGCAGUCC-G--UAC--GCUG-UGCCCCA
AAGV020859736.1/320-452        AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----AG-GG-CGC-----------------------------------------------------------------------------------------------------------------CUCGC-UUGC----U-CU-UCGUGCGGAAUCGAC--AUCAAGA-GAUUUCAGAAGCAUAAUUUUU---GUUGCCUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCCC
AAWR02028292.1/15486-15353     AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----GG-GG-CAG-----------------------------------------------------------------------------------------------------------------CUCAA-UUGC----U-CU-UCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUACUCG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--UCGG-CGCCCCU
AAKN02028628.1/12557-12424     AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----AG-GG-CAA-----------------------------------------------------------------------------------------------------------------CUCGU-UUGC----U-CU-GCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUUUCUG-GGCA---GCUAG-UGAUC-------------------------------------------GUU-G--GUC--CUGG-CGCCCUU
AASC02034979.1/62381-62245     UAAAAGGGCCUC-UGCCG----------------------------AUCA--UGGCACACGG----GA-UG-GCU------------------------------------------------------------------------------------------------------------------AAAC-GGCCGUAAG-UC-CUGUGCGGAAUCGCA--AUCAAGA-GAUUUCGGAGGCAAAAUUUUUA--UAUCUUGA-GGCU---GCUGG-UGCUC-------------------------------------------GCU-A--UGC--CCGG-CGCCCUU
AAQR03115726.1/70105-70238     AAAAGAGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----GG-GG-CAG-----------------------------------------------------------------------------------------------------------------CUCAA-CUGC----U-CU-UCGUGCAGAAUCGAC--AUCAAGA-GAUUUUGGAAGCAUAAUUUUUU--GGUACCUG-GGCA---GCUGG-UGAUC-------------------------------------------AUU-G--GUC--CCAG-CACCCAG
BK005205.1/1-134               AAAAAGGGCUUC-UGCUG----------------------------UGCU--UAGCACAGGC----GGAGU-GGU------------------------------------------------------------------------------------------------------------------GAUU-AUCA----CGCC-GCCUGCGGAAUCGCC--AUCAAGA-GAUUUCGGAAGCACAAUUUUU---AUAACUGG-GACU---GCCGG-UGAUC-------------------------------------------ACA-U--GUC--CCGG-CGUCCCG
AAGW02062789.1/6850-6716       AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----AG-GG-CGG----------------------------------------------------------------------------------------------------------------CUCUGU-UUGC----U-CU-UCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GAUACUGA-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CUGG-CGCCCGU
AADG06004967.1/92499-92362     AAAAAGGGUGCU-CGCUA----------------------------CUUUAAUAUCGCGUUA----GC-AC-GGU-----------------------------------------------------------------------------------------------------------------CAAGU-ACCA----U-GC-UAGCGGGGUAUGGCA--AUCAAGA-CAUACCCAGUACGUAAUUUUUG-UGAAUGCGA-GGCU---GUUGG-CUGCC------------------------------------------AUUU-U--GCA--CUGA-CGCCUCC
AACZ03008074.1/9530-9663       AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----AG-GG-CAA-----------------------------------------------------------------------------------------------------------------CUCGA-UUGC----U-CU-ACGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUAUUUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCUU
AAQY02000201.1/54989-54854     AAAAAGGGCAGG-CCUUG----------------------------CC----UAGGGCACAGU-AUGG-GU-GGC------------------------------------------------------------------------------------------------------------------CUCG-GCCG----U-CC-UUGUGGUGAAUCGCG--AUCAGGA-GAUUUGCCCUGCAUAAUUUCUG--AGCGGCCG-CGCU---GGAAUGGGCCC-------------------------------------------GUC-G--GGCUAAUUC-CAC-CGG
AAPE02033931.1/17932-17799     AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----AG-AG-CAG-----------------------------------------------------------------------------------------------------------------CCUGA-UUGC----U-CU-ACGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUACUUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CUGG-CGCCUGU
AADN03008246.1/6571-6445       AAAAAGGGCUUC-UGCCG----------------------------UGCG--UGGCACGGGG----G--GG-CUU-----------------------------------------------------------------------------------------------------------------------CGGC----C-GC-CCUCGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCACAAUUUUU---GUGGGAGG-GGUC---GCCGG-UAACC-------------------------------------------GCU-C--GUU--CUGG-CGCCCCG
AAGJ04082761.1/830-697         AAAAAGGGCUUC-UGCCG----------------------------CUUG--UGGCACAUGG----GA-AG-UCC-----------------------------------------------------------------------------------------------------------------AUAAU-GGGC----U-UC-CUGUGCGGAAUCACU--AUCAAGA-GAUUUCGGAAGCAUAAUAUUUG--UGACCUGU-GGCU---GUUAG-UUGUC-------------------------------------------UCU-U--GCA--CUGA-CGCCCUA
AAGU03057468.1/44726-44859     AAAAAGGGCUUC-UGUCG----------------------------UGAA-GUGGCACACGU----AG-GG-CAA-----------------------------------------------------------------------------------------------------------------CUCUA-UUGC----U-CU-AUGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCGUAAUUUUU---GUUCUCUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCUA
AAWZ02034328.1/8740-8879       AAAAAGGGCUUC-UGCCG----------------------------UGAG--UGGCACAUGG----AG-AG-GGAGGC----------------------------------------------------------------------------------------------------------UGCGGCCUG-UUCC----U-UU-CCGUGCGGAAUCGCU--AUCAAGA-GAUUUCGGAAGCAUAAUUUUU---GGGAACGG-GGAA---GCUGG-UAAUC-------------------------------------------GCG-U--GUU--CUGG-CUCCCCA
AP005284.3/44012-43888         AAAAAGGGUCGGUUGGCU----------------------------AUGU-AUGCCACAUCC----AU------------------------------------------------------------------------------------------------------------------------ACAUCC----------AU-GGGUGCUGUAUGGCU--AUCAAGA-CAUAUGGCCGGCAUAAUUUGUG-GAAAUAGAU-AGG----GUUGG-CUCGC-------------------------------------------U---A--CGG--CCGA-CCCUCAA
BK005202.1/1-134               AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGC----AG-GG-CAA-----------------------------------------------------------------------------------------------------------------CUCGA-UUGC----U-GU-GCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUAAUUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCUU
BK005204.1/1-133               AAAAAGGGCUUC-UGCUG----------------------------UGUG--UAGCACAGGA----GG-GG-UGG----------------------------------------------------------------------------------------------------------------UGUUUA-CCAC----U-CC-UCCUGCGGAAUCGCC--AUCAAGA-GAUUUCGGAAGCACAAUUUUU---AUAACUGG-GGCU---GCUGG-UGAUC-------------------------------------------ACU-C--GUC--CUGG-CGCCC-C
X13707.1/1-134                 AAAAAGGGCUUC-UGUCG----------------------------UGAG--UGGCACACGU----AG-GG-CAA-----------------------------------------------------------------------------------------------------------------CUCGA-UUGC----U-CU-GCGUGCGGAAUCGAC--AUCAAGA-GAUUUCGGAAGCAUAAUUUUUU--GGUAUUUG-GGCA---GCUGG-UGAUC-------------------------------------------GUU-G--GUC--CCGG-CGCCCUU
BK005203.1/1-127               AAAAAGGGCUUU-UGCCG----------------------------UGCG--UGGCACGGGG----G--GG-C--------------------------------------------------------------------------------------------------------------------UUCG---GC----C-GC-CCUCGCGGAAUUGAC--AUCAAGA-GAUUUCGGAAGCACAAUUUUU---GUGGGAGG-GGUC---GCCGG-UAACC-------------------------------------------GCU-C--GUU--CUGG-CGCCCCG
#=GC SS_cons                   :::::::(((((.<<<<<............................____..>>>>><<<<<....<<.<<.<<<_.............................................................................................................._______.>>>>....>.>>.>>>>><<<<<<<___.._______.>>>>>>>)))))----------..-------<.<<<-...<<<<<.-<<<<...........................................___.>..>>>..>>>>.>>>>>::
#=GC RF                        aAAAAGGGcgcc.cGccc............................agug..gggCgCAcug....gg.cc.gcuu..............................................................................................................ucauuca.agcg....g.cc.cagUGgGguAUgGCu..aUcAAGA.cAUauCcggcgCAUAAUUUUUg..uuauuugg.ggca...Gccgg.ugccc...........................................uuu.g..ggc..ccgg.Cgcccuu
//
# STOCKHOLM 1.0

#=GF AC   RF00549
#=GF ID   IRES_c-sis
#=GF DE   c-sis internal ribosome entry site (IRES)
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   Published; 10409733
#=GF SS   Predicted; ILM; Moxon SJ
#=GF GA   31.00
#=GF TC   31.80
#=GF NC   22.90
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   10409733
#=GF RT   Differentiation-induced internal translation of c-sis mRNA: analysis of
#=GF RT   the cis elements and their differentiation-linked binding to the hnRNP C
#=GF RT   protein.
#=GF RA   Sella O, Gerlitz G, Le SY, Elroy-Stein O
#=GF RL   Mol Cell Biol 1999;19:5429-5440.
#=GF CC   This family represents the c-sis 5'-UTR which contains three modules that
#=GF CC   can individually mediate internal ribosome entry. However, the full length
#=GF CC   sequence is required for maximal IRES activity. It is thought that the
#=GF CC   three IRES elements are somehow responsive to cellular changes and act to
#=GF CC   regulate the level of translation [1].
#=GF WK   c-sis_internal_ribosome_entry_site_(IRES)
#=GF SQ   10


X03494.1/498-1094  CGGAGCAGCCGCAGCUCACAGCC-----------------------CAGAGGACGCCCAGAGCGGC-AGCGCGCAGACAGACGGACCGACGGACUC-CGCCGCGUCCACCUGUCUGCCCGGCCCGGCACUGCGCGCA-CGGGCACGGCCG--AGCGCGGAGCAGCCGUGCCCGCCGCCCGGGCCCGCC---AAGGCGCACACGCUCCGGCCCCCCCCACCCGGCCCGGGCGGGAGUUUGCACCUCUCCCUGCCCGGGUACUCGGGCCGCCGCUGCAAAGCCAACUUUGGAAAAAGUUUUUGGGGGGAGACUUUGGCCUUGAGGUGCCCGGCUCUGCACUUUCCGACUUCGGGGGCCUUUCUAGAAAAUGUUGCAAAAAAGCUAAGCCAGCGGGCAGAGGAAAACGCCUAUAGCCGGCGAGUGAAGACGAACCAUCGGCUGCCGUGUUCUUUUUCCUCUUGGAGGUUGGAGUCCCCUGGGCGCCCCCACACGGCUAGACGCCUCGGCUGGUUCGCGACGCAGACCCCCGGCCGUGGAUGC-UCGCUCGGGCUCGGGAUCCGCCCAGGUAGC-GGCC--GGACCCUGGUCCCGCGCCCAGGCCCUCCCCAGCCCCCCAACGACGGAGCCGGGGC
BC053430.1/21-627  CGGAGCAGCCGCAGCUCGAAAC---------------------CCGCAGAGGAAGCCCAGAGUGGCGAGCGAGUGGGUAGAUAGACAGACUGACCCGAGCCGCGUCCACCUGUCGGCCCGGACCAGCCCAGCGCGCAGUGGGCGCG-CCGCGCUCUCGGAGCAGCCGUGCCCGCCGCUUGGGCCCUGCGCCAGGGCGCACACGCUCCCG-CCCCGCCACCCGGCCCGGGCGGGAGUUUGCACCUCUCCCUGCCCGGGUGUUCGGGCCGCCGCUGCAAAGCCAACUUUGGAAAAAGUUUUUUUUUGGAGACUUGGGCUUGGAGGUCCCCAGCUCUGCGCUUUCUGAUCUGGGGGUCCGUUCCAGAAAAUGUUGCAAAAAAGCUAAGCCAGCAGGCAGAGGAACACGCCUUUAGCGGGCGAGUGAAGACGAACCAUCGGCUGCCGUGUUCCUUUUCCUCUCUGAGGUUGGAGUCCCCUGCGCGCCCCCACACGGCUAGACGCCUUGGCUGGUUCGCGACGCAGCCCCCAGACUGUGGAUGC-UCGCGUGGGCUCGGGAUCCGCCCAGGUAGC-GGCUUUGGACCCCGGUCCCUUGUCCAGGUCCUCCCCAGCCCCCCAGCGACGGAGCCGGGGC
K01918.1/1-523     -----------------------------------------------------------------------------------------------------------GAAUUCAUGCCGGGCCCAGCCGAGCGCGCAGCGGGCACG-CCGCGCGCGCGGAGCAGCCGUGCCCGCCGCCCGGGCCCGCCGCCAGGGCGCACACGCUCCCG-CCCCCCUACCCGGCCCGGGCGGGAGUUUGCACCUCUCCCUGCCCGGGUGCUCGAGCUGCCGUUGCAAAGCCAACUUUGGAAAAAGUUUUUUGGGGGAGACUUGGGCCUUGAGGUGCCCAGCUCCGCGCUUUCCGAUUUUGGGGGCCUUUCCAGAAAAUGUUGCAAAAAAGCUAAGCCGGCGGGCAGAGGAAAACGCCUGUAGCCGGCGAGUGAAGACGAACCAUCGACUGCCGUGUUCCUUUUCCUCUUGGAGGUUGGAGUCCCCUGGGCGCCCCCACACGGCUAGACGCCUCGGCUGGUUCGCGACGCAGCCCCCCGGCCGUGGAUGCUGCACUCGGGCUCGGGAUCCGCCCAGGUAGCCGGCCUCGGACCCAGGUCCUGCGCCCAGGUCCUCCCCUGCCCCCCAGCGACGGAGCCGGGGC
M12783.1/288-917   CGGAGCAGCCGCAGCUCGCAGCUCGCAGCUCGCAGCCCGCAGCCCGCAGAGGACGCCCAGAGCGGCGAGCAGGCGGGCAGACGGACCGACGGACUCGCGCCGCGUCCACCUGUCGGCCGGGCCCAGCCGAGCGCGCAGCGGGCACG-CCGCGCGCGCGGAGCAGCCGUGCCCGCCGCCCGGGCCCGCCGCCAGGGCGCACACGCUCCCG-CCCCCCUACCCGGCCCGGGCGGGAGUUUGCACCUCUCCCUGCCCGGGUGCUCGAGCUGCCGUUGCAAAGCCAACUUUGGAAAAAGUUUUUUGGGGGAGACUUGGGCCUUGAGGUGCCCAGCUCCGCGCUUUCCGAUUUUGGGGGCCUUUCCAGAAAAUGUUGCAAAAAAGCUAAGCCGGCGGGCAGAGGAAAACGCCUGUAGCCGGCGAGUGAAGACGAACCAUCGACUGCCGUGUUCCUUUUCCUCUUGGAGGUUGGAGUCCCCUGGGCGCCCCCACACGGCUAGACGCCUCGGCUGGUUCGCGACGCAGCCCCCCGGCCGUGGAUGCUGCACUCGGGCUCGGGAUCCGCCCAGGUAGCCGGCCUCGGACCCAGGUCCUGCGCCCAGGUCCUCCCCUGCCCCCCAGCGACGGAGCCGGGGC
M19719.1/615-1244  CGGAGCAGCCGCAGCUCGCAGCUCGCAGCUCGCAGCCCGCAGCCCGCAGAGGACGCCCAGAGCGGCGAGCAGGCGGGCAGACGGACCGACGGACUCGCGCCGCGUCCACCUGUCGGCCGGGCCCAGCCGAGCGCGCAGCGGGCACG-CCGCGCGCGCGGAGCAGCCGUGCCCGCCGCCCGGGCCCGCCGCCAGGGCGCACACGCUCCCG-CCCCCCUACCCGGCCCGGGCGGGAGUUUGCACCUCUCCCUGCCCGGGUGCUCGAGCUGCCGUUGCAAAGCCAACUUUGGAAAAAGUUUUUUGGGGGAGACUUGGGCCUUGAGGUGCCCAGCUCCGCGCUUUCCGAUUUUGGGGGCCUUUCCAGAAAAUGUUGCAAAAAAGCUAAGCCGGCGGGCAGAGGAAAACGCCUGUAGCCGGCGAGUGAAGACGAACCAUCGACUGCCGUGUUCCUUUUCCUCUUGGAGGUUGGAGUCCCCUGGGCGCCCCCACACCCCUAGACGCCUCGGCUGGUUCGCGACGCAGCCCCCCGGCCGUGGAUGCUGCACUCGGGCUCGGGAUCCGCCCAGGUAGCCGGCCUCGGACCCAGGUCCUGCGCCCAGGUCCUCCCCUGCCCCCCAGCGACGGAGCCGGGGC
BC077725.1/20-647  CGGAGCAGCCGCAGCUCGCAGCUCGCAGCUCGCAGCCCGCAGCCCGCAGAGGACGCCCAGAGCGGCGAGCAGGCGGGCAGACGGACCGACGGACUCGCGCCGCGUCCACCUGUCGGCCGGGCCCAGCCGAGCGCGCAGCGGGCACG-CCGCGCGCGCGGAGCAGCCGUGCCCGCCGCCCGGGCCCCGCGCCAGGGCGCACACGCUCCCG-CCCCCCUACCCGGCCCGGGCGGGAGUUUGCACCUCUCCCUGCCCGGGUGCUCGAGCUGCCGUUGCAAAGCCAACUUUGGAAAAAGUUUUUUGGGGGAGACUUGGGCCUUGAGGUGCCCAGCUCCGCGCUUUCCGAUUUUGGGGGCCUUUCCAGAAAAUGUUGCAAAAAAGCUAAGCCGGCGGGCAGAGGAAAACGCCUGUAGCCGGCGAGUGAAGACGAACCAUCGACUGCCGUGUUCCUUUUCCUCUUGGAGGUUGGAGUCCCCUGGGCGCCCCCACACGGCUAGACGCCUCGGCUGGUUCGCGACGCAGCCCCCCGGCCGUGGAUGC-UCACUCGGGCUCGGGAUCCGCCCAGGUAGC-GGCCUCGGACCCAGGUCCUGCGCCCAGGUCCUCCCCUGCCCCCCAGCGACGGAGCCGGGGC
X02811.1/186-807   CGGAGCAGCCGCAGCUCGCAGCUCGCAGCCCGCAGC-------CCGCAGAGGACGCCCAGAGCGGCGAGCGGGCGGGCAGACGGACCGACGGACUCGCGCCGCGUCCACCUGUCGGCCGGGCCCAGCCGAGCGCGCAGCGGGCACG-CCGCGCGCGCGGAGCAGCCGUGCCCGCCGCCCGGGCCCGCCGCCAGGGCGCACACGCUCCCG-CCCCCCUACCCGGCCCGGGCGGGAGUUUGCACCUCUCCCUGCCCGGGUGCUCGAGCUGCCGUUGCAAAGCCAACUUUGGAAAAAGUUUUUUGGGGGAGACUUGGGCCUUGAGGUGCCCAGCUCCGCGCUUUCCGAUUUUGGGGGCCUUUCCAGAAAAUGUUGCAAAAAAGCUAAGCCGGCGGGCAGAGGAAAACGCCUGUAGCCGGCGAGUGAAGACGAACCAUCGACUGCCGUGUUCCUUUUCCUCUUGGAGGUUGGAGUCCCCUGGGCGCCCCCACACGGCUAGACGCCUCGGCUGGUUCGCGACGCAGCCCCCCGGCCGUGGAUGCUGCACUCGGGCUCGGGAUCCGCCCAGGUAGC-GGCCUCGGACCCAGGUCCUGCGCCCAGGUCCUCCCCUGCCCCCCAGCGACGGAGCCGGGGC
M64844.1/2257-2862 CGGAGCAGCCGCAGCUCGAAAC---------------------CCGCAGAGGAAGCCCAGAGUGGCGAGCGAGUGGGUAGAUAGACAGACUGACCCGAGCCGCGUCCACCUGUCGGCCCGGACCAGCCCAGCGCGCAGUGG-CGCG-CCGCGCUCUCGGAGCAGCCGUGCCCGCCGCUUGGGCCCCUGGCCAGGGCGCACACGCUCCCG-CCCCGCCACCCGGCCCGGGCGGGAGUUUGCACCUCUCCCUGCCCGGGUGUUCGGGCCGCCGCUGCAAAGCCAACUUUGGAAAAAGUUUUUUUUUGGAGACUUGGGCUUGGAGGUCCCCAGCUCUGCGCUUUCUGAUUUGGGGGUCCGUUCCAGAAAAUGUUGCAAAAAAGCUAAGCCAGCAGGCAGAGGAACACGCCUUUAGCGGGCGAGUGAAGACGAACCAUAGGCUGCCGUGUUCCUUUUCCUCUCUGAGGUUGGAGUCCCCUGCGCGCCCCCACACGGCUAGACGCCUUGGCUGGUUCGCGACGCAGCCCCCAGACUGUGGAUGC-UCGCGUGGGCUCGGGAUCCGCCCAGGUAGC-GGCUUUGGACCCCGGUCCCUUGUCCAGGUCCUCCCCAGCCCCCCAGCGACGGAGCCGGGGC
Y00389.1/1604-2152 CGGAGCAGCCGCAGCUCGCAGCUCGCAGCCCGCAGC-------CCGCAGAGGACGCCCAGAGCGGCGAGCGGGCGGGCAGACGGACCGACGGACUCGCGCCGCGUCCACCUGUCGGCCGGGCCCAGCCGAGCGCGCAGCGGGCACG-CCGCGCGCGCGGAGCAGCCGUGCCCGCCGCCCGGGCCCGCCGCCAGGGCGCACACGCUCCCG-CCCCCCUACCCGGCCCGGGCGGGAGUUUGCACCUCUCCCUGCCCGGGUGCUCGAGCUGCCGUUGCAAAGCCAACUUUGGAAAAAGUUUUUUGGGGGAGACUUGGGCCUUGAGGUGCCCAGCUCCGCGCUUUCCGAUUUUGGGGGCCUUUCCAGAAAAUGUUGCAAAAAAGCUAAGCCGGCGGGCAGAGGAAAACGCCUGUAGCCGGCGAGUGAAGACGAACCAUCGACUGCCGUGUUCCUUUUCCUCUUGGAGGUUGGAGUCCCCUGGGCGCCCCCACACGGCUAGACGCCUCGGCUGGUUCGCGACGCAGCCCCCCGGCCGUGGAUGC-UCACUCGGGCUCGGGAUC-------------------------------------------------------------------------C
Z81010.2/5780-6407 CGGAGCAGCCGCAGCUCGCAGCUCGCAGCUCGCAGCCCGCAGCCCGCAGAGGACGCCCAGAGCGGCGAGCGGGCGGGCAGACGGACCGACGGACUCGCGCCGCGUCCACCUGUCGGCCGGGCCCAGCCGAGCGCGCAGCGGGCACG-CCGCGCGCGCGGAGCAGCCGUGCCCGCCGCCCGGGCCCCGCGCCAGGGCGCACACGCUCCCG-CCCCCCUACCCGGCCCGGGCGGGAGUUUGCACCUCUCCCUGCCCGGGUGCUCGAGCUGCCGUUGCAAAGCCAACUUUGGAAAAAGUUUUUUGGGGGAGACUUGGGCCUUGAGGUGCCCAGCUCCGCGCUUUCCGAUUUUGGGGGCCUUUCCAGAAAAUGUUGCAAAAAAGCUAAGCCGGCGGGCAGAGGAAAACGCCUGUAGCCGGCGAGUGAAGACGAACCAUCGACUGCCGUGUUCCUUUUCCUCUUGGAGGUUGGAGUCCCCUGGGCGCCCCCACACGGCUAGACGCCUCGGCUGGUUCGCGACGCAGCCCCCCGGCCGUGGAUGC-UCACUCGGGCUCGGGAUCCGCCCAGGUAGC-GGCCUCGGACCCAGGUCCUGCGCCCAGGUCCUCCCCUGCCCCCCAGCGACGGAGCCGGGGC
#=GC SS_cons       :[[-[[[[[-[[[[[[[[-[[[--------------.......--[-[[[[[,(((((-(-((((((-((,<<<<<<<---<<<-<<<<<<<---<<<___>>>----->>>>>>>>>>->>>>->>>,,,<<-<<-<<<<<<<<<.<<<<____>>>>------>>>>>>>>>->>->>,))-)))))))-))))),,<<-<<<<<<<.<<<-<<_____>>--->>>>>>>>>>->>,,]]]]]-]----------]]]]]]]]]]]-]]]]]----]],<<<<<____>>>>>,,,,,{{{{{{{{{{{{{{{,,,,,[[[[[---[[[[[[[[----[[[-----[[[[[[,,,,,,,,,,,,,,,,<<______>>,,,<<<<<<--<<<<-<_____>-->>>>->>>>>>,,(((--(-((((((((((((((((((((<<<-<<<<<____>>>>>-->>><<<<___>>>>,,,,,,)))))))-))-----))))-))))))))--))),]]]]]]]]]-]]]]]]-]].]]]]],<<<<--<<<-<<<<---<<<<___._>>>>>>>>>>>-->>>>,,,}}}}}}}}-}}}}}}},,,<<<<-<<______>>->>>>:
#=GC RF            cGGAGcagccGcgGcucGcagcucgcAgcucgcAgc.......ccGcaGaGGAcGcccAGAGcggcGAGcggGcGGgcAGAcgGAccGacgGAcucGcGccgCgUccAcCcguCggCcgGgcCCAgCcgAGCGCGCAGcGGGCaCG.CCGcGcgCgCGGAGCAGCCGuGCCCgCCGCcCGGgCCCgccgCCAgggCgCACaCgCuCCcG.CCCCcCuACCCGgCCCGGGCgGGaGcUuGCACCuCuCCCUGCCCGGGUgcuCgagCcgCCgcugCAAAGCCAaCuuuGGAAaaaGuUUUUugggGGaGaccugGgccUuGAgGugcCCAGCuCcgCgCUUUccgAuuUuGGGGgCCuUUCcAGAAAAUGUUGCAAAAAAGCUAAGCCgGCgGgcaGAGGAAaACGCCugcAGCcGGCGAGcGAAGACGaaCCaccGaCuGCCGuGuuCcUccuCcUCUugGaggUUgGaGccCCCUGggCGCCCCCaCaCGGCUaGACGCCuCggCuGGuuCGCGACgCAGcCCCCcggCcGcgGaUGC.gcaCccGGgcUCGGGAuccgcccagGcAGc.GgCcucggaCCCaGgcCCugcgcCcaggucCuCCcccGccccccAGcGAcGGAgCcggggC
//
# STOCKHOLM 1.0

#=GF AC   RF00550
#=GF ID   HepE_CRE
#=GF DE   Hepatitis E virus cis-reactive element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15890906
#=GF SS   Published; PMID:15890906
#=GF GA   45.00
#=GF TC   45.70
#=GF NC   39.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019080; viral gene expression;
#=GF RN   [1]
#=GF RM   15890906
#=GF RT   The open reading frame 3 gene of hepatitis E virus contains a cis-reactive
#=GF RT   element and encodes a protein required for infection of macaques.
#=GF RA   Graff J, Nguyen H, Yu C, Elkins WR, St Claire M, Purcell RH, Emerson SU
#=GF RL   J Virol 2005;79:6680-6689.
#=GF CC   This family represents a cis-reactive element from Hepatitis E virus which
#=GF CC   is thought to be essential for "some step in gene expression" [1].
#=GF WK   Hepatitis_E_virus_cis-reactive_element
#=GF SQ   46


AB097811.1/5093-5243 GAAACAGUCAAACCUGUCCUUGAUCUUACUAGCUCUAUUAUAUACCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUUUGCUCUUCGUGCUUCUGCCUAUGCUGCCCGC
AB161719.1/5068-5218 GAGACAGUUAAACCUGUUUUAGACCUCACCAAUUCUAUUAUACAUCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUUUUCUGUUUUUGUUCCUCGUGCUUCUGCCUAUGCUGCCCGC
M80581.1/5023-5172   GAGUCAGUGAAGCCAGUGCUUGACCUGACAAAUUCAAUUCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AY575859.1/5097-5243 GAGACUAUUAAACCUGUGCUUGACCUUACAAACUCUAUCAUACAGCGGGUGGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGCUCUUCGUGCUUCUGCCUAUGCUGCCCGC
AB091394.1/5063-5209 GAGACUAUUAAACCUGUGCUUGAUCUAACAAAUUCCAUCAUACAGCGGGUGGAAUGAAUAACAUGU-UUUGUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGCUGUUCCUCGUGCUUUUGCCUAUGUUGCCCGC
X98292.1/5052-5201   GAGUCAGUAAAGCCAGUGCUCGACCUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUCUGUUGUUGCUCCUCAUGUUUUUGCCUAUGUUGCCCGC
AB080578.1/431-577   GAGACUGUCAAACCUGUACUUGACCUCACAAAUUCCAUCAUACAGCGGGUGGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAA--CACCAUGCGCCCUAGGGCUGUUCUGUUGCUGUUCUUCGUGCUUCUGCCUAUGCUGCCCGC
AF065061.1/40-189    GAGUCGGUAAAGCCAGUGCUUGACCUGACGAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUGUUGCCCGC
AB099347.1/5093-5243 GAAACAGUCAAACCCGUCCUUGAUCUUACUAGCUCUAUUAUAUACCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCUUCGUGCUUCUGCCUAUGCUGCCCGC
AB089824.1/5099-5245 GAAACCAUUAAACCUGUGCUUGACCUUACGAAUUCUAUCAUACAGCGGGUGGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGCUGUUGUUCCUCAUGCUUCUGCCUAUGCUGCCCGC
AP003430.1/5082-5228 GAGUCAAUUAAACCUGUGCUUGACCUUACAAAUUCUAUUAUACAGCGGGUGGAAUGAAUAACAUGU-CUUGUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGCUCUUCGUGCUUCUGCCUAUGCUGCCCGC
M73218.1/5053-5202   GAGUCAGUAAAACCAGUGCUCGACUUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGCUCCUCAUGUUUUUGCCUAUGCUGCCCGC
AJ272108.1/5093-5243 GAGACAAUUAAGCCUGUCCUUGACCUUACUAGCUCCAUUAUAUACCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCCGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCUUCGUGCUUCUGCCUAUGUUGCCCGC
AB108537.1/5074-5224 GAAACAGUCAAACCGGUCCUAGACUUAACUAACUCUAUCAUACAUCGGAUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUUUGUUUCUGCUCCUCGUGCUUCUGCCUAUGCUGCCCGC
AY594199.1/5101-5251 GAGACAAUUAAGCCUGUUCUUGACCUUACUAGCUCCAUCAUAUAUCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCUGCGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCCUCGUGUUUUUGCCUAUGCUGCCCGC
AF455784.1/5066-5212 GAGACUGUUAAACCGGUACUGGAUCUUACGAACUCCAUUAUACAGAGGCUAGAAUGAAUAACAUGU-CUUGUGCAUCGCCCAUGG-GAU--CGCCAUGUGCCCUCGGGCUGUUUUGCUGUUGUUCCUCGUGCUUUUGCCUAUGCUGCCCGC
AF459438.1/5053-5202 GAGUCAGUAAAACCAGUGCUCGACCUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AB074920.3/5083-5229 GAGACCAUUAAACCUGUGCUUGACCUUACGAAUUCCAUCAUACAGCGGGAGGAAUGAAUAACAUGU-CUUUUGCACCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGUUCCUCGUGCUUCUGCCUAUGCUGCCCGC
AF010422.1/22-171    GAGUCAGUAAAGCCAGUGCUCGAUCUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUUUGCCUAUGCUGCCCGC
U22532.1/1-90        -----------------------------------------------------AUGGAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCUAGACCAUGGGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUG-------C
AY204877.1/5012-5161 GAGUCUAUAAAACCAGUGCUCGACUUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGCUGCUCCUCAUGUUUCUGCCUAUGUUGCCCGC
AY245779.1/1-105     ----------------------------------------------GGGUGGAAUGAAUAACAUGUUCUUUUGCUCCUUGCAUGGCAAUGCCACCAUGCGCCCUCGGGCUCUUUUGUUUUUGCUCCUCCUGUUUUUGCUUAUGCUGCCCGC
M94177.1/5053-5202   GAGUCAGUGAAGCCAGUGCUCGACCUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUCUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AF051352.1/30-179    GAGUCUAUAAAGCCUGUGCUCGACUUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGCUGCUCCUCAUGUUUUUGCCUAUGUUGCCCGC
AB073912.1/5081-5227 GAGACUAUCAAACCUGUGCUUGACCUUACAAAUUCUAUCAUACAGCGGGUAGAAUGAAUAACAUGU-CUUGUGCAUUGCCCAUGG-GAU--CGCCAUGUGCCCUAGGGCUGUUCUGUUGUUGCUCUUCGUGCUUUUGCCUAUGCUGCCCGC
AB075971.1/25-175    GAAACAAUCAAACCUGUUCUUGACCUUACUAGUUCCAUUAUAUAUCGGAUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCCUCGUGCUUCUGCCUAUGCUGCCCGC
AF010418.1/22-171    GAGUCGGUAAAGCCAGUGCUUGACCUGACGAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGCUCCUCAUGUUUCUGCCUAUGUUGCCCGC
D11093.1/5053-5202   GAGUCGGUGAAGCCAGUGCUCGACUUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUGGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUCUGCCUAUCGUGCCCGC
M74506.1/5023-5172   GAGUCUGUUAAGCCUAUACUUGACCUUACACACUCAAUUAUGCACCGGUCUGAAUGAAUAACAUGU-GGUUUGCUGCGCCCAUGGGUUCGCCACCAUGCGCCCUAGGCCUCUUUUGCUGUUGUUCCUCUUGUUUCUGCCUAUGUUGCCCGC
X99441.1/5053-5202   GAGUCAGUAAAACCAGUGCUCGACCUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGCUCCUCAUGUUUUUGCCUAUGCUGCCCGC
AB080576.1/431-581   GAAACAGUCAAACCCGUCCUUGAUCUUACUAGCUCUAUUAUAUACCGGGUGGAGUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCUUCGUGCUUCUGCCUAUGUUGCCCGC
AF060669.1/5106-5252 GARAAUAUUAAACCUGUGCUUGACCUUACAAAUUCCAUCAUACAACGGGUGGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGCUCUUCGUGCUUUUGCCUAUGCUGCCCGC
AF051830.1/5053-5202 GAGUCAGUAAAACCAGUGCUCGACCUGACAAAUUCAAUUUGGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCACGGGUUCGCGAUCAUGCGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AF001276.1/35-184    GAGUCGAUAAAGCCAGUGCUUGACCUGACGAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGCUGUUCCUCAUGUUUUUGCCUAUGCUGCCCGC
AY115488.1/5097-5243 GAGACUAUUAAACCUGUGCUUGACUUAACAAACUCUAUCAUACAACGGGUGGAAUGAAUAACAUGU-CUUGUGCUUCACCCAUGG-GAC--CACCAUGCGCCCUAGGGCUAUUUUGUUGUUGUUCUUCGUGCUUCUGCCUAUGCUGCCCGC
AF010421.1/22-171    GAGUCUAUAAAGCCAGUGCUUGACUUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGUGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGCUGUUCUUCAUGUUUCUGCCUAUGUUGCCCGC
AB074915.3/5077-5227 GAAACUGUUAAACCUGUUUUGGAUCUCACCAAUUCCAUUAUACAUCGGGUGGAAUGAAUAACAUGUUCUUUUGCUCUGUGCAUGGAGAUGCCACCAUGCGCUCUCGGGCUCUUCUGUUUCUGCUCUUCGUGUUUUUGCCUAUGCUGCCCGC
L25547.1/5052-5201   GAGUCAGUGAAGCCAGUGCUCGACCUGACAAAUUCAAUCCUGAGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUCCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AF051351.1/28-177    GAGUCUAUAAAGCCUGUGCUCGACUUGACAAAUUCAAUCUUGUGUCGGGUAGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGCUGUUCCUCAUGUUUCUGCCUAUGCUGCCCGC
D11092.1/5053-5202   GAGUCAGUGAAGCCAGUGCUCGACCUGACAAAUUCAAUCCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGCUGUUGCUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AF185822.1/5002-5151 GAGUCAGUAAAACCAGUGCUUGACCUGACAAAUUCAAUUCUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGCUCCUCAUGUUUUUGCCUAUGCUGCCCGC
AF060668.1/5041-5187 GAGACUAUUAAACCUGUACUUGAUCUCACAAAUUCCAUCAUACAGCGGGUGGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGUUCCUCAUGUUUCUGCCUAUGCUGCCCGC
AF058684.1/39-188    GAGUCAGUAAAACCAGUGCUCGACCUGACAAAUUCAAUUUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUGCUGCCCGC
D10330.1/5053-5202   GAGUCAGUAAAACCGGUGCUCGACUUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGCGACCUCGGCCUAUUUUGUUGCUGCUCCUCAUGUUUUUGCCUAUGUUGCCCGC
AF076239.3/5053-5202 GAGUCAGUAAAACCAGUGCUCGACCUGACAAAUUCAAUCUUGUGUCGGGUGGAAUGAAUAACAUGU-CUUUUGCUGCGCCCAUGGGUUCGCGACCAUGGGCCCUCGGCCUAUUUUGUUGCUGUUCCUCAUGUUUCUGCCUAUGCUGCUCGC
AB074918.2/5099-5245 GAGACCAUUAAACCUGUGCUUGACCUUACGAAUUCCAUCAUACAGCGGGAAGAAUGAAUAACAUGU-CUUUUGCAUCGCCCAUGG-GAU--CACCAUGCGCCCUAGGGCUGUUCUGUUGUUGUUCCUCGUGCUUUUGCCUAUGCUGCCCGC
#=GC SS_cons         ::<<<<<<-<<<<____>>>>->->>>>>----------------<<<<<<<-<<<---<<<<<<-.-----<<-<<<---<<<<<<<-<<<______>>>---->>>>>>>-->>>---->>---->>>>>>------>>>->>>>>>>:
#=GC RF              GAGucagUugagcCuGUgcucGAccugaCaAAuUCaAUcaUauauCGGgugGAaUgAAUAaCAuGU.CUUUUgCugcgccCAugGgccugCgACCAUGcGccCUcggcCuaUUuugcUguUGcUCcUCaUGuUUcUGCCuAuGCugcCCGC
//
# STOCKHOLM 1.0

#=GF AC   RF00551
#=GF ID   bicoid_3
#=GF DE   Bicoid 3'-UTR regulatory element
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:15016447
#=GF SS   Published; PMID:15016447
#=GF GA   91.00
#=GF TC   95.50
#=GF NC   48.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0008359; regulation of bicoid mRNA localization;
#=GF RN   [1]
#=GF RM   15016447
#=GF RT   Secondary structure of the 3' UTR of bicoid mRNA.
#=GF RA   Brunel C, Ehresmann C
#=GF RL   Biochimie 2004;86:91-104.
#=GF CC   This family represents the core structure of the bicoid 3'-UTR and
#=GF CC   consists of domains II, III, IV and V which are known to be essential for
#=GF CC   correct transport and localisation of bicoid mRNA during oocyte and embryo
#=GF CC   differentiation [1].
#=GF WK   Bicoid_3'-UTR_regulatory_element
#=GF SQ   15


AC002512.1/12119-11569 GGCCGCACGGAUU-CCAGUGCAUAUCUUAGUGAUACUCCAGUUAA--CU-C-------UAU---------ACUUUCCCUGCAAUACGCUAUUCGCC-UUAGAUGUAUCUGGGUGGCUGCUCCAC-UAAAGCCCGGGAAUAUGCAACCAGUUACAUUUGAGGCCA-UU-U---GGGCUU-----AAGCGUAUUCCAUGGAAAGUU-AUCGUCCCACAUUUCGGAAAUUAUAUUCCG----AGCCAGCAAGAAAAUCU--UCUCUGUUACAA--UUUGACAUAGCUA-----AAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGG-CGUAAUCUCA-----UA-CAA--UG-------------AUUAC-CCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAA-AGUGUCUGACAUAAUCAAACAUUUGCGCAUUCUUUGACCA-AGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUG--CAGACCAUUUGUUUCAGAUUCGGAGAUUUUUUGCUGCCAAACGGAAUAAC---------------UAU-CAUAGCU-CACAUUCUAUUU--ACAUCACUAAGAAGAGCAUUGCAAUCUGUUAGGCC
AF466639.1/3212-3762   GGCCGCACGGAUU-CCAGUGCAUAUCUUAGUGAUACUCCAGUUAA--CU-C-------UAU---------ACUUUCCCUGCAAUACGCUAUUCGCC-UUAGAUGUAUCUGGGUGGCUGCUCCAC-UAAAGCCCGGGAAUAUGCAACCAGUUACAUUUGAGGCCA-UU-U---GGGCUU-----AAGCGUAUUCCAUGGAAAGUU-AUCGUCCCACAUUUCGGAAAUUAUAUUCCG----AGCCAGCAAGAAAAUCU--UCUCUGUUACAA--UUUGACAUAGCUA-----AAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGG-CGUAAUCUCA-----UA-CAA--UG-------------AUUAC-CCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAA-AGUGUCUGACAUAAUCAAACAUUUGCGCAUUCUUUGACCA-AGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUG--CAGACCAUUUGUUUCAGAUUCUGAGAUUUUUUGCUGCCAAACGGAAUAAC---------------UAU-CAUAGCU-CACAUUCUAUUU--ACAUCACUAAGAAGAGCAUUGCAAUCUGUUAGGCC
AF465792.1/2973-3522   GGCGACACGGAUU-CCAGUGCAUAUCUUAGUGAUACUCCAGUUAA--CU-C-------CAU---------ACUUUCCCUGCAAUACGCUAUUCGCC-UCAGAUGUAUCUGGGUGGUUGCUCCAC--UAAGCCCAGGAAUAACCAGCCAGUUACAUUUGAGGCCA-UU-U---GGGCUU-----AAGCGUAUUCCAUGGAAAGUU-GUCGUCCCAUAUUUCGAAAAUUAAAUUCCG----AGCCAGCAAGAAAAUCU--UCUCUGUUACAA--UUUGACAUAGCUA-----AAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGG-CGUAAUCUCA-----UA-CAA--UG-------------AUUAC-CCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAA-AGUGUCUGACAUAAUCAAACAUUUGCACAUUCUUUGACCA-AGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUG--CAGACCAUAUGUUCCAGUUUCGGAGAUUUUUUGCUGCCAAACGGAAUACU---------------UAU-AAAAACC-CACAUUCUAUUU--ACAUCACUAAGAAGAGCAUUGCAAUCUGUUUAGCC
AF466630.1/3213-3763   GGCCGCACGGAUU-CCAGUGCAUAUCUUAGUGAUACUCCAGUUAA--CU-C-------UAU---------ACUUUCCCUGCAAUACGCUAUUCGCC-UUAGAUGUAUCUGGGUGGCUGCUCCAC-UAAAGCCCGGGAAUAUGCAACCAGUUACAUUUGAGGCCA-UU-U---GGGCUU-----AAGCGUAUUCCAUGGAAAGUU-AUCGUCCCACAUUUCGGAAAUUAUAUUCCG----AGCCAGCAAGAAAAUCU--UCUCUGUUACAA--UUUGACAUAGCUA-----AAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGG-CGUAAUCUCA-----UA-CAA--UG-------------AUUAC-CCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAA-AGUGUCUGACAUAAUCAAACAUUUGCGCAUUCUUUGACCA-AGAAUAGUCAGCAAAUUAUAUUUUCAAUCAAUG--CAGACCAUUUGUUUCAGAUUCGGAGAUUUUUUGCUGCCAAACGGAAUAAC---------------UAU-CAUAGCU-CACAUUCUAUUU--ACAUCACUAAGAAGAGCAUUGCAAUCUGUUAGGCC
M32122.1/291-827       GCU-G-UAAUUUU-CCAA-GCAUUUUCAAUG--UA-UUUCCAUAA--G-----------AA---------ACUUCCUUGGUAAAACCUUCAUUGGUCUCAACUCUGUCUGGCUGGGCAUUUGCC--AAAGCCCAUGAGUGCCCAUCCAGACAUACUUGAGACAA-UAAU---GGGCUUAAGCUGAAGGUUUUACCGAAGAAGUU-UUCGUAUGAAAAUC-------U-CA-UGUA----AG---AUUC-AUU-UCUA-UAAUUUUGGCAC--CUUGGCAUAGCUUACAAAAAAACUGCACUGAUCUAAAUGGAAAAUGUUUCUCUUCCU-GAUAAUCGCACGCCUUU-CUUUUUG------GCCUGCCAUUAUCAGCCGAAGAUCGAACAUUUAAACAAUAAUACUCGUCAGAAUAUUUUUAAUU--CUUGCUAUGCCCC-GGUUU---UCAUGUU-ACAAUUGA--ACAUUCU-UCACGUGAGAAUUGUUCAAAUAUUGUACCACAAUAC-AUGAAUACCACA--UGCCUAAGUUAUC--GAAA-CGAAU--ACUA-UAUA-UUAC---------------UGG-AGGAUUUUCGUUU---UUUU-CUUAU-AAUUGAAAAUGGGUUGAAAAUUUACCAGUU
M32124.1/262-812       GGCGACACGGAUU-CCAGUGCAUAUCUUAGUGAUACUCCAGUUAA--CU-C-------CAU---------ACUUUCCCUGCAAUACGCUAUUCGCC-UCAGAUGUAUCUGGGUGGUUGCUCCAU-UAAAGCCCAGGAAUAUCCAGCCAGUUACAUUUGAGGCCA-UU-U---GGGCUU-----AAGCGUAUUCCAUGGAAAGUU-UUCGCCCCACAUUUCGGAAAUUAAAUUCCG----AGCCAUCAAGAAAAUCU--UCUCUGUUACAA--UUUGACAUAGCUA-----AAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGG-CGUAAUCUCA-----UA-CAA--UG-------------AUUAC-CCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAA-AGUGUCUGACAUAAUCAAACAUUUGCACAUUCUUUGACCA-AGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUG--CAGACCAUAUGUUCCAGUUUCGGAGAUUUUUUGCUGCCAAACGGAAUACU---------------UAU-AAAAACC-CAAAUUCUAUUU--ACAUCACUAAGAAGAGCAUUGCAAUCUGUUUAGCC
M32126.1/307-857       UGCCG-AGUUUUU-UUAAUGCAUUUUCUACUGACA-UAAACUUAA--GU-CCAAC---UAUUUGGAA---ACUUUAUUUGUAAAGCGCUCUUUGAUCUCAAUGCUGUCUGGCUGGACAUUUGCC--AAAGCCCAUGAACGCCCUACCAGACACUGUUGAGACAAAUA-U---GGGCUUUAAUUGAACGCUUUACAGAAGAAGUU-UA-U--AAAUAAAUACAA------AA-UGC---------AUUUCUUUCUUA--UAACUCAGGCCA--ACUGGCAUAGCAAGU---AAAACUGUACUGAUCUAAAUGAAAAAUGUUUCUCUUCCU-AAUAAUCGCAGGUCCUU-CAA--UGGACAUUAUCUGCCAUUAUCAGUCGAAGAUCGAACGUUUAACCAAUAAUGUUCUUCAGAAUAUUUUUAAG--CUUUGUUAUGCCAC-AGUUU---ACAUGUU--ACAAUUAA-ACAUUCU-UCACGUGAGAAUUGUUUACAAAUUGUCUCUAAACAC-AUGUGAAUCACA--GGCCUCAGUUAUC-UAAAC-GAAAU---CU--GUACUU-AC---------------UUU-CAGAAUGUAAGAG---AGUU--UUAUCAAUUGAAAAUGCAUUCAAAAUAUGU-GUCU
AF466626.1/3213-3763   GGCCGCACGGAUU-CCAGUGCAUAUCUUAGUGAUACUCCAGUUAA--CU-C-------UAU---------ACUUUCCCUGCAAUACGCUAUUCGCC-UUAGAUGUAUCUGGGUGGCUGCUCCAC-UAAAGCCCGGGAAUAUGCAACCAGUUACAUUUGAGGCCA-UU-U---GGGCUU-----AAGCGUAUUCCAUGGAAAGUU-AUCGUCCCACAUUUCGGAAAUUAUAUUCCG----AGCCAGCAAGAAAAUCU--UCUCUGUUACAA--UUUGACAUAGCUA-----AAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGG-CGUAAUCUCA-----UA-CAA--UG-------------AUUAC-CCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAA-AGUGUCUGACAUAAUCAAACAUUUGCGCAUUCUUUGACCA-AGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUG--CAGACCAUUUGUUUCAGAUUCGGAGAUUUUUUUCUGCCAAACGGAAUAAC---------------UAU-CAUAGCU-CACAUUCUAUUU--ACAUCACUAAGAAGAGCAUUGCAAUCUGUUAGGCC
AF466636.1/3213-3763   GGCCGCACGGAUU-CCAGUGCAUAUCUUAGUGAUACUCCAGUUAA--CU-C-------UAU---------ACUUUCCCUGCAAUACGCUAUUCGCC-UUAGAUGUAUCUGGGUGGCUGCUCCAC-UAAAGCCCGGGAAUAUGCAACCAGUUACAUUUGAGGCCA-UU-U---GGGCUU-----AAGCGUAUUCCAUGGCAAGUU-AUCGUCCCACAUUUCGGAAAUUAUAUUCCG----AGCCAGCAAGAAAAUCU--UCUCUGUUACAA--UUUGACAUAGCUA-----AAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGG-CGUAAUCUCA-----UA-CAA--UG-------------AUUAC-CCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAA-AGUGUCUGACAUAAUCAAACAUUUGCGCAUUCUUUGACCA-AGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUG--CAGACCAUUUGUUUCAGAUUCGGAGAUUUUUUGCUGCCAAACGGAAUAAC---------------UAU-CAUAGCU-CACAUUCUAUUU--ACAUCACUAAGAAGAGCAUUGCAAUCUGUUAGGCC
M32121.1/250-792       GGCUACACGGAUU-CCAGUGCACGUCAUAGGGAUACCCUAGUUUA--CU-C-------GAU---------ACUUUCCCUGUAAUACGCUUUUCGCC-UCAAUUGUAUCUGGGUGGCUGCUCCA--UAAAGCCCGGGAAUAUCCAACCAGUUACAUUUGAAGCCA-UU-U---GGGCUU-----UAGCGUAUUCCACAGAAAGUU-AUCGUCCCAC-------AACUUAUAUUCCG----AGCCAGCAAGAAAAUCU--UCUCUGUAACUA--UUUGACAUAGCUA-----AAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGG-CGUAAUCUUA-----UA-CAA--UG-------------AUUAC-CCUCAAAGAUCGAACAUUUAAGCAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAA-AGCGUCUGACAUAAUCAAACAUUUGCACAUUCUUCGACCA-AGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUG--CAGAUCAUGUGUUCCAGUUUCGGAGAUUUUUUGCUGUCAA-CGGAAUAAC---------------UAU-CCUACCCACACUGUCUAUUU--CUAUCACUUAGAAGAGCAUUGAAAUCUGUUUUGUU
M32123.1/262-812       GGCGACACGGAUU-CCAGUGCAUAUCUUAGUGAUACUCCAGUUAA--CU-C-------CAU---------ACUUUCCCUGCAAUACGCUAUUCGCC-UCAGAUGUAUUUGGGUGGUUGCUCCAC-UAAAGCCCAGGAAUAUCCAGCCAGUUACAUUUGAGGCCA-UU-U---GGGCUU-----AAGCGUAUUCCAUGGAAAGUU-UUCUCCCCACAUUUCGGAAAUUAAAUUCCG----AGCCAGCAAGAAAAUCU--UCUCUGUUACAA--UUUGACAUGGCUA-----AAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGG-CGUAAUCUCA-----UA-CAA--UG-------------AUUAC-CCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAA-AGUGUCUGACAUAAUCAAACAUUUGCACAUUCUUUGACCA-AGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUG--CAGACCAUAUGUUCCAGUUUCGGAGAUUUUUUGCUGCCAAACGGAAUACU---------------UAU-AAAAACC-CACAUUCUAUUU--ACAUCACUAAGAAGAGCAUUGCAAUCUGUUUAGCC
AF466631.1/3213-3763   GGCCGCACGGAUU-CCAGUGCAUAUCUUAGUGAUACUCCAGUUAA--CU-C-------UAU---------ACUUUCCCUGCAAUACGCUAUUCGCC-UUAGAUGUAUCUGGGUGGCUGCUCCAC-UGAAGCCCGGGAAUAUGCAACCAGUUACAUUUGAGGCCA-UU-U---GGGCUU-----AAGCGUAUUCCAUGGAAAGUU-AUCGUCCCACAUUUCGGAAAUUAUAUUCCG----AGCCAGCAAGAAAAUCU--UCUCUGUUACAA--UUUGACAUAGCUA-----AAAACUGUACUAAUCAAAAUGAAAAAUGUUUCUCUUGGG-CGUAAUCUCA-----UA-CAA--UG-------------AUUAC-CCUUAAAGAUCGAACAUUUAAACAAUAAUAUUUGAUAUGAUAUUUUCAAUUUCUAUGCUAUGCCAA-AGUGUCUGACAUAAUCAAACAUUUGCGCAUUCUUUGACCA-AGAAUAGUCAGCAAAUUGUAUUUUCAAUCAAUG--CAGACCAUUUGUUUCAGAUUCGGAGAUUUUUUGCUGCCAAACGGAAUAAC---------------UAU-CAUAGCU-CACAUUCUAAUU--ACAUCACUAAGAAGAGCAUUGCAAUCUGUUAGGCC
X55735.1/2601-3156     GGC-G-GCACAUU-UCAAUGAUUCUUCAAGUGAUACUAUAUAUAUUUCU-CACUUU--UAUCGGCA----ACUUUCUCUGCCAUACGUUCGUUGCU-UCGUUUGUUUUUGGUCGGGUGUUCCCCCAAAAGCCCAGGGAUACCCUGCUAAAACCAAACGAGGUGU-UU-UAUUGGGCUU-----GAACGUAUGCCAGAGAAAGUU-CU-UUCCCACAUUU-------UAAGUUCCUCAAAAGC--AAAGGAAUCUCU--GUACUUUAACAAAUUUUGUCAUAGCUA-----AAACCUGUACUUAUCGAAAUGCAAAAUGUUUCUCUUGGUUGGUAAUCAUA-----CA-AAAC-UG---------UAUUAUUACCAGCUAAAGAUUGAACAUUUAAACAA-----UUC-------------CGA---AUACGCCAUGACAAAAGCGU-UGGCUUGUUUCGACAUUUGGACAUUCUUUCUACA-AGAAAUGUCAGCAAAUUGUCUGCCAAGACAAAC--CA-AACAUUUGUUU-CGU--UCUAGGAUUCUUUU--ACU----GAAUUAUUUAUAUUAUAUCAUAUAUUUAUAUCCUAAGUUUCCAUUUGAAUAUCACUUCAAGUUGCAUUGAAAUCUGCUUAGCU
M32125.1/227-779       GCUGC-CGAGUUUUUUAAUGCAUUUUCUACUGACA-UAAACUGAA--GUGC-------CAUUAUUUGGAAACUUUAUUUGUAAAGCGUUCUUUGAUCUCAACGCUGUCUGGCUGGACAUUUGCC--AAAGCCCAUGAAUGCCCAACCAGACACUGUUGAGACGAAUA-U---GGGCUUUAAUUGAACGCUUUACAGAAGAAGUUUAUAAAUACACA----------UAAAAUGC----------AUUUCUUUCUUA--UAACUCAGGCCA--ACUGGCAUAGCAAGU---AAAACUGUACUGAUCUAAAUGAAAAAUGUUUCUCUUCCU-GAUAAUCGCACGUCCUU-CUA--UGGACAUUAUAUGCCAUUAUCAGUCGAAGAUCGAACGUUUAACCAAUAAUGUUCUUCAGAAUAUUUUUAAG--CUUUGUUAUGCCAC-AGUUU---GCAUGUUGCA---AUUAAACAUUCU-UCACGUGAGAAUUGUUUACAAAUUGUCUCUAAACAC-AUG-UGA-ACCACAGGCCUCACU--UAUCUAAACGAAAU---CU---GUACUUAC---------------UUU-CAGAAUGUAAGAU---AGUU--UUAUCAAUUGAAAAUGCAUUCCAAAUAUGUAUCUC
X78058.1/486-1031      GGC-G-GCAGAUU-UUAAUCAAACUUCAAGUGAUAUUCGCUCUUAC-CU-CUCUGCUUUAUCGAAA----ACUUUCUCUGCCAUGCGUUCGUUGCU-UCGUUUGUUUUUGGUUGGACAUUCCCCCAAAAGCCCAGGAAUUGCCUGCUAAAAUCAAUCGAGGUGU-UU-U-AUGGGCUU-----GAACGCAUGCCGGAGAAAGUU-AU-UUUCCCC-----------U-CAUUUUA----AGC--AAAGGAAUCCCCUGGCUCUGAUACAAA-UUUGUCAUAGCUA-----AAACCUGUCCUAAUCGAAAUGCAAAAUGUUUCUCUUGGC-GGUAAUCAUA-----UAACAAU-UG----UUUUAUAUAAUUACCAUCUAAAGAUUGAACAUUUAAACAA-----CUC-------------AGA---AUAUGCUAUGACAA-AGCGU-UGGCUUG-UCGGACAUUUGGACAUUCUUUCUGCA-AGAAAUGUCAGCAAAUCGUCUGCCGAAACAAGC--CA-AACAUUUGUU-CGU---CCUCGGAUUCCUUU--ACUGAUUUAUUUAU-------AUACCCAUUAU-UAUAUUUUAAGAUCGUCUUUUAAUAUCACUUCAAGUUGCAUUGAAACCUGUUUAGCU
#=GC SS_cons           [[[[-.[[[[[[[.-[[[[[[---[[[[[[[[[[,,,,,,,,,,,..,,.,.......,,,.........<<<<<<<-<<-<<<<<<<<----<<<.<<<<<<<<<-<<<<---<<<<-<<<__._________>>>->>->>-->>>>->>>>>>>>>>>>--.--.-...------.....->>>>>>>>->>->>>>>>>,.,,,,,,,,,,,,,,,,,,...,,(((((((....---..((((((((-(((..(-((((--((((..<<<<-<<<<<<<<.....--<<-<<-----<<<<<<-----<<<<<<<<-<<<<<<<.-<<<<<____.....__.___..__.........____>>>>>->>>-->>>>-->>>>>>>>----------->>>>>>---------->>->>.->>->>>>>>->>>.><-<<.<<-<<<---------<<<<<<<<<<<<_______.>>>>>->>-->>>>>--------------->>>..>>->>>,,))))--))))----))))))))))))..-----))))))),,...............,,,.,,,,,,,,,,,,,,,,,,,,..,,]]]]]]]]]]---]]]]]]-]]]]]]]--]]]]
#=GC RF                ggccg.gcggaUU.ccAaUgCAUaUccuAguGAuAcUcuAuuUAA..cU.C.......uAU.........ACUUucccuGcaAugCGcUauUuGcc.UcagcugugUcUGGuUGGgcauuccaC.uAAAGCCCaggaAugucCaaCCAgacacagcugAggCaA.Uu.U...GGGCUU.....gAgCGcaUucCauggaAAGUU.aUcgUcccAcAuUUcggA...UAuauUccg....AGC..gcaggaauaucu..ccacuguugCaa..uuuGaCAUaGCua.....AAaaCugUACUaaucgAaAUGaAAAAuGUUuCUCUUggg.gGUAAUCucA.....Ua.CAA..UG.........UgucAUUACCcccuaAAGAUCgAACaUUUAAaCAAUAAUAuUcgauAugAUAUUUUcaAuu.cuaUGCuAUGcCaa.aGUgu.uGaCaUaaUcaaAcAuuuGcaCaUUCUUUcAcca.AGAAuuGucagCaaaUUGUaUuuuaAaaCAAuG..CagacCAUuuGcuUcaguUuuggagaauuccugc..aCuAAcggAauaAc...............UaU.cAuAauuUaAgaUUcUAuUU..auaUCacUaggAAauGcAuUgaAAuccgcUuggcc
//
# STOCKHOLM 1.0

#=GF AC   RF00552
#=GF ID   rncO
#=GF DE   rncO
#=GF AU   Moxon SJ; 0000-0003-4644-1816
#=GF SE   PMID:8972772
#=GF SS   Published; PMID:8972772
#=GF GA   43.00
#=GF TC   43.50
#=GF NC   42.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0043488; regulation of mRNA stability;
#=GF RN   [1]
#=GF RM   8972772
#=GF RT   RNase III autoregulation: structure and function of rncO, the
#=GF RT   posttranscriptional "operator".
#=GF RA   Matsunaga J, Simons EL, Simons RW
#=GF RL   RNA 1996;2:1228-1240.
#=GF CC   This family represents a bacterial regulatory element (rncO) found in the
#=GF CC   rnc leader sequence. The rnc operon is negatively auto-regulated by
#=GF CC   transcript stability. rnc, the first gene in the operon codes for RNase
#=GF CC   III which cleaves the long rncO stem II leading to transcript degradation
#=GF CC   and a reduction in translation [1].
#=GF WK   rncO
#=GF SQ   18


CP000720.1/1337539-1337720   GAGCGAUAAAGUUGGCUCUCUUAU-GGGAGCCACUGCAAACGAAACAGUUUUGU----CUUGGUUAUUUUUG-------------------------------UCGGUCAGAC---CUGUUCCGUAUGCUGUAGUU-UUUGACGCAUUCUUGAUC----UAUUGGUAACUCAUGAAUCCCAUCGUAAUAAACAGGCUGCAGCGGAAGCUGGGCUACACUUUCCAAC
AM286415.1/1137336-1137517   AGCGAUAAAAGUUGGCUC-UUUUAUGGGGGCCACUGCAAACGAAACAGUUUUGU-CUU--------------GGUA--------UUAU------UGGCCGAUCA---------GACCUGUUCCGUCUGCUGUAGUU-UUUGACGCAUUCUUGAUC----UAUUGGUAACUCAUGAACCCCAUCGUAAUAAAUAGGCUACAGCGGAAGCUGGGCUACACUUUUCAAC
CP000653.1/3324072-3323909   GAAGUUUAAGGUUGGCGC-AGAGC-CAGUGCCACGGCACACGAAACCGCGUUGGUUUUC----------------------------U-----------------------CAGGUCGGUUUCGUGUGCUGCA-UU-UUUGACGCAUUC---AUU----UAUUGGUAUAGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUCAGC
CP000647.1/3179206-3179016   GAAGUUUUUGGUUGUCGCUCUGCC-GGGUGACACUGCACACGAAAGCGUAUUGG--UC--------------UGU-UUCAAAUUACUGUUUGAA--GCGAAUGCU------CAGGUCGGUUUCGUGUGCUGCA-UC-UUUGACGCAUUC---AUU----UAUUGGUAACGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGAAAGCUGGGCUACACUUUUCAUC
U48415.1/72-282              GAAGUUUUAGGUUG-CGC-CGUUU-GGUCGCCACGGCACACGAAACAGCGUUGG--UU-AUAGACAACCUUCUUUCCGCUGCAGCGAUGCGGCAGGACAGAUGACGUGUAUCAGGUCUGUUUCGUGUGCUGGA-UU-GUUGACGCAUUC---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
CP000243.1/2845964-2845756   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCG-----CUA-AACUGCAGCGAAGCAGUUAGCAGAGCUAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
CP000034.1/2599063-2598849   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUUCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGCUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
D64044.1/11691-11477         GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGGUAAACUGAAACUGCAGCGAACGAGUUAGCAGAACCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
AE014075.1/2967090-2966876   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGGUAAACUGAAACUGCAGUGAAGCAGUUAGCCGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
CP000266.1/2697918-2697704   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGCUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
CP000036.1/2601301-2601087   GAAGUUUAAGGUUGGCAC-CUUCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGGUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
BX571870.1/149010-148833     UCAAACUUAAACUGGCUC-CUAUA-AGGGGCCAGUGCAAACGCAACAGUUUUG---UCG-------------GGG----------GUU--------CCUGUAA--------CAGGUCUGUUGCGUGUGCGUUU-UUAUUUGACGAAUUC---UGACCGAUAUUGGUAGCACAUGAAUCCCAUCGUAAUUAACAGAUUGCAGCGUAAGCUGGGGUACACUUUUGAUC
ABEH02000006.1/190140-190351 GAAGUUUUAGGUUGGCGU-CGUUU-GGUCGCCACGGCACACGAAACAGCGUUGG--UU-AUAGACAACCUUCUUUCCGCUGCAGCGAUGCGGCAGGACAGAUGACGUGUAUCAGGUCUGUUUCGUGUGCUGGA-UU-GUUGACGCAUUC---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
CP001127.1/2726770-2726559   GAAGUUUUAGGUUGGCGC-CGUUU-GGUCGCCACGGCACACGAAACAGCGUUGG--UU-AUAGACAACCUUCUUUCCACUGCAGCGAUGCGGCAGGACAGAUGACGUGUAUCAGGUCUGUUUCGUGUGCUGGA-UU-GUUGACGCAUUC---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
CU928164.2/2878743-2878529   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGGUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
CP000946.1/1208700-1208914   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGGUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAACCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
AAMK02000008.1/26052-26266   GAAGUUUAAGGUUGGCAC-CUCCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGCUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGAUACACUUUUAAUC
CP001383.1/2739127-2738913   GAAGUUUAAGGUUGGCAC-CUUCA-GGUUGCCACGGCACACGAAACAGCGUUGGUCCCCAUAUACCGCUAAACUGAAACUGCAGCGAAGCAGUUAGCAGAGCCAUGUAUAUCAGGUCUGUUUCGUGUGCUGAA-UU-GUUGACGCAUUU---AUU----UAUUGGUAUCGCAUGAACCCCAUCGUAAUUAAUCGGCUUCAACGGAAGCUGGGCUACACUUUUAAUC
#=GC SS_cons                 ::::::::::::<<<<<<.<____.>>->>>>><<<<<<<<<<<<<<<------.-<<-<<<<<<-------<<<-<<<<<<______>>>>>>-->>>------>>>>>>-->>->>>>>>>>>>>>>>>--.--.------------...---....--------------------------------<<<<<<<<____>>>>>>>>:::::::::::::::
#=GC RF                      gAAguUUaAgGUUGGCgC.cUuua.gGucGCCAcgGCAcACGaAACaGcgUUGg.ccccauauacaguuaaacggacgCugcAgcgaugcaGcgaGccgaaucauguauauCAggUCuGUUuCGUgUGCcgaA.UU.uUUGACGCAUUc...AUu....UAUUGGUAuCgCAUGAAcCCCAUCGUAAUUAAccgGCUucAaCGgaAGCuggGcUACACUUUUaAuC
//
# STOCKHOLM 1.0

#=GF AC   RF00553
#=GF ID   SCARNA1
#=GF PI   snoACA35
#=GF DE   Small Cajal body specific RNA 1
#=GF AU   Marantidis E
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   45.90
#=GF NC   40.60
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. ACA35 belong to the H/ACA
#=GF CC   box class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail
#=GF CC   structure, conserved H/ACA-box motifs and is found associated with GAR1
#=GF CC   [2]. It is predicted to guide pseudouridylation of the U2 spliceosomal
#=GF CC   snRNA at residue U89 [2].
#=GF WK   Small_Cajal_body-specific_RNA
#=GF SQ   29


AL671190.10/55894-55730      CAGC-ACUUGA-----UACUAACCGAGCUAUCUGUA-UCCUCGUCUUGUUU-A---AAGGCU-U-GUGA--UA--UG--CUGUGGU-AGUUG--------GGUUGCAG-AA-GUGCG-AUAUUAAAGUAAAA-GCCAUGAGU-CUUUUAGGCCCAGUGUGUAAA-G----ACACAUUCUGAGUU-AUAA-CUCAGAGGCACAUUU
AL020997.1/124636-124801     CAGC-ACUUGA-----UACUAACCGAGCUGUCUAUA-UCCUAGCCUUGUGUCA---AAGGCU-U-GUGA--UG--UG--UUGUGAU-AGCUG--------GGUUUAAG-AA-GUGCA-AUAUUAAAACAAAA-GCCAUGAGU-CUUUUAAGCCCAGUGUGUAAA-G----AUACACUCUGAGUU-AUAA-CUCAGAGGCACAACU
AJ609484.1/1-166             CAGC-ACUUGA-----UACUAACCGAGCUGUCUAUA-UCCUAGCCUUGUGUCA---AAGGCU-U-GUGA--UG--UG--UUGUGAU-AGCUG--------GGUUUAAG-AA-GUGCA-AUAUUAAAACAAAA-GCCAUGAGU-CUUUUAAGCCCAGUGUGUAAA-G----AUACACUCUGAGUU-AUAA-CUCAGAGGCACAACU
AALT01582549.1/358-522       UAGC-ACUUGA-----UACUAGCCGAGCUAUCUGUG-UCCUAGCCUUGAUG-A---AAGGCU-U-GUGA--UA--CG--AUGUGAU-AGCUG--------GGUUUAAA-AA-GUGCA-AUAUUAAAACAAAA-GCCAUGAGU-CUUUUAAGCCCAGUGUGUAAA-G----AUACACUCUGAGUU-AUAA-CUCACAGGUACAGCU
AAYZ01435462.1/3762-3929     CAGC-ACUUGA-----UACUAACCGAGCUAUCUGUA-UCCUGGUCUUGUGACA---AAGGCU-U-GUGA--UAAGUG--UUGUGAU-AGCUG--------GGUUUAAA-AA-GUGCA-AUAUUAAAACAGAA-GCCAUGAGU-CUUUUAAGCCCAGAGUGUAAA-G----UCACACUCUGAGUU-AUAA-CUCAGAGGCACAACU
ABDC01243130.1/621-456       UAGC-ACUUGA-----UACUAACCAAGCUAUCUAUA-UCUUAGUCUCACGUCA---AAGGUU-C-GUGA--AG--UA--UUGUGAG-AGCUG--------GGUUUAAG-AA-GUGCA-AUAUUAAAACAAAA-GCCAUGAGC-CUUUUAAGCCCAGUGUGUAAA-G----AUACACUCUGAGUU-AUAA-CUCAAAGGCACAACU
AAIY01206707.1/10765-10603   CAGC-ACUUGA-----UACUAACCGAGCUAUCUAUG-UCCUAGCCUAUGUC-A---AAGGCU-U-GUGA--UG--UG--UUGUGAU-CGCUG--------GGUUUAAG-AA-GUGCA-AUAUUAAAACAA---GCCAUGAGU-CUUUUAAGCCCAGGGUGUAAA-G----CCACACUCUGAGUU-AUAA-CUCAAAGGCACAACU
AAPY01115810.1/1223-1386     UGGC-ACUUGA-----UACUCACCGAGCUGUCUAAA-UCCUGGUCUUGUCA-----GAGGCU-U-GUGA--UA--CG--CCGUGAC-AGCUG--------GGUUAAAG-AA-GUGCA-AUAUAAACACGAAA-GCCCUGAGU-CUUCGAAGCCCAGUGUGUGGA-G----ACACGCUCUGAGUU-AUAG-CUCAGAGGCACAGCU
AAFR03060621.1/25521-25687   AAGC-ACUUGA-----UACUAACCAAGCUAUCUGUA-UCCUGAUGCCGCUCCA---GAAGUU-G-G-GA--UG--UAUCUUGUGAU-AGCUG--------GGUUUUAU-AA-GUGCA-AUAUUAAAGUAA---ACCAUGAGU-CUUUUAAGCCCAGCAUGUGGA-GUUGAGCAUGC--UGGGUU-AUAA-CUCAAAGGUACAGCA
AAPN01310042.1/3555-3392     ACGC-ACUCGA-----UACUAACCGAGCCAUCUGGC-CC-UGGCCUCCCUG-C---GGGGCU-CCUGGG--GC--UGCCUUGUGGU-GGCUG--------GGUCUGAG-CA-GUGCA-AAAUUA-GCCAA---GCCGUGAGG-ACUCUGAGCUCAGCGUGGGGA-G----ACACACUCUGGGUU-AUAA-CUCAAAGGCACAGCC
AAVX01044606.1/1599-1436     AUGC-ACCAGA-----UACUAACCUGGCUAUCUAUG-UCAAAGCUCUGUUG-U---AGAUCU-G--AGA--CA-AUC--CUGUGAU-UGUUG--------GGUCCAAA-UG-GUGCA-AGAUUAAACCAA---GCCAUGAGUACAUAUUAGCUCAUCGUGCGCA-G----AAACACUAUGGGUU-AUAA-CUUAGAGGCACAAUG
BX927222.8/124697-124863     AUGC-ACCAGA-----UACUGACCUGUCUGCC-AGC-AGCUCAGUUUUUUU-C---ACACUGAU-GCCU--GC-AUG-ACUGUGGC-UGUCA--------GGUCCAAACCG-GUGCA-ACAAAAAACACAAG-ACCCUGAGA-U--UUAAGCCCUGAGAAAGAG-G---AACUCCUCAGGUGUU-AUAA-CUCAAGGGCACAUCA
ABDC01248697.1/770-617       GAGC-UCUC-------UGGUGUCUUUUCUUA-UAAG-GACACUGAUUCUAUCA---GAUGAG-G-G-UC--CC--UA-----------GCUG--------GGUUUAAG-AA-GUGCA-AUAUUUAAACAAAA-GCCAUGAAC-UUUGUAAGCCCAGUGUGUAAA-G----AUACACUCUGAGUU-AUAA-UUCAGAGGCAUAAUU
ABDC01297581.1/979-831       AAGCUAGAGGC-----UAGACACCUU------CGGU-GGUGGGUAUAGGUUUU---UGUCCC-U-GGUU--GC--UG-----------------------GGUUUGUG-UU-GUGCG-AUAUUAAAACAAAA-GCCAUGAGA-CUUGUAAGCCCAGUGUGUAAA-G----AUACACUCUGAGUU-AUAA-CUCAGAGGCACAGUU
ABDC01122790.1/1637-1789     AAUU-AC--AA-----UACU-ACCAAACA---AUGA-AAUAUUAGGUAGCC-----AUUUAA-A-AGUC--AC--AU--UU------AGCUG--------GGUUUAAG-AA-GUGCA-AUAUUAAAACAAAA-GCCAUGAGA-CUUGUAAGCCCAGUGUGUAAA-G----AUACACUCUGAGUU-AUAA-CUCAGAGGCACAGUU
AALT01405978.1/306-142       UAGC-AUUUGA-----UACUAGCCAAGCGAUCUGUG-UCCUAGCUUUGAUG-A---AAGACU-U-GUGA--UA--UG--AUGUGAU-AGCUG--------GGUUUAAG-AA-GUGCA-AUAUUAAAACAAAA-GCCAUGAUU-CUCUUAAGCCCAGCAUGUAAA-G----ACACACUCUGAGUU-ACAG-CACACAGGCAAAACU
ABDC01311173.1/2314-2479     AUGU-GCUU-----------UAAGAGGUAGAGGAAA-GGG-GAAGUCAAAGCA---GAUGUU---CCCU--AC--UC--CUGCCUU-UGUUAAACACAGCCUUUUAAG-AA-GUGCA-AUAUUAAAACAAAA-GCCAUGAGU-CUUCUAAGCCCAGUGUGUAAA-G----AUACACUCUGAGUU-AUAA-CUCAAAGGCACAAUU
AALT01399912.1/1832-1997     UAGC-CCUUAA-----UGCUAGCUGAGCUCUCUGUA-UUCCAGCCUUGAUG-A---CAGGCU-U-GUGG--UA--GC--GUGUGAG-AGCUG--------AGUUCAAG-AA-GCGUG-AUAUUAAAACAAAA-GCCAUGACU-UUUUGAAACCAGGCUUGCCAA-G----ACACGCUGUGAGUUCACAA-CUCAUCUGCACAAAU
AAKN02026384.1/16353-16190   CAGC-ACUUGA-----UACUAACCGAGCUGUCUAUA-UCCUGGCCUUAUAUCU---AAAGCU-U-GUGA--UA--UG--UUGUGAU-AGUUG--------GGUUGAAG-AA-GUGCA-AUAUUAAAACAAAA-GCCAUGAUC-A--UUAAGUCCAUUGUGUAAA-G----AUGCACUCUGAGUU-AUAA-CUCAAAGACACAACU
AAGV020447408.1/1046-883     CAAC-AUUUGA-----UAAUAACUGAGCUAUCUUUA-GCUUAGCUUUAUGUCC---AAGACU-C-GUGA--UG--UG--UUGUGAU-AGCUG--------GGUGUAAG-AA-CUGCU-CUAUCAACAGAA---GUCAUGAGC-CCUUUAUGCCCAGUAUGUAAA-G----ACACACUCUGAGUU-AUAA-CUCAAAGUCACAACA
AAKN02028641.1/76742-76577   CAGC-ACUUGA-----UACUAACCGAGCUAUCUAUA-UCCUGGCUUUAUAUCU---AAAGCU-U-GUGA--UA--UG--UUGUGAU-AGUUG--------GGUUGAAG-AA-GUGCA-AUAUUAAAGCAAAA-GCCAUGAGA-UCAUUAAGCCCAUUGUGUAAA-G----AUGCACUCUGAGUU-AUAA-CUCAAAGGCACAACU
AAKN02046889.1/258733-258563 AUGU-CCUUAAAGGUCCACGUGUUAAGCUAUCUAUA-UCCUGGCCUUAUAUCU---AAAGCU-U-GUGA--UA--UG--UUGUGAU-AGUUG--------GGUUGAAG-AA-GUGCA-AUAUUAAAGCAAAA-GCCAUGAGA-UCAUUAAGCCCAUUGUGUAAA-G----AUGCACUCUGAGUU-AUAA-CUCAAAGGCACAACU
AAPE02033950.1/32348-32184   CAGC-ACUUGA-----UACUAACCGAGCUAUCUACA-UCCUAGCCUUGUGUCA---GAGGCU-U-GUGA--UG--UG--UUGUGAU-AGCUG--------GGUUUAAG-AA-GUGCA-AUAUUAAAACAAAA-GCCGUGAGU-C-UGUUAGCCCAGUGUGUAAA-G----ACACACUCUGAGUU-AUAA-CUCAGUGGCACAACU
AADN03008214.1/139309-139474 GAGC-ACUUGA-----UACUAACCGAGCUAUCUGUAUCCCAGGUCUCCUCC-A---GAGGUC-U-GAGGUAUA--CU--UUGUGAU-UGCUG--------GGUCUGAA-AA-GUGCA-ACAUUAAAACAA---GCCCUGCAG-UGUUUAAGCUCAGUGUGUAAA-G----GAUGACACUGGGUU-AUAG-CUCAGAGGCACAGAA
AAPE02046649.1/14668-14826   CAGC-ACUUGA-----UACUAACUGAGCUGUCUGUG-UCCUAGCCUUGUGUCG---CAGGCG-U-GCGC--UG--UG--UGCUGAU-AACUA--------GAUUGAAC-AA-GUGCC-GUAGUAAAGCAA-A-ACCCUGAGU-C-UCUAAGCCCAGUGU------G----UAAGACACUGAGUU-AUAA-AUCGGUGGCAUACCU
AAQR03036882.1/538-700       CAGC-AUUUGA-----UACUAACUGAGCUAUCUAUA-UCUUAUCUUUGUGCCA---AAGGCU-U-AUGA--UG--UG--UUGUGAU-AGCU---------GGUGUACG-AA-GUACA-GUAUUAAAAUAA---AGUUAUAAG-UCUCUUAAUCCUGGUUGUAAA-G----AUACACCCUGAGUU-AUAA-CUCAAAGUUACAACU
AAWZ02032466.1/16322-16487   AAGC-ACUUGA-----UACUAACCAAGCCAUCUCUA-CUUUUGUUCUCUUAUAUAGAGUGCA-G-A-AG--UA--CAACUAGUGAUUGGCUG--------GGUCUAAA-AA-GUGCA-ACAUGAAAGUAA---GCCAUGUGA-U---UAAGCUCAAUGUGUGCA-G----GAUCACACUGGGUU-AUAA-CACAGCGGCACAUAC
AAGW02062815.1/2702-2537     CAGC-ACUUGA-----UACUAACCGAGCUAUCUGCA-UCCUGGUCUUGUGUCA---AAGGCU-U-GGGA--UG--UG--UUGUGAU-AGCUG--------GGUUUAAG-AA-GUGCA-AUAUCAAAACAAAA-GCCAUGAGG-CUUUUAAGCCCAGAGUGUAAA-G----ACACACUCUGAGUU-AUAA-CUCAGAGGCACAGCU
AAPE02024871.1/982-1146      CAGC-ACUCGA-----UACUAACCCAGCUAUCUGCA-UCCUAGCCUUGUGCCA---AAGGCU-U-GUGA--UG--UG--CUGUGAU-AACUG--------GGUUGAA--GAAGUGCAAUAUUAAAACAAA--AGCCGUGAGU-C-UUUAAGCCCAGUGUGU-AAAG----ACACACUCUGAGUU-AU-AACUCAGUGGCACAACU
#=GC SS_cons                 ::<<.<<<<--.....----<<<<-<<<<<<<<<<<.<<<-<<<<<<______...>>>>>>.-.>->>..>>..>>..---->>>.>>>>-........>>>>----.>>.>>>>-.--------------.(((,,,,,,.,,,,,,,,,,,,<<<<<<___._....>>>>>><<<<<<<_.___>.>>>>>>)))::::::
#=GC RF                      aaGC.aCuuGA.....UACUaACcaagCuguCcaua.uccUggccuuguuuCa...aaggcc.u.guga..ua..ug..uUGUGac.aGcuG........gGUuuAAg.aa.GuGCA.AUAUUAAAacAAAA.GCCaUGAGu.cuUuUAAGCCCAGuguguaAA.G....acacaCucUGaGUU.AUAA.CuCAgaGGCACAacu
//
# STOCKHOLM 1.0

#=GF AC   RF00554
#=GF ID   SNORA48
#=GF PI   snoACA48
#=GF DE   Small nucleolar RNA SNORA48
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00037
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300463;
#=GF DR   snoopy; Oryctolagus_cuniculus300515;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   9047361
#=GF RT   Mapping to nucleotide resolution of pseudouridine residues in large
#=GF RT   subunit ribosomal RNAs from representative eukaryotes, prokaryotes,
#=GF RT   archaebacteria, mitochondria and chloroplasts.
#=GF RA   Ofengand J, Bakin A
#=GF RL   J Mol Biol. 1997;266:246-268.
#=GF CC   The snoRNA ACA 48 has been identified to guide pseudouridylation of the
#=GF CC   residue U3797 in the 28S rRNA subunit. Its host gene EIF4A1 (eukaryotic
#=GF CC   translation initiation factor 4A1) is shared with U67 and snoRNA mgU6-77
#=GF WK   Small_nucleolar_RNA_SNORA48
#=GF SQ   24


AJ609447.1/1-134           UGUC-CCUGAC-CUGGGUAGAGUGGCAUCUGGU-UGGUGAUGCCCAUCUCAUAUCAGCCAGGGACAAAGCAAC--------UCCUUGUUCAUCCCAGCUUGGCUUUUGAUCCGUGC-CCAUGCCUGGUUCAUGCCUUGGACACAUA-
AC016876.10/19660-19526    UGUC-CCUGAC-CUGGGUAGAGUGGCAUCUGGU-UGGUGAUGCCCAUCUCAUAUCAGCCAGGGACAAAGCAAC--------UCCUUGUUCAUCCCAGCUUGGCUUUUGAUCCGUGC-CCAUGCCUGGUUCAUGCCUUGGACACAUAG
AC141001.6/11830-11964     UUUC-CCUGAC-CUGGGUAGAGUGGCAUCCAGU-UGGUGGUGCCCAUCUCAUAUCAGCCAGGGACAAAGCAAC--------CCCUUGUUCCUCCCAGCUUGGCUUUUCAUCUGUGC-CUAUGCCUGGUUCAUGCCUUGGACACAUUU
BS000596.1/82219-82353     UUUC-CCUGAC-UUGGGUAUAGUGGCAUCUGGU-UGGUGGUGCCCAUCUCAUAUCAGCCAGGGACAAAGCAAC--------CCCUUGUUCCUCUCAGCUUGGAUUUUCAUCUAUGC-CUAUGCCUGGUUCAUGCCUUGGACAUAUUA
AP005270.2/124772-124639   UGCC-UCUGAC-CUGGGUAGAGUGGCAUCUGGC-UG-UGACAUUCAUCUCAUAUCAGCCAGGGACAAAGCAAC--------CCCUUGUUUAUUUCAGCUUGGCCUUUUGUCUGUGC-CCAUGCCUGGUUCAUGCCUUGGACACACUA
AC121758.14/38724-38591    UGUU-CCCGAU-CUGG-UAGAGUAGCAUCUGGU-UGGUGGUGACCAUCUAAUACCAGCCAGGGACAAAGCAAC--------CCCUUGUUUAUCCCAGCUUGGCUUUUGGUCUGUUC-CCAUGCUUGGUUCAUGCCUUGGACACAUGG
AC130462.3/180762-180895   UGUC-CUUGAC-UUGGGUAGAGUGAUGUCUGGU-UGGUGCUGCCUAUCUCAUAUAAGCCAGGGACAAAUCAAU--------GCCUUAUUUAUUCCAGCUUGGCUUUUGGUCUGUGC-CCAUACCUGGUUUAUGCCUUGGACACAUG-
AC073149.5/38723-38590     UG-U-UCUGAC-AUGGGAAGAGUAGCUUCUGGU-UGGUGGAGCCCAUCUCACAUUAGCCAGAGACAAAGCAAC--------ACCUUGUUUAUCCCGGCUUGGCUUUUGGCCUGUGU-CCAUGACUGGUCCAUACCUUGGACACAUGG
AAPY01311076.1/837-971     UGUC-CCUGGC-CUGGGUAGAGUGGCAUCUGGC-AGGUGGUGCCCAUCUCAUAUCAGUCGGGGACAAAGCAAC--------UCCUUGUUCAUCCCAGCUUGGCUUUUGGUCAGUGC-UCUUGCCUGGUUCAUGCCUUGGACACAUGG
ABDC01224935.1/7470-7604   UGUC-CCAGCA-CUGGGUAGAGUGGCAUCUGGU-UAGUGGUGCCCAUCUCAUAUCAGCCAGGGACAAAGCAAC--------CCCUUGUUUAUCCCAGCUUGGCUUCUGGUCUGUGC-CUAUGCCUGGUUCAUGCCUUGGUCACAUGA
AANU01237122.1/783-650     UGUC-CCUGAC-CUGAGUAGAGUGGCAUCUGGU-UGGUGGUGCCCAUCUCAUAUCA-CCAGGGACAAAGUAAC--------CCCUUGUUCAUCCCAGCUUGGCUUCUCAUCUGUGC-CUACGCCUGGUUCAUGCCUUGGACACAUUA
AAFC03014409.1/12314-12180 CGUC-CCUGAC-CUGGGUAGAGUGGCACCUGGU-UGGUGGCGCCUGUCUCAUAUCAGUGAGGGACAAAACAAC--------UCCUUGUUUAUCCCAGCUUGGCUUUUGCUCUGUGC-CCAUGCCUGGUUCAUGCCCUGGACACAUGG
AACN010837001.1/124-258    AGUC-UCUGAC-CUGGGUAGAGUGGCAUCUGGU-UGGUAGUGCCUGCCUCAUAUUAGCCAGGGACAAAGCAAC--------GCCUUGUUUAUCCCAGCUUGGCUUUUGGUCUGUGC-CUGUGCCUAGUUCAUGCCCUGGACAUGUGG
AANG01159480.1/1892-2026   GGUC-CCUGAC-CUGGGUGGAGUGGCACCUGGU-CAGUGGUGCCAGCCUCAUAUCAGUCUGGGGCAAAGCAAU--------UCCUUGUUUAUCCCAGCUUGGCUUUUGGUUUGUGC-CGGUGCCUGGUUCAUGCCCUGGACACAUGG
AANN01359605.1/697-563     AAUU-GUUGUC-CUGGGUAGAGUGGCAUCUAGC-UUGUGGUGUCCAUCUCAUAUUAGCCAGGGAAAAAACAAU--------UCCUUGUUCAUCCCAGCUUGGCCUUUGGUCUGUGC-CCAUGCUUAGUUCCUGCCUUGGAUAUAUUG
AALT01042991.1/2189-2058   UGCC-UCUGUG-CUUGAUAGAGAGGAAUCUGGU-CAGUGGUACCCAUCUC---CUAGCCAGGGACAAAGCAAU--------UUCUUUCUUUUUCCAGAGUGGCUUUUGGUCUGUGC-CCUUACCUGGUUCAUGUGCUAUGAGUAGUA
AAFR03049834.1/1696-1839   CACC-CCUGACACUGGGUAGAGAGACACCUGGU-UGGUGGUGUUCUUCUCAUAUCAGUCAGGGGCAUAGCAACUGUAUAG-UCCAAGUUCAUCCCAGCUUGAUGCUUUGCUUGGUAGUCAUAGCUGGUUCAUGCCCUGGGCACAUAA
AAIY01028273.1/474-331     AACC-CCUGGCUAUGGGCAAAGAGACACCUGAU-UGAUGGUGGUGCUCUUAUAUCAGUCAGGGGCAAAGCAGACUGGCAGCCCUUUGUUCAUCCUAGCUUGAUGCCUGGAUUGUGG-CCAGAGCUGUUUCAUGCCUAGGACACAUUA
AAIY01141103.1/124-267     AGCC-CCUGGCUAUGGGCAAAGAGACACCUGAC-UGGUGGUGGUGCUCUUAUAUCAGUCAGGGGCAAAGCAGACUGGCAGCCCUUUGUUCAUCCUAGCUUGAUGCCUAGAUCGUGG-CCAGAGCUGUUUCAUGCCUAGGGCACAUAA
AAWR02013397.1/68679-68813 UGUC-CCUGAC-CUGGGUAGAGUGGCACCUGGU-UGGUGGUGCCUGUCUCAUAUCAGCCAGGGACAAAGCAGC--------UCCUUGUUCAUCCCAGCUUGGCUUUUGGUCUGUGC-CCAUGCCUGGUUCAUGCCCUGGACACAUGG
AAGV021032459.1/1225-1361  UGCCUCCCUAC-CUGGGUAGAGUGGCAUUUGGUAUGGUGGUGCUCAUCUCAUUUCAUCCAGGGACAGAGCAAC--------CCUUUGUUCAUCCCACCUUCGCUUUUGUAGCAUGC-CUAUGCCUGGUUCAUGCCUAGGACACACGG
AAPE02021711.1/46356-46491 UGUC-CUUUAC-CUGGGUAGAGUGGCACCUGGUUUGGUGAUACUUGUCUUGAAUCAGCCAGGGACAGAAAAAC--------UCCUUGUUUAUCCCAGCUUGGCUUUAGGUCUGUGC-CCAUGCCUGGCUAAUGCCUUGGACCAUGUG
AAGW02049572.1/32343-32212 UGUC-CCUGAC-UGGGGUAGAAUGGCUUUGGGU-UAGUGGUGCCCAU---CUAUCAGCCAGGGACAAAGCAAA--------CCCUUGUUUAUCCCAGCUUGGCUUUUGGUCUGUGC-CCCUGCCUGGGUCAUGCCUGGGACACACGG
AAQR03001358.1/4123-4257   UAUC-CUUGAC-CUGGGCAGAGUGACAUCUGGU-UGGUGGUGCCCAUCUCAUAUCAGCCAGGGGCAAAGCAAC--------CCCUUGCUUAUCCCAGCUUGGCUUCUGGUCUGUGC-CCAUGCUUGGUUCAUGCCUUGGACACAUGG
#=GC SS_cons               <<<<.<<<<--.<<<<---<<<-<<<<<<____.____>>>>>>--->>>--->>>>->>>>>>>>-------........----<<<<<<---------<<<---<<<-<<<-<<.____>>->>>->>>->>>->>>>>>:::::
#=GC RF                    uguC.cCuGaC.cUggGUAgAGuggcacCUGGU.UGGUGgugcccaUCUcAUAucAgcCaGgGacaAAGCAAc........uCCUuGuucaUCCCAGCUUGGcuUUUggucugUgc.CcAUgcCuggUucAUgCCUuggaCacAUua
//
# STOCKHOLM 1.0

#=GF AC   RF00555
#=GF ID   L13_leader
#=GF DE   Ribosomal protein L13 leader
#=GF AU   Barrick JE
#=GF SE   Predicted; Barrick JE, CMFinder
#=GF SS   Predicted; Barrick JE, CMFinder
#=GF GA   44.00
#=GF TC   44.30
#=GF NC   43.40
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   7517053
#=GF RT   Diverse mechanisms for regulating ribosomal protein synthesis in
#=GF RT   Escherichia coli.
#=GF RA   Zengel JM, Lindahl L
#=GF RL   Prog Nucleic Acid Res Mol Biol. 1994;47:331-370.
#=GF CC   This family is a putative r-protein leader autoregulatory structure [1]
#=GF CC   found in B. subtilis and other low-GC Gram-positive bacteria. It is
#=GF CC   located in the 5' untranslated regions of mRNAs encoding the L13-S9
#=GF CC   (rplM-rpsI) ribosomal protein operon.
#=GF WK   Ribosomal_protein_L13_leader
#=GF SQ   26


AE017333.1/151667-151724     GGUAUG--UAUUUCAA------CCCCACGA-UA-AGCCCCGGAA-ACUUA-UUGUG-----U-U------------------------------UUGAA-AUAGAAC
D64126.1/3296-3352           GGUAUG--UAUUUCAA------CCCCACGA-UA-AGCCCCGGAA--CUUA-UUGUG-----UUG-------------------------------UGAA-AUAGAAC
AL766844.1/88806-88887       GGUAU---UGUUUAC-------CCCAUUUGUAA-GGCCCCGGAA--CCUUUCAAAU---ACUCU---CGUGGACCGGAACAUCCACACCU-----GUAA-ACAAAAA
BA000017.4/2360375-2360306   GGUAU---UGUUU-UAUAUCCACCCCACGA-UA-AGCCCCGGAA-ACUUA-UUGUG-----U-U----------------------ACAAGAUAUAUAA-GCAGAAA
CP000024.1/101380-101466     GGUAU---UGUUUAC-------CCCAUUUGAAA-GGCCCCGGAA--CCUUCCAAAUAUACUUUU-CGAUGGGAAGGGACACCCAUCACUC-----GUAA-ACAAAAA
AP008934.1/716592-716659     GGUAU---UGUUUUAUAUCA--CCC-ACGA-UA-AGCCCCGGAA-UCUUA-UUGU-----GUA-----------------------ACAC-GAUAUAGAAGCACGUA
CP000003.1/1658075-1657991   GGUAU---UGUUUAC-------CCCAUUUGAAA-GGCCCCGGAA--CCUUCCAAAU--ACCU-U-CGAUGGGACGGAACACCCAUCACCU----UGUAA-ACAAAUA
CP000056.1/1637088-1637004   GGUAU---UGUUUAC-------CCCAUUUGAAA-GGCCCCGGAA--CCUUCCAAAU--ACCU-U-CGAUGGGAUGGAACACCCAUCACCU----UGUAA-ACAAAUA
AP006716.1/838593-838662     GGUAU---UGUUU-UAUAUCCACCCCAUGA-UA-AGCCCCGGAA-ACUUA-UUGUG-----U-U----------------------ACAAGAUAUAUAA-GCAAAUU
BA000028.3/159658-159716     GGCAUUU-UAUUUCUAA-----ACC-AUGA-UU-AGCCCCGGAA-UCUAA-UUAU-----GU-U-------------------------------AGAAUAUAAAUA
ABAF01000002.1/242115-242198 GGUAU---UGUUUAC-------CCCAUUUGAAA-GGCCCCGGAA--CCUUCCAAAU---ACU-UUUCGAUGGGAAGGAACACCCAUCACC-----GUAA-ACAAAAA
CP000422.1/1375781-1375721   GGUAU---UGUUUACCUC----CAC-AAAA-UA-AGCCCCGGAA-ACUUA-UUAA-----AG-U----------------------UGAG-----UUAA-ACAAAAC
AE017198.1/399439-399493     CGUAU---GUUUGU---------CC-ACGA-UA-GGCCCCGGAA-ACUUA-UUGU-----UU-G----------------------UCAA------ACA-GAAGAAA
CP000029.1/1844853-1844796   UGUUU---UAUAUCA-------CCCCACGA-UA-AGCCCCGGAA-ACUUA-UUGUG-----U-U----------------------ACAA------GAU-AUAUAAG
CR936503.1/1706111-1706054   GGUAU---UGUUUG--------CCCCACGA-UA-GGCCCCGGAA-ACUUA-UUGAG----UG-U----------------------CAAA------CAA-ACACAGA
CP000407.1/1794018-1793940   GGUAU---UGUUUAC-------CCCAUUUGAAA-GGCCCCGGAA--CCUUCCAAAU----AC-C----CGCGGACCGGAACAUCCGCCCA-----GUAA-ACAAAAA
CP000412.1/358213-358264     AGUAU-----GUUUG-------UCC-ACGG-UA-GGCCCCGGAA-ACUUA-UUGU-----AU-U-------------------------------CAAA-CUACGAA
CP000387.1/2039434-2039355   GGUAU---UGUUUAC-------CCCAUUUGUAA-GGCCCCGGAA--CCUUUCAAAU---AAC-U----CGCGGACCGGAACAUCCGCCCU-----GUAA-ACAAAAA
CP000233.1/1478833-1478779   GGUAU---UGUUUGC-------CCC-ACAG-UA-AGCCCCGUUAAUCUUA-UUGU-----AU-G-------------------------------UCAA-ACAUGUA
CP000423.1/2448021-2447965   GGUAU---UGUUUG--------CCCCACGA-UA-AGCCCCGGAA-ACUUA-ACGUG-----U-U----------------------CAAA------CAA-GCACAGA
X63912.1/137-202             GGUAUUGUUUUAUAUCAC----CACCACGA-UA-AGCCCCGGAA-ACUUA-UUGUG-----U-U----------------------ACUA----GAUAU-AGAAGCA
CP000033.3/307686-307736     AGUA----UGUUUG--------UCC-ACGA-UA-GGCCCCGGAA-ACUUA-UUGU-----UU-U--------------------------------CAA-ACUGCAA
AL591983.1/290233-290181     GGUAU---UGUUUG--------CCCCACAA-UA-AGCCCCGGAA-GGUUG-UUGUG-----U-U--------------------------------UAA-ACAAUAA
AM406671.1/2506490-2506412   GGUAU---UGUUUAC-------CCCAUUUU-UGUGGCCCCGGAA-ACCCA-AAAAU---ACUUU---GCAGGACUCUUACACCUGCU--------GUAA-ACAAAUU
AP010655.1/165619-165698     GGUAU---UGUUUGC-------CCCAUUUGAAA-GGCCCCGGAA-CCCUU-CAAAU---AAU-U----UGUGGACCGGAACAUCCACAUU-----GUAA-ACAUAAA
CP002222.1/932094-932148     GGUAU---UGUUUG--------CCCCACGA-UA-AGCCCCGGAAAUCUUA-UUGAG-----UGU--------------------------------CAA-ACAAACA
#=GC SS_cons                 :::::...<<<<<<<.......---<<<<<.<<.<<________._>>>>.>>>>>....--.-......................----.....>>>>.>>>::::
#=GC RF                      GGUAU...UGUUUac.......CCCcacgg.uA.gGCCCCGGAA.aCcUa.cugug....aU.U......................aCaa.....guAA.ACAaAaA
//
# STOCKHOLM 1.0

#=GF AC   RF00556
#=GF ID   L19_leader
#=GF DE   Ribosomal protein L19 leader
#=GF AU   Barrick JE
#=GF SE   Barrick JE, CMFinder
#=GF SS   Predicted; Barrick JE, CMFinder
#=GF GA   36.00
#=GF TC   36.30
#=GF NC   35.80
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   7517053
#=GF RT   Diverse mechanisms for regulating ribosomal protein synthesis in
#=GF RT   Escherichia coli.
#=GF RA   Zengel JM, Lindahl L
#=GF RL   Prog Nucleic Acid Res Mol Biol. 1994;47:331-370.
#=GF CC   This family is a putative r-protein leader autoregulatory structure [1]
#=GF CC   found in B. subtilis and other low-GC Gram-positive bacteria. It is
#=GF CC   located in the 5' untranslated regions of mRNAs encoding ribosomal protein
#=GF CC   L19 (rplS).
#=GF WK   Ribosomal_protein_L19_leader
#=GF SQ   10


BA000043.1/1221406-1221449 ACGAUGUUCCGCUG-CAAUGAAGAG-AUCAUUGGCAUGAACAUCUG
AP006627.1/2412709-2412672 ACGAUAUUCCGCUG-CUGCAG------UGUUGG-CAUGAAUGUCUG
AE017333.1/1781209-1781250 ACGAUGUUCCGCUG-UGCCGGUU--AACUCGCG-CAAGAGCAUCUG
AP008934.1/1590561-1590520 ACUAUGAUCCGCUG-CUAUAUUU---UGUCGAGGCAAGAACAUAGG
AE017355.1/3678229-3678186 ACGAUGUUCCGCUG-UAAUUUAUUUAGACUUUA-UAAGAGCAUCUG
AP006716.1/1732449-1732407 ACUAUGAUCCGCUG-CUAUAUGA--AUGUCUAGGCAAGAACAUAGG
BA000028.3/1580280-1580318 ACGAUGUUCCGCUGUCCCAU-------ACUUGUUCAUGAGCAUUAG
CP000046.1/1265245-1265287 ACUAUGAUCCGCUG-CUAUAUAU--UUGUCGAGGCAAGAACAUAGG
BA000004.3/2598726-2598685 ACGAUGUUCCGCUG-CAGGGGUA---GAAGCUGUCAUGAGCAUCUG
AL009126.3/1675981-1676022 ACGAUGUUCCGCUGUGCCGGUU---UUUGUGGC-CAAGAGCAUCUG
#=GC SS_cons               ::<<<<<<<---<<.<<<<____...___>>>>->>->>>>>>>::
#=GC RF                    ACGAUGuUCCGCUG.ccauguuu...uauauggGCAAGAgCAUCUG
//
# STOCKHOLM 1.0

#=GF AC   RF00557
#=GF ID   L10_leader
#=GF DE   Ribosomal protein L10 leader
#=GF AU   Barrick JE
#=GF SE   Predicted; CMFinder, Barrick JE, Moy RH
#=GF SS   Predicted; CMFinder, Barrick JE, Moy RH
#=GF GA   44.00
#=GF TC   44.10
#=GF NC   43.90
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   7517053
#=GF RT   Diverse mechanisms for regulating ribosomal protein synthesis in
#=GF RT   Escherichia coli.
#=GF RA   Zengel JM, Lindahl L
#=GF RL   Prog Nucleic Acid Res Mol Biol. 1994;47:331-370.
#=GF RN   [2]
#=GF RM   26101249
#=GF RT   Ribosomal protein L10(L12)4 autoregulates expression of the Bacillus
#=GF RT   subtilis rplJL operon by a transcription attenuation mechanism.
#=GF RA   Yakhnin H, Yakhnin AV, Babitzke P
#=GF RL   Nucleic Acids Res. 2015;43:7032-7043.
#=GF RN   [3]
#=GF RM   18247578
#=GF RT   Specific interactions of the L10(L12)4 ribosomal protein complex with
#=GF RT   mRNA, rRNA, and L11.
#=GF RA   Iben JR, Draper DE
#=GF RL   Biochemistry. 2008;47:2721-2731.
#=GF CC   This family is a putative r-protein leader autoregulatory structure [1]
#=GF CC   found in B. subtilis and other low-GC Gram-positive bacteria. It is
#=GF CC   located in the 5' untranslated regions of mRNAs encoding ribosomal
#=GF CC   proteins L10 and L12 (rplJ-rplL). A Rho-independent transcription
#=GF CC   terminator structure that is probably involved in regulation is included
#=GF CC   at the 3' end.
#=GF WK   Ribosomal_protein_L10_leader
#=GF SQ   97


AL766850.1/111629-111496     AGUUUCUGAUGAAACUGACCUAAGACAGUAGGG-GAG--CAGU---GCUCAUAAUA----------------------UUCCUACCGAGGCACA-A-AACGUCAUUAUA-----------------------------------------------------AAA-UAACGUAU-U-GUACUUUCGU-GUCUA-----------GGUU----UAGGUGCGAUUUUUUUG---UGCCUAU
AY026041.1/2528-2666         AUUAUAUUGCUAUUAAUACCUAAGACAGUAACG-GGG--UUAU---UCCCUUAAUU----------------------AUGUUACCGAGGAAAA--GACUUGUUUUAAA------------------------------------------------------AAACAUUUUUUUG-UUUUGUCCUU-GGUUUAG---------UGUU--ACUAGCCAAGGUUUU--UUAUUUUAUUU-
BA000045.2/1717397-1717540   UUUCAACCGAAUCCGCGACCGAAGACAGCAGGG-GCC--UUGA----CGCUUAAUC----------------------AGCCUGCCGAGGUUGG-C-ACAUGGGAAGUACGC-------------------------------------------------CUCC-AGGCUUUU-U-CCCUUUGCGC-CUCGCUUCG-------AAUA-UCGGCGGGGCGAUUUUUUUG---CCCAACC
AE009951.2/547935-547805     AUUGAAUAUAAAUCCAAACCAAAGACCGUAGGG-GGA--GAUA---AUCCUUAAAU----------------------AACCUACCGAGGUUGG-A-AGUUAGAUAUAC---------------------------------------------------------UAACCUCA-A-ACUCAACCCC-UGUU-C----------UUU----GCAAUAGGGGUAUAUUUU---UAGGAAA
BA000039.2/281279-281411     GACAACUCAAGACUAAAACCGAAGACCGCAGGG-GUCUGGCUG---AGACAUAAUC----------------------UUCCUGCCGAGGUUUG-C-GAAGUCCAUCCG------------------------------------------------------UU-GCGAUUGG-G-CGAUCGCCCC-GGCA------------CCCU-----UGCUGGGGUUUUUCUU---UCACUGA
AY026042.1/2271-2409         AUUAUAUUGCUAUUAAUACCUAAGACAGUAACG-GGG--UUAU---UCCCUUAAUU----------------------AUGUUACCGAGGAAAAGA-CUUGUUUUAAAAA--------------------------------------------------------ACAUUUUU-UUGUUUUGUCCU-UGGUUUAGU-------GUUA--CUAGCCAAGGUUUUUUAU----UUUAUUU
AE017355.1/112043-112186     GUGAAUUUAAUUAGUGUACCGUAGACAGUAGGU-GUC--AAUA----GACUUAAU-----------------------UUCCUACCUAGGUGUU-A-AUAUACGAAGCGGAAU------------------------------------------------UUUU-UUCUGUGA-C-UAUAUGCCUC-CAUGUCUAC-------AAGU-UGGGCAUGGAGGUUUUUAGU---GCACUUU
CP000001.1/106306-106449     GUGAAUUUAAUUAGUGUACCGUAGACAGUAGGU-GUC--AAUA----GACUUAAU-----------------------UUCCUACCUAGGUGUU-A-AUAUACGAAGCGGAAU------------------------------------------------UUUU-UUCUGUGA-C-UAUAUGCCUC-CAUGUCUAC-------AAGU-UGGGCAUGGAGGUUUUUAGU---GCACUUU
X53178.1/88-218              UUUAUUUAACUGGCUAUGCCAAAGACCGCAGGA-GCAA-UUAGGG-UUGCUUAAUU----------------------AACCUGCCGAGGUUGA-A-GCCUGAA----------------------------------------------------------------UCAAGA-U-UUGAGUUUGU-UGGGGAU---------UUGC--UUCCUUGACAGCUUUUAAU---GCUCUGC
CP000002.3/118828-118969     AAAAUAUGUCCAUUUAUACCGUAGACAGUAGGU-GCU--GAUA---AGGCUUAAU-----------------------UUCCUACCGAGGUGUA-U-AUAUAUCACAGCUCUAGCGUU-------------------------------------------ACGU-AUGCUUGU-A-UAUACAGCCU-CCAU--G---------UCGA-----AUGGAGGCUUUUUAUA---UGGAACA
CP000029.1/183820-183967     AUACUUGUGAUUAUUUUACCUAAGACAGUAGGA-GUUA-UUAA---UAACUUAAAA------------------CAGUAUCCUACCGAGGCUAA-A-AUUGACUUGAACGUG-------------------------------------------------AUGA-UUAAUGAU-C-UUUCAAGCAC-UUUUUGCC--------GUG--GGUAGAAAGUGCUUUUUUUA---UUGUGAU
AP008231.1/995841-995980     UGUAACUAAAUAGCAUUACCAGAGACAGCAGGU-GUUG-CACCG--CAACUGAAGC----------------------AUCCUGCCGAGGUAGU-C-CCCACAGUCUUC-----------------------------------------------------GUA-CUGUUGAU-C-UAUUUCGCUC-UGGCAAC---------CGAA--UUUGCCGGAGCUUUUUUGU---UGCAAGA
CP000003.1/819678-819814     GUUUUGAUAAAAAACUGACCUAAGACAGCAGGG-GAG--CAUG----CUCAUAAUA----------------------UUCCUGCCGAGGCACA-A-AACGUGAUUAAAG---------------------------------------------------AAAA-UAACGUAU-U-UGUACUUUCG-UGUCUA----------GGUU---UAGGUGCGAUUUUUUUUG---UACCUAG
BA000022.2/924051-923880     UUUAUUUAACUGGCUAUGCCAAAGACCGCAGGA-GCAA-UUAGGG-UUGCUUAAUU----------------------AACCUGCCGAGGUUGA-A-GCCUGAAUCAAGAUUUGAGUUUGUUGGGGAUUUGCUUCCUUGACAG------------------CUUU-UGAUCCUC-U-GCUUCAGCCC-C--GGC----------GAUC---GCCAAGGGGCAUUUUUAU---UGUGUGU
BA000016.3/2766858-2766732   AAAAGUGAAUGAAAGUUUCCGUAGACAGUAGGU-GCU--GAAA----GGCAUAACG----------------UAGAACAACCUACCGAGGGCAA-U-UAU--------------------------------------------------------------------AGUGUA-U-AUAAUAGUCU-UCCUAU----------GUCU---ACGGGAAGACUUUUCUUA---UUAUAUA
D50303.1/141-281             AAUAGAAUAUCAUUUAUACCGUAGACAGUAGGG-GCC--UAAC----CGCUUAAUU----------------------AUCCUACCGAGGUGUA-U-AUUAUCACAGCUAUUACGUU--------------------------------------------ACGU-AUGCUUGU-A-UAUACAGCCU-CCAUG-----------UCU-----CAUGGAGGCUUUUUAUA---UGGAAUC
BA000017.4/601773-601919     CUUAUUGUGAUUAUUUUACCUAAGACAGUAGGA-GUUA-UUUA---UAACUUAAAA-------------------UUUAUCCUGCCGAGGCUAA-A-AUUGACUUGAACGUG-------------------------------------------------AUGA-UCUAUGAU-C-UUUCAAGCAC-UUUUUGCC---------GUG-GGUAGAAAGUGCUUUUUUUA---UUAAUUU
AP006627.1/167869-168007     GGAAAUAGAAUAGUCAUACCGUAGACAGCAGGU-GCU--UCAU----AGCUUAAAU----------------------AUCCUGCCGAGGUGAG-C-GAAUAGAUCUCU------------------------------------------------------UU-UUACUAGA-G-CUUAAAGCCC-UCGUGUGUC-------UUCGUGC-CACGAGGGCUUUUCUAU---GGAAACU
AE017333.1/118632-118773     AAAAUAUGUCCAUUUAUACCGUAGACAGUAGGU-GCU--GAUA---AGGCUUAAU-----------------------UUCCUACCGAGGUGUA-U-AUAUAUCACAGCUCUAGCGUU-------------------------------------------ACGU-AUGCUUGU-A-UAUACAGCCU-CCAU--G---------UCGA-----AUGGAGGCUUUUUAUA---UGGAACA
BA000018.3/577527-577673     CUUAUUGUGAUUAUUUUACCUAAGACAGUAGGA-GUUA-UUUA---UAACUUAAAA-------------------UUUAUCCUGCCGAGGCUAA-A-AUUGACUUGAACGUG-------------------------------------------------AUGA-UCUAUGAU-C-UUUCAAGCAC-UUUUUGCC--------GUG--GGUAGAAAGUGCUUUUUUUA---UUAAUUU
CP000046.1/604895-605041     CUUAUUGUGAUUAUUUUACCUAAGACAGUAGGA-GUUA-UUUA---UAACUUAAAA-------------------UUUAUCCUGCCGAGGCUAA-A-AUUGACUUGAACGUG-------------------------------------------------AUGA-UCUAUGAU-C-UUUCAAGCAC-UUUUUGCC---------GUG-GGUAGAAAGUGCUUUUUUUA---UUAAUUU
AE017334.2/106314-106457     GUGAAUUUAAAUAGUGUACCGUAGACAGUAGGU-GUC--AAUA----GACUUAAU-----------------------UUCCUACCUAGGUGUU-A-AUAUACGAAGCGGAAU------------------------------------------------UUUU-UUCUGUGA-C-UAUAUGCCUC-CAUGUCUAC-------AAGU-UGGGCAUGGAGGUUUUUAGU---GCACUUU
BA000019.2/6323033-6323199   AAAACUAAAUAUGCAAAGCCGGAGACAGCAGGU-GCU---AAC----AGCUUAAAC----------------------ACCCUGCCGAGGUAAA-A-GCUCUCUUACUCAAUGUGACGUGAAAAAUAAUGCGUCGCUUUAGUAA-----------------UCAG-AGUCUUGA-G-ACUAAACCCC-GGCUG-----------AGA-----UAGUCGGGGUUUAUUGU---UGUACCC
AL596164.1/57905-58048       AACAAUCAAAUAUCCUUACCGUAGACAGUUGGC-GCG--UUUA---UCGCUUAAAU---------------------AUGCCACCCGAGGGAUU-U-CUUUUGAAGUGUGCGUC-----------------------------------------------CGCG-CGCAUUUC-A-CAAAAACCUC-UGGCGUC---------UAC---GGUGUCAGAGGUUUUUUGU---UGCUGAU
AL591974.1/66232-66375       AACAAUCAAAUAUCCUUACCGUAGACAGUUGGC-GCG--UUUA---UCGCUUAAAU---------------------UUGCCACCCGAGGGAUU-U-CUUUUGAAGUGUGCGUCC----------------------------------------------GCGU-GCAUUUUA---CAAAAACCUC-UGACGUC---------UAC---GGUGUCAGAGGUUUUUUGU---UGCUGAU
BA000033.2/568089-568235     CUUAUUGUGAUUAUUUUACCUAAGACAGUAGGA-GUUA-UUUA---UAACUUAAAA-------------------UUUAUCCUGCCGAGGCUAA-A-AUUGACUUGAACGUG-------------------------------------------------AUGA-UCUAUGAU-C-UUUCAAGCAC-UUUUUGCC--------GUG--GGUAGAAAGUGCUUUUUUUA---UUAAUUU
AE017225.1/106315-106458     GUGAAUUUAAAUAGUGUACCGUAGACAGUAGGU-GUC--AAUA----GACUUAAU-----------------------UUCCUACCUAGGUGUU-A-AUAUACGAAGCGGAAU------------------------------------------------UUUU-UUCUGUGA-C-UAUAUGCCUC-CAUGUCUAC-------AAGU-UGGGCAUGGAGGUUUUUAGU---GCACUUU
BA000034.2/939069-939204     GUUUUGAUAAAAAACUGACCUAAGACAGCAGGG-GAG--CAUG----CUCAUAAUA----------------------UUCCUGCCGAGGCACA-A-AACGUGAUUAAAGA--------------------------------------------------AAAU-AACGUAUU-U-GUACUUUCGU-GUCUA-----------GGUU----UAGGUGCGAUUUUUUUG---UACCUAG
BA000028.3/126602-126753     UAAAAAGAAUACGUUAUACCGUAGACAGCGGGG-GCU--UUAU----AGCUUAAUA----------------------AUCCUGCCGAGGUGUU-U-AUGAUGAAGGUAGUUUCGCGUUAAAAGCAU----------------------------------UGCU-AUCUGCCA-U-AUAUAAGCUC-UCAUG-----------UCUA----CAUGGGAGCUUUUUACA---UUUCUUA
AJ965256.1/781880-781752     AUUUAUAAUUGAAUAUUUCCUGAGAC-GUGGGU-GCC--GUUU----GGCUUAAUG-------------------CAUUGCCUGCCGAGGAUAC-A-AGACUUU--------------------------------------------------------------UUAAGGGU-U-UUCUAAGUCC-UUGUGC----------UUUG---GCAUAAGGACUUUAUUUU---UUUAGAA
AP006716.1/2471415-2471264   UUUAUUGUGAUUAUUUUACCUAAGACAGUAGGA-GUUA-UAGUA--UAACUUAAAA-------------------AUUAUCCUGCCGAGGCUAA-A-AUUGACUUGAACGUGUGAU---------------------------------------------CAUA-AAAAUGAU-C-UUUCAAGCGC-UUUUUGC---------CGUG-GGUAGAAAGUGCUUUUUUUA---UUGAGAA
AP006840.1/3290489-3290327   GAACUCCAUAGUGAACGACCGUAGACAGCAGGU-GCC--GCAC---AGGCCUAAGU----------GGCGUUUUCGCCAGCCCGCCGAGGUCGG-A-UGUCGCGCCUCCCGGGGCGCGCGCGU--------------------------------------CUGG-GUGCUACA-U-CUCAGACCUC-CGACUG----------GCUA---UGGUCGGAGGUCUUUCUU---CAUGUUC
CP000056.1/797961-798096     GUUUUGAUAAAAAACUGACCUAAGACAGCAGGG-GAG--CAUG----CUCAUAAUA----------------------UUCCUGCCGAGGCACA-A-AACGUGAUUAAAGA--------------------------------------------------AAAU-AACGUAUU-U-GUACUUUCGU-GUCUA-----------GGUU----UAGGUGCGAUUUUUUUG---UACCUAG
CP000023.1/505184-505320     AGGUUUGAAAAAAACUGACCUAAGACAGUUGGG-GAG--CUAG---ACUCGUAAAC----------------------AUCCAACCGAGGCACA-A-AACGUAACUAUUUU--------------------------------------------------UUUG-UGACGUAU-U-GUACUUUCGU-GUCUA-----------GGUU----UAGGUACGGUUUUUUUG---UGCCUAG
CP000017.1/800795-800931     GUUUUGAUAAAAAACUGACCUAAGACAGCAGGG-GAG--CAUG----CUCAUAAUA----------------------UUCCUGCCGAGGCACA-A-AACGUGAUUAAAG---------------------------------------------------AAAA-UAACGUAU-U-UGUACUUUCG-UGUCUA----------GGUU---UAGGUGCGAUUUUUUUUG---UACCUAG
CP000024.1/500366-500502     AGGUUUGAAAAAAACUGACCUAAGACAGUUGGG-GAG--CUAG---ACUCGUAAAC----------------------AUCCAACCGAGGCACA-A-AACGUAACUAUUUU--------------------------------------------------UUUG-UGACGUAU-U-GUACUUUCGU-GUCUA-----------GGUU----UAGGUACGGUUUUUUUG---UGCCUAG
BA000043.1/112875-113039     AAAUGAAUAUCAUUUGUACCGUAGACAGUAGGU-GCCU-GUUUG--AGGCUUAAU-----------------------UUCCUACCGAGGUAUG-U-GGACGAUAGAACAGCGCGCCCUGCGUCGGGGACGAG----------------------------CGGC-GGUGCGUU-G-AACGACACCU-CCAUGUCU--------ACGC--GGCAUGGAGGUUUUUUAUU---GAGCAGA
BA000004.3/151905-152040     AACAGGCGUUGAAACAUACCGUAGACAGUAGGU-GCG--UGAU---UCGCUUAAU-----------------------UUCCUACCGAGGUAAG-C-AAAUAGAUGAAAGU--------------------------------------------------CUUU-UGACUGGA-C-UCGUAUGCCC-UCAUG-----------UCUG----CAUGGGGGCAUUUUCGU---UGGCCUC
AP008934.1/2279664-2279517   GGUUAAUGUAUUAUUUUACCUAAGACAGUAGGA-GUUA-GUAA---UAACUUAAAA------------------UUUGAUCCUACCGAGGCUAA-A-AUUGACUUGAACGUG-------------------------------------------------AAGA-UUUUAGAU-C-UUUCAAGCAC-UUUUUGCC--------GUG--GGUAGAAAGUGUUUUUUUUA---UUGGAUA
ABAD01000005.1/124347-124212 AUACGGUUUAAAAAACUGCCUAAGACAGUAGGG-GAG--CUCG---ACUCAUAAAU----------------------AUCCUACCGAGGACAA-G-ACGUAUCAUGUAA---------------------------------------------------AAAG-AAGCGUAU-U-GUACUUUCGU-GUCUA-----------GGUU----UGGGCGCGUUUUUCUUU---UUGAAAA
AARG01000006.1/28069-28199   AUUAAAUAUAAAUCCAAACCAAAGACCGUAGGG-GGA--GGUA---AUCCUUAAAU----------------------AACCUACCGAGGUUGG-A-AGUUAGAUAUACU--------------------------------------------------------AACCUCAA-A-ACUUAACCCC-UGUCU-----------UUG-----UGAUAGGGGUAUAUUUU---UAGAAAA
CR936503.1/1649972-1649856   AGUUGGUUAUUUAUGCUACCGAAGACU-CAGGU-GCC--AAUA----GGCUUAAU-----------------------AUCCUGCCGAGGAAGA-U-ACGUUGA-----------------------------------------------------------------------A-AUCCCUCUCU-AUGUCU----------UGGU---GGACAUGGAGUUUUUUAU---UUUAUAA
CP000387.1/1124710-1124845   AAUGGUUUGAAAAAACUGCCUAAGACAGUAGGG-GAG--CUCG---ACUCAUAAAG----------------------AUCCUACCGAGGACAA-A-ACGUAUCAUGUAA---------------------------------------------------AAAG-AAGCGUAU-U-GUACUUUCGU-GUCUA-----------GGUU----UGGGCGCGUUUUUCUUU---UGGAAAA
AM263198.1/222190-222333     AACAAUCAAAUAUCCUUACCGUAGACAGUUGGU-GCG--UUUA---CCGCUUAAAU---------------------UUGCCACCCGAGGGAUU-U-CUUUUGAAGUGUACAUU-----------------------------------------------CGUG-UGCAUUCC-A-CAAAAACCUC-UGGCGUC---------UAC---GGUGUCAGAGGUUUUUUGU---UGCUGAU
CP000764.1/112625-112769     GUGAAUUUAAAUAGUGUACCGUAGACAGUAGGU-GCC--AAAU---UGGCUUAAU-----------------------UUCCUACCUAGGUGUU-A-AUAUACGAAACGGAA-------------------------------------------------UUUU-UUUCUGUG-A-CUAUAUGCCU-CCAUGUCUACA-----AGUU--AGCAUGGAGGUUUUUAGUG---CACUUUC
AABF01000026.1/2165-2294     AUUGAAUAUAAAUCCAAACCAAAGACCGUAGGG-GGA--GAUA---AUCCUUAAAU----------------------AACCUACCGAGGUUGG-A-AGUUAGAAUACU---------------------------------------------------------AACCUCAA-C-AUUCAACCCC-UGUCU-----------UUG-----UGAUAGGGGUAUAUUUU---UAGAAAA
CP000721.1/178210-178334     AAAAAGAAAAUAUUUUUUCCGUAGACAGUGGGU-GC----GAA---A-GCGUAAAG----------------UAUAACUGCCCGCCUAGGUAUA-U-AAU--------------------------------------------------------------------AGAUUG-U-AUUAUAGGCC-UUCCAU----------GUCU---GCGGAAGGUCUUUUUUAA---UAAAAGA
CP000027.1/909950-909818     UUUUAUAACUGAAUAUUUCCUGAGAC-GUGGGU-GCC--UUCG----GGCUUAAUA-------------------CGCUGCCUGCUGAGGAUAC-A-AGACUUUUUACUA----------------------------------------------------------AGGGUU-U-UCUUGAGUCC-UUGUGC----------UUUG---GCAUAAGGACUUUAUUUU---UUUAGAA
AAVW01000045.1/38162-37994   AAAACUAAAUAAGCCAAGCCGGAGACAGCAGGA-GCC---AAA----AGCUCAAAU----------------------AUCCUGCCGAGGUUAA-A-GCUCUAAUUGCCUGAAGUGCCACCCAUUGAGGUGUGAGUACUAACGUAU---------------UAUG-AGUUUUCC-U-AUGAAACCCC-GGCUC-----------GGA-----UAGCUGGGGUUAAUUGU---UUUUACA
CP000233.1/1271969-1271850   GUCAAGUUAAUAAUUCUACCUAAGACU-CAGGU-GGC--UAAC----GCCUUAAAU-------------------UUAUGCCUGCCGAGGAGUA-A-ACG-----------------------------------------------------------------------------UAUCUCUCUC-UGUGUCUUG-------GUGU--GGACAUAGAGCUUUUUAUU---UAUAAAA
CP000416.1/619497-619625     AAGUUAUGAAUUGAUCUACCUAAGACU-CAGGU-GAC--CAAAUU-GGUCUUAAUC--------------------ACCGCCUGCCGAGGCAGA-A-GUUUACUUAAAC------------------------------------------------------------------U-UUUGACUCCU-UAUGUCU---------UGGU---GGCAUAGGGAUUUUUUUA---UCCCACC
CP000557.1/110534-110684     AAACGAAUAUCAUUUGUACCGUAGACAGUAGGU-GCCU-UUUC---GGGCUUAAU-----------------------UUCCUACCGAGGUAUG-U-GGACGAUAGACAGCGCGCCAUCGAU---------------------------------------CGCG-GCGCGUUG-A-ACGAUACCUC-CAUGUCU---------ACGU---GGCAUGGGGGUUUUUCAU---UGAACUA
AE016830.1/2629755-2629626   GGUUAAUAAUUAACUGUACCGAAGACAGUAGGU-GAC--GCAA----GUCUUAAU-----------------------UUCCUACCGAGGACAA-U-UGUUGAG-----------------------------------------------------------UU-AUAUACAA-U-UCGGUCCCUC-UAUGUCU---------ACGG--UGGCAUGGAGUUUUGUUGU---UUUACAC
CP000413.1/383411-383534     AUUGUACAGUAAAUUCUACCUAAGACU-CGGGU-GGC--UAACG--UGCCUUAAU-----------------------AUCCCGCCGAGGCCAG-A-AAA------------------------------------------------------------------ACUAAGAG-U-UUUAUAACUC-CAUGUCU---------UUUU---GGCAUGGAGUUUUUAUUU---CGGCUGA
CP000423.1/2272168-2272048   UUGUGAUCAUUCACUCUGCCUAAGACU-CAGGG-GGC--GUAA----GCCUUAAUU----------------------AUCCUGCCGAGGUGGU-A-UCGGAAA-------------------------------------------------------------------CAC-U-AGAUACCUCU-AUGUCU----------UGGU---AGACAUGGAGUUUUUUUA---UAUUUAA
AAOX01000040.1/24511-24648   AAUAAAAUAACAUUUGUACCGUAGACAGCAGGU-GC----GAC---A-GCUUAAU-----------------------UUCCUGCCGAGGUCAU-A-CGAUAGAUUUUCUUUU------------------------------------------------GAAC-GGCUAUUG-U-AUACUUCCUC-CAUGUCU---------GCAA---GAUGUGGAGGUUUUUCUU---UGGACGG
AAXW01000042.1/7373-7246     AAUAAACUUUGGUUUAUACCGAAGACAGCAGGA-GCA--AAAU---UUGCUUAAAU----------------------AUCCUGCCGAGGUUGA-A-GCCUGAA----------------------------------------------------------GCC-AUAAAAUC-C-AGAAAAAUAG-UAGGU-----------UUU-----GCUUGCUAUUUUUAUGA---UGGGAUU
AAYW02000014.1/9896-10033    GUAUCCCCCGAUGAACUGCCGAAGACAGUAGGU-GCC--GGAU----GGCAUAAGU---------------UGAAAAACACCUACCGAGGAAUA-U-AUCGUUAAUAUU-----------------------------------------------------------AUUUUA-A-CUAUAUGCUC-UCUGUCU---------UAUC---GACAGAGAGCUUUUCUUA---UUUUAGC
AAVO02000011.1/72106-72239   GAUUAACAUAGAACGCUGCCGAAGACAGUAGGU-GCC--GAAA----GGCAUAAGG---------------AUUAAAACGCCUACCGAGGACUA-A-GUAUUCUAUUUAA-------------------------------------------------------------GAU-U-ACAGAGACCU-UACUGU----------CAU----GCAGUAAGGUUUUUUUAU---GUUUUGA
AAVP02000004.1/116049-115907 UAUAAAAGUAAUUGACUGCCGAAGACAGCAGGU-GCC--GUUA----GGCAUAAGG---------------UUGAGAACGCCUGCCGAGGAAGA-U-ACGAAUUCUUUU----------------------------------------------------UAAA-AAGAACAU-U-UGUAAACCUC-UGUGUC----------UUCU---GUCGCAGAGGUUUUUUGU---AUAGGCG
CP000232.1/2579880-2579746   UAACUAAAUAUUGGUUUGCCGUAGACAGCAGGU-GCC---AUC----GGCUUAAAU---------------------UUGCCUGCCGAGGUAAA-A-AAGUUAACCGUCU---------------------------------------------------AAAC-GGUUAGUC-A-GCUAUUGCCC-UCGCC-----------UGUC----UGCGGGGGCUUUAACUU---UUUAAGC
CP000412.1/1435213-1435084   GAUAAAGUAAAUUUCUAACCUAAGAC-GUGGGU-GGC--GUAA---AGCCUCAAUA--------------------CAAUCCCGCCGAGGCCAG-A-AGA--------------------------------------------------------------UAA-UGAAGAUU-G-UUAAACUCUC-CAUGUCU---------UUCU--UGGCAUGGAGGUUUUUAGG---CCUUGUA
AAXB02000001.1/13689-13836   UAACCUACUAAAGGACUGCCGAAGACAGUAGGU-GCUU-GAAA---GAGCGUAAGA------ACACAUUUUAUGCGGACGCCUACCGAGGAAAG-A-UCGAUACUAAAG-----------------------------------------------------------UAUGAC-U-UAUCAACCUC-UAUGUC----------UUUG---GAUAUAGAGGUUUUUUUA---CAUUUAU
AP008230.1/521594-521729     GAAUUGAAUAGCCUUCCACUGUAGACAGCAGGU-GCU--CUUA---GAGCUUAAUA----------------------UCCCUGCCGAGGUUGG-A-AAGAUAGCCUUAAG--------------------------------------------------UUAU-AUUGGGCC-U-UCUUAACCUC-UGCAG-----------UCA-----AAGCGGGGGUUUUUCUA---UUAGUGU
AAML04000002.1/58774-58902   UAAAAAAGAAUAGAUUUGCCGUAGAUAGUGGGU-GC----GAA---A-GCUUAAU-----------------------AUCCCGCCGAGGUUUU-A-GAUAAAU----------------------------------------------------------------UGAGAU-U-ACUAAAGCUU-UUGAUGUCUAC-----UUUU-GGCAACAAAAGCUUUUUAUA---AUGUUGC
CP000414.1/228096-228214     GUAAUUGAAUCCAUUUUGCCUAAGACU-CAGGU-GAU--GCUUG--CAUCUUAAU-----------------------AUCCUGCCGAGGAAGU-U-UAAAAAA--------------------------------------------------------------------------ACUUUUCCC-GUGUGUC---------UUCU--AGCGCACGGGAUUUCUUUU---GCAAAAU
AE015927.1/2761842-2761705   AGAAUUAAAGAAAAUAUACCGUAGACAGUAGGU-GCA---UUU----UGCAUAACG--------------GAUUAUCCAACCUACCGAGGGUUC-C-AAUAUAU-----------------------------------------------------------UA-CUUUUAGA-G-AGUAUUGGUU-UCUCCAU---------GUCU--ACGGAGGAACCUUUAAUUU---UUUAUAA
CP000393.1/409369-409180     AAAUUUCAAAUUCAAGAGCUAAAGACAGCAGGU-GCU---AAU----AGCUUAAU-----------------------UUUCUGCCGAGGUUCA-A-GAAUUAAUUAUUCAAAGAUAACAAUAGGGAGUUUUAUUAAAGACCCUAAUUUAAUUGCUUGAUUUGGA-UUUGAUAA-U-UCUUAGCCCU-GGCAGAU---------AGCUAAAUCUGCUAGGGUUUUUGAU---UUGGGUA
AADV02000089.1/397-567       GUGAAACUUUGGUUUAUUCCGAAGACAGCAGGG-GCA---ACU----UGCUUAAAU----------------------AUCCUGCCGAGGUUGA-A-GCCUGAAGAAAAUGACAUCUGAGUAAAUGGUAGGUUUUGCUAACUAUUUCU-------------CUGA-UUAAAUUG-G-ACUUCAGCCC-CGGCA-----------AAU-----UGUUAGGGGUUUAUUUU---UUUCCCA
CP000382.1/221728-221863     AUUAAAUAAGAUAAUACUCCGCAGACAGUAGGU-GC----GAA---A-GCAUAACG---------------GGGAACCAACCUACCGAGGAUUU-A-GAUAUUC---------------------------------------------------------GGUA-UUUUGGAU-A-UAUUAAGCCU-CUUCGU----------GUCU---GGGAAGAGGCUUUUAGUU---UUUGUUA
CP000422.1/1462150-1462024   UUAUAACUGAAUAAUUUACCUAAGACU-CAGGU-GGC--CAUGUUUGGCCUUAAUA-------------------UAUUGCCUGCCGAGGAACG-U-AUG-----------------------------------------------------------------------------AAACUAUUCG-UGUCUCAGAGUC----UUUC--UGGGGUACGAAUUUUUUUA---UGGUUCA
CP000727.1/3594486-3594357   GUAAAAAUGAAUAUAUCUCCGUAGACAGUGGGU-GU----UUU-----ACAUAAUU-----------AGUGAAAACUAAACCUACCUAGGAGUC-C-GAU--------------------------------------------------------------------AUAAAG-U-AUAUUGGGUC-UCUCUGU---------CUUA---CGGAGAGACCUUUAUUAU---UAUAAAU
CP000673.1/199491-199619     GUUGAAUAAGUAUAUUUUCCUUAGACAAUAGGU-GCA---AAA----UGCGUAACG--------------GUAAAACCAACCUAUCCAGGAUUC-C-AAUAUAA-------------------------------------------------------------------AGU-A-AAGGUGGUCU-CUCUGU----------GUCU---AUAGGGAGGCUUUUGAUU---UUUAUAU
AAYG02000011.1/287148-287284 UAAUAUAGCAAUUGACUGCCGAAGACAGCAGGU-GCC--GUAA----GGCAUAAGG----------------AGAAAACGCCUGCCGAGGAAGU-A-UGCGAAUUCAAUU----------------------------------------------------------UCGGAU-U-UGUAAACCUC-UGUGUC----------UUUG---GAUACAGAGGUUUUUAUU---UUGGCAG
CP000262.1/901322-901458     GUUUUGAUAAAAAACUGACCUAAGACAGCAGGG-GAG--CAUG----CUCAUAAUA----------------------UUCCUGCCGAGGCACA-A-AACGUGAUUAAAG---------------------------------------------------AGAA-UAACGUAU-U-UGUACUUUCG-UGUCUA----------GGUU---UAGGUGCGAUUUUUUUGU---ACCUAGC
CP000724.1/4592463-4592332   UUAAAAGUGAAUAUUUUGCCGCAGAAAGUAGGU-GC----GUU---A-GCUUAAAU----------------------AUCCUACCGAGGCUUU-G-GAUAAAU-------------------------------------------------------------------UUA-U-CAAAGAUCUC-UUUCUGUGUGACGUUAUUUA-CGCAGAGAGGGAUCUUUUUC---UGUAACG
AAVL02000037.1/2345-2494     GUGGUUUAAUACCAAUUGCCGAAGACAGUAGGU-GCC--UACG---GGGAUUUAUCCUUGACAAGGGCGUAAACUUAGUACCUACCGAGGAAUG-A-AGUUAUA--------------------------------------------------------------AGUAUGAC-U-GACAAUACCU-CUCUGU----------UUCG---GCAGAGAGGUUUUUUAUA---CUAUUGU
AE001437.1/3284087-3283956   AUUAAAUAUGUAAAUACUCCGUAGAAAGUAGGU-GC----GUG---A-GCGUAACG---------------GAUAACCAACCUACCGAGGAUUC-C-AAUAUAU----------------------------------------------------------------AUGAAA-G-UAUAUGGUCU-CUUCGUA---------CGUC--UGCGGAGGGGCCUUUAGUU---UAUUAUA
CP000239.1/1784776-1784931   CCACAGUCGAAUAGCGAGCCGAAGACAGCAGGG-GCC---AAG---GGGCUUAAU-----------------------GUCCUGCCGAGGUUUG-A-GCGGAGUGCUAAGGGAUCCCGUUGUGGACUGCU-------------------------------AGGU-UACGCUUG-U-CUCAAUGCGU-CUCGGC----------UAUG---GCUGAGGCGCAUUCUCUU---UGGCGGC
CP000240.1/1266102-1266261   CCCCAGUCGAAUAGCAAGCCGAAGACAGCAGGU-GCC--CGCG----GGCUUAAU-----------------------GUCCUGCCGAGGUUUG-A-GCGAAGUUCAAAGGGAUCCCUUCUUGGAUCGCUUUUG---------------------------AUGG-UGCGCUUA-U-CUCCAUGCGU-CUCGGC----------CACG---GCUGGGGCGCAUUCUGUU---UGGUAGA
CP000686.1/4176795-4176941   AGAUAUAUAUGCUAAGCGCCGCAGACAGCGGGU-GC----GUU---U-GCUUAAUG-------------GCUGCGUGCCGCCCGCCGAGGCAGC-U-UCCCAGGUCGAU-----------------------------------------------------------GCGACU-G-UAAGUUCGCG-GGUUGCUGCGUCUGU-GCGC--GGCAACCCGCGUUUUUAUC---UUCCAGA
ABCC02000059.1/1539-1392     UACCACAGUAUUGAAUGCCCUGAGACAGCAGGU-ACC--GUAA----GGUGUAAGG----------------CGAAAACGCCUGCCGAGGAACA-U-ACAAAACUCUGAUUAUU-----------------------------------------------UAUG-AUGAGAUU-U-UGCGAACCUC-UCUGUCU---------UUAC---GGCGGAGAGGUUUUUUGU---CCGGUCU
AE009948.1/1312489-1312356   AGUUUCUGAUGAAACUGACCUAAGACAGUAGGG-GAG--CAGU---GCUCAUAAUA----------------------UUCCUACCGAGGCACA-A-AACGUCAUUAUA-----------------------------------------------------AAA-UAACGUAU-U-GUACUUUCGU-GUCUA-----------GGUU----UAGGUGCGAUUUUUUUG---UGCUUAU
CP000033.3/347743-347864     AGUUAAUUGUAAAUUCUACCUAAGACU-CGGGU-GGC--AUGA---CGCCUCAAA-----------------------AUCCCGCCGAGGCCAG-A-AGAUAAU----------------------------------------------------------------GAAGAU-U-UUUAUGCUCC-AUGUC-----------UUUC----GGCAUGGAGUUUUUGCU---UUAAAAG
CP000885.1/4540490-4540346   CUUAAUUCUCACAAACUGCCGAAGACAGUAGGU-GCC--GUAA---UGGCAUAAGG----------------UGAGACCGCCUACCGAGGAAUA-G-AUUAAUCAAGCU----------------------------------------------------AAUA-UGCUAGAC-U-AAUAAUCUGU-CUCCUGU---------UUUC--GCAGGAGGCAGUUUUUUUU---AUUCCGU
ABAW02000017.1/196215-196085 AUCAAUGUUAUCAAUAUACCAUAGACAGUAACG-GC----AUA---A-GCUUAAUC----------------------AUGUUACCGAGGUUAG-A-GAUACGAAUAUA-----------------------------------------------------------AACGUA-C-UUUACACUCG-UAUGCUG---------UCUA-UUAGUAUGCGAGUGUUUUUA---UACUCUU
AP007281.1/360808-360926     UGAUUAAAUAUGACUCUGCCUAAGACU-CAGGU-GGC--GAAA----GCCUUAAUC-------------------GAAUGCCUGCCGAGGAAGA-A-AUGAAAG--------------------------------------------------------------------------UUCCUUCUC-UAUGUC----------UGCG---GUCAUAGGGAUUUUUUUA---UAAAUCC
AE009949.1/871512-871647     GUUUUGAUAAAAAACUGACCUAAGACAGCAGGG-GAG--CAUG----CUCAUAAUA----------------------UUCCUGCCGAGGCACA-A-AACGUGAUUAAAGA--------------------------------------------------AAAU-AACGUAUU-U-GUACUUUCGU-GUCUA-----------GGUU----UAGGUGCGAUUUUUUUG---UACCUAG
ABAX03000024.1/112177-112310 UUACUACAAGUAUCACUGCCGAAGACAGCAGGC-GCC--GUAU----GGCGUAACG----------------UAGAACGGCCUGCCGAGGAUGA-U-GAU--------------------------------------------------------------UAG-UAUUGAGC-U-AAUUGUGCCC-UUUGUCU---------UUGC--GGACAAAGGGCUUUUCUUA---UUCUUAU
AE008691.1/2189485-2189360   AAUUGAAUAUGAGAAAGACCGUAGACAGUGGGUUGUGC-GUACU--GCACGUAAA------------------------UCCCACCGAGGUUUU-U-UUAAGAU----------------------------------------------------------------AAAUUC-C-CUCUGGGGAU-CCUCGU----------GUCU---ACG-GGAUCCUUUUUAAA---UUUUUAA
CP000875.1/173523-173680     UCGGUACAAGAAAUACCACCGUAGACAGCAGGU-GCG--UUCG----CGCUUAAUG-----------AUGCCAAGCAUCGCCCGCCGAGGUAGC-U-GAUAGAUUAUUGCAAUCUUCCA-------------------------------------------CAC-AU-UUGUG-U-GCUACUGCCUCUGCGUGU---------CGUU--ACACUCAGGGCUUUUUUAU---UUGCCUG
CP000408.1/962606-962472     GAGGUUUGAAAAAACUGACCUAAGACAGUAGGG-GAG--CUGG---ACUCAUAAAC----------------------AUCCUACCGAGGCACA-A-AACGAUUAUUGAG----------------------------------------------------AUA-AACGUAUU-U-GUACUUUCGU-GUCUA-----------GGUU----UAGGUGCGAUUUUUUUG---UGCCUAG
AE005176.1/1302080-1301955   CGGUUCUAAAAGAACUGACCGAAGACAGUAGGG-GAC--GAAA----GUCAUAAAC----------------------UUCCUACCGAGGACAA-A-UAUCAAA----------------------------------------------------------------AUGAUA-A-UUGAACUCUC-UAUGUCU---------UUU---GUGUGUAGAGAUUUUUUAU---UUCUACA
CP000410.1/1215970-1215835   UACGGUUUAAAAAAACUGCCUAAGACAGUAGGG-GAG--CUCG---ACUCAUAAAU----------------------AUCCUGCCGAGGACAA-G-ACGUAUCAUGUAA---------------------------------------------------AAAG-AAGCGUAU-U-GUACUUUCGU-GUCUA-----------GGUU----UGGGCGCGUUUUUCUUU---UUGAAAA
AARN04000005.1/118564-118421 AACAAUCAAAUAUCCUUACCGUAGACAGUUGGU-GCG--UUUA---UCGCUUAAAU---------------------UUGCCACCCGAGGGAUU-U-CUUUUGAAGUGUGCGUC-----------------------------------------------CGCG-UGCAUUUU-A-CAAAAACCUC-UGACGUC---------UAC---GGUGUCAGAGGUUUUUGUU---GCUGAUC
AGMP01000043.1/38354-38485   AAGGUUUUGAAAAACUGACCUAAGACAGCAGGG-GAG--CGUG----CUCAUAAUA----------------------UUCCUGCCGAGGCACA-A-AACGUAAACUGA------------------------------------------------------AA-AAACGUAU-U-GUACUUUCGU-GUCUG-----------GGUU----UGGGUGCGAUUUUUUAU---UGCAUUC
AL935263.2/588900-589013     GGUUAAGUAAUAUCUCUACCUAAGACU-CAGGC-GGCU-UAAC---GGCCUUAAUC----------------------UACCUGCCGAGGACAU-U---------------------------------------------------------------------------------GUUUUUUCUC-UAUGUCU---------UGGU--GGACAUAGGGAUUUUUUUA---UAAAUCC
#=GC SS_cons                 :::::::::::::::::::::::::::<<<<<<.<<<..____..._>>>------......................->>>>>>---------.-.-------------...................................................----.--------.-.------<<<<.<<<<<<_.........____...>>>>>>>>>>::::::::...:::::::
#=GC RF                      auaaauuaAaaaaaauUaCCGAAGACAGcAGGu.GCc..uaaa...ugGCUUAAuu......................auCCUgCCGAGGuaua.A.aauuuaaUuaaag...................................................uuua.uuuuuuau.U.uuuaaacCcc.ugcugcu.........uuuu...gcagcaggGgUUUUUuUU...Uuuauua
//
# STOCKHOLM 1.0

#=GF AC   RF00558
#=GF ID   L20_leader
#=GF DE   Ribosomal protein L20 leader
#=GF AU   Barrick JE
#=GF SE   Predicted; CMFinder, Barrick JE, Moy RH
#=GF SS   Predicted; CMFinder, Barrick JE, Moy RH
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   7517053
#=GF RT   Diverse mechanisms for regulating ribosomal protein synthesis in
#=GF RT   Escherichia coli.
#=GF RA   Zengel JM, Lindahl L
#=GF RL   Prog Nucleic Acid Res Mol Biol. 1994;47:331-370.
#=GF CC   This family is a putative r-protein leader autoregulatory structure [1]
#=GF CC   found in B. subtilis and other low-GC Gram-positive bacteria. It is
#=GF CC   located in the 5' untranslated regions of mRNAs encoding initiation factor
#=GF CC   3 followed by ribosomal proteins L35 and L20 (infC-rpmI-rplT). A
#=GF CC   Rho-independent transcription terminator structure that is probably
#=GF CC   involved in regulation is included at the 3' end.
#=GF WK   Ribosomal_protein_L20_leader
#=GF SQ   43


AL766850.1/192353-192228   UGAGAAAAGCAGAAGUG-AGA-ACUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGCC--------CAACAUGUCAAGAUUCCAUCUAGGAAGAUUAUAUGUGCGGGCUUGA--UUUA---UCAAGUCCGCUUUCGUUUUUCUCU
CP000046.1/1757722-1757597 CGAACCAAGUAGAAGC--ACCCGCUUCUCACCUGUAGCGAC-GC--AUAAA--GC-AGUUGGCAGGU-----------UAAUCACAUUACACAUAACUGUGUAUAAGGAAGAGCGGGUAU----UUU------AUACCUGCUCUUCCUUUUUGCU
AE017334.2/4381448-4381328 UGGAACAAGUAGAAGC--ACCCGCUUCUCACCUGAUG-GAC-GC--AUUC---GC-AGUUUACAGGU--------------AAAUGUAUUUCUUACUUAAGAUUUUACAAGUGUGGGUGU----CGU------AUGCCCGCACUUUUUUUGUCGG
AJ249400.1/1495-1633       ACAAGAAAGAAGAAGCA-ACCCGCUUCUCGCCUCG---UUA-AC--AUGGA-UGU--UUU--CAGGCAAAAAAUUCAAACUUUCGUCGCGUUACUUGCGCGACUUUGAAUGUGCGGGAUUGC--UGAA-AAGCAG-CCCGUUUUUUUAUGGCCUC
AL596170.1/124519-124381   ACAAGAAAGAAGAAGCA-ACCCGCUUCUCGCCUCGUU--AACAC--G-AAC--GU-UUU---CAGGCAAAAAAUUCAAACUUUCGUCGCGUAACUUACGCGAUUUUGAAUGUGCGGGAUUGC--UGAA-AAGCAG-CCCGUUUUUUUAUGGCCUC
Z75208.1/12391-12521       AAUCACAAGCAGAAGC--ACCCGCUUCUCACCUGAUU-GAC-AC--AUGCA-UGU-AGUUGGCAGGU---------UGACCGUACAUUUUUAUUGAUACAGAUGUUCGUAGUGUGGGUGUU---UUAU----AAUGCCCACACUUUUUGUUUGCC
CP000002.3/2920264-2920132 AUCAACAAGCAGAAGC--ACCCGCUUCUCACCUGAUU-GAC-AC--AUUCU-UGU-AGUUGGCAGGUUAAA-----CGUACAUUUCUUAUUUUUCUAUGCAAUGUUCGCAGUGUGGGUGU----UUCG-----AUGCCCGCACUUUUUGUUUGCC
CP000029.1/1279603-1279480 CGAACCAAGUAGAAGC--ACCCGCUUCUCACCUGUGGCGAC-GC---UGAA--GC-AGUUGGCAGGU-----------CAAUCAUGUUACACAUUUAUUGUGUCUAAGAAGAGCGGGUA-----GUUA------UACUCGCUCUUCUUUUUGCUU
BA000034.2/1304115-1303992 UGAGAAAAGCAGAAGUG-AGA-GCUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCUAACAUGUCAAAUUCCUAUGGAAUAUUAUAUGUGCGGGCUUGA--UUUA---UCAAGUCCGCUUUCGUUUUUCUCU
BA000028.3/2183366-2183237 UAAGACAAGUAGAAGC--ACCCGCUUCUCACCUGAUU-GAC-ACCGAUUAU-GGU-AGUUGACUGGU------------UCCAACCUUUUAUUUAAAUGUAUUUGGAGAUGUGUGGGUGCG---UGUA----UGUACCGACACUUUUUUAAUUGC
AP006716.1/1282175-1282302 CGUACCAAGUAGAAAC--ACCCGUUUCUCACCUGUAGCGAC-GC--AUCAA--GC-AGUUGGCAGGU---------UAAUCAUGUCACACAUUAUAUGUGUAUGAGAGAAGAGCGGGCAU----UCU------AUGCUCGCUCUUUUUGCUUGGA
CP000023.1/997417-997295   UGAGAAAAGCAGAAGUG-AGA-ACUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCAACAUGUCAAAUCCUUAAAGGGAUAUUAUGUGUGCGGGCUUGU--AUAU----CAAGUCCGCUUUGUUUUUCUCUA
BA000016.3/2175416-2175297 GAUGUCAAGAAGAAAC--AGCCGUUUCUCACCUU-----ACAGCU-AUUAA-UGCUAGU---UUGGU---------CAUGAAUUUUAUUACAUUUGAUUUUGGUAAUAGAGGACGGCU------UAA--------AACCGUCCUUUUUUAUUUAU
X16188.1/136-267           UAACGAAAGCAGAAGC--GCCCGCUUCUCACCUGACC-GAC-GCU-AAGAA-GGC-UGUUGGCAGGUU--------GUUACGGUUCGCCAACUUUUUGUCCGAACGUCGUGCGCGGGUGCU---UUG-----UGCAUCCGCGCUUUUUCGUUGAG
X98458.1/1734-1872         ACAAGAAAGAAGAAGCA-ACCCGCUUCUCGCCUCGUU--AACAC--G-AAC--GU-UUU---CAGGCAAAAAAUUCAAACUUUCGUCGCGUACGUUACGCGAUUUUGAAUGUGCGGGAUUGC--UGAA-AAGCAG-CCCGUUUUUUUAUGGCCUC
AJ249399.1/1780-1918       ACAAGAAAGAAGAAGCA-ACCCGCUUCUCGCCUCGUU--AACAC--G-AAC--GU-UUU---CAGGCAAAAAAUUCAAACUUUCGUCGCGUAACUUACGCGAUUUUGAAUGUGCGGGAUUGCUGGAAA---GCAG-CCCGUUUUUUUAUGGCCUC
BA000043.1/2738703-2738570 UAACAAAAGCAGAAGCA-CCCCGCUUCUCACCUGACC-GAC-GCC-A-AGACGGC-UGUUGGCAGGUUG-------UUACGGUUCGUCAAUGCGAGUGUAAGGACGUACUGCGCGGGUGCU---UUG-----UGCAUCUGCGCUUUUUUUUGGGC
BA000004.3/3254375-3254248 CAAAGCAAGAAGGAGC--GCCCGCUUCUCACCUGAUC-GAC-GC--ACAGC--GC-AGUUGACAGGUC--------UACAUGUAAUAAUGUCUCAUGAUGACAAACAUGAGUGUGGGCGU----CGU------AUGCCCACACUCUUUUGUGUUG
AP006627.1/2820731-2820612 UAGAGCAAGAAGAAGC--GCCCGCUUCUCACCUGU---ACG-AC--AUUG---GU--UGC--CAGGU----------UAGAAACCGUCAGUUUGUUAAAAUGCUGAUUAAGUGUGGGUGC----CGU------GCGUCCACACUUUUUUCACGUU
AP008934.1/1132989-1133118 CGAACCAAGUAGAAGC--UCCCGCUUCUCACCUGUUGCGAC-GCU-AUAG---GC-AGUUGGCAGGU---------CUUAUAUAUACAUGUUAAUUUCAUGUGUAGAGAAGAGCGGGUAUA---UUA-----UAUACUCGCUCUUUUUGCUUGGG
AE015927.1/2410544-2410434 AACGUUAAGAAGAAACU-AGCCGUUUCUCACCUU----ACA-GC----AUA--GC-UAGU--AAGGU--------------UAUGAAAUCAGUUUAUUAUUUUGAUUAGAGGACGGCA------UUU---------GCCGUCUUUUUUUAUUUUA
CP000413.1/1403447-1403335 GAGAACAAGAAGAAGC--UCCCGCUUCUCGCCUA----AGU-UA--AUAU---UA--CCU-CUGGGC-------------------UGAUCGAUAAUAUCUGUUGAUUAAAAGCGGGCGUU---AAC-----UUUGCCCGCUUUUUUCUUGUCCU
ABDQ01000026.1/22638-22759 UUCGUUAAGAAGAAACUAAGCUGUUUCUCACCUU-----AC-AGC-AUUG---CU-AGU---AAGGUUAUA-----CAUUCAUUUUGAUUUGUUUUGUGUGAAUUGUAUAGGACGGCU------UAA--------AGCCGUCCUUUUUAUUUUGU
CP000382.1/964054-964181   UUCGUUAAGAAGAAACUAAGCUGUUUCUCACCUU----ACA-GC----ACA--GC-UAGU--AAGGUUAUACAUUCAUUUCAAGUUAUUUUAUUUUAUGUGAAUUGUAUAGGACGGCU------UAGA-------AGCCGUCCUUUUUAUUUUGU
AAOX01000069.1/1488-1614   GAGGAAAAGAAGAAGC--ACCCGCUUCUCACCUGGCU-GAC-GC--AAAGA--GC-AGUUGGCAGGUU--------UUACUGAAACAGCUUUUAACUUGUCGUUUCGUAAGUGUGGGUG-----AUUU------CAUCCGCACUUUUUUAUAUGU
CP000557.1/2749782-2749651 UAACGAAAGCAGAAGC--ACCCGCUUCUCACCUGACC-GAC-GCU-UAAGU-GGC-UGUUGGCAGGUU--------GUUACGGUUCGUCAAUGGUUUAUUCGAACAUCGUGCGCGGGUGCC---UUG-----UGCAUCCGCGCUUUUUUGUUAGG
CP000408.1/1212611-1212483 UGAGAAAAGCAGAAGUG-AGA-ACUUCUCGCCUU----GCG-AC--UAAC---GU--UGU--CUGGCUCUAC----GGAUUAAGAUUUCUUCGGAAAGAAUAAUGGUGUAGUGCGGACUUGU--UUAG----CAAGUCCGUUUCGUUUUUCUCGA
CR954253.1/1295361-1295250 GAGAACAAGAAGAAGC--CCCCGCUUCUCGCCU-----AAG-UU--AUUU---AA-CCUC--UGGGC-----------------AAAUCGAUAUUUUCUGUUGAUUUUAAAGGCGGGUGC----UAU------AUGCCCGCCUUUUUCUUGUCCU
CP000764.1/3327066-3326946 UAGAGCAAGUAGAAGC--ACCCGCUUCUCACCUGAUU-GAC-GC--AUUC---GC-AGUUAACAGGU--------------AAAUGUAUUUCUUACGUAAGAUAGUACAAGUGUGGGUGU----CGU------AUGCCCGCACUUUUUUUGUUCG
AAJS01000128.1/8-133       AUGAGAAAGCAGAAGU--GUGAACUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGCC--------CAACAUGUCAAGAUUCCAUCUAGGAAGAUUAUAUGUGCGGGCUUGA--UUUA---UCAAGUCCGCUUUCGUUUUUCUCU
CP000387.1/1505158-1505028 UGAGAAAAGCAGAAGUG-AGA-GCUUCUCGCCUU----GCG-AC--UAAC---GU--UGU--CUGGCUCUACA---GGAUUCAGUUUCAGUAAUGAAAUAUUAUCGUGUAGUGCGGGUUUGC--GUUA---GCAGGUCCGCACUUGUUUUUCUCU
CP000903.1/4407198-4407078 UUUGACAAGUAGAAGC--ACCCGCUUCUCACCUGAUG-GAC-GC--AUUC---GC-AGUUAGCAGGU--------------AAAUGUAUUUCUUACUAAAGAUAUUACAAGUGUGGGUGC----CGU------GUGCCCGCACUUUUUUUGUUCG
AARL02000322.1/352-214     ACAAGAAAGAAGAAGCA-ACCCGCUUCUCGCCUCGUU-AAC-AC--GAAC---GU--UUU--CAGGCAAAAAAUUCAAACUUUCGUCGCGUAAUUUACGCGAUUUUGAAUGUGCGGGAUUGC--UGAA-AAGCAG-CCCGUUUUUUUUAUGGCCU
CP000923.1/2066839-2066717 AGCAAUAAGUAGAAGC--GCCCGCUUCUCACCUU-----UC-AC--CGAGG--GU-GCA---AAGGUUU-------UUUCAAAAGUAGUUAUUGUUGUUUUGUUAUAAAGAAGCGGGUAU----UUCU-----AUAUCCGCUUUUAUUUUUUCAU
CP000410.1/862701-862832   UGAGAAAAGCAGAAGUG-AGA-GCUUCUCGCCUU----GUG-AC--AUUAA--GU--UGC--CUGGCCCUA-----CGGAUGAAAAGUUUCGAAGAAACGCUAUCAUAACGUGCGGGCUUGUA-UAUU--UACGAGUCCGCUAUUGUUUUUCUCU
CP000924.1/818075-818197   GCGAAUAAGUAGAAGC--GCCCGCUUCUCACCUU----UCA-CC----GAA--GG--UGC-AAAGGUUU-------CUUCAAAAGUAUUUAUCUUUGUUUUAUUGUAAAGAAGCGGGUAU----UUCU-----AUAUCCGCUUUUAUUUUUUCAU
AE004092.1/661402-661525   UGAGAAAAGUAGAAGUG-AGA-GCUUCUCGCCUU----GCG-AC--UUAG---GU--UGU--CUGGC----------CCUAACAUGUCAAAUUCCUAUGGAAUAUUAUGUGUGCGGGCUUGA--UUUA---UCAAGUCCGCUUUCGUUUUUCUCU
AE005176.1/1912587-1912462 GUUGAAAAGCAGAAGC--ACCCGCUUCUCGCCUUA----GA-GG--UUAUA--GC--CC---UGGGCAA-------ACGAAUGGAAUUAUUCAAAAACGAAUGUUUUCAUGAGCGGGGCGAG--AUUG----UCGUUCCGCUUUUGUUUUUCUUU
AE008691.1/1644338-1644220 GCGAAUAAGUAGAAGC--GCCCGCUUCUCACCUU-----UC-GCC-AUAG--GGC-AGA---AAGGU---------UUCUUCUUGAAAGUCAAAAGUAAUAUGGGCGAAGAAGCGGGUG-----GAU-------UAUCCGCUUUUAUUUUUUGAU
CP000033.3/1530046-1529934 GAGAACAAGAAGAAGC--ACCCGCUUCUCGCCUA-----AG-UU--AAGUA--AA-CCU--CUAGGC-------------------UGAUCGAUAAUUUCUGUUGAUUAAAGGCGGGGUGA---UAC-----UUAUCCCGCCUUUUUCUUGUCCU
AM263198.1/1836450-1836313 ACAAGAAAGAAGAAGCA-ACCCGCUUCUCGCCUCGUU-AAC-AC--GAAC---GU--UUU--CAGGCAAAAAAUUCAAACUUUCGUCGCGUAACUUACGCGAUUUUGAAUGUGCGGGAUUGC--U-GAAAAGCAG-CCCGUUUUUUU-AUGGCCU
AGMO01000014.1/41079-41205 UGAGAAAAGCAGAAGUG-AGA-ACUUCUCGCCUU----GCG-AC--UUAAA--GU--UGU--CUGGCC--------CAACAUGUUAAAGUUCCUGUGGAAUAUUAUGUGUAUACGGGCUUGA--UUUG---UCAGGUCCGUUUUUGUUUUUCUCA
CP001617.1/1367745-1367868 GAAAAAAAGCAGAAGC--ACCCGCUUCUCGCCUUG---GUG-AC--C-AGA--GU--CAU--CGGGCA--------GAUGAACGAUGAAUUGAUUCCCAUUAACGGGGUUGAGCGGGCGUA---CUA-----UGCGCCCGCUCUUUUUGUGAAUU
#=GC SS_cons               ::::::::::<<<<<<..____>>>>>>,<<<---...<<<.<<.._____..>>.->>>..-->>>-........-----------------------------------<<<<<<<<<<...____....>>>>>>>>>>:::::::::::::
#=GC RF                    uaaaaaAAGaAGAAGC..ACCCGCUUCUCgCCUua...gac.gC..aUaaA..Gc.aguu..CAGGcu........aaauuauauuuuuuuuuuuuauguuauuuuuaaaGgGCGGgcgug...Uuua....cacgcCCGCcuUUUUUUUuuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00559
#=GF ID   L21_leader
#=GF DE   Ribosomal protein L21 leader
#=GF AU   Barrick JE
#=GF AU   Moy RH
#=GF SE   Predicted; CMFinder, Barrick JE, Moy RH
#=GF SS   Predicted; CMFinder, Barrick JE, Moy RH
#=GF GA   36.00
#=GF TC   36.10
#=GF NC   35.70
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   7517053
#=GF RT   Diverse mechanisms for regulating ribosomal protein synthesis in
#=GF RT   Escherichia coli.
#=GF RA   Zengel JM, Lindahl L
#=GF RL   Prog Nucleic Acid Res Mol Biol. 1994;47:331-370.
#=GF CC   This family is a putative r-protein leader autoregulatory structure [1]
#=GF CC   found in B. subtilis and other low-GC Gram-positive bacteria. It is
#=GF CC   located in the 5' untranslated regions of mRNAs encoding ribosomal protein
#=GF CC   L21, a protein of unknown function, and ribosomal protein L27
#=GF CC   (rplU-ysxB-rpmA).
#=GF WK   Ribosomal_protein_L21_leader
#=GF SQ   38


AL596169.1/30615-30537       ACCAAGCUACAA-CCGCACA--GAGCUGGGUU-----------------AA-GUAUUUACC-----------------------UUGU------------------------GUAAGUC-CCCU--GUAA-UGGCGAGUCUUAGUAUAUGA
CP000002.3/2809177-2809103   CCCGUGCUACAA-CCGCUCA--GCACAGGCGUU----------------AA-GUGCU-U-------------------------UCUU---------------------------AGCC-CCCU--GUGACUGGCGAGUCUUAGUUUAUUA
X59528.1/1870-1945           CCAUUGCUACAA-CCGCUCA--GUACAGGUGUU----------------AA-GAGCU-U-------------------------UUAC---------------------------AGCC-CCCU-GGUAUCUGGCGAGUCUUAGUCUAAUA
BA000034.2/1289235-1289161   CAUCCUGUGCAA-CCGCGCG--AAAAUCGUUAUC---------------AA-GUAGAC--------------------------CAA---------------------------GUCUC-ACGA--UUCC-AGGCGAGUCUUCACAGAGGG
BA000004.3/3129240-3129168   CAAUGACUACAA-CCGCACA--GACUAGGUUUAUA--------------AAUG-G---A-------------------------UCUC-----------------------------CCUACCU--AGAA-UGGCGAGUCUGAGUAUAUGA
AL766850.1/177942-177863     CAUCCUGUGCAA-CCGCGCG--AAAAUCGUUAGAUU-------------AA-GUAGGGC-------------------------AAG--------------------------GCUCUC-ACGA--UUUAUAGGCGAGUCUUCACAGAGGG
AP006716.1/1307326-1307403   AGCUACAUACAA-CCGCUCA--AAUAUAGGUUU----------------AA-G-AACAUU------------------------UUUU------------------------UAUG-UCACCUA--UAUA-UGGCGUGACUUAUUAAUAUA
CP000023.1/400958-401034     CGUCCUGUGCAA-CCGCACG--ACUACUGUUUUUGU-------------AA-GUGGG-U-------------------------UCGU---------------------------CCCC-GCAG--UACU-AGGCGAGUCUUCACAGAGGG
AP006627.1/2726276-2726204   AUGAACUUACAA-CCGCGCA--GAUUAGGCGUUAA--------------AAUG-G---C-------------------------AUGU-----------------------------CCUGCCU--AUGA-UGGCGAGUCUGAUGUUAUGA
CP000029.1/1248763-1248687   AGCUACAUACAA-CCGCUCGC-AUACAGGUUG-----------------AA-GUACAAU-------------------------CAU--------------------------AUUGUC-ACCU--GUAUAUGGCGUGACUUAUUAUAUAG
AE017355.1/4241632-4241555   UAUAUGCUACAA-CCGCACA--AGACAGGUUCCCU--------------AA-A-GGCA--------------------------UGUA--------------------------UGUCU-ACCU-CGUUUUUGGCGAGUCUUAGUAAUUAA
CP000001.1/4296486-4296409   UAUAUGCUACAA-CCGCACA--AGACAGGUUCCCU--------------AA-A-GGCA--------------------------UUUA--------------------------UGUCU-ACCU-CGUUUUUGGCGAGUCUUAGUAAUUAA
CP000046.1/1733601-1733474   AGCUACAUACAA-CCGCUCAA-AUAUAGGUUC-----------------AA-GAACAUUUUUAAUGAAGAAAGCGAUUUUCCCACAGAGUGCAAACGCUUGACUCAAUAACGAAAUGUC-ACCU--AUGUAUGGCGUGACUUAUUAUACAG
BA000043.1/2624432-2624353   CCCGCACUACAA-CCGCUCA--GCGCGGGCGAUG---------------AA-GCGCUCCG------------------------UCU--------------------------UGGGCC-GCCUUGGCGC-UGGCGAGUCUGAGUCCAUGA
AAZZ01000006.1/107295-107382 GAUCCUGUGCAA-CCGCACG--AACAUCGUUGCUUGAUUAUUCAAGUUUAA-GUGG--U-------------------------UUGU----------------------------CCC-ACGA--UGCU-AGGCGAGUCUUCACAAAAAA
CP000233.1/981312-981236     UCACAUCUGCAA-CCGCACG--UUUUAAGUUU-----------------AA-GUAUCUCU------------------------UUAG--------------------------AGGUC-ACUA--CAUUACGGCGAGUCUAAGUAUUUUA
CP000557.1/2644089-2644009   CCCGUACUACAACCCGCUCA--GCGCGGGUUGUG---------------AA-GUGUUCCG------------------------GUUG--------------------------GAACC-GCCUUGACGC-UGGCGAGUCUGAGUUCAUAA
AAAK03000096.1/1617-1693     CCACAGCUACAA-CCGCUCA--GAACAAGUAAU----------------AA-GCACAGCA------------------------UAUG--------------------------CUGUC-ACUU--CGGA-UGGCGAGUCUAAGUAUAUCA
AP008934.1/1159200-1159273   AGCUACAUACAA-CCGCUCGG-AUUCAGGUUA-----------------AA-GUACA---------------------------UGUA---------------------------UGUC-ACCU--GAGUUUGGCGUGACUUAAAUUAUUA
CP000416.1/1005945-1005868   CCACAGCUGCAA-CCGCUCG--GAACGAGUUU-----------------AA-GUUUUCCGC-----------------------UUGC--------------------------GGAGC-ACUU--GUCUUCGGCGAGUCUAAGUCUAAAA
AE016830.1/931220-931295     CCACAGCUACAA-CCGCACA--GAACAAGUUUUU---------------AA-GCAUGA--------------------------GUAA--------------------------UCAUC-ACUU--GGGA-UGGCGAGUCUAAGUCUAGAA
AAOX01000015.1/104841-104922 ACCAAGCUACAA-CCGCUCA--GAGCAGGUAUUC---------------AA-GUUUUUGCUUU---------------------UUGC--------------------------AAAAC-GCCU--GCAAUUGGCGAGUCUUAGUCUAUAA
CP000413.1/725693-725773     UCACAUCUGCAA-CCGCACGUUUAUGGGGUAAG----------------AA-GAGAAUUAAC----------------------GUUA--------------------------AUUCC-ACCU--CAUA-CGGCGAGUCUAAGUAUUUUU
CP000387.1/1077610-1077697   AUUCCUGUGCAA-CCGCACG--AUCAUCGUUGCUCACUCUGUGAGAUAGAA-GUGG--U-------------------------UCGU----------------------------CCC-ACGA--UGCU-AGGCGAGUCUUCACAAAAUC
CP000764.1/3208747-3208670   UAUAUACUACAA-CCGCACA--AUGCAGGUGUAC---------------AA-AUGACAG-------------------------UCUA--------------------------UGUCU-ACCU-CGUGU-UGGCGAGUCUUAGUAAUUAU
CP000422.1/820542-820609     UCCACGCUACAA-CCGCACA--AAGUGAGUUUUA---------------AA-G-C------------------------------AUA-----------------------------GC-ACUU--ACUU-UGGCGAGUCUUAGAAUUAAG
ABCF01000098.1/6599-6680     CCCGUGCUACAA-CCGCUCA--AAUCAGGCAAU----------------AA-GCUUUUGUUGAA--------------------UAAC--------------------------AAAAC-GCCU--GUACUUGGCGAGUCUGAGUUUAUAA
BA000028.3/2073644-2073564   GUAAAACAGCAU-UCGUUGU--UUUUUGCUUAACAUUUU----------UA-AAAUCCG-------------------------UAUU--------------------------GGAUU-ACCU--AAAU-G-GCGAGUCUGAGUUGAAUG
AE009948.1/1379794-1379715   CAUCCUGUGCAA-CCGCGCG--AAAAUCGUUAGAUU-------------AA-GUAGAGC-------------------------AAG--------------------------GCUCUC-ACGA--UUUAUAGGCGAGUCUUCACAGAGGG
CP000407.1/761580-761668     CAUCCUGUGCAA-CCGCACG--AAUGCCGUUCUU---------------UC-GUUGAGAG------------------------UAGA---------------GUAAGUGGUUCGUCCC-ACGG--UACU-AGGCGAGUCUUCACAUCAAA
AE005176.1/1090513-1090586   CAUAAAGUGCAA-CCGCACGA-AGUUUCGUAUU----------------AA-GUGGC---------------------------AUAC---------------------------GCCC-ACG---AACAAAGGCGAGUCUAACAGUCGCU
AE017262.2/1556852-1556775   ACCAAGCUACAA-CCGCACA--GAGCUGGGUC-----------------AA-GUAUUUACUUC---------------------GUGU--------------------------AAAUC-CCCU--GUGA-UGGCGAGUCUUAG-UAUAUG
AF222894.1/255903-255828     AUGCAGCUUCAA-CCACUCA--AAAAAGGUUUAAAAAUA----------AAUGUUA----------------------------AUU-----------------------------UAU-ACCU--UAU--UGGUGAGUCUAAGUUGAUAA
AL591979.1/167146-167068     ACCAAGCUACAA-CCGCACA--GAGCUGGGUC-----------------AA-GUAUUUACUUC---------------------GUGU--------------------------AAAUC-CCCU--GUGA-UGGCGAGUCUUAGUAUAUGA
CP001184.1/243276-243198     AUGCAGCUUCAA-CCACUCA--AAAAAGGUUUCU---------------AA-A-UAAAUUUUU---------------------AAAA--------------------------UUUAU-ACCU--UAU--UGGUGAGUCUAAGUUGAUAA
CP000033.3/1314633-1314554   CCACAUCUGCAA-CCGCACG--GCUAGGGUUAG----------------AA-GACUUCUU------------------------GAGU------------------------AAGAAGC-ACCC--CAGUUCGGCGAGUCUAAGUAUUUUU
AL935263.2/1450556-1450629   CUACAGCUACAA-CCGCACG--GAUUGAGUCUU----------------AA-GAUCA---------------------------GCAA---------------------------UGGC-ACUU--ACAUUCGGCGAGUCUAAGUGAUUUA
AP010655.1/1229729-1229654   CAUCCUGUGCAA-CCGCACG--AAAAUCGCUUUU---------------AA-GCAGCUU-------------------------UCGU--------------------------AGCUC-ACGA--UUU--AGGCGAGUCUUCACGGAGGA
#=GC SS_cons                 ::::::::::::.:<<<-<<..<<<<<<<<----...............--.<-<<<<__........................____..........................>>>>>.>>>>..>>>>.>>>>>:::::::::::::::
#=GC RF                      aaccaucUACAA.CCGCuCa..aaauaGGuUuuu...............AA.Gugcauuu........................uaga..........................augcC.aCCu..auuu.uGGCGAGUCUUAgUAuAuaa
//
# STOCKHOLM 1.0

#=GF AC   RF00560
#=GF ID   SNORA17
#=GF PI   snoACA17
#=GF DE   Small nucleolar RNA SNORA17
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   29.00
#=GF TC   29.10
#=GF NC   28.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00029
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300412;
#=GF DR   snoopy; Homo_sapiens300290;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   9047361
#=GF RT   Mapping to nucleotide resolution of pseudouridine residues in large
#=GF RT   subunit ribosomal RNAs from representative eukaryotes, prokaryotes,
#=GF RT   archaebacteria, mitochondria and chloroplasts.
#=GF RA   Ofengand J, Bakin A
#=GF RL   J Mol Biol. 1997;266:246-268.
#=GF CC   snoRNA ACA 17 belongs to the H/ACA family of snoRNAs and is predicted to
#=GF CC   guide pseudouridylation of the 28S rRNA at positions U4659 and U4598. It
#=GF CC   shares the same host gene together with ACA43. NB This family has a high
#=GF CC   threshold value to exclude a large number of closely related sequences
#=GF CC   that do not appear to have conserved H and ACA boxes, and may be
#=GF CC   pseudogenes.
#=GF WK   Small_nucleolar_RNA_SNORA17
#=GF SQ   53


AL929577.9/115568-115437   UCUGCCCCUACAGGCGUUGCAGGUGUGGCUGC---UGUGUCACAUGUGUGUCAGUAGGUGGCAGAGAGGA--GAGAGGCUAUGUCUACGCUCAGUGUUC--UGAC--------CU-GUGAACA--UCUGAAUGAUUAGUAGCCUAACAUU
AC102195.14/77372-77241    CCUGCCCCUAGAGGCCUUGCAGGUGUGGCUGC---UGUGUCCCAUGUGGGUCAAUAGGUGGCAGAGAGGA--GAAAGGCUAUGUCUUCGGUCUGUGUUC--UGAC--------CU-AGGAACA--UCUGAAUGAUUAGUAACCUAACAUC
AC124719.3/60776-60645     ACUGCCCCUAGAGGCUUUGCAGGUGUGGCCGC---UGUGUCAUAUGUGUGUCAAUAGGUGGCAGGGAGGA--GAGUGACUAUGUCUAUGCUCAGUGUUC--UGAC--------CC-AUGAACA--UCAGAGUGAUUAGCAGCCUAACAUC
AL773512.6/105824-105955   UCUGCCUCUAGAGGCAUUGUAUGUGUGGCUGC---UGUGUCUCAUGUGUGUCAGUAGGUGGCAGAGAGGA--GACAGGCUAUGCCUACUCUCAGUGUAC--UUAU--------GU-AUAAACA--UCUGAAUGUUUUGAAGUCUAACAUU
AL592546.7/54124-53993     ACUGCCCCUGGAGGCAUUGCAGAUGUGGCUGC---UGUGUCACAUUUGUGUCAUUAGGUAGCAGCGAUUA--GAGAGGCUAUGUCUAUGCUCAGCGUUC--UGUC--------CC-AUGAACA--UUUGAAUGUUUAAUAGUCUGACUCU
AC044804.4/242661-242530   UUUGUCCCUAGAGGAGUUGCAGGUGUGGCUGC---UGUGUCACAUGGGUGUCAGUAGGUGGCAGAGAGGA--GAGAGGUUAUGUCUAUGCUCAGUGUUC--UGAU--------CU-GUGAACC--UCUGAAUGAUAGGUAGUUUAACAUA
AC147162.2/137638-137507   ACUGCCCCUAGAGGCAUUGCAGAUAUGGCGGC---UGUGUCACAUGUGUGCCAGUAGGUGGCAGAGAGGA--GAAAGGUUAUGUCUAUGCUCAAUGUUC--UGAU--------CU-AUGGACA--UCUGAAUAAUUAGUAGUCUAACAAU
AC160983.2/170827-170958   CCUUCCCCUAGAGGCUUUGCAGGUGUGGCUGC---UCUGUCACAUGUGUGUCAGUAGGUGGCAGAGAGUA--GAGAAGUUAUGUCUAUGCUCAGUGUUU--UGAC--------CU-GUGAAUA--UCUGAAUGAUUAGUAGCCUAACAAU
AC116747.10/162742-162873  CCUGCCCCUACCAGCAUUGCAGUUGUGGCUGC---UCUGUUGCAUAUGUGUCAGCAGGUGGCAGAGAGGA--GAGAGGCUGUGUCUAUGCUCAGUGUCC--UGAC--------CU-GUGAACA--UCUGAAUGAUUAGUAACCUCACAUU
AC124517.4/119239-119370   ACUGCCCCUAGAGGCAUUGCAGAUAUGGCGGC---UGUGUCACAUGUGUGCCAGUAGGUGGCAGAGAGGA--GAAAGGUUAUGUCUAUGCUCAAUGUUC--UGAU--------CU-AUGGACA--UCUGAAUAAUUAGUAGUCUAACAAU
AC125262.9/82422-82292     CCUGCCCCUAGAAGCACUGUACGUGUGGCUGC---UGUGUCACCGGUGUGUCAGUAGGUGGCAGAGAGGA--GACAGGCUGUGCCUAAGCUCAGUGUUC--UGAC--------CU-UUGAACA--GCUGAAUG-AUGGUAGCCUGACAUU
AC120020.9/24687-24556     CCUGCCCCUAGAGGCGUUGCAGGUGUGGCUGC---UGUGUCACAUGUGUGUCAGUAGGUGGCAGAGAGGA--AAGAGGCUAUGUCUACGCUCAGUGUUC--UGAU--------CU-GUGAACA--UCUGAAUGAUUAGUAGCCAAACAUU
AC156631.2/55855-55724     CCUGCUCCUAGAGGCAUUGUAGGUGUGGCUGC---UGUGUCACAUGCACGUCGGUAGGUGGCAGAGAGGA--GAGAGGCUACAUCUACACUCAGUGUUC--UGGC--------CU-GUGAAUG--UCUGCAUGAUUAGUAGCCUAAUAUU
AK090585.1/512-643         ACUGCCCCUAGAGGCGUUGCAGCUGUGGCUGC---CGUGUCACAUCUGUGUCAUUAGGUGGCAGAGAUUA--GAGAGGCUAUGUCUACGCUCAGCGUUC--UGCC--------CC-GUGAACG--UUUGAAUGUUUGAUAGUCUCACACU
AC154284.1/100289-100158   CCUGCCCCUAGAGGCGUUGCAGGUGUGGCUGC---UGUGUCACAUGUGUGUCAGUAGGUGGCAGAGAGGA--AAGAGGCUAUGUCUACGCUCAGUGUUC--UGAU--------CU-GUGAACA--UCUGAAUGAUUAGUAGCCAAACAUU
BX936366.8/102933-103064   CCUGCCCCUAGAGGUGUUUUAGGUGUGGCUGC---AGUGUCAUAUGUGUGUCAGUAGGUGGCAGAGAGGA--GAGAGGCUGUGCCUAUGCUCACUGUUC--AGAC--------CA-UUGAACA--UUUGAAUGAUCAGUAGCCUAACAUU
AC159299.2/205614-205483   UUUGUCCCUAGAGGAGUUGCAGGUGUGGCUGC---UGUGUCACAUGGGUGUCAGUAGGUGGCAGAGAGGA--GAGAGGUUAUGUCUAUGCUCAGUGUUC--UGAU--------CU-GUGAACC--UCUGAAUGAUAGGUAGUUUAACAUA
AL355987.31/5364-5233      ACUGCCCCUAGAGGCGUUGCAGCUGUGGCUGC---CGUGUCACAUCUGUGUCAUUAGGUGGCAGAGAUUA--GAGAGGCUAUGUCUACGCUCAGCGUUC--UGCC--------CC-GUGAACG--UUUGAAUGUUUGAUAGUCUCACACU
AC138288.13/66444-66575    CCUUCCCCUAGAGGCUUUGCAGGUGUGGCUGC---UCUGUCACAUGUGUGUCAGUAGGUGGCAGAGAGUA--GAGAAGUUAUGUCUAUGCUCAGUGUUU--UGAC--------CU-GUGAAUA--UCUGAAUGAUUAGUAGCCUAACAAU
AJ609434.1/1-132           ACUGCCCCUAGAGGCGUUGCAGCUGUGGCUGC---CGUGUCACAUCUGUGUCAUUAGGUGGCAGAGAUUA--GAGAGGCUAUGUCUACGCUCAGCGUUC--UGCC--------CC-GUGAACG--UUUGAAUGUUUGAUAGUCUCACACU
BC042667.1/532-663         ACUGCCCCUAGAGGCGUUGCAGCUGUGGCUGC---CGUGUCACAUCUGUGUCAUUAAGUGGCAGAGAUUA--GAGAGGCUAUGUCUACGCUCAGCGUUC--UGCC--------CC-GUGAACG--UUUGAAUGUUUGAUAGUCUCACACU
AC078860.19/16828-16700    AUUUUAC---AUAGCGCUGCAGAUGUGGCUGC---UGUGUCACAUUUGUGUUAUUAGGUGGCAGAGAGAA--GAGAGGCUAUGUCUAUGCUCAGUGUUC--UGCC--------CC-AUGAACA--UUUGAAUGUUUAAUAGUCAGACACU
AC131332.12/15646-15777    ACUGCCCCUAGAGGCUUUGCAGGUGUGGCCGC---UGUGUCAUAUGUGUGUCAAUAGGUGGCAGGGAGGA--GAGUGACUAUGUCUAUGCUCAGUGUUC--UGAC--------CC-AUGAACA--UCAGAGUGAUUAGCAGCCUAACAUC
AC160393.2/162851-162720   CUUGCUCCUAAAGGCAUUGCAGGUGUGACUGC---UGGGUCACCUGUACGUCAGUGGGUGGCAGAGUAGA--GAGAGGCUAUGUCUAUACUCAGUGUUC--UGAC--------CU-UCGAGCA--UCUGAAUGAUUAGUAGCCUAACACU
AC132335.3/147117-147248   ACUUUCCCUAGAGACACUGCAGAUGUGGCUGC---UGUGUCACCUGUGCAUCGGUAGGAGGCAGAGAGGA--GAGAGGCUAUGUCUACACUCAGGGUUC--UGCC--------CU-GUGAGUC--UCUGAAUGAUUGGCAGCCUAACACU
AC159274.2/136463-136332   ACUGCCCCUAGAGGUUUUGCAGGUGUGGCUGC---UGUGUCACAUGUGCAUCAGUAGGAGGCAGAGAGAA--GAGAGGCUAUGCCUGUGCUCAGUGUUC--UGAC--------CU-GUGAACA--ACUGAAUCAUUAGUAGCCUAACAGU
AL663042.5/46926-46793     CCUGCCCCUAGAGGUGUUGCAUGUAUGGCUGC---UGUGUCAUGUGUGCAUCAGUAGGUGGCAGAGAGGA--GAGAGUCUAUGUUCAGGCUCAGUGUUC--UGGC--------CU-AUGGACUUCUCUGAAUGAUUAGUGGCCUGACACA
AC155939.6/82555-82424     ACUGCACCUAGAGGUGUUGCAGGUGUGGCUGC---UAUGUCACAUGUGUGUCAGUAGGUGGCAGAGAAGA--GAAAGGCUAUGUUUACACUCAGUGUUC--UGAC--------CC-GCAUACA--UCUGAAUGAUAGGCAGCCUAACACU
AL671963.9/45705-45574     CCUGCCUCUGGAAGCAUUGCAGAUGUGACUGC---UGUGUCACAUGUGUGUCAGUAGGUGGCAGAGAGGA--GAGAGGCUAUGUCUACGCUCAGUGUUC--UAAC--------CG-AUGGGCA--UCUGAAUGGUUAUUAGCCUAACGUG
AC158351.4/104624-104493   CCUGCCCCUACCAGCAUUGCAGUUGUGGCUGC---UCUGUUGCAUAUGUGUCAGCAGGUGGCAGAGAGGA--GAGAGGCUGUGUCUAUGCUCAGUGUCC--UGAC--------CU-GUGAACA--UCUGAAUGAUUAGUAACCUCACAUU
AC122025.3/62844-62713     ACUGCCCCUAGAGGUUUUGCAGGUGUGGCUGC---UGUGUCACAUGUGCAUCAGUAGGAGGCAGAGAGAA--GAGAGGCUAUGCCUGUGCUCAGUGUUC--UGAC--------CU-GUGAACA--ACUGAAUCAUUAGUAGCCUAACAGU
AC122847.4/112382-112513   UUUGUCCCUAGAGGAGUUGCAGGUGUGGCUGC---UGUGUCACAUGGGUGUCAGUAGGUGGCAGAGAGGA--GAGAGGUUAUGUCUAUGCUCAGUGUUC--UGAU--------CU-GUGAACC--UCUGAAUGAUAGGUAGUUUAACAUA
AC139319.6/13901-14032     UUUGCCUCUAGAGGUAUUGCAGGUAUGGCUGC---UGUGUCACAUGUGCAUCAAGAGGUGGCAGAGGGGA--GAAAGGCUAUGUCUACACUCAGUGUUC--UAAC--------AU-GUGAACA--UCUGAAUGGUCAGUAGUCUAACAUU
AL732311.13/50067-49936    CCUGCUCCUAGAGGCGUUGCAGGUGUGGCUGC---UGUGUCACAUGUGCGUCAGUAGGUGGCAGAGAGAA--AAGAGGCUAUGUCUACGCUCAGUGUUC--UGCC--------CU-GUGAACG--UCUGAAUGAUUUGUAGCCUGACAAC
AL928643.6/100932-101063   CCUGCCCCUAGAGGUGUUUUAGGUGUGGCUGC---AGUGUCAUAUGUGUGUCAGUAGGUGGCAGAGAGGA--GAGAGGCUGUGCCUAUGCUCACUGUUC--AGAC--------CA-UUGAACA--UUUGAAUGAUCAGUAGCCUAACAUU
AL772346.5/72472-72603     CCUGCCCAUAGAGAUAUUGCAGGUUUGGCUGC---UGUGUCACAUGUGCGUCAGUAGGUGGCAGAGGGGA--GAGAGGCUAUGUCUAUGCUCAGUGUUC--AGAU--------CU-AGGAACU--UCUGAAUGUUUCUUAGCCUAACACU
BC046478.1/316-447         CCUGCUCCUAGAGGCGUUGCAGGUGUGGCUGC---UGUGUCACAUGUGCGUCAGUAGGUGGCAGAGAGAA--AAGAGGCUAUGUCUACGCUCAGUGUUC--UGCC--------CU-GUGAACG--UCUGAAUGAUUUGUAGCCUGACAAC
AC157950.2/130553-130423   CCUGUCCCUAGAGGCAUUGCAGGUGUGGCUAC---UGUGUCGCAUGUGUGUCAGUAGGUGGUAGAGAGG---GAAAGGCCAUGUCUACACUCAGUGUCC--UGAC--------CU-GGGAACA--UCUGAAUGAGCAGUAGCCUAACACU
AAHX01069608.1/34817-34686 CCUGCCCCUAGAGGCACUGCAGGUGUGGCUGC---UGUGUCACAUGUGCGUCAGUAGGUGGCAGAGAGGA--AAGAGGCUAUGUCUACGCUCAGUGUUC--UGAC--------CU-GUGAACA--UUUGAAUGAUUAGUAGCCUAAUAUU
AAPY01364388.1/271-141     CCUGCCCCUAGAGGCGUUGCAGAUGUGGCUGC---UGUGUCACAGCUGCGUCAGUAGUGGGCAGAGAGCA---AGAGGCUAUGUCUACGCUCAGUGUUC--UGAC--------UC-GUGAACA--UUUGAAUGAUUAGUAGCCUCACACU
AANN01080924.1/908-778     CCUGCCCCUAGAGGCGUUACAGAUGUGACUGC---UGUGUCACAUGUGUGUCAAUAGGUGGCAGAGAGAA--GAGAGGCU-UGUCUACGUCCAGUGCUC--UGAC--------CU-GUGAGCC--ACUGGGUGAUUGAUAGUCUGACACU
AAFC03086501.1/28639-28770 ACUGCCCCUAGAGGCGCUGCAGGCGUGGCUGC---CGUGUCACGUCUGCGUCAUGAGGUGGCAGAGAGGA--AAGAGGCUCGGUCUACGCCCAGUGUUC--UGGC--------CG-GUGGACA--UCUGGAUGAUUGAUAGUCUGACACU
AAYZ01571100.1/456-325     GCUGCCCCUCGAGGCGUUGCAGGUGCGGCUGC---UGUGCCGCACCUGUGUCAGCAGGUGGCAGAGAGCA--GUGCGGCUACGUCUACGCUCCGCGCCC--UGGC--------AC-GUGGGCU--UCGGAAUGAUUAGUAGGCGGACAGC
ABDC01163242.1/9845-9714   ACUUCUCCUAGAGGCAUUGCAGAUGUGGGUGC---UGUGUCACAUUUGUGUCAUUAGGUGACAGAGAGAG--GAGAGGCUAUGUCUACAUUCAGUGUUC--UGAC--------CC-AUGAAUG--UUUGAAUGAUUAAUAGUCUGCCAUA
AACN010677500.1/623-491    ACUGCCCCCAGAGGCGUUGCAGGUGUGGCUGCAUCUGUGUCACAUUUGUGUCAUUGGGUGGCAGAAAGAA--GAGAGGCU-UAUCUACGCCCAGUGUUC--AG-C--------UG-GUGAACG--UCUGGAUGAUUAAUAGUCUGACACU
AANG01443872.1/432-299     ACUGCCCCCAGAGGCGUUGCAGGUGUGGCUGCGUUUGUGUCACAUUUGUGUCAUUCGGCGGCAGAGAGAA--GGGAGGCU-UGUCUACGCCCAGCGUUC--CGGC--------UG-CAGAACG--UCUGGAUGAUUAAUAGCCUGACAGC
AAFR03005638.1/59378-59246 AUUGCCCCUAGAGGCGUUACAAAUUUGGCUGC---UGUGCCUCAUUUGUGUCAGUAGGUGGCAAAGAGAA---AGAGACUAUGUCUACGCUCAGUGCUC--UGAC--------CCAGUGAGCA-CUCAGAAUGAUUAAUAGCCUGACACU
AAPN01114604.1/4824-4957   GGUGCCCCUCGAGGCGUUGCAGAUGUGGCUGC---GGUGCCCCAUUUGUGUCAUGAGGUGGCAGAGAGGA--U-AAGGCUAUGUCUACGCUCCGUGUUCAAAAAU--------UU-GUGAGCA-CGCAGAAUGAUUAAUAGCCUGACAGU
AAIY01268469.1/912-1041    ACUGCCCCUAGAAGCAUUGCAG-CGUGGCCAC---CCUGCCACAGCUGUGUCAUUAGAGGGCAAAGAGAA--GAGGGGCUAUGUCUAGGCUCAGGGGUC--UGAC--------GU-G-AACCA--CCUGACUGACUGCUAGCCCCACAGU
AAWR02025983.1/946-1076    ACUGCCCCUAGAGGCGUUACAGAUGUGGCUGC---GGUGUCACAUUUGUGUCAUUGGGUGGCAGAGAGAA--GAGAGGCU-UGUCUACGCUCAGUGUUC--UGGC--------CU-GUGGACG--CCUGGAUGAUGAAUAGUCUGACACU
AAPE02023258.1/7569-7440   ACUGCCCCUAGAGGCAUUGUAGGUGUGGCUGC---CAUGUUGCACCUGCGUCAUUAGGUGGCAGAGAGCA--GAGAGGCU-UGCCUACGCCCAGCAUCC--UGG---------CU-GUGGGCG--CCUGGAUGGUUGACGGCCUGGCACU
AAQR03045159.1/6305-6174   AUUGUCCCUAGAGGAGUUGCAGAUGUGGCCGU---UGUGUCACAUUUGUGUCAUUAGGUGGCAGAGAGAA--AAAAGGCCAUGUAUACAUUCAGUGUUC--UGAC--------CU-AUGAAUG--UUUGAAUGAUUAAUAGUCUGACACA
AAWZ02037419.1/5349-5207   CUUGCCCCCAGAGGCGUUGCAGACACGGCUGU---CGUGCCAUGUUUGCGUCAUUGGGUGGCAAAGAGGAAAGAAAGGCUAUGUCUACGCUCAGUGCUC--UGAAAUGAAAAACC-GUGGGCA-CUCAGAAUGAUUUGUAGCCUGACAAA
#=GC SS_cons               :<<<<<<<<<<-<<<---<<<<-<<<<<<___...___>>>>>>->>>>>>>->>>>>->>>>>------..<-<<<<<<<<----<<<-<<<<<<<<<..____........__.__>>>>>..->>>>->>>--->>>>>>>>->:::
#=GC RF                    acUGCCCCuacAGgcgUUgCagguguGgCUGC...uGUGcCacaUcuGcguCAguaGGUGGCAgAGAGgA..GAcaGgCuacGUCUccgCuCaguGuuC..UGac........cu.gUGaaCa..UcuGaAuggUUaguaGcCugACAuu
//
# STOCKHOLM 1.0

#=GF AC   RF00561
#=GF ID   SNORA40
#=GF PI   snoACA40
#=GF DE   Small nucleolar RNA SNORA40
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   51.00
#=GF TC   51.00
#=GF NC   50.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300520;
#=GF DR   snoopy; Homo_sapiens300074;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   9047361
#=GF RT   Mapping to nucleotide resolution of pseudouridine residues in large
#=GF RT   subunit ribosomal RNAs from representative eukaryotes, prokaryotes,
#=GF RT   archaebacteria, mitochondria and chloroplasts.
#=GF RA   Ofengand J, Bakin A
#=GF RL   J Mol Biol. 1997;266:246-268.
#=GF CC   The snoRNA ACA 40 belongs to the H/ACA family of snoRNAs and guides the
#=GF CC   pseudouridylation of 28S rRNA subunit at position U4565. NB This family
#=GF CC   has a high threshold value to exclude a large number of closely related
#=GF CC   sequences that do not appear to have conserved H and ACA boxes, and may be
#=GF CC   pseudogenes.
#=GF WK   Small_nucleolar_RNA_SNORA40
#=GF SQ   28


AJ609445.1/1-126             UGCACUUAUGU--AUGUUUUUGU--UUAAC---GUGG-ACAAAGAC-UUAC-AGAUAGGUGCAAAAAAUAA--AUCCUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUAUAAGAAGGGAUAUU
AC020602.6/136573-136700     UGCACUUAUGU--AUGUUUUUGU--UUAACUU-GUGG-ACAAAGAC-UUAU-GGAUAGGUGCAAAAAAUAA--AUCCUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUAUAAGAAGGGAUAUU
AC055866.19/124993-124866    UGCACUUAUGU--AUGUUUUUGU--UUAACUU-GUGG-ACAAAGAC-UUAU-GGAUAGGUGCAACAAAUAA--AUCCUCUUUUGCAACCCAGAACUCAUUGUUCAGCAUGAGUUUUGAUACAUACAGGAAGGGAUAUU
AL590730.6/8553-8680         UGCACUUCUGU--AUGUUUUUGU--UUAACUU-GUGG-ACAAAGAC-UUGU-GGAUAGGUGCAAAAAAUAA--GUCCUCUUUUGCAACCUGGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUAUAAGAAGGGAUAUU
Z84480.1/104302-104429       UGCACUUAUGU--AUGUUUUUGU--UUAACUU-GUGG-ACAAAGAC-UUUA-GGAAAGGUGCAAAAAAUAA--AUCUUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUAUCAGAAUGGAUACU
AC090821.13/147314-147441    UGCACUUAUGU--AUGUUUUUGU--UUAAACU-GUGG-ACAAAGAC-UUAU-GGAUAAGUACAAAAAAUAA--AUCCUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUAAUACAUAUAGCCAGGGAAAUU
AC079802.6/80721-80594       UAGACUUGUGC--AUGUUUUUGC--UUAACUU-GUGG-AUAAAGUC-UUAC-AGACAGGUGCAAAAAAUAA--AUCCUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUAUAAGAAAGGACAUU
ABDC01191151.1/5291-5164     UGCACUUGUGU--UUGAUUUUGU--CUAACUU-GUGG-ACAAGGAC-UUAC-AGACAGGUGCAAAAAAUAA--AUCCUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUAUAAGAAGGAAUAUU
AAQQ01596999.1/8256-8383     AGCACUUGUGU--GUGUUUUUGU--UAAACUU-UUGG-ACAAAGAC-UUGU-GGACAAGUGCAAAAAAUAA--AUCCUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUACAAGCAGGUAUACU
AANU01107574.1/21156-21282   UGCACUUAUGU--AUGUUUUUGU--UUAACAU-GUGG-ACAAAGAC-UUAC-UGAUAAGAGCAAAAAAUAA--AUCUUC-UUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUAAUACAUAUAAGAAGGGAAAUU
AAIY01662003.1/3751-3877     UGCAUUUGUGU--UUGUGUUUGU--UUAAUUA-GUGG-ACAAACAC-UCAA-AGACAGGUGCAAGAA-UAA--AUCCUCUUUUGCAACCCAAAACUCAUUGUGCAGUAUGAGUUUUGAUACAGAUAAGAAGGGACAUG
AAYZ01416934.1/1611-1485     UGCACUAGUGU--AUGUUUUUGU--UUAAUUU-AUGG-ACAAAGAC-UGAC-AUAA-GGUGCAAAAAACAA--AUCCUCUUUUGCAACCCAGAACUCAUUGAUCAGUAUGAGUUUUGAUACAUAUAAGCAGGAAUAGU
AAFC03070145.1/80147-80021   AGCACUUGUGU--UUGUUUUUGU--UUAAUUU-GUGG-ACAAAGAC-UUAC-AGACAAGUGC-GAAAGUAA--AUCCUCUUUUGCAACCCACAACUCAUUGUUCAGUAUGAGUUUUGAUACAGAUAAGAAGGAACAUG
AALT01626182.1/322-448       AGCAUCUGUGU--GAGUGUUUGU--CUAAUGU-GUAG-ACAAAGAC-UUUG-AGACAGGUGC-AAAAAUAA--AUUCUCUUUUGCAACCCAGAACUCGUUGUUCUGUAUGAGUUCUGAUGCAUAUGAGAAGGAACAUG
AAPY01155136.1/459-584       AGCACUUGAAU--UUGUUUUUGU--CUGUCUU-UUAG-ACAAAGAC-ACAG-AA--AAGUGCAAAAAAUAA--AUCCUCUUUUGCAACCCAAAACUCAUUGUUUAGUAUGAGUUUUGAUACAUAUAAGAAGGAAUAUU
AC149606.6/161836-161712     AGCACUUGUAU--GGGUUUUUGU--UGAACUA-GUGG-GCAAAAAC-UGGA-AAACAAGUGC-AAGAACAA--AUCCUCUUUUGCAACCCAGAACUCAUUGUU--GUAUGAGUUUUGGUACAUGUAAGAAGGAAUAUC
AANN01814642.1/2983-3107     AGCACUUGUUU--GUUCGCUUUU--GUUAC-U-GAGC-AAAAGUGA-UU---AGACAAGUGCAAAAAAUAA--AUCCUCUUUUGCAACCCAGAGCUCAUUGUUCAGUAUGAGUUUUGAUACAUAUAAGAAGGAACAUG
AAPN01307029.1/41597-41472   AGCACUUCU-C--UUGUUCUUGU--UCAAUCU-GGGG-ACGAGGAC-UUAG-A-AAAAGUGCUCAGAACAA--ACCCUCUUUUGCAACCCACAGUUCAUGGCACAGUAUGAGCUGUGGUACAUAUAAGGAGGGACACC
AAFR03025134.1/18725-18853   UGCACUUCAUU--UAG-CUUUGUUUUUGAAUU-GUAG-ACAAAGAC-UUAA-AGACAAGUGCAAAGAACAA--ACCCUCUUUUGCAACCCACAACCCAUGGUUUUGUAUGAGUUGUGAUACAUACAAGAAGGGACAAU
AAWR02017934.1/92822-92949   AGCACUUGUGU--UUGUUUUUGU--UUAAUUU-GUGG-ACAAAGAC-UUAG-AGACAGGUGCAGAAAAUAA--AACCUCUUUUGCAACCCAGAGCUCAUUGUUCAGUAUGAGUUUUGAUACAGAUAAGAAGGAACAUU
AAGV020161066.1/8197-8325    GGCACUUGAGU--UUGUUUUUGU--CUGAUUU-GUAG-ACAAAGACCAGAU-AGACAGGUGCAAAGAAUAA--GUCCUCUUUCGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAGAUAAGAAGGGACAUA
AAKN02023925.1/26777-26646   GGCACUUGAGU--AUGUUUUUGUC-UUAACUUGGUGGACUAAAAAC-UUACUGAACAGGUGCAAAAAAUAA--AACCUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUAUAAGAAGGAAUAUU
AAHX01053335.1/98633-98760   AGCACUUGUGU--UUGUUUUUGU--UCAGCUG-UUGG-ACAAAGGC-AGGU-UGACAGGUGCAAAAAACAA--AUCCUCUUUUGCAACCCAGAACUCAUUGUUCAGUAUGAGUUUUGAUACAUACAAGAAGGAAUAUA
AAPE02025112.1/60951-60827   AGCACUUGUGU--UUGUUUUUGU----AAUUU-GUGG-ACAAAAAC--UAC-AUACGGGUGCUAAAAAUAA--AGCCUCUUUUGCAACCCAGAACUCAUUGCUCAGUAUGAGUUUUGAUACAUAUAAGAAGGAACAUG
AAQR03000688.1/141681-141809 GGCACUUGUGU--UUGUUUUUGU--CUAAC-U-GUGG-ACAAAGAC-UUAG-AGACAGGUGCAAAAAAAAAAAAUCCUCUUUUGCAACCCAGAACUCAUUGCUAAGUAUGAGUUUUGAUACAUGUAAGAAGGAAUAUC
AAEX03012728.1/174815-174940 CGCACUUGUAC--AUGUUUUUGU--UUAGC-U-GUGA-ACAAAGAC-UUA--GACUAAGUGCAAAAAAUAA--AUCCUCUUUUGCAACCCAGAACUCAUGGCUCAGUAUGAGUUUUGAUACAGAUAAGAAGGAACAAC
AAGW02026623.1/316-445       UGCACUUGUGUAUAUGUUUUUGU--UUAACUU-GUGG-ACAAAGAC-UGAC-AUACAGGUGCAAAAAAUAA--AUCCUCUUUUGCAACCCAGAACUCAUUGAUCAGUAUGAGUUCUGAUACAUACAAGCAGGAAUAGG
AACZ03124190.1/18098-17971   UACACUUGUUU--AUAUUUUUGU--UUAACUU-GUGG-ACAAAUAU-UUAU-AGACAGGUGCAAAAAAUAA--AUCCUCUUUUGCAACCCAGAACUCAUUGUUCGGUAUGAGUUUUAAUACAUAUAAGAAGGGAUAUU
#=GC SS_cons                 <<<<<<<<<-<..--<<<<<<<<..----<__.__>-.>>>>>>>>.----.>->>>>>>>>>--------..<<<<<-<<<<<-----<<<<<<<<<<________>>>>>>>>>>------->>>>>->>>>>:::
#=GC RF                      uGCaCcugugu..aUGucuUuGu..uUAAcuU.GUgG.aCaAagaC.UuAu.agacagGuGCaAAAAAuAA..gucCuCuuuugCAACCCagAaCuCaUUGuUcAGUAuGaGuUcuGAUACAUAcaagaAgGgacAuu
//
# STOCKHOLM 1.0

#=GF AC   RF00562
#=GF ID   SNORA49
#=GF PI   snoACA49
#=GF DE   Small nucleolar RNA SNORA49
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   35.00
#=GF TC   35.90
#=GF NC   33.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300456;
#=GF DR   snoopy; Echinops_telfairi300145;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF CC   The snoRNA ACA49 has no identified RNA target. NB genomic sequence 1-nt
#=GF CC   different from published.
#=GF WK   Small_nucleolar_RNA_SNORA49
#=GF SQ   21


AJ609476.1/1-135           CUUCCUCAGCCUUACUCCAGGG-ACUUUU--GUUGCCUGUAAAGUGCUCUGGCAUUGCCUGAGGAUAGAUGAGAAAGCACAUAUCCCUCCCCAGUAAGA-CGCUG-UU-UUCUUUUGGGGCCUACAAGUUGAGCUGACAGU
AC161348.2/116746-116614   CUUCCUCAGCCUUACUCCAGGG-GCUUCU----UGCCUGUAGAGUGCCCUGGCAUUGCCUGAGGAUAGAGGAGAAAGCACAGCUCCCUCCCUAGCAAGA-CUCUG-CU-UUCUUGUGGGGCCUACAGAUUGGGCUGACAGC
AC137590.2/61748-61613     CUUCCUCAGCCUUACUCCAGGG-ACUUUUU-GUUGCCUGUAAAGUGCUCUGGCAUUGCCUGAGGAUAGAUGAGAAAGCACAUAUCCCUCCCCAGUAAGA-CGCUG-UU-UUCUUUUGGGGCCUACAAGUUGAGCUGACAGU
ABDC01351852.1/5575-5707   AUUCCUCAGCCUUACUCCGGGG-GCUUUU----GUGCCGUAAAGCGCCCUGGCAUUGCCUGAGGAUAGACGAGGAAGCACACGUCCCUCCCCAGCAAGA-CUCCG-CU-UUCUUUUGGGGCCUGCAGGUGGAGCUGACAGU
AAYZ01181370.1/13699-13831 CUUCCUCAGCCUUACUCCAGGGCAGUUUU-----GUCUGUAAAGUGUCCUGGCAUUGCCUGAGGAUAAAUGAGAAAGCACAAAUCCCUCCCCAAGAAGA-UUCGA-AC-UUCUUCUGGGGCCUACAGAUUGAGCUGACAGU
AAPN01379069.1/4715-4581   CUUCCUCAGCCUUACUCCAGGG-GCUUUC---UUGCUCAUAGAGUGCCCUGGCAUUGCCUGAGGAUAAAUCAAAAAGCCCAUAUCCCUCCCCAGUAGGA-GCCUGAUU-UUCCUUUGGGGCCUACAGUUUGGGCUGACACA
AAFR03047157.1/53512-53378 CUUCCUCAGCCUUACUCCAGGG-ACUUUC---UUGUCCAUAGAGUGCCCUGGCAUUGCCUGAGGAGAAAGCAGAAAGCACAUUUCCCUCCCCAUUAAGA-GCCUG-AUCUUCUUUUGGGGCCUACAUUUGGAGCUGACAUU
AAIY01324387.1/596-728     CUUCCUCAGCCUUACUCCUGGG-CCUUCU-----CGCUGUGGAGUGCCCUGGCAUUGCCUGAGGAUAGAUAAGAAAGCCCGUGUCCCUCCCCAGGAAGAACCCAC-UU-UUCUUCUGGGGCCUACACAUUGAGCUAACAGU
AALT01218024.1/7446-7319   CUCCCUCAGCCUUACUCCAGGG-GCUUUU-----GCCUGUAGAGUGCCCUGGCAUUGCCUGAGGGUACAGGA-AAAGCGCACUUCCCUCCCCAGGAAGA-CUGUG-----UCCACUGGGGCCUACAAGGUGAGCUGACAGC
AANG01101869.1/958-1088    CUCCCUCAGCCUUACUCCGGAG-CCUUUU------GCCGUGAAGUGCUCCGGCAUUGCCUGAGGGUACAGGACCGAGCACACGUCCCUCCCCAGGAAGA-CUCUG-UG-UUCUCGUGGGGCCCACGGGUUGAGCUGACAGU
AAQQ01188056.1/286-160     CGUCCUCAGCCUUACUCCAGGG-GCUUUU---UUGCCUGUGAAGUGCCCUGGCAUUGCCUGAGGAUAUAAGAGAAAGCACGUGCCUCCCCAC---AAGG-CUCUG-AU-CUC----GUGGGCCACAGGCUGAGCUGACAGU
AANN01697580.1/2041-2171   CUCCCUCAGCCUUACUCCAAGG-GCUUUG-----UCCUGUGAAGUGCCUUGGCAUUGCCUGAGGGAACAGCA-ACAGCACACCUCCCUCCCCAGGAAGA-UUCUG-UU-CUCCUGUGGGGCCUGCAGCCUGCGCUGACAGC
AAPY01419740.1/662-788     CUUCCUCAGCCUUACUCCAGGG-GCUUUC----UGCCCGUAGAGUGCCCUGGCAUUGCCUGAGGAGACAGC-GAGAGCACGUUUCCCUCCCCAGGAAGA-CACUG-U---UCU-GUGGGGCCUAAAA--CGAGCUGACAGG
AAFC03064546.1/24513-24383 CUCCCUCGGCCUUACUCCAGGG-GCUUUU-----UGCUGUAAGGU-UCCUGGCAUUGCCGGAGGGUACAUGAACAAGCACGCAUCCCUCCCCAGGGAGA-CUCUG-CU-GUUCUCUGGGGCCUACACGUGGAGCUGACAGU
AAWR02035820.1/67057-67187 CUCCCUCAGCCUUACUCCAGGG-ACUUUU------GCUGUAAAGUGCCCUGGCAUUGCCUGAGGGCACAUGAAAAAGCACAUAUCCCUCCCCAGUAAGA-CUCUG-UG-UUCUUGUGGGGCCUACAGAUUGAGCUGACAGU
AAKN02056626.1/62753-62882 CGUCCUCAGCCUUACUCCAGGG-CCUUUG-------CUGUGAAGUGCCUUGGCAUUGCCUGAGGAUACAUGAGAAAGCACAUCUCCCUCCCCAGCAAGA-CGCUG-CU-UUCUUGUGGGGCCUACAGACUGUGCUGACAAC
AAGV020229427.1/710-577    CUUCCUCAGCCUUACUCCAGGG-GCUUUU---GUGCCUGUAGAGUGCCCUGGCAUUGCCUGAGGACAGAGGAGAAAGCACAUGUCCCUCCCCAGUAAGA-ACCUG-CU-UUCUUUUGGGGUCUACACAUUGAGCUGACAGG
AAPE02057366.1/1853-1723   CUCCCUCAGCCUUACUCCAGGG-GCCUUU------GCUGUAAGGUGCCCUGGCAUUGCCUGGGGGCACACGAAAAAGCGCACAUCCCUCCCCAGGAAGG-CUCCG-UU-CUCCUGUGGGGCCUACUGAUUGCGCUGACAGC
AAQR03035405.1/43779-43643 CUUCCUCAGCCUGACUCCAGGG-GCUUUGUUUUGUCUUGUGAAAUGCCCUGGUAUUGCCUGAGGAUAGACGAGAAAGCACAUGUCCUUCUCUGCCAAGA-CUCUG-UU-UUCUUUAAGGGCCUACGCGUUAAGCUGACAGU
AAGW02072069.1/8888-8756   CUUCCUCAGCCUUACUCCAGGG-UGGUUU----UGCCUGUAAAGUGCCCUGGCAUUGCCUGAGGAUAGAUGAGAAAGCACAGAUCCCUCCCCAGGAAGA-UUUGA-AC-UUCUUUUGGGGCCUACAGUUUGAGCUGACAGU
AAGU03086001.1/62185-62317 CUUCCUCAGCCUUACUCCAGAG-CCUUCU----CACCUGUAGAGUGCCCUGGCAUUGCCUGAGGAUAGAUGAGAAAGCACGUGUCCCUCCCCAGGAAGA-AUCCG-CU-UUCUUCUGGGGCCUACACAUUGAGCUGACAGU
#=GC SS_cons               ::<<<<<<<-<-----<<<<<<.<<<<<_...._______>>>>>->>>>>>---->->>>>>>>----------<<<-<<-------<<<<<<-<<<<._____.__._>>>>>>>>>>--------->>->>>::::::
#=GC RF                    CUuCCuCaGCCUUACUCCaGGG.gCuuuu....ugcCUGUaaaGcGCCCuGGCAUUGCCuGaGGauAaAugAgAAaGCACauaUCCCUCCCCaguaaGa.cuCuG.uu.uuCuucuGGGGCCUACAgauuGaGCuGACAgu
//
# STOCKHOLM 1.0

#=GF AC   RF00563
#=GF ID   SNORA53
#=GF PI   snoACA53
#=GF DE   Small nucleolar RNA SNORA53
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   38.00
#=GF TC   38.40
#=GF NC   37.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300847;
#=GF DR   snoopy; Gallus_gallus300026;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF CC   The snoRNA ACA53 belongs to the H/ACA family of pseudouridylation guide
#=GF CC   snoRNAs. RNA residues targeted for pseudouridylation by this molecule have
#=GF CC   not been identified. n.b: The GenBank accession number for 'Homo sapiens
#=GF CC   snoRNA ACA53 gene' (AJ609478) corresponds to a portion of snoRNA ACA24.
#=GF WK   Small_nucleolar_RNA_SNORA53
#=GF SQ   28


AC122188.4/123823-124068   AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUG---GGUCUUGGACUGAGUUCUACCUGU-AAAC-UUCUUGUUUCUUGUGG-UUCCAGU---CCAAGAAACGUCCAGCAACUUUGUUGGUUG--UAUAGUCG-AAGG------UGCUUGAGUCAUUGGCAUGUGAGACUAAUAUACCUGCAUGCUAGUCUUCAGGUUCUGAUGG-AAGUGACAUGCG-UG-AUGC---UGU-CAUG---UGU-UACUGUCAGGACUCGACUGGUGUGCGGACACG
X77337.1/5898-6146         AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUG---AAUCUUGAACUGAGUUCCACUUGU-AAAC-UUCUUGUUUCUUGUGG-UUCCAGUAGUCAAAGAAACAUCCAGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUAAGAGAAAUAUACCUGCAUGUUAGUCUAACGUAUCUGAUAG-AAAUGACAUGCA-UUUACUG----GC-CAUU---UGU-UACUAUCAGGACUCGACUCGUGUGCGGACAUU
AC140410.3/155965-155720   AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUG---GGUCUUGGACUGAGUUCUACCUGU-AAAC-UUCUUGUUUCUUGUGG-UUCCAGU---CCAAGAAACGUCCAGCAACUUUGUUGGUUG--UAUAGUCG-AAGG------UGCUUGAGUCAUUGGCAUGUGAGACUAAUAUACCUGCAUGCUAGUCUUCAGGUUCUGAUGG-AAGUGACAUGCG-UG-AUGC---UGU-CAUG---UGU-UACUGUCAGGACUCGACUGGUGUGCGGACACG
AC013283.23/46245-46493    AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUG---AAUCUUGAACUGAGUUCCACUUGU-AAAC-UUCUUGUUUCUUGUGG-UUCCAGUAGUCAAAGAAACAUCCAGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUAAGAGAAAUAUACCUGCAUGUUAGUCUAACGU-UCUGAUAG-AAAUGACAUGCA-UUUAUGC---UGC-CAUU---UGU-UACUAUCAGGACUCGACUCGUGUGCGGACAUU
AAFC03044145.1/50535-50782 CACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUGCC-CGUCUUGAGCUGAGUUCUACUUGU-AAAC-UUCUGGUUUCUUGUAG-UUCCAGU---CAAAGAAACAUCCAGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUAAGAUAAAUAUACCUGCAUGUUAGUCUUAGGU-UCUGAUAG-AAAUGACAUGCA-AUUAUGC---UGC-CAUU---UUU-UACUAUCAGGACUCGACUGGUGUGCGGACACU
AAPY01590511.1/1031-1273   AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUG---AAUCUUGAACUGAGUUCUACUUGU-AAAC---CUUGUUUCUUGUAG-UUCCAGU----CAAAAAACAUCCAGCAACUUUUUUGGUUG--UACAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAUAAAUAUACCUGCACAUUAGUCUAAGGU-UCUGAUAG-AAAUGACAUGCA-GUUAUGC---UGC-CAUU---UUC-CACUGUCAGGACUUGACUGGUGUGCGGACACU
ABDC01047524.1/1287-1527   AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUG---A-ACUUGAACUGAGUUCUGCCCGU-AAAC-UUCUUGUUUCUUGUAG-UUCCAGU---CAAA----CAUCCAGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAUAAAUACACCUGCAUGUUAGUCUAAAGU-UCUGAUAG-AAAUGACAUGCA-GUUAUGC---UGC-CAUU---UUA-UACUAUCAGGACUCGACUGGUGUGCGGACACU
AANG01096548.1/7299-7549   AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUGCU-AAUCUUGAACUGAGUUCUACUUGU-AAAC-UUUCUGUUUCUUGUAG-UUCCAGU---CAGAGAAACAUCCAGCAACUUCUUCGGUUG--UAUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAUAAAUAUACCUGCAUGUUAGUCCUAGGU-UCUGAUAG-AAAUGACAUGCA-AUUGUGC---UGC-CAUUUUUUUU-UGCUAUCAGGACUUGACUGGUGUGCGGACACU
AALT01573710.1/1508-1754   AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUGUC-AAUCUUGAACUGAGUUCUACUCGU-AAAC-UUUG-GUUUCUUGUAG-UUCCAGU---GAAAGAAACAUCCAGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAUCAAUAUACCUGCAUGUUAGUCUUAAGU-UCUGAUAG-AAAUGACAUGCA-AUUAUGC---UGC-CAUA---CUU-GACUAUCAGGACGUGACUGGUGUGCGGACACU
AAYZ01540850.1/807-1052    AACAUGCUUCCUUAGAUCCG-CCUUUGU-GGAUG---AAUCUUAAACUGAGUUCUACUGGU-AAAC-GUCCCGUUUCUUGUAG-UUCCAGU---UAUAGAGACAUCCGGCAACUUUUCUGGUUG--UACAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAGAAGUACACCUGCUUGCUAGUCCAACGU-UCUGAUGG-AAAUGGCAUACG-GUUGUGA---UGU-CAGU---UGG-UACUGUCAGGACCAGACUGGUGUGCGGACACU
AANN01072932.1/1055-1296   AACAUGCUGCCUUAGAUCCA-CCUUUGU-GGAUGUC-AGUCUUGAACUGAGUUCUGCUCGC-AAAC-UUCCUGUUUCUUGUAG-UUCCAGU---CAGAGA--CAUCCGGCAACUUUUUUGGUUG--UACAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAGAAAUACACCUGCAUGUUAGUCUCCAGU-UCUGGUGG-GAUGGCA--GCA-GC-CGGC---UGC-CAUU----CG-CUCCGCCAGGACUCGACUGGUGUGCGGACACG
AAFR03039542.1/22343-22105 AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUGCCAACUCUUGUUCUGAGUUCUACUUGC-UAAC-GUUU-GUUUCUUGUAG-UUCCAG----UCAAGAGGCAUCCAGCAACUUUACCGGUUG--UACUGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAUGAAUAUACCUGCAUAUUAGUCAUGCGU-UCUGAUAG-AAAUGGCAG------UGUGU-------CGUU---UCU-UACUAUCAGGACUUGAUUGGUAUGCGGACAGA
AAPN01022444.1/18048-17800 AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGUUGCC-CACCUUGAACUGAGUUCCGCCAGUUAAAC-UCUUUGUUUCUGGUAG-UUCCAGU----CAAGAGGCAUCCGGCAACUUCUUUGGUUG--UACAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUAAGAGAAAUAUACCUGCAUGUUAGUCAUACGU-UCUGAUUGCAAGUGACA-GCA-GCAUUGC--GUGU-CAUU---UCU-CACGAUCAGAGCCUGACUGGUGUGCGGACACU
AAQQ01564883.1/1001-1194   AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUG---AGUCUUGGGCUGAGUUCUACUUGU-AAAC-UUUCUUGUUCCUGUAGUUUCCAGU---CAAAGAA-CAUCCGGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UG-CUGAGUCAU-GGCAUGUGAGAUCA-UAUACCUGCAUGCUAGUCUCAGGU-----------------------------------------------------------UCUGAUGGGAAU-UGGCAUGC
AAIY01534107.1/1690-1880   AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUGUU-AAUUUUGAACUGAGUUCUACUUGU-AAAC-UUUGUGUUUCUUGUAG-UUCCAGU---CAAAGAAACAUCCGGCACCUUUUGUGGUUG--UACCCUCUUAAGG------UGCUUGAGUCAUUGGCAUGUGAGAGAACUAUACCUUCU---------------------------------ACU-GUUCUUU---GGU-UC-------------------------------UGAUGGAAAU
AALT01301038.1/2128-2374   AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUAUC-AAUCUCAAACUGAGUUUUACGGGU-AAAC-UUUG-GUUUCCUGUAG-UUCCAGU---GAAAGAAAUAUCCAGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGGUCAAUGUAUCUGCAAGUUAGUCUUAGGU-UCUGAUAG-AAAUGACAUGCA-AUUAUGC---UGC-CAUU---CUU-GACUAUCAGGACAUGACUGGUGUGCAGACACU
AALT01621535.1/4736-4982   CUUAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUGUC-AAUCUCAAACUGAGUUCUACUGGU-AAAC-UUUG-GUUUCCUAUAG-UUCCCGU---GAAAGAAACAUCCAGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UGCUUAAGUCAUUGGCAUGUGAGAUCAAUAUAUCUGCAAGUUAGUCUUAGGU-UCUGAUAG-AAAUGACAUGCA-AUUAUGC---UGC-CGUU---CUU-GACUAUGAGGACGUGACUGGUGUGCAGACACU
X77338.1/4681-4920         CACAUGCU--CCUAAGAUCA-CCUUUGU-GGAUGCC-CGUCUUGAGCUGAGU-CUACUUGU-AAAC-UCUG-GUUUCUUGUAG---UCAGU---CAAAGAAACAUCCAGCAACUUUUU-GGUUG---AUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUAAGAUAAAUAUACCUGCAUGUUAGUCUUAGGU-UCUGAUAG-AAAUGACAUGCA-AUUAUGC---UGC-CAUU---UUU-UACUAUCAGGACUCGACUGGUGUGCGGACACU
AALT01550119.1/1307-1558   AACAUACUUUCUUAGAUCUGGUCUUUGU-AGGUGAG-AAUCUUGAACCAGAUUCUAUGUGU-AAAU-UUUC-AUUUCUUCUUG-UUUCAGU---GAAAGAAACAUCCAGCCCCCUUUUGGGUUG--UAUAGUCA-AAGGUGCUAGCACAUGUGUCACUAGUACGUGAGAUGAAG-CAGCUGCAUGCUGGCCCUGGGC-CC--GAGAAGAAUGACCUGCA-AUUAUGC---UGC-AAUU---CUU-UAGCACAAAGUUUUGACUGGUGUGCAGACAUU
AALT01381857.1/4938-5172   UGGAUGGUGGGUUGAAUUCU-UGUUUUG-UUUUG---AAUAGGAGGAAAAGCUGUUUUUGU-G----UUUCU---CCUUAUAC-UAU--------GCUCAAUCA--GCUAGUCAUUCCAUGGCUUUAAGAUUAC-AAUG------UACUUGAGUCAUUGACAUGUGAGAUCAAUAUACCUGCAUGUUAGUCUUAAGU-UCUGAUAG-AAAUGACAUGCA-AUUAUGC---UGC-CAAA---CUU-GACUAUCAGGACGUGACUGGUGUGCAGACACU
AAIY01259312.1/6616-6395   C------UUCCUUAGAUCCA-CCUUUGU-GGAUGUU-AAUUUUGAACUGAGUUCUACUUGU-AAAC-UCUGUGUUUCUUGUGG-UUCCAGU---CAAAGAAGCAUCCGGCAACUUUUU-GGAUG--UACAGCCA-AAGG------UGCUUGAGUCAUUAAA----GAAAAGAACAAAAUGAAAGGAUGGUAACAUCA-----------------AAGGU-AUUGAGA---ACU-GGUA---UAA-AAUGAGAGAAAAAAUGCAAUUAUCACAAUUAU
AAWR02024772.1/36451-36700 AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGGUGUU-AGUCUUGAACUGUGUUCUACUUGU-AAAC-UUCUUGUUUCUUGUAG-UUCCGGU---CAGAGAAACAUCCAGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAUAAAUAUACCUGCAUGUUAGUCUUAUGU-UCUGAUAG-AAAUGACAUGCA-GUUGUGC---UGU-CAUU-UUUUU-UACUAUCAGGACUCGACUGGUGUGCGGACACU
AAHX01048238.1/9259-9504   AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUG---AAUCUUGAACUGAGUUCUACCUGU-AAAC-UUCUUGUUUCUUGUAG-UUCCAGU---CCAGGAAACAUCCAGCAACUUUGUUGGUUG--UACAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGACUAAUACACCUGCAUGUUAGUCCUCAGGUUCUGACGG-CAGUGACACGCG-UU-AUGC---UGU-CAUG---UGU-UACUGUCAGGACUCGACUGGUGUGCGGACACU
EU240282.1/2-242           CACAUGCU-CCUUAGAUCCA-UCUUUGU-GAGUA---UCUUUGU-GCUGAGUUCUGCUGGA-UAAC-UUCA-GUUUCUAGCAG-UUCCAGU-----CAAAGUUGCUCGGCAACUUUUUUGGUUG--UACGGUCA-AAGA------UGCUUGAGUCAUUGGCAUGUGAGAGUAAUAUAACUGCAUGUUAGCUUUCUGU-UCUGAUAA-AAGUG----ACUGUAAAUAUGAGAGU-CAUU---UAC-CGCUAUCAGGACAUGGCUGGUAUGCAGACAUU
AAQR03016715.1/34197-33956 AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUG---AAUUUUGAACUGAGUUCCGCUUGU-AAAC-UUCUUGUUUCUUGUAG-UUCCAGU---CAAA----CAUCCAGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAUAAACAUACCUGCAUGUUAGUCUAGGGU-UCUGAUAG-AAAUGGCAUGCA-GUUAUGC---UGC-CAUU---UUU-UACUAUCAGGACUUGACUGGUGUGCGGACACU
AACN010392928.1/139-385    UACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUGCU-AGUCUUGAACUGAGUUCUACUUGU-AAAC-AUUUGGUUUCUUGUAG-UUCCAGU----CAGGAAACAUCCAGCAACUUUUUUGGUUG--UAUAGUCA-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAUAAAUAUACCUGCAUGUUAGUCUUAGGU-UCUGAUAG-AAAUGACACGCA-AUUGUGC---UGC-CAUU---UUU-UGCUGUCAGGACUCGACUGGUGUGCGGACACU
AAPE02006914.1/22422-22175 AACAUGCUUCCUUAGAUCCA-CCUUUGU-GGAUGCC-AAUCUUGAACUGAGUUCUACUUGU-GAACUUUACUGUUUCUUGUAG-UUCCAGU----CAGGAAACAUCCAGCAACUUUUU-GGUUG--UACAGUCG-AAGG------UGCUUGAGUCAUUGGCAUGUGAGAUAAAUAUACCUGCAUGUUAGUCUUAGGU-UCUGAUAC-AAAUGGCAUGCC-AUUGUGC---UGC-CAUU---UUUGUACUAUCAGGACUUGACUGGUGUGCGGACACU
AAWZ02012449.1/18151-17919 AACAUGCUCCCUUAGAUCCA-UCUUUGUUUGAUG---UCUCUUGUGCUGAGUUCUGCUUA-------AACUU----UAAGUAG-UUCCAG----AUAAGAGGGAUCG-GCAACUUCAC-GGUUG--UACAGUCA-AAGA------UGCUUGAGUCAUUGGCAUGUGAGAACAAUACACCUUCACUCUAGUCUCAUGU-UCUGAUAG-AAAU---GACUU-UUAAUAC---AUGUCAUU---CUU-AACUAUCAGGAUUUAGCUGGAGUGUGGACAUG
#=GC SS_cons               :(((((((--(((((---((.((((((<.<<<<<--.--<<<<--<<<<-<--<<<<--<-.<<<<._____>>>>>-->>>>.-->>>>>...-->>>>-->>>>>><<<<<<_____>>>>>..>,,,,,)).))))......))-)))))-----)))))))-------------<<<<<--<-<<<<------.<<<<<<<<.---<<<-<-<<<._______...>>>.----...>->.>>>>>>>>>>---->>>>->-->>>>>:::::
#=GC RF                    aaCaUGcuUcCUuAgAUCCa.ccUUuGu.gGauGuu.aaUcuugaaCuGAGUUCuacuuGU.aAAc.UUuuUgUUuCUUguaG.UUCCaGu...caaagAAaCauCcagCaaCuUUuUugGuuG..uAuAGUCa.AAgg......uGCuUgAGUCAUUggCAuGuGAGAuaAAUAuAcCcgCAUGcUaGucuuaaGu.uCUGaugg.AAAugaCgugca.aUUaUGc...ugc.cAUu...cuu.caccauCAGgAcuugaCuGgUGUGcgGACAcU
//
# STOCKHOLM 1.0

#=GF AC   RF00564
#=GF ID   SCARNA11
#=GF PI   snoACA57
#=GF DE   Small Cajal body specific RNA 11
#=GF AU   Marantidis E
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   37.00
#=GF TC   37.20
#=GF NC   35.00
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. ACA57 belongs to the H/ACA
#=GF CC   box class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail
#=GF CC   structure, conserved H/ACA-box motifs and is found associated with GAR1
#=GF CC   [1]. ACA57 is predicted to guide the pseudouridylation of the U5
#=GF CC   spliceosomal RNA at position U43 [2].
#=GF WK   Small_Cajal_body_specific_RNA_11
#=GF SQ   24


AJ609487.1/1-136           UUGUCCUGGCC----UAUU----UUUCUGCU--CCCCUGUGCUCAGUUCUAACAG-GGU-AGUC--U---GGCAGGACACACAGCAA---UU-----C--CCUCUC--AGUUUAGGAGGGCCGUC--CUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
AC092184.7/50327-50196     UUGUCCUGGCC----UAGGCCA-UUUCUGCU--CCCCCGCGCUCAGUCCUAGCAG-AGU-AGUC--U---GGCAGGACGCACAGCAA---UC-U---C--CCUCUC--AGUUUAGGAGGGCCGUCUCCUAAGAAUAGGGCUGGC----A------GGAAAGGACAAU
AC006064.10/138690-138555  UUGUCCUGGCC----UAUU----UUUCUGCU--CCCCUGUGCUCAGUUCUAACAG-GGU-AGUC--U---GGCAGGACACACAGCAA---UU-----C--CCUCUC--AGUUUAGGAGGGCCGUC--CUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
AAHX01032860.1/31011-31146 UUGUCCUGUGC----C-UU----UUUCUGCU--ACCCUGUGCCCAGUCUUAACAG-GGU-AGUC--U---GGCAGGACACAUAGCAA---UU-U---A--CCUCUC--AGUUUAGGAGGGCUGUC--CUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
AAQQ01201309.1/4377-4515   UUGUCCUGGCC----UGUGCUU-UUUUUGCU---CCCUGUGCUCAGCUCUAACAG-GGU-AGUC--U---GGCAGGACACACAGCAG---UU-U---C--CCUCUC--AGUUUAGGAGAGCCAUC--CUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
AANG01080854.1/423-284     UUGUCCUUGCC----UAUGCUU-UGUCUGCU--CCCUUGUGCUCAGCUCUAACAG-GGG-AGUC--U---GGCAGGACACAGAGCAA---UC-U---C--CCUCUC--AGUUUAGGAGAGCCGUC--CUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAC
ABDC01192957.1/1309-1171   UUGUCCUAGCC----UAUGCUC-AUUCUGCU---CCCUGUGCUCAGUUCCAACAG-GGC-AGUC--U---GGCAGGACACACAGCAA---UC-U---C--CCUCUC--AGUUUAGGAGAGCUGUC--CUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
AAPY01657606.1/3438-3574   CUGUCCUGGCC----GGUGCU--UUUCUGCU--CCCCUGCACUCGGUUUU-GCAG-GGU-AGCC--U---GGCAGGACACACAGCAU---CC-----C--CCUCUC--AGUUUAGGAGAGCCGUC--CUAAGAAUGGGGCUGGCUCUUAAAGGCACGAGAGGACAGU
AAFC03022303.1/17401-17264 UUGUCCUGGCC----UGUGGUU-UUUCUGUU--CCCCUGUGCUCAGUUC--UCAG-GGG-ACUC--C---GGCAGGACGCACAGCAA---GC-U---C--CCUCUC--AGUUUAGGAGGGCCGUC--CUGAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAGU
AANN01528625.1/1227-1368   UUGUCCUGGCC----UAUGCUU-UUGCUGCU--CCCCUGUGCUCACUUCUGACAGAGGG-AGUC--U---GGCAGGACGCACAGUAA---UUCU---C--CCUCUC--AGUUUAGGAGGGCCAUC--CUGAGAAAAGGACUGGCUCUUAAAGGCACGAGAGGACAAC
AAIY01376073.1/3485-3344   UCGUCCUGGCCCCCGAGUG----UCCCUGCU--CCCCUGUGCUCAGCUGUGGCAG-GGG-GGCC--U-GAGGCAGGACGUACAGCAU---CU-----C--CCUCUC--AGUUUAGGAGGGCUGUC--CUAAGCACGGGGCUGGCUCUUAAAGGCACGAGAGGACAUU
AAPN01410804.1/2610-2752   CCGUCCCGGCC----CUUG----CAGCUGCC--CCCCUGUGCCGAGCUGUGGCGG-GGG-GGUG--UCCGGGCGGGACACACAGUAA---CC-CUAAC--CCUCUC--CAUUUAGGAGGGCCCCC--CCGAGGCUGGGGGUGGUCCUUAAAGGCAAGAGAGGACAAA
AAYZ01092047.1/678-814     UUGUCCUGACC----UCGG----CACCCUCUGUCGCCUAUGCUCAGUUGUCACAG-GGG-AGUC--U---GGCAGGACACA-AGCAC---UC-U---C--CCUCUG--AGCUUAGGAGA-CUUUC--CUAGGAGUGGGGCCAGUUCUUAAAGGCACGAGAGGACAAU
AALT01287000.1/5146-5006   UAGCUUUGUCC----CAUGCUU-UGCCUGCC---CAUUGUGCAUAGCUCCAACAG-UGA-AGUU--U---GGUGGAGUACACAACAC---UC-U---C--UCUCUCUAUGUAUAGGAGAGUUGUU--CUGAGCCUAUGGCUGACUCUUAAAGGCAUGAGAGGACAGU
AAFR03037693.1/44000-43864 AAGUCCAUGCU----UAUU------AUUGCU--UUCCUGCUUGCCACUGUAGCAG-GAG-GGCC--A-GAGGCAGGACUAAGAGCAAA--UC-U---U--CCUCUC--AGAUUAGGAGGGCUGUC--CUGAGA-UGGGGCUGACUCUUAAAGGCACAAGAGGACACU
AAKN02051621.1/20436-20572 GUGUCCUGGCC----UAUG----UUUGUGCU--CCCCUGUGCUCAGCUGUGACAG-GGU-AGUC--U---GGCAGGACGUACAGCAG---UU-U---C--CCUCUC--AGUUUAGGAGGGCUGUC--CUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
AAGV020153655.1/1614-1758  UCGUCCUGGCU----UAUGCUUUUUUCUGCU--CCCCUGUGCUCAGGUCUAACAG-GGG-AGUCGGU---AGCAUGACGCACAGGAA-AUCU-U---C--CCUCUC--AGUUUAUGAGGGCCAUC--CUAAGAAUAGGACUGGCUCUUAUAGGCACGAGACGACAGU
AAWR02029183.1/19489-19348 UUGUCCUGGCC----UAUGCUU-UCUCUGCU--CGCCUGUGCUCAGUUCUAACAG-GGG-CCUC--U---GGCAGGACACACAGCAA---UC-U---CUCCCUCUC--AGUUUAGGAGGGCCGUC--CUGAGAAUAGGUCUGGCUCUUAAAGGCACGAGAGGACAAU
AADN03001033.1/16904-17044 GUGUCCUGACCU---CAUCCUG-ACUCUUCC---CCUCAC-CGGAGCUGUGGUGG-UGG-GGUC--U-GGGGGUGGACACAGAUCAU---CU-UA--C--CCUCUC--AAGUUAGGAGGGUUGCU--GAAGAUGUUU-GCAAACCCUUAAAGGCAAGAGAGGACAUC
AAGW02051573.1/21026-20891 CUGUCCUGGCC----UGUG----CCUCUCCU--CGCCUGUGCCCAGUUCUCACAG-GGG-AGUC--C---GGCGGGACACACAGUAC---UC-U---C--CCUCUC--AGUUUAGGAGG-CCGUC--CUAAGAAUGGGGCUGGUUCUUAAAGGCACGAGAGGACAAU
AAQR03127877.1/2089-2226   UUGUCCUGGCC----UAUGCU--CUUCUGCU---CCCUGUGCUCAGUUCAAACAG-GGU-AGUC--U---GGCAGGACACACAAUAA---UC-U---C--CCUCUC--AGUUUAGGAGAGCCGUC--CUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
AAEX03015287.1/20864-21003 UGGUCCUUGCC----AGUGUUU-CUUCUGCU--CCCUUGUGUUGAGCUCUGACAG-AGG-AGUC--U---GGCAGGACACACAGCAA---UC-U---C--CCUCUC--AGUUUAGGAGAGCCGUC--CUAAGAAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
AAGU03041420.1/22663-22801 UUGUCCUGGCC----CCUGCUU-UCCCUGCA---CCCUGUGCUCAGCCCUAACAG-GGCAUGUG--U---GGCAGGACACACAGCAG---UC-U---C--CCUCUC--AGUUUAGGAG-GCCAUC--CUAAGUAUAGAGCUGGCUCUUAAAGGCACAAAAGGACAAU
AAPE02007003.1/20242-20104 UUGUCCUGGCC----UAUGGUU-UCUCUGCU--CACCUGUGCUCAGUAAA-ACAG-GGG-AGUC--U---GGCAGGACACACAGCAA---CC-U---C--CCUCUC--ACUUUAGGAGGGCCGUC--CUGAGUAUAGGGCUGGCUCUUAAAGGCACGAGAGGACAAU
#=GC SS_cons               :<<<<<<<-<<....-------.-----<<<..-<<<<<<___________>>>>.>>-.>>>-..-...>>>>>>>>>--------...--.-...-..<<<<<<..-<<<<--<<<<<<<<<<..<<<____>>>>>>->>>>>>>-->>>>-->>>>>>:::::
#=GC RF                    uuGuCcuggCC....uaUgcUu.uuuCUgCu..ccccuGuGCucAGuUcUaaCag.ggg.aGcc..U...GGcagGaCaCAcAGcAa...uc.U...C..CCUCUC..AGcuUAGgAGgGccgcC..cuaAGaauagGgcUggCcCUuAAAggCAcGAGAGGACAaU
//
# STOCKHOLM 1.0

#=GF AC   RF00565
#=GF ID   SCARNA3
#=GF PI   SCARNA25; snoHBI-100
#=GF DE   Small Cajal body specific RNA 3
#=GF AU   Marantidis E
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   47.00
#=GF TC   48.10
#=GF NC   45.30
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF CL   CL00018
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. This family includes the
#=GF CC   mouse H/ACA-box snoRNAs MBI-100 and MBI-114 identified in [2]. Both
#=GF CC   MBI-100 and MBI-114 are predicted to guide the pseudouridylation of
#=GF CC   position U40 in the U6 snRNA [2].
#=GF WK   Small_Cajal_body_specific_RNA_25
#=GF SQ   23


AL590723.13/6270-6128        AAUGGAAGCUGCU-GGAACCAGCCAUGUGGACAAAU-GAAAAAAUGCCUUUUGUCUACAGAUUGCAGCGAUCCUACAUAA-AUAUAUGGAGGUCUCUGUCUGGCUUAGGACAGCUGGCUAAGUC-UGAUCGUUCCCCUCCGUACAGC
AC118731.11/22104-22243      AAUGGAAGCUGC--GGAGUCAACCAUGCAGACAAAU-GAGAAGCUGUCUUUUGUCUGCAGAAGGCAGCAAUCCUACAUCA-ACAU--GGAGGUCUCUGUCUGACUUAGGAUAGCUGGCUAAGUC-CGAUCGUUCCCCUCCAUACAAC
AC134594.5/184549-184411     ACUGGAAGCUGC--AAAACCAACCAUGUAGACAAAG-GAGAAAAUGCCUUU-GUUUGCAGAAGGCAGCGGUCCUACAUGA-AUAU--GGAGGUCUCUGUCUGACUUAGAAUAGCUGGCUGAGUC-UGAUCGUUCACCUCCAUACAAC
AAHX01076216.1/3447-3308     AAUGGAAGCUGC--AGAGUCAACAUUGUAGACAAAU-GAGGAACUAUCUUUUGUCUGCAGAAGGCAGCGAUCCUACAUAA-ACAU--GGAGGUCUCUGUCUGACUUAGGAUAGCUGGCUAAGUC-UGAUCGUUCCCCUCCAUACAGU
AAYZ01576824.1/557-417       AAAGGAAGCUGCA-GGAAAUUACCAUGUGGACAAAU-GACAAAAAUCCUUUUGUCUACAGAUGGCAGCUUUCCUACAUGA-AUAU--GGGGGUCUCUGUCAGACUUCGGGCAGUUGGCUGAGUC-UGAUCGUUCCCCUCCAGACAGC
AAFR03026499.1/25128-24989   AAUGGAAGCUGCA-GGAACCAUCCAUGUGGACAAAU-GAAAUACU--UUUUUGUCUACAGUAUGCAGCCUUCCUAUAAAAUAUGU--GGAGGUCUCUGUCUGGUUUAGGACAGCUGACUAAGCU-UGAUCGUUCCCCUCCAUACAAU
AAPN01009016.1/3687-3551     ACUGGAAGCUGCC-GGAAACAACCAUGUGGACAAAU-GAA---AUGUCUUUUGUCUGCAUUCUGCAGCCUUCCUAUAAAA-AU-U--GGAGGUCUCUGUCUGGCUUAAAGCAGCUGGCUAAGCC-UGAUCGUUCCCCUCCAUACAAU
AANN01162527.1/493-356       AAGGGAACCUGUAGAAAACCAAUCAUGUGGACAGAG-GAGAAUACCCCUU--GUCCACACAUUGCAGUGUUCCUACAUAA-ACAU--GGAGGUCUCUGUCUGACUUUGGACAGCCA-CUGAGUC-AGAUCGUUC-CCUCCAUACAGU
AAIY01250371.1/763-898       AAUGGAAUCUGU-----AGGAACCAUGUGGGCAAAU-GAAAAAUACCUUU--GUCCUCAAAAUGCAGUGAUCCUACAGAA-AUGU--GGAGGGCUCUGUUUUUCUUAGGACAGCUGACUAAGGCUUGAUCAUUCCCUCCCAUAUAGC
AALT01348524.1/384-524       AAUGGAACCUGCAGUCGUCCCCCCGGGUGGGCAAAU-GCAGAGCUGUCUUUUGUCCCCCAAUUGCAGUGGUCCUACAGAA-ACAC--GGAGGUCUCUGUCGGACUUACAGCAGCUGC-UGAGCC-CGAUCGUUCCCCUCCACACAGG
AAHX01111367.1/31577-31712   UACGGAAGCUGU--AGAACCAGCCAUGAAGACAAGU-GAGAAACCACCUUCUGUCUACAGAAGGCAACAAUCCUGAAUAA-ACCU--GGAAAUCUUUGUCUGACUUCAGACAGCUGA----GUC-UAAUCGUUGCCUUCCUUACAAC
AANN01748800.1/863-988       AAGGGAACCAGC-----------CAUGUGAACAGAG-GAGAACACCCCU---GUCCACACAUUGCAUUGUUCCUACAUAG-ACAU--GGAGGUCUCUGUCUGACUUGGGCCAGCCA-CUAAGUC-AGAUCGUUCA-CUCCAGACAGU
AANN01719897.1/1253-1120     AUGGGUACCUGUAGAGAACCAACCAUGUGGACAAAG----AAUAUCC---CAGGCAACACACCGCAGUGUUCCUACAUAA-ACAC--GGAGGUCUCUGUCUGACUUUGGACAGCCA-CUAAGUC-AGAUCGUUC-CCUCCAUACAGU
AANN01623537.1/4809-4946     AAUGGAACCUGUAGAGAACCAACCACGUGGACAGCG-GAGAACACCCCUU--GUCCACACAUUGCAGUGUUCCUACAUAA-ACAU--GGAGGUCUCUGUCUGACUUAGGACAGCCA-CAAAGUC-AAAUUGUUC-CCUCAAUACAGU
AANN01595483.1/5658-5531     UUCGGAACCGGC---------AUAUGGCGGGCAGA--GUGAAGCACCCUCU-GUCUGCACUCCGCAGG-UUCCCACAUAA-ACAC--GGAGGUCUCUGUCUGACUCAGGACAGCCA-CUGAGCU-GGAUCGUUC-CCUCCAGACAGC
AAWR02036982.1/54993-54853   AAUGGAACCUGCA-GGAACUAACCAUGUGGACAAAU-GAAAAAAUGUCUUUUGUCUACAAAUUGCAGUGAUCCUACAUAA-ACAU--GGAGGUCUCUGUCUGGCUUAGGACAGAUGGCUAAGUC-UGAUCGUUCCCCUCCAUACAAC
EU240247.1/10-142            GUUGGGACCAGUU-GGGACCGGU--GGUGGGCAA---AAC---AAGUGUUUUGUCCACUCUU-GCAGUCUUCCUAGAGUA-AAGU--GGAGGUCUCUGUCUGCUUUAGGAGAGCCAACUAAACU-GGAUCGUUCCCCUCCAUACAUG
AAWZ02025377.1/20790-20921   AGUGGAAGUUGA--AUCAAU-----UGCAGGCAAAU-GAA---AUAUCUUUUGUCUGUGCUUUUCAGACUUCCUAGAAUA-AAGU--GAAGGUCUCUGUCUGGUUUAGAACAGCCAACUAAGCC-AGAUCGUUCCCCUUUGCACAUU
AAPE02010393.1/47003-46864   UAUGGAACCUGCA-GGAAUCAUCCAUGUGGACAAAU-GAA-AAAUGCCUUUUGUCUACAAAUUGCAGUGAUCCUACAUAA-ACAU--GGAGGCUUCUGUCUGGCUUAGGACAGCUGGCUAAGUC-UAAGGGUUCCCCUCCAUACAAC
AAGU03036908.1/5578-5718     AAUGGAAGCUGCA-GGAACCAACCAUGUGGACAAAU-GAAAAAAUGCCUUU-GUCUGCAGAAUGCAGCUAUCCUACAAAA-AUGU--GGAGGUCUCUGUCUGGCUUAGGACAGUUAACUAAGUCCUGAUCGUUCCCCUCCAUACAAC
AACN010336349.1/193-56       AAUGGAACCUGU----AACCAACCAUGUGGACAAAUGGAAAAACUGCCUUUUGUCUACAAAUUGCAGUGAUCCUACAUAA-AC-U--GGAGGUCUCUGUCUGGCUUAGGACAGCUGGCUAAGUC-UGAUCGUUCCCCUCCAUACAAC
AAGW02056585.1/119571-119431 AAUGGAAGCUGCA-GGAACCAACCAUGUGGACAAAA-GAGAAAAAUCCCUUUGUCUGCAGCAGGCAGCGAUCCUACAUAA-ACAU--GGAGGUCUCUGUCGGACUUAGGACAGCUGGCUAAGUC-UGAUCGUUCCCCUCCAUACAGC
AAQR03038539.1/10251-10390   AAUGGAAGCUGCA-GGCACCAAGCAUGUGGACAAAU-GAGAAAAUACCUUU-GUCUACAGAUUGCAGCAAUCCUACAUAA-ACGU--GGAGGUCUCUGUCUGACUUAGAACAGCUGGCUAAGUC-UGAUCGUUCCCCUCCAUACAUC
#=GC SS_cons                 :::<<<-<<<<<-.-----------<<<<<<<----.<<<_______>>>-->>>>>>>---->>>>>-->>>-------.----..<<<<<---<-<<<-<<<<<<<_________>>>>>>>.->>>->---->>>>>:::::::
#=GC RF                      AauGGaAgcuGca.agaAccAacCAuGugGaCAAAu.gagAAaauaccuuUUGuCcaCaaauugCagcguuCCUAcAuaA.AcaU..GGaGGUCUCUgUCUGgCUuaGGACAGCugaCuaAGcC.uGAuCGUUCCCCuCCAuACAgu
//
# STOCKHOLM 1.0

#=GF AC   RF00566
#=GF ID   SNORA35
#=GF PI   snoHBI-36
#=GF DE   Small nucleolar RNA SNORA35
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   39.00
#=GF TC   39.20
#=GF NC   38.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF CL   CL00034
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300835;
#=GF DR   snoopy; Loxodonta_africana300225;
#=GF RN   [1]
#=GF RM   11106375
#=GF RT   Identification of brain-specific and imprinted small nucleolar RNA genes
#=GF RT   exhibiting an unusual genomic organization.
#=GF RA   Cavaille J, Buiting K, Kiefmann M, Lalande M, Brannan CI, Horsthemke B,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Proc Natl Acad Sci U S A. 2000;97:14311-14316.
#=GF CC   The snoRNA HBI-36 snoRNA belongs to the H/ACA family of snoRNAs and is
#=GF CC   specifically expressed in the brain, specifically in the choroids plexus.
#=GF CC   No RNA target has been identified.
#=GF WK   Small_nucleolar_RNA_SNORA35
#=GF SQ   29


BX005219.12/41617-41744      CAGCACUGGCAAG-UGACCCAUUGG-ACUUUUUCUUGA---CCAAC-UGGGCAUCGA--GCAGUGCGAAAACAAAA-CCCUCC-GAAAGAUGGGAG--AGUC---ACACUGUG---GGCUA-CUCCCGCAUGCAGGUGGGUACAUAG
AC007025.2/13587-13714       CAGCACUGCCAAG-UGACCCAUUGG-GCUCCAUCUUGA---CCAAC-UGGGCAUCAA--GCGGUGCAAAAGCAAAU-CCCUCU-CAAAGCUGGGAG--AGUC---ACACCGUG---GGCUA-CUCCUGCAUGCAGCUGGGUACAUAU
AF357423.1/1-119             CA---------AG-UGACCCAUUGG-ACUUUUUCUUGA---CCAAC-UGGGCAUCGA--GCAGUGCGAAAACAAAA-CCCUCC-GAAAGAUGGGAG--AGUC---ACACUGUG---GGCUA-CUCCCGCAUGCAGGUGGGUACAUAG
AAPY01752721.1/3925-4052     AAGCACUGGCAAG-UGACCCAUUGG-GCUCCCUCUUGA---CCAAC-UGGGCAUCGA--GCAGUGCAAAAGCAAAU-CCCUCC-AAAAGCUGGGAG--AGUC---ACACUGUG---GGCUA-CUCCUGCAUGCAGGUGGGUACAUGU
AAHX01113643.1/8045-7918     UAGCACUGGCAAG-UGACCUGUUGG-ACUUUCUCUUGA---CCAAC-UGGGCAUCGA--GCAGUGCGAAAACAAAA-CCCUCC-GAAAGCUGGGAG--AGUC---ACACUGUG---GACUA-CUCCCGCAUGCAGGUGGGUACAUAA
AAQQ01371318.1/1437-1564     CAGCACUGGCAAG-UGACCCAUUGG-GCUUCCACCUGA---CCAAC-UGGGCAUCGA--GCAGUGCAAAAGCAAAU-CCCUCC-AAAAGCUGGGAG--AGUC---ACACCGUG---GGCUA-CUCCUGCAUGCGGGUGGGUACAUAU
AAYZ01551455.1/1076-1203     UAGCACUGGCAAG-UGACCCAUUGG-GCUUCUCCCUGA---CCAAC-UGGGCAUCGA--GCAGUGCAAAAGCAAAU-CCCUCC-AAAAGCUGGGAG--AGUC---ACGAUGUG---GGCUA-CUCCUGCAUGCAGGUGGGUACAUGU
AAIY01136125.1/1637-1509     UAGCACUGGCAAG-UGACCCAUUGG-GCUCCCCUUUGA---CCAAU-UGGGCAUCGA--GCAGUGCAAAAACAAAU-CCCACCGUAAAGCUGGGAG--AGCC---ACACUGUG---GGCUU-CUCUUGCAUGUAAGUGGGUACAUGU
AANN01739612.1/2062-2191     CAGCACUGGCAAG-UGACCCAUUGG-GCUUCUCCUUGA---CCAACUUGGGCAUCGA--GCAGUGCAAAAGUGAAU-CCCUCCCCAAAUCUGGGAA--AGUC---AUGCUGUG---GACUA-UUCCUGCAUGCAGGAGGGUACAUAA
ABDC01305761.1/337-463       CAGCACUGGCAAG-UGACCCAUUGG-GCUCCCCUUUGA---CCAAU-UGGGCAUCGA--GCAGUGCAAAAGCAAAU-CCCUCU-GGAAGCUGGGAG--AGUC---AU-CUGUG---GACUA-CUUCUGCAUACAGAUGGGUACAUCU
AANU01095683.1/6001-6128     CAGCACUGCCAAG-UGACCCAUUGG-GCUCCACCUUGA---CCAAC-UGGGCAUCGA--GCGGUGCAAAAGCAAAU-CCCUCU-CAAAGCUGGGAG--AGUC---ACACCGUG---GGCUA-CUCCUGCAUGCAGCUGGGUACAUAU
AAFC03083039.1/42492-42364   CAGCACUGGCAAA-UGACCCACUGG-GCUCCUCCUUGA---CCAAC-UGGGCGUAGA--ACAGUGCAAAAAUAAAU-CCCUCUGGAAAGCUGGGAG--AGUC---ACACUGUA---GGCUA-CUCCUGCAUGCAGGUGGGUACACAU
AAFR03051186.1/496-364       CAGCAUUGUUAAG-UGACCCACUGG-CCCUCCCUGUGG---CCAAC-UGGGCCUCAU-CACAGUGCAAGAGUAACUCCCCUCU-UUACAGAAGGGCCAGGCCU--GCUUUGUA---GGCUG-CCCCUUUUGGACUGGGGGUACAUCU
AALT01532742.1/3340-3212     CAGCAUUGUGCAG-UG-ACCUAUGG-UUUUUCCUGUAA---CCAUUUAGGUCUAAAA--GCAAUGCAACAGAAACU-UCCUUU-UUCCACGAGAAAC-AUCC---CUGCAGUG---GGUUG-UUCUUAUCGACAAGAGGGUACACAU
AANG01457386.1/801-673       CAGCAUUGUGCAA-UG-ACCUUUGG-UUUUUCUCAUAA---CCACUUAGGUCUGAAA--GCAAUGCAACAGAAACU-UCCUUU-UUCCACGAGAAAC-AUCC---CUGCGGUG---GGUUG-UUCCUAUCGACAGGAGGGUACACAU
AACN010612417.1/492-620      CAGCAUUGUGCAA-UG-GCCUUUGG-UUUUUCUCAUAG---CCAAUUAGGUCUGAAA--GCAAUGCAAGAGAAACU-UCCUUU-UUCCACGAGAAAC-UUCC---CUGUGGUG---GGUUG-UUCCUAUCGACAGAAGGGUACACAU
BX927065.8/52522-52392       AUGCACUGU---G-UGUAAUAUGUGGGUUGCCACCUAAUGGCAUUC-UGCUCUCAAA--UCAGUGCAAGAG-AAAC-CUCAGU-UUGCAGAAGGGCCAAAUC---AAACUAUU---GGUUAUUCCCUUUCGAAGGCUGAGAACAGAC
AC192392.3/134976-134848     CAGCAUUGUGCAA-UG-GCCUUUGG-UUUUUCUUGUAA---CCAGUUAGGUCUGAAA--CCAAUGCAAAAGAAAUU-UCCUUU-UUCCACGAGAAAC-AUCC---CUGCAGUG---GGUUG-UUCCUAUCGACAGGAGGUUACACGU
AANH01002229.1/3926-4055     CCGCACUGCCAAG-UGACUGGACGU-CCUCCUCCGUGG---UCGUC-CGAUCUCAUU--UCAGUGCCAGAA-AGAC-CUCAGU-UUGCAGAAGGGUU-GAGCUA-AACCAGUG---GGUCC-CCCCUUUCGAAGACUGAGAACAAAU
AAVX01300889.1/206-76        GUGCACAACUAAG-UG-ACUUGUUG-GCCAACUUGAGG---UCUUG-AAGUUUCAUU--CUUGUGCAAGAUUAAAC-UCCAGC-UUGCAGAAGGGCU-GAGCUUUAACCCAUG---GCUUC-UCCCUUUCGAAGGUUGGGGACAAAU
BAAE01143835.1/2104-1976     CUGCACCGCCAAG-UGACCGGACGA-CCUCCGCCGUGG---UCCUC-CGGUCUCAUU--CCGGUGCCAGAU-CAAC-CUCGGU-UUGCAGAAGGGUU-GGGUC--GAACCGUG---GCCCC-CCCCUUUCGAAAGCCGAGCACAGGU
AAKN02039767.1/5464-5337     CAGCACUGGCAAG-UGACCCAUUGG-GCUCCCUCUUGA---CCAAU-UGGGCAUCGA--GCAGUGCAAAAGCAAAU-CCCUCC-AUAAGCUGGGAG--AGUC---ACACUGUA---GGCUG-CUCCUGCAUGCAGGUGGGUACAUUC
AAWR02039288.1/127803-127931 CAGCACUGGCAAG-UGACCCGUUGG-GCUCCUCCUUGA---CCAAC-UGGGCAUCGA--GCAGUGCAAAAGCAAAU-CCCUCCACAAAGCUGGGAG--AGUC---AUGCUGUG---GGCUA-CUCCUGCAUGCAGGUGGGUACAUAU
AAGV021081572.1/560-432      CAGCAUUGUACAA-UG-GCCUUUGG-GUUUUAUUGUAA---CCAAUUAGGUCUGAAA--GCAAUGCAAAAGAAACU-UCCUUU-UUCCACGAGAAAC-AUCC---CUGCAGUG---GGUUG-UUCCUAUCGACAGAAGGAUACAUAU
AAPE02002646.1/53306-53179   CAGCACUGGCAAG-UGACCCACUGG-UCUCCUCCUUGA---CCAAU-UGGGCAUCGA--GCAGUGCAAAAGCAAAU-CCCUCC-GUUAGCUGGGAG--AGUC---AUUCUGUG---GGCUA-CUCCUGCAUGCAGGUGGGUACAUAU
AAGU03055879.1/60575-60446   CAGCACUGGCAAAGUGGCCCAUUGG-GCUCCCUCUUGA---CCAA--UGGGCAUCGA--GCAGUGCAAAAGCAAAU-CCCACCAUAAAGCCGGGAG--AGCC---ACACUGUG---GGCUAACUCCUGCAUGCAGGUGGGUACAUGU
AAWZ02007597.1/95966-95834   CUGCACUGCCAAA-GA-CCAGAUUG-UCUCUUCCAUGG---CCUU--CUGGUCUUCAUUCUAGUGCAAGAUAAACU-CCCUUC-UAGCAGAAGGGCU-AGGAC--UCUUUCUAAAGGCCUG-GUCCUUUCGAAGGCUGGGUACAUUA
AADN03005642.1/8014-7886     CUGCACUGGUCAU-UG-ACUAGCUG-GUCUUUCCCUGA---CCUCC-UGGUCUCAUU--CUAGUGCAAGAG-AAAU-CCCUUC-UAGCAGAAGGGCC-AGGCUC-UCUUUGUG---GCCUA-CCCCUUUCGAAUGCUGGGUACAACC
AAQR03176721.1/57131-57258   CAGCACUGGCAAG-UGACCCAUUGG-GCUUCCCCUUGA---CCAAU-UGGGCAUCGA--GCAGUGCAAAAGUAAAU-CCCUCU-GAAAGCUGGGAG--AGUC---ACACUGUG---GACUA-CUUCUGCAUGCAGAUGGGUACAUAU
#=GC SS_cons                 ::<<<<<<----<.-<-<<<<<<<<.-<________>-...>>>>-.>>>>>->---..->>>>>>----------.<<<--<.---<--<<<<<--.<<<<...________...>>>>-.->>>>>-->--->-->>>:::::::
#=GC RF                      caGCACuGucAAg.UGAcCcguuGG.gCUucccCuUGA...CCaac.cgGgCucaaA..gCaGUGCAAaAguAAAU.CCCuuc.uuacagaaGGgau.agcC...acaCuGUG...Ggcua.ccCCuuUcgaaaggUGGGUACAuau
//
# STOCKHOLM 1.0

#=GF AC   RF00567
#=GF ID   SNORD17
#=GF PI   snoHBI-43
#=GF DE   Small nucleolar RNA SNORD17
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   51.20
#=GF NC   40.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Cavia_porcellus300550;
#=GF DR   snoopy; Spermophilus_tridecemlineatus300315;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF CC   The snoRNA HBI-43 belongs to the C/D family of snoRNAs, guiding 2'O-ribose
#=GF CC   methylation at position U3797 of the 28S rRNA. Pseudouridylation in
#=GF CC   position U3797 is predicted to be guided by the H/ACA snoRNA ACA48.
#=GF WK   Small_nucleolar_RNA_SNORD17
#=GF SQ   19


AL808123.9/5649-5412         GUGAAAUGAUGAUUCUGUUUAUCCAUUCG-CUGAGU-AC-GCUG-CUCUGACCUUCUU-CCCAGUCUCGGUUC-CUGUUCU-GGGAGC--UUGGGGCUGA--GUAGC--CACCA--------GCCCU-GC-UCUC-UGC-AGUGUUCUAUUGUGGAUUGCUUGUGU-GCUGGC-AGGCUACUACUGGU--AAGAA--UGG-CUAGUGUCAGCAGG--GAUGGC-UCCU-C-----UCUG-----GGUUC--CAUC---UC-ACCAAGAUGAGUGGUGC--AAAUCU-GAUCAC
AL121585.22/69574-69338      GUGAAAUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-GC-GCUG-CACUGACCUUCUU-CCAAGCCUCAGUUC-CUGUUCU-AGGAAC--UUGAGGCUAU--GUAGC--CUGAAAAU-----GCCCU-GC-AGUC-UGC-AGUGUUCUACUGUGAACUGCUUGUGU-GUUGGC-AGGCUACC---GGU--AAGAA--UGG-UUGGUGUCAGCAGG--GACGGG-GCC--C-----UCUG-----AGACC--CAUC---UC-ACAAAGAUGAGUGGUGA--AAAUCU-GAUCAC
AF357317.1/1-221             --------------CUGUUUAUCCAUUCG-CUGAGU-AC-GCUG-CUCUGACCUUCUU-CCCAGUCUCGGUUC-CUGUUCU-GGGAGC--UUGGGGCUGA--GUAGC--CACCA--------GCCCU-GC-UCUC-UGC-AGUGUUCUAUUGUGGAUUGCUUGUGU-GCUGGC-AGGCUACUACUGGU--AAGAA--UGG-CUAGUGUCAGCAGG--GAUGGC-UCCU-C-----UCUG-----GGUUC--CAUC---UC-ACCAAGAUGAGUGGUGC--AAAUCU-GAU---
AAHX01025523.1/33959-33721   GUGAAAUGAUGAUUCUGUUUAUCCAUUCG-CUGAGU-AC-GCUG-CACUGACCUUCUU-CCCAGUCCCAGUUC-CUGUUCU-GGGAGC--UUGGGGCUGA--GUAGC--CUCCA--------ACCCU-GC-AAUC-UGC-AGUGUUCUACUGUGGAUUGCUUGUGU-GUUGGC-AGACUACUACUGGU--AAGAA--UGG-CUAGUGUCGGCAGG--GAUGGC-UCCCUC-----UCUG-----GGUUC--CAUC---UC-ACCAAGAUGAGUGGUGC--AAAUCU-GAUCAC
AANG01234717.1/5883-5647     GUGAAGUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-GC-GCUG-CACUGACCUUCUU-CCAAGCCUCGGUUC-CUGUUCU-AGGAAC--UCGGAGCUAU--GUAGC--CUCUAAAU-----GCCCU-GC-AGUC-UGC-AGUGUUCUACUGUGGACAGCUUGUGU-GUUGGU-AGACUACC---GGU--AAGAA--UGG-UUGGUGUCAGCAGG--GGUGGG-GCC--C-----UCUG-----GGUCC--CAUC---UC-ACCAAGAUGAGUGGUGG--AAAUCU-GAUCAC
ABDC01222884.1/3168-2932     GUGAAAUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-GC-GCUG-CACUGACCUCCUU-CCAAGCCUCAGUUC-CUGUUCU-AGAAAC--UUGGGGCUAC--AUAGC--CUCCAAAU-----GCCCU-GC-UCUC-UGC-AGUGUUCUACUGUCGACUGCUUGGGU-CUUGGU-AGACUAUU---GGU--AAGGA--UGG-UUGGUGUCAGCAGG--GAUAGG-UCC--C-----UCUG-----GGUCC--CAUC---UC-ACAAAGAUGAGUGGUGC--AAAUCU-GAUCAC
AAPY01642143.1/6685-6920     GUGAAAUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-GU-GCUG-UCCUGACCUCCUU-CCAAGUCUCAGUUC-CUGUUCU-AGGAAU--GUGGGGCCAC--GCAGC--CUCCAAAU-----GCCCU-AC-AGUC-UGC-AGUGUUCUACUGUGGGCUGUUUGUGU-GUUGGU-AGGCUGCU---GGC--AGGAA--UGG-UUGGUGUCAGCAGG--GAUGGG-GCC--------ACUU-----GGUCC--CAUC---CC-ACCAAGAUGAGUGGUGG--AAAUCU-GAUCAC
AAFC03076388.1/37157-36922   GUGAAAUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-GC-GCUG-CACUGACCUUCUU-CCAAGCCUGGGUUC-CUGUUCU-GGGAAC--UCUGGGUUAC--GUGGUUGCCAAAU-------GCCCU-GC-AGUC-UGC-UGUGUUCUACUGUGGACGGCUUGUGU-GUUGGU-GGACUACC---GGU--AAGAA--UGG-CUGGUGUCAGCAGG--GAUGGG-UCC--C-----UGUG-----GG-CU--CAUC---UC-ACCAAGAUGAGUGGUGG--AAAUCU-GAUCAC
AALT01059218.1/430-192       GUGAAAUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-AC-GCAGUCACUGAUCUUCUU-CCAAGCCUCAGUUC-CCGUUCU-GGGAAC--CUGAGUCUAC--GCAGC--CUCCAGUUGCCUUGCCUU-GC-AGUC-UGU-AGUGUUCUACUGUGGACAGCUUGUGU-GUUG-G-UGGCUGCU---GGU--AAGA---UGG-UUGGUGUCAGCAGG--GAUAGG-UCC--------UCCG-----GGUCC--CAUC---UC-ACUAAGAUGAGUGGUG---AAAUCU-GAUCAC
AAYZ01249466.1/2106-1873     GUGAAAUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-GC-GCUG-CACCAACCUUCUU-CCAAACCUCAGUUC-CUGUUCU-AGGAGC--GCGGGGCUGC--GUGGC--CUCCAGGC-----UCCCU-GC-AGCC-UGC-AGUGUUCUGCUGCCGGCUGCUGGGGG-GUC--U-GGGCUACU---GG---GAGAA--UGG-CUGGUGGUGGCAGG--GGUGAG-GCCC-C-----CUCG-----GGGCC--CAUC---UC-ACCGAGAUGAGUGGU-A--AGAUCU-GAUCAC
AAFR03003388.1/95306-95552   GUGAAAUGAUGAUGAAGUUUAUCCAUUCU-CUGAGU-GU-GCUG-CUCUGCCCUUCCU-ACAGCUCUGAGUUC-CUGUUCU-AGGAAC--UCUUGAGUUAU-GUAAC--CUCCAGAU-----ACCCU-CCAGACU-UGC-AGUGUUCUACUGUGGAUGGCAGGUGU-GUGUGG-UGGUCUUACUAGU---AGGAA--GAG-AUGGAGUUAGCAGA--GGUGAA-ACCC-CAUUAUUUGG-----GGUCC--CAUC---UU-ACCAAGACGAAUGACUG--GUGUCU-GAUCAC
AAQQ01173351.1/6265-6519     GUGAAAUGAUGAUUCAGUUUAUCCAUUCGGCUGAGU-GU-GCUG-CAUUGACCUUCUUCCCAAGCCUCAGUUC-CUGUUCUAAGAAACUUUUGGUGCUAU--GUAGC--CUCCAAAU-----GCCCUGGCAGAUC-UGC-AAUGGUCUAUUGCAGAUUGCUUGUGU-GGUGGU-AGCCCAUC---UGAUAAAAAG--UGGCUUGAUGUCUACAAA--GAAUGAUGCCC-A-----UGUG----UGGUUCGAAUUU---UU-ACCCAGAUGAGUGGGGGGCAAAUCUAGAUCAU
AAWR02026213.1/5119-5355     GUGAAAUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-GC-GCUG-CACUGAUCUUCUU-CCAAGCCUCGGUUC-CUGUUCU-AGGAAC--UCGGGGUUAC--GUAGC--CUCCAAAC-----ACCCG-GC-AGUC-UGU-GGUGUUCUACUGUGGACAGCUUGUGU-GUUGGU-GGACUACU---GGU--AAGAA--UGG-UUGGUGUCAGCAGG--GAUGGG-UCC--C-----UUGG-----GGUCU--CAUC---UC-ACCAAGAUGAGUGGUGG--AAAUCU-GAUCAC
AAKN02012610.1/175677-175875 GUGAAGUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-GC-ACC--CCACUACC-UUCU-UCAAGCCCC-GUUC-CUGUUCU-AGGGAC--UCAGGGCUCU--GCGGC--CCCCAGU------GCCUU-GC-GGCC-UGC-AGCGUUCUGCUGCAGGU-GCGUG-GU-GCAG-G-GGGCUGU----GGG--AG------GG-UGGACGGAGGCAG---------------------------------------------C-ACGAAGAUGAGUGGUG---GAAUCU-GAUCAC
AAWZ02013891.1/56008-56254   GUGAAAUGAUGAUGAAGUUUAUCCAUUCU-CUGAGUGUC-GCUG-CUCUGCCCUUCCU-GCUACGUUCAGGUCUCCGUUCU-GGGGUC--UUGGAUGAAA--G--GC--CUCCAGGC-----AUCUU-UC-AGCC-UUCUGGAGUUCUUCUGGGGGCUGGGAGCAUGGCUGGU-UGGCUGCU--GGCA--AGGCC--UGG-GCAGGGGCUGCGGGGCCAGAGC-ACCU-U-----UCUG----AGGGGC--UCUGACACCAACCAAGAAGAAUGAAA---CUGUCU-GAUCAC
AAPE02016204.1/51336-51100   GUGAAAUGAUGAUUGAGUUUAUCCAUUCG-CUGAGU-AC-GCUG-CACUGACCUUCUU-CCAAGCCUUGGUUC-CUGUUCU-AGGAAC--UCAGGGUUCA--GUAGC--CUCCAAAU-----GCCCU-GC-AGUC-UGU-GGUGUUCUACCAUGGACAGCUUGUGU-GUUGGU-GGACUACC---UGU--AAGAA--UGG-UUGGUGUCAGCAGG--GAUGGG-UCC--C-----UCUU-----GGGCU--CAUC---UC-ACCAAGAUGAGUGGUGG--AAAUCU-GAUCAC
AC172026.3/24408-24654       GUGAGGUGAUGAUGAAGUUUAUCCAUUCU-CUGAGU-GCAGUGG-CACUGCCCUCCUG-CAGCGCCCCGAUUC-CUGUUCU-AGGG----UCUGGGUGCCGUGCAGC--CUCCAGAG-----ACCCU-GC-AGUCUCCC-AGUGUGCUGCUGGGGGCUGCUGUGGU-GUGUGGCUGGCUGCC---UG---CAGGAGCCAA-GCAGUGCCGGCCGG--GUCAGG-GCCC-C-----UCUGUGGGGGGCUC--UGUC--ACC-ACUGAGACGAG-GGAUG--ACAUCU-GAUUGC
AAEX03013769.1/11938-12175   GUGAAGUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-GC-ACUG-UACUGACCUUCUU-CCAAGCCUUGGUUC-CUGUUCU-AGGAAC--UCGGGGCUAC--GUAGC--CUCCAAAU-----GCCCU-GC-AGUU-UGC-GGUGUUCUACCGUGGACAGCUUGUGU-GUUGGU-AGACUACU---GGU--UAGAA--UGG-UUGGUGUCAGUAGG--GAUGGG-GUCC-C-----UCUG-----GGUCC--CAUC---UC-ACCAAGAUGAGUGGUGG--AAAUCU-GAUCAC
AAQR03172061.1/1078-843      GUGAAAUGAUGAUUCAGUUUAUCCAUUCG-CUGAGU-GU-GCUG-CACUGACCUCCUU-CCAGGUCUCAGUUC-CUGUUCU-AGGAAC---UGGGGCUAU--GUAGC--CUCCAACU-----GCCCU-GC-AAUC-UGC-GGUGUUCUACUGCGGUCUGCUUGGGU-GUUGGC-AGACUAUC---GGU--AAGGA--UGG-UUGGUCUCAGCAGG--GACGGG-UCU--C-----UCUG-----GGUCC--CAUC---UC-UCAAAGAUGAGUGGUGA--AAAUCU-GAUCAC
#=GC SS_cons                 :::::::::[[[[[--[[[[--[[[[[[[.[[--[[.,,.((((.(((((((((((((.((,<<<<<<<<<<<.<<_____.>>>>>>..->>>>>>>,,..<<<<<..<<------.....<<<--.<<.<<<<.<<<.<<<<___>>>>>>>>>>>>>-->->>.------.>>>>>>>,...))-..)))))..-)).))))))-)))),<<..<<<<<<.-<<_._.....____.....>>->>..>>>>...>>.]]--]]-]]]]]]]---..]]]]--.]]]]]:
#=GC RF                      GUGAAAUGAuGauccAguuuAUCCauUCg.CUGAGu.gc.GcuG.CaccgccCuuCuu.ccaagccccgGuuC.CuGUUCU.aGGaaC..Ucggggcuau..GcaGc..CcCCAaau.....gCccU.gC.agcC.cgC.aGugUUCuaCuGcgGgcuGcuuguGc.GuugGu.gGgCugCu...ggu..aaGaa..uGg.gcgguGuCagCAGg..gacgGg.uCCc.c.....UcuG.....GGucC..cguc...cC.aCcaAGAcGAguGGugg..aaauCU.gauCaC
//
# STOCKHOLM 1.0

#=GF AC   RF00568
#=GF ID   SNORA26
#=GF PI   snoHBI-6
#=GF DE   Small nucleolar RNA SNORA26
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   40.00
#=GF TC   40.60
#=GF NC   39.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00032
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300924;
#=GF DR   snoopy; Loxodonta_africana300063;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF CC   The snoRNA HBI-6 belong to the H/ACA family of snoRNAs, guiding the
#=GF CC   pseudouridylation of position U4522 if the 28S rRNA. HBI-6 is the human
#=GF CC   orthologue of mouse MBI-6 snoRNA.
#=GF WK   Small_nucleolar_RNA_SNORA26
#=GF SQ   76


AC092814.2/136717-136838     AUGCCCUU--UU-AAGGUUG-AUGU----GG-UGCUUUAA-GAAGCUAACAU--------AGAAGGAUA-----AAGU-AAGUCUCUACAAAA--CCCAGAGA---------AGAGA-CU-GG-----AAAA-CUCC-UCUCUGG----------AUCCUGCC----UGGAGU-CACAGCU
AC104066.3/51055-51176       GUGCCCUU--UU-AAGGUUG-ACCC----AG-UGCUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGU-AAGUCUCCAUAAAA--CCCAGAGA---------AGAGA-CU-GG-----AAAG-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAACU
AL136367.10/60337-60471      GUGCCCUU--UU-AAGGUAG-ACGC----AG-UUUCGUAA-GAGGCUAACAC--------AUAAGGGUAAAUUAAAGU-AAGUCUCCAUAAAA--CCCAGAGAAGAGACAGAAGAGA-CU-GU-----GAAA-CUCC-UCUUUGG----------ACCCCAUC----UGGAGC-CACAGC-
AL121924.13/13903-13781      GUUCCCUU--UU-AAGGCUG-ACCC----AG-UGCUUUAA-GAGGCUGAUAC--------AGAAGGGUA-----AAGUUAAGUCUCCACAAAA--UCCAGGGA---------AGAGA-CU-GU-----GAAA-CUCA-UCUUAGA----------ACCUUGUA----UGGAGU-CACAGCU
AL050343.17/107475-107596    GUGCCCUU--UU-AAGGUUG-ACGC----AG-UGCUUUAA-GGGGCUAACAC--------AGAAGGGUA-----AAGG-AAGUCUCCAUAAAC--CCCAGAGA---------AGAGA-UU-GU-----AAAG-CUCC-UCUUUAG----------AACCUUUC----UGGAGU-CACACCU
AC104066.3/85942-86065       GUGCCCCU--UUUAAGGUUG-ACAC----AG-UGCAUUAA-G---------C--------AGAAGGGUU-----AAGU-AAGUCUCCAUAAAA--CCCAGAGA---------AGAGA-AU-GU-----AAAG-CUCC-UCUUUGGAGGAGCUAGACUCCUGUC----UGGAGU-CACAGCU
AC104843.3/81519-81640       GCACCCCU--UU-AAGGCUG-AUGC----AA-UGCUUUAA-GAGGCUAACAC--------AGAAGGGUG-----AAGC-CAGUCUCCUUAAAA--CCCAAAGA---------AGAGA-UU-GU-----AAAA-CUUC-UCUUUGG----------CUCCUGUC----UGGAGU-CACAGCU
AC003109.1/71088-70967       GCACCCCU--UU-AAGGCUG-AUGC----AA-UGCUUUAA-GAGGCUAACGC--------AGAAGGGUG-----AAGC-CAGUCUCCUUAAAA--CCCAAAGA---------AGAGA-UU-GU-----AAAA-CUUC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AL133229.40/63450-63329      GUGUCCUU--UU-AAGGUUG-ACAC----AG-UGCUUUAA-GAGCCUAACAC--------AGAAAGGUA-----AAGU-AAGUUUCCGUAAAA--CCCAGAAA---------UGAUA-UU-GC-----AAAA-UUCC-UCUUUGA----------AUCAUGUC----UGGAGU-CACAGCU
AC132607.4/131317-131438     GUGCCCUU--UU-AAGGUUG-ACAC----UG-UACUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGG-AACUCUCCAUCAAA--CCCAGAGA---------AGAGG-CU-CC-----ACAC-CUCC-UCUCUGG----------AUCCUGUC----UGGAGU-CACAGCU
AC157768.4/34378-34499       GUGCCCUU--UU-AAGGUUG-AUAC----UG-UACUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGG-AACUCUCCAUCAAA--CCCAGAGA---------AGAGG-CU-CC-----CCAC-UUCC-UCUCUGG----------AUCCUGUC----UGGAGU-CACAGCU
AC104794.4/72269-72155       GUGCC------U-AAGGUUA-ACAC----AG-CGCCUUAA-GAGGCUAACAC--------AGAAGGGCA-----AAGU-AAGUCUCCAUAAAA--CCCAGAGA---------AGA---CU-GU-----GAAC-C-CC-UCUCUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAFC03059112.1/4655-4776     GUGCCCUU--UU-AAGGUUG-ACAC----AG-UGCCUUAA-GAGGCUAACAC--------AGGAGGGUA-----AAGA-AAGUCUCCAUAAAA--CCCAGAGA---------AGAGA-UU-UU-----AGAA-CUCC-UCUCUGG----------AUCCUGUC----UGGAGU-CACAACU
AANG01294629.1/560-441       GUGCCCUU--UU-AAGGUUG-ACGC----AG-UGCCUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGU-AAGUCUCCAUAAAA--CCCAGGGA---------UGAGA-CU--------AAAA-CUCC-UCUCUGG----------AUCCUGUC----UGGAGU-CACAGCG
ABDC01192626.1/1120-1246     GUGCCCUU--UU-AAAGUUG-ACGC----AG-UGCUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGU-AAGUCUCCAUAAAA--CCCAGAGA---------AGAGA-UU-UUUUAAAAAAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAPY01080840.1/831-711       GUGCCCUU--UU-AAGGCUG-CCGC----AG-UGCUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGU-AAGUCUCCAUAAAA--CCCAGAGA---------AGAGA--U-GA-----UCAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAQQ01275709.1/3638-3517     GUGCCUUU--UU-AAGGUUG-ACGC----AG-UGCUUUAA-GAAGCUAACAC--------AGAAGGGUA-----AAGC-AAACCUCCAUAGAA--CCCAGAGA---------AGAGA-UU-GC-----AAAA-CUCU-UCUUUGG----------AUCCUGCC----UGGAGU-UACCAAU
AAIY01681363.1/743-865       GUGCCCUU--UU-AAGGUUG-CUGC----GG-UACUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGC-AAGUCUCCAUUAAA--CCCAGAGA---------UGAGG-UC-GG-----CAGAACUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAACU
AALT01155338.1/5220-5099     UUGCUCUU--UU-AAGGCUG-AUGC----AG-UGCUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGU-GAAUCUCCAUAAAA--CCCAGGGA---------GGAGA-UU-GU-----AAAA-CUUC-UCUCUGG----------AUCCUGUC----UGGAGC-CACAUCU
AANN01548915.1/871-998       GUGCCCUU--CUUAGGGUUG-AUGCUUUAAG-UGCUUUAA-GACGUUAACAU--------AGAAGGGUA-----AAGUUAAGUCUUCAUGAAA--CCCAGAGA---------AGAGA-UU-GU-----AAAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGUA
AANU01167777.1/14247-14117   GUGCCCUU--UU-AAGGUAG-ACAC----AG-UUUUUUAA-GCGGCUAGCAC--------AGAAGGGUA-----AAGU-AAGUCUCCAUAAAA--CCCGGAGAACAGACAGAAGAGA-CU-GU-----GAAA-CUCC-UCUUUGG----------AUGCCAUC----UGGAGC-CAUAGCA
AAYZ01011551.1/5063-4943     AGGCCCCC--GU-GCAGCUG-AUGC----UG-UGCAGUGU-GAGGCCAACAC--------AGGAGGGCA-----GAGG-AACCCUCCAUGACA--CCCAGGGA---------AGAGC-CU-GC-----CCA--CUCC-UCUCUUG----------AGCCUGCC----UGGAGG-CACAGCU
AAFR03034824.1/101255-101375 UAGCCUGU--UA-AAGCUGC-AGUG----CU-UUAAGAGG-CUAACCCAGAA--------UGAAGGGUA-----UAAU-AAUUCUCCAUUAAA--CCCAAAUC---------AGAGA-UU--U-----AAAA-CUCU-UUUUUGG----------AUCCUGUC----UGGAGU-UACAGUU
AAVX01051330.1/2876-2757     UUGCCCAU--CU-AA-GAUG-AACC----A--UGUCUUAA-GUGGCCAACAC--------AAAAGGGUA-----GAGCAGAUUCUCUCUAAAA--CCCAAAGCAA-------AAGAU-CA----------UG-UCUAUGCUUUGG----------AUCCUGUC----GAGAGG-AACAAUG
AAPN01028125.1/2930-2813     GUGCUCCC--UU-AGAGCUG--CUU-----G-UGCUCUAA-GGGG-CAACAC--------AGGAGGGAA-----UAAC-AUUCCUCUCUUAAA--CCCAGAGC---------UGAGG-CU--A-----AAAA-CUCU-CCUCUGG----------AUCCUGUC----GGGAGG-CACACUG
AC115823.18/163775-163655    GUGCCCUU--UU-AAGGUUG-UCGC----AG-UACUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGG-AACUCUCCAUAAAA--CCCAGAGA---------GGAAA-AC--U-----ACAC-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAAAU
AANU01285329.1/14928-15047   AUGCCCUU--UU-AAGGUUG-AUGU----AG-UGCUUUAA-GAAGCUAACAU--------AGAAGGAUA-----AAAU-AAGUCUCUACAAAA--CCCAGAGA---------AGAUA-UU-GG-----AACA---CU-CCUCUGG----------AUCCUGCC----UGGAGU-CACAGCU
AALT01195919.1/538-416       GUACCCUU--CU-AAAAUUG-AUGC----AGUUGCUUUAC-AUUGACAAUGC--------AGAAAGGUA-----AAGU-AAGAAUCUAUAAAA--CCUAGAGA---------GGAGA-UU-GU-----AAAA-CUCC-UCUUUGG----------AUUCCGCC----UGGAGA-CAAACUG
AAIY01305850.1/2017-2139     GUGCCCCU--UU-AAGGUUG-CUGC----AG-UGCUUUAA-GAGGGGAACAC--------AGACUGGCA-----AGGC-ACCCCUCCAUAAAA--CCCAGAGA---------CGAGG-UC-UG-----UGGAACUCU-UCUUUGG----------AGCCCAUC----UGGAGU-CACAGCU
AANN01231112.1/4311-4196     AUGCCCUU--UU-AAGG-------C----UU-UAAUUUAA-GAAGUUAACAU--------AGAAGGGUA-----AAGU-AAGUUUUCAUAAAA--CCCAGUGG---------AGAGA-UU-GU-----GGAA-CUCU-UCUUUGG----------AUCCUGUC----UGGAGU-UACAGUU
AAIY01697128.1/2417-2295     GUGCCCUU--GU-AAGGUUG-UUGC----AG-UACUUUAA-GAGGUGAACAC--------AGAAAGGCA-----AAAC-GAGUUUCCAUAAAA--CCCAGAGA---------UGAGG-UC-AC-----CAUAACUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAACU
AANN01321984.1/2338-2458     UUGCCCUU--UU-AAAGUUA-AUGC----AA-UGGUUUGA-GAGGCUAACAC--------AGAAGGGCA-----AAAU-AAGUGUCUAUAAAA--CCCAGGGA---------AGAGG-UU-AU-----AAAA-AUU--UUCUUGG----------AUCCUAUC----UGGACC-CAAGAAA
AANN01560516.1/946-827       UUAUCCUUACCU-AAAG----ACUC----AC-UG-UUUAA-GAAGCUAACAC--------AGAAGGGUA-----AAGU-AAGUCUCCAUAAAA--CCCAGGGG---------AGAGA-UU-AC-----AGAA-CUCU-UCUUUGG----------AUCCUGUC----UGGAGU-UACAGUU
AANU01259296.1/637-755       GUGCCCUU--UU-AAGGUUG-ACAC----AG-UGCCUUAA-GAGCCUAACAC--------AGAAG---U-----AAGU-AAGUUUCCAUAAAA--CCCAGAGA---------CUAUA-UU-GC-----AAAA-UUCC-UCUUUGG----------AUCAUGUC----UGGAGU-UACAGCU
AAIY01135236.1/1354-1232     GUGCCCUU--UU-AAGGUUG-CUGC----AA-UACUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGC-AAGUCUCCAUAAAA--CCUAGAGA---------UGAGG-UUGGU-----ACAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CAUAACU
AAHX01114487.1/3009-3129     GUGCCCUU--UU-AAGGUUG-UCAU----GG-CUCUUUAA-GAGGCUAACAC--------AAAAGGGUA-----AAGG-AAGUCUUCAUAAAA--CCCAGAGA---------GGAAA-AC--U-----GCAC-CUCC-UCUUUGG----------UUCCUGUC----UGGAGU-UACAGAU
AAFC03006239.1/27684-27803   GUGCCCUU--UU-AAGGUU---CGC----AG-UGCCUUAG-GAGGCUAACAC--------AGAAGGGUA-----AAGA-CAGUCUCCGUAAAA--UCCAGAGA---------AGAGA-CU-GU-----GGAA-CUCC-UCUUUGG----------AUCCUGGC----UGGAGU-CACAGCU
AAHX01101167.1/63554-63434   GUGCCCUU--UU-ACGGUUG-UCAU----GG-UACUUUAA-GAGGCUAACAC--------AAAAGGGUA-----AAAG-AACUCUCCAUAAAA--CCUAGAGA---------GGAAA-AC--U-----ACAC-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CAUCAAU
ABDC01035061.1/905-1025      GUGUCAUU--UU-AAAAUUG-UUGC----AG-UGCUUUAA-GAGGCUAAAAC--------AGAAGGGUA-----UAGU-AAU-CUUCAUAAAA--CCCAAAGA---------AGAGA-UU-UC-----AAAA-CUCC-UAUUUGG----------AUCCUGUC----UGGAGU-CACAGCG
AANN01590790.1/418-297       GUGCCCUU--UU-GAGGUUG-AUGC----AG-UUCUUAAA-AAGGCUAACAC--------AGAAGGGUA-----GAAU-UAGUCUUCAUAAAA--CCCAGAAA---------AGAGU-UU-AU-----AAAG-UUCC-UCUUUGU----------AUCCUGUC----UGGAAU-CACAGUU
AALT01630531.1/704-582       GUGCCCUC--CU-AAGACUG-UCUU----GG-UGCUUUCA-GAGACUCGUGU--------AAGAGGGUA-----AAAU-CAGGCUCUAUAAAA--CCCAGGGA---------GGAAA-CU-GU-----AAAAAUUCC-UCCUUGG----------AUUCUGUC----UGGAGU-CACAGCC
AANU01275726.1/973-851       GUUCCUUU--UU-AAGGCUG-GCCC----AG-UGCUCUAA-GAGGCUGAUAC--------AGAAGGAUA-----AAGUUAAGUCUCCACAAAA--CCCAGGGA---------AGAGA-CU-GU-----GAAA-CUCC-UCUUAGA----------ACCUUGUA----UGGAGU-CAUAGCC
AAPY01066966.1/3579-3699     GUGCCCUU--CU-AAGGCUG-CCGC----AG-UGCUUUAA-GAGUCUAACAU--------AGAAGGUUAA----AAGC-AAGACUCCAUAAAA--CUCAGAGA---------AGAGA-CU-GU-----AAAA-CUCC---UCUGG----------AACCUGUC----UGGAGU-CACAACU
AAPY01466542.1/454-574       UUUCCUGU--GC-CCUGGUG-ACGC----CA-UGCUUUUA-GAGGCUAACAC--------GGAAGGGUA-----AAAU-AAGUCUCCAUAAAA--UCCAGAGA---------AGAGA--U-GA-----UAAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAACU
AANN01720545.1/1692-1813     GUGCUCUU--UU-AAGAUUG-ACUC----AG-CGCUUUAA-GAGGCUAACAC--------AGAAGGGAA-----AAGU-AAGUCUCCAUAAAA--GGCAAGGG---------AGAGA-CU-GC-----AAAA-CUCU-UCUUUGG----------AUCCUGUC----UGCAGU-CACAGUA
AALT01366975.1/3882-4000     GUACCUUG--UU-GGGCUUG-AUGC----AA-UGCUUUUA-GAGGCUAACAC--------AG-AGGGUA-----AAGU-AAGUCUCCAUAAAA--CCCAGAGA---------AGA---UU-GU-----AAAA-UUCU-UCUCUGG----------AUCCUGUC----UGGAGU-CAAAGUG
AAIY01537984.1/1758-1881     GUGCCCUU--UU-AAGGUUG-CUGC----AG-UACUUUAA-GAGGCUAACAC--------AGAA-GGUA-----AAGC-AAGUCUCCAUAAAAAACCCAAAGA---------CAAGA-UC-GG-----UAGAACUCC-UCUUUGG----------AUCCUAUC----UGGAGU-CACAAGU
AAHX01044405.1/16728-16849   GUGCCCUU--UU-AAGGUUG-GUAC----UG-UACCUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGG-AACUCUCCAUAAAA--CCCAGAGA---------AGAGG-CU-CC-----ACUC-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGUU
AAIY01364204.1/641-767       GUGCCCUU--UU-AAGGUUG-CUGC----GG-UACUUUAA-GAGGCUAACAC--------AGAAGGGUAAAUA-AAGC-ACGUCUCCAUAAAA--CCCAGAGA---------CGAGG-UC-GG-----CAGAACUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAPY01398231.1/628-744       GUGCCCU--------GGUUG-ACGC----CA-UGCUUUUA-GAGGCUAACAC--------GGAAGGGUA-----AAAU-AAGUCUCCAUAAAA--UCCAGAGA---------AGAGA--U-GA-----UAAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGUCCACACCU
AAHX01111635.1/42213-42089   GUGCCCUU--UU-AAGGUUG-UUGC----AG-UACUUUAA-GAGGCUAACAC--------AGAAGGAUA-----AAGG-AAGUCUCCAUAAAA--CCCAGAGA---------GGAAA-AC--U-----GCAC-UUCC-UCUUUGG----------AUCCUGUCUGACUGGAGU-CACAGAU
AAHX01035522.1/62311-62430   GUGCCCUU--UU-AAGGUUG-UCGC----AG-UACUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGG-AAGUCUCCACAAAA--CCCAGAGA---------GGAAA-AC-UG-----CA---CUCC-UCUUUAG----------AUCCUGUC----UGGAGU-CACAGAU
AAWR02005238.1/34286-34165   GUGCCCUU--UU-AAGGUUG-ACGC----AG-UGCCUUAA-GAGGCUAACAC--------AGAAGGGCA-----AAGU-AAGUCUCCAUAAAA--CCCUGAGA---------GGAGA-UU-GU-----CAGA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAGV020589914.1/158-279      GUGCCCUU--UU-AAGGUUG-AUUC----AG-UACUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAUU-AAGUCUCCAUAAAA--CCCAGAGU---------GGAGA-UG-AU-----AAGA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAGV020885411.1/189-309      CUGCGCUU--UU-AAGGUUG-AUUC----UG-CAUUUGAA-GAGGCUAACAC--------AGAAG-GUA-----AAGU-AAGUCUCCAUAAAA--CCCAGAGA---------GGAGA-UU-AU-----AAAA-CUCC-UCUUUGG----------AUUCUGUC----UGGAGU-CACAGCU
AAHX01079130.1/33673-33553   GUGCCCUU--UU-AAGGUUG-UCGC----AG-UACUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGG-AAGUCUCCAUAAAA--CCCAGAGA----------GGGA-AA-AU-----GCAC-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGAU
AAKN02048776.1/18001-18119   UUGCCCUU--UU-AAGGUUG-ACAC----AG-UGCCUUCA-AAGGGUAAUAC--------AGAAGGGAA-----AAGA-AAGACUCCUUAAAG--CCCAGAUA---------AGAGA-UU---------AAA-CUCU-UCUUUGG----------GUCCUGUC----UGGAGU-CACAGGU
AAGV020380741.1/1292-1163    GUGCCCUU--UU-AAGAUUG-AUUC----AG-UGCUUUAA-GUGGCUAAUAUAAAAAUGUAGAAGGGUA-----AAUU-AAUUCUCCAUAAAA--CCCAGAGA---------GGAGA-UU-GU-----AAAA-CUUC-AUUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAGV020162099.1/3074-3191    GUGCCCUU--UU-AAGGUUG-ACUC----AG-UGCUUUAA-GAAGCUAACAC--------AGAAGGGAA-----AA-----GUCUCCAUAAAA--UGCAGAGA---------GGAGA-UU-GU-----AAAA-CUCC-CCUUUGG----------AUCCUGUC----UGGAAU-CAUAGCU
AAKN02028256.1/29613-29732   GUGCCCUU--UU-AAGGUUG-AUAC----AG-UGCCUUAA-GAGGCUAACAC--------AGAAGGGUA-----CAGG-AACCCUCCAUAAAA--CCCAGAGA---------AGAGA-C---U-----UACG-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAQR03113377.1/14484-14606   GUGCCCUU--UU-AAGGUUG-AUGC----AG-UGCUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGU-AAAUCUCCAUAAAA--CCCAGAGA---------AGAGAUUU-UU-----GAAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAWZ02023673.1/55636-55753   UUGCCCUC--UU-AGAGCUG-G--U----GG-UGCUUUAA-GUGGCCAAUAC--------AGAGGGGUA-----GAGA-AAUUCUCUUUUAAA--CCCAGAGG---------CAAG---G-AU-----GACA-CUUU-CCUCUGG----------AUCCUGUC----AGGAGG-AACAAAU
EU240310.1/17-134            UUGCCCUC--UU-AAGUCUG-U--C----AG-UGUCUUAA-GUGGCCAGUAC--------GGAGGGGUA-----UAAC-AGUUCUCUCUCAAA--CCCAGAGG---------UGAGG-CU-GA-------AA-CUCU-UCUUUGG----------AUCACGCU----GAGAGG-AACAUGU
AAQR03087120.1/6291-6170     GUGCCCUU--UU-AAGGCUG-AUGC----AG-UGCUUUAA-GGGAGGAACAC--------AGAAGUAUA-----AAGU-GAGUUUCCAUAAAA--CCCAGGGA---------AGAGA-UU-AU-----AAAA-CUCU-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAGW02023741.1/4342-4222     GUGCCCUU--UU-ACAGCUA-ACAC----AG-UGCUUUAA-GAGGCUAACAC--------AGAAGGGGA-----AACU-AAGUCUCCACAAAA--CCCAGAGA---------AGAGA-GU-GU-----G-AC-CUCU-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAGW02020979.1/14284-14404   GUGUCCUU--UU-AGAGCUG-ACAG----AG-UGCUUUAA-GAGGCUAACAU--------AUAAGUGGA-----AAGU-AAGUCUCCAUAAAA--CCCAGAGA---------AGAG--AU-GG-----UCGU-UUCU-UCUUUGG----------AUCCUGUC----UGGAGU-CAACAGA
AAGW02061513.1/11131-11251   GUGCCCUU--UU-AGAGCUG-ACAG----AA-UGCUUUAA-GAGGCUAGCAC--------AGAAGGGGA-----AAGU-AAGUUUGCAUCAAA--CCCAGAGA---------AGAGG-UU-GU-----C-AG-CUCA-UCUUUGA----------AUCCUGUC----UGGAGU-CACAGCU
AAQR03045919.1/16161-16283   UUAUUCUU--UU-AAGGUUG-AUGC----AG-UUCUUUAA-GAGACUAACAU--------GGAGGGGUA-----AAGU-AAAUCUCCAUAAAA--CCUGGAGA---------AGAGAUUU-UU-----AAAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAPE02033947.1/17066-17187   GUGCCCUU--UU-AAGGUUG-ACUC----AG-UGCCUUAA-GAGGCUAACAC--------AGAAGGGUA-----AACU-AAGUCUCCAUAAAA--CCCAGAGA---------AGAGA-UG-GU-----AAAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAGU03060179.1/762-883       GUGCCCUU--UU-AAGGUUG-CUGC----AG-UGCUUUA-AGAGGCUAACAC--------AGAAGGGUA-----AAGU-AAGACUCUAUAAAA--CCCAGAGA---------AGAGA-CU-GG-----AGAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAGW02029205.1/32790-32910   GUGCCCUU--UC-AGAGCUG-ACAG----AG-UGCUCUGA-GAGGCUAACAC--------AGAAAGGGA-----AAGU-AAGUCUCCAUAAAA--CCCAGAGA---------AGAG--AU-GG-----UCGU-UUCU-UCUUUGG----------AUCCUGUC----UGGAGU-CACAAAU
AAQR03158722.1/20477-20597   UUUCCUGU--CC----CUUACAUGC----AG-UGCUUUAA-GAGGCUAACAC--------AGAAGGGUA-----AAGU-AAAUCUCCACGAAA--CCCAGAGA---------AGAGAUUU-UU-----AAAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAPE02020099.1/15927-16045   GAGC---U--CA-AGAAAUG-ACUC----CG-UGCCUUAA-GAGGCUAACCC--------AGAAAGGUA-----AAGC-AAGUCUCCAUAAAA--CCCAGAGA---------AGAGA-UG-GU-----AAAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
AAGW02003126.1/50054-50172   GUGCCCUU--UU-AAAACUG-A--C----AG-UGCUUUAA-GAGGCUAACAC--------AGAAGGGGA-----AAGU-AAGUCUCCCUAAAA--CCCAGAGA---------AGAGA-UU-GU-----C-AU-CUCC-UCUUUGG----------AUCCUGUC----UGGAGA-UACAGCU
AAEX03009059.1/223-344       GUGCGCUC--CC-AAGGCUG-CCGC----AG-UGCCCUGG-GAGGCCAACAC--------AGAAGGGGA-----CAGC-AAGGCUCCAUGAAA--CCCAGGGA---------CGAGC-CC-GC-----AGAG-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCC
AAPE02005831.1/27958-28072   ----AUAA--CU-AAA---A-UUUC----AG-UGCCUUAA-GAGGCUAACAC--------AGAAGGGUA-----AACU-AAGUCUCCAUAAAA--CCCAGAGA---------AGAGA-UG-GU-----AAAA-CUCC-UCUUUGG----------AUCCUGUC----UGGAGU-CACAGCU
#=GC SS_cons                 :<<<<<<<..<<.---<<<<.-<-<....__.________.>-->->>>>--........>>>>>>>>>.....----.--<-<<<<<-----..-<<<<<<<.........-<<<-.<<.__.....__>>.>>>-.>>>>>>>..........--------....>>>>>-.>::::::
#=GC RF                      gugCCcuu..cu.AAGguug.acgC....AG.UgCuUUAA.GAGgCcaacAC........agaagGGca.....AAGu.AAgUCUCCaUAAAA..CCCAgAga.........aGAgA.uu.gu.....aAaa.cUCc.ucUuUGG..........AUCCUGUC....uGGAGU.cACAgcU
//
# STOCKHOLM 1.0

#=GF AC   RF00569
#=GF ID   SNORD19
#=GF PI   snoHBII-108
#=GF DE   Small nucleolar RNA SNORD19
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF CL   CL00048
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300820;
#=GF DR   snoopy; Echinops_telfairi300842;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   Homo sapiens C/D box snoRNA HBII-108: This snoRNA is the human orthologue
#=GF CC   of the mouse MBII-108 and is predicted to guide 2'O-ribose methylation of
#=GF CC   the small 18S rRNA on position G683. snoRNA HBII-108 is encoded in a
#=GF CC   nucleostemin (NS) gene intron like the HBII-210
#=GF WK   Small_nucleolar_RNA_SNORD19
#=GF SQ   22


AC154727.2/126995-126920   GAGGUAUGAGG--AAAAUAUC-GG-A-CAGUCU-GAU-UAC-CACUGA-AGACUGAUAAGAUCCAACUCUGACCUCAACAAAGCC
AC104446.2/142006-142080   CAUGGGUGAGG--U-ACGAGG-AA-A-CAGUCU-GAU-AGU-CACUGA-AGACUGAUUAGAUCCAACUCUGAUCUCAGCAAAGCC
AAYZ01025109.1/988-1063    GAGGUAUGAGG--AAAAUAUC-CA-A-CAGUCU-GAU-UGU-CAUUGA-AGACUGGUAAGAUCCAACUCUGACCUCAGCAAAACU
AALT01657539.1/13774-13698 GAGGUAUGAGG--AAAACAUCUGA-A-CAGUCU-GAC-UGU-CACUGA-AGACUGAUAAGAUCCAACUCUGACCUCAGCAAAAGC
AAQQ01595244.1/2462-2385   GAGGUAUGAGG--AAAACAUCUGA-A-CAGUCUUGAU-UGU-CACUGA-AGACUGAUAAGAUCCAACUCUGACCUCAACAAAGCC
AAPY01503610.1/2448-2523   GAGGUAUGAGG--AAGACAUCUGA-A-CAGUCU-GAU--GA-CACUGA-AGACUGAUAAGAUCCAACUCUGACCUCAGCAAAGCC
AAIY01362622.1/331-406     GAGGAAUGAGG--ACAACGUC-UA-A-CAGUCU-GAU-GGU-CGCUGA-AGACUGAUAAGAUCCAACUCUGACCUCAGAAGCAGC
AANN01012319.1/1728-1803   GAGGCAUGAUG--AAGAGUCU-GA-A-CAGUCU-GAU-CAU-CUCUGA-AGACUGAUAAGAUCCAACUCUGACCUCAGUAGAGUC
ABDC01345891.1/5381-5304   GACGUAUGAGG--AAAACAUC-UC-AGCAGUCU-GAU-UGU-CACUGAGAGACUGGUAAGAUCCAACUCUGACCUCAGCAGAGCC
AAFC03120533.1/11585-11661 GAGGUAUGAGG--AAAACAUCUGC-A-CAGUCU-UAC-UGU-CUGUGA-AGACUCGUAAGAUCCAACUCUGACCUCAGUGGGACC
AC189953.7/179736-179669   GAGGUAUGAGG--C---------U-A-CAGUCU-AAU-AGU-CACUGA-AGACUGAUUAGAUCCAACUCUGACCUCAGCACAGCC
AAFR03021759.1/98983-98907 GAGGUAUGAGG--AAAACAUCUAA-A-CAGUCU-GAAAUAC-CAUUGG-AGACUG-UAAGAUCCAACUCUGACCUCAGCCUAGGC
AAPN01330667.1/6031-5955   GAGGAAUGAGG--AAAAUAUCUGA-U-CAGUCU-GAUAUAC-CACUGA-AGACUG-UAAGAUCCAACUCUGACCUAAAACUUGCC
AAGV020246218.1/212-136    GAGGUAUGAGGA-AAACGUCU-GA-A-CAGUCU-GAU-UGU-CACUGA-AGACUGAUAAGAUCCAACUCUGACCUCAGUUAAACC
AAWR02008448.1/15319-15243 GAGGUAUGAGG--AAAACAUCUAA-A-CAGUCU-GAU-UGU-CACUGA-AGACUGAUAAGAUCCAACUCUGACCUCAGCAGAGUC
AAHX01086457.1/2753-2829   GAGGUAUGAGG--AAAAUAUC-GGAA-CAGUCU-GAU-UAU-CACUGG-AGACUGAUAAGAUCCAACUCUGACCUCAGCAAAGCC
AAPE02022331.1/3639-3715   GAGGUAUGAGG--AAAACAUCUGA-A-CAGUCU-GAC-UUU-CCCUGA-CGACUGAUAAGAUCCAACUCUGACCUCAACAAAGCU
AAWZ02009384.1/14786-14710 GAGCUAUGAGG--AAAACACAAAA-A-CAUACU-GAC-AUUCCUCUGA-AGACUG-UCAGAUCCAACUCUGAGCUCACAGUUCCU
AAGW02044176.1/47346-47422 GAGGUAUGAGG-AAAAUAUCU-GA-A-CAGUCU-GAU-UGU-UGUUGA-AGACUGGUAAGAUCCAACUCUGACCUCAGCAAAACC
AAQR03061766.1/26928-27004 GAGGUAUGAGG--AAAACAUCUGA-A-CAGUCU-GAU-UGU-CAUUGA-UGACUGAUAAGAUCCAACUCUGACCUCAGCAAAGCC
AAGU03030346.1/20671-20598 GAGGUAUGAGG--AAAAUAUGUGA-A-CAGUCU-GAU-UGU-CAGUGA-AGACUGAUAAGAUCCAACUCUGACCUCAG---AGCC
AAEX03012193.1/13579-13503 GAGGUAUGAGG--AAAACAUG-UG-AGCAGUCU-GAU-UUU-CAUUGA-AGACUGAUAAGAUCCAACUCUGACCUCAAUAAAGCC
#=GC SS_cons               <<<<_______..________.__._.______.___.___.______._______________________>>>>:::::::::
#=GC RF                    GAGGUAUGAGG..AAAAcAuc.gA.A.CAGUCU.GAU.ugU.CacUGA.AGACUGAUAAGAUCCAACUCUGACCUCAgcaaAgCC
//
# STOCKHOLM 1.0

#=GF AC   RF00570
#=GF ID   SNORD64
#=GF PI   snoHBII-13
#=GF DE   Small Nucleolar RNA SNORD64
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   40.00
#=GF TC   41.30
#=GF NC   39.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00069
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300359;
#=GF DR   snoopy; Oryctolagus_cuniculus300041;
#=GF RN   [1]
#=GF RM   11726556
#=GF RT   The IC-SNURF-SNRPN transcript serves as a host for multiple small
#=GF RT   nucleolar RNA species and as an antisense RNA for UBE3A.
#=GF RA   Runte M, Huttenhofer A, Gross S, Kiefmann M, Horsthemke B, Buiting K
#=GF RL   Hum Mol Genet. 2001;10:2687-2700.
#=GF RN   [2]
#=GF RM   11106375
#=GF RT   Identification of brain-specific and imprinted small nucleolar RNA genes
#=GF RT   exhibiting an unusual genomic organization.
#=GF RA   Cavaille J, Buiting K, Kiefmann M, Lalande M, Brannan CI, Horsthemke B,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Proc Natl Acad Sci U S A. 2000;97:14311-14316.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The human snoRNA HBII-13 belongs to the C/D family of snoRNAs. It is
#=GF CC   expressed mainly in the brain, but is also in the lungs, the kidneys and
#=GF CC   muscle. HBII-13 snoRNA has no identified RNA target and is encoded
#=GF CC   together with HBII-436, HBII-437, HBII-438A/B and the clusters of HBII-85,
#=GF CC   HBII-52 snoRNA in a 460 kb intron of the large, paternally expressed,
#=GF CC   transcription unit (SNURF-SNRNP-UBE3A AS). This is antisense to maternally
#=GF CC   expressed UBE3A gene (Runt et al., 2001).
#=GF WK   Small_nucleolar_RNA_SNORD64
#=GF SQ   17


AF019618.1/48-114            GGAUUUGUGAUGAGCUGUGUUUAC--UGAGCAUGAUG--AAGUAAA-GCUCAACGU--GAUUACUCUGAAGUCC
AL590560.9/76944-76878       GGAUUUAUAAUGAGCUGUGUUUAC--UGAGCAUUAUG--AAGUAAA-GUUCAAUAU--GAUUACUCUGAAGUCU
AF357424.1/1-46              ------------------GUUUAC--UGAGCAUGAUG--AAAUGAU-GCUCAAAAU--GAUUACUCUGAAG---
AAQQ01222593.1/1115-1049     GGAUUUAUGAUGAGCUAUGUUUAC--UGAGCAUGAUG--AAGUGAA-GCUCAAUAU--GAUUACUCUGAGGUCC
ABDC01422018.1/1541-1475     GGAUUUAUGGUGAGCUGUGUUUAC--UGAGCAUAAUG--AAGUGAA-GCUCAAAAU--GAUUAAUCUGAAGUCC
AAHX01005649.1/32396-32462   GGAUUAAUGAUGAGCUGUGUUUAC--UGAGCAUAAUG--AAAUGAC-GCUCAAAAU--AAUUACUCUGAAGUCU
AANG01133930.1/627-693       GGAUUUAUGAUGAGUUAUGUUUAC--UGAGUAUGAUG--AAGUGAA-ACUCAGUGU--GAGUACUCUGAAGUCC
AANU01239566.1/309-375       GGAUUUAUAAUGAUCUGUGUUUAC--UGAGCAUGAUG--AAGCAAA-GUUCAAUAU--UAUUACUCUGAAGUCU
AANN01394342.1/692-758       GGAUUUAUGAUGAGCUAUGUUUAC--UGAGCAUGAUG--AAAUGAA-GCUUGAUAU--GAGAACUCUGAGGUCC
AALT01596450.1/8655-8723     GAAUUCAUGAUGAGCUAUGUCUAC--UGAGCAUGAUG--AAGUAAA-GCUCGGUGUUUGAGUGCUCUGAAGUCC
AAKN02054627.1/21298-21366   GGACUGAUGAUGAGCUUUGUGUAC--UGAGUGUGAAUGAACAUGAG-GUUCACUGU--GAUUACUCUGAAGUUC
AAGV020498068.1/2598-2665    GGAUUUAUGAUGAGAUAUGUUUAC--UGAGCCUGAUG--AAAAGAAAGCUCACUGU--GAUUACUCUGAAGUCC
AAQR03118736.1/1837-1901     GGAUUCAUGAUGAGCU--GUUUAG--UAAGGAUAAAU--AAGUGAA-GUUCAAAAU--GAUUAUUCUGAAGUUC
AAGW02050371.1/181014-180948 GGAUUUAUGAUGAGCUGUAUUUAC--UGAGCAUAAUG--AAGGGAG-GCUCCAUGU--GAUUACUCUGAAGUCC
AAWZ02014467.1/17795-17738   GGCACACUG--GAGCUCAGUU-----UGAGCAUGAUG--AAAUGAA-GCUCAAA----UAGAACUUU--CUGCC
AAEX03002194.1/136274-136214 UGAU--AUGAUGAG----GUGUAC--UGAGCAUGAUG--AAGUGUA-GCUCAAUGU--AAGUACUCUAAAGUCC
AAGU03082774.1/13444-13512   GGACUUAUGAUGAGAUAUGCUGACUAUGAGCAUGAUG--AAGUGAA-GCUCAAUAU--GAUUUCUCUGAAUUCC
#=GC SS_cons                 <<<<<------<<<-----<<---..<<<<<______.._______.>>>>>----..>>--->>>--->>>>>
#=GC RF                      GGAuuuAUGAUGAGCUaUGUcUAC..UGAGCAUGAUG..AAgUGAA.GCUCAAuaU..gAuUACUCUGAagUCC
//
# STOCKHOLM 1.0

#=GF AC   RF00571
#=GF ID   SNORD65
#=GF PI   snoHBII-135
#=GF DE   Small nucleolar RNA SNORD65
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   41.00
#=GF TC   41.70
#=GF NC   40.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00057
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Oryzias_latipes300031;
#=GF DR   snoopy; Gasterosteus_aculeatus300007;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA HBII-135 belongs to the CD family of snoRNAs. It is the human
#=GF CC   orthologue of the mouse MBII-135 snoRNA and is predicted to guide
#=GF CC   2'O-ribose methylation of the small 18S rRNA at residue U627.
#=GF WK   Small_nucleolar_RNA_SNORD65
#=GF SQ   26


AC021876.5/63434-63504     AAAUAAUGAAAUCA---CCCA-AAAUAGCUGGAAUUACUGGCAGAUUGUGUAGCAAUAAACCUA---GUUUUCUGAAG
AC093484.2/162015-162087   AAAUGAUGAAAUCA---CCCA-AAAUAGCUGGAAUUACCGGCAGAUUGUGUAGUGGUGAACCUA-UGGUUUUCUGAAG
AL596181.10/69636-69565    AAAUGAUGAUAUCA---CCUA-AAAUAGCUGGAAUUACCGGCAGAUUG-GUAGUGGUGAGCCUA-UGGUUUUCUGAAG
AC016868.8/21258-21186     GUGUGAUGAAAUCA---CCCC-AAAUAGCUGGAAUUACCAGCAGAUUGUGUAGUGGUGAACCUA-CAAUUUUCUGAAG
ABDC01002234.1/21842-21770 AAAUGAUGCAAUCA---CUCA-AAAUAGCUAGAAUCACCAGCAAAUUUUGUAGUGGUGAACCUA-UGGUUUUCUGAAG
AANN01832263.1/8065-8137   AAAUGAUGAGAUCA---CCCA-AAAUAGCUGGAAUUACCGGCAGAGUGUGCAGUGGUGAGCCUA-AGGUUUUCUGAAG
AANG01607185.1/3082-3009   AAAUGAUGAAAUCG---CCUAAAAAUAGCUGGAAUUACCGGCAGAUUGUGUAGUGUUGAACCUG-UGGUUUUCUGAAG
AAFC03040867.1/16440-16367 CAAUGAUGAAAUCA---CCCAAAAGAAGCUGGAAUUACCGGCAGAUUGUGUAGUGGUGAACCUA-CGGUUUUCUGAGG
AAPY01717232.1/878-950     AAUUGAUAAAGACA---CCCA-AAAUAGCUGGAAUUACUGGCAGAUUAAGUAGUGGUGAACCUG-UGGUUUUCUGAAG
AAIY01670945.1/2472-2542   AUGUGAUGAAAUAA---CCUG-AAAUAGCUGGAAUUACCGGCAGAUGGUAUGGUGGUGAGUCUG---GUUUUCUGAAG
AAYZ01315227.1/502-575     CCAUGAUGAAAUUG---CCAAAAAAUAGCUGGAAUUACCGGCAGAUUGUAUGGUGGUGAGCCUG-UGGUUUUCUGAAG
AAVX01028731.1/116-47      GAAUGAUGAAACCA---ACUC-AAAUAGCUGGAAUUACCGUCAGAUUGUACAGUGUUGAGUA-A-UGAUUUUCUGA--
AAFR03054690.1/25696-25766 AAAUGAUGAGAUUC---ACCC-AAACAGCUGGAAUUACCGGCAGAUUGUUCAGUGGUGAGCCCG-CGGUUUUCUGA--
AAPN01320668.1/1718-1789   GGAUGAUGAAAGUU---ACCA-AAAUAGCUGGAAUUACCGGCAGAUGGAAUGGUGGUGAGCC-A-UGGUUUUCUGAAG
BAAF04066340.1/2308-2381   UAGUGAUGAAACUAA-ACUGA-AAAUAGCUGGAAUUACCGGCAGAUUGUUCAGUGGUGACUCUC--GGUUUUCUGAAU
AAHX01100517.1/24518-24447 AAAUGAUGAUAUCA---CCUA-AAAUAGCUGGAAUUACUGGCAGAUUA-CUAGUGGUGAGCCUA-CGAUUUCCUGAAG
AAKN02044276.1/21509-21579 AAAUGAUGAAAUAA---CCAA-AACUAGCUGGAAUUACCGGCAGAUUG-GCAGUGGUGA-CCCA-GGGUUUUCUGAAG
AAGV020452875.1/2316-2246  AAAUGAUGAGAUCA---CCAA-AAAUAGCUGGAAUUACCGGCAGAUGGUGUAGUGGUGAGCAUG---GUUUUCUGAAG
AAPE02062154.1/5566-5494   CAAUGAUGAAAUCA---CCCA-AAAUAGCUGGAAUUACCGGCAGAUUGUGUGGUGGUGAACUUA-CGGUUUUCUGAGG
AAGW02049334.1/40316-40389 CAAUGAUGAAAUCA---CCGAAAAAUAGCUGGAAUUACCGGCAGAUUGUGUGGUGGUGAGCCCA-AGGUCUUCUGAAG
AACN010050893.1/1752-1825  AAAUGAUGAGAUCA---CCCA-AAAUAGCUGGAAUUACCGGCAGAUUGUAUAGUGGUGAAUGUAAUGGUUUUCUGAAG
AAQR03057392.1/10113-10183 AAAUGAUGAAAUCA---CCCC-AAAUAGCUGGAAUUACUGGCAGAUUA--UAGUGGUAAACCUA-CAGUUUUCUGAAG
AAGU03082540.1/19827-19755 ACAUGAUGAGAUAA---CCCA-AAAUAGCUGGAAUUACCGGCAGAGUGUGUAGUGGUGAACCUG-UGGUUUUCUGAAG
AACZ03050570.1/28989-28917 AAAUGAUGAACUCA---CCUA-AAAUAGCUGUAAUUACCAGCAGAUUAUGUAAUGGCAAACCUA-CAGUUUUCUGAAG
EU094168.1/3-76            CAGUGAUGAGAACAAACCCCA-AAACAGCUGGAAUUACCGGCAGAGUC-CCCGUGGUGACUCCG--GUUUCUCUGAGU
JN899126.1/3-75            AAAUGAUGAAAUAA---CCCA-AAAAAGCUGGAAUUACCGGCAGAUGGUACAGUGGUGAACCUA-UGGUUUUCUGAAG
#=GC SS_cons               ::::::::::::::...::::.::::::::::::::::::::::::::::::::::::::::::.:::::::::::::
#=GC RF                    aAaUGAUGAaAucA...CCcA.AAAUAGCUGGAAUUACCGGCAGAUUGUgUaGUGGUGAaCCUa.uGGUUUUCUGAAG
//
# STOCKHOLM 1.0

#=GF AC   RF00572
#=GF ID   SNORD66
#=GF PI   snoHBII-142
#=GF DE   Small nucleolar RNA SNORD66
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   32.00
#=GF TC   32.00
#=GF NC   31.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300873;
#=GF DR   snoopy; Oryzias_latipes300087;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA HBII-142 is part of the C/D family of snoRNAs. It is the human
#=GF CC   orthologue of the mouse MBII-142 snoRNA and is predicted to guide
#=GF CC   2'O-ribose methylation of small 18S rRNA at residue C1272.
#=GF WK   Small_nucleolar_RNA_SNORD66
#=GF SQ   20


AL365219.17/28721-28796    GUCCUCUGAUGACUUCAUG-UUAGUGCCA-CCUGUCUGGGCCACGGAGAACCCAUGAUGGAACUGAGAAUCUGA-GGAA
AC087898.19/20875-20801    UUCCGCUGAUGACUUC-UG-UCAGUGCCA-CGUGUCUGGGCCACUGAGACCACAUGAUGGGAUUGAGGACCUGA-GGAA
AC078797.20/67061-67136    UUCCUCUGAUGACUUCCUG-UUAGUGCCA-CGUGUCUGGGCCACUGAGACACCAUGAUGGAACUGAGGAUCUGA-GGAA
AANU01242813.1/17396-17471 GUCCUCUGAUAACUUCGUG-UUAGUGCCA-CCUGUCUGGGCCACUGAGUACCCAUGAUGGAACCGAGGAUCUGA-GGAA
AANG01284517.1/9342-9417   UUCCGUUGAUGACUUCUUG-UUAGUGCCA-CGUGUCUGGGCCACUGAGACCGUGUGAUGGAACUGAGGAUCUGA-GGAA
AANN01513266.1/2600-2525   UUCCACUGAUGACGCUUUG-UUAGUGCCA-CGUGUCUGGGCCACUGAGACCCCAUGAUGGAACUGAGGAGCUGA-GGAA
AAYZ01187611.1/6223-6299   UUCCACUGAUGACUUUCUGUUUAGUGCCA-CGUGUCUGGGCCACUGAAUCCUCAUGAUGGAACUGAGGAUCUGA-GGAA
AAHX01070267.1/49076-49002 UUCCGCUGAUGACGUC-UG-UUAGUGCCA-CGUGUCUGGGCCACUGAGAGCACAUGAUGGGAUUGAGGAUCUGA-GGAA
BAAE01062600.1/4337-4262   CUCUGAUGAUGACUCCUGU-UUUGUGCCA-CGUGUCUGGGCCACUGAAUGCUCAUGAUGGCAAUGAGGAUCUGA-AGAA
AAPN01189324.1/1583-1659   CUCCGCUGACGAAUGCUUG-UUUGAGCCAUCGUGUCUGGGCCACUGACACCCCGUGAUGGAACUGAGGAUCUGA-GGAG
AAFR03062736.1/1625-1698   CUCCAGUGAUGACCUUUUG---AGUACCA-UGUGUCUGGGCCACUGAGAUACUGUGAUGGAGCUGAGGUUCUGA-GGAG
AAKN02012308.1/44499-44574 UUCCGAUGAUGACUUCUUG-UUAGUGCCA-CGUGUCUGGGCCACUGAGACCCCAUGAUGGAACUGAGGACCUGA-GGAA
CU462977.6/91080-91155     CUCCACUGAUGACCUUCAU-UAAGAGCCA-CGUGUCUGGGCCACUGAUCUACACUGAUGGGAUUGAGGAACUGA-GGAG
AAWZ02021625.1/80289-80213 CUUCUAUGAUGACCUCUUU-UUUGAGCCAUCGUGUCUGGGCCACUGACACACUGUGAUGGAGUUGAGGAUCUGA-GCAG
AACN010667949.1/85-160     UUCCACUGAUGACUUCUUG-UUAGUGCCA-CGUGUCUGGGCCACUGAGACCACAUGAUGGAACUGAGGAUCUGA-GGAA
AADN03005853.1/9118-9194   UUCUUGUGAUGAAUUCUAC-UUUGUGCCAUCGUGUCUGGGCCACUGAUACUUCAUGAUGGUAAAGAGGAUCUGA-GGGG
CAAB02011339.1/22139-22215 CUCCUGUGAUGACUGAUGC-UUUGUGCCA-CGUGUCUGGGCCACUGAAUGAUCGUGAUGGCUUUGAGGAUCUGAUGGAG
AAGW02014044.1/9328-9403   UUCCGUUGAUGACUUUCUG-AUAGUGCCA-CGUGUCUGGGCCACUGAGUCCUCAUGAUGGAACUGAGGAUCUGA-GGAA
EU094159.1/4-81            CUUCGCUGAUGACUCCCUG-UUCGUGCCGUCGUGUCUGGGCCACUGAGACCUGGUGAUGGAGAUGAGGAUCUGAGGAAG
JN899127.1/2-77            UUCCACUGAUGACUUCUUG-UUAGUGCCA-CGUGUCUGGGCCACUGAGACCCCCUGAUGGAACUGAGGAUCUGA-GGAA
#=GC SS_cons               <<<<_______________._________.____________________________________________.>>>>
#=GC RF                    cUCCucUGAUGACUUcuUg.UUaGUGCCA.CGUGUCUGGGCCACUGAgaccucaUGAUGGaAcUGAGGAUCUGA.GGAg
//
# STOCKHOLM 1.0

#=GF AC   RF00573
#=GF ID   SNORD67
#=GF PI   snoHBII-166
#=GF DE   Small nucleolar RNA SNORD67
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Takifugu_rubripes300018;
#=GF DR   snoopy; Gallus_gallus300091;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA HBII-166 belongs to the C/D family of snoRNAs. It is the human
#=GF CC   orthologue of the mouse MBII-166 and is predicted to guide 2'O-ribose
#=GF CC   methylation of snRNA U6 at residue C60.
#=GF WK   Small_nucleolar_RNA_SNORD67
#=GF SQ   15


AC115088.6/123021-122911       UGUGAGAGUGAUGAGUUGCAC---ACUGGUGGAGCCAUGGUAUCAGGUGAUACA-GGC-ACCACUCAGU-AU-CACCCUGGUGACAAAAUCAAGUGCACAGGGGCCAUCUGACUCACA
AANN01521896.1/8940-8830       UGUGAGAGUGAUGAGUUGCAC---ACUGGUGGAGCCACUGUAUCAGGUGAUACA-GGC-GCUGCUCAGU-AC-CACCCUGGCGACAAAAUCAAGUGCACAGGGGCCAUCUGACUCACA
AAPY01607636.1/641-751         UGUGAGAGUGAUGAGUUGCAC---ACUGGUGGGGCAACGGUGUCAGGUGAUACC-AGC-ACCACUCAGU-AC-CACCCUGGUGACAAAAUCAAGUGCACAGGGGCCAUCUGACUCACA
AANG01792695.1/556-445         UGUGAGAAUGAUGAGUUGCAC---ACUGGUGGUGCCACAGUGUCCGGUGACACG-GGC-ACCAGUCAGUUAC-CACCCUGGUGACAAAAUCAAGUGCACAGGGGCCAUCUGACUCACA
AAPN01125355.1/1356-1466       UGUGAGGGUGAUGAGUUGCAC---ACUGGUGGAGCCAAAGCAUCGGUCGAUGUG-GGC-GCCGCUCAGU-AU-CACCUUGGUGACAGAACCAGGUGCACAGGGGCCAUCUGACUCUCA
AAFR03038832.1/14502-14392     UGUGAGAGUGAUGAGUUGCAC---AUUAGUGUGGCCAUAGCAUCAGGUGAUGCA-GGC-UAUACUCAGU-AA-UAAACUGGUGACAAAGCCAUGUGCACAGGGGCCAUCUGACUCGCA
AANH01000144.1/7445-7558       GGUGAGAGUGAUGAGUUGCACUAAUCAGUUGGGGCGUUUGAUGCAGUGGCAUCGAUGC-CCCGAUCCGA-CC-CGACCUGAGGACA-CACUGUGUGCACAGGGGCCAUCUGACUCAAC
BAAF04066344.1/225-337         UGUGAGAGUGAUGAGUGGCACUGAAAAGUUGGCGU-GUUGUUGCAGUGGCAACAAAAC-CCCAAUCCGA-AC-CGCCAUGGGGACA-CACCAUGUGCACAGGGGCCAUCUGACUCCAC
CAAE01014581.1/7275709-7275822 UUUGAGAGUGAUGAGUUGCACGAAUCAGUUGGGGCGCUCGGUGCAGUGGCAACGGCGC-CCCAGUCCGA-GC-AGCGCUGAGGACACC-CUGGGUGCACAGGGGCCAUCUGACUCAAC
AAGV020455531.1/2-113          UGUGAGAGUGAUGAGUUGCAC---ACUGGUGGAGCCAUGGUAUCAGGUGAUACA-AGCCCCCACUCAGU-AU-UACUCUGUUGACAAAAUCAAGUGCACAGGGGCCAUCUGACUCACA
AAWR02037196.1/85385-85275     UGUGAGAGUGAUGAGUUGCAC---AAUGGUGAAGCCACAGUAUCAGGUGAUACG-GGC-AUCACUCAGU-AC-CACCCUGGUGACAAAAUCAAGUGCACAGGGGCCAUCUGACUCACA
AAWZ02018444.1/94508-94397     UGCGAGAAUGAUGAGUUGCACG--UUUGGUGGGGCU-GAGUGUCAGAUGACACA-AGC-ACCACUCAGA-AACCACCCUGAUGACAAUACCAAGUGCACAGGGGCCAUCUGACUCGCU
CAAB02000059.1/22013-21900     UUUGAGAGUGAUGAGUUGCACGAAUCAGUUGGGGUGUUUGAUGCAGUGGCAACAACAC-UCCAAUCCGA-UC-CAACCUGAGGACACGCACA-GUGCACAGGGGCCAUCUGACUCAAC
AADN03004572.1/34736-34846     UGCGAGAGUGAUGAGCUGCAC---UCUGGUGGAGCAACCAUGUCAGGUGACGUG-GUC-UCUGCUCAGA-AU-CUCCCUGAUGACAAAACUAGGUGCACAGGGGCCAUCUGACUCGCU
AL691489.21/136115-136225      UGUGAGAGUGAUGAGUUGCAC---ACUGGUGGAGCCAUAGUAUCAGGUGAUACA-GGC-ACCACUCAGU-AC-UACCCUGGUGACAAAAUCAAGUGCACAGGGGCCAUCUGACUCACA
#=GC SS_cons                   :::<-<<<-------------...<<<<<<<<-<<<---<<<<<____>>>>>-.>>>.->>>>->>>>.--.--------------------------------------->>>->:
#=GC RF                        UGUgAGaGUGAUGAGUUGCAC...acuGguGGaGccauaGuguCAGuuGacaCa.ggC.aCCacUCagu.ac.cacccUGguGACAaaAucAaGUGCACAGGGGCCAUCUGACuCaca
//
# STOCKHOLM 1.0

#=GF AC   RF00574
#=GF ID   SNORD69
#=GF PI   snoHBII-210
#=GF DE   Small nucleolar RNA SNORD69
#=GF AU   Marantidis E
#=GF SE   marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   37.00
#=GF TC   38.30
#=GF NC   35.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300500;
#=GF DR   snoopy; Oryctolagus_cuniculus300417;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA HBII-210 belongs to the C/D family of snoRNAs. It is the human
#=GF CC   orthologue of the mouse MBII-210 and is predicted to guide the 2'O-ribose
#=GF CC   methylation of large 28S rRNA on residue G4464.
#=GF WK   Small_nucleolar_RNA_SNORD69
#=GF SQ   11


AC104446.2/145501-145577   AAUGUGAAGCAAAUGAUGAUAAACUGGAUCUGACUGA----CUGUGCUGAGUCUGUUCAAUCCAACCCUGAGCUUCAUGUU
AC154727.2/125080-125001   AACAUGAAGCAG-UGAUGACAGAUUGGAUCUGACUUAACUGCUGUGCUGAGUUUGUUCAAUCCAACCCUGAGCUUCAUGUU
ABDC01345891.1/1521-1445   AACAUGAAGCAAAUGAUGAUAAACUGGAUCUGACUGA----CUGUGCUGAGUUUGUUCAAUCCAACCCUGAGCUUCGUGUU
AAYZ01417196.1/1128-1204   AACAUGAAGUAAAUGAUGAUACACUGGAUCUGACUGA----CUGUGCUGAGCUUGUUCAAUCCAACCCUGAGCUUCAUGUU
AANN01012319.1/4454-4530   ACCAUGAAGCAGAUGAUGAGAAACUGGGUCUGACAGA----CUGUGCUGAGUUUGUUCAAUCCAACCCUGAGCUUCAUGGU
AAIY01362622.1/3207-3282   GAUGUGAAGCAG-UGAUGAGAAACUGGAUCUGACUGG----CUGUGCUGAGUUUGUUCAAUCCAACCCUGAGCUUCACGUU
AAFR03021759.1/95855-95779 CACAUGAAGCAUAUGAUGACAAACUGGAUCUGAUAUU----CUAUGUUGAAUUUCUUCAAUCCAACCCUGAGCUUCAUGUU
AAPN01330667.1/4007-3933   AACAU-AAGCCUAUGAUGA-AAGUUGGAACUGACAUA----CCAUGCUGAGUUUGUUCAAUCCAACCCUGAGCUUCAUGUU
AAKN02001398.1/26445-26369 CCUAUGAAGCAAAUGAUGACAAACUGGAUCUGACUCA----CUGUGCUGAGUGUUUUCAAUCCAACCCUGAGCUUCAUGUU
AAPE02022331.1/5741-5817   CACAUGAAGCAAAUGAUGAUAAACUGGAUCUGACAGA----CUAUGCUGAGUUUGUUCAAUCCAACCCUGAGCUUCAUGUU
AAGW02044176.1/49228-49304 AACGUGAAGCAAAUGAUGAUAAAUUGGAUCUGAAUGA----CUGUGCGGAGUUUGUUCAAUCCAACCCUGAGCUUCAUGUU
#=GC SS_cons               <<<<<<<<<<___________________________....______________________________>>>>>>>>>>
#=GC RF                    aacaUGAAGCAaAUGAUGAuAAAcUGGAUCUGAcugA....CUgUGCUGAGUUUgUUCAAUCCAACCCUGAGCUUCAuguu
//
# STOCKHOLM 1.0

#=GF AC   RF00575
#=GF ID   SNORD70
#=GF PI   snoHBII-234
#=GF DE   Small nucleolar RNA SNORD70
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   48.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300782;
#=GF DR   snoopy; Gallus_gallus300095;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA HBII-234 belongs to the C/D family of snoRNAs. It is the human
#=GF CC   orthologue of the mouse MBII-234 and is predicted to guide 2'O-ribose
#=GF CC   methylation of the small 18S rRNA on position A512. It is hosted, together
#=GF CC   with HBII-95, by the core C/D box snoRNA protein encoding gene NOP5/NOP58.
#=GF WK   Small_nucleolar_RNA_SNORD70
#=GF SQ   21


AC147254.4/80430-80347       CUCAAUGU-U-GUCAAUGAUGCAU-CU---UAUUGGAACUGAAUU-UAAGUGAUCUAACCCA------UUCGUCACUACCACUGAGACAACAUUGAG
AC126934.4/123899-123813     UUCAUUGU-U-GUCAAUGAUGUAUACC---UUUUGGAACUGAAUC-UAAGUGAUUUAACAAAA----AUUCGUCACUACCACUGAGACAACAAUGAA
AC064836.7/15165-15252       UUCGUUGU-U-GUCAAUGAUGUAUUCU---UCUUGGAACUGAAUC-UAAGUGAUCUGACUCAAU---AUUCGUCACUACCACUGAGACAACGAUGAA
AC064836.7/16842-16926       UUCAAUGU-U-GUCAAUGAUGCAUUCU---UAUUGGAACUGAAUU-UAAGUGAUCUGACUCA------UUCGUCACUACCACUGAGACAACAUUGAG
AAFC03122356.1/4136-4222     UUCAAUGU-U-GUCAAUGAUGCAUUCU---UUUUGAAACUGAAUU-UAAGUGAUCUAACUCAA----AUUCGUCACUACCACUGAGACAACAUUGAG
AAPY01697198.1/233-321       UUCAUUGU-U-GUCAAUGAUGUAUUCU---UGUUGGAACUGAAUC-UAAGUGAUCUAACUCAAAU--AUUCGUCACUACCACUGAGACAACAAUGAA
AAYZ01352730.1/635-721       CUCAAUGU-U-GUCAAUGAUGCAUUCU---CAAUGGAACUGAAUU-UAAGUGAUCUGACUCAA----AUUCGUCACUACCACUGAGACAACAUUGAG
AAIY01449308.1/2140-2054     UUCAUUGU-U-GUCAAUGAUGUAUUCU---UGUUGGAAAUGAAUC-UAAGUGAUCUAACAAAU----AUUCGUCACUACCACUGAGAUGACAAUGAA
AANN01703169.1/274-359       ACCAAUGU-U-GUCAAUGAUGCAUUCA---UCC-GGAACUGAAUU-UAAGUGAUCUAACUCAA----AUUCGUCACUACCACUGAGACAACAUUGAG
AAPN01394254.1/830-918       CUCUUUGU-U-GUCAAUGAUGCAUUCA---UGUUGAAACUGAAUC-CAAGUGAUUUAACUGAACA--AUUCGUCACUACCACUGAGACAACACAAAA
AALT01509877.1/6732-6648     UCCAUUGU-U-GUCAAUGAUGUAU------UGUUGGAACUGAAUU-AAAGUGAUCGACUGCAUA---AUUCGUCACUACCACUGAGACAACAAUGAA
AAFR03042041.1/62388-62301   UUU--UGU-U-GUCAGUGAUGUACAUA---UGUUGGAACUGAAUCUUAAGUGAUAUCAUUUACCA--AUUCGUCACUACCACUGAGACAACACUGAA
AAZX01002711.1/12199-12116   UAUUUUAU----UCAAUGAUGAGUUCUG--UGUUUGAA---AAAA-UUAAUGAUGCACACAAUA---UUUCGUCACUACCACUGAGAAAAUAAAAAA
CR628393.11/8727-8637        UUAUCUGU-GCGUCUAUGAUGUUUCUG---UUCACCCAAUUCAAC-CAUGAGGUCACCAAACAGUU-AUUCGUCACUACCACUGAGACCACAAUUAU
AAGV020622443.1/4636-4725    UUCAUUGUGG-GUCAAUGAUGUAUUCU---UGUUGGAACUGAAUC-UAAGUGAUCUAACUUAAAG--AUUCGUCACUAUCACUGAGACAACGAUGAA
AAKN02019436.1/53252-53338   UUCAAUGU-U-GUCAAUGAUGCAUCCU---UAAUGCAACUGAGUU-UAAGUGAUCUAACUCAA----AUUCGUCACUACCACUGAGACAACGUUGAG
AAGU03009642.1/53180-53092   UUCAUUGU-U-GUCAAUGAUGUAUUCU---UGUCGGAACUGAGUC-UAAAUGAUCUAACUUAAAU--AUUCGUCACUACCACUGAGAUGACAAUGAA
AADN03005370.1/38306-38218   UAGUCUGU-U-GUCAAUGAUGGAUACC---UGUUGGAACUGAAUG-UAGCUGAUUUGAGUCAACA--UUUCGUCACUACCACUGAGACAACAGACAG
AAGW02042214.1/14113-14201   UUCAUCGU-U-GUCAAUGAUGUAUUCU---UGUUGGAACUGAAUC-CAAAUGAUCUAACUCAGAU--AUUCGUCACUACCACUGAGACAGCGAUGAA
AAEX03018026.1/118928-119013 UUCAAUGU-U-GUCAAUGAUGCAU-UC---UUUUGGAAUUGAAUU-UAAGUGAUCUAACUCAA----AUUCGUCGCUACCACUGAGACAACAUUGAG
AAGJ04142882.1/1874-1967     UCCACUUC-U-GUCAAUGAUGCAGAUAGAAUAUAGUAUGAGAUUA-UGAUGAUUAUCACAAAUUCUCAUUCGUCACUACCUCUGAGACAGAAAUGGA
#=GC SS_cons                 <<<<<<<<.<.<<<_____________..._______________.___________________..__________________>>>>>>>>>>>>
#=GC RF                      uucauUGu.u.GUCAAUGAUGuAUucu...UgUUGgAAcUGAAUu.UAAgUGAUcUaAcuaAaau..AUUCGUCACUACCACUGAGACaaCAaugaa
//
# STOCKHOLM 1.0

#=GF AC   RF00576
#=GF ID   SNORD71
#=GF PI   snoHBII-239
#=GF DE   Small nucleolar RNA SNORD71
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   34.00
#=GF TC   34.00
#=GF NC   33.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300812;
#=GF DR   snoopy; Loxodonta_africana300482;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA HBII-239 belongs to the family of C/D snoRNAs.It is the human
#=GF CC   orthologue of the mouse MBII-239 described and is predicted to guide
#=GF CC   2'O-ribose methylation of 5.8S rRNA on residue U14.
#=GF WK   Small_nucleolar_RNA_SNORD71
#=GF SQ   18


AC010653.10/104059-104144  UGUGU-GUU-GGAGGAUGAAAGUACGGAGUGAUCCAUCGGCUAAGUGUCUUGUCACAAUGCUGACACUC-AAACUGCUGACAGCACACG
AC122807.3/127086-127002   CGUGU-GCU-GGAGGAUGAA-GUAAGGAGUGAUCCAUCGGCUAAGUGUUUUCCCACUGUGCUGACACUC-ACAUUGCUGACAGUGCACG
AANG01668984.1/486-401     GGUGU-GCU-GGAGGAUGAAAAUACGGAGUGAUCCAUCGGCUAAGUGAUUUAUCACAAUGCUGAAACUC-AUAUUGCUGACAGCACACA
AAYZ01065789.1/754-669     UGUGU-GCU-GGAGGAUGAAAGUAAGGAGUGAUCCAUCGGCUGAGUGUCUUACCACAAUGCUGAAGCUC-ACACUGCUGACAGCACACA
AALT01270804.1/14576-14491 CGUGU-GUU-GGAGGAUGAAAGUACGGAGUGAUCCAUCGGCUAAGUGUUUUAUCACAAUGCUGAAACUC-AGGUUGCUGACAGCACACG
AAFR03032285.1/36420-36335 UGUGU-GUU-GGAGGAUGAAAACUUUGAGUGAUCCAUCGGCUGAGUGAUUUGUCACAAUGCUGAGACUC-AAGUUGCUGACAGCACACA
AAPY01318549.1/883-798     UGUGU-GUU-GGAGGAUGAAAAUAUGGAGUGAUCCAUCGGCUGAGUGUCUUAUCACAAUGCUGAAACUC-AACUUGCUGACAGCACACG
AAIY01530650.1/1620-1535   UGUGU-GCU-GGAGGAUGAAAACAAGGAGUGAUCCAUCGGCUGAGUGUCCUUUCACAAUGUCGAAACUC-GAAUUGCUGACAGCACACA
AAFC03018949.1/26979-27064 UGUGU-GCU-GGAGGAUGAAGAUACGAAGUGAUCCAUCGGCUGAGUGUUCUGUCACUAUGCUGAGACUC-GAAUGGCUGACAGCACACA
AAHX01098347.1/30704-30787 UGUGU-GCU-GGAGGAUGAA-GCAAGGAGUGAUCCAUCGGCUAAGUGUUUAC-CACUGUGCUGAAACUC-ACAUUGCUGACAGCGCACU
AAQQ01310605.1/2033-1951   UGUGU-GUU-GGAGGAUGAAAAUAAGGAGUGAUCCAUC-GCUAAGUGUCUA--CACGAUGCUGAAACUC-AAAUUGCUGACAGCACACA
AAPN01018749.1/27001-26915 UGUGU-GUU-GGAGGAUGAAAACUUUGAGUGAUCCAUCGGCUAAGUGACCUGUCACAGUGCUGAGACUCAAAACUGCUGACAACACACU
AAKN02026413.1/10226-10141 UGUGU-GUU-GGAGGAUGAAAAUAAGGAGUGAUCCAUCGGCUGAGUGUCUUAUCAUGAUGCUGAAACUC-AAUUUGCUGACAGCACACA
AAPE02023056.1/19145-19230 UGUGU-GUU-GGAGGAUGAAAAUACAGAGUGAUCCAUCGGCUAAGUGUUUUAUCACGAUGCUGAAACUC-AAAUUGCUGACAGCACACU
AADN03006341.1/17013-16927 AGUGCUGUU-GGAGGAUGAAGCCUUUGAGUGAUCCAUCGGCAGAGCUUGAUGUUGCUGUGCUGACACUC-GUGCUGCUGACAAUGCACU
AAGU03066274.1/1787-1872   UGUGU-GCU-GGAGGAUGAAAAUAAGGAGUGAUCCAUCGGCUAAGUGUCUUAUCACAAUGCUGAAACUC-GAAUUGCUGACAGCACACA
AAWZ02028829.1/28814-28729 UGUGC-UCUUGGAGGAUGAGGCCUGAGAGUGAUCCAUCGGCAGAGUGCCCAG-UGCAAUGGUGAAACUC-AUGCAGCUGACGGAGCACA
JN899129.1/1-86            UGUGU-GCU-GGAGGAUGAAAAUACGGAGUGAUCCAUCGGCCGAGUGUUUUAUCACAAUGCUGAAACUC-ACCUUGCUGACAGCACACG
#=GC SS_cons               :((((.(((.((,<<<<-<__________>->>>>,<<<<<---<<<______>>>--->>>>>,,,,,.,,,,,,))---))))))):
#=GC RF                    uGUGu.gcu.gGAGGAUGAAaauaagGAGUGAUCCAUCgGCuaAGuguuuUaUcaCaAUGCuGAaACUC.AaauUGCuGACagcaCACa
//
# STOCKHOLM 1.0

#=GF AC   RF00577
#=GF ID   SNORD72
#=GF PI   snoHBII-240
#=GF DE   Small nucleolar RNA SNORD72
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   43.00
#=GF TC   44.70
#=GF NC   39.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300852;
#=GF DR   snoopy; Gasterosteus_aculeatus300131;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA HBII-240 belongs to the CD family of snoRNAs. It is the human
#=GF CC   orthologue of the mouse MBII-240 and is predicted to guide 2'O-ribose
#=GF CC   methylation of the large 28S rRNA at residue U4590.
#=GF WK   Small_nucleolar_RNA_SNORD72
#=GF SQ   16


AC135079.9/151986-151906   AGCUUAUCAAUGAUGUCCUAAAAAA-UAAAUGUCUGAACAUAUGACUG-CUAUAAUGAUUUCAGCAUUUAA-CUGAGAUAAGCU
AB168634.1/2269-2348       AGCUUAUCAGUGAUGUUGUAAAAA--UAAAUGUCUGAACAUAUGAAUG-CAGUACUGAUUUCAGCAUUUAA-CUGAGAUAAGCG
AK124098.1/2478-2557       AGCUUAUCAGUGAUGUUGUAAAAA--UAAAUGUCUGAACAUAUGAAUG-CAGUAUUGAUUUCAGCAUUUAA-CUGAGAUAAGCG
AACN010405140.1/818-739    AGCUUAUCAAUGAUGUUGUAAAAA--UAAAUGUCUGAACAUAUGAAUU-UGAUACUGAUUUCAGCAUUUAA-CUGAGAUAAGCU
AAHX01013454.1/14613-14692 AGCUUAUCGAUGAUGUCCUAAAAG--UAAAUGUCUGAACAUAUGAAUG-CUAUACUGAUUUCAGCAUUUAA-CUGAGAUAAGCU
AAQQ01294809.1/310-389     AGCUUAUCGGUGAUGUUGUACAAA--UAAAUGUCUGAACAUAUGAAUG-CAAUAAUGAUUUCAGCAUUUAA-CUGAGAUAAGCU
ABDC01624612.1/609-532     AGCUUAUCAGUGAUGUUGUAAAAA--UAAAUGUCUGAACAUAUGAAUA-ACAU--UGAUUUCAGCAUUUAA-CUGAGAUAAGCU
AAIY01747932.1/696-617     AGCUUAUCGGUGAUGUUGUAAAAA--UAAAUGUCUGAACAUAUGAGUA-CAAUAAUGAUUUCAGCAUCAAA-CUGAGAUGAGCU
AAFC03009010.1/3782-3701   AGCUUAUCGGUGAUGUUCUAAAAAAAUAAAUGUCUGAACUUAUGAAUU-CAAUAUUGAUUUCAUCAUCUAA-CUGAGAUAAGCU
AAFR03031361.1/8719-8798   AGCUUGUCAGUGAUGUACUUUGAAA-AAAAUGUCUGAACAUAUGAAUU--AAUAGUGAUUUCAGCAUUUAA-CUGAGAUGAGCU
AANH01004731.1/3925-4003   UGCUUACCAAUGAUGCUG-AAAAA--UAAAUGUCUGAACAAAUGAUUU-CUAUA-UGAUAUCAACAUUUUCUCUGAGGUAAGCU
AAWR02016450.1/68382-68461 AGCUUAUCUGUGAUGUUGUAAAGA--UAAAUGUCUGAACAUAUGAAUU-CGAUACUGAUUUCAGCAUUUAA-CUGAGAUAAGCU
AAGU03020566.1/14414-14335 AGCUUAUCAGUGAUGUCAUAAAAA--UAAAUGUCUGAACAUAUGAAUA-CAAUACUGAUUUCAGCAUUUGC-CUGAGAUAAGCU
CR733210.1/707-786         AGCUUGUCAAUGAUGUUUCUUACU--AAAAUGUCUGAACAUAUGAACU-UCAUAGUGAUUUCAGUGCAUUA-CUGAGAUAAGCU
AAQR03055578.1/8380-8300   CUAUUAUCAGUGAUGUUGUAAAAA--UAAAUGUCUGAGCAUAUGAAUUACCAUAUUGAUUUCAGCAGUAGA-CUGAGAUUAAAA
AAPE02020502.1/9638-9559   AGCUUAUCAGUGAUGCUGUACAAA--UAAAUGUCUGAACAUAUGAAUU-CAAUAUUGAUUUCAACAUAUAA-CUGAGAUAAGCU
#=GC SS_cons               :<<<<<<<________________..______________________.______________________.____>>>>>>>:
#=GC RF                    AGCUuauCAgUGAUGUUgUAaAAA..UAAAUGUCUGAACAUAUGAAUu.caAUAuUGAUUUCAGCAUuUaA.CUGAGauaAGCU
//
# STOCKHOLM 1.0

#=GF AC   RF00578
#=GF ID   SNORD89
#=GF PI   snoHBII-289
#=GF DE   Small nucleolar RNA SNORD89
#=GF AU   Marantidis E
#=GF SE   marantidis E.
#=GF SS   Predicted; RNAalifold
#=GF GA   41.00
#=GF TC   42.00
#=GF NC   39.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300543;
#=GF DR   snoopy; Oryctolagus_cuniculus300130;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA HBII-289 belongs to the family of C/D snoRNAs. It is the human
#=GF CC   orthologue of the mouse MBII-289 and has no identified RNA target.
#=GF WK   Small_nucleolar_RNA_SNORD89
#=GF SQ   18


AC119809.10/32611-32502    GCUGAGGAGUGAUGACAU-AAAA-GGCCGAAUUGCAGUGUCUCC-AUCAACAGUUGGCUCUC--U---GAGCA--C-ACGAUGACAAAACCUCCUGAAGCGAGUCACU-GUC-UGACCUCAGU
AC013722.8/184033-183920   ACUGAGGAAUGAUGACAAGAAAA-GGCCGAAUUGCAGUGUCUCC-AUCAGCAGUUUGCUCUCCAU---GGGCA--C-ACGAUGACAAAAUAUCCUGAAGCGAACCACUAGUC-UGACCUCAGU
ABDC01304918.1/3845-3734   ACUGAGGAAUGAUGACACUAAAA-GGCCGAAUUGCAGUGUGUCC-AUCAGCAGUUUGCUCUC--U---GGGCA--C-ACGAUGACAAAAUCUCCUGAAGCGAACUAGUGGUC-UGACCUCAGU
AANG01205833.1/951-837     ACUGAGGAGUGAUGACAAUAAAA-GGCCGAAUUGCAGUGUGCCC-AUCAGCAGUUUGCUCUCUGU--GGGGCG--C-ACGAUGACAAAAUCUCCAGAAGCGAAUCACUGGUC-UGACCUCAGU
AAYZ01170191.1/5327-5218   ACUGAGGAAUGAUGACAGUAAAA-GGCCGAAUUGCAGUG--UCU-GUCAACAGUUUGCUCUC--U---GGGCA--C-ACGAUGACAAAAUCUCCUGAAGCGAACUACUGGUC-UGACCUCAGU
AAPY01027008.1/8-122       GCUGAGGAAUGAUGACAAUAAAAGGGCCGAAUUGCAGUGUGUCC-UAUAGCAGUUUGCUCUCUCU---GGGCA--C-ACGAUGACAAAAUCUCCUGAAGCGAAUCUCUGGUC-UGACCUCAGU
AAFC03010394.1/79139-79252 ACUGAGGAAUGAUGACACUAAAA-GGCCGAAUUGCAGUGUGCCC-CCUGGCAGUUGGCUCUCUCU---GGGUA--C-ACGAUGACAAAACCUCCUGAAGCGAACCUCUGGUC-UGACCUCAGU
AAQQ01025308.1/1204-1315   ACUGAGGAAUGAUGACAAGAAAA-GGCCGAAUUGCAGUGUCUCC-CUUAGCAGUUUGCUCUC--U---GGGUG--C-ACAAUGACAAAAUCACCUGAAGCGACCUACUGGUC-UGACCUCAGU
AAIY01076061.1/1256-1370   ACUGAGGAAUGAUGACAAUAAAA-GGCCGGAUUGCAGUGUCUCC-AUAAGCAGUUUGCUCUCUGU---GUGGAUGC-ACGAUGACAAAACCUCCUGAAGCGAACC-CUAGUC-UGACCUCAGU
AANN01761484.1/873-988     ACUGAGGAAUGAUGACAAUAAAA-GGCCGAAUUGCAGUGCCCCC-ACCAGCAGUUUGCUCUCUUU---GUGGAUGC-ACGAUGACAAAAUCUCCUGAAGCGAACCACU-GUCCUGACCUCAGU
AALT01411663.1/4348-4239   GCCGAGGAAUGAUGACAAUAAAA-GGCCGAAUUGCAGUGUCUCC--CCAGCAGUUGGCUCUC--U---GGGUG--C-ACGAUGACAAAACCCCCCGAAGCGAACCCC-AUUC-UGACCUCGGC
AAPN01148316.1/11303-11189 ACUGAGGAAUGAUGACAAUAAAA-GGCCGAAUUGCAGUGCUUCC-AUAAGCAGUUUGCUCUCUACAUGGAGCA--CAAUGA---CAAAGACUCCUGAAGCGAACUAUUGAUC-UGACCUCAGU
AAGV020441402.1/4362-4478  ACUGAGGAAUGAUGACAAUAAAA-GGCCGAAUUGCAGUGCCUCCAAAUUGCAGUUUGCUCUCUAU-AUGGAUG--C-ACGAUGACAAAAUCUCCUGAAGCGAACCACUGGUC-UGACCUCAGU
AAHX01059513.1/17513-17399 GCUGAGGAAUGAUGACAAUAAAA-GGCCGAAUUGCAGUGUCUCC-AUCAACAGUUUGCUCUCCGU-GUGGGCA--C-ACGAUGACAAAACCUCCUGAAGCGAGUCACU-GUC-UGACCUCAGU
AAWR02003365.1/26239-26352 ACUGGGGAAUGAUGACAGUAAAA-GGCCGAAUUGCAGUG--UCC-UCCAGCAGUUUGCUCUCUUG-UGGGGUA--C-ACGAUGACAAAAUCUCCUGAAGCGAACCACUGGUC-UGACCUCAGU
AAKN02027896.1/66040-65928 GCUGAGGAAUGAUGACAC-AAAA-GGCCGAAUUGCAGUGUCCCC-GUCUACAGUUUGCUCUCUGU---GGGCU--C-ACGGUGACAAAACUUCCUGAAGCGAAACAGCGCUC-UGACCUCAGC
AAQR03110130.1/1375-1490   ACUGAGGAAUGAUGACAAUAAAA-GGCCGAAUUGCAGUGUCUCC-AUCAGCAGUUUGCUCUCUGU-GUGGGCA--C-ACGAUGACAAAACCUCCUGAAGCGACCCACUGGUC-UGACCUCAGU
AAGW02007531.1/13538-13425 ACUGAGGAAUGAUGACAAUAAAA-GGCCGAAUUGCAGUGUCUCC-GUUAACAGUUGGCUCUCUGU---GGGCA--C-ACGAUGACAAAAUCUCCCGAAGCGAACCACCGGUC-UGACCUCAGU
#=GC SS_cons               [[[[[[[------[[[,,,,,,,.,<<______>>((((--(((.-((((,,<<-<<<<<_____...>>>>>..-.>><<-<______>->>))))-)-))--)))),]]].---]]]]]]]
#=GC RF                    aCuGaGGAAUGAUGacAauAAAA.GGCCGAAUUGCaguGucuCC.aucagCAGuUugCcCUCuau...GgGca..C.aCGaUgACAAAAccuCcugaAGCGaacCacugguC.UGACCuCaGu
//
# STOCKHOLM 1.0

#=GF AC   RF00579
#=GF ID   SNORD90
#=GF PI   snoHBII-295
#=GF DE   Small nucleolar RNA SNORD90
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   41.00
#=GF TC   41.90
#=GF NC   39.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300974;
#=GF DR   snoopy; Loxodonta_africana300518;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA HBII-295 belongs to the family of C/D snoRNAs. It is the human
#=GF CC   orthologue of the mouse MBII-295 and has no identified RNA target.
#=GF WK   Small_nucleolar_RNA_SNORD90
#=GF SQ   18


AC007066.4/164516-164622     AAGU----UUUCUAAGUGUCUAAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAAAA-UUUAAUUCAUCACUGAUACUCCUACUGUGGAAUCUGAAGACACUUGAAAACGU
AL929572.10/175094-174985    AAAUAAUGUUUUUAAGUGUCUAGUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAAAA-UUUAGUUCAUCAUUGAUUGUCCUAUUAUGAAAUCUGAAGACACUUGAAAAC-U
AAFC03111050.1/1381-1271     AAAUAAGUUUUCUAAGUGUCUAAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAAAA-UUUAAUUCAUCAUUGAUACUUCUACUAUGGAAUCUGAAGACACUUGAAAACUU
AANN01135589.1/606-496       AAAUUAGAUUUUUAAGUGUCUAAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGAUGAAAA-UUAAAUUCAUCACUGAUACUUCUACUGUGAAAUCUGAAGACACUUGAAAAACU
AAPY01745261.1/2883-2993     AAUUAAGUUUUCUAAGUGUCUGAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAAAA-CUUAAUUCAUCAUUGAUCCUCCUACUAUGGAAUCUGAAGACACUUGAAAGCAU
AAQQ01358583.1/359-469       GAAUAUGUUUUCUAAGUGUCUAAUGAUGA-GUUUCAUAGGGCAGAUUCUGAGAUGAAAA-UUUACUUCAUCAUUGAUACUCCUACUAUGAAAUCUGAAGACACUUGAAAACCU
AANG01754084.1/1570-1461     AAAUAAGUUUUCUAAGUGUCUAAUGAUGA-AGUUCAUAGGGCAGAUUCUGAGGUGAAAA-UUUCAUUCAUCACUGAUACUCCU-CUAUGGAAUCUGAAGACACUUGAAAACCU
AALT01485923.1/23521-23411   AAAUAAGUUUUUAAAGUGUCUAAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGAUGAAAA-UUGAAUUCAUCACUGAUACUUGUACUGUGAAAUCUGAAGACACUUAAAAACCU
AAYZ01222850.1/6201-6091     GAAGAAGUUUUUCAAGUGUCUCAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAAAA-UUUGAUUCAUCACUGAUACCCUAACUGUGAAUUCUGAAGACACUUGAAAACAU
AAFR03041314.1/160264-160153 UUUUGAGUUUUCUAAGUGUCUCAUGAUGAAAUUUCAUAGGGCAGAUUCUGAGAUGGGAA-UUGAAUUCAUCACUGAUAAAUAUUCUGUGAAAUCUGAAGACACAUGAAAAACU
AAPN01152521.1/3015-3126     AAUUAAAGUGCUAAAGUGUCUAAUGAUGAGGACUCAUAGGGCAGAUUCUGAGGUGAGCA-CUGAACUCAUCACUGAUAAUUGUUUGAUGCGAUCUGAAGACACUUGAAAGUCU
ABRN01365187.1/5441-5547     AAGU----UUUCUAAGUGUCUAAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAA-AAUUUAAUUCAUCAUUGAUACUCCUACUAUGGAAUCUGAAGACACUUGAAAACCU
AAKN02030304.1/77340-77450   AUAAAUGUUUUCUAAGUGUCUAAUGAUGA-GUUUCAUAGGGCAGAUUCUGAGGUGAAAA-UUUAGUUCAUCAUUGAUACUCUUUCUAUGGAAUCUGAAGACACUUCAAACCUA
AAWR02025687.1/6365-6255     AAAUAAGUUUUCUAAGUGUCUGAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAAAA-UUUAAUUCAUCACUGAUAGUCCUACUAUGGAAUCUGAAGACGCUUGAAAAUCU
AABR05100080.1/101248-101138 AAUAAUGUUUUCUAAGUGUCUAGUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAAAA-UUUAAUUCAUCAUUGAUUGUCCUAUUAUGAAAUCUGAAGACACUUGAAAACUA
AAPE02031984.1/129452-129562 UAAUGAGUUUUCUGAGUGUCUAAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAAAA-UCUAAUUCACCAUUGAUACUCCUACUAUGGAGUCUGAAGACACUUGAAAACCU
AAGW02054520.1/58849-58959   AAUUAAGUUUUCCAAGUGUCUCAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAAAA-UUUAGUUCAUCGUUGAUACCCCUACUAUGGAUUCUGAAGACACUUGAAAACCU
AAEX03006906.1/50218-50328   AAGUAAAUUUUCUAAGUGUCUGAUGAUGA-AUUUCAUAGGGCAGAUUCUGAGGUGAAAA-UUGUAUUCAUCAUUGAUAGUCCUAUUAUGGAAUCUGAAGACACUUGGAAACCG
#=GC SS_cons                 ::::::::::::<<<<<<<<<--------.<<<<<<<<<<<--<--<<-<-<<<<<<__._____>>>>>>->->>>-->>>>--->>>>>>>---->>>>>>>>>:::::::
#=GC RF                      aAauAAguUUUccaaGuGuCuaAUGAUGA.auuuCauagGgCAgAUuCUgAGguGaaAA.UUuAAuuCacCAcUGauAccCcuacUauGaaauCUGAaGaCaCuugAAAAccu
//
# STOCKHOLM 1.0

#=GF AC   RF00580
#=GF ID   SNORD91
#=GF PI   snoHBII-296A
#=GF DE   Small nucleolar RNA SNORD91 family
#=GF AU   Marantidis E
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   51.00
#=GF TC   53.30
#=GF NC   50.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; HBII-296A;
#=GF DR   snoRNABase; HBII-296B;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300936;
#=GF DR   snoopy; Echinops_telfairi300701;
#=GF RN   [1]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell. 2002;109:145-148.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. This family includes HBII-296A (SNORD91A) and
#=GF CC   HBII-296B (SNORD91B). They are close paralogues and share the same host
#=GF CC   gene (FLJ10534). Both snoRNAs and are predicted to guide 2'O-ribose
#=GF CC   methylation of the large 28S rRNA at position G4588 [3].
#=GF WK   Small_nucleolar_RNA
#=GF SQ   24


AC006435.7/3490-3399       UAGAGAAGUCAAUGAUGGUUUUAUUCAU-AUCGUCUGAACCUGUCUGAAGCAUCUCAGUGAUGCAAUCUCUGUGUGG-UUCUGAGACUUCU---CCA
AC006435.7/2333-2239       CUUAAGAGCCAAUGAUGUUUUUAUUCAA-AAUGUCUGAACCUGUCUGAAGCAUCCCAGUGAUGCAACUUCUGUGUGA-UACUGAGGCUUUUUUGCCA
AL604066.9/122672-122762   CUUAGGAGCCAAUAAUGUUUUUAUUCAA-AAUGUCUGAACCUGUCUGAAGCAUCCCAGUGAUGCAAAAU----GUUG-UACUGAGGCUUCUCUGCUA
AANG01158662.1/5412-5318   UCUAGGAGCCAAUGAUGUUUUUAUUCAC-AAUGUCUGAACCUGUCUGAAGCAUCCCAGUGAUGCAACCUCUGUGUGG-UGCUGAGGCUUCUCUGCCA
AAFC03038181.1/32658-32752 UUUAGGAGCCAAUGAUGUUUCCAUUCAA-AAUGUCUGAACCUGUCUGAAGCAUCCCAGUGAUGCAAACUCUGUGUGG-UGCUGAGGCUCCUGUGCCA
AAQQ01356717.1/1529-1435   CUUAGGAGCCAAUGAUGUUCUUAUUCAA-AAUGUCUGAACCUGUCUGAAACAUCUCAUUGAUGCAACUUCUGUGUGC-UGCUGAGGCUUCUCUGCCA
AAYZ01105433.1/696-601     CUUAGGAGCCAAUGAUGUUUUUAUUCAA-AAUGUCUGAACCUGUCUGAUGCAUCUCAGUGAUGCAAUCUUUGUAUUGCUGCUGAGGCUUCUCUGCCA
ABDC01240858.1/3725-3634   CAGAGAAGUCAAUGAUGGUUUUACCCAA-AAUGUCUGAACCUGUCUGAAGCAUCUCAGUGAUGCAGUCCCCGUGUGG-UUCUGAGACUUCU---CUA
AANN01330027.1/6135-6227   UAGAGAAGUCAAUGAUGUUUUUACCUAA-CAUGUCUGAACCUGUCUGAAGCAUCUCAGUGAUGU--UAUCUGUGUGG-UUCUGAGACUUCUCUGCUA
AADA01106034.1/182-88      CUUAUUAGGCAAUGAUGUUUUCAUUCCA-AAUGUCUGAACCUGUCUGAAGCAUCCCACUGAUGCAACCUUCGUGUGA-UACUGAGGCUUUUUUGCCA
AAIY01458109.1/1382-1474   UAGAGAAGUCAGUGAUGGUUUUACCCAG-AAUGUCUGAACCUGUCUGAAGCAUCUCAGUGAUGCGGCCUCU--GUGG-UGCUGAGACUUCUCUGAUA
AANU01110701.1/515-426     UGGAGAAGUCAGUGAUGGUUUUAUUCAU-GUUGUCUGAACCUGUCUGAAACAUC--GGUGAUGCAAUCUCUGGGUGA-UUCUGAGACUUCU---CUA
AALT01349646.1/581-675     AAGAGAAGUCAAUGAUGGUUUCAUCUAACAUUGUCUGAACCUGUCUGACGCAUCUCAAUGAUGCAGUGUUUGUG-GU-UUCUGAGACUUCUCUGUAU
AAFR03054580.1/13191-13098 UGGAGAAGCCAAUGAUGGUUUU-GCCAG-AAUGUCUGAACCUGUCUGAAGCAUCUUAGUGAUGCUACAUCCAUAUGG-CUCUGAGGCCUCUUUCUCU
AAPN01437579.1/109-203     UGGAGAAGCUAAUGAUGAGGAAAGCUAU-AAUGUCUGAACCUGGCUGAGGCAUCUUUGUGAUGCAUUCUCUUUUUAG-CUCUGAGGUUUCUCCAUAA
AAKN02033264.1/8112-8202   CUUAGGAGCCAGUGAUGUUUUUAUUCAU-AAUGUCUGAACCUAUCUGAAGCAUCGCCAUGAUGCAACAU----CUGU-UACUGAGGCUUCUUUGGCA
AAGV021021593.1/1092-998   UAGAGAAGUCAAUGAUGCUUUUACCAAA-AAUGUCUGAACCUGUCUGAAGCAUCUCAGUGAUGCAGUCUCUGUAUGG-UUCUGAGACUUCUCUGAGA
AAWR02013272.1/4663-4570   CUUAGGAACCGAUGAUGUUUUUAUUCAA-AAUGUCUGAACCUGUCUGAAGCAUCCCAAUGAUGC-AACUCUGUGUGG-UGCUGAGGCUUCUUUGCCA
AADN03007705.1/39231-39139 GCAAGAAGCCUGUGAUGUCUUA-GCCAC-AAUGUCUGAACCUGGCUGAAGGAUUCUUCUGAAGACACACACUUG-GG-CACUGAGGCUUCCAGGAGA
AAHX01064823.1/22327-22417 CUUAGGAGCCAAUGAUGUCUUUAUCCAA-AAUGUCUGAACCUGUCUGAAGCAUCUCAGUGAUGCACACU----GUUG-UGCUGAGGCUUCUCUGCUC
AACN010083780.1/1932-1838  UCUAGGAGCCAAUGAUGUUUUUAUUCAC-AAUGUCUGAACCUGUCUGAAGCAUCCCAGUGAUGCAAUCUUUCUGUGG-UGCUGAGGCUUCUCUGCCA
AAPE02038094.1/16004-16098 UUUAGAAGCCAAUGAUGUGUUUAUUCAA-AAUGUCUGAACCUGUCUGAAGCAUCCCAGUGAUGCUACCUCUGUGUGG-UGCUGAGGUUUCUCUGCCA
AAQR03150342.1/4164-4255   UAGAGAAGUCAAUGAUGACUUUGAAAAA-A-UGUCUGAACCUGUCUGAAGCAUCUCAGUGAUGCAAACCUUUUGUG---UCUGAGACUUCUCUGAGA
AAGW02049732.1/11737-11830 CUUAGGAGCCAAUGAUGUUUUUAUGCAA-AAUGUCUGAACCUGUCUGACGCAUCUCAGUGAUGC-AUCUCUAUGUGG-UGCUGAGGCUUCUCUGCCA
#=GC SS_cons               :::<<<<<<<__________________.________________________________________________.______>>>>>>>::::::
#=GC RF                    uuuAGaAGcCAAUGAUGuUUUuAuucAa.AAUGUCUGAACCUGUCUGAAGCAUCuCagUGAUGCAaucUcUgUgUGg.UuCUGAGgCUuCUcUGccA
//
# STOCKHOLM 1.0

#=GF AC   RF00581
#=GF ID   SNORD12
#=GF PI   SNORD106; snoHBII-99
#=GF DE   Small nucleolar SNORD12/SNORD106
#=GF AU   Marantidis E
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Marantidis E.
#=GF SS   Predicted; RNAalifold, Daub J
#=GF GA   43.00
#=GF TC   43.20
#=GF NC   42.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00044
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300989;
#=GF DR   snoopy; Oryzias_latipes300092;
#=GF RN   [1]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   12007400
#=GF RT   Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse
#=GF RT   cellular functions.
#=GF RA   Kiss T
#=GF RL   Cell. 2002;109:145-148.
#=GF RN   [4]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res. 2003;31:6543-6551.
#=GF CC   This family belong to the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. This family includes the human ortholog of mouse
#=GF CC   snoRNA HBII-99 and human snoRNA U106. In humans both HB11-99 and U106
#=GF CC   snoRNAs share the same host gene [1]. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs. HBII-99 is predicted to guide the 2'O-ribose methylation of 28S rRNA
#=GF CC   G3878 [2]. U106 contains conserved antisense elements which would predict
#=GF CC   U106 methylates residues G1536 and U1602 of 18S rRNA. However, these
#=GF CC   targets do not appear to be methylated and U106 might function as an RNA
#=GF CC   chaperone during rRNA folding [1]. A similar role has been suggested for
#=GF CC   the H/ACA snoRNAs U17a and U17b Rfam:RF00045 [1].
#=GF WK   Small_nucleolar_SNORD12/SNORD106
#=GF SQ   8


AL591711.22/138024-138113 GCUGGUGAA-CUGAUGAUAUCAUUUCUUUCCCCGUCAGAUCGACCCUGUUGAUCUCAAAUACUAAUUGCCAG-UUU-UGUCUGA--UGCAUCAGC
AL591711.22/137748-137836 AGGCAUG-U-GUGAUGACACAACUUUUUUCCCCAUCAGAUCGACCAUGUUGAUCACAUU-CUUUUAAGCCAG-UAU--GUCUGACAUGCCUGCCU
AL591711.22/136221-136311 GCUGGUGUAAAUGAUGAACUCACUUUUUUCCCCGUCAUAUCGACAGUGCUGAUGUUUUAAAACAUUUGCCAG-UUU-GUCCUGA--UAAACACCA
AY349607.1/2-78           G-----UAA-AUGAUGACUUCACUUUUUUCCCCAUCAGAUCGACAAUGCUGACGUCUUA-UAUU-UUGCCAG-UUA-GUUCUGA--UA------C
AL049766.14/57933-58022   GCCUUUGCAGCUGAUGAUACAGCUUCUUUCCCCAUCAGAUCGACCCUGUUGAUCUCUAC-ACUAUUGGCCAG-UUU-UGUCUGA--UGCAUUGGC
AL049766.14/57569-57659   GCUGGCAUAUAUGAUGACUUAGCUUUUUUCCCCGACAGAUCGACUAUGUUGAUCUAACU-UUUCUAAGCCAG-UUUCUGUCUGA--UAUGCCAGC
AL049766.14/56190-56278   GCUGGUGUAAAUGAUGACUUCACUUUUUUCCCCAUCAGAUCGACAAUGCUGACGUCUUA-UAUU-UUGCCAG-UUA-GUUCUGA--UACAUCGGC
CR390041.1/322-413        GCUGGUGUGGGUGAUGACUGAACUUUUUUCCCCAUCAGAGCGACAGUGUUGAUUACUCAUCACUCUAGCCAGGUCU-UGUCUGA--UGCACCAGC
#=GC SS_cons              <<<<<<<<<__________________________________________________.____________.___._______..>>>>>>>>>
#=GC RF                   GcugguguaaaUGAUGAcuuaACUUUUUUCCCCaUCAGAUCGACaaUGUUGAUcUcuua.uaUuuuuGCCAG.UUU.ugUCUGA..uacaccagC
//
# STOCKHOLM 1.0

#=GF AC   RF00582
#=GF ID   SCARNA14
#=GF PI   snoU100
#=GF DE   Small Cajal body specific RNA 14
#=GF AU   Marantidis E
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   40.00
#=GF TC   41.00
#=GF NC   39.20
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res. 2003;31:6543-6551.
#=GF RN   [3]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [4]
#=GF RM   16373490
#=GF RT   A computational screen for mammalian pseudouridylation guide H/ACA RNAs.
#=GF RA   Schattner P, Barberan-Soler S, Lowe TM
#=GF RL   RNA. 2006;12:15-25.
#=GF RN   [5]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. U100 belongs to the H/ACA
#=GF CC   box class of guide RNAs as it has the predicted hairpin-hinge-hairpin-tail
#=GF CC   structure and the conserved H/ACA-box motifs [2]. U100 is the human
#=GF CC   orthologue of mouse H/ACA snoRNA MBII-201 identified in [3] and also
#=GF CC   included in this family. U100 is predicted to guide the pseudouridylation
#=GF CC   of U2 snRNA at residue U7 [4].
#=GF WK   Small_Cajal_body_specific_RNA_14
#=GF SQ   22


AC055855.9/110736-110601     GUGACUGUUCCUGGUAUUGAUUGCAUUUG------UUAGUUGUACAGUGCAACCAUA--GAC-AGUCACACACAUUAAAA-CAGAUGGUUCCUGCCGACAGGGUCUGUAUAGUUAUCAGAUUUUCUGUGCGAUGGCUCCAUACAUG
AC135358.3/32139-32273       GUGACUGUACUUGGUAUUGAUUGCAUU-G------UUAGUUGUACAGUGCAACCGUA--GAC-AGUCACAUACAUCAAAA-CAGAUGGUUCCUGCCGACAGAGUCUGUAUAGUUGUCAGAUUUUCUGUGCGAUGGCUCCAUACAUA
BX005304.8/39970-39830       AAGUAUAUUU-UGUCAUAAAUUAAAAUGGUUGUACCAAGUUGUACAAUGCAACCAUA--GAU-AGUCACAUACAUCAAAA-CAGAUGGUUCCUGCCGACAGAGUCUGUAUAGUUGUCAGAUUUUCUGUGUGAUGGCUCCAUACAUC
AC115734.9/49995-49854       GUGAAUGUUUCUGAUAUUGAUUGCAUUUGCAUUUAUUAGUUGUAAAAUGCAAUGAUA--AAC-AGUCACAUACAUCAAAA-CAGAUGAUUCCUCCUGAAAGAAUCUGUAGAGUUGUCAAAUUUUCUGUGCAACAGCUCCAUACAUA
AAFC03019093.1/90754-90887   GUGACUGUUCCUGGUAUUGAUUGCAUUUG------UUGGUCGUACAGUGCAACCAUA--GGC-AGUCACAUACAUCAAAA-C--AUGGUUCCUGCCGACAGGGUCUGUAUAGUUAUCAGAUUUUCUGUGCGAUGGCUCCAUACAUG
AAYZ01062852.1/4067-3932     GUGACUGUUCCUGGUAUGGGUUGCAUUUG------UUAGUUGUGCGGUGUAACCAUA--GAC-AGUCACACACAUCAAAG-CAUGUGGUUCCUGCCGACAGAGUCUGUAUAGUUAUCAGAUUUUCUGUGCGAUGGCUCCAUACAUG
AAFR03022572.1/55067-55202   GUGACUGUACUUGGUAUUGGUUACAUUUG------UUAGUCACUGAGUGUAACCACA--GUC-AGUCACAUACAUCAACA-CAAGUGGUUCCUGCCGACAGGGUCUGUCUAGUUAUCAGAUUUCCUGUGCGAUGGUUCUGCACAUC
AANN01547278.1/1268-1401     GUGACUGUCCCUGGUACUGGUUGUAUCUG------UUAGUUGUACACUACAGCCUUG--GGA-AGUCACACACAUCAAAA-U--GUGGUUCCUGCCGACAGAGUCUGUAUAGUUAUCAGAUUCUCUGUGCGAUGGCUCCACACAUG
AAPN01423687.1/5814-5950     GUGACUGUACUUGGUACAGGUUGCAUUUG------UGAGUAGUCUGAUGCAACCACG--GCC-AGUCACGUACAUAAAAAUCCAGUGGUUCCUGCCGACAGGGUCUGUCUAGUGAUCAGAUUUCCUGUGCGAUGGCUCCGUACAAG
ABDC01123136.1/1381-1248     AUAAAAGUCU-AGCACAUGAUUGCAUU-G------UUAGUUGUACAGUGCAACCAUA--GAC-AGUCACAUACAUCAAAA-UACAUGGUUCCUGCCCACAGGGUCUGUAUAGUUAUCAGAUUUUCUGUGCGAUGGCUCCAUACAAG
AAHX01017478.1/14894-14760   GUGACUGUUUCAGGUAUUAAUUGCAUCCA------UUAGUUGUAAAAUGCAAUAU-A--GAU-AGUCACAUACAGCAAAA-CAAAUGGUUCUUCCUGAAAGAAUCUGUAGAGUUGUCAGAUUUUCUGGGCAAUGUCUUCAUACAUA
AALT01546168.1/2872-3005     GUGACUGGUCCUGGUAUGGGCUGCAUCUG------CGAGCCGUGCUGUGUAGCCGUU--GGC-GGUCACGUACAGCAAAG-C--AUGGUUCUUGCCGACAGGGUCUGUAGAGUCAUCAGACUUCCUGUGCGAUGGCCCCAUACAUC
AAIY01187655.1/336-202       GUGACUGAUCCUGGUAUUGAUUGCCUU-G------UCAGUUGUACAGGGCAACCAUG--GAC-AGUCACUCACAUCGAAA-CACGUGGUUCCUGCCGACAGGGUCUGUAUAGUGAUCAGAUUUUCUGUGCGAUGGUUCCAUGCAGA
CAAE01014712.1/350941-350810 GUGGCAGUUUUUAUU--UAGUUUCAGCAC------UGAGCAGUGUGCUGCAACUGGUGCAAC--GCCACACAGAUCGAGA-C---UGGUUCCUGCCGACAGGGCCUGUAAAGUCAUCGGUUUCCCUGUGCGAUGGUUCCAUACAUU
BX649250.6/111615-111744     GUGGUUAACCA--ACUGUUGCUGCAAGAC------UGAGCAGUGUUUUGCAGUAUUC--AAU-A-CCACACAGAGCAAGU-U---UGGUUCCUGCCGACAGGGCCUGUCAAGAUAUUGGGUUCUCUGUGCGAUGGUUCCAUACAUA
AAWR02001118.1/28579-28712   GUGACUGGUCCUGGUGUUGAUUGCUCUCG------UCAGUUGUACGGUGCAACCAUA--GGC-AGUCACACACAUCAAAA-C--AUGGUUCCUGCCGACAGGGUCUGCAGAGUUAUCAGAUUCUCUGUGCGAUGGCUCCAUACAUG
AAKN02051077.1/104593-104728 GUGACUGUUCCUGCUAAUGAUUGCAUUUG------UCAGUUGUACAGUGUAACCACA--GAC-AGUCACACACAUCAAAA-CAGAUGGUUCCUGCCGACAGAGUCUGUAGAGUUAUCAGAUUUUCUGUGCGAUGGCUCCAUACACU
AAGV020132002.1/1181-1045    GUGACUGUUCCUGGUAUUGAUUGCGUUUG------UUAGUUGUACAAUGCAACCGUG--GACCAGUCACACACAUUAAAA-CAAGUGGUUCCUGCCGACAGGGUCUGUAUAGUUAUCAGAUUUUCUGUGCGAUGGCUCCAUACAUG
AAPE02035601.1/24202-24065   GUUUCUCUCUCCCCUCUCCAUUCCUCUCUUU----UAAAAAAUCAAUAAAAACCAUA--GGC-AGUCACACACAUCAAAA-CAUAUGGUUCCUGCCGACAGGGUCUGUAUAGUUAUCAGAUUUCCUGUGCAAUGGCUCCAUACAUG
AAQR03026065.1/11715-11582   GUGACAGUUCUUGGUAAUGAUUGCAUU-G------UUAGUUGUACAGUGCAACCGUA--GAC-AGUCACAUACAUCAAAA-CACAUGGUUCCUGCCGACAGGGUCUGUAAAGCUAUCAGAUU-UCUGUGCGAUGGUUCCAUACAUG
AAWZ02031720.1/7869-8003     GUGGUUGCCAUGAAUAUUGGCUGCAUUUG------UGAGCAAUACAAUGCAGCCCUA--UGC-GGCCACAUACAUUAACA-AGACUGGAUCCUGCCGACAGCGUCUGCCUAGAUAUCAGAUU-CCUGUGCGAUGGUUCCAGACAUU
AAGU03071801.1/5084-4951     GUGACUGCUCCUGGUAUUGAUUGCACU-G------UUAGUUGUACAGUGCAACCGUA--GAC-AGUCACACACAUCAAAA-CACAUGGUUCCUGCCGACAGG-UCUGUAUAGUGAUCAGAUUUUCUGUGCGAUGGCUCCAUACAUG
#=GC SS_cons                 <<<<-<<<<--<<<<------<<<<<<__......__________>>>>>>>>>>--..>>>.>->>>>-----------.---<<<<--<<---<<<<<<<<<<<<<<____>>->>>>>-->>>>>->>-->>-->>>>:::::
#=GC RF                      GuGacugucccugguauugaUUgCacuug......UuAGuuGUacaguGcAaccaUa..gac.aGuCaCAuACAUcAAAA.cAaauGGUUCCUGCCGACAGgguCuGuauAGUuaUCaGauUUcCUGUGCGAUGGcUCCauACAUa
//
# STOCKHOLM 1.0

#=GF AC   RF00584
#=GF ID   SNORD105
#=GF PI   snoU105
#=GF DE   Small nucleolar RNA SNORD105
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   45.00
#=GF TC   52.50
#=GF NC   41.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00075
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Echinops_telfairi300870;
#=GF DR   snoopy; Rattus_norvegicus300866;
#=GF RN   [1]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res. 2003;31:6543-6551.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   U105 belongs to the C/D family of snoRNAs. It is encoded in an intron of
#=GF CC   the Suppressor of SWI4 1 homolog (Ssf-1) (Peter Pan homolog) gene. and is
#=GF CC   predicted to guide 2'O-ribose methylation of residue U799 of the small 18S
#=GF CC   rRNA subunit.
#=GF WK   Small_nucleolar_RNA_SNORD105
#=GF SQ   15


BC059277.1/353-435           CUCCUGUCUG--AUGAUGA-GCCCAU-UGCC-CUGAGCUCUUGUGAUG-CUGGCUUCAAAGUAAACGCUCUGAAGUGAAGGAGCA--GGGC
AY349606.1/1-85              CCCCUAUCUCUCAUGAUGA-ACACAUAUGCCUCUGAGCUGCUGUGAUUUCUGGCUUCAAAGUAAACGCUCUGAAG---AAGAGAU--GGGG
AAIY01432621.1/769-683       CUCCCCGCUCUCAUGAUGA-GCCCAUGUGCCUCUGAGCUGCCGUGAUU-CAGGCUUCAAAGUAAACGCUCUGAAGAAAUGGAGCC--GAGC
AACN010784424.1/382-296      CUCCCAGCUCUCAUGAUGA-ACCCAUAUGCCUCUGAGCUGCCAUGAUU-CUGGCUUCAAAGUAAACGCUCUGAAGAGAUGGAGCA--GAGG
AANG01184999.1/717-803       CCCCCAACUCUCACGAUGA-ACCCAUAUGCCUCUGAGUUGCCAUGAUU-CUGGCUUCAAAGUAAACGCUCUGAAGAGAUGGGGCG--GAGG
AAPY01626968.1/1830-1750     CCCCCAUCUCUCAGGAUGA-GCCCCUCUGCCUCUGAGCUGCCAUGAUU-CUGGCUUCAAAGUAAACGCUCUGAA------GAGAG--GGGG
AAQQ01144667.1/1988-1903     UCCUUGUCUCUCAUGAUGA-AACCCUGUGCCUCUGAGCUGCCAUGAUU-CUGGCUUCAAAGUAAACGCUCUGAAGAGACAG-GCA--GAGG
AAFC03050764.1/116399-116485 CUGCCAGCUCUCAUGAUGA--CCCUUGUGCCUCUGAGCUGCCAUGAUU-CUGGCUUCAAAGUAAACGCUCUGAAGAGAUAG-GCAGUGGUC
AALT01116036.1/270-351       UCCCCAAGUCUAAUGAUGAUACCCAAUUUCCUCUGAGCCACUGUUAUU-CUGGCUUCAAAGUAAAUGCUCUGAUG----AGA--U--GGGG
AAWR02017824.1/8739-8653     CCCCCAGCUCUGGUGAUGA-ACCCACGUGCCUCUGAGCUGUCGUGAUU-UUGGCUUCAAAGUAAACGCUCUGAAGAGAUGGGGCA--GAAG
AAKN02057568.1/14004-14088   GCCCCAUCUCUCAGGAUGA-ACCCCA-CGCCUCUGAGCCUCCAUGAUU-CUGGCUUCAAAGUAAACGCUCUGAAGAGAC-GGGCA--GAGG
AAGV020745740.1/1118-1033    UUCCCAGCUCUCGUGAUGA-CUCCAUGUGCCUCUGAGCUGCCAUGAUU-CUGGCUUCAAAGUAAACGCUCUGAAGAGAU-GGGCA--GAGG
AAQR03140867.1/13609-13525   CCCCCGUCUCUUAUGAUGA-ACCCAUUUGCUUCUGAGCUGCUGUGAUUUUUGGCUUCAAAGUAAACGCGCUGAAG---AAGAGUU--GGGA
AAHX01053575.1/70037-69954   CUCCUGUCUC--AUGAUGA-UCCCCACUGCC-CUGAGCUGUUGUGAUG-CAGGCUUCAAAGUAAACGCUCUGAAGCAAUGGAGCA--AGGC
AAPE02048878.1/10111-10025   CCCCCAGCUCUCUUGAUGA-ACCCAUGUGCCUCUGAGCUGCCAUGAUU-CUGGCUUCAAAGUAAACGCUCUGAAGAGAUGGGGCA--AAGG
#=GC SS_cons                 :<<<<-<<<<_________.____________________________._______________________________>>>>-..>>>>
#=GC RF                      cccccagCuCUcAUGAUGA.aCCCauaUGCCUCUGAGCUgCcaUGAUU.CUGGCUUCAAAGUAAACGCUCUGAAGaGAuaGaGca..gggg
//
# STOCKHOLM 1.0

#=GF AC   RF00586
#=GF ID   SNORA12
#=GF PI   snoU108
#=GF DE   Small nucleolar RNA SNORA12
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   41.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300802;
#=GF DR   snoopy; Loxodonta_africana300503;
#=GF RN   [1]
#=GF RM   16361266
#=GF RT   A novel experimental approach for systematic identification of box H/ACA
#=GF RT   snoRNAs from eukaryotes.
#=GF RA   Gu AD, Zhou H, Yu CH, Qu LH
#=GF RL   Nucleic Acids Res. 2005;33:e194.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   U108 belongs to the H/ACA family of snoRNAs. The sequence is predicted to
#=GF CC   guide the pseudouridylation of the U372 residue in the 28S rRNA subunit.
#=GF CC   However it has not been reported as a pseudouridylation site.
#=GF WK   Small_nucleolar_RNA_SNORA12
#=GF SQ   23


AC125101.3/38731-38592       UUGGGUGGUAGUGU--CUUCCUGGCGCAUUUGUUAAGUGUUCAAAUGGGCC-CGACUCUGCCACAUACAUUAUGCAGGAGCU--GGCAAAGGCUUAGAGACAAAGAAGUCUCUCU-UGAGUGUUUCCUA----------AUAACAGAUUGGCUCCC------
AP005857.3/135498-135653     UCUCGUGGUAGUUU-UCUUUUUGGCACAUUUGUUAAGUUUUCAAAUGGGCC-UAACACUGCCACAUGUAUUAUACUGGAGUU--GGCAAAGGCCUG-UGACAAUGAGAUAUCUCU-CAAGCCUUUCACGCCUUUCCUCUAUCAGAGAAUGGCUCCCACAUGU
AC015982.9/45601-45748       GGUUGUGGUGGUUU-UCUUUCUGGUACAUUUGUUAAGUUUUCAAAUGAGCC-UAACUCUGCCACAUAUAUCAUAUAGGAGCU--GGCAAAGGCUUGAUGACAAAGAGAUCUCUCU-CAAGCCUUUCCCAC---------AUCAGAGGCUGGCUUUCACACAC
AL138921.14/151404-151258    AGUUGUGGUGGUUU-UCUUUUUGGCACAUUUGUUAAGUUUUCAAAUGGGCC-UAACUCUGCCACAUAUAUAAUAUCGGAGAU--GGCAAAGGCUUG-UGACGGAGAUAUCUCUCU-UAAGCCUUUCCUGC---------AUCAGAGAAUGGCUCCCACAUGU
ABDC01397106.1/1705-1558     AAUUGUGGUGGUUU-UCUUUCUGGCACAUUUGUUAAGUUUUCAAAUGGGCC-UAACUCUGCCACAUAUAUUACAGUGGAGCU--GGCAAAGGCUUGGUGACAAAGAGAUCUCUCU-UAAGCCUUUUCUGC---------AUCAGAGAUUGGCUCCCACAUGU
AANG01051883.1/715-568       GGUUGUGGUGGUUU-UCUUUCUGGCACAUUUGUUAAAUUUUCAAAUGGGCC-UGACGCCGCCACAUAUAUUAUAUAGGAGCU--GGCAAGGGCUUGAUGACAGAGAGAUCUCUCU-CUAGCCUUUCCUGC---------AUCAGGGAUUGGCUCCCACAUGU
AAFC03096620.1/123807-123660 CAUUGUGGUGGUUU-UCUUUCUGGCACAUUUGUUAAGUUUUCAAAUGGGCC-UGACUCUGCCACAUAUAUUAUAUAGGAGCU--GGAAAAGGCUUGAUGACAAAGAGAUCUCUUU-CUAGCCUUUUCUGC---------AUCAGAGAUGGCCUCCCACAUGU
AANU01291874.1/4802-4655     GGCUGUGGUGGUUU-UCUUUCUGGUACAUUUGUUAAGUUUUUGAAUGAGCC-UAACUCCACCACAUGUAUUACAUAGGAGCU--GGCAAAGGCUUGAUGACAAAGAGAUCUCUCA-CAAGUCUUUCUCAC---------AUCAGAGGCUGGCUCUCACAUAU
AAHX01000509.1/115909-115767 UUUGGUGGUAGUGU--CUUCCUGGUGCAUUUGUUAAGUGUUCAAAUGGGCC-UGACUCUGCCACAUACAUUAUGUAGGAGCU--GGCAAAGGCUUAGAGACAAAG---UCUUUCU-UGAGUGUUUCCUA----------AUAACAGACUGGCUCCCAUAUGU
AAYZ01149322.1/1346-1201     AUUUGUGGUGGUUU-UCUCUCUGGCACAUUUGUCAAGUUUUCAAAUGGGCC-UGACUCCACCACAUACAUUGUAAGGGAGCU--GGCAAAGGCUCGAUGACAAAGACAUCUCUUC-UGAGCCCUU--UGC---------ACCAGAGCUUUGCUCCCACAUGU
AAPY01212984.1/5735-5588     AGUUGUGGUGGUUU-UCUUUCUGGCGCAUUUGUGAAGUUUUCAGAUGGGCC-UAACUCUACCACAUAUACGACGUCGGAGCU--GGGAAGGGCUGGGUGGCAAACAGGACUCCCU-GAAGCCUUUCCUGU---------AGCAGAGCUCGGCUCCCACAGGU
AANN01374393.1/1127-973      AGUGGUGGUAGUCC-UCCUCCUGGCACAUUUGUUAAGUUUUCAAAUGGGCU-UGACUCUACCACAUACAUUACUUAGGAGCU--GGCAAAGGCUUGAUGACAAAGAGACC--UCU-CAUCUCUCUCUUGCCUUCCCCUUGUCAGAUAUUGGCUCCUACAGAG
AALT01157768.1/566-710       AGUUGUGGUGGUUU--UCAUCUGGCGCAUUUGUUAAGUUUUCAAAUGGGCC-UGACUCUGCCACAUACAUUAUAGAGGAGCU--GGCAAGGGCUGGAGGACAGAGAGCUCUCUCG---AGCCGUUCCCGU---------GUCCCCGCUUUGCUCUGACAGAC
AAFR03043000.1/31137-31286   UGAUGUGGUAGUUU-UCUUUCUGGUCCAUUUGUGAAGUAU-CAAAUUGGCC-UGAUUCUACCACAUAGAUUAUGCAGGAGCA--AGC--AGUCUUGGGGAUGGUCAGGCCUCAUC-UGAGCCUUUCCCCCUUC--AGGUAUUGCU--UUAGCUCCUACAUGC
AAWR02012792.1/124037-124182 AGUUGUGGUGGCUU-UCUUUCUGGCGCAUUUGUUAAGUUUUCAGAUGGGCC-UGACUCUGCCACAUGUAUUAUUUAGGAGCU--GGCAAAGGCUUGAUGACAGAGAUAUCUCUCU---AGCCUUUCCUGC---------AUCAGCGAUUGGCUCUCACAUGU
AAKN02002808.1/29034-28890   GGUUGUGGUAGUUU--CUUUCUGGCACAUUUGUUAAGUUUUCAAAUGGGUC-UGACUCUACCACAUACAUUGUA-AGGAGCU--AGCAAAAGCUUAGAGACUGAAAUAUCUCUCU-UGAGCUUUUUUGU----------AUGAGAUAUUGGCUCUCACAAUC
AAGV020152435.1/2279-2424    AGUUGUGGUGGUUU-UCUUUCUGGUGCAUUCAUUAAGUUUUCAAAUGGGCC-UGAUUCUGCCACAUAUAAUAUAGAGGAACU--GGCAAAGGCUUGAUGAAAAAGAGAUUUUUUG-CUAGCCUUUCACA-----------UACCAGUUUGGUUCCCAUAUGU
AACN010730241.1/682-535      AGUUGUGGUGGUUU-UCUUUCUGGCACAUUUGUUAAAUUUUCAAAUGGGCC-UGACUCUGCCACAUAUAUUACAUAGGAGCU--GGCAAAGGCUUGAUGACACAGAUAUCUCUCU-CUAGCCUUUCCUGC---------AUUAGGCAUUGGCUCUCACAUGU
AAGU03026822.1/21335-21483   CGUUGUGGUGGUUU-UCUUUGUGGUACAUUUGUUAAGUUUUCAAAUGGCCCCUGACUCUGCCACAUAUAUUACACAGGAGCU--GGCAAAGGCUUGAUGAGAAAGAGAUCUCUCU-CUGGCUUUUCCCGU---------GUCAGAGAUUGGCUUCCACACGU
AAPE02026613.1/12720-12572   UCAUGUGGUGGUUU-UCUUCCUGGCACAUUUGUUAAGUUUUCAAAUGGGCC-UGACUCUGCCACAUAUAUUAUAUAGAAGCU--GGGAAAGGCUUGAUGACAAAGAGAUCUCCCUCUCUGGCCUUUCUGC---------AUCAGAGAUUGGCUCCCACAUGU
AAGW02060773.1/211129-210984 AUUUGUGGUGGUUU-UCUCUUUGGUCCAUUUGUUAAGUUUUCAAAUGGGCC-UGACUCGGCCACAUACAUUAUAAAGGAUCU--GGCAAAGGCUUGAUGACA--GAGAUUUCUGU-UGAGCCUAUCCUGC---------AUCACAGCUUGGCUCCCACAUGC
AAQR03047446.1/24248-24390   AAUUGUGGUGGUUU-UCUUUCUGGCACAUUUGUUAAGUUUUCAAGUGUACC-UAACUCUGCCACAUAUAUUAUAUCGGAGCU--GGCAAAGGCUUGAUGACAAAGAGAUCUUCU-----GCCUUUCCUCC---------AUC-AGAGAUGGCUCCCACAUGC
FM165411.1/1-140             ---UGUGGUGGUUUCUUUGUUUGGCAGAUCUGUAAUUGUAUCAGAGCGGCC-UGAAACUACCACAGAGAUCAAAAAGGAG--GG----AGGCUGUGCUGAGAACGUUUUC--AGG-CUCUCAGUUCUCAG---------CUUUUUAUUCAACUCCUAUAGAA
#=GC SS_cons                 ::::<<<<<<<---.-------<<<-<<<<<<_________>>>>>>->>>.----->>>>>>>------------((((((..<<<____>>>,,,,,,,,,,,,,,,,<<<<<.______________.........___>>>>>,,)))))):::::::
#=GC RF                      agUUGUGGugGUUU.UCUUUcUGGcacAUuUGUuAAGUUUUCAaAUgGgCC.UGAcUCcaCCACAUAuAUUAuAuAGGAGCc..gGcAAAGgCuUGaUGAcAAaGAgaUCucucu.uuaGccUUUCcugc.........aUcagagaUUgGCUCCcACAugu
//
# STOCKHOLM 1.0

#=GF AC   RF00588
#=GF ID   SNORD41
#=GF PI   snoU41
#=GF DE   Small nucleolar RNA SNORD41
#=GF AU   Marantidis E
#=GF SE   Marantidis E.
#=GF SS   Predicted; RNAalifold
#=GF GA   41.00
#=GF TC   41.70
#=GF NC   40.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00058
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300808;
#=GF DR   snoopy; Cavia_porcellus300883;
#=GF RN   [1]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell. 1996;85:1077-1088.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   snoRNA U41 belongs to the C/D family of snoRNAs. It is predicted to guide
#=GF CC   2'O-ribose methylation of the large 28S rRNA on residue U4276.
#=GF WK   Small_nucleolar_RNA_SNORD41
#=GF SQ   20


AC018761.6/51237-51168     UGGGAAGUGAUGACACC----UGUGACUGUUGA-UGUGGAACUGAUUUAUCGC----GUAUUCGUACUG-GCUGAUCCUG
AL135998.6/148355-148423   AGGGAAGUGAUGACAAC----UGUGACUGUUG--UGUGACACUGAUUUCUCUC----AUAUUUGUACUG-GCUGAUCCUG
AC191994.6/152635-152566   UGGGAAGUGAUGACACC----UGUGACUGUUGA-UGUGUCACUGAUUUCUCUC----GUAUUCGUACUG-GCUGAUCCUG
ABDC01213018.1/842-773     UGGGAAGUGAUGACACC----CGUGACUGCUGA-UGUGGCACUGAUUUCUCUC----GUAUUCGUACUG-GCUGAUCCCG
AAPY01153461.1/868-937     GGGGAAGUGAUGACA-C----UGUGACCGCUGA-CGUGGCACUGAUUUCUCUG----GUAUUCGUACUGGGCUGAUCCCG
AANG01677711.1/3755-3686   UGGGAAGUGAUGAUACU----CCCGACCCUUGA-CGUCACGCUGAUCUCUCGC----GUAUUCGUACUG-GCUGAUCCCG
AAFC03027664.1/79650-79580 CGGGAAGUGAUGAUACU----UAUGACUCCUGA-CAGUGCGCUGAUUUCUCACC---GUAUUCGUACUG-GCUGAUCCCG
AALT01503404.1/94-163      UCUGAAGUGAUGACACUG---UGUGAG-CCUGA-CCUCGCACUGAUUCCUCUU----GUAUUGGUACUG-GCUGAUCGGA
AAYZ01426181.1/2991-2922   CGGGAUGUGAUGAGACC----UGUGACCGCUGA-UGUGACCCUGAUUGCUGUC----GUAUUCGUACUG-GCUGAUCCCG
AC163703.4/111094-111025   UGGGAAAUGAUGAUGCC----UGUGACUGCUGA-CAAGACUCUGAUGUCUGUU----GUAUUCGUACUG-GCUGAUCCUG
AAHX01097686.1/36676-36745 UGGGAAAUGAUGAUGCC----UAUGACUGCUGA-CAAGACUCUGAUCACUGUC----GUAUUCGUACUG-GCUGAUCCUG
AAIY01335060.1/20-88       UGGGAAAUGAUGUUA-C----CUUGACCCUUGA-CAUCACGCUGAUUUUUCUU----GUAUUCGUACUG-ACUGAUCCCG
AANN01218035.1/1458-1385   CGGGAGGUGAUGACACU----CUGAACGCUUGAUCACCGCAAUGAUUUCUCACUGA-GUAUUCGUACUG-GCUGAUCCCG
AAFR03049193.1/60313-60382 UUGGAUGUGAUGGACAA----CUUACUGUUUGA-UGUCAAACUGAUCUUUGUA----GUAUUCAUACUG-UCUGAUCCUG
AAKN02038626.1/66168-66240 UGGGAAGUGAUGACAUACUUAUGUGACUGCUGA-CAU-GCCCUGAUUUCUCU----UGUAUUCGUACUG-GCUGAUCCCA
AAWR02041796.1/7931-8000   CGGGAAGUGAUGAUAUG----CAUGACCCCUGA-CAUCAAGCUGAUUUCUCGC----GUAUUCGUACUG-GCUGAUCCCA
AASC02024474.1/62087-62018 CUGGAAGUGAUGACAGC----UUUGAGCAUUGA-CA-CUUAAUGAUGUUUGCUA---GUAUUCGUACUG-UCUGAUCCGG
AAEX03012407.1/21080-21149 UGGGAAGUGAUGACACU----CAUGACCCUUGA-CAUCCUGCUGAUUUCUGAC----GUAUUCGUACUG-GCUGAUCCCA
AAQR03140515.1/8220-8288   UGGGAAGUGAUGACACC----UGUGACUGCUGA-UG-GGCACUGAUUUCUUGA----GUAUUCGUACUG-GCUGAUCCUG
AAPE02006874.1/14716-14784 AGGGAAGUGAUGACACU----CAUUACCUCUGA-UAU-UCGCUGAUUUCUAAC----GUAUUCGUACUG-GCUGAUCCCG
#=GC SS_cons               :<<<<____________....____________.___________________....____________._____>>>>:
#=GC RF                    ugGGAAGUGAUGAcAcu....ugUGACuguUGA.caUcaCaCUGAUUUCUcuc....GUAUUCGUACUG.GCUGAUCCcG
//
# STOCKHOLM 1.0

#=GF AC   RF00591
#=GF ID   SNORD77
#=GF PI   snoU77
#=GF DE   Small nucleolar RNA SNORD77
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00070
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Echinops_telfairi300160;
#=GF DR   snoopy; Oryctolagus_cuniculus300213;
#=GF RN   [1]
#=GF RM   15556860
#=GF RT   Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for
#=GF RT   modification of snRNAs in metazoa.
#=GF RA   Tycowski KT, Aab A, Steitz JA
#=GF RL   Curr Biol. 2004;14:1985-1995.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   U77 belongs to the C/D family of snoRNAs. It is predicted to guide
#=GF CC   2'O-ribose methylation of large 28S rRNA subunit at position A1521. The
#=GF CC   C/D snoRNAs U44, U47, U74, U75, U76, U78, U79, U80 and U81 share the same
#=GF CC   host gene as U77 (non-coding).
#=GF WK   Small_nucleolar_RNA_SNORD77
#=GF SQ   21


AL031584.2/110885-110818     GUACUAUGAUAGUUGCAUAGUUCAGCAGAU-UGA---AU-CAUCAAGAGAUUUA--AUAUUUGUCUGAUGUAUCU
AP004219.2/12572-12638       AUACUAUGAUGGUUGCAUAGUUCAGCAGAU-UGA---AUUCAUGAAGAGAUUUA--CAAU--GUCUGAUGUAGUU
AL136170.14/9004-8937        AUACUAUGAUGGUUGCAUAGUUCAGCAGAU-UUA---AU-CAUGAAGAGAUGUA--CUAUCUGUCUGAUGUAUCU
AC018515.7/88497-88433       AUACUAUGAUGUUUGCAUAGUUCAGCAGAU-UGA---AU-UAUGAAGAGAUCUA--CCAUUUGUCUGGUGU---U
AC012435.13/84027-83958      AUACUGUGACAGUUGCAUCGUUCAGCAGAU-UGA---GU-CACGAAGAGAUGUAUACCAUCUGUCUGAUGUAUCU
ABDC01166137.1/412-479       AUACCAUGAUGGUUGCAUAGUUCAGCAGAU-UGA---AU-CAUGAAGAGAUUUA--CCAUUUGUCUGAUGUAUCU
AANU01240317.1/5656-5589     AUACUAUGAUGGUUGCAUAGUUCAGCAGAU-UGA---AU-CAUGAAGAAAUGUA--CUGUGUGUCUGAUGUGUCU
AANG01024593.1/860-794       AUACUAUGAUGGUUGCAUAGUUCAGCAGAU-UGG---AU-CAUGAAGAGAUA-G--CUAUCUAUCUGAUGUAUCG
AAPY01728088.1/7352-7418     AUACUAUGAUGGUUGCAUAGUUCAGCAGAU-UGU---AU-CAUGA--AGAUGAGA-ACAUUUGUCUGAUGUAUCU
AAQQ01328837.1/160-225       AUACUGUGAUGGUUGCAUAGUUCAGCAGAU-UUA--AGU-CAUGAAGAAAUA-----UACUUUUCUGAUGUAUCU
AAFC03120161.1/28742-28810   AUACUGUGAUGGUUGCAUAGUUCAACAGAUAGGA---AU-CAUGAAAGAGAAAC--CAUUUUAUCUGAUGUAUCU
AAFR03026464.1/111644-111577 AUACUAUGAUGGUUGCAUAGUUCAGCAGAU-AUU---A---GUGAAGAAUACUUAUCUUAUUAUCUGAUGUAUCU
AANN01379367.1/1617-1554     AUACUAUGAUAGUUGCAUAGUUCAUCAGA---AA---GU-CCUGA--AGAGAUG--CACUUUGUCUGAUGUAUCU
AALT01136474.1/559-494       AUACGAUGAUGGUUGCAUAGUUCAGCAGAU-UG----GC-UGUGAAGAGAUGAA--CCAAU-GUCUGAUGUAUCU
AAPN01008930.1/67523-67455   AUACAGUGAUGCUUGCAUAGUUCAGCAGAU-GGAACAGU-GACGAAAUAUACCA--C--AUAAUCUGAUGUAUCU
AAWR02036950.1/21521-21454   AUACUAUGAUGGUUGCAUAGUUCAGCAGAU-UGA---AU-CAUGAAGAGAGAAA--CCAUUUGUCUGAUGUAUCU
AAGV020273689.1/1545-1610    ACAUAGUGAUGGUUGCAUAGUUCAGCAGAU-UGA---GU-UGUGA--AGAUAUG--UUAUUUGUCUGAUGUGUCU
AAGW02008585.1/14550-14617   AUACUAUGAUGGUUGCAUAGUUCAUCAGAU-UGA---AU-UCUGAAGAGAUGUA--UCAUUGGUCUGAUGUAUCU
AAPE02018271.1/30425-30358   AUACUGUGAUGCUUGCAUAGUUCAGCAGAU-UGA---AU-UCUGAAGAAAUGUA--CCACUUGUCUGAUGUAUCU
AAGU03036956.1/68003-68067   AUACUGUGAUGACUGCAUAGUUCAGCAGAU-UGC---AU----GAAGAGAUUUA--UCACUUGUCUGAUGUAUCU
AAQR03038677.1/8923-8990     AUACUAUGAUGGUUGCAUAGUUCAGCAGAU-UGA---AU-CAUGAAGAAAUUAG--CCAUUUGUCUGAUGUAUCU
#=GC SS_cons                 ((((,<<<<<--<<<<________>>>>--.---...>>.>>>,,,,<<<<<__.._>>>>>,,,,,,,))))::
#=GC RF                      AUACUauGAuGGUUGCAUAGUUCAGCAGAU.UGA...aU.CauGAAGagaucua..CgaucugUCUGAUGUAUCU
//
# STOCKHOLM 1.0

#=GF AC   RF00592
#=GF ID   SNORD78
#=GF PI   snoU78
#=GF DE   Small nucleolar RNA SNORD78
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   38.00
#=GF TC   38.20
#=GF NC   37.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Oryctolagus_cuniculus300266;
#=GF DR   snoopy; Oryctolagus_cuniculus300001;
#=GF RN   [1]
#=GF RM   15556860
#=GF RT   Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for
#=GF RT   modification of snRNAs in metazoa.
#=GF RA   Tycowski KT, Aab A, Steitz JA
#=GF RL   Curr Biol. 2004;14:1985-1995.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   U78 belongs to the CD family of snoRNAs. It is predicted to guide
#=GF CC   2'O-ribose methylation of the large 28S rRNA subunit at position G4593.
#=GF CC   The snoRNAs U44, U47, U74, U75, U76, U77, U79, U80 and U81, also of the
#=GF CC   C/D family, share the same host gene with U78 (protein non-coding).
#=GF WK   Small_nucleolar_RNA_SNORD78
#=GF SQ   19


AL591203.15/10035-10099      GUGUAAUGAUGUUGAUCAAAUGUCUGACCUGAAAUGAGCA-UGUAGACAA---AGGU-AACACUGAAGAA
BC055883.1/519-584           UUGUAAUGAUGUUGAUCAAAUGUCUGAGCUGAAAAUAACU-UGUAGACAA---UUUUUAACACUGAAGAA
AC073875.6/8012-8076         CUGUAAUGAUGUUGCUCAAAUAUCUGACCUGAAAUGAUUA-UAUAGACCA----AUUUAAUACUGAAGAA
AC092630.3/54523-54591       AUGUAAUAAUGUUCAUCAAAUGUCUGACCUGAAAUGAGCA-UGUAGACAAGUUAAUUUAACACUGAAGAA
AC143509.11/60610-60545      GUGUAAUGAUGUUGAUCAAAUGUCUGACCUGAAAUGAGCG-UGUAGACAG---AAGGUAACACUGAAGAA
AANN01730354.1/1287-1224     UUGUAAUGAUGUUGACCAAAUGUCUGACCUGAAAUAAGUA-UGUAGACAA-----GUUAACACUGAAGAA
AAQQ01328837.1/778-842       UUGUAAUGAUGUUGUUCAAAUGUCUGACCUGAAAUGAGCA-UGUAGACAA----GUUUUAUGCUGAAGAA
ABDC01272342.1/6406-6470     CUGCAAUGAUGUUGAUCAAAUGUCUUACCUAAAAUGAGCA-UGUAGACAA----AUUUAAUACUGAAGGA
AANG01024596.1/1235-1171     UUGAAAUGAUGUUGACCAAAUGUCUGACUGAAAGUGAGCA-UGUAGACAA----AUUUAACACUGAAGAA
AAFC03120161.1/29388-29452   UUGCAAUGAUGUUGAGCAAAUGUCUGACCUGAAAUUAGCA-UGUUGACAA----GUCUAACUCUGAAGAA
AAPY01728088.1/8008-8072     UUGUAAUGAUGUUGAUCAAAUGUCUGACCUGAAGUAAGCA-UGUAGACAA----ACAUAGCACUGAAAAG
AAIY01534871.1/1387-1323     UUACAAUGAUGUUUAACGAAUGUCUGACCUGAAGAGAGCA-UGUAGACAA----AUUUAACACUGAAAAG
AAYZ01154867.1/165-102       CUGUAAUGAUGUUGAUCAAAUGUCUGACCUGAAGCAAGCA-UGUGGACAA---GAGU--GUGCUGAAGAA
AAFR03026464.1/110530-110466 UUAUAAUGAUGU-CCUCAAAUGUCUGACCUGAAAUCAGCA-UGUAGAUAA---AUCACAGCACUGAAGUG
AAGV020273689.1/2172-2236    UUAAAAUGAUGGUGAUCAAAUGUCUGGCCUGAAAUGAACA-UGUAGAAAA----AUUUAAUACUGAAGAA
AAWR02036950.1/20825-20761   UUGUAAUGAUGUUGAUCAAAUGUCUGACCUGAAAUGAGCA-UGUAGACAA----AUUUAACACUGAAGAA
AAGW02032423.1/29510-29573   UUGUAAUGAUGUUGAUCAAAUGUCUGAUCUGAAAAGAGCA-UGUAGACAA---AUGU--GUACUGAAGAA
AADN03005691.1/152980-152914 UUGUAAUGAUGUUG-UCAAAUGUCUGACCUGAAACUACUAAUGUAGAUUUC--UUUUUUUUACUGAAAAA
EU094192.1/1-60              -UACAAUGAUGU-CUUCAAAUGUCUGACCUGAAAG-UCUA-UGUAGACAA----GCUUGCUUCUGAA--A
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::.:::::::::....::::::::::::::::
#=GC RF                      uUGuAAUGAUGUUGaUCAAAUGUCUGACCUGAAAugAGCA.UGUAGACAA....auUUAacACUGAAGAA
//
# STOCKHOLM 1.0

#=GF AC   RF00593
#=GF ID   snoU83B
#=GF DE   Small nucleolar RNA U83B
#=GF AU   Marantidis E
#=GF SE   Marantidis E, INFERNAL
#=GF SS   Predicted; RNAalifold_manual; Daub J
#=GF GA   35.00
#=GF TC   35.30
#=GF NC   34.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Gallus_gallus300027;
#=GF DR   snoopy; Loxodonta_africana300492;
#=GF RN   [1]
#=GF RM   10684929
#=GF RT   Characterisation of the U83 and U84 small nucleolar RNAs: two novel
#=GF RT   2'-O-ribose methylation guide RNAs that lack complementarities to
#=GF RT   ribosomal RNAs.
#=GF RA   Jady BE, Kiss T
#=GF RL   Nucleic Acids Res. 2000;28:1348-1354.
#=GF RN   [2]
#=GF RM   10684968
#=GF RT   The intron-containing L3 ribosomal protein gene (RPL3): sequence analysis
#=GF RT   and identification of U43 and of two novel intronic small nucleolar RNAs.
#=GF RA   Duga S, Asselta R, Malcovati M, Tenchini ML, Ronchi S, Simonic T
#=GF RL   Biochim Biophys Acta. 2000;1490:225-236.
#=GF CC   U83B belongs to the C/D family of snoRNAs. U83B like U83A has no
#=GF CC   documented RNA target and they share the same host gene with the C/D box
#=GF CC   snoRNA U43 (RPL3). N.B. U83A/B/C have no sequence similarity with the U83
#=GF CC   snoRNA that was cloned by Jady and Kiss (2000).
#=GF WK   Small_nucleolar_RNA_U83B
#=GF SQ   21


AJ238851.1/5294-5387         GCUGUGCAGUGAUGAGACCCUGGAAUGAGCGCUGGGCACAGCGCCCGAGUC-AGA--C--UGCGGAAGUA-UUCCUUGCUGCCUUCCUUCUGAGAACAGC
AL022326.1/46948-46856       GCUGUUCAGUGAUGAGGCC-UGGAAUGUGCGCUGGGCACAGCGCCCGAGAC-AGA--C--UGCGGAACCG-UUCCUUGUUGCCUUCCUUCUGAGAACAGC
AJ238851.1/3934-4027         GCUGUUCAGUGAUGAGGCCCUGGAAUGAGCGCUGGGCACAGCGCCCGAGUC-AGA--C--UGCGGAAAUG-UUCCUUGCUGCCUUCCUUCUGAGAACAGC
AF227523.1/526-433           GCUGUUCUGUGAUGAGGCUCUGGAAUGUGCGCUGGGCACAGCGCCCGAGAG-AGA--C--UGAGGAAUUA-UUCCCUGUUGCCUUCCUUCUGAGAACAGC
AACN010009543.1/958-1051     GCUGUUCGGUGAUGAGGCUCUGGAAUGAGCGCUGGGCGCAGCGCCCGAGUC-AGA--C--UGCGGAAACA-UUCCUUGCUGCCUUCCUUCUGAGAACAGC
AAPY01557070.1/195-288       GCUGUUCAGUGAUGAGGCCCUGGAAUGAGCGCUGGGCACAGCGCCCGAGUC-AUA--C--UGCGGAACCC-UUCCUUGUUGCCUUCCUUCUGAGAACAGC
AAIY01493238.1/1008-1101     GCUGUUCCGUGAUGAGACCCUGGAAUGAGCGCUGGGCACGGCGCCCGAGCC-AGA--C--UGCGGAAACG-UUCCUUGCUGCCUUCCUUCUGAGAACAGC
AAYZ01369362.1/4323-4231     GCUGUUCAGUGAUGAGGCC-UGGAAUGAGCGCUGGGCACGGCGCCCGAACU-CCC--C--UGUGGAACCA-UUCCCUGUUGCCUUCCUUCUGAGAACGGC
AAPN01198523.1/767-675       GCUGUUCAGUGAUGAGGCACUGGAAAAAGCGCCGGGCACGGCGCCCGACCC-CGA-----UGAGGAAUCC-UUCCUUGCUGCCUUCCUUCUGAGAACAGC
AANU01294177.1/9552-9458     GCUGUUCAGUGAUGAGGCU-CAGAGUGAGCGCUGGGCACAGCGCCCGAAUC-AGACAC--UGUGGAACCA-UUCUCUACUGCCUUCCUUCUGAGAACAGC
AALT01177781.1/612-705       GCCGUUCAGUGAUGAGACGC-GGAAUGAGCGCUGGGCACAGCGCCCGAGCC-ACA--CAGUGCGGAAGCA-UUCCAGCU-GCCUUCCUUCUGAGAACGGC
AAFR03059474.1/49781-49873   CUUGUUCAGUGAUGAAGUCAUGGAAUAAGCGCUGGGCACAGCGCCCGAGCC-UGA-----UGAGGAGAUA-UUCCUUGCUGCCUUCCUUCUGAGAACAGC
BAAF04045344.1/4422-4329     UUUUGUCAGUGACGAGACCACGGAACCUGCGCCAGGCAUGGCGCCUGAUCA-GUU--A--UGAAGAUAGU-UUCCAUGCUGCCUUCCUUCUGAGACGAGU
AADA01294197.1/3237-3331     GCUGUUCGUUGAUGAGGCU-CAGAGUGAGCGCUGGGUACAGCGCCCGAAUC-GGA--CAGUGUAGAACCA-UUCUCUACUGCCUUCCUUCUGAGAACAGC
AANH01011296.1/55625-55718   UGUUGUCAGUGAUGAGACCACGGAUCUUGCGUCAGGCAUGGCGCCCGACUA-ACA-----UGAGGAUACAUUUCCAUGCUGCCUUCCUUCUGAGACUACG
AAKN02031265.1/100993-100900 GCUGUUCCGUGAUGAGGCCUUGGAAUGCGCGCUGGGCACAGCGCCCGAGUC-AGA--C--UGAGGAACCA-UUCCCUGUUGCCUUCCUUCUGAGAACAGC
AAWR02025061.1/53134-53041   GCUGUUCGAUGAGGAGGCUCUGGAAUGAGCGCUGGGCACAGCGCCCGAGUC-AGA--C--UGCGGAAGCA-UUCCUAGCUGCCUUCCUUCUGAGAGCAGU
AAQR03016166.1/10353-10445   ACUGUUCAAUGAUGAGGCC-UGGAGUGUGCGCUGGGCACAGCGCCCGAGUC-AGA--C--UGCGGAAGCA-UUCCAUGUUGCCUUCCUUCUGAGAACAGC
AAGU03077394.1/9605-9699     GCUGUUCAGUGAUGAGGCUGUGGAAUGAGCGCUGGGCACAGCGCCUGAGUCAAGA--C--UGCGGAAACG-UUCCUUGCUGCCUUCCUUCUGAGAACAGC
AAWZ02017553.1/208705-208612 GCUGUUCAGUGAUGAGAUCAUGGAAUAUGCACUGGGCACAGUGCCUGAUAA-UAA--A--UGAGGAGUCG-UUCCAUGCUGCCUUCCUUCUGAGACCAGC
ADDD01113502.1/4207-4115     ACAGUUCGGUGAUGAAACCAUGGAAUAAGCGCUGGGCACAGCGCCUGACAU-CCG-----UGAGGAGUCA-UUCCAUGCUGCCUUCCUUCUGAGAACAAC
#=GC SS_cons                 <<<<<______________________________________________.___.._..__________.________________________>>>>>
#=GC RF                      gcuguUCaGUGAUGAGgCcaUGGAAUgaGCGCUGGGCACAGCGCCCGAguc.agA..c..UGaGGAaaca.UUCCuUGcUGCCUUCCUUCUGAGAacagc
//
# STOCKHOLM 1.0

#=GF AC   RF00594
#=GF ID   SNORD86
#=GF PI   snoU86
#=GF DE   Small nucleolar RNA SNORD86
#=GF AU   Marantidis E
#=GF SE   Marantidis E.
#=GF SS   Predicted; RNAalifold
#=GF GA   35.00
#=GF TC   36.30
#=GF NC   34.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300006;
#=GF DR   snoopy; Loxodonta_africana300505;
#=GF RN   [1]
#=GF RM   11594746
#=GF RT   U86, a novel snoRNA with an unprecedented gene organization in yeast.
#=GF RA   Filippini D, Renzi F, Bozzoni I, Caffarelli E
#=GF RL   Biochem Biophys Res Commun. 2001;288:16-21.
#=GF RN   [2]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   U86 belongs to the C/D family of snoRNAs. It is the human orthologue of
#=GF CC   Xenopus laevis U86 and has no identified RNA target. The snoRNAs U86, U56,
#=GF CC   U57 and HBII-55,of the C/D family, and the H/ACA box snoRNA ACA51 share
#=GF CC   the same host gene (NOL5A) with U86.
#=GF WK   Small_nucleolar_RNA_SNORD86
#=GF SQ   6


AJ311853.1/1-86           GAUCACGGUG--AUGGCUGACCAGGGCUCCCUGACCUAUACAGGCCUCUGCUAUGGGGGUGAUGGCCAGUCCUGGUGUCUGAGUGAUU
AL833804.16/187394-187479 GAUUACAAUG--AUGGCUGACCAGGGCAACCUGACCUAUACAGGCCUCUGCUAUGGGGGUGAUGGCCAGUCCUGGUGUCUGAGUGAUU
AY007719.1/710-795        GAUCACAGUG--AUGGUUGACCAGGGCUCCCUGACCUAUACAGGCCUCUGCUAUGGGGGUGAUGGCCAGUCCUGGUGUCUGAGUGAUU
AL663066.12/143691-143604 GAUAUUUAAGUCAUUUAACAUAUUUUGUUCUGGACCUAUACAGGCCUCUGCUAUGGGGGUGAUGUUCAGUCCUGGUGUCUGAGUGAUU
AC123851.4/99948-100029   UGCCUUUCAG--A----AGAAGAGGCGGACCUGACCUAUACAGGCCUCUGCUAUGGGGAUGAUGGCCAGUCCUGGUGUCUGAGUGAUU
AC154361.2/57260-57345    AUUUCAUCAG--AGAACACAAAAGAACAUUCUUAAAACUAAAUAGCUCUGCUAUGGGGGUGAUGGCCAGUCCUGGUGUCUGAGUGAUU
#=GC SS_cons              <<<<<<---<..<<-----<<<<<<<<<<<-<-<<<<---<<<<<____>>>->>->>>>->->>-->>>>>>>>>>>>--->>>>>>
#=GC RF                   gaucacuaaG..AuggcagAccaGgacucCCuGAcCuAUACAgGCCUCUGCuAUGGgGgUGaUGgCCagucCuggUgUCUGAgugauu
//
# STOCKHOLM 1.0

#=GF AC   RF00598
#=GF ID   SNORA76
#=GF DE   Small nucleolar RNA SNORA76
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:16373490. INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   36.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF CL   CL00034
#=GF DR   snoRNABase; ACA62;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300033;
#=GF DR   snoopy; Homo_sapiens300134;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   16373490
#=GF RT   A computational screen for mammalian pseudouridylation guide H/ACA RNAs.
#=GF RA   Schattner P, Barberan-Soler S, Lowe TM
#=GF RL   RNA. 2006;12:15-25.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   ACA62 (SNORA76) is a member of the H/ACA class of snoRNAs that guide the
#=GF CC   sites of modification of uridines to pseudouridines [1]. This snoRNA was
#=GF CC   identified by computational screening and its expression in mouse
#=GF CC   experimentally verified by Northern blot and primer extension analysis
#=GF CC   [2]. ACA62 is proposed to guide the pseudouridylation of 18S rRNA U34 and
#=GF CC   U105 [2].
#=GF WK   Small_nucleolar_RNA_SNORA76
#=GF SQ   22


AL663053.12/63895-64027      GCGCUG-CCUUUGAGCCCCCGGCCCACCUUCUCGUGGUGCCGGGGGUUAAGCUGCGGCGCCAUAACACUCUGCUAGCGCAUAACUGGGGCCGCC-UG---CCCUUCG-CGGGCGGCCCU-UUUAACCGCUAGCUACAGGC
AC022107.8/66266-66397       GCGCUG-CCUUUGUACCCCA-CCGUGCCUCCGCCUGGUGUCUGGGGUCAGGUUGCAGUGCCAGAGCA-CGUGCUUGCGCAUAAAUGGGGCAGCC-UGG--CCCCCUG-CGGAUGGUCCU-UUUAACCGCGAGCAACAAGG
AC025362.12/104850-104982    GCGCUG-UCUUUGAGCCCCCGCCGAGCUUCCUCGUGGCGCCGGGGGUCAAUCUGCAGCGCUAGAGCA-UGUGCUUGCGCAUAACUGGGGCCGCC-UGG--CCUCCCG-CGGGCGGCCUU-UUUAACCGCGAGCGACAAGA
AL672123.16/132758-132876    GUGCUG-CCUUUGAGCCCCCUGU---------AGU---GCCGGGGAUUAAGCUGCGGCGCCAUAGCACUUUGCAGGCGCAUAACUGGGGCCGCC-UG---UCUUUCC-CAGGCGGCCCU-UUUAAC--CUAGCUACAGGC
AAQQ01697664.1/466-335       GCGUUG-CCUUUGAGCCCCUGCUGCGCCUGCGCGUGGCGCCGGGGGUCAGGCUGCAGCGCCAGAGGA-CGUGCUCGCGCAUAACUGGGGCCGCC-UG---CCUCUCG-CUGGCGGCCCU-UUUAACCGCGAGCUACAUGG
ABDC01220433.1/3446-3579     GCGCUG-CCUUUGAGCCCCCGUAGCGCCUCCGCGUGGCGCCGGGGGUCAGGCUGCAGCGCCAGAGCA-CGGGCUCGCGCAUAACUGGGGCCGCC-UGCC-UCCUCCG-CGGGCGGCCCU-UUUAACCGCGAGCGACACAG
AAYZ01032340.1/3628-3759     GCGCUG-CCUUUGAGCCCCCGCUGCGUCUGCGCGUGGCGCCGGGGGUCAGGCUGCAGCGCCAGAGCA-AGGGCUCGUGCAUAACUGGGGCCGCC-GG---CCACUCG-CGGGCGGUCCU-UUUAAACGCGAGCGACACGG
AAFC03045555.1/64844-64976   GCGCUG-CCUUUGAGCCCCCGCCGCGCCUGCGCGUGGCGCCGGGGGUCAGGCUGCAGCGCCAGAGCA-CGUGCUCGCGCAUAACUGGGGUCGUCUGC---CCCCGCG-GCGGCGGCCCU-UUUAACCGCGAGCGACACGG
AAPY01361107.1/1811-1678     GCGCUG-CCUUUGAGCCCCCGCCGCGCCUGCGCGUGGCGCCGGGGGCCAGGCUGCAGCGCCAGAGCA-CAUGCUUGUGCAUAACUGGGGCCGUC-UGUC-CCUAACG-CGGGCGGUCCU-UUUAAACGCAAGCUACAUGG
AALT01505651.1/398-267       GCGCUG-CCUUUGAGCCCCCGGCG--CCUGCGCGUGGCCCCGGGGGUCAGGCUGCAGCGCCAGAGCA-CGGGCUCGCGCAUAACUGGGGCCGCC-AGCC-CCCCUCG-CCGGCGGCCCU-UUUAACCGCGAGCGACACGC
AC191241.1/59284-59418       GCGCUG-UCUUUGAGCCCCCGCCGCACCUCCGAGUAGCGCCGGGGGUCAGUCUGCAGCGCCAGAGCA-CGUGCUUGCGCAUAACUGGGGCCGCU-UGGCCCCCCCCG-CCGGCGGCCCU-UUUAACCGCGAGCUACAAUA
AAIY01663660.1/992-863       GUGCUG-CCUUUGAACCCGC--CGCGCCGGCCCGUGGCGCGGGGGGUUAAGCUGCAGCGCCAGAGCA-AGUGCUGGCGCAUAACUGGGGCCGCC-AA---GCCUCUG-CGGGCGGCCCU-UUUAACCGCCAGCGACACGG
AANG01166973.1/2746-2878     GCGCGGGCCUUUGUGCCCCCGCAGAGCCUGCGCGUGGCGCUGGGGGUCAGGCUGCAGCGCCAGAGCACG--GAUUGCGCAUAACUGGGGCCGCG-CG---GUCCUCG-CCAGCGGCCCUUUUUAACCGCGAGCCACACGU
AANN01601273.1/238-115       GCGCCG-CCUUUGAGCCCCCGC--CGCCUGC-AGUGGUGCCGGGGGUCAGGCUGCGGCGCCAGAGCA-GCCGCUCGUG-AUAACUGGGGCUCCG-CG---CUGCCGG-C----CGCCCU-UUUAGCCACAAGCCACAUGG
AAGV020220244.1/4142-4012    GCGCUG-CCUUUGAGCCCCCGUCGCGCCUGCGCGUGGCGCCGGGGGUUAAGCUGCAGCGCCAGAGCA-CGUGCUUGCGCAUAACUGGGGCCGCC-CG---ACCGUA--CGGGCGGCGCC-UUUAACCGCGAGCGACAAGC
AAWR02012489.1/59021-58890   GCGCUG-CCUUUGAGCCCCUGCUGCGCCUGCACGUGGCGCCGGGGGUCAGGCUGCGGCGCCAGAGUA-CGCGCUUGCGCAUAACUGGGGCCGCC-UC---CCGCUCG-CCGGCGGCCCU-UUUAACCGCGAGCGACAAGG
AAKN02045216.1/19074-19204   GCGCUG-CCUUUGAGCCCCC-GUGCGCCUGUGUGUGGCGCCGGGGGUCAAGCUGCGGCGCCAGAGAA-GGUGCUCGCGCAUAACUGGGGCCGCC-UG---CCGUUCG-CCGACGGCCCU-UUUAACCGCGAGCUACACGG
AABR05022670.1/19047-19179   GCGCUG-CCUUUGAGCCCCCGGCGCACCUUCUCGUGGUGCCGGGGGUUAAGCUGCAGCGCUAUAGCAUUUUGCUGGCGCAUAACUGGGGCCGCC-UG---CCUAUCG-CGGGCGGCCCU-UUUAACCGCUAGCUACAGGC
AAQR03042176.1/42356-42223   GCGCUG-CCUUUGAGCCCCCGCCGCGCUUCCUCGUGGCGCCGGGGGUCAGGCUGCAGCGCCAGAGCA-CAAGCUUGCGUAUAACUGGGGCCGCC-UGC--CUUCUCCGCGGGCGGCCCU-UUUAACCGCGAGCGACACGG
AAGW02039970.1/177966-178097 GCGCUG-CCUUUGAGCCCCCGUCGCGCCUGCGCGUGGCGCCGGGGGUCAGGCUGCAGCGCCAGAGCA-CGAGCUCGCCCAUAACUGGGGCCGCC-UG---UACCUCG-CAGGCCGCCCU-UUUAACCGCGAGCGACAGGG
AAPE02024657.1/45214-45083   GCGCUG-CCUUUGAGCCCCCGCUGCGCCUGCGUGUGGCGCCGGGGGUCAGGCUGCAGCGCCAGAGCA-GCUGCUUGCGCAUAACUGGGGCCUAC-GG---CGCUCUG-CCGGCGGCCCU-UUUAACCGCGAGCGACACGG
AAEX03006361.1/15732-15865   GCGCUG-CCUUUGAGCCCCCGCCGCGCCUGCGCGUGGCGCCGGGGGUCAGGCUGCAGCGCCAGAGCA-CGCGCUUGCGCAUAACUGGGGCCGCC-CGGU-UCCCCCG-CCGGCGGCCCU-UUUAACCGCGAGCGACACGG
#=GC SS_cons                 <<<<<<.<--<<<<-<<<<-----<<<<_______>>>>-->>>>->>>>--->>>>>>>-------.---<<-<<<<--<<<--<<<<<<<<<.<<..._______.>>>>>>>>>>>.->>>-->>>>->>:::::::
#=GC RF                      GCGCuG.CCUcuGaGCCCccGccGcgCcUgCgcGUgGcgCcgGGGGuCagGCUGCaGCGCCAGAGcA.uguGCUcGcGCAuaaCUgGGGCcGcc.cg...ccucucg.cgggCgGCCCu.UuuaAcCgCgAGCuACAaGg
//
# STOCKHOLM 1.0

#=GF AC   RF00599
#=GF ID   SNORA77
#=GF DE   Small nucleolar RNA SNORA77
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:16373490; INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   42.00
#=GF TC   42.00
#=GF NC   41.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; ACA63;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300872;
#=GF DR   snoopy; Homo_sapiens300230;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   16373490
#=GF RT   A computational screen for mammalian pseudouridylation guide H/ACA RNAs.
#=GF RA   Schattner P, Barberan-Soler S, Lowe TM
#=GF RL   RNA. 2006;12:15-25.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   ACA63 (SNORA77) is a member of the H/ACA class of snoRNAs that guide the
#=GF CC   sites of modification of uridines to pseudouridines [1]. This snoRNA was
#=GF CC   identified by computational screening and its expression in mouse
#=GF CC   experimentally verified by Northern blot and primer extension analysis
#=GF CC   [2]. ACA63 is proposed to guide the pseudouridylation of 18S rRNA U814
#=GF CC   [2].
#=GF WK   Small_nucleolar_RNA_SNORA77
#=GF SQ   19


AC091002.54/90660-90785      GCAGAUUCACUCUGCACCUGGCUG-CA-GCUCCA-GU-CUGGUGCUUUUUCCAUCUGCCAAAGAAACAGUCCAGAAUGCUGUGGCUUCCUCUG---CCUAUCAG--AGGCAGUGCAGCUGC-CUGGGGACACAGCC
AC006549.28/5389-5513        GCAGACUCACUCUGCAUCUGACUA-UA-CUUCCA-GG-CGGGUGCUUUUUCUGUCUGCCAGAUAAACAUUCCAGGGUGCUGUGGCCGCCUCA----CGUAUCCA--GAGUGAUGCAGCUCC-CUGGGGACACAGGU
AC114402.2/38652-38776       GCAGACUCACUAUGCACCUGACUG-UA-CUUCCA-GG-CAGGUGCUUUUUCUGUCUGCCAGAGAAACAUUCCAGGGUGCUGUGGCUGCCUCA----CCUAUCCA--GGGCGAUGCAGCUCC-CUGGGGACACAGGU
AAHX01070384.1/5143-5019     GCAGAUUCACUCUGCACCUGGCUG-UA-GCUCCA-GU-CUGGUGCUUUUUCCAUCUGCCAGAGAAACAAUCCGGGU-GCUGUGGCUGCCUCUG---CCUGUCAG--GGGCAAUACAGCGGC-CUGGGGACACAGCC
AACN010173765.1/229-104      GCAGACUCACUCUGCAUCCGGCUG-CA-GCCCCA-GG-CGGGUGCUUUUUCCGUCUGCCACAGAAACAUCCCGGGGUGCUGUGACCACCUCGU---CCUGUCAA--GGGUGAUACAGCCGU-CUGGGAACACAGGG
ABDC01398879.1/440-562       GCAGACUCACUCUGCAUCCGGCUG-CA-CUU-CA-GA-UGGGUGCUUUUUCUGUCUGCCAAAGAAAUAUUCCGGGU-GCUGUGGCUGCCUGA----CUUGUCAG--GGGCGAUGCAGCUGC-CUGGGGACACAGGG
AANG01808267.1/4288-4163     GCAGACUCACUCUGCACCUGGCUG-CA-GCCCCA-GG-CGGGUGCUUUUUCCGUCUGCCAGAGUAACAUCCCAGGGUGCUGUGACCACCUUGA---CCUGUCAU--GGGUGAUGCAGUUGU-CUGGGGACACGGUG
AANU01185244.1/867-743       GCAGACUCACUUGGAACCUGACUG-CA-ACUCAA-GA-UGGGUGCUUUUUCCUUCUGCCAGAAUAACAUUCUGGGGUGCUGUGGCCACCUGA----CCUGUCAA--GACUUAUGUAGCUGC-CCAGGAACACAGGG
AAYZ01185132.1/1302-1429     GCAGACGCACUCUGCACCUG-CCG-CA-GCCACU-GG-CAGGUGCUUUUUCCGUCUGCCAGAGAAGCCUUCCGGGU-GCCGUGGCCACUUCGACUCCACCUGUC--GGGUGAUGCGGCUGCUCCGGGGACACAGGG
AANN01733869.1/842-724       GCAGACUCACUCUGCACCCGGCUG-CA-GCCCCA-GG-CGGGUGCUUUUUCUGUCUGCCACAGUAACACUCCAGGC-GCUGCA----GUCAU----CUUGACAU--GGCAA-UACAGUUGC-CGGGGGACAAGGUG
AAFC03097062.1/1035-1156     GCAGACUCACUCUGCACCCAGCCG-CA-GCCCCA-GG-CGGGUGCUUUUUCCGUCUGCCACAGGAACUUGCGGGG--GCUGUGAC--CUCUGC---CCUGUUAC--GGGCAGCACAGCUAC-CCCGGUACACGGGU
AAIY01689832.1/401-526       GCAGACACACUCUGCCUCCGGCUGCCA-ACCUCA-GC-CCGGUGCUUUUUCUGUCUGCCAGAGAACCG-CCCGGCUUGCUGCGAGUGUCUUGG---CCUAUCUG--AGGUGGCACAGCUCU-CCGGGGACAUGUGU
AALT01589983.1/6451-6577     GCAGACUCACUCUGCACCCUGCUG-CA-UCACCAAGCAUGGGUGCUUUUUCUGUCUGCCACAGAAACAUGCCAGGG-ACUGGUACUGCUUUGA---CCUAUCAAAGUGGCGAAGCUG--CC-AUGGGGACACGGGG
AAPY01793489.1/1412-1525     GCAGACUCACUCUGCACCCGGCAG-CA-UUCCCA-GGGCGGGUGCUUUUGCCGUCUGC-AGAGAAACGUACAGCGU-GCGGCUCUUGACUGC--------------AGGCGAUGCAGCU---GCUGGGACACGGGU
AAWR02042381.1/6226-6351     GCAGACUCACUCUGCACCUGGCUG-CA-GCCCCA-GG-CGGGUGCUUUUUCUGUCUGCCACAGAAACGUUCCAGGGUGCUGUGACCACCUUGA---CCUGUCAA--GGGCGAUGCAGCUGC-CUGGGGACAUGGAG
AAGV020560117.1/1296-1420    GCAGACUCACUCUGCAUCCAACUG-CA-GCCCCA-GUCUGGGUGCUUUUUUCGUCUGCCAGAGAAACA-CCUGGCC-GCCAUGUGGGCCUCGA---CUUGUCGA--UGGCACUGCAGCUGG-CCGGGGACAGUGGU
AAKN02007363.1/102991-103119 GCAGACUCACUCUGCACUUGGCUG-UAGCCUCCA-GG-CAGGUGCUUUUUCUGUCUGCCAGAGAACCAUUCCAGGGAGCUGUGACAGCCUUGA---CCUGUCAGGGGGGCAGUGCAGCUUC-UUGGGGACAUAGAA
AAPE02057147.1/6917-6793     GCAGACUCACUCUGCACCCGGCUG-CA-GUCCCA-GA-CGGGUGCUUUUUCAGUCUGCCACAGAAACAUUCCAGGG-ACUGCGACUACCUUGA---CCUGUGCA--GGGUGACGCAGCUGC-CCGGGGACAUGGUG
AAQR03174539.1/7146-7273     GCAGACUCACUCUGCAUCCGCCUG-CA-GCCCCAAGG-CGGGUGCUUUUUCAGUCUGCCAGAGAAAUAGUCCAGGU-GCUGCAGCUGUCUGACCC-ACUGUCAA--GGGCAGUGCAGCUGC-CUGGGGACACGGGU
#=GC SS_cons                 <<<<<<-------<<<<<<<-<<<.__.____>>.>-.>>>>>>>------->>>>>>-----------<<<<<<<.<<<<<<--<<<<<___...________..>>>>>->>>>>>->>.>>>>>:::::::::
#=GC RF                      GCAGAcUCACUCUGCAcCcggCuG.CA.gcccCa.Gg.cgGgUGCUUUUUCugUCUGCCAgAGAAACaucCcgggc.GCuGcgaccgcccuga...CcUgUcaa..gggcgacgCaGCUgc.ccgGgGACAcaGgu
//
# STOCKHOLM 1.0

#=GF AC   RF00600
#=GF ID   SNORA79
#=GF DE   Small nucleolar RNA SNORA79
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:16373490; INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   55.00
#=GF TC   56.10
#=GF NC   54.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; ACA65;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300878;
#=GF DR   snoopy; Loxodonta_africana300475;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   16373490
#=GF RT   A computational screen for mammalian pseudouridylation guide H/ACA RNAs.
#=GF RA   Schattner P, Barberan-Soler S, Lowe TM
#=GF RL   RNA. 2006;12:15-25.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   ACA65 (SNORA79) is a member of the H/ACA class of snoRNAs that guide the
#=GF CC   sites of modification of uridines to pseudouridines [1]. This snoRNA was
#=GF CC   identified by computational screening and its expression in mouse
#=GF CC   experimentally verified by Northern blot and primer extension analysis
#=GF CC   [2]. ACA65 is proposed to guide the pseudouridylation of residue U31 in U6
#=GF CC   snRNA (Rfam:RF00026)[2].
#=GF WK   Small_nucleolar_RNA_SNORA79
#=GF SQ   25


AC010582.6/81476-81337     UGAUGACUGUUCUUCCUGUUGCCUUCAGACCU-GGCAUUAGGAUUUUAGGUCAUCAUAAAUUAAAAUUU-GAUUUU-CUUCACUCAGAGAAUAU-U-AGG--AUA-AUGGAGU----UAUCU----GUUC--UCUGAAAUUUGCGGAAUCAAACAUGU
AC126265.3/118626-118483   UGAUGACUGUUCCUCCUAUUGCCUUUAGAUAU-GGCACUAGGAUUUUAGGUCAUCAUAAAUUAAAAUU--GAUUUUUUUUCACUCAGAGAAUAU-U-AAG--AUA-CUGGGAU----UAUCUAUGUAUUC--UCUGAAAUUUGCGGGAUCAAACAGUU
AAFC03085126.1/12310-12453 UGAUGACUGUUCCUCCUAUUGCCUUCAGAUCU-GGCACUAGGAUUUUAGGUCAUCAUAAAUUAAAAUUU-GAUUUU-CUUCACUCAGAGGAUAU-U-AGG--AUA-AUGGAAU----UAUCUGUUUAUUC--UCUGAAAUUCGCGGAAUCAAACACCU
AAPY01357268.1/2436-2293   UGAUGACUGUUCCUCCUACUGCCUUCAAGCCU-GGCAGUAGGAUUUUAGGUCAUCAUAAAUUGAAAUUU-GAUUUU-CUUCACUCAGAGAAUAC-U-AAG--AUA-AUGGGAU----UAUCUGUUUAUUC--UCUGAAAUUUGCGGAAUCAAACAGUU
AANN01835968.1/5302-5159   UGAUGACUGUUCCUCCUCUUGCCUUCAGGUCU-GGCACUAGGAUUUUAGGUCAUCAUAAAUUAAAAUUU-GGUUUU-CUUCACUCAGAGAAUAU-U-AGG--AUA-AUGGGAU----UAUCUGUUUAUUC--UCUGAUAUUUGCGGAAUCAAACAUUU
AANG01129473.1/168-25      UGAUGACUGUUCCUCCUAUUGCCUUCACGUCU-GGCACUAGGAUUUUAGGUCAUCAUAAAUUUAAAAUUUGAUUUU-CUUCACUCAGAGAAUAU-U-AGG--AUA-AUGGGAU----UAUC-AUUUAUUC--UCUGAAAUUUGCGGAAUCAAACACUU
AALT01342459.1/799-658     UGAUGA-CGUUCCUCUCAUUGCCUAGAGCAUU-GGCACUGGGAUUUUAGUUCAUCAUACAUCAAACUU--GAUUUU-CUUCACUCAGAGAAUAU-U-GGG--AUA-AUGGGAU----UAUCUGUGUAUUC--UCUGAAAUUUGCGGAAUCAAACACUG
AAFR03018707.1/10108-10252 UGAUGACUGUUCCUCCUAUUGCCUAGAGCUCU-GGCAUUAGGAUUUUAUGUCAUCAUACAUUAAAAUUU-GACUUU-UUUCACUCAGAGAAUAUUU-GGG--AUA-AAUGGAU----UAUCCUUUUCUUC--UCUGAAAUUUGCGGAGUCAAACACUU
AAIY01601548.1/3201-3057   UGAUGACUGUGCCUCCUCUUGCCUUCAGACCU-GGCACUAGGGUUUUAGGUCAUCAUAAAUAAAAAAUU-GAUUUU-CUUCACUCAGAGAAUAA-U-AGA--AUA-AUGGGUU---UUAUCUGACUAUUC--UCUGAAAUUUGCGGAAUCAAACAGCU
AAQQ01695901.1/3622-3476   UGAUGACUGUUCCUCCUAUUGCUUAUAGGCUG-GGCACUAGGAUUUUAUGUCAUCAUAAAAUUAAUUU--GAUUUU-CUUCACUCAGAGAAUAU-U-AGG--AUA-AUGGGAUUUAUUAUCUGUCUAUUC--UCUGAAAUUUGCGGGAUCUAACACUU
AAVX01074621.1/2345-2488   CGAUGACUGUUCCUCCUGUAGCUUCAAGUCUC-AGCUGCAGGAUUUUAUGUUGUCGUAGAUCAAACCU--GACUUU-AUUCACUCGGAACGCAC-U-GGG--ACAUCUGGUAU----UGUCCAUCUGCGU--UUUGAAUUUUGCGGAGUCAGACAUGU
ABDC01400124.1/3450-3303   UGAUGGCUGUUCCUCUCACUGCUUGGAGCCUUAGGCGGUGGGAUUUUGAUCCAUCAUAUAUCAAAGCU--GACUUGUCUUCACUCAGAGCACCA-UGAGG--AUG-GGUUGGC----UAUCCAUUAGUGCCUUCUGAUUUUUGCGGAGUCAAACAAUU
AAFC03071173.1/56452-56305 UGAUGGCUGUUCCUCUCACUGCUUGGAGCCUUAAGUAGUGGGAUUUUAGUCCAUCAUAUAUCUAAACU--GACUUGUCUUCACUCAGGGCACCA-UGGGG--ACA-GGUUGGC----UGUCCGUUAGUGCCUUCUGAUUUUUGCGGAGUCAAACAAUU
AAFC03049649.1/69040-68900 UGAUGGCUGUUCUGCUCACUGCGUGCAGCCUUAAGUAGUGGGAUUUUAGUCCAUCAUAUAUCUAAACU--GACUUGUUUUCAUUCAGGGCACCA-U-GGG--UUA-GC---------UGUCUGUCACUGC-CUUUGAUUUUUGCAGACUCAAACAAUU
AAFC03094306.1/24807-24660 UGAUGGCUGUUCCUCUUACCGUUUGGAGCUCCGAGUAGUGGGAUUUUAGUCCAUCGUGCAUCUAAGCU--GACUUCUCUUCACUCUGGGCACCA-UGGGG--AUG-AGUUGGC----UGUCCGUUAGUGCCUUCUGAAUUUUGCGGAGUCAAACAAUU
AAFC03113610.1/4861-5003   UGAUGA-UGUUCCUCCUAUUGCCUUCAGGCCU-GACAUUAGGGUUUUAGGUCAUCAUAAAAUAAAAUUU-GCUUUUUCUUCACUCAGAGAAUAU-U-AGG--GUA-ACGGGAU----UGUCUACUUAUUC--UCUGA-AUUUGCAGAGUCAAACACUU
AAKN02053151.1/90466-90609 UGAUGACUGUUCCUCCUAUUGCUUUGAGGUUU-GGCACUAGGAUUUUAAGUCAUCAUAAAUUGAAAUUU-GAUUUU-CUUCACUCAGAGAAUAU-U-AGG--AUA-AUGGGAU----UAUCUGUCUGUUC--UCUGAAAUUUGCGGAAUCAAACAGUU
AAGV020611425.1/765-622    UGAUGACUCUUCCUCCUAUUGCCUUCAGGCCU-GGCAGUAGGAUUUUAGGUCAUCAUAAAUUAAAAUUU-GAUUUU-CUUCACUCAGAGAAUAU-U-AGG--AUA-AUGGGAU----UAUCUAUCUGUUC--UCUGAAAUUUGCGGAAUCAAACACAU
AAWR02019771.1/14857-14714 UGAUGACUGUUCCUCCUAUUGCCUUCAGGCCU-GGCACUAGGGUUUUAGGUCAUCGUAAAUUAAAAUUU-GAUUUU-CUUCACUCAGAGAAUAU-U-AGG--AUA-AUGGAAU----UAUCUGUUUAUUC--UCUGAAAUUUGCGGGAUCAAACAUUU
AAHX01045805.1/5078-5220   UGAUGACUGUUCCUCCUAUUGCCUAUAGGCAU-GGCACUAGGAUUUUAGGUCAUCAUAAAUUAAAAUU--GAUUUU-UUUCACUCAGAGAAUAU-C-AAG--AUA-AUGGGAU----UAUCUGUGUAUUC--UCUGAAAUUUGCGGGGUCAAACAAUU
AAPE02016522.1/17302-17445 UGAUGACUGUUCCUCCUAUUGCCUUCAGUCCU-GGCACUAGGAUUUUAGGUCAUCAUAUAUUAAAAUCU-GAUUUU-CUUCACUCAGAGAAUAU-U-AGG--AUG-AUGGGAU----UAUCUGUUUAUUC--UCUGAAAUUUGCGGAAUCAAACACUU
AAWZ02020193.1/2460-2315   UGAUGACUGUUCCUCUUGCUGUCAUAAGCCUUGGACAGUAAGAUUUUGUGUCAUCAGAUAUAAAAAUU--GGCCUUUCUUCACUCAA-GGUGUC-U-UGGAUGGG-UUUGGCU----GUCCUGUAGCACC--GUUGAACUUUGCGGGGUCAAACAUUU
AAGU03086581.1/15947-16093 UGAUGGCUGUUCCUCUCACUGCUUGGAGGCUUAGGCAGUGAGAUUUUAGUCCAUCAUAUAUCAAACCU--GGCUUGUCUUCACUCAGGGCACCA-U-GGG--AUG-GGUUGGC----UGUCCGUUAGUGCCUUCUGAUUUUUGCGGAGUCAAACAAUU
AAGU03025458.1/409-266     UGAUGACUGUUCCUCCUAUUGCCUUCAGACCU-GGCACUAGGAUUUUAGGUCAUCAUAGAUCAAAAUGU-GAUUUU-CUUCACUCAGAGAAUAU-U-AGG--AUA-AUGGGAU----UAUCUGUCUAUUC--UCUGAAAUUUGUGGAAUCAAACAGCU
AAGW02049089.1/15458-15601 UGAUGACUGUUCCUCCUAAUGCUUUCAAGCCU-GGCAUUAGGAUUUUAGGUCAUCAUAAAUUAAAAUUU-GAUUUU-CUUCACUCAGAGAUUAU-G-UGG--AUA-AUGGGAU----UGUCUGUCUGUUC--UCUGAAAUUUGCGGAAUCAAACAUUU
#=GC SS_cons               <<<<<<<<-----<<<<<-<<<<_________.>>>>->>>>>----->>>>>>>>------------..<<<<<<.------<<<<<<<<<<-.-.-<<..<<<._______....>>>>>--->>>>>..>>>>>------->>>>>>::::::::
#=GC RF                    uGAuGaccGUUCCuCcuauuGccUuaAGacuU.ggCaguagGaUUUUAgguCaUCaUAaAUuaAAauU..Gacuuc.cUUCACUCaGaGgacau.U.agG..aua.augGGaU....uauCcgUuugucC..uCuGAAaUUUGCggaguCAAACAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF00601
#=GF ID   SCARNA20
#=GF DE   Small Cajal body specific RNA 20
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:16373490
#=GF SS   Predicted; RNAalifold
#=GF GA   44.00
#=GF TC   44.00
#=GF NC   42.90
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; ACA66;
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   16373490
#=GF RT   A computational screen for mammalian pseudouridylation guide H/ACA RNAs.
#=GF RA   Schattner P, Barberan-Soler S, Lowe TM
#=GF RL   RNA. 2006;12:15-25.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. ACA66 (SCARNA20) is a member
#=GF CC   of the H/ACA class of snoRNAs that guide the sites of modification of
#=GF CC   uridines to pseudouridines. This snoRNA was identified by computational
#=GF CC   screening and its expression in mouse experimentally verified by Northern
#=GF CC   blot and primer extension analysis [2]. It is predicted to guide the
#=GF CC   pseudouridylation of residue U28 in U12 snRNA (Rfam:RF00007) [2].
#=GF WK   Small_Cajal_body_specific_RNA_20
#=GF SQ   5


AY152828.1/39544-39414   GGCCUCUCUCCCACGGGGCUGCGGGGGGCCCCUUUUCUCCUCGGCCAGGUCUGGAGGGCAAGAUCAGCCCUUGAAAAUCAU-U--GUCAGGACUGCCACAAGCUAG-CAGCCUUGUCUUCCUGCCUCAGACAUCU
AC104763.12/68286-68156  UGCCUCUCUCCCAUGGGCUUU-GGGGGGUCCCUGUUCUCCUUAGCCAAGGCUGGAGGCCAAGAGCAGCCCUCGAGGAUCGU-C--GUCAGGACUGCCACGAGUGGGGCAGCCUUGUUUUCCUGCCUCAGACAUGU
AJ630365.1/99155-99283   GGCCUCUCUCCCAUGGGGCUA-A-GAGGUCCCUUUUCUCCUUAGCCAGGGAUGGAGGCCAAGAUCAGCCUUUGAGGAUCAU-U--GUCAGGGCUGCCACAAGCUGG-CAGCCUUGUUUUCCUGCCUCAGACAUCU
AC084109.2/101118-100990 GGCCUCUUGUCCAUUGAGCUG-UGGGGAUCGUGUUCCUCCAUGGCCAGGGCUGGAGGCCAAGAUCAG-CUGUGAGGAGCAUUC--GUCAGGACUGCUAUGAGCAGG-CAGCCUUGUUU-CCGGCCUCAGACACUG
AC091752.2/95000-94868   GGCCUCUUGUCCAUUGAGCCA-UGGAGAUCACAUUCCUCCUUGGCCAGGGCUGGAGGCCAAGACAAGUCUGUGAGGAGCAUUCUCGUCAGGACUGCUGUGAGCGGG-CAGUCUUGUUUUCCGGCCUCAGACAUUG
#=GC SS_cons             <<<<<<<--<<<----<<<<-.<<<<<_________>>>>>->>>>->>>-->>>>>>>------------<<<<<-----.-..--<<<<-<<<<<_______>>.>>>->>>>-------->>>>>:::::::
#=GC RF                  ggCCuCuuucCCAUgGgGcca.gGGaGgUCccuuUuCuCCcUggCcAGGgcUgGaGGccAAGAucAGcCuuuGaGGAuCAU.c..GUCagGACuGCcAugAGcugG.CaGcCuuGUUUUCCuGCCuCaGACAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF00602
#=GF ID   SCARNA21
#=GF DE   Small Cajal body specific RNA 21
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:16373490
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   60.00
#=GF TC   65.90
#=GF NC   56.60
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; ACA68;
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF RN   [2]
#=GF RM   16373490
#=GF RT   A computational screen for mammalian pseudouridylation guide H/ACA RNAs.
#=GF RA   Schattner P, Barberan-Soler S, Lowe TM
#=GF RL   RNA. 2006;12:15-25.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   scaRNAs are a specific class of small nuclear RNAs which localise to the
#=GF CC   Cajal bodies and guide the modification of RNA polymerase II transcribed
#=GF CC   spliceosomal RNAs U1, U2, U4, U5 and U12 [1]. ACA68 (SCARNA21) is a member
#=GF CC   of the H/ACA class of snoRNAs that guide the sites of modification of
#=GF CC   uridines to pseudouridines. This snoRNA was identified by computational
#=GF CC   screening and its expression in mouse experimentally verified by Northern
#=GF CC   blot and primer extension analysis [2]. ACA68 is proposed to guide the
#=GF CC   pseudouridylation of residue U19 in U12 snRNA (Rfam:RF00007)[2].
#=GF WK   Small_Cajal_body_specific_RNA_21
#=GF SQ   24


AC009228.4/59361-59234     UGGCAUG-AUUUCCU-GCAGGUUGAGCUCAGCCAAGUACCACC--CCUCAG-UAAGCCUAGAGUAGAGGGGCCUGACA-------------UCCUUUCCUUAA-------------AUUAAACAAGGAG-CCUU-AUCCAGG--UUGUCCUAGUCUCAUACUU
BX640578.3/41476-41338     UGGCUUG-GUUUCCU-GGGGGGUGGGCUCAGUGCUCUCCACCCCCUCUCAGCUAAGCCUAGAGUAGAGAGGCCAGGUA-------------CGCACCUGGGUGGGAGAGGU----GCUUCUGC-AGGAG-CCUU-GCCUGGG--CUGGCCUAGCCUCACAUUU
AL121992.24/6341-6480      UGGCUCG-GUUUCCU-GGGGGGUGGGCUCAGUCUACACCACCUCCCCUCAGCCAAGCCUACAGUAGAGGGCCCAGGCA-------------UCCUCCCGUAUGGGAGAGGC----GUUUGAGUAAGGAG-CCUC-ACCUGGG--GUGUCCUAGCCUCACAUUU
AL646043.7/11714-11571     AGGCUCU-AUUUCCU-GGAAGGUGGGCCUAGCCUACCCCACUUCCCCUCAGCAGAGCCUAGAGUAAAGGGGCCAGGCC-------------UCCUCCCCAAUGGGAGAGAGAUGUGUUUGAAGAAGGAG-CCUC-ACUCGGG--CUGGCCUGGCUUCACAUUA
AL596125.27/8000-7857      AGGCUCU-AUUUCCU-GGGAGGUGGGCUUAGCCUACCCCACUUCCCCUCAGCAGAGCCUAGAGUAAAGGGGCCAGGCC-------------UCCUCCCCUAUGGGAGAGAGAGGUGUUUGAAGAAGGGG-CCUC-ACCCGGG--CCGGCCUGGCUUCACAUUU
AC104581.22/69359-69497    UGGCUCG-AUUUCCU-GGGGGGUGGUCUCAGCCCACUCCACCUCCCCUCAGCCGAGCCUAGAGUAGAGGGGCCAGGCA-------------UCCUCCCC-AGGGGAGGGGC----GUUGAAGCAAGGAG-CCUC-UCCUGGG--CUGUCCUAGCCUCACAUUU
AAHX01064572.1/17502-17363 AGGCUCU-AUUUCCU-GGGAGGUGGACUCAGCCUACCCCACUUCCCCUCAGCAGAGCCUAGAAUAAAGGGGCCAGGCC-------------UCCUCCCCUAUGGGAGAGGG----GUUUGAAGAAGGAG-CCUC-ACCCAGG--CUAGCCUGGCUUCACAUUU
ABDC01418608.1/4986-5124   UGGCUUG-GUUUCCU-GGGGGGUGGACUCAGCCUACUCCACCUCCCCUCAGCCGAGCCUAGAGUAGAGGGGCCAGGCA-------------UCCUUUCU-GGGGGAGAGGC----GUUUAUGUAAGGAG-CUUC-GCCUGGG--CUGUCCUAGCCUCACAUUU
AAQQ01673617.1/295-433     UGGCUCA-GUUUCCU-GGG-GGUGGGCUCAGCCUACACCACCUCCCCUCAGCUGAGCCUAGAAUAGAGGGGCCAGGCA-------------CCCUCCUUCAUGGGAGAGGU----AUUUAAGGAAGGCG-CCUC-GCCUGGG--CUGGCCUAGCCUCACAUUU
AANU01204662.1/3314-3175   UGGCUUG-AUUUCCUGGGGGGGUGGUCUCAGCCCACCCCACCUCCCCUCAGCCGAGCCUAGAGUAGAGGGGCCAGGCA-------------UUCUCCCC-AGGGGAGAGGU----GUUGAAGCAAGGAA-CCUC-UCCUGGG--CUGUCCUAGCCUCACAUUU
AADA01184538.1/2869-2731   UGGCUCG-AUUUCCU-GGGGGGUGGUCUCAGCCCACUCCACCUCCCGUCAGUCGAGCGUAGAGUAGAGGGGCCAGGCA-------------UCCUUUCC-AGGGGAGGGGC----GUUGAAGCAAGGAG-CCUC-UCGUGGG--CUGUCCUAGCUUCACAUUU
AAPY01712703.1/1836-1974   UGGCUCG-GUUUCCU-GGGGGGUGGGCUCAGCCUACCUCACCUCCCCUCAGACGAGCCUAGAGUGGAGGGGCCAGGCA-------------CCCUCCUC-CGUGGAGAGGC----GUUUAAGUAAAGAG-CCUC-GCCUGGG--CUGUCCGGGCCUCACAGUU
AAIY01313070.1/3664-3527   UGGCUCG-GUUUCCU-GGGCGGUGGGCUCAGCCUCCUCCACCUCCCCUCAGACGAGCCUAGAGGAGAGAGGCCAGGCU-------------UCCUCCCC--UGGGAGUGGC----UUUCAAGAAGGGAG-CCUC-GCCCAGG--CUGUCCUAGCCUCACACUU
AAFC03055699.1/17138-16999 UGGCUUG-GUUUCCU-AGGGGGUGGGCUCAGCCUCUGCCACCUCCCCUCAGCUGAGCCUAGAGCAGAGAGGCCAGGCG-------------CUCCCUACUGUGGGAGAGGC----AGGUGAGACAGGAG-CCUC-GCCUGGG--CUGUCCUUGCCUCACAGGC
AANG01159425.1/1572-1711   CGGCUUG-GUUUCCU-GGGGCGUGGACUCAGCCUGC-CCACCUCCCCUCAGCCGAGCCUAGAGCAGAGAGGCCUGGCU-------------UCCUCCCCCACAGGGCAGGU----GGUUGAGACAGGAA-CCUGGCCCCGGG--CUGGCCUCGCCUCACAUUU
AAYZ01280870.1/12479-12615 UGGCUCA-AUUUCCU-GGGGGGUGAGCUCAGCCUCCCCCACCCUCCCUCGCCUGAGCCUAAAGUAGAGGAGCCAGGCA-------------GGCACCACCCAG--AGAGAC----CUUUAAGUAAGGGG--CCU-CCCUUGG--CUGCCUUGACCUCACAUCA
AALT01405644.1/739-877     GGUCUCG-AUUUCCU-GGGGGGUGGGCUCAGUCUGUUCCACCUCCCCUCAGACUAGCCUAGAUCAAA--GGCAGGGUU-------------CUCUGCAUACUAGUAUGGUG----GGUCAAGAAAUCAGCGCCA-ACAUGGG--CUAUCCCUGCCAUACUUUU
AAFR03049850.1/23172-23323 AGGACCCUAUUUCCU-GGGGGGUGAGCUCAGUCUACCCCACCCCCCCUCAGUGGGUCCCAGAAUAGAAU-GCCAGGAUGGGUCUCACUCCUACCCCAUGAACA-GAGAGGA----GUGUGAGACAGACA-CCUG-CUCUGGC--CAGUACUGGCAACACAUGU
AAWR02013415.1/9829-9968   CGGCUCG-AUUUCCU-GGGGGGUGGGCUCAGCCUACCCCACCUCCCCUCAGACGAGCCCAGAGCAGAGAGGCUGGGCU-------------UCCUCCCCAACAGGAGAGGC----GGUUAAGACAGGAG-CCUC-GCCUGGG--CUGUCCUUGCCUCACAUUU
AAKN02049880.1/52363-52499 UGGCUCU-GUUUCCU-GGCAGGUGGACUUGGCUCCCUCCACCUUCCCUCAGUUGAGCCUAGAGUAGAGGGGCUGACUG-------------UCCU---GUGUGGGAGAGGU----AUUUAAGAAAGGAG-CCUU-GCCCGGG--CUGUCUCAGCCUCACAUUU
AAGW02049550.1/2920-2784   UGGCUCA-GUUUCCU-GGGGGGUGAGCUCAGCCUCCCCCACCUCCCCUCAGCUGAGCCUAGAGGAGACAGGCCAGGCA-------------CCUGCCCC--CUGGAGAGGC----GUUUAAGUAAGGAG-CCUC-GCC-UGG--CUGCCCUGGCCUCACAUUU
AAQR03002857.1/3077-3214   UGG-UUG-GUUUCCU-GGGGAGUGGGCUCAGCAUACCCCACCUCCCCUCAGCCAAGCCUAGAGUAGAGAGGCCAGGCA-------------UCCUCUCUGUGGGG-GAGGC----AUUCAAGUAAGGUG-CCUC-GCCUAGG--CUAUCCAAGCCUCACAUUG
AAEX03003635.1/15308-15448 UGGCUUG-GUUUCCU-GGGGCGUGGGCUCAGUGCGCCCCAUGUCCCCUCAGCCGAGCCUAGAGCACAGAGGCCUGGUC-------------CCCCUACU-ACGGGAGAGGC----GCUGGAGAUAGGAG-CCCU-GCCCUGGACCUGUCCUGGCCUCACAUUU
AAPE02045192.1/15898-16036 UAGCUCG-GUUUCCU-GGGAGGUGGGCUUAGUCUGACCCACCUCCCCUCAGACGAGCUGAGAGUAGAGAGGCCGGGCU-------------UCCUCCCC-AUGGGAGAGGU----GGUUACGAGAGGAG-CCUC-ACCUAGA--CUGUCCUUGCCUCACAUUU
#=GC SS_cons               :<<<<<<.-------.<<<<<<<<<<__________>>>>>>>>>>------>>>>>>---------<<<<<-<<<--.............-<<<------<<<<______....______________.>>>>.---->>>..---->>>->>>>>::::::
#=GC RF                    uGGcucg.aUUUCCU.GGgggGUGggCUCAGcCUacccCACcccCCCUCAGccgagCCUAGAguAgAGaGGCCaGgca.............ucCcccccaacgGGAGAGGu....guUuaAGaaAGGaG.CCcg.aCCugGg..CUGucCuaGCCuCACAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00603
#=GF ID   SNORD23
#=GF DE   Small nucleolar RNA SNORD23
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   64.00
#=GF TC   65.60
#=GF NC   63.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; HBII-115;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300008;
#=GF DR   snoopy; Pongo_pygmaeus300661;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. This family includes mouse MBII-115 identified in [2]
#=GF CC   and the human orthologue HBII-115 (SNORD23). There is currently no
#=GF CC   predicted target RNA for HBII-115 [3].
#=GF WK   Small_nucleolar_RNA_SNORD23
#=GF SQ   15


AK024486.1/3319-3428       UGCCCAGUGAUGACA-C-CAUCCUUGCUCCCCGUGC-CCCCCAG---GGG-CUAUGGGCGACACCAUGGCUGCCCCUGGGCUGGGCCAGU-GGGGCCAAU-GCCCAGGGGCUGAGGGCA
AF357349.1/1-99            -------UGAUAAC----CAUCCUUGCUCCCCGUGC-CUACUCG---GG--CUGUGGGCGACACCAUGGCUGCCC-UGGGCUGGGCCAGU-UGGGCCAUU-GCCUGGGGACUGAGGGCA
AAHX01004065.1/24142-24250 UGCCCGGUGAUGAUAAC-CAUCCUUGCUCCCCGUGC-CCUCUUG---GG--CUGUGGGCGACACCAUGGCUGCCC-UGGGCUGGGCCAGU-UGGGCCAUU-GCCUGGGGACUGAGGGCA
AAQQ01534227.1/350-242     UGCCCAAUGAUGACA-C-CAUCCUUGCUCCCCGUGC-CCCCAGG---GG--CUAUGGGCGACACCUUGGCUGCCCUUGGGCUGGGCCGGC-UGGGCCGUU-GCCUGGGGGCUGAGGGCA
AAPY01018131.1/311-201     UGCCCAGUGAUGAGA-C-CAUCCUUGCUCCCCAUGC-UCCCCAG---GGGGCUGUGGGUGACACUAUGGCUGCCCCCGGGCUGGGCCAGG-UGGGCCAGA-GCCCGGGGGCUGAGGGCA
AAYZ01216133.1/130-239     UGCCCUGUGAUGACA-C-CAUCCUUGCUCCCCGUGUGCCCCCCG---GGG-CUGUGGGUGACACCUUGGCUGCCC-CGGACUGGGCCAGG-UGGGCCAGU-GUCCGGGGGCUGAGGGCA
AACN010478572.1/777-885    UGCCCAGUGAUGAUA-CCCAUCCUUGCUCCCCGUGC-CCCCC-----GGG-CUGUGGGCGACAUCAUGGCUGCCCCCAGGUUGUGCCAGU-UGGGCUGAU-GCCUGGGGGCUGAGGGCA
AAFC03086458.1/7697-7588   UGCCCAGUGAUGACA-CCCAUCCUUGCUCCCCGUGU-CCGCAGG---GA--CUGUGGGCGACAUCACGGCUACCCCCAGGCGGGGCCGGU-UGGGCUAAU-GCCUGGGGGCUGAGGGCA
AANN01595469.1/181-294     UGCCCGGUGAUGACA-CCCAUCCUUGCUCCCCGUGC-CCUCCCAGCAGGG-CUUUGGGCGACAUCCUGGCUGCCCCUGGGCAGGGCCGGU-UGGGCUGAU-GCCUGGGGGCUGAGGGCA
ABDC01373885.1/646-756     UGCCCGGUGAUGACA-CCCAUCCUUGCUCCCCGUGC-CCCCCAG---GGG-CUGUGGGCGACA-CAUGGCUGCCCCCGGGCCAGGCUGGUUGGGGCCGGU-GCCCGGGGGCUGAGGGCA
AAIY01701293.1/348-242     UACCCGCUGAUGAUC-C-CAUCCUUGCUCCCCAGGC-CCUCCCG---GG--CAGUGGGCGACACUGUGGCUCCCC-UGGGCU-GGCCAGU-UGGGCUGAU-GCCUGGGGGCUGAGGGCA
AALT01144050.1/1322-1220   UGCCCGCUGAUGACA-C--AUCCUUGCUCCCCGUGC-CUGUU------GG-CUGUGGGUGACAUCCUGGCUGCCC-UGGGCCAAGCCAGU-GGG--CUAA-GCCUGGGGGCUGAGGGCA
AAGV020550780.1/807-698    UGUCCGGUGAUGACA-UCUAUCUUUGCUCUUCGUGC-CUCUCAG---GG--CCAUGGGCGACACUCUGGCUAGCUCUGGGCUGGGCCGGU-UGGGCCAGC-GCCUGGGGGCUGAGGGCA
AAWR02044380.1/7317-7425   UGCUCGAGGAUGACA-CUCAUCCUUGCUCCCCGUGC-CCCCAGG---GG--CUGUGGGCGACAUCGUGGCUGCCC-CGGGCUGGGCCAGU-UGGGCUGAU-GCCCGGGGACUGAGGGCA
AAQR03153932.1/31429-31540 UGCCCAGUGAUGAUA-CCCAUCCUUGCUCCCCGUGC-CUCCCAG---GGG-CUGUGGGCGACACCAUGGCUGCCCCCAGGACAGGCUGGU-UGGGCUAUUGGCCUGGGGGCUGAGGGCA
#=GC SS_cons               <<<<<__________._.__________________._______...___._______________________________________._________._____________>>>>>
#=GC RF                    UGCCCagUGAUGAcA.C.CAUCCUUGCUCCCCGUGC.CccCcaG...GGG.CUgUGGGcGACAccaUGGCUgCCCcuGGGCuGGGCCaGU.UGGGCcaaU.GCCuGGGGGCUGAGGGCA
//
# STOCKHOLM 1.0

#=GF AC   RF00604
#=GF ID   SNORD88
#=GF DE   Small nucleolar RNA SNORD88
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   46.00
#=GF TC   46.80
#=GF NC   45.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00071
#=GF DR   snoRNABase; HBII-180A;
#=GF DR   snoRNABase; HBII-180B;
#=GF DR   snoRNABase; HBII-180C;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300751;
#=GF DR   snoopy; Oryzias_latipes300016;
#=GF RN   [1]
#=GF RM   8764399
#=GF RT   Intron-encoded, antisense small nucleolar RNAs: the characterization of
#=GF RT   nine novel species points to their direct role as guides for the
#=GF RT   2'-O-ribose methylation of rRNAs.
#=GF RA   Nicoloso M, Qu LH, Michot B, Bachellerie JP
#=GF RL   J Mol Biol. 1996;260:178-195.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. This family includes mouse MBII-211 and MBII-180
#=GF CC   identified in [2] and the human orthologue HBII-180 (SNORD88). HBII-180 is
#=GF CC   predicted to guide the 2'O-ribose methylation of 28S rRNA C3680 [3].
#=GF WK   Small_nucleolar_RNA_SNORD88
#=GF SQ   35


AC152939.2/6387-6477         AGG--CUCCUGUGAUG--UUUAGCACUGGGCUCCAAACAC-CCUUGAGGAC----A-C---A-GUGCCCCU------CCAGGACCUUUGACACCU-GGAGAUC--UGAGGA-CCU
AF357325.1/3-89              CCC--CCCCUCUGAUG--UUCAGCACUGGGCUCUGACCAU-C-CUGAGGAC----A-U---G-GUGCCCC-------CAGGGACCUUUGACACCC-UGGGGUC--UGAGGGG---
AC152939.2/8747-8839         GAA--CCCCCAUGAUGUAUAUAGCACUGGGCUCUGACCAC-C-AUGGUGAU----A-U---G-UUGUGCCU------CCAGGACCUUUGACAUCC-AGGAGUC--UGAGGGGUUU
AC010325.7/135083-134993     GGG--CUCCCAUGAUG--UCCAGCACUGGGCUCUGAUCAC-CCCUGAGGAC----A-C---A-GUGCACC-------CCAGGACCUUUGACACCU-GGGGGUC--UGAGGGGCCC
AC010325.7/132197-132107     GGG--CCUCCAUGAUG--UCCAGCACUGGGCUCCGACUGC-CACUGAGGAC----A-C---G-GUGCCCC-------CCGGGACCUUUGACACCC-GGGGGUC--UGAGGGGCCC
AC010325.7/131787-131697     GGG--ACCCCGUGAUG--UCCAGCACUGGGCUCUGACUGC-CCCUGAGGAC----A-C---G-GUGCACC-------CCGGGACCUUUGACAUCC-GGGGUUC--UGAGGGGCCC
AC152939.2/8149-8238         GGA--CCCCUCUGAUG--UUCAGCACUGGGCUCUGACCAU-C-CUGAGGAC----A-U---G-GUGCCCC-------CAGGGACCUUUGACACCC-UGGGGUC--UGAGGGGCCC
AC152939.2/8432-8521         GGA--CCCCCUUGAUG--UCCAGCACUGGGCUCUGACCAU-C-CUGAAGAC----A-U---G-GUGCCCC-------CAGGGACCUUUGACACCC-UGGGGUC--UGAGGGGUCC
AANN01344612.1/471-561       GGG--CCCCCGUGAUG--UCCAGCACUGGGCUCUGACCAC-CCCUGAGGAC----A-U---G-GUGCCCC-------CCGGGACCUUUGACACCC-GGGGGUC--UGAGGGGCCC
ABDC01430049.1/209-119       GGG--CUCCAAUGAUG--UCUAGCACUGGGCUCCGAUCAC-CCCUGAGGAC----A-C---A-GUGCCCC-------CCAGGACCUUUGACACCU-GGGGGUC--UGAGGGGCCC
AANU01181926.1/15050-14960   GGG--CUCCCAUGAUG--UCUAGCACUGGGCUCCGAUCAC-CCCUGAGGAC----A-C---A-GUGCACC-------CCAGGACCUUUGACACCU-GGGAGUC--UGAGGGGCCC
AAPY01553556.1/872-961       GGG--UCCCCGUGAUG--UCCAGCACUGGGCUCUGACCAC-C-CUGAGGAC----A-U---G-GUGCCCC-------CCGGGACCUUUGACACCC-GGGGGUC--UGAGGGGCCC
AAIY01782013.1/208-298       UGG--CCCCCAUGAUG--UCUAGCACUGGGCUCCAAUUGC-CCCUGAGGAC----A-C---U-GUGCCCC-------CCAGGACCUUUGACACCU-GGGGGUC--UGAGGGGCCA
AAQQ01534077.1/26-117        GGA--CCCCUGUGAUG--UCUAGCACUGGGCUCUGACCAUUCUUUGAGGAU----A-A---G-GUGCCCC-------CCAGGACCUUUGACACCU-GGGGGUC--UGAGGGGUCC
AAFC03082890.1/21271-21362   GGG--CCCCUGUGAUU--UCCAGCACUGGGCUCUGAUCUC-CCGUGAGGAC----A-C---G-GUGCCCCC------CCAGGACCUUUGACACCU-GGGGAUC--UGAGGGGCUC
AANG01189622.1/185-87        GGG--CCCCCAUGAUG--UCCAGCAAUGGGGUUUGACCUC-CCCUGAGGAC----A-U---G-GUGCCCCCCCCCCCCCGGGACCUUUGACACCCAGGGGGUC--UGAGGGGCCC
AAFR03066872.1/23185-23275   GGG--CUCCCAUGAUG---CCAGCACUGGGCUCUGAGCCU-C--UGAGGACAAACA-C---G-GUGCCCC-------CCAGG-CCUUUGACUCCU-GGGGGUC--UGAGGAGCCC
AAPN01247065.1/315-403       GGG--UUUCCAUGAUG--UCUUGCACUGGGCUCUGAUCU----CUGAGGAC----AAC---G-GUGCACC-------CCAGGACUUUGACCCUCG-GGGAGUC--UGAGGAUGCC
CR381655.6/5580-5491         ACG--CUUCAGUGAUG--UUUAGCACUGGGCUCUGAGUUC-AUGUGUAGACA---A-A---A-GUGCAGU-------UUUG--CUCUUGACAUGG-CAGAACC--UGAGAAGUGU
BAAE01271509.1/641-731       CUU--CUCCGCUGAUGU-UUUAGCACUGGGCUCUGAGUCU-GCGUGAAGAG----G-C---U-GUGCAUC-------UUCGG-CCUGACAAGCCG-GGGUUUC--UGAGGAGAAC
AANH01004458.1/22842-22932   UCU--CUCCCCUGAUG--ACUUGCACUGGGCUCUGAGUCU-U-UUGAGGAGA---A-A---C-GUGCAUC-------UUUGGCCCUGACAAGCCA-AAGUUUC--UGAGGAGAAA
CAAE01014987.1/2016-2107     GCU--CUCCCAUGAUG--ACGUGCACUGGGCUCUGAGUCC-ACGUGGAGACG---A-G---C-GUGCAUG-------UCUGGCCCUGACAAGCCA-GAUCUUC--UGAGGAGAGC
AAWR02030771.1/8655-8565     GGG--CCCCCGUGAUG--UCCAGCACUGGGCUCCGACCGC-CCCUGAGGAC----A-C---G-GUGCACC-------CCGGGACCUUUGACACCC-GGGGGUC--UGAGGGGCCC
AAKN02046389.1/4459-4548     GGG--CCUCUGUGAUG--UCCAGCACUGGGCUCCGAGCUC-U-GUGAGGAC----A-U---G-GUGCCCC-------CCGGGACCUUUGACACCC-GGGGGUC--UGAGGGGCCC
AAGV020885884.1/241-331      CUG--CCCCCGUGAUG--UCCAGCACUAGGCUCUGACCAC-UCCAGGGGAC----A-C---U-GUGCCCC-------CUGGGACCUUUGACACCC-AGGGGUC--UGAGGGGCCC
AAGW02002644.1/45201-45291   GGA--CCUGUUUGACA--UCCAGCGCUGGGCUCUGACCAC-UCCUGAAGAC----A-C---U-GUGCUCC-------CUGGGACCUGUGACACUC-AGAGGUC--GGAGGGGGAU
AAPE02059342.1/8018-8108     GGG--CCCCUAUGAUG--UCUAGCACUGGGCUCUGACCUC-UCAUGAGGAC----A-C---U-GUGCCCC-------CUGGGACCUUUGACACCC-AGGGGUC--UGAGGGGCCC
AAQR03172564.1/15869-15960   --GACCCCCCAUGAUG--UCCAGCACUGGGCUCUCACUAC-CCAUGAGGAC----A-C---U-GUGCCCCC------CUGGGACCUUUGACACCC-AGGGGUC--UGAGGGGCCC
AAGU03012054.1/21927-21837   GGG--CCCCCAUGAUG--UCCAGCACUGGGCUCUGAUCAC-CCCUGAGGAC----A-C---A-GUGCCCC-------CCAGGACCUUUGACACCU-GGGGAAC--UGAGGGGCCC
AACZ03117470.1/998-1088      GGG--CUCCCAUGAUG--UCCAGCACUGGGCUCCGAUCAC-CCCUGAGGAC----A-C---A-GUGCACC-------CCAGGACCUUUGACACCU-GGGGGUC--UGAGGGGCCC
AABR05007302.1/150415-150504 GGA--CCCCUGUGAUG--UUCAGCACUGGGCUCUGACCAU-U-CUGAGGAC----A-U---G-GUGCCCC-------CGGGGACCUUUGACACCC-UGGGGUC--UGAGGGGUCC
CAAB02009639.1/6283-6374     GCU--CUCCCGUGAUG--ACGUGCACUGGGCUCUGAAUCU-GUUUGAGGAU----A-A---ACGUGCAUG-------UCUGGCCCUGACAAGCCA-GAGGUUC--UGAGGAGAAG
AACN010607826.1/898-808      GGA--CCCCCAUGAUG--UCCAGCACUGGGCUCUGACCUC-CCCUGAGGAC----A-C---A-GUGCCCC-------CCAGGACCUUUGACACCU-GGGGAUC--UGAGGGGCCC
AAWZ02023462.1/6377-6467     UUG--CUCUCAUGAUG--UA-AGCACUGGGCACAGACAAU-UGCUGUGGUG----A-UAAAA-GUGCCCC-------CAUG--CCUUUGACAUCA-UGGGGAC--UGAGGAGCAA
AADN03005464.1/22565-22474   ACC--UUCAAGUUAUA--U--AGCAGAGGGCUUUCAGCCU-CCCAGGUUAUA---A-G---U-GUUUCCU-------UCAGGACCUCUGCCAUCC-AGGUGCCCCUGAUGAGGCU
#=GC SS_cons                 <<<..<<<<_______..______________________.__________...._._..._._______.......__________________._______..___>>>>>>>
#=GC RF                      ggg..ccCccaUGAUG..UcuAGCACUGGGCUCUGAccac.cccUGAgGAc....A.u...a.GUGCcCC.......CcaGGACCUUUGACACCc.gGGgGUC..UGAgGggccc
//
# STOCKHOLM 1.0

#=GF AC   RF00606
#=GF ID   SNORD93
#=GF DE   Small nucleolar RNA SNORD93
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   60.00
#=GF TC   62.70
#=GF NC   54.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.52 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; HBII-336;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300350;
#=GF DR   snoopy; Cavia_porcellus300509;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. This family includes mouse MBII-336 identified in [2].
#=GF CC   The human orthologue HBII-336 (SNORD93) is predicted to guide the
#=GF CC   2'O-ribose methylation of 18S rRNA A576 [3].
#=GF WK   Small_nucleolar_RNA_SNORD93
#=GF SQ   17


AC146127.4/44893-44966     UGGCCAAGGAUGAGAACUC-UAAUCUGAUUUUAU--GUGCUUC-------------UGCUGUGAUGG-AUUAAAGGAUUUACCUGAGGCCA
AC117663.13/64140-64070    UGGCCAAGGAUGAGAACUC-UAACCUGACUGGAU--ACGCU----------------GCUGUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AC005682.2/110683-110610   UGGCCAAGGAUGAGAACUC-UAAUCUGAUUUUAU--GUGCUUC-------------UGCUGUGAUGG-AUUAAAGGAUUUACCUGAGGCCA
AAPY01584255.1/1738-1811   UGGCCAAGGAUGAAAAUUC-UAAUCUGAUUUGCU--AUGCUUC-------------UGCUCUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AAFC03129730.1/970-1042    UGGCCAAGGAUGAGAACCC-UAAUCUGAUUGGAU--ACCCU-C-------------UGCUCUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AANG01382327.1/4280-4351   UGGCCAAGGAUGAGAACUCUUAAUCUGAUUGGAU--AUGCU----------------UCUCUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AANN01508855.1/934-1001    UGGCCAAGGAUGAGAACUC-UAAUCUGAUUGGAU--UUACU-------------------CUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AAYZ01658959.1/746-819     UGGCCAAGGAUGAGAACCC-UUUGCUGAUUCAGU--UUGCUCC-------------UGCGCUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AALT01401044.1/674-745     UGGCCAAGGAUGAGAACUC--AAUCUGA-UGGAU--GUACUUC-------------CACUCUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AAFR03047799.1/14502-14426 UGGCCAAGGAUGAAAACCA-CAGUCUGAUUGGGC--AUGCUUUC----------CAUGCUCUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AAKN02039012.1/62316-62388 UGGCCAAAGAUGAGAACUC-UAACCUGAAUGGCU--GUGUU-C-------------UGCUCUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AAWR02014040.1/1918-1991   UGGCCAAGGAUGAGAACUC-UAAUCUGAUUGGAU--AUGCUUC-------------UGCUCUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AAGU03015482.1/95720-95646 UGGCCAAGGAUGAGAACUCUUAAUCUGAUUGGGC--AUGCUUG-------------UGCUCUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
AAQR03057360.1/38069-38137 UGGCCAAGGAUGAGAACUC-UAAUCUGAUUGGAU-------UC-------------UGCUCUGAUGG-AUUAAAGGAUUUACCUGAGGCCA
AACN010176650.1/1059-1130  UGGCCGAGGAUGAGAAAUC-UAAUCUGAUUGGAU--AUGCU----------------UCUCUGAUGGCGUUGAAGGAUUUACCUGAGGCCA
JN899136.1/2-75            UGGCCAAAGAUGAGAACUC-GAAUCUGAAUGGAU--AUCCUUC-------------UGCUCUGAUGG-GUUAAAGGAUUUACCUGAGGCCA
FM165396.1/10-97           UGGCCAGGGAUGAAAACAA-UCAUCUGAUUACUUGCAUACUUACAGUGUUAUGCAGAAGUCUGAUGG-AUUAAAGGAUUUU-CUGAGGCCA
#=GC SS_cons               :<<<<______________.______________.._______.............___________.__________________>>>>:
#=GC RF                    UGGCCAAGGAUGAgAACuc.UAAUCUGAUUggaU..aUgCUUc.............ugcUCUGAUGG.gUUAAAGGAUUUACCUGAGGCCA
//
# STOCKHOLM 1.0

#=GF AC   RF00607
#=GF ID   SNORD98
#=GF DE   Small nucleolar RNA SNORD98
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   50.00
#=GF TC   54.10
#=GF NC   43.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; HBII-419;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Loxodonta_africana300524;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. HBII-419 (SNORD98) is predicted to guide the
#=GF CC   2'0-ribose methylation of 18S rRNA G867 [3].
#=GF WK   Small_nucleolar_RNA_SNORD98
#=GF SQ   10


AC122539.4/111761-111697   GAGUUAUGAUGUGU--AAAUCCUAUUCCAUUGCUGAAA-UGCAGUGUGGAACAUAAUGAACUGAACUC
AL513534.17/133194-133260  GAGUUAUGAUGUGUGUAAAUCCUAUUCCAUUGCUGAAA-UGCAGUGUGGAACACAAUGAACUGAACUC
AAPN01032983.1/19495-19429 GAGUUAUGAUGUAUUUAAGUCCUAUUCCAUUGCUGAAA-UACAGUGUGGAACACGAUGAACUGAACUC
AAFR03050138.1/41907-41972 GAGUUGUGAUGAGU-AAAAUCCUAUUCCAUUGCUGAAA-UACAGUGUGGAACAUGAUGAACUGAGCUC
AAIY01311124.1/260-197     GAGUUGUGAUGUGU--AAAUCCUAUUCCAUUGCUGAAC-UGCAGUGUGGAA-AUGAUGAACUGAACUC
AAVX01111856.1/728-792     GGGUAAUGAUGUCU---AAUCCUAUUCCAUUGCUGAAAGCCCAAUGUGGAAAAAGACCAGCUGAACCC
BAAF04050323.1/9177-9113   GCCA-AUGAUGUGA--AAACCCUAUUCCAUUUCUGAAUUCUCAGUGUGGAAAAUUCCUGACUGAUGAC
AAWZ02019938.1/5000-5062   GAGUAAUGAUGCUU---AAACCUAUUCCAUUACUGAAA-UAAUCUGUGGAA-AACAAAAACUGAACUC
CR389762.1/394-457         GAGUGAUGAUGUUU--UAAACCUAUUCCAUUUCUGAAA-UAGUCUGUGGAA-AAAAAUAACUGAACUC
EU094120.1/5-71            GAGUUAUGAUGUAUUUAAGUCCUAUUCCAUUGCUGAAA-UACAGUGUGGAACACGAUGAACUGAACUC
#=GC SS_cons               <<<<__________..______________________._________________________>>>>
#=GC RF                    GaGuuAUGAUGUgU..AAAuCCUAUUCCAUUgCUGAAA.UaCAgUGUGGAAcAugAugAACUGAaCuC
//
# STOCKHOLM 1.0

#=GF AC   RF00608
#=GF ID   SNORD99
#=GF DE   Small nucleolar RNA SNORD99
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   60.00
#=GF TC   60.10
#=GF NC   59.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00064
#=GF DR   snoRNABase; HBII-420;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. HBII-420 (SNORD99) is predicted to guide the
#=GF CC   2'O-ribose methylation of 28S rRNA A2774 [3].
#=GF WK   Small_nucleolar_RNA_SNORD99
#=GF SQ   23


CR752656.3/1766-1839         ACUGGUCCAUGAUGAAACCCAUUAU-CA-GUGGACAU-CUAUGGAUGAGAAAUGCGGAUAUGGGACUGAGACCAGUU
AL513497.21/78318-78245      ACUGGUCCAGGAUGAAACCUAAUUU-GA-GUGGACAU-CCAUGGAUGAGAAAUGCGGAUAUGGGACUGAGACCAGCU
AANG01797529.1/1565-1492     ACUGGUCCAGGAUGAAACCUAAUCU-GA-GUGGACAU-CUAUGGAUGAUAAAUGCGGAUAUGGGACUGAGACCAGUU
AALT01584320.1/5415-5342     GCUGGUUCAGGAUGAAACCUUAUCU-GA-GUGGACAU-CUAUGGAUGAUAAAUGCGGAUAUGGGACUGAGACCUGCU
AANN01300916.1/940-1013      ACUGGUCAAGGAUGAAAACCUAUCU-CU-GUGGACAU-CAUUGGAUGAUAGAUGCGGAUAUGGGACUGAGACCAGUU
AAIY01690380.1/1263-1336     CCUGGUCAAGGAUGAAACCUAAUCU-GA-GUGGACAU-CUCCGGAUGAUAAAUGCGGAUAUGGGACUGAGACCAGCU
AAHX01233108.1/550-477       ACUGGUCUGUGAUGAAACCCAUUAU-CA-GUGGACAU-CUAUGGAUGAGAAAUGCGGAUAUGGGACUGAGACCAGUU
DQ096896.1/321-391           GCUGUGCGUGGAUGAAUCUCUUUUC-----UUGAGAC-UGUUGGAUGAAUCUUGCGGAUAUGGGACUGAGCGCAGCC
AAPN01440676.1/2690-2620     GCUGGUUAAGGAUGACACUCAAUG-----GUGGACAU-GUAUGGAUGACACUUGCGGAUAUGGGACUGAGACCAGCU
AAYZ01245008.1/2359-2288     GCUGGUCCAGGAUGAAUCCUACUGA----GUGGACAU-CUGUGGAUGAGCAGUGCGGAUAUGGGACUGAGACCAGCG
AAFR03060642.1/25942-25868   ACUGGUCAGUGAUGAAUCUCUUAUC-UG-GUGGACAUGCUUUGGAUGACACUUGCGGAUAUGGGGCUGAGACCAGUC
CR385068.11/103046-102975    ACUGAUCAAGGAUGAUA--GUAUAU-UG-AUGGUGAC-UGCUGGAUGAAACUUGCGGAUAUGGGACUGAGAUCAGUU
BAAF04001665.1/8391-8319     UCUGAUCCAUGAUGACUUCCAAACA-CAUGUGGAC---UGUUGGAUGAAGCAUGCGGAUAUGGGACUGAGAUCAGAC
AANH01002401.1/37077-37149   G-UGAUCUAUGAUGAUUCAAUACUA-AA-AUUGUGAC-UGCUGGAUGAAGCUUGCGGAUAUGGGACUGAGAUCAGCA
CAAE01014594.1/234729-234658 UCUGAUCUGUGAUGAUGCCUAAAUG-AU-GAGGAC---UGCUGGAUGAAGCUUGCGGAUAUGGGACUGAGAUCAGCC
AAVX01051885.1/355-282       GCUGGUCGAUGAUGACCUAUUUUAAAUU-GUGGACUU-CU-UGGAUGAUGCUCGCGGAUAUGGGACUGAGAUCAGCA
AAWR02028293.1/9717-9790     ACUGGUCCAGGAUGAAACCUAAUCU-GA-AUGGACAU-CUAUGGAUGAUAGAUGCGGAUAUGGGACUGAGACCAGCU
AAKN02028628.1/54612-54685   ACUGGUCCAGGAUGAAACCUAAUCU-GA-GUGGACAU-CUGUGGAUGAGAAAUGCGGAUAUGGGACUGAGACCAGUG
AAEX03001701.1/75141-75214   ACUGGUCCAGGAUGAAACCUAAUCU-GA-GUGGACAU-CUAUGGAUGAUAAAUGCGGAUAUGGGACUGAGACCAGCU
CAAB02003938.1/6191-6120     UCUGAUCUGUGAUGACACCAAAUCA-AU-GAGGAC---UGCUGGAUGAAGCUUGCGGAUAUGGGACUGAGAUCAGCC
AAGW02062791.1/16896-16969   ACUGGUCCAGGAUGAAUCCUAAUCU-GA-GUGGACAU-CUUUGGAUGAGAAAUGCGGAUAUGGGACUGAGACCAGCU
AEYP01008027.1/10809-10882   ACUGGUCCAGGAUGAAACCUAAUCU-GA-GUGGACAU-CUGUGGAUGAUAAAUGCGGAUAUGGGACUGAGACCAGCU
ADDD01076274.1/6439-6369     CCUGGUCAGUGAUGACACC---UUU-CU-UUGGAGAC-UGCUGGAUGAAUCCUGCGGAUAUGGGGCUGAGGCCAGGC
#=GC SS_cons                 <<<<<____________________.__.________._________________________________>>>>>:
#=GC RF                      gCUGgUCaAgGAUGAaaCcuaaUuu.ua.GUGGACAU.cuuUGGAUGAaaaaUGCGGAUAUGGGACUGAGAcCAGcu
//
# STOCKHOLM 1.0

#=GF AC   RF00609
#=GF ID   SNORD100
#=GF DE   Small nucleolar RNA SNORD100
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   58.00
#=GF TC   60.50
#=GF NC   57.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.09 -Z 549862.597050 CM SEQDB
#=GF CL   CL00073
#=GF DR   snoRNABase; HBII-429;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Oryzias_latipes300080;
#=GF DR   snoopy; Takifugu_rubripes300040;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. HBII-429 (SNORD100) is predicted to guide the
#=GF CC   2'O-ribose methylation of 18S rRNA G436 [3].
#=GF WK   Small_nucleolar_RNA_SNORD100
#=GF SQ   26


AK096147.1/2233-2308         GCUGUA-CAUGAUGACA-AC-U-GGCUCCCUCUACUGAACUGCCAUGAGGAAA-CUGCC----AUGUCACCC-------UUCUGAC--UACAGC
AL137783.12/18577-18652      GCUGUA-CAUGAUGACA-AC-U-GGCUCCCUCUACUGAACUGCCAUGAGGAAA-CUGCC----AUGUCACCC-------UUCUGAU--UACAGC
AAFC03068109.1/6499-6575     GCUGUA-CAUGAUGACA-AC-U-GGCUCCCUCUACUGAACCGUGGUGAGGAAA-CUGCC----AUGUCACCC------UAUCUGAC--UACAGC
AALT01102941.1/534-610       GCUGUG-CAUGAUGACA-AC-U-GGCUCCCUCUACUGAACCACUCUGAGGAAA-CUGCC----AUGUCACCC------AGUCUGAC--AACAGC
AANN01343682.1/116-192       GCUGUA-CAUGAUGACA-AC-U-GGCUCCCUCUACUGAACUGUCAUGAGGAAA-AUGCC----AUGUCACCC------AAUCUGAC--UGCAGC
AAIY01528082.1/2159-2234     GCUGUA-AAUGAUGACA-AC-U-GGCUCCCUCUACUGAG-UCUAGUGAGGAAA-UUGCC----AUGUCACCA------AUUCUGAC--UACAGC
AAFR03001093.1/89713-89630   GCUGUA-CAUGAUGACA-AC-UUGGCUCCCUCUACUGAUAAUAAUGAAGAGAA-CAGCC----AUGUCACCCAA--CAUAUCUGAGCGUACAGC
AAPN01046279.1/2999-2915     GCUGUA-CAUGAUGAUA-GC-UUGGCUCCCUCUACUGAA-AAUGGUGAGGAUAAUAGCC----AUGUCACCCAA-UAGUAUCUGAACGUACAGC
CAAE01015003.1/541630-541549 GGCAUC-ACUGAUGAUAAUC-U-GGCUCCCUCUACUGAU-UAUGGUGAGGAAA-GUGCC---ACUGUUACCCAA-UUUUGUCUGA---GAUGCA
CR759830.8/42467-42551       UGUAUC-UGUGAUGAUA-AU-UUGGCUCCCUCUACUGAA-GUCUCUGAGGAAAACUGCCA--UUCGUUACCCAAUUUCUUACUGA---GAUACU
BAAE01132893.1/96-14         UGUAUC-ACUGAUGAUA-AU-UUGGCUCCCUCUACUGAC-CUCUGUGAGGAGA-UGGCC---AUUGUUACCCAAUUUCUGUCUGA---GAUGCA
BAAF04047914.1/2634-2553     UAUUUC-UGUGAUGAUA-UC-CUGGCUCCCUCUGCUGAA-CAUCAUGUGGAAGUCUGCC---AUCGUUACCCA----AUGUCUGUC-UGAGAUA
CAAE01015003.1/541916-541832 CAUGUC-GCUGAUGAUA-UC-UUGGCUCCCUCUACUGAGUUUUAAUGUGGAAGUCUGCC---AUUGUUACCCAAUUUCUAUCUGA---GAUGUU
AAGV020962123.1/803-726      GCUGUA-CGUGAUGACA-AC-U-GGCUCCCUCUACUGAA-CCUGGUGAGGAAAACUGCC----ACGUCACCA------UUUCUGAC-UUACAGC
AAWR02015249.1/10509-10585   GCUGUG-CAUGAUGACA-AC-U-GGCUCCCUCUACUGAAUUGCCUUGAGGAAA-CUGCC----AUGUCACCC------UAUCUGAC--UACAGC
AAKN02045639.1/12641-12716   GCUGUG-CAUGAUGACA-AC-U-GGCUCCCUCUACCGAACUGUCUUGAGGAAA-AUGCC----AUGUCACCC-------UUCUGAU--GACAGC
AAWZ02013261.1/63232-63143   GCUGUACAGUGAUGACA-ACAU-GGCUCCCUCUACUGAAAUCUGUUGAGGAAAACAACCAUAAAUGUUACCCUU--UAUAUCUGAGUGUACAGC
CAAB02004398.1/5124-5043     UGCAUC-ACUGAUGAUGAUC-U-GGCUCCCUCUACUGAA-UAUUGUGAGGAAA-GUGCC---ACUGUUACCCAA-UGUUGUCUGA---GAUGCA
CAAB02004398.1/5420-5336     UUUAUC-GCUGAUGAUG-UC-UUGGCUCCCUCUACUGAGUUUCAAUGUAGAAGUCUGCC---AUUGUUACCCAAUUUUUGUCUGA---GAUAUG
AADN03003009.1/73791-73877   GCUGUACAAUGAUGAGACUU-U-GGCUCCCUCUACUGAU-ACUUGUGAGGAAAGCAGCCA--UAUGUUACCCAA--UACCUCUGAGAGUACAGC
AACN010870580.1/135-59       GCUGUA-CAUGAUGACA-AC-U-GGCUCCCUCUACUGAACUGCAGUGAGGAAA-CUGCC----AUGUCACCC------UAUCUGAU--UACAGC
AADN03003009.1/75024-75108   UGCAUC-UGUGAUGAAA-AU-UUGGCUCCCUCUACUGAA-ACAAAUGAGGAGAACUGCCUUAAUCGUUACCCAA--AUCUUCUGA---GAUGUU
AAPE02007475.1/212147-212072 GCUGUA-CAUGAUGACA-AC-U-GGCUCCCUCUACUGAAUUGGUGUGAGGAAA-CUGC-----CUGUCACCC------UAUCUGAC--UACAGU
AAGW02028778.1/11671-11596   GCUGUG-AAUGAUGACA-AC-U-GGCUCCCUCUACUGAGCUGCCUUGAGGAAA-CUGCC----AUGUCACCC-------UACUGAC--UACAGC
EU094059.1/1-77              UGU--A-CAUGAUGAUA-GC-UUGGCUCCCUCUACUGAA-AAUGGUGAGGAUAAUAGCC----AUGUCACCCAA-UAGUAUCUGA------ACG
EU094094.1/1-77              UGU--A-CAUGAUGAUA-GC-UUGGCUCCCUCUACUGAA-AAUGGUGAGGAUAAUAGCC----AUGUCACCCAA-UAUUAUCUGA------ACG
#=GC SS_cons                 <<<<<<.__________.__._.________________.___________________...____________..__________..>>>>>>
#=GC RF                      gcugUc.aaUGAUGAuA.aC.U.GGCUCCCUCUACUGAa.uauuaUGAGGAAAacuGCC...AaUGUuACCCAA..uuUaUCUGAc..gAcagc
//
# STOCKHOLM 1.0

#=GF AC   RF00610
#=GF ID   SNORD110
#=GF DE   Small nucleolar RNA SNORD110
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; Daub J
#=GF GA   64.00
#=GF TC   64.20
#=GF NC   51.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00076
#=GF DR   snoRNABase; HBII-55;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300980;
#=GF DR   snoopy; Loxodonta_africana300443;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. HBII-55 (SNORD110) is predicted to guide the
#=GF CC   2'O-ribose methylation of 18S rRNA U1288 [3].
#=GF WK   Small_nucleolar_RNA_SNORD110
#=GF SQ   16


AL833804.16/185705-185772  UUGCAAUGAU--GACUU----AU-AUAUCUGUCAAUCCCCUGAGAG------AUCACUGACGACUCCAUGUGUCUGAGCAA
AL049712.12/17737-17663    UUGCAGUGAU--GACUUGCGAAUCAAAUCUGUCAAUCCCCUGAGUG----CAAUCACUGAUGUCUCCAUGUCUCUGAGCAA
AF357318.1/1-59            ---------U--GACUU----AU-AUAUCUGUCAAUCCCCUGAGAG------AUCACUGACGACUCCAUGUGUCUGAGCAA
AAHX01025040.1/5155-5223   UUGCAAUGAU--GACUUG---AA-AAAUCUGUCAAUCCCCUGAGUG------AUCGAUGAUGACUCCAUGUUUCUGAGCAA
AAPY01184206.1/1603-1534   UUGCAGUGAU--GACUU----GU-UAAUCUGUCAAUCCCCUGAGUG----CAGUCACUGAUGUCUCCAUGUCUCUGAGCAA
AAYZ01171747.1/1290-1361   UUGCAAUGAU--GACUCAA--AA-AAAUCUGUCAAUCCCCUGAGUA----CUGCCAUUGAUGUCUCCAUGUCUCUGAGCAA
AAIY01405472.1/148-82      UUGCAGUGAU--GACUG--------UAUCUGUCAAUCCCCUGAGUG----CAGUCACUGAUGUCUCUAUGUCUCUGAGCAA
AAQQ01611468.1/10638-10566 UUGCAGUGAUCCGACUUG---UG-AAAUCUGUCAAUCCCCUGAGUG----UGAUCAUUGAUGUCUCAAUGUCUCUGAGCAA
AAFC03071760.1/10034-10105 UUGCAGUGAU--GACUUG-------AGUCUGUCAAUCCCCUGAGUGAGUUUAAUCACUGAUGUCUCCAUGUCUCUGAGCAA
AANN01172228.1/1197-1264   UUGCAAUGAU--GACUUG-------AUUCUGUCAAUCCCCUGAGUG----CAAUCGCUGAUGUCAGAGUGUCUCUGAGCAA
AALT01345847.1/1257-1190   UUGCAAUGAU--GACUUG-------GAUCUGUCAAUCCCGUGAGUG----CACUCAUUGAAGUCAACCUGUCCCUGAGCAA
AAKN02012840.1/32061-31991 UUGCAGUGAU--GACUUG---AG-AAAUCUGUCAAUCCCCUGAAUG----UAAUCACUGAUGUCUCCAUGUCUCUGAGCAA
AAGV020548465.1/2311-2242  UUGCGGUGAU--GACUU----GC-GAAUCUGUCAAUCCCCUGAGUG----CAGUCGCUGAUGUCUCCAUGUCUCUGAGCAA
AAEX03013839.1/36146-36079 UUGCAGUGAU--GACUUG-------AGUCUGUCAAUCCCCUGAGUG----CAAUCACUGAUGUCUCCAUGUCUCUGAGCAA
AAGW02060592.1/54316-54387 UUGCAAUGAU--GACUCAA--AA-UAAUCUGUCAAUCCCCUGAGUC----CUGUCACUGAUGUCUCCAUGUCUCUGAGCAA
AAQR03054003.1/2280-2210   UUGCAGUGAU--GACUU----UUCUUAUCUGUCAAUCCCCUGAGUG----CAGUCACUGAUGUCUCUGUGUCUCUGAGCAA
#=GC SS_cons               <<<<______..______...__.______________________....___________________________>>>>
#=GC RF                    UUGCAgUGAU..GACUUG...au.aaAUCUGUCAAUCCCCUGAGUG....cAaUCAcUGAUGUCUCcAUGUCUCUGAGCAA
//
# STOCKHOLM 1.0

#=GF AC   RF00611
#=GF ID   SNORD111
#=GF DE   Small nucleolar RNA SNORD111
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   46.00
#=GF TC   46.00
#=GF NC   45.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; HBII-82;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300813;
#=GF DR   snoopy; Homo_sapiens300593;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. HBII-82 (SNORD111) is predicted to guide the
#=GF CC   2'O-ribose methylation of 28S rRNA G3923 [3].
#=GF WK   Small_nucleolar_RNA_SNORD111
#=GF SQ   5


BX784024.10/48132-48213  GUGCCAGAAAUGAUGAUUAU--------CUUCAUGUCUCUUCUCUGACUGUUUGGUGAAGAGAGAUUUGUGA-------UAUCUGAUCUUCAUGCAC
AC010553.6/712-633       CAGCCUGAAGUGAUGAUUCAC-------AUUCAUGUCUCUUCUCUGAUAAAUUC--UUGAAGAAAAUUUUUG-----UGUGUCUGAUC---AGGCCU
AC106804.4/74513-74420   CAGCCUGAAAUGAUGACUCUUUAAAAAAUUUCAUGUCUCUUCUCUGACAUUUUUCUCUGGACACAGUUUUUGCCUUAUGAAUCUGAUC---AGGCUG
AC132945.3/142528-142616 CAGCCUGAAAUGAUGACCAUUU-----AAUUCAUGUCUCUUCUCUGACAUUCUCCUCUGGAGAUGAUUUUUGCCUUAUUGAUCUGAUC---AGGCUG
AF357319.1/1-64          ------------------AUUU-----AAUUCAUGUCUCUUCUCUGACAUUCUCCUCUGGAGAUGAUUUUUGCCUUAUUGAUCUGAU----------
#=GC SS_cons             <<<<<_________________....._____________________________________________________________..._>>>>>
#=GC RF                  caGCcuGAAAUGAUGAuUaUUU.....AaUUCAUGUCUCUUCUCUGACAuUuUccUcUGGAGAuAaUUUUUGCCUUAUguAUCUGAUC...AgGCug
//
# STOCKHOLM 1.0

#=GF AC   RF00612
#=GF ID   SNORD75
#=GF DE   Small nucleolar RNA SNORD75
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   50.00
#=GF TC   51.10
#=GF NC   48.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; U75;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300796;
#=GF DR   snoopy; Oryzias_latipes300025;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   9819378
#=GF RT   Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene
#=GF RT   and a member of the 5'-terminal oligopyrimidine gene family reveals common
#=GF RT   features of snoRNA host genes.
#=GF RA   Smith CM, Steitz JA
#=GF RL   Mol Cell Biol. 1998;18:6897-6909.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   U75 (SNORD75) belongs to the C/D class of snoRNAs which contain the C
#=GF CC   (UGAUGA) and D (CUGA) box motifs. Most of the members of the box C/D
#=GF CC   family function in directing site-specific 2'-O-methylation of substrate
#=GF CC   RNAs [1]. This family includes the mouse orthologue Z19. U75 is predicted
#=GF CC   to guide the 2'O-ribose methylation of 28S rRNA residue C4032 [3]. In
#=GF CC   humans U75 shares the same non-protein coding host gene (gas5) with 9
#=GF CC   other snoRNAs (U44, U47, U74, U76, U77, U78, U79, U80 and U81)[2].
#=GF WK   Small_nucleolar_RNA_SNORD75
#=GF SQ   5


AC025750.10/4277-4336    AUUUCUAUGGA----------AAAGAGGUGAAGUGGACAGAAGGGAUGUCUGAAAUUC----UAUCCUGAGGCU
CR759968.6/152594-152667 UGCCUUUGAUGAAUUAAAAAUGUAUAAGAGUAGUGGACAGAAGUGAUUUCUGAGAACAUUUUUAAUCUGAGGCA
CR759968.6/152857-152927 UGCCUAUGAUGAAUAAAAAU-GUAUAAGAGUAGUGGACAGGAGUGAUUUCUGAUAAUUUU--UACUCUGAGGCA
AJ224031.1/3-64          AGCCCAUGAUG----------GUAUGAGAGUAGUGGACAGAAGGGAUUUCUGAAAAACAC--UUUUCUGAGGCU
AF141346.1/1052-1111     AGCCUGUGAUG----------CUUUAAGAGUAGUGGACAGAAGGGAUUUCUGAAAUUC----UAUUCUGAGGCU
#=GC SS_cons             <<<<_______.........._______________________________________..________>>>>
#=GC RF                  aGCCuuUGAUG..........gUAUAAGAGUAGUGGACAGAAGgGAUUUCUGAaAaucuU..UAuUCUGAGGCu
//
# STOCKHOLM 1.0

#=GF AC   RF00613
#=GF ID   SNORD94
#=GF DE   Small nucleolar RNA SNORD94
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   60.00
#=GF TC   60.00
#=GF NC   47.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; U94;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300739;
#=GF DR   snoopy; Danio_rerio300149;
#=GF RN   [1]
#=GF RM   12215523
#=GF RT   Purified box C/D snoRNPs are able to reproduce site-specific
#=GF RT   2'-O-methylation of target RNA in vitro.
#=GF RA   Galardi S, Fatica A, Bachi A, Scaloni A, Presutti C, Bozzoni I
#=GF RL   Mol Cell Biol. 2002;22:6663-6668.
#=GF RN   [2]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res. 2003;31:6543-6551.
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   The members of this family belong to the C/D class of snoRNAs which
#=GF CC   contain the C (UGAUGA) and D (CUGA) box motifs. Most of the members of the
#=GF CC   box C/D family function in directing site-specific 2'-O-methylation of
#=GF CC   substrate RNAs [1]. U94 (SNORD94) is predicted to guide the 2'O-ribose
#=GF CC   methylation of C62 of the snRNA U6 (Rfam:RF00026)[2].
#=GF WK   Small_nucleolar_RNA_SNORD94
#=GF SQ   21


AC122200.4/154212-154076     CAGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAGUCAUGGGAGCUGAAUGUA----UGU-----GUUUUGCCUCUGUCCUGCAUGUGGCAGGCUGUUGG--CAUUCA--CAUACAUGAGACUGUUGCCUUAAUCUGAGCCUG
AY349593.1/1-137             CAGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAGUCAUGGGAGCUGAAUGUA----UGU-----GUUUCUCCUUUGUCCUGCAUGUGGCAGGCUGAUGG--GGAGCA--CUUACAUGAGACUGUUGCCUCAAUCUGAGCCUG
AALT01235424.1/874-738       CAGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAAUCAUGGGAGCUGAAUGUA----UGU-----GUUUUGCCUUUGUCCUGCAUGUGGCAGGUUGAUGG--CAGGCA--CUUACAUGAGACUGAUGCCUUAAUCUGAGCCUG
AAFR03048892.1/56230-56366   GAGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAAUCAUGGGAGCUGAAUGUA----UGU-----GUGUCUCUGCCCUCCUGCAUGUGGCAGGUUGAUGG--GGAGCA--CUUACAUGAGACUGGUGCCUAAAUCUGAGCCUC
AANG01204996.1/106-242       CAGGUUAUGAUGAUUGGCGCAGGGGUACGGACUUCAGUUGAUUCAUGGGAGCUGAACAUA----UGU-----GUUUCUCCUUUGUCCUGCAUGUGGCAGGAUGCUGG--UGAGCA--CUUACAGGAGACUGAUGCCUCAAUCUGAGCCUG
AAIY01402388.1/1061-1197     CAGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAGCCAUGGGAGCUGAAUGUC----AGU-----GUCUCUCCUCCGUCCUGCAUGUGGCAGGGUGCUGG--CGAGCA--CUGGCAUGAGACUGGUGCCUCAAUCUGAGCCUG
AAFC03072237.1/82864-82999   CAGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGA-UGAUGGGAGCUGAGUGUA----UGU-----GCUUCUCCUUCGUCCUGCAUGUGGCAGGAUGCUGG--UGAGCA--CUUACAUGAGACUUGUGCCUUAAUCUGAGCCUG
AAPY01106650.1/1635-1502     CAGGCAGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAGUCAUGGGAGCUGAAUGUA----CGU-----GCAUGUCGUCU-UCCUGCAUGUGGCAGG-UGAUGU--C-AGCA--CUUACAUGAGACUGUUGCCUCAAUCUGAGCCUG
AAPN01102371.1/411-276       GUGGCUGUGAUGAUCGGCGCAGGGGUACGGACCUCAGCUGCAUCAUGGGAGCUGAGUGUA----GGU-----GGGUCUC-UGAGUCCUGCACGUGGUAGGACGGAAG--AGAGCA--CUUACAUGAGACUGGUGCCUAAGUCUGAGCCUC
AANN01557999.1/7064-6931     AAGGCUGUGAUGAUUGGUGCAGGGGUAUGGCCCUCCACUAAGUCAUGGGAGCUGAAUGUA----UGU-----GUUUCUCCGUUGUCCUGCAUGUGGUGGGUUGAUGG--CAAGCA--CUU-CAUGAGAC--UUGCCUGACUCAGAGCUUG
AAVX01111653.1/632-495       CUGGCAAUGAUGAUUGGCGCAGGGGUACUUACCUCAGCUGGAUAAUGGGAGCUGAGUGCU----UGC-----GUCUUCUGCUCAGCCUACGUGUGGUGGGCUGUUCA-AGGAGCG--UCUGCACGAGAAAAACGCCUAAAUCUGAGCCAG
BX248136.12/139864-139999    GGAGCAAUGAUGAGUGGCGCAGGGGUACGUACCUCAGCUGA-UAAUGGGAGCUGAGUGUU----GAC-----UGCUCAAAAUCAGUGGACAUGUGGUCAGCUGGUUG-UAGGGUG--UCAGCACGAAAUUAUCGCCUUGA-CUGAGCUCC
AAGV020295740.1/1163-1028    CAGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAGUCAUGGGAGCUGAGUGUA----CGU-----GCGUCCCCCUCGUCCUGCACGUGGCAGGUCGGUGG--UGAGCA--CUGACACGAGACA-ACGCCUCAAUCUGAGCCUG
AAWR02003548.1/158125-157989 CAGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAGUCAUGGGAGCUGAGUGUA----UGU-----GUUUCUCCUUUGUCCUGCAUGUGGCAGGAUAACGG--CGAGCA--CUUACAUGAGACUGAUGCCUUAAUCUGAGCCUG
AAWZ02015154.1/51639-51496   GCAGCAAUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUAGAUCAUGGGAGCUGAGUGUG----AGUUUUCAGUGUCUGGCGUCGCUCGCAUGUGGCUUGCUUCCUGGACAGUGG--CUCACACGAGAAUGUUGCCUUAUGCUGAGCUGC
AAPE02048724.1/13460-13326   CAGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAGUUAUGGGAGCUGAGUGUA----CGU-----GUUUCUCCUCCGUCCUGCAUGUGGCAGUGCGGUGG--CGAGCA--CGUACAUGAGAU--AUGCCUCGAUCUGAGCCUG
AAGW02007279.1/87536-87670   CAGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAAUCAUGGGAGCUGAAUGUU----CGU-----GCUUCUCCUUUGUCCUGCACGUGGCAGGGUGAGGG--GGAGCA--CUUACAUGAGAC--UUGCCGCAAUCUGAGCCUG
AADN03004048.1/259088-258946 AUGGCAGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUAGAUCAUGGGAGCUGAGUGCAAACUGUU-----GAUUUCAGUGCAGCUGGCGUGUGGCUGGCUCACUG--GAAACAGGUUUGCAUGAGAACUUCGCCAAAGACUGAGCCAU
EU240253.1/1-141             U-GGCAAUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUAGAUCAUGGGAGCUGAGUGCAAACUGUU-----GAUUUCAGUGCAGCUGGCGUGUGGCUGGCUCACUG--GAAACAGGUUUGCAUGAGAACUUCGCCAAAGACUGAGCC-A
FJ916008.1/1-135             -AGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGAGUCAUGGGAGCUGAAUGUA----UGU-----GUUUCUCUUUUGUCCUGCGUGUGGCAGGCUAAUGG--GGAGCA--CUUACAUGAGACUGUUGCCUCAAUCUGAGCCU-
JN899137.1/1-135             CGGGCUGUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUGA-UCAUGGGAGCUGAGUGUA----UGU-----GUUUCUCCYUUGUCCUGCACGUGGCAGGAUGAUGG--CGAGCA--CUUACAUGAGACC-AUGCCUUGAUCUGAGCCCG
#=GC SS_cons                 <<<<<_______________________________________________________....___.....___________________________________..______..____________________________>>>>>
#=GC RF                      cgGGCugUGAUGAUUGGCGCAGGGGUACGGACCUCAGCUgaaUcAUGGGAGCUGAgUGUa....uGU.....GuuUcuccuuuguCcuGCAUGUGGcaGGcUgaugG..ugAgcA..cUuaCAuGAGAcuguUGCCUuAauCUGAGCCcg
//
# STOCKHOLM 1.0

#=GF AC   RF00614
#=GF ID   SNORA11
#=GF DE   Small nucleolar RNA SNORA11
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   36.00
#=GF TC   36.20
#=GF NC   35.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; U107;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300977;
#=GF DR   snoopy; Homo_sapiens300083;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF RN   [2]
#=GF RM   16361266
#=GF RT   A novel experimental approach for systematic identification of box H/ACA
#=GF RT   snoRNAs from eukaryotes.
#=GF RA   Gu AD, Zhou H, Yu CH, Qu LH
#=GF RL   Nucleic Acids Res. 2005;33:e194
#=GF RN   [3]
#=GF RM   16381836
#=GF RT   snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box
#=GF RT   snoRNAs.
#=GF RA   Lestrade L, Weber MJ
#=GF RL   Nucleic Acids Res. 2006;34:D158-D162.
#=GF CC   U107 (SNORA11) is a member of the H/ACA class of snoRNAs that guide the
#=GF CC   sites of modification of uridines to pseudouridines [1]. This snoRNA was
#=GF CC   identified by RT-PCR from blood cells and its expression confirmed by
#=GF CC   Northern blot analysis [2]. There is no predicted target for this guide
#=GF CC   snRNA [2].
#=GF WK   Small_nucleolar_RNA_SNORA11
#=GF SQ   35


AC113292.6/172404-172530     GGGGUGUGCUC------AGAGCAGGUGGCC-UGAAG-AAUGGCUUCUCUGUUUACAACACACCCAAGAAGAAUCUGGGACCA-UUGUAAUGAGGG-GCACAAG-CAGUUC---CCUCUCUGUGAAUGGAU---CCCCUACAUGU
AL731840.17/35857-35985      CGGGUGUGCUC------AGAGCAGGGGGCC-UGAGG-AAUGGCUCCUCUGUUUAUAACACACCCAAUAUAAACCUGGUCAUG-AUGUGAGGAGGGCUACAAAG-UUUGUUG--CCGUCCCCCAAACACAU---GUCCUACACAU
AC080089.5/42226-42352       GGGGUGUGCUC------AGAGCAGGGGGCU--GAAG-AAUGGCUCCUCUGUUUAUAACACAUGGAACAGGCAUCUGAGGUCA-CUGUGACAAGGGGCACAAAA-CUUGUGA--CUCCCUAA-GAACAAAU---GUCCUACAAGU
AK091003.1/832-962           GGGGUGUGCUC------AGAGCAGGGGGCC-CAAAG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAUCUGGGGUCA-UUGUGAUGAGGGCGUCAAACUUGUGGCUUCCCUAUGAACAAACGUCC----CCCAACACCU
AC016394.13/8497-8370        GGGGUGUGCUC------AGAGCAGGGGGCC-UAAAG-AAUGGCUCCUCUGUUUAUAACACACCCAACAGGAAUCUGGGGUCA-AUGUGAUGAGAGGCACAAAG-CUUGUGG--CCUCCCUACAAACAAAU---G-CCUACAUGU
AL121784.5/100385-100257     GGGGUGUGCUC------AGAGCAGGGGGCC-CGAAG-AAUGCCUCCUCUGUUUACAACACACCCAAUAGGAAUCUGGGGUCA-UUGUGACAAGGGACACAGAG-CUUGUGA--CCUCCCUACAAACAAAU---GCCCUACACAU
AL591503.9/129251-129379     GGGGUGUGCUC------AGAGCAGGGGGCC-UGAAG-AAUGCUUCUUCUGUUUACAACACACCCAAUAGGAAUCUGGGGUCA-UUGUGACGGGGGGCACAAAA-CUUGUGA--CCUCUCUAUGAACAAAU---GCCCCACAUGU
AK094541.1/1987-2114         GGGGUGUGCUC------AGAGCAGGGGGCC-UGAAG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAGCUGGGGUCA-UCGUGAUGAGGGGCACAAA--CUUGUGG--CCUCCCUACAGACAAAU---GCCCUACAUGU
ABDC01384620.1/249-377       GGGGUGUGCUC------AGAGCAGGGGGCC-UGAAG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAUCUCGGGUCA-CUGUCAUGAGGGACACAAAA-CUUGUGG--CCUCCCUAUGAACAAAU---GCCCUACAUGU
AADA01154100.1/3294-3421     GGGGUGUGCUC------AGAGCAGGGGGCC-UGAAG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAGCUGGGGUCA-UCGUGAUGAGGGGCACAAA--CUUGUGG--CCUCCCUACAGACAAAC---GCCCUACAUGU
AANU01283147.1/2890-2763     GGGGUGUGCUC------AGAGCAGGGGGCC-UAAAG-AAUGGCUCCUCUGUUUAUAACACACCCAACAGGAAUCUGGGGUCA-UUGUGAUGAGAGGCACGAAG-CUUGUGG--CCUCCCUACAAACAAAU---G-CCUACAUGU
AAQQ01366707.1/1100-973      GGGGUGUGCUC------AGAGCAGGGGGCC-UGAAG-AAU-GCUUCUCUGUUUACAACACACCCAACAGGAAUAUGGGGUUA-UUGUGACAAGGGCCACAAAA-AUUGUGG--CUUCCCUAUGAACAAAU---GCCCUACAUGU
AANG01131150.1/9026-8897     GGGGUGUGAUC------AGAGCAGGGGGCC-UGAAGAAAUGGCUCUUCUGUUUACAACACACCCAACAGGAAUCUGGGUUCG-UUGUGACAAGGGGCACAAAC-CUUGUGG--CUUUCCUAUGAACAGAU---ACCCUACAUGU
AAFC03094468.1/47841-47712   GGGGUGUGCUU------AGAGUAGGGGGCC-UGAAGAAAUGAGUCCUCUGUUUAUAACACACCCAACAGGAAUCUGGGUUCA-UUGUGACAAGGGGCACAAAA-CUUGUGG--CCUUUCUAUGAACAAAU---ACCCAAACACA
AAHX01024326.1/119730-119858 AGGGUGUGCUC------AGAGCAGGGGGCC-UGAGG-AAUGGCUCCUCUGUUUAUAACACACCCAAUACGAACCUGGUCAUG-AUGUGAGGAGGGCUACAAAG-UAUGUUG--CUGUCCUUCCCACACAU---GUCCUACAAUU
AAPY01738561.1/1419-1291     GGGGUGUGCUC------AGAGCAGGGGACC-UCAAG-AAUGGGUCCUCUGUUUAUAACACACCCAACAGAAAUCUGGGAUCA-UGAUGUUAAGGGACACAAAA-CUUGUAG--CCUCCCUAUGAACAAAU---ACCAUACAAGU
AAIY01387383.1/3172-3301     CGGGUGUGCUC------AGAGCAGGGGGCC-CAAAG-AAUGGCCCCUCUGUUUAUAACACACCCAAGAGGAAUCUGGGCUCAUUUGUAACCAGGAGCACACAA-CUUGUGG--CUUUCCUAUGAACAAAU---GCCUUACAUAU
AALT01602925.1/774-648       GUGGUGUGCUC------AGAGCAGGGGGCC-UAAAGAAAUGGCUCCUCUGUUUAUUACACACCAAACAGGAAUCUGGGUUUC-C--UGAUGAGGGUCACAAAA-CUUGUGA--CUUUCCUAUGAACA-AU---ACCCUACAGAU
AAYZ01539768.1/652-781       AGGGUGUGCUC------AGAACAAGGGACCUUGAAG-AACGGUUCCUCUGUUUACAGCACACCCAACAGCAAUGUGGGGAAA-UUGUGUUGAGGAGCAUAAAA-CAUGUGG--UCUGUUUGUGAACACAU---GUCCUACACAU
AC188110.1/209673-209800     GGGAUGUGCUC------AGAGCAGGGGGCC-UGAGG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAUCUGGGAUCA-CUGUGGCGAGAGGUACCAAAACUUGUAG--GCUUCCUAUGAACAAAC-----UCUACAUGU
AANN01707863.1/2420-2546     GGGGUGUUCUC------AGAGCAGGGGGCC-UGAAGAAAUGGCUUCUCUGUUUACAGUACACCCAACAGGAAUCUGAGUUCA-UUGG--CAGGGGGCAUAGAA--CUAUGA--CCUUCCUGUGAACAAAU---ACCGCACGUGU
CR974579.12/12128-11994      GGGGCGUGCUCAGACCGGGGGUGGGGGGCU-GAAGA-AAUGGCUCCUCUGUUUACAACACACCCAACGGGAAGCUGGGUUCA-CUGUGACAAGGGGCCCAAAA-CGCAUGG--CCUGUCUAUAAACAAAU---ACCCAACAUGG
AM055729.1/1-131             GGGGUGUGCUC------AGAGCAGGGGGCC-CAAAG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAUCUGGGGUCA-UUGUGAUGAGGG-CGUCAAA-CUUGUGG--CUUCCCUAUGAACAAACGUCCCCCAACACCU
AAKN02054121.1/69156-69028   GGGGUGUGCUC------AGAGCAGGGGCCC-UGAAG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAUCCAGGGCCA-UUGUGAAGAGGGCCACAACA-CUUGUGG--CCUCCCUAUGAGCAAAU---GCCCUACAUGU
AAWR02042438.1/44322-44451   GGGGUGUGCUC------AGAGCAGGGGACC-UGAAGAAAUGGCUCCUCUGUUUACAACACACCCAACAGGAAUCUGGGUUCA-UUGUGACAAGGGGCACAAAA-CUUGUGG--CCUUCCUAUGAGCAAAU---ACCCUACAUGU
AAGV020452296.1/866-994      GGGGUGUGCUC------AGAGCAGGGAGCC-UGAGG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAUCUGGGUUCA-UUGUUACAAGGAGCACAAAA-CUUGCGU--CCUUCCCAUGAACAAAU---GCCCUACACAU
AC239585.4/77797-77923       -GGGUGUGCUC------AGAGCAGGGGGCC-UGAAG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAGCUGGGGUCA-UCGUGAUGAGGGGCACAAAC--UUGUGG--CCUCCCUACAGACAAAU---GCCCUACAUGU
AAEX03005930.1/191049-190920 GGGGUGUGCUC------AGAGCAGGGGGCC-UGAAGAAAUGGCCCCUCUGUUUACAACACACCCAACAGGAAUCUGGGUUCA-UUGUGACAAGGGGCACAAAA-CCUGUGG--CCUUCCUAUGAACAAAU---ACCCUACAUGU
AC245177.1/27583-27457       -GGGUGUGCUC------AGAGCAGGGGGCC-UGAAG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAGCUGGGGUCA-UCGUGAUGAGGGGCACAAAC--UUGUGG--CCUCCCUACAGACAAAU---GCCCUACAUGU
AAQR03057237.1/558-430       GGGGUAUGCUC------AGAGCAAGGGGCC-UAAAG-AAUGGCUCCUCUGUUUAUAACAUGCCCAACAGGAAACUGGGAUCA-UUGUGAUGAGGGGCACAGAA-CUUGUGG--CCUCUCUAUCAACAAAU---UCCCUACAUGU
AAGW02064463.1/119579-119451 GGGGUGUGCUC------AGAGCAAGGGGCC-UGAAG-AAUGGCUCCUCUGUUUACAACACACCCAACAGGAAUCUUGGGUCA-UUGUGAUGAGGUCCAUAAAA-CUUGUGG--CCUCUUUACAAACUAAU---GCCCUACACAU
AAPE02015011.1/7858-7730     GGGGUGUGCUC------AGAGCAGGGUGCC-UGAAGAAAUGGCUCCUCUGUUUACAACACACCCAACAGGAA-CUGGGGUCA-CUGUGACAAGGGGCACAAAA-CGUGUGG--CCUUCCUGUGCACAAGC---ACCCUACAAGU
AAGU03000165.1/149452-149327 GGGGUGUGCUC------AGAGCAGGGGGCC-UGAAG-AAUGGC-UCUCUGUUUACAACACACCCAACAGGAAUCUGGGUUCA-UUGUGACAAGGGGCACAA---CUUGUGG--CCUUCCUAUAAACAAUU---GCCCUACACAU
AC007374.6/122865-122739     -GGGUGUGCUC------AGAGCAGGGGGCC-CGAAG-AAUGCCUCCUCUGUUUACAACACACCCAAUAGGAAUCUGGGGUCA-UUGUGACAAGGGACACAGAG-CUUGUGA--CCUCCCUACAAACAAAU---GCCCUACACA-
FJ915950.1/2-77              GGGGUGUGCUC------AGAGCAGGGGGCG-CGAAG-AAUGCCUCCUCUGUUUACAACACACCCAACAGUAAUCUGGG------------------------G-U-------------------------------C----AUU
#=GC SS_cons                 :<<<<<<<---......-<<<<<<<<<<<<._____.___>>>->>>>>>>>>---->>>>>>>------------<<<<--.-<<<--<<-<<<-<<<<<__._>>>>>-..>>>----->>->>>---...>>>>:::::::
#=GC RF                      GGGGuGUgCUC......AgagCaGgGGgCc.ugAAG.AAUgGcUCCuCuGuuuAcAAcACaCCCAAcAGGAAuCUGgGgucA.uuGuGAcgAgGggcacaaAa.cuugugg..cCuuccUAcgAaCaaAU...acCcuACAugU
//
# STOCKHOLM 1.0

#=GF AC   RF00615
#=GF ID   LhrA
#=GF DE   Listeria Hfq binding LhrA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Daub J
#=GF SS   Published; PMID:16682563
#=GF GA   100.00
#=GF TC   150.80
#=GF NC   35.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   16682563
#=GF RT   Identification of small Hfq-binding RNAs in Listeria monocytogenes.
#=GF RA   Christiansen JK, Nielsen JS, Ebersbach T, Valentin-Hansen P,
#=GF RA   Sogaard-Andersen L, Kallipolitis BH
#=GF RL   RNA. 2006;12:1383-1396.
#=GF CC   This RNA was identifed by screening for RNA molecules which
#=GF CC   co-immunoprecipitated with the RNA chaperone Hfq [1]. It appears to be
#=GF CC   transcribed from a region overlapping with predicted protein of unknown
#=GF CC   function (Lmo2257) and is located between a putative intracellular
#=GF CC   protease/amidase and a putative protein of the ribulose-phosphate 3
#=GF CC   epimerase family. Its is highly expressed in stationary growth phase but
#=GF CC   its function is unkown. It is proposed to be a regulatory RNA which
#=GF CC   controls gene expression at the post transcriptional level by binding its
#=GF CC   target mRNA in an Hfq dependent fashion [1]. This RNA molecule appears to
#=GF CC   be conserved amongst Listeria species but has not been identified in other
#=GF CC   bacterial species.
#=GF WK   Listeria_Hfq_binding_LhrA
#=GF SQ   10


AL591982.1/246434-246166   AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG
AL596172.1/30425-30158     AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUU-AUAAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUUAUGUCUAUGCCUCAUCCCGUUAUGCAUAGACGACCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG
AM263198.1/2311980-2311712 AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUAAAAAAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGACGCCAGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG
CP001175.1/288472-288740   AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG
AATL02000004.1/14657-14925 AGGAUAGAGUUUUACCUUGAUGAAAGUUUCAUUUUUAUUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGACGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG
AARQ02000001.1/48933-49201 AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUACUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG
FM242711.1/2352383-2352115 AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUAUUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGACGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG
AE017262.2/2341550-2341282 AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUAUUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGACGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG
AADR01000121.1/1123-1391   AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUAUUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGACGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG
AARN04000016.1/15498-15230 AGGAUAGAGUUUUACCUCGAUGAAAGUUUCAUUUUUAUUAAUGUGAUUUUCAUGGGGAUAAGACCCUAUCAUGGUUAUAAUGACUUUUGGUGUAUCCAUCUUCCAAUAGAAUGGCAACUAGUCAGACAUCUGUUUAGACACCAAAAUCAUUAUUUGUUUUCAUUCAUCUCAUUGGCCGUGUAGUUCAUGUCUAUGCCUCAUCCCGUUAUGCAUAGGCGCCCGAACAUGAUGGCAACGCUGGAAAUGUUUAUUUCGAGCGUCUUUUUUUG
#=GC SS_cons               ::<<<<<-<<<<<<<<<<-<<<<<<<<<-<<<<______>>>>->>>>>>>>>>>>>->>>>>>->>>>>,,,,,,<<<<<<<-<<<<<<<<<-----------<<<<<<-<<<<_____>>>>---->>>>>>--->>>>>>>>>>>>>>>>,,,,,,,,,,,,,,,,,,,,,<<<<<---<<<<-<<<<<<<<<_____________>>>>>>>>>--->>>>--->>>>>,<<<<<-<<<<<____>>>>>->>>>>:::::::::
#=GC RF                    AGGauaGAGucuuaCCccGauGaaagucUCauuUuuAuuaauGUgacuuuCauggGGAuaagaCCCuauCAUGGUUauaauGaCuuuuGGuGuAUCCAUCUUCCaacaGaAuGgCAACUAGcCaGACAuCuguuUAGaCaCCaaaauCauuauUUGUUUUCAUUCAUCUCAUUGGCCguGUAGuucAcGuCuauGCCUCAUCCCGUUAUGCauaGaCgcCcgaaCAUGacGGCAaCGCuGGaaauGUUUauuuCGaGCGuCUUUUUUUG
//
# STOCKHOLM 1.0

#=GF AC   RF00616
#=GF ID   LhrC
#=GF DE   Listeria LhrC
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Daub J
#=GF SS   Published; PMID:16682563
#=GF GA   110.00
#=GF TC   115.30
#=GF NC   107.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00114
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0045947; negative regulation of translational initiation;
#=GF RN   [1]
#=GF RM   16682563
#=GF RT   Identification of small Hfq-binding RNAs in Listeria monocytogenes.
#=GF RA   Christiansen JK, Nielsen JS, Ebersbach T, Valentin-Hansen P,
#=GF RA   Sogaard-Andersen L, Kallipolitis BH
#=GF RL   RNA. 2006;12:1383-1396.
#=GF RN   [2]
#=GF RM   25034691
#=GF RT   A multicopy sRNA of Listeria monocytogenes regulates expression of the
#=GF RT   virulence  adhesin LapB.
#=GF RA   Sievers S, Sternkopf Lillebaek EM, Jacobsen K, Lund A, Mollerup MS,
#=GF RA   Nielsen PK, Kallipolitis BH
#=GF RL   Nucleic Acids Res. 2014;42:9383-9398.
#=GF RN   [3]
#=GF RM   26176322
#=GF RT   The multicopy sRNA LhrC controls expression of the oligopeptide-binding
#=GF RT   protein OppA in Listeria monocytogenes.
#=GF RA   Sievers S, Lund A, Menendez-Gil P, Nielsen A, Storm Mollerup M, Lambert
#=GF RA   Nielsen S, Buch Larsson P, Borch-Jensen J, Johansson J, Kallipolitis BH
#=GF RL   RNA Biol. 2015;12:985-997.
#=GF RN   [4]
#=GF RM   27400116
#=GF RT   Two novel members of the LhrC family of small RNAs in Listeria
#=GF RT   monocytogenes with overlapping regulatory functions but distinctive
#=GF RT   expression profiles.
#=GF RA   Mollerup MS, Ross JA, Helfer AC, Meistrup K, Romby P, Kallipolitis BH
#=GF RL   RNA Biol. 2016;13:895-915.
#=GF CC   This RNA was identifed by screening for RNA molecules which
#=GF CC   co-immunoprecipitated with the RNA chaperone Hfq [1]. However, neither the
#=GF CC   stability nor the activity of LhrC is depending on the presence of
#=GF CC   Hfq[2][3]. LhrC is transcribed from the intergenic region between the
#=GF CC   protein coding genes cysK, a putative cysteine synthase and sul, a
#=GF CC   putative dihydropteroate synthase [1]. In Listeria monocytogenes four
#=GF CC   additional copies of lhrC have been identifed in the genome, three of
#=GF CC   which are located in tandem repeat upstream of the originally
#=GF CC   characterised lhrC [1]. This RNA molecule appears to be conserved amongst
#=GF CC   Listeria species but has not been identified in other bacterial species.
#=GF CC   The direct mRNA targets of LhrC are the virulence adhesion LapB, and the
#=GF CC   oligo-peptide binding protein OppA. The 3 conserved UCCC motifs common to
#=GF CC   all copies of LhrC are involved in the mRNA binding and
#=GF CC   post-transcriptional repression of the target genes. Interestingly, 2
#=GF CC   other Listerina monocytogenes sRNAs Rli22 and Rli33 contain two UCCC
#=GF CC   motifs and use them to repress oppA mRNA expression.[4]
#=GF WK   Listeria_Hfq_binding_LhrC
#=GF SQ   12


AL596164.1/23950-24060   AUAAGCUAACAACAAGCAAAACAAUU---CAUU---CU--U--UCCCCUUUUUAGAAUGAAAUUCCUAAACUCCC-U--UUU-UG-ACCAGUGUGGUUUACUCC--CUUUUU-CCACACUGGUUUUUUA
AL591974.1/32086-32197   AUAAGCUAACAACAAGCAAAACAUUU--UCAUU---CU--U--UCCCCUUUUUAGAAUGAAGAUCCCAAACUCCC-U--UUUUGA--CCAGUGUGGUUUACUCCCUUUUU---CCACACUGGUUUUUUG
AL596167.1/8204-8314     AUAAGCUAACAACAAGCAAAACAUUUU--CAUUU--CU--U--UCCC-UUUUUAGAAUGAAAAUCCCAAACUCCC-U--UUU-AG--CUAGUGCGGUUUACUCC--CUUUUU-CCGCGCUAGUUUUUUC
AADR01000023.1/5275-5162 AUAAGCUAACAACAAGCAAAACAUUUU--CAUUCUUCU--C--CCCCCUUUUUAGAAUGAAGAUCCCAAACUCCC-U--UUU-UG-ACCGAUGCGGUUUACUCC--CUUUU--CCGCAUCGGUUUUUUU
AL596164.1/23546-23655   AUAAGCUAACAACAA-CAAAACAUUUU--CAUU---CU--U--UCCC-CUUUUAGAAUGGAAAUCCCAAACUCCC-U--UUU-UA-GCCAGUGUGGUUUACUCC--CUUUUU-CCACACUGGUUUUUUA
AM263198.1/188916-189028 AUAAGCUAACAACAAGCAAAACAUUUU--CAUU---CU--UCCUCCCCCUAUUAGAAUGAAAAUCCCAACUCCCU-U--UUU-UG-ACCGAUGCGGUUUACUCC--CUUUU--CCGCAUCGGUUUUUUU
AL596164.1/24153-24267   AUAAGCUAACAACAAGCAUAACAUUUU--CAUU---CUUCU--CCCCCCUAUUAGAAUGAAAACCCUAAACUCCC-UUUUUU-UG-ACCGAUGCGGUUUACUCC--CUUUU--CCGCAUCGGUUUUUUU
AADR01000023.1/5482-5368 AUAAGCUAACAACAAGCAAAACAUUUU--CAUUCUUCU--C--CCCCCUUUUUAGAAUGAAGAUCCCAAACUCCC-U--UUU-UG-ACCAGUGUGGUUUACUCC--CUUUUU-CCACACUGGUUUUUUC
AL591974.1/32492-32605   AUAAGCUAACAACAAACAAAACAUUU-U-CAUU---CU--UCUCCCCCCUUUUAGAAUGAAAAUCCCAAACUCCCUU--UUU-UG-ACCGAUGCGGUUUACUCC--CUUUU--CCGCAUCGGUUUUUUU
AARU02000014.1/4738-4625 AUAAGCUAACAACAAACAAAACAUUUU--CAUU---CUUCU--CCCCCCUUUUAGAAUGAAAAUCCCAAACUCCC-U--UUU-UUGACCGAUGCGGUUUACUCC--CUUUU--CCGCAUCGGUUUUUUU
FM242711.1/982673-982783 AUAAGCUAACAACAAGCAAAACAUUUU--CAUUU--CU--U--U-CCCUUUUUAGAAUGAAAAUCCCAAACUCCC-U--UUU-AG--CUAGUGCGGUUUACUCC--CUUUUU-CCGCACUAGUUUUUUU
AE017262.2/237550-237663 AUAAGCUAACAACAAGCAAAACAUUUU--CAUU---CU--UCUCCCCCCUUUUAGAAUGAAGAUCCCAAACUCCC-U--UUU-UG-ACCAGUGUGGUUUACUCC--CUUUU-UCCACACUGGUUUUUUA
#=GC SS_cons             ::::::::::::::::::::::<<<<<..<<<<...<_.._..___________>>>>>>>>>>-----------.-..---.--.-<<<<<<<<<________.._____..>>>>>>>>>:::::::
#=GC RF                  AUAAGCUAACAACAAgCAAAACauuuu..Cauu...CU..U..uCCCCuUuUUAGaauGaaaauCCcAAACUCCC.U..UUU.ug.ACcgguGcGGUUUACUCC..CUUUU..CCgCaccgGUUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00617
#=GF ID   cHP
#=GF DE   flavivirus capsid hairpin cHP
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID:16474125
#=GF SS   Published; PMID:16474125
#=GF GA   40.00
#=GF TC   40.20
#=GF NC   39.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0006413; translational initiation;
#=GF RN   [1]
#=GF RM   16474125
#=GF RT   RNA secondary structure in the coding region of dengue virus type 2
#=GF RT   directs translation start codon selection and is required for viral
#=GF RT   replication.
#=GF RA   Clyde K, Harris E
#=GF RL   J Virol. 2006;80:2170-2182.
#=GF CC   cHP is a conserved RNA hairpin structure identified within the capsid
#=GF CC   coding region of several flavivirus genomes. These positive strand RNA
#=GF CC   genomes are translated as a single polypeptide and subsequently cleaved
#=GF CC   into constituent proteins, the first of which is the capsid protein. The
#=GF CC   cHP hairpin is located within the capsid coding region between two AUG
#=GF CC   start codons. The cHP cis element has been shown to direct translation
#=GF CC   start from the thermodynamically unstable first start codon [1]. The
#=GF CC   ability of cHP to direct initiation from the first start codon is
#=GF CC   proportional to its thermodynamic stability, is position dependent, and is
#=GF CC   sequence independent [1]. It has been demonstrated that both AUGs and the
#=GF CC   conserved cHP are necessary for efficient viral replication in human and
#=GF CC   mosquito cells [1].
#=GF WK   flavivirus_capsid_hairpin_cHP
#=GF SQ   59


U88237.1/1-43      AUGAAUAACCAACGAAAAAAGGCGAG--AAGU---ACGCCUUUCA--AUG
M84728.1/97-141    AUGAAUGACCAACGGAAAGAGGCGAA--AAAC---ACGCCAUUCAAUAUG
L04561.1/94-138    AUGAAUGACCAACGGAAAAAGGCGAG--AAAC---AUGCCUUUCAAUAUG
M19197.1/97-141    AUGAAUGACCAACGGAAAAAGGCGAG--AAAC---ACGCCUUUCAAUAUG
AF469176.1/1-45    AUGAAUAACCAACGGAAAAAGGCGAA--AACC---ACGCCUUUCAAUAUG
AF100466.2/88-132  AUGAAUAACCAACGGAAAAAGGCGAA--AAGC---ACGCCUUUCAAUAUG
AY744147.1/97-141  AUGAAUAACCAACGGAAAAAGGCGAG--AAAC---ACGCCUUUCAAUAUG
AF100465.1/86-130  AUGAAUAACCAACGAAAAAAGGCGAG--AAAC---ACGCCUUUCAAUAUG
M84727.1/97-141    AUGAAUGACCAACGGAAA-AAGGCGA--AAAA-CACGCCAU-UCAAUAUG
AF022440.1/97-141  AUGAAUAACCAACGGAAA-AAGGCGA--AAAA-CACGCCUU-UCAAUAUG
S75726.1/1-45      ---ACUAAAAAACCAGGAGGGCCCGG--UAAAAACCGGGCUAUCAAUAUG
U21057.1/69-116    AUGAUUAAAAAACCAGGAGGGCCCGG--UAAAAACCGGGCCAUCAAUAUG
U03696.1/69-116    AUGACUAAAAAACCAGGAGGGCCCGG--UAAAAACCGGGCCAUCAAUAUG
U03694.1/69-116    AUGACUAAAAAACCAGGAGCGCCCGG--UAAAAACCGGGCUAUCAAUAUG
AF416457.1/96-143  AUGACUAAAAAACCAGGAGGGCCCGG--UAAAAGCCGGGCUAUCAAUAUG
AY184212.1/96-143  AUGACUAAAAAACCACGAGGGCCCGG--UAUAAACCGGGCUAUCUAUAUG
AF080251.1/96-143  AUGACUAAAAAACCAGGAGGGCCCGGU-AAGA-ACCGGGCUAUCAAUAUG
AY453411.1/97-144  AUGUCUAAGAAACCAGGAGGGCCCGG--AAGAAACCGGGCCAUCAAUAUG
AB051292.1/97-144  AUGACUAAAAAACCAGGAGGGCCCGG--AAGAAACCGGGCCAUCAAUAUG
AF289817.1/68-115  AUGACUAAAAAACCAGGAGGGCCCGGG-AAAA-ACCGGGCCAUCAAUAUG
AY303794.1/96-143  AUGACUAAAAAACCAGGAGGGCCCGGG-AAAA-ACCGGGCUAUCAAUAUG
AY765264.1/97-144  AUGUCUAGGAAACCAGGAGGGCCCGGAGAUAA--CCGGGCUGUCAAUAUG
AY277251.1/92-139  AUGUCUAAGAAACCAGGAGGGCCCGG--AAAAAACCGGGCUGUCAAUAUG
AY688948.1/97-144  AUGUCUAAGAAACCAGGAGGGCCCGG--UAAAAACCGGGCUGUCAAUAUG
AY701412.1/55-102  AUGUCUAAGAAACCAGGAGGGCCCGGC-AAGA-GCCGGGCUGUCAAUAUG
AY278441.1/97-144  AUGUCUAAGAAACCAGGAGGGCCCGGC-AAGA-GUCGGGCUGUCAAUAUG
AY274504.1/97-144  AUGUCUAAGAAACCAGGAGGGCCCGGC-AAAA-GCCGGGCUGUCAAUAUG
AF161266.1/96-143  AUGUCUAAAAAACCAGGAGGACCCGG--GAAGCCCCGGGUCGUCAAUAUG
AY898809.1/96-143  AUGUCUAAAAAACCAGGAGGACCCGG--AAGAAACCGGGUCGUCAGUAUG
M16614.1/99-146    AUGUCUAAAAAACCAGGAAAACCCGG--UAGAAACCGGGUUGUCAAUAUG
AY152304.1/1-42    AUG---AACCAACGAAAAAAGGUGGU--UAGG---CCACCUUUCAAUAUG
AY152108.1/1-42    AUG---AACCAACGAAAAAAGGUGGU--UAGA---CCACCUUUCAAUAUG
AF289029.1/102-143 AUG---AACCAACGAAAAAGGGUGGU--UAGA---CCACCUUUCAAUAUG
M14931.2/102-143   AUG---AACCAACGAAAAAAGGUGGU--UAGA---CCACCUUUCAAUAUG
AY762084.1/93-137  AUGAACAACCAACGGAAGAAGACGGG--UCGA---CCGUCUUUCAAUAUG
AF226687.2/95-139  AUGAACAACCAACGGAAAAAGACGGG--UCGA---CCGUCUUUCAAUAUG
S75335.1/1-45      AUGAACGACCAACGGAAAAAGACGGG--UCGA---CCGUCUUUCAAUAUG
AY708047.1/95-139  AUGAACAACCAACGGAAAAAGACGGC--UCGA---CCGUCUUUCAAUAUG
AF309641.1/81-125  AUGAACAACCAACGAAAAAAGACGGC--UCGA---CCGUCUUUCAAUAUG
X70952.1/1-45      AUGAUCAACCAACGGAAAAAGACGGG--UCGA---CCGUCUUUCAAUAUG
AF180818.1/95-139  AUGAUCAACCAACGAAAAAAGACGGG--UCGA---CCGUCUUUCAAUAUG
AY376738.1/81-125  AUGAACAACCAACGAAAAAAGACGGG--UCGA---CCGUCUUUCAAUAUG
D00502.1/102-146   AUGAACAACCAACGGAAAAAGACGGG--UAAC---CCGUCUUUCAAUAUG
AY858044.2/95-139  AUGAACAACCAACGGAAAAAGACGGG--AAAA---CCGUCAAUCAAUAUG
AY099340.1/95-139  AUGAACAACCAACGGAAGAAGACGGG--AAAA---CCGUCUAUCAAUAUG
AB189127.1/95-139  AUGAACAACCAACGGAAAAAGACGGG--AAAA---CCGUCUAUCAAUAUG
AB189125.1/95-139  AUGAACAACCAACGGAAAAAGACGGG--UAAA---CCGUCUAUCAAUAUG
AB010982.1/1-45    AUGAACAACCAACGAAAAAGGACGGG--AAAA---CCGUCUAUCAAUAUG
AB010986.1/1-45    AUGAACAACCAACGAAAAAAGACGGG--AAAA---CCGUCUAUCAAUAUG
AB010990.1/1-45    AUGAACAACCAACGAAAAAAGACGGG--AAGA---CCGUCUAUCAAUAUG
X51710.1/1-45      AUGAAUAACCAACGAAAAAAUGCGAG--AAAA---ACGCCUUUCAAUAUG
AF038403.1/97-141  AUGAAUAACCAACGAAAAAAGGCGAG--AAAU---ACCCCUUUCAAUAUG
AF204177.1/97-141  AUGAAUAACCAACGAAAAAAGGCGAG--AAAU---ACGCCUUUCAAUAUG
AF022438.1/97-141  AUGAAUAACCAACGAAAAAAGGCGAA--AAAU---ACGCCUUUCAAUAUG
AF360862.1/1-45    AUGAAUAACCAACGGAAAAAGGCGAG--AAGU---ACGCCUUUCAAUAUG
AB189122.1/97-141  AUGAAUAACCAACGGAAAAAGGCGAG--AAAU---ACGCCUUUCAAUAUG
X51708.1/1-45      AUGAAUGACCAACGAAAAAAGGCGAG--AAGU---ACGCCUUUCAAUAUG
AF360863.1/1-45    AUGAAUAACCAACGAAAAAAGGCGAG--AGGU---ACGCCUUUCAAUAUG
AY692470.1/25-69   AUGAAUAACCAACGAAAAAAGGCGAG--AAGU---ACGCCUUUCAAUAUG
#=GC SS_cons       ::::::::::::::::<<-<<<<<<_..____...>>>>>>->>::::::
#=GC RF            AUGAaUAAcCAACGAAaAAaGgCgGG..AAAA...CcGcCuuUcAAUAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00618
#=GF ID   U4atac
#=GF DE   U4atac minor spliceosomal RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Marz M; 0000-0003-4783-8823
#=GF SE   PMID:19030770; Gardner PP
#=GF SS   Published; PMID:11911359
#=GF GA   53.00
#=GF TC   53.20
#=GF NC   52.90
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF CL   CL00007
#=GF DR   SO; 0000274; snRNA;
#=GF DR   GO; 0000244; spliceosomal tri-snRNP complex assembly;
#=GF DR   GO; 0000395; mRNA 5'-splice site recognition;
#=GF DR   GO; 0030624; U6atac snRNA binding;
#=GF DR   GO; 0030627; pre-mRNA 5'-splice site binding;
#=GF DR   GO; 0005690; U4atac snRNP;
#=GF RN   [1]
#=GF RM   15987817
#=GF RT   Evolutionary conservation of minor U12-type spliceosome between plants and
#=GF RT   humans.
#=GF RA   Lorkovic ZJ, Lehner R, Forstner C, Barta A
#=GF RL   RNA. 2005;11:1095-1107.
#=GF RN   [2]
#=GF RM   12409455
#=GF RT   Domains of human U4atac snRNA required for U12-dependent splicing in vivo.
#=GF RA   Shukla GC, Cole AJ, Dietrich RC, Padgett RA
#=GF RL   Nucleic Acids Res. 2002;30:4650-4657.
#=GF RN   [3]
#=GF RM   11911359
#=GF RT   A revised model for U4atac/U6atac snRNA base pairing.
#=GF RA   Padgett RA, Shukla GC
#=GF RL   RNA. 2002;8:125-128.
#=GF RN   [4]
#=GF RM   18390578
#=GF RT   Computational screen for spliceosomal RNA genes aids in defining the
#=GF RT   phylogenetic distribution of major and minor spliceosomal components.
#=GF RA   Davila Lopez M, Rosenblad MA, Samuelsson T
#=GF RL   Nucleic Acids Res. 2008;36:3001-3010.
#=GF RN   [5]
#=GF RM   19030770
#=GF RT   Evolution of spliceosomal snRNA genes in metazoan animals.
#=GF RA   Marz M, Kirsten T, Stadler PF
#=GF RL   J Mol Evol. 2008;67:594-607.
#=GF CC   U4atac is an essential component of the minor U12-type spliceosome complex
#=GF CC   which is required for removal of the rarer class of eukaryotic introns
#=GF CC   (AT-AC, U12-type) [1]. U4atac snRNA is proposed to form a base-paired
#=GF CC   complex with another spliceosomal RNA U6atac via two stem loop regions.
#=GF CC   These interacting stem loops have been shown to be required for in vivo
#=GF CC   splicing [2]. U4atac also contains an 3' Sm protein binding site which has
#=GF CC   been shown to be essential for splicing activity [2]. U4atac is the
#=GF CC   functional analog of U4 (Rfam:RF00015) in the major U2-type spliceosomal
#=GF CC   complex [2]. The drosophila U4atac snRNA has an additional predicted 3'
#=GF CC   stem loop terminal to the Sm binding site [3] which is not included in
#=GF CC   this model.
#=GF WK   U4atac_minor_spliceosomal_RNA
#=GF SQ   61


AAPP01019634.1/122532-122382   -ACCUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UCCAAUGAAC-GUCUAGU-GAGGG-CAUUG-CUGCUGACA--CCAAAGAUAUUA----------------------------------CCCCCG--CUC--ACU---GG-UC-GCCUG-----CGA-UC--AG-----GGU--U-CGG-AAUUUUUGGACCAAGGCCCCCUUACUUAACAGGGGGCCGU
AAPQ01006438.1/743481-743332   -ACCUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UUCAAUGAAC-GUCUAGU-GAGGA-CAUUG-CUGCUGACA--CCAAUGAUAUUA----------------------------------CCCCCG--CUC--GCC---GA-UC-GUUCG-----CGA-UU--GG-----AGU--U-CGG-AAUUUUUGGACCAGGCGCCCUUACUUUACAGGGCGCCGC-
AE014297.2/1020885-1020736     -ACCUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UUCAAUGAAC-GUCUAGU-GAGGA-CAUUG-CUGCUGACA--CCAAUGAUGACA----------------------------------CCCCCG--CUC--GCC---GA-UC-GUUCG-----CGA-UU--GG-----AGU--U-CGG-AAUUUUUGGACCAGGCUCCUUUACUUUACAGGGAGCCGC-
AAST01029695.1/1294-1145       -ACCUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UUCAAUGAAC-GUCUAGU-GAGGA-CAUUG-CUGCUGACA--CCAAUGAUAUCA----------------------------------CCCCCG--CUC--GCC---GA-UC--GUUCG----CGA-UU--GG-----AGU--U-CGG-AAUUUUUGGACCAGGCUCCCUUACUUUACAGGGAGCCGC-
AAKO01001557.1/51647-51498     -ACCUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UUCAAUGAAC-GUCUAGU-GAGGA-CAUUG-CUGCUGACA--CCAAUGAUAUCA----------------------------------CCCCCG--CUC--GCC---GA-UC--GUUCG----CGA-UU--GG-----AGU--U-CGG-AAUUUUUGGACCAGGCUCCCUUACUUUACAGGGAGCCGC-
AAEU02010290.1/66-215          -ACCUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UUCAAUGAAC-GUCUAGU-GAGGA-CAUUG-UUGCUGACA--CCAAUGAUAUUA----------------------------------CCCCCG--CUC--GUC---GA-UC--GUUCG----CGA-UU--GG-----AGU--U-CGG-AAUUUUUGGACUAGGCUUCCUUACUUUACAGGGAGCCGC-
AADA01241850.1/15965-15840     -ACCAUCCUU-UUCUUGGGG-UUGCAC-UACU-G-UCUAAUGAGU-GCAUAAU-GAGGG-CAGUA-UUGCUAAUGCCUAU-ACAA-----UGCACC----------------------------UGCAUCAAC----UA---GA-AC--UUU-------GC-UU--UA-----CCUU--GGUACAAUUUUUGGAAAA---------------------------
AL389925.10/20736-20611        -ACCAUCCUU-UUCUUGGGG-UUGCAC-UACU-G-UCUAAUGAGU-GCAUAAU-GAGGG-CAGUA-UUGCUAACGCCUAU-ACAA-----UGCACC----------------------------UGCAUCAAC----UA---GA-AC--UUU-------GC-UU--UA-----CCUU--GGUACAAUUUUUGGAAAA---------------------------
AADA01047294.1/887-1012        -ACCAUCCUU-UUCUUGGGG-UUGCAC-UACU-G-UCCAAUGGGU-ACCUAGU-GAGGG-CAGUA-CUGCUAACUCCUGC-ACAA-----CACACC----------------------------GAAAUCAAC----UA---GA-GC--UUU-------GC-UU--UG-----CCUU--GGUGCAGUUUUUGGAGAA---------------------------
AL135914.25/92223-92098        -ACCAUCCUU-UUCUUGGGG-UUGCAC-UACU-G-UCCAAUGGGU-ACCUAGU-GAGGG-CAGUA-CUGCUAACUCCUGC-ACAA-----CACACC----------------------------GAAAUCAAC----UA---GA-GC--UUU-------GC-UU--UG-----CCUU--GGUGCAGUUUUUGGAGAA---------------------------
AL161445.10/77816-77941        -ACCAUCCUU-UUCUUGGGG-UUGCAC-UACU-G-UCCAAAGAGC-AUGUAGU-GAGGG-CAGUA-CUGCUAACGUCUAC-ACAA-----CACACC----------------------------CACCUCAAC----UA---GA-GC--UUU-------GC-UU--UA-----GCUU--GGUGUAAUUUUUGGAAAA---------------------------
AADA01054074.1/15964-15839     -ACCAUCCUU-UUCUUGGGG-UUGCAC-UACU-G-UCCAAAGAGC-AUGUAGU-GAGGG-CAGUA-CUGCUAACAUCUAC-ACAA-----CACACC----------------------------CGCCUCAAC----UA---GA-GC--UUU-------GC-UU--UA-----GCUU--GGUGUAAUUUUUGGAAAA---------------------------
AC136636.6/172138-172014       -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAAC-GCGUAGU-GAGGG-CAGUA-CUGCUAACGCCUG--ACAA-----CACACC----------------------------UGCAUCGGU----UA---GA-GC--UCU-------GC-UU--UA-----CCUU--GGUGCAAUUUUUGGAAAA---------------------------
AAXN01018884.1/118-242         -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAAC-GAAUAGU-GAGGG-CAGUA-CUGCUAACGCCUG--ACAA-----CACACC----------------------------UGCAUCGGU----UA---GA-GC--UCU-------GC-UU--UA-----CCUU--GGUGCAAUUUUUGGAAAA---------------------------
AACN010332835.1/830-706        -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAAC-GCUUAGU-GAGGG-CAGUA-CUGCUGACGCCUG--ACAA-----CACGCC----------------------------CGCAUCGGC----UA---AA-GC--UCU-------GC-UU--UA-----CCUC--GGUGCAAUUUUUGGAAAA---------------------------
AAFC03121196.1/26240-26365     -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCGAUGAAC-GCUUAGU-GAGGA-CAGUA-CUGCUAACACCUAU-GCAA-----CACGCC----------------------------CGCACCGGC----UA---AA-GC--GCA-------GC-UU--UA-----UCAC--GGUGCAAUUUUUGGAAAA---------------------------
AAFR03008173.1/71752-71627     -ACCAUCCUU-UUCUUGGGG-UUGCGU-UACU-G-CCCAAUGAAC-GUUUAGU-GAGGA-CAGUA-CUGCUAACGCCUAA-ACAA-----CACGCA----------------------------CGCAUCUUU----UA---AA-GC--UUC-------GC-UU--UA-----ACAU--GGUGCAAUUUUUGGAACA---------------------------
AAPN01427475.1/38-163          -ACCGUCCUU-CUCUUGGGG-UGGCGC-UACU-G-UCCGAUGAAC-GUUUAGU-GAGGA-CAGUA-CUGCUAACGCUCAG-GCAA-----CACACU----------------------------CGCACCUGC----UA---GG-GC--UCC-------GC-CU--UA-----ACCG--GGUGCAAUUUUUGGAACC---------------------------
BAAF04053164.1/10519-10646     -ACCAUCCUA-GUCUUGGGG-U-GAAA-CGGGAAACUCAAUGAGC-GUCUAGC-GAGAG-UUCCC-UGCUGACACCAUUACCAACACAUU----------------------------------CGCAUCU------CC---UA-AA-CUUUAU----GUU-UA--GG------UUA-CGGUGCAAUUUUUGGAAA----------------------------
AANH01011402.1/5162-5288       -UCUUUCCUU-GUCAUGGGG-U-GGCU-UGGGGGACUCAAUGAAC-GCGUAGU-GAGAGCCUCCC-UGCUAACACCAGA-CCAACACAUG----------------------------------CGCGUCA------CC---CG-GGCGUCA-C----GCC-CG--GG-----CUAU--GACGCAAUUUUUGGAA-----------------------------
ABAV01030669.1/9778-9657       -AACGUCCUU-AUCGGGGGUUG-AGCG--GCA-G--UUCCGUGAUCGACAAGUGAGAA--UUGCUCUGCUGACAC--CUGAAACUACAACACUA-UG--------------------------U---------C-ACCA---CU-CU--GAAA------AG-GG-UUGGU-GC-----------AAUUUUUGGAAAA---------------------------
AACT01014164.1/14797-14663     AUU-GUCCUUAUCAAUGGGG-A-AGCGUUAUU-A-CUCAAGGAAC-GAUAAGU-GAGGG-UAGUACUGCUAACACCAUUUGUGAUUUAUCACACUC----------------------------CGCACCG------CUG-CUU-CC--UUGU------GG-AGUUGG-------UC--GGUGCAAUUUCUGGAUGG---------------------------
AABS01000098.1/66915-66782     -GUUGUCCUUAUCAAUGGGG-A-AGCGUUACA-A-UUCAAGGAAC-GAUAAGU-GAGGG-UUGUACUGCUAACACCAUUUGUGAUUUAUCACACCC---------------------------AAGCAUCA------CU---GC-UU-CAUUA-----GAA-GC--UG-------AU--GGUGCAAUUUCUGUACAG---------------------------
AAZX01007551.1/46173-46008     -UACAUCCUU-GUCUAGAGG-A-GCAU-AAGU-A-UUCAAUGAAC-GUAUAGU-GAGGG-UACUG-AUGCUGACA--CUAGUUAAAAAUUUUAACU-----------------------------GCAUCC--GCGAGUAAGGU-AUUUUAACG----AAU-AUCCACUC-GU-UUG-CGAUGCAAUUUUUGAAA--GCCUCUUUACUUCACAAGGGGCCA---
BAAB01203970.1/2470-2315       -AACUUCCUU-GUCUUGGGG-A-GCAU--AGU-G-CGCAGUGAUC-GUAAAGU-GAGAG-CACUU-CUGCUGACA--CCCACAAGUUAAACUUGUUACA---------------------CCCG--CGCC------CGG---CUGCC--GUAA------GGGAG-UCCG---A-------GCGCAAUUUUUGAC---GGGCACUCUUACUUUACAGAGGCCUUU
AAAB01008986.1/3372038-3372230 -UUCUUCCUU-GUCUUGGGG-A-GCAU--AAU-G-UCCAGUGAAC-GUGUAGU-GAGGG-CAUUG-AUGCUGACAAACCCAUCUUAAAGAGCAGGAUCUUGAAGGUCCUGUUUCUUUGUAAACCCCCGUCC--GUCGGU---UC-GC-UUUCAAA--CAGCUGU--ACCAGGU---G--GUCGGAAUUUUUGAA---GCGUCCCUUUACUUUACAAGGGAUGUG
AAFS01000016.1/19569-19724     -CACUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UCCAAUGAAC-GUCUAGU-GAGGG-CAUUG-CUGCUGACA--CCAAUUACAUUUA---------------------------------UUCCCG--UCU--GCC---AG-GC--CACUCACUGUGG-CU--GG-----UCU--U-CGG-AAUUUUUGGCCAAAGGCUCCCUUACUUUAUAGGGAGCCGC
AAIZ01001811.1/683-838         -CACUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UCCAAUGAAC-GUCUAGU-GAGGG-CAUUG-CUGCUGACA--CCAAUUACAUUUA---------------------------------UUCCCG--UCU--GCC---AG-GC--CACUCACUGUGG-CU--GG-----UGU--U-CGG-AAUUUUUGGCCAAAGGCUCCCUUACUUUAUAGGGAGCCGC
AANI01017162.1/86143-85990     -ACUUUUCUU-UUCUUGGGA-A-GCGG-AAAU-G-UUCAAUUAAC-GUCGAGG-CAGGA-GUGUG-UUGCUGACG--AAAACGUUGAAACAUUAA----------------------------UACACG--UUU--AAA---AA-UC--UUAG------GA-UU--AG-----CUU--U-CUA-AAUUUCUGGAAAUUAACUCCCAUACUUUAAGGUGGUCGU-
AANI01014648.1/138479-138633   -AUCUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UCCAAUGAAC-GUCUAGU-GAGGA-CAUUG-CUGCUGACA--CCAAUGAUAUAACAAAAAA---------------------------CCCCCG--UUC--GCU---GA-UC--UUC-------GA-UC--GG-----CGC--U-CGG-AAUUUUUGGAAAUAGACUCCCUUACUUUAUAGGGGGUCGU
AAPU01011105.1/262422-262573   -UCCUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UUCAAUGAAC-GUCUAGU-GAGGA-CAUUG-CUGCUGACA--CCAAUGAUAU-AAUAA------------------------------CCCCCG--CUC--GCU---GA-UC--UCUG-----CGA-UU--AG-----CGU--U-CGG-AAUUUUUGGAAA-AGACUCCCUUACUUCAUAGGGAGUCGU
AAPT01020183.1/127226-127384   -ACCUUCCUU-GUCUUGGGG-A-GCAG-AAAU-G-UCCAAUGAAC-GUAUAGU-GAGGA-CAUUG-CUGCUGACA--CCAAUGAUAUUAACAUCAG---------------------------CCCCCG--UUU--GCU---GA-UC-AUCUCG----UGA-UU--AG-----CUU--U-CGG-AAUUUUUGGAAAAAGGCCCCCUUACUUUAUAGGGGGUCGU
ABDC01347327.1/313-438         -ACCAUCCUU-UUCUUGGGG-UAGCGC-UACU-G-UCCAAUGAAC-GAAUAGU-GAGGA-CAGUA-CUGCUAACGCCUACACAACACAUC----------------------------------CGCAUCAAC----UA---GA-GC--UUU-------GC-UU--UA-----CUUU--GGUGCAAUUUUUGGAAAA---------------------------
AALT01476310.1/771-646         -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAAC-GUCUAGU-GAGGA-CAGUA-CUGCUAACACCUAA-ACAA-----CACGCU----------------------------CGCAUCAGU----UA---GA-GC--UCU-------GC-UU--UA-----UCUU--GGUGCAAUUUUUGGAAAA---------------------------
AANU01295318.1/748-623         -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAGC-GCAUAGU-GAGGG-CAGUA-CUGCUAACGCCUACACAACACACC----------------------------------CGCAUCAAC----UA---AA-GC--UUU-------GC-UU--UA-----CCUU--GGUGCAAUUUUUGGAAAA---------------------------
AANN01562320.1/870-745         -ACCAUCCUU-UUCUUGGGG-UUGCGU-UACU-G-UCCAAUGAGC-GCUAAGU-GAGGG-CAGUA-CUGCUAACACCUUAACAACACACU----------------------------------CGCAUCAAC----UA---GA-GC--UUU-------GC-UU--UA-----CCUU--GGUGCAAUUUUUGGAAAA---------------------------
AAIY01042223.1/294-419         -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-A-UCCAAUGAAC-GUGUAGU-GAGGG-UAGUA-CUGCUAACGCCUACGCAACACAUU----------------------------------CGCAUUAGU----UA---AA-GC--UCU-------GC-UU--UA-----UUUU--GAUGCAAUUUUUGGAAAA---------------------------
AAPY01611414.1/511-386         -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAGC-GCCUAGU-GAGGG-CAGUA-CUGCUAACGCCUGAACAACACACC----------------------------------CGCAUCAGU----UA---AA-GC--UCU-------GC-UU--UA-----UCUU--GGUGCAAUUUUUGGAAAA---------------------------
CAAE01014614.1/129416-129543   -GCUGUCCUU-GUCAUGGGG-UGGUUG-GGAG-G-CUCGAUGAAC-GUCUGGU-GAGGG-CCUCC-CUGCUGACACCAUAAUCAA-----CACGCA----------------------------CGCGCCG-----CCC---GG-GC--CUCG-----AGC-CC--GG-----ACCC--GGCGCAAUUUUUGGAACC---------------------------
AAVX01595596.1/659-533         -ACCGUCCUU-AUCUUGGGG-UUGUGC-UGCU-G-UUCGAUGAAC-GUGUAGU-GAGAG-CAGCA-CUGCUAACGCCAUCACAACACUGC-----------------------------------GCAUC-AC----CU---GG-AC--CCUG-----AGU-CC--AG-----UUA-CUGGUGCAAUUUUUGGAACC---------------------------
AANG01209374.1/1-113           -GGGG---------UU-------GCGC-UACU-G-UCCAAUGAAC-GUAUAGU-GAGGG-CAGUA-CUGCUAACGCCCUGCACAA-----CACACC----------------------------CGCAUCAAC----UA---AA-GC--UCU-------GC-UU--UA-----CCUU--GGUGCAAUUUUUGGAAAA---------------------------
AAWU01017057.1/6040-5883       -UUCCUCCUU-GUCUCGGGG-A-GCAU--AAC-G-UCCAAUGAAC-GUAUAGU-GAGGA-CGUUG-AUGCUGACACCCAGAUUAUACCAGGACCUAAUCGUCUUG----------GGAAAAACUCCCGCCCGAG--GUG--AUU-GC-UUUCGAA--CAGU-GG-CCA-----CCUG--GGCGGAAUUUUUGGAACG---------------------------
AAJJ01000001.1/47747-47867     -ACCUUCCUU-GUCUGGGGG-A-GCUG--AGU-G-UUCAAUGAUC-AACUAGU-GAGAC-CACUU-CUGCUAGCA--CCCAAACAUUUU-UCUCAU----------------------------CGCAC--------CC---GC-GC--CAA-------GU-GC--AG-----CGA----GUGCAAUUUUUGGAAAG---------------------------
DQ682679.1/205-355             -UUCCUCCUU-GUCUCGGGG-A-GCAU--AAC-A-UCUAAUGAAC-GUAUAGU-GAGGA-UGUUG-AUGCUGACACCCAGAUUGAACCAGGACAUCCUGGC-----------------GAUACCCCCGCUCGGG--GUG---GU-UGCUUUCGAA-CAGUG-AC--CA-----UCUG--GGCGGAAUUUUUGGAACG---------------------------
AAGE02008333.1/19499-19656     -CCCUUCCUU-GUCUUGGGG-A-GCAU--AAU-A-UCCAAUGAAC-GAAUAGU-GAGGG-UAUUG-AUGCUGGCACCCACAUUGAUACGAGCCUUUCGCGCUCGC----------ACUUAAACCCCCGCUCGG---GUG---GCCGC-UUUCGAACAGUGC-GC--UA-----CCUG--GGCGGAAUUUUUGGAACG---------------------------
AAZO01007334.1/46791-46906     -ACCUUCCUU-GUCUGUGGG-A-GUUC--GAC-GUUGCAAUGAUC-GUUUAGU-GAGCU-CGUC--GUGCUAACACAAUUAAUUA-----CGUCAU----------------------------CGUAC--------CC---GA-UU--AUA-------AA-UC--GA------------GUACAAUUUUUGAAGCU---------------------------
AAGV020469602.1/2323-2199      -ACCAUCCUU-UUCUUGGGG-UUGCGU-UACU-G-UCCAAUGAAC-GCCUAGU-GAGAG-CAGUA-CUGCUAACGCCUACACAACACACC----------------------------------CGCAUCG-----GUA---GA-GC--ACU-------GC-UU--UA-----UCUU--GGUGCAAUUUUUGGAAAA---------------------------
AASC02027737.1/1238-1108       -ACUGUCCUU-GUCUUGGGG-U-GCGA-GCUU-G-CUCAAGGAGC-GUUUAGC-GAGAG-CAAGA-CUGCUGACACCCUACAACUACAUGUUGUAGA-------------------------CACGCAUCG------CC---UC-CC--UC--------GG-GA--GG-----UCUG--GGUGCAAUUUAUGGGGGC---------------------------
AAKN02006802.1/64876-65001     -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAAC-GUUUAGU-GAGGA-CAGUA-CUGCUAACACCUGCACAACACAUU----------------------------------CGCAUCAAC----UA---AA-GC--UUC-------GC-UU--UA-----CCUU--GGUGCAAUUUUUGGAAAA---------------------------
CAAK05033158.1/3332-3460       -ACCUUCCUU-GUCUGGGGG-U-GGUU-UGGGCUGUUCAAUGAAG-GUUAACU-GAGAACAUCCC-UGCUAACACCUAA-CCAACACAAU---------------------------------CCGCAUCA------CC---UG-AACUAUUUU---GGUU-CG--GG-----CUAU--GGUGCAAUUUUUGGA------------------------------
AAWR02006087.1/50015-49891     -ACCAUCCUU-UUCUUGGGGCU-GCGC-UACU-G-UCCAAUGAGC-GCAUAGC-GAGGG-CAGUA-CUGCUAACGCCUAAACAACACACC----------------------------------CGCAUCA-----AUA---GA-GC--UCU-------GC-UU--UA-----CCUU--GGUGCAAUUUUUGGAAAA---------------------------
AAWZ02013490.1/81111-81235     -ACCGUCCUU-AUCUUGGGG-UUGCGC-UACU-G-UUCAAUGAAC-GUAUAGU-GAGAA-CAGUA-CUGCUAACGCCUAC-ACAA-----CACUUG----------------------------AGCAUCCC-----UG---GG-GU--CUAG------GC-CC--CA------ACG-UGGUGCAAUUUUUGGAAU----------------------------
AAGW02073287.1/24794-24920     -ACCAUCCUU-UUCUUGGGG-UUGCGU-UACU-G-UCCAAUGAAC-GCAUAGU-GAGGG-CAGUA-CUGCUAACGCCUGAACAACACGUU----------------------------------CGCAUCGGC----UA---AA-AU--UUCG------GU-UU--UA-----GCUC--GGUGCAAUUUUUGGAAAA---------------------------
AADG06006595.1/14072-13949     -UCUAUCCUU-GUCUUGGGG-GAGCAA--AGU-A-UUCAAUGAUC-GUUUAGU-GAGAG-UACUG-UUGCUGAAG--CCCAUUAUUAAUUUAAAUC----------------------------CGCAUC-------CU---CG-UG--UUAU------CA-UG--UG----------AGAUGCAAUUUUUGAAGGC---------------------------
CAAB02003742.1/18728-18856     -GCUUUCCUU-GUCAUGGGG-U-GGUU--GGGAAACUCAAUGAAC-GUAUAGU-GAGAGCUUCCC-UGCUAACACCAUAAUCGACACACA------C--------------------------ACGCGCCA-----CCC---GG-AC--CUUG-----AGU-CC--GG----ACCA--CGGCGCAAUUUUUGGAA-----------------------------
EU240318.1/2-119               -ACCGUCCUU-AUCUUGGGG-UUGCGC-GGCC-G-CUCGAUGAAC-GCGUGGU-GAGAG-CGGCA-CUGCUAACGCCUGA-GCAA-----CACACC----------------------------GAGCGCC------CG---CG-----UGCG---------CG--CG-------CG--GCGC-AAUUUUUGGAACC---------------------------
AAQR03093718.1/17057-17182     -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAGC-GCAUAGU-GAGGG-CAGUA-CUGCUAACACCUAC-ACAA-----CACGCU----------------------------CGCAUCAAU----UA---GA-GC--UUU-------GC-UU--UA-----UAUU--GGUGCAAUUUUUGGAAAA---------------------------
AAPE02048822.1/2601-2476       -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAAC-GCCUAGU-GAGGG-CAGUA-CUGCUAACGCCUAAACAACACGUU----------------------------------CGCAUCAGG----CC---GG-GC--UCU-------GC-UU--UG-----CCUU--GGUGCAAUUUUUGGAACA---------------------------
AAGJ04111208.1/10003-10134     -UCAGUCCUU-AUC-UUGGG-GAAGCAUGAUC-A-UUCAAUGAAC-GUAUAGU-GAGGA-UGAUUUUGCUAACACCAAUUACAAACACAUAC---------------------------------GUCACC------GC--CUA-CAGCUUCGG----CUGAUG-UGU------UUG--GU-GCAAUUUAUGGAAAA---------------------------
FJ916040.1/3-128               -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAGC-GCAUAGU-GAGGG-CAGUA-CUGCUAACGCCUACACAACACACC----------------------------------CGCAUCAAC----UA---AA-GC--UUU-------GC-UU--UA-----CCUU--GGUGCAAUUUUUGGAAAA---------------------------
U62822.1/2-128                 -ACCAUCCUU-UUCUUGGGG-UUGCGC-UACU-G-UCCAAUGAGC-GCAUAGU-GAGGG-CAGUA-CUGCUAACGCCUGAACAACACACC----------------------------------CGCAUCAAC----UA---GA-GC--UUUU------GC-UU--UA-----UUUU--GGUGCAAUUUUUGGAAAA---------------------------
#=GC SS_cons                   .::::<<<<<._____>>>>.>.<<<<.-<<<.<.<<<-----<<._____>>.-->>>.>>>>-.>>>>--------------------------...........................--<<<<<<.....-<<...<<.<<..____....._>>.>>..>>.....--->..>>>>>:::::::::::::...........................
#=GC RF                        .acCuuCCUU.gUCUUGGGG.a.Gcau.uAcu.G.ccCAAUGAaC.GUaUAGu.GAGgg.CagUa.augCUaACaCccuaAuaAuAuaaaaaaauu...........................cCGCgcCc.....gcc...gc.gc..UUua.....agc.gc..gg.....ccUg..GgcGCAAUUUUUGGAAaa...........................
//
# STOCKHOLM 1.0

#=GF AC   RF00619
#=GF ID   U6atac
#=GF DE   U6atac minor spliceosomal RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   PMID:10199569; Daub J, INFERNAL; PMID:18390578
#=GF SS   Published; PMID:11911359
#=GF GA   33.00
#=GF TC   33.00
#=GF NC   32.90
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00009
#=GF DR   SO; 0000274; snRNA;
#=GF DR   GO; 0000244; spliceosomal tri-snRNP complex assembly;
#=GF DR   GO; 0000395; mRNA 5'-splice site recognition;
#=GF DR   GO; 0030622; U4atac snRNA binding;
#=GF DR   GO; 0030627; pre-mRNA 5'-splice site binding;
#=GF DR   GO; 0005691; U6atac snRNP;
#=GF RN   [1]
#=GF RM   15987817
#=GF RT   Evolutionary conservation of minor U12-type spliceosome between plants and
#=GF RT   humans.
#=GF RA   Lorkovic ZJ, Lehner R, Forstner C, Barta A
#=GF RL   RNA. 2005;11:1095-1107.
#=GF RN   [2]
#=GF RM   11911359
#=GF RT   A revised model for U4atac/U6atac snRNA base pairing.
#=GF RA   Padgett RA, Shukla GC
#=GF RL   RNA. 2002;8:125-128.
#=GF RN   [3]
#=GF RM   10199569
#=GF RT   Conservation of functional features of U6atac and U12 snRNAs between
#=GF RT   vertebrates and higher plants.
#=GF RA   Shukla GC, Padgett RA
#=GF RL   RNA. 1999;5:525-538.
#=GF CC   U6atac is an essential component of the minor U12-type spliceosome complex
#=GF CC   which is required for removal of the rarer class of eukaryotic introns
#=GF CC   (AT-AC, U12-type) [1]. U6atac snRNA is proposed to form a base-paired
#=GF CC   complex with another spliceosomal RNA U4atac via two stem loop regions.
#=GF CC   These interacting stem loops have been shown to be required for in vivo
#=GF CC   splicing [2]. U6atac is the functional analog of U6 (Rfam:RF00026) in the
#=GF CC   major U2-type spliceosomal complex [2].
#=GF WK   U6atac_minor_spliceosomal_RNA
#=GF SQ   62


CAAA01028316.1/26512-26387     GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUUGGGCCU----AACA--AC-A-CAC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCACUGUUUUUU
AAYZ01599293.1/336-461         GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU----GACA--AC-A-CAC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCACUGUUUUUU
AAPY01744295.1/591-466         GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU----GACA--AC-A-CAC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCAAUGUUUUUU
AC183599.3/63444-63319         GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU----GACA--AC-A-CGC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCAUCGUUUUUU
BX649601.2/4054-3929           GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU----GACA--AC-A-CGC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCAUCGUUUUUU
AAIY01760151.1/509-384         GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU----UACA--AC-A-CGC---AUAU-GGUU-A---AGGCAUUGCCAC-CUACUUUGUG--GCAUC-U-------AACCACGGUUUUUU
AANU01299069.1/15065-14940     GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU----GACA--AC-A-CGC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCAUCGUUUUUC
BAAE01147435.1/439-566         GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAAU--GGCC-AUUUGGCC-----UGCA--AC-A-CAC---AUA--UGGUUA---AGGCAUUGCCAU-CUACUUCGUG--GCAUCUCU-----AACCAAGUUUUUUCU
AL928952.15/74115-73987        GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA-GGUCC-UAGUGGCC-----UUCA--AC-A-CAC---AUA--UGGUUA---AGGCAUUGCCAC-CUACUUCGUG--GCAUCUCU-----AACCAAGUUUUUUAU
AANH01007720.1/11181-11056     GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAUU-GGCCC-UUGUGGCC-----AUCA--AC-A-CAC---AUAC-GGUUA----AGGCACUGCCAC-CUACUUCGUG--GCAUC-UA-----UAACCA--AUUUUUU
AAPN01090305.1/573-700         GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGAGAAGGAUGGAAGA-GGUCC-UAGUGGCCU---UUACA--AC-A-CAC---AUAU-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCAAGUUUUUUU
AAFR03046662.1/75898-75771     GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGAUAAGGAUGGAAGA-GGUCC-UAGUGGCCU---UUACA--AC-A-CAC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUCUGUG--GCAUC-U-------AACCAUGUUUUUUU
CAAE01014979.1/1396163-1396289 GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA-GGCCC-CUGAGGCC-----UUCA--AC-A-CAC---AUAC-GGUUA----AGGCAUUGCCAC-CUACUUUGUG--GCAUC-UC-----UAACC-AAGUUUUUU
AAQQ01357191.1/625-500         GUGUUGUAUGAAAGGAGAGAAGUUUAGCACUCCCCUUGACAAGGAUGGAGAG--AGCC-CUCGGGCCU----GACA--AC-A-CGC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCAUCGUUUUUU
AANN01364098.1/913-791         GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAA---GAGGC-UUCGGCCU------GCA--AC-A-CAC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCGCCGUUUUUU
AAFC03110924.1/13969-14094     GUGUUGUAUGAAAGUAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCU-CUCGGGCCU----GACA--AC-A-CGC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCACUGUUUUUG
ABDC01122599.1/5804-5930       GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCUCUUGACAAGGAUGGAAGA--GGCU-CUCGGGCCU---GUACA--AC-A-CGC---AUAC-GGUU-G---AGGCGUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCAUCAUUUUUC
AANG01228883.1/1813-1689       CUGUUGUAUGAAAGGAGAGAAGGUUA-CACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU----GACA--AC-A-CGC---AUAU-GGUU-A---AGGCAUUGCCAC-CUACUUCAUG--GCAUC-U-------AACCAACGUUUUUC
ABAV01010855.1/55980-56108     GUGUUGUAUGAGCCGAGAGAAGGUUAGCAUCUCCCUCGAUAAGGACGAGAAA--AGUC-UUCGGACUU----UCAA--CCUA-CAA---CACG-UGGUUA---AGGCUAUGCCAC-CUACUUCGUG--GCAU--CU-----AACCAUUUUUAUUUU
AALT01218593.1/1417-1294       GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGCAUGGAA---GAGGC-UUUGGCCU-----UGCA--AC-A-CGC---AUAC-GGUU-U---AGGCACUGCCCC-CUACUUCGUG--GCAAC-U-------AACCAACGUUUUUA
AM444126.1/611-737             GUGUUCGUAGAAAGGAGAGACGGUUGGCAUYUCCCCUGACAGGGACGGGAAC--AGCC-UUCGGGCUUACCUGUUA--CC-A-CAC---AUCC-GGUUA----AGGCUUUCCACU------UCGGU--GGAUC-UC-----UAACCCAAUUUUUUU
AAVX01192849.1/1182-1306       GUAUCGUAUGAAAGAAGAGAAGGUUAACACUCCCCUUGAUAAGGAUGGAAGA-GGCCC-UUGUGGUC-----UUCA--CA-A-CAC---AUAA-UGGUUA---AGGCAUUGCCAC-UAACUUCGUG--GCAU--CU-----AACCA---GGUUUGU
AARH01009456.1/107284-107413   GUGUUCGUAGAAAGGAGAGAUGGUUGGCAUCUCCCCUGACAGGGACGGGAAC--AGCU-UUCGGGCUUCCCUGUUA--CC-A-CAC---AUCC-GGUUA----AGGCUCUCCACC-UUAUA--GGU--GGAUC-UA-----UAACCAAUUUUUUUU
AATU01001737.1/24057-24182     GUGUUCGUUGAGCCGAGAGAAGGUUAGCAUCUCCCUCGACAAGGACGGGAUU--GCGC-GUUUGCGUA----UCCA--AC-C-ACU---GGAU-GGUUUA---AGCUCUGUCAUC-CUUCUG-GAA--GAC---AU-----CUACCAGUUUUUUUU
AB006702.1/57908-57786         GUGUUCGUAGAAAGGAGAGAUGGUUGGCAUCUCCUCUGACAGAGACGGGAUU-UGACC-UUCGGGUCU----UUGA--AC-A-C-----AUCC-GGUU-A---AGGCUCUCCACA--UUCG--UGU--GGAUCUA-------AACCCAAUUUUUUU
AAQX01000572.1/261237-261360   GUGUUCGUUGAGCCGAGAGAAGGUUAGCAUCUCCCUCGACAAGGACGGGAUU--GCGC-GUAUGCGUA----UCCA--AC-C-ACU---GGAU-GGUUUA---AGCUCUGUCCUC-CUUCGU-GAA--GAC---AU-----CUACCA--GUUUUUU
AACV01010025.1/8651-8774       GUGUUCGUAGAAAGGAGAGACGGUUGGCAUCUCCCCUGACAGGGACGGGAAC--AGUC-UUCGGACUU----UCCU--CU-AGCAC---AUUG-CGGUUA---AGGCUACCCGCU------UCGGC--GGAU--CU-----UACCCAAAUUUUUUU
AAAA02014235.1/7862-7985       GUGUUCGUAGAAAGGAGAGACGGUUGGCAUCUCCCCUGACAGGGACGGGAAC--AGUC-UUCGGACUU----UCCU--CU-AGCAC---AUUG-CGGUUA---AGGCUACCCGCU------UCGGC--GGAU--CU-----UACCCAAAUUUUUUU
AASG02012151.1/2297-2169       GUGUUCGUAGAAAGGAGAGAUGGUUGGCAUCUCCCCUGACAGGGACGGGAAC--AGCC-UUCGGGCUUACCUGUUA--CCAA-CAC---AUCC-GGUUA----AGGCUACCCACU-UCU----GGU--GGAUC-UA-----UAACCCAAUUUUUUU
CR931738.1/64387-64518         GUGUUCGUGAAAAGGAGAGAUGGUUGGCAUCUCCCCUGACAGGGAUGGGAAC--AGCU-UUCGGGCUU----UCCU-GUU-A-CAC---ACCU-CGGUUA---AGGCUAUCCACCUCUUUGAGGUU--GGAUCUAU-----AACCCAAUUUUUUUU
AABS01000563.1/22545-22672     GUGUUGAAUAAAAGGAGAGCUGGUUAGCACUCCCCUUGAUAAGGACGGACAU-GUUGA-UUGGUUCAGC-CAUUCA--AU-A-CAU---AUAA-UGGAUA---AGGCACUGUCAC-CAU----GUG--GCAU--CU-----AUCCAUGUUUUGUAU
AACT01025174.1/9090-8972       GUGUUGAAAAAAAGGAGAGCCGGUUAGCACUCCCCUUGAUAAGGACGGAAAU-UGAUUGGUUCACCCU----UUCA--AU-A-CAU---AUAA-UGGAUA---AGGCACUGCCA---------UUG--GCAU--CU-----AUCCA---UAUUUUU
AACW02000079.1/158271-158139   UGGUUAAUAGAAAGGAGAGAACUUUGGCAAUCCCCUUGAGAAGGACGGAAU---GAGC-UUUUGCUCA---ACAUA--AC-A-CAC---CGUG-UGUGUUUGAAGGCAUCGCUCC------UCGGA--GCAUCUUGGCAUAUUGCCACUAUUUUUU
AAZX01006114.1/1257-1360       GUGUUGUAUGAAAGGAGAGAAGUUUAGCACUCCCCUAGACAAGGAUGGAA-----------------------------C-A-CAU---AUAC-UCGUAA---GGCACUGGUCGC-UUUAU--GCG--GCU---CU-----UACGA-CAUUUUUUU
BT013253.1/908-785             GUGUUCAUAGAAAGGACAGAUGACUGGCAUCACCGGCGACAGGGAUGGGAAU--AGCC-UUCGGGUU-----------------UU---ACCU-GU-CAU--CAAACAACAUUCU-ACUCUUUCGU--AUGCUUACC--AGUGUACACCUAUUUUU
AATT01000139.1/79978-80095     GUUAUGUAGAGAAGGAGAGAAGUUCGGCAGUCCCCAGGGCAUGGACGGACUC-GACCU-CAGAGGUUG----GAUU--UC-A-CUCCUGAAUU-UCCC-----------UGCACG-AAGGU--CUU--GCA-----------GGGAGCGACUUUGU
AAZO01001575.1/56592-56488     GUGUUGUAUGAAAGGAGAGACGGUUAGCACUCCCCUAGACAAGGAUGGAAUA--------------------------AC-A-CAU---AUAC-GGUU-A---AGGCACCGCUGC-CAC----GCA--GCACU-U-------AACCACAUUUUUUU
AAJJ01001449.1/7560-7468       GUGUAGUAUGAAAGGAGAGACGGUUAGCACUCCCCUAGACAAGGUUGGAAAC-----------------------------A-CAA---AUAC-GGUU-----------GAGCGU-CGC----ACA--CUC-----------AACCCCAUUUUUUU
AAPP01015683.1/52721-52818     GUGUUGUUUGAAAGGAGAGCAAGUUAGCACUCCCCUAGACAAGGAUGGAA-----------------------------C-A-CAU---AAAC-GGUC-----------GGCUGG-GCACAAGACAAAGCC-----------GACCACAAGUUUUU
AAAB01008834.1/2046617-2046743 GUGUCAUUUGAAAGGAGAGCAGGUUAGCACUCCCCUUGACAAGGAUGGAACACAUACC-CUGAGAUCA----GUGG--GC-A-CCC---AGAG-AAAA-C---CUGAUCUCGGCC-AUUUU--UUU--CGAUGAC-------UUUUAGGUUUUUGC
AAEU02000320.1/440756-440853   GUGUUGUUUGAAAGGAGAGCAAGUUAGCACUCCCCUAGACAAGGAUGGAA-----------------------------C-A-CAU---AAAC-GGUC-----------GGCUAG-GCACAAGACAAAGCC-----------GGCCACAAUUUUUU
AAQB01009459.1/49853-49949     GUGUUGUUUGGAAGGAGAGCAAGUUAGCACUCCCCUAGACAAGGAUGGAA-----------------------------C-A-CAU---AAAC-GAAC-----------GGCUAGGCACAAGACGA--GCC-----------GUUCACAAGUUUUU
AAGH01003552.1/12826-12730     GUGUUGUUUGGAAGGAGAGCAAGUUAGCACUCCCCUAGACAAGGAUGGAA-----------------------------C-A-CAU---AAAC-GGUC-----------GGCUAGGCACAAGACAA--GCC-----------GUCCACAAAUUUUU
AAKO01001003.1/37151-37250     GUGUUGUUUGGAAGGAGAGCAAGUUAGCACUCCCCUAGACAAGGAUGGAACA---------------------------------C---AUAA-GCGG-G---CGGCUAGGCACA-AGACAAA-----GCCG--U-------CCACAAAUUUUUUU
AAPU01010547.1/33911-34008     GUGUUGUUUGGAAGGAGAGCAAGUUAGCACUCCCCUAGACAAGGAUGGAA-----------------------------C-A-CAC---AAAC-GAAC------GGCUAGGCACA-AGACGAU-----GCC-----------GUUCACAAGUUUUU
AE014134.5/8389724-8389821     GUGUUGUUUGGAAGGAGAGCAAGUUAGCACUCCCCUAGACAAGGAUGGAA-----------------------------C-A-CAU---AAAC-GGUC-----------GGCUAG-GCACAGACAAAAGCC-----------GUCCACAAAUUUUU
AAGV020679998.1/1503-1377      GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU---GUACA--AC-A-CGC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCACUGUUUUUU
AAWR02025949.1/23784-23659     GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU----GACA--AC-A-CGC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUUGUG--GCAUC-U-------AACCACUGUUUUUU
AF459089.1/1-98                GUGUUGUUUGGAAGGAGAGCAAGUUAGCACUCCCCUAGACAAGGAUGGAA-----------------------------C-A-CAU---AAAC-GGUC------GGCUAGGCACA-GACAAAA-----GCC-----------GUCCACAAAUUUUU
U62823.1/1-125                 GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU----GACA--AC-A-CGC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCAU-CGUUUUU
AAPE02058594.1/5213-5338       GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCU-CUCGGGCCU----AACA--AC-A-CAC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCACUGUUUUUU
AAQY02000150.1/161480-161605   GUGUUCGUUGAGCCGAGAGAAGGUUAGCAUCUCCCUCGACAAGGACGGGAUU--GCGC-GUAUGCGUA----UCCA--AC-C-ACU---GGAU-GGUUUA---AGCUCUGUCCUC-CUCCGU-GAA--GAC---AU-----CUACCAGUUUUUUUU
AAEX03013616.1/398431-398554   GUGUUGUAUGAAAGGAGAGAAG---AGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUUGGGCCU----GACA--AC-A-CAC---AUAC-AGUUA----AGGCAUUGCCAC-CUACUUCGUG--GCAUC-C------UAACCAACGUUUUUU
AAGJ04126514.1/344-221         GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGAUAAGGACGGAAUU--CACC-CUCGGGUG------ACA--AC-A-CAC---AAAU-GGUU-A---AGGCACUGCCAC-UUACUUUGUG--GCAUC-U-------AACCACGUUUUUAC
AAGU03091125.1/29113-28988     GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUCGGGCCU----UACA--AC-A-CGC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUUGUG--GCAUC-U-------AACCACUGUUUUCU
AADN03007294.1/67995-68122     GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGAUAAGGAUGGAAGA-GGCCC-UAGUGGCCU---AUACA--AC-A-CGC---AUAC-GGUU-A---AGGCACUGCCAC-CUACUUCGUG--GCAUC-U-------AACCAUGUUUUUUC
AADG06005625.1/18064-17957     GUGUAGUAUGAAAGGAGAGACGUUUAGCACUCCCCUAGACAAGGAUGGAAUA---------------------------C-A-CAU---AUAAAUGGU-A---AGGCACUGUCGU-CCUUCG-GCG--ACACU-U-------ACCAAAUUUUUUUU
CAAB02028083.1/1473-1346       GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA-GGCCC-CUGUGGCC-----UUCA--AC-A-CAC---AUAC-GGUUA----AGGCAUUGCCAC-CUACUUCGUG--GCAUC-UC-----UAACCAAGUUUUUUU
AABR05098970.1/41388-41263     GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUUGGGCCU----AACA--AC-A-CAC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUUGUG--GCAUC-U-------AACCACUGUUUUUU
AAQR03101741.1/17340-17465     GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUUGGGCCU----AACA--AC-A-CGC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCAUG--GCAUC-U-------AAUCAUUGUUUUUU
AAWZ02010676.1/197194-197067   UAGUUGUAUGAAACAAGAGGAGGGUAGCAGUUCCCUUAAUAAGGAAAGUCAC--GGUC-CCAGGGUUC----UGUAGAAC-A-CAC---AUAU-GGUU-A---AGGCAUUGUCAC-UUACUGUGUC--GCAUA-U-------AACCAAGUAAUUUU
AL772282.9/116596-116471       GUGUUGUAUGAAAGGAGAGAAGGUUAGCACUCCCCUUGACAAGGAUGGAAGA--GGCC-CUUGGGCCU----AACA--AC-A-CAC---AUAC-GGUU-A---AGGCAUUGCCAC-CUACUUCGUG--GCAUC-U-------AACCACUGUUUUUU
#=GC SS_cons                   ::::::::::::::::::::::::::::::::::::::::::::::::::::..<<<<.____>>>>-....----..--.-.---...----.<<<<.-...------<<<<<<._______>>>..>>>--.-.......>>>>::::::::::
#=GC RF                        GUGUUguauGAAAGGAGAGAAGGUUAGCAcUCCCCUuGACAAGGAuGGAAaa..ggcC.uUcgGgccu....uacA..aC.A.Cac...AuAu.gguu.A...AGGCauugCccc.cuacuucggg..GcaUc.u.......aaccAauuUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00620
#=GF ID   HCV_ARF_SL
#=GF DE   Hepatitis C alternative reading frame stem-loop
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   80.00
#=GF NC   79.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   17299041
#=GF RT   Evidence for a functional RNA element in the hepatitis C virus core gene.
#=GF RA   McMullan LK, Grakoui A, Evans MJ, Mihalik K, Puig M, Branch AD, Feinstone
#=GF RA   SM, Rice CM
#=GF RL   Proc Natl Acad Sci U S A. 2007;104:2879-2884.
#=GF CC   The core protein-coding region of the Hepatitis C virus (HCV) genome
#=GF CC   contains a +1 alternative reading frame (ARF) and two proposed
#=GF CC   phylogenetically conserved RNA helix-forming stem loop structures [1]. The
#=GF CC   proteins translated from the ARF appear to be translated during the normal
#=GF CC   viral life cycle but are not essential to virus replication [1]. The two
#=GF CC   predicted stem loops included in this model (SLV and SLVI) are proposed to
#=GF CC   be important for HCV translation and repression [1]. These stem loops are
#=GF CC   located downstream of the IRES site but their functional role is unknown
#=GF CC   [1].
#=GF WK   Hepatitis_C_alternative_reading_frame_stem-loop
#=GF SQ   36


AF512996.1/25-177  AGAAAAACCAAACGUAACACCAGCCGUCGCCCACAGGACGUCAAGUUCCCGGGCGGCGGCCAGAUCGUUGGUGGAGUUUACUUGUUGCCGCGCAGGGGCCCUAGAUUGGGUGUGCGCGCGACGAGGAAGACUUCCGAGCGGUCGCAACCUCGA
AB061931.1/25-177  AGAAAAACCAAACGUAACACCAACCGCCGCCCACAGGACGUCAAGUUCCCGGGCGGUGGUCAGAUCGUUGGUGGAGUUUACCUGUUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCGCGACUAGGAAGACUUCCGAGCGGUCACAACCUCGU
D28833.1/213-365   AGACUAACCAAGAGAAACACCUACCGUCGCCCAAUGGACGUCAAGUUCCCGGGCGGCGGUCAGAUCGUGGGUGGAGUUUACUUGUUACCGCGCAGGGGCCCGAGAUUGGGUGUGCGCGCGACGAGGAAGACUUCCGAACGGUCCCAGCCCAGA
L38350.1/263-415   AGAAAAACCAAACGCAACACCAACCGCCGCCCACAGGACGUUAAAUUCCCGGGUGGGGGGCAGAUCGUGGGUGGAGUUUACUUGUUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCGCGACGAGGAAGACUUCCGAGCGGUCGCAACCUCGC
AY835332.1/49-201  AGACAAACCAAAAGAAACACCAACCGCCGCCCAAUGGACGUUAAGUUCCCGGGUGGCGGCCAGAUCGUCGGUGGAGUCUACUUAUUGCCGCGCAGGGGCCCUAGAUUGGGUGUGCGCGCGACGAGGAAGACCUCCGAACGGUCCCAGCCCAGA
AY859526.1/320-472 AGAAAAACCAAAAGAAACACCAACCGUCGCCCAAUGGACGUCAAGUUCCCGGGUGGCGGUCAGAUCGUUGGCGGAGUUUACUUGUUGCCGCGCAGGGGCCCCCGGUUGGGUGUGCGCGCGACGAGAAAGACUUCCGAGCGAUCCCAGCCCAGA
D37850.1/363-515   AGAAAAACCAAAAGAAACACUAACCGUCGCCCUAUGGACGUCAAGUUCCCGGGCGGCGGCCAGAUCGUUGGUGGAGUCUACUUGUUGCCGCGCAGGGGCCCGAGAUUGGGUGUGCGCGCGACGAGAAAGACCUCAGAACGGUCCCAGCCCAGA
D38078.1/363-515   AGAAAAACCAAAAGAAACACCAACCGCCGCCCACAGGACGUCAAGUUCCCGGGCGGUGGUCAGAUCGUCGGUGGAGUGUACUUGCUGCCGCGCAGGGGCCCCCGGUUGGGUGUGCGCGCAACAAGGAAGACUUCAGAACGAUCCCAGCCCAGA
D84263.2/363-515   AAAAGAAACCAAAGAAACACAAACCGUCGCCCACAGGACGUCAAGUUCCCGGGUGGCGGUCAGAUCGUUGGUGGAGUCUACUUGCUGCCGCGCAGGGGCCCCCGGUUGGGUGUGCGCGCGACGAGGAAGACUUCUGAACGGUCCCAGCCCAGA
AY835218.1/49-201  AGACUAACCAAAAGAAACUCUAACCGUCGCCCACAAGACGUUAAGUAUCCGGGCGGCGGCCAGAUCGUUGGCGGAGUAUACUUGUUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCGCGACAAGGAAGACUUCGGAGCGGUCCCAGCCACGU
AY622926.1/80-232  AGAAAAACCAGAAGAAACACAAACCGCCGCCCACAGGACGUUAAGUUCCCGGGUGGCGGCCAGAUCGUUGGCGGAGUUUACUUGCUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCACAACAAGAAAGACUUCCGAGCGAUCCCAGCCGCGU
AY835219.1/49-201  AGACUAACCAAAAGAAACACUAACCGCCGCCCACAGAACGUUAAGUUCCCGGGCGGUGGCCAGAUCGUUGACGGAGUAUACUUGUUGCCGCGUAGGGGCCCCCGGUUGGGUGUGCGCGCAACGAGGAAAACCUCCGAACGGUCCCAGCCACGU
L12355.1/338-490   AGAAAAACCAAAAGAAACACCAUCCGUCGCCCACAGGACGUCAAGUUCCCGGGUGGCGGCCAGAUCGUUGGUGGAGUAUACGUGUUGCCGCGCAGGGGCCCACGAUUGGGUGUGCGCGCGACCCGUAAAACUUCUGAAUGGUCACAGCCUCGC
AY838814.1/38-190  AGAAAAACCAAACGUAACACCAACCGCCGCCCCAUGGACGUCAAGUUCCCGGGUGGUGGCCAGAUCGUUGGCGGAGUUUACUUGUUGCCGCGCAGGGGCCCUCGGUUGGGUGUGCGCGCGACUCGGAAGACUUCGGAGCGGUCGCAACCUCGU
AB047639.1/365-517 AGAAAAACCAAAAGAAACACCAACCGUCGCCCAGAAGACGUUAAGUUCCCGGGCGGCGGCCAGAUCGUUGGCGGAGUAUACUUGUUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCACGACAAGGAAAACUUCGGAGCGGUCCCAGCCACGU
AB162873.1/209-361 AGACAAACCAAAAGAAACACAAACCGUCGCCCACAGGACGUUAAGUUCCCGGGCGGCGGUCAAAUCGUUGGUGGAGUUUACUUGUUGCCGCGCAGGGGCCCUCGUUUGGGUGUGCGCGCGACGAGGAAGACUUCGGAACGAUCCCAGCCCAGA
DQ061301.1/272-424 AGAAAAACCAAACGUAACACCAACCGCCGCCCACAGGACGUUAAGUUCCCGGGUGAUGGUCAAAUCGUUGGUGGAGUUUACUUGUUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCGCGACGAGGAAGACUUCCGAGCGGUCGCAACCUCGA
AY155455.1/37-189  AGACAAACCAAAAGAAACACCAUCCGUCGCCCACAGGACGUUAAGUUCCCGGGCGGUGGACAGAUCGUUGGUGGAGUAUACGUGUUGCCGCGCAGGGGCCCGCGAUUGGGUGUGCGCGCGACGCGUAAAACUUCCGAGCGGUCGCAGCCUCGC
D14669.1/49-201    AGAAAAACCAAAAGAAACACCAACCGUCGGCCACAAGACGUUAAGUUUCCGGGCGGCGGUCAGAUCGUUGGCGGAGUAUACUUGCUACCGCGCAGGGGCCCCAGGUUGGGUGUGCGUGCGACUAGGAAGACUUCCGAGCGGUCCCAACCUCGU
D84265.2/363-515   AGAAAAACCAAAAGAAACACUAACCGUCGCCCUAUGGACGUCAAGUUCCCGGGCGGCGGCCAGAUCGUUGGUGGAGUUUACUUGUUGCCGCGCAGGGGCCCUCGUUUGGGUGUGCGCGCGACGAGGAAGACUUCCGAACGGUCCCAGCCUAGA
AY051292.1/366-518 AGAAAAACCAAACGUAACACCAACCGACGCCCACAGAACGUUAAGUUCCCGGGUGGCGGCCAGAUCGUUGGCGGAGUUUGCUUGUUGCCGCGCAGGGGUCCCAGAGUGGGUGUGCGCGCGACGAGGAAGACUUCCGAGCGGUCACAACCUCGC
L48498.1/263-415   AGACAAACCAAAAGAAACACCAACCGCCGCCCACAGGACGUUAAGUUCCCGGGCGGUGGCCAGAUCGUUGGCGGGGUGUACUUGUUGCCGCGCAGGGGCCCCAGAGUGGGUGUGCGCGCGACGAGAAAGACCUCGGAGCGGUCCCAGCCGCGU
U94724.1/331-483   AGAAAAACCAAACGUAACACCAACCGCCGCCCAAUGGACGUUAAGUUCCCGGGUGGCAGCCAGAUCGUUGGCGGAGUUUACUUGUUGCCGCGUAGGGGCCCUAGAUUGGGUGUGCGCGCGACUAGGAAGACUUCGGAGCGGUCGCAACCUCGU
D88474.1/363-515   AGAAAAACCAAAAGAAACACCAACCGCCGCCCACAGGACGUCAAGUUCCCGGGUGGUGGUCAGAUCGUCGGUGGAGUUUACUUGUUGCCGCGCAGGGGCCCUCGUUUGGGUGUGCGCGCGACGAGGAAAACUUCUGAACGGUCCCAGCCUAGG
L38319.1/263-415   AGAAAAACCAAAAGAAACACUAACCGCCGCCCACAGGACGUUAAGUUCCCGGGCGGUGGCCAGAUCGUUGGCGGAGUAUACUUGCUGCCGCGCAGGGGCCCGAGAUUGGGUGUGCGCGCGACGAGGAAAACCUCCGAACGGUCCCAGCCACGU
AY155449.1/37-189  AGACAAACCAAAAGAAACACACCCCGUCGCCCACAGAACGUUAAGUUCCCGGGCGGCGGGCAGAUCGUUGGUGGAGUAUACGUAUUGCCGCGCAGGGGCCCACGGUUGGGUGUGCGCGCAGUGCGUAAGACUUCCGAGCGGUCGCAACCUCGC
Y13184.1/304-456   AGAAAAACCAAAAGAAACACCAACCGCCGCCCACAGGACGUCAAGUUCCCGGGCGGUGGUCAGAUCGUUGGUGGAGUUUACUUGUUGCCGCGCAGGGGCCCUAAAUUGGGUGUGCGCGCGACUCGGAAGAAUUCGGAACGGUCGCAACCCCGU
AY070167.1/229-381 AGAAAAACCAAAAGAAACACAAACCGCCGCCCACAGGACGUCAAGUUCCCGGGCGGUGGCCAGAUCGUUGGCGGAGUAUACUUGUUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCACGACGAGGAAGACUUCCGAACGGUCCCAGCCACGU
AY434111.1/271-423 AGAAAAACCAAAAGAAACACUAACCGUCGCCCACAGGACGUUAAGUUCCCGGGUGGCGGCCAGAUCGUUGGUGGAGUAUACCUGUUGCCGCGCAGGGGCCCCCGGUUGGGUGUGCGCGCGACUAGGAAGACUUCCGAACGGUCCCAGCCCAGA
AB162863.1/209-361 AGAAUAACCAAAAGAAACAUAUGCCGUCGCCCACAAGACGUUAAGUUUCCGGGUGGCGGCCAGAUCGUUGGCGGAGUAUACUUGUUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCGCGACAAGGAAGGCUUCGGAGCGGUCCCAGCCACGU
AY835205.1/49-201  AGAAAAACCAAAAGAAAUACUAACCGUCGCCCACAAGACGUUAAGUUUCCGGGCGGCGGCCAGAUCGUUGGCGGAGUAUACUUGUUACCGCGCAGGGGCCCUCGGUUGGGUGUGCGCGCGACAAGGAAGACUUCGGAGCGGUCCCAGCCACGU
X76411.1/53-205    AGAAAAACCAAAAGAAACACUAACCGCCGCCCACAGGACAUUAAGUUCCCGGGCGGCGGCCAGAUCGUCGGCGGAGUGUACUUGUUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCGCGACGAGGAAAACUUCCGAACGGUCCCAGCCACGU
AB162870.1/209-361 AGAAAAACCAAAAGAAACACCAACCGUCGCCCACAGGACGUUAAGUUCCCGGGUGGCGGUCAGAUCGUUGGUGGAGUUUACUUGUUGCCGCGCAGGGGCCCUCGGUUGGGUGUGCGCGCGACGAGAAAGACUUCUGAACGGUCCCAGCCCAGA
AY232732.1/329-481 AGAAAAACCAAAAGAAACACAAACCGCCGCCCACAGGACGUCAAGUUCCCGGGUGGUGGUCAGAUCGUUGGCGGAGUUUACUUGCUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCGCGACAAGGAAGACUUCUGAGCGAUCCCAGCCGCGU
D49756.1/367-519   AGAAUAACCAAAAGAAACACCAACCGUCGCCCACAGGACGUUAAGUUUCCGGGUGGCGGUCAGAUCGUUGGCGGAGUAUACUUGUUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCGCGACGAGGAAGACUUCCGAACGGUCCCAGCCGCGU
L38333.1/263-415   AGAAAAACUAAAAGAAACACUAACCGUCGCCCACAGGACGUUAAGUUCCCGGGCGGCGGCCAGAUCGUUGGCGGAGUUUACUUGUUGCCGCGCAGGGGCCCCAGGUUGGGUGUGCGCGCGCCAAGGAAGACUUCUGAACGGUCCCAGCCACGU
#=GC SS_cons       ::::::::::::::::::::::<<<<<<<<<<---<<<<_____>>>>-->>>>>>>>>>--<<<<<<<--<<<<<<<<-<<<<<<<<-<<<<<---<<<<______>>>>->>>>>>>>>>->>>->>>>>>>->>>>>>>>::::::::::
#=GC RF            AGAaaAACCAAAaGaAACACuAgCCgcCgCCCAcAGgaCGUuAAGucCCCGGGcGgcGGcCAGacCGuuGGcGgaGucuAccuGucGCCGCGCaGGGgCCCuaGgUUGGGuGuGCGCGCgaCgaggAagaCuuCugaaCGguCcCAgCCucGu
//
# STOCKHOLM 1.0

#=GF AC   RF00621
#=GF ID   CoTC_ribozyme
#=GF DE   Beta-globin co-transcriptional cleavage ribozyme
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Daub J
#=GF SS   Published; PMID:15565159
#=GF GA   58.00
#=GF TC   59.90
#=GF NC   57.90
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF RN   [1]
#=GF RM   11389836
#=GF RT   Multiple transcript cleavage precedes polymerase release in termination by
#=GF RT   RNA polymerase II.
#=GF RA   Dye MJ, Proudfoot NJ
#=GF RL   Cell. 2001;105:669-681.
#=GF RN   [2]
#=GF RM   15565159
#=GF RT   Autocatalytic RNA cleavage in the human beta-globin pre-mRNA promotes
#=GF RT   transcription termination.
#=GF RA   Teixeira A, Tahiri-Alaoui A, West S, Thomas B, Ramadass A, Martianov I,
#=GF RA   Dye M, James W, Proudfoot NJ, Akoulitchev A
#=GF RL   Nature. 2004;432:526-530.
#=GF CC   Transcription termination of RNA polymerase II transcripts is proposed to
#=GF CC   occur by a two stage process [1]. The first stage involves pre-termination
#=GF CC   cleavage (PTC) of the nascent transcript downstream of the poly(A) site.
#=GF CC   This process is also referred to as co-transcriptional cleavage (CoTC).
#=GF CC   The CoTC process in the human beta-globin gene has been shown to involve
#=GF CC   an RNA self-cleaving activity located in the 3' flanking region of the
#=GF CC   beta-globin gene. This Rfam model represents the catalytic core of the
#=GF CC   beta-globin CoTC ribozyme. The CoTC core is highly conserved in the 3'
#=GF CC   flanking regions of other primate beta-globin genes [2]. Functionally,
#=GF CC   this CoTC ribozyme resembles the 3' processive, self-cleaving ribozymes
#=GF CC   described for the protein-encoding genes from the myxomycetes Didymium
#=GF CC   iridis and Physarum polycephalum [2].
#=GF WK   Beta-globin_co-transcriptional_cleavage_ribozyme
#=GF SQ   10


AF205413.1/1614-1793 GCAUAGUGUUACUAUCAACAAC----CUUUACUUCAUUUA-CUUGUUCAAUAGCCAGGUAGGUAGAUGCUAGAUUCUAGAAAU----AAAAUAUGAGUCUCAAGUGGCCCUUGUCCCCUCUUCUACUCAAAUUCUGAAUCUAGUUGGCAAGAUUCUGAAAUCAAGGCAUAUAGUCGGU-------GAUGAUAGAAG----
U60902.1/53342-53532 GCAUAGUAUUACCAUCAGCAACACACCUUACCUUCGUUUUUUUCAUUCAGUACAUAGGU-GGUAGAUGCUAGACUGCAGGAAUGAAUAAAACAUGAGUCUCAGGUGGUCUCUGUCCCUUGUUUCAUCCUAAUUCU-AAUUUAGUUGGUAACAUUUUGAAAGUACUGCAUAUA-UCAGUA-UAAGUGAUGAUCGAA-----
AF205412.1/1675-1853 GCAUCCUGUUACCAUCAACAAC----CUUAACUUCAUUUA-CUUAUUCAAUAGCUGGGUAGGUAGAUGCUAGAGUCUACAAA-----AUAAAAUGAGUCUCAAGUGGUCCUUGUCCCCUCUCCUACUCAAAUUCUGAAUCUAGUUGACAAAAUUCUGAAAUCAAGGCAUAUAGUCAGU-------GAUGAUAGAAG----
AY034472.1/822-1013  GCAUAGUGUUACCAUCAACCAC----CUUAACUUCAUUUUUCUUAUUCAAUACCUAGGUAGGUAGAUGCUAGAUUCUGGAAAU----AAAAUAUGAGUCUCAAGUGGUCCUUGUCCUCUCUCCCAAUCAAAUUCUGAAUCUAGUUGGCAAGAUUCUGAAAUCAAGGCAUAUAAUCAGUAAUAAGUGAUGAUAGAAGGGUA
AF205410.1/1079-1269 GCACAGUGUUACCAUCAACAAC----CUUAACUUCAUUUU-CUUAUUCAAUGCCUAGGUAGGUAGAUGCUAGAUUCUGGAAAU----AAAAUAUGAGUCUCAGGUGGUCCUUGUCCUCUCUCCUAGUCGAAUUCUGAAUCUAGUUGACAAGAUUCUGAAAUCAAGGUGUAUAAUCAGUAAUACGUGAUGAUAGAAGGGUA
AF205411.1/1080-1270 GCACAGUGUUACCAUCAACAAC----CUUAACUUCAUUUU-CUUAUUCAAUGCCUAGGUAGGUAGAUGCUAGAUUCUGGGAAU----AAAAUAUGAGUCUCAGGUGGUCCUUGUCCUCUCUCCUAGUCGAAUUCUGAAUCUAGUUGACAAGAUUCUGAAAUCAAGGUGUAUAAUCAGUAAUACGUGAUGAUAGAAGGGUA
AF205408.1/1069-1260 GCAUAGUGUUACCAUCAACAAC----CUUAACUUUAUUUUUCUUAUUCAAUACCUAGGUAGGUAGAUGCUAGAUUUUGGAAAU----AAAAUAUGAGUCUCAAGUGGUCCUUGUCCUCUCUCCCAGUCGAAUUCUGAAUCUAGUUGGCAAGAUUCUGAAAUCAAGGCAUAUAAUCAGUAAUAAGUGAUGAUAGAAGGGUA
AF205409.1/1081-1271 GCAUAGUGUUACCAUCAACAAC----CUUAACUUCAUUUU-CUUAUUCAAUACCUAGGUAGGUAGAUGCUAGAUUCUGGAAAU----AAAAUAUAAGUCUCAGGUGGACCUUGUCCUCUCUCCUAGUCGAAUUCUGAAUCUAGUUGGCAAGAUUCUGAAAUCAAGGCGUAUAAUCAGUAAUACGUGAUGAUAGAAGGGUA
AF205415.1/1604-1783 GCAUAGUGUUACCAUCAACAAC----CUUAACUUCAUUUA-CUUAUUCAAUGGCCAGGUAGGUAGAUGCUAGAUUCUAGAAAU----AAAAUACAAGUUUCAAGUGGCCCUUGUCCCCUCUCCUACUCAAAUUCUGAAUCUAGUUGGCAAGUUUCCGAAAUCAAGGCAUAUAGUCAGU-------GAUGAUAGAAG----
U01317.1/64568-64759 GCAUAGUGUUACCAUCAACCAC----CUUAACUUCAUUUUUCUUAUUCAAUACCUAGGUAGGUAGAUGCUAGAUUCUGGAAAU----AAAAUAUGAGUCUCAAGUGGUCCUUGUCCUCUCUCCCAGUCAAAUUCUGAAUCUAGUUGGCAAGAUUCUGAAAUCAAGGCAUAUAAUCAGUAAUAAGUGAUGAUAGAAGGGUA
#=GC SS_cons         :::::::::::::::::::::[....[[[----[[[[[--.[[[[[[,,,<<<<<____>>>>>,(((((,<<<<--<<<---....-------<<<---<<<<_____>>>>---->>>>>>->>>>,,,<<<<<<<<<<________>>>>>>>>>>,,,,,))))),,,,,,,,,]]]]]]-]]]]]---]]]]:::
#=GC RF              GCAUAGUGUUACCAUCAACAAc....CuuAACUuCauuUu.cuuauuCAAuacCuAGGUaGguaGauGCcAGacucUggaAAU....AAAAuAUgaGUCUCagGUGGuCCcuGUCCuCucuccuaguCaAAuuCcGaaucuAGUUGgcAagauuCgGaaAucAAgGCauAUAaUCAGUaauaagUgauGaUAGaaGgGUA
//
# STOCKHOLM 1.0

#=GF AC   RF00622
#=GF ID   CPEB3_ribozyme
#=GF DE   Mammalian CPEB3 ribozyme
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published; PMID:16990549; INFERNAL
#=GF SS   Published; PMID:16990549
#=GF GA   60.00
#=GF TC   60.30
#=GF NC   59.80
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF RN   [1]
#=GF RM   16990549
#=GF RT   A genomewide search for ribozymes reveals an HDV-like sequence in the
#=GF RT   human CPEB3 gene.
#=GF RA   Salehi-Ashtiani K, Luptak A, Litovchick A, Szostak JW
#=GF RL   Science. 2006;313:1788-1792.
#=GF RN   [2]
#=GF RM   15565159
#=GF RT   Autocatalytic RNA cleavage in the human beta-globin pre-mRNA promotes
#=GF RT   transcription termination.
#=GF RA   Teixeira A, Tahiri-Alaoui A, West S, Thomas B, Ramadass A, Martianov I,
#=GF RA   Dye M, James W, Proudfoot NJ, Akoulitchev A
#=GF RL   Nature. 2004;432:526-530.
#=GF CC   The mammalian CPEB3 ribozyme is a self cleaving RNA located in the second
#=GF CC   intron of the CPEB3 gene which belongs to a family of genes regulating
#=GF CC   messenger RNA polyadenylation [1]. This ribozyme is highly conserved and
#=GF CC   found only in mammals [1]. The CPEB3 ribozyme is structurally and
#=GF CC   biochemically related to the human hepatitis delta virus (HDV) ribozyme
#=GF CC   (Rfam:RF00094) and the HDV ribozyme is proposed to have arisen from the
#=GF CC   human transcriptome [1]. There is currently only one other known self
#=GF CC   cleaving ribozyme in mammals, the CoTC motif (Rfam:RF00621)[2].
#=GF WK   Mammalian_CPEB3_ribozyme
#=GF SQ   12


AC113124.9/161461-161384     AGAGGAUAACAGGGGGCCACAGCAGAAGCGUUCACGUCGCGGCCCCUGUCAGAUUCUGGCGAAUCUGCGAAUUCUGCU
AC096310.9/197397-197321     AGAGGAUAACAGGGG-CCACAGCAGAAGCGUUCACGUCGCGGCCCCUGUCAGAUUCUGGUGAAUCUGCGAAUUCUGCU
AL158040.14/122218-122141    AGGGGAUAACAGGGGGCCACAGCAGAAGCGUUCACGUCGCAGCCCCUGUCAGAUUCUGGUGAAUCUGCGAAUUCUGCU
AAPY01211722.1/3878-3801     CGAGGAUAAUAGGGGGCCACAGCAGAAGCGUUCACGUCGCGGCCCCUGUCAGAUUCUGGUGAAUCUGCGAAUUCUGCG
AAFR03024585.1/20274-20351   AGUGGAUAACAGGGGGCCAUAGCAGAAGCGUUCACGUCGCGGCCCCUGUCAGAUUCAUAGGAAUCUGCGAAUUCUGCU
AAFC03085012.1/105656-105579 AAAGGAUAACAAGGGGCCAGAGCAGAAGCAUUCACGUCGCGGCCCCUGUCAGAUUCUGGUGAAUCUGCGAAUUCUGCU
AAIY01234049.1/2-76          UGAGCAUAAC--AGGGCCACCCCA-AAGCGUUCACAUUGUGGCCCCUGUCAGAUUCUGGUAAAUCUGCGAGUUCUGCU
AAGV020425402.1/596-519      AUAGAAGAUAAUGGGGCCACAGCAGAAGCAUUCAUGUUGCAGCCCUUGUGAGAUUCAAGUGAAUCUGUGAAUUCUGCU
AC190203.1/105322-105245     AGGGGAUAACAGGGGGCCACAGCAGAAGCGUUCACGUCGCGGCCCCUGUCAGAUUCUGGUGAAUCUGCGAAUUCUGCU
AAGJ04021094.1/6040-5967     AGGGGGGUCCCGGGGGCCAUUGAAGGAGCGUUCACGUCGCGGCCCCUGUCAGAU----GAAAAUCUGCGAAUCCUUCA
AAEX03015410.1/35073-34998   AGAGGAUAAC--GGGGCCACAGCAAAAGUGUUCACGUCAUGGCCCCUGUCAGAUUCUGGUGAAUCUGCAAAUUCUGCU
AAGJ04154883.1/9182-9255     AGAGGUACGCGGGGGGCCAUUGAAGGAGCGUUCACGUCGCGGUCCCUGUCAGAU----GAAAAUCUGCGAAUCCUUCA
#=GC SS_cons                 ::::::::::::<<<<<---AAAAAAA<<<__B____>>>->>>>>-b-<<<<<<<____>>>>>>>::::aaaaaaa
#=GC RF                      AGaGgAuAacagGGGGCCAcaGcAGAAGCGUUCACGUCGCGGCCCCUGUCAGAUUCugGuGAAUCUGCGAAUUCUGCu
//
# STOCKHOLM 1.0

#=GF AC   RF00623
#=GF ID   P1
#=GF DE   Pseudomonas sRNA P1
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   100.00
#=GF TC   110.70
#=GF NC   56.10
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF CC   This small RNA (sRNA) was computationally identified in the genome of the
#=GF CC   opportunistic pathogen Pseudomonas aeruginosa and its expression verified
#=GF CC   by northern blot analysis [1]. There appears to be two related copies of
#=GF CC   P1 sRNA in the P.aeruginosa PA01 genome and both copies appear to be
#=GF CC   located upstream of predicted glutamine synthetase genes. This sRNA
#=GF CC   appears to be conserved amongst several Pseudomonas species. P1 has a
#=GF CC   predicted Rho independent terminator at the 3' end but the function of P1
#=GF CC   is unknown [1].
#=GF WK   Pseudomonas_sRNA_P1
#=GF SQ   14


CP000075.1/5778074-5778253 ACCCCCGCUGUUGUUGCUCUACUGGGUUGCGAUCGAGCUUAGCCUCGUUCAUUUUUUUAUACAACAGCCCGUUAAAAACAGUAGACA-GGC-CGCUU----U--AG-CUC-UUAUUUAAGAUCGGUAAAAAACGGAA-UAAAACGCCCUAAAUAGCAGCAAAAAAGGCCAUAUGGCGCAGUUUUAGGGCAA
CP000076.1/6741850-6742029 ACCCC-GGUAUUAUUGCUGUUAUGGGUUUGAUUCGAGCUUAGCCUUGUUCAUUUUUUUACACAACACCCCCGUAAAAA-AUACAACACGGCCCGCUC----A--AG-CCU-GCGGUACCCAAGGCGGCCGAGCCCCA-AAAAACGCCCUGUUUUGCCCCAAAAGAGCCUUGCCAGCCCUUUAUUAGGGCAU
CP000712.1/5721262-5721441 ACCCU-CGUAUUAUUG-UGUUCUGGGUUGUGACCGAGCUUAGCCUUGUUCAUUUUUUUACACAACACUUCCGUAAAAA-AUAAAACACGGCACGUUU----G--AG-AUCACCCUUUCAGGCAGAAAUAGCGGAUAA-UGGCCUGCCCCGAUAUGCAGCAAAUCUGCCGUAGAUGUGCCAUUUCAGGGCGU
CT573326.1/5617189-5617368 ACCCU-CGUAUUAUUG-UGUUCUGGGUUGUGACCGAGCUUAUCCUCGUUCAUUUUUUUUCACAACCUCUCCGUAAAAA-AUAAAACACGCCCCGCUCGGGAU--AA-CCC-UUCAGGACGAAAAUAGCGGA---UAA-UGGCACGCCCUGAUAUGCAGCAAAUCUGCCGUAGAUGUGCCAUUUAAGGGCAU
AE016853.1/6038511-6038690 ACCCCCGCUAUUGUUGCUCUAUUGGGUUGCGAUCGAGCUUAGCCUCGUUCAUUUUUUUAUACAAUAACCCGUUAAAAAUAGAAGACA-GGC-CGCUC----A--CG-CUG-GCGAUCAAGACUGAAUAGAAACACGA-UAAAACGCCCUAAAUAGCGGCAAAAAAGGCCAUCUGGCGCAGUUUUAGGGCAA
AACY022960537.1/100-279    ACACC-CGUAUUAUUGCUGUUAUGGGUUUGAACCGAGCUUAGCCUUGUUCAUUUUUUUACACAAUAGCCCUGUAAAAA-AUUGAACACACCCCACUG----AGCAA-CCU-GAAAGAUCAACGUUUG--GAGCCCCC-UGAAAGGCCUUGAAAUGCCCCAAAAAUGGCCACCACGCCCCACUACAGGGCAU
CP000058.1/5571246-5571425 ACCCCCGCUAUUGUUGCUCUACUGGGUUGCGAUCGAGCUUAGCCUCGUUCAUUUUUUUAUACAACAACCCGUUAAAAAUAGAAGACA-GGC-CGCUC----U--AG-CUC-GUAUUUAACAGCGGUCAGAAACGGAA-UAAAACGCCCUAAAUAGCGGCAAAAAAGGCCAUAUGGCGCAGUUUUAGGGCAA
CP000680.1/348734-348555   ACACC-CGUAUUAUUGCUGUUAUGGGUUUGAACCGAGCUUAGCCUUGUUCAUUUUUUUACACAAUAGCUCUGUAAAAA-AUUGAACACACCCCAC-U----G--AG-CAC-CCUGUCGACAUGCGGGCAAAGCGCCUCUGAAAGGCCUUGAAACGCCCCAAAAAUGGCCAUCAUGCCCCACUACAGGGCAU
CP000926.1/5859447-5859626 ACCCU-CGUAUUAUUG-UGUUCUGGGUUGAGACCGAGCUUAGCCUUGUUCAUUUUUUUACACAACACCUCCGUAAAAA-AUAAAACACGGUGCACCGGAGAU--AG-CCC-U---UUACGCGGUAAAUAGCGGAUAA-UGCUUUGCCCCGAUAUGCAGCAAAUCUGCCGUAGAUGUGCCAUUUCAGGGCAU
CP000949.1/292483-292304   ACCCU-CGUAUUAUUG-UGUUUUGGGUUGAGACCGAGCUUAGCCUUGUUCAUUUUUUUACACAACACCUCCGUAAAAA-AUAAAACACGGCAUGUCGGAGAU--AG-CCC-UAUG---ACAGGGAAAUAGCGGAUAA-UGGCACGCCCCGAUAUGCAGCAAAUCUGCCGUCGAUGUGCCAUUUCAGGGCAU
CP000094.2/6072751-6072930 ACCCC-GGUAUUAUUGCUGUUAUGGGUUUGAUCCGAGCUUAGCCUUGUUCAUUUUUUUACACAACACCCCCGUAAAAA-AUACAACACGGCCUGCUC----A--AG-CCU-GCGGGUGGCGCGUCCUUCACGGAUAA-AAAAAUGCCCCAAAGUGCCCCAUAAAUGCCCUCGUGGCGCUUUUUCAGGGCAG
CP002585.1/6531139-6531318 ACCCC-GGUAUUAUUGCUGUUAUGGGUUUGAAUCGAGCUUAGCCUUGUUCAUUUUUUUACACAACACCCCCGUAAAAA-AUACAACACGGCCCGCUC----A--AG-CCC-GCGGGCGCCAAGACCCUUAAAGGGAA-AAAAACGCCCUAAAUUGCCUCAAAAAAGCCCUGAAGGUGCUUUUUUAGGGCAA
CP000744.1/397482-397303   ACCCG-UUGUUUGUAGAUGUUAUGGGGUUUGGCCGAGCUUAGCGUUGUUCAUUUUUUUACACAAUAGGCCUGUAAAAA-AUUGAACA-CGCGUUCCU---GA--ACACCC-UUCGACGCGAGGUUUUUUUCGGCUUU-UCGCCUGGC-GAAAAUGCCCUGAAAACGGCCUCAACGCCCCACAAGAGGGCGU
FM209186.1/327696-327517   ACCCG-UUGUUUGUAGAUGUUAUGGGGUUUGGCCGAGCUUAGCGUUGUUCAUUUUUUUACACAAUAGGCCUGUAAAAA-AUUGAACA-CGCACUCCUG--AA--CA-CCC-UUCGACGCGAGGUUUUUUUCGGCUUU-UCGUCCGGC-GAAAAUGCCCUGAAAACGGCCUCAACGCCCCACAAGAGGGCGU
#=GC SS_cons               :::::.:::::::::::::::::<<<<<<-----<-<----<<<<-<<<---<<<<<<<<___________>>>>>>>.>--->>>>->>>->->--....>..>>.>>>.--------------------------.----------------------------------<<<<-<_______>->>>>
#=GC RF                    ACCCc.cgUAUUaUUGcUGUUaUGGGcuuugacCGAGCUUAGCcUUGUuCAUUUUUUUAcACAAcAgccCugUAAAAA.AUaaaACACgGCaCgCUu....a..ag.CCC.uuaguuaagAaguuuuuaaaGgauaa.UaaaacGCCCuaAaaUGCagCAAAAauGgCcuuaacGcgCcaUUuuAGGgCgu
//
# STOCKHOLM 1.0

#=GF AC   RF00624
#=GF ID   P9
#=GF DE   Pseudomonas sRNA P9
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   43.00
#=GF TC   43.00
#=GF NC   42.80
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF CC   This small RNA (sRNA) was computationally identified in the genome of the
#=GF CC   opportunistic pathogen Pseudomonas aeruginosa and its expression verified
#=GF CC   by northern blot analysis [1]. P9 appears to be conserved in several
#=GF CC   Pseudomonas species in addition to Bordetella spp. In both Pseudomonas and
#=GF CC   Bordetella spp P9 appears to be located upstream of a predicted threonine
#=GF CC   dehydratase gene. P9 has a predicted Rho independent terminator at the 3'
#=GF CC   end but the function of P9 is unknown [1]. This sRNA also appears to be
#=GF CC   present in the Betaproteobacteria (Burkholderia and Ralstonia species).
#=GF WK   Pseudomonas_sRNA_P9
#=GF SQ   17


BX640440.1/318195-318270   AGCAU---UAUUACCGCCAUUCCAGCAGUGGCGGGUUAGCCUACGA-AUUCCCA------------GAAAACCCGCC-CUCGAGGCGGGUUUU
BX640426.1/81990-82065     AGCAU---UAUUACCGCCAUUCCAGCAGUGGCGGGUUAGCCUACGA-AUUCCCA------------GAAAACCCGCC-CUCGAGGCGGGUUUU
CP000075.1/1879751-1879678 AUUAU---UAUUACCGUCAUUCCAGUCAUGGCGGGUUAGCCGACG---UUUGCC------------AAAAACCCGCC-CUGGAGGCGGGUUUC
CP000058.1/1930990-1930918 AUUAU---UAUUACCGUCAUUCCAGUCAUGGCGGGUUAGCAGACG---UUUG-C------------AAAAACCCGCC-CUGGAGGCGGGUUUC
AE016853.1/4311676-4311749 AUUAU---UAUUACCGUCAUUCCAGUCAUGGCGGGUUAGCCGACG---UUUGCA------------AAAAACCCGCC-CUGGAGGCGGGUUUU
CP000076.1/3569953-3569881 AGCAU---UAUUACCGCCAUUCCU-UAUUGGCGGGCUUGCUGACG---ACUGCA------------CCCAACCCGCC-CUGGAGGCGGGUUUU
CP000438.1/4198088-4198015 AGCAU---UAUUACCGCCAUUCCAGCUAUGGCGGGUUAGCCAGCG---UCCACU------------CCGAACCCGCC-CUCGAGGCGGGUUCU
AE015451.1/3904826-3904753 AUUAU---UAUUACCGCCAUUAUCAGCUUGGCGGGCUAGCGCGUA---CGUGCA------------CCGAACCCGCC-CUGGAGGCGGGUUUU
CP000091.1/1636819-1636738 ---AU---UAUUAUCACCAUUCCUGGAAUGGUGGGUUAGCGCGCG---UCCUCAGAUCAGUUACCGCAAAACCCGCC-CU-GAGGCGGGUUUU
CT573326.1/3121484-3121408 AGCAUUAUUAUUACCGCCAUUAUCGGUUUGGCGGGCUAGCGCGUA---CGUGCA------------CCGAACCCGCC-CUGGAGGCGGGUUUU
CP000949.1/3244952-3244879 AUUAU---UAUUACCGCCAUUAUCAGUUUGGCGGGCUAGCGCGUA---CGUGCA------------CCGAACCCGCC-CUGGAGGCGGGUUUC
CP000094.2/2997820-2997896 AGCAU---UAUUACCGCCAUUCCUCAUUUGGCGGGCUAGCUCACGACUGCAGCA------------CCCAACCCGCC-CUAGAGGCGGGUUUU
CP002287.1/3961301-3961221 CUGAU---UAUUACCACCAUCAGGUCCAUGGUGGGUUAGCGCGCG---UCGGUACAUC---GCUACAUAAACCCGCC---AGAGGCGGGUUUU
CP002287.1/3297768-3297850 CUGAU---UAUUACCAUCAUUCCUGGAAUGGUGGGUUAGCGCGCG---ACCGCAACAG----UCACAGCCACCCGCCCCAAGAGGCGGGUUUU
CP000926.1/2789953-2790026 AUUAU---UAUUACCGCCAUUAUCAGCUUGGCGGGCUAGCGCAUA---CGUGCA------------CCGAACCCGCC-CUGGAGGCGGGUUUU
CP002585.1/3827107-3827034 AGCAU---UAUUACCGCCAUUCCUUAUUUGGCGGGUUAGCUGACG---GCUGCA------------CCCAACCCGCC-CUGGAGGCGGGUUUU
AM181176.4/3018216-3018292 AGCAU---UAUUACCGCCAUUCCUCAUUUGGCGGGAUAGCGCACG---GCUGUAC---------CCAAACACCCGCC-CUAGAGGCGGGUUUU
#=GC SS_cons               :::::...:::::<<<<<<<_______>>>>>>>-----------...------............--<<<<<<<<<._____>>>>>>>>>:
#=GC RF                    AuuAU...UAUUACCGCCAuUccugguaUGGCGGGuUAGCgcaCG...ucugCA............aaaAACCCGCC.CUaGAGGCGGGUUuU
//
# STOCKHOLM 1.0

#=GF AC   RF00625
#=GF ID   P11
#=GF DE   Pseudomonas sRNA P11
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   77.40
#=GF NC   49.40
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF CC   This small RNA (sRNA) was computationally identified in the genome of the
#=GF CC   opportunistic pathogen Pseudomonas aeruginosa and its expression verified
#=GF CC   by northern blot analysis [1]. P11 is located between a putative threonine
#=GF CC   protein kinase and putative nitrate reductase and appears to be conserved
#=GF CC   in several Pseudomonas species. P11 has a predicted Rho independent
#=GF CC   terminator at the 3'end but the function of P11 is unknown [1].
#=GF WK   Pseudomonas_sRNA_P11
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   15


CP000075.1/2450746-2450611 AGAU--GCGAGUUGGCACAAGCACUGCAUGG--UC-UCUUGCAGAUAAUUCAUAACACGCAGCCCUCAACGAUGAAGGCUGCGUC-UCCCGAGAGAACGGGACC-G-GACAAAGGCGUCCUCGUCAGGCCACUGACGGGACGCC
AE016853.1/2548871-2548734 GUGAACACGAGUUGGCACAAGCGCUGCAUAG--UC-CCUUUCAGAUCAUUCAUAACGCGCAGCCUUCAACGAUGAAGGCUGCGCC-UCCCGAGAGAACGGGACC-G-GACAAAGGCGUCCCCGUCAGGCAACUGGCGGGACGCC
AF112870.1/4018-4154       AAUAGCGCAAGUUGGCACGGCGCCUGCUUGGGUUC-UCCCGACAAUCGACAACAAAGCGCCUGCCUCAACGACGA-GGCGGCGUU-UCCCGACCGAACGGGACCUG-GACAAAGGCGUCCU-GC-UGGCAACA-GCGGGACGCC
CP000058.1/2429276-2429141 GAAUGCG--AGUUGGCACAGGCGCUGCAUUG--UC-UUGUGCAGAUCAUUCAUAACGCGUAGCCCUCAACGAUGAAGGCUGCGCC-UCCCGAUAGAACGGGACC-G-GACAAAGGCGUCCCCGUCAGGCAACUGGCGGGACGCC
CP000744.1/3650435-3650571 AAUAUCGCAAGUUGGCACGGCGCCUGCUUGGACUU-UCCCGACAAUCGACAACACAGCGCCGACCUCAACGACGA-GGCUGCGCU-UCCCGACCGAACGGGACCUG-GACAAAGGCGUCCU-GC-UGGCAACA-GCGGGACGCC
CP000680.1/2325584-2325446 CUUCGAGAAAGUUGGCACAGGCACUGCAUUG--UU-ACUGGCAGCAAACACAUAAAGCGCGACCUUCAACGAAGAAGGCUGCACU-UCCCGAUAGAACGGGACCUG-GACAAAGGCGUCCUCGCUAGGUGACUAGCGGGACGCC
AACY021569628.1/361-230    ------G--AGUUGGCACAAGGGCUGCAUUC--ACAACUACCACAAACCACAUAAAGCGCGACCUUCAACGACGAAGGCUGCACU-UCCCGAUAGAACGGGACC-UGGACAAAGGCGUCCUCGCUAGGUGACUAGCGGGACGCC
CP000304.1/2631424-2631562 GUAUUUCAGAAUUGGCACAGGCUCUGCAAAG--CA-AACGUCGAAGAUGACAUACGACCUGACCCUCAACGUGGAGCGGCAGGUU-UCCCGACUGAGCGGGACACG-GACAAAGGCGUCCUCACCGGAGAACCGGUGGGACGCC
CP001157.1/2336638-2336501 CAUCCGUGAAACUGGCACAGCCCCUGCAUCG-AGA-AAACCGACAGAUCACAUAA-GCAUUGCCUUCAACGUGGAGGGCAGUGUU-UCCCGACAGAACGGGAAU-G-GACAAAGGCGUCCUCGCUGGGUAACCGGCGGGACGCC
CP000094.2/1982387-1982251 CCCGCCGCGACUUGGCACAACCACUGCAU----UA-ACGUUUUCAACUGACAUAAAGCCCGACCUUCAACGACGAAGGCCAGGCU-UCCCGAGAGAACGGGACAAG-GACAAAGGCGUCCUCGCUAGGUAACUGGCGGGACGCC
AE004091.2/1928802-1928666 AACAGCGCAAGUUGGCACGGCGCCUGCUUGGGUUC-UCCCGACAAUCGACAACAAAGCGCCUGCCUCAACGACGA-GGCGGCGUU-UCCCGACCGAACGGGACCUG-GACAAAGGCGUCCU-GC-UGGCAACA-GCGGGACGCC
CP002727.1/3606931-3607057 UUUGAUGCUGAUUGGCACACUCCCUGCUCAU--GU-AUCCGCA-----GACAUCGAGCCUGUCGG----CACA---CGGCAGGCUCCCCGAAACGAAUCGGGACCG-GACAAAGGCGUCCUUGCACU-CACGGUGCAGGACGCC
CP002620.1/2870847-2870985 UUCCGAGAAAGUUGGCACAAGCGCUGCAUUG--UU-ACUGGCAGCAAACACAUAAAGCGCGACCUUCAACGAAGAAGGCUGCACU-UCCCGAUAGAACGGGCUCUG-GACAAAGGCGUCCUCGCUAGGUGACUAGCGGGACGCC
CP002585.1/2059414-2059278 CUUCGCGCCAGUUGGCACAACCACUGCAUAA-----UCCCUUUCAACAGACAUAAGGCAACGCCUCCAACGAUGAAGGCGGUGCU-UCCCGAGAGAACGGGACCAG-GACAAAGGCGUCCUCGCUAGCUUGCUAGCGGGACGCC
CP002881.1/2488319-2488457 GCAUUUCAAAAUUGGCACAGGCUCUGCAAAG--CA-AACGUCGAAGAUGACAUACGACCUGACCCUCAACGUGGAGCGGCAGGUU-UCCCGACUGAGCGGGACACG-GACAAAGGCGUCCUCACCGGAGAACCGGUGGGACGCC
#=GC SS_cons               :::::::::::(((<<<_______>>>,,,,..,,.,,,,,,,,,,,,,,,,,,,,<<<<<-<<-<<______>>->>->>>>>,.<<<<<______>>>>>,,,,.,,)))-<<<<<<<-<<<<<<____>>>>>>>>>>>>>
#=GC RF                    auuuuugcaAgUUGGCACAagcaCUGCauag..uu.acuugcaaAuaauacAUAaagCgcgaCcuuCAACGauGaagGccgcGcU.uCCcGAuaGAACgGGaccuG.GACAAAGGCGUCCUCGCcggguaAccgGCGGGACGCC
//
# STOCKHOLM 1.0

#=GF AC   RF00626
#=GF ID   Gurken
#=GF DE   Gurken localisation signal
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A, INFERNAL
#=GF SS   Published; PMID:15992540
#=GF GA   90.00
#=GF TC   95.30
#=GF NC   53.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0051028; mRNA transport;
#=GF RN   [1]
#=GF RM   15992540
#=GF RT   gurken and the I factor retrotransposon RNAs share common localization
#=GF RT   signals and machinery.
#=GF RA   Van De Bor V, Hartswood E, Jones C, Finnegan D, Davis I
#=GF RL   Dev Cell. 2005;9:51-62.
#=GF CC   Drosophila gurken mRNA is localized by dynein-mediated transport to a
#=GF CC   crescent near the oocyte nucleus, thus targeting the TGFalpha signal and
#=GF CC   forming the primary embryonic axes [1]. Gurken contains an RNA stem loop
#=GF CC   within the coding region that forms a signal for dynein-mediated RNA
#=GF CC   transport to the oocyte nucleus [1]. This hairpin is conserved in other
#=GF CC   drosophila species.
#=GF WK   Gurken_localisation_signal
#=GF SQ   3


AY051814.1/378-446         CAAAGUAAUUUUCGUGCUCUCAACAAUUGUCGCCGUCACAGAUUGUUGUUCGAGCCGAAUCUUACUUCU
L22531.1/397-465           CAAAGUAAUUUUCGUGCUCUCAACAAUUGUCGCCGUCACAGAUUGUUGUUCGAGCCGAAUCUUACUUCU
AAPP01019865.1/13195-13127 CAAAGUAAUUUUCGUGCUCUCAACAAUUGUCGCCGUCACAGAUUGUUGUUCGAGCCGGAUCUUACUACU
#=GC SS_cons               ::<<<<<<--<<<<-<<<<-<<<<<<<<<<_______>>>->>>>>>>--->>>>>>>>-->>>>>>::
#=GC RF                    CAaAGUAAUUUuCGUGCUCUCAACAAUUGUCGCCGUCACAGAUUGUUGUUCGAGCCGaAUCUUACUuCU
//
# STOCKHOLM 1.0

#=GF AC   RF00627
#=GF ID   P15
#=GF DE   Pseudomonas sRNA P15
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   78.10
#=GF NC   68.60
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF CC   This small RNA (sRNA) was computationally identified in the genome of the
#=GF CC   opportunistic pathogen Pseudomonas aeruginosa and its expression verified
#=GF CC   by northern blot analysis [1]. P15 is conserved across a wide range of
#=GF CC   Gammaproteobacteria. It appears to be consistently located upstream of a
#=GF CC   3-deoxy-7-phosphoheptulonate synthase gene. P15 has a predicted Rho
#=GF CC   independent terminator at the 3'end but the function of P15 is unknown
#=GF CC   [1].
#=GF WK   Pseudomonas_sRNA_P15
#=GF SQ   22


CP000058.1/2702335-2702218 CAACUCUUAUUAUGGGUAUUGGU---AUAGCCACU-GGCGCGCCUGAUACCCAU--CC--GGCGCCCAC--UUCA-AG--GGGACGCCAAC-CA-GA-G-AA-UUCUCU------A-----CCCCCGGUCGGC-UUCCCGACCGGGGG
CP000076.1/4113467-4113584 CAGCUUUUAUUUUGGGUAUUGGU---UUAGCCACU-GGCGCGCCUGAUACCCAA--CC--GGCGCCCAC--UUCA-AC--GGGUCGCCUAC-CA-GA-G-AA-AUCUCA------A-----CCCCCGGUCGGC-CUCCCGACCGGGGG
AE016853.1/3402134-3402251 CAACACUUAUUAUGGGUAUUGGU---UUAGCCACU-GGCGCGCCUGAUACCCAU--CC--GGCGCCCAC--UUCA-AG--GGGACGCCAAC-CA-GA-G-AA-UUCUCU------A-----CCCCCGGUCGGC-UACCCGACCGGGGG
CP000075.1/3478167-3478285 UAAUUCUUAUUAUGGGUAUUGGU---UUAGCCACU-GGCGCGCCUGAUACCCAU--CC--GGCGCCCAC--GUUA-AG--GGGACGCCAAC-CA-GA-G-AA-UUCUCU------AA----CCCCCGGUCGGC-UUCCCGACCGGGGU
CP000304.1/1386082-1386201 UGGUUAUUACUUUGGGUAUUGGU---UUAGCCACA-GGCGCGCCUGAUACCCCA--CA--GGCGCCCUA--GCAA-GG-AGGGUCGCC-AC-CA-GA-GCAG-UUUUCG------AA----CCCCCGGUCGGC-CACCCGACCGGGGG
CP000744.1/2276050-2275936 UAUUUCU----UCGGGUAUUGGU---UUAGCCACU-CCGGCGCCUGAUACCCCA--AC--GGCGCCCAC--GGUAUAC--GGGACGCCUAC-CC-UG-C-AC-ACGCAA------A-----CCCCCGGUCGGC-UCCCCGACCGGGGG
CP000438.1/2270208-2270094 UAUUUCU----UCGGGUAUUGGU---UUAGCCACU-CCGGCGCCUGAUACCCCA--AC--GGCGCCCAC--GGUAUAC--GGGACGCCUAC-CC-UG-C-AC-ACGCAA------A-----CCCCCGGUCGGC-UCCCCGACCGGGGG
CT573326.1/3362547-3362668 CAGCUUUUAUUUUGGGUAUUGGU---UUAGCCACUAGGCGCCGCUGAUACCCAC--AC--GGCGCCCAC-CUUCG-AG--GGGCCGCCGAA-CAUGA-G-AA-UACUCA------AA----CCCCCGGUCGGC-UCCCCGACCGGGGG
CP000680.1/3288041-3287918 UAUUACUUCUUU-GGGUAUUGGU---UUAGCCACA-GGCGCGCCUGAUACCCCA--CA-GGCGGCCUGA--GACA-GC--AGGGUCGCCAC-CA-AA-G-AC-GUUUUCCAGAAAA-----CCCCCGGUCGGC-AACCCGACCGGGGG
AACY022231095.1/248-372    GUAUUAUUUCUUUGGGUAUUGGU---UUAGCCACA-GGCGCGCCUGAUACCCCA--CA-GGCGGCCUAG--CAGA-AC--AGGGUCGCCAC-CA-GA-G-ACGUUUUCC------AGAAAACCCCCGGUCGGC-AACCCGACCGGGGG
CP000926.1/3131034-3131152 CAGCUAUUACUUUGGGUAUUGGU---UUAGCCACU-AG-GCGCC-GAUACCCAC--AC--GGCGCCCAC-CUUCG-AG--GGGCCGCCGAA-CAUGA-G-AA-UACUCA------AA----CCCCCGGUCGGC-UCCCCGACCGGGGG
CP001157.1/3396249-3396123 CGGCUAUUACUUCGGGUAUUGGUGGUUUAGCCACA-GGCGCGCCUGAUACCCCGUACA--GGCGCCC-C--AGCA-AGCAGGGUCGCCACCAGA-GCAG-UU-UUCGCA------AA----CCCCCGGUCGGC-AACCCGACCGGGGG
CP000949.1/3002877-3002998 CUGCUUUUAUUUUGGGUAUUGGU---UUAGCCACUAGGCGCCGCUGAUACCCAC--AC--GGCGCCCAC-CUUCG-AG--GGGCCGCCGAA-CAUGA-G-AA-UACUCA------AA----CCCCCGGUCGGC-UCCCCGACCGGGGG
CP000094.2/3510857-3510974 AAGCUUUUAUUUUGGGUAUUGGU---UUAGCCACU-GGCGCGCCUGAUACCCAA--CC--GGCGCCCAU--UUGA-AC--GGGUCGCCUAC-CA-GA-G-AU-UUCUCA------A-----CCCCCGGUCGGC-CUCCCGACCGGGGG
CP002585.1/2418757-2418639 CAGCUUUUAUUUUGGGUAUUGGU---UUAGCCACU-GGCGCGCCUGAUACCCAA--CC--GGCGCCCAU-UUUAA-AC--GGGUCGCCUUC-CA-GA-G-UU-UUC-CA------AA----CCCCCGGUCGGC-CUCCCGACCGGGGG
CP002881.1/1330807-1330926 UGGUUAUUACUUUGGGUAUUGGU---UUAGCCACA-GGCGCGCCUGAUACCCCA--CA--GGCGCCCUA--GCAA-GC-AGGGUCGCC-AC-CA-GA-GCAG-UUUUCG------AA----CCCCCGGUCGGC-CACCCGACCGGGGG
CP002727.1/4838909-4839030 CUCGUAUUUUUAUGGGUAUUGGU---UUAGCCACA-GGCGCGCCUGAUACCCCA--CA--GGCGCCCUA--GCAA-CUCAGGGUCGCCACCAGA-CA-G-UU-UCUCGA------AA----CCCCCGGUCGGC-CUCCCGACCGGGGG
AB333783.1/9871-9990       CGGCUUUUAUUUUGGGUAUUGGU---UUAGCCACA-GGCGCCGCUGAUACCCAC--AC-CGGCGCCCAC--UCCC-A---GGGCCGCCGAA-CACGA-G-AA-UACUCA------A-----CCCCCGGUCGGCCCUGCCUACCGGGGG
CP002290.1/2996764-2996882 CAGCUAUUACUUUGGGUAUUGGU---UUAGCCACU-AG-GCGCC-GAUACUCAC--CC--GGCGUCCAC--CUUAGAG--GGGCCGCCGAA-CAUGA-G-AA-UACUCA------AA----CCCCCGGUCGGC-UUCCCGACCGGGGU
AM181176.4/2370391-2370271 AAGUUUUUAUUUUGGGUAUUGGU---UUAGCCACU-GGCGCGCCUGAUACCUGA--AAUCGGCGGCCACUACUCA-AG--GGGUCGCCUAC-CA-GA-G-AA-AU--CU------AA----CCCCCGGUCGGC-UCCCCGACCGGGGG
CP002620.1/3593261-3593137 GUAUUACUUCUUUGGGUAUUGGU---UUAGCCAUA-GGCGCGCCUGAUACCCCA--CA-GGCGGCCUGA--GAAA-CC--AGGGUCGCCAC-CA-GA-G-ACGUUUUCCAG--AAAA----CCCCCGGUCGGC-AACCCGACCGGGGG
AE015451.1/3466159-3466041 CAGCUAUUACUUUGGGUAUUGGU---UUAGCCACU-AG-GCGCC-GAUACCCAC--CC--GGCGUCCAC-CUUCG-AG--GGGCCGCCGAA-CAUGA-G-AA-UACUCA------AA----CCCCCGGUCGGC-UUCCCGACCGGGGG
#=GC SS_cons               :::::::::::<<<<<<<<<<<<...---<<____._>>-->>>->>>>>>>>>..,,..<<<<<<<__..____.__..>>>->>>>,,,.,,.<<.<.__.__>>>,......,,....<<<<<<<<<<<_.___>>>>>>>>>>>
#=GC RF                    uaguUaUUauUuuGGGuauuGGc...UUAGCCACu.gGCGCgCCUgauaCCCaa..ca..GgcGCCcac..uuuA.ag..gGGuCgcCuAc.cA.gg.g.Aa.uuccca......AA....CCCCCGGuCGGC.uuCCCGaCCGGGGG
//
# STOCKHOLM 1.0

#=GF AC   RF00628
#=GF ID   RgsA
#=GF PI   P16;
#=GF DE   RgsA sRNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   61.30
#=GF NC   52.10
#=GF TP   Gene; sRNA
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0042542; response to hydrogen peroxide;
#=GF DR   GO; 0006979; response to oxidative stress;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF RN   [2]
#=GF RM   18405392
#=GF RT   Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas
#=GF RT   species.
#=GF RA   Gonzalez N, Heeb S, Valverde C, Kay E, Reimmann C, Junier T, Haas D
#=GF RL   BMC Genomics. 2008;9:167.
#=GF RN   [3]
#=GF RM   27381272
#=GF RT   RpoS-dependent sRNA RgsA regulates Fis and AcpP in Pseudomonas aeruginosa.
#=GF RA   Lu P, Wang Y, Zhang Y, Hu Y, Thompson KM, Chen S
#=GF RL   Mol Microbiol. 2016;102:244-259.
#=GF RN   [4]
#=GF RM   26858204
#=GF RT   The Role of the ncRNA RgsA in the Oxidative Stress Response and Biofilm
#=GF RT   Formation in Azotobacter vinelandii.
#=GF RA   Huerta JM, Aguilar I, Lopez-Pliego L, Fuentes-Ramirez LE, Castaneda M
#=GF RL   Curr Microbiol. 2016;72:671-679.
#=GF RN   [5]
#=GF RM   29473822
#=GF RT   RgsA, an RpoS-dependent sRNA, negatively regulates rpoS expression in
#=GF RT   Pseudomonas aeruginosa.
#=GF RA   Lu P, Wang Y, Hu Y, Chen S
#=GF RL   Microbiology. 2018;164:716-724.
#=GF CC   This small RNA (sRNA) was computationally identified in the genome of the
#=GF CC   opportunistic pathogen Pseudomonas aeruginosa and its expression verified
#=GF CC   by northern blot analysis [1]. P16 sRNA appears to be conserved across
#=GF CC   several Pseudomonas species and Azotobacter vinelandii. In these species
#=GF CC   it is consistently located downstream of a predicted TatD
#=GF CC   deoxyribonuclease gene. P16 has a predicted Rho independent terminator at
#=GF CC   the 3' end but the function of P16 is unknown [1]. It has been shown that
#=GF CC   this sRNA is transcribed from an RpoS-dependent promoter under positive,
#=GF CC   probably indirect GacA control in two Pseudomonas species. It was renamed
#=GF CC   RgsA (for regulation by GacA and stress).[2]RpoS mRNA expression is
#=GF CC   repressed by RgsA during the exponential phase. The Hfq RNA chaperone is
#=GF CC   required for the repression.[5]
#=GF WK   Pseudomonas_sRNA_P16
#=GF SQ   27


CP000075.1/1860063-1859868 CAAGGAGGGC-U-UUAGUAUUCCAAAACUGUUUAA-AAAA--CGAU--CAAAAGAC--ACUGGACGCUACGCCGUCCUGAACAAUACUUA-AGCUGCUG--ACGCG--U--CAU-CAUUCCCCAAAUGACUCGGCAGU-AGAGGUGCCAAAGGACUCGCGCGCCUUUGUUUUACUCCUAAUGGUCUUGACCCGGCUUCACCCCCC-AGAAUCCGG
CP000058.1/1911480-1911284 CAAGAAUCGC-U-UUAGUAUUCCAAAACUGUUUAA-AAAA--CGAU--CACAAGGC--ACUGGACGGUACGCCAUGCUGGGCAAUACUUA-AGCCACUG--ACGGG--U--CAU-CAUUCCCCAAAUGACUCGCCAGU-AAAGGUGCCUAAGGACUAGCGUGCCUUUGUUUUACUCCUAAUGGUCUUAACCCGGCUUCACCCCCCCAGAAUCCGG
AE016853.1/4332812-4333007 CAAGAAGCGC-U-UUGGUAUUCCAAAACUGUUUAA-AAAA--CGAC--CAAAAGAC--ACUGGACGGCGGCCCGUCCUGAGCAAUACUUAUAAGCGCUG--ACGCG--U--CAU--AUCCCCCAAAUGACUCGCCAGU-GGAGGUGCCAAUGGAUCAGCGCACCUUUGUUUUACUCCUAAUGGUCUUAACCCGGCUUCACCCCCC-AGAAUCCGG
CP000076.1/2006031-2005842 --CGAAGCGC----GCGUAUUCCAAAUUUGUUUAA-AAAA--CGAG--CAGGGGCA--ACUGGACUGAAUGCAAUAGUGAUCAAUACUUC-AACUGUCG--GCGGG--A--CAU--CUCCCCCAAGUGAAACGCCGAU-CAAGGUACCGAAGGAC-CGCGUGCCUUAGUUUUACUCCUAAUGGUCUUAACCCGGAUUCACCCCCC-AGAACCCGG
AACY022571736.1/225-33     CAGCAAAGGC-G-GACGUAUUCCAAAUCUGUUUAA-AAAA--CGAU--CAGAACCC--GCUGGAUACCCGUCAAUCCUGAUUAAUACUUG-GAAUGUUG--GCGCG--G--CAA--UCCCCCCAAGUGUUGCGCCGAU-AAAGGUGAUCAAGGAG-UGUUCGCCUUUGUUUAACUCCUAAUGGUCUUAACCCGGAUUC-CCCCCC-AGAGCCCGG
AAKV01000038.1/15932-16128 CAAGGACGGC-A-AGGGUAUUCCAAAUCUGUUUAA-AAAA--CCGC--CAGCCCUG--UCUGGACGCCCCACGAACAUGACCAAUACUGAAAGGUACUG--GCGCGCGG--UAU-CUCCCCCCAAGUACCCAGCCAGU-GAAGGUACCGAGGAAU--GCGUACCUUUGUUCCACUCCUAAUGGUCUUGACCCGGAUUCAUCCCCC-AGAACCCGG
AACY022994221.1/41-236     CAGCAGCGUC-C-GCGGUAUUCCAAAUCCGUUUAA-AAAA--C--U--CAGGCUUUGGCCUGGACGCUCGCUGAUCAUGGCUAAUACUGGAACUUACUGGUGUGCG--G--CAU-CUCCCCCCAAGUGCCCCGCCAGC-CAAGGUACCG-UGGAC-CGCGUACCUUG-AUUUACUCCUAAUGGUCUUAACCCGGAUUCAUCCCCC-AGAGUCCGG
AACY020827056.1/349-544    UCAGCAGCGC-GAUCUGUAUUCCAAAUCCGUUUAA-GAAU---GACGGCAAACGGC---CUGGACGUUCGGCAAUCUUCACCAAUACUGAGGAUUACUGGUGUGCG--G--CGU--AUCCCCCAAGCGCCCCGCCAGG-CAAGGUACCG-UGGAC-CGCGUACCUUG-AUUUACUCCUAAUGGUCUUAACCCGGUCUCAUCCCCC-AGAGGCCGG
CT573326.1/1693824-1693629 UAUGGAAUCA-A-GACGUAUUCCAAAUCUGUUUAA-AAAA--CGAU--CAACACAC--GCUGGCAGCGCGCCAAUCCUGGCCAAUACUUG-AAGUGUUG--GCGCG--G--CGCAUCCCCCCCAAGUGGCGCGCUGAU-AAAGGUGCCCAGGGAC-CGUGUGCCUUUGUUUUACUCCUAAUGGUCUUAACCCGGAUUCCCCCCCC-AGAACCCGG
AACY020343613.1/1832-2027  UCAGCAGCGCGC-UCUGUAUUCCAAAUCCGUUUAAGAAUG--CCGG--CAAAUGGC---CUGGACGUUCGGCAAUCUUCACCAAUACUGAGCAGUACUGGUGUGCG--G--CGU--AUCCCCCAAGCGCCCCGCCAGG-CAAGGUACCG-UGGAC-CGCGUACCUUG-AUUUACUCCUAAUGGUCUUAACCCGGUCUCAUCCCCC-AGAGCCCGG
CP000680.1/1799420-1799225 CAACAGCGUC-C-GCGGUAUUCCAAAUCUGUUUAA-AAAA--CACA--CGAUUUUG--CCUGGACGCUCGCCCAACAUGACCAAUACUGGAACUUACUG--GUGUG--UGGCAU-CUCCCCCCAAGUGCCCCGCCAGC-CAAGGUACCG-UGGAC-CGCGUACCUUG-AUUUACUCCUAAUGGUCUUAACCCGGAUUCAUCCCCC-AGAAUCCGG
CP000949.1/1689411-1689217 AAGCGGGCUC-G-GGCGUAUUCCAAAUCUGUUUAA-AAAA--CGAA--CAAUUGGC--ACUGGCACUGCGCCAAACCUGACCAAUACUAG-AAGUGUUG--GCGCG--G--CGC-AUCCCCCCCAGUGGCGCGUCGAU-AAAGGUGCUCACGGAC-CGCGUACCUUUGUUUUACUCCUAAUGGUCUUAACCCGGAUUCCUCCCCC-AGAACCCGG
CP001157.1/1479377-1479185 CAGCAACGGC-G-GAAGUAUUCCAAAACCGUUUAA-AAAA--UGAA--CAGCGCAU--ACUGGACUGGAGCCGAUCCACGACGAUACUUC-CUCUACUG--ACGUG--G--CAU---UUCCCCCGAUGCCAGGCCAGCCGAAGGCAUUCGAGGAA-CGCAUGCCUUCGCU-UACUCCUAACGCUUUUAACCCGGUUUCCUCCCCC-AGACUCCGG
CP000926.1/1682014-1681819 AACGGAACGG-C-GGCGUAUUCCAAAUCUGUUUAA-AAAA--CGAC--CAAUAUGC--ACUGGCACUGCGCCAAACCUGACCAAUACUUG-AAGUGUUG--GCGCG--G--CGCAUCCCCCCCAAGUGGCGCGCCGAU-AAAGGUGCUCAGGGAC-CGCGUACCUUUGUUUUACUCCUAAUGGUCUUAACCCGGAUUCCUCCCCC-AGAACCCGG
CP000438.1/2250681-2250485 CAAGGACGGC-G-AGGGUAUUCCAAAUCUGUUUAA-AAAA--CCGC--CAGCCCUG--UCUGGACGCCCCACGAACAUGACCAAUACUGAAAGGUACUGGCGCGCG--G--UAU-CUCCCCCCAAGUACCCAGCCAGU-GAAGGUACCG-AGGAA-UGCGUACCUUUGUUCCACUCCUAAUGGUCUUGACCCGGAUUCAUCCCCC-AGAACCCGG
AM181176.4/5174351-5174545 CAAGCGAAGC-G-CGCGUAUUCCAAAUCUGUUUAA-AAAA--CGAC--CAGUCGCG--ACUGGACUGAAUCGGAUACUGAUCAAUACUUC-AACUGUCG--GCGUG--A--CAU--CUCCCCCAAGUGAAGCGCUGAC-CUGGGUACCAACGGAC-CGCGUGCCCUUGUUUUACUCCUAAUGGUCUUAGCCCGGAUUCGCCCCCCCAGAACCCGG
CP002585.1/4953530-4953723 UAUCCGAAGC-G-AGCGUAUUCCAAAUUUGUUUAA-AAAC--CGCC--CCGGCCAG--ACUGGACGGGUUGGCAUACUGAUCAAUACUUG-AACUGUCG--GCGCG--A--CAU--CUCCCCCAAGUGACGCGCUGAU-GAAGGUACCAACGGAC-CGCGUACCUUUGUUUUACUCCUAAUGGUCUUAACCCGGAUUCACCCCCC-AGAACCCGG
CP002881.1/2787876-2788059 CAGCCAGCGA-GACAUGUAUUCCAAAUGCGUUUAA-AAAG--CGCG--GAAAUCCG--CCAGCAGACCGCUAAUGCAGCGUUAAUACUUG-AGUCACUG--GCUAG--G--CAA---UCCCCCCACUGCCUGGCCAGA-UGAGGUCGCC-UGGAU-UG-CGAUUUCA----UACUCCUAAUGGUCUUGGCCCGGUUUCU----CA-GGAAUCCGG
CP002620.1/1837409-1837215 CAACAGCGGC-C-GCGGUAUUCCAAAUCUGUUUAA-AAAA--CACC--CAAUUUUG--CCUGGACGCUCGCUCAUCAUGACCAAUACUGAAACGUACUGGUGUGCG--G--CAU--CUCCCCCAAGUGCCCCGCCAGC-CAAGGUACCG-UGGAC-CGCGUACCUUG-AUUUACUCCUAAUGGUCUUGACCCGGAUUCAUCCCCC-AGAAUCCGG
CP000712.1/4255404-4255598 AAUGAAACGU-U-GGCGUAUUCCAAAUCUGUUUAA-AAAA--CGUC--CAAUAUGC--ACUGGCACUGCGCCAAACCUGACCAAUACUUG-AAGUGUUG--GCGCG--G--CGC-AUCCCCCCCAGUGGCGCGCCGAU-AAAGGUGCUCAGGGAC-CGCGUACCUUUGUUUUACUCCUAAUGGUCUUAACCCGGAUUCCUCCCCC-AGAACCCGG
AE004091.2/3318663-3318859 CAAGGACCGC-A-AGGGUAUUCCAAAUCUGUUUAA-AAAA--CCGC--CAGCCCUG--UCUGGACGCCCCACGAACAUGACCAAUACUGAAAGGUACUGGCGCGCG--G--UAU-CUCCCCCCAAGUACCCAGCCAGU-GAAGGUACCG-AGGAA-UGCGUACCUUUGUUCCACUCCUAAUGGUCUUGACCCGGAUUCAUCCCCC-AGAACCCGG
AE015451.1/2229918-2229724 AACGAAACGU-U-GGCGUAUUCCAAAUCUGUUUAA-AAAA--CGUC--CAAUAUGC--ACUGGCACUGCGCCAAACCUGACCAAUACUUG-AAGUGUUG--GCGCG--G--CGC-AUCCCCCCCAGUGGCGCGCCGAU-AAAGGUGCUCAGGGAC-CGCGUACCUUUGUUUUACUCCUAAUGGUCUUAACCCGGAUUCCUCCCCC-AGAACCCGG
CP002290.1/4153073-4153266 AAUGAAACGU-U-GGCGUAUUCCAAAUCUGUUUAA-AAAA--CGUC--CAAUAUGC--ACUGGCACUGCGCCAAACCUGACCAAUACUUG-AAGUGUUG--GCGCG--G--CGC--AUCCCCCCAGUGGCGCGCCGAU-AAAGGUGCUCAGGGAC-CGCGUACCUUUGUUUUACUCCUAAUGGUCUUAACCCGGAUUCCUCCCCC-AGAACCCGG
CP002870.1/1725834-1725639 AAUGAAACGU-G-GACGUAUUCCAAAUUUGUUUAA-AAAU--CGAU--CAAUAUGC--ACUGGCACUGCGCCAAAGCUGACUAAUACUUG-AAGUGUUG--GCGCG--G--CGCAUCCCCCCCAAGUGGCGCGCCGAU-AAAGGUGCUCAGGGAC-CGCGUACCUUUGUUUUACUCCUAAUGGUCUUAACCCGGAUUCCCCCCCC-AGAACCCGG
CP000744.1/2256528-2256332 CAAGGAUGGC-A-GCGGUAUUCCAAAUCUGUUUAA-AAAA--CCAC--CAGCCCCG--UCUGGACGCCCCACGAACAUGACCAAUACUGAAAGGUACUGGCGCGCG--G--UAU-CUCCCCCCAAGUACCCAGCCAGU-GAAGGUACCG-AGGAA-CGCGUACCUUUGUUCCACUCCUAAUGGUCUUGACCCGGAUUCAUCCCCC-AGAACCCGG
CP002727.1/2932729-2932910 CAGACGCGGC-A-GGAGUAUUCCAAAUCCGUUUAA-A--G-----C--CGGC-------GUGGACGAUGGCUGCGGAUGACCAAUACUCAAUCGUACCG--GUGCG--G--CAU-AUUCCCCCAAGUGUCGCAGCGGC-CGAAGUGCCG-AGGAC-CGCGCACUUCG-UUUGACUCCUAAUGGUCUUGACCCGGAUUCCGUCCC---GAAGCCGG
CP000094.2/4687353-4687543 ACCGAAGCGA----ACGUAUUCCAAAUUUGUUUAA-AAACCCCGGC--CG--GCUA--ACUGGACUCGGCGCCAGACUGAUCAAUACUUG-AACUGUCG--G-GCG--A--CAU--CUCCCCCAAGUGUCGCGCCGGU-AAAGGUACCAAGGGAC-CGCGUGCCUUUGUUUUACUCCUAAUGGUCUUAACCCGGAUUCACCCCCC-AGAACCCGG
#=GC SS_cons               ::::::::::.:.::::::::::::::::::::::.::::..:(((..((,,,,,,..,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,<<<<..-<<-<..-..<<<.._________>>>->->>->>>>.<<<<<<<<<_______._>->>>>>>>>,,,,,,,,,,,,,)))))-----<<<<-<<<_______._>>>->>>>
#=GC RF                    cAagaAacGc.a.gauGUAUUCCAAAUcUGUUUAA.AAAa..Cgac..Caauauuc..aCUGGAcguucgccaAucaUGAcCAAUACUua.AagUgcuG..GcgcG..g..Cac..uuCCCCCAAguGcCucgCCagc.caAGGugcCgAaGGAc.cGCgcaCCUugGuUUUACUCCUAAuGgucUUAACCCGGauUCauCCCCC.AGAacCCGG
//
# STOCKHOLM 1.0

#=GF AC   RF00629
#=GF ID   P24
#=GF DE   Pseudomonas sRNA P24
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   100.00
#=GF TC   110.80
#=GF NC   94.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF CC   This small RNA (sRNA) was computationally identified in the genome of the
#=GF CC   opportunistic pathogen Pseudomonas aeruginosa and its expression verified
#=GF CC   by Northern blot analysis [1]. P24 is conserved across several Pseudomonas
#=GF CC   species and in Azotobacter vinelandii. It appears to be consistently
#=GF CC   located between a hypothetical protein gene and a transcriptional
#=GF CC   regulator gene (AsnC family) in the genomes of all these species. P24 has
#=GF CC   a predicted Rho independent terminator at the 3' end but the function of
#=GF CC   P24 is unknown [1].
#=GF WK   Pseudomonas_sRNA_P24
#=GF SQ   14


AAQW01000001.1/5129359-5129104 UUGCGCAAUCAAGGUUCUGGUGAGCAAUAUUAGCAAUCAUUG-GUCGCGCCUGGCGACG--U--AUUCUUUUACCCAGAUUCACGGCCCGGACAUCUCGUCCAUCACGGCUCGCCCAAUCAGGCCAGCCGUGGCCGCCGACCCUACAGGGUUGCGCCGGCCUCCGGGUUGCACACCGCCCAGAAGGUGGAGUGAGGUGAGCCGUCGCCAACAGCGCCGAGCCAGGACAGU-UACCCCAG-AAGGGA-GGUCGACGGGCCUCCCU
CT573326.1/5099291-5099037     UUGCGCAAGUGCUAUUUAUCAGAGCAAUCUUCGCAAUCCCCU-GCCGCACCAUUCGACC--U--AUCUUUAUCACCAGAAUCACUGCCCGGACAUCA-GUCCACGGCGACGCGCCCCAGACGGGCGGUCGCGGCCGGCCAUCCAACAGGAUCCGCCAGGCCCCCGGGCUACGCACUGUCCAGAAGACGGCGCGAGGUGAGCCGGUGUCACAAGCGCCGAGCACGGAC-GACAAUUCCCG-AAGGGA-GGCCGCAAGGCCUCCCU
AACY021957017.1/574-321        UUGCGCAAGCACUGUUUAUUGACGCAAUCUUCGCAAUCAUCU-GUCG--GACGUUGGCC--UGUAUCUUUAUCAACAGAAUCACCGCCUGGACA-ACAGUCCACUGCAGUUGGCCCAAUCAGGCCUGCUGCGGCCGCCGCCCCAGCAGGGUUGAGCCGGCCUCCAGGCUGCACACUGUCCACAAGACGGCGUGAGGUGAGCCAACGUCAAAAGCGUUGAGCCAGGAC-GA-AAUUCUCA-AGGGGC-GGCCGACGGGUCGCCCC
AP012280.1/5542719-5542464     UUGCGCAAUCAAGGUUCUGGUGAGCAAUAUUAGCAAUCAUUG-GUCGCGCCUGGCGACG--U--AUUCUUUUACCCAGAUUCACGGCCCGGACAUCUCGUCCAUCACGGCUCGCCCAAUCAGGCCAGCCGUGGCCGCCGACCCUACAGGGUUGCGCCGGCCUCCGGGUUGCACACCGCCCAGAAGGUGGAGUGAGGUGAGCCGUCGCCAAUAGCGCCGAGCCAGGAC-AGUUACCCCAG-AAGGGA-GGUCGACGGGCCUCCCU
AM181176.4/5924250-5923997     UUGCGCAAGCACUGUUUAUUGACGCAAUCUUCGCAAUCAUCU-GUCG--GGCGCAGGCGGGU--AUCUUUAUCAACAGAAUCACCGCCUGGACAACA-GUCCACAGCAGCUCGCCCAAUCAGGCCUGCUGCGGCCGCCACCUCAGCAGGGUUGAGCCGGCCUCCAGGCUGCACACUGUCCACAAGACGGCGUGAGGUGAGCCAACGUCAAAAGCGUUGAGCCAGGAC-GA-AGUUCUCA-AGGGGU-GGCCGACGGGUCACCCC
AE004091.2/4444952-4444697     UUGCGCAAUCAAGGUUCUGGUGAGCAAUAUUAGCAAUCAUUG-GUCGCGCCUGGCGACG--U--AUUCUUUUACCCAGAUUCACGGCCCGGACAUCUCGUCCAUCACAGCUCGCCCAAUCAGGCCAGCCGUGGCCGCCGACCCUACAGGGUUGCGCCGGCCUCCGGGUUGCACACCGCCCAGAAGGUGGAGUGAGGUGAGCCGUCGCCAACAGCGCCGAGCCAGGAC-AGUUACCCCAG-AAGGGA-GGUCGACGGGCCUCCCU
AE016853.1/5433294-5433054     UUGCGCAAGUGAUGUUUUAAUCGGCAAUAUUAGCAAUCCCCU-GCCACUGCCUCAGGCC--U--AUUCUUUUAAACAGAAUCACUGCCCGGACACAGCGUCCA--GCGACUCGCCAAAUCAGGCCAGUUGCGGCCUCCCACCCAACAGGGUGUGCCAGGCCCCCGGGCUACAUACUGUCCAGAAGACGGCAUGAGGUGAGCCGACGUCAAAAGCGUUGCGCCAGGAC-GA-AGCAUCUC-AAGGG--------GA-----CCCU
AEGG01000049.1/304292-304040   UUGCGCAAGUAAUGUUUUAAUCCGCAAUAUUAGCAAUCCUCU-GCCUUCGCCUCAGGCC--U--AUUCUUUUAACCAGAAUCACUGCCCGGACACAGCGUCCAGCGCGACUCGCCGAAUCAGGCCAGUCGCGGCCUCCCACCCAACAGGGUGUGCCAGGCCCCCGGGCUACAUACUGUCCAGAAGACGGCAUGAGGUGAGCCAACGUCAAAAGCGUUGCGCCAGGGC-GA-AGUAUCUC-AAGGG--GGCCAUUUGGUCCCCU-
AGFJ01000383.1/1309-1056       UUGCGCAAGUGCUAUUUAUCUGAGCAAUCUUCGCAAUCCUCUGUCGCAACCCGUCCG-G--U--AUCUUUAUCACCAGAAUCACUGCCCGGACAUCA-GUCCACGGCGACGCGCCCUAGGCGGGCGGUCGCGGCCAGCCAUCCAACAGGAUCUGCA-GGCCCCCGGGCUACACACCCUCCAGAAGACGGUGUGAGGUGAGCCGGCGCCACAAGUGCCGAGCACGGAC-GA-CAAUUCCU-GAAGGGAGGCCCUGUGGCCUCCCU
AGCS01000020.1/56915-56662     UUGCGCAAGUGCUAUUUAUCUGAGCAAUCUUCGCAAUCCUCU-GUCGCAACC--CGUCCGGU--AUCUUUAUCACCAGAAUCACUGCCCGGACAUCA-GUCCACGGCGACGCGCCCUAGGCGGGCGGUUGCGGCCAGCCAUCCAACAGGAUCUGCA-GGCCCCCGGGCUACACACCUUCCAGAAGACGGUGUGAGGUGAGCCGGCGCCACAAGUGCCGAGCACGGAC-GACAAUUCCUG-AAGGGA-GGCCCUGUGGCCUCCCU
CADW01000106.1/23307-23560     UUGCGCAAGUGGUGUUUUUACAAGCAAUCUUCGCAAUCCUCU-GUCUUCGCUGCGCGCC--U--AUUCUUAUCACCAGAAUCACUGCCCGGACAUAGAGUCCACUGCGGCCCGGCGAAUCAGGCCUGCCGCGGCCGCCAAUCCCACAGGGUUGAGCCGGCCCCCGGGCUACACACUGUCCAGAAGACGGAGUGAGGUGAGCCGGCGUCAAAAGCGCCGAGCACGGAC-AA-AAUCUCA--AAGGGC-GGCCGACGGGCCGCCCU
FM209186.1/1091343-1091598     UUGCGCAAUCAAGGUUCUGGUGAGCAAUAUUAGCAAUCAUUG-GUCGCGCCUGGCGACG--U--AUUCUUUUACCCAGAUUCACGGCCCGGACAUCUCGUCCAUCACGGCUCGCCCAAUCAGGCCAGCCGUGGCCGCCGACCCUACAGGGUUGCGCCGGCCUCCGGGUUGCACACCGCCCAGAAGGUGGAGUGAGGUGAGCCGUCGCCAACAGCGCCGAGCCAGGAC-AG-UUACCCCAGAAGGGA-GGUCGACGGGCCUCCCU
AEAO01000063.1/8359-8611       UUGCGCAAGUAAUGUUUUAAUCCGCAAUAUUAGCAAUCUUCU-GCCUUAGCCUCAGGCC--U--AUUCUUUUAAACAGAAUCACUGCCCGGACACAGCGUCCAGCGCGACCCGCCGAAUCAGGCCAGUCGCGGCCUCCCACCCGACAGGGUGUGUCAGGCCCCCGGGCUACAUACUGUCCAGAAGACGGCAUGAGGUGAGCCAGCGUCAAAAGCGCUGCGCCAGGAC-GA-AGUAUCUC-AAGGG--GGCCAUUUGGUCCCCU-
AGFS01026970.1/523-776         UUGCGCAAGUGCUAUUUAUCCGAGCAAUCUUCGCAAUCAUCU-GCCGCAGCC--UGUCCGGU--AUCUUUAUCCACAGAAUCACUGCCCGGACAUCA-GUCCACGGCGACGCGCCCUAGGCGGGCGGUCGCGGCCAGCCAUCCAACAGGAUCUGCA-GGCCCCCGGGCUACACACCUUCCAGAAGACGGUGUGAGGUGAGCCGGCGCCACAAGUGCCGAGCACGGAC-GACAAUUCCUG-AAGGGA-GGCCCAGCGGCCUCCCU
#=GC SS_cons                   <<<<____>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.<<<<_______>>>>,..,..,,,,,,,,,,,,,,,,[[[[[((((<<<<_____>>>>,,,<<<<<--<<<______>>>-->>>>><<<<<--<<<<<____>>>>>---->>>>>,,,)))),,<<<-<<<<<_____>>>>>->>>,]]]]]<<<<<<<<_____>>>>>>->>,,,,,,.,,.,,,,,,,,.,<<<<-.<<<<____>>>>->>>>
#=GC RF                        uugcGCAAgcaaugUUuuuaugaGCAAUaUUaGCAAUCaUcu.GccgcagccgucggCc..U..AUuuUUaUaacCAGAaUCaCcGCCCGGaCAucacGuCCAuuGCggCuCgCCcaAucaGGcCaGccGCGGCCgcCgacCCaACAGGgucuggccGGCCuCCGGGCUaCacACcguCCAgAAGacgGaguGAgGuGAGCCggCGcCAaaAgCGccGAGCcaGGAC.ga.aauucCua.AaGGGa.GGcCgacuGgCCuCCCu
//
# STOCKHOLM 1.0

#=GF AC   RF00630
#=GF ID   P26
#=GF DE   Pseudomonas sRNA P26
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   36.00
#=GF TC   36.00
#=GF NC   35.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF CC   This small RNA (sRNA) was computationally identified in the genome of the
#=GF CC   opportunistic pathogen Pseudomonas aeruginosa and its expression verified
#=GF CC   by northern blot analysis [1]. P26 is conserved across many
#=GF CC   Gammaproteobacteria species and appears to be consistently located between
#=GF CC   the DNA directed RNA polymerase (beta subunit) and 50S ribosomal protein
#=GF CC   L7/L12 genes. There are two eukaryotic sequences (AAGJ02000785.1 and
#=GF CC   AAAB01036679.1) included in this alignment which appear to be
#=GF CC   contamination.
#=GF WK   Pseudomonas_sRNA_P26
#=GF SQ   27


BA000037.2/3246217-3246162   UUACUUAGUCUCCUAGCCUAA-------------CGGCUAAU-GGCUGGUGGUUUUUUAACCACCGGCCU
U00006.1/46171-46232         ACCCUUCCGGUUGCAGCCUGAGA---AA-UC---AGGCUGAU-GGCUGGUGACUUUUUAGUCACCAGCCU
BX950851.1/255260-255321     ACCUUUCAGGUUGCAGCCUGA---UUUA----UUAGGCUGAU-GGCUGGUGACUUUUUAGUCACCAGCCU
CP000058.1/5240679-5240614   GACUUUGAGUGUCCAGCCCACGCGAUUA-GCGAAAGGCUGAU-GGCUGGUGGCUUUU--GCCACCGGCCU
CP000075.1/5416718-5416653   GAUUUUGAGUGUCCAGCCCACGCGUUUA-GCGAAAGGCUGAU-GGCUGGUGGCUUUU--GCCACCGGCCU
AE016853.1/678273-678338     GAUUUUGAGUGUCCAGCCCACGCGUUUA-GCGAAAGGCUGAU-GGCUGGUGGCUUUU--GCCACCGGCCU
CP000076.1/6375821-6375756   GACUUUGUGUCUCCAGCCCAAGCGUUAA-GCGAACGGCUGAU-GGCUGGUGGCUUUU--GCCACCGGCCU
CP000744.1/819985-820050     GACCUUGCGUCUACAGCCCGAGCGUCAA-GCGAAAGGCUGAU-GGCUGGUGGCUUUU--GCCACCGGCCU
AAVS01000001.1/114238-114178 UACGCUAAGUUCGCUGCCUGAGA---AA-UC---AGGCA-AG-GGCUGGUGAUUAUUUAAUCACCGGCCU
AAWQ01000063.1/22955-22899   UUGCAUAGUUUCUUAGCCUAA-------------CGGCUAAUUGGCUGGUGGUUUUUUAACCACCGGCCU
CP000304.1/879576-879641     GACUUUGCGUCUACAGCCCGAGCGACUC-GCGACAGGCUGAU-GGCUGGUGGCUCAU--GCCACCGGCCU
CT573326.1/502760-502825     GACUUUGCGACUCCAGUCCGAGCGUUAA-GCGAAGGGCUGAU-GGCUGGUGGCUUAU--GCCACCGGCCU
CP000680.1/4300164-4300099   CACCUUGCGUCUACAGCCCGAGCGACUC-GCACAAGGCUGAC-GGCUGGUGGCUUCU--GCCACCGGCCU
AP008232.1/217262-217320     ACCUUCCAGGUUGCAGCCUGA------A----UUAGGCUGAU-GGCUGGUGGCUUUUUGGUCACCAGCCU
AACY022708568.1/116-175      ACGCUAGGUUCGCUGCCUGAG-----UA----AUCAGGCAAG-GGCUGGUGAUUAUUUAAUCACCGGCCU
M38332.1/21-80               AUAACGCCGGUUGCAGCCCGAGA---AA-UC---AGGC--GU-GGCUGGUGACUUUUUAGUCACCAGCUU
ABEF01047555.1/1005-1070     GACCUUGCGUUUCCAGCCCAAGCGUUAA-GCUGAAGGCUGAU-GGCUGGUGGCUCUU--GCCACCGGCCU
BX571860.1/114672-114733     AGCUUUAAGUUAGCAGCCUGA---CUUG----AAAGGCUGAC-GGCUGGUGAUUAAAAAAUCACCAGCCU
CP000653.1/225700-225761     ACCCUUCCGGUUGCAGCCUGA---GAAA----UUAGGCUGAU-GGCUGGUGACUUUUUAGUCACCAGCCU
CP000305.1/267720-267781     AGCUUUGAGUUCGCAGCCUAA---CUUU----AUAGGCUGAU-GGCUGGUGACUUUUUAGUCAUCAGCCU
CP000020.2/2704298-2704243   UUACUUAGUUUCAUAGCCUAA-------------CGGCUAAU-GGCUGGUGGUUUAUUAACCACCGGCCU
CP001157.1/593671-593737     GAUCUUGCGUCUACGGCCUGCGCGCCCUUGCGUAAGGCUGAU-GGCUGGUGGCUGGA--GCCACCGGCCU
CP000926.1/555129-555193     GACUGUGCGAUGCCAGCCUGAGCGUUGA-GCGA-AGGCUGAU-GGCUGGUGGCUUAU--GCCACCGGCCU
CP000949.1/5243642-5243578   GACUUUGCGACUCCAGCCGGAGCGUUGA-GC-AAAGGCUGAU-GGCUGGUGGCUUAU--GCCACCGGCCU
CP000826.1/313159-313224     UGCUUUCUGAGUGCAGUCUGUUUUAACU-AAC--AGACUGAU-GGCUGGUGACUUUUUGGUCACCAGCCU
AALD02000042.1/9970-10030    AGCUUUGAGUUCGCAGCCUAA--CUUAU------AGGCUGAU-GGCUGGUGACUUUUUAGUCAUCAGCCU
CP000094.2/5718882-5718817   GACUUUGCUCCUCCAGCCCGAGCGUCAA-GCGACAGGCUGAU-GGCUGGUGGCUCUU--GCCACCGGCCU
#=GC SS_cons                 :::::::::::::<<<<<---<<.____.>>.--->>>>>--.<<<<<<<<<<______>>>>>>>>>>:
#=GC RF                      aacuUUgaGuuugCAGCCuGAGc.uuua.gC.aaAGGCUGAU.GGCuGGUGgCUUUUUAGcCACCgGCCU
//
# STOCKHOLM 1.0

#=GF AC   RF00632
#=GF ID   sxy
#=GF DE   sxy 5' UTR element
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF SE   Bateman A
#=GF SS   Published; PMID:17981840
#=GF GA   70.00
#=GF TC   71.30
#=GF NC   42.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   17981840
#=GF RT   RNA secondary structure regulates the translation of sxy and competence
#=GF RT   development in Haemophilus influenzae.
#=GF RA   Cameron AD, Volar M, Bannister LA, Redfield RJ
#=GF RL   Nucleic Acids Res. 2008;36:10-20.
#=GF WK   Sxy_5'_UTR_element
#=GF **   Wikipedia entry at: Sxy 5' UTR element
#=GF SQ   2


AAZI01000002.1/1639-1536 UUCUACUGACUCUUUUAAAAUAAUUAUUCAUUGGAGGUUUAAUAUGAAUAUAAAGGAUGAGCAUAUAGAUAGCGUUUGCUCCUUGUUAGAUCAGUUAGUAGGAA
AAZF01000018.1/1576-1473 UUCUACUGACUCUUUUAAAAUAAUUAUUCAUUGGAGGUUUAAUAUGAAUAUAAAGGAUGAGCAUAUAGAGAGCGUUUGCUCUUUGUUAGAUCGGUUAGUAGGAA
#=GC SS_cons             (((((((((((--(((((,,,,,,<<<<<<<____________>>>>>>>,,<<<<<<<<<<___________>>>>>->>>>>,)))))--))))))))))):
#=GC RF                  ucCuaCugaCcCUucuaaAAUAAUuauuCauUGGAGGUUUAAUauGaauaUAaagGacgagCAUAUAGAuAGCGcucgCuCcuuGuuagaUCgGucaGuaGgaA
//
# STOCKHOLM 1.0

#=GF AC   RF00634
#=GF ID   SAM-IV
#=GF DE   S-adenosyl methionine (SAM) riboswitch,
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Barrick JE
#=GF SE   Published; PMID:18369181
#=GF SS   Published; PMID:18369181
#=GF GA   38.00
#=GF TC   38.60
#=GF NC   37.10
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00012
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0046500; S-adenosylmethionine metabolic process;
#=GF RN   [1]
#=GF RM   18369181
#=GF RT   The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of
#=GF RT   SAM-I riboswitches.
#=GF RA   Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker
#=GF RA   RR
#=GF RL   RNA. 2008 Mar; [Epub ahead of print]
#=GF CC   SAM-IV is a mRNA element that regulates gene expression via direct sensing
#=GF CC   of S-adenosylmethionine (SAM or AdoMet). SAM-IV riboswitches share
#=GF CC   conserved nucleotide positions with the previously described SAM-I
#=GF CC   riboswitches sequence analysis and molecular recognition experiments
#=GF CC   suggest that SAM-I and SAM-IV riboswitches share similar ligand binding
#=GF CC   sites, but have different scaffolds.
#=GF WK   SAM-IV_riboswitch
#=GF SQ   40


AAAP01003574.1/1814-1929   GGUCAUGAG-UGCCAGCG---CGAAAC--CCCGGUU-UGCUGGC-CGGCAACCCUCC-----UCUCGC-GGCGGGGUGCC-CCGGGUGACGACCAGGCC--GC-AC-GCC-GACC-------------GGCGGGC--GGC-AAGCGCGGGGA
AAMN01000002.1/91115-91229 GGUCAUGAG-UGCCAGCG---ACAAGC--CCCGGCU-CGCUGGC-CGGCAACCCUCC-----AACCGC-GGUGGGGUGCC-CCGGGUGAAGACCAGGCG--GA-GC-GUC-GACC-------------GGCGC-C--CGC-AAGCACGGCAU
CP000454.1/2980407-2980520 GGUCACGAG-UGCCAGCG---CUAAAC--CCCGGUU-UGCUGGC-CGGCAACCCUCC-----AUUCGC-GGUGGGGUGCC-CCGGGUGACGACCAGGCC--G--GU-CCG-GAA--------------CGGACCC--GGC-AAGCGCGGAUC
AM420293.1/6539181-6539066 GGUCAUGAG-CGCCAGCG---UCAAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC-----AACCGC-GGUGGGGUGCC-CCGGGUGAGGACCUGGCC--G--GU-CGCGCAGG-------------GCGACCC--GGC-AAGCGCGGGCC
CP000580.1/1312753-1312635 GGUCAUGAG-UGCCAGCG---UCAAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC-----AACCGC-GGUGGGGUGCC-CCGGGUGAUGACCAGGUU--GA-GU-AGCCGUGA-----------CGGCUACGC--GGC-AAGCGCGGGUC
AP006618.1/5665640-5665528 GGUCAUGAG-CACCAGCG---CCAAGC--CCCGGCU-CGCUGGU-CGGCAACCCUCC------UCCGC-GGCGGGGUGCU-CCGGGUGACGACCUGGCC--GU-AC-CG--AAGA--------------CGGUGC--GGC-AAGUGCGGAUU
CP000474.1/2904762-2904875 GGUCACGAG-UGCCAGCG---CUAAAC--CCCGGUU-UGCUGGC-CGGCAACCCUCC-----AUUCGC-GGUGGGGUGCC-CCGGGUGACGACCCGGCC--G--GU-CCG-GAA--------------UGGAUGC--GGC-AAGCGCGGAUC
AACY020524451.1/3761-3655  GGUCAUGAG-UGCCAGCG---AUAAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC-----GACCGC-GGUGGGGUGCU-CCGGGUGAAGACCAGGCC--UG-A-------UAG-----------------UCA--GGC-AAGCGCGGGUC
CP000611.1/3736812-3736931 GGUCAUGAG-CGCCAGCG---UCAAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC-----AACCGC-GGUGGGGUGCC-CCGGGUGAUGACCAGGUU--GA-GU-AGCCAUCG----------CCGGCUGCGC--GGC-AAGCGCGGGUC
CP000325.1/1553430-1553311 GGUCAUGAG-CGCCAGCG---UCAAGC--CCCGGCU-UGCUGGU-CGGCAACCCUCC-----AACCGC-GGUGGGGUGCC-CCGGGUGAUGACCAGGUU--GA-GU-AGCCACAG----------UCGGCUACAC--GGC-AAGCGCGGGUC
AF052077.1/1481-1597       GGUCAUGAG-UGACAGUCA--UGAGGC--CCCGGCC-GACUGUC-CGGCAACCCUCC-----GUCCGU-GGCGGGGUGCC-CCGGGUGAAGACCAGGUC--GU-GG-ACA-GCAA-------------GGUCCAC--GGC-AAGCGCGGAUC
CP000509.1/3644126-3644238 CGUCACGAG-UACUGGCG---CGAAGC--CCCGGCU-GGCCAGU-CGGCAACCCUCC------UCCGC-GGCGGGGUGCC-CCGGGUGAGGACACGGCC--GA-CU-GCG-AC---------------CGCAGCC--GGC-AAGCGCGGACU
AE016958.1/3838572-3838694 GGUCAUGAG-CGCCAGCA---UCAAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC-----AACCGC-GGUGGGGUGCC-CCGGGUGAUGACCAGGUU--GA-GU-AGCCACCA-------CAACCGGCUAUCC--GGC-AAGCGCGGGUC
CP000656.1/5194683-5194802 GGUCAUGAG-UGCCAGCG---ACAAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC-----AACCGC-GGUGGGGUGCC-CCGGGAGACGACCAGGUUGAGU-AG-CCG-AACA-------------CGGCUAUAAGGC-AAGCGCGGGUC
CP000431.1/4627893-4628007 GGUCACGAG-UACCAGCG---UCAAGC--CCCGGCU-AGCUGGU-CGGCAACCCUCC------ACCGC-GGCGGGGUGCU-CCGGGUGACGACCAGGCU--GA-GG-UCCAUACC-------------GGACC-C--GGC-AAGCGCGGACU
CP000511.1/1643745-1643626 GGUCAUGAG-UGCCAGCG---AUAAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC-----AACCGC-GGUGGGGUGCC-CCGGGAGACGACCAGGUUGAGU-AG-CCG-GCCA-------------CGGCUAUAAGGC-AAGCGCGGGUC
BA000030.3/7291233-7291349 GGUCAUGAG-CGACAGUCA--UGAGGC--CCCGGCC-GACUGUC-CGGCAACCCUCC-----GUCCGU-GGCGGGGUGCC-CCGGGUGAAGACCAGGUC--GU-AG-GCA-GCGA-------------GGUCUAC--GGC-AAGCGCGGACC
CP000667.1/317960-317841   GGUCACGAG-CGCCAGCG---ACAAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCGUCGAGGUUCGC-GGUGGGGUGCC-CCGGGUGAUGACCGGGCC--UG-GC-GCG-GCG--------------CGCGUCG--GGC-AAGCGCGGACC
CT573213.2/4609200-4609314 CGUCUUGAG-UGCCAGCG---UUCAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC-----UUAUGC-AGCGGGGUGCC-CCGGGUGGUGACGAGGCC--G--CG-GCA-ACCC-------------CGCCGAC--GGC-AAGUGCCGACC
U00022.1/34579-34697       GGUCAUGAG-CGCCAGCG---UCAAGC--CCCGACU-UGCUGGC-CGGCAACCCUCC-----AACCGC-GUUGGAGUGCC-CC-GGUGAUGACCAGGUU--GA-GU-AGCCAGAA----------CCGGCUACGC--GGC-AAGCGCGAGUC
CP000480.1/1748393-1748264 GGUCAUGAG-CGCCAGCG---ACAAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC-----AACCGC-GGUGGGGUGCC-CCGGGUGAUGACCAGGUU--GA-GU-GGUUGACGGAUUCCUCCGUCGGCCGCAA--GGC-AAGCGCGGGUC
AAGP01000018.1/74571-74460 GUUCACGAG-UCGUGGCU---AUCGGUA-CCUGGCC-GGCCACG-CGGCAACCCGUC--------AUC-GACCGGGUGCC-CCAGGGAAAGAACGGGCC--CG-CA-CCA-CG---------------UGGUGCU--GGC-AAGAUUCGAUC
AY102616.1/3883-3767       GAUCAAGAA-GAUCAGCC---GCAAGCCCUUCGGCA-GGCUGAC-UGGCAACCGCGC------AUCGC-GCA-CGGUGCCCCCGAAGGAAGAUCGGCUC--UG-UA-CUC-AAAA-------------GAAUGCA--GAG-AAGAGCGAUUU
AP009044.1/1516225-1516341 GAUCAAGAA-GAUCAGCC---GCUAGCCCUUCGGCA-GGCUGAC-UGGCAACCGCGC------AUCGC-GCA-CGGUGCCCCCGAAGGAAGAUCGGCUC--UG-UA-CUC-AAAA-------------GAAUGCA--GAG-AAGAGCGAUUU
BA000035.2/1474355-1474472 GAUCAAGAA-GUUCAGCCU--CUAAGCCCUUCGGCA-GGCUGAC-UGGCAACCGCGC------AACGC-ACA-CGGUGCCCCCGAAGGAAGAUCCGCUC--UG-UA-CUC-AAAA-------------GACUGCA--GAG-AAGAGCGAUUA
CP000518.1/928910-928799   GCUCACGAG-CGGACGACUGUUCGGGUA-CCUGGCCCGUCGUCC-CGGCAACCGCGC-----GACCGCCGCA-CGGUGCC-CCAGGGGAAGAGCGGGCA--CG-A-------GCA-----------------UCG--UGC-AAGUGGUGGAC
CP000454.1/1479286-1479401 GGUCAUGAG-UGCCAGCG---AC-AGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC-----UUUCGC-GGCGGGGUGCC-CCGGGUGAAGACCUGGCC--UG-CCGGCC-AGUU-------------GGCGGCA--GGC-AAGCGCGAAGA
AP006618.1/396893-397006   GGUCAUGAG-UGCCAGCG---CAAAGC--CCCGGCU-CGCUGGU-CGGCAACCCUCC------UCCGC-GGUGGGGUGCU-CCGGGUGACGACCUGGCC--GC-CG-UCC-GACC-------------GGACG-C--GGC-AAGCGCGGACU
AACY020177622.1/1062-1175  GGUCAUGAG-UCUCAGUU---CAUAGC--CCCGGCU-AACUGAG-CGGCAACCCUCC------ACCAC-GGUGGGGUGCU-CCGGGUGAAGACCAGGUU--GA-UU-GCA-AAG--------------UGCAAUC--AGC-AAGCGUGGGUC
AAMN01000002.1/4575-4689   GGUCACGAG-UACCAGUG---UUCAGC--CCCGGCU-UGCUGGU-CGGCAACCCUCC------UCCGC-GGUGGGGUGCU-CCGGGUGACGACCUGGUC--GG-CU-GCA-GCAA-------------CGCAGUU--GGC-AAGCGCGGACU
CP000474.1/1618337-1618453 GGUCAUGAG-UGCCAGCA---CACAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC------UCCGC-GGUGGGGUGCC-CCGGGUGAAGACCUGGCC--UGUUC-GCACGCAA-------------GGCGACG--GGC-AAGCGCGAGGU
CP000431.1/6724422-6724302 GGUCAUGAG-UGCCAGCA---ACGAGC--CCCGGCU-AGCUGGC-CGGCAACCCUCC------ACCGC-GGUGGGGUGCC-CCGGGUGAUGACCUGGUU--UC-CU-GAUUCACA--------CAACAGUCGGGU--GAC-AAGCGCGGGUC
CT573213.2/4831346-4831458 UGUCACGAG-UGCCAACG---UCCAGC--CCCGGCU-UGUUGGC-CGGCAACCCUCC------ACCGC-GAAGGGGUGCC-CCGGGUGAGGACACGGCC--GC-AU-CCA-G----------------UGGAGGC--GGCAAAGCGCGGGCC
BA000030.3/8585292-8585400 GGUCAAGAG-CGUCAGCG---ACAAGC--CCUGGCU-UGCUGAC-CGGCAACCCUCG-----CGACGC-GGUGGGGUGCC-CCAGGUGACGACCGGACC--GG-A----U-GACC-----------------UUC--GGU-AAGCGCGAGGC
CP000480.1/1361993-1361882 CUUCACGAGACGCCGUCG---ACAAGC--UCCGACU-GGAUGGCGCGCCAACCCCAC-------GCUC-GU--GGGUGGC-UCGGAUGACGAAGCGGCC--UG-CA-CCA-CC---------------CGGUGCG--GGU-AAGAGCGCCUC
CP000656.1/5531569-5531680 GCUCACGAG-CGGACGACUGUUCGGGUA-CCUGGCCCGUCGUCC-CGGCAACCGCGC-----GACCACCGCA-CGGUGCC-CCAGGGGAAGAGCGGGCA--CG-C-------GGU-----------------GCG--UGC-AAGCGGUGGAC
CP000580.1/914360-914249   GCUCACGAG-CGGACGGCAGUUUGGGUA-CCUGGCCCGUCGUCC-CGGCAACCGCGC-----GACCACCGCA-CGGUGCC-CCAGGGGAAGAGCGGGCG--CG-G-------CUU-----------------ACG--UGC-AAGUGGUGGAC
CP000820.1/5910611-5910498 GGUCCUGAG-CGCCAGCG---UCAAGC--CCCGGCU-UGCUGGC-CGGCAACCCUCC------UCCGC-GGUGGGGUGCC-CCGGGUG-UGACCAGGCC--CG-CG-GCG-AACC-------------CGCCGUC--GGC-AAGUGCGGACC
CP000750.2/3280159-3280049 GGUCAUGAG-UGACAGCG---ACAAGC--CCUGGCU-CGCUGUC-CGGCAACCCUCC------UCCGC-GGCGGGGUGCC-CCAGGUGAAGACCCGGCC--GG-A---CG-AAAA-------------CG--UCC--GGC-AAGCGCGGAUC
CP000750.2/1351757-1351870 GGUCAUGAG-CGCCAGCG---ACAAGC--CCCGGCU-CGCUGGC-CGGCAACCCUCC------UCCGC-GGCGGGGUGCC-CCGGGUGACGACCUGGCC--GG-UG-CCG-ACG--------------UGGCGCC--GGC-AAGCGCGGACC
#=GC SS_cons               <<<<....<..<<<<<<.......<<........>>..>>>>>>.><<<..<<<.<<............>>..>>>.>>>..........>>>>..<<<..<<.<<.<<<..................>>>>>>>..>>>............
#=GC RF                    gguCAuGAG.ugccaGCg...auAaGc..cccGGCu.uGCuggc.CGGCAACCcucC.....aaccGc.GguggGGUGCC.CCgGGuGAaGaccaGGcc..gg.gg.ccc.aaaa.............gggcccc..ggC.AAGaGcgGauc
//
# STOCKHOLM 1.0

#=GF AC   RF00635
#=GF ID   HAR1A
#=GF PI   HAR1F; HAR1R; HAR1B
#=GF DE   Highly accelerated region 1A/1B
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:16915236; Eberhardt R
#=GF SS   Published; PMID:16915236;
#=GF GA   40.00
#=GF TC   44.30
#=GF NC   37.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 37.49 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   16915236
#=GF RT   An RNA gene expressed during cortical development evolved rapidly in
#=GF RT   humans.
#=GF RA   Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS,
#=GF RA   Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M
#=GF RA   Jr, Vanderhaeghen P, Haussler D
#=GF RL   Nature. 2006;443:167-172.
#=GF RN   [2]
#=GF RM   17040131
#=GF RT   Forces shaping the fastest evolving regions in the human genome.
#=GF RA   Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A,
#=GF RA   Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D
#=GF RL   PLoS Genet. 2006;2:e168.
#=GF WK   Human_accelerated_region_1
#=GF SQ   13


DQ860410.1/178-61            UGAAACGGAGGAGACGUUACAGCAACGUGUCAGCUGAAAUGAUGGGCGUAGACGCACGUCAGCGGCGGAAAUGGUUUCUAUCAAAAUGAAAGUGUUUAGAGAUUUUCCUCAAGUUUCA
AANU01093131.1/419-536       UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAGCUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGAAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
AAFC03066796.1/8405-8522     CGAAAUGGAGGAGAAAUUACAGCAAUUCAUCAGCUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGAAACCGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUUAAAUUUCA
AC152889.1/75335-75452       UGAAAUGGAGGAUAAAUUACAGCAAUUUAUCAAAUGAAAUUAUAGGUGUAGACACAUGUCAGCAAUGGAAACAAUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
DQ860412.1/770-887           UAAAAUGGAGGAGAAAUUACAGCAAUUUAUCAGCUGAAAUUAUAGGUGUAGACACAUGUCAGCCGUGGAAAUGGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
ABGA01067565.1/270-387       UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGAAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
ABRN01373532.1/4693-4810     CGAAAAGGAGGGGAAAUUACAGCAAUUCAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGGAACACUUUCUAUCAAAAUUAAAGUACUUAGCGAUUUUCCUUAAAUUUCA
ABRR01530888.1/207-324       UGAAACAGAGGAGAAAUUACAGCAAUUCAUCAACCGAAAUGAUAGGGAUAGACAUGUGUCGGCAGUGGAAACAGUUUCUAUCAAAAUUAAAGUAUUUAGAGACUUUCCUCAAAUUUCA
CABD02224489.1/391-508       UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGAAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
AAEX03014138.1/15195-15312   UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCGGUGCAAACAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
AACZ03124854.1/481-364       UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUGGAAAUAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
AAPE02054680.1/1732-1616     CGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAUCCGUGGAAACAGUUACGAUCAAAAUUAAAGUGUUUAGAGAUUUUCCUC-AAUUUUA
AADN03007856.1/620557-620674 UGAAAUGGAGGAGAAAUUACAGCAAUUUAUCAACUGAAAUUAUAGGUGUAGACACAUGUCAGCAGUAGAAACAGUUUCUAUCAAAAUUAAAGUAUUUAGAGAUUUUCCUCAAAUUUCA
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      uGAAAuGGAGGAGAaAUUACAGCAAUUuAUCAaCUGAAAUuAUAGGuGUAGACACAUGUCAGCaGUGGAAAcaGUUUCUAUCAAAAUUAAAGUaUUUAGAGAUUUUCCUCAAAUUUCA
//
# STOCKHOLM 1.0

#=GF AC   RF00636
#=GF ID   NRON
#=GF DE   ncRNA Repressor of NFAT (nuclear factor of activated T cells)
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; Gardner PP
#=GF SS   Predicted; Gardner PP
#=GF GA   50.00
#=GF TC   100.90
#=GF NC   32.70
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16141075
#=GF RT   A strategy for probing the function of noncoding RNAs finds a repressor of
#=GF RT   NFAT.
#=GF RA   Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P,
#=GF RA   Hogenesch JB, Schultz PG
#=GF RL   Science. 2005 Sep; 309:(5740)1570-3
#=GF WK   NRON
#=GF SQ   24


AADD01103245.1/5740-5371   GGGAGCGAAUGGCAUCGGGAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACACU-GCUGCCGCACAACCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACGCUUAUUUGCAUUCUUAUCAUGCCGGCAGCUCGCCC-UUAAAUACUGUUUCCACUACUGCUCCUUUACUG--UAAGUUUCCACCGAAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGUUAAAGA
AADA01286208.1/18105-17736 GGGAGCAAAUGGCAUCGGGAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACACU-GCUGCCGCACAACCAUAGCGACGGCAAAAUCAUUAGGCUAAUAACGCUUAUUUGCAUUCUUAUCAUGCCGGCAGCUCGCCC-UUAAAUACUGUUUCCACUACUGCUCCUUUACUG--UAAGUUUCCACCGAAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGUUAAAGA
AAHY01015175.1/6687-6318   GGGAGCAAAUGGCACCAGGAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCACAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUCACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCUGGAUGACAUAUUCACAACACU-GGUGCCGCACAACCAUGGCGACGGCAGAAUCAUUAGGCUAAUAACGCUUAUUUGCAUUCUUCUCAUGCCGCCAGCUCUCCC-UUAAAUACUGUUUCUACCACUGCUCCUUUACUG--UAACUUUCCACUCGACGGUAUUAACAGUAAUUAUUAGUGCUUUAGUGGAAUUU-UAAUGUUAAGAA
AANU01102576.1/963-594     GGGAGUGAAUGGCGUCGGGAACUUUGAAACUUUCCUUU-GUAUA-UUAUAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACCAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACACU-GCUGCCGCACAACCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACGCUUAUUUGCAUUCUUAUCAUGCCGGCAGCUCGCCU-UUAAAUACUGUUUCCACUACUGCUCCUUUACUG--UAAGUUUCCACCGAAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGUUAAAGA
ABDC01090171.1/2321-1952   GGCAGCAAAUGGCGCCGGGAACUCUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCUAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCAGGAUGACAUAUUCACAACACU-GCUGCCGCACAACCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCAUGCCAGCGGCUCGCCC-UUAAAUACUGUUUCUACUACUGCUCCUUUACUG--UAAGUUUCCACGGAAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGUUAAAGA
AAPY01835020.1/4591-4960   GGGAGCAAAUGGCGUUGGGAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACACG-GCUGCCGCACAGCCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCAUGCCGGCAGCUCUCCC-UUAAAUACUGUUUCCACUAGUGCUCCUUUACUG--UAAGUUUCCACUGGAAGAUAUUAACAGUAAUUAUGAGUACUUUAGUGGAAUUU-UAAUGCUAAAGA
AAFC03028358.1/51082-50713 GGGAGCAAAUGGCGUCGGGAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACAGA-GCUGCUGCACAACCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUCUCAUGCCGGCAGCUCUCCC-UUAAAUACUGUUUCUGCUAUUGCUCCUUUACUG--UAAGUUUCCACGGAAAGAUAUCAACAGUAAUUAUUAGUCCUUUAGUGGAAUUU-UAAUGUUAAAGA
AANN01817605.1/3408-3777   AAAAGCAAAUGGCAUCAGGAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACACU-GCUGCUGCACAACCAUGGCGACGGCACAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCAUGCCGGCAGCUCUCCC-UUAAACACUGUUUCUACUACUACUCCUUUACUC--UAAGUUUCCACGGGAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGUUGAAGA
AANG01442741.1/3287-2919   GGGAGCAAACGGCGUCGGGAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACACU-GGUGCCGCACAACCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCACGCUG-CAGCUCUCCU-UUAAAUACUGUUUCUACUAUUGCUCCUUUACUG--UAAGUUUCCACUGGAAGAUAUUAACAGUAAUUAUUACUACUUUAGUGGAAUUU-UAAUGUUAAAGA
AAIY01347731.1/1291-923    GGGAGCAAAUGGCUUCGGGAACUUCGAAAGUUUCCUUU-GUAGA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGAGUGCCGCAUGACAUAUUCACAACACU-GCUGC-GCACAACCAUGGCGACGGCACAAUCAUUACGCUAAUAACACCUAUUUGCAUUCUUAUCAUGCCGGCAGCUCUCCC-UUAAAUACUGUUUCUACUACUGCUCCUUUACUG--CAAGUUUCCAUCGAAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGUUAACGA
AAYZ01155974.1/2712-2344   GGGAGCAAAUGGCGUGGGGAACUUUGAAAGUUUCCUUU-GUAUA-UUACGUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCUGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCG-AUGACAUAUUCACAACACU-GCUGCCGCACAACCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUGAUCAUGCCGGCAGCUUUCCC-UUAAACACCAUUUCUACUACUGCUCUUUCCCUG--UAAGUUUCCACUGAAACAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGUUAAAGA
AAPN01381475.1/465-96      AGAAGCUAAUAGAGUCAGAAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCUAAAUUCACGGGUGCUGGAUGACAUAUUCACAACACU-GUUGCUGCACAACCAUGGCGAUGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCAUGCCAGCAGCUCUC-C-UUAAAUACUGUUUCAACCACUGCUCGUUUACUG--UAAGUUUCCACUGAAAGAUAUUAACUGUAAUUAUUAGUCCUUUAGUGGAAUUUUUAAUGCUAAAGA
AAFR03041416.1/45022-44651 AGGAGCUAAUCGUGUAGAAAACUUUGAAACUUUCCUUUUGUAUA-UUACAUUAAUCCAUAGAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCUGGAUGACAUAUUCACAACACU-GUUGCUGCACAACCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAGCAUGCCAGCAGCUCUCCUGUUAAAUACUGUUUCAACCACUGCUCGUUUACUG--UAAGUUUCCACUGAAAGAUAUUAACAGUAAUUAUUACUACUUUUGUGGAAUUU-UAAUGCAAAAAA
AAQQ01701148.1/3439-3781   GGGAGCAAAUGGCGUCGGAACUCUGGAACCUUCCCUUU-GGAUGGUUACAUUAAUCCAUAUAAGGAAAUCUCUUUUUAAUGAGGAGGUGAUGGAGUCUCAAACUCUCCCGACCCAUAAUUAGAGCAAACUAAU-GAAGCUGUGUUUUGACACACUUUCCAAACUCACGGGCGCCGG-CGACACACUCACAACACU-GCU--------------------GCAGAAUCAUUAGGCUAAUAACACUCGCUCGCAUCC----CGUGAAGCUCGCCCUCCC-UCAGACGCUGUUUCUGCACCCGC--CUGCCCUG--UG-GACUCCACU-GAAGAUAUCAACUGUGAUUAUGAGCACUUUUGUGGAAUUC-UAAUGUUAAGAG
AAWR02025746.1/67128-66759 GGCAGCAAAUGGCGUCGGGAACUUCGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCUGCGUGACAUAUUCACAACACU-GCCGCCGCACAGCCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCAUGCCGGCAGCUCUCCC-UUAAACACUGUUCUUACUAUUGCUCAUGUACUG--UAAGUUUCCACUGAAAGAUAUUAACAGUAAUUAUUAGUACUUCAGUGGAAUUU-UAAUGUUAAAGA
AAGV020078105.1/1086-1455  AGGAGCAAAUGGCGUCGGGAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACACU-GCUGCCGCACAACCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCAUGCCGGCAGCUCUCCC-UUAAAUACUGUUUCUACUAUUGCUCCUUUACUC--UAAGUUUCCACUGAAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGCUAAAGA
AAKN02030250.1/82861-83230 GCGAGCACAUGGCGCCAGGAACUUUGAAACUUGCCUUU-ACAUA-UUACAUGAAUCUAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAAGGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAACUCACGGGUGCCGGAUGACAUAUUCACAACACU-GCUGCUGCACAACCAUGGAGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCAUGCCGGCAGCUCUCCU-UUAAAUACUGUUUCUACUAUUGCUCCUUUACUC--GAAGUUUCCACGGGAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGUGAAGAA
AAEX03006877.1/91628-91998 GGGAGCAAACGGCGUCGGGAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACACUGGCUGCCGCACAACCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCACGCCGGCAGCUCUCCC-UUAAAUACUGUUUCUACCAGUGCUCCUUUACUG--UAAGUUUCCACUGAAAGAUAUUAACAGUAAUUAUUACUACUUUAGUGGAAUUU-UAAUGUUAAAGA
AAGU03017737.1/96303-96672 GGGAGCAAAUGGCAUCAGGAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCUAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACACU-GCUGCUGCACAACCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUCAUCAUGCCGGCAGCUUUCCC-UUAAAUACUGUUCCUACUAUUGCUCCUUUACUG--UAAGUUUCCACUGAAAGAUAUUAAUAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAACGUUAAAGA
AAGW02054415.1/9110-9478   GAGAGCAAAUGGUGUUGGGAACUUUGAAAGUUUCCUUU-GUAUA-UUACAUUAAUCCAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCG-AUGACAUAUUCACAACACU-GCUGCUGCACAACCAUGGUGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUGAUCAUGCCGGCAGCUUUCCC-UUAAAUACUGUUUCUACUACUGCUCUUACCCUG--UAAGUUUCCACUGAAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGUUAAAGG
AAPE02031918.1/50282-50651 GGGAGCAAGUGGCGUCGGGAACUUUGAAACUUUCCUUU-GUAUA-UUGCAUUAAUCCAUAGAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGGUGACAUAUUCACAACACU-GCCGCCGCACAGCCAUGGCGACGACAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCAUGCCGGCAGCUCUCCC-UUAAAUACUGUUUCUACUAUUGCUCCUUUGCUG--UAAGUUUCCACGGGAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUGGAAUUU-UAAUGUUAAAGA
AABR05099291.1/25863-26232 GGGAGAAAACGACAUCAGGAACUUUGAAACUUUCCUUU-GUCUG-UAACAUUAAUCCAUAUAAGAAAAUCUCCUUU-AAUGAGGAG-UGAUGUAGUCACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGAUGACAUAUUCACAACACU-GGUGCCGCACAGCCAUGGCGACGGCGGAAUCAUUAGGCUAAUAACGCUUAUUUGCAUUCUUCUCAUGCCACCAGCUCUCCC-UUAAAUGCUGUUUCUACCACUGCUCCUUUACUG--UGACUUUCCACGGGACGGUAUUAACAGUAAUUAUUAGCGCUUUAGUGGAAUUU-UAAUGUUAAGAA
AADN03007345.1/49387-49743 CCCCGCUCCACGCACCGG--------------CCCUUC-ACAUG-CUGCGUGUGUCCAUAUAAGAAAACCCCUUUU-AAUGAGAAG-CAAUAUAGUUAUGAACUCUCUAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCUGCAUGACAUAUUCACAACACU-ACUGCCGCACAGCCAUGGUGACAGCAGAAUCAUUAGGCUAAUAACGCUUAUUUGCAUUCUUAUCAUGCCAGCAGCAUGCCG-UUAAAUACUGCUUCA--CAGUGCUCGCUCACUGAGAAAGUUUCCACUGAAAGAUAUUAACAGUAAUUAUGAGUACUUCAGUGGAAUCUCUAACGUCAAGGA
AAQR03035688.1/87291-86922 GGCGGCAAAUGGUGUCAGAAACUUUGAAACUUUCCUUU-GUAUA-UUACAUUAAUCUAUAUAAGAAAAUCUCUUUU-AAUGAGGAG-UGAUGUAGUUACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCCGGGUGACAUAUUCACAACACU-GCUGCUGCACAGCCAUGGCGACGGCAAAAUCAUUAGGCUAAUAACACUUAUUUGCAUUCUUAUCAUGCCAGCAGCUCGCCC-UUAAAUACUGUUUCUACUACUGCUCCUUUCCUG--UAAGUUUCCACUGAAAGAUAUUAACAGUAAUUAUUAGUACUUUAGUAGAAUUU-UAAUGUUAAAGA
#=GC SS_cons               ................................................<<<<<.<<<<<..<<<.....<<<<<<.....>>>>>>.....<<<<<<<<...<<<....>>>.........<<<<<........<<<<.<<<<<....>>>>>>>>>..........<<<.<<.........................<<<<<........>>>>>..<<<<..........<<.<<<<.....>>>>.>>..........>>>>....>>...>>>.....................>>>>>....................................>>>>>>>>.....>>>..>>>>>.....>>>>>.......
#=GC RF                    GGGAGCaAAUGGCAuCaGGAACUUUGAAACUUUCCUUU.GUAUA.UUACAUUAAUCCAuAUAAGAAAAUCUCUUUU.AAUGAGGAG.UGAUGUAGUuACAAACUCUCCAGAGCCAUAAUUAGAGCAAACUAAUUGAAGUUGUGUUUUGACACACUUUCCAAAUUCACGGGUGCuGGAUGACAUAUUCACAAaACU.GgUGCCGCACAACCAUGGCGACGGCAaAAUCAUUAGGCUAAUAACGCUUAUUUGCAUUCUUaUCAUGCCGgCAGCUCuCCC.UUAAAUACUGUUUCuACuACUGCUCCUUUACUG..UAAgUUUCCACugaAaGaUAUUAACAGUAAUUAUUAGUaCUUUAGUGGAAUUU.UAAUGUUAAgaA
//
# STOCKHOLM 1.0

#=GF AC   RF00637
#=GF ID   mir-276
#=GF DE   microRNA mir-276
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase
#=GF SS   Predicted; WAR
#=GF GA   56.00
#=GF TC   57.60
#=GF NC   53.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000124;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus.
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF RN   [2]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF WK   MicroRNA
#=GF SQ   16


AAIZ01007696.1/7030-7122       CCUGGU--UUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUCAU--------AUUAUAAACUCGUAGGAACUUCAUACCGUGCUCUUGGA-AGACCAAAAGAC
AAEU02000190.1/4539-4630       CGAAGUCUUUUUACCAUCAGCGAGGUAUAGAGUUCCUACGUUCC-----------UAUUCAGUCGUAGGAACUUAAUACCGUGCUCUUGGA-GGACUGUCGACC
AAPU01011641.1/29322-29227     CGAAGUCUAUAUACCAUCAGCGAGGUAUAGAGUUCCUACGUGCAAA-------UUGCAAUAGUCGUAGGAACUUAAUACCGUGCUCUUGGA-GGGCUGUCGACC
AADK01021256.1/890-979         ACUGGU--AAUUACCACUAGCGAGGUAUAGAGUUCCUACGUAUG------------CUAACACUGUAGGAACUUCAUACCGUGCUCUUGGGUUUGCCAAAUUUC
AAFS01001503.1/12480-12386     CGAAGCCUCUUUACCAUCAGCGAGGUAUAGAGUUCCUACGUGCCG--------UAUCCAAAGUCGUAGGAACUUAAUACCGUGCUCUUGGA-GGGCUGUCCAUC
AAAB01013771.1/647-548         CAAAG---ACAACCCACCAGCGAGGUAUAGAGUUCCUAUGUGCCCAUUAGGCCGUUCGCUACUCAUAGGAACUUCAUACCGUGCUCUUGGA-UUGCUCUCAGCU
AAWU01010574.1/2274-2367       GUUGGU--GAUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUGCGA-------GUUCGAAAUCGGUAGGAACUUCAUACCGUGCUCUUGGC-UAGCCGAAAUUC
AAZX01001999.1/5300-5391       UAUGGUA-GAGAUCCAGCAGCGAGGUAUAGAGUUCCUACGUAGA-----------UUUCAGAAAGUAGGAACUUCAUACCGUGCUCUUGGACUUGCCGAAACAU
AAJJ01000143.1/58311-58223     UUUGGUA-GA---CCACUAGCGAGGUAUAGAGUUCCUACGU--G---------AUUUUUCGGCUGUAGGAACUUCAUACCGUGCUCUUGGAUUUACCGACCAUC
AAWU01046334.1/871-967         GAAAGUU-CAC--CCACUAGCGAGGUAUAGAGUUCCUAUGCGUUGUUUCG---AUUCGCUAUCCAUAGGAACUUCAUACCGUGCUCUUGGA-UGGCUUUCCGUU
AAGE02000417.1/11129-11035     UCGAGUU-AAU--CCGUCAGCGAGGUAUAGAGUUCCUAUGCGUUCGGA-----UAAAAUAUUCCAUAGGAACUUCAUACCGUGCUCUUGGA-UUGCUUGGAAGU
AAAB01008960.1/5047329-5047423 AGAGGU--GACUGCCAUCAGCGAGGUAUAGAGUUCCUACGGUAAUCG------AUUGAAACUUUGUAGGAACUUCAUACCGUGCUCUUGGA-UAGCCGUUUACC
AAZO01003220.1/6657-6747       UCGGGU--AUAAUUCAGCAGCGAGGUAUAGAGUUCCUACGUGCU---------UUGGUUAC--UGUAGGAACUUCAUACCGUGCUCUUGGAUGUGCCUAAUUCA
AAPP01019331.1/740947-741039   CCUGGU--UUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUAAC--------AUUAUAAACUCGUAGGAACUUCAUACCGUGCUCUUGGA-AGACCUAAAAUC
AAPT01020602.1/200228-200136   CCUGGU--UUUUGCCAUCAGCGAGGUAUAGAGUUCCUACGUUAAA--------UUUAAAUACUCAUAGGAACUUCAUACCGUGCUCUUGGA-AGACCAAAACAC
AAQB01008056.1/278056-277961   CGAAGCCUAUUUACCAUAAGCGAGGUAUAGAGUUCCUACGUGCAAA-------UUGCAAUAAUCGUAGGAACUUAAUACCGUGCUCUUGGA-GGGCUGUCGAAC
#=GC SS_cons                   :::<<<-.<<---<<<--<<<<-<<<<<--<<<<<<<<<<_____........__________>>>>>>>>>>-->>>>>->>>>-->>>-.>>>>>:::::::
#=GC RF                        aaagGca.aaaaaCCaucaGCgAGGuauAGaGuuCCuacgugaaa........auuaaaaaaucguaGGaaCuUcauaCCGuGCuCUuGGA.uugCcaaaaauu
//
# STOCKHOLM 1.0

#=GF AC   RF00638
#=GF ID   MIR159
#=GF DE   microRNA MIR159
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   74.00
#=GF TC   74.00
#=GF NC   73.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000010;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15200956
#=GF RT   Computational identification of plant microRNAs and their targets,
#=GF RT   including a stress-induced miRNA.
#=GF RA   Jones-Rhoades MW, Bartel DP
#=GF RL   Mol Cell. 2004;14:787-799.
#=GF RN   [2]
#=GF RM   17182867
#=GF RT   A diverse and evolutionarily fluid set of microRNAs in Arabidopsis
#=GF RT   thaliana.
#=GF RA   Rajagopalan R, Vaucheret H, Trejo J, Bartel DP
#=GF RL   Genes Dev. 2006;20:3407-3425.
#=GF RN   [3]
#=GF RM   15258262
#=GF RT   Novel and stress-regulated microRNAs and other small RNAs from
#=GF RT   Arabidopsis.
#=GF RA   Sunkar R, Zhu JK
#=GF RL   Plant Cell. 2004;16:2001-2019.
#=GF WK   MicroRNA
#=GF SQ   66


AP001800.2/28917-28720       AUGGAUGGAAGAGAGCGU-CCU--UCAGUCCACUCAUGGGCGG----UG----CU-AG--GGU-CGAAUUAG---------------CUGCCGACU-CAUUC-ACCCAC-AUG-CCA-AGCAA-GAAACGC--UUGAGA-----------------------------------------------------------------------------UAGCGAAGCUUA----------GCAGAUGAGUGAAUGAAGCGGGAGGUAA-C----------GUUCCGAU----CUCGCGCCGUCUUUGCUUGGACUG---AAGGGUGCUCCCUCCUCCUCGAUC
AP001800.2/44264-44453       GAAGAAGAAGACGAGCUC-CCU--UCGAUCCAAUCCAGGAGAG----GA----AG-U---GGUAGGAUGCAG---------------CUGCCGGUU-CAUGG-AUACCU-CUG-CAGUGCAUG-UCGUAGG----------------------------------------------------------------------------------------CUUGCACUU----------GCAUGGGUUUGCAUGACCCGGGAGAUGA-A----------CCCACCAU----UGUCUUCCUCUUAUGCUUGGAUUG---AAGGGAGCUCUACACCUCUCUCUC
AY884232.1/7-186             ---------GAGGUGCUC-CUU--UUAGUCCAAUACGGAGGGC----UG----AG-A---AGC-GGCUAGAG---------------CUGCCAUCU-CAUGC-AUUUAG-GCA-AUGCUUAAC-AUUUGACG-AAGAG---------------------------------------------------------------------------------AGGUUAAGC----------UUGGCCACUUGCAUGGUGUGGGAGCAAC-U----------CCUUCCGC----AUGCUUUGCUCGCCCAUUGGACUG---AAGGGAGCUCCUGGUUUU------
CU406292.1/220-493           GUUGUGGACGUUGAGCUC-CUU--UCGGUCCAAAAAGGGGUGU----UG----CU-GUG-GGU-CGAUUGAG---------------CUGCUGGGU-CAUGG-AUCCCG-UUA-GCCUACUCC-AUGUUCA--UCAUUCAGCUCGAGAUCUGAAAGAAACUACUCCAAUUUAUACUAAUAGUAUGUGUGUAGAUAGGAAAAUGAUGGAGUACUCGUUGUUGGGAUAGG----------CUUAUGGCUUGCAUGCCCCAGGAGCUGC-A----------UCAACCCU-------ACAUGGACCCUCUUUGGAUUG---AAGGGAGCUCUGCAUCUUUUGUCA
AY922324.1/461-652           UAUAUGUAGAGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-UCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-CCGAGUCGC-CAAAAUU--CAAA----------------------------------------------------------------------------------CUAGACUCG----------UUAAAUGAAUGAAUGAUGCGGUAGACAA-A----------UUGGAUCA------UUGAUUCUCUUUGAUUGGACUG---AAGGGAGCUCCCUCUCUCUUUUGU
AP002745.2/122724-122526     GAGGAGGAAGAGGAGCUC-CUU--UCGAUCCAAUUCAGGAGAG----GA----AG-U---GGUAGGAUGCAG---------------CUGCCGAUU-CAUGG-AUACCU-CUG-GAGUGCAUG-GCAGCAA----------------------------------------------------------------------------------------UGCUGUAGGCCUGCACUU-GCAUGGGUUUGCAUGACCCGGGAGAUGA-A----------CCCACCAU----UGUCUUCCUCUAUUGAUUGGAUUG---AAGGGAGCUCCACAUCUCUCUCGU
AP002745.2/130424-130234     UGAUGUGAGGAGGAGCUC-CUU--UCGAUCCAAUUCAGGAGAG----GA----AG-UG--GUG-GGAUGCAG---------------CUGCCGGUU-CAUGG-AUACCU-CUG-CA-GUUCAU-GCCG-------------------------------------------------------------------------------------------GUAGGCCUGCACUU-----GCAUGGGUUUGCAUGACCUGGGAGAUGA-A----------CCUGCCAU----UGUGUUCCUCUAUUGAUUGGAUUG---AAGGGAGCUCCGGCUACACCUAUC
AY884228.1/1-188             -----UUUAAGAGAGCUU-UCU--UCAGUCCACUCAUGGACGG----GC----GA-AG--GGUUUGGAUUAG---------------CUGCCGACU-CAUUC-AUUCAA-ACA-CAGUAGAAA-UUAAGGG--AGCAGU-----------------------------------------------------------------------------AUGGCUGCUAUU----------GUGAAUGUGUGAAUGAUGCGGGAGAUAA-A----------UUUCAUCC-----UUUUCUUCUCUGUGCUUGGACUG---AAGGGAGCUCCCUUUAAU------
AM474694.1/394-202           UGGGGGUUGAACAAGCUG-CCC--UCAUUCCAAAUUCAAAAGA----GU----AG-A---AGG-UGUUACAU---------------CUGCUGGUU-CAUGG-AUACCU-UUG-UAGUGUACA-GAUUAAU--AUAUC------------------------------------------------------------------------------CAAUG-------UCCCCU----UUAAGGGUUUGCAUGAAUGGGGAGAUGA-G----------GUUUCCUU-------CUUGACUUGUAAUUUGGUUUG---AAGGGAGCUCUGAUGACCCUUCUA
AY728415.1/7-185             ---------AAAGUGCUC-CUU--UUAGUCCAAUAAGGAGGGC----UG----AG-A---AGC-GGCUAGAG---------------CUGCCAUCU-CAUGC-AUUUAGGCAA-UGCUUAACA-UUUGGCA--AAGA----------------------------------------------------------------------------------GGUUUAAGC----------UUGGCCAGGUGCAUGGUGUGGGAGCAAC-U----------CCUUCCGC----AUGCUUUGUUCGCCCAUUGGACUG---AAGGGAGCUCCUGGUUUU------
AY551214.1/3-192             GGUUAUGAAGUGGAGCUC-CUU--UCGUUCCAAUGAAAGGUUU----AU----CU-GAA-GGG-UGAUACAG---------------CUGCUUGUU-CAUGG-UUCCCA-CUA-UUC-UAUCU-CAUAGGA--------------------------------------------------------------------------------------AAAGAGAUAGG----------CUUGUGGUUUGCAUGACCAAGGAGCCGA-A----------UCAACUCC------UUGCUGACCACUCUUUGGAUUG---AAGGGAGCUCUGCAUCUUGAUCCC
AM458581.1/27231-27413       UUACAUUGAAGAGAGCUU-UCU--UCAGUCCACUCAUGGGUGG----CA----GU-AG--GAU-UGAAUUAG---------------CUGCCGACUCCAUUC-AUCCAA-AUA-CUGUGUUAA-GGACUAC----------------------------------------------------------------------------------------CC-------A---------GUAAAUGAUUGAAUGAUGCGGGAGACAA-A----------UUGGAUCU------UAAGCUCCCUGUGCUUGGACUG---AAGGGAGCUCCCUUCACUGCAAUC
AK064418.1/273-459           UGUGUAAGAAGAGAGCUC-UCU--UCAGUCCACUCUCAGAUGG----CU----GU-AG--GGU-UUUAUUAG---------------CUGCCGAAU-CAUCC-AUUCAC-CUA-CCAGGAAAG-UUGC-----AGGAG-------------------------------------------------------------------------------UGUAUCUCUUG----------GUAGCGGACUGGAUGACGCGGGAGCUAAAA----------UUUAGCUC------UGCGCCGUUUGUGGUUGGACUG---AAGGGUGCUCCCUUGCUC------
AY775975.1/842-1033          UCGAUAGAUAGAGAGCUU-CCU--UGAGUCCAUUCACAGGUUG----UG----AU-AU--GAU-CCAAUUAG---------------CUUCCGAAU-CAUUC-AUCCAA-AUA-CUGAGUCAC-CAAAAUU--CAAA----------------------------------------------------------------------------------CUAAACUCG----------UUAAAUGAAUGUAUGAUGCGGUAGACAA-A----------UUGGGUUA------UUGAUUCUCUAUGAUUGGACUG---AAGGUAGCUCCCUCCCCUUUUUGA
AARH01017144.1/4716-4901     GAUUAGGGAGUGGAGCUC-CUU--GAAGUCCAAUAGAGGUUCU----UG----CU-G---GGU-AGAUUAAG---------------CUGCUAAGC-UAUGG-AUCCAC-AGU-CCUAUCUAU-CAAC-----------------------------------------------------------------------------------------CGAAGGAUAGG----------UUUGCGGCUUGCAUAUCUCAGGAGCUUU-A----------UUGCCUAA------UGUUAGAUCCCUUUUUGGAUUG---AAGGGAGCUCUAAACCCAUAACCC
CR962124.2/16450-16257       UGAAUGGUAAGAGAGCUU-UCU--UUAGUCCACUCAUGGGUGA----CA----AU-AA--GAUUUCAAUUAG---------------CUGCUGACU-CAUUC-AUCCAA-AUG-UUGAGUAAA-AUAU-----AUAGA------------------------------------------------------------------------------AACAUAUACUCA----------UCAAAUGAGUGAAUGAUGCGGGAGACAA-A----------UUGAAUCU------UAAGUUUCCUAUACUUGGACUG---AAGGGAGCUCCCUUUUCUUCCUUU
AASG02014601.1/2536-2726     UAUGGGAAGAAGGAGCUC-UCU--UCAGUCCAGUCCAAGGCGG----UU----GA-GG--GCUGGGACUUAG---------------CUGCUGACU-CGUUG-GUUCAA-GAG-CUCAUCAUC-AUCA-----AUGUG---------------------------------------------------------------------------------UAAGAGAUGU---------CUUUUUGAUCCAACGAAGCUGGAGCUGU-G----------UUCAGUUA-------UGGCUGUCAUGUCUUGGACUG---AAGGGAGCUCCCUCCAAUUCUUAC
AARH01000160.1/529592-529782 UAAUAGCUAAGAGAGCUU-UCU--UCAGUCCACUCAUGGGUGG----UA----GU-AG--GAU-UUAAUUAG---------------CUGCCGACU-CAUUC-AUCCAA-AUA-CUGAGUUAA-AGGACAAG-GAGAU------------------------------------------------------------------------------UACCC-------A---------GUAAAUGAGUGAAUGAUGCGGGAGACAA-A----------UUGAAUCC------UAAGCUUCCUGUACUUGGACUG---AAGGGAGCUCCCUUUCCUUUUAUA
AY728413.1/1-192             ---GGUGGGAGAGAGCUU-CCU--UCAGCCCACUCAUGGAUAG----GAGA--AA-GG--GGU-UGAAUUAG---------------CUGCCGACU-CAUUC-AUUCAA-GCA-CCAGUAGAA-AAAGGGG--AAUGGAUAU--------------------------------------------------------------------------UCUUUUGCUACU----------GUGAUUGUGUGAAUGAUGCGGGAGAUAA-U----------UUUACAUC----CCCUCUUUUUCUGUGCUUGGACUG---AAGGGAGCUCCUUCC---------
AB005233.1/55604-55413       GGUGGAGGAAGAGAGCUU-UCU--UCGGUCCACUCAUGGAGUA----AU----AU-GUGAGAU-UUAAUUGA---------------CUCUCGACU-CAUUC-AUCCAA-AUA-CCAAAUGAA-AGAAUUU--------------------------------------------------------------------------------------GUUCUCAUAUG----------GUAAAUGAAUGAAUGAUGCGAGAGACAA-A----------UUGAGUCU------UCACUUCUCUAUGCUUGGACUG---AAGGGAGCUCCCUAUUUUUAUCUU
AY775970.1/761-570           CAGAAAGAGAGGGAGCUC-CCU--UCAGUCCAAUCAAAGAGAA----UC----AA-U---GAUCCAAUUUGU---------------CUACCGCAU-CAUUC-AGUCAU-UUA-AC-GAGUCU-AGUU-----UGAAU------------------------------------------------------------------------------UUGGGUGACUCG----------GUAUGUGGAUGAAUGAGUCGGAAGCUAA-U----------UGGAUCAU------AUCACGACCUGUGAAUGGACUC---AAGGAAGCUCUCUCUAUAUAUUUU
AARH01006065.1/469812-470008 UUGUAAAUUUGGGAGCUU-UCU--UUGGUUCAAAAUGAGGAAA----GA----AA-GUG-GGU-AUACUCGU---------------CUGCUUGUU-CAUGG-AUACCU-CUG-GGU-UGCGC-AGGAUAUA-UUAGU------------------------------------------------------------------------------UAGGGCUACAGC----------UUAAGGGUUUGCAUGGCCAAGGAGACGU-U----------GCCUGCCU------UCUCCUUUCGUUUCUUGGAUUG---AAGGGAGCUCCUACAUGUAUCUCA
AARH01006065.1/463210-463415 UGAGGCUCAAUGGAGCUC-UCC--CCACUCCAUGCCUGAAAGG----AG----UUCGAU-GGUAGACCAUGG---------------CUGCUAGUU-CAUGA-AUACCC-UUG-GGUGCGCAG-AAUUAGC--AACGGUGCAGGCG----------------------------------------------------------------------AAGUUGCGCAGG----------CUAAGGGUCUGCAUGACCUAGGAGACGU-G----------GUUACCCU-------GACCCUUUUUGUAUUGGAGUG---AAGGGAGCUCGAUGGUCUUUCACC
AARH01006065.1/468133-468321 ACCAUUAAAUAGGAGCUU-GCU---CACUCCAGAUCUGAAAGG----AG----GU-GAUAGGA-AACCACUU---------------CUGCUACUU-CAUGA-AUACCC-GUG-GGUGUGCGC-GUAGCCA--UGGUG-------------------------------------------------------------------------------AGCUGCGCAGG----------CUAAGGGUCUGCAUGUGCUAGGAGAUGU-G----------GUUGCCUU-------GAUCUUUUUGGUCUUGGGGUG---AAGGGAGCUCCUAUAGUC------
AASG02000051.1/79825-80017   UUAGGCGUAAUGGUGCUC-UCU--UCACUCCUGUUGUAAAAGG----AG----GU-GAU-GGUAGGCCACGG---------------CUGCUAGUU-CAUGA-AUACCC-CUG-GCUGCGCAG-GAUUAAAGUAAUAA------------------------------------------------------------------------------AGUUUGCGCAGG----------CUAAGGGUUUGCAUGACCUGGGAGACGU-G----------GUUACCUU-------CUUCUUUUUUAUAUUGGAGUG---AAGGGAGCUCUGUUGUCU------
AASG02000051.1/89024-89224   UAUAUAUAUGCGGAGCUC-CUU--UUGGUCCAAAAUGAGGACU----CUGA--AA-GAG-GGCAUAGCAGGU---------------CUGCUAGUU-CAUGG-AUACCU-AUG-GGUUGCAGU-UGGAAACU-AACACA-----------------------------------------------------------------------------UUUUUGCGCAGC----------UUAAGGGUUUGCAUGACCUGGGAGACGU-G----------UUUCCCUU-------CCCCUUUCCUUAAUUGGAUUG---AAGGGAGCUCCUCCUGUUUAUUUG
AASG02000051.1/86758-86979   AUGCGUGCAUGGGGGCUC-UCUUCUAGCUCCGAUUCUGAAAGG----AG----AU-GAU-GGUGCGACAUGG---------------CUGCUAGUU-CAUGA-AUACCC-UUU-GGUGCGCAG-GUCAGUU--CUAUGUAGUUGGCAAAUGGCAAUG-----------------------------------------------------------GUGAUGCGCAGC----------CUAAGAGUAAGCAUCUGCUGGGAGCUCU-G----------UUUACCUU---UGAUAUUCUUUUUGGUAUUGGGGCG---AAGGAAGCUCCUAUAUUUACAUGU
AY775959.1/657-847           UAUGUACGGAGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-CCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-CCGAGUCUC-ACCA-----AAAUUG-----------------------------------------------------------------------------GAACAAGACUUG----------UUAAAUGAAUGAAUGAUGCGGUAGACAA-A----------UUGGAUCA------UUGAUUCUCUUUGAUUGGACUG---AAGGGAGCUCCCUUUCUUCUU---
AY775965.1/635-823           GAUAAAGAGAGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-CCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-CC-GAGUCA-CCAAAAU--UCGAG---------------------------------------------------------------------------------CAAGACUCG----------UUAAAUGAAUGAAUGAAGCGGUAGACAA-A----------UUGGGUCA------UUGAUUCUCUAUGAUUGGACUG---AAGGGAGCUCCCUCUAUAUUU---
AM434575.1/6317-6094         GGAACAGCUGAAGAGCUC-CUU--UUAGUCCAAUAAAGAGGGC----UG----AG-G---GGC-GGCCAGAG---------------CUGCCAUCU-CAUGC-ACUUGG-CUA-UGCUUAUUC-UUUUCUCA-AUCAAUUCGGUUCGAGUAUGGCUGUGGAGUGA---------------------------------------------------CAAAUGCUAAGU----------UUAGCCUGAUGCAUGACAUGGGAGCAAC-U----------CCUCCGCA-----CGCUUUGCCCACUCAUUGGACUG---AAGGGAGCUCCCAGGGCAGAUCUC
AP006665.1/46415-46593       AAUAGAAUGAAGGAGCUU-CCU--UCUGCCCAACCAUGGAUAU----AU----GU-GAG-GGA-AGCCUUUG---------------UUG-------CAAAA-AUA-AA-CUA-UUAUUCAUU-CAUUCAU-------------------------------------------------------------------------------------------------AU--------AUAAUUAUGUGAAUGAAGUGGAAGAUGU-A------UAUUUUGCAGCC------UUCUUUGGCUAUGUUUGGACUG---AAGGGAGCUCCUUCUUUCUGUUGC
AY884229.1/1-180             --AUAGAUAAGAGAGCUU-UUU--UCGGUCCACUUAUAGAUAG----UA----AU-AU--GAU-UUAAUUAG---------------UUACCGACU-CAUUC-AUCCAA-AUA-CUGAGUUAU-GAGCUAA----------------------------------------------------------------------------------------GAUUACCCA----------GUAAAUGAAUGAGUGAUGCGGGAGACAA-A----------UUAAAUCU------UAAACUUCCUAUCAUUGGACUG---AAGGGAGCUCCCUUUACU------
AY884231.1/6-193             ---------AGAGAGCUU-CUU--UCAGCCCACUCGUGGAUAG----GA----CA-AAGGGGU-UGAACUAG---------------CUGCCGACU-CAUUC-AUUCAA-GCA-CUAGUAGAA-AAAAAGGCGAACGGUGUU--------------------------------------------------------------------------UCUUUUGCUACU----------GUGAUUGUGUGAAUGAUGCGGGAGAUAA-U----------UUUCCAUC----CUCUCCUUUUCUGUGCUUGGACUG---AAGGGAGCUCCUUCC---------
AC012679.5/41369-41166       ACGAUGGAAGUAGAGCUC-CUU--AAAGUUCAAACAUGAGUUG----AG----CA-G---GGUAAAGAAAAG---------------CUGCUAAGC-UAUGG-AUCCCA-UAAGCCCUAAUCC-UUGUAAA--GUAAA------------------------------------------------------------------------------AAAGGAUUUGGU----------UAUAUGGAUUGCAUAUCUCAGGAGCUUUAA----------CUUGCCCUUUAAUGGCUUUUACUCUUCUUUGGAUUG---AAGGGAGCUCUACAUCUUCUUUCA
AM462844.1/17936-17742       UUGUGGAAGAAGGAGCUC-UCU--UUAGUCCAGUCCGAGACAG----CU----UC-AAG-GCUGAUACGUGG---------------CUGCUGACU-CGUUG-CUUCAA-GAA-CUCAUCACA-UASKCCUG-GAAAA---------------------------------------------------------------------------------GAUGGAUGG----------UUUUUUGAUCCAACGAUGCAGGAGCUGC-G----------UUCAGUUA-------UGGCUGUCACGUCUUGGACUG---AAGGGAGCUCCCUUGUAUUCCACA
AM457512.2/2227-2039         AGGGGCUUGUGGGAGCUU-CUUU-ACACUCCAGAACUGAAAGG---------------------AGAUACUA---------------CUGCUGGUU-CAUGA-AAACCU-AUG-GCUGCAUUC-UCUAUACU-GAAAU------------------------------------------------------------------------------UUUGUAUACAAA----------CUAUGGGUUUGCAUGAMCUUGGAGAAGU-G----------UUUGCUUU------UAUCUUUUCUGGCCUUGGAGUG---AAGGGAGCUCUCAUAACCGAUCUA
EF203471.1/100-300           UAGAUAUAGAAGGAGAUU-CUU--UCAGUCCAGUCAUGGAUAGAACAAG----AA-GAG-GGU-AGAAACAU---------------CUGCCGACU-CAUCC-AUCCAA-ACA-CUUCUGGUA-AAAAGAA--AAUAGA-----------------------------------------------------------------------------UUUUAUACCACA----------GUGGCUGUGUGAAUGAUGCGGGAGAUGU-U----------UUCAUCUC-------UCUUUAUCUGUGUUUGGACUG---AAGGGAGCUCCUUCUUUAUCUACA
AP009362.1/69443-69635       GUUUUGAAGGUAGAGCUCUUCU--GAAUUCCAAAGAGGAUCUA----AG----A---G--GGA-AAAUUGAG---------------CUGCUGAUC-UAUGG-AUCCCU-CAA-UCCUAUCUA-UUUU-----CAGAUUA----------------------------------------------------------------------------AUUUUAGAUAGG----------UUUGUGGUUUGCAUAUAUCAGGAGCUGC-A----------UUUACUCU-------UCUAGGAUCUUUAUUGGAAAG---AAGGGAGCUCUACACUUGAUAACC
AP009362.1/68028-68220       GUUCUGAAUGUAGAGCUUUUCU--GAAUUUCAAAGAGGAUCUG----AG----A---G--GGA-AAAUCGAG---------------CUGCUAAUC-UAUGG-AUCCCU-CAA-ACCUAUCUA-UUCUCAA--AAUAA-------------------------------------------------------------------------------UUUUAGAUAGG----------UUUGUGGUUUGCAUAUAUCAGGAGCUUC-A----------UUUACUCU-------UCUAGGAUCCUUAUUGGAAUG---AAGGGAGCUCUACGUUUGAUAACC
AASG02006722.1/5309-5498     ---------AAGGAGCUC-CUU--UCAGUCCAAUAUGGAGGGC----UU----AG-AA--GCG-GCAAAGAG---------------CUGCCAUCU-CAUGC-AUUAAGGCAA-UACUUGACA-AGUUUUUCACAGUG------------------------------------------------------------------------------AAAAUCUCAAGU----------UUGGCCUGGUGCAUGGUGUGGGAGCAAC-U----------CCUUCCCU------CCUUCCCCCACCCAUUGGACUG---AAGGGAGCUCCUUCUUUCAUUUUG
AARH01006425.1/130179-130368 GAUUAUGGAGUGGAGCUC-CUU--GAAGUCCAAUAGAAGCUCC----UG----CU-G---GGU-AGAUCGAG---------------CUGCUGAGC-UAUGA-AUCCCA-CAG-CCCUAUCACCAUCAGUC--------------------------------------------------------------------------------------AUUUUGAUGGG----------CCUGCGGCUUGCAUAUCUCAGGAGCUUU-A----------UUACCUAA------UGUUAGAUCUUUUUUUGGAUUG---AAGGGAGCUCUAAACCUUUGAUCU
AARH01008917.1/59768-59958   UAUAACUUAAUGGAGCUU-CCU--CCACUCCAAGUCUGAAAAG----GA----UGUGAG-GGUGUAUCACUG---------------CUGCAAACU-CAUGCAAUUCCC-AUA-AGAAGGCAU-GGUU-----------------------------------------------------------------------------------------UUUAUUGCAAU----------CUAAGGGCCUGCAUGAAUCUGAAGAAGU-G----------ACUGUCUA------GUUUUUUCUGGAUAUUGGAGAGAUCAAGGGAAAUCCACACACACUU---
AM432013.2/1939-2131         GGGGGAUUGAACAAGCUG-CCU--UCAUCCCAAAAUCAAAAGA----GU----AG-A---AGG-UGUUACAU---------------CUGCUGGUU-CAUGG-AUACCU-UUG-UA-GUGUAC-AGAUUAA--UAUAU------------------------------------------------------------------------------CUAAUGUCCACU----------UUAAGGGUUUGCAUGAAUGGGGAGAUGA-G----------GUUGCCUU-------CUUCACUUAUAAUUUGGUUUG---AAGGGAGCUCUGAUAGUCCUUCUC
AY775971.1/606-797           UAUAUUAAUGGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-CCAAUUAG---------------CUUCCGACU-CAUUC-AUACAA-AUA-CCGAGUCAC-AGAAAUC--UUAA----------------------------------------------------------------------------------CUGGACUCG----------GUAAAUGAAUGAAUGAUGCUGUAGACAA-A----------UUGGAUCA------UUGAUUCUCUCUGAUUGGACUG---AAGGGAGCUCCCUCUCUUUAGGUA
EF091572.1/1-172             ---------AGAGAGCUU-UCU--UUAGUCCACACAUGGGGAA----CG----AU-AG--GGU-UCAAUUUG---------------CUGCCGACU-CAUUC-AUCCAA-AUG-UUGAGGUCU-UGAU-----AAUCG------------------------------------------------------------------------------AGUGCCACCUCA----------GCAACUGAGUGAAUGAAGCGGGAGUACAAG----------UUGAGUCU------UGAGCUUCCUGUACUUGGACUG---AAGGGAGCUCC-------------
AASG02011104.1/6116-5917     AAUGGUUUAAGAGAGCUC-UCU--UCAGUCCACUCAUGGGCGG----GC----GA-AG--GUUUUGAAUUAU---------------CUGCCGACU-CAUUC-AUUCAA-ACA-CACUAGAAA-AGGGAGCAUUAAAG------------------------------------------------------------------------------AUAGCUGCUAUU----------GUGAAUGUGUGAAUGAUGCGGGAGAUAA-A----------UUUCAUAC-----UUCUCUUCUCUGUGCUUGGACUG---AAGGGAGCUCCCUUUAGCUGUAUC
AM471650.2/47253-47061       AGUGGUUUAAGAGAGCUU-CCU--UCAGUCCACUCAUGGAUGG----GU----UA-GG--GGUUUGGAUUAG---------------CUGCCGACU-CAUUC-AUUCAA-ACA-CAGUAGAAU-GGAA-------AUG------------------------------------------------------------------------------GAGUUUACUACU----------GUGAAUGUGUGAAUGAUGCGGGAGGUAA-A----------UUUCAUCC-----UUUUCUUGUCUGUGCUUGGACUG---AAGGGAGCUCCCUUCUACUGUUUU
AC069551.4/12020-12227       GAAGAAGAGGAAGAGCUC-CUU--GAAGUUCAAUGGAGGGUUU----AG----CA-GG--GUG-AAGUAAAG---------------CUGCUAAGC-UAUGG-AUCCCA-UAA-GCCUUAUCA-AAUUCAA--UAUAAUUGAU-------------------------------------------------------------------------GAUAAGGUUUUU----------UUUAUGGAUGCCAUAUCUCAGGAGCUUUCA----------CUUACCCCUUUAAUGGCUUCACUCUUCUUUGGAUUG---AAGGGAGCUCUUCAUCUCUCCAUC
AC005397.3/28936-28710       GUGUAACAGAAGGAGCUC-CCU--UCCUCCAAAACGAAGAGGA----CAAGAUUU-GA--GGA---------ACUAAAAUGCAGAAUCUAAGAGUU-CAUGU-CUUCCU-CAU-AGAGAGUGC-GCGGUGUU-AAAAG------------------------------------------------------------------------------CUUGAAGAAAGCACACUU----UAAGGGGAUUGCACGACCUCUUAGAUUC-UCCCUCUUUCUCUACAUAU---CAUUCUCUUCUCUUCGUUUGGAUUG---AAGGGAGCUCCUUUUCUUCUUCUC
AASG02019405.1/2563-2341     AGCAUUUUAAGAGAGCUU-UCU--UCAGUCCACUCAUGGGUGG----CG----GU-AG--GAU-UUAAUUAG---------------CUGCCGACU-CAUUC-AUCCAA-AUA-CUGAGUUAA-AAAG-----UUCAGAAAACAAAAGGGGCGGGUGCUGUAGAAAAG------------------------------------------------AAGGUUUACCCA----------GUAAAUGAGUGAAUGAUGCGGGAGACAA-A----------UUGAAUCU------UAAGCUUCCUGUACUUGGACUG---AAGGGAGCUCCCUUUACUGUUAUU
AASG02000468.1/24439-24641   AAUGGUGUGAGAGAGCUU-CCU--UCAGCCCACUCAUGGAUGG----GGGUA-AA-GG--GGC-UGAAGUAU---------------CUGCCGACU-CAUUC-AUUCAA-GCA-CUAGUAGAC-AAAGGGA--UUGGUACU---------------------------------------------------------------------------GUUUUAGCUACU----------GUGAUUGUAUGAAUGAUGCGGGAGAUAA-U----------UUUGCAUC-----CCUCUUUUUCCGUGCUUGGACUG---AAGGGAGCUCCUUCUUUCUACAGC
CU459032.2/137942-137752     AAUAGAUGAAGAGAGCUU-CCU--UCAGUCCACUCAUGGAAGG----GU----AA-GG--GGUUUGAAUUAC---------------CUGCUGACU-CAUUG-AUUCAA-ACA-CAAUAGACA-AUUAUGG-------------------------------------------------------------------------------------GGUUAUGCUAUU----------GUGAAUGUGUGAAUGAUGCAGGAGGUGA-A----------UUUCUUCC-------UUUUCUUCUUUGCUUGGACUG---AAGGGAGCUCCCUUUUUCUAUUUA
AASG02012489.1/1166-1359     GCUAAAGGAGUGGAGCUC-CUU--GAAGUCCAAUAGAGGAUCU----UG----AU-G---GGU-AGAUUGAG---------------CUGCUGAGC-UAUGG-AUCCCA-CAG-CCCUAUAAG-CAGAGAU--UAUAA-------------------------------------------------------------------------------UUUUGGAUAGG----------CUUGUGGCUUGCAUAUCUCAGGAGCUUC-A----------UUACCUUG------UAUUAGAUCCUUGUUUGGAUUG---AAGGGAGCUCUACAUCUCUCUCUC
AY775966.1/585-776           UAUAUUAAGGGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-UCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-UCGAGUCAC-CAAA-----AUUUG-------------------------------------------------------------------------------AACUAGACUCG----------UUAAAUGAAUGAAUGAUGCGGUAGACAA-A----------UUGGAUCA------UUGAUUCUCUCUGAUUGGACUG---AAGGGAGCUCCCUCUCUUUAGGUA
AY775967.1/620-808           UAGUUAGAAAGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-CCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-CCGAGUCAC-CAAAAUU--CAAA----------------------------------------------------------------------------------CUAGACUCG----------UUAAAUGAAUGAAUGAUGCGGUAGACAA-A----------UUGGGUCA------UUGAUUCUCUUUGAUUGGACUG---AAGGGAGCUCCCUCCCUCUUU---
AY775962.1/657-847           UAUGUAUGGAGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-CCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-CCGAGUCUC-ACCAAAAU-UCUAA---------------------------------------------------------------------------------CAAGACUUG----------UUAAAUGAAUGAAUGAUGCGGUAGACAA-A----------UUGGAUCA------UUGAUUCUUUUUGAUUGGACUG---AAGGGAGCUCCCUUUCUUCUU---
AY775957.1/547-737           UAAAUGUAGAGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----GA----UA-U---GAU-CCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-CCGAGUCGC-CAAAAUU--CAAA----------------------------------------------------------------------------------UUAGACUCG----------UUAAAUGAAUGAAUGAUGCGGUAGACAA-A----------UUGGAUCA------UUGAUUCUCUUUGAUUGGACUG---AAGGGAGCUCCCUCUCUCUUCUGU
AY775958.1/577-766           UAUAUGUAGAGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-CCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-CCGAGUCGC-UAAAAUC-------------------------------------------------------------------------------------GAACUAGACUCG----------UUAAAUGAAUGAAUGAUGCGGUAGACAA-A----------UGGAUCAU-------UGAUUCUCUUUGAUUGGACUG---AAGGGAGCUCCCUCUCUCUUCUGU
AY775974.1/600-788           UAUAUCGAGAGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-CCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-CCGAGUCAC-CAAAAUU--CGAA----------------------------------------------------------------------------------CUAGACUCG----------UUAAAUGAAUGAAUGAUGCGCUAGACAA-A----------UUGGAUCA------UUGAUUCUCUUUGAUUGGACUG---AAGGGAGCUCCCUUCCUUUUU---
AY775961.1/595-786           UAUAUGUAGAGAGAGCUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-CCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-CCGAGUCGC-CAAAAUU--CGAA----------------------------------------------------------------------------------CUAGACUCG----------UUAAAUGAAUGAAUGAUGCGGUAGACAA-A----------UUGGAUCA------UUGAUUCUCUUUGAUUGGACUG---AAGGGAGCUCCCUCUCUCUUCUGU
AY775964.1/559-748           UAUAUAGAUAGAGAGUUU-CCU--UGAGUCCAUUCACAGGUCG----UG----AU-AU--GAU-CCAAUUAG---------------CUUCCGACU-CAUUC-AUCCAA-AUA-CCGAGUCAU-CAAA-----AUUUC------------------------------------------------------------------------------AAUCUAAACUCG----------UUAAAUGAAUGAAUGAUGCGGUAGACAA-A----------UUGGAUCA------UUGAUUCUCUUUGAUUGGACUG---AAGGGAGCUCCCUCUCUUUUU---
AM427583.2/12150-11957       GGUUUUGGAGUGGAGCUC-CUU--GAAGUCCAAUAGAGGGUCU----UA----CU-G---GGU-AGAUUGAG---------------CUGCUGACU-UAUGG-AUCCCA-CAG-CCCUAUCCC-GUCA-----AUGGGGG----------------------------------------------------------------------------GCAUUGGAUAGG----------CUUGUGGCUUGCAUAUCUCAGGAGCUGC-A----------UUAUCCAA------GUUUAGAUCCUUGUUUGGAUUG---AAGGGAGCUCUACACCUCUCUCUC
AM454957.2/557-754           GGGGGUUUAUGGGAGCUC-CUUU-ACGCUCCAGUUCUGAAAGG----AG----AU-GAU-GGU-AUCCACAG---------------CUGCUGGUU-CAUGA-GUACCU-AUG-GCUGCACAA-UAUAUAUA-GCAAU------------------------------------------------------------------------------GUUGUGUGCAAA----------CUAUGGGUGUGCAUGACCUCGGAGAAGU-G----------GUUGCCUU-------GAUCUUUCUGGCCUUGGAGUG---AAGGGAGCUCUCAUAACCCUUCUA
AM457512.2/3648-3453         UGGGGUUCAAUGGAGCUC-UCU--UUGCUCCUAGCUAGAAGGA----GA----UG-AG--GGUAUGCCACAG---------------CUGCCAGUU-CAUGA-AUGCCC-AUG-GAUGCUCAA-GUUCUAG--CAUAU------------------------------------------------------------------------------GGUGAGAGCAAG----------CUAUGGGUGAGCAUGACUUGGGAGAUGA-G----------GGUACUUU-------GAUCUUUCUGGUAUUGGAGUG---AAGGGAGCUCUAUGGUUCUUACUU
EU549330.1/124-324           UAGAUAUAGAAGGAGAUU-CUU--UCAGUCCAGUCAUGGAUAGAAAAAG----AA-GAG-GGU-AGAAAUAU---------------CUGCCGACU-CAUCC-AUCCAA-ACA-CUCGUGGUA-GAGAAAC--GAUAA------------------------------------------------------------------------------AUUUAAACCGCA----------GUGACUGUGUGAAUGAUGCGGGAGAUAU-U----------UUUGAUCC------UUCUUUAUCUGUGUUUGGACUG---AAGGGAGCUCCUUCUUUUUCUACA
AY551216.1/17-209            GAUGAAGAAGAAGAGCUC-CCUU-UCGAUCCAAUUCAGGAGAG----GA----AG-U---GGUAGGAUGCAG---------------CUGCCGGUU-CAUGG-AUACCU-CUG-GA-GUGCAG-GGCAAAU----------------------------------------------------------------------------------------AG-------UCCUACCCUUUCAUGGGUUUGCAUGACUCGGGAGAUGA-A----------CCCGCCAU----UGUCUUCCUCUAUUGAUUGGAUUG---AAGGGAGCUCCUCUAGCUACAUCU
#=GC SS_cons                 ............<<<<<<.<<....<<<<<<<......<................................................<<.<<<....<<<<.....<.........................................................................................................................................>....>>>>...>>>.>>......................................>......>>>>>>>.....>>>>>>>>..............
#=GC RF                      uaugaagaAAagGAGCUC.CCU..UCAgUCCAAUcauGgAugg....ag....au.ga..GGU.agAaauAG...............CUGCcgacU.CAUgc.AUaCca.aUA.cccuugcaa.aauauaa..aAaAg..............................................................................auuuuugacAgg..........uUAaggGuuUGcAUGAcgcgGGAGAUga.a..........uUuaccuu......UuuucuuUcuuUgaUUGGAcUG...AAGGGAGCUCCuuuuuuuuuUuuc
//
# STOCKHOLM 1.0

#=GF AC   RF00639
#=GF ID   mir-515
#=GF PI   mir-373; mir-512
#=GF DE   microRNA mir-515
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00096
#=GF DR   MIPF; MIPF0000020;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   40


AANU01156321.1/745-831     UCUCGUGCUGUGACCCUUUAGAGG---GAAGCACUUUCUGUU----GUCUGA-AAACAAAGAAUGUGCAUC-CUUUCAGAGGGUUACUCUU-UGAGA
AADC01140615.1/1296-1380   UCUCAAGCUGUGA--CUGCAAAGG---GAAGCCCUUUCUGUU----GUCUAA-AAGAAAAGAAAGUGCUUC-CCUUUGGUGAAUUACGGUU-UGAGA
AADD01166738.1/2140-2226   UCUCAGGCUGUGUCCCUCUAGAGG---GAAGCGCUUUCUGUU----GUCUGA-AAGAAAAGAAAAUGGUUC-CCUUUAGAGUGUUACGCUU-UGAGA
AADD01166740.1/446-532     UCUCAAGCUGUGAGUCUACAAAGG---AAAGCGCUUUCUGUU----GUCUGA-AAGAAAAGAAAUCGCUUC-CCUUUGGAGUGUUACGGUU-UGAGA
AADD01166740.1/3349-3438   UCUCAGGUUGUGACCUUCUCGAGGAAAGAAGCACUUUCUGUU----GUCUGA-AAGAAAAGAAAGUGCUUC-CUUUCAGAGGGUUACGGUU-UGAGA
AANU01181659.1/6633-6719   UCUCAGGCUGUGACCCUCUAGAGG---GAAGCACUUUCUGUU----GUCUGG-AAGAAAAGAAUGCGCUUC-CCUUUAGAGGGUUACUCUC-UGAGA
AANU01181659.1/2591-2677   UUUCAGGCUGUGACCCUCUUGAGG---GAAGCACUUUCUGUU----GUCUGA-AUAAAAAGAAAGUGCUUC-CUUUUAGAGGCUUACGGUC-UGAGA
AANU01181659.1/8603-8689   UCUCAGGCUGUGACCCUCUAGAGG---GAAGCACUUUAUCUU----GUGUGA-AAGGAAAGAAAGCGCUUC-CCUUCAGAGGAUUACUCUU-UGAGA
AANU01181659.1/3404-3490   UCUCAGGCUCUAACCCUCUAGAGG---GAAGCGCUUUCUGUC----GUCUGA-GAGAGAAGAAAGUGCAUC-CUUUUAGAGGAUUACGGUU-UGAGA
AANU01181659.1/5786-5873   UCUCAGGCUGUGACUCUCCAGAGG---GAUGCACUUUCUUUU----AUGUGAAAAAAAAAGAAGGCGCAUC-CCUUUGGAGCGUUACGGUU-UGGGU
AANU01181659.1/12136-12222 UGUCAGGCUGUGACCCUCCAGAGG---GAAGCACUUUCUGUU----GUCUGA-AAGAAAGCAAAGCGCUCC-CCUUUAGAGGAUUACGGUU-UGAGU
AANU01181659.1/14614-14698 UCUCAGGCUGUGACUCUCCAAAGG---GAAGAAUUUUCUGUU----GCCUGA-AAG---AAAACGCACUUC-CCUUUCGAGUGUUACCGUUUUGAGA
AADD01166735.1/1220-1306   UCCCAUGCUGUGACCCUCUAGAGG---GAAGCACUUUCUGUU----GUCUGA-AAGAAACCAAAGCGCUUC-CCUUUGGAGCGUUACGGUU-UGAGA
AADD01166735.1/7661-7745   UCUCAGGCAGUGACCCUCUAGAUG---GAAGCACUGUCUGUU----GUCU---AAGAAAAGAUCGUGCAUC-CUUUUAGAGUGUUACUGUU-UGAGA
AADD01166735.1/8855-8942   UCCCAUGCUGUGACCCUCUAGAG----GAAGCACUUUCUGUUUGUUGUCUGA-GAAAAAACAAAGUGCUUC-CCUUUAGA--GUUACUGUU-UGGGA
ABBA01068200.1/49909-49819 UCUCAGGCUGUGGCCAUCUAGAGGUAAGAAGCACUUUCUGUU----GUCUUA-AAGAAAAGAAAGUCCUUUUUUUUUUUUUUUUUUUUUUU-UGAGA
AANU01181658.1/2015-2101   UUUCAUGCUGUGACUCUCUGGAGG---GAAGCGCUUUCUGUU----GUCUGA-AAGAAAACAAAGCGCUUC-UCUUUAGAGAGUUACGGUU-UGAGA
AANU01181649.1/9934-10020  UUUCAUGCUGUGACCCUACAAAGG---GAAGCCCUUUCUGUU----GUCUAA-ACUAAAAGAAAGUGCUUC-UCUUUGCUGGGUUACGGUU-UGAGA
AANU01181649.1/13118-13204 UCUCAUGCUGUGACUCUCUGGACA---GAAGCGGUUUCUGUU----GUCUGA-AAGAAAACAAAUCGCUUC-UGUCUAGAGUGUUUCGGUU-UGAGA
AANU01181649.1/17672-17755 UCUCAGGCUGUGACCAUCUACAGG---GAAGCACUUUCUAUG----GUCAGA----AAAAGAAAGUGCAUC-CUUUUAGAGUGUUACUAUU-UGAGA
AANU01181649.1/2975-3064   UCUCAGGCUGUGACUAUCUGGAGGUAAGAAGUGCUUACUGUU----GUCUUA-AAGAAAAGAAAGUGCUUU-CUUUCCGAGGGUUACGGUU-UGAGA
ABBA01184320.1/134-221     UCCCAUGCUGUGACCCUCCAAAGG---GAAGCGCUUUCUGUUU---GUUUUC-UCUUAAACAAAGUGCCUC-CCUUUAGAGUGUUACCGUU-UGGGA
AADC01140684.1/18074-18158 UCUCAUGAUGUGACCAUCUGGAGGUAAGAAGCACUUUGUGUU----UUGUGA-A-----AGAAAGUGCUUC-CUUUCAGAGGGUUACUCUU-UGAGA
AANU01181652.1/1375-1461   UAUCGGGCUGUGACCCUCUAAAGG---GAAGCGCUUUCUGUU----GUGUGA-AAGAAAACGAAGCGCUUC-UCUUUGGAGCGUUACAGUU-UGAGA
AANU01181651.1/3882-3966   CCUCAUGCAGUGACACUCUAAAUG---GCAGCACUGUCUGUG----GUCUAA-AACA--AGAUCGUGCAGC-CUUUUAGAGUGUUACUGUG-UGAGA
AANU01181661.1/11625-11711 UCUCAGUCUGUGACCCUCUAGAAG---GAAGCACUUUCUGUU----GUUUGA-AAGAAAAGAAAGUGCAUC-AUUUUAGAGGAUUACAGUU-UGAGA
AANU01181661.1/14497-14582 UCCCAGGCUGUGACUCUACAAAGG---AAAGCACUUUCUGUU----GUCG-A-AAGAAAAGAAAGCGCUUC-CCUUUUGAGAAUUACGGUU-UGAGA
AANU01181661.1/7385-7471   UCUCAUGCAGUCAUUCUCCAAUGG---GAAGCACCUUCUGUG----GUCUGA-AAGCAAGCAGAGGGCCUC-CUUUUGGAGCAUUACUGUU-UGAGA
AC200331.2/128607-128521   UCUCAUGAUGUGACCCUCUAGAGG---GAAGCACUUUCUGUU----GGCUAA-AAGAAAAGAAAGCGCUUC-CCUUCAGAGUGUUACGCUU-UGAGA
AC200331.2/109718-109632   UCUUAUGCUGUGACCCUCCAAAGG---GAAGAACUUUCUGUU----GUCUAA-AAGAAAAGAACGCACUUC-CCUUUAGAGUGUUACCGUG-UGAGA
AC200331.2/156950-156864   UCUCGUGCUGUGACCCACUAGAGG---GAAGCACUUUCUGUC----GUCUGA-AAGAAAAGAACGCGCUUC-CCUAUGGAGGGUUACCCUU-UGAGA
AANU01181654.1/1265-1351   UCUCAUGAUGUGACUCUCUAGAGG---AAAGCGCUUACUGUU----GGCUAA-AAAAAUAGGAAGCGCUUC-UCUUUAGAGUGUUACGCUU-UGAGA
AACZ03117218.1/20332-20246 UCUCAGGCUGUGACCCUCCAGAGG---GAAGUACUUUCUGUU----GUCUGA-GAGAAAAGAAAGUGCUUC-CCUUUGGACUGUUGCGGUU-UGAGU
AC011453.4/89941-89855     UCUCCUGCUGUGACCCUCAAGAUG---GAAGCAGUUUCUGUU----GUCUGA-AAGGAAAGAAAGUGCUUC-CUUUUUGAGGGUUACUGUU-UGAGA
AC011453.4/70442-70356     UCCCAUGCUGUGACCCUCUAGAGG---GAAGCGCUUUCUGUU----GUCUGA-AAGAAAAGAAAGUGCAUC-CUUUUAGAGGUUUACUGUU-UGAGG
AC011453.4/54650-54564     UCUCAUGCUGUGACCCUACAAAGG---GAAGCACUUUCUCUU----GUCCAA-AGGAAAAGAAGGCGCUUC-CCUUUGGAGUGUUACGGUU-UGAGA
AC011453.4/83493-83407     UCUCAGGCUGUGACCCUCUAAAGG---GAAGCGCUUUCUGUG----GUCAGA-AAGAAAAGCAAGUGCUUC-CUUUUAGAGGGUUACCGUU-UGGGA
AC011453.4/59401-59315     GCUCAGGCUGUGACCCUCUAGAGG---GAAGCACUUUCUGUU----GCUUGA-AAGAAGAGAAAGCGCUUC-CUUUUAGAGGAUUACUCUU-UGAGA
AADA01301557.1/9525-9439   UGUCAGGCUGUGUCCCUCUACAGG---GAAGCGCUUUCUGUU----GUCUGA-AAGAAAAGAAAGUGCUUC-CUUUUAGAGGGUUGCUGUU-UAAGA
EU086470.1/45033-45119     UCUCAUGCAGUCAUUCUCCAAAAG---GGAGCACUUUCUGUU----GUCUGA-AAGAAAACAAAGUGCCUC-CUUUUAGAGUGUUACUGUU-UGAGA
#=GC SS_cons               :<<<<----<--------<<<<<<...<<-<<---<<<<___....______.______>>>>--->>->>.>>>>>>-------->----.>>>>:
#=GC RF                    UCuCAuGCUGUGACcCUCuaaAgG...GAAGCaCUuUCUGUU....GUCUgA.AAgAAAAGAaAGuGCuUC.CcUuuaGAGugUUACugUU.UGaGA
//
# STOCKHOLM 1.0

#=GF AC   RF00640
#=GF ID   MIR167_1
#=GF PI   MIR167_2
#=GF DE   microRNA MIR167_1
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   57.00
#=GF TC   57.00
#=GF NC   56.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.97 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000023;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16040653
#=GF RT   Expression of Arabidopsis MIRNA genes.
#=GF RA   Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC
#=GF RL   Plant Physiol. 2005;138:2145-2154.
#=GF RN   [2]
#=GF RM   19939267
#=GF RT   High throughput approaches reveal splicing of primary microRNA transcripts
#=GF RT   and tissue specific expression of mature microRNAs in Vitis vinifera.
#=GF RA   Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del
#=GF RA   Fabbro C, Valle G, Policriti A, Morgante M, Pesole G, Pe ME, Horner DS
#=GF RL   BMC Genomics. 2009;10:558.
#=GF WK   MicroRNA
#=GF SQ   42


AACV01002433.1/39552-39424   CACCUUAAGCAGCUGAAGCUGCCAGCAUGAUCUGAUCUUUUGCGAUCUCUUUUUUUAUCU--GAAUAAGUU----------------------------------------------------------------------------------------------------GAUGGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA--UAUUG-----GGUUCCUAAGAUUCAGAUCGUGCUG-CG-CAGUUUCAUCUGCUAAUCGA
AY551191.1/7-170             UACCAGUAGCAGUU-AAGCUGCCAGCAUGAUCUUGUCUUCC---------------UCUC--UUAGGUUUC----------------------------------------------------------------------------------------------------AUAUAUAGUUAAUAAAUAUUUUAUAUAUUUCU-------------------------------------------------------------------------------------------------------------------UGUUCUUACAAGAUUAUAUGAUCAUAGCU--UAGAG-----AGAGAGAGAGA-CUAGGUCAUGCU--GG-UAGUUUCACCUGCUAAUGAU
AAAA02005241.1/62678-62404   ---UGUGAGAGAAUGAAGCUGCCAGCAUGAUCUGGUUGUCA---------------GGCA--UGAGCCAAA----------------------------------------------------------------------------------------------------UCUAUCCAUGGUGUUGGUGGUACUGAAAUUACCGCGUUUUCGAGGUUUUUCGUCGUGUCAACUUGCGAAGGGAAUUACGGGUUCUUGAU-GAGCAUUGGUGAUAGGAGGUGUGGGCUUGGUUAGUAGAGGUAGAAUUAUGAUUGUUCUUGUGAGUUUCAGUAAGAGGUGGGAGUGA--UUGGA-----AUUUGGCUCCA-UCAGAUCAUGUU---G-CAGCUUCACUCUCUCACCAC
AACV01005914.1/34613-34696   ---CAUAAGCAGGUGAAGCUGCCAGCAUGAUCUGAAAGCAU---------------CUCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCAGCGA-UCAGAUCAUCCG---G-CAGCUUCAUCUUCUCAUGGC
AM469063.2/4013-4114         CACCAAUAGCAGUUGAAGCUGCCAGCAUGAUCUAAGCUU-----------------UUCU--GUUGCCCAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C--CUUUC-----UCCAGGAAAGA-CUAGAUCAUGUG---G-CAGUUUCACCUGUUGAUGGA
AP003635.2/33923-34125       ---UGUGAGAGGCUGAAGCUGCCAGCAUGAUCUGGUCCAUGA-------------GUUGC--ACUGCUGAAUAUAUUGAAUUCAGCCAGGAGCUGCUACUGCAGUUCUGAUCUCG------------AUCUGCAUUCGUUGUUCUGAGCUAUGUAUGGAUUUGAUCGGUUUGAAGGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------AU--CCAUGUCUUUAAUUUCAUCGA-UCAGAUCAUGUU---G-CAGCUUCACUCUCUCACUAC
AC092076.7/52843-52692       CCAAGGGAACGAGUGAAGCUGCCAGCAUGAUCUAGCUCUGA---------------AUGA--UCAACAAGAUGUGCUCCCACACUGCCUU-------------------------------------------------------------CCUGUGGAUCUUGAGCUGUUGCUAGU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------C--UUGUG-----GUCAUGCCUUG-CUAGGUCAUGCUG-CGGCAGCCUCACUUCUUCCCAUU
AAAA02011018.1/78132-77981   CCAAGAGAAAGCGUGAAGCUGCCAGCAUGAUCUAACUUGCA---------------GACA--AGAAAUCAG----------------------------------------------------------------------------------------------------CUCAGCUCGCUGGUUUCGAACAGGA----------------------------------------------------------------------------------------------------------------------------------AGGCGGCUAGCUGAGGCUUCU--UCUGA-----GUACGUGAUGG-UUAGAUCAUGCUG-UGACAGUUUCACUCCUUCCCUGU
AL138648.2/73847-73962       ACAAGGGAACAAGUGAAGCUGCCAGCAUGAUCUAUCUUUGG---------------UUAAGAGAUGAAUGU----------------------------------------------------------------------------------------------------GGAAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------AU--AUUGC-----UUAAACCCAAG-CUAGGUCAUGCUC-UGACAGCCUCACUCCUUCCUGGU
AARH01033933.1/298-187       ACAAGGGAAAAGGUGAAGCUGCCAGCAUGAUCUAUCUUUGG---------------UUAG--AGAAGGAUA----------------------------------------------------------------------------------------------------GAAGCG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGA-----ACUAACCCUAG-CUAGGUCAUGCUC-UGACAGCCUCACUCCUUCCUAUU
AARH01002853.1/45908-46003   CACCACUAGCAGUUGAAGCUGCCAGCAUGAUCUAAAUUAAC---------------CUCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UU--CUUUA-----UCAAGGAUGGA-UUAGAUCAUGUG---G-UAGUUUCACCUGCUGAUGGC
AARH01001059.1/157614-157519 CACCACUAGCAGUUGAAGCUGCCAGCAUGAUCUAACUUCCU---------------UGCU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------U--CUUUA-----UCAAGGAUGGAUUUAGAUCAUGUG---G-UGGUUUCACCUGUUGAUGGC
AK067077.1/90-214            CACCACAAGUUGGUGAAGCUGCCAGCAUGAUCUGAUGAUGA---------------UGAU--GAUCCACCU----------------------------------------------------------------------------------------------------CUCUCAUCUGUGU----------------------------------------------------------------------------------------------------------------------------------------------------------UCUUGAUUA--AUUAC-----GGAUCAAUCGA-UCAGGUCAUGCU---G-UAGUUUCAUCUGCUGGUUGG
EU549023.1/125-488           ---UUUUAGAAGCUGAAGCUGCCAGCAUGAUCUGGUAAU-----------------CGCU--ACAUACGACAUACACACAUCACUAAACUUCUUUAUAAUUUAUGCACACACAUACAGCUCUUAAUGGCCACAACUCAAAGUUAUAAUUAGUGCAUGAUCUCUAGUUAUUUGACUGCUUUUAAUAUAUGUUUAUGGAUUCACGCAUGUGUGUGUAUGUACAUAAUUUACAUGCAUGCACUUUGUGUAUGGUACACA----------UCAAUUUGAACCCGUUCAAAAUUCUGUUUUUAUUAGUAUAUAUAUAGAUGUAUGUGGUGUGUGUGUCAGUGUGUGUGUGUG--UUUAU-----AGAUAGUAGUA-CUAGGUCAUCCU---G-CAGCUUCAGUCACUAAAUCA
FM163760.1/29-154            CACCGGCAUCUGAUGAAGCUGCCAGCAUGAUCUAAUUAGCU---------------UUCU--UUAUCCUUU----------------------------------------------------------------------------------------------------GUUGUGUUUCAUG----------------------------------------------------------------------------------------------------------------------------------------------------------ACGAUGGUU--AAGAG-----AUCAGUCUCGA-UUAGAUCAUGUU--CG-CAGUUUCACCCGUUGACUGU
FN595752.1/4932929-4932579   ---UUUGAGAGGUUGAAGCUGCCAGCAUGAUCUGGUGAAAC---------------AAAC--ACCAUCUCUUUCUUCUCUAACCCCAUGUCUGGAUUCGUCCACCGAU-------------------------CCAUUAUUAUAGACCAGGCCGCCCGUUUCCCAUGUAGUGAUCGAUAAUUAGGCUCGGGGUUUUCACUUUUUAGUGGGAUCUAAUCCUUAGGAUGGAUGUUUGUAUGGGUGGUAUAUAUCAUGGUGAGGUCUGUUUUCUAUUUUAAUUCUAACGGGGUUUUGAUUUAGCUGAGGGGGUAUAAUUCAUAGCCUAAUUCCAAAACCUAACUCCAUAG--AGAUA-----GGGUUCCAUGA-UCAGGUCAUCUU---G-CAGCUUCAAUCACUCACUCA
FN595511.1/254818-254935     CCAAGGGAAUAAGUGAAGCUGCCAGCAUGAUCUAGCUUUGG---------------CUAG--GGAUACAGA----------------------------------------------------------------------------------------------------GAAAGAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGAUCAGA-----GCUAACCCUAG-CUAGGUCAUGCCC-UGACAGCCUCACUCCUUCCUUCU
HM139495.1/532-415           CACCACAAGUGGAUGAAGCUGCCAGCAUGAUCUGAUCACAG---------------UAGU--UCUCUAGCU----------------------------------------------------------------------------------------------------GAUGAUGAU-----------------------------------------------------------------------------------------------------------------------------------------------------------------UUACAA--AACCU-----AGAGACAUGCA-UCAGAUCAUCUG---G-CAGUUUCAUCUUCUCAUGGC
HM139470.1/291-140           CCAAGGGAACGAGUGAAGCUGCCAGCAUGAUCUAGCUCUGA---------------AUGA--UCAACAAGAUGUGCUC--------------------------------------------------------------------------------------CCACACU------GCCUUCCUGUGGAUC------------------------------------------------------------------------------------------------------------------------------------------UUGAGCUGUUGCUAGUC--UUGUG-----GUCAUGCCUUG-CUAGGUCAUGCUGCGG-CAGCCUCACUUCUUCCCAUU
HM139546.1/212-340           CACCUUAAGCAGCUGAAGCUGCCAGCAUGAUCUGAUCUUUU---------------GCGA--UCUCUUUUUUUAUCUG-------------------------------------------------------------------------------------AAUAAGUUGAUGGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA--UAUUG-----GGUUCCUAAGAUUCAGAUCGUGCUG-CG-CAGUUUCAUCUGCUAAUCGA
HM139491.1/495-218           UGGUGUGAGAGAAUGAAGCUGCCAGCAUGAUCUGGUUGUCA---------------GGCA--UGAGCCAAAUCU---------------------------------------------------------------------------------------------AUCC------AUGGUGUUGGUGGUACUGAAAUUACCGCGUUUUCGAGGUUUUUCGUCGUGUCAACUUGCGAAGGGAAUUACGGGUUCUUGAUG--AGCAUUGGUGAUAGGAGGUGUGGGCUUGGUUAGUAGAGGUAGAAUUAUGAUUGUUCUUGUGAGUUUCAGUAAGAGGUGGGAGUGA--UUGGA-----AUUUGGCUCCA-UCAGAUCAUGUU---G-CAGCUUCACUCUCUCACCAC
GQ419050.2/128-252           CACCACAAGUUGGUGAAGCUGCCAGCAUGAUCUGAUGAUGA---------------UGAU--GAUCCACCUCUCUCA---------------------------------------------------------------------------------------UCUGUGU------UCU-----------------------------------------------------------------------------------------------------------------------------------------------------------------UGAUUA--AUUAC-----GGAUCAAUCGA-UCAGGUCAUGCU---G-UAGUUUCAUCUGCUGGUUGG
HM139510.1/528-442           CGCCAUAAGCAGGUGAAGCUGCCAGCAUGAUCUGAAAGCAU---------------CUCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCAGCGA-UCAGAUCAUCCG---G-CAGCUUCAUCUUCUCAUGGC
HM139456.1/595-444           CCAAGAGAAAGCGUGAAGCUGCCAGCAUGAUCUAACUUGCA---------------GACA--AGAAAUCAG----------------------------------------------------------------------------------------------------CUCAGCUCGCUGGUUUCGAACAGGA----------------------------------------------------------------------------------------------------------------------------------AGGCGGCUAGCUGAGGCUUCU--UCUGA-----GUACGUGAUGG-UUAGAUCAUGCUG-UGACAGUUUCACUCCUUCCCUGU
FM163792.1/118-233           ACAAGGGAACAAGUGAAGCUGCCAGCAUGAUCUAUCUUUGG---------------UUAAGAGAUGAAUGU----------------------------------------------------------------------------------------------------GGAAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------AU--AUUGC-----UUAAACCCAAG-CUAGGUCAUGCUC-UGACAGCCUCACUCCUUCCUGGU
GQ418989.2/150-264           CCCCAUUAAGAGCUGAAGCUGCCAGCAUGAUCUGAUGAGUG---------------UUUA--UUAGGUGAG----------------------------------------------------------------------------------------------------GGCAGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUGACUGC-----CAAAACAAAGA-UCAGAUCAUGCUG-UG-CAUUUUCCUCUGCUUGUGGC
GQ419008.2/150-264           CCCCAUUAAGAGCUGAAGCUGCCAGCAUGAUCUGAUGAGUG---------------CUUA--UUAGGUGAG----------------------------------------------------------------------------------------------------GGCAGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUGACUGC-----CAAAACAAAGA-UCAGAUCAUGCUG-UG-CAUUUUCCUCUGCUUGUGGC
HM139492.1/495-218           UGGUGUGAGAGAAUGAAGCUGCCAGCAUGAUCUGGUUGUCA---------------GGAA--UGAAACAAAUCUA--------------------------------------------------------------------------------------------UCCA------UGGUGUUGGUGGUACUGAAAUUACCGCGUUUUCGAGGUUUUUCGUCGUGUCAACUUGCGAAGGGAAUUACGGGUUCUUGAUG---AGCAUUGGUGAUAGGAGGUGUGGGCUUGGUUAGUAGAGGUAGAAUUAUGAUUGUUCUUGUGAGUUUCAGUAAGAGGUGGGAGUGA--UUGGA-----AUUUGGCUCCA-UCAGAUCAUGUU---G-CAGCUUCACUCUCUCACCAC
GQ419021.1/495-218           UGGUGUGAGAGAAUGAAGCUGCCAGCAUGAUCUGGUUGUCA---------------GGCA--UGAGCCAAAUCUA--------------------------------------------------------------------------------------------UCCA------UGGUGUUGGUGGUACUGAAAUUACCGUGUUUUCGAGGUUUUUCGUCGUGUCAACUUGCGAAGGGAAUUACGGGUUCUUGAUG---AGCAUUGGUGAUAGGAGGUGUGGGCUUGGUUAGUAGAGGUAGAAUUAUGAUUGUUCUUGUGAGUUUCAGUAAGAGGUGGGAGUGA--UUGGA-----AUUUGGCUCCA-UCAGAUCAUGUU---G-CAGCUUCACUCUCUCACCAC
GQ905535.1/138-252           CCAAGAUAAAGGGUGAAGCUGCCAGCAUGAUCUAACGACGGC-------------AUUGC--UCUGCUGCU----------------------------------------------------------------------------------------------------GCAGUG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------A--GGCUU-----GCGAGUGAUGG-UUAGAUCAUGCUG-UGACAGUUUCACUCUUUCCCUUU
FM163753.1/29-154            CACCGGCAUCUGAUGAAGCUGCCAGCAUGAUCUAAUUAGCU---------------UUCU--UUAUCCUUU----------------------------------------------------------------------------------------------------GUUGUGUUUCAUG----------------------------------------------------------------------------------------------------------------------------------------------------------ACGAUGGUU--AAGAG-----AUCAGUCUGGA-UUAGAUCAUGUU--CG-CAGUUUCACCCGUUGACUGU
GQ419026.1/530-416           CACCACAAGUGGAUGAAGCUGCCAGCAUGAUCUGAUCACAG---------------UAGU--UCUCUAGCU----------------------------------------------------------------------------------------------------GAUGAU------------------------------------------------------------------------------------------------------------------------------------------------------------------------UU--ACAAAAC-CUAGAGACAUGCA-UCAGAUCAUCUG---G-CAGUUUCAUCUUCUCAUGGC
HM139459.1/595-444           CCAAGAGAAAGCGUGAAGCUGCCAGCAUGAUCUAACUUGCA---------------GACA--AGAAAUCAG----------------------------------------------------------------------------------------------------CUCAGCUCGCUGGUUUCGAACAGGA----------------------------------------------------------------------------------------------------------------------------------AGGCGGCUAGCUGAGGCUUCU--UCUGA-----GUACGUGAUGG-UUAGAUCAUGGUG-UGACAGUUUCACUCCUUCCCUGU
GQ418996.2/150-264           AACCAUUAGGAGCUGAAGCUGCCAGCAUGAUCUGAUGAGUG---------------CUUA--UUAGGUGAG----------------------------------------------------------------------------------------------------GGCAGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUGACUGC-----CAAAACAAAGA-UCAGAUCAUGCUG-UG-CAGUUUCAUCUGCUUGUGGC
GQ905534.1/340-518           UCUUGCGAAUGAGUGAAGCUGCCAGCAUGAUCUAGCUCUGA---------------UUUG--GUUGGCACC----------------------------------------------------------------------------------------------------AUAUUAGCAGGCGUCCACGCACAGCUAGACUAGAGUGGC------------------------------------------------------------------------------------------------------CUCGCGCGCUCUCGUCUGGUCUGUGUCUCGCUUUG--UGCCU-----GCAAAUCGUUG-UUAGAUCAUGCA--UGACAGCCUCAUUCCUUCACAAU
GQ905545.1/103-218           UGGUGUGAGAGCUUGAAGCUGCCAGCAUGAUCUGGCUACUC---------------AAAC--GCCGCCGGCCU-----------------------------------------------------------------------------------------------CCCA-----AG-------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCUC--GAUCG-----GUGGCGCUUCA-CCAGAUCAUGUU---G-CAGCUUCACUCUCUCGCAAC
GQ418952.2/176-315           UAGUGUGAAUGAGUGAAGCUGCCAGCAUGAUCUAGCUCUGA---------------UUAA--UCGGCACUGUUGGCGUAC---------------------------------------------------------------------------------AGUCGAUUGA------CUAAUCG----------------------------------------------------------------------------------------------------------------------------------------------------------UCAGAUCUG--UGUGU-----GUAAAUCACUG-UUAGAUCAUGCA--UGACAGCCUCAUUUCUUCACACU
GQ419019.1/495-218           UGGUGUGAGAGAAUGAAGCUGCCAGCAUGAUCUGGUUUUCA---------------GGCA--UGAGCCAAAUCU---------------------------------------------------------------------------------------------AUCC------AUGGUGUUGGUGGUACUGAAAUUACCGCGUUUUCGAGGUUUUUCGUCGUGUCAACUUGCGAAGGGAAUUACGGGUUCUUGAUG--AGCAUUGGUGAUAGGAGGUGUGGGCUUGGUUAGUAGAGGUAGAAUUAUGAUUGUUCUUGUGAGUUUCAGUAAGAGGUGGGAGUGA--UUGGA-----AUUUGGCUCCA-UCAGAUCAUGUU---G-CAGCUUCACUCUCUCACCAC
GQ419007.2/150-264           AACCAUUAGGAGCUGAAGCUGCCAGCAUGAUCUGAUGAGUG---------------UUUA--UUAGGUGAG----------------------------------------------------------------------------------------------------GGCAGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUGACUGC-----CAAAACAAAGA-UCAGAUCAUGCUG-UG-CAGUUUCAUCUGCUUGUGGC
GQ905544.1/203-331           UGCUGUGAGAGGUUGAAGCUGCCAGCAUGAUCUGGCUGCUC---------------AGAC--GCCGGCGGGCGUCUCGAG----------------------------------------------------------------------------------UGCUCGCUCGAUCGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------CG--GUGAC-----GCUUGGAUUCA-CCAGAUCAUGUU---G-CAGCUUCACUCUCUCGCAGC
GU190713.1/187-298           ACAAGGGAAAAAGUGAAGCUGCCAGCAUGAUCUAUCUUCCG---------------UUAG--UAAGAUGCG----------------------------------------------------------------------------------------------------GAUGCU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUAUU-----GCUAACCCUAG-CUAGGUCAUGCUG-CGACAGCCUCACUCCUUCCUACU
FM163791.1/119-234           ACAGGGGAACAAGUGAAGCUGCCAGCAUGAUCUAUCUUUGG---------------UUAAGAGAUGAAUGU----------------------------------------------------------------------------------------------------GGAAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------AU--AUUGC-----UUAAACCCAAG-CUAGGUCAUGCUC-UGACAGCCUCACUCCUUCCUGGU
#=GC SS_cons                 ::::<-<<<--<-<<<-<<<<<--<<<<<<<<<<_______...............____..___________...............................................................................................________________.........................................................................................................................................................._________.._____.....___________._>>>>>>>>>>-...>.>>>>->>>->-->>>->:::
#=GC RF                      caaugugAGaggaUGAAGCUGCCAGCAUGAuCUggUuauua...............uuca..ucagacaauUu...............................................................................................uuuGauagauuuuuau..........................................................................................................................................................uuggauuau..uuuua.....auauaccaugA.UcAGaUCAUGCU...G.CAGCUUCAccCuCUcAcuau
//
# STOCKHOLM 1.0

#=GF AC   RF00641
#=GF ID   mir-154
#=GF PI   mir-368; mir-329; mir-379; mir-485; mir-654; mir-889
#=GF DE   microRNA mir-154
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   41.00
#=GF TC   41.00
#=GF NC   40.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000018;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction
#=GF RT   method.
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20944086
#=GF RT   Assessing the effect of the CLPG mutation on the microRNA catalog of
#=GF RT   skeletal muscle using high-throughput sequencing.
#=GF RA   Caiment F, Charlier C, Hadfield T, Cockett N, Georges M, Baurain D
#=GF RL   Genome Res. 2010;20:1651-1662.
#=GF RN   [4]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF WK   Mir-154_microRNA_precursor_family
#=GF SQ   121


AACN010166994.1/1346-1266    GAUACUCG-AAGGAGAGG-UUGUC-CGUGUUGUCUUCUCUUU-AUUUAUGAUGAA-ACAU---ACACGGGAAA-CCUCUU-UUUUAGUAUC
AAIY01699599.1/3898-3977     GGUACUUG--AAGAGUGG-UUAUC-CCUGUCCUGUUCGUUUU-GCUCAUGUCGAA-UCGU---ACAGGGUCAU-CCACUU-UUUCAGUAUC
AAIY01699599.1/3364-3441     GGUACUUA-A-CGCGAGG-UUGC--CUUGGUAUAUUCGGUUU-AUUGACGUGGAA-U-AU---ACAAGGGCAA-GCUCUC-UGUGAGUAUC
AAIY01699599.1/1723-1801     GGUACUUG-AA-GAGAGG-AUACC-CUUG-UAUGUUCACUCC-AUUCAUGACGAA-U-AU---ACAGGGGGAG-ACUCUUAUUUGCGUAUC
AAIY01699599.1/4687-4765     CCUACUUG--AGGAGAAA-UUACC-CUUGGUGUGUUGGCUUU-A-UCACGACAAA-UCAU---CCAAGGACAA-UUUCUU-GUUGAGUAUC
AAIY01699599.1/5227-5305     GGUGCUUA--AAGAAUGG-CUGUC-CGUAGUAUGGUCUCUAU-AUUUAUGAUGAU-UAAU---AUC-GGACAA-CCAUUG-UUUUAGUAUC
AACN010495881.1/108-187      GGUACUUG--AAGAGUGG-UUAUC-CCUGCUGUGUUCGCUGU-AUUUAUGACGAA-UCAU---ACAGGGACAU-CCAGUU-UUUCAGUAUC
AJ517767.1/636-714           GGUACUUG--AGGAGAGG-UUGUC-UGUGAUGAGUUCGCUUU-AUUAAUGACGAA-UAUA---ACACAGAUGG-CCU-GU-UUUCAAUACC
AADD01141100.1/3131-3209     GGUACUUG-A-AGGGAGA-UCGAC-CGUGUUAUAUUCGCUUU-AUUGACUUCGAA-UAAU---ACAUGGUUGA-UCU-UU-UCUCAGUAUC
AADD01141100.1/4257-4334     GGUACCUG--AAA-UAGG-UUGCC-UGUGAGGUGUUCACUUU-CUAUAUGAUGAA-UAUU---AUACAGUCAA-CCU-CU-UUCCGAUAUC
AADD01141100.1/2839-2915     GGUACUCG-GGGA-GAGG-UUACC-CGAGC-AACUUUGCAUC-U-GGACGACGAA-UGUU---GCUCGGUGAA-CCC-CU-UUUCGGUAUC
AADD01141100.1/3972-4050     GGUGCCUG--AGGAGAGG-UGGCC-UGUGUUGCAUUCACAGA-AAUCAUGACACA-CAAG---ACACGAGCGG-CCUCUC-UUC-AGUAUC
ABDC01257673.1/16756-16835   GAUAUUUG--AGGAGAGG-UUAUC-CUUGUUAUGUUCGCUUC-AUUCAUCAUGAA-UAAU---ACAUGGUUAA-CCUCUU-UUUGAAUAUC
ABDC01257673.1/21363-21442   GGUACUUG--AAGAGAAG-UUGUU-CGUGGUGGAUUCGCUUU-ACUUAUGACGAA-UCAU---UCACGGACAA-CACUUU-UUUCAGUACC
ABDC01257673.1/10494-10573   GGUGCUUG-AA-GAGAGG-AUACC-CUUUGUAUGUUCUCUUU-AUUAAUGGCGAA-U-AU---ACAGGGGGAG-ACUCUUAUUUGCGUACC
ABDC01257673.1/22503-22581   GGUACUUG--GAGAGAGG-CUGGC-CGUGAUGAAUUCGAUUC-A-UCAAAGCGAG-UCAU---ACACGGCUCU-CCUCUC-UUUUAGUGUC
ABDC01257673.1/23324-23403   GGUACUCG-GAGG-GAGG-UCGUC-CGUGGUGAGUUUGCAUUGUUUAAUAAUGCC-CAAU---ACACGGUCGA-CCU-CU-UUUCGGUAUC
ABDC01257673.1/7581-7660     GGUAUUUA--AAAAGUGG-AUAUU-CCUUCUAUGUUUAUGUU-AUUUAUGGUUAA-ACAU---AGAGGAAAUU-CCACAU-UUUCAGUAUC
ABDC01257673.1/14547-14626   CACACUGG--AGGAGCAA-UUACC-CUUGCUGUGUUCACUUU-AUUUGUGACUAA-CCAC---ACAAGGACGG-UUCCUU-UUUGGGUAUC
ABDC01257673.1/11708-11785   GGUGCUGG--AAGAGAGG-ACACC-CUUUGUAUGCUCUCUCU-AUUAAUGGCGAA-U-AC---ACAGGGGAG--ACUCUA-UUUGCAUAUC
ABDC01257673.1/8300-8379     GGUAUUUA--AAAGGUGG-AUAUU-CCUUCUAUGUUUACGUG-AUUCCUGGUUAA-UCAU---AGAGGAAAAU-CCAUGU-UUUCAGUAUC
ABDC01257673.1/7254-7333     GGAAUUCA--AAAGGUGG-AUGUU-CCUUCUAUGUUUACAGG-AUUUGUGGUUAA-UCAU---AGAGGAAAAU-CCACAU-UUUCAGCAUC
ABDC01257673.1/8622-8701     GGUAUUUA--AAAGGUAG-AUUCU-CCUUCUAUGAGUACAUU-AUUUACGAUUAA-UCAU---AGAGGAAAAU-CCACGU-UUUCAGUAUC
ABDC01257673.1/3779-3856     GGUACUCA-AAAGAGAGG-UUUUC-CCCGGCGAAUUCA--UU-GUUUAUGACGGA-UCAU---UCUUGGCCAA-CCUCUU-U-UCAGUGUC
AAIY01409313.1/1874-1796     GGUACUUG-AAUG-GAGG-UUGUC-CAUGGUGUGUUCAUUUU-AUUUAUGAUGAG-UAUU---ACAUGGCCAA-UCU-CC-UUUCAGUACU
AAIY01409313.1/249-170       GAUCCCUG--AGCAGGGG-UUGCU-CUUGGUGAAUUCGCUUU-AUUCUUGUUGAA-UCAC---ACAAAGGUAA-CUUUGG-UUUGCAUAUC
AAFC03087121.1/18127-18206   GGAACUUG--AAGAUAGG-UUAUC-CGUGUAGCCUUCGCUUU-ACUUGUGACGAA-UCAU---ACACGGUUCA-CCUAUU-UUUUAGUACC
AAFC03087121.1/18442-18522   GGUACUUG--AAGAGAGG-UCUUC-CAUGGUGCAUUCGCUUUAUUCUUUGACGAA-UCAU---ACAUGGUUGA-CCUUUU-UUUAGGUAUC
AAFC03087121.1/20572-20651   GAUCCUUG--AGCAGAGG-UUGCC-CUUGGUGAAUUCGCUUU-AUUUAUGUUGAA-UCAC---ACAAAGGCAA-CUUUUG-UUUGAGUAUC
AAFC03087121.1/24467-24545   GAUGCUUG--AGGAGAGG-UUGCC-CGUGGCCCGUUCGCAUU-CUUCAUGACGCA-CAAU---ACACGGUCGG-CCUCUC-UUC-GGUAUC
AAYZ01254084.1/2089-2167     GGUACUCA-G-AGCGAGG-UUGCC-CUGUGUAUAUUCCGUGU-AUUGACCUGCAG-U-AU---ACAAGGGCAA-GCUCUC-UGUGAGCACC
AADD01141098.1/2614-2692     GCUACUUG-A-AGAGAGG-UAAUC-CUUCAUGCAUUUGCUUU-ACUUGCAAUGAU-U-AU---ACAAGGGCAG-ACUCUC-UCUGGGGAGC
AAIY01408790.1/353-273       GGUACUUG--AAGAGAGG-UCUUC-CAUGAUGUAUUCACGUCAUUCCUUGAUGAA-UCAU---ACAUGUUUGA-CCUUUU-UUUAAGUAUC
AAQQ01350195.1/2022-2100     GCUACUUG-A-AGAGAGG-UUAUC-CUUUGUGUGUUUGCUUU-UCUUGCCAUGAA-U-AU---GCAAGGGCAA-GCUCUC-UGCGAGGAGC
AANN01196583.1/1560-1639     GGUAUUUA--AAAGGUGG-AUAUU-UCUUCUAUGUUUAUUGG-AUUCAUGGUUAA-ACGU---AGAGGAAGUU-CCACUU-UUUCAGUAUC
AANN01196583.1/1836-1915     GGUAUUUA--AAAGGUAG-AUUUU-CCCUCUGUGGUUACGUG-CUUGAUGGUUAA-UCAU---AGAGGAAAAU-CCACGU-UUUCAGUAUC
AANN01387447.1/2286-2206     GGUGCUUG--GAGAGAGG-UCUUC-CAUGAUGCAUUCGCUGGCAUUGGGUUCGAA-UCAU---ACAUGGAUGA-CCUUUU-UUUAAGUAAC
AANN01387447.1/1902-1824     GGUGCGUG-CAGG-GAGG-CUGGC-CACGGUGUGUUCAUUUU-CUUCACGAUGAG-UAUU---ACAUGGCCAG-UCU-CC-GUGUGGCACC
AACN010183773.1/1926-2004    GGUACCUG-GAAA-GGGU-UCGAC-CGCACUGCAUGUAUUUU-AUUAACAGCGUA-UGUA---ACAUGGUCGA-CUU-CU-UUUCAGUAUC
AAPY01740242.1/756-831       GGUGCUUG--AAGAGAGG-UCCUC-CAUGAUGCAUUCGCUUUAUUCUCUGACGA---UCA---ACAUAGU-GA-CCU-UU-UUU-AGUAUC
AANG01133030.1/803-880       GGUUCUAG--AAAAGAGG-UUACC-CGUGUU-UCUUCGCUCU-AUUCACGACGAA-GAAU---ACG-GGUGCA-CUUCUG-UUUGAGUAUC
ABBA01048514.1/248685-248607 GGUACUCG-AAUG-GAGG-UUGUC-CAUGGUGUGUUCAUUUU-AUUUAUGAUGAG-UAUU---ACAUGGCCAA-UCU-CC-UUUCGGUACU
ABBA01048514.1/249222-249142 GGUACUGG-U-GGAGAGG-UCUUC-CAUGAUGCAUUCGAUUUAUUUUUUGACCAA-UCCU---ACAUAGUGGA-CUCUUU-UGAAAGCAUU
AC121784.2/131190-131270     GGUACUUG-GAGG-GAGG-UUGCCUCAUAGUGAGCUUGCAUUAUUUAAUGAUGCC-CAAU---ACAGGAUAGA-CCU-GU-UUUCUGUAUC
AAHX01046584.1/23183-23106   CAUACUUG--AGGAGAAA-UUAUC-CUUGGUGUGUUUGCUCU---UUUGGAUGAA-UCAU---ACAAGGGUAA-UUUCUU-UUCGAGUAUC
AAHX01046584.1/15015-14936   GGUCCUUG-GAGG-GAGG-UUGUC-CAUAGUGAGUUUGCAUUAAUUAAUGAUGCC-CAAU---GCAGGGUCGA-CCU-CU-UUUCUGUGUC
AAQQ01350201.1/367-446       GGUACCUG-A-AGAGAGG-UUUUC-UGGGCUUGUGUUUCUGUGA-UGAGGAUGAA-ACAC---CCCCGGUUAA-CCUCUU-UCCCAGUAUC
AANG01662501.1/45-126        GGAACUUUUAAAGGAUGG-UCAUC-CCUACUGUACUUGCUUA-AUUUAUGGUGAA-UUUU---UGAAGUACAU-CCACGU-UUUCAGAACC
AANU01197804.1/1093-1013     GGUACUGG-U-GGAGAGG-UCUUC-CAUGAUGCCUUCAAUUUAUUCUUUUACCAA-UCCU---ACAUAGUGGA-CCCUUU-UGAAAGCAUU
AAPY01740243.1/526-604       GGUGCUCG-AGGA-GAGG-UCGCC-CGUGGCGCGUUCGCAUCCA-UCAUGACGCA-CAAU---ACACGGUCGA-CCU-CU-CUUCAGUACC
AANU01197805.1/74093-74169   GGUACUGG--AGGAGAGG-UUCUC-UGUGCU-UCUUCCCUUU-AUUUAUGGUGAA-AACU---AU--GGUGCA-CUUCUA-UUUGAGAAUC
AANU01197805.1/79709-79785   GCUGCUUG-A-AGAGAGG-UAAUC-CUCCCUGCUUUUGGUUU-ACUUGCAAUGAU-U-AU---ACAAAGGCAG-ACUCUC---UAGGGAGC
AANU01197805.1/77711-77790   CGCAUCUA-A-AAGGUGG-AUGUU-CCUUCUAUGCUUACAGG-AUUUAUGGUUAA-UCAU---AGAGGAAAAU-CCACAU-UGUCAGUAUC
AANU01197805.1/73797-73874   GGCCCUGG--AAGAGAAG-UUUCC-CCGG-UGUGUUCAUUUU-AUCUGUGACAAA-UCAU---UUCUGGCCAG-UCU-UU-UUGCAGUAUC
AADB02234051.1/94-172        GGUACUUA-AGGGGGAGG-UGGGC-UUUGA-AUAAUAAGUUU-AUUGACGUGGAA-U-AU---ACAAGGGCAA-GCUCUC-UGUGAGUAUC
AAYZ01254085.1/3260-3339     GGUGCUGG--GAGAGUGG-CUGUC-CCGGCUGUGGCCGCUGG-GCCUGUGAUGGA-UCAU---ACAGGGACAU-CCAGUU-UUUCAGCAUC
AAYZ01254085.1/5145-5224     GGUACUGA-GAGG-AAGA-UUGUC-UGUGGUGAGUUUGCGUUGUUCAGUGGUGCU-CAGU---ACACAGCCUA-CCU-CU-UUUUGGUAUU
AAFC03086346.1/2857-2779     GGUCCUUG-AAGA-GAGG-UAUUC-CCAGGUGAAUUUGUUUU-AGUUAUUACGAA-UCGG---UCUUGGCCAA-CCU-CU-UUGCAGUAUC
AAFC03086346.1/2564-2487     GGUACUAG--AAAAGAGG-UUGUC-UGUGUU-UCUUAGCUUU-GUUUAUGAUGAA-AAAU---AUG-GAUACA-CUUCUA-UUUGAGUAUC
AY865936.1/461-540           GGUACUUG--AAGAUAGG-UUAUC-CGUGUUGCCUUCGCUUU-AUUUGUGACGAA-UCAU---ACACGGUUGA-CCUAUU-UUUCAGUACC
AAGV020362611.1/1566-1643    GGUACUAG--AAAAGAAG-UUAUC-UGUGUU-UCUUCACCUU-AUUUAUGAUGGA-AAAU---AUG-GGUGCA-CUUCUA-UUUGAGUAUC
AAKN02051949.1/124580-124659 GGUCCUUG-GAGG-GAGG-UUGUC-CUUGGUGAGUUCACGUUACUUAGCGAUGCC-CGAU---ACAUGGUCCA-GCU-CU-UUUCAGUCUC
AAGV020430601.1/5233-5308    GGUUUUGA--CAC-GAGG-UGGCC-UGUGGUGGAUUUGCUUU-AUUUCUGACCCA-CAUC---GCACG-GCAA-CCU-CU-UUGCAG-AUC
AAKN02051949.1/110754-110833 GAUAUUUA--AAGGGUGG-AUAUU-CCUUCAAUGUUUAUGUC-AUUUAUGGUUAA-ACAC---AGAGGAAAUU-CCAUGU-UUUCAGUAUC
AAGV020430600.1/1205-1284    GGUACUUG-GAGG-GAGG-UUGUC-CGUGGUGAGUUCGCAUUAUCUAAUGAUGCC-CAAU---ACACGGUCGA-UCU-CU-UUUCGGUAUC
AAWR02020065.1/28565-28643   GGAACUUG-AG-G-AUGG-UCAUC-CCUACUGUGCUUGCUUU-AUUUAGGGUGAA-UUUU---UGAACUACGU-CCA-CUUUUUCAGAAUC
AAWR02020065.1/30944-31022   GCUACUUG-A-AAAGAGA-UUAUC-UUUCAUGUGUUUGCGUU-AUUUGUAAUGAA-U-CU---ACAAGGGCAG-GCUCCC-UCUGAGGAGC
AAWR02020065.1/25372-25448   GGAACUCA--AAAAGAGG-UUAUC-UGUGUU-UCUUCGCUUU-AUUUAUGAUGAA-AAAU---ACA-GGCGCA-CUUCUA-UUUGAG-AUC
AC121784.2/109026-109105     GGUACCGG--AAGAGAGG-UUUUC-UGGGUCUCUGUUUCUUUGA-UGAGAAUGAA-ACAC---ACCCAGCUAA-CCUUUU-UUUCAGUAUC
AAKN02051949.1/114894-114972 GCUACUUG-A-AGCGAGG-UUGCC-CUUUGUAUAUUCGGCUU-GUUGACACGGAA-U-AU---ACAAGGGCAA-GCUCUC-UGUGAGUAUC
AAKN02051949.1/112246-112324 GCUGCUUG-G-AGAGAGG-UUAGC-CUUUGUGUGUUUGCUGA-ACUGGCACUGAA-U-AU---GCCAGGGCAA-GCUCUC-UGCUAGGAGC
AAKN02051949.1/133749-133826 GGUGCCUG--AGGAGAGG-UUGCC-UGUGGCAUGUUCGCAUC-CCUUGUGACGCA-CAAU----CACGGUCAA-CCUCUC-UUC-AGGGCC
AC121784.2/122868-122947     GGUACUUG--GAGAGUGG-UUAUC-CCUGUCCUCUUCGCUUC-ACUCAUGCCGAA-UCGU---ACAGGGUCAU-CCACUU-UUUCAGUAUC
AAGV020362616.1/1264-1343    CAUAUUUG--AGGAGAGG-UUGUC-CAUCUUAAGUUCACCCC-AUUUGUCAUGAG-UAAU---ACCCAGUUAA-CCUCUU-UUUGAAUAUC
AAGV020362612.1/841-919      GCUACUUG-A-AGAAAGG-UGGUC-CUUCCUGUGGUUGCUUG-AUUUGUAAUGAA-C-GU---AUAAGACUAA-GCUCUC-UCUGAGGAGC
AAGV020362614.1/822-900      GGCGCUCA-C-AGCGAGG-UUACC-CUUUGUGUAUUCGGUUU-AUUGACGUGGAA-U-AU---ACAAGGGCAA-GCUCUC-UGUGAGCAUC
AAGW02077267.1/23775-23852   GGUACCUG--AAA-UAGG-UUGCC-UGUGAGGUGUUCACUCU-CUAUACGAUGAA-UAUU---AUACAGUCAA-CCU-CU-UUCCGGCGCC
AAQR03046512.1/14599-14678   GGUACUCA-AAGG-GAG-GUUGUU-CGUGGUGAGUUUGCAUCGUUUAAUGAUGCCCA-AU---AUAUGGUCUAAC-U-CU-UUUGGGUAUC
AL132709.5/86350-86274       GGUACUGG--AGGAGAGG-UUAUC-UGUGUU-UUUUCCCUUU-AUUUAUGAUGAA-AAAU---AU--GGUGCA-CUUCUA-UUUGAGAAUC
AAGU03025975.1/32125-32046   GAUAUUUA-A-GGAGAGG-UUAUC-UGUGUUCUGUUCACUUC-AUUCAUCAUAAA-UAAU---ACAUGGAUAA-CCUCUU-UCUGAAUAUC
AC208187.2/25743-25822       GGUAUUUG-AAGAUGCGG-UUGAC-CAUGGUGUGUACGCUUU-AUUUGUGACGUA-GGAC---ACAUGGUCUA-CUUCUU-C-UCAAUAUC
AADA01238809.1/43482-43561   GGUACUUA--AUGAGAAG-UUGCC-CGUGUUUUUUUCGCUUU-AUUUGUGACGAA-ACAU---UCGCGGUGCA-CUUCUU-CUUCAGUAUC
AAGU03025975.1/39962-39884   GCCACUUG-A-AGAGAGG-UUAUC-UUUUGUGUGUUUAUUUU-AUUUGUAAUGCA-G-AU---ACAAGGGCAA-GCUCUC-UCUGAGGAGC
CABD02116367.1/19466-19545   GGUACCUG--AAGAGAGG-UUUUC-UGGGUUUCUGUUUCUUU-AUUGAGGAUGAA-ACAC---ACCUGGUUAA-CCUCUU-UUCCAGUAUC
AAGW02077267.1/22999-23077   GGUACCUG-AAGG-GAGA-UCGAC-CGUGUUCCAUUCGCUCC-GCUGACUUCGAA-UAAU---AGAUGGUUGA-UCU-UU-CCUCGGUAUC
AAGW02077267.1/17943-18022   GGUGCUUG--AAGAUAGG-UUAUC-CGUGUUGCCUUCGCUGU-ACUCGUGACGAA-UCAU---ACACGGUUGG-CCUAUU-UUCCAGUACC
AAEX03006005.1/147851-147928 GCUACUUG-A-AGAGAGG-UUAUC-CUUCGUGUGUUUGUAUG-A-UUGUAAUGAA-U-AU---GCAAGGACAA-GCUCUC-UCCGAGGAGC
AL132709.5/98273-98194       GGUACUUG-GAGAGAUAG-UAGAC-CGUAUAGCGUACGCUUU-AUCUGUGACGUA-UGUA---ACACGGUCCA-CUA-AC-CCUCAGUAUC
AAPE02047294.1/11873-11793   GGUCCUUG--AGGAGAGG-UCUUC-CAUGAUGCAUUCACUGUACUAGUAGCUGAA-UCAU---ACAUGGUAGA-CCUGUU-UUCAAGUAUC
AAEX03006005.1/141193-141272 GGUGCCUG-G-GAAGAAG-UUGCC-CGUGUUAUUUUCGCUUG-AUACGUGCCGAA-ACAA---ACAUGGUGCA-CUUCUU-UCUCGGUAUC
AAEX03006005.1/152345-152424 CAUACUUG--AGGAGAAA-UUAUC-CUUGGUGUGUUCGCUGU-GUUUGUGAGGAA-UCAU---ACAAGGACAA-UUUCUU-UUUGAGUAUC
AAGW02077266.1/83917-83994   GAUACUUG-ACGGGGAGG-CUGUC-UGUGCUGUCUUCUCUUU-AUUUUUGAUGAA-ACAU---ACAGGGGAAC-GCGCGU-U---AGUCCC
AAPE02047294.1/28610-28535   GCUCCCUG-A-AGAGAGG-UUGUC-CUUCC-GUUGUUA--UU-AUUUGUGAUGUG-U-GU---UCAAGGGCAA-GCUCUC-UCCAGAGGGC
AAGW02077267.1/23236-23313   GGUGCUGA--GGG-GAGG-UUGUC-UGUGAUGAGUUCGCUGU-AUUAAAGCCGAA-UAUA---ACACAGAUGG-CCU-GU-UUUCAGCACC
AAEX03006005.1/142350-142427 GGUACUAG--AAAAGAGG-UUAUC-CGUGUU-UCUUCGCUUU-AUUUAUGACGAA-AAAU---ACG-GGUGCA-CUUCUG-UUUGAGUAUC
AAQR03046511.1/22259-22338   GAUACUUG-AAAA-GAGA-UUUUCCUUAAGUGAAUUUGUUGU-UUUUAUGACAAA-UCAU---UCUUAGCCAA-CCU-CU-AUUCAGUAUC
AAPE02047294.1/12164-12085   GGUGUGCG--CAGAUGGG-UUAUC-CGUGUUGCCUUCACUUU-AUUUGUCCCCAA-UCCU---CCAUGGUUCA-CCUAGC-UUUUAGUACC
AAQR03046511.1/22552-22628   ACUACUAG--AAGAGAGG-UUAUC-UGUGUU-UCUUCACUUU-AUUUAUGACAAA-AAAU---AU--GGUGCA-CUUCUA-UUUGCAUAUC
AL132709.5/95865-95787       GGUACUUG-GAGA-GAGG-UGGUC-CGUGGCGCGUUCGCUUU-AUUUAUGGCGCA-CAUU---ACACGGUCGA-CCU-CU-UUGCAGUAUC
AAGW02077267.1/14427-14502   GGUACU-G--AGG-GAGG-CUGUC-CGUGGUGAGUUCGCCUUAGGCGUUGAUGCC-CAAU---ACACGAUCGA-C---CU-CUUUGGUAUC
AAQR03046512.1/6198-6280     CAUACUUA--AGAGGAAA-ACAUC-CUUGGUAUGUUUACUUU-AUUUGUGAUGAA-UCAUCAUACAAGGACAA-UUUCUU-UUAGAGUAUC
AAGU03025975.1/35693-35615   GGUACUUA-G-AGUGAGG-UUACC-AUUUGUAUAUUCAGUUU-CUUGACAUGGAA-U-AU---ACAAGGGCAA-GCUCUC-UGUGAGCAUC
AAPE02047294.1/27347-27269   GGUACUUG-AA-AAGAGA-AUACC-CUUUGUAUGUUCACUUU-AUUAAUGGUGAA-U-GU---ACAGGGG-AG-ACUCUUAUUUGCGUAUC
AAQR03046512.1/488-566       GUUACUUG-A-AGAGAGG-UCGUC-UUUCAUUUGUUCACUUU-AUUAGUGGUGAA-U-AU---AUACGGGUAA-GCUCUC-UCUGAGGAGC
AAQR03046512.1/4777-4855     GGUACUUA-A-AGCGAGG-UUGCC-CUUUGUAUAUUCUGUUU-AUUGACAUGCAA-U-AU---ACAAGGGCAA-GCUCUC-UGUGAGUAUC
AL132709.5/87843-87764       GGUACCUG--AAAAGAAG-UUGCC-CAUGUUAUUUUCGCUUU-AUAUGUGACGAA-ACAA---ACAUGGUGCA-CUUCUU-UUUCGGUAUC
AAEX03006005.1/143202-143280 GAUGUUCG-AAAG-GAGG-UUGUC-CGUGAUGUAUUUGCUUU-GUUUAUGGCAGA-UAUU---GCACGGUUGA-UCU-CU-UUUCAUCAUC
EU434920.1/2521-2599         GGUACUUG--AGGAGAGG-UUGUC-UGUGAUGAGUUCGCUUU-AUUAAUGACGAA-UAUA---ACACAGAUGG-CCUGUU-UUC-AAUACC
AL132709.5/61554-61474       GGUACUGG-U-GGAGAGG-UCUUC-CAUGAUGCAUUCGAUUUAUUUUUUGACCAA-UCCU---ACAUAGUGGA-CUCUUU-UGAAAGCAUU
AY865927.1/23-102            GGUACUUG--AAGAGAAG-UUGUU-CGUGGUGGAUUCGCUUU-ACUUAUGACGAA-UCAU---UCACGGACAA-CACUUU-UUUCAGUACC
AL132709.5/66183-66105       GGUACUUG--GAGAGAGG-CUGGC-CGUGAUGAAUUCGAUUC-A-UCAAAGCGAG-UCAU---ACACGGCUCU-CCUCUC-UUUUAGUGUC
AL132709.5/56298-56222       GGUACUCG--GGGAGAGG-UUACC-CGAGC-AACUUUGCAUC-U-GGACGACGAA-UGUU---GCUCGGUGAA-CCCCUU-UUC-GGUAUC
AL132709.5/61017-60939       GGUACUCG-A-AUGGAGG-UUGUC-CAUGGUGUGUUCAUUUU-AUUUAUGAUGAG-UAUU---ACAUGGCCAA-UCUCCU-U-UCGGUACU
AC208187.2/29806-29886       GAUACUCG-AAGGAGAGG-UUGUC-CGUGUUGUCUUCUCUUU-AUUUAUGAUGAA-ACAU---ACACGGGAAA-CCUCUU-UUUUAGUAUC
AL132709.5/55165-55087       GGUGCCUG--AGGAGAGG-UGGCC-UGUGUUGCAUUCACAGA-AAUCAUGACACA-CAAG---ACACGAGCGG-CCUCUC-UUC-AGUAUC
AL132709.5/56006-55928       GGUACUUG--AAGGGAGA-UCGAC-CGUGUUAUAUUCGCUUU-AUUGACUUCGAA-UAAU---ACAUGGUUGA-UCU-UU-UCUCAGUAUC
AL132709.5/54880-54803       GGUACCUG--AAA-UAGG-UUGCC-UGUGAGGUGUUCACUUU-CUAUAUGAUGAA-UAUU---AUACAGUCAA-CCU-CU-UUCCGAUAUC
AL132709.5/73699-73621       GGUGCUUA--AAGAAUGG-CUGUC-CGUAGUAUGGUCUCUAU-AUUUAUGAUGAU-UAAU---AUC-GGACAA-CCAUUG-UUUUAGUAUC
EU616812.1/2503-2581         GAUACUUG--GAGAGAGG-CUGGC-CGUGAUGAAUUCGAUUC-A-UCUAAACGAG-UCAU---ACACGGCUCU-CCUCUC-UUCUAGUGUC
GU233960.1/1-52              GG-----------------UUGAC-CAUGGUGUGUACGCUUU-AUUUAUGACGUA-GGAC---ACAUGGUCUG----------------CU
GU233960.1/148-226           GGUACUUG-G-AGAGAGG-UGGUC-CGUGGCGCGUUCGCUUU-AUUUAUGGCGCA-CAUU---ACACGGUCGA-CCUCUU-UGC-GGUAUC
#=GC SS_cons                 <<<<<<-<.-<<<<<<<<.<<--<.<<<<----<<<<<____.________>>>>.>---...->>>>>-->>.>>>>>>.>>>->>>>>>
#=GC RF                      GgUaCuUg.AAagaGaGG.uugUC.CgUggUGUauUcgCUUU.AUUuAUGAcgAa.ucAU...AcAcGGucaa.CCuCuu.uUucaGuAuC
//
# STOCKHOLM 1.0

#=GF AC   RF00642
#=GF ID   mir-23
#=GF DE   microRNA mir-23
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.30
#=GF NC   43.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000027;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [2]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol. 2002;12:735-739.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-23_microRNA_precursor_family
#=GF SQ   22


CAAE01015023.1/589407-589480   GGGCUG-UGAGGGUUCCUGGCGUGCUGAUUUGUG-----ACCUA--UG---A-UAAAAUCACAUUGCCAGGGAUUACCACACCGCC
AF043897.1/1982-2056           UGGCUG-CUUGGGUUCCUGGCAUGCUGAUUUGUG-----ACUUA--AG---AUUAAAAUCACAUUGCCAGGGAUUACCACGCAACC
BAAF04082680.1/5350-5271       UGGCGG-GGAGGAUUCCUGGUGCCGUGAUUUGAUGCACAAAAAG--AA---AGAAAAAUCACAUUGCCAGGGAUUUCCACCUCUUC
CT027840.6/2697-2774           UGGCUG-UGUGGGUUCUUGGCAUGCUGAUUUGUG-----ACUGU--AGUAAAAAAAAAUCACAUUGCCAGGGAUUACCACACUACC
BX664751.9/59056-58982         CAGCUG-GAGGGAUUCCUGGCAGAGUGAUUUGGG-----AUUAU--AU---CAUAAAAUCACAUUGCCAGGGAUUUCCAACCAGCU
CAAE01012021.1/27791-27867     UAGCUG-GAGGGAUUCCUGGCAGAGUGAUUUGGC-----UGUGAUGUA---AUGUAAAUCACAUUGCCAGGGAUUUCCAACCAGCU
AY866326.1/317-389             GGCCGG-CUGGGGUUCCUGGGGAUGGGAUUUGCU-----GCCUA-------UCACAAAUCACAUUGCCAGGGAUUUCCAACCGACC
AANN01357153.1/1425-1351       GGGCUGGCUGGGGUUCCUGGGGAUGAGAUUUGUU-----UUUUA---G---UCACAAAUCACAUUGCCAGGGAUUACCAACCGUCC
AAVX01300477.1/943-1022        UGGCUGUGAGGUGUUCUUGUCAUUGUGAUUUGAGGCUA-AAAUC--AC---UGAGAAAUCACAUUGCCAGGGAUUCCCAUACAGCC
AAVX01508943.1/286-212         UGGUGG-GCUGGGUUCCUGGCAGAGUGAUUUGAU-----UUAAU--AA---UGUAAAAUCACAUUGCCAGGGAUUACCAACCCGUC
BX908735.10/1674-1753          UGGCGG-GGAGGGUUCCUGGCACCGUGAUUUGGUGGAUAAACAG--AA---AUGAAAAUCACAUUGCCAGGGAUUUCCACUCCUGC
BAAF04071179.1/1299-1375       CGGCCA-GGGGAAUUCCUGGCAGAGUGAUUUUUGA----GACUAC-AG---GACUGAAUCACAUUGCCAGGGAUUUCCAAUGGCUG
AAVX01114775.1/823-749         UGACUG-UGUGGGUUCCUGGCAUGCUGAUUUGUG-----ACAUG--AG---AUAAAAAUCACAUUGCCAGGGAUUACCACGUAGCC
AAPN01322484.1/282-356         CGGCGG-CUGGGGUUCCUGGUGAUGCGAUUUUCU-----UGUGC--UC---GCCAAAAUCACAUUGCCAGGGAUUUCCAACUGGCG
AAPY01721327.1/893-821         UGGCUGACUGGGGCUCCUGGGGAUGGGAUUGCUG-----CCUUU--------UAUAAAUCACAUUGCCAGAGAUUUCCAACUGACC
AC187115.2/53569-53495         UGGCUG-UUUGGGUUCCUGGCAUGAUGAUUUGUG-----AGUUA--AG---AUUAAAAUCACAUUGCCAGGGAUUACCACAUAGCC
AANH01003598.1/90472-90550     UGGUGG-GGAGGGUUCCUGGCACCGUGAUUUGAUGCAC-AAAGA--AA---AACAAAAUCACAUUGCCAGGGAUUUCCACUCCUUC
AC122794.3/96135-96063         GGACGG-CUGGGGUUCCUGGGGAUGGGAUUUGAU-----GCCAG-------UCACAAAUCACAUUGCCAGGGAUUUCCAACUGACC
AAFR03052006.1/45044-45116     GGCCGG-CUGGGGUUCCUGGGGAUGGGAUUUGAU-----UACUG-------CCACAAAUCACAUUGCCAGGGAUUUCCAACUGACC
AAYZ01075783.1/3205-3279       UGGCUG-CUUGGCUUCCUGGCAUGCUGAUUUGUG-----ACUUC--AG---AUUAAAACGACAUUGCCAGGGAUUACCACGCAACC
CAAE01014995.1/1246733-1246812 UGGCGG-GGAGGGUUCCUGGCACCGUGAUUUGAUGCAC-AAAGAC-AA---ACAAAAAUCACAUUGCCAGGGAUUUCCACCCUUUC
AAWZ02024153.1/17746-17672     UGCCAG-CUGGGGUUCCUGGUGAUGUGAUUUUAU-----UUUGG--UG---UUCAGAAUCACAUUGCCAGGGAUUUCCAACCAUCA
#=GC SS_cons                   ::::::.::::<<<<<<<<<------<<<<<___....._____..__...____>>>>>------>>>>>>>>>:::::::::::
#=GC RF                        UGGCuG.gugGGgUUCCUGGcAuuGUGAUUUGuu.....aauua..Ag...auaaAAAUCACAUUGCCAGGGAuUuCCAaccaaCC
//
# STOCKHOLM 1.0

#=GF AC   RF00643
#=GF ID   MIR171_1
#=GF DE   microRNA MIR171_1
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   48.00
#=GF NC   47.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.79 -Z 549862.597050 CM SEQDB
#=GF CL   CL00099
#=GF DR   MIPF; MIPF0000030;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12101121
#=GF RT   MicroRNAs in plants.
#=GF RA   Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP
#=GF RL   Genes Dev. 2002;16:1616-1626.
#=GF RN   [2]
#=GF RM   12202040
#=GF RT   Prediction of plant microRNA targets.
#=GF RA   Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP
#=GF RL   Cell. 2002;110:513-520.
#=GF RN   [3]
#=GF RM   15994906
#=GF RT   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa
#=GF RT   that are absent from Arabidopsis.
#=GF RA   Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL
#=GF RL   Plant Cell. 2005;17:2186-2203.
#=GF WK   MicroRNA
#=GF SQ   57


AAAA02020443.1/198-99        UGGAAAGAGCGAUAUUGGUGAGGUUCAAUCCGAUGAUUGGUUU-UACA--------------------------------------GCAGUGGUAAAAUCA-------------------------------------GUAU--CUGAUUGAGCCGCGCCAAUAUCUCUUCCUCUCCU
AC099399.2/24473-24353       UGGUAGCUAUGAUGUUGGCUCGGCUCACUCAGACGGCAUUGGC-GUGAUGCAAAGCAUG-----------------CAUGCGUGCUUGCUAGCUCACUUGU-------------------------------------GUUU--CUGAUUGAGCCGUGCCAAUAUCUUAGUGCUCUUU
AY551208.1/1-99              ---AACGCGAGAUAUUAGUGCGGUUCAAUCAAAUAGUCGUCCU-CUUA--------------------------------------ACUCAUGGAGAACGGU-----------------------------------GUUGU--UCGAUUGAGCCGUGCCAAUAUCACGCGGUAAACC
AM470860.1/34048-33952       UGGGAAGCGUGAUGUUGGGACGGCUCAAUCAAACCAAAGAUCU----C--------------------------------------AAUGGUUGAGUCCUU-------------------------------------UAAU--CUGAUUGAGCCGUGCCAAUAUCAUGUUCAAUACU
AM437215.2/7577-7677         UGAAGAAAGCGAUGUUGGUGAGGUUCAAUCUGAAGAUUGAUUU-AUGCU-------------------------------------UGAAUGUAAAAACUG-------------------------------------AUCU--CAGAUUGAGCCGCGCCAAUAUCACUUUUCUGUGG
AASG02000735.1/28318-28416   AUGCGUACGAGAUAUUGGUGCGGUUCAAUCAGAGAUCAU-UGC-UCUA--------------------------------------UAUAUAGAGCUUUUG-------------------------------------UUGU--UUGAUUGAGCCGUGCCAAUAUCACGUGCAUAUAU
AY728471.1/4-115             ----------GAUAUUGGCCUGGUUCACUCAGAUCACGACUUC-AGAG--------------------------------------CAAAGUGUCU-----UUCUUCUUCUUCUUCUUCUUCUUGUUUUAUGUUCGUUUGAU--UUGAUUGAGCCGUGCCAAUAUCUC----------
AC004392.1/107127-107027     UCAAAUACGAGAUAUUGGUGCGGUUCAAUCAGAAAACCGUACU-CUUU--------------------------------------UGUUUUAAAGAUCGG------------------------------------UUUAU--UUGAUUGAGCCGUGCCAAUAUCACGCGUUUAAAU
AY551252.1/1-120             --UAAAAAGAGGUAUUGGCGUGCCUCAAUCCGAAGGCAUGGCU-GAUUACAGGCACCUC-----------------GACCGAUCUAGCGCAUGCAGCCAUG------------------------------------UUUCU--UGGAUUGAGCCGCGUCAAUAUCUCUCCUUGCUUC
AM473187.2/3544-3427         UGGCUGCUGCGAUAUUGGCCCGGUUCACUCAGAUACAGGAUAC-ACCUACACUUCCA--------------------AAGAAAAAAAAAAAGGUGUACUUU-------------------------------------UGAU--UUGAUUGAGCCGUGCCAAUAUCUGAGUUCCCUUU
AARH01001039.1/225464-225596 GUGUCAUUGCGAUGUUGGCCCGGUUCACUCAGAGAAAAGACAC-CAUUUUUUUUCAAGAAGAUCA-----UCAAAGCUUGAAAGAAUAAUGGUGGUCGGUC-------------------------------------GUCU--CUGAUUGAGCCGUGCCAAUAUCUUAGUGCUCUUU
AC152351.7/84740-84636       CGAAAAAAGCGAUGUUGGUGAGGUUCAAUCCGAAGACGGAUUU-ACAUGUA---------------------------------UAGAGUUGUAAAAUACG-------------------------------------AUCU--CAGAUUGAGCCGCGCCAAUAUCACUUUUAUUAUU
AC154090.19/70773-70670      GUUGAGAUGAGAUAUUGGUGCGGUUCAAUCAGAAGGCAGUGCU-UUUAUA----------------------------------AUUCAAAAAGCUCUGUG-------------------------------------UUAU--UUGAUUGAGCCGUGCCAAUAUCACGUGUUAAUCA
AM486682.2/2891-2758         UAGUUACUGUGAUGUUGGCUCGGUUCACUCAGACAAAAAGAAA-AAAAAAAAGAAAAAGRAAAAA----CAAACACAYAUAUGCAUGCAUUUUUCUCUUUU-------------------------------------AGCU--UUGAUUGAGCCGUGCCAAUAUCUCAGUGCCUUUU
AASG02019837.1/638-762       UAGUGAUUGUGAUAUUGGCCUGGUUCACUCAGACAUGAAACCU-AUCCCUUCUCCUGCUUA-------------UUGCCUGAAUAGGGUGUUGUUGCUAUA-------------------------------------UGUU--UUGAUUGAGCCGUGCCAAUAUCUCAGUGCUGUUU
AY871043.1/1-86              -------GGGGAUGUUGGGAUGGCUCAAUCAUGUCAAAUCUCC-CAAAUU-----------------------------------AUGAUGUUGGGUCUUU-------------------------------------UAAU--CUGAUUGAGCCGUGCCAAUAUCAC----------
AASG02008156.1/3849-3747     CAACGAAAGCGAUGUUGGUGAGGUUCAAUCCGAAGACGGAUUU-ACACAU-----------------------------------UCUGUUGUAAAGGACG-------------------------------------AUCU--CAGAUUGAGCCGCGCCAAUAUCACUUUUCAUUAA
AY551249.1/18-146            GGGAGAGUGCGAUGUUGGCAUGGUUCAAUCAAACCGGGCAAAC-UUAUGCACUAGCUAAGCAA---------GAUGCAGGGAUAUGCAGUAUGGUUUUGUU-------------------------------------UGGU--CUGAUUGAGCCGUGCCAAUAUCACAAGCUUGCCU
AL606645.2/80760-80660       GUGGGAACGGGAUAUUGGUGCGGUUCAAUCAGAAAGCUUGUGCUCCGA--------------------------------------AGGCGAGGGGCUCCA-------------------------------------CUCU--UUGAUUGAGCCGUGCCAAUAUCACGUCGCCUUUG
AASG02006362.1/4770-4867     AGAAAGUGGGGAUGUUGGAAUGGCUCAAUCAAAUCAAA--UCU-CCCA--------------------------------------AAGUUUUGGGUCCUU-------------------------------------UAAU--CUGAUUGAGCCGUGCCAAUAUCCCCCAUAUUUAG
AM452855.1/37017-36917       GAAAGUAAGCGAUGUUGGUGAGGUUCAAUCCGAAGACGRAUUU-ACGAA-------------------------------------GAGCCGUAAAGAACG-------------------------------------AUCU--CUGAUUGAGCCGCGCCAAUAUCACUUUCUGCUAA
AASG02007113.1/1812-1912     GAGGAAAUCUGAUGUUGGCAUGGUUCAAUCAAAUCGAAGCACU-CAGCU-------------------------------------GCCUGCUGAGUUCUU-------------------------------------UAAU--CUGAUUGAGCCGUGCCAAUAUCGCCAUUCAGUCU
AY728466.1/4-80              ----------GAUGUUGGCAGAGCUCAAUCAAAUCAAA---GC-ACUC--------------------------------------AAUGGUUGGGUUCUU-------------------------------------UCAU--CUGAUUGAGCCGUGCCAAUAUCGC----------
AASG02001674.1/19617-19518   AAUCAAACGGGAUAUUGGUCCGGUUCAAUAAGAAAACAGUGCU-CAAA--------------------------------------AUGUUAUGGGCCCUG-------------------------------------CUUU--UUGAUUGAGCCGUGCCAAUAUCACGUGCACUGCU
AY728469.1/2-87              -------CGGGAUAUUGGUACGGUUCAAUCAGAAAGUAAUGCU-CCCAA-------------------------------------AAGUAUAGAGUACUA-------------------------------------UUGU--UUGAUUGAGCCGUGCCAAUAUCACGU--------
AARH01004445.1/202551-202452 UAUAUAACGAGAUAUUGGUGCGGUUCAAUCAGAUAGUAAUGCU-CCAU--------------------------------------AAGCAUAGAGCUCUA-------------------------------------UUGU--UUGAUUGAGCCGUGCCAAUAUCACGUAUAUGUUG
AASG02005726.1/12385-12489   UACAGGUGAAGGUAUUGGCGCGUCUCAAUCUGAUACAGAGCUA-AAUGGUA---------------------------------AAUUUAGAAUAGCCAUG-------------------------------------UAAU--UUGAUUGAGCCGCGUCAAUAUCUCCUUAAAUUUG
AY728474.1/2-89              -------AGCGAUGUUGGUGAGGUUCAAUCCGAAGACAGAUUU-ACACGA-----------------------------------GUGAAAGUAAAAUCCG-------------------------------------AUCU--CAGAUUGAGCCGCGCCAAUAUCACUU--------
AL133452.1/19161-19274       GAGUCCCUUUGAUAUUGGCCUGGUUCACUCAGAUCUUACCUGA-CCACACACGUA------------------------GAUAUACAUUAUUCUCUCUAGA-------------------------------------UUAU--CUGAUUGAGCCGCGCCAAUAUCUCAGUACUCUCU
AARH01006440.1/11723-11624   ACUAACUUGAGAUACUGGCUCGGUUCAACCUCAUCGUAGUCUU-GAUG--------------------------------------AAUGAUUCAAAUCUA-------------------------------------UGGU--UGGAUUGAGCCGCGCCAAUAUCGCAUGCUACUGC
AM447436.1/18502-18400       UAUGGGGGGAGGUAUUGGCGUGCCUCAAUUUAAAGACAUGGUU-AGAUGA-----------------------------------AGAGAUAUUAGCCAUG-------------------------------------UGAU--UUGAUUGAGCCGCGUCAAUAUCUCCUUUUGCACC
BT018211.1/119-253           GAGAGAGUGCGAUGUUGGCAUGGCUCAAUCAACUCGCCGGCCG-CGGGUGGCUUAGCUUAUUAAU----UCUGCGUUUUUGAUCGAGGUGCGGGCGCAGUG-------------------------------------UUU-AAUUGAUUGAGCCGUGCCAAUAUCACAACCUUCUCU
AC157488.1/72896-73001       AAGCAAGCAAGGUAUUGGCGCGCCUCAAUUUGAAUACAUGGCU-AUAAAAA--------------------------------UGCAUCAUAUCAGCCAUG-------------------------------------UAGU--UUGAUUGAGCCGCGUCAAUAUCUUGUUUCCAUCU
AASG02000279.1/67999-67862   GUGUCAUUGUGAUGUUGGCCCGGUUCACUCAGACAAAAACGAU-GUGUUUUCUCAAGCAUUUGUUUUUCGAAACGCUUGAUAUGUUAACACAAGCAUAAUG-------------------------------------GCCU--UUGAUUGAGCCGUGCCAAUAUCUUAGUGCUCUUU
AB011474.1/28147-28062       GAGUCCCUCUGAUAUUGGCCUGGUUCACUCAGAUUCUCUUUUA-----------------------------------------------------CUAAC-------------------------------------UCAU--CUGAUUGAGCCGUGUCAAUAUCUCAGUCCUCUCU
AC150705.17/109871-109755    UAGUUAAUGAGAUAUUGGCCUGGUUCACUCAGACCAAGUGAUA-AACCACUAAGAUA---------------------CAGUAUUGUACUUGUGUGGUUUU-------------------------------------GGGU--UUGAUUGAGCCGUGCCAAUAUCUCACUACUAUUU
AM485301.2/8595-8497         AGAAGGUGGGGAUGUUGGAAUGGCUCAAUCAAAUCAAAUCUCC--CAA--------------------------------------GGGUUUUGGGUCCUU-------------------------------------UAAU--CUGAUUGAGCCGUGCCAAUAUCAUCAUGUUCACU
AM446221.1/52246-52149       AGAUACACGAGAUAUUGAUACGGUUCAAUUAGAAAGCUG--UG-UUCU--------------------------------------AAGUUAAGAACUCUG-------------------------------------UUGU--UUGAUUGAGCCGUGCCAAUAUCACGUCCUACUUC
AC189627.2/36180-36072       AGUCCUCUUUGAUAUUGGCCUGGUUCACUCAGAUCUUCCAGAU-UACACACGU-----------------------------ACUAUAUACAUUCUCUCAG-------------------------------------UUAU--CUGAUUGAGCCGCGCCAAUAUCUCAGUGCUCUCU
AM470156.1/23164-23065       GCUUUCACGAGAUGUUGGUGCGGUUCAACCUAACUGUAGUGUC-CAUG--------------------------------------AAUGUAUCGACUCUG-------------------------------------AUGU--UUGGUUGAGCCGCGCCAAUAUCCCGUCUAUCUUA
FN595765.1/555787-555687     GGUAUUACGGGAUAUUGGUGCGGUUCAAUAAGAAAGCAGUGCU-CGCAA-------------------------------------UCUUUUUGAGUUCUG-------------------------------------GUUU--UUGAUUGAGCCGUGCCAAUAUCACGUGUCAUUGC
AY551247.1/10-146            UUGUAGCUAUGAUGUUGGCCCGGCUCACUCAGAUGGAUCAUCG-GUGCAGAAGAGUGCAUGAAUCUG-AUGCAGUCUCAGUGUAGUAUGCUCCAUGCUGGA-------------------------------------ACUU--CUGAUUGAGCCGUGCCAAUAUCUCAGCACCAUUU
AY551207.1/4-100             UCAAAUACGAGAUAUUGGUGCGGUUCAAUCAGAAAACCGUACU-CUUUU-------------------------------------GUUUUAAAGAUCGGU-------------------------------------UUAU--UUGAUUGAGCCGUGCCAAUAUCACGC----GUUU
AP003573.3/25796-25895       UGGAAAGAGCGAUAUUGGUGAGGUUCAAUCCGAUGAUUGGUUU-UACA--------------------------------------GCAGUGGUAAAAUCA-------------------------------------GUAU--CUGAUUGAGCCGCGCCAAUAUCUCUUCCUCUCCU
AY551248.1/8-128             UGGUAGCUAUGAUGUUGGCUCGGCUCACUCAGACGGCAUUGGC-GUGAUGCAAAGCAUG-----------------CAUGCGUGCUUGCUAGCUCACUUGU-------------------------------------GUUU--CUGAUUGAGCCGUGCCAAUAUCUUAGUGCUCUUU
EU549103.1/220-333           GAGUCCCUUUGAUAUUGGCCUGGUUCACUCAGAUCUUACCUGA-CCACACACGUA------------------------GAUAUUCAUUAUUCUCUCUAGA-------------------------------------UUAU--CUGAUUGAGCCGCGCCAAUAUCUCAGUACUCUCU
FM163807.1/196-297           GGUAACGCGAGAUAUUAGUGCGGUUCAAUCAAAUAGUCGUCCU-CUUAA------------------------------------CUCGUGGAGAACGGUG-------------------------------------UUGU--UCGAUUGAGCCGUGCCAAUAUCACGCGGUAAACC
AY728472.1/1-115             --------GCGAUGUUGGCCCGGUUCACUCAGAGAAAAGACAC-CAUUUUUUUUCAAGAAGAUCA-----UCAAAGCUUGAAAGAAUAAUGGUGGUCGGUC-------------------------------------GUCU--CUGAUUGAGCCGUGCCAAUAUCUU----------
AY728468.1/2-86              --------GGGAUGUUGGGAUGGCUCAAUCAUAUCAAAUCUCC-CAAACU-----------------------------------AUGAUGUUGGGUCGUU-------------------------------------UAAU--CUGAUUGAGCCGUGCCAAUAUCAC----------
AY728473.1/2-93              -------AGCGAUGUUGGUGAGGUUCAAUCCGAAGACGGAUUU-ACACGUGA-------------------------------AAGUAAUUGUAAAAUACG-------------------------------------AUCU--CAGAUUGAGCCGCGCCAAUAUCACUU--------
AY728470.1/5-86              --------GAGAUAUUGGUGCGGUUCAAUCAGAUAGUAAUGCU-CCAU--------------------------------------AAGCAUAGAGCUCUA-------------------------------------UUGU--UUGAUUGAGCCGUGCCAAUAUCAC----------
AY551251.1/1-100             GUGGGAACGGGAUAUUGGUGCGGUUCAAUCAGAAAGCUUGUGC-UCCGA-------------------------------------AGGCGAGGGGCUCCA-------------------------------------CUCU--UUGAUUGAGCCGUGCCAAUAUCACGUCGC-CUUU
ABXC01004438.1/173968-173868 AAACCUACGGGAUAUUGGCGCGGUUCAAUCAGAAAGCUUGCGC-UCCAA-------------------------------------AGCCCAGGGGCUCCA-------------------------------------CUCU--UUGAUUGAGCCGUGCCAAUAUCACGUCCUCGCUU
AP005441.3/32630-32710       ----------GAUAUUGGGGCGGUUCAAUCAGAAAGCUUGUGC-UCCGG-------------------------------------AAGCGAGGAGCUCUA------------------------------------CUCUU--UUGAUUGAGCCGUGCCAAUAUCA-----------
AECO01070604.1/1035-1121     GAGAGAGUGCGAUGUUGGCACGGUUCAAUCAAAUCGCCGGCCG-GGUU---------------------------------------------------GA-------------------------------------CUUG--UUGAUUGAGCCGUGCCAAUAUCACAACCUUCUCU
AY551250.1/5-106             GCGACGACGGGAUAUUGGGGCGGUUCAAUCAGAAAGCUUGUGC-UCCGG-------------------------------------AAGCGAGGAGCUCUA------------------------------------CUCUU--UUGAUUGAGCCGUGCCAAUAUCACGUCGCAUCCA
AAAA02023235.1/56013-55912   GCGACGACGGGAUAUUGGGGCGGUUCAAUCAGAAAGCUUGUGC-UCUGG-------------------------------------AAGCGAGGAGCUCUA------------------------------------CUCUU--UUGAUUGAGCCGUGCCAAUAUCACGUCGCAUCCA
#=GC SS_cons                 :::::::<--<<<<<<<<<--<<<<<<-<<_____________._____....................................._______________.....................................____..__>>->>>>>>-->>>>>>>>>-->:::::::::
#=GC RF                      uagaaaacGuGAUaUUGGccuGGUUCAaUCAGAuaacaaauuu.auaaa.....................................aaaauuuuaucuaua.....................................uuaU..UUGAUUGAGCCGUgCCAAuAUCuCguuucucUuu
//
# STOCKHOLM 1.0

#=GF AC   RF00644
#=GF ID   mir-27
#=GF DE   microRNA mir-27
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.20
#=GF NC   49.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000036;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [3]
#=GF RM   18256158
#=GF RT   MicroRNA profile of Marek's disease virus-transformed T-cell line MSB-1:
#=GF RT   predominance of virus-encoded microRNAs.
#=GF RA   Yao Y, Zhao Y, Xu H, Smith LP, Lawrie CH, Watson M, Nair V
#=GF RL   J Virol. 2008;82:4007-4015.
#=GF WK   miR-27
#=GF SQ   32


BAAE01159437.1/1557-1475     UUGGUGGAGGUGAAGGGCUUAGCUCGCUCUGUGAACAGUUCAG-UGAAA--ACUCGUGUUCACAGUGGCUAAGUUCCGCUCCUCAC
CAAE01015023.1/589695-589777 UCCAGCCAGGCACAGAGCUUAGCUGAU-UGGUGAACAGUGAUUGAUUUC--CUCUUUGUUCACAGUGGCUAAGUUCUGCACCUGAG
BAAF04082680.1/4929-4846     UCGCUAAAGGCACAGAGCUUAGCUAAU-UGGUGAGCAUUGAUCCCUGCUG-UGUGUUGUUCACAGUGGCUAAGUUCAGUGCCGGAG
CT027840.6/2845-2927         UCUGAGCGGGUGCAGAGCUUGGCUGAU-UGGUGAACGUGCAUGGCUUGU--GUUUUUGUUCACAGUGGCUAAGUUCUUCACCCGAA
AANN01293679.1/8845-8763     UCUGAUGAGGUGCAGAGCUUAGCUGAU-UGGUGAACAGUGACUGGUUUC--CGCUUUGUUCACAGUGGCUAAGUUCUGCACCUGAA
BX664751.9/57144-57062       UUUCGUGAGGUGCAGGACUUAGCUCACUCUGUGAACAGAUCUC-GGAUA--UCCUAUGUUCACAGUGGCUAAGUUCCGCUCCUCUG
BAAF04052671.1/6292-6371     UCUGGUCAGGCGUGGAACUUAGUUGAC-UUCUGAACAGAGUCU---UUC--AAGCGUGUUCACAGUGACUAAGUUCUUCUCUCGAG
CAAE01012021.1/28143-28225   UUGAGAGAGGGGCAGGACUUGGCUCGCUCCGUGAACAGUUCGGUCAGU---GUGAGUGUUCACAGUGGCUAAGUUCCGCUCCUCAC
AY866326.1/455-536           UGGCCUGAGGAGCAGGGCUUAGCUGC--UUGUGAGCAGGGUUCACUCCA--AGUCAUGUUCACAGUGGCUAAGUUCCGCCCCCCAG
AANN01357153.1/1239-1159     CGGCCUGGGGAGCAGGGCUUAGCUGC--UGGUGAACAGGGUGU-CACCG--AGUCUUGUUCACAGUGGCUAAGUUCCGCCCCCCUC
AAPN01152921.1/1247-1165     UCUGUCGCGGCGCAGAGCUUAGCUGAU-UGGUGAACAGUGAUUGCUGGA--CUCUUUGUUCACAGUGGCUAAGUUCUGCGCCCGCA
AANH01005391.1/487407-487325 UUUCUGAAGAUGCAGAAUUUAGCUCAU-UAGUGAGCAUUGAACCAAACA--GGAAUUGUUCACAGUGGCUAAGUUCAGUGUCUGAC
BAAF04071179.1/1519-1598     GCUGUGCGGCAGCAGGACUUAGCCCAC-AUGUGAACAGUGAGUGUA-----UGCCAUGUUCACAGUGGUUAAGUUCUGCCGCCACA
BAAF04073622.1/5313-5395     UGGGCUCAGAUGCAGGACUUAGUUCAU-UGGUGAGCAUUGAGCCACACA--GGAAUUGUUCACAGUGGCUAAGUUCAGUACCUGAC
AAPN01322484.1/470-549       GGUCCGGCGGAGCAGGGCUUAGCUGGC-CUGUGAACAG---UUAGUUCC--CUGCGUGUUCACAGUGGCUAAGUUCCGCCCCUCCA
AANH01005378.1/81241-81159   UUGACGGAGGGGCAGGACUUAGCUCGCUCCGUGAACAGUCCAG-UGAAA--GCCUGUGUUCACAGUGGCUAAGUUCCGCUCCUCAC
AAFR03052006.1/45216-45298   UGGCUUGAGGAGCAGGACUUAGCUGCC-UUGUGAACAGAGUCAGCAUCA--UAUUGUGUUCACAGUGGCUAAGUUCCGCUCCCCUU
AAFC03049555.1/15605-15685   UGGCCUGGGGAGCAGGGCUUAGCUGC--UUGUGAGCAGGUCCA-CAUCA--AAUCGUGUUCACAGUGGCUAAGUUCCGCCCCCCCA
CR847548.8/136623-136702     UUCUAGCAGGUGCAGAGCUUAGCUGAU-UGGUGAACAGUGAUUGAA-----CUCUUUGUUCACAGUGGCUAAGUUCUGCAUCUGAG
AAVX01257813.1/610-525       CCCCGUGCGGUGAAGGACUUAGCUAACUCUGUGAACAGAUAUCUGAAUGCCUUCAAUGUUCACAGUGGCUAAGUUCCGCACCUCAG
AAPY01721327.1/686-605       GGGCCUGAGGAGCAGGGCUUAGCUGC--UUGUGAGCAGCGUCCACACCA--AGCUGUGCUCACAGUGGCUACGUUCUGUCCUCCAG
AC187115.2/53333-53251       UCUGGUGAGGUGCAGAGCUUAGCUGAU-UGGUGAACAGUGAUUGUUUCC--CUCUUUGUUCACAGUGGCUAAGUUCUGCACCUGAA
AY866333.1/592-673           UGGCCUGAGGAGCAGGGCUUAGCUGC--UUGUGAGCAGGGUCCACACCA--AGUCGUGUUCACAGUGGCUAAGUUCCGCCCCCCCA
AF480561.1/2-79              ----CUGAGGAGCAGGGCUUAGCUGC--UUGUGAGCAGGGUCCACACCA--AGUCGUGUUCACAGUGGCUAAGUUCCGCCCCCCAG
AAHX01097732.1/7669-7751     UGGCCUGUGGAGCAGGGCUUAGCUGC--UUGUGAGCAAGGUCUACAGCAA-AGUCGUGUUCACAGUGGCUAAGUUCCGCCCCCUGG
CU138547.13/91679-91760      GUUGUGUGGUGUCAGGACUUAACCCAC-UUGUGAACAAUGCAUCGAAC---UUCAAUGUUCACAGUGGUUAAGUUCUGCCGCCCCU
AAWR02041732.1/2484-2565     UGGCCUGGGGAGCAGGGCUUAGCUGC--UUGUGAGCAGGGUCCACACCG--AGUCAUGUUCACAGUGGCUAAGUUCCGCCCCCCGG
AAKN02038501.1/44047-43965   UCUAACGAGGUGCAGAGCUUAGCUGAU-UGGUGAACAGUGAUUGGUUUC--CGCUUUGUUCACAGUGGCUAAGUUCUGCACCUGGG
AAGV020400005.1/5570-5488    UCUGACAAGGUGCAGAGCUUAGCUGAU-UGGUGAACAGUGAUUGGUUUC--CACCUUGUUCACAGUGGCUAAGUUCUGCACCUGAA
CU855875.13/5510-5593        UCGCUCACGGCGCAGAGCUUAGCUAAU-CGGUGAGCAUUGAUCCCUUAAG-AAAACUGUUCACAGUGGCUAAGUUCAGUGUCUGGA
CAAB02004947.1/150354-150272 UUUCUAAAGACACAGGACUUAGCUCAU-UAGUGAGCAUUGAACCCAACA--CAGAUUGUUCACAGUGGCUAAGUUCAGUGUCUGAC
AAWZ02024153.1/17341-17260   GAUGACAAGCCGUAGGGCUUAGCCCAC-CUGUGAACAGCAUUG-GAUUC--AGCCAUGUUCACAGUGGCUAAGUUCCGCUGCUUGG
#=GC SS_cons                 ::::::::::::::<<<<<<<<<<<--.--<<<<<<<____________.._____>>>>>>>-->>>>>>>>>>>::::::::::
#=GC RF                      UuucuugaGGuGCAGggCUUAGCUgau.UuGUGAaCAGugauuacauca..auuuuUGuUCACAGuGGCUAAGuuCuGCuCCugag
//
# STOCKHOLM 1.0

#=GF AC   RF00645
#=GF ID   MIR169_2
#=GF PI   MIR169_1
#=GF DE   microRNA MIR169_2
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.55 -Z 549862.597050 CM SEQDB
#=GF CL   CL00098
#=GF DR   MIPF; MIPF0000037;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15200956
#=GF RT   Computational identification of plant microRNAs and their targets,
#=GF RT   including a stress-induced miRNA.
#=GF RA   Jones-Rhoades MW, Bartel DP
#=GF RL   Mol Cell. 2004;14:787-799.
#=GF RN   [2]
#=GF RM   16040653
#=GF RT   Expression of Arabidopsis MIRNA genes.
#=GF RA   Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC
#=GF RL   Plant Physiol. 2005;138:2145-2154.
#=GF RN   [3]
#=GF RM   19939267
#=GF RT   High throughput approaches reveal splicing of primary microRNA transcripts
#=GF RT   and tissue specific expression of mature microRNAs in Vitis vinifera.
#=GF RA   Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del
#=GF RA   Fabbro C, Valle G, Policriti A, Morgante M, Pesole G, Pe ME, Horner DS
#=GF RL   BMC Genomics. 2009;10:558.
#=GF WK   MicroRNA
#=GF SQ   100


AARH01007968.1/101578-101471 AAAG----UUUGAUGC-AGCCAAGGAUGACUUGCCGACG---ACU-C--AAUUUUUGCUUCCA---------------------------------------------------------------------------------------------------------------------------------------------UAUG---GUAGAA---------------GAGAUGAAUAGGUUGGCAGGU-UU---UCCUU-GGCUACAUUUUC---CUUUCU
AARH01006471.1/67036-67151   AGGG----UUUGGU---AGCCAAGGAUGACUUGCCUAUU---UCC-U--CCAUAAGGCUUUAAAAAGCAU----------------------------------------------------------------------------------------------------------------------------------GAAAUGUGGUUUAGAGCUC-----------AAUUGAAGGGUUCAUAGGC-AGU-CU---ACUUU-GGUUA----------UCCUAG
AY551197.1/39-143            AGAA----UGAGGUUG-AGCCAAGGAUGACUUGCCGGGU---UUU-U--UUACCAAUGAAUCU---------------------------------------------------------------------------------------------------------------------------------------------------AAUUAAC---------------UGAUUCUGGUGUCCGGCAAGU-UG---ACCUU-GGCUCUGUUUCC---UUCUCU
AM433342.2/4348-4244         AGGG----UGGAAUUG-AGCCAGGGAUGACUGACCAUCA---UUU-U--UCAGUUGGUAUUUG------------------------------------------------------------------------------------------------------------------------------------------------AGGCUUUAAC---------------UGG---UCAUGCACGGCUGGU-UA---UCCCU-GUCUCCUUUAGC---UCCUCU
AM488015.2/3713-3611         AGGG----UGGAAUUG-AGCCAAGGAUGACUUGCCGUCC---UUU-G--CAKCAAGCAUUGAA--------------------------------------------------------------------------------------------------------------------------------------------------GCUUUAAC---------------UGG---GCAUGCACGGCUAGU-UA---UUCUU-GGCUCAUUUGGC---CCCUCU
AAAA02006935.1/54160-54031   AGAG----CAGGAUGC-AGCCAAGGAUGACUUGCCGGCC---GGC-G--AUGGCCGACGGCGAGGUUAAUU--------------------------------------------------------------------------------------------------------------------------------AAUUGGCCGGAGACUGGCAG----------UCCUUCUCUGUUGAUCCGGCAAGUUUG---UCCUU-GGCUACACCUUG---CUCUCU
AK241891.1/199-330           AGAA----CGGAAUGC-AGCCAAGGAUGACUUGCCGGUA---CGU-G--UAUGCAUGUUUCAAGGUACU------------------------------------------------------------------------------------------------------------------------------------AUAUGUGCCCCCAACUGUUUUA---GAUCCAUGCUGACAUUUUCCGGCAAGU-UG---UCCUU-GGCUACGUCUUG---UUCUUU
AACV01004468.1/73451-73625   AGCU----GAUUCGGU-AGCCAAGGAUGACUUGCCUAAU---GCC----UAUGUGCAUGUGUUUAUACGCUGCUCAUCUGCAUUUUGAUUAUCCCCU-----------------------------------------------------------------------------GAUCAGUCCUGUCGUCAAUUAUAUGUGUGUGUAGUACUCUGUA---------------CUCAUACAUAUAUAGGCAUGU-CU---UCCUU-GGCUAUUCGGAG--CGGCUCU
AB016889.1/42173-42024       ACAA----UAUUUGGU-AGCCAAGGAUGACUUGCCUGCU---UCU-C--UGAACAAAAUGGUCGAUGUCAUGUUUUGAAGUGACU----------------------------------------------------------------------------------------------------AUAAGUUAUACCAAGAAAUGACCAUUUUGUUU---------------AUAAAUAGACAUCAGGCAG---UC---UCCUU-GGCUAUCCUUAU---AUGUUC
AB016889.1/38601-38457       AUAU----UUGGU----AGCCAAGGAUGACUUGCCUGAC---UCU-U--UGUGUAAAAUGUUUAGUGUCUUGUUUGAAGUCAC--------------------------------------------------------------------------------------------------------UAUAAGUUGUAUCAAGCAAUGACCAUUUUGCU-----------UAUAAAAAAGAUAUCAGGCAG---UC---UCCUU-GGCUAUCCUU-----AUAUGU
AB016889.1/44813-44667       AUAU----UUGGU----AGCCAAGGAUGACUUGCCUGUU---UCU-U--UGAGUAAAAUGGGUUAGUGUCAUGUUUGACAAGUGAC--------------------------------------------------------------------------------------------------UAUAAGUUAUAUCAAGCAAUGACCAUUUUACUC---------------AUCAAAAGACAUCAGGCAG---UC---UCCUU-GGCUAUCCUU-----AUAUGU
AM423269.2/5504-5608         GGGG----UCGAAUUG-AGCCAAGGAUGGCUUGCCGUCA---UCU-G--CAGCAAGAGUUGGA------------------------------------------------------------------------------------------------------------------------------------------------GACUUUUAAC---------------UGU---GCGUGCACGGUUAGU-CA---UCCUU-GGCUCAUUUGGC---CCUUCU
AC186138.3/121840-121954     AAAG----UGAAAUGG-AGCCAAGGAUGACUUGCCGGUA---UAU-U--AGUUUGUCGCUAAAGCU------------------------------------------------------------------------------------------------------------------------------------------AACUAGCUUUAGU---------------UGUUGGGUACUCCCGGCAGGU-CA---UCCUUCGGCUAUAUUUGG---CUUUCU
AC186138.3/99196-99295       AAAG----UGGAAUGC-AGCCAAGGGUGAUUUGCCGGCA---GAU-A--UAUAUGAAUA--------------------------------------------------------------------------------------------------------------------------------------------------------UUCAUA---------------GAGAUGCAUGUGUCGGCAAGU-UC---CUCUU-GGCUACAUUUCG---CUUUCU
AC186138.3/116687-116941     AAAG----UGAGAUGA-AGCCAAGGAUGACUUGCCGGUAU-AAUA-G--UAAUUUGCCACAAAUCUAGAUAGCUAUUAGCUAUGUUUGGAUGGGCGGUGAGAUUAACAAAAUUACAGCAGCAUUGUGAUUUUGUUGAUGCUUUAAAGUGUAGUUUUUAUCAAAAUUACAGUGGUUCACUGUAAUUAUGAGAAUCUCACCGUCAAUCUAAAUAUGCAU---------------UUAGUUUCAUUUCCGGCAGGU-CA---UCCUUCGGCUAUAUUUGG---CUUUCU
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AARH01003557.1/353551-353722 AUAU----CGUGGCGC-AGCCAAGGAUGACUUGCCGGCA--AGCU-C--CUCACACGUAUUUUGUUUCGAGUUUCAUUGAUGGCAUUGCUAGAUA---------------------------------------------------------------------------------GAUAUAUAUGAUUUCGUAAUUCAAACUUUUGGGCCAUUGUC---------------UGGUUGAAAUGAUCGGCAAGC-UG---UCCUU-GGCUAUGUCUCU---AUUUCA
AM434595.1/14597-14697       UGAG----UGGAAUAG-AGCCAAGGAUGACUUGCCGGCA---ACU-G--CAGCAAGGCAUAGG---------------------------------------------------------------------------------------------------------------------------------------------------GUUUAAC---------------UGG---UCAUAACUGGCAAGC--A---UCUGA-GGCUCUAUUUCA---CCCUCU
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AY551193.1/37-274            CCAU----UGUUGUUC-AGCCAAGGAUGACUUGCCGGUA---GCU-U--GUAUUAUGAUUACUCUAUAUUCGAUUUAUAUUAUGGAGAUGAUGGUUUAUAUAUAUUUACUUAUCUACAUAGUUUUAGUUG-----------AUUUUUUUUCGUACGUAAUAUAAUACGAAAAAGUAUUUACUUAUUUAUAUAUGUGUGUUGGGGCAAGAAGUGUAAC---------------CAA---GCUAGCCCGGCAAGU-CA---UCUAU-GGCUAUGCAACU---GUCUCU
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AASG02001387.1/35857-35778   AAAG----UGCUAUGC-AGCCAAGGAUGACUUGCCGACU---AUG-U--GCAAUGUG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUGGCAAGU-UG---UCCUU-GGCUACAUGUUU---CUUUAU
AM428868.1/522-630           AGGG----UAGAAUCG-AGUCAAGGAUAACUUGCCGAUA---UAU-A--UUUGCAGAAGGCAUGC-------------------------------------------------------------------------------------------------------------------------------------------AGGGGCUUUUAGC---------------UAU---GUGUAACCGGCAAGU-UG----ACUU-GACUCAGUUUGU---CCCUCU
AASG02007020.1/8399-8148     AGGUC--GUGUAGUGC-AGCCAAGGAUGACUUGCCGGCU---AUA-G--UAGCCCUAGCUAAUAUAUAUAUAUUUGAAGAUCAAAUAGUUAUCUUUCUUUUUCAGUUAUGAAAGCUUUGCACUCUUUGCAAAU-----GAACAUACAUACACAUACUGUAGAUUUACAAGCAUAGACUUCUUGUGCCCUUAGUAUAUAUUUAUCUACGGUUAUUACUC------------AGCUAGUUGAUAGAUCGGCAAGU-CA---UCUCU-GGCUACUCAACU---GCCUCC
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AM444055.2/7771-7675         AAAG----UGGAUUGC-AGCCAAGGAUGACUUGCCGGCA---CUU-G--GCAUUAGGCA-----------------------------------------------------------------------------------------------------------------------------------------------------------CCA---------------UCGAUCAUCUUCCCGGCAAGU-UG---UUCCU-GGCUACAUUCUG---CUCUSU
AARH01007603.1/205939-205816 AUAG----UAGAAUGC-AGCCAAGAAUGAUUUGCCGGCG---CCG-G--CCAGCACUUGUUGCAAAGCAAC--------------------------------------------------------------------------------------------------------------------------------UAAGCAAGGGCUUCAAAU---------------GUUUUUGGCACCCCGGCAAGU-UG---UUCUU-GGCUACAUUUGG---AUAUCU
AARH01007603.1/200394-200284 AGAG----UGGAUUUG-AGCCAAGGAUGACUUGCCGCAG---AUGCA--UGGUCCUUGCUGCU---------------------------------------------------------------------------------------------------------------------------------------------GAUCACAUACCAA---------------GGGGGGUUUUGGGUGGCAAGC--A---UCCUU-GGUUCUCCUUCG---CUCUGU
AARH01007603.1/195565-195448 AGAG---UAGAGAUCG-AGCCAAGAAUGACUUGUCGGCA---GGC-U--AGCAAUUGCUACGU---------------------------------------------------------------------------------------------------------------------------------------------AUAGAGCAAUAUGUAU---------GCUAGAAUGAGUAUUCCGCCAGGU-CG---UUCUU-GGCUCAACUUUG---CUCUUC
AM430160.2/15218-15112       AGGG----UGGAAUCG-AGUCAAGGAUGACUUGCCGAUA---UAU-A--UUUGCAGGACUUGC---------------------------------------------------------------------------------------------------------------------------------------------AUGGGCYUUUAGC---------------UAU---GUGUCACCGGCAAGU-UG----ACUU-GACUCAGUUUGG---CCCUCU
AM430160.2/5320-5211         AGGG----UGGAAUUG-AGUCAAGGAUGACUUGCCGAUA---UAU-A--UUUGCAGAAGGGCA---------------------------------------------------------------------------------------------------------------------------------------------CGCAGGGGCCUUU---------------AGCYAUGUGUUACCGGCAAGU-UG----ACUU-GACUCUGUUUGG---CCCUCU
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AARH01000583.1/30205-30349   AGUC---UUGUUUGAU-AGCCAAGGAUGACUUGCCUGCU---ACU-U--GCAAGAGUUUCUGCAAAGAGAUCAGAACCAAAU-----------------------------------------------------------------------------------------------------------AUGCAUGGAAUUAUAUGUAAUGAAACUC---------------UUGUUUGAUUGCCAGGCAG---UC---UCCUU-GGCUAGCCUGAC--AGGCUCU
AM458937.2/4897-4993         AGGG----UGGAAUAG-AGCCAAGGAUGACUUGCCGGCA---UUU-G--CAGUAAGUCU----------------------------------------------------------------------------------------------------------------------------------------------------------AUAU---------------UAACUGGAACAGCCGGCAUGU-AA---UCC-U-GGCUCUAUUUGG---UCCUCU
AARH01003347.1/61128-61018   AGUG---AUGUUCGGU-AGCCAAGGACGACUUGCCCACA---CUA-U--GAGACAAGUGGUUA---------------------------------------------------------------------------------------------------------------------------------------------GAAUUAGCAACUU---------------CUUAAUUGGUUAUGGG-AAGU-C----UCCUU-GGCUAUGCUGAC--AGACUCU
AASG02003632.1/18444-18329   AGUUU-UUAGUUUGGU-AGCCAAGGAUGACUUGCCCACG---AUC-CAUUACUAAUUAGAGAC---------------------------------------------------------------------------------------------------------------------------------------------UAAGGUUUCAAUU---------------CUUUUUGGACUCUGGGC-AGU-UA---CCCUU-GGUUAUGCAGAC--AAACUCU
AASG02003632.1/10423-10310   AGUG---UUGUUUGGU-AGCCAAGGAUGACUUGCCCGCU---CCA-U--GCAUCGAAGUGGUU---------------------------------------------------------------------------------------------------------------------------------------------UCAAUUUUUUGAGA------------CACUUUUUCUGCUUCGGGCAG---UC---UCCUU-GGCUAUGCUGAC--AGACUCU
AM454465.1/33252-33371       AGAG----UGGAGUGC-AGCCAAGGAUGACUUGCCGGAA---UUC-A--CAUAUAGAGUGGAA---------------------------------------------------------------------------------------------------------------------------------------------UGAGGCAAUAGACCGGC------CUCUUCUCAUGGUGUCCCUGGCAGGU-UG---UCCUU-GGCUACCUUUCG---UUCUCU
AASG02003941.1/7763-7653     AUUC----UGUUUGAU-AGCCAAGGAUGACUUGCCCACU---CCA-C--UACUAAUUAGAGGCUGAU-----------------------------------------------------------------------------------------------------------------------------------------UAAGGCUUUAAUU---------------UUU---UGGAUUUGGGC-AGU-UA---UCUUU-GGUUAUGAGACA---GAUUCU
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AARH01011492.1/38551-38428   AGAG----UGUGAUUC-AGCCAAGGAUGACUUGCCGGCA---GCA-G--GUAAGAGCAAAGCUCCGUUU------------------------------------------------------------------------------------------------------------------------------------UUGGAAGUUCAAGGAUAU-----------CUUAACUUUUCCGGCCGGCAAGC-UG---UCCUU-GGCUACAUUGUA---CUCUCU
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AASG02009044.1/9839-9706     GAAG----UUUGAUGC-AGCCAAGGAUGACUUGCCGACU---GAU-U--UACAACUCCACUUUUUAUUCAUAUAUA----------------------------------------------------------------------------------------------------------------------UAUUUCAACAAAUAAUGAUCAUG---------------AAGAAGAAAAAGUUGGCAGGU-UG---UCCUU-GGCUACAUGUUU---CUUUCU
AARH01005671.1/55685-55803   AAAG----AUUGAUGC-AGCCAAGGAUGACUUGCCGACG---ACU-C--GUUUUUGCUUUCAUCAA------------------------------------------------------------------------------------------------------------------------------------------UAUACGCAUAAUUAA----------GAAGAGAUGAAUCCGUUGGCAGGU-UG---UUCUU-GGCUACAUUUUU---CUUUCU
AARH01009234.1/70403-70253   AGUC---UUGUUUGAU-AGCCAAGGAUGACUUGCCUGCU---ACA-U--ACAAGAGAUCAUUAUGCAUAAAUAGAACGAAAUAUG-----------------------------------------------------------------------------------------------------UACAUGGUAUUAAUUAAUGCAGUGAAAACUC---------------UUGUUUGGUUGCCAGGCAG---UC---UCCUU-GGCUAAGCUGAC--AGGCUCU
AARH01009234.1/70683-70558   AGUC---UUGUUUGGU-AGCCAAGGAUGACUUGCCUGCU---CCCUU--CAAGGAGGUUUCAUGAAAUGC-----------------------------------------------------------------------------------------------------------------------------------AGACAUGAUCUCUCGAAA-----------CCCCUGUUGGGUUUCAGGCGG---UC---UCCUU-GGCUAACUUGAC--AGGCUCU
AM488283.1/32022-31880       AGGUU--AUGUGGUGC-AGCCAAGGAUGACUUGCCGGCA---ACU-C--CCUUUAUUGUACUCAUGCAUGCUCAUA----------------------------------------------------------------------------------------------------------------------CUUAUACUGUUGUGGGCAUCAUUUAA--------GUGGCAAAAAUGGUGGUCGGCGAGU-CA---UUCUU-AGCUACAUUUCU---GCCUCA
AC189369.2/97764-97940       AAAG----UAGUGUGC-AGCCAAGGAUGACUUGCCGAUU---UGA-A--AUAUAUUUUUAAUACUUUACUAAGACAUCUUUUCAGUUUCAAAUUUGUC---------------------------------------------------------------------------UUGGAGAGGCUAGGAAGAAAUUACAAUUUAUUUCGUAGUUUAAA---------------GAAAAAAUAUGAUCGGCAAGU-UU---UCCUU-GGCUACAUGUUU---CUUUGU
AM432580.2/7944-7826         AAAG----UAUGGUGC-AGCCAAGGAUGACUUGCCGACU---CUC----UACUUAGCCAUCUGCCUUUC------------------------------------------------------------------------------------------------------------------------------------UCCAAGGAGGCUUGCA---------------GUACUGAUGAAGCCGGCAAGU-UG---UCUUU-GGCUACAUGCUU---CUUUCU
FN596751.1/559704-559603     AGUG----UGGAAUUG-AGCCAAGGAUGACUUGCCGGCA---GCU-G--CAGCAAGGCA--------------------------------------------------------------------------------------------------------------------------------------------------UUAAGGUUUAAC---------------UGG---CUAUAACUGGCAAGC--A---UCCGA-GGCUCUGUUUCA---CCCUCU
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FN596751.1/717184-717082     AGGG----UGGAUUUG-AGCCAAGGAUGACUUGCCGCCA---UCA-G--CAGCAAGCAUUGAA--------------------------------------------------------------------------------------------------------------------------------------------------GCUUUAAC---------------UGG---GCAUGGACAGCGAGU-UA---UUCUU-GGCUCAUGCGGC---CCCUCU
FN596751.1/755863-755763     AGGG----UGGAAUUG-AGCCAAGGAUGGCUUGCCGUCC---UUU-G--UCACUAUUUG----------------------------------------------------------------------------------------------------------------------------------------------------AGGCAUUAAC---------------UGG---UCACGCACGGAGGGU-UA---UCCUU-GACUCCUUUAGC---UCCUCU
AY551241.1/21-136            AGAA----CGGGAUGC-AGCCAAGGAUGACUUGCCGGCU---CCU-G--GUAUUGGGGGAAUCUCAG-----------------------------------------------------------------------------------------------------------------------------------------CUUUGCUGAAGCG---------------CCUUGGAGUUAGCCGGCAAGUCUG---UCCUU-GGCUACACCUAG---CUCUCU
AY551204.1/35-187            AUCA----UAUUUGGU-AGCCAAGGAUGACUUGCCUGUU---UCU-U--UGAGUAAAAUGGGUUAGUGUCAUGUUUGACAAGUGAC--------------------------------------------------------------------------------------------------UAUAAGUUAUAUCAAGCAAUGACCAUUUUACUC---------------AUCAAAAGACAUCAGGCAG---UC---UCCUU-GGCUAUCCUUAU--AUGUUCU
HM139566.1/394-276           AGGC----CAUGGUGC-AGCCAAGGAUGACUUGCCGAUC---GAU-C--GAUCUAUCUAUGAAGCUAAG-------------------------------------------------------------------------------------------------------------------------------------CUAGCUGGCCAUGGA---------------UCCAUCCAUCAAUUGGCAAGU-UG---UUCUU-GGCUACAUCUUG---GCCCCU
AY551240.1/52-183            AGAA----CGGAAUGC-AGCCAAGGAUGACUUGCCGGUA---CGU-G--UAUGCAUGUUUCAAGGUACUAUAUGUGC---------------------------------------------------------------------------------------------------------------------CCCCAACUGU------UUUAGAUC------------CAUGCUGACAUUUUCCGGCAAGU-UG---UCCUU-GGCUACGUCUUG---UUCUUU
AY551200.1/37-187            AUCA----UAUUUGGU-AGCCAAGGAUGACUUGCCUGAC---UCU-U--UGUGUAAAAUGUUUAGUGUCUUGUUUGAAGUCACUA----------------------------------------------------------------------------------------------------UAAGUUGUAUCAAGCAAUGACCAUUUUG----CU-----------UAUAAAAAAGAUAUCAGGCAG---UC---UCCUU-GGCUAUCCUUAU--AUGUUCU
AY551202.1/37-188            AACA---AUAUUUGGU-AGCCAAGGAUGACUUGCCUGCU---UCU-C--UGAACAAAAUGGUCGAUGUCAUGUUUUGAAGUGACU----------------------------------------------------------------------------------------------------AUAAGUUAUACCAAGAAAUGACCAUUUUGUUU---------------AUAAAUAGACAUCAGGCAG---UC---UCCUU-GGCUAUCCUUAU--AUGUUCU
AY551195.1/39-135            AAAA----UGAGAUUG-AGCCAAGGAUGACUUGCCGAUU---UUC-U--CAACGAAUCUUA-----------------------------------------------------------------------------------------------------------------------------------------------------------C---------------UGAUUAUGGUAUCCGGCAAGU-UG---ACUUU-GGCUCUGUUUCC---UUCCCU
GQ905552.1/156-295           GGAC----UACGGUGC-AGCCAAGGAUGACUUGCCGAUC---UAU-C--GUCGAUCAACGAGCGACGCCUCUGAUGUCU----------------------------------------------------------------------------------------------------------------GAUCUCGACAUCUAUCGUCGUCAGAC---------------CAUCAUCAUCUAUCGGCAAGU-UG---UUCUU-GGCUACACCGUG---GCUCCU
AY551205.1/30-204            AGCGU-CAUGUUUAGU-AGCCAAGGAUGACUUGCCUGAU---CUU-U--UUCGCCUCCACGAUUCAAUUUCAAAUUCAUGCAUUUUGGAUUAUUAU------------------------------------------------------------------------------ACCUUUUAAAGUAUAAUAGGUCAAAUAUCA--UG---------UUGAA-----UCUUGCGGGUUAGGUUUCAGGCAG---UC---UCUUU-GGCUAUCUUGAC--AUGCUUU
AY551203.1/30-206            AGAGU-CAUGUUUAAU-AGCCAAGGAUGACUUGCCUGAU---CUU-U--UUCACCUCCAUGAUUCAAUUUUAAGUUCGUGGAUUUUGGAUUAUUAU------------------------------------------------------------------------------GCGUUUAAAAGGUAUAAUAAUUUGAGAUCA--UG---------UUGAA-----UCUUGCGGGUUAGGUUUCAGGCAG---UC---UCUUU-GGCUAUCUUGACAUGCUUUCU
GQ419117.2/242-360           AGGC----CAUGGUGC-AGCCAAGGAUGACUUGCCGAUC---GAU-C--GAUCUAUCUAUGAAGCUAAG-------------------------------------------------------------------------------------------------------------------------------------CUAGCUGACCAUGGA---------------UCCAUCCAUCAAUUGGCAAGU-UG---UUCUU-GGCUACAUCUUG---GCCCCU
GQ905547.1/295-408           GGAC----UAUGGUGC-AGCCAAGGAUGACUUGCCGAUC---GAU-G--UGACGCCUCUUGAUCUC------------------------------------------------------------------------------------------------------------------------------------------GUCGUCGUCAGAU---------------CGUCGCCGAUCAUCGGCAAGU-UG---UUCUU-GGCUACACCGUG---GCUCCU
FM956490.1/302-402           AGAG----UAGAUUAC-AGCCAAGGAUGACUUGCCGGCG---UUU-A--UUCUUGCCAAUCCA-------------------------------------------------------------------------------------------------------------------------------------------------------CAU---------------UGUCAAAUUAGAUCGGCAAGU-UG---UCUUU-GGCUAUAGUUUG---UUCUUC
GQ468861.1/14-144            AGGC---GUGUUUAGU-AGCCAAGGAUGACUUGCCUACC---AAG-G--GUCUCAUUUUAAGGCAUUAUCUUCCUU-----------------------------------------------------------------------------------------------------------------------GGAUAAUGC-------------GUCUG----GAAUCCUCGACUGGUUAAUAGGCAG---UC---UCCUU-GGCCAACUUGAC--UGCCUCC
AY551201.1/49-220            AGUC---AUGUUUAGU-AGCCAAGGAUGACUUGCCUGAU---CUU-U--UUCACCUCCAUGAUUCAAUUUGUAAUUCAUGGGUUUUGGAUUAUUA--------------------------------------------------------------------------------UACAUUCAAAAGUAUAAUAAUUUGAAAUC-------------AUGUUG--AAUCUUGCGGGUUAGGUUUCAGGCAG---UC---UCCUU-GGCUAUCUUGAC--AUGCUUU
AY551246.1/52-182            AGCUC--GCAUCUGGU-AGCCAAGGAUGACUUGCCUGUG---UCU-C--UGCUCAUGUGCAGUAGAAGAAGAUG--------------------------------------------------------------------------------------------------------------------------CAUUUCUAGCUGCUUUCUGCA---------------UAUGUGAUCUCACAGGCAG---UC---UCCUU-GGCUAGCCUGAG--CGGCUCU
GQ905553.1/122-240           AGAA----CGGGAUGC-AGCCAAGGAUGACUUGCCGGCU---CCU-G--GAACCUGGAGGCGUCUCAGC-------------------------------------------------------------------------------------------------------------------------------------UU----GCUGUG---CUG---------UGGCUUAGAACUUAGUCGGCAAGUCUG---UCCUU-GGCUACACCUAG---UUCUCU
HM139585.1/245-135           UAUC----UCUGAU---AGCCAAGGAUGACUUGCCUGUG---UCC-U--CCCUGAAGGAUUAGCAA------------------------------------------------------------------------------------------------------------------------------------------UUUAAUGAUCCUU---------------UAAGCUGGUUCAUGGGCAG---UC---UCCUU-GGCUAGCCUGAG--UGGUUCU
AY551243.1/20-180            AGUC---UGUCUAGAU-AGCCAAGGAUGACUUGCCUGUG---GCC-U--CUUGGAGAGAGAGGUGUAGCUUAAUUAGCAGCAUGGUUUGA-------------------------------------------------------------------------------------------GCAUUGCUUGAUCGGUUGAUCGCUUCGCUUGCUCUG---------------CAUGAGAUCUUACAGGCAG---UC---UCCUU-GGCUAGUCUGGG--CGGCUCU
#=GC SS_cons                 :<<<....--------.<<<<<-<<<<<<<<<<<<<<__...___._..___________________________......................................................................................................................_______________________...............____________>>>>>>>>>.>>...>>>->.>>>>--------...>>>:::
#=GC RF                      AGag....UGuaaUGc.AGCCAAGGAuGACUUGCCgGca...uuu.u..uaauuauauauaauuauaauuuaauUu......................................................................................................................uuuauuuauauaugaauuuuaau...............uuaauuaguuuuCcGGCAAGU.Ua...UCCUU.GGCUAcaUuuag...cuCUCU
//
# STOCKHOLM 1.0

#=GF AC   RF00646
#=GF ID   mir-204
#=GF DE   microRNA mir-204
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   68.80
#=GF NC   56.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.98 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000042;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [2]
#=GF RM   17306260
#=GF RT   Identification and characterization of microRNAs from the bovine adipose
#=GF RT   tissue and mammary gland.
#=GF RA   Gu Z, Eleswarapu S, Jiang H
#=GF RL   FEBS Lett. 2007;581:981-988.
#=GF RN   [3]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF WK   MicroRNA
#=GF SQ   32


AAVX01052255.1/1202-1305     ACCAUCCAUGUGAGUGGCCCA-UGGGCUUCCCUUUGUCAUCCUAUGCCUGAAAUUAUAUGAAGG-GGGCUGGGAAGGCAAAGGGAUGUUCAAGUGUCAUCAGUGGC
AC126558.4/136520-136623     AGUCCUUCUUCAUGUGACUCG-UGGACUUCCCUUUGUCAUCCUAUGCCUGAGAAUAUAUGAAGG-AGGCUGGGAAGGCAAAGGGACGUUCAAUUGUCAUCACUGGC
CR450827.5/52029-51927       UAGUGACCAGUUUGUGACCUCCUGGGUUUCCCUUUGUCAUCCUAUGCCUGCA--GUUCCUGAUG-AGGCUGGGACAGCAAAGGGAGGUUCAGAUGUCGACCUGUAC
BAAE01064700.1/3191-3291     GGAGAUCCCUUCUGUGACCUG-UGGGCUUCCCUUUGUCAUCCUAUGCCUGGA---GCUUGGAUA-AGGCAGGGACAGCAAAGGGAUGCUCAGCUGUCACCACUGAC
AAVX01164390.1/969-1070      UGUCCACAACUGUGUGACCUG-UGGGUUUCCCUUUGUCAUCCUAUGCCUGGG--AGUAUCAGUG-AGGCAGGGGGGACAAAGGGGUGCUCAGCUGUCAACUCCAAC
AAFR03022736.1/24229-24330   UUCAACUGACUAUGUGACCUG-UGGGCUUCCCUUUGUCAUCCUAUGCCUGGA--AAUCAGAGUG-GGGCAGGGACAGCAAAGGGAUGCUCAGCUGUCGUCUUCUAC
AANH01011880.1/65628-65527   GGUUACCAAUCAUGUGACCCG-UGGGUUUCCCUUUGUCAUCCUUUGCCUGGA--GGUGUCUGUA-AGGCAGCGGCAGCAAAGGGAGGCUCAGCCAUCACUCACUUC
AC009562.9/144771-144872     UUCACCUGGCCAUGUGACUUG-UGGGCUUCCCUUUGUCAUCCUUCGCCUAGG--GCUCUGAGCA-GGGCAGGGACAGCAAAGGGGUGCUCAGUUGUCACUUCCCAC
CAAE01014652.1/7156-7055     AUCGUCCAGUCAUGUGACCUA-UGGACUUCCCUUUGUUAUCCUAUGCCUGGA--CUCAAAAAAG-GGGCUGGGAGGGCAAAGGGUUGCCCAGUUGUCAUACAGUCA
AAPN01089717.1/13112-13213   GCCGGUGAUCCUUGUGACUGC-UGAGCUUCCCUUUGUCAUCCUAUGCCUGGA--AGUCAAAAUG-GGGCAGGGACAGCAAAGGGAUGAUCAACCGUCACCUCCAAC
AAFC03027753.1/101899-102000 CUCCCCUGGCUGUGUGACCUG-UGGGCUUCCCUUUGUCAUCCUUUGCCCAGG--GUUCUGAGUG-GGGCAGGGACAGCAAAGGGGUGCUCAGUCGUCACCUCCCAC
AANH01001574.1/139065-138965 GUCGUCCUCCUCUGGGACCUA-UGGGCUUCCCUUUGUCAUCCUAUGCCUGGA---GCUCGGAUA-AGGCAGGGACAGCAAAGGGAUGCUCAACUGUCACCACCGAC
BX323080.10/77917-77816      CCUCCCUUGUCAUGUGACCUG-UGGACUUCCCUUUGUCAUCCUAUGCCUGGA--GUAAUAGAGG-GGGCUGGGAAGUCAAAGGGACGCUCAGGCGUCAUCAUUCGC
CAAE01014555.1/947630-947730 GACAGAGAACUCUGUGACCUG-UGGGCUUCCCUUUGUCAUCCUAUGCCUGGA---GCUCGGAUA-AGGCAGGGACAGCAAAGGGAUGCUCAGCCGUCACCACUGAC
AAYZ01172228.1/6125-6024     UUCACCUGGCUGUGUGACGUG-UGGGCUUCCCUUUGUCAUCCUUUGCCUAGG--GUUCUGAGCA-GGGCAGGGACAGCAAAGGGGGGCUCAGUCGUUACCCUCUGC
AAPN01357234.1/26856-26959   UAUCUCUCUCCAUGUGACCCG-UGGGCUUCCCUUUGUCAUCCUAUGCCUGAGAAUAUAUGAAGG-GGGCUGGGAAGGCAAAGGGACGUUCAACUGUCAUCACCAGC
BAAF04027114.1/6784-6888     UCCUCACCUUACUAUGACAUG-UGGACUUCCCUUUGUCAUCCUAUGCCUGGAAUCAAAUAAAAGGGGGCUGGGAAGGCAAAGGGAUGCUCAGCUGUCAUACAAGCA
AANH01001880.1/194334-194437 AUCAUCCGGUCAUGUGACUUA-UGGCCUUCCCUUUGUCAUCCUAUGCCUGGACUCAUACAAAAG-GGGCUGGGAAGGCAAAGGGACGCCCAGUCGUCAUACUAGCA
AANN01198559.1/1392-1493     CUCAGUUGGUACUGUGACUUG-UGGGCUUCCCUUUGUCAUCCUUUGCCUAGG--GUUAUGAGUA-GGGCAGGGACAGCAAAGGGGUGCCCACACAUCACUGUCACA
AAQQ01222771.1/904-1005      UUCACUUGAUCAUGUGACUUG-UGGGCUUCCCUUUGUCAUCCUUUGCCUAGG--GCUUUGAGUG-GGGCAGGGACAGCAAAGGGGUGCUCAGUCGUCACCUCCCAC
AAGV020630976.1/4916-5016    CCCAGCUGGCCAUGGGACCUG-UGGGCUUCCCUUUGUCAUCCUUUGCCUAGG---AUCCGAGUG-GGGCAGGGACAACAAAGGGGUGCUCAGGCGUCACCUCCACA
AAKN02016253.1/66521-66421   UUCACCCAGCCACGUGACUUG-UGGGCUUCCCUUUGUCAUCCUUUGCCUAGG---GCUCUGAUA-GGGCAGGGACUGCAAAGGGGUACUCAGUUGUCACCGUCUGC
AABR05009647.1/32943-33044   UCAGCUUGGACCUGUGACCUC-UGGGCUUCCCUUUGUCAUCCUUUGCCUAGG--CCUCUGAGUG-GGGCAAGGACAGCAAAGGGGGGCUCAGUGGUCACCUCUACU
AADN03005974.1/43587-43486   CUACUGAGACUGUGUGACCUG-UGGGCUUCCCUUUGUCAUCCUAUGCCUGGA--GAUCACAGUG-AGGCAGGGACAGCAAAGGGAUGCUCAGCUGUCGUCUCUUCC
AAWZ02027695.1/30269-30168   CUGCCUGGAUCACAUGACCUG-UGGGCUUCCCUUUGUCAUCCUAUGCCUGGA--GAUCGCAGAG-AGGCAGGGACAGCAAAGGGGUGCUCAGCUGUUGUCUCUAAC
AAGW02050442.1/67198-67299   UUCACCUGGCCAUGUGACUGG-UGGGCUUCCCUUUGUCAUCCUUUGCCUAGG--GUUCUGAGCA-GGGCAGGGACAGCAAAGGGGUGCUCAGUCGUCACCCUGCAC
AAQR03168651.1/25332-25231   UUCACCUGGCCAUGUGACGUG-UGGGCUUCCCUUUGUCAUCCUUUGCCUCGG--GCUCUGAGCA-GGGCAGGGACAGCAAAGGGGUGCUCAGUCGUCACCUCCACA
AAEX03002224.1/126026-126127 UUCAUCUGGCCAUGUGACUUG-UGGGCUUCCCUUUGUCAUCCUUUGCCUAGG--GUUCUGAGAG-GGGCAGGGACAGCAAAGGGGUGCUCAGUUGUCACCUCUCAC
AY866201.1/464-567           AGUCUUUCUUCAUGUGACUCG-UGGACUUCCCUUUGUCAUCCUAUGCCUGAGAAUAUAUGAAGG-AGGCUGGGAAGGCAAAGGGACGUUCAAUUGUCAUCACUGGC
AY866210.1/448-549           UUCACCCAGCCAUGUGACUUG-UGGACUUCCCUUUGUCAUCCUUCGCCUAGG--GCUCUGAGCA-GGGCAGGGACAGCAAAGGGGUGCUCAGUUGUCACUUCCCAC
AY866211.1/449-550           CUUCACUGGCCAUGUGACUUG-UGGGCUUCCCUUUGUCAUCCUUCGCCUAGG--GCUCUGAGCA-GGGCAGGGACAGCAAAGGGGUGCUCAGUUGUCACUUCCCAC
AY866209.1/453-554           CUUCACUGGCCAUGUGACUUG-UGGGCUUCCCUUUGUCAUCCUUUGCCUAGG--GCUCUGAGCA-GGGCAGGGACAGCAAAGGGGUGCUCAGUUGUCACUUCCCAC
#=GC SS_cons                 :::::::::::::<<<<<---.<<<<<-<<<<<<<<<--<<<<<-<<<<___..__________.>>>>>>>>>-->>>>>>>>>->>>>>--->>>>>:::::::
#=GC RF                      uucaucuaaucaUguGACuUg.UGggCUuCCCUUUGuCAUCCuuUGCCugGa..gaUaugAaug.gGGCagGGAcagCAAAGGGauGcuCAguuGUCaccucuuac
//
# STOCKHOLM 1.0

#=GF AC   RF00647
#=GF ID   MIR164
#=GF DE   microRNA MIR164
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   60.10
#=GF NC   59.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.65 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000045;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12101121
#=GF RT   MicroRNAs in plants.
#=GF RA   Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP
#=GF RL   Genes Dev. 2002;16:1616-1626.
#=GF RN   [2]
#=GF RM   12202040
#=GF RT   Prediction of plant microRNA targets.
#=GF RA   Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP
#=GF RL   Cell. 2002;110:513-520.
#=GF RN   [3]
#=GF RM   19939267
#=GF RT   High throughput approaches reveal splicing of primary microRNA transcripts
#=GF RT   and tissue specific expression of mature microRNAs in Vitis vinifera.
#=GF RA   Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del
#=GF RA   Fabbro C, Valle G, Policriti A, Morgante M, Pesole G, Pe ME, Horner DS
#=GF RL   BMC Genomics. 2009;10:558.
#=GF WK   MicroRNA
#=GF SQ   39


AACV01011958.1/3675-3793     AGGUUCUUGUUGGAGAAGCAGGGUACGUGCAA----------AAUGCACACCG--------------------------------------------------------------------------------GUUGGUCGAGCUAAUU-----------------------------------------------------AACAAGCUCUGA-----------------------------------CGACCAUGGUGAUCGA--------AUGCACGUGCUCCCCUUCUCCACCAUGGCCUU
AAAA02008438.1/26671-26540   UUGUGCAGGGUGGAGAAGCAGGGCACGUGAGC---------GGCCAUCCAGUGUAG-------------------------------------------------------------------------CUUCGCUGCGCGUCCAUGGC-----------------------------------------------------GGCGAACGCGCGUGA-----------------------------UCUGGAGUUUGGAUG--GU-------CGUUCAUGUGUCCGUCUUCUCCACCGAGCACUG
AY551227.1/10-103            CAAACCGUGCUGGAGAAGCAGGGCACGUGCUC----------GACGGC-------------------------------------------------------------------------------------GGGGCUGGCU--------------------------------------------------------------GGCCG-------------------------------------------GCCGGCUU--GC---------AGCAUGUGCGCUCCUUCUCCAGCAUGGCUUC
AARH01006944.1/110052-110208 GUGAGCAAGAUGGAGAAGCAGGGCACGUGCAU---------UACUAACUCAUGCACA-----------------------------------------------------------------------CAGAGUGAGAGAGACAUUUCUUGCUGGAGUUAUGACUCUU----------------ACCUACUAUAGAUUGUGUUGGCUUCA-------------------------------------------GCGAGUUA--GU-------UCUUCAUGUGCCUGUCUUCCCCAUCAUGAUCAC
AC002535.3/27880-27783       AUCUCCAUGUUGGAGAAGCAGGGCACGUGCAA----------ACCAA--------------------------------------------------------------------------------------CAAACACGAAAUCC----------------------------------------------------------GUCUC-------------------------------------------AUUUGCUU--AU--------UUGCACGUACUUAACUUCUCCAACAUGAGCUC
AC152057.11/32164-32084      UGAACCACGUUGGAGAAGCAGGGCACAUGCUU---------GAUUUUA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCAAAGUUCU--------GAGCAUGUGCUCUUGCUCUCCAUCAUGGAUUU
AACV01011837.1/11132-11244   CCGUGCACGGUGGAGAAGCAGGGCACGUGCAU---------UACCAUCCACUCGCCUGCCGGC-----------------------------------------------------------CGCCGGCCGCCAUUGCCA-------------------------------------------------------------------------------------------------------------------UGGAUG--GU-------UCUUCAUGUGCCCGUCUUCUCCACCGAGCACCA
AASG02020922.1/1372-1495     GUGAGCAAGAUGGAGAAGCAGGGCACGUGCAU---------UACUAACUCAUG--------------------------------------------------------------------------------CAUAAUUGAACAUACA-----------------------------------------------------UACAUACGCAUUUU------------------------------UCUUGCUGGAGGUUA--GU-------UCUUCAUGUGCCCGUCUUCCCCAUCAUGACCAC
AASG02000423.1/48609-48498   UAGUUCCUGCUGGAGAAGCAGGGCACGUGCAA----------ACCCCA-------------------------------------------------------------------------------------ACACUCCUUGGUUUCU-----------------------------------------------------UGAAUGCC-------------------------------------------AAUGGAAA--CUAUACUCUUUUGCACGUGCUCCCCUUCUCCAACAUGGUCUC
AM462494.2/40477-40359       AGCUCCUUGUUGGAGAAGCAGGGCACGUGCAG---------AUUUGCCUCACU--------------------------------------------------------------------------------UUUCCCCCUUUUUUCU-----------------------------------------------------UCUUUACUCCCA----------------------------------CCACCGCCCACAG--GC--------UUGCACGUGCUCCCCUUCUCCAACAUGGGUUC
AP004343.2/27453-27312       AGGACCGCGUUGGAGAAGCAGGGCACGUGCAU---------GCAUAUGUUCAUCAUCAUCUUCUUC-----------------------------------------------------CUCCUCCUCUAGCUCCAGCCUUGUGUGGGUU---------------------------------------------------GGAAGUUUA-------------------------------------------GAUAGAACUCGC-------ACUGCACGUGGUCUCCUUCUCCAUCCCGGUCUU
AC144541.12/12784-12878      UAGGUCUUGUUGGAGAAGCAGGGCACGUGCAAC-------CGUAGAUCUCUCU--------------------------------------------------------------------------------CAAACUU-------------------------------------------------------------------------------------------------------------------CAAUCUCAUU--------UUGCACGUGCUCCACUUUUCCAACUUGAUCUU
AY551190.1/11-112            UAACACUUGAUGGAGAAGCAGGGCACGUGCGA---------ACACAAAUGAA---------------------------------------------------------------------------------AUCGAUCGGUACUUGU-----------------------------------------------------UGA--------------------------------------------------UCAUAU--UU--------UCGCACGUGUUCUACUACUCCAACACGUGUCU
AL162351.1/12200-12368       AUGAGCAAGAUGGAGAAGCAGGGCACGUGCAU---------UACUAGCUCAUAUAUACACU---------------------------------------------------------------CUCACCACAAAUGCGUGUAUAUAUGCGGAAUUUUGUGAUAUAGAUG------------UGUGUGUGUGUUGAGUGUGAUGAUAUGG-------------------------------------------AUGAGUUA--GU-------UCUUCAUGUGCCCAUCUUCACCAUCAUGACCAC
AC150384.17/72119-72271      UUGAACAAGAUGGAGAAGCAGGGCACGUGCAA---------UACUAACUCAU---------------------------------------------------------------------------------GAACAUACACACAUGA-----------------------------------------------------UGGAAGUGAAUACAAAGAGAAUCUACAUUCUCUUAUGUUUCAUUUUUUUAAUUGAGUUA--GU-------UCUUCAUGUGCCCCUCUUCCCCAUCAUGACAAU
AARH01003031.1/58319-58482   GUGAGCAAGAUGGAGAAGCAGGGCACGUGCAC---------UACUAACUCAUG--------------------------------------------------------------------------------CACACAGAGAGGGAGACGCAUUUCUUGCUGGAGUUACGAGUUACGACUCUUACCUACUAUUGAUUUUGUUAGCUCCA-------------------------------------------GUGAGUUA--GU-------UAUUCAUGUGCCUGUCUUCCUCAUCAUGAUCAC
AASG02000861.1/36470-36555   CAGCUCUUGCUGGAGAAGCAGGGCACGUGCAA---------UUCCUUUCUUU---------------------------------------------------------------------------------CCCUCUC-------------------------------------------------------------------------------------------------------------------CGAAU--------------UGCACGUGCUCCACUUCUCCAACAUGGGUUU
AM449363.2/29982-30065       AAGCUCUUGAUGGAGAAGCAGGGCACGUGCAG----------UUCACAAAUUC--------------------------------------------------------------------------------UAAUCUG---------------------------------------------------------------------------------------------------------------------------CU--------CUGCACGUGCUCCCCUUCUCCAACAUGGGUUC
DQ090016.1/221-315           AGCUCCUUGUUGGAGAAGCAGGGCACGUGCAAUGU--UCUUGGCUCUCAAAUG--------------------------------------------------------------------------------CCAG----------------------------------------------------------------------------------------------------------------------UGAACC--CU--------UUGCACGUGCUCCCCUUCUCCAACAUGGGUUC
AM459087.2/8298-8457         UUGAGCAAGAUGGAGAAGCAGGGCACGUGCAU---------UACUAGCUCAU---------------------------------------------------------------------------------GCACCACAAACCAAUAAUCUUUUGCUCGAGUUAGACUC----------UUGCUUGCUGCUUUGAUUUUUUUUGUUAGCAC------------------------------------CAGCGAGAGUUG--GU-------UCUUCAUGUGCCCCUCUUCCCCAUCAUGACCAC
AC189579.2/50985-50886       UUACACUUGCUGGAGAAGCAGGGCACGUGCGA----------ACAAAUGAGAU--------------------------------------------------------------------------------CGAUCGGUAU--------------------------------------------------------------AUGUU-------------------------------------------GAUCAUAU--UU--------UCGCACGUGUUCUACUACUCCAACACGUGUGC
AC189657.2/5377-5278         UAUCACUUGCUGGAGAAGCAGGGCACGUGCGA----------ACAAAUGAGUU--------------------------------------------------------------------------------UGAGCAGUAC--------------------------------------------------------------AUUUU-------------------------------------------GAUCAAAU--AU--------UCGCACGUGUUCUACUACUCCAACACGUGUAU
FN596746.1/1162989-1163104   AAGCUCUUGAUGGAGAAGCAGGGCACGUGCAGUUCACAAAUUCUAAUCUGCUC--------------------------------------------------------------------------------UGCACGUGCAGUUCAC-----------------------------------------------------AAAUUCU----------------------------------------------AAUCUG--CU--------CUGCACGUGCUCCCCUUCUCCAACAUGGGUUC
HM139157.1/284-143           AGGACCGCGUUGGAGAAGCAGGGCACGUGCAU---------GCAUAUGUUCAUCAUCAUC------------------------------------------------------------------UUCUUCC--------------UCCUCCUCUAGCUCCAG------------------------CCUUGUGUGGGUUGGAAGUUUA-------------------------------------------GAUAGAACUCG-C------ACUGCACGUGGUCUCCUUCUCCAUCCCGGUCUU
HM139219.1/328-446           AGGUUCUUGUUGGAGAAGCAGGGUACGUGCAA---------AAUG-CACACCG--------------------------------------------------------------------------------GUUGGUCGAGCUAAUUAACAA-------------------------------------------GCUCUGACGACCA-------------------------------------------UGGUGAUC--GA--------AUGCACGUGCUCCCCUUCUCCACCAUGGCCUU
HM139324.1/344-475           UUGUGCAGGGUGGAGAAGCAGGGCACGUGAGC---------GGCCAUCCAGUGUAGCUUC------------------------------------------------------------------GCUGCGC--------------GUCCAUGGCGGCG--------------------------------AACGCGCGUGAUCU----GG---------------------------------------AGUUUGGAUG--GU-------CGUUCAUGUGUCCGUCUUCUCCACCGAGCACUG
FM163695.1/40-208            AUGAGCAAGAUGGAGAAGCAGGGCACGUGCAU---------UACUAGCUCAUAUAUACACUCUCACCA-------------------------------------------------CAAAUGCGUGUAUAUA--------------UGCGGAAUUUUGUGAUAUAGAU-------------GUGUGUGUGUGUUGAGUGUGAUG-----AUA-------------------------------------UGGAUGAGUUA--GU-------UCUUCAUGUGCCCAUCUUCACCAUCAUGACCAC
FM162585.1/105-191           UAGCCCUUGCUGGAGAAGCAGGGCACGUGCAA----------AGAAGGUCUUC--------------------------------------------------------------------------------AUUGA----------------------------------------------------------------------------------------------------------------------UAUAU--AU--------UUGCAUGUGCUCCUCUUCUCCAACAUGUGUUC
GQ905524.1/122-318           AGGACCACGCUGGAGAAGCAGGGCACGUGCAU---------GCACAUACGCCAUUCUCGAUCUCUCCUCUCCACCACUACUGCAUCUAGCUAUCUCCAUGGAUGGAUGUACGUAGCUCGGACUGGAUCGAUCG--------------GAGAAGCAAUAA----------------------------------GCUAGCGAGCUC-----AUG-------------------------------------CAUGCUGGCUG-UG--------CACGCACGUGGUCUCCUUCUCCAUCACGGUUCU
EU548721.1/245-342           AUCUCCAUGUUGGAGAAGCAGGGCACGUGCAA----------ACCAA--------------------------------------------------------------------------------------CAAACACGAAAUCC----------------------------------------------------------GUCUC-------------------------------------------AUUUGCUU--AU--------UUGCACGUACUCAACUUCUCCAACAUGAGCUC
HM139321.1/344-475           UUGUGCAGGGUGGAGAAGCAGGGCACGUGAGC---------GGCCAUCCAAUGUAGCUUC-----------------------------------------------------------------GCUGCGCG--------------UCCAUGGCGGCG---------------------------------AACGCGCGUGAUCU----GG---------------------------------------AGUUUGGAUG--GU-------CGUUCAUGUGUCCGUCUUCUCCACCGAGCACUG
GQ418713.2/344-475           UUGUGCAGGGUGGAGAAGCAGGGCACGUGAGU---------GGCCAUCCAGUGUAGCUUC------------------------------------------------------------------GCUGCGC--------------GUCCAUGGCGGCG--------------------------------AACGCGCGUGAUCU----GG---------------------------------------AGUUUGGAUG--GU-------CGUUCAUGUGUCCGUCUUCUCCACCGAGCACUG
FM163720.1/40-208            AUGAGCAAGAUGGAGAAGCAGGGCACGUGCAU---------UACUAGCUCAUAUAUACACUCUCACCA-------------------------------------------------CAAAUGCGUGUAUAUA--------------UGCGGAAUUUUGUGAUAUAGAU-------------GUGUGUGUGCGUUGAGUGUGAUG-----AUA-------------------------------------UGGAUGAGUUA--GU-------UCUUCAUGUGCCCAUCUUCACCAUCAUGACCAC
HM627261.1/237-151           CGGUUCUUGCUGGAGAAGCAGGGCACGUGCAA---------AAUCCUAA--------------------------------------------------------------------------------------UGAAG-----------------------------------------------------------------------------------------------------------------UAUUUACA--CU--------UUGCACGCGCUUUUCUUCUCCAACACGGGCUC
HM139198.1/328-446           AGGUUCUUGUUGGAAAAGCAGGGUACGUGCAA---------AAUG-CACACCG--------------------------------------------------------------------------------GUUGGUCGAGCUAAUUAACAA-------------------------------------------GCUCUGACGACCA-------------------------------------------UGGUGAUC--GA--------AUGCACGUGCUCCCCUUCUCCACCAUGGCCUU
AY728403.1/144-291           --------GAUGGAGAAGCAGGGCACGUGCAC---------UACUAACUCAUGCACACAGAGAGGGAGACGCAUUUCU------------------------------UGCUGGAGUUACGAGUUACGACUCU--------------UACCUACUAUU------------------------------------GAUUUUGUUAGCUCCA-------------------------------------------GUGAGUUA--GU-------UAUUCAUGUGCCUGUCUUCCUCAUC--------
FM163702.1/40-207            AUGAGCAAGAUGGAG-AGCAGGGCACGUGCAU---------UACUAGCUCAUAUAUACACUCUCACCA-------------------------------------------------CAAAUGCGUGUAUAUA--------------UGCGGAAUUUUGUGAUAUAGAU-------------GUGUGUGUGCGUUGAGUGUGAUG-----AUA-------------------------------------UGGAUGAGUUA--GU-------UCUUCAUGUGCCCAUCUUCACCAUCAUGACCAC
HM139187.1/284-143           AGGACCGCGUUGGAGAAGCAGGGCACGUGCAU---------GCAUAUGUUCAUCAUCUUC------------------------------------------------------------------UUCUUCC--------------UCCUCCUCUAGCUCCAG------------------------CCUUGUGUGGGUUGGAAGUUUA-------------------------------------------GAUAGAACUCG-C------ACUGCACGUGGUCUCCUUCUCCAUCCCGGUCUU
FM162587.1/172-265           UGGUGCAAGAUGGAGAAGCAGGGCACGUGCAU---------UACUGUCUCACA--------------------------------------------------------------------------------GCAGUGCCU-----------------------------------------------------------------------------------------------------------------UGAUUA--GU-------UCUUCAUGUGCCCCUCUUUUCCAUCAUGACCCU
#=GC SS_cons                 ::::<<--<-<<<<<<<<--<<<<<<<<<<<_.........____________................................................................................__________....___..................................................._________...........................................________..__.......__>>>>>>>>>>>-->>>>>>>>->-->>::::
#=GC RF                      auGacCauGaUGGaGAAGCAGgGCACgUGcau.........uacuAucucaUa................................................................................uaaacuagaa....uac...................................................guagauuua...........................................guuaGuUa..GU.......uaugCAcGUGCcCuuCUUCuCCAuCAUGgucuu
//
# STOCKHOLM 1.0

#=GF AC   RF00648
#=GF ID   MIR396
#=GF DE   microRNA MIR396
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   80.50
#=GF NC   79.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.01 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000047;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15200956
#=GF RT   Computational identification of plant microRNAs and their targets,
#=GF RT   including a stress-induced miRNA.
#=GF RA   Jones-Rhoades MW, Bartel DP
#=GF RL   Mol Cell. 2004;14:787-799.
#=GF RN   [2]
#=GF RM   16040653
#=GF RT   Expression of Arabidopsis MIRNA genes.
#=GF RA   Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC
#=GF RL   Plant Physiol. 2005;138:2145-2154.
#=GF RN   [3]
#=GF RM   15805478
#=GF RT   Cloning and characterization of microRNAs from rice.
#=GF RA   Sunkar R, Girke T, Jain PK, Zhu JK
#=GF RL   Plant Cell. 2005;17:1397-1411.
#=GF WK   Mir-396_microRNA_precursor_family
#=GF SQ   26


AASG02007435.1/277-442       CUUUGUAUUCUUCCACAGCUUUCUUGAACUGCAUCUAUUACA---------------------------------------------------GAACUGGUAGUAGUGCU------------------------------------------------------------UUUGCUUCCUUGCAAUUGCUUGCAUGCCACUGUACGGCU---------GGCUCCUUUUUUUUUUCUUCUUUUGUUUUG--------UUUUUGCGGUUCAAUAAAGCUGUGGGAAGAUACGAACA
AACV01005603.1/31253-31099   CUUUGUGAUCUUCCACAGCUUUCUUGAACUGCACGCAUGAUGAAUAAUCCCUU-----------------------------UGGUUAAUUGUGAUCUGGUCUCUGAGAG------------------------------------------------------------AUCGUAGUUAGACUCGAUCGGU------------------------------------------UGCAUUGGCAUCAG--------AGAGAGCAGUUCAAUAAAGCUGUGGGAAAUUGCAGAGA
AK066292.1/62-239            GGCCAUGCUCUCCACAGGCUUUCUUGAACUGUGAACUCGUGU---------------------------------------------------GUGCAUGCUCCUCAUAUAUUGUUCUAGAUCCCAUGCAUGAUGCAUAUCGAUCGAUCUGAUCUGAAUUAGGUCAUCGAUGCGCAUCUGGAUCC---------------------------------------------------------CCAUCU--------UGUUGAUAGUUCAAGAAAGUCCUUGGAAAACAUGGUGC
AASG02001279.1/18109-18241   UGUCAUGCUUUUCCACAGCUUUCUUGAACUUCUUCUUCUUCUUCUUCU--------------------------------------UCUUCUUAGAUUUCUUUCUCAUUG------------------------------------------------------------CCUAUAUCUUUCUUG---------------------------------------------------------AUGUGGC------ACAGAAUAAGUUCAAGAAAGCUGUGGGAGAACAUGGCAA
AB025611.1/629-764           GGUCAUACUUUUCCACAGCUUUCUUGAACUUUCUUUUUCAUU---------------------------------------------------UCCAUUGUUUUUUUCUUAAACAAAAGU----------------------------------------AAGAAGAAAAAAAACUUUAAGAU-----------------------------------------------------------UAAGCA--------UUUUGGAAGCUCAAGAAAGCUGUGGGAAAACAUGACAA
AAAA02018332.1/10514-10398   CUUUGUGGUCUUCCACAGCUUUCUUGAACUGCAUCUUUGAGA--------------------------------------------------GAGAUUAGCAUCCC----------------------------------------------------------------UAUGUGUGGAUUUUGC-------------------------------------------------------UUGCACG--------AGUGUGCAGUUCAAUAAAGCUGUGGGAAAUUACAGAGA
AM481354.2/2056-2230         UUGCAUGCUUUUCCACGGCUUUCUUGAACUUGGAACUUAGGU---------------------------------------------------GUGCUUCUCUCUCUUCU------------------------------------------------------------UCUUCUUCUUCUCCUUUCUCUCUACAUCCAUACGUAUGUUUCUCUUCAGAGAAUACUCUUAAUAUGAAAUUAAAUCUU--------AGUACGAAGUUCAAGAAAGCCGUGGGAAAAUAUGAAAU
AARH01007577.1/181152-181286 CUUUGUAUUCUUCCACAGCUUUCUUGAACUGCACCUAUUAGAUUAA------------------------------------------UGUUGAUGUUGUUGUGCGAUAU------------------------------------------------------------GCCAUGACCAUAUGACAUU-------------------------------------------------GUAUUCAUUU--------UUGCUGCGGUUCAAUAAAGCUGUGGGAAGAUACAAACA
AARH01007577.1/188194-188047 GGUCAUGCUUUUCCACAGCUUUCUUGAACUUCUUUGCCUUGCUUAAUCUG----------------------------------UGUAUAUAUAGAUCACUACAUGUACAGCUCCU-----------------------------------------------AUAUAUAUAAAUAUAUGUAUGU---------------------------------------------------------AUAGCG--------CCAUGGAAGCUCAAGAAAGCUGUGGGAGAACAUGGCAA
AC153121.15/48150-48253      GGUCAUGCUUUUCCACAGCUUUCUUGAACUUCUUU----------------------------------------------------------CGUAUCUUAAAUC-----------------------------------------------------------------UGUUUUCAAGAU-----------------------------------------------------------UAAAAG--------UCCUAGAAGCUCAAGAAAGCUGUGGGAGAAUAUGGCAA
AC153121.15/56895-56790      CUUUGUAUUCUUCCACAGCUUUCUUGAACUGCAUCCAAAUUG---------------------------------------------------AGUUCCUUUGCAU---------------------------------------------------------------------UGCCAUG------------------------------------------------------------GCCAUU--------GUUUUGCGGUUCAAUAAAGCUGUGGGAAGAUACAGAUA
AARH01002977.1/26105-26230   CUUGGUAUUCUUCCACAGCUUUCUUGAACUGCACCUAUUUGA---------------------------------------------------AUAUUGUUGUUGAUGUU------------------------------------------------------------GCCGUGCAUGUACAU---------------------------------------------------------AUGACAUUGUAUUUUUGUUGCGGUUCAAUAAAGCUGUGGGAAGAUACAAACA
AARH01002977.1/33014-32858   GGUCAUGCUUUUCCACAGCUUUCUUGAACUUCCUUGCCAUGCUUAACUUGUGUGUGUGUGU------------GUGUGUGUGUGUAGAUCACUAUAUAUCUGUAUAGUUA------------------------------------------------------------UACACAUUUAGCUAG---------------------------------------------------------CUAGCA--------CCAUGGAAGCUCAAGAAAGCCGUGGGAGAACAUGGCAA
AARH01003359.1/52522-52352   UUGCAUGCUUUUCCACGGCUUUCUUGAACUUGGCACUCAAGAGACAUGAGAGUAAAGGGCUAGGCUUUCUUUUCUAUUCCUUUCGUUCUUUGAAAUUUUCCUGUUCAAAG------------------------------------------------------------AAUCCAUACAUAUC----------------------------------------------------------AGUCUCU-----UUAGUACAAAGCUCAAGAAAGCCGUGGGAAAAUAUGAAAG
AC006250.4/85478-85629       CUCUGUAUUCUUCCACAGCUUUCUUGAACUGCAAAACUUCUUCAGAUUUUUU------------------------------UUUUUUUCUUUUGAUAUCUCUUACGCAU------------------------------------------------------------AAAAUAGUGAUUUUCUUCAUA--------------------------------------------UCUCUGCUCGAUU--------GAUUUGCGGUUCAAUAAAGCUGUGGGAAGAUACAGACA
AM489352.2/13768-13664       UGCCAUGCUUUUCCACAGCUUUCUUGAACUUCUUCUCCCUGU------------------------------------------------------UUGGUGGUCU----------------------------------------------------------------------CCUACGUUU---------------------------------------------------------ACCCAU--------CCACUGAAGUUCAAGAAAGCUGUGGGAAACCAUGGCUU
AM486009.2/272-384           UGUCAUGCUUUUCCACAGCUUUCUUGAACUACUUUUCCAUCU---------------------------------------------------ACCUGUUUGAUGA-----------------------------------------------------------------UCUUCUUCAUAAGG---------------------------------------------------------AGUGUG--------AAAUAGAAGCUCAAGAAAGCUGUGGGAGGACAUGGCAA
AM489352.2/7330-7448         CUUUGUAUUCUUCCACAGCUUUCUUGAACUGCAUUUUUC------------------------------------------------------AGACUACUGGUGUGUUUUU--------------------------------------------------------GUAUGCACUCAAAGUCA---------------------------------------------------------UUGUAA--------CAGUUGCGGUUCAAUAAAGCUGUGGGAAGAUACCAACA
GQ419588.1/34-211            GGCCAUGCUCUCCACAGGCUUUCUUGAACUGUGAACUCGUGU---------------------------------------------------GUGCAUGCUCCUCAUAUAUUGUUCUAGAUCCCAUGCAUGAUGCAUAUCGAUCGAUCUGAUCUGAAUUAGGUCAUCGAUGCGCAUCUGGAUCC---------------------------------------------------------CCAUCU--------UGUUGAUAGUUCAAGAAAGUCCUUGGAAAACAUGGUGC
FM164183.1/100-235           GGUCAUACUUUUCCACAGCUUUCUUGAACUUUCUUUUUCAUUUC----------------------------------------------CAU-----UGUUUUUUUCUUAAACAAAAGU----------------------------------------AAGAAGAAAA---------------AAAACU--------------------------------------------UUAAGAUUAAGCA--------UUUUGGAAGCUCAAGAAAGCUGUGGGAAAACAUGACAA
HM139796.1/344-460           CUUUGUGGUCUUCCACAGCUUUCUUGAACUGCAUCUUUGAGA--------------------------------------------------GAGAUUAGCAUCCCUAUG------------------------------------------------------------UGUGGAUUUUGCU-----------------------------------------------------------UGCACG--------AGUGUGCAGUUCAAUAAAGCUGUGGGAAAUUACAGAGA
GQ419538.1/118-272           CUUUGUGAUCUUCCACAGCUUUCUUGAACUGCACGCAUGAUGA-------------------------------------------------A--UAAUCCCUUUGGUUAAUUGUGAU--------------------------------------------CUGGUCUC---------------UGAGAGAUCGUAGUUAGA---------------------CUCGAUCGGUUGCAUUGGCAUCAG--------AGAGAGCAGUUCAAUAAAGCUGUGGGAAAUUGCAGAGA
GQ905608.1/114-231           CUUUGUGAUCUUCCACAGCUUUCUUGAACUGCAUCUCUCAGA---------------------------------------------------GGAGCGGCAGCUUCAAC------------------------------------------------------------UCCUCCACCCGCAUC---------------------------------------------------------AGCAGG--------UGCAUGCAGUUCAAUAAAGCUGUGGGAAACUGCAGAGA
GQ419544.1/118-272           CUUUGUGAUCUUCCACAGCUUUCUUGAACUGCACGCAUGAUGAA-----------------------------------------------UA----AUCCCUUUGGUUAAUUGUGAUCUG--------------------------------------GUCUCUGAGAGAUCG-----------UAGCUAGACUCGA-------------------------------UCGGUUGCAUUGGCAUCAG--------AGAGAGCAGUUCAAUAAAGCUGUGGGAAAUUGCAGAGA
FM164161.1/100-235           GGUCAUACUUUUCCACAGCUUUCUUGAACUUUCUUUUUCAUUUC-----------------------------------------------CA----UUGUUUUUUUCUUAAACAAAAGU----------------------------------------AAGAAGAAAAAAUACUUUAAGAU-----------------------------------------------------------UAAGCA--------UUUUGGAAGCUCAAGAAAGCUGUGGGAAAACAUGACAA
HM139865.1/34-211            GGCCAUGCUCUCCACAGGCUUUCUUGAACUGUGAACUCGUGU---------------------------------------------------GUGCAUGCUCCUCAUAUAUUGUUCUAGAUCCCAUGCAUGAUGCAUAUCGAUCGAUCUGAUCUGAAUUAUGUCAUCGAUGCGCAUCUGGAUCC---------------------------------------------------------CCAUCU--------UGUUGAUAGUUCAAGAAAGUCCUUGGAAAACAUGGUGC
#=GC SS_cons                 ::<<<<<-----<<<-<<<<<<-<<<<-<<<<<_________..................................................._________________............................................................_______________.........................................................______........____>>>>>->>>>->>>>>>->>>----->>>>>:::
#=GC RF                      uuccgUgcUcUUCCACgGCUUUCUUGAACUgccuacuuaagu...................................................auauuucuuuuUcauau............................................................uaugcaUcuauaUcu.........................................................aauuuu........uguuggcAGUUCAAgAAAGCcGUGGGAAAAcAcggaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00649
#=GF ID   mir-128
#=GF DE   microRNA mir-128
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   70.40
#=GF NC   47.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000048;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   16750530
#=GF RT   Identification of microRNAs from different tissues of chicken embryo and
#=GF RT   adult chicken.
#=GF RA   Xu H, Wang X, Du Z, Li N
#=GF RL   FEBS Lett. 2006;580:3610-3616.
#=GF WK   MicroRNA
#=GF SQ   18


AAYZ01088765.1/13723-13805   UGUGCAGUGGG-AAGGGGGCCGAUAC-ACUGUACGAGAGUGA-GUAGCAGGUCUCACAGUGAACCGGUCUCUUUCUCUACUGUGUC
AAYZ01289114.1/6650-6731     UGAGCUGUUGGAUUCGGGGCCGUAGC-ACUGUCUGAGAGGU---UUACAUUUCUCACAGUGAACCGGUCUCUUUUUCAGCUGCUUC
CU459063.8/87923-87839       GGAGUGCUGGGAGACGGGGCCGUGGC-ACUGUAUGAGAUUCAUGUAGGCUUUCUCACAGUGAACCGGUCUCUUUUUCCAGCCCUCA
AAPN01333292.1/110-29        UGAGCCGCUGGAUUCGGGGCCGAUAC-ACGGUCUGAGGGGU---UUACGAGUCUCACAGUGAACCGGUCUCUUUUUCAGUUGCUCC
AAVX01050759.1/9619-9536     GGAGCAGCUGGAGAGGGGGCCGUUAC-ACUGUAAGAGAGUGA-GUAGCAGGUCUCACAGUGAACCGGUCUCUUUCCCAGGGGCCAC
BAAF04005951.1/319-236       CAAGGGGCGGGACGCGGGGCCGGGAC-GCUGUCUGAGAGGCC-GCUACGAAUCUCACAGUGAACCGGUCUCUUUUCCCGCCCCUCA
BAAF04002274.1/1102-1018     GUGGCAGUAGAGGAGGGGGCCGUUAC-ACUGUCAGAGAUGUACUCUGAGGGUCUCACAGUGAACCGGUCUCUUUUCCUGCUGCUUC
AAPN01083252.1/12750-12833   UGGACAGCCGGAAGGGGGGCCGUUAC-ACUGUAAGAGAGUGA-GUACCAGGUCUCACAGUGAACCGGUCUCUUUCCCGACUGGAUC
AAFR03062124.1/28552-28469   UGUGCAGCAGGAAGGGGGGCCGUUAC-ACUGUCAGAGAGUGA-GUAGCAGGUCUCACAGUGAACCGGUCUCUUUCCCUGCUGUGGC
CAAE01014622.1/402657-402574 GGAGAGGCUGCAUACGGGGCCGGGAC-GCUGUUUGAGAGUCC-ACUAUGAAUCUCACAGUGAACCGGUCUCUUUUGCAGCCCCUUA
AAHY01081787.1/13703-13786   UGUGCAGUGGGAAGGGGGGCCGAUGC-ACUGUAAGAGAGUGA-GUAGCAGGUCUCACAGUGAACCGGUCUCUUUCCCUACUGUGUC
AADB02231623.1/453-371       UGUGCAGU-GGAAGGGGGGCCAAUCC-ACUGUAGGAGAGUGA-GUAGCAGGUCUCACAGUGAACCGGUCUCUCUCCCUACUGUGUC
CAAK05043402.1/2817-2901     UCAGUAGUAGGACAGGGGGCCGUUUCUACUGUCAGAGAUGCU-GCCACUCGUCUCACAGUGAACCGGUCUCUUUUCCUGCUAUUCA
CAAB02004088.1/15719-15636   AGAGAGCCUGGGUACGGGGCCGGGAC-GCUGUUUGAGAGUCC-UCUAUGAAUCUCACAGUGAACCGGUCUCUUUUCCAGCCCCUCA
AADN03002591.1/50849-50766   UGUCCAGCUGGAAGGGGGGCCGUUAC-ACUGUAAGAGAGUGA-GUAGCAGGUCUCACAGUGAACCGGUCUCUUUUCCUGCUGUGUC
FP236552.7/21756-21840       UCAGUAGUAGGACAGGGGGCCGUUUCUACUGUCAGAGAUGCU-GCCACUCGUCUCACAGUGAACCGGUCUCUUUUCCUGCUAUUCA
AC130551.4/164654-164571     UGUGCAGUGGGAAGGGGGGCCGAUGC-ACUGUAAGAGAGUGA-GUAGCAGGUCUCACAGUGAACCGGUCUCUUUCCCUACUGUGUC
AY865856.1/455-536           UGAGCUGUUGGAUUCGGGGCCGUAGC-ACUGUCUGAGAGGU---UUACAUUUCUCACAGUGAACCGGUCUCUUUUUCAGCUGCUUC
#=GC SS_cons                 :::::<<<<<<----<<<<<<<---<.<<<<<--<<<<____.________>>>>>>>>>>--->>>>>>>---->>>>>>:::::
#=GC RF                      ugaGcggcgGgAaagGGGGCCGuuaC.aCUGUaaGAGAGuua.guuacaggUCUCACAGuGAACCGGUCUCUUUucCcgccguuuc
//
# STOCKHOLM 1.0

#=GF AC   RF00650
#=GF ID   mir-153
#=GF DE   microRNA mir-153
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   68.00
#=GF NC   56.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000050;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [3]
#=GF RM   19170227
#=GF RT   Identification and expression profiling of microRNAs during bovine oocyte
#=GF RT   maturation using heterologous approach.
#=GF RA   Tesfaye D, Worku D, Rings F, Phatsara C, Tholen E, Schellander K, Hoelker
#=GF RA   M
#=GF RL   Mol Reprod Dev. 2009;76:665-677.
#=GF WK   Mir-153_microRNA_precursor_family
#=GF SQ   18


BAAF04053425.1/5508-5422       UGCGGUUGCCAGUGUCAU-UUUUGUGAUGUUGCAGCU--AGUAAUAUGAGCCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGAGACUGUG
AAPY01094601.1/1482-1395       AGCGGUGGCCAGUGUCAU-UUUUGUGACGUUGCAGCUA-GUGAUAUGAAGCCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGAGACUGUG
AABS01000027.1/231997-232081   UCUGUGUACGUGUGUCAU-UUUUCUAUU-AUGCAACU--UUUU-UUUCAUGUU-------AGUUGCAUAGUAACAAAAGUGAUCAUACGUUCGCAUG
AANH01011406.1/2584-2499       CAUAUCUGUCUGUGUCAU-UCUUGUGGU-UUGCAACU--AGUAGUCUGGCUCC-------AGUUGCAUAGUCACAAAAAUGAUCAUGGACUGAUGUG
AL928556.7/99188-99103         CACAGCUGUCUGUGUCAU-UUUUGUGGU-UUGCAGCU--AGUAGUCUGGUUCC-------AGUUGCAUAGUCACAAAAAUGAGCACAGACAGAUGUG
CAAE01015004.1/985676-985591   ACCAUCUCCCAGUGUCAU-UUUUGUGGU-UUGCAGCU--AGUACUCUGGCUCC-------AGUUGCAUAGUCACAAAAAUGAGCAUUGGCAGGUGUG
AANU01247847.1/3700-3615       CACAGCUGCCAGUGUCAU-UUUUGUGAU-CUGCAGCU--AGUAUUCUCACUCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGCAGGUGUG
AY865903.1/320-405             CACAGCUGCCAGUGUCAU-UUUUGUGAU-CUGCAGCU--AGUAUUCUCACUCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGCAGGUGUG
AY865902.1/114-199             CACAGCUGCCAGUGUCAU-UUUUGUGAU-CUGCAGCU--AGUAUUCUCACUCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGCAGGUGUG
AY865901.1/325-410             CACAGCUGCCAGUGUCAU-UUUUGUGAU-CUGCAGCU--AGUAUUCUCACUCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGCAGGUGUG
AY865904.1/433-519             AGCGGUGGCCAGUGUCAU-UUUUGUGAUGUUGCAGCU--AGUAAUAUGAGCCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGAAACUGUG
AY865906.1/428-514             AGCGGUGGCCAGUGUCAU-UUUUGUGAUGUUGCAGCU--AGUAAUAUGAGCCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGAAACUGUG
AY865905.1/428-514             AGCGGUGGCCAGUGUCAU-UUUUGUGAUGUUGCAGCU--AGUAAUAUGAGCCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGAAACUGUG
AAHY01155090.1/12968-13054     AGCGGUGGCCGGUGUCAU-UUUUGUGACGUUGCAGCU--AGUAAUAUGAGCCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGAAACUGUG
CAAE01014542.1/2489782-2489695 AGCGGUUGCCAGUGUCAUUUUUUGUGAUGUUGCAGCU--AGUAAUAUAAGCCA-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGAAACUGUG
AACT01065888.1/33880-33797     ACUGUUCACGAGUGUCAU-UUUAAUACU-AUGCAGCU--UUAA--AUAAUGUU-------AGUUGCAUAGUAAUAAAAGUGAUCAUGCGUUUACAAG
AAGJ04108136.1/11406-11314     CCCGCCAGCCCGA-UCAU-UUUUGUGUUUAUGCAACUUUUGUAUUUUCACCGAUCAGAGUAGUUGCAUAGUCACAAAAGUGA--UUGGGAGGGUUGG
AAWZ02011471.1/44569-44654     CACAGCCGUCAGUGUCAU-UUUUGUGAU-UUGCAGCU--AGUAAUCCUGGCCC-------AGUUGCAUAGUCACAAAAGUGAUCAUUGGCCGCUGUG
#=GC SS_cons                   ::<<<<--<<<<<<<<<<.<<<<<<<<<.-<<<<<<<..______________.......>>>>>>>-->>>>>>>>>>>>>->>>>>>-->>>>::
#=GC RF                        aacgccugCccguGUCAu.UUUuGUgau.uUGCAgCU..agUAuUuUaAuucc.......AGuUGCAUAgucACaAAAgUGAUCauggGaaggcguG
//
# STOCKHOLM 1.0

#=GF AC   RF00651
#=GF ID   mir-221
#=GF DE   microRNA mir-221
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   60.60
#=GF NC   58.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.50 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000051;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18256158
#=GF RT   MicroRNA profile of Marek's disease virus-transformed T-cell line MSB-1:
#=GF RT   predominance of virus-encoded microRNAs.
#=GF RA   Yao Y, Zhao Y, Xu H, Smith LP, Lawrie CH, Watson M, Nair V
#=GF RL   J Virol. 2008;82:4007-4015.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   19397817
#=GF RT   Parallel DNA pyrosequencing unveils new zebrafish microRNAs.
#=GF RA   Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL,
#=GF RA   Moura GR, Santos MA
#=GF RL   BMC Genomics. 2009;10:195.
#=GF WK   Mir-221_microRNA
#=GF SQ   47


AL831718.6/88302-88233       CAUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUU---UGUUAGGCAACAGCUACAU-UGUCUGCUGGGUUUCAG
AL831718.6/88895-88826       CAGUGGCUC-AGUAGCCAGUGUAGA-UCCUGUCUU---UGGUAAUCAGCAGCUACAUCUGGCUACUGGGUCUCUG
AANH01009585.1/5114-5044     CCUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUG--GUUAAAUUCAACAGCUACAU-UGUCUGCUGGGUUUCUG
AANH01009585.1/5625-5558     CGGUUGCUC-AGUAGGCAGUGUAGA-UCCUGUGUA-----GCAAUCAGCAGCUACAUCUGGCUACUGGGUCUCCG
AC194656.3/28401-28470       CAAUGGCUC-AGUAGCCAGUGUAGA-UCCUGUCUU---UCGUAAUCAGCAGCUACAUCUGGCUACUGGGUCUCUG
AAFR03036723.1/3502-3571     CAUGAACCU-GGCAUACAAUGUAGAAUUCUGUGUU---UAUUAAGUAACAGCUACAU-UGUCUGCUGGGUUUCAG
AAFR03036723.1/2919-2988     CAUUCGCUC-AGUAGUCAGUGUAGA-UACUGUCUC---UUUCCAUCAGCAGCUACAUCUGGCUACUGGGUCUCUG
AAQQ01365689.1/55-1          CAAUGGCCC-AGUAACCAGUGUAGA-UCCUGUCUU---UUGUAAUCAGCAGCUACAU----CUG-----------
BAAE01342535.1/103-172       UCUGGACCU-GGCAUACAGUGUAGUAUUCUGUGUG---CGUCCGUCUACAGCUACAU-UGUCUGCUGGGUUUCAG
BAAE01085056.1/1241-1173     CCUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUU---U-CAAUUCUACAGCUACAU-UGUCUGCUGGGUUUCUG
AC172026.3/74859-74931       UGGCUGCUC-AGUAGUCAGUGUAGG-AUCUGUCCGACAGUCUCACUAACAGCUACAUCUGAUUACUGGGUCACCA
AANN01137280.1/539-470       CAAUGGCUC-AGUAGUCAGUGUAGA-UCCUGUGUU---UUGUAAUCAGUAGCUACAUCUGGCUACUGGGUCUCUG
AAPN01358095.1/70-142        CGUCUGCUC-AGUAGUUGGUGUAGG-AUCUGUCUGACAUGAUUAAGAACAGCUACAUCUGAUUACUGGGUCACCG
AAPN01034572.1/4190-4257     CAAUCGCUC-AGUAGUCAGUGUAGA-UCCUGUAUU-----CUAAUCAGCAGCUACAUCUGGCUACUGGGUCUCUG
AALT01657316.1/439-370       CGUGAACCU-GGCACACAAUGUAGAUUUCUGUAUU---UAUUUAACAACAGCUACAU-UGUCUGCUGGGUUUCAG
AALT01657316.1/1356-1287     CAAUGACUC-AGUAGCCGGUGUAGA-UCCUGUGUU---UAGUAAUCAGUAGCUACAUCUGGCUACUGGGUCUCUG
AANH01006963.1/44202-44271   UCUGGACCU-GGCAUUCAGUGUAGGAUUCUGUGUG---UGUCAAUCUACAGCUACAU-UGUCUGCUGGGUUUCAG
AANH01006963.1/43986-44053   CGGGUGCUC-AGUAGUCAGUGUAGA-UCCUGUGCG-----GCUGGCAGCAGCUACAUCUGGCUACUGGGUCUCUG
AAVX01067207.1/2671-2602     CGGGUGCUC-AGUAGCUAGUGUAGG-AUCUGUUUU---GUCAUUUCUACAGCUACAUCUGGUUACUGGGUCUCUG
AAIY01624465.1/478-547       CAAUGGCUC-AGUAGCCAGUGUAGA-UCCUGUCUU---UUGUAAUCAGCAGCUACAUCUGGCUACUGGGUCUCUG
AAYZ01618848.1/488-419       CUUGAACCU-GGCAUACAAUGUAGAUUUCUGUAUU---UUCUGGGCAACAGCUACAU-UGUCUGCUGGGUUUCAG
AAPY01377193.1/1697-1628     CAUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUU---UGUUGGGCAACAGCUACAU-UGUCUGCUGGGUUUCAG
AANG01530718.1/118-187       CGUGAACCU-GGCAUACAAUGUAGAUAUCUGUGUU---UCUUGGGCAACAGCUACAU-UGUCUGCUGGGUUUCAA
CAAE01017358.1/322-252       CCUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUG--CUUGGAUUCUACAGCUACAU-UGUCUGCUGGGUUUCGG
CU550700.7/20157-20229       CUCUGGCCCUGGCACACAGUGUAUUGGUCUGUGUGU-GUGUGUGUCUACAGCUACAU-UGUCUGCUGGGUUUCAG
CAAK05045962.1/11661-11726   -----ACUC-AGUACUCGGUGUAGA-GUCUGUGUG--AUUCAGAAGAGCAGCUACAUCUGAAUACUGGGUCAGUG
CU550700.7/19683-19747       CCUGUGCUC-AGUGGUCAGUGUAGG-UCCUGC--------AGCGACAGCAGCUACAUCCGGCUACUGGGUCUCUG
AAGV020094308.1/2454-2385    CAAAGGCUC-AGUAGCCAGUGUAGA-UCCUGUCUU---UUGUAAUCAGCAGCUACAUCUGGCUACUGGGUCUCUG
CAAB02002407.1/76501-76568   UCUGGACCU-GGCAUAUAGUGUAGGAUUCUGUGUG-----UCAGUCUACAGCUACAU-UGUCUGCUGGGUUUCAG
AAGW02040329.1/185905-185974 CAUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUU---UUUUGGGCAACAGCUACAU-UGUCUGCUGGGUUUCAG
CAAB02002407.1/76211-76278   CAGUUGCUC-AGUAGUCAGUGUAGA-UCCUGUGGG-----GCUGUCAGCAGCUACAUCUGGCUACUGGGUCUCCG
AGAI01001682.1/35482-35550   CAAUCGCUC-AGUAGUCAGUGUAGA-UUCUGUCUU---U-ACAAUCAGCAGCUACAUCUGGCUACUGGGUCUCUG
AAWZ02029746.1/3142-3211     GGGCUGCUC-AGUAGUCGGUGUAGA-AUCUGUCUG---AUGAUACCCACAGCUACAUCUGAUUACUGGGUUUCCU
AAGU03070171.1/83261-83330   CAAUGGCUC-AGUAGCUAGUGUAGA-UCCUGUCUU---UUGUAAUCAGCAGCUACAUCUGGCUACUGGGUCUCUG
AAWZ02010876.1/97521-97453   CAGUCGCUC-AGUAGUCAGUGUAGA-UUCUGUCUU---C-UCAAUCAGCAGCUACAUCUGGCUACUGGGUCUCUG
ABQF01021060.1/73180-73249   CAUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUU---UGUUAAGCAACAGCUACAU-UGUCUGCUGGGUUUCCA
AAPE02021676.1/5049-4980     CUUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUU--U-GUUAAGCAACAGCUACAU-UGUCUGCUGGGUUUCAG
AAWZ02010876.1/96576-96509   CCUGAACCU-GGCAUACAAUGUAGAAUUCUGUUUG-----UUAAGCAACAGCUACAU-UGUCUGCUGGGUUUCAG
AGCE01118371.1/24202-24133   CAAUGGCUC-AGUAGCCAGUGUAGA-UCCUGUCUU---UUGUAAUCAGUAGCUACAUCUGGCUACUGGGUCUCUG
CAAB02004718.1/39836-39906   CCUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUG--CUUGGAUUCUACAGCUACAU-UGUCUGCUGGGUUUCCG
AAPE02021676.1/5735-5666     CAGUGGCUC-AGUAGUCAGUGUAGA-UCCUGUCUU---UUAUAAUCAGUAGCUACAUCUGGCUACUGGGUCUCUG
CAAB02004718.1/39554-39621   CAGUUGCUC-AGUAGGCAGUGUAGA-UCCUGUGUA-----GCAAUCAGCAGCUACAUCUGGCUACUGGGUCUCUG
AAQR03181317.1/33319-33250   CGAUGGCUC-AGUAGCCAGUGUAGA-UCCUGUCUU---UAGUAAUCAGUAGCUACAUCUGGCUACUGGGUCUCUG
CU207321.4/138521-138452     CAUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUU---UGUUGGGCAACAGCUACAU-UGUCUGCUGGGUUUCAG
CU855912.5/22126-22196       UGCAGACUC-AGUACUCGGUGUAGA-GUCUGUGUG--AUUCAGAAGAGCAGCUACAUCUGAAUACUGGGUCAGUG
AY866254.1/483-552           CAUGAACCU-GGCAUACAAUGUAGAUUUCUGUGUU---CGUUAGGCAACAGCUACAU-UGUCUGCUGGGUUUCAG
AY866255.1/442-511           CAGUGGCUC-AGUAGCCAGUGUAGA-UCCUGUCUU---UUGUAAUCAGUAGCUACAUCUGGCUACUGGGUCUCUG
#=GC SS_cons                 :::::<<<<.<<<<-<<<<<<<<<-.--<<<<___..._________>>>>>>>>>>->>>->>>>>>>>:::::
#=GC RF                      CauuagCcC.aGuAgcCAgUGUAGA.UUCUGugUu...UuuuaauCAaCAGCUACAuCUGgCUaCuGgGucUCuG
//
# STOCKHOLM 1.0

#=GF AC   RF00652
#=GF ID   MIR478
#=GF DE   microRNA MIR478
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.50
#=GF NC   49.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000052;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15994906
#=GF RT   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa
#=GF RT   that are absent from Arabidopsis.
#=GF RA   Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL
#=GF RL   Plant Cell. 2005;17:2186-2203.
#=GF WK   MicroRNA
#=GF SQ   17


AY728460.1/1-59 ---------------------------------AGUCUCCUAAUUUUUAGGGACUGAUGUUAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY884220.1/1-59 ---------------------------------AGUCUCCUAAUUUUUAGGGACUGAUGUUAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY884221.1/1-59 ---------------------------------AGUCUCCUAAUUUUUAGGGACUGAUGUUAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY728440.1/5-96 CCUUUUAGGGUUAAAACGUCAACAUUUUAGACGAGUCUCCUA-UUUUUAGGGACUGGUGUUAUUUUUUGACGUGUCUUCUAUUUUUAGGGACC
AY728467.1/5-95 CUUUUUAGGAAUAAA-CGUUAAUAUUUUAGACGAGUCUCCUAAAUUUUAGGGACUGAUGUCAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY851148.1/5-95 CUUUUUAGGGAUAAA-CGUUAAUAUUUUAGACGAGUCUCCUAAUUUUUAGGGACUGAUGUCAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY884224.1/1-59 ---------------------------------AGUCUCCUAAUUUUUAGGGACUGAUGUUAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY728439.1/4-95 CCUUUUAGGGUUAAAACGUCAACAUUUUAGACGAGUCUCUUA-UUUUUAGGGACUGGUGUUAUUUUUUGACGUGUCUUCUAUUUUUAGGGACU
AY851146.1/1-58 ---------------------------------AGUCUCCUAG-UUUGAGGGACUGAUAUCAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY728444.1/1-61 ------------AAGUAUCUUAUUUUUAGGAGCCGAUGUCAUUUUU----------------UU----GACAUGUCUUCUAUUUUUAGGGACC
AY851145.1/5-95 CUUUUUAGGGAUAAA-CGUUAAUGUUUUAGACGAGUCUCCUAAAUUUUAGGGACUAAUGUCAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY851147.1/5-95 AUUUUUAGGGAUAAA-CGUUAAUGUUUUAGACGAGUCUCCUAAAUUUUAGGGACUAAUGUCAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY851144.1/5-95 CUUUUUUGGGACAAA-CGUUAAUAUUUUAGACGAGUCUCCUAAUUUUUAGGGACUAAUGUCAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY728455.1/5-95 CUUUUUAGGGACAAA-CGUCAAUAUUUUAGACGAGUCUCCUAAUUUUUAGGGACUGGUGUCAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY728441.1/5-95 CUUUUUAGGGUUAAA-UGUCAAUAUUUUAGACGAGUUUUCUA-UUUUUAGGGUCUGGUGUUAUUUUUUGACGUGUCUUCUAUUUUUAGGGACC
AY884222.1/1-59 ---------------------------------AGUCUCCUAAUUUUUAGGGACUGAUGUUAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
AY884223.1/1-59 ---------------------------------AGUCUCCUAAUUUUUAGGGACUGAUGUUAUUUUU-AACGUGUCUCCUAUUUUUAGGGACC
#=GC SS_cons    :::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::
#=GC RF         CuUUUUaGGGauAAa.cGuuaAUaUUUuaGAcgAGUCUCCUAaUUUUUAGGGACUGaUGUuAUUUUU.aACGUGUCUcCUAUUUUUAGGGACC
//
# STOCKHOLM 1.0

#=GF AC   RF00653
#=GF ID   mir-22
#=GF DE   microRNA mir-22
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   59.00
#=GF TC   64.40
#=GF NC   48.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.43 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000053;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science. 2001;294:853-858.
#=GF RN   [2]
#=GF RM   15978578
#=GF RT   Identification of human fetal liver miRNAs by a novel method.
#=GF RA   Fu H, Tie Y, Xu C, Zhang Z, Zhu J, Shi Y, Jiang H, Sun Z, Zheng X
#=GF RL   FEBS Lett. 2005;579:3849-3854.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-22
#=GF SQ   12


CR353219.1/89-176          GGCUG-CCCGGCAGCAGUUCUUCAGUGGCAAGCUUUAUGUCCUUCUCUAGUAGC--UAAAGCUGCCAGUUGAAGAACUGUUGAAUGUAGCC
AY865971.1/460-544         GGCUG-AGCCGCAGUAGUUCUUCAGUGGCAAGCUUUAUGUCCUGA---CCCAGC--UAAAGCUGCCAGUUGAAGAACUGUUGCCCUCUGCC
AAFR03054554.1/22241-22157 GGCCG-AGCCACAGCAGUUCUUCAGUGGCGAGCUUUAUGUCUUGU---CCCAGC--UAAAGCUGCCAGUUGAAGAACUGCUGAGCUCUGCU
BAAF04035139.1/3478-3391   GGCUG-ACCCACAGCAGUUCUUCACUGGCAAGCUUUAUGUUCUCGUGCACCAGC--UAAAGCUGCCAGCUGAAGAACUGUUGUGGUCGGCU
BX890581.13/13018-12931    GGCUG-ACCUACCGUAGUUCUUCUCUGGCAAACUUUAUGACUCUGUCUUUACGC--UAAAGCUGCCAGCUGAAGAACUGUUGUGGUCAGCU
BAAF04020956.1/20-107      CGUUG-CCUCACAGUCGUUCUUCACUGGCUAGCUUUAUGUCCCACG--CCCCACCGUAAAGCUGCCAGUUGAAGAGCUGUUGUGUGUAACC
CT030218.5/50207-50290     CGUUA-CUUCACAGUCGUUCUUCACUGGCUAGCUUUAUGUGGCAG----CACCU--UAAAGCUGCCAGUUGAAGAGCUGUUGUGGGUAACC
CAAE01007790.1/7423-7510   GGCCG-ACCUACAGCAGUUCUUCACUGGCAAGCUUUAUGUCCUCGUGCAACCGC--UAAAGCUGCCAGCUGAAGAACUGUUGUGGUCGGCU
AANH01003046.1/62202-62289 GGCUG-ACCUACAGCAGUUCUUCACUGGCAAGCUUUAUGUCCUCAUCUACCAGC--UAAAGCUGCCAGCUGAAGAACUGUUGUGGUCGGCA
AAPN01147719.1/277-361     GGCUG-AGUCACAGCAGUUCUUCAGUGGCAAGCUUUACGUCCUGU---CCCAGC--UAAAGCUGCCAGUUGAAGAACUGUUGAACUCAGCC
ABPN01026389.1/1015-930    AGCUGAGCACA---CAGUUCUUCACUGGCAGCCUUAAGGUUUCUGUAGACAGGC--UAAACCUGCCAGCUGAAGAACUGCUCUGGCCAGCU
CAAB02004371.1/1413-1500   AGCUG-ACGCACAGGAGUUCUUCACUGGCAAGCUUUAUGUUCCUGUACACAUAC--UAAAGCUGCCAGCUGAAGAACUGCUCUGCUCAGCC
#=GC SS_cons               :<<<<.<<--<<<<<<<<<<<<<<-<<<<-<<<<<<<-<<____________>>..>>>>>>>>>>>-->>>>>>>>>>>>>>->>>>>>:
#=GC RF                    gGcuG.acucaCagcaGuUCUUCacUGGCaaGCUUuAUGcccuuguauacaagC..UaAAGCuGCCAGuuGAAGAaCugcuGugguCagCu
//
# STOCKHOLM 1.0

#=GF AC   RF00654
#=GF ID   mir-216
#=GF DE   microRNA mir-216
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   59.00
#=GF TC   59.10
#=GF NC   58.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.59 -Z 549862.597050 CM SEQDB
#=GF CL   CL00094
#=GF DR   MIPF; MIPF0000054;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   18511220
#=GF RT   Identification of novel chicken microRNAs and analysis of their genomic
#=GF RT   organization.
#=GF RA   Shao P, Zhou H, Xiao ZD, He JH, Huang MB, Chen YQ, Qu LH
#=GF RL   Gene. 2008;418:34-40.
#=GF RN   [3]
#=GF RM   12624257
#=GF RT   Vertebrate microRNA genes.
#=GF RA   Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP
#=GF RL   Science. 2003;299:1540.
#=GF WK   Mir-216_microRNA_precursor_family
#=GF SQ   33


AAPY01560157.1/6445-6357       AAGUGGCAGACUGGAAAAUCUCUGCAGGCAAAUGUGAUGUCACUG---AAGCAAUCACACACUUGCC-C-G-UAGAGAUUCUACAGU-CUGACAUC
AAFR03002982.1/16332-16244     GAGUUGCAGACUGGGAAAUCUCUGCAGGCAAAUGUGGUGUCGCUAU---AGUUAUCACACAAUUACC-C-G-UAGAGAUUCUGCAAU-CUGACAUC
AAPN01112677.1/27856-27944     GGCUGUGAAUCGGCUUAAUCUCAGCUGGCAACUGUGAGAUGCUAAC--CAAUUCUCCCACAGUGGCA-U-C-UG-GGAUUAUGCUAA-ACACAGCA
AAPN01112677.1/19396-19484     AAAUCGCAGACUGGGAAAUCUCUGCUGGCAAAUGUGGUGUCACGGU---AGCAAUCGCACAAUUACC-U-G-UAGAGAUUCUGCAAU-CUGGCUUU
AAIY01552317.1/295-382         GGCUGUGGGCUGGCUUAAUCUCAGCUGGCAACUGUGAGCUGUUCGU---GCAAUCCUCACAGUGGCC-U-C-UG-GGACUAUGCUAC-ACAGAGCA
CAAE01014563.1/1137339-1137250 UGUUGUGUUUUGGUGAAAUCUCAGCUGGCAACUGUGAGUCGUUCACU-AGCUGCUCUCACAAUGGCC-U-C-UG-GGAUUAUGCUAA-ACACAGCG
CAAE01014563.1/1138009-1137922 UUUAGGUUGACUGUUUAAUCUCUGCAGGCAACUGUGAUGGUGAUUU----UUAUUCUCACAAUCACC-U-G-GAGAGAUUCUGCAGU-UUAUUUAA
BAAF04071571.1/4838-4755       AGCUGUGAUCCAGUCAAAUCUCAGCUGGCAACUGUGAGUUUGGAGC-------ACCUCACAGCGCUA-G-C-UG-AGGUUCGCCUGA-AUGCAGCA
AANH01011241.1/47022-46939     AGCUGUGAUCCAGUUUAAUCUCAGCUGGCAACUGUGAGCUUUGAUC-------GCCUCACAGAGCCA-A-C-UA-AGAUUCACCUGA-ACGCAACA
AAVX01147466.1/944-1031        AAGCUACAGACUGGAUAAUCUCUGCAGGCAACUGUGAAGACCUGCC----UCUAUCUCACAAUAGCC-U-CCAG-AGGUUCUGUAGU-CUGUGGCA
CAAA01021685.1/51513-51601     CAUUGGCAGACUGGGAAAUCUCUGCAGGCAAAUGUGAUGUCACUG---AAGAAACCACACACUUACC-U-G-UAGAGAUUCUUCAGU-CUGACAAC
BX321898.29/72134-72045        AGCUGAUUUUUGGCAUAAUCUCAGCUGGCAACUGUGAGUAGUGUUUU-CAUCCCUCUCACAGGCGCU-G-C-UG-GGGUUCUGUCAC-ACACAGCA
BX321898.29/72434-72349        UAUAAACUGACUGGGUAAUCUCUGCAGGCAACUGUGAUGUGAUUAC--AG----UCUCACAUUGACC-U-G-AAGAGGUUGAGCAGU-CUGUUUAC
AANN01395871.1/902-990         GGCUAUGAAUUGGUUUAAUCUCAGCUGGCAACUGUGCGAUAUUCAU--ACAAUCCCCCACAGUGGUC-U-C-UG-GGAUUAUGCCAA-ACAAAGCA
AALT01617626.1/3023-3113       AGCUAUGAGUUGGUUUAAUCUCAGCUGGCAACUGUGAGAUGUUCAUACAAUUCCCCCCACAGUGGUC-U-C-UG-GGAUUAUGCUAA-ACAGAGCA
AANH01005109.1/23387-23300     UAAGGGCUGACUGGGUAAUCUCUGCAGGCAACUGUGAUGGUGCUUU--AAAU--UCUCACAAUGACC-U-G-GAGAGAUUCUGCAGU-UGCCUUUU
AAIY01782907.1/856-772         AAGUGGCAGACUGGGAAAUCUCUGCAGGCAAAUGUGACGUUGCUG---CCGAAAUCACACACUUGCC-C-G-UAGAGAUGCUGCAGU-CUGA----
BAAE01230816.1/685-599         CAAAGGCUGACUGGGUAAUCUCUGCAGGCAACUGUGAUGGUGAUUU--CA---UUCUCACAAUCACC-U-G-GAGAGAUUUUGCAGU-UUGUCUAA
AAVX01063793.1/485-397         UGCCAUGAACUGGCUUAAUCUCAGCUGGCAACUGUGAGUGUUUAAU--GGUUUCCCCCACAGUGGUU-G-C-UG-GGAUUAUGCUAA-ACACAGCA
AAYZ01065394.1/6883-6795       GGCUGUGAGUUGGCUUAAUCUCAGCUGGCAACUGUGAGAUAGUCUU--CCAAUCCCUCACAGUGGUC-U-C-UG-GGGUUAUGCUAA-ACAGAGCA
AACN010698325.1/574-662        AAGUGACAGACUGGAAAAUCUCUGCAGGCAAAUGUGAUGUCACUA---AAGAAAUCACACACUUACC-C-GUAG-AGAUUCUGCAGU-CUGACAUC
AAQQ01539574.1/518-430         AAGUGGCAGACUAGAAAAUCUCUGCAGGCAAAUGUGAUGUCACUG---AAGAAAUCACACACUUACC-C-GUAG-AGAUUCUUUGGU-CUGGCAGC
AAKN02040735.1/24209-24296     GAGUGGCAGACUGGAAAAUCUCUGCAGGCAAAUGUGAUGUCACUGA--AGAA--UCACACACUUACC-U-G-UAAAGAUUCUGCAGU-CUGACAGC
AY866221.1/470-558             GGCUGUGAGUUGGCUUAAUCUCAGCUGGCAACUGUGAGAUGUUCAU--ACAAUCCCUCACAGUGGUC-U-C-UG-GGAUUAUGCUAAACAGAGCA-
AAWR02003896.1/155482-155568   GGCUGUGAGUUGGUUUAAUCUCAGCUGGCAACUGUGAGAUGUUCAU----AAAUCCCCACAGUGGUC-U-C-UG-GGAUUAUGCUAA-ACAGAGCA
AAGV020516803.1/6245-6157      AAGUGGCAGACUGGAAAAUCUCUGCAGGCAAAUGUGAUGUCACUA---AAGAAAUCACACACUUACC-UAU-AG-AGAUUCUACAGU-CUGACAUC
AAQR03052253.1/13725-13637     GGCUGUGAGUUGGCUUAAUCUCAGCUGGCAACUGUGAGAUGUUCAU--ACAAUUCCUCACAGUGGUC-U-C-UG-GGAUUAUGCUAA-ACAGAGCA
AAHX01081871.1/22293-22381     AGCUAUGAGUUAGUUUAAUCUCAGCUGGCAACUGUGAGAUGUCCCU--AUCAUUCCUCACAGUGGUC-U-C-UG-GGAUUAUGCUAA-ACAGAGCA
AADN03003108.1/28627-28539     GAGUCACAGACUGGGAAAUCUCUGCAGGCAAAUGUGAUGUCUUUAU---AGCAAUCUCACAAUUACC-U-G-UAGAGAUUCUACAAU-CUGGCAUC
AAWZ02015728.1/1581-1492       AAGUCACAGACUGAGAAAUCUCUGCAGGCAAAUGUGAUGUCUUGAC--CAGCAAUCUCACAGUUACCAG-C-AG-AGGUUCUGCAAU-CUGGACUG
AAQR03052256.1/6761-6673       GAGUGGCAGACUGGAAAAUCUCUGCAGGCAAAUGUGAUGUCACUG---AAGAAAUCACACACUUACCAG-U-AG-AGAUUCUAUAGU-CUGUCACC
AAWZ02015727.1/100859-100771   GGCUGUGAAUUGGUUUAAUCUCAGCUGGCAACUGUGAGCAGUUUCC--AAAUCCUCUCACAGUGGUU-U-C-UG-GGAUUAUGCUAA-ACACAGCA
CAAB02004893.1/247202-247115   GUUACGUUGACUGUUUAAUCUCUGCAGGCAACUGUGAUGGUGUUUU----AUAUUCUCACAAUCACC-UGG-AG-AGAUUCUGCAGU-UUAUCUAA
#=GC SS_cons                   ::::::::<<<<<---<<<<<<<---<<----<<<<__________.._________>>>>---->>.-.-.>>.>>>>>--->>>>.>:::::::
#=GC RF                        aacUgucAgacuGuuuAAUCuCaGCaGGCAAcUGUGAugUuuuuau..AaaaaaUCuCACAgUgaCC.u.c.uG.aGAUUcUGCagu.cugaagca
//
# STOCKHOLM 1.0

#=GF AC   RF00655
#=GF ID   mir-28
#=GF DE   microRNA mir-28
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   54.00
#=GF TC   54.00
#=GF NC   53.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00086
#=GF DR   MIPF; MIPF0000057;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science. 2001;294:853-858.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-28_microRNA_precursor_family
#=GF SQ   29


AY865990.1/439-524           GGUCCUUGCCCUCAAGGAGCUCACAGUCUAU-UG-------AGUU-----A-----C-------CU-------UUCUG-A-------UUUUCC------CA-CUAGAUUGUGAGCUCCUGGAGGGCAGGCACU
AACN010336126.1/997-912      GGUCCUUGCCCUCAAGGAGCUCACAGUCUAU-UG-------AGUU-----G-----C-------CU-------UUCUG-A-------CUUUCC------CA-CUAGAUUGUGAGCUCCUGGAGGGCAGGCACU
AANU01277817.1/18509-18424   GGUCCUUGCCCUCAAGGAGCUCACAGUCUAU-UG-------AGUU-----U-----C-------CU-------UUGUG-A-------CUUUCC------CA-CUAGAUUGUGAGCUCCUGGAGGGCAGGCACU
AY865992.1/464-549           GGUCCUUGCCCUCAAGGAGCUCACAGUCUAU-UG-------AGUU-----G-----C-------CU-------UUCUA-A-------CUUUCC------CA-CUAGAUUGUAAGCUCCUGGAGGGCAGGCACU
AAHY01126390.1/23609-23694   GGUCCCUACCUUCAAGGAGCUCACAGUCUAU-UG-------AGUU-----G-----C-------CU-------UUCUG-A-------UUCUCC------CA-CUAGAUUGUGAGCUGCUGGAGGGCAGGCACU
AACN010000068.1/5570-5495    CUUUCCUGCCCUCGAGGAGCUCACAGUCUAG-UA-------UGUC-----U-----C-------------------------------AGCCC------UA-CUAGACUG-AGGCUCCUUGAGGGCAGGGAUC
AY865991.1/448-533           GGUCCUUGCCCUCAAGGAGCUCACAGUCUAU-UG-------AGUU-----U-----C-------CU-------UUCUG-A-------CUUUCC------CA-CUAGAUUGUGAGCUCCUGGAGGGCAGGCACU
AAFC03007218.1/22263-22187   UUUUCCUGCCCUCGAGGAGCUCACAGUCUAG-UA-------CGUC-----U-----C------------------------------AUCCCC------UA-CUAGACUG-AAGCUCCUUGAGGACAGGGAUC
AAPN01136267.1/2568-2487     AUUCCCUGCCCACAACGAGCUCACAGUCUAU-AU-------UAAU-----G-----U------------------CUG-U-------CUUUCC------CU-CUAGACUGCGAGCUCGUUGUGGGCAGGGAAU
AAIY01415377.1/560-486       UCUUCCUGCCCUCGAGGAGCUCACAGUCUAG-UA-------CGUG-----C-----C--------------------------------ACCC------UA-CUAGACUG-GCGCUCCUUGAGGACAGGGGUC
AAFR03055707.1/16355-16441   UUUCCUUGCUCUCAAGGAGCUCACAGUCUAA-UG-------GGGA-----G-----A-------AA-------GUCUACA-------GACAAU------CA-UUAUAUUGUAAGCUCCUGGAGGACAAGGAAC
AAPY01064819.1/112-40        UGUUCCUGCCCUC---GAGCUAACAGUCUAG-UA-------CGUC-----U-----U-------------------------------GUCCC------UA-CUAGACUG-AAGCUCCUUGAGGACAGGGACU
AANN01537336.1/417-509       GGUCCCUGCCCUCUAGAAGCUCACAGUCUAGUUG-------CGUUCAAGGU-----C-------AA-------AUCAU-U-------CACCCC------CAGCUAGAUUGUAAGCUCCUUGAGGGCAGUCACC
ABBA01017397.1/191881-191789 GGUCCCUGCCCUCUAGAAGCUCACAGUCUAG-UU-------GUGU-----U-----C-------AUGUGCAAGUCAUU-U-------ACCCCC------AG-CUAGAUUGUAAGCUCCUUGAGGGCAGUUACC
AANG01070166.1/4108-4200     GGUCCCUGCCCUCUAGAAGCUCACAGUCUAG-UU-------GCGU-----U-----C-------AU-------GUGCA-AGCCGUUCACCCCC------AG-CUAGAUUGUAAGCUCCUUGAGGGCAGUUACC
AAYZ01598458.1/215-123       GGCCUCUGCCCUCUAGAAGCUCACAGUCUAG-UUGUGUUCUCGUG-----C-----A-------AG-------UCAUU-C-------AGCCCC------AG-CUAGAUUGUAAGCUCCUUGAGGGCAGCUGCC
AAKN02023220.1/50087-50162   UUUUCCUGCCCUCGAGGAGCUCACAGUCUAG-UA-------UGUC-----U-----C-------------------------------UAUCC------UA-CUAGACUG-AGGCUCCUUGAGGACAGGGAUC
AAGV020456123.1/438-346      GGCCCCUGCCCUCUAGAAGCUCCCAGUCUAG-UU------GAGAU-----C-----C-------UG-------UGCAG-G-------UCUCUCACCCCCAG-CUAGAUUGUAAGCUCCUUGAGGGCAGUCACC
AC161581.3/175223-175148     CUUUCCUGCCCUCGAGGAGCUCACAGUCUAG-UA-------UGUC-----U-----C-------------------------------CUCCC------UA-CUAGACUG-AGGCUCCUUGAGGACAGGGAUC
AABR05028338.1/30311-30226   GGUCCCUACCCGCAAGGAGCUCACAGUCUAU-UG-------AGUU-----C-----C-------UU-------UUCUG-A-------UUCUCC------CA-CUAGAUUGUGAGCUCCUGGAGGGCAGGCACU
AY865988.1/401-486           GGUCCUUGCCCUCAAGGAGCUCACAGUCUAU-UG-------AGUU-----A-----C-------CU-------UUCUG-A-------CUUUCC------CA-CUAGAUUGUGAGCUCCUGGAGGGCAGGCACU
AAGW02008334.1/35341-35433   GGCCCCUGCCCUCUAGAAGCUCACAGUCUAG-UU-------GUGU-----U-----CGCGUGCACG-------UCAUU-C-------ACCCCC------AG-CUAGAUUGUAAGCUCCUUGAGGGCAGUUACC
AAGU03072740.1/37386-37478   GGUCCCUGCCCUCUAGAAGCUCACAGUCUAGUUG-------CGUU-----UAUGUGC-------AA-------GUCUU-U-------UACCCC------CAGCUAGAUUGUAAGCUCCUUGAGGGCAGUCACC
AC105235.7/18788-18712       UUUUCCUGCCCUCGAGGAGCUCACAGUCUAG-UA-------UGUC-----U-----C------------------------------AUCCCC------UA-CUAGACUG-AAGCUCCUUGAGGACAGGGAUG
AAPE02022836.1/51048-51140   GGCUCCUGCCCUCUAGAAGCUCACAGUCUAG-UUGUGUUCAUGUG-----C-----C-------AG-------UUGCU-U-------ACCCCC------AG-CUAGAUUGUAAGCUCCUUGAGGGCAGUCACC
AY865987.1/453-538           GGUCCUUGCCCUCAAGGAGCUCACAGUCUAU-UG-------AGUU-----U-----C-------CU-------UUGUG-A-------CUUUCC------CA-CUAGAUUGUGAGCUCCUGGAGGGCAGGCACU
AC115787.6/169871-169956     GGUCCCUACCUUCAAGGAGCUCACAGUCUAU-UG-------AGUU-----G-----C-------CU-------UUCUG-A-------UUCUCC------CA-CUAGAUUGUGAGCUGCUGGAGGGCAGGCACU
AP001838.4/124960-125052     GGUCCCUGCCCUCUAGAAGCUCACAGUCUAG-UUGUGUUCAUGUG-----C-----A-------AG-------UCAUU-U-------ACCCCC------AG-CUAGAUUGUAAGCUCCUUGAGGGCAGUUACC
AY865986.1/436-521           GGUCCUUGCCCUCAAGGAGCUCACAGUCUAU-UG-------AGUU-----G-----C-------CU-------UUCUG-A-------CUUUCC------CA-CUAGAUUGUGAGCUCCUGGAGGGCAGGCACU
#=GC SS_cons                 ::::<<<<<<<<<-<<<<<<<--<<<<<<<<.<<.......____....._....._.......__......._____._.......______......>>.>>>>>>>>-->>>>>>>->>>>>>>>>::::
#=GC RF                      ggUCcCUGCCCuCuAGgAGCUCACAgUCUAg.ug.......aguu.....u.....c.......au.......uucuu.u.......auccCC......ca.cUAGAuUGUAAGCUcCUuGaGGGCAGguAcc
//
# STOCKHOLM 1.0

#=GF AC   RF00656
#=GF ID   mir-205
#=GF DE   microRNA mir-205
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   60.90
#=GF NC   53.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000058;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12624257
#=GF RT   Vertebrate microRNA genes.
#=GF RA   Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP
#=GF RL   Science. 2003;299:1540.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [3]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF WK   Mir-205
#=GF SQ   29


AANG01030552.1/7420-7521     CCCCAGACAUUCCAUGUGUUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUC--GUACCCAACCAGAUUUC-AGUGGAGUGAAGUUCAGGAGG-CGUGGAGCAGA
AAVX01642942.1/416-517       ACUGAUGACAUCCAUGCU-UUCUGCUGUCCUUCAUUCCACCGGAGUCUGUGAC-AUAAACCAACCAGAUUUC-AGUGGGGUGAAGCACAUGAGA-CAUGGAACAAA
AANH01002613.1/123689-123785 CAAGGAAAAUCCCAUGUG----UUCUGUCCUUCAUUCCACCGGAGUCUGUCUG--UUUC-ACACCAGAUUUC-AGUGGUGUGAAGUGUAAGAGA-CAUGGGGAUAC
AANH01007448.1/5834-5732     UUUAACGAAACCCAUCCAUGUAUUCUAUCCUUCAUUCCACCGGAGUCUGUGUA-AAGUGCCAGUCAGAUUUC-AGUGGUUUGAAGAGUAAAACG-CAUGGAAUUCA
AAFR03023170.1/5678-5779     CUCAGGAUGAUCCAUGAAUUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUC--AUAUCUAAUCAGAUUUC-AGUGGAGUGAAGCAUAAGAGG-CAUGGAGUUGA
BAAF04011157.1/1235-1133     AACAGCAGGAAUAUUCCAUGUUUUCUGUCCUUCAUUCCACCGGAGUCUGUGCC-UGUAUGGAACCAGAUUUC-AGUGGUGUGAAGUGUAAAAGA-CAUGGGGAUAA
BAAE01019177.1/1941-2036     -------GAAAACAUCCAUGUCUUCUAUCCUUCAUUCCACCGGAGUCUGUAUA-GAGUGCCACUCAGAUUUC-AGUGGAUUGAAGAGUAAGAAA-CAUGGAAUAUG
AAVX01072421.1/1120-1016     CUUGAAGUGCAAUGGCACACUCUGGUGUCCUUCAUUCCACCGGGUCCUGUGUCCGAUUCUGAUCCAGAUUCCCAGUGAGAUGAAGCACAUGGGA-GGUGUCAAUGA
AAVX01185491.1/730-833       CAGCCGGUAAGCCAUGAUUUUUUGAUGCCCUUCAUUCCACCGGAAUCUGUACU-GGCAGAAAUCCGGAUUUC-AGUGAAAUGAGGAACAUUAGAACAUGGAUCCAA
AL929087.4/70181-70086       -------UAAAACUACUGUGCAUUCUAUCCUUCAUUCCACCGGAGUCUGUGUA-GUUGUUCAAUCAGAUUUC-AGUGGUGUGAAGUGUAGGAAA-CACGGAAAGAU
AALT01450952.1/1320-1220     AGAGGGGACCCAUCCACGUGGCUCCUGUCCUUCAUUCCACCGGAGUCUGUCUC--UGCA-CAACCAGAUUUC-AGUGGAGUGAAGAGCAGGAGG-CGUGGAGCGGA
AAPY01334591.1/2920-3021     UCUGAGACAAUCCAUGUGUUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUC--AUACCCAACCAGAUUUC-AGUGGAGUGAAGUUCAGGAGG-CAUGGAGCUGA
AAIY01330569.1/906-1007      CCCAAGACAAUCCAUGAAUUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUU--AUACCCAACCAGAUUUC-AGUGGAGUGAAGUUCAGGAGG-CAUGGAGCAGA
AAYZ01000262.1/7991-8092     CCCCAGACCAUCCAUGAGCUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUC--AUACCCAACCAGAUUUC-AGUGGAGUGAAGUUCAGGAGG-CAUGGAGCUGG
AAPN01396731.1/13477-13578   UUCGGAACGAUCCAUGGGUUUCUGUUGUCCUUCAUUCCACCGGAGUCUGUUUC--GUACCUAAUCAGAUUUC-AGUGGAGUGAAGCACAAGAGG-CAUGGAGUUGA
ABDC01034077.1/3824-3926     CCCCAGACAAUCCAUGUGCUUCUCUUGUCCUUCAUUCCACCGGAGUCUGGUCU-CAUACCCAACCAGAUUUC-AGUGGAGUGAAGUUCAGGAGG-CAUGGAGCUGA
AAFC03121357.1/8897-8998     CCUCAGAUAGUCCAUGUGCUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUC--GUACCCAACCAGAUUUC-AGUGGAGUGAAGUUCAGGAGG-CGUGGAACUGA
AY866204.1/444-544           CCUCGGGCAAUCCAUGUGCUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUC--AUACCCAACCAGAUUUC-AGUGGAGUGAAG-UCAGGAGG-CAUGGAGCUGA
AAKN02017853.1/245570-245471 GUCCAGGACCAUCCACGGGUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUG--CGGC--AACCAGACUUC-AGUGGAGUGAAGCUCAGGAGU-CGUGGAGCUGC
AAHX01077636.1/10495-10396   CCCCAGACAAUCCAUGGG-UCCUCCUGUCCUUCAUUCCACCGGAGUCUGUCUU--AUGC-CAACCAGAUUUC-AGUGGAGUGAAGCUCAGGAGG-CAUGGAGCUGC
AADN03001147.1/62076-62177   AGAUACACUACUAGGGCCUUCCUGAUGCCCUUCAUUCCACCGGAAUCUGUCAG-UGCAG-AAACCAGAUUUC-AGUGAAAUGAAGCCCAUCAGA-GAGGCAGCUCA
AAWZ02013773.1/18231-18332   ACAAAGAAUAUUCCAUGAGUUCUAUUGUCCUUCAUUCCACCGGAGUCUGUCUC--AUAUCUAAUCAGAUUUC-AGUGGAGUGAAGCACAAGAGA-CAUGGAGUUGA
AADN03008571.1/218014-218114 AUAAGGACAAUCCAUGGG-UUCUGUUGUCCUUCAUUCCACCGGAGUCUGUCUC--GUACCUAACCAGAUUUC-AGUGGAGUGAAGCACAAGAGA-CAUGGAGAUGA
CAAB02011054.1/6974-6872     UUCUGCAAGAAUAUUCCAUGUGUUCUAUCCUUCAUUCCACCGGAGUCUGUAUG-UGUAUUUAACCAGAUUUC-AGUGGUGUGAAGUGUAAGAGA-CAUGGUGAUGC
AAGU03032300.1/7683-7784     CCCCAGACAAUCCAUGCGUUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUC--AUACCCAAUCAGAUUUC-AGUGGAGUGAAGUUCAGGAGA-CAUGGAGCGGA
AAWZ02015481.1/79770-79870   CUAGCCACAGAUCCAGAGCUUG-GGUGCCCUUCAUUCCACCGGAAUCUGUCAC--CGCAAAAACCGGAUUUC-UGUGAAAUGAAGCCCACCAGG-CAUGGAAUUCU
AY866207.1/469-570           CCUCGGGCAAUCCAUGUGCUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUC--AUACCCAACCAGAUUUC-AGUGGAGUGAAGUUCAGGAGG-CAUGGAGCUGA
AY866208.1/458-559           CCUCAGGCAAUCCAUGUGCUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUC--AUACCCAACCAGAUUUC-AGUGGAGUGAAGUUCAGGAGG-CAUGGAGCUGA
AY866203.1/458-559           CCUCAGACAAUCCAUGUGCUUCUCUUGUCCUUCAUUCCACCGGAGUCUGUCUC--AUACCCAACCAGAUUUC-AGUGGAGUGAAGUUCAGGAGG-CAUGGAGCUGA
#=GC SS_cons                 ::::::::::::::::::::::<<<<<--<<<<<<<<<<<-<<<<<<<<____.._________>>>>>>>>.->>>>>>>>>>>-->>>>>::.:::::::::::
#=GC RF                      cuuaagauaauccauguguuUcUccUGUCCUUCAuuCCACCGgAgUCUGUcUc..auacccAACCAGAuUuC.AGUGGagUGAAGuuCAggAGa.CAUGGAgcuga
//
# STOCKHOLM 1.0

#=GF AC   RF00657
#=GF ID   mir-184
#=GF DE   microRNA mir-184
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   52.00
#=GF TC   52.30
#=GF NC   51.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.00 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000059;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   Mir-184
#=GF SQ   32


AY865940.1/104-187             CCAGUCACGUCCCCUUAUCACUUUUCCAG-CCCAGC-------UUUGUGA-CUGUAAGU--GUUGGACGGAGAACUGAUAAGGGUAGGUGAUUGA
CAAA01022586.1/26296-26214     CAGAUCCCCUUUCCUUAUCACUUUUCCAG--CCAGC-------UUUGUGA-CUCUAAGU--GUUGGACGGAGAACUGAUAAGGGUAGGUGACUGG
AAFS01000056.1/19415-19497     GUGCAUUCGUACCCUUAUCAU-UCUCGCG-CCCCGU-------GUGCAUU-AAAAGACA--ACUGGACGGAGAACUGAUAAGGGCUCGUAUCACC
AAGE02019030.1/3534-3452       GUGUAUUCGUACCCUUAUCAU-UCUUGCG-CCCCGU-------GUUAUAU-UGUUGGCG--ACUGGACGGAGAACUGAUAAGGGCCCGGGUCACC
AAVX01446026.1/144-63          CCACUUACAUUUCCUUAUCACUUUUCCAG-CCCAGC---------UGCAC-ACAGAUGU--GUUGGACGGAGAACUGAUAAGGGCUUGUUUCUGG
CAAE01014685.1/426159-426243   UCGCUCACAUCUCCUUAUCACUUUUCCAG-CCCAGC-------UAUAGCUUCUGAAUCC--GUUGGACGGAGAACUGAUAAGGGCAUGUGCAUGA
AAHX01056180.1/5344-5426       CCGACCACUUUCCCUUAUCAGUUUUCCAG--CCAGC-------UUUGUGA-CUGUAAAU--GUUGGACGGAGAACUGAUAAGGGUAAGUGACUGG
AAPN01248074.1/2985-3068       CCCAUCACGUCUCUUUAUCACUUUUCCAG-CCCAGC-------UUUCUGG-UUCUAGCC--GUUGGACGGAGAAUUGAUAAGGGUACGGGGUCGG
BAAE01193078.1/672-755         UCAAGCACAUCUCCUUAUCACUUUUCCAG-CCCAGC-------UAUCUGACAAACGUUU--GUUGGAC-GAGAACUGAUAAGGGUAUGUGCCUGG
AAAB01008980.1/6487239-6487319 GUGCACUCGAACCCUUAUCAU-UCUUUCG-CCCCGU-------GU--GCU-UUCUAACA--ACUGGACGGAGAACUGAUAAGGGCCCGGGUCACC
AANN01245614.1/108-185         CCGGUCCCCCGUCCUUGUCACUUUUCCAG-CCCAGC-------UU-------UGUGAGU--GCUGGACGGAGAACUGAUAAGGGUGGGCGGCCGG
AAZX01006282.1/1019-936        GUGCCUAAAGCCCCUUAUCAU-UCUCCUG-UCGAGU-------GUUAAAAUUCUCUACG--ACUGGACGGAGAACUGAUAAGGGCCCGAGGGUUA
AAZO01006369.1/2415-2497       UCUACUACGAUUCCUUGUCAU-UCUUCUG-UCCGGC-------GAGCUUU-CAUUAAAU--GUUGGACGGAGAACUGAUAAGGGCUCGUGGAUGA
AAYZ01335901.1/553-636         CCAAUCAUGUACCCUUAUCACUUUUCCAG-CCCAGC-------UUUGUGA-UUCUGACU--GUUGGACGGAGAACUGAUAAGCGUAGGUGAUUGU
AC147908.3/69916-69833         CCAGUAUCACUUCCUUAUCACUUUUCCAG-CCCAGC-------UUUUCAU-GACAAACU--GUUGGACGGAGAACUGAUAAGGCUGUGUGACUGC
BAAB01083504.1/1731-1651       GCAGUGACGUGCCCUUGUCAUUCUUCAGG-CCCUGU-------GU---AU-UUACAACU--ACUGGACGGAGAACUGAUAAGGGCACGCCGUGUA
AAJJ01000543.1/40724-40802     UUUCUUCCAGUCCCUUGUCAU-UCUCUCG-CCCGGU-------GU----A-UUUUAACA--ACUGGACGGAGAACUGAUAAGGGCUUGUGGGAAA
CR352253.9/159514-159598       UCGAACACGUCUCCUUAUCACUUUUCCAG-CCCAGC-------UAUCCAUUUAGUAUUC--GUUGGACGGAGAACUGAUAAGGGCAUGUGCCCGA
AAFR03045024.1/17871-17788     CCAGUCACAUCCCCUUAUCACUUUUCCAG-CCCAGC-------UUUCUAA-UGCUAAUU--GUUGGACGGAGAACUGAUAAGGGUAGGUGAUUGA
AAIY01348937.1/3812-3895       CCAGUCACAUCCCCUUAUCACUUUUCCAG-CCCAGC-------UGUGUGA-UUCUAAGU--GUUGGACGGAGAACUGAUAAGGGUAGGUGACUGA
AAPY01671193.1/13062-12979     CCGGCCACAUCCCCUUAUCACUUUUCCAG-CCCAGC-------UUUGUGA-CUCUGAGU--GUUGGACGGAGAACUGAUAAGGGUGGGUGACUGG
AANH01001588.1/36190-36106     UCGAGCACAUCUCCUUAUCACUUUUCCAG-CCCAGC-------UAUCUAUCAAAUGUUU--GUUGGACGGAGAACUGAUAAGGGUAUGUGUCUGA
AANG01143260.1/1786-1868       CCAGUCACAUUCCCUUAUCACUUUUCCAG--CCAGC-------UUUGUGA-CUCUAAGU--GUUGGACGGAGAACUGAUAAGGGUAGGUGGUUGU
AAPT01021532.1/10026-9944      GUGCAUUCGUACCCUUAUCAU-UCUCUCG-CCCCGU-------GUGGAUA-ACUAUACA--ACUGGACGGAGAACUGAUAAGGGCUCGUAUCACC
AAEU02000856.1/108964-108883   GUGCAUUCGUACCCUUAUCAU-UCUCUCG-CCCCGU-------GU-GCAU-UGAAGACA--ACUGGACGGAGAACUGAUAAGGGCUCGUAUCACC
AAWU01026464.1/17067-16985     GUGUAUUCGCACCCUUAUCAU-UCUUUCG-CCCCGU-------GUACUGU-UGUUUGCG--ACUGGACGGAGAACUGAUAAGGGCCCGGGUCACC
AADN03006053.1/41175-41092     CCGCUCUCACCCCCUUAUCACUUUUCCAG-CCCAGC-------UUCUUCG-CUCUGACU--GUUGGACGGAGAACUGAUAAGGGUGUGCGGGUGG
AAGJ04162502.1/17648-17739     UCUUUUAUCUUUCCUUAUCAU-UCUCUUG-CCCGGCCGAAUACUAUGUUA-UUGAAAUUGCGCUGGACGGAGAACUGAUAAGGGCUUAUAUAAGA
AADG06002732.1/85313-85396     GUGCCCAAAGCCCCUUAUCAU-UCUCCUG-UCCGGU-------GUAGAAUUGUUAGACG--ACUGGACGGAGAACUGAUAAGGGCCCGAGGGUCA
AAQR03026716.1/44271-44353     CCAGUCACAUCCCCUUAUCACUUUUCCAG-CCCAGC-------UGUGUGA-CUCUAGU---GUUGGACGGAGAACUGAUAAGGGUAGGUGGUUGA
CAAB02008852.1/41004-41088     UCAAGCUCAUCUCCUUAUCACUUUUCCAG-CCCAGC-------UAACUAUUGUAAAUUU--GUUGGACGGAGAACUGAUAAGGGUAUGUGUCUGA
AAGU03052093.1/7167-7250       CCAGUCACAUGCCCUUAUCACUUUUCCAGC-CCAGC-------UUUGUGA-CUCUAAAU--GUUGGACGGAGAACUGAUAAGGGUAGGUGAUUGA
#=GC SS_cons                   :::::::::::<<<<<<<<<-<<<<<<-<.-<<<<<......._______.________..>>>>>->>>>>>>->>>>>>>>>:::::::::::
#=GC RF                        ucgaucaCaUucCCUUAUCAuUUcUCcaG.CCCagC.......uuUguaa.uuuuaAcu..GcuGGACgGAgAACUGAUAAGGgcauGUGucuga
//
# STOCKHOLM 1.0

#=GF AC   RF00658
#=GF ID   mir-21
#=GF DE   microRNA mir-21
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   53.00
#=GF TC   65.40
#=GF NC   50.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000060;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16750530
#=GF RT   Identification of microRNAs from different tissues of chicken embryo and
#=GF RT   adult chicken.
#=GF RA   Xu H, Wang X, Du Z, Li N
#=GF RL   FEBS Lett. 2006;580:3610-3616.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [3]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues.
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF WK   MIRN21
#=GF SQ   11


BAAF04044466.1/2035-1963     UGUCAGAUAGCUUAUCAGACUGGUGUUGGCUGUUAAGAUUGCAAGG-CGACAACAGUC-UGUAGGCUGUCUGACA
AAVX01193435.1/262-191       UGUCAGAUAGCUUAUCAGACUGGUGUUGGCUGUUAGCUC-AGGUGG-CGACAACAGUU-GGUAGGCUAUCUGGCG
BAAF04048171.1/11412-11340   UGUCGGCUAGCUUAUCAGACUGGUGUUGGAGGUUCCAUU-UGCACGGCAACAACGGUC-UGUAAGCUGGCUGACA
AANH01008078.1/292800-292872 CGUCAGCUAGCUUAUCAGACUGGUGUUGGCUGUUCAAUCACCACGG-CAACAGCGGUC-UGUAAGCUGGCCGAAG
AAPN01116099.1/42432-42503   UAUCGGAUAGCUUAUCAGACUGAUGUUGACUGUUAGAUC-UCCUGG-CAACAGCAGUC-GAUGGGCUGUCUGACA
CAAE01007707.1/16214-16286   CGUCAGAUAGCUUAUCAGACUGGUGUUGGCUGUUGGGUCGUCAUGG-CAACAGCGGUC-UGUAAGCUGUCUGAAG
CR848791.15/19987-19917      UGUCAUGUAGCUUAUCAGACUGGUGUUGGCU--UUGAGU-UUUUGG-CAACAGCAGUCUAAUAGGCUGUCUGACA
ABQF01026541.1/60151-60222   UGUCGGAUAGCUUAUCAGACUGAUGUUGACUGUUGGAUC-UCAUGG-CAACAACAGUC-GGUAGGCUGUCUGACA
CAAB02007460.1/51060-51132   CAUCAGAUAGCUUAUCAGACUGGUGUUGGCUGUUAGGUUCCCAUGG-CAACAGCAGUC-UGUAAGCUGUCUGAAG
AM600961.1/11-82             UGUCGGGUAGCUUAUCAGACUGAUGUUGACUGUUGAAUC-UCAUGG-CAACAGCAGUC-GAUGGGCUGUCUGACA
AY865965.1/427-498           UGUCGGGUAGCUUAUCAGACUGAUGUUGACUGUUGAAUC-UCAUGG-CAACACCAGUC-GAUGGGCUGUCUGACA
#=GC SS_cons                 <<<<<<<<<<<<<<<--<<<<<-<<<<<-<<________.____>>.>>>>>->>>>>.->>>>>>>>>>>>>>>
#=GC RF                      ugUCaGauAGCuuAuCAGACuGgUGUuGgCuGUUagaUc.ucaugG.CaACAaCaGUC.ugUaaGCUguCuGAca
//
# STOCKHOLM 1.0

#=GF AC   RF00659
#=GF ID   mir-365
#=GF DE   microRNA mir-365
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   61.90
#=GF NC   52.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000061;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15735639
#=GF RT   Systematic discovery of regulatory motifs in human promoters and 3' UTRs
#=GF RT   by comparison of several mammals.
#=GF RA   Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES,
#=GF RA   Kellis M
#=GF RL   Nature. 2005;434:338-345.
#=GF RN   [2]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF WK   Mir-365_microRNA_precursor_family
#=GF SQ   9


ABBA01014956.1/33243-33152 ACAGCAAGAAAAAUGAGGGACUUUCAGGGGCAGCUGUGUUUU-CUGACUC-AGUCAUAAUGCCCCUAAAAA-UCCUUAUUGUUCUUGCAGUGUGC
AANU01212177.1/1330-1238   ACCGCAGGGAAAAUGAGGGACUUUUGGGGGCAGAUGUGUUUCCAUUCCAC-UAUCAUAAUGCCCCUAAAAA-UCCUUAUUGCUCUUGCAGUAUUC
AAVX01470594.1/166-258     ACAGCAAGAAAAAUUAGGG-UUUUUUGGGACAGCUAUGUUUUAUCUUCACAAGUCAUAAUGCCCCUAAAAA-UCCCUAUUUCUCAUGCAAUGGUC
AAVX01240641.1/1179-1241   GAA--------AAUGAGGGACUUUUGGGGGCAGGUGUGUUUCAGCUGCAU-AAUCAUAAUGCCCCUAAAAU-C----------------------
AANG01161851.1/1480-1570   ACAGCAAGAAAAAUGAGGGACUUUCAGGGGCAGCUGUGUUUU-CUGACUC-AGUCAUAAUGCCCCUAAAAAUCCCUUG--AGUUUGGCCAGUGUG
CU138533.13/80864-80956    UCCGCAGGGAGAAUGAGGGGCUUUUGGGGGCACUUGUGUUUCAGUUUCAC-CAUCAUAAUGCCCCUAAAAA-UCCUUAUUGCUCUUGCACUGAUC
AAPE02030584.1/10520-10428 ACAGCAAGAAAAAUAAGGGACUUUCAGGGGCAGCUGUGUUUUCUGACUCA-AGUCAUAAUGCCCCUAAAAA-UCCUUAUUGCUCUUGCAGUGGGC
CAAB02002081.1/60571-60479 GCAGCAAGAAAAGUGAGGGACUUUUAGGGGCAGCUGUGUUUUAUUAACCC-AGUCAUAAUGCCCCUAAAAA-UCCUUAUUGCUCUUGCAAUUGUC
AAWZ02011866.1/2166-2258   GCAGCAAGAAAAAUGAGGGACUUUCAGGGGCAGCUGUGUUUUACUAACCC-AGUCAUAAUGCCCCUAAAAA-UCCUUAUUGUUCUUGCAAUGUUC
#=GC SS_cons               :::<<<<<<--<<<<<<<<--<<<<<<<<<<<--<<<<____________.___>>>>->>>>>>>>>>>-.>>>>>>>>-->>>>>>:::::::
#=GC RF                    acAGCaaGaAAaaugaGGgACUUUuaGGGGCAGcUgUGUUUuauuuaCac.agUCAuAAUGCCCCuaAAAA.cCCucauugcuCuuGCAaugguc
//
# STOCKHOLM 1.0

#=GF AC   RF00660
#=GF ID   mir-214
#=GF DE   microRNA mir-214
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   53.00
#=GF TC   53.10
#=GF NC   52.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000062;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18511220
#=GF RT   Identification of novel chicken microRNAs and analysis of their genomic
#=GF RT   organization.
#=GF RA   Shao P, Zhou H, Xiao ZD, He JH, Huang MB, Chen YQ, Qu LH
#=GF RL   Gene. 2008;418:34-40.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MiR-214
#=GF SQ   8


AADB02000995.1/244869-244760 GGCCUGGCUGGACAGAGUUGUCAUGUGUCUGCCUGUCUACACUUGCUGUGCAGAACAUCCGCUCACCUGUACAGCAGGCACAGACAGGCAGUCACAUGACAACCCAGCCU
CAAE01014542.1/502955-502846 GCACCUGGCUGGAGGAGUUGCAGUGUGUCUGCCUAUCUCCACUUGCUGUGCAGAAUAUCCUCCAACCUGUACAGCAGGCACAGACAGGCAGAUAGACAUCAGCCCAUCGA
BAAF04061048.1/6848-6953     G---AAAAGAGCUAAAGUUGCAGUGUGUCUGCCUAUCUACACUUGCUGUGCAGAAUAUCCUCCAACCUGUACAGCAGGCACAGACAGGCAGAUAAACAA-AACAGAGCGC
AANH01005434.1/26064-26173   CCAACUGGCUGAAGGAGUUGCAGUGUGUCUGCCUAUCUACACUUGCUGUGCAGAAUAACCUCCAACCUGUACAGCAGGCACAGACAGGCAGAUAGACGUCAGCCUGCCCC
BAAF04076833.1/6408-6509     CGUCAGAC------CUGUUGUGGUGUGUCUGCCUGUCUACACUUGCUGUGCAGACCUUCUG--CUCCUGUACAGCAGGCACAGACAGGCAGACAGAUGGCAGCCCCCCCC
BX470128.8/142390-142495     GCCAUUGACUGAGAGC---GUUGUCUGUCUGCCUGUCUACACUUGCUGUGCAGAACUUCCU-GCACCUGUACAGCAGGCACAGACAGGCAGACAGAUGGCAGCCCGCCUG
CAAB02001273.1/58408-58515   GUGGCAGGAUGAGACUGUUGUGGUGUGUCUGCCUGUCUACACUUGCUGUGCAGACCUUCUG--CUCCUGUACAGCAGGCACAGACAGGCAGACAGAUGGCAGCCCCACUG
AY866218.1/423-532           GGCCUGGCUGGACAGAGUUGUCAUGUGUCUGCCUGUCUACACUUGCUGUGCAGAACAUCCGCUCACCUGUACAGCAGGCACAGACAGGCAGUCACAUGACAACCCAGCCU
#=GC SS_cons                 :<<___>>--------<<<<<<<<<<<<<<<<<<<<<<---<<<<<<<<<<<<_____________>>>>>>>>>>>>--->>>>>>>>>>>>>>>>>>>>>>:::::::
#=GC RF                      gccauugguuGaaagaGcuGccguguguCuGCCuguCuACACuuGCuGugCaGAacaUCcuCuaaCCuGuaCaGCagGCACaGacaGGCaGacacacggCagCccauCuu
//
# STOCKHOLM 1.0

#=GF AC   RF00661
#=GF ID   mir-31
#=GF PI   mir-72
#=GF DE   microRNA mir-31
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   56.00
#=GF TC   56.40
#=GF NC   52.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.58 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000064;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF RN   [2]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-31
#=GF SQ   28


AAPP01016551.1/245474-245363 CAAAUAAUGAAUUUGGCAAGAUGUCGGAAUAGCUGAGAGCACAGAGGAUCGAGCGAGU----------CAUCGACCGAGACGAAUUC--CAAAGCGGCUAUGCC-UCAUCUAGUCAAUUACAUUA
AASV01052250.1/993-1080      UCCGUUGGUAAAUUGGCAAGAUGUCGGCAUAGCUGACGUUGAAAAG----------------------------------CGAUUUU--GAAGAGCGCUAUGCU-GCAUCUAGUCAGUUGUUCAA
AADD01098494.1/16992-16914   GGAACUGGAGAGGAGGCAAGAUGCUGGCAUAGCUGUUGAA--------------------------------------------CUG--GGAACCUGCUAUGCCAACAUAUUGCCAUCUUUCCUG
AADE01001857.1/16402-16311   CAAAUAAUGAAUUUGGCAAGAUGUCGGAAUAGCUGAGAGCAAAAAGAA------------------------------GAUGAUUUG--AAAUGCGGCUAUGCC-UCAUCUAGUCAAUUGCAUUC
AAPT01021609.1/128313-128227 UCUGUUGGUGAAUUGGCAAGAUGUCGGCAUAGCUGACGUUUGAAA-----------------------------------GCGCAUC--UUAUAGCGCUAUGCU-GCAUCUAGUCAGUUAUUCAA
AC154049.1/4734-4855         CAAAUAAUGAAUUUGGCAAGAUGUCGGAAUAGCUGAGAGCACAGCGGAUCGAACAUUUUAUCGUCCGAAAAAAUGUGAUUAUUUUUG--AAAAGCGGCUAUGCC-UCAUCUAGUCAAUUGCAUUA
AAZX01004302.1/23296-23375   AUGAGCGUGUAGAAGGCAAGAUGUCGGCAUAGCUGAUGCUUU------------------------------------------UGA--AAUUUCGGCUGUGUC-ACAUCCAGCCAGCCAAACGC
AAJJ01000269.1/62248-62171   CGGGAGGCAGAGCAGGCAAGAUGUCGGCAUAGCUGAAGGU--------------------------------------------GUU--UGAAACGGCUAUGUC-UCAUCCGGCCAACUUAAGCC
AADK01000344.1/33937-34016   CCGGUGGCUGGGAAGGCAAGAAGUCGGCAUAGCUGUUUGA--------------------------------------------AUAAGAUACACGGCUGUGUC-ACUUCGAGCCAGCUCAAUCC
AAZO01004538.1/561-481       UAGACGGUGAGGUAGGCAAGAUGUCGGCAUAGCUGAAAUGAU-----------------------------------------UAUA--AUAUGCGGCUGUGUC-ACAUCGAGCCAGCUUGAGCC
AANI01013847.1/25203-25083   CAAAUAAUGAAUUUGGCAAGAUGUCGGAAUAGCUGAGAGCACAAAGUCAUAAAUCCAGAAUU-UCUAUUUUGUGUAUUUUUAUUGAG--UACAGCGGCUAUGCC-UCAUCUAGUCAAUUGCAUUC
AAPN01033181.1/1752-1830     AGAGCUGGAGAGAAGGCAAGAUGUUGGCAUAGCUGUUGAG--------------------------------------------UUA--AGAACCUGCUAUGCCGACAUGUUGUCAUCUUUCUUG
AAQB01006276.1/72264-72183   CUGUUUUUCGAAUUGGCAAGAUGUCGGCAUAGCUGAUAAUAUU----------------------------------------UUUA--GAAAAGCGCUAUGCU-GCAUCUAGUCAGUUUAUUCA
AAPU01009413.1/121752-121873 CAAAUAAUGAAUUUGGCAAGAUGUCGGAAUAGCUGAGAGCACAAAUAUCAUAGAAUCCAGAAUUUAUAUUUUGUGUAUUUUAUUGAG--UACAGCGGCUAUGCC-UCAUCUAGUCAAUUGCAUUC
AAQB01010380.1/1470-1552     CAACUAGUGGAUUUGGCAAGAUGUCGGAAUAGCUGAAAGUCACAC------------------------------------AAAAUC--AUAAAAUGUU----UGCCGUUUUGUUAUUGUUGUGA
AANH01007167.1/95060-94981   GGUCCAGGAAGGAAGGCAAGAUGUUGGCAUAGCUGUUAAA--------------------------------------------UUG-AAAUCCCUGCUAUAUCAACAUAUUGCCAUUUUUCUCU
AAFR03027366.1/158259-158181 AGAGCUGGAGAGGAGGCAAGAUGUUGGCAUAGCUGUUGAA--------------------------------------------CUG--AGAACCUGCUAUGCCAACAUAUUGCCAUCUUUCUUG
AAYZ01418306.1/450-372       GGAUCUGGAGAGAAGGCAAGAUGCUGGCAUAGCUGUUGAA--------------------------------------------CUG--AUAACCUGCUAUGCCAACAUAUUGCCAUCUUUCCUG
AANG01430048.1/646-568       AGAACUGGAGAGGAGGCAAGAUGCUGGCAUAGCUGUUGAC--------------------------------------------CUG--AGAACCUGCUAUGCCAACAUAUUGCCAUCUCUCUUG
AAIZ01001980.1/15086-15173   UCUGUUGGUAAAUUGGCAAGAUGUCGGCAUAGCUGAAGUUGAAAAG----------------------------------CGAUCUU--UGAGAACGCUAUGCU-GCAUCUAGUCAGUUAUUCAA
AAKN02003567.1/33096-33018   AGAACUGGAGAGGAGGCAAGAUGCUGGCAUAGCUGUUGAU--------------------------------------------GUG--AGAACCUGCUAUGCCAACAUAUUGCCAUCUUUCCUG
AADG06006981.1/17977-18057   CUGGGCGCCUCGAAGGCAAGAUGUCGGCAUAGCUGAUGCGAU-----------------------------------------UUUA--AAAUUCGGCUGUGUC-ACAUCCAGCCAACCGAACGC
AAWZ02010666.1/24551-24473   AGAGCUGGAGCGGAGGCAAGAUGUUGGCAUAGCUGAUGAG--------------------------------------------UUA--AGAACCUGCUAUGCCAACAUAUUGCCCUCUUUCCUG
AAGJ04172704.1/16120-16038   ACCAGUGGAGAAAAGGCAAGAUGUUGGCAUAGCUGUGAUUUAA----------------------------------------AUAU--UAACCCAGCUGUGUCUUCAUACUGCCAUUUAUUCAC
AC189661.2/146363-146285     AGAGCUGGAGGGGAGGCAAGAUGUUGGCAUAGCUGUUAAC--------------------------------------------CUA--AAAACCUGCUAUGCCAACAUAUUGUCAUCUUUCCUG
AE013599.4/13671391-13671304 UCCGUUGGUAAAUUGGCAAGAUGUCGGCAUAGCUGACGUUGAAAAG----------------------------------CGAUUUU--GAAGAGCGCUAUGCU-GCAUCUAGUCAGUUGUUCAA
AE014298.4/8887464-8887343   CAAAUAAUGAAUUUGGCAAGAUGUCGGAAUAGCUGAGAGCACAGCGGAUCGAACAUUUUAUCGUCCGAAAAAAUGUGAUUAUUUUUG--AAAAGCGGCUAUGCC-UCAUCUAGUCAAUUGCAUUA
AY866011.1/440-518           GGAACUGGAGAGGAGGCAAGAUGCUGGCAUAGCUGUUGAA--------------------------------------------CUG--GGAACCUGCUAUGCCAACAUAUUGCCAUCUUUCCUG
#=GC SS_cons                 ::::::::::::::<<<---<<<--<<<<<<<<____________....................................______.._______>>>>>>>>.->>>--->>>::::::::::
#=GC RF                      caaauaGugaAuuuGgCAAGAUGUCGGcAUAGCUGAuaguacAAA....................................auUuUg..aaAaaCgGCUAUgCC.uCAUcUaGcCAaUUuuauua
//
# STOCKHOLM 1.0

#=GF AC   RF00662
#=GF ID   mir-132
#=GF DE   microRNA mir-132
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   53.00
#=GF TC   54.70
#=GF NC   51.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000065;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   MiR-132
#=GF SQ   22


BAAF04037894.1/2153-2065   ACUGUCUCCAUGGUAACCGUGGCAUUAGAUUG-UUACUGUAGCAACAGCA----CC------ACUGGUAACAGUCUACAGCCAUGGUCGCUAGGG-GGCAA
BAAF04037894.1/2420-2326   AGUCAGUGCACCAAUACCUUGGCUCUAGACUGCUUACUGCUAAAAGUGCU----CCAA--AGUACAGUAACAGUCUACAGUCAUGGCUACUGACGCCUGGC
AAVX01086956.1/967-1051    CCUGGUUCCAUGGUGACCGUGGCUUUCGAUUG-UUAUUGUCAGUGUGGU--------------GUAGUAACAGUCUACAGCCAUGGUUGUUUGGA-CAGGA
AANG01158591.1/2876-2793   CGCGUCUCCAGGGCAACCGUGGCUUUCGAUUG-UUACUGUGGGAAC---------C------GGAGGUAACAGUCUACAGCCAUGGUCGCCCCGC-AGCAC
AAVX01172706.1/316-404     ACGUCAGUCACCAGCACCUUGGCUCUAGACUGAUUACUGUGUGUGUGUG------U------CUGAGUAACAGUCUACAGUCAUGGCUACUGAGGGUUGGC
BX663516.23/51989-52075    GCUGUCUCCAUGCUGACCGUGGCUUUAGAUUG-UUACUGUAGCGUUGGC------A------CGUGGUAACAGUCUACAGCCAUGGUCGCCAAGG-GGCAG
BX663516.23/51665-51759    UGUCAGAACUUCAUGACCUUGGCUCUAGACUGCUUACUGCUUAUGGAGU------CCGACAGUACAGUAACAGUCUACAGUCAUGGCUACUGAAGUCUGGC
BX088586.8/108540-108628   GCUGUCUCCAUGGCGACCGUGGCAUUAGAUUG-UUACUGUAGGAACAGAA----UU------UUUGGUAACAGUCUACAGCCAUGGUCGCUAGUG-GGCAG
AANH01000634.1/22334-22422 GCUGUCUCCAUGGCGACCGUGGCUUUAGAUUG-UUACUCUAGCAACAGC-----AG------CAUGGUAACAGUCUACAGCCAUGGUCGUUAGGGGCAGGU
AADB02296530.1/487-405     CGCGUCUCCAGGCAAACCGUGCUAUUCGAUUG-UUACUGUGGAACUGGA----------------GGUAACAGUCUACAGCCAUGGUCGCCCCGC-AGCAC
BAAF04066384.1/1751-1845   CGCUAGAGCAUCAGCACCUUGGCUUUAGACUGCUUACUGCUUAUACAAUCUCACAG------UACAGUAACAGUCUACAGUCAUGGCUACUGAAGCCUGGC
CAAE01008555.1/5373-5461   GUUGUCUCCAUGGUUACCGUGGCAUUAGAUUG-UUACUGUAGCAACUGCA----CC------AGCGGUAACAGUCUACAGCCAUGGUCGCUAGGG-GGCAA
ABDC01230941.1/4406-4323   CGCGUCUCCAGGGCAACCGUGGC-UUCGAUUG-UUACUGUGGGAACCGG---------------AGGUAACAGUCUACAGCCAUGGUCGCCCCGCAACAGG
ACBE01418795.1/3213-3125   GGGCAGCGCGCCGGCACCUUGGCUCUAGACUGCUUACUGCCCGGGCCGC------C------CUCAGUAACAGUCUCCAGUCACGGCCACCGACGCCUGGC
ABRQ01002353.1/3673-3585   GGGCAGUGCGCCGGCACCUUGGCUCUAGACUGCUUACUGCCCGGGCCGC------C------CUCAGUAACAGUCUCCAGUCACGGCCACCGACGCCUGGC
CAAB02009480.1/82904-82998 GGCCAGAGCAUCAGCACCUUGGCUUUAGACUGCUUACUGUUUAUACAGU------AUCACAGUACAGUAACAGUCUACAGUCAUGGCUACUGACGCCUGGU
CAAB02009480.1/83207-83296 GCUGUCUCCAUGGCGACCGUGGCUUUAGAUUG-UUACUCUUUGCAAUAGC----UC------CAUGGUAACAGUCUACAGCCAUGGUCGUUAGGGGCAGGU
CAAB02007213.1/16223-16129 GGUCAGCGCAUCAACACCUUGGCUCUAGACUGCUUACUGCUAAAACCGC------UCAUAAGUACAGUAACAGUCUACAGUCAUGGCUACUGACGCCUGAC
AAPE02038104.1/754-840     GGGCAGCGCGCCGGCACCUUGGCUGCAGACUGCUUACUGCCCGG--CGC------C------CCGAGUAACAGUCUCCAGUCACGGCCGCCGACGCCUGGC
AL603905.19/93367-93450    CGCGUCUCCAGGGCAACCGUGGCUUUCGAUUG-UUACUGUGGGAACCGG---------------AGGUAACAGUCUACAGCCAUGGUCGCCCCGC-AGCAC
HM627212.1/729-817         GGGCAGCGCGCCGGCACCUUGGCUCUAGACUGCUUACUGCCCGGGCCGC------C------UUCAGUAACAGUCUCCAGUCACGGCCACCGACGCCUGGC
HM627212.1/1013-1096       CGCGUCUCCAGGGCAACCGUGGCUUUCGAUUG-UUACUGUGGGAACCGG---------------AGAUAACAGUCUACAGCCAUGGUCGCCCCGC-AGCAC
#=GC SS_cons               ::::::::::::::::<<-<<<<----<<<<<.<<<<<___________......_......___>>>>>>>>>>---->>>>->>:::::::::::::::
#=GC RF                    ggugugucCAugguaACCuUGgCUuUAGAcUG.UUACuGUuugaacaGu......c......uauaGUAACAgUCUACAGcCAUGGucgCugagGccuggc
//
# STOCKHOLM 1.0

#=GF AC   RF00663
#=GF ID   mir-183
#=GF DE   microRNA mir-183
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   60.00
#=GF NC   48.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00093
#=GF DR   MIPF; MIPF0000066;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA. 2003;9:175-179.
#=GF RN   [2]
#=GF RM   12554860
#=GF RT   Numerous microRNPs in neuronal cells containing novel microRNAs.
#=GF RA   Dostie J, Mourelatos Z, Yang M, Sharma A, Dreyfuss G
#=GF RL   RNA. 2003;9:180-186.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   16


AABS01000291.1/71818-71726   ACUCUGGUGUUUUCGGUGUAUGGCACUGGUAGAAUUCACUGCCAA--------GC-CAGUGGUUC-AAC-AAGCGCCGUAAGCUGGAAACACUACUUUCUGCAG
AAYZ01118126.1/291-190       CCUGACUCCUGUUCUGUGUAUGGCACUGGUAGAAUUCACUGUGAACAAUCUCGGU-CAGUGAAUU-ACCGAAGGGCCAUAAACAGAGCAGAGACAGAUCCGCGA
BAAF04047675.1/11891-11992   AAUUCCUCCUAUUCUGUGUAUGGCACUGGUAGAAUUCACUGUCACAGCACUCUAU-CAGUGAAUU-ACCAUAGGGCCAUAAACAGAGUAGAGACAGAACCUCAG
AL590150.2/106933-106832     ACAGACUCCUGUUCUGUGUAUGGCACUGGUAGAAUUCACUGUGAAAGCACACUAU-CAGUGAAUU-ACCAAAGGGCCAUAAACAGAGCAGAGAAAGAACCACGU
AACT01062910.1/7572-7669     AGAAAAGUGUUGACGAAAUAUGGCACUAGUAGAAUUCACUGUAGA---CAACACC-CAGUGGUUUCAC--AGGCGCCAUAAAUUGAAAACAUUACUUUCUACAG
CAAE01014715.1/320476-320375 UCGUCCUCCUCGUCUGUGUAUGGCACUGGUAGAAUUCACUGUCUCGGCAUCCUCU-CAGUGAAUU-ACCACAGGGCCAUAAACAGCCUAGAGACCCACCCGCCC
AAFR03031888.1/52626-52727   CAUCACUCCUGUUCUGUGUAUGGCACUGGUAGAAUUCACUGUGAAAACACACUAU-CAGUGAAUU-ACCAAAGGGCCAUAAACAGAGCAGAGAAAGAUCCACAA
AAVX01005658.1/413-514       UCUGACUCCUGUUCUGUGUAUGGCACUGGUAGAAUUCACUGUGAAAACACACAAU-CAGUGAAUU-ACCAUAGGGCCAUAAACAGAGCAGAGAAAUAACCAGUU
AANH01009431.1/15599-15700   AAUGACUCCUGUUCUGUGUAUGGCACUGGUAGAAUUCACUGUGAGAGCUCACUAU-CAGUGAAUU-ACCAUAGGGCCAUAAACAGAGCAGAGAAAGAACCGCUU
AALT01103892.1/671-772       UGUCACUCCUGUUCUGUGUAUGGCACUGGUAGAAUUCACUGUGAACAGUCUGGGU-CAGUGAAUU-ACCGAAGGGCCAUAAACAGAGCAGAGACAGAUCCACGA
AAPY01581226.1/1863-1965     CGUGACUCCUGUUCUGUGUAUGGCACUGGUAGAAUUCACUGUGACAGUCUUCGGUUCAGUGAAUU-ACCGAAGGGUCAUAAACAGAGCAGAGACAGAUCCGCGA
CAAB02005445.1/236331-236430 AUCUCCUCCUGUUCUGUUUAUGGCACUGGUAGAAUUCACUGUCACAGCAUACU---CAGUGAAUU-ACCAUAGGGCCAUAAACAGCGUGGAGACACAUCCACGC
ADDD01009450.1/2612-2544     CUCCUGUUCUGUG-----UAUGGCACUGGUAGAAUUCACUGUGCAACCCCGCGGU-CAGUGAAUU-ACCAUAGGGC----------------------------
AY866343.1/452-553           CGUGACUCCUGUUCUGUGUAUGGCACUGGUAGAAUUCACUGUGAACAGUCUCGGU-CAGUGAAUU-ACCGAAGGGCCAUAAACAGAGCAGAGACAGAUCCACGA
AY866344.1/114-215           UGUGACUCCUGUUCUGUGUAUGGCACUGGUAGAAUUCACUGUGAACAGUCUCAGU-CAGUGAAUU-ACCGAAGGGCCAUAAACAGAGCAGAGACAGAUCCACGA
AY866346.1/463-564           CGUGACUCCUGUUCUGUGUAUGGCACUGGUAGAAUUCACUGUGAACAGUCUCGGU-CAGUGAAUU-ACCGAAGGGCCAUAAACAGAGCAGAGACAGAUCCUCGA
#=GC SS_cons                 :::::::::::::<<<<-<<<<<<--<<<<<--<<<<<<<<______________.>>>>>>>>>.>>>>---->>>>>>->>>>:::::::::::::::::::
#=GC RF                      auuuacuccUgUUCuGuGUAuGGCACuGGUaGAAuuCACUGUgaaaacucaCugU.CAGUGaaUu.ACCaaAGgGCCaUAAaCaGagcAgAgaaauauCcaCaa
//
# STOCKHOLM 1.0

#=GF AC   RF00664
#=GF ID   mir-223
#=GF DE   microRNA mir-223
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   73.00
#=GF TC   80.30
#=GF NC   56.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000067;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12624257
#=GF RT   Vertebrate microRNA genes.
#=GF RA   Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP
#=GF RL   Science. 2003;299:1540.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-223
#=GF SQ   19


AAFC03066285.1/26175-26068   CCCAGCCU----C-CUGCAGUGCCAUGCUCCGUGUAUUUGACAAGCUGAGUUGGACACUCCAUGUAG--UAG--UGUCAGUUUGUCAAAUACCCCAAGUGUGGCAUAUGCCUAGCA-G
AAFR03059733.1/788-675       UCUGGCCCAGAUC-CUUCAGUGCCACACUCCGUGUAUUUGACAAGCUGAGUUGGACACUCCGUGUCG--UAGAGUGUCAGUUUGUCAAAUACCCCAAGUGAGGCAUUUGCCUAGCA-A
AAHY01214491.1/9050-9159     UCUGGCCA----U-CUGCAGUGUCACGCUCCGUGUAUUUGACAAGCUGAGUUGGACACUCUGUGUGG--UAGAGUGUCAGUUUGUCAAAUACCCCAAGUGUGGCUCAUGCCUAUCA-G
AAIY01539231.1/5018-5127     CCUUGUCU----C-CUGCAGUGCCACGCUCCGUGUAUUUGAUAAACUGAAUUAGACACUCCAUGUGG--UAGAGUGUCAGUUUGUCAAAUACCCCAAGUGCGGCUCAUGCCUAGCA-A
AALT01652710.1/2269-2378     CCUGGUCU----U-CUUCAGUGUCACACUCCGCGUAUUUGACAAGCUGAAUUGGACACUCCAUGUGG--UAGAGUGUCAGUUUGUCAAAUACCCCAAGUGCGGCAUAUGUCUAACA-G
AANH01000582.1/391608-391499 UGUGGCG----GG-AUCAGGCCCCCCACUUAGUGUAUUUGACAAGCUGAGUUGGACACUCUGUAUCU--CUGAGUGUCAGUUUGUCAAAUACCCCAAGUGAGGUGUCACUUGUCUA-C
AANN01684196.1/3693-3802     CCUCACCU----C-UUGCAAUGUCACGCUCCGUGUAUUUGACAAGCUGAGUUAGACACUCCAUAUGG--AAGAGUGUCAGUUUGUCAAAUACCCCAAGUGCGGCAUAUGCUCAGCA-U
AAPN01125423.1/1862-1972     CGUGACC----ACACCGCAGUGCCGCGCUCCGUGUAUUUGACAAGCUGAGUUGGACACUCCGUGUGG--UUGAGUGUCAGUUUGUCAAAUACCCUAAGUGAGGCA-UUGCUCAGCCAC
BAAF04035315.1/6268-6159     ACUUCUG----AG-ACCAGGCCCCCCACUUAGUGUAUUUGACAAGCUGAGUUGGACACUCUAUCUCU--GUGAGUGUCAGUUUGUCAAAUACCCCAAGUGAGGUGUCACUUGUCGA-C
BX465863.11/57630-57725      UCCUCCU----GA-UCUAGACUCUUCUCUUAGAGUAUUUGACAGACUGUGGUUGACACUCGAUCUAA--AGGGGUGUCAGUUUGUCAAAUACCCCAAGAGAGG---------------
AAKN02052886.1/11821-11930   CCUGAUGU----C-UUGCAGUACCACACUCCGUGUAUUUGACAAGCUGAGUUGGACACUCCAUGUGG--UAGAGUGUCAGUUUGUCAAAUACCCCAAGUGCGGCACAUGCCUAGCA-G
AADN03003772.1/27092-27201   UGGUGACA----G-CUGCAGUGCAGCACUGCGUGUAUUUGACAAGCUGAGUUUGACACUCAGUCUGG--CAGAGUGUCAGUUUGUCAAAUACCCCAAGUGAGGCACUUGCUGAGCA-A
AAWZ02028490.1/3724-3834     AACGGAC----GC-ACGCAGGGCUUCCCUCCGUGUAUUUGACGAUCUGA-UCGCACACUCCGUCUGCACCAGAGUGUCAGUUUGUCAAAUAUACAAAGGGCGGCCUCUGACCCGCC-A
AAQR03171710.1/32631-32522   UUUGGCCU----C-CUGCAGUGCCACACUCUGUGUAUUUGACAGGCUGAGUGGAACACUCAGUUUAA--UAGAGUGUCAGUUUGUCAAAUACCCCAAGUGCGGCAUAUGCUGAACA-A
CAAB02000575.1/72816-72925   CGUUUGA----UG-ACCAGGCCCCUCACUUAGUGUAUUUGACAAGCUGUUCUUGACACUCUUUAUAC--GCGAGUGUCAGUUUGUCAAAUACCCCAAGUGAGGUGUCACUUGUCUG-C
DQ680072.1/138-247           CCUGGCCU----C-CUGCAGUGCCACGCUCCGUGUAUUUGACAAGCUGAGUUGGACACUCCAUGUGG--UAGAGUGUCAGUUUGUCAAAUACCCCAAGUGCGGCACAUGCUUACCA-G
AY866259.1/452-561           CCUGGCCU----C-CUGCAGUGCCACGCUCCGUGUAUUUGACAAGCUGAGUUAGACACUCCGUGUGG--UAGAGUGUCAGUUUGUCAAAUACCCCAAGUGCGGCACAUGCUUACCA-G
AY866260.1/406-515           CCUGGCCU----C-CUGCAGUGCCACGCUCCGUGUAUUUGACAAGCUGAGUUGGACACUCCGUGUGG--UAGAGUGUCAGUUUGUCAAAUACCCCAAGUGCGACACAUGCUUAGCA-G
AY866256.1/405-514           CCCGGCCU----C-CUGCAGUGCCACGCUCCGUGUAUUUGACAAGCUGAGUUGGACACUCCGUGUGG--UAGAGUGUCAGUUUGUCAAAUACCCCAAGUGCGGCAUAUGCUUACCA-G
#=GC SS_cons                 ::::::::....:.:::::<<<<<-<<<<--<-<<<<<<<<<<<<<<<------<<<<<<_______..__>>>>>>>>>>>>>>>>>>>>>->-->>>>->>>>>::::::::::.:
#=GC RF                      ucuggccu....c.cugcAgugCcaCgCUccGUGUAUUUGACaagCUGAGUUgGACACuCcaUgUgg..uaGaGUGUCAGuuuGUCAAAUACCCcAAGcGagGcacaUgcuuagca.a
//
# STOCKHOLM 1.0

#=GF AC   RF00665
#=GF ID   mir-290
#=GF PI   mir-72; mir-373; mir-512
#=GF DE   microRNA mir-290
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   53.00
#=GF TC   53.00
#=GF NC   52.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00096
#=GF DR   MIPF; MIPF0000068;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12919684
#=GF RT   Embryonic stem cell-specific MicroRNAs.
#=GF RA   Houbaviy HB, Murray MF, Sharp PA
#=GF RL   Dev Cell. 2003;5:351-358.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   15183728
#=GF RT   Human embryonic stem cells express a unique set of microRNAs.
#=GF RA   Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS,
#=GF RA   Moon SY, Kim VN, Kim KS
#=GF RL   Dev Biol. 2004;270:488-498.
#=GF WK   MicroRNA
#=GF SQ   27


AAIY01463435.1/1145-1228   UCAACCUGUAGCACUCAAACUUUGGGGGCACUUUCUGUUCUC---UAAGCUUG---GAAGUGCU-GCCUUCGUUUGGGGGUUACCGAUUGA
AC191152.6/69098-69179     UCGGCCUGUGCCACUCAAACUGUGGGGGCACU-UUCUGUUCU---AG-GUAGG---AAAGUGCC-GCCAUUUUUUGAGUGUCCCCGGCUGA
AAHY01059233.1/6026-5943   CCAGCCUGUGAUACUCAAA--CUGGGGGCUCU-UUUGGAUUU---UCAUCGGAAGAAAAGUGCC-GCCAGGUUUUGAGUGUCACCGGUUGA
AAHY01059233.1/4598-4519   CCAUAUAGCCAUACUCAAA--AUGGAGGCCCUAUCUAAGCUU---UUAAGUGG---AAAGUGCU-UCCCU--UUUGUGUGUUGCCAUGUGG
AAHY01059233.1/6294-6215   CUAUGUAGCGGCCAUCAAA--GUGGAGGCCCUCUCUUGAGCC---UGAAUGAG---AAAGUGCU-UCCAC--UUUGUGUGCCACUGCAUGG
AAHY01059233.1/6587-6507   UCAUCUUGCGGUACUCAAACUAUGGGGGCACUUUUUU---UU---UUCUUUAA---AAAGUGCC-GCCUAGUUUUAAGCCCCGCCGGUUGA
AAHY01059233.1/5731-5653   ACAUACAGUGUCGAUCAAA--GUGGAGGCCCUCUCCGCGGCU---UG-GCGGG---AAAGUGCA-UCCAU--UUUGUUUGUCUCUGUGUAC
AANU01181644.1/1881-1964   UCAGCCUGUGGCACUCAAACUGUGGGGGCACUUUCUGCUCUC---UGGUGAAA---AAAGUGCC-GCCAUGUUUUGAGUGUUACCGAUUGA
AANU01181644.1/2090-2169   UCACCCUGUGAUCCUCAAA-UGUGG-AGCACUAUUCUGAUGU---CCAAGUGG---AAAGUGCU-GCGACA-UUUGAGCGUCACCGG-UGA
AAQQ01482589.1/1853-1772   CCAGCCUGUGGUACUCACA-UGUGGAAGCACUCUUCUGACAU---CAGCAUGG---AAAGUGCU-ACCAUA-UUUGAGUGUCACCGGGGGG
AAPY01553483.1/1557-1477   CCAGCCUGUGGCCCUCAAA-UGUGGGAGCACUCUUCUGACGU---CA-AGUGG---AAAGUGCU-GCAACA-UUUGAGUGUCACCGGGGGC
AAPY01553483.1/1299-1220   CCAGGUGGUGGUCCUCAAA--AUGGAAGCACU-CCCCGUGGU---CUGCCUGG---AAAGUGCUUGCCAU--UUUGUGUGUCACUGUCUGA
AANG01678937.1/1502-1583   CUCUCCCGUGGUACUCAAA-UGUGGAAGCACUCUUCAGACAA---AUCAGUGA---AAAGUGCU-ACUAUA-UUUGGGUGUCACUGGUGGG
AANN01201868.1/2038-1956   CCGGUCUGCGACACUCAAACUGUGGGGGCACU-UUCUGGUGU---UCAGGAGG---GAAGUGCC-GCCAUGAUUUGAGUGUCACCGGUCGG
ABDC01467998.1/1214-1133   CCAUCCCGUGACACUCAAA-UGUGGGAGCACUCUUCUGGAAU---CUAGGUGG---AAAGUGCU-UCAACA-UUUGGGUGUCAUCGGUGGG
ABDC01467998.1/1387-1307   CCGACCUGUGGCACUCAAACUGUGGGGGCACU-UUCUG--UU---AUGUGACG---AAAGUGCC-GCUACUUUUUGAGUGUUACCGAUUGA
ABDC01467998.1/748-669     CAAGACCGUGUUACUCAAA--AUGGAGGCACUUCCCUUUGUC---UUCACUGG---AAAGUGCU-UCUGU--UUUGGGUCUCGCUGUUUGA
AAYZ01246660.1/323-242     CCAGCUUGCGGUACUCAAACUCUGGGGGCACU-UUUUGGUGU---GU-GUAGA---AGAGUGCC-GCCACGGUUUGAGUGUCGCCGGUGGA
AADA01143465.1/1018-937    UCAGCCUGUGGCACUCAAACUGUGGGGGCACUUUCUGA--CU---CUCUGGUG---AAAGUGCC-GCCAUCUUUUGAGUGUUACCGCUUGA
ABBA01068200.1/8347-8265   UCAUACUGGGAUACUCAAA--AUGGGGGCGCUUUCCUUUUUGUC-UGUACUGG---GAAGUGCU-UCGAUU-UUGGGGUGUCCCUGUUUGA
AAHX01003731.1/23420-23337 UCACCUGGUGGCACUCAAA-UGUAGGAGCGCUCUUCUGAUCUGGUUUAAGUGG---AAAGUGUU-GCAUCG-UUUGGGUGUCAUC-UGUGG
AAWR02030859.1/16491-16572 UCAGCCUGCGGGACUCAAA-UGUGGAAGCACUCUUCGAACAU---CGGGAUGG---AAAGUGCU-GCGACA-UUUGAGUGUCGCCGGUGGG
AAWR02030859.1/17098-17177 UCAGGCUGUGAGACUCAAA--AUGGGGGCGCUUGCCGUGUUC---GUGACAGG---AAAGUGCU-UUCAU--UUUGUGUGUCCCCGUUUGA
AAHX01003731.1/24835-24756 CGGUGUAGUAGCCAUCAAA--GUGGAGGCCCUCUCUUGGGCC---CGAGCUAG---AAAGUGCU-UCCAC--UUUGUGUGCCACUGCAUGG
AAPE02067262.1/7854-7774   UCAGCCUGUGGCACUCAAA-UGAGCAGGCACU-CUCCGAUGC---CCAGGCGG---AAAGUGCU-GCAACA-UUUGAGUGUCACCGGGGGG
AABR05005166.1/6218-6135   CCAACCUGUGAUACUCAAA--CUGGGGGCUCU-UUUGGGUUUUCUUUGGAAGA---AAAGUGCC-GCCAGGUUUUGAGUGUUACCGAUUGA
AAPE02067262.1/8025-7945   UCGGCUUGUGGGACUCAAACUGUGGGGGCACU-UUCUG--UG---CUGAGAGC---AAAGUGCC-GCCACAGUUUGAGUUCCACCGGCCGA
#=GC SS_cons               :<<<<<-<<<<<<<<<<<<.-<<-<-<<<-<<__________...________...__>>->>>.->->>-.>>>>>>>>>>>>->>>>>:
#=GC RF                    uCaccCuGuGgcaCuCAAA.UguGGggGCaCUuUucugauuu...uuaaguGG...AAAGUGCc.gCcaca.UUUGaGugcCaCCGgguGa
//
# STOCKHOLM 1.0

#=GF AC   RF00666
#=GF ID   mir-32
#=GF DE   microRNA mir-32
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   83.90
#=GF NC   55.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000069;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues.
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF RN   [3]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science. 2001;294:853-858.
#=GF WK   Mir-32_microRNA_precursor_family
#=GF SQ   8


AAHX01036962.1/16073-16142 GGGGAUAUUGCACAUUACUAAGUUGCAUGUUGUCACGGCCUCAAUGCAAUUUAGUGUGUGUGAUAUUCUC
AAVX01589492.1/985-916     GGAGGUAUUGCACACUACCAAGUUGCAUGUUGUGAGAGCCUGGGUGCAGCUUGGUGUGUGCGAUACUUUC
AAPN01052295.1/18887-18956 GGAGAUAUUGCACAUUACUAAGUUGCAUGUUGUCAAGGCCUCUGUGCAAUUUAGUGUGUGCGAUAUUUUC
AAIY01185602.1/2030-1961   GGAGGUAUUGCACAUUACUAAGUUGCAUGUUGUCACGGCCUCAGUGCAACUUAGUAUGUGUGAUAUUUUC
AAFR03054052.1/72588-72657 GGAGAUAUUGCACAUUACUAAGUUGCAUGUUGUCACGGCUUUAGUGCAAUUUAGUAUGUGUGAUAUUUUC
AAWR02025452.1/3351-3282   GGAGAUAUUGCACAUUACUAAGUUGCACGUUGUCACGGCCUCAGUGCAAUUUAGUGUGUGUGAUAUUUUC
AAWZ02000933.1/24032-23963 GGGGAUAUUGCACAUUACUAAGUUGCAUGUUGUCACGGGCUCAGUGCAAUUUAGUGUGUGCGAUAUUUUC
AY866030.1/492-561         GGAGAUAUUGCACAUUACUAAGUUGCAUGUUGUCACGGCCUCAAUGCAAUUUAGUGUGUGUGAUAUUUUC
#=GC SS_cons               <<<<<<<<<<<<<<<-<<<<<<<<<<<<<--<<____>>-->->>>>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                    GgagaUAUugCACAcUACuAAguUGCAcgUUGucAcGgCCUcagUGCAacUUaGUgUGUGcgAUAuuuuC
//
# STOCKHOLM 1.0

#=GF AC   RF00667
#=GF ID   mir-33
#=GF DE   microRNA mir-33
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   51.20
#=GF NC   47.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000070;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [3]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   miR-33
#=GF SQ   50


ABBA01055655.1/48509-48577       CUGUGGUGCAUUGUAGUUGCAUUGCAU----GUUCUGGU-GGUACCC----A-UGCAAUGUUUCCACAGUGCAUC-ACAG
AADB02018141.1/18034-18100       CCGCGGUGCAUUGCUGUUGCAUUGCAC----GUGU--GU-GAGGCGG----G-UGCAGUGCCUCGGCAGUGCAGC-CCGG
AAPU01011618.1/111826-111755     CGGAGGUGCAUUGUAGUCGCAUUGUCU----GUAUCCUU-UAUUCUCU--GC-GGCAAUACAACUGCAGUGCAAGCUCCG
CAAE01014738.1/1624047-1623979   CUGUGGUGCAUUGUAGUUGCAUUGCAC----GUCCGGCU-GAACACA----G-UGCAAUGGAUCUGCUCUGCAGU-ACAG
AASR01043351.1/997-930           CGAAGGUGCAUUGUAGUCGCAUUGUCU----GUUCCAAU-UG-CUUC----A-GGCAAUACAACUUCAGUGCAAG-CUCU
AAPT01020652.1/14236-14166       CGAAGGUGCAUUGUAGUCGCAUUGUCU----GUCCAAAA-AUUGCAU----GCGGCAAUACAACUGCAGUGCAAGCUCCG
AABS01001128.1/11040-10976       CCCUUGUGCAUUGUAGUUGCAUUGCAC---UGUUGCAUU------GU----G-GGUAAUGUGACAACAAUACAAC-CGGG
AAAB01008846.1/10052751-10052823 UUCGGGUGCAUUGUAGUUGCAUUGCAC---UUACCGUGU-UGGCAACA--GG-UGCAGUACUUCUGCAAUGCAACCCGAA
AAIZ01009364.1/25544-25613       CGCAGGUGCAUUGUAGUCGCAUUGUCU----GUCCAUCU-UGAUUUC----A-GGCAAUACAACUGCAGUGCAAGCUCUG
AACT01006707.1/8663-8725         CCUGGGUGCAUUGUAGUUGCAUUGCAC---UGUCAUAAU------------G-UGCAAUGUUACAUCAGUGCAAU-AUGG
BAAB01084098.1/1985-1918         CGAGAGUGCAUUGUAGUUGCAUUGCAC----CGGU--UC-CAUUAAC----G-UGCAAUAUGACUACAAGGCAAAUCCCG
AANH01004216.1/19959-19891       CUGUGGUGCAUUGUAGUUGCAUUGCAU----GGUCCUUA-AAGCCGA----G-UGCAAUGUGUCUGCAGUGCAGU-ACAG
BAAE01000948.1/5094-5161         CUGUGGUGCAUUGUAGUUGCAUUGCAU----GAUCCUGA-AG-CUGA----G-UGCGAUGCGUCUGCAGUGCAAU-ACAG
BAAF04067532.1/6545-6478         CUGCAGUGCAUUGUAGUUGCAUUGCAU----GUAU-GUU-UCUCAAA----G-UGCAAUGUACCUGCAGUGCAAC-ACAG
AAJJ01000068.1/107964-107901     CUUAGGUGCAUUGUAGUUGCAUUGCAU----GUUAUUCA-AA---------G-UGCAGUGUCUCUCCAGUGCAAC-UUAG
AAPN01437665.1/3526-3458         CUGUCGUGCAUUGUAGUUGCAUUGCAC----GUUCCGGC-AGUACUG----G-UGCAAUGUUCCCACAGUGCAUU-ACAG
AAYZ01315512.1/404-338           CCGUGCUGCAUUGCUGGUGCAUUGCAC----GUGU--GC-GCAGCAG----G-UGCAGUGCCUCGGCAGUGCAGC-CCGG
AAFR03065433.1/17202-17269       CUGGGGUGCAUUGUAGUUGCAUUGCAC----GUCG-UGU-CCGGGCC----G-UGCAAUGUUUCCACAGUGCAUC-CCAG
AAPN01422427.1/10575-10641       CUGUAGUGCAUUGUAGUUGCAUUGCAU----GUGU--CU-GACCAGG----G-UGCAAUGCCCCUGCAGUGCAAU-ACAG
AAWU01038467.1/41288-41214       CGUGGGUGCAUUGUAGUUGCAUUGCACG--UUUUGCGUU-CGAAAAGUCCAG-UGCAGUACUUCUGCAAUGCAAA-CCAG
AANH01011106.1/1499-1563         CUGUGGUGCAUUGUAGUUGCAUUGCAU----GUUG-----UCUGACG----C-UGCAAUGGAUCUCCUCUGCAAC-ACAG
AALT01070464.1/411-345           CCGCAGUGCAUUGCUGUUGUAUUGCAU----GUCU--GU-GAAGCGG----G-UGCAGUUCCUCGGCAAUGCAGC-CCGG
AAZX01017121.1/8029-8095         CGAGAGUGCAUUGUAGUUGCAUUGCAU----GAAUAUUU-GA---AA----G-UGCAGUACUUCUGCAGUGCAACCCUUG
AAPY01023874.1/2160-2093         CUGCAGUGCAUUGUAGUUGCAUUGCAU----GUCC-UGA-CAGUACC----A-UGCAAUGUUUCCACAGUGCAUC-ACAG
AAGE02018815.1/108790-108863     CCCGGGUGCAUUGUAGUUGCAUUGCACUUUUGCGUUCGA-UAACACG----G-UGCAAUACUUCUGCAAUGCAAGCCAGG
AAIY01417522.1/685-752           CGGGGGUGCAUUGUAGUUGCAUUGCAC----GUUCUGGC-AG-UGCC----G-UGCAAUGUUUCCACAGUGCAUC-CCAG
AANN01189516.1/304-372           CUGUGGUGCAUUGUAGUUGCAUUGCAU----GUUCUAGC-AGUACCC----G-UGCAAUGUUUCCACAGUGCAUC-ACAG
AC105358.8/20002-19934           CUGUGGUGCAUUGUAGUUGCAUUGCAU----GUUCUGGC-AAUACCU----G-UGCAAUGUUUCCACAGUGCAUC-ACGG
AAQQ01022475.1/405-337           CUGUGGUGCAUUGUAGUUGCAUUGCAU----GUUCUGGC-GGUACUC----G-UGCAAUGUUUCCACAGUGCAUC-CCAG
ABDC01612653.1/996-930           CUGCGGUGCAUUGUAGUUGCAUUGCAU----GUUC--UC-AGUACCC----A-UGCAGUGUUUCCACAGUGCAUC-CCAG
AAPP01019353.1/60482-60414       CGCAGGUGCAUUGUAGUCGCAUUGUCU----GUCCCACU-UG-CUCC----A-GGCAAUACAACUGCAGUGCAAGCUCUG
AANI01017473.1/521223-521153     CGGAGGUGCAUUGUAGUCGCAUUGUCU----GUCUCAAA-UUUGCCC----GCGGCAAUACAACUGCAGUGCAAGCUCCG
AAGV020569574.1/1591-1654        CCGCGGUGCAUUGCUGUUGCGUUGCAC----GUGUGUGC------GG----G-UGCAGUGCCUCUGCAGUGCAGC-CCGG
CAAB02000346.1/18927-18857       CUGUGGUGCAUUGUAGUUGCAUUGCACG--UCUGGCUGU-ACACACA----G-UGCAAUGAAUCUGCUCUGCAGU-ACAG
DQ483057.1/1273-1337             CCGCGGUGCAUUGCUGUUGCAUUGCAU----GUGU-----GAGGCAG----G-UGCAGUGCCUCGGCAGUGCAGC-CCGG
AAQR03015900.1/2680-2612         CUGUGGUGCAUUGUAGUUGCAUUGCAU----GUUCUAGC-AGUACCC----A-UGCAGUGUUUCCACAGUGCAUC-AUGG
ADDD01111004.1/5860-5928         CUGUAGUGCAUUGUAGUUGCAUUGCAU----GUGCUGGC-AGUAACU----G-UGCAAUGUUCCUGCAGUGCAGU-ACAG
AAGU03083241.1/16202-16138       CCGAGGUGCAUUGCUGUUGCAUUGCAC----GUGU-----GUGGCGG----G-UGCAGUGCCUCAGCAGUGCAGC-CCGG
AAEX03007288.1/12026-11958       CUGUGGUGCAUUGUAGUUGCAUUGCAU----GUUCUGGC-GGUACCC----G-UGCAAUGUUUCCACAGUGCAUC-AUGG
AAGJ04043287.1/21649-21718       CCAUGGUGCAUUGUCGUUGCAUUGCAU----GUGUCUCUAUACCCCU----A-UGUAGUGCAAGAACAGUGCAAU-AUGG
AAWZ02017587.1/61612-61680       CUGUAGUGCAUUGUAGUUGCAUUGCAU----GUUCUAGC-AGUAUUU----G-UGCAAUGUUUCCGCAGUGCAAU-ACAG
AAWZ02029214.1/2322-2388         CGGGGGUGCAUUGUAGUUGCAUUGCAU----GUGU--GG-CCAAGCU----G-UGCAAUGCCCCUCCAGUGCAGC-CCUG
CAAB02002948.1/84861-84794       CUGUGGUGCAUUGUAGUUGCAUUGCAU----GAUC-CUG-AACCUGA----G-UGCAAUGUAUCUGCAGUGCAGC-ACAG
AADG06000842.1/1176-1111         CAACUGUGCAUUGUAGUUGCAUUGCAU----GAAA-----UAUAACU----A-UGCAAUACUUCUACAGUGCAACUCUUG
CAAB02006724.1/156095-156163     CUGGGGUGCAUUGUAGUUGCAUUGCAU----GUGUGUCA-CAGAGGA----G-UGCAAUGUACCUGCACUGCAAC-ACAG
AC122129.9/71659-71593           CCGCGGUGCAUUGCUGUUGCAUUGCAC----GUGU--GU-GAGGCGG----G-UGCAGUGCCUCGGCAGUGCAGC-CCGG
AY866033.1/253-321               CUGUGGUGCAUUGUAGUUGCAUUGCAU----GUUCUGGU-GGUACCC----A-UGCAAUGUUUCCACAGUGCAUC-ACAG
AE014296.4/19791081-19791149     CGAAGGUGCAUUGUAGUCGCAUUGUCU----GUCCCAAU-UG-CUUC----A-GGCAAUACAACUUCAGUGCAAGCUCUG
AY866035.1/442-510               CUGCGGUGCAUUGUAGUUGCAUUGCAU----GUUCUGGU-GGUACCC----A-UGCAAUGUUUCCACAGUGCAUC-ACAG
AY866036.1/445-513               CUGCGGUGCAUUGUAGUUGCAUUGCAU----GUUCUGGU-GGUACCC----A-UGCAAUGUUUCCACAGUGCAUU-ACAG
#=GC SS_cons                     <<<---<<<<<<<<-<--<<<<<<<<<....________._______....>.>>>>>>>>-->->>>>>>>>--.->>>
#=GC RF                          CcguGGUGCAuUGuAGUUGCAUUGCac....GUuuuugu.uauaacc....g.uGCAAUGCuUCuaCAgUGCAac.ccgG
//
# STOCKHOLM 1.0

#=GF AC   RF00668
#=GF ID   mir-302
#=GF DE   microRNA mir-302
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   55.60
#=GF NC   54.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.03 -Z 549862.597050 CM SEQDB
#=GF CL   CL00096
#=GF DR   MIPF; MIPF0000071;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15183728
#=GF RT   Human embryonic stem cells express a unique set of microRNAs.
#=GF RA   Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS,
#=GF RA   Moon SY, Kim VN, Kim KS
#=GF RL   Dev Biol. 2004;270:488-498.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF WK   MicroRNA
#=GF SQ   44


AAFC03091296.1/1203-1135     ACACAACUU--AAACAU-GGAUGUAC-UUGCUUUCAAACUAAAA---AAGGAAGC-GCUUCC-AAGUUUC-GGGGAUGG
CAAA01211654.1/15598-15663   CCUUUACUU--UAACAU-GGAGGCAC-UUGCUGUGCAUU--UAA---AAAUAAGU-GCUUCC-AUGUUUG-AGU-GUGG
CAAA01211654.1/15470-15538   CCACCACUU--AAACGU-GGUUGUAC-UUGCUUUAGACCUAAGA---AAGUAAGU-GCUUCC-AUGUUUU-GGUGAUGG
CAAA01211654.1/15337-15404   CCUCUGCUU--UAACAU-GGGGUUAC-CUGCUGUGU-UAAACAA---AAGCAAGU-GCUUCC-AUGUUUC-AGUGGGGG
CAAA01211654.1/15207-15274   CUUCAACUU--UAACAU-GGGAAUGC-UUUCUGUCUCAUCGAAG----AGUAAGU-GCUUCC-AUGUUUU-AGUAGAAG
AADD01049814.1/10290-10224   CUUCAACUU--UAACAU-GGAAGUGC-UUUCUGUGACUU--UAA---AAGUAAGU-GCUUCC-AUGUUUU-AGUAGGAG
AAPY01684075.1/7919-7851     CCACCACUU--AAACGU-GGGAGUAC-UUGCUUUAUAACGGGGA---AAGUAAGU-GCUUCC-AUGUUUU-GGUGAUGG
AAHY01031685.1/1176-1109     CUUCAACUU--UAACAU-GGGAAUGC-UUUCUGUCU-CAUCUAA---GAGUAAGU-GCUUCC-AUGUUUU-AGUAGAAG
AAYZ01300380.1/1467-1400     CCUUUGCUU--UAACAU-GGGGGCAC-CUGCUGUGUA-CAACAA---AAGUAAGU-GCUUCC-AUGUUUC-AGUGGAGG
AANN01319001.1/1638-1703     CC---ACUU--AAACGU-GAAUGUUC-UUGCUUUGAAGCUAAAC---AAGAAAGU-ACUUUC-AUAUUUC-AGAGAUGG
AAFC03065343.1/37046-36982   UCACCACCU--AACCUG-GGAAGCGC-UUGCUUUGAAACUAUUA-------AAGU-GCUUCC-AUGUUUU-UGUGGUGA
AAPN01081641.1/13679-13747   CUUCUCCUU--UAACAU-GGAGGUGC-UUGCUGUGAGUUUGAAA---AAUUAAGU-GCUUCC-AUGUUUU-AGUUGAAG
AAPN01081641.1/13571-13636   CUGUCACUU--AAACGU-GGAUAAAC-UUGCUUUACUUUUA------AAGUAAGU-GCUUCC-AUGUUUU-AGUGAUGG
AAPY01419152.1/185-114       CUUUGACUU--UAACAU-GGAGGUAC-UCUCUGUGCCUUUUUAGAAAGAGUAAGU-GCUUCC-AUGUUUU-AGUGGAAG
AAHX01020222.1/16186-16122   CCUUCACUU--UAACAU-GGAGGCCC-UCGCUGUGCCUUUAAAA------UAAGU-GCUUCC-AGGUUUG-AGU-GUGG
AANN01821362.1/2160-2092     CCACCACUU--UAACAU-GGAGGCGC-UUGCUGUAUCAUCUUAA---GAAUAAGU-GCUUCC-AUGUUUU-AGUGUUGG
AANN01821362.1/2593-2523     CUUUAACUU--UAAUGU-GGAAGUGC-UUUCUGUGAUUCUAAAAUA-UAGUAAGU-GCUUCC-AUGUUUU-AGUGUAAG
AALT01320989.1/195-127       CCGCGACUU--UAACAU-GGAGGCAC-UUGCUGGGACCUGACCAA--AAAUAAGU-GCUUCC-AUGUUUU-AGU-GUGG
AALT01320989.1/475-405       CCUUCGCUU--UAACACGGGGGGCAC-UUGCUGUGUGCCCACAG---AAGUAAGU-GCUUCCUGUGUUUC-AGUGGAGG
AALT01320989.1/607-537       CUUUGACUU--UAACAU-GGGAGUGCUUUUCUGUGUGUUCUCAGA--GAGUAAGU-GCUUCC-AUGUUUG-AGUAGAAG
AAFR03016534.1/30625-30693   CCUCUGCUU--UAACAU-GGAAGUGC-UUGCUGUGAUUUUAAAA---AAUUAAGU-GCUUCC-AUGUUUG-AGUUGUGG
AAFR03016534.1/30106-30172   CUUCUACUU--UAACAU-GGAGGUAC-UUUCUGUGU--UUAAAA---AGGUAAGU-GCUUCC-AUGUUUU-GGUAGGAG
AAFR03016534.1/30254-30320   UCUCUGCUU--UAACAU-GGGGGUAC-CUGCUACGUAAU--AAA---AAGUAAGU-GCUUCC-AUGUUUC-AGUGGAGA
ABDC01525090.1/901-968       CCUUUGCUU--UAACAU-GGGGGUAC-AUGCUGUGUGAAUCAAA----AGUAAGU-GCUUCC-AUGUUUC-AGUGGAGG
AAIY01685397.1/7477-7410     CCUUUGCUU--UAACAU-GGGAGUAC-CUGCUGUGCAAA-AUGA---AAGUAAGU-GCUUCC-AUGUUUC-AGCGGAGG
AAIY01685397.1/7598-7532     CUUGGACUU--UAACAA-GGAGGCCC-UUUUACUAC--UUAAAA---AAGUAAGU-GCUUCC-UUGUUUU-AGUAAAAG
AAIY01685397.1/7173-7105     CCUCUACUC--UAACAC-GGCGGCAC-UUGCUGUGGCUUUUUGGA--AAUUAAGU-GCUUCC-AUGUUUG-AGU-GUGG
AANU01270256.1/2613-2682     CUUCAACUU--UAACAU-GGAAGUGC-UUUCUGUGACUUUAAAAU--AAGUAAGU-GCUUCC-AUGUUUU-AGUAGGAG
AADA01066072.1/27294-27227   CCUUUGCUU--UAACAU-GGGGGUAC-CUGCUGUGU-GAAACAA---AAGUAAGU-GCUUCC-AUGUUUC-AGUGGAGG
AAQQ01250562.1/1745-1679     CCUUUACUU--UAACAU-GGAGGCAC-UUGCUGUGACAUGAUAA----AAUAAGU-GCUUCC-AUGUUUG-AGU-GUGG
AAKN02038884.1/104365-104297 CCACCACU-U-AAACGU-GGACGUAC-UUGCUUUGGAAGCGAGA---AAGUAAGU-GCUUCC-AUGUUUC-GGUGAUGG
AAGV021030223.1/1436-1370    CCUCUACUU--UACAUU-GGAAGCAC--UGCUGUGA-GCUAUUU---UAUUAAGU-GCUUCC-CAUGUUUGAGU-GUGG
AAWR02036366.1/23003-22935   CCACCACUU--AAAUGU-GGGUGUUC-UUGCUUUGAAAUUAAAA---AAGAAAGU-ACUUCC-AUACUUU-AGAGAUGG
AAWR02000508.1/11188-11120   CCACCACUU--ACACAU-GGAUGCAC-UUGCUUUGACACUAAAA---AAGGAAGC-ACUCGC-AUGUUUU-AAUGAUGG
ADDD01113690.1/5635-5571     CCUCCGCUU--UAACAU-GGAGGUAC-CUGCUGCCU----ACAA---AAGUAAGU-GCUUCC-AUGUUUC-AGUGGUGG
AAGW02021863.1/25249-25316   UCUCUACUU--UAACAU-GGAGGCAC-UUGCUGUGCCAUGAUAA---AAAUAAGU-GCUUCC-AUGUUUG-AGU-GUGG
AAWZ02004954.1/27325-27392   CCACUACUU--UAAUAU-GAAAGUAC-UUGUUUUUGUUCCUUUU----AAAAAGU-GCUUUC-AUAUUUU-AGUGAUGG
AAGU03033948.1/12869-12803   CCUCUACU--UAAACAU-GGAGGCAC-UUGCUGUGA-CAUACUA---AAAUAAGUG-CUUCC-AUGUUUG-AGU-GUGG
AADN03003749.1/40360-40294   CCACAACUU--AAAUGU-GGAUGUGC-UUGCUUUGUUCU--GAA---AAGAAAGU-GCUUCC-AUGUUUU-AGUGAUGG
AADN03003749.1/40923-40855   CUUUUACUU--UAACAU-GGAGGUGC-UUUCUGUGAUUUUACAA---AAGUAAGU-GCUUCC-AUGUUUU-AGUAGAGG
AADN03003749.1/40025-39957   CCUCAACUU--UAACAU-GGAGGUAC-UUGCUGGACACCUGAAA---AAGUAAGU-GCUUCC-AUGUUUU-AGUUGUGG
AAEX03016829.1/107918-107850 CCACCACUU--AAACGU-GGAUGUAC-UUGCUUUGAAACUCAAA---AAGUAAGU-GCUUCC-AUGUUUU-AGUGAUGG
AAGU03033948.1/13326-13257   CUUUGACUU--UAACAA-GGAGGUCC-UUUCUGCUAUUUGUAAAA--AAGUAAGU-GCUUCC-UUGUUUU-AGUAGAAG
AAQR03142114.1/15713-15646   UCUCUACUU--UAACAU-GGAGGCAU-UUGCUGUGACAUAACAA---AAAUAAGU-GCUUCC-AUGUUUG-AGU-GUGG
#=GC SS_cons                 <<---<<<-..-<<<<<.<<<<<<<<._________________...______>>.>>>>>>.>>>>>--.>>>--->>
#=GC RF                      CCUCuaCUU..UAACau.GGagGcaC.UUGCUgUGaauuUAaAA...AAGUAAGu.gCuuCC.auGUUUu.AGuGGuGG
//
# STOCKHOLM 1.0

#=GF AC   RF00669
#=GF ID   mir-96
#=GF PI   MIR96
#=GF DE   microRNA mir-96
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   74.30
#=GF NC   47.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000072;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12919684
#=GF RT   Embryonic stem cell-specific MicroRNAs.
#=GF RA   Houbaviy HB, Murray MF, Sharp PA
#=GF RL   Dev Cell. 2003;5:351-358.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   11914277
#=GF RT   miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.
#=GF RA   Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L,
#=GF RA   Rappsilber J, Mann M, Dreyfuss G
#=GF RL   Genes Dev. 2002;16:720-728.
#=GF WK   Mir-96_microRNA
#=GF SQ   25


AY866347.1/676-753           UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAAA
AAPN01078070.1/2775-2698     UGGCCUCUUUUGGCACUAGCACAUUUUUGCUU-UUGUCUCUCU-GCUCUGAGCAAUCAUGUGUAGUGCCAAUAUGGGAAA
AY866348.1/656-733           UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAAA
AAFR03031888.1/53049-53126   UGGCCCGUUUUGGCACUAGCACAUUUUUGCUU-CUGUCUCUCU-GCUCUGAGCAAUCAUGUGUAGUGCCAAUAUGGGAAA
AAHX01029291.1/26553-26630   UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAAA
AAVX01227232.1/474-397       UUGCCCAUUUUGGCACUAGCACAUUUUUGCUU-UUGUAUAUGA-CUGUUGAGCAAUUAUGUGUAGUGCCAAUAUAGGAAA
CAAE01014715.1/320294-320219 UCGCCCAUUUUGGCACUAGCACAUUUUUGUUU-C-GUUUCUG--GCUGUCAGCAAUCGUGUGCAGUGCCAAUCUAGGACA
AF480568.1/1-78              UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAAA
AY866343.1/680-757           UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAAA
AAFC03026276.1/18887-18810   UGGCCGACUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAAA
CAAE01014535.1/342950-343027 UUGCCCAUUUUGGCACUAGCACAUUUUUGCUU-CUGUAUAUAU-ACUUUGAGCAAUUAUGUGUAGUGCCAAUAUAGGAGA
AL590150.2/106766-106689     UUGCCUGUUUUGGCACUAGCACAUUUUUGCUU-UUUUAUAUAU-ACCUUGAGCAAUUAUGUGUAGUGCCAAUAUGGGACA
AANH01001637.1/239663-239741 UGGCCCGUUUUGGCACUAGCACAUUUUUGCUUUGUCCCUUGUU-UGUUUGAGCAAACAUGUGUGGUGCCAAUUUAGGACA
AY866346.1/700-775           UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU---GUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAAA
BAAF04047675.1/12047-12125   UGGCCCGUUUUGGCACUAGCACAUUUUUGCUU-UUCUUUCUUGCUGUCUGAGCAAUCAUGUGUGGUGCCAAUAUGGGACA
AY866345.1/448-525           UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAAA
CAAA01210023.1/24901-24824   UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUGUGAGCAAUCAUGUGUAGUGCCAAUAUGGGAAA
AY866344.1/351-428           UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAAA
AAPY01581226.1/2090-2167     UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUUAUGUGCAGUGCCAAUAUGGGAAA
AAIY01697149.1/2365-2288     UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAGA
AALT01103892.1/894-971       UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAGAUGGGAAA
AAYZ01439986.1/3739-3662     UGGCCGACUUUGGCACUAGCACAUUUUUGCUU-GUGUCUCUCC-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGACA
AAGV020207254.1/1850-1927    UGGCCGAUUUUGGCACUAGCACAUUUUUGCUU-GUCUCUCUCU-GCUCUGAGCAAUCAUGUGCAGUGCCAAUAUGGGAGA
CAAB02005445.1/236493-236570 UUGCCCAUUUUGGCACUAGCACAUUUUUGUUU-CGUUUCCUGC-UGUUUGAGCAAUCAUGUGUAGUGCCAAUAUGGGACA
CAAB02000775.1/218086-218009 UCGCCCAUUUUGGCACUAGCACAUUUUUGCUU-CUGUAUGUAU-ACUUUGAGCAAUUAUGUGUAGUGCCAAUAUAGGAGA
#=GC SS_cons                 :::<<-<<-<<<<<<<<-<<<<<<--<<<<<<.--<<______.>>--->>>>>>-->>>>>>>>>>>>>>->>->>:::
#=GC RF                      UgGCCgauUUUGGCACuAgCACAUUUUUGCUu.gUgccUcUcu.gcUcUgAGCAAUcAUGUGcaGUGCCAAUaugGGAaA
//
# STOCKHOLM 1.0

#=GF AC   RF00670
#=GF ID   mir-105
#=GF DE   microRNA mir-105
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   53.00
#=GF TC   53.10
#=GF NC   52.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000074;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [2]
#=GF RM   11914277
#=GF RT   miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.
#=GF RA   Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L,
#=GF RA   Rappsilber J, Mann M, Dreyfuss G
#=GF RL   Genes Dev. 2002;16:720-728.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   20


AY866102.1/402-482         UGUGCAU-CGUGGUCAAAUGCUCAGACUCCUGUGGUG-GCUGCUCAUGCACCACGGAUGUUUGAGCAUGUGCUACGGUGUCUA
AADC01148833.1/6575-6495   UGUACAU-CGUGGUUUAACAGUCAAAUAUUAGUGUUA-GUUGCUCAUGCACCAUGAUUGCCUGAGUAUGUGCCAUGAUAUCUC
AALT01106831.1/106-184     AAAGAUC-UUCUGUCAAAUGUUCAUGUUCCU-UGGUG--CCCCUUAUGCACCGUGGAUGCUUGAGCAUGUGCUAUUGUGUCUA
AAIY01029761.1/2576-2497   UGUGCAU-UGUGGUCAAAUGCUCAGACUCCUGUUGUG-GCUGUUUGUGCACCAUGGAU-UUUGAGCAUGUGCUAUGGCGUCUA
CT797305.2/101964-101884   AGUGUGCCUGUGGUCAAAUGUUCUGACUAUUGUGGUG-ACUGCUCAUACACCAAGAAUGUCUGGCAAUGGACUAUA-UAUUUA
AAPY01458331.1/470-390     UAUAUAU-CAUGAUUAAAUGCUCAAACAUCAGUGGUA-GUUGCUCAUGUACCAUGAUUGUUUGAGUAUAUGCCAUGGUAUCUC
AAFC03107988.1/2045-2124   UGUGCAU-CAUAGUCAAAUGCUCAACCACCUAGUGUG-GCUGCUCAUACAC-CUGAUGGUUUAAGCUUGUACUGUGAUUUCAC
CAAA01059274.1/4642-4722   UGUGCAU-UUUAGCCAAGUGCUCAGAUGCUUGUGGUG-GCUGCUUAUGCACCACGAAUGCUUGAGCAUGUGCUAUGGUACCUA
AANG01462483.1/760-681     UGUGCAU-CAUGGUCAAAUGCUCAGACUC-CUUGGUG-GCUGCUUAUGUACCAUGAAUUUUUGAGCAUGUGCUAUGGUGUCUA
AANG01759982.1/244-164     UAUGCCU-UGUAGUCAAAUGAUCUGCCUAGUGUGGUG-GCUGCUUAUGCACCAUGGAUGUUUGAUAAUUGGCUAUGUAUCUAC
AAQQ01376207.1/2258-2178   UAUAUAU-CAUGGUGAAAUGCUCAAACAUCAGUGGUA-GUCAUUCAUGCACCACGAUUGUCUGAGUAUGUGCCAUGUUAUCCC
AANN01683306.1/428-348     UGUUCGU-CGUAGUCAAAUGCUCAGAUUCCUGUAGUG-GCUUCUGAUGUACUACAGCUGUCUGAGCAUGUGCCACGGCGUCUG
AANN01683306.1/2545-2466   UGCACAC-CGUGGUCAAAUGCUCAGGCU-CCGUGGUA-GUUGAUUAUGCACCACGGAUGUUUGAGCAUUUACAAUGGUGUCUA
AAKN02056081.1/11910-11990 UUUGUAC-UGCAGUGAAAUGCUCGGACUUCUGUGGUG-ACCACUCAUGCACUGCAGACUUUUGAGCAUGUGCUAUGGGUUCUA
AAWR02040596.1/7734-7654   UGUGCCU-UGUGGUCAAAUGUUCUGACUGCUGUGCUG-GCUGCUCAUGCACUAUGGAUGUUUGAUAAUAGGCUGCGUAUCUAC
AAWR02040596.1/10639-10559 UGUACAU-CACAGUAAAAUGCUCAAAC-AUCAAGGUUAGUUGGUCUUGCACCACGAUUGUCUGAGCAUGUACCAUGGUAUCCC
AAWR02040596.1/10151-10072 UGUGCAU-CACAGUCAAAUGCUCAAAUGCCUAUGGUG-ACUGUUCAGGCACCC-CGUUGUUUAAGCAUGUACCAUGAUUUCAC
AABR05011023.1/17864-17784 UGUGUAU-UGUAGUCAAGUGCUCAGAUGUCUGUGGUG-GCUGCUUAUGUAUCACGGAUGUUUGAGCAUGUGCUAUGGUAUCUA
AAEX03027060.1/7707-7627   UGUGCCU-UGUGGUCAAAUGUUCUACCUACUGUGGUG-GCUGCUCAUGCACCUCGGAUGUUUGAUAAUGGGCUAUGAAUCUAC
AAPE02015517.1/33682-33760 UGUGCAU-CAGAGUCAAAUGCUCAAAUGCCUAUGGUG-GUUAUUCAUGCACC-UGGUUAUUUAAGUAU-UACCAUGAUUUCAU
#=GC SS_cons               :::<<<<.<<<<<<---<<<<<<<<<<--<<<<<<<<.-<_______>>>>>>>>>-->>>>>>>>>>-->>>>>>>>>>:::
#=GC RF                    UGUgcac.caugGuCAAAUGcUCAgacucccguGGUg.GcUGCUcAUgcACCacggaUgucUGAgCAUGUgCcauggugcCua
//
# STOCKHOLM 1.0

#=GF AC   RF00671
#=GF ID   mir-138
#=GF DE   microRNA mir-138
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   63.10
#=GF NC   57.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.43 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000075;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF WK   miR-138
#=GF SQ   24


AAPN01441529.1/19449-19367   GGUGCUGCAGCUGGUGUUGUGAAUCAGGCCGACGAGCAGCGAGUCCUAAUACCCGGCUAUUUCACUACACCAGGGUUGCAUCA
AAYZ01057439.1/889-964       GGUGCGGCAGCUGGUGUUGUGAAUCAGGCCGUUGCCAAUC-------AGAGAACGGCUACUUCACAACACCAGGGUUGCACCC
BAAE01157223.1/2026-1944     UGUGUUGCAGCUGGUGUUGUGAAUCAGGCCGAUGACACACACCUCCUAAAAGCCGGCUAUUUCACAACACCAGGGUGGCACCG
AAHY01082616.1/260-185       UGUGGGACAGCUGGUGUUGUGAAUCAGGCCGUUGCCAAUC-------AGAGAACGGCUACUUCACAACACCAGGGCCACACUG
AAVX01140452.1/499-418       GGUGCUGCAGCUGGUGUUGUGAAUCAGGCCGGCA-AAAGCAGCUGCUACGAUCCGGCUAUUUCACAACACCAGGGUCGCACCG
AANH01000937.1/11718-11794   GGAGGGUCAGCUGGUGUUGUGAAUCAGGCCGCUG-----AGGUGUCGA-GACACGGCUUCUUCACAACACCAGGGUUCCUCCU
BX470170.5/95917-95835       UGUGCUGCAGCUGGUGUUGUGAAUCAGGCCGAUGUCACACGUCAGCGAUAACCCGGCUAUUUCACAACACCAGGGUGGCACCA
AAHX01319328.1/447-529       GUUGCUGCAGCUGGUGUUGUGAAUCAGGCCGACGAGCAACGCAUCCUCUUACCCGGCUAUUUCACGACACCAGGGUUGCACCC
AAPY01619641.1/874-793       GGUGCUGCAGCUGGUGUUGUGAAUCAGGCCGACGAGCAGCGCAUCUC-UUACCCGGCGAUUUCACGACACAGGUGCAUCAUAC
CAAE01013842.1/49188-49112   GGAGGGUCAGCUGGUGUUGUGAAUCAGGCCGCUG----ACACUACCAG--ACACGGCUUCUUCACAACACCAGGGUUCCUCCC
AAVX01130926.1/1014-940      GGUGCUGCAGCUGGUGUUGUGAAUCAGGCCGCCAUAUUUA--------CCGACCGGCUACUUCACAACACCAGGGUUGCACCU
DQ156151.1/39308-39226       UGUGCUGCAGCUGGUGUUGUGAAUCAGGCCGAUGCCACACACCUGCUAUAACCCGGCUAUUUCACAACACCAGGGUGGCACUG
AAFR03040115.1/139523-139605 GUUGCUGCAGCUGGUGUUGUGAAUCAGGCCGACAAGCAGCUCAUCCUAUUACCCGGCUAUUUCACUACACCAGGGUUGCAUCA
ABDC01224043.1/1530-1605     GGUGGGGCAGCUGGUGUUGUGAAUCAGGCCGUUGCCAAUC-------AGAGAACGGCUACUUCACAACACCAGGGCCGCACCG
AAFC03050427.1/7063-7138     GGUGGGGCAGCUGGUGUUGUGAAUCAGGCCGUCGCCAAUC-------AGAGAACGGCUACUUCACAACACCAGGGUCACACCC
AAIY01521032.1/4829-4754     GGUGGGGCAGCUGGUGUUGUGAAUCAGGCCGUGACCAAUC-------GGAAAACGGCUACUUCACAACACCAGGGUCGCACCC
AANN01222185.1/3411-3486     GGUGGGGCAGCUGGUGUUGUGAAUCAGGCCGGCGCCGAUC-------AGAGAGCGGCUACUUCACAACACCAGGGUCUCACCC
CAAK05039157.1/16818-16742   AGCAGGACAGCUGGUGUUGUGAAUCAGGCCGCCGUGGUGA------AAGGGUACGGCUUCUUCACAACACCAGGGUCUCACUU
AAGV020455273.1/411-336      GGUGGGGCAGCUGGUGUUGUGAAUCAGGCCGGCGCCCAUC-------GGAAAACGGCUACUUCACAACACCAGGGCCGCACCU
AAKN02012252.1/96136-96211   GGCGGGGCAGCUGGUGUUGUGAAUCAGGCCGUUGCCCAUC-------AGAGAACGGCUACUUCACAACACCAGGGUCUCACCC
ADDD01128007.1/11015-10940   CGUGCAGCAGCUGGUGUUGUGAAUCAGGCCGUCACCAGUC-------GGAGAACGGCUACUUCACAACACCAGGGUGGCACUG
AAGW02056045.1/49960-49885   GGUGCAGCAGCUGGUGUUGUGAAUCAGGCCGUUGCCACUC-------CGAGAACGGCUACUUCACAACACCAGGGUCGCACCC
AAWZ02031769.1/968-1050      GUUGCUGCAGCUGGUGUUGUGAAUCAGGCCGACAAAAAGCGCAUCUUACUAUCCGGCUAUUUCACUACACCAGGGUUGCAUCA
CAAB02001161.1/64061-64136   GGUGGGACAGCUGGUGUUGUGAAUCAGGCCGCCGCAGUCC-------AAGGAUCGGCUACUUCCCAACACCAGGGUCUCACCA
#=GC SS_cons                 :::<<<<<--<<<<<<<<<<<<<---<<<<<---<_____________>---->>>>>-->>>>>>>>>>>>>->>>>>::::
#=GC RF                      gGUGcggCAGCUGGUGUuGUGAAUCAgGCCGauGccaauCgcauccuagaaaaCGGCuAcUUCACaACACCAGGGccgCACcu
//
# STOCKHOLM 1.0

#=GF AC   RF00672
#=GF ID   mir-190
#=GF DE   microRNA mir-190
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   58.00
#=GF TC   59.70
#=GF NC   57.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00089
#=GF DR   MIPF; MIPF0000076;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   16698962
#=GF RT   Cloning and expression of new microRNAs from zebrafish.
#=GF RA   Kloosterman WP, Steiner FA, Berezikov E, de Bruijn E, van de Belt J,
#=GF RA   Verheul M, Cuppen E, Plasterk RH
#=GF RL   Nucleic Acids Res. 2006;34:2558-2569.
#=GF RN   [3]
#=GF RM   18583537
#=GF RT   MicroRNA discovery and profiling in human embryonic stem cells by deep
#=GF RT   sequencing of small RNA libraries.
#=GF RA   Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite
#=GF RA   A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R,
#=GF RA   Ruohola-Baker H, Tewari M
#=GF RL   Stem Cells. 2008;26:2496-2505.
#=GF WK   Mir-190_microRNA_precursor_family
#=GF SQ   29


AAAB01008807.1/2608463-2608553 -GG--ACAGUUUCGGUGAGAUAUGUUUGAUAUUCUUGGUUGUUAAGAUUU---CAAUUAUCACCCAGGAAUCAAACAUAUUAUUACCGUGACUGUCG
AADA01239194.1/26818-26902     -UG--CAGGCCUCUGUGUGAUAUGUUUGAUAUAUUAGGUUGUUAUUU---------AAUCCAACUAUAUAUCAAACAUAUUCCUACAGUGUCUUGCC
AADE01000851.1/6712-6801       -UG--GGGAUUCCAGUGAGAUAUGUUUGAUAUUCUUGGUUGUUACAUUCA---AGAGU-UCACCCAGGAAUCAAACAUAUUAUUACUGUGAUACCCG
AAFR03052180.1/90862-90947     -UC--CCUACUUCUGUGUGAUAUGUUUG--AUAUUGGGUUGUUUGAUUG-----GGAA-UCAACUAAAUGUCAAACAUAUUCUUACAGCGGUUGGGU
AAGE02010108.1/2182-2091       AGG--GUGAUUCCGGUGAGAUAUGUUUGAUAUUCUUGGUUGUUAAAUUUU---AUAUUAUCACCCAGGAAUCAAACAUAUUAUUACUGUGGUCAUCA
AAIY01445479.1/883-798         -AG--CCUGCUUCUGUGUGAUAUGUUUG--AUAUUGGGUUGUUGAAUUA-----GGAG-CCAACUAAAUGUCAAACAUAUUCUUACAGCGGUCAGCC
AAJJ01000811.1/4671-4587       -UG--UGAGUUGCUAUAAGAUAUGUUUGAUAUUCUUGGUUGUAUUUU--------UAAUUCACCCAGGAGUCAAACAUAUUAUUAUAGAAG-CGUCA
AANH01001186.1/51033-51124     -GG--CUAGAAGCUGUGUGAUAUGUUUG--AUAUUCGGUUGUUCUUGUGCUUCGUCGUGUCAACUAAAUAUCAGACAUAUUCCUACAGAGUCUGGCA
AANN01658794.1/906-991         -UG--UCUCCUUCUGUCUGAUAUGUUUG--AUAUUGGGUUGUUUAAUUA-----GGAA-CCAACUACAUGUCAAACAUAUUUUUACAGCAGUGGACA
AAPN01024655.1/497-582         -UG--CCCACCUCUGUGUGAUAUGUUUG--AUAUUAGGUUGUUACGCU------AGACCUCACCUGAAUAUCAGACAUAUUCCUACAGCGGCUGGGC
AAPQ01006550.1/54883-54794     -UG--AUGGUUCCAGUGAGAUAUGUUUGAUAUUCUUGGUUGUUUCAUUCA---AAAGU-UCACCCAGGAAUCAAACAUAUUAUUACUGUAGCCUUCG
AAPU01011510.1/87170-87258     -UA--ACGAUUCCAGUGAGAUAUGUUUGAUAUUCUUGGUUGUUACAUUCA---AAAGU-UCACCCAGGAAUCAAACAUAUUAUUACUGUGAUCGCU-
AAVX01028763.1/1639-1724       -UA--CAAGCGACUGUCUGAUAUGUUUGCUAUGUUAGGUUGUUACUC--------AAACUCAACGAUAUAUCAAACAUAUUUGUAUAGUUUCUUGUC
AAVX01176080.1/200-287         -UG--CCUGUCUCUGUGUGAUAUGUUUG--AUAUUAGGUUGUUUUUUGG----UUUAAAGCAACUAAAUAUUAGACAUAUUCCUACAGCGUCUGGCC
AAWU01013103.1/681-592         -GG--GUGAUUCCAGUGAGAUAUGUUUGAUAUUCUUGGUUGUUAAAUUUU---AUAUUAUCACCCAGGAAUCAAACAUAUUAUUACUGUGGUCAUC-
AAYZ01218204.1/4143-4058       -GG--CCCGCUUCUGUGUGAUAUGUUUG--AUAUUGAGUUGUUUAACUA-----GGUA-CCAACUAAAUGUCAAACAUAUUCUUAUAGCGGUGGGCA
AAZO01006982.1/10540-10462     --------UCAUCUCUGAGAUAUGUUUGAUAUUCUUGGUUGUUUUAUU------UAAUUUCAACCAAAUAUCGAACAUAUUUCAAGGCUGAAA----
AAZX01003157.1/32924-32997     --------UAUACUGCUAGAUAUGUUUGAUAUUCUUGGUUGUAUAAU--------AAUAACGACCAGGAAUCAAACAUAUUAUUACAGUG-------
BAAB01160920.1/3306-3391       -GCCGCGCGUCGUCG--AGAUAUGUUUGAUAUUCUUGGUUGUUUGUU-U------UGGAUCACCCGGGAAUCAAACAUAUUACU-CUACGACCGCGG
BAAF04125730.1/5227-5317       -UG--CUAGAGGCUGUGUGAUAUGUUUG--AUAUUCGGUUGUUCUUGUGCUUCAUCAUGUCAACUAAAUAUCAGACAUAUUCCAACAGACUCUGGC-
CAAA01007160.1/18747-18832     -UG--CCUGCUUCUGUGUGAUAUGUUUG--AUAUUGGGUUGUUAAAUUA-----UGAA-CCAACUGAAUGUCAAGCAUACUCUCACAGCAGUAAGGA
CAAE01014685.1/219901-219986   -UG--CAGGGCUCUGUCUGAUAUGUUUGAUAUAUUAGGUUGUUAUUC--------AGUCCCAACUAUAUAUCAAACAUAUUCCUACAGUGUCCCGCU
CAAE01015044.1/472022-472113   -GG--CCGGAGGCUGUGUGAUAUGUUUG--AUAUUCGGUUGUUCUUGUUCGCUUUGUCGUCAACUAAAUAUCAGACAUAUUCCUACAGAGUCUGGCA
CR361564.27/60035-60124        -UG--UUACAGACUAUGUGAUAUGUUUG--AUAUUCGGUUGCUUUCUUUA--UAUCAUGUCAACUAAAUAUCAGACAUAUUCCUAUAGACUGUGACA
AAEX03005350.1/184444-184529   -UG--CCUGCUUCUGUGUGAUAUGUUUG--AUAUUGGGUUGUUUAAUUA-----GGAA-UCAACUAAAUAUCGAACAUAUUCUUACAGCAGUGGGCA
AAQR03179159.1/3618-3534       -UG--CCUACUUCUGUGUGAUAUGUUUG--AUAUUGGGUUGUUUAAUUA-----GGAA-CCAACUAAAUGUCAGACAUAUUCUUAUAGCAGUAGGC-
AADG06002597.1/89381-89294     -GU--CUGGUUUCCGUAAGAUAUGUUUGAUAUUCUUGGUUGUUUUUU------AAAGAAUCGACCAGGAAUCAAACAUAUUAUUAUGGUGGUCAGAA
AC163616.3/177952-178037       -UG--CCUGCUUCUGUGUGAUAUGUUUG--AUAUUGGGUUGUUAAAUUA-----UGAA-CCAACUGAAUGUCAAGCAUACUCUCACAGCAGUAAGGA
AY865951.1/375-459             -UG--CAGGCCUCUGUGUGAUAUGUUUGAUAUAUUAGGUUGUUAUUU---------AAUCCAACUAUAUAUCAAACAUAUUCCUACAGUGUCUUGCC
#=GC SS_cons                   .:<..<<<<<<-<<<<--<<<<<<<<<<--<<<<<-<<<<<________.....______>>>>>->>>>>>>>>>>>>>>--->>>>->>>>>>>:
#=GC RF                        .ug..cccgccuCuGUguGAUAUGUuUGAUAuacuugGuUGUUuuauUu.....uaauauCAaCcAaguaUCAaACAUAUUcuUACaGuggcgggca
//
# STOCKHOLM 1.0

#=GF AC   RF00673
#=GF ID   mir-217
#=GF DE   microRNA mir-217
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   75.70
#=GF NC   59.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000077;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   12624257
#=GF RT   Vertebrate microRNA genes.
#=GF RA   Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP
#=GF RL   Science. 2003;299:1540.
#=GF WK   MicroRNA
#=GF SQ   27


AAHX01081871.1/29693-29795     ACAGUCAUUGUA---GUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGACUGGAUAAGACUCAGUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAG
AANG01681923.1/959-854         AUAAUUAUUAUAGAGUUUUUGAUGUCGUAGAUACUGCAUCAGGAACUGAUUGGAUAAGAAUGGGUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
BAAE01230814.1/1025-922        ACGAGGACGGAC--CUUUCUGGUGUGGAUGAUACUGCAUCAGGAACUGAUUGGCUGAUACUCAUUUGCCAACAGUACCUGGUGCAUUACCUUCAGCAUCGAAAGAA
AANH01005109.1/22353-22248     CGCUAGAGGAAAAACUCUCCGAUGCGGAUGAUACUGCAUCAGGAACUGAUUGGCUGAUGCUCAAAUGUCAACAGUACCUGAUGCAUUGCCUUCAGCAUCGCAAGAA
AAPN01112677.1/33155-33260     CAAAACCGAGCCGAGUUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGAUUGGAUAAUAAUCAGUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
AAIY01412982.1/1242-1137       UAACGUCACAAAGAGCUUUUGAUGUUGCAGGUACUGCAUCAGGAACUGAUCGGAUAAGUAUCUGUCACCAUCAGUUCCUAAUGCACUGCCUUCAGCAUCUAACUGA
BAAF04071571.1/3447-3342       GUGCUGACAGAACAGCCUCUGGUGUUGAUGAUACUGCAUCAUGAACUGAUGAGAAAAUGAAGAGAGGCCAUCAGUUCCUGAUGCACCGCCUUCAGCAUCCAGAGAC
AANH01011241.1/45727-45622     AACCUCUCGGCAGGUUCCCUGAUGUUGGUGAUACUGCAUCAGGAACUGAAUGGAGACCCAUGAGAGGCCAUCGGUUCCUGAUGCACGGUCCUCAGCAUCUGAAGAC
BX321898.29/71915-71810        GAGCUGCAUGAGAACUUUCUGAUGUUGGUGAUACUGCAUCAGGAACUGAUUGGAUGAUAUUCAGGAGCCAUCAGUUCCUGAUGCACUCCCAUCAGCAUCGAAAGAG
AAFR03002981.1/16291-16186     ACAGCCAUUUCUGAGAUUUUGAUGUCGUAGAUACUGCAUCAGGAACUGAUUGGAUAAUAUUCAGGCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
AAYZ01065394.1/1387-1282       AAUGUAUGAUUAAAGUUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGAUUGGAUACAAAUAUAUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
AANN01395868.1/720-823         CUUAUCACAGAG--UUUUUUGAUGUCGUAGAUACUGCAUCAGGAACUGAUUGUAUAAGAAUGUGCCACCAUCAGUUCCUAAUGCAUUACCUUCAGCAUCUAAACAA
ABDC01205979.1/1949-1844       ACAAGUAUUACACAGUUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGAUUGGAUAAGAGUCGGUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
AAHY01550462.1/749-646         AUAGUCAUUACA--GUUUUUGAUGUUGCAGAUACUGCAUCAGGAACUGACUGGAUAAGACUUAAUCCCCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
AAFC03081440.1/34025-34130     AUAAUUAACACAGAGUUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGAUUGGAUAAGAAUCGGUCACCAUCAGUUCCUCAUGCAUUGCCUUCAGCAUCUAAACAA
AALT01617638.1/400-505         GGUCUUAUUAUAAAGCUUUUGAUGUCGUAGAUACUGCAUCAGGAACUGAUUGGAUAAAAAUGGGUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
CAAE01014563.1/1136795-1136695 AUAAAGAAC-----CUUCUUGAUGUGGAUGAUACUGCAUCAGGAACUGAUUGGCUGAUGCUUAGUACCCAACAGUACCUGAUGCAUUGCCUUCAGCAUUGAAAGAA
AAEX03007534.1/182472-182367   UAUAAUUACUACGAGUUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGAUUGGAUAAGAAUGGGUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
AAGU03068078.1/94171-94276     AUAAUUUUUACAGAGUUUUUGACGUUGCAGGUACUGCAUCAGGAACUGAUCGGUUAAGUAUCCGUCACUGUCAAUUCCUAAUGCGCUGCCUUCAGCAUCUAAACAA
AAGW02006478.1/14128-14023     ACCUAAUUAUUACAGUUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGAUUGGAUAAGAAUCUGUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
AADN03003108.1/20570-20465     AAAGUCACUGCAGAGUUCUUGAUGUCGCAGAUACUGCAUCAGGAACUGAUUGGAUAAUAAUCAGUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
AAQR03052253.1/8294-8189       UGCAAGUAUUACACAGUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGAUUGGAUAAGAAUCAGUCACCAUCAGUUCCUCAUGCAUUGCCUUCAGCAUCUAAACAA
CAAB02004893.1/245981-245876   AAACAAUGAAGAGCCUUCUUGAUGCGGAUGAUACUGCAUCAGGAACUGAUUGGCUGAUGCUUUUUACCCAACAGUACCUGAUGCAUUGCCUUCAGCAUUGAAAGAA
AAWZ02015727.1/98447-98342     GUGUAGCCUUCAGAGCUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGAUUGGGGAAUAAUCAUGUACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
AACZ03152502.1/620-515         AUAAUUAUUACAUAGUUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGACUGGAUAAGAAUCAGUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
BX284627.4/50255-50360         ACAUAGUCAUUACAGUUUUUGAUGUUGCAGAUACUGCAUCAGGAACUGACUGGAUAAGACUUAAUCCCCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
AY866225.1/492-597             AUAAUUAUUACAUAGUUUUUGAUGUCGCAGAUACUGCAUCAGGAACUGAUUGGAUAAGAAUCAGUCACCAUCAGUUCCUAAUGCAUUGCCUUCAGCAUCUAAACAA
#=GC SS_cons                   ::::::::::::::::::::<<<<<-<-<<-<<-<<<<<<<<<<<<<<<-<<<--<<___>>----->>>>>>>>>>>>>>>>>>->>->>->->>>>>:::::::
#=GC RF                        auaauuauuaaagAguUUUUGaUGuuGcaGAuaCUGCAUcAGGaACUGaUuGGaUgauaaucagucaCCauCAGUuCCUgAUGCAUugCCuUCAgCAuCuAAAcAA
//
# STOCKHOLM 1.0

#=GF AC   RF00674
#=GF ID   mir-187
#=GF DE   microRNA mir-187
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   62.00
#=GF TC   68.30
#=GF NC   55.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000078;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   12624257
#=GF RT   Vertebrate microRNA genes.
#=GF RA   Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP
#=GF RL   Science. 2003;299:1540.
#=GF RN   [3]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   Mir-187_microRNA_precursor_family
#=GF SQ   20


AALT01600757.1/702-806       GGGCUCACCAAGACUCCGUGUGUUACCUCGGGCUACAACACGGGACCCGGGCGCUA-CUCCGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACACAGGUCCGCA
CAAE01015012.1/372800-372873 -------------------------CCAGGGGCUGCAACACAGGACAUGGGUCUUGCCUCUGCCCGCCGCUCGUGUCUUGUGUUGCAGCCAGUGGAACU----------
AAFC03051911.1/20036-20139   GGCUCCC-CACGACACGGUGUGAGACCUCGGGCUACAACACGGGACCCGGGCGCUG-CUCCGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACGCAAGUCCGCA
AAHY01137150.1/64474-64371   GGGCUCA-CAGGAUACAAUGCGGGUCCUCAGGCUACAACACAGGACCCGGGCGCUG-CUCUGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACGCAGGUCUGCA
BAAE01104282.1/99-8          ----------------UUGGUUGGGCCAGCGGCUGCAACACAGGACAUGGGUCCUGCUUCUCCUCCC-GCUCGUGUCUUGUGUUGCAGCCAGUGGAGCUCCCUGUCCGU
BX927241.19/109900-110007    AGACGAA-GGUGACCUGUGGCUGGGCCAGGGGCUGCAACACAGGACAUGGGAGCUGUCUCUCACUCCCGCUCGUGUCUUGUGUUGCAGCCAGUGGAACGGCUACACUGU
AAPN01052341.1/8485-8382     UGUGUUG-UCCAUCAUCUUGUGAGACCUCCGGCUACAACAGAGGACACAGGAGCUU-UUCAGAACC---CUCGUGUCUUGUGUUGCAGCCAGAGGAGCACAUCUAUUCG
AAYZ01085202.1/4617-4513     GGAUUCACCGUGACACAGUGUGGGACCUCGGGCUACAACCCAGGACCCGGGCGCUG-CUCUGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACACAGGUUUGCA
AY866178.1/469-573           AGGCUCACUAUGACACAGUGUGAGACCUCGGGCUACAACACAGGACCCGGGUGCUG-CUCUGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACGCAGGUCCGCA
AAFR03010221.1/8167-8270     GGUUUGU-CAUCAUGUAUUGUGAGACCUCUGGCUACAACACAGGACACGGGAGCUU-UUCUGAACC---CUCGUGUCUUGUGUUGCAGCCAGAGGGGCACAUCUUUGCG
ABDC01264301.1/2060-1957     GGCCCGC-CAUGACACGGUGUGAGACCUCGGGCUACAACACAGGACCCGGGCGCUG-CUCUGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACGCAGGUCCGCA
AAQQ01333660.1/699-803       GGGCCCACUGUGACAUGGUGUGAGUCCUCGGGCUACAACACAGGACCCGGGCGCUG-UUCAGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACACAGGUCUGCA
AAWR02022308.1/206632-206529 GUGCCCG-CAAGACACGGUGUGAGACCUCGGGCUACAACACGGGACCCGGGCGCUG-CUCCGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACGCAGGUCCGCA
AAKN02020391.1/22749-22852   CUGAGCU-CAUGAUACAGUGUGAGUCCUUGGGCUACAACACAGGACCCGGGCGCUG-AUUUGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACACAGGUCUGCA
AADN03001852.1/531649-531752 GGUUUGC-UCUAAACUAUUGUGAGACCUCCGGCUACAACACAGGACAUGGGAGCUU-UUCUGAACC---CUCGUGUCUUGUGUUGCAGCCAGAGGGGCACAUCUUUUCA
AAWZ02000931.1/55275-55378   ACUUUUU-UAUGAAUUCUUGUGAGACCUUUGGCUACAACACAGAACAUGGGCGCUU-UCUUGGACC---CUCGUGUCUUGUGUUGCAGCCAGAGGGGCACAUCUUGGCA
AAGU03013622.1/2338-2441     -GGCUCACCAUGACAUGGUGUGAGACCUCGGGCUACAACACAGGACCCGGGUGCUG-CUCUGACCC---CUCGUGUCUUGUGUUGCAGCCGGGGGGACACAGGACCGCA
CAAB02003131.1/32211-32104   GCUGAAG-GUGGCCAUUUGGCCGGGCCAGGGGCUGCAACACAGGACAUGGGUCAUGCCUCUGCCCACCGCUCGUGUCUUGUGUUGCAGCCAGUGGAGCUGCCUGUCUUC
AAPE02009267.1/25442-25546   AGGCUCACCUUGACACGGUGUGAGACCUCGGGCUACAACACGGGACCCGGGCGCUG-CUCCGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACGCAGGUCCGCA
AC125096.3/60283-60386       GGGCUCA-CAGGAUACAAUGCGGGUCCUCAGGCUACAACACAGGACCCGGGCGCUG-CUCUGACCC---CUCGUGUCUUGUGUUGCAGCCGGAGGGACGCAGGUCUGCA
#=GC SS_cons                 :::::::.:::::::::::::::::<<<--<<<<-<<<<<<<<<<<<<<<<_____._________...>>>>>>>>>>>>>>>>->>>>-->>>::::::::::::::
#=GC RF                      gguuuca.uauGAcauauuGUgaGaCCucgGGCUACAACACaGGACacGGGugCUg.cUCUGacCC...CUCguGUCUuGUGUUGCAGCCaGaGGgaCacAuguuugca
//
# STOCKHOLM 1.0

#=GF AC   RF00675
#=GF ID   mir-145
#=GF DE   microRNA mir-145
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   60.00
#=GF NC   59.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000079;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [2]
#=GF RM   14573789
#=GF RT   Reduced accumulation of specific microRNAs in colorectal neoplasia.
#=GF RA   Michael MZ, O' Connor SM, van Holst Pellekaan NG, Young GP, James RJ
#=GF RL   Mol Cancer Res. 2003;1:882-891.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-145
#=GF SQ   13


AADC01055700.1/27332-27419   CACCUUGU-CCUCAC-GGUCCAGU-UUUCCCAGGAAUCCCUUAGAUG--CUAAGAU---GGGGAUU-CCUGGAAAUACUGUUCUUGAGGUCAUGGUU
CT029999.12/82723-82635      UUCCUCAU-CCCCGG-GGUCCAGU-UUUCCCAGGAAUCCCUUGGGCA-AUCGAAAG---GGGGAUU-CCUGGAAAUACUGUUCUUGGGGUUGGGGGU
BAAF04072768.1/17019-16930   CUCCUCUC-UCCUGG-GGUCCAGU-UUUCCCAGGAAUCCCUUGGGCUGUCAAAAAA---GGGGAUU-CCUGGAAAUACUGAUCUUGGGGGUGGGGCU
AAPN01425210.1/4552-4467     CCACCGUG--UCUCA-GGUCCAGU-UUUCCCAGGAAUACAU-AGGUG--CUGAGAU---GGGGAUU-CCUGGAAAUACUGUUCUUGAGGUCAUGGCU
AANH01007327.1/2171-2260     UUCCUCUC-UCCUGG-GGUCCAGU-UUUCCCAGGAAUCCCUUGACCU--AUCAGAAA-GGGGGAUU-CCUGGAAAUACUGUUCUUGGGGGCGGGGCU
AANG01343499.1/5356-5446     CCUUUGUC-CCUCAC-GGUCCAGUUUUUCCCAGGAAUCCCUUAGAUG--CUAAGAU--GGGGGAUUCCCUGGAAAUACUGUUCUUGAGGUCAUGGUU
AAGV020415915.1/2-83         ---CGUGU-CCUCAC-GGUCCAGU-UUUCCCAGGAAUCCUU-AGAUG--CUAAGAU---GGGGAUU-CCUGGAAAUACUG--UCUUGAGGUCACGGU
CAAB02010650.1/42467-42377   AUCCUCUC-UCCUGG-GGUCCAGU-UUUCCCAGGAAUCCCUUGACAU--UUCAGAACAGGGGGAUU-CCUGGAAAUACUGUUCUUGGGGGCGGGGCU
AAWZ02012097.1/17386-17298   UUACUGUGUCCUCGG-GGUCCAGU-UUUCCCAGGAAUCCCUUAGAUG--AUAAGAG---GGGGAUU-CCUGGAAAUACUGUUCUUGGGGUCAUGGCU
AAEX03003103.1/475200-475114 CGCCGUGU-CCUCAC-GGUCCAGU-UUUCCCAGGAAUCCCUUAGAUG--CUAAGAU---GGGGAUU-CCUGGAAAUACUGUUCU-UGAGGUCAUGGU
AY865899.1/453-539           CACCUUGU-CCUCAC-GGUCCAGU-UUUCCCAGGAAUCCCUUAGAUG--CUAAGAU---GGGGAUU-CCUGGAAAUACUGUUCU-UGAGGUCAUGGU
AC125157.4/168663-168751     CCACCUUG-UCCUCACGGUCCAGU-UUUCCCAGGAAUCCCUUGGAUG--CUAAGAU---GGGGAUU-CCUGGAAAUACUGUUCUUGAGGUCAUGGCU
AY865896.1/427-513           CACCUUGU-CCUCAC-GGUCCAGU-UUUCCCAGGAAUCCCUUAAAUG--CUAAGAU---GGGGAUU-CCUGGAAAUACUGUUCU-UGAGGUCAUGGU
#=GC SS_cons                 :::<<<<<.<<<<<<.<<--<<<<.-<<-<<<<<<<<<<<<______.._______...>>>>>>>.>>>>>->>->>>>-->>>>>>>>>>>>>::
#=GC RF                      cucCcccc.cCcccg.gGUCCaGU.UUUCCCaGGaaUCCcuUagaug..cUaAGAu...ggGGAuu.CCuGGAAAUACuGUUCucgggGgggggGcU
//
# STOCKHOLM 1.0

#=GF AC   RF00676
#=GF ID   mir-127
#=GF DE   microRNA mir-127
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   111.00
#=GF TC   117.30
#=GF NC   41.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000080;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15854907
#=GF RT   RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus.
#=GF RA   Davis E, Caiment F, Tordoir X, Cavaille J, Ferguson-Smith A, Cockett N,
#=GF RA   Georges M, Charlier C
#=GF RL   Curr Biol. 2005;15:743-749.
#=GF RN   [2]
#=GF RM   15891114
#=GF RT   Clustering and conservation patterns of human microRNAs.
#=GF RA   Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A,
#=GF RA   Brownstein MJ, Tuschl T, Margalit H
#=GF RL   Nucleic Acids Res. 2005;33:2697-2706.
#=GF RN   [3]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells.
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [4]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-127
#=GF SQ   5


AAFC03050876.1/55038-55134 UUUGAUCACUGUCUCCAGCCUGCUGAAGCUCAGAGGGCUCUGAUUCAGAAAGAUCAUCGGAUCCG-UCUGAGCUUGGCUGGUCGGAAGUCUCCUCAUC
AY865922.1/435-531         UGUGAUCACUGUCUCCAGCCUGCUGAAGCUCAGAGGGCUCUGAUUCAGAAAGAUCAUCGGAUCCG-UCUGAGCUUGGCUGGUCGGAAGUCUCAUCAUC
AY865925.1/378-474         UGUGAUCACUGUCUCCAGCCUGCUGAAGCUCAGAGGGCUCUGAUUCAGAAAGAUCAUCGGAUCCG-UCUGAGCUUGGCUGGUCGGAAGUCUCCUCAUC
EU499599.1/1788-1884       UUUGAUCACUGUCUCCAGCCUGCUGAAGCUCAGAGGGCUCUGAUUCAGAAAGAUCAUCGGAUCCG-UCUGAGCUUGGCUGGUCGGAAGUCUCAUCAUC
AY865920.1/437-533         UGUGAUCACUGUCUCCAGCCUGCUGAAGCUCAGAGGGCUCUGAUUCAGAAAGAUCAUCGGAUCCGU-CUGAGCUUGGCUGGUCGGAAGUCUCCUCAUC
#=GC SS_cons               :::<<<--<<<---<<<<<<-----<<<<<<<<<-<<-<<<<<<<<_____>>-->>>>>>->>-.>>>>>>>>>>>>>>>->>>-->>>::::::::
#=GC RF                    UgUGaccACcGUcUCCaGCCUGcUGaaGCuCaGaGGGcuCcGauuCAGAAAGaUcauCgGaUCCG.uCuGaGCuuGGCuGGUCgGAAguCUcaUcAUc
//
# STOCKHOLM 1.0

#=GF AC   RF00677
#=GF ID   MIR168
#=GF DE   microRNA MIR168
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   66.00
#=GF TC   67.70
#=GF NC   65.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000081;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12101121
#=GF RT   MicroRNAs in plants.
#=GF RA   Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP
#=GF RL   Genes Dev. 2002;16:1616-1626.
#=GF RN   [2]
#=GF RM   12202040
#=GF RT   Prediction of plant microRNA targets.
#=GF RA   Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP
#=GF RL   Cell. 2002;110:513-520.
#=GF RN   [3]
#=GF RM   15994906
#=GF RT   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa
#=GF RT   that are absent from Arabidopsis.
#=GF RA   Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL
#=GF RL   Plant Cell. 2005;17:2186-2203.
#=GF RN   [4]
#=GF RM   19555436
#=GF RT   Cloning and characterization of small RNAs from Medicago truncatula
#=GF RT   reveals four novel legume-specific microRNA families.
#=GF RA   Jagadeeswaran G, Zheng Y, Li YF, Shukla LI, Matts J, Hoyt P, Macmil SL,
#=GF RA   Wiley GB, Roe BA, Zhang W, Sunkar R
#=GF RL   New Phytol. 2009;184:85-98.
#=GF WK   MicroRNA
#=GF SQ   10


AASG02009178.1/8089-7934 UUACCGGCGGUCUCUAAUUCGCUUGGUGCAGGUCGGGAACUGAUU--GGCUUUUCUAUUUCUAAUGAUUU-----CCAG---GCGGCGAAAAGUUAU--------------UGGUCAAGAUUAGAUGGAA--------AGU--GA-AUUGGAUCCCGCCUUGCAUCAACUGAAUCGAAGACC-GGGGUGAAG
AB020744.1/40369-40244   UUACCGGCGGUCUCGGAUUCGCUUGGUGCAGGUCGGGAACUGAUUG-GCUGACACCGACACGUGUCUUG---------------UCAUGGUUGGU------------------------------UU-------------------GUGAGCUCCCGUCUUGUAUCAACUGAAUCGGAGUCC-GAGGUGAAA
AC126012.22/66241-66365  CUUCUUUCGAUCUCUGAUUUGCUUGGUGCUGGUCGGGAACCAUU---ACAUCCACAGUUUCCGUAGAAAC--------------UUUCCCU----------------------------------------------UAGU--AA-AUUGGACCCCGUCUUGCAUCAAUCGAAUCAGAGGUC-GCGGUGAAU
AK063802.1/109-212       GGCGCCGCCGCCUCGGGCUCGCUUGGUGCAGAUCGGGACCCGCC---GCCGCCGCUG------------------------------CCGG----------------------------------------------GG--------CCGGAUCCCGCCUUGCACCAAGUGAAUCGGAGCCG-GCGUAGCGC
AY728396.1/1-121         ----------------AUUCGCUUGGUGCAGGUCGGGAACUGAUUC-GGCGAUUUGAUUGCCAGAUGGCU--------AAACACGAUUGGCUGU----------------GAGGCAAAUUAUAAAAAGAA--------AGA--GA-AUUGGAUCCCGCCUUGCAUCAACUGAA-------------------
AY728397.1/1-145         ----------------AUUCGCUUGGUGCAGGUCGGGAACUGAUUC-GGCGAUUUGAUUGCCAGAUGGCU--------CGACAUGACUGGUUGUUGUGGAAAAAGAAAAGGAAGGAAACAGGAAAAAAAACAAAGAAUAGC--GA-AUUGGAUCCCGCCUUGCAUCAACUGAA-------------------
CU302337.1/59396-59285   CUCACUUCAACCUCUGAUUCGCUUGGUGCAGGUCGGGAACCAUU---ACAUCCACAGUUUCC---------------------------CU----------------------------------------------CGGU--AA-AUUGGAUCCUGCCUUGCAUCAAUCGAAUCGGAGGCU-GCAGUGAAU
CU302345.1/65608-65728   CACUUCGCGGUCUCUAAUUCGCUUGGUGCAGGUCGGGAACCACU---ACAUCCGCUGUUUUCGUAGAAA----------------------CCGGC------------------------------------------GGU--GA-AUUGGAUCCCGCCUUGCAUCAACUGAAUCGGAGGCC-GCGGUGAAU
DQ108858.1/128-268       UCACCAUCGGGCUCGGAUUCGCUUGGUGCAGGUCGGGAACCAAUUCGGCUGACACAGCCUCGUGACUUUU--------------AAACCUUUAUUGG---------------------------UUUGUG--------AGCAGGG-AUUGGAUCCCGCCUUGCAUCAACUGAAUCGGAUCCUCGAGGUGUA-
AM444929.2/2171-2317     CUUACGGUGGUCUCUAAUUCGCUUGGUGCAGGUCGGGAACCGACUUCGCCGCUCCGGCAGCGCCGGAGGCACGCGGCGGCCUACGAUUGGUUGCUG------------------------------------------AGC--GAAUUCCGAUCCCGCCUUGCAUCAACUGAAUCGGAGACG-GCGGUGAUG
#=GC SS_cons             ::::::::::::<<--<<<<--<<<<<<<<<<-<<<<<-<<_____._______________________..............____________.............................__...........___..__.___>>->>>>>->>>>>>>>>>-->>>>-->>::::.:::::::::
#=GC RF                  uuacCugCgGuCUCugaUUCGCUUGGUGCAGGUCGGGAACcgaUUc.GccgauuCuguuuCcagauaguU..............gauugguUguUg.............................ua...........AGu..GA.AUUgGAUCCCGCCUUGCAUCAAcUGAAuCGGAGaCu.GcGGUGaau
//
# STOCKHOLM 1.0

#=GF AC   RF00678
#=GF ID   mir-140
#=GF DE   microRNA mir-140
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   94.00
#=GF TC   98.20
#=GF NC   69.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000085;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16750530
#=GF RT   Identification of microRNAs from different tissues of chicken embryo and
#=GF RT   adult chicken.
#=GF RA   Xu H, Wang X, Du Z, Li N
#=GF RL   FEBS Lett. 2006;580:3610-3616.
#=GF RN   [2]
#=GF RM   15800047
#=GF RT   Kaposi's sarcoma-associated herpesvirus expresses an array of viral
#=GF RT   microRNAs in latently infected cells.
#=GF RA   Cai X, Lu S, Zhang Z, Gonzalez CM, Damania B, Cullen BR
#=GF RL   Proc Natl Acad Sci U S A. 2005;102:5570-5575.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   14


BAAF04008549.1/880-978         UCUCUGUCUCCGGUGUCACGUCAGUGGUUUUACCCUAUGGUAGGUGACAUCAUGCUGUUCUACCACAGGGUAGAACCACGGACGGGAUGUUGGGAGGUG
AAVX01038725.1/2937-3034       CUUUCCACU-CUGUGACCUACCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACAGGCUACUGAGAUUCU
AAPN01171234.1/21212-21309     UGUCUCUCU-CUGUGUCCUGCCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACAGGAUACCGGGACGCU
BX890570.11/109089-108991      UGUUUGUCUCCUGUGUCCCGUCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACGGGAUGUCUGGAGGUG
CAAE01014566.1/1204272-1204174 UCUCUGUCUCUGGUGUCACGUCAGUGGUUUUACCCUAUGGUAGGUGACAUCAUGCUGUUCUACCACAGGGUAGAACCACGGACGGGAUGUCGGAGGGUG
AANH01008603.1/57229-57132     UCUUGUCUC-CGGUGUCGCGUCAGUGGUUUUACCCUAUGGUAGGUGACAUCAUGCUGUUCUACCACAGGGUAGAACCACGGACGGGAUGUCGUGAGGUG
AAHX01098220.1/19370-19467     UGUCUCUCU-CUGUGUCCUGCCAGUGGUUUUACCCUAUGGUAGGUUACAUCAUGCUGUUCUACCACAGGGUAGAACCACGGACAGGAUACUGGAGCACC
ACTA01018935.1/111755-111658   UCUGUCUCU-CUGUGUCCUGCCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACAGGAUACCGAGGCACC
AADN03006300.1/10985-10888     UGCGUCUCU-CCGUGUCCUGCCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACGGGAUGCCGGGGCUGC
AAWZ02031409.1/32112-32209     UUCCUCUCU-CUGUGUCCUUCCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACGGGAUGCCGGGGCUCU
EU116273.1/131-229             UGUUUGUCUCCUGUGUCCCGUCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACGGGAUGUCUGGAGGUG
AC132126.3/17780-17683         UGUCUCUCU-CUGUGUCCUGCCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACAGGGUACUGGAGCACC
AY865886.1/365-462             UGUCUCUCU-CUGUGUCCUGCCAGUGGUUCUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACAGGAUACCGGGGCACC
AY865885.1/385-482             UGUCUCUCU-CUGUGUCCUGCCAGUGGUUUUACCCUAUGGUAGGUUACGUCAUGCUGUUCUACCACAGGGUAGAACCACGGACAGGAUACCGGGGCACC
#=GC SS_cons                   :::::::::.::::::<<<<<<<<<<<<<<<<<<<<-<<<<<<<--<<<______>>>>>>>>>>->>>>>>>>>>>>>>>>>>>>:::::::::::::
#=GC RF                        UgUuucuCU.CuGUGUCccgcCaGuGGuuuuaCCCuAuGGuaGgUuaCgUCAUGCcGuuCuaCCaCaGGGuagaaCCaCgGgcggGAUaccGggacauu
//
# STOCKHOLM 1.0

#=GF AC   RF00679
#=GF ID   mir-210
#=GF DE   microRNA mir-210
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   51.00
#=GF TC   52.00
#=GF NC   50.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000086;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15800047
#=GF RT   Kaposi's sarcoma-associated herpesvirus expresses an array of viral
#=GF RT   microRNAs in latently infected cells.
#=GF RA   Cai X, Lu S, Zhang Z, Gonzalez CM, Damania B, Cullen BR
#=GF RL   Proc Natl Acad Sci U S A. 2005;102:5570-5575.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   Mir-210_microRNA
#=GF SQ   26


AAJJ01000173.1/48564-48466   CUGAAUCUCACUGCAGCUGCUGGACGCUGCACAAGAUUAGAUAUUUUAGAACUCUUGUGCGUGUGACAGCGGCUAUUGUGGGUAUUCUUA-UUCAACAAU
BAAE01058508.1/297-393       UCUAAAAGCAGGUAAGCCACUGACUAACGCACAUUGUGCGUGUGAC-AGAUCCACUGUGCGUGUGACAGCGGCUAACCUGGU-UUUGGGA-AAACCUCUG
AAPP01019211.1/33278-33184   ACGGUGCUUAUUGCAGCUGCUGGCCACUGCACAAGAUUAGACUU---AAGACUCUUGUGCGUGUGACAGCGGCUAUUGUAAG-AGGCCAU-AGAAGCAAC
AAAB01008958.1/106879-106786 AAGAAAUUCAUUGCAGCUGCUGACCACUGCACAAGAUUAGAAUG----CGACUCUUGUGCGUGUGACAACGGCUAUUAUGGG-UUUUCAA-AAUCAUUUU
AAVX01157710.1/252-349       UCCAAAAGCAAGUGAGCCACUGACUAACGCACAUUGCGCUGUGUUUGAAUACCACUGUGCGUGUGACAGCGGCUAACUUGCU-CUUAGGA-CGGCACCUG
BAAB01031372.1/2361-2266     --GAAGUCCAAAGCAGCUGCUGGCCACUGCACAAGAUUAGUCAAGUUUAUACUCUUGUGCGUGUGACAGCGGCUAUUGCGGG-CAUUUCA-UUGGCUGCG
AAZX01004912.1/9254-9160     AUGGACCCCAGUGCAGCUGCUGGCCACUGCACAAGAUUAGACAU---AAGACUCUUGUGCGUGUGACAGCGGCUAUGAUGGG-GCUUCCG-UGACACAGC
AAIY01719786.1/340-435       UCCAGGUGCAGGGCAGUCCCUGCCCACCGCACACUGCUCUGUGCC--AGACCCAUUGUGCGUGUGACAGCUGCUGAUCUGUC-CCUGGGU-UGCACGAUC
AAFR03066236.1/16417-16509   UCCGGCCGCAGGGGAGCCACUGACUAACGCACAUUGCGCUC---A--GGACCCACUGUGCGUGUGACAGCGGCUACCGUGCA-ACCGGCC-CGCAGCUGG
AAZO01006118.1/235-143       GGAAAACCCAUGGCAGCUGCUGGACACAGCCCAAGAUUAGU-UU---AAGACUCUUGUGCGUGA-ACAUCAGCUAGUGUGGG-GUUUCAA-CACGGCAUA
AAWU01026010.1/9946-9852     CUGAAUCUCAUUGCAGCUGCUGACCACUGCACAAGAUUAGA-UU---AUGACUCUUGUGCGUGUGACAACGGCUAUUGUGGGCAUUCCAA-AUCAACCAG
AAGE02019443.1/85298-85205   GUGAAUCUCAUUGCAGCUGCUGACCACUGCACAAGAUUAGA-UU---AUGACUCUUGUGCGUGUGACAACGGCUAUUGUGGG-CAUUCCG-AGUCAUCCA
AAPT01021333.1/33432-33528   UCGGAGCUUAUUGGAGCUGCUGGCCACUGCACAAGAUUAGAUUCAA-AAGACUCUUGUGCGUGUGACAGCGGCUAUUGUAAG-AGACCAG-AUAACAUCA
AJ330328.1/223-318           UUCAGGCGCAGGGCAGUACCUGCCCACCACACAUUGGGCUGACCC--AAGACCACUGUGCGUGUGACAGCGGAUGAUCUGUG-CCUAGGC-AGAACGAAC
AAHY01067274.1/26421-26326   UCCAGGCUCAGGACAGCCACUGCCCACCGCACACUGCGUUGCUCC--GGACCCACUGUGCGUGUGACAGCGGCUGAUCUGUC-CCUGGGC-AGCGCGAAC
AAQB01008838.1/8331-8425     ACGGUACUUAUUGCAGCUGCUGGCCACUGCACAAGAUUAGACUU---AAGACUCUUGUGCGUGUGACAGCGGCUAUUGUAAG-AGGCCAG-AAAACGACC
AAIZ01004338.1/5853-5947     UCGGUACUUAUUGCAGCUGCUGGCCACUGCACAAGAUUAGAUUU---AAGACUCUUGUGCGUGUGACAGCGGCUAUUGUAAG-AGGCCAU-AUUAGCAUC
AANI01015309.1/4850-4756     GCGGUACUUAUUGCAGCUGCUGGCCACUGCACAAGAUUAGACUC---AAGACUCUUGUGCGUGUGACAGCGGCUAUUGUAAG-AGACCAG-AGAAACAGC
CAAE01014688.1/325191-325288 UCUGAAAGCAGGUGAGCCACUGACUAACGCACAUUGUGCCAGUUGACAGUUCCACUGUGCGUGUGACAGCGGCUAACCUGGU-UUUGGGG-ACACCUCCU
AANH01001617.1/62500-62403   UCUAAAAGCAGGUAAGCCACUGACUAACGCACAUUGUGCCAGUGUCCAAAUUCACUGUGCGUGUGACAGCGGCUAACCUGGU-UUUGGGA-GCACUUCUC
AAKN02056356.1/47090-47185   UCCAGGCGCAGGGCAGCCACUGCCCACCGCACACUGCGCUGCUCC--CGACCCACUGUGCGUGUGACAGCGGCUGAUCUGUC-CCUGGGC-AGCGCGAGC
AL928892.6/129366-129463     UCUGAAAGCAGGUAAGCCACUGACUAACGCACAUUGCGCCUAUUCUCCACUCCACUGUGCGUGUGACAGCGGCUAACCAGCU-UUUGGAUCUGCACCUG-
CAAB02005932.1/3542-3453     UCUAAAAGCAGGUGAGCCACUGACUAACGCACAUUGCGCCAGUUGACAGUUCCACUGUGCGUGUGACAGCGGCUAACCUGGU-UUUGGGA-A--------
AADG06004206.1/5125-5031     AUGGACCCUAAUGCAGCUGCUGGCCACUGCACAAGAUUAGACAU---AAGACUCUUGUGCGUGUGACAGCGGCUAUGAUGGG-GUUUCCA-CGAAACAAC
AP006284.2/26902-26807       UCCAGGCGCAGGGCAGCCCCUGCCCACCGCACACUGCGCUGCCCC--AGACCCACUGUGCGUGUGACAGCGGCUGAUCUGUG-CCUGGGC-AGCGCGACC
AAWZ02002961.1/110385-110298 UCCAGGAGCAGAUGAGCCACUGACUAACGCACAUUGUGCUUCUCGU-GUCCCCACUGUGCGUGUGACAGCGGCUAACCUGCU-UUUCGGA----------
#=GC SS_cons                 ::::<<<<<<<<--<<<<<<<<-<<<-<<<<<<-<<_________.._____>>->>>>>>>>->->>>>>>>>-->>>>>>.>>:::::.:::::::::
#=GC RF                      ucgAgcccCAgggcAGCcgCUGaCCAccGCACAagguuagauuuu..AaaaCccuUGUGCgUGUGACAGcgGCUAaccUGgg.gcUugaa.agaaacauc
//
# STOCKHOLM 1.0

#=GF AC   RF00680
#=GF ID   mir-224
#=GF DE   microRNA mir-224
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   80.40
#=GF NC   45.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000088;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF RN   [2]
#=GF RM   12554860
#=GF RT   Numerous microRNPs in neuronal cells containing novel microRNAs.
#=GF RA   Dostie J, Mourelatos Z, Yang M, Sharma A, Dreyfuss G
#=GF RL   RNA. 2003;9:180-186.
#=GF RN   [3]
#=GF RM   15891114
#=GF RT   Clustering and conservation patterns of human microRNAs.
#=GF RA   Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A,
#=GF RA   Brownstein MJ, Tuschl T, Margalit H
#=GF RL   Nucleic Acids Res. 2005;33:2697-2706.
#=GF WK   MiR-224
#=GF SQ   5


AADB02037484.1/327553-327473 GGGCUUUCAAGUCACUAGUGGUUCCGUUUAGUAGAUGAUUGUGCAUUGUUUCAAAAUGGUGCC-CUAGUGACUACAAAGCCC
AAYZ01416179.1/584-505       GGGCUUUCAAGUCACUAGUGGUUCCGUUUAGUAGAUGGU-UUGCAUUUCUUCAAAAUGGUGCC-CUAGUGACUACAAAGCCC
AANG01462441.1/2365-2285     GGGCUUUCAAGUUACUAGUGAUUCCGUUUAGUAGAUGGCUGUGCAUUGUUUCAAAAUGGCCCC-CUAGUGACUACAAAGCCC
AAQQ01376165.1/3609-3529     GGGCUUUCAAGUCACUACUGUUUCCGCUUAGUAGAUGGUUGUACAUUGUUUCAGAAUGGUGCC-CUAGUGACUACAAAGCAC
AAGV020950165.1/982-903      GUGCUUUCAAGUCACUUGUCUACCA--UUAGUAGAUGGUUGUGCAUUGUUUCAAAAAUGGUACCCUAGUGACUACAAUGCCC
#=GC SS_cons                 <<<<<<<--<<<<<<<<<-<<<<<<<<<<-<-<<<--<<_____>>-->>>>->>>>>>>>>>.>>>>>>>>>-->>>>>>>
#=GC RF                      GgGCuuuCAaGucaCuaGUGgccCcguuuAGUagaUGguUgUGCauUguuuCAaaaugGggcC.CuaGugaCuACaaaGCcC
//
# STOCKHOLM 1.0

#=GF AC   RF00681
#=GF ID   mir-198
#=GF DE   microRNA mir-198
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   85.80
#=GF NC   49.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000090;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA. 2003;9:175-179.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   15652478
#=GF RT   Phylogenetic shadowing and computational identification of human microRNA
#=GF RT   genes.
#=GF RA   Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E
#=GF RL   Cell. 2005;120:21-24.
#=GF WK   Mir-198_microRNA_precursor_family
#=GF SQ   3


AB119283.1/66690-66751 UCAUUGGUCCAGAGGGGAGAUAGGUUCCUGUGAUUUUUCCUUCUUCUCUAUAGAAUAAAUGA
AY866280.1/427-488     UCACUGGUCCAGAAGGGAGCUAGGUACUUGUGAUUUUUCCUUCUUUUCUGUAGAAUAAAUGA
AY866279.1/540-601     UCAUUGGUCCAGAGGGGAGCUCGAUACCUGUGAUUUUUCCUUCUUUUCUGUAGAAUAAAUGA
#=GC SS_cons           (((((--((((((((((((,<<<____>>>,<<____>>,))))))))))--))---)))))
#=GC RF                UCAuUGGUCcAGAgGGGAGcuaGgUaCCugUGAUUUUUCCUUCUUcUCUgUAGAAUAAaUGA
//
# STOCKHOLM 1.0

#=GF AC   RF00682
#=GF ID   mir-144
#=GF DE   microRNA mir-144
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   74.10
#=GF NC   48.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000093;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   16750530
#=GF RT   Identification of microRNAs from different tissues of chicken embryo and
#=GF RT   adult chicken.
#=GF RA   Xu H, Wang X, Du Z, Li N
#=GF RL   FEBS Lett. 2006;580:3610-3616.
#=GF RN   [3]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   miR-144
#=GF SQ   22


AADC01129597.1/744-828       UGGGGCCCUGGCUGGGAUAUCAUCAUAUACUGUAAGUUUGCGA-UGAGACACUACAGUAUAGAUGAUGUACUAGUCCGGGCACCCC
CAAE01014557.1/33500-33585   UUGUGCCCUGGACAGGAUAUCAUCUUAUACUGUAAGUUUAAUAAAGUGACACUACAGUAUAGAUGAUGUACUAUCCAGGGCUUCAU
AAFR03044825.1/5551-5467     CGGGGCCCAGGCCGGGAUAUCAUCGUAUACUGUAAGUUUGCAA-UGAGACACUACAGUAUAGAUGAUGUACUGGCGAGGGCCGCCU
BX548073.8/159549-159634     UUGCUCUCUAGACAGGAUAUCAUCGUAUACUGUAAGUUCAUUAUUGAGACACUACAGUAUAGAUGAUGUACUAUCCAGGGGGUCAA
AAVX01587350.1/53-138        UUGUGCUCUGGGCUGGAUAUCAUCAUAUAUUGUAAGUUCACAAUUCAGACACUACAGUAUAGAUGAUGUACUACACAGGGCUACAC
AANN01574826.1/86-2          CAGGGCCUUGGUUGGGAUAUCAUCAUAUACUGUAAGUUUGUGA-UGAGACACUACAGUAUAGAAAAUCUACUAGCCCGGGUUCCCU
AAFC03123225.1/17133-17217   CAGGGCCCUGACUGGGAUAUCAUCAUAUACUGUAAGUUUGCAA-CGAGACACUACAGUAUAGAUGAUGUACUAGUCCGGGUGCUCC
AANH01000562.1/126228-126313 UUGUGCCCCGGACAGGAUAUCAUCUUAUACUGUAAGUUUAUUAAAGAGACACUACAGUAUAGAUGAUGUACUAUCCAGGGUCUCAU
AAPN01323131.1/344-260       CGGGGCCCUGGCGGGGAUAUCAUCGUAUACUGUAAGUUUGCUA-UGAGACACUACAGUAUAGAUGAUGUACUAGCCCGGGUGCCCC
AANG01161467.1/4827-4743     CAGGAUCCUGGCUGGGAUAUCAUCAUAUACUGUAAGUUUGCGA-UGAGAUACUACAGUAUAGAUGAUGUACUAGUCCGGGUACCCC
AAHX01064968.1/4371-4455     CAGGGCCUUGGCUGGGAUAUCAUCAUAUACUGUAAGUUUGUGA-UGAGACACUACAGUAUAGAUGAUGUACUAGUCUGGGUACCCC
AAEX03006671.1/2727-2643     CGGGGCCCUGGCUAGGAUAUCAUCAUAUACUGUAAGUUUGCGA-CAAGAUACUACAGUAUAGAUGAUGUACUAGUCCGGGUCCCCA
AADN03007690.1/39192-39108   CGCCGCCCUGGGCUGGAUAUCAUCAUAUACUGUAAGUUCACUA-UGAGACACUACAGUAUAGAUGAUGUACUCCCCUGGGCUGCAC
AAPE02030653.1/27404-27320   CAGGGCCCUGGCUGGGAUAUCAUCGUAUACUGUAAGUUUGCAA-UGAGACACUACAGUAUAGAUGAUGUACUAGUCCGGGCACCCU
CAAB02013240.1/35503-35588   UUGUGCCCUGGACAGGAUAUCAUCUAAUACUGUAAGUUUAUUAAAGAGACACUACAGUAUAGAUGAUGUACUAUCCAGGGGUUCAG
BC152081.1/387-472           UUGCUCUCUAGACAGGAUAUCAUCGUAUACUGUAAGUUCAUUAUUGAGACACUACAGUAUAGAUGAUGUACUAUCCAGGGGGUCAA
AC024267.18/54766-54682      UGGGGCCCUGGCUGGGAUAUCAUCAUAUACUGUAAGUUUGCGA-UGAGACACUACAGUAUAGAUGAUGUACUAGUCCGGGCACCCC
FQ233014.1/322-406           CAGGGCCUUGGCUGGGAUAUCAUCAUAUACUGUAAGUUUGUGA-UGAGACACUACAGUAUAGAUGAUGUACUAGUCUGGGUACCCC
AY865895.1/403-487           UGGGGCCCUGGCUGGGAUAUCAUCAUAUACUGUAAGUUUGCGA-UGAGACACUACAGUAUAGAUGAUGUACUACUCCGGGCACCCU
AY865894.1/413-497           UGGGGCCCUGGCUGGGAUAUCAUCAUAUACUGUAAGUUUGUGA-UGAGACACUACAGUAUAGAUGAUGUACUAGUCCGGGCACCCC
AY865893.1/442-526           UGGGGCCCUGGCUGGGAUAUCAUCAUAUACUGUAAGUUUGCGA-UGAGACACUACAGUAUAGAUGAUGUACUAGUCUGGGCACCCC
AY865892.1/431-515           UGGGGCCCUGGCUGGGAUAUCAUCAUAUACUGUAAGUUUGCGA-UGAGACACUACAGUAUAGAUGAUGUACUAGUCCGGGCACCCU
#=GC SS_cons                 ::::::<<-<<<<<<<<<<<<<<<-<<<<<<<<<-<_______._______>>>>>>>>>>>>>>>>>>>>>>>>>->>:::::::
#=GC RF                      uaGgGCCCUGgcugGgAuAUCaUCauAUACUGUAAGUUUguuA.uGAGACACUACAGUAUaGAuGAUgUaCcagcCaGGGuacCcu
//
# STOCKHOLM 1.0

#=GF AC   RF00683
#=GF ID   mir-143
#=GF DE   microRNA mir-143
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   75.90
#=GF NC   48.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.09 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000094;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol. 2002;12:735-739.
#=GF WK   Mir-143
#=GF SQ   18


AANG01343499.1/3909-4014     CAGCGGCGCCCUGUCCCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCGGGA-AGGGAGAAGUUGUUCUGCAGC
CT029999.12/84446-84345      GAUCUAC----AGUCGUCUGGCCCGCGGUGCAGUGCUGCAUCUCUGGUCAACUGGGAGUCUGAGAUGAAGCACUGUAGCUCGGGA-GGACAACACUGUCAGCUCAUA
BAAF04072768.1/17225-17120   GGUUCUGGUCCAUCUCUGCUGCCCAUGGUGCAGUGCUGCAUCUCUGGUCAGUUGAUAGUCUGAGAUGAAGCACUGUAGCUCGGGA-CGGAGGGCAGGAGUCUCAGUC
AALT01067568.1/1206-1307     GGGAACC----UGUCUCCCGGCCUGGGGUGCAGUGCUGCAUCUCUGGUCAGCUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGA-AGGGGGAAGCUGCUCUCCGGG
AANH01007327.1/1417-1521     UGCAGUCAGUCAUCCCUGUGGCCCAUGGUGCAGUGCUGCAUCUCUGGUCAGUUGGUAGUCUGAGAUGAAGCACUGUAGCUCGGGA-CG-GAGGACAGAAAUCCCGGU
AAFR03012464.1/24867-24972   UAUUCCUCCUCUGUCUCCCAGCCCGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGUGAGUCUGAGAUGAAGCACUGUAGCUCGGGA-AGGGAGGAACUGUCCAACUCA
AAPN01425211.1/1518-1413     GACCUCUCCGAUGUCUCCCAGCCCAAGGUGCAGUGCUGCAUCUCUGGUCAGUUGUGAGUCUGAGAUGAAGCACUGUAGCUCGGGA-AGGGAGGAGCUGUCCAGCCGG
AAVX01064725.1/2024-2127     GACGGCCAACACAUCAAUCAGCCAGAGGUGCAGUGCUGCAUCUCUGGUUAGUUGUGAGUCUGAGAUGAAGCACUGUAGCUCUGGA-GGAUG--AACACUGCAUCAAU
AADC01055700.1/25604-25709   GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGA-AGAGAGAAGUUGUUCUGCAGC
AAHX01095471.1/4798-4697     GAGCGCC----UGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGA-AGGGAGAAGAUGUUCUGCAGC
AAIY01705731.1/1779-1674     ACAUGGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCGGGA-AGGGAGAGGUUGUUCGACGCC
AAWR02002266.1/32907-32802   CGCCGGCGCCCUGUCCCCCGGCCCGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGA-AGGGAGAAGUUGUUCUGCGGC
AAGV020415914.1/1647-1752    AGCACGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCGGGA-AGGGAGAAGUUGUUCUGCGGG
AAWZ02012097.1/18626-18521   ACCCCCUUCAAUGUCUCCCAGCCCAAGGUGCAGUGCUGCAUCUCUGGUCAGUUGUGAGUCUGAGAUGAAGCACUGUAGCUCGGGA-AGGGAGGAACGAAGCAACGAA
AAEX03003103.1/476600-476495 GCAGUGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCGGGA-AGGGAGAAGUUUUUCUGCAGC
CAAB02010650.1/42697-42591   AUUGUCGGUAUGUUCCUGUGGCCCACGGUGCAGUGCUGCAUCUCUGGUCAGUUGGUAGUCUGAGAUGAAGCACUGUAGCUCGGGACACGGGAGAGACGCACCUGCAC
AY865888.1/449-554           GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGA-AGAGAGAAGUUGUUCUGCAGC
AY865887.1/449-554           GCGCAGCGCCCUGUCUCCCAGCCUGAGGUGCAGUGCUGCAUCUCUGGUCAGUUGGGAGUCUGAGAUGAAGCACUGUAGCUCAGGA-AGAGAGAAGUUUUUCUGCAGC
#=GC SS_cons                 :::::::::::::::<<----<<<<<<-<<<<<<<<<<<<<<<<-<<<<______>>->>->>>>>>>>>>>>>>>>->>>>>>-.----->>::::::::::::::
#=GC RF                      gauuuucgcccugUCccccaGCCcGaGGUgCAGUGCUgCAUCUCUGgUcAGUUGggAGuCUGAGAUGaAGCACUGuAGCuCgGGA.aGggaggAguuguucuucagc
//
# STOCKHOLM 1.0

#=GF AC   RF00684
#=GF ID   mir-122
#=GF DE   mir-122 microRNA precursor
#=GF AU   Nawrocki EP
#=GF SE   Nawrocki EP
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   76.90
#=GF NC   50.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000095;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol. 2002;12:735-739.
#=GF RN   [2]
#=GF RM   15003116
#=GF RT   Expression profiling of mammalian microRNAs uncovers a subset of
#=GF RT   brain-expressed microRNAs with possible roles in murine and human neuronal
#=GF RT   differentiation.
#=GF RA   Sempere LF, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V
#=GF RL   Genome Biol. 2004;5:13-13.
#=GF RN   [3]
#=GF RM   16459310
#=GF RT   miR-122 regulation of lipid metabolism revealed by in vivo antisense
#=GF RT   targeting.
#=GF RA   Esau C, Davis S, Murray SF, Yu XX, Pandey SK, Pear M, Watts L, Booten SL,
#=GF RA   Graham M, McKay R, Subramaniam A, Propp S, Lollo BA, Freier S, Bennett CF,
#=GF RA   Bhanot S, Monia BP
#=GF RL   Cell Metab. 2006;3:87-98.
#=GF CC   miR-122 is miRNA precursor family MIPF:MIPF0000095 that appears to be
#=GF CC   vertebrate specific. In mammals, miR-122 is enriched in liver cells where
#=GF CC   it has been implicated as a regulator of fatty-acid metabolism in mouse
#=GF CC   studies. The hairpin precursors (represented here) are predicted based on
#=GF CC   base pairing and cross-species conservation -- their extents are not
#=GF CC   known. In this case the mature sequence is excised from the 5' arm of the
#=GF CC   hairpin.
#=GF WK   MiR-122
#=GF SQ   26


X13234.1/4754-4827           CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAACUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGU
DQ520616.1/152-225           CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAACUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGU
AAFC03017519.1/1096-1169     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAACUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGU
AADD01160241.1/3920-3993     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-UAAACUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGC
AAFR03031600.1/238986-238913 CAGAGC-UAUGGAGUGUGACAAUGGUGUUUGUG-UC-CAGUCUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGU
AADA01016860.1/1549-1476     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-UAAAUUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGC
AAYZ01033453.1/5054-5127     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAACUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGC
ABDC01112703.1/3466-3539     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAACUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGC
AANN01785848.1/4194-4121     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAUCUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGU
AANU01184262.1/8235-8162     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-UAAACUAUCAAACGCCAUUAUCACACUAAAUAGCUACUAC
AC157910.4/167449-167376     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAACCAUCAAACGCCAUUAUCACACUAAAUAGCUACUGC
AAPN01246572.1/7878-7805     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAGUCUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGU
AANG01179765.1/2963-3036     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UG-CAAACUGUCAAACGCCAUUAUCACACUAAAUAGCUACUGU
CAAE01014533.1/512064-512137 CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CUUUCUUUCAAACGCCAUUAUCACACUAAAUAGCUACAGU
BAAE01201314.1/775-848       CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUU-UC-CUGCCUAUCAAACGCCAUUAUCACACUAAAUAGCUACAGU
AAHX01095574.1/22624-22551   CAGAGC-UCUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAAACAUCAAACGCCAUCAUCACACUAAACAGCUACUGC
AANH01004711.1/32344-32417   CGGAGC-UUUGGAGUGUGACAAUGGUGUUUGUG-UC-CUGUGUAUCAAACGCCAUUAUCACACUAAAUAGCUACGGU
CR925730.6/26724-26798       CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUA-UCAUCUGUCGUCAAACGCCAUUAUCACACUAAAUAGCCACGGU
AAQQ01527039.1/1708-1635     CAGAGCUUGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAACUAUCA-ACGCCAUUAUCACACUAAAUAGCUACUGU
AAVX01098255.1/690-764       AGUGAC-UAUGGAGUGUGACAAUGGUGUUUGUAAUC-ACUGACAUCAAACGCCAUUAUCACACUAAAUAAACACGGC
AAKN02019883.1/8431-8358     CAGAGC-UAUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAACUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGC
CAAB02003098.1/124229-124302 CAGAGC-UAUGGAGUGUGACAAUGGUGUUUGUU-UC-CUUUCUUUCAAACGCCAUUAUCACACUAAAUAGCUACAGU
AC243550.3/65293-65220       CAGAGC-UAUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAUCUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGG
AAWZ02019592.1/2386-2459     UGGAGC-UGUGGAGUGUGACAAUGGUGUUUGUA-UC-CAAUCCGUCAAACGCCAUUAUCACACUAAAUAGCUACUGC
DQ520615.1/152-225           CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAACUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGU
AAPY01002717.1/2720-2647     CAGAGC-UGUGGAGUGUGACAAUGGUGUUUGUG-UC-CAAGCUAUCAAACGCCAUUAUCACACUAAAUAGCUACUGC
#=GC SS_cons                 :::<<<.<<<--<<<<<<<-<<<<<<<<<<<__.__.________>>>>>>>>>>>->>>>>>>-->>>>>>:::::
#=GC RF                      cAGagC.UgUGGAGUGUGACaAUGGuGUUUGUg.UC.caaacUAUCAAACgCCAUuAUCACACUAAAcAGcuACuGu
//
# STOCKHOLM 1.0

#=GF AC   RF00685
#=GF ID   mir-36
#=GF PI   mir-35; mir-39
#=GF DE   microRNA mir-36
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   48.80
#=GF NC   47.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00088
#=GF DR   MIPF; MIPF0000096;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [3]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF WK   MicroRNA
#=GF SQ   46


AC084525.1/3063-3169         AUUCA-UGUGGAGCCUGGACCUGUACCGGGUUCUCUUUG-U-GGUGAUAUGACAACUCAUAACC--AUUCCUUAUCACCGGGAGACAAC-CUGGUA------UAGGUCCAGCGACUCUG
AC084525.1/3698-3802         UGAAA-GCAGGUCCCAAAUGCCUUGGUGGUUUUUCGCCG-U-AGUGAUACAACAUCGAAGCCA----UACGAUAUCACCGGGUGAAAAA-CUCCCA------AGGUCGGGACAUUUUUA
AC084525.1/3341-3445         CUGUA-UCCCCUGCC-CUCACCCCAGCGGGUUUUCAUCG-C-AGUGAUAUGACGCAUUCAAACC--AUUUCUUAUCACCGGGUGUCAAU-CAGCUA------GGGUGUGGGC-GCGGGU
AC084525.1/3241-3340         UAUUC-CAGAGAUGCAGGGAGCCCAACUGGUUCUCACUG-C-AGUGAUAAGCUAUGUUACA--------GUCUAUCACCGGGUGAAAAA-CGGUUA------GGCUCUUUAA-GCAUCU
AC084525.1/3582-3679         CCUUC-GGCCCAGUUCCGGACACUCGCAGGUUUUUGCUU-C-GGUGAUAUU----CGAAGAG------CCGUUAUCACCGGGUGAAAAU-UUGCAA------GUGUCCGGUA-ACUGGA
AC084525.1/3820-3919         CCCUU-AGUCCAGUUCUGGACAUUCGCGGGUUUUUUCCUUC-GGUGAUAUU----CGAAGAA------UCGCUAUCACCGGGUGAAAAC-UUGCAA------GUGUCUUGCUUCGACUG
AAGD02001682.1/66886-66788   ACUCC-UCGGUCGGAUCGGACCUACACUGGUUUUCGCUG-C-GGUGAUACUU---CGAGAA-------UGAUUAUCACCGGGUGAAAAU-CAGGGC------AGGUCCGAUUCCACCGA
AAGD02001682.1/68488-68391   UUAUC-UGGUCGGAU-CGGACCUCCACUGAUUUUCGCUU-C-GGUGAUAUUU---CAAGAA-------CGAUUAUCACCGGGUGAAAAU-CAGGGC------AGGUCCGAUUCCCCAUU
AAGD02001682.1/68606-68507   UCCUC-CUGGUCGGAUCGGACCUCCACUGGUUUUUGCUG-C-GGUAAUAUUU---CUCAGAA------UCAAUAUCACCGGGUAAAAAU-CAGGGC------AGGUCCGAUUCCAGCCA
AAGD02001682.1/65818-65720   UGCUC-UC-UGUGACGAGAGCCACGCC-AAUUCUUACCG-C-GGUAAUAGAAC--UGCAUAG------UUUCUAUCACCGGGUGAAAAU-UCGGCU------CGGAUCUCUUAACAGAC
AAGD02001682.1/67443-67345   UACUC-CCUAAUGAC-GGGAACCGUGCUGGUUUCGAACU-C-GGUAAUAGACCAGAAGAAA---------GCUAUCACCGGGUGGAAAC-UGGUAC------GGGUCCCCGAGUCGUGC
AL110499.1/17533-17636       UUUAA-GUGGGUCCCAGAGACCUUGGUGGUUUUUCUCUG-C-AGUGAUAGAUACUUCUAACAA----CUCGCUAUCACCGGGUGAAAAA-UCACCU------AGGUCUGGAG-CCUCCU
AL110499.1/17164-17259       U-------GUGAGCCAGGUCCUGUUCC-GGUUUUUUCCG-U-GGUGAUAACGCAUCCAAAAG------UCUCUAUCACCGGGAGAAAAA-CUGGAG------UAGGACCUGUGACUCAU
AL110499.1/16941-17042       GCUCC-ACCGCUGUCGGGGAACCGCGCCAAUUUUCGCUU-C-AGUGCUAGACCAUCCAAAG-------UGUCUAUCACCGGGUGAAAAU-UCGCAU------GGGUCCCCGACGCGGAA
AL110499.1/17409-17507       CCGAA-CCUCCUGUC-CGCACCUCAGUGGAUGUAUGCCA-U-GAUGAUAAGAUAUCAGAAA--------UCCUAUCACCGGGUGUACAU-CAGCUA------AGGUGCGGGU-ACAGGU
AAGD02000354.1/140549-140446 GUUUA-ACAGGUCCCCAUGACCUUGGUAGUUUUCCGCCG-C-AGUGAUAUACCAUCAAUCAA-----AACGAUAUCACCGGGUGAAAAA-CUACCA------AGGUCGGGUCACCUGUC
AAGD02000354.1/140770-140671 UAUUU-CUGAGAUCCAGAGAGCCCAACUGUUUCUUUCCC-C-GGUAAUAAAC---UUCAACA------CGACUAUCACCGGGUAUGAAU-CAGUUA------GGCUCUUCUGGUAUCUU
AAGD02000354.1/140669-140569 AAA-----CCCUGCC-CGUAACCUAGUUGAUGUUCAUCG-C-AGUGAUAUGACGCAUCAGUAC---AUUCCUUAUCACCGGGUGUACAU-CAGCUA------GGGUGCGGGUUCAGGUU
AAGD02000354.1/140925-140842 ----------------------AUACCGGUUUAACUUCG-U-GGUGAUAUGACACAUAUUACA----UUCUUUAUCACCGGGAGUAAAA-CUGGUA------UAGGAUCUGCGACUCGC
CAAC02000527.1/132358-132458 UUUCA-UGGUCUGGGUCGGACCUUUGCCAAUUUUCUCCG-C-GGUGAUACUCCAAUGCGAC--------GAUUAUCACCGGGUGAAAAC-UGGUAG------AGGUCCGAGCCAGUCAG
CAAC02000527.1/134345-134446 AUUAU-UCCGAUGGUCUGGAUCGGACC----UUUCUCUG-C-AGUGAUAUUCC--AAAAUCG------UGGUUAUCACCGGGUGAAA-A-CUGGUAGAGGUGCGAUCUAGCCGGGCCUU
CAAC02000527.1/132866-132967 UCCAA-UGGUCUGGGUCGGACCUCCGCUGUUUUUCUCCG-C-GGUGAUACUCCAAAGAAAG-------UCGUUAUCACCGGGUGAAAAC-UGGUAG------AGGUCCGAUUCAGUCGG
CAAC02000527.1/135017-135118 ACUGU-UAGUCUGACUCGGUCCUGCGCCACUUUCCACCG-C-GGUGAUAUUCCAAGCAAAA-------CGGUUAUCACCGGGUGAAAAU-UGGUAC------AGGUCCGAUCCUCUUCU
CAAC02000527.1/134902-135002 CACAG-AAGGUUGAAUUGGACCUCUGCUGGUUU-CGCGG-C-GGUGAUACUUUGUACUGAU-------UGAUUAUCACCGGGUGAAAAC-UGGUAG------AGGACCUUGUAGACUAU
CAAC02000527.1/132702-132803 UCCGA-AGGACUGGAUCGGACCUCCGCUGGUUUUUCCCG-C-GGUGAUAUUCCGAAGCAAG-------UGGUUAUCACCGGGUGAAAAC-UGGUAG------AGGUCCGAUCCAGUCGU
ABEG02001577.1/117227-117133 --------CUGAGGCGGGAACCG-AGCUGAUUU-CUCUA-CUGGUGAUAAGUCCGAUCAUAG------UGUUUAUCACCGGGAGUAAAU-CUGCUC------UGGUCCCGUCUCGGGAU
ABEG02001354.1/20483-20384   UCGUU-UCCAGAGCCAGGACCUGUUCCAGUUUUUUUCCG-C-GGUAAUAACG---CGAGCAA------GUCCUAUCACCGGGAGAAAAA-CUGGAG------UAGGUCCUGCGACUCUA
ABEG02001577.1/117330-117229 UAUUC-AGGGUUGGAUCGGACCUUUGCUGGUUUCUGCCG-C-GGUGAUAUUUC--UAUUUCG------UGAUUAUCACCGGGUAAAAAUACAGCAG------AGGUCCGGUCCUUCCUU
ABEG02001577.1/113842-113741 UAUUC-UGGGAUGGAUGGGGCCUGUGCUGGUUUUUGCCG-C-GGUGAUACUUCAACGUGAU--------GAUUAUCACCGGGUGAAAAUACGGCAC------AGGUCCAAUCCUGCCUU
ABEG02001577.1/118517-118418 -UCUAUUCGGCCGGAUCGGACCUAUGCUGGUUUUCACCG-C-GGUUAUACUU---CUAACAA------UAAUUAUCACCGGGUUAAAAC-UUGCAG------AGGUCCGGUCCGGCCUU
ABEG02001577.1/111440-111366 ----------------UGCGCUGG------UUUUUGCCG-C-GGUGAUAUUCCAACGUCAU--------GAUUAUCACCGGGUGAAAAU------A------CAGCACAGGCCCAAUCC
ABEG02008718.1/1588-1487     UCUUU-AAUUGCGUAGGGGAACCAAGCUAGUUCUUACCG-C-GGUGCUACAACAAGCAUAA-------CAUCUAACACCGGGUAAAAAC-UAGCUC------GGGUCCCCCUUGCAACA
ABEG02001577.1/113460-113366 ------UCCUGAGAC-GGGAACCGAGCUGAUUUCACUUU-C-GGUGAUAUGUC--CAUGAUG------CGCCUAUCACCGGGUGUAAAU-UGGCUC------GGGUCCCGUCUCGGGAU
ABEG02008718.1/1138-1030     AGUUU-AGCAGGUCUUGUGACCUCGGUGGUUUCUUGCCG-C-GGUGAUAUGCACAUUCACUUCCAUAAUUGAUAUCACCGGGUGAAAAA-UCACCA------AGGUCGACGAUUCUGUU
JN251327.1/12-117            CUGUA-UCCCCUGCC-CUCACCCCAGCGGGUUUUCAUCG-C-AGUGAUAUGACGCAUUCAAACC--AUUUCUUAUCACCGGGUGUCAAU-CAGCUA------GGGUGUGGGCGCGGGUA
JN251346.1/369-473           UGAAA-GCAGGUCCCAAAUGCCUUGGUGGUUUUUCGCCG-U-AGUGAUACAACAUCGAAGCCA----UACGAUAUCACCGGGUGAAAAA-CUCCCA------AGGUCGGGACAUUUUUA
JN251352.1/253-351           CCUUC-GGCCCAGUUCCGGACACUCGCAGGUUUUUGCUU-C-GGUGAUAUU----CGAAGAG------CCGUUAUCACCGGGUGAAAAU-UUGCAA------GUGUCCGGUAACUGGAC
JN251350.1/253-351           CCUUC-GGCCCAGUUCCGGACACUCGCAGGUUUUUGCUU-C-GGUGAUAUU----CGAAGGC------CCGUUAUCACCGGGUGAAAUU-UUGCAA------GUGUCCGGUAACUGGAC
JN251329.1/369-473           UGAAA-GCAGGUCCCAAAGGCCUUGGUGGUUUUUCGCCG-U-AGUGAUACAACAUCGAAGCCA----UACGAUAUCACCGGGUGAAAAA-CUCCCA------AGGUCGGGACUCUGCAU
JN251324.1/133-237           UUAUC-GCGGAUCUCUCUGGCCUUGGAGGUUUCUCAUCG-U-AGUGAUACAAAACCAAAACCA----UACGAUAUCACCGGGUGAGAAU-CUUCCA------AGGUAGGAGGAUCCUGC
JN251343.1/369-473           UGAAA-GCAGGUCCCAAAUGCCUUGGUGGUUUUUCGCCG-U-AGUGAUACAACAUCGAAGCCA----UACGAUAUCACCGGGUGAAAAA-CUCCCA------AGGUCGGGACUCUGCAU
JN251345.1/133-237           UUAUC-GCGGAUCUCUCUGGCCUUGGAGGUUUCUCAUCG-U-AGUGAUACAAAACCAAAACCA----UACGAUAUCACCGGGUGAGAAU-CUUCCA------AGGUAGGAGAAUCCUGC
JN251333.1/253-351           CCUUC-UCCCCAGUUCCGGACACUCGCAGGUUUUUGCUU-C-GGUGAUAUU----CGAAGAG------CCGUUAUCACCGGGUGAAAAU-UUGCAA------GUGUCCGGUAACUGGAC
JN251330.1/12-117            CUGUA-ACCCCUGCC-CUCACCCCAGCGGGUUUUCAUCU-C-AGUGAUAUGACGCAUUCAAACC--AUUUCUUAUCACCGGGUGUAAAU-CAGCUA------GAGUGUGGGCGCGGGUA
JN251329.1/253-351           CCUUC-AGCCCAGUUCCGGACACUCGCAGGUUUUUGCUU-C-GGUGAUAUU----CGAAGAG------CCGUUAUCACCGGGUGAAAAU-UUGCAA------GUGUCCGGUAACUGGAC
JN251334.1/11-117            UCUGU-AUCCCCUACCCUCACCCCAGCGGGUUUUCAUCG-C-AGUGAUAUGACGCAUUCAAACC--AUUUCUUAUCACCGGGUGUCAAU-CAGCUA------GGGUGUGGGCGCGGGUA
#=GC SS_cons                 :::::.::::::::::<<<<<<<-<<<<<<<<<<<<<<-.<.-<<<<<<_____________......____>>>>>>->>>>>>>>>>.>>>>>-......>>>>>>>::::::::::
#=GC RF                      uuuua.uccgguGucucggaCCuuagCuGuUUuucaCCG.C.GGUGAUAuuaCAucuaAaaa......ucguUAUCACCGGGugaaAAa.CaGcua......aGGuccggucuccucuu
//
# STOCKHOLM 1.0

#=GF AC   RF00686
#=GF ID   mir-338
#=GF DE   microRNA mir-338
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   54.60
#=GF NC   48.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.30 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000097;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [2]
#=GF RM   20300190
#=GF RT   Characterization of the Melanoma miRNAome by Deep Sequencing.
#=GF RA   Stark MS, Tyagi S, Nancarrow DJ, Boyle GM, Cook AL, Whiteman DC, Parsons
#=GF RA   PG, Schmidt C, Sturm RA, Hayward NK
#=GF RL   PLoS One. 2010;5:e9685.
#=GF RN   [3]
#=GF RM   20483914
#=GF RT   Discovery of microRNAs and other small RNAs in solid tumors.
#=GF RA   Meiri E, Levy A, Benjamin H, Ben-David M, Cohen L, Dov A, Dromi N, Elyakim
#=GF RA   E, Yerushalmi N, Zion O, Lithwick-Yanai G, Sitbon E
#=GF RL   Nucleic Acids Res. 2010;38:6234-6246.
#=GF RN   [4]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   miR-338
#=GF SQ   21


BAAE01013935.1/90-171          GGCUGGUCCCAGAAACAACAUCCUGGUGCUGCCUGAGUGU--GUAAUGCAAACUCCAGCAUCAGUGAUUUUGUUGCUGGGGGCG
BAAF04036435.1/2170-2253       GUUGUCUCCUGGAAACAACAUCCUGAUGCUGUCUGGGUGUGGAAAAGCAGAACUCCAGCAUCAGUGAUUUUGUUGCUGGGGGAG
BAAF04103498.1/7620-7539       GGCCACUUCCUGAAACAAUAUCCUGGUGCUGCCCGAGUGC--GGCUCACAGACUCCAGCAUCAGUGAUUUUGUUGCAGGCGGUG
BX571959.8/68448-68530         GGUGCCUGCUGAGAACAAUAUCCUGAUGCUGAAUGAGUGUG-UUGAAGGAAACUCCAGCAUCAGUGAUUUUGUUGCCAGAGGAG
CAAA01219673.1/10354-10432     GGCCGUCCUCCCCAACAAUAUCCUGGUGCUGAGUGGGUG-----CACAGUGACUCCAGCAUCAGUGAUUUUGUUGAAGAGGGCA
CAAE01014738.1/1400351-1400433 GUCACCUGCGGGGAACAACAUCCUGAUGCUGUCUGAGUAUG-UGGUACAGAACUCCAGCAUUAGUGAUUUUGUUGCCAGUGGGA
AAFR03029132.1/115398-115317   GGCCUUCCUCCCCAACAAUAUCCUGAUGCUGAGUGAGCGG--CACAUGGAGACUCCAGCAUCAGUGAUUUUGUUGAAGAGGGUG
AAVX01041385.1/4416-4496       GUUCAUUUCUGGUAACAAUAUCCUGAUGCUGUCCGAGUA---UGUGGAAAAGCUCCAGCAUCAGUGAUUUUGUUGCUAGUGGUG
AANH01004322.1/123577-123496   GGUCUUUCCCUGCAACAACAUCCUGGUGCUGCCUGAGUAA--UUGUCAAAAACUCCAGCAUCAGUGAUUUUGUUGCGGGGGGAG
AANN01126736.1/1031-1108       GGCCGUCCUCCCCAACAACAUCCUGGUGCUGAGUGA------UGAUCAACAACUCCAGCAUCAGUGAUUUUGUUGCAGAGGGCA
BX323027.8/66170-66089         GGUUUCUCCCUGCAACAAUCUCCUGAUGCUGCCUGAGUGU--UUUUCUUCCACUCCAGCAUCAGUGAUUUUGUUGCCGGAGGUC
AAYZ01406815.1/2366-2288       GGCCGCCCGCCCCAGCAACAUCCUGGUGCUGAGUGGGGA-----CAUAGUACCUCCAGCAUCAGCGAUUUUGUUGGCGAGGGCG
AANH01012267.1/23040-22957     GGUUGCUUCAUGGAACAAUAUCCUGGUGCUGCCUGAGUAAUCCACUUAAAGACUCCAGCAUCAGUGAUUUUGUUGCAGGCGGUG
CAAE01014705.1/537256-537337   GGUCACUUCCUGGAACAAUAUCCUGGUGCUGCUCGAGUGU--UCCCUACAGACUCCAGCAUCAGUGAUUUUGUUGCAGGCGCUG
BX547935.12/10590-10671        GGUGUCUCCUGGCAACAAUAUCCUGGUGCUGCCUGAGUAC--AUCUCACAGACUCCAGCAUCAGUGAUUUUGUUGCCGGGGGAA
AAVX01571211.1/489-569         GUUCGUUCCUUGCAACAACAUCCUGAUGCUGCCAGAGCGG--GUCU-GGUGGCUCCAGCAUCAGUGAUUUUGUUGCAGGGAGCG
AADB02019003.1/88-9            GGCUGUCCUCUCCAACAAUAUCCUGGUGCUGAGUGA--UG--ACUCAGGCGACUCCAGCAUCAGUGAUUUUGUUGAAGAGGGCA
AANG01169639.1/1040-961        GGCCGUCCUCCCCAACAAUAUCCUGGUGCUGAGUGAUGAC--ACAUACAAC--UCCAGCAUCAGUGAUUUUGUUGAAGAGGGCA
AAKN02047347.1/124236-124157   GGCCGUCCUCCCCAACAAUAUCCUGGUGCUGAGUGA--UG--ACACAGGCAACUCCAGCAUCAGUGAUUUUGUUGAAGAGGGCA
AAWZ02002277.1/77672-77753     GCUCCUUGUCCUCAACAAUAUCCUGGUGCUGAGUGAGUGG--CACUCAAAGACUCCAGCAUCAGUGAUUUUGUUGAAGAGGGUG
CAAE01014593.1/786787-786868   GGAUUCUCCCUGCAACAACAUCCUGGUGCUGCCUGAGUCA--CUUUCACAAACUCCAGCAUCAGUGAUUUUGUUGCGGGGGGCA
#=GC SS_cons                   :::::::::::::<<<<<-<<<<<<<<<<<<---<<<<__.._________>>>>>>>>>>>>>->>>->>>>>::::::::::
#=GC RF                        GgucuuUcccugcAACAAuAUCCUGgUGCUGacUGAGuau..uuuuuaaaaaCUCCAGCAuCAGUGAUUUUGUUGcaGggGGug
//
# STOCKHOLM 1.0

#=GF AC   RF00687
#=GF ID   mir-136
#=GF DE   microRNA mir-136
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   63.00
#=GF TC   68.60
#=GF NC   51.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000099;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15183728
#=GF RT   Human embryonic stem cells express a unique set of microRNAs.
#=GF RA   Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS,
#=GF RA   Moon SY, Kim VN, Kim KS
#=GF RL   Dev Biol. 2004;270:488-498.
#=GF RN   [2]
#=GF RM   15891114
#=GF RT   Clustering and conservation patterns of human microRNAs.
#=GF RA   Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A,
#=GF RA   Brownstein MJ, Tuschl T, Margalit H
#=GF RL   Nucleic Acids Res. 2005;33:2697-2706.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol. 2002;12:735-739.
#=GF WK   MicroRNA
#=GF SQ   2


AAFC03050876.1/56719-56800 UGAGCCCUCGGAGGACUCCAUUUGUUUUGAUGAUGGAUUCUUACGCUCCAUCAUCGUCUCAAAUGAGUCU-UCAGAGGGUUCC
AANN01125399.1/1347-1429   CGAGCCCUCUGAGGACUCCAUGUGUUUUGAUGAUGGAUUCUUAAGCUCCAUCAUCGUCUCAAAUGAGUCUUUCAGAGAGUUCC
#=GC SS_cons               :<<<<<<<<<<<<<<<<<-<<<<<---<<<<<<<<<<_________>>>>>>>>>>--->>>>>>>>>>>->>>>>>>>>>>:
#=GC RF                    uGagCcCuCuGagGaCuCCauuuGUUUuGauGauGGaUUCUUAaGCuCCauCauCgUCUCaaauGaGuCuuuCaGaGgGuuCC
//
# STOCKHOLM 1.0

#=GF AC   RF00688
#=GF ID   MIR394
#=GF DE   microRNA MIR394
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   60.20
#=GF NC   59.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000100;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15200956
#=GF RT   Computational identification of plant microRNAs and their targets,
#=GF RT   including a stress-induced miRNA.
#=GF RA   Jones-Rhoades MW, Bartel DP
#=GF RL   Mol Cell. 2004;14:787-799.
#=GF RN   [2]
#=GF RM   15200956
#=GF RT   Computational identification of plant microRNAs and their targets,
#=GF RT   including a stress-induced miRNA.
#=GF RA   Jones-Rhoades MW, Bartel DP
#=GF RL   Mol Cell. 2004;14:787-799.
#=GF RN   [3]
#=GF RM   16954541
#=GF RT   MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent
#=GF RT   RNA polymerase-2 mutant.
#=GF RA   Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, Poethig RS,
#=GF RA   Henderson IR, Jacobsen SE, Wang W, Green PJ, Meyers BC
#=GF RL   Genome Res. 2006;16:1276-1288.
#=GF WK   Mir-394_microRNA_precursor_family
#=GF SQ   19


AASG02000377.1/56114-56246   CUUAC---AGAGCU-UAUUGGCAUUCUGUCCACCUCC-------UUUAUCAAU--AGAACAAUUUCUCU-CUUUUAUUUUCCCUGUCAUAUAUGCAUAUUUACAUAUUUAUAUGGAGGUGGGCAUACUGCCAACUGAGCUCUGUUGG
AM428484.2/52366-52463       CUCAC---AGAGUU-UAUUGGCAUUCUGUCCACCUCCC------AUC--------UCUUGAAAAUCUC----UCUUUUCUCUCUGU---------------------------GGAGGUGGGCAUACUGCCAACCAAGCUCUGUUGG
DQ908352.1/346-226           CUUAC---AGAGUU-UAUUGGCAUUCUGUCCACCUCCA------AUCAUGGAA--ACAAAAAAACCCUU--GUCUUUUUGCUCUCUGAUCUCA------------UCUUUCAUGGAGGUGGGCAAACUGCCAACUGAGCUCUGUUGG
AASG02008916.1/699-813       GUUGC---AGAGCCAUUUUGGCAUUCUGUCCACCUCCAUAAAUCUAAGAUCAC--UUCUUGGUGUCCAA-UAUUUCUGGUCUUUGU--------------------------UGGAGGUGGCCAGCAUGUCAAACUGGCUCUGUAAA
AM454446.1/19563-19456       UUUAC---AGAGCCAAUUUGGCAUCCUGGCCGCCUCCA------AACGCUUGU-GGGCGCCAAWUCAGA--AGAAUUGGUAUAUAU---------------------------GGAGGUGGACAGAAUGCCAAAAUGGCUCUGUAAU
AC026234.4/7432-7316         CUUAC---AGUCAU-CUUUGGCAUUCUGUCCACCUCCUU--CUAUACAUAUAU--GCAUGUGUAUAUAU--AUAUGCGUUUCGUGUGAA--------------------AGAAGGAGGUGGGUAUACUGCCAAUAGAGAUCUGUUAG
AARH01002882.1/31556-31654   CUUAC---AGAGUU-UAUUGGCAUUCUGUCCACCUCCU-------------AU--CUUUAGAAAUUAGA--AUAUCUCUUUCAUAU---------------------------GGAGGUGGGCAUACUGCCAACCGAGCUCUGUUGG
AM434426.2/19562-19468       UUUAC---AGAGCCACUUUGGCAUGCUGGCCACCUCCA--------------------AAAGAAUAUAG--GCCCAUGAUGUGCAU---------------------------GGAGGUGGACAGAAUGCCAAAAUGGCUCUGCAAC
AC189318.1/31773-31892       CUUAC---AGAGUU-CUUUGGCAUUCUGUCCACCUCCUU-UCUGAAUAUAUUU--GUGUAUAAGUGUAC--GCAACUACGUUGUGUUUUG------------------UGUGAGGAGGUGGGCAUACUGCCAAUAGAGAUCUGUUAG
AARH01001039.1/148774-148676 CUUAC---AGAGUU-UUUUGGCAUUCUGUCCACCUCCA----UCUGU-----------AGAAACUACAA--GUUGUUCUACUUUCU---------------------------GGAGGUGGGCAUACUGCCAACUGAGCUCUGUUGG
AC009978.3/24986-25106       CUUAC---AGAGAU-CUUUGGCAUUCUGUCCACCUCCUC-UCUCUAUAUUUAU-GUGUAAUAAGUGUAC--GUAUCUACGGUGUGUUUCG------------------UAAGAGGAGGUGGGCAUACUGCCAAUAGAGAUCUGUUAG
AC189295.2/85926-86037       CUUAC---AGAGAU-CUUUGGCAUUCUGUCCACCUCCC---CUACCUAUGUAU--AUGUGUAUUAUCUA--CGUUGUGUUUUGUGAG------------------------GGGGAGGUGGGCAUACUGCCAACAGAGAUCUGUUAG
HM139771.1/249-360           CUUACU-GAGAGUU-CUUUGGCAUUCUGUCCACCUCCU----UGUCGAAUCCU--CAGAGACAGAAAUCUCAUAUCUGUUGAUCUU---------------------------GGAGGUGGGCAUACUGCCAAUGGAGCUGUGUAGG
EU549400.1/212-328           CUUAC---AGUCAU-CUUUGGCAUUCUGUCCACCUCCU----UCUAUACAUAU--AUGCAUGUGUAUAU--AUAUAUGCGUUUCGUGUGA------------------AAGAAGGAGGUGGGUAUACUGCCAAUAGAGAUCUGUUAG
GQ905603.1/88-204            CUUACUGAAGAGUU-CCUUGGCAUUCUGUCCACCUCCU---CUCGCCGAUCUU---GCAGAAAGUUUAC-CAGUUCUGUUGCAUUUUU----------------------UUUGGAGGUGGGCAUACUGCCAAUGGAGCUGUGUAGG
HM627266.1/300-201           CUUAC---AGAGUU-UAUUGGCAUUCUGUCCACCUCCA-------------AU-CUGCAGAAACUACAA--GUUGUUUUACUUUCU---------------------------GGAGGUGGGCAUACUGCCAACUGAGCUCUGUUGG
GQ905604.1/109-220           CUUACU-GAGAGUU-CCUUGGCAUUCUGUCCACCUCCC----UUCUUGACGAUCUUGCAGAAAGUUUGC--UUUUUUUGUUUGUUU---------------------------GGAGGUGGGCAUACUGCCAAUGGAGCUGCGUAGG
EU549419.1/151-271           CUUGC---AGAGAU-CUUUGGCAUUCUGUCCACCUCCUC-UCUCUAUAUUUAU-GUGUAAUAAGUGUAC--GUAUCUACGGUGUGUUUUG------------------UAAGAGGAGGUGGGCAUACUGCCAAUAGAGAUCUGUUAG
EU549408.1/151-271           CUUAC---AGAGAU-CUUUGGCAUUCUGUCCACCUCCUC-UCUCUAUAUUUAU-GUGUAAUAAGUGUAC--GUAUCUACGGUGUGUUUUG------------------UAAGAGGAGGUGGGCAUACUGCCAAUAGAGAUCUGUUAG
#=GC SS_cons                 :::::...:::::<.--<<<<<<---<<<<<<<<<<<_....___________..______________..________________........................__>>>>>>>>>>>--->>>>>>--->::::::::::
#=GC RF                      CUUAC...AGAGuu.uuUUGGCAUUCUGuCCACCUCCu....UcuauAuuuaU..ugaaaaAaaUauau..aUuUuUuuuuuuUgUu........................auGGAGGUGGgCAuACUGCCAAuaGaGcUCUGUuaG
//
# STOCKHOLM 1.0

#=GF AC   RF00689
#=GF ID   MIR390
#=GF DE   microRNA MIR390
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   77.00
#=GF TC   78.20
#=GF NC   75.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000101;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15608278
#=GF RT   ASRP: the Arabidopsis Small RNA Project Database.
#=GF RA   Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD
#=GF RL   Nucleic Acids Res. 2005;33:D637-D640.
#=GF RN   [2]
#=GF RM   15632092
#=GF RT   Computational prediction of miRNAs in Arabidopsis thaliana.
#=GF RA   Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V,
#=GF RA   Sundaresan V
#=GF RL   Genome Res. 2005;15:78-91.
#=GF RN   [3]
#=GF RM   16040653
#=GF RT   Expression of Arabidopsis MIRNA genes.
#=GF RA   Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC
#=GF RL   Plant Physiol. 2005;138:2145-2154.
#=GF RN   [4]
#=GF RM   16040653
#=GF RT   Expression of Arabidopsis MIRNA genes.
#=GF RA   Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC
#=GF RL   Plant Physiol. 2005;138:2145-2154.
#=GF WK   Mir-390_microRNA_precursor_family
#=GF SQ   16


AM484368.2/7952-7807         UGGGAGAAUCUGUUAAGCUCAGGAGGGAUAGCGCCAUGAG--CCAUGAU--GAAAAUGAUUGUUGAGUU----GAAAAUUUUUUCUAGCUUGUUUUUUGGGUCAUCAUUUUGUGUGUGUGGCGCUAUCUAUCCUGAGUUUCACGGGWUCUUCUU
AC133007.4/86351-86434       UGGAACAAUCCUUGAAGCUCAGGAGGGAUAGCGCCUCGAA------------------------------------------------------------AUCAAAC----------UAGGCGCUAUCUAUCCUGAGCUCCAUGGUUUGUUCUU
AASG02008232.1/8506-8369     UGGAAGAAUCUAAUAAGCUCAGGAGGGAUAGCGCCAUGGA--UGGAUAU--GUGUUUUUAUGAAUAUGACUCGUCUUUUCUUGGCUUGCUUUUUUU-A-UCUCUUCU----------AUAGCGCUAUCCAUCCUGAGUUUCAUUGGUUCUUCUU
AARH01003823.1/151507-151375 UGGGAGGAUCUGUUAAGCUCAGGAGGGAUAGCGCCAUGAG-CUGAUGAUAAGUUGAUGUUUGAUGGGU-------UAAUCUCAACAUAAUCAAUCU---AGUCAUUA----------GUGGCGCUAUCUAUCCUGAGUUCUAUAGGUUCUCCUU
AC143338.29/35527-35410      UGAAAGAAUCUGUUAAGCUCAGGAGGGAUAGCGCCAUAGA--AUGUCUU----CUUUUUUUGG----------------UUCCAUUUUAUUGAUUG----AUCUUCU----------CUUGCGCUAUCCAUCCUGAGUUUCAUGGCUUCUUCAU
AARH01003029.1/551541-551656 UGGAAGAAUCUGUUAAGCUCAGGAGGGAUAGCGCCCUAAG-----------GAUAAUCAUGGG----------------CUCUUUUUAUGUGGUUU-UUGAUUCUCA----------GUGGCGCUAUCCAUCCUGAGUUUCAUUGCUUCUUCUU
AARH01000472.1/96655-96783   CGGGAGAAUCUGUUAAGCUCAGGAGGGAUAGCGCCAUGAGCAUGACAAA--GUCUAUGUUUGAGUU----------AAUCUCAACAAAAUCAAUCC---AGUCAUCA----------GUGGCGCUAUCUAUCCUGAGUUCUAUGGGUUCUCCUU
AASG02000259.1/53979-54102   AUGGAGACUCUGUUAAGCUCAGGAGGGAUAGCGCCGUGAA--GAUCAUU-GAUAUAUUAUUGU----------------CCAAACAAAACAUAUGUAU-AGUCUUUA----------GUGGCGCUAUCCAUCCUGAGUUUCACAGGUUCUUCUU
AB025632.1/22985-23104       GAGAAAUAGCUAUAAAGCUCAGGAGGGAUAGCGCCAUGGC--UCACCAG-------UGCUGUAU---------------GUUUUGUAUAUGCGUACAUGUAUAUCUG----------UUGGCGCUAUCCAUCCUGAGUUCCAUAGCUUCUUCUU
AC004683.3/59307-59209       GAGAAGAAUCUGUAAAGCUCAGGAGGGAUAGCGCCAUG-A--UGAUCAC--AUUCGUUAUCUA----------------------------------------UUUU----------UUGGCGCUAUCCAUCCUGAGUUUCAUUGGCUCUUCUU
AC189355.2/75830-75939       GAGAAGUAGCUGUAAAGCUCAGGAGGGAUAGCGCCAUGAC--UCAUCAC------------------------------CAUUACUAUAUGUCUUU-G-UAUAUGUA----------AUGGCGCUAUCCAUCCUGAGUUCCAUGGCUUCUUCUU
FN594967.1/1358179-1358055   UGGGAGAAUCUGUUAAGCUCAGGAGGGAUAGCGCCACUAC--GCUUAAA----CCAUUUUUAUUUU-----------UUUUGGAAAUGGGUUUUUU-U-GGUUGUUG----------GUUGCGCUAUCCAUCCUGAGUUUCAUUGGUUCUUCUU
GQ419265.1/720-637           UGGAACAAUCCUUGAAGCUCAGGAGGGAUAGCGCCUCGAA------------------------------------------------------------AUCAAAC----------UAGGCGCUAUCUAUCCUGAGCUCCAUGGUUUGUUCUU
FM163953.1/147-245           GAGAAGAAUCUGUAAAGCUCAGGAGGGAUAGCGCCAUGAU---GAUCAC--AUUCGUUA----------------------------------------UCUAUUUU----------UUGGCGCUAUCCAUCCUGAGUUUCAUUGGCUCUUCUU
HM627264.1/214-342           UGGGAGAAUCUGUGAAGCUCAGGAGGGAUAGCGCCAUGAGCAUGACAAA--GUCUAUGUUUGAGUU----------AAUCUCAACAAAAUCAAUCC---AGUCAUCA----------GUGGCGCUAUCUAUCCUGAGUUCUAUGGGUUCUCCUU
AC189543.2/98818-98914       GAGAAGAAUCUGUAAAGCUCAGGAGGGAUAGCGCCAUCAU---GAUCAC--ACACAU------------------------------------------CGAUAUUU----------UUGGCGCUGUCCAUCCUGAGUUUCAUUGGCUCUUCUU
#=GC SS_cons                 :::::::::<-----<<<<<<<<<-<<<<<<<<<<_____.._______.._____________..............._________________._.________..........__>>>>>>>>>>->>>>>>>>>----->:::::::::
#=GC RF                      ugGaAGAAUCUgUuAAgCUCAGGAGGGAUAGCGCcAUgAa..ugauaAu..guuuaUuuUugau...............cUuuacuaaauuuaUuu.u.uaUcuUua..........uUgGCGCUAUCCAUCCUGAGuUuCAUuGgUUCUUCUU
//
# STOCKHOLM 1.0

#=GF AC   RF00690
#=GF ID   MIR408
#=GF DE   microRNA MIR408
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   64.00
#=GF TC   64.90
#=GF NC   62.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000102;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15258262
#=GF RT   Novel and stress-regulated microRNAs and other small RNAs from
#=GF RT   Arabidopsis.
#=GF RA   Sunkar R, Zhu JK
#=GF RL   Plant Cell. 2004;16:2001-2019.
#=GF RN   [2]
#=GF RM   19939267
#=GF RT   High throughput approaches reveal splicing of primary microRNA transcripts
#=GF RT   and tissue specific expression of mature microRNAs in Vitis vinifera.
#=GF RA   Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del
#=GF RA   Fabbro C, Valle G, Policriti A, Morgante M, Pesole G, Pe ME, Horner DS
#=GF RL   BMC Genomics. 2009;10:558.
#=GF RN   [3]
#=GF RM   19939267
#=GF RT   High throughput approaches reveal splicing of primary microRNA transcripts
#=GF RT   and tissue specific expression of mature microRNAs in Vitis vinifera.
#=GF RA   Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del
#=GF RA   Fabbro C, Valle G, Policriti A, Morgante M, Pesole G, Pe ME, Horner DS
#=GF RL   BMC Genomics. 2009;10:558.
#=GF WK   Mir-408_microRNA_precursor_family
#=GF SQ   8


AARH01001232.1/22607-22493 AGA----GACA-GAUGAAGACGGGGAACAGGCAG---------------------------------------AGCAUG---GAUG-----GAGCUACUAAC-------------------------------------------------------------AGAAG------UACUUGUUUUGGCUCU-ACCCAUGCACUGCCUCUUCCCUGGCUUG-UGGCUCUUCCUUUUCU
AASG02001473.1/22877-22996 AGAAACAGACA-GACAAAGACUGGGAACAGGCAG---------------------------------------UGCAUG---GAUG-----GGGCUACUAAC-------------------------------------------------------------AGAAAA-----CAUCUGUUUUGGCUCU-ACCCCUGCACUGCCUCUUCCCUGGCUUC-CGGUUCUUCUUUUUGU
AC136840.24/84429-84307    AGUUAAUGACAGGACAAAGACAGGGAACAUGCAG---------------------------------------AGCAUG---GAUG-----AAACUAUCGAC-------------------------------------------------------------AGUGAAGG---AAACUGUUGUGGCUCC-ACUCAUGCACUGCCUCUUCCCUGGCUUA-UAAUCUGUUUUUAUUA
AM434998.2/53932-53808     AAAUGGAGACAAGAGGAAGACGGGGACGAGGUAG---------------------------------------UGCAUG---GAUG-----GAACUAUUAAC-------------------------------------------------------------AGAAGAAUGUUAAGCUGUUUUUGCUCU-ACCCAUGCACUGCCUCUUCCCUGGCU-C-UGUCUCUCCUUUACUC
AK228004.1/1596-1471       AAGCGGUAAUGAGAGAGAGACAGGGAACAAGCAG---------------------------------------AGCAUG---GAUU-----GAGUUUACUAA-------------------------------------------------------------AACAUUAAACGACUCUGUUUUGUCUCU-ACCCAUGCACUGCCUCUUCCCUGGCUCC-CUCUUUUUUUCUCUAU
GQ379191.1/170-351         GAUUGGAGAGGAGAG-GAGACAGGGAUGAGGCAGAGCAUGGGAUGGGGCUAUCAACAGAUGUAGAUUAUUCCUUGCACAAGAGAUGAUGAUGAGCUGUGAAUGAGU-----------------------------------------------------UCUGAGAGAUGGCUGGUGUUGUUGUUGCUCCCUCCCCUGCACUGCCUCUUCCCUGGCUCCCCUGCACACCUCUCUCU
AY730704.1/10-135          AAGCGGUAAUGAGAGAGAGACAGGGAACAAGCAG---------------------------------------AGCAUG---GAUU-----GAGUUUACUAA-------------------------------------------------------------AACAUUAAACGACUCUGUUUUGUCUCU-ACCCAUGCACUGCCUCUUCCCUGGCUCC-CUCUUUUUUUCUCUAU
GQ905616.1/68-256          GGUUGGUUUUGAUUUGGAGACAGGGAUGAGACAG---------------------------------------AGCAUG--GGAUG-----GGGCCAUCAACAAAGUGGAGGGACUAGCUUGCGAGGCAGAAAGAAGGUGCCAGUGCCGGUGCCUCCCCGGUGAAACGAUGAUGGGAGUGUUGUUGCUCCCUCCCCUGCACUGCCUCUUCCCUGGCUCC-GAUCCCCCACCGUUGC
#=GC SS_cons               ::::::::::::::::<<<-<<<<<<<-<<<<<<.......................................-<<<<<..-<---.....<<_____________.....................................................____________________________>>---->>>>>>->>>>>>->>>>>>>->>>:.::::::::::::::::
#=GC RF                    aauUGGugAugAgAugGAGACaGGGAagAgGCAG.......................................aGCAuG..aGAUG.....GaGCUaucAAcaAau.....................................................ugUGAgAaaaagaUGgaauUGUUgUuGCuCcCuCCCaUGCACUGCcUCuUCCCuGGCUCC.uuucuCuccucuuUuu
//
# STOCKHOLM 1.0

#=GF AC   RF00691
#=GF ID   mir-146
#=GF DE   microRNA mir-146
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   54.00
#=GF NC   49.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000103;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol. 2002;12:735-739.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   15800047
#=GF RT   Kaposi's sarcoma-associated herpesvirus expresses an array of viral
#=GF RT   microRNAs in latently infected cells.
#=GF RA   Cai X, Lu S, Zhang Z, Gonzalez CM, Damania B, Cullen BR
#=GF RL   Proc Natl Acad Sci U S A. 2005;102:5570-5575.
#=GF RN   [4]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   miR-146
#=GF SQ   33


CAAE01015006.1/213889-213798 AGG--AGUGCUCUGCUGUGAGAACUGAAUUCCAUAGAUGGUGACAUUUG----UAUGUGUCAUCU-AUGGGCUCAGUUCUUUUGGCUUGGUACUGUUUU
AC008388.7/35916-36002       GUG--UAUCCUCAGCUUUGAGAACUGAAUUCCAUGGGUUG-UG-UCAG-------UGUCAGACCUGUGAAAUUCAGUUCUUCA-GCUGGGAUAUCUCUG
BX005397.20/24549-24637      CUG--AGCUCUUGGCUUUGAGAACUGAAUUCCAAGGGUGUCUGCUU-------UAUAUUCAGCCCACGGAGUUCAGUUCUUAA-GUUUGGAUGCUCACG
AAFR03025019.1/59826-59741   ------GCAUCUGGCUCUGAGAACUGAAUUCCAUAGGCUG-UGAGCUC-----AUGCAAAUGCCCUAGGAAGUCAGUUCUGGA-GUCCGGUGACCUCGA
CT025772.15/118748-118837    UUG--AGCACUUUUCCCUGAGAACUGAAUUCCAUAGAUGG-UGUUCAU-----GAAAAGUUCAUCUAUGGGCUCAGUUCUUCU-GGCAAUCUGUUUAAU
BAAE01103753.1/1540-1630     AGA--AGUGCUCUACUAUGAGAACUGAAUUCCAUAGAUGGUAGCUUUUC----UAGGUGUCAUCU-AUGGGCUCAGUUCUUUU-GGCAUGGUACUGGUU
AANH01005121.1/10850-10759   AUG--AGUGUUGUACUAUGAGAACUGAAUUCCAUAGAUGGUGGCAUCUU----CAGGUGUCAUCU-AUGGGCUCAGUUCUUUUGGUACGGUACUAAUUU
AAPN01141106.1/3079-3169     AUGC-GGUGCUUGGCUCUGAGAACUGAAUUCCAUAGGCUG-UGAGUUG-----AUGAGGAUGCCCUAGGGAUUCAGUUCCACA-GCCCAGCAACCCACA
AAPN01152393.1/27352-27260   CAG--UACGCUCAGCUUUGAGAACUGAAUUCCACGGGUUG-UGAUUGCAAC--UCUGACAGACCCGUGGGGCUCAGUUCUUGA-GCUGGGGUACCUCUG
AAIY01333564.1/1864-1775     UUU--GGUCCCUGGCUCUGAGAACUGAAUUCCAUAGGCUG-UGAGCUC-----UAGCAAAUGCCCUAGGAGCUCAGUUCUGGU-GCCCGGCAGGCCGUG
AAFR03012754.1/25474-25388   UUG--UAUCUUCAGCUUUGAGAACUGAAUUCCAUGGGUUG----UCUU-----UGUAUCAGACCUAUGAAACUCAGUUCUUCA-GCUGGAAUAUCUCUG
AAVX01275541.1/618-713       UGG--CAGCUCCAGCUGUGAGAACUGAAUUCCAUGGGCUGGUCACGCAGUUUUCUUCCUCAGUCCAUAGUAGUCAGUUCUUCC-GUUUGGCUGCUUGAU
AAYZ01153033.1/3261-3350     UUG--GUUGCCUGGCUCUGAGAACUGAAUUCUAUAGGCCG-UGAGCUC-----UAGCAGAUACCCUAGGGACUCAGUUCUGGU-GCCUGGCUGGGCUGC
AANN01666952.1/959-1048      UUG--GCCACCUGGCUCUGAGAACUGAAUUCCAUAGGCUG-UGAGCUC-----UAGCAAACGCCCUAGGGACUCAGUUCUGGU-GCCCGGCUGUGCUAU
ABDC01238493.1/6154-6243     UUG--GCCACCUGGCUCUGAGAACUGAAUUCCAUAGGCUG-UGAGCUC-----UAGUGAAUGCCCUAGGGACUCAGUUCUGGU-GCCUGGCUGUGCCAC
AAPY01213417.1/4703-4792     CCG--GCCACCUGGCUCUGAGAACUGAAUUCCAUAGGCCG-UGAGCUC-----CAGCAGAUGCCCUAGGGACUCAGUUCUGGU-GCCCGGCUGCGCAGU
AANG01052378.1/2905-2994     UUG--GCCACCUGGCUCUGAGAACUGAAUUCCAUAGGCUG-UAAGCUC-----AAGCAAAUGGCCUAGGGACUCAGUUCUGGU-GCUCGGCUGUGCUAU
CAAA01220328.1/4488-4574     GUG--UAUCCCCAGCUCUGAGAACUGAAUUCCAUGGGUUA----UAUC-----AAUGUCAGACCUGUGAAAUUCAGUUCUUCA-GCUGGGAUAGCUCUG
AAFC03000506.1/621-535       GUG--UAUCCUCAGCUUUGAGAACUGAAUUCCAUAGGUUG----UGUC-----AGUGUCAGACCUGUGAAGUUUAGUUCUUUA-GCUGGGAUAUCUCUA
AADA01134315.1/4724-4812     UUG--GCCACCUGGCACUGAGAACUGAAUUCCAUAGGCUG-UGAGCUC-----UAGCAAU-GCCCUGUGGACUCAGUUCUGGU-GCCCGGCAGUGCUAC
AAKN02016522.1/10507-10417   CUG--GCCAUCUGGCUUUAAGAACUGAAUUCUGUAGGCUG-UGAGCUC-----CAGCAAAUGCCUUAGGGACUCAGUUCUGGAAACCUGGCUGUGCUGC
AAGV020197496.1/364-278      GUG--UAUCCCCAGCUUUGAGAACUGAAUUCCAUGGGUUU----UCUC-----AAUGUCAGACCUGUGAAAUUCAGUUCUUCA-GCUGGGAUAUCUCUG
AABR05018978.1/7743-7657     GUG--UAUCCUCAGCUCUGAGAACUGAAUUCCAUGGGUUAUAGCAA---------UGUCAGACCUGUGAAGUUCAGUUCUUUA-GCUGGGAUAGCUCUA
AAGU03026742.1/175862-175773 CUG--GCCACCUGGCUCUGAGAACUGAAUUCCAUAGGCUG-UGAACUC-----UAGCAGAUGCCCUAGGAACUCAGUUCUGGU-GCCCGGCUGUGCUGC
AADN03006667.1/347156-347063 GUG--UAUCCUCAGCUUUGAGAACUGAAUUCCAUGGGUUGUAAUUGAAUCC--UUUGUCAGACCCAUGGGGCUCAGUUCUUCA-GCUUGGAUAUUUCUG
AADN03004045.1/26172-26268   UUGGCAGUUCCCAGCUCUGAGAACUGAAUUCCAUGGACUGGUUUCAAUUCCA-UGCGUUCAGUCCAUGGUAUUCAGUUCUCUA-GCUUGGCUGCAUCAA
AAGW02060858.1/19148-19237   UUG--GCCACCUGGCUCUGAGAACUGAAUUCCAUAGGCCG-UGAGCUC-----UAGCAAAUGCCCUGGGGACUCAGUUCUGGU-GCCCGGCUGUGCUGC
AAWZ02005630.1/5439-5350     AUG--GUUGCCUAGCUCUGAGAACUGAAUUCCAUAGGCUUUAG-AAUA-----AUUGAAACGCCCCGUGGAUUCAGUUCUACA-GCUAGGCAGCAACUA
AAWZ02023959.1/1703-1799     CUGGCAGUUCCAAGCUUUGAGAACUGGUUUUCGUGGACUGGUUUCCAUUUAG-UCUUCUCAGUCCAUAAUGCUCAGUUUUCCA-GCUUGGCUGCACCUG
CAAB02001937.1/426747-426656 UAG--AGUGCUCCGCCAUGAGAACUGAAUUCCAUAGAUGGUGACAUUUG----UAUGCUUCAUCU-AUGGGCUCAGUUCUUUUGGCUCGGUACUGUCCA
AAEX03015486.1/23854-23943   CUG--GCCACCUGGCUCUGAGAACUGAAUUCCAUAGGCUG-UGAGCUU-----GAGCAAACAGCCUAGGGACUCAGUUCUGGU-GCCCGGCUGUGCUCU
AAPE02031084.1/12272-12361   UUG--GCCACCUGGCUCUGAGAACUGAAUUCCAUAGGCUG-UGAGCUC-----UAGCAAAUGCCCUAGGGACUCAGUUCUGGU-GCCCGGCUGUGCUAC
AADN03004970.1/43219-43309   CUG--GCUGCUUGGCUUUGAGAACUGAAUUCCAUAGGCGUUAAAGCAU-----CCAAAAAUGCCCUAUGGAUUCAGUUCUGCA-GUUGGGCAGCAAAUA
#=GC SS_cons                 :::..::::<<-<<<----<<<<<<<<-------<<<<__._______.....________>>>>------->>>>>>>>---.>>>->>:::::::::
#=GC RF                      uUG..aguaCcugGCUuUGAGAACUGAAUUCCAUgGgcUG.Ugaucuu.....uaugaaaugcCcuagGgacUCAGUUCUuua.GCcugGcUguuucuu
//
# STOCKHOLM 1.0

#=GF AC   RF00692
#=GF ID   MIR171_2
#=GF DE   microRNA MIR171_2
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   65.10
#=GF NC   63.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00099
#=GF DR   MIPF; MIPF0000104;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15994906
#=GF RT   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa
#=GF RT   that are absent from Arabidopsis.
#=GF RA   Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL
#=GF RL   Plant Cell. 2005;17:2186-2203.
#=GF RN   [2]
#=GF RM   20398412
#=GF RT   Discovery and comparative profiling of microRNAs in a sweet orange
#=GF RT   red-flesh mutant and its wild type.
#=GF RA   Xu Q, Liu Y, Zhu A, Wu X, Ye J, Yu K, Guo W, Deng X
#=GF RL   BMC Genomics. 2010;11:246.
#=GF RN   [3]
#=GF RM   12101121
#=GF RT   MicroRNAs in plants.
#=GF RA   Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP
#=GF RL   Genes Dev. 2002;16:1616-1626.
#=GF RN   [4]
#=GF RM   16040653
#=GF RT   Expression of Arabidopsis MIRNA genes.
#=GF RA   Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC
#=GF RL   Plant Physiol. 2005;138:2145-2154.
#=GF WK   MicroRNA
#=GF SQ   7


AARH01006308.1/48604-48716 UGGAGAAGUAGACACGGUGUGAUAUUGGUCCGGCUCAUCUUCUGUGCAUAA-GCAUCUGAAGUUCUUCACUC-AUG--------AAGACGAGCCGAAUCAAUAUCAC-UCUUGUAUGCUUCUUC
AAAA02021855.1/30025-30132 AGAACAGGAAGACAUGGCAUGGUAUUGACUUGGCUCAUCUC--AGCAACAGCAAACUGCAUG--CAGCGCU---GG---------AGGUGAGCCGAGCCAAUAUCACUUCAUGUCCUCUUUUGU
EF424185.1/156-34          UGAAGAGGCAGACAAGGUGUGGUAUUGGUUCGGUUCAUCUCUCUCUCUCUCUGUCUCUCUGAUGAGGAAAACUCUAAUUAGUAAGAGGCGAGCCGAAUCAAUAUCAC-UCUUGUAUUUCUCGUU
AASG02011537.1/4995-5113   UAGAGAAGUAGACAUGGCGUGAUAUUGGUCCGACUCAUCUCUCUCUCUCUCUCUCUCUCUCUAACUUAGAGAGUUCUUCA----GAGGCGAGCCGAAUCAAUAUCAC-UCUUGUAUGCUUCUUU
AARH01005111.1/17672-17565 UGGAGAAGCAGACAUGGCGUGGUAUUGAUCCGGCUCAUCUUCUGUAUUU---GCAUCAGAAGUUCUUCGCU---GA---------AGACGAGCCGAAUCAAUAUCAC-UCUUGUACGCUUCAUU
AM438992.1/34547-34650     UGGAGAAGUAGACAUGGUGUGGUAUUGGUUCGGCUCAUCUUCUUUCAUU--------CAUUUUCAUCGGCU---CA--------AAGACGAGCCGAACCAAUAUCAC-UCUUGUAUGCUUCUUU
AL662954.2/104399-104487   AGAAGAAGAGGACAUGGUUUGGUAUUGUUUCGGCUCAUGUCGUUCACAC-------------------------AG---------AUGUGAGCCGAACCAAUAUCAC-UCAUGUAUUCUUCAUU
#=GC SS_cons               ::::<<<<<--<<<<<---<<<<<<<<-<<<<<<<<___________________________________...__........_____>>>>>>>>->>>>>>>>-.->>>>>-->>>>>:::
#=GC RF                    uGaAgAaGcAGACAuGGugUGgUAUUGguuCGGCUCAUCUcuuuuucucuauguaUcucuuguucuuagcu...ua........aAGgcGAGCCGaauCAAUAuCAC.UCaUGUAUgCuUcuUU
//
# STOCKHOLM 1.0

#=GF AC   RF00693
#=GF ID   mir-147
#=GF DE   microRNA mir-147
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.10
#=GF NC   44.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.91 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000105;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   18402656
#=GF RT   Hidden layers of human small RNAs.
#=GF RA   Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub
#=GF RA   CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y
#=GF RL   BMC Genomics. 2008;9:157.
#=GF RN   [3]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   MicroRNA
#=GF SQ   64


BX931191.1/437-506             AAUCUAGUGGA-AUC-ACUUCUGC-ACA-------AACUUG---ACU---ACUGAAAU---CAGUGUGC---GGAAAUGCUU-CUGCUACAUU
AAFC03018591.1/6229-6298       AAUCUCAUGGA-AAC-AUUUCUGC-ACA-------AACUCG---AUU---AUGGAUAC---CAAUGUGC---CAAAAUGCUU-UUGCUACAUU
ABDC01001199.1/1794-1723       ACUCCAGAGAA-AAC-GUUUCUGC-GCACA-----CCCCAG---ACU---ACCGAAAC---CAAUGUGU---GGAAAUGCUU-CUGCUGCGUU
ABBA01075050.1/41249-41181     UAUUUCGUGGA-UG--AUUUCUAC-ACA-------GACUAG---GCC---AUAGAAAC---CAGUGCGU---AGAAAUGCUU-CUGUUACAUG
AY866123.1/404-475             AAUCUAAAGAA-AAC-AUUUCUGC-ACACA-----CACCAG---ACU---AUUGAAGC---CAGUGUGU---GGAAAUGCUU-CUGCCACAUU
AADD01093451.1/1636-1571       AAUCUUAUGGA-AAC-AUUUCUGC-ACA------------C---AAU---AAAGAAAC---UAGUGUAC---AGAAAUGUUUACUUGUCUAUG
AAPY01498171.1/7435-7366       AAUCUAGGGAA-AAG-AUUUCUGC-ACA-------AACCAG---ACU---UUGGAAAC---UAAUGUGU---GGAAAUGCUU-CUGCUGCAUU
CAAE01014581.1/5651544-5651616 AGUCUAACAGA-AUC-CUUUCUGC-ACA-------AACUAG---AAUGAUUUGACACU---CAGUGUGC---GGAAACGCUU-CUGCUCCACU
AANN01839719.1/1424-1493       AAUUUAGAGAA-ACC-AUUUUCAG-ACA-------CGCCAG---ACU---AUUGAAAU---GCUUGUGU---GGAAAUGCUU-CGGCUGCAUU
AAQQ01100588.1/1420-1352       UAGGUAGG-GA-AAC-AUUUCUGC-ACA-------GACUAG---ACC---AGAGAAAC---CAGUGUGU---GAAAAGGUUU-GUGAUACGUG
AAIY01216105.1/2209-2140       CAUCCAGGGGA-AAC-ACUU--CC-ACAUG-----AGCUAG---AUU---ACGGAAAC---CUGUGUGC---AUAAAGGCUU-CUGCUACAUU
AANH01000229.1/71291-71222     AGUGCAACAGA-AUC-CUUUCUGC-ACA-------CACUUU---GCG---UUGACACU---CGGUGUGC---GGAAAUGCUU-CUGCUCCACU
AAIY01448215.1/220-289         UGUCUUGUGAG-AAC-AUUUAUGC-ACA-------AAGUAG---ACA---AUAUGUAC---CAGUGUGU---AGAUAUGCUU-UUCCUGUGUU
AAFR03018157.1/230013-230082   AAUCUAGUGGA-AAC-AUCUCCGC-ACA-------AACUAG---ACU---ACUGAAAC---CAGUGUGC---GGAAGUGCUU-CUGCUACAUU
AAHX01006722.1/12190-12258     AAUCUAGUGGA-AAC-ACUUCUGC-ACA-------AACUCG---AUU---U-UGAUGC---CAGUGUGC---AGAAAUGCUU-CUGCUACAUU
AANN01661338.1/2315-2243       AAUCGAGUGGG-AAC-ACUUCUGC-ACAGCU----AGAUAG---AUU---AUAAGUGC---GGGUGCGC---AGAAGUGCUU-CUGCUGCAUU
AANG01714059.1/489-419         AAUCUUGCAAA-AAC-AUUUCUGC-ACA-------AACUAG---AUU---AUGGAUAC---CAGUGUGC--CAAAAAUAUUU-CUGCUGCAUC
AAYZ01657527.1/870-937         AAUCUAGUGGA-AAC-AUUUC--C-ACA-------GACUCA---AUU---AUGGGUGG---CAGUGUGC---AGAAGUGCUU-CUGCUACAUU
AACN010573528.1/732-801        AGUCUAGAGGA-AGC-AUUUCUGC-ACA-------CACCAG---ACU---AUUGAAAU---CAGCGUGU---GGAAAUGCUU-UCGCUACAUU
AAIY01799330.1/435-507         AGUCCAGGGGA-AACACUUCCACC-GCACG-----AGCUAG---GUU---ACGGAAAC---CAGUGUUC---GGGAAGGCUU-CUGCUACAUU
BAAF04016950.1/22862-22934     AGUCUAACAGA-AUC-CUUUCUGC-ACA-------AACUAGGAUGUU---UUUACGGU---CAGUGUGC---GGAAAUGCUU-CUGCUUAACU
AAFR03003088.1/227501-227425   UAUCUAGCAGA-AAC-AUUUCUGC-ACAAACCACAAAGUAU---ACA---ACUAAACC---CAGAGUGU---AGAAAUGUUA-CUGCUACAUU
AAPY01675107.1/268-337         AGUCUAGUGGA-AAC-ACUUCUGC-ACC-------AACUAG---AUU---AUGGGUAU---CAGUGUGC---GGAAAUGCUU-CUGCUACAUU
AAFC03110925.1/4203-4133       AGCCUUAGGAAAAAU-AUUUCU-U-ACUA------GAUUAG---AUU---AUGGAAAG---GAGUGUGU---AGAAAUGCAU-CUGCUACAUA
AANG01591628.1/889-825         AAUCUAACGGA-AAC-AUUUCUGC-ACA------------A---ACU---AAAGAAAC---UAAUAUGU---GAGAAUACUU-CUGCUAUAUU
AAIY01165272.1/221-150         AAUCCAGGGGA-AAC-ACUUCCGC-CGCCG-----AGAUAG---GUU---ACGGAAAC---CAGUGUUC---GGGAAGGCUU-CUGCUACAUU
AAFR03041724.1/84993-84924     AAUGUAGUGGA-AAC-AUAUCUGC-ACA-------AAGCAA---AUU---ACUAAAAU---AAGUGUUU---GGAAGUAUUU-CCGUUAUAUU
AAVX01307041.1/135-202         AAUCUCCCGGA-AUC-AUUUCUGC-ACA-------AACUCG---GUA---CUGGAA-----CAGUGUGC---GGAAAUGCUU-CUGGUACAUU
ABDC01643817.1/885-818         UAUUUAGUGGA--UC-AUUUCGUC-AUA-------GACUA----ACC---ACAGAAAC---UGGUGUGA---GGAAAUGCUG-CUGCUACUAA
AALT01540283.1/872-940         AAUCCAG-GGA-AAC-AUUUCAGC-ACA-------GAGUUG---AGU---ACGGAGAC---CAGUGUAU---GGAAAUGCUU-CUGUUUCAGG
AANU01115274.1/8719-8650       AAUCUAGUGGA-AAC-AUUUCCGC-ACA-------AACUAG---AUU---CUGGACAC---CAGUGUGC---GGAAGUGCUU-CUGCUGCAUU
AAFC03064072.1/45006-44940     UAUUUGGUGUA--GC-AUUUCUGC-AUA-------GACUGG---AUU---AUGGAAAC---CUGUAU-----AGAAAUGCUU-CUGCUGUAUA
AANU01292740.1/18422-18491     GUAUUUCAUGG-AUG-AUUUCUGC-ACA-------GAGUAG---GCC---AUAGAAAC---CAGUGUGU---GGAAAUGCUU-GUUACAUGUU
AALT01554324.1/2524-2592       GAUCCAG-GGA-AAC-GUUUCAUC-GCA-------GACUCG---AGU---ACGGAGAC---CAGUGUAU---GGAAAUGCUU-CUGCUACAGU
AAIY01580043.1/888-817         CAUCAUUAGAA-ACA-CUUCCGCC-GCACA-----AGCUAG---GUU---AUGGAAAC---CAGUGUUC---GGGAAGGCUU-CUGCUACAUU
AAIY01810045.1/447-519         AUCCAGGGGAA-AAC-ACUUCCGCCGCACG-----AGCUAG---GUU---ACGGAAAC---CAGUGUUC---GGGAAGGCUU-CUGCUAUAUU
AAPN01075732.1/1773-1705       AAUCCAGCGGA-AUC-ACCUCUGC-ACA-------AACUCG---UCU---UCUGAA-C---CAGUGUGC---GGAGAUGCUU-CCGCCGCAUU
AAPY01600069.1/1541-1474       UUCCUAGUGGA-AC--AUUUCUGC-AUG-------GACUAG---ACC---AUAGAAAU----AGUGUGU---AGAAACACUU-CUGCUGCAUG
BC049633.1/371-439             AAUCUAGUGGA-AAC-AUUUCUGC-ACA-------AACUAG---A-U---GUUGAUGC---CAGUGUGC---GGAAAUGCUU-CUGCUACAUU
AAWR02029570.1/15403-15467     AGUCUAACGGA-AAC-ACUUCUGC-ACA------------A---ACU---GAAGACAC---CAGUGUGU---GGAAAGGUUU-CUGCUACAUG
AAGV020068496.1/506-569        AAUGCAGUGGA-AAC-CUUUCCAA-ACA----------------AAU---AUGGAUAU---CAGUGUGC---AGAAAUGCUU-CUGCUGAACU
AAWR02026698.1/2322-2389       GAUCUAGUGGA-AAC-AUUUCUGC-ACA--------ACUAG---AAU---AUUCAAAC---UGGUUUG----AGAAAUGCUU-CUGUAACAAU
AAGV020749547.1/2494-2563      AAUCUAGUGAA-AAC-AUUUGUAC-ACC-------CACCAG---AUG---AUAAAAAC---CAGUGUGU---GGAAAUGCAU-CUAGUAUGUA
AAWR02019028.1/76654-76723     AAUGUUAAGGA-GAC-CAUUCUGC-ACA-------AACUGG---AGU---AUGGAUAU---CAGUGUGC---CGAAAUGCUU-CUGCUACAUU
AAKN02021930.1/38377-38445     AAUCCAGUGGA-AGU-AUUUCUAC-ACA-------AACUAG---AGC---CUGCAUAC---CAGUGUGU---AG-AGUGCUU-CUGCUGUUCU
AAGV020162996.1/809-878        UAUCUACUGGG-AAC-AUUUCUGC-AUA-------AAUUUC---ACC---AUAGAUAC---CAGUGUGU---AGAAGUGCUU-AGAAUUUACC
AAKN02027666.1/17442-17511     AAUCUAGCGGA-AAC-ACUUCCGG-ACA-------GGCUUG---GGU---CUGGACAC---CAGUGUGC---GGAAGUGCUU-CUGCUAAGUU
AAWR02025623.1/4499-4430       AGUCUUGAGGA-AGC-AUUUCCGC-ACA-------CGCCAC---GCU---AUCGAGAC---CAGCGUCU---GGAAACGCGU-CUGCUACAUU
AAWR02004081.1/100914-100982   UAUCUAGUAGA-A-C-AUUUCUGC-AUA-------GACUAG---ACC---AUAGAAAC---UAGUGUAU---GGAAAUGCUU-CUGCUGCAUG
AAGV020259291.1/6833-6764      AAUCUAAUGAC-AAC-GUGUGUAC-GCC-------CACCAG---AGG---AUAAAAGC---CAGUGUGU---AGAAAUGCAU-GUGCUACAUA
AAKN02005203.1/37099-37168     ACUCUACAGAA-AAC-AUUUCUGC-ACA-------AACCAG---ACU---AUUGAAUC---CAGUGUGG---GGCGAUGCUU-CUGCUACAUU
AAGV020401132.1/719-787        AGUCUAGAGGA-AAC-AUUUCUGC-ACA--------ACUAG---AAU---AUUCAAAC---UUGUAUGA---GGAAAAGCUU-CUGUCACAGU
AAPE02005277.1/58174-58243     UAUCUAGUGGA-A-C-AUUUCUAC-UUA-------GACCAG---ACU---ACAGAAACA--CAGUGUAU---GGAGAUGCUU-CUGCUACAUG
AAEX03010097.1/60191-60260     AAUCUAGUGGA-AAC-AUCGCUGC-ACA-------AACUCG---AUU---AUGGAUAC---CAGUGUGC---GGAAAUGCUU-CUGCUACAUU
AAGU03000998.1/82402-82333     GAUUUAGUGGA-AAC-ACUUCCGC-ACA-------AACUAG---AUU---AUGGAUAC---CAGUGUGU---GGAAAUGCUU-CUGCAACAUU
AL031669.28/23303-23371        GGUCUAGUGGA-AAC-AUUUCUGC-ACA--------ACCAG---AAU---ACUCAAAC---UAGCAUGA---GGAAAGGCUU-CUGUAACAGU
AAGU03079720.1/12036-11968     AAUCUAGUGGA-AAC-ACUUCUGC-ACA-------AACUAG---AUU---G-UGGACA---CAGUGUGC---GGAAAUGCUU-CUGCUACAUU
AAEX03011796.1/88817-88889     AUUCUUAUGGA-AGC-AUUUCUGU-ACA-------AACUAG---AUU---AUGAAUAU---CAGUGUGCCAAAAAAAUGCUU-CUGCUAUAUC
CAAB02000082.1/10885-10813     AGUCUAACAGA-AUC-CUUUCUGC-ACC-------AACUAG---AAU---GAUUUAACACUCAGUGUGC---GGAAACGCUU-CUGCUCCACU
AAQR03050990.1/1633-1565       UACUUAGUGGG--UC-AUUUCUGC-AUA-------GACUCG---ACU---GUAGAACC---CAGUGUGA---GGAAAUGCUU-CUGCUAUGUG
AAWZ02029364.1/18093-18024     AAUCUAGUGGA-AUC-ACUUCCGC-ACA-------AACUAG---AUG---AAUGAAAC---CAGUGUGC---GGAAAUGCUU-CUGCUACAUU
AAGW02054599.1/3783-3852       AAUCCAGAGAG-AGC-AUUUCUGC-ACA-------CACCAG---ACU---AUUGCAAG---CAGUGUGC---GGAAAUGCUU-CCGUUACAUU
ADFV01042782.1/25340-25276     AAUCUUAUGGA-AAC-AUUUCUGC-ACA------------C---AAU---AAAGAAAC---UAGUGUAC---AGAAAUGUUU-AUUUGUCUAU
AAEX03015921.1/21466-21402     AAUAUAAUGGA-AAC-AUUUCUGC-ACA------------A---ACU---AAGGAAAU---UAAUGUAU---GGAAUUAUUU-CUGCUAUAUU
#=GC SS_cons                   ::::::::<<<.--<.<<<<<<<<.<<<.......______...___...________...___>>>>>...>>>>>>>->>.>:::::::::
#=GC RF                        AAUCUAGuGGA.AAC.aUUUCugc.ACA.......AACUAG...AuU...AUgGAAAC...CAGUGUgc...aGAAAuGCUU.CUGCUACAUU
//
# STOCKHOLM 1.0

#=GF AC   RF00694
#=GF ID   mir-137
#=GF DE   microRNA mir-137
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   57.00
#=GF TC   59.70
#=GF NC   51.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00092
#=GF DR   MIPF; MIPF0000106;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing.
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF WK   Mir-137
#=GF SQ   28


AASS01044470.1/198-98          CGUCGCCAAUCUCC--AAUGGCCACGUGUAUGCUCGUAGCUAUAACCUGAAA---UCCA-AAUGUUAUUGCUUGAGAAUACACGUAGUUCA--CCGA-G-AUUUGUUCAGC
AAZO01004444.1/55394-55292     AUUAUUUAUAACUUG-GUUGGUCACGCGUAUUCUUGGGGAAUUAACACACCAAA-AGAG--AUGUUAUUGCUUGAGAAUACACGUAGCUGA--CAAG-U-UUGAGCAUCAC
BAAE01237923.1/971-872         ACGGAAAGACUCUC--UUCGGUGACGGGUAUUCUUGGGUGGAUAAUACGGAU---CACG--UUGUUAUUGCUUAAGAAUACGCGUAGUUGA--GGAG-A-GUCCUCUCUUC
AJ324266.1/117-18              GUCCUCUGACUCUA--GUCGGUGACGGGUAUUCUUGGGUGGAUAAUCCGGAU---GACG--UUGUUAUGGUUUAAGAAUACGUGUAUUCAA--GGAA-A-GUACAAGGUCG
AAGE02007773.1/15500-15400     CAUCGAGCAACUUG--GUUGGCCACGCGUAUUCUUGGGUUAUUAACACACUGUU-UAUG--UUGUUAUUGCUUGAGAAUACACGUAGUUGA---CAA-G-UGUUUCACAUC
BAAB01088495.1/2035-1938       UAAAUAACACGCUU--GGAGGUCACGCGUAUUCUUGGGGAAUUAACACAUAUG--UGAG--AUGUUAUUGCUUGAGAAUACACGUAGCUGA--CAAG-----GAGUAAUGC
CAAE01013623.1/560-657         CUCUAUGCUCCGAU--CUCGACCACGGGUAUUCUUGGGUUGAUAAUACAGAU---GUGG--AUGUUAUUGCUUGAGAAUACGCGUAGUCGA--G--U-G-GAUGCUUUAUC
AANH01004180.1/20978-21076     CCGUUUGCUCCCGU--CUCGACCACGGGUAUUCUUGGGUUGAUAAUACAGAU---GUCG--AUGUUAUUGCUUGAGAAUACGCGUAGCUGA--G-CG-G-AAGCCAUCACC
BAAE01218049.1/3115-3015       ACCACUUGCUCCCGU-CUCGACCACGGGUAUUCUUGGGUUGAUAAUACAGAU---GUCG--AUGUUAUUGCUUGAGAAUACGCGUAGCUGA--GCGG-A-AGCCAUUGUCA
AANH01003094.1/38438-38337     GCCCCUUUGCUCCGGUCUCGACCACGGGUAUUCUUGGGUUGAUAAUACAGAU---GUGG--AUGUUAUUGCUUGAGAAUACGCGUAGUCGA--GUGG-A-GGCUUCAUCAU
AAJJ01002111.1/15264-15166     AAAUGGUAACUU-G--GUUGGUCACGUGUAUUCUUGGGUAAUUAACACAUAUUC-AGGG--AUGUUAUUGCUUGAGAAUACACGUAGCUGA--C--A-A-GUGACAACAGC
BAAF04031315.1/5933-5836       UUUAUUGCUCCGGU--CUCGACCACGGGUAUUCUUGGGUUGAUAAUACAGAU---AUGG--AUGUUAUUGCUUGAGAAUACGCGUAGUCGA--G--U-G-GAAGCUCCAAC
AAPT01021618.1/1643-1543       AAAUUAAAAUCUGA--AAUGGCCACGUGUAUGCUCGUAGCUAUAACCUGAACAA-UCAA--AUGUUAUUGCUUGAGAAUACACGUAGUUAA--C-AA-G-AUUGCCUCAAC
AL929343.7/129004-128905       UAUAAAGGACUCUC--UUCGGUGACGGGUAUUCUUGGGUGGAUAAUACGGCU---CUCG--UUGUUAUUGCUUAAGAAUACGCGUAGUCGA--GGAG-A-GUCAUGUCGGC
AAPP01018794.1/261725-261826   AACCUGGAAUCUCC--AAUGGCCACGUGUAUGCUCGUAGCUAUAACGUGAAAUG-CGAA--AUGUUAUUGCUUGAGAAUACACGUAGUUCA--GAGA-G-AUUUGUUCAGC
AAPN01296459.1/4449-4348       AGCCCCCAGCCCCU--UUCGAUGACGGGUAUUCUUGGGUACAUAAUACGGAU---GGCG--CUGUUAUUGCUUGAGAAUACGCGUAGUCGAGGGAGA-G-GCACCGACGUC
AAAB01008900.1/2515482-2515584 CAUCGCAAAACUUG--GUUGGCCACGCGUAUUCUUGGGUUACUAACACACUGUU-UAUG--UUGUUAUUGCUUGAGAAUACACGUAGUUGA--CUAGUG-UUGUACAUCGA
AAFR03049204.1/9121-9021       AUUGCCUAGCCCCC--CGCGAUGACGGGUAUUCUUGGGUAGAUAAUACCAAU---GGCG--CUGUUAUUGCUUGAGAAUACACGUAGUCGA--GGGGAG-GCCUCUUCGAC
AAZX01005510.1/7421-7321       ACAUCGGAGACCAG--GUUGGCGACGCGUAUUCUUGGGGAAUUAACACACAUA--CGCG--CUGUUAUUGCUUGAGAAUACACGUAGUUUG--CCUG-G-UCGAUCUCUGC
AAWU01042674.1/5306-5206       UCGUCGAGAACUUG--GUUGGCCACGCGUAUUCUUGGGUUACUAACACACUGUU-UAUG--UUGUUAUUGCUUGAGAAUACACGUAGUUGA--C-AA-G-UGUUCCACAUC
AAPU01010131.1/289658-289758   AAAUUGGAAUCGGC--AAUGGCCACGUGUAUGCUCGUAGCUAUAACUGGUAC---AAUCAAAUGUUAUUGCUUGAGAAUACACGUAGUUA----GCCAG-AUUCGCCCAAC
AAQB01009904.1/3815-3716       CACAAGAAUCUUUU--AAUGGCCACGUGUAUUCUUAUAGCUGUAACCUGUUA---UACAAAAUGUUAUUGCUUGAGAAUACACGUAGUUA----ACU-A-GAUUCGUUCAA
CAAK05033301.1/18518-18419     UUUCUGAGGCUCUC--UUCGGUGACGGGUAUUCUUGGGUGGAUAAUACGGCU---CUCG--UUGUUAUUGCUUAAGAAUACGCGUAGUUGA--GGAG-A-GUCAUUGUCGA
AK094607.1/564-663             GUCCUCUGACUCUC--UUCGGUGACGGGUAUUCUUGGGUGGAUAAUACGGAU---UACG--UUGUUAUUGCUUAAGAAUACGCGUAGUCGA--GGAG-A-GUACCAGCGGC
AADG06002845.1/74264-74364     ACUUCAUAGGCCAG--GUUGGCGACGCGUAUUCUUGGGGAAUUAACACACAUU--UGCG--CUGUUAUUGCUUGAGAAUACACGUAGUUUG--CCUG-G-UCGUUCACUCC
AAGJ04108966.1/34551-34651     ACUAUCCAGACCUC--AUG-AUUACAGGUAUUCUCGAGUGAAUAAUACAGAAAAGCCUG--AUGUUAUUGCUUGAGAAUACACGUAGUAUA--CG-G-G-UCACUCACCGC
AGAI01068243.1/879-978         GCUUUCUGACUCUC--UUCGGUGACGGGUAUUCUUGGGUGGAUAAUACGGAU---UACG--UUGUUAUUGCUUAAGAAUACGCGUAGUCGA--GGAG-A-GUACCGGCGGC
AAWZ02011060.1/18103-18003     ACUGACUAGCUCCC--UUCAAUAACGGGUAUUCUUGGGUAUAUAAUACAGAU---GGCG--UUGUUAUUGCUUGAGAAUACGCGUAGUUGA--GGGG-AUGCUGAUUCAUC
#=GC SS_cons                   ::::::::<<<<<<..<<<<<<-<<<-<<<<<<<<<<<--<-<<<<<<<___...__>>..->>>>>>-->>>>>>>>>>>->>>->>>>>..>>>>.>.>>:::::::::
#=GC RF                        aauuuuuagccccc..cucggccACGgGUAUuCUcGgGuaaaUAAcacggAu...uacg..augUUAuUGCuUgAGaAUACaCGUAgccga..gggg.g.gcuuuuucaac
//
# STOCKHOLM 1.0

#=GF AC   RF00695
#=GF ID   MIR398
#=GF DE   microRNA MIR398
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   55.50
#=GF NC   54.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000107;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15200956
#=GF RT   Computational identification of plant microRNAs and their targets,
#=GF RT   including a stress-induced miRNA.
#=GF RA   Jones-Rhoades MW, Bartel DP
#=GF RL   Mol Cell. 2004;14:787-799.
#=GF RN   [2]
#=GF RM   15258262
#=GF RT   Novel and stress-regulated microRNAs and other small RNAs from
#=GF RT   Arabidopsis.
#=GF RA   Sunkar R, Zhu JK
#=GF RL   Plant Cell. 2004;16:2001-2019.
#=GF RN   [3]
#=GF RM   16040653
#=GF RT   Expression of Arabidopsis MIRNA genes.
#=GF RA   Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC
#=GF RL   Plant Physiol. 2005;138:2145-2154.
#=GF RN   [4]
#=GF RM   19942686
#=GF RT   Conservation and divergence of microRNAs and their functions in
#=GF RT   Euphorbiaceous plants.
#=GF RA   Zeng C, Wang W, Zheng Y, Chen X, Bo W, Song S, Zhang W, Peng M
#=GF RL   Nucleic Acids Res. 2010;38:981-995.
#=GF WK   Mir-398_microRNA_precursor_family
#=GF SQ   14


AAAA02021799.1/7230-7143     GGAGUUCCUACAGGGGCGAGC---UGGGA-ACACACG------------------GUGAUG----------------------------AGGCGGUCU-GGUC--------UUUC------GUGUGUUCUCAGGUCGCCCCUGCCGGGACUCU
AM426431.2/9842-9931         AGGUGUCCUACAGGAGUGACC---UGAGAAUCACAUG------------------CCCGCA---------------------------UCACCCAUCU-UUGC--------UCUC------AUGUGUUCUCAGGUCGCCCCUGCUGGACUCCC
CR962131.2/106004-106111     UUCUAUCUCAGAGGAGUGACAC--UGAGA-ACACAAGAUU----GAUUAAUCAU-AUAAUG----------------------------UAUUUGGUU-GUUA-CUAGUU-GAUU------UUGUGUUCUCAGGUCACCCCUUUGAGUCAACC
AP006112.1/24509-24640       GUUUAUCUCAGAGGAGUGAGCU--UAAGA-ACACAAGCUGCAUUGGUUUGAAUU-GUUAUAUCAUAUACUAGAAUCUAG--------UAUAUCUUUAU-GUUA-CUAAUU-UAUC------UUGUGUUCUCAGGUCACCCCUUUGAGGUAACC
AK220694.1/69-183            UGGAUCUCGACAGGGUUGAUA---UGAGA-ACACACGAGC----AAUCAACGGCUAUAACGACG-----------------------CUACGUCAUUGUUACAGCUCUCG-UUUC------AUGUGUUCUCAGGUCACCCCUGCUGAGCUCUU
AC006284.4/38811-38707       UGAAAUUUCAAAGGAGUGGCA---UGUGA-ACACAUAUCC----UAUGGUUUCUU--------------------------------CAAAUUUCCAU-UGAA-ACCAUUGAGUU------UUGUGUUCUCAGGUCACCCCUUUGAAUCUCCC
AACV01021213.1/28360-28246   GCUGAACCCAGAGGAGUGGUAC--UGAGA-ACACAGGUGCC---AAUACAAUGU-AUGGUG-----------------------------AGCUACUG-UAUAAUGGAGU-AAUUCUGUAACUGUGUUCUCAGGUCACCCCUUUGGGUUUCUU
AARH01004353.1/90880-90989   GUACACCCCAGAGGAGUGGCUCC-AGAGA-ACACAGGGGG----UUGGUUUU---CUAGCU--------------------------GUAAGCUACAA-GAUGGACAAAG-CACU------CUGUGUUCUCAGGUCACCCCUUUGGGGCACCC
AARH01003834.1/508642-508739 AGGAUUCCUACAGGAGCGACC---UGAAA-UCACAUGUGG----GCUGCACCCUC--------------------------------CUGGGUUAUCU-UGAG--------CAAC------AUGUGUUCUCAGGUCGCCCCUGCCGGGCUUUC
AASG02014986.1/899-1036      AGGAUUCCUACAGGAGCGACC---UGAGAAUCACAUGUGGAC--AUUCUUAGCU-AUAUAUACCCUUAUCAUCUUCUCUUAUUUUGGGUUUAUUGUAC-UUUG-GUGUUC-UUUC------AUGUGUUCUCAGGUCGCCCCUGCCGGGCUUUC
AC136507.19/33604-33700      AGAUGUUCUACAGGGUCGACA---UGAGA-CCACAUGA-----------------AGCUAU--------------------------CAUAUUUGUCU-AUGU-UAUCCA-ACUC------AUGUGUUCUCAGGUCGCCCCUGCUGAAUUUUC
AARH01000462.1/173558-173473 AGGGUUCCGACAGGAGCGGCC---UUGGG-UCACAUGU----------------------G--------------------------GCGGCAUCCAA-UGUA--------CUUC------AUGUGUUCUCAGGUCGCCCCUGCCGGGCUUCC
AASG02002548.1/28926-28824   GUACACCCCAGAGGAGUGGCUCCCUGAGA-ACACACGUGC----A----------UUGGCU--------------------------CUCACCUUUUG-UAGU-UCCACU-GCAC------CUGUGUUCUCAGGUCACCCCUUUGGGGCACCC
AM470404.1/7821-7717         GUACACCCCAAGGGAGUGGCACC-UGAGA-ACACCGGUUG----UGUUGGCUGC-GCCAAG--------------------------CUCUGCUAGCU-AAUG--------CAUU------UUGUGUUCUCAGGUCACCCCUUUGGGGCACCA
#=GC SS_cons                 ::::::<<--<<<<-<<<<--...-<<<<.<<<<<<____....__________.______..........................___________.____.______.____......>>>>>>>>>>--->>>>->>>>-->>::::::
#=GC RF                      agaaaUCCcAcAGGAGuGaca...UGAGA.aCACAuGugg....aaUuuaauuU.aUaaug..........................cuuauuUauau.uuua.uuaauu.uaUC......aUGUGuUCUCAGGuCaCCCCUgugGGgcuucC
//
# STOCKHOLM 1.0

#=GF AC   RF00696
#=GF ID   mir-203
#=GF DE   microRNA mir-203
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   66.00
#=GF TC   71.30
#=GF NC   58.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000108;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12624257
#=GF RT   Vertebrate microRNA genes.
#=GF RA   Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP
#=GF RL   Science. 2003;299:1540.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MiR-203
#=GF SQ   10


AAFR03013559.1/2925-3004     GCUGCCCUGGUCCAGUGGUUCUUAACAGUUCAACAGUUCUGUGUAGAGA-UUGUGAAAUGUUUAGGACCACUUGAUCUGGG
AANN01327868.1/1449-1528     GCGCGUUGGGGCCAGUGGUUCUUAACAGUUCAACAGUUCUGUAGCGCAA-UUGUGAAAUGUUUAGGACCACUAGCUCCGGC
AAVX01234553.1/1127-1048     GUCUCCCUGGUGCAGUGGUUCUAAUCAGUUCAACAGUUCUCUAUCGAAA-UUGUGAAAUGUUUAGGACCACUUGACCUGGG
AAVX01626047.1/560-639       GUCCUUUGGGUGCAGUGGUUUUCAACAGUUCAACAGUUCUUUAUUAACA-UUGUGAAAUGUUUAGGACCACUUGAUCCAAA
BAAE01000181.1/2185-2106     GUCAUUCUGAUUAAGUGGUUCUCAACAGUUCAACAGUUCUUUGAGAAAA-UUGUGAAAUGUUUAGGACCACUUGACCAGUC
BX255913.8/25815-25737       UCCUCUUUGGCCGAGUGGUUCUCAACAGUUCAACAGUUCUUU-UGAUGA-UUGUGAAAUGUUCAGGACCACUUGAUCAGAC
CAAA01071497.1/6544-6465     GCGCGCCUGGUCCAGUGGUUCUUGACAGUUCAACAGUUCUGUAGCACAA-UUGUGAAAUGUUUAGGACCACUAGACCCGGC
CT027758.7/42576-42497       GUCCCUCUGGUGCAGUGGUUCUUAACAGUUCAACAGUUCUAUCUCAAAA-UUGUGAAAUGUUUAGGACCACUUGACCAGAG
CAAB02010027.1/2469-2546     UCCUCUCUGGUCCAGUGGUUCUCAACACUUCUACAGU---GGGAAGACAUAUGUGAAAUGUUUAGGACCACUGGCCCCGGG
AADN03004812.1/594539-594460 GCCUCCUUGGUGCAGUGGUUCUUAACAGUUCAACAGUUCUCUAUCAUAA-UUGUGAAAUGUUUAGGACCACUUGACCAGCG
#=GC SS_cons                 ::::<<<-<<<--<<<<<<<<<-<<<<-<<<-<<<______________._>>>>>>->>>>->>>>>>>>>-->>>->>>
#=GC RF                      GccucccUGguccAGUGGUuCUuAACAGUUCAACAGUUCUuUauaaaaA.UUGUGAAAUGUUUAGgACCACUuGacCaggg
//
# STOCKHOLM 1.0

#=GF AC   RF00697
#=GF ID   mir-186
#=GF DE   microRNA mir-186
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   53.00
#=GF TC   53.00
#=GF NC   52.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000109;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA. 2003;9:175-179.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   16766679
#=GF RT   Identification and characterization of two novel classes of small RNAs in
#=GF RT   the mouse germline: retrotransposon-derived siRNAs in oocytes and germline
#=GF RT   small RNAs in testes.
#=GF RA   Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N,
#=GF RA   Imai H
#=GF RL   Genes Dev. 2006;20:1732-1743.
#=GF RN   [4]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF WK   Mir-186_microRNA_precursor_family
#=GF SQ   19


AAFC03040431.1/43745-43653   UGCUUC--UCACUUUCCAAUAAGGUAUCCUUUU-GGGCUGAAACUUUCCAUGCUCAGUUUCAGCUCAAAGGUGAAUUU----AUUUUGGAAAGUUCACAC
AAPN01067101.1/12973-13059   UUGCUCA-UAACUUUCCAAAGAAUUCUCCUUUU-GGGCUU------UCUAUGCUUGGUCACAGCCCAAAGGUGAAUUU-----UUUGGGAAGUUUGAGCU
AY865945.1/420-505           UGCUUG--UAACUUUCCAAAGAAUUCUCCUUUU-GGGCUU------UCUGGUUUUAUUUUAAGCCCAAAGGUGAAUUU-----UUUGGGAAGUUUGAGCU
AAXM01004409.1/377-286       UUCUCG--CAGCUUUCCAAAAAAUUAGCCUUUU-GUGGUGAAAUUUUCCAUGCUUAGUUUCAGCCCAAAGGUGAUUUU-----UUUUGCAAAGUUCGAGA
AAFR03042129.1/13240-13326   UUGCUCA-CAACCUUCCAAAGAAUUCUCCUUUU-GGGCUU------UUGAUUCUUAAUUUCAGCCCAAAGGUGAAUUU-----UUUGGGAUGUUUGAGCU
CAAA01202455.1/12062-12147   UGCUUA--CAACUUUCCAAAGAAUUCUCCUUUU-GGGCUU------UCUCAUUUUAUUUUAAGCCCUAAGGUGAAUUU-----UUUGGGAAGUUUGAGCU
AANN01553095.1/1575-1661     UGCUUA--UAACUUUCCAAAGAAUUCUCCUUUUUGGGCUU------UCUGAUUUUGUUUUAAGCCCAAAGGCGAAUUU-----CUUGGGAAGUUUGAGCU
AAQQ01434948.1/1749-1657     UGCUUC--UAACUUUCCAAUAAUGUAUCCUUCU-GGGCUGAAACUUUCCAUCCUUCGUUUCAGCUCAAAGGUAAAUUU----AUUUUGGAAAGUUCACAC
ABDC01349456.1/5826-5918     UGCUUC--UAACUUUCCAAUAAGGUUUCCUUUA-GGGCUGAAACUUUCCGUGCUUCGUUUCAGCGCAAAGGUGAAUUU----AUUUUGGAAAGUUCGCAC
AADD01064057.1/7183-7274     UGCUUC--UAACUUUCCAAUAAGGUAU-CCUUU-GGGUUGAAACUUUCCAUGCUUCAUUUCAUCUCAAAGGUGAAUUU----AUUUUGGAAAGUUCACAC
AANG01342151.1/693-785       UGCCUC--UAAUUUUCCAAUAAGGUAUCCUUUU-GGACUGAAACUUUCCAUGCUUGGUUUCAACUCAAAGGUGAGUUU----AUUUUGGAAAGUUCAUAC
AAKN02005099.1/172878-172964 UUGCUCG-UAACUUUCCAAAGAAUUCUCCUUUU-GGGCUU------UCUGGUUUUAUGUUAAGCCCAAAGGUGAAUUU-----UUUGGGAAGUUUGAGCU
AAWR02002340.1/29052-28960   UGCUUC--UAACUUUCCAAUAAGGUAUCUUUUU-GGGCUGAAAGUUUCCGUGCUUAGUUUCAGCUCAAAGGUGAAUUU----AUUCUGGAAAGUUCACAC
AAGV020303356.1/7437-7522    UUGCUU--GUACUUUCCAAAGAAUUCUCCUUUU-GGGCUU------UCUGAUUUUAUUUUAAGCCCAAAGGUGAAUUU-----UUUGGGAAGUUUGAGCU
AACN010052403.1/1704-1612    --UGCCUCUAACUUUCUAAUAAGGUAUCCUUUU-GGACUGAAACUUUCCGUGCUUAGUUUCAGCUCAAAGGUGAAUUU----AUUUUGGAAAGUUCGUAC
AAQR03048750.1/25469-25565   GUUUUG--CAGCUUUCCAAAAAAUUAGCCCUUU-GUGGUGAAAUUUUCCAUGCUUGGUUUCAGCCCAAAGGUGAUUUUUUUUUUUUUGCAAAGUUUGAGA
AAGU03004798.1/46533-46625   UGCUCC--UAACUUUCCAAUAAAGUAUGUUUUG-GGGCUGAAACUUUCCAUGCUUAGUUUCGGCUCGAAGGUGAAUUU----AUUUUGGAAAGUUCACAC
AADA01218450.1/19335-19428   UUCUUG--CAGCUUUCCAAAAAAUUAGCCCUUU-GUGGUGAAAUUUUCCAUGCUUGGUUUCAGCCCAAAGGUGAUUUU---UUUUUUGCAAAGUUUGAGA
AADN03001062.1/48120-48212   AUGCUCU-UAACUUUCUGAAAAAUUCUUCUUUU-CAGCUGAAAUUUUCCAUGCUUGGUCUCAGCUGAAAGAUGAAUUU-----CUUUAGACAGUUGAGCA
#=GC SS_cons                 ::<<<<..-<<<<<<<<<<<<<<<<<<<<<<<<.<<<<<<____________________>>>>>>>>>>>>>>>>>>....->>>>>>>>>>>>>>>>:
#=GC RF                      Uuccuc..uAacuUUCCaAaaAauucucCuUUu.GgGcUgAAAuUUUCcaUgCUUagUUUcAgCcCaAAgGgggauuU....auuUuGGAAaguUgaggu
//
# STOCKHOLM 1.0

#=GF AC   RF00698
#=GF ID   mir-489
#=GF DE   microRNA mir-489
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   60.00
#=GF NC   58.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000111;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [4]
#=GF RM   16698962
#=GF RT   Cloning and expression of new microRNAs from zebrafish.
#=GF RA   Kloosterman WP, Steiner FA, Berezikov E, de Bruijn E, van de Belt J,
#=GF RA   Verheul M, Cuppen E, Plasterk RH
#=GF RL   Nucleic Acids Res. 2006;34:2558-2569.
#=GF WK   Mir-489_microRNA_precursor_family
#=GF SQ   19


AANH01002320.1/123232-123323 UGGUGGUGGCCUGGUGGUCGUAUGUAUGACGUCAU-UUACUUCA-AUGUUU-GGAGUGACAUCAUAUGUACGGCUGCUAAACUGCUACAUGGGAC
AC161368.2/144688-144779     CAGUGGCAGCUUGGUUGUCAUAUGUGUGAUGACAC-UUUCUAAA-GUCUUCCAGAAUGACACCACAUAUAUGGCAGCUAAACUGUUACA-UGGAA
AAHX01028271.1/83263-83172   CAGUGGCAGCUUGGUUGUCGUAUGCGUGAUGACAC-GUUCUCGU-GUAUUCCAGAAUGACAUCACAUAUAUGGCAGCUAAACUGUUACA-GGAAC
AANN01186766.1/1891-1983     UGGUGGCAGUUUGGUGGUUGUAUGUGUGGCAUCAC-UUACUGGA-AUUUUUAUGAGUGACAUCACAUAUACAACUGCUAAUGUGCUACACGGAAC
AAQQ01558075.1/3986-3895     UGGUGGCAGCGUGGCUGUUGGAUAUAUGGCGUCAU-UUACUUGA-ACUUUUGGAAGUGACAUCAAAUAUCCAGCAGCUAAACUGCCAUG-GGGGA
ABDC01215275.1/2133-2041     UAGUGGCAGCUUCGUUGUUGUAUAUGCGGCGCCAUUUAACUUGA-ACCUUUAGUAGUGACAUCACAUAUACGGCAACUAAGCUGCUACA-UCGAG
AAFC03096979.1/8554-8645     CAGUGGCAGCUUGGUGGUCGUAUGUGUGGCGCCAU-CUACUGGA-ACGUUUAGGAGUGACAUCACAUAUAUGGCGACUAAACUGCUGCA-UAGGA
AAYZ01157617.1/703-611       UGGUGGCAGCUUGGUGGUCGUAUGUGUGGUGUCAU-UCACUUGA-AUCCUUAGGAGUGACAUCACAUAUACGGCAGCUAAACUGCUACAAGGGAC
AC097628.2/22907-22817       UGGUGGUGGCUUGGUGGUCGUAUGCAUGACGUCAU-UUACUUCG-AUGAUU-GGAGUGACAUCAUAUGUACGGCUGCUAAACUGCUACA-AGAGA
BX537314.17/2373-2283        GAGUGGUGGCCUGGUGGUCGUAUGUAUGACGUCAU-UUACUUCA-AAGUUU-GGAGUGACAUCAUAUGUACGGCUGCUAAACUGCUACA-UGGCU
AAGV021023725.1/1512-1422    UGGUGGCAGCUUGGUGGUCGUAUGUGUGGUGCCAU-UUAUUUAA-CCUUUA-GAAGUGACAUCACAUAUACGGUGGCUAAACUGCUACAUGGGA-
AAWR02013812.1/76228-76136   UGGUGGCAGCUUGGUGGUCGUAUGUGUGGCGCCAU-UUAUUUGACCCCUUUAGGAGUGACAUCACAUAUACGGCGGCUAAACUGCUACA-UAAGA
AAGW02035404.1/47502-47411   UGGUGGCAGCUUGGUGGUCGUAUGUGUGGUGCCAU-UCACUUGA-ACCUUUAGGGGUGACAUCACAUAUACGGUGGCUAAACUGCUACAAGGGA-
AAQR03012714.1/72381-72290   UGGUGGCAGCUUGGUAGCCGUAUGUGUGGCGCCAU-UUACUUGA-AUCUUUAGAAGUGACAUCACAUGUACGGCAGCUAAUCUGCUACA-CAGAA
AAGU03015880.1/90724-90815   GGGUGCCAGCUUGGCGGUUGUAUGUGUGGCGCCAU-UUACUUGA-ACUCUUAGGAGUGACAUCACAUAUACGGUGGCUAAACUGCUCCA-UGGAC
AAEX03009311.1/293619-293528 UGGUGGCAGCUUGGUGGCCGUAUGUGUGGCGCCAU-UUACUUGA-ACCUUUAGGAGUGACAUCACAUAUACGGCGGCUAAACUGCUACA-UAGGA
BL000001.1/92070999-92070908 UGGUGGCAGCUUGGUGGUCGUAUGUGUGACGCCAU-UUACUUGA-ACCUUUAGGAGUGACAUCACAUAUACGGCAGCUAAACUGCUACAUGGGA-
AADN03002013.1/193612-193703 ACGUGGUGGCUUGGUGGUCGUAUGUAUGACGUCAU-UUACUUGG-ACUUUUAGGAGUGACAUCAUAUGUACGGCUGCUAAACUGCUGCAUGGGA-
AAWZ02000509.1/42756-42847   GCGUGAUGGCUUGGUGGUCGUAUGUAUGACGUCAU-UUACUUGU-UCUUUUAGGAGUGACAUCAUAUGUACGGCUGCUAAACUGCCACAUGGGA-
#=GC SS_cons                 ::<<<<<<<-<<<<<<<<<<<<<<<<<<<-<-<<<.<<______.________>>>>>->->>>>>>>>>>>>>>>>>>>->>>>>>>:.:::::
#=GC RF                      ugGugGcaGCuUgGuuGucGuAuguguGgcGuCAu.ucACUugA.auuUUUaggagUGACAcCacauaUaCggCagCuAaACugCuaCA.ugGaa
//
# STOCKHOLM 1.0

#=GF AC   RF00699
#=GF ID   mir-134
#=GF DE   microRNA mir-134
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   53.00
#=GF TC   59.70
#=GF NC   35.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000112;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15183728
#=GF RT   Human embryonic stem cells express a unique set of microRNAs.
#=GF RA   Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS,
#=GF RA   Moon SY, Kim VN, Kim KS
#=GF RL   Dev Biol. 2004;270:488-498.
#=GF RN   [2]
#=GF RM   15891114
#=GF RT   Clustering and conservation patterns of human microRNAs.
#=GF RA   Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A,
#=GF RA   Brownstein MJ, Tuschl T, Margalit H
#=GF RL   Nucleic Acids Res. 2005;33:2697-2706.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   miR-134
#=GF SQ   6


AY865928.1/353-425         CAGGGUGUGUGACUGGUUGACCAGAGGGGCAUGCACUGUGUUCACCCUGUGGGCCACCUAGUCACCAACCCUC
AANG01133004.1/6671-6743   CAGGGUGUGUGACUGGUUGACCAGAGGGGCAAGCGCUCUGUUCACCCUGUGGGCCACCUAGUCACCGACCCUC
AAFC03087121.1/13343-13415 CAGGGUGUGUGACUGGUUGACCAGAGUGGCCAGCACUCGGUUCACCCUCUGGGCCACCUAGUCACCAACCCUC
AAGU03025975.1/25285-25215 CUGGGUUUGUGUUUGGUCAACCAGAGGG-CACGUGCUCUGUUCACCCCAUGGGCC-CCUAUUCACCAACCUUG
AAQR03046512.1/13099-13171 CAGGGUGUGUGACUGGUUGACCAGAGGGGCAUGCAGUCUUUCCACCCUGUGGGCCACCUAGUCACCAACCCUC
AY865927.1/406-478         UAGGGUGUGUGACUGGUUGACCAGAGGGGCAUGCACUGUGUUCACCCUGUGGGCCACCUAGUCACCAACCCUC
#=GC SS_cons               :<<<<<--<<<<<<<<-<<-<<<-<<<<----<<_____>>--->>>>->>>-->>->>>>>>>>-->>>>>:
#=GC RF                    CaGGGUgUGUGacUgGUuGACCAGaGGGGCAugcacUcUguUCACCCugUGGGCCaCCuAguCACCAACCCuc
//
# STOCKHOLM 1.0

#=GF AC   RF00700
#=GF ID   mir-375
#=GF DE   microRNA mir-375
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   60.50
#=GF NC   38.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000114;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   Mir-375
#=GF SQ   9


BAAE01195317.1/70-137      CUUCACGUUGAGCCUCACGUACAAUACCUGA--AGAUGA--GUUUUGUUCGUUCGGCUCGCGUUACGCAGGU
AAFR03041735.1/930-997     ACCCGCGCCGAGCCCCUCGCACAA-ACCGGA---CCUGAGCGUUUUGUUCGUUCGGCUCGCGUGAGGCGGAG
AJ334771.1/142-209         GCCAGCGACGAGCCCCUCGCACAA-ACCGGA---CCUGAGCGAUCUGUUCGUUCGGCUCGCGUGAGGCACGG
CU929360.7/11656-11724     CUUUACGUUGAGCCACACGCACAAUACAUGU---GGAUUCAGUUUUGUUCGUUCGGCUCGCGUUAAGCAAGU
CU468956.14/114092-114163  UCUCACGUUGAGCCACACGCACAAUGCCUGCAGAUGAAAGGGUUUUGUUCGUUCGGCUCGCGUUACGCAGAU
AC139023.15/92020-91953    CCCCGCGACGAGCCCCUCGCACAA-ACCGGA---CCUGAGCGUUUUGUUCGUUCGGCUCGCGUGAGGCAGGG
ADDD01145945.1/3688-3620   CCUGGCGUCGAGCCCCACGUGCAAGACCUGA---CCUGAACGUUUUGUUCGUUCGGCUCGCGUUAGGCAGGU
CAAB02019320.1/404-472     CUUCACGUUGAGCCUCACGCACAAUACCUGA---AGAUGAAGUUUUGUUCGUUCGGCUCGCGUUAUGCAGGU
AAWZ02019678.1/18867-18799 CCUCGCGUCGAGCCCCACGCACAAGACCUGA---CGUGAAUGUUUUGUUCGUUCGGCUCGCGUUAGGCAGGU
#=GC SS_cons               ....<<<.<<<<<<...<<.<<<<.<<..............>>.>>>>.>>...>>>>>>>>>.........
#=GC RF                    ccUcaCGucGAGCCaCACGCACAAuACCuGA...cgugAaaGUUUUGUUCGUUCGGCUCgCGuuAgGCAGGu
//
# STOCKHOLM 1.0

#=GF AC   RF00701
#=GF ID   mir-126
#=GF DE   microRNA mir-126
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   78.70
#=GF NC   48.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000115;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15891114
#=GF RT   Clustering and conservation patterns of human microRNAs.
#=GF RA   Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A,
#=GF RA   Brownstein MJ, Tuschl T, Margalit H
#=GF RL   Nucleic Acids Res. 2005;33:2697-2706.
#=GF WK   Mir-126
#=GF SQ   12


AAFC03086494.1/264-192     UGACGGGACAUUAUUACUUUUGGUACGCGCUGUGACAC-UUCAAACUCGUACCGUGAGUAAUAAUGCGCUGUCA
AANH01004778.1/8857-8785   UCGCGGCCCAUUAUUACUUUUGGUACGCGCUAUGCCAC-UCUCAACUCGUACCGUGAGUAAUAAUGCACUGCGA
CR361566.16/83189-83116    UCACAGUCCAUUAUUACUUUUGGUACGCGCUAGGCCAGACUCAAACUCGUACCGUGAGUAAUAAUGCACUGUGG
AAFR03005634.1/12031-12103 CAAUGGGUCAUUAUUACUUUUGGUACGCGCUGUGACAC-AUCAAACUCGUACCGUGAGUAAUAAUGCGCCAUUG
AAPN01325297.1/2349-2421   CAACUGCCCAUUAUUACUUUUGGUACGCGCUGUGACGC-UUCAAACUCGUACCGUGAGUAAUAAUGCGUGGCUG
AAVX01058805.1/2145-2073   UGACAGCCCAUUAUUACUUUUGGUACGCGCUGUGACAC-UUCAAACUCGUACCGUGAGUAAUAAUGCACAGUGG
AALT01124964.1/452-524     CGACGGGCCAUUAUUACUUUUGGUACGCGCUGUGACAC-UGCAAACUCGUACCGUGAGUAAUAAUGCGCCGUCG
AAHX01020484.1/11419-11347 UGACAGCACAUUAUUACUUUUGGUACGCGCUGUGACAC-UUCAAACUCGUACCGUGAGUAAUAAUGCGUGGUCA
ABRP01267729.1/87-15       CGACGGAACAUUAUUACUUUUGGUACGCGCUGUGACAC-UUCAAACUCGUACCGUGAGUAAUAAUGCGCUGACG
ABRQ01610658.1/2102-2030   CGACGGGGCAUUAUUACUUUUGGUACGCGCUGUGACAC-GUCAAACUCGUACCGUGAGUAAUAAUGCGUUGUCG
EU221177.1/65651-65724     UUACGGUUCAUUAUUACUUUUGGUACGCGCUAGGCCAGUCUCAAACUCGUACCGUGAGUAAUAAUGCACUGUGG
AAWZ02037629.1/473-401     CCGCGGUCCAUUAUUACUUUUGGUACGCGCUGUGCCAC-UUCAAACUCGUACCGUGAGUAAUAAUGCGCUGAGG
#=GC SS_cons               ........<<<<<<<<<<<.<<<<<<<.<...<<.......>>..>.>>>>>>>.>>>>>>>>>>>........
#=GC RF                    uaACgGucCAUUAUUACUuUuGGUACGCGCUGuGACAC.uUCaAACUCGUACCgUgAGUAAUAAUGCgcuGugg
//
# STOCKHOLM 1.0

#=GF AC   RF00702
#=GF ID   mir-182
#=GF DE   microRNA mir-182
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   87.40
#=GF NC   52.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00093
#=GF DR   MIPF; MIPF0000116;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19170227
#=GF RT   Identification and expression profiling of microRNAs during bovine oocyte
#=GF RT   maturation using heterologous approach.
#=GF RA   Tesfaye D, Worku D, Rings F, Phatsara C, Tholen E, Schellander K, Hoelker
#=GF RA   M
#=GF RL   Mol Reprod Dev. 2009;76:665-677.
#=GF WK   MicroRNA
#=GF SQ   17


AAPN01078068.1/4329-4245     UCCUGCUGUGUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUAAUGGGAUCCGGUGGUUCUAGACUUGCCAACUAUGGCCCGAGG
ABDC01155768.1/2022-1938     UCCCACCGCUUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUCAUGGGAUCCGGUGGUUCUAGACUUGCCAACUCUGGUGCGAGG
BAAE01056755.1/3488-3572     UCUAGUGGUGUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUAGAUGGAUCCGGUGGUUCUAGACUUGCCAACUACUGCUUGAGA
BAAF04047675.1/12269-12354   UCCUGUGGUGUUUGGCAAUGGUAGAACUCACUCUGGUGGUGCUGGAAGGAUCCGGUGGUUCUAGACUUGCCAACAACUGACUUGAG
AAIY01755693.1/720-804       CCGCGCCGCCUUUGGCAAUGGUAGAACUCACACUGGU-GAGGAAAUGGGAUCCGGUGGUUCUAGACUUGCCAACUACGGUGCCGGG
AANN01116974.1/651-567       UCCCACAGUUUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUAAUGGGAUCCGGUGGUUCUAGACUUGCCAACUACGGUGUGAGG
AAFR03031888.1/60307-60391   UCCUGCUGUGUUUGGCAAUGGUAGAACUCACACUGGU-GAGAUAAUGGAAUCCGGUGGUUCUAGACUUGCCAACUACGGCUUGAGA
AAVX01309390.1/833-917       UCCGGCUGUGUUUGGCAAUGGUAGAACUCACACUGGU-GAGAUAGUGGGAUCCGGUGGUUCUAGACUUGCCAACUACAGCCUGGGA
AL590150.2/105838-105754     UCUGAUGGUAUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUAGUCAGAUCCGGUGGUUCUAGACUUGCCAACUACUACCUGAGA
AAYZ01439986.1/1308-1225     UCCCACCCUCUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUA-UGGGAUCCGGUGGUUCUAGACUUGCCAACUAUGGUGUGUGG
AC192810.3/155763-155679     UCCCUCCGUUUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUAACAGGAUCCGGUGGUUCUAGACUUGCCAACUAUGGGGCGAGG
AC161538.7/136149-136233     UCCCACCAUUUUUGGCAAUGGUAGAACUCACACCGGU-AAGGUAAUGGGACCCGGUGGUUCUAGACUUGCCAACUAUGGUGUAAGU
AY866175.1/416-500           UUCCCCCGUUUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUAACAGGAUCCGGUGGUUCUAGACUUGCCAACUAUGGGGCGAGG
AY866174.1/448-532           UCCCCCUGUUUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUAAUGGGAUCCGGUGGUUCUAGACUUGCCAACUACGGGGCGAGG
AAGU03016903.1/2927-2843     UCGCACCGUGUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUAAUGGGAUCCGGUGGUUCUAGACUUGCCAACUACGGGCCAAGG
AAQR03184844.1/5054-5138     UCCCACCAUUUUUGGCAAUGGUAGAACUCACACUGGU-GAGGUAAUGGGAUCCGGUGGUUCUAGACUUGCCAACUAUGGUGCACGG
CAAB02005445.1/236719-236803 UCCCACAGUGUUUGGCAAUGGUAGAACUCACUCCGGU-GGGCUAGAAGGAUCCGGUAGUUCUAGAAUUGCCAACAACUGACCGAGA
#=GC SS_cons                 :::::::::::<<<<<<<-<-<<<<<<---<<<<<<_._____________>>>>>>>>>>>>-->>>>>>>>:::::::::::::
#=GC RF                      UCccacuGUuUUUGGCAAUGGUAGAACUCACaCuGGU.GAGgUAaugGGAUCCgGuGGUUCUAGACUUGCCAACUAcgGugugaGg
//
# STOCKHOLM 1.0

#=GF AC   RF00703
#=GF ID   mir-139
#=GF DE   microRNA mir-139
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   63.00
#=GF TC   64.90
#=GF NC   44.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000117;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF WK   MicroRNA
#=GF SQ   5


AAFR03050545.1/7759-7826 GUGUAUUCUACAGUGCAUGUGUCUCCAGUGUGACU---AAGGGACUGGAGAUACAGCCCUGUUGGAAUAAC
AAPN01104066.1/4648-4582 GUGUAGUCUACAGUGCAUGUGUCUCCAGGGACACU---AGACAGCUGGAGACACAGCUCUGUUGGA-UACA
AY866119.1/405-472       GUGUAUUCUACAGUGCACGUGUCUCCAGUGUGGCU---CGGAGGCUGGAGACGCGGCCCUGUUGGAGUAAC
CAAB02006820.1/7703-7773 CUGUAUUCUACAGUGCAUGUGUCUCCAGUAUGUUAGUAAUGCUACUGGAGACUCAGCUCUGUUGGAAUAAC
AAWZ02031977.1/6685-6618 CUGUAUUCUACAGUGCAUGUGUCUCCAGUGUUUUC---CAGCGACUGGAGAUACGGCCCUGUUGGAAUAAC
#=GC SS_cons             :::<<<<<<<<<<-<<-<<<<<<<<<<<<______..._____>>>>>>>>>>>>>>->>>>->>>>>>::
#=GC RF                  gUGUAuUCuACAGUGCAuGuGUCUCCAGuGUgucu...aaGcgaCUGGAGACaCaGCuCUGUUgGAaUAAc
//
# STOCKHOLM 1.0

#=GF AC   RF00704
#=GF ID   MIR397
#=GF DE   microRNA MIR397
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   55.30
#=GF NC   54.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000120;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19939267
#=GF RT   High throughput approaches reveal splicing of primary microRNA transcripts
#=GF RT   and tissue specific expression of mature microRNAs in Vitis vinifera.
#=GF RA   Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del
#=GF RA   Fabbro C, Valle G, Policriti A, Morgante M, Pesole G, Pe ME, Horner DS
#=GF RL   BMC Genomics. 2009;10:558.
#=GF RN   [2]
#=GF RM   19903869
#=GF RT   Rice MicroRNA effector complexes and targets.
#=GF RA   Wu L, Zhang Q, Zhou H, Ni F, Wu X, Qi Y
#=GF RL   Plant Cell. 2009;21:3421-3435.
#=GF WK   Mir-397_microRNA_precursor_family
#=GF SQ   7


AP004126.4/29756-29641     AGGGAAGGCAUUAUUGAGUGCAGCGUUGAUGAACCUGC--CGGCCGG---CUAAAUUAAUUAGCAAGAAAGU------CUGAAACUGGCUCAAAG---GUUCACCAGCACUGCACCCAAUCACGCCUUUG
AL049656.1/63294-63188     UGAAUGAACAUCAUUGAGUGCAUCGUUGAUGUAAUUUUACUUAUUUUA--UUCCAUUGUUGAAUUAAUUAA-----------------AGAAGUA----UAUAUCAGCGUUGCAUUCAAUUAUGUUUUUC
AP003766.3/37038-37149     AUCAAAUGCAUCAUUGAGUGCAGCGUUGAUGAA-CAACGGUAACCGGU--CCAUGUUGAUGCGCAU------------UUGGCCGGUGAUCUGAU---CAUCAUCAGCGCUUCACUCAAUCAUGCGUUUG
AARH01002083.1/50091-50204 UAAUUAUACACCAUUGAGUGCAGCGUUGAUGAAAUUCUCUUGUUAGC---UUACUUAGCUAUUUUCUCACG-------AUGGCGUGGAAUCA------UUUCACCAGCGCUGCAUUCAACCAUGUUUUUC
AM477433.2/15503-15382     GAAGAAAACAUCAUUGAGUGCAGCGUUGAUGAAACUGAAGUAUUCCAUUUUUCAGCUUCUUUGAAGUCC-G-------GCAAGAUGGGUUCUGGUUGAUUCCAUUGGCGCUGCACUCAAUCAUGUCUUUU
AC012392.1/95144-95040     UGAAUGAACAUCAUUGAGUGCAGCGUUGAUGUAAUUUC-GUUUUGUU---UUUCAUUGUUGAAUGGAUUAA-----------------AAGAAUU----UAUACCAGCGUUGCGCUCAAUUAUGUUUUUC
AARH01004614.1/50089-49970 UGGAGAACCAUCAUUGAGUGCAGCGUUGAUGAAAUCCU-CCAUUUUG---UGCUAUUAAACUGUUACCAACCCUUUAUGGGGCAUGGCAUCA------UUUCACCAGCGCUGCAUUCAAUCAUGUUUUUC
#=GC SS_cons               :::::<<<<<<-<<<<<<<<<<<<<<<<-<<<_______________..._____________________......._________________...__>>>->>>>>>>>>>>>>>>>->>>>>>:::
#=GC RF                    ugaaaAggCAUCAUUGAGUGCAGCGUUGAUGaAAuUuuagUauUuug...UUauaUUgaUuuguaaucaAg.......guGgcauGGgaUcAgau...uUuCAcCAGCGCUGCACUCAAUCAUGccUUUc
//
# STOCKHOLM 1.0

#=GF AC   RF00705
#=GF ID   mir-202
#=GF DE   microRNA mir-202
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   68.00
#=GF TC   69.80
#=GF NC   56.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000121;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   Mir-202_microRNA_precursor_family
#=GF SQ   13


AANH01008757.1/2123-2037   CUCGCUGUUCCUUUUUCCUAUGCAUAUACCUUUUUCAGAUGUAACUUUAAAGAGGUAUAGGGCAUGGGAAAAUGGGGCUGCAGAGGU
AC149072.1/21212-21298     CUCGCUGUUCCUUUUUCCUAUGCAUAUACCUCUUUGAAAAAUGAAUGUAAAGGGGCAUAGGGCAUGGGAAAAUGGCGCAGCUGAGCC
AAIY01420185.1/327-241     CCCGUCCUGCCUUUUUCCUAUGCAUAUACUUCUUUGAGGGUCUGGUCCAAAGAGGUAUAGCGCAUAGGACAACGGCGCGGCGGUCUC
AAQQ01476817.1/2066-2152   CUCGCCGUUCCUUUUUCCUAUGCAUAUACUUCUUUGAGGAUCUGGCCUAAAGAGGUAUAGGGCAUGGGAAAAUGGGGCGGUGAGUCC
BAAF04099470.1/3897-3811   CUCGCUGUUCCUUUUUCCUAUGCAUAUACUUCUUUGACAUGUAACUUUAAAGAGGCAUAAGGCAUGGGAAAAUGGGGCUGCAGAGGU
CAAK05035699.1/2366-2452   CUCGCUGUUCCUUUUUCCUAUGCAUAUACCUCUUUGACAUGCUGCUUUAAAGAGGCAUAGGGCAUGGGAAAAUGGGGCGGCAGAGGU
AL592071.13/6491-6405      CCCGCCGUUCCUUUUUCCUAUGCAUAUACUUCUUUGAGGAUCUGGCCUAAAGAGGUAUAGGGCAUGGGAAAACGGGGCGGUCGGGUC
AAGU03077051.1/12175-12089 CUCGUCGUUCCUUUUUCCUAUGCAUAUACUUCUUUGAGGAUCUGACCUAAAGAGGUAUAGGGCAUGGGAAAAUGGGGCGACGGGGUC
AAPE02037764.1/12393-12307 CUCGCGGUUCCUUUUUCCUAUGCAUAUACUUCUUUGAGGGUCUGGCCUAAAGAGGUGUAAGGCAUGGGAAAAUGGGGCGGCGAGGUU
ADDD01006267.1/5678-5764   CUCGUUGUUCCUUUUUCCUAUGCAUAUACUUCUUUGAGAGUUUGAUCUAAAGAGGCAUAGAGCAUGGGAAAAUGGGGCGACUGAGGU
AABR05014223.1/10479-10393 CUGGCUGUUCCUUUUUCCUAUGCAUAUACUUCUUUGUGGAUCUGGUCUAAAGAGGUAUAGCGCAUGGGAAAAUGGAGCAGUGAGAUC
AAEX03015731.1/4402-4316   CUCGCUGUUCCUUUUUCCUAUGCAUAUACUUCUUUGAGGGUCUGGCCUGAAGAGGUGUAAGGCAUGGGAAAAGGGGGUAACGAGGUC
AAWZ02022446.1/5908-5822   CUCAUUGUUCCUUUUUCCUAUGCAUAUACUUCUUUGAGAAUCUGAUCUAAAGAGGCAUACGGCAUGGGAAAAUGGGGCAAUUGAGGU
#=GC SS_cons               ::::<<<<<<<-<<<<<<<<<<<-<<<<<<<<<<<<___________>>>>>>>>>>>>-->>>>>>>>>>>->>>>>>>:::::::
#=GC RF                    CUCGccGucCCUUUuUCCuAUGCAUAuaCcuCUUugAgaaucuGaucuaAAGagGuaUAggGCAUgGGAaAAuGGggCggcagaguu
//
# STOCKHOLM 1.0

#=GF AC   RF00706
#=GF ID   mir-263
#=GF DE   microRNA mir-263
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   47.00
#=GF TC   47.20
#=GF NC   46.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00093
#=GF DR   MIPF; MIPF0000122;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF WK   MicroRNA
#=GF SQ   23


AAPQ01006581.1/272485-272396   UAGCUGACUUUGA-GUCUUGGCACUGGGAG-AAUUCAC-AGUUG---AUUUU--AUUA-U--UCUGUGGUUCUGCGGGUGCC-AAAAUUUA-AUC-AACAGCUC
AAZX01007729.1/30972-30882     AGCUUGGGUUCUG-UCAAUGGCACUGGAAG-AAUUCAC-GGGGGA--AUUUAGCAACAGU--CCCGUGGAACU-CCCGUGUC-AUACACAG-CGU---CCGGCU
AAPP01019315.1/707685-707774   CUGCUGUCUUUGA-AUCUUGGCACUGGGAG-AAUUCAC-AGUUG---AUUUU--AUUA-U--UCUGUGGUUCUGCGGGUGCC-AAAAUUGA-AAU-AAUGGCCU
AAGE02001908.1/33266-33358     GGACCAAUUACGA-ACCUUGGCACUGGGAG-AAUUCAC-AGGCGC--UAUUUGCUAUCAU--UCUGUGGAUCUUUUCGUGCC-AUCGUUUA-AAU--UCGGUCA
AAKO01002647.1/151787-151698   GAUCUCGACACAG-UUAAUGGCACUGGAAG-AAUUCAC-GGGGUA--AUUUUUAUACA-A--CCCGUGA-UCUCUUAGUGGC-AUCUAUGG-UGC---GAGAAU
AAIZ01003707.1/23266-23174     UUGCUGGCAUUGG-CUCUUGGCACUGGGAG-AAUUCAC-AGUUG---GUUUUCAUAUA-U--UCUGUGGUUCUGCGGGUGCCCAAAAUCGA-AUG-UUCGGCUC
AAQB01006403.1/367480-367390   CAUCUCGGCACAG-UUAAUGGCACUGGAAG-AAUUCAC-GGGGUU--UUUAUUUAACACA--CCCGUGA-UCUCUUAGUGGC-AUCUAUGG-UGC---GGGAUU
AAPT01020730.1/183758-183669   UACUGC-CAUUAC-AUCUUGGCACUGGGAG-AAUUCAC-AGUUG---GUUAUAUAAUA-U--UCUGUGGUUCUGCGGGUGCC-AAACUGUA-AUG--UGUGGAC
AAJJ01000157.1/103377-103289   GAGCAUAGGCCUG-CGAAUGGCACUGGAAG-AAUUCAC-GGGGU---UCUUC---GCACU--CCCGUGG-ACUUUGAGUGCC-AUCCUCAGAGCC--CUUGUCC
BAAB01015424.1/819-730         AAGCCCACGCUGU-UCCUUGGCACUGGGAG-AAUUCAC-AGGAG----UUGUAAUUCAUA--CCCGUGAAUUUCCCGAUGCC-UUAGCUCA-GUG---UGGUCA
AAAB01008960.1/3840022-3840116 UGACCAAUUAUGG-ACCUUGGCACUGGGAG-AAUUCAC-AGUGGAUCGUACCAUAUCGUU--UCUGUGGAUCUUUUCGUGCC-AUCGUUCA-GAU--UUGGUGC
AAGE02027430.1/4828-4738       GCUCCUAGUACAC-GUAAUGGCACUGGAAG-AAUUCAC-GGGUA---UAUUUUGAAAU-C--CCCGUGU-UCUGGCAGUGGC-AUCCCUGG-UAC-UAAGGUGA
AAST01017609.1/1860-1768       UUGCUGACUUUGAAGUCUGGGCACUGGGAGAAAUUCAC-AGUUG---ACCUUUAUUAU----UUUGUGGGUCUGCGGGUGCC-AAAACUUA-AAA-ACCGGCUU
BAAB01106279.1/2818-2907       GAUCCAAGCACAG-GCAAUGGCACUGGAAG-AAUUCAC-GGGUU---CAGUUUAUAUAUU--CCCGUGA-UCUCUUAGUGGC-AUCACUGG-UGC---AGGACG
AAQB01006546.1/140884-140979   CUGCUCACAAUGC-AUCUUGGCACUGGGAG-AAUUCAC-AGUUG---AUUCUUAUUCGAUAUUCUGUGGUUCUGCGGGUGCC-AAAAUCUA-AUGUUUGAGCUG
AAAB01008944.1/325742-325831   UCCCCUGGUACAU-GUAAUGGCACUGGAAG-AAUUCAC-GGGAU---UUUUUUCAACAUU--CCCGUGU-UCUCUUAGUGGC-AUACCUAG-UAC---AGGGUA
AAKO01000155.1/113509-113420   UUGCUGACUUUGA-GUCUUGGCACUGGGAG-AAUUCAC-AGUUG---ACUUG--AUUA-U--UCUGUGGUUCUGCGGGUGCC-AAAACUUA-AAA-ACCGGCUU
AAWU01014939.1/4076-3988       UCCCUUUGUACAC-GUAAUGGCACUGGAAG-AAUUCAC-GGGUA----UGAUUUAAUAUC--CCCGUGU-UCUGGCAGUGGC-AUCCCUGG-UAC---AAGGCA
AAZX01003415.1/15982-15890     GAGGUUCUGGCGG-GUCUUGGCACUGGAAG-AAUUCACAGAUGU---GCGGUUGUGUGUA--AUCGUGGAUCUUGCAAUGCC-AUUACCCG-CUG--GGACUCU
AADE01000074.1/40884-40796     CAUCCCGGCACAG-UUAAUGGCACUGGAAG-AAUUCAC-GGGGU---UUUUCAAUACA-A--CCCGUGA-UCUCUUAGUGGC-AUCUAUGG-UGC---GGGACU
AANI01016237.1/287949-288037   CAUCUCGGCACAG-UUAAUGGCACUGGAAG-AAUUCAC-GGGGU----UUUUAUAACACG--CCCGUGA-UCUCUUAGUGGC-AUCUAUGG-UGC---GGGAUA
AAZO01001458.1/4323-4412       UUUUUUUUUGUGA-AACUUGGCACUGGAAG-AAUUCAC-AGAUA---GAAAAUGAAAA-A--UC-GUGGGUCUUUUGGUGCC-AAAGUUCA-CGG--AAUAAAU
AEKZ01007636.1/20182-20272     AAGGUUCUGGCGG-GUCUUGGCACUGGAAG-AAUUCAC-AGAUG---UGCAGUGUAUA-A--UC-GUGGAUCUUGCAAUGCC-AUCACUUG-CUG-GAUACCGA
#=GC SS_cons                   ::<<<<-<<<<<<.<---<<<<<<<---<<.---<<<<.<<<__..._____________..>>>>>>>-->>--->>>>>>.>--->>>>.>>>..->>>>::
#=GC RF                        uagcccaccucgg.gucuUGGCACuGGaAG.AAUuCAC.gGgug...auuuuuauauauu..cCcGUGgaUCUuuuaGUGCC.Auaacccg.agg..ugggcuu
//
# STOCKHOLM 1.0

#=GF AC   RF00707
#=GF ID   mir-197
#=GF DE   microRNA mir-197
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   62.00
#=GF NC   57.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000123;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA. 2003;9:175-179.
#=GF WK   MicroRNA
#=GF SQ   5


AANG01018453.1/1208-1282   GGCUGUGCCGGGUAGAGAGGGC------AGUGGGAGGUAAGAGCUCUUCACCCUUCACCACCUUCUCCACCCAGCAUGGCC
X96549.1/7710-7779         GGCUGUGCUGGGUAGAAAGGGC------AGGGGGAGGUAAGCCCUCUUCCCCCUUCACCUCCCU-----CCCAGCAUUGCU
ABRR01264916.1/11491-11417 GGCUGUGUCGGGUAGAGAGGGC------AGUGGAAGGUCAGAGCUCUUCGCCCUUCACCACCUUCUCUACCCAGCACGGCU
ABVD01022248.1/5649-5577   GGUUGUGCAGGGUAGAG--GGC------AGUGGGAGGUAAGAGCUCUUCACCCUUCACCACCUUCUCCACCCAGCAUGGCC
ABRQ01203185.1/1385-1305   AGCUGUGCCGGGUAGAGAGGGCUGUGGGAGGGGGAGGUAAGAUUUCUCCACUAUUUACCACCUUUUCUACCCAGCACGGCU
#=GC SS_cons               <<<<<<<<<<<<<<<<<<<<<-......-<<<<--<<<<<<____>>>->>>-->>>>-->>>>>>>>>>>>>>>>>>>>>
#=GC RF                    gGccguGccGGGuaGaGagGGC......AGuGgGAGGuaaGAucUCuuCaCCcUuCaCCACCcuCuCuaCCCggCacggCc
//
# STOCKHOLM 1.0

#=GF AC   RF00708
#=GF ID   mir-450
#=GF DE   microRNA mir-450
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   61.50
#=GF NC   58.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000128;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   MicroRNA
#=GF SQ   21


AC004383.1/124989-124899     AAACGAUACUAAACUGUUUUUGCGAUGUGUUCCU-AAUAUGCACU----AUAAAUAUAUUGGGAACAUUUUGCAUGUAUAGUUUUGUAUCAAUAUA
AC004383.1/125160-125070     GAAAGAUGCUAAACUAUUUUUGCGAUGUGUUCCU-AAUAUGUAAU----AUAAAUGUAUUGGGGACAUUUUGCAUUCAUAGUUUUGUAUCAAUAAU
AC004383.1/124827-124736     GUAAGAUGCAGAAUUAUUUUUGCAAUAUGUUCCUGAAUAUGUAAU----AUAAGUGUAUUGGGAUCAUUUUGCAUCCAUAGUUUUGUAUCAACAUA
AAHX01102601.1/65549-65639   GCCAGAUGCUGAACUAUUUUUGCGAUGUGUUCCU-AAUAUGUACU----AUGAGUGUAUUGGGGACGCUUCGCAUUCAUGGUUCUGCAUCAGUCAU
AAHX01102601.1/65682-65772   GAGAGAUGCGGAGCUGUUUUUGCGAUGUGUUCCU-AAUGUGUGCU----ACAAUUAUAUUGGGAACAUUUUGCAUAAAUAGUUUUACAUCGACACA
AAHX01102601.1/65843-65933   AUCAGAUACGGAAUUCUUUUUGCAGUAUGUUCCUGUAUAAG-AAC----AUAAGCGUAUUGGGAACAUUUGGCAUACAUAAUUUUGUAUCAAUAUA
AAIY01247667.1/488-575       UAAAGAUGCUCAACUAUUUUGGCAUUGAGUUCUC-AAUAUAUAAU----ACAGCUAUAUUGGGAAGAUUUUGCG---AUAGUUUUGUAUCAAUAUA
AAIY01247667.1/662-753       UGGAGGCACAAACUUAUUUUUGUAAUAUGUUCUUGAGUAUGUAAC----AUAAAUGCCUUGGGAACAUUUGGUACCCAUGGUUUCGUAUCGAUACA
AAHY01210345.1/8126-8036     GAGAGAUACUGAGCUGUUUUUGCGAUGUGUUCCU-AAUAUGUGCU----AUAAUUAUAUUGGGAACAUUUUGCAUAAAUAGCUUUGUGUCAAUACA
AACN010723377.1/501-591      GAAAGAUGCUGAACUGUUUUUGCGAUGUGUUCCU-AAUAUGCAGU----AUGAACAUAUUGGGAGCAUUUUGCAUGCAUGGUUUUGUAUCAAUAUA
AANN01800872.1/333-426       GUGUGUG-UGUGUGUGUGUGUGUGAUGUGUUCCU-AAUAUGCAGUUUAGAUAAAUAUAUUGGGAGCACUUUGCAUGCAGACAAAAAGCUGGAGGGA
AAQQ01708411.1/190-100       AAAAGAUGCUGAACUAUUUUUGCGAUGUGUUCCU-AAUAUGUAAU----AAGAAUGUAUUGGGAACAUUUUGCAUUUGUAGUUUUGUAUCAAUAAU
AAYZ01306302.1/1275-1185     GAAAGAUGCUAAACUGUUUUUGCGAUAUGUUCCU-AAUAUGCACU----AUAACUAUAUUGGGAACAUUUUGCAUGCAUAGUUUUGUGUCAGUGUA
AAFC03117779.1/23903-23812   GUAAGAUGCAAAAUUAUUUUUGCAAUAUGUUCCUGAAUAUUUAAU----AUAAGUAUAUUGGGAACAUUUUGCAUCCAUAGUUUUGUAUCAGUAUU
AAGV020284255.1/3919-3829    GAAUGAUGCAAAACUAUUUUUGUGAUGUGUUCCU-AAUAUGAAAU----AUAAGUGUAUUGGGAAUAUUUUGCAUCCAUGGUUUUGUAUCAAUAAG
AAKN02053360.1/153259-153169 GAAAGAUGCUAAACUGUUUUUGCGAUGUGUUCCU-AAUAUGUACU----AUAAAUAUAUUGGGAGCAUUUUGCAUGCAUAGUUUUGCAUCAAUAUA
AAWR02034052.1/47385-47294   GGAAGGUACAAAAUUAUUUUUGCAAUAUGUUCCUGAAUAUGUAAU----AUAAGUGUAUUGGGAACAUUUUGCAUCCAUAGUUUUGUAUCAAUAUU
AAPE02002186.1/137315-137405 GAAAGAUGCUAAACUAUUUUUGUGAUGUGUUCCU-AAUAUGCAGU----AUAAAUAUAUUGGGAGCAUUUUGCAUGCAUGGUUUUGUAUCAAUAUA
AAGW02046793.1/82212-82121   GCAAGGUGCAGAAUUAUUUUUGCAAUAUGUUCCUGAAUAUGUAAU----CUAAGUGUAUUGGGGACAUUUUGCAUCCAUAGUUUUGUAUCGAUAUG
AAQR03131452.1/4974-4883     GUAAGGUGCAGAAUUAUUUUUGCAAUGUGUUCCUGAAUAUGUCGU----GUAAGUAUAUUGGGAACAUUUUGCAUCCAUAGUUUUGUAUCAAUAUA
AAGU03084141.1/49841-49751   GAAAGAUGCUAAACUAUUUUUGCGAUGUGUUCCU-AAUAUGUAAU----AUAAGUAUAUUGGGAACAUUUUGCAUUGAUAGUUUUGCAUCAAUAUA
#=GC SS_cons                 ::::::<<<-<<<<<<<---<<<<<-<<<<<<<<.<<<<<<____...._____>>>>>>>>>>>>>>->>>>>--->>>>>>>->>>::::::::
#=GC RF                      gaaAGaugCugaacuaUUUUUGcgAUguGuUCCu.AAUauguAaU....AUAAauauAUUgGGAaCacUUcgCAUucAuaguucUGcaUCAAUAua
//
# STOCKHOLM 1.0

#=GF AC   RF00709
#=GF ID   mir-455
#=GF DE   microRNA mir-455
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   52.00
#=GF TC   53.10
#=GF NC   50.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000129;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19397817
#=GF RT   Parallel DNA pyrosequencing unveils new zebrafish microRNAs.
#=GF RA   Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL,
#=GF RA   Moura GR, Santos MA
#=GF RL   BMC Genomics. 2009;10:195.
#=GF RN   [2]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues.
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF WK   Mir-455_microRNA_precursor_family
#=GF SQ   5


CAAK05008291.1/8173-8258   UCCCUGAAGUGAGGGUAUGUGCCCUUGGACUACAUUGUGGAGGCCAGCACCAUGCAGUCCAUGGGCAUAUACACUUACUUCAUGGC
AL445543.20/79842-79927    UCCCUGGCGUGAGGGUAUGUGCCUUUGGACUACAUCGUGGAAGCCAGCACCAUGCAGUCCAUGGGCAUAUACACUUGCCUCAAGGC
CR931814.13/136829-136744  UCCCUGGUGUGAGGGUAUGUGCCCUUGGACUACAUCGUGGAAGCCAGCACCAUGCAGUCCAUGGGCAUAUACACUUGCCUCAAGGC
CAAB02000485.1/24681-24596 UCCCUGAUGUGAGAGUAUGUGCCCUUGGACUACAUCGUGGAAGCCAGCACCAUGCAGUCCAUGGGCAUAUACACUUUCCUCAAGGC
AFTD01094266.1/62198-62114 UCCCUGGUGUGAGCGUAUGUGCCUUUGGACUACAUCGUGGACGC-AGCACCAUGCAGUCCACGGGCAUAUACACUUGCCUCAAGGU
#=GC SS_cons               ::::<<<-<--<<-<<<<<<<<<<<<<<<<<-<<<-<<<________>>>->>>->>>>>>>>>>>>>>>>>->>-->->>>::::
#=GC RF                    UCCCuGguGUGaGgGuauguGCCcguGGaCuACaucGuGGAaGCCAGCaCCauGCaGuCCacgGGCauauaCACuUgCccCaaGGc
//
# STOCKHOLM 1.0

#=GF AC   RF00710
#=GF ID   mir-44
#=GF DE   microRNA mir-44
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.90
#=GF NC   45.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000132;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   6


AAGD02000348.1/78845-78938     GAGAAUGGCCGAUCUGGAUGUGCUCGUUAGUCAUAGACGAAUCACAGAAAA-CAGUCAUAUGACUAGAGACACAUUCAGCUUGGCCUGGAUCUCA
AAGD02000348.1/73452-73360     AAAACGUGCCACGCUGGAUGUGCUCGUUAGUCAUAAUAACCUCAUUUAGU--AAGGCUUAUGACUAGAGACACAUUCAGCUUGGCGCCGAACUAU
Z70213.1/3656-3563             ACCAUGUGCCACGCUGGAUGUGCUCGUUAGUCAUAAUAUCCUCCACAAAGC-AAGGACUAUGACUAGAGACACAUUCAGCUUGGCGCCGAAUGCA
Z70213.1/12643-12735           GAAAAUGGCCAAUCUGGAUGUGCUCGUUGGUCAUAGACG--UCAACACGAACUGUUCAUAUGACUAGAGACACAUUCAGCUUGGCCUGCUUCUCU
CAAC02000450.1/2292163-2292069 GAGAAGGGCCGAUCUGGAUGUGCUCGUUAGUCAUAGACGAAUCACACUUGAAAGGUCAUAUGACUAGAGACACAUUCAGCUUGGCCUGGAUCUCA
ABEG02004077.1/66776-66685     GGAAACUGCCACGCUGGAUGUGCUCGUUAGUCAUAGUAG--CCUAUCCUGA-ACGGCCUAUGACUAGAGACACAUUCAGCUUGGCUCCGAUAUCA
#=GC SS_cons                   :::::<<<<<<-<<<<<<<<<<<<<--<<<<<<<<________________.______>>>>>>>>>>>->>>>>>>>>>->>>>>>::::::::
#=GC RF                        gaaAaggGCCaagCUGgAUGUGCUCGUUaGUCAUAguagaaUCaauaaaaa.aaGucaUAUGACuAGAGACACAUuCAGcUuGGCccggAucUca
//
# STOCKHOLM 1.0

#=GF AC   RF00711
#=GF ID   mir-449
#=GF DE   microRNA mir-449
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.10
#=GF NC   44.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00087
#=GF DR   MIPF; MIPF0000133;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   Mir-449_microRNA_precursor_family
#=GF SQ   56


AAIY01660884.1/5468-5556       CUGGAUGUGA-UGAGUUGGCAGUGUAUUGUUAGCUGGUUGA-----AUAUGUGAGUAGCA--------------CCAGCUAAC--G--UGCAGCUGCUAACUUAUU-GCA--GACC
AAIY01660884.1/5347-5436       UGGCCAGAAU-CAGGUAGGCAGUGUACUGUUAGCUGGCUGU-----GUUGGGUCAAUUCA--------------GCAGCCACG--A-CUACC-CUGCCA-CUUGCU-UCUGGAUAA
AAHX01013086.1/6230-6320       CUGUGUGCGA-UGGGUUGGCAGUGUAUUGUUAGCUGGUUGA-----GUAUGUAAAAGGCA--------------CCAGCUAAC--A--UGCAACUGCUCUCCUAUU-GCACAUACA
AAHX01013086.1/6116-6205       UUGCCAGACU-CAGGUAGGCAGUGUGUUGUUAGCUGGCUGC-----GUUGGGUUAAGUAA--------------GCAGCCACA--G-CUACC-CUGCCA-CUUGCU-UCUGGACGG
AAHX01013086.1/4699-4790       GUGGGUGUGU-CAGACAGGCAGUGCAUUGCUAGCUGGCUGU----UAGAACUUCGUCCCA--------------ACAGUGGCU--AGCUGCA-CUACCC-UCUGCU-GCACUUAGA
AALT01534765.1/2819-2909       CUGGGUGUGA-UGAGUUGGCAGUGUAUUGUUAGCUGGUUGG-----AUAUGUGAAUAGCA--------------UCAGCUAAC--A--UGCAACUGCUUGCUUAUU-GCAUCUACG
AALT01534765.1/2698-2787       UACCCUGAGU-CAGGUAGGCAGUGUAUUGUUAGCUGGCUGC-----UUUGGAUCAGUUCA--------------GCAGCCACA--A-CUACC-CUGCCA-CUUGCU-UCUGGACAA
AALT01534765.1/1607-1697       UUGGAUGUGU-CGGCUUGGCAGUGCACCGCUAGCUGGCUGU-----UGUAAUCUCCCUGG--------------ACAGCUGCU--AGUUGCA-CUUCCC-UCUGCU-GCAUCCAUU
AANN01422130.1/1413-1504       UUGGAUGUGU-CAGGGAGGCAGUGCAUUACUAGCUGGCUGU----UAUCGUGUCAUUUUA--------------ACAGCUGCU--AGUUGCA-CUCCCC-CCUGUU-GCAUGCAUA
AAPN01209390.1/1892-1981       CUGUGUGCGA-UAGUUUGGCAGUGU-UUGUUAGCUGGUUGA-----AUAUUUAAAUGGCA--------------CCAGCUGAC--A--GACAGCUGCUUUCCUAUU-GCAUGUACC
AAPN01209390.1/1753-1843       UUACCUGGGU-CAAGUAGGCAGUGUGAUGUUUGCUGGCUGC-----UUUGAAUCGAUUCA--------------GCAGCCACC-GU--UACU-CUGCCA-CUUGCUACUAGGCGGA
AAPN01209390.1/379-468         AAGAAUGUGC-CGGUUUGGCAGUGCUUUGCUAGCUGGCUGUU---CAAUAAAUGAUUCCA--------------GCAGCUGGU-----UGCA-C-GCCCCACUGUC-ACAAUCCAA
AAFC03029384.1/3106-3197       UUGAAUGUGU-CAGGUAGGCAGUGCAUCUCUAGCUGGCUGU----UAAAAUUUCUUUUUA--------------ACAGUUGCU--AGUUGCA-CUCCCC-UCUGUU-GCAUUCAUA
AC091977.3/122948-122862       UGGGAUGUGU-CAGGUAGGCAGUGUAUUGCUAG-CGGCUGU-----UAAUGA---UUUUA--------------ACAGUUGCU--AGUUGCA-CUCCUC-UCUGUU-GCAUUCAGA
ABBA01015737.1/36023-35937     UGGGAUGUGU-CAGGUAGGCAGUGUAUUGCUAGC-GGCUGU-----UAAUGAUUUUAACA--------------GUAGCU-AG--U--UGCA-CUCCUC-UCUGUU-GCAUUCAGA
AAQQ01588713.1/1895-1807       UGAUCUGAAU-CAGGUAGGCAGUGUAUUGUUAGCUGGCUGC------UUUGGUCAAGUCA--------------GCAGCCACA--G-CUACC-CUGCCA-CUUGCU-UCUGGAUAA
AAPY01138081.1/497-406         UUGGAUGUGU-CAGGUUGGCAGUGCAAUGCUAGCUGGCUGU----UGUAAUUCCAUUUUA--------------ACAGUUGCUAGU--UACA-CUGCCC-UCUGUU-GCAUUCAGA
AAFR03035385.1/18957-18868     CUGCUUGUGA-UGGGAUGGCAGUGUAUUGUUAGCUGGUUGA-----CUAUCUGAACGUG---------------CCAGCUAAC--A--UGCAACUGCUAUCCCAUU-GCAUUUCCC
AAFR03035385.1/19098-19010     UUGCCAGGGU-CAGGUAGGCAGUGCGCUGUAAGCUGGCUGC------UUGGCUCAAUUUA--------------GCAGUCAGG--A-CUGCC-CUGCCA-CUUGCU-CCUGGACUC
AAVX01082942.1/951-861         UUGUGCUUGG-UGGGAAGGCAGUGUAACGUUAGCUGGUUGU-----GGUUGUAUAUGUUA--------------CCAGUUAAC--U--UGCUGCUGCCCUCUUACC-ACACAUGGA
AAVX01082942.1/500-413         GUGUGUGGGU-UGAUUAGGCAGUGUAAUGUUAGCUGGCUGC-----A-AUGUAGGAAUCA--------------GCAGCUACA-----AGCA-CUACCACAUUAGC-UCAUGAUUU
AAVX01082942.1/1090-1000       GUGCCAGAGU-CUGGAAGGCAGUGUACAGUUAGCUGGCUGC-----UUGGUGUUUGGACA--------------GCAGCCGCUACG--UAUU-CCGCCA-CUUGCC-UCGUGGUCU
CAAE01014999.1/1949699-1949612 CCGCGGGCGG-CUGGUAGGCAGUGUCAUGUUAGCUGGUUGG-----UUCCGU---UAGCA--------------CCAGUUUAC--C--UGCCACUGCUCUCCAACC-ACCUGCAAA
AC193609.2/87034-86948         CUGUGUGCGG-UGGGGUGGCAGUGUA-UGUUAGCUGGUUGA-----AACUCU---UGACA--------------UCAGCUAAC--A--CGCAGUUGCUAACCUGCU-CCACAUACC
AC193609.2/87195-87108         GACCCUGUGG-CUGGAAGGCAGUGUGCUGUUAGC-GGCUGC------UGUGCUGAAUGGA--------------GCAGUCACU--A-CCACA-CUGCCA-CCUGCU-GCAGGGAUA
AC193609.2/86167-86082         CUGUGUGUGA-UGAUUAGGCAGUGUAUUGUUAGUUAGCUGC------UCUUCAUACACCA--------------GCAACUAAC-----UACA-CUGCCACAUUA---GCACAUCAC
AANU01256425.1/34046-33956     CUGUGUGUGA-UGAGCUGGCAGUGUAUUGUUAGCUGGUUGA-----AUAUGUGAAUGGCA--------------UCAGCUAAC--A--UGCAACUGCUGUCUUAUU-GCAUAUACA
AC159207.2/92222-92132         CUGUGUGUGA-UGGCUUGGCAGUGUAUUGUUAGCUGGUUGA-----GUAUGUGAGCGGCA--------------CCAGCUAAC--A--UGCGACUGCUCUCCUAUU-GCACACACA
ABDC01177373.1/3735-3646       UGACCUGAAU-CAGGUAGGCAGUGUAUUGUUAGCUGGCUGC-----UUUGGGUCAAGUCA--------------GCAGCCACU--A-CUACA-CUGCCA-CUUGCU-UCUGGACAA
AANH01010052.1/23105-23020     AUGUGGGCGG-CUGGUAGGCAGUGUCUUGU----UAGCUGG------UCAAUUCUGCGCC--------------CCAGCUUAC--C--UGCUGCUGCCCUCCAGCU-GUCCAUCUA
AAZX01003771.1/10900-10991     AAGCGACCGG-CGUGUUGGCAGUGU--GGUUAGCUGGUUGU-----GUAGCUUAUAGAAAG------------CACGACCGCUAUC--GACA-CUGCAAUUAUGAC-GGUCGCGAU
AAQA01000334.1/14819-14733     CGGGGAUUUA-CCGGGUGGCAGUG--UGGUUAGCUGGUUGU-----CAGCAUAUCGGACA--------------ACGGCUAUC--A--U-CA-CUGCCGUCCUGGU-UUUCCUAAA
AAAB01008859.1/3300834-3300927 GAGGCAAUAUACGCUCUGGCAGUGUGG--UUAGCUGGUUGUG--UGGUUUUCCCAUCUUC--------------ACAGCCACUAUC--CGCC-CUGCCGUCGCGCU-AAUGCCCAA
AANI01014607.1/367710-367617   AUUGGCUAUG-CGCUUUGGCAGUGU--GGUUAGCUGGUUGU-----GUGGCCAAUUGACAAA----------UCACAGCCACUAUC--UUCA-CUGCCGCCGCGAC-AAGCUAUGA
AAJJ01000475.1/25339-25252     UAGCGAUGUA-CACGGUGGCAGUGUGG--UUAGCUGGUUGU-------GUUUUUUUGAUC--------------ACGACCACUAUC--CAUA-CUCCCUCCAUGAA-UAUCGUUAA
AADE01000147.1/85680-85577     AUUGGCUAUG-CGCUUUGGCAGUGU--GGUUAGCUGGUUGU-----GUAGCCAAAAUAUUGCCUUUGACCAUUCACAGCCACUAUC--UUCA-CUGCCGCCGCGAC-AAGCCAUAA
AAZO01004205.1/1293-1391       GUCGUCGUGC-AGCAUUGGCAGUGU--GGUUAGCUGGUUGUG--UGGUGAUAACAAUAAAAUA--------GUCACAACCACUAUC--UUCA-CUGGCAACGUAAC-ACGGCAAAA
AAQB01008630.1/408110-408004   AUUGGCUAUG-CGCUUUGGCAGUGU--GGUUAGCUGGUUGUGUAGCCAAUUAAAUUGCCAAAACAA--UAAACCACAGCCACUAUC--UUCA-CUGCCGCCGCGAC-AGGCCAUGA
AAPP01019533.1/13885-13988     AUUGGCUAUG-CGCUUUGGCAGUGU--GGUUAGCUGGUUGU-----GUAGCUGGUGCUCGUUGGCAAUUAAUUCACAGCCACUAUC--UUCA-CUGCCGCCGCGAC-AAGCUAGAG
AAGV020398386.1/850-759        CUGGGUGUGU-CAGGUAGGCAGUGCUUUGCUAGCUGGCUGU----UAUAAUUUUAUUUUA--------------ACAGUUGCU--AGUUGCA-CUCCCC-UCUGUU-GCAUUCAAA
AAKN02031494.1/12165-12258     UUGGAUGUGA-CAGAUAGGCAGUGCAUUGCUAGCUGGCUGUU--AAGAUUUUUCAUUUUA--------------GCAGUUGCU--AGUUGCA-CUCCUC-UCUGUU-GCAAUCAGA
AAKN02031494.1/12810-12899     CUGUGUGUGA-UGGGCUGGCAGUGUAUUGUUAGCUGGUUGA-----AUAUAUAUUA-UUA--------------GCAGCUAAC--A--UACAACUGCUAUCUUAUU-GCAUAUACA
AAWR02016364.1/4252-4337       UUGGAUGUGU-CAGGUAGGCAGUGCAUUGCUAGCUGGCUAU-----UUCAUUUUAA--CA--------------GUUGCUGGU-----UGCG-CUCCCC-UCUGUU-GCAUUCGAA
AE014297.2/5926659-5926761     AUUGGCUAUG-CGCUUUGGCAGUGU--GGUUAGCUGGUUGU-----GUAGCCAAUUAUUGCCGUUG-ACAAUUCACAGCCACUAUC--UUCA-CUGCCGCCGCGAC-AAGCUAAAG
AP009026.1/9014-8925           CAGGGUAGAC-CGCGUUGGCAGUGU--GGUUAGCUGGUUGU-----GUAUGGAAAUGACA--------------ACAGCCACUAAC--GACA-CUGCUCCUGCGUG-CACCCUAAA
CAAB02011574.1/9059-8972       CAGCGGGUGG-CUGGUAGGCAGUGUCAUGUUAGCUGGUUGA-----UUCUGU---UCUCG--------------CCAGUUUAC--C--UGCUACUGCUCUCCAACC-ACCAGCAAA
AAGU03020867.1/27393-27303     CUGUGUGUGA-UGGGUUGGCAGUGUAUUGUUAGCUGGUCGA-----AUUGAUAAGUGGCA--------------UCAGCUAAC--A--UGCAGCUGCUAACUUAUU-GCAUAUGCU
AAQR03013218.1/12074-12165     UUGGAUGUGU-CGGGUAGGCAGUGCAUUGCUAGCUGGCUGU----UGUAAUUUCACUUUA--------------ACAGUUGCU--GGUUGCA-CUCCCC-UCUGUC-GCGUUCAGA
AADG06005308.1/87357-87449     UUGCGAUUGG-CAUGUUGGCAGUGU--UGUUAGCUGGUUGU-----GUGGCUACAUUGUAU-----------AUACGACCGCUAUC--GGCA-CUGCAAUUAUGAC-GAUCGUAGG
AAQR03013218.1/13225-13314     GGAUCCGAAU-CAGGUAGGCAGUGUAUUGUUAGCUGGCUGC-----UUUGCAUCGAGUCC--------------GCAGCCAUA--A-CUACC-CUGCCA-CUUGCU-UCUGGAUAA
AAWZ02010283.1/10129-10219     GUGUGUGUGG-UGGAAUGGCAGUGUAUUGUUAGCUGGAUGA-----GUAUCUCAAUGCCC--------------CCAGCUGAC--A--UUCAGCUGCCAAUCUACG-GCACAUAUU
AACZ03174975.1/1653-1737       UGACCUGAAU-CAGGUAGGCAGUGUAUUGUUAGCUGGCUGC------UUGGGUCAAGUCA--------------GCAGCCACA--A-CUACC-CUGCCA-CUUG-----AGGGGGA
AACN010038305.1/3346-3436      CCGUGUGUGA-UGGGUUGGCAGUGUAUUGUUAGCUGGUUGA-----AUAUAUGAAUGGCA--------------UCAGCUAAC--A--UGCAACUGCUAUCUUAUU-GCAUAUACA
AAGW02030810.1/75800-75711     UGACCUGAAG-CAGGUAGGCAGUGUAAUGUUAGUUGGCUGC-----UUUGGGUCAAGUCA--------------GCAGCCACA--G-GUACG-CUGCCA-CUUGCC-UCUGGCUAA
AAGW02030810.1/75679-75589     CGGUGUGUGA-UGAGGUGGCAGUGUAUUGUUAGCUGGUUGA-----AUAUGUGUGUGAUA--------------UCAGCUAAC--A--UACAACUGCUAUCUUAUU-GCAUUUACA
AAWZ02010283.1/10791-10878     CUGUAUGUGA-UGGUUUGGCAGUGUACUCUUAGUUAGCUGU------UGUAUAUAUUACA--------------GCAACUAAA-----UACA-CUUCCAUAUUAUU-GCAUGACUU
#=GC SS_cons                   :::<<<<<<<.<<<<--<<<<<<<<<<-------<<<<<<<.....______________..............>>>>>>>--..>..>>>>.>>>>>-->>>>>>.>>>>>::::
#=GC RF                        uUGcgugcga.cgggUuGGCAGuGuauUGUUAGCugGcUGu.....gUauuuuaauuucA..............aCAgCcacu..a..uaCa.CUGCCaucccguc.gcacgaaaA
//
# STOCKHOLM 1.0

#=GF AC   RF00712
#=GF ID   mir-460
#=GF DE   microRNA mir-460
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   82.60
#=GF NC   56.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000134;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16750530
#=GF RT   Identification of microRNAs from different tissues of chicken embryo and
#=GF RT   adult chicken.
#=GF RA   Xu H, Wang X, Du Z, Li N
#=GF RL   FEBS Lett. 2006;580:3610-3616.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   MicroRNA
#=GF SQ   8


AAFR03030363.1/8341-8416   CUUUAUAGAACCUGCAUUGUACACACUGUGUGUUUUCAUUCC-CAUGCACAGCGCAUACAAUGUGGAUACUAUAAGA
BAAE01241804.1/395-319     CUUUACAGUUCCUGCAUUGUACACACUGUGCAUAUAUGUUACAUAAGCACAGCGCAUACAAUGUGGAUGCUGUGCUA
AJ550897.1/27759-27835     UUUUACAGUUCCUGCAUUGUACACACUGUGCAAAUCAUUUCUGGAAGCACAGCGCAUACAAUGUGGAUGCUGUGCUG
AL929518.16/147724-147648  CUCCUCGGCUCCUGCAUUGUACACACUGUGCGGAAAACAUGGACAUGCACAGCGCAUACAAUGUGGAUGCUGUGGAG
AAPN01052000.1/412-337     CUGUAUAGAACCUGCAUUGUACACACUGUGUGUCUC-GCUCUCUGCACACAGCGCGUACAAUGUGGAUACUAUAGAA
AANH01005365.1/54234-54158 CUUUACAGCUCCUGCAUUGUACACACUGUGCGUAGAAGUUACGUAAGCACAGCGCAUACAAUGUGGAUGCUGUGCUA
AAWZ02031896.1/1692-1616   CCUUAUAGGACCUGCAUUGUACACACUGUGUGUAUGGACUGGAGGUGCACAGCGCAUACAAUGUGGAUGCUAUAGAA
AADN03002318.1/51312-51236 CUAUAUAGCACCUGCAUUGUACACACUGUGUGUGUUAACUGGAAAUGCACAGCGCAUACAAUGUGGAUUCUGUAGAA
#=GC SS_cons               :::::<<<<--<<<<<<<<<<--<-<<<<<<_______________>>>>>>->-->>>>>>>>>>-->>>>:::::
#=GC RF                    CUuUAcaGcuCCuGCAUUGUACACACUGUGcGuauaaauUauauAugCACAGCGCAUACAAUGUgGAUgCugUagaA
//
# STOCKHOLM 1.0

#=GF AC   RF00713
#=GF ID   mir-239
#=GF DE   microRNA mir-239
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   56.90
#=GF NC   52.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000135;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [3]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF WK   MicroRNA
#=GF SQ   9


Z67754.1/1218-1322             ACUCUACACGUUUGCAAUUUUUGUACUACACAUAGGU-ACUGGACAAUUUUCA-AAAUAUAUCCAGUGUCUA-GUCUAGUGCAA-ACAUUGCUCG--GUGUUGUUUGAAAA
Z67754.1/178-79                CAGCGAC--AGAUGCAAUUUUUGUACUACACAAAAGU-ACUGGUCAUUUAAGU--UGAGG-CUCAGCACUUUUGUGGUGUGCAA-AAAUGGCAAG--UUGCUUU--UAUCU
AAGD02001685.1/9995-9897       AAUCCAA--GAUUGCGAUUUUUGUACUACACAUAGGU-ACUGGACACUG--AG-AUUUGUAUCCAGAAUCUA-UUCUAGUGCAA-AAAUUGCUCU--GGAUUCU--UUUUU
CAAC02000438.1/1163532-1163436 GUAGGACAGACAUGCAAUUUUUGUACUGCACAAAAGU-ACUGACUAUUU------------CUCAGCGCUUUUGUCCAGUGCAA-GAAUGGCAAGAGCUGGUCCAUUUUUU
CAAC02000438.1/1164613-1164718 GAUCCAAGUUUAUGCGAUUUUUGUACUACAAUUAGGU-ACUGGACACCAGCAGCGAGUGUAUCCAGAAUCUA-UACUAGUACAA-AAAUAGCUAA--CAGGAUUAAGAUUU
AAGD02001685.1/11081-11181     ACAAGAC-AACUUGCAAUUUUUGUACUGCACAAAAGC-UCUGACUGCUC--UG-AUAUGG-CUCAGCACUUU-UGUCUGUGCAA-AAAUGGCGAA--UAUCUGUCUUUCUU
ABEG02005018.1/33548-33648     AUUCCAC-AAAAUGCGAUUUUUGUACCGAUUAUAGGCAACUGAUUUUUG------AACGUUUUCAGUGCCUA-UUUCAGUACAAUAGAUUGCUAA--GUAAGGGACACUUU
ABEG02003040.1/26892-26995     AGCCUAA--AAAAGCGAGUUUUGUACUAAACAUAGGU-ACUGAAAUAAAAUAUUUUAUUUACUCAGUUCCUA-GUCUAGUGCAA-GGGUUGCUAA--UGGGUUAAUUGGUU
ABEG02001091.1/1868-1968       -AACUGACAAGUUGCAGUUUUUGUACUUCACAAGAGU-ACUGGCGGUUC--AG-GUCCGG-CUCAGAACUUUUGUGGGGUGCAA-GAACAGCAAA-ACUGUCAU--ACUUU
#=GC SS_cons                   :::::::.:::::<<<<<<<<<<<<<<<----<<<<<.-<<<<______..__.________>>>>->>>>>.--->>>>>>>>.>>>>>>>:::..::::::::::::::
#=GC RF                        aauCuAa.aAaaUGCcAUuuUUGuACugCACAuAGGu.ACUGgauauUu..ag.auauGuAccCAGuaCCUa.gUccaGUgCAA.aaAUgGCuAa..uuguuuuauuuuUU
//
# STOCKHOLM 1.0

#=GF AC   RF00714
#=GF ID   MIR535
#=GF DE   microRNA MIR535
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   56.00
#=GF TC   57.00
#=GF NC   53.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000136;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19942686
#=GF RT   Conservation and divergence of microRNAs and their functions in
#=GF RT   Euphorbiaceous plants.
#=GF RA   Zeng C, Wang W, Zheng Y, Chen X, Bo W, Song S, Zhang W, Peng M
#=GF RL   Nucleic Acids Res. 2010;38:981-995.
#=GF WK   Mir-535_microRNA_precursor_family
#=GF SQ   4


AASG02028037.1/959-869     CAUCAUUUGUUGACAACGAGAGAGAGCACGCUUGUUAGCCU-UCAUGUAAGGA----ACAUGGUUGCACACCAGCGUGCUCCCUAUCGUUGUCAAU----------
AASG02007689.1/8432-8332   CUUAGUUGGUUGACGACGAGAGAGAGCACGUUUGUCAGCAG-UCAUGCAAUGG----ACAUGUCUGUCUACAUGCGUGCUCUCUUUUGCCGUCAUACAAUUUUCUC
AAAA02031907.1/20463-20366 --------GGUGACAACGAGAGAGAGCACGCCGGUGCGGCGGUCACGGUGAGCCGGCCCGCGGCGGCGUACCUGCGUGCUUUCUCCCGUUGUCACUGCCAUACACA
AM489362.2/576-677         UGCAAUUGCUUGACAAAGAGAGAGAGCACACUUGUUAGCAU-UCAUGUGAGGUA---ACAUGACUGUGUACAGGUGUGCUUUCUCUCGCUGUCAUACAAUCUUCUC
#=GC SS_cons               ::::::::::<<<<<<<<-<<<<<<<<<<<<--<<------.<<<<<_______..._>>>>>------>>-->>>>>>>>>>>>->>>>>>>>::::::::::::
#=GC RF                    cauaaUUgguUGACaaCGAgAGagAGCACGcUuGUuaGcau.cCauGuaAaGua...aCauGgcuGugUACaugCGUGCUcuCUcUCGuuGUCAuucaauuuuaua
//
# STOCKHOLM 1.0

#=GF AC   RF00715
#=GF ID   mir-383
#=GF DE   microRNA mir-383
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   84.60
#=GF NC   43.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000137;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF WK   Mir-383_microRNA_precursor_family
#=GF SQ   6


AAFR03038294.1/87558-87630     CUCCUCAGAUCAGAAGGUGAUUGUGGCUUUCGGUAGACAUGGAACAGCCACAUCACUGGCUGGUCAGAAAGAG
AAPN01276053.1/1242-1314       CUCCUCAGAUCAGAAGGUGAUUGUGGCUUUGGGUAGCUACUAAGCAGCCACAACACUGCCUGGUCAGAAAGAG
AC084838.7/42301-42373         CUCCUCAGAUCAGAAGGUGAUUGUGGCUUUGGGUGGAUAUUAAUCAGCCACAGCACUGCCUGGUCAGAAAGAG
AC124198.2/165455-165527       CUCCUCAGAUCAGAAGGUGACUGUGGCUUUGGGUGGAUAUUAAUCAGCCACAGCACUGCCUGGUCAGAAAGAG
AADN03003935.1/1006669-1006597 CUCCUCAGAUCAGAAGGUGAUUGUGGCUUUGGGUAAAUAUUGAGCAGCCACAGCACUGCCUGGUCAGAAAGAG
AAWZ02012881.1/60819-60747     CUCCUCAGAUCAGAAGGUGAUUGUGGCUUUGCUUUUAUAUGAAACAGCCACAGCACUGCCUGGUCAGAAAGAG
#=GC SS_cons                   :::<<<-<<<<<<--<<<<-<<<<<<<<<<<<_______>>>>-->>>>>>>>>>>>-->>>>>>----->>>
#=GC RF                        CUCCUCAGauCaGAAgGUGAcUGUGGCUUuggGUagAUAccaAaCAGCCACAgCACuGcCuGguCAGAAAGAG
//
# STOCKHOLM 1.0

#=GF AC   RF00716
#=GF ID   mir-3
#=GF DE   microRNA mir-3
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00084
#=GF DR   MIPF; MIPF0000140;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF WK   Mir-3_microRNA_precursor_family
#=GF SQ   11


AAIZ01001618.1/39320-39392   GAUCCUGGGAUGCAUUUUGUGCAGUUAUG--UCUACGUG----AUCAUCCUCAUCACUGGGCAAAGUGUGUCUCAGGAU
AAIZ01001618.1/39190-39258   UAUUAUACGAUAAACUUUGUUCAGUUUUG--CCAAC-------UUGCUUG-CAGCACUGGGUGAAGUUUGUCUUAUAAU
AAPU01010225.1/183837-183766 ACUUUUGGGAUGCAUUUUGUGCAG--AUG--UCUAACGAU---UGGAAACCCAUCACUGGGCAAAGUGUGUCUCAAAAU
AAPU01010225.1/183969-183894 UAUUAUAAGGUAAACUUUGUUCAGUUUUG--CCGGGUUCUAU-GUUGUGCGCAUCACUGGGUGAAGUUUGUCGUAUAAU
AAGH01003023.1/8387-8456     AAUUAUACGACAAACCUUGUUCGGUUUUG--CCAAU-------UUCCAAGCCAGCACUGGGUAAAGUUUGUCCUAUAAU
AAGH01003023.1/8499-8566     GAUCCUGGGAUGCAUCUUGUGCAGUUAUG--UUCCA-------AUC--UCACAUCACUGGGCAAAGUGUGUCUCAAGAU
AAPT01006453.1/2658-2730     GCUUUUGGGAUGCAUUCUGUACAGUAAUG--UUGACUCU----UGUAAAACCAUCACUGGGCAAAGUGUGUCUCAAAAU
AAPT01006453.1/2524-2600     CAUUAUAUGGCAAACCUUGUUCAGUUUUG--ACAACUUUGUUUCUGUGCAUCAUCACUGGGUGAAGUUUGUCGUAUAAU
AAPP01018770.1/56641-56712   GAUCUUGGGACGCAUUUUGUGCAGUUAUGCACCAAA-------AAUAUAUCCAUCACUGGGCAAAGUGUGUCUCAGGAU
AAQB01006291.1/71735-71659   GAUUUUGGGAUGCAUUUUGUGCAGUUAUG--UCUUCAUGUGAUAAUUCUCUCAUCACUGGGCAAAGUGUGUCUCAUAAU
AANI01014795.1/39022-39093   GCUUUUGGGAUGCAUUUUGUGCGGUUAUG--UCUGCCU-----CCAAAACCCAUCACUGGGCAAAGUGUGUCUCAAAAU
#=GC SS_cons                 :<<<<<<<<<<<<<<<<<<<-<<<<-<<<..________....________>>>->>>>->>>>>>>>>>>>>>>>>>>
#=GC RF                      gAUucUGcGAugcAcuUuGUgCAGUUaUG..uCaacuuu....uuuauacuCAuCACUGGGCaAagUgugUCgCAgaAU
//
# STOCKHOLM 1.0

#=GF AC   RF00717
#=GF ID   mir-315
#=GF DE   microRNA mir-315
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   57.00
#=GF TC   57.40
#=GF NC   53.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000141;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF RN   [2]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [3]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF WK   MicroRNA
#=GF SQ   16


AASU01006755.1/588-667       CACUUAUAUAAUUUUGAUUGUUGCUCAGAAAGCCCUUAUUGUUUACCAGU-UGGCUUU-GAGC--UAAU-GGAACCAG-AGAAGUG
AAFS01000172.1/91075-90992   CACUUAUCUAUUUUUGAUUGUUGCUCAGAAAGCCCUUAUAAUUAACCAGU-UGGCUUUCGAGCAAUUAUCAAAGCCAA-AUAAGUG
AAGE02021501.1/12488-12571   UUUCUAUAAAAUUUUGAUUGUUGCUCAGAAAGCCGUGCAUUUGAAACGGG-UCGCUUUCGAGCAGUAAUCAAAGUCAA-AUAAAAC
AAZX01000470.1/15987-15906   GCUCUCUAUGCUUUUGAUUGUUGCUCAGAAAGCCUCGAUAUCGA---UAC-UGGCUUUCGGGCAAUAAUCAUAAUCACGGGAGAGU
AAJJ01004236.1/2476-2553     UUCCUUU-UGCUUUUGAUUGUUGCUCAGAAAGCCGGGUGUUAGAAA------GGCUUUCGGGCAAUAAUCAUUUCCAA-AGAGGAC
AAAB01006400.1/15231-15314   UUUGUAUAAAAUUUUGAUUGUUGCUCAGAAAGCCGUGUCGAUUAAGCAAU-UCGCUUUCGGGCAGUAAUCAAAGUCAA-AUACAAC
AAPP01019348.1/396602-396519 CACUUAUAUAAUUUUGAUUGUUGCUCAGAAAGCCCUUAUAAAUUAUUAGC-UGGCUUUCGAGCAAUAAUUGAAACCAA-AUAAGUG
AANI01017430.1/85121-85040   CGCCUAUAUCAUUUUGAUUGUUGCUCAGAAAGCCCUG--CAUUCAAUACU-UGGCUUUCGAGUAAUAAUCGAAACCAA-AUAAGCG
AAPU01011669.1/1431-1347     CCCUUAUAUAAUUUUGAUUGUUGCUCAGAAAGCCCGUAAUUUAACUUAACAUGGCUUUCGAGUAAUAAUCGAAACCAA-AUAAGGC
AAPT01020729.1/201657-201576 CGCUCAUAUAAUUUUGAUUGUUGCUCAGAAAGCCUUUCACUUGA--CACU-UGGCUUUCGAGUAAUAAUCGAAACCAA-AUAAGCG
AAEU02004141.1/4128-4045     CACUUAUAUAAUUUUGAUUGUUGCUCAGAAAGCCCUUACUAUUUAACAGC-UGGCUUUCGAGCAAUAAUUGAAACCAG-AUAAGUG
AAKO01002852.1/220904-220985 CACUUAUAUAAUUUUGAUUGUUGCUCAGAAAGCCCUU--AUUGUACCAGU-UGGCUUUCGAGCAAUAAUUGAAACCAG-AUAAGUG
AAWU01022757.1/12051-12134   UUUCUAUAAAAUUUUGAUUGUUGCUCAGAAAGCCGUGCAUUCGAAACAUU-CCGCUUUCGAGCAGUAAUCAGAGUCAA-AUAAAAC
AAPQ01006582.1/536778-536860 CACUUAUAUAAUUUUGAUUGUUGCUCAGAAAGCCCUAUUAUCUA-ACAGC-UGGCUUUCGAGCAAUAAUUGAAACCAG-AUAAGUG
AE014296.4/18854071-18854154 CACUUAUAUAAUUUUGAUUGUUGCUCAGAAAGCCCUCAUUGUUUACCAGU-UGGCUUUCGAGCAAUAAUUGAAACCAG-AUAAGUG
AADG06004063.1/7218-7138     GCUCUUUAUGCUUUUGAUUGUUGCUCAGAAAGCCUUGAUUAUGA---UAU-UGGCUUUCGGGCAAUAAUCAUAAUCAC-GAAAGGG
#=GC SS_cons                 :<<<<<<----<<<<<<<<<<<<<<<-<<<<<<<________________._>>>>>>>>>>>>>>>>>>>>>>----.>>>>>>:
#=GC RF                      cccuUauAUaauUuuGAUUGuUGCuCAGAAAGCCcUuauuuuuaAacAau.UGGCUUUCGaGCAaUAAUCaaAacCAa.auAaggg
//
# STOCKHOLM 1.0

#=GF AC   RF00718
#=GF ID   mir-431
#=GF DE   microRNA mir-431
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   95.00
#=GF TC   101.80
#=GF NC   59.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000142;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19784364
#=GF RT   Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic
#=GF RT   stem cells and neural precursors.
#=GF RA   Goff LA, Davila J, Swerdel MR, Moore JC, Cohen RI, Wu H, Sun YE, Hart RP
#=GF RL   PLoS One. 2009;4:e7192.
#=GF WK   Mir-431_microRNA_precursor_family
#=GF SQ   9


AAIY01393072.1/1321-1434     UCUUGGUCGUCC-UGCGGGCUGUCUUGCAAGCCGUCAUGCAGGCCACCUUGACGGUAACGUUGCAGGUCGCCCUGCCGGGCUUCUCGCAAGACGACAUCCUCGUCGUUCACAAUG
AAYZ01391476.1/1833-1946     GCCCGUGCGUCC-UGCGAGGUGUCUUGCAGGCCGUCACGCAGGCCACUCUGACGGUAACGUUGCAGGUCGUCUUGCAGGGCUUCUCGCAAGACGACAUCUUCAUCGCCAACGACG
AY986480.1/2211-2098         UCCUGCGCGUCC-UGCGAGGUGUCUUGCAGGCCGUCAUGCAGGCCACACUGACGGAAACGUUGCAGGUCGUCUUGCAGGGCUUCUCGCAAGACGACAUAUUCAUCACCCUCGACG
AY986481.1/101-214           UCCUGCGCGUCC-UGCGAGGUGUCUUGCAGGCCGUCAUGCAGGCCACACUGACGGAAACGUCGCAGGUCGUCUUGCAGGGCUUCUCGCAAGACGACAUAUUCAUCACCCUCGACG
AL117190.6/121123-121236     UCCUGCUUGUCC-UGCGAGGUGUCUUGCAGGCCGUCAUGCAGGCCACACUGACGGUAACGUUGCAGGUCGUCUUGCAGGGCUUCUCGCAAGACGACAUCCUCAUCACCAACGACG
BK001261.1/4964-4851         UCCUGCGCGUCC-UGCGAGGUGUCUUGCAGGCCGUCAUGCAGGCCACACUGACGGUAACGUUGCAGGUCGUCUUGCAGGGCUUCUCGCAAGACGACAUCUUCAUCCCCAACGACG
AAPE02047295.1/126788-126675 GCCUGCGCGUCC-UGCGAGGUGUCUUGCAGGCCGUCAUGCAGGCCACACUGACGGUAACGUUGCAGGUCGUCUUGCAGGGCUUCUCGCAAGACGACAUCACUCCCGAUGACGUGC
AAQR03046506.1/15537-15650   UCCUGCUCGUCC-UGCGAGGUGUCUUGCAGGCCGUCAUGCAGGCCACACUGACGGUAACGUUGCAGGUCGUCUUGCAGGGCUUCUCGCAAGACGACAUCCUCAUCACCAACGACG
AAGU03025978.1/2463-2350     UCUUGAUCGUC-CUGCGGGGUGUCUUGCAGGCCGUCAUGCAGGCCACCUUGACGGUAACGUUGCAGGUCGCCCUGCGGGGCUUCUCGCAAGACGACAUUCUCCUCGUUAACGAUG
#=GC SS_cons                 :::<<-<<<<<-.<<<<<<<-<<<<<<<<<<-<<-<-<<<<<<<<________>>>---->>>>>->->>->>>>>>>>>>->>>>>>>->>>>>>>::::::::::::::::::
#=GC RF                      uCcuGcucGuCC.uGCGaGgUGuCuuGCagGCCGUCAuGCaggCCACacUGACGGcAACGuuGCaGGUCGuCcuGCagGgCUcCuCGCaAGaCgaCaUcuUcaUCacuaaCGAcg
//
# STOCKHOLM 1.0

#=GF AC   RF00719
#=GF ID   mir-326
#=GF DE   microRNA mir-326
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   92.50
#=GF NC   86.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000143;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-326_microRNA_precursor_family
#=GF SQ   7


AACN010575653.1/202-296    CUCCUCUGUCUGUUGGGCUGGAGGCAGGGCCUUUGUGAAGGCGGGUGGUGAUCGGAUCGCCUCUGGGCCCUUCCUCCAGCCCAGAGGCGGAUUCA
AAYZ01294195.1/2778-2684   GCCACCCGUCUGUUGGGCUGGGGGCAGGGCCUUUGUGAAGGCGGGUUGUGCUCGGAUCGCCUCUGGGCCCUUCCUCCAGCCCCGAGAUGGAUUCA
AAWR02018146.1/14357-14451 CUCGUCUGUCUGUUGGGCUGGAGGCAGGGCCUUUGUGAAGGCGAGUUGUGCUGGGAUCGCCUCUGGGCCCUUCCUCCAGCCCAGAGGCGGAUUCA
AAKN02051174.1/76507-76600 CUCCUCUGUCUGCUGGGCUGGGGGCAGGGCCUUUGUGAAGGCGGGU-GUGCAAAGAUCGCCUCUGGGCCCUUCCUCCAGCCCCGAGGCGGAUUCA
AC111086.18/5159-5253      CUCAUCUGUCUGUUGGGCUGGGGGCAGGGCCUUUGUGAAGGCGGGUUAUGCUCAGAUCGCCUCUGGGCCCUUCCUCCAGUCCCGAGGCAGAUUUA
DQ314865.1/18155-18249     CUCAUCUGUCUGUUGGGCUGGAGGCAGGGCCUUUGUGAAGGCGGGUGGUGCUCAGAUCGCCUCUGGGCCCUUCCUCCAGCCCCGAGGCGGAUUCA
AAQR03001071.1/20442-20536 CUCAUCUGUCUGUUGGGCUGGAGGCAGGGCCUUUGUGAAGGCGGGUUGUGCUCAGAUCGCCUCUGGGCCCUUCCUCCAGCCCCGAGGCGGAUUCA
#=GC SS_cons               :::<<<<<<<<-<<<<<<<<<<<<<<<<<<<<----<-<<<<<<____________>>>>>>>->>>>>>>>>>>>>>>>>>>>>>>>>>>>:::
#=GC RF                    cucauccGccuGccGGGcuGGgGGcaGGGcccUUGUGAaGGcGgGUugUGcucaGAcCgCCuCUgggCCCugCCcCCagCCCggaggCggauUcA
//
# STOCKHOLM 1.0

#=GF AC   RF00720
#=GF ID   mir-317
#=GF DE   microRNA mir-317
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   63.40
#=GF NC   58.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.94 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000144;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [2]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF WK   MicroRNA
#=GF SQ   12


AAWU01003687.1/17257-17344     GAAUUUCGGCUACCGGGAUAC-ACCCUGUGCUCGCUUUGCAUUC-----GAAACUAGUGAACACAGCUGGUGGUAUCUCAGUGGCCCUGAUCCG
AAQB01008630.1/421628-421538   GUGCAACUGCCACUGGGAUAC-ACCCUGUGCUCGCUUUGAAUAU-UGUGCAAACAAGUGAACACAGCUGGUGGUAUC-CAGUGGCCGUUUUUUG
AANI01014607.1/383695-383607   GUGCAAUUGCCGCUGGGAUAC-ACCCUGUGCUCGCUUUGAAUUG---UGCAAGCAAGUGAACACAGCUGGUGGUAUC-CAGUGGCCGUUGGCAG
AAAB01008859.1/3281503-3281595 ACGUCUCUGCCACUGGGAUAC-UCCUUGUGCUCGCUGUGCAUAUCGAUUCAAACUAGUGAACACAUCUGGUGGUAUCUCAGUGGCCGGGAUGAG
AAJJ01000475.1/38254-38168     GGUGGGGCGGUGCUGGGGACC-ACCCUGUGUUUACUCUGUAUUU------CGACCAGUGAACACAGCUGGUGGUAUCUCAGUUUCUUCCCAUCA
AAPU01011031.1/18314-18227     GUGCAAUUGCCGCUGGGAUAC-ACCCUGUGCUCGCUUUGAGUUU---AUGUUGCAAGUGAACACAGCUGGUGGUAUC-CAGAGGCCGUUG-ACA
AAIZ01005964.1/1594-1504       GUGCAACUGCCGUUGGGAUAC-ACCCUGUGCUCGCUUUGAAUAU-GGUGCAAGCAAGUGAACACAGCUGGUGGUAUC-CAAUGGCCGUUCUGCA
AAPP01019533.1/3894-3984       GUGCAUCGGCUGCUGGGAUAC-ACCCUGUGCUCGCUUUGAAUGA-AAUGCAAGCAAGUGAACACAGCUGGUGGUAUC-CAGUGGCCGUUUUGCA
AAPT01018372.1/102669-102760   GUGCAAUUGCCACUGGGAUAUUGCCCUGUGCUCGCUUUGAAUAU-UGUGUAAGCAAGUGAACACAGCUGGUGGUAUC-CAGUGGCCGUUUGGCG
AC009183.5/112559-112649       AUGCAACUGCCAUUGGGAUAC-ACCCUGUGCUCGCUUUGAAUGA-AAUGCAAGCAAGUGAACACAGCUGGUGGUAUC-CAGUGGCCGUUUGGCA
AP009026.1/37151-37063         GCUAUCGAACGACCGGGUGCC-ACGCUGUGCUCUCUCGAAAAUU-AUGGCG---GAGUGAACACAGCUGGUGGUAUCUCAGUUGUUCCCUAGUU
AEKZ01010478.1/7049-6959       GCUCUCGGAGAACAGGGAGCC-ACUCUGCGUUCACUCGGUGGGU--AAUGAAGCGGGUGAACACAGCUGGUGGUAUCUCAGUUUUCUGAGGGCG
#=GC SS_cons                   :<<<<<<-<<<<<<<-<<<<<.<<<<<<<<-<<<<<<_______._________>>>>>>->>>>>-->>>->>>>>->>>>>>>->>>>>>::
#=GC RF                        GcccggcuGccaCuGGGauaC.aCcCUGuGcUCgCucuGaAuuu.aaugcaAgCgaGuGAACaCAGCUgGuGGuauCUCaGuggCcgccgggca
//
# STOCKHOLM 1.0

#=GF AC   RF00721
#=GF ID   MIR475
#=GF DE   microRNA MIR475
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   100.00
#=GF TC   103.60
#=GF NC   77.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000145;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15994906
#=GF RT   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa
#=GF RT   that are absent from Arabidopsis.
#=GF RA   Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL
#=GF RL   Plant Cell. 2005;17:2186-2203.
#=GF WK   MicroRNA
#=GF SQ   4


AY728408.1/5-100         CAUCCUGAUCAAUGGCCAUUGUAAGAGUAGAAGGAUCCAUGAAGCAA----------------------------AACAUUGACUCCUGAUAUUCCACUCUUACAGAGUCCAUUGAUUAAGAUG
AY728406.1/1-120         -AUCUUGAUCAAUGGCCAUUGUAAGAGUAGAAGGAUCCAUGAAGCAAUAACUCUCUUUGCUGAAAUGUGCGACCAAAUA--GACUCUUGAUAUUUCAUUCUUACAGUGCCCAUUGAUUAAGAU-
AY728407.1/4-123         CAUCUUGAACAAUGGCCAUUGUAAGAGUA-AGUGGUCCAUGAGUCAAUAACUCUCUUUGCAGAAAUGCAUGACAAAGCAUUGACUCCU---AUUUCACCCUUACAAUGUCCAUUGAUUAAGAGG
AARH01001365.1/1380-1503 CAUCUUGAUCAAUGGCCAUUGUAAGAGUAGAAGGAUCCAUGAAGCAAUAACUCUCUUUGCUAAAAUGUGUGAUAAAACAUUGACUCCUGGUAUUUCACUCUUACAGUGCCCAUUGAUUAAGAUG
#=GC SS_cons             <<<<<<<<<<<<<<<-<<<<<<<<<<<<-<<<-----<<-<<--<<<<---------<<<______>>>--------->>>>-->>->>--->>>->>>>>>>>>>>>->>>>>>>>>>>>>>>
#=GC RF                  CauCuugauCaauGGCCacuGuaaGaGuAgaagGaUCCaUGaagCaauAACUCUCUUcgCugAAAUGcguGAcaAAacauuGACuCcuGaUAuucCaCuCuuaCaguGuCCauuGauuaaGauG
//
# STOCKHOLM 1.0

#=GF AC   RF00722
#=GF ID   mir-451
#=GF DE   microRNA mir-451
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   54.00
#=GF TC   54.00
#=GF NC   53.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000148;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18619946
#=GF RT   Role of MicroRNA miR-27a and miR-451 in the regulation of
#=GF RT   MDR1/P-glycoprotein expression in human cancer cells.
#=GF RA   Zhu H, Wu H, Liu X, Evans BR, Medina DJ, Liu CG, Yang JM
#=GF RL   Biochem Pharmacol. 2008;76:582-588.
#=GF RN   [2]
#=GF RM   18765229
#=GF RT   MIR-451 and Imatinib mesylate inhibit tumor growth of Glioblastoma stem
#=GF RT   cells.
#=GF RA   Gal H, Pandi G, Kanner AA, Ram Z, Lithwick-Yanai G, Amariglio N, Rechavi
#=GF RA   G, Givol D
#=GF RL   Biochem Biophys Res Commun. 2008;376:86-90.
#=GF RN   [3]
#=GF RM   18849488
#=GF RT   miR-451 regulates zebrafish erythroid maturation in vivo via its target
#=GF RT   gata2.
#=GF RA   Pase L, Layton JE, Kloosterman WP, Carradice D, Waterhouse PM, Lieschke GJ
#=GF RL   Blood. 2009;113:1794-1804.
#=GF RN   [4]
#=GF RM   20218812
#=GF RT   miR-451 enhances erythroid differentiation in K562 cells.
#=GF RA   Bruchova-Votavova H, Yoon D, Prchal JT
#=GF RL   Leuk Lymphoma. 2010;51:686-693.
#=GF RN   [5]
#=GF RM   20679397
#=GF RT   Defective erythroid differentiation in miR-451 mutant mice mediated by
#=GF RT   14-3-3zeta.
#=GF RA   Patrick DM, Zhang CC, Tao Y, Yao H, Qi X, Schwartz RJ, Jun-Shen Huang L,
#=GF RA   Olson EN
#=GF RL   Genes Dev. 2010;24:1614-1619.
#=GF RN   [6]
#=GF RM   20679398
#=GF RT   miR-451 protects against erythroid oxidant stress by repressing
#=GF RT   14-3-3zeta.
#=GF RA   Yu D, dos Santos CO, Zhao G, Jiang J, Amigo JD, Khandros E, Dore LC, Yao
#=GF RA   Y, D'Souza J, Zhang Z, Ghaffari S, Choi J, Friend S, Tong W, Orange JS,
#=GF RA   Paw BH, Weiss MJ
#=GF RL   Genes Dev. 2010;24:1620-1633.
#=GF RN   [7]
#=GF RM   20699384
#=GF RT   Conserved vertebrate mir-451 provides a platform for Dicer-independent,
#=GF RT   Ago2-mediated microRNA biogenesis.
#=GF RA   Yang JS, Maurin T, Robine N, Rasmussen KD, Jeffrey KL, Chandwani R,
#=GF RA   Papapetrou EP, Sadelain M, O'Carroll D, Lai EC
#=GF RL   Proc Natl Acad Sci U S A. 2010;107:15163-15168.
#=GF WK   Mir-451_microRNA
#=GF SQ   19


AANG01161467.1/4651-4580     CUUGGGAAUGGCGAGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAACGGUUCUCUUGCUGC-ACCCAGA
CAAE01014557.1/33640-33712   GCCGGGGAGGGCCGUCAAA-CCGUUACCAUUACUG-AGUUUCAGUAAUGGUAAGGGUUCCGCGGCCCU-CGCUCCA
BAAE01003505.1/1574-1502     ACAGAGCGGGGCCGUCAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAAGGGUUCCACGGCCUCUGCUCAAA
AAFR03044825.1/5420-5349     GGGCAGCCUGGCGGGGAAA-CCGUUACCAUUACUG-UGUU-UAGUAAUGGUAAGGGUUCUCCCGCUGC-GCUGAGU
BX548073.8/159677-159748     ACAGAGAGAGGCGGCGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAAGGGUUCUGCUGCCUU-UUCUCAA
AAVX01465249.1/530-602       CUGGGGGGUGUCAAUCAAA-CCGUUACCAUUACUUGUAUU-AAGUACUGGUAAGGGUUAUAUUGCUGC-CUCCGAU
AANH01000562.1/126354-126425 CAGAGGAGAGGCCGUCAAA-CCGUUACCAUUACUG-AGUUUCAGUUAUGGUAAGGGUUAUACGGCC-C-UCGCUCA
AAPN01323131.1/127-56        CGAGGGUCUGGCGAGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAACGGUUCUCUGGCUGG-GCCCACC
AAFC03123225.1/17309-17380   ACUUGGGGUGGCGAGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAACGGUUCUCUUGCUGC-ACCCAGA
AACN010082587.1/2136-2207    CUUGGGGAUGGCGAGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAAUGGUUCUCUUGCUGU-ACCCACA
AAKN02033337.1/59671-59742   CUUGGGGAUGGCGAGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUGACGGUUCUCUUGCUGC-UCCCCGA
FQ225534.1/495-566           UUUGGGAAUGGCGAGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAAUGGUUCUCUUGCUGC-UCCCACA
AC024267.18/54588-54517      CUUGGGAAUGGCAAGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAAUGGUUCUCUUGCUAU-ACCCAGA
AC198613.3/123210-123281     CUUGGGAAUGGCAAGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAAGGGUUCUCUUGCUAU-AUCCAGA
AL669840.5/57978-58049       CUUGGGAAUGGCGAGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAACGGUUCUCUUGCUGC-UCCCACA
AAGU03065334.1/21722-21651   CUUGGGAAUGACGAGGAA-ACCGUUACCAUUACUG-AGUU-UAGUAAUGGUAAUGGUUCUCUUGCUGC-AUCCAAA
CAAB02013240.1/35643-35715   GCAGGGGAGGCCCGUCAAA-CCGUUACCAUUACUG-AGUUUCAGUUAUGGUAAGGGUUCCACGGCUCU-CGCUCAA
AADN03007690.1/39022-38951   CACAUGGCUGGCAGGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAACGGUUCUGCUGACAG-CCAGGCA
AAQR03132753.1/823-894       UGUGGGAAUGGCAAGGAAA-CCGUUACCAUUACUG-AGUU-UAGUAAUGGUAACGGUUCUCUUGCUGC-ACCCAAA
#=GC SS_cons                 :::::<<<<<<<<<<--<<.<<<<<<<<<<<<<<<.____.>>>>>>>>>>>>>>>>>-->>>>>>>>.>>:::::
#=GC RF                      cuugGgggcggCggggAAA.CCgUUACCAUUACUg.AGUU.cAGUAAUGGUAAcGGUUCUcccGccgc.ccccaaA
//
# STOCKHOLM 1.0

#=GF AC   RF00723
#=GF ID   mir-448
#=GF DE   microRNA mir-448
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   74.00
#=GF TC   74.70
#=GF NC   51.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000149;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   Mir-448_microRNA_precursor_family
#=GF SQ   19


AALT01302712.1/526-635       GCAGGGAGG-UUGAACAUCCUGCAUAGUGCUGCCAGGAAAAUCC--CGUUAUAGUAAAA--G--GGCACUGACUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCUGCCCACUUCGUCG
AAPY01023583.1/1050-940      GUGGAG-AC-UUGUAGGUUCUCCGCAGUUCUGCCAGGAAGCCCU--GAUAAUUAUUUCGCAG--GGGGCUGUCGGGCUGCAUGUGGGGGAUGGCCCACUGCUCUGCCUCCCCAGUCA
AANN01153638.1/692-581       AGCGGGGAC-UUGUAGGUUCUCCGCAGCUCUGCCAGGAACCCCU--GAUAGUUGUUCCUCAG--GGGGCUGUCCGGCUGCAUGUGGGGGAUGGCCCACUUCUCCGCCUCCCCCGUCA
AAFC03097322.1/50759-50869   GCGGAGACU-UGUA-GGUUCUCCGCAACUCGGCCAGGAAUCCCU--GAUAGUUGUUUCGUAA--GGGGCUGUCGGGUUGCAUGUGGGGGAUCGCCCACUUCUCCGCCUCCCCAGUGA
AAIY01435447.1/95-210        GUGGGGAGGCUUGAACAUCCUGCAUAGUGCUGCCAGGAAACCCCCUACUCUCAUAAUAAG-AGAGCGGCAGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCCACCCACUUCGCCA
AANU01095693.1/44445-44335   GCCGGGAGG-UUGAACAUCCUGCAUAGUGCUGCCAGGAAAUCCC--UAUUUCAUACUAAG-A--GGGGCUGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCAGCCUACUUCGUCA
AAHX01113655.1/6710-6821     ACGGGGAGG-UUGAACAUCCUGCAUAGUGCUGCCAGGAAAUCCC--UACUUCAUACUAAGAG--GGGGCUGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCGGCCCACUUCGUCA
AAQQ01707153.1/1229-1340     GCCGGGAGG-UUGAACAUCCUGCAUAGUGCUGCCAGGAAAUCCC--UAUUUCAUACUAAGAG--GGGGCCAGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCGGCCCACUUCGUCG
Z75407.2/3338-3448           GCGGAGACU-UGUA-GGUUCUCCGCAACUCUGCCAGGAACCCCU--GAUAGUUGUUGCGCAA--GGGGCUGUCAGGUUGCAUGUGGGGGAUAGCCCACUUCUCCGCCUCCCCAGUCA
AAWR02039291.1/142114-142225 GCGGGGAGG-UUGAACAUCCUGCAUAGUGCUGCCAGGAAAUCCC--CAUUUUAUACUAAGAG--GGGGCUGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCCGCCCGCUUCAUCA
AAKN02056344.1/88521-88410   AGGGGGGAC-UUGUAGGUUCUCCGCAACUCGGCCAGGAAGCCCU--GAUAGUCGUUUCGCAA--GGGGCUGUCUGGCUGCAUGUGCGGGAUGGCCCACUUCUCGGCCUCCCCGGUCA
AC192993.3/32053-32163       GCCGGGAGG-UUGAACAUCCUGCAUAGUGCUGCCAGGAAAUCCC--UAUUUCAUAUAAGA-G--GGGGCUGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCAGCCCACUUCGUCA
AL808014.8/123489-123600     ACGAGGAGG-UUGAACAUCCUGCAUAGUGCUGCCAGGAAAUCCC--UACUUCAUACUAAGAG--GGGGCUGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCUGGCCCACUUCGUCA
CU856526.4/19058-19169       GCGGGGAGG-UUGAACAUCCUGCAUAGUGCUGCCAGGAAAUCCC--UAUUUUAUACUAAGAG--GGGGCUGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCUGCCCACAUCAUCG
AAGU03077096.1/884-774       GUGGAGACU-UGUA-GGUUCUCCGCAGCUCUGCCAGGAACCCCU--GGUAGUUGUUUCGCAA--GGGGCUGUCUGGCUGCAUGUGGGGAAUGGCCCACUUCUCUGCCUCCCCAGUCA
AAPE02002642.1/41916-41806   GCAGGGAGG-UUGAACAUCCUGCAUAGUGCUGCCAGGAAAUCCC--UAUUUAUACUAAGA-G--UGGGCUGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCUGCCCACUUCGUCG
AAEX03026796.1/214387-214496 GCAGGGAGG-UUGAACAUCCUGCAUAGUGCUGCCAGGAAAUCCC--UAUUUUAUACUAA--G--GGGGCUGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCCGCCCACUUCAUCG
AAQR03176722.1/33762-33872   GCGGGGAGG-UAGAACAUCCUGCAUAGUGCUGCCAGGAAAUCCC--UAUUUCAUACUAAA-G--GGGGCUGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCAGCUCCCUUCGUCA
AAGW02041448.1/56610-56721   GCAGGAAGG-UUGAACAUCCUGCAUAGUGCUGCCAAGAAAUCCC--UAUUUCAUACCAAGAG--GGGGCUGGCUGGUUGCAUAUGUAGGAUGUCCCAUCUCCCAGCCCACUUCAUCA
#=GC SS_cons                 :::<<<<<<.<---<<<<<<<<<<<<-<<<-<<<<<-----<<<..________________..>>>->>>>>----->>>>>>>>>>>>>>>--->>>>>>>::::::::::::::
#=GC RF                      GcgGgGagg.UuGAacaUcCucCacAGugCUGcCaGGAAauCCc..uAUuuuauauuaagAg..gGGGCuGgCuGGUUGcaUguGgaGgAuguCCCAccuCcCuGCCcaCuucGUCA
//
# STOCKHOLM 1.0

#=GF AC   RF00724
#=GF ID   mir-282
#=GF DE   microRNA mir-282
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   51.00
#=GF TC   53.20
#=GF NC   50.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000150;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF WK   Mir-282_microRNA_precursor_family
#=GF SQ   15


AAZO01006369.1/2671-2577       GAAGAAGCCGUUGGAAAAGCCUCUCCCAGGCUUUGUCUGUUUAAAUAAUUA---------AGACAAAGACAUAGCCUGGUAAAGGCUAAACUGAUGCUUCUUAU
AANI01013986.1/5805-5711       AAUUUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCAUUCGAUAU---------ACGGUCAGACAUAGCCUAUGAGAGGUUAGGUGUACCAAGGGGAC
AASV01000010.1/1373-1467       AGUUUCCUUUUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCAUUCGAAAG---------CCGAUCAGACAUAGCCUAUAAGAGGUUAGGUAUACCAAGGCGAA
AAFS01004981.1/3653-3558       AUGUGCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCAUUUGAAAA--------CCCGAUCAGACAUAGCCUAUAAGAGGUUAGGUGUACCAAGGAAGA
AADK01036842.1/1094-1185       AAUCGGGACUUUGACCUAGCCUCUCCUUGGCUUUGUCUGAACCGUUA--G----------UAGCUCAGACAUAGCCUGAUAGAGGUUACGUUUUGUCCCUUUCC
AAPT01020493.1/70677-70773     GAAUUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCACUUUUUCAA-------UUCAAUCAGACAUAGCCUAUGAGAGGUUAGGUGUACAAAUGGAUC
AAGE02015982.1/5597-5494       UCGCACAGGUGUAAUCUAGCCUCUCCUAGGCUUUGUCUGUUACCUUCCUUGGGAAUUCCACUAGCCAGACAUAGCCUGACAGAGGUUAGGUGAAAUCUGAAAAG
AAZX01009495.1/283-193         AUCGAGCGACGUGAUUUAGCCUCUCCUAGGCUUUGUCUGUCAGUGA---A----------AAAACGAGACAUAGCCUAGAAUAGGUUAGGUCGGGGCUCGUUCA
AAAB01008960.1/3551826-3551733 AGUAACAGAGCUAAUCUAGCCUCUUCUAGGCUUUGUCUGUACAGUUUCUG----------CAAACCAGACAUAGCCUGUCAGAGGUUAGGUGAAAUCUGCUAGC
AAJJ01000207.1/45613-45525     CACUGAGGUGUAGAGGUAGCCUCUCCUAGGCUUUGUCUGUGAAUUUG---------------GCCGAGACAUAGCCUGAUUGAGGCUAACUUUAGCCUUAGCAC
AAPP01019299.1/59627-59721     AAUUUCCUUAUAGAUCUAGCCUCUACUAGGCUUUGUCUGUGCAUUCGAAAG---------UCGAUCAGACAUAGCCUAUAAGAGGUUAGGUGUACCAAGGCGAC
AAPU01011488.1/130621-130527   CAUUUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCAUUUGAUAU---------AAGAUCAGACAUAGCCUAUGAGAGGUUAGGUGUAGCAAGGGGUC
AAQB01009652.1/11236-11325     UAUAUCCUUAUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCAUUU--------------GGAUUCAGACAUAGCCUAUGAGAGGUUAGGUGUACCAAGGAGAA
JN211061.1/1417-1511           AGUUUCCUUCUAAAUCUAGCCUCUACUAGGCUUUGUCUGUGCAUUCGAAAG---------CCGAUCAGACAUAGCCUAUAAGAGGUUAGGUGUACCAAGGCGAA
AADG06002953.1/100558-100468   ACAGAGUAACUUGAUUUAGCCUCUCCUAGGCUUUGUCUGUAUAUAA---A----------GAACGGAGACAUAGCCUAGAAUAGGUUAGGUCAGGGCUCGUUCA
#=GC SS_cons                   :::::<-------<<<<<<<<<<<--<<<<<<-<<<<<<____________........._____>>>>>>->>>>>>-->>>>>>>>>>>------->:::::
#=GC RF                        aauuaccuuaUuaAucuAgCCUcUcCuAGGCUUUGUCUgUgcAuUugauaa.........aaaaucAGACAUAGCCUauaAgAGGuUaggUguAaucugguuaa
//
# STOCKHOLM 1.0

#=GF AC   RF00725
#=GF ID   mir-iab-4
#=GF DE   microRNA mir-iab-4
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   47.00
#=GF NC   44.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000151;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila.
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010; [Epub ahead of print]
#=GF WK   Mir-iab-4_microRNA_precursor_family
#=GF SQ   8


AAAB01008850.1/675464-675547 GUGCCGCUUCAUGAACGUAUACUGAAUGUAUCCUGAGUGC----U-ACUUAUCCGGUAUACCUUCAGUAUACGUAACAAGAGGCGACAC
AAFS01000023.1/145076-145159 GUGCGACUUCGUAUACGUAUACUGAAUGUAUCCUGAGUGU----A-UCCUAUCCGGUAUACCUUCAGUAUACGUAACACGAGGAAACAC
AAJJ01001135.1/10616-10533   GUUAAACCCCCUGUACGUAUACUGAAUGUAUCCUGAGUGU----U-UUCUGUCCGGUAUACCUUCAGUAUACGUAACAGGAGGCCACAU
AASW01019415.1/3125-3208     GUGCGACCUCGUAAACGUAUACUGAAUGUAUCCUGAGUGU----A-UCCUAUCCGGUAUACCUUCAGUAUACGUAACACGAGAUAGCAC
AAGE02017255.1/44731-44648   GUACUGCUUCAUGAACGUAUACUGAAUGUAUCCUGAGUGC----U-AUCUAUCCGGUAUACCUUCAGUAUACGUAACAGGAGGCUGCAC
EU365400.1/852-939           GCGUCGCCUUCUGUACGUAUACUGAAUGUAUCCUGAGUGCGCGAU-UCUUGUCCGGUAUACCUUCAGUAUACGUAACAGAAGAUGACAC
M32109.1/1878-1961           GUGCGACCUCGUAAACGUAUACUGAAUGUAUCCUGAGUGU----A-UCCUAUCCGGUAUACCUUCAGUAUACGUAACACGAGAGAGCAC
AADG06003606.1/22467-22551   GUGAAACCCCCUGUACGUAUACUGAAUGUAUCCUGAGUGU----AUUUCUGUCCGGUAUACCUUCAGUAUACGUAACAGGAGGCUACAC
#=GC SS_cons                 ::::::::<<<<<<<<<<<<<<<<<<-<<<<-<<<--<<_...._.___>>-->>>->>>>->>>>>>>>>>>>->>>>>>::::::::
#=GC RF                      GUgcaaCcuccUGuaCGUaUaCUGaaUGUaUCCuGAGugu....u.uccuaUCCgGUAuACCuuCAGuAuACGuAaCAggaGguaaCAC
//
# STOCKHOLM 1.0

#=GF AC   RF00726
#=GF ID   mir-87
#=GF DE   microRNA mir-87
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   76.40
#=GF NC   52.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.00 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000152;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12812784
#=GF RT   Temporal regulation of microRNA expression in Drosophila melanogaster
#=GF RT   mediated by hormonal signals and broad-Complex gene activity.
#=GF RA   Sempere LF, Sokol NS, Dubrovsky EB, Berger EM, Ambros V
#=GF RL   Dev Biol. 2003;259:9-18.
#=GF RN   [2]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF RN   [3]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [4]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF WK   MicroRNA
#=GF SQ   8


AC093196.2/166565-166468     --ACACAUUUCAUUCGCGCCUGUAUCUUGCUGAACCGCUGCCA-UUAUGGCCAACGAUCC-GGUUGAGCAAAAUUUCAGGUGUGUGAGAAAUGUGUUUAGCA-
AAPP01015726.1/103265-103169 ---CAUAUUUCAUUCGCGCCUGUAUCUUGCUGAACCGUUACCG-AUAUGGCACAGAAUCC-GGUUGAGCAAAAUUUCAGGUGUGUGAGAAAUUUGUUAAGCA-
AAFS01000157.1/47452-47549   ---CAUAUUUCAUUCGCGCCUGUAUCUUGCUGAACCGUAGCCA-UAAUGGUCUUUCAUCCCGGUUGAGCAAAAUUUCAGGUGUGUGAGAAAUUUGUUAAGCA-
AAQB01006451.1/125766-125668 ---CAUAUUUCAUUCGCGCCUGUAUCUUGCUGAACCGUUACCAAUUGUGAUCUUCAUUUCCGGUUGAGCAAAAUUUCAGGUGUGUGAGAAAUUUGUGACGGU-
AANI01013753.1/102284-102383 --GCAUAUUUCAUUCGCGCCUGUAUCUUGCUGAACCGUUACAA-UUGAGACAUCUAAAUCCGGUUGAGCAAAAUUUCAGGUGUGUGAGAAAUUUGUAGCGGUA
AASV01010644.1/57-152        CGGCACAUUCA--UCGCGC-UGUAUCU-GCUGAACCGCUGCCA-UCAUGGCCAACGAUCC-GGGUGAGCAAAAUUUCAGGUGUGUGAGAAAUGUGUUUAGCA-
AAPQ01007348.1/296047-295950 --GCAUAUUUCAUUCGCGCCUGUAUCUUGCUGAACCGUUGCCA-UUAUGGCCUACGAUCC-GGUUGAGCAAAAUUUCAGGUGUGUGAGAAAUUUGUUUAGCA-
AAPT01021688.1/518352-518253 --GCAUAUUUCAUUCGCGCCUGUAUCUUGCUGAACCGUUACCA-UUGUGACAUCCAAAUCCGGUUGAGCAAAAUUUCAGGUGUGUGAGAAAUUUGUAGCGGCU
#=GC SS_cons                 ..:<<-<<<<<---<<<<<<<<-<<-<<<<<-<<<<<--<<<_.____>>>--------->>>>>->>>>>->>-->>>>>>>>--->>>>>->>:::::::.
#=GC RF                      ..gCauauuuCAUUCgCgCCuGUauCuuGCuGaaCCGuUgcCA.UuaUGgcauacaAuuCCGGuuGaGCaaAauUUCaGGuGuGUGAGaaauuuGUuaaGca.
//
# STOCKHOLM 1.0

#=GF AC   RF00727
#=GF ID   bantam
#=GF DE   microRNA bantam
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   67.20
#=GF NC   64.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00091
#=GF DR   MIPF; MIPF0000153;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17543122
#=GF RT   Computational and transcriptional evidence for microRNAs in the honey bee
#=GF RT   genome.
#=GF RA   Weaver DB, Anzola JM, Evans JD, Reid JG, Reese JT, Childs KL, Zdobnov EM,
#=GF RA   Samanta MP, Miller J, Elsik CG
#=GF RL   Genome Biol. 2007;8:R97.
#=GF RN   [2]
#=GF RM   20817720
#=GF RT   Functional shifts in insect microRNA evolution.
#=GF RA   Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S
#=GF RL   Genome Biol Evol. 2010;2:686-696.
#=GF WK   bantam_microRNA
#=GF SQ   11


AADE01000186.1/73475-73386   AUUUGACUACGAAACCGGUUUUCG------AUUUGGUUUGACUGUUUUUUAUACA---AGUGAGAUCAUUUUGAAAGCUGAUUUUGU--CAAUGAAUACCA
AAAB01008946.1/56994-57090   AUGUAAUCACAGAACCGGUUUUCAUUUUCGAUCUGACUUAUUUUUUUCACAAACA---AGUGAGAUCACUUUGAAAGCUGAUUUUGU-ACAAUUAAUUCAA
AAZX01004974.1/17134-17222   GUAUAUAGACGAAACUGGUUUUCA------CAAUGAUUUGACAGAUGUAUUUGAU---UCUGAGAUCAUUGUGAAAGCUGAUUUUGU--UCCGA-AUUCAG
AAWU01005949.1/119500-119406 AAGCAAUCACAGAACCGGUUUUCAUUUUCGAUCUGACUUAUUUGAUUUAACAG-----AGUGAGAUCAUUUUGAAAGCUGAUUUUGUACGGAGA-ACUCAA
AAGE02003301.1/208408-208314 AAGUAAUCACAGAACCGGUUUUCAUUUUCGAUCUGACUUAUUUGAUUUA-ACAAG---AGUGAGAUCAUUUUGAAAGCUGAUUUUGU-ACGGAG-AUUCCA
AAJJ01000881.1/39195-39283   UCAGCGAGACGAAACUGGUUUUCA------CAGUGAUUUGACAGAUAUAUUUGAU---UCUGAGAUCAUUGUGAAAGCUGAUUUUGU--UCAUU-AAUCAU
BAAB01089624.1/1303-1392     AAGGAACUACGAAACUGGUUUUCA------UAAUGAUUUGACAGAUUGUUUUGUA--UUCUGAGAUCAUUGUGAAAGCUAAUUUUGU--UCCUG-GUACAA
AAZO01005717.1/66950-67042   AAAGGAAAACGAAACUGGUUUUCA------CAAUGAUUUGCCAGAUAGUUUUUGUUAUUCUGAGAUCAUUGUGAAAGCUGAUUUUGU--UAUGGAACUCCA
AAPU01011505.1/2277-2366     AUUUGACUACGAAACCGGUUUUCG------AUUUGGUUUGACUGUUUUUUUAUAC--AAGUGAGAUCAUUUUGAAAGCUGAUUUUGU--CAAUG-AAUAAC
FJ485607.1/993-1082          AUUUGACUACGAAACCGGUUUUCG------AUUUGGUUUGACUGUUUUUCAUACA---AGUGAGAUCAUUUUGAAAGCUGAUUUUGU--CAAUGAAUACCA
AADG06002975.1/37219-37131   UAUCGAAAACGAAACUGGUUUUCA------CAAUGAUUUGACAGAUAGAUUCGAU---UCUGAGAUCAUUGUGAAAGCUGAUUUUGU--UGAAA-AGUCGA
#=GC SS_cons                 ::::::::<<<<<<-<<<<<<<<<......<--<<<<<<-<<<____________...>>>->>>>>>-->>>>>>>>>>->>>>>>..:::::.::::::
#=GC RF                      AaauaAuuACgaAACcGGUUUUCa......cuaUGauUUgacuGaUuuauuuaau...aguGAGauCAUUguGAAAGCUgAUUuuGU..uaaug.AuUCaa
//
# STOCKHOLM 1.0

#=GF AC   RF00728
#=GF ID   mir-81
#=GF DE   microRNA mir-81
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   67.10
#=GF NC   59.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00091
#=GF DR   MIPF; MIPF0000154;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   11679672
#=GF RT   An extensive class of small RNAs in Caenorhabditis elegans.
#=GF RA   Lee RC, Ambros V
#=GF RL   Science. 2001;294:862-864.
#=GF RN   [3]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   9


AAQA01000482.1/18100-18000     AAAAAAGUUGGUGGGGGCAGUAGGCCUUCACCAUGAUCUACAGAAUGCU---AUCAUUUUGAGUCUGAGAUCAUUGUGAAAGCUAUUUGCCUUCUACCGUCUCC
AAGD02002337.1/175857-175956   UAAAAAAGUUCUUCUAGCGACAGGUUUUCCCUGUGAUCUGCAGAGUACAA--AGAAAUACA--UCUGAGAUCAUCGUGAAAGCCAGUUGUUUCCAAGAACUCCU
AAGD02002337.1/178830-178730   ACUGCCCUCGUGGCCAGCAGUCGGUUUUCACCUUGAUCUG-AGAGCUAAA--CAUAAUGCUUAUCUGAGAUCAUCGUGAAAGCUAGUUGCAGGUACACAGGCUC
CAAC02000448.1/1314112-1314010 UAUGCCAUCGUGAUUAACGGUCGGUUUUCACCUUGAUCUG-AGAGCAAUAACCAGAAUGCUUAUCUGAGAUCAUCGUGAAAGCUAGUUGUUACUUCACUCGGCU
CAAC02000448.1/1311085-1311186 AUAAAAAGUUCUUCUAGCGACAGGUUUUCGCCGUGAUCUGCAGAGUUCCA--UGAAGAAAACAUCUGAGAUCAUCGUGAAAGCCAGUUGCUUAAGAGGACUCAU
FO080846.1/14198-14299         AGUGCCAUCGUGCCCAACAGUCGGUUUUCACCGUGAUCUG-AGAGCAAUC-CAAAAAUGCUUUUCUGAGAUCAUCGUGAAAGCUAGUUGUUGGUCUACGGGCUU
FO080846.1/18477-18379         GAAAUAGGUUCUUUUAGCAACCGGUUUUCUCUGUGAUCUACAGAAUGAC-----AGCUAAUCGUCUGAGAUCAUCGUGAAAGCCAGUUGUUUUUAUGAACUCUU
ABEG02000016.1/4017-4115       AAAAUAUGUUCUCCUAGCAACAGGUUCUCACUGUGAUCUGCAGAGUAUA---AAGCCUACA--UCUGAGAUCAUCGUGAAAGCCAGUUGCUUACGAACUAAAUU
ABEG02000016.1/7077-6979       AUUGCCAACGUGGUCAACAGUCGGUUUUCACCUUGAUCUG-AGAGCUAU---CUGAAUGCUA-UCUGAGAUCAUCGUGAAAGCUAGUUGUUGUUUCACAGGGCC
#=GC SS_cons                   ::::::::<<<<<--<<<<<<-<<<<<<<<<-<<<<<<<-<<<<<<<___.._____>>>--->>>>>>>>>>>->>>>>>>>>->>>>>>--->>>>>:::::
#=GC RF                        aaaaaaaucgcgcuuagCaacagGuuuUCaCcgUGAUCUGCAGAgcaaua..aaaAaugcuuaUCUGAGAUCAuCGuGAaagCcAguuGcuuuugcgcguucuu
//
# STOCKHOLM 1.0

#=GF AC   RF00729
#=GF ID   mir-278
#=GF DE   microRNA mir-278
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   61.00
#=GF TC   62.40
#=GF NC   60.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.00 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000155;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [2]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF WK   Mir-278_microRNA_precursor_family
#=GF SQ   9


AAGE02001172.1/33036-33136     UAAUGGUUCUGGUGCGAACGGACGAUAGUCUUCAGCGGCCGUGCAUUUGAUAGA-----AUUGGUCGGUGGGACUUUCGUCCGUUUGUAACCGCCGUUUGCGACGA
AAWU01001740.1/43930-44034     UUCUGGUCUUGGUGCGGACGGACGAUAGUCUUCAGCGACCGUGCCAU-UUGAAAACCCUUUGGGUCGGUGGGACUUUCGUCCGUUUGUAACCGCCAGUUGCAACGA
AANI01014820.1/6361-6262       UUUAUGGUACGGUGCGACCGGAUGAUGGUUCACAACGACCGUGCAUA-CUUUUA-----ACUGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAACGA
AAAB01008986.1/7850728-7850827 UAUACGGUACGGUACGGACGGACGAUAGUCUUCAACGACCGUUCCGU-UUGACA-----CGAGGUCGGUGGGACUUUCGUCCGUUUGUAAGGCCAGCUGCAUCGAG
AADE01012656.1/560-657         GUAAUGGUACGGUGCGACCGGACGAUGGUUCACAACGACCGUGUCUC-UUAAA------CU-GGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAGCGA
AAQB01007950.1/807758-807661   GUAAUGGUACGGUGCGACCGGAUGACGGUUCACAACGACCGUGUCAA-UUUUA------CU-GGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAACGA
AAPU01010248.1/305747-305847   UUUAUGGUACGGUGCGACCGGAUGAUGGUUCACAACGACCGUACAGUUUUUUCA-----ACGGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAACGA
AAPT01020762.1/231816-231717   CUGAUGGUACGGUGCGACCGGAUGACGGUUCACAACGACCGUGCUUA-UUUUUA-----ACUGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAGCGA
JN211059.1/1988-2085           GUAAUGGUACGGUGCGACCGGAUGAUGGUUCACAACGACCGUGUCAU-UUAAA-------CGGGUCGGUGGGACUUUCGUCCGUUUGUAACGCCAUUUGUCAACGA
#=GC SS_cons                   :::::<<<----<<<<<-<<<<<<<-<<<<<-<<-<<<<<_______.______.....___>>>>>->>>>>>>->>>>>>>->>>>>-->>>::::::::::::
#=GC RF                        uuaauGgcacGGUgCgaaCGGacGaUaGUccaCaaCGaCCGUgccuu.uUuaaA.....auuGGuCGGuGggACuUuCguCCGUuuGuAAcgcCauuUgucaacGA
//
# STOCKHOLM 1.0

#=GF AC   RF00730
#=GF ID   mir-277
#=GF DE   microRNA mir-277
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   72.70
#=GF NC   69.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000156;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing.
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF WK   Mir-277_microRNA_precursor_family
#=GF SQ   12


AAIZ01005963.1/2133-2034       UUGA--AGGUUUU--GGGUUGCGUGUCAGGAGUGCAUUUGCAC------UGAAACAUUC--------------UGAAGCUUGUAAAUGCACUAUCUGGUACGACAUUCC-AGAACGUACAAUCUU
AAGE02012646.1/3549-3655       AACU--UAGUUUU--GGAGUGCGUGUCAGAAGUGCAUUUACAU------AGGUAUUUCCCGU-------UUAGCAGUAUUUGUAAAUGCACUAUCUGGUACGACAUUCC-AGAAUCAACAAUCAU
AAZX01003771.1/6490-6590       UAGA--AGGCAGGCUGGGGCUCGUGCCAGAUGCGCGUUUACAC-----GAGAGCC-----------------CUGAAUACUGUAAAUGCACUAUCUGGUACGACAUCUCUCCUGCCGCCUCUCCU
AAJJ01000475.1/30018-29916     CGGA--ACGUGGU--GGGCUCCGUGCCAGAUGCGCGUUUACAC------UGCACCGUUCU-----------AAAGAAUUCUGUAAAUGCACUAUCUGGUACGACAGCCC-ACUACGUGCACUCGU
AAZO01001184.1/8581-8481       AAAU--CCGCGUC--GAAAUGCGUAUCAGAUGCGCGUUUACAA------GUUUUUUUUU-------------UAAUCAUCUGUAAAUGCACUAUCUGGUACGACAUUUC-GGUUUGCGAAUUCCU
AAAB01008859.1/3298972-3299077 UCCU--GAGUUUU--GGGGUACGUGUCAGAGGUGCAUUUACAU------CGAACUAUUCCA--------GUUGAGGUAUUUGUAAAUGCACUAUCUGGUACGACAUUCC-AGAAUCGAUAAUCGA
BAAB01014298.1/12019-12140     UUGAUUACGCCUC--GGGGUUCGUGCCAGGAGUGCGUUUGCAAAGAGGCCGACAUGUUUGCGUUAUUGCAAUGUUAACACUGUAAAUGCACUAUCUGGUACGACAUCCC-GGGGCGUGUAGCAAC
AAQB01008630.1/409672-409572   UUGA--AGGUUUU--GGGCUGCGUGUCAGGAGUGCAUUUGCAC------UGAAAAUUUC-------------UAAAAGCUUGUAAAUGCACUAUCUGGUACGACAUUCC-AGAACGUACAAUCUU
AAPT01018372.1/115739-115839   GAGA--CAGUUUU--GGGCUGCGUGUCAGGAGUGCAUUUGCAC------UGAAACAUUC-------------UGAAAGCUUGUAAAUGCACUAUCUGGUACGACAUUCC-AGAACGUACAAUCUU
AAWU01003689.1/17698-17805     CUCU--UAGUUUU--GGAGUGCGUGUCAGAAGUGCAUUUACAU------AGGUAUUUUCCCG------UUUAGCAGUAUUUGUAAAUGCACUAUCUGGUACGACAUUCC-AGAAUCAACAAUCAA
FJ485605.1/1009-1108           UUGA--AGGUUUU--GGGCUGCGUGUCAGGAGUGCAUUUGCAC------UGAAACUAUC--------------UGAAGCAUGUAAAUGCACUAUCUGGUACGACAUUCC-AGAACGUACAAUCUU
AFJA01006014.1/57581-57676     ACAG--GGCAGUU--GGGGCUCGUGCCAGAUGCGCGUUUACAC------GGGCCC------------------UGAAUACUGUAAAUGCACUAUCUGGUACGACAUCUC-UCCUGUCACCGCCAC
#=GC SS_cons                   ::::..::<<<<<..<<<<--<<<<<<<<<<<<<<<<<<<<<_......__________.............________>>>>>>>>>>>>->>>>>>>>>--->>>>.>>>>>::::::::::
#=GC RF                        uuga..aagcccc..GGggUuCGUgcCAGaaGuGCaUUUaCAc......uGaaauuUUc.............uuaaaauuUGuAAAuGCaCuAuCUGguACGACAccCC.ggggcguacAaUcau
//
# STOCKHOLM 1.0

#=GF AC   RF00731
#=GF ID   mir-155
#=GF DE   microRNA mir-155
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   58.00
#=GF TC   58.80
#=GF NC   52.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.64 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000157;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MiR-155
#=GF SQ   17


AF402776.1/238-302             CUGUUAAUGCUAAUCGUGAUAGGGGUUUUU-------GCCUCCAACUGACUCCUA-CA-UAUUAGCAUUAACAG
AAPN01114009.1/559-624         UCGUUAAUGCUAAUCGUGAUAGGGGUUUUC------UCUGUCUGACUGACCCCUG-CC-CGUUAGCAUUAGCAA
AANH01000396.1/166544-166481   AAGUUAAUGCUAAUCGUGAUAGGGGUUUU---------UCUUCAUCAGACACCUAACA-UGUUAGCAUUAGCUU
CAAE01014581.1/3640492-3640429 GAGUUAAUGCUAAUCGUGAUAGGGGUUGGC-------GGUUCCCA--GGCACCUAGCA-UGUUAGCAUUAGCUC
BAAF04006741.1/10216-10153     AUGUUAAUGCUAAUCGUGAUAGGGGUUGC---------AAUUAAUCUGACACCUAACA-UGAUAGCAUUAGCUU
AAVX01187381.1/1334-1270       GAUUUAAUGCUAAUUGUGAUAGGGGUUGUA-------AAUUUUGACCAGCUCCUA-CA-UGUUAGCAUUAGCUC
AY096003.1/159-223             CUGUUAAUGCUAAUUGUGAUAGGGGUUUUG-------GCCUCUGACUGACUCCUA-CC-UGUUAGCAUUAACAG
AANN01428292.1/2182-2119       CUGUUAAUGCUAAUCGUGAUAGGGGUUUU--------UACUUUGACUGACUCCUA-CA-UGUUAGCAUUAACAG
AAFR03036553.1/2910-2839       UUGUUAAUGCUAAUCGUGAUAGGGGUUUUUCUUUUUGACUUCGAACUGACUCCUA-CA-UGUUAGCAUUAACAG
AAWR02022821.1/16129-16193     CUGUUAAUGCUAAUCGUGAUAGGGGUUUUU-------ACCUCGGACUGACUCCUA-CA-UGUUAGCAUUAACAG
CU571081.7/40496-40433         GGUUUAAUGCUAAUCGUGAUAGGGGUUUA---------GUGCUGAUGAACACCUA-UGCUGUUAGCAUUAAUCU
AF182318.1/354-418             UUGUUAAUGCUAAUCGUGAUAGGGGUUUUU-------ACCUCUGAAUGACUCCUA-CA-UGUUAGCAUUAACAC
CAAB02000121.1/1558-1620       GAGUUAAUGCUAAUCGUGAUAGGGGUUGU----------UGGUUACAGGCACCUAGCA-UGUUAGCAUUAGCUU
AAWZ02018358.1/34180-34116     GCAUUAAUGCUAAUCGUGAUGGGAGUUUUU-------GUCUCUGGCUGACUCCUA-CA-UGUUGGCAUUGAAAA
AAGW02015109.1/10371-10307     CUGCUAAUCCUGCCUGUGAUAGGAGAUUUC-------AUCUCUGACAGACUUCUA-CA-UGUUAGCAUUAACAG
AAGU03032697.1/15972-15909     CUGUUAAUGCUAAUCGUGAUAGGGGUUUUU-------ACCUCAAGC-AACUCCUA-CA-UGUUAGCAUUAACAG
AAGW02039016.1/1519-1582       CUGCUAAUGCUAUUCUCGAUAGGAGUCUU--------UUCUCUGACAGAUUCUUA-CA-UGUUAACAUUAACAG
#=GC SS_cons                   :<<<<<<<<<<<<<--<<-<<<<<<<<___.......__________>>>>>>>>.>>.->>>>>>>>>>>>>:
#=GC RF                        uuguUAAUGCUAAUCGuGAUAGGgGuuUUu.......aucUCugACugaCuCCUA.Ca.UGUUAGCAUUAacag
//
# STOCKHOLM 1.0

#=GF AC   RF00732
#=GF ID   mir-305
#=GF DE   microRNA mir-305
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   70.10
#=GF NC   67.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000158;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17543122
#=GF RT   Computational and transcriptional evidence for microRNAs in the honey bee
#=GF RT   genome.
#=GF RA   Weaver DB, Anzola JM, Evans JD, Reid JG, Reese JT, Childs KL, Zdobnov EM,
#=GF RA   Samanta MP, Miller J, Elsik CG
#=GF RL   Genome Biol. 2007;8:R97.
#=GF RN   [2]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus.
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF WK   Mir-305_microRNA_precursor_family
#=GF SQ   14


AASW01038426.1/5288-5201       UGUCUCCCAUGUCUAUUGUACUUCAUCAGGUGCUCUGGUGUGUCUCG--UAACCCGGCACAUGCUGAAGUACACUCAAUAUGAGGCGAUU
AAZO01007192.1/28953-29038     UGGUCUUUACGUUGAUUGUACUUCAUCAGGUGCUCUGGUAGUUCUUA--AAUCCAGGCAUCUGGUGUAGUACUAUUAAUCU--AAGAUCU
AAPU01010637.1/244417-244330   UCUCCCCCAUGUCUAUUGUACUUCAUCAGGUGCUCUGGUGUCAGUGG--AAACCCGGCACAUGUUGAAGUACACUCAAUAUGCGGUGAUU
AADK01007727.1/11338-11424     ACCGCCGCACGCCCAUUGUACUUCAUCAGGUGCUCUGGUGAUCAUAG---UUCCAGGCGCUUGUUGGAGUACACUUACCGUGUCGGCGGU
AAWU01017841.1/823-910         AAUGUCACAUGUCUAUUGUACUUCAUCAGGUGCUCUGGUUGCUUUCG--AUACCCGGCACAUGUUGGAGUACACUUAAUGUGCUGACAGU
AAAB01008980.1/2241127-2241216 UUUGUCACAUGUCUAUUGUACUUCAUCAGGUGCUCUGGUGGAUUUGAGAAAACCCGGCACAUGUUGGAGUACACUCUAUGUGCUGACAAG
AAZX01002044.1/14551-14465     GAGGCUGCAUGUUAAUUGUACUUCAUCAGGUGCUCUGGUGAUUUUG---AUACCCGGUGCCUGUUGGAGCGCAAUUCAUAUGAUUGUGCC
AAJJ01000649.1/41392-41476     UCUGUCACAUGUCUAUUGUACUUCAUCAGGUGCUCUGGUAUACUUU----UUCCCGACACCUGUUGGAGUGCACUAAUUAUG-UGGCUCG
AAPT01020969.1/276028-276115   UGUCUCCCAUGUCUAUUGUACUUCAUCAGGUGCUCUGGUGUCACUCG--UAACCCGGCACAUGUUGAAGUACACUCAAUAUGCGGUGAUU
AAPP01015737.1/35950-36037     UGUCUCCCAUGUCUAUUGUACUUCAUCAGGUGCUCUGGUGUCCACCG--UAACCCGGCACAUGUUGAAGUACACUCAAUAUGAGGCGAAU
AAIZ01002385.1/22659-22572     UGUCUCCCAUGUCUAUUGUACUUCAUCAGGUGCUCUGGUGUGUCCUG--UAACCCGGCACAUGUUGAAGUACACUCAAUAUGUGGCGAAG
AAQB01006829.1/458206-458118   UGUCUCCCAUGUCUAUUGUACUUCAUCAGGUGCUCUGGUGUCCGUUU-GUAACCCGGCACAUGUUGAAGUACACUCAAUAUGUGGCGAUC
AC008354.3/37595-37682         UGUCUCCCAUGUCUAUUGUACUUCAUCAGGUGCUCUGGUGUGUCUCG--UAACCCGGCACAUGUUGAAGUACACUCAAUAUGAGGCGAUU
AEAC01002177.1/15555-15469     GAGGCUGCAUGUUAAUUGUACUUCAUCAGGUGCUCUGGUGAACUCG---AUACCCGGCACCUGUUGGAGCGCAAUUCAUAUGACUGUGCC
#=GC SS_cons                   :<<<<<<<<<<<----<<<<<<<<<<<<<<<<<-<-<<_________..___>>->>>>>>>>>>>>>>>>>>---->>>>>->>>>>>:
#=GC RF                        ucugcccCAugucuAUuGuaCUuCAcCAgGuGCUCUGGUguuuuUug..aaaCCcGGCaCcUGgUGaAGuaCacUuaauaUGagggcagu
//
# STOCKHOLM 1.0

#=GF AC   RF00733
#=GF ID   mir-296
#=GF DE   microRNA mir-296
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   73.30
#=GF NC   67.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.21 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000159;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   miR-296
#=GF SQ   12


AAFC03013470.1/95871-95794   AGGAC-CCUUCCGGAGGGCCCCC-CCCAAUCCUGUUGUGCUU-GGUUCAGAGGGUUGGGCGGAGGCUUUCCUGAAGG-GUCU
AADC01142343.1/121944-121865 AGGAC-CCUUCCAGAGGGCCCCCCCUCAAUCCUGUUGUGCCU-AAUUCAGAGGGUUGGGUGGAGGCUCUCCUGAAGGGCUCU
AL929537.17/90687-90766      AGGGC-CUUUCUGGAGGGCCCCCCCUCAAUCCUGUUGUGCUC-GCUUCAGAGGGUUGGGUGGAGGCUCUCCUGAAGGUGUCC
AANN01541123.1/984-904       AAGAGUCUUUCUAGAGGGC-CCCUGACAAUCCUUUUGUGCUCUAAUUCAGAGGGUUGAUAGGGAGCUCUCUGGAAAGGCUCU
ABDC01114716.1/6053-5974     AAGAC-CCUUCUAGAGGGCCCCUCCUCAAUCCUGUUGUACUA-GAUCCAGAGGGUUGGGCGGAGGCUCUCCUGAAGGCCUCU
AAIY01647257.1/5699-5630     ------CCUUCUGGGAGGCCCCUUUCCAAUCCUGUUGUGCCU-GGGUCAGAGGAUUGGGGAGAGGCUUUCCUGAAGG-----
AANG01240597.1/1468-1389     ACGGGUCCUUCCGGAGGGCC-CCCCCCAAUCCUGUUGUGCUC-AAUUCAGAGGGUUGGGUGGAGGCUUUCCUGAAAGGCUCG
AAPY01465435.1/668-589       AGGAC-CCUUCCGGAGGGCCCCCCCUCAAUCCUGUUGUGCUU-GGUUCAGAGGGUUGGGUGGAGGCUCUCCCGAAGGGCUCU
AAKN02054782.1/64637-64559   AGGGU-UCUUCCAGAGGGCCCCCCCUCAAUCCUGUUGUGCUA-AGUUCAGAGGGUUGGGUGGAGGCUCUCCAGAAGG-ACUC
AAWR02038939.1/5748-5671     AGGAC-UCUUCCGGAGGGCC-CCCCCCAAUCCUGUUGUGUUU-GAUUCAGAGGGUUGGGUGGAGGCUUUCCUGAAGG-CUCU
AAGU03078189.1/5617-5538     AGGAC-CCUUCUGGAGGGCCCCCCCUCAAUCCUGUUGUGCCU-GAUUCAGAGGGUUGGGUGGAGGCUUUCCUGAAGGGCUCU
AAEX03014051.1/107852-107775 AGGGC-UCUUCCGGAGGGC-ACCCCCCAAUCCUGUUGUGCUG-GAUUCAGAGGGUUGGGUGGAGGCUUUCCUGAAGG-GCUG
#=GC SS_cons                 :<<<<.<<<<<-<<<<<<<<<<<<<<<<<<<<<-<<<_____.____>>>>>>>>>>>>>>>>>>>>>>>>->>>>>->>>>
#=GC RF                      AgGgg.ccUUCugGaggGCCcCccccCAAuCCUGuUGUGCUu.gaUUCAgAGGgUUGggggGgGGCucuCcuGAAgggccCc
//
# STOCKHOLM 1.0

#=GF AC   RF00734
#=GF ID   mir-52
#=GF DE   microRNA mir-52
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   71.70
#=GF NC   40.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000160;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF WK   Mir-52_microRNA_precursor_family
#=GF SQ   5


AL023835.1/60854-60953         UCCAACUCUAACAGUCCACCCGUACAUAUGUUUCCGUGCUUGACAGCGAAGCUCAAUCACGUUACAAUGAAAGGGUAGCCGGUUAUUGAAGUUGGGUCUU
AAGD02004810.1/56-151          ACCCUCUACUACCGUCCACCCGUACAUAUGUUUCCGUGCUUGACA-UUGUGCUCAAUCACGUUACAAUAUAUGGGUCGCCGG---UCUUAGGCGGUUCUU
CAAC02000470.1/1061940-1062037 UCCCGCUCUGACAGUCCACCCGUACAUAUGUUUCCGUGCUUGACA-UAGAGCUCAAUCACGAUACAAUGAGCGGGUAGCCGGUCAUCG-AGUCGGAACAU
Z68760.4/4495-4396             CCCGAUUCUGACAGUCCACCCGUACAUUUGUUUCCGUGCUUGACUUCAAAGCUCAAUCACGGCACAAUAUAUGGGUCGCCAGUCAUUGUAGUCGGAAUUU
ABEG02004146.1/13598-13695     UUCGGCUCUGACAGUCCACCCGUACAUAUGUUUCCGUGCUUGACA-AUGAGUUCAAUCACGUCACAAUUUAUGGGUCGCCGGUCAUUG-AGUUGAACAUU
#=GC SS_cons                   :<<<<<<<<<<<-<-<-<<<<<<-<<<-<<<---<<<<-<<<<<_.____>->>>>->>>>-->>>>>>->>>>>>->->->>>>-->->>>>>>:::::
#=GC RF                        ucCggcucugaCaGUCCaCCCguAcauauGuUUCCGuGCuuGaCa.uagaGcuCaaUCaCGuuaCaauguacGGGuaGCCgGucaUuguagccGgaucuU
//
# STOCKHOLM 1.0

#=GF AC   RF00735
#=GF ID   mir-367
#=GF DE   microRNA mir-367
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   77.90
#=GF NC   67.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000162;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF WK   Mir-367_microRNA_precursor_family
#=GF SQ   13


AAHX01020222.1/16082-16015   CCGUCACUGCUGCUAAUCUGCAACUCUGUUGAGCACACACUGGAAUUGCACUUUAGCAAUGGUGAUGG
AAFR03016534.1/30777-30844   CCACUACUGUUGCUAACAUGCAACUCUGUUCUAUGUAAACGGGAAUUGCACUUUAGCAAUGGUGAUGG
AAPY01684075.1/7711-7646     CCGUCACUGUUGCUAGUGUGCAACUCUG-GGGACACGGC-UGGAAUUGCACUUUAGCAAUGGUGACGG
AC113952.9/51027-50960       CCGUCACUGUUGCUAACAUGCAACUCUGUUGAAUAGAAAUUGGAAUUGCACUUUAGCAAUGGUGAUGG
AAPN01081641.1/13870-13937   CCAUUACUGUUGCUAACAUGCAACUCUGUUAUGUAUAAACUGGAAUUGCACUUUAGCAAUGGUGAUGG
AANN01821362.1/2035-1968     CCACUACUGUUGCUAAUGUGCAACUCUGUUCAGUACCAAUUGGAAUUGCACUUUAGCAAUGGUGAUGG
AAIY01685397.1/7052-6985     CCACUACUGUUGCUAACAUGCAACUCUGUUCAAUUUAAAUUGGAAUUGCACUUUAGCAAUGGUGACGG
AALT01320989.1/82-15         CCACGACUGUUGCUAAUCUGCAACUCUGUUCAGCUCACACUGGAAUUGCACUUUAGCAAUGGUGAUGG
AAWR02019160.1/24457-24524   CCAUCACUGUUGCUAAUAUGCAACUCUGUUCAAUACAAACUGGAAUUGCACUUUAGCAAUGGUGACGG
AAKN02038884.1/104135-104068 CCGCCACUGUUGCUAGUGUGCAACUCUGCUGCGUGCACCCUGGAAUUGCACUUUAGCAAUGGUGACGG
AC106864.5/11031-10964       CCAUUACUGUUGCUAAUAUGCAACUCUGUUGAAUAUAAAUUGGAAUUGCACUUUAGCAAUGGUGAUGG
AAWZ02004954.1/27683-27750   CCUUUACUGUUGCUAAUGUGCAACUCUGUUAUGUAUAAUCUGGAAUUGCACUUUAGCAAUGGUGAUGG
AADN03003749.1/39886-39819   CUAAUACUGUUGCUAACAUGCAACUCUGUUGUAUAAAAAUUGGAAUUGCACUUUAGCAAUGGUGAUGG
#=GC SS_cons                 <<<-<<<<<<<<<<<<--<<<<<-<<<<-<________>->>>>->>>>>-->>>>>>>>>>>>->>>
#=GC RF                      CCgucACUGUUGCUAauaUGCAACUCUgUugaaUauAaacuGGAAUUGCACUuUAGCAAUGGUgAcGG
//
# STOCKHOLM 1.0

#=GF AC   RF00736
#=GF ID   mir-320
#=GF DE   microRNA mir-320
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   48.90
#=GF NC   47.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.00 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000163;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF WK   Mir-320
#=GF SQ   55


AL139142.10/89349-89268      AAAGUAACUAGAUUGGCCUUCUCUUCCCGGUCCUUCCUGGAG-U-UGG-GAAAAGCUGG--GUU----GA-GGGAGCGUUAAAAAAAAAUUA
ABDC01199707.1/8369-8288     AAAUGAGAAUGGUUGGCUUUCUCUUCCCGGUUCUUCCCAGAA-U-CGG-GAAAAGCUGG--GCU----AA-GAGAGUGGAGAAAAACAAAAA
AAIY01395053.1/6996-7062     ---------------GCCUUCUCUUCCCGGUUCUUCCCGGAG-U-CGG-GAAAAGCUGG--GUU----GA-GAGGGCGAAAAAAGAUGAGGG
AC091038.9/133705-133624     UGCAUUAAAAAUGAGGCCUUCUCUUCCCAGUUCUUCCCAGAG-U-CAG-GAAAAGCUGG--GUU----GA-GAGGGUAGAAAAAAAAUGAUG
ABDC01023147.1/176-96        UGGCAGGCCCCUUAGCC-UUCUCUUCCCAGUUCUUCCUGGAG-U-CGG-GAAAAACUAG--GAG----GG-GGGUGGAGGAGAAAAAAAGAA
ABDC01120233.1/908-827       CUUAAAGGGUUUCUGGCCUUCUCUUCUCAGUUCUUCCCAGAG-U-CAG-GAAAAGCUGG--GUU----GA-GAAGGCAAGAAAAAAACAACA
ABDC01287788.1/350-431       AAAUAAAAUUAUGAGAGCUUCUCUUCCUGGUUCUUCCCAGAA-U-UGG-GAAAAGCUGG--GUU----GA-GAAGGUAAAAAAAAAAAAAAA
ABDC01183875.1/2602-2521     AAAUGUUAGGAAGAGGCCUUCUCUUCCCAGUUCUUCCCGGAG-U-UGG-GAAAAGCUGG--GUU----GA-GGGAUGGUGGGGAGGAAGAUU
ABDC01268212.1/395-314       CAGGAAUAUAAAUUGGCCUUCUCUUCCCAGUUCUUCCAGGAG-U-UGG-GAAAAGCUGG--GUU----GA-GAGGGCAAAGAAAAAAGAAAA
ABDC01417450.1/2718-2799     AGACUGGCCUGGGCAGCCUUGUAUUCCUGGUUCUUCCCAGAG-U-UGG-GAAAAGCUGG--GUG----GA-GAGGGCGAGGAAGGGAAAAAA
AANU01166576.1/19424-19343   UAAACAUAUUUUAAGGCCUUCUCUUCCUGGUUUUUCCCAGAG-U-CAG-GAAAAGCUGG--ACU----GA-GAGGGCAAAAGGAAAAAACAA
ABDC01284545.1/2682-2601     AAAUAUAGUGUAUGGGCAUUCUCUUCCCGGUUCUUCCCGGAG-U-CAG-GAAAAGCUGG--GUU----GA-GAGGGCGAAAAAAAUUAACAA
AADC01148566.1/3420-3500     AAAUGUAUCAAUAAGCA-UUCUCUUCCCAGUUCUUCUUGGAG-U-CAG-GAAAAGCUGG--GUU----GA-GAGGAGCAGAAAAGAAAAAAG
ABDC01264990.1/524-443       ACAAAGGGGAGCUUGGCCUUCUCUUCCCAGUUCUUCCUGGAA-U-CAG-GAAAAGCUGG--GUU----GA-GAGGGCAAAAAAAAAAAAAAA
AANU01213722.1/4489-4404     AAAUAAUACUUCUGGGCCGUCUCUUCCUGGUUCUUCCCAGAG-U-CAG-GAAAACCUGG--AUUGAAAGA-GUGGUUUAAAAAAAAAAAAAA
ABBA01056241.1/284887-284967 AAUACAAUAAACUUCUU-UUCUCUUCCCUGGUCUUCCUGGAG-U-AAG-UAAAAGCUGG--AUU----GA-GAGGGUGAAACGACAACAACA
ABDC01304918.1/4988-5069     UAAAGAUACACAGAGGACUUUUCUUUCCAGUUCUUCCCAGAG-U-AGG-GAAAAGCUGG--AUU----GA-GAGGGCAGCAAAGAAAAAAAA
ABDC01114138.1/1771-1852     UACAAACACUGGGAGGCCUUCUCUUUCCAGUUCUUCCUGAAG-U-CGG-GAAAGGCUGA--GUU----GG-GGGGUGGGGGAGGAAUACAUU
ABDC01497176.1/772-854       UAAAACCUUCUUCUCAGCUUCUCUUCCUAGUUCUUCUGG-AG-U-CCG-GAAAAGCUGGUGGGG----GA-GAGGGGUGUUGGACAAAAACA
ABDC01019201.1/208-290       UAAAAAGUCUUUCUCGCCUUCUCUUCCCGAUUCUUCCUGGAA-U-CAG-GAAGAGCUGU--GUU----GAGGAAGGGAAAAUAAAAAGUAUC
ABDC01218323.1/525-445       AAUUUCUGCAAUAAGACUUUCUCUUCUCAGUUCUUC-UGGAA-U-CAG-GAAAAGCUGG--GUU----GA-GAAGGCAAAAAAAAAGAAUUU
ABDC01387161.1/2650-2569     AAGUUUGCUGCUUUGGCCUUCUCUUCCUGCUUCUUCCCGGAG-U-CGG-GAAAAACUGA--GUU----GA-GAGGGCGGGAAAAAAAAAAAA
ABDC01439707.1/377-296       UAGAAAAAUUCAUCCAGCUUCUCUUCCAGGUUCUUCCUGGAG-U-CAG-GAAAAGCUGG--UUU----GA-GAGGGGGAAAAAAAAAAAGAA
AANU01240291.1/12793-12712   AACUAGAUUGGCCUUGCCUUCUCUUCCCGGUUCUUCCUGGAG-U-UGG-GAAAAGCUGG--GUU----GA-GGGGGCAUUUAAAAAAUAAUA
ABDC01148153.1/3275-3194     AAAACUUAAAAUUCAGCCUUCUCUUCCCAGUUCUUCCCAGAG-U-CAA-GAAAAGCUGG--GUU----AA-GAGGGUGGAAAAAAAAAAAAA
AAYZ01017732.1/506-425       CUGCGUUUCCCCUCCGCCUUCUCUUCCCGGUUCUUCCCGGAG-U-CGG-GAAAAGCUGG--GUU----GA-GAGGGCGAAAAAGCUGGCUUG
ABDC01260937.1/591-510       UUAAAAAAAUUAGGAGCUUUCUCUCCCCAGUUCUUCCUGGAG-U-UGG-GAAAAGCUGG--GUU----GA-GAAGGUGAAAAAAAAAAAAAA
ABDC01272608.1/588-669       AAGUCAUGGACUGUGGCCUUCUUUCCCUAGUUCUUCCCAGAG-U-CUG-GAAAAUCUGG--GUU----GA-UAGGGCAAAAAUAUAUACAUA
AC188406.3/123881-123963     AAAUGAGAGUCCUCGGCCUUCUCUACCCAGUUCUUCCCAUAG-UCGGG-GAAAAGCUGG--GUU----GA-GAGGGCGAAAAAAAAAAAAAA
ABDC01258284.1/7200-7119     UAAUCUGCUUUAUCACCUUUCUCUUCCCGGUUCUUCCUGGAA-U-CAG-GAAAAACUGG--GUU----GA-GAGGGCAGGAAAAAAAAAUCU
ABDC01127582.1/5308-5389     UAAUUAAACUUUUAGGCCUUUUCUUCCCGGUUCUUCCCACAG-U-CAG-GAAUAGCUGG--GUU----GA-GAGGAAAAAUAAAAUUAAAAA
AANU01225385.1/6419-6500     GUAAGAAUAAUAAGGGUCUUCUCUUCCCAGUUCUUCCCAGAA-U-UGG-GAAAAGGUGG--AUU----GC-GGGGGGCAGAGACGAAGAGAA
AAFC03042574.1/60836-60755   AAAAACGAAAAAGAGGCCUUCUCUUCCCGGUUCUUCCCGGAG-U-CGG-GAAAAGCUGG--GUU----GA-GAGGGCGAAAAAGGAAGAGGG
AANN01464117.1/252-333       ACCUCGCCCCCCUCCGUCUUCUCUUCCCGGUUCUUCCCGGAG-U-CGG-GAAAAGCUGG--GUU----GA-GAGGGCGAAAAAAGAAGAGGA
AALT01227351.1/12789-12708   CCGCACUCCCCUUCCGCCUUCUCUUCCCGGUUCUUCCCGGAG-U-CGG-GAAAAGCUGG--GUU----GA-GAGGGCGAAAAAGGAAGAGCG
AAQQ01616155.1/1785-1866     CCUCGCUGCCCCUCCGCCUUCUCUUCCCGGUUCUUCCCGGAG-U-CGG-GAAAAGCUGG--GUU----GA-GAGGGCGAAAAAGGAUGAGGG
AC073389.10/66673-66592      AAAAUUAAAAAUUAGACUUUCUCUUCCUGGUUCCUAGCAGAG-U-CAG-GAAAAGCUUU--GUU----GA-GAGGGCGGGGUGAAAAAAACU
AC092809.2/84279-84199       AAUUCUGUCUCUUAGGCUUUCUCUUCCCAGAU-UUCCCAAAG-U-UGG-GAAAAGCUGG--GUU----GA-GAGGGCAAAAGGAAAAAAAAA
AL451048.13/22140-22059      CAAAUGUAUCAAUAAGCCUUCUCUUCCCAGUUCUUCUUGGAG-U-CAG-GAAAAGCUGG--GUU----GA-GAGGAGCAGAAAAGAAAAAAG
AY316117.1/70377-70296       AAAAGCCAAAACCUAGCCUUCUCUUCCUGGUUCUUCCUGAAG-U-CAG-GAAAAGCUGG--GUU----GA-GAGGAUGAAAUAUAAUAAUAA
AC185996.2/125842-125761     ACAUUAAAAAUGUUGGCCUUCUCGUCCCAGUUCUUCCCAAAG-U-UGA-GAAAAGCUGG--GUU----GA-GAGGAUGAAAAGAAAAAAAAA
EF445004.1/162621-162702     AAAAUGGCAUGACAGGCCUUCUCUUUCCAGUUCUUCCCAGAA-U-UGG-GAAAAGCUGG--GUU----GA-GAGGGUAAGAAAAGAAAAACA
AC008635.6/28164-28246       AAAUACCUCCAUGGGGCCUUCUCUUCCCAGUUCUUCCUGGAG-U-CGGGGAAAAGCUGG--GUU----GA-GAAGGUGAAAAGAAAAAACAA
AC005815.1/140174-140255     UCAAAAAUAAAUUAAUCCCUCUCUUUCUAGUUCUUCCUAGAG-U-GAG-GAAAAGCUGG--GUU----GA-GAGGGCAAACAAAUUAACUAA
AL590323.4/1289-1370         AAGAUCUUGACAUAAGCCUUCUCUUCUCAGUUCUUCCCCAAG-U-UAG-GAAAAGCUGA--GUU----GA-GAGGGGAAAAAAAAAUCUUAA
AAQR03081442.1/13914-13833   UUAAAAAAAAAAUAGGCCUUCUCUUCCCAGUUCUUCCCAGAG-U-CAG-GAAAAGCUGG--CUU----GA-GAGGAAGAAAAAAAGUCCUUA
AAQR03153470.1/136-214       AAGUCAUGGACUGUGACCUUCUUUU---AGUUCUUCCCAGAG-U-CUG-AAAAAGCUUG--GAU----GA-GAGAGCAAAAAAGAAAAUAAA
AAQR03054575.1/20654-20573   ACAAUGCUAUAAUCUCACUUCUCUUCCCAGUUCUCCCCAGA-GU-CGG-GAAAAGCUGA--GUU----GA-GAAGGGAAAAAAUAAAUGAUA
AAQR03106219.1/1742-1822     AAAAAAAAAAGUAGGGACUUCUCUUCCCGGUUCUGCCCUAAG-U-UGA-GAAAAGCUGG---UU----GA-GAGGAUGGAAAAACAUUACUG
AAQR03069578.1/1604-1684     CAAACAAACUGGGAGGCCUUCUCGUCCCAGUUCUUCCUGGAG-U-CAA-GAAAGGAUGA--G-U----GA-GACGGUAAGGGAAAAAAACAU
AABR05051681.1/28252-28333   GCCUCGCUGUCCUCCGCCUUCUCUUCCCGGUUCUUCCCGGAG-U-CGG-GAAAAGCUGG--GUU----GA-GAGGGCGAAAAAGGAUAUGGG
AAQR03042600.1/1678-1759     AAAGGAAAGAAAUAGGCCUUCUAUUCCUGGUUUUUCCCAGAG-U-UGG-GAAAAGCUGG--GUU----GA-GAAAGCAAAUAAAUAAAUAGA
AADA01205229.1/3012-3093     AAAAAAUACUUCAGGGCCGUCUCUUCCUGGUUCUUCCCAGAG-U-CAG-GAAAAACUGG--GUU----GA-AAGGGUGUUUAAAAAAAAAAC
AAQR03052516.1/37536-37617   ACAAAACACUUUUCAGCCUGCUCUUCCCGGUUCUUCCCUGAG-A-UGG-GAAAACCUGG--GUU----GA-GAGGGUGCCCUGUCCCAAAAG
ACBE01123145.1/11982-12063   GCCUCGCUCCCCUCCGCCUUCUCUUCCCGGUUCUUCCCGGAG-U-CGG-GAAAAGCUGG--GUU----GA-GAGGGCGAAAAAGGAAGAGGG
#=GC SS_cons                 :::::::::::::::::<<<<<<--<<<<<<<-<<<<<<___._.>>>.>>>->>>>>>..>--....>>.>>>>:::::::::::::::::
#=GC RF                      aAAaaaaacuuuuagGCCuUCUCUUCCcaGuUCUUCCcgGAG.U.cgG.GAAAAgCugG..GUU....GA.GAgGGugAaAAAAaAAAAaaA
//
# STOCKHOLM 1.0

#=GF AC   RF00737
#=GF ID   mir-322
#=GF DE   microRNA mir-322
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   79.80
#=GF NC   62.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000164;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   15325244
#=GF RT   Altered expression profiles of microRNAs during TPA-induced
#=GF RT   differentiation of HL-60 cells.
#=GF RA   Kasashima K, Nakamura Y, Kozu T
#=GF RL   Biochem Biophys Res Commun. 2004;322:403-410.
#=GF RN   [3]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF WK   Mir-322_microRNA_precursor_family
#=GF SQ   11


AAIY01107643.1/134-218       CGGGGGGAUGCAGCAGCAAAUUCAUGUUUUGGAGUGUUGUACAAAGUUCAAAACGUGAAGCGCUGCUACACCCCCUCGCGGGAAA
AAFC03117779.1/30433-30350   CGAGGGGAUGCAGCAGC-AAUUCAUGUUUUGAAGUGCUUUAAACGGUUCAAAACGUGAGGCGCUGCUAUACCCCCUUGCGAGGAA
AALT01307157.1/2319-2402     CGAGGGGAUGCAGCAGC-AAUUCAUGUUUUGAAGUGCUUUCAAAGAUUCAAAACGUGAGGCGCUGCUAUACCCCUUUGGGGGGAA
AADA01203598.1/1-80          ----GGGAUACAGCAGC-AAUUCAUGUUGUGAAGUGUUCUAAAUGGUUCAAAACGUGAGGCGCUGCUAUACCCCCUCGUGGGGAA
AAKN02053360.1/159470-159387 CGAGGGGAUGCAGCAGC-AAUUCAUGUUUUGAAGUAUUCUAAACUGUUCAAAACGUGAGGCGCUGCUAUACCCCCUCGUGGGAAA
AC004383.1/131269-131186     CGAGGGGAUACAGCAGC-AAUUCAUGUUUUGAAGUGUUCUAAAUGGUUCAAAACGUGAGGCGCUGCUAUACCCCCUCGUGGGGAA
AABR05185947.1/34859-34941   CGAAGGGAUGCAGCAGC-AAUUCAUGUUUUGGAGUAUUGCCAA-GGUUCAAAACAUGAAGCGCUGCAACACCCCUUCGUGGGAAA
AAPE02002186.1/131059-131142 CGAAGGGAUACAGCAGC-AAUUCAUGUUUUGAAGUGCUUUACAUAGUUCAAAACGUGAGGCGCUGCUAUACCCCCUCGAGGGGAA
AAGU03084141.1/55529-55446   CGAGGGGAUGCAGCAGC-AAUUCAUGUUUUGGAGUGCUCUACAAGGUUCAAAACGUGAGGCGCUGCUAUACCCCCUCGCGGAGAA
AAEX03026927.1/1385-1302     CGAGGGGAUGCAGCAGC-AAUUCAUGUUUUGAAGUGCUUUAAAUGGUUCAAAACGUGAGGCGCUGCUAUACCCCUUCGUGGGGAA
AAGW02046793.1/88303-88220   CGAGGGGAUGCAGCAGC-AAUUCAUGUUUUGAAGUGCUAUGAUUCAUUCAAAACGUGAGGCGCUGCUAUACCCCCUCGCGGGGAA
#=GC SS_cons                 <<<<<<<-<<-<<<<<<.--<<<<<<<<<<<<<-<<<_____>>>->>>>>>>>>>>>>-->>>>>>->>->>>>>>>:::::::
#=GC RF                      CGagGGGAugCaGCaGC.AAcuCauGuuuuGaaGcguUuUaaacgguuCaaaaCguGagGCGCuGCuAcaCCCCcuCGuGGGgAA
//
# STOCKHOLM 1.0

#=GF AC   RF00739
#=GF ID   MIR476
#=GF DE   microRNA MIR476
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   68.00
#=GF TC   70.10
#=GF NC   61.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000166;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15994906
#=GF RT   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa
#=GF RT   that are absent from Arabidopsis.
#=GF RA   Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL
#=GF RL   Plant Cell. 2005;17:2186-2203.
#=GF WK   MicroRNA
#=GF SQ   2


AARH01008219.1/136656-136748 GCUAGUAAUCCUUCUUUGCAAAGUCAUUUAUUAUUUUUCCUUCAAUUACUAUAAUCAAUGACUUUGCAAAGAUAGAUUUACUAGCUAAAUCUU
AARH01001853.1/174434-174342 GCUAGUAAUUCUUCUUUGCAAAAUCAUUAAUUAUCCUAGCUCUAAUUACUAUAAUUAAUGGCUUUGCAAAGAUAGAUUUACUAGCUAAAUCUU
#=GC SS_cons                 <<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<<<<--<<<______>>>-->>>>>>>>>>>>>>>>>>>>>>->>>->>>>>>>>::::::::
#=GC RF                      GCuaGuaaUcCuuCuuuGCaaagcCauugauuauuuuagCUuuAAcuaCUauaaucaauGgcuuuGCaaaGaUaGgUuuaCuaGCUAAAUCUU
//
# STOCKHOLM 1.0

#=GF AC   RF00740
#=GF ID   mir-370
#=GF DE   microRNA mir-370
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   68.70
#=GF NC   50.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.06 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000167;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15183728
#=GF RT   Human embryonic stem cells express a unique set of microRNAs.
#=GF RA   Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS,
#=GF RA   Moon SY, Kim VN, Kim KS
#=GF RL   Dev Biol. 2004;270:488-498.
#=GF WK   Mir-370_microRNA_precursor_family
#=GF SQ   6


AAYZ01216249.1/13302-13374 AGACAGAAAAGCUGGGUCACUUCUCUGCAGUUGCACAGCUCAUGAGUGCCUGCUGGCGUGGAAUCUG----CUC--UCU
ABDC01401092.1/3492-3570   AGACAGAGAGGCCAGGUCACGUCCCUGCAGUUACACAGCUCAUGAGUGCCUGCUGGGGUGGAACCUGGUCUGUCUGUCU
AAFC03050875.1/5952-6030   AGGCAGAGAAGCCAGGUCACGUCUCUGCAGUUACACCGCUCACGAGUGCCUGCUGGGGUGGAACCUGGUCUGUCUGUCU
AC121784.2/13792-13870     AGACGGAGAGACCAGGUCACGUCUCUGCAGUUACACAGCUCAUGAGUGCCUGCUGGGGUGGAACCUGGUUUGUCUGUCU
AC226390.3/2976-2898       AGACAGAGAAGCCAGGUCACGUCUCUGCAGUUACACAGCUCACGAGUGCCUGCUGGGGUGGAACCUGGUCUGUCUGUCU
AAGW02077265.1/5369-5446   AGACAGAGAGGCCAGGUCACGUCUCUGCAGUUGCACGGCUC-UGAGUGCCUGCUGGGGUGGAACCUGGUCAGUCUGUCU
#=GC SS_cons               <<<<<<<-<<<<<<<<<--<--<<<-<<<<-<<<-<<_____>>->>>->>>>->>>-->-->>>>>>>>>->>>>>>>
#=GC RF                    aGaCaGagaggCcaGGuCACgUCcCUGCaGUuaCACgGCUCAcGAGugCCuGCUGgGGUGGAaCCugGccuguCuGuCu
//
# STOCKHOLM 1.0

#=GF AC   RF00741
#=GF ID   mir-378
#=GF DE   microRNA mir-378
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   80.80
#=GF NC   51.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000168;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   8


ACBE01041034.1/733-792       ----CUCCUGACUCCAGGUCCUGUGUGUUACCUCGAAAUAGCACUGGACUUGGAGUCAGAAGGC--
AC022100.7/39101-39036       AGGGCUCCUGACUCCAGGUCCUGUGUGUUACCUAGAAAUAGCACUGGACUUGGAGUCAGAAGGCCU
AADA01026617.1/1519-1583     -GGGCUCCUGACUCCAGGUCCUGUGUGUUACCUAGAAAUAGCACUGGACUUGGAGUCAGAAGGCCU
AAWR02002261.1/122823-122758 AGGGCUCCUGACUCCAGGUCCUGUGUGUUACCUCGAAAUAGCACUGGACUUGGAGUCAGAAGGCCU
ABRO01277839.1/2055-1991     -GGGCUCCUGACUCCAGGUCCUGUGUGUUACCUCGAAAUAGCACUGGACUUGGAGUCAGAAGGCCU
AAQQ01293120.1/2430-2365     AGGGCUCCUGACUCCAGGUCCUGUGUGUUACCUCGAAAUAGCACUGGACUUGGAGUCAGAAGGCCU
AANU01185315.1/11930-11995   AGGGCUCCUGACUCCAGGUCCUGUGUGUUACCUCGAAAUAGCACUGGACUUGGAGUCAGAAGGCCU
AC153155.6/10103-10038       AGGGCUCCUGACUCCAGGUCCUGUGUGUUACCUCGAAAUAGCACUGGACUUGGAGUCAGAAGGCCU
#=GC SS_cons                 :<<-<<-<<<<<<<<<<<<<<---<<<<<<________>>>>>>->>>>>>>>>>>>>>->>->>:
#=GC RF                      AGGGCUCCUGaCUCCagGUCCUGUGUGuUaCCUcGAAAuAgCACUGGACuuGGAGuCAGAAGGCCU
//
# STOCKHOLM 1.0

#=GF AC   RF00742
#=GF ID   MIR162_2
#=GF PI   MIR162_1
#=GF DE   microRNA MIR162_2
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   60.10
#=GF NC   57.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000169;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12101121
#=GF RT   MicroRNAs in plants.
#=GF RA   Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP
#=GF RL   Genes Dev. 2002;16:1616-1626.
#=GF WK   MicroRNA
#=GF SQ   10


AB006708.1/30672-30582     CGCUGGAGGCAGCGGUUCAUCGAUCAAUUC-CUGUGAAUAUUUAUUUUUGUUUACAAAAG-------------------------------CAAGAAUCGAUCGAUAAACCUCUGCAUCCAGC
AARH01009108.1/35255-35165 CACUGGAGGCAGCGGUUCAUCGAUCUUUUC-CUGAAGAUUUUUUUGUUUUACACGAACAA-------------------------------CACGAACCGAUCGAUAAACCUCUGCAUCCAGU
AAAA02014213.1/20842-20957 C-CUGGGCGCAGUGGUUUAUCGAUCUCUUCCCUG------CCUUGUGCUGCUCCGAUCGAUGCCCGUGCUGAUUCUUGAUAAUAUACAACGCAGGAAUCGAUCGAUAAGCCUCUGCAUCCAGA
EF512306.1/364-454         CACUGGAGGCAGCGGUUCAUCGAUCUCUUC-CUGGGAAUUUGGUGUGAAAAAUCACAGAA-------------------------------CAUGAAUCGAUCGAUAAACCUCUGCAUCCAGC
AM451502.1/2540-2627       CACUGGAUGCAGCGGUUCAUCGAUCUCUUC-CUGAAA---UUGUUGUGAAAAAAGCAGAU-------------------------------CAAGAAUCGGUCGAUAAACCUCUGCAUCCAGC
AL357612.1/61691-61604     CGCUGGAGGCAGCGGUUCAUCGAUCUCUUC-CUGUGAACACAU---UAAAAAUGUAAAAG-------------------------------CAUGAAUAGAUCGAUAAACCUCUGCAUCCAGC
AARH01005287.1/78295-78385 CACUGGAGGCAGCGGUUCAUCGAUCUCUUC-CUGGCCAAUUUUUUGUUUAGCACGAAAAA-------------------------------CAUGAACCGAUCGAUAAACCUCUGCAUCCAGC
AASG02018381.1/677-582     CACUGGAGGCAGCGGUUCAUCGAUCUCUUC-CUGGAAGAUUUUGUUGUGAAACAAAAAUA--------------------------AAACGCAUGAAUCGAUCGAUAAACCUCUGCAUCCAGC
AC189332.2/56556-56647     UGCUGGAGGCAGCGGUUGAUCGAUCUCUUU-GUGGGAAUUUUUGAAAAACAAAAUUAAAA------------------------------GCAUGAACAGAUCGAUAAACCUGUGCAUCCAGC
AC137819.22/96449-96538    CACUGGAUGCAGCGGUUCAUCGAUCUGUUC-CUG--AAUUUUGUUUGUCUCGUAAAACAA------------------------------ACAUGAAUCGGUCGAUAAACCUCUGCAUCCAGC
#=GC SS_cons               ::<<<<<-<<<<-<<<<-<<<<<<<--<<<.-<<__________________________.............................._>>->>>-->>>>>>>->>>>->>>>->>>>>:
#=GC RF                    CaCUGGagGCAGcGGuUcAUCGAuCUcUUC.CUGgaaAuuuuuuuuuuuaaauagaaaaA..............................gCAuGAAUcGaUCGAUAAaCCUCUGCAuCCAGc
//
# STOCKHOLM 1.0

#=GF AC   RF00743
#=GF ID   mir-308
#=GF DE   microRNA mir-308
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   52.00
#=GF TC   54.40
#=GF NC   50.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000171;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus.
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF WK   MicroRNA
#=GF SQ   11


AASW01005636.1/598-536         CUCGCAGUAUAUUUUUGUG-UUUUGUUUCGUUUUGCAAC-----UCAAAUCACAGGAUUAUACUGUGAG
AAAB01008986.1/1063449-1063512 UUCGCAGUAUAUCCCUGUGAGUUUGCUACUU-UUCAAUGG----UCAAAUCACAGGAGUAUACUGUGAG
AAGE02006324.1/6463-6527       UUCGCGGUAUAUUCUUGUG-GCUUGAUGCAU-UUGAAAAAUC--UCAAAUCACAGGAGUAUACUGUGAG
AAWU01008421.1/27722-27788     UUCGCAGUAUAUUCUUGUG-GCUUGAUGUGU-UAGAAAUCGUGCUCAAAUCACAGGAGUAUACUGUGAG
AAPU01010142.1/147078-147139   CUCGCAGUAUAUUUUUGUG-UUUUGUUUAUU-AUAAAAA-----UCAAAUCACAGGAUUAUACUGUGAG
AADE01001573.1/8261-8200       CUCGCAGUAUAUUUUUGUG-UUUUGUUGUGU-CUGAAACG-----CAAAUCACAGGAUUAUACUGUGAG
AAQB01006264.1/2824-2886       CUCGCAGUAUAUUUUUGUG-UUUUGUUCAAU-UUGUCAAC----UCAAAUCACAGGAUUAUACUGUGAG
AAPP01018749.1/259662-259723   CUCGCAGUAUAUUUUUGUG-UUUUGUUUGGU-UUGAAAC-----UCAAAUCACAGGAUUAUACUGUGAG
AAPT01021578.1/175719-175657   CUCGCAGUAUAUUUUUGUG-UUUUGUUUAUU-UUUGAAAA----UCAAAUCACAGGAUUAUACUGUGAG
AAKO01000634.1/21607-21545     CUCGCAGUAUAUUUUUGUG-UUUUGUUUCGU-UUUGCAAC----UCAAAUCACAGGAUUAUACUGUGAG
AAIZ01001989.1/16305-16366     CUCGCAGUAUAUUUUUGUG-UUUUGUUGUGU-CUGAAACG-----CAAAUCACAGGAUUAUACUGUGAG
#=GC SS_cons                   <<<<<<<<<<<<<<<<<<<.<<<<<______.________...._>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                        cUCGCAGUAUAuUcuUGUG.uuUUGuUuugU.UUgaAAaa....UCAAauCACAggAuUAUACUGUGAg
//
# STOCKHOLM 1.0

#=GF AC   RF00744
#=GF ID   mir-361
#=GF DE   microRNA mir-361
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   92.00
#=GF NC   50.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000172;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues.
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF RN   [2]
#=GF RM   15538371
#=GF RT   A pancreatic islet-specific microRNA regulates insulin secretion.
#=GF RA   Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer
#=GF RA   S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M
#=GF RL   Nature. 2004;432:226-230.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [5]
#=GF RM   20668074
#=GF RT   Identification and analysis of expression of novel microRNAs of murine
#=GF RT   gammaherpesvirus 68.
#=GF RA   Zhu JY, Strehle M, Frohn A, Kremmer E, Hofig KP, Meister G, Adler H
#=GF RL   J Virol. 2010;84:10266-10275.
#=GF RN   [6]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   Mir-361_microRNA_precursor_family
#=GF SQ   5


AAHY01200939.1/6585-6654     GAAGCUUAUCAGAAUCUCCAGGGGUACUUAGUAUUUGAA-AAGUCCCCCAGGUGUGAUUCUGAUUUGUUUC
AALT01577813.1/141-211       GGAGCUUAUCAGAAUCUCCAGGGGUACUUGUACUUUGAAAAGGUCCCCCAGGUGUGAUUCUGAUUUGCUUU
AAWR02034316.1/233867-233797 GGAGCUUAUCAGAAUCUCCAGGGGUACUGAUAAUUUUAAAAAGUCCCCCAGGCGUGAUUCUGAUUUGCUUC
FP102371.5/56574-56504       GGAGCUUAUCAGAAUCUCCAGGGGUACUUAUAAUUUGAAAAAGUCCCCCAGGUGUGAUUCUGAUUUGCUUC
AAGW02041908.1/7575-7505     GGAGCUUAUCAGAAUCUCCAGGGGUACUUACAAUUUGAAAAAGUCCCCCAGGUGUGAUUCUGAUUUGCUUC
#=GC SS_cons                 <<<<<--<<<<<<<<<-<<-<<<<-<<<<___________>>>>->>>>->>--->>>>>>>>>-->>>>>
#=GC RF                      GgaGCUUaUCaGaaUCUCCAGGGGUaCuuAuAAUUUgAAAaaGuCCCCCAGGUGUGAuuCuGAuUUGCuuC
//
# STOCKHOLM 1.0

#=GF AC   RF00745
#=GF ID   mir-499
#=GF DE   microRNA mir-499
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   83.00
#=GF NC   53.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000173;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [2]
#=GF RM   16698962
#=GF RT   Cloning and expression of new microRNAs from zebrafish.
#=GF RA   Kloosterman WP, Steiner FA, Berezikov E, de Bruijn E, van de Belt J,
#=GF RA   Verheul M, Cuppen E, Plasterk RH
#=GF RL   Nucleic Acids Res. 2006;34:2558-2569.
#=GF RN   [3]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF RN   [4]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [5]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [6]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [7]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues.
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF WK   MicroRNA
#=GF SQ   19


AALT01096934.1/620-533       CCGGGCGGGUGGCCG-UUAAGACUUGCAGUGAUGUUUAACUCC-UCA-CACGUGAACAUCACAGCAAGUCUGUGCUGCUGCCUGUCCUCUU
AAIY01738857.1/91-1          CCGGGCGGGUGGCCGUUUAAGACUUGCAGUGAUGUUUAAACUUCUGUCCACGUGAACAUCACAGCAAGUCUGUGCUGCUUCUCGUCCCCAC
AAPN01135512.1/158-246       CUGGGGGGGCAGCGG-UUAAGACUUGUAGUGAUGUUUAGCUCA-UCUCCACGUGAACAUCACUGCAAGUCUGUGCUGCUUCUCCCCUCCUC
BAAF04004562.1/510-599       CUGGGGCUGAGACAG-UUAAGACUUGCAGUGAUGUUUAGGGCAAUGAUGACAUGAACAUCACUUUAAGUCUGUGCUGACUCUUCUCUUUUU
CR555298.10/129727-129639    CUGAGAGGGAGGCAG-UUAAGACUUGCAGUGAUGUUUAGAGAA-AUGUCACAUGAACAUCACUUUAAGUCUGUGCUGGCUCCUGUUCUGAG
AAFR03012197.1/530-442       CCGGGCGGGCAGCUG-UUAAGACUUGCAGUGAUGUUUAAUUCU-UCUCUAUGUGAACAUCACAACAAGUCUAUACAGUUUCCCGGCUCCAU
AANH01006124.1/24032-23943   CUGAGACGGAGGCAG-UUAAGACUUGCAGUGAUGUUUAGGGCAAUGAUCACAUGAACAUCACUCUAAGUCUGUGCUGGCUCCUCUCUCCUU
AANG01236757.1/1287-1374     CUGGGCGGGCGGCUG-UUAAGACUUGCAGUGAUGUUUAACUCC--UCUCUUGUGAACAUCACAGCAAGUCUGUGCUGCUUCCCGUCCGCAC
AAGV020171441.1/1913-2001    CUGGGCGGGUGGCCG-UUAAGACUUGCAGUGAUGUUUAACUCC-UCUGCAUGUGAACAUCACAGCAAGUCUGUGCUGCCUCCCGUCCCUAC
CR847953.10/25811-25900      AAGAGAGUGAGCCAG-UUAAGACUUGCAGUGAUGUUUAGGUAAUCUGACCCAUGAACAUCACUUUAAGUCUGUGCUGGCUCAGCUUUCACC
AAKN02039379.1/66044-66132   CUGGGCGGGCGGCUG-UUAAGACUUGCAGUGAUGUUUAAUUCC-UCUCCACGUGAACAUCACAGCAAGUCUGUGCUGCUUCCCGUCCCCAU
AC134996.3/177640-177728     UUGGGUGGGCAGCUG-UUAAGACUUGCAGUGAUGUUUAGCUCC-UCUCCAUGUGAACAUCACAGCAAGUCUGUGCUGCUGCCUGCCCCCAU
AC200084.7/132719-132631     UUGGGCGGGCAGCUG-UUAAGACUUGCAGUGAUGUUUAACUCC-UCUCCACGUGAACAUCACAGCAAGUCUGUGCUGCUUCCCGUCCCUAC
AL132825.35/10839-10927      UUGGGCGGGCGGCUG-UUAAGACUUGCAGUGAUGUUUAACUCC-UCUCCACGUGAACAUCACAGCAAGUCUGUGCUGCUUCCCGUCCCUAC
AAWZ02005874.1/63980-64069   UUGAGGGGGAGGCAG-UUAAGACUUGCAGUGAUGUUUAGAAAAUUUACUACAUGAACAUCACUUUAAGUCUGUGCUACUUCUUUCCUUAUC
CAAB02004652.1/105583-105494 CUGGGAUGGAGGCAG-UUAAGACUUGCAGUGAUGUUUAGGGCAAUGAUCACAUGAACAUCACUUUAAGUCUGUGCUGGCUCCUCUCCUCAU
AAPE02019276.1/61456-61544   CUGGGCGGGCGGCCG-UUAAGACUUGCAGUGAUGUUUAACUCC-UCUCCACGUGAACAUCACAGCAAGUCUGUGCUGCUUCCUGUCCCCGA
AAQR03054338.1/7644-7731     CUGGGCGGGCGGCUG-UUAAGACUUGCAGUGAUGUUUAACUCC--UCUCGCGUGAACAUCACGGCAAGUCUGUGCUGCUUCCCGUCCUCAG
AADN03007831.1/85999-85910   UUGAGGGAGCGGCAG-UUAAGACUUGUAGUGAUGUUUAGAUAAUGUAUUACAUGAACAUCACUUUAAGUCUGUGCUACUUCUCUCCUCAUU
#=GC SS_cons                 :::::::<<<<<<<<.---<<<<<<<--<<<<<<<<<<_____.________>>>>>>>>>>-->>>>>>>--->>>>>>>>:::::::::
#=GC RF                      cuGgGaGgGcggCaG.UUAAGACUUGCAGUGAUGUUuAaauca.uuuucAcgUgAACAUCACauCAAGUCUGUGCuGccgCcuguCuccau
//
# STOCKHOLM 1.0

#=GF AC   RF00746
#=GF ID   mir-454
#=GF DE   microRNA mir-454
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   71.20
#=GF NC   67.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000174;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [2]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   20733160
#=GF RT   Deep sequencing of the small RNA transcriptome of normal and malignant
#=GF RT   human B cells identifies hundreds of novel microRNAs.
#=GF RA   Jima DD, Zhang J, Jacobs C, Richards KL, Dunphy CH, Choi WW, Yan Au W,
#=GF RA   Srivastava G, Czader MB, Rizzieri DA, Lagoo AS, Lugar PL, Mann KP, Flowers
#=GF RA   CR, Bernal-Mizrachi L, Naresh KN, Evens AM, Gordon LI, Luftig M, Friedman
#=GF RA   DR, Weinberg JB, Thompson MA, Gill JI, Liu Q, How T, Grubor V, Gao Y,
#=GF RA   Patel A, Wu H, Zhu J, Blobe GC, Lipsky PE, Chadburn A, Dave SS
#=GF RL   Blood. 2010;116:e118-e127.
#=GF RN   [5]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [6]
#=GF RM   18256158
#=GF RT   MicroRNA profile of Marek's disease virus-transformed T-cell line MSB-1:
#=GF RT   predominance of virus-encoded microRNAs.
#=GF RA   Yao Y, Zhao Y, Xu H, Smith LP, Lawrie CH, Watson M, Nair V
#=GF RL   J Virol. 2008;82:4007-4015.
#=GF RN   [7]
#=GF RM   18469162
#=GF RT   A microRNA catalog of the developing chicken embryo identified by a deep
#=GF RT   sequencing approach.
#=GF RA   Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML
#=GF RL   Genome Res. 2008;18:957-964.
#=GF RN   [8]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF WK   Mir-454_microRNA_precursor_family
#=GF SQ   17


AAVX01227898.1/233-348       AGC--GGGUUACCCCGGCAGCUGAAACCCUAUCUAUAUUGCGUCUGCUUUGAAUUUCUGC-CUUAAGUAGUGCAAUAUCGCUUAUAGGGU----UUUGG-CCCCGGGUUCG---AGCAUCAAGAGCC
AAIY01209324.1/410-527       CUU--UUUAAUUACCAGAUCCCAGAAGCUUAUUGAUAUU--CUCUGCUGUGUAAAUAUCU-CUUGAGUAGUGCAGUAUUGCUUGUAGGCUAAAAACCCA-ACAUUGGGAAG---AACAGUGAGCAAG
BAAF04080581.1/3530-3641     CUC--CCCAGAGCCUUGCAGAUGGGACCCUAUCAAUGUUGCCUCUGCUCUCAGCAGCAUU-UCUCAGUAGUGCAAUAUUGCUUAUAGGGU----GUCGU-CUGUGGGGGAC---UACCUC----GUG
AAFR03045417.1/66257-66371   GUU--GAUAAUUAAUAGAUCCAUGAACCCUAUCAAUGUGGUCUCUGCUGUGUACAUAGCU--GUAAGUAGUGCAAUAUUGCUUAUAGGGU----UUUAG-UUUUUGGAAAG---AACAGUGGCCAAG
AC091299.2/31120-31004       UUGAGAAUUAAUCCUAAUUCUUGGGACCCUAUCAGUAUUGCCUCUGCUGUCCACUGUGUU--CAGAGUAGUGCAAUAUUGCUAAUAGGGU----UUUAG-GUUUUAGGUUG---UACCUUCAGUCAG
BX957246.7/151285-151170     GAU--AAAUGCAUCUUGCAGGCGAGACCCUAUCAAUAUUGCCUCUGCUUUUCUCACUGUUUAUGGAGUAGUGCAAUAUUGCUUAUAGGGU----CUUGA-CUUUAAGGCUAAUCUGCAAU----AUC
AANH01010010.1/101669-101555 GUC--CACGUGCCCUCGCAGAUGAGACCCUAUCAAUGUUGCCUCUGCUUUCACUUGAGUCAACAGAGUAGUGCAAUAUUGCUUAUAGGGU----CUUGC-CUGUGAGGGAGG-CUCCCCG----GGC
AAPN01410228.1/3072-2958     UGU--GGAUAUUACCAGAUCCUGGAACCCUAUCGAUAUUGUCUCUGCUGUGUAAAUAGCU--GUGAGUAGUGCAAUAUUGCUUAUAGGGU----UUUAG-UGUUUGGGAAA---ACCAUUGGGCAGA
AAVX01021344.1/1948-2058     ACU--UUUGACACUCAAGUACUGGGACCCUAUCGAUAUUGCCUCUGCUUUGUAGAUGGCU--GUGAGUAGUGCAAUAUUGCUUAUAGGGU----UUCAG-UGCUUGGGAAC---UUCAAC----AGU
AAQQ01354557.1/209-98        UCU--GUUUAUCACCAGAUCCUAGAACCCUAUCAAUAUUGUCUCUGCUGUGUAAAUAGCU--CUGAGCAGUGCAAUAUUGCUUAUAGGGU----UUUGG-UAUUUGGAAAG---AACAAUG---AGG
AAGV020132411.1/1224-1110    CCU--GUUUAUUACCAGAUCCUAGAACCCUAUCGAUAUUGUCUCUGCUGUGUAAAUAGCU--CUGAGUAGUGCAAUAUUGCUUAUAGGGU----UUUAG-UGUUUGGGAAG---AACAAUGGGCAGG
AAWR02012955.1/98530-98416   CCU--GUUAACCACCAGAUCCUAGAACCCUAUCGAUAUUGUCUCUGCUGUGUAAAUCGCU--CUGAGUAGUGCAAUAUUGCUUAUAGGGU----UUUGG-UGUUUGGGAAG---AACAAUGAGGAGG
AC099850.7/126354-126468     UCU--GUUUAUCACCAGAUCCUAGAACCCUAUCAAUAUUGUCUCUGCUGUGUAAAUAGUU--CUGAGUAGUGCAAUAUUGCUUAUAGGGU----UUUGG-UGUUUGGAAAG---AACAAUGGGCAGG
AC194680.6/59690-59576       UCU--GUUUAUCACCAGAUCCUAGAACCCUAUCAAUAUUGUCUCUGCUGUGUAAAUAGUU--CUGAGUAGUGCAAUAUUGCUUAUAGGGU----UUUGG-UGUUUGGGAAG---AACAAUGGGCAGG
ADDD01030165.1/4010-4124     UUC--C---UAACCUUAAGGAUGAGACCCUAUCAAUAUUGCCUCUGCU-UUUGUGCUCAG--GGUAGUAGUGCAAUAUUGCUUAUAGGGU----CUUUUCUUUUGAGGGUAUUCUUCAUGGAGAGAA
AAWZ02023259.1/25574-25460   CCU--GUGAGAACUCUGAGGAUAAGACCCUAUCAAUAUUGCCUCUGCUUCUGUGCUGGAU--UCAAGUAGUGCAAUAUUGCUUAUAGGGU----CUUUU-CUUUGGGGAGG---CGCUCUUCGUGGG
CAAB02012616.1/1355-1471     --UUCCCUGUGGCCUUACUGGUGAGACCCUAUCAAUGUUGCCUCUGCUUUCACAUGUGUUCACUCAGUAGUGCAAUAUUGCUUAUAGGGU----CUUGC-CUCUGAGGGCA---GACCUUCCUCAGA
#=GC SS_cons                 <<<..<-------<<<<---<<<<<<<<<<<<<<<<<<<<<--<<<<<____________..___>>>>>->>>>>>>>>--->>>>>>>....>>>>>.--->>>>----...----->---->>>
#=GC RF                      ccu..cuuuauuaCcagaugccgagACCCUAUCaAUaUUGcCUCUGCUuUguaaauaguU..uugAGUAGUgCAAuAUuGCUUAUAGGGU....cucgg.uuuuugGGaag...aaCauggagcagg
//
# STOCKHOLM 1.0

#=GF AC   RF00747
#=GF ID   mir-283
#=GF DE   microRNA mir-283
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   51.10
#=GF NC   49.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.59 -Z 549862.597050 CM SEQDB
#=GF CL   CL00094
#=GF DR   MIPF; MIPF0000175;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus.
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF RN   [2]
#=GF RM   12844358
#=GF RT   Computational identification of Drosophila microRNA genes.
#=GF RA   Lai EC, Tomancak P, Williams RW, Rubin GM
#=GF RL   Genome Biol. 2003;4:R42.
#=GF RN   [3]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF RN   [4]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [5]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [6]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [7]
#=GF RM   17543122
#=GF RT   Computational and transcriptional evidence for microRNAs in the honey bee
#=GF RT   genome.
#=GF RA   Weaver DB, Anzola JM, Evans JD, Reid JG, Reese JT, Childs KL, Zdobnov EM,
#=GF RA   Samanta MP, Miller J, Elsik CG
#=GF RL   Genome Biol. 2007;8:R97.
#=GF RN   [8]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing.
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF RN   [9]
#=GF RM   20817720
#=GF RT   Functional shifts in insect microRNA evolution.
#=GF RA   Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S
#=GF RL   Genome Biol Evol. 2010;2:686-696.
#=GF WK   MicroRNA
#=GF SQ   11


AAIZ01007486.1/1906-2003       CUCACGAUUCUCAAAGGUAAAUAUCAGCUGGUAAUUCUGGGAGCUAAGCAAGAU---AUGAAACACUCGGAAUUUCAGUUGGUAUCGACUUUUUUGAAUUG
AAAB01008851.1/1388883-1388790 AGUUCGACC--GAAAGGUAAAUAUCAGCUGGUAAUUCUAGGCUAUCAAUCCA-----UCGUGCAUCCCGGGAUUUCAGCUGAUAUCCACUUUUCCGUCGAG
AAZX01000006.1/24204-24295     CUGUCCAGUCACGUAGUCAAAUAUCAGCUGGUAAUUCUGGGAU----ACUUA-----UUAUGCAGCCCAGGAUUCUUGCUGGUAUCCGGUUACGAACUGGC
AAQB01006319.1/8842-8742       UAACGAAUUCUCAAAGGUAAAUAUCAGCUGGUAAUUCUGGGAGCUAUGCCUAGAUAUUUGAAACACUCGGAAUUUCAGUUGGUAUCGACUUUUUUGAAUUG
AAGE02004323.1/32427-32333     U--UCGACU--GAAAGGUCAAUAUCAGCUGGUAAUUCUGGGCUUACCCCACCGU--UAUACGCUUCCCGGAAUUCCAACUGAUAUCCACUUUUUAGUCGAG
AAWU01005348.1/2399-2495       UGUUCGGCU--GAAAGGUCAAUAUCAGCUGGUAAUUCUGGGCUUUCCAAACCCG--UUGUCGCUUCCCGGGAUUCCAACUGAUAUCCACUUUUUAGUCGAA
AAEU02002163.1/2268-2170       UACACGAUUCUCAAAGGUAAAUAUCAGCUGGUAAUUCUGGGAGCUAAGCCUAAA--UAUGAAACACUCGGAAUUUCAGUUGGUAUCGACUUUUUUGAAUUG
AAPT01019076.1/29962-29865     CACCCGAUUCUCAAAGGUAAAUAUCAGCUGGUAAUUCUGGGAGCAAUGCCAAAU---AUGAAACACUCGGAAUUUCAGUUGGUAUCGACUUUUUUGAAUUG
AAPP01015897.1/30328-30230     CACCUGAUUCUUAAAGGUAAAUAUCAGCUGGUAAUUCUGGGAGCUAUGCCUGAU--UAUGAAACACUCGGAAUUUCAGUUGGUAUCGACUUUUUCGAAUUG
AC010706.8/145153-145251       CACACGAUUCUCAAAGGUAAAUAUCAGCUGGUAAUUCUGGGAGCUAAGCCUAAA--UAUGAAACACUCGGAAUUUCAGUUGGUAUCGACUUUUUUGAAUUG
AADG06003899.1/23792-23703     UAAUCUGGUGAUGUAGUCAAAUAUCAGCUGGUAAUUCUGGGAUUUUGAC-----------AAUAACCCAGGAUUCUUGCUGGUAUCCGGCUACGAACUGGA
#=GC SS_cons                   ::::::::::::<<<<<<--<<<<<<<<<<<--<<<<<<<<_____________.._________>>>>>>>>->>>>>>>>>>>-->>>>>>::::::::
#=GC RF                        uauuCgAuUcucaaAgguAAAUAuCAGCuGgUAAUuCuGGGAuuUaaaccuaau..UaUgaaaaaCCCgGaAUUcCaGCUGgUAUCcacuUuuuaGaagug
//
# STOCKHOLM 1.0

#=GF AC   RF00748
#=GF ID   mir-433
#=GF DE   microRNA mir-433
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   85.00
#=GF TC   91.40
#=GF NC   48.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000177;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF RN   [2]
#=GF RM   15891114
#=GF RT   Clustering and conservation patterns of human microRNAs.
#=GF RA   Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A,
#=GF RA   Brownstein MJ, Tuschl T, Margalit H
#=GF RL   Nucleic Acids Res. 2005;33:2697-2706.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   19784364
#=GF RT   Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic
#=GF RT   stem cells and neural precursors.
#=GF RA   Goff LA, Davila J, Swerdel MR, Moore JC, Cohen RI, Wu H, Sun YE, Hart RP
#=GF RL   PLoS One. 2009;4:e7192.
#=GF WK   Mir-433
#=GF SQ   5


AAYZ01700633.1/78-170        CCCGGGAGAAGUACGGUGAGCCUGUCAUUAUUCAGAGAGGCGAGAUCCUCUGUGUUGAGCAGGAUCAUGAUGGGCUCCUCGGUGUUCUCCAGG
AY986480.1/1332-1240         CCGGGGAGAAGUACGGUGAGCCUGUCAUUGUUCAGAGAGGCUAGAUCCUCCUUGUUGAGAAGGAUCAUGAUGGGCUCCUCGGUGUUCUCCAGG
EU499599.1/674-766           CCGGGGAGAAGUACGGUGAGCCUGUCAUUAUUCAGAGAGGCUAGAUCCUCUGUGUUGAGAAGGAUCAUGAUGGGCUCCUCGGUGUUCUCCAGG
AAPE02047295.1/124925-124833 CCCGGGAGAAUUACGGUGAGCCUGUCAUUAUUCAGGGAGGCUAGAUCCUCUGUAUUGAGAAGGAUCAUGAUGGGCUCCUCGGUGCUCUCCAGG
AAGW02077263.1/414-506       CCCGGGAGAAGUACGGUGAGCCUGUCAUUAUUCAGAGAGGCUAGAUCCUCGCUGCUGAGAAGGAUCAUGAUGGGCUCCUCGGUGUUCUCCAGG
#=GC SS_cons                 ::::<<<<<----<<<-<<<<<<<<<<<--------<<<________>>>---------------->>>>>>>>>>>->>>---->>>>>:::
#=GC RF                      CCcGGGaGaAgUACGgUGaGCCuguCauUAUUCAGAGaGGCuAGAUCCuCugUguUGAGaAGGAUCauGaugGGCuCCuCGGUGuuCuCCAGG
//
# STOCKHOLM 1.0

#=GF AC   RF00749
#=GF ID   mir-208
#=GF DE   microRNA mir-208
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   61.10
#=GF NC   54.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.00 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000178;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA. 2003;9:175-179.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [4]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [5]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [6]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [7]
#=GF RM   16698962
#=GF RT   Cloning and expression of new microRNAs from zebrafish.
#=GF RA   Kloosterman WP, Steiner FA, Berezikov E, de Bruijn E, van de Belt J,
#=GF RA   Verheul M, Cuppen E, Plasterk RH
#=GF RL   Nucleic Acids Res. 2006;34:2558-2569.
#=GF WK   MiR-208
#=GF SQ   17


AAYZ01095204.1/9868-9789   UCUCCCCUCAGGGAAGCUUUUUGCUCGCAUUAUGUUUC---UCAUCCAAAUAUAAGACGAACAAAAGGUUUGUCUGAGAGCAG
AAFR03022197.1/70154-70233 UCUCCUCUCAGGGAAGCUUUUUGCUCGGGUUAUGUUUU---GGAUCUGAAUAUAAGACGAACAAAAGGUUUGUCUGUGUGCAG
AANH01005510.1/7154-7076   UUGUCUAGCAGAUCAGCUUUUUGUUUGUGUUAUGUUCA---UA-CUAAAAUGUAAGACGAACAAAAAGUUUGUCUGUUGGAUG
AAFR03022200.1/17966-18045 UCCUGUGACAGGUGAGCUUUUGGUCCGGGUUAUACCUG---AUGCAUGUGUAUAAGACGAGCAAAAAGCUCGUUGGUCGGAGG
BX000358.11/72775-72853    UCUACUGACAGAGAAGCUUUUUGUUUGUGUUAUGUUUA---UU-UUCAAAUGUAAGACGAACAAAAAGUUUUUCUGUUAGUAG
AAPN01031605.1/4571-4492   UCCUGUGACAGACAAGCUUUUGGCCCAGAUUAUACCUG---ACAUUCCCGUAUAAGACGAGCAAAAAGCUUGUUGGUCAGAGG
L15351.1/22841-22920       UCCUUUGACGGGUGAGCUUUUGGCCCGGGUUAUACCUG---ACACUCACGUAUAAGACGAGCAAAAAGCUUGUUGGUCAGAGG
BAAE01155469.1/5362-5284   UCGUCUGGCAGAUCAGCUUUUUGUUUGUGUUAUGUUCC---UA-CUACAAUGUAAGACGAACAAAAAGUUUUUCCGUUGGAUG
L12104.1/28954-29033       GCUCCUCUCGGGGAAGCUUUUUGCUCGCGUUAUGUUUC---UCAUCCGAAUAUAAGACGAACAAAAGGUUUGUCUGAGGGCUG
DQ227285.1/14652-14731     UCUCCUCUCAGGGAAGCUUUUUGCUCGCGUUAUGUUUC---UCAUCCGAAUAUAAGACGAACAAAAGGUUUGUCUGAGGGUAG
GU324919.1/21603-21682     UCCUGUGACGGGCGAGCUUUUGGCCCGGGUUAUACCUG---AUGCUCACGUAUAAGACGAGCAAAAAGCUUGUUGGUCAGAGG
DQ227286.1/13629-13708     UCCUGUGACGCAUGAGCUUUUGGCUCGGGUUAUACCUG---AUGCUCACGUAUAAGACGAGCAAAAAGCUUGUUGGUCAGAGG
CT025533.11/42898-42977    GCUCCUCUCAGGGAAGCUUUUUGCUCGCGUUAUGUUUC---UCAUCCGAAUAUAAGACGAACAAAAGGUUUGUCUGAGGGCUG
AF130771.1/159-238         UCUCCUCUCAGGGAAGCUUUUUGCUCGCGUUAUGUUUC---UCAUCCGAAUAUAAGACGAACAAAAGGUUUGUCUGAGGGCAG
CAAB02005568.1/9492-9414   UCGUCUAGCAGAUCAGCUUUUUGUUUGUGUUAUGUUCC---AA-CUAAAAUGUAAGACGAACAAAAAGUUUGUCUGUUAGGUG
AAWZ02031816.1/9825-9907   UCCUCUAACAAGGAAGCUUUUGGCUCGGGUUAUAUUUUAGAAUGGCAGUGUAUAAGACGAGCAAAAAGCUUGUUGGUUGGAGG
AAQR03175805.1/1765-1686   UCUCCUCUCAGGGAAGCUUUUUGCUCGAAUUAUGUUUC---UCAUUCAAAUAUAAGACGAACAAAAGGUUUGUCUGAGGGCAG
#=GC SS_cons               ::::<<<<<-<<<<<<<<<<<-<<-<<--<<<<<<___...________>>>>>>-->>->>->>>>>>>>>>>->>>>>:::
#=GC RF                    UCuucugaCAggcaAgCuUUUuGcUCGgGUUAuguUUc...uuauucaaauaUAAGACGAgCAAAAaGcUugucuGucagaaG
//
# STOCKHOLM 1.0

#=GF AC   RF00750
#=GF ID   mir-458
#=GF DE   microRNA mir-458
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   81.70
#=GF NC   63.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000179;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18469162
#=GF RT   A microRNA catalog of the developing chicken embryo identified by a deep
#=GF RT   sequencing approach.
#=GF RA   Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML
#=GF RL   Genome Res. 2008;18:957-964.
#=GF RN   [2]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF RN   [3]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF WK   MicroRNA
#=GF SQ   7


AANH01006599.1/90205-90129   GUGUGGACGGCAGCGCCAUUUUCAGAGCUAUAAGUGUGAAGU-GGUCAUAGCUCUUUAAAUGGUACUGCCGUGUGCAC
BAAF04063537.1/2161-2085     CUGCAGACUCCAGCGCCAUUUUCAGAGCUAUAAGUGUGAAGU-GAUGAUAGCUCUUUCAAUGGUACUGCAGUAAGCAU
CAAE01013759.1/80040-80116   GUGCAGACGGCAGCGCCAUUUUCAGAGCUAUCAGUGCCAGCG-GGUCAUAGCUCUUUAAAUGGUUCUGCUGUAGGCAC
BX322629.9/12571-12494       GUGCAGAUAGCAGCGCCAUUUACAGAGCUAUAAGCAUCAUAGUUGUCAUAGCUCUUUGAAUGGUACUGCCAUAUGCAC
AADN03006674.1/322433-322356 GUGCAGAUGGCAGCGCCAUUUUCAGAGCUAUAAACAGCGUCAUUGUCAUAGCUCUUUGAAUGGUACUGCCAUAUGUAC
CAAB02019872.1/7521-7596     CUGCAGACAGCAGCGCCAUUUUCAGAGCUAUCAGU--CAACGUGGUCAUAGCUCUUUAAAUGGUACUGCUGUAGGCAC
AAWZ02012080.1/11427-11350   GUGCAGAUGGCAGCGCCAUUUUUGGAGCUAUAAACACUCUCACUGUCAUAGCUCUUUGAAUGGUACUGCCAUAUGUAC
#=GC SS_cons                 <<<<--<<<<<<<-<<<<<<<--<<<<<<<<________________>>>>>>>>-->>>>>>>->>>>>>>-->>>>
#=GC RF                      gUGCAGAcgGCAGCgCCAUUuUCaGAGCUAUAAguaucaacaugGUcAUAGCUCuUUaAAUGGuACUGCcgUAuGCAc
//
# STOCKHOLM 1.0

#=GF AC   RF00751
#=GF ID   mir-12
#=GF DE   microRNA mir-12
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   58.00
#=GF TC   59.30
#=GF NC   55.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.51 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000181;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20075255
#=GF RT   Functional and evolutionary insights from the genomes of three parasitoid
#=GF RT   Nasonia species.
#=GF RA   Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK,
#=GF RA   Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK,
#=GF RA   Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA,
#=GF RA   Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM,
#=GF RA   Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN,
#=GF RA   Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P,
#=GF RA   Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D,
#=GF RA   Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG,
#=GF RA   Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards
#=GF RA   R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach
#=GF RA   D, Gibson JD, Gilbert DG, Graur D, Grunder S, Hagen DE, Han Y, Hauser F,
#=GF RA   Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM,
#=GF RA   Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim
#=GF RA   J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R,
#=GF RA   Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA,
#=GF RA   Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA,
#=GF RA   Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV,
#=GF RA   Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA,
#=GF RA   Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R,
#=GF RA   Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson
#=GF RA   J, Rosenberg M, Sackton TB, Sattelle DB, Schluns H, Schmitt T, Schneider
#=GF RA   M, Schuler A, Schurko AM, Shuker DM, Simoes ZL, Sinha S, Smith Z, Solovyev
#=GF RA   V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y,
#=GF RA   Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW,
#=GF RA   Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin
#=GF RA   F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA
#=GF RL   Science. 2010;327:343-348.
#=GF RN   [2]
#=GF RM   20817720
#=GF RT   Functional shifts in insect microRNA evolution.
#=GF RA   Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S
#=GF RL   Genome Biol Evol. 2010;2:686-696.
#=GF WK   MicroRNA
#=GF SQ   7


AASS01036731.1/488-415     UACGGUUGAGUAUUACAUCAGGUACUGGUGUGCCUGAAAUCCAACAACCAGUACUUGUGUCAUACUACGCCGUG
AAZX01000006.1/25515-25586 AGGGUGUGAGUAUUACAUCAGGUACUGGUGU--CUUUUUUUCAGCGACCAGUACUUGUGUUAUACUUGCGUUCG
AAJJ01005828.1/1033-1102   AGGGUUUGAGUAUUACAUCAGGUACUGGUUCGGU----UUUGAAAAACCGGUCCCUGAGUAACACUUACAUUCU
AADE01000788.1/13719-13792 UACGGCUGAGUAUUACAUCAGGUACUGGUGUGCUUUAAAUCCAACAACCAGUACUUAUGUUAUACUACGCCGUG
AAPT01019076.1/28140-28067 UACGGUUGAGUAUUACAUCAGGUACUGGUGUGCCAUUUAACCAACAACCAGUACUUAUGUCAUACUACGCCGUG
AAKO01004048.1/21405-21478 UACGGUUGAGUAUUACAUCAGGUACUGGUGUGCCUGAAAUCCAACAACCAGUACUUGUGUCAUACUACGCCGUG
AELG01001534.1/18803-18733 UGGGUGUGAGUAUUACAUCAGGUACUGGUGUGAU---AUUCAGACAACCAGUACUUGUGUUAUACUUACGCUCA
#=GC SS_cons               <<<<<<--<<<<<-<<<<-<<<<<<<<<<<<____________>>->>>>>>>>>>>>>>->>>>>-->>>>>>
#=GC RF                    cgcGggUGAGUaUUACauCAgGuACuGGUGuGcuuuaaaUccAaCAACCaGUaCuUguGUuAuACUaaccCgcg
//
# STOCKHOLM 1.0

#=GF AC   RF00752
#=GF ID   mir-14
#=GF DE   microRNA mir-14
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   72.00
#=GF TC   73.90
#=GF NC   65.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000182;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [2]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus.
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF WK   Mir-14_microRNA_precursor_family
#=GF SQ   6


AAFS01000078.1/28520-28458     UGUGGGAGCGAGACGGGGACUCACUG------UGCUUUUGAAG-UAGUCAGUCUUUUUCUCUCUCCUAUA
AAGE02012112.1/774-706         UGUGGGAGCGAGAUUAAGGCUUGCUGGUCAUUUAUUACACUCG-AAGUCAGUCUUUUUCUCUCUCCUAUU
AAAB01008984.1/6108898-6108965 UGUGGGAGCGAGAUUAAGGCUUGCUGGUUAU-CACGUUAAACG-UAGUCAGUCUUUUUCUCUCUCCUAUC
AAQB01006270.1/561771-561833   UGUGGGAGCGAGACGAGGACUCACUG------UGCUUUUUAUA-UAGUCAGUCUUUUUCUCUCUCCUAUA
AASS01019587.1/1264-1325       UGUGGGAGCGAGACGGGGACUCACUG------UGCUUAUUAAA-UAGUCAGUCUUUUUCUCUCU-CUAUA
AAWU01029067.1/5309-5242       UGUGGGAGCGAGAUUAAGGCUUGCUGGUUU--CACGUUCGAGUAAAGUCAGUCUUUUUCUCUCUCCUAUU
#=GC SS_cons                   <<<<<<<<-<<<<--<<<<<<-<<<<____..___________.>>>>->>>>>>-->>>>->>>>>>>>
#=GC RF                        uGUGGGAGCGAGAuuaaGaCUuaCUgGUua..UaCuUuuuAag.uAGuCAGuCuuUUUCUCUCUCCUAUa
//
# STOCKHOLM 1.0

#=GF AC   RF00753
#=GF ID   mir-503
#=GF DE   microRNA mir-503
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   56.00
#=GF TC   57.20
#=GF NC   51.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000183;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction
#=GF RT   method.
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   19196471
#=GF RT   Cloning, characterization and expression analysis of porcine microRNAs.
#=GF RA   Reddy AM, Zheng Y, Jagadeeswaran G, Macmil SL, Graham WB, Roe BA, Desilva
#=GF RA   U, Zhang W, Sunkar R
#=GF RL   BMC Genomics. 2009;10:65.
#=GF RN   [5]
#=GF RM   19917043
#=GF RT   MicroRNA identity and abundance in porcine skeletal muscles determined by
#=GF RT   deep sequencing.
#=GF RA   Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C,
#=GF RA   Thomsen B
#=GF RL   Anim Genet. 2010;41:159-168.
#=GF RN   [6]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF RN   [7]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [8]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [9]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [10]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction
#=GF RT   method.
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [11]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   Mir-503_microRNA_precursor_family
#=GF SQ   14


AAHX01102601.1/60779-60849   UGCCCUAGCAGCGGGAACAGUACUGCAGUGAGUGUUUGGUGCCCUGGAGUAUUGUUUCCGCUGCCUGGGUA
AANN01675780.1/1012-1082     UGCCCUAGCAGCGGGAACAGUACUGCAGUAAGCGAUCAGGGCUCUGGAGUAAUGUUUCUGCCGCUUGAGCA
AAIY01107643.1/326-392       UGCCCUAGCAGCGGGAACAGUACUGCAGUGAAUAC----UAGUCUGGAGUAUUGUUGCUGCUGCCCUGGCA
CR380839.1/11557-11627       UGCCCUAGCAGCGGGAACAGUUCUGCAGUGAGCGAUCGGUGCUCUGGAGUAUUGUUUCCGCUGCCAGGGUA
AALT01307157.1/2625-2695     UGCCCUAGCAGCGGGAACAGUACUGCAGUGAGUAAUCUGUACCCUGGAGUAUUGUUUCUGCUGCCCGGGCA
AAFC03117779.1/30081-30011   UGCCCUAGCAGCGGGAACAGUACUGCAGUGGGCAAUUGGUGAUCUGGAGUAUUGUUUCUGCUGCCCGGGCA
ABDC01117506.1/5521-5451     UGCCCUAGCAGCGGGAACAGUACUGCAGUGAGUGAUCAGUGCUCUGGAGUAUUGUUGCUGCUGCCAGGGUA
AAGV020284257.1/2168-2098    UGCCCUAGCAGCGGGAACAGUACUGCAGCAGGUGAUUGGUGCUCUGGGGUAUUGUUCCUGCUGCCUGGGCA
AAWR02034053.1/1603-1533     UGCCCUAGCAGCGGGAACAGUACUGCAGUGGGCGAUCGGUGCUCUGGAGUAUUGUUCCUGCUGCCCGGGCA
AAKN02053360.1/159109-159039 UGCCCUAGCAGCGGGAACAGUACUGCAGUGAGGGAUUUGUGCUCUGGAGUGUUGUUUCUGCUGCCAGGGCA
AC004383.1/130956-130886     UGCCCUAGCAGCGGGAACAGUUCUGCAGUGAGCGAUCGGUGCUCUGGGGUAUUGUUUCCGCUGCCAGGGUA
CU468475.7/117225-117155     UGCCCUAGCAGCGGGAACAGUACUGCAGUGGGCGAUCGGUACUCUGGGGUAUUGUUUCUGCUGCCCGGGCA
AAGU03084141.1/55286-55218   UGCCCUAGCAGCGGGAACAGUACUGCAGCGGGCGCUC--GGCUCUGGAGUAUUGUUGCCGCUGCCCGGGCA
AAPE02002186.1/131373-131443 UGCCCUAGCAGCGGGAACAGUACUGCAGUGGGUUAUCCGUAUUCUGGAGUAUUGUUUCUGCUGCCCGGGUA
#=GC SS_cons                 <<<<<--<<<<<<<<<<<<<<<<<-<<<---<<<_____>>>->>>->>>>>>>>>>>>>>>>>-->>>>>
#=GC RF                      UGCCCUAGCaGCgGgAACAguaCuGCAGUGagcgAUcgGcgcUCUGGaGuauUGUUcCcGCuGCCuGGGCA
//
# STOCKHOLM 1.0

#=GF AC   RF00754
#=GF ID   mir-279
#=GF DE   microRNA mir-279
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   62.00
#=GF TC   62.40
#=GF NC   59.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00095
#=GF DR   MIPF; MIPF0000184;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [2]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus.
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF RN   [3]
#=GF RM   20817720
#=GF RT   Functional shifts in insect microRNA evolution.
#=GF RA   Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S
#=GF RL   Genome Biol Evol. 2010;2:686-696.
#=GF RN   [4]
#=GF RM   20075255
#=GF RT   Functional and evolutionary insights from the genomes of three parasitoid
#=GF RT   Nasonia species.
#=GF RA   Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK,
#=GF RA   Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK,
#=GF RA   Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA,
#=GF RA   Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM,
#=GF RA   Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN,
#=GF RA   Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P,
#=GF RA   Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D,
#=GF RA   Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG,
#=GF RA   Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards
#=GF RA   R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach
#=GF RA   D, Gibson JD, Gilbert DG, Graur D, Grunder S, Hagen DE, Han Y, Hauser F,
#=GF RA   Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM,
#=GF RA   Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim
#=GF RA   J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R,
#=GF RA   Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA,
#=GF RA   Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA,
#=GF RA   Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV,
#=GF RA   Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA,
#=GF RA   Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R,
#=GF RA   Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson
#=GF RA   J, Rosenberg M, Sackton TB, Sattelle DB, Schluns H, Schmitt T, Schneider
#=GF RA   M, Schuler A, Schurko AM, Shuker DM, Simoes ZL, Sinha S, Smith Z, Solovyev
#=GF RA   V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y,
#=GF RA   Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW,
#=GF RA   Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin
#=GF RA   F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA
#=GF RL   Science. 2010;327:343-348.
#=GF WK   Mir-279_microRNA_precursor_family
#=GF SQ   12


AAPP01019575.1/159482-159391 UACUACUACUGUUUUUAGUGGGUGAGG-GUCCAGUGUUUCACAUUGAUUUCUG----UAUUUGUGACUAGAU-CCACACUCAUUAAUAACGGUA---GUUC
AAJJ01000015.1/255293-255381 AAUUUGAUCCGUUCUUGAUGGGUUCGG-GUCUAGUGG--CACGGUUUUUUCA-----ACUUCGUGACUAGAU-CCACACUCAUUAAGGAAGUUU---CACA
AAGE02017556.1/117017-116925 CAUCCCAACGGUUGUCGAUGGGUGUGA-AUCUAGUGUUUCACAUGAUUUUCGAUA-GCC--UGUGACUAGAU-CCACACUCAUUAACAAAAGUU---GCCG
AAJJ01003219.1/11291-11201   UGGAGCUCUCGGUGUAAGCCAGUGUUCAGUCUAUUGUUUCACAUUGGUUUCG-------AUUGUGACUAGAUCGAACACUCGCUUGCAACCUGG---GUUU
AAZX01001678.1/20489-20404   CCAGCCGAUUGUACUGAGUGAGUGAUG-GUCUGGUG-----CACGGUUUAUC-----GAUCUGUGACUAGAU-CCACACUCAUUAAGUACGUUC---GGCU
AAWU01001985.1/8444-8349     GCUUCCCACUAUUGUCGAUGGGUGUGA-AUCUAGUGGUUCACAUGAGCUUUGCC--A-AACUGUGACUAGAU-CCACACUCAUUAACAAGAGUGCUCGGAA
AADE01000363.1/2006-2100     UCAUACUACUGUUUUUAGUGAGUGAGG-GUCCAGUGUUUCACAUUGAUUUUCUUA-GUAUUUGUGACUAGAU-CCACACUCAUUAAUAACGGUA---GUUC
AAPT01018378.1/277640-277732 CCGUAUUACUGUUUUUAGUGGGUGAGG-GUCCAGUGUUUCACAUUGUUUAUUUG---UAUUUGUGACUAGAU-CCACACUCAUUAAAAACGGUA---GUUC
AANI01014375.1/46325-46420   GCGUACUACUGUUUUUAGUGAGUGAGG-GUCCAGUGUUUCACAUUCGUUUUUUCAAGUAUUUGUGACUAGAU-CCACACUCAUUAACAACGGUA---GUUC
JN211060.1/1022-1116         UCAUACUACUGUUUUUAGUGGGUGGGG-GUCCAGUGUUUCACAUUGAUUUUCUUA-GUAUUUGUGACUAGAU-CCACACUCAUUAAUAACGGUA---GUUC
AADG06007490.1/6579-6668     UUGUUCGAUGGCCUUGGAUGGGUUUGA-AUUCAG---UCCACGUU--UUUUAUUU-UUAUUCGUGACUAGAU-CCACACUCAUCCAAGGAAAUC---GAGC
AEKZ01010226.1/4670-4585     UUUCCUGAAUUUGCCAAAUGAGUGAAG-GUCUAGUG---CACAGAAAAUGAA-------AUUGUGACUAGAU-CCACACUCAUUAAGUACGUUC---AGGU
#=GC SS_cons                 ::::<<<<<<<<<<<<<<<<<<<<<<<.<<<<<<----<<<<<___________...____>>>>>>>>>>>.>>>>>>>>>>>>>>>>>>>>>...>>::
#=GC RF                      uuuuccgaccguuguuaauGaGUGugg.gUCuAGUGuUuCACaUuguUUUuauu...uAuUuGUGaCUaGAu.ccaCACuCauuaacaacgguc...gguu
//
# STOCKHOLM 1.0

#=GF AC   RF00755
#=GF ID   mir-542
#=GF DE   microRNA mir-542
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   88.00
#=GF TC   89.90
#=GF NC   49.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000185;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF RN   [2]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction
#=GF RT   method.
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   Mir-542_microRNA_precursor_family
#=GF SQ   5


AAHX01102601.1/64448-64532 GGAUCUCAGACGUCUCGGGGAUCAUCAUGUCACGAGAUACCACUGCGCACUUGUGACAGAUUGAUAACUGAAAGGUCUGGGAGCC
AAIY01425199.1/1318-1400   AGACCUUAGGCAUUUCGGGGAUC--CCUGUCAUGGGAUACCACUGCAUACUUGUGACAGAUUGAUAACUGAAAGGUUUAGGGCCU
CU468475.7/112254-112170   AGACCUCAGACGUCUCGGGGAUCAUCAUGUCACGAGAGACCACUGUGCACUUGUGACAGAUUGAUAACUGAAAGGUCUGGGAGCC
AC004383.1/125994-125910   AGAUCUCAGACAUCUCGGGGAUCAUCAUGUCACGAGAUACCAGUGUGCACUUGUGACAGAUUGAUAACUGAAAGGUCUGGGAGCC
AFSB01204397.1/3395-3479   AGACCUCAGACAUUUCGGGGAUCAUCAUGUCACGAGAUACCACUGUGCACUUGUGACAGAUUGAUAACUGAAAGGUCUGGGAGCC
#=GC SS_cons               :::<<<<<<<<-<-<<<<--<<<<---<<<<<<<<<-<<<____>>>-->>>>>>>>>--->>>>-->>>>->->>>>>>>>:::
#=GC RF                    AGAcCucaGaCauuuCgGGGauCaUCauGuCacgaGAcaCCAcUGugcACuuguGaCaGAUuGauAACuGaAaGGuCuggGggCc
//
# STOCKHOLM 1.0

#=GF AC   RF00756
#=GF ID   mir-299
#=GF DE   microRNA mir-299
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   73.00
#=GF TC   75.30
#=GF NC   61.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.96 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000186;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15891114
#=GF RT   Clustering and conservation patterns of human microRNAs.
#=GF RA   Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A,
#=GF RA   Brownstein MJ, Tuschl T, Margalit H
#=GF RL   Nucleic Acids Res. 2005;33:2697-2706.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-299_microRNA_precursor_family
#=GF SQ   6


AACN010183773.1/1196-1258  AAGAAAUG-GUUUACCGUCCCACAUACAUUUUGAGUAUGUAUGUGGGACGGUAAACCGCUUCUU
ABDC01257670.1/1456-1394   AAGAAGCG-GUUUACCGUCCCACAUACAUAUAGAAAAUGUAUGUGGGACGGUAAACCAUUUCUU
CAAA01169866.1/64-2        AAGAAAUG-GUUUACCGUCCCACAUACAUUUUGAGUAUUGUUGUGGGACGGUGAACCGCUUGUU
AANU01197805.1/63515-63453 AAGAAGCG-GUUUACCGUCCCACAUACAUAUUGAAAAUGUAUGUGGGACGGUAAACCAUUUCUU
AADD01141097.1/32192-32254 AAGAAAUG-GUUUACCGUCCCACAUACAUUUUGAAUAUGUAUGUGGGAUGGUAAACCGCUUCUU
AAIY01428934.1/3553-3616   AAGACCUGUGGUUACCGUCCCACAUACAUUUUAGAUGUGUAUGUGGGAUGGUAAACCGCUUCUU
#=GC SS_cons               <<<<<<<<.<<<<<<<<<<<<<<<<<<<<_______>>>>>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                    AAGAaguG.GuUuACCGUCCCACAuacAuuUUGAAuaUguaUGUGGGACGGUaAaCCgcuUCUU
//
# STOCKHOLM 1.0

#=GF AC   RF00757
#=GF ID   mir-275
#=GF DE   microRNA mir-275
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   63.00
#=GF NC   59.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000187;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17933784
#=GF RT   Anopheles gambiae miRNAs as actors of defence reaction against Plasmodium
#=GF RT   invasion.
#=GF RA   Winter F, Edaye S, Huttenhofer A, Brunel C
#=GF RL   Nucleic Acids Res. 2007;35:6953-6962.
#=GF RN   [2]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus.
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF RN   [3]
#=GF RM   12844358
#=GF RT   Computational identification of Drosophila microRNA genes.
#=GF RA   Lai EC, Tomancak P, Williams RW, Rubin GM
#=GF RL   Genome Biol. 2003;4:R42.
#=GF RN   [4]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF RN   [5]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [6]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [7]
#=GF RM   20075255
#=GF RT   Functional and evolutionary insights from the genomes of three parasitoid
#=GF RT   Nasonia species.
#=GF RA   Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK,
#=GF RA   Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK,
#=GF RA   Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA,
#=GF RA   Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM,
#=GF RA   Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN,
#=GF RA   Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P,
#=GF RA   Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D,
#=GF RA   Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG,
#=GF RA   Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards
#=GF RA   R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach
#=GF RA   D, Gibson JD, Gilbert DG, Graur D, Grunder S, Hagen DE, Han Y, Hauser F,
#=GF RA   Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM,
#=GF RA   Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim
#=GF RA   J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R,
#=GF RA   Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA,
#=GF RA   Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA,
#=GF RA   Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV,
#=GF RA   Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA,
#=GF RA   Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R,
#=GF RA   Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson
#=GF RA   J, Rosenberg M, Sackton TB, Sattelle DB, Schluns H, Schmitt T, Schneider
#=GF RA   M, Schuler A, Schurko AM, Shuker DM, Simoes ZL, Sinha S, Smith Z, Solovyev
#=GF RA   V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y,
#=GF RA   Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW,
#=GF RA   Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin
#=GF RA   F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA
#=GF RL   Science. 2010;327:343-348.
#=GF RN   [8]
#=GF RM   18714353
#=GF RT   The silkworm (Bombyx mori) microRNAs and their expressions in multiple
#=GF RT   developmental stages.
#=GF RA   Yu X, Zhou Q, Li SC, Luo Q, Cai Y, Lin WC, Chen H, Yang Y, Hu S, Yu J
#=GF RL   PLoS One. 2008;3:e2997.
#=GF RN   [9]
#=GF RM   18977439
#=GF RT   Identification of conserved microRNAs in Bombyx mori (silkworm) and
#=GF RT   regulation of fibroin L chain production by microRNAs in heterologous
#=GF RT   system.
#=GF RA   Cao J, Tong C, Wu X, Lv J, Yang Z, Jin Y
#=GF RL   Insect Biochem Mol Biol. 2008;38:1066-1071.
#=GF RN   [10]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing.
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF RN   [11]
#=GF RM   19699294
#=GF RT   A discovery of novel microRNAs in the silkworm (Bombyx mori) genome.
#=GF RA   Yu X, Zhou Q, Cai Y, Luo Q, Lin H, Hu S, Yu J
#=GF RL   Genomics. 2009;94:438-444.
#=GF RN   [12]
#=GF RM   20229201
#=GF RT   Novel microRNAs in silkworm (Bombyx mori).
#=GF RA   Cai Y, Yu X, Zhou Q, Yu C, Hu H, Liu J, Lin H, Yang J, Zhang B, Cui P, Hu
#=GF RA   S, Yu J
#=GF RL   Funct Integr Genomics. 2010;10:405-415.
#=GF RN   [13]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [14]
#=GF RM   20817720
#=GF RT   Functional shifts in insect microRNA evolution.
#=GF RA   Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S
#=GF RL   Genome Biol Evol. 2010;2:686-696.
#=GF WK   Mir-275_microRNA_precursor_family
#=GF SQ   15


AASW01038426.1/5456-5366       AAAAGUCUCCUACCUUGCGCGCUA-AUCAGUGACC-GGGGCUGGUU-----UUUUAUA-UACAGUCAGGUACCUGAAGUAGCGCGCGUGGUG-GCA-G-ACA
AAQB01006829.1/458431-458336   CCUUGUCUCUUACCUUGCGCGCUA-AUCAGUGACC-AGGGCUGAGUAAUUUUAUUCAA-UACAGUCAGGUACCUGAAGUAGCGCGCGUGGUU-UUA-G-ACC
AAWU01017837.1/19596-19687     GAAUCCUUCCGAUAGCGCGCGCUA-AGCAGGAACC-GGGACUUGGU-----CAUUCGCUAGCAGUCAGGUACCUGAAGUAGCGCGCGUGAUC-GGA-A-GUG
AAPT01020969.1/275887-275981   CGUCGUCGUUUACCGCGCGCGCUA-AUCAGUGACC-GGGGCUGGUUU--UGAUUAUCC-CACAGUCAGGUACCUGAAGUAGCGCGCGUGGUG-GCCAG-ACG
AAPU01010637.1/244569-244475   GUCCGUCUUUUACCGUGCGCGCUA-AUCAGUGACC-GGGGCUGGUUU---CGAUUAUCUCACAGUCAGGUACCUGAAGUAGCGCGCGUGGUGGCUA-G-ACG
AADK01007727.1/11210-11296     AGCAGGCGGCAGCGCCGCGCGCUA-CUCCGGCGCC-AGGACU---G-----UCCUCAC-CG-AGUCAGGUACCUGAAGUAGCGCGCGGUGUC-UCC-U-CCU
AAAB01008980.1/2232223-2232317 UGAGCCGUCUAAUGACACGCGCUA-AGCAGGAACC-GGGACUUGGUA--CACAUUCGCUAGCAGUCAGGUACCUGAAGUAGCGCGCGUUAUU-CGG-C-UCA
AAZX01002044.1/14734-14647     ACAGCCAGUUUGCAACUCGCGCUA-CUCCGGUACU-UACGACUGUG-----CAUUCGA-U-AGUC-AGGUACCUGAAGUAGCGCGCGCUGCG--AC-U-GGA
AAJJ01000649.1/41251-41341     UGUUGCCUGUUGCUACGCGUGUUACCUCAGU-ACC-UAGGCUGGGG-----UUUUUCG-AA-AGUCAGGUACCUGAAGUAGCGCGCGCAGCG-GUG-GUGCA
AAGE02001651.1/96625-96717     GUAUCCUUUCGAUUUCGCGCGCUA-AGCAGGAACC-GAGACUUUGU-----CAUUUGCUAGCAGUCAGGUACCUGAAGUAGCGCGCGUGAUC-AAACA-GGA
AAIZ01002385.1/22802-22712     GAAAGUCUCCUACCAUGCGCGCUA-AUCAGAGACC-GGGGCUGGUU-----UUUUCAC-UGCAGUCAGGUACCUGAAGUAGCGCGCGUGGUG-CUA-G-ACA
AAPP01015737.1/35785-35873     UCCAGUCUCCUACCUUGCGCGCUA-AUCAGUGACC-GGGGCUG--G-----UUUUUGC-AACAGUCAGGUACCUGAAGUAGCGCGCGUGGUG-GCA-G-ACA
AANI01016257.1/59564-59470     CGCCGUCUUUUACCGUGCGCGCUA-AUCAGUGACC-GGGGCUGGUUU--UGGUUAUCC-CACAGUCAGGUACCUGAAGUAGCGCGCGUGGUGGCCA-G-ACG
JN211058.1/1181-1271           UAAAGUCUCCUACCUUGCGCGCUA-AUCAGUGACC-GGGGCUGGUU-----UUUUAUA-UACAGUCAGGUACCUGAAGUAGCGCGCGUGGUG-GCA-G-ACA
AADG06004977.1/9496-9406       CUUGUCGUG-CGCAACGCGCGUUA-CUCGGGUACUUUAGGCUGUGCC---AAUUUCGA-AUCAGUCAGGUACCUGAAGUAGCGCGCGCUGCG---G-C-GAA
#=GC SS_cons                   ::::<<<<--<<<<<<<<<<<<<<.--<<<--<<<.--<<<<<___....._______.__>>>>>->>>-->>>--->>>>>>>>>>>>>>.-->.>.>>:
#=GC RF                        uuaugccuuucgCcgcGCGCGCUA.aUCaGugACC.ggGgCugguu.....uuUUcga.aacaGuCAGGUACCuGAAGUAGCGCGCgcgGcg.uua.g.gca
//
# STOCKHOLM 1.0

#=GF AC   RF00758
#=GF ID   mir-346
#=GF DE   microRNA mir-346
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   80.60
#=GF NC   40.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.63 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000188;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:360-365.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   Mir-346_microRNA_precursor_family
#=GF SQ   5


AAIY01391882.1/1153-1058   UCUGUGUUGGGCGCCUGUCUGCCCACCUGCCUGCCUCUCUGUCA-UCUGAAGGAGGCAGGGGCCGGGC-UGCAGCUGCCUGGGCAGAGCGGCUCCUGC
CT030647.17/44422-44325    UCUGUGUUGGGCGUCUGUCUGCCCGAGUGCCUGCCUCUCUGUUGCUCUGAAGGAGGCAGGGGCUGGGCCUGCAGCUGCCUGGGCAGAGCUGCUCCUUC
AC199143.7/141552-141455   UCUGUGGUGGGCGUCUGUCUGCCCGCAUGCCUGCCUCUUUGUUGCUCGGAAGGAGGCAGGGGCUGGGCCUGCAGCUGCCUGGGCAGAGCGGCUCCUGC
AL732479.6/57414-57317     UCUGUGUUGGGCGUCUGUCUGCCCGCAUGCCUGCCUCUCUGUUGCUCUGAAGGAGGCAGGGGCUGGGCCUGCAGCUGCCUGGGCAGAGCGGCUCCUGC
AABR05055792.1/21624-21527 UCUGUGUUGGGCAUCUGUCUGCCUGAGUGCCUGCCUCUCUGUUGCUCUGAAGGAGGCAGGGGCUGGGCCUGCAGCUGCCUGGGCAGAGCUGCUCCUUC
#=GC SS_cons               :::::<<<<<<<<-<<<<--<<<<<----<<<<<<<<-<<__________>>>>>>>>>>--->>>>>-->>>>->>>>>->>>::::::::::::::
#=GC RF                    UCUGUGcugGGCguCuGuCUGCCcgaaUGCCuGCCuCUcuGUugcUCuGAagGaGGCaGGGGCcgGGCcUgCaGCcGCCuGggCAGAGCgGCUCCUgC
//
# STOCKHOLM 1.0

#=GF AC   RF00760
#=GF ID   mir-342
#=GF DE   microRNA mir-342
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   51.00
#=GF TC   53.60
#=GF NC   46.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000190;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [4]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues.
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF RN   [5]
#=GF RM   17306260
#=GF RT   Identification and characterization of microRNAs from the bovine adipose
#=GF RT   tissue and mammary gland.
#=GF RA   Gu Z, Eleswarapu S, Jiang H
#=GF RL   FEBS Lett. 2007;581:981-988.
#=GF RN   [6]
#=GF RM   19267191
#=GF RT   Identification and characteristics of cattle microRNAs by homology
#=GF RT   searching and small RNA cloning.
#=GF RA   Long JE, Chen HX
#=GF RL   Biochem Genet. 2009;47:329-343.
#=GF RN   [7]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [8]
#=GF RM   18230126
#=GF RT   New miRNAs cloned from neuroblastoma.
#=GF RA   Afanasyeva EA, Hotz-Wagenblatt A, Glatting KH, Westermann F
#=GF RL   BMC Genomics. 2008;9:52.
#=GF WK   MicroRNA
#=GF SQ   10


AAYZ01348637.1/771-867     GGACUUGGGCUUGAGGGGAGGGGUGCUCUCUGUGCCUGAGGGACAUGGC-AAUGGAACUGUCUCACACAGACAUCGCACCC-UCCCCUCUGCCUGCUCA
AAFC03050755.1/31465-31562 GGAAGCGGGUGCGAGGCGAGGGGUGCUAUCUGUGGUUGAG-GACACGGCAAAUGAAACUGUCUCACACAGAAAUCGCACCCAUCUCCUCGGCCCGCCUU
AALT01532195.1/130-32      AGACCUGGGCUCAAGGUGAGGGGUGCCAUCUGUGACUGAGGGACAUGGCCAAAGGAAUUGUCUCACACAGAAAUCGCACCCGUCACCUUGGUACUGCCC
AACN010082176.1/1129-1227  GAAACUGGGCGCAAGGUGAGGGGUGCUAUCUGUGAUUGAGGGACAUGGCAAAUAGAAUUGUCUCACACAGAAAUCGCACCCGUCACCUUGGCCCGCCUA
AC122029.4/7275-7177       GAAAAUGGGCUCAAGGUGAGGGGUGCUAUCUGUGAUUGAGGGACAUGGUCAAUGGAAUUGUCUCACACAGAAAUCGCACCCGUCACCUUGGCCUGCUGA
AC192208.3/111651-111553   GAAACUGGGCUCAAGGUGAGGGGUGCUAUCUGUGAUUGAGGGACAUGGCUAAUGGAAUUGUCUCACACAGAAAUCGCACCCGUCACCUUGGCCUACUUA
AAGU03026017.1/85012-84914 GACCCUGGGCUCAAGGUGAGGGGUGCUAUCUGUGAUUGAGGGACAUGGUACAUAGAAUUGUCUCACACAGAAAUCGCACCCGUCUCCUUGGCCUGCUUA
AAGW02075757.1/8372-8276   GAACCUGGGCUCGAGGUGAGGGGUGCUCUCUGUGCGUGAGGGACAUGGC-AAUCGAAUUGUCUCACACAGAAAUCGCACCC-UCUCCUCGGCCUGCUCA
AAPE02046801.1/21345-21247 GAACCUGGGCGCAAGGUGAGGGGUGCUAUCUGUGAUUGAGGGACAUGGCACAUAGAAUUGUCUCACACAGAAAUCGCACCCGUCACCUUGGCCCAACUC
AAQR03046438.1/36527-36625 GAAAUUGGGCUUAAGGUGAGGGGUGCUAUCUGUGAUUGAGGGACAUGGACAAUGGAACUGUCUCACACAGAAAUCGCACCCGUCACCUUGGCCUGCUUA
#=GC SS_cons               ::::::<<<<-<<<<<<<<-<<<<<<--<<<<<<-----<<<<<<_____________>>>>>>->>>>>>---->>>>>>->>>>>>>>>>>>:::::
#=GC RF                    GaAauUggGcucgaGGuGaGGGGuGCUauCuGuGauUGAGgGaCaUGGcaaAugGAAuuGuCcCACaCaGaAAUCGCaCCCguCaCCucggCccgcuua
//
# STOCKHOLM 1.0

#=GF AC   RF00761
#=GF ID   mir-340
#=GF DE   microRNA mir-340
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   65.20
#=GF NC   64.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.34 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000191;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:360-365.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   17965199
#=GF RT   In vitro and in silico annotation of conserved and nonconserved microRNAs
#=GF RT   in the genome of the marsupial Monodelphis domestica.
#=GF RA   Devor EJ, Samollow PB
#=GF RL   J Hered. 2008;99:66-72.
#=GF RN   [4]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF WK   Mir-340_microRNA_precursor_family
#=GF SQ   31


AC169700.1/140375-140471     AAUUUAUACAAGGCAUGACUGUAAUAUAAUGAAUCUGAUUU-UUCUG--UGUG--ACU-UGUGG--AAUC-A--AUCCU-AUUUCUUUAUAAUCACAUCUUGUAUAUUA
AACN010226306.1/818-721      UCUUUGUACCUGAUGCGAUUAUAAAGCAAUGAGACUGAUUG-UCAUG--UGUC--GGU-UGUGG--GAUC-C-GUCUCA-GUUACUUUAUAGCCGUGCCUGGUACCUAA
AAFR03033110.1/48153-48249   UUAAUGUAUGAGGUGUGACAAUAAGGUAACGAUACUGAUUU-CCAUG--UUAG--UCU-GGUGG--AAUU-A-GCCUC--AUUACUCUAUAGUCACACCUUAUAAAUUC
AANG01281249.1/484-388       AUGAAAAAUGAGAUGUGACUAUAAAGUGAUGAAACUGAUUU-UCACA--UGUG--GCC-UGUGG--GAUU-U-CCUUGA--UUACUUUUUAGUCAUGCCUUGUAUUAGU
AAPY01204703.1/899-994       AAAAAAUACAUGGCAUGACUAUAAAGUAAUGAGACAAAUUU-UCAUG--UGUA--G---CUUGG--AUUA-CUGUCUCA--UUAGUAUAUAGUCACAUCCUGUCUUGAG
AAFR03012620.1/32411-32507   AACACACACAAGGUGUGACUAUAAAGUAAUGAAACCAAUUU-UCAUG--UAUG--GCU-UAUGG--AAUC-A-GUCUUA--UUUCAUCAUACUCACAUCUUGUGUAUGU
AAFR03008051.1/35072-34981   AUAUCAUACGAGGUGUGACUAUAACAUAAUGAGAUUGAUUU-UCAUG--UGUG--ACU-UUUGG--AAUC-A-AUCUCA-------UUAUAGAAAUGCCUUAUGUCAUA
AALT01005382.1/1156-1059     AAAAAAUACAUGGCAUGACUAUAAAGUAAUGAGACAAGUUU-UCAUG--UGUG--GCU-UGUGU--UACUGA-GUCUCA--UUAGUAUAUAGUCACAUCCUGUCUCAAG
AAFR03025299.1/56825-56733   UACAUGAACUCGGUAUGACUAUAAAGUAAUGAAAUUGAUUU-UCGUG--UGUG--ACU-UAUGG-AAGUC-C-GUUUCA--UUACCUUAUAGUCACACC-----CCAAA
ABDC01266727.1/454-548       UUUAAGGAAGAGGUGUGACUAUAAAGCAGUGAGACUGAU-G-UGGGG--UGUG--CAG-CUUCUGGAAUC-A-GUCUCA--UUACUUUCUACUCUCACC---UCUGAGA
AAFR03024491.1/9819-9913     UGAUCA----AGGUGUGACUAUAAAGUAAUGAGAUUGAUU--UCUGUGGUAUA--GUAAAUGGA--AAUC-A-GUUUCA--UUACCUUACAGUCACAUCUAAUCUUCUA
AAFR03044565.1/87831-87735   CUUCAGCAUGAGGUGUGAUUACAAAGGAAUGAAACUGUUUU-UCUUA--UGUG--GUU-UGUGG--AAUU-G-GU-UCU-GUUACUUUGUAGUUAUAUAUCAUAGAUCU
AAFR03025629.1/19404-19498   GGUGUAUCUAUGGUAUGACUAUAAAGCAAUGAUACUGAUUC-UCCAU--UUGG--GUU-AUGGA--AAUC-A-GUCUCA--UUACCUUAUAGUUGCAC--UGGGUCUUC
AAHX01063758.1/23051-23148   CACUUGUACUCGGUGUGAUUAUAAAGCAAUGAGACUGAUUG-UCAUG--UGUC--GUU-UGUGG--GAUC-C-GUCUCA-GUUACUUUAUAGCCAUACCUGGUAUCUUA
AAIY01703130.1/1510-1607     CGCUUGUAUCUGGUGUGAUUAUAAAGCAAUGAGACUGAUUG-UCAUG--UGUA--GCU-UGUGG--GAUC-C-GUCUCA-GUUACUUUAUAGCCAUACCUGGUAUCUUA
AAFC03080208.1/50415-50512   AAAACAUACAUGGCAUGACUAUAAAGUAAUGAGACGAGUUU-UCAUA--UGCG--GCU-UGUAU--UACUGA-GUCUCA--UUAAUAUAUAGUCACAUCCUGUUUCGAG
AC158769.2/163667-163764     AAAACAUACAUGGCAUGGCUAUAAAGUAAUGAGACAAGUUU-UCAUG--UGUG--G---CUUGGUUUAUUGA-GUCUCA--UUAAUAUAUAGUCAUAUCCUGUCUCAAG
AAQQ01168328.1/1653-1750     UUUAAGGAAGAGGUAUGAGUAUAAAGCAGUGAGACUGAUU--UGAGA--UGUGCAGCU-GCUGG--AAUC-A-GUUUCG--UUACUUUCUACUCUCACCUCUGAGACAG
AC200335.2/106893-106989     AAUUUAUACAAGGCAUGACUGUAAUAUAAUGAAUCUGAUUU-UUCUG--UGUG--ACU-UGUGG--AAUC-A-AACCUA-UUUCUAU-AUAAUCACAUCUUGUAUAUUA
AANN01309615.1/1178-1081     AAAACAUACAUGGCAUGACUAUAAAGUAAUGAGACAAGUUUUUCACA--UCUG--GC--UGUGU--UACUGA-GUCUCA--UUAGUGUAUAGUCAAAUCCCGUCUCAAG
AAKN02055594.1/55874-55971   CACUUGUACCUGGUGUGAUUAUAAAGCAAUGAGACUGAUUG-UCAUU--UGUC--UUU-UGUGG--GAUC-C-GUCUCA-GUUACUUUAUAGCCAGACCUGGUAUCUUA
AAWR02006601.1/58623-58527   GACUUGAAUAUAGUAUGAUUAUGAAAUAAUAAGACUAAUUU-UGACA--UGUG--GUU-UAUGU--AAUU-G-GUUUCA--UUACUUGAUAGCCACACUUGAGACUUUA
AAWR02011473.1/193267-193171 AGGAAAUAUGAGGUGUGACUAUCAAGGGAUGAAACUGAUUU-UCCCA--UGUG--GCU-UGUGG--GAUU-U--CCUGG-AUUACUUUUUAGUCAUGCCUUAUAUUAGU
AC069137.6/16222-16127       GGCUAGAAUACAGUAUGAUUGUGAAGUAAUAAGACUAAUUU-UGACA--UGUG--GUU-UGUGG--AAUU-G-GUUUCA--UUACUU-AUAGUCACAUUUGAGGCUUUA
AC018356.26/45515-45611      AGGGAAUAUGAGAUGUGACUAUAACGUGAUGAAACUGAUUG-UCACA--UGUG--GCU-UGUGG--GAUU-U-C--UCAGAUUACUUUUUAGUCAUGUUUUGUAUUAGU
AC026413.5/105797-105700     CGUUUGUACCUGGUGUGAUUAUAAAGCAAUGAGACUGAUUG-UCAUA--UGUC--GUU-UGUGG--GAUC-C-GUCUCA-GUUACUUUAUAGCCAUACCUGGUAUCUUA
AAGU03055997.1/112380-112283 CCAGAGUAUGCAGUAUGAAUAUAAAAUAGUGUGCCCAGUUU-UCUUG--UGUG--GUU-UGUGG-AAACU-G-GUCACA-UUGC-UUUAUAGCCACACCACAUAUAUUU
AAQR03004710.1/72078-71984   UUUAAGGAAGAGGUGUGAUUAUAAAGCAGUGAGACUGAUU--UGGGG--UGUGCAGCU-UCUGG--AAUC-A-GUCUCA--UUACUUUCUACUCUCACC---UCUGAGA
AAGW02065628.1/38933-38836   CAUUUGUACCUGGUGUGAUUAUAAAGCAAUGAGACUGAUUG-UCAUA--UGUU--GUU-CAUGG--GAUC-C-GUCUCA-GUUACUUUAUAGCCAUACCUGGUACCUUG
AAGU03013135.1/33713-33810   GGCAGAUACAGAAUGUGACUAGAAAGCAAUGAGUCUAGUAU-UUGUG--UGUG--GUG-CAUGG-AAACC-A-GCCUCA--UUACUUUAUAAUCACACUCUGCGUAGCA
AAGU03047370.1/11364-11460   AAAAUAUAUAAGGUAUGAAUAUAAAGUAAUGAGAUGAUUUU-CCUUA--CGUA--GUU-UAUGG--AAAU-A-GUCUC--GUUAUUUCCCAGUUAUACCUUAUCUAUUU
#=GC SS_cons                 :::::<<<<<<<<<<<<<<<<<<<<<---<<<<<<-<<<<-.<<<<<..____..___.>>>>>..>>>>.-.>>>>>>..--->>>>>>>>>>>>>>>>>>>>>::::
#=GC RF                      aaaauauacgaGgugUGacUAuAaaguAAUGAgacUgaUuU.ucacg..UGUG..GuU.cgugg..aAuc.a.gucUCA..UUAcuuUaUAguCAcacCucguauauua
//
# STOCKHOLM 1.0

#=GF AC   RF00762
#=GF ID   mir-412
#=GF DE   microRNA mir-412
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   88.00
#=GF NC   51.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.80 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000192;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15310658
#=GF RT   A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain.
#=GF RA   Seitz H, Royo H, Bortolin ML, Lin SP, Ferguson-Smith AC, Cavaille J
#=GF RL   Genome Res. 2004;14:1741-1748.
#=GF RN   [2]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction
#=GF RT   method.
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [5]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   MicroRNA
#=GF SQ   9


AAIY01437686.1/1059-969    CUGGGGUACGGGGAUGGCUGGUCGACCAGUUGGAAAGUAAUUUUUUAUAAUGUAUUUCACCUGGUCCACUAGCCAUCAGUGCCCACUGCAG
ABDC01257675.1/5683-5773   CUGGGGUAUGGGGACGGAUGGUCGACCAGUUGGAAAGUAAUUGUCCCCAAUGUACUUCACCUGGUCCACUAGCCGUCCGUACCCACUGCCG
AAFC03087121.1/23475-23564 CUGGGGUACA-GGACGGAUGGUCGACCAGUUGGAAAGUAAUUGUUUCUAAUGUACUUCACCUGGUCCACUAGCUGUCCGUACCCACUGCAG
AAPY01359978.1/1472-1562   CUGGGGUACAGGGACGGGUGGUCGACCAGUUGGAAAGUAAUUGUCUCUAAUGUACUUCACCUGGUCCACUCGCCGUCCGUACCCGCUGCAG
AALT01091711.1/638-727     CUGGGGUACA-GGAUGGAUGGUCGACCAGUUGGAAAGUAAUUGUGUCGAAUGUACUUCACCUGGUCCACUAGCCGUCCGCACCCACGGCGG
AL132709.5/56152-56062     CUGGGGUACGGGGAUGGAUGGUCGACCAGUUGGAAAGUAAUUGUUUCUAAUGUACUUCACCUGGUCCACUAGCCGUCCGUAUCCGCUGCAG
AC121784.2/138820-138909   CUGGGGUAUG-GGACGGAUGGUCGACCAGCUGGAAAGUAAUUGUUUCUAAUGUACUUCACCUGGUCCACUAGCCGUCGGUGCCCGCUGCAG
AAGU03025975.1/14212-14122 CUGGGGCGCGGGGAUGGAUGGUCGACCAGUUGGAAAGUAAUUGUUUAUAAUGUACUUCACCUGGUCCACUAGCCGUCGGUGCCCACUGCAG
AAPE02047294.1/8472-8383   CUGGGGUACA-GGAUGGGUGGUCGACCAGUUGGAAAGUAAUUGUUUCUAAUGUACUUCACCUGGUCCACUAGCCGUCCGUAUCCACUGCCG
#=GC SS_cons               :::<<<<<<---<<<<<<<<<<<<<<<<<-<<<--<<<<<<<<____>>>>->>>>>>>->>>>>>>>>>>>>>>>>->>>>>>:::::::
#=GC RF                    CUGGGGuacagGGacGGcugGucGaCCaGUuGgAAaGuaauugUuUccaauGuaCuuCaCCuGGuCgaCuagCCguCcguaCCCaCuGCaG
//
# STOCKHOLM 1.0

#=GF AC   RF00763
#=GF ID   mir-339
#=GF DE   microRNA mir-339
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   60.30
#=GF NC   58.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.72 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000193;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [4]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:360-365.
#=GF RN   [5]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [6]
#=GF RM   19170227
#=GF RT   Identification and expression profiling of microRNAs during bovine oocyte
#=GF RT   maturation using heterologous approach.
#=GF RA   Tesfaye D, Worku D, Rings F, Phatsara C, Tholen E, Schellander K, Hoelker
#=GF RA   M
#=GF RL   Mol Reprod Dev. 2009;76:665-677.
#=GF RN   [7]
#=GF RM   19170227
#=GF RT   Identification and expression profiling of microRNAs during bovine oocyte
#=GF RT   maturation using heterologous approach.
#=GF RA   Tesfaye D, Worku D, Rings F, Phatsara C, Tholen E, Schellander K, Hoelker
#=GF RA   M
#=GF RL   Mol Reprod Dev. 2009;76:665-677.
#=GF RN   [8]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF RN   [9]
#=GF RM   19633723
#=GF RT   Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed
#=GF RT   upon viral infection.
#=GF RA   Glazov EA, Kongsuwan K, Assavalapsakul W, Horwood PF, Mitter N, Mahony TJ
#=GF RL   PLoS One. 2009;4:e6349.
#=GF RN   [10]
#=GF RM   19917043
#=GF RT   MicroRNA identity and abundance in porcine skeletal muscles determined by
#=GF RT   deep sequencing.
#=GF RA   Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C,
#=GF RA   Thomsen B
#=GF RL   Anim Genet. 2010;41:159-168.
#=GF RN   [11]
#=GF RM   20180025
#=GF RT   Cloning and characterization of microRNAs from porcine skeletal muscle and
#=GF RT   adipose tissue.
#=GF RA   Cho IS, Kim J, Seo HY, Lim do H, Hong JS, Park YH, Park DC, Hong KC, Whang
#=GF RA   KY, Lee YS
#=GF RL   Mol Biol Rep. 2010;37:3567-3574.
#=GF RN   [12]
#=GF RM   20433717
#=GF RT   Deciphering the porcine intestinal microRNA transcriptome.
#=GF RA   Sharbati S, Friedlander MR, Sharbati J, Hoeke L, Chen W, Keller A, Stahler
#=GF RA   PF, Rajewsky N, Einspanier R
#=GF RL   BMC Genomics. 2010;11:275.
#=GF RN   [13]
#=GF RM   15325244
#=GF RT   Altered expression profiles of microRNAs during TPA-induced
#=GF RT   differentiation of HL-60 cells.
#=GF RA   Kasashima K, Nakamura Y, Kozu T
#=GF RL   Biochem Biophys Res Commun. 2004;322:403-410.
#=GF RN   [14]
#=GF RM   15634332
#=GF RT   New human and mouse microRNA genes found by homology search.
#=GF RA   Weber MJ
#=GF RL   FEBS J. 2005;272:59-73.
#=GF WK   Mir-339_microRNA_precursor_family
#=GF SQ   14


ABDC01170433.1/932-839       UCGGGGCCGGCGCUCUCCCCGUC-UCCAGGAGCCCACGUCUGCUUUCCUCUGAGCUUCUCGACGACAGAGCCGGCGCCCGUUCCAGCGUU-UGCGC
AAPY01369443.1/857-762       ACGGGGUGGCCACUCUCCCUGUCCUCCAGGAGCUCACGUGCGCCUGCCUGUGAGCGCCUCGACGACAGAGCCGGUGUCCGCCUCAGUGUCCGCAUC
AAFC03028593.1/22710-22804   CUGGGGCAGCCGCUGUCCCUGUCCUCCAGGAGCUCACUUGGUCCGGCC-GUGCGCUCCUCGAGGCCAGAGCCCGUGUCUGCUUCCCGCCAGCACCA
AANG01816334.1/313-220       CUGA--CAGCCGCUCUCCCUGUCCUCCAGGAGCUCACUUACAUCCGGCCGUGAGCUCCUCGAGGCCAGAGCCCGCGUCUGCCUCCACUCAGCGCCA
AAYZ01411525.1/5602-5507     GCGCGACGGCCGCCCUCCCUGUCCUCCAGGAGCUCACGUCAGCCUGCCUGUGAGCGCCUCGACGACAGAGCCGGCGUCCGCCACAGUGCUGUCGAC
AAWR02040473.1/4828-4923     CCGUGGCAGCCGCUUUCCCUGUCCUCCAGGAGCUCACUUACAUCCGGCCGUGAGCUCCCCGAGGCCAGAGCCCGUGUCUGCCUCAUUGUCAGCGCC
AAGV020651181.1/406-501      ACGUGGCAGCCGCUCUCCCUGUCCUCCAGGAGCUCACGUGGGUCAGGCUGUGAGCGCCUCGAGGGCAGAGCCCGCGUCUGCCUGCGCGCCCAGCGC
AAKN02032234.1/100244-100339 GAUGGGUGGCCGCCCUCCCUGUCCUCCAGGAGCUCACGUAUGCCUGCUUGUGAGCGCCUCGAUGACAGAGCCGGCGUCCGCCUCUGUGUCUGCAGC
AC146112.3/143647-143552     GCGGGGCGGCCGCUCUCCCUGUCCUCCAGGAGCUCACGUGUGCCUGCCUGUGAGCGCCUCGACGACAGAGCCAGCGCCUGCCCCAGUGUCUGCGCC
AC161058.2/17435-17530       ACGGGGUGGCCACUAUCCCUGUCCUCCAGGAGCUCACGUAUGCCUGCCUGUGAGCGCCUCGGCGACAGAGCCGGUGUCCACCCCUGCACUGUCCAC
AAQR03120007.1/7201-7295     UCGGGGCGGCCGCUCUCCCUGUCCUCCAGGAGCUCACGUGUGCCUACCUGUGAGCGCCUCGACGACAGAGCCGGUGCCCGUCCCAGUGUC-UGCAC
AABR05030987.1/5615-5710     ACGGGGUGGACACCGUCCCUGUCCUCCAGGAGCUCACGUAUGCCUGCCUGUGAGCGCCUCGACGACAGAGCCAGAGUCCACCCCUGCACUGCCCAA
AAEX03004350.1/131722-131815 CUCUGGCAGCCGCCCUCCCUGUCCUCCAGGAGCUCACUUAUAUCUGGCCGUGAGCUCCUCGAGGCCAGAGCCCGCGUCUGCC--UCCACUCAGCAC
AAPE02056646.1/5003-4908     AUCGGGCAGCCGCUCUCCCUGUCCUCCAGGAGCUCACCUGCGUCCGGCCGUGAGCUCCUCGGGGCCAGAGCCCGCGUCUGCCUCCGUGCCAGCGCC
#=GC SS_cons                 ::<<<<<<<<<<<<--<-<<<<<-<<-<<<<<<<<<<<-<<____>>->>>>>>>>>>>->>->>>>>->-->>>>>>>>>>>>::::::::::::
#=GC RF                      acggGGcgGcCgCccUCCCuGuCCuCCaGGaGCuCaCgUgcgcCugcCcGuGaGCuCCuCGacGaCaGAGCCgGcGgCcgCCccaguguuauccac
//
# STOCKHOLM 1.0

#=GF AC   RF00764
#=GF ID   mir-191
#=GF DE   microRNA mir-191
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   51.00
#=GF TC   51.10
#=GF NC   50.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000194;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:360-365.
#=GF RN   [2]
#=GF RM   15345052
#=GF RT   Microarray analysis of microRNA expression in the developing mammalian
#=GF RT   brain.
#=GF RA   Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P,
#=GF RA   Constantine-Paton M, Horvitz HR
#=GF RL   Genome Biol. 2004;5:R68.
#=GF RN   [3]
#=GF RM   16766679
#=GF RT   Identification and characterization of two novel classes of small RNAs in
#=GF RT   the mouse germline: retrotransposon-derived siRNAs in oocytes and germline
#=GF RT   small RNAs in testes.
#=GF RA   Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N,
#=GF RA   Imai H
#=GF RL   Genes Dev. 2006;20:1732-1743.
#=GF RN   [4]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [5]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [6]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [7]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues.
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF RN   [8]
#=GF RM   17306260
#=GF RT   Identification and characterization of microRNAs from the bovine adipose
#=GF RT   tissue and mammary gland.
#=GF RA   Gu Z, Eleswarapu S, Jiang H
#=GF RL   FEBS Lett. 2007;581:981-988.
#=GF WK   miR-191
#=GF SQ   5


AAYZ01449103.1/1170-1080  AGCUGGACAGCGGGCAACGGAAUCCCAAAAGCAGCUGUUGUCUCGAGAGCAUUCCAGCUGCGCUUGGAUUUCGUUCCCUGCUUUCCUGCCC
AAPN01354695.1/4366-4456  AGCUUGACAGCAGGCAACGGAAUCCCAAAAGCAGCUGUUGUCUCCAGAGCAUUCCAGCUGCAGUUGGAUUUCGUUCCCUGCUAUCCUGCAA
CT010508.10/218074-218164 GGCUGGACAGCGGGCAACGGAAUCCCAAAAGCAGCUGUUGUCUCCAGAGCAUUCCAGCUGCACUUGGAUUUCGUUCCCUGCUCUCCUGCCU
AC137630.9/69177-69087    GGCUGGACAGCGGGCAACGGAAUCCCAAAAGCAGCUGUUGUCUCCAGAGCAUUCCAGCUGCGCUUGGAUUUCGUCCCCUGCUCUCCUGCCU
AAWZ02016383.1/6922-6832  GGUUUGAUAGUGGGCAACGGAAUCCCAAAAGCAGCUGUUUUCCUCUUAAAGUUCCAGCUGCACUUGGAUUUCGUUCCUUGCUUUCCUACCC
#=GC SS_cons              <<<-<<<-<<<<<<-<<<<<<<<<<-<<--<<<<<<<-<<<_______>>>--->>>>>>>-->>>>>>>>>>>>->>>>>>->>>->>>:
#=GC RF                   gGcUgGacaGcgGGCaaCGgaauCCCaaAAGCaGCuGUugcCuccagAgcaUUCCaGCuGCacuuGGauuuCGuuCCCcgCuuuCcUgCcu
//
# STOCKHOLM 1.0

#=GF AC   RF00765
#=GF ID   mir-337
#=GF DE   microRNA mir-337
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   49.00
#=GF NC   46.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.41 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000195;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:360-365.
#=GF RN   [2]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-337_microRNA_precursor_family
#=GF SQ   6



ABRP01372708.1/596-690   GCCGUAACAAGUAGGAGGGGGGUGAGAACGGCCUCAUCCAGGAGUUGAU-GC-CAGUUACCCAGCGCCUAGAUGAUGCCUUUCUUCACCCCCUUC--AG
AANG01662487.1/1879-1974 GCCGUAGUCAGUAGGUGGGGGGUGAGAACGGCUCCAUACAGGAGUUGAC-GCACAGUUAUCCAGCUCCUAUAUGGCGCCUUUCCUCAUCCCCUUC--AA
AAPY01359946.1/778-872   CCCAUAGUCAGC-GUUGGGGGGUAGGAACGGCUUCAUACAGGAGUUGGU-GCGCAGUUACCCGGCUCCUAUAUGACGCCUUUCUUCACC--CUCCAGCC
AC152063.5/103745-103649 AGUGUAGUGAGAAGUUGGGGGGUGGGAACGGCGUCAUGCAGGAGUUGAUUGCACAGCCAUUCAGCUCCUAUAUGAUGCCUUUCUUCACCCCCUUC--AA
AL117190.6/114606-114701 CCCGUAGUCAGUAGUUGGGGGGUGGGAACGGCUUCAUACAGGAGUUGAU-GCACAGUUAUCCAGCUCCUAUAUGAUGCCUUUCUUCAUCCCCUUC--AA
AAGW02077262.1/1537-1633 CCCGCGGUCGGUAGUUGGGGGAUGGGAACGGCUUCAUACAGGAGUUGAUUGCACAGUCAUCCAGCUCCUAUAUGAUGCCUUUCUUCAUCCUCUUC--AA
#=GC SS_cons             ::::::::::::::::<<<<<<<<<<<<-<<<-<<<<<-<<<<<<<<<_._________>->>>>>>>>->>>>>->>>->>>->>>>>>>>>::..::
#=GC RF                  accgUAgUcAGuAGuugGGGGguGgGaaCGGCuuCauaCaGGaGuuGgU.GCaCAGUuAccCagCuCCuAuauGauGCCUuuCUcCacCCCCuuC..aa
//
# STOCKHOLM 1.0

#=GF AC   RF00766
#=GF ID   mir-335
#=GF DE   microRNA mir-335
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   84.30
#=GF NC   63.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.24 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000196;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [4]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [5]
#=GF RM   19267191
#=GF RT   Identification and characteristics of cattle microRNAs by homology
#=GF RT   searching and small RNA cloning.
#=GF RA   Long JE, Chen HX
#=GF RL   Biochem Genet. 2009;47:329-343.
#=GF WK   MicroRNA
#=GF SQ   9


AAGU03016925.1/62310-62403 UCUUUUGGGCGGGGGUCAAGAGCAAUAACGGAGAAUGUCUGU----GAUGAACCAUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUCCCCGCG
AAFC03120087.1/25191-25098 ACUUUUGGGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGU----CAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUGUACUCA
AALT01453348.1/471-564     UCAUUUGGGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGU----CAUAAACCGUUUUUCAUUAUUGCUCCUGACCGCCUCUCAUUUAUUGGACUCC
AANN01534930.1/9517-9612   UCUUUUGGGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUU--UCAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUUUCAUUGGCUAUAUUCA
AAPY01581132.1/4913-4820   UCUUUUGGGCGAGGAUCAAGAGCAAUAACGAAAAAUGUUUGU----CAUAAACCGUUUUUCAUUAUUGCUCCUGACCUUCUCUCAUUUGCUAGCUUCA
AC007938.1/151529-151622   UGUUUUGAGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGU----CAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUUGCUAUAUUCA
AC146699.5/3373-3276       UCUUUUGGGCGGGGGUCAAGAGCAAUAACGAAAAAUGUUUGUUUUUCGUAAACCGUUUUUCAUUAUUGCUCCUGACCCCCUCUCAUGGGUUAUAGCCA
AAGV020321978.1/1313-1221  UUUUUUGGGCG-GGAUCAAGAGCAAUAACGAAAAAUGUUUGU----CAUAAACCGUUUUUCAUUAUUGCUCCUGACCUUCUCUCAUUUGCUGUAUUCU
AAGW02039138.1/3555-3647   UCUUUUGGGCGGGAGUCAAGAGCAAUAACGAAAAAUGUUUGU----CAUAAACCGUUUUUCAUUAUUGCUCCUGACCUCCUCUCAUUG-CUAUAGUCG
#=GC SS_cons               :::::<<<<-<<<<<<<<-<<<<<<<<<-<<<<<<<<<<<__....___>>>->>>>>>>>->>>>>>>>>->>>>>>>>->>>>:::::::::::::
#=GC RF                    UcuUUuGgGCGGgGGuCaAGaGCaauaaCGaaaaacGuuuGU....cAUaaaCCguuuuuCAuuauuGCuCCuGaCCcCCUCcCaUuuGcUauauuCa
//
# STOCKHOLM 1.0

#=GF AC   RF00767
#=GF ID   mir-150
#=GF DE   microRNA mir-150
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   63.30
#=GF NC   59.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000197;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [2]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues.
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF RN   [3]
#=GF RM   15345052
#=GF RT   Microarray analysis of microRNA expression in the developing mammalian
#=GF RT   brain.
#=GF RA   Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P,
#=GF RA   Constantine-Paton M, Horvitz HR
#=GF RL   Genome Biol. 2004;5:R68.
#=GF RN   [4]
#=GF RM   16766679
#=GF RT   Identification and characterization of two novel classes of small RNAs in
#=GF RT   the mouse germline: retrotransposon-derived siRNAs in oocytes and germline
#=GF RT   small RNAs in testes.
#=GF RA   Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N,
#=GF RA   Imai H
#=GF RL   Genes Dev. 2006;20:1732-1743.
#=GF RN   [5]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [6]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [7]
#=GF RM   18392026
#=GF RT   Discovering microRNAs from deep sequencing data using miRDeep.
#=GF RA   Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S,
#=GF RA   Rajewsky N
#=GF RL   Nat Biotechnol. 2008;26:407-415.
#=GF WK   MiR-150
#=GF SQ   17


AALT01365871.1/7873-7792   CUCCUCAGGGCCCUGUCUCCCAACCCUUGUACCAGCGCU---GCCA-AG--UUGCUGGUACAGGUU--UGGGG-G-GCAGGGACCUGGGGAC
AC010619.7/88039-87956     CUCCCCAUGGCCCUGUCUCCCAACCCUUGUACCAGUGCUG-GGC-UCAG--ACCCUGGUACAGGCC--UGGGG-G-ACAGGGACCUGGGGAC
AAYZ01332954.1/116-31      CUCCUCACGGCCCUGUCUCCCAACCCUCGUACCAGUGUUG-CACAAUAG--ACACUGGUACAGGAU--UGGGG-GCUCAGGGACCUGGGGAC
AAPN01015410.1/1836-1922   CCCCUCGGCGCCCCCUCUCCCAACCCUUGUACCAGAGCAU-AAACUGAA--CCCCUGGUACGGGGCCGUGGGA-G-AGGGGGAGCCGGGGCC
AAFR03057352.1/4345-4428   CCCUCCGGGGCCCCUUCUCCCAACCCUUGUACCAGAG-UC-CAUCAGAG--ACCC-GGUACGGGCU-GUGGGG-G-ACGGGGAGUCGGGGCU
AAFC03061346.1/17848-17932 CUCCUCACGGCCCUGUCUCCCAACCCUUGUACCAGUG-UG-UGUCUCAG--ACCCUGGUACAGGUA--CGGGGAG-GCAGGGACCUGGGGGA
AAPY01553607.1/1213-1296   CUGCCCUCGUCCCCGUCUCCCAACCCUCGUACCAGGGCCA-UGC-UCAG--ACCCUGGUGCAGGGA--UGGGG-G-GCAGGGCCGUGGGGAC
AANG01189373.1/867-783     CUCCUCACGGCCCUGUCUCCCAACCCUUGUACCAGUGCUG-UGGCUCAG--UCCCUGGUACAGGUA--UGGGG-G-GCAGGGACGUGUGGAC
AAQQ01016809.1/78-162      UUCCUCAAGGCCCUGUCUCCCAACCCUUGUACCAGUGCUG-UGCCUUAG--ACCCUGGUACAGGUC--UGGGG-G-UCAGGGACCUGUGGAC
ABDC01415302.1/6674-6591   CUCCUCAUGGCCCUGUCUCCCAACCCUUGUACCAGUGCUG-CCC-UCAG--ACCCUGGUACGGGCG--UGGGG-G-GCAGGGACCUGGGGAC
AACN010859833.1/100-16     CUCCUCUCGGCCCUGUCUCCCAACCCUUGUACCAGUGCUG-UGCCUCAG-UACCCUGGUACAGGCA--UGGGG-G-GCAGGGACU-GGGGAC
AANH01011205.1/15427-15513 UUCCUUGGUCUGGUCACUCCCAAUCCUUGUACCAGUGUCGUUACCACGGUGACGCUGG-ACAGGUU--UGGGG-G-GGGCUGUGCCAAGGAC
AAWR02030682.1/18969-18885 CUCCCCACGGCCCUGUCUCCCAACCCUUGUACCAGUGCUG-UGCCUCGG--UCCCUGGUACAGGCA--UGGGG-G-GCAGGGACCUGGGGGC
FP102665.5/106834-106751   CUCCUCUCGGCCCUAUCUCCCAACCCUUGUACCAGUG-CG-UGCCUCAG--UCCCUGGUACAGGAA--UGGGG-G-GCAGGGACCUGGGGAC
AC150897.2/224703-224619   CUUCUCAAUGCCCUGUCUCCCAACCCUUGUACCAGUGCUG-UGCCUCAG--ACCCUGGUACAGGCC--UGGGG-G-AUAGGGACUUGGGAAC
AAPE02058383.1/6045-6125   CUCCUCAAGGCCCCGUCUCCCAAC-CCUGUACCAUGG-UG-UGC--CAG--UCCCUGGUACAGGCA--UGGGG-G-GCAGGGACCUGGGGAC
AABR05007347.1/8135-8219   CUUCUCAAGGCCCUGUCUCCCAACCCUUGUACCAGUGCUG-UGCCUCAG--ACCCUGGUACAGGCC--UGGGG-G-ACAGGGACUUGGGGAC
#=GC SS_cons               :<<<<<<-<-<<<<<<<<<<<<---<<<<<<<<<<-<<<<._____>>>..->->>>>>>>>>>--..>>>>>.>.>>>>>>->->>>>>>:
#=GC RF                    CuCCcCgaggCccuguCuCCCaACCCuuGUACCAGuGcug.ugcCucag..aCcCUGGUACagGuu..uGGGg.G.acaggGAcccGgGGaC
//
# STOCKHOLM 1.0

#=GF AC   RF00768
#=GF ID   MIR405
#=GF DE   microRNA MIR405
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   104.00
#=GF TC   104.20
#=GF NC   103.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.58 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000198;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15258262
#=GF RT   Novel and stress-regulated microRNAs and other small RNAs from
#=GF RT   Arabidopsis.
#=GF RA   Sunkar R, Zhu JK
#=GF RL   Plant Cell. 2004;16:2001-2019.
#=GF WK   MicroRNA
#=GF SQ   13


AF128396.1/25475-25594   UUAACCCAUUUAA----CAACUCAGUCCAUCAA-----AUUAAAUGAGUUAUGGUU-GACCCAACUCAUUUAACAAAAUGAGUUGGGUC-AACCAUAACUCAUUUAACC--CUAAACUCAUUUGAUU-AUGAGU
AC007843.6/49983-50104   UUAAACCGUUUAA----CAACUCAACCCAUCAA-----AUUAAAUGAGUUAUGGGUUGACGCAACUCAUUUUAUUAAAUGGGUUGGGUCAACCUAUAACUCAUUUAAUC--AUAAACUCAUUUGAUU-AUGAGU
AL161581.2/10009-9888    UUAACCCAUUUAA----CAACUCAACCCAUCAA-----AUUAAAUGAGUUAUGGGUUGACCCAAUUCAUUUAACAAAAUGAGUUGGGUCAACCCAUAACUCAUUUGAUU--AUGAGUUGAGUUGAGU-UGGGUU
AC002534.1/7083-7194     ----------AAA----UGGGUUAACCCAUCAA-----AUUAAAUGAGUUAUGGGUUGACCCAACUCAUUAUGUUAAAUAGGUUGGGUCAACCCAUAACUUAUUUAAUU--CUAAACUCAUUUAAUU-AUGAGU
AC006951.6/55866-55745   UUAACCCAUUUAA----CAAUUUAAUCCAUCAA-----AUUAAAUGAGUUAUGGAUUGACACAACCCAUUUUGUUAAAUGGGUUGUGUCAAUCCAUAACUCAUUUAACC--CUAAACUUAUUUGAUU-AUGAGU
AC002131.1/21060-21186   UUAAUUAAAUUAU----UAUUUAAAUGGGUUAACCCAUAUUAAAUGAGUUAUAGGUAGACCCAACCUAUUUAACAAAAUGAGUUGGGUCAACCCAUAACUCAUUUAACC--UUAAACUCAUUUGAUU-AUGAGU
AL162508.1/25569-25690   UUAAAUGGGUUAA----CAUCUCAAACCAUUAA-----AUUAAAUGAGUUAUAGGUUGACCCAACACAUUUAACAAAAUGAGUUGGGUCAACCCAUAACUCAUUUAUUC--UUAAACUCAUUUGAUU-AUAAGU
AC007123.1/41517-41641   UUAACCCAUUUAA----CAACUCAACCCAUCAA-----AUUAAAUGAGUUAUGGGUUGACCCAACUCAUUUUGUUAAAUGAGUUGGGUCAACCCAUAACUCAUUUUGUUAAAUGAGUUGGGUCAACCCAUAACU
AC007887.9/131110-131238 UUAAAUGAGUUAUGGGUUGACCCAACUCAUUUU-----GUUAAAUGAGUUAUGGGUUGACCCAACUCAUUUUGUUAAAUGGGUUGGGUCAACCCAUAACUCAUUUAAUUUGAUGGGUUGAGUCAACCCAUAACU
AL162874.1/39868-39989   UUAAUUCAUUUAA----CAACUCAACCCAUCAA-----AUUAAAUGAGUUAUGGGGUUACCCAACCCAUUUAACAAAAUGAGUUGGGUCAACUCAUAACUCAUUUAACC--AUAAACUCAUUUGAUU-AUAAGU
AB028616.1/15879-15998   UUAACCCAUUUAA----CAACUCAACCCAUCAA-----AUUAAAUGAGUUAUAGGUU-GACCAACCCAUUUAACAAAAUGGGUUAGUC-AACCUAUAACUCAUUUAACC--CUAAACUCAUUUGAUU-AUGAGU
AB028616.1/7811-7932     UUAACCCAUUUAA----AACCUCAACCCAUCAA-----AUUAAAUGAGUUAUGAGUUGAUCCAACCCAUUUAACAACAUGAGUUGGGUCAACCCAUAACUCAUUUAAUU--CUAAACUCAUUUGAUU-AUGAAU
AC189263.2/67212-67332   GUCAACCAUUAAC----CCAUCUAACCUUUUUA-----AUUUAAUGGGUCAUGGGUCAACCCAACCUAUUUAAU-AAAUGGGUUGGGUUGACCCAUGACUCAUUAACAG--UAAACCCAUUUGGGUU-UUGGGU
#=GC SS_cons             :::::::::::::....::::::::::::::::.....:::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>::::..::::::::::::::::.::::::
#=GC RF                  UUAAaccAuUUAa....caacUcAAcccAUcAA.....AUUaAAUGaGUuAUGGGUuGacCCAACccAUUuaauaaAAUggGUUGGguCaACCCAUaACuCAUUuAauu..uUAAacUcAuUuGAuU.AUgAgU
//
# STOCKHOLM 1.0

#=GF AC   RF00769
#=GF ID   mir-331
#=GF DE   microRNA mir-331
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   100.00
#=GF TC   103.40
#=GF NC   48.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000199;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-331_microRNA_precursor_family
#=GF SQ   5


AALT01654326.1/921-1014    GGACUUUGGUUUGUUUGGGUUUGUUCUAGGUAUGGUCCCAGGGAUCCCAGAUAAAACCAGGCCCCUGGGCCUAUCCUAGAACCAACCUAAACUC
AANN01801584.1/619-712     GCCUUUGGUUCUGUUUGGGCUUGUUCUAGGUACGGUCUCAGGGAUCCCAGAUCAAACCAGGCCCCUGGGCCUAUCCUAGAACCAACCUAAACUC
AC122901.4/85573-85480     GAGUCUGGUUUUGUUUGGGUUUGUUCUAGGUAUGGUCCCAGGGAUCCCAGAUCAAACCAGGCCCCUGGGCCUAUCCUAGAACCAACCUAAACCC
AC084879.23/106118-106025  GAGUUUGGUUUUGUUUGGGUUUGUUCUAGGUAUGGUCCCAGGGAUCCCAGAUCAAACCAGGCCCCUGGGCCUAUCCUAGAACCAACCUAAGCUC
AGCE01060485.1/37978-38071 GAGUUUGGUUUUGUUUGGGUUUGUUCUAGGUAUGGUCCCAGGGAUCCCAGAUCAAACCAGGCCCCUGGGCCUAUCCUAGAACCAACCUAAACUC
#=GC SS_cons               ::::::::::::<<<<<<<<<-<<<<<<<<---<<-<<<<<<<___________________>>>>>>>>>--->>>>>>>>->>>>>>>>>::
#=GC RF                    GaguuUgGuUuUGuuugGGuuUGuuCuaGGUAuGGUCcCaGGGAUCCCAGAUcAAACCAGGCCCCuGgGCCUAUCCuaGaaCCaaCCuaaaCuC
//
# STOCKHOLM 1.0

#=GF AC   RF00770
#=GF ID   mir-330
#=GF DE   microRNA mir-330
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   95.00
#=GF TC   99.80
#=GF NC   81.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000200;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:360-365.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [4]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [5]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [6]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   Mir-330_microRNA_precursor_family
#=GF SQ   6


CAAA01027766.1/2291-2387   ACCCUUUGGC-GAUCUCUGCCUCUAAGGGCCAGAGUCUUAGGCUCUUC-AAGAUCCAUCGAGC-AAAGCACAGGGCCUGCAGAGAGGUAGCGCUCUGCUC
AANU01182576.1/213-309     GAUCUUUGGC-GAUCACUGCCUCUCUGGGCCUGUGUCUUAGGCUCUGC-AAGAUCAACCGAGC-AAAGCACACGGCCUGCAGAGAGGCAGCGCUCUGCCC
AAHX01004186.1/15942-15846 ACCCUUUGGC-GAUCUCUGCCUCUCUGGGCCUGUGUCUUAGGCUCUUC-AAGAUCUAACGAGC-AAAGCACAGGGCCUGCAGAGAGGUAGCGCUCUGCUC
AAIY01734125.1/577-673     GAUCUUGGGC-GAUCACUGCCUCUCUGGGCCUGUGUCUUAGGCUCUGC-GUGUUCGACCGAGC-AAAGCACACGGCCUGCAGAGAGCCAGCGCUCCGCUC
AAWR02030508.1/26139-26041 GAUCCUUGGCGUU-CACUGCCUCUCUGGGCCUGUGUCUUAGGCUCUUCAAAGAUCAACCGAGCAAAAGCACACGGCCUGCAGAGAGGCAGCGCUGCGCUC
AAGV020131910.1/223-319    GAUCUUGGGC-GAUCACUGCCUCUCUGGGCCUGUGUCUUAGGCUCUGC-AAGAUCAACCGAGC-AAAGCACACGGCCUGCAGAGAGCCAGCGCUGCGCUC
#=GC SS_cons               :::::::<<<.<<-<-<<<<<<<<<<<<<<<<<<<-<<<--<<<<___.__________>>>>.->>>>>>>->>>>-->>>>>>>>>>>->->>->>>:
#=GC RF                    gauCuUugGC.gaUCaCugcCuCucuGGGCCuGuGUCuuAGGCuCUuC.AAGAUCaAcCGaGC.AaaGCaCacGGCCUGCagaGaGgcaGCGCucuGCcC
//
# STOCKHOLM 1.0

#=GF AC   RF00771
#=GF ID   mir-185
#=GF DE   microRNA mir-185
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   95.00
#=GF TC   95.30
#=GF NC   92.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000202;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15800047
#=GF RT   Kaposi's sarcoma-associated herpesvirus expresses an array of viral
#=GF RT   microRNAs in latently infected cells.
#=GF RA   Cai X, Lu S, Zhang Z, Gonzalez CM, Damania B, Cullen BR
#=GF RL   Proc Natl Acad Sci U S A. 2005;102:5570-5575.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [4]
#=GF RM   20158877
#=GF RT   Analysis of deep sequencing microRNA expression profile from human
#=GF RT   embryonic stem cells derived mesenchymal stem cells reveals possible role
#=GF RT   of let-7 microRNA family in downstream targeting of hepatic nuclear factor
#=GF RT   4 alpha.
#=GF RA   Koh W, Sheng CT, Tan B, Lee QY, Kuznetsov V, Kiang LS, Tanavde V
#=GF RL   BMC Genomics. 2010;11:S6.
#=GF RN   [5]
#=GF RM   18548309
#=GF RT   Identification and characterization of new microRNAs from pig.
#=GF RA   Kim J, Cho IS, Hong JS, Choi YK, Kim H, Lee YS
#=GF RL   Mamm Genome. 2008;19:570-580.
#=GF RN   [6]
#=GF RM   19917043
#=GF RT   MicroRNA identity and abundance in porcine skeletal muscles determined by
#=GF RT   deep sequencing.
#=GF RA   Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C,
#=GF RA   Thomsen B
#=GF RL   Anim Genet. 2010;41:159-168.
#=GF RN   [7]
#=GF RM   15345052
#=GF RT   Microarray analysis of microRNA expression in the developing mammalian
#=GF RT   brain.
#=GF RA   Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P,
#=GF RA   Constantine-Paton M, Horvitz HR
#=GF RL   Genome Biol. 2004;5:R68.
#=GF RN   [8]
#=GF RM   16766679
#=GF RT   Identification and characterization of two novel classes of small RNAs in
#=GF RT   the mouse germline: retrotransposon-derived siRNAs in oocytes and germline
#=GF RT   small RNAs in testes.
#=GF RA   Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N,
#=GF RA   Imai H
#=GF RL   Genes Dev. 2006;20:1732-1743.
#=GF RN   [9]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   Mir-185_microRNA_precursor_family
#=GF SQ   5


AAIY01387213.1/2963-3043 GGGGGUGAGGGGCUGGAGAGAAAGGCAGUCCCUGAUGGUCCCCUCCCCAGGGGCUGGUUUUCCUCUGGUCCUUCCUUCCCA
AAFC03097072.1/7852-7932 GGGGGUGAGGGACUGGAGAGAAAGGCAGUUCCUGAUGGUCCCCUCCCCAGGGGCUGGCUUUCCUCCGGCCCCUCCUUCCUG
AAGV020977699.1/729-650  GGGGCCGAGGGACUGGAGAGAAAGGCAGUUCCUGAUGGUGCCU-CCCCAGGGGCUGGCUUUCCUCUGGUCCUUCCCUCCCA
AC002491.1/33761-33841   GGGGGCGAGGGAUUGGAGAGAAAGGCAGUUCCUGAUGGUCCCCUCCCCAGGGGCUGGCUUUCCUCUGGUCCUUCCCUCCCA
AC003060.1/93739-93660   GGGGGUGAGGGAUUGGAGAGAAAGGCAGUUCCUGAUGGUCCCCUCC-CAGGGGCUGGCUUUCCUCUGGUCCUUCUCUCCCA
#=GC SS_cons             <<<<<-<<<<<<<<<<<<-<<<<<<<<<<<<<<<--<<______>>->>>>>>>>>>>>>>>>>>>>>>>>>>>->>>>>:
#=GC RF                  GGGgguGagGGgcugGaGAGaaaGcCaGucCCuGAUGGUcCCcUCCCCaGGggCuGgCuuuCCuCcggcCCcuCccuCCCA
//
# STOCKHOLM 1.0

#=GF AC   RF00772
#=GF ID   mir-328
#=GF DE   microRNA mir-328
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   80.60
#=GF NC   71.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.00 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000203;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:360-365.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [4]
#=GF RM   15538371
#=GF RT   A pancreatic islet-specific microRNA regulates insulin secretion.
#=GF RA   Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer
#=GF RA   S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M
#=GF RL   Nature. 2004;432:226-230.
#=GF RN   [5]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [6]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [7]
#=GF RM   19917043
#=GF RT   MicroRNA identity and abundance in porcine skeletal muscles determined by
#=GF RT   deep sequencing.
#=GF RA   Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C,
#=GF RA   Thomsen B
#=GF RL   Anim Genet. 2010;41:159-168.
#=GF WK   MicroRNA
#=GF SQ   13


AAFC03022836.1/10329-10246 UGGAGCGGGGGGGCAGGAGGGGCUCAGGGAGAUAGUGUGUGCUGCCCCUGGCCCUCUCUGCCCUUCCGUCCCCUGUUCCUGAAC
CAAA01078944.1/1505-1422   UGGGGCAGGGGGGCAGGAGGGGCUCACGCAGAAAGUAUCUACAGCCCCUGGCCCUCUCUGCCCUUCCGUCCCCUGCCCCCAAGU
AC040160.4/136429-136512   UGGAGUGGGGGGGCAGGAGGGGCUCAGGGAGAAAGUGCAUACAGCCCCUGGCCCUCUCUGCCCUUCCGUCCCCUGCUCUUGGCC
AAYZ01109814.1/701-618     UGGGGCAGGGGGGCAGGAGGGGCUCAGGGAGGAGAGACAUGCAACCCCUGGCCCUCUCUGCCCUUCCGUCCCUGGCCCCCGAAC
AAPY01319435.1/939-1022    UGGAGCGGGGGGGCAGGAGGGGCUCAGGGAGGAAGCCUGUAUAGCCCCUGGCCCUCUCUGCCCUUCCGUCCCAGUUCCCACCCA
AANN01235694.1/888-971     UGGAGCAGAGGGGCAGGAGGGGCUCAGGGAGAAAGUGUAUGUCACCCCUGGCCCUCUCUGCCCUUCCGCCCCCUGUUUCUAGAC
ABDC01234803.1/9089-9006   UGGAGCAGGGGGGCAGGAGGGGCUCAGGGAGAAAGUGUGUGCAGCCCCUGGCCCUCUCUGCCCUUCCGCCCCCUGUUCCCAGAC
AC140074.2/123408-123491   UGGGGCAGGGGGGCAGGAGGGGCUCAGGGAGAAAGUAUCUACAGCCCCUGGCCCUCUCUGCCCUUCCGUCCCCUGUCCCCAAGU
AAGW02067912.1/8740-8658   UGGAGCGGGGGGGCAGGAGGGGCUCAGGGAGAAA-AGUGUGCAGCCCCUGGCCCUCUCUGCCCUUCCGUCCCUGUUUCCAGACU
AAQR03153104.1/6331-6414   UGGAGCAGGGGGGCAGGAGGGGCUCAGGGAGAAAGUGUGUAUAGCCCCUGGCCCUCUCUGCCCUUCCGCCCCCUGUUCUCACAG
AABR05076001.1/84639-84556 UGGGGCAGGGGGGCAGGAGGGGCUCAGGGAGAAAGCAUCUACAGCCCCUGGCCCUCUCUGCCCUUCCGUCCCCUGUCCCCAAAU
AAPE02038693.1/1176-1093   UGGAGCAGGGGGGCAGGAGGGGCUCAGGGAGGAAGUAUGUGAAGCCCCUGGCCCUCUCUGCCCUUCCGUCCCCCGUUCCCGGAC
AAPN01317755.1/481-398     CGGGGGGGGGGGGGGGGGGGGGGAGAAAAAAAAAAAUUUUUUUUUUUUUUCCCCCCCCCCCCCCCCCCCCCCCCUUUUUAAAAA
#=GC SS_cons               :<<<<<-<<<<<<<<<<<<<<<<-<<<<<-<---<______>-->>>>>>>>>>>>>>>>>>>>>>->>>>>::::::::::::
#=GC RF                    UGGggcaGggGGGcaGgggGGGcUcAgGgAGAAAguaUuUacagCcCcUggCCCcccCugCCCccCCgccCCcugUuccaaaau
//
# STOCKHOLM 1.0

#=GF AC   RF00773
#=GF ID   mir-298
#=GF DE   microRNA mir-298
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   75.80
#=GF NC   45.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.31 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000206;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12919684
#=GF RT   Embryonic stem cell-specific MicroRNAs.
#=GF RA   Houbaviy HB, Murray MF, Sharp PA
#=GF RL   Dev Cell. 2003;5:351-358.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [4]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   MicroRNA
#=GF SQ   5


AADC01142343.1/122563-122476 UCAGGUCUUCAGCAGAAGC-AGGGAGGUUCUCCCAGUGGUUUUCCUUGACUGUGAGGAACUAGCCUGCUGCUUUGCUCAGGAGUGAGCU
AL929537.17/90228-90312      CCAGGCCUUUGGCAGAGGA-GGGCUGUUCUUCCCUUGAGUUUU--AUGACUGGGAGGAACUAGCCUUCU-CUCAGCUUAGGAGUGGGCC
ABDC01114716.1/6703-6619     UUAGGCCUUUAUCGGAAGCAAGGCUGUUCU----AGUCGUCUUCCUGGACCACGAGGAACUUGCCUGUUGCUUUGCUUAGGACUGAGCU
AAQR03050726.1/73824-73737   UUAGGCCUUUAACAGAAGU-GAGCCAGUUCUCCCUGGGCUCUUGCUUGAUCUUGAGGAACUUGCCUAUUGCUUUGCUCAGGACUGAGCU
ACFV01097969.1/11783-11870   UCAGGUCUUCAGCAGAAAC-AGGAUGGUUCUCCCAGUGGUUGAUCUCCACUGUGAGGAACUGGCCUGCCGCUUUGCUGGGGAGUGAGCU
#=GC SS_cons                 <<<--<<<--<<<<<<<<<.<<<<<<<<<<<<<<---<<<<______>>>>>>>>>>>>>->>>>>>>>-->>>>>>->>>-->>>:::
#=GC RF                      ucAGGcCuUuagCagAagc.aGGccGuUccuCccaguggUcUUuCUugAccggGaggAaCUggCCugcuGCUcuGcuuaGgAgUgaGCU
//
# STOCKHOLM 1.0

#=GF AC   RF00774
#=GF ID   mir-360
#=GF DE   microRNA mir-360
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   64.00
#=GF TC   66.70
#=GF NC   58.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.29 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000210;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [3]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF WK   MicroRNA
#=GF SQ   5


AAGD02000028.1/247908-247796   AAAUUGUCAAAAAGGCGAUCAGGGUUUUGUGACCGUUGUUACGGUCAAUUU-CAUUCAG---AAGCUAUGACCGUAAUCCCGUUCACAACAUCUUGUUUAGCU-UGACUCAUGAAUUG
CAAC02000521.1/3689146-3689258 UAUUCCAUAAAAAAGCGCCUAGGGUUUUGUGACCGUUGUUACGGUCAAUUC-AUGUCUG---ACACAAUGACCGUAAUCCCGUUCACAACACCUUGUGUGGCU-UGAAUAAUGAAAUU
FO080886.1/6709-6821           CAUUCUGUUAGGAAGC-AUCAAUGUGUUGUGACCGUUGUUACGGUCAAUUUGCAAAUUG---AAAAAAUGACCGUAAUCCCGUUCACAAUACAUUGUUCGUUU-UCUCCAAAGGUGAU
ABEG02001210.1/41217-41109     AUAUUUCUUGAACGGC-AUCAAGGUUUUGUGACCGUUGUUACGGUCAUUUCAACAUGUA-------ACUGACCGUAAUCCCGUUCACAACACAUUGUUUGUCGAUUCGUCAUGAAA-U
AEHI01030914.1/111-1           UAAUUGUGAAUUGAGUGAAUUUGAUUUUGUGACCGUUAUUACGGUCAUUUU-CCAUUUAUUCAUAUUUUGACCGUAAUUCCGACCACAACAUCUUAUUCGCUC-GCAAU-----UUUU
#=GC SS_cons                   ::::::::::::<<<<<<-<<<<<<-<<<<<<-<<--<<<<<<<<<<____._______...______>>>>>>>>>>-->>->>>>>>->>>>>>->>>>>>.::::::::::::::
#=GC RF                        uAaUuuuuaAaagggcgaucaaggUUUUGUGaCCGUUgUUACGGUCAaUUu.caaUuUg...AaAuaaUGACCGUAAucCCGuuCACAACAccuugUucgccc.uuaaUaAuGAauuU
//
# STOCKHOLM 1.0

#=GF AC   RF00775
#=GF ID   mir-432
#=GF DE   microRNA mir-432
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   73.60
#=GF NC   47.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000211;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction
#=GF RT   method.
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   19784364
#=GF RT   Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic
#=GF RT   stem cells and neural precursors.
#=GF RA   Goff LA, Davila J, Swerdel MR, Moore JC, Cohen RI, Wu H, Sun YE, Hart RP
#=GF RL   PLoS One. 2009;4:e7192.
#=GF WK   Mir-432_microRNA_precursor_family
#=GF SQ   6


AAFC03050876.1/56533-56626 UGACUCCUCCAAGUCUUGGAGUAGGUCAUUGGGUGGAUCCUUUAUUUCCCUAUGUGGGCCACUGGAUGGCUCCUCCAUGUCUUG-GCGGAGGUCA
CAAA01088145.1/20377-20284 UGGCUCCUCCACUUCUUGGAGUAGAUCAGUGGGCAGCUCUUGCAUUUCCUGGUGGGGGCCACUGGAUGGCUCCUCCACUUCUUG-GAGUAGAUUA
CAAA01088145.1/20764-20680 UGAUUCCUCCAUGUCUUGGGGUAGAUCGUUAGAUGAUGCCUC---------ACAGGGGUCGCUGGAUGGCUCCUCCACUUCCCG-GAGUAGAUCA
AY865932.1/8-101           UGACUCCUCCAGGUCUUGGAGUAGGUCAUUGGGUGGAUCCUCUAUUUCCUUACGUGGGCCACUGGAUGGCUCCUCCAUGUCUUG-GAGUAGAUCA
AANN01125399.1/1129-1222   GGACCCCUCCACGUCUUGGAGUAGGUCAUUGGGUGGAUCCGUGUUUUCGCUACGUGGGCCACUGGAUGGCUCCUCCAUGUCUUG-GCGGAGGUCA
AAIY01403620.1/1283-1377   CAGCUCUUCCAUUUCCUGGAGUGAGCCACUGGGUGGCUCCCUACUUUGCUGGGCUGGGCCACCGGCCGGCUGCAUCACUUCCUGCGCGUGGCUGC
#=GC SS_cons               ::::::<<<<<<<-<-<<<<<--<<<<<<<-<<<<<-<<<_______________>>>>>>>>->>>>>>>->>>>>->->>>>.>>>:::::::
#=GC RF                    uGaCUCcuCCacgUcUUGGaGUAgGuCauuGgGuGGauCCuuuaUUUccuuauguGGgCCaCcGgauGgCucCuCCAcgUcguG.GaguAGaUcA
//
# STOCKHOLM 1.0

#=GF AC   RF00776
#=GF ID   mir-540
#=GF DE   microRNA mir-540
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   97.30
#=GF NC   55.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.21 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000212;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   MicroRNA
#=GF SQ   2


AAQQ01350179.1/20-102    CCUUGGGGCUGGGCCCAGGGUCACCCUCUGACUCUGCGGCCACGGGCAGACAGGGCAGAGGUGGAGU-UGGGCCAGCCCUGGGG
AC152063.5/103464-103381 CCCUGGGGCUGGGCCAAGGGUCACCCUCUGACUCUGUGGCCAAGGGUAGACAGGUCAGAGGUCGAUCCUGGGCCUACUCUGGGG
#=GC SS_cons             :::::::::<<<<<<<<<<<<<--<<<<<<<<-<<<<-<<<___>>>-->>>>>>>>>>>>-->>>>>>>>>>>>>::::::::
#=GC RF                  CCuUGGGGCugGGCCcaGgguCACCCuCuGaCUCuGuGgCCAaGGGcAGaCaGGuCaGaGGUgGaccCugGGCCcaCuCUGGGG
//
# STOCKHOLM 1.0

#=GF AC   RF00777
#=GF ID   mir-541
#=GF DE   microRNA mir-541
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   46.30
#=GF NC   39.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000213;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction
#=GF RT   method.
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [2]
#=GF RM   16973894
#=GF RT   Mouse microRNA profiles determined with a new and sensitive cloning
#=GF RT   method.
#=GF RA   Takada S, Berezikov E, Yamashita Y, Lagos-Quintana M, Kloosterman WP,
#=GF RA   Enomoto M, Hatanaka H, Fujiwara S, Watanabe H, Soda M, Choi YL, Plasterk
#=GF RA   RH, Cuppen E, Mano H
#=GF RL   Nucleic Acids Res. 2006;34:e115.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [5]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [6]
#=GF RM   20944086
#=GF RT   Assessing the effect of the CLPG mutation on the microRNA catalog of
#=GF RT   skeletal muscle using high-throughput sequencing.
#=GF RA   Caiment F, Charlier C, Hadfield T, Cockett N, Georges M, Baurain D
#=GF RL   Genome Res. 2010;20:1651-1662.
#=GF WK   Mir-541_microRNA_precursor_family
#=GF SQ   10


AAYZ01254085.1/10311-10400   GCCA--ACGUCAGGGAAAGGAUUCUGCUGUCGGUCCCACUCCAAAGUUCACAAAAUGGGU-GGUGGGCACAGAAUCCAGACCCUGCUUGUGGC
AANG01133006.1/4131-4221     CCCA--AACUCAUGCCAGGGGUUCUGCGGUCGGCCCCCCUCCCGAAGUUCCCCAAACAGGUGGCGGGCACAGAGUGCAGACUCUGUGUGUGGC
AANN01107744.1/773-685       GCCA--AAGUCAGGGAAAGGAUUCUGCUGUCGGUCCCACUCCACGACUCGCAGAC-GGGU-GGUGGGCACAGAAUCCAGACUCUGCUUAUGGC
AANU01197803.1/2974-3063     GCCA--ACGUCAGGGAAAGGAUUCUGCUGUCGGUCCCACUCCAAAGUGCAUAGAAUGGGU-GGUGGGCACAGAAUCCGGACUCUGCUUGUGGC
AAGV020430601.1/5595-5683    GCCG--ACGUCAGGGAAAGGAUUCUGCUGUCGGUCCCACUCCAAAGUUUGCAAAAUGGGU-GGUGGGCACAGAAUCCAGACUCUGCUG-UGGC
AC121784.2/137943-138032     GCCA--AAAUCAGAGAAGGGAUUCUGAUGUUGGUCACACUCCAAGAGUUUUAAAAUGAGU-GGCGAACACAGAAUCCAUACUCUGCUUAUGGC
AL132709.5/57108-57019       GCCA--ACGUCAGGGAAAGGAUUCUGCUGUCGGUCCCACUCCAAAGUUCACAGAAUGGGU-GGUGGGCACAGAAUCUGGACUCUGCUUGUGGC
AAGU03025975.1/15199-15110   GCCA--AUGUCAGAAAAAGGAUUCUGCUGUCGGUCCCACUCCAAAUGUCUCAGAAUGGGU-GGUGGGCACAGAAUCCGGACUCUGCUUGUGGC
AAEX03006005.1/168837-168928 GUCGUGACACCAGGGAGAGGAUUCUGCUGUGGGUCCCACCCCAAAGUUCGCAAAAUAGGU-GGUGGGCACAGAAUCCAGACUCUGCUUGUGGC
AACZ03097072.1/25810-25899   GCCA--ACGUCAGGGAAAGGACUCUGCUGUCGGUCCCACUGCAAAGUUCACAGAAUGGGU-GGUGGGCACCGAAUCCGGACUCUGCCUGUGGC
#=GC SS_cons                 <<<<..-<<-<<<<<---<<<<<<<<-<<<<-<-<-<<<<<_______________>>>>.>>>->>>>>>>>>>>>--->>>>>->>->>>>
#=GC RF                      GCCa..AcgUCaGggAAaGGauUCuGcuGucGgUCcCaCccCAaAauUcacAaAAuggGu.GGcGggCaCaGAauCCaGAccCuGccgguGGC
//
# STOCKHOLM 1.0

#=GF AC   RF00778
#=GF ID   MIR473
#=GF DE   microRNA MIR473
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   52.00
#=GF TC   52.00
#=GF NC   51.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.48 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000214;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15994906
#=GF RT   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa
#=GF RT   that are absent from Arabidopsis.
#=GF RA   Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL
#=GF RL   Plant Cell. 2005;17:2186-2203.
#=GF RN   [2]
#=GF RM   20230504
#=GF RT   Identification of grapevine microRNAs and their targets using
#=GF RT   high-throughput sequencing and degradome analysis.
#=GF RA   Pantaleo V, Szittya G, Moxon S, Miozzi L, Moulton V, Dalmay T, Burgyan J
#=GF RL   Plant J. 2010;62:960-976.
#=GF WK   MicroRNA
#=GF SQ   6


AM424499.2/17212-17291     AUUG---CUCACUCUUUCUCAAGGGCUUCUAGCAUUGCC--------------------AGUAACAAAA--------UGGCAAGCUCGAAGUCUUUG-GGGAGAGUGG---ACAA
AM424499.2/17051-17153     GUUG---CUCACUCUCCCUCAAGGGCUUCUGCACUUUGGCCAUGGCCAUAUACCAAUGUGGGGCAAGUGGG------AAAGAGGGUAGAAGCUCUUGAGGGGGACUGA---AGAA
AY728388.1/84-183          AUUG---UUCACUCUCCCUC-AAGGCUUCCAACGCAAUAACCAGCUACGUA--------CAUGUAACUGUGUUACGGCUGCAGGCUUGAGGCCUUUGGGGGAGAGUGG---UCAA
AASG02001028.1/43237-43323 UUCAUUCUUCACUCUCCCUCAAGGGCUUCUGUGUGUUUU--------------------UUGGUCGAAA--------GACCAAUUCAGAGGUCCUGUAGGGAGAGUGGAUAAUAU
AY728389.1/1-100           --UG---CUCGCUCUCCCUC-AGGGCUUCCAACGCAGUAAGCAGGUACGUG--------CAUGUCAGCAUAUUCUCGCUGCAGGCUCGAGGUCUUUG-GUGAGAGUAGUGAUCAA
AASG02004731.1/12744-12666 AUUG---UUCACUCUCUC-UGAAGGCUUCAAACAGUCUC--------------------CAGCUGGCC---------U--CAAGUUUGAGGCCUUUG-GUUAGAGUGGACAAAAG
#=GC SS_cons               ::::...:<<<<<<<<<<-<<<<<<<<<<______________________........____________......__________>>>>>>>>>>->>>>>>>>>>...::::
#=GC RF                    aUUG...uuCACUCUccCUcaAgGGCuUCuaacauUuuaacaaGguaaguu........cagGuaAauaug......uagCAgGuUaGAgGCCcUugAGggAGAGUGg...AcAa
//
# STOCKHOLM 1.0

#=GF AC   RF00779
#=GF ID   MIR474
#=GF DE   microRNA MIR474
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   48.10
#=GF NC   47.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.03 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000215;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15994906
#=GF RT   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa
#=GF RT   that are absent from Arabidopsis.
#=GF RA   Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL
#=GF RL   Plant Cell. 2005;17:2186-2203.
#=GF WK   Mir-474_microRNA_precursor_family
#=GF SQ   11


AARH01021309.1/1506-1605     CCAAGAGCU---GUUGGGUCUGGCUCGGCUGCCAGACUCAACGCU--------------AUUGGGUCCA--------GCUGUCCAGCCAAACCCAAU---GCCCAACCAAAUCCAAU---AGCGUUGGGUC
AARH01002585.1/127261-127166 UCUAAAAGG--UGUUGGGUUUGGCUGGGCAGCGAGAUCCAAUGCU--------------AUUAGGUCUU--------GC----UUGGGGGU----UGGCUGCCCAGCUAGACCCACCAAUC---UUGGAUC
AARH01008738.1/175548-175428 UCCAAAAGU--UGUUGGGUCUUGUUGGGCAACGUGAUCUAAUGCUAUGAACCCAACGCCAUUAGGUCUU--------GCUGGACAAUGCUAUUAGAUUCUGGCAAGUCAGACCCAACAAUAUUUUUUGACU
AARH01008738.1/175225-175331 AGACCCACCAAUCUUGGGUCAAGCUGGGCAACGAGACCCAAUGCG--------------AUUGGGUCAG--------GCUGGGAAGCCAGACCCAAC--UUCUCAGCAGGACCCAAUAGCGUUGGGUCUUA
AARH01003136.1/362522-362625 UCCAAAAGU--UGCUGGGUUUGGCUGGGCAGGCGGACCCAAUGCU--------------AUUGGGUUCA--------GCAGGACCCAACACUUCUUUCCUUCUCUUCUAUCACCAGC---ACCCUUUGAAA
AY728392.1/1-107             UUCAAAAGU--UGUUGGGUUUGGCUGGGCAGCCAGAUCCAGUGCU--------------AUUGGGUCCU--------GUUAGACAACGCUAUUUGGUCUUGUCAAGCUAGAUCCAACAUUACUUUUUGACU
AARH01007580.1/103082-102983 UCAAUGCUA--UUAGGUCUAG--UUUUUCUGCUAGACCCAAUGCU--------------AUUGGGUCUA--------UUUUUGCAG-----CCAGAUCCAAAACUAUUUUGGAUCUGACUUAGCAUUGUUA
AARH01005763.1/41169-41075   UCAAAAGCU---GCUGGGUCUGGCUGGACAGCCAGACCCAAAUCG---------------------CUU--------CCAAUU-GGUGCUGGGUUUGGCUGCUCAGCCAGACCCAGC---AGCUUUUGGCA
AARH01005758.1/50942-50847   UCCACAAGC--UAUUGAGUCUGGCUGGGUAGCCGGACCCAAUGUU--------------AUUGGGUUUU--------GCUGGGCUGUUGAACCCAAG--UUUUCUUCUAAAA--------GC-UGUUGGGU
AARH01015563.1/5266-5377     UCCAAAAGU--UGUUAGGUCUGAUUGGGUAGUAGGACCCAACGCU--------------AUUGGGUCCUACUAGGAGACAGAACCCAACGUUUCUUUCCUCCUCUUCUAUCACCAGC---ACCCUUUGAAA
AARH01006145.1/4584-4504     UCCAAAAGU--UGUUGGGUCUGGCUGGCAGCC-GGACCCAACGCU--------------AUUGGGUCC-----------------------------GGCUGCCAGCAGGACUCAAU---GCUAAU-GAGU
#=GC SS_cons                 ((-((((((..-((((((((((((((((((((,<<<<<<<<<___..............>>>>>>>>>,........,,<<<<________>>>>,,))))))))))))))))))))---))))))-))::
#=GC RF                      uCcAaaggu..UguuGGgucugGcugggcagcggGACCCAAuGCU..............aUUGGGUCcu........gCugggCagugcuacccaaugcugcccagCcagacCCaacAaUaccuuUUGaua
//
# STOCKHOLM 1.0

#=GF AC   RF00780
#=GF ID   MIR477
#=GF DE   microRNA MIR477
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   65.20
#=GF NC   63.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.07 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000216;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15994906
#=GF RT   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa
#=GF RT   that are absent from Arabidopsis.
#=GF RA   Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL
#=GF RL   Plant Cell. 2005;17:2186-2203.
#=GF WK   MicroRNA
#=GF SQ   3


AY728433.1/1-85            --------CAAUCUCCCUCAGAGGCUUCCAAUAUCUC---AGUUUA--------UAGUAAUU---GCUUCAAAUAAUGAGAAUGUUGGAUGCCUUUGGGUGAGAUUG-------
AASG02000511.1/21598-21512 GAAGCUUCCAAUCUCCCUCAAAGGCUUCCAACA----------------------UACAUCCAUGACCG----CUAUGGGAAUGGUGGAUGCCUUUGGGGG-GAUUGAAGGCUU
AM458660.1/10017-9919      GAAGGCUCCAACUUCCCUCAAAGGCUUCCAAUAUUCCAGCAGACUACUAUUGGC---------------UUAGAUAUGGUAACGUUGGGAGCCUGCGAGGGAAACUGAAGCCUU
#=GC SS_cons               ::<<<<-<<<<<<<<<<<<-<<<<<<<<<<<<<____...______........._______..._________________>>>>>>>>>>>>>->>>>>>>>>>>>->>>>:
#=GC RF                    GAaGgcUcCAaucuCcCuCAgAGGCuuCCAacaUuuC...AGauUA.........aauAauu...aCuuuuAauuAUGggAAuguUGGaaGCCUcuGaGgGagauUGgAgcCuU
//
# STOCKHOLM 1.0

#=GF AC   RF00781
#=GF ID   mir-505
#=GF DE   microRNA mir-505
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   84.00
#=GF TC   84.40
#=GF NC   63.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.53 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000217;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach.
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF WK   Mir-505_microRNA_precursor_family
#=GF SQ   5


AAIY01284167.1/1220-1137 GAUGCGCCCAGUGGGGGAGCCAGGAAGUAUUGAUGUUUCCGCCAGUUUAGCAUCAACAUUUGCUGCUUUCCUCUCUGGAGCAUC
AANN01119226.1/350-433   GAUGCACCCAGUGGGGGAGCCAGGAAGUAUUGAUGUUUCUGCCAGUUUAGCUUCCACACUUGCUGGCUUCCUCUGCGGAGCAUC
ABBA01066083.1/4722-4805 GAUGCACCCAGUGGGGGAGCCAGGAAGUAUUGAUGUUUCUGCCAGUUUAGCGUCAACACUUGCUGGUUUCCUCUCUGGAGCAUC
AAGV020468390.1/163-80   GAUGCACCCGGUGGGGGAGCCAGGAAGUAUUGAUGUUUCUGCCAGUUUAGCGUCAACACUUGCUGGUUUCCUCUCUGGAGCAUC
CU682339.17/39753-39670  GAUGCACCCAGUGGGGGAGCCAGGAAGUAUUGAUGUUUCUGCCAGGUUAGCGUCAACACUUGCUGGUUUUCUCUCUGGAGUAUC
#=GC SS_cons             <<<<<--<<<<-<<<<<<<<<<<-<<<<-<<<<<<<<___________>>>>>>>>->>>>->>>>>>>>>>>->>>>->>>>>
#=GC RF                  GauGCACCCggUGgGGgagCCaGGaaGuAuuGacGuuUCuGCCAGuUUagCguCaaCaCuuGCuGGcuuCCuCUccGGAGCauC
//
# STOCKHOLM 1.0

#=GF AC   RF00782
#=GF ID   MIR480
#=GF DE   microRNA MIR480
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000218;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15994906
#=GF RT   Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa
#=GF RT   that are absent from Arabidopsis.
#=GF RA   Lu S, Sun YH, Shi R, Clark C, Li L, Chiang VL
#=GF RL   Plant Cell. 2005;17:2186-2203.
#=GF WK   MicroRNA
#=GF SQ   69


AARH01038611.1/438-287       UAAUCUAUUUAA-GAACAAAUCCUUAU----UUAAU-UAUGAUAGACACAUACACAUGACUGCUCAGAAUCAUUUAUUAUCAUAAAUCCGACUACAUCAUUAACAUU-GAAAAACAAAA---GAU---AAUUACU---------GUG-U---GAACAAU--AA---UUUU-U-----U-AAGA--UUUGAAU
AARH01001401.1/198347-198199 AAUUUAUUUAAG-GAC-AAAUCCUUAU----UUAGU-UAUGGUAAACACAUACACGUGACUGCUCAGAAUCAUUUAUUAUCAUAAAUCCGACUAUAUCAUUAACAUU-GAAAAAC---AAAUGAU---AAUUACU---------GUG-U---GAACAAU--AA-----UU-U-----U-UUAA--GAUUUGA
AY728446.1/1-140             UAAUAUGUUUGG-GGU-UGAUCCUUGU----UUAGU-UAUAAUAGACCC--ACACCUGACUGCUUAGAAUUAUUUGUUAUCGCAUAUCCGACUACAUUAUUGACGUU-GAAAAAC---A---GAG---AACUACU---------ACA-U---C----AU--UG-----AC-G-----U-UGAA--CCAUAAA
AARH01006100.1/347236-347094 UAAUCUGUUUGG-GGC-AGAUCCUCAU----UUAGU-UAUGGCAGAACC--ACAUUUGACUACUCAGAAUCACUUGUUAUCACAAACUUGACUACAUCAUUGACAUU-AAAAAAC---A---UAGGACAACUAUU---------GUG-U---G----AA--UA-----UU-G-----U-UGAG--CCGGCCA
AARH01013737.1/1242-1112     UAAUUUAUUU-G-AGU-C-AGAUUUCA----UUUGUCUAUGAUAGACCC--AUAUAUGACUGCUCAGAAUCGUCUGUUAUUGUAAGUCUGACUAUAUCAUUAAUAUU-AAAAAAC---A---AAA---AACAACU-----------------A----CU---------AU-G-----U---AA--AUAAUAA
AARH01032743.1/998-855       UAAUCUAUAUGU-GGC-AAAUUUUUAU----UUAGU-UGUGAUAGAUCC--ACACCUAACUGAUCAGAAUUACUUGUUAUUGCAAGUUUGACAACAUCAUUGACACU-GAAAAAU---A---GAGGACAACUACU---------GUG-U---G----AU--UA-----AU-A-----AAAAUU--UUAGAUU
AARH01003636.1/20164-20023   UAAUCUAUUUGG-GGC-AUAUUCUCAU----UUAGU-UAUGAUAGAUCC--ACACUUGAUUGCUUAAAAUCACCUGUUAUUACAUGUUCGACUAUAUUAUUAACAUU-GAAAAGU---U---GAG---GACAACU---------ACU-G---U----AU--GA-----AU-A-----A-UAAUUUUUUGAGA
AARH01003658.1/93782-93646   UAAUUUUUUUGG-GGC-AUGUUAUUAU----CUAAU-UAUAGCAGAUUC--ACAUCUAACUGCUCAAAAUCAUUCAUUAUCGUAAGCCCGACUAUAUCAUUGACACU-CAAA------A---UAU---AAUUGAA---------AGA-A---A----AG--GU-----UU-A-----U-UAAA--UUAUGAU
AARH01002127.1/80234-80373   AAUACAUCUAUU-AGG-CUAUCCUCAU----UUAGU-UAUGGCAGAACC--ACACUUGACUGCUUAGAAUCAUUCAUUAUCGCUAGCCUGACUACAUUAUUAACACU-AAAAAAC---AAAGGAG---AACUACU---------AU-----------AU--GA-----AC-A-----A-UAAG--UUUUUAA
AARH01008360.1/238545-238689 UAAUCUAUUUGG-GGC-AGAUCCUCAU-----UAGU-UAUGGAAAACCC--AUACCUGACUACUCAGAAUCACCCAUUAUCGCAAUCUCGACUACAUCAUUGACAUU-GAAAAAU---A---AAGGACAACUACU---------GUG-U---UAACAAU--AA-----CU-U-----U-UUAA---UAUUUU
AARH01000445.1/80933-80801   UAAUCUGUUUGG-GAC-AUAUCCUCAU----UUAGU-UAUGAUAGAGCC--ACACUUUGCUAUUUAGAAUCACCCGUUAUCGCAAGCCCGGCAACAUCAUUGACAUU-GAAAAAC---A---GAG---GACAACU---------A------------AU---------GU-G-----U--GAA--CAAUAAA
AARH01003018.1/4272-4408     UAACAUAUUUGG-AGC-AUAUCUUUAU----UUAGU-UAUCACAGAC----ACACUUGACUGCUUAGAAUCAUCCAUUAUCGUAAGUCCAACUACAUUAUUAACAUU-GAAAAAC---A---GAGGACAACUACU---------AUA-A---C---------------UU-U-----U-UGAG--AUUUUAA
AARH01021567.1/639-508       UACUAU-GCUUG-GGC-CAAAACUCAU----UCAGU-UAUAGUAGACUC--ACAUCUGACUGCUUAGAAUCACAUAUUAUCGCAAAUCCAACUACAUCAUUGACAUU-GAAAAAC---A---UAG---GAC-------------AAG-C---A----UU--UU-----GC-A-----U-ACG-----AUAAC
AARH01003020.1/64102-63971   UAAUCUGUUUAG-GGC-AAAUCU-CAU----CUAGU-UGUGGUAGAUUC--AUACCUAACUGCUGAGAAUCACCCGUUAUCACAAGCCCGACUAUAUUAUUGAUACU-GAAAAAC---A---GAG---GACAAUU---------A------------AU--CU-----GU-G---------AA--CAAUAAC
AARH01009831.1/190998-190860 UAAUCUGUAUGG-GGA-AGAUCCUCAU----CUGGU-UAUGACAGAUCC--ACACCUAACUGCUCACAAUCACUCAUUAUCGCAAGCCCGACUACACCAUAGACACU-GAAAAAC---A---GAG---GACAACU---------AUGAA---C----AA--UA-----AC-U-----U-UUUA----AGAUU
AARH01010190.1/77283-77144   UCAUCUAUUUAG-AGC-AAAUCAUCAU----UUAAU-UAUGACAGAACC--ACAUUUGACUGUUUAAAAUCACUUAUUGUCGCAAGUCUUACUACAUCAUUGACAUU-GAAAAAU---A---AAG---GAUAACU---------ACU-G---U----AU--AA-----AU-A-----A-UAAU--UUUUUAA
AARH01018697.1/4780-4636     UGACAUGCUGGG-AAC-AUAGCCUCAU----UUAGU-UAUGAUAAAUCU--ACAUUUGACCAUUCAAAAUUAUUUGUUAUCACAAGUCUAGUUAUAUCAUUGAUAUU-GAAAAAC---A---AAU---GACAACU---------AUU-U---UUUAAUU--UA-----UU-U-----U-UUAG-UUUAUAAA
AARH01001061.1/246026-245885 UAAUCUGUUUAG-AAC-AGAUCCUCAU----UUAGU-UAUGACAAACUC--ACACCUAACUACGUAAAAUUACUUGUUAUCACAAGAUCAACUACAUCAUUGACAUU-GAAAAAC---A---AAG---GACAACU---------AUU-G---U----AU--GA-----AU-A-----A-UAAUUUUUUGAAA
AARH01003204.1/96505-96652   UAAUAUGUUUGG-AGC-AAAUCCUCAU----UUAGU-UAUGACAAAUUC--AUACCUGACUGUUUAAAAUCACUCGUUAUCGCAAGCCCGACUACAUCAUUGAUAUU-GAAAAAU---A---GAGAACAACUACA---------AUG-U---G----AA--UA-----AC-AACUUUU-UAAA--AUUUUAA
AARH01001894.1/31814-31962   AUAUUUAUUAGG-GGC-AAAUUCUUAU----UUAGU-UAUGGCAGAUCC--ACACCUGACUGCUCAAAAUCAAUCGUUAUCACAAGAUCGACUACAUCAUUCACAUU-AAAAAAC---A---AAG---AACAACUGCUGUUUGGAUA-A---U----AU--GU-----UU-U-----U-GAGA--UUUUAAU
AARH01009821.1/67326-67459   UAAUUAGUUUGA-GGC-AGAUCAUUAU----UUAAU-UGUAGCAAACUC--ACACCUGAUUACUCAAAAUCACCUAUUAUUGCAAGUCCGACUACAUCAUUGACAUU-GAAAAAC-------------AAGUG-U---------AUA-C---U----UU--GA-----GA-U-----U-UUAA---UUAGAG
AARH01004351.1/82409-82539   CUAUUCG---GG-GGC-AGAUUCUCAU----UUAGU-UAUGGUAGACAA--ACACUUAAUUGCUUAAGGUCACUCGUUAUCGCAAGUUCGACUAUAUCACUGACAUU-GAAAAAC-------------AACGACU--------CAUA-A---A----AU--AU-----AU-U-----U-UG-----CAAAAA
AARH01001998.1/62222-62364   UAAUCUAUAUGU-GGC-AAAUUUUUAU----CUAAU-UGUGAUAGAUCC--ACACCUAACUGCUCAGAAACACUUGUUAUUAUAAGCUCGACUAUAUUAUUGACACU-GGAAAAU---A---GAUGACAACUACU---------GUG-U---G----AU--UA-----AU-A-----A-UUAU--UUAAGAU
AARH01006056.1/11548-11410   UAAUCUAUUUGG-GGC-AGAUCCUCAU----UUAGU-UAUGACAGACUU--ACACCUGAUUUCUUAGAAUCACUCGUUAUCACAAGCCCGAUUAUAUCAUUGACAUU-GAAAAAC---A---GAA---AAUAAUU---------AUU-G---U----GU--GA-----AU-G-----U-U-AG--UGAGCCA
AARH01001107.1/539365-539228 GAUCUCUUUGGG-GGC-AAAUCCUUAU-----UUGC-UAUGACAUAACU--ACAUUUGACUACUCAAAAUCAUUUGUUAUCACAAGCCCGACUACAUCAGUGACAUU-AAGAAAU---A---GAG---GACAACU---------AU--U---U----UU--CA-----GU-A-----U-AUAA--GUUGGAA
AARH01008106.1/34454-34306   UAAUCUGUCCAG-GGA-AAAUCUUCAU----CUAGU-UAUGACAAACCC--ACAUUUGACUACUCAGAAUCACCCGUUAUUGCAAGCUCGACUACAUCAUUGACACU-AAAAAAC---A---AAGAACAACUACU---------AUG-U---GAACAAUAACU-----UU-U-----U-AAGA--UUUAAAU
AARH01014972.1/819-698       UAAUUUGUUUGG-GAC-AAAUCCUCAU----CUAGU-UAUAAUAGACUC--ACACCUGACUGCUUAAAAUCACUAGUUAUUGUAGGAUUGACUACAUCAA----------------------------AAUUGAU---------UGG-U---U----UU--UU-----GU-U-----U-UCAA--AGAGAUU
AARH01003934.1/49894-50031   CAAUCUGUUUGG-GGC-AAAUCCUCAU----UUAGU-UAUGACAAGCCC--ACACUUAAUUGCUUAGAAUCACUCGUUAUCAUAAACACAAUUACAUCAUUAACAUU-GAAAAAC---A---AAG---AACAAUU---------A---C---U----AU--GU-----GA-A-----U-AAUA--ACUUUUU
AARH01002154.1/24791-24659   CAAUUUGUUUAG-UGC-AGAUCCUCAU----UUAAU-UAUGACAAACCC--ACACCUGACUACUUAGAAUCAUCCGUUAUCAUAAGCUCGACUAUAUCAUUGACAUA-GAAAAAC---A---AAA---GA---CA---------A---A---U----AU--U------GU-G-----U--GAA--UAAUAAA
AARH01008115.1/75970-75827   UAAUCUUUCUGG-GAU-AGAUCCUCAU----AUAGU-UGUAGCAGACUC--ACACCUGAUCGUUCAGAAUCACACGUUAUCGUAAGCCCGACUAUUUUAUUGACACU-AAAAAUC---A---GAG---GACAACU---------ACC-U---U----AU--AA-----AC-A-AUAAU-UUUU--UAAGAUU
AARH01009696.1/35613-35487   UAAUCAAUA---------AAUUUUUAU----UUAGU-UAUGACAAAUUC--AUACCUGACUGCUCAGAAUCACCCGUUAUCACAAGCCCGACUACAUCAUUGAUAUU-GAAAAAC---A---CAU---GUAUAUU---------UUG-A---A----AU--UU------------------UA--AUUAAAA
AARH01004344.1/180894-181028 CAAAUAAUUUGU-GGU-GUGUUCUUAU----UUAGU-UAUGGCACAGCC--ACACCUAACU----AUAAUUAUUUGUUAUCGCAGGUC-GACUAUAUUAUUAACAUU-GAAAAAC---A---UAU---GACAAUU---------AUU-G---U----AU--AA-----AC-A-----A-UAUC--UUUUUGA
AARH01005271.1/31192-31323   UAAUUUGUCUAG-GGC-AGAUCCUCAU----CUAGU-CAUGGCAGACCC--GCACCUGACUGCUCAUAAUCACCCGUUAUCGCAAGCACAACUACAUCAUUGACAUU-AAAAAAC---A---UAG---GA----U---------A------------AU--UG-----UU-A-----U-GUGA--AUAAUAA
AARH01003811.1/47507-47368   UGAUCUAUUUAU-AAU-GAAUCAUUUU----CUAAU-UAUGACAGACUU--ACAUCUAACUACUCAGAAUUAUCUGUUAUCAUAAAUCCGACUAUAUCAUUAAUAUU-GAAAAAU---A---AAA---GACAAUA---------AUU-U---U----UU--AA-----GA-U-----G-UUAA--CUGGAAU
AARH01001852.1/64526-64387   UUAUUUAUCUAG-AAU-AAAUCCUUAU----CUGGU-UAUGACAGACUC--ACAUUUUAUUGCCUAUAAUCAUUUGGUAUCGCAAGUCGGAUUAUAUUAUUGAUACU-AAAAAAU---A---GAG---GACAACU---------AUU-G---C----AA--AU-----AA-U-----A-ACUU--UUAAAGA
AARH01006766.1/11342-11476   UAAUUUAUUUGU-GGC-AAAUAUUUGU----UUAGU-UAUGGCAGAUUC--ACAUCUGACUACUCAAAAUCAUCCGUUAUCACAAGUUGGACUAUAUCAUUUACAUU-GAAAAAC---A---UAA---AACAACU----------------------AU--UG-----UC-U-----G-AAUA--AUAAUUU
AARH01023002.1/3181-3328     UAAUCUAUUUGG-GGC-AGAUCCUCAU----UUAGU-UAUGACAGACUC--AUACUUAACUGCUUAAAAUCACUCGUUAUCACAAGUGUGACUGCAUCAUUGACAUU-GAAAAAC---A---GAGGACAACUACU---------GUG-U---G----AA--UAAUAACUU-U-----U-UGAA--AUUUUAA
AARH01000552.1/37835-37689   UAAUCUAUUUAG-GGC-AGAUCAUCUU----GUAGU-UAUGACAGAUCC--ACACCUGACUACUUAAAAUCAAUCGUCAUCAUAAGUCUGACUACAUUAUUGACAUU-GAAAACA---AAG-GAU---AACUAUU---------GUG-C---G----AA--UAAUAAUGU-U-----U-UGAG--AUUUUAA
AARH01009782.1/57783-57649   UAAUUUGUUUGA-GAC-AGAUCUUCAU----CUAGC-UAUGGUAAACUC--ACAACUGACUGCUCAAAAUCACUCGUUAUCGCAAGUCCGACUACAUCAUUGACCUU-GAAAAAC---A---AAG---GACAACU-----------G-U---U----GU---------GU-G-------AAAA--AUAAUUU
AARH01028948.1/1155-1020     UAAUCUGUUAGG-AGC-AAAUCCUUAU----UUAGU-UAUGGCAGAUCC--ACACCUGACUGCUCAAAAUCACUCGUUAUCAUAAGACCGACUACAUCAUUGACAUU-AAAAAAU---A---AAG---AACAACU---------A---C---U----GU--UU-----GG-A-----U---AA--UAAGUUU
AARH01037666.1/594-461       UAAUUUAUUUGG-GGC-UGAUCCUCGU----CUAGC-UAUGACAGACCC--ACACUUAACUGCUCAGAAUCAUCUGUUAUUGCAAGUCUGACUACAUUAUUAACAUU-GAAAAAA---C---AGA---AGAUAAU-------------U---A----CU---------GU-G-----U--GAA--CAAUAAC
AARH01003549.1/244411-244280 UAAUUUGUUUAG-GGC-AAAUCCUCAU----UUAGU-UAUGAUAAACUU--AUAUCUGCUUGCUUAAAAUCACAUGUUAUCGCAAGCCCGGCUAUAUCAUUGACAUU-GAAAAAU---A---AAG---GACAACU---------A------------CU---------GU-G-----U--GAA---CAAUAA
AARH01002753.1/98464-98322   UAAUUCGUUUUG-GCC-AGAUCCUCAU----UUAGU-UAUGGUCGAUUC--ACACAUAACUACUCAAAAUCACCCGUUAUCACAAGUCUGACUAUAUCAUUGACAUU-GAAAAAC---A---GAGAAAAACUAUU---------GUG-U---G---AAU--AU-----UG-G-----U--GAG--CUGACUA
AARH01006065.1/547150-547283 UAAUCUUUUUGG-AGU-AGAUCCUUAU----UUAGU-UAUGGUAAACUC--GCACCUAACUACUCAGAAUCACCCCUUAUCGCAAGCUUGACUAUAUUAUUGAUAUUAAAAAAAU---A---AAG---GACAACU----------------------AU--U------AC-G-----U-U-AA--CAAUAAC
AARH01003623.1/207196-207065 UAAUCUGUUUAA-AUC-AAAUUCUUAU----UUAGU-UAUGACAAACUC--ACAUCUGACGGCUUAGAAUCACCUGUUAUCACGAGCCUGACUAUAUUAUUGACAUU-UAAAAAC---A---GAA---AAC-------------A------------AU--UA-----CU-A-----U-AUAA--ACAAUAA
AARH01004408.1/226185-226316 UAAUUUGUUUGG-AAC-AGAUCCUCAU----UUAAU-UAUAACAAACCC--ACACCUGGAUGCUCAGAAUCACCCGUUAUCAUAAGUCUGUGUACUUCAUUGACAUU-GAAAAAC---A---------AAUGACA---------A---C---C----AC--UA--------------U-CUAA--AUAAUAA
AARH01008247.1/33347-33210   UAAUAUGUUUGG-G-C-CAAAUUUCAU----UUUGU-UAUGAUAGACUC--AUACAUAACUGCUUAGAAUCACGUGGUAUCGCAAGUCCAACUACAUUAUUGACAUU-GAAAAAC---A---AAG---AACAAGC---------AUU-U---U----GU--AU------U-A-----U-UUCA--CCAUUUU
AARH01006741.1/27207-27062   UAAUCUAUUUGG-GAC-AGAUCCUCAU----UUAGU-UAUGACAGACUC--AUACUUAACUGCUUAGAAUCACUUGUUAUCACAAGUCUGACUACAUCAUUGACAUU-GAAAAACAAAA---GAC---AACUACU---------GUG-U---GAAUAAU--AA-----CU-U-----U-UUAA---UAUUUU
AARH01006070.1/68431-68299   UAAUUUAUUUGG-GGC-CGAUCCUCGU----CUAGC-UAUGACAGACCC--ACACUUAACUGCUCAGAAUCAUCUGUUAUUGCAAAUCUGACUACAUUAUUAACAUU-GAAAAA---------AU---AG--AAG---------ACA----------AU--UA-----CU-G-----U-AUGA--ACAAUAA
AARH01003800.1/186862-186723 UAACACAUCUCG-GGU-AGAUUCUUAU----CUAGU-UAUGAAAAACUC--AUACCUGACCGCUCAAAAUCACUCAUAAUUACAAGCCUGACUAAAUCAUUGAAAAU-GAAAAAU---A---CAA---GACAACU---------ACU-A---A----AU--AA-----AC-A-----A-AAGC--UUUUAAG
AARH01007537.1/9661-9514     UAAUUUGUUUGG-AGA-AAAUUCUCAU----UUAGU-UAUGAAAUAUCC--ACACUUGAAUGCUUAAAAUCACCUAUUAUUACAAGUCCAACUAUAUCAUUGACAUU-GAAAAAC---A---UGGAAUAACUACU---------ACG-U---U----AA--CAGUAACUU-U-----U-UGAG--AUUUUAA
AARH01008919.1/96973-96841   UAAUCUGUUUGA-GAC-AUAUUCUCAU----GUAAU-UAUGACAAACUC--AUACUUAACUGCUCAGAAUCAUUUGUUAUCAUAUACCCGACAAUAUCAUUAACAUU-AAAAAAU---A---GAG---AACAACU----------------------AU--U------GU-G-------UGAA--CAAUAAC
AARH01022391.1/1714-1859     UAAUUUGUUUGA-GGC-AGAUCCUCAU----UUAAU-UAUAGCAGACCC--ACACUUGACUGCUCAGAAUCAUUUAUUAUCGCAAGUCCGACUAUUUCUCUAGCAUU-GAAAAAC---A---AAGGACAAUUACU---------AUG-UGGAC----AA--UA-----AC-U-----C-GAGA--UCAUAAA
AARH01008873.1/15309-15442   UAAUUUGUUUAG-GGC-AGAUUCUUAU----UUAGU-UAUGAUAGACAC--ACA--UGGAUACUUAGGAUCACUUGUUAUCACAAGUCUUUCUAGAUCAUUGACAUU-GAAAAAU---A---GAU---AACAACU---------A------------CU--GU-----GU-G-----A-AUAA--AAAAAAU
AARH01006378.1/61715-61584   UAAUUUGUUUAU-GAC-AAAUCCUCAU----UUAGU-UAUGGUUGACCC--AUACUUGACUGCUUAGAAUCACCCAUUAUCACAAGUCCGACUACAUCAUUGACAUU-GAAAAAC---A---AAG---GACAACU----------------------AU--UG--------U-----G-UGAA---UAAUAA
AARH01008349.1/100667-100812 UAAUUUAUUUGA-GGC-AAAUCCUCAU----UUAAU-UAUAACAGACCC--ACACCUGACUGUUCAGAAUCACCUAUUAUCACAAAUCCGACUACUUCUUUGGCAUU-UAAAAAC---A---AAGAACAAUUACU---------AUG-UGGAC----AA--UA-----AC-U-----U-GAGA--UCAUAAA
AARH01006655.1/39596-39739   UGAUCUGUUUUG-AAC-AGAUUCUCAU----UUAGU-UGUGUCAGAUUU--AUACUUGACUGCUCAAAAUCAUCUAUUAUUGCAAGCCUAACCACAUCAUUGACAUU-GAAAAAC---A---GAGGACAACUACC---------AUG-U---A----AA--UA-----AUAA-----U-UUUU--UGAGAUU
AARH01009121.1/43835-43702   UAGUCCAUAAAU--AA-UAUACCUCAU----UUAAU-UAUGGCAGACUC--ACACCUAACUAUUUAAAAUCACCUAUUAUCACAGAUCCAACUACAUCAUUAACAUU-GAAAAAC---A---UAG---GAUCACU---------A-------C----UG--UG-----U--------G-AAUA--UUGGUGA
AARH01008741.1/93181-93043   UAAUUUGUUUUGUAGC-AGAUUCUCAUCUAGUUAGU-UAUAAUAUACUC--AUACUUCAUUAUUCAGAAUCGUCAGUUAUUGCAAGUCCGAUUAUAUCUUUGAUAUU-GAAAAAC---A---GA----AAGAACA----------------------AU--UA-----UC-G-----U-GUAA--ACAAAAA
AC182654.2/60670-60814       CAAUCUAUUUGA-GGC-AGAUCCUCAU----UUAGU-UCUGGCCGAUUC--ACACAUAACUUCUCAAAAUCACUCGUUAUUACAAGUCUGACUA--UCAUUGACAUU-GAAAAAC---A---GAGAAAAACUAUU---------AUG-U---G-AAUAU--UG-----GCAA-----G-CUGA--CUGGUUA
AARH01000731.1/21244-21385   UAAUCUGAUUGA-GGC-AAAUCCUCAU----UUAGU-UAUGACAAACCC--ACACUUGACUGCUUAGAAUCACCCGUUAUCACAAGCUCGACUACAUCAUUGACAUU-GAAAAAU---AAAGGAG---AACUACU---------GUA-U---G----AA--UA-----AU-A-------ACUU--UCUGUUA
AARH01005222.1/20484-20615   CAAUUUGUUUGG-GGC-AAAUCCUCAU----UUAAU-UAUAACAGACUC--ACACCUGAUUGCUUAGAAUCACCUAUUAUUGCAAACUCAACUACAUCAUUGACAUU-GAA-----------------AAAUAAA---------AGA-C---A----AC--UU-----GU-A-----U-GUUA--ACACUAA
AARH01008739.1/72963-72816   CAAUCUAUUUAG-GGC-AGAUUCUUAU----UUAGU-UAUGGCAGACUC--AAACCUGAAUGCUCAGAAUCACUUGUUAUUACAAGCUCGAAUAUAUCAUUGACAUU-GAAAAAC---A---GUGGACAACUACU---------GUG-U---G----AA--UAAUAACUU-U-----U-UGAA--AUUUUAA
AARH01004367.1/93891-94034   UAAUCUGUUCGG-GGU-ACAUUCUUAU----UUAGU-UAUGACAGACUC--ACACCUGCUUGUUUAGAAUCAUCCGUUAUUACAAACUCGACUACAUCAUUGACAUU-GAAAAAC---ACAUGAC---AACUACC---------CUG-U---G----AG--UA-----AU-G----AU-UUUU--UGAGAUU
AARH01008389.1/51770-51913   UAAUCUAUAUGG-AGC-AUAUCCUCAU----UUAGC-UAUGUCAGGCCC--ACAUCUGAAUACUCAUAAUUACUUGUUGUCGUAAGCCCAACUACAUCAUCGACAUU-GAAAAAU---A---GAGGAUAGUUAUU---------GUG-U--GC----AU--AG-----UG-A-----C-UUUU--UUAAAUU
AARH01007846.1/3077-2946     UAAUCUGUCUGG-AAA-AAAUCCUCAU----CUUAU-UAUAGCAUACCC--ACAACUGUCUGCUCAGAAUCAUUCAUUAUUGCAAGUCCAACUACAUCAUUGAGAUU-GACAAAU---A---AAG---GAUAACU---------A------------CU---------UU-G-----U---CA--ACAAUAA
AARH01027276.1/529-391       UAAUUUGUUCAA-GGC-AUGUUAUUAU----CUAAU-UAUGACAGAUUC--AUAUCUAACUGCUCAGAAUCAUUCAUUAUCAUAAGUCCGACUACAUCAUUGACACU-UAUAAA----A---UAU---AAUUGGA---------AGA-A---A----AG--GU-----UC-A-----U-CAAA--UUAUGAU
AARH01003818.1/296844-296710 CAAUUUGUUUGU-GAC-AAAUUCUCAU----UUAAU-UGUGACAAACUC--AUACCUAAUUGCUCAGAAUUACUCAUUAUCGCAAGUCUGACUACAUCGUUGACAUU-GGAAAAC---A---AAA---GACAACU---------A------------AU--GU-----GU-G-----A-ACAA---UAAAUU
AARH01003453.1/7596-7734     UAAUCUAUUUGA-GAU-AUAUCUUUAU----UUAAU-UAUGAUAGAUCC--ACAUUUGAUUGCACAGAAUCAUCAAUUAUCGCAAAUUCGACUACAUCAUUGACAUU-GAAAAAC---A---GAA---GACAACU---------AUU-A---C----GU--GA-----AU-A-------AUAA--CUUUUUA
#=GC SS_cons                 :::<<<<<<--<.-<<.--<<---<<<....-<<<<.<___________..________________________________________________________._______..._...___...>>>>>--.........>>>.-...-....>>..--.....>>.-.....>.-->>..->>>>::
#=GC RF                      UAAucuauuUgg.Ggc.AaaucCUcau....UUagU.uAUGacAgAcuC..ACACcUgACUGCUcAgAAUCAcuuGUUAUCaCAAGuccGACUAcAUCAUUGACAUU.GAAAAAC...A...gAg...aAcuACU.........aug.u...u....au..ua.....gc.u.....c.uuaa..uuagaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00783
#=GF ID   mir-484
#=GF DE   microRNA mir-484
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   57.00
#=GF TC   59.60
#=GF NC   38.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.85 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000219;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues.
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF RN   [4]
#=GF RM   15978578
#=GF RT   Identification of human fetal liver miRNAs by a novel method.
#=GF RA   Fu H, Tie Y, Xu C, Zhang Z, Zhu J, Shi Y, Jiang H, Sun Z, Zheng X
#=GF RL   FEBS Lett. 2005;579:3849-3854.
#=GF RN   [5]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [6]
#=GF RM   20433717
#=GF RT   Deciphering the porcine intestinal microRNA transcriptome.
#=GF RA   Sharbati S, Friedlander MR, Sharbati J, Hoeke L, Chen W, Keller A, Stahler
#=GF RA   PF, Rajewsky N, Einspanier R
#=GF RL   BMC Genomics. 2010;11:275.
#=GF WK   Mir-484_microRNA_precursor_family
#=GF SQ   15


AAHX01062820.1/36411-36347   CUCGUCAGGCUCAGUCCCCUCCCGAUAAACCUCAAAAUAGGGGGUUAUCUGGGGGAU--CGGUGGCA
AAPY01325197.1/1143-1078     CUCGUCAGGCUCAGUCCCCUCCCGAUAAAGCCCUAAAUAGGAUCCU-CCUGGGGGGCGACCCUAGUU
AALT01092469.1/602-536       CUCGUCAGGCUCAGUCCCCUCCCGAUAAACCCCUAAAUAGGGACCUUCCCCCGGGGGCGCCCCGGCU
AANN01741400.1/199-264       CUCGUCAGGCUCAGUCCCCUCCCGAUAAAUCC-UAAAUCCGGACCUUCUGGGGGGCUGACCCCAGCU
AAFC03020163.1/150857-150791 CUCGUCAGGCUCAGUCCCCUCCCGAUAAACCUCUAAAUAGGGACCUUCCCGGGGGGCUACCUCGGCU
AAYZ01087935.1/68-134        CUCGUCAGGCUCAGUCCCCUCCCGAUAAACCUGGAAAAAAGCACCUUCCCGGGAGGAGACUCAGACU
AACN011076480.1/157-91       CUCGUCAGGCUCAGUCCCCUCCCGAUAAACCCCUAAAUAGGGACCUUCCCAGGGGGAGACCCCGGCU
AAWR02036416.1/5025-4959     CUCGUCAGGCUCAGUCCCCUCCCGAUAAACCCCUAAAUAGGGACCUUCCCGGGGCGCGAUCCCGGCU
AAKN02007627.1/182653-182587 CUCGUCAGGCUCAGUCCCCUCCUGAUAAAUUCCUAAAUAGGUUCCUUUGCGGGGGAAUUCCCUUUUU
AC164291.2/38618-38684       CUCGUCAGGCUCAGUCCCCUCCCGAUAAACCUCAAAAUAGGGUCUUACCUAGGGGGCUGGCGGCGUA
BC033900.1/36-102            CUCGUCAGGCUCAGUCCCCUCCCGAUAAACCCCUAAAUAGGGACUUUCCCGGGGGGUGACCCUGGCU
AAGU03087402.1/51180-51114   CUCGUCAGGCUCAGUCCCCUCCCGAUAAAACCCUAAAUAGGGACCUUCCAUGGGGGUGACCGUGGCU
AAPE02043441.1/20653-20719   CUCGUCAGGCUCAGUCCCCUCCCGAUAAACCCUUAAAUAGGGACCUUCCCGGGGGGCGGCCCCGGCU
AAQR03077636.1/5966-5900     CUCGUCAGGCUCAGUCCCCUCCCGAUAAACCCUUAAAUAGGGACUUUCCCGGGGGGUGAUUCUGGCU
ABVD01026394.1/3000-2934     CUCGUCAGGCUCAGUCCCCUCCCGGUAAAUCCCUAAAUAGGGACCUUCCUGGGGGGCGACCCUGGCU
#=GC SS_cons                 :::<<<<<<----<<<-<<<<<<<--<<<-<<<<____>>>>-->>>-->>>>>>>->>>>>>>>>:
#=GC RF                      CUCGucaGGCUCAGucCCCUCCcgAUaAaccCcuAAAUagGgaCcUuCCcgGGGGGugaCCCuggCU
//
# STOCKHOLM 1.0

#=GF AC   RF00784
#=GF ID   mir-486
#=GF DE   microRNA mir-486
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   69.00
#=GF TC   71.60
#=GF NC   68.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000220;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF RN   [2]
#=GF RM   15978578
#=GF RT   Identification of human fetal liver miRNAs by a novel method.
#=GF RA   Fu H, Tie Y, Xu C, Zhang Z, Zhu J, Shi Y, Jiang H, Sun Z, Zheng X
#=GF RL   FEBS Lett. 2005;579:3849-3854.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [5]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   MicroRNA
#=GF SQ   12


AAFC03025383.1/28550-28617 GGGUCCUGUACUGAGCUGCCCCGAGGCCCUUCGCUGUGCCCAGCUCGGGUCAGCUCAGU-ACCGGGCGC
AAYZ01062575.1/1218-1151   GGAUCCUGUACUGAGCUGCCCUGAGGUCCUUGCUUGUGCCCAGCUCGGGGCAGCUUAGU-ACAGGAUGC
AALT01613538.1/133-200     GGAUCCUGUACUGAGCUGCCCCGAGGCCCUUUCUUGUGCCCCACUAGGGGCAGCUCAGU-ACAGGAUGC
AADA01053888.1/632-565     GCAUCCUGUACUGAGCUGCCCCGAGGCCCUUCAUGCUGCCCAGCUUGGGGCAGCUCAGU-ACAGGAUAC
ABDC01344599.1/5816-5751   GGGUCCUGUACUGAGCUGCCCCGAGGCCCU--GUAUUGCCCCGCUCGGGGCAGCUCAGU-ACAGGGUGC
AAIY01232422.1/5210-5143   GGAUCCUGUACUGAGCUGCCCCGAGGUCCUUCUUUGAGCCCAGCUCGGGGCAGCUCAGU-ACAGGAUGC
AANN01184510.1/3098-3031   GGAUCCUGUACUGAGCUGCCCCGAGGUUCUUUCUUGUGCCCAGCUCGGGGCAGCUCAGU-ACAGGAUGC
AAWR02023968.1/18344-18411 GGAUCCUGUACUGAGCUGCCCCGAGGCCCUUCACUGUGCCCAGCUCGGGGCAGCUCAGU-ACAGGAUGC
AC113133.5/13542-13475     GCAUCCUGUACUGAGCUGCCCCGAGGCCCUUCAUGCUGCCCAGCUCGGGGCAGCUCAGU-ACAGGAUAC
AC126445.5/51298-51231     GGGUCCUGUACUGAGCUGCCCCGAGGUCCUUCACUGUGCUCAGCUCGGGGCAGCUCAGU-ACAGGAUGC
ABRT010741278.1/1111-1044  GGAUCCUGUACUGAGCUGCCCCGAGGCCCGUCAUUGUGCCCCGCUCGGGGCAGCUCAGUU-CCAGAUGC
AAPE02033713.1/5817-5884   GGAUCCUGUACUGAGCUGCCCCGAGGUUCUUCAUUGCACCCGGCUCGGGGCAGCUCAGU-ACAGGAUGC
#=GC SS_cons               <-<<<<<<<<<<<<<<<<<<<<<<<__________________>>>>>>>>>>>>>>>>.>>>>>>>->
#=GC RF                    GGauCCuGUACUGAGCUGCCCCGAGGcCCUUcaUugUGCCCaGCUCGGGGCAGCUCAGU.ACaGGauGC
//
# STOCKHOLM 1.0

#=GF AC   RF00785
#=GF ID   mir-90
#=GF DE   microRNA mir-90
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   68.00
#=GF TC   70.30
#=GF NC   44.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000221;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679672
#=GF RT   An extensive class of small RNAs in Caenorhabditis elegans.
#=GF RA   Lee RC, Ambros V
#=GF RL   Science. 2001;294:862-864.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [4]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [5]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [6]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF RN   [7]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF RN   [8]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   5


AAGD02006260.1/1037-942      GGGCCU-CA--CUUCGAGCGGUAUUCAACGACUAUCUCAACCGAUA-UACAUACCAAC-CGAGUUGAUAUGUUGUUU-GAAUGCCCCUUGAACUCGAGGCCC
Z22175.1/9773-9676           GGGCGC-CA--UUUCGAGCGGCUUUCAACGACGAUAUCAACCGACAACUCACACUUUUGCGUGUUGAUAUGUUGUUU-GAAUGCCCCUUGAAUUGGAUGCCA
CAAC02000525.1/201175-201268 -CGCACUCA--UUUCAAGCGGCUUUCAACGACUAUAUCAACCAAAU----CAAGCUAGAUACGUUGAUAUGUUGUUU-GAAUGCCCCUUGAGAUUUUGGAGU
CAAC02000525.1/202893-202799 CAGCAC-CA--UUUCAAGCGGCCUUCAACGACUAUAUCAACCGAAU----CCAAAUUCGCGAGUUGAUAUGUUGUUUUGAAUGUCACUUGAGGUUUUUGCUU
ABEG02000481.1/15171-15268   -GGCGC-CAAGUUUCGAGCGGCUUUCAACAACGAUAUCAACCGAUU-UUCAGUAAAUUGCGAGUUGAUAUGUUGUUU-GAAUGCCCCUUGAGUUGGUUGCCC
#=GC SS_cons                 :<<<<<.-<..-<<<<<<-<<<-<<<<<<<<<-<<<<<<<<<<-<<._______>>--->>->>>>>>>>>>>>>->.>>>->>>->>>>>>->->->>>>:
#=GC RF                      gggCgc.Ca..ucuCaaGCGGcuuuCaaCgaCuauauCaaCCGAcg.uucauAacguugCGaGuuGauauGuuGuUu.GaaUgCCcCuuGaguuugucGccu
//
# STOCKHOLM 1.0

#=GF AC   RF00786
#=GF ID   mir-289
#=GF DE   microRNA mir-289
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   53.60
#=GF NC   33.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000222;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17994087
#=GF RT   Evolution of genes and genomes on the Drosophila phylogeny.
#=GF RA   Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC,
#=GF RA   Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM,
#=GF RA   Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW,
#=GF RA   Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D,
#=GF RA   Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak
#=GF RA   SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK,
#=GF RA   Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S,
#=GF RA   Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A,
#=GF RA   Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher
#=GF RA   AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD,
#=GF RA   Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC,
#=GF RA   Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey
#=GF RA   J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S,
#=GF RA   Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter
#=GF RA   GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz
#=GF RA   MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J,
#=GF RA   Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P,
#=GF RA   Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S,
#=GF RA   Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L,
#=GF RA   Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky
#=GF RA   E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L,
#=GF RA   McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P,
#=GF RA   Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S,
#=GF RA   Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M,
#=GF RA   Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli
#=GF RA   D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D,
#=GF RA   Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie
#=GF RA   MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S,
#=GF RA   Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz
#=GF RA   MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M,
#=GF RA   Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W,
#=GF RA   Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W,
#=GF RA   Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E,
#=GF RA   Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang
#=GF RA   J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A,
#=GF RA   Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K,
#=GF RA   Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A,
#=GF RA   Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A,
#=GF RA   An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A,
#=GF RA   Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C,
#=GF RA   Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y,
#=GF RA   Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De
#=GF RA   Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M,
#=GF RA   Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D,
#=GF RA   Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR,
#=GF RA   Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez
#=GF RA   N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L,
#=GF RA   Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P,
#=GF RA   Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X,
#=GF RA   Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P,
#=GF RA   Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T,
#=GF RA   Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V,
#=GF RA   Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N,
#=GF RA   Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E,
#=GF RA   Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F,
#=GF RA   Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N,
#=GF RA   Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N,
#=GF RA   Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y,
#=GF RA   Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk
#=GF RA   T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q,
#=GF RA   Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W,
#=GF RA   Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I
#=GF RL   Nature. 2007;450:203-218.
#=GF WK   MicroRNA
#=GF SQ   3


AAEU02000202.1/398546-398448 GAGUUUACAGUAAAAUAAAUAUUUAAGUGGAGCCUGCGACUCCAGUCCCU-CUGACUGACUGGGGUAAGUCUCUCGAGCGUUUGUUGGCACGUAAAAGAC
AAFS01003071.1/3815-3716     GAGUUUACAGUGAAAUAAAUAUUUAAGUGGAGCCUGCGACUGGGACUCCAGCUCUCCGACUGGGCUAACUCACUUGAGCGUUUGUUGGCACGUAAAAGAC
AAPT01020646.1/98474-98545   GAGUUUACAGUAAAAUAAAUAUUGAAGUGG-----GCC----------UGG-----GGAAG--------UCACUUGAACGUUUGUUGGCACGUAAAAGAC
#=GC SS_cons                 :::<<<<<-<<--<<<<<<--<<<<<<<<<<<<<<-<<---<<<<______>>>>->>--->>>>>--->>>>>>>>>-->>>>>>--->>>>>>>::::
#=GC RF                      GAGuuuaCAGuaAaauaaaUAcucaaGuGgagCCcGCgAcUcggguuccaGcccgccGAcugGGcuAAguCaCuugagCGuuuguuGGCaCGuaaaAGAC
//
# STOCKHOLM 1.0

#=GF AC   RF00787
#=GF ID   mir-288
#=GF DE   microRNA mir-288
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   91.40
#=GF NC   42.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000223;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17994087
#=GF RT   Evolution of genes and genomes on the Drosophila phylogeny.
#=GF RA   Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC,
#=GF RA   Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM,
#=GF RA   Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW,
#=GF RA   Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D,
#=GF RA   Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak
#=GF RA   SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK,
#=GF RA   Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S,
#=GF RA   Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A,
#=GF RA   Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher
#=GF RA   AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD,
#=GF RA   Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC,
#=GF RA   Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey
#=GF RA   J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S,
#=GF RA   Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter
#=GF RA   GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz
#=GF RA   MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J,
#=GF RA   Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P,
#=GF RA   Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S,
#=GF RA   Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L,
#=GF RA   Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky
#=GF RA   E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L,
#=GF RA   McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P,
#=GF RA   Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S,
#=GF RA   Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M,
#=GF RA   Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli
#=GF RA   D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D,
#=GF RA   Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie
#=GF RA   MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S,
#=GF RA   Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz
#=GF RA   MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M,
#=GF RA   Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W,
#=GF RA   Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W,
#=GF RA   Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E,
#=GF RA   Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang
#=GF RA   J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A,
#=GF RA   Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K,
#=GF RA   Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A,
#=GF RA   Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A,
#=GF RA   An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A,
#=GF RA   Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C,
#=GF RA   Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y,
#=GF RA   Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De
#=GF RA   Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M,
#=GF RA   Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D,
#=GF RA   Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR,
#=GF RA   Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez
#=GF RA   N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L,
#=GF RA   Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P,
#=GF RA   Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X,
#=GF RA   Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P,
#=GF RA   Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T,
#=GF RA   Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V,
#=GF RA   Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N,
#=GF RA   Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E,
#=GF RA   Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F,
#=GF RA   Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N,
#=GF RA   Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N,
#=GF RA   Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y,
#=GF RA   Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk
#=GF RA   T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q,
#=GF RA   Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W,
#=GF RA   Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I
#=GF RL   Nature. 2007;450:203-218.
#=GF WK   MicroRNA
#=GF SQ   7


AASV01027319.1/2097-2001     CGGUCAUGUCGUAAUUAGCGGAGCACGGCAU-UGCCGGCGAUAAUUAAUGACGGUGGUCACGUUGGUUUCAUGUCGAUUUCAUUUCAUGACACGGCCG
AAPU01010689.1/172508-172412 UGGACGCGUCGUAAUUAGCUGUGCACAGCGU-UGCUGGCGAUAAUUAAUGACGUUGGUCACGUUGGUUUCAUGUCGAUUUCAUUUCAUGACACGGCCG
AAQB01006401.1/336794-336697 CCCUCAGGUCGUAAUUAGCAGCGCACAACAUUCGUCGGCGAUAAUUAAUGACGUUGGUCACGUUGGUUUCAUGUCGAUUUCAUUUCAUGACACGGCCG
AAFS01000334.1/6651-6555     UGGCCAUGUCGUAAUUAGCAGGGUACAGCGU-UGCCGGCGAUAAUUAAUGACGUUGGUCACGUUGGUUUCAUGUCGAUUUCAUUUCAUGACACGGCCG
AAPP01015693.1/87835-87739   AGGUCAUGUCGUAAUUAGCAGGGCACAGAAU-UGCCGGCGAUAAUUAAUGACGUUGGUCACGUUGGUUUCAUGUCGAUUUCAUUUCAUGACACGGCCG
AAPT01020977.1/42229-42133   UGGCCGUGUCGUAAUUAGCUGUGCAGAACGU-AGCUGGCGAUAAUUAAUGACGUUGGUCACGUUGGUUUCAUGUCGAUUUCAUUUCAUGACACGGCCG
AANI01016239.1/44496-44592   CAGCCGCGUCGUAAUUAGCUGUGCACAACGU-UGCUGGCGAUAAUUAAUGACUUUGGUCACGUUGGUUUCAUGUCGAUUUCAUUUCAUGACACGGCCG
#=GC SS_cons                 :<<<<-<<<<<<<<<--<<<<<<--<<<<<<.-<<<<<<<-<<_____>>->>>>>>>->>>>>>-->>>->>>-->>>------->>>>>>->>>>:
#=GC RF                      uggcCauGuCguaauUAgCaGggcACagcgu.ugccggcGAuaAUUAAugACgcugguCacgcuGGUucCAuGuCGauuUCAUUUCauGaCaCGgccG
//
# STOCKHOLM 1.0

#=GF AC   RF00788
#=GF ID   mir-287
#=GF DE   microRNA mir-287
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   89.50
#=GF NC   45.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000224;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12844358
#=GF RT   Computational identification of Drosophila microRNA genes.
#=GF RA   Lai EC, Tomancak P, Williams RW, Rubin GM
#=GF RL   Genome Biol. 2003;4:R42.
#=GF WK   MicroRNA
#=GF SQ   9


AAKO01001640.1/35443-35535     GGACGCCGUGGAUGUAUGGGU-GUGUAGGGUCGGAAAUUUUGCACACAUUUACAAUAAUUGUAAAUGUGUUGAAAAUCGUUUGCACG-ACUGUGA
AADE01001319.1/26535-26625     GAGACAGUCUUAUGUGUGAGU-GUG--GGGCCUGAAAUUUUGCACACAUUUACAAUAAUUGUAAAUGUGUUGAAAAUCGUUUGCACA-ACUGUGA
AAPT01009679.1/245-326         -----------ACACAUACAU-GCAUAAUGCUUGAAAUUUUGCACACAUUUACAAUAUUUGUAAAUGUGUUGAAAAUCGUUUGCACA-ACUGUGA
AAQB01006734.1/267050-266959   GUAAUAUGUAUAUGUAUUGC---UGUAAAGUCUGAAAUUUUGCACACAUUUACAAUUAUUGUAAAUGUGUUGAAAAUCGUUUGCACAAACUGUGA
AAPP01015675.1/1283611-1283521 UAUAGGGCUGUGUGUAUUGGUAGUG---GGUCUGAAAUUUUGCACACAUUUACAAUAAUUGUAAAUGUGUUGAAAAUCGUUUGCACA-ACUGUGA
AAPQ01007040.1/1493379-1493287 GUGGACGCUGGAUGUAUGGGU-GUGUGGGCUCUGAAAUUUUGCACACAUUUACAAUAAUUGUAAAUGUGUUGAAAAUCGUUUGCACG-ACUGCGA
AAEU02000290.1/178244-178333   GCAAGCCGUGGAUGUAUGGGU-GUG---GGUCUGAAAUUUUGCACACAUUUACAGUAAUUGUAAAUGUGUUGAAAAUCGUUUGCAUG-ACUGUGA
AANI01016269.1/16786-16878     CUUUCGCACACACACAAACGU-GCAUAAUGUUUGAAAUUUUGCACACAUUUACAAUAAUUGUAAAUGUGUUGAAAAUCGUUUGCACA-ACUGUGA
AAPU01010664.1/17553-17645     CUCCCACGCACACACACACGC-GCAUAAUGUUUGAAAUUUUGCACACAUUUACAAUAAUUGUAAAUGUGUUGAAAAUCGUUUGCACA-ACUGUGA
#=GC SS_cons                   ::::::::::::::::::<<<.<<<<<<<---<<<--<<<<<-<<<<<<<<<<<_____>>>>>>>>>>>>>>>>->>>>>>>>>>>.->>::::
#=GC RF                        guaauacguauAuguAuaggu.GuGuaagGUcuGAAAUUUugCACACAUUUACAAUAAUUGUAAAUGUGUugAAAAUCgcuugCaCa.AccGUGA
//
# STOCKHOLM 1.0

#=GF AC   RF00789
#=GF ID   mir-286
#=GF DE   microRNA mir-286
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   40.10
#=GF NC   39.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.26 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000225;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multispecies survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF WK   MicroRNA
#=GF SQ   14


AAIZ01001618.1/39462-39558     UUAAAAUUAAAUGGCGAUUGUCGGUUUGGUCGCUUU----UU-------ACCAGGGUUCCGA----UCAAGC------------GAAGUGACUAGACCGAACACUCGUG--CUAUAAUUUUAGAAU
AAPU01010225.1/183664-183561   UUAAAAUUAAAUGGCGAUUGUCGGUAUGGUCUCUUU----UUCA----ACAUAUACACCAAACAUUCUAUAU------------AAAGUGACUAGACCGAACACUCGUG--CUAUAAUUUUAAAAU
AAPT01006453.1/2821-2925       UUAAAAUUAAAUGGCGAUUGUCGGUAUGGUCGCUUUUGAACCUA----AACUCUAUAUACAA----UAUAUA-----------UAAAGUGACUAGACCGAACACUCGUG--CUAUAAUUUUAAAAU
AAGE02008291.1/17656-17755     AAGUCCUGGG---GCGAUUGUCGGCUUAGUCGCUGU----AUCAUUUCAACUGCUGUGCAGU----UCUUCG------------CUAGUGACUAGACCGAACACUCGUA--UC-CCAGGCCUUUAC
AAPQ01007044.1/1205305-1205207 UUAAAAUUGAAUGGCGAAUGUCGGUAUGGUCUCUUU----UUCA----AAGAA-GGUUUCGA----UCGAGC------------GAAGUGACUAGACCGAACACUCGUG--CUAUAAUUUUAAAAU
AAWU01011011.1/918-843         UUUGGG-------GCGAUUGUCGGACUAGUCGCUUC----UU----------------GAAA----UCAGCC------------CAAGUGACUAGACCGAACACUCGCG--U-----CCUAAAACU
AAQB01006291.1/71587-71475     UUAAAAUUGAAUGGCGAUUGUCGGUAUAGUCUCUUUU---UCCA----AAAAUCUUGUUUGU----UUUUGCCAAUCUAAUAAGAAAGUGACUAGACCGAACACUCGUG--CUAUAAUUUUAAAAU
AAAB01008980.1/6864363-6864282 UUGGG--------GCGAUUGUCGGACUAGUCGCUGU----CG--------CAGUCAUUCGGU----UUCACC------------UUAGUGACUAGACCGAACACUCGCG--U------CCUAAACG
AAAB01008968.1/493523-493599   UUAGG--------GCGAAUGUCGGAGUAGUCGCUUG----UG-------------AUUGAAU----UGACAA------------AAAGUGACUAGACCGAACACUCGUA--U------CCUAAAUC
AAGE02018252.1/93413-93512     AUCGUUAUUUGGGGCGAUUGUCGGACUAGUCGCUGC----GUAC----AAAACGGAACUAUU----UCAA--------------CUAGUGACUAGACCGAACACUCGCGUCCUAAAGCACGAUCAG
AAWU01006018.1/401-308         AGUCCUGGG----GCGAUUGUCGGCUUGGUCGCUGU----CUUU----ACCCGAGGCACAGU----UGCACU------------UCAGUGACUAGACCGAACACUCGUA--U--CCUAGGACUUAC
AAPP01018770.1/56774-56877     UUAAAAUUGAAUGGCGAUUGUCGGUAUGGUCGCUUU----UUCACAAAAAAAUUGGUUACCA----ACAAGC------------GAAGUGACUAGACCGAACACUCGUG--CUAUAAUUUUAAAAU
AANI01014795.1/39192-39293     UUAAAAUUAAAUGGCGAUUGUCGGUAUGGUCGCUUU----UUCA----AACAAUAUACCAUUAU--CUAUAU------------AAAGUGACUAGACCGAACACUCGUG--CUAUAAUUUUAAAAU
AAEU02000463.1/592259-592161   UUAAAAUUGAAUGGCGAAUGUCGGUAUGGUCUCUUU----UU-C----AAAAGAGGUUUCGA----UCAAGC------------GAAGUGACUAGACCGAACACUCGUG--CUAUAAUUUUAAAAU
#=GC SS_cons                   <<<<<<<<<----<<<<-<<<<<<<<<<<<<<<<<<....____....______________....______............>>>>>>>>>>>>>>>->>>->>>>-..--->>>>>>>>>:::
#=GC RF                        uugggguugaAuGgCGAUUGUCGGucUaGUCgCUuu....uuca....AAaaauauuuuagu....Uuaaau............aaAGuGACuAgaCCGAACACUCGcG..cUAcaaccccaaaAu
//
# STOCKHOLM 1.0

#=GF AC   RF00790
#=GF ID   mir-358
#=GF DE   microRNA mir-358
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   72.40
#=GF NC   52.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000226;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [3]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [4]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF RN   [5]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   3


AAGD02001646.1/15888-15778   AAAUUCACCG--CGGAUGGCGACCUGGCCA-GGCAUUCCAACUGUCCAUCCAA-GUACUUUAUCGGACAAUUGGUAUCCCU-GUCAAGGUCUCAAUCCUCU--CGGCGAGCUUUUUCC
CAAC02000446.1/155814-155700 UUACUCCCCAUUCGGAUUGAUACCCGACUUCCGGAUACCAAAUGUCAUAUCCA---ACUCGUUUCGUCAAUUGGUAUCCUUAGUCGUGGUCUCAAUCUGUACACGGCGAGAGUGUUGU
FO080489.1/41094-40983       AAACUCGCGA--CGGCUGGCGACCUGGCCA-GGCAUUCCAACUGUCAAACUUACAAAGCUUUCUCGACAAUUGGUAUCCCU-GUCAAGGUCUCAAUCCGUU--CAGCGAAUUCGUUGU
#=GC SS_cons                 ::::<<-<-<..<<<<<-<-<<<<<<<<--.<<-<<-<<<<-<<<<_______.___________>>>>->>>>->>->>-.>>>>->>>>->->>>>>>-..-->->>:::::::::
#=GC RF                      aaAcUCaCcg..cGGaUgGcgaCCcGaCca.gGcaUuCCaacUGuCaaaccuA.aaAcuuuuuucGaCAAuuGGUAuCCcU.GuCgaGGucUCAAuCCgcu..CgGCGAguuugUUgu
//
# STOCKHOLM 1.0

#=GF AC   RF00791
#=GF ID   mir-357
#=GF DE   microRNA mir-357
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   81.00
#=GF NC   54.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000227;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [3]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [4]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF RN   [5]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF RN   [6]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   5


AAGD02001646.1/15527-15437 CUGCCU-------AA-CAGCGGAUUCCAGUAAC-UCUGAGCAUAUACAUGAAGUUUCAAAA-CAAUGUAAAUGCCAGUCGUUGCUGGAAUUCG-------------AUAAGCAC
CAAC02000548.1/42047-42159 CUACAUCAGAAGAGA-CAGCGAAUCCCGGCAAUCACCGUGCAUUUUCAUCUACCAGAGGCACUAAUGAAAAUGCCAGUCAUUGACGGAAUUCGUUGAAUCUGGAAUUAAAGCAU
FO080489.1/40778-40669     ACGCUGUACUACUCACCAGCGGAUCCCUACAAC-GCUGCGCAUAUGCAUGAACACAAUGAA--AAUGUAAAUGCCAGUCGUUGCAGGAGUUCGCAUACAGUAGUA-AAAUGCGC
ABEG02009086.1/2940-2832   UAUUCUCUGCCUGAACGUGCGAAUCCCUGUAAU-ACUGUGCAUAUACAUGU---CAUGUAACUAAUGUAAAUGCCAGUCGUUGCAGGAAUUCGCUAAA-AGUCAGCUAAAAAUC
ABEG02003760.1/30507-30615 AUGUGUCUGUACUAACAUGCGAAUCCCUGUAAU-ACUGUGCAUAUACAUGUCAUACAACUA---AUGUAAAUGCCAGUCGUUGCAGGAAUUCGCUAAAAGU-CAGCUAAAAAUC
#=GC SS_cons               :<<<--<<<<<<<---<<<<<<<<-<<<-<<<<.<<<<-<<<<<<<<<<____________.__>>>>>>>>>>>>>>->>>>->>>->>>>>>>>-->>>>>>>----->>>:
#=GC RF                    acgcuucugcacuaACcaGCGaAucCCuGcAAc.aCuGuGCAUcUaCAUguaauaaaaaaA.uAAUGuAgAUGCCaGuCgUUgcaGGAaUuCGCugAaagugcaguuAAAgcgc
//
# STOCKHOLM 1.0

#=GF AC   RF00792
#=GF ID   mir-490
#=GF DE   microRNA mir-490
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   85.00
#=GF TC   88.60
#=GF NC   74.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.02 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000229;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   18230126
#=GF RT   New miRNAs cloned from neuroblastoma.
#=GF RA   Afanasyeva EA, Hotz-Wagenblatt A, Glatting KH, Westermann F
#=GF RL   BMC Genomics. 2008;9:52.
#=GF RN   [4]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF WK   MicroRNA
#=GF SQ   19


AAFR03031771.1/89803-89676   GAGGUGCCACAUUGCAUUUGAAAAUUCAUGUUUCAA-CUUCAUGGAUCUCUU-GGUGGG-UCAAGUU--UAGGAAUAU---ACCAACC-UGGAGGACUCCAAGCUGUUGAGCUAUCCAAAAGCAACAGAUAUGAAUA
AAPN01246488.1/31456-31583   AGGAGCCACGGGAGACUUGGAAAGUUCACGGUUCGA-CGCCAUGGAUCUCCA-GGUGGG-UCAAGGU--UAGAGACGC---ACCAACC-UGGAGGACUCCAUGCUGUCGAGCUGAUCACGAGCAACAGACGCAAGAG
AAQQ01772082.1/825-951       UUAUGAGACUGCCUGUUUGG-AAGUUCAUUGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCACGUU--UAGAGGUUA---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACAAGCAGCGGAUACUUCCA
AAIY01755813.1/1336-1204     ACCUUGAAUGAGUUUUACAAAAUUAACGUGGUUCGACCACCAUGGAUCUCCAAGGUGGGGUCCCGAG-AUAGAUGCAC---ACCAACCAUAGUGGACUCCAUGCUGUUGAGCUAUUCACAAGCAAGCGAUGCUUCCU
AAYZ01127575.1/844-971       CUCACUUUCCAGAGGCCUGGCUGGUUCAUUGUUCGG-CACCAUGGAUCUCCA-GGUGGG-UCACGUU--UAGAGAUAC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACAAGCAGCGGACACUUCUA
AAPY01592915.1/408-535       ACGAGGACUUGCUGGUUUGGAAAGUUCAUUGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCACGGU--UAGAGAUAC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACAAGCAGCGGACACUUCCA
AC113246.15/27115-26988      UGGAAGCCUGGCUGAUUUGGAAAGUUCAUUGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCACGUU--UAGAUAUAC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACAAGCAGCGGAACUUCUAA
AANN01372443.1/381-254       UGGAGACCUUGCUGGCUUGCAAAGUUCAUUGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCACGUU--UUGAGAUAC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCAUAAGCUGCGGAUACUUCCA
AALT01594938.1/2782-2655     UGGACACCUGGCUGGCUUGGAAAGUUCAUUGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCACGUU--UAGAGAUAC---ACCAACC-UGGAGUACUCCAUGCUGUUGAGCUGUUCACAAGCUACGGAUGCUCUAA
AAKN02015558.1/78118-77991   UGGAGGCCUCGCUGGUGUGGAAAGUUCAUUGUUCGG-CACCAUGGAUCUCCA-GGUGGG-UCACGGU--UAGAAAUAC---ACCAACC-UGGAGGACUCCAUGCUGUCGAGCUGUUCAUGAGCAGCGGACACUUCCA
AC009264.6/134142-134269     UGGAGGCCUUGCUGGUUUGGAAAGUUCAUUGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCAAGUU--UAGAGAUGC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACAAGCAGCGGACACUUCCA
AC192819.2/133290-133417     UGGAGGCCUUGCUGGUUUGGAAAGUUCAUUGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCAAGUU--UAGAGAUGC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACACGCAGCGGACACUUCCA
AAPE02016781.1/150232-150105 UGGAGACCCUGCUGGUUUGGAAAGUUCAUUGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCACGUU--UUCAGAUAC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACAAUCAGCGGACACUUCUA
AADN03000373.1/281679-281808 UGGAGGCAGUGCUGUCUUCAUAAGUUCAUGGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCAAGAUUAUAGAGAUAC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACAAGCAGCGGAAGCCAAUA
AAQR03083508.1/23983-23856   UGGAGGCCUGGCUGGUUUGGAAAGUUCAUUGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCAAGUU--UAGAGAUAC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACAAGCAGCGGACACUCCUA
AAEX03010240.1/209595-209468 UGGAGACCUUGCUGGUGUGCAAAGUUCAUUGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCACGUU--UAGAGAUAC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACGAGCAGCGGACACUUCUA
AAGU03080504.1/9775-9648     UGGAGACCUUGCUGGUUUGGAAAUUACAUGGUUCGA-CACCAUGGAUCUCCA-GGUGGG-UCACGGU--UACAGGUAC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACAAGCAGCGGACACUUCUA
AAWZ02027502.1/382053-381924 UGGAAACAAUGCUGGUUUGAUAUGUUCAUGCCUCAA-CACCAUGGAUCUCCA-GGUGGG-UCAAGAUUAUAGAGAAAC---ACCAACC-UGGAGGACUCCAUGCUGUUGAGCUGUUCACAAGCUACAAGAACCAAUU
AAMC01093731.1/12746-12874   UAAAAACAUUUUCUUUGUCAUUAUGUCAUUUUUUGA-CACCACAGAGGGGUG-UCUUCC-UCAGGAA--AAAAAAAACCUGAGGAAGA-CACCCC--UCUGUGGUAUCGAAAUGUUGACAUAAUAAAGAAAAUGUUU
#=GC SS_cons                 ::::::::::::::::::::::::::::::<<<<<<.<<<<<<<<<<<<<<<.<<<<<<.<______.._________...>>>>>>>.>>>>>>-->>>>>>>>>>>>>>>:::::::::::::::::::::::::
#=GC RF                      uggAaacauugcuguUuUggaAAguUCAUuguUCgA.CAcCAuGGAucucca.GGUgGG.UCAaGuu..UAgAgAuAC...ACCaACC.uggaggACUCCaUGgUGUcGAgcUGUUCACAAGCaacaGAuAcUucua
//
# STOCKHOLM 1.0

#=GF AC   RF00793
#=GF ID   mir-497
#=GF DE   microRNA mir-497
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   100.00
#=GF TC   105.80
#=GF NC   53.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000231;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17306260
#=GF RT   Identification and characterization of microRNAs from the bovine adipose
#=GF RT   tissue and mammary gland.
#=GF RA   Gu Z, Eleswarapu S, Jiang H
#=GF RL   FEBS Lett. 2007;581:981-988.
#=GF WK   Mir-497_microRNA_precursor_family
#=GF SQ   8


CR933731.5/80171-80282       CCACCCCAGUCCUGCCC-CCGCCCCAGCAGCACACUGUGGUUUGUACGGCACUGUGGCCACGUCCAAACCACACUGUGGUGUUAGAGCGAGGGUAUGGGAGGCACCGAUGAGC
AAFR03049810.1/89806-89695   CAAAUCCCAUCCUGCCU-CCGCCCCAGCAGCACACUGUGGUUUGUUCAGUGUUAUGGCCAAGUCCAAACCACACUGUGGUGUUAGAGCGAGGGUAGGGGAGGCACCGCCAUCG
AALT01598296.1/191-302       CCCGUCCAGUCCUGCUC-CCGCUCCAGCAGCACACUGUGGUUUGUACGGCACUGUGGCCACGUCCAAACCACACUGUGGUGUUAGAGCGAGGGUGGGGGAAGGCACCGCUGAG
AAQQ01673553.1/1157-1046     ACCCACCCGUCCUGCCC-CCGCCCCAGCAGCACACUGUGGUUUGUACGGCACUGUGGCCACGUCCAAACCACACUGUGGUGUUAGAGCGAGGGUGGGGGAGGCACCGCUGAGG
AY865955.1/85-196            CCACCCCGGUCCUGCUC-CCGCCCCAGCAGCACACUGUGGUUUGUACGGCACUGUGGCCACGUCCAAACCACACUGUGGUGUUAGAGCGAGGGUGGGGGAGGCACCGCCGAGG
AY865956.1/128-240           CCACCCCGGUCCUGCUCCCCGCCCCAGCAGCACACUGUGGUUUGUACGGCACUGUGGCCACGUCCAAACCACACUGUGGUGUUAGAGCGAGGGUGGGGGAGGCACCGCUGAGG
AAEX03003597.1/206554-206443 CCACCCCAGUCCUGCUC-CCGCCCCAGCAGCACACUGUGGUUUGUACGGUACUGUGGCCACGUCCAGACCACACUGUGGUGUUAGGGUGAGGGUGGGGGAGGCACCGCUGAGG
AAGU03065644.1/46021-45910   CCACCCGAGUCCUGCUC-CCGCCCCAGCAGCACACUGUGGUUUGUACGGCACUGUGGCCACGUCCAAACCACACUGUGGUGUUAGAGCGAGGGUGGGGGAGGCACCGCAGAGG
#=GC SS_cons                 :::::::::<<<<<<<<.-<<<-<-<<<<-<<<<-<<<<<<<<<-<<<<<______>>>-->>->>>>>>>>>->>>>->>>>->->>>->>>>>>>>:::::::::::::::
#=GC RF                      ccacuCcaguCccgCcc.CCGCcCCagCaGCaCaCuGuGGuuuGUaCGGcAcUgUGgCCAcGuCCaaaCCaCaCuGuGGuGuuAGAGCGAggGuggGgGAGGcAcCgcugagg
//
# STOCKHOLM 1.0

#=GF AC   RF00794
#=GF ID   mir-42
#=GF DE   microRNA mir-42
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   92.50
#=GF NC   54.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.71 -Z 549862.597050 CM SEQDB
#=GF CL   CL00088
#=GF DR   MIPF; MIPF0000233;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   Mir-42_microRNA_precursor_family
#=GF SQ   5


AAGD02000348.1/78552-78654     AAACCCUUGUCGGACCUUUGUGGAUGUUUCCUUUUUCGGUGAAGUUGUUCCGUUGAAUUAUCUUCUUCACCGGGUUAACAUCUACAGAGGUCCUCGAGGGUUU
Z70213.1/12424-12524           AACCC-UUCGCGGACCUUUGUGGGUGUUUGCUUUUUCGGUGAAGUUGUCUUCCGUAGCU-UCUUCUUCACCGGGUUAACAUCUACAGAGGUCCAAAAAGGGGU
CAAC02000450.1/2292468-2292373 UAACCCUUGUCGGACCUUUGUGGGUGUUCGCCUUUUCGGUGAAGUUAC------UGAAU-GCUUCUUCACCGGGUUAACAUCUACAGAGGUCCUAAAGGGUUC
ABEG02004077.1/72498-72594     CAACCCUUGUCGGACCUUUGUGGAUGUUUGCCUUUUCGGUGAAGUUUC-----AAAAGA-UAUUCUUCACCGGGUUAACAUCUACAGAGGUCCUGAAGGGUUU
ABLE03028485.1/7422-7326       GAGACGCCGUUGGACCUCCGUGGAUGUUUGCUUUUGCGGUGAAGAGGU----GAUAACG-GGCGCUUCACCGGGUUAACAUCUACAGAGGUCC-GGGCGUCUU
#=GC SS_cons                   ::<<<<<<---<<<<<<<<<<<<<<<<<-<<<----<<<<<<<<____...._______.____>>>>>>>>>>>->>>>>>>>>>>>>>>>>-->>>>>>::
#=GC RF                        aAgcCcucgucGGaCCucuGugGauGuuugCcUUUuCGGuGaaGuugu....uauAAuu.ucuuCuuCaCCGgGcUaaCauCuaCagaGGuCCuagagGgcuu
//
# STOCKHOLM 1.0

#=GF AC   RF00795
#=GF ID   mir-43
#=GF DE   microRNA mir-43
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   57.40
#=GF NC   51.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000234;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF RN   [2]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [3]
#=GF RM   11679672
#=GF RT   An extensive class of small RNAs in Caenorhabditis elegans.
#=GF RA   Lee RC, Ambros V
#=GF RL   Science. 2001;294:862-864.
#=GF RN   [4]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [5]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [6]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [7]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [8]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   4


AAGD02000348.1/78685-78788     AAAGAGGCGAUUCUGCCCGUGACAACAAGAAACUUGUGAUU-AUGCCUAGAGAAUGAA-GAAGGGACAUAUCACAGUUUACUUGCUGUCGCAGGCGGUG-UCAUCUG
Z70213.1/12528-12626           UAUUGGCACUAGUCGCCCGUGACAUCAAGAAACUAGUGAUU-AUGCCAAACC-------ACAGGGACAUAUCACAGUUUACUUGCUGUCGCGGGCGGUGCUGAGUUU
CAAC02000450.1/2292316-2292219 AAGAGGCGAUU-CUGCCCGUGACAUCAAGAUGCUUGUGAUU-AUGCGAAAAU-------GUUGGGACAUAUCACAGUUUACUUGCUGUCGCAGGCGGAUUAUUGCUA
ABEG02004077.1/72634-72740     AAAGUGGUGUCACUGCCCGUGAUAUCAAGGAACUUGUGAUUUAUGCCAUAACUAACAUAACCUCGACAUAUCACAGUUUACUUGCUGUCGCAGGCAGGUGUUACUGA
#=GC SS_cons                   ::::<<<<<<--<<<<<<<<<<<<-<<<<<<<<<-<<<<<-.<<<<____________._____>->>>>>>>>>>>>>->>>>->>>>>>>>>>>>--->>>>>>:
#=GC RF                        aAaggggcgcuaccGCCcGuGacauCaaGaaaCuuGuGauU.auGCcaaAauaAauAa.auaggGACauauCaCaGuuuACuuGCuguCgCgGGCgguuugcgccca
//
# STOCKHOLM 1.0

#=GF AC   RF00796
#=GF ID   mir-48
#=GF DE   microRNA mir-48
#=GF AU   Burge S; 0000-0002-2506-927X
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A; WormBase
#=GF SS   Predicted; WAR; Burge S
#=GF GA   70.00
#=GF TC   83.90
#=GF NC   57.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000235;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [4]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [5]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [6]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF RN   [7]
#=GF RM   21085120
#=GF RT   Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs.
#=GF RA   Jan CH, Friedman RC, Ruby JG, Bartel DP
#=GF RL   Nature. 2011;469:97-101.
#=GF RN   [8]
#=GF RM   21177960
#=GF RT   Computational and experimental identification of mirtrons in Drosophila
#=GF RT   melanogaster and Caenorhabditis elegans.
#=GF RA   Chung WJ, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS,
#=GF RA   Lai EC
#=GF RL   Genome Res. 2011;21:286-300.
#=GF RN   [9]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   Mir-48
#=GF SQ   4


Z81551.1/5922-5825           AAA--CUCCCGGGAACUUGAGGUAGGCUCAGUAGAUGCGAAUUGAA------------CGGUAUCUCACAUCCACCAGCCUAGCUCGCAUUCCCAGAGUUUACGGUAUU--GUU
AAGD02012077.1/7529-7641     AAAUCCAUACCGGAUGUUGAGGUAGGCUCAGUAGAUGCGAUCAGAGUUGUGCCU-CAGGCGUUCCUCACAUCUUCUUGCCUAACUCGCCUUCCUUUAUGUUUAACCUUUUUUCU
CAAC02000462.1/389258-389362 AGAACCAUUCGGGAUGUUGAGGUAGGCUCAGUAGAUGCGAGGAGA--------U-CCACCAUUCCUCACAUCGUCUGUCCUAACUCGCCUUCCCUUGUGCUUCAAUAUUUCUUU
ABEG02012626.1/224-111       AAAGACAUGAGAGAAGUUGAGGUAGGCUCAGUAGAUGCGAACGUAAAUGAGCCCACAUCGGCCUUUCACAUCCACUUGCCUUCCUCGCCUUUCCAAAUGUUUCACUUUUCAAUU
#=GC SS_cons                 :::::<<<<-<<<<<<-<<<<-<<<<<<-<<<-<<<<-<<<_____________._________>>>->>>>->>>>>>>>>->>>>->>>>>>->>>>:::::::::::::::
#=GC RF                      AAAaccauccgGGAagUuGAGGuAGGccCaGuAGAUGCGAguagAaaUGaGCCu.CaacgGUuucUCACAUCuaCuggCCUaaCUCgCcuUCCcagaugUUucAaUuUUuuuUU
//
# STOCKHOLM 1.0

#=GF AC   RF00797
#=GF ID   mir-355
#=GF DE   microRNA mir-355
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   68.00
#=GF TC   70.10
#=GF NC   46.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000236;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF RN   [2]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF RN   [3]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [4]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF WK   MicroRNA
#=GF SQ   4


Z70037.1/4531-4414           UUGAGAUUAAUAAU--GUCAAGAAUUGAAUGGUUUGUUUUAGCCUGAGCUAUGAGUCAUCGGAAUAUGCAUAGCUUCUUGCUAAAACAUGCCAAUCAAUCUUAAUUGACGAAGUUUUUGA
CAAC02000450.1/748458-748341 CUACUGAUUAUGAUUAGUCAGCAAUCGGAUGGUUUGUUUUAGCCUGAGCUAUGUGUUAUUG-CAUAUUCAUAGCUACUUGCUAAAACAUACCAAUCGA-GUUGACUGACAUUCUUUGUUA
AAGD02000378.1/7048-7160     AAGUUGAUAUUUAUGUCAUUUG--UCGAAUGGUUUGUUUUAGCCUGAGCUAUGUGUUAUUG-CACAUACAUAGCUUCUUGUUAAAACAUACCAAUCGGUU----AAAUGAACCUUUUUGA
ABEG02004287.1/24539-24424   AUUCUUAUUCUAAGUCAUCAAAAG-GGAAUGGUUUGUUUUAGCCUGAGCUAUGUGUUAUUG-CACAUACAUAGCUACUUGUUAAAACAUACCAAUCCA-AUGAACUGA-CUGCUAUUUGG
#=GC SS_cons                 :::::::::::::<--<<<<<---<<<<-<<<<<<<<<<<<<<--<<<<<<<<________.______>>>>>>>->-->>>>>>>>>>>>>>->>>>------>>>>>>::::::::::
#=GC RF                      auguugaUaaUaAuuugucaggAaucGaAuGGuuuGuuuuagCCUGaGCuauGuGUuAUuG.cAuAUaCauaGCuuCUUGcuaaaaCauaCCaAuCgaUuUuaAcugacaaucUuUuUgA
//
# STOCKHOLM 1.0

#=GF AC   RF00798
#=GF ID   mir-49
#=GF DE   microRNA mir-49
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   63.50
#=GF NC   49.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000237;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [4]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [5]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF RN   [6]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF RN   [7]
#=GF RM   21177960
#=GF RT   Computational and experimental identification of mirtrons in Drosophila
#=GF RT   melanogaster and Caenorhabditis elegans.
#=GF RA   Chung WJ, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS,
#=GF RA   Lai EC
#=GF RL   Genome Res. 2011;21:286-300.
#=GF RN   [8]
#=GF RM   21129974
#=GF RT   MicroRNAs both promote and antagonize longevity in C. elegans.
#=GF RA   de Lencastre A, Pincus Z, Zhou K, Kato M, Lee SS, Slack FJ
#=GF RL   Curr Biol. 2010;20:2159-2168.
#=GF RN   [9]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   4


Z48006.1/9366-9462           UUUUGAAAAAGACCACC-GUCCGCAGUUUGU-UGUGAUGUGCUCCAAGCAAUCAU-GAGUCUGAAGCACCACGAGAAGCUGCAGAUGGAGGUUCUGAUUU
CAAC02000448.1/477630-477533 AACCGAAACCAUUUGCC-AUCCGCAGUUUUU-UGUAGUGUGCUCCGCGCCAUCUUAGUGCCCGAAGCACCACGAGAAGCUGCAGAUGGAAGUUUUGGUUG
AAGD02000772.1/52926-52830   -UUUAGAACAAUCUACCGAUCCGCAGUUUCU-UAUGAUGUGCUCCGAGCCAACAU-GUGUUCGAAGCACCACGAGAAGCUGCAGAUGGAGGAGUUUGUUC
ABEG02000562.1/30536-30439   UUUAGAAACAGUUGGCC-GUCCGCGGUUUUUUUGUGUAGUGCUCCGCACCAUCGA-GUGUUCGAAGCACCACGAGAAGCUGCAGAUGGAGAAGCUUGUUU
#=GC SS_cons                 :::::<<<<<--<<-<<.<<<-<<<<<<<<<.<<<<--<<<<<-<<-<<______.__>>->>->>>>>>>>>>>>>>>>>>->>>>>->>---->>>>>
#=GC RF                      uuuuggaaccauccaCC.auCCGCaGuuucu.uGuGauGuGCuCCGagCcAuCau.GuGcuCGAaGCaCCaCgagaagCuGCAGauGGAgguuuUgguuc
//
# STOCKHOLM 1.0

#=GF AC   RF00799
#=GF ID   mir-354
#=GF DE   microRNA mir-354
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   50.50
#=GF NC   37.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000238;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF WK   MicroRNA
#=GF SQ   4


AL132876.4/135332-135222     CCAGAGCCGACUAAGCACCUUGGUGCGGCUGCAGACGGGUAUCCGGCUCGACGUUC-----AUACAUCAC-GAC-UUCUUUCCUUUUACC-UUGUUUGUUGCUGCU-CCUAUUGGUUUUG
CAAC02000482.1/154225-154116 CCAGAGCCGACUAAGUGCCUUGGUGCGGCUACAGACGGGUAUCCGGCUCGAUGUUC-----AUACACCGC-GAC--UCUUUCCUUUUACC-UUGUUUGUUGCUGCU-CCUUUUGGUUUUG
AAGD02005008.1/3108-3217     CCAGAGCCGACUAAGCGCCUUGGUGCGGCUGCAGACGGGUAACCGGCUCGACGUUC-----AUUCAUCACCGAC-U-CUUUCCUUUUACC-UUGUUUGUUGCUGC--CCUUAUGGUUUUG
ABEG02002754.1/34274-34392   CCAGAGCCGAUUAAGCACCUUGGUGCGGCUGCAGACGGGUAACCGGCUCGACGUUCAUCACAUCAUCCGC-GACCUUCUUUCCUAUUACCCUUGUUUGUUGCUGCCACUAUUUGGUUUUG
#=GC SS_cons                 :<<<<<<<<<-----------<<-<<<<<-<<<<<<<<<<<---<<---<<-<<<_....._________.>>>.->>--->>--->>>>.->>>>>>>->>>>>-.>>-->>>>>>>>>
#=GC RF                      CCagagCCgacUAAGcaCCUUGGUGCgGCUgCagaCgGGuaaCCGGCUCGacGuuC.....AUacauCaC.gaC.UuCUUUCCUuUuaCC.UuGuuuGcUGCuGCu.CCuuuuGGuuuuG
//
# STOCKHOLM 1.0

#=GF AC   RF00800
#=GF ID   mir-353
#=GF DE   microRNA mir-353
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   83.60
#=GF NC   42.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000239;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF WK   MicroRNA
#=GF SQ   4


AY948598.1/42-155          UGUUGAAGUAUUGCAAAA-GCAAAGGACGGGCACAAUUGCCAUGUGUUGGUAUUAUUGCUUCAAGUUAUUUGAAGCUGUAAUAUCAAUAAGCAUGUCUCGUGUGAAGUCCGACAA
AAGD02001045.1/15690-15804 UGUCGAAGUUAUGCGAAAUAUAAAGCGUGGAAGCAAUUGUCAUGCGUUGGUCUUAUAGUUUCAAGUUAUUUGAACCUUUGAAAUCGAUAAGCAUGCCUCGUUAGAAGUGCGACAA
DQ789493.1/47-161          UGUCGAAGAUAUGCAAAAUAAAAAGCAUGGGCACAAGUAUCAUGUGUUGGUAUCAUUGUUUCAAGUUAUUUGUUGCUAUGGUAUCGAUAAGCAUGCUACGUGUGAAGUGCGACAA
ABEG02000967.1/5860-5746   UGUCGAAGUUAUGCAAAAGAAUAAGCAUGGUCACAUCUGUCAUGUGUUGUUACCUUGAUUUCAAGUUAUUUGAGAUUAUGGUAUCGAAAAGCAUGCCUCGUGAAAAAUGCGACAA
#=GC SS_cons               ::::::::::::::::::::::::<<<<--<<<<------<<<<<<<<<<<<<<<<<<<<<<<<_____>>>>>>>>>>>>>>>>>>>-->>>>>---->>>>--->>>>:::::
#=GC RF                    UGUcGAAGuuaUGCAAAAuAaaAAGcacGGgcaCAauUguCauGcgucGguaccaugGcuuCaaGUUAUuuGaagCcaugguacCgacAAgCauGccuCGugcgAAgugCGACAA
//
# STOCKHOLM 1.0

#=GF AC   RF00801
#=GF ID   mir-280
#=GF DE   microRNA mir-280
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   85.00
#=GF TC   89.00
#=GF NC   51.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000240;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12844358
#=GF RT   Computational identification of Drosophila microRNA genes.
#=GF RA   Lai EC, Tomancak P, Williams RW, Rubin GM
#=GF RL   Genome Biol. 2003;4:R42.
#=GF WK   MicroRNA
#=GF SQ   8


AASS01023700.1/2698-2599     UGGGCUUUUUAUGUAUUUUACGUUGCAUAUGAAAAUGAUAUUUAUAGUAAACAGAUUAUUUUUAUAUGCAGGUAU--AUGCAAGUCGAGGUCCUGCACACUG
AAIZ01001347.1/100621-100715 CGGCUUUU--AUGUAU-UUACGUUGCAUAUG-AAAUGAUAUUUAUAGUAAACAGAUUAUUU-UAUAUGCAGGUAU--GUGCAGCUGAAGAGCCUGUCCAUUG
AANI01014841.1/76079-76175   UGGCUUUU--AUGUAU-UUACGUUGCAUAUG-AAAUGAUAUUUAUAGUAAACAGAUUAUUU-UAUAUGCAGGUAUACAUGCCAGAGCAGUGCAUGCAACUGC
AAQB01006287.1/166688-166782 UGGCUUUU--AUGUAU-UUACGUUGCAUAUG-AAAUGAUAUUUAUAGUAAACAGAUUAUUU-UAUAUGCAGGUAU--GUGCAACCGAAGCAGCAGAAGCCAG
AAPT01021476.1/37912-38002   UGGCUUUU--AUGUAU-UUACGUUGCAUAUG-AAAUGAUAUUUAUAGUAAACAGAUUAUUU-UAUAUGCAGGUAU----ACA--UGCAACUCCUUCUCAAUG
AAPU01010189.1/60454-60360   UAGCUUUU--AUGUAU-UUACGUUGCAUAUG-AAAUGAUAUUUAUAGUAAACAGAUUAUUU-UAUAUGCAGGUAU--ACAUGCCAGGCCGGCCAGUGCAUGC
AAKO01000485.1/3586-3680     UGGCUUUU--AUGUAU-UUACGUUGCAUAUG-AAAUGAUAUUUAUAGUAAACAGAUUAUUU-UAUAUGCAGGUAU--AUGCAAGUCGAGGUCCUGCACACUG
AAPP01018712.1/27830-27743   UGGCUUUU--AUGUAU-UUACGUUGCAUAUG-AAAUGAUAUUUAUAGUAAACAGAUUAUUU-UAUAUGCAGGUAU--AUGCA-------AGCCUGAACAACU
#=GC SS_cons                 :<<<<<<<..-<<<<<.-<<<-<<<<<<<<<.<<<<<<<-<<<<___>>>>--->>>>>>>.>>>>>>>>>>>>-..>>>>>---->>>>>>>:::::::::
#=GC RF                      UgGcccuc..AuGcau.UuaCGuuGCauaug.aaaugauAuuuaUAGuaaaCAGauuauuu.uauauGCagGuaU..augCaaguggagggCcuGuacauug
//
# STOCKHOLM 1.0

#=GF AC   RF00802
#=GF ID   mir-207
#=GF DE   microRNA mir-207
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.40
#=GF NC   49.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000241;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human.
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA. 2003;9:175-179.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   MicroRNA
#=GF SQ   6


AB183426.1/6611-6689         AAGG----CAGGGGUGAGGGGCUGCGGGAGGAGCCGGGCGGAGGCUGCGGCUUGCGCUUCUCCUGGCUCUCCUCCCUCUCUUU
AAFC03003387.1/34783-34701   AAGGACCCUUGGGGCGAGGGGCUGCGGGAGGAGCCGGGCGGAGGCUGCGGCUUUCGUUUCUCUGGUCUCUCCUCCUCCUCUUU
ABBA01065072.1/33420-33342   GAGG----CAGGGGCGAGGGGCUGCGGGGGGAGCCGGGCGGAGACUGCGGCUUUUGGUUUCGCUUUCUCUGUUUCCCCUCCCU
AAQQ01038110.1/88-165        GAGG----CAGGGGCGAGGGGCUGCGAGAGGAGCCGAGC-GAGGCUGCUGCUUUCGCUUCUCCUGUCUCCCCUCCCUCUCUUU
AAGW02033449.1/226-303       GAGG----CAGGGGCGAGGGGCUGCGGGAGGAGCCGGGCGG-UGCUGCGGGUUUCGCUUCUCCAGUCUCCCCUCCUUCUCUUU
AAEX03007936.1/261346-261421 GAGC----CAGGGGCGAGGGGCUGCGGGGGGAGCGGGGCGGAGGCUGCGGCC---GCUUCUCCGGUCUCUCCUCCUUCCCUUU
#=GC SS_cons                 :<<<....-<<<<<-<<<<<<--<<<<<<<<<<<<<<<<-<______>->>>>>->>>>>>>>>->>->>>>>>>>>>>>>>:
#=GC RF                      gagG....caGggGCGaGGgGCUGcggGgGgagCcggGCGGAGGCUGCGGCcugcGcuuCcCccggCUCcCCuCCccCuCcuU
//
# STOCKHOLM 1.0

#=GF AC   RF00803
#=GF ID   mir-425
#=GF DE   microRNA mir-425
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   77.20
#=GF NC   52.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000242;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17965199
#=GF RT   In vitro and in silico annotation of conserved and nonconserved microRNAs
#=GF RT   in the genome of the marsupial Monodelphis domestica.
#=GF RA   Devor EJ, Samollow PB
#=GF RL   J Hered. 2008;99:66-72.
#=GF RN   [2]
#=GF RM   15538371
#=GF RT   A pancreatic islet-specific microRNA regulates insulin secretion.
#=GF RA   Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer
#=GF RA   S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M
#=GF RL   Nature. 2004;432:226-230.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [5]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [6]
#=GF RM   20360741
#=GF RT   The genome of a songbird.
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF WK   Mir-425_microRNA_precursor_family
#=GF SQ   5


AANN01668557.1/686-771     GAGAGGCGGUGGAAUGACACGAUCACUCCCGCUGAGCGGGCCCGCACACGCCGUCUGGGAAUGUCGUGGUCCGCCCGGCGCUCUUU
AAFR03030218.1/13947-14031 AAAGUGCUUUGGAAUGACACGAUCACUCCCGUUGAGCGGACAGCCAAGAAGCCAUCGGGAAUAUCGUG-UCCGUCCAAUGCUCUUU
CT010508.10/218540-218624  AAAGUGCUUUGGAAUGACACGAUCACUCCCGUUGAGUGGGCACCCAAGAAGCCAUCGGGAAUGUCGUG-UCCGCCCAGUGCUCUUU
AC137630.9/68702-68618     AAAGCGCUUUGGAAUGACACGAUCACUCCCGUUGAGUGGGCACCCGAGAAGCCAUCGGGAAUGUCGUG-UCCGCCCAGUGCUCUUU
AAWZ02016383.1/4845-4762   GAAUGGUUUUGGAAUGACACGAUCACUCCCGCUGAGCGAGCAGAGCCACGGCCA-CGGGGAUGUCGUG-UCUGUCCAAAACUAUUU
#=GC SS_cons               :::::<<<<<<<---<<<<<<<<---<<<<<________________________>>>>>-->>>>>>.>>--->>>>>>>:::::
#=GC RF                    aAAguGcguuGGAAUGACACGAuCACuCCCGuUGAGcGGGCAcccaaaaagCcAuCGGGaAUgUCGUG.UCcGcCCaacgCUcUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00804
#=GF ID   mir-240
#=GF DE   microRNA mir-240
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.40
#=GF NC   48.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000243;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF WK   MicroRNA
#=GF SQ   3


AAGD02000008.1/9523-9408     CUACAAUUCUACCU-AAAACUGUUUUCGAAUCGGGAGUUUCGUGGCCUGAAUGCGUGAACGCUUGUGCUUUAGCAUACUGGCCCCCAAAUUUUCGCUUUGAAUUCUAGUUGUCUUUU
CAAC02000535.1/798371-798483 CGCUGUCUUUAUUUUGAAACUGUUUUCAAAUCGAGAAUUUCGAGGCCUGAAUGCAAGAACCGUUUU----GAGCAUACUGGCCUCCAAAUUUUCGCUUUGAAUUUUAGUUACGCGUG
FO080457.1/9205-9316         UGCUAUUUCGUUGUUAGAAACUUUUUCAAAUCGAGGAUUUUGAGACUAGAAUGCUUGAAUUGUACU-----AGCAUACUGGCCCCCAAAUCUUCGCUUAGAAAUACAGUUCACAAUU
#=GC SS_cons                 :::::::::::::::::<<<<<--<<<<<<-<<<<<<<<<-<-<<<<-<-<<<<____________....__>>>>->->>>>->->>>>>>>>>->>>>>>--->>>>>:::::::
#=GC RF                      cgcuauuUcuauuUUaaAAcugUUUUCgAAUCGaggaUUUcGaGGCcuGAAUGCauGAAcugUuuU....uAGCAUACUgGCCcCCAAAucuuCGCUUcGAAuUucagUUaucuaUu
//
# STOCKHOLM 1.0

#=GF AC   RF00805
#=GF ID   mir-351
#=GF DE   microRNA mir-351
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   100.00
#=GF TC   118.30
#=GF NC   66.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000244;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20668074
#=GF RT   Identification and analysis of expression of novel microRNAs of murine
#=GF RT   gammaherpesvirus 68.
#=GF RA   Zhu JY, Strehle M, Frohn A, Kremmer E, Hofig KP, Meister G, Adler H
#=GF RL   J Virol. 2010;84:10266-10275.
#=GF RN   [4]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [5]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:360-365.
#=GF RN   [6]
#=GF RM   16766679
#=GF RT   Identification and characterization of two novel classes of small RNAs in
#=GF RT   the mouse germline: retrotransposon-derived siRNAs in oocytes and germline
#=GF RT   small RNAs in testes.
#=GF RA   Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N,
#=GF RA   Imai H
#=GF RL   Genes Dev. 2006;20:1732-1743.
#=GF RN   [7]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   Mir-351_microRNA_precursor_family
#=GF SQ   2


AAHY01210347.1/2526-2428 CAUGGCACCUCCGUUUCCCUGAGGAGCCCUUUGAGCCUGGAGUGAAAAAAAAAAACAGGUCAAGAGGCGCCUGGGAACUGGAGAAGAGUGUUAAACUUC
AABR05186732.1/234-138   CAUGGCACCUCCAUUUCCCUGAGGAGCCCUUUGAGCCUGAGGUGAAAAAAAAA--CAGGUCAAGAGGCGCCUGGGAACUGGAGAAGAGUAUUAACUUCU
#=GC SS_cons             ::<<<-<<<<<<<-<<<<<--<<<-<<<-<<<<<-<<<<________________>>>>>>>>>->>>->>>>>>>>->>>>>---->>->>>::::::
#=GC RF                  CAuggCaCCuCCgUuuCCCUGaGGAGCCCcuuGaGCCuGaaGUGAAAAAAAAAAACaGGuCaagAGGCGCCuGGGaaCcGGaGAAGAGuaccaAauUuu
//
# STOCKHOLM 1.0

#=GF AC   RF00806
#=GF ID   mir-350
#=GF DE   microRNA mir-350
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   76.00
#=GF NC   45.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000245;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15538371
#=GF RT   A pancreatic islet-specific microRNA regulates insulin secretion.
#=GF RA   Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer
#=GF RA   S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M
#=GF RL   Nature. 2004;432:226-230.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [4]
#=GF RM   20668074
#=GF RT   Identification and analysis of expression of novel microRNAs of murine
#=GF RT   gammaherpesvirus 68.
#=GF RA   Zhu JY, Strehle M, Frohn A, Kremmer E, Hofig KP, Meister G, Adler H
#=GF RL   J Virol. 2010;84:10266-10275.
#=GF RN   [5]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [6]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:360-365.
#=GF RN   [7]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   Mir-350_microRNA_precursor_family
#=GF SQ   11


AAWR02039510.1/16310-16408   AAACCCUUUGCUCCUAUAAGAGUAAA-GUGCACGCGCUUUGGGACAGU-GAGGAAGAUGAUGUUCACAAAGCCCAUACACUUUUACUCUUUAGGAGAGCCA
AANN01799551.1/1515-1613     AAAAACUUUGCUCCUACAAGAGUAAA-GUGCACGUGCUUUGGGACAGU-GAAUAAAAUAAUGUUCACAAAGCCCAUACACUUUUACCCUUUAGGAGAGCCG
AAGW02026533.1/115483-115385 AAAAUAUUUGCUCCUACAAGAGUAAA-GUGCAUGCGCUUUGGGACAGU-GAGGAAAAUAAUGUUCACAAAGCCCAUACACUUUUACCCUUUGGGAGAGUUG
AC144905.10/206783-206881    AGAUGCCUUGCUCCUACAAGAGUAAA-GUGCAUGCGCUUUGGGACAGU-GAGGAAAAUAAUGUUCACAAAGCCCAUACACUUUCACCCUUUAGGAGAGUUG
AAPY01728940.1/2419-2322     AGAUGCCUUGCUCCUACGAGAGUAAACGUGCAC-UGAUUUGGGACAGUGGAAGAGAAUAAUGUUCACAAGGCC-AUACACUUUUACCCUG-AGAAGAGUUG
AAQQ01687215.1/1109-1011     AAAUAUCUUGCUCCUACAAGAGUAAA-GUGCACGCGCUUUGGGACAGU-GAGGAAAAUAAUGUUCACAAAGCCCAUACACUUUCACCCUUUAGGAGAGUUG
AC239692.1/34871-34960       AAAAACUUUGCUCCUACAAGAGUAAA-AUGCAGGUGCUUUGCGACAGU-GAGGAAAA---------GAAAGCCCAUACAUUUUAACCCUUUAGGAGAGUUG
ABBA01109437.1/411-500       AAAAACUUUGCUCCUACAAGAGUAAA-AUGCAGGUGCUUUGCGACAGU-GAGGGAAAGAA---------AGCCCAUACAUUUUAACCCUUUAGGAGAGUUG
AANU01168227.1/13622-13711   AAAAACUUUGCUCCUACAAGAGUGAA-GUGCAGGGGCUUUGGGAUAGU-GAGGAAAA---------UAAAGCCCAUACACUUUGACCCUUUAGGAGAGUUG
AAFC03070376.1/47198-47100   AACAACUUUGCUCCUGCAAGAGUGAA-AUGCACGUGCUUUGGGACAGU-GAAGACAAUAAUGUACACAAAGUCCAUACACUUUUACCCAUUAGGAGAGUUG
AAEX03005247.1/304791-304693 AAAACCUUUGCUCCUACAAGAGUAAA-GUGCACGCGCUUUGGGACAGU-GAAGAAAAUAAUGUUCACAAAGCCCAUACACUUUUACCCUUUAGGAGAGUUG
#=GC SS_cons                 ::::::::::<<<<<<-<<<-<<<<<.<<<---<-<<<<<<<<<<<__.___________>>>>>->>>>>>->--->>>>>>->>->>>>>>>>>:::::
#=GC RF                      AAAaacuUUGCuCCuacaaGAGuaaa.guGCAcGuGCuuugGgaCaGU.GAgGAaAAuAAuGucCAcaaaGCCCAUACacuuuuaCcCuuuaGGaGAGuuG
//
# STOCKHOLM 1.0

#=GF AC   RF00807
#=GF ID   mir-314
#=GF DE   microRNA mir-314
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   77.00
#=GF NC   33.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000246;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17994087
#=GF RT   Evolution of genes and genomes on the Drosophila phylogeny.
#=GF RA   Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC,
#=GF RA   Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM,
#=GF RA   Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW,
#=GF RA   Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D,
#=GF RA   Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak
#=GF RA   SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK,
#=GF RA   Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S,
#=GF RA   Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A,
#=GF RA   Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher
#=GF RA   AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD,
#=GF RA   Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC,
#=GF RA   Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey
#=GF RA   J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S,
#=GF RA   Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter
#=GF RA   GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz
#=GF RA   MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J,
#=GF RA   Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P,
#=GF RA   Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S,
#=GF RA   Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L,
#=GF RA   Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky
#=GF RA   E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L,
#=GF RA   McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P,
#=GF RA   Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S,
#=GF RA   Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M,
#=GF RA   Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli
#=GF RA   D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D,
#=GF RA   Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie
#=GF RA   MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S,
#=GF RA   Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz
#=GF RA   MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M,
#=GF RA   Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W,
#=GF RA   Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W,
#=GF RA   Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E,
#=GF RA   Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang
#=GF RA   J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A,
#=GF RA   Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K,
#=GF RA   Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A,
#=GF RA   Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A,
#=GF RA   An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A,
#=GF RA   Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C,
#=GF RA   Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y,
#=GF RA   Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De
#=GF RA   Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M,
#=GF RA   Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D,
#=GF RA   Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR,
#=GF RA   Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez
#=GF RA   N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L,
#=GF RA   Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P,
#=GF RA   Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X,
#=GF RA   Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P,
#=GF RA   Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T,
#=GF RA   Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V,
#=GF RA   Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N,
#=GF RA   Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E,
#=GF RA   Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F,
#=GF RA   Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N,
#=GF RA   Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N,
#=GF RA   Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y,
#=GF RA   Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk
#=GF RA   T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q,
#=GF RA   Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W,
#=GF RA   Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I
#=GF RL   Nature. 2007;450:203-218.
#=GF WK   MicroRNA
#=GF SQ   6


AAEU02000214.1/163018-162929 UCGUAACUUGUGUGGCUUCGAAUGUACCUAGUU-GAGG--AAAA----ACCCCAUGUCGGAUUUUGUUACCUCUGGUAUUCGAGCCAAUAAGUUCGG
AANI01017486.1/342740-342830 UCGUAACUUGUGUGGCU-UGAAUGUACCUGGUU-GAGGAACGAA----UUCAACGUUUGGAUUUUGUUGCCUUUGGUAUUCGAGCCAAUAAGUUCGG
AAPU01011627.1/156896-156990 UCGUAACUUGUGUGGCUUCGAAUGUACCUCGUCGAGCG--AAAAGCGAAUUCAUUGUUGGAUUUUGUUGCUCUUGGUAUUCGAGCCAAUAAGUUCGG
AAPT01020574.1/773332-773257 UCGUAACUUGUGUGGCUUCGAAUGUACCUGGCU-AAGG-----------AAAGUUGGAUUU--------CCU-AGGUAUUCGAGCCAAUAAGUUCGG
AAFS01000446.1/64778-64866   UCGUAACUUGUGUGGCUUCGAAUGUACCUAGUU-GAGG--AAAA----CUCCGAAAU-GGAUUUUGUUACCUCUGGUAUUCGAGCCAAUAAGUUCGG
AAPP01019289.1/431088-431175 UCGUAACUUGUGUGGCUUCGAAUGUACCUAGUU-GAGG--AAAA-----AUCAGUUUGGAU-UUUGUUACCUCUGGUAUUCGAGCCAAUAAGUUCGG
#=GC SS_cons                 :<<-<<<<<<<-<<<<<-<<<<--<<<<-----.<<<<..-<<<....-<<<______>>>->>>---->>>>->>>>>>>>>>>>>>>>>>>>>>:
#=GC RF                      UCGUaaCuuguGuGGCuUcGaaUGuaCCUaGUu.gagG..aaaa....auccauuguuggaUuuuGUUaCcucuGGuauuCgaGCCaauaaGuuCGG
//
# STOCKHOLM 1.0

#=GF AC   RF00808
#=GF ID   mir-86
#=GF DE   microRNA mir-86
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   52.70
#=GF NC   46.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000247;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [4]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [5]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [6]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF RN   [7]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF RN   [8]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   5


AL132860.1/102935-102838     CGUGUCCACGCCGUCUAAGUGAAUGCUUUGCCACAGUCUUCGAUGUUCUGAAAUGAAGCCUGGGCUCAGAUUCGCUUAGGCCGGAGUUUGACACGGCA
AAQA01000542.1/5785-5693     GGUGAGCUGGCCAGUUAAGUGAAUGCUUUGCCACAGUCUUAGAAAUUGA----UUAAG-CUGGGCUAAGGUUCACUUAGGCUGGACGCUAUAACCGCA
AAGD02000059.1/34982-35079   CGAGUCGGCGCCGUCUAAGUGAAUGCUUUGCCACAGUCUUCGACCAUGUCAAAUGAAGCCUGGGCUAAGAUUCGCUUAGGCCGGCGUUUUUCGACACG
CAAC02000515.1/635706-635609 CGAGUCAAUGCCGUUUAAGUGAAUGCUUUGCCACAGUCUUCGAUCAUGUCACAUGAAGCCUGGGCUUAGAUUCACUUAGGCCGGCGUUCCUUGACUCA
ABEG02004129.1/28875-28969   CGAGUCGGCGCCGUCUAAGUGAAUGCUUUGCCACAGUCUUCGACCAUGUCAAAGGAAGCCUGGGCUCAGAUUCGCUUAGGCCGGCGUU---CGACACG
#=GC SS_cons                 :<<<<<<<<<<<<<<<<<<<<<<<-<<--<<<-<<<<<<<<<___________>>>>>>>>>>>>-->>>>>>>>>>>>>->>>>>>---->>>>>>:
#=GC RF                      cGcgucggcgCCGccuaaGcGaauGCuUUGCCACaGgCuucgAuaaUgucAaAcgaaGcCuGGGCUaaGauuCgCuuaggCCGGcgcuuaucgacgCa
//
# STOCKHOLM 1.0

#=GF AC   RF00809
#=GF ID   mir-241
#=GF DE   microRNA mir-241
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   52.10
#=GF NC   48.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000248;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [4]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   Mir-241_microRNA_precursor_family
#=GF SQ   4


Z81551.1/7696-7601           CGGGGGUGUCAAAGUUGAGGUAGGUGCGAGAAAUGACGGCAUCCAUAUAGUAAUCGUUCAUUGUCUCUCAGCUGCUUCAUCUGUG---ACAUG---GCUACG
CAAC02000462.1/386402-386495 AGACGGUGUCAAAGCUGAGGUAGGUGUGAGAAAUGACGAAAGGCUCUUAAUCGU--UUCAUUGUCUCGCAGCUGCUUCAACUGUG---AUUUA---CCGACG
AAGD02012077.1/6135-6233     GCGACGUGUCAAAGUAGAGGUAGGUGCGAGAAAUGACGGAACCUCACAAAUCAUCGUUCAUUGUCUCGCAGCUGCUUCAACUGUGCCCACUGA---CGCAAA
ABEG02011887.1/1393-1489     AAGGGGUGUCAAAGUAGAGGUAGGUGCGAGAAAUGACGG--GCAUCGUGCAAAUCGUUCAUUGUCUCCCAGCUACUUCAACUGUG---AUUUCAACCCUUUG
#=GC SS_cons                 ::::<<-<<<<-<<<<<<<<<<<-<<<<<<<<<<<<_____________________>>>>>->>>>>>>->>>>>>>>>>>->>...>>---...>>::::
#=GC RF                      aagaggUguCaAaGuuGagGcaGGuGcGaGaaauGaCGgaAucuuuuuAauaAUCGUuCauuGuCuCgCaGCugCuuCaaCuGuG...acuua...ccuaug
//
# STOCKHOLM 1.0

#=GF AC   RF00810
#=GF ID   mir-85
#=GF DE   microRNA mir-85
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   58.00
#=GF TC   59.00
#=GF NC   56.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.44 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000249;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [4]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [5]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [6]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF RN   [7]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF RN   [8]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   5



ABLE03020284.1/3941-4049     UAUAGAGCGCUCAUCCGGGAGCCCGGCUUUUCAUUUGUUUGAAACCAGCCAAGACGAGUAUGGUGGUUACAAAGUAUUUGAAAAGUCGUGCUCUGGAAAGAGGAACUCA
Z66520.1/16076-16181         UAUAGAAUUUUGGCGUCGGAGCCCGAUUUUUCAAUAGUUUGAAACCAGUGUACACAUAAA---UGGUUACAAAGUAUUUGAAAAGUCGUGCUCUGAAAAUGAAUUCUUA
AAGD02000337.1/3974-4079     GAAGACGUUCUGAAGUCGGAGCCCGUCUUUCCAAUAUUUUGAAACCAGUACUCAUGCAAA---UGGUUACAAAGUAUUCGAAAAGGCGUGCUCUGAGAAGAGCUCUUCG
CAAC02000442.1/497969-497866 UCAAAAAACAGUACCCCGGUGCCCGCUUUUUCAGUAGUUUGAAACCAGAG-AU-GAUAGU---UGGUUACAAAGUAUUUGAAAAGGCGUGCACUGGGUAAAUUUUGAAU
ABEG02003023.1/27618-27723   CGAGGUUCGGUCACCACGGUGCCCGACUUUUCAAUAUUUUGAAACCAGUUAUUCUGAGAA---UGGUUACAAAGUAUUUGAAAAGCCGUGCACUGUAAGAAUCUCUCUU
#=GC SS_cons                 ::::::::::::::<<<<<<<<<<<<<<<<<<<<<<-<<<<-<<<<<_____________...>>>>>->>>>->>->>>>>>>>>>>>>>>>>>>>::::::::::::
#=GC RF                      uaaagaauuuuuAcccCgGaGCcCGgcUUUuCaaUagUUUGAAACCAGuuaauauguaaA...UGGUUACAAAGuAUuuGaAAAgcCGuGCuCuGggAAaAuuUuuuua
//
# STOCKHOLM 1.0

#=GF AC   RF00811
#=GF ID   mir-84
#=GF DE   microRNA mir-84
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   94.10
#=GF NC   47.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000250;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF RN   [2]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [3]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [4]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [5]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [6]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF RN   [7]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   Mir-84_microRNA_precursor_family
#=GF SQ   4


Z68131.1/3383-3285         -----CUACUAUUCAUCAUAC-GUCUGCCUGUGGCAUCUGAGGUAGUAUGUA-AUAUUGUAGACUG-UCUAUAAUGUCCACAAUGUUUCAACUAACUCGGCUGUUCU--------
CAAC02000532.1/88618-88505 UUGCUAUAUAUUCAGCCGUACUGUCUGAAAAUAACAUCUGAGGUAGUUUGCA-AUGCUGUCGACGUAACUGAAAAGUCAACAUCAUUCCAACUUCCUCGGCUGUUCAAAAGGCUA
AAGD02011097.1/57200-57312 AUUUUCUAUAUUCUACGAAACAGUCUAACAGAAGCAUCUGAGGUAGUUUGUA-AUGCUGUCGACGC-ACUGUAAUGUCUACAUCAUUUCAACUGCCUCGGCUGUUUUUAGACUUU
ABEG02000526.1/67837-67950 CUGCUCUAUACUUCUAAAGAUUGUCUCAAAGUAACAUCUGAGGUAGUUUGGAAAUGCUGUCGACGC-AUUGUGAUGUCAACAACAUUUCAACUAACUCGGCUGUUUCAUGAGAUU
#=GC SS_cons               ::::::::::::::::::::::::::::::::<<<<-<<<<<<<<<<-<<-<.<<<-<<<-<<<__.________>>>->>>->>>>->>>>>>>>>>>>->>>>::::::::::
#=GC RF                    uUgcUcUAUauUucauaAuAcuGUCUgaaaguaaCAUCuGAGguAGUuUGuA.AuGcUGUcGACgu.acUguAAuGUCaACAaCaUUUCAACUacCUCgGCUGuuuuaagaguUu
//
# STOCKHOLM 1.0

#=GF AC   RF00812
#=GF ID   mir-83
#=GF DE   microRNA mir-83
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   51.00
#=GF TC   61.70
#=GF NC   42.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000251;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [4]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [5]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [6]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF RN   [7]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF RN   [8]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   4


CAAC02000544.1/241286-241176 GCAGAAGGCACCACUCGAAAAAACUGAGUUUAUGUGUGUACUU-GACGGC-GAUCAGAGCAACGAUCUAGCACCAUAUAAAUUCAGUGUUUUCGUGGACA-GAGAGCCAAGUUU
AAGD02003239.1/24857-24749   CCAGUAGGCACCACUCGGAAAAACUGAGUUUAUGUGUGUACUU-GACGGC-CACUCGAGCAACGAUCUAGCACCAUAUAAAUUCAGUAUUUUCGUG--GA-GAGAGCCAAUUUU
ABEG02005358.1/2141-2251     AUCGAAGGCACCACUCGGAAAAACUGAGUUUAUUUGAGUACUUAGACGGC-CAUUAGAGCAACGAUCUAGCACCAUAUAAAUUCAGUAUUUUCGUG--GAUGAGAGCCUAUUUU
FO080377.1/15999-16108       UUUAAAAGCACCACUCGGAACCACUGAAUUUAUGUGUGUACUU-GACGGCCAACAAGAGCAUCGAUCUAGCACCAUAUAAAUUCAGUAAUUUCGCG--UC-GAGAGCUAUUCUG
#=GC SS_cons                 ::::::<<<----<-<<<<<<<<<<<<<<<<<<<<<-<<-<<-.<<<<__.___________>>->>->>->>>>>>>>>>>>>>>>>>>>>>>->..--.---->>>::::::
#=GC RF                      uuagaAgGCACCACUCGgaaacaCuGaguuuauguGuGuACuU.GaCGGC.aAuuaGAGCAaCGAuCUaGCaCCacauaaacuCaGuguuucCGuG..ua.GAGAGCcaauuUu
//
# STOCKHOLM 1.0

#=GF AC   RF00813
#=GF ID   mir-11
#=GF DE   microRNA mir-11
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   51.30
#=GF NC   48.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.71 -Z 549862.597050 CM SEQDB
#=GF CL   CL00083
#=GF DR   MIPF; MIPF0000252;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20807255
#=GF RT   Next-generation small RNA sequencing for microRNAs profiling in the honey
#=GF RT   bee Apis mellifera.
#=GF RA   Chen X, Yu X, Cai Y, Zheng H, Yu D, Liu G, Zhou Q, Hu S, Hu F
#=GF RL   Insect Mol Biol. 2010;19:799-805.
#=GF RN   [2]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [3]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus.
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF RN   [4]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus.
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF RN   [5]
#=GF RM   20817720
#=GF RT   Functional shifts in insect microRNA evolution.
#=GF RA   Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S
#=GF RL   Genome Biol Evol. 2010;2:686-696.
#=GF RN   [6]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing.
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF RN   [7]
#=GF RM   20229201
#=GF RT   Novel microRNAs in silkworm (Bombyx mori).
#=GF RA   Cai Y, Yu X, Zhou Q, Yu C, Hu H, Liu J, Lin H, Yang J, Zhang B, Cui P, Hu
#=GF RA   S, Yu J
#=GF RL   Funct Integr Genomics. 2010;10:405-415.
#=GF WK   Mir-11_microRNA_precursor_family
#=GF SQ   15


AAPP01019528.1/447265-447343   GCACUUGCCAAGAACUC-UCUCUGUGACUUG----------UGUCCUUUUU--U------UC------GA----------AAC---UCACAUCACAGUCUGAGUUCUUGCUGAGAGC
AAPQ01006441.1/419197-419271   GCACUUGCCAAGAACUU-UCUCUGUGACCUG----------CGU---GUAC--U------GA------AA----------AGC----CGCAUCACAGUCUGAGUUCUUGCUGAGCGC
AAPT01019388.1/147488-147568   CCACUCGUCAAGAACUC-UCUCUGUGACUUG----------CGU---GAAC--U------UUCAUGUGAA----------AAU----CGCAUCACAGUCUGAGUUCUUGCUGAGCGC
AAPU01010953.1/16155-16075     GCACUUAACAAGAACUU-UUUCUGUGACCUG----------CGU---GAAU--UCCUAUAUG------CA----------AAC----CGCAUCACAGUCUGAGUUCUUGCUUAGCGC
AAFS01000036.1/6151-6079       CCUCUUGUCAAGAACUU-AUUCUGUGACCUG----------CGU---GACA--U------U--------U----------AGC----CACAUCACAGUCUGAGUUCUUGCUGAGCGU
AAGE02023911.1/46406-46483     GUGCCGCGCGAGAACUC-CGGCUGUGACCUG----------UGU---ACAC--U------UU------AUC-------CAAAU----CACAUCACAGUCUGAGUUCUUGCUUGGAGG
AAAB01008987.1/3180576-3180487 GCAUCCGGCAAGAACUUGGAACUGUGAUCUGUGUGGUUAUUAGC---CGCG--U------UC------GA----------AGCUCUUCACAUCACAGUCUGAGUUCUUGCUCGAUGG
AAWU01011517.1/5912-5834       GUGCCGCGCGAGAACUC-CGGCUGUGACCUG----------UGU---GCCCCGU------GU------UG----------AACU--UCACAUCACAGUCUGAGUUCUUGCUUGGCGC
AAQB01008624.1/142840-142924   CUUCUUGUCAAGAUCUC-UCUCUGUGACCUG----------CGU---GAGA--U------UU------AUCAUAUAUGAAAAC----CGCAUCACAGUCUGAGUUCUUGCUGAGCGG
AASS01008809.1/103-177         GCACUUGUCAAGAACUU-UCUCUGUGACCCG----------CGU---GAAC--U------UA------AA----------AGC----CGCAUCACAGUCUGAGUUCUUGCUGAGUGC
BAAB01121158.1/452-382         UUUUGUGGCUAGCACUC-GACAUGUGACCUG----------UGU---UCGG--U------A--------------------AU----CACAUCACAGUCAGAGUUCUAGCUACACGG
AAZX01002631.1/4523-4598       ACUCCCUGGUGGGACUC-UGUCUGUGACUUG----------UGU---AGUC--U------UG------AA---------UGGU----CACAUCACAGGCAGAGUUCUAGUUAGGUGG
AAJJ01003245.1/4924-4995       AUGCAUU-CUGGGAUUC-UGACUGUGACCUG----------UGU---GUGU--C------U--------G----------AUU----CACAUCACAGGCAGAGUUCUAGCUAUGCGU
AE014297.2/17448293-17448219   GCACUUGUCAAGAACUU-UCUCUGUGACCCG----------CGU---GUAC--U------UA------AA----------AGC----CGCAUCACAGUCUGAGUUCUUGCUGAGUGC
AEKZ01001463.1/24443-24522     GUACCCUGAUGGAGCUC-UGGCUGUGACUUG----------UGU---GUUA--A------CU------GAAU-----UAAAAU----CACAUCACAGGCAGAGUUCUAGUUAGGUAA
#=GC SS_cons                   :<<<<<<-<<<<<<<<<.---<<<<<<--<<..........-<<...____.._......__......__.........._>>....>>-->>>>>>--->>>>>>>>>->>>>>>:
#=GC RF                        gcaCccggCaAGAACUc.uauCUGUGACCuG..........uGu...gaau..U......Uu......aa..........AaC....CaCAUCACAGUCUgAGUUCUuGCuggGugg
//
# STOCKHOLM 1.0

#=GF AC   RF00814
#=GF ID   mir-316
#=GF DE   microRNA mir-316
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   98.30
#=GF NC   60.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000254;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF RN   [2]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [3]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF WK   MicroRNA
#=GF SQ   4


AAPP01019276.1/25939-25851   AAAUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGGCGUUUAAUUCAAACAACGACAGGAAAGGGAAAAAGGCGUAUUUACUAUGAGUUU
AAPU01011629.1/100796-100883 AAGUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGACGUUUUA-UUGAACAACGGCAGGGAAGGGAAAAAGGCGUAUUUACUAUGAAUUA
AC010571.8/20592-20504       AAAUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGGCGUUUCAAUUCCACAACGACAGGAAAGGGAAAAAGGCGUAUUUACUAUGAGUUU
AANI01017487.1/102971-103058 AAGUUCUAGUCGAUUUGUCUUUUUCCGCUUACUGGCGUUUUA-UUGAGCAACGACAGGAAAGGGAAAAAGGCGUAUUUACUAUGAAUUU
#=GC SS_cons                 <<<<<<<<<<-<<<-<<<<<<<<<<<-<<<-<<<<<<<<__________>>>>>>>>-->>>>>>>>>>>>>>->>>->>>>->>>>>>
#=GC RF                      aaauuCuaGuCgauUuGuCuuuuuCCGCuuACuGcCGuuUuAaUuaaaCaaCGgCaGGaaaGGGaaaaaGgCgUauuUaCuaUGaauuu
//
# STOCKHOLM 1.0

#=GF AC   RF00815
#=GF ID   mir-244
#=GF DE   microRNA mir-244
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   61.00
#=GF TC   67.00
#=GF NC   60.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.53 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000256;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [4]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF WK   MicroRNA
#=GF SQ   4


CAAC02000589.1/1456779-1456876 ACCCAAAUUUCUCGAUUUCUUUGGUUGUACAAAGUGGUAUGGC----UCUCU---------UGCUCAUACCGCUUUACAGCUAAAGGAAUCGAUUGAUUUUGGAAACAUUU
AAGD02001046.1/36887-36781     UCUCCAGUUUCUCGAUCUCUUUGGUUGUACAAAGUGGUAUGGC----ACUUCUCAAUAGUCUGCUCAUACCGCUUUUCGGCUAAAGGAAUCGAGUCUUUGGUGUCAUUAAU
ABEG02000979.1/83062-83165     GCCCCA-UUUCUCGAUCUCUUUGGUUGUACAAAGUGGUAUGGCAAUUUCAUUAAA----AAUGCUCAUACCGCUUUUCAGCUGAAGGAAUCGUGU--UUGUGGGUAAUUAG
FO080107.1/15169-15068         CCUCCA-UAUCUCAAUCUCUUUGGUUGUACAAAGUGGUAUGGC----UCAUCGAA----UAAGCACAUACUGCUUUUCAGCUAAAGGAAUUGAGAUUUUGUAGGCUUUUUC
#=GC SS_cons                   :<<-<<<<<<<<<<<<<<<<<<<<<<<---<<<<<<<<<<<<<....________....___>>->>>>>>>>>>>->>>>>>>>>>>>>>>>>>>>>>>->>::::::::
#=GC RF                        uCcCcagcgccuCGaucuCuuugGuuGUACaaaGuGGuauGGC....uCuuuaaA....uauGCuCauaCCgCuuuuCagCuaaaGggauCGaggcgcugugGauauuuau
//
# STOCKHOLM 1.0

#=GF AC   RF00816
#=GF ID   mir-245
#=GF DE   microRNA mir-245
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   90.60
#=GF NC   43.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.26 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000257;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   3


Z75542.1/9021-9117         CUGAAUUCAAUGUUGGAGAGCUAUUUGCAAGGUACCUAAUUGUUUGAUUAUUGAUUCUCAAUUGGUCCCCUCCAAGUAGCUCUAUUGCAUUGUUUGC
AAGD02005327.1/11068-11161 AAGUACUCAAUGUCGAAGAGCUGCUUGCAAGGUACCUAAUUGUUUGCACAU---UUCUCAAUUGGUCCCCUCCAAGUAGCUCUAUUGCAUUGUUUGU
ABEG02007251.1/323-418     AAAAAUUCAAUGCCGUGGAGCUGCUUGCAAGGUACCUAAUUGUUUGAA-AUUCAUUCUCAAUUGGUCCCCUCCAAGUAGCUCUAUUGCAUUGUGUUU
#=GC SS_cons               ::::::::::<<<-<<<<-<<<<-------<<-------<<<---<<________>>->>>------->>------>>>>->>>>->>>::::::::
#=GC RF                    aagaAuUCAAuGccgcaGAGCugcUUGCAAGGUACCUAAuuGUUUGaauAUUgAUuCUCaaUUGGUCCCCUCCAAGcaGCUCuguUgCaUUGUuUgu
//
# STOCKHOLM 1.0

#=GF AC   RF00817
#=GF ID   mir-80
#=GF DE   microRNA mir-80
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   93.10
#=GF NC   46.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000258;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [3]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [4]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   4


Z22175.1/1056-957            AUGGACACUCGUUCGCUCAGCUUUCGACAUGAUUCUGAACAAUCCGCAA-GCCCAUGUUGUUGAGAUCAUUAGUUGAAAGCCGAAUGAUC-AGAGAUAUCCA
AAGD02008136.1/2438-2337     UCGGACACUCUUUCGCUCAGCUUUCGACAUGAUUCUAAACAAUACGUCGAGACAAUGUUGUUGAGAUCAUUAGUUGAAAGCCGAACGAUUUUGAGAUAUCCA
CAAC02000525.1/186793-186693 UUGGACACUCUUUCGCUCAGCUUUCGACAUGAUUCUAAACAAUACGCUGUCGCAAUGUUGUUGAGAUCAUUAGUUGAAAGCCGAACGAUU-CGAGAUAUCCA
ABEG02000481.1/4033-3933     UCGGACACUCUUUCGCUCAGCUUUCGACAUGGUUCUGAACAAUACGCAUUGCAUAUGUUGUUGAGAUCAUUAGUUGAAAGCCGAAUGAUU-UGAGAUAUCCA
#=GC SS_cons                 ::<<<--<<<--<<<-<<-<<<<<<<<<<<<<<-<<-<<<<<<<___________>>>>>>>->>>>>>>-->>>>>>>>>->>->>>--.->>>--->>>:
#=GC RF                      uuGGaCACuCuUuCgCuCAGCuuuCgaCauGauUCuaaaCaacaCGcaaugacaAuguuGuuGaGauCauUAGucGaaaGCCGaAcGaUu.uGaGAUAuCCA
//
# STOCKHOLM 1.0

#=GF AC   RF00818
#=GF ID   mir-318
#=GF DE   microRNA mir-318
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   80.90
#=GF NC   53.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00084
#=GF DR   MIPF; MIPF0000259;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17994087
#=GF RT   Evolution of genes and genomes on the Drosophila phylogeny.
#=GF RA   Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC,
#=GF RA   Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM,
#=GF RA   Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW,
#=GF RA   Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D,
#=GF RA   Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak
#=GF RA   SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK,
#=GF RA   Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S,
#=GF RA   Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A,
#=GF RA   Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher
#=GF RA   AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD,
#=GF RA   Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC,
#=GF RA   Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey
#=GF RA   J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S,
#=GF RA   Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter
#=GF RA   GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz
#=GF RA   MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J,
#=GF RA   Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P,
#=GF RA   Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S,
#=GF RA   Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L,
#=GF RA   Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky
#=GF RA   E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L,
#=GF RA   McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P,
#=GF RA   Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S,
#=GF RA   Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M,
#=GF RA   Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli
#=GF RA   D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D,
#=GF RA   Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie
#=GF RA   MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S,
#=GF RA   Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz
#=GF RA   MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M,
#=GF RA   Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W,
#=GF RA   Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W,
#=GF RA   Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E,
#=GF RA   Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang
#=GF RA   J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A,
#=GF RA   Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K,
#=GF RA   Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A,
#=GF RA   Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A,
#=GF RA   An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A,
#=GF RA   Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C,
#=GF RA   Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y,
#=GF RA   Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De
#=GF RA   Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M,
#=GF RA   Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D,
#=GF RA   Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR,
#=GF RA   Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez
#=GF RA   N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L,
#=GF RA   Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P,
#=GF RA   Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X,
#=GF RA   Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P,
#=GF RA   Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T,
#=GF RA   Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V,
#=GF RA   Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N,
#=GF RA   Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E,
#=GF RA   Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F,
#=GF RA   Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N,
#=GF RA   Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N,
#=GF RA   Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y,
#=GF RA   Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk
#=GF RA   T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q,
#=GF RA   Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W,
#=GF RA   Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I
#=GF RL   Nature. 2007;450:203-218.
#=GF WK   MicroRNA
#=GF SQ   5


AAPP01019505.1/87887-87819 UUUGUGGGAUACACACGGUUCAGUUGUGUCACUUUUG-CGA-GCAUCACUGGGCUUUGUUUAUCUCAUAAG
AAPU01010980.1/46750-46818 UUUAUGGGAUACACUAAGUUCAGUUUUGUCAGAUGU--CCAAGCAUCACUGGGCUUUGUUUAUCUCAUAAG
AC008357.8/142603-142670   UUUAUGGGAUACACACAGUUCAGUUUUGUCACACUU--CAA-GCAUCACUGGGCUUUGUUUAUCUCAUGAG
AAQB01008603.1/8840-8771   UUUAUGGGAUACACCAAGUUCAGUUUUGUCGCAUUCCACGA-GCAUCACUGGGCUUUGUUUAUCUCAUAGA
AADE01000241.1/35557-35624 UUUAUGGGAUGCACCAAGUUCAGUUUUGUCACAUUU--CGA-GCAUCACUGGGCUUUGUUUAUCUCAUAAG
#=GC SS_cons               :<<<<<<<<<<<<<<<<<<<<<<<--<<<_______..___.>>>-->>>>>>>>>>>>>>>>>>>>>>>:
#=GC RF                    UuuaUGgGAUacACaaaGuuCAGUUUUGuCAcAUUU..CgA.gCAUCACUGggCuuuGUuuAUCuCAuaaG
//
# STOCKHOLM 1.0

#=GF AC   RF00819
#=GF ID   mir-246
#=GF DE   microRNA mir-246
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   68.60
#=GF NC   53.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000260;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   4


AAGD02006381.1/5542-5435       GUUCAGUCCAAACAA--UAGAACAGCACCUGGCCGAUUUCAUGUAAUAUCUG--AAAAGAAAAGA-UAUUACAUGUAUCGGGUAGGAGCUGUUUGAGUAAAGGAUCUUUCGAA
Z69385.1/30335-30444           UCAGCAUCUGAAUUA--UAAAACAUCGCCUAACCGUUGUCAUGUAAUAUUUCCCAGAGAAAAUGA-UAUUACAUGUUUCGGGUAGGAGCUGUUCAAACUUUGGACAUUGGCAU
CAAC02000470.1/1130830-1130722 GAAAAGUCCUAGUGA--UAAAACAGCACCUGGCCAAUAUUAUGUAAUAUCAG--AAGCAAAUUGAUUAUUACAUGUAUUGGGUAGGAGCUGUUCAAGCUAUGGUUAAAUGGGU
ABEG02006090.1/15964-15857     GAAUUUAUCUCACAAAGUACGAGAGCACCUGGCCGAAAUCAUGUAAUA--UUGCAAUGAGUUC---UAUUACAUGUUCCGGGUAGGAGCUGUCGAAGAUGUGAACGUUUUAAU
#=GC SS_cons                   :::::::<<<<<<--..---<<<<<<-<<<<-<<<<<<-<<<<<<<<<<<_____________>>.>>>>>>>>>>>>>>>->>>>->>>>>>--->>>>->>::::::::::
#=GC RF                        gaAuagucccagcaA..UAaaACAgCACCUggCCGauaUcAUGUAAUAucuugCAAagAAauuga.UAUUACAUguauCGGGuAGGAGcUGUuuAAgcuguggAuauuuuaAu
//
# STOCKHOLM 1.0

#=GF AC   RF00820
#=GF ID   mir-248
#=GF DE   microRNA mir-248
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   51.00
#=GF TC   75.30
#=GF NC   34.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000262;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   4


AAGD02008733.1/82049-82151 UUUUUUGGCAGAGAUUACGAUUAGCGAUAUCCAGCCGUUGUAUUCAAUAGCGCAU-UUGAGUACACGUGCACGGAUA-CGCUCAUCGUUUUUGUAUUGCCACUUC
AC084497.1/17009-17113     UUGCAAACUGAUAUUCACGAUAAGCGCUAUCCUUCCGUUGUAUUCAAGCUUGGUUGUCGAGUACACGUGCUCGGAUAACGCUCAUCGAGUCUGAUCGGUUAUGUU
ABEG02000017.1/12298-12402 UUUCUUGGCAGUUAUCACGAUCAGCGCUAUCCAGCCGUUGUAAUCAAGAACGGAGGUUGACUACACGUGCACGGAUAACGCUCAUUGUCAUAGGUUGCCAUUUUU
FO080097.1/20339-20236     UUUCCCGGCUGCAACUACGGUAAGCGGUAUCCAGCCGAUGUUUUCAAUACUGCAU-UUGAAUACACGUGCACGGAUAACGCUCAUUGUUUUUCGCAUGCCAAUUU
#=GC SS_cons               ::::::<<<<<<----<<<<<-<<<<<<<<<<--<<<-<<<<<<<_____________>>>>>>>>>->--->>>>>>>>>>->>>>>----->>>>>>::::::
#=GC RF                    UUucuuGccggcaaUuaCgaUaAGCGcUAUCCagCCGuUGUacUCAAuauuGgauGUuGAguACACGUGCaCGGAUAgCGCUCAucGuuuuuggccggCuauuUU
//
# STOCKHOLM 1.0

#=GF AC   RF00821
#=GF ID   mir-249
#=GF DE   microRNA mir-249
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   66.00
#=GF TC   69.30
#=GF NC   65.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000263;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [4]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [5]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   4


AAGD02000048.1/2070-2177     AUUACUUCUAUUUUGU--UUUCUACGUGACUAGCAACGCACAAAAGUU-UCUGUGCGACAAA-UAU-GAAAUUUUGUCACAGGACUUUUGAGCGUUGCUAGUUGAAAGAAGAU
CAAC02000521.1/486552-486442 AUUUGUUAUUUUGUGCGCCCUCAAUGCUACUAGCAACGCUCAAAAAUC-ACUGUACGACAAAUGAC-UAUAUUUUGUCACAGGAUUUUUGAGUGUUGCUAGUCGGAGAAGGGC
ABEG02000018.1/14232-14122   AACUUUUAUUUUUUUGUCUCUCUGAGCUACUAGCAACGCU-AGAAGUCUACUGUUAGACAGAGUACAGAAAUUUUGUCACAGGACUUUUGAGCGUUGCUGGUU-AAUGAGAGC
FO081649.1/314-204           CAUAUUGUGUAUCUAUACUCUUGA-ACGACUAGCAACGCACAAACGUCUUCUGUGCGACAACAUCU-GAAUGUUUGUCACAGGACUUUUGAGCGUUGCCAGUCGAAAGAGGAA
#=GC SS_cons                 ::::::::::::::::::<<<<----<<<<<<<<<<<<<<<<<<<<<<--<<<<--<<<<<<<<__.__>>>->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>--->>>>::
#=GC RF                      aauuuUuauuuUuUauaCccucuAugcgaCuaGCaaCGCuCaaaaGucUaCuGugcGaCaaacuau.gAaguUuuGuCaCaGgaCuuuuGaGCGuuGCuaGucgAAagaggau
//
# STOCKHOLM 1.0

#=GF AC   RF00822
#=GF ID   mir-274
#=GF DE   microRNA mir-274
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   79.40
#=GF NC   55.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000264;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12844358
#=GF RT   Computational identification of Drosophila microRNA genes.
#=GF RA   Lai EC, Tomancak P, Williams RW, Rubin GM
#=GF RL   Genome Biol. 2003;4:R42.
#=GF RN   [2]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [3]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF WK   MicroRNA
#=GF SQ   7


AASS01003576.1/752-851       UCCUGUGUUGCAGUUUCGUUUUGUGACCGACACUAACGGGUA---AUUGUUUG--------GC-----------C-AGCAG-------GAU-------UACUCGUUUUUGCGAUCACAAAUCAUGAAAUUGCAGCAA
AAFS01001069.1/28638-28734   UCCCGUGCUGCAGUUUCAUUUUGUGACCGACACUAACGGGUA---AUGGCU-G--------GC-----------C-GC-AG-------GAC-------UACUCGUUUUUGCGAUCACAA-UACUGAAAUUGCAGCAA
AANI01017486.1/215294-215400 CUGUUUGUUGCAGUUUCGGUUUGUGACCGACACUAACGGGUA---GUUGGGGC--------AC-----------C-UCGAA-------UACGCUGUUUUACUCGUUUUUGCGAUCACAAAUUCUGAAAUUGCAACGA
AAQB01007682.1/34817-34703   UAUCCUGUUGCAGUUUCAUUUUGUGACCGACACUAACGGGUA---GUAACGGGUUAACAAAGU-----------C-GUUUUUCUGGCCUUU-------UACUCGUUUUUGCGAUCACAAAUUCUGAAAUUGCAGCAA
AAPP01019289.1/330187-330287 AGAAAUGUUGCAGUUUCGUUUUGUGACCGACACUAACGGGUA---UUUUACAG--------GA-----------CAUACAG-------GAU-------UACUCGUUUUUGCGAUCACAAAUCCUGAAAUUGCAGCAA
AAPU01011627.1/22605-22713   UCCUGUGUUGCAGUUUCGGUUUGUGACCGACACUAACGGGUAGUUGAGGCAUC--------UCGUAUU------C-GCUGU-------UUU------AUACUCGUUUUUGCGAUCACAAAUUCUGAAAUUGCAACGA
AAPT01020611.1/127253-127143 GUGCGUGUUGCAGUUUCGGUUUGUGACCGACACUAACGGGUA---GUUAAAGG--------GCAUCCUCGCAUUC-UGCUG-------GCU-------UACUCGUUUUUGCGAUCACAAAUUCUGAAAUUGCAACGA
#=GC SS_cons                 :::::<<<<<<<<<<<<<<-<<<<<<-<<-<<--<<<<<<<<...<<<<<___........__..........._.>>---.......>>>.......>>>>>>>>-->>>>->>>>>>--->>>>>>>>>>>>>>:
#=GC RF                      uuuuuuGcuGCaguuuCggUuuGuGaCCGACaCUaaCGgGua...gucgcagg........gc...........C.gcuau.......gac.......uaCuCGuuUUuGCGAuCaCaaAUuccGaaauuGCagCaA
//
# STOCKHOLM 1.0

#=GF AC   RF00823
#=GF ID   lsy-6
#=GF DE   microRNA lsy-6
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   60.70
#=GF NC   49.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000265;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF WK   Lsy-6_microRNA
#=GF SQ   4


Z73905.1/23766-23837       CAUC-AAAUGCGUCUAGUAUCAAAAUCAUGU-AAA--AACUGUAAAACAGAUUUUGUAUGAGACGCAUU-UCGAUGA
AAGD02004319.1/33986-34061 CCACCGACUGCUUCGAAUACCAAAAUCAUGGGUAAUCUACAGUAUGCCAGAUUUUGUAUGAGACGCAUU-CAGUGGC
AC099762.1/87386-87313     CCACAGAAUGCGUCCAGUAUCAAAAUCACAUCAAA--GAGAAUACGGUGGAUUUUGUAUGAGACGCAUU-CCGUGGC
ABEG02002378.1/16264-16335 CCACAGAAUGCGUCGAAUAUCAAAAUCAUGUCAAA--AUAUG---GAUAGAUUUUGUAUGAGACGCAUUUCCGUGGC
#=GC SS_cons               <<<<-<<<<<<<<<<-<<<-<<<<<<<-<<<<___..________>>>>>>>>>>>>>>->>>>>>>>>.>->>>>:
#=GC RF                    CcaCaGAaUGCgUCcAaUAUCAAAAUCAugucaAA..aAcaGUAugacaGAUUUUGUAuGgGAcGCAuU.CcGugGc
//
# STOCKHOLM 1.0

#=GF AC   RF00824
#=GF ID   mir-50
#=GF DE   microRNA mir-50
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   49.00
#=GF TC   49.00
#=GF NC   48.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00089
#=GF DR   MIPF; MIPF0000266;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [4]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [5]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF RN   [6]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF RN   [7]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   5


AAQA01001434.1/1796-1718     AUGCAGUG--------UUGAUAUGUCUGAUAUUCUUGGGUUGU--------GCAAAGUC--AACCAGCAUCUCAGACGUAUCGG---------CCACUGUGUAUUG
AAGD02001051.1/27617-27516   ACCCACCCCCUGGCCGCUGAUAUGUCUGGUAUUCUUGGGU--UCGAUACUCUGAAAAACG-AACCAAAGUAGCAGACGUAUCGACGGCCGG-GAGGGUGGGAAUUU
CAAC02000589.1/893157-893260 UUCCACCCACCGGCCGCUGAUAUGUCUGAUAUUCUUGGGUUAUCUG-AUAAUGAUUGUUGUAACUCAAGUAUUAGACGUAUCGACGGCCGG-CUGGGUUGGAAUCA
ABEG02000979.1/99685-99586   UCUCACCCACCGGCCGCUGAUAUGUCUGGUAUUCUUGGGU---UCA-UUCCUUACUCUGA--ACCAGUUUAUUAGACGUAUCGACGGCCGGAUCGGGUGAGAAUUU
FO080942.1/98206-98306       UCCUGCCCGCCGGCCGCUGAUAUGUCUGGUAUUCUUGGGU--UUGA-ACUUCCAGCGUUG-AACCCGCAUAUUAGACGUAUCGACGGCCGG-CGGGGCAGGUAAUG
#=GC SS_cons                 ::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<---<<<<<..<<__.____________>.>>>>>>->>>>>>>>>>>>>>>>>>>>>>>.>->>>>>>::::::
#=GC RF                      uuccacccgCcGGCCGcuGauauGuCugguauUCUcgGGu..ucua.auuuuuAauguug.aaCCcgaauaccaGaCguauCggCGGCCgG.cuggguggGaAuUu
//
# STOCKHOLM 1.0

#=GF AC   RF00825
#=GF ID   mir-344
#=GF DE   microRNA mir-344
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   51.00
#=GF TC   51.00
#=GF NC   50.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.50 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000267;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [2]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   Mir-344_microRNA_precursor_family
#=GF SQ   35


AAHY01695386.1/13-108        CUGCAGCCAGGGUUU--UUACCAGUCAGGCUCCUGGCUAGUAUUCCAGGUAC-C-AGCUGGUACCUG-A-UCUAGCCA-AAGCCUGACUG--U---AAGCCCUGAACA
AC117644.6/139679-139776     GUAAACACAGGGAUU--UUGCAAGUCAGGCUCCUGGCUGG-AGUCCAGCUUU-C-AGCUGGGUCCAGGC-UCUAGCCA-GGGCCUGACUGCAU---GAUGCUCAGUAG
AC117644.6/172227-172322     CUGAAGAGAGGGGUU--UUGCCAGUCAGUCUCCUGGCUGG-AGUCCAGCUCU-A-AGCUGGUUCCAGGC-UCUAGCCA-GGACCUGACUA--C---AACCUACUUAGC
AAHY01062139.1/21833-21743   GUACAGAAGGAUU----UGAUCAGUCAGGCUGCUGGCUAU-AUUCCAGGA-C-A-AGUCUGGUCCUG-A-UAUAGCCA--AGCCCGACUG--U---AUGGUGCCAAAG
AAHY01062139.1/6908-6814     CUGCAGGGAAGGAUU--UGAUCAGUCAGGCUUCUGGCUAU-AUU-CCAGGAC-UUACCUGGUCCUGG-A-UAUAACCA-AAGCCUGACUA--U---AUGGUGCUAAAG
AAHY01062139.1/5076-4986     UGGGAAGGAU----U--UGAUCAGUCAGGCUUCUGGCUAU-AUUUCAGGACU-C-AUCUG-GUCCUGGG-UAUAAUCA-AAGCCCGACUG--U---AUGGUAGUAAAG
AAHX01005727.1/134541-134447 CUGCACAGAGACAUC--UGAUCAGUCAGGCUACUGGUUAU-UUU-CCAGGAC-UUAUCCGGUCCUGG-G-UAUAACCA-AAGCCCGACUG--A---AUAGUGUUAAAU
AAHX01005727.1/128160-128063 CUGCAGGGUUAAAAC--UGAUGAGUCAGGCUACUGGUUAU-AUUCCAGGGCU-U-AUCC-AGUUCUGAG-UAUAACCA-AAGCCUGGCUG--AAUGGUGUUAAAUAAA
AAHX01446007.1/851-774       ----------AUC--------CAG-CAGGCUACUGGCUAU-AUU-CCAGGAC-CUAUCUGGUCCUGG-A-UAUAGCCA-AAGCCCGACUG--A---AUGGUGUUAAAU
AAHY01149168.1/2858-2952     CUGAAGGGUAAGAUU--UGAUCAGUCAGGCUGCUGGCUAU-ACUCCGGGAAU-U-UUCUGGUCCUGG-A-UAUAACCA-CUGCCAGACUG--A---AUGGUGCUAAAG
AC091333.6/33249-33343       CUUCUGCAAGGGUUU--UUUUCAGUCAGGCUGCUGGCUAG-AGUACAGCUAU-C-AGCUGGUACCUG-A-UCUAGUCA-AAGCCUGACAG--U---AAACUGCUCCAG
AC091333.6/80056-80144       CUGCAGCCAGGAUUU--UCAUCAGUCAGGCUCCUGGCUAA-AGUUCAGCU------UUC---AGCUG-CAUUUAGCCA-AAGCCUGACUG--U---AAGCUGCUCCAG
AC091333.6/142701-142795     CUGCAAGAAAAGAUU--UUAUCAGUCAAGCUUCUGGCUAU-AUUUCAGGACU-U-AUCU-GGUCCUGGG-UAUAACCA-AAGCCUGCUUG--U---UUGCUAUUAAAG
AC091333.6/187520-187614     CUGCAGGGGAAGAUU--UCAUCAGUCAGGCUGCUGGCUAU-ACACCAGGACU-U-AUCU-GGUCCUG-GAUAUAACCA-CUGCCAGACUG--A---AAGGUGCUAAAG
AC091333.6/185372-185462     CAGGGAAGAU----U--UCAUUAGUCUGGUUGCUGGCUAU-AUU-CCAGGAC-UUAUCUGGUCCUGG-A-UAUAACCA-CUGCCAGACUG--A---AUGGUGCUAAAG
AC091333.6/176173-176264     UGGGGGGGUGAGCCU--UUAUCAGUCAGGCUGCUGGCUA----UCCAUGUCU-U-GUCU-AGUCCUGCA-UAUAGCCA-AAGCCAGACUG--A---AUGGUGAUAAAG
AC119249.7/44803-44897       CUGCAGUGAGAUAUA--UGUUCAAGCAGGCUGCUGGCUAU-AUU-CCAGAACUC-AUCUGGUCCUGG-A-UAUAACCA-AAGUCUUAUUG--U---AUGAUGCUAAAG
AAHY01444869.1/376-470       CCACUGAGAAGGAUU--UGAUCAGUCAGGCUUCUGGCUAU-AU-CCCAGGACUC-AUCUGGUCCUGG-G-UAUAACCA-AAGCCCGACUG--U---AUGGUACUAAAG
AAHY01152159.1/1182-1272     AUGGAAGGAU----U--UGAUCAGUCAGGCUUCUGGCUAU-AUUCCAGGACU-U-ACCUGGUUCUGG-A-UAUAACCA-AAGCCUGACUA--U---AUGGUGCUAAAG
AAXM01007418.1/188-97        CCUCAGGGCU--UUU--AUACUUGUUAGACU-CUGGCUAG-AGUACACUAAU-C-GGCUGGUACCUG-A-UCUGGCCA-AAGCCUGACUU--U---AAACUGCUUAAA
AAHY01190415.1/585-499       CUGUAGCCAGUGUUU--UAAC-AGUCAGACUUCUGGCUAG-AGUCCAGCUCU-C-AAGUG------G-G-UCUAGCCA-AAC-CUGACUA--U---AAGCUGCUCCAG
AAHX01005728.1/38074-37984   AUGGAAGGAU----U--UGAUCAAUCAGGCUGCUGGCUAU-AUUCCAGGACU-U-AACUGAUCCCGG-G-UAUAACCA-AAACCUGAUUC--U---AUGGUACUAAAG
AAHX01005728.1/46044-45950   CUGCAGGGAGGAAUU--UGAUCAGUCAGGCUGCUGGCUAU-UUUCCAUGACU-U-AUCUAGUUCUGG-A-UAUAACCA-AAGCUCAACUG--U---AUGGUGCUAACG
AAHX01005752.1/4103-4007     AUUCACAUAGAAUUU--CUGUCAGUCAGGCUCCUGGCAGG-AGUCCAGCUCU-C-AGCUGGUUCCAGGC-UCUAGCCAGGGGCUUGACUG--C---AAGCUGCUCAUC
AAHX01005728.1/16836-16742   CUGCAGGGAGAGAUC--UGAUCAGUCAGGCUGCUGGUUAU-AUU-CCAGGAC-UUAUCUGGUCCUGG-G-UAUAACCA-AAGCCCGACUG--U---UAAAUAAAAGGA
AC127317.3/68397-68491       CUCUAGUGAGAGUUU--UUACCAGCCAAGUUCCUGGGUGU-UGUUGAGGUCU-C-AACUGGUUCAGU-U-UAUAACCA-AAGCUUGCCUG--U---GAGGUGCUCAAA
AC091333.6/135033-135127     CUGCAGGGAAGGAUU--UGAUCAGUCAGGCUUCUGGCUAU-AUU-CCAGGAC-UUACCUGGUCCUGG-A-UAUAACCA-AAGCCUGACUA--U---AUGGUGCUAAAG
AC138549.3/136705-136799     CCACUGGGAAGGAUU--UGAUCAGUCAGGCUUCUGGCUAU-AUUUCAGGAC-UC-AUCUG-GUCCUGGG-UAUAAUCA-AAGCCCGACUG--U---AUGGUAGUAAAG
AC091333.6/120106-120198     CUGUACAGAAGGAUU--UGAUCAGUCAGGCUGCUGGCUAU-AUUCCAGGA-C-A-AGUCUGGUCCUG-A-UAUAGCCA--AGCCCGACUG--U---AUGGUGCCAAAG
AC138549.3/121511-121605     CUGCAGGGAAGGAUU--UGAUCAGUUAGGCUUGUGGCUAU-AUUCCAGGAAU-U-AUCUGGUUCUGG-G-UAUAACCA-AAGCCAGACUG--A---AUGGUACUAAAG
AAHX01005728.1/35413-35319   CUUCAGGGAGAGAUU--UGAUCAGUAAGGCUACUGGCUAU-AUU-CCAGGACUC-AUCUGGUCCUGG-G-UAUAACCA-AAGCAUGACUA--U---ACGGUUCUAAAA
AAHX01005745.1/4362-4270     CUGCAGGGCU--UUU--UUUCCUGUUAGGCUUCUGGCUAG-AGUCCACUAAU-U-UUCUGGUACCUG-A-UCUGGCCA-AAGCCUGACUA--U---AACCUGCUCCAG
AAHX01005728.1/185-91        CUGCACGGAGAGAUC--UGAUCAGUCAGGCUACUGGCUAU-AUU-CCAGGAC-CUAUCUGGUCCUGG-A-UAUAGCCA-AAGCCCGACUGAAU---GGUGUUAAAU--
AABR05009223.1/8214-8123     GUGGGGAGAGAUCUG----AUCAGUCAGGCUGCUGGUUAU-AUUCC-AGGAC-U-UAUCUGUCCUAG-G-UAUAACCA-AAGCCCGACUG--U---UAAAUAAAAGUA
AABR05009333.1/17036-16944   ----CCUUAGGGGUUUUUUUCCUGUUAGACUUCUGGCUAG-AGUCCACUAAU-C-UUCUGGUACCUG-A-UCUGGCCA-AAGCCUGACUA--U---AACCUGCUCCAG
#=GC SS_cons                 ::::::::::<<<<<..----<<<<<<<<<<--<<<<<<<.<<--<<<<<<<.<.____>>>>>>>>.>.>>>>>>>>.->>>>>>>>>>..-...>>>>>:::::::
#=GC RF                      cUgcAgggAgagcuu..UuAUcAGUcaGGCUuCUGGcUAu.AuUcCcgggcc.c.AuCUgggcccgG.a.UaUAgCCA.AAGCCugACUg..U...aagcugcUaAAg
//
# STOCKHOLM 1.0

#=GF AC   RF00826
#=GF ID   mir-55
#=GF DE   microRNA mir-55
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   67.30
#=GF NC   51.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000270;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   5


Z69788.1/18474-18378         AGAUUUGGAACUU--AAUGGGACUCGGCAGAAACCUAUCG-GUUAUACUUUUUG--GAUAUGCUAUACCCGUAUAAGUUUCUGCUGAGCCCCUU-AUUCCUGU
AAGD02007434.1/173562-173660 AGACUCGGAAAGUCGCAUGGGACUCGGCAGAAGC-ACUUGGGGUAUACUUCACA--GAGUAACUAUACCCGUAUUUGUUUCUGCUGAGCCCCUG-ACACCAGU
ABEG02000165.1/125157-125253 AGGUUUGGUAGUC--GCUGGGACUAGGCGGAAGUAUAGAG-GGUAUACUUCAUC--AAGUAACUAUACCCGUAUAUAUUUCUGCUUAGCCCCUG-ACACCAUC
JN251415.1/333-432           UGAAUCGUCACUA--AGGGGGACUCGGCGGAAAA-UAUGGUGGUAUACUACACAGUGAAUAGAUAUACCCGUAUAUUUUUCUGCCGAGCCCCUCCACGACAUC
JN251398.1/333-432           UGAAUCGUCACAA--AGGGGGACUCGGCGGAAAA-UAUGGUGGUAUACUACACAGUGAAUAGAUAUACCCGUAUAUUUUUCUGCCGAGCCCCUCCACGACAUC
#=GC SS_cons                 :::::::::::::..:<<<<<-<<<<<<<<<<<<.<<<<<-<<<<<<<<<____..___>>>->>>>>>>>->>>->>>>>>>>>>>>->>>>>.::::::::
#=GC RF                      aGAuUuGgaAcuu..aggGGGACucgGCaGaaac.uaucGuGguauacuccAua..GAagagcuauacCCgUauauguuuCuGCcgaGCCCCcc.AcacCAuu
//
# STOCKHOLM 1.0

#=GF AC   RF00827
#=GF ID   mir-77
#=GF DE   microRNA mir-77
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   57.20
#=GF NC   51.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000272;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   5


AAGD02000430.1/4126-4038     AAAUAAAAAGAGCUGUUAGUUUGGAUGGCUGUGCUCUGAGGAAAC-ACG-------------GUGUCAUUUCAUCAGGCCAUAGCUGUCCAAA--ACU---CGUUUCC
AAGD02003971.1/5795-5695     AACUGUAAAGAGCUGUUAGUUUGGAUGGCUGUGCUCUGAGGAAAU-ACG----GCUCAUAAAAUGUCAUUUCAUCAGGCCAUAGCUGUCCAAAUUAUCA--AUGUUCG
Z81124.1/29149-29248         GCAUCUGCCAAACCGCCCGUUUGGAUGGUUGUGCUCUGAGGAAAU-ACG-------CACAGAAUGUCAUUUCAUCAGGCCAUAGCUGUCCAAAUUGGUAUAGAGUUUG
CAAC02000490.1/201259-201155 AAUUCCAAAGAGCUGUGAAUUUGGAUAGCUGUGCUCUGAGGAAAUAACAAUAGUCACACCCCAUGUCAUUUCAUCAGGCCAUAGCUGUCCAAAUUUCU---CGGUUCG
ABEG02000262.1/43428-43334   CCAAAAAUAGAGCCAAUAAUUUGGAUGGCUGUGCCUUGAAGAAAU-ACA---------GUUAGUGUCAUUUCAUCAGGCCAUAGCUGUCCAAAUUGUU---AGGUUCG
#=GC SS_cons                 :::::::::<<<<<<<<<<<<<<<<<<<<<<<<--<<<<-<<<<<.<<<......._______>>>->>>>>->>>>-->>>>>>>>>>>>>>>>>>>...->>>>>:
#=GC RF                      aaauauAaaGagccgccaguuuGGaugGcuguGCUcuGagGaaau.aCa.......cAuauaauGuCauuuCAuCagGCCauagCcguCCaaacuggc...aggcuCg
//
# STOCKHOLM 1.0

#=GF AC   RF00828
#=GF ID   mir-75
#=GF DE   microRNA mir-75
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.30
#=GF NC   49.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000273;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   4


AAGD02008731.1/12413-12314     GACCACAUGCAUUGAUGAGUUGAAGUCGGUUAUAAGCUUAAAUACAGAACAUACCCGUUGUUAUUAAAGCUACCAACCGACUUCAGAUCAUACUUUGCAU
CAAC02000448.1/1374161-1374062 UUUUUUCUGCGAGACCGAAUUGCAGUCGGUUGCAAGCUUCAAUACAGACAAUGGUUCUUGAUAUUAAAGCUACCAACCGCCUUCAAAUCGUGCAUCGCGA
FO081414.1/34313-34409         UUCUUGUUGCUUUGAAGAAUUGCAGUCGGUUGCAAGCUUAAAUACAAAUCCGAA---UUGUUAUUAAAGCUACCAACCGGCUUCAAGUCUGAAAGAGCAG
ABEG02000016.1/53957-53860     UUAAUCCUGCCUCGACGAGUUGAGGUCGGUUGCAAGCUUCAAUACAUUUAUGAA--AUUGAUAUUAAAGCUACCAACCGGCUUCAAAUCGAAAAGUGCGU
#=GC SS_cons                   ::::::::<<<<<--<<<-<<<-<<<<<<<<<--<<<<<-<<<<<<<__________>>>->>>>->>>>>-->>>>>>>>>->>>->>>-->->>>>::
#=GC RF                        uuuuuuuUGCgccgacGaauuGaaGcCGGuuGcAaGCuuaaauaCagauaauAauuacuGuuauuAaaGCuACCaaCCGgCuUCaaAuCguAgagcGCau
//
# STOCKHOLM 1.0

#=GF AC   RF00829
#=GF ID   mir-149
#=GF DE   microRNA mir-149
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   86.00
#=GF NC   49.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000274;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse.
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol. 2002;12:735-739.
#=GF WK   MicroRNA
#=GF SQ   3


AANU01125201.1/15673-15585 GCCGGCGCCCAAGCUCUGGCUCCGUGUCUUCACUCCCGUGUUUGUCCGAGGAGGGAGGGAGGGACGGGGGCUGUGCUGGGGCAGCCGGA
CAAA01040434.1/8905-8817   GCCAGUGCCCAGGCUCUGGCUCCGUGUCUUCACUCCCGUGUUUGUCCGAGGAGGGAGGGAGGGACGGGGGCGGUGCUGGGGCAACUGGA
AAFC03011974.1/2395-2483   GCCGGCGCCCAGGCUCUGGCUCCGUGUCUUCACUCCCGUGUGUGUCCACCGAGGGAGGGAGGGACGGGGGCUGUGCUGGGGCGGCCGGG
#=GC SS_cons               :<<<<<<<<<-<<<-<-<-<<<<<<-<<<<<-<<<<<-<-<<<____>>>->>>>>>>>>>>->>>>>>->->->>>->>>>->>>>>:
#=GC RF                    GCCgGcGCCCAgGCUCUGGCcCCGuGcCucCACuCCCGuGcgcGUCCgcgGaGGGaGGgaGgGaCGGgGGCuGUGCcGGGGCagCcGGa
//
# STOCKHOLM 1.0

#=GF AC   RF00830
#=GF ID   mir-74
#=GF DE   microRNA mir-74
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   47.20
#=GF NC   44.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00090
#=GF DR   MIPF; MIPF0000275;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [3]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF RN   [4]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF WK   MicroRNA
#=GF SQ   4


CAAC02000448.1/1381014-1380917 AAAAGGUC---CGCACUUUUGGGCUUCCAUA-UCUUUCCCAGCUCCUCUCAUUUACUAUGGAUGCUGGCAAGAAAUGGCAGUCUAGAUGUGCAAAAUCCUGC
ABEG02000016.1/58502-58409     AAAGGAU----AGCACGUUUGGGCUUCCAUUAUCUUUCCCAGC--AGGUUCACGAACGU--AUGCUGGCAAGAAAUGGCAGUCCACAUGUGUAAAUCCUCGA
ABEG02000016.1/58630-58535     AUCAGCCCCGUCACACAAAUGGGCUUCCUUU-UCGUUCCCAGC-UGAAUUUCUAAUCAU----GCUGGCAAGACAAGGCAGUCUACUUGUGUGACGGGGCAA
FO081414.1/30902-30998         AAAUGGUUCAAAAAACGUUCGGGCUUCCAUC-UCUUUCCCAGCCUACAUC--UCAACCUGG--GCUGGCAAGAAAUGGCAGUCUACACGUUUUUCAACCAAA
#=GC SS_cons                   ::::::::::::<<<<<<-<<<<<<-<<<<-.<<<<--<<<<<._______________....>>>>>->>>>->>>>->>>>>->>>>>>>::::::::::
#=GC RF                        AaaaGgUcCauagcACguucgGgCUUCCaUu.UCuUUCCCAGC.uauaUuuuUuAacaU....GCUGGCAaGAaAuGGCAGuCcAgacGUgcaAaaucuuaA
//
# STOCKHOLM 1.0

#=GF AC   RF00831
#=GF ID   mir-73
#=GF DE   microRNA mir-73
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   64.90
#=GF NC   54.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00090
#=GF DR   MIPF; MIPF0000276;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF RN   [2]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF WK   MicroRNA
#=GF SQ   7


AAGD02008731.1/16399-16304     A-------GGUCCC--UCAAACGACUGAGCUUCCACGUC-AAGCCUCAGCUAUCGAAUGAA-AAAUUGCUGGCAAGAUGUAGGCAGUUCAGUUGU-AUG----CGGAGACCA
CAAC02000572.1/13001-13103     UAAAAAA-CGUCCCAAAAUUCCGAUCCGGCUUCCACAUC-GAGCCUCAGCUAGA---UCCAUAACUUGCUGGCAAGAUGUUGGCAGUCGCAUUGG-AUA---AAGGAGACAC
CAAC02000448.1/1381310-1381211 -AGUGAGCGGUCCC--UCAAACAACCGAGCUUCCCCGUC-AAGCCACAGCUAUC---UCUG-ACAUUGCUGGCAAGAUGUUGGCAGUUCAGUUGU-AUG---ACGGAGACCA
ABEG02001837.1/1967-1873       A-------AUUCCC--UUCCUCUUCAGGACUGCCGGGUCUGUGCCCCAGCUAUG---ACUA--UUUUGCUGGCAAGUUUUCGGCAGUUCAGAAGGUGUC---UUGGGGAUCA
FO081414.1/30624-30726         CAGUGAG-AGUCCC--ACACACGACUGGACUUCCAUAUC-GAGCCACAGCUAUC---AACG-AAUUUGCUGGCAAGAUGUAGGCAGUUCAGUUGU-GCGUUUAUGGAGACCA
ABEG02001837.1/2575-2473       UUUUU---UGUCCCAAUCCCCCUUCAGGACUGCCGAGUCUCUGCCCCAGCUAUC---AGUAGUAUAUGCUGGCAAGAUUUAGGCAGUUCAGAAGGUGUU---UCGUGGACUU
ABEG02000016.1/58784-58683     ACGAAGC-GGUCCU--UAAUACGACUGAGCUUCCACAUC-AGACCACAGCUAUUCACAAAA-AAAAUGCUGGCAAGAUGUAGGCAGUUCAGUUGU-AUG----CGGUGACCA
#=GC SS_cons                   :::::::.:<<<<<..---<<<<<<-<<<<<<<<<<<<<.--<<--<<<<____...____._____>>>>>>-->>>>>->>>>>>>>->>>>>.>--...-->>->>>::
#=GC RF                        aaguaaa.agUCcC..ucaccCgaCuGgaCUgCCacauC.aaGCCaCAGCUAUc...aauA.AauuUGCUGGCAAGauguaGGcAGucCAGucGg.gUg...acGgaGAcca
//
# STOCKHOLM 1.0

#=GF AC   RF00832
#=GF ID   mir-71
#=GF DE   microRNA mir-71
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   48.60
#=GF NC   47.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.00 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000278;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [2]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing.
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF RN   [3]
#=GF RM   18714353
#=GF RT   The silkworm (Bombyx mori) microRNAs and their expressions in multiple
#=GF RT   developmental stages.
#=GF RA   Yu X, Zhou Q, Li SC, Luo Q, Cai Y, Lin WC, Chen H, Yang Y, Hu S, Yu J
#=GF RL   PLoS One. 2008;3:e2997.
#=GF WK   Mir-71_microRNA_precursor_family
#=GF SQ   12


AADK01011192.1/8467-8525   UGAAAGACAUGGGUAGUGAGAUGUCCC------------GUACAUCU---AAAAUUCUCACUACCUUGUCUUUC
AAWT01027656.1/43691-43744 UGAAAGACACGGGUAGUGAGAUAUGG----------------AUUUU---UCAUCUC-UAUAUUCGUGUCUUUC
AAJJ01001714.1/2180-2239   UGAAAGACAUGGGUAGUGAGAUGUUUAAUU---------AAUAAAUU---UUGUCUC--ACUACCUUGUCUUUC
AAQA01000505.1/22871-22929 UGAAAGACAUGGGUAGUGAGACGUUA-------------GAAUUUCAAGGUCGUAUC--ACUAUUCUGUUUUUC
AAZX01013101.1/18156-18214 UGAAAGACAUGGGUAGUGAGAUGCUUACC----------UCGGAUUC---GCGUCUC--ACUACCUUGUCUUUC
AAZO01007079.1/39885-39949 UGAAAGACAUGGGUAGUGAGAUGUUGGUUCACGUG----UCAUUUUU---ACCUCUC--ACUACCUUGUCUUUC
AAGE02012793.1/18335-18272 AGAAAGACAUGGGUAGUGAGAUAGUUUCACCCUA-----UUGCACUG---GGAUCUC--ACUACCUUGUCUUUC
AAWU01020422.1/11289-11221 AGAAAGACAUGGGUAGUGAGAUAGUUUUACCCUGCAUUCGAAAACCG---GGAUCUC--ACUACCUUGUCUUUC
AASC02030054.1/9912-9965   UGAAAGACAUGGGUAGUGAGAUGUUU---------------UGCAGA---UCAGCUC--ACUACUCUGUCUUUU
Z81505.2/5532-5477         UGAAAGACAUGGGUAGUGAGACGUCG-------------GAGCCUCG---UCGUAUC--ACUAUUCUGUUUUUC
AEKZ01001511.1/388-331     UGAAAGACAUGGGUAGUGAGAUGUUC-------------UCACGCUA---UCGCGUCUCACUAUCUUGUCUUUC
AAGJ04087467.1/19918-19860 UGAAAGACAUGGGUAGUGAGAUUUGACUA----------UCACAAAA---CAAUCUC--ACUAUUCUGUUUUUC
#=GC SS_cons               :<<<<<<<<-<<<<-<<<<--<_______..........________...__>-->>..>>->>>>>>>>>>>>
#=GC RF                    UGAAAGACAUgGGUAGUGAGAugUUuuua..........uaaaauuu...ucaUcUC..ACUACCcUGUCUUUC
//
# STOCKHOLM 1.0

#=GF AC   RF00833
#=GF ID   mir-70
#=GF DE   microRNA mir-70
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   77.00
#=GF NC   63.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000279;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [3]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   4


AAGD02012111.1/237549-237430 UCAGAUGAACGAGGAGAACAGCUAUAGGAAUACCGUUGAUGCAUUACACUAAACAUUUGAAAGAUGUAAUACGUCAUUUGGUGUUCCUAUAGUU--ACCCGUUCAACUUUUAUUCUUCUUCU
CAAC02000558.1/449438-449320 UAUUUUCAAAACGGAUGU-AUCUCUAGGAACAGCCAUCAUGUAAGACAUUUCUAAC-UGAAAGAUGUAAUACGUGAUU-GGUGUUCCCAGAGUUUACCGUUUCCUUCUUUUAUUUUUCCAAA
ABEG02011397.1/567-448       AUUUAAUGGCAGAAUUGG-AACUUCUGAACCACCACUGACGAAUCACAUUGAAACU-AAAGAGAUGUAAUACGUCAUUUGGUGUUUCCGAAGUUUAUACUGUCAAGUUUAGCUUACUUUAAC
FO081382.1/32412-32297       UCAAAAUAAAACGAUGAA-AACUAUCGAAAUACUAUCGACGAAUAACACUUAUGA----AGAAAUGUAAUACGUCGUU-GGUGUUUCCAUAGUUUGAAUUGUUUAUUCCAUUAUUUUUGAGC
#=GC SS_cons                 :::::::::::::::::<.<<<<<<-<<<<<<<<<<<<<<<<<<-<<<<<<_____.____>>>>>>->>>>>>>>>>->>>>>>>>->>>>>>>:::::::::::::::::::::::::::
#=GC RF                      UcuuAuuAAaAaGauuaa.AaCUcuaGgAacACCaauGAcGuAuuACAuuuAaaAu.ugAaagaUGUAaUaCgUCauuUGGUguUcCCagAGuUuAaacUGUucAuuUUuUaUUuUUuuAac
//
# STOCKHOLM 1.0

#=GF AC   RF00834
#=GF ID   mir-268
#=GF DE   microRNA mir-268
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   68.90
#=GF NC   56.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000280;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12769849
#=GF RT   Computational and experimental identification of C. elegans microRNAs.
#=GF RA   Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J
#=GF RL   Mol Cell. 2003;11:1253-1263.
#=GF WK   MicroRNA
#=GF SQ   4


AC084551.1/15618-15523   GGAAGUGUCUUUGAAGCGGCAAGAAUUAGAAGCAGUUUUGGUGUCAGACACACUCACUGACUCACUGCUUCUUGUUUUU-CUUCUUCUUCUUCUUCU
AAGD02001159.1/8939-8861 GGAAGUGGCUUUGAAGCGGCAAGAAUUAGAC---------GGGGUGGCUCGACA--CCACCA------GUCUUGUUUUUUUCU-UUCUUUUUCUCCC
Z75526.1/15593-15687     GGAAGUGGCUUUGAAGCGGCAAGAAUUAGAAGCAGU-UUGGUGUCAGACACACU-ACUCACUCACUGCUUCUUGUUUUUUCUGCUUUCUUUGCUUUU
ABEG02009404.1/1631-1543 GGAAGUGGCUUUGAAGCGGCAAGAAUUAGAAGCAGUUUUGGUGUCAG--------ACACACUCACUCCUUCUUGUUUUUUCUUCUCUUUUUCCUUUU
#=GC SS_cons             ::::::::::::<<<<<<<-<<<<<<-<<<<<<<<<.---<-<<<<<_______._>>>>>->>>>>>>>>>->>>>>>->>>>>>>::::::::::
#=GC RF                  GGAAGUGgCUUUgaaGcgGCaagaauUaGaaGcaGu.UUGGuGucgGacacACu.ACcgaCuCaCugCuuCuUguuuuuUCcgCuucuUuUuCUuuu
//
# STOCKHOLM 1.0

#=GF AC   RF00835
#=GF ID   mir-58
#=GF DE   microRNA mir-58
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   59.30
#=GF NC   45.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000282;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [3]
#=GF RM   11679672
#=GF RT   An extensive class of small RNAs in Caenorhabditis elegans.
#=GF RA   Lee RC, Ambros V
#=GF RL   Science. 2001;294:862-864.
#=GF RN   [4]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF WK   Mir-58_microRNA_precursor_family
#=GF SQ   4


AAGD02012439.1/31637-31733   GCUCGCCAUAUCCAUUGCCCUACUAUUCGCAUCUCAUCACUUCCUCCAGUAA-------UAUAAGGAUGAGAUCGUUCAGUACGGCAAUGGAAAGAGCUAUAUA
CAAC02000451.1/314460-314357 GCUCGCCAUAUCCAUUGCCCUACUAUUCGCAUCUCAUCACUCCAGUAUAUAUAUAUAUAUAUAAGGAUGAGAUCGUUCAGUACGGCAAUGGAAAGAGCUAAACG
ABEG02008254.1/6499-6403     GCUCGUCAUAUCCAUUGCCCUACUCUUCGCAUCUCAUCACUUCGUCCGCCAA-------UAUAAGGAUGAGAUCGUUCAGUACGGCAAUGGAAAGAGCUAUAAC
FO081657.1/16188-16284       GCUCGUCAUAUCCAUUGCCCUACUCUUCGCAUCUCAUCACUUCGUCCAAUAC-------CAUAGGGAUGAGAUCGUUCAGUACGGCAAUGGACUGAGCUAGAGU
#=GC SS_cons                 ::::::::::<<<<<<<<<-<<<<---<<-<<<<<<<<-<<___________.......____>>>>>>>>>>>>--->>>>->>>>>>>>>::::::::::::
#=GC RF                      GCUCGuCAUAuCCauuGCCCuaCuaUUCGCauCuCauCACuuCauccaauAa.......uAUAaGGauGaGauCGUUCaGuaCGGCaauGGaaaGAGCUAuAuu
//
# STOCKHOLM 1.0

#=GF AC   RF00836
#=GF ID   mir-250
#=GF DE   microRNA mir-250
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   57.00
#=GF TC   59.90
#=GF NC   56.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000283;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   4


Z72511.1/6583-6503           UCGGACCACGCCUUCAGUUGCCUCGUGAUCCGCCAAACACAAUAAAUGGACGAAUCACAGUCAACUGUUGGCAUGGUGCUC
AAGD02011065.1/159359-159279 UCGGACCGCCCCUUCAGUUGACUCGUGAUCCGCCGACUUUGAUAUAUGGACGAAUCACAGUCACCUGAUGGUACGGUCUUU
CAAC02000606.1/999512-999434 UCGGACCACGCCUUCAGUUGCCUCGUGAUCCGCCGAAUCUG--UAAUGGACGAAUCACAGUCAACUGUUGGCACGGUCCUU
ABEG02010263.1/2814-2892     UUCGACCACGCCGGCAGUUGCCUGUUGAUCCGCCGCAAUUA--UGAUGGACGAAUCACAGUCAACUGUUGGCACGGUCUUU
#=GC SS_cons                 ::<<<<<<-<<<--<<<<<<-<<-<<<<<-<<<<<___________>>>->>->>>>>>>->>>>>>-->>>->>>>>>::
#=GC RF                      UcggaCCgCgCCuuCaGuUGcCUcgUGaUCCGCCgaauuUaAUaaAuGGACGAAuCAcAGUCAaCuGuUGGcAcGGuccUU
//
# STOCKHOLM 1.0

#=GF AC   RF00837
#=GF ID   mir-251
#=GF DE   microRNA mir-251
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   84.50
#=GF NC   55.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.04 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000284;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF WK   MicroRNA
#=GF SQ   4


Z68005.1/28031-28127         ACUUUCAAUGA-CCCCUUGUUAAGUAGUGGUGCCGCUCUUAUUAG-GUUGAAAAGUAAUAAGAGUAGUUCACUACUUAUCAAGGUGAAAUUUGAAAUUU
AAGD02002327.1/50319-50415   GUUCCAAAUAA-CCCCUUGUUAAGUAGUGGUGCCGCUCUUAUUAGAAUCCAGAA-UAAUAAGAGUCGCUCACUGCUUAUCAAGGUGAAAUUUGGGUUUU
CAAC02000543.1/114114-114021 GUCCCAAAUGA-CAUCUCGUUAAGUAGUGGUGCCGCUCUUAUUAGAAUUAUCAAGUAAUAAGAGUUGUUCGCUACUUAACGAGAGGAAAUUUGGA----
ABEG02000546.1/102770-102673 UAUUCAAAGGACCCCCUUGUUAAGUAGUGGUGCCGCUCUUAUUAG-AUGAGAUAGUAAUAAGAGUUGCUCACUACUUAUCAAGGUGAGUUUUGAUGUUU
#=GC SS_cons                 :::<<<<<<--.<-<<<<<-<<<<<<<<<<-<<-<<<<<<<<<<___________>>>>>>>>>>->>>>>>>>>>>>->>>>>->-->>>>>>:::::
#=GC RF                      auuccaaaugA.CccCuuGUuaaGuaGuGgUgCCgCuCuuauuaGAaUuaaaaAGuaauaaGaGuuGcuCaCuaCuuauCaaGguGAaauuuggaaUUU
//
# STOCKHOLM 1.0

#=GF AC   RF00838
#=GF ID   mir-252
#=GF DE   microRNA mir-252
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.30
#=GF NC   49.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000285;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF WK   MicroRNA
#=GF SQ   10


Z66521.1/2054-1944             ACUAUUCCAGGGGUCUCUUUCAGUU--AUAAGUAGUAGUGCCGCAGGUAA---------CCGCCAGUCUAAAA--GGC-UUACCUACUGC-CU-UCUGCUUAA-------AAUUGAAAUAUUGAUGACCAUUGA
AAQA01000035.1/130050-130151   ACAAUCCUCAAGGAUAAGUC--AUU--CUAAGUAGUAGUGCCGCAGGUAA---------CAAC----AAUUGA---GU-UUACCUGUUCU-CU-GCUACUUAA-------CAU--GACCAUCCAUGCUUGAACA
AAGD02000357.1/21908-22018     UUUAUUCUUGAGGUCUCUUUCAGUU--AUAAGUAGUAGUGCCGCAGGUAA---------CCACUCAAAUAUAU--GGU-UUACCUACUGC-CU-UCUGCUUAG-------AAUUGAAAUAUCGAUGACCGUACU
CAAC02000450.1/1710699-1710587 AUUCCAACCGAGGUCUCUCCCAGUU--AUAAGUAGUAGUGCCGCAGGUAA---------CCGCUUCCAGAAAAUUGGU-UUACCUACUGC-CU-UCUGCUUAG-------AAUUGGGAUUUUGAUGACCGUCUA
AAZX01009285.1/3883-4013       AAAUUUUCGCAAAAUCCCGUCCUGUUCCUAAGUACUAGUGCCGCAGGAGUGACUAGAUUGGGCUAGAAAUUAC--CGCGUCUCCUGCUGCUCA-AGUGCUUAUCAAUGGUUCGGGACGCACGACAAUGUAUACU
AAWU01043189.1/6884-6779       AGAUCAGCGGAUGAUAAGAAUUCUUUACUAAGUACUAGUGCCGCAGGAGA----------------GAUUUGA------ACCCCUGCUGC-CCAAGUGCUUAUC-----GAAGAGUUCCACUCGUACAUCGAAC
AAGE02003685.1/79138-79037     UCUGGUGAUUGAUAAGAAUUCUUUA--CUAAGUACUAGUGCCGCAGGAGA----------------GAUUUGA------ACCCCUGCUGC-CCAAGUGCUUAU-------CGAAGAGUUCCCCUCGUACAUCGU
ABLF02022130.1/7910-7799       UUCUACAAUAACGCAUAUUCUGUUC--CUAAGUACUAGUGCCGCGGGAGU---------GAUAUCCGUUUUUU--GUA-UCUCCUGCAGCUCA-AGUGCUUAU-------CAACGGGAAACAGCGCACCGACCU
AAGJ04018203.1/7463-7569       UUCAUCUUGAGUCCACGUUGCCGAU--CUAAGUAGUAGUGCCGCAGGUAC-------------UGAUUUUUAA--GUG-AUACCUGUACA-CG-GCUACUUAC-------AUUGGCAACGAGCUGGAAAAUCAA
ABEG02007476.1/32771-32878     AUUCCUUUUUUGGUCUCUUUCAGUU--AUAAGUAGUAGUGCCGCAGGUAA------------CCGAUUUCAAU--GGU-UUACCUACUGC-CU-CCUGCUUAG-------AAUUGAAAUUUCGAUGACCGUCUU
#=GC SS_cons                   :::::::::::::::::<<<<<<<<..-<<<<<<<-<<-<<-<-<<<<<<.........--<<<_________..>>>.>>>>>>->->>.>>.->>>>>>>-.......>>>>>>>>::::::::::::::::
#=GC RF                        auuuuuucuaAagauuauuuCccuu..cUAAGUAgUaGUGCCGCAGGuga.........gagCcaaaauUUaa..gGc.ucaCCUGCUGC.Cu.acUGCUUAu.......aaggGaaacacugaugaacaUacu
//
# STOCKHOLM 1.0

#=GF AC   RF00839
#=GF ID   mir-452
#=GF DE   microRNA mir-452
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   94.90
#=GF NC   69.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.48 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000287;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20733160
#=GF RT   Deep sequencing of the small RNA transcriptome of normal and malignant
#=GF RT   human B cells identifies hundreds of novel microRNAs.
#=GF RA   Jima DD, Zhang J, Jacobs C, Richards KL, Dunphy CH, Choi WW, Yan Au W,
#=GF RA   Srivastava G, Czader MB, Rizzieri DA, Lagoo AS, Lugar PL, Mann KP, Flowers
#=GF RA   CR, Bernal-Mizrachi L, Naresh KN, Evens AM, Gordon LI, Luftig M, Friedman
#=GF RA   DR, Weinberg JB, Thompson MA, Gill JI, Liu Q, How T, Grubor V, Gao Y,
#=GF RA   Patel A, Wu H, Zhu J, Blobe GC, Lipsky PE, Chadburn A, Dave SS
#=GF RL   Blood. 2010;116:e118-e127.
#=GF WK   Mir-452_microRNA_precursor_family
#=GF SQ   4


AAHY01212658.1/43863-43947 GCUAAGCAGUUACAACUGUUUGCAGAGGAAACUGAGACUUUAUAACUAUGUCUCAGUCUCAUCUGCAAAGAGGUAAGUGCUUUGC
AANN01683404.1/5649-5565   GCUAGGCACUUACAACUGUUUGCAGAGGAAACUGAGACUCUGUACCCGUGGCUCAGUUUUCUUUGCAAAGGAGUAAGUGCUUUGC
AANG01462441.1/3814-3730   GUUAUGCACUUACAACUGUUUGCAGAGGAAACUGAGACUUUGUAACUACAUCUCACUCUCAUCUGCAAAGGAGUAAGUGCUUUGC
U92285.1/12-96             GCUAAGCACUUACAACUGUUUGCAGAGGAAACUGAGACUUUGUAACUAUGUCUCAGUCUCAUCUGCAAAGAAGUAAGUGCUUUGC
#=GC SS_cons               <<<<<<<<<<<<<---<-<<<<<<<<-<<<<<<<<<<<___________>>>>>>>>>>>->>>>>>>>->->>>>>>>>>>>>>
#=GC RF                    GcuaaGCacuuaCAACuGuuuGCaGaGGagacuGaGacUuUgUAaCuauguCuCagucuCauCuGCaaaGaaGuaaguGCuuugC
//
# STOCKHOLM 1.0

#=GF AC   RF00840
#=GF ID   mir-374
#=GF DE   microRNA mir-374
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   69.00
#=GF TC   69.10
#=GF NC   68.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.21 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000288;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [2]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF WK   Mir-374_microRNA_precursor_family
#=GF SQ   13


AAFC03073181.1/1998-1928    ACAUCGGCCAUUAUAAUACAACCUGAUAAGUGUUACAGCACUUAUCAGGUUGUAUUGUAAUUGUCUGUGUA
AACN010065303.1/2609-2539   ACAUCGGCCAUUAUAAUACAACCUGAUAAGUGUUGUAGCACUUACCAGGUUGUAUUGUAAUUGUCUGUGUA
AANU01175070.1/1285-1355    ACAUCGGCCAUUAUAAUACAACCUGAUAAGUGUUACAGCACUUAUCAGAUUGUAUUGUAAUUGUCUGUGUA
AJ421479.1/16189-16259      ACUCGGGUGGAUAUAAUACAACCUGCUAAGUGUUCUAGCACUUAGCAGGUUGUAUUAUCAUUGUCCGAGGU
AALT01656114.1/3449-3379    GCUCGGAUGGAUAUAAUACAACCUGCUAAGUGUACUACCACUUACCAGGUUGUAUUAUUAUCGUCCGUGUU
AAGV020234407.1/12295-12225 ACUCAGAUGGAUAUAAUACAACCUGUUAAGUGUCCUAGCAUGAACCAGAUUGUAUUGUCAUUGUUCGUGUC
AAKN02029926.1/5039-5109    ACAUAGGCCUUUAUAAUACAACCUGAUAAGUGUUAUAACACUUACCAGAUUGUAUUGUAAUUGUCUGUGUA
AAEX03026520.1/10525-10455  ACUCGGAUGGAUAUAAUACAACCUGCUAAGUGUCCUAGCACUUAUCAGGUUGUAUUAUCAUUGUCCGUGGC
AABR05180221.1/17862-17792  ACUCGGAUGGAUAUAAUACAACCUGCUAAGUGUUCUAGCACUUAGCACGUUGUAUUAUUAUUGUCCGAGGC
AC002418.1/95571-95641      ACAUCGGCCAUUAUAAUACAACCUGAUAAGUGUUAUAGCACUUAUCAGAUUGUAUUGUAAUUGUCUGUGUA
AAPE02004040.1/21776-21839  ---CAGAUGUAUAUAAUACAACCUGGUAAGUGGCCCAGCACUUACCAGGUUGUACUAUCAUUGUUUG----
AGCE01104029.1/14237-14307  ACUCGGAUGGAUAUAAUACAACCUGCUAAGUGUCCUAGCACUUAGCAGGUUGUAUUAUCAUUGUCCGUGUC
AAGU03047897.1/27799-27869  GCUCGGAUGAAUAUAAUACAACCUGCUAAGUGUCCUAGCACUUAUCAGGCUGUAUUAUCAUUGUCCGUGUC
#=GC SS_cons                <<<<<<<<----<<<<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>>>>---->>>>>>>>:
#=GC RF                     aCacgGacgaaUAuAAUACAACCUGcUaAGUGcucUAgCACUuAgCAGGUUGUAUUaUaAUUguCcguGua
//
# STOCKHOLM 1.0

#=GF AC   RF00841
#=GF ID   mir-384
#=GF DE   microRNA mir-384
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   61.00
#=GF TC   61.00
#=GF NC   60.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000289;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15538371
#=GF RT   A pancreatic islet-specific microRNA regulates insulin secretion.
#=GF RA   Poy MN, Eliasson L, Krutzfeldt J, Kuwajima S, Ma X, Macdonald PE, Pfeffer
#=GF RA   S, Tuschl T, Rajewsky N, Rorsman P, Stoffel M
#=GF RL   Nature. 2004;432:226-230.
#=GF WK   Mir-384_microRNA_precursor_family
#=GF SQ   16


AAFC03097915.1/116760-116663 UGUUAUAUCAGGCAUUAUAAAUAAUUCCCAGGCAAUAUUUAGAAUGGCCACAAGC-----CAUUU-UUA-GGAUUGGUUGAGAAUUAUUUACAAUA-CCCAACUCG
ABDC01432121.1/672-585       UGUUAAAUCAGGAAUUGUAAACAAUUCCUAGGCAAUGUGUAUAAUGUUUGUAAGU-----CAUUC-CUA-GA----------AAUUGUUCACAAUG-CCUGUAACA
CAAA01218287.1/25473-25560   UGUUAAAUCAGGAAUUGUAAACAAUUCCUAGGCAAUGUGUAUAAUGUUGGUAAGU-----CAUUC-CUA-GA----------AAUUGUUCACAAUG-CCUGUAACA
Z84470.1/130382-130295       UGUUAAAUCAGGAAUUUUAAACAAUUCCUAGACAAUAUGUAUAAUGUUCAUAAGU-----CAUUC-CUA-GA----------AAUUGUUCAUAAUG-CCUGUAACA
AANU01174943.1/9038-9125     UGUUAAAUUAGGAAUUGUAAACAAUUCCUAGGCAAUAUGUAUAAUGUUCAUAAGA-----CAUUC-CUA-GA----------AAUUGUUCAUAAUG-CCUGUAACA
AANG01128599.1/11891-11804   UGUUAAAUCAGACUUUGCAAACAAUUCCUAGGCAAAACUUAAAAGGCCUGAAAGC-----AUUUU-UUA-GA----------AGCUAUUUACAAGG-CCUGAAUUA
AAKN02020573.1/67489-67587   UGUUAUACCAGGCAUCAUAAAUAAUUCUUAGGCAAUAUUUAAAAUGGCUGCAAGC-----CAUUU-UUA-UGAUUGAUUCAGAAUUAUUUACAAUGUCCUGCUCAA
AAQQ01334929.1/3073-3171     UGUCAUAUCAGGCAAUAUAAAUAAUUUCUGGGCAAUAUUCAGAAGGACUGCAAGC-----UGUUU-UUA-GGACUGGCUAAAACUUAUUUACAAUACCCUGUUCAC
AAGV020551934.1/1830-1927    UGUUAUAUUAGGCAUUAUAAAUAAUUCCUAGGCAAUAUUUAGACUGGCUGCAAGC-----CAAUU-UUA-GAAUUGGCUAAGAAUUAUUUACAAUA-CUUUUACAA
AAHX01093778.1/1883-1786     UAUUAUAUCAGGCAUUAUAAAUAAUUUCUAGGCAAUUUUUAAAAUGACUGCAAGA-----CAGUU-UUA-GGAUUGGCUAAGUGUUAUUUACAGUA-UCUUGCCCA
AAPE02042867.1/28541-28454   GGUGUGAUUAGGGAGUGUAAAUAAUUUCUGAGUAAUGUUUAAAAUAGCCAUAAAC-----AGUUCCCUA-GA----------GAGUAUCCACAC-A-CCUGCAUUA
AAGW02031858.1/37839-37741   UGUUAUAUCAGGCAUUAUGAAUAAUUCCUAGGCAAUAUUUAGAAUGGCUGAAAGC-----CAUUU-UUA-GGAUUGGCAAAGAAUUAUUUACAAUACCCUGCUCAC
AAGU03017009.1/14305-14217   GGUGUGAUAAGGAAUUGUAAAUAACUCCAGGGUAAUGUUUAAAAUGGUCACAAAC-----AGUUC-CCUAGA----------AACUAUUCACAAUG-CCUCCAUUA
AAEX03005433.1/621745-621842 UGUUAUAUCAGGCAUUAUAAAUAAUUCCUAGGCAAUAUUUAGAAUGGCUGCAAGC-----CAUUU-UUA-GAAUUGGAAGAGAAUUAUUUACAAUA-CCUUGCUCA
AACZ03042055.1/5853-5942     GAAUCAAUCUGGCAUUAUAAACAAUUCAAAGGCAAUUUUUAGAAUGAAAGCAAGC-----AAUUCUCUA-UG----------AAUCCUUUACAAUGCCCAGAAUAA
AAQR03028908.1/5511-5605     UGUUGUAUCAGGCAUUAUAAAUAAUUCCUAGGCAAUAUUUAGAAUGGCUGCAAGCCAUAGAAUUGGCUA-AG----------AAUUAUUUCAAAUACCCUGCUCCC
#=GC SS_cons                 ::::::::<<<<-<<<<<-<<<<<<<-<<<<<-<<<---<<_________>>---.....->>>>.>>>.>-..........>>>>>>>->>>>>-.>>>>:::::
#=GC RF                      UGUUauAUcaGGcAuUguAAAuAauUCcuaggCAAuaUUUaaAAUGgcuGuAAGC.....aaUUc.cua.ga..........AauUaUUUacAaUa.CCuguaucA
//
# STOCKHOLM 1.0

#=GF AC   RF00842
#=GF ID   MIR403
#=GF DE   microRNA MIR403
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   70.40
#=GF NC   69.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.47 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000290;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19939267
#=GF RT   High throughput approaches reveal splicing of primary microRNA transcripts
#=GF RT   and tissue specific expression of mature microRNAs in Vitis vinifera.
#=GF RA   Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del
#=GF RA   Fabbro C, Valle G, Policriti A, Morgante M, Pesole G, Pe ME, Horner DS
#=GF RL   BMC Genomics. 2009;10:558.
#=GF WK   Mir-403_microRNA_precursor_family
#=GF SQ   13



AEWC01015763.1/50884-50977   GCAUAUUUCACGUUUGUGCGUGAAUCUAAC----------------AAC-CCUUUUCA--UCAG-------------------AAAAACUGUUGUUGUU-UGCUAGAUUCACGCACAAACUCGUAAUAUGUAU
AFSA01297085.1/784-909       GCUUAUUUUGUGUUUGUGCGUGAAGCUAACGAUGUAACCAGGUGGUUGAAUCGAUGCUGAUCUA--UGAAUUAAACUGAU--GCCGGAG-GAUAUGUU--CGUUAGAUUCACGCACAAACUCGUAAUACGUCU
AM425370.2/5256-5142         GCACAUCUCAAGUUUGUGCGUGAAUCAAAC----------------CCCAUCGUAGCCGUCCAUAUCUUCGUGUACUAAU--CACGGGGCGAUUCGACGCCGUUAGAUUCACGCACAAACUCGCGAUCUGUCC
AM425370.2/6875-6790         ACAAACCUCGAGUUUGUGCGCGAAUCCAAC----------------CCC-UCA-----------AUCUUCUUUCA--------AAGGGGUG-----------UUAGAUUCACGCACAAACUCGGGAUCUGUCU
AM486228.2/8178-8064         GCACAUCUCAAGUUUGUGCGUGAAUCAAAC----------------CCCAUCGUAGCCGUCCAUAUCUUCGGGUACUAAU--CACGGGGCGAUUCGACGGCGUUAGAUUCACGCACAAACUCGUGAGUUCUGA
AARH01003570.1/90995-91093   UCCUAUCUCUGGUUUGUGCGUGGAUCUGAG----------------GCCAUCACAACCGUCCAC------------------UACACGACCACCCAAUGGCUUUAGAUUCACGCACAAACUCGCGAUCUGUCU
AARH01004350.1/142675-142577 UCAUAUCUCUAGUUUGUUCGUGGAUCUGAC----------------GCCAUCACAACCGUUCAU------------------UUCACGACCAUCCAAUGGCGUUAGAUUCACGCACAAACUCGCGAUCUGUCU
AM473558.1/14784-14680       G---AUGAGGAGUUUGUGCGUGACUCUAAA----------------ACCGCCU-----GAUCUAAA--CCUUUUCCCGAU--GCGAUACCUUUUCUAUGGUCUUAGAUUCACGCACAAACUCGUAAUCUGUCU
AARH01001226.1/54332-54202   GCAUAUUUCAGGUUUGUGCAUGAAUCUAAUAUAGCUA-AAAAAAUCCCAUCAAACACAAAUUAAAAUACUAGAUAGCAAUCAGCACUAG-UUUAGUAUAGUAUUAGAUUCACGCACAAACUCGUAAUCUGUCU
AC002337.3/49345-49460       GUAU-UACAUGUUUUGUGCUUGAAUCUAAU----------------UCAACAGGCUUUAUGUAAGAGAUUCUUUAACAAUUCCUAUAAUCUUUGUUGUUGGAUUAGAUUCACGCACAAACUCGUAAUCUGUCU
AASG02004953.1/3036-2929     ACGUAUCUCUAGUUUGUGCGUGAAUCGAGC----------------CCCAUCA-------UCAAGGCCGUUCAUUUUGAG--GCCCCACGAAUCCAAUGGUGUUAGAUUCACGCACAAACUCGUGAUCUGUCU
FN595246.1/600181-600266     ACAAACCUCGAGUUUGUGCGCGAAUCCAAC----------------GCC-UCG-----------AUCUUCUUUCA--------AAGGGGUG-----------UUAGAUUCACGCACAAACUCGGGAUCUGUCU
FN595246.1/602611-602725     GCACAUCUCAAGUUUGUGCGUGAAUCAAAC----------------CCCAUCGUAGCCGUCCAUAUCUUCGGGUACUAAU--CACGGGGCGAUUCGACGCCGUUAGAUUCACGCACAAACUCGUGAUCUGUCC
#=GC SS_cons                 <<<-<<<---<<<<<<<<<<<<<<<<-<<<................-<<---------<-<___________________.._____>->-------->>->>>->>>>>>>>>>>>>>>>--->>>->>>::
#=GC RF                      gCauAUcUcaaGUUUGUGCGUGAAUCuAAc................uCcAuCauaaCuGuuCAaAauuuuuuauAcuaAU..gaaagagCgaUuuuaUgGugUUAGAUUCACGCACAAACuCGUgAUcuGuCU
//
# STOCKHOLM 1.0

#=GF AC   RF00843
#=GF ID   mir-228
#=GF DE   microRNA mir-228
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   46.30
#=GF NC   41.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00093
#=GF DR   MIPF; MIPF0000292;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [2]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [3]
#=GF RM   12769849
#=GF RT   Computational and experimental identification of C. elegans microRNAs.
#=GF RA   Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J
#=GF RL   Mol Cell. 2003;11:1253-1263.
#=GF WK   MicroRNA
#=GF SQ   4


AAGD02004629.1/4581-4485     AUCCUAUC--UUGUUCGCAAUGGCACUGCAUGAAUUCACGG--AUGCAUUGCGACAGACCGCGGAUCAUGCGGUACCAUAGCGGACAGUGGUGAGAUAUUG
CAAC02000563.1/426449-426353 AUCCCACC--CUGUUCGCAAUGGCACUGCAUGAAUUCACGG--AUGCAAAGCGACAGACCGCGGAUCAUGCGGUACCAUAGCUGACGGUGGUGAGAUCAGA
FO081292.1/23963-24061       UCCUUAUC--CCGUUCGCAAUGGCACUGCAUGAAUUCACGGCUAUGCAUAACGACAGACCGCGGAUCAUACGGUACCAUAGCGGACGGUGAUGAGGUUAAU
ABEG02002540.1/19179-19082   UCCUCUCAGCCUGUUUGCAAUGGCACUGCAUGAAUUCACGG--AUGCAUUGCGACAGACCGCGGAUCAUGCGGUACCAUAGCUGACAG-UGAGUGGUCUCU
#=GC SS_cons                 :<<-<<<<..<<<<<<<<-<<<<-<<<<<<<<<-<<<-<<<..-<<________>>-->>>->>>>>>>>>>>>->>>>->>>>>>>>->>>>->>:::::
#=GC RF                      ucCucacc..ccGuccGCAauGGcaCcGcauGaAucCACGG..AuGcAuagcGACaGACCGcGgauCaugCgGuACCauAGCggaCggUggugaGgUuauu
//
# STOCKHOLM 1.0

#=GF AC   RF00844
#=GF ID   mir-67
#=GF DE   microRNA mir-67
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   51.60
#=GF NC   45.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000293;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18977439
#=GF RT   Identification of conserved microRNAs in Bombyx mori (silkworm) and
#=GF RT   regulation of fibroin L chain production by microRNAs in heterologous
#=GF RT   system.
#=GF RA   Cao J, Tong C, Wu X, Lv J, Yang Z, Jin Y
#=GF RL   Insect Biochem Mol Biol. 2008;38:1066-1071.
#=GF RN   [2]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing.
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF WK   Mir-67_microRNA_precursor_family
#=GF SQ   14


AABU01002766.1/2608931-2608865 GACUCACUCAACCUGGGUGUGAUGUU--AUUUCGAUAUGGUAUC--------------CAUCACAACCUCCUUGAGUGAGC-GA
AADE01000567.1/57238-57304     GACUCACUCAACCUGGGUGUGAUGUU--AUUUCGAUAUGGUAUC--------------CAUCACAACCUCCUUGAGUGAGC-GA
AADK01002680.1/19047-19115     UACUCACUCAACCUGGGUGUGAUGUGUGCACUCGUUGCUCGGCC--------------CAUCACAACCUCCUUGAGUGAGC-GA
AAQB01006297.1/299092-299025   GACUCACUCAACCUGGGUGUGAUGUUAUUUAU-AAUAUGGUAUC--------------CAUCACAACCUCCUUGAGUGAGC-GA
AAAB01008986.1/7425506-7425447 CACUCACUCAACCUGGGUGUGAUGCU--UUUU-------UGAAU--------------CAUCACAACCUCCUUGAGUGAGC-GA
AAGE02001157.1/148024-147965   CACUCACUCAACCUGGGUGUGAUGCU--UAUU-------UGAAU--------------CAUCACAACCUCCUUGAGUGAGC-GA
AAWU01001681.1/9094-9035       CACUCACUCAACCUGGGUGUGAUGCU--UAUU-------UGAAU--------------CAUCACAACCUCCUUGAGUGAGC-GA
AAJJ01001473.1/10807-10747     GACUCACUCAACCUGGGUGUGAUGUGUUUGCU--------GUAC--------------CAUCACAACCUCCUUGAGUGAGC-GA
AAZX01010522.1/11245-11164     AACUCACUCAACCUGGGUGUGAUGCUUGCCCG-UGAAAUUGAACAGGGCCCUUGCGGUCAUCACAACCUUUUUGAGUGAGC-GA
AAZO01000007.1/12339-12398     CACUCACUCAACUUGGGUGUGUUACG--UAAG-------UGAUU--------------CGCCACAACCUCCUUGAGUGAGC-GU
AAGD02001338.1/23885-23949     AACUCGUUCUGC-UGGUUGUUAUGCUGAAACA----GAAAGAAG--------------CAUCACAACCUCCUAGAAAGAGUAGA
CAAC02000485.1/290134-290201   AACUCAUUCUGC-UGGUUGUUAUGCUGACAAUUGAUGAU-UAAG--------------CAUCACAACCUCCUAGAAAGAGUAGA
ABEG02000805.1/33315-33248     AACUCAUUCUGC-UGGUUGUUAUGCCAAACAUUGAAAUU-UAAG--------------CAUCACAACCUCCUAGAAAGAGUGGA
AADG06000212.1/10340-10415     GACUCACUCAACCUGGGUGUGAUGCUUGCCUGUGUAUCAGGCCC-------UAGCGGUCAUCACAACCUUUUUGAGUGAGC-GA
#=GC SS_cons                   ::<<<<<<<<<---<<<<<<<<<<________.___________..............>>>>>>>>>>--->>>>>>>>>:.::
#=GC RF                        aACUCaCUCaACCUGGgUGUGAUGCUuauauu.gaaaauuGAac..............CAUCACAaCCUCCUuGAGuGAGC.GA
//
# STOCKHOLM 1.0

#=GF AC   RF00845
#=GF ID   MIR158
#=GF DE   microRNA MIR158
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   44.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000294;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12101121
#=GF RT   MicroRNAs in plants.
#=GF RA   Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP
#=GF RL   Genes Dev. 2002;16:1616-1626.
#=GF RN   [2]
#=GF RM   16040653
#=GF RT   Expression of Arabidopsis MIRNA genes.
#=GF RA   Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC
#=GF RL   Plant Physiol. 2005;138:2145-2154.
#=GF RN   [3]
#=GF RM   16954541
#=GF RT   MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent
#=GF RT   RNA polymerase-2 mutant.
#=GF RA   Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, Poethig RS,
#=GF RA   Henderson IR, Jacobsen SE, Wang W, Green PJ, Meyers BC
#=GF RL   Genome Res. 2006;16:1276-1288.
#=GF WK   MicroRNA
#=GF SQ   2


AC002328.2/10346-10445 ACACGUCAUCUCUGUGCUUCUUUGUCUACACUUUUGGAAAAGGUGAUGAUAUCAUUGCUUUUCCCCAAAUGUAGACAAAGCAAUACCGUGAUGACGUUAU
AC011708.8/49978-50077 ACACGUCAUCUCUGUGCUUCUUUGUCUACAAUUUUGGAAAAAGUGAUGACGCCAUUGCUCUUUCCCAAAUGUAGACAAAGCAAUACCGUGAUGAUGUCGU
#=GC SS_cons           ::::::::<<-<-<<<---<<<<<<<<<<<-<<<-<<<<<<<<<<<<<____>>>>>>>>>>>>>->>>>>>>>>>>>>>--->>>->->>:::::::::
#=GC RF                ACACGUCAuCUCUGugCUUCuuuGuCuaCaauuuUGGgaaggGcgauGAuauCaucgCccuucCCCaaauGuaGaCaaaGCAAcaCCGUGaUGAuGUuaU
//
# STOCKHOLM 1.0

#=GF AC   RF00846
#=GF ID   mir-64
#=GF DE   microRNA mir-64
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   48.90
#=GF NC   42.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000295;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF WK   MicroRNA
#=GF SQ   4


AAGD02000398.1/736-840     UUAA----CCAGAGGCCUCGCCGAAUAUGACACUGACGCUUAAUAUGGACCGAUCUCCC----CCGGAUCCAUA--AAAGCUCAGUGUCAAACUCGGCGAGUGCCCCGCCCCCUA
FO080824.1/92980-93089     CUCC----CCGCUGACCUCGCCGAAUAUGACACUGAAGCGUU-ACCGAACCGUUUUCCCACACCUGGAUUCGGUGCAACGAUCAGUGGCAUGCUCGGCUAGCGCCAGUUAAGUAU
FO080824.1/93130-93233     ----AGCCAUGGAGCCUUCGCCGAUUAUGACACUGAAGCGUA-ACCGAACA------CCAUAUUUUGAGAUUCUGCUACGCGCAGUGCCAUGCUCGGCGCGUUGGCUCCAUUAAA
ABEG02005734.1/14156-14049 ----AACUCCUUGGGCCUCGCCGGUUAUGACACUUAAGCUAA-UCUGAACCAAUUUAGAACUAUAGGAUUCAGU--UUAGAUAAGUGGAAUAGUCGGCGAGAGUCCGGAGACGUU
#=GC SS_cons               ....::::::::::::::<<<<<<-<<<<<<<<<<--<<<<<.<<<<_______________________>>>>-->>>>>->>>>>>>>>>->>>>>>::::::::::::::::
#=GC RF                    ....AaCucCggaGgCCUcGCCGauuaUGaCACUgAAgCgua.acuGAACcgaUuUcccAcauuuGGAUuCaguGCuacGcUcAGUGuCAuacuCGGCgAGuGuccggcaacaua
//
# STOCKHOLM 1.0

#=GF AC   RF00847
#=GF ID   mir-62
#=GF DE   microRNA mir-62
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   68.90
#=GF NC   39.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000296;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   Mir-62_microRNA_precursor_family
#=GF SQ   4


Z50006.1/11828-11887         AGGUGAGUUAGAUCUCAUAUCCUUCCGCAAAAUGGAAAUGAUAUGUAAUCUAGCUUACAG
AAGD02009525.1/92624-92565   AGGUGGGUUAGAUCCCAUAUCCUUCCGCGUAAUGGAAAUGAUAUGUAAUCUAGCUUACAG
CAAC02000438.1/250486-250427 AGGUGGGUUAGAUCCCAUAUCCUUCCGCUUGAUGGAAAUGAUAUGUAAUCUAGCUUACAG
ABEG02001466.1/4507-4448     AGGUGAGUUAGAUAUCGUAUCCUUCCGCUUAAUGGUAAUGAUAUGUAAUCUAGCUUACAG
#=GC SS_cons                 ::<<<<<<<<<<<--<<<<<<-<<<<<_____>>>>>-->>>>>>-->>>>>>>>>>>::
#=GC RF                      AGGUGaGuUAGAUcuCaUAUCCUuCCGCuUAAUGGaAAUGAUAuGUAAUCUAgCuUACAG
//
# STOCKHOLM 1.0

#=GF AC   RF00848
#=GF ID   mir-61
#=GF DE   microRNA mir-61
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   46.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000297;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [3]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF WK   Mir-61_microRNA_precursor_family
#=GF SQ   4


Z72511.1/6725-6639           UAUCGCUGAACCUCGAGAUGGGUUACGGGGCUUAGUCCUUCCUCCGUAUGGCAAUGACUAGAACCGUUACUCAUCUCGAGGUUUCGG--
AAGD02011065.1/159499-159415 UAUCGGUC--UUCCGAGUUGGGUCACGGCGCUUAGUCCUUCCGACAUAUGGCAAUGACUAGAACCUUGGCUCAGCUCGGGACUCCGA--
CAAC02000606.1/999667-999581 GAUCGGUG--UCUCGAGCCGAGUUAAGGCUAAUAGUCCUUCCGGUGUAUGGUAAUGACUAGAACCUUGACUCUGCUCGAGUUACUGAGC
ABEG02010263.1/2679-2765     CAU-GUUGAACUUCGAGUUGGGUCACGGUGCUUAGUCCUUCCAACAGUCGGUAAUGACUAGAACCGUGACUCAGCUCGAGGAAGC-GGC
#=GC SS_cons                 ::<<<<<<..-<<<<<<<<<<<<<<<<<----<<<<<-<<<<_______>>->>->>>>>--->>>>>>>>>>>>>>>>>->>>>>>::
#=GC RF                      uAuCGgug..ucuCGaGcuGgGucacGGugcuuaGuCCuuCCgacauauGGuaaUGaCuaGAACCgugaCuCagCuCGaggcacCGaGc
//
# STOCKHOLM 1.0

#=GF AC   RF00849
#=GF ID   mir-60
#=GF DE   microRNA mir-60
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   69.30
#=GF NC   46.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000298;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF RN   [2]
#=GF RM   11679672
#=GF RT   An extensive class of small RNAs in Caenorhabditis elegans.
#=GF RA   Lee RC, Ambros V
#=GF RL   Science. 2001;294:862-864.
#=GF RN   [3]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF WK   MicroRNA
#=GF SQ   4


AC084475.1/24584-24513     UUCUUGAGCUGGAAAGGUGACAUAAAAUCAUGUCCAAGCACGCGAUAUUAUGCACAUUUUCUAGUCCAAGAC
AAGD02011425.1/10260-10331 UUCUUGAGCUAGAAAGGUGACAUAAAAUCAUGUAUAACAACGCGAUAUUAUGCACAUUUUCUAGACCAAGAC
ABEG02001647.1/9658-9587   CUCUUGAGCUGGAAAGGUGACAUAAAAUCAUGUCAGAGAACGCGAUAUUAUGCACAUUUUCUAGUCCAAGAC
FO080708.1/16773-16702     UUCUUGAACUGGAAGAGUGCCAUAAAAUCAUGACAAAGUACGUGAUAUUAUGCACAUUUUCUAGUUCAAGAC
#=GC SS_cons               :<<<<<-<<<<<<<<<<<<-<<<<<-<<<-<<________>>->>>->>>>>>>>->>>>>>>>>->>>>>:
#=GC RF                    UUCUUGAgCUgGAAagGUGaCAUAAAAUCAuGucaAAgaACgcGAUAUUAUGCACAuuUUCuAGccCAAGAC
//
# STOCKHOLM 1.0

#=GF AC   RF00850
#=GF ID   mir-259
#=GF DE   microRNA mir-259
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   53.30
#=GF NC   43.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000299;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [2]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF RN   [3]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF WK   MicroRNA
#=GF SQ   4


Z73973.1/9529-9429       UCAGUCAUUGAAACGAGUAAAUCUCAUCCUAAUCUGGUAGCAUCUUUCGAACCUU--GCCACCGAUUUGGCAUGGGAUUGACUUGUUAAAUAGUGACUUUUUU
AC084639.1/15370-15472   AUAGUCAUCGAAACGAGUAAAUCUCAUCCUAAUCUGGUUGCAUUUUCAAUACUUUUUGCUACCGAUUUGGUUUGGGAUUGGCUUGUCUAGUAUUGACAUUUUA
AAGD02004316.1/7095-6995 AUAGCCGACGGAACGAGUAAAUCUCAUCCUAAUCUGGUUGACACAACACAAGGAAGUGCUACCGAUUUGGCUUGGGAUUGACUUGUGGAA--AUGGCUUUUUA
ABEG02002421.1/4034-4136 AUUGUCAGUGAAACGAGUUAAUCUCAUCCUAAUCUGGUCGCAUCACAAAACUUACCUGCUACCGAUUUGGCUUGGGAUUGACUCGUUGAAUUUUGACUAUUGU
#=GC SS_cons             :::<<<<<-<-<<<<<<<-<<<<<<<--<<<<--<<<<-<<________________>>->>>>-->>>>-->>>>>>>->>>>>>>--->->>>>>::::::
#=GC RF                  aUaGuCacugAaaCgaGuaaauCuCaUCCuaaUCuGGuuGcaucauuaaaauuauuUgCUaCCgAUuugGcuuGgGauuGaCucGuugAAuaguGaCuuUUuu
//
# STOCKHOLM 1.0

#=GF AC   RF00851
#=GF ID   mir-230
#=GF DE   microRNA mir-230
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   63.50
#=GF NC   50.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000306;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [2]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF RN   [3]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF WK   MicroRNA
#=GF SQ   2


CAAC02000521.1/3562400-3562495 AAAAUGCCUUACCGAUACUUGGUCGACAAUUUAAUAGUAUCUGAU--UAAUUGAUGGAUAGUAUUAGUUGUGCGACCAGGAAAUGGUAUGAGCAUUUC
FO080955.1/21083-21180         UUGAUGUAAUGCCGUCACUUGGUCGGCGAUUUAAUAUUAUCAGAACAUAGGAAAUUGUUAGUAUUAGUUGUGCGACCAGGAGACGGUAUUCGCAUAUU
#=GC SS_cons                   :::<<<<<<<<<<<<<-<<<<<<<<<<<<<-<<<<<<<<<<<_____________>>>>>>>>>>>>>>>>->>>>>>>>->>>>>>>>>->>>>:::
#=GC RF                        aaaauGccaugCCgucACuuGGuCGgCgauUuaauacuauCcGAacAUAauaaAUgGauaguauuagucGcGCGaCCagGAgacGGcaugagCauaUu
//
# STOCKHOLM 1.0

#=GF AC   RF00852
#=GF ID   mir-231
#=GF DE   microRNA mir-231
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   71.80
#=GF NC   48.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000307;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   4


CAAC02000486.1/217689-217765 CAAUGUUGUUCUGUCUGUUUCCAUAGCUUAUAUUGU-------AAGGUACUUAUAAGCUCGUGAACAACAGGCAGGACAACUGG
AAGD02000085.1/638-717       CGAUGUUGUUCUGACUGUUUCCAUAGCUUAUAUUGUCUC----AAAAUGCAUAUAAGCUCGUGAACAACAGGCAGGACAACUGG
ABEG02000475.1/1322-1404     CAU-GUUGUUCUGACUGUUUCAAAAGCUUAUAUUGUUCGUUCAAAGUUACUUAUAAGCUCGUGAUCAACAGGCAGGACAACUAU
FO080424.1/6436-6354         CAG-GUUGUUCUGACUGUUUCAAAAGCUUGUAGUAUCUUAAUAAAUAAACAUAUAAGCUCGUGAUCAACAGGCAGAACAACUCG
#=GC SS_cons                 ::<.<<<<<<<<<-<<<<<<<<--<<<<<<<<___________________>>>>>>>>-->>>-->>>>>->>>>>>>>>>::
#=GC RF                      CAa.GUUGUuCUGaCUGUUUCaAaAGCUUaUAuUgUcuuaauAAAgauACaUAuAAGCUCGuGAuCAACAGGCAGgACAACuag
//
# STOCKHOLM 1.0

#=GF AC   RF00853
#=GF ID   mir-304
#=GF DE   microRNA mir-304
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   98.40
#=GF NC   59.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000308;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF RN   [2]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [3]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF WK   MicroRNA
#=GF SQ   5


AABU01002771.1/4690658-4690745 GCAGCAUUGAAUAAUCUCAAUUUGUAAAUGUGAGCG-GUU-UAAG-CCAUUUGACGCACUCACUUUGCAAUUGGAGAUUGCUCGAGACUGC
AADE01000788.1/13102-13189     GCAGCAUUGAAUAAUCUCAAUUUGUAAAUGUGAGCG-AUU-UGAG-GCAUUUGACACACUCACUUUGCAACUGGAGAUUGCUCGAAACUGC
AANI01016408.1/101204-101292   GCAGCAUUGAUUAAUCUCAAUUUGUAAAUGUGAGCGAUUU-UAAA-GUAUUUGACGCACUCACUUUGCAAUUGGAGAUUGCUCGAGAUUGC
AAPT01019076.1/28722-28634     GCAGCAUUGAAUAAUCUCAAUUUGUAAAUGUGAGCG-AUUAUUAA-GAAUUUGACGCACUCACUUUGCAAUUGGAGAUUGCUCGAGAUUGC
AAQB01006319.1/7240-7152       GUAACAUUGAUUAAUCUCAAUUUGUAAAUGUGAGCG-AUU-UAAAUCCAUUCGAUGCACUCACUUUGCAAUUGGAGAUUGCUCGAGAUUGC
#=GC SS_cons                   <<<<--<<<<-<<<<<<<---<<<<<<<-<<<<<-<.--<.<<<<.___>>>>>-->->>>>>>>>>>>>--->>>>>>>->>>>-->>>>
#=GC RF                        GcagCAuuGaauaauCuCAAUuuGuaaaUGuGaGCG.aUu.ugaa.gcAuucgacgCACuCaCuuugCaauUGGaGauugCuCgagAcugC
//
# STOCKHOLM 1.0

#=GF AC   RF00854
#=GF ID   mir-5
#=GF PI   mir-4
#=GF DE   microRNA mir-5
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   87.40
#=GF NC   44.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000309;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF RN   [2]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [3]
#=GF RM   11679670
#=GF RT   Identification of novel genes coding for small expressed RNAs.
#=GF RA   Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T
#=GF RL   Science. 2001;294:853-858.
#=GF RN   [4]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF WK   Mir-5_microRNA_precursor_family
#=GF SQ   6


AADE01001895.1/3489-3560         GCUAAAAGGAACGAUCGUUGUGAUAUGCGUUAAUU-CACCGUUACAUAUCACAGUGAUUUUCCUUUAUAGCGC
AABU01002766.1/12601692-12601624 GCUAAAAGGAACGAUCGUUGUGAUAUGAGUUGUUU----CCUAACAUAUCACAGUGAUUUUCCUUUAUAACGC
AAPP01018770.1/57095-57166       GCUAAAAGGAACGAUCGUUGUGAUAUGCGUUUAUC-CCUCGUUACAUAUCACAGUGAUUUUCCUUUAUAACGC
AAPT01006453.1/3132-3204         GCUAAAAGGAACGAUCGUUGUGAUAUGCGUUCAUUAAAUCGUUACAUAUCACAGUGAUUUUCCUUUAUAGCGC
AASS01023484.1/3619-3686         GCUAAAAGGAACGAUCGUUGUGAUAUGAGUUGUUC-----CCAACAUAUCACAGUGAUUUUCCUUUAUAUCGC
AAQB01006291.1/71265-71193       GCUAAAAGGAACGAUCGUUGUGAUAUGCGUUAGAUUCACCGUUAUAUAUCACAGUGAUUUUCCUUUAUAGCGC
#=GC SS_cons                     <<<<<<<<<<<-<<<<<<<<<<<<<<<________.________>>>>>>>>>>>>>>>>>>>>>>->>>>::
#=GC RF                          GcUAAAAGGAACgAUCguUGUGAUAUGcGUUaaUu.cauCgUuACAUAUCACAguGAUuUUCCUUUAUAgCGC
//
# STOCKHOLM 1.0

#=GF AC   RF00855
#=GF ID   mir-254
#=GF DE   microRNA mir-254
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   71.90
#=GF NC   59.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000310;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF WK   MicroRNA
#=GF SQ   4


Z66567.1/13696-13591         ------GCACGGACUAUGCAUAUUGCCGCCUACAGAAGCAUAGAUUUCCACAAACC-AUUCGAGGUGUUUGUGCAAAUCUUUCGCGACUGUAGGCGGCGAACAUGCAGUUU----UU
AAGD02002330.1/90281-90171   AGCACU------AGAAUGCAUAUCGCCGCUUACAGAAGCGUGGAUUUUCACAUACCAAUCGGAAGUGUCUGUGCAAAUCUAUCGCAACUGUACACGGCGAUACUGCAGUUAUUGAAC
CAAC02000541.1/544760-544867 CUCCAC------UCUAUGCGGGUUGCCGUAUACAGAAGCAUCGAUUUUCACACGCC-AU--GAUGCGCCUGUGCAAAUCUUUUGCAACUGUAUACGGCGAUUUAGCAGACCAUAUUG
ABEG02000001.1/96464-96354   CACUUA------AAAAUGCAUAUUGCCGCCUACAGAAGCAUAGAUUUUCACAUACCGAUCUGAAGAGUUUGUGCAAAUCUGUCGCAUCUGUAGGCGGCGAUUAUGCAGUCAUUUGAG
#=GC SS_cons                 ::::::......::::<<<<--<<<<<<<<<<<<<--<<<--<<<<<<<<<<<<<<._______>->>>>>>>>>>>>>--->>>-->>>>>>>>>>>>>--->>>>::::::::::
#=GC RF                      caCuuu......aauAuGCauaucGCCGccuaCaGAAGCgUaGauuugCaCacgCC.AUcuGAaGuGcguGuGcaaauCUuUcGCaaCuGuaggCGGCgauuauGCaGuuauUaauu
//
# STOCKHOLM 1.0

#=GF AC   RF00856
#=GF ID   mir-232
#=GF DE   microRNA mir-232
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   66.00
#=GF NC   52.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000311;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   3


AAGD02004292.1/20644-20547     AAGUCUGAUUGUCGGAUCUCCGUAGUUUCGAUCAUUUUAUCCU-AUCUCCAACAAAGCGAUAAAUGCAUCUUAACUGCGGUGAUCUGAAUUCUU-GGACA
Z68748.1/3269-3172             AAGUUCAAUUUUUGGAUCCCUGCAGUUUCGAUGAUUUUAUCCUUAAUUCUGAAGAUGUGAUAAAUGCAUCUUAACUGCGGUGAUCUAGAUCAU--GAACA
CAAC02000470.1/1099567-1099662 AAUUCAAGAUUUCGGAUCUCCGUAGUUUUGACCAUUUUAUCCA-ACCU--AAUAAUGUGAUAAAUGCAUCUUAACUGCGGUGAUCUGGAUUUUGUGAAC-
#=GC SS_cons                   ::<<<<----<<<<<<<<-<<<<<<<<--<<<---<<<<<<__.______________>>>>>>--->>>-->>>>>>>>->>>>>>>>-----.>>>>:
#=GC RF                        AAguccaauUuccgGauCuCcGcaGuuUcGaucAUuuuauCCu.AucUCuaAuaAuGuGauaaaUGCauCUUaaCugCgGUGauCuggaUuuUu.ggacA
//
# STOCKHOLM 1.0

#=GF AC   RF00857
#=GF ID   mir-233
#=GF DE   microRNA mir-233
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   30.00
#=GF TC   30.00
#=GF NC   29.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000312;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   4


Z67738.1/505-408               AUA---UAGCAUCUUUCUGUCUCGCCCAUCCCGUUGCUCCAAUAUUCUAACAACAA--GUGAUUAUUGAGCAAUGCGCAUGUGCGGGAUAGACUGAUGGCUGC
CAAC02000532.1/1029462-1029561 ---AAUAAGCAUUUUUCUGUCCCGCGCAUCCCUUUGUUCCAAUAUUCAAACCAGUAGAAAGAUUAUUGAGCAAUGCGCAUGUGCGGGACAGAUUGAAUAGCUG
AAGD02005858.1/36439-36537     CUG---AAGCGUCUCUCUGUCCCGCUCAUCCUGUUGUUCCAAUAUUCCAACAGCCC-AGUGAUUAUUGAGCAAUGCGCAUGUGCGGGACAGAUUGUAUGCUGC
ABEG02000526.1/114240-114337   UCA---AAGCGUCUUUCUGUCUCGCCCAUCCCGUUGUUCCAAUAUUCCAACAACAA--GUGAUUAUUGAGCAAUGCGCAUGUGCGGGACAGACUGAUGUCUGC
#=GC SS_cons                   :::...:::::<<--<<<<<<<<<<<<<<-<<<<<<<<<-<<<<-<<_________.___>>->>>>>>>>>>>>->->>>>>>>>>>>>>>-->>:::::::
#=GC RF                        uua...aAGCaucUuuCuGuCcCGCcCauCCcguuGcuCCaauaUuCuAACaacaa.AguGaUuauuGagCaacgCGCauGgGCGgGaCaGauUgaauacugc
//
# STOCKHOLM 1.0

#=GF AC   RF00858
#=GF ID   mir-306
#=GF DE   microRNA mir-306
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.90
#=GF NC   45.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000313;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12919683
#=GF RT   The small RNA profile during Drosophila melanogaster development.
#=GF RA   Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B,
#=GF RA   Gaasterland T, Meyer J, Tuschl T
#=GF RL   Dev Cell. 2003;5:337-350.
#=GF RN   [2]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [3]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF WK   MicroRNA
#=GF SQ   7


AADE01000148.1/25176-25258     CACUUUGCCGGCUCAGGUACUUAGUGACUCUCA---AUGCUUUCGACAU--CU--------UGAGAGUCUCUCUGUGCCUGCACUGGCGGUGGUGC
AABU01002759.1/4710601-4710519 CCACUCGAUGGCUCAGGUACUUAGUGACUCUCA---AUGCUUUUGACAU--UU--------UGGGGGUCACUCUGUGCCUGUGCUGCCAGUGGGAC
AAPP01015742.1/196327-196245   CCACUUGGUAGCUCAGGUACUUAGUGACUCUCA---AUGCAUUUGACAU--UU--------UGGGAGCCACUUUGUGCCUGGGCCAUCAGUGCGAC
AAPU01010522.1/87951-88041     ACACGCUGCAGCUCAGGUACUUAGUGACUCUCA---AUCACAUAUUGCU--UUGCAUACUUUGAGGGUCGCUCUGUGCCUGUGCCGCCCGUGUUGC
AAPT01019705.1/15024-15115     ACACGUUGCUGCUCAGGUACUUAGUGACUCUCAAUUCAACAUUGUAUUG--CA--CGCCUUUGAGGGUCGCUCUGUGCCUGUGUUGCACGUGUUGC
AANI01016236.1/76413-76323     ACACCCCGCUGCUCAGGUACUUAGUGACUCUCA---AUCAUCUAUUGCU--UUGCAUACCUUGAGGGUCGCUCUGUGCCUGUGCCGCCUGUGCUGC
AAQB01008360.1/26170-26086     UGCCUAAACAGCUCAGGUACUUAGUGACUCUCA---AAGAAUAUAUCUAGACU--------UGAGAGACGCUCUGUACCUAGACUGUUGUGUCUGC
#=GC SS_cons                   <<<<<-<<<<<<-<<<<<<<--<<<<<<<<<<<...<<<<____>->>>..--........>>>>>>>>>>>-->>>>>>>->>>>>>>>>>>:::
#=GC RF                        ccaccuggcgGCUCAGGuACUUAGcGaCuCuCA...augcauUugacau..uU........UGaGaGuCgCUCUGUgCCUGuGCcgccggugguGC
//
# STOCKHOLM 1.0

#=GF AC   RF00859
#=GF ID   mir-234
#=GF DE   microRNA mir-234
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   55.10
#=GF NC   47.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00092
#=GF DR   MIPF; MIPF0000315;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [2]
#=GF RM   12747828
#=GF RT   MicroRNAs and other tiny endogenous RNAs in C. elegans.
#=GF RA   Ambros V, Lee RC, Lavanway A, Williams PT, Jewell D
#=GF RL   Curr Biol. 2003;13:807-818.
#=GF WK   MicroRNA
#=GF SQ   4


Z81468.1/1975-1876           AACACAAAAAAUGAUCAAACGGUAUUCCAGAGUUGAUAAUAAAAAUGCG-UCAGUCCGCAAUCUAUUAUUGCUCGAGAAUACCCUUUGACUA--CUAUGUGUA
AAGD02003360.1/7138-7240     GUGGUGAACCAAGCUCAAACGGUAUUCGACGGUGAAUAAUAAAAAUGACAUUGCGACUCAUUCUAUUAUUGCUCGAGAAUACCCUUUGACACGGUUCACCUUU
CAAC02000444.1/319384-319479 GACUCUAGCAAAGAUCAAACGGUAUUCCUGAGUGAAUAAUAAAAAUGAG-UC------CAUUCUAUUAUUGCUCGAGAAUACCCUUUGACAAGCUGAAAAGUG
ABEG02008127.1/4482-4381     AUGCAACAAUCAGCUCAAACGGUAUUCUUUGGUUAAUAAUAAGGAUGGCAUCACGACUCAUUAUAUUAUUGCUCAAGAAUACCCUUUGACAAA-UGUCGCGUG
#=GC SS_cons                 ::::::::::::::<<<<<-<<<<<<<--<<<<-<<<<<<<--<<<<<<_______>>>>>>->>>>>>>>>>>-->>>>>>>->>>>>::::.:::::::::
#=GC RF                      auguuaaAaaaaGaUCAAACGGUAUUCuagaGuuaAUAAUAAAaaUGggAUcacgaccCAuucUAUUAUugCucgAGAAUACCCUUUGACaag.UuaagugUg
//
# STOCKHOLM 1.0

#=GF AC   RF00861
#=GF ID   mir-488
#=GF DE   microRNA mir-488
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   68.00
#=GF TC   77.60
#=GF NC   48.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000318;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   Mir-488_microRNA_precursor_family
#=GF SQ   5


AANU01240492.1/126475-126557 GAGAAUCAUCUCUCCCAGAUAAUGGCACUCUCAAACAAGUUUCCAAGUUGUUUGAAAGGCUAUUUCUUGGUCAGAUGACUCUC
AADB02001007.1/970631-970549 GAGAAUCAUCUCUCCCAGAUAAUGGCACUCUCAAACAAGUUUCCAAAUUGUUUGAAAGGCUAUUUCUUGGUCAGAUGACUCUC
AAIY01694145.1/4368-4450     GAGAAUCCUCUCUCCCAGAUAAUGACACUCUCAGACAAGAGUCCAAGUUGUUUGAAAGGCUAUUUCUUGGCCAGAAGACUCUC
AAYZ01007634.1/3646-3565     GAGGAUCAUCUCUCCCAGAUAAUGGCACUCUCAAACGAGUUUCCAG-UUGUUUGAAAGGCUAUUUCUUGGUCAGAAGACUCUC
AAHX01076190.1/26229-26147   GAGAAUCCUCUCUCCCAGAUAAUGGCACUCUCAAACAAGUUUCUACAUUGUUUGAAAGGCUGUUUCUUGGUCAGAAGACUCUC
#=GC SS_cons                 <<<<-<<-<<<--<<-<<<-<<<<<<-<<-<<<<<<<<_________>>>>>>>>->>>>>>>>>>>->>-->>>->>->>>>
#=GC RF                      GaGaAuCauCuCUCCCaGaUaaugGCACuCuCaaaCaaGuuUCcAaauuGuuuGaAaGGCuauuuCuUGGuCaGaaGaCuCuC
//
# STOCKHOLM 1.0

#=GF AC   RF00862
#=GF ID   mir-491
#=GF DE   microRNA mir-491
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   60.10
#=GF NC   52.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000319;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF WK   Mir-491_microRNA_precursor_family
#=GF SQ   5


AACN010707222.1/279-362  UUGACUUAGCUGGGUAGUGGGGAACCCUUCCAUGAGGAGUAGAACACUCCUUAUGCAAGAUUCCCUUCUACCUGACUGGGUUGG
AAHY01037827.1/9529-9612 UUGACUUAGCUGGGAAGUGGGGAACCCUUCCAUGAGGAGUAGAACACUCCUUAUGCAAGAUUCCCUUCUACCUGACUGAGUUGA
CR937052.2/62844-62927   UUGACUUAGCUGGGAAGUGGGGAACACUUCCGUGAGGAGUAGAGCACUCCUUAUGCCAGAUUCCCUUCUACCUGGCUGGGUUGA
AAIY01312167.1/1228-1146 UUGAUUUAGCUAGGUAGUGGGGAACCUUCCCACAAGGAGUAGAACACAUGUUAUGU-AACUGCCCUUCUACCUGACUGGGUGGA
AL445624.3/151725-151642 UUGACUUAGCUGGGUAGUGGGGAACCCUUCCAUGAGGAGUAGAACACUCCUUAUGCAAGAUUCCCUUCUACCUGGCUGGGUUGG
#=GC SS_cons             ::<<<<<<<-<<<<<<<-<<<<<<--<<<-<<<<<<<<<<_____>>>>>>>>>>->>>->>>>>>->>>>>>>->>>>>>>::
#=GC RF                  UUgaccuaGCugGGuaGUgGGGaaCccuuCCaugagGaGuAGAACaCuCcuuauGcaagauuCCCuUCuaCCugaCugggucGa
//
# STOCKHOLM 1.0

#=GF AC   RF00863
#=GF ID   mir-BART17
#=GF DE   microRNA mir-BART17
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   100.00
#=GF TC   112.80
#=GF NC   50.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000321;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16540699
#=GF RT   A combined computational and microarray-based approach identifies novel
#=GF RT   microRNAs encoded by human gamma-herpesviruses.
#=GF RA   Grundhoff A, Sullivan CS, Ganem D
#=GF RL   RNA. 2006;12:733-750.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   2


AJ507799.2/139894-139995 GUUGAACAGGAUGUGGCACCCUAAGAGGACG-CAGGCAUAC-AAGGUUAUUACCCAGUCCUUGUAUGCCUGGUGUCCCCUUAGUGGGACGCAGGCCUAGGUAGC
AY037858.1/134283-134386 CUUACGCGGCCUGCGGAACCCUAAGAGGGGGGCCUGCACGCCGAGGUUAUUUCCCAGCCCUUCGAUGCAUGGUCCCCCCUUAGUGGACUGCAGGCCCAUGUAGC
#=GC SS_cons             ::::::::<--<<<<---<<<<<<<-<<<<<-<<<<<<<<<-<<<<____________>>>>>>>>>>>>->>>>>>->>>>>->>-->>>>-->:::::::::
#=GC RF                  gUUaaaCaGgauGcgGaACCCuaaGAGGggggCagGCauaccaaGGUUAUUuCCCAGuCCuuguauGCcuGGuccCCCCuuaGUGGaacgCaGGCCuAuGUAGC
//
# STOCKHOLM 1.0

#=GF AC   RF00864
#=GF ID   mir-BART20
#=GF DE   microRNA mir-BART20
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   100.00
#=GF TC   102.10
#=GF NC   42.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000322;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16557291
#=GF RT   Epstein-Barr virus microRNAs are evolutionarily conserved and
#=GF RT   differentially expressed.
#=GF RA   Cai X, Schafer A, Lu S, Bilello JP, Desrosiers RC, Edwards R, Raab-Traub
#=GF RA   N, Cullen BR
#=GF RL   PLoS Pathog. 2006;2:e23.
#=GF RN   [2]
#=GF RM   20219930
#=GF RT   Comprehensive analysis of Rhesus lymphocryptovirus microRNA expression.
#=GF RA   Riley KJ, Rabinowitz GS, Steitz JA
#=GF RL   J Virol. 2010;84:5148-5157.
#=GF WK   MicroRNA
#=GF SQ   2


AY037858.1/143731-143811 GAGGGCCAGUUGAAGCAGGCAUGUCUUCAUUCCUGAUUUCCUGAUGGCAUGAAACACAUGGCCUGUUCCUAUUGGCACCUU
AJ507799.2/148327-148406 UAGGGCCUAUUGUAGCAGGCAUGUCUUCAUUCCUGCGUACCGAAUGGCAUGAAG-GCACAGCCUGUUACCAUUGGCACCUU
#=GC SS_cons             :<<<<<<-<<-<<<<<<<<<-<<<<<<<<<-<<____________>>->>>>>>->>>-->>>>>>>>>->>->>>->>>:
#=GC RF                  uaGGGCCaauUGuagCaGGCAuGucuuCauUCCUGauUuCCuaAUGGCauGaagcaCauaGCCuGuuaCuauUGGCACCuU
//
# STOCKHOLM 1.0

#=GF AC   RF00865
#=GF ID   MIR169_5
#=GF DE   microRNA MIR169_5
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   44.30
#=GF NC   43.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00098
#=GF DR   MIPF; MIPF0000323;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19939267
#=GF RT   High throughput approaches reveal splicing of primary microRNA transcripts
#=GF RT   and tissue specific expression of mature microRNAs in Vitis vinifera.
#=GF RA   Mica E, Piccolo V, Delledonne M, Ferrarini A, Pezzotti M, Casati C, Del
#=GF RA   Fabbro C, Valle G, Policriti A, Morgante M, Pesole G, Pe ME, Horner DS
#=GF RL   BMC Genomics. 2009;10:558.
#=GF RN   [2]
#=GF RM   17659282
#=GF RT   Cloning and characterization of microRNAs from Brassica napus.
#=GF RA   Wang L, Wang MB, Tu JX, Helliwell CA, Waterhouse PM, Dennis ES, Fu TD, Fan
#=GF RA   YL
#=GF RL   FEBS Lett. 2007;581:3848-3856.
#=GF WK   MicroRNA
#=GF SQ   6


AAAA02026104.1/123-1       --AAUAAGAACCACUCAGGCUAGCC-AAGGAG--ACUGCCCAUG-AACCA------------GCUUAAAGGAUCAUU------AAAUUG-CUAAUCCUUC----AGGGAGGA-CACAGGCAAGUCAUCCUUGGCUAUCAGA----GAUAAGUCCUUA---
AACV01018924.1/19093-19233 GUGACAAGAAUCACUCAGGCUAGCC-AAGGAG--ACUGCCCAUGAAACCU------------GCUGAAAGGAUCAUUUUCUGAAUAAUAAUUAAUGAUCCUUACACACAAGGACACAGGCAAGUCAUCCUUGGCUACCAGA----GCUAAACCCUUGUCU
AASG02003632.1/6210-6338   AAGAGAAGAGUCUGCCAGACUAGCC-AAGGAG--ACUGCCCG---AAGC-------------AGAAAAAGGGUCUC-------AAAAA--CUGAAGCCACUUAGAUGCAUCG-GGCGGGCAAGUCAUCCUUGGCUACCAGACAACGCC--ACUCUUUUCU
AARH01003347.1/61012-61135 UCGAGAAGAGUCUGUCAGCAUAGCC-AAGGAG--ACUUCCCAUA--ACCA------------AUUAAGAAGUUGCU-------A-AUU--CUAACCACUUG---UCUCAUAG-UGUGGGCAAGUCGUCCUUGGCUACCGAA----CAUC-ACUCUUAUCU
AY551246.1/188-45          AGGAUGAGAGCCGCUCAGGCUAGCC-AAGGAG--ACUGCCUGUGAGAUCACAUAUGCAGAAAGCAGCUAGAAAUGC-------AUCUU--CUUCUACUGCACAUGAGCAGAGACACAGGCAAGUCAUCCUUGGCUACCAGA---UGCGA-GCUCUCAUCG
AM447150.1/70671-70532     GAGAUAAGAGCCGGUCAGUUUAGCCGAAGGAAUGACUGCCUAAA-GACCACGGAAUC-----GCUUUGUGGAUAAUU------ACAUU--CAGUGUUUUGAAACCUGGUGGA-UUUAGGCAAGUCAUCCUUGGCUACCAGA----CGAG-ACUCUUUAUC
#=GC SS_cons               <-<<<<<<<<<<--<--<-----<-.<-<<-<..--<<<<<<<<._____............______________......._____..______________________.>>>>>>>>-->-->>->->---->-->-....>---.>>>>>>>>>>
#=GC RF                    gaGacaAGaGccaguCAGgcUAGCC.AAGGAg..ACUGCCcgug.aAcCA............gcuaaaAGGaUuau.......AuAuU..CUaauucUucauAuaugcAgag.cacgGGCAAGuCAUCCUUGGCUACCAgA....gaua.gCuCUuguCc
//
# STOCKHOLM 1.0

#=GF AC   RF00866
#=GF ID   mir-BART3
#=GF DE   microRNA mir-BART3
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   66.50
#=GF NC   52.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.09 -Z 549862.597050 CM SEQDB
#=GF CL   CL00097
#=GF DR   MIPF; MIPF0000324;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16557291
#=GF RT   Epstein-Barr virus microRNAs are evolutionarily conserved and
#=GF RT   differentially expressed.
#=GF RA   Cai X, Schafer A, Lu S, Bilello JP, Desrosiers RC, Edwards R, Raab-Traub
#=GF RA   N, Cullen BR
#=GF RL   PLoS Pathog. 2006;2:e23.
#=GF RN   [2]
#=GF RM   16540699
#=GF RT   A combined computational and microarray-based approach identifies novel
#=GF RT   microRNAs encoded by human gamma-herpesviruses.
#=GF RA   Grundhoff A, Sullivan CS, Ganem D
#=GF RL   RNA. 2006;12:733-750.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   2



EU828627.1/838-913       UUUGGUGGGACCUGAUGCUGCUGGUGUGCUGUAAAUAAGUGCCUAGCACAUCACGUAGGCACCAGGUGUCACCAGG
AADB02183564.1/4826-4752 UUUGGUGGAACCUAGUGUUAGUGUUGUGCUGUAAAUAAGUGUCCAGCGCACCAC-UAGUCACCAGGUGUCACCGGA
#=GC SS_cons             :<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<____________>>>>>>>>>>>->>>->>>>>>>>->>>>>>>:
#=GC RF                  UuuGGuGgaaCCugguGcuaguGguGuGCugUAAAUAAGUGuCcaGCaCacCacGuaguCaccaGGuGuCaCCaga
//
# STOCKHOLM 1.0

#=GF AC   RF00867
#=GF ID   mir-BART5
#=GF DE   microRNA mir-BART5
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   100.00
#=GF TC   107.30
#=GF NC   44.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000326;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16557291
#=GF RT   Epstein-Barr virus microRNAs are evolutionarily conserved and
#=GF RT   differentially expressed.
#=GF RA   Cai X, Schafer A, Lu S, Bilello JP, Desrosiers RC, Edwards R, Raab-Traub
#=GF RA   N, Cullen BR
#=GF RL   PLoS Pathog. 2006;2:e23.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20219930
#=GF RT   Comprehensive analysis of Rhesus lymphocryptovirus microRNA expression.
#=GF RA   Riley KJ, Rabinowitz GS, Steitz JA
#=GF RL   J Virol. 2010;84:5148-5157.
#=GF WK   MicroRNA
#=GF SQ   2


AJ507799.2/139661-139749 GCUCUGUGGCACCUCAAGGUGAAUAUAGCUGCCCAUCGACGUAUCGCUGGAAACCGGUGGGCCGCUGUUCACCUAAAGUGACGCAAGGU
AY037858.1/134008-134096 UUGCUGCGGCACCGUAAGGUGAAUAUAGCUGCCCAUUGAUGUCUGUUUAGAACCCGGUGGGCCGCAGUUCACCUACAGUGACGCAGUGA
#=GC SS_cons             <<<<<<<<-<<<----<<<<<<<<---<<-<<<<<<<<________________>>>>>>>>->>->>>>>>>>--->>>->>>>>>>>
#=GC RF                  gcgcuGcGGCaCCuuAaGGuGaauAUAGCUGCCCaucGAuGUaUguuUaGAAaCCgguGGGCCGCaguuCaCCuAaAGuGACgCagcgc
//
# STOCKHOLM 1.0

#=GF AC   RF00868
#=GF ID   mir-BART15
#=GF DE   microRNA mir-BART15
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   83.00
#=GF TC   87.50
#=GF NC   37.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000327;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16557291
#=GF RT   Epstein-Barr virus microRNAs are evolutionarily conserved and
#=GF RT   differentially expressed.
#=GF RA   Cai X, Schafer A, Lu S, Bilello JP, Desrosiers RC, Edwards R, Raab-Traub
#=GF RA   N, Cullen BR
#=GF RL   PLoS Pathog. 2006;2:e23.
#=GF RN   [2]
#=GF RM   20219930
#=GF RT   Comprehensive analysis of Rhesus lymphocryptovirus microRNA expression.
#=GF RA   Riley KJ, Rabinowitz GS, Steitz JA
#=GF RL   J Virol. 2010;84:5148-5157.
#=GF WK   MicroRNA
#=GF SQ   2


AY037858.1/133863-133941 UGUGCCGCUUCGAGGUAAACAUCGGCUUACUGAAGUCUCUUAGUAAGGUCAGUGGGCCUGUUUCCCUCACAGAGACACA
EF102892.1/879-956       UGUGCCGCUUGGAGGGAAACAU-GACCACCUGAAGUCUGUUAACCAGGUCAGUGGUUUUGUUUCCUUGAUAGAGACACA
#=GC SS_cons             <<<<-<-<<---<<<<<<<<<--<<-<--<<<<--<<<<_____>>>>>>>>-->->>>>>>>>>>>--->>->->>>>
#=GC RF                  uGuGCCGCuUgGagGgaaaCaUcggCcuaCuGaAGuCugUUAaucaGguCaGUGguccuGuuucCcugAuaGAGACaCa
//
# STOCKHOLM 1.0

#=GF AC   RF00869
#=GF ID   mir-BART7
#=GF DE   microRNA mir-BART7
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   88.00
#=GF TC   92.50
#=GF NC   56.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000328;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16557291
#=GF RT   Epstein-Barr virus microRNAs are evolutionarily conserved and
#=GF RT   differentially expressed.
#=GF RA   Cai X, Schafer A, Lu S, Bilello JP, Desrosiers RC, Edwards R, Raab-Traub
#=GF RA   N, Cullen BR
#=GF RL   PLoS Pathog. 2006;2:e23.
#=GF RN   [2]
#=GF RM   16540699
#=GF RT   A combined computational and microarray-based approach identifies novel
#=GF RT   microRNAs encoded by human gamma-herpesviruses.
#=GF RA   Grundhoff A, Sullivan CS, Ganem D
#=GF RL   RNA. 2006;12:733-750.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   2


AJ507799.2/146425-146510 UCCAGUGUCCUGAUCCUGGACCUUGACUAUGAAACAAUUCUAAAAAAAUGCAUCAUAGUCCAGUGUCCAGGGACAGUGCACUCGGA
AY037858.1/141820-141903 UCCCGUGUCUUGAUCCUGGGCAUGGGCUAUGAAACAGUUCU-AACAAUUGGAUCAUAG-CCAGUGUCCAGGGACGGUGCACCGGGA
#=GC SS_cons             <<<<<<<<-<<<-<<<<<<<<<<-<<<<<<<<--<<-<<______>>->>-->>>>>>>>->>->>>>>>>>->>>->>>>>->>>
#=GC RF                  uCCgGuGuCcuGAuCCuGGaCcuuGaCuauGaAACaauuCUAAAaaaauGgAuCauaGuCCagUGuCCaGGgACagUgCaCcgGGa
//
# STOCKHOLM 1.0

#=GF AC   RF00870
#=GF ID   mir-423
#=GF DE   microRNA mir-423
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   59.40
#=GF NC   54.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000329;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues.
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF RN   [2]
#=GF RM   19170227
#=GF RT   Identification and expression profiling of microRNAs during bovine oocyte
#=GF RT   maturation using heterologous approach.
#=GF RA   Tesfaye D, Worku D, Rings F, Phatsara C, Tholen E, Schellander K, Hoelker
#=GF RA   M
#=GF RL   Mol Reprod Dev. 2009;76:665-677.
#=GF RN   [3]
#=GF RM   19633723
#=GF RT   Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed
#=GF RT   upon viral infection.
#=GF RA   Glazov EA, Kongsuwan K, Assavalapsakul W, Horwood PF, Mitter N, Mahony TJ
#=GF RL   PLoS One. 2009;4:e6349.
#=GF WK   Mir-423_microRNA_precursor_family
#=GF SQ   4


AACN010109711.1/39-119    AGGAAGUUAGGCUGAGGGGCAGAGAGCGAGACUUUU-CUAUUUUCCAAAAGCUCGGUCUGAG-GCCCCUCAGUCUUGCUUCCU
AALT01504263.1/495-419    AGGAAGUUAGGCUGAGGGGCAGAGAGCGAGACUUUU-CUAUUUUCCAAAAGCUCGGUCUGAGAGCCCCUUCGUGUG-----CU
AAPY01128697.1/4155-4231  AGGAAGGUGGGCUGAGGGAC--AGAGUGAAGCUCUUCUUUUUUUCCAAAAGCUUGGUCUAA--GGCCCU--GUCUUGCUUCCU
AC104984.14/146492-146412 AGGAAGUUAGGCUGAGGGGCAGAGAGCGAGACUUUU-CUAUUUUCCAAAAGCUCGGUCUGAG-GCCCCUCAGUCUUGCUUCCU
#=GC SS_cons              <<<<<<<-<<<<<<<<<<<<--<<<-<<<<-<<<<<._________>>>>>>>>>->>>---.>>>>>>>>>>>>->>>>>>>
#=GC RF                   aGGaaGcUaggCugaGGGgCAGaGaGcGaGaCuuuu.cUaUUUUCCaaaaGCuCgGuCugAG.GcCCCucaGucuugCuuCCu
//
# STOCKHOLM 1.0

#=GF AC   RF00872
#=GF ID   mir-652
#=GF DE   microRNA mir-652
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   76.20
#=GF NC   74.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.02 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000333;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20668074
#=GF RT   Identification and analysis of expression of novel microRNAs of murine
#=GF RT   gammaherpesvirus 68.
#=GF RA   Zhu JY, Strehle M, Frohn A, Kremmer E, Hofig KP, Meister G, Adler H
#=GF RL   J Virol. 2010;84:10266-10275.
#=GF WK   Mir-652_microRNA_precursor_family
#=GF SQ   13


ABVD01051371.1/1994-2090   UGUGCAGCCUGUGCACAUCACAAUUCCAG---GGGGUGCCAUUCACA---UCGACCACACUGUGACUGGU-ACCCUCUGGAGUUGUGCAGUGCACAACCUGGCC
AACN010214799.1/755-660    UGUGUGGGCUGUGUGCUCCACAACUCCAC----GGGUGUCAUUCACA---UAGACUACACUGUGAAUGAU-GCCACCUAGAGUUGUGCAGUACACAACCUUCAC
ABRN01090407.1/4522-4617   UGUUCAGGUUGCUCACUGCAUAAUCCUAG---AGGGCUCCAUUCACA---UGGAGUAUGGUGUGAAUGGU-GCC-CUUAGAGUUGUGCAGUGCACAACAUGCCC
ACBE01245880.1/1926-2022   UGGCCAGGUUGUGCACUGCACAACUCUAGAA---GGUACCAGUCACA---GUGUGAUCUAUGUGCAUGGU-GCCCUCUAGAAUUGUGUAGUGCACAAGCUGCAC
ABRT010494874.1/190-94     GCAACAGGUUGUGCACUGCACAACUCCAA---GGGGUGCCAGUCACAUUGCAGACUCUG---UGAAUGGUGACC-CCUUGAGUUGUGCAGUGUACAGUCUGUAC
ABGA01152213.1/4819-4914   UGCACAGGUUGUGCACUGCACAACUCCAA---GGGAUGCCAAUCACAUUGCAGACUAUG---UGAAUGGU-GAC-CCUGGAGUUGUGCAGUGCACAGUCUGUAC
ABRR01183245.1/1634-1731   ACGAAUGGCUAUGCACUGCACAACCCUAGGAGAGGGUGCCAUUCACA---UAGACUGUAAU-UGAAUGGC-GCC-ACUAGGGUUGUGCAGUGCAUAGCCAUUCG
AANU01095443.1/40917-41014 ACGAAUGGCUAUGCACUGCACAACCCUAGGAGAGGGUGCCAUUCACA---UAGACUAUAAU-UGAAUGGC-GCC-ACUAGGGUUGUGCAGUGCACAACCUGCAC
AALT01529428.1/6713-6810   AUGAAUGGCUGUGUCCUACACAACCCUAGUAGAUGGUGCCAUUCACA---UAGACUAUAAU-UGAAUGGC-GCC-ACUAGGGUUGUGCAGUGCACAGCCUAUAC
ABRP01145045.1/4347-4444   AUGAGCGGCUAUGUACUGCACAACCCUAGGAAUGUGUGCCAUUCACA---UAGACUAAAAU-UGAAUGGC-GCC-ACUAGGGUUGUGCAGUGUACAACCUACAC
AAHY01203960.1/259-162     AGGAACAGCUAUGUACUGCACAACCCUAGGAGGGGGUGCCAUUCACA---UAGAGUAUAAU-UGAAUGGC-GCC-ACUAGGGUUGUGCAGUGUACAGCCUACAC
AAKN02039981.1/11479-11382 ACGAAUGGCUAUGCACUGCACAACCCUAGGAAGGGGUGCCAUUCACA---UGGACUAUAAU-UGAAUGGC-GCC-ACUAGGGUUGUGAAGUGUACAACCUACAC
AL360224.14/82487-82584    ACGAAUGGCUAUGCACUGCACAACCCUAGGAGAGGGUGCCAUUCACA---UAGACUAUAAU-UGAAUGGC-GCC-ACUAGGGUUGUGCAGUGCACAACCUACAC
#=GC SS_cons               :::::::::::<<<<<<<<<<<<<<<<<<--.--<<<<<<<<<<<--...<<_____>>--.>>>>>>>>.>>>.->>>>>>>>>>>>>>>>>>::::::::::
#=GC RF                    uggaaaGGcUgugcaCugCACAAccCuAggA.aGGgcgCCAuuCACA...uaGAcUauaaU.UGaaUGGc.gcC.acUaGggUUGUGcaGugcaCAacCUgcaC
//
# STOCKHOLM 1.0

#=GF AC   RF00873
#=GF ID   mir-550
#=GF DE   microRNA mir-550
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   61.40
#=GF NC   49.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000334;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-550_microRNA_precursor_family
#=GF SQ   3


AADB02010436.1/149995-150091   UGAUGCUUUGCUGGCUGGUGCAGUGCCUGAGGGAGUAAGAGCCCUGUUGUUGUCAGAUAGUGUCUUACUCCCUCAGGCACAUCUCCAGCGAGUCUCU
AACC02000087.1/2375233-2375137 UGAUGCUUUGCUGGCUGGUGCAGUGCCUGAGGGAGUAAGAGCCCUGUUGUUGUAAGAUAGUGUCUUACUCCCUCAGGCACAUCUCCAACAAGUCUCU
AANU01125643.1/4981-5077       UGAUGCUUUGCUGGCUGGUGCAGUGCCUGAGGGAGUAAGAGCCCUGUUGUUGUAAGAUAGUGUCCUACUCCCUCAGGCACAUCUCCAGCAAGUUCCU
#=GC SS_cons                   :::::::<<<<<<<--------<<<<<<<<<<<<<<<<<<-<-<<<<<_______>>>>>->>>>>>>>>>>>>>>>>>>---->>>>>>>::::::
#=GC RF                        UGAUGcUuuGcuGGcUGGUGcAGuGCCuGaGGGaGuagGaGCcCugucGUUGUaAgacaGUGuCcuaCuCCCuCaGGCaCAUcUCCagCaaGUcucU
//
# STOCKHOLM 1.0

#=GF AC   RF00874
#=GF ID   mir-BART12
#=GF DE   microRNA mir-BART12
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   101.30
#=GF NC   39.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000335;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16557291
#=GF RT   Epstein-Barr virus microRNAs are evolutionarily conserved and
#=GF RT   differentially expressed.
#=GF RA   Cai X, Schafer A, Lu S, Bilello JP, Desrosiers RC, Edwards R, Raab-Traub
#=GF RA   N, Cullen BR
#=GF RL   PLoS Pathog. 2006;2:e23.
#=GF RN   [2]
#=GF RM   20219930
#=GF RT   Comprehensive analysis of Rhesus lymphocryptovirus microRNA expression.
#=GF RA   Riley KJ, Rabinowitz GS, Steitz JA
#=GF RL   J Virol. 2010;84:5148-5157.
#=GF WK   MicroRNA
#=GF SQ   2


AY037858.1/143257-143352 UUCCUGGAGCCGGUGACCUGAGACCCACCCUUCUCGACGGGGCAGGUGUUAUAAGUGUCCUGUAGAGUAUGGGUGUGGUUUUAGUGCACGCGGGAG
AJ507799.2/147879-147973 UCCGUGUAGCUGGUGACCUAACACCCGCCCAUCACCACCGGACAGAUUCUGAACUUGUCCUGUGGUGUU-UGGUGUGGUUUUGGGGUACGCAGGAG
#=GC SS_cons             :::::::::<<<<<<-<<<<<-<<<<<<<---<<<<<<-<<<<<--<<___>>-->>>>>->>>>>>---->>>>->>>->>>>>->>>->>>:::
#=GC RF                  UuCgUGuAGCcGGugAcCuaagaCCCaCCCaUCuCcaCgGGaCaGauguUacaauuGuCCUGugGaGUauuGGuGUGGuUuuaGgGcaCGCgGGAG
//
# STOCKHOLM 1.0

#=GF AC   RF00875
#=GF ID   mir-692
#=GF DE   microRNA mir-692
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   42.00
#=GF TC   42.00
#=GF NC   41.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000336;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   MicroRNA
#=GF SQ   11


AC125143.4/44733-44813       AACCAGC-GCAGACUG--GCGCGC-CCCAGGGAUCU--------CUGGGUG--AGUAUCUCUUUGAGCGCCUCACUCUCAAGCACAACUAGGAGG
AAHY01107679.1/13131-13051   AACCAGC-GCAGACUG--GCGCGC-CCCAGGGAUCU--------CUGGGCG--AGUAUCUCUUUGAGCGCCUCACUCUCAAGCACGACUAGGAGG
CT990572.1/76704-76784       AACCAGU-GCAGACUG--GCACGC-CCCAGGGAUCU--------CUGGGCG--AGUAUCUCUCUGAGCGCCUCACUCUCAAGCACGACUAGGAGG
S89400.1/567-644             AACCAGU-GCAGACUG--GCGUGG-CCCAGGCAUCU--------CUGGGCG--AGUAUCUCUUUGAGCGCCUCACUCUGAAGCACGACU---AGG
AANU01291939.1/123983-124065 CAACCUCAACAGGCUG--G-CCGG-CCCGGAGG-CUGGG-----CUGGGUG--AGUAUCUCUUCGAAAGGCUCACUCUCAAGCACGACUAAGAGC
AY466472.1/450-534           CAACCUCCACAGGCUG--G-GUGG-CCCGGAGGCUGGG------CUGGGCGAGUAUCUCUCUUCGAAAGGCUCACUCUCAAGCACGACUAAGAGC
AAYZ01435150.1/829-738       CAACAUCCACAGAGUGCAGCCCCG-CCAGGGAGCCCAGGCUGGCCUGGGCG--AGUGCCUCUUCGAAAGGCUCACUCUGAAGCACGACUAGGGGU
AAKN02053482.1/190185-190264 CCUCCGC---AGGCUG--GACGGUCCCCAGG---CUGGG-----CUGGGCG--AGUACCUCUUUGAAAGGCUCACCCUUAAGCACGACUAGGAGG
AAGV020070009.1/1724-1649    CCUCAGC---AGGCUG--GCUGGCCCACAGG---CC--------C-GGGUG--GGUAUCUCUUUGAAAGCCCCACCCUCAAGCACAACUAGGAGC
AAHX01057570.1/24684-24764   UACCAGC-GCAGACUG--GCGUGG-CCCAGGCAUCC--------CUGGGCG--AGUAUCUCUUUGAGUGCCUCACUCUCAAGCACGACUAGGAGG
AACN010285857.1/14-94        -AACCUCCGCAGGCUG--G-CC-C-CCCCCAGG-CUGGG-----CUGGGCG--AGUAUCUUUUCGAAAGGCUCAUUCUCAAGCACGACUAGGAGC
#=GC SS_cons                 :::::<<.--<<<-<<..<-<<<<.<--<<<<<<<<--......<_____>..>>->>>>>>-->->>>>->>>->>>--->>::::::::::::
#=GC RF                      cAaCagC.aCAGgCUG..gcccgc.CCCaggggcCugG......CUGGGcG..aGUgccucuUuGAgcggCuCACcCUcAAGcACGACUAGGAGg
//
# STOCKHOLM 1.0

#=GF AC   RF00876
#=GF ID   mir-684
#=GF DE   microRNA mir-684
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000337;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF WK   MicroRNA
#=GF SQ   28


AAHY01017673.1/7990-8076   -UGUAGGGCA--AU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--UGA--AC----AAAAU----G--A-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGCGUCUUGC
AAHY01033490.1/12295-12382 AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--UGA--AC----AAAAU----G--A-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGUGUCUUGU
AAHX01070223.1/10164-10077 AUGUAGGGCA--AC--CUGUCUUUAAGUAGGGAUAAAUUACUCU--UGA--AC----GAAGU----G--A-----UCCUAGAUAGU-UUUCCCUUC-AAGCCAAGCGUCUUGU
AALT01227370.1/542-629     AUGUAGGGCG--AU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--AAA--AG----AAAUG----A--A-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGCGUCUUGU
AANU01171090.1/4870-4959   AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--AAA--AC----AAAAA----GGAA-----UCUUAGAUAGU-UUUCCCUUC-AAGUCAAGCGUCUUGU
AAQQ01308870.1/13316-13401 AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGGUAAAUUACUCU--UAA--AA----AAGAU----U--C-------CUAGAUAGU-UUUCCCUUC-AAGUCAAGCGUCUUGU
ABDC01385734.1/1611-1522   AUGUAGGGUA--AU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--AAA--AA----GAAAA----UGAA-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGUGUCUUGU
AAPY01680387.1/926-1017    AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGAUAAACUACUCU--UAA--AG----AAAAAAAGGA--A-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGUGUCUUGU
AAYZ01205875.1/2300-2212   AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGGUAAAUUACUCU--UAA--AA----AAAAU----G-AA-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGCGUCUUGU
AAIY01051207.1/594-681     AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGGUAAACUACUCU--CAC--AG----AAAAG----A--A-----GCCUAGAUAGU-UUUCCCUUC-AAGUUAAGCGUCUUGU
AANN01819085.1/911-824     AUGCAGGGCA--AU--CUGUCUUUAAGUAGGGGUAGAUAACUCU--AAA--AG----AAAUG----A--A-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGCGUCUUGU
AADB02009763.1/68566-68477 AUGUAGCGCA--AU--CUGUCUUUAGGUAGGGAUAAAUUACUCU--AAA--ACAA--AAAAC----A--A-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGUGUCUUGU
AC150624.3/11004-11092     AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGGUAAAAUACACU--AAA--AG----AAAUG----A--A-----UCCUAGAUAUUCUUUUCCUUC-AAGUCAAAUGUCUUGU
AAFC03101346.1/44581-44494 AUGUAGAGCG--AU--CUGUCUUUAAGCAGAGAUAAAUUACUCU--AAA--AG----AAAUG----A--A-----UCCUGGAUAGU-UUUCUCUAC-UAGUCAAGCAUCUUGU
AAPN01333701.1/324-413     AUGUAGGGCAGUCU--CUGUCUUUAAGUAGGGGUAAAUUACUCU---AA--AG----AAAUG----G--A-----UCCUAGAUAGU-UUUCCCUUCAAAGUCAAGCGUCUUGU
AAFR03016021.1/93939-94027 AUGUAGGGCA--AUCUCUGUCUCUCAGUAGGGAUAAAUUACUAU---AA--AG----AAAAU----G--A-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAACAUCUUGU
AANG01811140.1/860-946     AUGUAGGGUG--AU--CUGUCUCAAAUAG-GAACAAAUUACUCU--AAA--GG----AAAUA----A--A-----UCCUAGAUAGU-UUUCCACUC-AAGUCAAGCAUUUUGU
AC191239.1/20428-20340     AGGCAGGGCA--GU--CUGUCUUCAAGUGGGGGUAAAUGACUGU--AAA--ACAGA-AAAAA----A--A-----UCCUAGA--GU-UUUCCCUUC-AAGUCAAGCAUCUUGU
AB220475.1/911-1000        AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--AAA--ACAA--AAAAG----A--A-----UCUUAGAUAGU-UUUCCCUUC-CAGUCAAGCGUCUUGU
AAWR02013748.1/51824-51911 AUGCUGGGCA--GU--CUGUCUUUAAGUAGGGGUAAAUUACUCU--AAA--AG----AAAUU----A--A-----UCUUAGAUAGU-UUUCCCUUU-AGGUCAAGUGUCUUGU
AAKN02048266.1/17804-17715 AUGUAGGGCA--AU--CUGUCCUUAAGUAGGAAUAAAUUACUCUUUUUA--AA----AAAAU----A--A-----UUCUAGAUAGU-UUUCCCUUU-AAGUCAAGUGUCUUGU
AAGV020257289.1/820-733    AUAUAGGGCA--CU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--AAA--AG----AAAUG----A--A-----UACUAGAUAGU-UUUCCCUUC-AAGUCAAGCAUCUUGU
AJ720405.1/915-999         UUGUAGAGCA--AU--CUGUCUA--AGUAGGGGUAAAUUACUCU--UAA--AA----AAAAA----A--------UCCUAGGUAGU-UCUCCCUUC-UAGUAAAGCGUCUUGU
ABRR01297734.1/791-878     AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--AAA--AG----AAAUG----A--A-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGUGUCUUGU
AC015909.14/132622-132530  AGGUAGGGUA--AU--CUGUCUUUAAGUAGGGAGAAAUUGCUCU--AAA--AA----AAAAA----A--AAAGAAUCCUAGAUAGU-UUUCCCUUC-AAGUCAAGCAUCUUGU
BC062713.1/862-951         AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--AAAACAA----AAAA--------G---AAUCCUAGAUAGU-UUUCCCUUC-AAGUCAAGCGUCUUGU
BT021041.1/859-946         AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--AAA--AG----AAAUG----A--A-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGCGUCUUGU
BC102379.1/902-989         AUGUAGGGCA--AU--CUGUCUUUAAGUAGGGAUAAAUUACUCU--AAA--A----GAAAUG----A--A-----UCCUAGAUAGU-UUUCCCUUC-AAGUCAAGCGUCUUGU
#=GC SS_cons               :::<<<<<<<..--..-<<-<<<-----<<<<<-<<<<<<-<<<..--<..__...._____...._.._.....>--->>>>>>>.>>>>>>>--.>>>->>-->>>>>>>:
#=GC RF                    AUGuagGgcg..AU..CUGUCuuUAAGUaGGGaUaaAuuaCuCu..aAa..Aa....AAAaa....a..A.....uCCUaGauagU.uuuCCCuUC.aaGUCAAGcguCuugU
//
# STOCKHOLM 1.0

#=GF AC   RF00877
#=GF ID   mir-592
#=GF DE   microRNA mir-592
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   81.50
#=GF NC   53.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000340;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF WK   Mir-592_microRNA_precursor_family
#=GF SQ   5


AAHY01052276.1/107953-108040   UAUUAUGCCAUGACAUUGUGUCAAUAUGCGAUGAUGUGUUGUGAUGGCACAGCGUCAUCACGUGGUGACGCAACAUCAUGACGUAAGA
AACC02000001.1/1404789-1404876 UAUUAUGCCAUGACAUUGUGUCAAUAUGCGAUGAUGUGUUGUGAUGGCACAGCGUCAUCACGUGGUGACGCAACAUCAUGACGUAAGA
AAYZ01212552.1/5149-5062       UAUUAUGCCAUGACAUUGUGUCAGUAUGCGAUGAUGUGUUGUGAUGGCACAGCGUCAUCACGUGGUGACACAGCAUCAUGACAUAAAA
AAQQ01768898.1/161-74          UAUUAUGCCAUGACAUUGUGUCAGAAUGCGAUGACUGGUUGCGAUGGCACAGCGUCAUCACGUGGAGACGCAACAUCAUGACGAAAGA
AAPN01131115.1/15145-15229     UAUUAUGCCACAACACUGUGUCACUAUGUGAUG---UGUUGUGAUGGCACAGCCUCAUCACAUAGUAAUGCAACAUCAUGACAUAAAU
#=GC SS_cons                   ::<<<<<-<<<<<--<<<<<<<<-<<<<-<<<<<<<<--<<<<____>>>>>>>>>>>>->>>>->>>>>>>>-->>>>>->>>>>::
#=GC RF                        UAuuacGCCauGaCAuuGcGucaacacGcGauGacgcGUuGuGAUGGCaCagcguCauCACgugGugaCgCaaCAuCauGACguaaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00878
#=GF ID   mir-456
#=GF DE   microRNA mir-456
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   78.40
#=GF NC   47.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000341;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16750530
#=GF RT   Identification of microRNAs from different tissues of chicken embryo and
#=GF RT   adult chicken.
#=GF RA   Xu H, Wang X, Du Z, Li N
#=GF RL   FEBS Lett. 2006;580:3610-3616.
#=GF RN   [2]
#=GF RM   18256158
#=GF RT   MicroRNA profile of Marek's disease virus-transformed T-cell line MSB-1:
#=GF RT   predominance of virus-encoded microRNAs.
#=GF RA   Yao Y, Zhao Y, Xu H, Smith LP, Lawrie CH, Watson M, Nair V
#=GF RL   J Virol. 2008;82:4007-4015.
#=GF RN   [3]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning.
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   MicroRNA
#=GF SQ   5


BX004877.10/47607-47503    AUUUCCGCUGGC-------UGGUUGUGUG-------UGCAGGCAUCUUUCCAGUCUACAUGUGGAUCCAGGAGUCUGCAGGCUGGUUAGAUGGUUGUCACGUACCCAGCAAACAUCACA
AAVX01070382.1/1647-1554   UUUGAAGCCAC--------UGUGUGUGAG-------AGCAGGUAUCUUCCCAGCCUACACGUAGGUCCUGAAAUCUGCAGGCUGGUUUGAUGGUUGUCUUGCACACA----------GC
AANH01010790.1/61460-61563 CAGGUGGCUGC--------UGGCUCUGUG-------AGCAGGCAUCUUCCUAGCCUACAUGUAGAUCCAGGAAUCUGCAGGCUGGUUAGAUGGUUGUCACAUGUCUAGCUGUCUUCAUC
BAAF04097110.1/5066-4963   CAGGCAGCUGC--------UGGCUCUGUG-------AGCAGGCAUCUUCCCAGCCUACAUGUAGAUCCAGCCGUCUGCAGGCUGGUUAGAUGGUUGUCACAUAUCUGGCUGUCGUCAUC
AAPN01283735.1/3703-3587   AAGAGAGGGAGAGAGAGUGGGGAUGGGGGAAGCAAAUGCAAGCAUCU--CAGUCUUAAAUGUGGAUUCUUAAAUCUGCUGUUUCGUUAGUUGGUUGUCAUUCAUUCAUGUGCUAUCUGC
#=GC SS_cons               :::::::::::........<<<<<<<<<<.......-<<<<-<<<<<--<<<<<<<----<<<<<<______>>>>>>>>>>>>>-->>>>>->>>>>>>>>>>>>>::::::::::::
#=GC RF                    aagguaGcuag........uGggugcguG.......agCAgGCAuCuUcCcagccuAcAUGuaGaucCugaAauCugCaggcugGUUaGaUGGuUGuCacgcaccCagcuGucaUCauc
//
# STOCKHOLM 1.0

#=GF AC   RF00879
#=GF ID   mir-615
#=GF DE   microRNA mir-615
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   68.80
#=GF NC   59.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000342;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-615_microRNA_precursor_family
#=GF SQ   6


AANU01281206.1/16723-16818 CUCGGGAGGGGCGGAA-GGGGGGUCCCCGGUGCUCGGA-UCUCGAGGGUGCUUAUUGUUCGGUCCGAGCCUGGGUCUCCCUCUUCCCCCCAACCC-CCC
AC021667.21/117732-117827  CUCGGGAGGGGCGGGA-GGGGGGUCCCCGGUGCUCGGA-UCUCGAGGGUGCUUAUUGUUCGGUCCGAGCCUGGGUCUCCCUCUUCCCCCCAUCCC-CCC
AF490843.1/112503-112598   CUCGGGAGGGGCGGGA-GGGGGGUCCCCGGUGCUCGGA-UCUCGAGGGUGCUUAUUGUUCGGUCCGAGCCUGGGUCUCCCUCUUCCCCCCAACCC-CCC
AC012531.11/171554-171649  CUCGGGAGGGGCGGGA-GGGGGGUCCCCGGUGCUCGGA-UCUCGAGGGUGCUUAUUGUUCGGUCCGAGCCUGGGUCUCCCUCUUCCCCCCAACCC-CCC
ABRP01242037.1/11752-11658 CUCGGGAGGGGCGGGA-GGGGGGUCCCCGGUGCUCGG-AUCUCGAGGGUGCUUAUUGUUCGGUCCGAGCCUGGGUCUCCCUC-UCCCCCCACCCC-UCA
ABRQ01001814.1/3563-3468   CUCGGGAGGGGC-GGGAGGGGGGUCCCCGGUGCUCGGA-UCUCGAGGGUGCUUAUUGUUCGGUCCGAGCCUGGGUCUCCCUCU-CCCCCCACCCCUUCA
#=GC SS_cons               ::::<<-<<<<-<<<<.<<<<<<---<<-<-<-<--<-.-<-<<<<-<_______>->>>>>-->-->->>->>--->>>>>>>>>>>>>---->.>>:
#=GC RF                    CUCGGgAGGGGCGGGa.gGgGGGUCCCCGgUGCcCGGA.UCUCGagGgUGCUUAUcGcuCGGUCCGAgCCcGGGUCUCCCcCcuCCCCCCAaCCC.cCa
//
# STOCKHOLM 1.0

#=GF AC   RF00882
#=GF ID   MIR811
#=GF DE   microRNA MIR811
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   87.00
#=GF TC   87.10
#=GF NC   86.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000347;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16959252
#=GF RT   Rice embryogenic calli express a unique set of microRNAs, suggesting
#=GF RT   regulatory roles of microRNAs in plant post-embryogenic development.
#=GF RA   Luo YC, Zhou H, Li Y, Chen JY, Yang JH, Chen YQ, Qu LH
#=GF RL   FEBS Lett. 2006;580:5111-5116.
#=GF WK   MicroRNA
#=GF SQ   5


AC090873.4/23607-23796   GGAAACUUGAAAACUACCGUUAGAUCGAGAAAUGGACGUCCGAGAUUCGUCCACGUCACCAUGAGUUAAAAUUUAACUCGCAGAUUCACUCCUGAGUUAAACUUUU-ACUGGGAGUUAAAUUUUAACUCAUGGUGACGUGGGCGAAUCUCGAACGUUCGUUUCUGGAUCCAACGGUAGUUUCCAAGUUUCC
AP004679.3/152682-152871 GGAAACUUGAAAACUACCGUUAGAUCGAGAAAUGGACGUCCGAGAUUCGUUCACGUCAUCAUGAGUUAAAAUUUAACUCGCAGAUUCACUCAUGAGUUGAAAUUUU-ACUGGGAGUUAAAUUUUAACUCAUUGUGACGUGGACGAAUCUCGGACGUCCAUUUCUCGAUCCAACGUUAGUUUCCAAGUUUCC
AC145323.3/30444-30632   UAAUUUUCAUCCUACACCGUUAGAUCGAGAAAUGGACGUUCGAGAUUCGUCCACGUCACCAUGAGUUAAAAUUUAACUCUCAG--UAAAUUUUAACUCAUGAGUGAAUCUGCGAGUUAAAUUUUAACUCAGGGUGACGUGGACGAAUCUCGGACGUCUAUUUCUCGAUCCAACGGUGUAGAAUGAGAGUUG
AAAA02007199.1/7486-7297 GGAAACUUGGAAACUACCGUUGGAUCGAGAAAUGGACGUCCGAGAUUCGUCCACGUCACCAUGAGUUAAAAUUUAACUCGCAGAUUCACUCAUGAGUUAAAAUUUU-ACUAGGAGUUAAAUUUUAACUUAUGGUGACGUGGAUGAAUCUUGGACGUCUAUUUCUCGAUCCAACAGUAGUUUCCAAGUUUCC
U72726.1/1587-1398       GGAAACUUGGAAGCUAUCGUUGGAUCGAGAAAUGGAUGUCCGAUAUUCGUCCACAUCAACAUGAGUUAAAAUUUAACUCUCAUUAAAAUUUUAACUCAUAAGUGAA-UCUGCGAGUUAAAUUUUAUCUCUUGGUGACGUGGACGAAUCUUGGACAUCCAUUUCUCGAUCUAACGGUAGUUUCUAAGUUUCC
#=GC SS_cons             <<<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-<<<_______________________._>>>->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>->>>>>>>>>
#=GC RF                  ggaaacucgaaagccaccGuugGauCgaGaaaugGacGucCgagauuCGucCaCguCaccauGaGuuaaaauuuaaCuCucagauuaAuUuuuaauuuaaaauuuu.acuggGaGuuaaauuuuaaCuCaugguGacGuGgaCGaaucucGgaCguCcauuuCucGauCcaaCgguggcuuccgaguuucc
//
# STOCKHOLM 1.0

#=GF AC   RF00883
#=GF ID   MIR820
#=GF DE   microRNA MIR820
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   150.00
#=GF TC   154.30
#=GF NC   141.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000348;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16959252
#=GF RT   Rice embryogenic calli express a unique set of microRNAs, suggesting
#=GF RT   regulatory roles of microRNAs in plant post-embryogenic development.
#=GF RA   Luo YC, Zhou H, Li Y, Chen JY, Yang JH, Chen YQ, Qu LH
#=GF RL   FEBS Lett. 2006;580:5111-5116.
#=GF RN   [2]
#=GF RM   18353984
#=GF RT   Genome-wide analysis for discovery of rice microRNAs reveals natural
#=GF RT   antisense microRNAs (nat-miRNAs).
#=GF RA   Lu C, Jeong DH, Kulkarni K, Pillay M, Nobuta K, German R, Thatcher SR,
#=GF RA   Maher C, Zhang L, Ware D, Liu B, Cao X, Meyers BC, Green PJ
#=GF RL   Proc Natl Acad Sci U S A. 2008;105:4951-4956.
#=GF RN   [3]
#=GF RM   19903869
#=GF RT   Rice MicroRNA effector complexes and targets.
#=GF RA   Wu L, Zhang Q, Zhou H, Ni F, Wu X, Qi Y
#=GF RL   Plant Cell. 2009;21:3421-3435.
#=GF WK   MicroRNA
#=GF SQ   2


AAAA02028768.1/22398-22218 CGGCCUCGUGGAUGGACCAGGAGCUCGACAUUCCUUAAGGUCGUUCUUUCCGACCCAUACAAGGUUCCGCUGCCUGCAUUGUUCCAAGAGUGUCUUGGACAAAAGCAGGAAGUGGAACCUUGUUAAGGUCGGAACGAACUGCCUUAAGGAAGUCGAUGCUCCAGGUCCGUCCACGAGGACG
AACV01001046.1/6839-6659   CGGCCUCGUGGAUGGACCAGGAGCUCAACAUUCCUUAAGGUUGUUCUUUCAAACCCAUACAAGGUUCCACCGCCUGCAUUGUUCCAAGAGUGUCUUGGAUGAAAGUAGGAAGUGGAACCUUGUUAGGGUUGGAACGAACUGCCUUAAGGAAGUCGAUGCUCCAGGUCCGUCCAGGAGGACG
#=GC SS_cons               <<-<<<<<<<<<<<<<<<-<<<<<<<<<<-<<<<<<<<<<<-<<<<-<<<<<<<<---<<<<<<<<<<<<--<<<<<-<<<<-<<<<<_____>>>>>>>>>-->>>>>-->>>>>>>>>>>>--->>>>>>>>->>>>->>>>>>>>>>>>>>>>->>>>>->>>>>>>>>>>>>>>->>
#=GC RF                    cggccucguggacggaccAggagcucgacAuuccuuaaggcuguucuuuccgacccAuacaagguuccgcugccugcAucguuccaagAgugucuuggacgaAAgcaggAAgcggaaccuuguuAaggucggaacgaacugccuuaaggaagucgaugcuccAgguccguccacgaggAcg
//
# STOCKHOLM 1.0

#=GF AC   RF00884
#=GF ID   MIR815
#=GF DE   microRNA MIR815
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   63.00
#=GF TC   64.60
#=GF NC   62.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000349;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16959252
#=GF RT   Rice embryogenic calli express a unique set of microRNAs, suggesting
#=GF RT   regulatory roles of microRNAs in plant post-embryogenic development.
#=GF RA   Luo YC, Zhou H, Li Y, Chen JY, Yang JH, Chen YQ, Qu LH
#=GF RL   FEBS Lett. 2006;580:5111-5116.
#=GF WK   MicroRNA
#=GF SQ   3


AAAA02017903.1/18477-18397 UUUUUUAGACUC-UUAAUUUCUUUUUCU---AGGAUGAACUCUUAGGGUGUGUUUGAGGAGAAGGGGAUUGAGGAGAUUGGGGAG
AC134346.3/9712-9789       AUUCCCAAUCUUCUCUAUUUCCUUCUCCUCAAACACAGCCU----GGGAGUGUUU---GAGAAGGGGAUUGAGGAGAUUGGGAAG
AC144455.5/110578-110658   UUUUUUAGACUC-UUAAUUUCUUUUUCU---AGGAUGAACUCUUAGGGUGUGUUUGAGGAGAAGGGGAUUGAGGAGAUUGGGGAG
#=GC SS_cons               <<<<<<<<<<<<.<<-<<--<<<<<<<<...-<<<<<-<<<_____>>>->>>>>-->>>>>>>>-->>->>->>>>>>>>>>>>
#=GC RF                    cUucccAauCUc.UcaAUUUCcUUcUCu...AagAcaaaCuCUUAGgGuGugUuuGAgGAgAAgGGGAUUgAGgAGauUgggaAg
//
# STOCKHOLM 1.0

#=GF AC   RF00885
#=GF ID   MIR821
#=GF DE   microRNA MIR821
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   166.00
#=GF TC   166.00
#=GF NC   165.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000350;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16959252
#=GF RT   Rice embryogenic calli express a unique set of microRNAs, suggesting
#=GF RT   regulatory roles of microRNAs in plant post-embryogenic development.
#=GF RA   Luo YC, Zhou H, Li Y, Chen JY, Yang JH, Chen YQ, Qu LH
#=GF RL   FEBS Lett. 2006;580:5111-5116.
#=GF WK   MicroRNA
#=GF SQ   5


AACV01018463.1/3730-4003 GAUAUCAACUGAAAAAGUCAUCAACAAAAAAGUUGAAUAACUCAUCAACAUCUAAAACUUUUAUUUUGGUUAUUUCUUCAUACGACAAAGUGAUAGUAACAUUAUUCACAAAAUUGACAUAACUCUUAUCUGGUUUUAUAAACUAUAACACAUAUAUGUAAAAUUUGUGAAUAAU-UUUCUAACAUUUUGUCAGAUGAAGAAACAACAAAAAUAAAAGUUUUAGAUCUUGAUGAGUUAUUCAACUUUGUUGUUGAUGACUUUUUCAAUUGAAAUC
AACV01007306.1/1382-1655 GAUAUCAGCUGAAAAAGUCAUCAACAAAAAAGUUGAAUAACUCAUCAAGAUCUAAAACUUUUAUUUUGGUCAUUUCUUCAUACGACAAAGUGAUAGUAACAUUGUUCACAGAAUUGACAUAUCUCUUAUCUGGUUUUAUAAACUAUAACACAUAUAUGUAAAAUUUGUGAAUAAUAUUACUAACAUUUCGUCAGAUGAAGAAAUAA-AAAAAUAAAAGUUAUAGAUCUUGAUGAGUUAUUCAACUUUGUUGUUGAUGACUUUUUCAAUUGAAAUC
AACV01016110.1/2831-2557 GAUUUCAAUUGAAAAAGUCAUCAACAAAAAAGUUGAAUAACUUAUCAAGAUCUAAAACUUUUAUUUUUGUUAUUUCUUCAUCCGACGAAAUGUUAGUAAUAUUAUUCACAAAUUUUACAUAUAUGUGUUAAAGUUUAUAAAACCAGAUAAGAGAUAUGACAAUUUUAUAAAUAAUGUUACCAUCACUUUGUCGUAUGAAGAAAUAACCACAAUAAAAGUUUUAGAUCUUGAAGAGUUAUUCAACUUUGUUGUUGAUGACUUUUUCAGUUGAUAUC
CR855018.1/30195-30469   GAUAUCAACUGAAAAAGUCAUCAACAACAAAGUUGAAUAACUCAUCAAGAUCUAAAACUUUUAUUUUGGUCAUUUCUUCAUACGACAAAGUGAUAGUAACAUUGUUCACAAAAUUGACAUAUCUCUUAUCUAGUUUUAUAAACUAUAACACAUAUAUGUAAAAUUUGUGAAUAAUAUUACUAACAUUUCGUCGGAUGAAGAAAUAACAAAAAUAAAAGUUUUAGAUCUUGAUGAGUUAUUCAACUUUGUUGUUGAUGACUUUUUCAAUUGAAAUC
DQ352453.1/118693-118421 GAUUUCAACUGAAAAAGUCAUCAACAACAAAGUUGUAUAACUCAUCAAGAUCUAUAACUUUUAUUUUGGUCAUUUCUUUAUCUGACAAAGUGAUAGUAACAUUGUUCACAAAAUUCAUAUAU--CUCGUCUGGUUUUAUAAACUAUAACACAGAUAUGUCAAUUUUAUGAACAAUGUUACUAAUACUUCGUCGGAUGAAGAAAUGACAAAAGCAAAAGUUAUAGAUAUUGAUGAGUUAUACAACUUUGUUAUUGAUGACUUUUUUAGUUGAAAUC
#=GC SS_cons             <<<-<<<<-<<<<<<<<<<<<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<<<<<-<<<<<<<<<<<<--<-<<<<<<<<<<--<<<-<<<<<-<<<<<<-<<<<<<<<<<<<-<<-<<<<<<--------<<<<<_____>>>>>-------->>>>>>->>->>>>>>>>>>>>->>>>>>->>>>>->>>-->>>>>>>>>>>--->>>>>>>>>>>>->>>>>>>>>>>>>>>>>>>>>>>>>>->>>>>>>>>>>>>>>>>>->>>>->>>
#=GC RF                  GauauCaacuGaaaaaGuCauCaacaaaaaaGuuGaauaaCucauCaagauCuaaaaCuuuuauuuugGuuauuuCuucauacGaCaaaguGauaGuaacauuguucacaaaauuuacauaucUcUuaUcugGuuUuauAaaCcauAacAcAuauauguaaaauuugugaacaauauuaCuaaCacuuuGuCggaugaaGaaauaAcaaaaauaaaaGuuuuaGaucuuGaugaGuuauuCaaCuuuGuuguuGauGaCuuuuuCaauuGaaauC
//
# STOCKHOLM 1.0

#=GF AC   RF00886
#=GF ID   MIR807
#=GF DE   microRNA MIR807
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   166.00
#=GF TC   166.00
#=GF NC   165.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.35 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000352;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16959252
#=GF RT   Rice embryogenic calli express a unique set of microRNAs, suggesting
#=GF RT   regulatory roles of microRNAs in plant post-embryogenic development.
#=GF RA   Luo YC, Zhou H, Li Y, Chen JY, Yang JH, Chen YQ, Qu LH
#=GF RL   FEBS Lett. 2006;580:5111-5116.
#=GF WK   MicroRNA
#=GF SQ   30


AACV01017840.1/11427-11253 AACCACACUAUCAAUGAAUGGAUUCACCCGUGAGAUGACGUGUUUGUUU--------CACC-AGGACGAGGAUGUGGCAUCAUAUUACUAGCCAUCGCACGAAAUUAAUAG-GA--UG--G--CACGUCCUCAUCUUAGAUGGAACAACCACGUCAUCUCAC-GGGUGGAUCC----AUUCAUUGAUAGUGUGGUU
AP001111.1/164351-164176   AUCCACACUAUCAAUGAAUGUAUUCACCCGUGAUAUGACAUGGCUGUUC--------CACUUAGGACGAGGAUGUGGCAUCCUAUUAUCAGUCAUUGCACGAAAUUAAUAG-GA--UG--C--CACGUUCUCAUCCUAGGUGGAACAACCACGUCAUCUUAU-AGGUGAAUCC----AUUCAUUGAUAGUGUAGUU
AP004734.2/105507-105332   AACCACAUAUUCGAUGAAUGGAUUCACCCGUGAGAUGAAGUGGUUGUUU--------CACCUAAGAUGAAGACAUGGCAUCCUAUUACCAGCCAUCGCACGAAAUUAAUAG-GA--UA--C--CACAUCCUCAUCCUAAAUGGAACAACCACGUCAUCUUAC-GGCUGAAUCC----AUUCAUCAAUAGUGUAGUA
AP005170.3/107018-107193   UACUACACUAUCGAUGUAUAGAUUUACCCGCGAGAUGAUGUGGUUGUUU--------CACCUAGGACGAGGACAUGGCAUCCUAUUACCAGCCAUUGCACGAAAUUAAUAU-GA--UG--C--CACGUCCUCAUACUAGAUGAAACAACCACAUCAUAUCAC-GGGUGAAUCC----AUUCAUCGAUAGUGUGGUU
AACV01004560.1/65192-65367 UAGUGUAGUUUCAAUGAAUGAAUUCACCUGCGAGAUGACAUGACAGUUU--------CACCUAGGACAAGGACAUGGCAUCCUAUUACCAGCAAUCGCACGAAAUUAAUAG-GA--UG--C--CACGUCCUCAUCCUAGAUGGAACAAUCAUCUCAUCUCAC-AGGUGAAUCC----AUUCAUUGAUAGCGUGGUU
AC134885.1/97791-97616     AACCACACUAUCGAUGGAUGGAUUCACCCACAAGAUGAUGUGACUGUUU--------CACCUAGGACGAGGACAUGGCAUCGUAUUAACAGCCAUCACACGAAAUUAAUAG-GA--UG--C--CACGUCCUCAUCUUAUAUGGAACAACCACAUCAUCUCAC-GGGUAAAUUC----AUUCAUCAAUAGUGUGGUU
AP004053.3/94478-94302     AACCACACUAUCAAUGAAUGGAUUCACCCGUGAGAUGAUGUGACUGUUU--------CAUCUAGGACGAGGACAUAUCAUCCUAUUACCAGCCAUCGCACGAAAUUAAUAG-GG--UG--C--CACAUCCUCAUCCUAGAUGGAACGACCACGUCAUCUCAAAAGGUGAAUCC----AUACAUCGACAGUGUAGUU
AP004270.3/4275-4450       AACCACACUAUCGAUGAAUGGAUUCACUCACGAGAUGACGUGGCUGUUU--------CACCUAGGACGAGGUCAUGGCAUCCUAUUAUCAGCUAUCACACGAAAUUAAUAG-GA--UG--C--UACGUCCUCAUCCUAGAUGGAACAACCAUGUCAUCUCAC-GGGUGAAUCC----AUUCAUCGAUAAUAUGGUU
AC150702.2/71785-71606     AACCAUACUAUCAAUGAAUGGAUUCACCCGUGAUAUAACGUGGUUGUUU--------CACUUAGAACGAGGAUGUGACAUCCUAUUACCAGCCAUCGCACGAAAUUAAUAG-GA--UG--C--CACGUCCUCAUCCUAGGUGGAACAGCCAGGUCAUCUCAC-AGAUGAAUCGAUCCAUUCAUUAAUAGUUUGGUU
AL954829.6/81559-81734     AACCACACUAUCAAUGAAUGGAUGCAUCUGUGAUAUGACGUGGUUGUUA--------CACCUAGGAUAAGGACGUGACAUCCUAUUACCAGCCAUCGCAUGAAAUUAAUAG-GA--UG--C--CACGUCUUUAUCCUAGGUGGAACAACCAUGUUAUCUCAU-AGACGAAUCC----AUUUAUUGAUAGUGUGGUU
AP004363.3/37957-38132     AACCACACUAUCAAUGAAUGGAUUCAGCCGUGAUAUGACGUGGGUGUUC--------CACUUAGGACAAGAACAUGGCAUCCUAUUACCAGCCAUCGCAUGAAAUUAAUAG-GA--UG--C--CACGUCCUCAUCCUAGGUGAAACAACCAUGUCAUCUCAC-AUGUGAAUCU----GUUCAUUGAUAGUUUGGUU
AP005439.3/52644-52827     AACCACACUAUCAAUAAAUAGAUUCACCCGCGAGAUGACGUGACUAUUUCACUGUUUCAUCUAGGAUGAGGAUAUGGCAUCCUAUUACCAGCCAUCGCACAAAAUUAAUAG-AA--UG--C--CACGUCCUCAUCCUUAAUGGAACAACCACGUUAUCUCAU-GGGUGAAUCC----AUUCAUCGAUAGUGUGAUU
AACV01022739.1/14066-14235 AACCACACUAUCGAUGAAUGGAUUCACCCGUGAGAUGACGUGGUUGUUC--------CAUCUAGGAUGAGGACGUGGUAUCCUAUUAAUUUC----GUACAGG--UAAUAG-GA--UG--C--CAUGUCCUCGUCCUAAGUGAAACAGCCACGUCAUCUCGC-GGGUGAAUCC----AUUCAUUGAUAAUGUGGCU
CR855159.1/38055-38229     AAUCAUACUAUCAAUAAAUGGAUUCACCCGUGAUAUAACGUGGUUGUUC--------CACUUAGGACAAGAACGUGGCAUCCUAUUACAAGCCAUUGCACAAAAUCAA-AG-GA--UG--C--CACGUCCUCAUCAUAGGUGGAACAACCACGUCAUCUCAC-AGGUGAAUCC----AUUCAUUGAUAGUGUGGUU
AACV01013589.1/3463-3638   AACCACACUAUCGAUAAAUGGAUUCACCUACGAAAUGACAUGGUUGCUU--------CACCUAGGACAAGGACAUGGCAUCAUAUUACCAGCCAUCGCACGAAAUUAAUAG-GA--UG--C--CAUGUUCUCAUCCAAGAUGGAACAACCACGUCAUCUCAU-GAGUGAAUCC----AUUCAUCAAUAGUGUGGUU
AACV01010087.1/24904-25078 AACCGCACUAUCAAUGAAUGAAUUCACCCGCGAGAUGAUGUGACUGUUU--------CAACUAGGACGAGAACAUGGCAUCUUAUUACUAGCCAUCCCAUGAAAUUAAUAG-GA--UG--C--CACGUCAUCAUC-UAGAUAAAACAACCACGUCAUCUCAU-GUGUGAAUCC----AUUCAUCGAUAGUGUGGUU
AL731891.2/51910-51737     AACCACAUUAUCAAUGAAUGGAUUCACCCGUGAUAUGACGUGGUUGUUC--------CACUUAGGAUAAGGAUGUGACAU--UAUUAUCAGCCAUCGCACGAAAUUAAUAG-GA--UG--C--CACGUUCUUAUUCUAGGUGAAACAACCACGUCAUCUCAC-AGUUGAAUCC----AUUCAUUGAUACCAUGGUU
AACV01024453.1/6666-6840   AACCACACUAUCGAUGAAUGAAUUCACCCGCAAGAUGAUGUGGAUGUUU--------CACUUAGGACGAGGACAUAGCAUCCUAUUACCAGCCAUCGCACGAAAUUAAUAG-GA--UG--U--CACAUCCUCAUCCUAA-UGGAACAACCACAUCAUCUCAC-GGGUGAAUCC----GUUCAUCGAUAAUGUGUUU
AL732532.4/96533-96359     AACCGCACUAUCGAUGAAUGGAUUCACCCGCGAGAUGACGAGGUUGUUU--------CACCUAGGACGAGGACAUGGCAUCCUAA-ACCAGCCAUUACACGAAAUUAAUAG-GA--UG--U--CACGUUCUCCUCCUAGAUGGAACAACCACGUCAUCUCAC-GAGUGAAUCC----AUUCAUCAAUAGUGUGGUU
CR855138.1/21768-21943     AACCACACUAUCAAUAAAUGGAUUCACUCAUGAGAUGACGUGGUUGUUU--------CACUUAGGACGAGGACAUGACAUCCUAUUACCAGCCAUCGCACGAAAUUAAUAG-GA--UG--U--AACAUCCUCAUCUUAGAUGGAACAACCACGUCAUCUCAC-GGGUGAAUCU----AUUCAUCAAUAGAGUGGUU
AACV01019713.1/44151-44326 AACCACACUAUCAAUGGAUAGAUUCACCCGCGAAAUGACGCGGUUGUUU--------CACCUAGGACAAGGACAUGGCAUCCUAUUACCAGCCAUCGCACGAAAUUAAUAG-GA--UG--C--CACGUCCAUAUCCUAGAUGAAACAACCACGUCAUAUCAU-GGGUGAAUUC----AUUCAUUGAUAGUAUGAUU
AP004684.3/11483-11308     AACCACAAUAUCAAUGAAUGGAUUAACUCGUGAUAUGACGUGGCUGUUC--------CACUUAGGACAAGGACGUGGCAUCCUAUUACCAACCAUCGCACGAAAUUAAUAG-GA--UG--C--CUCGUCCUCAUCCUAGGUAGAACAACCACGUCAUCUCAC-AGGUGAAUUC----AUUCAUUGAUAGUGUGGUU
AP003268.4/58292-58117     AACCACACUAUCGAUGAAUGGAUUCACUCGCGAGAUGAUGUGGUUGUUU--------CACAUAGGACGAGGACAUGGCAUCAUAUUACCAGCCAUCAGACAAAAUUAACAG-GA--UG--C--CACGUCCCCAUCCUAGAUGGAACAACCACGUCAUCUCGC-GGGUAAAUCC----AUUCAUGGAUAGUGUGGUU
DQ355953.1/18436-18259     AACCACACUAUCAAUGAAAGGAUUCACCCGCGAGAUGACGUGGCUGUUU--------CACAUAGGACGAGGGCGUGGCAUCCUAUUACCAGCCAUCGCACGAAAUUAAUAG-GAUAUG--C--CACAUCAUCAUCCUAGAUGGAAUAACUACGUCAUCACAC-GGGUGAAUCC----AUUCAUCGAUAGUGUGGUU
AC136226.2/81550-81375     AAUCACACUAUCAAUGAAUUGAUUCACCCGUGAUAUGGCGUGGCUGUUC--------CACUUAUGACGAGGACGUGGCAUCUUAUUACCAGCCAUCACACGAAAUUAAUAG-GA--UG--C--CAUAUUCUCAUCCUAGGUGUAACAACUACGUCAUCUCAC-AUGUGAAUCC----AUUUAUUGAUAGUGUGGUU
AP003614.2/25317-25492     AACUACACUAUCGAUAAAUGGAUUCACGUGCGAGAUGAUGUGGCUGUUU--------CACCUAGGACGAGGACAUGGCAUUCUAUUACCAGCCAUCGCGCGAAAUUAAUGA-GA--UG--C--CACGUCCUCAUUCUAGAUGGAACAACCACGUCAUCUCAC-GGGUGAAUCU----AUUCAUCGAUAGUGUAGUU
AP003572.3/39300-39125     AACCACACUAUCAAUGAAUGGAUUCACCCGCGAGAUGACCUAACUGUUU--------CACCUAGGACGAGGACUUGGCAUCCUAUUACCAGCAAUCGCACGAAAUUAAUAG-GA--UG--C--CACGUCCUCAUCCUAGAUGGAACAACCACGUCAUCUCAC-AGGUGAAUCU----AUUCGUCGAUAGUGUGGUU
AL731759.2/40028-40202     AACUACACUAUCGAUUUAUAGAUUCACUCGCGAGAUGAUAUGGCUGUUU--------CACCUAGGACGAGGACAUGACAUCCUAUUA-UAGCCAUCGCACGAAAUUAAUAAUGA--UG--A--CACGUCCUCAUCCUAGAU-AAACAACCACGUCAUCUCAC-GGGUGAAUCC----AUUCAUCGAUAGUGUGGUU
AC118981.1/41759-41582     AAUCACACUAUCAAUGAAUGGAUUCACCCGCGAGAUGAUGUGGCUCUUU--------CACAUAAGACGAGGACAUGGUAUCCUAUUACUAGCCAUCUCACGAAAUUAAUAG-GA--UAUAC--UACGUCAUCAUCCUAAAUGGAGCAACCACGUCAUCUCAC-GGGUGAAUCC----AUUCAUCGAUAGUGUGUUU
AP004040.3/47321-47498     AACCACACUAUCAAUGAAUGGAUUCACCCGCGAGAUGAUGUGGCUCUUU--------CACAUAGGACGAGGACAUGACAUCCUAUUACCAGCCAUCUCACGAAAUUAAUAG-GA--UA--UACCACGUCAUCAUCCUAGAUGGAGCAACCACGUCAUCUCAC-GGGUGAAUCC----AUUCAUCGAUAGUGUGGUU
#=GC SS_cons               <<<<<<<-<<<<<<<-<<<-<<<<<<<<-<<<<-<<<<<-<<<<<<<<-........-<<-<<-<<----<<<---<<<<<<<<<<<------<<________>>>>>>>>.>>..>>..>..--->>>---->>->>->>-->>>>>>>>->>>>>->>>>.->>>>>>>>-....>>>->>>>>>>->>>>>>>
#=GC RF                    aaccacacuauCgaugaauggauuCaccCgcGagauGacguGgcuguuu........CaccuaGGacgAGGacaUGgCauCcuauuaccAGCcauCgCACGAAauuaauag.Ga..uG..c..CACguCcUCAuCcuagguGgaacagcCacguCauCuCgc.ggguGaaucc....auuCaucGauaGugugguu
//
# STOCKHOLM 1.0

#=GF AC   RF00887
#=GF ID   mir-802
#=GF DE   microRNA mir-802
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   63.30
#=GF NC   59.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000353;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16973894
#=GF RT   Mouse microRNA profiles determined with a new and sensitive cloning
#=GF RT   method.
#=GF RA   Takada S, Berezikov E, Yamashita Y, Lagos-Quintana M, Kloosterman WP,
#=GF RA   Enomoto M, Hatanaka H, Fujiwara S, Watanabe H, Soda M, Choi YL, Plasterk
#=GF RA   RH, Cuppen E, Mano H
#=GF RL   Nucleic Acids Res. 2006;34:e115.
#=GF RN   [2]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   Mir-802_microRNA_precursor_family
#=GF SQ   13


AAHY01130307.1/4530-4436       GUCCUAUUAUUUGCAAUCAGUAACAAAGAUUCAUCCUUGUGU-CAAUCAUACAACACGGAGAGUCUUUGUCACUCAGUGUAAUUAAUAGCCUUCAC-
AANU01260813.1/2882-2789       GUUCUGUUAUUUGCAAUCAGUAACAAAGAUUCAUCCUUGUGU-CCAUCAUGCAGCAAGGAGAAUCUUUGUCACUUAGUGUAAUUAAUAGC-UGGA-C
AADB02020342.1/3191453-3191360 GUUCUGUUAUUUGCAGUCAGUAACAAAGAUUCAUCCUUGUGU-CCAUCAUGCAACAAGGAGAAUCUUUGUCACUUAGUGUAAUUAAUAGC-UGGA-C
AAFC03120329.1/37567-37474     AGACUAUUAUUUGCAAUCAGUAACAAAGAUUCAUCCUUGUGU-CCAUCAAGCAACAAGGAGAAUCUUUGUCACUAAGUGUAAAUAAUAGC-UACA-C
AANG01245245.1/9417-9510       CUUCUAUUAUUUGCAGUCAGUAACAAAGAUUCAUCCUUGUGU-CUGUCAAGCAACAAGGAGAAUCUUUGUCACUUAGUGUAAUUAAUAGC-UGUA-C
AAPY01680918.1/2148-2241       UUUCUAUUAUUUGCGGUCAGUAACAAAGAUUCAUCCUUGUGU-CCAUCAUGCAACAAGGAGAAUCUUUGUCACUUAAUGUAAAUAAUAGC-UGCA-C
ABDC01068180.1/1689-1782       UUUCUAUUACUUGCAGUCAGUAACAAAGAUUCAUCCUUGUGU-CCAUGAUGCAGCAAGGAGAAUCUUUGUCACUUGGUGUAAUUAAUAGC-UGGA-C
AANN01549372.1/6202-6294       CUUCUAUUAUUUGCAGUCAGUAACAAAGAUUCACCCUUGUGU-CAAUAA-ACAGCAAGGGGAAUCUUUGUCACUUAGUGUAAUUAAUAGC-UGGA-U
AAIY01234787.1/6341-6434       CGUCUAUUACUUGCAGUCAGUAACAAAGAUUCAUCCUUGUGU-CCAUCGAGCAGCAAGGAGAGUCUUUGUCACUUAGUGUAAUUAAUAGC-UGUG-C
AAYZ01304398.1/3837-3931       UUUCUAUUAUUUGCAGUCAGUAACAAAGAUUCAGCCUUGUGUCCCUUCAUGCAACAAGGAGAAUCUUUGUCACUUAGUGUAAUUAAUAGC-UGCA-C
AAQQ01243660.1/144-237         UCUCUGUUAGUUGCAGUCAGUAACAGAGAUUCAUCCUUGUGU-CGAUCACGCAACAAGGGGAAUCGCUGUCACUUCCUGUAAUUAAUGGC-CACA-C
AAPN01075186.1/3091-3184       UUUCUGUUUCUUGCAGUCAGUAACAAAGAUUCAUCCUUGUGU-CCUGUAAGCAACAGGGAGGGUCUUUGUCACUGAGUGCAAUUAAUGGU-GGCC-G
AAWR02022935.1/72940-73033     CUUCUAUUAUUUGCAAUCAGUAACAAAGAUUCAUCCUUGUGU-CCAUCAAGCAACAAGGAGAAUCUUUGUCACUUAGUGUAAUUAAUAGC-UGCG-C
#=GC SS_cons                   :::<<<<<<-<<<<<---<<<-<<<<<<<<<<-<<<<<<<<<._______>>->>>>>>>>>>>>>>>>>->>>--->>>>>->>>>>>:.::::.:
#=GC RF                        uuuCuauuauuugCagUCaGuAaCaaaGauuCAuCCuuGuGc.CcaucAugCAaCaaGGaGaauCuuuGuCaCuuAguGcaauuaauaGc.ugca.c
//
# STOCKHOLM 1.0

#=GF AC   RF00888
#=GF ID   mir-770
#=GF DE   microRNA mir-770
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   52.00
#=GF TC   53.00
#=GF NC   50.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000355;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   4


AAFC03050876.1/23581-23676 GAGCUACCCUUCCCUG---CCUCCAGUGCCAUGUGUCCGGGCCAUGUGAGCAGAGCUUUGUGGGCCUGAGGUGGCUCUGGGGCUUCAGGGC-UCUGCUGU
AAWR02020057.1/98240-98339 CAGGAGCCGCCCUUCCGUGCCUCCAGCACCACGUGUCUGGGCCAUGUGAGCAAGGUCACAUGGGCCCGAUGUGGUGCUGGGGGCGGCAGGGCUCUGCUCU
AC107681.15/170-75         AAGCCAC---CUUCUG-UGCCCCCAGCACCACGUGUCUGGGCCACGUGAGCAACGCCACGUGGGCCUGACGUGGAGCUGGGGCCGCAGGGGUCUGAUGGC
AL117190.6/92505-92602     CAGGAGCCACCUUCCG-AGCCUCCAGUACCACGUGUCAGGGCCACAUGAGCUGGGCCUCGUGGGCCUGAUGUGGUGCUGGGGCCUCAGGGG-UCUGCUCU
#=GC SS_cons               ::<<<<<---<<<<<<.<<-<<<<<<<<<<<<--<<<<<<-<<<<<<<-<<___>>>>>>>>>->>>>>>>>>>>>>>>>>>->>>>>>>>---->>>>>
#=GC RF                    aAggcgccauccccug.cGCCcCCaGcgCCacGUguCcGGGCCacguGAGCaaaGCCacguGGGCCgGacguGGcgCuGGgGcCgcagggguucugcgcc
//
# STOCKHOLM 1.0

#=GF AC   RF00890
#=GF ID   mir-668
#=GF DE   microRNA mir-668
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   47.40
#=GF NC   40.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000357;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [2]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF WK   MicroRNA
#=GF SQ   6


AAHY01103470.1/48096-48031 GGUAAGUGUGCCUCGGGUGAGCAUGCACUUAAUGUAGGUGUAUGUCACUCGGCUCGGCCCACUACC
AANG01133004.1/7218-7278   GGUAAGUGCGUCUCGGGUGAGCAUGCGAUUACGGUGGUAGCAUGUCACUC-----GGCCCACUACC
AAFC03087121.1/13899-13959 GGUAAGUGUGUCUCGGGUGAGCAUGCAAUGAACGUGCUCGCAUGUCACUC-----GGCCCACUACC
AAWR02020065.1/43983-44043 GGUAAGUGCGUCUCGGGUGAGCAUGCAAUUGAUGUAGUAGUAUGUCACUC-----GGCCCACUACC
ABRP01151524.1/11446-11506 GGUAAGUGCGUCUCGGGUGAGCAUGCGAUUAAAGUGGUAGUAUGUCACUC-----GGCCCACUACC
AL132709.5/66341-66276     GGUAAGUGCGCCUCGGGUGAGCAUGCACUUAAUGUGGGUGUAUGUCACUCGGCUCGGCCCACUACC
#=GC SS_cons               <<<<-<<<-<<<--<<<<<<-<<<<<<<<<<___>>>>>>>>>>>>>>>>.....>>>->>>>>>>
#=GC RF                    GGUAAGUGcGcCUCGgGUGAGCAUgCacuuaAuGuagguGcAUGUCACuC.....GgCCCACUACC
//
# STOCKHOLM 1.0

#=GF AC   RF00891
#=GF ID   mir-671
#=GF DE   microRNA mir-671
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   49.70
#=GF NC   47.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000358;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-671_microRNA_precursor_family
#=GF SQ   3


AACC02000108.1/937834-937908 GGAAGAGGAGGAAGCCCUGGAGGGGCUGGAGGUGAUGGAUGUUUUCCUCCGGUUCUCAGGGCUCCACCUCUUUCG
AAFC03048436.1/8400-8474     GGAAGAGGAGGAAGCCCUGGAGGGGCUGGAGGUGAUGGAUGUUUUCCUCCGGUUCUCAGGGCUCCACCUUUUCCG
AK056331.1/2331-2405         GGAAGAGGAGGAAGCCCUGGAGGGGCUGGAGGUGAUGGAUGUUUUCCUCCGGUUCUCAGGGCUCCACCUCUUUCG
#=GC SS_cons                 :<<<<-<<-<<-<<<<<<<--<<<<<<<<<<<-<<<____>>>-->>>>>>>>>>>>>>>>>>->->>>->>>>:
#=GC RF                      GGaagAgGAGGAaGCCCuGGAgGggCuGGaGGUgauGGAUguuUUCCuCCgGuuCuCaGGGCuCCACCucuuuCG
//
# STOCKHOLM 1.0

#=GF AC   RF00892
#=GF ID   mir-551
#=GF DE   microRNA mir-551
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.30
#=GF NC   49.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000360;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [3]
#=GF RM   18511220
#=GF RT   Identification of novel chicken microRNAs and analysis of their genomic
#=GF RT   organization.
#=GF RA   Shao P, Zhou H, Xiao ZD, He JH, Huang MB, Chen YQ, Qu LH
#=GF RL   Gene. 2008;418:34-40.
#=GF WK   MicroRNA
#=GF SQ   20


AADB02005341.1/767470-767385 CUCUCCUGGCCCAUGAAAUCAAGCGUGGGUGAGACCU-GGUGCAGAA-CGGG-AAGGCGACCCAUACUUGGUUUCAGAGGCUGUGAGAA
AANU01224302.1/10050-9965    GCCGGGUGACCCUGGAAAUCCAGAGUGGGUGGGGCCU-GUCUGACCA-UUUC-UAGGCGACCCACUCUUGGUUUCCAGGGUUGCCCUGG
AANU01299462.1/9531-9616     CUCUCCUGGCCCAUGAAAUCAAGCGUGGGUGAGACCU-GGUGCAGAA-CAGG-AAGGCGACCCAUACUUGGUUUCAGAGGCUGCGAGAA
AADB02000071.1/283609-283524 GCCGGGUGACCCUGGAAAUCCAGAGUGGGUGGGGCCA-GUCUGACCG-UUUC-UAGGCGACCCACUCUUGGUUUCCAGGGUUGCCCUGG
AC113454.8/87576-87661       CUCUUGUGGCCCAUGAAAUCAAGCUUGGGUGAGACCU-GGUGCAGAA-CAGG-AAGGCGACCCAUACUUGGUUUCAGUGGCUGCAAGAA
AAIY01691459.1/5449-5364     GUCUCGUGGCCCAUGAAAUCAAGCAUGGGUGAGACCU-GGUGCAGAA-CAGG-AAGGCGACCCAUACUUGGUUUCAGAGGCUGCGAGAA
AALT01062645.1/1860-1775     CUCUCUUGGUCUAUGAAAUCAAGCGUGGGUGAGACCU-GGUGCAGAA-CAGG-AAGGCGACCCAUACUUGGUUUCAGAGGCUGAGAGAA
AACN010030455.1/2051-1966    CUCUCCUGGCCCAUGAAAUCAAGUGUGGGUGAGACCU-GGUGCACAG-CGGG-AAGGCGACCCAUACUUGGUUUCAGAGGCUGCGAGAA
AAFC03024756.1/83868-83783   UUCUCCUGGCCUAAGAAAUCAAGCGUGGGUGAGACCU-GGUGCAGAA-CAGG-AAGGCGACCCAUACUUGGUUUCAGAGGCUGUGAGAA
AAYZ01509825.1/715-799       CUCUCGUGGCCCGUGAAAUCAAGCGUGGGUGAGACCU-GGUGCAGAA--GGG-AAGGCGACCCAUACUUGGUUUCAGAGGCUGUGAGGA
AANN01687869.1/1924-1838     CUCUCCUGGCCCAUGAAAUCAAGCCUGGGUGAGACCU-GGUACAGAA-CAAGAAAGGCGACCCAUACUUGGUUUCAGAGGCUAUGAGGA
AAPN01098875.1/4087-4172     CUCCUGUGGCCCCAGAAAUCAAGGAUGGGUGAGACCU-CUUGCACAA-GUGG-AAGGCGACCCAUACUUGGUUUCAGGGGCUUCCGGAA
AANG01000350.1/4480-4395     GCCAGGUGACCCUGGAAAUCCAGAGCGGGUGAGGCCU-GUCCGACCA-UUUC-UAGGCGACCCACUCUUGGUUUCCCUGGUUGCCCUGG
AAFR03046841.1/43899-43813   CUCCCGUGGCCCCAGAAAUCAAGGAUGGGUGAGACCUCGUGUGCAAA-CUGA-AAGGCGACCCAUACUUGGUUUCAGGGGCUUCGAGAA
AAVX01059360.1/184-266       CCUGAAAGGCCUCAGAAAUCAAGGGUGGGUGAGGCCU-AUGAUAUAC-AAGG-AAGGCGACCCAUACUUGGUUUCCUAGGACU---GGG
AANH01008111.1/58748-58665   ACUGCCUUCCCUUAGAAACUAAGCGUGGGUGUGGCCU-GGAAAAGAAACACG----GCGACCCAUCCUUAGUUUCUGAGGUCACGCGGG
BAAE01149217.1/2073-2150     GCUGCACGCUCUUAGAAGCCAAGUGUGGGUGUG-CCC-UGAAAAAAA-UGAG-----UGACCCAUCCUUAGUUUCUGAG---GCGUAGA
AAKN02050963.1/24909-24994   CUCUUGUGGCCCAGGAAAUCAAGCGUGGGUGAGACCU-GGUGCGGAA-GGGG-AAGGCGACCCAUACUUGGUUUCAGAGGCUGCAAGAA
AAGV020087505.1/1612-1697    GUCCCGUGGCCCGUGAAAUCAAGCGUGGGUGAGACCU-GGUGCAGAA-CGGG-AAGGCGACCCAUACUUGGUUUCAGAGGCUGCGAGAA
CAAK05038038.1/4296-4214     CCUGUGUUGCCUUAGAAACCAAGCAUGGGUG---UGG-CCUGAAUCC-UCCA-AUGGCGACCCAUCCUUGGUUUCUGAGGCUGUACAGA
#=GC SS_cons                 :<<<<<<<<<<--<<<<<<<<<<-<<<<<<<---<<<._________._>>>.---->->>>>>>->>>>>>>>>>-->>>>>>>>>>:
#=GC RF                      cccucgcggCCcuuGAAAuCAAGcgUGGGUGaGaccc.ggugaAgAA.uggg.AAGGCGACCCAcaCUUGgUUUCagaGGccgcgaggA
//
# STOCKHOLM 1.0

#=GF AC   RF00893
#=GF ID   MIR854
#=GF DE   microRNA MIR854
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   49.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000361;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17189346
#=GF RT   A family of microRNAs present in plants and animals.
#=GF RA   Arteaga-Vazquez M, Caballero-Perez J, Vielle-Calzada JP
#=GF RL   Plant Cell. 2006;18:3355-3369.
#=GF WK   Mir-854_microRNA_precursor_family
#=GF SQ   3


AB046429.1/6389-6609   CGGAUGAGGAUAGGGAGGAGGAGUAUGAUACGAGCAUGUAUCAUUUCAGUGAGCACGUACCUCCAGCGCGGGAGAGCAAGAGCUUGAGUGAAGCUCAUAGAAACAACAGUAAGUUGCAGAGGUGGUGCAAGAAACAAGAUAGGCUACUUAUCAAGUGCUUCAAAGCCAUCACGUUUCUGACGGACAAGAUAAGCUGCUUCUCUUCUACUACAGCUAUUCCG
AB046426.1/52871-52651 CGGAUGAGGAUAGGGAGGAGGAGUAUGAUACGAGCAUGUAUCAUUUCAGUGAGCACGUACCUCCAGCGCGGGAGAGCAAGAGCUUGAGUGAAGCUCACAGAAACAACAGUAAGUUGCAGAGGUGGUGCAAGAAACAAGAUAGGUUACUUAUCAAGUGCUUCAAGGCCAUCACGUUUCUGACGGACAAGAUAAGUUGCUUCUCUUCUACCACAGCUAUUCCG
AB046428.1/51158-51378 CGGAUGAGGAUAGGGAGGAGGAGUAUGAUACGAGCAUGUAUCAUUUCAGUGAGCACGUACCUCCAGCGCGGGAGAGCAAGAGCUUGAGUGAAGCUCACAGAACCAACAGUAAGUUGCAGAGGUGGUGCAAGAAACAAGAUAGGCUACUUAUCAAGUGCUUCAAAGCCAUCACGUUUCUGACAGACAAGAUAAGCUGCUUCUCUUCUACUACAGCUAUUCCG
#=GC SS_cons           <<<<------<-<<<<<<<<<<<<<_________________________________________________________________________________________________________________________________________________________________________>>>>>>>>>>>>->->------->>>>
#=GC RF                CGGaUGAGGAuAGgGagGaGgaGuaUGAUACGAGCAUGUAUCAUUUCAGUGAGCACGUACCUCCAGCGCGGGAGAGCAAGAGCUUGAGUGAAGCUCAcAGAAaCAACAGUAAGUUGCAGAGGUGGUGCAAGAAACAAGAUAGGcUACUUAUCAAGUGCUUCAAaGCCAUCACGUUUCUGACgGACAAGAUAAGcugCuuCuCuuCuACuaCAGCUAUuCCG
//
# STOCKHOLM 1.0

#=GF AC   RF00894
#=GF ID   mir-790
#=GF DE   microRNA mir-790
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   63.00
#=GF TC   67.80
#=GF NC   51.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000362;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [3]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   2


CAAC02000563.1/419309-419243 GACUGCUUGGCACUCGCGAACACCGCGGUCGAA----GUUACUCGCGGAGUUAGCCAGUGUCAACCAGAUG
AAGD02008557.1/4565-4635     GACUGCUUGGCACUCGCGAACACCGCGAUCUUAUCAGAUAAAUCGCGGAGUUAGCCGGUGGCAACCAGGCG
#=GC SS_cons                 <<<<<-<<<<<<<--<<-<<<-<<<<<<______________>>>>>>->>>->>-->>>>>>>->>>>>:
#=GC RF                      gcCUGCUUGgCACUCGCGAACACCGCGaUCuuAUCAGaUaAauCGCGGAGUUAGCCaGUGcCAACCAGgcG
//
# STOCKHOLM 1.0

#=GF AC   RF00895
#=GF ID   mir-786
#=GF DE   microRNA mir-786
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   55.00
#=GF NC   47.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000363;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF WK   Mir-786_microRNA_precursor_family
#=GF SQ   2


CAAC02000535.1/798499-798589 GGGACCCUUCCCAACAAAAUCUCAAAUAGUGGCAUUUACACAAGCAAUGGUAUGUAAUGCCCUGUACGAGAUUUGGUUGGUGAGAAGUCUC
FO080457.1/9344-9433         GGGAUAGUUCCCGAUCGAAUAUCAGUUGG-GGUAUUUACAAAAAGACAAAAUUGUAAUGCCCUGAAUGAUGUUCAAUCGGUGAUGAAUCUC
#=GC SS_cons                 <<<<<-<<--<<<<<-<<<<<<<--<<<<-<<<<<<-<<<____________>>>>>>>>>>>>>-->>>>>>>->>>>>-->>-->>>>>
#=GC RF                      GgGacacuUCCCgacagaaucuCAauuaGUGGcauuUaCaaAAagAauaauauGuaaugCCCugaAuGagauucagucGGUGagaAguCuC
//
# STOCKHOLM 1.0

#=GF AC   RF00896
#=GF ID   mir-787
#=GF DE   microRNA mir-787
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   52.00
#=GF TC   53.60
#=GF NC   51.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000364;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [3]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   2


Z66561.1/828-917             GAUGUAUCAGUGGACGAAAGAUAC-AUACGAUCUUACAUC-UUCAAAAUGGUAUGUAAGCUCGUUUUAGUAUCUUUCGUCUCUGAUCACAUU
CAAC02000541.1/600113-600022 CCUCAAAAUGGAGAAGAAGGAAACUAGACAAUCUUACAUAGCUCAAAAUAAUCUGUAAGCUCGUCUUAGUUUUCCUCUCCUCUCUAGGGAAU
#=GC SS_cons                 <<<-<----<-<<<<<<<<<<<<<<<<<<<<-<<<<<<_______________>>>>>>->>>>>->>>>>>>>>>>>>>>->->->>>:::
#=GC RF                      gccguAaauguaGacGaaggauaCuagaCgaUCuuaCaUaGuUCAAAAUaaUauGuaaGCucGucUuaGuauccuuCguCuCugaaggcAaU
//
# STOCKHOLM 1.0

#=GF AC   RF00897
#=GF ID   mir-675
#=GF DE   microRNA mir-675
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   61.00
#=GF TC   64.40
#=GF NC   59.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000365;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17237358
#=GF RT   The imprinted H19 noncoding RNA is a primary microRNA precursor.
#=GF RA   Cai X, Cullen BR
#=GF RL   RNA. 2007;13:313-316.
#=GF RN   [2]
#=GF RM   18402656
#=GF RT   Hidden layers of human small RNAs.
#=GF RA   Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub
#=GF RA   CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y
#=GF RL   BMC Genomics. 2008;9:157.
#=GF WK   Mir-675_microRNA_precursor_family
#=GF SQ   11


AADB02013519.1/46039-46111 CCCAGGGUCUGGUGCGGAGAGGGCCCACAGUGGACUUGGUGACGCUGUAUGCCCUCACCGCUCAGCCCCUGGG
AANU01093282.1/4296-4224   CCCAGGGUCUGGUGCGGAGAGGGCCCACAGUGGACUUGGUGACACUGUAUGCCCUCACCGCUCAGCCCCUGGG
AC013548.13/138280-138351  CCCAGGGACUGGUGCGGAAAGGGCCCACAGUGGACUUGGU-ACACUGUAUGCCCUAACCGCUCAGUCCCUGGG
AF190054.1/443-515         CCCAGGGGCUGGUGCGGGAAGGGCCCACAGUGUGCUUGGUGACACUGUAUGCCUUAACCGCCCAGUCCCUGGG
AF214115.1/794-866         CCCAAGGACUGGCGCGGAAAGGGCCCACAGUGGACGCUUGUGCACUGUAUGCCCUAACCGCUCAGCCCCUGGG
AF190056.1/465-536         CCCAGGGUCUGGCGCGGAGA-GGCCCACAGCGUACUUGGUGACACUGUAUGCCUUCACCGCUCAGCCCCCGGU
AF190055.1/453-521         CCCAGGG-CUGGCGCGGAAAGGC--CACAGUGGACUUGUUCACGCUGUAU-GCCUAACCGCUCAGCCCCUGGG
AY044827.1/35459-35529     CCCAGGGGCUGGCGCGGC-AGGGCCCCCGGUGUCCUUGGUGGCACUGUGCGCCCUCGCCGCUC-GCCCCUGGG
AF190057.1/504-575         CCCAAGGGCCGGCGCGGAAAAGGC-CACAAUUGCCUCGGUUACCUUGUAUGCCCUCACCGCUCAGCCCCUGGG
AAKN02038607.1/34464-34536 CCCAGGACCUGGCGCGGAGAGGGCCCACAGUGGACUUGGUGACACUGUAUGCCCUAACCGCUCAGCCCCUGGG
AAWR02038016.1/7687-7615   CCCAGGGGCUGGCGCGGAGAGGGCCCACAGUGCACUCAGUGACACUGUAUGCCUUCACCGCUCAGCCCCUGGG
#=GC SS_cons               <<<<<<<-<<<<-<<<<--<<<<<--<<<<<<__________>>>>>>-->>>>>-->>>>>>>>->>>>>>>
#=GC RF                    CCCaGGGuCuGgcGCGGAaAGGGCCCaCaGuGgaCUuGGUgACaCuGuAUGCCCUaACCGCuCaGCCCCuGGG
//
# STOCKHOLM 1.0

#=GF AC   RF00898
#=GF ID   mir-242
#=GF DE   microRNA mir-242
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   42.00
#=GF TC   42.20
#=GF NC   41.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000366;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   2


AAGD02011159.1/4161-4091     AGAAUAUUGCGUAGGCCUUUGCUUCGAAAGA-AACACUUUACUGUUCGCAGCAAUCUCCUCCGCAAUAUUUU
CAAC02000582.1/173061-172992 AGAAUAUUGCGUAGGCCUUUGUUUCGAAAGACCCAAAAAUU--GUUCGCAGCAAUCUCCUUCGCAAUAUUUU
#=GC SS_cons                 <<<<<<<<<<<-<<<---<<<<<-<<<<___.____________>>>>->>>>>--->>>->>>>>>>>>>>
#=GC RF                      AgAAUAUUGCGUAGGCCUUUGcUUCGAAAGA.aaaAauuUuCUGUUCGCAgCAAUCUCCUuCGCAAUAUUuU
//
# STOCKHOLM 1.0

#=GF AC   RF00899
#=GF ID   mir-235
#=GF DE   microRNA mir-235
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   47.10
#=GF NC   44.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000367;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode
#=GF RT   species.
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   2


AAGD02010739.1/10351-10420 GAUCAGGCCUUGGCCGAAUGCAUAUAUUGCUC------AGUUGAAUUGCUAAUAUUGCACUCGCCCCGGCCUGAUC
DQ498827.1/14793-14718     GAUCCGGCCAUGGCCAAUUGCAUAUAUUGCUUUUACUUUUUCAAAAUGCGAAUAUUGCACUUUCCCUGGCCAGAUC
#=GC SS_cons               <<<<<<<<<--<<-----<<<<-<<<<________________________>>>>>>>>---->>-->>>>>>>>>
#=GC RF                    GAUCcGGCCaUGGCCaAuUGCAUAUAUUGCUuUUACUUuuUuaAAaUGCuAAUAUUGCACUuuCCCuGGCCgGAUC
//
# STOCKHOLM 1.0

#=GF AC   RF00900
#=GF ID   mir-255
#=GF DE   microRNA mir-255
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   65.10
#=GF NC   46.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000368;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [3]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF WK   MicroRNA
#=GF SQ   2


AC084561.1/3609-3711       AUUUUGUUAGAUGU-------CUCUUCAUUAUCAGGUAAGAAAUCUUUGUAGUUUUCCGCGAGUCAACGUGAAAACUGAAGAGAUUUUUUACAGAUUCCG-GAGGAGCA-----------UC
AAGD02012095.1/86646-86750 ---------AACGUUAUACUGAU----AAAAUCAGGUAAGAAAUCUUUGUGGUUUUCCGUGUUUAAACGCGAAAACUGAAGAGAUUUUUUACAGAUUCUGC----AUAAUUUUCGAUUCGUC
#=GC SS_cons               .........::::::::::::<<....--------<<<<<<<<<<<<<-<<<<<<<<<<________>>->>>>>>>>->>>>>>>>>>>>>---------....>>:::::::::::::::
#=GC RF                    .........aAuGUUAUAcUGcu....AaaAUCAGGuaagaaauCuuuGuaGuuuuCCGuGuuUaAACGuGaaaaCugAagaGauuuuuuaCAGAUUCuGc....agaAUUUUcGAUUcGUC
//
# STOCKHOLM 1.0

#=GF AC   RF00901
#=GF ID   MIR845_1
#=GF DE   microRNA MIR845_1
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   88.90
#=GF NC   66.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.83 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000369;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17299599
#=GF RT   High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent
#=GF RT   birth and death of MIRNA genes.
#=GF RA   Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS,
#=GF RA   Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC
#=GF RL   PLoS One. 2007;2:e219.
#=GF RN   [2]
#=GF RM   17182867
#=GF RT   A diverse and evolutionarily fluid set of microRNAs in Arabidopsis
#=GF RT   thaliana.
#=GF RA   Rajagopalan R, Vaucheret H, Trejo J, Bartel DP
#=GF RL   Genes Dev. 2006;20:3407-3425.
#=GF WK   MicroRNA
#=GF SQ   2


AL031326.1/29579-29495 GCGUUUCCAUCACGUCGAUUGCUGUCAGAGCCACGCCU-----AUGAAGAAUUUGUGCGGCUCUGAUACCAA-UUGAUGCUAUGGAAACAU
AL031326.1/26214-26124 CGGUUUCCAUCACGUCAAUUGCUAUCAGAGCAACGCAUGAUGUAUAAUAACUAAGCGUCGCUCUGAUACCAAAUUGAUGCAAUGGAAACAU
#=GC SS_cons           ::<<<<<<<<--<<<<<<<<<-<<<<<<<<<<<<<<__________________>>>>>>>>>>>>>>->>>->>>>>>-->>>>>>>>::
#=GC RF                ggGuuuCCauCACguCaauuGCuauCaGaGCcgCgCaUGAUGUAUaAuaAaUaaGcGcgGCuCuGauaCCaaAuuGauGCaauGGaaaCAU
//
# STOCKHOLM 1.0

#=GF AC   RF00902
#=GF ID   mir-791
#=GF DE   microRNA mir-791
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   77.10
#=GF NC   51.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000370;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [3]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF WK   MicroRNA
#=GF SQ   3


CAAC02000521.1/3575831-3575916 GAAUUCUCGAUCACCGUAUCACGUGUGGCCAAAGUCAAAUCCAU-UAUUGAACAUUGGCACUCCGCUGAUUUGGUGAUCGACUUUUC
ABEG02000049.1/8382-8468       CAAUUCUCAGUUACCUUAUCACGUGUUGCUAAAGUUCAAUACAUUUAGUGAACUUUGGCACAACGCUGAUUAGGUGACUGAUUAUUU
FO081142.1/5009-5093           GAACCUUCGAUUACCUUAUCCGUUGUAGCCAAAGUUCAACGAAG-C-GGCAACUUUGGCACUCCGCAGAUAAGGCAAUCGAUUGUUU
#=GC SS_cons                   :<<---<<<<<<<<<<-<<<<------<<<<<<<<<________._____>>>>>>>>>------->>>>->>>>>>>>>>--->>:
#=GC RF                        gAAuucUCGgUcaCCuUAUCacgUGUaGCcAAaGUucAAuacAu.uAgugaACuUUgGCACucCGCuGAUuaGGugAcCGAuUaUUu
//
# STOCKHOLM 1.0

#=GF AC   RF00903
#=GF ID   mir-359
#=GF DE   microRNA mir-359
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   56.70
#=GF NC   53.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000371;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [3]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF WK   MicroRNA
#=GF SQ   2


AAGD02000048.1/3335-3244     CUCGAUAAA-CUUCAUUGGUCAGAGCAACACGCAGUCACAUAAGUUUCUGAAAUGUGUCACUGGUUUUCCUCUGACUAAUUGAAGAUAUCGAG
CAAC02000521.1/484549-484635 GAC---AAAUCUUCAUCCGUCAGAGCAUAUCUCAGUUACACAACUUCCUAAAUAGUGUCACUGGUUAUCCUCUGUCGAAAUGAAGAU---GUC
#=GC SS_cons                 <<<-----<.<<<<<<<<<<<<<<<<<<<<<-<<<<-<<<<<<_________>>>>>>->>>>>>>>>>>>>>>>>>->>>>>>>->--->>>
#=GC RF                      guCGAUAAa.CuuCauucGuCaGaGcauaaCuCaGuuaCacaagUUuCUaAAuuguGuCaCuGGuuaugCuCuGaCgAaauGaaGAuAUcGac
//
# STOCKHOLM 1.0

#=GF AC   RF00904
#=GF ID   mir-392
#=GF DE   microRNA mir-392
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   87.80
#=GF NC   53.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000372;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15317971
#=GF RT   Patterns of flanking sequence conservation and a characteristic upstream
#=GF RT   motif for microRNA gene identification.
#=GF RA   Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB
#=GF RL   RNA. 2004;10:1309-1322.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [3]
#=GF RM   21307183
#=GF RT   Improved annotation of C. elegans microRNAs by deep sequencing reveals
#=GF RT   structures associated with processing by Drosha and Dicer.
#=GF RA   Warf MB, Johnson WE, Bass BL
#=GF RL   RNA. 2011;17:563-577.
#=GF WK   MicroRNA
#=GF SQ   3


Z70208.1/24353-24423           UUCAGUCAGCAUUCGUGGUUGAGGAUAUCGAACACAAAAAAAGAUAUCAUCGAUCACGUGUGAUGACAGAU
AAGD02008034.1/12297-12367     AUCUGGCGGUUUACAUGGUAGAAGAUAUCAGUAUAAAAAAUAGAUAUCAUCGAUCAUGUAUGCUGUCAGAU
CAAC02000474.1/1909133-1909203 AUCUGACAUCUCACAUUAUUGAGGAUAUAAACUAAAUAAAGAAAUAUCAUCGAUCAUGUGAGCUGUUAGAU
#=GC SS_cons                   :<<<<<<<-<<<<<<<<<<<<<-<<<<<<_____________>>>>>>->>>>>>>>>>>>>->>>>>>>:
#=GC RF                        aUCuGaCagcucaCgUGgUuGAgGAUAUcAAuuaaAaAAAaAgAUAUCAUCgAuCAcGugagcuGuCaGAU
//
# STOCKHOLM 1.0

#=GF AC   RF00905
#=GF ID   mir-789
#=GF DE   microRNA mir-789
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   100.00
#=GF TC   115.60
#=GF NC   66.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.46 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000373;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF WK   MicroRNA
#=GF SQ   2


Z82285.1/29139-29043     UGUCCUGAAGGCGGACAAUUGAUGACUCAGGCAGGGACUAAUCAUGAUUGUCGAUUUAGUCCCUGCCUGGGUCACCAAUUGUCGGCCCCCGCGGACA
AL132952.2/268954-268858 UGUCCUGAAGGCAGGCAAUUGAUGACCCAGACAAGGACUAAUCAAGAUUGUCGAUCUAGUCCCUGCCUGGGUCACCAAUUGUCGGCCCCCGCGGGCA
#=GC SS_cons             :<<<<<<--<<<-<<<<<<<<-<<<<<<<<-<<-<<<<<<<<<_________>>>->>>>>>->>->>>>>>>>->>>>>>>>->>>-->>->>>>:
#=GC RF                  UGccccGAAGGcaGgcaauuGAuGacccaGacaaGGacuaaucAaGAUUGUcgauuuaguCCcugcCuggguCacCaauugcCGgCCccCgcgggCA
//
# STOCKHOLM 1.0

#=GF AC   RF00906
#=GF ID   MIR1122
#=GF DE   microRNA MIR1122
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   77.00
#=GF TC   77.00
#=GF NC   76.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.99 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000382;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17543110
#=GF RT   Cloning and characterization of microRNAs from wheat (Triticum aestivum
#=GF RT   L.).
#=GF RA   Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q
#=GF RL   Genome Biol. 2007;8:R96.
#=GF WK   MicroRNA
#=GF SQ   12


CT009587.1/113990-114124 GAAAUACUCCCUUCGUCCGAAAAUACUUGUCAUCAAAAUAA-AUAUAAGAGGAUGUAUUUAGAUAUAUUUUAGU-UCUAAAUACAUUCAAUUUUAUCCAUUUUGAUGACAAGUAUUUUCGGACGGAGGGAGUA-UAUU
AB238931.1/2749-2883     GUAGUACUCCCUCCGUCCGAAAAUACUUGUCAUCAAAAUGG-ACAAAAAGGGAUGUAUUUAGAACUAAAAUACA-UCUAGAUACAUCCCCUUUUAUUCAUUUUGAUGACAAGUAUUUCCGGACGGAGGGAGUA-CAUC
AY963808.1/10854-10724   CACAUACUCCCUCCGUCCGGAAAUACUUGUCAUCAAAAUGG-AUAAAAGGGGAUGUAUCUAGACAUAUUUUAGU-UCUAGAUACAUCUCUUUUUAGUCACUUUGAUGACAAGUAUUUUCGGACGGAGGGAGUA-----
AF459085.1/1867-1743     UAAAUACUCCCUCCGUCCGGAAGUACUUGUCGUCAAAAUGG-AAAGAAAUGGAUGUAUCUAGAACUAAAAUACG-UCUAGAUACAUCC----------AUUUCUAUGACAAAUAAUUCCGGACGGAGGGAGUA-UAAU
DQ871219.1/236267-236133 UACGUACUCCCUCCGUCCCAAAAUUCUUGUCUUAGAUUUGU-CUAAAAACGGAUGUAUCAAGUCACGUUUUAGU-AUUAGAUACAUCCGUAUCUAGACGAAUCUAAGACAAGAAUUUUGGGACGGAGGGAGUA-CAAG
AF548379.1/5968-6092     AUUAUACUCCCUCCGUCCGAAAUUAUUUGUCGGAGAAAUG-----------GAUGUAUCUAGACGUAUUUUAGU-UCUAGAUACAUCCAUUUUUAUCCAUUUCUGCAACAAGUAGUUCCGGACGGAGGGAGUA-UCAU
AF277239.1/1056-1188     CAAAUACUCCCUCCGUCCCAAAAUUCUUGUCAUAGAUUUGU-CUAAAUACGGAUGUAUCUAGUCAUGUUUUAGU-GUUAGACACAUUCAUAUCUAAACAAAUCUAAGACNAGAAUUUUGGGACGGAGGGAGUA---UU
AY821732.1/670-536       CAUGUACUCCCUCCGUCCCAAAAUUCUUGUCUUAGAUUUGU-CUAAAUACGGAUGUAUCAAGUCACGUUUUAGU-AUUAGAUACAUCCGUAUCUAGGCAAAUCUAAGACAAGAAUUUUGGAACGGAGGAAGUA-UAAG
DQ145552.1/803-667       UAGUUACUCCCUCCGUCCGGAAAUACUUGUCACCAAAAUGGAUAAAAGGGGGAUGUAUCUAGAUGUAUUUUAGU-UCUAGAUACAUUUCUUAUUAUCCAUUUUGAUGACAAGUAUUUUCGAACGGAGGGAGUACGUUU
DQ267106.1/58607-58473   AAUGUACUCCUUUUGUCCUAAAAUUUGUGUCUUAGAUUUGU-CUACAUACGAAUGUAUUUAUUCACAUUUUAGU-GUUAGAUACAUUCGUAUUUAAAUAAAUUUAAGAUAAGAAUUUUGGGACAGAGGAAGUA-UAUA
EF059989.1/343417-343552 GCUGUACUCCCUCCGUCCAACAAAAGAUGUCUCAAGUUUGU-CAAAAUUUGGAUGUAUCUAGACAUGACUUAGUGUAUAGAUGCAUUCAAAUUUAGUCAAAAUUGAGACAUCCUUUGUUGGACGGAGGAAGUA-CCAU
AY083681.1/2466-2333     --ACUACUCCCUCCGUCACAAAAAGGAUGUCUCAAGUUUGU-UUGAAUUUGGACGAAUCUAUAUAUUAAAUAGUGUCUAGAUACAUCCAAGUUUAGACAAAUUUGAUACAUCCUUUUCGGGACGGAGGGAGUA-CAUG
#=GC SS_cons             ::::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<--------.---------<<<<<<<<<<<<___________.>>>>>>>>>>>>----------------->>>>>>>>>>>>>>>>>>>>>>>>>>>>>.::::
#=GC RF                  uaaaUACUCCCUCCGUCCggaAaugcuUGUcuuaaAuuUGu.auAaAuauGgAuGuaUcuAgacaUauuuUAGU.ucUagAuaCaUcCauaUUUAuaCAaaUuuaagACAagcauUuccGGACGGAGGGAGUA.uauu
//
# STOCKHOLM 1.0

#=GF AC   RF00907
#=GF ID   mir-941
#=GF DE   microRNA mir-941
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   106.40
#=GF NC   57.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000387;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [2]
#=GF RM   19784364
#=GF RT   Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic
#=GF RT   stem cells and neural precursors.
#=GF RA   Goff LA, Davila J, Swerdel MR, Moore JC, Cohen RI, Wu H, Sun YE, Hart RP
#=GF RL   PLoS One. 2009;4:e7192.
#=GF WK   MicroRNA
#=GF SQ   2


AADB02020304.1/29478-29390 CCCGGCUGUGUGCACAUGUGCCCAGGGCCCGGGACAGCGCCACGGAAGAGGACGCACCCGGCUGUGUGCACAUGUGCCCAGGGCCCGGG
ABBA01021431.1/13824-13912 CCCGGCUGUGUGGACAUGUGCCCAGGGCCCAGGACAGCGCCACGGAAGAGGACACACCCGGCUGUGUGGACAUGUGCCCAGGGCCCAGG
#=GC SS_cons               <<<<<<<-<<-<-<<<<<<<<-<<-<<<<-<<<---<<<<<-<____>->>->>>->>>>>>>->>->>>>>>>>-->>>->>->>>>>
#=GC RF                    CCcGGCcGuGUGgaCauGugCcCaGgGCCcgGGAcAGcGCCACGGAAGAGGACgCACCcGGCcGuGUGcaCauGuGcCCaGgGcCCgGG
//
# STOCKHOLM 1.0

#=GF AC   RF00908
#=GF ID   MIR529
#=GF DE   microRNA MIR529
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   83.80
#=GF NC   68.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000388;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17635765
#=GF RT   MicroRNAs in loblolly pine (Pinus taeda L.) and their association with
#=GF RT   fusiform rust gall development.
#=GF RA   Lu S, Sun YH, Amerson H, Chiang VL
#=GF RL   Plant J. 2007;51:1077-1098.
#=GF RN   [2]
#=GF RM   18687877
#=GF RT   A diverse set of microRNAs and microRNA-like small RNAs in developing rice
#=GF RT   grains.
#=GF RA   Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C
#=GF RL   Genome Res. 2008;18:1456-1465.
#=GF WK   Mir-529_microRNA_precursor_family
#=GF SQ   3


AAAA02013151.1/14888-14754 UCGUGAAGGCUAAAUGGAGAAGAGAGAGAGUACAGCUUUGGGCGGUUUAGUUGUUAGAUGGUGGAAGUACUUGCGACGCCUACUACCCUUUUCACCAAGGCUGUACGCUCCCUCUUCUUCUCUUAGCUU--UUUAUG
AAAA02006244.1/79559-79429 ACAUCGAGGCUAAAGGAAGAAGAGAGAGAGUACAGCCUUAGU----UCAGAUCACAUAUGACU--AUCUUUUGCGAGUCUGAUCGAUACUCUGAUGAAGGCUGUACCCUCUCUCUUCUUCUCUUAGCUUCUUGAUGC
AY946855.1/130-4           AU--CGAGGCUAAAGGAAGAAGAGAGAGAGUACAGCCUUAGU----UCAGAUCACAUAUGACU--AUCUUUUGCGAGUCUGAUCGAUACUCUGAUGAAGGCUGUACCCUCUCUCUUCUUCUCUUAGCUUCUUGAU--
#=GC SS_cons               ::::<<--<--<<-<<<<<<<<<<<<<<-<<<<<<<<<____...._________________..________________________________>>>>>>>>>->>>>>>>>>>>>>>->>-->---->>::::
#=GC RF                    acaUcaAGGCUaaAgGaaGaaGaGaGaGAGuaCaGCcuUaGu....UcAGaUcacAuAUGacu..AucuuUUGCGAguCugAucgauacUcUgAugAagGCuGuaCcCuCuCuCuuCuuCcCuuAGCUUCUugauug
//
# STOCKHOLM 1.0

#=GF AC   RF00909
#=GF ID   mir-883
#=GF DE   microRNA mir-883
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   63.50
#=GF NC   57.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000389;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   17989215
#=GF RT   RNA sequence analysis defines Dicer's role in mouse embryonic stem cells.
#=GF RA   Calabrese JM, Seila AC, Yeo GW, Sharp PA
#=GF RL   Proc Natl Acad Sci U S A. 2007;104:18097-18102.
#=GF RN   [3]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   MicroRNA
#=GF SQ   3


AAHY01211886.1/6262-6339 U-GCAAUGCAUUACUGAGAAUGGGUAGCAGUCACUUUGUACUA-UGAGUAACUGCAACAUCUCUCAGUAUUGUAAGGUUC
AAHY01211887.1/3534-3610 -UGCACUAUAAUGCUGAGAG-AAGUAGCAGUUACUUUAUUCUA-UAAGUAACUGCAACAGCUCUCAGUAUUGUAAGGCUC
AAHX01115170.1/8183-8259 U-GCACU-CAAUGCUGAGAG-AAGUAGCAGUUACUUUUUACUCUUAAGUAACUGCAACAUCUCUCAGUAUUGUAAGGCUC
#=GC SS_cons             :.<<--<<<<<<<<<<<<<<.--<<-<<<<<<<<<<_______._>>>>>>>>>>->>-->>>>>>>>>>>>>>-->>::
#=GC RF                  U.GCAcugcaauaCuGaGaG.aaGuAGCaGuuaCuuUaUaCUa.UaaGuaaCuGCAaCAuCuCuCaGuauugcaAGGCUC
//
# STOCKHOLM 1.0

#=GF AC   RF00910
#=GF ID   mir-873
#=GF DE   microRNA mir-873
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   93.40
#=GF NC   46.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000390;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   Mir-873_microRNA_precursor_family
#=GF SQ   3


AAHY01034958.1/42063-42139 GUGUGCAUUUGCAGGAACUUGUGAGUCUCCUAUUGAAAAUAGACAGGAGACUGACAAGUUCCCGGGAACACCCACAA
AAHX01036096.1/13504-13428 GUGUGCAUUUGCAGGAACUUGUGAGUCUCCUAUUGAAAAUGGACAGGAGACUGACAAGUUCCCGGGAACACCCACAA
AL158072.9/123404-123328   GUGUGCAUUUGCAGGAACUUGUGAGUCUCCUAUUGAAAAUGAACAGGAGACUGAUGAGUUCCCGGGAACACCCACAA
#=GC SS_cons               :::<<<____>>><<<<<<<<<-<<<<<<<<-<<_______>>->>>>>>>>->>>>>>>>>-<<<____>>>::::
#=GC RF                    GUGuGCAUUUGCaGGaaCuuGuGaGuCuCCuAucGAAAAUggaCaGGaGaCuGaCaaGuuCCCGGGAACACCCACAA
//
# STOCKHOLM 1.0

#=GF AC   RF00911
#=GF ID   mir-672
#=GF DE   microRNA mir-672
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   60.00
#=GF NC   59.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000391;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF RN   [2]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [3]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   Mir-672_microRNA_precursor_family
#=GF SQ   7


ABDC01238457.1/396-297     GAUGGUGAUUUGGCCCUUUAGUUUUGAGGUUGGUGUACUGUGUG-UGAGUACACAUAU--UUAUCACACACAGUCACUAUCCUCGAAACUAAGGGUGCACAUC
AANG01619273.1/1456-1357   AUAUGGUGUCUAGCCCUUUAGUUUUGUGGUUGAUGUACUGUGUG-CAAGUAUAUACAU--UUAUCACGUGCAGUCAUUGUCUUUGAAAGUGAGCAUGCAUCUU
AAGV020467248.1/1689-1588  GAUGGCAAUCUAGCCCUUUAGUUUUGAGGUUGGUGUACUGUGUG-UGAGUAUAUAUAUACUUAUCACACACAGUAGCUAUCUUCAAAAGUGAGGGUGCACAUC
AAKN02029883.1/10222-10321 GAUGGUUAUACAGAACUUUAGUUUUGAGGUUGGUGUACUGUGUGUGGG-UAUACAUAU--UUAUCCCACACAGCCACUAUGUUUCAAAGCAAAGGUGCACAUC
AAWR02034187.1/41002-40903 GAUGGCGAUCUAGCCCUUUAGUUUUGAGGUUGGUGUACUGUGUG-UGAGUAUAUAUAU--UUAUCACACAUAGGCAAUAUCUUUGAAAGUGAGGGUGCACGUC
AAHX01111751.1/5045-4946   GAUGGUGAUCUAGCCCUUUAGUUUUGAGGUUGGUGUACUGUGUG-UGAGUAUACAUAU--UUAUCACACACAGUCGCCAUCUUCGAAAGUGAGGGUGCACAUC
AL671963.9/91658-91559     GAUGGUGAUCUAGCCCUUUAGUUUUGAGGUUGGUGUACUGUGUG-UGAGUAUACAUAU--UUAUCACACACAGUCACUAUCUUCGAAAGUGAGGGUGCACAUC
#=GC SS_cons               ::::::::::::::<<<<<<-<<<<<<<<-<<<<<-<<<<<<<<.<<<__________..___>>>>>>>>>>>>>>>>->>>>>>>>->>>>>>::::::::
#=GC RF                    gAugGuuAUcUAGccCuucaGuuucgaggUugguGUaCuGuGuG.uGaGUAUAuAUAU..UUAuCaCaCaCaGuCaccaUccucgaaagugagGgUGCAcaUc
//
# STOCKHOLM 1.0

#=GF AC   RF00912
#=GF ID   mir-877
#=GF DE   microRNA mir-877
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   49.00
#=GF NC   43.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000392;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   17964270
#=GF RT   Mammalian mirtron genes.
#=GF RA   Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC
#=GF RL   Mol Cell. 2007;28:328-336.
#=GF RN   [4]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   MicroRNA
#=GF SQ   13


AANU01228141.1/3731-3646     GUAGAGGAGAUGGCGCAGGGG--ACACGGGCU--AAGACUCGGGG------GUUCCUGGGACCCUCAGACAUGUGU-CCUCUUCUCCCUCCUCCCAG
AADB02009988.1/731206-731291 GUAGAGGAGAUGGCGCAGGGG--ACACGGGCA--AAGACUUGGGG------GUUCCUGGGACCCUCAGACGUGUGU-CCUCUUCUCCCUCCUCCCAG
AAHY01132265.1/16958-16874   GUAGAGGAGAUGGCGCAGGGG--ACACAAGGU--AGGCCUUGCGG------GUCUGUGGA-CCCUUGGACAUGUGU-CCUCUUCUCCCUCCUCCCAG
AANG01354420.1/2007-2092     GUAGAGGAGAUGGCGCAGGGG--ACAUGGGCU--AAGAGUUGGGG------GUUCCUGGAACCUUUGGACAUGUGU-CCUCUUCUCCCUCCUCCAGG
ABDC01371804.1/471-554       GUAGAGGAGAUGGCGCAGGGG--ACAC-AGGU--AAGACUUGGGG------UUCUUGGGG-CCCUUGAACAUGUGU-CCUCUUCUCCCUCCUCCCAG
AAFC03013893.1/72422-72338   GUAGAGGAGAUGGCGCAGGGG--ACACGGGCU--AAGACUGGGGG------CUCCCGGGA-CCCCCCAACAUGUGU-CCUCUUCUCCCUCCUCCCAG
AACN010926608.1/195-110      GUAGAGGAGAUGGCGCAGGGG--ACAUGGGCU--GAGACUUGGGA------GUUCCUAGAACCUCUAGACAUGUGU-CCUCUUCUCCCUCCUCCAGG
AAIY01783760.1/194-278       GUAGAGGAGAUGGCGCAGGGG--ACACGGGCG--GAGACU-GGGG------CUGGCUGGGGUCCUCCAACAUGUGU-CCUCUUCUCCCUCCUCCCAG
AB113357.1/20621-20705       GUAGAGGAGAUGGCGCAGGGG--ACACGGGCC--AAGACUAG-GG------GUUGCUGGGACCUCCCGACAUAGGU-CCUCCUCUCCCUCCUCCCAG
AAQQ01546407.1/17-106        GUAGAGGAGAUGGCACAGGGG--ACAUGGUCUGCGAGACUUGGGGGGAGGGGCCUCUAGG-CCCUCAGACAUGAGU-CCUCUUCUUCCUCC---CAG
AANN01156499.1/1623-1711     GGAGAAGGUAAAGAACAUGACAUACAUGGGCU--AGAGUUUGGGG------GUUCCUGGAACCUUUGAACAUGUUUCCUUAUCUUCUCUCCUCCUAG
BX883048.1/162947-162863     GUAGAGGAGAUGGCGCAGGGG--ACACAAGGU--AGGCCUUGCGG------GUCUGUGGG-CCCUUGGACAUGUGU-CCUCUUCUCCCUCCUCCCAG
AAWR02009855.1/2715-2800     GUAGAGGAGAUGGCGCAAGGG--ACACAAACG--AAGACUUGGGG------GUUCCUGGGACCUUCAGACAUAUGU-CCUCUUCUCCCCCCUCCCAG
#=GC SS_cons                 :::<<<<<<--<<-<-<<<<<..<<<<_____..___________......_____________________>>>>.>>>>>->->>>>>>>>::::
#=GC RF                      GUAGAGGaGAUGGCGCAgGGG..AcacGGGcu..AAGacUUGGGG......gUuucUGGgACCcUuagACAUgugU.CCUcUUCUCCCuCCUCCcAG
//
# STOCKHOLM 1.0

#=GF AC   RF00914
#=GF ID   mir-674
#=GF DE   microRNA mir-674
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   119.20
#=GF NC   53.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000394;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF RN   [2]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [3]
#=GF RM   16973894
#=GF RT   Mouse microRNA profiles determined with a new and sensitive cloning
#=GF RT   method.
#=GF RA   Takada S, Berezikov E, Yamashita Y, Lagos-Quintana M, Kloosterman WP,
#=GF RA   Enomoto M, Hatanaka H, Fujiwara S, Watanabe H, Soda M, Choi YL, Plasterk
#=GF RA   RH, Cuppen E, Mano H
#=GF RL   Nucleic Acids Res. 2006;34:e115.
#=GF RN   [4]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   MicroRNA
#=GF SQ   2


AAHY01019858.1/11200-11299 GGCCUAGUCAUCACCCUGAGCCUUGCACUGAGAUGGGAGUGGUGUAAGGCUCAGGUAUGCACAGCUCCCAUCUCAGAACAAGGCUCGGGUGUGCUCAGCU
AAHX01024498.1/50044-50143 GGCCUAGUCCUCACCCUGAGCCUUGCACUGAGAUGGGAGUGGUGUAAGGCUCAGGUAUGCACAGCUCCCAUCUCAGAACAAGGCUCGGGUGUGCACAGCU
#=GC SS_cons               ::::::::::::::<<<<<<<<<<<--<<<<<<<<<<<<<<<<<<<--<<____>>->>>>>>>>>>>>>>>>>>>-->>>>>>>>>>>:::::::::::
#=GC RF                    GGccUAGUcaUcAcCCcGaGCCuuGcACuGaGauGGGaGcgGuGcaAGgCUcAGGcAugCaCcgCuCCCauCuCaGAACaaGGCuCgGGUGUGcacAGcU
//
# STOCKHOLM 1.0

#=GF AC   RF00915
#=GF ID   mir-760
#=GF DE   microRNA mir-760
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   76.00
#=GF NC   36.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000395;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [2]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   7


AADC01005182.1/14823-14903 GGCG-CGUCGCCCCCCUCAGUCCACCAGAGCCCGGAUACCUCAGAAAUUCGGAUUCUGGGUUCUGUGGGGAGCGAAAUGCAA
ABDC01171198.1/108-187     GGCGGUGUCGCCCCCCUCAGUCCACCAGAGCCCGGAUGCCUCAGAAAUUCGG-CUCUGGGU-CUGUGGGGAGCGAAAUGCAG
AAIY01391264.1/968-890     GGCG-CGUCGCCCCGCUCAGUCCGCCAGAGCGCGGAUGUCUCCGAAAUUCGG-CUCUGGGU-CUGUGGGGUGCGAAAUGCAA
AC134918.5/80739-80661     GGCG-CGUCGCCCCCCUCAGGCCACCAGAGCCCGGAUACCUCAGAAAUUCGG-CUCUGGGUCUGUGG-GGAGCGAAAUGCAA
AAKN02004112.1/23939-24017 GGUA-CGGCGCCCCCCUCAGUCUGCCAGAGCCCGGAUGCCUCAGAAAUUCGG-CUCUGGGU-CUGUGGGGGACGAAAUGCAA
ABSL01211407.1/9538-9616   GGCG-CGUCGCCCCCCUCAGUCCACCAGAGCCCGGAUACCUCAGAAAUUCGG-CUCUGGGUCUGUGG-GGAGCGAAAUGCAA
AL049796.28/42934-42856    GGCG-CGUCGCCCCCCUCAGUCCACCAGAGCCCGGAUACCUCAGAAAUUCGG-CUCUGGGUCUGUGG-GGAGCGAAAUGCAA
#=GC SS_cons               ::<<.--<<<<-<<<<-<<<--<-<<<<<<<<-<<<<_________>>>>>>.>>>>>>>-->>>->>>>->>>-->>>:::
#=GC RF                    GGcg.cGuCGCCCCcCUcagUCcaCCaGaGCCCGgauacCUCAGAAauuCGG.CuCuGGgUccuguGgGGaGCGAAaugCAA
//
# STOCKHOLM 1.0

#=GF AC   RF00917
#=GF ID   mir-708
#=GF DE   microRNA mir-708
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   70.10
#=GF NC   69.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.86 -Z 549862.597050 CM SEQDB
#=GF CL   CL00086
#=GF DR   MIPF; MIPF0000397;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [3]
#=GF RM   20935160
#=GF RT   Next-generation sequencing identifies the natural killer cell microRNA
#=GF RT   transcriptome.
#=GF RA   Fehniger TA, Wylie T, Germino E, Leong JW, Magrini VJ, Koul S, Keppel CR,
#=GF RA   Schneider SE, Koboldt DC, Sullivan RP, Heinz ME, Crosby SD, Nagarajan R,
#=GF RA   Ramsingh G, Link DC, Ley TJ, Mardis ER
#=GF RL   Genome Res. 2010;20:1590-1604.
#=GF WK   Mir-708_microRNA_precursor_family
#=GF SQ   21


AACN010115628.1/268-181    AACUGCCCUCAAGGAGCUUACAAUCUAGCUGGGGGUGAACGGCUUGCAC-----AUGAACGCAACUAGACUGUGAGCUUCUAGAGGGCAGGGA
AAIY01519317.1/2158-2071   GACUGCCCUCAAGGAGCUUACAAUCUAGCUGGGGCUAAAAGACUUGCAC-----ACAAACACAACUAGACUGUGAGCUUCUAGAGGGCAGGGA
AAYZ01001621.1/4751-4664   AGCUGCCCUCAAGGAGCUUACAAUCUAGCUGGGGCUGAAUGACUUGCAC-----GAGAACACAACUAGACUGUGAGCUUCUAGAGGGCAGAGG
AANN01537336.1/506-419     GACUGCCCUCAAGGAGCUUACAAUCUAGCUGGGGGUGAAUGAUUUGACC-----UUGAACGCAACUAGACUGUGAGCUUCUAGAGGGCAGGGA
AAPN01374968.1/10334-10242 CCCUGCCCACAAGGAGCUUACAGUCUAGAGGGGGGGAAAUAUAUAUUAAUGUCUGUCUCCCCUUCUAGACCGUAAGCUUCUUGUGGGCAGGGA
AY865990.1/521-441         GCCUGCCCUCCAGGAGCUCACAAUCUA-GUGGGAA--AAUCAGAAAGGU--------AACUCAA-UAGACUGUGAGCUCCUUGAGGGCAAGGA
AANG01285199.1/10387-10307 GCCUGCCCUCCAGGAGCUCACAAUCUA-GUGGGAAAGUCUGAAAGGCAA----------CUCAA-UAGACUGUGAGCUCCUUGAGGGCAAGGA
AALT01512689.1/4650-4730   GCCUGCCCUCCAGGAGCUCACAAUCUAGUGGGGAAGUCA------GCAU-----GGCAACUC-AAUAGACUGUGAGCUCCUUGAGGGCAAGGA
AAPY01689043.1/421-341     GCCUGCCCUCCAGGAGCUCACAAUCUAGUGAGAAAGUCA------GGAA-----GGCAA-CUCAAUAGACUGUGAGCUCCUUCAGGGCAGGGA
AY865992.1/546-466         GCCUGCCCUCCAGGAGCUUACAAUCUA-GUGGGAAAG--UUAGAAAGGC--------AACUCAA-UAGACUGUGAGCUCCUUGAGGGCAAGGA
CAAA01059217.1/1247-1327   GCCUGCCCUCCAGCAGCUCACAAUCUA-GUGGGAG--AAUCAGAAAGGC--------AACUCAA-UAGACUGUGAGCUCCUUGAAGGUAGGGA
AY865991.1/530-450         GCCUGCCCUCCAGGAGCUCACAAUCUA-GUGGGAA--AGUCAGAAAGGA-----A---ACUCAA-UAGACUGUGAGCUCCUUGAGGGCAAGGA
AY865987.1/535-455         GCCUGCCCUCCAGGAGCUCACAAUCUA-GUGGGAA--AGUCACAAAGGA-----A---ACUCAA-UAGACUGUGAGCUCCUUGAGGGCAAGGA
AY865994.1/541-461         GCCUGCCCUCCAGGAGCUCACAAUCUA-GUGGGAA--AGUCAGAAAGGU-----A---ACUCAA-UAGACUGUGAGCUCCUUGAGGGCAAGGA
AY865986.1/518-438         GCCUGCCCUCCAGGAGCUCACAAUCUA-GUGGGAA--AGUCAGAAAGGC-----A---ACUCAA-UAGACUGUGAGCUCCUUGAGGGCAAGGA
AC160527.9/84987-85074     GACUGCCCUCAAGGAGCUUACAAUCUAGCUGGGGGUAGAUGACUUGCAC-----UUGAACACAACUAGACUGUGAGCUUCUAGAGGGCAGGGG
AAKN02012362.1/20992-20912 GCCUGCCCUCCAGGAGCUCCCAAUCUA-GUGGGAAAGUCUU-----AAA-----AGUAACUCAA-UAGACUGUGAGCUCCUUGAGGGCAAGGA
AAGV020456123.1/349-436    GACUGCCCUCAAGGAGCUUACAAUCUAGCUGGGGGUGAGAGACCUGCAC-----AGGAUCUCAACUAGACUGGGAGCUUCUAGAGGGCAGGGG
AP001838.4/125049-124962   AACUGCCCUCAAGGAGCUUACAAUCUAGCUGGGGGUAAAUGACUUGCAC-----AUGAACACAACUAGACUGUGAGCUUCUAGAGGGCAGGGA
AANU01189273.1/88875-88788 AACUGCCCUCAAGGAGCUUACAAUCUAGCUGGGGGUAAAUGACUUGCAC-----AUGAACACAACUAGACUGUGAGCUUCUAGAGGGCAGGGA
ABRR01099085.1/1908-1995   AACUGCCCUCAAGGAGCUUACAAUCUAGCUGGGGGUAAACGACUUGCAC-----AUGAACGCAACUAGACUGUGAGCUUCUAGAGGGCAGGGA
#=GC SS_cons               ::<<<<<<<<-<<<<<<<<<<<-<<<<<-<<-<--<<--<<_____>>-.....->>-->->>->>>>>->>>>>>>>>>>->>>>>>>>:::
#=GC RF                    gccUGCCCuCaAGgAGCUcaCaAUCUAguuGGGaaggaaugaauagcaa.....accAACuCaAcUAGACuGugAGCUcCUuGaGGGCAgGGA
//
# STOCKHOLM 1.0

#=GF AC   RF00918
#=GF ID   mir-872
#=GF DE   microRNA mir-872
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   46.00
#=GF TC   46.00
#=GF NC   45.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000399;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   Mir-872_microRNA_precursor_family
#=GF SQ   6


AAFR03055299.1/38289-38205 UUUCUGUUCACAGUGCUACCACUUAGUUCAGGUCCUCAUUUUCUCUUGCCUGGACUAUUGAAGUAGCCUUCACUGAACUGGUCUC
AAQQ01543934.1/2534-2614   UACUUGUUAGAA-GGUUACUUGUUAGUUCAGGACCUCAUUAUUUCCUGCCUGAACUAUUGUAGUAGCCUCCU---AACUGGUCAC
AAYZ01052122.1/818-897     UACUUGUUAGAA-GGUUACUUGUUAGUUCAGGACCUUGUUAUU-CUUGUCUGAACUAUUGUAGUAGCCUCCU---AACUGGUCUC
ABDC01451942.1/2331-2411   UACUUGUUAGAA-GGUUACUUGUUAGUUCAGGACCUCAUUAUUUUUUGCCUGAACUAUAGCAGUAGCCUCUU---AACUGGUGUC
AL772277.13/13725-13805    AACUUGUUAGAA-GGUUACUUGUUAGUUCAGGACCUCAUUACUUUCUGCCUGAACUAUUGCAGUAGCCUCCU---AACUGGUUAU
AAWR02015956.1/93482-93561 UACUUGUUAGAA-GGUUACUUGUUAGUUCAGGACCUCGUUAUUUCUUGCCUGAACU-UUGCAGUAGCCUCCU---AACUGGUCUC
#=GC SS_cons               :<<<-<<<<<-<.<<<<<<<---<<<<<<<<<________________>>>>>>>>>---->>>>>>>>->>...>>>->>>:::
#=GC RF                    UaccUGUUagaA.gGcUACuugUUAGUuCAGGaCCUCAUUaUUUcuUGCCUGaACUAUUGuaGUAgCcUccu...AACUggucuC
//
# STOCKHOLM 1.0

#=GF AC   RF00919
#=GF ID   mir-874
#=GF DE   microRNA mir-874
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   69.50
#=GF NC   37.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000401;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [2]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF WK   Mir-874_microRNA_precursor_family
#=GF SQ   4


AAFC03124123.1/10967-10892 UUAGCCCUGCGGCCCCACGCACCAGGGUAAGAGAGA--CUCACUUCCUGCCCUGGCCCGAGGGACCGACUGGCUGGGC
AANG01341167.1/1542-1465   UUAGCCCUGCGGCCCCACGCACCAGGGUAAGAGAGAGUCUCGCUUCCUGCCCUGGCCCGAGGGACCGACUGGCUGGGC
AAHX01089817.1/5137-5212   UUAGCCCUGCGGCCCCACGCACCAGGGUAAGAGAGA--CUCGCUUCCUGCCCUGGCCCGAGGGACCGACUGGCUGGGC
AC004021.1/119249-119172   UUAGCCCUGCGGCCCCACGCACCAGGGUAAGAGAGACUCUCGCUUCCUGCCCUGGCCCGAGGGACCGACUGGCUGGGC
#=GC SS_cons               :::<<<<--<<<<<<<-<<--<<<<<<<<__________________>>>>>>>>-->>->>>>>>>------->>>>
#=GC RF                    UUAGCCCUGCGGcCCCACGCACCaGGGuaAGAGAGAaUCUCgCUUCCugCCCuGGCCCGAGGGaCCGACUGGCUGGGC
//
# STOCKHOLM 1.0

#=GF AC   RF00920
#=GF ID   MIR444
#=GF DE   microRNA MIR444
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   110.00
#=GF TC   111.60
#=GF NC   107.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000402;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17543110
#=GF RT   Cloning and characterization of microRNAs from wheat (Triticum aestivum
#=GF RT   L.).
#=GF RA   Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q
#=GF RL   Genome Biol. 2007;8:R96.
#=GF RN   [2]
#=GF RM   18353984
#=GF RT   Genome-wide analysis for discovery of rice microRNAs reveals natural
#=GF RT   antisense microRNAs (nat-miRNAs).
#=GF RA   Lu C, Jeong DH, Kulkarni K, Pillay M, Nobuta K, German R, Thatcher SR,
#=GF RA   Maher C, Zhang L, Ware D, Liu B, Cao X, Meyers BC, Green PJ
#=GF RL   Proc Natl Acad Sci U S A. 2008;105:4951-4956.
#=GF RN   [3]
#=GF RM   18312648
#=GF RT   Identification of novel and candidate miRNAs in rice by high throughput
#=GF RT   sequencing.
#=GF RA   Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK
#=GF RL   BMC Plant Biol. 2008;8:25.
#=GF WK   Mir-444_microRNA_precursor_family
#=GF SQ   4


AK063114.1/148-276 UGCAAUUGGGGGCAGCAAGCUAGAGGUGGCAACUGCAUAAUUUGCAAGAAA-UUGU------------------UGG----------------------------------------CUGAAGAUCAUACCGAUGAUAUUCUUGCAAGUUAUGCAGUUGCUGCCUCAAGCUUGCUGCCUCCUGUUGCC
CU406550.1/236-400 UGCAUAUGGUGGCACCAAGCAUGAGGUUACAACUGCAUUACUUGCAAGGGAAUCACAAGUCACAAGAAACACAUGUUAUUACAAUGGAUAAUCAA----------------------UGGGUCAUCAUACU-AUGACUUUCUUGCAAGUUGUGCAGUUGUUGCCUCAAGCUUGCUGCCUCCGUCUGUC
AK066992.1/189-316 UGCAAGUGGAGGCGGCAAGCUAGAGACAGCAACUGCAUAUCUUGCAAGAAAAUC--------------------GGU----------------------------------------UUUAUGGCCAUACCGAUGAUUUUCUUGCAAGCUGUGCAGUUGUUGUCUCAAGCUUGCUGCCUCCCUUUGCC
AK249841.1/242-414 CGCAUGUGGCGGCACCAAGCAUGAGGCAACAACUGCAGUACUUGUGGGGAAGGCACAAG---------------UAGGACACCAACAUUACCUGCAAGCAAGACGCAAAAUUAAUAGAACAUCACCAUACUUGUGGCUUUCUUGCAAGUCGUGCAGUUGCUGCCUCAAGCUUGCUGCCUCCCUUUGCC
#=GC SS_cons       :<<<<--<<<<<<<-<<<<<--<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<_____..............._____________________......................_________________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-->>>>>->>>>>>>-->>>>:
#=GC RF            uGCaggUGGcGGCacCaaGCauGaGGcagCaaCuGCacgacuuGcaaGaaagucacAAG...............uauaauACaAacauUAauuaa......................uuuaucAuCAUACuuaUgacuuuCuugCaagucguGCaGuuGcugCCuCAAGCuuGCuGCCgCCuucuGCC
//
# STOCKHOLM 1.0

#=GF AC   RF00921
#=GF ID   mir-665
#=GF DE   microRNA mir-665
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   52.10
#=GF NC   42.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000404;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   6


AAHY01103461.1/3314-3221   AGAACAGGGUCUCCUUGAGGGGCCUCUGCCUCUAUCCAGGAUUAUGUUUUUAUGACCAGGAGGCUGAGGUCCCUUACAGGCGGCCUCUUACUCU
AADB02016115.1/2057-2147   AGAGGAGGGUCUCCUCGAGGGGUCUCUGCCUCUACCCAGGACU---CUUUCAUGACCAGGAGGCUGAGGCCCCUCACAGGCGGCUUCUUACUCU
AAYZ01391475.1/1433-1523   GGAGGAGGGUCUCCUUGAGGGGCCUCUGCCUCUCCCCAGGGCU---CCUCUGUGACCAGGAGGCUGAGGCCCCUCACAGGCGGCUUCUCACUAU
AAPY01359946.1/1294-1384   GGAGGAGGGUCUCCUUGAGGGGUCUCUGCCUCUCCCCAGGACU---CUUCCGUGACCAGGAGGCUGAGGCCCCUCACAGGCGGCUUCUUACUCU
AAFC03050876.1/48735-48825 GGAGGAGGGUCUCCUUGAGGGGUCUUGGCCUCUGCCCAGGACU---CUUUCAUGACCAGUAGGCCGAGGCCCCUCACAGGCGGCUGCUUACUCU
AAQQ01350179.1/242-331     AGAGAAGGGUUGCCUUGAGGGGCCGCUGCCUCUAACCAGGACU----UUGCAUGACCAGGAGGCAGAGGCCCCUCAUAGGCGGCCUCUUACUCU
#=GC SS_cons               :::::::::<<-<<<<<<<<<<<<<<<<<<<<<---<<-<<__...___>>->>---->>>>>>>>>>>>>>>>>>->>>->>:::::::::::
#=GC RF                    aGAggAGGGucuCCuuGaGGGGcCucgGCCucuacCCaGggcU...cUUccauGACCAggaGGCcgaGgCCCCuCacaGGCggCuuCUUACUcU
//
# STOCKHOLM 1.0

#=GF AC   RF00922
#=GF ID   mir-673
#=GF DE   microRNA mir-673
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   100.40
#=GF NC   33.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000405;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   MicroRNA
#=GF SQ   2


AAHY01103461.1/17656-17581 GAGGGGCUCACAGCUCUGGUCCUUGGAGCUCCAGAGAAAAUGUUGCUCCGGGGCUGAGUUCUGUGCACCCCCCUUG
AAHX01046579.1/14940-14865 GAGGGGCUCACAGCUCCGGUCCUUGGAGCUCCAGAGAAAAUGUUGCUCCGGGACUGAGUUCUGUGCACCCCCCUUG
#=GC SS_cons               <<<<<<--<<<<<--<<<<<<<<-<<<<<--<<_______>>-->>>>>>>>>>>>->-->>>>>---->>>>>>:
#=GC RF                    gaGGGGCUCaCaGCUCcgGuCCuUGGaGCUCCaGAGAAAAuGUUGCuCCgGGaCugAGUUCuGuGCACCCCCCuuG
//
# STOCKHOLM 1.0

#=GF AC   RF00925
#=GF ID   MIR1027
#=GF DE   microRNA MIR1027
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   miRBase; Daub J
#=GF SS   Predicted; RNAalifold; Daub J
#=GF GA   150.00
#=GF TC   172.10
#=GF NC   80.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.52 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000414;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17601824
#=GF RT   Common functions for diverse small RNAs of land plants.
#=GF RA   Axtell MJ, Snyder JA, Bartel DP
#=GF RL   Plant Cell. 2007;19:1750-1769.
#=GF WK   MicroRNA
#=GF SQ   2


ABEU01006583.1/57263-57122 GUGCAAGAGCAGAUACUUAAGUCGAAGAGCAUCUUUCUAUCUUCUCUUCCAAUCUAUUGAUCUGCCCUUCCAAUACUAUCAGAUCAAUAGAUUGGAAGAGCAGAUCGAAAAAUGCUCUCACCUUAAGGAGAGACAGCGACUC
ABEU01006585.1/184-43      GUGCAAGAGCAGAUACUUAAGUCGAAGAGCAUCUUUCUAUCUUCUCUUCCAAUCUAUUGAUCUGCCCUUCCAAUACUAUCAGAUCAAUAGAUUGGAAGAGCAGAUCGAAAAAUGCUCUCACCUUAAGGAGAGACAGCGACUC
#=GC SS_cons               :::::::::::::::<<<<<<--<<-<<<<<<-<<<<-<<<<-<<<<<<<<<<<<<<<<<<<<<_______________>>>>>>>>>>>>>>>>>>>>>->>>>->>>>->>>>>>>>-->>>>>>:::::::::::::::
#=GC RF                    GUGCAAGAGCAGAUACuuaaGUCGaAGaGCauCuuuCUauCuUCuCuuCCaauCuauuGauCuGCCCUUCCAAUACUAUCaGauCaauaGauuGGaaGaGCaGauCGaaaAauGCuCuCACCuuaaGGAGAGACAGCGACUC
//
# STOCKHOLM 1.0

#=GF AC   RF00926
#=GF ID   MIR1151
#=GF DE   microRNA MIR1151
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   120.00
#=GF TC   151.80
#=GF NC   94.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000415;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17538623
#=GF RT   miRNAs control gene expression in the single-cell alga Chlamydomonas
#=GF RT   reinhardtii.
#=GF RA   Molnar A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC
#=GF RL   Nature. 2007;447:1126-1129.
#=GF WK   MicroRNA
#=GF SQ   2


ABCN01001818.1/8177-8320 GUGGUGUGUGCCGCUCACCGGCCACGGCAGUCCGGGGCUCAUAACCUGUUAACGCGCGCAGCCCGCAGGCAGUCCCUGCGGGCCGCGCGGUGCUAACGGGUUGUGGGACCCGGACUGACGCGGCUGGCAUGUGACA-GGCCCCAC
ABCN01001818.1/6412-6556 GUGGAGCGUGUCUCUCACCGGCCGCGGCAGUCCGGGGCUCAUAACCUGUUGACGCGCGCAGCCCGCGGGCAGUCCCUGCGGGCCGCGCGGCGCUAACGGGGUGUGGGACCCGGACUGACGCGGCCGGCAUGUGGCAACGUAUCGU
#=GC SS_cons             <<<<-<<<<<<<<<---<<<<<<<<<-<<<<<<<<<-<<<<<<<<<<<<<<-<<<<<<<-<<<<<<<<<_____>>>>>>>>>->>>>->>>->>>>>>>>>>>>>>->>>>>>>>>->>>>>>>>>--->>>>>>->>>->>>>
#=GC RF                  gcggagcgugccgcucAccggccgcggcaguccggggcccacaacccguugAcgcgcgcAgcccgcgggcAguccccgcgggccgcgcggcgccaacggguugugggAcccggacugAcgcggccggcAugcggcaacgcaccgc
//
# STOCKHOLM 1.0

#=GF AC   RF00927
#=GF ID   mir-582
#=GF DE   microRNA mir-582
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   106.00
#=GF NC   65.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000417;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF WK   MicroRNA
#=GF SQ   7


AANU01256201.1/20665-20762 AUCUGUGCUCUUUGAUUACAGUUGUUCAACCAGUUACUAAUCUACCUAAUUGUAACUGGUUGAACAACUGAACCCAAAGGGUGCAAAGUAGAAACAUU
ABDC01143060.1/9478-9381   AUCUGUACUCUUUGGUUACAGUUGUUCAACCAGUUACUAAUCUAACAAAUUGUAACCAGUUGAACAACUGAACCCAAAGGGUGCAAAGUAGAAACAUU
AAQQ01491097.1/18175-18272 AUCUGUACUCUUUGGUUACAGUUGUUCAACCAGUUACUAAUCUAACUAACUGUAACCGGUUUAACAACUGAACGCAAAGGGUGCAAAGUGGAAAAAUU
AALT01573678.1/1712-1809   AUCUGUACUCUUUAGUUACAGUUGUUCAACCAGUUACUAAUCUAGCGAACUGUAACCAGUUGAACAACUGAACCUGAAGGGUGCAAAGUGGAAGCAUU
AAKN02031390.1/26225-26322 AUCUGUACUCUUUGGUUACAGUUGUUCAACCAGUUACUAAUUUAACUAAUUGUAACCGGUUGAACAACUGAACCCAAAGGGUGCAAAGUGAAAACAUU
AAHX01012929.1/14288-14385 AUCUGUACUCUUUGGAUACAGUUGUUCAACCAGUUACUAAUCUAACUAAUUGUAACCUGUUGAACAACUGAACCCAAAGGGUGCAAAGUUGGAAACAU
AC012315.5/114825-114728   AUCUGUGCUCUUUGAUUACAGUUGUUCAACCAGUUACUAAUCUAACUAAUUGUAACUGGUUGAACAACUGAACCCAAAGGGUGCAAAGUAGAAACAUU
#=GC SS_cons               :::<<<<<<<<<<<----<<<<<<<<<<<<--<<<<<______________>>>>>-->>>>>>>>>>>>---->>>>>>>>>>>:::::::::::::
#=GC RF                    AUCuGuaCuCuuuGguUACaGuuGuucaaCCAGuuaCUAAUcUAaCuAAuUGuaaCcgGuugaaCaaCuGAACcCaaaGgGugCaAAGUaGAAAcAuU
//
# STOCKHOLM 1.0

#=GF AC   RF00928
#=GF ID   mir-590
#=GF DE   microRNA mir-590
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   62.00
#=GF TC   63.10
#=GF NC   60.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000418;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF WK   Mir-590_microRNA_precursor_family
#=GF SQ   10


AANU01190949.1/13092-13188 UAGCCAGUCAGAAAUGAGCUUAUUCAUAAAAGUGCAGU---AUGGUGGAGUCAGUCUGUAA--UUUUAUGUAUAAGCUGGUCUCUAACUGAAACGUGCAGCA
AAQQ01313324.1/3303-3207   UAGCCAGUCAGAAAUGAGCUUAUUCAUAAAAGUACAGU---AUCAUCCAGUAAGUCUGUAA--UUUUAUGUAUAAGCUGGUCUCUGACUGAAGCACGCAACA
AAPN01308740.1/1340-1245   AAGCCAAUCAGAAAUGAGCUUAUCCAUAAAAGUACAGU---AUCGUC-AGUAAACCUGUAC--UUUUAUGGAUAAGCUAGUCUCUGAUUGAAACACGCAACA
AAPY01718744.1/4971-4879   UAGACAGUCAGAAGUGAGCUUAUUCAUAAAAGUAC-------AGUAUAAUACAACAAGUAA--CUUUAUGUAUAAGCUAGUCUCUGAUUGAAACAUGCAACA
AC091000.2/90050-89952     GAGC-AGUCAGAAAUGAACUUGCUCAUAAAAGUACAGUAGCAGUGAGCAGUAAGUCUGUAA--UUUUAUGUAUGAGCUGGUUUCUGACUAAAACGCGCAGCA
AF139987.1/67501-67594     CUAGCAACCAGAAAUGAACUUAUUCAUGAAAGUACAGU---AGCACACAGUGAGUCUAUAA--UUUUAUGUAUACACUGGUCUCUGG---AAGCAUGUGUCU
AANG01014751.1/283-382     UAGCCAAUCAGAAAUGAGUUUAUUCAUGAGAGUAUAGUA--UUCUUUUAAAAGCUCUAUCUGUCCUAAUAAGUGGUUUUGUGUUUGGUUGAAACCUUCCAUA
AAGV020627533.1/2369-2273  UAGCCAAUCCGAAAUGAGCGUAUUCAUAAAAUUACAGU---AUAAUCCAGCUAGCCUGUAA--UUUUAUGUAUAAACUAGUCUCUGAUUGAAACAUGCAACA
AC091403.3/33174-33078     UAGCCAAUCAGAAAUGAGCUUAUUCAUAAAAGUACAGU---AUAAUCCAGUAAACCUGUAA--UUUUAUGUAUAAGCUAGUCUCUGAUUGAAAAAUGCAACA
AC200709.3/54642-54738     UAGCCAGUCAGAAAUGAGCUUAUUCAUAAAAGUGCAGU---AUGGUGAAGUCAAUCUGUAA--UUUUAUGUAUAAGCUAGUCUCUGAUUGAAACAUGCAGCA
#=GC SS_cons               ::::<<<<<<<<-<<-<<<<<<<-<<<<<<<-<<<<<-...-<<<_____>>>-->>>>>-..>>>>>>>->>>>>>>->>->>>>>>>>::::::::::::
#=GC RF                    uAGcCaguCaGAAauGAgcuuauUCAUaAaaGuacAGU...AucguuuAgcgaauCUguaa..uuUuAUGuauaagcUagucUCuGacuGAAACaUGCaaCA
//
# STOCKHOLM 1.0

#=GF AC   RF00929
#=GF ID   mir-574
#=GF DE   microRNA mir-574
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   89.50
#=GF NC   77.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000419;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [4]
#=GF RM   19917043
#=GF RT   MicroRNA identity and abundance in porcine skeletal muscles determined by
#=GF RT   deep sequencing.
#=GF RA   Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C,
#=GF RA   Thomsen B
#=GF RL   Anim Genet. 2010;41:159-168.
#=GF WK   MicroRNA
#=GF SQ   3


AANN01784293.1/568-492 CGCGGGGCGUGUGAGUGUGUGUGUGUGAGUGUGUGUCGCUC---GGUCCACGCUCGUGCACACACCCGCACGCCCGCGCC
AB210286.1/35542-35465 UGCGGG-CGUGUGAGUGUGUGUGUGUGAGUGUGUGUCGCUCC-GGGUCCACGCUCAUGCACACACCCACACGCCCGCACU
AC108044.5/88266-88343 UGCGGG-CGUGUGAGUGUGUGUGUGUGAGUGUGUGUCGCUC-CGGGUCCACGCUCAUGCACACACCCACACGCCCACACU
#=GC SS_cons           <<<<<<.<<<<<<-<-<<<<<<<<<<<<<<<<<--<<____.._>>-->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>::
#=GC RF                cGcGGG.CGuGuGAGUGuGuGuGuguGaGuGuGUGuCGCUC..GGgUCCaCgCuCaugCaCaCaCCCaCaCGCCCgCgCu
//
# STOCKHOLM 1.0

#=GF AC   RF00931
#=GF ID   mir-879
#=GF DE   microRNA mir-879
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   96.30
#=GF NC   49.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000421;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   MicroRNA
#=GF SQ   2


AAHY01042346.1/1999-2074   UUCUAGGUCCAGAGGCUUAUAGCUCUAAGCCUUGGAUGAAAGAGGCUUAUGGCUUCAAGCUUUCGGAGCUGGAGAC
AAHX01028040.1/10798-10873 UUCUAGAUCCAGAGGCUUAUAGCUCUAAGCCUUGGAUAAAAGAGGCUUAUGGCUUCAAGCUUUCGGAGCUGGCGAC
#=GC SS_cons               <<<<<<-<<<--<<<<<<--<<<<-<<<<<<<<________>>>>>>>>->>>>-->>>>>>-->>>->>>>>>::
#=GC RF                    uuCuaGauCCAGagGCuuAUaGCuCuaaGCCuuGGAUaAAAgaGGCuuaUgGCuUCaaGCuuUCGGaGCugGagAC
//
# STOCKHOLM 1.0

#=GF AC   RF00932
#=GF ID   mir-471
#=GF DE   microRNA mir-471
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   109.60
#=GF NC   63.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000423;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   MicroRNA
#=GF SQ   2


AAHY01211886.1/3511-3588   AGCAGUGCUUUACGUAGUAUAGUGCUUUUCACAUUAAACAAAAAGUGAAAGGUGCCAUACUAUGUAUAGGAAGGCUUA
AAHX01115171.1/16979-17056 AGCAGUGCUUUACGUAGUAUAGUGCUUUUCACAUUACACAAAAAGUGAAAGGUGCCAUACUAUGUACAGGAAGGCUUA
#=GC SS_cons               :::::::<<-<<<<<<<<<<-<<<<<<<<<<<-<<______>>->>>>>>>>>>>->>>>>>>>>>->>:::::::::
#=GC RF                    AGCAGUGCuUuaCguaGuauAGugCuuuuCaCAuuAaACAAaaAGuGaaagGugCCauaCuauGuauaGGAAGGCUUA
//
# STOCKHOLM 1.0

#=GF AC   RF00933
#=GF ID   mir-875
#=GF DE   microRNA mir-875
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   74.10
#=GF NC   63.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000424;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus.
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [2]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   MicroRNA
#=GF SQ   9


AANU01254699.1/42635-42560   UUAGUGGUACUAUACCUCAGUUUUAUCAGGUGUUC--CUAAAAUCACCUGGAAAUACUGAGGUUGUGUCUCACUGAAC
AADB02011901.1/592222-592147 UUAGUGGUACUAUACCUCAGUUUUAUCAGGUGUUC--UUAAAAUCACCUGGAAACACUGAGGUUGUGUCUCACUGAAC
AAHY01121086.1/51266-51342   UCUGUGGUACUAUACCUCAGUUUUAUCAGGUGUUCA-UUAAAAUCACCUGAAAAUACUGAGGCUAUGUUUCACUGAGC
AAPY01575258.1/7396-7320     UCAGUGGUACUAUACCUCAGUUUUAUCAGGUGUUCU-UUAAAAUCACCUGGAAAUACUGAGGUUGUGUUUCACUGAAC
AANN01737513.1/1623-1546     UUAGUGGUACUAUACCUCAGUUUUAUCAGGUGUUUCUUUAAAAUCACCUGGAAACACUGAGGUUGUGUUUCACUGAAC
AAFR03006570.1/12434-12510   UCUGUGGUACAAUACCUCAGUCUUAUCAGGUGUUAA-UUAAAAUCACCUGGAAAUGCUGAGGUUGCGUUUCACUGAAC
AAHX01050033.1/28442-28518   UCUGUGGUACUAUACCUCAGUUUUAUCAGGUGUUCA-UUCAAAUCACCUGAAAACACUGAGGCUGCGUCCCACUGAAC
AAPN01034672.1/28336-28412   UUAGUGGUACAAUACCUCAGUCUUAUCAGGUGUUCU-UUCAAUUCACCUGGCAAUACUGAGGUUGUGUCUCACUGAAC
AAIY01412163.1/1644-1720     UUGGUGGUACUAUACCUCAGCUUUAUCAGGUGUUCU-UUAUAAUCACCUGGAAAUACUGAGGUUGAGUUUCACUGAAC
#=GC SS_cons                 <<<<<<--<<---<<<<<<<<-<<-<<<<<<<____._______>>>>>>>->>->>>>>>>>--->>-->>>>>>::
#=GC RF                      UcaGUGGUaCuAUaCCUCaGuUUUAuCaGGUGUUcu.UUAAAAUCACCuGgAAAuaCuGAGGuUGuGuuUCACugAAC
//
# STOCKHOLM 1.0

#=GF AC   RF00934
#=GF ID   mir-463
#=GF DE   microRNA mir-463
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   106.40
#=GF NC   51.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000425;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [3]
#=GF RM   15901636
#=GF RT   MicroRNA Mirn122a reduces expression of the posttranscriptionally
#=GF RT   regulated germ cell transition protein 2 (Tnp2) messenger RNA (mRNA) by
#=GF RT   mRNA cleavage.
#=GF RA   Yu Z, Raabe T, Hecht NB
#=GF RL   Biol Reprod. 2005;73:427-433.
#=GF WK   MicroRNA
#=GF SQ   2


AAHY01211885.1/3872-3952   ACCCUGCUUUACCUAAUUUGUUGUCCAUCAUGUAAAACAUAAAUGAUGAUAGACACCAUAUAAGGUAGAGGAAGGUUCACU
AAHX01115171.1/13053-13133 ACCCUGUUUUACCUAAUUUGUUGUCCAUCAUGUAAAAUUUAAGUGAUGAUAGACGCCAAUUUGGGUAGAGGAAGGCUCACU
#=GC SS_cons               ::::::<<<<<<<<<<<-<<-<<<<<<<<<<___________>>>>>>--->>>>->>->>>>>>>>>>>:::::::::::
#=GC RF                    ACCCUGcuuuaCCuaauUuGUuGuCCauCauGUAAAAuuUAAauGauGAUAGaCaCCauauuaGGuagagGAAGGuUCACU
//
# STOCKHOLM 1.0

#=GF AC   RF00935
#=GF ID   mir-876
#=GF DE   microRNA mir-876
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   93.00
#=GF NC   62.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000430;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   MicroRNA
#=GF SQ   3


AACN010229644.1/1222-1302  UGAAGUGCUGUGGAUUUCUUUGUGAAUCACCAUAUCUAAGCUAAUGUGGUGGUGGUUUACAAAGUAAUUCAUAGUGCUUCA
AAHY01034957.1/14912-14992 UCACGUGCUAUGGAUUUCUCUGUGAAUCACUAUAUCAAAUCUAGUGUGGUAGUGGUUUACAAAGUAAUUCAUAGUGCUUCA
AAHX01036095.1/17291-17211 UCAAGUGCUGUGGAUUUCUCUGUGAAUCACCAUAUCAAAUCUAAUGUGGUGGUGGUUUGCAAAGUAAUUCAUAGUGCUUCA
#=GC SS_cons               <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<_________________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                    ugaaGugCuguGgauuuCucuGugaauCaCcaUAUCaAAuCUAaUGUGGugGuGguuuaCagaGuaauuCacaGugCuuca
//
# STOCKHOLM 1.0

#=GF AC   RF00936
#=GF ID   mir-744
#=GF DE   microRNA mir-744
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   80.50
#=GF NC   45.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000431;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16973894
#=GF RT   Mouse microRNA profiles determined with a new and sensitive cloning
#=GF RT   method.
#=GF RA   Takada S, Berezikov E, Yamashita Y, Lagos-Quintana M, Kloosterman WP,
#=GF RA   Enomoto M, Hatanaka H, Fujiwara S, Watanabe H, Soda M, Choi YL, Plasterk
#=GF RA   RH, Cuppen E, Mano H
#=GF RL   Nucleic Acids Res. 2006;34:e115.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-744_microRNA_precursor_family
#=GF SQ   5


AAHY01093966.1/11357-11258 GGCUGGGCAAGGUGCGGGGCUAGGGCUAACAGCAGUCUUACUGACGGUUUCCUGGAAACC-ACACACAUGCUGUUGCCACUAACCUCAACCUUACUCGGUC
AAHX01064429.1/28843-28942 GGCUGGGCAAGGUGCGGGGCUAGGGCUAACAGCAGUCUUACUGAGGGUCUCCUGGAGACC-ACACACAUGCUGUUACCACUAACCUCAACCUUACUCCGUC
AAFC03122196.1/37207-37108 GGUUGGGCGGGGUGCGGGGCUAGGGCUAACAGCAGGCUCACUGACGGUUUCCCGGAAACC-ACGCACAUGCUGUUGCCACUAACCUCAACCUUACUCGGUC
DQ015703.1/62228-62327     GGUUGGGCAAGGUGCGGGGCUAGGGCUAACAGCAGUCUUACUGAAGGUUUCCUGGAAACC-ACGCACAUGCUGUUGCCACUAACCUCAACCUUACUCGGUC
ABRQ01516308.1/352-451     GGUUGGGCAAGGUGCGGGGCUAGGGCUAACAGCAGUCUCACUGAAGGUUUCCUGGAAACCA-CACACAUGCUGUUGCCACUAACCUCAACCUUACUCGGUC
#=GC SS_cons               ::<<<<<<<<<<<--<<<<----<<<-<<<<<<<-----------<<<<<<___>>>>>>.------->>>>>>>>>>----->>>>->>>>>>>>>>>::
#=GC RF                    GGccGgGcaaGGuGCGgGGCUAGGGcUaaCaGCaGuCUuACUGAaGGuuuCCuGGaaaCC.ACaCACAuGCuGuugCCACUAACCcCAaCCuugCcCggUC
//
# STOCKHOLM 1.0

#=GF AC   RF00937
#=GF ID   mir-653
#=GF DE   microRNA mir-653
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   70.30
#=GF NC   69.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000435;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat.
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF WK   MicroRNA
#=GF SQ   12


AANU01288201.1/25475-25570     UUCAUUCCUUCAGUGUUGAAACAAUCUCUACUGAACCAG-CUUCAA--ACAAAUUCACUGGAGUUUGUUUCAAUAUUGCAAGAAU-GAUAAGAUGGAAGC
AAHY01051069.1/93453-93550     UUCAUUCUUUCAGUGUUGAAACAAUCUCUACUGAACCAAGCUCCAAA-GCGAGUUCACUGGAGUUUGUUUCAGUAUUGCAGGAGU-GCUAAGUGUGAAGC
AACC02000014.1/1175297-1175392 UUCAUUCCUUCAGUGUUGAAACAAUCUCUACUGAACCAG-CUUCAA--ACAAGUUCACUGGAGUUUGUUUCAAUAUUGCAAGAAU-GAUAAGAUGGAAGC
AAQQ01558075.1/2832-2735       UUCAUUCCUUCAGUGUUGAAACAAUCUCUACUGAACCAGGCUCCAAA-CCAAGUUCACUGGAGUUUGUUUCAAUAUUGCAAGAAU-GAUAAAAUUGAAGC
AAFC03096979.1/9216-9311       CUCAUUCCCUCAGUGUUGAAACAAUCUCUGUUGAACCAU-GUUACA--GGAAGUUCACUGGAGUUUGUUUCAACAUUGGAGGAAU-GAUAAGAUGCUACU
AALT01658113.1/578-675         UUCAUUUUUUCAGUGUUGAAACAAUCUCUGCUGAACCAGACUGCAAA-UCAAGUUCACUGGAGUUUGUUUCAAUAUUGGAAGAAU-GUUAAUAUGAUACU
AANN01380427.1/400-497         CUCAUUCCUUCAGUGUUGAAACAUUCUCAGCUGAACCAGACUCCAAA-CCAAGUUCACUGGAGUUUGUUUCAAUAUUGCAAGAAU-GAUAAUAUGAUGCU
AAHX01028271.1/82616-82518     UUCAUUCUUUCAGUGUUGAAACAUUCUCUACUGAACCAAGCUCCAAA-ACAAGUUCACUGGGGUUUGUUUCACUAUUGCAAGAAUUGCUAAGUAUGAAGC
ABDC01215275.1/1099-1003       CUCAUUCCUUCAGUG-UGAAACACUCUCUAGUGAACCAGGCUUCAAA-CGAAAUUCACUGGAGUUUGUUUCAAUAUUGCAAGAAU-GGUAAGAUUGAAGC
AAWR02013812.1/75511-75414     CUCAUUCCUUCAGUGUUGAAACAAUCUCUGCUGAACCAGGCUCCAAA-CUACGUUCACUGGAGUUUGUUUCAAUAUUGCAAGAAU-GAUAAAAUUGAUGC
AAGV021023725.1/902-805        CUCAUUUCUUCAGUGUUGAAACAAUCUCUGGUGAGCUAA-GUCCCAAGUCAUGUUCACUGGAGUUUGUUUCAACACUGUAUGAAU-GAUUAAAUUUAUGC
ACBE01071805.1/1503-1600       CUCAUUCCUUCAGUGUUGAAACAAUCUCUAUGGAACCAGGCUCCAAA-CCAAGUUCACUGGAGUUUGUUUCAAUAUUGCAAGAAU-GGUAAGAUUGAUGC
#=GC SS_cons                   :<<<<<<<<-<<<<<<<<<<<<<<-<<<<<-<<<<<___________.____>>>>>->>>>>->>>>>>>>>>>>>>->>>>>>.>>::::::::::::
#=GC RF                        uuCauuccuUCaguguuGaaaCaaUCuCcacuGaaCCAggcUccaAA.ucAaGuuCaCugGaGUuuGuuuCaacacuGcaggaau.GaUAAgAuugaagc
//
# STOCKHOLM 1.0

#=GF AC   RF00939
#=GF ID   mir-504
#=GF DE   microRNA mir-504
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   97.10
#=GF NC   60.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000437;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   21346006
#=GF RT   An evolutionarily conserved, alternatively spliced, intron in the p68/DDX5
#=GF RT   DEAD-box RNA helicase gene encodes a novel miRNA.
#=GF RA   Moore HC, Johnston M, Nicol SM, Bourdon JC, Thompson AM, Hutvagner G,
#=GF RA   Fuller-Pace FV
#=GF RL   RNA. 2011;17:555-562.
#=GF RN   [4]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF WK   Mir-504_microRNA_precursor_family
#=GF SQ   6


AANU01115486.1/42717-42635 GCUGCUGUUGGGAGACCCUGGUCUGCACUCUAUCUGUAUUCUUACUGAAGGGAGCGCAGGGCAGGGUUUCCCAUACAGAGGGC
AAHY01210867.1/281-199     GCUCCUGUUGGGAGACCCUGGUCUGCACUCUAUCUGUAAACUUACUGAAGGGAGAGCAGGGCAGGGUUUCCCAUACAGAGGGC
AALT01458873.1/10731-10813 GCUGCUGUUGGGAGACCCUGGUCUGCACUCUAUCUGUAAGCAUUUUUAAGGGAGCGCAGAGCAGGGUUUCCCAUACAGAGGGC
AAHX01114801.1/334-252     GCUGCUGUUGGGAGACCCUGGUCUGCACUCUGUCUGGAAACUUACAGAAGGGAGAGCAGGGCAGGGUUUCCCAUACAGAGGCA
AAGV021074623.1/492-410    GCUGCUGUUGGGAGACCCUGGCCUGCACUCUGUCUGUAUGUUUAUUGAAGGGAGCGCAGGGCAGGGUUUCCCAUACAGAGGGC
Z82193.1/8683-8601         GCUGCUGUUGGGAGACCCUGGUCUGCACUCUAUCUGUAUUCUUACUGAAGGGAGUGCAGGGCAGGGUUUCCCAUACAGAGGGC
#=GC SS_cons               ::::<<<<<<<<<<<<<<<<-<<<<<-<<<<-<<-<<<____>>>->>-->>>>->>>>>->>>>>>>>>>>>->>>>:::::
#=GC RF                    GCUgCuGuuGGGagaCCCuGGcCuGCACuCuaucUguaaacuuacugaAGgGaGaGCaGgGCaGGGuuuCCCaUaCaGAGGgc
//
# STOCKHOLM 1.0

#=GF AC   RF00940
#=GF ID   mir-327
#=GF DE   microRNA mir-327
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   59.80
#=GF NC   53.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000438;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   14691248
#=GF RT   Identification of many microRNAs that copurify with polyribosomes in
#=GF RT   mammalian neurons.
#=GF RA   Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G
#=GF RL   Proc Natl Acad Sci U S A. 2004;101:360-365.
#=GF WK   MicroRNA
#=GF SQ   2


AAHY01113307.1/12135-12074 AUGCCCUUAUAACUUGAGGGGCAUGAGGAUAGUCAGUAGUCCAACAUCCCUCUUGAUGGCAC
AAHX01100216.1/4169-4109   AUGCCCUCAU-CCUUGAGGGGCAUGAGGGUAGUCAGUAGCCUGAUGUCCCUCUUGAUGGCAC
#=GC SS_cons               :<<<<-<<<------<<<<<<<<<--<<<<________>>>>->>>>>>>>>->>>->>>>:
#=GC RF                    AUGCCCUcAUAaCUUGAGGGgcaUGAgGguAGUCAGUAgcCcaAuguCCCUCUUgAUGGCAC
//
# STOCKHOLM 1.0

#=GF AC   RF00941
#=GF ID   mir-434
#=GF DE   microRNA mir-434
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   113.70
#=GF NC   58.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000439;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15854907
#=GF RT   RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus.
#=GF RA   Davis E, Caiment F, Tordoir X, Cavaille J, Ferguson-Smith A, Cockett N,
#=GF RA   Georges M, Charlier C
#=GF RL   Curr Biol. 2005;15:743-749.
#=GF RN   [2]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction
#=GF RT   method.
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [3]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [4]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [5]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   Mir-434_microRNA_precursor_family
#=GF SQ   2


AAHY01103463.1/29559-29466 UCGACUCUGGGUUUGAACCAAAGCUCGACUCAUGGUUUGAACCAUUACUUAAUUCGUGGUUUGAACCAUCACUCGACUCCUGGUUCGAACCAUC
AAHX01046580.1/10858-10765 UUGACUCUUGGUUUGAACCACAGCUCGACUCAUGGUUUGAACCAUUGUCAAACUCGUGGUUUGAACCAUCACUCGACUCCUGGUUUGAAUCAUC
#=GC SS_cons               ::::::::::<<<<<<<<<<-<<-<<<<-<-<<<<<<<<<<<<<<__________>>>>>>>>>>>>>>->->>>>>>-->>>>>>>>>>::::
#=GC RF                    UuGACUCUuGguuugaaCCaaaGCuCGaCuCauGGuuugaaCCauUauuaAAuUCguGGuuugaaCCauCaCuCGaCuCCuGGuucgaacCAUC
//
# STOCKHOLM 1.0

#=GF AC   RF00942
#=GF ID   mir-1224
#=GF DE   microRNA mir-1224
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   69.20
#=GF NC   47.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000440;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [2]
#=GF RM   17964270
#=GF RT   Mammalian mirtron genes.
#=GF RA   Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC
#=GF RL   Mol Cell. 2007;28:328-336.
#=GF RN   [3]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF WK   MicroRNA
#=GF SQ   11


AAHY01126206.1/91640-91724 GUGAGGACUGGGGAGGUGGAGGGUAGCAUCAUUAGAGC-CAGAGCUCUGUCUCAGCUC-CCUCU-CCCCCCACCUCUUCUCUCCUCAG
AANU01300318.1/4618-4534   GUGAGGACUCGGGAGGUGGAGGGUGGCGCCGCCGGGGC-CAG-GCGCUGUCUAAGCUCGCUUCU-CCCCCCACCUCCUCUCUCCUCAG
AAFC03060523.1/41664-41749 GUGAGGACUCGGGAGGUGGAGGGUGGCGCUGCCAGGGC-CAGGGCACUGUCUCAGCUCGCUUCU-CCCCCCACCUCCUCUCUCCUCAG
AAQQ01259737.1/1179-1264   GUGAGGACUCGGGAGGUGGAGGGUAGUGUCACCAGAGC-UAGAGUGAUGUCUCAGCUCACUUCU-CCCCCCACCUCCUCUCUCCUCAG
ABDC01030158.1/9889-9974   GUGAGGACUCGGGAGGUGGAGGGUGGCAUCGUCAGGGC-CUGGACGCUGUCUUAGCUCGCUUCU-CCCCCCACCUCCUCUCUCCUCAG
AAYZ01168547.1/11688-11773 GUGAGGACUCGGGAGGUGGAGGGUAUCAUUGCCAGAGC-CGGGAUGCUGUCUCAACUCGCUUCU-CCCCCCACCUCCUCUCUCCUCAG
AAPY01267440.1/1166-1249   GUGAGGACUCGGGAGGUGGAGGGCGGCGUCGCCAGGGC-CGG-GCGCCGUCUCAGCCC-GCUCG-UCCCCCACCUCCUCUCUCCUCAG
AANN01718197.1/501-583     GUGAGGACUCGGGAGGUGGAGGGUGGCGCUGGCAGGCC-CCG-GCGCCGGCUCAGCUCGC--CU-CCCCCCACCUCCUCUCUCCUCAG
AAIY01561587.1/204-118     GUGAGGACUUGGGAGGUGGAGGGCGGCGUGGCCGGCCCGGCGGGCGCCGUCUCAGCUCGCCGCG-CCCCCCACCUCCUCUCUCCUCAG
AAGV020421475.1/1984-2069  GUGAGGACUCGGGAGGUGGAGGGUGGCCUCUUGAGGGC-CGG-GCGUUGUCUCAGUUCGCUUCUUCCCCCCACCUCCUCUCUCCUCAG
AC061705.16/19231-19147    GUGAGGACUCGGGAGGUGGAGGGUGGUGCCGCCGGGGC-CGG-GCGCUGUUUCAGCUCGCUUCU-CCCCCCACCUCCUCUCUCCUCAG
#=GC SS_cons               :<<<<<<----<<<<<<<<<<<<-----------<<<<._______________>>>>------.>>>>>>>>>>>>---->>>>>>:
#=GC RF                    GuGaGGaCUcGGGaGGuGGaGGGUgGcgucgccAGggC.caGgGcgcuGUCUcAGccCGcuUCu.CCCcCCaCCuCCUCUCuCCuCaG
//
# STOCKHOLM 1.0

#=GF AC   RF00943
#=GF ID   MIR824
#=GF DE   microRNA MIR824
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   100.00
#=GF TC   152.80
#=GF NC   82.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000442;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17182867
#=GF RT   A diverse and evolutionarily fluid set of microRNAs in Arabidopsis
#=GF RT   thaliana.
#=GF RA   Rajagopalan R, Vaucheret H, Trejo J, Bartel DP
#=GF RL   Genes Dev. 2006;20:3407-3425.
#=GF RN   [2]
#=GF RM   17299599
#=GF RT   High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent
#=GF RT   birth and death of MIRNA genes.
#=GF RA   Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS,
#=GF RA   Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC
#=GF RL   PLoS One. 2007;2:e219.
#=GF RN   [3]
#=GF RM   17704216
#=GF RT   MicroRNA-mediated regulation of stomatal development in Arabidopsis.
#=GF RA   Kutter C, Schob H, Stadler M, Meins F Jr, Si-Ammour A
#=GF RL   Plant Cell. 2007;19:2417-2429.
#=GF RN   [4]
#=GF RM   19815687
#=GF RT   Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in
#=GF RT   Arabidopsis.
#=GF RA   Moldovan D, Spriggs A, Yang J, Pogson BJ, Dennis ES, Wilson IW
#=GF RL   J Exp Bot. 2010;61:165-177.
#=GF WK   Mir-824_microRNA_precursor_family
#=GF SQ   12


AF389288.1/313-970     CUUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUACACCAAUACCCCCCAGUCUCUAAAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAACAUAGCUAGUUCGACAUACCAUACUACCCUUUUUAAAA---CUAUCCUAUAUGUUUGAUGCUAGCAUAGCGUAAUUUUGUGUUCUCAUGGUG---CAGCAGGGUUAGUUUAUUGUGUACCUCUAGAUAUAUAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGCCAAAAACUUUUAAAAAUU--AGUGAUCUGUUCCCCAAACCCCCAUUCAAUAAGAAAGGUCUACCUGUAGC-UCACAGUCACAGCUAUUAGAGCUGUCCUUGCUUCUUUGGGUUUACUGUUUUAGUUAAUUAGUUAC-CCUAUGAAAGUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUU-UUUAUUUGUAUUCGAACUAGUCCAAGCCGAUUCUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUCUAAAAUUGGGGAGU-GG-GGAGAUGUUUGGUUA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUGGAGG
AC189548.2/18653-19283 CUCGAGUUGUCUUUCAUGUCUAGACCAUUUGUGAGAAGGGAUUUUUUGUUUGCACCGUUCACCC-CAC--UCUCAAUCUGUAGUGAGU----------AUUAAGGAAAAUAGCUUGUUCAACAUAUCACACUACUCUUUUAGAAA---CAAAACUAUAUUUUAGAUGCUUUUCCAGCUUGAUAU-ACGUUGUUUUGUUA---U-GUAUACCUGUAUUCUCCCGGCUACCAAAACGUUAAGAAAUAAGGUGAACAUCUCCCCAAAACCUGCAUCCAAUUAGAAAGGUCUAGGUCACAGCCAUUACUUGCUAUCUCUCGAUUAAGCUAUUUUAUUUCUAUCAUCAUCAUCAGAUCAUUCAGGAGU-UAAGUAUAAAAUAAAAUACAUUA----AGUCCAUUCAUGACAUUUCUGGAUGCUGCAUACAUAAUAUU--UUGUUUUUGGACUAUGCCAC---ACUUCGGACAGACAUUUUUCCUACG--AGAUGUCAAACCUCU-GUCUGGAGUGUUAGAGGUAUUUCA---UGAUAGCUAAGAACUUG---AAUCUUGCACUACUUAGCUACACUAGUUUACUUCAUAGUAAAU-AACUUGGGGAGUGG-GGAAGGUGCUGGGUUAUUAGUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUUGAGG
FM164211.1/27-684      CUUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUACACCAAUACCCCCCAGUCUCUAAAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAACAUAGCUAGUUCGACAUACCAUACUACCCUUUUUAAAA---CUAUCCUAUAUGUUUGAUGCUAGCAUAGCGUAAUUUUGUGUUCUCAUGGUG---CAGCAGGGUUAGUUUAUUGUGUACCUCUAGAUAUAUAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGCCAAAAACUUUUAAAAAUU--AGUGAUCUGUUCCCCAAACCCCCAUUCAAUAAGAAAGGUCUACCUGUAGC-UCACAGUCACAGCUAUUAGAGCUGUCCUUGCUUCUUUGGGUUUACUGUUUUAGUUAAUUAGUUAC-CCUAUGAAAGUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUU-UUUAUUUGUAUUCGAACUAGUCCAAGCCGAUUCUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUCUAAAAUUGGGGAGU-G-GGGAGAUGUUUGGUUA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUGGAGG
FM164206.1/41-590      CUUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUGCACCAAUACCCACCAAUCUCUAUAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAAAAUAG-UAGUUCAACAUACCACACUACCCUUUUAAGUAGUAUCAUCCUAUAUGUUAUCUGCUACCUUAGCUAAAUUUUGCGUUCUCAUGGUGCUGCAGUAGGGUUAGUUUCUUGUGUACCUCUAGAUAUACAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGUCAAAA-----------CU--AGUGAUCUGUUCCCCUUGAU---------------------------------------------------------------------------------------------------------AUUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUUUUUCAUUUGUAUUCGAACUAGUCCAAGCCGAUUCUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUCUAAAAUUGGGGAGUG--GGGAGAUGUUUGGUUA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUGGAGG
FM164213.1/41-590      CUUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUGCACCAAUACCCACCAAUCUCUAAAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAAAAUAG-UAGUUCAACAUACCACACUACCCUUUUAAGUAGUAUCAUCCUAUAUGUUAUAUGCUACCUUAGCUAAAUUUUGCGUUCUCAUGGUGCUGCAGUAGGGUUAGUUUCUUGUGUACCUCUAGAUAUACAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGUCAAAA-----------CU--AGUGAUCUGUUCCCCUUGAU---------------------------------------------------------------------------------------------------------AUUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUUUUUCAUUUGUAUUCGAACUAGUCCAAGCCGAUUCUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUCUAAAAUUGGGGAGUG--GGGAGAUGUUUGGUUA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUGGAGG
FM164204.1/27-664      CUUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUACACCAAUACCCCCCAGUCUCUAAAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAACAUAGCUAGUUCGACAUACCAUACUACCCUUUUUAAAA---CUAUCCUAUAUGUUUGAUGCUAGCAUAGCGUAAUUUUGUGUUCUCAUGGUG---CAGCAGGGUUAGUUUAUUGUGUACCUCUAGAUAUAUAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGCCAAAAACUUUUAAAAAUU--AGUGAUCUGUUCCCCAAACCCCCAUUCAAUAAGAAAGGUCUACCUGUAGC-UCACAGUCACAGCUAUUAGAGCUGUCCUUGCUUCUUUGGGUUUACUGUUUUAGUUAAUUAGUUAC-CCUAUGAAAGUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUU-UUUAUUUGUAUU--------------------CUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUCUAAAAUUGGGGAGU-G-GGGAGAUGUUUGGUUA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUGGAGG
FM164231.1/41-590      CUUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUGCACCAAUACCCACCAAUCUCUAUAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAAAAUAG-UAGUUCAACAUACCACACUACCCUUUUAAGUAGUAUCAUCCUAUAUGUUAUCUGCUACCUUAGCUAAAUUUUGCGUUCUCAUGGUGCUGCAGUAGGGUUAGUUUCUUGUGUACGUCUAGAUAUACAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGUCAAAA-----------CU--AGUGAUCUGUUCCCCUUGAU---------------------------------------------------------------------------------------------------------AUUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUUUUUCAUUUGUAUUCGAACUAGUCCAAGCCGAUUCUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUCUAAAAUUGGGGAGUG--GGGAGAUGUUUGGUUA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUGGAGG
FM164236.1/41-590      CUUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUGCACCAAUACCCACCAAUCUCUAUAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAAAAUAG-UAAUUCAACAUACCACACUACCCUUUUAAGUAGUAUCAUCCUAUAUGUUAUCUGCUACCUUAGCUAAAUUUUGCGUUCUCAUGGUGCUGCAGUAGGGUUAGUUUCUUGUGUACCUCUAGAUAUACAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGUCAAAA-----------CU--AGUGAUCUGUUCCCCUUGAU---------------------------------------------------------------------------------------------------------AUUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUUUUUCAUUUGUAUUCGAACUAGUCCAAGCCGAUUCUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUCUAAAAUUGGGGAGUG--GGGAGAUGUUUGGUUA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUGGAGG
FM164232.1/27-684      CAUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUACACCAAUACCCCCCAGUCUCUAAAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAACAUAGCUAGUUCGACAUACCAUACUACCCUUUUUAAAA---CUAUCCUAUAUGUUUGAUGCUAGCAUAGCGUAAUUUUGUGUUCUCAUGGUG---CAGCAGGGUUAGUUUAUUGUGUACCUCUAGAUAUAUAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGCCAAAAACUUUUAAAAAUU--AGUGAUCUGUUCCCCAAACCCCCAUUCAAUAAGAAAGGUCUACCUGUAGC-UCACAGUCACAGCUAUUAGAGCUGUCCUUGCUUCUUUGGGUUUACUGUUUUAGUUAAUUAGUUAC-CCUAUGAAAGUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUU-UUUAUUUGUAUUCGAACUAGUCCAAGCCGAUUCUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUCUAAAAUUGGGGAGU-G-GGGAGAUGUUUGGUUA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUGGAGG
FM164199.1/41-590      CUUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUGCACCAAUACCCACCAAUCUCUAUAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAAAAUAG-UAGUUCAACAUACCACACUACCCUUUUAAGUAGUAUCAUCCUAUAUGUUAUCUGCUACCUUAGCUAAAUUUUGCGUUCUCAUGGUGCUGCAGUAGGGUUAGUUUCUUGUGUACCUCUAGAUAUACAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGUCAAAA-----------CU--AGUGAUCUGUUCCCCUUGAU---------------------------------------------------------------------------------------------------------AUUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUUUUUCAUUUGUAUUCGAACUAGGCCAAGCCGAUUCUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUAUAAAAUUGGGGAGUG--GGGAGAUGUUUGGUUA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUGGAGG
FM164218.1/41-590      CUUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUGCACCAAUACCCACCAAUCUCUAAAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAAAAUAG-UAGUUCAACAUACCACACUACCCUUUUAAGUAGUAUCAUCCUAUAUGUUAUAUGCUACCUUAGCUAAAUUUUGCGUUCUCAUGGUGCUGCAGUAGGGUUAGUUUCUUGUGUACCUCUAGAUAUACAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGUCAAAA-----------CU--AGUGAUCAGUUCCCCUUG---------------------------------------------------------------------------------------------------------AUAUUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUUUUUCAUUUGUAUUCGAACUAGUCCAAGCCGAUUCUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUCUAAAAUUGGGGAGUG--GGGAGAUGUUUGGUUA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUUUCAUGAACA
FM164221.1/41-590      CUUGAGUUGUCUCUCAUGUCUAGACCAUUUGUGAGAAGGGAGUUUUUGUUUGCACCAAUACCCACCAAUCUCUAUAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAAAAUAG-UAGUUCAACAUACCACACUACCCUUUUAAGUAGUAUCAUCCUAUAUGUUAUCUGCUACCUUAGCUAAAUUUUGCGUUCUCAUGGUGCUGCAGUAGGGUUAGUUUCUUGUGUACCUCUAGAUAUACAUUCUCUUGCUGCGUAGGGUUCCCAAGCUGUCAAAA-----------CU--AGUGAUCUGUUCCCCUUGAU---------------------------------------------------------------------------------------------------------AUUCUGAUCCUUCAGAAGUU-AGGUAUAGAAGUAAGUCGAUUAAGUUCAUUCAUGACUUUUCCAGAUGUUGCAUACAUAACUUUUUUUCAUUUGUAUUCGAACUAGUCCAAGCCGAUUCUCAAAAUCAUAUAAAAUCAUUUACACCUUGGUCAUGGUAGCUAAGAAUAUUGUAUCUAAAAUUGGGGAGUG--GGGAGAUGUUUGGUAA-UAUUCCCUUCUCAUCGAUGGUCUAGAUGUGCGAGGUGACUCUCAUGGAGG
#=GC SS_cons           <<<<<<<<<<<<<-<<<<<<<<<<<<<<<-<<<<<<<<<<<<<--------<<<<<-------<-<<<--<<<<_______________________________________________________________________...___________________________________________________..._____________________________________________________________________________________..__________________________________________________._______________________._______________________....______________.____________________________.________________________________________________________________._________________________________________________________________________________________________>>>>>>>>.---->>>>>-------.->>>>>>>>>>>>>->>>>>>>>>>>>>>>->>>>>>>>>>----->>>:
#=GC RF                CucGAGUuguCUCUCAugUCUAGACCAUuUgUGAGAAGGGAgUUUUUGUUUgCAcCAAUAcCCCCCAcUCUCucaAUUUGUAAGAAGUAUUAUGCUCAAUUAAGGAAaAUAGCUAGUUCAACAUAcCAcACUACcCUUUUaAaaA...uuAUcCUAUAUGUUagaUGCUAucuUAGCuuAAUUUUGcGUUcUcAUGGUG...cAGuAGGgUUAGUUUcUUgUGuAccUCUAGAUAUAuAuUcUcUUGcUGcGUAGgGUUCCcAAGCUGuCAAAAAaUUuuAAAaauU..AGUgAUcugUUcccCuugauauCauUCaAUaAgaaaggUuUAuuUgUAgC.UCAuagUCAcAgCuaUuAGagcU.UaauUguuuauUugggUuuAuUg....AGUuaAUUagUuAC.uuUaUGaAAgUcugAUcCUUcAGAAGUU.AGGUAUAGAAgUAAGUCGAUUAAgUUCAuUCAuGAcUUUUcCAGAUGUUGcAUAcAUAACUUUU.uUcAuuUGUAUUcGAAcUAgUcCAAGCcGAUucUcAAAAUCAUAUAAAAUCAUuUACAcCUUGGUcAUGgUAGcUAAgAAUAUUGUAUcUAAAAUUGggGAgUGG.GGGAGgUGcUuGGUUA.UAuUCCCUUCUCAuCgAUGGUCUAGAugUGCGAGgugACUCUCAUGgaGG
//
# STOCKHOLM 1.0

#=GF AC   RF00945
#=GF ID   mir-1226
#=GF DE   microRNA mir-1226
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   76.00
#=GF NC   65.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000444;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17964270
#=GF RT   Mammalian mirtron genes.
#=GF RA   Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC
#=GF RL   Mol Cell. 2007;28:328-336.
#=GF WK   MicroRNA
#=GF SQ   2


ABDC01287930.1/4361-4436 UGGGGGGCAGCCAGGACUGGAUGGGGUAGCUGGGAAGGGCCAGAAGGGUGGCCUCACUCAGCCCUGUGUUCCCUAG
AC139667.5/127698-127624 GUGAGGGCAUGCAGGCCUGGAUGGGGCAGCUGGGAUGGUCCAAAAGGGUGGCCUCAC-CAGCCCUGUGUUCCCUAG
#=GC SS_cons             :::<<<<<<<<<<<<<<<<<-<<<<<<-<<<-<<_____>>----->>>->>>>>>>->>>>>>>>>>>>>>>>::
#=GC RF                  uuGaGGGcacgCaGGgCuGGAuGgGGcAgCuGGGAaGGuCCAaAAGgGuGgCCuCaCUCaGcCCuGcguuCCCuAG
//
# STOCKHOLM 1.0

#=GF AC   RF00946
#=GF ID   mir-1225
#=GF DE   microRNA mir-1225
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   79.90
#=GF NC   57.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000445;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17964270
#=GF RT   Mammalian mirtron genes.
#=GF RA   Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC
#=GF RL   Mol Cell. 2007;28:328-336.
#=GF WK   MicroRNA
#=GF SQ   7


AAHY01131651.1/4809-4902   GUGGGUACGGCCCAGUGGGGGGGAGAGGGACACACCCUGGGUCU----CGCGAG-C-----CCAGGGUGCAGCCGGACUGACCGAGCCCCUGUGCCGCCCCCAG
AC145332.48/12658-12564    GUGGGUACGGCCCAGUGGGGGGGAGAGGGACGCACCCUGGGCCC----AGGGGAGC-----CCGGGGUGCAGCCGGACUGACGGAGCCCCUGUGCCGCCCCCAG
AANN01125789.1/79-170      GUGGGUACGGCCCAGUGGGGGGGAGAGGG--ACGCCCUGGGCCCACGUAG-----C-----CCGGGGCGCAGCCGGACUGACCGAGCCCCUGUGCCGCCCCCAG
AAFC03060160.1/33630-33722 GUGGGUACGGCCCAG--GGGGGGAGAGGGACGCACCCUGGGCCC----AG-----CAGAGCCCAGGGCGCAGCCGGACUGACCGAGCCCCUGUGCCGCCCCCAG
AAWR02040073.1/645-739     GUGGGUACGGCCCAGUGGGGGGGAGAGGGACACGCCCUGGGCUC----AGGUGAGC-----CCAGGGUGCAGCCGGACUGACUGAGCCCCUGUGCCGCCCCCAG
AF483210.1/36797-36891     GUGGGUACGGCCCAGUGGGGGGGAGAGGGACACACCCUGGGCCC----AGGUGAGC-----CCAGGGUGCAGCCGGACUGACCGAGCCCCUGUGCCGCCCCCAG
L43619.1/955-1044          GUGGGUACGGCCCAGUGGGGGGGAGAGGGACACGCCCUGGGCUC----UG-----C-----CCAGGGUGCAGCCGGACUGACUGAGCCCCUGUGCCGCCCCCAG
#=GC SS_cons               :::::::::::::::<<<<<<<<<-<<<<_______________....______._.....__________________________>>>>->->>->>>>>>:
#=GC RF                    GUGGGUACGGCCCAGuGGGGGGGaGaGGGACaCaCCCUGGGccc....aGguga.C.....CCaGGGuGCAGCCGGACUGACcGAGCCCCuGuGCCGCCCCCaG
//
# STOCKHOLM 1.0

#=GF AC   RF00947
#=GF ID   mir-929
#=GF DE   microRNA mir-929
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   68.80
#=GF NC   51.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000447;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17543122
#=GF RT   Computational and transcriptional evidence for microRNAs in the honey bee
#=GF RT   genome.
#=GF RA   Weaver DB, Anzola JM, Evans JD, Reid JG, Reese JT, Childs KL, Zdobnov EM,
#=GF RA   Samanta MP, Miller J, Elsik CG
#=GF RL   Genome Biol. 2007;8:R97.
#=GF RN   [2]
#=GF RM   20817720
#=GF RT   Functional shifts in insect microRNA evolution.
#=GF RA   Marco A, Hui JH, Ronshaugen M, Griffiths-Jones S
#=GF RL   Genome Biol Evol. 2010;2:686-696.
#=GF RN   [3]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF WK   MicroRNA
#=GF SQ   15


AABU01002551.1/121293-121380 AG--UCCUGGUGGAGCUCAAAUUGACUCUAGUAGGGAGUCC--UUUAA-----U-GAGCGACUCCCUAACGGAGUCAGAUUGAGCUGC--AAAGGAGC------GA
AAPQ01006437.1/316769-316856 AG--UCCUGGUGAAGCUCAAAUUGACUCUAGUAGGGAGUCC--UUCCA-----U-AAGCGACUCCCUAACGGAGUCAGAUUGAGCUAC--AAAGGAGC------GA
AAFS01002785.1/3282-3188     AU--UCCUGCAGCAGUUCAAAUUGACUCUAGUAGGGAGUCC--UUUUA-----UUGAGCGACUCCCUAACGGAGUCAGAUUGAAUUAC--CAAGGAACAGACAACA
AAPP01019549.1/24317-24405   --CUUCCUGGCGCAGUUCAAAUUGACUCUAGUAGGGAGUCC--UUUUA-----ACGAGAGACUCCCUAACGGAGUCAGAUUGAAUUAC--AAAGGAGC------GA
AAJJ01001068.1/14929-15018   --CAUCUUAAUCGGGGUCAAAUUGACUCUAGUAGGGAGUCC--GUUACUU---UAUAGCGACUCCCUAACGGAGUCAGGUUGACUCCCUUUGAGG---------GA
AAQB01008629.1/27335-27241   --CUUCCUGCGGCAGUUCAAAUUGACUCUAGUAGGGAGUCC--UUUAU-----AUAAGCGACUCCCUAACGGAGUCAGAUUGAAUUAC--AAAGGAACAACAACAA
AAZO01002930.1/51339-51442   UG--ACUCAGUCGGUGUCAAAUUGACUCUAGUAGGGAGUCCAGCUUUUAUUAAAAUGGCGACUCCCUAACGGAGUCAGAUUGACUCCUUCUGGGAAAACCAGCUGG
AANI01014363.1/204913-205006 AU--UCCUGCCGCAGUUCAAAUUGACUCUAGUAGGGAGUCC--UUUCA-----C-GAGCGACUCCCUAACGGAGUCAGAUUGAAUUAC--AAAGGACCCAGACAAC
AAPT01020159.1/382171-382077 --CUUCCUGCUGCAGUUCAAAUUGACUCUAGUAGGGAGUCC--UUUUA-----ACGAGCGACUCCCUAACGGAGUCAGAUUGAGUUAC--AAAGGACCAAGUCAAC
BAAB01013302.1/660-751       UG--AGCUCACGGAUGUUAAAUUGACUCUAGUAGGGAGUCC--GUUCC-------GCGCGACUCCCUAAUCGAGUCAGGUUGACUUCUUU---GAUGCUAAAUCGA
AAPU01011179.1/143817-143911 --UUUCCUCAUGCAGUUCAAAUUGACUCUAGUAGGGAGUCC--UUUUU-----UUUAACGACUCCCUAACGGAGUCAGAUUGAAUUUC--AGAGGACCCAGACAAC
AAAB01008089.1/34548-34645   --GCCUACUCGUGGGAUUAAAUUGACUCUAGUAGGGAGUCC--UUUUAUAC----GAGCGACUCCCUAACGGAGUCAGAUUGAUUCCGGUAGUGCACCUGUCCACA
AAWU01005610.1/5708-5616     UG--CCUACGACUGGCCCAAAUUGACUCUAGUAGGGAGUCC--UUGUGUAC----GAGUGACUCCCUAACGGAGUCAGAUUGAGCCCG--CUAGGAGC---AAGGA
AAGE02012461.1/76734-76637   UG--CCUACGACUGGUCCAAAUUGACUCUAGUAGGGAGUCC--UUGUGUAC----GAGUGACUCCCUAACGGAGUCAGAUUGAACCCGGUAGGAUGGAACCCCCUA
AAZX01003135.1/832-932       GA--ACUUAACUGGGGUCAAAUUGACUCUAGUAGGGAGUCC--CUGCAUUCAAUAUGGCGACUUCCUAACAGAGUCAGGCUGACUCCU-UUUAAGACGCUCACCGA
#=GC SS_cons                 ::..::::::::<<<<<<<--<<<<<<<<--<<<<<<<<<<..<____.....___>>->>>>>>>>>-->>>>>>>>-->>>>>>>:.:::::::::::::::::
#=GC RF                      ug..ucuuaaugcggguCAAAuUGACUCuAGUAGGGAGUCC..uUuua.....uagaGcGACUCCCUAACgGAGUCAgAUUGacccgu.uaaaGgAacuaaacaga
//
# STOCKHOLM 1.0

#=GF AC   RF00948
#=GF ID   mir-996
#=GF DE   microRNA mir-996
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   86.10
#=GF NC   59.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00095
#=GF DR   MIPF; MIPF0000449;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs.
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [2]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus.
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF WK   MicroRNA
#=GF SQ   5


AAAB01008898.1/1736227-1736132   UUAUUCUCCGCUUU-GUAGGCGUGCAUGUUUUCUAGUACACG-UU------UUCAGUUAAAGU-----UUCGUGACUAGAUUACAUGCUCGUCUAUAAUACUGAGAUCG
AABU01002774.1/21461087-21461183 UCUGACUCUAUUUU-GUCGGCGAACAUGG-AUCUAGUGCACG-GUG----GUUCAUGAUUAAG-----UUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAG
AAQB01008976.1/70319-70416       CUUGACUCUAUUUU-GUCGGCGAACAUGG-AUCUAGUGCACGGUUU----GUUCAUGAUUAAG-----UUCGUGACUAGAUUUCAUGCUCGUCUAUUAAGUUGGGUCAG
AAWU01001985.1/4335-4234         UUGAACUCAAUUUUCGUCGGCGUGCAUGU-AUCUGGUGCACG-GUUUUCAGUUGCAAUAUAGC-----UUCGUGACUAGAUUACAUGCUCGUCUAUGAAGUUGGGACCG
AAGE02017556.1/112272-112170     AGAAACUCAAUUUUCGUCGGCGUGCAUGA-AUCUGGUGCACG-GUU----UUCCAGUUGUAAUAUCGCUUCGUGACUAGAUUACAUGCUCGUCUAUGAAGUUGAGAUCC
#=GC SS_cons                     :<<<<<<<-<<<<-.<<-<<<<<<<<<<<.<<<<<<<-<<<<.___...._____________.....__>>>>>>>>>>>->>>>>>>>>>>->>->>>>->>>>>>>
#=GC RF                          ucgggCuCuacuuU.gucGgCGagCauGg.auCuaGugCaCG.gUu....gUucauuuauAau.....UUCGuGaCuaGauUcCauGcuCGuCUauuaaguUGaGcccg
//
# STOCKHOLM 1.0

#=GF AC   RF00949
#=GF ID   mir-983
#=GF DE   microRNA mir-983
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   99.60
#=GF NC   50.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000450;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [2]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila.
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010; [Epub ahead of print]
#=GF WK   MicroRNA
#=GF SQ   3


AABU01002762.1/6384496-6384594 UAUUAUAUUGCAAUAAUUAAAUAAUACGUUUCGAACUAAUGAUUUUCAGUUCAUUCAUUAGGUAGUUACGCAUUAUCUAGUUGUUGUAAACAUUCAACU
AAST01038470.1/3387-3484       UAAUAUCUUGCAGUAAUUUAGUAAUACCUUUCGAACACAUGAUUUUCAG-UCAUUCAUGAGUUCGUCAGGUAUUAUCUAGUUAUUGUAAACAUUCAACU
AAPQ01005960.1/9641-9544       UAUUAUGUUACAGUGAUUUAAUAAUUCGAUUCGAAGUUAUGUGCUUUA-AUCAUUCAUAAAUGCGAAACGGAUUAUUAAGUUAUUGUUAACAUUCAACU
#=GC SS_cons                   :::::::<<<<<<<<<<<<<<<<<<-<<<--<---<<<<<<<____________>>>>>>>--->-->>>->>>>>>>>>>>>>>>>>>::::::::::
#=GC RF                        UAuUAUauuaCaauaauucgauaauaCguUUCGAAcucauGauuUUcAGaUCAUuCaugaguucGuuacGuauuaucgaguuauuGuaaACAUUCAACU
//
# STOCKHOLM 1.0

#=GF AC   RF00950
#=GF ID   mir-927
#=GF DE   microRNA mir-927
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   63.60
#=GF NC   52.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000452;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila.
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010; [Epub ahead of print]
#=GF RN   [2]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs.
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [3]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes.
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF WK   MicroRNA
#=GF SQ   14


AABU01002771.1/5147484-5147409 UGUAGA-GUUUUAGAAUUCCUACGCUUUA-CCG---UGG--CAUACGAAAUUCGGCAAAGCGUUUGGAUUCUGAAACC-CUACC
AAPP01018483.1/24549-24624     UGUGGA-GUUUUAGAAUUCCUACGCUUUA-CCG---UUG--CAUAUGAAAUUAGGCAAAGCGUUUGGAUUCUGGAACC-CUAUG
AAQB01006885.1/24835-24758     UGGUAGCGUUUUAGAAUUCCUACGCUUUA-CCG---UCG--CCUACGAAACUCGGCAAAGCGUUUGGAUUCUGAAACAUUAUCU
AANI01016453.1/2288-2211       UCGUAUCGUUUUAGAAUUCCUACGCUUUA-CCG---UCG--UGUCCGAAAUUUGGCAAAGCGUUUGGAUUCUGAAACGAUAUAU
AAPT01021373.1/57544-57621     UUGUAUUGUUUUAGAAUUCCUACGCUUUA-CCG---UCG--UAUACGAAAUUUGGCAAAGCGUUUGGAUUCUGAAACGGUAUGU
AADE01004638.1/1941-2017       UGUAGU-GUUUUAGAAUUCCUACGCUUUA-CCGU--UGC--AAAACGAAAUUCGGCAAAGCGUUUGGAUUCUGAAACC-CUAUG
AAZX01009215.1/528-602         GAUAUUUGUUUUAGAAUUCCUACGCUUUA-CCG-----G--UUUUUAAAAAU-GGCAAAGCGUUUGAAGUCUAAAACAAAAGCA
AAPU01009479.1/6268-6193       CGUAUC-GUUUUAGAAUUCCUACGCUUUA-CCG---UCG--UAUACGCAAUUUGGCAAAGCGUUUGGAUUCUGAAACA-AUAUA
AAGE02001795.1/170457-170536   AUGGUUUGCUUUAGAAUUCCUACGCUUUA-CCG---UGAUUUGUUGAAAGUUUGGCAAAGCGUUUGGGUUCUGAAACGAAACAU
AAZO01006968.1/5752-5674       GGUUUC-GAUUUAGAAUUCCUACGCUUUA-CCUUUUUUA--UAUAUAAUAUU-GGCAAGGCGUUUGAAUUCUGAAUCCGAAUCA
AAJJ01000142.1/38254-38325     -CGUUUCGGUUUAGAAUUCCUACGCUUUA-CCG--------UGUGAAAGGCU-GGCAAAGCGUUUGGAUUCUGAAUCGAACCU-
AADK01018362.1/2316-2242       CU-UUUUGCUUUAGAAUUCCUACGCUUUA-CCG---UUG--CCAAGUAGUUG-GGCAAAGCGUUUGGAUUCUAAAACGAAAUA-
AAEU02001931.1/46128-46205     CUGUAGAGUUUUAGAAUUCCUACGCUUUA-CCG---UCG--CAUACGAAAUUCGGCAAAGCGUUUGGAUUCUGAAACCCUACCG
AAAB01008811.1/1452829-1452907 AUGGUUUGUUUUAGAAUUCCUACGCUUUACCCG---UGA--UUAAAGUAGUGCGGCAAAGCGUUUGGAUUCUGAAACGAAACGU
#=GC SS_cons                   :<<<<<<<<<<<<<<<<<<--<<<<<<<-.<<<...___..___________>>>->>>>>>>-->>>>>>>>>>>>>>>>>>:
#=GC RF                        ucguuucGuUUuAGAAUuCCUACGCUUUA.CCg...Uug..uaUaugAAaUUcGGCAAAGCGUUUGgAUUCUgAAaCgaaacgu
//
# STOCKHOLM 1.0

#=GF AC   RF00951
#=GF ID   mir-1302
#=GF DE   microRNA mir-1302
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   62.00
#=GF TC   62.00
#=GF NC   61.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.81 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000456;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells.
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF WK   MicroRNA
#=GF SQ   24


AADB02040854.1/117-168       UUCGUAGCAUAAAUAUGUCCCAAGCUUAGUUUGGGACAUACUUAUGCUAAAA
AANU01215031.1/1246-1297     UGUGUAGUAUAAGUAUAUCCCAUGCAAUAUUUGGGACAUACUUAUACUAAAA
ABDC01016108.1/1474-1423     UUUUCAGUAUAAGUAUGUCCCAUGCAAUGUUUGGGACAUACUUAUACUACAA
AAFC03060092.1/44141-44192   UUUGUAGUAUAAGUAUGUCCCAUGCAAUAUUUGGGAUAUACUUAUACUAAAA
AANG01363935.1/486-537       UUUUAAGUAUAAGUAUGUCCCAUGCAAAAUUUGGGAUAUACUUAUAUUAAAA
AC198040.3/136227-136176     UUUUCAGUAUAAGUAUGUACCAUGCAAUAUUUGGCACAUAUUUAUACUAAAA
AAQQ01361603.1/494-443       CUUUCAAUAAAAGUAUGUCCUAUUCAAUAUUUGGGACAUACUUAUGCUAAAA
AAGM01000063.1/190-241       UUUUUAGUAUAAAUGUGUUCCAUGCAAUAUUUGGGACAUACUUAUGCUAUAA
AAPY01581013.1/9561-9612     UUUCUAGUAUAAGUGUGUCCCAUGUAAUAUUUGGGAUAUACUUAUACUAAAA
AAHY01751933.1/571-520       UUUUUAGCGUAAGUAAGUCCCAUGCAACAUUUGGGAUAUACUUAUACUAAAA
CR956397.19/96142-96192      UUU-CAGCAUAAGUAUGCCCCAUGCAAUAUUGGGGACAUACUUAUGCUAAAA
CT954314.7/17189-17240       UUUUUAGUAUAAGUAUGUCCCAUGCAAUAUUUGGUAUAUACUUAUACUAAAA
AC188792.2/147259-147208     UUUUAAGUAUAGGUAUGUCCCAUGCAAUUUUGGGGAUAUAGUUAUACUAAAU
AAYZ01377391.1/551-602       UUUUAAAUAUAAUUAUGUACCAUGAAAUAUUUGGGAAAUACUUAUACUAAAA
AAGL01003462.1/373-424       UUUUUAGGAUAAGUAAAUCCCAUUCAAUAUUUGUGACAUACUUAUCCUAAAA
AANN01711679.1/739-790       UUUUUAGUAUAAGUAUGUCUCAUGUAGUAUUUGAGAUAUACUUGCACUAAAA
AAIY01008039.1/1905-1956     UUUCUAAUGUAAGUAUGUCUCAGGCAAUAUUUGGGGCAUAUUUAUAUUAAAA
AC138552.3/125966-126017     UUAAACGUAUAAGUAUGUCCUGUGAAAUAUUUAGGACAUACUUAUGCUAAAA
AAPN01324572.1/326-377       UUUUUAGGAUAAGUAUGUCCCAUGCCAUGUUUGGGAUAUACAUAUACUAAAA
AALT01502983.1/2427-2376     AUACUUGUAUAAGUAUGUCCCAUGCAAUAUCUGGGACAUACUUAUACUAACA
AC099315.3/137568-137619     UGUUUAGUAUAAGUAUGUCCCAUGCAAUAUUUAGGAUGUACUAAUACUAAAC
AAKN02054411.1/136817-136767 UUU-UAGUACAAAUAUGUCCCAUGUAAUAUUCGGGACAUACUUAUGCUAAAA
ABVD01694939.1/1003-1054     UUUUUAGUAUAAGUAUGUCCCAUGCAAUAUUUGGGACAUACUUAUACUAAAA
AACN010404620.1/57-6         UUUUUAGUAUAAGUAUGUCCUAUGCAAUAUUUGGGACAUACUUAUACUAAAA
#=GC SS_cons                 :::::<<<<<<<-<<<-<<<<<________>->>>>->>>->>>>>>>::::
#=GC RF                      UUUUUAGuAUAAGUAUGUCCCAUGCAAUAUUUGGGAcAUACUUAUaCUAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF00952
#=GF ID   mir-650
#=GF DE   microRNA mir-650
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   44.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000457;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF WK   Mir-650_microRNA_precursor_family
#=GF SQ   11


AADB02020447.1/169830-169924 CAGUGCUGGGGUCUCAGGAGGCAGCGCUCUCAGGA-CGUCACCACCAUGGCCUGGGCUCUGCUCCUCCUCACCCUCCUCACUCAGGGCACAGGUGA
AANU01210640.1/17305-17211   CAGUGCUGGGGUCUCAGGAGACAGUGCUGUCGGGA-CGUCUCCACCAUGGCCUGGGCUCUGCUCCUCCUCACCCUUCUCACUCAAGGCACAGGCGA
AANU01210630.1/14314-14220   CAGUGCUGGGAUCUCAGGAGGCAGCGCUCUCAGGA-CGUCUCCACCAUGGUCUGGGCUCUGCUCCUCCUCACCCUCCUCACUCAGGGCACAGGUGA
AANU01210643.1/9228-9138     CAGUGCUGGGGUGUCAGGAGGCAGCGCUCUCAG-----UCUCCACCAUGGCCUGGGCUCUGCUCCUCCUCACUCUCCUCACUCAUGGCACGGGUGA
AANU01210639.1/1550-1456     CAGUGCUGGGGUCUCAGGAGGCAGCGCUCUCGGGA-CAUCUCCACCAUGGCCUGGGAUCUGCUCCUCUUCACCCUCCUCACUCAGGGCACAGGUGA
AANU01210636.1/4993-4899     CAGUGCUGGGAUCUCAGGAGGCAGCGCUCUCAGGA-CUUCUCCACCAUGGUCUGGGCUCUGCUCCUCCUCACCCUCCUCACUCAGGGCACAGGUGA
AAIY01160283.1/783-691       CUGUGUGAG---CUCAGAAGGCAGGACUCACAGGACCGUCACCACCAUGGCCUGGUCCCCUCUCCUCCUCACCCUCCUUGCUCACUGCACAGGUAA
AAFR03055934.1/84564-84656   CAGCUGAGGGGCCUCAGGGGGCAGAGCUCUGGGG--UGUCUCCACUAUGGUCUGGGUUCCUCUCCUUC-CCCCCUCCUCACUGACCCGCCUGAGGG
AAWR02038310.1/94361-94267   CAGGGUUGGGGUCUCAGAAGGCAGUGCUCUUGGGA-CGUCUCCACCAUGGCCUGGGCUCUGCUCCUCCUCACCCUCCUCACUGAGGGCACAGGUGA
AAGV020034474.1/1514-1420    CAGCAUUGGGUUCUCAGUGGGCAACACUCUUGGGG-CAUAUCCACCAUGGCCUGGGCUCUGCUCCUCCUUACCCUCCUCACUCAGGGUACAAGUGA
AC099533.36/186809-186903    CAGUGCUGGGGUCUCAGGAGGCAGCACUCUCGGGA-CGUCUCCACCAUGGCCUGGGCUGUGCUCCUCCUCGCCCUCCUCACUCAGGACACAGGUGA
#=GC SS_cons                 ::<<<<<<<<<<---<<<<<<-<<<<--<<<<<<-.<<<_______>>>->>>>>>--->>>>>>>>>>->>>>>---------->>>>>::::::
#=GC RF                      CAGugccgGGguCUCaGgaGGCaGcgCUcccaGGA.cgucuCCACCacgGCCugggcUCcgCuCCucCuCacCCuCCUCACUcAgggcaCaGGuGA
//
# STOCKHOLM 1.0

#=GF AC   RF00953
#=GF ID   mir-1497
#=GF DE   microRNA mir-1497
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   99.50
#=GF NC   33.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000458;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20370911
#=GF RT   miRTRAP, a computational method for the systematic identification of
#=GF RT   miRNAs from high throughput sequencing data.
#=GF RA   Hendrix D, Levine M, Shi W
#=GF RL   Genome Biol. 2010;11:R39.
#=GF RN   [2]
#=GF RM   18339653
#=GF RT   Altered miRNA repertoire in the simplified chordate, Oikopleura dioica.
#=GF RA   Fu X, Adamski M, Thompson EM
#=GF RL   Mol Biol Evol. 2008;25:1067-1080.
#=GF WK   MicroRNA
#=GF SQ   2


AABS01000309.1/72950-73023 UAGCGCAACCACUUGUGAAUCUCCAACACUCGGCUUUGUCCACGACUUUGUUGAAGAAUUGCAGGUGGUAGGUG
AACT01066312.1/9231-9159   AAGCGUAACCUCUUGUAAAUCUCCAACACUAAGCUUGGUUAC-AGCUCUGUUGAAGAAUUGCAGGUGGUAGGUG
#=GC SS_cons               :::<--<-<<-<<<---<-<<<-<<<<<____________________>>>>>->>>->--->>>->>>->:::
#=GC RF                    uAGCGuAACCuCuUGUaAAUCUCCAACACUaaGCUUuGUuaaCaaCUuUGUUGAAGAAUUGCAgGUGGUAGGUG
//
# STOCKHOLM 1.0

#=GF AC   RF00954
#=GF ID   MIR1446
#=GF DE   microRNA MIR1446
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   68.80
#=GF NC   62.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000459;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18363789
#=GF RT   Stress-responsive microRNAs in Populus.
#=GF RA   Lu S, Sun YH, Chiang VL
#=GF RL   Plant J. 2008;55:131-151.
#=GF WK   MicroRNA
#=GF SQ   7


AARH01006471.1/315430-315326 CCAACUUCUUCUGAACUCUCUCCCUCAACUGCUACUCUAGA----UCUUGCCA-AUCCCUGUCAAGUGUUUCUGUGUAGCAGUCGAGG---UGAGAG-G----UUCAGGAAAUGUUGG
AARH01005504.1/48344-48242   CCAAUUUCUUCUGAACUCUCUCCCUCAACCGCCACUCUAGA----GGUUGGCA---CCUUGUCAAUUGUUUCUGUGUAGCGGUCGAGG---UGAGGG-G----UUCAGAACAUGUUGG
AARH01005504.1/53010-52906   CCAACUUCUUCUGAACUCUCUCCCUCAACCGCUACUCUAGA----GCUUGGCA-AUCCUUGUCGAUUGUUUCUGUGUAGCGGUUGAGG---UGAGGG-G----UUCAGAACAUGUUGG
AARH01006483.1/21782-21887   CCAACUUUUUCUGAACUCUCUCCCUCAACUGCUAUUCUAGA----GCUUGUUA-AUCCUUGUCAAGUGUUUCCCUGUAGCAGUCGAGG---CGAGGG-GG--UUUCGGAAAAUGUUG-
AARH01005504.1/162893-162997 CCAACUUUUUCUGAACUCUCUCCCUCAACUGCUAUUCUAGA----GCUUCCUG-AGCUAACCCUUGUGUUUCUGUGUAGCAGUCAAGG---UGGGAG-G----CUCAGAAAAUGUUGG
EU124734.1/81383-81275       CCAGAGUUUUCUGAACUCUCUCCCUCAAUGGCUGUUCAUAUAAUAUAUGCUGCUACUUUGCAGCUUAAUUAAAUAACAGCUUUGGGGG---UUUGA--G----UCCAGAAAACUCUUG
AM482260.2/9267-9159         CUGGCAUUUUCUGAACUCUCUCCCUCAUUGGCUUUCUAAGC----UUGUC-UG-AACAUCUAGAGAAAAGGG--AGAAGCUGAGGAAGCCGUGAGGGA-AGAUUUCAGAAAAUGUUGG
#=GC SS_cons                 <<<<<---<<<<<<<<-<<<<<<<<<-<<<<<<<<------....<<-<<-<<._____>>->>->>-------->>>>>>>>->>>>...->>>>>.>....>>>>>>>--->>>>>
#=GC RF                      CcagcuUuUuCuGaaCUCuCucCCuCAaccGCugcUcuAGa....ucuugucg.AucuUcgucaagaaUuucuuugcaGCggucGaGG...UgaGaG.G....uuCaGaAAAUgcugG
//
# STOCKHOLM 1.0

#=GF AC   RF00955
#=GF ID   mir-1829
#=GF DE   microRNA mir-1829
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   52.20
#=GF NC   43.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000460;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18392026
#=GF RT   Discovering microRNAs from deep sequencing data using miRDeep.
#=GF RA   Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S,
#=GF RA   Rajewsky N
#=GF RL   Nat Biotechnol. 2008;26:407-415.
#=GF RN   [2]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [3]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF WK   MicroRNA
#=GF SQ   3


Z69660.1/8193-8134   AAGCGAAAUUCAAGAUGGUUGUAAAACAUCGAGUACUACAACCACUGGAAUUUCUCUAUU
Z79601.1/10621-10562 AAGGGGACUUCUAAUUGUUUGUAAAAAAUCGAGUAUUACAACCAUUGGAAUUUCUCUAUU
Z78542.1/11427-11486 AAGCGAUCUUCUAGAUGGUUGUAAAACAUCGAGUAUUACAACCACUGGAAUUUCUCUAUU
#=GC SS_cons         :<<-<<<<<<<<<<-<<<<<<<<<-<<_____>>->>>>>>>>>>>>>>>>>>>->>:::
#=GC RF              AAGcGaacUUCuAGaUGGUUGUAaAAcAUCGAgUAuUACAACCACUgGAAuuuCUCUAUU
//
# STOCKHOLM 1.0

#=GF AC   RF00956
#=GF ID   MIR1444
#=GF DE   microRNA MIR1444
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   90.50
#=GF NC   74.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000461;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18363789
#=GF RT   Stress-responsive microRNAs in Populus.
#=GF RA   Lu S, Sun YH, Chiang VL
#=GF RL   Plant J. 2008;55:131-151.
#=GF WK   MicroRNA
#=GF SQ   3


AARH01003581.1/172299-172213   UUUAUCACUUGAAUGUUGACCGAAUAUGGAUGAAAAGUUGUUUUCUGUUUCCUUUCCUCCACAUUCGGUCAAUGUUCCAGUGAUGAG
AARH01004320.1/1047188-1047272 UUUAUCCCUCGAAUAUUGAUCGAAUAUGUAUGAAAUAUGAUGGUUAUAUG--UUUCAUUCACAUUCGGUCAACGUUCGAGUGAUAAA
AARH01028621.1/1186-1102       UUUAUCCCUCGAAUAUUGAUCGAAUAUGUAUGAAAUAUGAUGGUUAAAUG--UUUCAUUCACAUUCGGUCAACGUUCGAGUGAUAAA
#=GC SS_cons                   <<<<<<-<<<<<<--<<<<<<<<<<-<<-<<<<<<<_____________>..>>>>>>->>->>>>>>>>>>-->>>>>>->>>>>>
#=GC RF                        uuuauCcCucGaaUauuGacCGaauAuGuauGaaacaUgaUggUuaaaUg..uuuCauuCaCauuCGguCaacGuuCgaGUGauaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00957
#=GF ID   mir-663
#=GF DE   microRNA mir-663
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   43.00
#=GF TC   43.10
#=GF NC   42.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000462;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17989710
#=GF RT   MicroRNA expression profiles of human leukemias.
#=GF RA   Takada S, Yamashita Y, Berezikov E, Hatanaka H, Fujiwara SI, Kurashina K,
#=GF RA   Watanabe H, Enomoto M, Soda M, Choi YL, Mano H
#=GF RL   Leukemia. 2008;22:1274-1278.
#=GF RN   [3]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF WK   Mir-663_microRNA_precursor_family
#=GF SQ   12


AADB02401928.1/128606-128514 CCUUCCGGCGUCCCAGGCGG---GGCGCCGCGGGACCGCCCUCG--UGU-CUG--UGGCGGUGGGAUCCCGCGGCCGUG-UUUUCCUGGUGGCCCGGCCAUG
AANU01134169.1/389-297       CCGUUCGGCGUCCCAGGCGG---GGCGCUGCGGGACCGCCCUCG--UGU-CUG--UGGCGGUGGGAUCCCGUGGCCGUG-UUUUCCUGGUGGCCCGGCCGCG
AADA01107823.1/4742-4834     CCUUCCGGCAUCCCAGGCGG---GGCGCCGCGGGACCGCCCUCG--UGU-CUG--UGGCGGUGGGAUCCCGCGGCCGUG-UUUUCCUGGUGGCCCGGCAUGC
AANN01386973.1/23-114        CCGGCCGGCGUCCCGGGCGU---GGG--UGCGGGACCGCCCUCUGUGGU-CUU--GGGCGGUGGGAUCCCGCGUG-UUG-UUUUCCCGGUGGCCCGGCCGUG
AACN010370390.1/1027-942     CCGGCCGGCGUCCCGGGC------GU--CGCGGGACCGCCCUCG--UGC-UGG--UGGCGGUGGGAUCCCGUG--CGCG-UUUACCCGGUGGCCCGGCUCGC
AAFC03108961.1/714-625       CCGGUCGGCGUCCCAGGC------GUGUCGCGGGACCGCCCUCG--UGU-GUGGGUGGCGGUGGGACCCCGCGCUGGUU---UUCCUGGUGGCCCGGCCGUG
ABDC01574561.1/1024-1114     CCGGCUGGCGUCACGGGC------ACGCCGCGGGACCGCUCCCG--UGUGUUG--GGGCGGUGGGAUCCCGCGGCGUUG-UUUUCCCGGUGGCCCGGUCGCG
AANG01520510.1/529-614       CCGGCUGGCGCCGCGGGC------GU--CGCGGGACCGCCCUCG--UGC-UGG--UGGCGGUGGGAUCCCGUG--CACG-UUUACCCGGUGGCCUGGCUCGC
AALT01140430.1/629-540       CCGGCCGGCGUCCCGGGCGU----GGGCGCGGGA-CCGCCCUGG--UCU-GUG--G-GCGGUGGGAUUCCCGUGCGUUG-UUUUCCCGGCGGCCCGGUCGCC
AAQQ01470949.1/458-377       CGGGUUGGCGUCGCGGGCGG---U-----GCGGGACCGCCCUCG--CG---UG--UGGCGGUGGGACCCCGC----UUG-UUUUCCCGGCGGCCCGACUCUG
AAYZ01634401.1/742-656       GGCUCCGGUGUCC---CAGG---CAUGUCACGGGACCGCCCAGG--UGU-GGG-----CGGUGGCAUCCCGUGUCUGUU-UUCCGGGAGGGACCCGGCUUUC
AAPY01840898.1/591-497       CCGGCCGGCGUCCCCGGGGGAUGCGCCGUGCGGGACCGCCCUCG--UG---UG--UGGCGGUGGGACCCCGCGUGUGCUCUCCCCCGGCGGGCUCCGUCGUC
#=GC SS_cons                 ::::<<<<-<<<<<<<<-<<...-<<<<<<<<<<<<<<<<-<<<..___.___..>>>->>>>>-->>>>>>>>>->>-.>>-->>>>>->>>>>>>:::::
#=GC RF                      ccggccGGCGuCcCgGGcgg...ugcgccgcGGGaCCgCCCuCg..UGU.uuG..cGgCGGuGGGAuCCCgcggcugcg.ccUuCCcGguGgCCCggccguc
//
# STOCKHOLM 1.0

#=GF AC   RF00958
#=GF ID   mir-498
#=GF DE   microRNA mir-498
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   90.10
#=GF NC   75.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000463;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-498_microRNA_precursor_family
#=GF SQ   5


AANU01181661.1/3192-3315     AAUCCUCCUUGGGAAGUG-AAGCUCAGGCUGUGAUUUCAAGCCAGGGGGCGUUUUUC-UGUGACUGGAUGAAAAGCACCUCCGGGGCUUGAAGCUCACAGUUUGAGAGCAAUCAUCUAAGGAAGUU
AADB02020212.1/391438-391561 AACCCUCCUUGGGAAGUG-AAGCUCAGGCUGUGAUUUCAAGCCAGGGGGCGUUUUUC-UAUAACUGGAUGAAAAGCACCUCCAGAGCUUGAAGCUCACAGUUUGAGAGCAAUCGUCUAAGGAAGUU
AAYZ01246662.1/336-215       GAGAGGCAUCGGG-AGUC-CAGCUCGGUGUGUGGUUUCAAGCUGGGGGGUGUUUUUA-UGACCGAGCUGAGAAAGCACCCC-AAAGCUUGAUACUCACACACUGAGACACAGCAUCCAAAGUCCUG
ABDC01595467.1/1102-983      CCGUCUUUCCGGAGUG---CAGCUCAGGCUGUGAUUUCAAGCUCGGGGGUGCUUUCUGUAACUCUG---AAAAAGGACCUCCAAGCCUUGAACAUCACAAUCUGAGGCAAACCAUCUAGAUUUAAA
AAPY01017646.1/369-247       CGGCGGCCUCGUGCAGCACAAGCUCAGGCUGUGGUUUCAAGCUGGAGGGUGCUUUCG-GGACUUCGGU-GGGAAGCACCG-CCAGGCUUGACCCACACAGCUUGGGACCAGUCAUCCGGGACUGCC
#=GC SS_cons                 :::::<<<<<<<<---<<.---<<<<<<<<<<<<<<<<<<<<<-<<<<<-<<<<<<<.___________>>>>>>>->>>>>->->>>>>>>>->>>>>>>>>>>>-->>---->>>>>>>>::::
#=GC RF                      aagccgccccgggaAGug.aAGCuCaggcUGUGacuUCAAGCcaGGgGGuGcUUucc.ugacucuGguuggaAAgCACCcCCaggGCUUGAagcuCACAgccuGaGAccaAuCAuccggggcuguu
//
# STOCKHOLM 1.0

#=GF AC   RF00959
#=GF ID   mir-612
#=GF DE   microRNA mir-612
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   77.80
#=GF NC   65.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000464;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF WK   Mir-612_microRNA_precursor_family
#=GF SQ   6


AANU01213855.1/10814-10715 UCUCAUCUGGACCCCACUGG-GGAGGG-CUUCUGAGCUCCUCAGCACUGGCAGGAGGGGCUCCAGGGGCC-----CUCC-CUCCAUGG-CAGCCAGGACAGGACUCUCA
AANG01068065.1/2277-2377   UCUCCUCUGGACUCUGCUGGAGAAGGG-CUACUGGGCUCCUCAGGGCUGGCUGGAGGGGUC-CAGGAGUC-----CUCCCCUCGUGAG-AGGCCAGGACAGGACUCCUG
ABDC01368197.1/2724-2822   UCUCAUCUGGAUCUUGCUGG-GGAGGGGCUUCUGAGUUCCUCAGCGCUGGCAGGAGGUGCUCCAGGGACC----AGUCC-CAUAACAG---GCCAAGA-AGGACUCGUG
AACN010257726.1/951-847    UCUCAUCUGGACCCUGCUGU-GGAGGGGCCACUGAACUCCUCAGGGUCAACAGGAGAGGU-CCAGCCGCCUCCAUCCCC-UCCAUGAG-AGCCCAGGCCAGGACUCCUG
AAWR02037820.1/23695-23793 UCUCAUCUGGACCUUGCUGG-AAAGGGGCUUCUCAGCUCCUCAGG-CUG--ACGGGGGGGUCCAGGGGCC-----CUCU-CCCCAUGAGAAGCCGGGACAGGACUCCUG
AC000353.27/232388-232487  UCCCAUCUGGACCCUGCUGG-GCAGGG-CUUCUGAGCUCCUUAGCACUAGCAGGAGGGGCUCCAGGGGCC-----CUCC-CUCCAUGG-CAGCCAGGACAGGACUCUCA
#=GC SS_cons               <<<--<<<<<---<<<--<<.<<<<<<-<<<<<<<<<<<<<<-<<____>>-->>>>>>>>->>>>>>>>.....>>>>.>>--->>>.--->>>>>--->>>::::::
#=GC RF                    uCcCAuCuGGAccccgCUgg.GgagGGGCccCuGggccCCucAGcgcUggCAggaGGggccCCaGggGCC.....cucC.cccaacgg.aagCCaGgaCAgGaCUCuug
//
# STOCKHOLM 1.0

#=GF AC   RF00960
#=GF ID   mir-661
#=GF DE   microRNA mir-661
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   73.40
#=GF NC   38.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000465;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF WK   Mir-661_microRNA_precursor_family
#=GF SQ   4


AADB02012369.1/40293-40205 GGAGAGGCU--G-----UGCUGUGGGGCAGGCGCAGGCCUG---------AGCCCUGGUUUCGGGCUGCCUGGGUCUCUGGCCUG-C-GCGUGACUUUGGGGUGGCU
AANU01106914.1/19156-19059 GGAGAGGCU--G-----UGCUGUGGGGCAGGCGCUGGCCUGGGUGGCCUGAGCCCUGAUUUUGGGCUGCCUGGGUAUCUGGCCCG-U-GCGUGACCUUGGGGCGGCU
ABDC01279171.1/1188-1088   GGCGCAGCCCUG-----UGCUGUGGGACAGGCACUUGCUCACACUGCCUGGGCCCUGGGUCCAGGCUGCCUGGGUCUCUGGCCAG-CAGUGUGACCUUGGGGAGGCU
AAQR03179319.1/18024-18127 GGAGGUGCA--GCCCUGUGCUGUGGGGCAGGCUCUUGUUGUGGUGGCUGGGGCCCUGAUUCUGCGCUCCCUGGGUCUCUGGCCAGCA-GCGUGACCUUGGAGAUGCC
#=GC SS_cons               :::::<<<<..-.....-<<<-<--<<<<-<<<<<<<<<-<---------<<<<<-<<<________>>>->>>->>>->>>>>>.>.>>->>->>-->->>>>>>>
#=GC RF                    GGaGagGCc..G.....UgCcGuGGGGCaGGCgCugGccugggugGCuuGagCCCUGgcUuuggGCUgcCUGGGUcucUggCcaG.c.GCGuGACCUUgGgGcgGCc
//
# STOCKHOLM 1.0

#=GF AC   RF00961
#=GF ID   mir-581
#=GF DE   microRNA mir-581
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   103.50
#=GF NC   74.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000466;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [3]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF WK   MicroRNA
#=GF SQ   2


AADB02008818.1/469768-469863 GUUAUGUGAAGGUAUUCUUGUGUUCUCUAGAUCAGUGCUUUUAGAAAAUUUGUGUGAUCUAAAGAACACAAAGAAUACCUACACAGAACCACCUGC
AANU01256485.1/2117-2022     GUUCUGUGAACGUAUUCUUGUGUUCUGUAGAUCAGUGCUUUUAGAAAAUUUGUGUGAUCUAGAGAACACAAAGAAUACCUACACAGAACCAUCUGC
#=GC SS_cons                 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<____________________>>>>>>>>>>>>>>>>->>>>>>>>>>>>>>>>>>:::::::
#=GC RF                      GuucuGuGgagGuauuCuuGuGuuCucuaGauCaGUGCUUUUAGAAAAUUUGUGuGauCuagaGaaCaCaAaGaauaCcucCaCagaaCCAuCUGC
//
# STOCKHOLM 1.0

#=GF AC   RF00962
#=GF ID   mir-586
#=GF DE   microRNA mir-586
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   81.40
#=GF NC   63.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000467;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [3]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF WK   MicroRNA
#=GF SQ   2


AADB02010026.1/2568853-2568757 AUGGGGUAAAACCAUUAUGCA--UUGUAUUUUUAGGUCCCAAUACAUGUGGGCCCUAAAAAUACAAUGCAUAAUGGUUUUUCACUCUUUAUCUUCUUAU
AANU01242546.1/57934-58032     AUGGGGUAAAACCAUUAUGCAUAUUGUAUUUUUAGGUCCCAAUACGUGUGGACCCUAAAAAUGCAAUGCAUAAUGGUUUUAUACUCUUUAUCUUCUUAU
#=GC SS_cons                   ::<<<<<<<<<<<<<<<<<<<--<<<<<<<<<<<<<<<<<<_____>>->>>->>>>>>>>>>>>>>>>>>>>>>>>>>>>>->>>:::::::::::::
#=GC RF                        AUGgGguaaaaccauuauGcauAuuGcauuuuuaGGccccaAUAcaugUgggcCCuaaaaaugCaaugCauaaugguuuuacACcCUUUAUcUUcUUAU
//
# STOCKHOLM 1.0

#=GF AC   RF00963
#=GF ID   mir-642
#=GF DE   microRNA mir-642
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   109.40
#=GF NC   70.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000468;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF WK   MicroRNA
#=GF SQ   2


AANU01182572.1/256-352 AUCUGAGCUGGGAGGGUCCCUCUCCAAAUGUGUCUUGGGGUGGGGGAUCAAGACACAUUUGGAGAGGGAACCUCCCAACUCGGCCUCAUUGAACUCU
AC006132.1/34274-34370 AUCUGAGUUGGGAGGGUCCCUCUCCAAAUGUGUCUUGGGGUGGGGGAUCAAGACACAUUUGGAGAGGGAACCUCCCAACUCGGCCUCUGCCAUCAUU
#=GC SS_cons           ::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<_________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>::::::::::::::
#=GC RF                AUccGaGcuGGGaGGgucccucuccaaauGuGucuuGgGGUGGGGGAcCaagaCaCauuuggagagggacCCuCCCagCuCggccUcauugAacauU
//
# STOCKHOLM 1.0

#=GF AC   RF00964
#=GF ID   mir-938
#=GF DE   microRNA mir-938
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   86.80
#=GF NC   52.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000469;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [3]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF WK   Mir-938_microRNA_precursor_family
#=GF SQ   2


AANU01172051.1/35182-35264   GAAAGUGUACCAUGUGCACUUAAAGAUGAAGCCGGUGCACCUUCAUGAACUGUGGUACACCUUUAAGAACUUGGUCCACCUUC
AADB02013021.1/931796-931878 GAAGGUGUACCAUGUGCCCUUAAAGGUGAACCCAGUGCACCUUCAUGAACCGUGGUACACCUUUAAGAACUUGGUAUGCCUUC
#=GC SS_cons                 <<<<<<<<<<<<-<<---<<<<<<<<<<-<<<<-<<-<<______>>->>->->>>->>>>>>>>>>->>->>>>>>>>>>>>
#=GC RF                      GaagGuguaCCaUGuGCaCuuaaaGguGAacCCaGuGCaCCUUCAuGAaCuGUGguACacCuuuaaGAaCUuGGuacaCcuuC
//
# STOCKHOLM 1.0

#=GF AC   RF00965
#=GF ID   mir-549
#=GF DE   microRNA mir-549
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   111.70
#=GF NC   79.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000470;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-549_microRNA_precursor_family
#=GF SQ   2


AANU01256848.1/66356-66262   AGACAUGCAACUCAAGAAUAUAUUGAGAGCUCAUCCAUAGUUGUCACUGUCUCAGAUCA-UGACAAUUAUGGAUGAGCUCUUAAUAUAUCCCAGGC
AADB02016766.1/139001-139096 AGACAUGCAACUCAAGAAUAUAUUGAGAGCUCAUCCAUAGUUGUCACUGUCUCAAAUCAGUGACAACUAUGGAUGAGCUCUUAAUAUAUCCCAGGC
#=GC SS_cons                 :::::::::::::::::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<______________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>:::::::
#=GC RF                      AGACAUGCAACUCAAGAauauauugaGaGCuCauCCauaguuGuCaCUGUCUCAaAUCAguGaCaacuauGGauGaGCuCucaauauauCCCAGGC
//
# STOCKHOLM 1.0

#=GF AC   RF00966
#=GF ID   mir-676
#=GF DE   microRNA mir-676
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   52.60
#=GF NC   49.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000471;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos.
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF RN   [2]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [3]
#=GF RM   20224791
#=GF RT   Discovery of novel microRNAs in female reproductive tract using next
#=GF RT   generation sequencing.
#=GF RA   Creighton CJ, Benham AL, Zhu H, Khan MF, Reid JG, Nagaraja AK, Fountain
#=GF RA   MD, Dziadek O, Han D, Ma L, Kim J, Hawkins SM, Anderson ML, Matzuk MM,
#=GF RA   Gunaratne PH
#=GF RL   PLoS One. 2010;5:e9637.
#=GF RN   [4]
#=GF RM   20498841
#=GF RT   Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an
#=GF RT   unexpectedly complex subcellular distribution of miRNAs and tRNA 3'
#=GF RT   trailers.
#=GF RA   Liao JY, Ma LM, Guo YH, Zhang YC, Zhou H, Shao P, Chen YQ, Qu LH
#=GF RL   PLoS One. 2010;5:e10563.
#=GF WK   MicroRNA
#=GF SQ   6


AAHY01214974.1/4619-4531   CUUUGCCUGAAUGCAUGACUCUACAACCUUAGGACUUGCAGAAUUAAAGGAAUGCCGUCCUGAGGUUGUUGAGCUGUGCGUUUCUGGGC
AANU01068099.1/275-187     UCUCACCUGAAUGCAUGACUCUUCAACCUCAGGACUUGCAGAAUUAAUGGAAUGCCGUCCUAAGGUUGUUGAGUUGUGCGUUUCUGGGC
AAYZ01448796.1/363-450     CUCAG-CUGAAUGCGUGACUCUGCAACCUCAGGACUUGCAGGAUUAAGAGAAUGCCGUCCUAAGGUUGUUGAGUUGUGCGUUUCUGGAC
AAWR02039725.1/65437-65349 CCUCACCAGAAUGCAUGACUCUUCAAUCUCGGGACUCGCAGAAUUAAUGGAAUGCCGUCCUAAGGUUGUUGAGUUCUGCGUUUCUGGGC
AAGV020395671.1/1356-1444  CGUCACCUGAACUCAUGACUCUUCAACUUCAGGACUUGCAGAAUUAAUGGAAUGCCGUCCUAAGGUUGUUGAGUUCUGCGUUUCUGGGC
AAHX01111573.1/7948-8036   CUUCACCUGAAUGCAUGACUCUGCAACCUUAGGACUUGCAGAAUUAACAGAAUGCCGUCCUGAGCUUGUCGAGCUAUGCGUUUCUGGGC
#=GC SS_cons               :::::<<<<<<<<<<<<-<<<-<<<<<<<-<<<<<--<<<____________>>>->>>>>->>>>>>>->>>->>>>>>>>>-->>>:
#=GC RF                    cuUcaCCcgaacgCacgACuCUgCaaccucaGGaCUUGCaGAAUUAAugGAAuGCCGuCCuaagguuGcUGaGuuguGcguuuCUgGGC
//
# STOCKHOLM 1.0

#=GF AC   RF00967
#=GF ID   mir-281
#=GF DE   microRNA mir-281
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   96.10
#=GF NC   44.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000472;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18339653
#=GF RT   Altered miRNA repertoire in the simplified chordate, Oikopleura dioica.
#=GF RA   Fu X, Adamski M, Thompson EM
#=GF RL   Mol Biol Evol. 2008;25:1067-1080.
#=GF RN   [2]
#=GF RM   20370911
#=GF RT   miRTRAP, a computational method for the systematic identification of
#=GF RT   miRNAs from high throughput sequencing data.
#=GF RA   Hendrix D, Levine M, Shi W
#=GF RL   Genome Biol. 2010;11:R39.
#=GF WK   Mir-281_microRNA_precursor_family
#=GF SQ   2


AACT01013310.1/6369-6451   UGUCAAGUGCGUGUCGGAGGGUUAUUUCAUGCCGGUC-UAGCAUUGCGCUGUCAUGGAGUUGCUCUCUCAUUGGCGCUAUGGCU
AABS01000211.1/21157-21238 UGUCCAGUGCGUGUCGGAGAGUAAUUUCAUGUUAGUGACAUCAC--UACUGUCAUGGAGUUGCUCUCUUAUUAGCGCUGAGGCC
#=GC SS_cons               :<<<-<<<<<--<<-<<<<<<<-<<<<<<<<-<<<<_._________>>>>->>>>>>>>->>>>>>>->>-->>>>>-->>>:
#=GC RF                    UGuCaaGuGCGUguCgGaGaGuuauuuCauGucaGug.uAuCAuUGuaCugUCauGgaguUgCuCuCuuauUaGCgCuauGgCu
//
# STOCKHOLM 1.0

#=GF AC   RF00968
#=GF ID   mir-626
#=GF DE   microRNA mir-626
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   55.00
#=GF NC   42.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000474;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [3]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF WK   MicroRNA
#=GF SQ   6


AANU01297252.1/2538-2632 ACCGAUAUCUUUGUCUUAUUUCUGAGCUGAGGG----GU---UAU-UU-UUAUGCA--GUCUAAAUGAUCUCAGCUGUCCGAAAAUGUCUUCAAGUUUAAAGGCUU
AANG01136823.1/1111-1209 ACUAACAUCCUUAUCUAGUUUCUGACCUUAGGGGGCAGU---AGU-UC-UUGUACA--GUCUGACUUGUUUCAGCUGUUAGAAAAUGUCUUUAUCUUUGAAGUCUU
AAFC03068996.1/4318-4415 ACUAAUAUCCUUGUGUUGUUUU-GGUCUAAGGAG---GU---AGUAUU-UUUUGUGACGUGUGAAUUCUUUCAGAUGUCUGAAAAUGUGUUUAGCUUUGAAGGCUU
AACN010460612.1/284-379  AACUAAAUUCUUACCU-GUUUCUGAUUUUAGGA----GCUAGUAU-UUCUUAGGCA--GUCUCAAUUCUCUCAGUUGUCUGAAAGUGUCU--AUCUUCAAAGCCUU
AAWR02001476.1/4012-3914 GCCAAUAUCCUUGUCUUUUUUCUUAUCUUAGGAG---GU---GAUAUU-UCUUGUGCUGUCUGAAUUCUGUCAGCUAUCUGAAAAUGUCUUUAGCCUUGAAGACUU
AC073657.5/46523-46616   ACUGAUAUAUUUGUCUUAUUUGAGAGCUGAGGA----GU----AU-UU-UUAUGCA--AUCUGAAUGAUCUCAGCUGUCUGAAAAUGUCUUCAAUUUUAAAGGCUU
#=GC SS_cons             ::::::::::::<<<<<------<<<-<<<<<<-...--...-<<.<<.<<--<<<..--<<-<______>->>->>>-->>>>>>->>>>>>-->>>->>>>>::
#=GC RF                  AcuaAuAUccUUGcCUugUUUcUgacCUgAgGaG...GU...aau.Uu.UuaUgca..GUCUgAAUuaUuUCAGcuguCugAaAauGuCuUcAucgucaaAGgCUU
//
# STOCKHOLM 1.0

#=GF AC   RF00969
#=GF ID   mir-556
#=GF DE   microRNA mir-556
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   94.40
#=GF NC   85.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000475;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   2


AANU01239714.1/9369-9275 GAUAGUAAUGAGAAAGAUGAACUCAUUGUAAUAUGAGCUUCAUUUAUGCAUUUCAUAUUACAAUUAGCUGAUCUUUUUUUUUUUUUUUUUUUUUU
AL512785.7/29781-29875   GAUAGUAAUAAGAAAGAUGAGCUCAUUGUAAUAUGAGCUUCAUUUAUACAUUUCAUAUUACCAUUAGCUCAUCUUUUUUAUUACUACCUUCAACA
#=GC SS_cons             ::::::<<<<<<<<<<<<<<<<<-<<-<<<<<<<<<<______________>>>>>>>>>>->>->>>>>>>>>>>>>>>>>:::::::::::::
#=GC RF                  GAUAGUaauaagaaaGaugagCuCauUGuaauauGagCUUCAUUUAUaCAUuuCauauuaCaauUaGcucauCuuuuuuauuauUauuUUuaaua
//
# STOCKHOLM 1.0

#=GF AC   RF00970
#=GF ID   mir-648
#=GF DE   microRNA mir-648
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   94.30
#=GF NC   32.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000476;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   2


AANU01211035.1/10592-10499   AGCACAGACGCCUCCAAGUGUGCAGGGCACUGAUGGGGGCCAGGGCAGGCCCAGCCAAAGUGCAGGACCUGGCACUUAGUCGGAGGUGAGGAUG
AADB02020410.1/572431-572338 AUCACAGACACCUCCAAGUGUGCAGGGCACUGGUGGGGGCCGGGGCAGGCCCAGCGAAAGUGCAGGACCUGGCACUUAGUCGGAAGUGAGGGUG
#=GC SS_cons                 ::::::::<<<<<<<<<<<<<-<<<<<<<<<-----<<<<<______>>>>>------>>>>>---->>>>>>>>>>---->>>>>>>::::::
#=GC RF                      AuCACAGACgCcuCCaaGuGcGCaGGGCaCuGaUGGGGGCCaGGGCAGGCCCAGCgAAaGuGCAGGACCuGgCaCuuAGUCGGagGcGAGGaUG
//
# STOCKHOLM 1.0

#=GF AC   RF00971
#=GF ID   mir-578
#=GF DE   microRNA mir-578
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   101.60
#=GF NC   82.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000477;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


AADB02007897.1/76733-76828 A-GAUAAAUCUAUAGACAAAAUACAAUCCCGGACAACAAGAAGCUCCUAUAGCUCCUGUAGCUUCUUGUGCUCUAGGAUUGUAUUUUGUUUAUAUAU
AANU01272999.1/14644-14739 -GGAUAAAUAUAUAGACAAAAUACAAUCCUGGACUAUAAGAAGCUCCUAUAGCUCCUGUAGCUUCUUGUGCUCUGGGAUUGUAUUUUGUUUAUAUAU
AADA01074106.1/5191-5105   A-GAUAAAUCUAUAGACAAAAUACAAUCCCGGACAACAAGAAGCU---------CCUGUAGCUUCUUGUGCUCUAGGAUUGUAUUUUGUUUAUAUAU
#=GC SS_cons               :.:::::<<<<<<<<<<<<<<<<<<<<<<<<<<--<<<<<<<<<<______________>>>>>>>>>>-->>>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                    A.GAUAAauauauagaCaaaauaCaauCCcgGaCaacaaGaaGCuccUAUAGcUCCUGUaGCuuCuuguGCuCcgGGauuGuauuuuGucuauauau
//
# STOCKHOLM 1.0

#=GF AC   RF00972
#=GF ID   mir-651
#=GF DE   microRNA mir-651
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   65.50
#=GF NC   63.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000478;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   4


AANU01236884.1/24642-24546 AAGCUAUCACUGCUUUUUAGAAUAAGCUUGACUUUUGUUCAAAUAAAAACGCAAAAGGAAAGUGUAUCUUAAAAGGCAAUGACAGUUUAAUAUGUUU
AADB02035301.1/5277-5373   AAUCUAUCACUGCUUUUUAGGAUAAGCUUGACUUUUGUUCAAAUAAAAAUGCAAAAGGAAAGUGUAUCCUAAAAGGCAAUGACAGUUUAAUGUGUUU
ABDC01066543.1/12126-12221 AAGCUAUCAUUGCCU-UUAGGGCAAGCUUGACUUUUGUUCAAAUAGACAUGCAAAAGUCAAGUGUACCUUAAGAGGGAAUGAUAGUUUAAAAUCGUU
AAWR02023234.1/3089-3185   AAGCUAUGAUUGCCUUUUAAGGCAAGCUUGACUUUUGUGCUUAUAGAAAUGCAAAUGCCAAGCUUGUCUUAAAAGACAAUGACAGUUUAAUAUUCUC
#=GC SS_cons               <<<<<-<<<<<<<<<<<<<<<<<<-<<<<--<<<<<<<____________>>>>>>>-->>>>->>>>>>>>>>>>>>>>>>->>>>>:::::::::
#=GC RF                    aagCuAucauugccuuuuagGgcaAgCuuGACuuuuGuuCaaAUAaAaAugCaaaaGuaaaGcgugcCcuaaaaggcaaugacaGcuuAAuaUuuUu
//
# STOCKHOLM 1.0

#=GF AC   RF00973
#=GF ID   mir-597
#=GF DE   microRNA mir-597
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   53.50
#=GF NC   49.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000479;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   4


AANU01127382.1/23707-23611   UACUUACUCUACAUGUGUGUCACUUGACGACCACUGUGAAGAGAGUAAAAUGUACAGUGGUUC--UCUU--GGGGCUCAAGCGUAACGUAGAGUGCUGGUC
ABDC01288249.1/2841-2939     UACUUAUUCUACCUGUGUAUCAUUUAAUGACCAGUGUGAGGGGAAUAAAAUGUACUGUGGUUCUCUUUU--GCGGCUGAAGAGUAAUGUAGUGUUCAGGUC
AAWR02024110.1/252315-252218 UACUUAUUAUACAUGUGUGUCAUUUGGUGACCAGUGUGCGAGAAAUAAAAUGUAUAGUGGUUC--UCUUUUGUGGC-UAAUAGAAUUGUAGUGUGCAGGUU
AC103834.2/165358-165454     UACUUACUCUACGUGUGUGUCACUCGAUGACCACUGUGAAGACAGUAAAAUGUACAGUGGUUC--UCUU--GUGGCUCAAGCGUAAUGUAGAGUACUGGUC
#=GC SS_cons                 :<<<<<<<<<<<<<-<<-<<<<<--<<-<<<<<<<<<<______________>>>>>>>>>>-..>>--..>>>>>->>------>>>>>>>>>>-->>>:
#=GC RF                      UaCucacucuaCguGugUGuCacUuGaugaCCacuGugaagaaAaUAAAAUGuaCaguGGuuC..uCUU..guGgCUcaAgaGuAacGuagagugCagGuc
//
# STOCKHOLM 1.0

#=GF AC   RF00974
#=GF ID   mir-607
#=GF DE   microRNA mir-607
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   95.00
#=GF TC   97.60
#=GF NC   92.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000480;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF WK   MicroRNA
#=GF SQ   3


AADB02013263.1/1948053-1948148 UUGCCUAAAGUCACACAGGUUAUAGAUCU--GGAUU-GGAACCCAGGGAGCCAGACUGCCUGGGUUCAAAUCCAGAUCUAUAACUUGUGUGACUUUGGG
AANU01012646.1/6912-7007       UCGCCCAAAGUCACACAGGUUAUAGAUCU--GGAUU-GGAACCCAGGUAGCCAGACUGCCUGGGUUUGAAUCCAGAUCUGUAACCUGUGUGACUUUGGA
ABBA01021824.1/3353-3451       UUGCCUAAAGUCACACAGGUUAUAGAUCUUGGGAUUGGGAACCCAGGGAGCCAGACUGCCUGGGUUCAAAUCCAGAUCUAUAACUUGUGUGACUUUGGG
#=GC SS_cons                   :::::<<<<<<<<<<<<<<<<<<<<<<<<..<<<<<.-<<<<<<<<<<<<_____>>>>>>>>>>>>->>>>>>>>>>>>>>>>>>>>>>>>>>>>>::
#=GC RF                        UugcccaaaGucacacagGuuauaGaucu..GGauu.ggaacccaGGcaGccAgACugCCuggguucaaauCCagauCuauaaCcugugugaCuuuggg
//
# STOCKHOLM 1.0

#=GF AC   RF00975
#=GF ID   MIR845_2
#=GF DE   microRNA MIR845_2
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   80.50
#=GF NC   79.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000481;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17721507
#=GF RT   The grapevine genome sequence suggests ancestral hexaploidization in major
#=GF RT   angiosperm phyla.
#=GF RA   Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne
#=GF RA   N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C,
#=GF RA   Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B,
#=GF RA   Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C,
#=GF RA   Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M,
#=GF RA   Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G,
#=GF RA   Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A,
#=GF RA   Scarpelli C, Artiguenave F, Pe ME, Valle G, Morgante M, Caboche M,
#=GF RA   Adam-Blondon AF, Weissenbach J, Quetier F, Wincker P
#=GF RL   Nature. 2007;449:463-467.
#=GF WK   MicroRNA
#=GF SQ   2


AM480503.2/2487-2357 AGAACGCACAUUAAUUAUCCCUAGGGCCAUGGGAUAAACAAAAACCUUGAAAAAACAAGUUAGCACACCCUAGAAUGGUUCUAGCACGAUUACUAACCUAUGGCUCUGAUACCAAUUGAUGGGAAAAACUC
AM438450.2/9360-9490 AUAACCAACAUUAAUUAUCCCUGGGGCCAUGGGAUAAACAAAAACUCUGCAAAACCAAGUUAGCACACCCUAGAAUGGUUCUAGCACAAUUACUAACCUAUGGCUCUGAUACCAAUUGAUGGGAAAAACCU
#=GC SS_cons         ::::::::<<<<<<<<-----<<<<<<<<<<<<--------------<<---<<-<<--<<<<______>>>>-->>->>---->>---------->>>>>>>>>>>>----->>>>>>>>::::::::::
#=GC RF              AuAACgaACauuaauuAUCCCuaGgGCCaugGGAUAAACAAAAACuuuGaAAaaaCaAGuuaGCACACCCuagAAuGGuuCUAGCaCaAUUACUAACCuauGGCuCugAUACCaauugauGGGAAAAACuu
//
# STOCKHOLM 1.0

#=GF AC   RF00976
#=GF ID   mir-583
#=GF DE   microRNA mir-583
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   68.00
#=GF TC   69.50
#=GF NC   66.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000482;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [3]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF WK   MicroRNA
#=GF SQ   3


AANU01187000.1/6932-7006   AACUCGCACAUUUACCAAAGAGGAAGGUCCCAGUACUGCAGGGAUCUUAGCAGUACUGGGACCUACCUCUUUGGU
ABGA01020288.1/16391-16317 AACUCACACAUUUACCAAAGAGGAAGGUCCCAGUACUCCAGGGAUCUUAGCAGUACUGGGACCUACCUCUUUGGU
AC104123.2/90919-90845     AACUCACACAUUAACCAAAGAGGAAGGUCCCAUUACUGCAGGGAUCUUAGCAGUACUGGGACCUACCUCUUUGGU
#=GC SS_cons               :::::::::::::<<<<<<<<<<<<<<<<<<<<<<<<<<__________>>>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                    AACUCaCACAUUuaCCaaaGaGGaaGGuCCCaguaCugCAGGGAUCUUAGcaGuacuGGGaCCuaCCuCuuuGGu
//
# STOCKHOLM 1.0

#=GF AC   RF00977
#=GF ID   mir-600
#=GF DE   microRNA mir-600
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   80.20
#=GF NC   50.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000484;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


AANU01127189.1/17617-17693 GUGUCUCCAGCUUCACAGGAAGGCUCUUGUCUGUCAGGCAGUGGA-GUUAC----AGA-CAAGAGCCUUGCUCAGGCCAGCCC
AAGV020251216.1/651-733    GUGGCUCCAGCCUCACAGGGAAACUUGUGUCUAUCAGGUACCAGAAGUCACUCACAGAGCUAGGGCCUUGCCCAGGCCAGGCU
AC007172.6/99775-99855     GUGGCUCCAGCUUCAUAGGAAGGCUCUUGUCUGUCAGGCAGUGGA-GUUACUUACAGA-CAAGAGCCUUGCUCAGGCCAGCCC
#=GC SS_cons               ::<-<<---<<<<---<<-<<<<<<<<<<<<<----<<<______.>>-->---->>>.>>>>>>>>>>->>->>>>->>->:
#=GC RF                    GUGgCUCCAGCcUCAcaGGaaggCucuuGUCUgUCAGgcAgugGA.guuACUuACAGA.CaagaGccuuGCuCAgGCCAGcCc
//
# STOCKHOLM 1.0

#=GF AC   RF00978
#=GF ID   mir-638
#=GF DE   microRNA mir-638
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   54.40
#=GF NC   46.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000486;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-638_microRNA_precursor_family
#=GF SQ   6


AADB02020051.1/340879-340978 GUGAGCGGGCGCGGCAGGGAUCGCGGGCGGGUGGCGGC-CUAGGGCGCGGAGGGCGGACCGGGAAUGGCGCGCCGUGC-G-CCGCCGGCGUAACUGCGGCGCU
AANU01122668.1/894-795       GUAAGCGGGCGCGGCAGGGAUCGCGGGCGGGCGGCGGC-CUAGGGUGCGGAGGGCGGACCGGGAAUGGCGCUCCCUGC-G-CCGCCGGCGUAACUGCGGCGCU
AAQQ01596178.1/458-359       GUGAGCGAGCGCGGCGGGGACUGCGGGAGGGCGGCGGC-CUAGGGCGCGGAGGGCGUACCGGGAAUGGCGCUCCCUGC-G-CCGCCGGCGUAACUGCGGCGUU
ABGA01233823.1/6469-6367     GUGAGCGGGCGCGGCAGGGAUCGCGGGCGGUCGGCGGCCCUAGGGCGCGGAGGGCGGACCGGGAAUGGCGCGCCCUGGCGCCCGCCGGCGUAACUGCGGCGCU
ABRQ01087111.1/310-211       GUGAGCGAGCGCCGCGGGGACGGUGGGAGGGCGGCGGC-CUAGGGCGUUGAGGGCGGCCCGGGAAUGGCGCGCCCUGC-G-CCGCCGGCGUAACUGCGGCGCU
ABRN01352993.1/11133-11034   GUGAGCGAGCGGGGCGGCGACAGCGGGCAGGCGGCGGC-CUAGGGCGCGGAGGGCGGACCGGGAAUGGCGCGUCCUGC-G-CCGCCGGCGUAACUGCGGCGCU
#=GC SS_cons                 ::::::::<<<<-<-----------------<<<<<<<.<<<<<<<<<<___________________>>>>>>>>>>.>.>>>>>>--------->->>>>:
#=GC RF                      GUgAGCGaGCGCgGCaGgGAuuGcGGGcgGgcGGCGGC.cuagGGcGcgGAGGGCGgACCGGGAAUGGcgCgCCcugg.G.CCGCCgGCGUAACUGCGGCGCU
//
# STOCKHOLM 1.0

#=GF AC   RF00979
#=GF ID   mir-553
#=GF DE   microRNA mir-553
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   75.70
#=GF NC   49.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000487;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


AANU01219886.1/10436-10503 CUUCAAUUUUAUUUGAAAAAGGUGAGGUUUUGUUUUGUCUGAGAAAAUCUCACUGUUUUAGACUGAGG
ABDC01323916.1/3871-3934   CAUAUAUUCAAAAACAAAAAGGUGAGGUUUUGUUUUG-CUUAGAGAAUCUUGCUGUUUUAUUUUA---
AL663111.8/4549-4616       CUUCAAUUUUAUUUUAAAACGGUGAGAUUUUGUUUUGUCUGAGAAAAUCUCGCUGUUUUAGACUGAGG
#=GC SS_cons               ::::::::::::<<-<<<<-<<<<<<<<<<<-<<______>>->>>>>>>>>>>->>>>->>::::::
#=GC RF                    CuUcaAUUuuAuuuuAAAAaGGuGAGgUUuUGUuUUGUCUgAGAaAAuCUCgCUGUUUUAgacUgAGG
//
# STOCKHOLM 1.0

#=GF AC   RF00980
#=GF ID   mir-643
#=GF DE   microRNA mir-643
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   55.30
#=GF NC   52.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000488;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF WK   MicroRNA
#=GF SQ   2


AANU01181804.1/9985-9889       ACCAACUGAUACGCAUUAUCUACGUGAGCUAGAAUACAAGUAGUUGGUGUCUUCAGAGACACUUGUAUUCUAGCUCAGGUAGAUACUGAAUGGAAAA
AADB02020208.1/1305278-1305374 ACCAAGUGAUAUUCAUUGUCUACCUGAGCUAGAAUACAAGUAGUUGGCGUCUUCAGAGACACUUGUAUGCUAGCUCAGGUAGAUAUUGAAUGAAAAA
#=GC SS_cons                   .........<<..<<.<<<<<<<.<<<<<<<<.<<<<<<<<.<<<...<....>...>>>>>>>>>>>.>>>>>>>>.>>>>>>>.>>..>>.....
#=GC RF                        ACCAASUGAUAYKCAUURUCUACSUGAGCUAGAAUACAAGUAGUUGGYGUCUUCAGAGACACUUGUAUKCUAGCUCAGGUAGAUAYUGAAUGRAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF00981
#=GF ID   mir-939
#=GF DE   microRNA mir-939
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   82.50
#=GF NC   55.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000490;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-939_microRNA_precursor_family
#=GF SQ   3


AF205589.5/40457-40538   UGUGGGCAGGGCCCUGGGGAGCUGAGGCUCUGGGGGUGGCCGGGGCUGACCC-UGGGCCUCUGCUCCCCAGUGUCUGACCGCG
AC195294.3/96374-96294   UGUGGGCAGGGCCCUGGGGAGCUGAGGCUCUGGGGGUGGCCGGGGCUGACCC-UGGGCCUCUGCUCCCCAGUGUCUGACCGC-
AANU01106867.1/8590-8508 UGUGGGCAGGGCCCUGGGGAGCUGAGGCUCUGGGGGUGGCCGGGGCUGACCCCUGGGCCUCUGCUCCCCAGUGUCUGACCGUG
#=GC SS_cons             :<<<<---<<<<-<<<<<<<<<-<<<<<<<---<<<<<<<____>>>->>>>.->>>>>>>->>>>>>>>>->>>>-->>>>:
#=GC RF                  UgcGGGCAgGgCCCuGGGGaGCUGaGGCcCUGGGGGugGCCGGGGCcGaCCC.UGgGCCuCUGCuCCCCaGUGcCcGACCgcg
//
# STOCKHOLM 1.0

#=GF AC   RF00983
#=GF ID   mir-662
#=GF DE   microRNA mir-662
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   60.50
#=GF NC   55.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000492;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF WK   MicroRNA
#=GF SQ   14


AADB02017031.1/91068-90974 GCUGUUGAGGCUGCGCAGCCAGG-CCCUGACGGUGGGGUGGCUGCGGGCCUUCUGAAGGUCUCCCACGUUGUGGCCCAGCAGCGCAGUCACGUUGC
AANU01106367.1/1414-1320   GCUGUUGAGGCUGUACAGCCAGG-ACCUGACGGUGGGGUGGCUUCGGGCCUUCUGCAGGUCUCCCACGUUGUGGCCCAGCAGCGCAGUCACGUUGC
AANN01248073.1/3014-2920   GCUGUUGAGGCUGCGCAGCCAGG-AGCUGAUGGUGGGGUGACUUCGUGCCUUCUGCAGGUCCCCCACAUUCUGGCCCAGCAGCGUGGUCACGUUGU
ABDC01468449.1/1430-1524   GCUGUCGAGGCCGCGGAGCCAGG-AGCUGACGGCCGGGUGGCUGCGGGCCUUCCACAGGUCCCCCGCGUUGGGCCCCAGCAGCGUGGUCACGUUGC
AAPY01721895.1/962-868     GCUGUCGAGGCUGCGUAGCCAGG-AGCUGACGGCUGGGUGGCUGCGGGCCUUCUGCAGGUCUCCCACGUUAGGGCCCAGCAGUGUGGCCACGCUGC
AALT01295375.1/837-931     GCUGUUGAGGCUGCGCAGCCAGG-AGCUGAUGGUCGGGUGGCUGCGCGCCUUCCGCAGGUCCCCCACGUUCUGGCCCAGCAGUGUGGUCACAUUGU
AAQQ01317942.1/2514-2420   GCUGCUGAGGCUCCGCAGCCAGGAGCUGACCG-UGGGGUGGCUGCGGGCCUUCUGCAGGUCCCCCACAUUCUGCCCCAGCAGGGUGGUCACGUUGC
AAIY01729442.1/929-835     GCUGCUCAGACUGCGAAGCCAGG-AGCUGAUGGUGGGGUGGCUGCGUGCCUUCUGCAGGUCCCCCACGUUCUGACCCAGCAGCGUGGUCACAUUGC
AAFC03000824.1/48766-48860 CCGAUUGAGGCUGCGGAGCCAGG-AGCUGAUGAUGGGGUGGCUCCGAGCCUUCUGCAGGUCCCCCACGUUCGGACCCAGCAGCGUCGUCACGUUGC
AANG01147031.1/255-349     CCUGUUGAGGCUGCGCAGCCAAG-AGCUGAUGGUCGGGUGGCUCCGUGCCUUCUGUAGGUCCCCCACGUUCUGGCCCAGCAGUGUCGUCACAUUGC
AAYZ01695173.1/800-894     ACUGUUGAGGCUGCCGAGCCAGG-AGCGGAUGGCCGGGUGGCUGCGGGCCUUCUGCAGGUCCACCACGUUCUGACCCAGCAGCGUGGUCACGUGGC
AAWR02040130.1/14530-14436 GCUGUUGAGGCUGCGGAGCCAGG-AGCUGAUGGUGGGGUGGCUGCGAGCCUUCUGCAGGUCCCCCACAUUCUGGCCCAGCAGCGUCGUCACGUUGC
AAGU03068835.1/1169-1075   GUGGUUCAGGCUGCGGAGCCAGG-AGCUGAUGGUGGGGUGGCUGCGCACCUUCUGUAGGUCCCCCACGUUCUGGCCCAGCAGUGUCGUCACGUUGU
AAQR03077873.1/5015-5107   UG--UUGAGGCUGUGUAGCCAGG-AGCUGACAGUGGGGUGGCUGCGAGCCUUCCGCAGGUCCCCCACGUUCUGCCCCAGCAGCGUGGUCACAUUGC
#=GC SS_cons               <<---<<-<<<<<<<<-<<--<<.<<-<<<<<-<<<<<-<<<<-<<<_____>>>-->>>>>>>>>>>>>>->>>>-->>->>>>>>>>->>-->>
#=GC RF                    gcuGUcGAGgCcgcgcAGCCAGG.cccggacGGugGGGUGgCugCggGCCUUccGcAgGuCCCCcaCguucuggCCCAGCAgcgcgGcCACgUUgc
//
# STOCKHOLM 1.0

#=GF AC   RF00984
#=GF ID   mir-576
#=GF DE   microRNA mir-576
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   90.60
#=GF NC   73.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000493;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414. Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF WK   MicroRNA
#=GF SQ   2


AADB02007245.1/34316-34413 UACAAUCCAACGAGGAUUCUAAUUUCUCCACGUCUUUGGUAAUAAGGUUUGGCAAAGAUGUGGAAAAAUUGGAAUCCUCAUUCGAUUGGUUAUAACCA
AANU01270069.1/11195-11292 UACAAUCCAGUGAGGAUUCUAAUUUCUCCACAUCUUUGGUAAUAAGUUUUGGCAAAGAUGUGGAAAAAUUGGAAUCCUCAUUGGAUUGGUUAUAAUAC
#=GC SS_cons               ::<<<<<<<<<<<<<<<<<<<<<<<-<<<<<<<<<<<<-<<<______>>>->>>>>>>>>>>>->>>>>>>>>>>>>>>>>>>>>>>::::::::::
#=GC RF                    UAcaauccagcGaGGauuccaauuucuccacgucuuuGGcaaUAAGuUuugGCaaagacguggaAaaauuggaauCCuCgcuggauugGUUAUAAuaa
//
# STOCKHOLM 1.0

#=GF AC   RF00985
#=GF ID   mir-640
#=GF DE   microRNA mir-640
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   97.00
#=GF NC   74.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000494;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


AC092067.2/49912-50007   GUGACCCUGGGCAAGUUCCUGAAGAUCAGACACAUCAGAUCCCUUAUCUGUAAAAUGGGCAUGAUCCAGGAACCUGCCUCUACGGUUGCCUUGGGG
AC195612.4/185993-185898 GUGACCCUGGGCAAGUUCCUGAAGAUCAAACACAUCAGAUCCCUUAUCUGUAAAAUGGGCAUGAUCCAGGAACCUGCCUCUAUGGUUGCCUUGGAG
AADA01086534.1/2954-3048 -UGACCCUGGGCAAGUUCCUGAAGAUCAGACACAUCAGAUCCCUUAUCUGUAAAAUGGGCAUGAUCCAGGAACCUGCCUCUACAGUUGCCUUGGGG
#=GC SS_cons             ::::<<<-<<<<<<<<<<<<<--<<<<<----<<<<<<<<_____>>>>>---->>>---->>>>>>>>>>>>------------>>>>>>->>>:
#=GC RF                  GUGAcCCUgGGCaaGuuCCuGAAGauCagACACauCaGauCCCUUauCuGUAAAauGGGCAuGauCCaGGaaCCUGCCUCUAcgGuuGCCcUGGgG
//
# STOCKHOLM 1.0

#=GF AC   RF00986
#=GF ID   mir-920
#=GF DE   microRNA mir-920
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   47.50
#=GF NC   38.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.97 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000495;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17573847
#=GF RT   Analysis of gene expression in normal and neoplastic human testis: new
#=GF RT   roles of RNA.
#=GF RA   Novotny GW, Nielsen JE, Sonne SB, Skakkebaek NE, Rajpert-De Meyts E,
#=GF RA   Leffers H
#=GF RL   Int J Androl. 2007;30:316-326.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   4


AADB02014749.1/234282-234356 GUAGUUGUUCUACAGAAGACCUGGAUGUGUAGGAGCUAAGACACACUCCAGGGGAGCUGUGGAAGCAGUAACACG
AANU01253677.1/16443-16369   GUAGUUGUUCUGCAGAAGACCUGGAUGUGGAAGAGCUAAGACACACUCCAGGGGAGCUGUAGAAGCGGUAACACG
AAFC03002330.1/135300-135226 GUAGCUGCUCUUCAGGAGACCUGGGUGUGGAGACACUAAGUCAAACUCCAGGAGACUUGUGGAAGUGGUAACACU
AANN01623347.1/2384-2310     GUGACUGCUCUAUAGGAAACCUGGUUGUGGAGGAACUGAGUCAAACUCUAGGAGAGAUGUGGAAGUGGUAGAGAC
#=GC SS_cons                 <<--<<<<<<<<<<<----<<<<<<<<<<____________>>>>->>>>>>---->>>>>>->>>>>-->>:::
#=GC RF                      GuAGcugcUCuacAgaAGACCUGGaUgUGGAGGAaCUAAGuCAcACuCCAGGaGAgcUgugGAAgcggUAaCAcu
//
# STOCKHOLM 1.0

#=GF AC   RF00987
#=GF ID   mir-589
#=GF DE   microRNA mir-589
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   103.10
#=GF NC   77.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000496;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-589_microRNA_precursor_family
#=GF SQ   2


AADB02010408.1/405496-405594 UCCAGCCUGUGCCCAGCAGCCCCUGAGAACCACGUCUGCUCUGAGCUGGGUACUGCCUGUUCAGAACAAAUGCCGGUUCCCAGACGCUGCCAGCUGGCC
AANU01170262.1/1936-1838     UCCAGCCUGUGCCCAGCAGCCCCUGAGAACCACGUCUGCUCUGAGCUGGGUACUGCCUGUUCAGAACAGACGCUGCUUCCCAGACGCUGCCAGCUGGCC
#=GC SS_cons                 :<<<<<---------<<<<<--<<<-<<<<<-<<<<<<-<<<<<<<-<<<_____>>>>>>>>>>->>>>>>-->>>>>->>>-->>>>>-->>>>>::
#=GC RF                      UccaGccUGUGcccAGcaGccccuGAGaaccAcgucuGcucuGagcUgGGUAcUGCCcgcuCagaACagacgcugguuCcCagAcgCugCcAgCuggcc
//
# STOCKHOLM 1.0

#=GF AC   RF00988
#=GF ID   mir-657
#=GF DE   microRNA mir-657
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   94.00
#=GF NC   49.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000498;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF WK   Mir-657_microRNA_precursor_family
#=GF SQ   2


AANU01217966.1/9444-9541 GUAUAGCAGGGCUGGGAGGAGAGGGUCCUGGAGAAGCGUGGACGGCUCCAGGUGGGUUCUGGCAGGUCCUCACCCUCUCUAGGCCCCAUUCUCAUCUG
AADB02050593.1/5582-5485 GUGUAGUAGAGCUAGGAGGAGAGGGUCCUGGAGAAGCGUGGACCGGUCCGGGUGGGUUCCGGCAGGUUCUCACCCUCUCUAGGCCCCAUUCUCCUCUG
#=GC SS_cons             :::::::::::::::::<----<<<-<<<<<<<<------<<<----<<<<_______>>>>--->>>------->>>>>>>>->>>--->:::::::
#=GC RF                  GUaUAGuAGaGCUaGGAGGAGAGGGUCCugGaGaAGCGUGgaCgGgUCCgGGUGGGUUCcGGCAGGucCUCACCCuCuCuaGGCCCCAUUCUCaUCUG
//
# STOCKHOLM 1.0

#=GF AC   RF00989
#=GF ID   mir-492
#=GF DE   microRNA mir-492
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   75.50
#=GF NC   74.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000499;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs.
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [2]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach.
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [3]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF WK   Mir-492_microRNA_precursor_family
#=GF SQ   14


AADB02015429.1/35076-35191 CA--ACUACAGCCACUACUACAGGACCAUCGAGGACCUGCGGGACAAGAUUCUUGGUGCCACCAUUGAGAACGCCAGGAUUGUCCUGCAGAUCAACAAUGCUCAACUGGCUGCAGAUG
AANU01270091.1/20339-20224 --UGACUACAGCCACUACUACAAGACCUUCGAGGACCUGCGGGACAAGAUUCUUGGUGCCGUCAAUGAGAACUCCAGGAUUGUCCUGCAGAUCAACAAUGCCUGUCUGGCUGCAGAUG
BC116088.1/417-532         --CGACUACAGCCACUACUUCAAGACCAUAGAGGACCUGCGGGACCAGAUUCUCGGUGCCACCAUUGAGAACUCCAAGAUAGUCCUGCAGAUCGACAAUGCCCGUCUGGCUGCAGAUG
AADA01319369.1/12481-12596 --UGACUACAGCCACUACUACAAGACUAUCCAGGACCUGCGGGACAAGAUUCUUGGUGCCACCAUUGAGAACUCCAGGAUUGUCCUGGAGAUCGACAACGCCCGUCUGGCUGCAGAUG
DQ289548.1/23-138          CA--ACUACAGCCACUACUACAGGCCCAUCGAGGACCUGCGGGACAAGAUUCUUGGUGCCACCAUUGAGAACUCCAGGAUUGUCCUACAGAUCGACAACACCCAUCUGGCUGCAGAUG
AANG01593139.1/635-750     CA--ACUACAGCCCCUACUUCAAGACCAUCAAGGAGCUGCAGGACAAGAUUCUUGUGGCCACCAUUAAGCACUCCAAGAUUGUCCUGCAGAUUGACAAUGCCUGUCUGGCUGCAGAUG
AAIY01817548.1/749-634     --CGACUACAGCCACUACUACGAGACCAUCGAGGACCUGCGGCACCAGAUUCUCGGUGCCACCAUCCAGAACUCCAAGGUUGUGCUGCAGAUCGACAACGCCCGCCUGGCGGCGGAUG
BC088424.1/441-556         --UGAUUACAGCCAGUACUUCAAGACCAUCGAGGACUUGCGCGACAAGAUCCUUGGCGCCACCAUUGAGAACUCCAAGAUAGUCCUACAGAUCGACAAUGCCCGCCUGGCUGCAGAUG
BC085304.1/444-559         --AGAUUACAACCACUACUUUAAGACCAUCGAGGACUUGCGCGACAAGAUUCUUGGUGCCACCAUUGACAACUCCAAGAUUGUCCUACAGAUUGACAAUGCUCGCCUGGCUGCAGAUG
AAYZ01143552.1/22927-22812 --CGACUACAGCCACUAUUUUAAGACCAUCGAGGAUCUACGUGAUAAGAUUCACGGGGCCACCAUUGACAACUCCAAGAUCGUCCUGCAGAUCGACAAUGCCCGUCUGGCUGCAGAUG
X82579.1/440-555           --AGACUAUAGCGCCUACAUGACGACCAUCCAGGACCUGCGAGAUAAGAUUCUUGGUGCCACCAUAGAGAACUCAAAGAUUGUUCUGCAAAUUGACAAUGCCCGGCUGGCUGCAGAUG
AB050955.1/348-463         --AGACUACAGCAAAUAUUUUGAUACUAUUGAUGACCUCCGGAAUAAGAUACUUUCUGCAACUAUUGAAAACUCCAAGUACAUUUUGCAGAUCGACAAUGCCAGGUUGGCAGCUGAUG
AAWR02017948.1/49448-49563 --CGACUACAGCCACUACUUCAAGACCAUCGAGGAGCUGCGGGACAAGAUUCUUGGGGCCACCAUUGAGAACUCCAAGAUUGUUCUGCAGAUCGACAAUGCCCGUCUGGCUGCAGAUG
AAGV020823453.1/493-607    --GGUCUUGAAAUAGUUUU-CAAGACCAUUCAUGACUUGCGUGACAAGAUUUUUGGUGCCACCAUUAAGAACGCCAAGAUUGUCCUGUAGAUCAAGAAUCCCCAUCUGGCUGUAGAGA
#=GC SS_cons               ..:::<<-<<<<<<---------<--<-<----<<-<<<<<<<<<<<---<<<<<<-<----<_____>-->->>>>>>>>>>>>>>>>>->>---->->-->--->>>>>>->>:::
#=GC RF                    ..aGACuACaGCcacUAcUucAAgACcAUcgAgGAccUgCgggAcaaGAUuCuugguGCCACcAUUgAgAACUccaaGauugUccuGcAgAUCGACAAUgCCcGuCugGCuGCaGAUG
//
# STOCKHOLM 1.0

#=GF AC   RF00990
#=GF ID   mir-552
#=GF DE   microRNA mir-552
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   71.20
#=GF NC   66.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000501;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF WK   Mir-552_microRNA_precursor_family
#=GF SQ   2


AANU01100315.1/28426-28332 -ACCAUUCAAAUAUACCACAGUUUGUUUGACCAUUAACCUGUUUGUUGAAGAUGCCUUUCAACGGGUGACUGGUUAGACAAACUGUGGUAUAUUCA
AC158329.1/2884-2979       AACCAUUCAAAUAUACCACAGUUUGUUUAACCUUUUGCCUGUUGGUUGAAGAUGCCUUUCAACAGGUGACUGGUUAGACAAACUGUGGUAUAUACA
#=GC SS_cons               ::::::::::<<<<<<<<<<<<<<<<<<<<<<--<<<<<<<<<<<--<_______>-->>>>>>>>>>>-->>>>>>>>>>>>>>>>>>>>>>:::
#=GC RF                    AACCAUUCAAauauaCCaCaGuuuGucugaCCaUucgCCcGuuggUUGAAGAUGCCUUccaaCgGGcgaCUGGucagaCaaaCuGuGGuauauaCA
//
# STOCKHOLM 1.0

#=GF AC   RF00991
#=GF ID   mir-599
#=GF DE   microRNA mir-599
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   56.30
#=GF NC   46.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000502;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF WK   MicroRNA
#=GF SQ   11


AANN01737513.1/1490-1396   AGAGACAUGCUGUCCACAGUGUGUUUGAUAAGCUGACAUGGGACAGGAA-UUCUUUUCACUGUUUUGUCAGUUUAUCAAACCCAUACCUGGAUGAU
AAQQ01055001.1/924-830     AAAGAUAAGUGGUCCAUUGUGUGUUUGAUAAGCUGACAUGGGACAGAGA-UUCUUUUCACUGUUGUGUCAGUUUAUCAAACCCAUACCUGGAUGAC
AAPY01575258.1/7264-7170   GAGGACAUGCUAUCCACAAUGUGUUUGAUAAGCUGAUAUAGGACAGGGA-UUUUUUUCACUGUUGUGUCAGUUUAUCAAACCCAUAUCUGGAUGAU
AAFR03006570.1/12574-12668 AAGGACAAACUGUCCAGAGUGUGUUUGAUAAUCUGACAUGGGACAGAGG-UUCUUUUCACUGUUGUGUCAGUUUAUCAAACCCAUACCUGGAUACC
AC121598.3/75982-76076     AAAGAUGUGCUGUCCACAGUGUAUUUGAUAAGAUGACAUAGGAGAGGAA-CUUCUUUCACCUUUGUGUCAGUUUAUCAAACCCAUACCUGGAUGAC
AAPN01034672.1/28470-28563 AAACACACUGUCCUCAGUGC--GUUUGAUAAGCUAACAUGAGACAGGAGCUUUUUUUCACGGUUGUGUCAGUGUAUCAGACACAAGCCUGAGCACC
ABRQ01087343.1/1788-1694   ACCUACAUGCUGUCCACAGUGUGUUUGAUAAGCUGACAUGGGACAGGAU-UUCUUUUCACUGUUGUGUCAGUUUAUCAAACCCAUACCUGGACGAC
AP005625.2/32064-31970     AAAGACAUGCUGUCCACAGUGUGUUUGAUAAGCUGACAUGGGACAGGGA-UUCUUUUCACUGUUGUGUCAGUUUAUCAAACCCAUACUUGGAUGAC
AC023933.9/63274-63180     AAAGACAUGCUGUCCACAGUGUGUUUGAUAAGCUGACAUGGGACAGGGA-UUCUUUUCACUGUUGUGUCAGUUUAUCAAACCCAUACUUGGAUGAC
AC026827.6/166296-166202   AAAGACAUGCUGUCCACAGUGUGUUUGAUAAGCUGACAUGGGACAGGGA-UUCUUUUCACUGUUGUGUCAGUUUAUCAAACCCAUACUUGGAUGAC
AANG01418749.1/382-288     ACAGACAUGCUGUCCAUAGUGUGUUUGAUAAGCUGACAUGGGACAGGGA-UUCUUUUCACUGUUGUGUCAGUUUAUCAAACCCAUACCUGGACGAC
#=GC SS_cons               :::::::::::<<<<<-<<<<<<<<<<<<<<<<<<<<<<--<<<<<<<<._____>>>->>>>>>>>>>>>>>>>>>>>>>-->>>>>>>>>>:::
#=GC RF                    AaagAcAugcUgucCacgGuguGuuuGauaagCuGaCacgGgacaGGaa.UUcUUuuCACuguuguGuCaGuuuauCaaaCcCauaCcuGgacgac
//
# STOCKHOLM 1.0

#=GF AC   RF00992
#=GF ID   mir-593
#=GF DE   microRNA mir-593
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   82.40
#=GF NC   52.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000503;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF WK   MicroRNA
#=GF SQ   2


AANU01285987.1/6423-6324     CCCCCAGAGUGUGUCAGGCAUCAGCCAGGCAUCGCUCAGCCCCUUUCCCUCUGGGGGAGCAAGGAGUGGUGCUGGGUUUGUCUCUGCUGGGGUUUCUCCU
AACC02000001.1/381414-381315 CCCCCAGAAUCUGUCAGGCACCAGCCAGGCAUUGCUCAGCCCGUUUCCCUCUGGGGGAGCAAGGAGUGGUGCUGGGUUUGUCUCUGCUGGGGUUUCUCCU
#=GC SS_cons                 :<<<<<<-------<<<<-<<-<<<<-<<<<<<<<<<-----<<<<<<<____>>>>>>>--->>>>>>>>>>->>>>->>->>>>>>>>>>::::::::
#=GC RF                      CCCCCaGAaUgUGUCaGgCacCagCCAgGCaccgCuCAGCCCgcucCCCUCUGGGGgagcAAGGaGcgguGCcGGGcuUguCcCuGCuGGGGUUUCUCCU
//
# STOCKHOLM 1.0

#=GF AC   RF00993
#=GF ID   mir-1473
#=GF DE   microRNA mir-1473
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   92.70
#=GF NC   50.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000504;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20370911
#=GF RT   miRTRAP, a computational method for the systematic identification of
#=GF RT   miRNAs from high throughput sequencing data.
#=GF RA   Hendrix D, Levine M, Shi W
#=GF RL   Genome Biol. 2010;11:R39.
#=GF RN   [2]
#=GF RM   18339653
#=GF RT   Altered miRNA repertoire in the simplified chordate, Oikopleura dioica.
#=GF RA   Fu X, Adamski M, Thompson EM
#=GF RL   Mol Biol Evol. 2008;25:1067-1080.
#=GF WK   MicroRNA
#=GF SQ   2


AACT01064472.1/104323-104400 ACGUGGGUCUGGCUCCCAAAUCUUCGAUCUUGUGAGAUAUA------UUCUCAAGCUCGGUUUUAUGGGUGCCGCAUCCAACGA
AABS01000095.1/49734-49651   GCGCGGCUCUGGCACCCACGUAUUCGAUCUUGCGAGAGAUAAAGGACAUCUCAAGCUCGGGUUUAUGGGUGUUGGACCAAGCGG
#=GC SS_cons                 :<<<<<<<<<<<<<<<<<---<<<<<<-<<<<-<-<____________>->>>>>->>>>>>--->>>>>>>>>>>>>>->>>:
#=GC RF                      aCGcgGgucuggCaCCCaaaUacuCGaUCuuGugAgAuAUAAAGGAcauCuCaaGCuCGgguUUAuGGGuGccggacCcAgCGa
//
# STOCKHOLM 1.0

#=GF AC   RF00994
#=GF ID   mir-1255
#=GF DE   microRNA mir-1255
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   65.00
#=GF NC   64.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000506;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells.
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   10


AADB02006467.1/217743-217678 UCUUACGGAUGAGCAAAGAAAGUGGUUUCUUAAAAU-----GGAAUCUACUCUUUGUGAAGAU-GC--UGUGAA
AANU01269624.1/9-80          UCUCAAGGAUGAGCAAAGGAAGUAGUUUUUUUAGAUUCCAAAGAAACUACCUACUUUGCUCAU-CU-UUGAGAA
ABDC01417052.1/3023-2958     UCUUAUGGAUGAGCAAAGAGAGUGGUUUCUUAAGAU-----GGAACCUACUUUUGGUGAACAU-GC--UGUGAA
AAFC03122281.1/6641-6708     UCUCAUGGAUGAGCAAAGAAAGUGGUUUCUUGAAAU-----GGAGUCUACUCUCGGUGAAGAU-GCGAUGAGGA
AANG01676531.1/2754-2819     UCAUACGGAUGAGCAAAGAAAGUGGUUUCUUGGGAU-----AGAAUCUACUCUUGGUGAAGAU-GC--UGUGAA
AC187354.5/97864-97931       UCUUAUGGACGAGCAAAGGAAGUGGUUUCUUGAGAC-----AGAAUCUACUUCUGGUGAAGAUACU-AUGAGAA
AC199862.3/67944-67879       UCUUAUGGAUGAUCAAAGAAAGUGGUUUCUUGAGAU-----AGAAUCUACUCCUGUUGAAAGU-GC--UGUGAA
AAGV020889804.1/238-303      UCUUAUGGAUGAUUAAAAAAAGUAGUUUCUUGAGAU-----GGAAUCUACUUUUGGUGAAGAU-AC--UGUGAA
AAWR02008080.1/187905-187970 UCUUAUGCAUGAGCAAAGAAAGUGGUUUCUUGAGAU-----GGAAACUGCUCUUGGUGAAGAU-GC--UGUGAA
ABVD01165354.1/722-787       UCUUAUGGAUGAGCAAAGAAAGUGGUUUCUUGAGAU-----GGAAACUACUCCUGGUGAAGAU-GC--UGUGAA
#=GC SS_cons                 <<<<<-<-<<---<<--<<-<<<<<-<<<<______.....>>>>->>>>>->>-->>--->>.->..>>>>>:
#=GC RF                      UCuuAuGGAuGAGCAAAgaAaGUgGUUUCuUgAGAU.....aGAAuCuACuuucGGUGAAgaU.gC..UgaGAA
//
# STOCKHOLM 1.0

#=GF AC   RF00995
#=GF ID   mir-616
#=GF DE   microRNA mir-616
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   71.00
#=GF TC   71.60
#=GF NC   70.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000507;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-616_microRNA_precursor_family
#=GF SQ   3


AADB02015149.1/16440-16344 UUAGGUAAUUCCUCCACUCAAAACCCUUCA--GUGACUUCCAUGACAUGAAAUAGGAAGUCAUUGGAG-GGUUUGAGCAGAGGAAUGACCUGUUUUAAAA
AANU01280868.1/9459-9362   UUAGGUAAUUCCUCCUCUCAAAACCCUCCA--AUGACUUCCCUGACAUGACAUAGGAAGUCACUGGAGAGUUUUGAGCAGAGGAAUGACCUGUUUUAAAA
AAWR02035787.1/215-128     GAAGGCCAUUG-UCAACUCAAAACCCUUCACUCUGGUUUUCCUG----------GGAAGCCUUUGGAG-GGUUUGAGCAGAGCAGUGACUUGAUUGAUUU
#=GC SS_cons               ::<<<<<<<<<<<<--<<<<<-<<<<<<<<..<<<<<<<<<_____________>>>>>>>>>>>>>>.>>>>>>>>-->>>>>>>>>>>>:::::::::
#=GC RF                    uuagGucauuccuCcaCuCaaAacCCucCa..guGgcuucCcUGAcAUGAaAUAGgaagcCacuGgaG.GguuuGaGCAGaggaaugaCcuGuUUuAaaa
//
# STOCKHOLM 1.0

#=GF AC   RF00996
#=GF ID   mir-631
#=GF DE   microRNA mir-631
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   48.20
#=GF NC   38.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000508;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   7


AANU01184627.1/708-782     GUGGAGAGCCUGGUUAGACCUGGCC-CAGACCUCAGCUACACAAGCUGAUGGACUGAGUCAGGG-GCCACA-CUCUCC
AADB02016646.1/28909-28983 GUGGGGAGCCUGGUUAGACCUGGCC-CAGACCUCAGCUACACAAGCUGAUGGACUGAGUCAGGG-GCCACA-CUCUCC
AANG01142762.1/3613-3543   GGGGAGCC-UGGUC--AACUUGGCC-CAGACCUCAGCUAUAU-AGCUGAUGGGCUGAGUCAGAG-GGCCGA-GGCUCU
ABDC01359619.1/2826-2751   GUGGGGAGCCUGUGUUAGAUCUGACUUAGGCCUCAGCCACACAAGCCGAUGGACUGAGUCGGGC-CACACU-CUCCCU
AAFC03077567.1/33091-33015 AGGGGGAGCCCAGUUAGACCUGGCU-UAGACCUCAGCUUCACAAGCUGAUAGACUGAGUCAGGGGGCCAAAGCUCUCC
AAWR02000950.1/80261-80332 GGGGAGCCAG---UAAGACCUGGCC-CAGACCUCAGCUAUACAAGCUGAUGGACUGAGUCAGGG-GUCCAA-GGCUCU
AAGV020186756.1/428-355    CAGGGAGC-CUAGCCAGACCCAGCU-CAGACCUCAGCUAGGCAUGCCGAGGGGCUGAAUUGGGG-GCCAAG-GCUUCC
#=GC SS_cons               ::<<<<<<--<<<<----<<<<<<<.<<<-<<<<<<<<_____>>>>>>->>->>>->>>>>>>.>>>>--.>>>>>>
#=GC RF                    guGGgGggccuGgcuAgAccccGcc.cAGACCUCaGCuAcACAaGCuGAUGGACUgAguCgggg.gcCaaa.ccCcCC
//
# STOCKHOLM 1.0

#=GF AC   RF00997
#=GF ID   mir-942
#=GF DE   microRNA mir-942
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   78.00
#=GF TC   78.90
#=GF NC   76.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000511;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF WK   MicroRNA
#=GF SQ   2


AANU01203167.1/13489-13404 AUUAAGAGAGUACCUUCUCUGUUUUGGCCAUGUGUGUACUCACAGCCCCUCACACGUGGCCGAAACAGAGAAGGUACUUUCCUAAU
AL391476.20/31705-31790    AUUAGGAGAGUAUCUUCUCUGUUUUGGCCAUGUGUGUACUCACAGCCCCUCACACAUGGCCGAAACAGAGAAGUUACUUUCCUAAU
#=GC SS_cons               <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<______________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                    auuagGagaGuacCuuCuCuGuuucGGCCacGuGuGUACUCACAGCCCCUCaCaCguGGCCgaaaCaGaGaaGguaCucuCcuaau
//
# STOCKHOLM 1.0

#=GF AC   RF00998
#=GF ID   mir-562
#=GF DE   microRNA mir-562
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   68.00
#=GF TC   68.00
#=GF NC   67.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.87 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000512;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18945293
#=GF RT   Annotation of 390 bovine miRNA genes by sequence similarity with other
#=GF RT   species.
#=GF RA   Strozzi F, Mazza R, Malinverni R, Williams JL
#=GF RL   Anim Genet. 2009;40:125.
#=GF WK   Mir-562_microRNA_precursor_family
#=GF SQ   14


AANU01247092.1/5986-6080     AGUGAAAUUGCUGGGUCAUAUGGU---CAG-------UCU-A-C-UUUCAGAGUAAUUGUGAAAGUAUUUUUCAAAGUAGCUGUA-CCA-U-UUG-CAUUCCCUGUGGCAAU
AAQQ01366971.1/167-263       AGUGGAAUUAUUGGAUCAUAUGGU---AAC-------UCU-AGC-UUUUAGAGAAAUUACCAGACUAUUUUCAAAAGUGGCUGUA-CCA-UUUUG-AAAUUCCACCAGCAAU
ABDC01056296.1/123-28        AGCGGAAUUGCUGGAUUGUAUGGU---AAA-------UUU-AAC-UUUUUAAGAAACUACCAAACUACUUUCUAAAGUGGCUGUA-CCA-U-UUA-CAUUUCUACCAGCAAU
AAFC03007787.1/22317-22219   AGUGAAAUUGCUGGUUCAAAUGGUAAACUG-------UUUAA-C-UUUUUGAGGAACUGCCAGACUGUUUUCAAAAGUGACUGCA-CCA-U-UUG-CAUUACCACUAGUAGU
AADB02007034.1/32865-32763   AAUGCAAUUGCUGGGUGAUAUGGU---GAGUCCAUUUUUA-G-U-UUUUAAAGGAAUUGCCAAACUAUUUUCCAGAACAACUGUA-CCA-U-UUUGCAUCUCCACUGGCAAU
AALT01290003.1/153-246       AGUGAUAUUGCUGGGUCA-AAUGG---GAG-------CUA-G-U-UUUUUGAGAAAUAUCCAUAUUUUUUUUCAAAAAGGCUGUC-CAU-U-UUA-CAUUACCACCAGCAGU
AAWR02012610.1/25155-25060   AAUGCAAUUGCUGGGUUGUAUGGU---AAG-------UCC-A-U-UUUGAAGGGAACUACAAAACUAUUUUCCAGAGUGGCUGUA-CCA-UUUUA-CAUUCCCACCAGCAAU
AAGV020907890.1/392-297      AGUGGAAUAGCUGGGUCAUAUGGU---AAC-------UUU-A-A-AUUUUGAGUAACUGCCAAAAUGUUUCCCAAUGUGGCUGUA-CCA-UUUUA-UAUUCCCACUGGCAAU
AAKN02020707.1/24919-24824   AGUGAAAUUCCUGGGUAAUAAUGG---UAG-------UUA-A-C-UUUUUGAGGAACUUCCAAACUGUUUUCCAAAGUGGCUGUUGCAU-U-CUA-UAAUCCCACCAGUAAU
AAPE02002811.1/16357-16255   AGUAGAAUUGCUGGGCCACAUGGU---AAGUCUAUGUUUU-A-C-UUUGUGAGGAAUUGGCAGAUUCCUUACCAAAGUGACUGUA-CCA-U-UUUCCCCUCCCACUAGCAAU
AAGW02070197.1/117139-117237 AGUACAAUUGCUAGGUCACAUGUUAA-CUG-------UUUAA-C-UUUAUAAGAAAUUGUCAAACUCUUUUUCAAAGUGACUGCA-CCAAU-UUG-CAUCCCUAUCAGCAAU
AF312225.1/187734-187828     AGUGAAAUUGCUAGGUCAUAUGGU---CAG-------UCU-A-C-UUUUAGAGUAAUUGUGAAACUGUUUUUCAAAGUAGCUGUA-CCA-U-UUG-CACUCCCUGUGGCAAU
AACN010734815.1/162-257      AGUGCAGUUGCUGGGUCAUAUGGU---AAG-------GCC-A-U-UUUUGAAAUAACUUCCAAAGUAUUUUCCAGAGUGGUUGUA-CCA-UUUUA-CAUUCUUAUUAGCAAU
AAGU03018309.1/72381-72285   AGUGGAAUUGCUGGGUCAUAUGUU---AAG-------UGA-A-UAUUUAUAAGAAACUGUCAAAUUGUUUUCCAAAGUGCCUGUA-CCA-UUUUG-CAUUCCCAUAAGCAAU
#=GC SS_cons                 ::::::<<<<<<<<<-<<-<<<<<...<<<.......-<<.<.<.<<<-<<<<<<-<<____>>->>>>>>-->>>>>>>>>>->.>>>.>.->>.---->>>--->>>>>>
#=GC RF                      AGUGaAAuugCuGGgUcauAuGGu...cag.......Ucc.a.c.uuUugaAgcAAuugccAaacUguUucccAaaguggcugUa.CCa.U.Uug.cAuUcCCAcuaGcaaU
//
# STOCKHOLM 1.0

#=GF AC   RF00999
#=GF ID   mir-924
#=GF DE   microRNA mir-924
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   65.40
#=GF NC   57.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000513;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17573847
#=GF RT   Analysis of gene expression in normal and neoplastic human testis: new
#=GF RT   roles of RNA.
#=GF RA   Novotny GW, Nielsen JE, Sonne SB, Skakkebaek NE, Rajpert-De Meyts E,
#=GF RA   Leffers H
#=GF RL   Int J Androl. 2007; [Epub ahead of print]
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   4


AANU01220613.1/9696-9748     AAUAGAGUCUUGUGUUGUCUUGCUUAAAGGCCAUCCAACCUAGAGUCUAUACC
ABDC01308946.1/589-641       AAAAGACACUUGUGAUGUCUUGCUUAAAGGCCAUUCAAUCCAGACCCUGCACC
AADB02009236.1/102624-102676 AAUAGAGACCUGUGAUGUUUUGCUUAAAGGUCAUCCAAUCUGGGCCCUGCACC
AC099845.2/38615-38667       AAUAGAGUCUUGUGAUGUCUUGCUUAAGGGCCAUCCAACCUAGAGUCUACAAC
#=GC SS_cons                 ::<<<--<<<-<-<-<<--<-<<<____>>>->-->>->>->>>-->>>::::
#=GC RF                      AAuAGAGuCuUGUGAUGUCUUGCUUAAAGGCCAUCCAACCUaGaguCUaCACC
//
# STOCKHOLM 1.0

#=GF AC   RF01000
#=GF ID   mir-580
#=GF DE   microRNA mir-580
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   85.00
#=GF TC   89.00
#=GF NC   80.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000515;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-580_microRNA_precursor_family
#=GF SQ   2


AANU01264423.1/57736-57640   AUAAAAUUUCCAGUUGGAACCUAAUGAUUCAUCAGACUCAGAUAUUUAAGUUAACAGUAUUUGAGUCUGAUGAAUCAUUAGGUUCCAGUCAGAAAUU
AADB02008662.1/290777-290681 AUAAAAUUUCCAAUUGGAACCUAAUGAUUCAUCAGACUCAGAUAUUUAAGUUAACAGUAUUUGAGAAUGAUGAAUCAUUAGGUUCCGGUCAGAAAUU
#=GC SS_cons                 ::::<<<<<<--<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<_________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-->>>>>>
#=GC RF                      AUAAaauuuccAgccGGaaccuaauGauucaucaggcucagauacuUAAGUUAAcaguaucugagccugaugaauCauuagguuCCggccAgaaauu
//
# STOCKHOLM 1.0

#=GF AC   RF01001
#=GF ID   mir-609
#=GF DE   microRNA mir-609
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   85.00
#=GF TC   89.00
#=GF NC   79.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000516;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   2


AC196383.7/152636-152729 UGCUCUGCUUUUCCUAGGGUGUUGCUCUCAUCUCUGGUCUAUAAUGGGGUAAAU-GUAGAGAUGAGGGCAACAGCCUAGGAACAGCAGAGGAACC
AL139341.9/49625-49531   UGCUCGGCUGUUCCUAGGGUGUUUCUCUCAUCUCUGGUCUAUAAUGGGUUAAAUAGUAGAGAUGAGGGCAACACCCUAGGAACAGCAGAGGAACC
#=GC SS_cons             ::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<____________________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>:::::
#=GC RF                  UGCuCuGCuguuCCuaGGguGuugCcCuCauCuCugGUcUAUAAUGGGuUAAAUAGcaGaGauGaGgGcaaCacCCuaGGaacaGCaGaGGAAcc
//
# STOCKHOLM 1.0

#=GF AC   RF01002
#=GF ID   mir-936
#=GF DE   microRNA mir-936
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   58.30
#=GF NC   50.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000517;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   4


AANU01193828.1/9097-9000     UCAAGGACACUGGGACAGGAGAGGGAGG-AAUCGCAGAAAUCACUC-CAGGAGCAACUGAGAGACCUUGCUUCUACUUUACCAGGUCCUGCUGGCCCAGA
AAWR02007614.1/358786-358882 GAGAGGCUGUUGG-ACAGUGGAGGGAGGGAGUCCCAGGG-CAGCUCCCAGAGGCC-CUGAGACACUGUGGUUCUGAUUUCCUAGGACCCGCUGGCCCAGA
U76590.1/184-281             UCAAGGCCACUGGGACAGUAGAGGGAGG-AAUCGCAGAAAUCACUC-CAGGAGCAACUGAGAGACCUUGCUUCUACUUUACCAGGUCCUGCUGGCCCAGA
AAQR03047049.1/25293-25390   UUGAAGCUGCUGGGGCAGGAGAGGGAGG-AGGCACAGAAGUAGGUC-CAGGAGCCACUGAUGGACUUUGCUUCUGCUUUACCAGGUCCUGCAGGCCCUGA
#=GC SS_cons                 ::::<<<<<--<<<<<<<<<<<<<<<<<.--<<-<<<---<<-<__.__>>>---->>>->>-->>>>->>>>>>>>------->>>>>-->>>>>::::
#=GC RF                      uuaAGGccacUgGGgCagcaGagggagG.AaucaCaGaaaccacUC.CAgggGCaACuGAgagACcuuGcuuCugcuUUaCcAGGcCCcGCuggCCCaGA
//
# STOCKHOLM 1.0

#=GF AC   RF01003
#=GF ID   mir-563
#=GF DE   microRNA mir-563
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   49.50
#=GF NC   42.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000519;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   7


AANU01196930.1/13971-14049     AGCAAAGAAGUGUGUUGCCCUCCAGGAAAUGUGUGUUGCUCUGAUGUAAUUAGGCUGACAUACAUUUCCCUG--GUAGCCA
AADB02003081.1/3311081-3311159 AGCAAAGAAGUGUGUUGCCCUCUAGGAAAUGUGUGUUGCUCUGAUGUAAUUAGGUUGACAUACGUUUCCCUG--GUAGCCA
AACN010216273.1/3-81           AGCAAAGAGGUAUGUUGCCCUCUAGGAAAUGUAUGUCACACUGGAGUAAUUAGACUGACAUGCAUUUCCCUG--GUGGCAA
AAFC03065393.1/93779-93701     AGCAAAGAGGUAUGUCGCCCUGUAGGAACUGUAUGUCACUUUAGGGUGAUUAGGCUGACAUGCAUUUCCCUG--AUGGAAA
AAQQ01168018.1/4796-4718       AGCAAAGAUGUAUGUUGCCCUCCAGGAAAUGUAAGGUGCUCAGAUGUAAUUAGGCUGACCUGUAUUUUCUUG--GUAAACC
AANN01468185.1/1521-1601       AACAAAGAGGUAUAUUGCCCUUCAGGAAAUGUGUGUCACUUAGGAAUAAUUAGGCUGACAUGUGUUUUCUUGAUGCAAAUG
AAYZ01500923.1/2406-2483       AGCAAAGGGGUUAUUUCCCCUAAGAAAAAUG-GUGUUGCUCUGGCGUAUUUUGGCUGACAUGCGUUUCCCUG--GUGGCAG
#=GC SS_cons                   ::::::::::<<-<<<<<<-----<<<<<<<<<<<<<<-<<<<<<___>>>>>>->>>>>>>>>>>>>>-->..>>>>>>>
#=GC RF                        AGCAAAGAgGugUguugCCCUcuAGgAAAuGuauGucaCucugguGUAauuaggCugaCaugCaUUUcCcUG..Gcagcca
//
# STOCKHOLM 1.0

#=GF AC   RF01004
#=GF ID   mir-557
#=GF DE   microRNA mir-557
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   72.40
#=GF NC   62.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000520;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   2


AADB02000990.1/319523-319593 AAAUUUGGAGGCCUGGGGCCCUCCCUGCUGCUGGAGAAGUGUUUGCACGGGUGGGCCUUGUCUUUGAAAGG
AANU01240052.1/14687-14757   AAAUUUGGAGGCCUGGGGCCCUCCCUGCUGCUGGACAAGUGUCUGCAUGGGUGAGCCUUAUCUUUGAAAGG
#=GC SS_cons                 :::<<--<<<<<--<<<<<<<-<<<<<<-<<<_____>>>---->>>->>>->>>>>>>>>>>>-->>:::
#=GC RF                      AAAUUUGgaGgcCUggGGCcCUCCCUGCUgCUGGAgAAGuGUuUGCAuGGGUGgGCCuuguCuuUGAAAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01005
#=GF ID   MIR530
#=GF DE   microRNA MIR530
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   85.00
#=GF TC   87.60
#=GF NC   84.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000521;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18363789
#=GF RT   Stress-responsive microRNAs in Populus.
#=GF RA   Lu S, Sun YH, Chiang VL
#=GF RL   Plant J. 2008;55:131-151.
#=GF WK   MicroRNA
#=GF SQ   3


AARH01010693.1/61395-61566 GCCAAUAUGUUGCCUUUAUCUGCAUUUGCACCUGCAUCUUUUGCGUUUG----UUUUGUUUUUGA-----CUCCACAAACAAAAUCAAGUUCUGUCGAUACAGUAUGUGGGACAAUUAGAUAUGGAAACUAAUAAGCUUAGUUGAGGUGCAGGUGCAAGUGCAGGUGAAUGCCAUUUUGGU
AARH01003925.1/6653-6796   GCCAACAUGUUGCCUUUAUCUGCAUUUGCACCUGCACCUUACUUGUUUCUUUCUUUUGUUUUUGA-----CUCCAAAACCAAAAGUAAGUU----------------UGAAACAU--------UAAAAC----AAGCUU----GAGGUGCAGGUGCAGGUGCAGGUGAAUGCCAUGUUGGU
AASG02002502.1/29848-29672 GCCAAUAUGUUGCCUUUAUCUGCAUUUGCACCUGCACCUUAAGUUUCUUUGUUUCUUCUUCUUCUUUUUUCUUUUUUAAGAAGUCUACUUCUUCUAAAUUAUGGGUUUUCAAUAUAUAGAGGAUUGAAACAAGCAAAUA----UAGGUGCAGGUGUGAGUGCAGGUGAAUGCCAUUUUGGU
#=GC SS_cons               <<<<<<<<<--<<-<<<<<<<<<<<<<<<<<<<<<<<<<--------------<<<<<<<<<<<_.....___>>>>>>>>>>>-------------------------------------------------------....->>>>>>>>>>>>>>>>>>>>>>>>>->>>>>>>>>>>
#=GC RF                    gCCAAcAUGUUGCCUUuAuCUGCAuuuGCACCUGCAcCUUaugugUuUuUuUuucUUguUuuuga.....CUccaaaAacAAgauuAagUuuUcUaaAUuauGuaUuUgaaAcAuaUAGAuaauuaAAcuAAuaAgcUu....gAGgUGCAGGUGCaagUGCAGgUgAAUGCCAUgUUGGu
//
# STOCKHOLM 1.0

#=GF AC   RF01006
#=GF ID   mir-601
#=GF DE   microRNA mir-601
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   101.90
#=GF NC   57.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000522;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome.
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [4]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome.
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [5]
#=GF RM   19889580
#=GF RT   Profiling of molecular pathways regulated by microRNA 601.
#=GF RA   Ohdaira H, Nakagawa H, Yoshida K
#=GF RL   Comput Biol Chem. 2009;33:429-433.
#=GF WK   Mir-601_microRNA_precursor_family
#=GF SQ   3


AANU01127169.1/9531-9609   UGCAUGAGUUCAUCUUGGUCUAGGAUUGUUGGAGGAGUCAGAAAAAUUACCCCAGGGAUCCUGAAGUCAUUGGGGUGGA
AL445489.10/45367-45289    UGCAUGAGUUCGUCUUGGUCUAGGAUUGUUGGAGGAGUCAGAAAAACUACCCCAGGGAUCCUGAAGUCCUUUGGGUGGA
AACZ03069357.1/63028-63106 UGCAUGAGUUCAUCUUGGUCUAGGAUUGUUGGAGGAGUCAGAAAAACUACCCCAGGGAUCCUGAAGUCCUUUGGGUGGA
#=GC SS_cons               :::::::::<<<<<<------<<<<<<-<<<<-<<<<_________>>->>>>>>->>>>>>---------->>>>>>:
#=GC RF                    UGCAUGAGUuCauCuUGGUCUaGGauuGuuGGAGGaGUCAGAAAAACuACCCCagGgauCCuGAAGUCcUUugGguGgA
//
# STOCKHOLM 1.0

#=GF AC   RF01007
#=GF ID   mir-624
#=GF DE   microRNA mir-624
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   86.40
#=GF NC   67.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000523;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-624_microRNA_precursor_family
#=GF SQ   2


AANU01225849.1/16803-16900 AAUGCUGUUUCAAGGUAGUACCAGUAUCUUGUGUUCAGUGGAACCAAGGUAAACACAAGAUACUGGUAUUACCUUGAGAUAGCAUUAACACCUAAGUG
AL121808.4/109696-109792   AAUGCUGUUUCAAGGUAGUACCAGUACCUUGUGUUCAGUGGAACCAAGGUAAACACAAGGUAUUGGUAUUACCUUGAGAUAGCAUUA-CACCUAAGUG
#=GC SS_cons               <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<--<<____>>-->-->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>::::::::::::
#=GC RF                    aauGcugucucaaGGuaguaccaguaccuuGuGuucAGuGGAAcCaAGgUAaaCaCaagguacugguacuaCCuugagacagCauuAacAccUAAGUG
//
# STOCKHOLM 1.0

#=GF AC   RF01008
#=GF ID   mir-636
#=GF DE   microRNA mir-636
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   56.70
#=GF NC   54.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000524;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-636_microRNA_precursor_family
#=GF SQ   5


AAPY01605159.1/3524-3428 UGGCGGCCGGGGC----GGGAGCACGCGGGCGGGGCCGGCCCGGCUGCCUGGCUUAACCCUGACGUGCC---GCUCGUCCC-GCCUGCAGCCCUAGGCGGCGUCG
AANN01800487.1/2280-2183 UGGCGGCCUGGGCGGGCGGGAGCACGCGGGCGGGG--CGCGGCCCGACGCCGGCACCCUGACGU-UCGGCUCGC---UCCC-GCCCGCAGCCCCAGGCGGCGUCG
AAFC03064261.1/3392-3478 UGGCGGCCUGGGCGGGCGGGAGCACGCGGGCGGGGCCGCCGA--------ACCCUGACGCGC----------CGCUGUCCCUGUCCGCAGCCCUAGGCGGCGUCG
AF015189.1/238-140       UGGCGGCCUGGGC----GGGAGCGCGCGGGCGGGGCCGGCCCCGCUGCCUGGAAUUAACCCCGC-UGUGCUUGCUCGUCCC-GCCCGCAGCCCUAGGCGGCGUCG
AC200524.3/68408-68310   UGGCGGCCUGGGC----GGGAGCGCGCGGGCGGGGCCGGCCCCGCUGCCUGGAAUUAACCCCGC-UGUGCUUGCUCGUCCC-GCCUGCAGCCCUAGGCGGCGUCG
#=GC SS_cons             ::<<-<<<<<<<<....--------<<<<<<<<<<<-<<<--<<<-<<--<<______>>-->>.->>>--->>>->>>>>.>>>>>>->>>>->>>>->>::::
#=GC RF                  UGGCGGCCuGGGC....GGGAGCaCGCgGGCGGGgccggccacgcugccuggaauuacccucgc.UgcgcUugcccguCCC.GCCcGCAGCCCuaGGCGGCGUCG
//
# STOCKHOLM 1.0

#=GF AC   RF01009
#=GF ID   mir-M7
#=GF DE   microRNA mir-M7
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   73.70
#=GF NC   59.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000526;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16912324
#=GF RT   Marek's disease virus encodes MicroRNAs that map to meq and the
#=GF RT   latency-associated transcript.
#=GF RA   Burnside J, Bernberg E, Anderson A, Lu C, Meyers BC, Green PJ, Jain N,
#=GF RA   Isaacs G, Morgan RW
#=GF RL   J Virol. 2006;80:8778-8786.
#=GF RN   [2]
#=GF RM   18430245
#=GF RT   Deep sequencing of chicken microRNAs.
#=GF RA   Burnside J, Ouyang M, Anderson A, Bernberg E, Lu C, Meyers BC, Green PJ,
#=GF RA   Markis M, Isaacs G, Huang E, Morgan RW
#=GF RL   BMC Genomics. 2008;9:185.
#=GF RN   [3]
#=GF RM   18256158
#=GF RT   MicroRNA profile of Marek's disease virus-transformed T-cell line MSB-1:
#=GF RT   predominance of virus-encoded microRNAs.
#=GF RA   Yao Y, Zhao Y, Xu H, Smith LP, Lawrie CH, Watson M, Nair V
#=GF RL   J Virol. 2008;82:4007-4015.
#=GF RN   [4]
#=GF RM   18842708
#=GF RT   Sequence conservation and differential expression of Marek's disease virus
#=GF RT   microRNAs.
#=GF RA   Morgan R, Anderson A, Bernberg E, Kamboj S, Huang E, Lagasse G, Isaacs G,
#=GF RA   Parcells M, Meyers BC, Green PJ, Burnside J
#=GF RL   J Virol. 2008;82:12213-12220.
#=GF WK   Mir-M7_microRNA_precursor_family
#=GF SQ   2


AF147806.2/140284-140356 UGGAUGG----CGUUGUCUCGUAGAGGUCCAGAUCUCUCCUGUUGGCAACUCGAAAUCUCUACGAGAUAACAGUUUG
AF147806.2/140161-140233 ----GGAGAACUGUUAUCUCGGGGAGAUCCCGAUCUCUCCUACCAGCAACUCGAGAUCUCUACGAGAUUACAGUUUU
#=GC SS_cons             :::::::::::<<<<<<<<<<<<<<<<<<-<<<---<<______>>---->>>->>>>>>>>>>>>>>>>>>:::::
#=GC RF                  UGGAuGaGAACuGUuaUCUCGuaGAGaUcCcGAUCUCuCCUauuaGCAACUCgAgAuCUCuaCGAGAuaACaGUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF01010
#=GF ID   mir-632
#=GF DE   microRNA mir-632
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   62.50
#=GF NC   46.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000527;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-632_microRNA_precursor_family
#=GF SQ   16


AANU01121461.1/7744-7651   CGCCUCCUGCCGC-AGUGCCUGACGGGAGGCG-GA---GCGGCGAACGAGGCCGUCGGCCAUUUUGUGUCUGCUUCCUGUGGGAC-GCGGUCGUAGCCGU
ABDC01629241.1/373-466     CGCCUCCCGCCGC-AGUGGCUGACGGGAUGCG-GA---GCAGCAAACGAGGCCGUCGGCCAUUUUGUGUCUGUUUCCUGUGGGAC-GCGGUGGUAGCCGU
AAFC03094946.1/3397-3490   CUCCUCCGGCCGC-AGAGCCUGACGGGAGACA-GA---GCAGCGAGCGAAGGCGUCGGCCAUUUUGUGGAUGUUUCCUGUGGGAC-GCGGUGGUGGCGGU
AANN01619229.1/133-226     CGCCCCUGGUCGC-GGUGCCUGCCGGGAGGUA-GA---GCGCCGAACGGGAGCGUCGGCCAUUUUGUGCCUGUUUCCUGUGGGAC-GCGGCGGUGGCAGU
AALT01115250.1/29-124      CGCCCCUGGCCGCAGUUGGCCGACGGGAGGCA-GA---GCGCCGAGCGAGGGUGUCGGCUUUUUUGUGUCUGUUUCCUGUGGGGGGGCGGUGGUGGCCGU
AAFR03044718.1/61849-61755 CGCCCGUGGCCGC-GUUGCCUGACGGGAAGCG-GAGGGGCGAGGAGCGAGGCGUUCGGCCAUUUUGUGUCU--UUCCUGUGGGAC-GCGGCGGCGUUUGU
AAYZ01474155.1/733-640     CCACU-CGGUCGC-GGGGACUGACGGGAAGCGCGA---GCCGCGAACGAGGGUGUCGGCCAUUUUGUGUCUGUUUCCUGAGGGAC-GCGGUGGUAGCCGU
AAGV020133793.1/2039-1946  CGCCUCUGGCCGC-AGUGCCUGACGGGAGGCG-GA---GAGGCGAAAGAGACUGUCCGCCAUUUUGUGUCUGUUUCCUGUGGGAC-GCGGUCAUAACCGU
AAWR02013117.1/4030-3937   CGCCUCCAGCCGC-AGUGGCUGACGGGAGGCG-GA---GCAGCGAACGAGGGCGUCGGCCAUUUUGUGCCUGUUUCCUGUGGGAC-GCGGCGGUGGCGGU
AL591146.21/50773-50865    CAGCUCUCACCGC-GGUGGCUGAUGGGAGGUG-GA---G-AUAGAACGAGGGUGUCGGCCAUUUUGUGUCUGUUUCCUGCGGGAC-GCGCUGGUGGCGGU
AC005899.1/59750-59843     CGCCUCCUACCGC-AGUGCUUGACGGGAGGCG-GA---GCGGGGAACGAGGCCGUCGGCCAUUUUGUGUCUGCUUCCUGUGGGAC-GUGGUGGUAGCCGU
AABR05021132.1/7681-7773   CAGCUCUCGCCGC-GGUGGCUGACGGGAGGUG-GA---G-AUAGAACGAGGGUGUCGGCCAUUUUGUGUCUGUUUCCUGCCGGAC-GUGGUGGUGGCGGU
AAQR03133166.1/747-840     CGCCCCCCGCCCC-AGUGCCUGACGGGAGUCA-GA---GCAGCGAACGAGGCCGUCGGCCAUUUUGUGUCUGUUUCCUGUGGGAC-GCGGUGGUGUCCGU
AAGU03054505.1/2398-2491   CGCCCCCGGCCGC-AGUGCAUGAUGGGAAGUG-GA---GCGGCUAACGAGGCCGUCGGCCAUUUUGUGUCUGUUUCCUGUGGGAC-GUGGUGGUAGCCGU
AAGW02049927.1/9157-9250   CGCCUCCCGCCGC-AGUGCCCGACGGGAGGCG-GA---GCCGCGAACGAGGGUGUCGGCCAUUUUGUGUCUGUUUCCUGUGGGAC-GCGGUGGGAGCCGU
AACN010804236.1/315-407    CGCCUCCGGCCGC-AGUGCCUGACGGGAG-CA-GA---GCGGCGAACGAGGGCGUCGGCCAUUUUGUGUCUGUUUCCUGUGGGAC-GCGGUCGUGGCCGU
#=GC SS_cons               <<-<<-<-<<<<<.-<<-<<--<<<<<<<<<<.<<...-<<--------<<<<___>>>>------>>>>>>>>>>>>>>>>->>.>>>>>->->>->>:
#=GC RF                    CgcccccggcCGC.aguGcCUGaCgGGaggcg.Ga...GCggcGAACGAGGccGUCggCCAUUUUGcGuCugccuCCuGuGgGac.GCGgcggUggCcGU
//
# STOCKHOLM 1.0

#=GF AC   RF01011
#=GF ID   mir-605
#=GF DE   microRNA mir-605
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   85.00
#=GF TC   90.00
#=GF NC   76.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000528;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-605_microRNA_precursor_family
#=GF SQ   2


AANU01015199.1/6910-6992     -ACCCUAGCUUGGUUCUAAAUCCCACGGUGCCUUCUCCUUGGGAAAAACAGAGAAGGCACUGUGGGAUUUAGAACCAAGUUAGG
AADB02013075.1/328353-328435 G-CCCUAGCUUGGUUCUAAAUCCCAUGGUGCCUUCUCCUUGGGAAAAACAGAGAAGGCACUAUGAGAUUUAGAAUCAAGUUAGG
#=GC SS_cons                 :::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<--<<_______>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                      gACCCuagCuuGguuCuaaauCcCacgGuGCCuuCuCCUuGGGAAAAACaGaGaaGGCaCcguGgGauuuaGaacCaaGcuaGG
//
# STOCKHOLM 1.0

#=GF AC   RF01012
#=GF ID   mir-628
#=GF DE   microRNA mir-628
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   69.50
#=GF NC   50.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000529;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   9


AANU01108781.1/6856-6762  AUAGCUGUUGUGUCACUUCCUCAUGCUGAC-AUAUUUACUAGAGGGUAAAAUUAAUAACCUUCUAGUAAGAGUG-GCAGUCGAAGGG--AAGGACUCAU
AADB02222703.1/291-386    AUAGCUGUUGGGGCACUUCCUCAUGCUGAC-AUAUUUACUAGAGGGUGAAAUUAAUAACCCUUUAUUAAGAGUGGGCAGCCAAAGGG--AAGGCUUAAU
AALT01279890.1/1250-1156  AUAGCUGUUGUAUUUCUUUCUUAUGCCGACAAUAUUUACUAGA-GGUGGAAUGAAUAACCAUCUAGUAAGAGUG-GCAGUCCAGGGG--AAGGACUCUU
AANN01484297.1/1287-1379  GUUGUGUGUGUGUUGCAUCCUCAUGCUGAC-AUAUUAGUGAGAGGAC--AAUCUGUAGCCCCCUAGUAAGAGUG-GCGGUCAAAGGG--AAGGGCUCAU
AAYZ01314872.1/976-882    ACAACUAUUGUAACACUUUCUCUUGCUGCA-GUGUUUCCUAGAGGGUAAAAUUCAUAAUCUUAUAGUAGGAGUG-GAGGUUGAAGAC--AAGGGCCCAU
AC158997.2/147317-147409  AGAGCUGUUGUGUCACUUCCUCAGGCAGAC-AUAUUUACUAGAGGGU--GAUCCACAACCUUCCAGUAAGAGAG-GCAGCAGAAGGG--AGGGGCUCAC
AC018926.10/145080-144986 AUAGCUGUUGUGUCACUUCCUCAUGCUGAC-AUAUUUACUAGAGGGUAAAAUUAAUAACCUUCUAGUAAGAGUG-GCAGUCGAAGGG--AAGGGCUCAU
AAHX01055315.1/6564-6660  AGAGCUGUUGUGUCGCUUCCUCAUGCUGAC-AUAUUUACGAGAGGGUGCAAUUCAUAACCUUCUGGUAAGAGUG-GCAGUUGAGGGGUUGGGGAUUUAG
AAGU03071490.1/4013-3919  AAAGCUGUUGUGUCACUUCCUCAUGCUGAC-AUGUUUACUAGAGGGUAAAACUGAUAACCGUCUAGUAAGAGUG-GCAGUCGAAGGG--AAGGGCUCAU
#=GC SS_cons              ::::::::<<-<<<-<<<<<<--<<<<<-<.<<-<<<<<<<<<<<<<__________>>>>>>>>>>>>>->>>.->>>->>-->>>..>>>>>>->>:
#=GC RF                   AuAGCUgUuGUgccaCuucCuCAcgCuGAC.auAuuuacuagagGGuaaAAUuaAUAaCCcucuaguaagAguG.GCaGUcgAAgGg..aaGggcUCau
//
# STOCKHOLM 1.0

#=GF AC   RF01013
#=GF ID   mir-577
#=GF DE   microRNA mir-577
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   76.70
#=GF NC   64.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000530;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   2


AANU01270381.1/2571-2666 UGGGGGAAUGAAGAGUAGAUAAAAUAUUGGUACCUGAUGAGUGUGAGGCCAGGUUUCAAUACUUUAUCUGCUCUUCAUUUUCCCAUAUCUACUUAC
AC122938.3/47747-47842   UGGGGGAGUGAAGAGUAGAUAAAAUAUUGGUACCUGAUGAAUCUGAGGCCAGGUUUCAAUACUUUAUCUGCUCUUCAUUUCCCCAUAUCUACUUAC
#=GC SS_cons             <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<_____________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>:::::::::::
#=GC RF                  uGGGggaguGaaGaGcaGauaaaguauuGgcaCCuGAUGAaUgUGAGGcCaGGugcCaauacuuuauCugCuCuuCacuccCCCaUAUcUAcUUAc
//
# STOCKHOLM 1.0

#=GF AC   RF01014
#=GF ID   mir-1306
#=GF DE   microRNA mir-1306
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   79.90
#=GF NC   56.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000531;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells.
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [2]
#=GF RM   18849523
#=GF RT   In-depth characterization of the microRNA transcriptome in a leukemia
#=GF RT   progression model.
#=GF RA   Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M,
#=GF RA   Yung E, Piper J, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst
#=GF RA   M, Hansen CL, Marra MA, Humphries RK
#=GF RL   Genome Res. 2008;18:1787-1797.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   MicroRNA
#=GF SQ   8


BC070985.1/229-302           GAGCCUCCACCACCUCCCCUGCAAACGUCCAGUGACGCAGAGGUAAUGGACGUUGGCUCUGGUGGUGAUGGACA
AAFR03062526.1/78612-78539   GAGCCUCCACCACCUCCCCUGCAAACGUCCAGUGACGCAGACGUAAUGGACGUUGGCUCUGGUGGUGCUGGACA
AAVX01501338.1/278-205       CCGCCUCCACCACCUCCCCUGCAAACGUCCAGUGAGGCCGAGGUUAUGGACGUUGGCUGCGGUGGUGAUGGACU
AANH01001823.1/103357-103430 GCACCUCCACCACCUCCCCUGCAAACGUCCAGUGACGCAGAGGUAAUGGACGUUAGCUCUGGUGGUGAUGGAUA
BX088551.7/56646-56573       GCACCUCCACCACCUCCCCUGCAAACGUCCAGUGACGCAGAGGAAAUGGACGUUAGCUCUGGUGGUGAUGGACA
BC150109.1/107-180           CAGUCUCCACCACCUCCCCUGCAAACGUCCAGUGAUGCAGAGGUAAUGGACGUUGGCUCUGGUGGUGAUGGACA
BC009984.2/450-523           CAGUCUCCACCACCUCCCCUGCAAACGUCCAGUGGUGCAGAGGUAAUGGACGUUGGCUCUGGUGGUGAUGGACA
AAGW02067123.1/18910-18983   AAGUCUCCACCACCUCCGUUGCAAAUGUCCAGUGAUGCAGUGGUAAUGGACAUUGGCUCUGGUAGUGAAGAACA
#=GC SS_cons                 :::<<--<<<<<<<------<<-<<<<<<<<---<<______>>-->>>>>>>>->>--->>>>>>>-->>:::
#=GC RF                      gaGcCUCCACCACCUCCcCUGCAAACGUCCAGUGacGCAGAGguAAUGGACGUUGGCUcUGGUGGUGAUGgACA
//
# STOCKHOLM 1.0

#=GF AC   RF01015
#=GF ID   mir-885
#=GF DE   microRNA mir-885
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   85.00
#=GF TC   86.10
#=GF NC   78.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000532;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414..
#=GF RN   [2]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis.
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF WK   Mir-885_microRNA_precursor_family
#=GF SQ   3


AAPN01033075.1/1325-1251 CUGUGCUCUUUCCACUAGGCCACGCUGCUUCUCAAAGAAUGAGAAGCAGCGUGGCCUAGUGGAAAGAGCACAGGU
AAGV021057099.1/191-264  CCACACUCUCUCCAUUACACUACCCUGCCUCUU-CUCCACGAGAGGCAGCUGGGUGUAGCGGAUAGAGCACGGGU
AC090841.2/112558-112485 CCGCACUCUCUCCAUUACACUACCCUGCCUCUU-CUCCAUGAGAGGCAGCGGGGUGUAGUGGAUAGAGCACGGGU
#=GC SS_cons             <<<--<<<<<<<<<<<<<<<<-<<<<<<<<<<<.______>>>>>>>>>->>>>>>>>>>>>>>>>>>-->>>::
#=GC RF                  CcGcaCUCUuUCCacUAcgCcAccCUGCcUCUc.cuccAugAGAgGCAGCgggGcgUAguGGAaAGAGCACgGGU
//
# STOCKHOLM 1.0

#=GF AC   RF01016
#=GF ID   mir-584
#=GF DE   microRNA mir-584
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   62.00
#=GF TC   62.00
#=GF NC   61.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.59 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000533;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF WK   Mir-584_microRNA_precursor_family
#=GF SQ   16


AANU01185361.1/45786-45882   UAGGGUGACCAGCCAUUAUGGUUUGCCUGGGACUGA-----GG-AAUUUGCUGG----GAUA-UG--------------------------UCA-GUUCC-AGGCCAACCAGGCUG-GUUGGUUUCCCUGAAGCAAC
AAPY01567440.1/5861-5765     UAGGAUGACCAACCAACCUGGUUUGCUUGGGACUGU-----GC-AGGCUCCCAG----GAUA-G---------------------------ACA-GUCCU-AGGUAAACCAGGAUAAGUUGGUUACCCUAGGGCUGG
AC068547.7/82954-82858       UAGGGUGACUAGCCAUCAGGGUUUGCCUGGGACUGU-----CC-UGUGUCCUGGGAAACACU-GA----------------------------A-GUCCC-AGGCAAACCAGGAAG-GUUGGUCAC--UGAAGCCUC
AANG01682402.1/3939-4034     UAGGGCGACCAGUUGUCCCGGUUGGCCUGCGACUGA-----GG-UGUUUUGCCA----ACUA-GG--------------------------ACA-GUCCC-AGGCAAGCCGGAG-A-GUUGGUCACCCUAAAUCUGG
AAFC03076184.1/35990-36088   AGGGAUGACCAACUGUCCUGGUUUGCCUGGGACUGA-----GG-GGUUACUGAG----GACA-CG--------------------------UGAAGUCCCUGGGCAAACUGGAGUG-GUUGGUUCAUUCUAGCUUUU
CT954319.9/106515-106393     UAGGGUCACCAACUGUCCCAGUUUGCCUGAGACUGA-----GG-AAUUUCCUGG----CAUA-CAGAUGUUCCAUACCAGUGCCAGGACAGUUA-GUUCC-AGGCAAACUGGGACA-GUUGGUCACCCAGGUGCCCA
AC123970.3/75714-75835       UAGGAUGACCAACUGUCCUGGUUUGCCUGAAACAGA-----GG-CAUUUCCCAG----GACA-CAGGACUCUUUGAA-AGCUAAAAGCAGGACA-GUUCU-GGGUAAUCCAGAACA-GUUGGUCAUUCUAAUUAAAA
AAHX01054361.1/29631-29525   CAGGUUGAUCAAGUGCCCUGGUUUGCCUGGGGCUGA----GGG-UUUUUCCAGG----GCAG-GGGACU-----------------UUCUUUCA-GUUCU-GGGCAAACCAGGGUG-GUUGGUCACCCUAGUGAUAA
AAGV020769799.1/1706-1607    UAGGGCAACCAGCUGUCCCGGUUUGCCCAGGACUUG-C-ACAG-UUUUUGUAGG----AAAC-CU-------------------------UUUG-GUCCU--GGCAAGCUGGGACA-GCUGGUCACCCUAAAGCCCA
AAWR02024077.1/7850-7748     UAGAGUCACCAACUGUUCAUGUUUGCCUGGGACUGA-----GG-AAUUUCCCAG----GAUG-CAGGA--------------------CUUUCA-GUCUU-AGGCAAACCUGGGUG-GUUGGUAACUCAGAUUCCAA
AC091940.3/3034-2938         UAGGGUGACCAGCCAUUAUGGUUUGCCUGGGACUGA-----GG-AAUUUGCUGG----GAUA-UG--------------------------UCA-GUUCC-AGGCCAACCAGGCUG-GUUGGUCUCCCUGAAGCAAC
AACN011030071.1/202-108      UAGGGUAACCAACUGUCCCAGUUUGCCUGGGGCUCU-----UG-CAGUUCUGGA----A--U-UG--------------------------GAA-GCCCC-UGGCAAACAGAGCUG-GCUGGUCACCCUGGACCACU
AAGW02052704.1/266971-267071 UAAGAGGACGAACUAUCCUGGUUUGCCUGGAACUUU-----AC-UGGUGUUUGC----AUGA-GAAA----------------------UCCCA-GUCCC-CGGCAAUCCAGGAGA-GUUGGUCCUUUUACCACCUC
AAPE02003505.1/78976-78875   UAGGGUGACCAACCACUCCGGUUUGCCUGGGACAGGGAACUUU-CAGUAUUAAA----GCUA-GG--------------------------CCA-GUCCC-AGGCAAACUGGGAGA-GUGGGUCCCCAUAGGUCUAG
AAGU03087302.1/19644-19749   UAGGGGGGCCACCCAUCCCAGUUUGCCUGGGACUGA-----GG-GGUUUCCUGG----GAUG-CUAAUA-----------------CUGGGGCA-AUCCC-AGGCAAACCAGGAUA-GUUGGUCACCCUAUCGAGAG
AAQR03098083.1/1549-1453     UAGGGUGAUCAGCCAUCAGGGUUUGCCUGGAACUGU-----CCUAUGUCCUAGG----ACACUGG--------------------------ACA-GUUCC-AGACAAGCCAGGAAG-GCUGAUCAU--UGAUACCUC
#=GC SS_cons                 <<<<<<<<<<<<<<<---<<<<<<<<<<<<<<<<<<.....-<.-<<<______....>>>-.>-..........................>>>.>>>>>.>>>>>>>>>>--->>.>>>>>>>>>>>>>:::::::
#=GC RF                      uaGGgugACCAgCcgUCCcgGuUUGCCuGGgACuga.....gg.ugucucuugg....gaca.ca..........................uca.GUcCC.aGGCAAaCcgGGacg.GcUGGUcacCCuaaugcuaa
//
# STOCKHOLM 1.0

#=GF AC   RF01018
#=GF ID   mir-569
#=GF DE   microRNA mir-569
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   73.10
#=GF NC   44.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000535;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-569_microRNA_precursor_family
#=GF SQ   13


AANU01299587.1/22836-22741   GGUAUUGUUAGAUUAAUUUUGUGGGACAUUAACAACAGCAUCAGCAGCAACAUCAGCUUUAGUUAAUGAAUCCUGGAAAGUUAAGUGACUUUAUUU
ABDC01040335.1/2625-2530     AGUGUUGUUAGAUUAAUUUUGUGGGACAUUAACAACAGCAUCAGCAGCAACAUCAGCCUUAGUUAAUGAAUCCUGACAAGUUAAGUGACUUUAUUU
AAQQ01653799.1/497-402       AGUAUUGUUAGAUUAAUUCUGUGGGGCAUUAACAAGAGCAUCAGCAGCAACAUCAACUUUAGUUAAUGAAUCCUGGUGAGUUAAGUGACUUUAUUU
AAIY01309527.1/1347-1442     GGUAUUGUUAGAUUCAUUUUGUGGGACAUUAACAACAGCAUCAGCAGCAACAUCGACUUUAGUUAAUGAAUCCCAGCGAGCUAAGUGACUCUAUUU
AAPY01270675.1/874-783       GGCAUUGUUAGAUUAUUUUG-UGGGACAUUAACAACACCAUCAGCAGCAGCAACU---UUAGUUAAUGAAUCUUGGCAAGUUAAGUGACUUUAUUU
AANN01582903.1/10569-10474   AGUAUUGUGCGAUUAAUUUUGCGGGGCAUUAACUAAAGCAUCAGCAGCGGCAUUGACUGUAGUUAAUGAAUCCUGGCGAGUGAAGUAACUCUGUUU
AAGV020084471.1/1533-1438    GGUAUUGUUAGAUUAAUUUUGUGGAACAUUAACAAAAGCAGCAGCAGCAACAUCAACUUUAGUUAAUGAAUCCUAGUGAGUUAAGUGACUUUAUUU
AAKN02051025.1/41128-41033   GGUAUUGUUAGAUUAAUUUUGUGGGACAUUAACACUAGCAUCAGUAGCAAUAUUCACUUGACAUAGUGAAUCCUGCUGAGUUAAGUGACUUUAUUU
AC026315.15/26111-26206      GGUAUUGUUAGAUUAAUUUUGUGGGACAUUAACAACAGCAUCAGAAGCAACAUCAGCUUUAGUUAAUGAAUCCUGGAAAGUUAAGUGACUUUAUUU
AC121268.7/120021-119927     GUUAUUGUUAGAUUAAUUUUGUGGGACAUUAACAACACCAUAGGCAGCAACAUCAACCUUAGCUAAUGAAUCCGGGCUAGUUAAAUGA-UCUAUUU
AAGW02014437.1/168391-168480 AGUACUGCUAGAUUAAUCUUAUGGGACAUUAACAACACCAUCAACAGCAAC----G--UUAGUUAAUGAAUCUUGGUGAGUGAAAUGACUCUCUUA
AAPE02018140.1/149254-149349 GGUAUUGUUAGAUUAAUUUUGUGGAACAUUAACUACAGCAUCAACAGCAACAGCAUCUUUAGUUAAUGAAUACUGGCGAGUUAAGUGACUUUAUUU
AACN010147712.1/871-966      GGUAUUGUUAGAUUAAUUUUGUGGGACAUUAACUACAGCAGCAGCAGCAACAUCAACUUUAGUUAAUGAAUCCUGGCGAGUUAAGUGACUUUAUUU
#=GC SS_cons                 <<<<--<<<<--<<<<<<<<-<<<<<<<<<<<<---<<<________________>>>--->>>>>>>-->>>>>->>>>>>>>->>>>-->>>>:
#=GC RF                      aguaUUGuuaGAuuaauucgGcgGgaCauuaaCaAcaGcAUCAGcAGCAACAucagCuUUAGuuaauGAAucCcggcgaguuaaGugaCUuuauuU
//
# STOCKHOLM 1.0

#=GF AC   RF01019
#=GF ID   mir-922
#=GF DE   microRNA mir-922
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   48.00
#=GF NC   39.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000536;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17573847
#=GF RT   Analysis of gene expression in normal and neoplastic human testis: new
#=GF RT   roles of RNA.
#=GF RA   Novotny GW, Nielsen JE, Sonne SB, Skakkebaek NE, Rajpert-De Meyts E,
#=GF RA   Leffers H
#=GF RL   Int J Androl. 2007;30:316-326.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   12


AANU01297564.1/18238-18318 -GUGGCGUUCUCUC-UCUCCCUGUCCUGGACUGGGGUCAGACCGUGCCCC---GAGGAGAAGCAGCAGAGAAUGAGACUACGUCGU
ABDC01218976.1/123-206     A-UGGAGUUUUCUC-UCUUCUAAUCCUGAAACAGGGUCAGACUCUGCCCUAAUGAGGAGAAGCAGCAGAGAAUGGGACUGCAUCAU
AAYZ01250604.1/2148-2070   AUUGGAGUUUUCUC-UUCCCCAGUCCUAGAAUAGGGUAAGAUC--UCCCC---AAGGAGAAGCAGCAGAGAAUG-GACAUUGUAGG
AANG01598532.1/4255-4333   A-CGGAGUUUUCUC-UCUCA--GUCCUGAAAUAGAGUCAGACUGCACCCU---GAGGAGAAGCAUUAGAGGAUGGGAGUACAUUGU
AAFC03007273.1/63604-63529 G-UGGAGUUUUCUC-UCUCCCAGUCCUGGAACAGGGUCAC-----ACCCU---GAGGAGAAGCAUCAGAGAAUGGGACUGAGUCAU
AAGV020523561.1/2930-3011  -GUAGAGUUUUUUUCUCUCUCAUUCCUGGAAUAGGGUCAGACUGAGCCCU---GAGGAGAAACACCAGAGAAUAGGACUACAUUGU
AAWR02011835.1/10566-10486 A-UGGAAUUUUCUC-UCUCCCCAUCCUGAAAUAGGGUCAAACUGUGCCCU---GAGGAGAAGCAGCAGAGAAUUGGACUACAUCAU
D86979.3/3461-3541         A-UGGCGUUUUCCC-UCUCCCUGUCCUGGACUGGGGUCAGACUGUGCCCC---GAGGAGAAGCAGCAGAGAAUAGGACUACGUCAU
CU468995.15/173245-173166  G-UGGGGUUUUCUG-UCUC-CAAUCCUGGAAUAGGGUCAGAGUGUGCCCU---GAGGAGAAGCAGCAGAGAAUGAGACUGCAUCAC
AAQR03186177.1/3192-3114   A-UGGAAUUUUCUC-UCUCCUAAUCCUGGAACAGGGUCAGACU--ACCCU---GAGGAGAAGCAGCAGAGAAUGGGACUGUAUCAU
AAPE02025206.1/46170-46094 A-UGGAGCUUUCUC-CCUCCCAGUCCUGAAAUAGGGC-AGACCAUGCCCU---GAGGAGAAGCAGCAGAGGACGGGACA---CUGU
AAGW02013764.1/27447-27524 -UUGGAGUUUUCUC--CUCCCAGGCCUGGAAUAGGGUCAGACU--GCCCU---GAGGAGAAGCAGCAGAGACUGGGACUACAUUGU
#=GC SS_cons               :.<<<<<<--<<<<.<<<<-<<<<<<<----<<<<<<________>>>>>...>>>>---->>>>-->>>>-->>>>-->>>>>>:
#=GC RF                    A.uggcguUUUCuc.uCuCcccguCCUGgAAcaGGGcCAGAcUgugCCCu...gAGGAGAAgcggCAGaGaAUggGACUacgucaU
//
# STOCKHOLM 1.0

#=GF AC   RF01020
#=GF ID   mir-572
#=GF DE   microRNA mir-572
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   53.40
#=GF NC   46.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000537;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF WK   Mir-572_microRNA_precursor_family
#=GF SQ   4


AANU01106553.1/9481-9426 UCGGGGCCGCCGCGGACGGAAGGGCGCCUCUGCUUCGUCCGCUC---GGCGGUGGCCCA
AC006230.11/71210-71265  UCGGGGCCGCUGCGGGCGGAAGGGCGCCUGUGCUUCGUCCGCUC---GGCGGUGGCCCA
AC009065.8/9556-9611     UCGGGGCCGCUGCGGACGGAAGGGCGCCUGUGCUUCGUCCGCUC---GGCGGUGGCCCA
AAQR03078035.1/3483-3425 UAGGGGCCGCAGCGGACGGAAGGGCGCCCCCGCUUCGUCCGCUCUGUGGCUACGGCCUA
#=GC SS_cons             :::<<<<<<<<<<<<<<<<<-<<<<<____>>>>>-->>>>>>>...->>>>>>>>>>:
#=GC RF                  UcGGGGCCgCcGCGGgCGGAAGGGCgCCUccGCUUCGUCCGcUC...GGCgGcGGCCCA
//
# STOCKHOLM 1.0

#=GF AC   RF01021
#=GF ID   mir-558
#=GF DE   microRNA mir-558
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   99.90
#=GF NC   69.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000538;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-558_microRNA_precursor_family
#=GF SQ   3


AADA01295085.1/2655-2563   -UGUGUGUGUGUGUGUGUGGUUAUUUUGGUAUAGUAGCUCUAGACUCUAUUAUAGUUUCCUGAGCUGCUGUACCAAAAUACCACAAAUGGGCUG
AANU01293252.1/20582-20675 GUGUGUGUGUGUGUUUGUGUUUAUUUUGGCAUAGUAGCUCUAGACUCUAUUAUAGUUUCCUGAGCUGCUGUACCAAAAUACCACAAACUGCCUG
AL133243.3/127094-127187   GUGUGUGUGUGUGUGUGUGGUUAUUUUGGUAUAGUAGCUCUAGACUCUAUUAUAGUUUCCUGAGCUGCUGUACCAAAAUACCACAAACGGGCUG
#=GC SS_cons               ::::::::<<-<<<-<<<<<<-<<<<<<<<<<<<<<<<<<--<<--<<<___>>>-->>-->>>>>>>>>>>>>>>>>>>>>>>>->>>->>::
#=GC RF                    gUGUGUGUGcGcguguGuGguUauuuuGGuacaGcaGCuCUAGaCUCuaUUAuaGUUuCCUGaGCugCuguaCCaaaauacCaCaAacgGgCUG
//
# STOCKHOLM 1.0

#=GF AC   RF01022
#=GF ID   mir-611
#=GF DE   microRNA mir-611
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   42.80
#=GF NC   36.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000539;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   8


AAPY01121631.1/1482-1548   AAAAUGGUGAGAGGGUUAAGGGGAGUGCCCAGCACCGCC-GUG----AGGACCGCUGGGGACCUGACCCCAC
AANG01067506.1/3627-3557   AAGAUGGUGAGAGGGUUGAGGGGCGUCCCGGACAGGGCU-GUGAUGAGGACCCCCUCGGGGCCCGUCCCACA
AAGV020393512.1/1077-1144  GAAAUGGUGAGAGGUUUGAGGGGAGCUCAGGACCGGGUUGUGG----AGAACCCCUCGAGGCCCGUCCCUCA
AAWR02037690.1/14951-14885 AAAAUGGUGAGAGGGCUGAGGGGAGUUCCCGACAGGGCU-GUG----GGGACCCGUCGGUGCCCGUCCCACG
AC194778.9/2215-2149       AAAAUGGUGAGAGGGUUAAGGGGAGUUCCCGACGGAGAU-GCG----AGGACCCCUCGGGGUCUGACCCACA
AF523117.1/947-881         AAAAUGGUGAGAGCGUUGAGGGGAGUUCCAGACGGAGAU-GCG----AGGACCCCUCGGGGUCUGACCCACA
AAGW02063772.1/20623-20689 AAAAUGGUGAGAGGGAUGAGGGGAGUUCUGAGCAGGGCG-GAG----AGCACGGCUCGGGGUCUGAUUCACA
AAQR03147834.1/21629-21695 AAAAUGGUGAGAACGAUAAGGGGAGUUCUGGACAGAGUU-GCG----AAGACCGCUCGGGGCCUGACCGACC
#=GC SS_cons               :::::<<<-<<-<--<<-<<<<<--<<<<__________.>->....>>-->>>>>->>-->>>->>>::::
#=GC RF                    AAAAUGGuGaGAGGGcUGAGGGGAGuuCcgGACaGgGcU.guG....aggACCCCUCGgGGCCuGaCCCACa
//
# STOCKHOLM 1.0

#=GF AC   RF01023
#=GF ID   mir-940
#=GF DE   microRNA mir-940
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   57.80
#=GF NC   44.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000540;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [2]
#=GF RM   18945293
#=GF RT   Annotation of 390 bovine miRNA genes by sequence similarity with other
#=GF RT   species.
#=GF RA   Strozzi F, Mazza R, Malinverni R, Williams JL
#=GF RL   Anim Genet. 2009;40:125.
#=GF WK   MicroRNA
#=GF SQ   8


AANU01106553.1/13297-13390 GUGGGGUGUGGGCCCGGCCCCAGGAGCGGGGCCUGGGCAGCCCCGUGUGUUGAGGAAGGAAGGCAGGGCCCCCGCUCCCCGGGCCUGACCCCAC
AADB02017038.1/91332-91239 GUGAGGUGUGGGCCCGGCCCCAGGAGCGGGGCCUGGGCAGCCCCGUGUGUUGAGGAAGGAAGGCAGGGCCCCCGCUCCCCGGGCCUGACCCCAC
ABDC01172738.1/2318-2410   GUGGGGUACGGGCCGGGCCCCAGGAGCGGGGCCUGGGCAGCCCCGUGUGUUGAGGAAGGAAGGCAGGGCCCCCGCUCCCCGGGCCCG-CCCCAC
AANG01611018.1/655-562     GUGUGGUGUAGGCCGGGCCCCAGGAGCGGGGCCUGGGCAGCCCUGUGUGUUGAGGAAGGAAGGCAGGGCCCCCGCUCCCCGGGCCCGACCCCGU
AACN011000899.1/397-304    GUGGGGUGCAGGCCGGGCCCCGAGAGCGGGGCCUGGGCAGCCCUGUGUGUUGAGGAAGGAAGGCAGGGCCCCCGCUCCCCGGGCCUGACCCUGU
AAFC03056637.1/2486-2393   GUGGGGUGUGGGCUGGGCCCCAGGAGUGGGGCCUGGGCAACCCUGUGUGUUGAGGAAGGAAGGCUGGGCCCCCGCUCCGCGGGCCUGACCCCAG
AAQQ01317791.1/554-462     UUGGGGUAUGUGUUUGGCGCCAGGAGCAGGGCCUGGGCAGCCCCAUGUGUUGAGGA-GGAAGGCAGGGUCCCUGGUCCCCAGGCCCAACCCCAC
AAWR02040062.1/56457-56364 GUGGGGUGUGGGCCGGGCCCCAGGAGUGGGGCCUGGGCAGCCCCGUGUGUUGAGGAAGGAAGGCAGGGCCCCCGCUCCCUGGGCCCGACCCCAU
#=GC SS_cons               <<<<<<<-<<<<<<<<<-----<<<<<<<<<<<<--<<--<<<<_________>>-->>--->>->>>->>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                    guGgGGugcggGcccGgccccAGGagcGGGGCCcGGGCAgCCCcgUGUGUUGAgGAAGGAAGGCAgGGcCCCCgcuCCcCgggCccgaCCcCac
//
# STOCKHOLM 1.0

#=GF AC   RF01024
#=GF ID   mir-944
#=GF DE   microRNA mir-944
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   82.90
#=GF NC   75.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000541;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   2


AANU01277874.1/26225-26138 GUUCCAGACACAUCUCAUCUGAUAUACAAUAUUUUCUUAAAUUGUAAAAAGAGAAAUUAUUGUAUAUCAGAUGAGAUGUGUCUGGGGU
AC063939.15/50344-50431    GUUCCAGACACAUCUCAUCUGAUAUACAAUAUUUUCUUAAAUUGUAUAAAGAGAAAUUAUUGUACAUCGGAUGAGCUGUGUCUGGGAU
#=GC SS_cons               :<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<____________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>:
#=GC RF                    GccCCaGaCaCauCuCauCcGauguaCaauacuuuCucAAAUUGUAaAAAgaGaaaguauuGuacauCgGauGaGauGuGuCuGGggU
//
# STOCKHOLM 1.0

#=GF AC   RF01025
#=GF ID   mir-934
#=GF DE   microRNA mir-934
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   80.30
#=GF NC   73.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000542;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   2


AANU01115620.1/11777-11859 AGGAAUAAGGCUUCUGUCUACUACUGGAGACACUGAUAGUGUAAAACCCAGAGUCUUCGGUAAUGGACGGGAGCCUUAUUUCU
Z97632.3/23636-23554       AGAAAUAAGGCUUCUGUCUACUACUGGAGACACUGGUAGUAUAAAACCCAGAGUCUCCAGUAAUGGACGGGAGCCUUAUUUCU
#=GC SS_cons               <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<___________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                    aGgaauaaGGCucCcGuCcacuaCcGgaGaCgCuGgUAGUaUAAAACcCaGcGuCucCgGuagugGaCgGgaGCCuuauucCu
//
# STOCKHOLM 1.0

#=GF AC   RF01026
#=GF ID   MIR828
#=GF DE   microRNA MIR828
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   51.30
#=GF NC   49.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.21 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000544;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17182867
#=GF RT   A diverse and evolutionarily fluid set of microRNAs in Arabidopsis
#=GF RT   thaliana.
#=GF RA   Rajagopalan R, Vaucheret H, Trejo J, Bartel DP
#=GF RL   Genes Dev. 2006;20:3407-3425.
#=GF RN   [2]
#=GF RM   20407027
#=GF RT   MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana.
#=GF RA   Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S,
#=GF RA   Smith LM, Dasenko M, Givan SA, Weigel D, Carrington JC
#=GF RL   Plant Cell. 2010;22:1074-1089.
#=GF RN   [3]
#=GF RM   20407023
#=GF RT   Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA
#=GF RT   loci within the Arabidopsis genus.
#=GF RA   Ma Z, Coruh C, Axtell MJ
#=GF RL   Plant Cell. 2010;22:1090-1103.
#=GF WK   Mir-828_microRNA_precursor_family
#=GF SQ   4


AM481109.2/2574-2468     AAAGUUUCUUGCUCAAAUGAGUAUUCCAAACAACAGCUUGUGAAGCAAUGAUUACUGUCAUAGUCUCUGCAUGUGGAUUGUU-----GUUGAGAUGCUCAUUUGAGGAAGCA
AL161571.2/157498-157597 AAUGUUUCUUGCUUAAAUGAGUAUUCCAUGUAA------------AAAUGAUUCACUCACUCGUAUGGGUGGGUUGGGUUUUCUCUUCAUGAGAUGCUCAUUUGAGCAAGCA
AC189237.1/100224-100330 AAUGUUUCUUGCUUAAAUGGGUAUUCCAUGAAAGUGAUUC-----ACACUCACUAUGUAGACCUAACUACGAGUCGAUUUCUCUCUUCAUGAGAUGCUCAUUUAAGCAAGCA
AC168149.8/75695-75613   AAUGUUUCUUGCUCAAAUGAGUAUUCCA----------------------------AUCACAGUUGCAGAUCUUUGUUUUCUGCUGAC-UGAGAUGCUCAUUUGAGCAAGCA
#=GC SS_cons             ::::<<-<<<----<<<<<<<<<<<-<<<___________.....___________________________________________>>>->>>>>>>>>>>>>>->>:::
#=GC RF                  AAuGUUUCUuGCUuAAAUGaGuAUuCCAuguAAcaGaUUg.....aaAugauuuaugUaauagUaucuGcguGUuGaUUuuUcucuucaUGAgAUgCuCAUUUgAGcAAGCA
//
# STOCKHOLM 1.0

#=GF AC   RF01027
#=GF ID   mir-765
#=GF DE   microRNA mir-765
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   63.70
#=GF NC   39.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000545;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-765_microRNA_precursor_family
#=GF SQ   2


AADB02000969.1/939661-939774 UUUAGGCGCUGAUGAAAGUGGAGUUCAGUAGACAGCCCUUUUCAAGCCCUACGAGAAACUGGGGUUUCUGGAGGAGAAGGAAGGUGAUGAAGGAUCUGUUCUCGUGAGCCUGAA
AANU01239435.1/26313-26426   UUUAGGGGCUGAUGAAAGUGGAGUUCAGUAGACAACCCUUUUCAAGCCCUGCAAGAAACUGGGGUUUCUGGAGGAGAGGGAAGGUGCUGAAGGGGCUGCUCUCGUGAGCCUGAA
#=GC SS_cons                 :::::<<<<<-<<<<-<<--<<-<<<<<<<--<--<<<<<<<<<<<<<<<<________>>>>>>>>----->>>>>>>>-->->>>>>>>--->>-->>->>>>->>>>>:::
#=GC RF                      UUUAGggGCuGacGaAagUGGaGuuCagcaGACAaCCcucucCaagCCCcgCaAGAAACcgGGGcuuCUGGAGgagagGGAAGGugcuGaaGGauCUGcuCuCguGaGCccGAA
//
# STOCKHOLM 1.0

#=GF AC   RF01028
#=GF ID   mir-633
#=GF DE   microRNA mir-633
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   80.60
#=GF NC   58.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000546;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-633_microRNA_precursor_family
#=GF SQ   3


AADB02018606.1/558040-557943 AACCUCUCUUAGCCUCUGUUUCUUUAUUGCGGUAGAUACUAUUA--ACCUAAAAUGAGAAGGCUAAUAGUAUCUACCACAAUAAAAUUGUUGUGAGGAUA
AAFR03007371.1/244369-244465 AACUCUUCUCUACCUGACUUUCUUCAUA--GGUAGAUAAUAUUAUAAUAUAAUAUCUAGAGGAUAAUAAUAUCUACC-UUUCAAAGUUGUUAUGAGGCUC
AANU01178929.1/20913-20816   AACCUCUCUUAGCCUCUGUUUCUUUACUGUGGUAGAUACUAUUA--GCCUAAAAUAAGAAGGCUAAUAGUAUCUACCACAAUAAAAUUGUUGUGAUGAUA
#=GC SS_cons                 :::::::::::::::::::::::::::<<-<<<<<<<<<<<<<<..-<<<_________>>>->>>>>>>>>>>>>>->>::::::::::::::::::::
#=GC RF                      AACcucUCUuagCCUcugUUUCUUuAuuGuGGUaGaUacUaUUa..accUAAaAUaagaAggcuAAuAguAuCuACCACaauAAAaUUGUUgUGAgGaUa
//
# STOCKHOLM 1.0

#=GF AC   RF01029
#=GF ID   mir-649
#=GF DE   microRNA mir-649
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   82.00
#=GF TC   84.50
#=GF NC   80.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.19 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000547;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF WK   MicroRNA
#=GF SQ   5


AANU01210828.1/12529-12433 GCCCUAGCCAAAUACUGUAUUUUUUAUCAACAUUUGGUUGAAAAACAUCUGUGUAUUAGUA---------------AACCUGUGUUGU---------------UCAAGAGUCCGCUGUGCUUUGCUG
ABDC01582119.1/894-798     ACAUCCUGUGAAUACUGUAUUUUUGAUUUGCAUUUGAUUGAAAAAAUUGUGUAUGUAAGUG---------------GACCCAUGUUGU---------------UCAAGGGUCAACUGUAUACAUAUG
AC188307.1/109548-109440   UCCC---ACAAAUACUGUACUUUUGAUCUGCAUUUGGUUAAAAAAUAUCUGUGUAUAAGUGGACCCUCACAGUUCAAACCCAUGUUGU---------------UCAAGGGCCAACUGUAUUUCUACA
AC233974.1/5721-5832       GCAUCUCCCAGAUACUGUAUUUUUUAUCUGCUUUUGGUUGAAAUAAAUAUGCAUAUAAGUG---------------AACCCAUGCAGUUCAAGCCCAUGUUGUUCAAGUGUCAACUGUAUCUAGUAG
AC002472.8/78421-78325     GGCCUAGCCAAAUACUGUAUUUUUGAUCGACAUUUGGUUGAAAAAUAUCUAUGUAUUAGUA---------------AACCUGUGUUGU---------------UCAAGAGUCCACUGUGUUUUGCUG
#=GC SS_cons               ::::<<<<-<<<<<<-<<<<<<<<<<-<<<<<<--<<<<----<<<<<____>>>>>----...............>>>>->>>>>>-...............>>>>>>>>-->>->>>>>>->>>>
#=GC RF                    gcauccgccagauaCUGuaccuuugaUcggCauUUGGuugAAAcauauaUGuauaugAGUg...............aaCCcauGccgU...............ucaaggguCaaCUGuaucuagcgg
//
# STOCKHOLM 1.0

#=GF AC   RF01030
#=GF ID   mir-422
#=GF DE   microRNA mir-422
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   80.90
#=GF NC   58.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000548;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15325244
#=GF RT   Altered expression profiles of microRNAs during TPA-induced
#=GF RT   differentiation of HL-60 cells.
#=GF RA   Kasashima K, Nakamura Y, Kozu T
#=GF RL   Biochem Biophys Res Commun. 2004;322:403-410.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   3


AANU01097154.1/12100-12011 GAGAGAAGCACUGGACUCAGGGUCAGAAGGCCUGAGUCUCCCUGCUGCAGAUGGGCUGUGUGUCCCUGAGCCAAGCCUUGUCCUCCCUGG
AC015914.8/92261-92350     GAGAGAAGCACUGGACUUAGGGUCAGAAGGCCUGAGUCUCUCUGCUGCAGAUGGGCUCUCUGUCCCUGAGCCAAGCUUUGUCCUCCCUGG
AAEX03016203.1/17206-17121 GAGGGAGUG-CUGGACUCAGAGGUAGAAAACCUGCUGCUGUCUGCUC---CUGGGCUAAGUAUCCCUGAGCCAACUCUUGUCCUCUCAAA
#=GC SS_cons               <<<-<<<<<--<<<-<<<<<<<<<<<<-<<<<<--<<<<<______>->>>>>>>>>->>>>>>>>>>>>>>>->>>>>--->>>:::::
#=GC RF                    GaGagaggcACuGGACucaGgGgcagaAggCCuGaggcucuCUGCUgcagccgGGccaucugcCcCugaGCCaAgccuuGUCCuCcCugg
//
# STOCKHOLM 1.0

#=GF AC   RF01031
#=GF ID   mir-639
#=GF DE   microRNA mir-639
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   44.70
#=GF NC   40.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000549;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   6


AANU01214979.1/724-821     UGGCCGACGGGGCGCGCGCGGCCGGGAGGGGCGGGGCGGACGCACAGCCGCGUUUAGUCUAGCGCAGCGGUCGCGAGCGCUCUGGGUAUCCUGUCCUG
ABDC01432807.1/299-396     UGGCCGGCGGGGCGCGCGCGACAGGGAGGGGCGGGGCGGACGCGGAGCCGCGGUUAGUCUGGCGCAGCGGUCGCGAGCGCGUUAGGCGACCCGUGCUG
AAWR02041705.1/28905-28810 UGGCUGGU-GGGCGAGCGCGGCAGGGAGGGGCGGGGCAGGCGUGGAGCCGCGGGUAGUCUCGCGCGGCCGUCGCGAGCGCUG-GAGGAUCUUUGGUAC
AC009004.6/14944-14847     UGGCCGACGGGGCGCGCGCGGCCUGGAGGGGCGGGGCGGACGCAGAGCCGCGUUUAGUCUAUCGCUGCGGUUGCGAGCGCUGUAGGGAGCCUGUGCUG
AAGW02074592.1/1761-1665   UGGCCGGUGGCGCGCCCGAGGCGGGGUGGGGCGGGGCGAG-GGGGAGCUGCAGUUAGUCCGGCGCGACGGUCGCGAGCGCGCGAGGAUCCCCGUGCCG
AAQR03140354.1/1125-1028   UGGUCAUCAGGGCGCGCGCAGCAGGGAGGGGCGGGGCGGACUCAGAGCCGCGGUUAGUCUAGCGCCGCGGUCGCGAGCGCGUUAGGUGGCUGCUGUGG
#=GC SS_cons               ::<<<--<<-<<<<<-<<<<<<<<----<-<<-<<<<<<<<<<______>>>>>>->>>>->>->-->>>>>>>>->>>>>->>>>>:::::::::::
#=GC RF                    UGgccGgcgGgGCGCgCGcggCcgGGAGGGGcGgGgCggaCgcagAGCcgcGucuAGuCcagCGCaGcgGucgCGAGCGCcucgggcauCcugugcug
//
# STOCKHOLM 1.0

#=GF AC   RF01032
#=GF ID   mir-554
#=GF DE   microRNA mir-554
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   43.50
#=GF NC   37.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000551;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF WK   MicroRNA
#=GF SQ   4


AANU01226456.1/6829-6734   ACCUGAGUAACCUUUGCUAGUCCUGACUCAGCCAGUACUGAUCUUAC-ACUGGCAGUGG---GUCAGGGUUCAUAUUUUGGCAUCUCUCUCUGGGCAUCU
ABDC01184603.1/13192-13285 ACCUGAGUGACCUUUGCUAGUCCUAACUCAGCCAGGACUGGUCUCAGACGUGGUGAUGA----UCAGGGUUCA--UUUUGGCAUCCCUCUCUGAACACCU
AAQR03162163.1/5313-5216   ACCUGGGUAGCUUAUGCUGGUCUUAACUCAGCCAGGACUGGUCAUGU-GUGGGCAGGGGAUGGUCAGGGUUAAUGGGGUGGCAUC-CUGUCUGGGCCCUG
AL365436.26/38903-38998    ACCUGAGUAACCUUUGCUAGUCCUGACUCAGCCAGUACUGGUCUUAG-ACUGGUGAUGG---GUCAGGGUUCAUAUUUUGGCAUCUCUCUCUGGGCAUCU
#=GC SS_cons               :::::::::::::::<<---<<<<<<<<<<<<<<<<___________.>>>>>>-->>>...>>>>>>>----------->>::::::::::::::::::
#=GC RF                    ACCUGaGUAaCcUuUGCUaGuCcUgACuCagCCaggACUGGUCuUau.ccuGGcaauGg...GUcAgGgUUcAUauuuUGGCAUCuCUcUCUGggCaucu
//
# STOCKHOLM 1.0

#=GF AC   RF01033
#=GF ID   mir-767
#=GF DE   microRNA mir-767
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   74.30
#=GF NC   55.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000552;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis.
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [2]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach.
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   Mir-767_microRNA_precursor_family
#=GF SQ   14


AANU01106645.1/4647-4756   GCUUUUAUAUUG--UAGGUUUUUGCUCAUGCACCAUGGUUGUCUGAGCAUGCAGCAUGCUUGUCUGCUCAUACCCCAUGGUUU-CUGAGCAGGAAUCUUCA-UUGUCUACUGCU
AAFC03107988.1/1770-1879   GUCUUUGUAUUA--UAGGUUUUUGCUCAUGCACCAUGGUUGUCUGAGCAUGCAGCAUGCUUGUCUGCUCAUACCCCAUGGUUC-CUGAGCAGGAACCGUCA-CUGCUUACUGUU
AAQQ01376207.1/2059-1948   UUUAUAUUAUUGUAUAGGUUUUUGCUUAUGCACCAUGGUUGUCUGAGCAUGCAGCAUGCUUGUCUGCUCAUACGCCAUGGUUC-CUGAGCAGGAGCCUUCA-UUAACUACUGCU
AANG01462482.1/1257-1148   GCUUUUAUAUGC--UAGGUUUUUGCUCAUGCACCAUGGUUGUCUGAGCAUGCAACAUGCUUGUGUGCUCAUACCCCAUGGUUC-CUGAGCAGAAAACUUCA-UUGCCCAGUGCU
AAPY01458331.1/263-157     UAUCUUGUUUUG--UAGGUUUUUGCUCAUGCACCAUGGUUGUCUGAGCAUGCAGUGUGUUUGUCUGCUCAUUCCCCAUGGUUC-CCGAGCAGGAACCUUUG-UUGCCUACU---
AC091452.2/111889-111783   GAAUCCAUAU-----AGGUUUUUACUCAUGCACCAUGGUUGUCUGAGCACAUAACAUGCUUGUCUGCUCAUACCCUAUGGUUC-CUGAAGAGGAAUCUUAA-CUGUCUACUGCU
AANN01683306.1/1622-1513   ACCUUUGUGGGA--UUGGUUUUUGCUCCUGCACCAUGGUUGUCUGAGCACGGAGCAUGCUUGUCUGCUCAUACGCCAUGGUUC-GUGAGCAGGAACCUCCA-CUGCCCACCACG
AAHX01006705.1/22154-22047 GAAACCACAU-----AGGCUUUUGCUCAUGCACUGUAUUUGUCUGAGCAUGCACCAUGCUUGUCUGCUCAUACCUCAUGGUUC-CUGAGCAGGAAUCUUUUUUUUUCUGUUUCU
ABDC01642751.1/245-138     GCUUUUGUAUUA--UAAGUUUUUGCUCAUGCGCCAUGG-UGUCUGAGCAUGCAGCAUGCUUGUCUG-UCAUAUCUCAUGGUUUUCUGAGCAGGACCCUC-A-UUGCCUACUAUU
AAKN02056081.1/10707-10816 UUGUAUUCUUUA--UAGGCUUUUGCUCAUGCACCAUGGUUGUCUGAGCACGCAGCAUGCUUGUCUGCUCAUACCCCAUGGUUC-CUGAGCAGGAACCUUCA-CUGCCUACUAGU
AAWR02040596.1/10427-10318 GCUUUUGUAUUA--UAGGUUUUUGCUCAUGCACCAUGGUUGUCUGAGCAUGCAGCAUGCUUGUCUGCUCAUACUCCAUGGUUC-CUGAGCAGGAACCUUCA-UUGCCUACUGAC
AF274857.3/27844-27735     GCUUUUAUAUUG--UAGGUUUUUGCUCAUGCACCAUGGUUGUCUGAGCAUGCAGCAUGCUUGUCUGCUCAUACCCCAUGGUUU-CUGAGCAGGAACCUUCA-UUGUCUACUGCU
AAEX03027060.1/10112-10004 ACUUUUGUAUUC--UAGGUUUUUGCUCACACA-CAUUGUUGUCUGAGCAUGCAGCAUGCUUGUAUACUCAUAUCCCAUGGUUC-CUGAGCAGAAAACUUCA-UUGCCUACAGCU
AAPE02015517.1/33407-33515 GUUUUUGUAUUA--UAAGUUUUUGCUCAUGCACCGUGGUUGUCUAAGCAUGCAGCAUGCUUGGCUGCUCACACCCCGUAUUUC-CUGAGAAGGAACUU-UA-UUGCCUACUGCU
#=GC SS_cons               <<----<<<-<-..-<<<<<<<<<<<<<-<-<<<<<<<--<<-<<<<<<-<<<<_____>>>>->>>>>>->>->>>>>>>->.->>>>>>>>>>>>>-->.->>>----->>:
#=GC RF                    gcuuuugcaUua..UaGguuuuugCuCaUGCaccauggUUGuCuGaGCaUgcagCAUGCcugccuGCuCaUaCcccaugguUC.cuGaGcaggaacCuUca.uugcCUAcUgcu
//
# STOCKHOLM 1.0

#=GF AC   RF01034
#=GF ID   mir-618
#=GF DE   microRNA mir-618
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   miRBase; Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   68.60
#=GF NC   50.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000553;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-618_microRNA_precursor_family
#=GF SQ   5


AANU01112357.1/15114-15214 UUCUUGUUCACAACCAAACUCUACUUGUCCUUCUGAGUGUGAUUACGCCCAUGGAGUAGCUCAGGAGGCAAACAGGGUUACCCUGUGGAUAGGUCUGAAAA
ABGA01129596.1/1254-1354   CUCUUGUUCACAGCCAAACUCUACUUGUCCUUCUGAGUGUAAUUAUGUACAUGCAGUAGCUCAGGAGACAAGCAGGGUUACCCUGUGGACGAGUCUGAAAA
AC068798.26/62891-62791    CUCUUGUUCACAGCCAAACUCUACUUGUCCUUCUGAGUGUAAUUACGUACAUGCAGUAGCUCAGGAGACAAGCAGGUUUACCCUGUGGAUGAGUCUGAAAA
CABD02084991.1/4451-4351   CUCUUGUUCACAGCCAAACUCUACUUGUCCUUCUGAGUGUAAUUAUGUACAUGCAGUAGCUCAGGAGACAAGCAGGGUUACCCUGUGGAUGAGUCUGAAAA
AACZ03084217.1/94201-94301 CUCUUGUUCACAGCCAAACUCUACUUGUCCUUCUGAGUGUAAUUACGUACAUGCAGUAGCUCAGGAGACAAGCAGGGUUACCCUGUGGAUGAGUCUGAAAA
#=GC SS_cons               ::<<<<<<<<<<<---<<<<<<-<<<<<<-<<<<<<<<---<<<-<<____>>->>>->>>>>>>>>>>>>>->>>>>>--->>>>>>>>>>>::::::::
#=GC RF                    cUCucgucCaCagCCAaaccCuAcuuGuCCucCuGaGcGUaacuAcguaCAcgcaguAgCuCaGgaGaCaagCaGgguuACCcuGuGgacgaGUCUGAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01035
#=GF ID   mir-887
#=GF DE   microRNA mir-887
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   94.00
#=GF NC   64.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000554;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


ABDC01026404.1/4653-4575   GUGCAGGCCCUUGGAAGCCCCAUUAGACACUCCAUUUUACACUUGGCGUGAAGGGGCUCCAAUCCAAGGCUUUGUGCAG
AC091872.3/26278-26356     GUGCAGAUCCUUGGGAGCCCUGUUAGACUCUGGAUUUUACACUUGGAGUGAACGGGCGCCAUCCCGAGGCUUUGCACAG
AAQR03064444.1/26611-26533 GUGCAGGUCCUUGGAAGCCCCAGUAGACCCUAUAUUUCACAUUUUGAGUGAACAGGCUCCAUUCUAAGGUUUUGCUUAG
#=GC SS_cons               <<<<<<<-<<<<<<<<<<<<--<<---<-<_________________>->>>->>>>>---->>>>>>>->>>>>>>::
#=GC RF                    GuGCAgguCCUuGGgaGCCccauUAGACuCUauAUUUuACAcUUgGaGUGAacgGGCuCCAucCCaAGGcuuUGCaCAG
//
# STOCKHOLM 1.0

#=GF AC   RF01036
#=GF ID   mir-567
#=GF DE   microRNA mir-567
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   52.00
#=GF TC   54.60
#=GF NC   50.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000555;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates.
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   9


AANU01279133.1/11007-11100 GGAUUCUUACAGGACACUAUGUUCUUCCAGGACAGAACAUUCUUUGCUAUUUUGUA-CU-GGAAGAACAUGCAAAACUUUAAAAAAA----GUUAUUGCU
AADB02004619.1/64331-64234 GGAUUCUUAUAGGACAGUAUGUUCUUCCAGGACAGAACAUUCUUUGCUAUUUUGUA-CU-GGAAGAACAUGCAAAACUAAAAAAAAAAAAAGUUAUUGCU
ABDC01160933.1/3144-3236   GGAUUCUCCUAGGACAGUACAUUCUUCUAGGACAGGACACCCUUUGCUACUUUGUA-CU-GGAAGAACAUGCAGCACU--GAAAAAAU---AUUAUUGCU
AANG01703138.1/1221-1311   GCGAGAUUACAGAAGA--GGGUUCUUCUAGGACAGUAUGCCCUUUGCCUUUUUGUA-CU-GGAGGAACAUGAGGAGCUAGAAAGAG-----GGUCGUGCU
AAFC03050676.1/19640-19728 AGGUGCAUUGACAAGG----GCUCUUCUAGGGUAGUACACUCUUUGUUGUUUUAUA-CU-GGGAGAGCAUGUAGAACUCAAAAGAU-----GUUUUUGCU
AAWR02012002.1/82097-82003 AUGGACUCGUG---GAGGGGGUUCUUCUAGGACAGUACACUCUUUGCUAUUUUGUACCU-GGAAGAAUGUGCAGAA-CAAAAAAAAAAAAUGUUAUUGCG
AAPE02028785.1/56374-56470 CUGGACCCGUGGAAGA--GGAUUCUUCCAGGGCAGCAUACCUUUUGCUAUUUUGUA-CUUGGAAGAACACGAGGAACUAAAAAAAAGAAAUGUUAUUGCU
AAQR03138419.1/4645-4737   GGAUUCUUCUAGGACAGCACAUUCUGCUAGAACGGAUUGCCGUUUGCUGUUUUGUA-CU-GGAAGAACAUGCAGCACUAAAAAAAU-----GUUAUUGAU
AACZ03024758.1/51058-50961 GGAUUCUUAUAGGACAGUAUGUUCUUCCAGGACAGAACAUUCUUUGCUAUUUUGUA-CU-GGAAGAACAUGCAAAACUAAAAAAAAAAAAAAAAAAAGUU
#=GC SS_cons               ::::::<<<<<<----<<<<<<<<<<<<<<-<<<<<<<<_____>>--->>>>>>-.>>.>>>>>>>>>>>>---->>>>>>::::::...:::::::::
#=GC RF                    ggauuCuucuaGgAgAGcauguUCuuCcAGGaCAGaacacucUUugCUauuUUGuA.CU.gGaaGAacaugCAGAACuagaaAAAaAA...GuUauUGcU
//
# STOCKHOLM 1.0

#=GF AC   RF01037
#=GF ID   mir-644
#=GF DE   microRNA mir-644
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   66.50
#=GF NC   50.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000556;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF WK   MicroRNA
#=GF SQ   3


AANU01276459.1/12864-12955 -UUUUAUUUAGUAUUCUUCCAUCAGUGUUCAUAAGGGAUGUUGGUCUGUAGUUUUCUUAUAGUGUGGCUUGCUUAGAGCAAAGGUGGUUCCCU-
AL109923.29/43467-43560    UUUUUUUUUAGUAUUUUUCCAUCAGUGUUCAUAAGGAAUGUUGCUCUGUAGUUUUCUUAUAGUGUGGCUUUCUUAGAGCAAAGAUGGUUCCCUA
ABGA01346441.1/4610-4703   CUGAUAUUUAGUAUUUUUCCGUCAAUGUUCAUAAGGGAUGUUGGUCUGUAGUUUUCUUAUAGUGUGGCUUUCUUAGAGCAAAGGUGGUUCCCUA
#=GC SS_cons               ::::::::::::::::::<<<<<--<<<<<-<<<<<<<-<<<<<-<<<<<<_____>>>>>>->>>>>>>>>>>>>>>>>-->>>>>:::::::
#=GC RF                    uUuuUaUUUAGUAUUuUUCCacCAguGuuCAuaaGggaUGuugcUCuguagUUUUCuuauaGUguggCuccCuuaGagCaAAGguGGUUCCCUA
//
# STOCKHOLM 1.0

#=GF AC   RF01038
#=GF ID   mir-1307
#=GF DE   microRNA mir-1307
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   60.30
#=GF NC   38.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000558;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells.
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [2]
#=GF RM   19144710
#=GF RT   Identification of novel Epstein-Barr virus microRNA genes from
#=GF RT   nasopharyngeal carcinomas.
#=GF RA   Zhu JY, Pfuhl T, Motsch N, Barth S, Nicholls J, Grasser F, Meister G
#=GF RL   J Virol. 2009;83:3333-3341.
#=GF WK   MicroRNA
#=GF SQ   7


AACN010169582.1/393-294    ACAGCCACUGCCUACCAAUCUCGACCGGACCUCGACCGGCUCGUCUAUGUUGCCAAUCGACUCGGCGUGGCGUCGGUCGUGGUAGAUAGGCGGUCAUACA
ABDC01066567.1/2169-2070   GCUGCCACUGCCUACCAAUCUCGACCGGACCUCGACCGGCUCGUCUGUAUUGCCAAUCGACUCGGCGUGGCGUCGGUCGUGGUAGAUAGGCGGUCAUACA
AAFC03098458.1/36666-36765 ACUGCCACUGCCUACCAAUCUCGACCGGACCUCGACCGGCUCGUCUAUAUUGCCAAUCGACUCGGCGUGGCGUCGGUCGUGGUAGAUAGGCGGUCAUACA
AANG01052568.1/1920-1821   ACUGCCACUGCCUACCAAUCUCGACCGGACCUCGACCGGCUCGUCUAUGUUGCCAAUCGACUCGGCGUGGCGUCGGUCGUGGUAGAUAGGCGGUCACACA
AC190201.3/81203-81302     ACUGUCACUGCCUACCAAUCUCGACCGGACCUCGACCGGCUCGUCUGUGUUGCCAAUCGACUCGGCGUGGCGUCGGUCGUGGUAGAUAGGCGGUCAUGCA
BC007087.1/72-171          ACUGUCACUGCCUACCAAUCUCGACCGGACCUCGACCGGCUCGUCUGUGCUGCCAAUCGACUCGGCGUGGCGUCGGUCGUGGUAGAUAGGCGGUCAUGCA
AAGW02060888.1/16091-15992 ACUGCCACUGCCUACCAAUCUCGACCGGACCUCGACCGGCUCGUCUGUGUUGCCAAUCGACUCGGCGUGGCGUCGGUCGUGGUAGAUAGGUGGUCACACA
#=GC SS_cons               :::<--<<<<<<<<-<-<<<-<<<<<<<-<<-<<-<<<--<<<----<<____>>-->>>-->>>>>->>-->>>>>>>->>>->->>>>>>>>-->:::
#=GC RF                    AcugccaCcGCCuacCAacCUCGaCCGgACCUCGACCGGcuCGUcUauguUGccaAUCGacUCGGCGUGGcGcCGGuCGUGguAGAuaGGCgGucAcacA
//
# STOCKHOLM 1.0

#=GF AC   RF01039
#=GF ID   mir-937
#=GF DE   microRNA mir-937
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   47.50
#=GF NC   40.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000560;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer.
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF WK   MicroRNA
#=GF SQ   9


AANU01106925.1/1175-1090   AGCACUGCCCCCGGUGAGUCAGGGUGGGGCUGGCCCCCUGCUUCGCGCC--CAUCCGCACUCU--GACUCUCCAC---CUGCCUGCAGGAGCU
ABDC01348805.1/1662-1747   AGCACUGCCUCCGGUGAGUGAGGGUGGGGUAGGCCUCCCACCUGGUGCC--CAUCUGCUCUCU--GACCCUCUUC---CUGCCCUCAGGAGCU
AAQQ01060996.1/829-746     AGCACUGCCCCCGGUGAGUGAGGGCGGGACUGGCCUCCUACCUCCAG-C--UGCUGUC-CUCU--GACCCUGUGC---CUGCCCUUAGGAGCU
AAFC03099350.1/6667-6578   AGCCCUGCCCCCGGUGAGUGAGGGUGUGG-CUGCCACCCCCACUUGGGCCUGGCCCUCCCCCU--GACCCUCUGCACCCACCCCCCAGGAGCU
AAWR02021814.1/51032-50947 AGCACUGCCCCCGGUAAGUGAGGGUGUGGC--UGCCCCUGCCUUGUGCU--GCUCCGUUUUCU--GACUGUCUGCA-UCCACCCUCAGGAGCU
AC105219.6/15753-15838     AGCACUGCCCCCGGUGAGUCAGGGUGGGGCUGGCCCCCUGCUUCGUGCC--CAUCCGCGCUCU--GACUCUCUGC---CCACCUGCAGGAGCU
AC116487.14/30147-30229    AGCGCUGCCCCCGGUAAGUGAGGGUGGGACUGG---CUUUAUCCCCUAC--CUGCUGCCCUUU--GACCUUUUGU---CUGUCUGCAGGAGCU
AC195637.4/37515-37430     AGCACUGCCCCCGGUGAGUCAGGGUGGGGCUGGCCCCCUGCUUCGUGCC--CAUCCGCGCUCU--GACUCUCUGC---CCGCCUGCAGGAGCU
AAEX03008940.1/1041-956    GGCACUGCCCCCGGUGAGUGAGGGUGCGG-CAGCCCCUGGC-UCGUGCC--UGGCCGUGCCCUGACCCUCCGCAC---CCACCCGCAGGAGCU
#=GC SS_cons               <<<-<<<<----<<<<<<<<<<<<<<-<<-<<<------<<_____>>>..>>->>->>>>>>..>>>>>--->>...>----->>>>-->>>
#=GC RF                    aGCaCUGcCCCCGGcgaGucAGgGcGggGCcggcCcCcugcuUcgugcc..cguCcgCgCcCU..gaCucUcUgC...CuaCCcgCAGGAGCu
//
# STOCKHOLM 1.0

#=GF AC   RF01040
#=GF ID   mir-573
#=GF DE   microRNA mir-573
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   84.20
#=GF NC   50.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000561;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF WK   MicroRNA
#=GF SQ   2


AADB02006286.1/27859-27761 UUUAGCGGUUUCUCCCUGAAGUGAUGUGUAACUGAUCAGGAUCUACUCAUGUCGUCUUUGGUAAAGUUAUGUCGCUUGUCAGGGUGAGGAGAGUUUUUG
AANU01231817.1/17907-17809 UUUAGAGGUGUCUCCCUGAAGUGAUGCAUAACCGAUCAGGAUCUACUCAUGUCAACUUUGGUAAAGUUAUGUUGCUUGUCAGGGUGAGGAGAGGUUUUG
#=GC SS_cons               ::::::::<<<<-<<<<<<<<<<<<--<<<<<--<<<<<<----<<____>>---->>>>>>--->>>>>>>>>>>-->>>>>>->>>>::::::::::
#=GC RF                    UUUAGaGGucuCUCCCuGaaGugauGuauaaCuGauCaggAUCUaCUCAUGuCaaCuuuGguAAAGuuaugucgCuUGuCaGGGUGaggAGAGuUUUUG
//
# STOCKHOLM 1.0

#=GF AC   RF01041
#=GF ID   mir-604
#=GF DE   microRNA mir-604
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   62.70
#=GF NC   34.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000562;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF WK   MicroRNA
#=GF SQ   2


AADB02013021.1/988989-989082 AGAGCAUCGUGCUUGACCUUCCACGCUCUCGUGUCCACUAGCAGGCAGGUUUUCUGACACAGGCUGCGGAAUUCAGGACAGUGCAUCAUGGAGA
AANU01172048.1/7070-7163     AGAGCAUCGUGCUUGACCUUCCACGCUCCCGUGUCCACUAGCAGGCAGGUUUUCUGACACGGGCUGCGGGAUUCAGGACAGCGCAUCACGGAGA
#=GC SS_cons                 :<<<<<<-<<-<<<<<---<<<-<<<-<<<<<<<<----<<<______>>>---->>>>>>>>-->>>>>>->>>>>>>->>>>->>:::::::
#=GC RF                      AGaGCgcCGuGCcuGaCCUucCACGCUCccGuGuCCACUagCAGGCAGGcuUUCUGaCaCggGCUGCGGgaUuCagGaCAgcGCAuCAuGGAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01042
#=GF ID   mir-891
#=GF DE   microRNA mir-891
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; RNAalifold
#=GF GA   54.00
#=GF TC   54.20
#=GF NC   53.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000420;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   MicroRNA
#=GF SQ   7


AL358174.12/10771-10693    CCUUAAUCCUUGCAACGAACCUGAGCCACUGAUUCAGUAAAAUACUCAGUGGCACAUGUUUGUUGUGAGGGUCAAAAGA
AC193538.2/129585-129508   CCUUAAUCCUUGCAACUUACCUGAGUCAUUGAUUCAGUAAAACAUUCAAUGGCACAUGUUUGUUGUGAGGGUCAAAAG-
AL445258.4/159413-159335   CCUUAAUCCUUGCAACUUACCUGAGUCAUUGAUUCAGUAAAACAUUCAAUGGCACAUGUUUGUUGUUAGGGUCAAAAGA
CU464034.1/156317-156240   CCUUAAUCCUUGCAACGAACCUGAGCCAUUGAUUCAGUAAAAUACUCAGUGGCACAUGUUUGUUGUGGGGGUCAAAAG-
AANU01202537.1/38748-38670 CCUUAAUCCUUGCAACUUACCUGAGUCAUUGAUUCAGUAAAACAUUCAAUGGCACAUGUUUGUUGUUAGGGUCAAAAGA
ABRT010818628.1/1390-1467  CUUCAAUCCUUGCAACAAACCUGUGGCAGUGAGUCAUUAAAACA-UCAUUGCCACAUGUCUGUUGUGAGGGUCAAGGGA
ABRQ01519725.1/3315-3237   CGUUAAUCCUUGCAACAGAUCUGUGUCAGUGAGUUAGUACAGGGGUCAGUGACACAGAUUUGUCGUGAGGAUUAAAUGA
#=GC SS_cons               :::::<<<<<<<<<<<--<<-<<-<<<<<<<<_____________>>>>>>>>->>->>-->>>>>>>>>>>:::::::
#=GC RF                    CcUUAAuCCuugCaACaaAcCUGaGcCAcUGAuUCAGUAAAAcAuUCAgUGgCACAUgUUUGUuGugaGGgUCAAAaGA
//
# STOCKHOLM 1.0

#=GF AC   RF01043
#=GF ID   MIR1023
#=GF DE   microRNA MIR1023
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   miRBase; Wilkinson A, Daub J
#=GF SS   Predicted; RNAalifold
#=GF GA   90.00
#=GF TC   125.90
#=GF NC   83.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000396;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17601824
#=GF RT   Common functions for diverse small RNAs of land plants.
#=GF RA   Axtell MJ, Snyder JA, Bartel DP
#=GF RL   Plant Cell. 2007;19:1750-1769.
#=GF WK   MicroRNA
#=GF SQ   4


ABEU01008017.1/44527-44387   ----UGUAGAAGAUGCAGCUUGCAGAUU-AUCAUCCACUCUCUCCGUUUCCCUUCCCACAGCUAUCAUCCG-GACUAG-----CAUUUCCUGUACAUAC---------------------UAGGGAAGGGAAAUGGAGAGAGUGUAUAAUGAAUUGCAUGCUUGAUUGCUGAG----
ABEU01004783.1/104781-104949 GGAGCG-AUUGGAC-CACCUUGCAGUUUCAUGGCACACUCUCUCCAUUUCUCUACCGUUCAUGCAGCGGUUGAUCGAUUGGGUUGCUGGUUG-AUUGAUCGAUCGAUGGUCAGGA----GUUGGA-AGAGAAUUGGAGAGAGUGCAUUGUGAAUUGCGGGGUUGACGAGGCGGAGGG
ABEU01011925.1/25350-25179   GAAGCGCGGCGGGC-CAGCUUGCAAUUUCAUGACACACUCUCUCCAUUUCUCUGCCUGUCAUGACUUGGUUGAUCGAUGGAGCGGUGGUUUUCAUUGCCCGAUUGAGGAUCAGGA----GUUGGGGAGAGAAUUGAAGAGAGUGCAUUGUGAAUUGCAAGCUCCUCCUUUCUUUUCG
ABEU01004286.1/181899-181732 ---GCGCAGUU-ACACAGCUUGCAUUUC-GGUGUCCACUCUCUCCGUUUCCCUUCCCAUGAUGGCUAGCCUUGAGUAAGUACAUAUGUUUUGAACACAUGUAUGCUUGCUUAAAAUCCUUUGUCGGAGGGAAUCGGAAAGAGUGUACAAUGAAUUGCAAGCUUGAUUGAUUCG----
#=GC SS_cons                 ...:::::::::::::<<<<<<<<<<<<.<<<<<-<<<<<<<<<<<-<<<<<<<<<<---------------<<<<<<<<___________________>>>>>>>>--------....--->>>>>>>>>>->>>>>>>>>>>->>>>>>>>>>>>>>>>>:::::::::::....
#=GC RF                      ...GCGcAGugGACaCAgCuuGCAauUu.acuguaCACUCUCUCCgUUUCcCUuCCcaUaAUGacuaGguUggucgAucgaguuaUuuuUUGuAuagAucgaUcgacGaUcAggA....gUugGGaAGgGAAUcGGAGAGAGUGuacagugAauUGCaaGcUUgAuuguUuuG....
//
# STOCKHOLM 1.0

#=GF AC   RF01044
#=GF ID   mir-345
#=GF DE   microRNA mir-345
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   65.00
#=GF TC   67.20
#=GF NC   64.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000189;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing.
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [3]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   Mir-345_microRNA_precursor_family
#=GF SQ   10


ABDC01284659.1/800-896     ACCCAAACCCCAGGUCUGCUGACUC-UAGUCCAGUGCUCGUGAUGGCUGGUGGGCCCUGAACUAGGGGUCUGGAGGCCCUGGGUUUGAAUGUC-GCCAG
AALT01091699.1/386-481     ACCCAAACC-CAGGCCGGCUGACUCUUAGUCCAGUGCUCGUGAAGGCUGCUGGGCCCUGAACUGAGGGUCUGGAGG-CCUGGGCUUGACUGUC-AACAG
AAIY01055903.1/172-268     AACCAGGCC-CAGGCCUGCUGACUCCUAGUCCAGUGCUCGUGAUGGGCAUAGGGCCCUGAACUAGGGGUCUGGAGG-UCUGCGCUUGAAUAUCGACAAG
AAFC03086528.1/21560-21655 ACCCAAACC-CAGGUCUGCUGACUCCUAGUCCAGUGCUUGUGAUGGCUGGUGGGCCCUGAACUAGGGGUCUGGAGG-CCUGGGUUUGAAUAUC-ACCAG
AAYZ01540228.1/2113-2017   AUGCAAACCCCAGGUCUGCUGACUCCUCGUCCAGUGCUCGAGAUGGCUGCUGGGCCCUGAACUGGGGGUCUGGAGG-CCUGGGUUUGAAUAUC-GCCAG
AC152061.6/175970-176065   ACCCAAGUC-CAGGCCUGCUGACCCCUAGUCCAGUGCUUGUGGUGGCUACUGGGCCCUGAACUAGGGGUCUGGAGA-CCUGGGUUUGAUCUCC-ACAGG
AL135838.6/146068-145972   ACCCAAACCCUAGGUCUGCUGACUCCUAGUCCAGGGCUCGUGAUGGCUGGUGGGCCCUGAACGAGGGGUCUGGAGG-CCUGGGUUUGAAUAUC-GACAG
AC193024.5/98698-98794     AUGGAAACCCUAGGUCGGCUGACUCCUAGUCAAGGGCUCGUGGUGGCUGGUGGGCCCUGAACGAGGGGUCUGGAGG-CCUGGGUUUGAAUAUC-ACCAG
AAGU03026008.1/70278-70183 GACCCAACC-CAGGUCUGCUGACUCCUAGUCCAGUGCUUGUGAUGGCCAUUGGGCCCUGAACUAGGGGCCUGGAGG-CCUGGGUUUGAUUAUC-GCCAG
AAPE02046792.1/6668-6573   ACCCAGACC-CAGGUCUGCUGACUCCUAGCCCAGUGCUUGUGAUGGCUGGUGGGCCCUGCAUUAGGGGUCUGGAGG-CCUGGGUGUGAAUAUC-GCCAG
#=GC SS_cons               :::::::::.<<<<<<<-<-<<<<<<<<<<-<<<<<<<<<__________>>>>>>>>>->>>>>>>>>>->->>>.>>>>::::::::::::.:::::
#=GC RF                    AcccAAACC.caGGcCuGCUGaCuCcuaGuCCaGgGCucgUGAUGGcUguuggGCcCuGAaCuagGgGuCUGGaGg.CCuggGuUUGAaUaUC.accAG
//
# STOCKHOLM 1.0

#=GF AC   RF01045
#=GF ID   mir-544
#=GF DE   microRNA mir-544
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   68.00
#=GF TC   68.00
#=GF NC   67.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000436;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [2]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes.
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF WK   Mir-544_microRNA_precursor_family
#=GF SQ   24


AANU01242105.1/21434-21526   AUAUGGAU--------UACCUUGGGAGCUUGUUAAAAU-GCAGAUUCUGAUUCA--------------G-GA-------AGUCUG--AGAUUCUGCAUUUCUAUCAAGUUCUCAGGUGAUGCUGAU
AAPY01824234.1/1936-1833     ACAGAAAU--------CACCCAGGAAUCUUGUUAAAAU-GCAGAUUCUGAUUCAGUAGGG-CUGGCACG-G---------GGCCC--AGAUUCUGCAUUUCUAACAAGCUUCCAGGUGAUUAGAAU
AAQQ01373685.1/1858-1765     --------ACAUAAAUCACCUGGAGAUCUUGUUAAAAA-GCAGAUUCUGAUUCA--------------G-UU------AAGCCUG--AGACUCUGAAUUUUUAACAAGCUCCCAGGUGAGGCUGAU
AAFC03005951.1/71350-71259   AUAUGAAU--------CACCAGGGGAUCUUGUAAGAAC-ACAGAUUCUGAUUCG--------------G-G---------GAGCU-GAGAAUCUGCAUGUCUAACAAGCUCCCAAGUGAUGCUUUG
ABDC01231707.1/6020-6119     AGACCAGU--------CACUCAGGGAUCUUGUUAAAAU-GCAGAUUCUGACACA--------------G-GAGGUCUGAACGCUG--AGAUUCUACAUUUCUAACAAGCUCUCAAGUGACUCUAAU
AL139239.18/39922-39830      ACAUAAAC--------CACCCAGGGGUCUUGUUAGAAU-GCAGGUUCUGAUUUCAU---------UAGG-G---------GCCUG--AGAUUCUGCAAUUCUAGCAAGCUCCCAGGUG---ACAUU
AANG01731304.1/847-757       AAAUGGAU--------CAC-UGGAGAUCUUGUUAAGAC-GCAGAUUCUAAUUCA--------------GUG---------GCCCA--GGAUUCUGCAUUUCUAACAAGCUCGCAAGUGAUGCCAGU
AANN01547993.1/591-693       AUACAAGU--------CAUUU-GGGAUCUUGUUAAAAU-GCAGAUUCUGAUUAAAUGAAU-UUGACAUA-G---------GUCUG--AGAUUUUGCAUUUUUAACAAGCUCCCAGGUGAUGCGUAU
AAIY01079206.1/3124-3027     ACAGAAAU--------CACCUGGGGAUCUUGUUAAAAU-GCAGAUUUGGAUGUAAUA-------GGUUU-U---------GGCUC--AGAUUCUGUAAUUUUAACAAGCUCCCAGGAGAUGCUGAU
AAYZ01265095.1/3165-3062     AUAGGAAU--------UGCCUAGGAAUCUUGUUAAAAU-GUAGAUUCUGAUUCAGCAGGC-CUGGCCUG-G---------GGCCA--AGAUUCUGCAUUUCUAACCAGCUCCCAGGUGAUUAGAAC
AC197607.1/132974-132877     AUACAAAU--------UGCACUGAGAUCUUCUUAAAAC-GCAGAAUCUGAUUCUGGG-------GCUGG-A---------ACCUG--AGGUUCUGCAUUUCUAACAGGUUCACAGGCAAUGUCAAU
AAHX01113444.1/3509-3405     AUGAGUAU--------CACCUAGGGAGCUUGUUAAAAU-GCAGAUUCUAAUUCAGGGAGGUUGAGGUGG-G---------GCUUG--GGAGCCUACAUUUCUAAUAAGUUCCCAGGUGAUGUCUUU
CR974431.11/197555-197451    AUGCGAAU--------CACCUGGGGAGCUUGUUAAAAU-GCAGAUUCUGAUUCAGCGGGUCUGGGGUGG-A---------GCCCG--AGAGUCUGCAUUUCUAACGAGCCUCCAGGUGGUGCGGGC
AC159930.3/84189-84292       AUUUGAAU--------CACUAGAUGAACUUAUUAAAAU-GCAGAAUCUGACUCAUUAGGU-CUGGCUAU-G---------GUCCA--AGAUUCUACAUUUCUAACAAGUUCUAGGGUGAUUCAAAU
AALT01428581.1/2178-2089     AUGUAGAU--------CACCUGGGGAUCUUGUUAAAAU-GCAGAUUCUGGUUCA--------------A-U--------AGGAAU--GAAUUCUGCAUUUCUAACAGGACCCCAU--GAUUUUAAU
AC148207.4/60804-60907       AUUUGAAU--------CACCACAGGAACUUAUUAAAAU-GCAGAAUCUGACUCAUUAAGU-CUGGCUAU-G---------GCCCA--AAAUUCUACAUUUCUUACAAGUUCCAGGGUGAUUCAAAU
AAWR02025360.1/73860-73949   -----CAGUG---AGUCACCUGGGGAGCUUGUUAAAAU-GCAGAUUCUGAGAUG--------------G-G---------GCCUG--AGAGUCUGCAUUUCUCACAAGCUCCCAGGUGCUAACUU-
AAGV020377152.1/1916-1825    AUAAGAAU--------CACCUAGGGAGCUUGUUAAAAU-GCAGAGUCUUAAUCA--------------G-U---------AGGCAUGAAAUUCUGCAAUUUUAACAUGUUCUCAGG-GAUGGUGCU
AAKN02051949.1/117559-117649 AUUUUCAU--------UACCUAGGGAUCUCGUUAAAAA-CCAGAUUCUGAUGCA--------------G-G---------GACCA--AGAUUCUGUAUUUUUAGCAAGUUGUCAAGUGAUGCUAAU
AC121784.2/124851-124941     AUAUUCGU--------CACCUAGGGAUCUUGUUAAAAA-GCAGAGUCUGAUUGA--------------G-G---------GGCCA--AGAUUCUGCAUUUUUAGCAAGCUCUCAAGUGAUGCUAAU
AL132709.5/72941-72851       AUUUUCAU--------CACCUAGGGAUCUUGUUAAAAA-GCAGAUUCUGAUUCA--------------G-G---------GACCA--AGAUUCUGCAUUUUUAGCAAGUUCUCAAGUGAUGCUAAU
AAEX03006005.1/153692-153782 AUUUUCAU--------CACCUAGGGAUCUUGUUAAAAG-GCAGAUUCUGAUUUA--------------G-G---------GACCA--AGAUUCUGCAUUUUUAGCAAGUUCCCAAGUGAUGCUAGC
AAGW02077267.1/8650-8740     AUGGUCAU--------CACCAAGGCAUCUUGGUAGAAA-GCAGAUUCUGAUUCC--------------G-G---------GACCA--AGAUUCUGCAUUUUUAGCAAGUUCUUGAGUGCUGCCGCA
AAGU03051271.1/73223-73133   AUAUAAAU--------CACUU-GGGAUCUUGCUAAAAAAGCAGAUUCUGGUUUG--------------A-A---------ACCUA--AGAGUCUGCAUUUCUAACAAGCUCUCAGGUGAUGUCGAG
#=GC SS_cons                 :::::<<<........<<<---<<<<-<<<<<<<<<<<.<<<<<<<<<______.............._._........._____..>>>>>>>>>->>>>>>>>>>>->>>>-->>>>>>:::::
#=GC RF                      Auauacau........CaCcuaGgGAuCUUGuUAaAAc.gCAGAcUCuGAUUcA..............G.g.........GcCua..aGAgUCUGcAgUUuUAaCAAGcUCcCAgGuGaugcuaaU
//
# STOCKHOLM 1.0

#=GF AC   RF01046
#=GF ID   WLE3
#=GF DE   Wingless localisation element 3 (WLE3)
#=GF AU   Brown C
#=GF SE   Predicted
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   55.00
#=GF NC   43.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://mrna.otago.ac.nz/cgi-bin/tt_data_browse/RNAMotif?PatID=T0202;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0006403; RNA localization;
#=GF RN   [1]
#=GF RM   18045835
#=GF RT   A stem-loop structure in the wingless transcript defines a consensus motif
#=GF RT   for apical RNA transport.
#=GF RA   dos Santos G, Simmonds AJ, Krause HM
#=GF RL   Development 2008;135:133-143.
#=GF WK   Wingless_localisation_element_3_(WLE3)
#=GF SQ   10


S67383.1/2071-2114         UGCUUGCAUACUGCUUUGGCCAGGACCAAAACGUAUGCGAAGUG
DQ778986.1/830-873         UGCUUGCACACUGCUUUGGCCAGGACCAAAACGUAUGCGAAGUG
DQ778975.1/672-715         UGCUUGCAUACUGCUUUGGCCAGGACCAAAACGUAUGCAAAGUG
AY128458.1/2363-2406       UGCUUGCAUACUGCUUUGGGCAGGACCAAAACGUAUGCGAAGUG
AE014134.5/7315711-7315754 UGCUUGCAUACUGCUUUGGGCAGGACCAAAACGUAUGCGAAGUG
DQ778977.1/640-683         UGCUUGCAUACUGCUUUGGCCAGGACCAAAACGGAUGUGAAGUG
DQ778976.1/640-681         UGCUCGCAUACUGCUUUGGCCAGGACCAAAACGUAUGUGGAG--
DQ778982.1/694-735         UGCUUUCAUGUUGCUUUGGCCGGGCUCAAAGCAGAUGGAAAG--
DQ778983.1/809-850         UGCUUGCAUUUCGCUUUGCCCAGCUGCAAAACGCAUGUUAAG--
DQ778987.1/872-913         UGCUUGCAUUCCGCUUUGCCCAGCUGCAAAACGCAUGUUAAG--
#=GC SS_cons               <<<<<<<<<<<-<-<<<<<______>>>>>->>>>>>>->>>>>
#=GC RF                    UGCUUgCAUaCUGCUUUGGCCAGGaCCAAAACGuAUGcgAAGUG
//
# STOCKHOLM 1.0

#=GF AC   RF01047
#=GF ID   HBV_epsilon
#=GF PI   HBV
#=GF DE   HBV RNA encapsidation signal epsilon
#=GF AU   Chen A
#=GF AU   Brown C
#=GF SE   Chen A, Brown C
#=GF SS   Published; PMID:12409471
#=GF GA   45.00
#=GF TC   46.60
#=GF NC   44.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF CL   CL00104
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   17206754
#=GF RT   Hepatitis B virus replication.
#=GF RA   Beck J, Nassal M
#=GF RL   World J Gastroenterol. 2007;13:48-64
#=GF RN   [2]
#=GF RM   12409471
#=GF RT   The apical stem-loop of the hepatitis B virus encapsidation signal folds
#=GF RT   into a stable tri-loop with two underlying pyrimidine bulges.
#=GF RA   Flodell S, Schleucher J, Cromsigt J, Ippel H, Kidd-Ljunggren K, Wijmenga S
#=GF RL   Nucleic Acids Res. 2002;30:4803-4811
#=GF RN   [3]
#=GF RM   9857345
#=GF RT   Structure and function of the encapsidation signal of hepadnaviridae.
#=GF RA   Kramvis A, Kew MC
#=GF RL   J Viral Hepat. 1998;5:357-367
#=GF CC   The HBV RNA encapsidation signal epsilon (HBV_epsilon) is an element
#=GF CC   essential for HBV virus replication.
#=GF WK   HBV_RNA_encapsidation_signal_epsilon
#=GF SQ   32


X85254.1/1849-1909   UGUUCAUGUCCUACUGUUCAAGCCUCUAAGCUGUGCCUUAGGUGGCUUUAGGGCAUGGACA
AB048704.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGUUGUGCCUUGGGUGGCUUUAGGACAUGGACA
X75657.1/1847-1907   UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AB036910.1/1847-1907 UGUUCAUGUCCCACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AB032431.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AY090457.1/1850-1910 UGUUCAUGUCCCACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
X02496.1/1849-1909   UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AB033554.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AB033556.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
D00330.1/1847-1907   UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AF090842.1/474-534   UGUACAUGUCCCACUUUUCAAGCCUCCAAGCUGUGCCUUGGAUGGCUUUGGGGCAUGGACA
M32138.1/1849-1909   UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUAGGACAUGGACA
X69798.1/1847-1907   UGUUCAUGUCCCACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AY090460.1/1850-1910 UGUUCAUGUCCCACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AF100309.1/1849-1909 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AB073858.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUAGGGCAUGGACA
AB064310.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUAGGGCAUGGAUA
AF297621.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUAGGGCAUGGACA
AY123041.1/1721-1781 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
X75658.1/1847-1907   UGUUUAUGUCCCACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AY090454.1/1850-1910 UGUUCAUGUCCCACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
X65259.1/1849-1909   UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUAGGGCAUGGACA
AF223965.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
X02763.1/35-95       UGUACAUGUCCCACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AF160501.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUAGGGCAUGGAUA
AB014381.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUAGGACAUGGACA
X51970.1/1847-1907   UGUACAUGUCCCACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
D00329.1/1847-1907   UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
AF405706.1/1847-1907 UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUAGGGCAUGGAUA
AM282986.1/1847-1907 UGUACAUGUCCCACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
V01460.1/1338-1278   UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
X04615.1/1847-1907   UGUUCAUGUCCUACUGUUCAAGCCUCCAAGCUGUGCCUUGGGUGGCUUUGGGGCAUGGACA
#=GC SS_cons         <<<<<<<<<<<<<------<<<<<<<<<<<<___>->>>>>>->>>>>>>>>>>>>>>>>>
#=GC RF              UGUuCAUGuCCcACUGUUCAAGCCuCCAAGCUGUGCCUUGGgUGGCUUUgGGgCAUGgACA
//
# STOCKHOLM 1.0

#=GF AC   RF01050
#=GF ID   Sacc_telomerase
#=GF DE   Saccharomyces telomerase
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:15242611
#=GF SS   Published; PMID:15242611
#=GF GA   80.00
#=GF TC   102.90
#=GF NC   37.40
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00004
#=GF DR   URL; http://telomerase.asu.edu/;
#=GF DR   SO; 0000390; telomerase_RNA;
#=GF RN   [1]
#=GF RM   15242611
#=GF RT   A phylogenetically based secondary structure for the yeast telomerase RNA.
#=GF RA   Dandjinou AT, Lévesque N, Larose S, Lucier JF, Abou Elela S, Wellinger RJ
#=GF RL   Curr Biol. 2004;14:1148-1158.
#=GF RN   [2]
#=GF RM   18073191
#=GF RT   The telomerase database.
#=GF RA   Podlevsky JD, Bley CJ, Omana RV, Qi X, Chen JJ
#=GF RL   Nucleic Acids Res. 2008;36:D339-D343.
#=GF WK   Telomerase_RNA_component
#=GF SQ   13


AM296234.1/1-1165          CAAAGGAAGAUAGGUAACCUAUUAAGAUGUC-AGCGGCUGUUGCGUUUGCUUAGUUGUUUUUUUUUUU-----AGUAU-UU-GUUUUUUGUACAUUUUCCGUUUGAAUUUUCUAUCAUGCAAGCCUCAGAGAUUUGGUAGAUGCUUAAUGAUGUAAAGGUUGCGUUGAAUUUUGAAUUGUUCUCUCAAGUUAGCAGGCAG-GUGCAC---UUUUCUCUUU-UACGAAGGACUUCGAGUGCACUGGGGUCAGCAUAGAUA-CUUGUGUGUAUAUAUAUU-UGUGGUUU-UUGUUAUUUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUU-GAAAGAUGGC--CACCAUAAAUUCUUAAAA-GUGGUAUCGCAUUUAGCCCCC---------------------------------------CUUC-GUACCAAUUCUGUUUUC-GUCUCAAGCUCUUCAUUA--CUACAGCG--------CA-AGUCUACCAUUACCACACCCACACACAGAUAUCACGGCUAAU-GUUUAUUAGUUAAGUUUCCAUGAGCUCACUCUUUAUUCUUUUCCUCGUUUUCUUAUACCUAGUAUGUUUUCUGACGCUUUUUGAAGUGACAGAAAAAA---GGAGUUUA-AAUUAGAUUUGCAAA-CGGACGGUACUA--AAUACCGUCACU-UUUACGUCUAACUUAUCGUUAACUCUGCAAAAAGAAAACAAGAAAAAGAAAA-UCAGUGAAUA-GGAGUAUAU---AUAGAAAUGGUUUAUUCUAU--------UUUUUUUUCGUUUUU-CAGUAGAUUUUCGCCUUUAAA-AGAAUAAAUUCCAUU----AAAAAAAGGUAAAAAGAAAAAUCUAUUCACUGAACUUGC-CGAUAGAAUUUGCAAAUGUGUCAAGUGCAUC-AAGGAGAAGAU----AGAGG-AGAAACUCGAUUAGGCAAACAAGCCAAAAGGCAAGGAUAC-CCC-------------------UUCUCAAGCAUUG-UUAGGUUUAUGGGCUACCAGUAAGCG-----AAAAAUGAUACAGGACGAAAAAAACAUAAUUCGAGAUUUUUCAG-GAUGGAUUUUUUUAGGUAU--CUAUCAAAA-CUAUU-CUGAUGA-UCAAUACAGUAUUUUUGU-CGCAUUAUUAUUACGGUA-GU-GUAGACAUUAGUUUCCAAGCGGAAGAAACUGUGUGUUCAUUUUAUGGAUUUU-CGUGUUGUACGAUUUUUUUCAGUUGCGUUAGCAACUAC-G--UGCCCACAAUACU--UCCGAUGCAUUUAGAUAAUUUUUGGAAA--CA-UU
AY639010.1/1-1163          UAGAGGAAGAUAGGUAGCCUAUUAAAAUGUC-AGCGGCUGUCGCGUUUGCUUAGUUG--UUUUUUUUU-----AGUAU-UU-GUCGUCUGUACAUUUUCCGUUUGAAUUUUCUAUCAUGCAAGCCUCAGAGAUUUGGUAGAUGCUUAAUGAUGUAGAGGUUGCGAUGAAUUUUGGAUUGUUCUCUCAAGUUAGCAGGCAG--GUCAC---UUUUCUCUUU-UACGAAGGACUUCGAGUGCACUGGGGUCAGCAUAGAUA-CUUGUGUGUACGUAUAUU-UGUGGUUU-UUGUUAUUUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUU-GAAAGGUGGC--CACUAUAAAUUCUUAAAAAGUGGCACCGCAUUUAGCCCCC---------------------------------------CUUC-GUACCGAUUCUGUUUUC-GUCUCAAGCUCUUCAUUA--CUACAGCG--------CA-AGUCUACCAUUACCACACCCACACACAGAUAUUACGGCUAAU-GUUUAUUAGUCAAGUUUCCAUGAGCUCACUCUUUAUUCUUUUUCUCGUUUUCUUAUACCUAGUAUUUUUUCUGACGCUUUUUGAAGUGACAGAACAAA---GGAGUUUA-AAUUAGAUUUGCAAA-CGGACGGAACUA--AAUACUGUCACU-UUUAUGUCUAACUUAUCGUUAACUCUGCAAAAAGAAAAUAAGAAAAAGAAAA-UCAGUGGAUA-GGAGUAUAU---AUAGAAAUGAUUUAUUCUAG--------UUUUUUUUCGUUUUU-CAGUAGAUUUUCGCCUUCAAA-GGAAUAAAUUCCAUU----AAGAAAAGGUAAAAAGAAAAAUCUAUUCACUGAACUUAC-UGAUAGGAUUUGCAAAUGUGUCAAGUGCAUC-AAGGAGAAGAU----AGAGG-AAAAACCU-AUUAGGCAAACAAGCCAAAAGACAAGGAUAC-CCU-------------------UUCUCAAGCAUUG-UUAG-UUUAUGGGCUACUAGUAAGCG-----AAGAAUGAUACAGGAUGAAAAAAACAUAUUAUGAGAUUUUUCAG-GAUGGAUUCUUUUAGGUAU--CUAUCGAAA-CCAUU-CUGAUGA-UCAAUACAGUAUUUUUGU-CGCAUUCUUAUUACGGUACGU-GCARACAUUAGUUUCCAAGCGGAAGAAACUGUGUGUUCAUUUUAUGGAUUUU-CGUGUUGUACGAUUUUUGUCAGUUGCCUCAACAACUAC-G--UGCCCACAAUACU--UCCGAUGCAUUCAGAUAAUUUUUGGAAA--CAUUU
AY639011.1/1-1215          AUGAGGAAGAUGCGUCGCCUAUUAAAAUGUCUGGCGGCUGUUACAUUUGCUUUCUAGCACUUUUCUAUUCU--CGUUU-CC-UUUUUUUGUACCUUCCCCUUUUGAAUUUUCCAUCGUAUAAGCCUCAGAAAUUUGGUAGACACUUAAUGAUGAAUAGGUUGGGUUAGAUUU-GAUUUGAGAUCUUGAGUCACCAGGCAGUCCCAA-------UUUUUUU-UACGAAAUAUUAGGAGUGUGCUGAUGUCAGCAUAGAUG-AUGUAUUAUACAUGUUUUGUGUGGUU---UGCUAUAUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUU-GAGA-GCAGCA-UGCCACAGAUGCUUGGAUUUUACUAUUGGAUUUUGCUGCCGGAAUAGGGCUU-UCGGGACACUUA------UUCCUUUGCUUAAG-ACCAACUCUGUUUUC-GCCUUUGCCCCUUCAUCA--UUA---UA---CAAAAU---GUCUACCAUUACCACACCCACACAUUGAUAUUAUGACUAAUUGUUUAUUAGCUAAGUUCCCAU-G-GCCACUUUUUACU-UUUUUCUCAUUUUCUUAUUUUUAUUAUAUUUUCUGUCACUUCU-GAAGUGACGGAAAAGA---GGAGUUUG-AAUUAGAUUUGCAAAACGGGCGGUAUCAAGAAUACUGUCACUCUAUAUGUCUAAUUUAUCGUCAACUCUGCAAAAAGAAAAUAGGAAGAAGAAAA-UAGGCGGAUA-AGAGUAUAU---AGAGAAAUGAUUUAUUCUAUUUUU-UUUUUCUUUUUCGUUUUU-CAGUAGAUUUUUGCCUUUCGAGAGAAUAAAUUCCACU------AAAAAGGGUUAAAGAAAAAUCUAUUCACUGAACUUAU-UGAUGAAAACUUUAAAUGCGUCAAGUACAUCAAAAGAGGAAAC----AGAGGGAAAGAACCAGGUUGGCAAACAAGCAAAAAGGCAAGGACGAACCU-------------------UCCUCAAGCACUGAAU-GUUUUGCGAGUGAAUGGUAAGCGCGAGAAAUGAUGAUACAAGUUG-AAAAGACAUAAUUUGAGAUUUUUCAA-AAUAGAUUAUUUUAGACAU-CCUACUUUAAUCAUUU-UUGAUGAAUCAAUACGGUAUUUUUGU-CGCUUCCUUAUUACAGUAA-U-GCAGACAUUAACUUCUGAGCGGAAGGAACCGUGUGUUCAGUUUAUGGAUUUU-CGUGUAAAGCGUUUUUU--CGGUUGCGAUAGCAGUUACUUACUUUCCUCGAUGCC--UUUGAUGCAUUCAGAUAAUUUUUGGAA---CAUUU
AY639012.1/1-1215          AUGAGG-AGGUCGGUUACCUAUUAAGAUGUC-CAUGGUCGUCACGUUUAGUUACUAGUAUUUUUUCUCUUU--UGUUU-CU-GUUUUUUGUGCAUUUUCCAUUUGAGUUUUCUAUUGU-UGAGCCUCAGAUAUUUGGUAGACGCUUAAUGGUGGAAUGAUUGGACCGGAUUUAGGGUUGUGUUCUCAGAUUGGCGGGCAGUUACACUGGUUGUUGUUUUUUAACGAAGGGCUAUGAGUGCGCUGGUGUCAGUGUAGAUA-CAUAUGUAUGCG--UACA-UGUGGUUU-UUGUUGUUCUUCUACUUAUAGAUCGCU-----------------AAAAUCUGAGUUU-GA-GAAAUGCGGGACCAUCCAUGUCCGAAUAUAACUGACGCAUUUUGUAGCUAGAACACGUUUU-UCCUACAA-UUA------UCCCGCUCCUCUUAGAAAAAUUCUGCUUUC-ACUCCAA-CUCUUCAUCA--UUU---UAUAAGAAUUU---GUCUACCAUUACCACACCCACACACAAACAUUACGGCUAGUAGUUUAUUAGUCAAAUUUCCAUGGCCACACAUUUUGUC-UUUUUCUCGUUUUCUUAU------UGUGUUUUCUGUCACUGUG-AAAGUGACGGAGAAAA--AGGAGUUUGGAAUCAGAUUUGCAAAACGGGCUGUAUCAAUAAUACUGUCAUUCCUAAUGUCUGAUUCAUCGUCAACUCUGUAAAAAGAGAACAAGAAAGGDAAAA-UUGAUGGGCA-AAAGUAUAU---AUAGAAAUGGUUUAUUCCCG---------UUUUUUCCAUUUCU-CAGUAGAUUUUUCCCUUUUGCGAGAAUAAAUUGACACUUGAACAAAAAGCUUCGAAGAAAAAUCUAUUCACUGAACUUAUAU-AUAGAAAAAUCAAAUGUGCUAAGUAUAUUUAAAAUGGAAACAAAUAGGGGGAAAGAGAUAGGUAGAUAAACAGCCCAAGGGACAAGGACAC-CCU-------------------UCCUCAGGCACUGAAUAUAUUGGAGAGUGGACAGUAACAG-----AGAAAUGAUACAAGAUG-GAAAGCCAUAAAUUGAGAUUU-UCUUGAAUGGGUUCAUUUAGAUAUUUCUC-UUUAGCCAUUU-UUGAUAA-UCAAUACAGUAUUCUUGUUCCCAUCCUUGUCAGAUUAAGGAAGGAACAUUAAUU-CCAAACAGGAAAAACUGUGUGUUCACUUCGUGGGUUUG-CGUGUUGUACAUUUC-CUUCAUCCGUGUUGGCGGUUACUU--UCCUCAAUAUACC--UUCAGUGCAUACA---AAUUUUUGGAA---CAAUU
U14595.1/11-1168           GAGAGGAAGAUAGGUACCCUAUGAAAAUGUC-AAUGGCUGUUGCGUUUGCUUAAUCGUAUUUUUUUUUUUUUCAGUCC-GU-GUUUUUUGUACAUUCUACGUUUGAGUUUUCCAUCAUGCAGGCCUCAGAAAUUUGGUAGGCACUCGAUGGUGAAGAGAUAGUGUCGGAUUUCGGAUUGAUCUUUCA-GUUGAUAGCCUGC-UGCUC---UUUUCUUU---UCCAAAGAAUUUCGAGUAUGCUGGUGUCAGUGUAGAUG-CUUGUGUGUGCGCA-AUU-UGUGGUUUUUUAUUGUGUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUUAGAAA-AUGCA--AACCGUAAAUUCUUAAACACUGCUAUUGCAUUUAGUUGCUAAAGCAGUGUUU-UUGAACUUAUUCCUGUUAUUCCUU--CUUC-GUACCGAUCCUCUUCUC-GACCUAACCUUUUAAUUACCAUG---GG--------A--AGCCUACCAUCACCACACCCACACACAAAUGUUACAGCUAAUUGUUUAUUAGCAAAGUUUGCACGAGUUCGCUGUUUAUU-UUUUUCUCGUUUUCUUAUACCUAGUAUUUUUUCUGACACUGUUUAAGGUGACAGAAAAAA--AGGAGUUUA-AGUUAGAUUUGCAAA-CAGACGGUGCUA--AGCGCUGUCAC--UUUAUGUCUAUCUUAUCGUUAACUCUGGAAAAAGAAAAA-GGAAAAAGAACG-UCAGGGAACA-UGAGUAUAU---AUAGAAAUGGUUUAUUCUAG---------UUUUUUCCGUUUUUUCAGUAGAUUUUUGCCUUUAAA-AGAAUAAAUCCCACU----ACAAAAAGGUAAAAUAAAAAAUCUAUUCACUGAACUUAC-UGAUGAAAUUUCCAAAUGUGCCCCGUACAUCGAACGAUGUGAC----AGAG--AAAAAUACGAGUAGGUAAAUAAGCCAAAAGGCAAGGGUGU-CCU-------------------UUCUUAAGCAUCGGUUAGGUUUGCGGGCGAUCAGUAACUG-----AACAAUGACACAAGAUC--AAGAACGUAAUUUGAGAUUUUUCAA-GAUGG-UUUUUUUAGGUAU--CUAUUAAAA-CUACU-UUGAUGA-UCAAUACGGUAUUUUUGU-CGCAUU-------------------------AUUUUCCAAGCGGAAGGAACCGUGUGUUCAUUUUAUGAAUCUU-GGUGUUGUAU--------UCA----------CAGCUACU---UCUCC-UAAUGCC--UUCGAUGCAUUUAGAUAAUUUUUGGAAA--CAUUU
AY639013.1/1-1219          GAGAGGAAGGU-AGUAACCUAAUAAUACGUC-AGCGACUGGUAUGUUUGCCUGCCCUUUUUUUA----------UUUU-GCUUGUCAAUGUAUUUUUUCCAUUUGAGUUUUCUGUUG-AUAAGCCUCAGAGUUUUGGUAGGCGCCUAGUGGUGGAAUGGUUGGGCUGGAAUCGGAAUUGAGAUGUGAUGUUAACGGGCCAUCGUGCA---UCUUUUUUAAAUUUUGAGCAAUUUGAGUACGCUAGUGCCACUAUGCAUGUUUCAUGUAUACAUGUAUG-CGCGGUUU-CUGUUCUUGUCGUACUUAUAGAUCGCUACGUUAUUUCAAUUUUGAAAAUCUGAGUCC-UGG-GAGUGCGGAGCCAUGCAUACAUGUACUUUAUUGUUGCAUAGUAUUGCUAGAGUACACUUU-CUCCAUGA-UUGU---CUGU-CUU--CUUUA-CACCAGUUCUGUUUUCUGUCUUAACCUCUUCACUA--UCA---UG---GAAAGU---UUCUACCAUUACCACACCCACACACGAACAUUAAGGCUAAUCGUU-AUUAGUUCAAUCUCCAU-A-GCCACACUC-------UUUUUUUCUUCC----------AAUAUUUUCCGUCGCUUUC-CAAGUGACAGAAAAAA-AAGGAGUUUG-AAUUAGGCUUGCAAAAGGGACAAUAUAUAUGAUACUGUCACUCCUAAUGUCUAAUUUAUCGUCAACUCUGUAA--AGGAAGCAAGAAAGAGAAAGGUUGCUGGAAAUAAAAUUUGUACAAACAAGACGGUUUAUUCUAG----------UUAUUCCAUUUUU-CAGUAGAUUUUUGCCUUUUACUAGAGUCAAUUUAACCA--GUAUAAAAGGUUCAAGGAAAAAUCUAUUCACUGAACUUAU-CA--CGAAACCUCAAAUGUGUCAGACGCAUUAAAAAGAUAAAU----------CAAAAAAACGGUAUGCAAGCGAGUCAAAAGACUGGUACUC-CCUUCGUUUCCUGUCCCAUUUUGCCUCAAGCAUUGAAUAAGUUUGCGAGCGAAUAAUAACCG----GGGAAAUGAUACAA-GAG-AAAAUCCAUAAUUUGGGAUCU-UCUUGGAUGGAUUCAUUUAUGUAU--UUAUUUG--CUCAUUUUUGAGGA-UCAAUACAAUAUUCUUGU-CCUAUCCUUGCUAAAGUAAAGAACGGGCAUUAAUUUCUGAACGGAAAGAAUUGUGUGUUCACUUUAUGG--UUUUCGCAUUGUACAUUUUUC--AACUUGCAUGAGCAG--UCGG--UUUCCUCAAUACUUUUUCGGUGCUUACGAAUAAUUUUUGGAACUUCAAUU
AY639014.1/1-1196          GAGAGGAAGGU-GGUAACCUAAUAACACGUC-AGCGACUGGUAUGUUUGCUUGCCCUUUUUUAA----------UUUG-CU-UCUCAAUGUAUUUUUUCCAUUUGAGUUUUCUGUUG-AUAAGCCUCAGAGUUUUGGUAGGCGCCUAGUGGUGGAACGGUUGAGCCGGAAUCGCGAUUGAGAUGUGAUGUUAGUGGGCCAUUGUGCA---UCUUUUUUAUAUUUUGGGCAAUGCGAGCACGCUAGUGCCA-----------------------GUAUG-CGCGGUUU-CUGUUCUUAACGUACUUAUAGAUCGCUACGUUAUUUCAUUUUUGAAAAUCUGAG-CC-CGGGGAGUGCGGAUCCAUACAUACAUGUAAUUUGUUGUUGC-AGUAUU-GCUAGAGUACAUUUUUCUCCGCGA-UUGU---CUGU-CUU--CUUUA-CACCAGUUCUGUUUUCCGUCUCAACCUCUUCAUUA--UUA---UG---GAAAGC---AUCUACCAUUACCACACCCACACACGAACGUUAAGGCUAAUCGUU-AUUAGUUGAAUCUCCAUA-----GCCAAG-----CUCUUUUUUUUUUC----------AAUGUUUUCCGUCGCUUUC-CAAGUGACAGAAAAAA--AGGAGUUUG-AAUUAGGCUUGCAAAAGGGGCAAUAUCAAUGAUACUGUCACCCUUAAUGUCUGAUUUAUCGUCAACUCUGUAA--AGGAAACAAGAGAGAGAAAGGUUGGUGGAGAUUAAAUCUGUAGAAAGAGGAAGGUUUAUUCUAG----------UUAUUCCAUUUUU-CAGUAGAUUUUUGCCUUUUACUAGAAUUAAUUUAACCA--AUAUAAAAGGUUCAAGGAAAAAUCUAUUCACUGAACUUAU-UA--GAAAACCUCAAAUGUGUUGGAUGCAUUGAAAAGAUUAAC----CAAA---AAAAAAAAGGCACGCAAGCAGGUCAAAAGACUAGGACUC-CCUUCGUUUCCUUUCCCAUUUUGCCUCAAGCAUCGAAUAAGUUUGCGAGCAAAACAUAACCG----GGCAAAUGUUACAA-GAG-AAAAUACAUGAUUUGGGAUCU-UCUUGGAUGGAUUUGUUUACAUAUUUCU--UUACUCAUUUU-UUGAGGA-UCAAUACAAUAUUCUUGU-CCCAUCCUUGCUAAAGUAAAGAACGGGCAUUAAUUUCCGAACAGAAAGAAUUGUGUGUUCACUUUAUGG--UUUUCGCAUUGUACUUUUCCU---ACUUGCAUUAGCAGUUGUUU--GGCUCACUACUUU-UUUCGAUGCUCACGAAUAAUUUUUGGAACCUCAUUU
AABY01000040.1/50453-51617 CAAAGGAAGAUAGGUAACCUAUUAAAAUGUC-AGCGGCUGUUGCGUUUGCUUAGUUGUUUUUUUUUUU-----AGUAU-UU-UUUUUUUGUACGUUUUCCGUUUGAAUUUUCUAUCAUGCAAGCCUCAGAGAUUUGGUAGAUGCUUAAUGAUGUAAAGGUUGCGUUGAAUUUUGGAUUGUUCUCUCAAGUUAGCAGGCAG-GUGCAC---UUUUCUCUUU-UACGAAGGACUUCGAGUGCACUGGGGUCAGCAUAGAUA-CUUGUGUGUACGUAUAUU-UGUGGUUU-UUGUUAUUUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUU-GAAAGAUGGC--CACCAUAAAUUCUUAAAA-GUGGUAUCGCAUUUAGCCCCC---------------------------------------CUUC-GUACCAAUUCUGUUUUC-GUCUCAAGCUCUUCAUUA--CUACAGCG--------CA-AGUCUACCAUUACCACACCCACACACAGAUACCACGGCUAAU-GUUUAUUAGUUAAGUUUCCAUGAGCUCACUCUUUAUUCUUUUCCUCGUUUUCUUAUACCUAGUAUGUUUUCUGGCGCUUUUUGAAGUGACAGAAAAAA---GGAGUUUA-AAUUAGAUUUGCAAA-CGGACGGUACUA--AAUACCGUCACU-UUUACGUCUAACUUAUCGUUAACUCUGCAAAAAGAAAACAAGAAAAAGAAAA-UCAGUGAAUA-GGAGUAUAU---AUAGAAAUGGUUUAUUCUAU---------UUUUUUUUGUUUUU-CAGUAGAUUUUCGCCUUUAAA-AGAAUAAAUUCCAUU----AAAAAAAGGUAAAAAGAAAAAUCUAUUCACUGAACUUGC-UGAUAGAAUUUGCAAAUGUGUCAAGUGCAUC-AAGGAGAAGAU----AGAGG-AAAAACUCGAUAAGGCAAACAAGCCAAAAGGCAAGGAUGC-CCU-------------------UUCUCAAGCAUUG-UUAGGAUUAUGGGCUACCAGUAAGCG-----AAAAAUGAUACAGGACAGAAAAAACAUAAUUCGAGAUUUUUCAG-GAUGGAUUUUUUUAGGUAU--CUAUCAAAA-CUAUU-CUGAUGA-UCAAUACAGUAUUUUUGU-CGCAUUACUAUUACGGUA-GU-GCAGACAUUAGUUUCCAAGCGGAAGAAACUGUGUGUUCAUUUUAUGGAUUUU-CGUGUUGUACGAUUUUUUUCAGUUGCGUUAGCAACUAC-G--UGCCCACAAUACU--UCCGAUGCAUUUAGAUAAUUUUUGGAAA--CAUUU
AABZ01000048.1/19811-18596 AUGAGGAAGAUGCGUCGCCUAUUAAAAUGUCUGGCGGCUGUUACAUUUGCUUUCUAGCACUUUUCUAUUCU--CGUUU-CC-UUUUUUUGUACCUUCCCCUUUUGAAUUUUCCAUCGUAUAAGCCUCAGAAAUUUGGUAGACACUUAAUGAUGAAUAGGUUGGGUUAGAUUU-GAUUUGAGAUCUUGAGUCACCAGGCAGUCCCAA-------UUUUUUU-UACGAAAUAUUAGGAGUGUGCUGAUGUCAGCAUAGAUG-AUGUAUUAUACAUGUUUUGUGUGGUU---UGCUAUAUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUU-GAGA-GCAGCA-UGCCACAGAUGCUUGGAUUUUACUAUUGGAUUUUGCUGCCGGAAUAGGGCUU-UCGGGACACUUA------UUCCUUUGCUUAAG-ACCAACUCUGUUUUC-GCCUUUGCCCCUUCAUCA--UUA---UA---CAAAAU---GUCUACCAUUACCACACCCACACAUUGAUAUUAUGACUAAUUGUUUAUUAGCUAAGUUCCCAUG--GCCACUUUUUACU-UUUUUCUCAUUUUCUUAUUUUUAUUAUAUUUUCUGUCACUUCU-GAAGUGACGGAAAAGA---GGAGUUUG-AAUUAGAUUUGCAAAACGGGCGGUAUCAAGAAUACUGUCACUCUAUAUGUCUAAUUUAUCGUCAACUCUGCAAAAAGAAAAUAGGAAGAAGAAAA-UAGGCGGAUA-AGAGUAUAU---AGAGAAAUGAUUUAUUCUAUUUUUUUUUUUCUUUUUCGUUUUU-CAGUAGAUUUUUGCCUUUCGAGAGAAUAAAUUCCACU------AAAAAGGGUUAAAGAAAAAUCUAUUCACUGAACUUAU-UGAUGAAAACUUUAAAUGCGUCAAGUACAUCAAAAGAGGAAAC----AGAGGGAAAGAACCAGGUUGGCAAACAAGCAAAAAGGCAAGGACGAACCU-------------------UCCUCAAGCACUGAAU-GUUUUGCGAGUGAAUGGUAAGCGCGAGAAAUGAUGAUACAAGUUG-AAAAGACAUAAUUUGAGAUUUUUCAA-AAUAGAUUAUUUUAGACAU-CCUACUUUAAUCAUUU-UUGAUGAAUCAAUACGGUAUUUUUGU-CGCUUCCUUAUUACAGUAA-U-GCAGACAUUAACUUCUGAGCGGAAGGAACCGUGUGUUCAGUUUAUGGAUUUU-CGUGUAAAGCGUUUUUU--CGGUUGCGAUAGCAGUUACUUACUUUCCUCGAUGCC--UUUGAUGCAUUCAGAUAAUUUUUGGAA---CAUUU
AAEG01000107.1/89228-88071 GAGAGGAAGAUAGGUACCCUAUGAAAAUGUC-AAUGGCUGUUGCGUUUGCUUAAUCGUAUUUUUUUUUUUUUCAGUCC-GU-GUUUUUUGUACAUUCUACGUUUGAGUUUUCCAUCAUGCAGGCCUCAGAAAUUUGGUAGGCACUCGAUGGUGAAGAGAUAGUGUCGGAUUUCGGAUUGAUCUUUCA-GUUGAUAGCCUGC-UGCUC---UUUUCUUU---UCCAAAGAAUUUCGAGUAUGCUGGUGUCAGUGUAGAUG-CUUGUGUGUGCGCA-AUU-UGUGGUUUUUUAUUGUGUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUUAGAAA-AUGCA--AACCGUAAAUUCUUAAACACUGCUAUUGCAUUUAGUUGCUAAAGCAGUGUUU-UUGAACUUAUUCCUGUUAUUCCUU--CUUC-GUACCGAUCCUCUUCUC-GACCUAACCUUUUAAUUA--CCA---UG--------GGAAGCCUACCAUCACCACACCCACACACAAAUGUUACAGCUAAUUGUUUAUUAGCGAAGUUUGCACGAGUUCGCUGUUUAUU-UUUUUCUCGUUUUCUUAUACCUAGUAUUUUUUCUGACACUGUUUAAGGUGACAGAAAAAA--AGGAGUUUA-AGUUAGAUUUGCAAA-CAGACGGUGCUA--AGCGCUGUCAC--UUUAUGUCUAUCUUAUCGUUAACUCUGGAAAAAGAAAAA-GGAAAAAGAACG-UCAGGGAACA-UGAGUAUAU---AUAGAAAUGGUUUAUUCUAG---------UUUUUUCCGUUUUUUCAGUAGAUUUUUGCCUUUAAA-AGAAUAAAUCCCACU----ACAAAAAGGUAAAAUAAAAAAUCUAUUCACUGAACUUAC-UGAUGAAAUUUCCAAAUGUGCCCCGUACAUCGAACGAUGUGAC----AGAG--AAAAAUACGAGUAGGUAAAUAAGCCAAAAGGCAAGGGUGU-CCU-------------------UUCUUAAGCAUCGGUUAGGUUUGCGGGCGAUCAGUAACUG-----AACAAUGACACAAGAUC--AAGAACGUAAUUUGAGAUUUUUCAA-GAUGG-UUUUUUUAGGUAU--CUAUUAAAA-CUACU-UUGAUGA-UCAAUACGGUAUUUUUGU-CGCAUU-------------------------AUUUUCCAAGCGGAAGGAACCGUGUGUUCAUUUUAUGAAUCUU-GGUGUUGUAU--------UCA----------CAGCUACU---UCUCC-UAAUGCC--UUCGAUGCAUUUAGAUAAUUUUUGGAAA--CAUUU
AY737252.1/615-1829        AUGAGG-AGGUCGGUUACCUAUUAAGAUGUC-CAUGGUCGUCACGUUUAGUUACUAGUAUUUUUUCUCUUU--UGUUU-CU-GUUUUUUGUGCAUUUUCCAUUUGAGUUUUCUAUUGU-UGAGCCUCAGAUAUUUGGUAGACGCUUAAUGGUGGAAUGAUUGGACCGGAUUUAGGGUUGUGUUCUCAGAUUGGCGGGCAGUUACACUGGUUGUUGUUUUUUAACGAAGGGCUAUGAGUGCGCUGGUGUCAGUGUAGAUA-CAUAUGUAUGCG--CACA-UGUGGUUU-UUGUUGUUCUUCUACUUAUAGAUCGCU-----------------AAAAUCUGAGUUU-GA-GAAAUGCGGGACCAUCCAUGUCCGAAUAUAACUGACGCAUUUUGUAGCUAGAACACGUUUU-UCCUACAA-UUA------UCCCGCUCCUCUUAGAAAAAUUCUGCUUUC-ACUCCAA-CUCUUCAUCA--UUU---UAUAAGAAUUU---GUCUACCAUUACCACACCCACACACAAACAUUACGGCUAGUAGUUUAUUAGUCAAAUUUCCAUGGCCACACAUUUUGUC-UUUUUCUCGUUUUCUUAU------UGUGUUUUCUGUCACUGUG-AAAGUGACGGAGAAAA--AGGAGUUUG-AAUCAGAUUUGCAAAACGGGCUGUAUCAAUAAUACUGUCAUUCCUAAUGUCUGAUUCAUCGUCAACUCUGUAAAAAGAGAACAAGAAAGGAAAAA-UUGAUGGGCA-AAAGUAUAU---AUAGAAAUGGUUUAUUCCCG---------UUUUUUCCAUUUUU-CAGUAGAUUUUUCCCUUUUGCGAGAAUAAAUUGACACUUGAACAAAAAGCUUCGAAGAAAAAUCUAUUCACUGAACUUAUAU-AUAGAAAAAUCAAAUGUGCUAAGUAUAUUUAAAAUGGAAACAAAUAGGGGGAAAGAGAUAGGUAGAUAAACAGCCCAAGGGACAAGGACAC-CCU-------------------UCCUCAGGCACUGAAUAUAUUGGAGAGUGGACAGUAACAG-----AGAAAUGAUACAAGAUG-GAAAGCCAUAAAUUGAGAUUU-UCUUGAAUGGGUUCAUUUAGAUAUUUCUCUUUAGC-CAUUU-UUGAUAA-UCAAUACAGUAUUCUUGUUCCCAUCCUUGUCAGAUUAAGGAAGGAACAUUAAUU-CCAAACAGGAAAAACUGUGUGUUCACUUCGUGGGUUUG-CGUGUUGUACAUUUCCU-UCAUCCGUGUUGGCGGUUACUU--UCCUCAAUAUACC--UUCAGUGCAUACA---AAUUUUUGGAAC--AAUUU
AY547299.1/91-1310         GAGAGGAAGGU-AGUAACCUAAUAAUACGUC-AGCGACUGGUAUGUUUGCCUGCCCUUUUUUUA---------UUUU-GCU-UGUCAAUGUAUUUUUUCCAUUUGAGUUUUCUGUUG-AUAAGCCUCAGAGUUUUGGUAGGCGCCUAGUGGUGGAAUGGUUGGGCUGGAAUCGGAAUUGAGAUGUGAUGUUAACGGGCCAUCGUGCA---UCUUUUUUAAAUUUUGAGCAAUUUGAGUACGCUAGUGCCACUAUGCAUGUUUCAUGUAUACAUGUAUG-CGCGGUUU-CUGUUCUUGUCGUACUUAUAGAUCGCUACGUUAUUUCAAUUUUGAAAAUCUGAGUCC-UGG-GAGUGCGGAGCCAUGCAUACAUGUACUUUAUUGUUGCAUAGUAUUGCUAGAGUACACUUU-CUCCAUGA-UUGU----CUGUCUU--CUUUA-CACCAGUUCUGUUUUCUGUCUUAACCUCUUCACUA--UCA---UG---GAAAGU---UUCUACCAUUACCACACCCACACACGAACAUUAAGGCUAAUCGUU-AUUAGUUCAAUCUCCAUAGCCACACUCUU---------UUUUUCUUCC----------AAUAUUUUCCGUCGCUUUC-CAAGUGACAGAAAAAAAAAGGAGUUUG-AAUUAGGCUUGCAAAAGGGACAAUAUAUAUGAUACUGUCACUCCUAAUGUCUAAUUUAUCGUCAACUCUGUAA--AGGAAGCAAGAAAGAGAAAGGUUGCUGGAAAUAAAAUUUGUACAAACAAGACGGUUUAUUCUAG----------UUAUUCCAUUUUU-CAGUAGAUUUUUGCCUUUUACUAGAGUCAAUUUAACCA--GUAUAAAAGGUUCAAGGAAAAAUCUAUUCACUGAACUUAU-CA--CGAAACCUCAAAUGUGUCAGACGCAUUAAAAAGAU-AAA----U-----CAAAAAAACGGUAUGCAAGCGAGUCAAAAGACUGGUACUC-CCUUCGUUUCCUGUCCCAUUUUGCCUCAAGCAUUGAAUAAGUUUGCGAGCGAAUAAUAACCG----GGGAAAUGAUACAA-GAG-AAAAUCCAUAAUUUGGGAUCU-UCUUGGAUGGAUUCAUUUAUGUAU--UUAUUUGCU-CAUUU-UUGAGGA-UCAAUACAAUAUUCUUGU-CCUAUCCUUGCUAAAGUAAAGAACGGGCAUUAAUUUCUGAACGGAAAGAAUUGUGUGUUCACUUUAUGG-UUUU-CGCAUUGUACAUUUUUC--AACUUGCAUGAGCAGUCGGUU--UCCUCAAUACUUU--UUCGGUGCUUACGAAUAAUUUUUGGAACUUCAAUU
BK006936.2/307597-308754   GAGAGGAAGAUAGGUACCCUAUGAAAAUGUC-AAUGGCUGUUGCGUUUGCUUAAUCGUAUUUUUUUUUUUUUCAGUCC-GU-GUUUUUUGUACAUUCUACGUUUGAGUUUUCCAUCAUGCAGGCCUCAGAAAUUUGGUAGGCACUCGAUGGUGAAGAGAUAGUGUCGGAUUUCGGAUUGAUCUUUCA-GUUGAUAGCCUGC-UGCUC---UUUUCUUU---UCCAAAGAAUUUCGAGUAUGCUGGUGUCAGUGUAGAUG-CUUGUGUGUGCGCA-AUU-UGUGGUUUUUUAUUGUGUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUUAGAAA-AUGCA--AACCGUAAAUUCUUAAACACUGCUAUUGCAUUUAGUUGCUAAAGCAGUGUUU-UUGAACUUAUUCCUGUUAUUCCUU--CUUC-GUACCGAUCCUCUUCUC-GACCUAACCUUUUAAUUA--CCA---UG--------GGAAGCCUACCAUCACCACACCCACACACAAAUGUUACAGCUAAUUGUUUAUUAGCAAAGUUUGCACGAGUUCGCUGUUUAUU-UUUUUCUCGUUUUCUUAUACCUAGUAUUUUUUCUGACACUGUUUAAGGUGACAGAAAAAA--AGGAGUUUA-AGUUAGAUUUGCAAA-CAGACGGUGCUA--AGCGCUGUCAC--UUUAUGUCUAUCUUAUCGUUAACUCUGGAAAAAGAAAAA-GGAAAAAGAACG-UCAGGGAACA-UGAGUAUAU---AUAGAAAUGGUUUAUUCUAG---------UUUUUUCCGUUUUUUCAGUAGAUUUUUGCCUUUAAA-AGAAUAAAUCCCACU----ACAAAAAGGUAAAAUAAAAAAUCUAUUCACUGAACUUAC-UGAUGAAAUUUCCAAAUGUGCCCCGUACAUCGAACGAUGUGAC----AGAG--AAAAAUACGAGUAGGUAAAUAAGCCAAAAGGCAAGGGUGU-CCU-------------------UUCUUAAGCAUCGGUUAGGUUUGCGGGCGAUCAGUAACUG-----AACAAUGACACAAGAUC--AAGAACGUAAUUUGAGAUUUUUCAA-GAUGG-UUUUUUUAGGUAU--CUAUUAAAA-CUACU-UUGAUGA-UCAAUACGGUAUUUUUGU-CGCAUU-------------------------AUUUUCCAAGCGGAAGGAACCGUGUGUUCAUUUUAUGAAUCUU-GGUGUUGUAU--------UCA----------CAGCUACU---UCUCC-UAAUGCC--UUCGAUGCAUUUAGAUAAUUUUUGGAAA--CAUUU
#=GC SS_cons               :::::::::::::::::{{,,,,,,,,,[[[.---[[[[-----[[[[[[-[[[[----[[[[--------..-[[[[.--.------[[[[[------[[[[[[----------[[-[[[[[--[[[[,,,,,((((((((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<_________...__________._________________________>>>,,,,,,,,,,.,,,,,,,,,,,,,,,,,,.<<<<<<--.--<<-<<-<<<<-<<<<--<<<<____.................___>>>>>>>>--.>>>>->>->>-.->>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,.,,,......,,,,,,..,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,,,,,,,,,..,,,...,,...,,,,,,...)))))))),,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<_____>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<-<<<<___.__>>>>->>>>>>>,,..,<<<<<<--.<<<<<<<<----------<<<<-<<<_____>>>->>>>--------->>>>>>>>------->>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,.,,,,,,,,,...,,<<<<<<<<AAAAAAAA__.........______>>>>>>>>.,<<<<<<<<<<___________aaaaaaaa_______...._________________>>>>>>>>>>,,]]]]-]]]]].]]----------]]]]]]------]]]]]----------]]]]....-----.-]]]]----]]]]-]]]]]]-]]]]----]]],,,,,,,,.,,,...................,,,,,,,[[[[[[[,,,,,,,,,,,,,,,,,,,,,,,,,,.....,,,,,,,,(((((-(((.------(((((--((((,,,,,,,,,.,,,,,,,,,,,,,,,,,,,..,,,,,,,,,.,,,,,.,<<<___.>>><<<<<<<-<<<<<<<._____________________.__________________>>>>>>>-->>>>>>>,))))--)))))------.)))-))))),,,,,,,,.,,,,<<<<____>>>>,,,,,,..,,,,,,,,,,,,,..,]]]]]]],,,,,,,,,,,,,,,}}:::..:::::
#=GC RF                    aaGAGGAAGaUagGUaaCCUAuUAAaAUGuC.agcGGcuGuUacGuUUGcUugcccgUauuUuuUUuUUuU..agUuu.cU.uuUuuuUGuacaUUuUcCaUUUGAgUUUUCuAUcgUguaaGCCUCAGAaAUUUGGUAGgcgCUUAAUGgUGaAaaGgUUGgGuuGGAuUUuGgaUUGagaUcUcAaGUUaacaGgCaGUuuuaaa...UuUUuUUUuu.UacgAAGaAuUuuGAGUacGCUGGUGcCAguaUAgAUg.cUuaUGUaUaCguaUAUu.uguGGuUU.uUgcUcuuuuucUACUuAUAGAUgGCU.................AAAAUCUgAGUUU.gaaagagugcg.aaCCauaaAUuCuUgaAuauUacUaUuGCAUuUuguuGCuAgAguAcauUUU.uucuacua.UUa......uucCuU..CUUuaguACCAAUUCUGUUUUC.GuCuuAAcCUCUUcAUuA..uUA...ug...gAAaau...gcCUACCAUUACCACACCCACACACaaAuAUUAcGgCUAaUuGUUUAuUAGcuaAgUUUcCAUGaguuCACuuUUUAUU.UUUUUcUcgUUUUCUUAUaccUAguAUaUUuUCuGuCaCuuUu.aAaGuGACaGAaAAAA..AGGAGUUUg.AguuAGauUUGCAAAAcGGaCgGuauuAAuAauaCcGuCACUCuUuAUguCUaacUUAUCGUcAACUCUGuAAAAAGAAAAcAaGAAAaAGAAAa.UugguGgAuA.agAGUaUAU...AuagAaAcGGUUUAUUCUAg.........UUUuUUCCgUuUuu.CAGUAGAUUUUUGCCUUUuAauAGAAUaAAUUcaAcu....aaaAAAAGGUuaAAaGAAAAAUCUAUUCACUGAACuuac.cgAUaaAAauuuCAAAuGUGucaaguaCAUuaAAagaggaaAc....AGAGG.AaAaaaacaggcaggCAAaCAagCCAAAAGaCAAGGAcac.CCU...................ucCUCAAGCAucGaaUAggUUUGcGaGcgAauAGUAAccG.....AaaAAUGAuaCaaGgcg.AAAAaaCauaAUUuGaGAUUUUUCau.gAUGGAUUuuUUUAggUAU..CUAUUuaaa.cuuUU.UUGAuGA.UCAAuACgGUAuUuuuGu.CgCAUccUUauUAaAgUAAgu.acagaCAUUAaUUUCcaAaCggaAagAACcGUgUGUuCauUUuauGGAUUUU.cgcGuuGuaCauUUuUu.UcAucuGcgUuAgCaguUAcUu..UuucCacaAUaCu..UuCgaUGCAUucAgAUAAUUUUUGGAAa..CAuUU
//
# STOCKHOLM 1.0

#=GF AC   RF01051
#=GF ID   c-di-GMP-I
#=GF PI   GEMM_RNA_motif
#=GF DE   Cyclic di-GMP-I riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Weinberg Z
#=GF SS   Published; PMID:17621584
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0035438; cyclic-di-GMP binding;
#=GF RN   [1]
#=GF RM   17621584
#=GF RT   Identification of 22 candidate structured RNAs in bacteria using the
#=GF RT   CMfinder comparative genomics pipeline.
#=GF RA   Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER,
#=GF RA   Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR
#=GF RL   Nucleic Acids Res. 2007;35:4809-4819.
#=GF RN   [2]
#=GF RM   18635805
#=GF RT   Riboswitches in Eubacteria Sense the Second Messenger Cyclic Di-GMP
#=GF RA   Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR
#=GF RL   Science 2008;321:411-413.
#=GF CC   GEMM was predicted in a large-scale screen for bacterial structured RNA
#=GF CC   regulatory elements. Genes associated with GEMM are involved in a diverse
#=GF CC   array of functions, including chemotaxis regulation, signal transduction,
#=GF CC   secretion and chitin.
#=GF WK   Cyclic_di-GMP-I_riboswitch
#=GF **   seedtax: Bacteria; Viruses; unclassified sequences
#=GF SQ   155


CP000644.1/4016040-4015954   UAGAGUAAAGGGCAAACCGA-U-C-GAA---A-GGUCGGGACGCAAAGCCA--C-CGGUCUA-AGGGUG---UAGA---------------------------------UA-CCUAAGACAGCGG-AGCUGCCAAC
CP000141.1/90445-90359       UGUCGAUAAAGGCAAAACCG-G-C-GAA---A-GCCGGUGACGCAAAGCUA--CAGGGGCUA-AAGCGA---AUUU---------------------------------UC-GCCAUGCCAGCC--AGCUGCCGAA
AP009389.1/804550-804637     UUCCUAAAAGGGCAAACCAU-U-C-GAA---A-GAAUGGGACGCAAAACCU--U-GGGUCUA-AGGCAGC--AAAG---------------------------------CU-GCUAUGAUUGCCA-GGUUGCAGGA
CP000724.1/790814-790902     UGUUGAUAAAGGCAAACUUA-U-U-GAA---A-AAUAAGGACGCAAAGCUA--U-GGAUCUA-AGGGAAGU-UGUA---------------------------------UU-CCUAUGAUUGCCA-GGUUGCCGAA
CP000612.1/1107064-1107147   AAAAUUAAAAGGCAAACUUU-C-C-GAA---A-GGAAAGGACGCAAAGCCA--C-GGGCCUA-AGGACA---U------------------------------------UG-UCUAUGGUAGCCG-GGCCGCCUUA
CP000232.1/1536251-1536164   AUCAACAAAGGGCAAACCUG-U-C-GAA---A-GGCAGGGACGCAAAGCCA--U-GGGCCUA-AAGCCCG--ACAA---------------------------------GG-GCUAUGGUUGCCA-GGUUGCCGGU
AASZ01001000.1/4254-4168     AUAGCGAAAGGGCAAAGUCA-C-C-GAA---A-GAUGGCGACGCAAAACCG--U-GGAUCUA-AAGCCA---UUUA---------------------------------UG-GCCAAGAUAGCCA-GGUUACCGAA
CP000679.1/1202000-1202089   AUAUCGAAAGGGCAAACCUG-U-C-GAA---A-GGCAGGGGCGCAAAGCCA--U-GGGCCUG-UCGGAAG--UAAA-------------------------------ACUU-CCUAUGGUUGCCA-GGCUGCCGAA
ABCF01000005.1/23265-23355   UUAACGAAAAGGCAAACUUG-C-U-GAA---A-GGCAAGGACGCAAAACCA--C-AGAUCUA-AAGAUUG--CUAG------------------------------AGCAA-UCCAAGAUGGCUG-GGUUACCGAA
AAOX01000001.1/400824-400906 UAUUGAAAAAGGCAAACUUA-U-U-GAA---A-AAUAAGGACGCAAAGCCG--C-GAGUCUA-AGGC-----GUAA------------------------------------GCUAUGAUAGUCG-GGCUGCCAGG
CP000462.1/551681-551596     UAGAGUAAAGGGCAAACCGG-U-C-GAA---A-GGUCGGGACGCAAAGCCA--C-CGGUCUA-AGGGUU---CAU----------------------------------AA-CCUAAGACAGCGG-AGCUGCCAUC
CP000673.1/3897171-3897085   UCCGACAAAGGGCAAACUUG-C-C-GAA---A-GGUAAGGACGCAAAGCCG--A-GGGUCUA-AAGUGC---GAGA---------------------------------GC-AUUAUGACAGUCU-GGCUGCCGUA
AACY020365487.1/1679-1764    UAGAGUAAAGGGCAAACCGG-U-C-GAA---A-GGUCGGGACGCAAAGCCA--C-CGGUCUA-AGGGUU---CAU----------------------------------AA-CCUAAGACAGCGG-AGCUGCCAUC
CP000568.1/3637613-3637528   UUUUGAAAAGGGCAAAUCUA-U-C-GAA---A-GAUAGAGACGCAAAGCCAA-C-GAGUCUA-AGGUG----GAAA----------------------------------C-ACUAUGACGGUCG-GGUUGCCAAA
AAOH01000011.1/15155-15071   GUUCGUAAAGGGCAAACUUA-G-U-GAA---A-AUUAAGGACGCAAAGCUA--U-UGGUCUA-AGGGUA---UU-----------------------------------UA-CCUAUGAUUGCAA-AGCUGCCAAC
AAWL01000017.1/11338-11251   ACAUAAGUUGGGCAAACCCG-G-C-GAA---A-GCCGGGGACGCAAAGCCA--U-GGGUCUA-AGGACAU--UGGG---------------------------------UG-UCUAUGAUCGCCA-GGUUGCCAAU
CR555306.1/718866-718950     CUCUGAAAAAGGCAAACCCG-U-C-GAA---A-GGCGGGGACGCAAAAUCA--C-CGGUCUA-CAGGG----GUCG----------------------------------C-CCCAUGACAGCGG-GAUUGCCAGG
CP000478.1/4546395-4546307   ACCUGUAAAGGGCAAACCAU-C-C-GAA---A-GGGUGGGACGCAAAGCCG--C-UGGCCUA-AGUCCCCC-GCGU---------------------------------GG-GAUAUGGCAGCAG-GGUUGCCAGG
CR378670.1/196774-196861     GUAUGUAAAGGGCAAACUAG-U-C-GAA---A-GGCUAGGACGCAAAGCUA--C-CGGUUUA-AGGGUUA--UUAA---------------------------------GA-CCUAUGACAGCGG-AGCCGCCAUA
CP000482.1/3118185-3118275   GCCUGAAAAAGGCAAACCAU-U-C-GAA---A-GGAUGGGGCGCAAAACCA--C-UGGUCUA-AAUCCCG--GAAA------------------------------UUCGG-GACAUGACAGCAG-GGCUGCCGGG
CP000469.1/3587317-3587229   UAGUGUAAAAGGCAAACCAA-U-C-GAA---A-GAUUGGGACGCAAAGCCU--C-CGGUCUA-AGGGUUCG-UUUG---------------------------------UA-CCUAUGAUAGCGG-GGAUACCACA
AAPH01000029.1/24025-23938   GUAUGUAAAGGGCAAACUAG-U-C-GAA---A-GGCUAGGACGCAAAGCUA--C-CGGUUUA-AGGGUUA--CACA---------------------------------GA-CCUAUGACAGCGG-AGCCGCCAUA
AAXG02000005.1/131709-131618 GCGGGAAAAGGGCAAACCGG-C-U-GAA---A-GGCCGGGACGCAAAGCCA--G-GAGGCUA-AAGCGGAG-GGAA------------------------------ACGCC-GCCAUGCCCGUCC-GGUUGCCGCA
AP008230.1/5220217-5220127   UAAAGUCAAGGGCAAACCUG-C-C-UAA---A-GGCAGGGACGCAAAACCGU-A-GGAUCUA-AGGUGCU--UAAA-------------------------------AGGU-GCUAUGAUAGCCU-GGUUGCCAAU
AAOJ01000002.1/319461-319551 GUCACGAACUGGCAAAUUAA-U-U-GAA---A-GAUUAAGACGCAAAACCA--C-CGGCCUA-AAAAUUAU-GUUA-------------------------------AUAA-UUCAAGGUAGCGG-GGUUACCGAA
AAOU01000011.1/39728-39638   GUCACGAACUGGCAAAUUAA-U-U-GAA---A-GAUUAAGACGCAAAACCA--C-CGGCCUA-AAAAUUAU-GUUA-------------------------------AUAA-UUCAAGGUAGCGG-GGUUACCGAA
AE014299.1/1112481-1112574   CACCGUAUUGGGCAAACUAA-U-U-GAA---A-AAUUAGGACGCAAAGCCU--C-CGGUCUA-AGGUUG---UAAA--------------------------GGGAUGUUA-ACUAAGAUAGCGG-GGUUGCUUAA
DQ124694.1/7633-7720         GCAUGAUAAAGGCAAACUGAAC-U-GAA---A-AGUCAGGACGCAAAGCCU--C-CGGUCUA-AUAGCU---GCAA---------------------------------UG-CUAAUGAUAGCGG-GGUUACCAAG
CP000083.1/4612611-4612693   GCUUGAUAAGGGCAAAUCUA-A-U-GAA---A-GUUAGAGACGCAAAGUUA--C-CGGUCUA-AUGG-----GAAA------------------------------------CCUAUGAUAGCGG-GACUGCAAAU
CP000753.1/3685694-3685606   GCGUGUAAAAGGCAAACCAG-U-U-GAA---A-AACUGGGACGCAAAGCCU--C-CGGUCUA-AGGGUUCG-UCUG---------------------------------UA-CCUAUGAUAGCGG-GGAUACCACA
CP000563.1/3606440-3606352   GCGUGUAAAAGGCAAACCAG-U-U-GAA---A-AACUGGGACGCAAAGCCU--C-CGGUCUA-AGGGUUCG-UCUG---------------------------------UA-CCUAUGAUAGCGG-GGAUACCACA
BA000028.3/2580327-2580243   CUCAGAAAAAGGCAAACCUA-U-U-GAA---A-GAUGGGGACGCAAAGUCA--C-AGAUCUA-AGGUA----UUUU----------------------------------U-ACUAAGAUGGCUG-GACUAUCUGG
CP000444.1/3427742-3427655   UAUUGUGAAAGGCAAACCAA-U-U-GAA---A-GAUUGGGACGCAAAGCCU--C-CGGUCUA-AGGGUCG--UUUG---------------------------------UA-CCUAUGAUAGCGG-GGAUACCGCA
CP000446.1/3357377-3357290   UAUUGUGAAAGGCAAACCAA-U-U-GAA---A-GAUUGGGACGCAAAGCCU--C-CGGUCUA-AGGGUCG--UUUG---------------------------------UA-CCUAUGAUAGCGG-GGAUACCGCA
CP000721.1/4634346-4634259   UAUUGAUAAUAGCACACUUG-C-C-GAA---A-GGUAGGGCCGCAAAGCUA--U-GGGUCUA-AAGAAAU--UCAU---------------------------------UU-UCAAUGAUUGCCA-GGUUGCCAAA
AAVO02000002.1/48259-48176   AUAGCAUAAAGGCAAACCUG-C-U-GAA---A-GGCAGGGACGCAAAGCCA--C-GGGUCUA-AGGUC----GUGA----------------------------------G-ACUAAGGCAGCC--GGUUGCCGCA
AM180355.1/3266964-3266879   AAAAUUAAAUGGCAAAAUUA-G-G-GAA---A-UCUAAUGACGCAAAACUA--UAGGGAUUA-AAGCUU---UUA----------------------------------AA-GCCAUAUCAGCC--AGUUGCUAAA
AAML04000014.1/594909-594824 AAAAUUAAAUGGCAAAAUUA-G-G-GAA---A-UCUAAUGACGCAAAACUA--UAGGGAUUA-AAGCUU---UUA----------------------------------AA-GCCAUAUCAGCC--AGUUGCUAAA
ABDW01000004.1/131179-131263 AUAAUAUAUUGGCAAAUCUA-G-A-GAA---A-UUUAGAGACGCAAAGCUA--AAGGGGCUA-AGGUUA---UA-----------------------------------UA-ACUAUGCUAGCC--AGUUGCCAAA
AAND01000010.1/47376-47291   UCACGCACAGGGCAAACCAC-U-U-GAA---A-AAGUGGGACGCAAAGCUU--C-CGGCCUA-AACCAC---UCG----------------------------------UU-GGUAUGGUAGCGG-GGUUACCGAU
Y10550.1/784-870             AGCAGAUAAAGGCAAACCUG-C-G-GAA---A-CGCAGGGACGCAAAGCCA--U-G-GCCUA-AGGUACU--GACG---------------------------------GU-GCUACGGUUGACA-GGUUGCCGAA
AAJM01000107.1/5655-5567     AAAAUAAAUAGGCACACUGU-U-C-GAA---A-GGAUAGGUCGCAAAGCUA--A-GAGUCUA-AGGUAAU--GAAA--------------------------------AUU-ACUAUGAUAGUCU-GGUUGCAGUU
CP000246.1/1695696-1695613   UAAAAAAAUGGGCAAAAUUA-G-A-GAA---A-UCUAAUGACGCAAAGCUA--UAGGGACUA-AGGUU-----UAU----------------------------------A-ACUAUGUCAGCC--AGUUGCCAAA
ABDY01000007.1/25749-25832   UAAAAAAAUGGGCAAAAUUA-G-A-GAA---A-UCUAAUGACGCAAAGCUA--UAGGGACUA-AGGUU-----UAU----------------------------------A-ACUAUGUCAGCC--AGUUGCCAAA
ABDV01000006.1/21251-21334   UAAAAAAAUGGGCAAAAUUA-G-A-GAA---A-UCUAAUGACGCAAAGCUA--UAGGGACUA-AGGUU-----UAU----------------------------------A-ACUAUGUCAGCC--AGUUGCCAAA
ABDX01000004.1/24814-24897   UAAAAAAAUGGGCAAAAUUA-G-A-GAA---A-UCUAAUGACGCAAAGCUA--UAGGGACUA-AGGUU-----UAU----------------------------------A-ACUAUGUCAGCC--AGUUGCCAAA
BA000016.3/1510292-1510209   UAAAAAAAUGGGCAAAAUUA-G-A-GAA---A-UCUAAUGACGCAAAGCUA--UAGGGACUA-AGGUU-----UAU----------------------------------A-ACUAUGUCAGCC--AGUUGCCAAA
CP000485.1/435376-435460     CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUAUGCUAGCC--AGUUACCGGA
AAEW02000001.1/146764-146686 CUCCGAUAAAGGCAAAACCG-G-A-GUA---A-UCCGGUGACGCAAAGCCA--C-GGGUC-----CUGU---UUG----------------------------------AC-AG---GAUCGCCG-GGUUCCCGAA
AATC01005788.1/229-145       UUUUGUAAAAGGCAAAAUAA-A-U-GAA---A-AUUUAUGACGCAAAGCCA----AGGUCUA-AGAGCU---AUA----------------------------------UG-CUUAUGAUAGCUA-GGUUGCACAA
ABCH01000059.1/9246-9159     UCACGCACAGGGCAAACCAC-U-U-GAA---A-GGGUGGGACGCAAAGCCA--C-CGGCCUA-AACCAAA--UUUA---------------------------------UU-UGAUAGGUAGCGG-GGUUACCGAU
CP000002.3/378607-378693     AGCAGAUAAAGGCAAACCUG-C-G-GAA---A-CGCAGGGACGCAAAGCCA--U-G-GCCUA-AGGUGCU--GACG---------------------------------GU-GCUACGGUUGACA-GGUUGCCGAA
CP000382.1/1871611-1871526   CAACGAUAAAGGCAAAUUUA-G-U-GAA---A-ACUAGAGACGCAAAGCUA--AAGGGCCUU-CCUUAG---UUA----------------------------------UU-AAGAUGGCAGCC--AGUUACCGAA
AAWD01000198.1/2303-2217     UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CA-UGGUAGGUAGCGG-GGUUACCGAU
AAWE01000118.1/3454-3368     UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CA-UGGUAGGUAGCGG-GGUUACCGAU
AE003852.1/1860690-1860776   UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CA-UGGUAGGUAGCGG-GGUUACCGAU
AAUT01000003.1/5810-5896     UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CA-UGGUAGGUAGCGG-GGUUACCGAU
CP000142.2/1987037-1987116   UCCCGAUAAAACCAAACCUG-U-C-GCA---A-GACAGGGACGGAAAGCAA--C-GGAUC-----UUCG---AACC---------------------------------AG-AA---GAUGGCCG-AGCUGCCGAA
AAKJ02000030.1/26337-26423   UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CG-UGGUAGGUAGCGG-GGUUACCGAU
AAKI02000072.1/12068-12154   UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CG-UGGUAGGUAGCGG-GGUUACCGAU
AATY01000002.1/114977-114891 UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CG-UGGUAGGUAGCGG-GGUUACCGAU
AAUU01000047.1/27433-27347   UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CG-UGGUAGGUAGCGG-GGUUACCGAU
AAUR01000002.1/72158-72244   UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CG-UGGUAGGUAGCGG-GGUUACCGAU
AAWF01000029.1/2517-2603     UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CG-UGGUAGGUAGCGG-GGUUACCGAU
CP000627.1/1413802-1413888   UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CG-UGGUAGGUAGCGG-GGUUACCGAU
AAWG01000002.1/25205-25291   UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CG-UGGUAGGUAGCGG-GGUUACCGAU
AAEN01000023.1/138415-138499 CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AE017355.1/421273-421357     CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AAAC01000001.1/914180-914264 CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AE017225.1/397305-397389     CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AAER01000042.1/136402-136318 CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AE017334.2/397292-397376     CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AAES01000043.1/103414-103498 CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AE016879.1/397292-397376     CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AAEQ01000043.1/90673-90589   CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
CP000001.1/414665-414749     CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AAEO01000030.1/151854-151938 CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AAEP01000046.1/103744-103828 CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
AAMR01000021.1/11847-11762   UCACGCACAGGGCAAAUCAC-U-U-GAA---A-GAGUGAGACGCAAAGCUU--C-CGGCCUA-AACCAC---UCG----------------------------------UU-GGUAUGGUAGCGG-GGUUACCGAU
AAZW01000020.1/21384-21469   UCACGCACAGGGCAAAUCAC-U-U-GAA---A-AGGUGAGACGCAAAGCUU--C-CGGCCUA-AACCAC---UCG----------------------------------UU-GGUAUGGUAGCGG-GGUUACCGAU
AAEK01000003.1/195166-195078 GAAAUAAAUCGGCACACUAU-U-C-GAA---A-GGAUAGGUCGCAAAGCUA--A-GAGUCUA-AGGUAAUA-CAUA---------------------------------UU-ACUAUGAUAGUCU-GGUUGCAAUU
AAPS01000039.1/21459-21548   UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUG-AACCAUA--UUAC------------------------------GAUAU-GG-AAGGUAGCGG-GGUUACCGAU
AAWQ01000045.1/17416-17505   UCACGCACAGGGCAAACCAU-C-C-GAA---A-GGGUGGGACGCAAAGCCU--C-CGGCCUG-AACCAUA--GUAG------------------------------UAUAU-GG-AAGGUAGCGG-GGUUACCGAU
BA000031.2/1078742-1078653   UCACGCACAGGGCAAACCAU-C-C-GAA---A-GGGUGGGACGCAAAGCCU--C-CGGCCUG-AACCAUA--GUAG------------------------------UAUAU-GG-AAGGUAGCGG-GGUUACCGAU
CP000103.1/2175552-2175465   AUCUGUAAAAGGCAAAUCUC-G-C-GAA---A-GCGGGGGACGCAAAGUCA--U-CGGUCUA-CCGGGCU--CAAG---------------------------------GC-CCCAGGACGGCAG-GACUGCCAGA
CP000312.1/1445209-1445126   UUUAAAAUUCGGCAAAAUUA-G-A-GAA---A-UCUAAUGACGCAAAGCUA--UAGGGACUA-AGGUU-----UAU----------------------------------A-ACUAUGUCAGCC--AGUUGCCAAA
CP000698.1/247508-247587     CCGACGAAAAGGCAAAGCAC-G-G-GCA---A-CCGUGUGACGCAAAGCUA--C-CUGUC-----CAGU---UGCA---------------------------------AC-UG---GAUAGAGG-GGCUGCCGAA
AAKK02000061.1/16343-16432   UCACGCACAGGGCAAACCAU-U-C-GAA---A-GGGUGGGACGCAAAGCCU--C-CGGCCUG-AACCAU---AAUA-----------------------------CUAUAU-GG-AAGGUAGCGG-GGUUACCGAU
CP000510.1/1867279-1867369   GCUGGAAAAAAGCAAAUUAA-G-G-GAA---A-CCUUAAUACGCAAAACCA--C-CGGCCUG-UUGAUUG--ACUA------------------------------UUUAG-UCUAUGGCAGCGG-AGUUACCAAG
AE017194.1/504284-504368     CAGCGAGAAAGGCAAACUGG-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
CP000606.1/1879203-1879288   CUCUCGAAACGGCAAGCAUU-A-A-GUA---A-UUAAUGUACGCAAAGCCA--C-AGGCCCU-AAUUGC---AUA----------------------------------GC-AAAAGGGUGGCUG-GGUUACCGAA
AAWP01000006.1/124156-124245 UCACGCACAGGGCAAACCAU-U-C-GAA---A-GGGUGGGACGCAAAGCCU--C-CGGCCUG-AACCAUC--GAAU------------------------------UAGAU-GG-AAGGUAGCGG-GGUUACCGAU
BA000037.2/2327906-2327994   UCACGCACAGGGCAAACCAU-U-U-GAA---A-AAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---ACGU------------------------------UUUUU-GGUA-GGUAGCGG-GGUUACCGAU
AY855346.1/29246-29151       AAACUAAAUCGGCAAAACUA-G-A-GAA---A-UUUAGUGACGCAAAGCUA--UAGGGACUA-AGAUUUA--UAAA-------------------------AUUCUUAUAA-AUUAUGCCAGCC--AGUUGCCAAA
CP000116.1/532900-532975     AUCCCGAAAGGGCAAACCCG-C-C-GCG---A-GGCGGGGGCGCAAAGCGA--C-CGGUC-----UC-----GAAA------------------------------------GA---GAUAGCGG-CGCUGCCGUG
CP000148.1/824437-824354     UUUCCGAAAGGGCAAACUUC-G-G-GUA---A-CCGGGGGACGCAAAGCCA--C-GGGUC-----CUGAC--UCCA------------------------------UGGUC-AG---GAUAGCCG-GGUUGUCGAA
AE016877.1/408156-408240     CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUGAGGACGCAAAACUA--CAGGAGCUA-AGGUC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
CP000109.2/325943-326021     AGAAAAUUUUGCCAAACUUG-U-U-GUG---A-AGCAAGGACGGAAAGCCA--U-GGGUC-----UCAA---UGG----------------------------------UU-GA---GAUCGCCA-GGUUGCCAAA
AE017180.1/1100143-1100060   UUUUCGAAGAGGUAAACCCC-G-G-GUA---A-CCGGGGGGCACAAAGCUG--C-GGGUC-----CCGCCU-GAAA-------------------------------CAGC-GG---GACAGCCG-GGUUGGCGAA
AANZ01000050.1/14174-14099   CCUCGAAAAAGGCAAACCGA-U-C-GUG---A-GGUCGGGACGCAAAGCCA--A-GGGCC-----AC-----GUAA------------------------------------GU---GGACGCCA-GGCUGCCGAA
CP000450.1/861386-861306     AACCGACAAAGGCCAACCUG-U-C-GUG---A-GGCAGGGGCGCAAAGUUU--C-CGAUC-----CUGAU--UGCA---------------------------------UC-AG---GAAAGCGG-GACUGCCGAA
AAOW01000010.1/54987-54913   CUCUCGAAAAGGCAAAACCC-G-A-GUA---A-UCGGGUGACGCAAAGUCA--C-GGGUC-----CCA-------A----------------------------------U-GG---GACAGCCG-GACCGCCACA
AP009179.1/1220413-1220339   UCUAAUAUAUGCCAAACCUG-U-U-GCG---A-AACAGGGACGGAAAGCCA--C-GGGUC-----UCA------------------------------------------U-GAA--GAUAGCCG-GGUUGCCAGA
AL954747.1/1707540-1707622   AACCGACAAAGGCUAAUCUG-U-C-GUA---A-GGCAGGGGCGCAAAGUUU--C-CGGUC-----CUGAUCCAUGA---------------------------------UC-AG---GAAAGCGG-GACUGCCGAA
AAMX01000014.1/21204-21112   UUGUUUAACUGCCAAACUCA-U-C-GCG---A-GAUGAGGACGGAAAGCCA--C-GGGUCUC-AGAGUGU--GUUG----------------------------AGAUGUA-UCUCAGAUAGCCG-GGUUGCGGAA
CP000302.1/2534228-2534317   UGCUGUGGAAGGCAAACCAG-U-U-UUA---AAGACUGGGACGCAAAGCCU--C-CGAUCUA-AAGGUUUG-CUUG---------------------------------UA-CCUAUGAUAGCGG-GGAUCCCACA
CP000503.1/3966333-3966251   CUGACGAACAGGUACACCCG-U-U-GUG---A-GACGGGGUCGCAAAGCUU--C-GGGUC-----UUGA---UUUU---------------------------------UU-AUUAAGAUAGCCG-GGUUGCCGAA
CP000284.1/503076-502984     AAAUGUUAAGGGCAACCUUG-G-UUGAA---AAACCAAGGACGCAAAGUCA--C-CGGUCUA-AGGUAA---GCAG-----------------------------CUUGCU-ACUAUGACAGCGG-AACCGCCAUA
AE015927.1/477013-477088     CCACGAUAAAGGCAAAACUA-U-U-GAA---A-GAUAGUGACGCAAAGCUA--UAGGGUCUG-UA---------AA---------------------------------------AUGACAGCC--AGUUAUCGAA
AP006840.1/3227495-3227385   CAGCGAUAAAGGCACACCCG-C-C-GAA---A-GACGGGGCCGCAAAGCCA--C-GGGGCUA-CAGGAA---GCGG---------GCGCCGCCCUGCCGGGUCUCCCGCCU-CCCAUGCUAGCCG-GGCUGCCGCU
AAXV01000001.1/231054-230969 GGGAAAGAUAGGCAAAUUUA-C-U-AAA---A-AGUAAAGAUGCAAAGCUA--C-AGGUCUA-AGGGAA---UAA----------------------------------GU-ACUUAGAUGGCUA-GGUUGCAAAA
CP000282.1/989437-989348     CAACGAUAAAGGCAAACCCG-C-G-GUA---A-CGUGGGGACGCAAAGCCA--G-UGCCCAA-CUACUU---GUAA------------------------------UUUAA-GAUUGGGUCGAAC-GGUUACCGAA
BX842649.1/31567-31484       UUUGCCUCAAGGCAAACCGU-C-G-GAA---A-CGGCGGGACGCAAAGCUA--AAGGGGUGU-CGGUGC---AAAG---------------------------------CC-AC---GCCAGCC--AGCUGCCAAA
CP000267.1/4400341-4400428   CAAGUUCAAAAGCACACCCGAU-C-GAA---A-GACGGGGUCGCAAAGCUU--C-CGGCCUG-ACGCAU---UCGU---------------------------------GC-GAAGUGGUAGCGG-GGUUGCCCAA
AAXY01000014.1/263-343       CUAACCAGCAGCCAAACCAU-U-U-GUG---A-GGAUGGGACGGAAAGCCA--A-GGAUC-----UCUGG--GGAA---------------------------------AA-GA---GACAGCCU-GGUUGCCUAG
BA000004.3/597582-597667     CCUUGAAAAAGGCGAGUGUU-U-G--AA---A-UGGAAAGACGCAAAGCUG--C-GAGUCUG-AAAUCC---UUCU---------------------------------GA-AUAGGGAUAGUCG-AGUUGUCAAA
BX294141.1/222899-223010     CCCUGACAAAGGCAAACCGU-U-C-GAG---A-GGACGGCACGCAAAACCA--C-GGGUCCG-UGAGUCG--GUCG---------AUCGCAUUGUUUGCGUUCGGCUUGGC-UUCAGGAAAGCCG-AGUUGCCGUG
CP000112.1/841128-841197     CGAGAAUCAAGCCAACCCGC-C-U-C-------AGGCGGGACGGAAAGCCA--C-GGGUC------------UUUC--------------------------------A--------GACAGCCG-GGUUGCCUCG
CP000764.1/420958-421045     GGGCGAGAAAGGCAAACUCG-U-G-GAA---A-CAUAAGGCUGCAAAACUG--UAGGGCUUA-AGGUCAA--GAGA---------------------------------AG-GCGAAGCUAGUC--AGUUACCGAA
CP000251.1/2466924-2466841   CACGCUUCAGGGCAAUUCAC-C-C-GUACCCA-GGGUGAAGCGCAAAGCCG--C-GGGUC-----CGGU---GAAC---------------------------------GC-CG---GACGGCCGUGGCCGCCGUG
CT573072.1/491002-491095     GAUUGAAAAAGGCAAACCAA-C-C-GCA---A-GUUUGGGACGCAAAGCCA--U-GGGUCUU-AAGCGUG--AGUU---------------------------CUUUAUAC-GUAAAGAUUGCCA-GGUUGCCGAA
DQ898548.1/1361-1448         CCCGUUUCAGGGCAAACUCA-C-C-GAA---A-GGUGGGGACGCAAAGCCU--C-CGGUCUA-CGGGAC---GCAU---------------------------------GUGCCUAUGACAGCGG-GGUUGCCGGU
CP001186.1/4695548-4695460   AAAAUAAAUGGGCACACUGU-U-C-GAA---A-GAAUAGGUCGCAAAGCUA--A-GAGUCUA-AGGUAAUA-AAAA---------------------------------UU-ACUAUGAUAGUCU-GGUUGCAGUU
ABDT01000056.2/21523-21607   AAGUAUUAAUGGCAAAAUUA-G-A-GAA---A-UCUAAUGACGCAAAGCUA--UAGGAGCUA-AAGUU----AAAA----------------------------------A-ACUAUGCUAGCC--AGUUGCUAAC
CP000853.1/1736753-1736673   ACAAUAAAUGGGCAAACCU-----------------AGGGACGCAAAGCUU--G-A-GUCUA-CGGUUAU--CUCA-----------------------------AAGAUA-AUUACGAUCGUUC-AGCUGCAUAG
CP000821.1/3858383-3858465   CUACGAUAAAGGCAAAACCG-G-G-GUA---A-CCCGGCGACGCAAAACCA--G-UGCCC---AGGCA----GAGA----------------------------------U-GCGGGGGUCGAAC-GGUUACCGAA
CP000891.1/3806662-3806574   GCGUGUAAAAGGCAAACCAG-U-U-GAA---A-AACUGGGACGCAAAGCCU--C-CGGUCUA-AGGGUUCG-UCUG---------------------------------UA-CCUAUGAUAGCGG-GGAUACCACA
CP001336.1/1127881-1127794   AUUCGACAAUAGCAAACCUG-G-C-GAA---A-GCCAGGGACGCAAAGCUA--U-GGGUCUU-CCUGGAU--ACAC---------------------------------UC-CUGAUGAUCGCCA-AGCUACCGAA
CP000923.1/2190645-2190558   UGUUGAAAAAGGCAAACUCG-U-C-GAA---A-GGCGGGGACGCAAAGCCA--C-GGGUCUA-AAGCGAU--AGUU---------------------------------UU-GCUAUGAUAGCCG-GGCUGCCAAC
CP000885.1/1430070-1430158   UUAUAAAUUUAGCAAACUAA-U-U-GAA---A-GAUUAGGACGCAAAGCUA--U-GGGUCUA-AGGAUAUC-AUAA---------------------------------UA-UCAACGAUUGCCA-GGUUACAGAA
CP001176.1/4733001-4732913   AAAAUAAAUGGGCAUACUAU-U-C-GAA---A-GGAUAGGUCGCAAAGCUA--A-GAGUCUA-AGGUAAU--GAAA--------------------------------AUU-ACUAUGAUAGUCU-GGUUGCAGUU
CP001215.1/397645-397729     CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
ABCC02000002.1/64098-64013   AAAAAUAAUUAGCAAAACUG-G-U-GAA---A-GCUAGUGACGCAAAGCUA--CAGGGAUUU-CUCUCU---AAAA---------------------------------AG-AG-GUGUCAGCC--AGCUGCAUGA
ABED02000012.1/2557-2651     GCAAUUUUUUGGCAAACUUG-U-C-GAA---A-GGCAAGGACGCAAAGCCA--UAGGGGCUA-AGGUUCG--GGGC--------------------------AUUUCCCGG-AUGAUGCCAGCC--GGUUGCUUCC
CP001052.1/1667937-1667858   GCGCAGUUUGGGCAAACCCG-G-A-GCG---A-UCCGGCGACGCAAAGCUA--CAGGGAC-----UCCC---UUGC---------------------------------GG-GA---GUUUGCC--AGUUGCCCGC
CP000859.1/2080979-2081056   UCAUGCUAAAGCCAAACUCC-G-G-GCG---A-CCGGAGGACGGAAAGCAA--C-GGGUCUU-AA-------UAUA---------------------------------------AAGACAGCCG-GGCUGCCAUG
AE008691.1/706140-706227     CUUCGAUAAGGGCAAACCCG-U-C-GAA---A-GGCGGGGGCGCAAAGCCA--C-GGGCCUA-AAUCCCU--GAUU---------------------------------GG-GACAUGGUAGCCG-GGCUGCCGAA
CP001177.1/464065-464149     CAGCGAGAAAGGCAAACUGG-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
CP000961.1/1418939-1419059   AAUGUACAAAGGCAAACCAA-U-C-GAA---A-GGUUGGGACGCAAAGCUU--C-CGGUCUA-AGGGGAU--AGUGUUUGAGAGGGUCGCACUCUUAACGUUAUUUUGGUA-CCUAUGAUAGCGG-GGAUGUUACA
ABAX03000005.1/232139-232052 AAUUUUCAUCGGUAAAGCUG-C-C-GAA---A-GGCAGUGACACAAAGCCA--A-GGGUCUA-AAGUCUUA-CAUA---------------------------------AG-ACUAUGACAGCC--GGUUGCCACA
CP001089.1/2534834-2534760   UCACCGAAAAGGCAAAAUCC-A-G-GGG---A-CUGGAUGACGCAAAGCCA--C-CUACC-----CGG-------A----------------------------------C-CG---GGAAGAGG-GGUUACCGAA
CP000903.1/416914-416998     CAGCGAGAAAGGCAAACUUA-U-G-GAA---A-CAUGAGGACGCAAAACUA--CAGGAGCUA-AGGUC----GAAG----------------------------------G-GCUAAGCUAGCC--AGUUACCGGA
CP001233.1/1807824-1807910   UCACGCACAGGGCAAACCAU-U-C-GAA---A-GAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---AAGA---------------------------------CA-UGGUAGGUAGCGG-GGUUACCGAU
CP000924.1/1541170-1541083   UGUUGAAAAAGGCAAACUCG-U-C-GAA---A-GGCGGGGACGCAAAGCCA--C-GGGUCUA-AAGCGAU--AGUU---------------------------------UU-GCUAUGAUAGCCG-GGCUGCCAAC
CP000884.1/4023666-4023571   UUUGCGCACCAGCACACCCG-UAC-GAA---A-GGCGGGGUCGCAAAGCCU--C-CGGUCUA-CCCCCG---CCCU-------------------------UUGACGGGCG-GGCAUGACAGCGG-GGUUGCCAGG
CP001098.1/769828-769735     CUCCGGAAAUGGUAAACCCA-U-C-GAA---A-GGUGGGGACACAAAGUCA--C-GGGCCUGUAGCCGG---UUAU---------------------------UUUUAACC-GGUAUGGCAGCCG-GACUGCCGAA
CP001139.1/1780753-1780835   UCACGAACAUGGCAAACUAC-A-U-GAA---A-AUGUAGGACGCAAAGCUU--C-CGGCCUA-AGUA-----UUUA------------------------------------UAUAAGGUAGCGG-GGUUGCCGAC
CP001124.1/2736237-2736160   CACACGAAAAGGCAAACCCA-G-G-GUA---A-CCUGGGGACGCAAAGCCA--C-CUGUC------CAG---CAUU---------------------------------CU-G----GAAAGAGG-GGUUGUCGAA
CP000851.1/4449140-4449058   UGAUGAAAAAGGCAAAACCU-G-U-GAA---A-GCAGGUGACGCAAAGCAU--C-CAGCCUA-AGGG-----GACA------------------------------------CCUAUGGCAGUGG-CGCUACCGCA
CP001390.1/3356677-3356601   UAACGAUAAUACUAAACCAU-U-C-GCG---A-GAAUGGGGCGGAAAGCCUAUA-GGGUCUC-A--------AGCA-----------------------------------------GACAGCCG-GGUUGCCGAA
CP001598.1/397192-397276     CAGCGAGAAAGGCAAACUGA-U-G-GAA---A-CAUUAGGACGCAAAACUA--CAGGAGCUA-AGGCC----GAAA----------------------------------G-GCUACGCUAGCC--AGUUACCGGA
CP003056.1/2189771-2189855   AAUUGAAAAAGGCAAAUUCA-U-C-GAA---A-GGUGGAGACGCAAAGCUA--AAGGGACUA-AAGUCA---GA-----------------------------------UG-ACCAUGUCAGCC--AGUUACCGAU
CP002457.1/712651-712733     CUGACGAACAGGUACACCCG-U-U-GUG---A-GACGGGGUCGCAAAGCUU--C-GGGUC-----UUGA---UUUU---------------------------------UU-AUUAAGAUAGCCG-GGUUGCCGAA
CP002469.1/1123237-1123149   UCACGCACAGGGCAAACCAU-U-U-GAA---A-AAGUGGGACGCAAAGCCU--C-CGGCCUA-AACCAG---ACGU------------------------------UUUUU-GGUA-GGUAGCGG-GGUUACCGAU
AAKH03000018.1/618060-617954 GUCACACUUUGGCAAACCCU-U-U-GAA---A-AAAUGGGACGCAAAGCCU--C-CGGUCUG-UCGGUCAA-GAAA---------------GCUCAUAAAGCCCUCUUACA-CCUAGGAUAGCGG-GGUUACCAAU
#=GC SS_cons                 :::::::::::<<---<<<<.<.<.___..._.>>>>>>--->>--<<<<-..<.<<<<<--.--<<<<...____.................................>>.>>--->>>-->>>.>>>>::::::
#=GC RF                      uaaugaaAAaGGCAAAcccg.c.c.GAA...A.ggcgggGACGCAAAgCca..c.gGguCUA.Aggccc...gaaa.................................gg.gcuAuGacAGCcg.gGcUGCCgaa
//
# STOCKHOLM 1.0

#=GF AC   RF01052
#=GF ID   Arthropod_7SK
#=GF DE   Arthropod 7SK RNA
#=GF AU   Gruber A; 0000-0003-1219-4239
#=GF AU   Stadler PF; 0000-0002-5016-5191
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:18566019
#=GF SS   Published; PMID:18566019
#=GF GA   44.00
#=GF TC   44.40
#=GF NC   42.50
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00013
#=GF DR   SO; 0000274; snRNA;
#=GF RN   [1]
#=GF RM   18566019
#=GF RT   Arthropod 7SK RNA.
#=GF RA   Gruber AR, Kilgus C, Mosig A, Hofacker IL, Hennig W, Stadler PF
#=GF RL   Mol Biol Evol. 2008;25:1923-1930.
#=GF WK   7SK_RNA
#=GF SQ   19


AAKO01001600.1/88983-88539     GGAAGUGUAU-------UCUGUGAUUGU------UCUGUACA-UUGAUCGAUAUUCAGGUAACUGC----AUCUGCUUAUCAGAUCUGUUCAGAGCCGACCCUCCGUCACAC-----CUUUGUGUUUCCCAGUAAUUCUGCCUGGCGUUGCCGUGGC-UCCUCGUUC-GGAUCGGCUUUCCGCUGCCUUCCGCUGGAUGACGACGGGUUAUC-CGGCGGUCGACGCACGGUC-AUGCA--------------CCCCC----GAUCCGUCGCC-C--CCUCCAC------CCCGCGGAUUCCGGUCU-------------CGACCGGUA---GCCGUAUUGGGCGGGG-ACGGG---------------CGGCGG--U-CCGGUG-CUGAAGCCGGCGACAGUUGCCCGAGUCAGCCACUUUCAAAAUUUGUUGGUUAA----------GUAACUUAGUAGCUUAGCUUCGGAUUUUCGUAACAAAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AASS01022392.1/2223-2667       GGAAGUGUAU-------UCUGUGAUUGU------UCUGUACA-UUGAUCGAUAUUCAGGUAACUGC----AUCUGCUUAUCAGAUCUGUUCAGAGCCGACCCUCCGUCACAC-----CUUUGUGUUUCCCAGUAAUUCUGCCUGGCGUUGCCGUGGC-UCCUCGUUC-GGAUCGGCUUUCCGCUGCCUUCCACUGGAUGACGACGGGUUAUC-CGGCGGUCGACGCACGGUC-AUGCA--------------CCCCC----GAUCCGUCGCC-C--CCUCCAC------CCCGCGGAUUCCGGUCU-------------CGACCGGUA---GCCGUAUUGGGCGGGG-ACGGG---------------CGGCGG--U-CCGGUG-CUGAAGCCGGCGACAGUUGCCCGAGUCAGCCACUUUCAAAAUUUGUUGGUUAA----------GUAACUUAGUAGCUUAGCUUCGGAUUUUCGUAACAAAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AE014297.2/3300718-3300274     GGAAGUGUAU-------UCUGUGAUUGU------UCUGUACA-UUGAUCGAUAUUCAGGUAACUGC----AUCUGCUUAUCAGAUCUGUUCAGAGCCGACCCUCCGUCACAC-----CUUUGUGUUUCCCAGUAAUUCUGCCUGGCGUUGCCGUGGC-UCCUCGUUC-GGAUCGGCUUUCCGCUGCCUUCCACUGGAUGACGACGGGUUAUC-CGGCGGUCGACGCACGGUC-AUGCA--------------CCCCC----GAUCCGUCGCC-C--CCACCAC------CCCGCGGAUUCUGGUCU-------------CGACCGGAA---GCCGUAUUGGGCGGGG-ACGGG---------------CGGCGG--U-CCGGUG-CUGAAGCCGGCGACAGUUGCCCGAGUCAGCCACUUUCAAAAUUUGUUGGUUAA----------GUAACUUAGUAGCUUAGCUUCGGAUUUUCGUAACAAAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AAEU02002383.1/6635-6191       GGAAGUGUAU-------UCUGUGAUUGU------UCUGUACA-UUGAUCGAUAUUCAGGUAACUGC----AUCUGCUUAUCAGAUCUGUUCAGAGCCGACCCUCCGUCACAC-----CUUUGUGUUUCCCAGUAAUUCUGCCUGGCGUUGCCGUGGC-UCCUCGUUC-GGAUCGGCUUUCCGCUGCCUUCCGCCGGACAACGACGGGUUAUC-CGGCGGUCGACGCACGGUC-ACGCA--------------CCCCC----GAUCCGUCGCC-C--CCUCCAC------CCCUCGGAUUUCGGUCU-------------CGACCGGGA---GCCGUAUUGGGCGGGG-ACGGG---------------CGGCGG--U-CCGGUG-CUGAAGCCGGCGACAGUUGCCCGAGUCAGCCACUUUCAAAAUUUGUUGGUUAA----------GUAACUUAGUAGCUUAGCUUCGGAUUUUCGUAACAAAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AAPQ01006440.1/1136576-1136132 GGAAGUGUAU-------UCUGUGAUUGU------UCUGUACA-UUGAUCGAUAUUCAGGUAACUGC----AUCUGCUUAUCAGAUCUGUUCAGAGCCGACCCUCCGUCACAC-----CUUUGUGUUUCCCAGUAAUUCUGCCUGGCGUUGCCGUGGC-UCCUCGUCC-GGAUCGGCUUUCCGCUGCCUUCCGCCGGACAACGACGGGUUAUC-CGGCGGUCGACGCACGGUC-ACGCA--------------CCCCC----GAUCCGUCGCC-C--CCUCCGC------CCCGCGUAGUCCGGUCU-------------CGACCGGGA---GCCGUAUUGGGCGGGG-ACGGG---------------CGGCGG--U-CCGGUG-CUGAAGCCGGCGACAGUUGCCCGAGUCAGCCACUUUCAAAAUUUGUUGGUUAA----------GUAACUUAGUAGCUUAGCUUCGGAUUUUCGUAACAAAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AAPP01015714.1/90347-90803     GGAAGUGUAU-------UCUGUGAUUGU------UCUGUGCA-UCGAUCGAUAUACAGGUGAUU-C----AUCUGUUUAUCAGAUCUGCUCAGUGCCGACCCUCCGUCACAC-----CUU--UGUUUCCCAGUAAUUCUGCCUGGCAUUGCUGAGGCGACAUAGUUC-GGUUCGGCUUUCCGAUGCCUCCGCCGAG-GGACGACGGGUCCUUUCGGCGGCAGACGCACGGUU-GUGUU--------------CCAGU----GAUCCGUCUCC-C--CCUUCGC------UCCGCGGAUUUCGGUCAGGACAUUUGUCUACGACUGCAA---UACGAUUUGAGCGGAG-GCGGG---------------CGGCGG--CGCUGGUG-CUGAAGCCGACGACAGUUGCCCGAGUCAGCCAUUUUCAAAAUUUCUUGGUUAA----------GUAACUUUGUAGCUUAGCUUCGGAUUUUCGUAAUAUAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AAIZ01000943.1/6063-5615       GGAAGUGUAU-------UCUGUGAUUGU------UCUGUGCA-UCGAUCGAUAGAUAGAUAGUC------AUCUGUUUAUCAGAUCUGCUCAGUGCCGACCCUCCGUCACAC-----CUU--UGUUUCCCAGUAAUUCUGCCUGGCAUUGCUGUGGCAACAUUGUUCUGGAUUGGCUUUCCCGCUGCCUUUGCUAG-CGACGACGGGUCGUU--AGCAACAGACGCACGGUC-AUGCG--------------CUGGU----CCUCCACCACC-C--ACUCCGC------CUCGCGGACUCCAGUCA-------UCUCCACGACUGGAG---CACGCAUAGGAUGGGGCUCGGG---------------CGGUGG--UGCCGGUG-CCGAAGCCAACAACAGUUGCCCACGUCAGCCAUUUUCAAAAUUUCUUGGUUAA----------GUAACUUUGUAGCUUAGCUUCGGAUUUUCGUAAUAUAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AAFS01000135.1/65623-66071     GGAAGUGUAU-------UCUGUGAUUGU------UCUGUGCA-UCGAUCGAUAGAUAGAUAGUC------AUCUGUUUAUCAGAUCUGCUCAGUGCCGACCCUCCGUCACAC-----CUU--UGUUUCCCAGUAAUUCUGCCUGGCAUUGCUGUGGCAACAUUGUUCUGGAUUGGCUUUCCCGCUGCCUUUGCUAG-CGACGACGGGUCGUU--AGCAACAGACGCACGGUC-AUGCG--------------CUGGU----CCUCCACCACC-C--ACUCCGC------CUCGCGGACUCCAGUCA-------UCUCCACGACUGGAG---CACGCAUAGGAUGGGGCUCGGG---------------CGGUGG--UGCCGGUG-CCGAAGCCAACAACAGUUGCCCACGUCAGCCAUUUUCAAAAUUUCUUGGUUAA----------GUAACUUUGUAGCUUAGCUUCGGAUUUUCGUAAUAUAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AANI01017847.1/66245-66700     GGAAGUGUCU-------UCUGUGAUUGU-U---CUCUGUGCA-UUGAUCGAUAUAUAGAUGCCC------AUCUGUUUAUCAGAUCUGCUCAGUGCCGACCCUCCGUCACAC-----UU---UGUUUCCCAGUAAUUCUGCCUGGCAUUGCUGUGGCAACAGGUUUU--GAUUGGCUUUCCGCUGCCUUU-GCUAC-CGACGACGGGUCGAA-UAGCAACAGACGCACGGUU-AUGCA--------------UCAGC--CCAACCCACCGCC-CAACCUUCGC----CUCGCGCGUAUUUCAGUCG-------CUUUUGAGAUUGAUG--AUGCGUAUAGGCAACGGGUUGGG---------------CGGGGG-GCGCUAAUG-UUGAAGCCAACAACAGUUGCCCAAGUCAGCCAUUUUCAAAAUUUCUUGGUUAA----------GUAACUUUGUAGCUUAGCUUCGGAUUUUCGUAAUAAAUUUGCUGUUCAGAACACUUCCAUUC--UCGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AAPU01010442.1/29217-29677     GGAAGUGUCU-------UCUGUGAUUGU-U---CUCUGUGCA-UUGAUCGAUAUAUAGAUGCCC------AUCUGUUUAUCAGAUCUGCUCAGUGCCGACCCUCCGUCACAC-----UU---UGUUUCCCAGUAAUUCUGCCUGGCAUUGAUGUGGCAACACGUUCU--GAUUGGCUUUCCGCUGCCUUU-GCUAA-CGACGACGGGUCGAU-UAGCAACAGACGCACGGUC-AUGCA--------------UCAGC--ACCACCCACCGCC-CAACCUCCGCCCCUCUCACGCGUAUUUCAACCG---------CUUCUGGUUGAGGAUGCGUGUAUAGGUAACGGGUUGGG---------------CGGGGGGCCGCUAAUG-UUGAAGCCAACAACAGUUGCCCAAGUCAGCCAUUUUCAAAAUUUCUUGGUUAA----------GUAACUUUGUAGCUUAGCUUCGGAUUUUCGUAAUAAAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AAPT01021824.1/81029-80568     GGAAGUGUCU-------UCUGUGAUUGU-U---CUCUGUGCA-UUGAUCGAUAUAUAGAUAUGC-C----AUCUGUUUAUCAGAUCUGCUCAGUGCCGACCCUCCGUCACAC-----UU---UGUUUCCCAGUAAUUCUGCCUGGCAUUGCUGUGGC-AACAGGUUU-CGAUUGGCUUUCCGCUGCCUUU-GCUAC-CGACGACGGGUCGAU-UAGCAACAGACGCAUGGUUAACGCA--------------UCUGCAUCCACCCCGCCGCC-CAACCUCCGC----CUCUCGCGUAUCUUAGUCU---------UCGAUGAUUGGGGUGCGUAGCAUAGGUAACGGGUUGGG---------------CGGGGGGCCGCUAAUGCUUGAAGCCAACAACAGUUGCCCAAGUCAGCCAUUUUCAAAAUUUCUUGGUUAA----------GUAACUUUGUAGCUUAGCUUCGGAUUUUCGUAAUAAAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGUCG---AGCAAUUUGCCC-AUUCUUUU-G
AAQB01009643.1/33348-32856     GGAAGUGUAU-------UCUGUGAUUGC------UCUGUGCAUUUGAUCGAUAUGCGGAUAGUUCUAUCUGUCUGUUUAUCAGAUCUGCUCAGUGCCGACCCUCCGUCACACACACCUGU--UGUUUCCCAGUAAUU-UGCCUGGCAUUGCUGUGGCGACAUGCUUUCCGAUUGGCUUUCCGAUGCCUUUGCCCAU-CGACGACGGGUCGUAUGGGCAAGAGACGCACGGUC-AUGCAAAUAGCUUUCCCACCCACA----AACCCACUACUUCCGGCUCCGU------CUCGCGAAUUUCGAUCA--------AUCUCUGAUUGGAA---UGCGUAUAGAUUGGAG-UUGGGGGCGGAGGGCCGCGGGGGCGCCGC-UAGAUG-UUGAAGCCAACGGCAGUUGCCCAAGUCAGCCAUUUUCAAAAUUUCUUGGUUAA----------GUAACUUUGUAGCUUAGCUUCGGAUUUUCGUAAUAUAUUUGCUGUUCAGAACACUUCCAUGU--ACGCGGCAUUGCCG---AGCAAUUUGCCC-AUUCUUUU-G
AAGE02007486.1/266367-266708   GGAGGUGUGUGUCUUCGUCUGUGAUGGCACGAUAACUGAACA-UUGAUCGCUUUAC-----GUGUU----A---GUUU-GCAGAUCUGCUCAGU---GGCAACCCGUCACACCUAAAAUA--CAACUCUGGCAGUCCGGAUCUGGUAUCACGGG----------------------------UGAACUCUCGCUGCACGGCGCCGGGCCGAA-----------CGCACGAUUGAUGUC---------------------------------------------------------------------------------------------------------------------------------------------AUUUGUGAUACAAGACUACUGCCGUUCUUACCCAACUCUUUCCAAAUUGUUGAGUAUAAAAUCGUAAUUUAAUACAGAUAGCUUAGCUUCGGAUU------AAAAUUACAUUGUUCAGAACGCUUCCAUAUCACUAGGGCACCGCCG---AGCGGUCGGCCC-AUUCUUUU-G
AAWU01029926.1/3773-4101       GGAGGUGUGUGUCUUCGUCUGUGAUGGCACGAUAACUGAACA-UUGAUCGCUUUG--------UUA----G----UUU-GCAGAUCUGCUCAGU---GGCAACCCGUCACAC-----UCU-UGAUAAACGGCAGUCCGGAUCUGGUAUCACGGG----------------------------UGAACUCUCGCUGCACGGCGCCGGGCCGAA-----------CGCACGAUUGAUGUC---------------------------------------------------------------------------------------------------------------------------------------------AUUCGUGAUACAAGAC----GCUGCCCAGACCCAACUAUUUCUCAAAAUUGUUGAGUAU-AUCGUAAUUUAAUACAGAUAGCUUAGCUUCGGAUU------AAAAUUACAUUGUUCAGAACGCUUCCAUAUCACUAGGGCACCGCCG---AGCGGUCGGCCC-AUUAUUUU-G
AAAB01008933.1/721432-721748   GGAGGUGUGUGUCUUCGUAUGUGAUGGCACGAUAACUGAACA-UUGAUCGCCAAA------AACAGUUUAG----UUU-GCAGAUCUGUCCAGU----GGCAUGCGUCACAA----------CUCUAAUGGUAGUCUUUCUUCUGUGUCAUCGG----------------------------UGAUCUCUCGCUGCACGGCGACGGGCCGUA-----------CGCACGAUUGAUGUC---------------------------------------------------------------------------------------------------------------------------------------------AUCUGUGACACGAGAUU--------------CUACCGCCAUACGAAAUUAGUUGAAAUU-----GUAAUUAUACAAGUUAGCUUAGCUUCGGAUU------AAAAUUACAUUGUUCAGAACGCUUCCAUAUCACUCGGGCACUGCCG---AGCAGUUGGCCC-AUUCUUUUUG
AAZX01010227.1/22096-21793     GGAAGUGUGUG------CUAGUGAUGGCAC---AGCUGAACA-UUGAUCGCUAAC------UAGUAGAU-A----UAUGGCAGAUCUGCUCAGU----GGGUGUUGUCACGU---------------------GGUCGCUUCAAGUAGCUUGUGCUCGGCUCCCGAU-------GCGCCUACAAACCGAGGCCUGUCUCGUGGCCCCUGGCACCUGUAGGCC-CGCACGGUCGAGUCU----------------------------------------------------------------------------------------------------------------------------------------------------UCACGUCGCUCCUCGAACU-----ACCGCGAUUUCCAAAUUGGGGGGCAAUC----------GAAUAGGUCAGACGAGGUAAUU---------------------------GUCGCUUCCAUAU--ACAAGGCGCUGCAGUUCUGCAGUGUGCCC-UUUUUGUC-G
AAJJ01000164.1/55572-55821     GGAGGUGUGUG------UCAGUGAUGGCAC---AGCUGAACA-UUGAUCGCUUUA------GUUCA----G-----UAGGCUGAUCUGCUCAGU---AACGUGCGGUCACGU---------------------GGUCGAUCCAGCAACCAAUGG---------------------------------------ACUCUGACGAUGCCCUAGU-----------CGCACGUCAGUCAUC------------------------------------------------------------------------------------------------------------------------------------------------------CUCUGGUUUCUUGAACG-----UCCGCCAUUUCCAAAUUUGGGGGGUUAC----------GGAUGGGUUUCAUUUAG--------------------------------AACACCUCCAAUA---AUCGGCACUGCAGUUACGUAGUUCGCC--AUUUUUUC-A
AAZO01004201.1/24393-24636     GGAAGUGUGUGUGUC--UUAGUGAUGGCAC---UGCUGAACA-UUGAUCGCU---------CCCACUUC-A-------GGCAGAUCUGCUCAGU--UAAGGUGUAGUCACGU---------------------GGUUUACUUUAGCAGUUCAGG---------------------------------------GACCUCCCGAUGCUACAAAU----------CGCACGGUGGAUGGU----------------------------------------------------------------------------------------------------------------------------------------------------CCCGAGGACUCCUCGAUUGCCGCGAUUCCAAAUUGUUAGGCGUGAGGUUAAU-----------------------------------------------------------CGAACUUCCAUAU---AUCGGUACUACUGUG-UGUAGUUUGCCA-GUUUUUUU-C
AADG06004967.1/71451-71138     GGAAGUGUGUG------CUAGUGAUGGCAC---AGCUGAACA-UUGAUCGCUAAC-----GUAGAA----A----UAUGGCAGAUCUGCUCAGU----GGGUGUUGUCACGU---------------------GGUCGCUUCAAGUAGCUUGUGUUUGGCUCCCGAUUGCGCGUGCAAGUUCGUGGUGUUUUGCUUUAAGCAUCAUCUCGGAUCUGCACGCC-UGCACGGUUGAGUCC---------------------------------------------------------------------------------------------------------------------------------------------------UUCACGUCGCUCCUCGAACU-----ACCGCGAUUUCCAAAUUGGGGGGCAAUC----------GAAUAGGUCAGACGAGGUUAUAAUUU-----------------------GUCGCUUCCAUAU---ACAGGCACUGCAGAUAAGCAGUAUGCCAUGUUUUUUUU-
#=GC SS_cons                   <<<<<<<<--.......---<<<<<---.-...--<<<-<<<.--<<<<<<<<--<<<<_______...._>>>>-->>>>->>>>>>>->>>------------>>>>>--.....---..-----------------------------------.---------..-------------------------------------------.-------------------------..............-----....-----------.-..-------......-----------------.............---------...----------------.-----...............------..-.------.-----------------------------------------------------..........-------------------------------------------------->>>>>>>>----..----<<<<<<<<__..._>>>>>-->>>:.::::::::.:
#=GC RF                        GGAAGuGUgU.......UCUGUGAUuGc.C...auCUGugCA.UUGAUCGcuauacaGaUaauuaa....AuCugUUuagCAGAUCUGcUCAGUGCCGACccuccGUCACAc.....uUU..UgUUUCCcAgUaaUUcugcCUGGcAUugcuGugGC.aCaucgUuu..GAUuGGCUUUCcguugcCUuUcgCuauacGaCGACGGGUcgua.caGCAauaGACGCACGGUuGAUGca..............cCagc....aAuCCacCgCC.C..cCUCCGC......CuCGCGgAUUuCgGUCa.............uGAuUGgaa...uacGuAUaGGuuGgGG.uuGGG...............cGGcGG..u.CagaUG.uugAaGccaacaacaGuugcCCaAGuCAGCcAUUUuCAAAaUUUguuGguUAa..........GuAacuuugUAGCUUAGCUUCGGAUUUUCGUAAuAAAUUUGCUGUUCAGAACaCUUCCAUaU..AcgcGGCAcUGCcG...AGCAgUUUGCCC.AUUcUUUU.G
//
# STOCKHOLM 1.0

#=GF AC   RF01053
#=GF ID   Deinococcus_Y_RNA
#=GF DE   Deinococcus radiodurans Y RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Gardner PP
#=GF SS   Published; PMID:10766734
#=GF GA   80.00
#=GF TC   163.40
#=GF NC   45.40
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000405; Y_RNA;
#=GF RN   [1]
#=GF RM   10766734
#=GF RT   Ro ribonucleoproteins contribute to the resistance of Deinococcus
#=GF RT   radiodurans to ultraviolet irradiation.
#=GF RA   Chen X, Quinn AM, Wolin SL
#=GF RL   Genes Dev. 2000;14:777-782.
#=GF WK   Y_RNA
#=GF SQ   2


AE000513.1/1272031-1271906 GCUCUGGGCCGAAGUGGUCACGGUUACUUCUCCAACCUCAAUGGGCGGAAGCGGUGCAAGCCGUUCCGGGUUCGAUUCCCGGCAUGAAGUGGCCCGUCCGUGACCCGAACCCUUGUCCAGAGCACU
AF233656.1/1-126           GCUCUGGGCCGAAGUGGUCACGGUUACUUCUCCAACCUCAAUGGGCGGAAGCGGUGCAAGCCGUUCCGGGUUCGAUUCCCGGCAUGAAGUGGCCCGUCCGUGACCCGAACCCUUGUCCAGAGCACU
#=GC SS_cons               ((((((((-(((-((((((((((--(((((,,,,,,,,,,,,,,,,,,,,,<<<<____>>>>,,<<<<<_______>>>>>,,,)))))-------))))))))---))--))))))))))):::
#=GC RF                    GCuCuGGgCCgaAGuGGuCaCGGUUaCuuCUCCAACCUCAAUGGGCGGAAGCGGcGCAAgCCGUUCCGGGUUCGAUUCCCGGCAUGaaGuGGCCCGUCCGuGaCCCGAaCCCucGcCCaGaGCACU
//
# STOCKHOLM 1.0

#=GF AC   RF01054
#=GF ID   preQ1-II
#=GF PI   COG4708
#=GF DE   preQ1-II (pre queuosine) riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:18305186; Weinberg Z, Meyer MM, Gardner PP
#=GF SS   Published; PMID:18305186; Gardner PP
#=GF GA   42.00
#=GF TC   43.00
#=GF NC   39.50
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0008616; queuosine biosynthetic process;
#=GF RN   [1]
#=GF RM   18305186
#=GF RT   Confirmation of a second natural preQ1 aptamer class in Streptococcaceae
#=GF RT   bacteria.
#=GF RA   Meyer MM, Roth A, Chervin SM, Garcia GA, Breaker RR
#=GF RL   RNA. 2008;14:685-695.
#=GF RN   [2]
#=GF RM   17621584
#=GF RT   Identification of 22 candidate structured RNAs in bacteria using the
#=GF RT   CMfinder comparative genomics pipeline.
#=GF RA   Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER,
#=GF RA   Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR
#=GF RL   Nucleic Acids Res. 2007;35:4809-4819.
#=GF WK   PreQ1-II_riboswitch
#=GF SQ   14


ABAC01000009.1/939-843     UGUGCUAUACUAGU-AAGGUUGA-------AUGAA--U-CAAC-CCUUGGUGCUUAG-CUUCUUUCACCAAGCAUAUUACACGCGG------------------AUAA--CCGCCAAAGGAGAAAAG--AUG
AAJR01000052.1/12937-13050 UGUGAUAUACUUAG-UAAGUUGU-------UUUAC--A-CAAC-CCUUGAUGCUUAGUUCCCUUUCAUCAAGCAUAUUACAAACGUUAGAAGU----GUUAACUGUCUAAACGUUAAAGGAGAAAUU--AUG
AM406671.1/1746216-1746111 UCUGCUAAAAUAAA-AACGUUGCU----CAAUAGUGAGUUAAC-CCUUGAGCCUUCA-UCCCUUUGCUCAAGCAUAUUAUAGGCGA------------------AUUUUGUCGCCAAAGGAGAACCU-UUUG
CP000260.1/602445-602560   UAUGGUACAAUGUA-ACCGUUGC-------UUU----G-CAAC-CCUUGGUGCUUAGUUCCCUUUCACCAAGCAUAUUAGAAACGUAGAUAGCUUUUGAGAGUUAUCCAGACGUUAAAGGAGAAAAA--AUG
CP000003.1/587341-587456   UAUGGUACAAUGUA-ACCGUUGC-------UUU----G-CAAC-CCUUGGUGCUUAGUUCCCUUUCACCAAGCAUAUUAGAAACGUAGAUAGCUUUUGAGAGUUAUCCAGACGUUAAAGGAGAAAAA--AUG
CP000425.1/786495-786601   UCUGUUAAAAUAAA-AACGUUGCU----CAAUUGCGAGUCAAC-CCUUGAGCCUUCU-UCCCUUUGCUCAAGCAUAUUAAACGCGA-----------------CAUUUUGUCGCCAAAGGAGAGUAU-UUUG
CP000387.1/1493003-1492897 UGGGGGAAUCAACU-AAUGAUGCUCCUCUCAUGUGAUG-CAAC-CCUUGGCGCUUAG-CUUCUUUCGCCAAGCAUAUUACACGCGG-------------------UAAAGCCGCUAAAGGAGAAAAC--AUG
CP000407.1/1534158-1534056 UAUGCUAUACUAAUCAACGUUGUUGA-UAAAUUCA--A-UGAC-CCUUGGGGCUUGC-UCACUUUACCCAAGCAUAUUUUA--AGC------------------UUUUUCGCU--AAAGGAGAAUUU-UAUG
CP000423.1/2043279-2043181 ACACCAAAACUGAA-AACGGAAGG----CAAU----CC-UUCCACGACGAUACUUACUUUCCUUUGAUCGUCGUUACUAC--UGGC------------------AUA---GCCACAAAGGAGAACAAACAUG
CP001033.1/966317-966413   UGUGCUAUACUAGU-AAGGUUGA-------AUGAA--U-CAAC-CCUUGGUGCUUAG-CUUCUUUCACCAAGCAUAUUACACGCGG------------------AUAA--CCGCCAAAGGAGAAAAG--AUG
FQ312042.1/2132413-2132509 UGUGCUAUACUAGU-AGGGUUGA-------AUAAA--G-CAAC-CCUUGGUGCUUAG-CUUCUUUCACCAAGCAUAUUACACGCGG------------------GCAA--CCGCCAAAGGAGAAAAG--AUG
AE014133.2/1474191-1474095 UAUGCUAUACUGGA-UAAGUUGU-------CUG----A-CAAC-CCUUGGUGCUUAUUUCCCUUUCACCAAGCAUAUUACAAACGG-------------------UAGAUCCGUUAAAGGAGAAACA--AUG
CP000114.1/925396-925509   UGUGAUAUACUUAG-UAAGUUGU-------UUUAC--A-CAAC-CCUUGAUGCUUAGUUCCCUUUCAUCAAGCAUAUUACAAACGUUAGAAGU----GUUAACUAUCUAAACGUUAAAGGAGAAAUU--AUG
FQ312029.1/941296-941392   UGUGCUAUACUAGU-AAGGUUGA-------AUGAA--U-CAAC-CCUUGGUGCUUAG-CUUCUUUCACCAAGCAUAUUACACGCGG------------------GCAA--CCGCCAAAGGAGAAAAG--AUG
#=GC SS_cons               ::::::::::::::.:::<<<<<......._____..>.>>>>.,<<<<<<<_____._______>>>>>>>---------<<<<<..................______>>>>>::::::::::::..:::
#=GC RF                    UauGcuAuAcUaaa.AAcGuuGc.......aUuaa..g.CaaC.CcuuGgugCUUAg.UccCUUUcacCaagCAUAUUAcAagcGg..................aUauagcCgcuAAAGGAGAAaau..AUG
//
# STOCKHOLM 1.0

#=GF AC   RF01055
#=GF ID   MOCO_RNA_motif
#=GF DE   Moco (molybdenum cofactor) riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Barrick JE, Weinberg Z
#=GF SS   Published; PMID:18363797
#=GF GA   36.00
#=GF TC   36.00
#=GF NC   35.80
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0048037; cofactor binding;
#=GF RN   [1]
#=GF RM   18363797
#=GF RT   A widespread riboswitch candidate that controls bacterial genes involved
#=GF RT   in molybdenum cofactor and tungsten cofactor metabolism.
#=GF RA   Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR
#=GF RL   Mol Microbiol. 2008;68:918-932.
#=GF RN   [2]
#=GF RM   17621584
#=GF RT   Identification of 22 candidate structured RNAs in bacteria using the
#=GF RT   CMfinder comparative genomics pipeline.
#=GF RA   Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER,
#=GF RA   Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR
#=GF RL   Nucleic Acids Res. 2007;35:4809-4819.
#=GF WK   Moco_RNA_motif
#=GF SQ   160


CP000141.1/711593-711712     AAAAAUAAGCUGCUC-CG-AGUAUUU-U-C-ACCUA-AAGCU----UUA------------------------------------GGCCAUGGUGAAAAUACC------------------------------------------------------------------------------AAAGGGUACUAC---CG-GGAAACCGGGGUGCCUCC-CGUUU---U-GGAAAGGAG-U-UAUCAAAGCGCCUUU
CP000448.1/1172054-1171931   AAAAGAAUAGAGCUC-CG-AGCCUUAUU-A-AUCUA-AAGAC----UGCG-----------------------------------GUUCAUGAUUAUAGGGCC------------------------------------------------------------------------------UAUAGGUAU-AA---GU-GGAAACGCUUAUGCCUCC-CCGUAUUGU-GGAAAGGAG-U-ACUUAUUUAGCUGUU
AP009389.1/593165-593047     AAAAAUCAUACUCUC-CG-AGCCAGG-U-A-ACCUA-AAGCU----CGA------------------------------------CGCCAUGGU-ACCUGGCC-----------------------------------------------------------------------------GGCAGGGUGU-AC---CG-GGAAACCGGUGUGCCUUC-CAUUG---C-GAAAAGGAG-A-GCUGGAUUUGGGACC
CP000482.1/935247-935365     AUGCCAUGUUAUCUC-CG-AGCCUUG-C-C-ACCUA-AAAGG----AAAA-----------------------------------CCUCAUGGU-GCACGGCC------------------------------------------------------------------------------AACGGGUUU-CG---CU-GGAAACAGCGGAGCCUCC-CUUC----A-GGAAAGGAGCU-UGUCCUCGUUAGAGA
AACY022724149.1/127-8        AACAGAUAAUUUCUC-CG-AUUCAUU-CAU-GCCUA-AUGCG----CC-------------------------------------CGCAAAGGCAGGAUGAAC-----------------------------------------------------------------------------GAAAGGGUCA-GC---AU-GGAAACGUGCUGGCCUCC-CGUUU---U-GGAAAGGAG-A-CCUCCUAUGUUGGAC
CP000148.1/2016583-2016702   AUUUAAAACCGUCUC-CG-AGCCGCG-G-C-GCCUA-AAGGG---AACAU-----------------------------------CCCCAUGGCGGUCCGGCC------------------------------------------------------------------------------UAUGGGUAU-CG---CU-GGAAACGGCGUUGCCUUC-CUUA----U-GCAAAGGGG-A-CCCAGCGACGCGGAG
AE017180.1/2979275-2979393   AUAUUUUGUUAUCUC-CG-AGCCCAU-C-C-GCCUACCAGGA----ACAU-----------------------------------UCCCACGGC-GGCCGGCC------------------------------------------------------------------------------GACGGGUGU-UG---CU-GGAAACGGCAGCGCCUCC-CCUC----U-GGAAAGGAG-A-UUCCGGGCCACGUGC
CP000142.2/2958797-2958678   UACAGAACACGUCUC-CG-AGUCUU--A-A-GCCUA-AAAGG---AUGGA-----------------------------------CCUCAUGGCUGACGGGCC-----------------------------------------------------------------------------GGCAGGGUUU-CG---CU-GGAAACGGCGGAGCCUCC-CUUU----C-GGAAAGGAG-A-UAUUUGCAUUUUGAG
CP000232.1/1884333-1884198   UUGAAUAGUCAUCUC-CG-AGCCGGU-G-C-UCCUA-AGGGC----UGUC-----------------------------------GCCUAUGGAACACCGGCC----UGGGUUUC----------------------------------------------------------GUACCCA--UGGGGUAG-GU---CG-GGAAACGGGCCUGCCUCC-CUUUGC-UC-GGAAAGGAG-A-UUCCCCAUGGCUUCU
AAWL01000002.1/83580-83714   UAUGGAAUACGCCUU-CG-AGCCUGU-C-C-GCCUA-AAGGU----AGCG-----------------------------------UCCCAUGGCAGACUGGCC----UGGGCCCG----------------------------------------------------------ACGCCCA--CGGGGUAU-AG---UU-GGAAACGGCUAUGCCUUC-CCAGUU--U-GAAAAGGAG-G-UAGACAAAUGAUUAG
CP000627.1/583753-583892     GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AAKJ02000036.1/5658-5797     GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AAKI02000041.1/24441-24302   GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AAUR01000042.1/26458-26319   GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AAWE01000035.1/31834-31695   GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AAWF01000006.1/90475-90336   GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AAUU01000009.1/30696-30557   GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AAWD01000062.1/12304-12165   GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AE003852.1/1093019-1093158   GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AAUT01000027.1/30681-30542   GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AAWG01000034.1/4112-3973     GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
BA000031.2/2204413-2204280   UGGUUGCCAUAACUC-CG-AGCUCAC-U-A-UGCUA-AGUCC----GA-------------------------------------GGAUAAGCAUUUUGAGCC---AGUGACAUA----------------------------------------------------------CUGUCAC--AAGGGCAU-GA---UU-GGAAAUGGCCAUGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
AAWQ01000033.1/29657-29524   UGGUUGCCAUAACUC-CG-AGCUCAC-U-A-UGCUA-AGUC-----UGAG------------------------------------GAUAAGCAUUUUGAGCC---AGUGACAUA----------------------------------------------------------CUGUCAC--AAGGGCAU-GA---UU-GGAAAUGGCCAUGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
AAWP01000079.1/7183-7050     UGGUUGCCAUAACUC-CG-AGCUCAC-U-A-UGCUA-AGUCC----AA-------------------------------------GGAUAGGCGUCUUGAGCC---AGUGACAUA----------------------------------------------------------CUGUCAC--AAGGGCAC-AA---UU-GGAAAUGAUUAUGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
ABCH01000027.1/16237-16374   UAACUGCCAUAACUC-CG-AGCUCUA-C-G-CGCUA-AGUCGA--ACCAA-----------------------------------AGAUAAGCUUCUAGAGCC---AGUGACAAU----------------------------------------------------------UUGUCAC--AAGGGCAU-AA---UU-GGAAAUGAUUGUGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
AATY01000030.1/31957-31818   GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------GUAAAUAUGCGUUGUAAGCC---AGUGGCAGA----------------------------------------------------------AUGUCAC--AAGGGCAG-GA---UU-GGAAAUGAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
CP000444.1/4455501-4455368   CGAAUGACGGUUCUC-CG-AGCUUGC-C-U-ACCUA-AGUC-----GACA------------------------------------GAUAUGGGGGUGUAGCC----GUGGCAAUA---------------------------------------------------------AGGCCAC--UGGGGUGA-GU---AA-AGAAAUGCACUCGCCUCC-CACACU--U-GGAAAGGUG-A-UCAUGUCUCAAUUAC
CP000446.1/294832-294965     CGAAUGACGGUUCUC-CG-AGCUUGC-C-U-ACCUA-AGUC-----GACA------------------------------------GAUAUGGGGGUGUAGCC----GUGGCAAUA---------------------------------------------------------AGGCCAC--UGGGGUGA-GU---AA-AGAAAUGCACUCGCCUCC-CACACU--U-GGAAAGGUG-A-UCAUGUCUCAAUUAC
CP000720.1/3203744-3203598   ACUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
ABCQ01000014.1/60025-59878   AUAUUAAUCAAACUC-CG-AUCCUUAAC-G-AUCUA-AAUUU---AUAAAA--------------------------------UUAAAUAUGAUCUUAAGGACU--CAUAGCAUUUUA----------------------------------------------------AAUUUGCUAU--AAGGGUUU-AA---UC-AGAAAUGAUUAGGCCUCC-CGUAUU--U-GGAAAGGUG-U-UUAUGCAACUUCAAG
AE014299.1/4641235-4641102   CAGCUGACGGUUCUC-CG-AGCUUGC-C-U-ACCUA-AGUC-----AACA------------------------------------GAUAUGGGGGUGUAGCC----GUGGCAAUA---------------------------------------------------------AGGCCAC--UGGGGUGA-GU---AA-AGAAAUGCUCUCGCCUCC-CACACU--U-GGAAAGGUG-A-UCAUGUCUCAAUUAC
BA000037.2/1214618-1214768   GGGUUGCCAUAACUC-CG-AGCUUAA-C-U-UGCUA-AGUUA---UUUUAUUUCAAU---------------------GAUGGAAUGAUAAGCAGCUUAAGCC---AGUGACAUG----------------------------------------------------------AUGUCAC--AAGGGCGU-AA---UU-GGAAAUGACUACGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
BX936398.1/1419284-1419430   GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
CP000305.1/3199155-3199009   GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
ABAT01000001.1/487948-487802 GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
AAUB01000157.1/9443-9589     GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
CP000308.1/1219676-1219822   GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
AE009952.1/3330087-3329941   GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
AAYU01000002.1/139698-139844 GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
AAYV01000015.1/91236-91382   GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
CP000668.1/2886890-2886744   GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
AAYS01000002.1/351853-351707 GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
AL590842.1/1306720-1306866   GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
AAYT01000002.1/511253-511107 GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
ABCD01000002.1/667524-667378 GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
AAYR01000003.1/37187-37041   GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
AE017042.1/1078165-1078019   GCUGAACAUAAACUC-CU-AGCCUUA-G-C-GUCUA-CGUUG---UCUUUUUUGU-------------------------AUUGGCAAUAUGAUGUUCUGGCC----GUGGCCUU----------------------------------------------------------AAGCCAC--CAGGGUGCAAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
CP000606.1/101467-101601     GAAACGACGGUUCUC-CG-AGCUUUC-U-C-UCCUA-CGUC-----CACA------------------------------------GAUAGGGAGAUUAAGCC----GUGGCAAUA---------------------------------------------------------GUGCCAC--CGGGGUGA-GG---AA-AGAAAUUGACUCACCUCC-CCUUAC-UU-GGAAAGGUG-A-UCAUGUCUCAACUAC
CP000462.1/1732669-1732808   AAACUAGAUGAACUC-CG-AGCGGUU-U-U-GCCUA-AGUCC----UCA------------------------------------UGAUAGGGGGAAACCGCC---GUCAGCCGAUGU-----------------------------------------------------UCGAGCUGU--AAGGGUCA-GG---AA-AGAAAUGCCCUGGCCUCC-CGUAUU--U-GGAAAGGUG-U-UUAUGUCGCCACUGC
CP000644.1/2971207-2971068   AAACUAGAUGAACUC-CG-AGCUGUU-U-U-GCCUA-AGUCC----UUG------------------------------------GGAUAGGGGAAAGCCGCC---GUCAGCCGAUGU-----------------------------------------------------UCGAGCUGU--AAGGGUCA-GG---AA-AGAAAUGCCCUGGCCUCC-CGUAUU--U-GGAAAGGUG-U-UUAUGUUGCCACUGC
AM286415.1/3151770-3151626   ACUGAGCACAAACUC-CU-AGCCUUA-G-U-GUCUA-CGUUG---UUGCGUUUA---------------------------UGGACAAUAUGAUGCUCUGGCC----GUGGCUUC----------------------------------------------------------AAGCCAC--CAGGGUGCGAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUUAC
CP000563.1/321974-322107     CCGGUGACGGUUCUC-CG-AGCUUGC-C-U-ACCUA-AGUC-----GAAA------------------------------------GAUAUGGAGGUGUAGCC----GUGGUAAUA---------------------------------------------------------AUGCCAC--CGGGGUGG-GA---UA-AGAAAUGCUCUCACCUCC-CACACU--U-GGAAAGGUG-A-UCAUGUCUCAAUUAC
CP000753.1/319215-319348     CCGGUGACGGUUCUC-CG-AGCUUGC-C-U-ACCUA-AGUC-----GAAA------------------------------------GAUAUGGAGGUGUAGCC----GUGGUAAUA---------------------------------------------------------AUGCCAC--CGGGGUGG-GA---UA-AGAAAUGCUCUCACCUCC-CACACU--U-GGAAAGGUG-A-UCAUGUCUCAAUUAC
CP000507.1/4159189-4159323   UCAAUGACGGUUCUC-CG-AGCUCCU-G-C-ACCUA-AGUC-----AAUG------------------------------------GAUAUGGUGUUUGAGCC----GUGGCGCG----------------------------------------------------------GUGCCAC--CGGGGUGG-GG--UGC-AGAAAUGGCUUCACCUCC-CGAUAC-UU-GGAAAGGUG-A-UCAUGUCUCAACUUC
CP000469.1/309677-309810     CGAAUGACGGUUCUC-CG-AGCUUGC-C-U-ACCUA-AGUC-----GACA------------------------------------GAUAUGGGGGUGUAGCC----GUGGUAAUA---------------------------------------------------------AGGCCAC--UGGGGUGA-GU---AA-AGAAAUGCACUCGCCUCC-CACACU--U-GGAAAGGUG-A-UCAUGUCUCAAUUGC
AASA01000098.1/11609-11765   AUUUAUUGAAGACUC-CG-AGCAUUA-U-U-UCCUA-ACUCU---AAAAAUUAAAGA--------------------CAAAUUUUUGAUAUGGAAUUUAUGCCAGUAACAGCAUA----------------------------------------------------------AAGCUGUUCAAAGGAUA-AC---UU-AGAAAUGGGUUGUCCUCU-CGUGUU--U-AGAAAGGUG-U-CAAAUGCAGUCUAUU
AAPS01000028.1/5735-5869     UGGUUGCCAUAACUC-CG-AGCUCAC-U-AUUGCUA-AGUCC----UU-------------------------------------GGAUAAGCGUUUUGAGCC---AGUGGCAUA----------------------------------------------------------CUGUCAC--AAGGGCAU-GA---UU-GGAAAUGGCCAUGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
CP000503.1/268441-268574     CCAGCGACGGUUCUC-CG-AGCUUGC-C-U-ACCUA-CGUC-----AAUA------------------------------------GAUAUGGAGGUGUAGCC----GUGGUAAUA---------------------------------------------------------AUGCCAC--CGGGGUGA-GU---AA-AGAAAUGCUCUCACCUCC-CACACU--U-GGAAAGGUG-A-UCAUGUCUCAAUUAC
CP000681.1/424831-424964     CCAGCGACGGUUCUC-CG-AGCUUGC-C-U-ACCUA-CGUC-----AAUA------------------------------------GAUAUGGAGGUGUAGCC----GUGGUAAUA---------------------------------------------------------AUGCCAC--CGGGGUGA-GU---AA-AGAAAUGCUCUCACCUCC-CACACU--U-GGAAAGGUG-A-UCAUGUCUCAAUUAC
AAKK02000029.1/45601-45467   UGGUUGCCAUAACUC-CG-AGCUCAC-U-AUUGCUA-AGUCC----GA-------------------------------------GGAUAAGCGUUUUGAGCC---AGUGGCGUA----------------------------------------------------------CUGUCAC--AAGGGCAU-GA---UU-GGAAAUGGCCAUGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
CP000447.1/97810-97942       GAUCUGACGGUUCUC-CG-AGCUUUU-U-G-CCCUA-CGUC-----AAU-------------------------------------GAUAUGGGCAGUUAGCC----GUGGUAAUU---------------------------------------------------------UUGCCAC--CGGGGUGA-GU---AA-AGAAAUGCACUCACCUCC-CACACU--U-GGAAAGGUU-A-ACAUGUCCCAACUAC
AAZG01000002.1/216987-216847 UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUU---CAUCG-----------------------------------AAAUACGGC-GACAAGCC----AAUAACGCCG------------------------------------------------------UGUGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CCAUAU-UU-AGAAAGGUG-U-AGAAUGCAAUCCAUU
CP000653.1/1402015-1402149   GAUGAAAACAUACACUCU-AGCCUUG-A-C-GCCUG-UGUC-----ACAU------------------------------------GAUAUGGCGCCCUGGCC----GUGGCGGUU---------------------------------------------------------UCGCCAC--CAGGGUAC-AG---AA-AGAAAUGACUGUGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000302.1/114598-114731     GCAUUGACGGUUCUC-CG-AGCUUCU-U-A-UCCUA-AGUC-----UUUA------------------------------------GAUACGGGUCAUUAGCC----GUGGUAAUA---------------------------------------------------------AUGCCAC--CGGGGUGA-GU---AA-AGAAAUGCACUCACCUCC-CGCACU--U-GGAAAGGUU-A-ACAUGUCUCAACUAC
CP000671.1/754622-754762     UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUU---CAUCG-----------------------------------AAAUACGGC-GACAAGCC----AAUAACGCAG------------------------------------------------------UUCGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CCGUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
BX571864.1/57269-57413       CUAUGGAAUUAACUC-CU-AGCCUCU-G-C-AUCUA-AGUCA---CUUUUUAC----------------------------ACAGCGAUAUGAUGUUUUGGCC----GUGACCACU---------------------------------------------------------GAGUCAC--CAGGAUGUGAG---GC-AGAAAUGCCCACGUCUCC-CAUGUU--U-GGAAAGGUG-U-UAUGGUGAAACAACU
AAZD01000003.1/249903-250044 UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUUC--ACAAA-----------------------------------AAAUACGGU-GGCAAGCC----AAUAACGCGG------------------------------------------------------UACGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CCAUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
AAZE01000014.1/10673-10814   UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUUC--ACAAA-----------------------------------AAAUACGGU-GGCAAGCC----AAUAACGCGG------------------------------------------------------UACGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CCAUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
AAZI01000004.1/68933-69074   UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUUC--ACAAA-----------------------------------AAAUACGGU-GGCAAGCC----AAUAACGCGG------------------------------------------------------UACGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CCAUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
L42023.1/1745366-1745226     UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUU---CAUAG-----------------------------------AAAUACGGU-GGCAAGCC----AAUAACGCGC------------------------------------------------------UACGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CCGUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
CP000312.1/1962720-1962561   AUUAGUAUAACUCUC-CA-AGCUUAA-A-G-AUCUA-AGGAG----AAGG-----------------------------------UUCUAUGAUUUUUAAGCC----UGGAUUACUAAAUUAUUUAA-----------------------------------CAUUAAGUUGGUAAUCCA--CAGGGUAA-GG---UU-UGAAAGAAUUUUGCCUCC-ACGUAUUUU-GGGAAGGAG-A-AUAAGCAAAAGUAAA
AAZF01000005.1/174554-174413 UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUUC--AGAAG-----------------------------------AAAUACGGU-GGCAAGCC----AAUAACGCCG------------------------------------------------------UGUGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CCAUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
AP006840.1/3132643-3132508   GAUGUGAUCACGUCC-CG-AGUCAUG-C-G-ACCUG-UACCC----GAUG-----------------------------------GGGUAUGGUCGCCUGACCG-GUCCCGGUCG----------------------------------------------------------UACCGGG-CCAGGGUUG-UC---GG-GGAAACCUGGCGGCCUCC-CGU-----U-GGAAAGGGG-C-GGAACUGCGGGAGAU
CP000612.1/2515252-2515370   AAAUUAAUAGUACUC-CG-AGCUUAG-G-C-ACCUA-AGAU-----AGUA------------------------------------AUUAUGGUUCUUAAGCC-----------------------------------------------------------------------------GUUAGGGUUU-GU---CU-GGAAACGGGCAGGCCUCC-CAAUG---C-GGAAAGGAG-A-AACACAUUAUGCCAA
AP008232.1/1475425-1475565   AGGUAUACAUAACUC-CU-AGCCUUU-A-C-GCCUA-AGUGG---CCCGUCAU-----------------------------GAGCCAUAGGGGGUUCUGGCC----GUGGCGAA------------------------------------------------------------GCCAC--CAGGGUGCAGG---GU-AGAAAUGCCGGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UACUGUGUCACAACU
AE014613.1/2146005-2145861   AACCACAAUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUAUGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AL627268.1/76072-76216       AACCACAAUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUAUGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AAZH01000018.1/19134-18993   UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUUC--ACAAG-----------------------------------AAAUACGGU-GGCAAGCC----AAUAACGCGC------------------------------------------------------UACGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CCGUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
CP000672.1/374985-374845     UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUU---CAUAG-----------------------------------AAAUACGGU-GGCAAGCC----AAUAACGCGC------------------------------------------------------UACGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUGUCCUCU-CCGUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
AAZJ01000004.1/67324-67464   UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUU---CAUAG-----------------------------------AAAUACGGU-GGCAAGCC----AAUAACGCGC------------------------------------------------------UACGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUGUCCUCU-CCGUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
AAEW02000009.1/8135-8014     UACUAUCAAGAUCUC-CG-AGCCUGC-C-CCCCCUA-CGGAG---GUUGC-----------------------------------CUUUAAGGG-GACAGGCC------------------------------------------------------------------------------UCAGGGUUG-CA---UU-GGAAACGGUGUGGCCUCC-CAGUCU--U-GGAAAGGAG-A-UUCUUACCAUGCGCU
ABEJ01000007.1/41426-41570   AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUAUGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
ABAN01000005.1/160757-160613 AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUAUGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AE017220.1/899104-899248     AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUAUGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AAXB02000020.1/32320-32165   AAAUACAAGGUUCUC-CGAAGCCUUC-A-U-GCCUA-AGAUC---CAUAAAAA----------------------------UUGUGAUGAUGGGAUGUUGGCC----AGGAAUGACAGGU------------------------------------------------CUGUCAGUUCCU--CAGGGUAG-AU---AG-GGAAACGUAUCUGCCUCC-CGCGUAUUU-GGAAAGGAG-A-GCAGCACCUUUGCUU
CP000647.1/905889-906027     AUAACCUGUUAACACUCU-AGCCUCU-U-C-GCCUG-UGUC-----AAAA------------------------------------GAUAUGGCGAUUUGGCC----GCGACGCCGCC-----------------------------------------------------GGUUGUCGC--CAGGGCGU-GG---AA-AGAAAUGACCGCGUCUCC-CGUAUU--U-GGAAAGGUG-U-AUAUGGCCUCACAGC
CP000724.1/1069180-1069304   AUGAUAUUAAUUCUC-CG-AGCUUAUGA-C-UCCUA-AUAGA---UCAAUG---------------------------------GUCUGAUGGAGUGCAAGCC-----------------------------------------------------------------------------UGUAGGGUAU-UG---UU-GGAAACAAUAAUGCCUCC-CAUAG---C-GGAAAGGAG-U-GCGCAAAUCUAAUGC
AJ312124.1/15932-16050       UAUACACAGAUUUUC-CG-AGUCGUC-A-U-UUCUA-AAGCC----AA-------------------------------------GGCCAUGAAAUGCUGACC------------------------------------------------------------------------------AGUGGGCCU-UU---UG-AGAAAUUGGGGGGCCUCC-CAUAUU--U-GGAAAGGAG-A-AUCUUAAACCACUGG
BA000007.2/939277-939421     UUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUAUGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
ABEI01000004.1/118460-118604 AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUACGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
ABAO01000011.1/6431-6575     AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUACGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
ABEL01000001.1/615181-615325 AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUACGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AE016827.1/1003377-1003526   AGAAAUUUUAUAUAC-CG-AGCUUGU-A-C-GCCUA-AGUUU---UUAAAUUUA--------------------------UUUGAAAAUAAGGCGGCAAUGCC----AGCAAUGAAU------------------------------------------------------UUUAUUGCU--CAGGGAUAAUG---UG-GGAAACGACUUAUCCUCU-CAUCUU--C-AGAAAGGUA-U-CAAAUGCAAUCUAUU
AAXG02000019.1/34077-33936   CAAUUCAAUAUUCUC-CG-AGCCCCU-G-C-GCCUA-CGGC-----UUU-------------------------------------GCUAUGGCGCCCGGGCC----GUGGACGCCUCC--------------------------------------------------ACGGUGUCCUU-UCAGGGUCU-GU--GCU-GGAAACGGACAGGCCUUC-CGUGUU--U-GAGAAGGAG-A-GGUUUUUUCAGGCUG
U00096.2/816135-816279       AUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
X70420.1/73-217              AUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AP009048.1/817334-817478     AUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000158.1/1582667-1582794   GUUGGAAAUUCGCUC-CG-AGCCGUU-C-C-GCCUA-AAGCG---CCGUUUCC-----------------------------CGGUGUCAUGGCGGCCCGGCC-------------------------------------------------------------------------------GAGGGUGG-CA---GUUGGAAACCCUGCCGCCUCC-CGUGCU--U-GGAAAGGAG-C-CAUGCGAUGACACAU
AE014075.1/839533-839677     UUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000468.1/781456-781600     UUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000036.1/682934-683078     UUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AE014073.1/755896-756040     UUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000243.1/779855-779999     UUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000038.1/805998-806142     UUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000247.1/832790-832934     UUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AE005174.2/940930-941074     UUAACCACUAAACACUYU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUAUGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000698.1/4162311-4162191   GAAACUGACGCUCUC-CG-AGCUGUA-G-C-GCCUA-AAAGGU--UUGUA-----------------------------------CCUGAUGGCGC-ACGGCC------------------------------------------------------------------------------UAUGGGUUC-UG---CC-GGAAACGGCAGCGCCUCC-CUUU----U-GGAAAGGAGAA-ACCGCAGCGUUGCAA
CP000026.1/2029594-2029450   AACCACAAUAAACACUCU-AGCCUCU-G-C-ACUUG-GGUCA----UUUU-----------------------------------UGAUAUGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
BX950851.1/3157560-3157412   AUGAGAAUCAAACUC-CU-AGCCUUG-G-U-GCCUA-AGUGA---UGCGCUUAUU-------------------------GCGCGUGAUACGGUGCCUUGGCC----GUGGCCUUC--------------------------------------------------------GUGGUCAC--CAGGGUGCGAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UUAUGGUGAGUCAAC
CP000510.1/2652936-2652780   UUUUAAAACCAGCUC-CG-AGCUUAA-U-AAAACUA-AGUUU---CCUUUUUA----------------------------AGGUAAAUAAGUCUGUUAAGCC---GCUUGUCUGACAUUU----------------------------------------------UGGUCAGCGCAAG--AAGGGUAA-AG---AG-AGAAAUGUCUUUGCCUCC-CGUAUU--U-GGAAAGGAA-C-UUAACAUGAGCCAAC
CP000679.1/1094763-1094897   UUUUGAAAAUCUUUC-CG-AGCCAUU-G-CAACCUA-AAAAG---AGGGGUUUU--------------------------UCCCUCUUCAUGGUGCUUUGGCC-----------------------------------------------------------------------------GAUAGGGUGC-AGGUUUG-GGAAACCACUGCGCCUCC-CGCUU---U-GGAAAGGAA-A-GAUUUAAAGGAUACU
AAOE01000024.1/17701-17833   CAUUAAGCAAUACAC-CG-AGUGACA-G-GGCGCUA-AGUGG----UCU------------------------------------CCAUAAGCCCUUGUCACC----UCGCAGUA-------------------------------------------------------------GCGA--CAGGGUAG-CG--AUU-GGAAACGGCGUUGCCUCC-CGUGUU--U-GGAAAGGUG-A-AUAAUGUUACAGGAU
CP000746.1/1838749-1838596   UCAAUUUUCGUUUAC-CG-AGCUUGU-G-U-GCCUA-AGUUC---UUCCGGUUAUC----------------------CGGCGCGGAAUAAGGCAGCAACGCC----AGCGAUGCGG------------------------------------------------------UUUAUCGCU--CAGGGAUC-CG---UU-GGAAACAGUUGGUCCUAC-CGAUUU-UU-GUAAAGGUA-U-UCAAUGCAAUCUAUU
CP000266.1/795717-795862     UUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG--GAA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000388.1/2608745-2608595   CAGGUGGUUUAACUC-CG-AGCCUUC-A-U-ACCUA-AAUC-----AGAA------------------------------------GACAAGGUAUGUUGGCC----GCGAAGUGCGUUCGCAA-----------------------------------------GAAUGUGUCAUUCGC--CAGGGUUG-UG---AG-AGAAAUCAAACAGCCUCC-CCGUAA-GU-GCCAAGGCG-A-UAAGGCCCGGCAACU
CP000360.1/5126307-5126444   CUAGGAACGUGUUUC-CG-ACGUUCG-C-U-GCCUA-CGG------AAUA-------------------------------------CUAAGGCAUCGGGCGC----GGUAUCCAUCUUU-------------------------------------------------GUAGAUGGAUC--GAGGGUGA-CG---AA-GGAAACUUCGCCGCCUCC-CGUU----U-GGAAAGGAA-G-CACCUCGGCGCAUGC
CP000478.1/38745-38855       AGAACGGUCGCUCCC-CG-AGCCGCC-G----------GGUC----UAA------------------------------------GGCU--UUUGCGGCGGCC-----------------------------------------------------------------------------GGCAGGGUGU-GC---CU-GGAAACGGGCAUGCCUCC-CGUUG---C-GGAAAGGGG-A-GCAGGUCAAACCGGG
CR522870.1/3382961-3382835   UUAAGAAUAUAACUC-CG-AGCUAAA-A-G-GCCUU-CGGUUUCUGCAUG-----------------------------------GAUCAUGGUCUGC-AGCC-----------------------------------------------------------------------------GUUAGGGUUG-UA---CU-GGAAACGGUUCAGCCUUC-CACCAC-UU-GAAAAGGAG-UCUGUAUGAAUGUCUCA
AAMR01000039.1/24877-24725   CAGUUGCCAUAACUC-CG-AGCUCUC-G-CAUGCUA-AGUCG---CACAGUGGUAUU--------------------UGCUGUACCGAUACGCAUCAAGAGCC---AGUGACAUG----------------------------------------------------------UUGUCAC--AAGGGCUU-AA---UU-GGAAAUGAUUAUGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
AAPH01000008.1/168857-169008 UAGCUGCCAUAACUC-CG-AGCUUUG-G-U-CACUA-CGUUU---UCUGUUUUUCUU--------------------AAAUCAGAAUAUAUGUGUUCAGAGCC---AGUGACAUA----------------------------------------------------------CUGUCAC--CAGGGUCA-AU---UU-AGAAAUGAAUCGGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCCAUGGCGCAACAA
AAOJ01000002.1/672485-672316 UAACUGCCAUAACUC-CG-AGCAUUU-U-U-CACUA-AGUUA---CUAAGCGAUGUUGGACAUUAA--UAUAUACGUUCAAAAGUUGAUAGGUGAUUAAUGCC---AGUGACGAU----------------------------------------------------------UUGUCAC--CAGGGUUU-AU---UU-AGAAAUGAAUUGACCUCC-CGUAUU--U-GGAAAGGUG-U-UCCGUGGCGAAACAA
AAOU01000009.1/42833-43004   UAACUGCCAUAACUC-CG-AGCAUUC-U-U-CACUA-AGUUA---CUAAGCGAUGUUGGACUUAUAUAUAUAUACGUUCAAAAGUUGAUAGGUGAUUAAUGCC---AGUGACGAU----------------------------------------------------------UUGUCAC--CAGGGUUU-AU---UU-AGAAAUGAAUUGACCUCC-CGUAUU--U-GGAAAGGUG-U-UCCGUGGCGAAACAA
ABDX01000019.1/7621-7434     AUUAGUAUAAAUCUC-CA-AGCUUAA-A-G-AUCUA-AGGAG----AAGG-----------------------------------UUCUAUGAUUUUUAAGCC----UGGAUUACUAAAUUAUUUAACAUUAAGUUUAAUA-------AGAGCUUAAAUUGUUAAUUUGGGGGUAAUCCA--CAGGGUAA-GG---UU-UGAAAGAAUUUUGCCUCCACGUAUU--UUGGGAAGGAG-A-AUAAGCAAAAGUAAA
AAND01000029.1/42323-42171   CAGUUGCCAUAACUC-CG-AGCUCUC-G-CAUGCUA-AGUCG---CACAGUGGUAUU--------------------UGCUGUACCGAUACGCAUCAAGAGCC---AGUGACAUG----------------------------------------------------------UUGUCAC--AAGGGCUU-AA---UU-GGAAAUGAUUAUGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
AC150248.3/31115-31259       AUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AAZW01000021.1/37268-37420   CGGUUGCCAUAACUC-CG-AGCUCUC-G-CAUGCUA-AGUCG---CACAGUGGUAUU--------------------UGCUGUACCGAUACGCAUCAAGAGCC---AGUGACAUG----------------------------------------------------------UUGUCAC--AAGGGCUU-AA---UU-GGAAAUGAUUAUGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
AB017192.1/8307-8501         AUUAGUAUAAAUCUC-CA-AGCUUAA-A-G-AUCUA-AGGAG----AAGG-----------------------------------UUCUAUGAUUUUUAAGCC----UGGAUUACUAAAUUAUUUAACAUUAAGUUUAAUAAGAACUUAAAUUGUUAAUUGGUUUAAUUGGGGUAAUCCA--CAGGGUAA-GG---UU-UGAAAGAAUUUUGCCUCCACGUAUU--UUGGGAAGGAG-A-AUAAGCAAAAGUAAA
BA000016.3/2073405-2073211   AUUAGUAUAACUCUC-CA-AGCUUAA-A-G-AUCUA-AGGAG----AAGG-----------------------------------UUCUAUGAUUUUUAAGCC----UGGAUUACUAAAUUAUUUAACAUUAAGUUUAAUAAGAACUUAAAUUGUUAAUUGGUUUAAUUGGGGUAAUCCA--CAGGGUAA-GG---UU-UGAAAGAAUUUUGCCUCCACGUAUU--UUGGGAAGGAG-A-AUAAGCAAAAGUAAA
AM933172.1/829612-829756     AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUACGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000924.1/904376-904493     UUAUUACUUAUUCUC-CG-AGUCUAU-A-A-UCCUA-AGGC-----AAGA------------------------------------GCUAUGGAUUAUAGGCC-----------------------------------------------------------------------------GAUAGGGUAG-UG---CU-GGAAACGGUGCUGCCUCC-CGCC----U-GGAAAGGAG-A-AUAGGAAGGCUGCUA
CP000800.1/865089-865233     AUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AM933173.1/847519-847663     AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUACGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CU928145.2/876431-876575     AUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000826.1/1451002-1451144   CUGAAACCAAAACUC-CU-AGCCUCU-G-G-GCCUA-CGUUG---UUCUUGU------------------------------GAACAAUAUGGCGCUUGGGCC----GUGGCGAAG--------------------------------------------------------UCAGCCAC--CAGGGUGCAGA---GC-GGAAACGCUCGCAUCUCC-CGACUU--U-GG-AAGGUG-U-UAUGGUGCCGCAACU
AE006468.1/870506-870650     AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUACGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000853.1/2630463-2630586   AUAACUAAAUAUCUC-CG-AGUUCAU-C-GAUCCUA-AUACCU--GUUUU-----------------------------------CGUAAUGGUCUAUGAGCC-----------------------------------------------------------------------------UGUAGGGUAU-UG---UG-GGAAACUUCAAUGCCUCC-CAUUG---U-GGAAAGGAG-U-ACUAUGCAGAUCCCU
CP000057.2/1827000-1826859   UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUUC--AGAAG-----------------------------------AAAUACGGU-GGCAAGCC----AAUAACGCCG------------------------------------------------------UGUGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CCAUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
CP000927.1/4176112-4176249   CGAUGAAACUCGCUC-CG-AGCGUCC-C-G-GCCUA-ACGCGC--AUCCG-----------------------------------CGCCAAGGCCGGGCCGCCG--CGCCGGUAC-----------------------------------------------------------GCCGGC--AAGGGUGA-CG---GG-GGAAACGCCGUCGCCUCC-CUUGCU--U-GGAAAGGAG-C-CCGCAUGGGACGUCU
ABDU01000042.2/353622-353816 AUUAGUAUAAAUCUC-CA-AGCUUAA-A-G-AUCUA-AGGAG----AAGG-----------------------------------UUCUAUGAUUUUUAAGCC----UGGAUUACUAAAUUAUUUAACAUUAAGUUUAAUAAGAACUUAAAUUGUUAAUUAGUUUAAUUGGGGUAAUCCA--CAGGGUAA-GG---UU-UGAAAGAAUUUUGCCUCCACGUAUU--UUGGGAAGGAG-A-AUAAGCAAAAGUAAA
CU928160.2/865804-865948     AUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AE004439.1/728600-728451     AUUAUCGCAUAACUC-CG-AGCUUAU-U-UAACCUA-CGUUU---CUACAAU-------------------------------AGAAAUAAGGUGGUAAUGCC----AAUAGCAUAAAA--------------------------------------------------CUUGUGCUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CGUAUU-UU-AGAAAGGUG-U-GACAUGCAAACAAUU
CP000851.1/5004542-5004406   AGGUUGACGGUUCUC-CG-AGCUUCU-U-A-CCCUA-CGUCG----AGAC-----------------------------------AGAUAAGGGUUUUUAGCC----GUGGCAAUA---------------------------------------------------------ACGCCAC--CGGGGUGA-GA---AA-AGAAAUGAUCUCACCUCC-CCUUAC-UU-GGAAAGGUG-A-UCAUGUCCCAACUAC
CP000891.1/327352-327485     CCGGUGACGGUUCUC-CG-AGCUUGC-C-U-ACCUA-AGUC-----GAAA------------------------------------GAUAUGGAGGUGUAGCC----GUGGUAAUA---------------------------------------------------------AUGCCAC--CGGGGUGG-GA---UA-AGAAAUGCUCUCACCUCC-CACACU--U-GGAAAGGUG-A-UCAUGUCUCAAUUAC
CP000923.1/1425277-1425394   UUAUUACUUAUUCUC-CG-AGUCUAU-A-A-UCCUA-AGGC-----AAGA------------------------------------GCUAUGGAUUAUAGGCC-----------------------------------------------------------------------------GAUAGGGUAG-UG---CU-GGAAACGGUGCUGCCUCC-CGCC----U-GGAAAGGAG-A-AUAGGAAGGCUGCUA
CP000857.1/847673-847817     AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUAUGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
AP009240.1/898974-899118     AUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000879.1/408780-408659     AUUUUAUAAUGUCUU-CG-AUCUAGG-U-U-ACCUA-CGGAA----UUCA-----------------------------------UUCUAUGGUGACUUAGAC-----------------------------------------------------------------------------GAUAGGGUAU-AG---AA-GGAAACUUCUAUGCCUCC-CGCAUU--A-GGAAAGGAG-A-CACAUUAUGAACCGG
CP000020.2/1036399-1036547   UGGCUGCCAUAACUC-CG-AGCUCAA-G-C-UACUA-AGUUG---UUUUUUAAGA------------------------AGCACUCAAUAUGUAGCGUGAGCC---AGUGACAAUU---------------------------------------------------------CGGUCAC--AAGGGUUU-GU---UU-GGAAAUGAACAAGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
AE016795.3/3156082-3155932   GGGUUGCCAUAACUC-CG-AGCUUAA-C-U-UGCUA-AGUUA---UUUUAUUUCAAU---------------------GAUGGAAUGAUAAGCAGCUUAAGCC---AGUGACAUG----------------------------------------------------------AUGUCAC--AAGGGCGU-AA---UU-GGAAAUGACUACGCCUCC-CGUGUU--U-GGAAAGGUG-U-UCCGUGGCGCAACAA
AALD02000070.1/3698-3534     ACUGAACAUAAACUC-CU-AGCCUUG-G-U-GCCUA-CGUUG---UCCCGAGCCGCGAAUAUGC-------GUUUCGUUUAUGGACAAUAGGGUGCUCUGGCC----GUGGCUUU----------------------------------------------------------AAGCCAC--CAGGGUGCGAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUGAC
AAKH03000004.1/5826-5965     GCUUGGCCUUAACUC-CG-AGCUUAC-C-G-CGCUA-AGUUU---AAACCU--------------------------------UUAAAUAUGCGUUGUAAGCC---AGUGACCGC----------------------------------------------------------UUGUCAC--AAGGGCAG-AA---UU-GGAAAUAAUUUUGCCUCC-CGUAUU--U-GGAAAGGUG-U-UCUGUGGCGCAACAA
AALC02000040.1/35583-35747   ACUGAACAUAAACUC-CU-AGCCUUG-G-U-GUCUA-CGUUG---UCCGGUGUCGCGAAUACGU-------UUUUCGUUUACCGGCAAUAUGAUGCUCUGGCC----GUGGCUUU----------------------------------------------------------AAGCCAC--CAGGGUGCGAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUUAC
ACSL01000009.1/10801-10941   UUUAACGCAUAACUC-CG-AGCUUGU-U-UAGCCUA-AGUUU---CAUCG-----------------------------------AAAUACGGC-GACAAGCC----AAUAACGCCG------------------------------------------------------UGUGUUAUU--CAGGGAUA-CG---CU-GGAAACGGUUUAUCCUCU-CCAUAU-UU-AGAAAGGUG-U-AAAAUGCAAUCCAUU
AALF02000023.1/11913-12057   ACUGAACAUAAACUC-CU-AGCCUUG-G-C-GUCUA-CGUUG---UCUCGUUCG---------------------------CGAACAAUAUGAUGCUCUGGCC----GUGGCUUU----------------------------------------------------------AAGCCAC--CAGGGUGCGAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUCAC
AALE02000011.1/37751-37896   ACUGAACAUAAACUC-CU-AGCCUUA-G-U-GUCUA-CGUUG---UUGUGUUUU--------------------------UCUAACAAUAUGAUGCUCUGGCC----GUGGCUUU----------------------------------------------------------AAGCCAC--CAGGGUGCGAG---GU-AGAAAUGCCUGCAUCUCC-CGUAUU--U-GGAAAGGUG-U-UAUGGUACAACUGAC
AP008230.1/4378234-4378102   AAUUGAAUAGUUUUC-CG-AGCUCCU-U-U-GUCUA-AAAGA----CUA------------------------------------UCUCAUGACGGAGGAGCC----UGAGCAAA----------------------------------------------------------CCGCUCA--CGGGGUCA-GU---CA-GGAAACCAGCUGGCCUUC-ACUGA---U-GAAAAGGAA-G-CAGAAAAUACAGGAU
CP000886.1/2253727-2253583   AACCACAGUAAACACUCU-AGCCUCU-G-C-ACCUG-GGUCA----UUUU-----------------------------------UGAUACGGUGCUUUGGCC----GUGACAACGUUUA-------------------------------------------------ACGUUUGCCAC--CAGGGCGC-AG---GA-AGAAAUGACUCCGCCUCC-CGUAUU--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000821.1/5381607-5381473   GCCCUGACGGUUCUC-CG-AGCUUUU-U-G-UCCUA-CGUC-----AACA------------------------------------GAUACGGACGCUAAGCC----GUGGCAAUA---------------------------------------------------------ACGCCAC--CGGGGUGU-GA---AC-AGAAAUGCUCUCACCUCC-CCUUAC-UU-GGAAAGGUG-A-UCAUGUCUCAACUAC
CP000034.1/768837-768693     UUAACCACUAAACACUCU-AGCCUCU-G-C-ACCUA-GGUC-----AACU------------------------------------GAUACGGUGCUUUGGCC----GUGACAAUGCUCGU-----------------------------------------------AAAGAUUGCCAC--CAGGGCGA-AG---GA-AGAAAUGACUUCGCCUCC-CGUAUC--U-GGAAAGGUG-U-ACAUGGCUUCACAAC
CP000436.1/881170-881033     AAAAACUGACGACUC-CG-AGCUUGU-U-G-ACCUA-AGUU-----GCAA------------------------------------AAUAAGGU-UGCAAGCC---U-GUAACAUUGUC---------------------------------------------------AAAUGUUGC--ACAUGGUAC-AA---CU-AGAAAUGGUUGUGCCACU-CCCUU---U-AGAAAGGUG-U-CGAAAAUAAAACUUU
#=GC SS_cons                 ::((-(----(((((.(,.,<<<<<<.<.<.<<<--.-<<<<....____...................................>>>>-->>>>>>>>>>>,....<<<<<___..........................................................__>>>>>..,,<<<<<<.<<...<<.<____>>>>>>>>>>><<.______.._.>>,,,)))).).)----)-))::::::
#=GC RF                      auucacauaaaaCuC.Cg.AGCcuaa.c.c.acCUA.Agucg....aaag...................................cgauAuGgugguuagGCC....guggcuau..........................................................uagccac..cAGGGcga.ag...uu.gGAAAcaacuucgCCUCC.CGUaUU..U.GGAAAGGaG.u.uuaaggagaaauaaa
//
# STOCKHOLM 1.0

#=GF AC   RF01056
#=GF ID   Mg_sensor
#=GF DE   Magnesium Sensor
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Gardner PP
#=GF SS   Published; PMID:17381304
#=GF GA   40.00
#=GF TC   41.40
#=GF NC   36.60
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   17381304
#=GF RT   A Mg2+-responding RNA that controls the expression of a Mg2+ transporter.
#=GF RA   Groisman EA, Cromie MJ, Shi Y, Latifi T
#=GF RL   Cold Spring Harb Symp Quant Biol. 2006;71:251-258.
#=GF RN   [2]
#=GF RM   16615891
#=GF RT   An RNA sensor for intracellular Mg(2+).
#=GF RA   Cromie MJ, Shi Y, Latifi T, Groisman EA
#=GF RL   Cell. 2006;125:71-84.
#=GF RN   [3]
#=GF RM   18248433
#=GF RT   Regulation of magnesium homeostasis in Salmonella: Mg(2+) targets the mgtA
#=GF RT   transcript for degradation by RNase E.
#=GF RA   Spinelli SV, Pontel LB, Garcia Vescovi E, Soncini FC
#=GF RL   FEMS Microbiol Lett. 2008;280:226-234.
#=GF CC   The Magnesium sensor RNA element is a cis-regulatory element that
#=GF CC   regulates the expression of the magnesium transporter protein MgtA. It is
#=GF CC   located in the 5' UTR of this gene. The element adopts different
#=GF CC   structures depending on the presence or absence of Mg2+, this has the
#=GF CC   affect of regulating whether transcription reads through the mgtA coding
#=GF CC   region or stops within the 5' UTR.
#=GF WK   Magnesium_responsive_RNA_element
#=GF SQ   4


U07843.1/1597-1709         CUUACCGGAGG-CGACAUGGACCCUGAACCCACCCCUCUCCCGCGAUGGAGAAUUUUCCUUUUCCGGUAAGCCUGCCUCU--GCUGUCUUACCGG--UG-UGUAAGACAGUGACACAAU
CP000653.1/495640-495750   CUUACCGGAGG-CUGUAUGGACCCUGAUCCCACCCCUCUCCCGCGAUGGAGAAU---CUCUUUCCGGUAAGCCAGCCCUC--GCUGUCUCACCGG--UGAUGUGAGGCAGCAACGUCAU
CP000247.1/4704294-4704409 CUUACCGGAGG-UUAUAUGGAACCUGAUCCCACGCCUCUCCCUCGACGGAGAUUAAAACUUUUCCGGUAAGCCCGUCUUUUCACGGCGUUACCGGA-UG-CGUAAGGCCGUGACGUUUU
CP000647.1/5085745-5085861 CUUACCGGAGAUAGUUAUGGACCCCGAUCCCACUCCUCAUCCUCGAUGGAGCAACCUUUCUUUCCGGUAAGCCUGUUUAAC-ACUGCUUUACCGGAAAG-CGUAAAGCAGUGACGUCCU
#=GC SS_cons               (((((((((((.,,,,,<<<_________>>>,,,,<<<<<______>>>>>,,,,,,,,)))))))))))----------.<<<<<<<<<<____.__._>>>>>>>>>>::::::::
#=GC RF                    CuuaCCGGagg.uuaUAuGGAcCCuGAuCCCaCuCCuCucCCuCGAuGgaGaauuuuuuuuuuCCGGuaaGCCuGucUuuu.gCuGccuuaCCGGA.uG.uGuaaggCaGcgACgUuaU
//
# STOCKHOLM 1.0

#=GF AC   RF01057
#=GF ID   SAH_riboswitch
#=GF DE   S-adenosyl-L-homocysteine riboswitch
#=GF AU   Wang J
#=GF SE   Published; PMID:18374645
#=GF SS   Published; PMID:18374645
#=GF GA   37.00
#=GF TC   37.10
#=GF NC   36.50
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0046498; S-adenosylhomocysteine metabolic process;
#=GF RN   [1]
#=GF RM   18374645
#=GF RT   Riboswitches that sense S-adenosylhomocysteine and activate genes involved
#=GF RT   in coenzyme recycling.
#=GF RA   Wang JX, Lee ER, Morales DR, Lim J, Breaker RR
#=GF RL   Mol Cell. 2008;29:691-702.
#=GF WK   SAH_riboswitch
#=GF SQ   52


AAFX01048275.1/188-258         CA-UUAG-CUGAGGAGCGCUGCAACUCCGG------------------------------------------------UUUACGGAACCAGGCUCAGCAA--------------------------------------------------AUGAAAC-GGCGCUCGUUCCAA
AAFX01122445.1/162-87          ----GCU-UCGAGGAGCGCUGCGACUUGCGU----------------------------------------------GGUUUGCAAGCCAGGCUCGGAGCA-U-------------------------------------UCGA------CAGGAAC-GGCGCUCACCCACU
AASZ01000145.1/12763-12838     CCUGUGU-GCGAGGAGCGCUGCGACAG---C----------------------------------------------UUAA---CUGCCAGGCUCGCCCACUG-------------------------------------GAUC-----AAUGCAAC-GGCGCUCGUAAAUA
AASZ01001430.1/3908-3830       C-----A-CCGAGGAGCGUUGCAACGGGAC------------------------------------------------AAGGUCCCGCCAGGCUCGGU--G-AGGG------------------------------CUCCAUAA-----GUUUCAAC-GGCGCUUACUCUGA
AASZ01004975.1/320-450         CCUCCCA-CCGAGGAGCGCUGCAACCCCAUUAUUAAAUCGGCACCUGCGGUCGGGUUUCGACCACAGGUGCCGAUUUAGUCGCGGGGCCAGGCUCGGUGAG-G-------------------------------------AGGUAU-CUUCAACGAC-GGCGCUCACUCUGA
AATN01000007.1/45143-45222     ------A-CUGAGGAGCGUUGCGACAGGUU---------------------------------------------------UUCCUGCCAGGCUCAGU--A-GAUUGA---------------------------AGGACAAUUU---AAAUACAAC-GGCGCUCAGUCAUC
AATN01000007.1/46422-46509     -----GC-CUGAGGAGCGCUGCAACGGUUAGCAGAU-----------------------------------AUUAACUCGCUAACCGCUAGGCUCAGGC-A-A-------------------------------------UCAUU---UAGAUUAAC-UGCGCUCAUUCAAU
AATN01006348.1/58-129          ----AAU-CCGAGGAGCGCUGCAAGGCUGUC---------------------------------------------GUCCCACAGUUUCAGGCUCGGAUU-------------------------------------------------CAUCAAAC-GGCGCUCAUCCCAC
AATO01000357.1/409-538         C---CCG-CCGAGGGGCGCUGCGACCAUGGACCUGCGGCCCGAGCCGCGAAGCCGCGCACACGUCCGUGCGCGCCUGCGAUCCCUGGCCAGGCUCGGCAGG-GCGU-------------------------------UCCUUCA-----GCGACAAC-GGCGCCCGGACCAA
AATO01002448.1/1018-1089       ----AAU-CCGAGGGGCGCUGCAGGGCUGUC---------------------------------------------GUUCGACAGUUUCAGGCUCGGAUU-------------------------------------------------UCUCAAAC-GGCGCUCAUCCAAC
CP000555.1/3494432-3494509     A---CUU-UCGAGGAGCGUUGCAACUCCCG-------------------------------------------------CCCGGGAGCCAGGCUCGAAAGU-C-------------------------------------AUCCC--CCGAUGCAAC-GGCGCUCACCCGCA
AE017282.2/144280-144199       ----GCG-CCGAGGAGCGCUGCGACGGCCCG----------------------------------------------UCGAGGGCCGCCAGGCUCGGCGGG-G-------------------------------------ACAAUCGGUUUUCCAAC-GGCGCUCUGUUUAU
CP000453.1/2565212-2565295     C---GCC-CCGAGGAGCGCUGCAACAGGGCC----------------------------------------------GCCGGCCCUGCCAGGCUCGGGGAU-GGCG-------------------------------CCCCAUC-----GUUCCAAC-GGCGCUCAGCGAAA
AAOF01000009.1/53442-53352     C---UCG-CCGAGGAGCGCUGCAACAGGACACG-----------------------------------------UCUUGGAUUCCUGCCAGGCUCGGCGAU-UAUCG-----------------------------GGACCUUU-----AAACCAAC-GGCGCUCGGUUCAG
CP000352.1/177418-177491       C---ACU-CCGAGGAGCGUUGCAACGGAUGGC--------------------------------------------CUCGCCUUCCGCCAGGCUCGGAAU-------------------------------------------------GUUUCAAC-GGCGCUCGCAGUUC
AACY020581805.1/324-399        U---CUU-CCGAGGAGCGUUGCAACCGCCACU-------------------------------------------UUAGCUUGGCGGCCAGGCUCGGAACC------------------------------------------------GUGACAAC-GGCGCUCACCCGCA
AM406670.1/4083393-4083321     C---CUG-CCGAGGAGCGCUGCGACCCGAAA----------------------------------------------UCACGCCGGGCCAGGCUCGGCAAC------------------------------------------------CGAACAAC-GGCGCUCGCAAACC
CP000090.1/239471-239552       C---ACU-CCGAGGAGCGUUGCAACGGAUCGUGGC-------------------------------------GUAACAUGCCCUCCGCCAGGCUCGGACUG------------------------------------------------UCUUCAAC-GGCGCUCGCUGAUC
CP000113.1/8035799-8035872     G---ACU-UCGAGGAGCGCUGCGAGGCCGG-------------------------------------------------ACCCGGCCCCAGGCUCGAAGCG-G-------------------------------------AAUC------ACCCAAC-GGCGCUCACCUGUA
CP000089.1/57505-57435         U---CUG-CCGAGGAGCGCUGCGACCCUUU-----------------------------------------------AAUUCGGGGGCCAGGCUCGGCAA-------------------------------------------------UGAUCAAC-GGCGCUCGCAAACC
CP000116.1/2591667-2591597     G---GUU-CCGAGGAGCGCUGCGACGG---U----------------------------------------------UCAC---CCGCCAGGCUCGGGAC--G-------------------------------------CUUC-----CUUUCAAC-GGCGCUCACGUUUU
CP000304.1/4264519-4264605     C---CAC-CCGAGGGGCGCUGCAGCAGGUU-----------------------------------------------CCAGAACCUGUCAGGCUCGGAUGG-GGCGUU---------------------------UCCUCGAAC-----GCAUCAAC-GGCGCCCAUUCGCA
AL646052.1/107656-107582       A----UU-CCGAGGAGCGUUGCAACGGACCGGC-----------------------------------------AUCCGCCCGGCCGCCAGGCUCGGAA--------------------------------------------------GUUCAAAC-GGCGCUCGCACUAU
CP000103.1/2909965-2909888     C---AGA-CCGAGGAGCGCUGCAACGGGCA-------------------------------------------------UUGUCCCGCGAGGCUCGGCAAG-G-------------------------------------AAGGA--UCGCUACAAC-GGCGCUCGUUCAUU
CP000316.1/4339043-4338971     C---UUC-CUGAGGAGCGUUGCAACCCACA------------------------------------------------UCACGUGGACCAGGCUCAGGAC-----------------------------------------UUC-----AUUGCAAC-CACGCUCACCCGCA
CR555306.1/1088385-1088448     U-----G-CCGAGGAGCGCUGCGAGAC--------------------------------------------------UUCC---GUCCCAGGCUCGGC-------------------------------------------CCU-----UCAAAAAC-UGCGCUCACCUUAA
AM260479.1/256130-256245       C---ACU-CCGAGGAGCGUUGCAACGGAUGGAGGCCUGCGAAGCACAUCGCG---CGGCCGGCGGCACAGCCGCCCCAUGCCAUCCGCCAGGCUCGGACUG------------------------------------------------UCUUCAAC-GGCGCUCGCUGAUC
CP000744.1/550599-550494       C---CGU-UCGAGGGGCGCUGCAGCAGGCC-------------------------------------------------UAGGCCUGUCAGGCUCGAACGG-AGCGCGCUCUCAGGCC------GGCCUCGCCGGUCUGUCAAC-----GCACCAAC-GGCGCCCAUUCGCA
CP000539.1/650534-650615       C---UUU-CCGAGGAGCGUUGCAGCGUCCCCAG------------------------------------------CACGGCGGGGCGCGAGGCUCGGAAGU-C-------------------------------------AUAC-----CCAGCAAC-GACGCUCACCCACG
CP000267.1/475493-475563       U---CUU-CCAAGGAGCGUUGCAGUCGGCC-----------------------------------------------ACAUGGCCGGUCAGGCUUGGAUG-------------------------------------------------ACCCCAAC-GACGCUCACCUGAU
CT573326.1/5348242-5348337     C---CGG-CCGAGGGGCGCUGCAGCAGGUU--------------------------------------------------CGUCCUGUCAGGCUCGGUCGG-GGCGUUGUCCGC---------------GCAGCGGACGCUCAA-----CGCACAAC-GGCGCCCAUUCGCA
AE015451.1/5667868-5667964     C---UGU-CCGAGGGGCGCUGCAGCAGGCU--------------------------------------------------AGGCCUGUCAGGCUCGGAUGG-GGCGUUGCUCGC--------------UCCCGCGAGCGCUUAA-----CGCACAAC-GGCGCCCAUUCGCA
CP000680.1/478968-478877       C---CGU-CCGAGGGGCGCUGCAGCAGGUCGGU-----------------------------------------CGACACCGGUUUGUCAGGCUCGGAUGG-GGCGU----------------------------UAACCAUAC-----GCAUCAAC-GGCGCCCAUUCGCA
CP000450.1/2008790-2008713     U---UGUACCGAGGAGCGCUGCAACGGUCU---------------------------------------------------AUCUCGUGAGGCUCGGACAA-A-------------------------------------UGAACA-ACCCAACAAC-GGCGCUCUUUCACU
CP000086.1/3610417-3610350     G---UUU-CCGAGGAGCGUUGCGACGGGCC--------------------------------------------------CCGCCCGCCAGGCUCGGAAA-------------------------------------------------UGGUCAAC-CGAGCGGUGUGUCU
AE016853.1/5771306-5771415     C---UGU-CCGAGGGGCGCUGCAGCAGGUU--------------------------------------------------UACCCUGUCAGGCUCGGAUGG-GGCGUUGUUUGUCAGGUUG-AUCACAGCCGGCAAGCCUUAAA-----CGCACAAC-GGCGCCCAUUCGCA
CP000076.1/6604864-6604970     C---UGU-CCGAGGGGCGCUGCAGCAGGCA--------------------------------------------------UGACCUGUCAGGCUCGGAUGG-GGCGUUGUUGGUACAGG----GCUCCCUGUAUGGACACUAAA-----CGCACAAC-GGCGCCCAUUCGCA
CP000529.1/516171-516245       U---CUC-CUGAGGAGCGUUGCAACCCACG------------------------------------------------GCAUGUGGUCUAGGCUCAGGAC--U-------------------------------------UCUA-----UUUGCAAC-CACGCUCACCCGCA
DQ996270.1/1772-1706           ----UUU-CCGAGGAGCGUUGCGACGGGCA-------------------------------------------------CCGGCCCGCCAGGCUCGGAAA-------------------------------------------------UCUUCACCAGGCGGUGGCCCG--
CP000542.1/736268-736181       C---GCU-CCGAGGAGCGUUGCAGCGCCUCCCACCGG----------------------------------CAGGGCCGGCGGGGCGUGAGGCUCGG-GC--A-------------------------------------UCAU-----CUGGCAAC-GACGCUCAUCCACA
CP000075.1/499723-499613       C---UGU-CCGAGGGGCGCUGCAGCAGGUU--------------------------------------------------UUCCCUGUCAGGCUCGGAUGG-GGCGUUGUUUGCCAGGACGAUCCUCGACCGGCAAACCUUAAA-----CGCACAAC-GGCGCCCAUUCGCA
ABCT01000021.1/8794-8876       C---CGU-UCGAGGAGCGUUGCGACACACCCAUG----------------------------------------CUUUUUUGGGGUGCUAGGCUCGAACAA-G-------------------------------------AAAU------AAACAAC-GGCGCUCACGCUUC
CP000884.1/6586554-6586470     C---UCU-CCGAGGAGCGUUGCAGCGGCCCCCACA-------------------------------------CAUCAGGCGUGGUCGCGAGGCUCGGAGUC-A-------------------------------------UA-------CCUGCAAC-GACGCUCGCCCACG
CP001068.1/3828986-3829069     C---AUU-CCGAGGAGCGUUGCAACGACCGGCCCAAG---------------------------------UUCAGACGGGGCGGCCGCCAGGCUCGGAAG--------------------------------------------------UUCAAAC-GGCGCUCGCAGUAU
CP000949.1/538083-537987       C---UGU-CCGAGGGGCGCUGCAGCAGGGU--------------------------------------------------CAUCCUGUCAGGCUCGGAUGG-GGCGUUGUCCGC--------------UCCCGCGGACGCUCAA-----CGCACAAC-GGCGCCCAUUCGCA
CP001111.1/740018-739937       ----CUG-CCGAGGGGCGCUGCGACCGGAUCC--------------------------------------------CUUGAGGCCGGCCAGGCUCGGCCAG-GU----------------------------------GGUACU-----GCAACAAC-GGCGCCCGGCCAGA
AAUJ02000001.1/4967434-4967338 C---CAU-CCGAGGAGCGUUGCAGCGUUCCCCAGCCAGCCA-------------------------UGAGCUGGCCUGCGCGGGGCGUGAGGCUCGGAUUU----------------------------------------CAU-----CCCGCAAC-GACGCUCGCCCACG
CP001157.1/337304-337216       C---CUU-CCGAGGGGCGCUGCAGCAGGCCUG--------------------------------------------CCAACGGCCUGUCAGGCUCGGAAGG-GGCGU----------------------------UUUCCGAAC-----GCAUCAAC-GGCGCCCAUUCGCA
CP002271.1/7720690-7720757     C---AAC-CUGAGGAGCGCUGCAACGGGGA--------------------------------------------------CUUCCCGCCAGGCUCAGGUU-------------------------------------------------CAUGUAAC-GGCGCUCGCUGACU
CU914168.1/185982-185906       C---AUU-CCGAGGAGCGUUGCAACGGACCGGCA----------------------------------------UGCGCCCGGCCCGCCAGGCUCGGAAG--------------------------------------------------UUCAAAC-GGCGCUCGCACUAU
CP001715.1/470000-469928       C---AAU-CCGAGGAGCGCUGCAGGGCCGUC---------------------------------------------GAUCGACGGUUUCAGGCUCGGAUU-------------------------------------------------CCUUAAAC-GGCGCUCAUCCGAC
CP000094.2/5940642-5940740     C---UGU-CCGAGGGGCGCUGCAGCAGGUU--------------------------------------------------CAACCUGUCAGGCUCGGAUGG-GGCGUUGACCGGC------------UCAGGCCGGACACUAAA-----CGCACAAC-GGCGCCCAUUCGCA
#=GC SS_cons                   :...<<<.<<<<------------<<<<<<_..............................................____>>>>>>------>>>>>>>:.:.....................................::::.....::::::::.::::::::::::::
#=GC RF                        C...ccu.CCGAGGAGCGCUGCAACgggccu..............................................uuucggcccGCCAGGCUCGGaggg.g.....................................uaaa.....ucuaCAAC.GGCGCUCauuCaca
//
# STOCKHOLM 1.0

#=GF AC   RF01059
#=GF ID   mir-598
#=GF DE   microRNA mir-598
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   70.00
#=GF NC   69.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000393;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF WK   Mir-598_microRNA_precursor_family
#=GF SQ   24


ABDC01461977.1/439-343       GCUUGACGAUGCUGCUGAUGCUGGCGGUGACACCGAUGGCGUGAGCUGGAG------ACAGGGUGCUACGUCAUCGUUGUCAUCGUCAUCAUCAU--CACCCGAG
AAPY01193946.1/257-353       GCUUGAUGAUGCAGCUGAUGCUGGCGGUGAUGCCGAUGGUGCGAGCUGGAA------AUGGGGUGCUACGUCAUCGCUGUCAUCGUCACCAUCAU--CAUCUGAG
AAIY01363772.1/1668-1573     GUUUGAUGAUACUGCUGAUGCUGGUGGUGAUGCCGAUGGUGUGAGCUGGAA------AUGGGU-GCUACGUCAUCGUUGUCAUCGUCGUCAUCAU--CAUCCGAG
AAFC03106541.1/8060-7964     ACUUGAUGGUACUGCUGAUGCUGGUGGUGAUGCCGAUGGUGCGAGCUGGAC------GGUGGGUGCUACGGCAUCAUUGUCGUCGUCAUCGUCAU--CAUCCAAG
ABAV01011112.1/56268-56173   UGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGA-UGAUGAUG------AUGAUGAUCAUCAUCAUCAUCAUCAUCAUCAUCAUCAG--CAGCAGCA
AACY021001521.1/13-108       UGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGA-UGAUGAUA------AUGAUGAUGAUCAUCAUCAUCAUCAUCAUCAUCAUGAU--GAUGAUGA
AC134429.3/110743-110844     UGGUGGUGAUGAUGGUGAUGAUGGUGAUGGUGAUGAUGAUGA-UGAUGAAAGUCAUCAUUGUCUUCAUCAUCAUCACCACCACCACCAUCAUCAU--CAUCAUCU
AAQB01006273.1/290291-290386 UGAUGAUGAUGCUGGUGAUGGUUAUGAUGAUGAUGAUGAUGAUGCU-GAUG------CUGGUCUAGUGCAUCCUCAUCGUCAACAUCAUCAUCAU--CGUUGUCA
AAFR03021066.1/3131-3034     UAAUGAUAAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGA-UAAUGAUG------AUGAUGAUGAUCAUCAUCAUCAUCAUCAUCAUCAUCAUAGCAUUUAUA
AAPN01393926.1/7541-7636     UGAUGAUGAUGAUGAUGAUGAUGAUGAUGACAAUGAUGGUGC-UGUUGCAG------UGGAUGAUCAUCAGUAUCAUAAUCAUCAUCAUCAUCAU--CAACAACA
AM409476.1/115-209           UGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGA-UGAUGAUG------AUGAGA-UAAGCAUCCUCAUCAACAGCAUCAUCCUCAU--CAUCAUAU
CAAE01007994.1/29433-29335   UAAUGAUGAUGAUGAUGAUGAUGAUGACGAUGAUUAUUAUUAUUAUUAUUAUU----AUUAUUAUUAUUAUUAUUAUCAUCGUCAUCAUCAUCAU--CAGACACC
AC171141.2/74913-74999       UACAGUUACCAUUGCUGAUGGUGAUGAUGAUGAUGAUGGUGA-------UG------AUGAUCA---UCAUCCUCAUCGUCAUCAUCAUCAUCAU--CUACUAAU
CT033813.18/79235-79330      UGUUGUUGUUGCAGUUGAUGAUGAUGAUGAAGAUGGU-GUGUGUGUUUGAU------GAAAGCUGCUUCACACCCGUCAUCAUCAUCAUCAUCAU--CAUCUAAA
AAZO01003431.1/583-678       AAGUCACGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGACAUUUAAUUAAU------UUUUUUUUUUAU-UCAUCAUCAUCAUCAUCAUCAUUAU--UAUUUUCG
AAQQ01172656.1/53-139        AAUUGAGAGUCAGAGUGAUGAUGAUGAUGAUGAUGAUGAUGA-------UA------AAAAUAA---UCAUCAUCAUCAUCAUCAUCAUAAUUAU--UAUUAUUA
AAWR02032193.1/1951-1855     AUUUGAUGAUACUGCUGAUGCUGGCAGUGAUGCCGAUGGUGCGGGCUGGAA------AUGGGGUGCUACGUCAUCGUUGUCAUCGUCAUCAUCAU--CAUCCAAG
AASC02024498.1/33738-33833   UGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUAA-UGAUGAUG------AUGAUCAUCAACAUCAUCAUCAUCAUCAUCAUCAUCAU--CAUUCAUA
AAKN02003336.1/127088-127184 GUUUGACGAUGCUGCUGAUGCUGGCGGUGACGCCGAUGGUGCGAGCUGGAC------AUGGGGUGCUACGUCAUCGUUGUCAUCGUCAUCAUCAU--CAUCAGAG
AAPE02001941.1/95493-95589   AUAUGAUGAUGCUGCUGAUGCUGGUGGUGACGCCGAUGGUGCGAGCUGGAA------AUGGGGUGCUACGUCAUCGUUGUCAUCAUCAUCAUCAU--CAUCUGAG
AF131215.2/12542-12446       GCUUGAUGAUGCUGCUGAUGCUGGCGGUGAUCCCGAUGGUGUGAGCUGGAA------AUGGGGUGCUACGUCAUCGUUGUCAUCGUCAUCAUCAU--CAUCCGAG
AAGU03044570.1/13872-13967   GUUUGAUGAUACUGCUGAUGCUGGCGGUGAUGCCGAUGGUGGGAGCUGGAA------AUAGGU-GCUACGUCAUCGUUGUCAUCGUCAUCAUCAU--CAUCUGAG
AAWZ02021618.1/24776-24871   UAAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGAUGA-UGAUGAUG------AUGAUCAUCAUCAUCAUCAUCAUCAUCAUCAUCAUCAU--CAUCAUCA
AAGJ04166118.1/694-608       UGCUGCUGAUUCUGAUGAUGAUGGCGGUGAUGAUGAUUGUGA-------UU------AUCAUCA---UCACCAUCAUCAUCAUCAUCAUCAUCAU--CAUCAAUA
#=GC SS_cons                 :::::::::::::<-<<<<<-<<<<<<<<<<<<<<<<<<<<<-<<<_____......_______>>>>>>>>>>>>>>>>>>>>>>>>->>>>>-..>:::::::
#=GC RF                      uaaUGAUGAUgaUGaUGAUGaUGauGaUGaugauGAugauGagugcUGaaa......AUgauuugcauCaucaUCaucauCAuCauCAUCAUCAU..CAUcaaaa
//
# STOCKHOLM 1.0

#=GF AC   RF01061
#=GF ID   mir-548
#=GF DE   microRNA mir-548
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   90.00
#=GF TC   90.00
#=GF NC   89.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.46 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000317;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome.
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing.
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20459774
#=GF RT   Ultra-high throughput sequencing-based small RNA discovery and discrete
#=GF RT   statistical biomarker analysis in a collection of cervical tumours and
#=GF RT   matched controls.
#=GF RA   Witten D, Tibshirani R, Gu SG, Fire A, Lui WO
#=GF RL   BMC Biol. 2010;8:58.
#=GF RN   [4]
#=GF RM   20733160
#=GF RT   Deep sequencing of the small RNA transcriptome of normal and malignant
#=GF RT   human B cells identifies hundreds of novel microRNAs.
#=GF RA   Jima DD, Zhang J, Jacobs C, Richards KL, Dunphy CH, Choi WW, Yan Au W,
#=GF RA   Srivastava G, Czader MB, Rizzieri DA, Lagoo AS, Lugar PL, Mann KP, Flowers
#=GF RA   CR, Bernal-Mizrachi L, Naresh KN, Evens AM, Gordon LI, Luftig M, Friedman
#=GF RA   DR, Weinberg JB, Thompson MA, Gill JI, Liu Q, How T, Grubor V, Gao Y,
#=GF RA   Patel A, Wu H, Zhu J, Blobe GC, Lipsky PE, Chadburn A, Dave SS
#=GF RL   Blood. 2010;116:e118-e127.
#=GF WK   Mir-548_microRNA_precursor_family
#=GF SQ   11


AL391356.22/22986-23069  UAUUAGGUUGGUCCAAAAGUAAUUACAGUUUUUGUCUUUGAAAGUAAUGUCAAAAACUGUGAUUACUUUUGCACCAACCUAAUA
AL390966.14/78822-78741  UAUUAGGUUGGUGCAAAGGUAUUUGUGGUUUUUGUCAUUAAA-GUAAUG-CAAAAGCCACAAAUACCUUUGCACCAACCUAAUA
AP004582.2/69378-69295   UAUUACGUUGGUGCAAAAGUAAUUGCCAGUUUUGCCAUUGAAAGUAAUGGUAAAACUCGCAAUUACUUUUGCACCGACCUAAUA
AC009121.8/57560-57477   UAUUAGGUUGGUGCAAAAGUAAUUGUGGUGUUUGCCAUUGAAAGUAAUGACAAAAACCGCGAUUACUUUUGCACCAACCUAAUA
AC005411.1/13879-13796   UAUUAGGUUGGUGCAAAAGUAAUCGCGGUUUUUGUCAUUGAAAGUAAUAGCAAAAACUGCAAUUACUUUUGCACCAACCUAAAA
AC110921.9/174283-174200 AUUUAGGUUGGUGCAAAAGUAAUUGUGGUUUUUGCCAUUGAAAGUAAUGGCAAAAACCACAGUUUCUUUUGCACCAACCUAAUA
AADA01335449.1/302-219   UAUUAGGUUGGUGCAAAAGUAACUGUGGUUUUUGCCAUUGAAAGUAAUGGCAAAAACCGCAGUUACUUUUGCACCAACCUAAUA
AC187360.3/56085-56002   UAUUAGGUUGGUGCGAAAGUAAUUGCAGUUUUUGCUAUUACUUUUGACAGCAAAAACUGCAGUUACUUUCGCACCAACCUAAUA
AC098811.3/48288-48205   UAUUGGGUUGGUGCAAAAGUAAUUGUGGUUUUUGACAUUUCUUUUAAUGGCAAAACCCACAAUUACUUUUGCACCAAUCUAAUA
CT954305.14/33966-34049  UAUUAGGUUGGUGCAAAGGUAAUUGUGGUUUUUACCAUUGAAGGUAAUGGCAAAACCUCCAAUUACUUUUGCACCAACCUAAUA
CAAA01099159.1/1144-1227 UAUUAUGUUGGUACAAAAGUAAUUGUGGUUUUUGCCAUUAAAAGGAAUGGCAAAACCCGCAAUUACUUUUGCAUCAACCUAAUA
#=GC SS_cons             <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                  uauuagGuuGGugCaaaaGuaauuGcgGuuuuuGccauugaaagcaauggCaaaaaCcgCaauuaCuuuuGcaCCaaCcuaaua
//
# STOCKHOLM 1.0

#=GF AC   RF01064
#=GF ID   mir-253
#=GF DE   microRNA mir-253
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   75.30
#=GF NC   64.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000286;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF RN   [2]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF RN   [3]
#=GF RM   19460142
#=GF RT   Dynamic expression of small non-coding RNAs, including novel microRNAs and
#=GF RT   piRNAs/21U-RNAs, during Caenorhabditis elegans development.
#=GF RA   Kato M, de Lencastre A, Pincus Z, Slack FJ
#=GF RL   Genome Biol. 2009;10:R54.
#=GF RN   [4]
#=GF RM   20062054
#=GF RT   Comprehensive discovery of endogenous Argonaute binding sites in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo
#=GF RA   GW
#=GF RL   Nat Struct Mol Biol. 2010;17:173-179.
#=GF WK   MicroRNA
#=GF SQ   4


CAAC02000488.1/1601400-1601301 AUUUUUCGAGUUUCAGUCCUUCUCACACACCUCACUAACACUA-ACUACAGAUUUCUAGAUGUUAGUAGGCGUUGUGGGAAGGGCGGAGAUGACGAAUACU
AAGD02012098.1/83849-83750     UUAGUUCGAGUUUCCACCCUUUUCACACACCUCACUAACACUA-AACACAGAUUGAUAGAUGUUAGUAGGCGUUGUGGGAAGGGCGGCGAUGACGAGCACA
FO080929.1/10410-10311         AUUGUUCCGAUCGCCGCUCUUUUCACACACCUCACUAACACUG-ACCACCGAUGCAUAGAUGUUAGUAGGCGUUGUGGGAAGGGCGGCGACAGUGAACGUC
ABEG02001496.1/14085-13985     CUCAUUCGAUGUUCCACCCUUUUCACACACCUGACUAACACAAAACCGCAGAUGUAUUGAUGUUAGUAGGCGUUGUGGGAAGGGUGGCGAUGAUGAGCAUA
#=GC SS_cons                   ::<<<<<--<<<<<<<<<<<<<<<<<<<-<<<-<<<<<<<<<<.____________>>>->>>>>>>>>>->->>>>>>>>>>>>>>>>>>--->>>>>::
#=GC RF                        aUcguuCgagucgCcgccCuucuCaCaCACCucaCuaaCaCua.AccaCaGAUuuauaGAuGuuaGuaGGCGUuGuGggaaGggcgGcgacgauGaacgua
//
# STOCKHOLM 1.0

#=GF AC   RF01065
#=GF ID   23S-methyl
#=GF DE   23S methyl RNA motif
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:17621584; Weinberg Z
#=GF SS   Published; PMID:17621584; Weinberg Z
#=GF GA   50.00
#=GF TC   50.90
#=GF NC   43.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   17621584
#=GF RT   Identification of 22 candidate structured RNAs in bacteria using the
#=GF RT   CMfinder comparative genomics pipeline.
#=GF RA   Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER,
#=GF RA   Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR
#=GF RL   Nucleic Acids Res. 2007;35:4809-4819.
#=GF WK   23S_methyl_RNA_motif
#=GF SQ   19


CP000262.1/316897-316995   CA-UUCGUUGGUUUAAAUCA----AACCUGUUA------UGAUUUAAGUUA-GCGAGUC-----ACCAUCAACCACAUUGUUUGCUGAGCAUGACUCCGAGCAGUGUGGUUUUUUA
CP000423.1/889561-889673   UU-AUUUUUAACUUUUAUCAGGGCUAGCUUUUGGGUAAUUGAUAAAAGUUU-GCGAUAAAUUACUUCACUAACGUAUCGCUUCGCUGAGUGCG-CUCCGAAGCAAUGCGUUUUUUU
AAJS01000102.1/3910-3812   GA-UUUGUUAGUUUAAAUCA----AACCUGUUA------UGAUUUAAGCUA-ACAAACC-----ACCAUAAACCACAUUGUUUGCUGAGAUUGACUCCGAGCAGUGUGGUUUUUUU
CP000387.1/1761216-1761121 CC-UUCAUUGGUUUACCUCA----AACCUGUUG------UGAUGUAAGUUA-AUGAAGC--------CUUAACCACGCUGUUUGCUGAGCUUGACUCCGGGCAGUGUGGCUAUUUU
AE016830.1/2578241-2578137 UU-UUCAUUGGUUUUUAUCAGG--GUCCUGUUC------UGAUAAAAGUUA-GUGAAGAGACC-UUCACUAACGUAACGACUCGCCGUGGUAGACACCGAGACGGUACGUUUUUUU
AAFV01000025.1/9216-9314   CA-UUCGUUGAUUUAAAUCA----AACCUGUUA------UGAUUUAAGUUA-GCGAGUC-----ACCAUCAACCACAUUGUUUGCUGAGCAUGACUCCGAGCAGUGUGGUUUUUAA
CP000408.1/1609304-1609205 GAUUUCAUUGAUUUAACUCA----AACCUGUUG------UGAGUUAAGUGA-AUGAAUC-----AUCAUUCACCAUGCUGUUUGCUGAGCUUGACUCCGGGCAGUGUGGCUAUUUU
CP000416.1/1433094-1432993 CG-UUUGGCGGUCGAUAUCA----GCGUUUAAC------UGUUAGCGGCAG-ACAAGUAGCAC-UUCACUAAAGUAGUUCCUCGCCGUGCCCA-CACCGAGGAGCUGCUUUUUUUG
CR936503.1/496018-496118   UU-UUCCCUAACUUUUAUCAG---AAUACUUUU------UGAUAAAAGCUA-GUGAUGAAAU--GACACUAACGUAGUUUCUCGCCGUGAAUAAC--CGAGGGACUACGUUUUUUU
AAAK03000109.1/29-133      UU-UUCAUUGGUUUUUAUCAGG--UUCCUGUUC------UGAUAAAAGUUA-GUGAGAAGAGC-UUCACUAACGUAACGACUCGCAGUGACUGACACCGAGUUGAUACGUUUUUUU
CP000705.1/649443-649549   UCGUUUGAUAAUUGACAUCGAAUAUAAGUGUUU------CGUUGGUAAUUA-UCAAGGAGUAC-UUCAUUAAAGCAGCGUUUCGCCGUGCCCA-CACCGAGACCCUGCUUUUUUUA
CP000233.1/1171100-1171001 CG-GUUGUUAGUAAUUAACG----GAACUGU--------CGUUAGUUGCUAUAUAAUUGUAC--UUCAUUAACGUAGCUGUUCGCCGUGCCCA-CACCGAAUGGCUACGCUUUUUU
ABAB01000011.1/28504-28409 GU-UUCGCUGAUUUACUUCA----AACCUGUUG------UGAGGUAAGUUA-ACGAUGC--------CUUAACCACGCUGUCUGCUGAGCUUGACUCCGGGCAGUGUGGCUAUUUU
CP000419.1/269671-269768   CA-UUCACUAUUUUAAAUCU----AACCUGUCA------UGAUUUAAGCUA-AUGAAUG-----UCCAU-AACCAUGUCGUCUGCUGAGCUUGACUCCGGGCGAUAUGGCAUUUUU
CP000114.1/1597742-1597644 GA-UUUGUUAGUUUAAAUCA----AACCUGUUA------UGAUUUAAGUUA-ACAAACC-----ACCAUAAACCACAUUGUUUGCUGAGAUUGACUCCGAGCAGUGUGGUUUUUUU
CP000425.1/1179760-1179664 UA-UUAAUUUGUUUCAAUCU----UUCCUGUUA------UGAUUAAAGCAA-AUUAGUC-----CCCC--AACUAGACUUCUUGCUGAGAUUGACUCCGAGGGGUCUAGUUUUUUU
AE009949.1/349483-349581   UA-UUCGUUGGUUUAAAUCA----AACCUGUUA------UGAUUUAAGUUA-GCGAGUC-----ACCAUCAACCACAUUGUUUGCUGAGCAUGACUCCGAGCAGUGUGGUUUUUUA
AL935263.2/1998551-1998453 CG-UUUGGUAGUUAACAUCG----ACAUGU---------CGUUGGUGACUA-CCGAGUUGUAC-UUCAUUAACGUAGCGUUUCGCCGUGCCCA-CACCGAAAUACUACGUUUUUUU
AP010655.1/448210-448309   -UAAUCAUUGUUUUAAAUCA----AACCUGUUA------UGAUUUAAGAUA-AUGAAAGC----ACCGCACACCACGUUACCUGCUGAGCUGGACUCCGGGUUCCGUGGUUCUUUU
#=GC SS_cons               :<.<<<<<<<<<<<<<<<<<...._________......>>>>>>>>>>>>.>>>>>>----..------<<<<<<<<<<<<<<--<<<_____>>>>>>>>>>>>>>>>>:::::
#=GC RF                    uc.uUcguuaguuuucauCa....aaccUgUUa......uGaugaaagcua.acgAagaaua..uuCAuUAaCgccgcugcucGCuGaGcuugACuCCgagcagcggcGuUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01066
#=GF ID   6C
#=GF PI   390
#=GF DE   6C RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:17621584; Weinberg Z
#=GF SS   Published; PMID:17621584; Weinberg Z
#=GF GA   47.00
#=GF TC   47.00
#=GF NC   46.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.35 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0043934; sporulation;
#=GF RN   [1]
#=GF RM   17621584
#=GF RT   Identification of 22 candidate structured RNAs in bacteria using the
#=GF RT   CMfinder comparative genomics pipeline.
#=GF RA   Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER,
#=GF RA   Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR
#=GF RL   Nucleic Acids Res. 2007;35:4809-4819.
#=GF RN   [2]
#=GF RM   18477385
#=GF RT   Biocomputational prediction of small non-coding RNAs in Streptomyces.
#=GF RA   Pánek J, Bobek J, Mikulík K, Basler M, Vohradský J
#=GF RL   BMC Genomics. 2008;9:217.
#=GF WK   6C_RNA
#=GF SQ   18


CP000518.1/5128853-5128778 UGUGCA-UCAGCCCGA--------CCCCCCG---GGGCUGAUAC--AC-----GACGACCUCCGCCUCCUCCCCCCCU--GGCGGGGGUCGUCCCUU
CP000717.1/4112461-4112386 GGUGUA-UCAGUCCGA--------CCCCCCG---GGGCUGAUGC--AC-----GACGACCCUCGCCUCCUCCCCCCCU--GGCGGGGGUCGUCCCUU
CP000088.1/153000-152926   CGGG-A-CCGACUCUU--------CCCCCCG---GAGUCGGACCG-UCG----GACGGCCCCCGCCUU-UCCCCCCU---GGCGGGGGCCGUCCCCU
CP000325.1/4706815-4706738 GGUGCA-UCAGUCCGA--------CCCGCCG---GGGCUGAAGC--AC-----GACGACCUCCGCCUCCUCCCCCCCCCUGGCGGGGGUCGUCCCUU
CT573213.2/7144301-7144387 CGAGAC-CCGGCCCGAGACGGGCAGCCCCCAUACGGGCCAUGUC--CC-----GAGGCGACCCCCGCACUCCCCCCUG--UGGGGGUCGCCUCCCCC
CP000656.1/1438737-1438813 UGUGCA-UCAGCCCGA--------CCCCCCG---GGGCUGAUAC--AC-----GACGACCUCCGCCUCCUCCCCCCCCU-GGCGGGGGUCGUCCCUU
BX927148.1/314706-314782   G-----CCCCGGCACAAUCC----CCCCCCGU--UGCCGGG-------UUACUGACGGCCCGCGC-AC-ACCCCCCCCGAGGCGCGGGCCGUCCCUU
BX248346.1/285807-285731   GGUGUA-UCAGUCCGA--------CCCCCCG---GGGCUGAUGC--AC-----GACGACCCUCGCCUCCUCCCCCCCCU-GGCGGGGGUCGUCCCUU
CP000479.1/459952-460027   GGUGUA-UCAGCCCGA--------CCCCCCG---GGGCUGAUGC--AC-----GACGACCCUCGCCUCCUCCCCCCCU--GGCGGGGGUCGUCCCUU
AP006618.1/368553-368627   CGUG-U-UCAGCCCGA--------CCCCCCG---GGGCUGAACC--CC-----GACGGCCCCAGCCUCCUCCCCCCCC--GGCUGGGGCCGUCCUCU
CP000481.1/2259193-2259120 GGGGGU-GCGGCUCUU--------CCCCCCA---GAGCCGUACCGGGC-----AGUGGCCCCCGCU---ACCCCCCC---GGCGGGGGCCACUCCUU
CP000480.1/6241207-6241132 GGUGUA-UCAGCCCGA--------CCCCCCG---GGGCUGAUAC--GC-----GACGACCUCCGCCUCCUCCCCCCCU--GGCGGGGGUCGUCUUCU
AAOB01000010.1/29207-29282 CACGCG-GCAAUUUUGAUU-----CCCCCCAAU-CAAUUGCCGCG-GU-----GGCGGUGCCUAU----UCCCCCCA----AUGGGCGCCGCCCCUC
CP000667.1/4593132-4593060 AGUGGU-UCGGCUCAC--------CCCCCCCG--GAGCCGGACC--CC-----GACGACCCCCGUCU--UCCCCCC----GACGGGGGUCGUCCCUU
AM420293.1/403498-403572   CCUGGU-UCAGCUCGA--------CCCCCCG---GAGCUGAACCG-CC-----GACGACCCCCGUCCC-UCCCCCCU---GGCGGGGGUCGUCUUGU
CP000431.1/4571458-4571533 CGAUGU-UCAGCCCGA--------CCCCCCG---GGGCUGAACA--CU-----GACGACCCUCGCCUCCUCCCCCCCU--GGCGAGGGUCGUCCUCU
CP000750.2/1818012-1817941 CGCGGC-CCGGCUCAU--------CCCCCCC---GAGCCGGACCG-UC-----GACGGCCCCCGC----UCCCCCCCA---GCGGGGGCCGUCUCCA
CP000850.1/5005718-5005646 AGUGGU-UCGGCUCAA--------CCCCCCCG--GAGCCGAACCC-CC-----GACGGCCCCCGUC---UCCCCCC----GACGGGGGUCGUCCCUU
#=GC SS_cons               :<<<<<.<<<<<<<__........_______...>>>>>>>>>>..>>.....<<<<<<<<<<<<<__._________..>>>>>>>>>>>>>::::
#=GC RF                    cGcGcc.cCgGcccga........CCCCCCg...gggCcGgggC..gC.....GacGgccCcCGCcuc.UCCCCCCcu..gGCGgGggcCguCCCuU
//
# STOCKHOLM 1.0

#=GF AC   RF01067
#=GF ID   ATPC
#=GF DE   ATPC RNA motif
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:17621584; Weinberg Z
#=GF SS   Published; PMID:17621584; Weinberg Z
#=GF GA   45.00
#=GF TC   45.50
#=GF NC   41.20
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17621584
#=GF RT   Identification of 22 candidate structured RNAs in bacteria using the
#=GF RT   CMfinder comparative genomics pipeline.
#=GF RA   Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER,
#=GF RA   Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR
#=GF RL   Nucleic Acids Res. 2007;35:4809-4819.
#=GF WK   ATPC_RNA_motif
#=GF SQ   90


AACY022975089.1/331-241      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UCUCAGACCCAUUCUUAAAACA------AAGGAUGU-CCAA--GCGUG
AANO01000002.1/213710-213621 -C-CCGGGCCGGUCGGCCGU--UCUG-CUAAAUCUCC-UGCGCGC----AGGUCCGGUCUG----AACCGGGCCCGUCUCCCCAGC-------GGAGAUGU-CCCAG-GCGCC
AACY023014890.1/144-235      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAUAU----AAUCAGACCCAUUCUUAAAAGA------AAGGAUGU-CCAA--GCGUG
CP000551.1/1400761-1400670   -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAACA-----UAUCAGACCCAUUCUUAUAAAGA-----AAGGAUGU-CCAA--GCGUG
AACY021408792.1/724-634      -U-UUACAAAGAGUCUGUAA--UCUGGCAAAAUAACUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUCUUUAAAAGA------AAGGAUGU-CCAA--GCGUG
AACY020475809.1/184-95       -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAA-A------AAGGAUGU-CCAA--GCGUG
AACY020366270.1/955-865      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAUAA------AAGGAUGU-CCAA--GCGUG
AACY022720715.1/258-347      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAC-A------AAGGAUGU-CCAA--GCGUG
AACY020440440.1/1895-1986    -U-UUACAAAAGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAUAU----AAUCAGACCCAUUCUUAAAAGA------AAGGAUGU-CCAA--GCGUG
AACY023399400.1/427-337      -U-UUACAAAGUGUCUGUGA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAUUA------AAGGAUGU-CCAA--GCGUG
AACY021337351.1/585-497      -A-UCGCCUGAGAACGGCGA--UCUG-CUAAACACAUCCGCGCGC----AGGUCCGGAAUUGC--ACCCGGGCCCGUUCCUUC----------GGGAAUGU-CCCU--GCGCG
AACY021392813.1/673-582      -U-UUACAAAGGUUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAUAAA-----AAGGAUGU-CCAA--GCGUG
AACY020952548.1/514-426      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAA--------AAGGAUGU-CCAA--GCGUG
CT978603.1/1639132-1639041   -U-UCGCCCUAACCCGGCGA--UCUG-CUAAACACUUC-GCGCGC----AGGUCCGGCUGCU---GACCGGGCCCUUCCCUGCUCCC------AGGGUUGU-CCCAG-GCGCU
AACY021269415.1/780-870      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAUACA------AAGGAUGU-CCAA--GCGUG
AE017126.1/1464170-1464078   -U-CAGAGAUAAAUUAUUUU--UCUGGCAAAAC-U-----CUUGCGAAUAGCUUCGAUUUUC----UUCGAACGCAUCUUAAUUAACUA----UGAGAUGUACCCCUCGCA--
AACY022493886.1/188-98       -U-UUACAAAGGGCCUGUAA--UCUGGCAAAAUAUUUAAUCGCGU----AGGUCUGAAGU-----AAUCAGACCCAUUCUUAAAAAA------AAGAAUGU-CCAA--GCGUG
AACY023934638.1/484-394      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAACUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAACA------AAGGAUGU-CCAA--GCGUG
AACY020909425.1/791-700      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCAAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUACAAAGA-----AAGGAUGU-CCAA--GCGUG
AACY023521305.1/408-502      -C-UCGCCGUUAA--GGCGA--UCUG-CUAAACACUUCUGCGCGU----AGGUCCGACGCUCAUGACUCGGGCCCGCUCUCUUGCAACA----GAGAGUGU-CCCU--GCGCA
AACY022233316.1/279-367      -U-UCGCUGAAUUUCGGCGA--UCUG-CUAAACACAUCCGCGCGC----AGGUCCGAAUUGC---AACCGGGCCCUCUCCUUCCU---------GGAGUGU-CCCU--GCGCG
AACY023994678.1/252-162      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAUCA------AAGGAUGU-CCAA--GCGUG
CT971583.1/1847828-1847738   -U-UCGCAGGUCCCCCGCGA--UCUG-CUAAACACAUC-GCGCGC----AGGUCCGGGUGG----AACCGGGCCCGCCCUCCAUCGU------GAGGGUGU-CCCGG-GCGCG
AACY021948974.1/781-691      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAACU------AAGGAUGU-CCAA--GCGUG
AACY023949218.1/166-254      -U-UCGCCAAUUGAUGGCGA--UCUG-CUAAACACAUCCGCGCGC----AGGUCCGGCGAUC---ACCCGGGCCCGCUCCUUCA---------AGGAGUGU-CCCU--GCGCG
AACY022185424.1/51-146       -A-GAGCAUCAUUA-GGUUC--UUUAGGUACUUUUGAACCUGCGC----AGGUCCGAUGAG----UUUCGGGCCCAUUUCAAAAAAAAUUU--UGAGAUGUCCCCC--ACGCA
AACY022741752.1/495-405      -U-UUACAAAGGGUCUGUAA--UCUGGCACAAUAUCUAAUCGCGU----AGGUCUGACAA-----UAUCAGACCCAUUCUUAAAUUAA------AGGAUGU-CCAA--GCGUG
AAOK01000001.1/272018-272108 -U-UCGCAGGUCCCCAGUGA--UCUG-CUAAACACUUC-GCGCGC----AGGUCCGGGUGG----AACCGGGCCCGCCCUCCAUCGU------GAGGGUGU-CCCGG-GCGCG
AACY020483706.1/2020-1930    -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAAGC------AAGGAUGU-CCAA--GCGUG
CP000110.1/2006437-2006349   -A-UCGCCUGAGAACGGCGA--UCUG-CUAAACACAUCCGCGCGC----AGGUCCGGCAUUGC--ACCCGGGCCCGUUCCUUC----------GGGAAUGU-CCCU--GCGCG
BX569690.1/142368-142456     -U-UCGCCAUUUGAGGGCGA--UCUG-CUAAACACGUCCGCGCGC----AGGUCCGGAUAGC---ACCCGGGCCCGCUCCUUUC---------AGGAGUGU-CCCU--GCGCG
CP000097.1/500648-500736     -U-UCGCUUUUACCUGGCGA--UCUG-CUAAACACAUCCGCGCGU----AGGUCCGGACUGC---AACCGGGCCCUCUCUUCAC---------AAGAGUGU-CCCU--GCGCG
AACY021024843.1/187-280      -U-UUACAAAAGGCAAAUAA--UCUGCCAAAAUACCUAAUCGCGU----AGGUCUGAAAA------AUCAGGCCCAUCCUAAAUAAACUAG--UAGGAUGU-CCAA--GCGCG
AACY022343928.1/741-831      -U-UUACAAAUUGUCUGUAA--UCUGGCACAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUUAAUUA------AAGAAUGU-CCAA--GCGUG
AACY022813017.1/10-100       -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAAUA------AAGGAUGU-CCAA--GCGUG
AACY022005619.1/269-363      -C-UCGCCGUUAA--GGCGA--UCUG-CUAAACACUUCUGCGCGU----AGGUCCGACGCUCAUGACUCGGGCCCGCUCUCUUGCAAUA----GAGAGUGU-CCCU--GCGCA
AACY023865758.1/295-388      -U-UUACAAAAGGCAUAUAA--UCUGCCAAAAUACCUAAUCGCGU----AGGUCUGAAAA------AUCAGGCCCAUUCUAAAUUAACUAG--UAGGAUGU-CCAA--GCGCG
AACY023549611.1/122-29       -U-UUACAAACUGCAAAUAA--UCUGCCAAAAUACCUAAUCGCGU----AGGUCUGAAAA-----AUUCAGACCCAUUCUUAAAUAAAAA---AAGAAUGU-CCAA--GCGUG
AACY020675193.1/883-793      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAACUAAUCGCGU----AGGUCUGAGAA-----UAUCAGACCCAUUCUUAAAAGA------AAGGAUGU-CCAA--GCGUU
AANP01000006.1/228716-228805 -U-UCGCCGGUCCCAGGCGA--UCUG-CUAAACACUUC-GCGCGC----AGGUCCGGGUGG----AACCGGGCCCACUCCUUUCAG-------GGGAGUGU-CCCGG-GCGCG
CP000554.1/476761-476851     -C-AAGGCCUAACCCCUCGG--UCUGGC-AAAC-UCCAUGCGCGC----AGGUCCGGCUU-----GUUCGGGCCCAUCUCACAAUCUC-----CGAGAUGU-CCCUG-GCGCU
AATZ01000001.1/790249-790161 -U-UCGCUAUGCCCUAGCGA--UCUG-CUAAACACAUCCGCGCGC----AGGUCCGGACUGC---AUCCGGGCCCUCUCUUUCA---------AAGAGUGU-CCCU--GCGCG
AACY021266296.1/418-513      -U-UUACAAAAGGCAUAUAA--UCUGCCAAAAUACCUAAUCGCGU----AGGUCUGAAAA-----AUUCAGACCCAUUCUUAAUUAGAUUAAU-AGAAUGU-CCAA--GCGCG
AACY022742986.1/269-179      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAUUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAGAGA------AAGAAUGU-CCAA--GCGUG
AACY022155955.1/727-815      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----A-GUCUGAAAA-----UAUCAGACCCAUUCUUAAAAC-------AAAGAUGU-CCAA--GCGUG
AACY023503137.1/1263-1172    -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAACCA-----AAGGAUGU-CCAA--GCGUG
AACY021530526.1/86-176       -U-UUACAAAUAGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAUA-----UAUCAGACCCAUUCUUAAAAGA------AAGGAUGU-CCAA--GCGUG
AACY022018649.1/93-3         --UUUACAAAGAGUCUGUAA--UCUGGCAAAAUGUCUAAUCGCGU----AGGUCUGAAUA-----UAUCAGACCCAUUCUUAAAAUA------AAGGAUGU-CCAA--GCGUG
AACY022857722.1/372-278      -U-UUACAAAGAGCAUAUAA--UCUGCCAAAAUACCUAAUCGCGU----AGGUCUGUUAA-----GUUCAGACCCAUUCUUUAAAAAACAA--AAGGAUGU-CCAA--GCGUG
AACY020382975.1/1484-1393    -U-UCGCUCUAACCCGGCGA--UCUG-CUAAACACUUC-GCGCGC----AGGUCCGGCUGCU---GACCGGGCCCUUCCCUGAUUCC------AGGGUUGU-CCCAG-GCGCC
DQ366722.1/21796-21886       -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAAGA------AAGGAUGU-CCAA--GCGUG
AACY020086170.1/686-595      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAAAAA-----AAGGAUGU-CCAA--GCGUG
CP000435.1/2030820-2030724   AC-GGCCUUUUCGA-AGGCUCGUCUG-CUAGAAAAUUUUGCGCGC----AGGUCCGACCAUCAACAUUCGGGCCCACUUUCCUCAGU------GAAGGUGU-CCCU--GCGCA
AACY021760761.1/233-323      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCAAAUCACGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAACA------AAGGAUGU-CCAA--GCGUG
CP000111.1/1442726-1442635   -U-UUACAAAGGGUCUGUAA--UCUGGCAAGAUAUCUAAUUGCGU----AGGUCUGAAAAA----UAUCAGACCCAUUCUUAAAAGA------AAGGAUGU-CCAA--GCGUU
AACY024102189.1/255-345      -U-UUACAAAGAGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAUA-----UAUCAGACCCAUUCUUAAAAGA------AAGGAUGU-CCAA--GCGUG
AACY021918327.1/821-730      -U-UUACAAAGAGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAUAU----AAUCAGACCCAUUCUUAAAAGA------AAGGAUGU-CCAA--GCGUG
AACY023183283.1/237-147      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAUAGA------AAGGAUGU-CCAA--GCGUG
AACY023958478.1/34-121       -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGUAAU------AUCAGACCCAUUCUUAAAA--------AAGGAUGU-CCAA--GCGUG
AACY022465503.1/660-750      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCAAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAACG------AAGGAUGU-CCAA--GCGUG
AACY021624316.1/138-48       -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAUA-----UAUCAGACCCAUUCUUAAAACA------AAGGAUGU-CCAA--GCGUG
AACY020707597.1/209-296      -U-UCGCCUUUUCGAGGCGA--UCUG-CUAAACACAUCCGCGCGC----AGGUCCGGCGCUC---GAUCGGGCCCACUCCAGAA----------GGAGUGU-CCCA--GCGCG
AACY021521877.1/109-199      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----AAUCAGACCCAUUCUUAAAACA------AAGGAUGU-CCAA--GCGUG
AACY023512896.1/872-782      -U-UUACAAAAGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAUUA------AAGGAUGU-CCAA--GCGUG
AACY020981383.1/179-89       -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----AAUCAGACCCAUUCUUAUAACA------AAGGAUGU-CCAA--GCGUG
AACY022790400.1/739-829      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAAAA------GAGAAUGU-CCAA--GCGUG
AACY021130268.1/288-198      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAACCA------AAGAAUGU-CCAA--GCGUG
AACY023863377.1/614-702      -A-UCGCCUGAGAACGGCGA--UCUG-CUAAACACAUCCGCGCGC----AGGUCCGGCAUUGC--ACCCGGGCCCAUUCCUUC----------GGGAAUGU-CCCU--GCGCG
AACY020965060.1/80-170       -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAAUA------AAGAAUGU-CCAA--GCGUG
AACY023483958.1/1059-969     -U-UUACAAAGUGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----CAUCAGACCCAUUCUUAAAACA------AAGGAUGU-CCAA--GCGUG
AACY020496228.1/1944-1850    -C-UUGCCGUUAA--GGCGA--UCUG-CUAAACACUUCUGCGCGU----AGGUCCGACGCUCAUGACUCGGGCCCGCUCUCUUGCAACA----GAGAGUGU-CCCU--GCGCA
AACY020535675.1/6729-6818    -U-UCGCCGGUCCCCGGCGA--UCUG-CUAAACACAUC-GCGCGC----AGGUCCGGGUGG----AACCGGGCCCACUCCUCUCAG-------GGGAGUGU-CCCGG-GCGCG
AACY022427862.1/360-448      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAACA--------AAGGAUGU-CCAA--GCGUG
AACY021587358.1/670-580      -U-UUACAAAGAGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAACA-----UAUCAGACCCAUUCUUAAAAGA------AAGGAUGU-CCAA--GCGUG
AACY023061039.1/52-140       -U-UCGCCUUUUGAGGGCGA--UCUG-CUAAACACAUCCGCGCGC----AGGUCCGGAUAGC---ACCCGGGCCCGCUCCUUUC---------AGGAGUGU-CCCU--GCGCG
AACY023989245.1/664-754      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAACA------AAGAAUGU-CCAA--GCGUG
CP000552.1/1428005-1427917   -U-UUACAAAGGGCCUGUAA--UCUGGCAAAAUAUUUAAUCGCGU----AGGUCUGAAAA-----AUUCAGACCCAUUCUUAAAA--------AAGAAUGU-CCAA--GCGUG
AACY020316069.1/902-812      -U-UUACAAAGUGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAU-----UAUCAGACCCAUUCUUAAAUAA------AAGAAUGU-CCAA--GCGUG
AACY023868456.1/1237-1331    -U-UUACAAAACGCAUAUAA--UCUGCCAAAAUACCUAAUCGCGU----AGGUCUGAAAA------AUCAGGCCCAUUCUAAAUACAUUAAA-UAGAAUGU-CCAA--GCGCG
AACY020690792.1/637-727      -U-UUACAAAAGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----AAUCAGACCCAUUCUUAAAUUC------AAGGAUGU-CCAA--GCGUG
AACY023371655.1/1240-1332    -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAUAUA---UAUCAGACCCAUUCUUAAAAUA------AAGGAUGU-CCAA--GCGUG
AACY023505252.1/458-368      -U-UUACAAAGAGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAG-----UAUCAGACCCAUUCUUAAAAAA------AAGGAUGU-CCAA--GCGUG
AACY023185794.1/205-293      -U-UCGCCUUUUGAGGGCGA--UCUG-CUAAACACAUCCGCGCGC----AGGUCCGGACGAC---AACCGGGCCCGCUCCUUCC---------GGGAGUGU-CCCU--GCGCG
CP000576.1/1376525-1376435   -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAA-----UAUCAGACCCAUUCUUAAAACA------AAGGAUGU-CCAA--GCGUG
AACY020366492.1/1087-1175    -U-UUGCCUUUUGAGGGCGA--UCUG-CUAAACACAUCCGCGCGC----AGGUCCGGAAAAC---ACCCGGGCCCGCUCCUUUC---------AGGAGUGU-CCCU--GCGCG
AACY022540081.1/139-48       -U-UUACAAAGAGUCUGUAA--UCUGGCACAAUAUCUAAUCGCGU----AGGUCUGAAUA-----UAUCAGACCCAUUCUUAUAAAGA-----AAGGAUGU-CCAA--GCGUG
AAUA01000001.1/645961-645867 -A-CCUCCUCAGAUCGCCCG--UCUG-CUAAAACCUUCUGCGCGC----AGGUCCGGUCAUCAGGAUUCGGGCCCACUUUCUCUAGA------GACAGUGU-CCCU--GCGCA
AACY020087986.1/449-359      -U-UUACAAAGGGUCUGUAA--UCUGGCAAAAUAUCUAAUCGCGU----AGGUCUGAAAG-----UAUCAGACCCAUUCUUAAUUUA------AAGAAUGU-CCAA--GCGUG
BX548174.1/1390580-1390488   -U-UUACAAAGGGCCUGUAA--UCUGGCAAAAUAUUUAAUCGCGU----AGGUCUGAAAA-----AUUCAGACCCAUUCUUAAAAAAAA----AAGAAUGU-CCAA--GCGUG
BX548175.1/1556654-1556564   -C-CAGGCCUAACCCCUCGG--UCUGGC-AAAC-UCCAUGCGCGC----AGGUCCGGCUU-----GUUCGGGCCCAUCUCACAAUCUC-----CGAGAUGU-CCCUG-GCGCU
#=GC SS_cons                 .:.<<<<<_______>>>>>..------------------(((((....,<<<<<<<____....__>>>>>>><<<<<<<______......>>>>>>>,.,,,,..)))))
#=GC RF                      .U.ucgccaaaagucggcga..UCUGGCaAAAuAucUaaucGCGc....AGGuCcGaaaau....aauCgGaCCCauccuuaaaaaa......aaggauGU.CCca..gCGCg
//
# STOCKHOLM 1.0

#=GF AC   RF01068
#=GF ID   mini-ykkC
#=GF DE   Guanidine-II riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:17621584; Weinberg Z
#=GF SS   Published; PMID:17621584; Weinberg Z
#=GF GA   32.00
#=GF TC   32.00
#=GF NC   31.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   17621584
#=GF RT   Identification of 22 candidate structured RNAs in bacteria using the
#=GF RT   CMfinder comparative genomics pipeline.
#=GF RA   Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER,
#=GF RA   Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR
#=GF RL   Nucleic Acids Res. 2007;35:4809-4819.
#=GF RN   [2]
#=GF RM   28001368
#=GF RT   Biochemical Validation of a Second Guanidine Riboswitch Class in Bacteria.
#=GF RA   Sherlock ME, Malkowski SN, Breaker RR
#=GF RL   Biochemistry. 2017;56:352-358.
#=GF RN   [3]
#=GF RM   28529131
#=GF RT   The Structure of the Guanidine-II Riboswitch.
#=GF RA   Huang L, Wang J, Lilley DMJ
#=GF RL   Cell Chem Biol. 2017;24:695-702.
#=GF CC   Simpler in structure and has fewer highly conserved nucleotide positions
#=GF CC   than the ykkC-yxkD leader.[1] Despite this each of its two stem-loop
#=GF CC   structures directly bind free guanidine. Therefore, mini-ykkC RNA motif
#=GF CC   represents a distinct class of guanidine-sensing RNAs.[2] Its crystal
#=GF CC   structure was also determined.[3]
#=GF WK   Mini-ykkC_RNA_motif
#=GF SQ   72


CP000462.1/2127857-2127812 CCUCGGGGACGACCUC-GAGGCCUCCUGAUACG--------CAGGGACGACCCUG
CP000781.1/1410192-1410143 AGGCCGGGACGACCCG-GCCAUUCCCUCGGGACCCGG----CCGGGACGACCCGG
BA000040.2/4473825-4473773 UGGGAGGGACGGCCCU-CCUAUCCACCAGCAUAUCAGCCG-CGGGGACGACCCUG
BX572600.1/144591-144548   --UCGAGGACGACCUC-AA--AAUCACCUUUUCGG------CCGGGACGACCCGG
CP000572.1/1233467-1233513 GCCCGGGGACGACCCC-GGGCCGUCGAUGUUCAAC-------GGGGACGACCCCA
CP000283.1/2608526-2608481 GCUCGAGGACGACCUC---CCAAUCACCCUUUCGG------CCGGGACGACCCGG
CP000058.1/4535822-4535869 AGCAACGGACGACCGU-UGCGUAGAUAGAUCAAUA------GCGGGACGGCCCGC
CP000390.1/1077820-1077866 GUGCAGGGACGGCCUU-GCUUUCUUCUAUCCGGA-------UGAGGACGGCCUCA
CP000563.1/3324894-3324846 GCUUAGGGACGACCCU-AAACAUGCCUUAAUUUGGU-----AGGGGACGACCCCU
CP000075.1/4724000-4724047 AGCAACGGACGACCGU-UGCGUAGAUUGAUCAAUA------GCGGGACGGCCCGC
CP000444.1/1985002-1985050 GCUUAGGGACGACCUU-AAAUACGCCGAUAUCAAUU-----UGGGGACGACCCCG
CP000614.1/2627011-2626967 GCCCGGGGACGGCCCC-GGGCCGUUCGCUUCAAC--------GGGGACGACCCC-
CP000463.1/3411592-3411635 --UCGAGGACGACCUC-AA--AAUCACCCUUUCGG------CCGGGACGACCCGG
CP000270.1/1349405-1349446 UCGUAAGGACGACCUU-GCGUUUUCACGAAC-----------GGGGACGGCCCC-
CP000076.1/5115332-5115385 UCGCGAGGACGACCUC-GCGACUCAUUCGAGCGAUCAAUUCCGGGGACGACCCCA
AM286690.1/2165346-2165394 CCCUGGGGACGACCCC-GGCGGCCAAGGCUAUAAAG-----ACGGGACGGCCCGU
CP000453.1/2185364-2185316 GGCCGGGGACGACCCU-GGCCGCCAGAACGAAAACG-----GCGGGAGGACCUGG
CP000264.1/1252874-1252827 CCGCCGGGACGACCCG-GCCAUGUACGGGUAGUUG------UCAGGACGACCUGC
CP000089.1/88477-88521     CUUCCGGGACGACCCG-GAGGCAAAAGAAUCCGG--------CGGGACGACCCG-
CP000749.1/1273916-1273962 AUGUGGGGACGACCUC-ACCGCUCUAAUUAAUAA-------UGAGGACGACCUCA
CP000151.1/2708127-2708083 GCCCGGGGACGACCCC-GGGUCAUUCGCUUCAAC--------GGGGACGGCCCC-
BA000045.2/3187382-3187335 CGGUGGGGACGACCCC-ACCCUUCGCAAAGUUUCG------CGGGGACGACCCCG
CP000468.1/4784334-4784380 UUUGCAGGACGACCUG-CAAACGCGUCUUUUCACC-------GGGGACGGCCCCA
CP000627.1/1043227-1043274 AAGUGAGGACGACCUC-ACCGCUCCAUCUUUUCUU------CGGGGACGACCCCA
CP000137.1/143273-143224   CGACCGGGACGGCCCG-GUCGCUUCCCUGGGGCACAG----CCGGGACGACCUGG
AE015451.1/1897147-1897096 CGGUGAGGACGACCUC-ACGACGCACCGCGUGACCACUC--CGGGGACGGCCCCA
BX950851.1/2171199-2171246 CGCGAUGGACGACCAU-CAUGCGGAUCGCAUUUUG------GCGGGACGACCUGC
CP000712.1/4533467-4533518 CUGUGAGGACGACCUC-ACGACGCACCGCGUGACCAUUC--CGGGGACGGCCCCA
CP000301.1/5064909-5064861 CGGCCGGGACGACCCG-GCCGAACAAGGAGCAUGAG-----CCGGGACGGCCCGG
AL954747.1/2389357-2389307 GAUUGAGGACGACCUC-AUCUUCGGGACAAUCUACUAU---CCGGGACGACCUGG
CP000086.1/1166409-1166455 GCCCGGGGACGACCCC-GGGCCGUCGAUGUCCAAC-------GGGGACGACCCCA
BX571660.1/26855-26903     CCCCUAGGACGACCUA-GAGGGUGACUUCACCGAUG-----AUGGGACGACCCAA
CP000438.1/3579539-3579491 GAAGCGGGACGACCCG-UUUUCCCUCUUUCAUUGCG-----CGGGGACGACCCUG
DQ472473.1/1294-1250       UUUGCAGGACGACCUG-CAAACGCUUCUUUCACC--------GGGGACGGCCCC-
CP000469.1/1970735-1970783 GCUUAGGGACGACCCU-AAAUACGCCGAUAUCAAUU-----UGGGGACGACCCCG
BX571872.1/300724-300678   UAUCCGGGACGACCUG-GAUAUACUGCCGUUUUC-------UGGGGACGACUCCA
CP000781.1/4652689-4652739 GGACGCGGACGGCCGC-GUGCCCUUGCGUAUCGAGCGG---CGGGGACGACCUCG
CP000463.1/1374094-1374142 CGGCCGGGACGACCCG-GCCGACCAGGGAGCAUGAG-----CCGGGACGACCCGG
CP000301.1/3222813-3222860 CCAAGAGGACGACCUC-CCAAUCACCCAAAUGACG------CAGGGACGACCCUG
CP000091.1/1606547-1606501 GCCGCGGGACGACCCG-UGGCCGAUACGCAACCG-------GCAGGACGACCUGC
CP000744.1/3522595-3522547 GAAGCGGGACGACCCG-UUUUCCUUCUUUCAUUGCG-----CGGGGACGACCCUG
CP000697.1/2991257-2991208 GCCGGGGGACGACCCCACGGCCGGGACGAUCGCCCG-----CGAGGACGGCCUCG
CP000282.1/1459875-1459918 UGUUUAGGACGACCUA-AGCAGGCUCUCAAU----------GCGGGACGACCCGC
BA000032.2/787493-787539   AAGUGAGGACGACCUC-ACCGCUCUAUCUUUUCUC-------GGGGACGACCCCA
CP000758.1/2644355-2644400 CGGGAAGGACGGCCUU-CCCGCUUCUUCAACGA--------ACGGGACGGCCCGU
CP000230.1/336937-336985   AGGCGGGGACGACCCC-GCUGGAGGUGUUUUUCAGG-----CGGGGACGACCCCG
CP000458.1/2537252-2537208 GCCCGGGGACGACCCC-GGGCCAUUCGCUUCAAC--------GGGGACGGCCCC-
BX572597.1/162305-162257   CGGCCGGGACGACCCG-GCCGCACAGGGAGCAUGAG-----CCGGGACGACCCGG
AP007255.1/1410478-1410525 GGGCCGGGACGACCCG-CCCCUUUUCCCCUCACCU------CCGGGACGGCCCGG
CT573326.1/1469842-1469791 CUGUGAGGACGACCUC-ACGACGCAGUGCGUGAUCGCUA--CGGGGACGGCCCCA
CP000038.1/4603316-4603362 UUUGCAGGACGACCUG-CAAACGCCUCUUUUCACC-------GGGGAUGGCCCCA
AE017180.1/755444-755400   CGGCGGGGACGACUCC-GCCGCCCGAACAUCCAC--------GGGGACGACCCC-
CP000753.1/3410159-3410111 GCUUAGGGACGACCCU-AAAUACGCCUAAUCUAACA-----UGGGGACGACCCCU
AAFY01000765.1/857-899     CUCGCAAGACGACUUG-CGAGAUGUAAGCAAU----------CGGGACGGCCCG-
CP000115.1/2219778-2219829 GCGGAAGGACGACCUU-UCGUAUCCCACACAACCACGCG--CGGGGACGGCCCUG
CP000388.1/1686454-1686408 AAAUGAGGACGACCUC-AUCCCUCGCGCUUUUCU-------CUGGGACGACCCAG
BX640439.1/167183-167227   GCGCCGGGACGACCCG-GCGCGUGUACUGGCC---------UGAGGACGACCUCG
CP000283.1/2440543-2440591 CGGCCGGGACGACCCG-GCCGAACAGGGAGCAUGAG-----CCGGGACGACCCGG
X69949.1/348-394           UUUGCAGGACGACCUG-CAAACGCCUCUUUUCACC-------GGGGACGGCCCCA
CP000720.1/4139495-4139449 UGGCUGGGACGACCCA-GUUACGCAUCUGUUUUU-------CGGGGACGGCCCCG
CP000440.1/2556910-2556866 GCCCGGGGACGACCCC-GGGUCAUUCGAUUCAAC--------GGGGACGGCCCC-
CP000026.1/4331173-4331217 GUUACAGGACGACCUG-UAAACGCUAUUCUCACC--------GGGGACGGCCCC-
BA000012.4/3864269-3864318 GCGCGGGGACGACCCC-GCGCCUCCCCAAGAAUUCGG----UCGGGACGACCCGC
CP000826.1/463043-463087   UAAACGGGACGACCUG-UUUACGCAUCUGUAUCC--------GGGGACGACCCC-
AE007869.2/1627110-1627159 GCGCGAGGACGACCUC-GGCCAAAUCGGCGACAGCAU----GCGGGACGGCCCGG
CP001044.1/953099-953146   UGCCGUGGACGACCUC-GGCAUGCAUGACCACGUG------GCGGGACGACCCGC
CP000304.1/2181100-2181054 AACCACGGACGGCCGU-GGCACUGAUGAAUAAAG-------GCGGGACGGCCCGC
CP000680.1/1523071-1523024 CACCACGGACGACCGU-GGCACAUGACGAAUGACG------GCGGGACGGCCCGC
CP000790.1/1077239-1077193 AAGUGAGGACGACCUC-ACCGCUCUUAUCACUAU-------CGGGGACGACCCCA
AM747720.1/2630566-2630522 GCCCGGGGACGACCCC-GGGUCAUUCGCUUCAAC--------GGGGACGGCCCC-
CP000094.2/1515933-1515886 CGUCGGGGACGACCCC-GGCGCUCAUCGAAAAACU------GCGGGACGGCCCGC
CP000094.2/1858450-1858398 ACGCGGGGACGACCCU-GCGGCUCAAUCGAGUUUUCAAUC-UGGGGACGGCCCCG
#=GC SS_cons               <<<<<<<<____>>>>.>>>>--------------......<<<<<____>>>>>
#=GC RF                    ccgcggGGACGACCcc.gcggCucaccgauuuacc......cgGGGACGACCCcg
//
# STOCKHOLM 1.0

#=GF AC   RF01069
#=GF ID   purD
#=GF DE   purD RNA motif
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:17621584; Weinberg Z
#=GF SS   Published; PMID:17621584; Weinberg Z
#=GF GA   41.00
#=GF TC   42.10
#=GF NC   40.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   17621584
#=GF RT   Identification of 22 candidate structured RNAs in bacteria using the
#=GF RT   CMfinder comparative genomics pipeline.
#=GF RA   Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER,
#=GF RA   Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR
#=GF RL   Nucleic Acids Res. 2007;35:4809-4819.
#=GF WK   PurD_RNA_motif
#=GF SQ   21


CP000538.1/1181299-1181426   GU-GU--GAUUU---ACCGUGUUCUGUGGCAUUGUUUG-AGCUUUGAAA--------AAAGCGAGAAGU-UGCAG-CCUUUAA--AAAUU-A-CCUAGCGGUUUUCU--UUGACUU-UU--UG-----GGGUCAAUCUU---UGUUAAA----CGGCUGUUUGGGU
BX571659.1/149379-149509     GU-AGAUGAUCU---UGUGUGUUCGGUGUUUCCGUUUGUAGCCU-CUA----------AGGUGAGGAUU-UGCCG-CCU-AAU--AGGUCGC-UCUUGUCUGAGUUG--UUGGCUU-UUUUUG-----GGGCCACGCAA---CUUGGUAA---CGCCCGCUCGGGC
CP000776.1/211827-211937     GU-GA--GAUUU--UUGUGCGA--CGUGGCCGA------------GUUA---------------UUGGU-UGCG-ACCUGAUA--AAAUU-U-CCUAACUGCAAGA---UUGGCUU-UU--UC-----GGGCCGAUUCU---UUUUACGCAC-CGCUCACUUGGGU
AL111168.1/1179643-1179770   GU-GU--GAUUU---ACCGUGUUCUGUGGCAUCGUUUG-AGCUUUGAAA--------AAAGCGAGAAGU-UGCAG-CCUUUAA--AAAUU-A-CCUAGCGGUUUUCU--UUGACUU-UU--UG-----GGGUCAAUCUU---UGUUAAA----CGGCUGUUUGGGU
AAFY01021399.1/242-110       GU-AG-AAUUCU---UGUGUGU-CGGUGUCAUCGUUUG-AGAUA-UGUUAACUC----UGUCGAGAUGA-UGCCG-CCUUUAG--AGGAUUC-UCUCUUCACCCAAAU-UCGGCUU-UU--AGAACC-AAGCCAG-------UGCGAAA----CGGCUACUCGGGC
CP000025.1/1300422-1300549   GU-GU--GAUUU---ACCGUGUUCUGUGGCAUCGUUUG-AGCUUUGAAA--------AAAGUGAGAAGU-UGCAG-CCUUUAA--AAAUU-A-CCUAGCGGUUUUCU--UUGACUU-UU--UG-----GGGUCAAUCUU---UGUUAAA----CGGCUGUUUGGGU
AE017125.1/579127-578994     GU-AGU-AAUCU--UUGUGUGU-CGGUGUUUGCGCUUG-AGCUA-CUUUGAGA-----UAGUGAGCAUU-CGCCG-CCUAAUG--AGAUU-C-UCUUAACCCUAUUU--GUGGCUU-UU--UU-----AGGCUACGCAAAUCGGGGUAA----CGCUCAUUUGGGG
AAFY01000382.1/216-327       GU-AA-AUAUGU---GGUGUGC--AGCG------UUUG-------CUUUUAGCAUUU-----------U-CGCU--CCUAAA---ACAUAGU-UCUUAUGUGCUAGUG-UUGGCUU-UUA--------GGGCCAGUUAGA--UGGUUAA----CGGCUACUUGGAA
CP000767.1/541301-541429     GU-AC-AGGUGC---UAUGCG--AUGUGAUUUCGUUUG-AGUGC-GAAA---------GUGCGAGAGAU-UGCA-ACCUUGAG--GCGCUUG-UCUAUUUGCAAGA---UUGGCUU-UG--UUUAC--GGGCCACUCUU---UUAUGCG---ACGCUCACUUGGGU
AAFL01000002.1/145370-145243 GU-GC--GAUUU---ACCGUGUUCUGUGGCGUCGUUUG-AGUUUCGAAA--------GAAGCGAGAAGU-UACAG-CCUUUAA--AAAUC-G-CCUAACGGUUUUCU--UUGACUU-UU--UG-----GGGUCAAUCUU---UAUUAAG----CGGCUGUUUGGGU
CP000487.1/1253234-1253105   GU-AC--GCAAA--UGGUGUGA-U-GCGAUCUCGUUUGUAGCCA-UUUU---------UAGCGAGAGAU-UGCGA-CCUAAAG--UUUGA-G-UCUAUCUGCAAGG---UUGGCUUUUUA-UU----AGGGCCGAUUCUA-CUGCGUAA----CGGCCAUUUGGGU
CP000241.1/1226355-1226241   GU-AGU-GGUUUU--UGUGUGAU-GGCA-UUU-------------UUU-----------------AAAUCUGCC--CCUAAG--AAAAUC-C-UCCUAGCCUUAUUAGUGUAGGUU-UGU-UG-----AACUUAUGCGCA--UGUAAAAGUAGCGGUCAUCUGGGU
AP009179.1/1946938-1946809   GU-AGUCGGGCC---GGUGUGU-AGACAUUUUCGUUCG-AACGGGGUAA--------CCCGUGAGAAAU-UGCCU-CCUAAA---GGCCCGC-UCUCUCCUGCAUCG--UUGGCUU-UUU-UA-----GGGCCGA-------CUUUAACAGAACGGCCACUCGGGC
AM260522.1/1390694-1390581   GU-AGU-GGUUUU--UGUGUGAU-GGCA-UUU-------------UUU-----------------AAAUCUGCC--CCUAAU--AAGAUU-C-UCCUAGCCUUAUUGGUGUAGGUU-AU--UG-----AACUUAUGCACA--UGUAAAAGUAGCGGUCAUCUGGGU
AAFJ01000002.1/15726-15851   GU-GC--GAUUU---ACCGUGU-CUGUGGCGUCGUUUG-AGUUUCGAAA--------GAAGCGAGAAGU-UGCAG-CCUUUAA--AAAUU-G-CCUAGCG-ACUUUU--UUGACUU-UU--UG-----GGGUCAAUCUU---UGUAAAA----CGGCUACUUGGGU
CP000768.1/424659-424532     GU-GU--GAUUU---ACCGUGUUCUGUGGCAUCGUUUG-AGCUUUGAAA--------AAAGCGAGAAGU-UGCAG-CCUUUAA--AAAUU-A-CCUAGCGUUUUUCU--UUGACUU-UU--UG-----GGGUCAAUCUU---GGUUAAA----CGGCUGUUUGGGU
AAFY01003596.1/87-211        GU-AGUUGUUCU---UGUGUGC--AUCGGUUUUGUUUG--AAGC-AUUA---------GCUU-AGAAAC-UGAU--CCUAAU---AGA-CAC-UCGCUUUGCCACAU--UAAGCCUUUG--AGAACCAAGGCUAA------UUGUGAAA----CGCUCACUCGGUU
AP009178.1/1349332-1349200   GU-AGAUUUUGG---UGUGUGU-CGGUGACUCCGUUUG-AGCCAGGGACGC------CUGGCGAGGAGC-CGCCG-CCUAAU---CCAAAAC-UCGCUCCCUCUUCU--UAUGGUC-UUA-GG-----GACCAUGGCAU---UGCGCGA---ACGCCCGCUCGGGC
CP000153.1/424860-424993     GUAAU--GCUCU---UGUGUGU-CGGUGCUAUCGUUUG-AGAUA-UGUUUACUC----UGUCGAGAUAA-UGCCG-CCGAUAA--AGAGC-ACUCUCUUCGCCCAAAU-ACGGCUU-UU--AGAACC-AAGCCAA------CUGCGAGA----CGGCUACUCGGGC
CP000792.1/1502338-1502210   GU-AU--GGGUGCC--UUGCGA--UGUGGCUUCGUUUG-AGCCU-UAAAC--------A-GCGAGAAGU-UGCA-ACCUUUU-GGUAUCC-A-UCUAUUUGCAAGA---UUGGCUU-UG--UUUAU--GGGCCACUCUU---CUAUGCG---ACGCCCACUUGGGU
CP000932.1/480470-480599     GU-GU--GAUUU---ACCGUGUUCUGUGACUUCGUUUG-AGUUUUGAAA--------AAAGCGAGAAGC-UGCAG-CCUUUAA--AAAUC-A-CCUAAUGGCAUACU--UUGACUU-UU--UGA----GGGUCAG----A-CACUUAUACUC-CGGCCAUUUGGGU
#=GC SS_cons                 ::.<<..<<<<<...-------.<<<<<-<<<<-----.-<<<<.____.........>>>>-->>>>-.>>>>>.-------..>>>>>.>.>-------------..<<<<<<<.__..__.....>>>>>>>::::...:::::::....:::::::::::::
#=GC RF                      GU.ag..ggucu...ugUGUGu.cgGcggcuuCGUUUG.AGccu.uuua.........aggCGAGaagU.ugCcg.CCUaaaa..agacc.c.uCUauuugcuauau..uuGGCuu.UU..Ug.....ggGCCaauCuu...UguuaaA....CGgCcAcUUGGGu
//
# STOCKHOLM 1.0

#=GF AC   RF01070
#=GF ID   sucA
#=GF DE   SucA RNA motif
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:17621584; Weinberg Z
#=GF SS   Published; PMID:17621584; Weinberg Z
#=GF GA   40.00
#=GF TC   41.20
#=GF NC   36.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   17621584
#=GF RT   Identification of 22 candidate structured RNAs in bacteria using the
#=GF RT   CMfinder comparative genomics pipeline.
#=GF RA   Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER,
#=GF RA   Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR
#=GF RL   Nucleic Acids Res. 2007;35:4809-4819.
#=GF WK   SucA_RNA_motif
#=GF SQ   35


X91877.1/1118-1200             UUGCGAUCCGCUAACCGGUCAAGCCGUGUCGCGGAAGGUUGAAU-----------AACC--CGCUGAA--CUCCGGCAUUCCCGG-AG-AAU-AGUGA-GCG
AACY023318756.1/1434-1516      GAUCAAUUCGUGAAGCGGUAUAGCCGUAGAGCGGAUGGUUUU-------------AACCACAGUUUUUA-AUCGGGAAA--CCCG-AU-GAAAGGUGA-GCA
CP000458.1/1665648-1665730     UCGCAAUCCGCUAAACGGUCAGGCCGUGUCGCGGAAGGUUGAGU-----------AACC--CGCUAUU-UCUCGAGAAG--CUCGAAGAAA--GGUGA-GCG
CP000555.1/2159060-2158977     UCGCAAUCCGCCAACCGGUCCAGCCGUGUCGCGGAAGGUUUUUC-----------AACC--AGCCAAC-GUCCUGGAUA--CCAG-GGUGAAAGGUGA-GCG
CP000267.1/2549148-2549056     UCGC-AUCCGCCAAACGGUCAAGCCGUGACGCGGAAGGUUUUUAAAAACAGCUUUAACC--AGCUCAA-GUUUCCUGCA--GGGA-AACGGA-GGUCA-GCG
CP000352.1/2222407-2222325     UUGCAAUCCGCUAACCGGUCGAGCCGUGUCGCGGAAGGUUGAUG-----------AACC--CGCUUAA--CUCCGGCAUUCCCGG-AG-AAU-AGUGA-GCG
AACY023427272.1/974-893        UUGCGUUCUGCUAAUCGGUGAAGCCGUGUCGCAGAUGGUUUA-------------AACCACAGUUU---UUUUCGGGAUACCCGAUGAAA---GGUGA-GCA
CP000316.1/2758688-2758597     UCGC-AUCCGCUAAUCGGUCCAGCCGUGUUGCGGAAGGUUAAUCAACCA-GCUUUAACC--AGCUAAU-GUUUCCCCAA--GGGA-AACGGA-GGUCA-GCG
CP000512.1/3588834-3588752     UCGC-AUCCGCCAACCGGUUCAGCCGUGUCGCGGAAGGUUUUAC----------CAACC--AGCUAAU-GCUUCCCGCA--GGGA-AGCGGA-GGUCA-GCG
CP000539.1/1894099-1894180     UCGC-AUCCGCCAACCGGUUCAGCCGUGACGCGGAAGGUUUGUU-----------AACC--AGCUAAC-GCUUCCUUCA--GGGA-AGUGGA-GGUCA-GCG
AAFX01033646.1/36-119          UCGC-AUCCGCCAUCCGGUUCAGCCGUGUCGCGGAAGGUUUCUC----------AAACC--AGCCAAU-GCCUCCCGCA--GGGA-GGCGGAAAGUAU-GCG
CP000572.1/1733374-1733456     GCGCAAUCCGCUAAACGGUCAGGCCGUGUCGCGGAAGGUUGAGU-----------AACC--CGCUAUU-UCUCGAGAAG--CUCGAAGAAA--GGUGA-GCG
AACY023317617.1/166-85         UCGC-AUCCGCCAACCGGUCCAGCCGUGUCGCGGAAGGUAGUUC-----------AACC--AACUAAU-GUUCCCUGAA--GGGG-AGCGAA-GGUCA-GCG
AACY020696236.1/616-535        UCGC-AUCCGCCAACCGGUUCAGCCGUGUCGCGGAAGGUUUCUC-----------AACC--AGCUAAU-GCUUUCCCAA--GGAA-AGCGGA-GGUCA-GCG
AACY020173447.1/1452-1533      UUGCGUUCUGCUAAUCGGUAAAGCCGUGUCGCAGAUGGUUUU-------------AACCACAGUUU---UUUUCGGGAUACCCGAUGAAA---GGUGA-GCA
AL646052.1/1348533-1348615     UUGCGAUCCGCUAACCGGUCAAGCCGUGUCGCGGAAGGUUGAUG-----------AACC--CGCUGAA--CUCCGGCAGACCCGG-AG-AAA-GGUGA-GCG
CP000151.1/1635431-1635513     UCGCAAUCCGCUAAACGGUCAGGCCGUGUCGCGGAAGGUUGAGU-----------AACC--CGCUAUU-UCUCGAGAAA--CUCGAAGAAA--GGUGA-GCG
CP000614.1/1585413-1585495     UCGCAAUCCGCUAAACGGUCAGGCCGUGUCGCGGAAGGUUGAGC-----------AACC--CGCUAUU-UCUCGAGAAG--CUCGAAGAAA--GGUGA-GCG
CU207211.1/1785563-1785482     GUGCAAUCCGCUAAACGGUCAGGCCGUGUCGCGGAAGGUUGAAU-----------AACC--CGCUAAU--CUCGCGAAG--CGCGAAG-AAA-GGUGA-GCA
CP000090.1/2250076-2249994     UUGCGAUCCGCUAACCGGUCAAGCCGUGUCGCGGAAGGUUGAAU-----------AACC--CGCUGAA--CUCCGGCAUACCCGG-AG-AAA-AGUGA-GCG
CP000270.1/1834738-1834820     GCGCAAUCCGCUAAACGGUCAGGCCGUGUCGCGGAAGGUUCUGU-----------AACC--CGCUAUU-UCUCGAGAAA--CUCGAAGAAA--GGUGA-GCG
AACY021530903.1/764-682        GAUCAAUUCGUAAACCGGUUAAGCCGGAGAGCGAAUGGUUUU-------------AACCACAGUUUUUA-UUCGGGAAA--CCCG-AU-GAAAGGUGA-GCA
CP000529.1/1977317-1977408     UCGC-AUCCGCUAAUCGGUUCAGCCGUGUUGCGGAAGGUUAAUUAACCA-GCUUUAACC--AGCUAAU-GUUUCCCAAA--GGGA-AACGGA-GGUCA-GCG
CP000269.1/1701914-1701996     GUGCAAUCCGCUAACCGGUCAGGCCGUGCCGCGGAAGGUUAAAU----------UAACC--CGCUAAU--CUCGCGAAA--CGCGAAG-AAA-GGUGA-GCA
CP000542.1/4367133-4367052     UCGC-AUCCGCCAACCGGUCCAGCCGUGUCGCGGAAGGUUUUCC-----------AACC--AACUCAU-GCUUUCCGCA--GGAA-AGCGCA-GGUCA-GCG
AACY023344455.1/936-854        GAUCAAUUCGCGAAACGGUAUAGCCGCGUAACGAAUGGUUUU-------------AACCACAGUUUUUA-AUCGGGAAA--CCCG-AU-GAAAGGUGA-GCA
CP000655.1/832933-833015       GAUCAAUUCGUGAAACGGUACAGCCGUGUAACGAAUGGUUAU-------------AACCACAGUUUUUA-UUCGGGAAA--CCCG-AU-GAAAGGUGA-GCA
BX640448.1/54616-54535         CUGCUAUCCGCUAAACGGGAAGCCCGUGUCGCGGAAGG--UUUU-------------CCUGCAUCGUAU-CGAGUGAAG--CACU-CG-UCAAGGUGAAGCG
AACY020300513.1/953-871        UCGC-AUCCGCCAAUCGGUCCAGCCGUGUCGCGGAAGGUUGUUU-----------AACC-AGUUCAAA-GUUUCCUGCA--GGGA-AACGGA-GGUCA-GCG
CP000884.1/3831654-3831736     UCGC-AUCCGCCAAUCGGUACAGCCGUGUCGCGGAAGGUUCCAC----------AAACC--AGCUAAU-GCCUCCUUCA--GGGA-GGCUGA-GGUCA-GCG
CP001043.1/1962243-1962161     GCGCAAUCCGCUAAACGGUCAGGCCGUGUCGCGGAAGGUUCAGU-----------AACC--CGCUAUU-UCUCGAGAAG--CUCGAAGAAA--GGUGA-GCG
AAUJ02000001.1/2879809-2879727 UCGC-AUCCGCCAAUCGGUACAGCCGUGUCGCGGGAGGUUCCAC----------AAACC--AGCUAAU-GCUUUCCGAA--GGAA-AGCGGA-GGUCA-GCG
CP001503.2/2183445-2183363     GCGCAAUCCGCUAAACGGUCAGGCCGUGUCGCGGAAGGUUGAGC-----------AACC--CGCUAUU-UCUCGAGAAG--CUCG-AAGAAA-GGUGA-GCG
CU914168.1/1698650-1698569     UUGCGAUCCGCUAACCGGUCAAGCCGUGUCGCGGAAGGUUGAUG-----------AACC--CGCUGAA-CUCCGGCAGA--CCCG-GAGA-A-GGUGA-GCG
CP001644.1/1260235-1260317     UUGCGAUCCGCUAACCGGUCAAGCCGUGUCGCGGAAGGUUGAUG-----------AACC--CGCUGAA--CUCCGGCAGACCCGG-AG-AAA-AGUGA-GCG
#=GC SS_cons                   :(((,,<<<<<----<<<<___>>>>---->>>>>,<<<<____...........>>>>..<<<<---.<<<<<<<___..>>>>.>>>---.>>>>,.)))
#=GC RF                        ucGCaAUCCGCuAAaCGGucaAgCCGUGUcGCGGAAGGUUuuuu...........AACC..cgcuaau.gcuccggaAa..ccgg.agcgaA.ggugA.GCg
//
# STOCKHOLM 1.0

#=GF AC   RF01071
#=GF ID   OLE
#=GF DE   Ornate Large Extremophilic RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:17164334; Weinberg Z
#=GF SS   Published; PMID:17164334; Weinberg Z
#=GF GA   50.00
#=GF TC   57.20
#=GF NC   45.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17164334
#=GF RT   Identification of a large noncoding RNA in extremophilic eubacteria.
#=GF RA   Puerta-Fernandez E, Barrick JE, Roth A, Breaker RR
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:19490-19495.
#=GF WK   OLE_RNA
#=GF SQ   20


AATC01006218.1/714-103     UGUUAAAAUAGAAAAAGUGGUGCAUUAUUCUAGU-GAUAUU--GCCUACUAUGAGGGUGGGGCUAAAAAUCCACUAAAGGGCACA-UCGUUGAAGUUUCUUGUUUGUGCGCAAAAC-GCCCAGUUAUGCGUGUUUUCAGGGAGUA-------------------------------AAGAUUG-CCGGGAUAUAUGUAACGGCAUACAUAGAAAGACCCGACAAUCGCGGAGACUUUAUUCAGUAUAG-------AUU------------------------------------UUAUGCAGUUUGAAGU--GUAACCUAUCAUUUUCAUAC-----------GGGAUGUAUGGAAAU-AUAGAGUAGCCUGUCUUGA-GUGAGAG-U-AUUGGGAU-UA-GCA------------------UCAAAGAGGUAU-CGUAUUUG-GCCAAAUGCGAUGUUCCUUC-----UUGCUAUGAAA-UUAC-GAUUGCAAAAAAGACUAAUAGUAGAACCAA--UAUUUUAAGGAAAACUUCUAGAAUGUUUAUUCAGACAUGAAUAGGAAAGUCUAGGGAUUAAGGUACGGAUUUGAGUGGCAAUCUGGUAUUCUC--AAAUUUC-UGUGAGAAUGUUUUGU-UAAAUGGAAACAGCUA-AACAGUAAUGUU-UAGUACA-AAACAGAGAAAUUCGACUAGACCU-AAACCGUAAAAUUUACUUAGACUUUUA-CCACUUAAUCCAUAUAUUUU
CP000568.1/1011746-1011099 AUGCUUGUAAGACAGGGUGGUGCAGUAUUCUAGU-CAGUACU-ACCGGUUCUGAAGACGGGCCUAAAAAUCCGUUAAAGGGCACA-UCGAUGAAGUUCCUUGUGCUGGCUUGCUAC-GCCCAGUGGUGGGCUGGUGCUGGGAGUU-------------------------------AAGGUUU-AGGGGCAACCCGCAAUGGCAUGCGGGCAUUGACCCCUUUACCGUGGAGACCCGACCUUGUGGGAGUAAA-GUACACUGCAAGCAUAAUAAUUUUGUCAGUGUGUAAACACUUCUACGAG-CCGGGA-GAGAACCUGUUUUGCGAUACC---------AUUUAUUGGUGUUGUG-GACAGAGUAGCCUGCCUUGA-GUGAGGU-U-GG-CGGAU-AA-UGGU--------------------CAGGUGUAU-AGGUAUUG-GCCGAUACAUAUACACUAUA-----GCAGUUUGAAA-CCAA-UCUUGCAAAAGAGGCUAGGAACCGGAUAG---ACUGUCGGGGAAAGCCCCUAGACUGUUCGU----UAA---GCGAGUUAUGCUGGGGAUUGAAGUGUGGACUA-AGUGGUAAUCAGGCCCCGCUC-CCUUUAA-AGGGGCGGCUGAAGGUUUAAAGGGAAACCGCUGAAAUGGCGACAUU-CAGUACC-UUCUGUGGAAAUCAUGCCUGACCU-AAGCCGCAAAAUUUACUCAGCAUAAUG-CCACCCUGUAUUAUAGCGUU
AE001437.1/2182120-2181516 AAUUAAUAUAUUCAAUGUGGUGCAGUAUUCUAGU-CAGGGAA-AUGCUUUUUGAAGGCGGGGCUAAAAAUCCGCUAAAGGGCACA-UCGAUGAAGUUCCUGGUGCUGGCCUUAGAAUGCCCAGUCUUGGGCUUGUGCUGGGAGUU-------------------------------AAAAAAGCUGGGGC-ACUCGCAAUGGCAUGCGACAAAUGACCCUACUUUUGUGGAGGCCAAUUAUUGUAUAUUGAGAGAGAU-------------------------------AUUCAAUAUACGAA-AUUGGG-GUAAACCUGCAAUGUGGUGUA----------------AAAGCUAUG-UGCAGUGUAGCCUGCCUUGA-GUGGUAU-G-GG-GAGAG-GA-GA------------------UAAACAAGUCAAA-AAUUUUAG-GCCUAAGUUUUUGUACUAUU-----GAACUCUGAAA-CCUA-UGUUGCAAAAGAGGCUAAGAAAGCAUCUA---ACUGUUGAGGAAAACUCCUAGACUGU--------UUU-------GGUAAAAUGAGGAUUGCAGUGCGGACUU-AGUGGCAAUUCAGUCCUGAAA-GUGGCAA-CACUUCAGCUCGGAUAUUAAAGGGAAACCGCUA-UAUGGCGACGUA-UAGUUAU-UCGUGGGGAAAGCCUACUGAACCU-AUGCCGUAAGAUUUACUUAUUUUGUUA-CCACAUUGAUGUUAUGUUUU
AARF01000383.1/4229-3835   GUAUAUCUGUUAUGGAGUGGUACAGUAUUCAA-U-CAGUCU--ACCGUUUCCGAGGGCGGACCUAAAAAUUUGUUAAAGGGCACA-UCGAUGAAGUUCCUGAUGUUGGCUUCCGGC-GCCCAUUUGGGGGUUGAUGCU--GAAU------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAACCA--------------------------------------------------UUCCCUUUA-------------------------------------------------------------------------------------------------------------------AAAGAGGCUAAGAAACGGUUAAAG-GCUGCCUAGGAAAGCCCCUAGACUGUUCAU---GAUU---AUGGGGCUUUCUGGGGAUUAUAGUGUGGACUG-AGUGGUCAUCUAGUCUGAUGG-CCGGCGGGCGGCAUCAAGACAGACAUGAAGG-AAACCGCCCAUUUGGCGACAAAAGGGUGUCCCGCUUGGGAAAACCUGCUGGACCU-AAGCCACAGCGUUUACUC-GCGAGCCA-ACACUCUGAUUCCAUGACUU
CP000141.1/1776967-1776358 AAAUAGCACGGGACGGCUGAUGCAGUAUCCUAGU-CGGACCC-GCACCUUUCGAAGACGGGCCUAAAAAUCCGUCGC-GGGCACA-UCGAUGAAGUUCCUGGUGCUGGCUUACGAC-GCCCAGUCGGGGGCUGGUGCUGGGAGUU-------------------------------AAGGUUG-GAGGGCGAGCCGCAAUGGCAUGCGGGCGUGGACCCUCCUUCCACGGAGACCCAAGUGCGUGGGGAGUAU------------------------------------UCACGAACUACGGC-UUGGGA-UUAAACCUGCACGUGGGGGC-------------------GUGCUACGUGCAGUGUAGCCUGCCUUGA-GUGAAAU-G-GG-GGGAU-AU-UAG-----------------GUUAAGGGGAGAA-GCCGAACGGGCCCUUAGGCUUCGAACCUU------CUAAUUGAAA-CCCA-UUUUGCAAAAGAGGCUAGAUUGGUGCGGGA--GCCGUCGGGGAAAUCCUCUAGGCUGUUUGGC---CCG--GCCAAGGUCUUACGGGGAUUGCAGUAUGGACUA-AGUGGUGAUCCAGUUCCGCAG-CGGGUAA-CCCUGCGGCAGAAGCUUUAAAGGGAAACCGCCUCCUCGGUGACGA-GAGGUAGC-UUCUGGGGAAAUCCUACUGGACCUUAAGCCAUAAAAUUAACCCGUAAGGCUA-UCAGCCGUCCUGGCUACCUG
CP000232.1/1558967-1558347 UACCAUGUUUUGGUGGGUGGCGCAGUAUUCUAGU-CAAGACC-ACCAUCUUUGAAGGCGGGCCUAAAAAUCCGUCAA-GGGCACA-CCGAUGAAGUUCCUGGUGCUGGCUGCCGAC-GCCCAGUCGGGGGUUGGUACUGGGAGUU-------------------------------AAGGAGG-GGGGGCGAUCUACAAUGGCAUGUAGGCGUGGACCCUCCCUCCGUGGAGACCCAAGUUCGUGGGAAA-GUUCCGCGGCAGGA------------------------GCAAAUACUAUGGC-UUGGGGUGGAAACCUGCAGUUGGUACUG---------------AGGGUGCUGGCUGCAGUGUAGCCUGCCUUGA-GCGGCAG-G-GG-UGGAU-GC-AGGCGA--------------UAAGCC-UAUCAC-GAUUUUC--GCCGAAAAUCGUGGAG----------UAAGCGGAAA-CCCC-UGUUGCAAAAGAGGCUAGAAGAUGGAUGGG--AUUGCCGGGGAAAACCCCUAGACUGUUUAC---CACG--UGUAAGGCUGGCCGGGGAUUAAAGUAUGUGCUA-AGUGGUAAUCCAGUCCUGCUA-CCGGUGA-CGGCGCAGGGCAGCCUUUAAAGGGAAACCGCCAUGACGGCGACG-CAUGGUAGG-CUACCGGGAAAACCUACUGGACCU-AAGCCAUAACAUUUAUCCGGCCAGUCG-CCACCCACCCGUAAUUUUCA
BA000004.3/2908975-2908348 GUCUUUUAGAAUAAGAGUGGUGCAGUAUUCUAGU-CAAUCCU-CCA-UUCUUGAAGGCGGGGCUAAAAAUCCGCCAAAGGGCACA-UCGAUGAAGCUCCUUGUGAUGGCUUGAGGC-GCCCAGCCUUGGGUCAUUGCUGGGAGAA-------------------------------AAGGUAG-UAGGGCGAUCCACAAAGGCAUGUGGGCGAUGACCCUCCUACUGUGGAGGCCUUUUUCUCUGCUGCUUAUGUAUGGAC----------------------------AUAGG-GCAAGAGC-AAAGGGUAUGAACCUGCGAAGGCAAGCU------------AGGGAGCUUGUCA--GCAGCGUAGCCUGCCUUGA-GUGGAGU-A-GAGGGGAU-UA-UGGG----------------UUUUGAAGCAAUC-CGCUGUCG-GCCAACAGCCA-UUGCCUCUCUAGUACCAUAUGAAA-UCUG-CUCUGCAAAAGAGGAUAAGAGAAUGGCAAGGGAUUGCCGAGGAAAACUCCUAGACUGUUCC----AUGG----GGACAUUUAAAGAGGAUUACAGUGUGGACUA-AGUGGUAAUCCAGUCUGGCGU-UUGGUGA-CAGCGCCAAGUUCAACAUAAAGGGAAACCGCCAGCGCGGCGACGCACUGGUGUU-GAAUUGGGAAAUCCUACUGGACCU-AAGCCACAGAGUUUACUCUUUAAAUGA-CCACUCUCAUACAUACGCAG
CP000448.1/671338-671925   AGAAA--ACUGGCAAAAGGUUGCAGUAUUCUAGU-CAACCCUAUACAAUUUCGAAGACGGGCCUAAAAAUCCGUAAA-GGGCACA-UCGAUGAAGCUUCUGGUGCCGGCUUGUGAC-GCCCAGUCAGGGGUCGGUGCUGGGAGUU-------------------------------AAGAGUGCAGGGGCAAUCCGCAACGGCAUGCGGGCAUGACCCCUGUAUUCGUGGAGGCUCUUCAC-GGUAU-------------------------------------------------GACCAGUGAAGGGA---AAACCUGCAUUCCGGUAU------------------AAGCUGGG-UGCAGUGUAGCCUGCCUUGA-GUGGUGG-C-GG-CGGAU-GA-ACU-----------------CUAGUGGGUAAUC-AUAUCCCG-GCCAGGAUAUAAUUGCCU---------GUUCUGAAA-CCGGGUGCUGCAAAAGAGGCUAGAAUUGAUGUGG---GUUGUUGAGGAAAACUCCUAGACUGUGUGUU--GCGG--AACAUAGUUUGUCGGGGAUUAAAGUGUGUACUU-AGUGGUAAUCCAGCCCCAUAA-GUGGCAA-CGUUAUGGAGCAGGCG-UAAAGGGAAACCGCCCUUAUGGCAACAUUCGGGUGAC-CUGCUGGGAAAACCUGCUGGACCU-AUGUCGCAGCGUUUACUCGACAGAC-A-ACCUUUUGCCAGA--ACUUU
AP008230.1/2178750-2178172 AAUCUUCUUUGAAC-UAGGGUGCGCUAUUCUAGUGCGUAAA--AUGACUGUCGAAGGCGGGCCUAAGAAUCCGCUAA-GGGCAUA-CCGAUGAAGUUCCUGGUGGUGGCUUUCGAC-GCCCAGUCGAGGGUUGCUGCUGGGAGUU-------------------------------AAGGAU--GAGGGGGAUCUGCAAUGGCAUGCGGGCGAU-ACCCUC-UUCCGUGGAGGCCUAAGUUCGUGGCUGCU----------------------------------------UUUGGUUACGGC-UUGGGGUAUGAACCUGCAUUAGGAAG--------------------GAACUUAGUGCAGUGUAGCCUGCCUUGAGGUGGAGA-A-GUUGGGAG-GG-C-------------------UGAAGGAACUUCU-GUUCAUUG-GCCGAUGAGCUUAAGUUU----------GCCUGAAAUUCUU-UUCUGCAAAAGAGGCUAGACCGUCACGGA----GCGUGAAGGAAAACUUCUAGAGCGA------------------AAACCAACGAGGAUUAAAGUGCGUUCUU-AGUGGCGAUCAAGUGCUGGAA-AUGGUGA-CAUUCUGG-GCUGAGGGAAAAGGGAAACCGCCUGUCAGGAAACUG-CAGGAGCU-CAGU-GGGAAAACCUACUUGACCU-AUGGCGCAAUAUUUAUUCGUUGGUGU--CCUAAGGUUCAAAGAGCAGC
CP000612.1/1147663-1148270 UAUAACUUAAAAAUAAGUGAUACAGUAUCCUAGU-CAGCAUU-ACCU-UUCUGAAGGCGGGCCUAAAAAUCCGUUAA-GGGCACA-UCGAUGAAGUUCCUGGUGCUGGCUUUUGAC-GCCCAGUUGGGGGCUGGUACUGGGAGUU-------------------------------AAGGGGA-UGGGGCGACCUACAACGGCAUGUGGGCAUCGACCCCGUCCCCGUGGAGACCCAAGUGCGUGGGGAGUCGGAAA--------------------------------CGGCAAACUAUG-GCUUGGCU-GUUAACCUGCA-UGUGGUAGG-----------------AAGCUGCG-UGCAGUGUAGCCUGACUUGAAGUGGUAC-U-GG-UGGAU-AU-C--U----------------CUGGUACAAUAUA-AAAUACGG-GCCCGUAUUUUAUAUUGUG---------GGUUGAAA-CCUU-UGCUGCAAAAGAGUCUAAGAA-AGAUUAAU--GCUGUUGAGGAAAACUCCUAGGCUGUUCGGC--ACUU--GCCGGGGCAGAUCAGGAAUUAAAGUGUGGACUA-AGUGGUAAUCUAGCCCUGAGA-GCGGUAA-CGCCUCAGAUAG-GGUUUAAUGGGAAACCGCCGGUU-UGGCGACAGCCGGUACC-GCUAUGGGAAAACCUGCUGGACCU-AAGCCACAACAUUUACCUGAUCUGCUACUCACUUAUCUAAAAUUUACA
AP006840.1/1989962-1989287 UGAUCGCGGAUUAUGGGUGGCGCAGUAUCCUAGU-CAGUACU-ACCUUUUCCGAAGGCGGGCCUAAAAAUCCGCAAA-GGGCACAUUCGAUGACGUCUCUGGUGCUGGCCGCCGAU-GCCCAAUCGGGGGUUGGUGCUGGGGAUUCAGCGAACCGGGCCGUUCUGGUCCGACGCUGCCGGAUU-GAGGGCGACCCGCAACGGCAUGCGGGCCCCGACCCUCCUUCCGUGGAGGCCUGCACGCGCGGCGGUCGCGCCAAUGUGAGC------------------------GAUGCGGCUGCGGU-GCAGUG--UAGACCUGCAUGCGGUACCG------AAACAUGGUGAGGUGCUGGGUGCAGCGUAGCCUGCCUUGA-GUGGGCG-U-GG-CGGAU-GC-GACCGUGGGCGUAAUGGCCCGGUAACCCCUGCC-GGACGCCG-GCCAGCUGAGGGCGGGGGCG---AUGGAAGCUGAAA-CCAC-GCCUGCAAAAGAGGCUAGGAAAAGGUGUG----UUGUCGAAGAAAAUUCCUAGGCUGCUC-----GAAA-----GAGGUCUGGCAAGGAUUGUAGUGUGGUCUA-AGUGGUAAUCCAGCCCUGCCG-GUGGCGA-CACGGCAGCUGGGCCA-UAAAGGGAAACCGCCGUGGCGGCGACGCUGCGGA-GG-CCCUGGGGAAAUCCUGCUGGACCU-AAGCCACAAGAUUUACUUGCCAGGCUG-CCACCCAUAAUUUUAUGUAU
AP009389.1/1231411-1232030 CUAGCUUUUAUGAUAAGUGACGCAGUAUCCUAGU-CAGAUAA-ACCU-UUUUGAAGGCGGGCCUAAAAAUCCGUCA-AGGGCACA-UCGAUGAAGUUCCUGGUGCUGGCUAUCGAC-GCCCAGUCGGGGGCUGGUACUGGGAGUU-------------------------------AAGGGGG-UGGGGCGACCUGCAAUGGCAUGUGGGCGUUGACCCCGCCCCCGUGGAGACCCAAGUGCGUGGGCAGCCAUGCCGGCUUUACCGGG--------------------UGGUCAACUAUG-GCUUGGGA-UUAAACCUGCA-UGUGGUUAA-----------------AAGCUGCG-UGCAGCGUAGCCUGCCUUGA-GUGGUAU-G-GG-UGGAU-AU-CG-GUAU-------------UACAUACGCGUCC-G-CCAUGG-GCCCGUGGACGGCCGUGUGG-------UGAUUGAAA-CCUA-UACUGCAAAAGAGGCUAGAAA-AGGUGUAA--UCUGUCGAGGAAAACUCCUAGGCUGUCUGG---GGUA---CCAGGGCGGGCCGGGGAUUAAAGUGUGGACUA-AGUGGUAAUCUAGCCCCGGU--GCGGCAA-CG-AUCGGAGACAGCUUUAAAGGGAAACCGCCGGUU-UGGCGACAGCCGGUAGC-UGUUUGGGAAAACCUGCUAGACCU-AAGCCACAAUAUUUACCCGGUCCGCUG-UCACUUAUCUAAUAAUACCG
CP000724.1/2545152-2545750 AGGUGUUUUAGUAGUAGUGGUGCAGUAUUCUAGU-CAAUUAA-CCUAGUUUGGAAGGCGGGGCUAAAAAUCCGUUGAAGGGCACA-UCGAUGAAGUUCCUGGUUUUGGCUGCCGAC-GCCCAGUUGGGGGUUAUUUCUGGGAGU--------------------------------AAAGAGAUGGGGGCGAUCCACAAUGGCAUGUGGGCGAUGACCCUCCCUCUGUGGAGACUACCUUA-GAAACAU---------------------------------------------UGUUUUAAAAGUGGGA--GAAACCUGCAGAAUAUGAAA-----------------GACAUAAACUGUAGUGUAGCCUGCCUUGA-GUGGCAU-A-GG-UGGAU-AA-GUAG------------------AUCAGUUUCUU-GAAAUCAGGGCCCGACGGAGAGGAUCAUC-----GCUAUUUGAAA-CCUA-UGCUGCAAAAGAGGCUAAGAGUUAGCUUA---AUUGCUGAGGAAAACUCCUAGACUGUUCU----UUUC--U-AGAAGUAUAUUAAGGAUUACAGUGCGGACUA-AGUGGUAAUCCAGUCCUAUCU-CUGGCGA-CAAGAUAGAUAUCAUUUUAAAGGGAAACCGCUACUUUGGCGACAG-GUAGUAGU-GAUUUGGGAAAUCCAACUGGACCU-AAGCCGUAAGAUUUACUUAGUAUACUA-CCACUACUAUCAGCUGAUAG
AE015927.1/1705719-1705109 UUUCUAAUAGGAAAAGGUGGCACAGUAUUCUAGU-CAGGUAA-GUAUUUCUUGAAGGCGGGGCUAAAAAUCCGCCAAAGGGCAUA-UCGAUGAAGCUUCUGGUGCUGGCUUAUGAC-GCCCAGUUAUGGGCUGGUGCUGGGAGU--------------------------------AAGAAGGAUGGGGCGGC-CGCAAUGGCAUGCG-CAACUGACCCUACCUUCAUGGAGACCAUUAAUUGUGUUUUAGGUUAGUC-------------------------------GCCUAUUGUACGAU-AAUGGA-UUAAACCUGUAUUGUGGUUAA-----------------AAGCUAUG-UGCAGUGUAGCCUGCCUUGA-GUGAUGU-A-GG-GAGAG-GU-AAU------------------AUCAA---CUUU-AACCUUUG-GCCAAAGGUUAAAGCUCUUG------GUUACUGAAA-CCUA-CAUUGCAAAAGAGGCUAGAGAUAUACCUA---ACUGUCGAGGAAAUCUCCUAGACUGUUCCA---UUUU-GUAUGAAGUGAAUUAAGGAUUAUAGUGCGGACUA-AGUGGUAAUCCAGUCCUACUUAUUGGUAA-CAAAGUAGAUAGGGUAUUAAAGGGAAACCGUCAAAAUGGCGACAUUUUGGUUAC-UCUAUGGGAAAGCCUACUGGACCU-AAGCCGUAAGGUUUACUUAAUUUACUG-CCACUUUUUUCUGGAAAAUU
CP000679.1/1996671-1997302 UACAAGAUGGGAUAGGGUGAUGCAGUAUCCUAGU-CAGAGUG-GCUGCUUUCGAAGGCGGGCCUAAAAAUCCGCCAAAGGGCACA-CCGAUGAAGUUCCUGGUUUUGGCUUCUGAC-GCCCAGUCAGGGGUUGAAGCUGGGAGU--------------------------------AAGGGAU-AAGGGAGUCCUGCAAUGGCAUGCAGGAUGGAACCCUUUUCCCGUGGAGGCUAACGCACAAAAAGAAAACU-----------------------------------AAAUUCUUUUUGUGCGUUAGU--AAAACCUACCACCAGGUACAUCUAUAAUUAAGUAGAUGUGCUUGG-GGUAGUGUAGCCUGCCUUGA-GCGAAAU-A-GA-CGGAU-GG-CCGAAU--------------UUAUGGCUCCUCU-AAAAAUAGGGCCCGUUUUUAGAGGAGUCU----UGAGGCCUGAAA-UCUA-UUUCGCAAAAGAGGCUAGAAAGCAUGCCC---UCUGUCGAGGAAAGCUCCUAGGCUGUGCCGA---CUU--UCGGCUUUACGAAGGGGAUUAAAGUGCGGACUU-AGUGGCGAUCUGGUUGUGUGU-UGGGCAA-CCGCACACCCAGACUUUUAAAGGGAAACCGCCU-CCUGGCGACGGG-AGGUAAG-UUUGGGGGAAAUCCUACCAGACCUUAAGCCGCAAAAUUUACCCUUCGUAAAA-UCACCCUAUCCCAUAAAUUU
CP000726.1/1940272-1939665 AAGUAUAUAAAUAAAGGUGGUGCAGUAUUCUAGU-CAGGUAA-GUAUAUCUUGAAGGCGGGGCUAAAAAUCCGCUAAAGGGCACA-UCGAUGAAGCUUCUGGUGCUGGCUUACGAC-GCCCAGUUGUGGGCUGGUGCUGGGAGA--------------------------------AAGAAGG-CUGGGGCAAUCACAAAGGCAUGUGGCAACUGACCCUACCUUCGUGGAGGCCAUUGAUUGUGUAUAGGGAGAGAU-------------------------------UCCCUAUGGACGAC-AAUGGA-UUAAACCUGCAAUGUGGCGAG-----------------CAGCUAUG-UGCAGUGUAGCCUGCCUUGA-GUGGUGG-G-GG-GAGAG-GUUAAG-----------------UUUAAA---UCUA-AAGGUUAG-GCCAAACCUUUAGGCUAUUG------CUUGCUGAAA-CCUC-CAUUGCAAAAGAGGCUAGAGAUAUACCCA---ACUGCCGAGGAAAUCUCCUAGACUGUUCU-----AUA----CGAGGUAUAUUGGGGAUUACAGUGCGGACUA-AGUGGCAAUCCAGUCCUAUUU-CUGGUGA-CAGGGUAGGUAAAGCAUUAAAGGGAAACCGUCAAAAUGGCGACAUUUUGAUUGU-UUUACGGGAAAUCCUACUGGACCU-AAGCCGCAAGGUUUACUCAAUACACUA-CCACCUUUUAAAAUUACAUA
ABCF01000017.1/6762-7377   CUACAACUUAAUAGGGAUGGUGCAGUAUUCUAGU-CAAUCU--ACCAGUUCUGAAGGUGGGCCUAAAAAUCCACUAAAGGGCACA-UCGAUGAAGUUCCUUGUUUCGGCUUGAGGC-GCCCAGCCUUGGGUCGAAGCUGGGAGU--------------------------------AAGGUAC-AAGGGCGAUCCACAAUGGCAUGUGGGCGUUGACCCUUGCACCGCGGAGGUUCCGUUCUGGGCCGGCAAGUU----------------------------------GCAUGAGCAACAGAACGGAGU-AUAGACCUGCGAUGCGGUGA------------------CAACCGCU-AGCAGCGUAGCCUGCCUUGA-GUGAAGU-GUGAGGGGAU-UA-UGG-----------------UUACAAGGUACAC-AUCAGUUG-GCC-AUUGAUAUGUGCUUUU--UCGCCCAUAUGAAA-UCCA-CUUUGCAAAAGAGGCUAAGAACAUGGUUAAAGGUUGCUGAGGAAAACUCCUAGACUGUUCCC---AUUU---GUGACAUAUAUUGAGGAUUAUAGUGCGGACUA-AGUGGUAAUCCAGUCUAACUG-CUGGUGA-CACAGUUAAGUCGGGUUUAAAGGGAAACCGCCGGUAUGGCGACAU-CCGGUACC-UGAUUGGGAAAACCUACUGGACCU-AAGCUGCAAUUUUUACUCAAUGUAUGA-CCAUCCCUUUACAUAUUUGA
CP000924.1/1154773-1155375 UGAAAAGAAAGGCAAAGUGGUGCAGUAUCCUAGU-CAGAGGC-GCUAAUCCCGAAGACGGGCCUAAAAAUCCGUCAA-GGGCACA-UCGAUGAAGUUCCUGGUGCUGGCUUUCAAC-GCCCAGUUGGGGGCUGGUGCUGGGAGUU-------------------------------AAGGAGG-GGGGGCGAUCCACAAUGGCAUGUGGGCGUUGACCCUUCCUCCGCGGAGACCUACUUGCGUGGCUUUU----------------------------------------ACAGGCUACG-GGGUAGGA--UGAACCUGUCUCGCGGCCAU----------------AAAGCUGCG-GACAGUGUAGCCUGCCUUGA-GUGAUUC-G-GG-UGGAUAUC-AGU------------------UGUAAGCCA-UA-AUUCAAAGAGCUCUUGAAUUACUGGCUAU-----UGCUGAUGAAA-CCCG-AAUUGCAAAAGAGGAUAGGGGUUAGUCCC---UCUGUUGAGGAAAACUCCUAGGCUGCGCCU---UGCC---GGGCGGCAUAUUGGGGAUUACGGUGCGGACUA-AGUGGUAGUCCAGUCUUACCU-UUGGCGA-CAAGGUAAAAGCGGGCUUAAAGGGGAACCGCUG-AACGGCGACGUU-CAGUGCA-CGCUUGGGAAAUCCUACUGGACCU-AAGCCGCAAAGUUUACCCAAUAUGCUA-CCACUUUGCCUUUAUACAUG
CP001348.1/2259506-2258874 UUGACAAAAAAACAGGGUGGCGCAGUAUUCUAGU-CAGUACU-GACGAUUCUGAAGACGGGCCUAAAAAUCCGUUUAAGGGCAUA-UCGAUGAAGUUCCUUGUGUCGGCUUGUUAC-GCCCAGUGGUGGGUUGAUGCUGGGAGUU-------------------------------AAGGCUU-AGGGGCGAUCCGCAAUGGCAUGCGGGCGUGGACCCCUUUUCCGUGGAGACCCUUACUUGUGGAAGAAAAGUCAAGCUUUUGCUUGCC------------------ACCUCGACUACGAA-AAGGGA-UUAAACCUGUUAUGCGGUG----------UCUUUAUGAUGGCUGUG-AACAGUGUAGCCUGCCUUGA-GUGAAAUCA-GG-UGGAU-AA-UGG-------------------AUCAGAUGCUUCAUGUAUUG-GCCGAUAUAUAAGCAUUAUU-----GCUAUUUGAAA-CCCU-UUUUGCAAAAGAGGCUAGGAAUCGUUUUG---ACUGCCGGGGAAAACCCCUAGACUGUUCUU---AAU----AAGUGGUUUAUUGGGGAUUAAAGUGUGGACUA-AGUGGUAAUCAGGCCCCGUAA-ACGGAGA-CG-UACGGUGAUGUGUUUAAAGGGAAACCACUGGUUUGGCGACAUUCCAGCACA-UAUCAGGGAAAUCCUGCCUGACCU-AAGCCGCAAAAUUUACUCAAUAAACUG-CCACCUGUUUUUCUAUUAAA
CP000923.1/1561222-1561822 UGAAAAGAAAGGCAAAGUGGUGCAGUAUCCUAGU-CAGAGGU-GCUAAUUCCGAAGACGGGCCUAAAAAUCCGUCAA-GGGCACA-UCGAUGAAGUUCCUGGUGCUGGCUUUCAAC-GCCCAGUUGGGGGCUGGUGCUGGGAGUU-------------------------------AAGGAGG-GGGGGCGAUCCACAAUGGCAUGUGGGCGUUGACCCUUCCUCCGCGGAGACCUACCUGCGUGGCUUUU------------------------------------------AAGCUACG-GGGUAGGA--UGAACCUGUCUCGCGGCCAU----------------AAAGCUGCG-GACAGUGUAGCCUGCCUUGA-GUGAUUC-G-GG-UGGAUAUC-AGU------------------UGUAAGCCG-UA-AUUCAAAGAGCUCUUGAAUUACUGGCUAU-----UGCUGAUGAAA-CCCG-AAUUGCAAAAGAGGAUAGGGGUUAGUCCC---UCUGUUGAGGAAAACUCCUAGGCUGCGCCU---UGCC---GGGCGGCAUAUUGGGGAUUACAGUGCGGACUA-AGUGGUAAUCCAGUCUUACCU-UUGGUGA-CAAGGUAAAAGCGGGCUUAAAGGGGAACCGCUG-AACGGCGACGUU-CAGUGCC-CGCUUGGGAAAUCCUACUGGACCU-AAGCCGCAAAGUUUACUCAAUAUGCUA-CCACUUUGCCUAUAUAUUAC
#=GC SS_cons               ::::::::::::::::::::::::::::::::::.:::::::.::::::::::::<<<<<<________>>>>>>,,,,,,,,,,.,,,,,,,,,<<<<<-<<<<<<<<<<<<<<<._____>>>>>>>>>>>>>>>->>>>>,,...............................,,<<<<<.-<<<<----<<<<<______>>>>>------->>>>->>>>>,,,,,,,<<<<<-<<<<<<<<<<<<_______...............................__>>>>>>>>>>>>.>>>>>,.,,,,,,<<<<<-<<<<<<<<_................_>>>>>>>>.>>>>>,,,,,,,,<<<<<--.<<<<<<<.<.<<.-----.<<.<<<.................----<<<<<<<<<.<<<<<<__.____>>>>>>>>>>>>>>>-.....->>>>>-----.>>>>.>>>>>>---->>>>>,,,,,,,,,,,,,,...,,,,,,<<<_____>>>,,,,,,,,,<<<<...____...>>>>(((((((((((--------(((((----.--------((((((,<<<<<-.<<<____.>>>>>>>><<<<<<<<-------------<<<<<<<<<____>>>>>>>>>>>>.>>>>>,,,,,,,,,,))))))---.---)))))-------))))))))))):.::::::::::::::::::::
#=GC RF                    uaauauuuuagaaagaGUGGUGCAGUAUuCUAGU.CAguauu.accuuUUuuGAAggCGGgcCUAAAAAuCCGccAAAGGGCACA.UCGAUGAAGuucCugGugccggCucccgac.GCCCAgucggggGccggugCUgGgagUU...............................AAGGggg.agGGGcgAuccgCAAuGGCAUGcgggcauuGACCCcucccCCGUGGAGacccccucccGuggccgccaaguaau...............................aaggcggccaCggg.ggggga.uuaAACCUGccucgcggccca................agggccgcg.ggCAGuGUAGCCUGCCUuGA.Guggcgu.g.Gg.uGGAU.gc.ccg.................uuaacgggccccc.acccgcuG.GCCagcgggugggggcccgu.....gcgggcUGAAA.cCca.cgcugCAAAAgAGGCUAggAauagguuua...acUGUcGaGGAAAaCuCCUAGaCUGUucgc...aaua...gcgaggccugccGgGGAUUAaAGUGcGgACUa.AGUGGUAAUCcaGccccgccu.ccGGugA.CggggcggcgggggcuuUAAAGGGAAACCgCcggcgcGGcgACgcgccgGuagc.ccccgGGGAAAuCCUgCugGACCU.AAGcCgCAAaaUUUACcCggcaggcca.cCAcuuuuuuuuauaauuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01072
#=GF ID   TMV_UPD-PK3
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   34.00
#=GF TC   34.10
#=GF NC   33.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.00 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00055;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   3934645
#=GF RT   Five pseudoknots are present at the 204 nucleotides long 3' noncoding
#=GF RT   region of tobacco mosaic virus RNA.
#=GF RA   van Belkum A, Abrahams JP, Pleij CW, Bosch L
#=GF RL   Nucleic Acids Res. 1985;13:7673-7686.
#=GF RN   [2]
#=GF RM   8355685
#=GF RT   A phylogenetically conserved sequence within viral 3' untranslated RNA
#=GF RT   pseudoknots regulates translation.
#=GF RA   Leathers V, Tanguay R, Kobayashi M, Gallie DR
#=GF RL   Mol Cell Biol. 1993;13:5331-5347.
#=GF RN   [3]
#=GF RM   8608444
#=GF RT   A central pseudoknotted three-way junction imposes tRNA-like mimicry and
#=GF RT   the orientation of three 5' upstream pseudoknots in the 3' terminus of
#=GF RT   tobacco mosaic virus RNA.
#=GF RA   Felden B, Florentz C, Giege R, Westhof E
#=GF RL   RNA. 1996;2:201-212.
#=GF WK   UPSK_RNA
#=GF SQ   25


U30944.1/6092-6122    AGUG--UUUUUCUCUCCACUUAAAUCGAAGAGA
X72587.1/563-593      AGUG--UUUUUCCCUCCACUUAAAUCGAAGGGU
AJ223596.1/5826-5856  AGUG--UUUGCCGUUCCACUUAAAUCGAAACGG
X82130.1/6266-6296    AGUG--GCUAUCCCUCCACUUAAAUCGAAGGGU
AY751781.1/621-651    AGUG--UUUCGGCUUCCACUUAAAUCGAAAGCC
M81486.1/3404-3434    AGUG--UUUUCAUGUCCACUUAAAUCGAACAUG
AJ295948.1/6376-6406  AGAG--UUUUUCCCUCCUCUUAAAUCGAAGGGC
AM040955.1/6093-6123  AGUG--UUUUAUCCUCCACUUAAAUCGAAGGAU
AB127937.1/964-994    AGUG--CUUUCCCGUUCACUUAAAUCGAACGGU
AB089381.1/6287-6317  AGUG--UUUAUCCCUCCACUUAAAUCGAAGGGC
AJ132578.1/6804-6834  AGUG--CUUUCCAGUUCACUUAAAUAGAACUGG
Z97873.1/5659-5689    AGUG--UUUUGAAGUCCACUUAAAUAGAACUUC
AF165884.2/2227-2257  AGUG--UUUUUCUGUCCACUUAAAUCGAACAGA
AF035633.1/1264-1294  AGUG--UUUUCGGCUCCACUUAAAUCGAAGCCC
AJ223597.1/2737-2767  AGUG--UUUUUCGUUCCACUUAAAUCGAAACGA
AB017503.1/6087-6117  AGUG--UUUUCCUCUCCACUUAAAUCGAAGAGG
S68164.1/1326-1356    AGUG--UUUUUCUCUCCACUUGAAUCGAAGAGA
AF155507.2/6248-6278  AGUG--UUUUUCCCUCCACUUAAAUCGAAGGGU
AB261167.1/6350-6380  AGUG--UUUUUCCGUCCACUUAAAUCGAACGGC
AF321057.1/6425-6455  AGAG--UUUUUCCCUCCUCUUAAAUCGAAGGGA
AF103781.1/547-576    AGUG--UUUUUCUCUCCACUUAAAUCGAAGAG-
AAMG01000647.1/78-108 AGUG--UUUUUCCCUCCACUUAAAUCGAAGGAU
AF103782.1/729-757    AGUG---UUUUCCCUCCACUUAAAUCGAAGGG-
AM398436.1/6246-6275  AGUG---UUUACUCUCCACUUAAAUCGAAGAGU
D13438.1/6370-6402    AGUGUUUUUUUCCCUCCACUUAAAUCGAAGGGU
#=GC SS_cons          <<<<..____AAAAAA>>>>::::::a:aaaaa
#=GC RF               AGUG..UUUUUCcCUCCACUUAAAUCGAAGgGu
//
# STOCKHOLM 1.0

#=GF AC   RF01073
#=GF ID   GP_knot1
#=GF DE   Gag/pol translational readthrough site
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   48.00
#=GF TC   48.00
#=GF NC   47.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00047;
#=GF DR   PKBASE; PKB00078;
#=GF DR   PKBASE; PKB00079;
#=GF DR   PKBASE; PKB00088;
#=GF DR   PKBASE; PKB00098;
#=GF DR   PKBASE; PKB00099;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0039705; viral translational readthrough;
#=GF RN   [1]
#=GF RM   2402881
#=GF RT   RNA pseudoknots: translational frameshifting and readthrough on viral
#=GF RT   RNAs.
#=GF RA   ten Dam EB, Pleij CW, Bosch L
#=GF RL   Virus Genes. 1990;4:121-136.
#=GF RN   [2]
#=GF RM   8076609
#=GF RT   Pseudoknot-dependent read-through of retroviral gag termination codons:
#=GF RT   importance of sequences in the spacer and loop 2.
#=GF RA   Wills NM, Gesteland RF, Atkins JF
#=GF RL   EMBO J. 1994;13:4137-4144.
#=GF WK   Gag/pol_translational_readthrough_site
#=GF SQ   7


M18247.1/2424-2485   UAGGAGAGUCAGGGC-CAGGACCCCCCCCCUGAGCCCAGGAUAACCUUAAAAAUAGGGGGGCA
M77193.1/3206-3267   UAGGGAGGUCAGGGC-CAGGAGCCCCCCCCUGAGCCCAGGAUAACUCUUGAAGUUGGGGGGCA
AF411814.1/2228-2289 UAGGGGGGUCGGGGU-CAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCAAAGUAGGGAGGCA
J02034.1/2580-2641   UAGGGGUGUCAGGGCUCUGGAGCCCCCCCC-GAGCCCCGGCUAACUCUAUCUGUAGGGGGGCA
M26927.1/2191-2251   UAGGGGAGUCAGGGU-UCGGACCCCCUCCCCGAACCUAGGGUAACACUGACUGUGGAGGGGA-
AY099324.1/2582-2643 UAGGGGAGACGGGGU-UCGGACCCCCUCCCCGAGCCCAGGGUAACUUUGAAGGUGGAGGGGCA
AF053745.1/2288-2348 UAGGGAAGUCGGGGC-UCAGACCCCCUCCCUGAGCCUAGGGUAACUUUGUCUGUGGAGGGGA-
#=GC SS_cons         :::::::::::<<<<.<<<<_AAAAAAA>>>>->>>>::::::::::::::::::aaaaaaa:
#=GC RF              UAGGGGaGUCaGGGc.caGGAcCCCCcCCCugAgCCCAGGaUAACucUaaauGUaGgGGGGcA
//
# STOCKHOLM 1.0

#=GF AC   RF01074
#=GF ID   RF_site1
#=GF DE   Putative RNA-dependent RNA polymerase ribosomal frameshift site
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   40.00
#=GF TC   41.60
#=GF NC   38.80
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00240;
#=GF DR   PKBASE; PKB00044;
#=GF DR   PKBASE; PKB00046;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   12038685
#=GF RT   Biological properties and molecular characterization of beet chlorosis
#=GF RT   virus (BChV).
#=GF RA   Hauser S, Stevens M, Beuve M, Lemaire O
#=GF RL   Arch Virol. 2002;147:745-762.
#=GF RN   [2]
#=GF RM   8030201
#=GF RT   Nucleotide sequence of cucurbit aphid-borne yellows luteovirus.
#=GF RA   Guilley H, Wipf-Scheibel C, Richards K, Lecoq H, Jonard G
#=GF RL   Virology. 1994;202:1012-1017.
#=GF RN   [3]
#=GF RM   1840612
#=GF RT   Nucleotide sequence analysis and genomic organization of the NY-RPV
#=GF RT   isolate of barley yellow dwarf virus.
#=GF RA   Vincent JR, Lister RM, Larkins BA
#=GF RL   J Gen Virol. 1991;72:2347-2355.
#=GF WK   Ribosomal_frameshift
#=GF SQ   4


AF352024.1/1581-1620 GGGAAAUGGACUGAGCGGCGCCGACCGCCA-AACAACCGGC
EF521839.1/1666-1705 GGGAAACGGGA-AGGCGGCGGCGUCCGCCGUAACAAACGCA
X76931.1/1482-1521   GGGAAACGGGC-AGGCGGCGGCGACCGCCGAAACAACCGCA
AF473561.1/1475-1514 GGGAAACGGGA-GAGCGGCAGCGCCCGCCGAAACAACCGCA
#=GC SS_cons         :::::::::::.:<<<<<__AAA_>>>>>::::::::aaa:
#=GC RF              GGGAAACGGGa.gGGCGGCGGCGaCCGCCGaAACAACCGCA
//
# STOCKHOLM 1.0

#=GF AC   RF01075
#=GF ID   TLS-PK1
#=GF DE   Pseudoknot of tRNA-like structure
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   80.00
#=GF TC   109.20
#=GF NC   37.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00138;
#=GF DR   PKBASE; PKB00164;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045069; regulation of viral genome replication;
#=GF RN   [1]
#=GF RM   6328450
#=GF RT   Nucleotide sequence of the 3'-terminal tRNA-like structure in barley
#=GF RT   stripe mosaic virus genome.
#=GF RA   Kozlov YuV, Rupasov VV, Adyshev DM, Belgelarskaya SN, Agranovsky AA,
#=GF RA   Mankin AS, Morozov SYu, Dolja VV, Atabekov JG
#=GF RL   Nucleic Acids Res. 1984;12:4001-4009.
#=GF RN   [2]
#=GF RM   1935928
#=GF RT   tRNA-like structures. Structure, function and evolutionary significance.
#=GF RA   Mans RM, Pleij CW, Bosch L
#=GF RL   Eur J Biochem. 1991;201:303-324.
#=GF RN   [3]
#=GF RM   8623558
#=GF RT   Comparisons of the genomic cis-elements and coding regions in RNA beta
#=GF RT   components of the hordeiviruses barley stripe mosaic virus, lychnis
#=GF RT   ringspot virus, and poa semilatent virus.
#=GF RA   Solovyev AG, Savenkov EI, Agranovsky AA, Morozov SY
#=GF RL   Virology. 1996;219:9-18.
#=GF WK   Transfer_RNA-like_structures
#=GF SQ   2


M81486.1/3496-3591   AUUGGUAUGUAAGCUACUUCUUCCAGUAGCUGCGUCAUAACAUCAAGGUUAUGCAUACUGAGCCGAAGCUCAGCUUCGGUCCUCCAA-GGAAGACCA
AY787207.1/2721-2816 AUUGGUAUGUAAGCUACAACUUCCGGUAGCUGCGUCACACU-UUAAGAGUGUGCAUACUGAGCCGAAGCUCAGCUUCGGUCCCCCAAGGGAAGACCA
#=GC SS_cons         :((((((((,,<<<<<<__AAAAA_>>>>>>,,,,<<<<<<______>>>>>>))))))))-<<<<<<_____>>>>>>:::::::::aaaaa::::
#=GC RF              AuugGuauGUAaGCuaCaaCUUCCaGuaGCuGCGUCacaccAUuAAGgguguGCauaCugaGCCGaaGCUCAGCuuCGGUCCuCCAAgGGAAGACCA
//
# STOCKHOLM 1.0

#=GF AC   RF01076
#=GF ID   RF_site2
#=GF DE   Polymerase ribosomal frameshift site
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   70.00
#=GF TC   84.00
#=GF NC   32.60
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00218;
#=GF DR   PKBASE; PKB00233;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   10073689
#=GF RT   North American and European porcine reproductive and respiratory syndrome
#=GF RT   viruses differ in non-structural protein coding regions.
#=GF RA   Allende R, Lewis TL, Lu Z, Rock DL, Kutish GF, Ali A, Doster AR, Osorio FA
#=GF RL   J Gen Virol. 1999;80:307-315.
#=GF RN   [2]
#=GF RM   8517032
#=GF RT   Lelystad virus, the causative agent of porcine epidemic abortion and
#=GF RT   respiratory syndrome (PEARS), is related to LDV and EAV.
#=GF RA   Meulenberg JJ, Hulst MM, de Meijer EJ, Moonen PL, den Besten A, de Kluyver
#=GF RA   EP, Wensvoort G, Moormann RJ
#=GF RL   Virology. 1993;192:62-72.
#=GF WK   Ribosomal_frameshift
#=GF SQ   2


AY588319.1/7400-7471 UUUAAACUGUUAGCCGCCAGCGGCUUGACCCGCUGUGGCCGCGGCGGCCUAGUUGUGACUGAAACGGCGGUA
AY612613.1/7689-7760 UUUAAACUGCUAGCCGCCAGCGACUUGACCCGCUGUGGUCGCGGCGGCUUGGUUGUUACUGAAACAGCGGUA
#=GC SS_cons         ::::::::::::<<<<<<-<<<<<<____AAAAAAA>>>>>>>>>>>>:::::::::::::::aaaaaaa::
#=GC RF              UUUAAACUGuUAGCCGCCAGCGgCuUGACCCGCUGUgGcCGCGGCGGCuUaGUUGUuACUGAAACaGCGGUA
//
# STOCKHOLM 1.0

#=GF AC   RF01077
#=GF ID   TLS-PK2
#=GF DE   Pseudoknot of tRNA-like structure
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   42.00
#=GF TC   42.60
#=GF NC   38.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00139;
#=GF DR   PKBASE; PKB00057;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045069; regulation of viral genome replication;
#=GF RN   [1]
#=GF RM   16453568
#=GF RT   The three-dimensional folding of the tRNA-like structure of tobacco mosaic
#=GF RT   virus RNA. A new building principle applied twice.
#=GF RA   Rietveld K, Linschooten K, Pleij CW, Bosch L
#=GF RL   EMBO J. 1984;3:2613-2619.
#=GF RN   [2]
#=GF RM   1935928
#=GF RT   tRNA-like structures. Structure, function and evolutionary significance.
#=GF RA   Mans RM, Pleij CW, Bosch L
#=GF RL   Eur J Biochem. 1991;201:303-324.
#=GF RN   [3]
#=GF RM   8608444
#=GF RT   A central pseudoknotted three-way junction imposes tRNA-like mimicry and
#=GF RT   the orientation of three 5' upstream pseudoknots in the 3' terminus of
#=GF RT   tobacco mosaic virus RNA.
#=GF RA   Felden B, Florentz C, Giege R, Westhof E
#=GF RL   RNA. 1996;2:201-212.
#=GF WK   Transfer_RNA-like_structures
#=GF SQ   4


AB354955.1/1390-1455 GUGUCUUGGAUCGCGCGGGUCAAAUGUAUAUGGUUCAUAUACAUCCGCAGGCACGUAAUAAA-GCGA
AB083196.1/6281-6347 GUGUCUUGGAGCGCGCGGAGUAAACAUAUAUGGUUCAUAUAUGUCCGUAGGCACGUAAAAAAAGCGA
EF375551.1/6292-6357 GUGUCUUGGUUCGCGCGGGUCAAGUGUAUAUGGUGCAUAUACAUCCGUAGGCACGUAAUAAA-GCGA
DQ355023.1/6272-6337 GUGUCUUGGAACGCGCGGGUCAAAUAUAAGUGGUUCACUUAUAUCCGUAGGCACGAAAAAUU-GCGU
#=GC SS_cons         <<<<<<----AAAA<<<<-----<<<<<<<<_____>>>>>>>>>>>>>>>>>>::::::::.aaaa
#=GC RF              GUGuCUUGGAuCGCgCGGGucAAaugUAuaUGGUuCAuaUAcauCCGcAGgCACGuAAaAAA.GCGA
//
# STOCKHOLM 1.0

#=GF AC   RF01078
#=GF ID   PK-PYVV
#=GF DE   3'-terminal pseudoknot in PYVV
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   65.00
#=GF TC   74.60
#=GF NC   35.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00259;
#=GF DR   PKBASE; PKB00260;
#=GF DR   PKBASE; PKB00261;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   15218192
#=GF RT   Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite
#=GF RT   genome and conserved 3'-terminal structures among members of the genus
#=GF RT   Crinivirus.
#=GF RA   Livieratos IC, Eliasco E, Muller G, Olsthoorn RC, Salazar LF, Pleij CW,
#=GF RA   Coutts RH
#=GF RL   J Gen Virol. 2004;85:2065-2075.
#=GF WK   Potato_yellow_vein_virus
#=GF SQ   3


AJ508757.2/3834-3892 CGGUAGAAAAGAUGGUUUGAAAACCACGCCUUCUACCAAUAUAGUAAAUAAAUAGGCGG
AJ704619.1/2027-2082 CGGUAGAAAAGAUGGUGUUUAAACCACGCCUUCUACCAAUAUAGUAAAUAAAUAGG---
AJ557129.1/5283-5339 A-GUAGAAAAGUUGGUGCUUAGACCACGCCCUCUACCGUAAUAAUAGAUAAAUAGGCG-
#=GC SS_cons         :<<<<<<-----<<<<______>>>>AAAAA>>>>>>::::::::::::::::aaaaa.
#=GC RF              cGGUAGAAAAGaUGGUgUuuAAACCACGCCUUCUACCAauAUAgUAAAUAAAUAGGCG.
//
# STOCKHOLM 1.0

#=GF AC   RF01079
#=GF ID   RF_site3
#=GF DE   Putative RNA-dependent RNA polymerase ribosomal frameshift site
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   50.00
#=GF TC   60.10
#=GF NC   33.40
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00042;
#=GF DR   PKBASE; PKB00043;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   2466700
#=GF RT   Nucleotide sequence and organization of potato leafroll virus genomic RNA.
#=GF RA   van der Wilk F, Huisman MJ, Cornelissen BJ, Huttinga H, Goldbach R
#=GF RL   FEBS Lett. 1989;245:51-56.
#=GF RN   [2]
#=GF RM   2402881
#=GF RT   RNA pseudoknots: translational frameshifting and readthrough on viral
#=GF RT   RNAs.
#=GF RA   ten Dam EB, Pleij CW, Bosch L
#=GF RL   Virus Genes. 1990;4:121-136.
#=GF RN   [3]
#=GF RM   2732710
#=GF RT   Nucleotide sequence of potato leafroll luteovirus RNA.
#=GF RA   Mayo MA, Robinson DJ, Jolly CA, Hyman L
#=GF RL   J Gen Virol. 1989;70:1037-1051.
#=GF RN   [4]
#=GF RM   8502558
#=GF RT   Structural requirements for efficient translational frameshifting in the
#=GF RT   synthesis of the putative viral RNA-dependent RNA polymerase of potato
#=GF RT   leafroll virus.
#=GF RA   Kujawa AB, Drugeon G, Hulanicka D, Haenni AL
#=GF RL   Nucleic Acids Res. 1993;21:2165-2171.
#=GF WK   Ribosomal_frameshift
#=GF SQ   2


D13954.1/1664-1702 UUUAAAUGGGCAAGCGGCACCGUCCGCCAAAACAAACGG
Y07496.1/1663-1701 UUUAAAUGGGCGAGCGGCACCGCCCGCCAAAACAAACGG
#=GC SS_cons       :::::::::::::<<<<__AAAA>>>>::::::::aaaa
#=GC RF            UUUAAAUGGGCaAGCGGCACCGuCCGCCAAAACAAACGG
//
# STOCKHOLM 1.0

#=GF AC   RF01080
#=GF ID   UPD-PKib
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   39.00
#=GF TC   39.90
#=GF NC   34.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00202;
#=GF DR   PKBASE; PKB00118;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF RN   [1]
#=GF RM   10603167
#=GF RT   Molecular characterization of a new furovirus mainly infecting rye.
#=GF RA   Koenig R, Pleij CW, Huth W
#=GF RL   Arch Virol. 1999;144:2125-2140.
#=GF RN   [2]
#=GF RM   9714254
#=GF RT   Genome properties of beet virus Q, a new furo-like virus from sugarbeet,
#=GF RT   determined from unpurified virus.
#=GF RA   Koenig R, Pleij CW, Beier C, Commandeur U
#=GF RL   J Gen Virol. 1998;79:2027-2036.
#=GF WK   UPSK_RNA
#=GF SQ   4


AJ271839.1/3358-3389 GGUGCUUGCUAUUUCACCUAAAUCGAAAUAGC
AB033689.1/7019-7050 GGUGCUUGUUAGUUCACCUAAAUCGAACUAAC
U64512.1/3276-3307   GGUGCUUUUAUGUUCACCGAAAUCGAACAUAC
AJ749657.1/3098-3129 GGUGCUUGUUAUUUCACCUAAAUCGAAAUAAC
#=GC SS_cons         AAAA:::<<<<<<<aaaa_______>>>>>>>
#=GC RF              GGUGCUUGUuagUUCACCUAAAUCGAAcuaAC
//
# STOCKHOLM 1.0

#=GF AC   RF01081
#=GF ID   SBWMV1_UPD-PKe
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   38.00
#=GF TC   39.00
#=GF NC   32.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.31 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00197;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF RN   [1]
#=GF RM   10603167
#=GF RT   Molecular characterization of a new furovirus mainly infecting rye.
#=GF RA   Koenig R, Pleij CW, Huth W
#=GF RL   Arch Virol. 1999;144:2125-2140.
#=GF WK   UPSK_RNA
#=GF SQ   3


AJ132576.1/6778-6803 AGCCUAUUAGUACGGGUUGAGUACAA
AF361641.1/1314-1339 AACCUAUUUGCUCGGGUUGAGUGCAA
AF146279.1/6754-6779 AGCCUAUUUGUACGGGUCGAGUACAA
#=GC SS_cons         <<<<<__AAAA__>>>>>::::aaaa
#=GC RF              agCCUAUUUGUaCGGGuuGAGUACAA
//
# STOCKHOLM 1.0

#=GF AC   RF01082
#=GF ID   SBWMV1_UPD-PKh
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   32.00
#=GF TC   32.30
#=GF NC   31.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.33 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00200;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF RN   [1]
#=GF RM   10603167
#=GF RT   Molecular characterization of a new furovirus mainly infecting rye.
#=GF RA   Koenig R, Pleij CW, Huth W
#=GF RL   Arch Virol. 1999;144:2125-2140.
#=GF WK   UPSK_RNA
#=GF SQ   2


AJ132577.1/3357-3381 GUCUAACAUGUCGGGCAGAGACACG
AF361641.1/1235-1259 GUCUAAUUUGUCGGGCUGAGACAAA
#=GC SS_cons         AAAA::<<<<<<aaaa___>>>>>>
#=GC RF              GUCUAAcuUGUCGGGCuGAGACAag
//
# STOCKHOLM 1.0

#=GF AC   RF01083
#=GF ID   UPD-PK2
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   32.00
#=GF TC   32.00
#=GF NC   31.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00059;
#=GF DR   PKBASE; PKB00063;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF RN   [1]
#=GF RM   8666266
#=GF RT   The complete sequence of a Singapore isolate of odontoglossum ringspot
#=GF RT   virus and comparison with other tobamoviruses.
#=GF RA   Chng CG, Wong SM, Mahtani PH, Loh CS, Goh CJ, Kao MC, Chung MC, Watanabe Y
#=GF RL   Gene. 1996;171:155-161.
#=GF RN   [2]
#=GF RM   7931178
#=GF RT   Similarities between the secondary structure of satellite tobacco mosaic
#=GF RT   virus and tobamovirus RNAs.
#=GF RA   Gultyaev AP, van Batenburg E, Pleij CW
#=GF RL   J Gen Virol. 1994;75:2851-2856.
#=GF WK   UPSK_RNA
#=GF SQ   4


AM055643.1/1046-1066 CGUGGUGCAUACGAUAAUGCA
X82130.1/6244-6264   GCUGGUGCAUACGAUAAUGCA
U34586.1/6451-6471   CGUGGUGCAUACGAUAAUGCA
X55295.1/733-753     CGUGGUGCAUACGAUAAUGCA
#=GC SS_cons         AAA::<<<<<aaa___>>>>>
#=GC RF              CGUGGUGCAUACGAUAAUGCA
//
# STOCKHOLM 1.0

#=GF AC   RF01084
#=GF ID   TLS-PK3
#=GF DE   Pseudoknot of tRNA-like structure
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   45.00
#=GF TC   53.60
#=GF NC   41.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00134;
#=GF DR   PKBASE; PKB00136;
#=GF DR   PKBASE; PKB00137;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045069; regulation of viral genome replication;
#=GF RN   [1]
#=GF RM   7214524
#=GF RT   Near identity of 3- RNA secondary structure in bromoviruses and cucumber
#=GF RT   mosaic virus.
#=GF RA   Ahlquist P, Dasgupta R, Kaesberg P
#=GF RL   Cell. 1981;23:183-189.
#=GF RN   [2]
#=GF RM   6628363
#=GF RT   Three-dimensional models of the tRNA-like 3' termini of some plant viral
#=GF RT   RNAs.
#=GF RA   Rietveld K, Pleij CW, Bosch L
#=GF RL   EMBO J. 1983;2:1079-1085.
#=GF RN   [3]
#=GF RM   1935928
#=GF RT   tRNA-like structures. Structure, function and evolutionary significance.
#=GF RA   Mans RM, Pleij CW, Bosch L
#=GF RL   Eur J Biochem. 1991;201:303-324.
#=GF RN   [4]
#=GF RM   8289279
#=GF RT   Solution structure of the 3'-end of brome mosaic virus genomic RNAs.
#=GF RT   Conformational mimicry with canonical tRNAs.
#=GF RA   Felden B, Florentz C, Giege R, Westhof E
#=GF RL   J Mol Biol. 1994;235:508-531.
#=GF WK   Transfer_RNA-like_structures
#=GF SQ   8


AF325738.1/2039-2167 GCUGCCCUUGGGUUU-UACUCCUUGAACCCUUCGGAAGAACUC----------UUUG---GAGUUCGUACCA-GUACCUCACAUAGUGAGGUAAUAAGACUGGUGGGCAG--CGCCUAGUCGAAAGACUAGGUG--AUC-UCUAAGGAG
AF127976.1/2067-2194 GGUACCCUUGAAAUC-ACCUCCUAGAUUUCUUCGGAAGGGCUUCG--------UGAG---AAGCUCGUGCAC-GGUAAUACAC-UGAUAUUACC--AAGAGUGCGGGUAUC-GCCUGUGG--UUUUCCACAGGUUCUCC-AU-AAGGAG
AB183261.1/1984-2112 GGUGCCUUUGAGAGU-UACUCUUUGCUCUCUUCGGAAGAACCC----------UUAG---GGGUUCGUGCAU-GGGCUUGCA--UAGCAAGUCU--UAGAAUGCGGGUACCGUACAGUGUUGAAAAACACUGUAAAUCU-CUAAAAGAG
AB194808.1/1958-2087 GUUGCCUUUGAGAGU-UACUCCUUGCUCUCUUCAGAAGUUCUC----------UACC---GAGAACGUGCAG-UGGCUGUCA--UAGACAGCCU-UCAGACUGCGGGCAAC-GUCAGUUCCAUAAGGAACUGAUAAUCUCCAAAAGGAG
D10044.1/3265-3405   GGUGCCUUUGAACCCUUUAUCCCGGGGUUCUUCGGAAGGUGAGACUUGUCCAUGUAGAGUCUCGCCGUGCAC-GGUAUCACAC-UGAUGAUACCUUCAGAGUGCAGGCAUC-GCCUACGG--UUUUCCGUAGGU--UCC-CCCUAGGGG
AJ276479.1/3234-3353 GGCGCCUUUGAAACC-AUCUCCUAGGUUUCUUCGGAAGGAC------------UUCG-----GUCCGUGUACUUCUAGCACA--AGGUGCUAGU-UUAGAGUACGGGCAUC-CCCCCGUU-----UUGCGGGGGUCUCU-AA-AAGGAG
AM183114.1/3233-3357 GGUGCCUUUGAAACC-AUCUCCUAGGUUUCUUCGGAAGGAC------------UUCG-----GUCCGUGUACUUCUAGCACA--AGAUGCUAGUUUCAGGGUACGGGCACC-CCCCCC-UCAUUUAAUGGGGGGCCUCC-UC-AAGGAG
AM183117.1/3235-3356 GGCACCUUUGAAACC-AUCUCCUAGGUUUCUUCGGAAGGAC------------UUCG-----GUCCGUGUACUUCUAGCACA--ACGUGCUAGUUUCAGGGUACGGGUGCC-CCCCCAUU----UUCGUGGGGGCCUCC-AA-AAGGAG
#=GC SS_cons         (((((((,,<<<<<<.__AAAAAA>>>>>>,,,,,,,<<<<<<..........____...>>>>>>,,<<<<.-<<<<<<__..___>>>>>>------->>>>))))))).<<<<<<<<______>>>>>>>>:::::.:::aaaaaa
#=GC RF              GguGCCcUUGagacc.uucUCCUuggucuCUUCGGAAGgaccc..........UuaG...gggucCGUGcac.ggucccgCA..ugacgggacuUucAGagugCgGGCacC.ccCcgcggcauauuccgcgGgguaUCc.uuaAAGGAG
//
# STOCKHOLM 1.0

#=GF AC   RF01085
#=GF ID   TLS-PK4
#=GF DE   Pseudoknot of tRNA-like structure
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   80.00
#=GF TC   136.90
#=GF NC   58.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00135;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045069; regulation of viral genome replication;
#=GF RN   [1]
#=GF RM   7214524
#=GF RT   Near identity of 3- RNA secondary structure in bromoviruses and cucumber
#=GF RT   mosaic virus.
#=GF RA   Ahlquist P, Dasgupta R, Kaesberg P
#=GF RL   Cell. 1981;23:183-189.
#=GF RN   [2]
#=GF RM   6628363
#=GF RT   Three-dimensional models of the tRNA-like 3' termini of some plant viral
#=GF RT   RNAs.
#=GF RA   Rietveld K, Pleij CW, Bosch L
#=GF RL   EMBO J. 1983;2:1079-1085.
#=GF RN   [3]
#=GF RM   1935928
#=GF RT   tRNA-like structures. Structure, function and evolutionary significance.
#=GF RA   Mans RM, Pleij CW, Bosch L
#=GF RL   Eur J Biochem. 1991;201:303-324.
#=GF WK   Transfer_RNA-like_structures
#=GF SQ   2


K01778.1/151-266 AAGAUAUCUGUACCGUCUUCUCCCCGACGGUUUCAAUCCAUAGCUUCACGUUGUGUAGCGUAGGUGGAAGGUAUCGUGUGGUGU--AUAAACACCACAUAGUCUCUUAGGGGAGACCA
K01776.1/83-200  AAGAUAUCUGUACCGCCUGCUCCCCGGUGGUUUCGAUCCAUGGCUUCACGAUGUGUUGCAUAGAUGGAAGAUAUCGUGUGGUGUUGAAAAACACCACAUAGUCUCUUAGGGGAGACCA
#=GC SS_cons     ::(((((((,,<<<<<<__AAAAAA>>>>>>,,,,,<<<<<-<<<-<<_____>>->>>---->>>>>)))))))<<<<<<<<<______>>>>>>>>>:::::::::aaaaaa::::
#=GC RF          AAGauauCuGUaCCgcCUuCUCCCCGgcGGuUUCaAuCCauaGCuUCaCGaUGuGUaGCaUAGauGGaaGauauCguGuGGuGuugAaAAaCaCCaCauAGUCUCUUAGGGGAGACCA
//
# STOCKHOLM 1.0

#=GF AC   RF01087
#=GF ID   PK-repZ
#=GF DE   Pseudoknot of the regulatory region of the repZ gene
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   44.00
#=GF TC   46.30
#=GF NC   42.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00170;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   9565606
#=GF RT   An RNA pseudoknot as the molecular switch for translation of the repZ gene
#=GF RT   encoding the replication initiator of IncIalpha plasmid ColIb-P9.
#=GF RA   Asano K, Mizobuchi K
#=GF RL   J Biol Chem. 1998;273:11815-11825.
#=GF WK   Regulatory_region_of_repZ_gene
#=GF SQ   6


AB021078.1/294-442   AAGGAAAACCCCCACUAUCUUUCUUACGAACUUGGCGGAACG-ACGAAAGAUAGUGGGGGC-CUCACAGAAUACGGGUAAAGUAUA-AUGAAACCGUACCAGAGAUUCAACCCUGUGCAGUGUAUAAAUACACGGCACAAUCGCUCCGCCAU
M20413.1/189-337     AAGGAAAACCCCCACUAUCUUUCUUACGAACUUGGCGGAACG-ACGAAAGAUAGUGGGGGC-CUCACAGAAUACGGGUAAAGUAUA-AUGAAACCGUACCAGAGAUUCAACCCUGUGCAGUGUAUAAAUACACGGCACAAUCGCUCCGCCAU
M20412.1/189-336     AAGGAAAACCCCCACAAUCUUUC-GACGAACUUGGCGGGACG-GAGAAAGAUUAUGGGGGC-CUCACAGAAUACGGGUAAAGUAUA-AUGAAACCGUACCAGAGAUUCAACCCUGUGCAGUGUAUAAAUACACGGCACAAUCGCUCCGCCAU
M93062.1/561-709     AAGGAAAACCCCCACUAUUUUUCCU-CGAACUUGGCGGAACG-CAGAAAAAUAAUGGGGGC-CUCACAGAAUACGGGAUAAGUAUAUAUGAAACCGUACCAGAGAUUCAACCCUGUGCAGUGUAUAAAUACACGGCACAAUCGCUCCGCCAU
AY686591.1/9038-8888 AAGGAAAACCCCCACUAUCUUUCCUCGAACUUUGGCGGACUC-GUGAAAGAUAGUAGGGGCGUUCACAGAAUACGGGAUAAGUAUAUAUGAAACCGUACCAGAGAUUCAACCCUGUGCAGUGUAUAAAUACACGGCACAAUCGCUCCGCCAU
M93064.1/561-711     AAGGAAAACCCCCAUAAUCUUCCUGUCGAACUUGGCGGAACGCACAGAAGAUUAUGGGGGC-CUCACAGAAUACGGGAUAAGUAUAUAUGAAACCGUGUCAGAGAUUCAACCCUUCGCAGUGUAUUAACGCACGGCAUUCUGUUUCCGCCAU
#=GC SS_cons         :<<<----<<<<<<<<<<<<<<<_________AAAAAAA_AA.A_>>>>>>>>>>>>>>>>.>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::aaa:aaaaaaa:
#=GC RF              AaGGAAAACCCCCacuaucuuuCuuacGAAcUUGGCGGAAcg.aaGaaagauaguGGGGGC.CuCACAGAAUACGGGauAAGUAUAUAUGAAACCGUAcCAGAGAUUCAACCCUgUGCAGUGUAUAAAUACACGGCAcAAUcgcUCCGCCAU
//
# STOCKHOLM 1.0

#=GF AC   RF01088
#=GF ID   TLS-PK5
#=GF DE   Pseudoknot of tRNA-like structure
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   70.00
#=GF TC   79.50
#=GF NC   33.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00240;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045069; regulation of viral genome replication;
#=GF RN   [1]
#=GF RM   2584952
#=GF RT   Nucleotide sequences of 5' and 3' non-coding regions of pepper mild mottle
#=GF RT   virus strain S RNA.
#=GF RA   Avila-Rincon MJ, Ferrero ML, Alonso E, Garcia-Luque I, Diaz-Ruiz JR
#=GF RL   J Gen Virol. 1989;70:3025-3031.
#=GF RN   [2]
#=GF RM   1935928
#=GF RT   tRNA-like structures. Structure, function and evolutionary significance.
#=GF RA   Mans RM, Pleij CW, Bosch L
#=GF RL   Eur J Biochem. 1991;201:303-324.
#=GF WK   Transfer_RNA-like_structures
#=GF SQ   3


AB000709.2/6252-6319   GUCGUUGGGAUGGAACGCAAUUAAAUACAUGUGUGACGUGUAUUUGCGAACGACGUAAUUAUUUUUCA
L35074.1/577-644       GUCGUUAGGAUGGAACGCAAUUAAAUACAUGUGUGACGUGUAUUUGCGAACGACGUAAUUAUUUUCAG
AAMG01002274.1/151-217 GUCGUCUGGAUGAAACACAAG-AUUUACACGUGUGACGUGUAUAUGUGGGCGACGUAAAAUUUUUACU
#=GC SS_cons           <<<<<<----AAAAA<<<----<<<<<<<<<_____>>>>>>>>>>>>>>>>>>:::::::::aaaaa
#=GC RF                GUCGucuGGAUGgAACGCAAuUAaaUACAcGUGUGACgUGUAuuUGCGgaCGACGUAAuuaUUUUucu
//
# STOCKHOLM 1.0

#=GF AC   RF01089
#=GF ID   PK-repBA
#=GF DE   Pseudoknot of the regulatory region of the repBA gene
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   45.00
#=GF TC   47.80
#=GF NC   42.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00179;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0006412; translation;
#=GF RN   [1]
#=GF RM   7543895
#=GF RT   The replication of an IncL/M plasmid is subject to antisense control.
#=GF RA   Athanasopoulos V, Praszkier J, Pittard AJ
#=GF RL   J Bacteriol. 1995;177:4730-4741.
#=GF RN   [2]
#=GF RM   10074073
#=GF RT   Analysis of elements involved in pseudoknot-dependent expression and
#=GF RT   regulation of the repA gene of an IncL/M plasmid.
#=GF RA   Athanasopoulos V, Praszkier J, Pittard AJ
#=GF RL   J Bacteriol. 1999;181:1811-1819.
#=GF WK   Regulatory_region_of_repBA_gene
#=GF SQ   7


U27345.1/557-680         AACCCCCUGAUCCUAU-UUCAGAACUUUGGCCGGCUC-GGA----AUAGAAUCAGGGGGUGCAA--ACUGCCCA-CUGGCAGA-AAGGAUUAUAGCAAAUGCGUACCCUAUUGCAAUACAGCCCGGCCAAUAUG
AY422214.1/51958-52081   AACCCCCUGAUCCCUGUAGAAAA-CUUUGGCCGGUCU-ACU----CAGGAAUCAGGGGGUGCAA--ACUGCCCA-CUGGCAGA-AAGGAUUAUAGCAAAUGCGUAACCUAUUGCAAUACAGCCCGGCCAAUAUG
AF550415.2/54744-54867   AACCCCCUGAU-UCAU-CCUCUCACUUUGGCCGGUCA-GAG----AUGAAAUCAGGGGGCGCAA--ACUGCCUUGCUGGCAGA-AAGGAUUAUAGCAAAUGCGUACCCUAUUGCAAUACAGCCCGGCCAAUAAG
AY150843.2/66153-66280   AAGCCCCCGAAUCUCUAUUCACAAUCUUGG-CGGAUG-GGUUUAGAGAGAAUCAGGGGCUCAAA-UACUGGCUG-CUGCCAGC-AAGGAUUAUAACGCAUGUACAAUCCAAAUCAAGCCUU-CCGACCCGCCAU
AE017044.1/1577-1455     AACCCCCUGAAAUCUG---CUUCAACUUGGCGGGAGA-GA-----CAGAGAUCAGGGGGUCCAAAAGCAGGCGC-UGGCCUGUGAAGGAUUAUAGCAAAUGCAUAACCUAACACAACCCCU-CAGACUCGCCAU
CP000654.1/141918-142038 AACCCCCUGAU-AUCU-UUCUCA-ACUUGG-CGGAAG-GGU----AGAU-AUCAGGGGGUCCAAAAGCAGGCGCGAUGCCUGUGAAGGAUUAUAACGCAUGCACCAUAGAAAACAAUAC---CCGGCCGCCCUA
CP000718.1/1687-1567     AACCCCCCGAUUUCUA-GCUAUCAACUUGGCGGAAGGUGAC----UAGACAUCGAGGGGU-------UAGGUAU-AAACCUAUGAAGGAUUAUAACGCAUGUUUGCUCUAAAACAACCCCAUUCUGCCAUAAGC
#=GC SS_cons             :<<<<<<<<<<-<<<<.<<<-<<___AAAAAAAA_>>.>>>....>>>>->>>>>>>>>>::::..::::::::.::::::::.::::::::::::::::::::::::::::::::::::::aaaaaaaa::::
#=GC RF                  AacCCCCuGAuucccu.gccaccAacUUGGCcGGagg.ggc....agggaaUCaGGGGguccAA..aCuGgCuu.cuGcCaGu.AAGGAUUAUAaCaaAUGcaUaauCuAaaaCAAuaCaucCCGgCCaauaau
//
# STOCKHOLM 1.0

#=GF AC   RF01090
#=GF ID   RF_site4
#=GF DE   Edr gene ribosomal frameshift signal
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   45.00
#=GF TC   50.30
#=GF NC   37.10
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00257;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0006452; translational frameshifting;
#=GF RN   [1]
#=GF RM   15767280
#=GF RT   Characterization of the frameshift signal of Edr, a mammalian example of
#=GF RT   programmed -1 ribosomal frameshifting.
#=GF RA   Manktelow E, Shigemoto K, Brierley I
#=GF RL   Nucleic Acids Res. 2005;33:1553-1563.
#=GF WK   Ribosomal_frameshift
#=GF SQ   7


AAIY01557043.1/3331-3396     GGGAAACUCCCAGGCCCCGCUGUAGAGGGACCGUCAGCGGCCGGGCCAG---AAAGAAUGAGGUCCCCA
AB260975.1/11458-11523       GGGAAACUCCCUGGCCCCGCUGUAGAGGGACCCCCAGCGCCCGGGCCUG---AACCAGAAAGGUCCCCC
BC050659.2/1365-1433         GGGAAACUCCCCGGCCCCGCUGUAGAGGGACCUUCAGCGACCGAACCAGCUUAGGCAAAAGAGUCCCCA
AAKN02016859.1/6843-6908     GGGAAACUCCCCGGCCCCGCUGUAGAGGGACCAUCAGCGACCGGGCCGG---AAAUCAUAAGGUCCCAA
AJ006464.1/1390-1455         GGGAAACUCCCCGGCCCCGCUGUAGGGGGACCUUCAGCGACAGGGCCAG---AACGAAUAAGGUCCCCA
BL000001.1/93251221-93251286 GGGAAACUCCCCGGCCCCGCUGUAGAGGGACCUUCAGCGACCGGGCCAG---AAAUAAUAAGGUCCCCA
AAQR03013182.1/99107-99042   GGGAGACUCCCCGGCCCUGCUGUAGAGGGACCUUCAGCGACUGAGCCAG---AAAUAAUAAGGUCCCCA
#=GC SS_cons                 ::::::::::::<<<<<<<<<<____AAAAAAAA>>>>>--->>>>>::...:::::::aaaaaaaa::
#=GC RF                      GGGAAACUCCCcGGCCCCGCUGUAGAGGGACCuUCAGCGaCcGGGCCaG...AAauAAuAAGGUCCCCA
//
# STOCKHOLM 1.0

#=GF AC   RF01091
#=GF ID   PK-SPCSV
#=GF DE   3'-terminal pseudoknot in SPCSV
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   36.00
#=GF TC   36.40
#=GF NC   35.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.45 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00265;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   15218192
#=GF RT   Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite
#=GF RT   genome and conserved 3'-terminal structures among members of the genus
#=GF RT   Crinivirus.
#=GF RA   Livieratos IC, Eliasco E, Muller G, Olsthoorn RC, Salazar LF, Pleij CW,
#=GF RA   Coutts RH
#=GF RL   J Gen Virol. 2004;85:2065-2075.
#=GF WK   Sweet_potato_feathery_mottle_virus
#=GF SQ   2


AJ428555.1/8163-8223 CGGUUUUCCUAAAUCGUCGUGAGACGGACCUUGGAAAACCUAGUAUUUAAAUAACUAGGUC
AJ428554.1/9347-9407 CGGUUUUCCUAAAUCGUCGUGAGACGGACCUUGGAAAACCUAGUAUUUAAAUAACUAGGUC
#=GC SS_cons         :<<<<<<<<-----<<<<____>>>>AAAAA->>>>>>>>::::::::::::::::aaaaa
#=GC RF              CGGUUUUCCUAAAUCGUCGUGAGACGGACCUUGGAAAACCUAGUAUUUAAAUAACUAGGUC
//
# STOCKHOLM 1.0

#=GF AC   RF01092
#=GF ID   GP_knot2
#=GF DE   Gag/pol translational readthrough site
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   80.00
#=GF TC   86.00
#=GF NC   53.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00048;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0039705; viral translational readthrough;
#=GF RN   [1]
#=GF RM   8076609
#=GF RT   Pseudoknot-dependent read-through of retroviral gag termination codons:
#=GF RT   importance of sequences in the spacer and loop 2.
#=GF RA   Wills NM, Gesteland RF, Atkins JF
#=GF RL   EMBO J. 1994;13:4137-4144.
#=GF WK   Gag/pol_translational_readthrough_site
#=GF SQ   2


M54993.1/172-232     UAGGGCCGUCAGGGUUCUCCCGCCCUCCGUGAACCCAGGCUAAAAGUUAAGGUAGGGGGGC
DQ003591.1/2531-2591 UAGGGCCGUCAGGGUUCUCCCGCCCUCCGUGAACCCAGGCUAAAAGUUAAGGUAGGGGGGC
#=GC SS_cons         :::::::::::<<<<<<-<__AAAAAAA>->>>>>>::::::::::::::::::aaaaaaa
#=GC RF              UAGGGCCGUCAGGGUUCUCCCGCCCUCCGUGAACCCAGGCUAAAAGUUAAGGUAGGGGGGC
//
# STOCKHOLM 1.0

#=GF AC   RF01093
#=GF ID   RF_site5
#=GF DE   Ma3 gene ribosomal frameshift signal
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   35.00
#=GF TC   36.00
#=GF NC   34.60
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00258;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0006452; translational frameshifting;
#=GF RN   [1]
#=GF RM   16407312
#=GF RT   A functional -1 ribosomal frameshift signal in the human paraneoplastic
#=GF RT   Ma3 gene.
#=GF RA   Wills NM, Moore B, Hammer A, Gesteland RF, Atkins JF
#=GF RL   J Biol Chem. 2006;281:7082-7088.
#=GF WK   Ribosomal_frameshift
#=GF SQ   12


AAQQ01394808.1/251-310     GGGAAACGGGAGCCGGGCUUGGGACAAGAGCCAUCCCAAGUCCAAGGCCAAGUAGGCUCU
AY121806.1/1715-1774       GGGAAACGAGGCAGGGGCUGGGGCCAUGAGCCAUCCCAAGCCCUGGGAAACAUAGGCUCA
AAPY01451866.1/2180-2239   GGGAAACGAGAUAGGGGCUGGGGCCAUGAGCCACCCCAAGCCCUGGGAAGCAUAGGCUCA
ABDC01277479.1/317-258     GGGAAACGAGAUGGGGGCUGGGGCUAUGAGCCAUCCCGAGCCCUAAGAAGCAUAGGCUCA
AANN01419562.1/5008-4949   GGGAAACGAGCAGGGGGCUGGGGCAGUGAGCCAACCCAAGCCCUAGGAAGCAGAGGCUCG
AAIY01564318.1/499-558     GGGAAACGGGGUGGGGGCUGGGGCAGUGAGCCACCCCAGGCCUUAAGCAGUACAGGCUCA
AAWR02040610.1/2027-2086   GGGAAACGGGAGCUGGGCUUGGGACAAGAGCCAUCCCAAGCCCAAGGCCAAGUAGGCUCA
AAGV020672825.1/603-544    GGGAAACGGGAGCCGGGCUUGAGACGCGAGCCAUCCCAAGCCCAAGCCCAGGCAGGCUCA
AC216924.3/17795-17736     GGGAAACGGGAACUGGGCUUGGGACAAGAGCCAUCCCAAGUCCAAGGCCAAGUAGGCUCG
AL136329.1/63782-63841     GGGAAACAGGAGCUGGGCUUGGGAGAAGAGCCAUCCCAAGCCCAAGACCAAGUAGGCUCC
AAQR03179762.1/22803-22744 GGGAAAAGAGGAUAGGGCUUGGGACAUGAGCCACCCCGAGUCCUCAGGUGAAUAGGCUCU
AAPE02015504.1/48430-48489 GGGAAACGGCGACCGGGCUUGGGACAAGAGCCAUCCCAAGUCCAAGGCCAGAUAGGCUCA
#=GC SS_cons               :::::::::::::<<<<<<<<<<<___AAAAA_>>>>>>>>>>>::::::::::aaaaa:
#=GC RF                    GGGAAACGgGaacuGGGCUuGGGacAuGAGCCAuCCCaAGCCCaAGGcaaaAUAGGCUCa
//
# STOCKHOLM 1.0

#=GF AC   RF01094
#=GF ID   RF_site6
#=GF DE   Polymerase ribosomal frameshift site
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   90.00
#=GF TC   154.00
#=GF NC   38.80
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00128;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   2388833
#=GF RT   The carboxyl-terminal part of the putative Berne virus polymerase is
#=GF RT   expressed by ribosomal frameshifting and contains sequence motifs which
#=GF RT   indicate that toro- and coronaviruses are evolutionarily related.
#=GF RA   Snijder EJ, den Boon JA, Bredenbeek PJ, Horzinek MC, Rijnbrand R, Spaan WJ
#=GF RL   Nucleic Acids Res. 1990;18:4535-4542.
#=GF WK   Ribosomal_frameshift
#=GF SQ   2


X52374.1/1045-1162     UUUAAACUGUUGAGAGGUGCCUGGAGCGCCUGCAGGCAUCUCUGUUUUCAAAAUGGCGCAUACCAGUCUUCAAGGUCAAAACAUUAUAUUGAUUUGGCAACUGAGUAUAAUGCAGGCA
AY427798.1/14184-14301 UUUAAACUGCUGAGAGAUGUCUGGUGCGCCUGCAGACAUCUCUGUUUUCAAAAUGGCGCGUAUCAGUCGUCACGAUCUAAGCAUUAUAUUGAUUUGGCGACUGAGUACAACGCAGGCA
#=GC SS_cons           ::::::::::::<<<<<<<<<<<____AAAAA>>>>>>>>>>>:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::aaaaa:
#=GC RF                UUUAAACUGuUGaGaGauGcCuGGuGCGCCUGCaGgCauCuCuGUUUUCAAAAUGGCGCaUAuCAGUCuUCAaGaUCuAAaCAUUAUAUUGAUUUGGCaACUGAGUAuAAuGCAGGCA
//
# STOCKHOLM 1.0

#=GF AC   RF01095
#=GF ID   PK-CuYV_BPYV
#=GF DE   3'-terminal pseudoknot of CuYV/BPYV
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   60.00
#=GF TC   89.90
#=GF NC   34.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00262;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   15218192
#=GF RT   Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite
#=GF RT   genome and conserved 3'-terminal structures among members of the genus
#=GF RT   Crinivirus.
#=GF RA   Livieratos IC, Eliasco E, Muller G, Olsthoorn RC, Salazar LF, Pleij CW,
#=GF RA   Coutts RH
#=GF RL   J Gen Virol. 2004;85:2065-2075.
#=GF WK   Cucumber_yellows_virus
#=GF SQ   2


AB085612.1/7844-7899 CGUUUGGUCGAAUGCUACUAGAGCAGCCUGACCAAACUAGUAUUAGUAAAUAAAGG
AB085613.1/7552-7607 CGUUUGGUCGAAUGCUACUAGAGCAGCCUGACCAAACUAGUAUUAGUAAAUAAAGG
#=GC SS_cons         :<<<<<<<<---<<<<_____>>>>-AAA>>>>>>>>::::::::::::::::aaa
#=GC RF              CGUUUGGUCGAAUGCUACUAGAGCAGCCUGACCAAACUAGUAUUAGUAAAUAAAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01096
#=GF ID   PK-HAV
#=GF DE   HepA virus 3'-terminal pseudoknot
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   50.00
#=GF TC   54.00
#=GF NC   45.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00265;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   15218192
#=GF RT   Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite
#=GF RT   genome and conserved 3'-terminal structures among members of the genus
#=GF RT   Crinivirus.
#=GF RA   Livieratos IC, Eliasco E, Muller G, Olsthoorn RC, Salazar LF, Pleij CW,
#=GF RA   Coutts RH
#=GF RL   J Gen Virol. 2004;85:2065-2075.
#=GF WK   Pseudoknot
#=GF SQ   2


AB020564.1/7423-7477 UUAAACAAAUUUUCUUAAAAUUUCUGAGGUUUGUUUAUUUCUUUUAU-CAGUAAAU
X15462.1/90-145      UUAAACAAACCUUCUUAAAAUUUCUGAGAUUUGUUUAUUUUGCAUAUUCAGUAAAU
#=GC SS_cons         :<<<<<<<<<<_________AAAAAAA>>>>>>>>>>:::::::::a:aaa:aaa:
#=GC RF              UUAAACAAAucUUCUUAAAAUUUCUGAggUUUGUUUAUUUuuuuUAUUCAGUAAAU
//
# STOCKHOLM 1.0

#=GF AC   RF01097
#=GF ID   RF_site8
#=GF DE   Gag/pro ribosomal frameshift site
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   43.00
#=GF TC   43.00
#=GF NC   42.90
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00107;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   2402881
#=GF RT   RNA pseudoknots: translational frameshifting and readthrough on viral
#=GF RT   RNAs.
#=GF RA   ten Dam EB, Pleij CW, Bosch L
#=GF RL   Virus Genes. 1990;4:121-136.
#=GF RN   [2]
#=GF RM   7585244
#=GF RT   Analysis of the role of the pseudoknot component in the SRV-1 gag-pro
#=GF RT   ribosomal frameshift signal: loop lengths and stability of the stem
#=GF RT   regions.
#=GF RA   ten Dam EB, Verlaan PW, Pleij CW
#=GF RL   RNA. 1995;1:146-154.
#=GF RN   [3]
#=GF RM   9237911
#=GF RT   Base-pairings within the RNA pseudoknot associated with the simian
#=GF RT   retrovirus-1 gag-pro frameshift site.
#=GF RA   Du Z, Holland JA, Hansen MR, Giedroc DP, Hoffman DW
#=GF RL   J Mol Biol. 1997;270:464-470.
#=GF RN   [4]
#=GF RM   9490779
#=GF RT   Mutational analysis of the RNA pseudoknot involved in efficient ribosomal
#=GF RT   frameshifting in simian retrovirus-1.
#=GF RA   Sung D, Kang H
#=GF RL   Nucleic Acids Res. 1998;26:1369-1372.
#=GF WK   Ribosomal_frameshift
#=GF SQ   4


AB181392.1/1897-1948 GGGAAACGGACUGAGGGGCCAGCCCCAGGCCCCGAAACAAGCUUAUGGGGCG
AF252389.1/572-623   GGGAAACGGGUGGAGGGGCCAGCCCCAGGCCCCGAAACAAGCUUAUGGGGCG
U85505.1/2460-2511   GGGAAACGGGAUGAGGGGCCAGCCCCAGGCCCCGAAACAAGCAUAUGGGGCA
M80216.1/1954-2005   GGGAAACUGGGUGAGGGGCCAGCCCCUGGCCCCGAAACAAUGUUAUGGGGCA
#=GC SS_cons         ::::::::::::::<<<<<<_AAAAAA>>>>>>::::::::::::aaaaaa:
#=GC RF              GGGAAACGGGuUGAGGGGCCAGCCCCAGGCCCCGAAACAAGcUUAUGGGGCa
//
# STOCKHOLM 1.0

#=GF AC   RF01098
#=GF ID   RF_site9
#=GF DE   Gag/pro ribosomal frameshift site
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   70.00
#=GF TC   70.40
#=GF NC   63.80
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00080;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   2402881
#=GF RT   RNA pseudoknots: translational frameshifting and readthrough on viral
#=GF RT   RNAs.
#=GF RA   ten Dam EB, Pleij CW, Bosch L
#=GF RL   Virus Genes. 1990;4:121-136.
#=GF RN   [2]
#=GF RM   1309954
#=GF RT   An RNA pseudoknot and an optimal heptameric shift site are required for
#=GF RT   highly efficient ribosomal frameshifting on a retroviral messenger RNA.
#=GF RA   Chamorro M, Parkin N, Varmus HE
#=GF RL   Proc Natl Acad Sci U S A. 1992;89:713-717.
#=GF RN   [3]
#=GF RM   7723043
#=GF RT   The structure of an RNA pseudoknot that causes efficient frameshifting in
#=GF RT   mouse mammary tumor virus.
#=GF RA   Shen LX, Tinoco I Jr
#=GF RL   J Mol Biol. 1995;247:963-978.
#=GF RN   [4]
#=GF RM   8759314
#=GF RT   A characteristic bent conformation of RNA pseudoknots promotes -1
#=GF RT   frameshifting during translation of retroviral RNA.
#=GF RA   Chen X, Kang H, Shen LX, Chamorro M, Varmus HE, Tinoco I Jr
#=GF RL   J Mol Biol. 1996;260:479-483.
#=GF WK   Ribosomal_frameshift
#=GF SQ   2


M15122.1/3396-3444 AAAAAACUUGUAAAGGGGCAGUCCCCUAGCC-CCGCUCAAAAGGGGGAUG
DQ917496.1/479-528 AAAAAACUGGUAAAGGGGCAGUCCCCUAGCCGCCACUCAAAAGGGGGGAG
#=GC SS_cons       ::::::::::::::<<<<<_AAAAAAA_>>>->>::::::::aaaaaaa:
#=GC RF            AAAAAACUuGUAAAGGGGCAGUCCCCUAGCCGCCaCUCAAAAGGGGGauG
//
# STOCKHOLM 1.0

#=GF AC   RF01099
#=GF ID   PK-IAV
#=GF DE   Pseudoknot of influenza A virus gene
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   47.00
#=GF TC   47.30
#=GF NC   44.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00273;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   17090581
#=GF RT   An RNA conformational shift in recent H5N1 influenza A viruses.
#=GF RA   Gultyaev AP, Heus HA, Olsthoorn RC
#=GF RL   Bioinformatics. 2007;23:272-276.
#=GF RN   [2]
#=GF RM   20200490
#=GF RT   A family of non-classical pseudoknots in influenza A and B viruses.
#=GF RA   Gultyaev AP, Olsthoorn RC
#=GF RL   RNA Biol. 2010;7:125-129.
#=GF WK   Influenza_virus_pseudoknot
#=GF SQ   32


X52146.1/523-570   UUCCAGGACAUACUGCUGAGGAUGUCAAAAAUGCAGUUGGAGUCCUCA
AY585441.1/497-544 UUCCAGGACAUACUAAUGAGGAUGUCAAAAAUGCAAUUGGAGUCCUCA
AY060138.1/501-548 UUCCAGGACAUAUUGAUGAGGAUGUCAAAAAUGCAGUUGGGGUCCUCA
CY009104.1/511-558 UUCCAGGACAUACUGUUGAGGAUGUCAAAAAUGCAAUUGGGGUCCUCA
DQ226120.1/497-544 UCCCAGGACAUACUGAUGAGGAUGUCAAAAAUGCGAUUGGGGUCCUCA
AY060139.1/501-548 UUCCAGGACAUACUAAUGAGGAUGUCAAAAUUGCAGUUGGGGUCCUCA
CY022369.1/508-555 UUCCAGGACAUACUGAUGAGAAUGUCAAAGAUGCAGUUGGGGUCCUCA
EF155266.1/497-544 UUCCAGGACAUAAUGAAGAGGAUGUCAAAAAUGCAAUUGGGGUCCUCA
M55482.1/508-555   UUCCAGGACAUACUGAUGAGGAUGUCAAAAAUGCAGUUGGGGCCCUCG
CY014802.1/523-570 UUCCAGGACAUACUAGCGAGGAUGUCAAAAAUGCAAUUGGAAUCCUCA
AF509066.1/500-547 UUCCAGUACAUACUGAUGAGGAUGUCAAAAAUGCAAUUGGGGUCCUAA
EF101744.1/484-531 UUCCAGGACAUACUGAUGAGGAUGUCAAAAAUGCAAUUGGGACCCUCA
AY664746.1/497-544 UUCCAGGACAUACUGACAAGGAUGUCAAAAAUGCAAUUGGGGUCCUCA
EF124593.1/482-529 UUCCAGGACAUACUGAUGAGGAUGUCAAAAUUGCAAUUGGGGUACUCA
CY011284.1/510-557 UUCCAGGACAUACUAAUGAGGAUGUCAAAAAUGCAAUUGGGAUUCUCA
DQ493173.1/482-529 UUCCAGGACAUACUGGUGAGGAUGUCAAAAAUGCAAUUGGCGUACUCA
DQ321190.1/482-529 UUCCAGGACAUACUGAUGAGGAUGUCAAAAAUGCAAUUGGCGUCCUCG
M80958.1/523-570   UUCCAGGACCUACUAGUAAGGAUGUCAAAAAUGCAAUUGGAAUCCUCA
AY300997.1/497-544 UGCCAGGACAUACUACAGAGGAUGUCAAAAAUGCAAUUGGAAUCCUCA
DQ376792.1/523-570 UUCCAGGACAUACUAAGGAGGAUGUCAAAGAUGCAAUUGGGGUCCUCA
AY585447.1/497-544 UACCAGGACAUUCUACAGAGGAUGUCAAAAAUGCAAUUGGAGUCCUCA
AY737300.1/508-555 UUCCAGGACAUACUGGUGAGGAUGUCAAAAAUGCAAUUGGCAUCCCCA
AF098574.1/503-550 UUUCAGGACAUACUGAAGAGGAUGUCAAGAAUGCAAUUGGGGUCCUCA
AY651575.1/494-541 UUCCAGGACAUAAUGGUGAGGAUGUCAAGAAUGCAAUUGGCGUCCUCA
AY241635.1/497-544 UGCCAGGACAUUCUGCGGAGGAUGUCAAAAAUGCAAUUGGGAUCCUCA
DQ299857.1/523-570 UUCCAGGACAUGCUAACGAGGAUGUCAAAAAUGCAAUUGGGGCCCUCA
AJ293940.1/487-534 UUCCAGGACAUACUGGUGAGGAUGUCAAAAAUGCAAUUGAGGCCCUCA
CY022785.1/508-555 UGCCAGGACAUUCUGGAGAGGAUGUCAAAAAUGCAAUUGGAAUCCUCA
AF508712.1/494-541 UGCCAGGACAUUCUCAUGAGGAUGUCAAAAAUGCAAUUGGAAUCCUCA
CY014263.1/482-529 UUUCAGGACAUACUGGUGAGGAUGUCAAAAGUGCAAUUGGCGUCCUCA
M80944.1/523-570   UUCCAGGACAUACUAACGAGGAUGUCAAAAAUGCAAUUGAGAUCCUCA
AY241631.1/497-544 UGCCAGGACAUUCUGCAGAGAAUGUCAAAGAUGCAAUUGGAAUCCUCA
#=GC SS_cons       :<<<<<___________AAAAAA_____________>>>>>aaaaaa:
#=GC RF            UuCCAGGACAUACUGauGAGGAUGUCAAAAAUGCAAUUGGaGUCCUCA
//
# STOCKHOLM 1.0

#=GF AC   RF01100
#=GF ID   PK-BYV
#=GF DE   3'-terminal pseudoknot in BYV
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   50.00
#=GF TC   59.10
#=GF NC   34.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00268;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   15218192
#=GF RT   Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite
#=GF RT   genome and conserved 3'-terminal structures among members of the genus
#=GF RT   Crinivirus.
#=GF RA   Livieratos IC, Eliasco E, Muller G, Olsthoorn RC, Salazar LF, Pleij CW,
#=GF RA   Coutts RH
#=GF RL   J Gen Virol. 2004;85:2065-2075.
#=GF WK   Beet_yellows_virus
#=GF SQ   2


AF056575.1/15429-15468 CUCCUAGCGAAGUCCCGCUAGGAAGAAAAAAUAAGGGCCG
AF190581.1/15429-15468 CUCCUAGCGAAGUCCCGCUAGGAAGAAAAAAUAAGGGCCG
#=GC SS_cons           :<<<<<<<___AAAA_>>>>>>>:::::::::::aaaa::
#=GC RF                CUCCUAGCGAAGUCCCGCUAGGAAGAAAAAAUAAGGGCCG
//
# STOCKHOLM 1.0

#=GF AC   RF01101
#=GF ID   TLS-PK6
#=GF DE   Pseudoknot of tRNA-like structure
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   44.00
#=GF TC   47.70
#=GF NC   31.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00130;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045069; regulation of viral genome replication;
#=GF RN   [1]
#=GF RM   3645545
#=GF RT   tRNA-like properties of tobacco rattle virus RNA.
#=GF RA   van Belkum A, Cornelissen B, Linthorst H, Bol J, Pley C, Bosch L
#=GF RL   Nucleic Acids Res. 1987;15:2837-2850.
#=GF RN   [2]
#=GF RM   1935928
#=GF RT   tRNA-like structures. Structure, function and evolutionary significance.
#=GF RA   Mans RM, Pleij CW, Bosch L
#=GF RL   Eur J Biochem. 1991;201:303-324.
#=GF WK   Transfer_RNA-like_structures
#=GF SQ   3


X03686.1/1866-1905 AGGGGUAAAACCCCUCGCCUACGUAAGCGUUAUUACGCCC
S82444.1/61-100    AAAGGUAAAACCCCUCGCCUACGUAAGCGUUAUUACGCCC
X51828.1/3335-3374 AGGGUUAAACCCUUCCGCCUACGUAAGCGUUAUUACGCCC
#=GC SS_cons       :::::::::::::::<<<___AAAAA>>>:::aaaaa:::
#=GC RF            AGGGgUAAAACCccUCGCCUACGUAAGCGUUAUUACGCCC
//
# STOCKHOLM 1.0

#=GF AC   RF01102
#=GF ID   PK1-TEV_CVMV
#=GF DE   5'-leader pseudoknot of TEV/CVMV
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   40.00
#=GF TC   42.70
#=GF NC   38.70
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00277;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0002190; cap-independent translational initiation;
#=GF RN   [1]
#=GF RM   15911616
#=GF RT   Cap-independent translation of tobacco etch virus is conferred by an RNA
#=GF RT   pseudoknot in the 5'-leader.
#=GF RA   Zeenko V, Gallie DR
#=GF RL   J Biol Chem. 2005;280:26813-26824.
#=GF WK   Tobacco_etch_virus
#=GF SQ   2


M15239.1/38-74   CGAAUCUCAAGCAAUCAAGCAUUCUACUUCUAUUGCA
AJ237843.3/24-59 CGAAU-UCAAGCAAUCAAGCAUUCAAGCGCUCUUUUA
#=GC SS_cons     :<<<<<<___AAAAA__>>->>>>:::::::aaaaa:
#=GC RF          CGAAUCUCAAGCAAUCAAGCAUUCuAguuCUaUUuuA
//
# STOCKHOLM 1.0

#=GF AC   RF01103
#=GF ID   UPD-PKc
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   40.00
#=GF TC   44.30
#=GF NC   34.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://wwwbio.leidenuniv.nl/~Batenburg/pkbget.html;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   9714254
#=GF RT   Genome properties of beet virus Q, a new furo-like virus from sugarbeet,
#=GF RT   determined from unpurified virus.
#=GF RA   Koenig R, Pleij CW, Beier C, Commandeur U
#=GF RL   J Gen Virol. 1998;79:2027-2036.
#=GF RN   [2]
#=GF RM   8623558
#=GF RT   Comparisons of the genomic cis-elements and coding regions in RNA beta
#=GF RT   components of the hordeiviruses barley stripe mosaic virus, lychnis
#=GF RT   ringspot virus, and poa semilatent virus.
#=GF RA   Solovyev AG, Savenkov EI, Agranovsky AA, Morozov SY
#=GF RL   Virology. 1996;219:9-18.
#=GF RN   [3]
#=GF RM   8608444
#=GF RT   A central pseudoknotted three-way junction imposes tRNA-like mimicry and
#=GF RT   the orientation of three 5' upstream pseudoknots in the 3' terminus of
#=GF RT   tobacco mosaic virus RNA.
#=GF RA   Felden B, Florentz C, Giege R, Westhof E
#=GF RL   RNA. 1996;2:201-212.
#=GF RN   [4]
#=GF RM   9223489
#=GF RT   The role of the pseudoknot at the 3' end of turnip yellow mosaic virus RNA
#=GF RT   in minus-strand synthesis by the viral RNA-dependent RNA polymerase.
#=GF RA   Deiman BA, Kortlever RM, Pleij CW
#=GF RL   J Virol. 1997;71:5990-5996.
#=GF RN   [5]
#=GF RM   15033563
#=GF RT   The tRNA-like structure of Turnip yellow mosaic virus RNA is a
#=GF RT   3'-translational enhancer.
#=GF RA   Matsuda D, Dreher TW
#=GF RL   Virology. 2004;321:36-46.
#=GF WK   UPSK_RNA
#=GF SQ   2


AF146278.1/6828-6856 UCUGUUUUUCGAACAGAUGUAAAUCGAAG
AJ298069.1/3470-3498 UCUGUUUUUCGAACAGAUGUAAAUCGGAG
#=GC SS_cons         <<<<<_AAAAAA>>>>>::::::aaaaaa
#=GC RF              UCUGUUUUUCGAACAGAUGUAAAUCGaAG
//
# STOCKHOLM 1.0

#=GF AC   RF01104
#=GF ID   SBWMV2_UPD-PKb
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   39.00
#=GF TC   42.20
#=GF NC   31.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00201;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   10603167
#=GF RT   Molecular characterization of a new furovirus mainly infecting rye.
#=GF RA   Koenig R, Pleij CW, Huth W
#=GF RL   Arch Virol. 1999;144:2125-2140.
#=GF WK   UPSK_RNA
#=GF SQ   3


X81639.1/3422-3450   GGCGUUCUACAGUACGUUUAAACUGUAGG
AJ749657.1/3135-3163 GGCGUUCCACAGUACGUUUAAACUGUGGG
AJ012006.2/3398-3426 GGCGUCCCGCAGUACGUUUAAACUGUAGG
#=GC SS_cons         ::<<<_AAAAAAA>>>:::::aaaaaaa:
#=GC RF              GGCGUUCcACAGUACGUUUAAACUGUAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01105
#=GF ID   SBWMV2_UPD-PKl
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   39.00
#=GF TC   41.70
#=GF NC   34.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.50 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00204;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   10603167
#=GF RT   Molecular characterization of a new furovirus mainly infecting rye.
#=GF RA   Koenig R, Pleij CW, Huth W
#=GF RL   Arch Virol. 1999;144:2125-2140.
#=GF WK   UPSK_RNA
#=GF SQ   2


X81639.1/3336-3362 AGAGUUAUCAUACUCUAUAAACUAUGA
L07938.1/3336-3362 AGAGUUAUCAUACUCUAUAAACUAUGA
#=GC SS_cons       <<<<___AAAAA>>>>::::::aaaaa
#=GC RF            AGAGUUAUCAUACUCUAUAAACUAUGA
//
# STOCKHOLM 1.0

#=GF AC   RF01106
#=GF ID   SBWMV1_UPD-PKb
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   38.00
#=GF TC   39.50
#=GF NC   35.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00194;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   10603167
#=GF RT   Molecular characterization of a new furovirus mainly infecting rye.
#=GF RA   Koenig R, Pleij CW, Huth W
#=GF RL   Arch Virol. 1999;144:2125-2140.
#=GF WK   UPSK_RNA
#=GF SQ   2


AJ012005.1/6980-7004 CGUAGUACAGUGCGUUAAACUGUAC
L07937.1/6932-6956   CGCUGUACAGUGCGUUAAACUGUAC
#=GC SS_cons         <<<_AAAAAAA>>>::::aaaaaaa
#=GC RF              CGcuGUACAGUgCGUUAAACUGUAC
//
# STOCKHOLM 1.0

#=GF AC   RF01107
#=GF ID   SBRMV1_UPD-PKf
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   39.00
#=GF TC   42.10
#=GF NC   32.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00187;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   10603167
#=GF RT   Molecular characterization of a new furovirus mainly infecting rye.
#=GF RA   Koenig R, Pleij CW, Huth W
#=GF RL   Arch Virol. 1999;144:2125-2140.
#=GF WK   UPSK_RNA
#=GF SQ   2


AF146278.1/6748-6774 GCCGCUGGGAUUGCGGAUUAUAAAUCG
AF146279.1/6723-6749 GCCGCUGGGAUUGCGGAUUAUAAAUCG
#=GC SS_cons         :<<<<___AAAA>>>>::::::aaaa:
#=GC RF              GCCGCUGGGAUUGCGGAUUAUAAAUCG
//
# STOCKHOLM 1.0

#=GF AC   RF01108
#=GF ID   BMV3_UPD-PK1
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   38.00
#=GF TC   40.80
#=GF NC   35.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00154;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   7684465
#=GF RT   Contributions of the brome mosaic virus RNA-3 3'-nontranslated region to
#=GF RT   replication and translation.
#=GF RA   Lahser FC, Marsh LE, Hall TC
#=GF RL   J Virol. 1993;67:3295-3303.
#=GF WK   UPSK_RNA
#=GF SQ   2


X58459.1/594-619   GAGCCCCUGACUGGGUUAAAGUCACA
J02042.1/1829-1854 GAGCCCCUGACUGGGUUAAAGUCACA
#=GC SS_cons       :<<<<<_AAAAA>>>>>::aaaaa::
#=GC RF            GAGCCCCUGACUGGGUUAAAGUCACA
//
# STOCKHOLM 1.0

#=GF AC   RF01109
#=GF ID   SBRMV1_UPD-PKd
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   33.00
#=GF TC   35.50
#=GF NC   30.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00185;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   10603167
#=GF RT   Molecular characterization of a new furovirus mainly infecting rye.
#=GF RA   Koenig R, Pleij CW, Huth W
#=GF RL   Arch Virol. 1999;144:2125-2140.
#=GF WK   UPSK_RNA
#=GF SQ   2


AF146278.1/6806-6826 CGUGGCCAUCACGAUAGAUGG
AJ298068.1/6775-6795 CGUGGCCAUCACGAUAGAUGG
#=GC SS_cons         <<<__AAAAA>>>:::aaaaa
#=GC RF              CGUGGCCAUCACGAUAGAUGG
//
# STOCKHOLM 1.0

#=GF AC   RF01111
#=GF ID   SBWMV2_UPD-PKk
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   35.00
#=GF TC   36.30
#=GF NC   33.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.26 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00203;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   10603167
#=GF RT   Molecular characterization of a new furovirus mainly infecting rye.
#=GF RA   Koenig R, Pleij CW, Huth W
#=GF RL   Arch Virol. 1999;144:2125-2140.
#=GF WK   UPSK_RNA
#=GF SQ   4



AJ749657.1/3076-3096 CGUGGUCUUCGCGAUAGAAGA
AJ132579.1/3124-3144 CGUGGUCUUCACGAAAGAAGA
X81639.1/3363-3383   CGUGGUCUUCACGAUAGAAGA
AJ749658.1/1294-1314 CGUGGUCUUCACGAUAGAAGA
#=GC SS_cons         <<<__AAAAA>>>:::aaaaa
#=GC RF              CGUGGUCUUCACGAUAGAAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01113
#=GF ID   BMV3_UPD-PK3
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   36.00
#=GF TC   37.00
#=GF NC   33.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00156;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   7684465
#=GF RT   Contributions of the brome mosaic virus RNA-3 3'-nontranslated region to
#=GF RT   replication and translation.
#=GF RA   Lahser FC, Marsh LE, Hall TC
#=GF RL   J Virol. 1993;67:3295-3303.
#=GF WK   UPSK_RNA
#=GF **   seedtax: Viruses; unclassified sequences
#=GF SQ   2



X01678.1/2648-2670 ACUUUGGCUAAGUUUAAAAGCUU
X58459.1/659-681   ACUUUGGCUAAGGUUAAAAGCUU
#=GC SS_cons       :<<<_AAAA>>>::::::aaaa:
#=GC RF            ACUUUGGCUAAGuUUAAAAGCUU
//
# STOCKHOLM 1.0

#=GF AC   RF01114
#=GF ID   TMV_UPD-PK1
#=GF DE   Pseudoknot of upstream pseudoknot domain (UPD) of the 3'UTR
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Pseudobase
#=GF SS   Pseudobase
#=GF GA   33.00
#=GF TC   33.90
#=GF NC   31.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   PKBASE; PKB00053;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF DR   GO; 0046782; regulation of viral transcription;
#=GF RN   [1]
#=GF RM   7684465
#=GF RT   Contributions of the brome mosaic virus RNA-3 3'-nontranslated region to
#=GF RT   replication and translation.
#=GF RA   Lahser FC, Marsh LE, Hall TC
#=GF RL   J Virol. 1993;67:3295-3303.
#=GF WK   UPSK_RNA
#=GF SQ   2


Z96945.1/505-526     ACGGAUUGUGUCCGUAAUCACA
EF375551.1/6216-6237 ACGGAUUGUGUCCGUAAUCACA
#=GC SS_cons         ::<<<_AAAA>>>:::::aaaa
#=GC RF              ACGGAUUGUGUCCGUAAUCACA
//
# STOCKHOLM 1.0

#=GF AC   RF01116
#=GF ID   Yfr1
#=GF DE   Cyanobacterial functional RNA 1
#=GF AU   Voss B
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:17941988
#=GF SS   Published; PMID:17941988
#=GF GA   38.00
#=GF TC   38.30
#=GF NC   37.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17941988
#=GF RT   A motif-based search in bacterial genomes identifies the ortholog of the
#=GF RT   small RNA Yfr1 in all lineages of cyanobacteria.
#=GF RA   Voss B, Gierga G, Axmann IM, Hess WR
#=GF RL   BMC Genomics. 2007;8:375.
#=GF RN   [2]
#=GF RM   16168080
#=GF RT   Identification of cyanobacterial non-coding RNAs by comparative genome
#=GF RT   analysis.
#=GF RA   Axmann IM, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR
#=GF RL   Genome Biol. 2005;6:R73.
#=GF WK   Yfr1
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   37


BA000039.2/1862773-1862841   GCGGAGAC--ACAC--GUUUCCGUUCACUCCUCACACCACACCCCGCCUGGACAGUUAUUGGUUCGGGCGGCU-
CP000100.1/1899750-1899688   GCGGAGAC--AAAU--GUUUCCGUUCACUCCUCACACCACACUUCGCCCGGGCAAC-----GCUCGGGCG-UU-
AAVW01000068.1/4156-4092     GCGGAGAC--AGAU--GUUUCCGUUCACUCCUCACACCACACUCCGCCCGGA-CUAUU---GUCUGGGCGGUU-
BX569691.1/8565-8510         GUGCGGGC--AAU---GCCCACAC--ACUCCUCACACCCCCC--GGCCCGG--CGCGC-----UCGGGCU-UU-
CP000239.1/814199-814136     GCGGAGAC--GCAU--GUUUCCGUUCACUCCUCACACCAUCCGCCGCUCGAC-GUCGA----GUCGGGCGGUU-
BA000045.2/931736-931675     GCGGAGAC--GCAU--GUUUCCGUUCACUCCUCACACCAUGUUCCGCCCGG--UCGCU-----CCGGGCGGUU-
AANP01000004.1/175334-175390 GUGGGGGC--UUCG--GCCCACAC--ACUCCUCACACCCCCC--GGCCCGA--CGCGU-----UCGGGCU-UU-
CP000110.1/1765916-1765972   GUGCGGGC--UUCG--GCCCACAC--ACUCCUCACACCCCCC--GGCCCGG--CGCGA-----UCGGGCU-UU-
CP000393.1/5071155-5071224   --GGAGACUCUUAAGAGUUUCCCUUCACUCCUCACACCACACUCCGCCCGGA-CCUUUUUAGUUUGGGCGGUU-
CP000111.1/980239-980186     AUG-GGG---GAAA---CCC-CAU--ACUCCUCACACACUAAAUCGCCCGA--UUAU------UCGGGC--UUU
AANO01000005.1/42936-42880   GUGGGGGC--UCCG--GCUCGCAC--ACUCCUCACACCAACCC--GCCCGG--CGCGU-----CCGGGCA-UU-
CP000435.1/875873-875817     --GUGCGGG-CUUCGGCC-UACAC--ACUCCUCACACCCCCC--GGCCCGA--CGCGU-----UCGGGCU-UU-
BA000022.2/2960900-2960963   GCGGAGAC--GUAA--GUUUCCGUUCACUCCUCACACCACACUCCGCCUGGAUGAU-----GUUCGGGCGGUU-
CP000554.1/826928-826872     GUGAGGGC--UACG--GCCCACAC--ACUCCUCACAC-ACACC-GGCCCGA--CGAGC-----UCGGGCU-UU-
CP000097.1/728301-728246     GUGCGGGC--UAGC--GCCCACAC--ACUCCUCACACCCCC---GGCUCGA--CGCGU-----UCGAGCU-UU-
CP000240.1/1399746-1399809   GCGGAGAC--GCAU--GUUUCCGUUCACUCCUCACACCAUCUUCCGCUCGGC-GUCAA----GUCGGGCGGUU-
AAVU01000041.1/49291-49227   GCGGAGAC--GUAU--GUUUCCGUUCACUCCUCACACCACACUCCGCCUGGA-CUAUU---GUUCGGGCGGUU-
CP000576.1/977377-977324     AUG-GGG---GAAA---CCC-CAU--ACUCCUCACACACUAAAUCGCCCGA--UUAA------UCGGGC--UUU
CT978603.1/664633-664578     GUGCGGCG--CUU---CGCCGCAC--ACUCCUCACACCACCAC--GCCCGG--CGAGC-----CCGGGU--UUU
CT971583.1/1467225-1467281   GUGCGGGC--GUAU--GCCCACAC--ACUCCUCACACCCCCC--GGCCCGA--CGCGU-----UCGGGCU-UU-
CP000117.1/3283425-3283489   GCGGAGAC--GCAU--GUUUCCGUUCACUCCUCACACCACACUCCGCCCGGA-CUACU---GUUCGGGCGGUU-
CP000552.1/1002151-1002098   AUG-GGG---GAAA---CCC-CAU--ACUCCUCACACACUAAAUCGCCCGA--UUUA------UCGGGC--UUU
AADV02000124.1/3571-3634     GCGGAGAC--AAAC--GUUUCCGUUCACUCCUCACACCACACUCCGCCCGG--CAUUA---GUUCGGGCGGUU-
AAUA01000001.1/164327-164383 GUGCGGGC--CUCU--GCUCGCAC--ACUCCUCACACCCCCC--GGCCCGG--CGCGA-----UCGGGCU-UU-
AACY020227538.1/1465-1409    GUGCGAGC--CUUG--GCUCACAC--ACUCCUCACACCCCCU--GGCCCGA--CGCGU-----UCGGGCU-UU-
AACY024060802.1/260-316      GUGCGGGC--CUAG--GUCCACAC--ACUCCUCACACCCCCC--GGCCCGA--CGAGC-----UCGGGCU-UU-
AACY020831335.1/308-365      GUGCGGGCC-CCUG--GCCCUCAC--ACUCCUCACACCCCCU--GGCCCGG--CGCGU-----CCGGGCU-UU-
AACY020103989.1/439-386      AUGGGGGA--------UUCCCCAU--ACUCCUCACACACUAAAUCGCCCGA--UUAA------UCGGGCU-UU-
AACY022240010.1/143-197      GUGUGGCU--UC----GGCCUCAC--ACUCCUCACACCACCC--CGCCCGG--CGCGC-----CCGGGCU-UU-
AACY022959795.1/142-197      GUGCGGCU--UUA---CGCCGCAC--ACUCCUCACACCACCA--CGCCCGG--CGCGC-----CCGGGUU-UU-
AACY020153858.1/1667-1614    AUGGGG----UUAU----CCCCAU--ACUCCUCACACACUAAAUCGCCCGA--UUAA------UCGGGCU-UU-
AACY021641331.1/457-511      AUGGGG-----GAA--AACCCCAU--ACUCCUCACACACUAAAUCGCCCGA--UUAA------UCGGGCU-UU-
AACY023914069.1/155-103      AUGGGG----GAAA----CCCCAU--ACUCCUCACACAAUAAU-CGCCCGA--UUUA------UCGGGCU-UU-
AACY023854694.1/865-917      AUGGGG----GAAA----CCCCAU--GCUCCUCACACACAAAU-CGCCCGA--UUUA------UCGGGCU-UU-
CP000095.2/1191112-1191170   GUGAGAGC--CUUU--GCUCUCAC--ACUCCUCACACUUAAAAAUGCCCGA--CUUGU-----UCGGGUU-UU-
BX548174.1/1000797-1000744   AUG-GGG---GAAA---CCC-CAU--ACUCCUCACACACCAAAUCGCCCGA--UUUA------UCGGGC--UUU
CP001037.1/6896974-6896910   GCGGAGAC--AAAU--GUUUCCGUUCACUCCUCACACCACACUCCGCCCGGA-CUACU---GUUCGGGCGGUU-
#=GC SS_cons                 <<<<<<<<..____..>>>>>>>>..------------------<<<<<<<.._____.....>>>>>>>.::.
#=GC RF                      guGgGggc..uuAu..gccCcCac..ACUCCUCACACCaCAcuccGCCCGa..cuugu.....uCGGGCg.UU.
//
# STOCKHOLM 1.0

#=GF AC   RF01117
#=GF ID   ciona-mir-92
#=GF DE   Ciona microRNA mir-92
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   101.40
#=GF NC   39.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000509;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20370911
#=GF RT   miRTRAP, a computational method for the systematic identification of
#=GF RT   miRNAs from high throughput sequencing data.
#=GF RA   Hendrix D, Levine M, Shi W
#=GF RL   Genome Biol. 2010;11:R39.
#=GF WK   MicroRNA
#=GF SQ   2


AACT01001449.1/20206-20286   GUAUCAAUAUGCCUAGACCAGACAAAGUGUAUUGCGUUGUUGCAAUCGUAUUGCACUUGUCCCGGUCUAAGCAUUUGGUAA
AABS01000020.1/506273-506353 GUACCUGCAUACUUAGGCCUGGCGAAGUGCAUUGCGUUGUCAUGGUCGUAUUGCACUCGUCCCGGUCUAUGUAUCUGGUAA
#=GC SS_cons                 :<<<<<<-<<<<-<<<<<<-<<<<<-<<<<<-<<<<<<_____>>->>>>->>>>>>>>>>-->>>>>>->>>>>>>>>>:
#=GC RF                      GuacCaguaugCuuaGaCCaGaCgaAGuGcaUugCGuuGUuauaaUCGuaUugCaCucGuCCCGGuCuaaGcaucuGguaA
//
# STOCKHOLM 1.0

#=GF AC   RF01119
#=GF ID   sR32
#=GF DE   Small nucleolar RNA sR32
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   50.70
#=GF NC   35.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987815
#=GF RT   The Cm56 tRNA modification in archaea is catalyzed either by a specific
#=GF RT   2'-O-methylase, or a C/D sRNP.
#=GF RA   Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A
#=GF RL   RNA. 2005;11:1051-1063.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ248283.1/67950-68006     AGAAAUGAUGAGCUUGGCCGCUACCCGAUCGAUGAGGGU-UAAACUCCGGUGCUGAUC
BA000001.2/58901-58957     GGAGAUGAUGAGCUUGGCCGCUACCCGAGUGAUGAGGGC-CAAACUCCGGUGCUGAUC
AE009950.1/1886961-1886904 UGAGAUGAUGAGCUUGGCCGCUUCCCGAGUGGUGAGGGUCUAAACUCCGGUGCUGAUG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::.::::::::::::::::::
#=GC RF                    uGAGAUGAUGAGCUUGGCCGCUaCCCGAguGaUGAGGGu.uAAACUCCGGUGCUGAUc
//
# STOCKHOLM 1.0

#=GF AC   RF01120
#=GF ID   sR33
#=GF DE   Small nucleolar RNA sR33
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.60
#=GF NC   35.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.37 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10736225
#=GF RT   Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs:
#=GF RT   lessons from the Pyrococcus genomes.
#=GF RA   Gaspin C, Cavaille J, Erauso G, Bachellerie JP
#=GF RL   J Mol Biol. 2000;297:895-906.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3



BA000023.2/582159-582106   UCGCAUGAUGUGGAAUCCGGGAACUGA--CUGUGAUGAAAUGCGCGAGCACUGAGU
BA000001.2/1623026-1622971 UGACGUGAUGAGGAAUCGGGGAGCUGAAGCUAUGAUGAGAUCCGCCAACGCUGAUU
AE009950.1/1754536-1754482 AUGUAUGAUGAGGAAUCGGGGAGCUGA-GAUGUGAUGAAAUCCAUCAGAGCUGACU
#=GC SS_cons               :::::::::::::::::::::::::::.::::::::::::::::::::::::::::
#=GC RF                    uuGcaUGAUGaGGAAUCgGGGAGCUGA.GcUGUGAUGAaAUcCGccAGcGCUGAuU
//
# STOCKHOLM 1.0

#=GF AC   RF01121
#=GF ID   sR38
#=GF DE   Small nucleolar RNA sR38
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   69.60
#=GF NC   35.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


BA000001.2/1016391-1016333 GUAGGCGAUGAUUUGACUCCGGAAAAGCUGAAUGAUGAUGAAGUCCAGCCCGAAUGAGC
AJ248286.2/158357-158415   AUAGGCGAUGAUUUGACUCCGGAAAAGCUGAGCGAUGAUGAAGUCCAGCCCGAAUGAGC
AE009950.1/998550-998608   GGAGGCGAUGAUUUGACUCCGGAAAAUCUGAUCGAUGAUGAAGUCCAGCCCGAAUGAGC
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GuAGGCGAUGAUUUGACUCCGGAAAAgCUGAucGAUGAUGAAGUCCAGCCCGAAUGAGC
//
# STOCKHOLM 1.0

#=GF AC   RF01122
#=GF ID   sR39
#=GF DE   Small nucleolar RNA sR39
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   65.40
#=GF NC   33.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987815
#=GF RT   The Cm56 tRNA modification in archaea is catalyzed either by a specific
#=GF RT   2'-O-methylase, or a C/D sRNP.
#=GF RA   Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A
#=GF RL   RNA. 2005;11:1051-1063.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AJ248284.1/236815-236761   GGCGAUGAAGAAAAUUUCGCUAGCUGAAAAGU-----GAUGAGUACCCUCGCAACUGAGC
BA000001.2/1411664-1411723 GGUGAUGAGGAAAAUUUCGCUAGCUGAAGUGAAAGAUGAUGAAUACCCUCGCAACCGAGC
AP006878.1/832424-832370   GGCGAUGACGACAAUUUCGCUAGCUGACCGGU-----GAUGACUACCCUCGCAACCGAGC
DQ516907.1/5418-5363       GGCGAUGAUGACAAUUUCGCUAUCUGAUUCUG----UGAUGACUACUCCCGCAGCUGAGC
M97860.2/1902-1843         GGCGAUGAAGAUAAUUUCGCUAGCCGAAAAAUAAGAUGAGGAGUACCCUCGCAACUGAGC
#=GC SS_cons               ::::::::::::::::::::::::::::::::....::::::::::::::::::::::::
#=GC RF                    GGCGAUGAaGAaAAUUUCGCUAGCUGAaaagu....UGAUGAgUACCCUCGCAACuGAGC
//
# STOCKHOLM 1.0

#=GF AC   RF01123
#=GF ID   sR35
#=GF DE   Small nucleolar RNA sR35
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   74.60
#=GF NC   37.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.00 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3



CP002372.1/138861-138916 AUUGAUGAUGAAUACGGGGCCACCUGAGUGAUGAUGAAAUUUC-CCCAAUGCUGAUA
BA000001.2/902264-902320 AAAAAUGAUGAGUACGGGGCCACCUGAGCGGUGAUGAGGUUUCUCCCAAGUCUGAUU
AJ248286.2/41891-41835   UAAAAUGAUGAGUACGGGGCCACCUGAAUGGUGAUGAGGUUUCUCCCAAGGCUGAUU
#=GC SS_cons             :::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  aaaaAUGAUGAGUACGGGGCCACCUGAGUGGUGAUGAGGUUUCUCCCAAggCUGAUu
//
# STOCKHOLM 1.0

#=GF AC   RF01124
#=GF ID   sR36
#=GF DE   Small nucleolar RNA sR36
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   72.50
#=GF NC   32.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.16 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11359559
#=GF RT   A guided tour: small RNA function in Archaea.
#=GF RA   Dennis PP, Omer A, Lowe T
#=GF RL   Mol Microbiol. 2001;40:509-519.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AJ248287.2/214684-214738   GUGGAUGAGGAGAGGGUAGGUAGCUGAG----UUAUGAUGAACUAAUCGGCCCCCGACA
BA000001.2/530081-530027   GUGGAUGAAGAGAGGGUAGGUAGCUGAU----CUGUGAUGAACUAAUCGGCCCCUGACA
AP006878.1/1829976-1829923 GGGGAUGAUGUGAGGGUAGGUGGCUGAG----AAGUGAUGACCUAAUCGGCC-CUGACC
DQ223723.1/12457-12515     UGGGAUGAUGUGAGGGUAGGUGGCCGAGAGACCGAUGAGGAGCUAAUCGGCCCCUGACC
AE009950.1/329170-329116   GUGGAUGAAGAAAGGGUAGGUAGCUGAG----CGGUGAUGAUCUAAUCGGCCCCUGACA
#=GC SS_cons               ::::::::::::::::::::::::::::....:::::::::::::::::::::::::::
#=GC RF                    GuGGAUGAuGaGAGGGUAGGUgGCUGAG....cgGUGAUGAaCUAAUCGGCCCCUGACa
//
# STOCKHOLM 1.0

#=GF AC   RF01125
#=GF ID   sR4
#=GF DE   Small nucleolar RNA sR4
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   78.30
#=GF NC   34.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.10 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3



CP000077.1/2217166-2217111 GUUGAUGAGCACAUUCUUUUCUGAUUUAAUGAAGAAAGUGGCCAGGUCUGAGGUAG
AF195098.1/1-56            GUUGAUGAGCACAUUCUUUUCUGAUUUAAUGAAGAAAGUGGCCAGGUCUGAGGUAG
ADKL01000252.1/892-837     CUUGAUGAGUACACUCUUUGCUGAUUCAAUGAGGAGAGUGGCCAGGGCUGAAGAGG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    gUUGAUGAGcACAuUCUUUuCUGAUUuAAUGAaGAaAGUGGCCAGGuCUGAGGuaG
//
# STOCKHOLM 1.0

#=GF AC   RF01126
#=GF ID   sR41
#=GF DE   Small nucleolar RNA sR41
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   54.00
#=GF TC   57.60
#=GF NC   53.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.10 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987815
#=GF RT   The Cm56 tRNA modification in archaea is catalyzed either by a specific
#=GF RT   2'-O-methylase, or a C/D sRNP.
#=GF RA   Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A
#=GF RL   RNA. 2005;11:1051-1063.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


CP001463.1/675109-675057   GCGGAUGAUGAUGAAUCAAACCUGAU-UGAUGAAGAGCCCUAUGAGCGCUGACG
CP002565.1/1609578-1609526 GCCGAUGAUGAUCGAGCUGUUCUGAG-UGGUGAUGAGCCCUAUGAGUCCUGAGG
BA000001.2/630833-630885   GCGGAUGAUGAAGGCUAAUUUCGGAU-UGGUGAAGAGCCCUAUGAGCGCUGACG
AJ248287.2/97964-97912     GCGGAUGAUGAGCUAGUAAUUCUGAG-CGAUGAAGAGCCCUAUGAGCGCUGACG
AE009950.1/1155596-1155544 ACGGAUGAUGAAAUGUAAAGACGGAA-AGAUGAAGAGCCCUAUGAGCGCUGACG
CP003117.1/1641606-1641553 GCCGAUGAAGAGAAGAGUUCGCUGAUCCGAUGAUGAGCCCUAUGAGUCCUGAGG
CP000477.1/1557383-1557435 GCCGAUGAUGACACCAGGUCUCUGAA-AUGUGAUGAGCCCUAUGAGUUCUGAGG
#=GC SS_cons               ::::::::::::::::::::::::::.:::::::::::::::::::::::::::
#=GC RF                    GCgGAUGAUGAuauaugauuuCUGAu.uGaUGAaGAGCCCUAUGAGcgCUGAcG
//
# STOCKHOLM 1.0

#=GF AC   RF01127
#=GF ID   sR42
#=GF DE   Small nucleolar RNA sR42
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   38.00
#=GF TC   38.50
#=GF NC   34.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ248284.1/107848-107786   UAUGGUGAUGAUCUUCACGGUACCCUGAG--AGACCCUCGAUGAUGAGCCCCCUCUCAACUGACC
BA000001.2/1615276-1615214 UGUGAUGAUGAUCUUCACGGUACCCUGAG--AGGCGCUCGAUGAUGAGCCCCCUCUCAACUGAUC
AE009950.1/1747694-1747630 CUUGAUGAUGAACUUCACGGUACCCUGAGUUCUAAAAACGAUGAUGAGCCCCCUCUCGUCUGAUU
#=GC SS_cons               :::::::::::::::::::::::::::::..::::::::::::::::::::::::::::::::::
#=GC RF                    uuUGaUGAUGAuCUUCACGGUACCCUGAG..agacacuCGAUGAUGAGCCCCCUCUCaaCUGAUc
//
# STOCKHOLM 1.0

#=GF AC   RF01128
#=GF ID   sR43
#=GF DE   Small nucleolar RNA sR42
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   58.50
#=GF NC   35.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.19 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


BA000001.2/236067-236012   UGA-GAUGAAGAAAAAGCACCUCCACUGAG-------U-----GA-UGAUGACACGCCCACGGUCUGAUC
AJ248283.1/250988-250933   GGA-GAUGAAGAGAAAGCACCUCCACUGAU-------U-----GA-UGAUGAAACGCCCACGGUCGGAUU
AE009950.1/1805498-1805554 GGACGAUGAAGAGAAAGCACCUCCACGGAU-------A-----GA-UGAAGAAACGCCCACGGACUGAGU
CP001463.1/1593382-1593322 GCA-GAUGAGGAGAAAGCACCUCCACUGAG-------UAUUGCGA-UGAAGAUACGCCCACGACCUGAUG
CP001398.1/582989-582925   GGACGAUGACGAGAAAGCACCUCCACUGAGACCGGCGU-----GAGUGCUGAGACGCCCACGGUCGGAGU
AP006878.1/1593134-1593070 GGACGAUGAGGAGAAAGCACCUCCUCUGAGACCGGCGU-----GAGUGCUGAGACGCCCACGGUCUGAGU
#=GC SS_cons               ::::::::::::::::::::::::::::::.......:.....::.::::::::::::::::::::::::
#=GC RF                    GGACGAUGAgGAGAAAGCACCUCCACUGAG.......U.....GA.UGauGAgACGCCCACGGuCuGAgu
//
# STOCKHOLM 1.0

#=GF AC   RF01129
#=GF ID   sR44
#=GF DE   Small nucleolar RNA sR44
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   59.80
#=GF NC   36.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ248285.1/36404-36458     GGCAAUGAUGAAAUCGGUCUUGUCCGAG-GAGUGAUGAUAGUGGUCACCGCUGAGC
X59857.1/407-462           GGCUAUGAGGAAAUCGGUCUUAGCUGAGCUUAUGAUGAAAGUGGUCACCGCCGAGC
BA000001.2/1327988-1327934 GGCGAUGAGGAGAUCGGUCUUGUCUGAA-GAAUGAUGAAAGUGGUCACCGCUGAGC
#=GC SS_cons               ::::::::::::::::::::::::::::.:::::::::::::::::::::::::::
#=GC RF                    GGCuAUGAgGAaAUCGGUCUUGuCuGAG.gaaUGAUGAaAGUGGUCACCGCuGAGC
//
# STOCKHOLM 1.0

#=GF AC   RF01130
#=GF ID   sR46
#=GF DE   Small nucleolar RNA sR46
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   69.80
#=GF NC   33.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AJ248283.1/57376-57436     GGCAAUGAGGAAUGAAUCCAAUGCUGAGCAAAGGCAAUGAUUGACCCCAGAGUGGCCGAGC
BA000001.2/49019-49079     GGCAAUGAGGAAUGAAUCCAAUGCUGAGCUUAGGCAAUGAUUGGCCCCAGAGUGGCCGAGC
AE009950.1/9297-9237       GGCGAUGACGACUGAAUCCAAUGCUGAGCAAAGGCGAUGAUUGGCCCCAGAGUGGCUGAGC
AP006878.1/87729-87781     CGCGAUGAUGAGUGAAUCCAAUGCUGAUGA-----GAUGAUGAGCCCCAAAC---CUGAGC
CP000855.1/6375-6323       UGCGAUGAUGAGUGAAUCCAAUGCUGACGG-----GAUGAUGAACCCCGAAC---CUGAGC
CP002372.1/1418715-1418660 UGCGAUGAUGAAUGAAUCCAAUGCUGAACU-----GAUGAUUGACCCCAGAGUGGCUGAGC
CP002952.1/765075-765127   CGCGAUGAUGAGUGAAUCCAAUGCUGACGG-----GAUGAUGAACCCCAAAC---CUGAGC
#=GC SS_cons               :<<---<<<______>>>---->>::::::.....::::::::::::::::::::::::::
#=GC RF                    gGCGAUGAuGAaUGAaUCCAAUGCUGAgca.....GAUGAUugaCCCCAgAgUGGCUGAGC
//
# STOCKHOLM 1.0

#=GF AC   RF01131
#=GF ID   sR47
#=GF DE   Small nucleolar RNA sR47
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   36.40
#=GF TC   37.50
#=GF NC   35.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.55 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


BA000001.2/266350-266296   ACCGAUGA-AGAGCCUUUUGGGCCCUGA-GAGAUGAUGAAAGCCCCCCUAU-CUGAGG
AJ248288.1/153186-153240   GAUGAUGA-AACUCCUUUCGGGCACUGA-UCCGUGAUGAAGGCCCUCCUAU-CUGAGC
D88253.1/2344-2290         GAUGAUGA-AGAACCUUUCGGGCCCUGA-UGGAUGAUGGAGGCCUCCCUAU-CUGAGG
L22346.1/2711-2655         GCCGAUGAGGGAGUCUUUCGGGCCCUGA-UUGGUGAUGAGGGCCUCCCUAUCCCGAGG
AJ248286.2/52940-52994     UCCGAUGA-GGAGCGAGCCCGGCCCUGA-GCGAUGAUGAGAGCUACCACUA-CUGAGG
BA000001.2/1117042-1116988 GCCGAUGA-GGAACGAGCCCGGCCCUGA-AGGAUGAUGAAAGCUACCACUA-CUGAGG
AE009950.1/893919-893864   GCCGAUGA-AGAGCGAGCCCGGCCCUGAGGAGAUGAUGAAAGCUACCACUU-CUGAGG
CP001857.1/353158-353105   GCCGAUGA-UGAGCUAAUCCGCCACUGA-GCGGUGAUGAGGGCCAC-GGAU-CUGAGG
#=GC SS_cons               ::::::::.:::::::::::::::::::.::::::::::::::::::::::.::::::
#=GC RF                    GCCGAUGA.aGAGCcuuUCgGGCCCUGA.gcGaUGAUGAAGGCCaCCcuAU.CUGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01132
#=GF ID   sR48
#=GF DE   Small nucleolar RNA sR48
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   47.50
#=GF NC   33.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987815
#=GF RT   The Cm56 tRNA modification in archaea is catalyzed either by a specific
#=GF RT   2'-O-methylase, or a C/D sRNP.
#=GF RA   Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A
#=GF RL   RNA. 2005;11:1051-1063.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AJ248287.2/274259-274205 CUCGAGGAUG---AUCCCACCCUUGGCUGAAGUGUGAUGAUGUCUCGU-GGUUCUGAGA
X79777.1/10-68           CUUCUUGAUGUGGAACCCACCCUUGGCUGAAUGAUGAUGAGGCCUCGUGGGUUCCGAAG
#=GC SS_cons             :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  CUuguuGAUGUGGAuCCCACCCUUGGCUGAAuggUGAUGAgGuCUCGUGGGUUCuGAgg
//
# STOCKHOLM 1.0

#=GF AC   RF01133
#=GF ID   sR3
#=GF DE   Small nucleolar RNA sR3
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   41.00
#=GF TC   42.10
#=GF NC   40.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.87 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   19


BA000001.2/535542-535480   A----U---AGGCGAUGAUGA-GC------UCCAUCCCUACCUGAGUUG--------------------UGAUGAA-UGUAGCGCGCUCUGA-----GCAACC-
AJ248287.2/209210-209272   AA-AGG---C---GAUGAUGA-GC------UCCAUCCCUAUCUGAGUUG--------------------UGAUGA-CUGUAGCGCGCUCUGA-----GCUACA-
L77117.1/260391-260453     A----UCGCC---AAUGAUGA-CGAUUGGCUU-------UGCUGAGUCUG-------------------UGAUGAACCGU-AUGAGCACUGA-----GGCGAU-
Y18930.1/78510-78450       -CGGGG---A---AAUGAUGA------GGGUUCC---AGAGCUGAAGCG--------------------UGAUGAAUGGU-UGACACGCUGACCCCG------C
BA000001.2/1099694-1099748 G----G---C---GAUGAUGA-AUAGCAAGCC-------AGCUGAAGAG--------------------UGAUGAAGUGA-ACACCCCCUGA-----G-----C
L77117.1/467007-466953     G----G---C---AAUGAUGA-AAAGAGGGUU-------AGCUGAACUG--------------------UGAUGAUACUU-ACCCGAACUGA-----G-----C
AJ248286.2/84133-84079     G----G---C---GAUGAUGA-GUAGCAAGCC-------ACCUGACCUA--------------------UGAUGAGGUGAACA-CCCCCUGA-----G-----C
AE000782.1/2141683-2141629 C----G---G---CGUGAUGA-UUGACGGGUC-------UGCUGAGCGG--------------------UGAUGACCCGU-UGGAGCUCUGA-----C-----C
AY047491.1/12-66           C----G---G---UGUGAUGA-CCAAUGGGUC-------UGCUGAAGUG--------------------UGAUGACCCGU-UGGAGCUCUGA-----C-----C
CP000254.1/1849259-1849314 G----C---A---GAUGAUGA-CAAAUGGGUC-------UUCUGAUUUGG-------------------UGAUGAUCCGU-UGGAGCACUGA-----U-----G
CP000780.1/742645-742701   G----C---A---GAUGAUGA-ACAAUGGGUC-------UGCUGAAAUUG------------------AUGAUGACCCGU-UGGAGCACUGA-----U-----G
CP000559.1/1002954-1003010 G----C---G---UAUGAUGAACUAUCGGGUC-------UACUGAUUUGA-------------------UGAUGACCCGC-UGGAGCACUGA-----U-----C
CP000562.1/1074852-1074794 G----C---A---CGUGAUGA-ACAAUGGGUC-------UCCUGACGAACG----------------GAUGAUGACCCGU-UGGAGCACUGA-----U-----G
CP000300.1/175892-175966   A----U---A---AAUGAUGA-ACAACGGGUC-------UACUGAGAUCUGCUCGACGGAGUGGGUCGGUGAAGAGCCGU-UGGAGCACUGA-----U-----G
CP000477.1/799971-800043   C----U---G---GAUGAUGA-GCAACGGGUC-------UGCUGAGCCAUCCCGACGG--GGAUGGUGUUGAUGAUCCGU-UGGAGCACUGA-----G-----A
AM114193.2/215332-215260   A----A---A---UAUGAUGA-GCAACGGGUC-------ACCUGAAGCUGCCCGACGG--GGUAGCUUGUGAGGAACCGU-UGGAGCGCUGA-----U-----U
CP000099.1/1909489-1909415 A----U---A---AAUGAUGA-ACAACGGGUA-------UACUGAAUCUUUCCCGACGGGGCAAGAUAAUGAGGAACCGU-UGGAGCACUGA-----U-----A
AE008384.1/2153609-2153535 A----U---A---AAUGAUGA-ACAACGGGUC-------UACCGAGUCUUUCCCGACGGGGCAGGACAAUGAGGAACCGU-UGGAGCACUGA-----U-----A
AE009950.1/1226581-1226635 G----G---C---GAUGAUGA-AUAGCAAGCC-------ACCUGAAGAG--------------------UGAUGAGGUGA-ACACCCCCUGA-----G-----C
#=GC SS_cons               :....:...:...::::::::.::::::::::.......::::::::::....................:::::::::::.:::::::::::.....:.....:
#=GC RF                    a....g...a...aAUGAUGA.acAaCGGGUC.......agCUGAguug....................UGAUGAaCCGU.UGGAGCaCUGA.....G.....c
//
# STOCKHOLM 1.0

#=GF AC   RF01134
#=GF ID   sR30
#=GF DE   Small nucleolar RNA sR30
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   38.00
#=GF TC   41.30
#=GF NC   33.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


BA000001.2/963521-963465   GUGGAUGAUGAGUAGUCGGAAGGCUGAGCUGAUGAUGAAGGACGCCCAUGUCUGAUC
AJ248285.1/293100-293155   GUGGAUGAUGAUUAGUCGGAAGGCUGAAGUG-UGAUGAAGGACGCCCAUGGCUGAAC
AE009950.1/1035617-1035561 GUGGAUGAUGAGUAGUCAGAAGGCUGAGUUGAUGAUGAAGGACGCCCACGCCUGACU
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GUGGAUGAUGAgUAGUCGGAAGGCUGAGuUGAUGAUGAAGGACGCCCAuGuCUGAuc
//
# STOCKHOLM 1.0

#=GF AC   RF01135
#=GF ID   sR24
#=GF DE   Small nucleolar RNA sR24
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   36.00
#=GF TC   37.80
#=GF NC   35.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ248286.2/118705-118759   CCCUAUGAUGAGAGAGCUGUUAAAUGAUUGAUGAUUAGAGGAUGGCUGGCUGAGG
BA000001.2/1057034-1056980 CCCUAUGAUGAGAGAGCUGUUAAAUGAGCGGUGAUUAAAGGAUGGCUGGCUGAGG
AE009950.1/823496-823550   CCCUAUGAUGAGAGAGCUGUUAAAUGAGUGGUGAUUAGAGGAUGGCUGGCUGAGG
#=GC SS_cons               <<___________________________________________________>>
#=GC RF                    CCCUAUGAUGAGAGAGCUGUUAAAUGAgUGgUGAUUAgAGGAUGGCUGGCUGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01136
#=GF ID   sR28
#=GF DE   Small nucleolar RNA sR28
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   40.40
#=GF NC   37.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11359559
#=GF RT   A guided tour: small RNA function in Archaea.
#=GF RA   Dennis PP, Omer A, Lowe T
#=GF RL   Mol Microbiol. 2001;40:509-519.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


BA000001.2/1484845-1484791 AGGAAUGAUGACCGGUUUCGGGACUGAACGAUGAUG-ACACCAGCUAUCGCUGACC
AF254825.1/1-53            --GGAUGAUGACCGGUUUCGGGACUGAGCUAUGAUG-ACACCAGCUAUCGCUGACU
CP000077.1/808273-808328   GUUCAUGAUGAGCUUGACCGGGAAUGAAUGGUGAUGUAAAGGCACGUGUGCUGAUU
U95207.1/9-63              GCCGAUGAUGAGUGGCUUCGGGUCCGAGGGGUGAGG-ACACCAGCUAUCGCUGAGG
AP006878.1/558878-558824   GCCCGUGAUGAGUGGCUUCGGGUCCGAGCGGUGAGG-ACACCAGCUAUCGCUGAGG
DQ202294.1/425-479         AGAGAUGAUGACCGGUUUCGGAUCCGAUGGAUGAGG-ACAUCAGCUAUCGCUGAUC
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::.:::::::::::::::::::
#=GC RF                    GuugAUGAUGAgCGGuUUCGGGaCuGAgcGGUGAuG.ACAcCAGCUAUCGCUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF01137
#=GF ID   sR21
#=GF DE   Small nucleolar RNA sR21
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   63.60
#=GF NC   31.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11359559
#=GF RT   A guided tour: small RNA function in Archaea.
#=GF RA   Dennis PP, Omer A, Lowe T
#=GF RL   Mol Microbiol. 2001;40:509-519.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


BA000002.3/277650-277585   GGGAGUGAUGAGGGUUAAAAGCGC-CGACUCUGGGUAGCAUGGGGAAGGCCAGGACAGCUGACCAUA
CP000077.1/1993127-1993062 AAGACUGAUGAUGAUUUUCACUGGGCAGGGCAAGAUUG-AUGAUUGAGCCCUGGAUAACUGAUUAUG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    ggGAgUGAUGAgGgUUuuaAguGgGCggggCugGgUuGCAUGggggAGgCCuGGAuAgCUGAuuAUg
//
# STOCKHOLM 1.0

#=GF AC   RF01138
#=GF ID   sR23
#=GF DE   Small nucleolar RNA sR23
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   57.90
#=GF NC   36.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.00 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987815
#=GF RT   The Cm56 tRNA modification in archaea is catalyzed either by a specific
#=GF RT   2'-O-methylase, or a C/D sRNP.
#=GF RA   Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A
#=GF RL   RNA. 2005;11:1051-1063.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6



CP002952.1/1713086-1713138 GGAUGAUGACUCUGGAGCCCCCUGA-UCUGUGAAGA-GGUUUCGCGGGGCUGACC
CP002779.1/1194791-1194843 GGAUGAUGAGUCUGGAGCCCCCCGA-GUUGUGAGGA-GAACUUGCGGGGCUGACC
AJ248288.1/156856-156803   AGAUGAUGAAUCUGGAGCCCCCUGA-GUGAUGAUGAGCAGUCUGCGGAGCUGAUA
BA000001.2/262667-262720   AGAUGAUGAAUCUGGAGCCCCCUGA-UCGGUGAUGAUCAGUCUGCGGAGCUGAUA
AP006878.1/1371731-1371783 GGAUGAUGAGUCUGGAGCCCCCUGA-GAGGUGAAGA-GGUUUCGCGGGGCUGACC
AE009950.1/278287-278341   GAAUGAUGAAUCUGGAGCCCACUGAUUUAAUGAUGACCUGUUCGCGGGGCUGAUG
#=GC SS_cons               :::::::::::::::::::::::::.:::::::::::::::::::::::::::::
#=GC RF                    GGAUGAUGAaUCUGGAGCCCCCUGA.uugGUGAuGAugagUUcGCGGGGCUGAuc
//
# STOCKHOLM 1.0

#=GF AC   RF01139
#=GF ID   sR2
#=GF DE   Small nucleolar RNA sR2
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   42.00
#=GF TC   48.90
#=GF NC   41.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.00 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


AE000782.1/2111100-2111040 AUAGGUGAUGAAUCUAGCAGGAUCUGA-GCCGUGGCGAUGAUGACGGCUGUACUCUCUGAUU
L77117.1/22583-22529       GCGGAUGAUGAACGGAGUAGCUGCUGA-GCUAUGAUGA--UUGAUGGGCGAA----CUGACG
CP000745.1/387458-387404   GUGGAUGAUGAACGGAGUAGCUUCUGA-UUUAUGAUGA--AAGAUGGGCGAG----CUGACA
CP000743.1/1513977-1513922 GUGGAUGAUGACCGGAGUAGCUUCUGACUUUGUGAUGA--AAGAUGGGCGAG----CUGACA
CP000077.1/1212722-1212774 UAUUGUGAUGAGAG--AAUAUAUCUGA-ACGGUGAAGAAGUGGA--GCGACU----CUGAGG
BA000023.2/1235481-1235429 CCAUGUGAUGAAAA--AAAUUAGCAGA-UUGGUGAAGAAGUGGA--GCGACU----CUGAGG
CP000682.1/1630929-1630876 UAUAGUGAUGAAAG-GGAUUUAGCCGA-GUAGUGAGGAAGUGGA--GCGACU----CUGAGG
AE006641.1/755722-755775   UGUUGUGAUGAAAG-GGAAAGAUCAGA-UCUGUGAAGAAGUGGA--GCGACA----CUGAGG
#=GC SS_cons               :::::::::::::::::::::::::::.::::::::::::::::::::::::....::::::
#=GC RF                    uuggGUGAUGAAaGgAGaAguAUCUGA.ucuGUGAuGAAGugGAUGGCgGca....CUGAgg
//
# STOCKHOLM 1.0

#=GF AC   RF01140
#=GF ID   sR20
#=GF DE   Small nucleolar RNA sR20
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   44.60
#=GF NC   41.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


CP000077.1/458753-458807   UUUAAUGAUGAAAAGAGGGUCGCAUGAU---AGAUGAUGACCGCUGGAAAUA---CUGAAA
BA000001.2/1401921-1401976 GGCGAUGAUGAGGCCUCGAUUGGCUGAAU--CGAUGAUUG--AGAGGGACU-UGGCUGAGC
AJ248284.1/246620-246563   CGCGAUGAUGAAGCCUCGAUUGGCUGAAUCGCGAUGAUUG--GGAGGGACU-UGGCCGAGC
CP000682.1/117691-117745   AUCAGUGAUGAGAAGAGGGUCGUAUGAUU--AG-UGAUUAGCGCUGGAAAUU---CUGAAA
BA000023.2/418330-418276   UUUGAUGAUGAUAAGAGGGUCGAAAGAU---CGAUGAUAUACGCUGGAAAAA---CUGAUU
AE009950.1/1484450-1484505 AGCAAUGAUGAAGCCUCGAUUGGCUGAUU--UGAUGAUUG--GGAGGGACU-UGGCUGAGC
#=GC SS_cons               :<<__________________________.._____________________...____>>
#=GC RF                    ugcgAUGAUGAaaagagGaUuGgaUGAUU..cGAUGAUUgaCGguGGaAaUA...CUGAgc
//
# STOCKHOLM 1.0

#=GF AC   RF01141
#=GF ID   sR18
#=GF DE   Small nucleolar RNA sR18
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   53.70
#=GF NC   39.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AF195112.1/1-54            AAGUGAUGACAGAACCCCGGCUUGAA--AGAUGAUAGAGCCGUGUGAG-AACUGAUC
AF254834.1/5-60            UGAUGAUGAUACAGCCAGGACCCUGAUGGGAUGAU-GAGUGGUGGGCUUAGCUGAUG
BA000001.2/1131168-1131223 UAAUGAUGAAACAGCCAGGACCCUGAUGGGAUGAU-GAGUGGUGGGCUUAGCUGAUG
BA000023.2/2234271-2234324 AGAUGAUGACUGAACCCCGGCUAGAU--CGAUGAUAUAGCCGUGUGAG-AGCUGAUU
AE009950.1/808508-808453   UGAUGAUGAAACAGCCAGGACCCUGAUGAGAUGAU-GAAUGGUGGGCUUAGCUGACG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::.:::::::::::::::::::::
#=GC RF                    uGAUGAUGAcAcAGCCagGgCccuGAUGaGAUGAU.GAGugGUGgGcuUAGCUGAUg
//
# STOCKHOLM 1.0

#=GF AC   RF01142
#=GF ID   sR19
#=GF DE   Small nucleolar RNA sR19
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   59.50
#=GF NC   33.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ248284.1/214425-214363   GCAUAUGAUGAGCUUUCCCUACGGCCCGAGC-UCACGCGAUGAGGAAUACAGCCAGGGCUGAUU
BA000001.2/1433294-1433356 GCUCGUGAUGAGCUUUCCCUACGGCCCGAGC-UUAGGCGAUGAGGAAUACAGCCAGGGCUGAUU
AE009950.1/1520328-1520391 GCUUAUGAUGAACUUUCCCUACGGCCUGAGCGUCACGCGAUGAGGAAUACAGCCAGGGCUGAUG
#=GC SS_cons               :::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::
#=GC RF                    GCuuaUGAUGAGCUUUCCCUACGGCCcGAGC.UcAcGCGAUGAGGAAUACAGCCAGGGCUGAUu
//
# STOCKHOLM 1.0

#=GF AC   RF01143
#=GF ID   sR16
#=GF DE   Small nucleolar RNA sR16
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   79.10
#=GF NC   33.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.83 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2



CP000077.1/2196893-2196945 GAAUGAAGACGUUCCACCCGAGCGAGUGAUGAGCGAAACGGUUAAUACUGAUG
AF195110.1/1-53            GAAUGAAGACGUUCCACCCGAGCGAGUGAUGAGCGAAACGGUUAAUACUGAUG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GAAUGAAGACGUUCCACCCGAGCGAGUGAUGAGCGAAACGGUUAAUACUGAUG
//
# STOCKHOLM 1.0

#=GF AC   RF01144
#=GF ID   sR17
#=GF DE   Small nucleolar RNA sR17
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   36.00
#=GF TC   36.50
#=GF NC   35.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.38 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


BA000001.2/689901-689953 UGCGAUGAUGAGA--GCGAACUGCACUGAAAAGUGAUGACAGGGCCUUG--CUGAGC
AF195111.1/1-57          AGAAAUGAAGACUAAAAAACCGGCUGAGAUAAGUGAUGACGACGUCUCGCACUGAUC
CP000077.1/794012-793956 AGAAAUGAAGACUAAAAAACCGGCUGAGAUAAGUGAUGACGAGCUCUCGCACUGAUC
AJ248287.2/46690-46638   UGCGAUGAUGAAA--GCGAACUGCACUGAAAAGUGAUGAGAGGGCCUCG--CUGAGC
AE009950.1/531855-531802 CGCGAUGAAGAAA--GCGAACUGCUCUGAGAGAUGAUGAAAAGGGC-CUAACAGAGC
#=GC SS_cons             :::::::::::::..::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  aGcGAUGAaGAaa..GcGAaCuGCucuGAuAAGUGAUGAcaaGGuCUCGcACUGAgC
//
# STOCKHOLM 1.0

#=GF AC   RF01145
#=GF ID   sR14
#=GF DE   Small nucleolar RNA sR14
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   38.00
#=GF TC   40.40
#=GF NC   34.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


AF195108.1/1-55            -GCUGUGAAGACGCUAGACUUA--GACUGACUC-AUGAUGAAG-GGCCAAAGCUCAGAGC
AJ248283.1/65278-65224     UCCGAUGAUGA--UG-GAUCAACCGGCUGAGUG-GUGAUGAAGUCCGCAUCAC-CUGAGG
BA000001.2/56243-56188     ACCAAUGAUGA--CG-GAUCAACCGGCUGAUCGAAUGAUGACGUCCGCAUCAC-CUGAGG
CP000682.1/1693002-1693054 UGCUGUGAAGA--GG-AAUCUG--GUCUGAUCC-AUGAUGAAG-GGCCAAAGCUCAGAGC
BA000023.2/1296396-1296450 UGCUGUGAAGAGGCUAGAUAUA----CUGAAUUUGUGAUGAAG-GGCCAAAGCUCGGAGC
AP006878.1/316188-316134   UCCGAUGAUGA--CG-GAUCAACCGGCCGAACG-GUGACGACAUCGGUCUUGU-CUGAGG
AE009950.1/1889591-1889645 CCCAAUGAUGA--UG-GAUCAACCGGCUGAA-GUAUGAUGAGGUCCGCAUCAC-CUGAGG
AE006641.1/829583-829636   UGCUGUGAAGA--CC-UAGCUA-GGUCUGAAGA-GUGAUGAGG-GGCCAAAGCUCGGAGC
#=GC SS_cons               :::::::::::..::.::::::.::::::::::.:::::::::.::::::::::::::::
#=GC RF                    UgCuGUGAaGA..Cg.GAUCuA.CGgCUGAaug.GUGAUGAaG.gGcCAaaGCUCuGAGc
//
# STOCKHOLM 1.0

#=GF AC   RF01146
#=GF ID   sR15
#=GF DE   Small nucleolar RNA sR15
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   47.90
#=GF NC   29.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.59 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


BA000002.3/1357410-1357474 CGGGAUGAAGACUACUCCCCAGACCGAGGCAAGUCUCGAGAUGACGACAAUUCCUUUAGCAGACC
AF195109.1/1-55            AGUGAUGAGGA-------ACCAACGAGAGCUAGUUU---GAUGGCUUCGACGCUCUGCUCUGAAA
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    cGgGAUGAgGACUACUCCcCagACggggGCuAGUcUCGAGAUGgCguCgAuuCcuUuagCuGAcc
//
# STOCKHOLM 1.0

#=GF AC   RF01147
#=GF ID   sR12
#=GF DE   Small nucleolar RNA sR12
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   38.00
#=GF TC   39.60
#=GF NC   35.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AF195106.1/1-62            GAAUGAAG-AACCCAACCUUAUCUGAGGUUAUGAUG---ACAGGUUGUUCGUCAGAUCGAUGUGAG
BA000001.2/1732056-1732107 GGAUGAUG-AGCGUUUACCGGUCUGA-GCUGUGAUG---AUAUCG-GCACU-------G-UCUGAC
AF254842.1/1-50            GA-UGAUG-AGCGUUUACCGGUCUGA-GCUGUGAUG---ACAUCG-GCACU-------G-UCUGA-
AE006641.1/2189456-2189402 AAGUGAUGUAGCAGGGACGUA-CUGAAGC--UAAUGUGGAAAGAGUAUAAA-------GA-CUGAC
AE009950.1/1849496-1849445 GGAUGAUG-AGCGUUUACCGGUCUGA-GUUGUGAUG---AUACUG-GCACU-------G-UCUGAC
#=GC SS_cons               ::::::::.:::::::::::::::::::::::::::...::::::::::::.......::::::::
#=GC RF                    GAAUGAUG.AGCguuuACcugUCUGAgGcUGUGAUG...AcAggGUGuACu.......GAUCUGAc
//
# STOCKHOLM 1.0

#=GF AC   RF01149
#=GF ID   sR10
#=GF DE   Small nucleolar RNA sR10
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   69.00
#=GF NC   34.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AJ248286.2/162377-162324   AGCGAUGAUGAACUACUCCCGGCUGAGCUGUGAUGAACCACCUACCGGCUGAGG
BA000001.2/1013073-1013126 ACUAAUGAUGAACUACUCCCGGCUGAGGGGUGAUGAACCACCUACCGGCUGAGG
AP006878.1/274146-274093   CCCGAUGAAGAACUACUCCCGCCUGAAGUGUGAUGAGCCACCUACCGGCGGAGG
AE009950.1/1001864-1001811 GCAGAUGAUGAGCUACUCCCGGCUGAAAGAUGAUGAACCACCUACCGGCUGAGG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    aCcGAUGAUGAACUACUCCCGGCUGAgggGUGAUGAACCACCUACCGGCUGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01150
#=GF ID   sR11
#=GF DE   Small nucleolar RNA sR11
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   40.20
#=GF NC   36.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.87 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


BA000002.3/840962-840900   GCCGAUGAUGUCUACUCCCGACUACGACACGCCGUGGGGAUGAGUUGAAGGCAUUUG--GCUGAG
BA000001.2/544644-544590   CGGGAUGAUGACUUUGCCGAG-UGC-------UGAGCUGGUGAUGAGUAAACAGUCG--UCUGAC
AJ248287.2/202677-202731   UGGGAUGAUGACUUUGCCGAG-UGC-------UGAGGAAGUGAUGAGUAAACAGUCG--CCUGAC
AF195105.1/1-56            GAAUGUGAUGAUGGGUCGAUGUUAC-------UGAUUAGUUGAUGAGAUUAUCUCCG--GCUGAG
BA000023.2/1261884-1261826 GCAGAUGAUGAGCUUGACCACUUAUG------AAACUAGAUGAUUUAUUAAAGGUAGCCUCUGAU
CP000077.1/1152448-1152506 UUUAGUGAUGAGCUUGACCGCAUAUG------AAAAUUGAUGAUUUAAUAAAGGUAGCCUCUGAU
AE009950.1/497425-497371   GGGGAUGAUGAGUUUGCCGAG-UGC-------UGAGCUAGUGAUGAAUAAACAGUCG--CCUGAC
AE006641.1/794185-794127   UUAAAUGAUGAGCUUGACCACUUAUG------AAGCUAGAUGAUAUAAUAAAGGUAGCCGCUGAG
#=GC SS_cons               ::::::::::::::::::::::::::......:::::::::::::::::::::::::..::::::
#=GC RF                    gcaGAUGAUGAguuuGCCcaguUACG......uGaguaGaUGAUuuGAuaAcaGUcG..gCUGAg
//
# STOCKHOLM 1.0

#=GF AC   RF01151
#=GF ID   snoU82P
#=GF DE   Small nucleolar RNA U82P
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   42.00
#=GF TC   45.70
#=GF NC   39.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=HUM30096;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10684968
#=GF RT   The intron-containing L3 ribosomal protein gene (RPL3): sequence analysis
#=GF RT   and identification of U43 and of two novel intronic small nucleolar RNAs.
#=GF RA   Duga S, Asselta R, Malcovati M, Tenchini ML, Ronchi S, Simonic T
#=GF RL   Biochim Biophys Acta. 2000;1490:225-236.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   14


BC036582.1/1156-1210         GGGGUGAUGAAGGCCUGCACCUGG----UCCCCUCCCCAACU-CUGCUCUGCUCCUGAAG
AANU01294177.1/11152-11098   GGGGUGAUGAAGGCCUGCACCCGG----CCCCCUCCCCAACU-CUACUCUGCUCCUGAAG
AANN01257832.1/1121-1175     GGGGUGAUGAAGGUGUGCACCGGG----GAUCCUCCCCAACU-CUGCUCUGCUCCUGAAG
AANG01249677.1/3745-3691     GGGGUGAUGAAGGCCUGCGCCCCG----CCCCCUCCCCAACU-CUGCUCUGCCCCUGAAG
AAFC03020685.1/16339-16284   GGGCUGAUGAAGGCUGGCACCUGG---GCCCCCUCCCCAACU-CUGCUCUGCUCCUGAAG
AAYZ01369362.1/5081-5029     GGGGUGAUGAAGGCCUGCACCCGG----CCCCUGCCC--ACU-CUGCUCUGCUCCUGAAG
AAPY01024276.1/1622-1675     CGGGUGAUGAAGGCCGGCACCCGG-----CCCUGCCCCAACU-CUGCUCUGCUCCUGAAG
AAPN01049857.1/5928-5873     GGGCCGAUGAAGGGCUGAGCCGAG---ACCCCCUCCCCAACU-GUGCUCUGCUCCUGAAG
AAFR03059474.1/48492-48551   GUGCUGAUGAAGGGCUGCCCCCCCCACUCCCUCUCCCCAACUGCUGCUCUGCUUCUGAAG
AAHX01051776.1/36978-36924   AGGGUGAUGAAGGCCUGCACCAGG----CCCCUUCCCCAACU-GUGCUCUGCUCCUGAAG
AAGV020489277.1/1364-1418    GAGGUGAUGAAGGCUUGGCCCCGG----CCCCCUUCCCAACU-CUGCUCUGCUCCUGAAG
AAKN02031265.1/103464-103410 GGGGUGAUGAAGGCCUGCACCCGC----CCCCUUUCCCAACU-CUGCUCUGCUCCUGAAG
AAGU03077394.1/7967-8021     GGGUUGAUGAAGGCCUGUGCCCGG----CCCCCUCCCCAACU-CUGCUCUGCUCCUGAAG
EU094091.1/1-54              G-GCCGAUGAAGGGCUGAGCCGAG---ACCCCCUCCCCAACU-GUGCUCUGCUCCUGAA-
#=GC SS_cons                 ::::::::::::::::::::::::....::::::::::::::.:::::::::::::::::
#=GC RF                      GGGgUGAUGAAGGcCUGcaCCcGG....CCCCCUCCCCAACU.CUGCUCUGCUCCUGAAG
//
# STOCKHOLM 1.0

#=GF AC   RF01152
#=GF ID   sR1
#=GF DE   Small nucleolar RNA sR1
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   46.70
#=GF NC   43.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   12


AJ248287.2/14879-14825     GGC-AAUGAUGAAGCCU-UCCGCACCUGAACG-GUGAGGAGUGGACG---GCUUCCUGA---GC
AE000782.1/711263-711211   GCC-GAUGAUGACUGAUGGGCGAC-CUGAGAA-AUGAUGAAAGGGAG---A--GUCUGA---GG
BA000001.2/762168-762222   GGC-GAUGAUGAAGCCU-UCCGCACCUGAAUG-AUGAGGAGUGGACG---GCUUCCUGA---GC
BA000002.3/143608-143554   GCC-GAUGAUGAGUUCUAGCCUUA-CGGACAC-GUGAAGACAGUGGC-CAG--GCCUGA---GG
L77117.1/29609-29554       GCA-GAUGAUGACGUUUAUCCCCGUCUGAGUU-AUGAUGA--GUAGC-AAGCCGGCUGA---UG
BA000001.2/1328943-1328887 GGC-GAUGAUGAGUGAUGGGCGAA-CUGAAAACAUGAUGAAGGUAGG-UGAUCU-CUGA---GC
CP000077.1/1175551-1175494 GGCUAAUGAUGAGGGUUAAAAGCG-CUUAUUG-AUGAUGA---ACCU-CUACCUACUGAAGAGC
AF254826.1/2-57            GGC-GAUGAUGAGUGAUGGGCGAA-CUGAGAA-GUGAUGAUGGUAGG-UGAUCU-CUGA---GC
AP006878.1/1626447-1626391 UGC-GAUGAUGAGUGAUGGGCGAA-CCGACCG-GUGAGGAAGGAAAGGUGAUCG-CUGA---GC
BA000023.2/1214437-1214490 CCC-GAUGAUGAUGGUUAAAAGCG-CUUAUCG-GUGACGA---GCCU-CUACCUGCUGA---GG
AE009950.1/1288110-1288166 GGC-AAUGAUGAGUGAUGGGCGAA-CUGAAAUAGUGAUGACGGUAGG-UGAUCU-CUGA---GC
AE009950.1/678049-678103   GGC-GAUGAUGAUGCCU-UCCGCACCUGAUUG-GUGAGGAGUGGACG---GCUUCCUGA---GC
#=GC SS_cons               :::.::::::::::::::::::::.:::::::.::::::::::::::.:::::::::::...::
#=GC RF                    GGC.GAUGAUGAggGaUggcCGca.CUGAuug.GUGAuGAagGuagg.cgACCUcCUGA...GC
//
# STOCKHOLM 1.0

#=GF AC   RF01153
#=GF ID   sn3060
#=GF DE   Small nucleolar RNA sn3060
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   48.90
#=GF NC   35.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Caenorhabditis_elegans300129;
#=GF RN   [1]
#=GF RM   12372436
#=GF RT   Location of 2(')-O-methyl nucleotides in 26S rRNA and methylation guide
#=GF RT   snoRNAs in Caenorhabditis elegans.
#=GF RA   Higa S, Maeda N, Kenmochi N, Tanaka T
#=GF RL   Biochem Biophys Res Commun. 2002;297:1344-1349.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AM051017.1/1-66              GCUUCUGUGAUCGACAACAAACCCAGCUCUCUGAAUGAUUGUGAGGUUAAGAAAACAGCUGAGAAG-
AAGD02011076.1/1329-1395     GCUUCUGUGAUCGACAACAAACCCAGCUCUCUGAAUGAUUGUGAGGUUAAGAAAACAGCUGAGAAGC
CAAC02000606.1/140971-140905 GCUUCAGUGAUCGACAACAAACCCAGCUCUCUGAAUGAUUGUGAGGUUAAGAAAACUGCUGAGAAGC
#=GC SS_cons                 <<<<<_________________________________________________________>>>>>
#=GC RF                      GCUUCuGUGAUCGACAACAAACCCAGCUCUCUGAAUGAUUGUGAGGUUAAGAAAACaGCUGAGAAGC
//
# STOCKHOLM 1.0

#=GF AC   RF01155
#=GF ID   snoR101
#=GF DE   Small nucleolar RNA snoR101
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   40.70
#=GF NC   36.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300006;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AJ505631.1/1-68              GGGAUACACUUGAUCUCUGAACUUCACAGGUAAGUUCGCUUGUUGAUAACUACUGGUCUGCUGAUGCU
AASG02007650.1/11125-11063   GGUUUACACUUGAUCUCUGAACUUC--AGGUAAGUUCACUUGUGGAUAAUUCAUGAA---CUGAUGCC
AM463855.1/5770-5834         GGCUUACACUUGAUCUCUGAACUUC--AGGUAAGUUUACUUGUUGACAAGUA-UACAUUACUGAUGCU
AARH01002882.1/376548-376486 GUCUUACACUUGAUCUCUGAACUUC--AGGUAAGUUCACUUGUUGACAAGCUCU---UUACUGAUGCC
AY973954.1/12-75             GUCUUACACUUGAUCUCUGAACUUC--AGGUAAGUUCAUAUGUGGACA--UAUUUCAUUGCUGAUGCA
#=GC SS_cons                 :::::::::::::::::::::::::..:::::::::::::::::::::::::::::::::::::::::
#=GC RF                      GgcUUACACUUGAUCUCUGAACUUC..AGGUAAGUUCACUUGUuGAcAAgUacUgcaUUgCUGAUGCu
//
# STOCKHOLM 1.0

#=GF AC   RF01156
#=GF ID   SNORD123
#=GF DE   Small nucleolar RNA SNORD123
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.80
#=GF NC   44.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; SNORD123;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16990247
#=GF RT   snoSeeker: an advanced computational package for screening of guide and
#=GF RT   orphan snoRNA genes in the human genome.
#=GF RA   Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2006;34:5112-5123.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   12


AAIY01246169.1/1638-1707     GGUGAAAAUGAUGAAUUCUGGGUCUCUGA-G-UCAUGUGACCUGAAAAA-GGCCAUCCAUUUCCUGAUUCACC
AAPY01265923.1/1643-1574     GGUGAAAAGGAUGAAUUCUGGGGCGCUGA-U-CACUGUGACUUGAAAAA-CGCCAUCCAUUUCCUGAUUCACC
AAFR03010505.1/107885-107953 GGUGAAAAUGAUGAAUUCUGGGGAACUGA-U-UCAUGUGACUUGAAA-A-GGCCAUCCAUUUCCUGAUUCACC
AANG01319836.1/252-322       GGUGAAAAUGAUGAACCGUGGGGCGCUGAUU-UCAUGUGACUUGAAAAA-CGCCAUCCAUUUCCUGAUUCACC
AAPN01041052.1/6593-6661     GGUGAAAAUGAUGAAUAUUGGGGAACUGA-U-UUAUGCGACUUGAAA-A-GGCCAUCCAUUUCCUGAUUCACC
AANN01573202.1/12896-12825   GGUGAACGUGAUGAACUUUGGGGCGCUGA-UUUCACGUGACUUGAAAAAACGCCAUCCAUUUCCUGAUUCACC
AAVX01470676.1/421-489       UGUGAACUUGAUGACUUAAAGGGGGCUGAAA-UAAUCUGA--UGAAAAA-UGCCAUCCAUUUCCUGAUUCACA
AAGU03019324.1/7109-7042     GGUGAAAAUGAUG-AGUCUGGGGCUCUGA-U-CCAUGUGACUUGAAA-A-GGCCAUCCAUUUCCUGACUCACC
AAGW02031224.1/511-442       GGUGAAGAUGAUGACUCCUGGGGGGCUGA-U-UCAUGUGACUUGAAAAA-GGCCAUCCAUUUCCUGAUUCACC
FM165401.1/10-78             GGUGAAAAUGAUGAAUUCUGGGGUGCUGA-C-UCAUGUGAUCUG-AAAA-UGCCAUCCAUUUCCUGAUUCACC
AK095831.1/758-827           GGUGAAAAUGAUGAAUUCUGGGGCGCUGA-U-UCAUGUGACUUGAAAAA-UGCCAUCCAUUUCCUGAUUCACC
AACN010043475.1/1202-1134    GGUGAAAAUGAUGAACCCUGGGGCGCUGA---UCACGUGACUUGAAAAA-CGCCAUCCAUUUCCUGAUUCACC
#=GC SS_cons                 <<<<<<_______________________._._________________._________________>>>>>>
#=GC RF                      GGUGAAaAUGAUGAAuucUGGGGcgCUGA.u.UcAUGUGACUUGAAAAA.uGCCAUCCAUUUCCUGAUUCACC
//
# STOCKHOLM 1.0

#=GF AC   RF01157
#=GF ID   sn1185
#=GF DE   Small nucleolar RNA sn1185
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   67.20
#=GF NC   52.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=CEL30007;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12372436
#=GF RT   Location of 2(')-O-methyl nucleotides in 26S rRNA and methylation guide
#=GF RT   snoRNAs in Caenorhabditis elegans.
#=GF RA   Higa S, Maeda N, Kenmochi N, Tanaka T
#=GF RL   Biochem Biophys Res Commun. 2002;297:1344-1349.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AM050842.1/3-68                AUCGGUGAUGUGAUAUCCAGUUCUGCUACUGAGUUAUUGUGAAGAUUAACUUUCCCCGUCUGAGAU
AAGD02000356.1/28674-28739     AUCGGUGAUGUGAUAUCCAGUUCUGCUUCUGAAUGGUUGUGAGGAUUAACUUUCCCCGUCUGAGAU
CAAC02000450.1/1739599-1739534 AUCGGUGAUGUGAUAUCCAGUUCUGCUACUGAAGCGUUGUGAAGAUUAACUUUCCCCGUCUGAGAU
ABEG02001356.1/1765-1830       AUCAGUGAUGUUACAUCCAGUUCUGCUACUGAGUUGUUGUGAAGAUAAUCUUUCCCCGUCUGAGAU
DQ789405.1/1-66                AUCGGUGAUGUGAUAUCCAGUUCUGCUACUGAAGCGUUGUGAAGAUUAACUUUCCCCGUCUGAGAU
#=GC SS_cons                   <<<____________________________________________________________>>>
#=GC RF                        AUCGGUGAUGUGAUAUCCAGUUCUGCUACUGAauuGUUGUGAAGAUUAACUUUCCCCGUCUGAGAU
//
# STOCKHOLM 1.0

#=GF AC   RF01158
#=GF ID   SNORD108
#=GF DE   Small nucleolar RNA SNORD108
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   46.00
#=GF TC   46.50
#=GF NC   44.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.24 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; HBII-437;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11726556
#=GF RT   The IC-SNURF-SNRPN transcript serves as a host for multiple small
#=GF RT   nucleolar RNA species and as an antisense RNA for UBE3A.
#=GF RA   Runte M, Huttenhofer A, Gross S, Kiefmann M, Horsthemke B, Buiting K
#=GF RL   Hum Mol Genet. 2001;10:2687-2700.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY055807.1/1-71              GCUUAAUGAUGAGAAUCAUUAUUUCUUGAAUUGGAUGACACUUUCCAUUCCUGCAAAGGGAG-CGUGAGGGC
AANU01099487.1/56230-56160   GCUUAAUGAUGAGAAUCAUUAUUUCUUAAAUUGGAUGACACUUUCCAUUCCUGCAAAGAGAG-CCUGGGGUC
AANG01133945.1/1523-1593     GCUUUAUGGUCAGACUCCUUGUUUCUUGACUCUGAUGAUAGUGUUCAUUCCUACAAAGGGAU-UCUCAGGUU
AAWR02000803.1/234424-234495 GCUUUAUGAUCAGACUCAUUGUUUCUUGAGCCUAAUGACAGCUUUCAUUCUUGCAAAGGGAAAUCUGAGGUC
#=GC SS_cons                 <-<<__________________________________________________________._____>>->
#=GC RF                      GCUUuAUGAUgAGAaUCAUUaUUUCUUGAaUuuGAUGACAgUUUuCAUUCCUGCAAAGGGAg.ucUGAGGUC
//
# STOCKHOLM 1.0

#=GF AC   RF01159
#=GF ID   snoU18
#=GF DE   Small nucleolar RNA U18
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   47.00
#=GF TC   47.20
#=GF NC   46.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.54 -Z 549862.597050 CM SEQDB
#=GF CL   CL00047
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=DRO30005;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11726521
#=GF RT   Release of U18 snoRNA from its host intron requires interaction of Nop1p
#=GF RT   with the Rnt1p endonuclease.
#=GF RA   Giorgi C, Fatica A, Nagel R, Bozzoni I
#=GF RL   EMBO J. 2001;20:6856-6865.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   16


AJ784359.1/4-73              ACUGUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UU-UA-UAUUGAUUAAA--AACC-UUCCA-AU---UACUGAG-CA-A-
AAPQ01006572.1/223606-223676 CCUAUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UU-UA-UAUUGAUUAAA--AACC-UUCCA-AU---UACUGAG-AA-AA
AAKO01000106.1/14068-14138   UGACUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UU-UA-UAUUGAUUAAA--AACC-UUCCA-AU---UACUGAG-CA-AA
AAPT01020876.1/13987-13917   ACGCUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UU-UA-UAUUGAUUAGA--AACC-UUCCA-AU---UACUGAGUUA-A-
AANI01017473.1/69861-69791   ACAUUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UU-UA-UAUUGAUUUCA--AACC-UUCCA-AU---UACUGAGUUA-A-
AAPU01011615.1/691001-690930 ACUAUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UU-UAACAUUGAUUAGA--AACC-UUCCA-AU---UACUGAG-CA-AA
AAPP01019276.1/169366-169295 ACUGUGAUGAAAUUAAUUGGUCCGUGUUUAUGAAUUU-UA-CGUUGAUUAAA--AACC-UUCCA-AU---UACUGAG-CACA-
AAQB01006196.1/437455-437385 UAUUUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UU-UA-AGUUGAUUAAA--AAUC-UUCCA-AU---UACUGAU-UG-UU
AAIZ01003783.1/8636-8707     CCUCUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UUAUC-CAUUGAUUAAA--AACC-UUCCA-AU---UGCUGAG-CACA-
AASV01045658.1/508-438       UUGUUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UU-UC-CAUUGAUUAUA--AAUU-CUCCA-AU---UACUGAA-CA-AG
AAFS01000468.1/27664-27734   UUUCUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UU-UA-CAUUGAUUAUA--AAUU-CUCCA-AU---UGCUGAC-AA-AU
AAEU02000204.1/549677-549602 CCUAUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA-UU-UA-AAUUGAUUACAGAAAUC-UUCCA-AUUACUACUGAG-CA-AA
AAWU01009725.1/50032-49961   CAAAUGAUGAAAUUAAUUGGUCCGUGUUGAUGAA-UU-UU-GUUUGAUUAAA--GUUUACUCCA-AU---UACUGAU-CG-UU
AAGE02008153.1/52713-52643   UUUAUGAUGAAGUUAAUUGGUCCGUGUUGAUGAA-UU-U--CGUUGAUUAUA--AUUUCCUCCA-AU---UACUGAU-UU-UC
AAAB01008844.1/977795-977724 UCUGUGAUGAAAAUAUUUGGUCCGUGUUUAUGAA-AU-UG-UAUGAUUUUAU--AGCA-AUCCAUAU---UUCUGAU-AC-GU
AAZX01002090.1/12487-12423   AUAAUGAUGAAAUUCAUUGGUCCGUGUUGCUGUU-UU-GU-CACUGAUGA---------UUACC-AU---UCCUGAU-UA-AA
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::.::.::.:::::::::::..::::.:::::.::...:::::::.::.::
#=GC RF                      ucuaUGAUGAAAUUAAUUGGUCCGUGUUUAUGAA.UU.Ua.caUUGAUUAaA..Aacc.uUCCA.AU...UaCUGAg.ca.aa
//
# STOCKHOLM 1.0

#=GF AC   RF01160
#=GF ID   sn2841
#=GF DE   Small nucleolar RNA sn2841
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   60.70
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Caenorhabditis_elegans300017;
#=GF RN   [1]
#=GF RM   12372436
#=GF RT   Location of 2(')-O-methyl nucleotides in 26S rRNA and methylation guide
#=GF RT   snoRNAs in Caenorhabditis elegans.
#=GF RA   Higa S, Maeda N, Kenmochi N, Tanaka T
#=GF RL   Biochem Biophys Res Commun. 2002;297:1344-1349.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AY948666.1/1-72 CUGCGGUGACGAUCAACUCUUACCUACUAUGACAAAAACAAUGGUUAGACGUUACUCGUACUGUCUGAGCAG
DQ789448.1/2-72 CUGCUGUGACGAU-AAUCCUUACCUACUAUGACAAAAACAAUGGUUAGACGUUACUCGUACUGUCUGAGCAG
#=GC SS_cons    <<<<________________________________________________________________>>>>
#=GC RF         CUGCuGUGACGAUCAAuuCUUACCUACUAUGACAAAAACAAUGGUUAGACGUUACUCGUACUGUCUGAGCAG
//
# STOCKHOLM 1.0

#=GF AC   RF01161
#=GF ID   SNORD5
#=GF DE   Small nucleolar RNA SNORD5
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   55.70
#=GF NC   54.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; mgh28S-2409;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   20


AJ609488.1/1-73              GUUCAGAUGAUGAAUUUAACUGUUCAACUGCUGAAUGAUA--ACGGGCAUGAACUAAAA-CUUAAUU--CUGACAGAG
AANG01072514.1/867-795       GUUCACAUGAUGAAUUUAACUGUUCAACUGCUGAAUGAUU--ACAGACAUGAACUAAAA-CUUGAUU--CUGACGGAG
AAPY01155118.1/654-725       GCUCAGAUGAUGAAUUUAACUGUUCAACUGCUGAAUGAU---GCAGACAUGAACUAAAA-CUUAAUU--CUGACAGUG
AAYZ01416934.1/837-767       GUUCAGAUGAUGAAUUCA--UGUUCAACUGCUGAAUGAUU--ACAGACAUGAACUAAAA-CUUAAUU--CUGAAAGAG
AAFC03070145.1/78070-78000   GUUCAGAUGAUGAAUUUAA-UGUUCAACUGCUGAAUGAU---ACAGAUAUGAACUAAAA-CUUAAUU--CUGAUAGAG
AAIY01662003.1/5367-5439     GUUCAUGUGAUGAAUUUAACUGUUCAACUGCUGAAUGAU---ACAGACAUGAACUAAAAUCUUCAUU--CUGAUUGAG
AC155259.1/220384-220314     GUUCAGAUGAUGAAUUCAACUGUUCAACUGCUGAAUGAG---CCAAACAUGAACUAACA--UUAACU--CUGACAGAA
AANN01814642.1/4675-4746     GUUUGCAUGAUGAGUGUUACUGUUCAACUGCUGUGUGAU---ACAGACGUGAACUAAAG-CUUUAUU--CUGACAGCU
AAFR03025134.1/19564-19634   GUUCAAAUGAUGAAUUCUUUUGUUCAACUGCUAAGUGAU---AGAAACAUGAACUGAAA--UGAAUU--CUGAUAGAA
AAPN01307029.1/40503-40434   AUUCAAGUGAUGACAUUAU-UGUUCAACUGCUAAGUGAU---GUAGAUAUGAACAAAAA--GGAAUU--CUGAGGGGU
ABDC01023157.1/26873-26808   AAUGUAAUUAUUAAUUUCAGUAUUUA----CUGAGUGAU-----AGACAUAAACUAAAA-CUUGAUU--CUGACAGAA
AAKN02037651.1/18789-18860   GUUUACAUGAUGAAUUUAACUGUUCAACUGCUGCAUGAU---ACAAACAUGAACUAAAA-CUUAAUU--CUGACAGCU
AAGV020161067.1/318-387      AUUCAGAUGAUGAAUUUAACUGUUCAACUGCUGUCUGAUA--CAG---AUGAACGAAAG-CUUAAUU--CUGACAGCU
AABR05151178.1/2494-2565     GUUCAGAUGAUGAAUUAAACUGUUCAACUGCUGUAUGAU---ACAGACAUGAACUAAAA-UUUAAUU--CUGACAGAA
AAGW02008739.1/15962-15890   GUUCACAUGAUGAAUUUAAAUGUUCAACUGCUGAAUGAUU--ACAGACAUGAACUAAAA-CCUAAUU--CUGACCGAG
AADN03001015.1/70703-70632   GUUCAUGUGAUGAAUAUUUCUGUUCAACUGCUGAGUGACU---CAGAAAUGAACUAAAU-UUCAAUU--CUGAUUAGA
AAEX03012728.1/176447-176518 GUUCACAUGAUGAAUUUAACUGUUCAACUGCUGAAUGAU---ACAGACAUGAACUAAAA-CUUAAUU--CUGACAGAG
AC194638.4/198160-198086     AUUCAGAUGCUGAAUUUAACUGUUCAACUGCUGAACCACUCGACAGACAUGAACGAAAA-CUUAAUU--CUGACAGAG
AAWZ02006558.1/137034-136962 GUUCUUGUGAUGACAUUCCUAGUUCAACUGCUGAGUGAUU--CCAGAAAUGAACUAAAA-CUAAAUACUCUGAUUG--
AAPE02025112.1/59627-59556   GUUCAGAUGAUGAAUUUAACUGUUCAACUGCUGAAUGAU---ACAGACAUGAACUAAAA-CAUAAUU--CUGACAGCU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::...:::::::::::::::::.:::::::..:::::::::
#=GC RF                      GUUCAgAUGAUGAAUUUaacUGUUCAACUGCUGAgUGAU...aCAGACAUGAACUAAAA.CUuaAUU..CUGAcaGag
//
# STOCKHOLM 1.0

#=GF AC   RF01162
#=GF ID   sn668
#=GF DE   Small nucleolar RNA sn668
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   40.60
#=GF NC   38.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.80 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=CEL30006;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12372436
#=GF RT   Location of 2(')-O-methyl nucleotides in 26S rRNA and methylation guide
#=GF RT   snoRNAs in Caenorhabditis elegans.
#=GF RA   Higa S, Maeda N, Kenmochi N, Tanaka T
#=GF RL   Biochem Biophys Res Commun. 2002;297:1344-1349.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


CAAC02000503.1/360912-360848 AGUCUAUGAUGUUUUUUCAAGACGGGACCGACUUGUGAAUGAUGCAUAACAGAAUUGCUGAGACU
AAGD02001661.1/7945-8009     AGUCUGUGAUGUUUUUUCAAGACGGGACCGACUUGUGAAUGAUGCAUAACAGAAAUGCUGAGACU
ABEG02005695.1/32372-32436   AGUCAGUGAUGUUUUUUCAAGACGGGACCGACUUGUGAAUGAUGCAUAAUCGAAAUGCUGAGACU
FO081502.1/41179-41243       AGUCAAUGAUGUUUUUUCAAGACGGGACCGACUGGUGAAUGAUGCAUAAAUGAAAUGCUGAGACU
AY948665.1/1-65              AGUCAAUGAUGUUUUUUCAAGACGGGACCGACUGGUGAAUGAUGCAUAAAUGAAAUGCUGAGACU
DQ789514.1/1-65              AGUCUAUGAUGUUUUUUCAAGACGGGACCGACUUGUGAAUGAUGCAUAACAGAAUUGCUGAGACU
#=GC SS_cons                 <<<<_________________________________________________________>>>>
#=GC RF                      AGUCuaUGAUGUUUUUUCAAGACGGGACCGACUuGUGAAUGAUGCAUAAcaGAAaUGCUGAGACU
//
# STOCKHOLM 1.0

#=GF AC   RF01163
#=GF ID   snoR64a
#=GF DE   Small nucleolar RNA snoR64a
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   43.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.69 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300090;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AJ505626.1/1-73            AUACUUUGCCAAGUUGUUGAAUGCUCAGA---UUUU--UC----UGGGUUUUAUGAUUCA-----CUUGUAUAGGAAGAUCUGAUGA
AASG02000099.1/88757-88676 AUUAUUUGCCGAAUCAUUGAAUGCUCAGU---UUCU--UUGUAUUGAGUAUUAUGAUUCUUUCUCUUUGUAUAGGAAGAUCUGAUGC
AARH01001054.1/12320-12396 AUCUUUUG---AAUUGUUGAAUGCUCAGACACUUAU--UU----GGGUUCUUAUGAUUUAGAUU-CUUGAAUAGGAAGAUCUGAUGC
AM450475.1/13027-12949     UGAAUAUCGAGAGUUGUUGAAUACUCAGA---UUUCGAUC----UGAGUAGCAUGAUUCUUUUC-UUUGAAUAGGAAGAUCUGAUGC
#=GC SS_cons               :::::::::::::::::::::::::::::...::::..::....::::::::::::::::::::.::::::::::::::::::::::
#=GC RF                    auaaUUUGccGAgUUGUUGAAUGCUCAGa...UUuU..Uu....UGgGUauUAUGAUUCuuuuu.uUUGuAUAGGAAGAUCUGAUGC
//
# STOCKHOLM 1.0

#=GF AC   RF01164
#=GF ID   SNORD107
#=GF DE   Small nucleolar RNA SNORD107
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   55.90
#=GF NC   46.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; HBII-436;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11726556
#=GF RT   The IC-SNURF-SNRPN transcript serves as a host for multiple small
#=GF RT   nucleolar RNA species and as an antisense RNA for UBE3A.
#=GF RA   Runte M, Huttenhofer A, Gross S, Kiefmann M, Horsthemke B, Buiting K
#=GF RL   Hum Mol Genet. 2001;10:2687-2700.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   13


AY055806.1/1-75              GGUUCAUGAUGACACAGGACCUUGUCUGAACA-UAAUGAUUUCAAAAUUUGAGCUUAAAAAUGACACUCUGAAAUC
AAQQ01467875.1/529-602       GGUUCAUGAUGACACAGGACCUUGUCUGAAUA-UGAUGAUUUCAAAAUUUGAGCUUAAAU-UGACACUCUGAAAUC
AAPY01669620.1/1915-1842     GGUUCAUGAUGACACUGGACCUUGUCUGAAAA-AAGUGAUUUCAAAAUUUGAGCUUAAA-AUAAUACUCUGAAAUC
AAYZ01696736.1/453-527       GGUUCAUGAUGACACAGGACCUUGUCUGAAAAUUAAUGAUUUCAAAAUUUGAGCUUAAA-ACGACAUUCUGAAAUC
AALT01596450.1/6400-6473     GAUUAAUGAUGAUACAGGACCUUGUCUGAAUA-UACUGAUUUCAAAAUUUGAGCUUAAA-AUAAUAUUCUGAAAUC
AAHX01005649.1/27994-28065   GAUUUAUGAUGACAUGGGACCUUGUCUGAACA-CAAUGAUUUCAAAAAUUGAGCUUAGA---GUGACUCUGAAAUC
AANN01394341.1/3716-3789     GAUUCAUGAUGACAUUGGACCUUGUAUGACUA-AAAUGACAUCAAAAUUUGAGCUUAG-AAUUAUACUCUGAAAUC
AAHY01495030.1/174-105       GAUUUAUGAUGAUAUAGGACCUUGUCUGAAUA-UAAUGAUUUCAAAAAUUGAGCUUA-----CAGUGACUGAAAUC
AAWR02000803.1/232527-232600 GGUUCAUGAUGAUACAGGACCUUGUCUGAACA-AAGUGAUUUCAAAAUUUGAGCUUAAA-AUGACAUUCUGAAAUC
AAGV020498068.1/119-191      GAUUCAUGAUGACACAGGACCUUGUUUGAAAA-UAAUGAUAUUAAACUUUGAGCUUAA--ACCACACUCUGAAAUC
AACN010194540.1/1302-1373    GGUUCAUGAUGACAUAGGACCUUGUCUGAACA-UAAUGA-UUCAAAAUUUGAGCUUAA--AUGACACUCUGAAAUC
AAQR03178258.1/44616-44545   GGUUCAUGAUGACAUAGGACCUUGUCUGAACA-UAAUGAUUUCAAAACUUGAGCUUAAAAUG---ACACUGAAAGC
AAPE02056879.1/48016-47944   GGUUCAUGAUGACACAGGACCUUGUCUGAACU-UCAUGAUCUCAAAACAUGAGCUUGGAUAUGUCA--CUGAAAUC
#=GC SS_cons                 <<<<____________________________.__________________________.____________>>>>
#=GC RF                      GaUUcAUGAUGACAcAGGACCUUGUCUGAAuA.uAAUGAUUUCAAAAuUUGAGCUUAAA.AugAcAcUCUGAAAuC
//
# STOCKHOLM 1.0

#=GF AC   RF01165
#=GF ID   sn2317
#=GF DE   Small nucleolar RNA sn2317
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   73.90
#=GF NC   40.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Caenorhabditis_elegans300070;
#=GF RN   [1]
#=GF RM   16344563
#=GF RT   Organization of the Caenorhabditis elegans small non-coding transcriptome:
#=GF RT   genomic features, biogenesis, and expression.
#=GF RA   Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z, Wang Y, He H, Cai L, Sun H, Liu
#=GF RA   C, Li B, Bai B, Wang J, Jia D, Sun S, He H, Cui Y, Wang Y, Bu D, Chen R
#=GF RL   Genome Res. 2006;16:20-29.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948658.1/3-77            UGUCAAUGAUGUCUAAAAAAUUACUACGAUUUAAUUCGAAUUGCUGUGAGAUC-AAUCUUAUACAA---UUCUGAGACA
DQ789434.1/1-68            UGUCAAUGAUGUCCUAA-----UCUACGAUUUAAUUCGAAUUGAUGUGAGAUG-AAUCACUGA-AAA----CUGAGACA
AAGD02000367.1/6414-6343   CGUCAAUGAUGUCCUAA-----UCUACGAUUUAAUUCGAAUUGCUGUGAGAU--AAUCUGAUGCAAAACAACUGAGACU
ABEG02001368.1/10678-10608 GGUCAAUGAUGUCCUAA-----ACUACGAUUUAAUUCGAAUUACUGUGAGAUAAAAUCAUAUAUGC---AACUGAGACA
#=GC SS_cons               :<<<_____________....._______________________________.____________...______>>>:
#=GC RF                    uGUCAAUGAUGUCcuAA.....aCUACGAUUUAAUUCGAAUUGcUGUGAGAUa.AAUCuuAUAcAA...aaCUGAGACA
//
# STOCKHOLM 1.0

#=GF AC   RF01166
#=GF ID   sn3071
#=GF DE   Small nucleolar RNA sn3071
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   40.60
#=GF NC   35.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=CEL30019;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16344563
#=GF RT   Organization of the Caenorhabditis elegans small non-coding transcriptome:
#=GF RT   genomic features, biogenesis, and expression.
#=GF RA   Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z, Wang Y, He H, Cai L, Sun H, Liu
#=GF RA   C, Li B, Bai B, Wang J, Jia D, Sun S, He H, Cui Y, Wang Y, Bu D, Chen R
#=GF RL   Genome Res. 2006;16:20-29.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AY948662.1/1-76 GAUCUAUGAUGAGACUUUCACGACGGUCUUCCGAUGUAAUA-CAUACCUGUGGAUAUCUUUACGUGAAGCUGAGAUC
DQ789449.1/1-77 GAUCGAUGAUGAGACUUUCACGACGGUCUUCCGAUGAAAUAUCAAAGCUGUGGAUAUCUUUACGUGAAGCUGAGAUC
#=GC SS_cons    <<<<_____________________________________________________________________>>>>
#=GC RF         GAUCuAUGAUGAGACUUUCACGACGGUCUUCCGAUGuAAUAUCAuAgCUGUGGAUAUCUUUACGUGAAGCUGAGAUC
//
# STOCKHOLM 1.0

#=GF AC   RF01167
#=GF ID   sn2429
#=GF DE   Small nucleolar RNA sn2429
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   74.70
#=GF NC   36.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=CEL30012;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16714446
#=GF RT   Evolution of small nucleolar RNAs in nematodes.
#=GF RA   Zemann A, op de Bekke A, Kiefmann M, Brosius J, Schmitz J
#=GF RL   Nucleic Acids Res. 2006;34:2676-2685.
#=GF RN   [2]
#=GF RM   16344563
#=GF RT   Organization of the Caenorhabditis elegans small non-coding transcriptome:
#=GF RT   genomic features, biogenesis, and expression.
#=GF RA   Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z, Wang Y, He H, Cai L, Sun H, Liu
#=GF RA   C, Li B, Bai B, Wang J, Jia D, Sun S, He H, Cui Y, Wang Y, Bu D, Chen R
#=GF RL   Genome Res. 2006;16:20-29.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AM051011.1/2-76            UGGGAAUGAUGACCUUCUG-UGUAGGAAUCUCAAUGAGUG-ACUGUGACAUAAAAAUGCAGUAAAUUCACUGACCCC-
DQ789441.1/1-77            UGGGAAUGAUGACUUUCUGUUGUAGGAAUCUCAAUGAGCG-ACUGUGAUAUAAAAAUGCAGUAAUCUCACUGACCCCA
AAGD02001642.1/71286-71210 UGGGAAUGAUGACUUUCUGUUGUAGGAAUCUCAAUGAACG-ACUGUGAUAUAAAAAUGCAGUAAUCACUCUGACCCAA
ABEG02002894.1/20434-20357 UGGGAAUGAUGAUUUUCUGUUGUAGGAAUCUCGAUGAGCGUACACUGAUAUCAAAAUGCAGUAAUCUCGCUGACCCCA
#=GC SS_cons               <<<<____________________________________._________________________________>>>>
#=GC RF                    uGGGAAUGAUGAcUUUCUGUUGUAGGAAUCUCAAUGAGcG.ACugUGAUAUaAAAAUGCAGUAAucuCaCUGACCCCa
//
# STOCKHOLM 1.0

#=GF AC   RF01168
#=GF ID   SNORD126
#=GF DE   Small nucleolar RNA SNORD126
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   66.10
#=GF NC   52.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.08 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; SNORD126;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16990247
#=GF RT   snoSeeker: an advanced computational package for screening of guide and
#=GF RT   orphan snoRNA genes in the human genome.
#=GF RA   Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2006;34:5112-5123.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AAYZ01187716.1/225-149     GGUUUGCCAUGAUGAGAUGCAUGUUCAGUCCGUGUUUCAGCUGAUGACCCUGAUUAAACACAUGCUCUGAGCAGACU
AACN010729405.1/784-708    AGUUUGCCAUGAUGAAAUGCAUGGUGAGUCCGUGUUUCAGCCGAUCACCCUGGUCAAACACAUGCUCUGAGCAGACU
AAHY01113754.1/39386-39310 AGUUUGCUAUGAUGAAAUGCAUGUGAAGUCCGUGUUUCAGCUGAUCACACUGAUUAUACACAUGUGCUGAGCAGACA
AAFR03022281.1/33862-33938 UGUCUGCCAUGAUGAAAUGCAAUUUCAGUCCGUGUUUCAGCUGAUUACCCUGAUUGCAUGCAUACUCUGAGCAGACU
AAPN01395706.1/2381-2305   CCCCUGCCUUGAUGAAAUGCAUGUUCAGUCCGUGUUUCAGCUGACCACCCUGAUUAUACACAUGCGCUGAGCAGGAG
AL355075.6/193439-193515   AGUUUGCCAUGAUGAAAUGCAUGUUAAGUCCGUGUUUCAGCUGAUCAGCCUGAUUAAACACAUGCUCUGAGCAGACU
#=GC SS_cons               <<<<<<<_______________________________________________________________>>>>>>>
#=GC RF                    cgucUGCCAUGAUGAAAUGCAUGUUaAGUCCGUGUUUCAGCUGAUcACCCUGAUUAaACACAUGCuCUGAGCAgacg
//
# STOCKHOLM 1.0

#=GF AC   RF01169
#=GF ID   SNORD112
#=GF DE   Small nucleolar RNA SNORD112
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   58.00
#=GF TC   58.10
#=GF NC   57.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00069
#=GF DR   snoRNABase; 14q(0);
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12045206
#=GF RT   Identification of tandemly-repeated C/D snoRNA genes at the imprinted
#=GF RT   human 14q32 domain reminiscent of those at the Prader-Willi/Angelman
#=GF RT   syndrome region.
#=GF RA   Cavaille J, Seitz H, Paulsen M, Ferguson-Smith AC, Bachellerie JP
#=GF RL   Hum Mol Genet. 2002;11:1527-1538.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   13


AADB02016115.1/24955-25031   UG-GACCAAUGAUGAGACA--GUGUUUAUGAACAAAAGAUCAUGAUUAAUCCAGUUCUGCACA-AAACACUGAGGUCCAUU
AANG01132981.1/497-573       UG-GACCAAUGAUGACGAA--GUGUUUAUGAACAAAGCAUCAUGAUUAAUCCAGUUCUGCGCA-AAAUACUGAGGUCCAUU
AAQQ01697068.1/858-934       UG-GGCCAGUGAUGAGAAA--GUGUCUAUGAACAAAGGAUCGUGAUUAAUCCAGUUCUGCGCA-AAAUACUGAGGUCCAUU
AAPY01359948.1/6379-6455     UG-GACCAAUGAUGAGCAA--GCCUUUGUGAACAAAGGACCACGUUUAAUCCAGUUCUGCAGG-AAAUACUGAGAUCCAUU
AANU01283640.1/2332-2403     UG-GACCAGUGAUAAGAAC--GUGUU-AGGAACCAAAGAUUAUGAGUAAUCUAGUUUUGUAUA-----UCUGAGGUCCAUU
AAFC03050876.1/69355-69431   GG-GAUCUAUGAUGAAAAA--GUGUUUAUGAACAAAGGGUCGUGAUUAAUCCAGUUCUGCACA-AAGUACUAAGGUCCAUU
AAGV020923945.1/1278-1355    GU-GAAAUAGGAAGAGAAA--GUGUUGAUGAACAAAGGAUCGUGAUUAAUCCAGUUCUGCACAGAAAUACGGAGGUCCAUU
AAWR02020062.1/16730-16808   UG-GACCCAUGAGGAGAGAAAGUGUUUACGAACAAAAGAUGGUGAUUAAUCCUGUUCUGCGCA-AAGUACUGAGGUCCAUU
ABRN01400946.1/2385-2461     UG-GACCAAUGAUGAGAAA--GUGUUUGUGAACAAAGGAUCAUGAUUAAUCCAGUUCUGCGCA-GAAUACUGAGGUCCAUU
ABRT010568606.1/1153-1229    UG-GACCCAGGAUGAGACC--GUAUUUACGAACAAAGAAUCUCGAUUCAUCUGGUUCUGCACA-AAAUACUGAGGUCCAUC
ABRO01195545.1/6059-6137     UG-GACCAGUGAUGACAGACAAUGUUUAUGAACAAAGGCUCGUGAUUAAUCCAGUUCUGCACA-GACCGCACAGGUCCAUG
ABVD01661372.1/403-480       UGCGACUAAUGCUGAGACA--GUUUUUAUGAACAAAGGAUCGCGACUAACUCAGUUCUGCACA-AAAUGCUGAGGUCCAUC
AAEX03006004.1/437847-437923 UG-GACCAAUGAUGACAAG--GUGUUUAUGAACAAAGGAUCAUGAUUAAUCCAGUUCUGCGCA-AAAUACUGAGGUCCGUU
#=GC SS_cons                 <<.<<<<____________..__________________________________________._________>>>>>>::
#=GC RF                      uG.GAcCaAUGAUGAgAaA..GUgUUUAUGAACAAAGGAUCaUGAUUAAUCCAGUUCUGCACA.AAAUACUGAGgUCCaUU
//
# STOCKHOLM 1.0

#=GF AC   RF01170
#=GF ID   snoU61
#=GF DE   Small nucleolar RNA U61
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   55.90
#=GF NC   52.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.70 -Z 549862.597050 CM SEQDB
#=GF CL   CL00067
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [2]
#=GF RM   12520043
#=GF RT   Plant snoRNA database.
#=GF RA   Brown JW, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Huttenhofer A,
#=GF RA   Kastenmayer JP, Green PJ, Shaw P, Marshall DF
#=GF RL   Nucleic Acids Res. 2003;31:432-435.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


AC005314.3/53885-53968       GAGCUGUGAGGAA--AAAAUCGUGUGCCAGAGAU----------------GGUUAAUCCAUCGCUGACGGUAAUACACA-ACCCUCUAAGAAGUUCUGAGCUU
AP006141.1/89421-89503       AAUCUGUGAUGAA--AAUUUACUGUGCCGAAGACGAGUCUU---------U-----CUCGUCGGUGAUGGU-U--CACA-ACCCUCUAAGAAGUUCUGAGCUC
AJ532487.1/8-90              GGGCUGUGAGGAAAGAAAACCUUGUGCCGGAGGC----------------GG---AUGCGCCGGUGUCGGUAACACAAA-AUCCUCUAAGAAGUUCUGAGCUC
AASG02003152.1/15705-15613   CAGCCGUGAUGAA--AAAAACUUGUGUCCUUGAGACGGUUUUCUUAUAGAA-----AUCGUCUUUGACGGC--AACACA-ACCCUCUAAGAAGUUCUGAGCUG
AC146791.12/25263-25194      GAGCUAUGACGAA--AAAA-ACUGUGCUGGAG------------------------CUCGUCGAUGAUGG-----CGCA-AUCCUCUAAGAAGUUCUGAGCUU
AARH01009456.1/204753-204840 AUGCUGUGAUGAA--AUUC-UGUGUUCCAGAGACGGUCUCAGA----UGAG-----GUCGUCUUUGACGGU--UACACA-ACCCUCUAAGAAGUUCUGAGCUU
AARH01008371.1/237205-237118 AUGCUGUGAUGAA--AUUC-UGUGUUCCGGAGACGAUCUCAGA----UGAG-----GUCGUCUUUGACGGC--UGCACA-AACCUCUAAGAAGUUCUGAGCUU
ABXC01000468.1/77526-77612   UGGCGAUGAGGAAAGAAAUUCGUGUGCCGGAGGCGUCCGCU---------G-----GACGCCGGUGUUGGU--UCCACAAAUCCUCUAAGAAGUUCUGAGCCA
#=GC SS_cons                 <<<<_________..__________________________........._....._______________..______.___________________>>>>
#=GC RF                      gaGCuGUGAuGAA..AAaaucuUGUGCCggAGAcgaucuuu.........g.....uuCGUCguUGAcGGU..uaCACA.AcCCUCUAAGAAGUUCUGAGCuc
//
# STOCKHOLM 1.0

#=GF AC   RF01171
#=GF ID   snoR4
#=GF DE   Small nucleolar RNA snoR4
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   81.90
#=GF NC   37.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12520043
#=GF RT   Plant snoRNA database.
#=GF RA   Brown JW, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Huttenhofer A,
#=GF RA   Kastenmayer JP, Green PJ, Shaw P, Marshall DF
#=GF RL   Nucleic Acids Res. 2003;31:432-435.
#=GF CC   This model is based on the Medicago trunculata homolog of Arabidposis
#=GF CC   thaliana snoR4 which is included in Rfam model RF00147 (along with mouse
#=GF CC   and other species). This sequence was obtained from the plant snoRNA
#=GF CC   database.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AC150706.4/101845-101922 GGGAUAUGAGGAUAAAAAAAUUCAAAUGUGA--CAUCCAGUCUUACUACAUACGUGGUGAUUGAUCGACUAUCUGAUCCC
D90215.1/1270-1191       CUAACAAGGGGAUAAAAAAAUUCAAAUGUGAAACAACUAAUAUUCAAAUGUACGACGACCUUAAACAGCUCGGUGAAACU
#=GC SS_cons             ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  gggAuAuGgGGAUAAAAAAAUUCAAAUGUGAAACAuCuAgUaUUcauAugUACGugGugcUUgAuCggCUcggUGAuaCu
//
# STOCKHOLM 1.0

#=GF AC   RF01172
#=GF ID   sn2343
#=GF DE   Small nucleolar RNA sn2343
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   89.90
#=GF NC   38.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Caenorhabditis_elegans300004;
#=GF RN   [1]
#=GF RM   16344563
#=GF RT   Organization of the Caenorhabditis elegans small non-coding transcriptome:
#=GF RT   genomic features, biogenesis, and expression.
#=GF RA   Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z, Wang Y, He H, Cai L, Sun H, Liu
#=GF RA   C, Li B, Bai B, Wang J, Jia D, Sun S, He H, Cui Y, Wang Y, Bu D, Chen R
#=GF RL   Genome Res. 2006;16:20-29.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948660.1/1-78            CGGCUGUGAUGAUUUCCUA-UUGCCGUUUACCCGUCUGAGGAAAACCGUGCUUGAUACAACUUGGAAA--AGGCUGAGCCG
AAGD02003714.1/6065-5988   CGGCUAUGAUGAUUUCCUA-UUGCCGUUUACCCGUCUGAGGAAAACCGUGCUUGAGACUUUUGGAAGU--UGGCUGAGCCG
CAAC02000520.1/80909-80829 CGGCUGUGAUGAUUUCCUACUUGCCGUUUACCCGUCUGAGGAAAACCGUGCUUGACGAUUUUGGAAAAUUAGGCUGAGCCA
#=GC SS_cons               <<<<_______________.________________________________________________.._______>>>>
#=GC RF                    cGGCUgUGAUGAUUUCCUA.UUGCCGUUUACCCGUCUGAGGAAAACCGUGCUUGAuacuuuUgGaAaa..aGGCUGAGCCg
//
# STOCKHOLM 1.0

#=GF AC   RF01173
#=GF ID   snoU105B
#=GF DE   Small nucleolar RNA U105B
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   49.00
#=GF TC   49.90
#=GF NC   46.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.01 -Z 549862.597050 CM SEQDB
#=GF CL   CL00075
#=GF DR   snoRNABase; U105B;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300769;
#=GF RN   [1]
#=GF RM   16990247
#=GF RT   snoSeeker: an advanced computational package for screening of guide and
#=GF RT   orphan snoRNA genes in the human genome.
#=GF RA   Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2006;34:5112-5123.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   13


AABR05151673.1/128645-128724 CCCCAUGCAUCUGAUGAGAGCUUUGCUGCUGAGAUUGUGUGAUUGCUCAGACUCAAAGUAAACGCCCUGAUGCAUGCGCA
AAEX03012427.1/37620-37541   UCAUGUGCGGCUGAUGACAGUGUUCCAGCUGAGGGUCUGUGAUUGCUCAGUCUCAAAGUAAACGCUCUGACGCACUGUGG
AAFC03026210.1/28436-28510   CCAUGUGCAGCUGAUGACAGCACAGCUGCUGAGACUCUAUGAUUGCUCAGUCUCAAAGUAAA-----UGACGCACUGUGG
AAIY01448758.1/1752-1673     UGAGAUGUGGCUGAUAACAGUAUUAUGGGUGAGACUCUGUGAUUGCUCAAUCUCAAAGUAAACGCCCGGACAAUCCCUGG
AALT01065961.1/259-180       GUAUGUGCAGCUGAUGACAGCAUCGCUGCUGAGACUCGAUGAUGGCUCAGCCUUAAAGUAAACGCUCUGAUGCACAUCAC
AANG01184999.1/1981-2060     CCACGUGUGGCUGAUGACAACGCUCCUGCUGAGGCUCUGUGAUUGUCCAGUUUCAAAGUAAACGCCCUGACGCACUGUGG
AANU01122753.1/5340-5266     CCGCGUGCGGCUGAUGACAGCACUCCUGCUGAGACUCUGUGAUUGCUGUGUCUC-----AAACGCCCUGACGCACUGGGA
AAPE02048878.1/8840-8761     CUGUGUGCGGCUGAUGACAGUGCUGCUACUGAGACUCCAUGAUUGCUCAGUCUCAAAGUAAACGCCCUGACGCACCAUGA
AAPY01626968.1/365-287       UACCGUGCGG-UGAUGACAGUGCAGCUGCUGAGACGCUGUGAUUUCUCAGUCUCAAAGUAAACGCCCUGAGGCACGUGGG
AAQQ01144667.1/568-490       CCUUGUGCGACUGAUGACAGCACAGCUGCUGAGACUCCGUGAUUGCUCA-UCUCAAAGUAAACGCUCUGAUGCACUGCCC
AAWR02017824.1/7471-7392     CUCCAUGUGGCUGAUGACAGCGCUGCUGCUGAGACUCUGUGACUGCUCAGUGUCAAAGUAAACGCUCUGACGCACCGUGG
ABDC01292888.1/2468-2547     CCCAGUGCGGCUGAUGACAGCACUUCCGCUGAGGCUCUGUGAUUGCUCAGUCUCAAAGUAAACGCCCUGACGCGCCCUGG
AC020931.6/95709-95787       CCACAUGCGGCUGAUGACAGCACUUCUGCUGAGACGCUGUGAUUGCUCUGUC-CAAAGUAAACGCCCUGACGCACUGUGG
#=GC SS_cons                 ::::(((((<<<<____>>>>,,,,,,,<<<<<____________>>>>>,,,,,,,,,,,,,,,,,,,,))))):::::
#=GC RF                      ccauGuGcggCUGAUGACAGcacugCUGcUGAGACUCUGUGAUUGCUCAgUCUCAAAGUAAACGCcCUGAcgCaCugugg
//
# STOCKHOLM 1.0

#=GF AC   RF01174
#=GF ID   snoU43
#=GF DE   Small nucleolar RNA U43
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.30
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.42 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=DRO30008;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17994087
#=GF RT   Evolution of genes and genomes on the Drosophila phylogeny.
#=GF RA   Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC,
#=GF RA   Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM,
#=GF RA   Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW,
#=GF RA   Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D,
#=GF RA   Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak
#=GF RA   SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK,
#=GF RA   Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S,
#=GF RA   Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A,
#=GF RA   Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher
#=GF RA   AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD,
#=GF RA   Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC,
#=GF RA   Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey
#=GF RA   J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S,
#=GF RA   Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter
#=GF RA   GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz
#=GF RA   MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J,
#=GF RA   Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P,
#=GF RA   Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S,
#=GF RA   Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L,
#=GF RA   Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky
#=GF RA   E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L,
#=GF RA   McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P,
#=GF RA   Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S,
#=GF RA   Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M,
#=GF RA   Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli
#=GF RA   D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D,
#=GF RA   Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie
#=GF RA   MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S,
#=GF RA   Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz
#=GF RA   MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M,
#=GF RA   Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W,
#=GF RA   Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W,
#=GF RA   Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E,
#=GF RA   Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang
#=GF RA   J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A,
#=GF RA   Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K,
#=GF RA   Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A,
#=GF RA   Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A,
#=GF RA   An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A,
#=GF RA   Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C,
#=GF RA   Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y,
#=GF RA   Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De
#=GF RA   Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M,
#=GF RA   Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D,
#=GF RA   Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR,
#=GF RA   Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez
#=GF RA   N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L,
#=GF RA   Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P,
#=GF RA   Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X,
#=GF RA   Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P,
#=GF RA   Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T,
#=GF RA   Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V,
#=GF RA   Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N,
#=GF RA   Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E,
#=GF RA   Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F,
#=GF RA   Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N,
#=GF RA   Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N,
#=GF RA   Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y,
#=GF RA   Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk
#=GF RA   T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q,
#=GF RA   Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W,
#=GF RA   Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I
#=GF RL   Nature. 2007;450:203-218.
#=GF RN   [2]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   11



AEAB01027627.1/3905-3978     AUGAUGAUU--------UAGAAAAUUUAUGGUUAGAU-AUA-CUGAAUAA-CCUUGAUGAA--C---UUAUUCUAGGGCGGUCUGAUUUU
AADG06002824.1/6841-6765     AUGAUGAUUA-CA--UUUUUAAUGUUUAUGGUUUUAAAA---CUGAAUAA-CCAUGAGGAU--A----AAUUCUAGGGCGGUCUGAUAUU
AEVX01005495.1/1202-1277     AUGAUGAUUU-AG--A-UUAAAAGUUUAUGGUU----UUCGUCUGAAUAA-UCUUGACGAU--A---AUAUUCUAGGGCGGUCUGAUUUU
AJ784369.2/7-85              AUGAUGAGUA-UA--C-UAGAAGAUUUAUGGUUAGAACACAUAUGAUUAA-CCGUGAUUAU--C----UCAACUAGGGCGGACUGACCAA
AAEU02000017.1/580975-581052 AUGAUGAUU--UA--C-UAGAAGAUUUAUGGUUAGAACACAACUGAUUAA-CCGUGAUUAU--C----UCAACUAGGGCGGACUGACUAA
AAPP01019560.1/78790-78713   AUGAUGAGUA-AA--C-UAGAAAAUUUAUGGUUAGAACACA-AUGAAUAA-CCUUGAUUAA--A----UUAACUAGGGCGGACUGAUCAA
AAPU01010962.1/18103-18022   AUGAUGAGGAACA--G-UUAAAAUUUUAUGGUUAGAACACAUAUGAUUAA-CCGUGAUUAU--CA--AUUAACUAGGGCGGACUGACUCG
AADE01000237.1/3017-2936     AUGAUGAUAA-AA--GGUAAAAAAUUUAUGGUUAGAAACUGUAUGAUCAA-CCGUGAUUAUUAC----UUUACUAGGGCGGACUGACUAA
AANI01017147.1/264213-264131 AUGAUGAGAA-ACAGU-UAAAAUUUUUAUGGUUAGAACACAAAUGAUCAA-CUGUGAUUAUGAC----UUAACUAGGGCGGACUGAUUUG
AAPT01018771.1/29442-29360   AUGAUGAGGAACA--G-UUAAAUUAUUAUGGUUAGAACACAUAUGAUAAAACCGUGAUUAU--UA--AUUAACUAGGGCGGACUGAUUUG
AAQB01009437.1/229446-229526 GUGAUGAAUU-UA--G-U-UAUCAAUUAUGGUUAGAACAAACAUGAUUU--CCGUGAUUAU--CAAUUAUAACUAGGGCGAACUGACUAA
#=GC SS_cons                 ::::::::::.::..:.:::::::::::::::::::::::::::::::::.::::::::::..:....::::::::::::::::::::::
#=GC RF                      AUGAUGAuua.aa..g.UaaAAaaUUUAUGGUUAGAAcAcAuaUGAuuAA.CCgUGAUuAU..c....UuaaCUAGGGCGGaCUGAuUua
//
# STOCKHOLM 1.0

#=GF AC   RF01175
#=GF ID   snoU83D
#=GF DE   Small nucleolar RNA U83
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   80.00
#=GF NC   39.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=DRO30010;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


AJ784370.1/4-84              UGGAUGAUGAAACGAUGGUAUCUGAAUGAGC-AAA-UUAUUGUUGAGAAGCCUUU-UACCA--U--CUGCUGCCUUCCUUCUGAUCGG
AAPP01019560.1/78347-78267   UGGAUGAUGAUACGAUGGUAUCUGAAUGAGC-AAA-UUCCUGUUGAAAAGCCUUC-UACCA--U--CUGCUGCCUUCCUUCUGAUCAG
AAQB01009437.1/229861-229942 UGGAUGAUGAUAAGAUGGUAUCUGAAUGAGCUAAA-UUACUGUUGAGAAGCCUUG-UACCA--U--CUGCUGCCUUCCUUCUGAUCAA
AAIZ01002917.1/47541-47622   UGAAUGAUGAUACGAUGGUAUCUGAAUGAGC-AAAAUUCUUGUUGAAAAACCUUC-UACCA--U--CUGCUGCCUUCCUUCUGAUCGG
AAEU02000017.1/581399-581477 UGGAUGAUGAAAAAUUGGUAUCUGAAUGAGC-AAA-UUAUUGUUG--AAACCUUU-GAGCA--U--CUGCUGCCUUCCUUCUGAUCGG
AANI01017147.1/263803-263726 UGGAUGAUGAUGAGAUGGUAUCUGAAUGACC-------UUUGUCGAAAAACCUAC-UACCAUUU--CUGCUGCCUUCCUUCUGAUCGC
AAPT01018771.1/29024-28947   UGAAUGAUGAUAAGAUGGUAUCUGAAU------AU-AUGUUGUCGAAAAGCCUUC-UACCA--UCACUGCUGCCUUCCUUCUGAUAUC
AAPU01010962.1/17699-17623   UGUAUGAUGAGAAUUUGGUAUCUGAAUGACC--------CUGUCGAAAAUCUUGUAUACCA--UA-CUGUUGCCUUCCUUCUGAACAC
#=GC SS_cons                 <<_____________________________.___.___________________._____.._..___________________>>:
#=GC RF                      uGgAUGAUGAuAagaUGGUAUCUGAAUGAgC.AAA.uUauUGUuGAAAAaCCUuu.UACCA..U..CUGCUGCCUUCCUUCUGAUCag
//
# STOCKHOLM 1.0

#=GF AC   RF01176
#=GF ID   snR78
#=GF DE   Small nucleolar RNA snR78
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   48.20
#=GF NC   44.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.52 -Z 549862.597050 CM SEQDB
#=GF CL   CL00063
#=GF DR   snornadb; snR78;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   9891049
#=GF RT   Seven novel methylation guide small nucleolar RNAs are processed from a
#=GF RT   common polycistronic transcript by Rat1p and RNase III in yeast.
#=GF RA   Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y,
#=GF RA   Caizergues-Ferrer M, Bachellerie JP
#=GF RL   Mol Cell Biol. 1999;19:1144-1158.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


AJ010801.1/1-82                UCCCUUGAUGACCAAAAUAAAUUUUUACAAACUAGAGUUUCUGAAU---CUUUUGUGAUUAGAA---CGUUUAUU--------CUUAUUU--CUGAGG
AAZN01000292.1/3733-3648       UCCAUUGAUGACCAUGAUAAAAACAUACAAACUAGAGUUUCUGAA----CUUUAAUGAUUAGAAAACUGAUCAUG--------CAUAUCUCACUGAGG
AACF01000013.1/101212-101134   UCCGUUGAUGACCAUAUCAAA-AUAUACAAACUAGAGUUUCUGAAU----UUUAAUGAUUAGGA---AUUUGAUU---------AAAUC--ACUGAGG
CR382124.1/956328-956411       ACUUGUGAUGACUUCAUUUCA-AAAUACAAACUAGAGUUUCUGAAUAAAAAUUUAUGAUUAGAA---ACG-AAUG--------CAAAUAA-ACUGAAG
AJ617346.1/2-72                AUCUUUGAUGACCAUUUUUUA-AAAUACAAACUAGAGUUUCUGAUU---AAUUUAUGAUUUCAA---AUU--------------CUUG----CUGA--
CR380959.2/771671-771580       UUCGUUGAUGACUCUUGAUAAACAAUACAAACUAGAGUUUCUGAAC---AAUCAUUUAGUAGAA---UUGUUAGUGAUUAGGACAUAUCUUACUGAGG
AACE03000004.1/1105816-1105901 UCCGCUGAUGACCAAGAUUAA-AUAUACAAACUAGAGUUUCUGAAU---AUCUAAUGAUUAGAAAACUGAUCAUG--------CAUUGCAUACUGAGG
AE016815.5/489238-489315       GCCGCUGAUGACCAAAGAUAU--UUUACAAACUAGAGUUUCUGAUG---GUCACGUGAUUAGGA---ACUAUCUU--------GCUAU----CUGAGG
#=GC SS_cons                   :<<__________________.________________________..._______________...________........_______._____>>
#=GC RF                        uCCguUGAUGACcauaauUAA.auAUACAAACUAGAGUUUCUGAAu...auUUaaUGAUUAGAA...auuUuAUu........CaUAUcu.ACUGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01177
#=GF ID   snR67
#=GF DE   Small nucleolar RNA snR67
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   62.70
#=GF NC   35.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00053
#=GF DR   snornadb; snR67;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300033;
#=GF RN   [1]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science. 1999;283:1168-1171.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   16


AF064279.1/1-82              UAACAUGAUGACUAAGUUGUCGCCCCAA---GCGGAUC----------UUU----------------------GAA--A------UGACUGAUUUUACAAA----CAA---CAAACACUGAAAAUUCUGAAA
AAZN01000148.1/12872-12778   UAACAUGAUGACCAAGUUGUCGCCCCAA---GCGGAUCGACUAUCUUUUUA----------------------GAA--A------UGACAGACUACUACAA----CAUAGCCAAACACUGAAAAUUCUGAAA
AADM01000162.1/1080-1164     CAUUAUGAUGA-UAAGUUGUCGCCCCAA---GCGGAUU----------UCG----------------------AAAUUA------UGAACGAUUCGACAAU----AUAGC-CAAACACUAAUGUUUCUGAUC
AAPO01000010.1/296734-296826 UAUAAUGAUGACAACGUUGUCGCCCCAAACGGAGGAUC----------CUU----------------------UUC--AGGACGCUGACCGAUUCGAUAAA----UUAGC-CAAACACUGAAAAUUCUGACU
AAFM01000009.1/58038-58124   UACAGUGAUGAC-AACAUGUCGCCCCAA---GCGGAGG----------CCUCUUCAG----------------GCA--C------UGACCGAUUCGAUUCA----AGC---CAAACACUGAAAAUUCUGAGU
AACG02000007.1/85543-85462   UAACAUGAUGAC-UAGUUGUCGCCCCAA---GCGGAUC----------UUU----------------------GAA--A------UGACUGAUUUAACAAA----ACA-A-CAAACACUGAAAAUUCUGAAA
CR382121.1/185563-185648     GAUUAUGAUGAC--CGCUGUCGCCCCAA---ACGGAUU----------UCG----------------------AAAAUA------UGAACGAUUCGACUAGCA--UUAGC-CAAACACUGAAAAUUCUGAUC
AAFO01000004.1/83419-83510   UUAAAUGAUGAC-AAGCUGUCGCCCCAG---ACGGAGG----------CUCCUUUUCAGG-------------ACA--A------UGACCGAUUCGAUUUA----UUAGC-CAAACACUGAAAAUUCUGAAC
CP000500.1/204939-205028     UACAGUGAUGAC-ACGAUGUCGCCCCAA---ACGGAGG----------CUCCUAUUCAGG-------------ACG--A------UGACCGAUUCGAUUCA----AGC---CAAACACUGAAAAUUCUGAUC
AACF01000010.1/111499-111400 AUAGAUGAUGAC-AAGCUGUCGCCCCAA---ACGGAUC----------CUCUCUGUCACACACAGAGG-----GAG--A------UGACCGAUCAUUGACA----UUAGC-CAAACACUGAAAAUUCUGAAU
AAFT01000085.1/352609-352700 UUAUGUGAUGAC--CGCUGUCGCCCCAG---ACGGAGGAUCCUUUUC-AGG----------------------ACC--A------UGACCGAUUCGACAAA----UAGCCAAACACACUGAAAAUUCUGAAC
CR380956.2/1157269-1157167   UAUUAUGAUGACUAAGUUGUCGCCCCAA---GCGGAAA----------GGGUUCACCGACAAUGGAACCCGUUAUU--A------UGACAGACUACUACAA----CCA----AAACACUGAAAAUUCUGAAC
AACE03000001.1/368840-368755 CCUAAUGAUGAC-AAGCUGUCGCCCCAA---GCGGAUU----------UCG----------------------AAAGCA------UGAACGAGUCGACUAA----AUUAGCCAAACACUGAAAAUUCUGAUC
CR382138.2/2180107-2180014   UACCGUGAUGAC-ACGCUGUCGCCCCAA---ACGGAGGCUCCUUUUA-CAG----------------------GACU-A------UGACCGAAUCGAUUUU----AUGCCAAACACACUGAAAAUUCUGAAG
AE016814.2/570456-570373     UUAGGUGAUGAC--AGUUGUCGCCCCAA---ACGGAUU----------CGC----------------------AAA--A------UGAACGAUUCGACUACAAUGCCA---AACACACUGAAAAUUCUGAUU
AAFN02000078.1/376063-376155 UUGAAUGAUGACAAAAUUGUCGCCCCAG---UCUGAAUACCUUUUC--AGG----------------------GUG--A------UGACUGAA-CGACAAUCU--AUAGC-CAAACACUGAAAAUUCUGAUC
#=GC SS_cons                 ::::::::::::.:::::::::::::::...:::::::..........:::......................:::..:......::::::::::::::::....:::::.:::::::::::::::::::::
#=GC RF                      uauaAUGAUGAC.AaGuUGUCGCCCCAA...gCGGAuu..........cug......................gaa..A......UGACcGAuUcgauaaa....uuagc.CAAACACUGAAAAUUCUGAac
//
# STOCKHOLM 1.0

#=GF AC   RF01178
#=GF ID   snoR77Y
#=GF DE   Small nucleolar RNA snoR77Y
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   52.00
#=GF TC   53.50
#=GF NC   50.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00057
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12136108
#=GF RT   A novel gene organization: intronic snoRNA gene clusters from Oryza
#=GF RT   sativa.
#=GF RA   Liang D, Zhou H, Zhang P, Chen YQ, Chen X, Chen CL, Qu LH
#=GF RL   Nucleic Acids Res. 2002;30:3262-3272.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   21


AAAA02011059.1/20497-20416   GA--GCCUGUGAUGAUUAGCAUAUU----GUUGGAAUUACCGUCGGAUU---AUCA---AAUGACGAC--A-----UUUGUCUGGCU--UCCUGAGGCUUAAU
AASG02011273.1/5793-5709     AG--GCCAAUGAUGAUUUCUUUUUA----GUUGGAAUUACCGGCUGAAU---UUCA---UUUGAUGUC--AAUU--UUAGACUGGCU--UUCUGAGGCUUCAU
AARH01006125.1/83661-83576   GA--GCCGAUGAUGAUUGUUUAUUUA--UGUUGGAAUUACCGGCUGAAU---UUCA--CAUUGAUGUC-AA-----UCUUACUGGCU--GUCUGAGGCUUCAU
AM483106.2/1366-1281         AA--GCCAAUGAUGAUUUUGUCUGA----UCUGGAAUUACCGGCUGAAU---UUUG--CUUUGAUGUC--AAAU--UUUGACUGGCU--UUCUGAGGCUUCAA
CU062477.6/15802-15711       AA--GCCGAUGAUGAUGAAACUUGA----ACUGGAAUUACCGUCUGAAUAGAUUUAUUCUUUGAUGUA--AAUU-UCUUGGCUGUGG--UACUGAGGCUUUGC
AC131239.20/38708-38798      AA--GCCUAUGAUGAUAAAA-CAUA----UCUGGAAUUACCGUCUGAAUAGAUUUAUUCUUUGAUGUA--AAUU-UCUUGGCUGUGG--UACUGAGGCUUCUG
ABXC01006880.1/57239-57321   AC--UCCUUUGAUGAUUAGCUAUAC---AUCUGGAAUUACCGUCAGAUU---UACU---UGUGACGAC--A-----UUUGUCUGGCU--UUCUGAGGAUUUAU
ABXC01002952.1/3490-3408     AA--GCCAAUGAUGAUUAGCUAUAC---AUCUGGAAUUACCGUCAGAUU---UACU---UAUGACGAA--A-----AUUGUCUGGCU--UGCUGAGGCUUAUG
AARH01001267.1/61415-61503   A---GCCAAUGAUGAUUGUUUUUGUU-UAGUUGGAAUUACCGGCUGAAU---CUCA--UUUUGAUGUC--A-UU--UUAUACUGGCUGUGUCUGAGGCAUCAU
AASG02013750.1/2808-2721     AA--GCCAGUGAGGAUUUCUUUUAUU-UAGUUGGAAUUACCGGUUUAAU---UUCA---UUUGAUGUC--AAUU--CUAAAGUGGCU--AUAUGAGGCUUCAU
BT065282.1/900-981           GA--GCCAAUGAUGAUUAGCAUACA----UCUGGAAUUACCGUCAGAUU---UACU---UAUGACGAA--A-----AUUGUCUGGCU--UGCUGAGGCUUAAC
ABEU01004381.1/198994-198909 AG--ACCAGUGAGGAUC----UUUA----UUUGGAAUUACCGGCUGAAGG-UUUUA--CUCAAAUCUG--AAUGCUGAGAACUGGCU--GACUGAGGUCUUCC
BT084578.1/886-969           AA--GCCAAUGAUGAUUAGCUAUUAC--AUCUGGAAUUACCGUCAGAUU---UACU---CGUGACGAA--A-----AUCGUCUGGCU--UUCUGAGGCAUAUU
ABIM01003022.1/5516-5601     GA--GCCAAUGAGGAUUGUUUAUAUU-UAGUUGGAAUUACCGUCUGAAU---UCU----UUUGAUGUC--A-UU--UUAGACUGGUU--UUCUGAGGUUCCGU
AC235231.1/103306-103383     AA--GCCGAUGAGGAUUAGAUUUGA----AUUGGAAUUACCGUCUGAAC---AU------CUGAUGAG--AG------UUUCUGGCU--GACUGAGGCUUCGU
AC235267.1/40195-40271       AA--GCCGAUGAGGAUUAGAUUUAA----AUUGGAAUUACCGUCUGAUC----------UUUGAUGAG--AAUU--U----CUGGCU--GACUGAGGCUUCGU
AP009154.1/18595-18675       GA-UGCCAAUGAUGACUUA-AUUGA----AUUGGAAUUACCGUCUGAAU-----CA---AUUGAUGUG--ACUU--UCUGGCUG--U--UUCUGAGGCUCAAU
ABEU01011083.1/97260-97174   GA--GCCGAUGAUUAUUG----UUA----AUUGGAAUUACCGGCUGAUGG-UUUCA---AUGUAAGCCAGAAUGCUGUGAACUGGCU--GACUGAGGCUUUCG
AK117712.1/553-641           GAUUACCGAUGAUGAUUAUUGCUAAA--CUAUGGAAUUACCGUCUGAGU---UUAUU-CUUUGACGAG--AA----AAACGCUGGCU--UACUGAGGUUUCCC
ABCN01002957.1/108986-109064 GG--ACCGGUGAUGAUUAAAAUUAUUAAAUAUGGAAUUACCGUCCGAUU---UA------AUGAGGAG--A---------ACUGGCU--GCCUGAGGUCCACA
AJ310377.1/1109-1028         AA--GCCUAUGAUGAUUAGCAUAUU----GUUGGAAUUACCGUCAGAUU---AUCA---AAUGACGAC--A-----UUUGUCUGGCA--UCCUGAGGCUUUAU
#=GC SS_cons                 <<..<<<__________________....____________________...____..._________..____..___________..______>>>>>:::
#=GC RF                      aa..GCCaAUGAUGAUUauuuuUua....uuUGGAAUUACCGuCUGAaU...UUca...UuUGAuGuc..AAUu..uUugaCUGGCU..uuCUGAGGCuucau
//
# STOCKHOLM 1.0

#=GF AC   RF01179
#=GF ID   snoU83
#=GF DE   Small nucleolar RNA U83
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.70
#=GF NC   48.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.33 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2003;31:2601-2613.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AC155101.19/100605-100523    UUCCAAUGAUGAGAUCGAUGGAAAAUGUGUUAGG---GUAUGAACAUUGAUGAUU---U--ACUAUACCA-UACUGCCUUCCUUCUGAGGAA
AARH01007481.1/123778-123693 UGCCAUUGAUGAAAGAACUGGUAUAUUUGUCACGAAUGAUGAAGCUGUGAUUACA---A--ACUUACCAC-UACUGCCUUCCUUCUGAGGCU
AASG02001268.1/26859-26944   UGCCGGUGAUGAAAGAAAUGGUAAAUUAGUCACU---CAUGACAAAUUUGUGAUUACAG--ACAUACCAC-UACUGCCUUCCUUCUGAGGCU
BT017923.1/466-551           GGCCAAAGAUGAAAUAUGUGGAUGCUAUUUCUGUA-UGACGUCUCACGUCUGAUU---AC-AAAACCCAU-UACUGCCUUCCUUCUGAGGCC
AC108499.3/93788-93708       GGCCUAUGAUGAUCAAUGUGGAAACCUUU---CU---CUCUGAAAUCUUGUGAGG---AC-AUACCCUAC-UACUGCCUUCCUUCUGAGGUC
FN595756.1/3108538-3108621   UGCUGAUGAUGA-AACAAAGGAUACUUUGUAAUG----UAUGAGAAAUCAUGAUU---ACAACUAUACCUCUACUGCCUUCCUUCUGAAGCU
AJ490436.1/3-83              GGCCUAUGAUGAUCAAUGUGGAAACCUUU---CU---CUCUGAAAUCUUGUGAGG---AC-AUACCCUAC-UACUGCCUUCCUUCUGAGGUC
#=GC SS_cons                 :<<<______________________________...__________________...__._________._________________>>>:
#=GC RF                      ugCCaAUGAUGAaAaAaaUGGAAAaUUUgUcAcu...guuugAaaauUuaUGAuu...AC.AcaaucCAc.UACUGCCUUCCUUCUGAGGcu
//
# STOCKHOLM 1.0

#=GF AC   RF01180
#=GF ID   snoR110
#=GF DE   Small nucleolar RNA snoR110
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   44.60
#=GF NC   40.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300016;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AJ505681.1/1-83        GCUAAAUUUAGUGCCGCC-UUGUCUUUUCA-AGUUUUCUCCUU---UUGUAUGUAAGGA-AUCACUUUUAUACUUGGUGGCAUAAAUCU
AC189353.2/34023-33935 GCUACAUUUAGUGCCGCCUUUGUCUUUUCAAAGUUUUCUCCUUUUUUUGUAUUUAAGGACAUUACUGUUUUACUCGGUGGCAGAAAUCU
#=GC SS_cons           :::::::::::<<<<<<<---<<--------<<<--<-<<<<<___________>>>>>->-->>>----->>-->>>>>>>:::::::
#=GC RF                GCUAaAUUUAGuGCCgCCUUUGuCUUUUCAAaGuUUuCuCCuuUUUUUGUAUuUaaGGacaUuaCuuUUuUaCUuGGuGGCauAAAUCU
//
# STOCKHOLM 1.0

#=GF AC   RF01181
#=GF ID   snR77
#=GF DE   Small nucleolar RNA snR77
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   54.20
#=GF NC   42.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00057
#=GF DR   snornadb; snR77;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   9891049
#=GF RT   Seven novel methylation guide small nucleolar RNAs are processed from a
#=GF RT   common polycistronic transcript by Rat1p and RNase III in yeast.
#=GF RA   Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y,
#=GF RA   Caizergues-Ferrer M, Bachellerie JP
#=GF RL   Mol Cell Biol. 1999;19:1144-1158.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   15


Z69299.1/1-84                  UCAUAUGAUGAUUAUAACAAAAACAAAAGCUGGAAUUACUGGCUGAACGAGUAUAUGUUGAU--ACGUUUUUGC---ACUA-U-CCUGACC
AACI02000031.1/7633-7716       AUGAAUGAUGAUUAUAACAAAAACAAAAGCUGGAAUUACUGGCUGAACGAGUAUAUGUUGAU--ACGUUUUUGC---ACUA-U-CCUGACU
AACA01000204.1/8000-7917       UUAUAUGAUGAUUAUAACAAAAACAAA-GCUGGAAUUACUGGCUGAACGAAUAUAUGUUGAU--AAGUUUUUGCA--ACUA-U-CCUGACU
AAZN01000292.1/3455-3372       CUAAAUGAUGAUG-UAACAAAAACAAAAGCUGGAAUUACUGGCUGAACGAUUAUAUGUUGAU--ACGUUUUUGC---ACUA-UUUCUGAUU
CR382124.1/956620-956705       UACUAUGAUGAUCCUUACAAAAACAAAAGCUGGAAUUACUGGCUGAAAGACUACGUGUUGAU--AAGUUUUUGGCA-AUAA-G-ACUGAUU
AADM01000093.1/237924-238006   CUUAAUGAUGAUU-GAACAAAAACAAA-GCUGGAAUUACUGGCUGAACGAUUAUAUGUUGAU--AAGUUUUUGC---ACUA-UUUCUGAAU
AAVQ01000001.1/1457885-1457967 UACUAUGAUGACU-UAACAAAAACAAAAGCUGGAAUUACUGGCUGAAUCUCUAU-GAUUGAU--ACGUUUUUGCA--ACUC-U-ACUGAUC
AAPO01000086.1/18704-18621     UAUUAUGAUGAUU-UAACAAAAACAAA-GCUGGAAUUACUGGCUGAAUCUCUAU-GAUUGAU--AAGUUUUUGCAAAACGC-U-UCUGAUA
AAFM01000013.1/140629-140710   UUAGAUGAUGACU-UAACAAAAACAAA-GCUGGAAUUACUGGCUGAAUCUCUAU-GAUUGAC--AAGUUUUUGC---ACUA-UUUCUGAUU
AAFT01000027.1/99956-99875     UAUUGUGAUGAUA-CAACAAAAACAAA-GCUGGAAUUACCAACUGAAUCUCUCU-GAUUGAU--AAGUUUUUGC---AUUA-UUACUGAAG
AACF01000013.1/100989-100904   UUUUAUGAUGAUCAUCUCAAAAACAAAAGCUGGAAUUACUGGCUGAACGAGUAUAUGUUGAU--ACGUUUUUGCA--ACUA-UUACUGAUU
CR382139.2/220120-220199       UAUUAUGAUGAUU-UAACAAAAACAAA-GCUGGAAUUACUGGCUGAAACUCUAU-GAUUGAU--AAGUUUUUGC---ACU--U-CCUGAUA
CR380959.2/771358-771273       UUUUAUGAUGAUUCAAUCAAAAACAAAAGCUGGAAUUACUGGCUGAACGACUACAUGUUGAUAAAGUUUUUGGC---ACAA-CAACUAAA-
AACE03000004.1/1106015-1106097 CAUUAUGAUGAUUA-AACAAAAACAAA-GCUGGAAUUACUGGCUGAAUACUUCGAUGUUGAU--AAGUUUUUGC---ACUACU-UCUGAAU
AE016815.5/489394-489476       UCGAGUGAUGAAU-UAACAAAAACAAAAGCUGGAAUUACUGGCUGAAUUUAUCUGUGUUGAU--ACGUUUUUGC---ACUA-C-UCUGACU
#=GC SS_cons                   :::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::..::::::::::...::::.:.:::::::
#=GC RF                        UuuuAUGAUGAUu.uAACAAAAACAAAAGCUGGAAUUACUGGCUGAAugacUauauGUUGAU..AaGUUUUUGC...ACuA.u.uCUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF01182
#=GF ID   SNORD11
#=GF DE   Small nucleolar RNA SNORD11
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   57.40
#=GF NC   52.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.85 -Z 549862.597050 CM SEQDB
#=GF CL   CL00103
#=GF DR   snoRNABase; HBII-95;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300762;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   19


AC064836.7/31785-31868       -GUGUUCAAUGAUGAUUU--CUAUUUG---UUU----GCCUGAUUUCCUUU-UGGAUAA-UGAAGGCAUCUUUAGUCACUACCUCUUCUGAGACAC
AAFC03122356.1/14349-14432   -GUGUUCGAUGAUGAUUU--UUAUUUG---UAU----GCCUGAUUUCCUUU-CGGAUAG-UGAAGGCAUCUUUAGUCACUACCUCUUCUGAGACAC
ABDC01102575.1/7482-7565     -CAGUUCAGUGAUGAUUU--UUGUUUG---UUU----GCCUGAUUUCCUUU-UGGAUAA-UGAAGGCAUCUUUAGUCACUACCUCUUCUGAGACAC
AAPY01283634.1/685-768       AGUGU-CAAUGAUGACUU--UUAUUUG---UUU----GCCUGAUUUCCUUU-UGGAUAA-UGAAGGCAACUUUAGUCACUACCUCUUCUGAGACAC
AANN01299364.1/1497-1580     -GUGUUAGAUGAUGAUUU--UUAUCUG---UAU----GCCUGAUGUCCUUU-UGGAUUA-UGAAGGCAUCUUUAGUCACUACCUCUUCUGAGACAC
AAQQ01276055.1/322-401       -GUGUUCAAUGAUGAUU------UUUG---UUU----GCUGGAUUUCCUUU-UGGAUAA-UGAAGGCAUCUUUAGUCACUACCUCUUCUGAGACAC
AANG01224129.1/249-332       -GUGUUCAAUGAUGAUUU--UAAUUAU---UAU----GCUUGAUUUCCUUU-UGGAUAA-UGAAGGCAUCGUUAGUCACUACAUGUUGUGAGACAA
AALT01509875.1/1637-1555     -GUGUUCAAUGAUGAUUU--UUGUUUG---CAU----GCCUGAU-UCCUUU-UGGUUAA-UGAAGGCAUCUAUAGUCACUACCUCUUCUGAGACAC
AAFR03042041.1/46276-46193   -GUGAUCUGUGAUGAUUU--UAAUUUG---UUU----GCCUGACUUCCUUU-UCAAUAA-UGAGGGCAACUUUAGUCACUACCUCUUCUGAGACAC
AAIY01263621.1/2209-2122     -GUGUUCAGUGAUGAAUU--UUAUUUG---CUUGGUUGCCUGACUUCCUUU-GGGAUCA-UGGAGGCAUCUUUAGUCACUACCUCUUCUGAGACAC
AAPN01394254.1/11353-11436   -GUGAUCGGUGAUGAUUU--GGAUUUG---UUU----GCCUGACUUCCUUUGUGGAUAA-UGAAGGCAAC-UCAGUCACUACCUCUUCUGAGACAC
AAGV020290171.1/4538-4621    -GUGUUCAAUGAUGAUUU--UUAUUUG---UGU----GCCUUACUUCUUGU-UGGAUAA-UGAAGGCAUCUUUAGUCACUACCUCUUCUGAGACAC
AAQR03079580.1/3274-3356     -UGGUUCAAUGAUGAUUU--UUGUUUG----UU----GCCUGAUUUCCUUU-UGAAUAA-UGAAGGCAUCUUUAGCCCCUACCUCUUCUGAGACAC
AAHX01060272.1/22200-22117   -GUGUUCAAUGAUGAUUU--CUGAUGC---CUU----GCCUGAGUUCAUUU-UGAAUAA-UGAGGGCAGCUUCAGUCACUACCUCUUCUGAGACAC
AAEX03018026.1/131279-131362 -GUGUUCAAUGAUGAUUC--UAAUGUG---UAU----GCCUGAUUUCCUUU-UGGAUAG-UGAAGGCAUCUUUAGUCACUACCUCUUCUGAGACAC
AAPE02003157.1/9655-9738     -GUGUUCGAUGAUGAUUU--UUACUUG---UAU----GCCUGAUUUCCUUU-GGGAUAA-UGAAGGCAUCUUUAGUCACUACCUCUUCUGAGACAC
AADN03005370.1/30193-30108   -GUAGUCUGUGAUGAUGUAGUUCUUGG---UUG----GCCUGAAUCCUUUU-UGGAAUA-UGAGGGCAACUUAAGUCACUACCUCUUCUGAGACAC
AAWZ02015300.1/4623-4536     -GCAUUCAAUGAUGAUUC--AUUUCUGAAGUUU----GCCUGAUUUCAUCU-UUGAAAAGUGAAGGCAACUCUAGUCACUACCUCUUCUGAGAUGC
EU240222.1/2-82              -GU---CUGUGAUGAUGUAGUUCUUGG---UUG----GCCUGAAUCCUUUU-UGGAAUA-UGAGGGCAACUUAAGUCACUACCUCUUCUGAG--AC
#=GC SS_cons                 .<<<<_____________.._______...___....______________._______.________________________________>>>>
#=GC RF                      .guGuUCaAUGAUGAUUU..uUaUUUG...UuU....GCCUGAuUUCcUUU.UGGAUaA.UGAAGGCAuCUUUAGUCACUACCUCUUCUGAGaCac
//
# STOCKHOLM 1.0

#=GF AC   RF01183
#=GF ID   SNORD19B
#=GF DE   Small nucleolar RNA SNORD19B
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   51.60
#=GF NC   48.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF CL   CL00048
#=GF DR   snoRNABase; HBII-108B;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16990247
#=GF RT   snoSeeker: an advanced computational package for screening of guide and
#=GF RT   orphan snoRNA genes in the human genome.
#=GF RA   Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2006;34:5112-5123.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   17


ABDC01345891.1/4294-4211   GGAUGGUUGAAAUAUGAUGAGUUUACAAAAUCUUGAU-UUAAAAAAA-UGAAAAAUUACAAGAUCCAACUCUGAUUUCAUCCGGAG
AAFC03120533.1/12388-12469 AGAUGGGUGAAACAUGAUGAGUGUACAAAAUCUUGAU-UAAAA--AA-UGAAAACUUAUAAGAUCCAACUCUGAUUUCAUCCAGAA
AACN010086138.1/143-224    GAAUGGCUGAAAUAUGAUGAGCAUACAAAAUCUUGAU-UAAAA--AA-UGAGAAUUUAUAAGAUCCAACUCUGAUUUCAUCCAGAG
AAQQ01595244.1/1480-1396   CAAUGGUUGAAAUAUGAUGAGUAUGCAAAAUGUUGAUUUUUAAAAAA-UGAAAGACAAUAAGAUCCAACUCUGAUUUCAUCCAGAG
AAYZ01025109.1/1765-1846   UGAUGGUUGAAAUAUGAUGAG--UAUAGAGUCUUGAU-UUCAAAAAA-UGAAAAGAUACAAGAUCCAACUCUGAUUUCACCCAAAG
AALT01657539.1/12894-12813 CGAUGGCUGAAGCAUGAUGAGUAUGUAAAAUCUUGAU---AAUAGAA-UGAAAACAGAAAAGAUCCAACUCUGAUUUCAUCCAGAG
AANN01012319.1/2357-2440   GGUUGGCUGAAAUAUGAUGAGUGUAGUAAAUUUGAUC-UUAAAAACA-UGAAAGUUUGUGAGAUCCAACUCUGAUUUCAACCAGAG
AAPY01503610.1/3331-3412   AUAUAGUUGAAAUAUGAUGAGUGUACAAAAU-UUGAU-GUAAAA-AA-UGAAAAAUGUUAAGAUCCAACUCUGAUUUCAACUCAGG
AAHX01086457.1/3836-3915   UGAUGAUUGAAAUAUGAUGAGCAUACAAAAUGUUGAU-UACAG-----UGAAAAACAGUAAGAUCCAACUCUGAUUUCAUUAAAGA
AAFR03021759.1/98276-98197 UUUGGGUUGAAAUAUGAUGAACACUGAAAA-CUAGAU-GGAAUUG----UGAAGAUCACAAGAUCCAACUCUGAUUUCACCCAGAG
CAAA01053942.1/45659-45581 UGAUGAUUGAAAUGUGAUGAGUACACAAA-UGUUGAU-GAAAG-----UGAAAAACAUGAAGAUCCAACUCUGAUUUCAUUAAAAA
AAPN01330667.1/5443-5363   UCUGGGUUGAACUGUGAUGAAACUGAUCGCUCUGGAU-ACAAGAG----UGAAGAAUACAAGAUCCAACUCUGAUUUCAUCCCAUU
AAKN02001398.1/27645-27565 GGAUGGUUGAAAUAUGAUGAGUAUAUGAGAAGUUGAG-UUAA---AA-UGAAAAAUAAAAAGAUCCAACUCUGAUUUCAUCCAGAG
AAWR02008448.1/14428-14347 GGAUGGCUGAAAUAUGAUGAGUCUACAAAAUCUUGAU-UAAAA--AA-UGAAAACUUAUAAGAUCCAACUCUGAUUUCAUCCAGAG
AAGW02044176.1/48131-48214 UGACGGUUGGAAUAUGAUGAGUAUGCAGAAUCUUGAU-UUUAAAAAA-UGAAAAGUUACAAGAUCCAACUCUGAUUUCAUCCUAAG
AC104446.2/143509-143592   UUUUGGUUGAAAUAUGAUGAGUGUACAAAAUCUUGAU-UUAAGUGAA-UGAAAAAUUACAAGAUCCAACUCUGAUUUCAGCCAGAG
JN899098.1/1-85            AGAUGGGUGAAAUAUGAUGAGUAUACAAAAUCUUGAU-UUAAAAAAACUGAAAGCUUGUAAGAUCCAACUCUGAUUUCAUCCAGCA
#=GC SS_cons               :::<<<_______________________________._________.________________________________>>>:::
#=GC RF                    ugAuGGUUGAAAUAUGAUGAGuaUAcAAAAUcUuGAU.uuAAaAaAA.UGAAAAAuuAuAAGAUCCAACUCUGAUUUCAuCCagAG
//
# STOCKHOLM 1.0

#=GF AC   RF01184
#=GF ID   snR79
#=GF DE   Small nucleolar RNA snR79
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   58.20
#=GF NC   50.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.66 -Z 549862.597050 CM SEQDB
#=GF DR   snornadb; snR79;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300003;
#=GF RN   [1]
#=GF RM   9891049
#=GF RT   Seven novel methylation guide small nucleolar RNAs are processed from a
#=GF RT   common polycistronic transcript by Rat1p and RNase III in yeast.
#=GF RA   Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y,
#=GF RA   Caizergues-Ferrer M, Bachellerie JP
#=GF RL   Mol Cell Biol. 1999;19:1144-1158.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   18


AJ010802.1/1-84                ---UUAAUGAUGAUAGCAUGAUUUAUGUUGCUCGAAG------------UUAAUCGAUGUGAGC-ACAA-UGAUUUCUCA--AGACUACAACGGUAUCUGAAU
AAZN01000268.1/117161-117076   --UUAUAUGAUGAUAC-AAAUAUAUUGUUGCUCGAAGA-----------UUUAUCGAUGUGAGC-ACA--UGAUUUCUCAAUAGACUACAACGGUAUCUGAAU
AADM01000279.1/19853-19939     --UUUGAUGAUGAUAC-AAAU--UAUGAUGCUUGAAGAGU---------UUUCUCACUGUGAGC-ACAA-UGAUUUCUCAAUAGACUACAACGGUAUCUGAAA
AACF01000007.1/69722-69637     --UUAAAUGAUGACAAUUUGU-UAACGUGGCUCGAAGA-----------UUAUUCGAUGUGAGC-ACA--UGAUUUCUCAAUAGACUACAACGGUAUCUGAUU
AAFO01000049.1/295349-295263   --UUAAGUGAUGAUAA----A--AGUGUGUCUUUAAGGUUUAA------ACACCUAAUGUUAGC-ACAA-UGAUUUCUCAAUAGACUACAACGGUAUCUGAUU
AAVQ01000001.1/1604795-1604883 --UUAAGUGAUGAUAACUUGA--UUAGUGUAUCGAAGGUCUA-------CGGAUCACUGUGAGC-ACA--UGAUUUCUCAAUAGACUACAACGGUAUCUGAAA
CR382126.1/1839223-1839134     -A-UAUAUGAUGAUAAACCAUUUUAGAUGUCUCGAAGAAUU--------UAUUUCAAUGUGAGC-ACA--CGAUUUCUCAAUAGACUACAACGGUAUCUGAUU
CU329670.1/2705952-2706037     --UACGCUGAUGACACUGUAUUUGAU---GCUGG-AGAAU---------CCGUUCGGUGAAGGC-ACAA-UGAUUUCUCAAAAGACUACAACGGUAUCUGAGU
AAPO01000083.1/37264-37176     --UUGCAUGAUGACAAUUUGA--CAAGUGUCUUUAAGAUCGA-------AAGAUCAGUGUGAGC-ACA--UGAUUUCUCAAUAGACUACAACGGUAUCUGAUU
AATM01000036.1/34063-34139     --UGUGGUGAUGACAACCU-UUUUAU---GCUUGAA----------------UACUAUGAGAGC-AUA--AGAUUUCUCA-AAGACUACAACGGUAUCUGAGC
AAFM01000009.1/206343-206266   ---UCUCUGAUGAU-CCAAACAUUAU---GCUUGAA---------------UCUCCGUGUGAGC-AUA--CGAUUUCUCAAUAGACUACAACGGUAUCUGACG
AAFT01000026.1/250563-250640   ---UUAAGGAUGACACCAAAUUUCGUGUUGCUUGAAGA-----------UUUUUCGCUGUAAGCCACA-----------AAUAGACUACAACGGUAUCUGACU
CR382128.1/956260-956186       CUUGACAUGAUGAUAUCGAAAACCUU---UCUUGAA-----------------CUCCUGAGAG-------UGAUUUCUUA-UAGACUACAACGGUAUCUGAUU
CR382137.2/1314996-1314907     ---UUUAUGAUGAUAACCUGAUUACAGUGUCUUUAAGUUCUU-------CGGAUCGAUGUGAGC-ACA--UGAUUUCUCAAUAGACUACAACGGUAUCUGAUA
AACE03000008.2/886365-886279   ---UGUAUGAUGAUAA-AACUGUCAUGUUGCUCGAAGA-----------UUUUUCGAUGUGAGC-GCAAACGAUUUCUCAAUAGACUACAACGGUAUCUGAUU
CR380959.2/1142643-1142545     --UUCGAUGAUGAUAAUAUGUUACAUGUUGCUUGAAGACAGUCCGAUGGGCUGGCACUGUGGGC-ACAA-UGAUUUCUCAAUAGACUACAACGGUAUCUGAGU
AAFN02000004.1/75742-75828     ---UUAGUGAUGACAA----U--ACUGUGUCUUUAAGGUAAUUU-----ACUCCUAAUGUUAGC-ACAA-UGAUUUCUCAAUAGACUACAACGGUAUCUGAUU
AE016820.4/1171098-1171018     --UUAUAUGAUGAUAA-UUAC--UAU---GCUCGAAGA-----------UAUUUCGAUGUGAGC-AUA--CGAUUUCUCAAUAGACUACAACGGUAUCUGAUA
#=GC SS_cons                   ..::::::::::::::::::::::::::::::::::::::.........:::::::::::::::.:::..:::::::::::::::::::::::::::::::::
#=GC RF                        ..UUuuaUGAUGAUAacauguuuuauGUggCUuGAAGauu.........uuuuuCgaUGUGAGC.ACA..uGAUUUCUCAAUAGACUACAACGGUAUCUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF01185
#=GF ID   snR75
#=GF DE   Small nucleolar RNA snR75
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   43.00
#=GF NC   39.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.82 -Z 549862.597050 CM SEQDB
#=GF CL   CL00045
#=GF DR   snornadb; snR75;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   9891049
#=GF RT   Seven novel methylation guide small nucleolar RNAs are processed from a
#=GF RT   common polycistronic transcript by Rat1p and RNase III in yeast.
#=GF RA   Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y,
#=GF RA   Caizergues-Ferrer M, Bachellerie JP
#=GF RL   Mol Cell Biol. 1999;19:1144-1158.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   61


AJ010798.1/1-83                UU--A---UGAUGAGAUAUUUAUAGAUGACGAGUCUGAUCA----------UUC--GU---------------------GAAG-AC--A-CAACUAU----UAAAAUU-----ACCAUUCAUGCCUU-UCUGAAG
AAZN01000292.1/2990-2905       UU--UA-GUGAUGA-AUACUUAUAGAUGACGAGUCUGAUCUA--------CUUU--GU---------------------GAAG-AC--A-AAACUAU----UUUUAAU-----UCCAUUCAUGCAUU-UCUGAAA
CR382124.1/957132-957216       UCGAA---UGAUGAGCU-UUUAUAGAUGACGAGUCUGACUA----------UUCAGUU---------------------GAAG-AC--A-CAACUAU----UUUAAU------ACCAUUCAUGCAUU-UCUGACU
AACF01000013.1/100529-100445   UCCAA---UGAUGAGACCUUU-UAGAUGACGAGUCUGAUCU----------UUGAAGU---------------------GAAG-AC--A-AAUCUAA----UUUAAU------ACCAUUCAUGCCUU-UCUGAGA
AATM01000016.1/35659-35741     UU--UG-CCAAUGAGGAAUUACUAGAUGACGAGUCUGAUG-----------UCC--AU---------------------GACG-AA--A-CGACUCU----AUAAAUU------CCAUUCAUGCCUU-ACUGAGG
CU329670.1/527190-527270       UC--U---CAAUGAGGAAUAAUUAGAUGACGAGUCUGAUUC----------AAU--AU---------------------GAAG-AA--A-AGACUCU----UAAAAUU------CCAUUCAUGCUAA--CUGAGA
AACW02000245.1/159431-159514   UU--A---UGAUGA---ACUCUUAGAUGACGAGUCUGACGA----------GUC--AUUCAAU----------------GUUG-AU--A-AAACUCU----UUUAAU------ACCAUUCAUGCUUU-ACUGAAA
AAVQ01000001.1/1458293-1458382 UA-GA---UGAUGA--UUCUUUUAGAUGACGAGUCAGAAUU----------UCG--GGAUACCCG------------UUGAUG-AC--A-AAACUUU----UUUAAU------ACCAUUCAUGCUUU-UCUGAUU
AAFU01001217.1/1599-1511       UU--U---UUCUGUGAUGACUCUAGAUGACGAGUCUGAUUC----------GGG--AUUCCCGC--------------UGAAG-AC--A-AAAACUU----UUAACU------ACCAUUCAUGCCUU-UCUGAUA
AAID01002090.1/2659-2574       UU--A---UGAUGA-GCAUUUUUAGAUGACGAGUCUGAUUG----------GAG--UUUUCCAU---------------GUUG-AC--A-ACAUCAA----AAUUAU------ACCAUUCAUGCCUU--CUGAAU
AAFT01000027.1/99620-99532     AU--U---ACAUGAUGAUUACUUAGAUGACGAGUCAGAAUC----------GGG--AUUCCCGU--------------UGACG-AC--A--ACCUUU----UUUAAUU-----ACCAUUCAUGCCUU-UCUGAGU
AAFM01000013.1/140949-141035   AC--A---AGAUGA---UCUCUAAGAUGACGAGUCAGAUCC----------GGG--AUACCCGC--------------UGAUG-AC--A-ACACUUA----UUUUAAU-----ACCAUUCAUGCCUU-UCUGAUA
AADM01000093.1/238419-238513   UU--ACAGUGAUGA--UAUCCUUAGAUGACGAGUCUGAUUC----------GAG--GUUUUUCUCG-----------CUGAAG-AC--A-ACACUUU----UUUUUUU----UACCAUUCAUGCAUU-UCUGACU
ABAS01000006.1/940284-940196   GU--U---ACAUGAUGAUUGCUUAGAUGACGAGUCUUAUGC----------GAG--UUUUCGAU---------------GCAG-AC--A-ACCUUCU----UUUAAUA-----ACCAUUCAUGCUUU-CCUGAUU
AAPO01000086.1/18114-18023     UU--G---AAGUGAUGAUUACCUAGAUGACGAGUCAGAACC----------UCG--GGUUUCCCG------------UUGAUG-AC--A-ACCUUUU----UUUUAAU-----ACCAUUCAUGCAUU-UCUGAUU
AM270078.1/67439-67352         AU--U---AGAGGAUGAUUCCCUAGAUGACGAGUCUUAUUC----------GAG--UUAUCGAU---------------GCAG-AC--A-ACAUCUU----UUUUAU------ACCAUUCAUGCAUU-UCUGAAA
AARE01002242.1/721-809         UC--A---UGAUGA-UUUCCUUUAGAUGACGAGUCUUAUAC----------GAG--UUUUCGAU---------------GCAG-AC--AACAUCUUU----UUUUUAU-----ACCAUUCAUGCAAA-ACUGACA
AAJN01000109.1/73745-73659     CC--A---CAAUGAUGAUCUCCUAGAUGACGAGUCUUAUUC----------GAG--UUAUC------------------GAUG-CA--G-ACACUAU---CUUUUUUU-----ACCAUUCAUGCAUU-UCUGACA
AAKE03000005.1/1118422-1118509 AC--A---CUGUGAUGAUUCCCUAGAUGACGAGUCUUAUUC----------GAG--UUAUCGAU---------------GCAG-AC--A-ACAUUCU----UUUUUU------ACCAUUCAUGCAUU-UCUGACG
AACQ01000006.1/123917-124007   AU--G---UGAUGA--UUUUACUAGAUGACGAGUCAGAACC----------UCG--GGUUUCCCG------------UUGAUG-AC--A-AACUUUU---AUUUAAUU-----ACCAUUCAUGCAUU-UCUGAUC
AACD01000097.1/11630-11717     CU--C---ACAUGAUGAUCUUCUAGAUGACGAGUCUUAUUU----------GAG--UUUUCAAU---------------GCAG-AC--A-ACA-UCU----UUUUUUU-----ACCAUUCAUGCAAA-ACUGACA
AAIH02000128.1/1199-1286       CU--C---ACAUGAUGAUUUCCUAGAUGACGAGUCUUAUUC----------GAG--UUAUCGAU---------------GCUG-AC--A-CCA-UCU----UUUUUUU-----ACCAUUCAUGCAUU-UCUGACU
ABAR01000009.1/661755-661844   GU--U---ACAUGAUGAUCCCCUAGAUGACGAGUCUUAUAC----------GAG--UUUUCGAU---------------GCAG-AC--A-ACCUUUU----UUUAAUU----AACCAUUCAUGCUUU-ACUGAAU
AATX01000061.1/19122-19208     UC--C---UCAUGAUGAUCUCUUAGAUGACGAGUCCUAUUCG-------AGUAC--UC---------------------GAUG-CG-GA-CAACCUU----UCUUUUU-----ACCAUUCAUGCAUU-UCUGAAC
AAIW01000358.1/17398-17311     UU--U---AUGUGAUGAUCUCUUAGAUGACGAGUCCUAUACGAG----UACUCG--AU---------------------GCGG-AC--A-CCCUUCU----UAUUUU------ACCAUUCAUGCCUU-UCUGAAA
ABBB01000034.1/251365-251282   UC--A---UGAUGA---UCUCUUAGAUGACGAGUCCUAUUCG-------AGUAC--UC---------------------GAUG-CG-GA-CAACCUU----UCUUUUU-----ACCAUUCAUGCAUU-UCUGAAC
AACM02000292.1/22980-23063     UC--C---UGAUGA---ACAAUCAGAUGACGAGUCUUAUCC----------GAG--UUUUC------------------GAUG-CA--G-ACACCCU----AUUUACU-----ACCAUUCAUGCAUUCUCUGAAU
AAIM02000027.1/316344-316260   UC--C---UGAUGA-ACCCUU-UAGAUGACGAGUCUUAUAC----------GAG--UUUUCGAU---------------GCAG-AC--A-CAAUCCU----ACUUUA-------CCAUUCAUGCAUUUCCUGAC-
AAKD03000029.1/281090-281175   CC--G---UGAUGA---UUCCCUAGAUGACGAGUCUUAUUC----------GAG--UUAUCGAU---------------GCAG-AC--A-ACAUCUU----UUUUUAU-----ACCAUUCAUGCAAA-ACUGACU
AAJI01001102.1/179871-179781   CU--A---UGAUGA---UUCCCUAGAUGACGAGUCUUAUUC----------GAG--UUUUCGAU---------------GCAG-AC--A-AUUUUUU----UUUUUUUUUAAUACCAUUCAUGCUUU-UCUGAAA
AACA01000204.1/7585-7505       UU--A---UGAUGAGAUAUUUAUAGAUGACGAGUCUGAUCU----------UUC--GU---------------------GAAG-AC--A-CAA--CU----AUUAAUU-----ACCAUUCAUGCCUU-UCUGAAA
CR382127.1/989516-989433       AU--A---UGAUGA---UUCCCUAGAUGACGAGUCAGAAUG----------GGG--CUUCCCCU--------------UGACG-AU--A-CAA--AC----UUUUAAU-----ACCAUUCAUGCCUU--CUGAAA
AAGI01000315.1/11447-11360     UG--G---AGAUGAUGCGACUUCAGAUGACGAGUCUGACGG----------GCU--CGCCCUGU---------------GACG-AC--C-UCAUUUA----AAAUAU-------CCAUUCAUGCCUUUUCUGAUC
AAXI01000054.1/31430-31511     AA--A---UGAUGA----ACACUUGAUGACGAGUCCGAUGG----------GUU--CGCCCGGU---------------GAAG-AC--U-UAAAUCA----AAAUAU-------CCAUUCAUGUCAA--CUGAUC
AADS01000356.1/83584-83477     AA--G---GGAUGA---UCUUUUAGAUGACGAGUCUGAAUACGUC-GGCGUGAG--GUUUCCUCUCGUCGAUCUUCCUUGAUG-AU--A-CAU--CU----UUUAAAU-----ACCAUUCAUGCAUA-UCUGACU
AACE03000004.1/1106384-1106474 AA--G---UGAUGA-UUACCC-UAGAUGACGAGUCUGAUCC----------GGG--GUUUUUCCCG-----------CUGAAG-AC--A-AACUAAC----UAAAUAU-----ACCAUUCAUGCAUU-UCUGAUU
CR380959.2/770723-770635       --CUA---UGAUGA-ACCCUUUUAGAUGACGAGUCUGAAUA----------GUU--UUUUAUUA--------------UGAAG-AC--A-CAUCUAU----AAAUUAU-----ACCAUUCAUGCAUU-UCUGAGU
EU780931.1/3-91                -C-CA---UGAUGA--UCCCUUUAGAUGACGAGUCUUAUCG----------GGG--AUUCCCCA--------------UGCAG-AC--AACCUUUUU----UUUUAAU-----ACCAUUCAUGCAUU-UCUGAAA
CR382139.2/220568-220656       AA--A---AGAUGA--UCUCCUUAGAUGACGAGUCAGAAUU----------UCG--GGAUUCCCG------------UUGAUG-AC--A-ACCUUUU----UUUAAU------ACCAUUCAUGCAAA-UCUGAUA
AM920437.1/1346884-1346970     CU--A---UGAUGA-UACCAUUUAGAUGACGAGUCUGAUUC----------GAG--UUUUCGAU---------------GCUG-AC--A-CAAUCUU----UUUAAU------ACCAUUCAUGCCUU-UCUGACA
ABBT01000198.1/255809-255896   CU--A---UGAUGA---UUCCCUAGAUGACGAGUCUUAUUC----------GAG--UUUUCGAU---------------GCAG-AUAAA-AAAUUUU----UUUUAAU-----ACCAUUCAUGCUUU-UCUGAAA
ABRJ01000399.1/35593-35507     CU--A---UGAUGA---UUCCCUAGAUGACGAGUCUUAUUC----------GAG--UUUUCGAU---------------GCAG-AC--A-AUUUUCU---UUUUUAAU-----ACCAUUCAUGCUUU-UCUGAAA
ABHV01000190.1/63334-63422     AC--A---UGAUGA---ACCCCUAGAUGACGAGUCUUAUCC----------GAG--UUUUCGAU---------------GCAG-AC--A-ACUUUUU----UUAUAUUA--AUACCAUUCAUGCUUU-UCUGAAA
ACBU01001064.1/83137-83226     CU--A---UGAUGA---UCCCCUAGAUGACGAGUCUUAUUC----------GAG--UUUUCGAU---------------GCAG-AC--A-ACCUAUUUUUUUAUAAAU-----ACCAUUCAUGCUUU-UCUGAAA
ABKH01000207.1/32876-32965     AC--A---UGAUGA---ACUCCUAGAUGACGAGUCUUAUCC----------GAG--UUUUCGAU---------------GCAG-AC--A-CCCUUUU----UUUAUAUUA-AUACCAUUCAUGCUUU-UCUGAAA
FN392322.1/110356-110270       AA--A---AGAUGA--UACUCUUAGAUGACGAGUCAGAUUU---------CGUG--UUUCACGA--------------UGACG-AU--A-CAA--CC----UUUUUUU-----ACCAUUCAUGCAUU-UCUGAUA
CU633895.1/1470274-1470357     UU--A---UGAUGA-----CUCUAGAUGACGAGUCCUAUAC----------GGG--AUUCCCGA--------------UGCGG-AC--A-ACCUAUU----UUUUAU------ACCAUUCAUGCCUA-UCUGAAA
CABE01000024.1/563849-563942   AA--G---UGAUGAUCUUUAUCUAGAUGACGAGUCAGAAUCU--------CGGG--UUUCCCGU--------------UGAUG-AC--A-ACUAUUUU--UAUUAAUU-----ACCAUUCAUGCAUU-UCUGAUU
ABWI01000681.1/3384-3300       AU--G---UGAUGA----CAUCUUGAUGACGAGUCUUAUUC----------GAA--UUCUCGAU---------------GCAG-AC--A-CAAACAU----UUAAAUA-----ACCAUUCAUGCCAA-ACUGAAC
ABVF01000212.1/14233-14148     UU--G---UGAUGA----CAUCUUGAUGACGAGUCUUAUUC----------GAA--UUCUCGAU---------------GCAG-AC--A-CAAAUAU----UUCAAAU----AACCAUUCAUGCCAA-ACUGAAC
ABJE01000834.1/14883-14801     UC--C---UGAUGA-----ACACAGAUGACGAGUCCUACAC----------GGU--UUUACCGA--------------UGCGG-AC--A-ACC--UA----UUUUAAU-----ACCAUUCAUGCCUU-ACUGAAC
ABFE01001339.1/82173-82065     UU--A---UGAUGA-G-AUAUUUAGAUGACGAGUCUGAACCAUGAUAGGCAGAG--UUUCUCUGUCUGUC--UGAACAUGACG-AC--U-CAACUAA----AAUUAU------ACCAUUCAUGCUUU-UCUGAUU
ABHY02000006.1/989997-990077   UU--C---CAAGGA-GGAACUAUAGAUGACGAGUCUGAAUA----------UUU--CU-----U---------------GAUG-AA--A-CAGACUC----UUUAAUU------CCAUUCAUGCUUA--CUGAGG
AATT01000026.1/6566-6482       UC--A---AAAUGA-GGAAAC---GAUGACGAGUCAGACGA----------GU---UUCUCGAU---------------GCUG-CA--U-AAUCUUU----UUUUUUA-----UUCAUUCAUGCCAAAACUGAUU
ABDG02000025.1/1667597-1667516 AU--G---UGAUGA----UUUUUAGAUGACGAGUCCUAUUC----------GGG--UUUCC------------------GAUG-AG--G-AUACAAU----CUUUUUU-----ACCAUUCAUGCAUUUCCUGAU-
ABSB02003537.1/1511-1431       CC--G---UGAUGA-GA-AAUUUAGAUGACGAGUCUGAUCC----------GAG--AAAUCGAU---------------GUUG-AC--A-AAA---------AAAAUA-----ACCAUUCAUGCCUU--CUGAAA
AACS02000007.1/1746582-1746690 CA--A---AGAUGA--AUUCUUUAGAUGACGAGUCUGAGCUAUGAUGGUCAGAG--UUUCUCUGGCCUGA--CGGUUCUGACG-AU--A-CAA-UCU----UUAAUUU-----ACCAUUCAUGCUUU-UCUGAAC
AFQF01002514.1/154985-154901   UC--C---UGAUGA-ACCCUU-UAGAUGACGAGUCUUAUAC----------GAG--UUUUCGAU---------------GCAG-AC--A-CAA--UC----UUACUUU-----ACCAUUCAUGCAUUUCCUGAC-
AACU03000132.1/431363-431444   UC--C---UGAUGA-----UUCUAGAUGACGAGUCUUAUUC----------GGG--UUUCC------------------GAUGCAG--A-CAACAAA----ACUUACU-----ACCAUUCAUGCCUUAACUGAA-
AE016815.5/489655-489738       CU--G---UGAUGA--UCUCCAUAGAUGACGAGUCUGAUUC----------GAG--CUUCUC-----------------GCUG-AA--G-ACACACA----CACAAUU------CCAUUCAUGCAUU-UCUGAGC
AAFN02000003.1/318992-318904   AC--G---UGAUGA---UUACCUAGAUGACGAGUCAGAACU----------UCG--GGUUUCCCG------------UUGAUG-AC--A-ACCUUUU----UUUAAUU-----ACCAUUCAUGCAUU-UCUGAUC
#=GC SS_cons                   ::..:...::::::..:::::::::::::::::::::::::..........:::..::::::::...............::::.::..:.:::::::....:::::::.....::::::::::::::.:::::::
#=GC RF                        uu..a...uGAUGA..uuuuuuUAGAUGACGAGUCUgAuuc..........GaG..uUUuCcau...............GaaG.Ac..A.aaacUuU....UUUuauU.....ACCAUUCAUGCaUU.UCUGAau
//
# STOCKHOLM 1.0

#=GF AC   RF01186
#=GF ID   SNORD127
#=GF DE   Small nucleolar RNA SNORD127
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A, Daub J
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   47.50
#=GF NC   39.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.99 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; SNORD127;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300770;
#=GF RN   [1]
#=GF RM   16990247
#=GF RT   snoSeeker: an advanced computational package for screening of guide and
#=GF RT   orphan snoRNA genes in the human genome.
#=GF RA   Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2006;34:5112-5123.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   13


AACN010948193.1/172-257    UGGCAACUAUGAUGAAAGAUUUGCUCUGUAUGU--AAUAUAUUUUAUUACUACAUGAAGACAGCAGUCCCUCUAAACUGAUGUUGCCA
AAPY01351447.1/97-181      UGGCAACUGUGAUGAAAGAUUUGGUCUGUAUGU--GAUAUAUU-UAUUACUAAAUGUGGACAACAGUCCCUCUAAACUGACGUUGCCA
AC159621.2/106632-106547   UGGCAACUGUGAUGAAAGAUUUGGUCUAUACAG--UAAUAUAUUUAUUACUACAUGAGGACAACAGUCCCUCUAAACUGAUGUUGCCA
AALT01578859.1/299-379     UGGCAACUGUGAUGAAAUACUUGGUCUGUAUGU--AA-----UGCAUUACUAAAUGAAGACAACAGUCCCUCUAAACUGACGUUGCCA
AANN01169539.1/189-118     UGGCAACUAUGAUGAAGUAUUUGGUCUGUAU----------------UACUAAAUGAAGACAACAGUCCCUCUAAGCUGAUGUUGCCA
AAPN01154590.1/2818-2731   GGGCAACCGUGAUGACAGGUUCAGUCUGUAUGUGUAAUGGGUUUCAUUACUACAUGAAGACACCAGUCCCUCUAAGCUGAUGUUGCCG
AAWR02032993.1/22776-22859 UGGCAACUAUGAUGAAAGAUUCAGUCUGUAUGU--AAU--GUCUUGUUACUAAAUGAAGACAACAGUCCCUCUAAACUGAUGUUGCCA
AAKN02027477.1/59206-59291 UGGCAACUAUGAUGAAAAAUUUGAUCUGAAUGU--AAUACAUUUUAUUACUAAAUGAGGACAACAGUCCCUCUAAACUGAUGUUGCCA
ABQO010086764.1/3146-3231  UGGCAACAGUGAUGACAGGUUUGGUCUGUAUGU--AAUAUAUUUUAUUACUACAUGAAGACACCAGUCCCUCUAAGCUGAUGUUGCCA
AL121809.6/149441-149356   UGGCAACUGUGAUGAAAGAUUUGGUCUGUAUGU--AAUAGAUUUUAUUACUAAAUGAGGACAACAGUCCCUCUAAACUGAUGUUGCCA
BX935454.2/93-178          UGGCAACAAUGAUGACAGGUACUGUAACUGUAU--GUGAUAUUUCAUUACUGCAUGGAGACACCAGUCCCUCUAAACUGAUGUUGCCA
AAGW02023552.1/64585-64503 UGGCAACUAUGAUGAAAAAUUUGGUCUGUAUGU--AAUAUGUUUUAUUAC---AUGAGGACAACAGUCCCUCUAAACUGAUGUUGCCA
AAPE02022122.1/33833-33918 UGGCAACUAUGAUGAAAGAUUUGGUCUGUAUGU--AAUAUAUUUAAUUACUGAAUGAAGACAACAGUCCCUCUAAACUGAUGUUGCCA
#=GC SS_cons               <<<<<<<__________________________..______________________________________________>>>>>>>
#=GC RF                    uGGCAACuaUGAUGAaAgAUUUgGUCUgUAUGU..aAuauaUUUuAUUACUAaAUGAaGACAaCAGUCCCUCUAAACUGAUGUUGCCa
//
# STOCKHOLM 1.0

#=GF AC   RF01188
#=GF ID   snR56
#=GF DE   Small nucleolar RNA snR56
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   54.00
#=GF TC   54.10
#=GF NC   53.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.31 -Z 549862.597050 CM SEQDB
#=GF CL   CL00049
#=GF DR   snornadb; snR56;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science. 1999;283:1168-1171.
#=GF CC   Checked in using file
#=GF WK   Small_nucleolar_RNA
#=GF SQ   16


AF064268.1/2-88                UAACAUGAUGAAAAAAUAUAUUAACACAGACCUGUACUGAACU---------UUUCGAAGUUUUGCAGAUAACAA---UAUUG-CUUUUUUUCUCUGACU
AAZN01000252.1/47075-47158     UAUCAUGAUGAAAAAAUAUUUUAACACAGACCUGUACUGAACC---------UUUUG--GUUUUGCAGAUAAACGA--UAUUG-CCUUU--UUACUGAUU
AADM01000047.1/81966-82047     CUAAGUGAUGAAAACAUAUUU-UACACAGACCUGUACUGAACU-----------UUG---UCAUGCAGAUAAACGA--UAUUG-CCUUUUUUUUCUGAUU
CR382125.1/1819986-1819898     UAACGUGAUGAAACA-AAUUU-UACACAGACCUGUACUGAAUUCUCUU----UUUUGA-AUCAUGCAGAUAAACAC--UUUUG-CCUUUU-UUUCUGAUC
AACF01000110.1/7118-7204       UACAAUGAUGAGAGAAAUGU----UACAGACCUGUACUGAACUAACAUUU--UUUAG---UUAUGCAGAGAAACUA-CUAUUG-CCUUU--UUGCUGAGA
AATM01000050.1/82502-82429     UCAUAUGAUGAUAAAACAUU-----ACAGACCUGUUCUGAAUU-----------UCG-----UUGAGGAUAACCUA--UAUUG-CCUUU--UUACUGAGA
AAFT01000054.1/52963-53050     UACAAGGAUGAUACAAAA------CACAGACCUGAUCUGACAGAGUCCU---CGUGGCUCUUAUGCAGAUAAAAUG--UAUUG-CCUUUUUUUGCUGAUG
ABBB01000204.1/168240-168161   UUCCGUGAUGAAACA-CCUUU-UACACAGACCUGUUCCGAAAC---------AGAUA-----AUGUGGAUAAAAAA-AUGUUG---CCUUCCUUCUGAUA
AAIW01000435.1/28302-28380     UACAAUGAUGAAAAC-CCUUUAUACACAGACCUGUUCCGAAAC---------A------AUUAUGUGGAUAAAAGA--UGUUG---CCUUCCUUCUGAAA
CU329670.1/5148555-5148474     UAUUGUGAUGAUACCAAUUA------CAGACCUGUUCC-AAUGCAA------AUCUG--UAUAUGAGGACAACCUA-AUAUUG-CCAUUA-UUUCUGAGU
AAFM01000026.1/10445-10516     UAAAAUGAUGAAAAA-CCUU----CACAGACCUGUACUGAUCA-----------CUG---ACGUGCAGA-AAACC---AAUUG---CCU--AUUCUGAGU
AACE03000002.2/979440-979351   UUUCAUGAUGAGAAAAUUUAUUAACACAGACCUGUACUGAACU---------UUUCAA-GUCAUGCAGAUAACAAUAUUAUUGCCUUUUUAUUUCUGAUU
CR380947.2/448337-448240       UUUUAUGAUGAGAAGAAAUAUUUACACAGACCUGUACUGAUUCCUGUUUUGAACCAGG-ACUAUGCAGAUAACCGUAUUAUUG-CCUUUUUUUUCUGAUA
CR382135.2/1370717-1370634     UUAAAUGAUGAUAAA-AAUA---ACACAGACCUGUACUGAUUCUAUUUA---AAUAGA-UACAUGCAGAUAAAAU---UAUUG---CCU--UUUCUGACA
AE016820.4/1741517-1741439     UCACAUGAUGAAAAA-UAAA----CACAGACCUGUACUGAUCUC--------CUUUGGAGUAAUGCAGA-AAUGUU--UAUUG---CCU--UUACUGAUA
AACS02000002.1/2856238-2856150 UUUCGUGAUGAUAAAACUUU------CAGACCUGUUCUGAAGGCGGCUUC--GGUCGAUCUUUUGAGGACAACCUA--UAUUG-CCUUUUUUAUCUGAUC
#=GC SS_cons                   ::::::::::::::::::::...:::::::::::::::::::::........::::::.:::::::::::::::::..:::::.::::::::::::::::
#=GC RF                        UaacAUGAUGAaAaaAaaUu...ACACAGACCUGUaCUGAacuc........uuUuGa.guuaUGcAGAUAAacua..UAUUG.CCuUUUuUUuCUGAua
//
# STOCKHOLM 1.0

#=GF AC   RF01189
#=GF ID   sn1502
#=GF DE   Small nucleolar RNA sn1502
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   88.70
#=GF NC   40.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=CEL30008;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16714446
#=GF RT   Evolution of small nucleolar RNAs in nematodes.
#=GF RA   Zemann A, op de Bekke A, Kiefmann M, Brosius J, Schmitz J
#=GF RL   Nucleic Acids Res. 2006;34:2676-2685.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948667.1/1-86            -GUCCGUUGAUGACAA-CAUACAUACACCAUUACGAUCUCUGAAGACUUCGUG-CUGAUCAUGUAUCCAUGCAACACCAACUGAGGACA
DQ789431.1/1-87            UGUCCUGUGAUGACAA-CAUACAUACACCAUUACGAUCUCUGAAGACUUCGUG-CUGAUCAUGUAUCCAUGCAACACCAACUGAGGGCA
AAGD02011809.1/15532-15445 UGUCCGCUGAUGACAC-CUUACAUACACCAUUACGAUCUCUGAAGACUUCGUGACUGAUCAUGUUUCCAUGCAACACCAACUGAGGACG
ABEG02001590.1/71951-72038 UGUCCGCUGAUGACAACCUUACAUACACCAUUACGAUCUCUGAAGACUUCGUG-CUGAACAUGUUUCCAUGCAACACCAACUGAGGACG
#=GC SS_cons               <<<<<___________.____________________________________.______________________________>>>>>
#=GC RF                    cGuCCguUGAUGACAa.CuUACAUACACCAUUACGAUCUCUGAAGACUUCGUG.CUGAuCAUGUuUCCAUGCAACACCAACUGAGGaCg
//
# STOCKHOLM 1.0

#=GF AC   RF01190
#=GF ID   snR50
#=GF DE   Small nucleolar RNA snR50
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   49.60
#=GF NC   41.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.43 -Z 549862.597050 CM SEQDB
#=GF DR   snornadb; snR50;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   9090058
#=GF RT   Analysis of the DNA sequence of a 34,038 bp region on the left arm of
#=GF RT   yeast chromosome XV.
#=GF RA   Rad MR, Habbig B, Jansen G, Hattenhorst U, Kroll M, Hollenberg CP
#=GF RL   Yeast. 1997;13:281-286.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ223034.1/8-96            UAGAAUGAUGAAAGAGGUAGCAAUUUGCAGCAGAUUUUUCGUGAUUGAAUCAAACAAAGAUUAACCUUUACAGAACCGCUACACUGAUA
AACI02000236.1/11645-11732 UAAAAUGAUGAAAGAGGUAGCAAUUUGCAACAGAU-UUACAUGAUCGAAUCAAACAAAGAUUAACCUUUACAGAACCGCUACACUGAUA
AACH01000741.1/1390-1477   UAGAAUGAUGAAAGAGGUAGCAAAAUGUAACAGAAUUUUCAUGACUGAAACAAACAA-GAUUAACCUUUACAGAACCGCUACACUGAUA
#=GC SS_cons               <<_____________________________________________________________________________________>>
#=GC RF                    UagAAUGAUGAAAGAGGUAGCAAuuUGcAaCAGAuUUUuCaUGAuuGAAuCAAACAAAGAUUAACCUUUACAGAACCGCUACACUGAuA
//
# STOCKHOLM 1.0

#=GF AC   RF01191
#=GF ID   SNORD121A
#=GF DE   Small nucleolar RNA SNORD121A
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   44.10
#=GF NC   43.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.80 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; SNORD121A;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16990247
#=GF RT   snoSeeker: an advanced computational package for screening of guide and
#=GF RT   orphan snoRNA genes in the human genome.
#=GF RA   Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2006;34:5112-5123.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   26


AAQQ01544386.1/1713-1633   GUCCAGAAAACAAUGAUGUGAUAA--UUUCCAAGCACAUAUCUGAU-GUUUCCAUG-UGGAAUU-UAAU--UA---CUGAG-UUUCCUGGAC
AANG01431959.1/798-716     GUCCAGAAAACAAUGAUGUGAUAC--UUUCCAAGCACAUAUCUGAU-GAUUCCAUG-UGGAAUU-CAAC--UACU-CUGAG-UUUCCUGGAC
AAPY01565688.1/821-739     GUCCAGAAAACAAUGAUGUGAUAA--UUUCCAAGCACAUAUCUGAU-AAUUCCAUG-UGGAAUU-UAAC--CACU-CUGAG-UUUCCUGGAU
AAIY01116190.1/1086-1167   GUCCAGAAAACAAUGAUGUGGCAA--UUUCCAAGCACAUAUCUGAU-GAUUUCAUG-UGGAAUC-AACU--ACU--CUGAG-UUUCCUGGAC
AANN01292285.1/1361-1279   GUCCAGAAAACAAUGAUGUGGUAA--UUUCCAAGCACAUAUCUGAU-GAUUCCAUG-UGGAAUU-CAAU--UACU-CUGAG-UUUCCUGGGC
ABDC01388884.1/521-437     GUCCAGAAAACAAUGAUGUGAUAA--UUUCCAAGCACAUAUCUGAUUGACUCCAUG-UGGAAUU-UAAC--UACU-CUGAGUUUUCCUGGAC
AAYZ01708269.1/397-317     AUCCAGAAAACAGUGAUGUGAUAA--AUUCCAAGCACAUAUCUGAU-GAUUCCAUG-UGGAAAG-CAGC--UA---CUGAG-UUUUCUGGAC
AALT01140248.1/1685-1765   GUCCGGGAAACAAUGAUGCGAUCA--UUUCCAAGCACAUAUCUGAU-GAUGCCAUG-UGGAAAU-AAAC--U-C--CUGAG-UUUCCUGGAC
AAFC03131486.1/552-472     GUCCAGAAAACAAUGAUGUCAUAA--UUUCCAAGCACAUAUCUGAC-AGUUCUGUG-CAGAAUU-CAAC--CA---CUGAG-UUUUCUGGAU
AAHY01035230.1/8607-8684   AUCCCGGAAACAAUGAUGUG---A--UUUCCAAGCACAUAGCUGAU-GAUUCCAUG-UGGAAUU-UUAC--CA---CUGAG-UUUCCUGGGC
AAPN01283415.1/1235-1153   GUCCAGAAGACAGUGAUGUGGUAU--UUUCCAAGCACAUAUCUGAU-UGGCAUGUG-UGGAAAU-CAUUA-UUU--CUGAG-UUUUCUGGAA
AAFR03026988.1/26117-26033 GUCCAGGAUACAAUGAUGUCAUAG--UUUCCAAGCACAUAUCUGAU-UAUUAAAUGUUGGAAUA-CAUCUGUUU--CUGAG-UUUUCUGGAC
AAVX01094312.1/469-550     AUCCAGGAAACAAUGAUGUU---U--AAUUCAAGCACAUAUCUGAACACUUUUAUG-UGGAUAG-UCCCAUUGG--CUGAG-UUUCCUGGAU
AANU01165025.1/4195-4275   CUGGAAAAGACAAUGAUGUU-UUA--UUUCCAAGCACAUAUCUGAG-UUGUAUGUG-UGGACAG-CACU--GAAA-CUGAG-UCUU-UCCAC
AAGV020483149.1/848-766    GUCCAGAAAACAAUGAUGCAUUAA--UUUCCAAGCACAUAGCUGAU-GAUUCCAUG-UGGAUUU-CAAC--UACU-CUGAG-UUUUCUGGAC
AAKN02030392.1/28310-28233 CUGGAAAAGACAAUGAUGUA------CUAUCAAGCACAUAUCUGAA-GUGAGUGUG-UGGACAG-CACU--AAC--CUGAG-UCUUUUCCAU
AAWR02016008.1/33739-33657 GUCCAGAAGACAAUGAUGUGGUAA--UUUCCAAGCACAUAUCUGAU-GAUUCCGUG-UGGAAUU-CAAC--UACU-CUGAG-UUUUCUGGAC
AAEX03007942.1/69924-69842 GUCUGGAAAACAAUGAUGUGAUAA--UUUCCAAGCACAUAUCUGAU-GAUUCCAUG-UGGAAUU-CAGC--UACU-CUGAG-UUUUCUGGAC
AAQR03161553.1/4942-5026   GUCCAGAAAACAAUGAUGUGAUAA--UUUCCAAGCACAUAUCUGAU-GAUUCCAUG-UGGAAUAAUAAC--UACA-CUGAGUUUUCCUGGAU
AL139113.21/156153-156072  GUCCAGAAAACAAUGAUGUGGUAA--UUUCCAAGCACAUAUCUGAU-GAUUCCAUG-UGGAAUU-UAAC--UAC--CUGAG-UUUCCUGGAC
AAGU03018613.1/67261-67340 GUCCAGAAAACAAUGAUG---UAA--UUUCCAAGCACAUAUCUGAU-AAUUCCAUG-UGGAAUA-CAAC--UACU-CUGAG-UUUCCUGGAC
AC213112.3/34407-34491     GUCCAAAAUACAAUGAUGUUGUCU--UUUCCAAGCACAUAUCUGAU-UGCGCUAUG-UGGAAAA-UGAC--UGUUGCUGAGUGAUUUUGGAU
AAGW02033468.1/46234-46154 GUCCAGAAGACAAUGAUGUGAUAA--ACUCCAAGCACAUAUCUGAU-GAUUCCAUG-UGGAAUG-UAAC--UA---CUGAG-AUUUCUGGAU
AABR05123959.1/14690-14612 AUUCCGGAAACAAUGAUGUG---A--UUUCCAAGCACAUAUCUGAU-GAUUCCAUG-UGGAAUU-UUAA--CUA--CUGAG-UUUCCUGGGC
AAPE02037193.1/38026-38108 GUCCAGAAAACAAUGAUGUGUUUA--UUUCCAAGCACAUAUCUGAU-GCUUCCAUG-UGGAAUU-CAAC--UACU-CUGAG-UUUUCUGGGC
AAWZ02026386.1/14752-14667 GGCCAGCAGACUAUGAUGUGAUAUUCUUUCCAAGCACAUAUCUGAC-UGCUGCAUG-AGGAAAC-AAAC--UGUUUCUGAG-UCUUCUGGCC
#=GC SS_cons               <<<<<<-<<<<_____________..____________________._________._______.____..___..____>.>>>->>>>>>
#=GC RF                    gucCAGAAgACAAUGAUGUgaUAa..UUUCCAAGCACAUAUCUGAu.gauUccAUG.UGGAAuu.uAac..uau..CUGAG.UcUuCUGgac
//
# STOCKHOLM 1.0

#=GF AC   RF01192
#=GF ID   SNORD11B
#=GF DE   Small nucleolar RNA SNORD11B
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   51.50
#=GF NC   49.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.48 -Z 549862.597050 CM SEQDB
#=GF CL   CL00103
#=GF DR   snoRNABase; HBII-95B;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16990247
#=GF RT   snoSeeker: an advanced computational package for screening of guide and
#=GF RT   orphan snoRNA genes in the human genome.
#=GF RA   Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2006;34:5112-5123.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   37


AANN01433628.1/978-1063      UGAU-GGCAAUGAUGAUUUUUAA--ACUUA---UUGUUUACCUGAUAAG-UAAAUAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
AAQQ01276054.1/1184-1267     UGAU-GGCAAUGAUGAUUUUUAG--AGUUA---UUGUUCACCUGAUAA---AAACAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
AAFC03122356.1/13561-13646   UGAU-GGCAGUGAUGAUUUUUAA--AUGUA---UUGUUCACCUGAUAA-AUAAAUAUGAAGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCGUCU
AAYZ01276509.1/4776-4861     UGAU-GGCGAUGAUGAUUCUCCC--ACUU----GGGUUCACCUGAUAAUCUAAAUAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAAGCCAUCU
AALT01509876.1/472-388       UGAU-GGCUAUGAUGAUUUUAAA--AUUUACACUUG----CCUGAUAAG-UAAAUAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
AANG01224100.1/1739-1820     UGAU-GGCAAUGAUGAUUUUUAA--AUUUA---CUAAUCACCUGACAA-----AUAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
AC126934.4/111575-111495     AGGU-GGCAAUGAUGAUUUUU-----CUUA--UUUGUUCACCUGACAAU----AUAUGAAGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
AAFR03042041.1/48307-48221   UGAU-GGCAGUGAUGAUGAUUUU--A--UAUUGAUUCUCACCCGAUU-UACAAAUAUGAGGGUA-UAUAGUCACUA-CCUCAUCUGAUGCCAUCU
AAHX01060272.1/22747-22668   AGGU-GGCAAUGAUGAUAAUUUU--ACUCA------UUCACCUGACAAU----AUCUGAAGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
AAPN01394254.1/9386-9468     CGAU-GGCGAUGAUGAUUUCUAG--AUUU----UUGCUCUCCUGAUG---UAGCCGUGAGGGUG-CAAAGUCACUA-CCUCAUCUGAUGCCAUCU
AAIY01263621.1/3423-3343     UGGU-GGCGAUGAUGAUUU----------AUCUUAACUCAUCUGA-AAUACAAGCAUGAGGAUG-UACAGUCACUA-CCUCAUCUGAUGCCACUC
BAAE01004788.1/3214-3131     UGGC-AGUGCUGAUGAUGUCGAC--AGUUG---UCUUCAACCUGA--AUAUCCCCGUGUGGGUU-UUCAGUCACUA-CCUCAUCUGA-ACUGUCA
CAAE01018048.1/627-544       UGGC-AGUGGUGAUGAUGACGAC--AGUUG---UCUCUAUCCUGAAA--GCCAACGUGUAGGUU-UUCAGUCACUA-CCUCAUCUGA-ACUGUUC
CR628393.11/8368-8286        AACA-AGCUGUGAUGAUGAUGAC--CAUGC--GUCAUUUUGCUGAAA----AAUCAUGAGGCUU-UUUUGUCACUA-CCUCAUCUGA-GCUUGUU
AANH01007122.1/13744-13660   CGAC-CGUUGUGAUGAUAAUGGC--UUGUU--GUCUUUACCCUGAAA--CAAAUCAUGUGGGUU-UUCAGUCACUA-CCUCAUCUGA-ACAGUCG
AANU01248796.1/503-590       UGAU-GGCAAUGAUGAUUUACAC--UUACU--GUUGUUCACCUGAUAACAUAAAUAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCA
AAWR02007034.1/19160-19245   UGAU-GGCAGUGAUGAUUUUUCA--ACUUA---UUGUUCACCUGAUAA-ACAAACAUGAAGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
AAGV020290171.1/3732-3815    UGAU-GGCAAUGAUGAUUUUUUU--AAC-----UUGCUCACCUGAUA-UGCACAUAUGAGGGUG-UAUAGUCACUA-CCUCAUCUGAUGCCAUCU
ABRN01138500.1/10345-10430   UGAU-GGCAAUGAUGAUUUUUUA--AUGUA---UUGCUCACCUGAUAA-AUAAAUAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
ABRT010283008.1/3255-3341    UGAU-GGCAGUGAUGAUUUUUAC--AGUUA---UUCAUCACCUGAUAACGUAAAUAUGAGGGUG-UUCAGUCACUA-CCGCAUCUGAUGCCAUCA
ABRP01237890.1/344-427       UGAU-GGCCGUGAUGAUUCUUAA--ACUUA---UUGUUCACCUGAUAA---AUAAAUGAAGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
ABRO01216921.1/4543-4625     UGAU-GGCAAUGAUGAUUUUUAU--GCU-----CUGUUUACCUGAAA--GCAAAUAUGAGGGUA-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
ABQO010948697.1/1347-1264    UGAU-GGCAAUGAUGAUUUUAU---A-UUG---AUUCUCACCUGAUA-UAUAAAUAUGAGGGUU-UACAGUCACUA-CCUCAUCUGAUGCCAUCU
AAKN02019437.1/1770-1853     UGAU-GGCGAUGAUGAUUUUUAC--AUGUA---UUGUUCACCUGAUGA---CAGUAUGAGAGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
ABVD01300951.1/365-454       UGAU-GGCAGUGAUGAUUUUUUUUAACUUAU-UAUGUUCACCUGAUA-UGCAAAUAUGAGGGUG-UACCGUCACUA-CCUCAUCUGAUGCCAUCU
ABQF01010158.1/104804-104884 UGAU-GGCAGUGAUGAUUCCUAU--A-------UUGUUUUCCUGAUG-UUCAGACAUGAGGGUG-CACAGUCACUC-GCUCAUCUGA-GCCAUCU
ABPL01055166.1/575-492       GGCCUAGCAGUGAUGAUGAUGAC--ACUAA--GUCACUUUCCUGAAC----AUGACUGAUGGUU-UUAAGUCACUA-CCUCAUCUGA-GCUGGCA
AAVX01012835.1/960-875       CUGC-AGUGAUGAUGACGACGAC--UAUG----UCACUUUCCUGAUUA-AAUACUGUGAUGGUAUUUCAGUCACUA-CCUCAUCUGAGACUGCUA
AAPE02003157.1/8188-8272     UGAU-GGCAAUGAUGAUUUUUAA--ACUUA----UGUUCACCUGAUAA-AUAAAUAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
AC064836.7/30066-30155       UGAU-GGCAAUGAUGAUUUUUAC--ACUUAUUGUUGUUCACCUGAUAACAUAAAUAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCA
AAWZ02015300.1/6474-6388     UGGU-GGCAGUGAUGAUUCUUGU--GAUG----CUGCAUUCCUGAUAUACAAACUGAAGGGCUG-CAUAGUCACUACCCUCUUCUGAUGCCAUCU
CAAB02002627.1/31663-31746   UGAC-AGUGGUGAUGAUGAUGAC--AUUUG---UCUCUAUCCUGAAA--GCUAAUGUGUAGGUU-UUCAGUCACUA-CCUCAUCUGA-ACUGUCU
AAGU03009642.1/42250-42172   UGAU-GGCAGUGAUGAUUUAA------------UUGUUCACCUGA-AAUACAAAUAUGAGGGUG-UACAGUCACUA-CCUCAUCUGAUGCCAUCU
AADN03005370.1/31284-31201   UGAU-GGCAGUGAUGAUUCCUA------UAUUGUGGUUUUCCUGAUG-UACAAAUGUGAGGGUG-CACAGUCACUA-CCUCAUCUGA-GCCAUCU
AAGW02042214.1/29956-30040   UGAU-GGCGAUGAUGAUGCUUAC--ACUU----CGGUUCACCUGAUAACAUAA-CAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUUU
AAQR03032726.1/753-667       UGAU-GGCAGUGAUGAUUUUUAU--ACUUA---CCAUUCACCUGAUAAGACAAAUAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCA
AAEX03018026.1/130318-130396 UGAU-GGCAAUGAUGAUUUUUAA--GCUUA------CUCACCUGAUAA-----AUAUGAGGGUG-UUCAGUCACUA-CCUCAUCUGAUGCCAUCU
#=GC SS_cons                 :<<<.<<<_______________.._____..._______________________________.___________.___________>>>>>>:
#=GC RF                      UGau.gGCaaUGAUGAUuuUuac..auUua...UuguUcaCCUGAuAAuauAAauAUGAGGGUg.UUCAGUCACUA.CCUCAUCUGAUGCcauCu
//
# STOCKHOLM 1.0

#=GF AC   RF01193
#=GF ID   snoR20a
#=GF DE   Small nucleolar RNA snoR20a
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   42.00
#=GF TC   43.80
#=GF NC   41.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12520043
#=GF RT   Plant snoRNA database.
#=GF RA   Brown JW, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Huttenhofer A,
#=GF RA   Kastenmayer JP, Green PJ, Shaw P, Marshall DF
#=GF RL   Nucleic Acids Res. 2003;31:432-435.
#=GF RN   [2]
#=GF RM   12736310
#=GF RT   The high diversity of snoRNAs in plants: identification and comparative
#=GF RT   study of 120 snoRNA genes from Oryza sativa.
#=GF RA   Chen CL, Liang D, Zhou H, Zhuo M, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2003;31:2601-2613.
#=GF CC   This family is based on the Oryza sativum homolog of Arabidposis thaliana
#=GF CC   snoR20 (which is included in model RF00351). The O.sativum sequence was
#=GF CC   obtained from the plant snoRNA database. The name originally given to the
#=GF CC   O.sativum homolog in PMID:12736310 is Z160a.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AJ490367.1/4-94            GCCUUU-GAUGACAUGAUGGUUUCAGAACUGGCACACA-UCGUUGUUGCCAGAGCUAUGUUGAUAUUGCU-CAUGAACUAGGACGGUCUGAGGC
AARH01002868.1/80604-80517 GCCUAU-GAUGACAAACUUGAGUUUCACUGAAAGCAAG-UCAAUGAAUUUGCAUAAUUGUUGAAAUU----CAUGAACUAGGACGGUCUGAGGC
AM450475.1/12728-12644     GCCUAU-GAUGAUA-GUUUGAAUAUUAACUGAAAUGCA-AAAGCAUUUGCA--UUCAUGUUGAAAUU----CAUGAACUAGGACGGUCUGAGGC
AASG02000099.1/88593-88520 GCCAUU-GAUGACU-GUUUGUUUUUCAACUGAAAC------------------UAAAUGUUGAAAUUAUUAUACGAACUAGGACGGUCUGAGGC
AAAA02009241.1/11429-11518 GCCAACACAUGAUA---AGGUUUCAGAAUUAGCAUACAGUUGUUGUUUCUGGAGCUUUGUUGAUACUAAU-UAUGAACUAGGAUGGUCUGAGGC
#=GC SS_cons               <<<___._______._______________________._______________________________.____________________>>>
#=GC RF                    GCCuaU.GAUGAcA.GuUuGuuUuuuAAcUgaaAcAcA.UcauUGUUUuuagAuauaUGUUGAaAUUauU.cAUGAACUAGGACGGUCUGAGGC
//
# STOCKHOLM 1.0

#=GF AC   RF01194
#=GF ID   sn2903
#=GF DE   Small nucleolar RNA sn2903
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   52.50
#=GF NC   43.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.72 -Z 549862.597050 CM SEQDB
#=GF CL   CL00066
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Caenorhabditis_elegans300127;
#=GF RN   [1]
#=GF RM   16714446
#=GF RT   Evolution of small nucleolar RNAs in nematodes.
#=GF RA   Zemann A, op de Bekke A, Kiefmann M, Brosius J, Schmitz J
#=GF RL   Nucleic Acids Res. 2006;34:2676-2685.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


Z72511.1/19566-19656         GAGCGGUGAUGAAUGCACGUAUUGCUCUGACACCUCUUAUGUUAGCGGUAAAUUUCCGUGCCGCGAUGAGUCCACUAGGAUCUCUGAGCUC
DQ789428.1/2-92              GAGCGGUGAUGAAUGCACGUAUUGCUCUGACACCUCUUAUGUUAGCGGUAAAUUUCCGUGCCGCGAUGAGUCCAAUUGGAUCUCUGAGCUC
AAGD02011065.1/170533-170623 GAGCGGUGAUGAAUGCACGUAUUGCUCUGACACCUCUUAUGUUAGCGGUAAAUUUCCGUGCCGCGAUGAGUCCACUUGGAUCUCUGAGCUC
AM051015.1/2-92              GAGCGGUGAUGAAUGCACGUAUUGCUCUGACACCUCUUAUGUUAGCGGUAAAUUUCCGUGCCGCGAUGAGUCCACUAGGAUCUCUGAGCUC
#=GC SS_cons                 <<<<___________________________________________________________________________________>>>>
#=GC RF                      GaGCGGUGAUGAAUGCACGUAUUGCUCUGACACCUCUUAUGUUAGCGGUAAAUUUCCGUGCCGCGAUGAGUCCAcUuGGAUCUCUGAGCuC
//
# STOCKHOLM 1.0

#=GF AC   RF01195
#=GF ID   snR52
#=GF DE   Small nucleolar RNA snR52
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.70
#=GF NC   43.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.00 -Z 549862.597050 CM SEQDB
#=GF DR   snornadb; snR52;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300050;
#=GF RN   [1]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science. 1999;283:1168-1171.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AJ223033.1/15-106          UACUAUGAUGAAUGACAUUAGCGUGAACAAUCUCUGAUACAAAAUCGAAAGAUUUUAGGAUUAGAAAAACUUAUGUUGCCUUCCUUCUGAAA
AABY01000024.1/7397-7488   UACAAUGAUGAAUGACAUUAGCGUGAACAAUCUCUGAUACAAAAUCGAAAGAUUUUAGGAUUAGAAAAACUUAUGUUGCCUUCCUUCUGAAA
AACH01000015.1/15664-15755 CACUAUGAUGAAUGACAUUAGCGUGAACAAUCUCUGAUACAAAAUCGAAAGGUUUUAGGAUUAGAAAAACUUAUGUUGCCUUCCUUCUGAAA
AACI02000291.1/11268-11177 UACUGUGAUGAAUAACAUUAGCGUGAACAAUCUCUGACACAAAAUCGAAAGAUUUUAGGAUUAGAAAAACUUAUGUUGCCUUCCUUCUGAAA
AACG02000002.1/62928-63018 UACUAUGAUGAAUGACAUUA-CGUGAACAAUCUCUGAUACAAAAUCGAAAGAUUUUAGGAUUAGAAAAACCUAUGUUGCCUUCCUUCUGAAA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    uACuaUGAUGAAUGACAUUAGCGUGAACAAUCUCUGAuACAAAAUCGAAAGaUUUUAGGAUUAGAAAAACuUAUGUUGCCUUCCUUCUGAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01196
#=GF ID   snoZ30a
#=GF DE   Small nucleolar RNA Z30a
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   83.10
#=GF NC   34.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=DRO30015;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11842100
#=GF RT   The Schizosaccharomyces pombe mgU6-47 gene is required for
#=GF RT   2'-O-methylation of U6 snRNA at A41.
#=GF RA   Zhou H, Chen YQ, Du YP, Qu LH
#=GF RL   Nucleic Acids Res. 2002;30:894-902.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   10


AJ007735.1/1-92              AGCCAAUGAUGAUUAAACCACAAAU--GCA--GGGAGUGGGCAGCUGGCAACAGUUGGCGCACGCAUGACCAGCAACUAAUCUUCUCGCUGAC-GCG
AASS01022858.1/652-560       AGCCAAUGAUGAUAAAACCACAAAU--GGA--GGGAGUGGGCAGCUGGCAACAGUUGGCUCACGCAUGACCAGCAACUAAUCUUCUCGCUGACGGCA
AAEU02000846.1/77664-77572   AGCCAAUGAUGAUAAAACUAUGAAU--GUA--GGGAGUGGGCAGCUGGCAACAGUUGGCGCACGCAUGACCAGCAACUAAUCUUCUCGCUGAUGGCA
AAPQ01006057.1/692543-692451 AGCUUAUGAUGAUAAAACUAUUAAU--GCA--GAGAGUGGGCAGCUGGCAACAGUUGGCGCACGCAUGACCAGUAACUAAUCUUCUCGCUGAUGGCA
AAFS01002680.1/4226-4317     CCCACAUGAUGUUAAACCCAAAGUG--AAA--GGGAGUGCGCAUCUGGCAACAGUUGGCGCACGCAUGACCAAUAACUAAUCUUCUCGCUGAU-GGA
AAPP01017258.1/46530-46615   AAA--AUGAUGA---AACC-UUACU--UCA--GGGAGUGGGCAGCUGGCAACAGUUGGCGCACGCAUGACCAGAUUCUAAUCUUCUCGCUGAU-UUC
AAPT01018964.1/183168-183075 ACCAACUGAUGAAAGACACAAACUUCAUUU--GGGAUUGCGCAAUUGGCAACAAUUGGCGCACGCAUGACCAUAGACUAAUCUUCUCGCUGAU-GGC
AAQB01006833.1/398045-397955 GCCACAUGACGAUUUG-CUUUUUGU--AAA--GAGAGUGGGCAGCGGGCAACCGUUGGCCCACGAAUGACCAGUUACUAAUCUUCUCGCUGAU-GGU
AANI01016931.1/5301-5209     UCCAGCUGAUGAC-AAACCAAAUCU--UCAAUGGGAUUGCGCAAUUGGCAACAAUUGGCGCACGCAUGACCAUAGACUAAUCUUCUCUCUGAU-GGC
AAPU01008519.1/41898-41989   AGCCGAUGAUGAAAUCAACUUCAGU--UU---GGGAUUGCGCAAUUGGCAACAAUUGGCGCACGCAUGACCAUUGACUAAUCUUCUCUCUGAUGGCU
#=GC SS_cons                 :<<______________________..___.._____________________________________________________________.>>:
#=GC RF                      agCaaAUGAUGAuaaAAccAuaaaU..uuA..GGGAgUGgGCAgcUGGCAACAgUUGGCgCACGCAUGACCAguaACUAAUCUUCUCGCUGAU.Gca
//
# STOCKHOLM 1.0

#=GF AC   RF01197
#=GF ID   snR39
#=GF DE   Small nucleolar RNA snR39
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   42.40
#=GF NC   39.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.69 -Z 549862.597050 CM SEQDB
#=GF CL   CL00054
#=GF DR   snornadb; snR39b;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science. 1999;283:1168-1171.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


X94605.1/2-96              UUUAGUGAUGAUACUGCCGAUU----CUGGCA-UUCCAAAAAGUGACUAGC---AAAAU---UGCGAUGUUGUCAACUUAAAUUACACCAUCUUUCGGGGCUGAUA
AACH01000077.1/3889-3986   UUUAGUGAUGAUACUGCCGAUU----CUGGCA-UUCCAAAAAGUGACUAGC---AUUAUAAAUGCGAUGUUGUCAACUUAAAUUACACCAUCUUUCGGGGCUGAAU
AACA01000192.1/11990-12087 UUUAGUGAUGAUACUGCCGAUU----CUGGCA-UUCCAAAAAGUGACUAGCGUUAUAAA---CGCAAUGUUGUCAACUUAAAUUACACCAUCUUUCGGGGCUGAUU
AAZN01000229.1/74905-74806 UGAAGUGAUGAUAAAUGUCAUUAACAGUGACAUUUUCAACUAGUGACUAGC---UAUUU---AGCAAUGUUGUUUACUAAAAUUACACCAUCUUUCGGGGCUGAUU
#=GC SS_cons               ::<<__________________....______.__________________..._____...__________________________________________>>
#=GC RF                    UucaGUGAUGAUAcugccgAUU....cUGgCA.UUcCAAaaAGUGACUAGC...aauau...uGCaAUGUUGUcaACUuAAAUUACACCAUCUUUCGGGGCUGAug
//
# STOCKHOLM 1.0

#=GF AC   RF01198
#=GF ID   snoR69Y
#=GF DE   Small nucleolar RNA snoR69Y
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   46.20
#=GF NC   43.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.37 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol. 2001;311:57-73.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AC167403.2/76867-76775     UGCGA---CAAUGACGAUAAAUG---UGAUCCCAGCUC--UAUGAGACCG---------UAA-GGUCCAAGAAUAAACUUAGUU-CCAACACACAUUUGUCUGAGCC----UCUCG
AC069159.8/55260-55355     UCUCGAGGUGAUGAUGAUAACAUA--UAAUCCCAGCUC--UAUGAGACCUUUUG-----U---GGUCAAGGAGUAUAACUAUGUUCAUACAUUUAU----CUGAGCC----UUAGA
AC172870.1/115717-115624   UAAGG---UGGUGAUGAUAAUAUA--UAAUCCCAGCUC--UAUGAGGCCUUUUG-----U---GGUCUAGGAGUACAACUAUGUUCA---AUACAUGUAUCUGAACC----UUUUA
AM460399.2/62309-62412     AAUUGUUGCAAUGAUGAUAAAUGU--UAAUCCCAGCUCAUUAUGAGACCUUUCAUU---GAAAGGUCCAGGAGUAGACUCAAUG---AACACAUAU----CUGAGCCUCUGCAAUU
AASG02008443.1/3761-3660   AAUAGCAGCGAGGAUGAUAAAUGUUUUAAUCCCAGCUCAUUAUGAGACCUUUUUG----UAA-GGUCUGGGAAUUGAAAUACAGUCUCACAUUUAU----CUGAGC-----UUAUU
AARH01003141.1/37515-37613 UGCUG--GCUAUGAUGAUCAUUGA--UAAUCCCAGCUC--UAUGAGAUCUUCAAUUG--UAA-GGUCUAGGAGUAUUAUAUGUUUUCAAUUUCUGC----CUGAGCC----UAAUA
AC182564.2/17000-17102     UUUAGCAGUGAUGACGAGAACAC---UAAUCCCAGCUC--UAUGAGGCCUUCUUUGUGUUAA-GGUCACGGAUAAUACUCUUCAAUCUCGAUCUUUUU--CUGAGC-----UUAGC
#=GC SS_cons               <<<<<___________________..____________.._______________....___._________________________________...._______....>>>>>
#=GC RF                    ugugguaGcgAUGAUGAUAAauga..UAAUCCCAGCUC..UAUGAGACCUUuuau....UAA.GGUCuaGGAgUAuAauuauuuuccaAcAUaUaU....CUGAGCC....ucaca
//
# STOCKHOLM 1.0

#=GF AC   RF01199
#=GF ID   snR58
#=GF DE   Small nucleolar RNA snR58
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   76.90
#=GF NC   64.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.85 -Z 549862.597050 CM SEQDB
#=GF CL   CL00077
#=GF DR   snornadb; snR58;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300024;
#=GF RN   [1]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science. 1999;283:1168-1171.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ223032.1/9-104           CUUUAUGAUGAUAUUCUUUACGAACUUUU-AGACGUUAGACUUCUGAAGGAGAUUAGACCCUCCUAUGGAAGAGAAACUC-GUUAAACUUAUCUGAGU
AABZ01000203.1/11569-11665 UUUUAUGAUGAUAUCCUUUACGAACUUUUCAGACGUUAGACUUCUGAAGGAGAUUAGACCCUCCUGUGGAAGAGAAACUC-GUUUAACUUAUCUGAAU
AACA01000158.1/4253-4156   UCCUAAGAUGAUAUUCUUUACGAGCUUUUUGGACGUUAGACUUCUUAAGUAGAUUAGGUUAUCUUGUGAAAGAGAAACUCACCCCAACAAGUCUACAU
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::
#=GC RF                    uuuUAuGAUGAUAUuCUUUACGAaCUUUUuaGACGUUAGACUUCUgAAGgAGAUUAGacccUCcUGUGgAAGAGAAACUC.guuuAACuuaUCUgaaU
//
# STOCKHOLM 1.0

#=GF AC   RF01200
#=GF ID   SNORD125
#=GF DE   Small nucleolar RNA SNORD125
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   56.00
#=GF TC   62.30
#=GF NC   53.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00067
#=GF DR   snoRNABase; SNORD125;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16990247
#=GF RT   snoSeeker: an advanced computational package for screening of guide and
#=GF RT   orphan snoRNA genes in the human genome.
#=GF RA   Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2006;34:5112-5123.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   16


ABDC01061241.1/1976-1882     AAGCCUAGCAGCCC-UCCUGAUGAUUCU--UCU-U--CCUGAGCG-----CUCUAG---UGAUGAGC----AAACUGAGCCUCUAAGAAGUUGACUGAAGGGGUUGCUUCCUC
AAQQ01192494.1/1039-943      AACUGAAGCAGCCCCUCCUGAUGAAUCU--UCU-U--CCUGAGCA-----GCUCCAG--UGAUGAGC----AAACUGAGCCUCUAAGAAGUUGACUGAAGGGGCUGCUUCCUC
AALT01311275.1/7233-7329     GACCCUCGCAGCCCCUCCUGAUGAUUCU--UCU-U--CCUGAGUG-----GCUCCAG--UGAUGAGC----AAACUGAGCCUCUAAGAAGUUGACUGAAGGGGCUGCUUCCCC
AAIY01078682.1/1436-1532     AAGCGUGGCAGCCUCUCCUGAUGAUCCU--UCU-U--CCUGAGCG-----GCUCCAG--UGAUGAGC----AAACCGAGCCUCUAAGAAGUUGACUGAAGGGGCUGCUUCCCC
AAFC03028295.1/24957-24861   AACGCAGGCAGCCUCUGCUGAUGACCCU--UCU-U--CCUGAGUGG----CUCUGG---UGAUGAGC----AAACUGAGCCUCUAAGAAGUUGACUGAAGGGGCUGCUUCCUC
AAYZ01146934.1/10710-10614   GGCUCCAGCAGCCCCUCCUGAUGAUCCC--UCU-U--CCUGAACG-----GCUCCAG--UGAUGAGC----AAACUGAGCCUCUAAGAAGUUGACUGAAGGGGCUGCUUCCUC
AAHY01090323.1/17268-17364   AACCUUGGCAGCCCCUCUUGGUGAUUCC--UCC-U--CCUGAGUGG----CUCCAA---UGAUGAGC----AAACUGAGCUUCUAAGAAGUUGACUGAAUGGGCAGCUCUGCC
AANN01154657.1/2369-2467     GACUCACGCAGCCCCUCCUGAUGAUCCU--UCU-U--CCUGAGUG-----GCUCCAG--UGAUGAGCCA--AAACUGAGCCUCUAAGAAGUUGACUGAAGGGGCUGCUUCCUC
AAPN01414510.1/3377-3476     AGCCCUGGCCGCCUCUCCUGAUGACUCUUCUCU-U--CCUGACUG-----GCUCCAG--UGAUGAGUA---AACCUGAGCCUCUAAGAAGUUGACUGAAGAGGCCGCGGGGGA
AABR05046572.1/96751-96847   AACCGUGGCAGCCCCUCCUGAUGAUUCC--UCU-U--CCUGAGUG-----UCUCCAG--UGAUGAGC----AAACUGAGCCUCUAAGAAACUGACUAAAGGGGCAGCUUCCUC
AACN010830067.1/665-761      GAGCCAAGCAGCCUCUCCUGAUGAUUCU--UCU-U--CCUGAGUGG----CUCUAG---UGAUGAGC----AAACUGAGCCUCUAAGAAGUUGACUGAAGGGGCUGCUUCCUC
AAPE02038438.1/20128-20224   GAACUGAGCAGCCUCUCCUGAUGAUUCU--UCU-U--CCUGAGCAG----CUCUCG---UGAUGAGC----AAACUGAGCCUCUAAGAAGUUGACUGAAGGGGCUGCUUCCUC
AC138066.34/81656-81751      ACCCCUGGCAGCCCCUCCUGAUGAUUCU--UCU-U--CCUGAGCA-----CGCUCA---UGAUGAGC----AAACUGAGCCUCUAAGAAGUUGACUGAAGGGGCUGCUUCCCC
AAWZ02027449.1/32053-32150   UAAGAAGGUGGCCUCUCGUGAUGACCCC--CCUCU--CCUGAAGCAGAUGGGUUGG---UGAUGAUC----GAAC----CCUCUAAGAAGUUGACUGAAGAGGCUGCUUGGCU
AAGU03075197.1/119928-120024 AACCCAGGCAGCCUCUCCUGAUGAUCCU--UCU-U--CCUGAGCAG----CUCUAG---UGAUGAGC----AAACUGAGCCUCUAAGAAGUUGACUGAAGGGGCUGCUUCCCC
AADN03007146.1/11098-10994   CCAGGGAACAGCCUCACGUGAUGAUCCU--UCU-CUCCCUGAUGG-----CUCCGAUGGUGAUGGACAUCAACCCAAAGCCUCUGAGAAGUUGACUGAGGAGGCUGUUUCCUG
#=GC SS_cons                 ::::::<<<<<<<<<_____________..___._..________....._______..________....____________________________>>>>>>>>>:::::
#=GC RF                      aaaccuaGCaGCCcCUCcUGAUGAuuCU..UCU.U..CCUGAgug.....cuucaag..UGAUGAgC....AAACuGAGCCUCUAAGAAGUUGACUGAAGgGGCuGCuUccuc
//
# STOCKHOLM 1.0

#=GF AC   RF01201
#=GF ID   snR40
#=GF DE   Small nucleolar RNA snR40
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   42.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00054
#=GF DR   snornadb; snR40;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   7667877
#=GF RT   Antisense snoRNAs: a family of nucleolar RNAs with long complementarities
#=GF RT   to rRNA.
#=GF RA   Bachellerie JP, Michot B, Nicoloso M, Balakin A, Ni J, Fournier MJ
#=GF RL   Trends Biochem Sci. 1995;20:261-264.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   18


Z71564.1/474-570               GUAAAUGACGAGAAAAAAGCUGUGCACCAGUCUGAACAUGGAUGCCA--CAAGUACUCAGGUGUCCUAUGAAGCAU---UAAGUAU--ACCCAAAUU-UCUGAUC
AACG02000180.1/13913-13817     GAAAAUGACGAGAAAAAAGCUGUGCACCAGUCUGAACUUGGACGCCA--GAUGUACUCAGGCGUCCUAUGAAGCAU---UAAGUAU--ACCCAAAUU-UCUGAUC
AAZN01000021.1/10523-10428     GAAAAUGACGAGACAAACGCUGUGCACCAGUCUGAUAUCAGGUCCUA--AAUGUACUCAGGA-UUCGAUGAAGUAU---CAAGUAU--ACCCAAAUU-UCUGAUC
AACF01000363.1/646-549         GAAAGUGACGAGAGAAACGCUGUGCACCAGUCUGAACUUGGCACCUAACAAUGUACUCAGGUG-CCCAUGAAGUAU---UAAGUAU--ACCCAAAUU-UCUGAUU
CR382125.1/1171339-1171430     UCCAAAGACGAGAGAAACGCUGUGCACCAGUCUGAACG-UG----CU--AAAAUGUACUCUAGCACUCUGAAGCAU---UAAGUAU--ACCCAAAUU-UCUGAGG
AADM01000021.1/38814-38722     UCAAGUGAUGAGUGAAAUGCUGUGCACCAGUCUGAAA----GGGCCA--CAAGUACUC-GUGGCCCGUUGAAGCAU---UAAGUAA--ACCUAUAUUAUCUGAUG
AABZ01000174.1/12255-12350     GAAAAUGACGAGAAAAAAGCUGUGCACCAGUCUGACAU-GGACGCCA--CAAGUACUCAGGUGUCCUAUGAAGCAU---UAAGUAU--ACCCAAAUU-UCUGAUC
CP000497.1/358606-358529       UUAAGUGACGACA-AAACGCUGUGCACCAGUCUGA-----------------GUACUCAUACG---CAUGACAGAC---CCAGUAU--ACCCAAAUU-UCUGAUA
DQ115396.1/8340-8429           UUAAGUGAUGAGAAUUACGCUGUGCACCAGUCCAAGC---GGAAAUU--UUUGUACUC---UCUGCUCUGACG-AC---UCAGUAU--ACCCAUAUU-CCUGAUU
AAFM01000054.1/140217-140293   UUAAAUGAUGACA-AAACGCUGUGCACCAGUCUGA-----------------GUACUC----AUUGCAUGAUAGAC---CCAGUAU--ACCCAAGUU-UCUGAUA
AAFT01000015.1/83616-83540     CAUGAUGAUGACA-AAACGCUGUGCACCAGUCAGA-----------------GUACUC----UUUUCAUGAUCGAU---ACAGUAU--ACCCAUAUU-CCUGACA
AACQ01000170.1/2388-2308       UUUAAUGAUGACAAGAUCGCUGUGCACCAGUCUGA-----------------GUACUCAACUG---CAUGACAGAC---CCAGUAUAUACCCAAAUU-UCUGAUC
AAPO01000074.1/76364-76438     UGCAAUGAUGACAAUCAUGCUGUGCACCAGUCGGAAC--------------------------UUAAAUGACAGAC---CCAGUAUAUACCCAAAUU-UCUGAUU
AACE03000005.3/1082925-1082831 GUAUAUGACGAUAGAAAUGCUGUGCACCAGUCUGAAAGUACUAAACC--UUUGUACUC--UAGUACGUUGAAGCAU---UAAGUAU--ACCCAAAUU-UCUGAUA
CR382137.2/1045753-1045676     CUAAAUGACGACA-AAACGCUGUGCACCAGUCUGA-----------------GUACUCAAAAG---CAUGAUAGAC---CCAGUAU--ACCCAAAUU-UCUGACA
CR380959.2/403349-403256       UGAUAUGACGACAAAAUAGCUGUGCACCAGUCUGAA-----AGGAUA--CCAGUACUC-GGUAACCGUUGAAGUAUAUCUAACUAU--ACCCAAAUU-UCUGAUA
AE016818.2/266474-266566       GCACAGGACGAGAGAAAUGCUGUGCACCAGUCUGAACG--UACUACA--CUUGUACUC--UAGUACUCUGAAGCAU---CAAGUAU--ACCCAAAUU-UCCGAUG
U26015.1/1-97                  GUAAAUGACGAGAAAAAAGCUGUGCACCAGUCUGAACAUGGAUGCCA--CAAGUACUCAGGUGUCCUAUGAAGGAU---UAAGUAU--ACCCAAAUU-UCUGAUC
#=GC SS_cons                   :::::::::::::::::::::::::::::::::::::...:::::::..:::::::::.:::::::::::::::::...:::::::..:::::::::.:::::::
#=GC RF                        uuaaAUGAcGAgAgaAAcGCUGUGCACCAGUCUGAac...gaugcca..cauGUACUC.gguguccuaUGAaGgAU...uaAGUAU..ACCCAAAUU.UCUGAUa
//
# STOCKHOLM 1.0

#=GF AC   RF01202
#=GF ID   sn2991
#=GF DE   Small nucleolar RNA sn2991
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   66.30
#=GF NC   39.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Caenorhabditis_elegans300033;
#=GF RN   [1]
#=GF RM   12372436
#=GF RT   Location of 2(')-O-methyl nucleotides in 26S rRNA and methylation guide
#=GF RT   snoRNAs in Caenorhabditis elegans.
#=GF RA   Higa S, Maeda N, Kenmochi N, Tanaka T
#=GF RL   Biochem Biophys Res Commun. 2002;297:1344-1349.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


U70870.1/2038-1941           AUUUCUAGAUGAUGGAAGAGCAGUGAAAGAUCUUUGAAGAGCCGAAUGUUCAGAAUCAACAGAUACCAAUGAAGCAUCUGUAUCUCCUGACGAGAAAU
CAAC02000447.1/926003-925906 AUUUCUGGAAGAUGGAAGAGCAGUGAACGAUCUUUGAAGAGCUGAAUGCUCAGAGUCAACAGAAACCAGAGCAGCAUCAGUGUCUCCAGAUGAGAAAU
AAGD02003554.1/75595-75692   AUUUCUGGAUGAUGGAAGAGCAGUGAAAGAUCUUUGAAGUGCUGAAUGUUCGGAAUCAACAGAAACAAGAGCUGCAUCUGUAUCUCCUGAAGAGAAGU
ABEG02005932.1/17993-17896   AUUUCUAGAUGAUGGAAGAGCAGUGAAUGAUCGUUGAAGUGCCGAAUGUUCAGAAUCAACAGAGACUAAAGCAGCAUCAGUAUCUCCAGAUGAAAAGU
#=GC SS_cons                 <<<<<<______________________________________________________________________________________>>>>>>
#=GC RF                      auuuCuaGAuGAUGGAAGAGCAGUGAAaGAUCuUUGAAGuGCuGAAUGuUCAGAAUCAACAGAaACuAaaGcaGCAUCaGUAUCUCCaGAuGaGaaau
//
# STOCKHOLM 1.0

#=GF AC   RF01203
#=GF ID   snR47
#=GF DE   Small nucleolar RNA snR47
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   61.00
#=GF TC   66.80
#=GF NC   54.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   snornadb; snR47;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300039;
#=GF RN   [1]
#=GF RM   8797828
#=GF RT   The RNA world of the nucleolus: two major families of small RNAs defined
#=GF RT   by different box elements with related functions.
#=GF RA   Balakin AG, Smith L, Fournier MJ
#=GF RL   Cell. 1996;86:823-834.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   17


U56648.1/1-99                  ---AUAUAUGAUGAUA-UCCUAUAAC-AACAACAACAUGAAUUUCUUCGUCCGAAUCCUUUAUAGGUGGAAACA--AACUUUGACAAUAGCUUUUUAACACUGAUA
AADM01000045.1/22801-22708     ---UAAUAUGAUGAAA-CCCAAUUAC-AACAACAACAUGAAUUUCUUCAGCCGA--CCAAAAUAGGAGGAACCA--AACUUUGACA---GCUUUUUAACCCUGAUU
AACF01000157.1/2944-2847       ---UUUUAUGAUGAUAAACAAAUAAC-AACAACAACUUGAAUUUCUUCAACCGA--UAAUUAUAGGAGGAUAAAU-UACUUUGACA-UAGCUUUUUAACCCUGAUC
AAZN01000317.1/31446-31541     ---UUUGAUGAUGAUA-G-CCUUAAU-AACAACAACUUGAAUUUCUUCAACCGAAACA---ACAGGUGGAAACAAUUAUUUUGACA-UAGCUUUUUAACCCUGAUC
CR382126.1/1700717-1700622     ---UUUUAUGAUGAUA-C-ACCUAAC-AACAACAACAUGAAUUUCUUCAACCGA--UCAACUCAUGAGGAAUCCU-UAUUUUGACA-UAGCUUUUUAACCCUGAUC
CP000499.1/1393929-1394024     GAAUACUCUGAUGAAU-AAUUAUAAC--AAAACAAC--GAAUUUCUUCACCUGAAUCA---CCAUGUGGAAUAAA-CAUAAUUUCA-GAGCUUUUUAACACUGAUU
AACQ01000059.1/130089-130179   ---UUAAAUGAUGAAU-GAUUAUUU---ACAACAAC--GAAUUUCUUCACCUGAAAUA---CCAUGUGGAUAAA--AAUAAUUUCA-GAGCUUUUUAACACUGAUU
AAPO01000038.1/21288-21189     ---UAAAUUGAUGAAUCGAUUAUUUAUAACAACAAC--GAAUUUCUUCACCUGAAAAAAAACCGUGUUGAUAAAUUAAUAAUUUCA-GAGCUUUUUAACACUGAAU
AAFT01000029.1/86929-87017     GUGUAUGAUGAUGAAU-UAUUAU---------CAAC--GAAUUUCUUCACCUGAAUCA---CCAUGUGGAUUAUC-AAUAAUAUCA-GAGCUUUUUAACCCUGACA
AACE03000004.1/255309-255214   ---UCAUAUGAUGAAA-AACGAUUAC-AACAACAACUUGAAUUUCUUCAACCGA--UUUACAUAGGAGGAACCUUAUUCUUUGACA---GCUUUUUAACCCUGAUU
CR382138.2/574814-574907       UAAUUUACUGAUGAAU-UAUUA--AU--ACAACAAU--GAAUUUCUUCACCUGAAUCA---CCAUGUGGAAUAAA-AAUAAUAUCA-GAGCUUUUUAACACUGAAU
CR380957.2/1168535-1168437     ---UAUUAUGAUGAUA-AAAACUAAC-AACAACAACUUGAAUUUCUUCAACCGA--AUAACCCAGGAGGAUACAAUUACUUUGACAAUAGCUUUUUAACCCUGAUA
CABE01000024.1/1717129-1717222 ---UCUAAUGAUGAAU-GAUUAU-UU-AACAACAAC--GAAUUUCUUCAGCUGAAAUA---ACGUGUGGAAAAAAACAAUAACUCA-GAGCUUUUUAACACUGACU
FN392321.1/1844377-1844462     ---UUGGAUGAUGAAC-AUUUUU--------ACAACAUGAAUUUCUUCACCUGAAAUA---UUAUGUGGAUUCAG-U---AAAACA-GAGCUUUUUAACCCUGACA
CR382132.1/2836259-2836176     ---UUUACUGAUGAUA-AAAAU------ACAACG--UUGAAUUUCUUCAACUGAAACC---UCGUGUGGAG------AUAAGUACA-GAGCUUUUUAACCCUGAUA
AAFN02000033.1/162533-162627   ---UUUAAUGAUGAAU-GAUUAUUUU-AACAACAAC--GAAUUUCUUCACCUGAAAUA---CCAUGUGGAAACAACAAUAAUUUCA-GAGCUUUUUAACACUGAUU
AE016820.4/1087646-1087733     ---UAGCGUGAUGAAA-A-CGC--ACAAACAACAACUUGAAUUUCUUCAGCCGA--CU-ACACAGGAGGAACCAU-----UUGACA---GCUUUUUAACCCUGAGC
#=GC SS_cons                   ...:::::::::::::.:::::::::.:::::::::::::::::::<<<_________..._____>>>::::::.::::::::::.:::::::::::::::::::
#=GC RF                        ...UuuuaUGAUGAaa.aauuaUaac.AACAACAACuUGAAUUUCUUCaaCuGAAaua...acAuGuGGAaaaAa.aAuuaUgaCA.gAGCUUUUUAACcCUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF01204
#=GF ID   snR65
#=GF DE   Small nucleolar RNA snR65
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   40.90
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 36 -Z 549862.597050 CM SEQDB
#=GF DR   snornadb; snR65;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300019;
#=GF RN   [1]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science. 1999;283:1168-1171.
#=GF RN   [2]
#=GF RM   15306656
#=GF RT   Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the
#=GF RT   Saccharomyces cerevisiae genome.
#=GF RA   Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM
#=GF RL   Nucleic Acids Res. 2004;32:4281-4296.
#=GF RN   [3]
#=GF RM   9106664
#=GF RT   The family of box ACA small nucleolar RNAs is defined by an evolutionarily
#=GF RT   conserved secondary structure and ubiquitous sequence elements essential
#=GF RT   for RNA accumulation.
#=GF RA   Ganot P, Caizergues-Ferrer M, Kiss T
#=GF RL   Genes Dev. 1997;11:941-956.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AF064277.1/1-100           UAAAAUGAUGAUUUUUUUA-AACACAA-UUUAUGCUAGAUAGUAUCUGAAAGCAUUCAAACUUUAUGAUUACAGUGUUUUCGACAGUUUUAAAUCUCUGAAC
AABY01000060.1/33829-33929 UUAAAUGAUGAUUUUUUUUGAACACAA-UUUAUGCUAGAUAGUAUCUGAAAGCAUUUAAACUUUAUGAUUAUAGUGUUUUCGACAGUUUUAAAUCUCUGAAU
AACI02000034.1/7813-7912   UAAAAUGAUGAGUUUUUUG-AACACAAUUUUAAGCUAGAUAGUAUCUGAAAGCAUUUAAACUUUAUGAUUACAGUGUUUUCGACAGUUUUAA-UCUCUGAGA
AABZ01000039.1/17906-17807 UUUAAUGAUGAUUUUUUUG-AACACAAUUUUAUGCUAGAUAGUAUCUGAAAGCAUUUAAACUUCAUGAUUAUAGUGUUUUCGACAGUUUUA-AUAUCUGAAA
AACA01000006.1/87789-87885 UAUAAUGAUGAGUUUUUUG-AACAC-U-UAUAUGCUAGAUAGUAUCUGAAAGCAUUUAA-CUUUAUGAUUACAGUGUUUUCGACAGUUUUAA-UCUCUGAAA
#=GC SS_cons               :::::::::::::::::::.:::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UaaAAUGAUGAuUUUUUUg.AACACAa.UuUAuGCUAGAUAGUAUCUGAAAGCAUUUAAACUUuAUGAUUAcAGUGUUUUCGACAGUUUUAAAUcUCUGAaa
//
# STOCKHOLM 1.0

#=GF AC   RF01205
#=GF ID   snR62
#=GF DE   Small nucleolar RNA snR62
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   61.40
#=GF NC   44.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34 -Z 549862.597050 CM SEQDB
#=GF CL   CL00055
#=GF DR   snornadb; snR62;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science. 1999;283:1168-1171.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AF064274.1/1-100         UUUUAUGAUGAAUUUAUGUUUUCAAUCUUAUCUACAUUAUCUGAAUUAAUAGCUAACAAUAGUUAUAAUGGAAGAUAUACGACUAUCAACAAUUCUGAAA
AACH01000555.1/3655-3754 UUUCAUGAUGAAUUUGUGUUUUUAAUCUUAUCUACAUUAUCUGAAUUAAUAGCUAACAAUAGUUAUAAUGGAAGAUAUACAACUAUCAAUAAUUCUGAAA
#=GC SS_cons             <<<______________________________________________________________________________________________>>>
#=GC RF                  uuuuAUGAUGAAUUUaUGUUUUuAAUCUUAUCUACAUUAUCUGAAUUAAUAGCUAACAAUAGUUAUAAUGGAAGAUAUACaACUAUCAAuAAUUCUGaaa
//
# STOCKHOLM 1.0

#=GF AC   RF01206
#=GF ID   snoR109
#=GF DE   Small nucleolar RNA snoR109
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   34.00
#=GF TC   34.60
#=GF NC   33.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300014;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AJ505680.1/1-101             CGGCUGUAGCUAGAUUGAAU---------AAGAAGCU-AUCGGCCGGUGGUCGCGUAGAG-GGAUUUAGAUCUCUCCGGUCGAUUCAUCUGCUUACCGAGUUUCUUACAUUU
AARH01010739.1/234432-234534 CGGCUGUAGCUAUAUCAAAU---------GAGAUGCUAACUGGCCGGCUGUUGUGUGAGGUGGAUUUUCCCAUCUCCGAUUGACUGAUCUGCUUACCGAGCCUCUCACAAUC
AC148915.2/27731-27645       UGGCUGUAGCUAUAUUAAAUCG-------AAGAAUCUUACUGGCCGGUUAUUGU----GA--------------CUCUGUCGAUAAAUCUGCUUACCGAGUUUCUCACAUUU
AASG02000807.1/14902-14812   CGGCUGUAGCUAUAUCAAUUU--------CAGAAGCUAACUGGCCGGUUGUUGUUUUUGA------------G-AUCCAUCGACAUAUCUGCUUACCGAGCUUCUUAUAUUU
AP007291.1/29018-29107       UGGCUAUAGCCAAAUCAAAUCGAG-----GAGAAGCUAACUGGCCGGUUGUUGC----GA------------G-UUUCGUCAACAAAUCUGCUUACCGAGCUUCUCACAUUU
AM431816.2/2981-3076         UGGCUGUAGCUAUAUCAAAUCAAAUGGCUGAGAAGUUAACUGGCCGGUUGUCGU----GA------------AUCUCUGUCGACAAAUCUGCUUACCGAACUUCUCACAUUU
#=GC SS_cons                 :::::::::::::::::::::........<<<<<<<<----<<<-<<<<<<<<_______............________>>>>->>>>->>>----->>>>>>>>::::::
#=GC RF                      uGGCUGUAGCUAuAUcAAAUc........gAGAagCUAACUgGCCGguuGUcGugUaaGa............ucuuCugUCgACaaauCUGCuUACCGAGcuUCUcACAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01207
#=GF ID   snR73
#=GF DE   Small nucleolar RNA snR73
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.30
#=GF NC   36.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00056
#=GF DR   snornadb; snR73;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   9891049
#=GF RT   Seven novel methylation guide small nucleolar RNAs are processed from a
#=GF RT   common polycistronic transcript by Rat1p and RNase III in yeast.
#=GF RA   Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y,
#=GF RA   Caizergues-Ferrer M, Bachellerie JP
#=GF RL   Mol Cell Biol. 1999;19:1144-1158.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AJ010796.1/1-103             GUUUAUGAUGAUU-UCCACAU---UUCACGACGGUCAACUGCGUUUUUCGA-A-UGUUUAUCGAUU-AACUUUGAUGAUAUUUCGCCUGUGACAGGGCGUGGUACUGAGC
AACF01000013.1/100163-100061 GUUUAUGAUGAUU-UAAUUUU---AUCACGACGGUCAACUGUGUUCUUCUACU-UGUUUAUUGAAG-AACGUUGAUGAUAUUU-GCCUGUGACAGGGCAUUGAUCUGAUC
CR382124.1/957592-957696     GUUUAUGAUGAUUAUCCACUU---UUCACGACGGUCAGCUGUUAUCCCCGA-AAUGUUUAUUUGGG-GAUGUUGAUGAUAUUUUGCCUGUGACAGGGCGUGGUACUGAUU
AAZN01000292.1/2511-2408     GUUUAUGAUGAAUUUACUUUU---AUCACGACGGUCAACUGCGUUUCUUUACC-UGUUUAAUUAAGAAACUUUGAUGAUAACU-GCCUGUGACAAGGCAUGAUACUGA-C
CR380959.2/770154-770049     GUUUAUGAUGAUU-ACCACUUAUUAUCACGACGGUCAACUGCGUUCUUCGA-U-UGUUUAUCUUAG-AACUUUGAUGAUAUUCUGCCUGUGACAGGGCGUGGAACUGAUU
#=GC SS_cons                 :::::::::::::.:::::::...:::::::::::::::::::::::::::.:.::::::::::::.:::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      GUUUAUGAUGAuU.ucCacUU...aUCACGACGGUCAaCUGcGuUcuUCgA.u.UGUUUAuuuaaG.aACuUUGAUGAUAuUUuGCCUGUGACAGGGCgUGGuaCUGAuc
//
# STOCKHOLM 1.0

#=GF AC   RF01208
#=GF ID   snoR99
#=GF DE   Small nucleolar RNA snoR99
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   41.00
#=GF TC   41.10
#=GF NC   40.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300140;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   9


AJ505676.1/1-103           GUGCUUAAUAGGAUUGAACAAAGUCCCU-CAAAU--CUUG--AUCCAUCUGU--CACUUUGUCAGCAG---UCUUAAUUGGUUUCUUGCU-GAUCAUUAUAUGAUGGGAAAUAA
AC189545.1/54648-54751     GUGCU-AAUAGGAUUGAACAAAGUCCC---AAAU--AUUGUAAUCCAUCUGUUUCACUUUGUCAGCAG---ACUUAAUUGGUGUCUUGCU-GAUCAUUUUAUGAUGGGAUAUGG
AARH01003329.1/32990-33097 GUGCU-CUAGGGGGUGAAAGAGUCCCUG-AUAUUUAAUUAACAUCCAUCCGUUUCACUUUGUCAGCAG---UAUUGUUUGGUUUCUUGCU-GAUCAUUAGAGGGUGGAAUAUUA
AM424485.2/33101-33205     GUGCU--UCAGGGAUGAACAAGUCCCUGAUAUGU--AAUCUUAUCCAUCUAUUUCACUUUGUCAGCAA---UC-UAUUUUGUAUUUUGCU-GAUCAUUUGCGGAUGGAACAUCC
AC155101.19/100263-100159  UUGCUUAU--GGGAAGAAUGCGUCCCUU-AUAUG--CAAAUUAUCCAUCUGCUUCACUUUGUCAGCUC---UGUUUUCUUAUAUUUUGCU-GAUCAUUUUAGGAUGGAAAAGUA
AASG02014320.1/3869-3974   GUGCU--UUAGGGAUGAACAAGUCCCUAAUAAAU--AUCG--AUCCAUCCAU--CACUUUGUCGGCAAUAUUCGUUUUUGGUUUGUUGCCUGAUCAUUUAAGGGUGGAAUAUGC
AACV01012416.1/22338-22437 GUGCCUAA--GGGAUGAACAGGUCCCC-----AU--AGUUACAUCCAUUUCGUUCACUUUGUUGGCUA---AUAACACUAAUUUUUAGCU-GAUCAUUA-AGGAUGGGAAAUCU
CT990489.3/73281-73181     UUGCU--UUAGGGAUGAACAAGUCCCU----GAU--AAUUUAAUCCAUUCAU--CACUUUGUCAGCAUC--ACAAUUUUUAUGUUUUGCU-GAUCAUUAUCGGAUGGUACAAGU
AAAA02017482.1/36664-36567 GUGCC--UGUGGGAUGAACAGGUCCCA-----AU--AUUUACA-CCAUUUUAUUCACUUUGUCAGCUA---AU-GGUCAUAUUUUUAGCU-GAUCAUUG-AGAAUGGGAAAUAC
#=GC SS_cons               :::::.::::::::::::::::::::::.:::::..:::::::<<<<<<-----------<<<<<<<<...______________>>>>>.>>>-------->>>>>>::::::
#=GC RF                    GUGCU.auuaGGGaUGAAcAaGUCCCuu.uaaaU..AuUuuuAuCCAucuauUUCACUUUGUCaGCaa...ucuuuuuUugUuUuuuGCu.GAUCAUUuuAGgaUGGaAaAUua
//
# STOCKHOLM 1.0

#=GF AC   RF01209
#=GF ID   snR76
#=GF DE   Small nucleolar RNA snR76
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   59.00
#=GF NC   51.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00071
#=GF DR   snornadb; snR76;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   9891049
#=GF RT   Seven novel methylation guide small nucleolar RNAs are processed from a
#=GF RT   common polycistronic transcript by Rat1p and RNase III in yeast.
#=GF RA   Qu LH, Henras A, Lu YJ, Zhou H, Zhou WX, Zhu YQ, Zhao J, Henry Y,
#=GF RA   Caizergues-Ferrer M, Bachellerie JP
#=GF RL   Mol Cell Biol. 1999;19:1144-1158.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   15


AJ010799.1/3-106               UGGAAAUGAGGAUCCACAGCACUGGGCACUGAGGGGGAAACAAAUA----------UCCUUUCAAAUGAGUGACAAUGCUUU---A-GCGGGCCU-AGAAAACCCGCGCAACUGA--UCCA
AABY01000226.1/9021-8920       UGGAGAUGAGGAUCCACAGCACUGGGCACUGAGGGGGACAAUUG------------UCCUUU-AAAUGAGUGACAAUGCUUUU--A-GCGGGCCU-AGAAAACCCGCGCAACUGA--UCCA
AACA01000204.1/7787-7681       UGGAGAUGAGGAUCCACAGCACUGGGCACUGAGAAGGAACAAAAUGUA--------UCCUAUCGAAUGAGUGAUAAUGCUUU---AAGUGGGCCU-AGAAAACCCACGUUACUGA--UCCA
AABZ01000605.1/944-1046        UGGAGAUGAGGAUACACAGCACUGGGCACUGAGAAUGAACUUUA------------UUCUUUCGAAUGAGUGACAAUGCUUU---AAGCGGGCCU-AGAAAACCCGCGCUACUGA--UCCA
AACF01000013.1/100770-100670   UGAAGAUGAGGAUCCAUAGCACUGGGCACUGAGUAUAAUAAU--------------UUUUAUUGAAUGAGUGACAUGCUUAC---AAGAGGGCCU-AGAAAACCCUCGCUACUGA--UUCA
AAZN01000292.1/3240-3132       UGAAGAUGAAGAGUCACAGCACUGGGCACUGAUAAAUUAAUAAAAUUUUU------UUUUGCAAAAUGAGUGACACCGCUUU---AAGUAGGCCU-AGAAAACCUACGCUACAGA--UUCA
AADM01000093.1/238202-238298   UAA--AUGACGAAGCAUAGCACUGGGCACUGAG----UCAAUAA------------AUUUUGGCUAUGAGUGACACUGCUUU---AAGUGGGCUU-AGAAACCCCACGCUACUGA--UUUU
CR382124.1/956903-957002       UUGAAAUGAGGAGUCAUAGCACUGGGCACUGAAAUAU-------------------UUAAAAAAUAUGAGUGACACCGCUUUUUAUGGUAGGCCUCAGAAACCUGCCGUGACUGA--UCAA
AACQ01000006.1/123666-123761   UGAUUAGGAUGAAUUAUCGCACUGGGCACUGAAUAUA----------------------UAUUUUAUGAGUGACAAUGCAUUUU-AGGUGGGCCUCAGAAACCCACUGUAACUGA--UUCA
AAFT01000027.1/99798-99708     UCA--AUGAGGAAUUAUUGCACUGGGCACUGAUUAAA------------------------CUUUAUGAGUGACAACGCAUUU--CGGUGGGCCUCAGAAACCCACUUUAACUGA--UUGA
AAVQ01000001.1/1458070-1458158 UUU--AUGAAGAAUUAUUGCACUGGGCACUGAAUAAU--------------------------UUAUGAGUGACAACGCAUUU--CGGUGGGCCUCAGAAACCCACCUUAACUGA--UCAA
AACE03000004.1/1106202-1106301 UUCAAAUGACGAGCCACAGCACUGGGCACUGAGUAUUAA-----------------UACAAGUACAUGAGUGACACUGCUUU---UAGUGGGCCU-AGAAAACCCACAUAACUGAUUUUAA
CR380959.2/771032-770918       UGGAUAUGACGAUUCACAGCACUGGGCACUGAAUUUUAAUUUCCACAAAUGGAAUUAUUUUGCAUAUGAGUGACAAUGCUUU---UAGUAGGCCU-AGAAAACCUACGCAACUGA--UCCG
AE016815.5/489532-489619       CGGAAAUGACGAGGUACAGCACUGGGCACUGAA----------------------------CGGCAUGAGUGACAAUGCUUA---UGGCGGGCCUCAGAAACCCGCCGUGGCCGA--UCCG
AAFN02000003.1/319237-319143   UGAAUAGGAUGAAUUAUUGCACUGGGCACUGAU-----------------------UUCAAAUACCUGAGUGACAAUGCAUUUU-AGGUGGGCCUCAGAAACCCACCGUAACUGA--UUCA
#=GC SS_cons                   <<<<______________________________________..............__________________________...__________.___________________..>>>>
#=GC RF                        uggaaAUGAgGAuucAuAGCACUGGGCACUGAauauuaaauu..............uuuuauuauAUGAGUGACAauGCUUU...aaGuGGGCCU.AGAAAaCCuaCGuaACUGA..ucca
//
# STOCKHOLM 1.0

#=GF AC   RF01210
#=GF ID   snoU13
#=GF DE   Small nucleolar RNA U13
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   46.00
#=GF TC   46.00
#=GF NC   45.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00081
#=GF DR   snoRNABase; U13;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   1748306
#=GF RT   Three pseudogenes for human U13 snRNA belong to class III.
#=GF RA   Baserga SJ, Yang XD, Steitz JA
#=GF RL   Gene. 1991;107:347-348.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   34


X58062.1/52-155              AUCCUUUUGUAGUUCAU-GAGU-GUGAUGAUUGUG-UGUUCAUACGCU-UGUGUGAGAUGUGCCACCCU-U--GAACCUUGUUACG-ACAUUGGCACAUUA-CCCG-UCUGAUC
AANU01284163.1/3535-3432     AUCCUUUUGUGGUUCAU-GAGU-GUGAUGAUUGGG-UGUUCACACGUU-UGUGUGAGAUGUGUCACCCU-A--CAACCUUGUUACG-ACGUCGGCACAUUC-CCCA-UCUGACC
AANG01408182.1/948-1051      AUCCUUUUGUAGUUCAU-AAGC-GUGAUGAUUGGG-UGUUCACGCCGU-UGUGUGACAUGUGCCACCCU-U--AAACCUUGUUACG-ACGCUGGCACAUUA-CCCG-UCUGACG
AC097004.3/70903-71006       AUCCUUUUGUAGUUCAU-GAGC-GCGAUGAUUGGG-UAUUCAUGUGCA-UAUGUGAGAUGUGCCACCUC-U--GAACCUUGUUACA-ACCUUGGCACAUUA-CCCA-UCUGACC
ABDC01170469.1/6451-6554     AUCCUUUUGUAGUUCAU-AAGC-GUGAUGAUUGGG-UUUUCACGCGCA-UGCGUGAGAUGUGCCUCCCU-C--AAACCUUGUUACG-ACGUCGGCACAUUA-CCCG-UCUGACG
AANN01269190.1/335-232       AUCCUUUUGUAGUUCAU-AAGU-GUGAUGAUUGGG-UUGUCAUGCGAC-UGCGUGAGGUGUGCCACCCA-U--AAACCUUGUUACG-ACGUCGGCACAUUA-CCCG-UCUGACA
AAHX01367010.1/743-640       AUCCUUUUGUAGUUCGU-AAGC-AUGAUGAUUGGG-UGUUCACGUGUA-UGUGUGAGAUGUGCCACCCU-U--GAACCUUGUCAAG-ACAUCGGCACAUUA-CCCA-UCUGAUA
ABEF01050803.1/757-653       AUCCUCUUGUAGUUCAU-GAGC-GUGAUGAUUGAG-UAUUCAUGUGCA-UGUGUGAGAUGUGCCACUGUCU--GAACCUUGUUACA-ACCUUGGCACAUUA-CCUG-UCUGACC
AAYZ01100208.1/606-709       AUCCUUUUGUGGUUCAU-AAGC-GUGAUGACUGGG-UUUGCACACGGC-UGUGUGACAUGUGCCUCCCU-C--CAACCUUGUUACG-ACGUCGGCACAUCA-CCCU-UCUGACU
AAIY01193208.1/4278-4175     AUCCUUUUCUGGUUCAU-AAGC-AUGAUGAUUGGG-UUUUCAUGCAUU-UGUGUGACAUGUGCCUCCCA-U--AAACCUUGUUAUG-ACCUCGGCACAUUA-CCUA-UCUGACA
AC188098.1/141934-142037     AUCCUUUUGUAGUUUAU-AAGC-AUAAUGGUUGGG-UUUUUAUAUGCA-UGUGUGAAAUGUGCUUCCCU-C--AAACCUUGUUACA-AUGUCAGCACAUUA-CCCA-CCUGACA
AAFC03001691.1/8729-8625     AUCCUUUUGUAGUUCAU-GAGC-AUGAUGAUUGGG-UGUUCAUGCUGC-UGCGUGACAUGUGCCUCCCUGC--AAACCUUGUUACG-ACACCGGCACGUUA-CCCG-UCUGACG
AC109163.16/134442-134339    AUCCUUUCUGGUUCAUA-AAGC-GUGAUGAUUGGG-UGUUCACGCCAU-UGCGUGACAUGUGCCGCCCA-U--AAACCUUGUUACG-ACGUGGGCACAUUA-CCCG-UCUGACA
AAQQ01433553.1/582-482       AUCCUU---UAAUUCAC-AAGC-AUGAUGAUUGGG-UGUUCACACUAU-GGUGUGAGAUGUGCCUCCUC-U--UAACCUUGUUACG-ACAUUGGCACAUUA-CCUG-UCUGACA
AALT01503801.1/6075-6178     AUCCUUUUCUGGUUCAU-AAGC-AUGAUGAUUGGG-CUUUCACACUUU-UGUGUGAUAUUUGCCUCCCU-U--AAAUCUUGUUACA-CAUUUGGCACAUUA-CCCU-UCUGACA
AAPY01046963.1/1015-1116     AUCCUUUUGUGCUUCAU-AAAC-AUGAUGACUGAG-AGUUCA--CGCC-AUUGUGAGAUGUGCCUCCCU-U--GAGCCUUGUUACG-ACGUUGGCACAGUA-CCCA-UCUGACA
AC166008.4/67799-67695       AUCCUUUUGCAGUUCAU-AAUU-GUGAUAACUGGG-AGUUCAUGCGCA-UGUGUGAGAUGUGCCUCCCU-C--AAACUUUGUUUCG-ACGUCAGCACAUUA-CCUGAUGUGAAA
AAFR03003990.1/101440-101338 AUCCUUCUG--GUUCAU-ACAA-GUGAUGACUGGG-UUUUCACGCGUU-UGUGUGAGAUGUGCCGCCCU-UACUUUUCUUGUUACG--CAUAGGUACAUUA-CCCG-UCUGAUU
AC198097.2/98038-98133       ACCCA--------GCCU-AAGC-AUGAUAAUUGAG-UGUUCAGGUGCA-CGUGUGAGAUGUGGCACCAU-G--GAACCCUGGUAUG-ACGUCGGUACGUGA-CCCG-UCUGACA
AAPN01297596.1/744-648       AUCCUUUCG--GUUCAU-UAAAAAUGAUGAUUGGG-UUGCCACGCGCC-UGCGUGAGAUGUGCCGCCCU-U-------UUGUUACG--CAUGCGCACAUUA-CCCU-UCUGAUC
CR550308.6/107309-107404     AUCCUUGAG--GUUCAUACAAC-AUGAUGAUUGGU-CUAUCACGACUG-UUCGUGAAAUGUGCAGCCCU---------UUGUUACG-AC-GUGGCACAUUG-ACCG-UCUGAUU
AC123543.3/156568-156464     AUCUUUUUGUAGUUUGU-AAGC-GUGAUGACUGGG-AGCUCAUGCGCA-UGCAUGAGAUGUGCCUCCCU-C--AAACUUUGUUUUG-ACAUCAUCACAUUA-CCUGAUGCGAAA
AF291825.1/1-89              A----------CUUUAU-AAGC-GUGAUGAUUGGG-UGUUC------C-CGUGUGAGAUGCGCCACCCU-C--GAACCUUGUUACGGACGUCAGCACAUUG-CGCG-UCUGACA
AANH01013020.1/3888-3987     AUCUUUCUG--GUUCAU-GAGU-AUGAUGAUUGGUGCGUUCACGGACCCUCCGUGAAAGGCGCAGCCCU-C----UCCUUGUUACG---CUCUGCGCCUCA-GCCC-UCUGACC
BAAE01258468.1/762-664       AUCCUU---CGGUUCAU-CAAA-AUGAUGAUUGGUGCGUUCACGGUCC-UUCGUGAAAGGUGCUGCCUU-C-----ACUUGUUACG--CUUAAGCGCCUCAGCCCU-UCUGAUC
AAKN02043638.1/81388-81489   ---AUCCUCAGGUUCAU-AAGC-GUGAUGAUUGGG-UGUUCAUGCUCCAUGCAUGACAUGUGCCUCCUU-U--GAACCUUGUUACG-ACCUUGGCACAUUA-CCCA-UCUGACG
AAGV020977746.1/713-610      AUCCUUUUGUGGUUCAU-AAGU-AUGAUGAAUGGG-UGUUCACGCGCU-UGUGUGAGAUGUGCCUCCCU-C--CAACCUUGUUACG-ACGUGGGCACAUUA-CCCG-UCUGACA
AAWR02024066.1/307117-307014 AUCCUUUUGUAGUUCAU-GAGC-GUGAUGAUUGGG-UGUUCACGCGGC-UGUGUGACAUGUGCCACCCA-C--AAACCUUGUUACG-ACGUGGGCACAUUA-CCCA-UCUGACG
AAPE02026601.1/17288-17185   AUCCUUUUGUAGUUCAU-AAGC-GUGAUGAUUGGG-UAUUCACGCUGC-UGUGUGAGAUGUGCCUCCCA-C--GAACCUUGUAACA-CCUUUGGCACAUUA-CCUG-UCUGACG
AAQR03101782.1/4678-4781     AUCCUUUUGUAGUUCAU-AAGC-GUGAUGAUUGGG-UUUUCAUGCGCA-UGCGUGAGAUGCGCCUCCCA-C--AAAUCUUGUUACG-ACGUCGGCACAUUA-CCCU-UCUGACA
AADA01186519.1/6096-6199     AUCCUUUUGUAGUUCAU-GAGC-GUGAUGAUUGGG-UGUUCAUACGGU-UGUAUGAGAUGUGCCACCCU-U--GAACCUUGUUACG-ACGUGGGCACAUUA-CCCG-UCUGAUC
AAEX03016441.1/933670-933773 AUCCUUUUGUAGUUCAU-GAGC-GUGAUGAUUGGG-GGCUCAUGCCGU-UGUGUGACAUGUGCCUCCCU-G--AAACCUUGUUAUG-ACCAUGGCACAUUA-CCCA-UCUGACA
AAGU03045296.1/76017-75914   AUCCUUUUUCGGUUCAU-AAGC-GUGAUGAUUGGG-UUUUCAUACGUC-UGUGUGAUAUGUGCCUCCCC-C--AAACCUUGUUACG-ACGUCGGCACAUUA-CCCG-UCUGACG
FJ915995.1/2-105             AUCCUUUUGUGGUUCAU-GAGC-AUGAUGAUUGGG-UGUUCACACGUU-UGUGUGAGAUGUGCCACCCU-A--CAACCUUGUUACG-ACGUCGGCACAUUC-CCCA-UCUGACC
#=GC SS_cons                 :::::::::::::::::.::::.::::::::::::.::::::::::::.::::::::::::::::::::.:..:::::::::::::.::::::::::::::.::::.:::::::
#=GC RF                      AUCCUUUUGugGUUCaU.aAGc.gUGAUGAUUGGG.ugUUCAcGcgcu.UGuGUGAgAUGUGCCuCCCU.u..gAACCUUGUUACG.ACgUcGGCACaUUA.CCCg.UCUGAca
//
# STOCKHOLM 1.0

#=GF AC   RF01211
#=GF ID   SNORD124
#=GF DE   Small nucleolar RNA SNORD124
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   41.90
#=GF NC   38.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; SNORD124;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16990247
#=GF RT   snoSeeker: an advanced computational package for screening of guide and
#=GF RT   orphan snoRNA genes in the human genome.
#=GF RA   Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH
#=GF RL   Nucleic Acids Res. 2006;34:5112-5123.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   18


AAFC03094834.1/33076-32973   UGGUUCCAAGGAAGGGAUGAUGUUCCAAUUGAAACUC-AAGAAAAGGAUUCUGAG-----CCUCAGAGCUUUGAAGGAGCCACU-CGUUCCCUGACCUUCCUUGAAGUAGU
AAFR03029930.1/44054-43950   UAAUUUCAAGGGAGGAAUGAUGUUCAAAGUGAAGCCCUAAGAAAAGGAACCUGAG-----UCUCAGGUCUGUGAUGGAGUUACU-UUCUUCCUGACCUUCCUUGACCUGAA
AAHX01065923.1/31199-31096   GGAUUUCAAGGAAGGGAUGAUGUUUUUACUAAGACCC-AAGAAAAGGAUUCUGAG-----CCUCAGAGCUUUGAAGGAACCACU-UGGUCCCUGACCUUCCUUCAGAAAGU
AAHY01095698.1/223417-223314 GGAUUCCAAGGAAGGGAUGAUGUUCUUAAUAAGACCC-AAGAAAAGGAUUCUGAG-----CCUCAGAGCUUUGAAGGAACCGCU-UGCUCCCUGACCUUCCUUCAGGAAAU
AAIY01452890.1/1686-1583     GGGCUCCAAGGAAGGAAUGAUGUUCUGAUUGGGUUUC-AAGAAAAGGAUCCUGAG-----CCUCAGAGCUCUGAAAGAGCCACU-UAAUCCCUGACCUUCCUGGAGGCAGA
AAPY01741688.1/713-816       UGAGCCCAAGGAAGGGAUGAUGUUCCAAAUGAGACCC-AAGAAAAGGAUUCUGAG-----CCUCAGAGCUUUGAAAUAGCUACU-UGGUCCCUGACCUUCCUUGAGGCAAA
AAQQ01352631.1/541-644       GGAUUCCAAGGAAGGGAUGAUGUUCUAAUUGAGACUC-AAGAAAAGGAUUCUGAG-----CCUCAGAGCUUUGAAGGAACCAUG-UGGUCCCUGACCUUCCUUAAGACAAA
AAYZ01120778.1/6607-6509     UGACCCCAAGGAAGGAAUGAUGUUCC-CCUGAGACUC-AAGAAAAGGAUUCUGAG-----CCUUGG--CUUUGAGGGUGCCACU-UGAUCCCUGACCUUCCUG--GGCAAA
ABDC01229624.1/3267-3164     UGAUUCUAAGGAAGGGAUGAUGUUUCAAAUGAGACUC-AAGAAAAGGAUUCUGAG-----CCUUAGGGCUUUGAAGGAGCCACU-UGGUCCCUGACCUUCCUGGAGGCAAG
AANG01163107.1/2118-2015     UGAUUCUAAGGAAGGGAUGAUGUUCCAAUCGACACUC-AAGAAAAGGAUUCUGAG-----CCUCAGAGCUUUGAAGAAGCCACU-UGAUCACUGACCUUCCUUGAGGCAAA
AAVX01272865.1/749-641       ACAGUGAGAGGAAGGAAUGAUGUGCU-AAAAAUUCCC-AAGAAAAGGACUCUGAUUGAAUCUGCUUCACUCUGAUUGAACUAUGGUUAUUUCUGACCUUCCUCCAGCGUGG
AAWR02012686.1/22839-22942   UGAUCCCAAGGAAGGGAUGAUGUCCCAGUUGAGACUC-AAGAAAAGGAUUCUGAG-----CCUCAGAGCUUUGAAGGAGCCGCU-UGGUCCCUGACCUUCCUUGAGGCAAA
AAKN02042390.1/48826-48725   AGGACCCCAGGAAGGGAUGAUGUUCUACUUAAGACUC-AAGAAAAGGAUUCUGAG-----CCUCGG-GCUUUGAAGGAGCCCUC-UGGUCCCUGACCUUCCUCA-CCCAAG
AAGV020566448.1/482-584      UGAUUCCAAGGAAGGGGUGAUGUUCCAGUUCAGUCCC-AAGAAAAGGAUCCUGAG-----CCUUAGGGCUCUGAAGGAGCCACU-UGGUC-CUGACCUUCCUUUAUACAAA
AAPE02041565.1/1006-905      UGAAUCCAAGGAAGGAAUGAUGUUCCAAUUGAGACUC-AAGAAAAGGAUUCUGAG-----CCUCAGAGCUUUGAAGGAGACACU-GG--CUCUGACCUUCCCUGAGAUGAU
AAEX03006469.1/16909-17012   GGAUUCCAAGGAAGGGAUGAUGUUCCAAUUGAGACUC-AAGAAAAGGAUUCUGAG-----CCUCAGAGCUUUGAAGGAGCCACU-UGAUCACUGACCUUCCUUGAGGCAAA
AAGU03055077.1/77109-77006   UUAUUCUAAGGAAGGAAUGAUGUUUCAAUUGAGUCUC-AAGAAAAGGAUCCUGAG-----CCUUAGAGCUUUGAAAGAGCCACU-UGGUCCCUGACCUUCCUUGAGACAAA
AC102799.9/53508-53611       UGGUCUCAAGGAAGGGAUGAUGUUCCAGUUGAGACUC-AAGAAAAGGAUUCUGAG-----CCUCAGAGCUUUGAAGGAGCCACU-UGGUCCCUGACCUUCCUAGAGGCAAA
#=GC SS_cons                 ::::::::<<<<<<<______________________._________________.....________________________.__________>>>>>>>:::::::::
#=GC RF                      ugAuUccAAGGAAGGaAUGAUGUUCuAAuUgAgaCuC.AAGAAAAGGAUUCUGAG.....CCUCaGagCUuUGAagGAgCcAcu.UgaUccCUGACCUUCCUugAggcaAa
//
# STOCKHOLM 1.0

#=GF AC   RF01212
#=GF ID   sn2524
#=GF DE   Small nucleolar RNA sn2524
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   44.70
#=GF NC   42.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.05 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Caenorhabditis_elegans300032;
#=GF RN   [1]
#=GF RM   12372436
#=GF RT   Location of 2(')-O-methyl nucleotides in 26S rRNA and methylation guide
#=GF RT   snoRNAs in Caenorhabditis elegans.
#=GF RA   Higa S, Maeda N, Kenmochi N, Tanaka T
#=GF RL   Biochem Biophys Res Commun. 2002;297:1344-1349.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


CAAC02000445.1/763027-763135 UCUUGAGAAGACUCACGUAAAACUGGAAUCCAGAAUUUUGUCUUUUUGAUCUUUGUUGAUUUUUACAAGGAACGCAUCCACAAAGUCGUCGCCUUCUUCGUUAACCACA
FO080121.1/14749-14854       UAUUGAGAGAACAUACGUAAAACUAGAGUC---AAUGCCUUCUUUCUUGUCCUUCUCCAUUUUUACAAUAAAUGCGUCUACAAAAUCGUCGCCUUCUUCACUGAGAGUA
#=GC SS_cons                 <<<.......................................................................................................>>>
#=GC RF                      UauUGAGAaaACauACGUAAAACUaGAaUCcAGAAUguugUCUUUuUgaUCuUUgUugAUUUUUACAAgaAAuGCaUCuACAAAaUCGUCGCCUUCUUCauUaAgaauA
//
# STOCKHOLM 1.0

#=GF AC   RF01213
#=GF ID   snoR103
#=GF DE   Small nucleolar RNA snoR103
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   51.20
#=GF NC   44.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300008;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF RN   [2]
#=GF RM   11266566
#=GF RT   Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana.
#=GF RA   Qu LH, Meng Q, Zhou H, Chen YQ
#=GF RL   Nucleic Acids Res. 2001;29:1623-1630.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   11


AJ505678.1/1-106           CGCAAGUAUGUGUUUC-UGCUGUAAAUAUGGACGUAUAAUGAUA--UGUAGGCU---UUUAGGUGGGCAUUUUGUUAGCU-GCUAUUUGCUCAUAAAGGA-CCUACUGACAUUU
AASG02028280.1/167-271     ACUUAGUAUGUGUACC-UGCUGUAAAUAUGGACCAAUAGCAAUA--UGUAGGC----UUUAGGUGGGUAUCUAAUGAGUU-UCAGCUUGCCCAUAAAGGA-CCUACUAAUAGUU
AARH01007526.1/26843-26947 ACUUGAUAUGUGUACC-UGCUGUAAAUAUGGACGAACAGCAAUA--UGUAGGC----UUUAGGUGGGUGUCUAUUGAGUU-UCAGAUUGCCCAUAAAGGA-CCUACUCACAUUC
AM469124.2/20325-20429     CUUCAGUACGUGUACU-UGCUGUAAAUAUGGACGUACAUUAAUA--UGCGGGC----UUUAGGUGGGCAUGCGAUGAGUA-UAAGGGUGCCCAUAAAGGA-CCUGCAGACAUAG
AP004509.1/56301-56405     CUUAGUUAUGUGUACC-UGCUGUAAAUAUGGACAGAAAACAACA--UGUGGGC----UUUAGGUGGG-AUUCUUUAAGUUAUAAGAUUACCCAUAAAGAA-CCUACAUACAUUU
CT990559.2/48366-48470     UUAAGAGAUGUGUUUC-UGCUGUAAAUAUGGCUGGAGAACAAUU--GGUAGGC----UUUAGCUGGGCAGCCAAUGAGUA-UUGGAUUGCCCAUAAAGAU-UCUACUAACAUUG
AAAA02011738.1/164-269     UGCAUGAGUUGCCUCC-UACUGUAAAUAUGGACAAAGAGUAAAGU-UGAUGGAA---UUUAGGUGGGCAUUAUGCUAGUU-GUAGA-UGCUCAUAAAGGA-CCAUCAUACAUGC
CR855028.1/62851-62744     CUGCAUUAGUUGCAUCUUGCUGUAAAUAUGGGCAAAUACUAAAGU-UGAUGGGA---AGUAAGUGAGUGUUCUUCAAGUC-CAGAAUC-CUCACAAAAGAACUGUCGCAUAGUC
AC150446.8/83046-82943     CUUAAGUAUGUGUACU-UGCUGUAAAUAUGGACAGAGAGCAAUU--CGUGGGC----UUUAGGUGGG-AUUGACUCAGUU-UCAAAUUACUCAUAAAGAU-CCCACGCAUAUUC
AC189375.2/28568-28457     UUAAGCAAUGCGACCU-UGCUGUAAAUAUGGACGAACAUUGAUACUUGUAGGCUUUUUUUAGGUGGGCACUCUUUAAGUU-CUUUGAUGCUCAUAAAGGACCCUACGUAUAUGA
AK288810.1/1847-1741       UUGCGUGAGUUGCACCUUGUUGUAAAUAUGGACAGAAAGUAAGGU-AGAUGGAA---UUUAGAUGAGUAUUAUGUGAGUC-ACUGG-UGCUCAUAAAGGA-CCAUCGCUCAUUU
#=GC SS_cons               ::::::::::::::::.:::::::::::::::::::::::::::..:<<<<<--...<<<--<<<<<<<___________.______>>>>>>>-->>>-.>>>>>::::::::
#=GC RF                    uuuaauuAugUGuacc.UGCUGUAAAUAUGGACaaAuAauAAua..uGugGGca...uuUAGgUGgGcaUucuuUaAGUu.uuagauugCcCAuAAAgaA.CCcaCuuAcAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01214
#=GF ID   snR51
#=GF DE   Small nucleolar RNA snR51
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   44.30
#=GF NC   43.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00058
#=GF DR   snornadb; snR51;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300057;
#=GF RN   [1]
#=GF RM   10024243
#=GF RT   A computational screen for methylation guide snoRNAs in yeast.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Science. 1999;283:1168-1171.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   17


AF064263.1/1-107             UAUUAUGAUGAUUUUUUU--AUAUUCACACUGUACUAGAUUGGUCUCUUUAACGAAGGGGCUAAUUGAUGACUACAAAAUAAAAAAUAACUGAUUUAAUGACUCUGAAA
AACI02000085.1/16775-16669   UACUAUGAUGAUUUUUUU--AUAUUCACACUGUACUAGAUUAGUCUCUUUAACGAAGGGACCAAUUGAUGACUACAACAUAAAAAAUAACUGAUUUAAUGACUCUGAGA
AACG02000032.1/77804-77909   ---UAUGAUGAUUUUUUUUUAUAUUCACACUGUACUAGAUUGGUCUCUUUUACGAAGGGACCAGUUGAUGACUACAAAAUAAAAAAUAACUGAUUUAAUGACUCUGAGA
AAZN01000219.1/32906-32813   UAUCAUGAUGAUUUUUU---AUAUUCACACUGUACUAGAUAG-----UUUAAUUA------CUAUUAAUGACUACACUAAACAAAAA-ACUGAUUUAAUGACUCUGAUA
AAPO01000004.1/60171-60081   UUCUAUGAUGAUUUUUUACAAUAUUCACACUGUACUAGAAG------UUUUACUU----------CAGUGACUACACCAUAAAAAA--ACUGAUUUAAUGACUCUGAUU
AAFT01000028.1/118550-118461 UUGCAUGAUGAUUCUUC---AUAUUCACACUGUACUAGAAG-----UUUCUGCUU----------CGGUGACUACAAAAACACAAAA-ACUGAUUUAAUGACUCUGAUA
AACF01000016.1/90301-90395   UUUUGUGAUGAUUUUUGACUAUAUUCACACUGUACUAGG------AAUUUAAGUA-------UUUCGAUGAAUACAUCAACCAAAAA-ACUGAUUUAAUGACUCUGAUA
AACQ01000010.1/38808-38899   UUUGGUGAUGAUUUUUUUA-AUAUUCACACUGUACGAGAGG-----UUUCUGCCU----------CCCUGACUACAUCAAUAAAAAU-ACUGAUUUAAUGACUCUGAAA
AAFM01000056.1/195642-195728 UUCGAUGAUGAUUUUUU---AUAUUCACACUGUACGAGGGGG---A----GACUU----------CAAUGACUACAAAAAC--AAAAUACUGAUUUAAUGACUCUGAGG
CR382123.1/1365047-1365148   UUUCGUGAUGAUUUUCUU--AUAUUCACACUGUCUAAGAGUGC--AGUUUAAGUAC--UGUAUCUCAAUGAACACACAAACGAAAAA-ACUGAUUUAAUGACUCUGAUU
AAVQ01000002.1/773358-773446 UUCUAUGAUGAUCCAAUUUUAUAUUCACACUGUACGAGA-----------AGCUAG-----CCUUCACUGACUACGACCA---AAAU-ACUGAUUUAAUGACUCUGAUG
AADM01000009.1/44435-44532   CUGAAUGAUGAUUCCAU---AUAUUCACACUGUGUGAUGCCU---AGUUUAGUUAC---UACGGU-AAGGAUCACGACAAACAAAAA-ACUGAUUUAAUGACUCUGAUG
CR382137.2/1146776-1146868   UUUUAUGAUGAUUCCUUUU-AUAUUCACACUGUACGAGGAGU---UUUUCGGCUU----------CAUUGACUACAAACAU--AAAAUACUGAUUUAAUGACUCUGAUG
CR380957.2/800130-800029     UUCAGUGAUGAUUCUAUUCUAUAUUCACACUGUGUGAGGCCU---AGUUUAAUUAC---UAUGGUCAAUGGUCACAAACAAGAAAAA-ACUGAUUUAAUGACUCUGAGU
AACE03000007.1/762993-762893 UACUGUGAUGAUUUUCU---AUAUUCACACUAUCUAAGAAUGC--AGUUUAACUAC--UGUACUUCAAUGAACCUAAAAACGAAAAA-ACUGAUUUAAUGACUCUGAUC
AE016815.5/578738-578837     UGCUGUGAUGAUUUUUU---UUAUUCACACUGUCUAAGGGUGC--AGUUUAACUAC--UGCACAUCGAUGAACACACUUACAAAAA--ACUGAUUUAAUGACUCUGAUC
AAFN02000068.1/97293-97383   UUUUAUGAUGAUUUUUUUA-AUAUUCACACUGUACGAGAAG-----UUUCUGCUU----------CACUGACUACAUAAACAAAAA--ACUGAUUUAAUGACUCUGAAA
#=GC SS_cons                 ::::::::::::::::::..:::::::::::::::::<<---...--<______>-...----->>:::::::::::::::::::::.:::::::::::::::::::::
#=GC RF                      UuuuaUGAUGAUUUUuUU..AUAUUCACACUGUacuAGaaug...auuUUaacUaa...auuuauCaaUGAcUACAaaAAaaAAAAa.ACUGAUUUAAUGACUCUGAua
//
# STOCKHOLM 1.0

#=GF AC   RF01215
#=GF ID   snoR97
#=GF DE   Small nucleolar RNA snoR97
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   40.40
#=GF NC   39.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300138;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AJ505674.1/1-108           C--UUGUAUCUUAGUGCUUGUAGUCUGAAAAAACUCAUAAAUUCUCAGUGUUC-UCAUCAGCUUCCGUCUCC----UUAACC-AUGAGACUUGAGUUAAACAAGAUCACUACAUUA
AAAA02021081.1/8772-8665   UAAGUUUCU-GUUUUGUGUGUAGGCUGAAAAAGCUCGGAGAUU-G-UGUGUUG-ACAUCAGCUUC-GUCUCU--UUAUGUCU-GUGAGAUGGGAGUUAAAUGACAGCACGAAAUUC
AARH01005974.1/1135-1242   C--CUCUGUAAAUGGGUUUAGAGUCUGAAAAA-CUCAGACAGU-G-UGUGUUG-UCAUCAGCUUC-UUCUCCCGCAUAACCC-ACGAGAUUGGAGUUAAAUAACAGCACUACAUCC
AASG02001178.1/42223-42328 C--UUUCCU-CAUGGGUUUAGGGUCUGAAAGA-CUCAGACAGU-U-GGUGUUG-UCAUCAGCUUC-AUCUCU-AUAAUACCC-ACGAGAUAGGAGUUAAAUAACAGCACUAAAUUU
AP009482.1/31951-32059     A--UGUAAUUAGUGGGUUUAGGGUCUGAAAAA-CUCAGAAAAU-U-AGUGCUGUUUAUCAGCUUC-UUCUCUUGAAUAAUUCAACGAGA-UGGAGUUAAAUCAUGGCACUAAAUGU
AP003723.3/35951-36055     --AGUUUCU-GAUUUGCCGGGAGGCUGAAAAAGCUCGGAGAUU-G-UGUGUUG-ACAUCAGCUUC-GUCUCU---AUUAACC-GUGGGAUGGGAGUUAAAUGACAGCACGAAAUUC
FN595759.1/223869-223764   C--UUGCAU-GGUGGGUAUGGAGGCUGAAAAA-CUCAGAAAGU-UAGGUGUUG-UAAUCAGCUUC-UUCUCCCCUUUA--CC-ACGAGACUGGAGUUAAAUGCCAUCACUACAUUA
#=GC SS_cons               :..::::::.::::::::::::::::::::::.::::::::::.:.<<<<<<<.-----<<<<<<.-<<<<_._________.__>>>>-->>>>>>------>>>>>>>::::::
#=GC RF                    c..uUuuaU.aaUggGUuUggAGuCUGAAAAA.CUCAGAaAuU.u.gGUGcug.ucAUCAgCUuc.uUCuCu.auauuAuCC.AuGaGAuuggAGuUAAAUaAcagCACcAaAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01216
#=GF ID   snR87
#=GF DE   Small nucleolar RNA snR87
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.70
#=GF NC   36.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00046
#=GF DR   snornadb; snR87;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300056;
#=GF RN   [1]
#=GF RM   16484372
#=GF RT   Accumulation of unstable promoter-associated transcripts upon loss of the
#=GF RT   nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae.
#=GF RA   Davis CA, Ares M Jr
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3262-3267.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


Z28007.1/2587-2479       GUAACUGAAUGAUGAUAUAAUUUGCGAUCUAGGGCUAAUCACUUGGAACACCGCCAUGUUCUAUAUGGGUGAUUAGCGAAGUGCGAAAAAUUUUUUAUCUGAUAUUUUC
AACH01002005.1/735-843   GUAAUUGAAUGAUGAUAUAAUUUGCGAUCUAGGGCUAAUCAUUUGGAACACCGCCAUGUUCUAUAUGGGUGUUUAGCGGAGUGCGAAAAGUUUUUUAUCUGACGUUUUU
AACA01000080.1/6450-6342 GUAAUUAAAUGAUGAUAUAAUUUGCGAUCUAGGGCUAAUCACUUGGAACACCGCCAUGUUCUUUAUGAGUGUUUAGCGAAAUGCGAAAAUUUUUUUAUCUGACAUUACU
AACI02000338.1/2769-2661 UCUAAUGAAUGAUGAUAUAAUUUGCGAUCUAGGGCUAAUCACUUUGAACACCGCCAUGUUCUAUAUGGGUGCUUAGCGAAAUGCGAAAAGUUUUUUAUCUGACGAUUUC
#=GC SS_cons             ::<<_____________________________________________________________________________________________________>>::
#=GC RF                  guaauUgAAUGAUGAUAUAAUUUGCGAUCUAGGGCUAAUCAcUUgGAACACCGCCAUGUUCUaUAUGgGUGuUUAGCGAAaUGCGAAAAgUUUUUUAUCUGAcauuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01218
#=GF ID   snR41
#=GF DE   Small nucleolar RNA snR41
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   68.80
#=GF NC   40.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00068
#=GF DR   snornadb; snR41;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   7667877
#=GF RT   Antisense snoRNAs: a family of nucleolar RNAs with long complementarities
#=GF RT   to rRNA.
#=GF RA   Bachellerie JP, Michot B, Nicoloso M, Balakin A, Ni J, Fournier MJ
#=GF RL   Trends Biochem Sci. 1995;20:261-264.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   18


U26016.1/1-110               UCCCCUAUGAUUAAAAAUUAUUAAUCAUAU-ACCAAUUGUUCCGACUGAAUAGU-GGUU--UAACUACAUGUCGACAAC----CCUUUU---UCGUUAAGUUUCAGCCUUGUAUGAGGGGU
AACI02000085.1/17223-17114   UCUCCUAUGAUUAAAAUUUUUUAAUCAUAU-ACCAAUUGUUCCGACUGAAUAGU-GAUU--UAACUAUAUGUCGACAAC----CCUUUU---UCGUUAAGUUUCAGCCUUGUAUGAGGAGA
AACH01001819.1/54-160        ACCUCUAUGAUUAAAAUCUAUUAU---UAU-ACCAAUUGUUCCGACUGAAUAGU-GGUU--UAACUAUAUGUCGACAAC----CCAUUU---UCGUUAAGUUUCAGCCUUGUAUGAGGGGU
AACF01000016.1/89825-89933   UUACCUGUGAUUAAACAUUUUCCA--AUAU-ACCAAUUGUUCCGACUGAAUAGU-GGUUA-UAACUGCAUGUCGACAAC----CUUUUU---UCGUUAAGUUUCAGCCUUGUAUGAGGUUU
AAZN01000219.1/33424-33313   ACUAAUAUGAUUAAACAUUACAUUCCAUAU-ACCAAUUGUUCCGACUGAAUAGUAGGAU--UUCCUGCAUGUCGACAACA---CCUUUU---UCGUUAAGUUUCAGCCUUGUAUGAUUUUA
AADM01000009.1/43988-44094   CCAGCAGUGAUUAUAUGCAUU------UAU-ACCAAUUGUUCCGACUGAAUAGU-GUUA--CUACUGCAUGUCGACACUUUG-CAUCUA---UCGUUAAGUUUCAGCCUUGUAUGAGCUAG
CR382123.1/1364446-1364554   UUUGCGGUGAUUAAUGUGAGAAUA----UU-ACCAGUUGUUCCGACUGAAUAGU-UGUA--UAACUACGGGUCGACAAU----CUCUUUUUAUCGUUAAGUUUCAGCCUUGUAUGAGCACC
AAPO01000004.1/60759-60664   UCGGCGAUGAUUAA--------UUGCAUUU-ACCAAUUGUUCCAACUGAAUUUU-----------CACAGGUUGACAAUAA--GCAUUA---UCGUUAAGUUUCAGCCUUGUAUGAGCCGA
AACQ01000009.1/38184-38281   UUGGCUAUGAUUA----UUUGCAUUAUAUU-ACCAAUUGUUCCAACUGAAUA------------UCCCGGGUUGACAACC---GCAUUA---UCGUUAAGUUUCAGCCUUGUCUGAGCCUU
AAFT01000028.1/118950-118858 AGGGCGAAGAUUA--------UUUGCAUUU-ACCAAUUGUUCCAACUGAAU-------------CACCGGGUUGACAAUC---GCAUUA---UCGUUAAGUUUCAGCCUUGUAUGAGCCCU
AAVQ01000002.1/772920-773014 CUGGCGGUGAUUA-------UUUGCUAUUU-ACCAAUUGUUCCAACUGAAU------------GUUCCGGGUUGACAACA---GCAUUA---UCGUUAAGUUUCAGCCUUGUAUGAGCCUU
AAFM01000056.1/195271-195363 GACUCUAUGAUUA---------UUUGCUUU-ACCAAUUGUUCCAACUGAAU------------UUUCCGGGUUGACAACA---GCAUUA---UCGUUAAGUUUCAGCCUUGUAUGAGUGUC
AACG02000032.1/77343-77451   UCCCCUAUGAUUAAACAUUUUUAAUCAUAU-ACCAAUUGUUCCGACUGAAUAGU-GGUU--UAACUAUAUGUCGACAAC-----CCUUU---UCGUUAAGUUUCAGCCUUGUAUGAGGGGC
CR380957.2/800598-800486     UUGUCAGUGAUUAUUGAUUUUUUAAACCAUUACCAAUUGUUCCGACUGAAUGGU-GUAU--U--CUAUAUGUCGACAACUAUAUCUCUA---UCGUUAAGUUUCAGCCUUGUAUGAGACAA
AACE03000007.1/763415-763304 CUGGCUAUGAUUA-UUUCUAUUUUCCAU-U-ACCAAUUGUUCCGACUGAAUAGU-UGUUAUUUACUACGGGUCGACAUCAU--AGAUUA---UCGUUAAGUUUCAGCCUUGUAUGAGCUAG
CR382137.2/1146317-1146411   UUGGCAGUGAUUA-------UUUGCUAUUU-ACCAAUUGUUCCAACUGAA------------CUAUCCGUGUUGACAACA---GCAUUA---UCGUUAAGUUUCAGCCUUGUAUGAGCCUA
AAFN02000068.1/96702-96798   UUGGCGAUGAUUA-----UUUGCAUUUUAU-ACCAAUUGUUCCAACUGAAUA------------ACCCGGGUUGACAACC---GCAUUA---UCGUUAAGUUUCAGCCUUGUAUGAGCCAC
AE016815.5/578386-578485     CUGGCAAUGAUUAACGUGAGAUCA--------CCAAUUGUUCCGACUGAAUAGU-GUUU-----CUACGUGUCGACAUU----CUCUAA---UCGUUAAGUUUCAGCCUUGUAUGAGCCUG
#=GC SS_cons                 ::<<<_________________________._______________________.____..___________________...______...________________________>>>::
#=GC RF                      uuggCuaUGAUUAaauuuuuuuuaucaUaU.ACCAAUUGUUCCgACUGAAUAGU.gguu..UaacUaCauGUcGACAAca...ccaUUa...UCGUUAAGUUUCAGCCUUGUAUGAGccuu
//
# STOCKHOLM 1.0

#=GF AC   RF01219
#=GF ID   snoR100
#=GF DE   Small nucleolar RNA snoR100
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   52.80
#=GF NC   48.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300005;
#=GF DR   snoopy; Arabidopsis_thaliana300197;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   9


AJ505677.1/1-117           GAAUGAUUGUAGCAUGGUACUGUGCACGGAAACUGAAUCAUG----GGUUUCAAAUGUCUGUGCCUGCUCUGAGUUCCUUAUUGGUUCUUUGAUUUGC-GGGCCUGAUUUGAACCCACAUUU
AF370437.1/575-689         CAAUGAAGGUAGCAUGGUAUGGUGCACGGAAAUCGAA-UUUC----AGGUCUACUUGUCUGCCCCCUCUGAUGUCCCUUGUUGC-GGCUUUGAUUUGG-GGGCCUGGUUCCGACCCACAUUU
AM468511.2/12308-12196     GAAUGAAGGAAGCAUGGUAAUGUGCACAGAGAUUGAAUUCUA----AGGUCAUCAUGUCUGCUCUCUCUGAUGCCUUUC---GG-GGCUUUGAUUUGG-GGGCCUGGAUCAGACCUACAUUU
AASG02009538.1/7602-7720   CAAUGAAGGUAGCAUGGUAAUGUGCACAGAGAUUGAAUUCUCUU-UGGGUCUACAUGUCUGCUCCCUCUGAUGCCUCUCUUGGU-GGCUUUGAUUUGG-GGGCCUGGUUCUGACCCACAUUU
AARH01001401.1/4929-4813   UGAUGAAGGAAGCAUGGUAAGGUACACGGAAAUUGAAGUUUU----GGGUCGGCAUGUCUGCUCCCUCUGAUGCCUCUCUUUGGAGGAUAUGAUUUGG-AGGCCUGGUUUAGACCCACAUUU
AACV01011996.1/14445-14335 AGAGGAAGGAAGCAUGGUAGUGUGCACGGAGAUUCACCACAA-----GGUCUGCAUGUCUGCCUGCAGUGACGCCUUCG------GGCUUUGAUCUCGCGGGCCUGGAUUUGACCCACAUUU
AY765859.1/595-489         CAAUGAAGGAAGCAUGGUAAUGUGCACAUAAAUUAAUUU-------GGGUCUCUAGGCCUGCCC-CUCUGAUGCCAUUU------GGCUUUGAUUUAG-GGGCAUGGUUUUACAACAAAACG
AAAA02004628.1/70247-70362 AGAGGAAGGAAGCAUGGUAGUGUGUACAGAGAUGGAUUGAUUUUGUUGGUCUGCAUGUCUGCCUGCGGUGAUGCCUUCG------GGCUUUGAUCUCGCGGGCCUGGAUUUGACCCACACUU
AC189332.2/59172-59288     UAAUGAAUGUAGCAUGGUACUGUACACGGAAACUAAAUCAUG----AGUUUGAAAUGUCUGUGCCCUCUCUGAGUACCUAAUCGGUUCUUUGAUUUGC-GGGCCUGGUUUAAACCCACAUUC
#=GC SS_cons               :::::::::::<<<<______>>>>-----------------....<<<<<-----<<<-<<<_____________________.>>>--->>>----.->>>>>:::::::::::::::::
#=GC RF                    uAAUGAAGGaAGCAUGGUAaUGUGCACgGAaAUUgAaUuaUu....aGGUCuacAUGUCUGccCcCucUGAuGcCuuuuuuugg.ggCUUUGAUUUgG.GGGCCuGGuUUugACCCACAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01220
#=GF ID   snoR104
#=GF DE   Small nucleolar RNA snoR104
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   41.90
#=GF NC   38.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300009;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


AJ505679.1/1-118           GGGGAGCAUCAAAGAGUUGUGAUGU-UAUCUGAUACAAUCUUCCUA---AAUAAACACUCUGCAUUUCCUGCUUGCGGAAGC-UGAGCUUUGUUCCGCGAGUCUCAUAUCUGCAAAGACACCA
AASG02000087.1/59626-59510 GGGGAGCAUCUGAAAGCUGAGAUGC-UACCUGAUAAAAUCUUCCUA---GAGAAAACUCUGUAUUUUCCUGCUUGUGGUACU-UGAGCAA-GUAUUGCGAGUCUCAAAUCUUCAGAGACAGAA
AC182669.2/108315-108430   GGGGAGCACCUAAGAGCUGAGAUGC-UACCCGAUACAACCUUCCUA---GAGAAAACUCUGUAGUUUCCUGCUUGUAGUGCU-UAAGCAA--UCCUGCAAGCCUCAAAUGUUCAGAGACAUGA
AP009295.1/65720-65603     GGGGAACAUCUACGAGGUCAGAUGU-UGCCCGAUACAAACUUCCCAC--ACUAAAACUCUAUCAUAAGAUGCUUGAGGUACU-UGAGUGA-GUUCUUCAAGCUGUUGAUCAGGAGGCACAUAA
AC120508.3/18102-17987     AGGUAGGAUUCAAAAGAGAAGAUGCCUACCUGAUACAAUCUUCCUAG--AGUAAAGUUGUCAUUUC--CUGCUUGUGGUAUUGUUAGCAA-GUCCUGCAAGUCUCAAAUGUCAAGACAGCU--
AAAA02010780.1/20651-20539 AUGCAGCAUUCAAAAGAG---AUGCCUACCCGAUACAAUCUUCCUAU--AGUAAAGUUGUUACUUC--CUGCUUGUGGUAUUGUUAGCAA-GUCCUGCAAGUCUCAAAUGACAAGACAGUG--
AC016779.5/77587-77470     AAGGAGGAUGUGAGAGUUAGCAUUCCUGCCUGAUACAAUCUUCCUAG--AUUUAAUCUGCCAUUUUGUUUGCUUGCUGAACUAUUAGACA-GUUUUGCUGGCCUUAGUGGGCAGGACAUCA--
FN595749.1/1529576-1529695 GGGGAGCAUCCUAAAGCUGAGAUGU-UACCUGAUACAAUCUUCCUACAAAAAAAACAUCUGGAUUUUCGUGCUUGUUGUUUC-UAAGCAA-GCUCUACAAGCCUCAAGUUACCAGAGACAUGA
#=GC SS_cons               <<<-<<<<<<<________>>>>>>.>->>>----------------..--------<<<----------<<<<<<<<-<<<.______>.>>->>>>>>>>----------->>>:::::::
#=GC RF                    ggGgAGcAUcuaAgAGuUgagAUgC.UACccGAUACAAUCUUCCUAu..AauAAAacucuuauuUuuccUGCUuGcgGuacu.UuAGcaa.guuCcgCaAGCCUcAaaUgucaagagAcauaA
//
# STOCKHOLM 1.0

#=GF AC   RF01221
#=GF ID   snoU6-47
#=GF DE   Small nucleolar RNA U6-47
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   54.00
#=GF TC   54.70
#=GF NC   51.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=CEL30005;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16714446
#=GF RT   Evolution of small nucleolar RNAs in nematodes.
#=GF RA   Zemann A, op de Bekke A, Kiefmann M, Brosius J, Schmitz J
#=GF RL   Nucleic Acids Res. 2006;34:2676-2685.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AAGD02011855.1/9652-9519 AAGCAAUGAAGAGUAAUUUGA-CACGAAA-------------UGGCGUCAUAUCGUUGACACUCCAAAAAAGACUGCAAAUUCCAAU---UCGUUUCGGAAUACAGUCCGUCGACGAG-AUGGGCGAUCGUCUAAUCUUCUCUCUGAGCUUU
FO080775.1/3726-3608     CAGCUAUGACGAGUUCUUG----ACGACA-------------UGACGUCA--UCACUGACAAUUAAAGAUAG---------UUCCCU---UCGUUCGGGUUGACUAUC-GUCGGAGAU-GUGGACGAGCGCCUAAUCUUCUCUCUGAGCUGU
ABEG02000242.1/3587-3450 AUGCGAUGAAGAGACUGAUGAUCACGAAAAC---------CCUGACGUCUUAUCAUUGACACCUAAAGAC--CCAUCGGAUUCCGAA---UCGUUAGGAAAACGGGGUCGUCGAUGAGUGUGGGCGAGCGACUAAUCUUCUCUCUGAGCAUU
DQ789438.1/2-142         GAGCAAUGACGAUUUUCGAUU-CACAAAACGGUUUAGCAUCAGGACACAAAGUGCUCGUCACUUUGUAACAG--------UUUCCAGUCGUCGUUUGGCAGAAACCGU-UUUGAUGAU-GUGACCGAGCGACUAAUCUUCUCUCUGAGCUCA
DQ789550.1/1-116         GAGCAAUGACGAUUCUUGU---CACGA-------------------GUCGUAUCAUCGAAGCGCAUAGUU----UUUGGCUGUCGUU---UAGAGC----UGAAAAUGUUUCGACGGC-GUGAUCGAUUGACUAAUCUUCUCUCUGAGCU--
#=GC SS_cons             <<<<_________________._______.............______________________________.._____________...____________________________.____________________________>>>>:
#=GC RF                  gaGCaAUGAcGAgUuuuguga.CACGAAA.............uGACGUcauAUcaUuGACACuuaaAgAuAG..uucggaUUuCgau...UCGUUuGGaAaaAaaauucgUCGAuGAu.GUGguCGAgCGaCUAAUCUUCUCUCUGAGCucu
//
# STOCKHOLM 1.0

#=GF AC   RF01222
#=GF ID   sn2417
#=GF DE   Small nucleolar RNA sn2417
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   111.90
#=GF NC   35.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=CEL30011;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16344563
#=GF RT   Organization of the Caenorhabditis elegans small non-coding transcriptome:
#=GF RT   genomic features, biogenesis, and expression.
#=GF RA   Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z, Wang Y, He H, Cai L, Sun H, Liu
#=GF RA   C, Li B, Bai B, Wang J, Jia D, Sun S, He H, Cui Y, Wang Y, Bu D, Chen R
#=GF RL   Genome Res. 2006;16:20-29.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948656.1/6-128           GAGGAGUUGAUGAGAACUCUAAUCCAUUCUCUGAGCGAGAAGGAUGGCCGAAGCGGGUUCGCAUUUGAGGCAUUAAGGUAGACGACAGAGUUCUUCUGGAAACUACUGCCUCGCGCUGACGUC
DQ789410.1/2-123           GAGGAGUUGAUGAGAACUCUAAUCCAUUCUCUGAGCGAGAAGGAUGGCCAAAGCGGGUUCGCAUUGAAGGC-UUAAGGUAGACGAAAGAGUUCUUCUGACGACUACUGCCUUGCGCUGAAGCC
ABEG02000948.1/42456-42335 GAGGAGUUGAUGAAAACUCUAAUCCAUUCUCUGAGCGAGAAGGAUGGCCGAAGCGGGCUCGCAUUAGAGGCAU-AAGGUAGACGACAGAGUUCUUCUGAAGACUACUGCCUCGCGCUGAAACC
#=GC SS_cons               ::<<_____________________________________________________________________________________________________________________>>
#=GC RF                    GAGGAGUUGAUGAgAACUCUAAUCCAUUCUCUGAGCGAGAAGGAUGGCCgAAGCGGGuUCGCAUUagAGGCAUUAAGGUAGACGAcAGAGUUCUUCUGaagACUACUGCCUcGCGCUGAagCC
//
# STOCKHOLM 1.0

#=GF AC   RF01223
#=GF ID   snR13
#=GF DE   Small nucleolar RNA snR13
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   47.00
#=GF TC   48.60
#=GF NC   43.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00045
#=GF DR   snornadb; snR13;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300051;
#=GF RN   [1]
#=GF RM   981937
#=GF RT   Medicosocial aspects of ankylosing spondylarthritis.
#=GF RA   Rubens-Duval A, Lubetzki D
#=GF RL   Rev Rhum Mal Osteoartic. 1976;43:7-9.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


U16692.1/354-477         AGGAAGUUUUUUCCUUUUUAUAUGAUGAAUAUGAGUGCAUUUGGCUCGAGUUGCUGUUUGGCUUUUGCCAAAUCAGUAACGGUGUGGAAAAACUCAAGCUACCUUUUUUUACUUUUAUCUGACC
AACI02000088.1/9635-9513 AGGAAGUUUUUUCCUUUUAACGUGAUGAAUAUGAGUGCAUUUGGCUCGAGUUACUGUUUGGCGUUUGCCAAAUCAGUAACGGUGUGGAAAAACUCAAGCUACCUU-UUUUACUUUUAUCUGAUC
#=GC SS_cons             :<<_______________________________________________________________________________________________________________________>>
#=GC RF                  AGgAAGUUUUUUCCUUUUuAuaUGAUGAAUAUGAGUGCAUUUGGCUCGAGUUaCUGUUUGGCuUUUGCCAAAUCAGUAACGGUGUGGAAAAACUCAAGCUACCUUUUUUUACUUUUAUCUGAcC
//
# STOCKHOLM 1.0

#=GF AC   RF01224
#=GF ID   snoR80
#=GF DE   Small nucleolar RNA snoR80
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   46.70
#=GF NC   42.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00038
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300204;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   9


AJ505652.1/1-127           ACCAAUUCUGAGGGA-UAAAAACAGUUCCUUCAGGUAUAAUGGCUUGUGA-CGCUAUAUUG-----------GUUGUG-GUA-UAUCCUGAUCUUUUUGCUUUUUUCCA-UGCCUUUUGAUCCUGGAAAUGCCUCGCACAUUA
AC189511.1/15225-15099     ACCAAUUCUGAGGGA-UAAAUACAGUUUCUUCAGGUAUAAUGGCUUGUGA-CGCAAUAGUU------------UUGUG-GUA-UAUCCUGAUCAUCUUGCUUUUUCUCAGUGCCUUUUGAUCCUGGAAAUGCCUCGCAUAUUG
CU459035.1/58207-58333     ACCAAUUCUGAAGGA-UUUA-AUUGUUCCUUUUGGUGUAAUGGCUCG-GA-CGCUAAAUUG-----------AUUGUGUG-GUGAUCCUGAUUUUUUGGUUUUACUUCAAUACCAUUUGGUCUUGGAAACGCCUCAUACAUUU
AARH01008775.1/79980-79856 ACCAAUUCUGGGGGA-UUA--UCGGUUCCUCUUGGCAUAAUGGCUCGGGUGCUAUAUCCAG-----------UUUGUG-GCC-UAUCCUGAUU--AAUGGCUGAUAUCAGUGCCAUCUAAUCCUGGAAACACCACGUACAUUU
AP006087.1/71365-71244     ACCAAUUCCGAAGGA-UGUGU-UAGUUCCUUACGGUAUAAUGGCUCG-GA-CGCUAAAUCAU----------CAUGUG-GUG-A-UCCUGAUUUAUGGGU----UUUCAAUACCAUUUGAUCUUGGAAACGCCUCAAACAUUU
AASG02005717.1/6669-6538   ACCAAUUCUGGUGGA-UAAUA--AGUUCCUCUUGGUAUAAUGGCUUGGG--UGCUAUAGUUAAAGUCU----CUUGUG-GCU-UAUCCUGAUUAAUGGCUUUUUCUGUCAUGUCAUCUAAUCCUGGAAACACCACAUACAUUU
AAAA02020787.1/8963-9097   ACCAAUUCCGGAGGA-UUAUU-CAGUUCUUCACGGUAUAAUGGCUCG-GA-CGCCAGAUGAUAUUCUUCUGAUGUGUG-UCA-UAUCCUGAUU--GUUGGCGUUCUUGGUGCCAGUCUAAUCCUGGAAACGCCACAUAUAUUC
AM467034.1/3412-3536       ACCAAUACUGGGGGUUUGAAAACAGUACCUCCAGAUGUAAUGGCACGGG--CGCUACAUCCAAA--------AUUGUG-GCC-A-UCCUGAUC-GGUGAU----UUUUAGUAUCAUUUGAUCCUGGAAACACCUCAUACAUUU
AC135559.4/53248-53117     ACCAAUUCUGGAGGA-U----ACUGUUCCUCACGGUGUAAUGGCUCG-GA-CGCUAGAUGAUAUUCUUUGA-UGUGUG-GUCAUAUCCUGAUU--GUUGGUGUUCUUGGUGCCAUUCUAAUCCUGGAAACGCCACAUAUAUUU
#=GC SS_cons               :<<<--<<-<-<<<<.__________>>>>->->>----->>>-------.-----------..........--<<-<.<<-.<--<<-<<<<-----<<___________>>----->>>>-->>-->->>>->>:::::::
#=GC RF                    ACCAAUuCUggaGGa.UuAaaAcaGUuCCuccuGgUaUAAUGGCUcGgGA.CGCUAuAuuau..........uuuGUG.Gca.uAUCCUGAUcuuuuugcuuUuuUUcaaugccaUuUgAUCCUGGAAaCgCCuCauAcAUUu
//
# STOCKHOLM 1.0

#=GF AC   RF01225
#=GF ID   ACA64
#=GF DE   Small nucleolar RNA ACA64
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; ACA64;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300765;
#=GF RN   [1]
#=GF RM   16373490
#=GF RT   A computational screen for mammalian pseudouridylation guide H/ACA RNAs.
#=GF RA   Schattner P, Barberan-Soler S, Lowe TM
#=GF RL   RNA. 2006;12:15-25.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   30


BC028232.1/151-277           GUUGGUUGAAAAUCGCCCCCGGCUUUGGCC-GUGGCCGCGGGUGAGAU-U-CGGCGCCC-AGAGCCCCC-----GGGGGCCUC--AGCUCACCGC-GCGCUG-CC-CCAUGUG-CGGCGGUGAAACCCAGGCCCCGACAGGC
ABDC01310736.1/270-396       GUUGGUUGAAAAUCACCCCCGGCUUUGGCC-GUGGCCAGGGGUGAGAU-G-CGGCGCCC-AGAGCCAGU-----AGGGGCCUC--AGCUCAGCGC-CCACUG-CC-UCGUGUG-CGGCGGUGAAACCCAGGCCCCGACAGGC
AANG01147281.1/396-522       GUUGAUUGAAAAUCACCCGCGGCUUUGGUC-GUGGCCGCGGGUGAGAU-U-CGGCGCCC-AGAGCCACC-----GGGGGCCUC--AGCUCACCGC-CCACUC-GU-CGGUGUG-GGGAGGUGAAACCCAGGCCCCGACAAGC
AAFC03057820.1/30291-30417   GUUGGUUGAAAAUCACCUUCGGCUCUGACC-AUGGCCGCAGGUGAGAU-U-CGGCGCCC-AGAGCCACU-----GGGGGCCUU--AGCUCACUGC-CCGCUU-CU-CUGUGUG-GGGAUGUGAAACCCAGGCCCCGACACGC
AANU01174700.1/2922-2796     AUUGGUUGAAUAUCACCCCCAGCUUUGGCC-AUGGCCAUGGGUGAGAU-U-UGGCACCC-AGAGCCUCC-----AGGGGCCUC--AGCUUAUUGU-GCACUG-CC-CCAUGUG-CAGCUGUGGAACCCAGGCCCUGAUGGGC
AAQQ01680967.1/1813-1688     GUUGGUUGAAAAUCACCCUCGGCGCUGGCG-GUGGCCGUGGGUGAGAU-U-CGGCGCCC-AGAGCCUCC-----AGGGGCCUC--AGCUCGCCGC-CCACUA-C--CAGUGUG-GGAAGGCGAAACCCAGGCCCCGACAUCC
AAYZ01019396.1/2534-2660     GUUGGUUGAAAAUCGCCC-UGGCUUUGGCC-GUGGCUAUGGGUGAGAU-U-CAGCGCCU-AGAGCCACC-----AGGAGCUUC--AGCUCACCGC-CCACAG-UUUCAAUGUG-GAGAGGUGAAACCCAGGCUCCGACAGGU
AAHY01131654.1/34983-34856   GUUCGUUGAAAAUCACCCUCGGCUUUGGCCUGUAGCCGGGGGUGAGAU-U-CGGCGCCC-AGAGCCA-C-----AGAGGCCUC--AGCUCACCGC-CCGCUG-CCCCGGUGUG-GGAGGGUGAAACCCAGGCCCCUACAUUC
AAHX01062910.1/10994-10867   GUUCGUUGAAAAUCAUCCUCGGCUUUGGCCUGUGGCCGGGGUUGAGAA-U-CGGCGCCC-AGAGCCA-C-----AGAGGCCUC--AGCUCACCCC-CUGCUG-CCCCAGUGUG-GGAGGGUGAAACCCAGGCCCCUACAUUC
AAIY01686160.1/334-461       GCUAGCUGAAAAUCGCCUGCGGCGUCACCC-GUGGCCGCGGGUGAGAU-U-CGGCGCCC-AGAGCAACC-----AGGGGCCUU--AGCUCGCCGC-CUACUG-CCUGCGUGUA-GGCGGCCGAAACCCAGGUCCCAACAGGC
AALT01092335.1/844-721       GCCCGCUGAAAGUCACCUGCGGCCUUGCCC-GUGGCCAUGGGUGAGAC-U-CGGCGCCC-AGAGC--AU-----GGGGGCUUU--AGCUCACCGC-CCACU---UUUGGUGUG-GGGAGGUGAAACCCAGGCCCCGACAGCG
AANN01385508.1/1150-1026     GUCUGUAGAAAAUCACCUUCAGCCUCUACC-GUGGCAGUGGGUGAGAU-C-CGGCACCU-AAAGCCAUC------AGGGCCUU--AGCUCACAGC-CUGC---CCGCAGUGCG-CGCAGAUGAAGCCCAGGCCCCGACACGC
AAPY01642506.1/1023-889      GUUGGCUGAAAAUUAUCCCCGGCUCUGACU-AUGGCCACAGAUGAGGU-U-UUGUGCUC-AGAGGGACCAAACUAGGGGUCUC--AGCUCAAUGCUCUACUGUCCUCGGUGUA-GAGUGGUGAAACUCAGGCUCUUACAAGU
BX931113.2/241-369           ACAGUCUGAAAAUCACCUGCGGUCU--CCC-GUGGCCCCCGGUGAGAUAA-CCGUGCCG-ACAGCAUA------GGGAACAUCAAAGCUUAUUGC-CCACGG-UGACAGUGUGUGGGGAGUGAAACCCAUGUUCCCAUAACC
BX548038.9/118324-118450     ACAAUCUGAAAAUUACCUUUGGCAU--UUU-GUUGCGAUGGGUAAGAU-UAUUGUGCCA-ACAUUAAUU-----CGGUACAUU-UAGCUUAUUGC-CAACUU-CA-UGUAGUU-GUGCAAUGAAACCCAUGUGCCUACAUUA
BAAF04126678.1/1431-1302     UCAGCCUGAAAAUGUUCUCCGGUUU-GACC-GUAACCUGAGGUCAGAUAU-CUGAGCCC-ACAGCACGG-----CGGCCCAUU-AAGCUUAUCGU-CUGCUCCUGUGUAGGCA-GGCCGAUAAAACCCAUGGGCCUACAAAG
AAKN02007400.1/46917-47042   GUUUGUUGAAAAUCACCCCCGGCUUUGGCC-GUAGUCGCGGGUGAGAU-U-CGGCGCCC-AGAACGUCC-----AGGGUCCUC--AGCUCACCGC-CCACUG-C--CGGUGUG-GGUGGGUGAAACCCAGGCCCCGACAUCC
AAWR02040077.1/15855-15729   GUUGGUUGAAAAUCACCUGCGGCUUUGGCU-GUGGCCGUGGGUGAGAU-U-CGGCGCCC-AGAGCCACC-----GGAGGCCUC--AGCUCACCGC-CCACUU-CU-CAGUGUG-GGGAGGUGAAACCCAGGCCCCGACACGA
AAGV020932280.1/1237-1110    GUUGGUUGAAAAUCACCCGCGGUUCUGACC-GUGGCUGCUGGUGAGAU-U-CGGCGCCC-AGAGCCACC-----UGGGGCCUC--AGCUCCCCGC-CCACUG-CCUCAGUGUG-AGCGGGUGAAACCCAGGCUCCGACAUUC
AAGU03005336.1/17295-17422   ACUGGUUGAAAAUUACCAGCAGUUUCGCCU-GUGGCUGCGGGUGAGAU-U-CUGCACCC-AGCGCCACC-----AGGGGCCUC--ACCUCACCGC-CGACUG-CCUUUGUGUG-AGUAGCUGAAACCCAGGCCCCAACAGGC
AAQR03077995.1/1528-1654     GUUGGUUGAAAAUCACCCCCGGCUUUGGCU-GUAGCCGGGAGUGAGAA-G-CGGCGCCU-AGAGCCAGC-----AGGGGCCUC--AGCUCACCGC-CCACUG-CC-UCGUGUG-CGGGGGUGAAACCCAGGCCCCGACAGGU
AAPE02019978.1/133289-133167 GUUGGUUGAAAAUCACCCGCGGCCUUGGCC-GUGACUGUGGGUGAGAU-U-CGGCGCCC-AGAGCCACC-----UGGGGCCUC--AGCUCACUGU-CCACA-----CGAUGUG-GGGAGGUGAAACCCAGGCCC-GACACGC
AAGW02022955.1/65666-65792   GUUGGUUGAAAAUCACCC-UGGCUUUGGCC-AUGGCUGUGGGUGAGAU-U-CCGCGCCU-AGAGCCUCC-----AGGAGCCUC--AGCUCACCUC-CCAUUG-CUCUGGUGUG-GAGAGGUGAAACCCAGGCCCCGACAAGU
AAEX03004635.1/19307-19181   GUUGGUUGAAAAUCACCUGCGGCCCUGCCC-GUGGCCGCGGGUGAGAU-U-CGGCGCCC-AGAGCCACC-----GGGGGCCUC--AGCUCACCGC-CCACUG-GU-CCUUGUG-GAGAGGUGAAACCCAGGCCCCGACAAGC
AACZ03005313.1/59405-59277   GUUGGUUGAAAAUCACCCCCGGUUUUGGCC-GUGGCCGCGGGUGAAAU-U-CGGCGCCCAAGAGCCUCC-----GGGGGCCUC--AGCUCACCGC-GUGCUG-CCGCCAUGUG-CGGCGGUGAAACCCAGGCCCCGACAGGG
AAWZ02035474.1/15477-15348   ACUGUCUGAAAAUCGCCUUUGGCCUUUUCA-AUGGCUUUGGGUGAGAUAU-UGGUGCCC-ACAGCAAA------GGGAAUGUU-UAGCUUAUUGC-CCUCAA-GCCUGAGGAGUGUGCAAUAAAACCCAUGUUCCUAUACUC
EU094028.1/5-134             GCCGUCUGAAAGUCGCCCGCGGCCUGACCC-GUGGCCGCGAGUGAGACCC-CGGCGCCC-ACAGACAC------AGGGGCCUA-AAGCUUGUCGC-CCACCG-CCCUGUCGUGUCGGCGACAAAACCCGGGCCCCGACAGGC
EU240332.1/6-134             ACAGUCUGAAAAUCACCUGCGGUCU--CCC-GUGGCCCCCGGUGAGAUAA-CCGUGCCG-ACAGCAUA------GGGAACAUCAAAGCUUAUUGC-CCACGG-UGACAGUGUGUGGGGAGUGAAACCCGUGUUCCCAUAACC
EU094033.1/5-134             GCCGUCUGAAAGUCGCCCGCGGCCUGACCC-GUGGCCGCGAGUGAGACCC-CGGCGCCC-ACAGACAC------GGGGGCCUA-AAGCUUGUCGC-CCACUG-CCCUGUAGUGUCGGUGACAAAACCCAGGCCCCGACAGGC
JN899079.1/7-132             GUCGUUUGAAAAUCACCUGCGGCUUUGGCC-UUGGCCGUGGGUGAGAU-U-CCCCGCCU-AAAGUCACC-----AGGAGCCUU--AGCUCACCGC-UCACU---CUCGGUGUG-GGGAGGUGAAACCCAGGCCCCGACACGC
#=GC SS_cons                 ::::<<<<<<--<<<<----<<<<______.__>>>>---->>>>-->.>.>>>>----.---------.....-<-<<<<<-..---<<<<<--.-<<<__._______>>>.---->>>>>----->>>>>->:::::::
#=GC RF                      guuggccGaaAAUcacCuuCgGccUUGaCc.GUggCcgugGgugAGAu.u.CggcGCCc.AgAGccacc.....aGGggCcUc..AGCUcaccGC.CcaCUg.ccucggUGug.gggaggugAAACCCAgGccCCgACAagc
//
# STOCKHOLM 1.0

#=GF AC   RF01226
#=GF ID   snoZ5
#=GF DE   Small nucleolar RNA Z5
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; Wilkinson A
#=GF GA   60.00
#=GF TC   65.40
#=GF NC   51.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00045
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Drosophila_melanogaster300049;
#=GF RN   [1]
#=GF RM   15288778
#=GF RT   Different expression strategy: multiple intronic gene clusters of box
#=GF RT   H/ACA snoRNA in Drosophila melanogaster.
#=GF RA   Huang ZP, Zhou H, Liang D, Qu LH
#=GF RL   J Mol Biol. 2004;341:669-683.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


AJ010684.1/1-113             CUCAAAUGAUGAUUCAGAUGACGAGACUGA-AGGAACAAAU-UCUC--GACUUGGCGCUGUAUUUUUCAGUG---C---CUCGUU---AUAU----AUUUGUUCA-UUUAA-GAUGAUUCGGCGAUCUGAUG
AAEU02000113.1/4030-4142     CUCAAAUGAUGAAACAGAUGACGAGACUGA-AGGAACGAAU-UCUC--GACUUGGCGCUGUAUUUUUCGGUG---C---CUCGUU---AAAU----AUUUGUUCA-UUUAA-GAUGAUUCGGCAAUCUGAUG
AAPU01010632.1/32660-32544   CACAAAUGAUGAGACUGAUGACGAGACUGA-AGGGACAUUU-UCUC--GAUUUGACGUUGUAUUUUUCAAUGUAAU---AUCGUA---CAAU----AUUUGUUCA-UUUAAAGAUGAAUCGGCAAUCUGAUG
AADE01000150.1/100636-100752 CACAAAUGAUGAAACUGAUGACGAGACUGA-AAGAACAUUUUUCUC--GACUUAACGUUGUAUCUUUCAAUG---U---UUCGUUGAACAAU----AUUUGUUCA-UUAAA-GAUUAUUCGGCAAUCUGAUG
AAPP01015683.1/83206-83322   CUCAUAUGAUGAGACUGAUGACGAGACUGA-AGGAACAUUU-UCUC--GACUCUGCAUUGUAUUUUUCAAUG---C---CUUGUUGAACUAU----AUUUGUUCU-UUUAAAGAUGAAACGGCAACCUGAUG
AAPT01021723.1/153906-153790 CACAAAUGAUGAUACUGAUGACGAGACUGA-AGAAACAUUU-UCUC--GGUUUUGUACUGUAUCUUUCAAUG---CAAUCUCGAA---CAAU----AUUUGUUCC-UUUAAAGAUGAACCGGCAAUCUGAUG
AANI01016249.1/27966-27850   CACAAAUGAUGAAACUGAUGACGAGACUGA-AGGAACAUUU-UCUC--GAUUUUAUGUUGUAUAUUUCGACG---UAAUUUCGAA---CAAU----AUUUGUUCAUUUUAA-GAUGAAUCGGCAAUCUGAUG
AAQB01006358.1/65907-66026   UGCCAAUGAUGAGACUGAUGACGAGACUGAAACGAACAGAU-UCUCUUGAUUUUCCAUUGUAUUUUUCAAUG---U---UUAAUU---GAACUAUAAUUUGUUCAUUUUAA-GAUGAUUUGGCG-UCUGAUG
#=GC SS_cons                 ::<<__________________________.__________.____..________________________..._...______...____...._________._____.__________________>>
#=GC RF                      CaCaAAUGAUGAaACUGAUGACGAGACUGA.AgGAACAuuU.UCUC..GAuUUuacguUGUAUuUUUCAAUG...u...uUcGuu...cAAU....AUUUGUUCa.UUUAA.GAUGAuuCGGCAAUCUGAuG
//
# STOCKHOLM 1.0

#=GF AC   RF01227
#=GF ID   snoR83
#=GF DE   Small nucleolar RNA snoR83
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   40.30
#=GF NC   39.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300121;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AJ505656.1/1-130           AUCCCAGCUAAGUUUG-AUGA----AGUACUUAU-------CUGAUUCAUGUGAGGCCUAAACUAA-AGCUGCGAGUUUCGCUGAUA-AUACCUUCUUCUCUUUUAUCCC----------AGAAGGUGUUUUAUUAGUAACUCU-GCUUACAUAU
AC155335.1/33339-33211     AUCCCAGCUAAG-UUG-AUGA----GGUACUUAU-------CUGAUUCAUGGGAGGCCUAAACCAA-UGUUGCAAGUUUCGCUGAUA-AUACCUUCUUCUUUUUAAUCCC----------AGAAGGUGUUUUAUUAGUAACUUC-GCUUACAUUU
AM429090.2/11963-11843     AUCCCAAAUAAA--UG-AUUA----UGUGUUUAU-------UUGAUUCAUGGGAGGCAGACAUCAA-GAAUGGGAG-UUCGCUGAUA-GCACCUUUUGUUUU------CC----------AGAAGGUGUUUUAAUAGUACCUCA-CCAGACAUAU
AASG02017340.1/2450-2308   AUCCCAGAUAAG-CUG-AGUAUUUAAGUGCUUUU-------CUGAUUCAUGGGAGGCCGAUAAUAA-UGCUGGAAGUUUCGCUGAUA-AUGCCUUUUUCUUUUCUGUUUGAGAUUGCUUUGAAAGGCAUU-UGUUAGUAACUUCGCCAUACAUAA
AARH01010454.1/31951-31833 AUCCCAGUUAAUGUUG-UUAUC---AAUGAUUAU-------CUGAUUCAUGGGAGGCAAAUAACAA-A-UUGGGAG-UUCGCUGAUA-GCACCUUUUUUA--------------------AAAAGGUGUUUUACUAGUACCUCA-CCAUACAUGU
CT963106.2/108769-108631   AUCCCAGUUAAGAUUGAAUUU----UUUUCAAGUGAUUACACUGAUUCAUGGAAGGCCAACAAUAAGUGUUGGAAGUUUCGCUGAUAAAUGCCUUUAAUUGAUUU-UACA----------UCAGGGUGUU-UACUAGUAACUUUACCGCACACUC
AK241461.1/451-573         AUCCCGGAUUAACUCG-CUUA----GCUGUUCUU-------CUGAUUCAUGGGAGGCCGAGAUCGA-UGCUGGCAGUUUCGCUGAUA-GCCCCUUCCUCUU-------AC----------UGGAGGUGCUUCAUUAGUAACUGG-CCACACAAUA
#=GC SS_cons               :<<<<<---------<.<<<<...._____>>>>.......>------->>>>>------------.----<<<<<<<--<<<<<<<.<<<<<<<<<________.____..........>>>>>>>>>-->>>>>>>>>>>>-.>>::::::::
#=GC RF                    AUCcCaGaUAAgaUUG.auga....agUgcucau.......CUGAUUCAuGgGAGGCcaAuAauAA.uGuUGggAGuUUCgCUgaua.acgCCuucuuuUuuUuu.Uucc..........agaaGGcguUUuauuAGuAaCUcu.cCauACAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01228
#=GF ID   snoR111
#=GF DE   Small nucleolar RNA snoR111
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   38.00
#=GF TC   39.50
#=GF NC   34.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300017;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AJ505682.1/1-130             AAAAUGGGGCAAGAGA-GAGUAACGGUGUCUCUGAGUCCUUGAUGAACCGGCGAGGGAAAUCAAUCU-----GGCCGAGAUAUCGUUUCAGUCGUUCUUUGUUUUGGUUUACGAUCUGAUUGUUGCUCGUCCACAU
AARH01010739.1/167276-167404 UCAAUGGGAUGAGAGACGGAUAC-AGUGUCUCUUUCGCUCGAAAGAA---CAGAGGUAGAACAAAUGUAA-UGGCCGAGAUAUCGUUUCAGUCGUCAUUCUUU--GAUUGACGAUUCGAUUGUUGCUCGUCCACAU
AASG02008398.1/9109-8983     ---AUGAAGGGACAGG-AAUUAGGAAUGUCUCUUUGUCUGGAACAGA---GGGAGGUAUAUCAAUUUCGGUAGGCCGAGAUAUCGUUUCAGUCGUCAUU--CUUCCAUUGACGAUUCGAUUGUUGCUCGUCCACAU
AM485814.2/5099-4974         --AA---AAUGAGAGACGAAUGUGAAUGUCUCGUCAUUGAUAACAAG---AGGAGGUAGAGAGAACGGAA-AGGC-GAGAUAUCGUUUCAGUCGUCAUUUCUCUGGAUUGGCGAUUCGAUUGUUGCUCGUCUACAU
AC162440.26/27224-27101      CAGAAUGAUGAAGAGACCAUUAA-UUUGUCUCCGCCGUCGUUUUAACA--UUGAGGUAUAACAA--------CGCCGAGUCAUCGUUUCGAUCGUCAUUUGUUUCG-UUGGCGAUACGAUUGUUUCUCGUCUACAA
AP008240.1/7403-7525         GUGUUAAUGGU-GAGACUGUUGAAAGUGUCUU--ACCGUUGUGAAUA---UUGAGGCAUAUCGAAUC-----GGC-GAGUCAUCGUUUCGGUCGUCCUUUGUUU-GGUUGGCGAUACGAUUGUUACUCUUCUACAU
#=GC SS_cons                 :::::<<<<<<-<<<<<<________>>>>>>-->>>>>>-------...-----------------.....<<-<<<<--<<<<-----<<<<<<<-<<_____>>->>>>>>>->>>>----->>>>->>::::
#=GC RF                      uaaAuggggggAgAGaCgauUaaaagcGuCUcuuccccccuaauaaa...uuGAGGuAuAucaAauu.....gGCCGAGauAUCGUUUCagUCGucaUuugUUUugaUugaCGAuuCGAUUGUUgCUCGUCcACAU
//
# STOCKHOLM 1.0

#=GF AC   RF01229
#=GF ID   SNORA84
#=GF DE   Small nucleolar RNA SNORA84
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   46.00
#=GF NC   41.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; SNORA84;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   28


AAFC03094193.1/47121-46989   GCCC-UGUGGUUACUGGAUGCUGUUGUGC---AGGUACAG-CUCUCCAGUGG-AUAUG-AG--GGGC-UAGA-GCAAUC-C---UGUGAUA-UAU-GCAUGGGGGCUGUUUCUCCUCAGCAGCU-GCCAUAGCCCGGUCACUGAUA-CAUGA
AAPY01017333.1/488-620       GCCC-UGUGGUUGCUGGGUGCUGUUGUGC---AAGUACAG-CUCUCCGGUGG-AUACU-AU--GGGC-AACA-GCAAUC-C---UGUGAUU-UAU-GCAUGGGGGCUGUUUCUUCUCAGCAGCC-GCCAUAGCCCGGUCACUGGUA-CAUGG
ABDC01226143.1/6122-6253     GCCC-UGUGGUUGCUGGAUGCUGUUGUGC---AGGUACAG-CUAUCCAGUGG-AUA-CAAU--GGGC-UAUA-GUAUUC-C---UGUGAUU-UAU-GCAUGGGG-CUGUUUAUUCUCAGCAGCU-GCCAUAGCCCGGUCACUGGUA-CAUGG
AAQQ01533914.1/1480-1612     GCCC-UGUGGUUGCUGGAGGCUGUUGUGC---UGGUACAG-UUCUCCAGUGG-AUA-CAGU--GGGC-CAGA-GCAAUC-C---UGUGAUU-UAU-GCAUGGGAGCUGUUUGUCCUCAGCAGCU-UCCAUAGCCCGGUCAUUGGUA-CAUGG
AC129306.5/112792-112924     GCCC-UGUGGUUGCUGGAGGCUGUUGUGU---AGGUACAG-CUUUCUAGUGG-AUA-CAAU--GGGC-AAGA-GAAAUC-C---UUUGAUU-UAU-GCAUGGUAGCUGUUUCUUCUCAGCAGCU-GCCAUAGCCCGGUCAUUGGCA-CAUUA
AAYZ01650745.1/1075-943      GCCC-UGUGGUUGCUGGAGACUGUUGUGC---CAGUACAG-CUCUCCAGUGG-AUA-CAAC--GGGC-CAGA-GCAACC-C---UGUGAUG-UAU-GCAUGGAGGCUGUUUCUCUUCCGCAGCC-GCCAUAGCCCGGUCACUGGGA-CAUGG
AANN01508860.1/2074-1942     GCCC-UGUGGUUACUGGAUGCUGUUGUGU---AAGUGCAG-CUCUCCAGUGG-AUAUAAAG--GG-C-UACA-GCAACU-C---UGUGAUU-UAU-GCAUGGGGGCUGUUUCUCCUCCGCGGCC-UCCAUAGCCCGGUCACUGAUA-CAUGA
AALT01251133.1/1178-1047     GCCC-UGUGGUUUCUGGAUGCUGUUGUUC---AUGUACAG-CUCUCCAGUGG-AUA-GAAG--GGGC-CAGA-GUGAUU-C---UGUGAUU-UAU-GCAUGGGG-CUGUUCUUCCUCAGCAGUC-GCCAUAGCCCGGUCACUGAGA-CAUGG
AAIY01679074.1/2049-2182     GCCC-UGUGGUUGCUGGGGGCUGUUGUUC---AAGUACAG-CUUUCCAGUUG-AUGGCAAU--GGGC-CAGA-GCAAUG-C---UGUGAUG-UGU-GCAUGGGGGCUGUUCCUUUUCAGCAGCC-UCCAUAGCCCGGUCACUGGUA-CAUGG
AANG01752618.1/2209-2077     GCCC-UGUGGUUACUGGAUGCUGUU-UGC---AGGUACAG-CUCUCCAGUGG-AUGUGAGG--GGGC-CACA-GCAAUC-C---UGUGAUU-UAU-GCAUGGGGGCUGUUUCUCCUCAGCAGCC-ACCAUAGCCCGGUCACUGAUA-CAUGG
AAPN01343940.1/6882-7015     GCCU-UGUGGUUACUGGUUGCUGU--UAU---UGAUGCAG-UACUCCAGUUG-AUAGAAAC--UGGC-CAAAAGUAAUU-C---UGUGAUU-UUUUGCAUGGAGUCUGUAAUUCCUCAGCAGCC-UCCAUAGCCCGGUCACAGUUA-CACAA
BAAE01083321.1/397-530       GCCU-GGUGGUUCCUAGAGUCAGC-GUCA---CAGUGCUG-AACUGUAGGUU-UUAUUGAC--AGGC-ACAAAUCGACU-C---UGCAAUGUUAU-GCAUGGAAGCUGCCACUAU--AGCAGCUCUCCAUAGCCCGGUUGCAGAUA-CAAAA
AAFR03064834.1/47797-47667   GCCC-UGUGGUUCCUGGAAGCCGGUG-GU---CAGUCCGG-CCUUUCCGGGU-GUA-GACG--GGCC-CAGA-GAAAGG-CAGCAGUGAUG-GAU-GCGUGG-GUCUGCACGCU---GGCAGCC-CCCACAGCCCGGUCACUGCCA-CAGGC
AC099740.2/57684-57822       GCCU-CGUGGUUCCCAGAGUCGGCUGACUCCAAAGUGCUG-AUCUGUGGGUUUUUGUCAAC--AGGCGCACA-UUAAGU-C---UGUGAUUUUAU-GCAUGGAAG-CUGCCACCAUAGCAGCCU-UCCAUAGCCCGGUCUCAGAUA-CAUUU
CR352215.34/145558-145420    UGCCUUGUGGUUCCUUAAGACAGCU-CAU---CGGUGCUGAUGCUUGAGGUU-GUGUUUGACGGGCA-CACA-UUGAUCUC---UGCAAUU-UAAUGCGUGGUGGCUGACAUUUCCAUGCAGCU-UCCACAGCCCGGUUGCAGAAA-CAUGU
CAAE01014737.1/587233-587095 GCCU-UGUGGUUCCUAGAGUCAGCUUGUUCCUCGGUGCUG-AACUGUGGGGUUUUGUCAAC--AGGCGCACA-UUAGUU-C---UGUGAUAUUAA-GCAUGGGAG-CUGCCACCAUAGCAGCCU-CCCACAGCCCGGUCGCAGAUA-CACGC
AAKN02038452.1/148883-149015 GCCC-UGUGGUUGCUGGGGGCUGUUGUUC---AGGUACAG-CACUCCAGUGG-GUA-CAAU--GGGC-CACA-GCAAUC-C---UGUGAUU-UUU-GCAUGGCAUCUGUGUUUCCUCAGCAGCU-GCCAUAGCCCGGUCACUGGUA-CAUGG
AAGV020349331.1/763-896      GCCC-UGUGGUUGCUGGAUGCUGUUGUGC---AAGUACAG-CUCUCCAGUGC-AUAGCAGU--GGGC-CAGA-GCAAUC-C---UGUGGUU-UAU-GCAUGGGGUCUGCUCUCCCUCAGCAGUC-GCCAUAGCCCGGCCACUGGCA-CAUGG
AAWR02016182.1/17013-17145   GCCC-UGUGGUUACUGGAUGCUGUUGUGC---ACGUACAG-CUCUCCAGUGG-AUGUGAGG--GG-C-CAGA-GCAAUC-C---UGUGAUG-UAU-GCAUGGGGGCUGUUUCUCUUCAGCAGCA-ACCAUAGCCCGGUCACUGAUA-CAUAG
AAHX01090248.1/15133-15001   GCCC-UGUGGUUGCUGGAGGCUGUUGUGC---CAGUACAG-UUCUCCAGUGG-AUA-CAAU--GGGC-UAGA-AAAACC-C---UUUGAUU-UAU-GCAUGGGAGCUGCUUCUUCUCAGCAGCU-GCCAUAGCCCGGUCAUUGGUA-CAUUG
AACZ03069523.1/65944-65813   CCCC-UGUGGU-GCUGGAUGCUGUUGUGC---AUGAACAG-CUCUCCAGUGG-AUUCG-AU--GGGC-CCCA-GCAAUC-U---UGUGAUU-UAU-GCAGGGAGGGUGCUUCUCCUCAGCAGCU-GCCAUAGCCCGGUCGCUGGUA-CAUGA
AADN03006376.1/135621-135487 GGCC-UGUGGUUACUGGACACUGGUUUGU---GUGUGCAG-UGCUUCAGUUG-GAAGAAAU--GGCC-CAAAAGUGAUA-C---UGUGAUU-UAC-GCAUGGAGUCUGUGAUGUGUGAGCAGCU-UCCAUAGCCCGGUCACAGUUA-CAGAC
AL136097.10/127422-127290    GCCC-UGUGGUUGCUGGAUGCUGUUGUGC---AUGGACAG-CUCUCCAGUGG-AUUCG-AU--GGGC-CAUA-GCAAUC-C---UGUGAUU-UAU-GCAUGGAGGCUGCUUCUCCUCAGCAGCU-GCCAUAGCCCGGUCGCUGGU-ACAUGA
AAGW02048252.1/133084-133216 GCCC-UGUGGUUGCUGGAGGCUGUUGUGC---AAGUACAG-CUCUCUAGUGG-AUG-CAAU--GGGC-CAGA-GCAAUC-C---UGUGAUU-UUU-GCAUGGCGGCUGUUUCUCUUCAGCAGCC-GCCAUAGCCCGGUCACUGGAA-CAUGG
AAQR03117429.1/10920-11052   GCCC-UGUGGUUGCUGGAUGCUGUUGUGC---AGGUACAG-CUAUCCAGUGG-AUA-CAAU--GGGC-CAUA-GCAAUC-C---UGUGAUU-UAU-GCAUGGGGGCUGUUUCUGCUCAGCAGCU-UCCAUAGCCCGGUCACUGAUA-CAUGG
AAEX03000684.1/82462-82593   GCCC-UGUGGAUACUGGAUGCUGUU-UGC---AGGUACAG-CUCUCCAGUGG-AUGUGAAG--GG-C-CAGA-GCAAUC-C---UGUGAUU-UAU-GCAUGGGGGCUGUUUCUCCUCAGCAGCC-GCCAUAGCCCGGUCACUGAUA-CAUGG
AAGU03085235.1/107993-108126 GCCC-UGUGGUUACUGGAUGCUGUUGUGC---AGGUACAG-CUCUCCAGUGG-AUAGCAAU--GGGC-CAGA-GCAUUA-C---UGUGAUG-UAU-GCAUGGGGGCUGUUCCUCCUCAGCAGCC-GCCAUAGCCCGGUCACUGGUA-CAUGG
AAWZ02009361.1/42791-42659   GCCC-UGUGGUUACUGGACGCUGUUCUCU---CAGUACGG-UGCUUCAGUUA-GUAGAAAU--GGGC-CAAAAGUAAUG-C---UUUGACU-UAC-GCAUGGAGUCUG--ACUUGUUAGCAGCC-UCCAUAGCCCGGUCAUUGUGA-CACUU
#=GC SS_cons                 <<<<.--<<-<<<<<<<<-<<<<<_____...____>>>>.>-->>>>>>>>.->>-----..>>>>.----.------.<...-<<<<<<.---.<<<<<<-<<<<<<<_______>>>>>>>.->>>>->>-->>>>>>->:::.:::::
#=GC RF                      GcCc.UGugGcccCuggaugCuGcUgugu...aaGUgCaG.cuCuccaGggg.auauuAAu..gGgC.cAaA.guAAuu.C...UguGAuc.UAU.GCaUGGaggCuGcuuuuucUcagCaGcc.uCCAuAGCCCggUCacuGauA.CAuga
//
# STOCKHOLM 1.0

#=GF AC   RF01230
#=GF ID   snoR77
#=GF DE   Small nucleolar RNA snoR77
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   47.00
#=GF TC   47.50
#=GF NC   45.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300109;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AJ505648.1/1-133             AGGCAACCUACUUGUUAAUAAAACAAUGACAUGAGAGGUGUUUAACUGCUCCUAGAUCAAAUUAUGCUUCUGCUCUUCAGACUUGCUGAGAU----------UUUAUCGUCUUUGAAGCUGGUCUAGUAGUCUUAAGCACAUU
AARH01003870.1/147742-147873 AGGCAGCCUCUUUGCUGAAAAGAAGAUAGCAAAGAAGGUGUUAAACUGCUCGUACAUUAAUUUGU-CUUAUGCUCUUCAGACUUGCUGAGAC----------UUCUCUGUCUUUGAAGCUGGUCUAGUAAGCCUAAGCACAUC
AASG02001200.1/36745-36620   AGGCAGCCUCUUUGCUGAUAUUAAAAUAGCUAAGAAGGUGUUUAACUUCUCGUAUAUCAAU--GU-CUUUUGCUCUUCAGAUUUGCUGAG-U------------CU-UAUCCUUGAAGCUGGUCUAGUAAGCUUAAGCACAUU
AK059482.1/298-435           AGGCAGCCCCUUUGUCUGA-UUUCAAUGGCAAUGGAGGUGUUGCGUUGCUCGGAGAGUGAUU----CUUCUGCUCUUCAGAUUAGCUGAGAGGGUAGGCUUGCUUUCCCUCGUUGAAGCUUGUCUAGUAGUCUUAAGAACAUU
AM479372.1/704-585           AGGCAGCCCCCUUAGCCCU-AGCCAUGGC-AAGGGAGGUGUUAUUCUUCUCAGAUAUCGAU-----CUUUUGCUCUUCAGACCUGCCGAA----------------CCAUUCUUGAAGCUGGUCUAGUAAGCAUAAGUACAUU
#=GC SS_cons                 :<<<<-<<<<<<<<<<<_________>>>>>>>>>->>>>>>--------------------.--.<<<--<<<----<<<<<-<<<--<<<..........______>>>----->>>->>>>>---->>>-->>>::::::
#=GC RF                      AggCAGCCcccuuGccgauAauacAAcggCaagggAGGUGuuaaacUgCUCguAuAuuaAuU.gU.CUUuUGcuCUUCAGAccuGCuGAGac..........uUuuccguCuUUGAaGCUggUCUAGUAagCuUAAGcACAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01231
#=GF ID   snoR74
#=GF DE   Small nucleolar RNA snoR74
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   44.40
#=GF NC   42.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300106;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   9


AJ505651.1/1-133           GAAAAAGCAGAGUUCUG-UUGCAAUUU--G-----A-CAGAUCUCACGUAUACUUCAGGGAAAUUGAAUUG-GUCAUCGUGAUUGGGUGAAUCUAUGUUUAUAUAUCU-CAUAACUAU-AAGAUUCAGUACAUGAUGGUACAUUG
AC189572.1/58368-58500     GAAAAAGCAGAGGUUUG-AAGCAAUUU--------A-CAGAUCUAACGUAUACUUCAGGGACAUUGAAUUG-GUCAUCGUGAUUGGGUGAAUCUUAGUUUCAUUUUCU-UAUAGCUUUAAAGAUUCAGUACAUGAUGGUACAUUG
AASG02000124.1/14817-14956 AAAAAAGCAGGGGCUUG-UUGUAUCCU--UUGUGAA-CAGGCCUCUCGUAAACGUCAGGGAAAUUAAUGUU-UUCAUUGUUAUUGGGUGAACCUCUGUUUUUUGAUUUAUUUGUCGCUGAAGGUUCAGUAAAUAAUGGAACAUUU
AARH01003623.1/36913-37042 AAAAAAGCAGGGGCCUGUUGCCUAUGU--G-----AACAGGCCUCUCGUAAACUUCAGGGAAAUCAGUUA----CAUUGUUAUUGGGUGAACCUCUGUUU---UAUUU-UAUGUGGCUGAAGGUUCAGUAAAUGAUGACACAUUU
AM445900.2/26639-26766     AAAAAAGCAGGGGCUUG-UUGCCUUUGUGG-----A-CAGGUCUCUCGUAAACUUCAGGGAAAUU-AGUUG---CAUUAUUAUUGGGUGAACCUCUGGAGUUUUUUGU-GAUGG-----AAGGCUCAGUAAAUAAUGGCACAUUG
AP006441.3/41776-41647     AAAAAAGCAGGAUGCUGUUCUCUCUAU--A-----AGCAGUAUCUUCGUAACCUUUAGGAACAUC---AUG-UUCAUCGUUAUUGGGUGAACCG--GUGGACACAGCU-CAAUGUUGA-CUGGUUCAGUAAAUGAUGGCACAUUU
AAAA02026690.1/50545-50678 AGAAAAGCAGGAUGUUGUUCUCUAUAU--A-----AGCAUUGUCCUCGUAAACUUCAGGAAUAUCAGAGUGAGUCAUUGUUCUUGGGUGAAUCAA--UUGACACAGCU-UGAUGUUAA-UUGGUUCAGUAAAUGAUGACACAAUU
AF034618.1/2078-2211       UAAAAAGCAGGGUCCUA-UUGCCUUAU--UGUGA-A-UGGGCCUCUCGUAAACGUCAGGGAAAUC-AAUUG-UGUAUUGUUAUUGGGUGAACC--ACUUGAGUUUUCU-CUAUGAUGGCA-UGUUCAGUAAACGAUGCUACAUUG
X57297.1/5111-5240         AAAAAAGUAGGGAUCUG-GUGCAAUUU--CUGA--A-CAUGCCUCUUGUAAACUUUAGGGAUAAGGAUAUG---CAAUGUUAUUUGGUGAACU--UGUUGAGUUGUCC-UGAUGAUUGAU-AGUUCAGUAAAG--UGCGUGAGUA
#=GC SS_cons               ::::<<<---<<-<<<<._________.._....._.>>>>->>-------->>>----------------.<<<<<<<<<------<<<<<<<______________.___________>>>>>>>--->>>>>>>>>::::::
#=GC RF                    aAAAAaGCAGgGuccUG.UugCaaUuU..u.....A.CAgguCccUCGUAAACuUCAGGGAaAUuaAauUG.gcCAUcgUuAUUGGGUGAaccuauGUUgauuuaUcU.uauuguuuuaaagguUCAGUAaAcgAUGgcACAuUu
//
# STOCKHOLM 1.0

#=GF AC   RF01232
#=GF ID   snoR442
#=GF PI   snoU40
#=GF DE   Small nucleolar RNA R442
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   64.30
#=GF NC   33.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=DRO30007;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15987805
#=GF RT   Genome-wide analyses of two families of snoRNA genes from Drosophila
#=GF RT   melanogaster, demonstrating the extensive utilization of introns for
#=GF RT   coding of snoRNAs.
#=GF RA   Huang ZP, Zhou H, He HL, Chen CL, Liang D, Qu LH
#=GF RL   RNA. 2005;11:1303-1316.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   10


AADE01000002.1/234888-234842 UGCAAGCCUGUUGGGUGUGAUUACGGCUUGUCAUAGUUACUCUGAUU
AAEU02000439.1/170562-170607 UGCAAGCCUGUUGGGUGUGAUU-CAGCUUGUCAUAGUUACUCUGAUC
AANI01014595.1/210739-210785 UGCAAGCCAGUUGGGCGUGAAUCACGCUUGUCAUAGUUACUCUGAGA
AAPP01019597.1/125491-125536 UGCAAGCCUGUUGGGCGUGACU-UCGCUUGUCAUAGUUACUCUGAUU
AAPQ01006793.1/350792-350747 UGCAAGCCUGCUGGGUGUGACU-CCGCUUGUCAUAGUUACUCUGAUC
AAPT01018383.1/64068-64114   UGUAAGCCAGUUGGGCGUGAAUUUGGCUUGUCAUAGUUACUCUGAGA
AAPU01011132.1/61912-61958   CGCAAGCCUGUUGGGCGUGAUUUAUGCUUGUCAUAGUUACUCUGAGA
AAQB01009407.1/110311-110355 AUCAAGCCUGUUGGGUGUGAUU-UUGCU-GUCAUAGUUACUCUGAGC
AE014297.2/25689021-25689066 CGCAAGCCUGUUGGGUGUGAUU-CUGCUUGUCAUAGUUACUCUGAUC
AJ543998.1/1-46              CGCAAGCCUGUUGGGUGUGAUU-CUGCUUGUCAUAGUUACUCUGAUC
#=GC SS_cons                 :::::<<<_____>>><<<<<_.______>>>>>:::::::::::::
#=GC RF                      uGCAAgCCUGUUGGGcGUGAuU.cuGCUUgUCAUAGUUACUCUGAuc
//
# STOCKHOLM 1.0

#=GF AC   RF01233
#=GF ID   snoU109
#=GF DE   Small nucleolar RNA U109
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   43.00
#=GF TC   43.20
#=GF NC   42.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; U109;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16361266
#=GF RT   A novel experimental approach for systematic identification of box H/ACA
#=GF RT   snoRNAs from eukaryotes.
#=GF RA   Gu AD, Zhou H, Yu CH, Qu LH
#=GF RL   Nucleic Acids Res. 2005;33:e194.
#=GF RN   [2]
#=GF RM   7225127
#=GF RT   Pseudouridine residues in the 5'-terminus of uridine-rich nuclear RNA I
#=GF RT   (U1 RNA).
#=GF RA   Reddy R, Henning D, Busch H
#=GF RL   Biochem Biophys Res Commun. 1981;98:1076-1083.
#=GF RN   [3]
#=GF RM   12912925
#=GF RT   A common sequence motif determines the Cajal body-specific localization of
#=GF RT   box H/ACA scaRNAs.
#=GF RA   Richard P, Darzacq X, Bertrand E, Jady BE, Verheggen C, Kiss T
#=GF RL   EMBO J. 2003;22:4283-4293.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   26


AM055742.1/1-134           UUGCAUGUGGAA---------AUGUCUGCUUCUCAUUCC-UUG--G-GAGCAGGAAUAUGUUCAUAACAUGCUACAUUA-AC-------AAAGGAGUUCUCAGGGCUGCCAACCUUCUAGUAAAGGUUGAGUGGUAGUAUAUUUCUCCAACAUAA
AAFC03012751.1/570-436     UCGCAUGUGGAA---------AUGUCUGCUUCUCAUUCCUUUG--G-AAGCAGGAAUACGUCCAUAACAUGCUACAUUA-AA-------AAAGGAGUUCUCAGGGCUGCCAACCUUCCAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAUAA
ABDC01105195.1/1988-2122   UUGCAUGUGGAA---------AUGUCUGCUCCUUAUUCC-UUC-GG-GAGCAGGAAUACAUUCAUAACAUGCUACAUUA-AA-------AAAGGAGUUCUCAGGGCUGCCAACCUUACAGUUGAGGUUGAGUGGUAGUAUAUUUCUCCUACAUAA
AADA01032425.1/12845-12711 UUGCAUGUGGUA---------AUGUCUGCUCUUCAUUCCUUUG--G-GAGCAGAAAUACAUCCAUAACAUGCUAAAUUA-AA-------AAAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUGGUAGUAUAUUACUCCUACAUAA
AAIY01155199.1/1916-1782   CUGCAUGUGGAA---------AUAUCUGCUCCUCAUUUC-GUU-AG-GAGCAGGAAGACAUCCAUAACAUGCUACAUUA-AU-------AAAGGAGUUCUCAGGGCUACCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCUUACACAA
AAQQ01025945.1/7271-7137   UUGCAUGUGGAA---------AUGUCUGCCCCUCAUUUC-UUC-AG-GGGCAGGAAUGCAUCCAUAACAUGCUACAUUA-AC-------AAAGAGGUUCUCAGGGCUGCCAGCCUUAUAGUAGAGGCUGAGUGGUAGUAUAUUUCUCCUACAUAA
AACN010521667.1/155-289    CUGCAUGUGGAA---------AAGUCUGCUCCUCAUUCU-UUG-GG-GAGCAAGAAUACAUCCAUUACAUGCUACAUUA-AA-------AAAGGAGUUCUCAGGGCUACCAGCCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAUAU
AANG01809596.1/3729-3863   UGGCAUGUGGAA---------AUGUCUGCUCCUCAUUCCUUUG--G-GAGCAGGAAGACAUCCAUUACAUGCUACAUUG-AA-------AAAGGAGUUCUCAGGGCUGCCAGCCUUACAGUAGAGGCUGAGUAGUAGUAUAUUUCUCCUACAUAG
AAPY01288712.1/832-964     UUGCAUGUGGAA---------ACGUCUGUUCUGCAUUCU-UUU--G-GAGCAGGAAUACAUCCAUCACAUGCUACAUUG-AG--------AAGGAGUUCUCAGGGCUGCCGACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAUAA
AL592403.6/87724-87858     UUGCAUGUGGAA---------AUACCUUCUCCUCAUUCUAUUU--G-GAGCAGGAAUGCAUCCAGAACAUGCUACACUA-AA-------AGAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAGAA
AAHX01075576.1/2850-2716   UUGCAUGUGGAA---------AUACCUUCUCCCCAUUCUCUUU--G-GAGUAGGAAUGUAUCCAGAACAUGCUACACUA-AA-------AGAGGAGUUCUCAGGGCUGCCAGCCUUCUAGUAGAGGUUGGGUGGUAGUAUAUUUCUCCUACAGAA
AANU01221802.1/12812-12946 UUGCAUGAGGAA---------GUAUCUGCUCUUCAUUCCUUUG--G-GGGCAGAAAUACAUCUAUCACAUGCUAAAUUA-CA-------AAAGGAGGUCUCAGGGCCGCCAACGUUUCAAUAGAGGUUGAGUGGUAGUAUAUUACUCCUAUAUAA
AALT01635921.1/820-679     UUGCAUGUGAAA---------AUGCCUGCUUCUCAUUCC-UUU-AG-GGGCAGGAAUACAUCCAUAACAUGCUACAUUA-AAAAGGAAAAAAGGAGUCUUCAAGGCUACCAAACUUACAUUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACACAA
AANN01279194.1/758-890     UUGCAUGUGGAA---------ACGUCUUCUGCUCAUUCCUUUG--G-GCGCAGG-AUAUAUCC-UUACAUGCUACAUUA-AG-------AAAGGAGUUCACAGGGCUGCCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAAAA
AAFR03013540.1/37441-37297 CUGCAUGUUGGACUUUUUAA-AGUCAUACUUCUUAAUGCAAUA--G-AAGUAUGAAUAUAACCAGUACAUGCUAUAUAA-AAAU-----AUAGGAGUUUUCAGGGCUGCCAACCUUGCAGUAAAGGUUGAGUAGUAGUAUAUUUCUCCUACAUCA
AAYZ01413806.1/796-664     UUGCAUGUGGAAG--------UUUCUUUCUCCUCACUCC-UGU--G-GAGGAGGAAUGCAUCCAUUACAUGCUACAUUA-GC---------AGGAGUUCUCAGGGCUGCCGGCCUGCCAGGAGAGGCUGGGCAGUAGUAUAUUGCUCCAACACAA
AAPN01018558.1/7732-7871   UUGCAUGAUGGAAACCAA---UUUUCAGCUCUUUGUUCU-UUA-AG-GAGCAUGAAUAUAUCCAUAACAUGCUACAUAA-AU--------GAGGAGCUGUCAGGGCUGCCAGCCUUUUAGUUAAGGCUGUGUGGUAGUAUAUUUCUCCAACACUG
AAKN02019979.1/23970-23835 UGGCAUGUGGAA---------AUGCCUUCUCCUCAUUCC-UUG-UG-GAGCAGGAAUAUAUCCAUGACAUGCUACAUUA-AAA------AAAGGAGUUGUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUGGUAGUAUAUUUCUCCUACAUUA
AAWR02003035.1/86430-86564 UUGCAUGUGGAA---------AUGUCUGCUCCUCAUUCCUUUG--G-GGGCAGGAACACAUCCGUAUCAUGCUACAGUA-AA-------AAAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAUAA
AAGV020307937.1/641-507    UUGCAUGUGGAA---------AUGUCUGCUCCUCAUUCU-UUU-AG-GAGCAGGAAUAUAGCCAUAACAUGCUACAUUA-AA-------AUAGGAGUUCUCAGGGCUGCCAAUCUUGCAGAAGAGGUUGAGUGAUAGUAUAUUUCUCUUACAUUA
AAWZ02032644.1/10370-10504 CUGCAUGAUGGAAACU-----UGUCAUUCUUCUUUCUUC-UG---G-GAGAAUGAAUAUUCCUUCA--AUGCUAUAAAA-AU-------CAAGGAGUUUUCAGGGCCACCUGCCUUGGAGUAGAGGCUGAGUGGUAGUAUAUUUCUCCUACAUUA
AAGU03001560.1/48063-48198 UGACAUGUGGAA---------AGGUCUGCUCCUCAUUCC-UUU-AG-GAGCAGGAAUACAUCUAUAACAUGCUACACUAUAA-------AAAGGGGUUUUCAGGACUGACAACUUUACAGUAGAGUUUGAGUGGUAGUAUAUUUCUCCUACAUUA
AAPE02000595.1/29599-29732 UUGCAUGUGGAAAU-------AUGUCUGUUCCUCAUUCCUUUG--G-GAGCAGGAAUACCUCCAUAACAUGCUACAUAA-----------AAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUUCUCCUACAUAG
AAQR03037363.1/5502-5637   UUGCAUGUGGAA---------AUGUCUGCUCCUCAUUCC-UUU--GAGAGCAGAAAUACGUCCAUAACAUGCUACAUUA-AAA------AGAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUAGUAGUAUAUUACUCCUACAGAA
AAGW02054189.1/12164-12297 UUGCAUGUGGAA---------AUGCCUUCUCCUCAUUCC-UUU--G-GAGCAGGACAACAUCCAUAACAUGCUAUAUUA-AC-------AAAGGAGUUCUCAGGGCUGCCAACCUUACAGUAGAGGUUGAGUGGUAGUAUAUUUCUCCUACACAA
AADN03004144.1/23237-23093 CUGCAUGUUUCAAAAAAACACAAUUCUGCUCCUUAUUCC-CUUAAG-GAGCAUGAAUAUAUCUAUAACAUGCUACAGAA-AA-------CAAGGAGUCUUCAGGGCUGCCAGUCUUCAAGUAAAGGCUGAGUGGUAGUAUAUGCCUCCUACAUUC
#=GC SS_cons               ::<<<<<<----.........---<<<<<<<<_______.___..>.>>>>>>>------------>>>>>>-------.--.......---<<<<--------<<--<<<<<<<<______>>>>>>>->-->>--------->>>>:::::::
#=GC RF                    UUGCAUGugGaA.........AugccugCucCUcAUUcc.UUu..G.gaGcaggAAUAcAUCcAUaaCAUGCUAcAuuA.Aa.......AaAGGaGUUcUCAGGgCUGCCagcCUcacAGUAgAGgcuGAGUaGuAGUAUAUUuCuCCUACAuaA
//
# STOCKHOLM 1.0

#=GF AC   RF01234
#=GF ID   SNORA47
#=GF DE   Small nucleolar RNA SNORA47
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   46.30
#=GF NC   44.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.10 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; HBI-115;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300758;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF RN   [2]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   20


AC008581.11/95393-95256    UGGAGGACUGAGAAGGUGAGGCAGUUUU-GCCCCGUGCUGCCUUCCACCGGUUAAGACCUCCAAAAUCGAAGGGCUGCCCAGGCAGAGGAUGUCC-CCUUGCCACCCUUG------GAGGGGCAGCGCUG-UGCUGGCCGACAUUUG
ABDC01238968.1/714-577     UGGAGGACUGAGAAGGUGAGGCAGUUCU-GUACUGUGCUGCCUUCCACUGGUUAAGACCUCCAAAAGUGAAGAGCUGCCCAGGCAGAGGAUGCCC-CUCUGCCACCCUCA------GAGGGGCAACGCUG-UGCUGGCCGACAUUUC
AAQQ01634086.1/1372-1509   UGGAGGACUGAGAAGGUGAGGCAGUCUC-AUACCAUACUGCUUUCUACUGGUUAAGACCUCCAACAGCGAAGGGUUGCCCAGGCAGAGGAUGUCC-CUCUGCCAACUUCG------GAGGGGCAGCACUG-UGCUGGCCGACAUUUG
AAPY01231828.1/609-746     UGGAGGACUGAGAAGGUGAGGCAGUCCU-GUGCCAUGCUGCCUUCCACUGGUUAUGACCUCCGAAAGCAAAGGGCUGCCCAGGCAGCGCACGUCC-CUCUGCCACCCUCA------GAGGGGCAGCACUG-UGCUGGCUGACAUUUG
AAFC03042691.1/8218-8081   CGGAGGACUGAGAAGGUGAGGCAGUUCU-GAACCAUGCUGCCUUCCACUGGUUAAGACCUCCGAGAGCGAAGGCCUGCAGAGGCAGAGGAAGUCC-CUCUGCCGCCCCCA------GAGGGGCAGCACUG-UGUUGGCCGACACUUG
AANG01760272.1/2045-2180   CGGAGGACUGAGAAGGUGAGGCAGUUA--GCACUGUGCUGACUU-CACCGGUUAAGACCUCCAAGAGCGAAGGCCUGCCUAGGCAAAGGAUGUCC-CUCUGCUGCCCUUG------GAGGGGCAGCGCUG-UGCUGGCCGACAUUUG
AAIY01172864.1/10733-10870 UGGAGGACUGAGAAGGUGAGGCAGCUCU-GUACCAUGCUGCCGUCCACUGGUUAAGGCCUCCGAAAGUGAAGGGUCGCCAGGGCAGAGGAUGCCC-CUCUGCCACCUUCA------GAGGGGCAGGGCUG-UGCUUGCCGACAUUGU
CAAA01163729.1/4429-4566   UGGAGGACUGAGAAGGUGGAGCAGUUCU-GUACCGUGCUGCCUUCCAUUGGUUAAGACCUCCAACAGUAAAGGGCUGGCCGGCCAAAGAAUGUCC-UCUCUAUCACCGUG------GAGGGGCAGCACUG-AGCUGGCCCACAUUGU
AALT01067225.1/502-637     UGGAGG-CUGAGAAGGUGAGGCAGCUCA-GUACCAUGCUGCUUUUCAUUGGUUAAGACCUCCGAGAGCAAAGGC-AGCCAAGGCAGAGCACGCCC-CUCUGCUACCUUCA------GAAGGGCAGCGCUG-UGUUGGCUGACAUCUG
AAPN01106423.1/5677-5812   UGGAGGACUGAGAAGGUAAGGCAGUUUCUCUACCAUGCUGCCUCUUACUGGUUAGAGCCUCCUACAUUAAAU---------CGCA-AAAGCAUCUCACGUGCCUCCUGUGAAUUGGGAGGGACCUUACUG-CAUUUGCACACAUCAU
AAKN02048524.1/27402-27265 UGGGGGUCUGAGAAAGUGAGGCAGCUCU-GCACCAUGCUGCCUUCCACCGGUUAAGGCCUCCGACAGCAAACGGUUGCCCAGGCAGAGAAUGUCC-CUUUGCUACCCUCA------GAGGGACAGCACUG-UCUUGGUCAACAUUUA
AAGV020489675.1/4828-4964  UGGAGGACUGAGAAGGUGAGGCAGAUCU-GUACCAUGCUGCUUUCCACUGGUUAAGACCUCCCAGAGUGAAGGG-UGCCAAGGCAGAGGAUGUCC-CUCUGCCACCCUUG------GAGGGGCAGCACUG-UGCUGGCCAACAUUUG
AAWR02003118.1/1523-1660   UGGAGGACUGAGAAGGUGAGGCAGUCCU-GUACCGUGCUGCCUUCUACCGGUUAAGACCUCCGAGAGUGAAGGCCUGCCGAGGCAGAGGAUGUCC-CUCUGCCGCCCUCG------GAGGGGCAGCCCUG-UGCUGGCCGACAUUUG
AAEX03002137.1/5220-5357   CGGAGGACUGAGAAGGUGAGGCAGCCCA-GUGCUGUGCUGUCUUCCACCGGUUAAGACCUCCGAGAGUGAAGGCCUGCCAAGGCGGAGGAUGUCC-CUCUGCCACCCUUG------GAGGGGCAGUGCUG-UGCUGGCCAACAUUUA
AAWZ02003636.1/38036-37905 CGGAGGACUGAGAAAAUAAGGCAGUUG----CACGUACUGCAUU-UAUUGGUUAUCACCUCCAAAAUCAAAAUGGUGCAAACGCAAAUCAUGUUC-CU---UUGACCAUA------UAGGAAUAUGGCUGCUGGUUGCAUAUACAGU
AAQR03040110.1/22717-22580 UGGAGGACUGAGAAAGUGAGGCAGUUCU-GUACCAUGCUGCCUUCCACUGGUUAAGACCUCCGAAAGUGAACGGCUGCCCAGGCCGAGCAUGUCC-CUCUGCCACCCUCG------GAGGGGCAGCGCUA-UGCUGGCCAACAGUUG
AABR05079405.1/10776-10913 UGGAGGACAGAGAAGGUGGAGCAGUUC--AUACCGUGCUGCCUUCCAUUGGUUAAGACCUCCAACAGUAAAGGGCUAGCCAGGCAAAGAACAUCCUCUCCAGCGCCCUGG------AGGGGGCAGUACUG-UGCUGGCCCACAUUGU
AC202792.4/210215-210344   UGGAGGACUGAGAAGGUAAGACAGUUUUAACUUGGUACUGUAUCUUACUGGUUAUGGCCUCCGAAAUUAUAAGGGUGCAAUGGCA----AUUCAU-GUUUCCCUCCCGAC------AUGAGGGAAAGCGA-U----GCUG-CAUUUG
AAPE02000689.1/28882-29019 CGGAGGACUGAGAAGGUGGGGCAGUUCU-GUACCAUGCUGCCUUCCACUGGUUAAGACCUCCAAGAGCAAAGGCCUACCAAGGUAGAAGAUGUCC-CUCUGUCACCUGUA------GAGGGGCAGCACUG-AGCUGGCCGACAUUUG
AAGW02003014.1/18596-18463 UGGAGGACUGAGAAGGUGA-GCAGCGC--CUGCCAUGCUGCCUCCCACCGGUAAGGACCUCCAACAGCAAAGGGCUGCCU-GGCAGAGGCCGCCC-CUCUGCCACCUCCG------G-GGGGCAGCGCUG-CGCCAGCCCACAGUCU
#=GC SS_cons               :<<<<<--------<<<<<<<<<<<___._______>>>>>>>-->>>>-------->>>>>-------------------<<<--<<-<<<---.--<<<<<-<<____......__>>>>>>>--->>.>->>->>>::::::::
#=GC RF                    UGGAGGACUGAGAAgGUGagGCAGcUcu.guaccaUgCUGCcuUcCACcGGUUAagACCUCCaAaAguaAAgGgcUGCcaAgGCAgagaacgUcC.cUcugccaCCcuua......gAGGggcagcaCug.uGcugGCcgACAUUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01235
#=GF ID   snR68
#=GF DE   Small nucleolar RNA snR68
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   128.50
#=GF NC   45.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00079
#=GF DR   snornadb; snR68;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10547039
#=GF RT   Structure and biogenesis of small nucleolar RNAs acting as guides for
#=GF RT   ribosomal RNA modification.
#=GF RA   Filipowicz W, Pelczar P, Pogacic V, Dragon F
#=GF RL   Acta Biochim Pol. 1999;46:377-389.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


Z38059.1/58140-58275       UAUCAUGAUGAGCAUUU-AUUUUACUGCGUUAUCGUAUUGACGGGGG-CUGUUUAAGUACAGU-CUGUUUUAUAAUCUAUAUUCAUUUAUAUUUUAUAUUUCUUACCGAGGAAAUUGACUCUUAACAGAUUUGCUGAAA
AABY01000004.1/79246-79110 UACCAUGAUGAGCAUUU-AUUUUACUGCGUUAUCGUAUUGAUGGGGG-CUGUUUAAGUACAGUGUUGUUCUAUAAUCUAUAUUCAUUUAUAUUUUAUAUUUCUUACCAAGGAAAUUGACUUUUAACAGAUUUGCUGAAA
AACI02000464.1/2130-2267   UAUCAUGAUGAGCAUUUUAUUU-ACUGCGUUAUCGUAUUGACGGGGGACUGUUUUAUUACAGUCUUGCUUUAUAAUCUAUAUUCAUUUAUAUUUUAUAUUUCUUACCGAGGAAAUUGACUUCUAACAGAUUUGCUGAAA
AACH01000600.1/2227-2363   UAUCAUGAUGAGCAUUUUAUUUUACUGCGUUAUCGUAUUGACGGGGG-CUGUUUAAGUACAGCUUUGCUUUAUAAUCUAUAUUCAUUUAUAUUUUAUAUU-CUUACCAAGGAAAUUGAAUUUUAACAGAUUUGCUGAAA
AF064280.1/1-136           UAUCAUGAUGAGCAUUU-AUUUUACUGCGUUAUCGUAUUGACGGGGG-CUGUUUAAGUACAGU-CUGUUUUAUAAUCUAUAUUCAUUUAUAUUUUAUAUUUCUUACCGAGGAAAUUGACUCUUAACAGAUUUGCUGAAA
#=GC SS_cons               ::::::::[-[[[[,,,.,,,,,,<<-<<<<<______>>>>>->>,.(((((--(((-(((,,,,,,,,<<<<<--<<<<______>>>>-->>>>><<<<<<____>>>>>>))))))---))))),,,]]]]-]::
#=GC RF                    UAuCAUGAuGaGCaUUU.AUUUUACuGCGuuaUCGUAUugaCGGgGG.CuGuuUaaguACaguuuUGuUuuauaaUCuauaUUCAUUuauaUUuuauauuuCuuACCgagGaaauuGacuuuUaaCaGAUUuGCuGaAA
//
# STOCKHOLM 1.0

#=GF AC   RF01236
#=GF ID   snoU19
#=GF DE   Small nucleolar RNA U19
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.30
#=GF NC   42.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300151;
#=GF RN   [1]
#=GF RM   12477388
#=GF RT   Experimental RNomics: identification of 140 candidates for small
#=GF RT   non-messenger RNAs in the plant Arabidopsis thaliana.
#=GF RA   Marker C, Zemann A, Terhorst T, Kiefmann M, Kastenmayer JP, Green P,
#=GF RA   Bachellerie JP, Brosius J, Huttenhofer A
#=GF RL   Curr Biol. 2002;12:2002-2013.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ505662.1/1-144             AUCUGGCUUAGUUAGGAGGCAUAAAUCAAUC----UUGAUCAUCAAUACUUUACUGUAUUGUAUUGAUCUAUUUGACUUGAGGUCUUUUUGAGGAGGAGCUUUGCUUCUGCUAAGUAUCAAGCUUCUCCCAAGCAGCCUCAGACAUAU
AARH01005662.1/240390-240253 AGCUGGCUUAGUUAGGAGGCAGAAAUCAAAU----UAGAUCGAAAGAUGUUU----UGUCU--UCGGUCGUUUCAAUCUAAGGCCCGUUUGAGGGGACAAUUUUGCUCUUUUCAUUACCAGUUGUCCUCCAAGCAGCCUUUGACAUUC
AM466283.1/77958-77813       AUUUGGCUUAGUUAGGAGGCACAAAUCAAAACAUAUGGAUCAAAAGUAUCUUAGAUUGAUGCCUUGAUC-UUAAAAACUAAGGUCUUUUUGAGUGGACUCUCUUGUUACUUUC-CCAUCAAUUGUCCUUCAAGCAGCCUUAGACAUUC
#=GC SS_cons                 :::<<-<<<______>>>->>,,,,,,,,,,....,,<<<<<---<<<<<_______>>>>>-->>>>>--------<<<<<<<---<<<<-<<<<<<<<<___________________>>>>>>>>>>>>>-->>>>>>>::::::
#=GC RF                      AucUGGCUuAGUUAGgAGGCAuAAAUCAAau....UaGauCgaaAgcaccUUAguuUggugcaUcGauCuuUuuaAucugaGGcCuuuUUGAGggGacgcuuUuguUcuuuUcAuuAuCAagcguCccCCAAgCAgCCucagACAUuc
//
# STOCKHOLM 1.0

#=GF AC   RF01237
#=GF ID   snR161
#=GF DE   Small nucleolar RNA snR161
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   54.90
#=GF NC   45.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00036
#=GF DR   snornadb; snR161;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300048;
#=GF RN   [1]
#=GF RM   15306656
#=GF RT   Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the
#=GF RT   Saccharomyces cerevisiae genome.
#=GF RA   Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM
#=GF RL   Nucleic Acids Res. 2004;32:4281-4296.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   10


Z35905.1/390-230             UAAAUAUACAACAC----CCAGUAUUUUUGGCUGCCCGUG-UCUUUCUCUACCACGGGUAGUCUCUCUAAGCUGGCAGAUAGAUG--------------UUUAUUGAACCGCUUAAGUUCCGUUGUGA-AGUUUUCGUCUUUC--AGGCUGUAUUU-CAUAACACUACUGUAGUUCACACAUAC
AY737251.1/371-211           UAAAAAUACAACAC----CCAGUAUUUUUGGCUGCCCGCG-UAUUUCUCACCUACGGUUAGUCUCUCUAAGCUGGCAGAUAGAUG--------------UUUAAUGAACCACUUAAGUUCCGUUGUGA-AGUUUUUAGCCUUU--CAGGUGUAUUU-CAUAACACUACUGUAGUUCACACAUAC
AABZ01000048.1/20077-20240   GUAAAAUACAACAC----CCAGUAUUUUUGGCUGCUCGCG-UAUCUCCCACUCAUGGGUAGUCUCUCUAAGCUGGUAGAUAGAUAU-------------UUUAAUGAACCACUUAAGUUCCGUUGUGA-AGUUUCUCGUCUCUUUAGGCUGUAUUU-CAUGACACUACUGUAGUUCACACAUAU
AACI02000039.1/22783-22621   UAAAAUACAAACAC----CCAGUAUUUUCGGCCACCCGCG-UAUCACUCACCCGUUGGUGGCCUCUCUAAGCUGGCAGAUAGACG--------------UUCAAUGAACCACUUAAGUUCCGUUGUGA-AGUUGUUAGUCUUUAAAGACUGUAUUU-CAUGACACUACUGUAGUUCGCACACAC
AACA01000196.1/11253-11093   GUAAAGUAUAAC-C----CCAGUAUCAUUGACUGCCCGCG-CAACAAUCACUCGCGGAUGGUCACUCUAAGCUGGCAGAUAGACGU-------------CUCGAUGAACCACUUAAGUUCCGUUGUGA-AGUUUUUGCCCUUC--AGGCUGUAUUU-CAUGACACUACUGUAGUUCACACACCC
AADM01000270.1/138465-138625 ACAUACCAAACAAG----CCAGUAUCAUUGGCUGUCUGCG-UAUCCCCAACUCACAGACGGUCUCUCUAAGCUGGUAGAUCGAAAACCU----------AAAUACGAACAACUUAAGUUCUGUCGUAGUGGCUCCUAA---UA--U--CCAAGCCC-UAUGACACUAUUGUGGUUCAAACAGCU
AAZN01000162.1/50026-50186   UUAAUUAGCAACAC----CCAGUAUCAUUGGCUGUUUUAA-UUUCACCAACAUCAUAACGGUCUCUUUAAUCUGGCAGAUAAAAUAUUUUUA-------AUUAUUGGACGACUUAAGUUCCGCUGUUG-AAUUUA---GUUGU--AAU----GUUC-AUUAGCUUUACUGUUGUCUAUACAUCC
CR382122.1/609777-609614     CAAGUAAAAAUCAA----CCAGUAUAUUUGGCUGGCCAAGGCAUCUUCAACUCUUGGCUAGUCUCUCUAAGCUGGGAGAAUAAAUCUUAUC--------AGUCUUGAACAAUUUAAGUUCUGUUAUCC-GAUCUUCAA-------AAAUUAUAUCGAUAUAACCCUAUCGUUGUUCAAACAAAU
AACE03000004.1/345368-345208 AAACAAAAAAUUAA----CCAGUAUCAUUGGCUGCCUGUA-GAUCACCAACAUACGGGCGGUCCCUCUAAGCUGGAAGAAGAAACCUUUC---------UUAUUAGAACAGCCUAAGUUCUGUCGUGC-GAA---CCAGUCCC--AACACG-UUC--CAUGACACUAAUGUCGUUCUAACAAUA
AE016814.2/677544-677375     UAAAACUACAAAACUUGACCAGUAUCAUUGGCUGUCUGGG-UAUCACUUACAUCCGGACGGUCUCUCUAAGCUGGGAGAUAGAUCCCCGCCAAACUUUUGGCGGAGAGCAAUCUAAGUUCUGUUGC-----UUGUGAGGCCUC---ACCUCCA-----GCAACACUAAUGUUGCUCGCACAUUU
#=GC SS_cons                 ::::::::::::::....<<<<<-------<<<<<<<<<<.___________>>>>>>>>>>-------->>>>>--------------..........-----<<<<<-<<---------<<<<<<<.<<<---<<-<<___.._>>->>->>>>.>>>>>>------>>->>>>>:::::::
#=GC RF                      uaAaaauAaAacAc....CCAGuAUcaUUGgCugcCcgcg.uAUCaCuaACucgcgGgcaGuCUCUCUAAgCUGGuAGAUagAaucuuu..........uuuaauGaaCaaCUUAAGUUCuGuugugg.gguUuucaagcuuu..Agccuguaccc.cauaaCACUAcUGuuGuuCacACAuau
//
# STOCKHOLM 1.0

#=GF AC   RF01238
#=GF ID   snR70
#=GF DE   Small nucleolar RNA snR70
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   55.00
#=GF TC   55.40
#=GF NC   53.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00059
#=GF DR   snornadb; snR70;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300058;
#=GF RN   [1]
#=GF RM   10547039
#=GF RT   Structure and biogenesis of small nucleolar RNAs acting as guides for
#=GF RT   ribosomal RNA modification.
#=GF RA   Filipowicz W, Pelczar P, Pogacic V, Dragon F
#=GF RL   Acta Biochim Pol. 1999;46:377-389.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   9


U51033.2/34867-34704       UGAUAUGAUGAUU--UGUUGUCGACCGGGCGGACAUA--UUAGUAUCUGUUAAAGGGUCGCC-GUCUACUC-UCAUCGUUCUUUU-GUGUACAAAUUUUUUAAAGGAGCGAUGUUGAUGGCAUUAUGGUUCUUUAGUGGAGAAUUGAUGAUUGGUCACAAGACAUCUGAUU
AABY01000114.1/30471-30635 UAAUAUGAUGAUU--UGUUGUCGACCGGGCGGACAUA--UUAGUAUCUGCUAAAGGAUCGCC-AUCUACUUCGCAUCGUUCUUUU-GUGUACAAAUUUUUUAAAGGAGCGGUGUUGAUGGCAUUACGGUUCUCUAGUGGAGAAUUGAUGAUUGGUCACAAGACAUCUGAUU
AACI02000085.1/17022-16859 UAAUAUGAUGAUU--UGUUGUCGACCGGGCGGACAUA--UUAGUAUCUGUUGAGGAAUCGUC-AUCUACUACGCAUCGUUCUUUU-GUGUACAAAUUUUU-AAAGGAGCGGUGUUGAUGGCAUUAUGGUUCUAAAGUGGAGAAUUGAUGAUUGGUCACAAGACAUCUGAUU
AACH01001819.1/243-406     CAAUAUGAUGAUU--UGUUGUCGACCGGGCGGACAUA--UUAGUAUCUGCUGGAGAACCGCC-AUCUACUUUGCAUCGUUCUUUU-GUGUACAAAUUUUU-AAAGGAGCGGUGUUGAUGGCACUACGGUUUUUUGGUGGAGAAUUGAUGAUUGGUCACAAGACAUCUGAUU
AACG02000032.1/77562-77719 CAAUAUGAUGAUU--UGUUGUCGACCGGGCGGACAUA--UUAGUAUCUGCUAGAGAGCCGCC-AUCUACUC-GCAUCGUUC---U-GUGUACAAAUUUUU-AA--GAGCGGUGUUGAUGGCACUACGGUUCUUUGGUAGAGAAUUGAUGAUUGGUCACAAGACAUCUGAUU
AACF01000016.1/90047-90207 UUAAAUGAUGAUU--AUUUAUCGACCGGGCGGACAUA--UUAGUAUCAUCGAAGGAAUAGCU-GGGCAUUG-UUAUCUUUCUUUU-GUGUACAAAUUUUA-AAAGGAAAGGUAGCU-UAGCA-UAUUGUUUCUUUGUUGAGAAUUGAUGAUUGGUCUCAAGAUAGCUGACU
AAZN01000219.1/33176-33012 AAAUGUGAUGAUU--UGUUGUCGACCGGGCGGACAUA--UUAGUAUCUUAGGUAAGGUAGUU-UUACAAUUUAAGUUUCCCUUUCAGUGUACAAAUUUUUUGAAGGGGGGAUGGUAA-AACAUCAUUAUCUUAUCUUUGAGAAUUGAUGAUUGGUCACAAGAUAUCUGAUU
CR380957.2/800407-800238   AAAUAUGAUGAUUAUUUUUGUCGACCGGGCGGACAUAGUUUAGUAUCUGUUGGGUGGUAGCUGUUGCAAUUUAAGUUCUCUUCUU-GUGUACAAAUUUUUAAAGAGGAGGAUGGCAGUGGCAUUAUUAUCACCUGGCAGAGAAUGGAUGAUUGGUCACAAGAUAGCUGAUU
AF064282.1/1-164           UGAUAUGAUGAUU--UGUUGUCGACCGGGCGGACAUA--UUAGUAUCUGUUAAAGGGUCGCC-GUCUACUC-UCAUCGUUCUUUU-GUGUACAAAUUUUUUAAAGGAGCGAUGUUGAUGGCAUUAUGGUUCUUUAGUGGAGAAUUGAUGAUUGGUCACAAGACAUCUGAUU
#=GC SS_cons               ::::::<<<<---..--<<<<-<<<<<--------<<..<<<<<-<<<-<<<<<<<<<<<<<.<<<------<<<<<<<<<<<<<._______________>>>>>>>>>>>>>->>>>>>----->>>>>>>>>>->>>-->>>>>>>-->>>>>>>>>-->>>>:::::
#=GC RF                    uaAUAUGaugAUU..UguuGuCGaCCgGGCGGACAua..uuaguAuCcgccaggggaccGcc.gucuAcUuugcaucgccccuuu.GUGUACAAAUUUUUuaaaggggcgaugcugacggCAuUAugguccccuggUgGaGAauugaugAUuGGuCaCaaGAcauCUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01239
#=GF ID   snR49
#=GF DE   Small nucleolar RNA snR49
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.80
#=GF NC   42.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00038
#=GF DR   snornadb; snR49;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300010;
#=GF RN   [1]
#=GF RM   15306656
#=GF RT   Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the
#=GF RT   Saccharomyces cerevisiae genome.
#=GF RA   Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM
#=GF RL   Nucleic Acids Res. 2004;32:4281-4296.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


Z71666.1/727-896           AUGGGACUUUAUCUCCAUGACUAUGCCAUUUCUAGGUAGCCUAUGGUAAACGAAUCCCGUAGAUUA---------UUC-AC-ACGU--UUGUUGUCUUUGUUGACAACAACA-CAGAGUAAGAAAAAGCAAA-AGA--UUUAUCUCUUUU--GUCCAUCUUUUUUUUAUUUUGAAGGCGUGUAACAUUU
AACA01000197.1/7672-7842   AUGGGAAUUUAUCUCCAUGACUAUGCCAUUUCUAGGUAGUCUAUGGUAAACAGCUCCCGUAAAUUA---------UCC-ACCACGU--UUGUUGUCUUAAUCGACAGCAACA-CAGAGUAAGAAGAAGCAAA-AGA--UUUAUUUCUUUU--CUCCAUCUUUUUUUUAUUUUGAAGGCGUGUAACAUCU
AACI02000264.1/1524-1695   AUGGGACUUUAUCUCCAUGACUAUGCCAUUUCUAGGUAGUCUAUGGUAAACGACUCCCGUAAAUUA---------UCC-AC-ACGU--UUGUUGUCUUAACUGACAGCAACA-CAGAGUAAGAAGAAGUGAA-AGAGAUUUAUCCCUUUC--GCCCAUCUUUUUUUUAUUUUGAAGGCGUGUAACAUCU
AACH01000736.1/1244-1414   GUGGGACUUUAUCUCCAUGACUAUGCCAUUUCUAGGUAGUCUAUGGUAAACGAAUCCCGUAGAUUA---------UCC-AC-ACGU--UUGUUGCCUUAAUUGACAACAACA-CAGAGUAAGAAGAAGGGAAGAAU--UUUUUUUCUUUC--GUCCAUCUUCUUUUUAUUUUGAAGGCGUGUAACAUCU
AACF01000082.1/45350-45178 AUGGGAUUUUAUCACCAUGUCUAUGCCAUCUCUAGGUAGAUUAUGGUAAACGAAUCCCAGAGACUA---------GCAUAC-ACGUUAGUCCUGUCCGUGAGGAUGGGACGACCAGAGUGACACGGGAAUGA-ACU--UCUA---GUUCGCAUACCCAUCCCGUUGCAUUUUGAAGCCGUGUGACAUUC
AAZN01000146.1/7292-7465   UUGGGACUUUAUCUCCAUAGCUAUGACGAGUACAGGUAGUU-GUGGUAAACGAAUCCCAGAUAUUAGAAUUCAUUUCU-AC-GCGU--UAUUGUAUCUUUG-AUGCAAUAAA-CAGAGUGUUAAGA---ACA-ACU--UUUAGUUAUUUU--AUUCAACUUCUUUGCAUUUUGAAGACGUGUUACAUUA
#=GC SS_cons               <<<<<<--------<<<<<<<<<--<<_______>>>>>>>->>>>-------->>>>>>------.........---.((.((((..<<<<<<<<______>>>>>>>>,,.,,,,<<<<<<<<<<<-<<<.<<_.._______>>>>>..------>>>>>>>>>>>,,,,,,,)))))):::::::
#=GC RF                    guGGGacUUUAUCuCCauggCuaUGcCAuuUcUAGguaGccUauGGUAAACGAauCCCacAaAUUA.........uCc.aC.aCGc..uugcugucuuuauugacagcaaaA.CAGAgugagaagaggagga.agu..UUUAuuUcuucc..aucCAuccucuucucauUUUGAAGgCGuGuaACAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01240
#=GF ID   snR85
#=GF DE   Small nucleolar RNA snR85
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.90
#=GF NC   36.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00024
#=GF DR   snornadb; snR85;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15306656
#=GF RT   Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the
#=GF RT   Saccharomyces cerevisiae genome.
#=GF RA   Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM
#=GF RL   Nucleic Acids Res. 2004;32:4281-4296.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


X80835.1/7645-7470         UACUAGCACAUAUGUCAAAUUCCUAAUUAACGUU----U-----UUUAUAUUCAUCGUUUCUUAGAGCCGUAAUUGUGCUGAUAUCAAU-AUCAGGGAAGAACAUACCAUAUAGAGGUGUCAAGUACACCGAACGAUCGUGGU-GCUCCCUCAGCCACGGGCGUGCUUGGACGCUAUUCCCACAUAU
AABY01000008.1/67645-67824 UAUUAGCACAUAUGUCAAAUUCCUAAUUAACGUUUAAUU-----UUUAUACCCAUCGUUUCUUAGAGCCGUAAUUGUGCUGAUAUCAAA-ACCAGGGAAGAACCUACCAUAUAGAAGUGCUAAAUGCACUUAACGAUCGCGGC-GCCUCCUCGGCCACGGGCGUGUUUGGACACUAUUCCCACAUAU
AACH01000096.1/3948-3770   UACUAGCACAUAUGUCAAAUUCCUAAUUAACGUUUUAUU-----UUUAUAUCCAUCGUUUCUUAGAGCCGUAAUUGUGCUGAUAUCAUA-UCCAGGGAAGAACCUACCAAUAAAAGUUGCCAAGUGCAAUG-ACGCUCGCGGC-GUCUCCUAGGCCAUGGGCGUGUUCGGAAACUACUCCCACAUAC
AACI02000115.1/14713-14893 CACUAGCACAUAUGUCAAAUUCCUAAUUAACGUU----UUAUUCUUUAUAUCCAUCGUUUCUUAGAGCCGUAAUUGUGCUGAUAUCAAU-ACCAGGGAAGGACACACAGCAAACAUUUGCUGGAUCCACGUCACACCCGUGGC-GACUUCUCGGCCACGGGCGUAUUUGGACCUUUUUCUCACAUAC
AACA01000849.1/94-274      CACUAGCACAUAUGUCAAAUUCCUAAUUAACGUUAUAUU-----UAU-UAUCCGUCGUUUCUUAGAGCCGUAAUUGUGCUGAUAUCAAACUCCAGGGAAGGACACACAGCAAGCGAUUGCUGGGCCCACCUCGCGCCCCUGGCAUCUUUCUCCGCCACGGGCGUGUCCGGGCCUUCUUCCCAUACCC
#=GC SS_cons               :::<<<<<<<------------<<<<--<<<<_______.....___________>>>>-->>>>--------->>>>>>>--------.----(((((-------(((,,,,,,<<<<<_____>>>>>,,<<<--<<-<<<._________>>>->>-->>>,,,)))------)))))::::::
#=GC RF                    uAcuaGCaCaUAUGUCAAAUUCCuaaUUaaCGUUuuAUU.....UuUAUAUcCAUCGuuUCuuaGAGCCGUAAUuGuGCugAUAUCAAa.acCAGGGaaGaACauACcguAaAaAgguGcuaagUgCaccuaaCGcuCguGGc.gcuUuCUcggCCAcGGGCGuGUUcgGAcauUauuCCCAcAUAc
//
# STOCKHOLM 1.0

#=GF AC   RF01241
#=GF ID   SNORA81
#=GF DE   Small nucleolar RNA SNORA81
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   46.40
#=GF NC   42.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; HBI-61;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   16361266
#=GF RT   A novel experimental approach for systematic identification of box H/ACA
#=GF RT   snoRNAs from eukaryotes.
#=GF RA   Gu AD, Zhou H, Yu CH, Qu LH
#=GF RL   Nucleic Acids Res. 2005;33:e194.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   28


AC112907.7/62863-62686     ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUGCA---GACACUAGGACCAUGUCUUGGUUUUUGCAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAAAG----UAA--CAGCACUAGAUUGU-AAA-GACUGGGGUGGA--CCUCUUUCUUAAUGUCCAAUGUCCUUUGUCUUAAGA-UUUGGUGCAAUAUCU
ABDC01304434.1/1589-1766   ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUACA---GAAACUAGGACCAUGUCUUGGUUUUUGUAAUAAUGCUAGCAGAGUAC-ACACAGGAAGAAAAG----UAA--CUGCACUGGAUUGU-AAA-GACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUUUGUCUUAAGA-UUCGGUGCAAUAUAU
AALT01246665.1/603-780     ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUGCA---GAAACCAGGAAUACAUCUUGGUUUUUGCAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAAAG----UAA--CUGCACUAGAUUGAAUUG--ACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUUUGUCUUAAGA-UCUGGUGCAAUAUGU
DQ351284.1/3156-3333       ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUACA---GAAACUAGGAUCACAUCUUGGUUUUUGUAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAGAG----UAA--CUGCACUAGAUUGUAAAG--ACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUUUGUCUUAACG-UUUGGUGCCAUAUAU
AAYZ01178903.1/11910-11732 ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUACA---GAAACUGGGACCAUGUCUUGGUUUCUGUAAUAAUGCUAGCAGAGUAC-ACACAGGAAGAAAAG----CAA--CUGCACUAGAUUUUGAAA-GACUGGGGUGGA--CCUCUUUCUUAAUGUCCAAUGUCCUUUGUCUUAAAA-UCUGGUGCAAUAUGU
CAAA01081857.1/4337-4160   ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUGCA---GGAACUAAGAUUCUAUCUUGGUUUUUGUAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAAAG----UAA--CUGCACUGGAUUGCAAAG--ACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUAUGUCAUAAGA-UUCGGUGCAAUAAGU
AAQQ01260144.1/2844-3023   ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUGCA---GAAGCUAGGAUCAUAUCUUGGUUUUUGCAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAAAU----UAA--CUGCACUGUAUCCUAAAAAGACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUUUGUCUUAAGA-UUUGGUGCAACAUAU
AANU01260585.1/21240-21063 ACUUUAUUGUAUA--AACACUGUGCUAAAAUGGCA---GAAACUAGGACCAUAUCUUGGUUUUUGUAAUAAUGCCAGCAGAGUAU-ACACAAGAAGAAAAG----UAA--CUGCACUAGAUUGU-GAA-GACUGGGGUGGA--CCUGCUUCUUAAUGCCCAGUGCCCUUUGUCUUAAGA-UUUGGUGUAGUAUAU
AAFC03092164.1/72731-72907 ACCUUCUUGU--AUAAGCACUGUGCUAAAAUUACA---GAAACCAAGAU--AGCCUUGGUUUUUGUAAUAAUGCUAGCAGAGUAUUACACAAGAAGAAGAG----GAA--CUGCACUAGAUU--GUAAAGACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUUUGUCUUAAGA-UUUGGUGCAAUAUGU
AANN01199082.1/1089-1266   GCCUUCUUGUAUA--AGCACUGUGCUAAAAUUACA---GAAACUUUGAUUUCAUCUUGGUUUUUGUAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAAAG----UA---CUGCACUAAAUUAGAAAA-GACUAGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUUUGUCUUAAGA-UUUGGUGCAAUACUG
AAIY01159036.1/14517-14337 UCCUUCUUGUAUA--AGCACUGUGCUAAAAUUACA---GAAACUGGGGCACUGUCUUGGUUUUUGUAAUAAUGCUAGCAGAGUAC-ACACAGGAAGGAAAU----UGAAACUGCACCCGGUCUGGAAA-GACUGGGGCGGA--CCUCUUUCUUAAUGUCCAAUGUCCUUCGUCUUAAGA-UUUGGUGCGAUAAAU
AAHX01072068.1/2687-2507   ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUGCA---GAAACUAGGAUUAUGUCUUGGUUUUUGUAAUAAUGCUAGCAGACUGC-ACACAAGAAGAAGAGUAAUUAA--CUGCUCUGGGUUCCAAAA--ACUGGG-UGGA--CCUCUUUCCUAAGGUCCAGUGUCCUUUGUCAUAAGA-UUCGGGGCAAUAAGU
AADA01184916.1/1518-1342   ACUUUAUUGUAUAUAAGCACUGUGCUAAAGUUGCA---GGAACUGGGACCAUAUCUUGAUUUUUGUAAUAAUGCCAGCAGAGUAC-ACACAAGA---AAAG----UAA--CUGCACUAGAUUGU-GAA-GACUGGGGUGGA--CUUGCUUCUGAAGGUCCAGUGCCCUUUGUCUUAAGA-UUUGGUGUAGUGUAU
AAFR03036229.1/2466-2648   ACCUUCUUGUUUCAAAGCACUGUGCUAAAAUUGCA---AAAAUUAAGGCAAUGCCUUGGUCUUUGUAAUAAUGCUAGCACAGUAU-AUACAAGAAGAAGAA----CAA--AUGCACUAGAUCGAAAAAAGACUUGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUGUGUCUUAAGAUCCUAGUGCGAUAUCU
AANG01283486.1/3720-3559   ACCUUCCUUCAUAUAAGCACUGUGUCAAAACUGCG---GAAACUAGGAUCACAUCUUGGUUUUUGUAAUAAUGUUGGCAGAGUA---CACAC---------------A--CUGCACUAGAUUGU-GAA-GACUUGGGGGGGGGCCUCUCUCUUAAUGUCC-------UUCAUCUCAAGA-UUUGAUGCAGUAUGU
AAGV020221721.1/2036-2213  ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUGCA---GAAACUAAGAUUAUUUCUUAGUUUCUGUAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAAAG----UAA--CUGCACUAGAUUGUAAAG--ACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUUUGUCUUAAGA-UUUGGUGCAAUAUGU
AAWR02011630.1/19855-20032 ACCUUCUUAUUUA--GGCUCUGAGCUGAAAUUGCA---GAAACUCU-AUCAUAUCUUAGUCUUUGUAAUAAAGCUAGCAGAGUAA-ACACAGGAAGAGAGG----CAA--CUCUCCCAGGUAGUAGAAAAACUGAGAUGAA--CCUCUUUCUGAA-GUGCGGGCUACUUCAUUCUAAGA-UUUGGUACAAUAAUA
AAKN02012344.1/12135-12312 ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUGCA---GAAACUAGGAUCAUGUCUUGGUUUUUGUAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAAAG----UAA--CUGCACUAGACCCUAAA--GACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUUUGUCUUAAGG-UUUGGUGCAAUAUGU
AAGW02010594.1/2355-2526   ----GCCAAGGUA--AA-AGUGUAUUAAGAUGGAAAGGGAAACUAGGACCAUGACGUGGUUUUUGUAAGAAUGCUAGCAGGGUAC-ACACAAGAAGAG-------UAA--UUGCACUGGAUUAGAAAU--ACUGGGGUGGG--CCUCUUUU-UAAUGUCCAGUGUCCUUUGUCUUAACA-UUUGGUGCAAUGUGU
EU240324.1/1-181           ACCUUCUUGU--CAAAGCACUGUGCUAAAAUUACA---GAAGCUGAGGCUGAGCUUUGGGUUCUGUAAUAAUGCUAGUAGAGUAC-ACGCAAGAAGAAGAA----AAAGGAUGCUCUGGAUC-GAAAAUGACCGGGGUGGA--CCUCUUUCUUAAUGUCCGUUGUCCUGUGUCAGAAGA-UCCGGUGCAACAGUU
AAGU03048771.1/3050-3227   UCCUUCUUGUAUA--AGCACUGUGCUAAAAUUACA---GAAACGAGGACUGUGUCUUGGUUUUUGUAAUAAUGCUAGCAGAGUAC-ACACAGGAAGAAAAG----U--AACUGCACUAGAUC-GGAAA-GACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUUUGUCUUAAGA-UUGGGUGCGAUAAAA
AAWZ02024796.1/52852-52674 CACUUCUUGU--ACAAGCACUGUGCUAAAACUAUG---GAAGUCGGGGUUCUGCCUCUUCCUCUGUAGUAAUGCUAGCAUGGUAC-ACACGAGAAGAAAAG----UAA--AUGCACUGGAUCUGUAAAAGACUAGGGUGGA--CCUCUUUCUUAAUGUUCAGUGUCCUG-GUCUGGAGA-CUUGGUGCAACACUA
AAEX03017258.1/19485-19305 ACCUUCUUUUGUAUAAGCAUUGCGCUAAAAUCGCA---GAAACCGGGAUCAUACCUUGGUUUCUGUAAUGAUGUUAGCAGACUA--ACAUAAGAAGAAAAG----UAA--CUGCAUUAGAGUCU-AAA-GACUGGAGUGAACCUCUCUCUCUUAGUGUCCAGUGUCCUUUGUCUUAAGG-CAUGAUGCACUAUGU
AAPE02024657.1/36263-36440 ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUGCA---GAAACUAGGAUCACAUCUUGGUUUUUGUAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAAAG----UAA--CUGCACUAGAUGAUAAA--GACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUUUGUCUUAAAA-UUUGGUGCAUCAUGU
AF357409.1/1-164           ----------------GCACUGUGCUAAAAUUGCA---GGAACUAAGAUUCUAUCUUGGUUUUUGUAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAAAG----UAA--CUGCACUGGAUUGC-AAA-GACUGGGGUGGA--CCUCUUUCUUAAUGUCCAGUGUCCUAUGUCAUAAGA-UUCGGUGCAAUAAGU
AM055745.1/1-178           ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUGCA---GACACUAGGACCAUGUCUUGGUUUUUGCAAUAAUGCUUGCAGAGUAC-ACACAAGAAGAAAAG----UAA--CAGCACUAGAUUGU-AAA-GACUGGGGUGGA--CCUCUUUCUUAAUGUCCAAUGUCCUUUGUCUUAAGA-UUUGGUGCAAUAUCU
FJ915993.1/2-179           ACCUUCUUGUAUA--AGCACUGUGCUAAAAUUGCA---GACACUAGGACUAUGUCUUGGUUUUUGCAAUAAUGCUAGCAGAGUAC-ACACAAGAAGAAAAG----UAA--CAGCACUAGAUUGU-AAA-GACUGGGAUGGA--CCUCUUUCUUAAUGUCCAAUGUCCUUUGUCUUAAGA-UUUGGUGCAAUAUCU
L22740.1/5-73              A---------------------------------------------------------------------------------CA----------------------------GCACUAGAUG---UAA-GACUGGGU--GA--CCUCUU--CUAAUGUCCAAUGUCCUUUGUCUUAAGA-UUUGGUGCA------
#=GC SS_cons               :::::::::::::..::::<<-<<<<<--<<<<--...<<-<<<<<<<<___>>>>>>>>->>----->>>>-->>>>>->>---.---------------....---..-<<<<<<<<<--------.----<-<-<<<<..______________>>>>->->--------------.>>>>>>>>>::::::
#=GC RF                    ACCUUCUUgUaUA..AGCACuGuGCuaAAauugCA...gAAaccagGgcuaUgcCcugguUUcUGUAAcaauGCuaGCaGaGUAc.ACACAAGAAGAAAAG....uAA..cuGCaCuggaUuguaaAA.GACUgGgGuGga..CCUCUUUCUUAAUGucCaGuGuCCUUUGUCUUAAGA.uccgGuGCaAUAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF01242
#=GF ID   snR36
#=GF DE   Small nucleolar RNA snR36
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   43.00
#=GF TC   43.70
#=GF NC   40.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00035
#=GF DR   snornadb; snR36;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   7630735
#=GF RT   Characterization of three new snRNAs from Saccharomyces cerevisiae: snR34,
#=GF RT   snR35 and snR36.
#=GF RA   Samarsky DA, Balakin AG, Fournier MJ
#=GF RL   Nucleic Acids Res. 1995;23:2548-2554.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   10


Z75093.1/322-141             UUGCCCUGUGCCUCGCUCGGUUGU----UAAUUGCCA---AUAUU--ACGAUCUUGAGCUGGA-UGACAAAAAAAUAAAAAUACA--------UUUU-AUUUUU--UUGAUCAACGGGCUAAAACAA-------U--UAGACUUCU-UUGAGUACGAGGAUAUCGCUAUUUUUA-----UCUCACGGUAU-CGUA--UUGUAAUUAGAACGUCUCAUAUCA
AABY01000157.1/7666-7486     UUGCCCUGUACCUCGCUCGGUUGC----UAAUUGUCA---AUAUU--ACAAUCUUGAGCUGGA-UGACAGAAAUAUGAAAAUGAA--------UUUU-AU-UUU--CUGAUCAAUGGGCUAAAACAA-------C--UAGACUUCU-UUGAGUACGAGGAUAUCGCUAUUUCUU-----UCUCACGGUAU-CGUA--UUGUAAUUAGAAUGUCUCAUAUCA
AACH01000064.1/11375-11554   UUGCCCUGUUCCUCGCUCGGUUGU----UAAUUGUCA---AUAUU--ACAAUCUUGAGCUGGA-UGUCAGAGAAACGACAAUUAA--------CUUU--GUUUG--CUGAUCAAUGGGCUAUAAAAA-------C--UAGACUUCU-UUGAGUACGAGGAUACCAUUCUUUUU------UCUCACGGUAU-CGUA--UUGUAAUUAGAAUGUCUCAUAUUA
AACA01000382.1/3439-3617     CCGCCCUGUGCCUCGCUCGGUUGU----CAAUCGUCA---AUAUU--GCAAUCUUGAGCUGGA-UGAUCUAAGAAUGGCAAUGAA--------UUUU--GCUUU--CUGGUCAAUGGGCUAUAACAA-------C--UAGACUUCU-UUGAGUACGAGGAUAUCAUUAUUUUU-------CUCACGGUAU-CGUA--UUGUAAUUAGAAUGUCUCAUAUUA
AACI02000001.1/14209-14385   CUGCCCUGUGCCUCGCUCGAUUGG----UAAUUAUCA---AUAUU--ACAAUCUUGAGCUGGA-UGAUUGGAAAUGAAAAUAAAA--------UUUC----UUU--CUGAUCAAUGGGCUAUAGCAA-------C--UAGGCUUCU-UUGAGUACGAGGAUAUCAUUAGUUU-------UCUCACGAUAU-CGUA--UUGUAAUUAGAAUGUCUCACAUCA
AACF01000129.1/9129-8948     UUGCCCUGUGCCUCGCUCGGUUGA----AGUUUCUCUACCAUAUU--UCAAUCUUGAGCUGGA-UGAUUCGAAUUUUUCUUC-----------UGAA--AAUUU--CUUAUUAAUGGGCUAUAUUAA-------UGAUAAACUUCU-UUGAGUACGAAUGUAUCGCUUUUUU-------UUUCACGAUAUUAUUU--UUGUAAUUAGAACGUUUCACAUUC
AAZN01000268.1/54129-53930   UUGCCCUUUGCCUCGCUCGAUUUU----AAUCAUCCA---AUAUU--AGAAUCUUGAGCUGGAUGUCUAUGUUUUUUGAGAUAUA---CCAAUUUCG-AAAAAA--AUUAGAUAUGGGCUAUAAGAAACCACAAU--UAGACUUCU-UUGAGUACGAAGGUAUCGAUGAAUCUAUUCAUCUCGAUGGUAC-CCUACUUUGUAAUUAGAAGCUCUAACAU--
CR382123.1/461240-461047     ACGCCCUGUACCUCGCUCGGUUGA----ACGUACCUC---ACACU-UUCAAUCUUGAGCUGGA-UGGUUAAUGUUUGUUAUUCGACUACGAACCAACAAAACAUUUUUGACCAAUGGGCCAUAUCAA-------U--UUGACUUCUUUUGAGUACGAAAAGGCCUUUCUUUGA------AUCAAUGACCU-UAAA--CCGUAAUUAGAAGCUCACACACUC
AADM01000273.1/19677-19495   UUGCCCUGUGCCUCGCUCGGCUAG-----ACCUGUCA---GUGGU--UUAGUCUUGAGCUGGA-UGAUUGU----CUUCUCUUUA--------UGAG--CAGCA--CAA-UCAAUGGGCUAAAUUAAUCU----U--GCGACUUCUUUUGAGUACGAUUUUACCAGUAAGCUCAGCGCUGCAAAUGGUAA-ACCC---CGUAAUUGGAACGUCCAACACCU
AACE03000009.1/692100-692283 UUGCCCUGUGCCUCGCUCGGUUGUGUUCCUAUUUUUC---UGAUAAUGCAAUCUUGAGCUGGA-UGGUCCAAAGAUGUC--ACAA---------GAC--UCUUUAUGGGACCAAUGGGCUAUAGAAAUUU----U--UUGACUUCUUUUGAGUACGAAAUUACC----UUUUG------CUCCAUGGUU--UAUU--UCGUAAUUAGAAUGUCUUACAUUA
#=GC SS_cons                 ::((((,,,,<<--<<<<<<<<<<....-<<<_____...__>>>..>>>>>>-->>>>->>,.<<<<<<<<<<<-<<<<_____........>>>>..>>>>>..>>>->>>,,))))--------.......-..-<<<<<<<-.------<<<<-<<<<<<_________......______>>>>>.>---..>>>>----->>>->>>>:::::::
#=GC RF                      uUGCCCUGUgCCUCGCUCGguugc....aaguuuuca...auacu..gcaauCUUGAGCUGGA.uggccgaagguuggcgauaaA........cgcc..accuu..cggAccaAUGGGCUAuAauAA.......U..UaGaCUUCU.UUGAGUACgaagguacCauUauuUuu......uuucAuGguac.caua..ucGUAAUUAGAAuGuCucAcAUua
//
# STOCKHOLM 1.0

#=GF AC   RF01243
#=GF ID   snR33
#=GF DE   Small nucleolar RNA snR33
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   47.50
#=GF NC   42.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00027
#=GF DR   snornadb; snR33;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   8265354
#=GF RT   SnR31, snR32, and snR33: three novel, non-essential snRNAs from
#=GF RT   Saccharomyces cerevisiae.
#=GF RA   Balakin AG, Schneider GS, Corbett MS, Ni J, Fournier MJ
#=GF RL   Nucleic Acids Res. 1993;21:5391-5397.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


L22435.1/168-350           AAGCUUAAUGCCCUCUUUGUACGAUGGUGUCACUCUAAAAUUAU-UU-AGGUAAUUUAAUUGGAUGUGAUAUCAAGCACUAGUUUUGUUUGGAGGAGCAGAGAUUGAAAGCCUAGCUUUUACACCGGUUUGAGUCGGUUCCUUCGU---UUUCUUAGUUGGAAUUGAUAUAGAAGUGUGUGGACAAUC
AABY01000200.1/15394-15212 AAGCUUAAUGCCCUCUUUGCACAAUGGUGUCACUCUAAAAUUAU-UU-AUAUAGUUUAAUUGGACGUGAUAUCAAGCAUUAUUUUCGUUUGGAGGAGCAGAGAUUGAAAGCUUAGCUUUUACACCGGUUUGAGUCGGUUCCUUCGU---UUUCUUAGUCGGAAUUGAUAUAGAAGUGUGUGAACAAUU
AACI02000300.1/6456-6274   AAGCUUAAUGCCCUCUUUGUACG-CGAUGUCACUCUAAAGUUAU-UUUAUAUAACUUAGUUGGAUGUGAUAUCCAGCACUUUUUUCGUUUGGGAGAGCAGAGAUUGAAAGCCUAGCUUUUACACCAGUUUGAGUCGGUUCCUUCGU---UUUUUCAGUCGGAAUUGAUAUAGAAGUGUGUGAACAAUU
AABZ01000064.1/7080-7262   AAGCUUAAUGCCCUCUUUGUACAACGAUAUCACUCUGAAGUUAUAUU-AUAUAAUUUAGUUGGAUGUGAUAUCAAGCACUAUUUUUGUUAGGGGGAGCAGAGAUUGAAAGCGAAGCUUUUACACCAGUUUGAGUCGGUUCCUUCAU---UUU-UCAGUCGGAGUUGAUAUAGAAGUGUGUGAACAAUU
AACA01000006.1/53848-53662 AAGCUUCAUGCCCUCUUUGUACAGCGGUAUCACUCUAAAGUUAU-UUUAUAUAAUUUGGUUGGAUGUGAUAUCCAGCACUAUUUUUGUUUGGAGGAGCAGAGAUUGAAAGCCUAGCUUUUACACCGGUUUGAGUCGGUCCCUUCGUAUUUUUUUCAGUCGGGGUUGAUAUAGAAGUGUGUGAACAAUU
#=GC SS_cons               :::::::::::<<<<<---------<<<<<<<<<<<<<<<<<<<.__.__>>>>>>--->>>>>->>>>>>>>----------------->>>>>-----------------------<<<<<<--------<<<<<<<<<_____...__________>>>>>>>>>-------->>>>>>::::::
#=GC RF                    AAGCUUaAUGCCCuCuUUGUACaauGauauCaCuCuaaaguuau.UU.AuauaacuUAguugGaUGuGauauCaAGCAcUAuUUUuGUUugGaGGAGCAGAGAUUGAAAGCcuAGCUUuuaCaCCgGUUUGAguCgguuCCUUCgU...UUUuUuAGUcGGaauuGauAUAGAAGUGuGugaACAAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01244
#=GF ID   snR4
#=GF DE   Small nucleolar RNA snR4
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   37.00
#=GF TC   38.30
#=GF NC   35.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snornadb; snR4;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   8797828
#=GF RT   The RNA world of the nucleolus: two major families of small RNAs defined
#=GF RT   by different box elements with related functions.
#=GF RA   Balakin AG, Smith L, Fournier MJ
#=GF RL   Cell. 1996;86:823-834.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


U57010.1/1-186             AACUAUUACAGUCGAUGAGGAUAGGUUAUAGUUCAUGUGU-AACAUCUGUGUUUUAAAAUAACUCUAGUUAUCCGGGGCGUUUUUCAC-AAA-GUUUG--UGUAAGAUGCU-UUCCUGGGUCGAUGUGGAUUGUGCCGUGGCCUUUUUCACCACCUUUAUAGCGGUGCUUU-AACUAUUAAUAACUGAGGCUG
AACI02000291.1/4750-4936   AACUAUUACAGUCGAUGAGGAAAGGUUAUAGUUCAUGUGU-AACAUCUGUGUUUAAAAAUAACUCUAGUUAUCCAGAGCAUUUUUCAC-AAGUGUUUG--UGUAAGAUGCU-UUUCUGGGUCGAUGUGGAUUGUGCCGUGGCCUUUUUCACCACCUUUAUAGCGGUGCUUU-GACUAUUCAUUACUGAGGCUG
AABZ01000008.1/9856-9673   AACUAUUACAGUCGAUGAGGAUAGGUUAUAGUUCAUGUGU-AACAUCUGUGUUUGAAAAUAACUCUAGUUAUCCGAAUCAUUUUUCGC-AAGUGUUUG--UGGAGUAUG----UUCUGGGUCGAUGUGGAUUGUGCCGUGGCCUUUUUCACCACCUUUAUAGCGGUGCUUU-AACUAUUAUUAACUGAGGCUG
AAZN01000373.1/5727-5915   AACUAUUACAGUCGAUGAGGAUAGGUUAUAGUU-AUGUUU-AACAUCUGUGUUCGAGAG-AACUCUAGUUAUCCAUUCUGUUCAAAUCUAAGUUCUUAACUUUGAAUUGAAACAAUUGGGUCGAUGUGGAUUGUGCCGUGGC-UGUUUCACCACCUUAAUAGCGGUGCUUUUAACUAGUAUAAACUGAGGCUG
AACF01000088.1/17675-17856 AACUAUAACAGUCGAUGAGGAGAGGCUUUAGUUCAUGUGUUAACAUCCGAACUCAAAAAU-----UUGAGAUUUAACGGUUCCAGAGGCAUUUAUUUU--UGUAAGUGUCU-UAUUGGGACCGAUGUGGAUUGUACCGUGGC--UUUUCACCACCUUUAUAGCGGUGCUUU-GGUUAUAAUCAACUGAGGCUG
#=GC SS_cons               ::::::::[[[[[,,((((((-(((((((((((((-----.--((((,,,,,,,,,,,,,<<<____>>><<<<<<<<<<<<<<-<<<.<<____>>>..>>->>>>>>>-.-->>>>>>>,)))))))))))-----)))))))))))),<<<<________>>>>,,,,.,,,,,,,,,,,,,,,,]]]]]
#=GC RF                    AACUAUuACaGuCGAuGaggauaGGcuauaguuCaUGUgU.AACauCuGuguUuaAAAAUaaCUCUaGuuacccggggcguccuucgc.aagUgUuug..cguaggacgcu.uucccggguCGauGuGgauugUgCCGuggCCuuuuuCaCCaCCUUuAUAGCGGuGCUUU.aAcUAuuAuuAACUGAGgCuG
//
# STOCKHOLM 1.0

#=GF AC   RF01245
#=GF ID   snR9
#=GF DE   Small nucleolar RNA snR9
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   58.00
#=GF TC   60.20
#=GF NC   53.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00036
#=GF DR   snornadb; snR9;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   2905424
#=GF RT   Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: viable
#=GF RT   sextuple mutant.
#=GF RA   Parker R, Simmons T, Shuster EO, Siliciano PG, Guthrie C
#=GF RL   Mol Cell Biol. 1988;8:3150-3159.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


M20765.1/237-423           GGGAAUAUAAUACUAAAUACUCUGUUAUAUAGAACUUUCUACGCCUUUUCCUCUAUGGCUAUGAAAGCGUGGACAACGGAGAUCAAAUAGACCAAUUACUGAAUAUGGCUUUUGACAUAUCUUCUUCUUCAUGGGUGAGGAUUAAG-CUGAUAUCCUGACCCACCUAUCAUUAGUCCUUCAGACAUAC
AABY01000088.1/34426-34241 GGGAAUAUAAUACUAAAUACUCUGUUAUAUAGAACUUUCUAUGCCUUUUCCUCUAUGGCUAUGGAAGCGUGGACAACGGAGA-CAAAUAGACCAACCACUGAAUAUGGCUUUUGACGCUUCUUCUUCUCGGUGGGUAGGGAUUAAG-CUGAUAUCCUGACCCGCCUAUCAUUAGUCCUUCAGACAUAC
AACG02000010.1/70750-70564 GGGAAUAUAAUACUAAAUACUCUGUUAUAUAGAACUUUCUAUGCCUUUUCCUCUAUGGCUACGGAAGCGUGGACAACGGAGACAAAUUAACCAAUUUAAUGAAUAUGGCUUUUGACAAAUCUUCUUCUCGGUGGGUAAGGACGAAA-CCGAUAUCCUGACCUGCCUGUCAUUAGUCCUUCAGACAUAC
AACI02000041.1/11601-11416 GGGAAUAUAAUACUAAAUACUCUGUUAUAUAGAACUUUCUAUGCCUUUUCCUCUAUGGCUAUGGAAGCGUGGACAACGGAGA-CAAAUAGACGAACUAAUGAAUAUGGCUUUUGACAAAUCUUCUUCUCGGUGGGUAAGGACGAAA-CUUAUAUCCUGACCUGCCUGUCAUUAGUCCUUCAGACAUUU
AACH01000555.1/5395-5581   GGGAAUAUAAUACUAAAUACUCUGUUAUAUAGAACUUUCUAGGCCUUUUCUUCUAUGGCUAUGAAAGCGUGGACAACGGAGAU-AAAUAGACAAAAUACUGAAUUUGGCUUUUGACAAAUCUUCUUCUCGGUGGGUGAGGUCGAAAACUGAUGUCCUGACCUGCCUGUCAUAAGUCUUUCAGACAUAC
#=GC SS_cons               :::::::::::::::::::<<<<<<--------<<<<<<<<<<<<___________>>>->>>>>>>->>----->>>>>>-----------------<<<<<---<<<<-------------------<<<<<<<-<<<<_____.______>>>>->>>>>>>------->>>>->>>>>::::::
#=GC RF                    GGGAAUAUAAUACUAAAUACuCuGuUAUAUAGAaCuuucuauGCCUUUUCcUCUAUGGCUauggaagCGuGGACAaCgGaGAucAAAUAgaCaAAuUAcuGaaUaUGgCuUUUGACAaAUCUUCUUCUcGGcgGGuaaGGaugAAa.CUgAUAuCCuGaCCcgCCUgUCAUuaGuCcuuCagACAUAc
//
# STOCKHOLM 1.0

#=GF AC   RF01246
#=GF ID   snR81
#=GF DE   Small nucleolar RNA snR81
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   52.50
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00025
#=GF DR   snornadb; snR81;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15306656
#=GF RT   Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the
#=GF RT   Saccharomyces cerevisiae genome.
#=GF RA   Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM
#=GF RL   Nucleic Acids Res. 2004;32:4281-4296.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


Z74794.1/3074-3261     AGGUUAGGGACUGCAAAAGAAGCGGCGAGGCAGCCCACAUCAAGUGGAACUACACAGACUUCCUUGUCGCGAUACUACGGUCCCAAGAGCAAUCCUAACAAGCAAUUACAUAUUCCCCCGCUGAACCUGUACAGUCCACGGAUGGUGCAGAAGUUAUAUGAUUUGGGGGAAGACGCUUUUUCACAUCU
AACH01001718.1/854-667 AUCUCAGGGACAGCAAAAGAAGCGGCAAGAGAGCCCACGAUAAGUGGAACUACACAGACUUCCUUGCCGCGAUACUACGGUCCCCAGAACAAUCCUAACAAGCAAUUACAUAUUCCCCCGCUGAACCUGUGCAGUCCAUGGACGACGCUGAUACUAUAUGAUUCGGGGGAAGACGCUUUUUCACAUCU
AACI02001270.1/259-72  ACGUCAGGGAUUGCAAAAGAAGCGGCGAGGCGGCCCACGCCAAGUGGAACUACACAGACUUUCUCGCCGCGAUACUACGAUCCCCAGAAUAAUCCUAAUAAGCAAUUACAUAUUCCCCCGCUGAACCUGUGCCGUCCACGGACGGCGCUGACGCUAUAUGAUUCGGGGGAAGACGCUUUUUCACAUCU
#=GC SS_cons           ::::::(((((((--------(((((((((-((,<<<<_____>>>>,,<<____>>,))-)))))))))-------)))))))------------<<-<<<<-----------<<<<<<---<-<<-<<<<-<<<____>>>->>>>->-->->-------->>>>>>----->>>>->>:::::::
#=GC RF                AugUcAGGGaccGCAAAAGAAGCGgCgaGgcaGCCCaCgucAAGuGGAACuACACaGACuUcCucGcCGCGAUACUACgguCCCcAGAacAAUCCUaacaaGCAAUUACAUAUUCCCCCgCUGaAcCUGugcaguCCAcGGacGgcgCuGAugcuAUAUGAUUcGGGGGAAGACGCuuUuuCACAUCU
//
# STOCKHOLM 1.0

#=GF AC   RF01247
#=GF ID   snR32
#=GF DE   Small nucleolar RNA snR32
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.60
#=GF NC   44.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF DR   snornadb; snR32;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300006;
#=GF RN   [1]
#=GF RM   8265354
#=GF RT   SnR31, snR32, and snR33: three novel, non-essential snRNAs from
#=GF RT   Saccharomyces cerevisiae.
#=GF RA   Balakin AG, Schneider GS, Corbett MS, Ni J, Fournier MJ
#=GF RL   Nucleic Acids Res. 1993;21:5391-5397.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   11


U10398.3/28338-28525           AACAUCAUAAUUA-UAUCGC-GAAUGUACUACUAGUAUAUGCA-G-----UUU--UCUU-------AAAAUUGCA---GGG--AA--UGACUAAA-AGC-CCACGUUU------------UUCCCACUUU---UAGU----AGUAC-UGAAGCGUAGAUAGAUU-----GAACGUUGCUGGGCGCCUGGUGUUGAUCAUUUCUGAAAUGA-----GAU--AUUGGGAAUCAGCUGUAUCUACAUUU
AABY01000073.1/24549-24361     AACAUCAUAAUUA-UAUCGC-GAAUGUACCACUACUCUAUGCA-GU----UUU--UCUU-------AAAAUUGCA---GGG--AA--UGGCUAAACAAU-CCAUACUU------------UUCCCACUUU---UAGU----AGUAC-UGAAGCGUAGAUAGAUU-----GAACGUUGCUGGGCGCCUGAUGUUGAUCAUUU-UGAAAUGA-----GAU--AUUGGGAAUCAGCUGUAUCUACAUUU
AACH01000131.1/10994-11183     AACAUCAUAAUUA-UAUCGC-GAUUGUACCACUAGUAUAUGCAAC-----UUU--UCUU-------AAGAUUGUA---GGG--AA--AGGCUAAC-CGAACCAUACUU------------UUCCCAUUUU---AAGU----GGUAC-UAAAGCGUAGAUAGAAU-----GAACGUUGCUGGGCGCCUGAUGUUGAUUAUUUUUAAAAUGA-----GAC--AUUGGGAAUCAGCUGUAUCUACAUUU
AACI02000057.1/7740-7551       AACAUCAUAAUUA-UAUCGC-GAAUGUACUACCACUACAUGCA-GCU---UUU--UCAU-------AAGGUUGCA---GGG--AA--UGGCUAAA-UGUUCUAUGUUU------------UUCCCAUUUU---UGGU----AGUGC-UGAAGCGUAGAUAGAUU-----GAACGUUGCUGGGCGCCUGAUGUUGAUCAUUU-UGAAAUGA-----GGU--AUUGGGAAUCAGCUGUAUCUACAUUU
AACA01000258.1/7199-7388       AACAUCAUAAUAA-UAUCGC-GAAUGUACCACUAACAUAUGCA-GCU---UUU--UCUU-------AAAGUUGUA---GGG--AA--UGGCUAAAUAUU-CUAUGCUU------------UUCCCAUUUU---UAGU----AGUGC-UCAAGCGUAGAUAAAUU-----GAACGUUGCUGGGCGCCUGAUGUUGAUCGUUUC-GAAAUGA-----AAU--AUUGGGAAUCAGCUGUAUCUACAUUU
AAZN01000029.1/18837-18636     AACAUCAUUUUUA-UAUCGCAGAUGCACUACCAAUUUAACUGA-UCUCACUUC--UUAU-------GAGUUUCAG---GAGAUGA--ACUCGAUUUUGU-UUCAAGGU------------UCCUCUUGGU---UUGG----UACUG-UUAAGCGUAGAUCAAAUAA---GAACGUUGCUGGGCGCCUGGUGCUGACCAUAU--UGUAUGGGUUGAGGC--AUUGGGAAUCAGCUGUAUCUAUAUCU
CR380953.1/573348-573145       AACAUCAUUUUUAUUAUCGC-CUGUGACAGUACUAUCAGGAGA-UU----GUGAUUCUUUAUGAAUUGCUUUUUCCAUGUG--GA---AAUAAUC-UUU-CAAUGUUU----------UUUCCCCAUAUC---GGUA----CUGUU-CGAAGCGUAGAUAGACUUAAA-GAACGUUGCUGGGCGCCUGGUGUUGA---UAUCUUACAUGA-----GAU--ACUGGGAAUCAGCUGUAUCUACAUCU
CR382124.1/668790-668986       AACAUCAAUAUUA-U--CGC----UCCACGGUUAUCCCUGUGU-A-----AGA--UUUC-------GUUCUGCGC---GGG--GACCGGGUUAUG-UGUUGUUCACUA-----------UUUCCUGGUUU---UAAUAAUUUGUGU-UGAAGCGUAGAUUUAAUACCAAGUACGUUGCUGGGCGCCUGAUAUUGAGUCAAUUUGAUU-AU-----GAUCUAUUGGGAAUCAGCUGUAUCUACAUUU
AACF01000039.1/56929-56724     AACAUCAUUUUUA-AAUCGC-CAAUGCAAUACCAUGAUAAGGG-UC----UUUUUUCUU----AAUUAAGAACCU---GAG--AG--AGAUUCAU-UUA-CUAUGUCUCUUUGAAAAAUACUUUCUUCUCGUUUGGU----AUUUG-UUUAGCGUAGAUUAAUA-----GAACGUUGCUGGGCGCCUGAUGUUGAUUCAAUAUAU---GA-----GAC--AUUGGGAAUCAGCUGUAUCCACAUUU
AADM01000200.1/18092-17904     AACAUCAUUUUAA-C-UCGC-UCACACUGGUCCUAACUUUUAA-C------------AU------------UCAG---UGG--GG--AGAGACAC-UUC-ACGAGUCU------------CCUCAGGUUUUGCAGGG----CCGGUAAGAAGCGUAGAGAGAAUUCAA-GAGCGUUGCUGGGCGCCUGGCGUUGAUUUUCU-UCGGAAAAGAUGAGAC--UCUGGGAAUCAGCUGUUUCUACAUAU
AACE03000003.1/1021105-1021294 AACAUCAU--UUU-UAUCGC-UCACACUGACCCCAUACUC----------UUU--UUUU-------AGA-----G---AGG--GA--AGACGCAA-UUU-UCGAGUUC------------CUUCUGGUUU-UCGGGG----UCGGUAAGAAGCGUAGACAGAAUCUCAAGACCGUUGCUGGGCGCCUGAUGUUGAUUUUUUUCAUAAAAAGAGGAUAC--AUUUGGAAUCAGCUGUUUCUACAAUU
#=GC SS_cons                   :::::::::::::.:::(((.----(((((((((,,,,,<<<<.--....<<<..____.......>>>-->>>>...<<<..<<..-<<<____.___.____>>>-............>>>>>,,,,,...))))....))))).----)))------------...<<<<<----------<<--<<<<<--<<<<<_____>>>>>.....>>>..>>-->>------->>>->>:::::::
#=GC RF                        AACAUCAUuuUUA.UAUCGC.uaaugcacccccauuauacgga.uc....uuu..UcuU.......aaauUuccg...ggG..gg..aggcuaaa.Uuu.cuaugccU............ccCccauuUU...uggg....ggugc.ugAAGCGUAGAUagAaUua...GaaCGUUGCUGGGCGCCUGguguuGAucauuUuUaaaauga.....gac..acUGGGAAUCAGCUGuAuCUACAUuU
//
# STOCKHOLM 1.0

#=GF AC   RF01248
#=GF ID   snR8
#=GF DE   Small nucleolar RNA snR8
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   60.10
#=GF NC   36.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00039
#=GF DR   snornadb; snR8;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   2905424
#=GF RT   Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: viable
#=GF RT   sextuple mutant.
#=GF RA   Parker R, Simmons T, Shuster EO, Siliciano PG, Guthrie C
#=GF RL   Mol Cell Biol. 1988;8:3150-3159.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   11


M20764.1/402-590             AUGAUACAUAUUAAACAUGCCUUCUAUUCACUGUGCCAUCU-------UACAU-CCGU-AGGUGAUCAGAGGGGAAAAGAAGAGCUAGAGCAACUCCCAC----------------------------ACUCAU-GAGCGU-CCUCAUACUGUUCUGGGCGCUUCUCACAGGUGCUUCUUUUAGUGUCUCCCAUUG-GCCCAGAUCGGUA-CUGCGCGAGUGAGAUAUCU
AACH01001103.1/771-582       AUGAUACAUAUUAAACAUGCCUUCUAUUCACUGUGCCAUCU-------UACAU-CCGU-AGGUGAUCAGAGGGGAAAAGAAGAGCUAGAGCAACUCCCAC----------------------------ACUCAU-GAGCGU-CCUCAUACUGUUCUGGGCGCUUCUCUCAGGUGCAUCUUUUAGCAUCUUUCAUUG-GCCCAGAUCGGUAGCUGCGCAAGCGAGAUAUUC
AACA01000336.1/10189-9996    AUGAUACAUAUUAAAAAUGCAUUCUAUUCACUGUGCCAUCUAUAU---UACAU-CCGU-AGGUGAUCAGAGGGGAAAAGAAGAGCUAGAGCAACUCCCAC----------------------------ACUCGU-GAGCGU-CCUCAUACUGUUCUGGGUGCUUCUCACAGGUGCUUCUUUUAGCACCUCCCAUUG-GCCCAGAUCGGUAGCUGCGCAAGCGAGAUAUCC
AAZN01000271.1/10970-11147   GUGAUAC-----GAAAAUGCAUUCUAUUCACUGUGCCAUCUG------UUUUU-CUAU-AGGUGAUCAGAGGGGAAAAGAAGCGCUAGAUAGACACCCAC----------------------------GCUCAU-GAGCGUACCUCAUACUGUUUUAAGUGU-------UAUAAUUUUUAUUGUUAAUACCCA--C-GCUUAGAUCAGUAUCUGCGCAAGUGAGACAUCU
CR382123.1/649568-649394     ACGAAACAUAUUA---AUGCCUUCUAUUCACUGUGCCAUCU-------GAUACACCGU-AGAUGAACAGAGGGGAAAAGAACGGCUAGAUGAAAAUUC-U----------------------------AUCCGC-GAGCGUACCUCAUACUGAUUAAAGUACUUAACUA---------UUUU----UCAUCAAUUG-GCUUUAAUUGGUAGCUGCGUGAGCGGGACAUUC
AADM01000109.1/82414-82578   GUGAUACGAAAUUUAUA-GCCUUCUAUUCACUGUGCCAUCUU------AGUAU-CCGU-AGAUGAUCAGAGGGGAAAAGAACGGCUAG----ACUAAUAU----------------------------UGGCGC-GAGCGU-CCUCAUACUGUCCGAAUCGAAU----------AGCAUUGUCU-----------G-GGUUCGGUCGGUAACUGCGCAAGCGCUACAAAC
AACF01000052.1/41759-41971   CCGAUACAUAUAAAACAUGCAUUCUAUUCACUGUGCCAUCUG------UCAAU-UUGUUAGAUGAUCAGAGGGGAAAAGAAGAGCUAGAGCAAUGGUUACGGAAUGGUAGCAAUACCAUAUCGUGAUCUCUAAU-GAGCGU-CCUCAUACUGUCCAAGGUGUUCAACCA---UUUUACAAUGAAUA----UUUAUG-GCCUUGGUCGGUAACUGCGCAAGUGAGAUAUUU
CR382138.2/946011-946171     UUUUUCUUUGAUACGAAAGCUUCCUAUUCACUGCACCAUUCU------UUAAU-CAAU-GAGUGACUGGAGGGGAAAAGGAAAGCGAGAAAGAAACAU---------------------------------CGAAUAACGU-CCUCAUACUAAGUUUGCUUGUA-------------UUUUG-------------U-AGCAUAUUUGGAUUCUGCGUUUUCGAAACAUGC
CR380958.2/1164869-1165060   AUACGAAAUAUUUAA-AUGCCUUCUAUUCACUGUGCCAUCUUUUU---CAAGU-AGUU-AGAUGAUCAGAGGGGAAAAGAAGCGCUAGAUCAAAUUUUUC----------------------------G--AAU-GAGCGU-CCUCAUACUGUUCAUGGUAAUUCGUUUGCUUAGAGACACAUCUAUUCAUAAUUUGGCCAUGAUCGGUAACUGCGCGAUUUGAACAUUA
AACE03000006.2/492326-492155 UUGAUACGAAAUAUUAA-GCCUUCUAUUCACUGUGCCAUCUCUAUUUAUACUU-CCGU-AGAUGAUCAGAGGGGAAAAGAAGCGCAAGACUGAAAAA----------------------------------CGC-AAGCGU-CCUCAUACUGAACAAGGUACUUUUCUU---------UUUU---------CAUUG-GCCUUGGUUGGUAACUACGUGAGCGAGACAACC
AE016818.2/1255565-1255727   UUGUUCAGUGAUACGAAAGCCUUCUAUUCACUGUGCCAUCU-------AGUUU-CCGU-AGAUGAUCAGAGGGGAAAAGAAG-GCGAGAGCGA-----------------------------------AUUCAC-GAGCGU-CCUCAUACUGAGUAGGGUACUUAACUA-------UCUAGA------------UG-GCCCUAUUUGGUAACUGCGCGAGGGAGACAUAG
#=GC SS_cons                 ::::::::::::::::::<<-<<-------<<-<<-<<<<<_......_____.____.>>>>>-->>->>-------->>-->>---------------............................-<<<<<.--<<<-.-------<<<-<<<<<<<-<-------...--<<______>>--....----->.>>>>>>>->>>------>>>-->>>>>::::::
#=GC RF                      aUgaUAcaUAuUaaaaAuGCcUuCUAUUCACUGuGCCAuCuu......uaaaU.ccgU.aGaUGAUCaGAGGGGAAAAGaAgaGCuAGAucaAaauuuAc............................acucgc.GAGCGU.CCUCAUACuGuccagGgcgcUuaaCua...uacuucuuUuaguA....uuauUg.gcCcuggUCgGUAaCUGCGCaAgcgagAcAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01249
#=GF ID   snR190
#=GF DE   Small nucleolar RNA snR190
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   42.40
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00044
#=GF DR   snornadb; snR190;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300054;
#=GF RN   [1]
#=GF RM   2850487
#=GF RT   Characterization of an SNR gene locus in Saccharomyces cerevisiae that
#=GF RT   specifies both dispensible and essential small nuclear RNAs.
#=GF RA   Zagorski J, Tollervey D, Fournier MJ
#=GF RL   Mol Cell Biol. 1988;8:3282-3290.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   10


Z49425.1/3177-2988         GGCCCUGAUGAUAAUGGUGUCUCUUCUUUCCUCGUCCGAUUCGACCAUGACGACAAGGGAUUUUAUCUCGUUCUCUU-AAUGCGAAUGAUUUUGAAAA----GAUGUUGCUUCUGUGACAUUU-----UUUUU-UAAUCAUUUGUGUUUGCAAACGGGAACUUUUCUUGCCAGUGUU-AUAC---AACACAUGCAG--A---UCUGAGCC
AABY01000001.1/58183-58381 GGCCCUGAUGAUAACGGUGUCUCUUCUUUCCUCGUCCGAUUCGACCAUGACGACAAGGGAUUUUAUCUCGUUCUCUU-AAUGCGGAUGGUUUUGGAAAGGUAGAUAUUGCUUCGGUGAUGUUUGUCCAUUUUU-UAAUCAUUUGCGUUUGCAAACGGGAACUUUUCUUGCCAGUGUU-AUAC---AACACAUGCAG--A---UCUGAGCC
AABZ01000130.1/3235-3036   GGCCCUGAUGAUAACGGUGUCUCUUCUUUCCUCGUCCGAUUCGACCAUGACGACAAGGGAUUUUAUCUCGUUCUCUU-AAUGCGAGUGAUUUUGAAAAGGUGAAUAUUGCUUCGGUGAUAUCUCUUCCUUUUCAUGAUCAUUAGUGUUUGCAAACGGGAACUUUUCUUGCCAGUGUU-AUAC---AACACAUGCAG--A---UCUGAGCC
AACI02000020.1/23732-23928 GGCCCUGAUGAUAACGGUGUCUCUUCUUUCCUCGUCCGAUUCGACCAUGACGACAAGGGAUUUUAUCUCGUUCUCUU-AAUGCGAGUGGUUUUA-AAAGAUAGAUAUUGCUUCGGCGAUAUUU-UCCCUUUUC-UUACCACUUUCAUUUGCAAACGGGAACUUUUCUUGCCAGUGUU-AUAC---AACACAUGCAG--A---UCUGAGCC
AACG02000042.1/74682-74484 GGCCCUGAUGAUAACGGUGUCUCUUCUUUCCUCGUCCGAUUCGACCAUGACGACAUGGGAUUUUAUCUCGUUCCCUU-AAUAUUAGUGGUUUUGAGAAGAUGAACAUCACCUCGGUGACGUUU-UUCUUUCUCUUAGCCAUUGGUGUUUGCAAACGGGAACUUUUCUUGCCAGUGUU-AUAC---AACACAUGCAG--A---UCUGAGCC
X96815.1/457-646           GGCCCUGAUGAUAAUGGUGUCUCUUCUUUCCUCGUCCGAUUCGACCAUGACGACAAGGGAUUUUAUCUCGUUCUCUU-AAUGCGAAUGAUUUUGAAAA----GAUGUUGCUUCUGUGACAUUU-----UUUUU-UAAUCAUUUGUGUUUGCAAACGGGAACUUUUCUUGCCAGUGUU-AUAC---AACACAUGCAG--A---UCUGAGCC
M21124.1/146-335           GGCCCUGAUGAUAAUGGUGUCUCUUCUUUCCUCGUCCGAUUCGACCAUGACGACAAGGGAUUUUAUCUCGUUCUCUU-AAUGCGAAUGAUUUUGAAAA----GAUGUUGCUUCUGUGACAUUU-----UUUUU-UAAUCAUUUGUGUUUGCAAACGGGAACUUUUCUUGCCAGUGUU-AUAC---AACACAUGCAG--A---UCUGAGCC
ABPO01000129.1/4050-4248   GGCCCUGAUGAUAACGGUGUCUCUUCUUUCCUCGUCCGAUUCGACCAUGACGACAUGGGAUUUUAUCUCGUUCUCUU-AACGUAAGUGGUUUUGAGAAGAUAUAUGUUACUUCGGUGAUGUUU-UUCUUUCUUUAAGCCAUUUGUGUUUGCAAACGGGAACUUUUCUUGCCAGUGUU-AUAC---AACACAUGCAG--A---UCUGAGCC
AAZN01000409.1/41203-41387 GGCUUUGAUGAUAACGGUGA-UCUUCUUUCCCAGUCCGAUUCGACCAUGACGACAUGGGGUUCUACC--ACGUUCUU-GGUUUUGGCCGGUUUUAUACUGUU----UUCUUUAUUGAU------UAUAGUUGA-AAUUGGUUUUAACCUACAUG---GAACUUUUCUUGCCAAGUACCAAGA---GUACUAA-CAAUUA---UCUGAGCC
CR380959.2/619578-619761   UGCUUUGAUGAAAACGGUAA-UCUUCUUUCCCAGUCCGAUUCGACCAUGACGAUCAGGGUUUCUACCACGUCCAUCUUUCUCUG--ACUUGACUCUCU-CU-----UCUCUUCGGAGGA-----UUG-GGAGG-AUAGG---AUGGGAUUGUGA---GGACUUUUCUUGCCAGUGUA-UUACGUAUACACAA-CAA--AGACUCUGAGCA
#=GC SS_cons               (((---(((,,,,,,,,,<<<<<<<------<<<<<____________>>>>>->>>>>>>,,,,<<<<<<<-----.<<<<<<<<<<<<<--<<<<<<--<<<<<<<<<____>>>>>>>>>.--->>>>>>.->>>>>>>>>>>>>---->>>>>>>,,,,,,,<<<<--<<<<<.____...>>>>>-->>>>..)...))---)))
#=GC RF                    gGCccUGauGAuAAcGGUguCuCuuCUUUCCucGuCCGAUUCGACCAUGaCgacaaGgGauUuUAuCcCGuucucUU.ggcgccagugguuuUgggacgaUggacgucgcUUcggcgacgucc.Uuucguccc.uaaccacuggcgccUgcAaaCGgGaACUUUUCuuGCCAGuguu.AuAc...aacaCAuGCaa..a...uCUGAGCc
//
# STOCKHOLM 1.0

#=GF AC   RF01250
#=GF ID   snR189
#=GF DE   Small nucleolar RNA snR189
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   53.70
#=GF NC   37.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00021
#=GF DR   snornadb; snR189;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   3290853
#=GF RT   Sequence and genetic analysis of a dispensible 189 nucleotide snRNA from
#=GF RT   Saccharomyces cerevisiae.
#=GF RA   Thompson JR, Zagorski J, Woolford JL, Fournier MJ
#=GF RL   Nucleic Acids Res. 1988;16:5587-5601.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


X62452.1/873-682           AACAAAAUAAUUUACAUUCCAAGGACCGGUAUUAUUGUAGGGGAUUUGUGACUUUCAAGGCAACGUCCUCUCUACAACCGAGUUCGAGAAUAAGUACAAAUGGCUCUUUUUGUUAUUCGAAAGCUUACAAGUUCUGGUAUAUUCUAUAUACUCACUU----AUUACUUUCAAGUAC-UUCACACGGGCCUGACAUCU
AABZ01000039.1/16243-16432 AACAAAAUAUUUUACAUUCCAAGGACCGGUAUUAUUGUAGGGGAUUUGUGACUUUCAAGGCAAUGUCCUCUCUACAACCGAGUUCAAGAAUAAGCAU-AACGGCUCUUUUUGUUAUUCGAAAGCUUACAAGAUGCAGUAUCUUC-GUAUACUCUCCU----AUCACUUUCUAGUAC-UUCACACGGGCCUGACAUCU
AACA01000006.1/89474-89283 AAUAAAAUAAUUUACA-UCUAAGGACCGGUAUUAUUGUAGGGGAUUUGUGACUUUCUAGGCAAUGUCCUCUCUACAACCGAGUUCGAGAAUAAAUACCAAUGGCUCUUUUUGUUAUUCGAAAGCUUACAAGGUAUAGCGUAUUUUAUAUGCUUUCUUU---AUCACUUUCCAGUAC-UUCACACGGGUCUAACAUUU
AACI02000034.1/9484-9289   AAUAAAAUAAUUUACAUUUCAAGGACCGGUAUUAUUGUAGGGGAUUUGUGACUUCCAAGGCAACGUCCUCUCUACAACUGAGUUCGAGAAUAAAUUCCAAUGGCUCUUUUUGUUAUUCGAAAGCUUACAAGUUGUAGUAUAUU-UAUAUGCUCUCUUCUUACUUACUUUCAAGUACUUUCACAUGGGCCAAACAGAU
#=GC SS_cons               ::::::::::::::::::::::<<<<<<<<--------<<<<<<<---<<-<<_____>>>>-->>>>>>>----->>>>->>>>----------------<<<<<-------<<<<-<<<<<-----<<<<---<<<<<<<___>>>>>>>->>>>-...---->>>>>->>>>-.------->>>>>::::::::
#=GC RF                    AAuAAAAUAaUUUACAUUccAAGgaCCGGuAUUAUUGUaGgGGauUUGuGACuUuCaAgGCaAuguCCuCuCUACAaCCGAGuuCgAGAAUAAauaccAAuGGCuCUUUUUGUuauuCGaaaGCUUACaaGgUauaGcauauUcUauaugCuccCuuu...aUuACuuuCaaguaC.UUCACAcGgGCCuaACAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF01251
#=GF ID   snR3
#=GF DE   Small nucleolar RNA snR3
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Published; PMID:9106664; Wilkinson A
#=GF GA   40.00
#=GF TC   40.30
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF CL   CL00040
#=GF DR   snoRNABase; snR3;
#=GF DR   snornadb; snR3;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300040;
#=GF RN   [1]
#=GF RM   6197184
#=GF RT   A U4-like small nuclear RNA is dispensable in yeast.
#=GF RA   Tollervey D, Wise JA, Guthrie C
#=GF RL   Cell. 1983;35:753-762.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


Z49629.1/469-662             AACUUUGUCCUAAAGUACUAAUCCACCGCAUUAGACAGUACGAAGAUCGAGCUAUUUAUUUGAACACUCGGUCUUAUUCGUGAUAAGCGUAAUGU--GGAGAGAUCAAUUUC-CGGGUCAUUUAU-AAGAACUCGAGUGGAUUGCUAGUUGUUUUGAUUAGCUGAAUGAGACUCGAGUGUCAGAAGAUGACUAUAUUU
AABZ01000024.1/46395-46589   AACUUUGUCCUAAAGUACUAAUCCACCGCAUUAGACAGUACGAAGAUCGAGCUAUUAAUUUGAACACUCGAUUUUAUUCGUGAUAAGCGUAAUGU--GGAGAGAUCAAUUUUUCAGGUCAUUUAU-AAGAACUCGAGUGGAUUGCUGAUUGUUUUGGUCAGCUGAAUGAGACUCGAGUGUCAGAAGAUGACUAUAUUU
AACA01000267.1/4921-4730     AACUUUGUCCUAAAGUACUAAUCCACCGCAAUAGACAGUACGAAGAUCGAGCUAUUAAUUUGAACACUCGGUCUUA-UCGUGAUAAGCGU--UGU--GGAGAGAUCAAUUUUUCAGGUCAUUUAU-AAGAACUCGAGUGGAUUGCUGAUUGUUUUGAUUGGCAGAAUGAGACUCGAGUGUCAGAAAAUGACUAUAUUU
AAZN01000275.1/150002-149819 AACUUUGUCCAAAAGU----UUCCACCGCAAUAGACAGUACGAGAUUUGAGCUUUUUAUUCU--CACUCAGAUUUA-UCGUGAUAAGCGGUUUUUAAGGAUAGAUCAAAUU-----GUCACUCAUUAAGAACUCGAGUGGAUUACGUUAGGCUUCCUAAC--UAAAUGAGACUCGAGUGUCAGAGAGUGCCUAUAUUU
#=GC SS_cons                 :<<<<<<___>>>>>>,,,,,,,,,<<<----------<<<<<<<<<<<<<_______________>>>>>>>>--.>>>>>------------>..>>-------------.--<<<<<<<<--.----<<<<<<<<-----<<<<<<<_____>>>>>>>-------->>>>>>>>------>>>>>>>>::::::
#=GC RF                      AaCuuugUCCcaaaGuACUAaUCCACCgCAaUAGACAGuaCGaagaccGaGCUaUUuAUUugAACACuCggucuUA.uCGugAUAAGCGuaaUgu..GGAgAGAUCAAuUUu.CagGuCacucAU.AAGAaCuCGaGuGGAUUGCcggccGuUUuggccgGCugAAUGAGaCuCGaGuGUCAGAgaguGaCcAUAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01252
#=GF ID   snR5
#=GF DE   Small nucleolar RNA snR5
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Published; PMID:15075370; Wilkinson A
#=GF GA   45.00
#=GF TC   46.40
#=GF NC   40.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00038
#=GF DR   snornadb; snR5;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   2905424
#=GF RT   Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: viable
#=GF RT   sextuple mutant.
#=GF RA   Parker R, Simmons T, Shuster EO, Siliciano PG, Guthrie C
#=GF RL   Mol Cell Biol. 1988;8:3150-3159.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   11


AAFW02000032.1/134926-135122 AUCAUUCAAUAAACUGA-UCUUCCGGAUUACCAUGCUUAAGACAU--CACGCCUCCAUAUGUCUAUAUAAAGCGCAAAUGGCUGGAAGUAGACCAAUUUUUUUU-GUUCCUAGCUUUUCAUUAUUGAAAUCUAAUCCAGUUUUAAUGGUUUUUCUUAAUUAAGAA--AACAAAUUA-UCAUUGGUUCGCUCUAGGUGUACAUAU
AACG02000027.1/92648-92843   AUCAUUCAAUAAACUGA-UCUUCCGGAUUACCAUGCUUAAGACAU--CACGCCUCCAUAUGUCUAUGUCAAGCGCAAAUGGCUGGAAGUAGACCAAUUUCUUU--GUUCCUAGCUUUUCUUUAAUGAAAUCUAAUCCAGUUUUAAUCGCUUUUUCUUCAUUGAGA--AGCAAAUUA-UCACUGGUUCGCUCUAGGUGUACAUGU
X89633.1/18639-18835         AUCAUUCAAUAAACUGA-UCUUCCGGAUUACCAUGCUUAAGACAU--CACGCCUCCAUAUGUCUAUAUAAAGCGCAAAUGGCUGGAAGUAGACCAAUUUUUUUU-GUUCCUAGCUUUUCAUUAUUGAAAUCUAAUCCAGUUUUAAUGGUUUUUCUUAAUUAAGAA--AACAAAUUA-UCAUUGGUUCGCUCUAGGUGUACAUAU
AAEG01000065.1/19439-19634   AUCAUUCAAUAAACUGA-UCUUCCGGAUUACCAUGCUUAAGACAU--CACGCCUCCAUAUGUCUAUAUAAAGCGCAAAUGGCUGGAAGUAGACCAAUUUUUUU--GUUCCUAGCUUUUCAUUAUUGAAAUCUAAUCCAGUUUUAAUGGUUUUUCUUAAUUAAGAA--AACAAAUUA-UCAUUGGUUCGCUCUAGGUGUACAUAU
AACH01000317.1/2583-2779     AUCAUUCAAUAAACUGA-UCUUCCGGAUUACCAUGCUUAAGACAU--CACGCCUCCAUAUGUCUAUAUAAAGCGCAAAUGGCUGGAAGUAGACAAAUUUCUUUU-GUUCCUAGCUUUUCAUUAUUGAAAUCUAAUCCAGUUUUAAUAGUUUUUCUUUAGUAAGAA--AACAAAUUA-UUAUUGGUUCGCUCUAGGUGUACAUAU
AABY01000003.1/33852-34047   AUCAUUCAAUAAACUGA-UCUUCCGGAUUACCAUGCUUAAGACAU--CACGCCUCCAUAUGUCUAUAUAAAGCGCAAAUGGCUGGAAGUAGACCAAUUUUUCU--GUUCCUAGCUUUUCAUUAUUGAAAUCUAAUCCAGUUUUAAUAGUUUUUCUUUAUUAAGAA--AACAAAUUA-UCAUUGGUUCGCUCUAGGUGUACAUAU
AACI02000485.1/4961-5155     AUCAUUCAAUAAACUGA-UCUUCCGGAUUACCAUGCUUAAGACAU--CACGCCUCCAUAUGUCUAUGUAAAGCGCAAAUGGCUGGAAGUAGACCAAUCUCUUUU-AUUCCUAGCUUUUCAUUAUUGAAAUCUAAUCCAGUUUUAAU--ACUUUCUUCAUUAAGAA--AACAAAUUA-UCAUUGGUUCGCUCUAGGUGUACAUAU
AAZN01000136.1/17454-17631   UACACUAAAAAAACUGAAACUUCCGGAAUACCAAGCUUA-GACAUACUACACCUCGAUAUGUCA--AUAAAGCACAAAUGGCUGGAAGAAGAUUAAAAUUU-------CCUAGCUUUCCAGCAAUGGAAUCUAAUCCAAUUUUCAAGUU------UCUUUU---------AUUUGA-AUAUUGGUUCGCUCUAGGUGUAUAUUC
AACF01000029.1/72947-73140   AGAAUACCAAAACUGAC-CCUUCCGGAUUACCAAGCUUAGACGUGA-AACGCCUCCA-CACGUCAAUUCAAGCGCAAAUGGCUGGAAGUAGAAAAAAAGCUACUAGCUCCUAGCUUUCCAGCAAUGGAAUCUAAUCCAGACUUGAC---CUGUUUUCUUUUAAGC--ACGU-GUCU-UGUCUGGUUCGCUCUGGGAGUAUAUAC
CP000496.1/2518769-2518943   CUCAUUACAUAUAUCUC-ACUUCCGGAUUACCA-GCGACACUGAU--AACUCCUCCGU-----UUAGUUAAGCAAAAAUGGCUGGAAGGAGAACAAAUGUCAC-----CAUCAUUU------------AUAUAAUCCAGAUUUAAU---GUGAAUUUUCUAAUUCAUACCCUGUUAAUAUUUGGUUCGCGUGAUGGGUACAUCG
CR382126.1/308047-308236     CAUAUUUUUUAAAACAC-UCUUCCGGAUUACCA-GCUG-UGGCAU--UGUUCCUCCAUAUGUUCACAA-CAGCAAAAAUGGCUGGAAGUAGAAAAACUGGC----GGUUCAACGCUAGGUUUCAGGGUAUAUAAUCUACCUCGAUAGGUUUUUUUACAGGCGAGA--UACUAUAUC-UGGCUA-UACUAUCUUGGUGGUUCGCU
#=GC SS_cons                 :::::::::::::::::.:<<<<<---------<<<<<-<<<<<<..___________>>>>>>----->>>>>--------->>>>>---------------..---(((((,,<<<<<____>>>>>,,,,,,<<<<<--<<<<---<<<<<<<____>>>>>..>>--->>>>.-->>>>>,,,,,,))))):::::::::
#=GC RF                      aucAUUcaAUAAAcuga.uCUUCCGGAUUACCAcGCuuAgGacau..uACgCCUCCAUauguCcAuaUaaaGCgcAAAUGGCUGGAAGuAGAacAAuuuuUuu..GuUCcuaGcUUucCauUAauGgaAUcUAAUCCAguUUuaaugGUuuuucuuuauUaagaa..aaCaaauua.UuacUGGUUCGCUCuagGuGUAcAUau
//
# STOCKHOLM 1.0

#=GF AC   RF01253
#=GF ID   snR46
#=GF DE   Small nucleolar RNA snR46
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   43.00
#=GF TC   43.70
#=GF NC   42.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00021
#=GF DR   snornadb; snR46;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300062;
#=GF RN   [1]
#=GF RM   8797828
#=GF RT   The RNA world of the nucleolus: two major families of small RNAs defined
#=GF RT   by different box elements with related functions.
#=GF RA   Balakin AG, Smith L, Fournier MJ
#=GF RL   Cell. 1996;86:823-834.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


Z72815.1/1165-1361         AUGGCCUCUUCGAAGAUCCGUAGAUUUUG---CAUUUUUG--CGGUGGUUUAUGGAUUCAAAGCGAGGCCUAAAUU-AACGAUCAUGUCUUUGCU-A-----UUAUAUC------A-GAGGGCAUAUCAUUGAAUUU---CCGAUUUCCAAAGGGAAGAAAAUAAAUAAAG---UUGUGCUAUUUCCAUGCAUC-CUUUUUUCUUUCAUUCAAUGACACAUAC
AABY01000137.1/29506-29307 AUGGCCUCUUCGAAGAUCCGUAGAUUUUG---CAUUUUUG--CGGUGGUUUAUGGAUUCAAAGCGAGGCCUAAAUU-AACGAUCAUGUCUUUAUU-AUUUUUUUAUAAA------A-GAGGACAUAUCAUUGAAUUU---CCGAUUUCCAAAGGGAAGAAAACAAAUAAAG---CUGUGCCAUUUC-AUGCAUU-CCUUUU-CUUUCAUUCAAUGAUACAUAC
AACA01000278.1/3590-3786   AUGGCCUCUUCGAAGAUCCGUAAACUUUG---CAAAUUUG--UGGUGGUUUAUGGAUUCAAAGCGAGGCCUAAAUU-AACGAUCAUGUCUUUAUU-U-----UUUUAAA------AAGAGGGCAUAUCAUUGAAUUU---CCGAUUUCCAAAGGGAAGAAAAUAAAUAAAG---CUGUGCUAU-UCCGUGCACU-UCUUUUUCUUUUAUUCAAUGAUACAUUU
AACH01000553.1/3305-3502   AUGGCCUCUUCGAAGAUCCGUAAACUUUG---CAUACUUG--CGGUGGUUUAUGGAUUCAAAGCGAGGCCUAUAUA-AACGAUCAUGUCUUUUCU-A-----CUUUUUAUAA---A-GGGGGCAUAUCAUUGAAUUUU--CCGAUUUCCAAAGGGAAGAAAACGAAUAAGG---UUGUG---UUGUCAUGCACU-UCUUUUUCUUUCAUUCAAUGACACAUAU
AACI02000653.1/4337-4144   AUGGCCUCUUCGAAGAUCCGUAAACUUUG---CAUAUUUG--UGGUGGUUUAUGGAUUCAAAGCGAGGCCUAAAUU-GACGAUCAUGUCUUUAUUCU-----UUUUAAG------A-GAGGGCAUAUCAUUGAAAUU---UCUAAUUUCCAAAGGGAAAAAAAAACUAAAG---CUGUGCUAUUUCAUGCGCUC-CUUUUUUUGU----UCAAUGACACAUUU
AACF01000167.1/9584-9795   AUGGCCUCUUCGAAGAUCCUUAAACUUUGAUACAAAUGUGUCUUGUGGUCUAGGGAUUCAAAGCGAGGCCUAUAUUGAAAGUGUAUGUCAUGGUA-C-----AAAAACAAAAAAAU-UGUGACAUCUCAUUGACUUAGGUUCCAUAUAUUUAUGGACUUGUAUU-GUGAGGAUUUAGAGCCAUUUC-GGGCUCUACCUUAUUACAUU--UCAAUGAUACAUUU
#=GC SS_cons               ::<<<<<<-------<<<<<<<<<<<<<<...<<____>>..>>>->>>>>>>>>>>------->>>>>>,,,,,,.,,,,,,,<<<<<<<<___._....._______......_.>>>>>>>>-<<<<<<<<<--...-------------<<<<<<<<<------<<<...--<<<<_________>>>>-.>>>>>>>>>>>>>>>>>>>>>:::::::
#=GC RF                    AUGGCCuCUUCGAAGauCCguagacuucg...CauaUuuG..cggUggucuacGGauUCAAAGCGaGGCCUAaAUU.AAcGaucauGuCcucauu.a.....uuauAaa......a.gagGaCauauCauuGaauUu...uCgAUuUccaaAgggaagaaaauaAaUAagG...uuguGCuAUUUCcauGCacu.CcuuuuucuuucauuCaauGauACAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01254
#=GF ID   snR34
#=GF DE   Small nucleolar RNA snR34
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   40.70
#=GF NC   36.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00042
#=GF DR   snornadb; snR34;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300041;
#=GF RN   [1]
#=GF RM   7630735
#=GF RT   Characterization of three new snRNAs from Saccharomyces cerevisiae: snR34,
#=GF RT   snR35 and snR36.
#=GF RA   Samarsky DA, Balakin AG, Fournier MJ
#=GF RL   Nucleic Acids Res. 1995;23:2548-2554.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


U19729.2/1781-1983         GAAUCAAAAAUUUAUUUUUUACACGGAAACGAUGCCACAGUUGACUGAACCUGUCUUCUAACAGUAGUUAAUUGCCAGUAUUUCAAACAAGAUUUGAAAUACGAGUUUCCCAGAAUAAUUU--A----------UUUGGACAGGAUAGGAAGUCCGAUUUCUGUGUUGUCUC---AAAC-GAGGCGAUAGAAUUGGGAUGUCGAAGAAAGUCUACAUUA
AABY01000020.1/14589-14385 AAUCAAAAAAUUUAUUUUUUACACGGAAACAAUGCCACAGUUGACUGAACCUGUCUUCUAACAGUAGUUAAUUGCCAGUGUUUCAAACAAGAUUUGAAAUACGAGUUUCCCAGAAUAAUUUUCA----------UUUGGACAGGAUAGGAAGUCCGAUUUCUGUGUUGUCUC---AAGC-GGGGCGAUAGGAUUGGGAUGUCGAAGAAAGUCUACAUUA
AACG02000015.1/23258-23463 AAUCAAAAAAUUUAUUUUUUACACGGAAACAAUGCCACAGUUGACUGAACCUGUCUUCCAACAGAAGUUAAUUGCCAGUGUUUCAAACAAGAUUUGAAAUACGAGUUUCCAAGAACAAUUU--U-------AAUUUUGGACAGGAUAGGAAGUCCGAUUUCUGUGUAGUCUC---AAGC-GAGGCGAUAGAAUUGGGAUGUCGAAGAAAGUCUACAUUA
AACF01000003.1/29422-29628 GAAUCAAUAAUG---------CACGGAAACAAUGCCACAGUUGGCUGAACCUGUCUUCUAACAGUAGCUAAUUGCCAGUGUUUCAAAUA-UAAUUGAAAUACCAGUUUCCCAGAUUAACAU--AAUCAUUAUAUUUUGGACAGGAUAGGAAGUCCGAUGUCUGUGUACCUUCAUUAAAUGGAGGGGAUAGACAUGGGAUGUCGAAGAUAGUCUACAUUU
#=GC SS_cons               ::::::::::::::::::::::::<<<<----------<<<<<<<<<---<<<<______>>>>>>>>>>>>>------->>>>---------------------------------<<<<..-.......---<<---------------<<<<-<-<<<<--<<<<<<<<...____.>>>>>>>>>>>>->->>>>------>>>>>>::::::::
#=GC RF                    aAauaAAaAAUuUAUUUUUUACACGgaaACAAUGCCACaguuggCugAACCuGuCUUCuAaCaGcaGcuaauuGCCAGUguuuCAAAcAAgAuUUGAAAUACgAGUUUCCcAGAauAacuu..a.......uAUuuUGGACAGGAUAGGAAguCCGaUuuCuGUgucgccuC...AAac.GaggcgauaGaauuGGGauGUCGAAgaaaguCUACAUUa
//
# STOCKHOLM 1.0

#=GF AC   RF01255
#=GF ID   snR35
#=GF DE   Small nucleolar RNA snR35
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   41.80
#=GF NC   35.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00028
#=GF DR   snornadb; snR35;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300063;
#=GF RN   [1]
#=GF RM   7630735
#=GF RT   Characterization of three new snRNAs from Saccharomyces cerevisiae: snR34,
#=GF RT   snR35 and snR36.
#=GF RA   Samarsky DA, Balakin AG, Fournier MJ
#=GF RL   Nucleic Acids Res. 1995;23:2548-2554.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   11


Z75131.1/340-137           AUACAAAAUUAAUCGUGCGGAUUAAU-AA-UCCAGGACUAUAAAACCGUGUUGUUUAU-AUCGAGUCUCUU-UUGGUA---U--AAGCGUCAAGUCCAUCGGAGAGAUCAUCA--UUUUGUUCAUCUUAAUGCCCUUUUGUGUAGG------AAAUUGAG-----GGAAGUUUAGGCUUCUC--AACAUUUUAAGACG---CCUAUGCAAGGGCUGGUAGGACAGACAUGC
AABZ01000977.1/1380-1584   AUACAAAAUUAAUCGUGCGGAUUAAU-AA-UCCAGGACUAUAAAACCGUGUUGUUUAU-AUCAAGUCUUUU-UUGGUA---U--AAGCGUCAAGUCCAUCGGAGAGAUCAAUA--UUUUGUUCAUCUUAACGCCCUUUUGUGUAGA------AGGUUGAG-----CGGAGCGUAAGCUUUUC-UUAACAUUUGAAACG---UCUAUGCAAGGGCUGGUAGGACAAACAUGC
AACI02000292.1/2431-2225   AUACAAAAUUAAUCGUGCGGAUUAAU-CA-UCCAGGACUAUAAAACCGUGUUGUUUAU-AUCGAGUCUUUU-UCGGUA---U--AAGCGUCAAGUCCAUCGGAGAGAUCAAAA-AUUUUGUUCAUCUUAACGCCCUUUUGUGUAGA------AAGUUGAG-----UAAAGCGCAAGCUUUUCUUUACAUUUCAAAACU---UCUACGCAAGGGCUGGUAGGACAAACAUGC
AACA01000231.1/7126-7331   AUACAAAAUUAAUCGUGCGGAUUAAU-AA-UCCAGGACUAUAAAACCGUGUUGUUUAU-AUCGAGUCUUUU-UCGGUA---U--AAGCGUCAAGUCUAUCGGAGAGAUCAAAAAAUUUCGUUCAUCUUAACGCCCUUUUGUGUAGA------AAGUCGAG-----CAGAGUGCAAACUCUUC--UUGGCAUUGAAACU---UUUACGCAAGGGCUGGUAGGACAGACAUGC
AAEG01000064.1/26266-26063 AUACAAAAUUAAUCGUGCGGAUUAAU-AA-UCCAGGACUAUAAAACCGUGUUGUUUAU-AUCGAGUCUCUU-UUGGUA---U--AAGCGUCAAGUCCAUCGGAGAGAUCAUCA--UUUUGUUCAUCUUAAUGCCCUUUUGUGUAGG------AAAUUGAG-----GGAAGCUUAGGCUUCUC--AACAUUUUAAGACG---CCUAUGCAAGGGCUGGUAGGACAGACAUGC
AAZN01000301.1/56993-57206 AAAUAUAAUUAAUCGUGCGGAUUAAU-AA-UCCAGGACUCUAAAACCGUGUUGUUUAA-AUUGAUCAUGCG-UUGAUU---U--AAGCGUCAAGUCCAUCGGAGAGAUCAUCA--U---GUUCAUCUUAAUGCCCUUUUGUAUGAGCCACUUUUGCUGCAUUAUAGGUACCUUUGGGUAUU---UAUGGUGUGGUAUAUAGCUUUUGCAAGGGCUGGUAGGACAGACAUUC
AADM01000108.1/37439-37249 AAAAACCAAUAAUCGUGCGGAUUAUC-AA-ACCAGGACUAUAAAACCGUGUUGCUAGU-AUGCCUUUUCUAUGGUGUAAUUC--UAGCGUCAAGUCCAUCGGAGAGAACA-----UCUCGUUCAUCUUAGCGCUCUUUUGUGCAUC------GAG----U-----GGUCCCAUUAGGGCCGA------------GAUC---GUUGUGCAAGGGCCGGUAGAACGUACAUCU
AACF01000019.1/74170-74353 AAGUAUUAUUAAUCGUGCGGAUUAAU-UAAUCCAGGACUCUAAAACCGUGUUGCUUGA-AUUAAUUUCUAU-UUAGUU---CCCAAGCGUCAAGUCCAUCGGAGAGAUCAUCA---UUGGUUCAUCUUAGCGCCCUUUUGU--------------UUUAG-----UUGCUUUUAUA----UC--ACAACUUUG-------------GUGAGGGCUGGUAGAACUGACAUCU
CR382124.1/608616-608422   AUAUUUAUAAUAUCGUGCGGA------AA-UCCAGGACUAUAAAACCGUGUUGCUUCGUUGCGAUUUUUUAUUUGCAU---G-CAAGCGUCAAGUCCAUCGGAGAGAUCAA----UAUCGUUCAUCUUAGCGCCCUUUCUGUUGAA-----UAAAUUGGG-----AAAAGCCUA-GCU--UC--UUCUCACCA---CA---UACAAUGGAGGGCUGGUAGAUCGGAUAUCC
AE016816.3/547860-547685   AACCAAUAAAAAUCGUGCGGAUUUUUGCA-UCCAGGACUCUAAAACCGUGUUGCUAGG-GCCGCGCGCUAC-GCGGCC---A--CAGCGUCAAGUCCAUCGGAGAGAUCAG-----UUGGUUCAUCUCAACGCCCUUUCUUCCUGC------CGG----G-----CG------------CUC------------ACUG---GCAGGGGGAGGGCUGGUAGAACAGACAUUC
L33803.1/201-404           AUACAAAAUUAAUCGUGCGGAUUAAU-AA-UCCAGGACUAUAAAACCGUGUUGUUUAU-AUCGAGUCUCUU-UUGGUA---U--AAGCGUCAAGUCCAUCGGAGAGAUCAUCA--UUUUGUUCAUCUUAAUGCCCUUUUGUGUAGG------AAAUUGAG-----GGAAGUUUAGGCUUCUC--AACAUUUUAAGACG---CCUAUGCAAGGGCUGGUAGGACAGACAUGC
#=GC SS_cons               :::::::<<<<<<<_____>>>>>>>.,,.<<<-<<<<--------------<<<<<<.<<<<<<_____>.>>>>>>...>..>>>>----->>>>--->>>----------..---------<<<<<--<<<<<--<<<<<<<<......---<<<<<.....-<<<<<____>>>>>->..------>>>>----...>>>>>>>>>>>>>--->>>>>:::::::::
#=GC RF                    AuAuAaaauuaaUCGUGCGGAuuaau.aA.uCCAGGACUaUAAAACCGUGUUGcUugg.accgagUuUuuc.ucgguc...c..aAgCGUCAAGUCCAUCGGaGAGAUCAucA..UuUuGUUCAucuuAacGCCCUUUugugcggg......aagccggg.....uggagcuUaagcuccUc..uauauuccggaAua...cccgcgcaAGGGCUGGUaggaCagACAUuc
//
# STOCKHOLM 1.0

#=GF AC   RF01256
#=GF ID   snR43
#=GF DE   Small nucleolar RNA snR43
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Published; PMID:18332121; Wilkinson A
#=GF GA   60.00
#=GF TC   60.10
#=GF NC   55.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00027
#=GF DR   snornadb; snR43;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   8797828
#=GF RT   The RNA world of the nucleolus: two major families of small RNAs defined
#=GF RT   by different box elements with related functions.
#=GF RA   Balakin AG, Smith L, Fournier MJ
#=GF RL   Cell. 1996;86:823-834.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   20


X59720.2/107708-107500       CACUCCUGUUUCUGCCUCAUGUCUU-----UUAAAACGCUUCCACGGGA-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCCGU-UUACACAUUUUGAUACAACCGUAG-A-CGGCGUCUCGUUUCAAAGACCGUGUGGUUGUCUAUCAGUAUAU-ACUCAUUG-----UGUUUUUCAA----AAAAU--------CUCUGGGUUGUUUAGAU-GCCACUAUAUUU
AABZ01000112.1/9647-9855     CACUCCUGUUUCUGCCUCAUGUCCUU----UUACAACGCUUCCACGGGA-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCCGU-AUACACAUUUUGAUACAACCGUAU-A-CGGCGUCUCGUUUCAAAGAUCGUGUGGUUGUCUAUCGAUAUAU-ACUCAUUG-----UGUUUUUAG-----AAAAC--------CUUUGGGUUGUUUAGAU-GCCACUAUAUUU
AABY01000162.1/1359-1151     CACUCCUGUUUCUGCCUCAUGUCCUU----UUACAACGCAUCCACGGGA-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCCGU-UUACACAUUUUGAUACAACCGUAU-A-CGGUGUCUCAUUUCAAAGAUCGUGUGGUUGUCUAUCAAUAUAU-ACUCACUA-----UGUUUUUCAA----AAAAC---------UCUGGGUUGUUUAGAU-GCCACUAUAUUU
AACI02000137.1/4593-4383     CACUCCUGUUUCUGCCUCAUUUCCCC---UUUUAAACGCUUCCACGGGU-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCCGU-UUACACAUUUUGAUACAACCGUAG-A-CGGCGUCUCGUUUCAAAGAUCGUGUGGUUAUCUAUCGUUAUGU-ACUCAUUG-----UUUUCAAAAA----AUAAU--------CUCUGAGUUGUUUAGAU-GCCACUAUAUUU
AACG02000009.1/53495-53284   CACUCCUGUUUCUGCCUCGUGUCCU-----UUUAAACGCUUCCACGGGA-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCUGU-UCACACAUUUUGAUACAACCGUGA-A-CAGUGUUCCGUUUCGAAGAUCGUGUGGGUUUCUAUCGUUUCGU-ACUCAUUG-----UGUUUUCAAAA-AAAAAAU--------CUUUGAGUUGUUUAGAU-GCCACUAUAUUU
Z86109.1/3914-3708           CACUCCUGUUUCUGCCUCGUGUCCU-----UAGAAACGCUUCCACAGGA-CA-CGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCUAU-UCACACAUUUUGAUACAACCGUGA-A-CAGUGUUCCGUUUCGGAGAUCGUGUGGGUUUCUAUCGUUACGU-ACUCAUUG-----UGUUUU--CA----AAAAU--------CUCUGAGUUGUUUAGAU-GCCACUAUAUUU
AACF01000094.1/6899-6696     CUCUCCGAUUUCUGCCUCAUUUUCUU----UU-----GCUUCAAUAGAUUCA-UGGGUUCUAAUUUUUGGAGAAGAAUAAGCUGUAUGACGACUCAAUUCACACAUUUUGAUACAACCGUGA-U-UGA-G---CGUGGUGCAGAUCGUGAGAUUACUUC---AUUCGA-CUUGAUUA-----AUUCAAUUUAU-UGUUUAU--------UUUUCAAGAUUUGGAGU-GACUCUACAUUU
CR382121.1/752772-752561     CACUCCUGAUUCUGCCCCAUGUUCUU----U-----CUCUUCCAUAGAU-UAAUGGGUUCUGUUUAU-GGAGAAGAUAAAGCUGGUGAAUGGUGCGC-CUGCGC-CUUUGAUACAACAGUGG-GAUGC-ACUUCAUUUACCAGAUCGUGAGAACACAUU---AAACGA-CUUGUCUGA---CUUUAUUUUCG----AAUAUCCAAUAGCCUGACGAGACUUGAUGU-GCCUCUAUAUUU
AAZN01000184.1/27875-28075   CACUCCUAUUUCUGCCCCAUAUUCCC----CU----UUCUUCUAUGGAU-UAAUGGG-UCUAACGAU-GGAGAAGAAAAAGCCAAUGAAUGGUUCAA-UUACAACUUUUGAUACAUCCGUAA-U-UGA-ACUUCAUUUGUUGGAUCGUGUAGUUGAGUU---GUACAA-UUUCUUAA-----UUCCAAUAUG----UUAAU---------UAAGGAAACGCAAUUC-UCUUCUAUAUUC
AADM01000355.1/4342-4146     CCCUCCUAUUUCUGCCCCACAUUCUU----UA----CGCUACCAUAGAA-UAAUGGGUUCUAUUAAU-GGAGAAGAGAAAGCCUGCUAACGCAUUAC-CUACAC-UUUUGAUACAACCGUGG-G-UUUUUG--UGUUGACAGGAUCGUGUGUAAGGGCC---AAACAC-CUUUAAGA-----UUAGCU--------AAUUA--------UCUUAGAGAUAUGGUGC-UUCACUACAUUU
AAPO01000014.1/230229-230440 CACUCCUGUUUCUGCCUCAAAUCCGU----UU----UGUUUCUAUAGGA-UUAUGGGUUCUGGUGAU-GGAGAAGAUCAAGCCAUGAAAUGGGCUUA-UACCAACUUUUGAUACAUCCGGUA-U-UUGUCU--UGUUUCAUGGAUCGUGUGGAUGAUUUUGUAUCCGU-UGUGUGGAGC-AAUAUCAAUAUAAAGUUUGAU-------AUUGA-GCCUGAUCGGUC--CCACUACAUUA
AAVQ01000001.1/924370-924575 CACUCCUGUUUCUGCCCCAAAUUCUU----UU---ACACAGCCAUAGAA-UUAUGGGUUCUACUUAU-GGAGAAGAAAAAGCCAUUCAACGAACUUC-GGACAC-UUUUGAUACAACCGUCC-G-UUG-UU--UUUUGGGUGGAUCGGGUGGUUAGGCUUUGUAUCCU-UGCGUGACU--GACUCGGAACGU----UCCGG--------GAAAGUCUGAUCGGUCU--CCACUAUAUUU
AAFM01000047.1/164975-164781 ACCUCCUGUUUCUGCCUCAAGUUCUU----UU-----UUCACCAUAGAA-UAUUGGGUUCUGUUUAG-GGAGAAGAUAAAGCUGGUUGAAG--ACAA-CGACAC-CUUUGAUACAACCGUCGCU-UGU-----UUUUGACCAGAUCGUGUGGACAGGCCCAACCUUGA-AGGCAU-A-----UCGGCUCAUU----GCCCG--------U--UGUCGGUUUGGUCU--CCACUACAUCU
AACE03000004.1/744835-745036 CACUCCUGUUUCUGCCUCAUACUCUU----UC----UACUUCCAUAGAU-UAAUGGGUUCUAGUUAU-GGAGAAGAUAAAGCCAGGGGAUGACCUUU-CCACAA-CUUUGAUACACACGUGG-A-UGG-GCUUCAUUGUCUGGAUCGUGAGAACACAUU---GAAUGA-CUUCUUGC-----AAUUUCUAUA----AUUGA--------GCAAGAAGACUCAAUGU-CUCUCUAUAUUC
CR382139.2/961528-961315     CACUCCUGUUUCUGCCUCAGAUUCUU----AU-----GUUUCCAUAGAA-UUAUGGGUUCUGUUUAU-GGAGAAGAUUAAGCCUGUUAACGGAGCUU-GGACAC-UUUUGAUACAACCGUCC-A-UGU-UC--UUUUAGCAGGAUCGUGUGGUUAGAUUUGUCCGUGUGUGAUACACUCGAUAAUGGUUAGU----UCCAAAUG-ACGAGAAAAUCUGGCAAAUCU--CCACUACAUAU
AAFN02000078.1/177466-177681 AACUCCUGUUUCUGCCUCAGAUUCGUGCUUUCAUAUGGAAGCAAUGGGA-UUAUGGGUUCUGGUGAU-GGAGGAAAUCAAGCCAUCGAACAGACAAU-UGCUAC-CUUUGAUACAACCAGCU-U-UUGUUUUUUGUUUUAUGGAUCGUGUGG-UCGACUUGUAUCCGU-AGUUGGUU-----UGUUGUGUGAU--UACAAU--------AUUCAAUGAACUGAUCGUCCCACUAUAUUU
AE016814.2/333453-333261     CACUCCUAUUUCUGCCCCAUCUUCUU----AU-----UACUCCAUAGAU-UAAUGGGUUCUAGUAAA-GGAGAAGAAAAAGCCGUGGAAUGGCUUCC-CG----CACUUGAUACUUCG--CG-G-UUUAGCUUCAUUCCGCGGAUCGUGUGUA-GUGGCAGGUUAU---CCGGCUGC-----AGCAUUU-------UAUGU--------GCAGUCGGGCU-GUCAU-UGCUCUAUAUUU
HE576754.1/979444-979647     CUCUCCGAUUUCUGCCUCAUUUUCUU----UU-----GCUUCAAUAGAU-UCAUGGGUUCUAAUUUUUGGAGAAGAAUAAGCUGUAUGACGACUCAAUUCACACAUUUUGAUACAACCGUGA-U-UGA-G---CGUGGUGCAGAUCGUGAGAUUACUUC---AUUCGA-CUUGAUUA-----AUUCAAUUUAU-UGUUUAU--------UUUUCAAGAUUUGGAGU-GACUCUACAUUU
U56644.1/1-209               CACUCCUGUUUCUGCCUCAUGUCUUU----UAA-AACGCUUCCACGGGA-CA-UGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCCGU-UUACACAUUUUGAUACAACCGUAG-A-CGGCGUCUCGUUUCAAAGACCGUGUGGUUGUCUAUCAGUAUAU-ACUCAUUG-----UGUUUUUCAA----AAAAU--------CUCUGGGUUGUUUAGAU-GCCACUAUAUUU
AJ003086.1/1-207             CACUCCUGUUUCUGCCUCGUGUCCUU----AGA-AACGCUUCCACAGGA-CA-CGGGUUCUAAUUAU-GGAGAAGAUCAAGCUUUGAAAUGGCCUAU-UCACACAUUUUGAUACAACCGUGA-A-CAGUGUUCCGUUUCGGAGAUCGUGUGGGUUUCUAUCGUUACGU-ACUCAUUG-----UGUUUU--CA----AAAAU--------CUCUGAGUUGUUUAGAU-GCCACUAUAUUU
#=GC SS_cons                 ::<<<<---------<<<<<<<<<<_....__...._________>>>>.>>->>>>----------.>>>>,,,,,,,,,<<<<<<<<<<<<<<<<.<<<<________________>>>>.>.>>>->>-->>>>>>>>>>-----<<<<--<<<<<---------.<<<<<--<.....-<<<<<____....>>>>>........>-->>>>>---->>>>>.->>>>:::::::
#=GC RF                      CACUCCUGUUUCUGCCuCAugucCuU....Uu....cgcuuCcAUaGga.caAUGgGUUCUaaUuAU.GGAGAAGAuaAAGCcggggaAcGgcccgc.ccaCACauUUUGAUACAACCGugg.g.cggugcuUCgUuccccgGAUCGUGuGguUgccucUguauacgu.ccucauug.....ucuuuuuaua....aaaag........cuuugaggauuUgaggc.gcCaCUAuAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01257
#=GF ID   snR31
#=GF DE   Small nucleolar RNA snR31
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   48.20
#=GF NC   43.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00026
#=GF DR   snornadb; snR31;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   8265353
#=GF RT   Identification and functional analysis of a novel yeast small nucleolar
#=GF RT   RNA.
#=GF RA   Dandekar T, Tollervey D
#=GF RL   Nucleic Acids Res. 1993;21:5386-5390.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


Z75186.1/359-138             GAAGCAAAAUUACACCAUGAGUUCCUAUUAACGUCAGCCUCU--UUUGUACUCAUAA-UGUGGCU-UCGGAUGUUUGA-UGGGCGUUGCUUCAGU-GCGUACGGCUCAUGGUAGAUUAAU----------UAUUAGAAAGAUGUAUCUCCAGCUGUUGAUAUUAGAGGGGGAAGCCUUUCUCUUUCACCUCGCC-----UUUUUAAACACCUGAUACAGUUGGUCAUGAUUCGUUCUACAUUU
AABY01000003.1/33612-33389   GAAGCAAAAUUGUACCAUGAGUUCCUAUUAACGUCAGCCUCC--UUUUCCCUCAUAAGUAUGGUU-UUGGAUGUUUGA-UAGGCGUCGCUUCAAU-GCGUACGACUCAUGGCAGAUUAAUU---------UAUUAGAAAGAUGUAUCUCCAGCUGUUGAUAUCAGAGGGGGAAGCCUUUCUCUUUCACCUCGCC-----UUUUUAAACACCUGAUACAGUUGGUCAUGAUUCGUUCUACAUUU
AACH01000317.1/2350-2128     GAAGCAAGAUUGGACCAUGAGUUCCUAUUAACGUCAGCCUUC--UUUUUCCCAUAAG-GACGGUU-UCAGAUGUUUGA-UAGGCGUUGCUUCAGU-ACGUACGACUCAUGGCAGAUUAAUU---------UAUUAGAAAGAUGUAUCUCCAGCUGUUGAUCUUAGAGGGGGAAGCCUUUCUCUUUCACCUCGCC-----UUUUUAAACACCUGAUACAGUUGGUCAUGAUUCGUUCUACAUUU
AACG02000027.1/92408-92183   GAAGCAAAAUUGUGCCAUGAGUUCCCAUUAACGUCAACCUCU--UUUUCUUCCAUAGGGAUGGUUUUUAGAUGUCUGA-UGGGCGUUGCUUCAGUUGCGUAUGACUCAUGGUAGAUAAAUU---------UACUAGAAAGAUGUAUCUCCAGCUGUUGAUAUUAGAGGGGAAAGCCUUUCUCUUUCACCUCGCU-----UUUUUAAACACCUGAUACAGUUGGUCAUGAUUCGUUCUACAUUU
AACI02000485.1/4731-4508     GAAGCAAAAUUAGGCCAUGAGUUCCCGUUAACGUCAACCUCCU-UCUCUUCCGUAAG-AACGGUU-UUCGAUGUUUGA-UGGGCGUUGCUUCAGC-ACGUUCGACUCAUGGCAGAUAAAUU---------UAUUAGAAAGAUGUAUCUCCAGCUGUUGAUCUUAGAGGGGGAAGCCUUUCUCUUUCACCUCGCA-----UUUUAAAAAAUCUGAUACAGUUGGUCAUGAUUCGUUCUACAUUC
AACF01000029.1/72679-72443   AAUUAACUCAAAUGGCAUGUGUUCCUGUCGACGUCAUCUUACUCUUUACUUCUGUGA-GUGAGAUUUCCGAUGUCCAAACAGG--GUGAUUGUUU-CCCUCAAAUGCAUGCCAGAUAAAGUGCCCUUGGGUACAAGAAAGAUGUAUCUCCAGCUGUUGAUA--AGAGGGGGAAGCCUUUCUCUUCCACCUCGCCAAAAUUUUCAAAACUCCUGAUACAAUUGGUCAUGAUUCUUUCUACAUUC
AADM01000109.1/102001-101793 AAAACAUUAAACAACCAUGCGUUCCA-CUGGCGUCACUAGUA--CGUACUACUAUCG-UUCUGGU-UU-GAUGUCAAU-UUUUUAUGGUGGUUUU-UUUAGCGAUGCAUGGGAGAUAAAUG---------GUUU---AAGAUGUAUCUCCAGCUAUUGAAG---UGAGGGAAAGCCUUUUUCUUUCCCCCAGCC-----------AAAAUCUGAUAUAGUUGGUCAUGUUUCUUGCGACAAAU
AACE03000006.2/473757-473963 UAUACAAA---CAACCAUGUGUUCCA-CCGGCGUCACUGUAG--GCUUCCUUCCAUGCCUACGGU-UA-GAUGCUUGA-AUUUCUUUGGUGGCAU-UCUGUCGACACAUGGAAGAUUGAUU---------UUAG-GUAAGAUGUAUCUCCAGCUAUUGAAC---GCGG-GAAAGCCUUUCUCUUUC-CUGCCCC-----------AAAAACUGAUAUAGUUGGUCAUAAUUCUUGCAACAUCA
#=GC SS_cons                 ::::::::::::::((((((((,<<<<<<<<<<<<<<<<---..-<<________>>.--->>>>.--->>>>->>>>.>>>><<<<<<______.>>>->>>))))))))----------.........----<<<<-<<-------<<<<<<<<--------<<<<-<<<<<_______>>>>>->>>>---.....---------------->>>>>>>>------->>->>>>::::::
#=GC RF                      aAagcAaaAuuauacCAUGcGuUcccgucggCgUCAcccUuu..ucuucuucuauag.uuugggU.UuaGAuGUccga.cgggcgucGcUucauU.gCguacgaCgCAUGguAGAUaAAUu.........UauuaGaAAGAUGUAUCUCCAgCUGUUGAuaUuAGaGGGGgAAGCCUUUCUCUUcCACCuCGCc.....UUUuuAAAaAcCUGAUACAGuUGGUCAUGAUUCuUuCuACAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01258
#=GF ID   snR10
#=GF DE   Small nucleolar RNA snR10
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   70.00
#=GF TC   107.90
#=GF NC   64.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00031
#=GF DR   snornadb; snR10;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   6197183
#=GF RT   Yeast contains small nuclear RNAs encoded by single copy genes.
#=GF RA   Wise JA, Tollervey D, Maloney D, Swerdlow H, Dunn EJ, Guthrie C
#=GF RL   Cell. 1983;35:743-751.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   15


Z72610.1/833-1077              AACGCAAAUUUAACAGCCAUUCGUAACAC-GU-ACA-GUAUCUCGUCGAGGUUGAACCCC--UCCGGGGCGUUCUUGACCCAUGAAGAAUGUGGAUUG-GUGUUGCA----AUAUA----------UUUAU-U-AUUGGCU--------------------UGGACUGGAGA-ACAA-----A------U-UUAUCGAUCUUGGGUGCAACAGUCUUUCUGUC--GUCUGUUUUU-----UAGCAGAUCUAAGGG--UUUACCUUCGUGUGCCCGGAUGAGGACCGUUGCAAGGAUUGAUAAUACAACU
AABZ01000003.1/45202-44958     AACGCAAAUUUAACGGCCAUUCGCAACAU-AU-ACA-GUAUCUCAUCGAGGUUGAACCCC--UCCGGGGCGUUCUUGACCCAUGAAGAAUGUGGAUUU-GUGUUGUA----AUAUA----------UUUAU-U-AUUAGCU--------------------UGGACCGGAGA-ACAA-----A------U-UUAUCGAUCUUGGGUGCAACAGUCCUUCUGUC--GUCUGCUUUA-----UAGCAGAUCUAAGGG--UUUACCUUCGUGUGCCCGGAUGAGGACCGUUGCAAGGAUUGAUAAUACAUUU
AACA01000537.1/2766-2521       AACGCAAAUUUAACAGCCAUUCGCAGCAC-GU-ACA-GUAUCUCAUCGAGGUUGAACCCC--UCCGGGGCGUUCUUGACCCAUGAAGAAUGUGGAUUU-GUGUUGCA----GUAUA----------UUUAC-U-ACUGGCU--------------------UGGACUGGAGA-ACAA-----A------G-UUAUCGAUCUUGGGUGCAACAAUCUUUCUGUC--GUCUGUUUUU----AUAGCAGAUCUAAGGG--UUUACCUUCGUGUGCCCGGAUGAGGACCGUUGCAAGGAUUGAUACGACAUCU
AADM01000052.1/7763-8010       AACGCAAAUUCA-CAGCCAUUCGCAGUGCAUA-ACA-GCAUCUCCUUGAGGUCGAACCCC--UCCGGGGCGUUCUUGGCCCAUGACAAGUGUAGAUAGUGUGCUGCC----UUUUU----------AUUAA-GCUAUAGCU--------------------UGGACUGGAGA-AGAA-----A------U-UUACUGAUCUUGGGUGCGACGGCUCAUGUGUU--GCUUGUCUUC----GUGGCAGGUCUAAGGG--AUUGCCUUCGUGCGCCCGUAUGGGAGUUGUUGCAAUGAUCACUAAUACAAAU
CR382125.1/1700339-1700595     AACGCAAAACUCACAGACAUUCGCAGCGC-AU-AAAAGCAUCCUCUUGAGGUUGAACCCC--UCCGGGGCGUUCUUGGCCCAUGAAAAGUUGGGAUAU-GUGUUGCA----GUUUG----------CAUAA-C-UAUUUUCG-----------------GAUGUACUGGAGA-ACGAAUCCCA------U-CGAAUGGUCUUGGGUGCAGCGACUCAUCUGUU--GCUUGGUCUUA--GUUACCAGGUCUAAGGG--UUUACCUUCGUGUGCCCGUAUGAGAGUGGCUGCAAGGAUCAGUCGAACAAAC
AACF01000138.1/19155-18890     AACGCAAAAACA-CAGCCAUUCACAACAU-AUAACA-GUAUCUCAUUGAGGUUGAACCCC--UCCGGGGCGUUCCGGUCCCAUGACAAAUGUAGAAUU-GUGUUGUAAACUAAAAA----------UUCAU-U-UUUUUGUUUUAU---------UUUGCCUGUGCUGGAGA-AUAA-----ACUUUUCU-UUAUUGGUCUCGGGUGCAACAAUUCUUCUGUC--GUUUGCCUUC-----GUGCAAAUCUAAGGG--UUUACCUUCGUGUGCCCGUAUGGGAGUCGUUGCAAGGAUCACUAAUACAUUU
AAFM01000016.1/250023-249797   AACGCAAAUUCA-CAGCCAUUCGCAAC-G-CU-AAU-GCAUUCCUUUGAGGUUGAACCCU--UA--UGGCGUUCU-GACCCAUGACCAUA--GGAGUA-UAGUUGUC----GAAAG----------------U-GUCAGAA--------------------UGGACUGGAGA-ACAA------------U-UGGUUGAUCUUGGGUGCAGCACCUCAUCGGUA---AAUACU---------UGUAUUUCUAAGGG--UUUACCUUCGUGUGCCCGUAUGGGAGGUGGUGCAAUGAUCAGCUGUACAUUU
AAVQ01000002.1/1147703-1147933 AACGCAAAUUUCACAGCCAUUAGCAACGC--U-AAA-GCAUUCCUUUGAGGUUGAGCCCA--UUAC-GGCGCUCU-GACCCAUGACCAU--UGGGAUA-UUGUUGU-------GGA-----------UACU-U-CCGUCGG--------------------UGGACUGGAGA-ACAA------------U-CGGUUGAUCUUGGGUGCAGCAUUCCAUCUGUA--A----AUACU-----UGUUAUUUCUAAGGG--AUUACCUUCGUGUGCCCGUAUGGGGUUUGGUGCAAUGAUCAGCUGUACAUCG
AAFT01000001.1/74020-74263     AACGCAAAUUCA-CAGACGUCCACAACGU--U-ACA-GCAUCCCGUAGAGGCUGAACCCA--UUAC-GGCGUUCU-GGCCCAUGACCACUGGGGUAUU---GUUGUA----UUGGAGGGCGCAAGCUCUCC-U-CUUGCGG--------------------CGGACUGGAGA-ACAA-----C--------UGGUUGAUCUUGGGUGCGAUAUUCCAUCGGCG---AAUAC--UU-----U-GUAUUUCUAAGGG--ACUGCCUUCGUGCGCCCGUAUGGGGAGUGUUGCAAUGAUCAGCUAUACAUGU
AAZN01000229.1/53179-53449     AACGCAAAUUUCACAGCCAAUCGCAACAUAUA-ACA-GUAUCACAUCGAGGUUGAACCCC--UCCGGGGCGUUCUUGACCCAUGACAUUUGUUGAUUU-GUGUUGCA----ACGAU----------UCUGAUA-UUUUUUAAUGUUAGAGUUGUCUUUGCUUGGACUGGAGA-AUAA-----ACU--AUA-UAAAUGAUCUUGGGUGCAACGAUUCAUCUGUU--GUCUGUCUUU-----GUGCAGAUCUAAGAG--UUUACCUUCGUGUGCUCGUAUGGGAGUGGUUGCAAGGAUCAUUAAUACAUCU
AACE03000009.1/471521-471264   AACGCAAAUUUCACGGCCAUUCGCAACAUAUA-ACA-GCAUCCCCUCGAGGUUGAACCCC--UCCGGGGCGUUCUUGACCCAUGACAAGCGUGGAUAUUGUGUUGCC----UUUCG----------CUUUUGC-GAAGUCUGU---------------GCCUGGACCGGAGA-GCAA-----AC----CG-UUACUGAUCUUGGGUGCAACGUUCCAUCUGUU--GUUUGUCCUU----GUGGCAGAUCUAAGGGAUUUUACCUUCGUGUGCCCGUAUGGGGAUCGUUGCAAUGAUCGUUAAUACAUCU
CR382136.2/435988-436222       AACGCAAAACCA-CAGCCAUUCACAAC-G-UU-AAU-GCAUUCCCUUGAGGUUGAACCCA--UUA-UGGCGUUCUUGACCCA--UGACCAUCGGAAUA-UAGUUGU-------GUU----------UUUUU-C-ACUGGA---------------------UGGACUGGAGA-AAAA-----U------U-UGGUUGAUCUUGGGUGCAGCACUCCAUCUGUU--GAAUAAUUUA-----U-UUGUUUCUAAGGG--AUUACCUUCGUGUGCCCGUAUGGGGAGUGGUGCAAUGAUCAGCUGGACAUAU
AE016819.5/317647-317411       AACGCAAAUUCA-CAGCCACUCGUAGCAC-AU-ACA-GCAUCCCCUUGAGGUUGAACCCC--CCCGGGGCGUUCUUGACCCAUGACAAGCGCGGAUAU-GUGUUGC---------C----------UUUAU-G-C-UUGCU--------------------UGGACUGGAGA-ACAA-----A------UCCAACUGGUCUUGGGUGCAGCGGCCCAUCCGUG---CCUGGCCUU------GCCAGGCCUAAGGG--ACUGCCUUCGUGCCCCCGUAUGGGGGCUGCUGCAAGGAUCAGUUGAACAUUA
AAFN02000069.1/73765-74015     AACGCAAAAUUCACAGCCAUUAACAACGU--C-AAA-GCGUUCCUUCGAGGUUGAACCCAAUUAUUUGGCGUUCUUGACCCA--UGACCUUUGGAAUA-UUGUUGUA----CUUUA----------UGUUU-U-AUUUGA---------------------UGGACUGGAGAAAAAA-----A------U-UCAUUGAUCUUGGGUGCAGCAUCUCAUCUGUUUUGAGAUUAACUUUGUUUUAAUUUCCUAAGGG--UUAACCUUCGUGUGCCCGUAUGGGAGAUGGUGCAAUGAUCAGUGAGACAUUU
X03372.1/207-451               AACGCAAAUUUAACAGCCAUUCGUAACAC-GU-ACA-GUAUCUCGUCGAGGUUGAACCCC--UCCGGGGCGUUCUUGACCCAUGAAGAAUGUGGAUUG-GUGUUGCA----AUAUA----------UUUAU-U-AUUGGCU--------------------UGGACUGGAGA-ACAA-----A------U-UUAUCGAUCUUGGGUGCAACAGUCUUUCUGUC--GUCUGUUUUU-----UAGCAGAUCUAAGGG--UUUACCUUCGUGUGCCCGGAUGAGGACCGUUGCAAGGAUUGAUAAUACAACU
#=GC SS_cons                   :::::::::::::((((((,,,<<<<<<<.-<.<<<.----------<-<<<<<<<<<<<..____>>>->>>>-->>>>>-------->>>>-----.>>>>>>>,....,,<<<.........._____.>.>>,,,,,....................)))-)))----.----.....-......-.(((((((((-------((((-((((((--(((..,<<<<<<___....._>>>>>>,,,,,<<<..<____________>>>>,)))))))))-))))----))))))))):::::::
#=GC RF                        AACGCAAAuuuaACaGcCaUUcgCAaCac.uc.aca.GcAUcuCaUuGAGGuuGAaCCCc..UccggGGCGuUCUUgaCCCAUGAcaaaugugGAuuu.guGuUGca....auggg..........uuUau.c.ccUuuuu....................uGgACuGGAGA.AcAA.....A......u.uggcuGaUCUUGGGUGCaaCagccCcuCuguc..GccugccuUu.....uggcaggUCUAAGGG..cUUACCUUCGUGUgCCCGgauggGggcuGuuGCAAuGAuCagccauACAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01259
#=GF ID   snR63
#=GF DE   Small nucleolar RNA snR63
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   53.00
#=GF NC   44.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00061
#=GF DR   snornadb; snR63;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300052;
#=GF RN   [1]
#=GF RM   10547039
#=GF RT   Structure and biogenesis of small nucleolar RNAs acting as guides for
#=GF RT   ribosomal RNA modification.
#=GF RA   Filipowicz W, Pelczar P, Pogacic V, Dragon F
#=GF RL   Acta Biochim Pol. 1999;46:377-389.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


Z74123.1/1919-1665         UUUAAUGAUGAAGAUUUUAAUU-UUCCGUUGGUCUAUUAAGAACAGAAGUACUUCAAAACUACUUUUUAAGACCAUCCUUUUACAGUAUUU-UUUCAAUAUUGUAAAACUUCUCAUUUACUUUGUGUCUUUAUGAUCUCAUCGUUCUGGUGGACCAUAAUC-AGACGCACGGUAUACUUCGUU--UCUGUUGGAGAAUAUUGGGAGUCUUUUAAUGUGAUGAGUGGCCAACAUAACCUUAUAGUCAUAGUUACACUGAUU
AABY01000419.1/584-331     UUUAAUGAUGAAGAUUUUAAUU-UUCCGUUGGUCUAUUAAGAACAGAAGUACUUCAAAACUACUUUUUAAGACCAUCCUUUUGCAGUAUUU-UUUUGAUAUUGUAAAACUUCUCACUUACUGUGUGCCUU-AUGGUCUCGUCGUUCUGAUGGACCGUAAUC-AGACGCACAGUAUACUUCGUU--UCUGUUGGAGAAUAUUGGGAGUCUUUUAAUGUGAUGAGCGGCCAACAUAACCUUUUAGUCAUAGUUACACUGAUU
AABZ01000568.1/3571-3319   UUUAAUGAUGAAGAUUUUAAUU-UUCCGUUGGUCUAUUAAGAACAGAAGUACUUCAAAACUACUUUUUAAGACCAUCCUUUUACAGUAUUU-CU--AGUAUUGCAAAACUUCUCAUUUACUCUGCGUCUUUAUGAUGUCAUCGUUCUGAUGUGUCGUGAUC-AGAUGCUAAGUAUACUUCAUU--UUUGUUGGAGAAUAUUGGGAGUCUUUUAAUGUGAUGAAUGGCCAACAUAACCUUAUAGUCAUAGUUACACUGAUU
AACI02000012.1/27730-27474 UUAAAUGAUGAAGAUUUAAAUUAUUCCGUUGGUCUAUUAAGAACAGAAGUACUUCAAAACUACUUUUUAAGACCAUCCUUUUACAGUAUUU--UUUAAUAUUGUAAAACUUCUCAUUUACUUUGUGUCUUUAUGGUCUCAUCGUUCUGAUGGAUUGUAGUU-GGACGCGAGGUAUACUUCAUUGAUAUGUUGGAGAAUAUUGGGAGUCUUUUAAUGUGAUGAGUGGCCAACACAACCUUAUAGUCAUAGUUACACUGAUU
AACA01000285.1/12444-12701 UAAAAUGAUGAAGAUUUUAAUU-UUCCGUUGGUCUAUUAAGAACAGAAGUACUUCAAAACUACUUUUUAAGACCAUCCUUUAACAAUGUUUCUUUUAAUAUUGUUAAACUUCUCAUUUACUUUGCGUCUUUAUGGUCUCAUCGUUCUGAUGGAUCGUAAUUUAGACACGAGGUAUACUUCAUUAAUUUGUUGGAGAAUAUUGGGAGUCUUUUAAUGUGAUGAGUGGCCAACACAACCU-AUAGUCAUAGUUACACUGAUU
AF064275.1/1-255           UUUAAUGAUGAAGAUUUUAAUU-UUCCGUUGGUCUAUUAAGAACAGAAGUACUUCAAAACUACUUUUUAAGACCAUCCUUUUACAGUAUUU-UUUCAAUAUUGUAAAACUUCUCAUUUACUUUGUGUCUUUAUGAUCUCAUCGUUCUGGUGGACCAUAAUC-AGACGCACGGUAUACUUCGUU--UCUGUUGGAGAAUAUUGGGAGUCUUUUAAUGUGAUGAGUGGCCAACAUAACCUUAUAGUCAUAGUUACACUGAUU
#=GC SS_cons               ::::{{{{{<<<<<<____>>>.>>>,{{{{{{{-{{{----{{{<<<<<<_________>>>>>>,,[[[[[,,,,,<<<<<<<<<<<<_.____>>>>>>>>>>>>,,((((,,,<<<<<<<<<<<<<<<<<<<<-<<<<_____>>>>>>>>>>>>--.>>>>>>>>>>>>,,<<<<<__.._____>>>>>,,,,,,))))]]]]],,,,}}}----}}}}}}}}}},,,,,,,,,,,}}}}}:::::::::::::
#=GC RF                    UuuAauGauGaagauUUuAauu.uuCCGuuGGuCUacuAAGAaCagaaGuaCUUCAAAACuaCuuuUUaaGaCCAUCCuuuugCaguauuU.uUUuaauacuGcaaaaCUuCuCAuUuaCccuGcGuCuuuacGgucUCauCGUUCUGauGgacCguaaUc.aGaCgCaggGuaUACuuCaUU..UuUGUuGgaGAAUAUUGgGaGuCuuUUAAuGuGAUGaguGgCCaaCAuAACCUUAUAguCauAGUUACACUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01260
#=GF ID   snR11
#=GF DE   Small nucleolar RNA snR11
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   42.00
#=GF TC   42.30
#=GF NC   40.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF CL   CL00022
#=GF DR   snornadb; snR11;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   3327689
#=GF RT   A yeast small nuclear RNA is required for normal processing of
#=GF RT   pre-ribosomal RNA.
#=GF RA   Tollervey D
#=GF RL   EMBO J. 1987;6:4169-4175.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


Z47815.1/14842-15099         AAUAAUGUCUUUUAUA---AUAGACACCCAGAGUCACGAUUCGUCUUGGUUUUAGAGA-UUCUGUUUCGACAGUU-UUUUUAGGCGGUGGACGUAUAUAGUUUACUUAAUCGUUUACU-AUACGGUGGAGUACUAAUAC----UAUUUCACUGUCGUGCUCGCGGUUGAUCUUAGAUAAAUAUAUUUCUUUUUCAU------------------AAAGAAAGUGA-GUGGAUCUUCCCUGGAAGUACGA---AUAAUGUACUUAUGAUUAGAUUCUCUUCACGCACAUAC
AACI02000295.1/4050-3790     AACAAUGUCUUUUAUA---AUAGACACCCAGAGUCACGAUUCGUCUUGGUCUUAGAAAAUCCUGUUUCGGCAGUUUUUUUUAGGCAGUGGACGUAUAUAGUUUACUUAAUCGUUUACU-GUACGUUGAAAUACUAAUAC----UAUUUCACUGUCGUGCUCGCGGUUGAUCUUAGAUAAAUAUAUUUCUUUUUCAUA-----------------AAAGAAAGUGG-GUGGAUCUUCCCUGGAAGUACGA---UCAAUGUACUUAUGAUUAGAUCCUCUUCACGCACAUAC
AACH01000003.1/9678-9937     AACAAUGUCUUUUAUA---AUAGACACCCAGAGUCACGAUUUGUCUUGGUCCUAAAAAAUUCUGUUACGACAGUU-UUUAUAGGCGGUGGACCUAUAUAGUUUACUUAAUCGUUUACU-AUACGGUGGGGUACUAAUAC----UAUUUCACUGUCGUGCUCGCGGUUGAUCUUAGAUAAAUAUAUUUCUUUUUCAGA-----------------AAAGGAAGUGA-GUGGAUCUUCCCUGGAAGUACGA---UCAAUGUACUUAUGAUUAGAUCCUCUUCACGUACAUCU
AACA01000120.1/9107-9355     AACAAUGUCUUAAUUG---AUAGACGCCCAGAGUCACGAUUCGUCUUAGUUUUAGAAAAUUCUAUUUCGAUAGUUUUUUUUAGACGGUGGACGUAUAUAGUUU------------ACU-AUACGGUGGGGUACUAAUAC----UAUUUCACUGUCGUGCUCGCGGUUGAUCUUAGAUAAAAAAAUUUCUUUUUUAUA-----------------AAAGGAAGUGA-GUAGAUCUUCCCUGGAAGUACGA---UCAAUGUACUUAUGAUUAGAUUUUCUUCACGCACAUAC
AAZN01000216.1/9623-9352     AACAAUGUCUUUUAU----AUAGACACCCAGAGUCACGAAACGUUCUGGUCUUUG-UACCGGUGGAUGUCUAUAC-UAUUUAUGUUUU--AUUUAUUUAGAAUAUUAAAUUGUGU------ACGGUCAUAGCAGAAUACCACUGUUAUGAUUGUCGUGCUCGCGGUUGAUCUUAGAUCAA----UGUUUGUUGAACCUUACCAAUAUGGGGUACACAGACGGUAAAGUUUAUCAAUGCUGGGGGUACUAAUUUUAUUGUGCCUUUUAUUCGGUAUCCUUUACUAACAUCU
AACF01000002.1/137514-137744 UACAAUGUCUUUUAUAAGAAUAGACACCCAGAGUCACGAUUCGUUUUUC-GGAUG---------------------AAAUAUGCCAGUGAACGUAUAUAUUCCAUUC----GUGGAAUCAUACGGUAGGAUACUCGA------UAUUCUACUGUCGUGCUCGCGGUUGAUCUUAGAUUAA-------UCCUUGUAAA-----------------AGGAAUUUGGA-AUGUAUCUACCCUGGAAGUAUGAA--UUAAUAUACUUAUAAUUAGAUCCAUCUUCACUACAAAC
#=GC SS_cons                 ::::::::::::::::...::(((((-((------((((,,<<<<<----<<<<<<<<---<<<<____>>>>--.>>>>>>>>---->>>>>,,<<<<<<--<<______>>-->>>.>>><<<<<<<<<<_______....>>>>>>>>>>))))------))-))-))),,,,,,,,,,,,<<<<<<<______.................>>>>>>><<<<.<-<<<<<<-------<<<<<<<_...____>>>>>>>------>>>>>>->->>>>::::::::
#=GC RF                      AACAAUGUCUUUUAUA...AUAGACaCCCAGAGUCACGAuucGUcuUggUccuagagaauucuguuucgacaguu.ucuuuaggcagUggACgUAUauaguuUacUuAAUuguuuacu.auACggUgggauacuAAuAC....uaucccAcuGUCGUGCUCGCGGUuGAUCUUAGAUaAAuAuAugucucUUuuAua.................Agagacaguga.GUggAuCuuccCUGGagGuAcgA...UuAaugUaCcuaUgAUUaGaUccuCUucacuuACAuac
//
# STOCKHOLM 1.0

#=GF AC   RF01261
#=GF ID   snR82
#=GF DE   Small nucleolar RNA snR82
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   60.00
#=GF TC   63.50
#=GF NC   50.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00040
#=GF DR   snornadb; snR82;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300020;
#=GF RN   [1]
#=GF RM   12853629
#=GF RT   Computational identification of non-coding RNAs in Saccharomyces
#=GF RT   cerevisiae by comparative genomics.
#=GF RA   McCutcheon JP, Eddy SR
#=GF RL   Nucleic Acids Res. 2003;31:4119-4128.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


Z72621.1/2505-2772           AUGGCUCUUCAACACAUUUCAACAUGUUCAAGUAAUUUGUGUUAGUGGAUGACCAUUUAGGGGCUGCUGGC----CUGGUU---ACCGGGAGUUUUUCUUGG-AUCCAA----GCUAGCUUUUCCGUC--------UGAUUAUCCUUAAGCUUCACAAAUUAC--AAUUUUUCCCACGCAUUAAGAAAUAAGCUCAAGAUGCCUAAAAUAAG-UUCU-A-UCCCGCCUUUUUUCGCUAACAAUGACUGAGUA-UUCCCACAGUCUAUAGUUUGAUAGUAGAUGGGCGGAAAUUU
AABZ01000003.1/73091-72822   AAGGCUCUUCAACACAUUUCAACAUGUUCAAGUGAUUUGUGCUAGUGGAUGAGCAUUUUGGGACGACUGGC----UUGGUU---AUCGGGAGUUUUUCUUGA-AUCCAA----GCUAGUUUUCUCUCG--------UGAUUAUCCUUAAGCUUCGCAAAUUAC--ACUUUAUCCCACGCAUUAAGAAAUAAGCUCAAGAUGCCUAGAAUUAG-UUUUUA-UCCUGCCUUUUUUCGCUAACAAUGACUGAGUAUUUCCCACAGUCUAUAGUUUGAUAGUAGACGGGCAGACAUUU
AACI02000309.1/1028-1298     ACGGCUCUUCAACACAUUUCAACAUGUUCAAGUGGUUUGUGGUAGUGGGUGAACAUUUUGGGACUAUCAAC----UUGGUU---CUCGGGAGUUUUUCCUGAGACUCAG----GUAGGUUUUUCUGUG--------UGGUUAUCCUUAAGCUUCACAAAUUAC--AACUUAUCCCACGCAUUAAGAAAUAAGCUCAAGAUGCCUAAAAUAAGUUUUU-A-UCCUGCCUUUUUUCGCUAACAGUGACUGAGUAUUUCCCACAGUCUAUAGUUUGAUAGUAGAUCGGCAGAAAUUU
AACA01000219.1/3705-3437     AAGGCUCUUCAACACAUUUCAACAUGUUCAAGUGAUUUGUGCAAGUGGAUAGACAUUGUGGAUUAGUUGGC----UUGGUU---CUCGGGAGUUUUUCUUGGGAGCCGA----ACUGGUUUCUCUGUG--------UGGUUAUCCUUAAGCUUCGCAAAUUAC---ACUUUACCCACGCAUUAAGAAAUAAGCUCAAGAUGCCUAUAAUAAG-UUUA-AAUCCUGCCCUUUUUCGCUAACAGUGACUGAGUA-CCUCCACAGUCUAUAGUUUGAUAGUAGAUGGGCAGAAAUUU
AAZN01000244.1/218286-217999 AAGGCUCUUCAACACAUUUCGACAUGCUCAACGUAGGUUUUCUAAUUAUUUCUGUUGGAUGAAUCGUAUGAUAAUUCGGUUUAUAUUAAGAGUUUUUCUUAGUUAUUGAAUAUUCAAACUUUUCACUUAAAGUCUAAUAGGA---UUAUGUUGGAUAUUUUGGCUUACAAAUCCCACGCAUUAAGAAAUAAGCUCAAGAUGCCUAUAUUAAA-UUUU-A-CAACGCCUUUUUUCGCUAACAACGGCUGAAACACAUCCACAGUCUGUAGUUUGAUAGUAGAUGGGCGCAAAUUC
#=GC SS_cons                 ::<<<<<<<------<<<<<---<<<<----<<<<<<<<<<--<<<<<<<<<-<<----<<<<--<<<<<<....-<<<--...-<<<<<<<___>>>>>>>--->>>-....>>>>>>-->>>>---........>>->>>>>>---->>>->>>>>>>>>>..------------>>>>--->>>>>------>>>>->>>---------.----.-.--<<<<<<-----------<<<-<<<<<-<_______>->>>>>------>>>--------->>>>>>::::::
#=GC RF                      AaGGCuCuuCAACACauuuCaACauGcUCAAgugauuugugcuaGuGGauggacaUuuugGgguugccgGc....UcGgUU...accggGagUUUuuCcugguaucCgA....gCcggcUUccCcgUu........ugaccauCCUUAagCuucacaaaucac..aAcuuauCCCACgCauUAAGaaauAAGCUCaaGaUGCCUAuAaUAAg.UUUu.A.ucccGCCcUUUUUCGCUAACaauGaCuGAGuauuuuCCACaGuCUaUAGUuuGAUAGUAGAUgGGCggAAAUUu
//
# STOCKHOLM 1.0

#=GF AC   RF01262
#=GF ID   snR44
#=GF DE   Small nucleolar RNA snR44
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   33.00
#=GF TC   33.60
#=GF NC   32.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00035
#=GF DR   snornadb; snR44;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15306656
#=GF RT   Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the
#=GF RT   Saccharomyces cerevisiae genome.
#=GF RA   Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM
#=GF RL   Nucleic Acids Res. 2004;32:4281-4296.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


U56645.1/1-211             CUCCGGGCUGAUAACUAGAUGGUGUGAUCGGGC-AGUAUACUAAUUUAUACUGGACAAAGAC-UCGUAAAAGAUGUUCUUUGUGCUUAGUCCCAUACUGUUUUUUAAGUGUCCGGGAUAUUUAAUCCCAUGUGGAAAUGCUUCUUACACGGUUAUGGAUUACACCUCAUGU-GUAGCUACUAUAUCCAUUACCGUUUACUUUUCCUCAAAAUCU
AABY01000020.1/57086-56876 CUCCGGGCUGAUAACUAGAUGGUGUGAUCGGGC-AGUAUACUAAUCUAUACUGGACAAAGAC-UCGUAAAAGAUGUUUUUUGUACUCAGUCCCAUACUGUUUUUUAAGUGUCCGGGAAAUUCAACUCCAUGUGGAAAUGCUUCUUACACGGUUAUGGAUUACAUUUUACAU-GUAGUUACUAUAUCCAUUACCGUUUACUUUUCCUCAAAAUUU
AACH01002147.1/1226-1016   UUCCGGGCUGAUAACUAGAUGGUGUGAUCGGAC-AGUAUAAUAAUUUAUACUGAACAAAGAC-UUUCAAAAGAUGUUCUUUGUGCUCAGUCCCAUACUGUUUUUUAAGUGUCCGGGAAAUUCAAUCCCAUGUGGAAAUGCUUCUUACACGGUCAUGAAUUACACUUCGCGU-GUAGCUACAAUAUCCAUUACCGUUUACUUUUCCUCAAAAUUU
AACI02000064.1/20206-19995 UUCCGGGCUGAUAACUAGAUGGUGUGAUCGGACCAGUAUAAUAACUUAUACUGGACAAAGAC-UCCUAAGGGAUGCUCUUUGUACUCAGUCCCAUACUGUUUUUUAAGUGUCCGGAAAAUUCAAUCCCAUGUGGAAAUGCUUCUUACACGGUCAUGAAUUACACUUCGCGU-GUAGCUACAAUAUUCAUUACCGUUUACUUUUCCUCAAAAUUU
AACG02000134.1/16938-16731 UUCCGGGCUGAUAACUAGAUGGUGUGAUCGGAC-AGUAUACUAAUGUAUACUGGACAAAGAC-UCCUAAAAGGUGAUCUUUGUACUCAGUCCCAUACUGUUUUUUAAGUGUCCGGGAAAUACAAUACCAUGUGGAAUCGCAUCUUACACGGUCAUGAAUUACACUUCAAGU-GUA---ACAAUAUUCAUUAGCGUUUACUUUUCCUCAAAAUUU
AACA01000309.1/269-61      UUCCGGGCUGAUAACUAGAUGGCGUGAUCGGAC-AGUAUACUAAUGUAUACUGGACAAAGAC-UCCUAACAGGUGAUCUUUGUACUCAGACCCAUACUGUUUUUUAAGUGGCCGGGAAAUACACUACCAUGUGGAAUCCCAUCUUACACGGACAUGAAUCACACUUCAAGUAGUA---ACAAUAUUGAUUAACGGUUACUUACCCUCAAAAUUU
AAZN01000172.1/34417-34237 UCCCGGACUGAUAACUGGAUGGUUUGAUCGGAU-AGUGUCA-----AAUGCU--AAAAUGUCUUCCUAUUGGAU-UUCAUU----UCAGUCCCAUACUGUCUUUUAAGUGUCCGGGAGAAUGA-----AUGUGGAAAUGCUUCUUACACGGUUUGAAAU------UUUG---------UCAGUAUUCCAAACCGUUUACUUUUCCUCGACAUCU
#=GC SS_cons               ::((((((--------((((((((((---((((.,<<<<<______>>>>>,<-<<<<<<<<.<<______>>->->>>>>>>->,,,))))))))))))))-------))))))-----------------<<<<------------<<<<-<<<<<<<<<<<_____>>.>>>-------->>>>>>->>>>------>>>>::::::::::
#=GC RF                    uUCCGGgCUGAUAACUagaugGuguGAUCGGac.AGuauaaUAAUuuauaCUGgaCaaaGaC.uCcUAAaaGaUGuuCuuuGuaCUcAguCCCacaCugucuUUUAAGUGcCCGGGAaAuucAaUaCCAUGUGgaaaugCuUCUUACACGguuauggauuaCacUUcaagu.GuaGcUACaAUauccauuacCGuUUACUuucCCUCAAAAUuU
//
# STOCKHOLM 1.0

#=GF AC   RF01263
#=GF ID   snR191
#=GF DE   Small nucleolar RNA snR191
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   46.00
#=GF TC   46.90
#=GF NC   45.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00043
#=GF DR   snornadb; snR191;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12810910
#=GF RT   A snoRNA that guides the two most conserved pseudouridine modifications
#=GF RT   within rRNA confers a growth advantage in yeast.
#=GF RA   Badis G, Fromont-Racine M, Jacquier A
#=GF RL   RNA. 2003;9:771-779.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   11


Z71668.1/1563-1290         UACCAAACCUUUUUGUCAGGGUGCUUCU-CUAUCCGUUUUAGGAUA---AACUUA-UC-UACAGAAGUGUCUGUUACUGUUUUGGAAGAGUAAUACUGUUC-GCUUA-UCCAU-AUUUCCCCGUUCUGGGGAAGCCUC-AUGGGUAAA-UUAGAAGGACAACCUUUGUUUUAAAGGU-AUACCUUCGCU---UUUUA------GAACAGCGAGGAUCUUAUGAGUUGAGCUUUUGUUAUUUGAGACUU--------UAUCUC-GGGC--UCCAUACAAUAUGUUCGUAGUAAAGAUCCUCACAAUU
AABY01000051.1/17563-17291 UACCAAACCUUUUUGUCAGGGUGCUUCU-CUAUCC-UUUUAGGAUA---ACUUUA-UC-UACAGAAGUGUCUGUUACUGUUUUGGAAGAAUAAUACUGUUC-GCUUA-UCCAU-AUUUCCUCGUUCUGAGGAAGCUUAAAUGGAUAAA-CUAGAAGGACAACCUUUGUUUUAAAGGU-AUACCUUCGCU----UUUA------GAACAGUGAGGAUUUUAUGAGUUGAGCUUUUGUCACUUGAGAUUU--------UGUCUC-AGGC--ACCAUACAAUAUGUUCGUAGUAAAGAUCCCCACAAUU
AACI02000264.1/7638-7365   UACCAAACCUUUUUGUCAGGGUGCUUCU-UUAUCCGU-UUAGGAUA---ACCUUU-UC-UACAGAAGUGUCUGUUACUGUUUUGGGAGAGUAAUACUGCUC-GCUUA-UCCAU-AUUUCCUCGUUCUGAGGAAGCCUA-AUGGAUAAA-UUAGAAGGAUAACCUUUGUUUUAAAGGU-AUACCUUCGCU----UUUA------GAGCAGCGAGGAUCUUAUGAGUUGAGCUUUUGUUAUUUGAGUUUUG-------UUUCUC-AAGU-AUCCAUACAAAAUGUUCGUAGUAAAGAUCCUCACAAUU
AACH01002253.1/53-321      UACCAAACCUUUUUGUCAGGGUGCUUCU-CUGUCCUUUCUAGGACA---ACUUUA-UC-CACAGAAGUGUCUGUUACUGUUUUGGUAGAGUAAUACUGUUC-GCUUA-UCCUU-AUUUCCUCGUUCUGAGGAAGCCUG-AUGGAUAAC-UGAGAAGGAUAACCUUUGUUUUAAAGGU-AUACCUCCUCU---UUUUA------GAACAGUGAGGAUCUUAUGAGUUGAGCUUUUGUUACCU-----UU--------UUCUUG-GGUA--UCCGUACAAUAUGUUCGUAGUAAAGAUCCUCACAACU
AACA01000197.1/13773-13499 UGCCAAACCUUUUUGUCAGGGUGCUUCU-UUGUUCGUUCUAGAACA---ACUUUA-UC-UACAGAAGUGUCUGUUACUGUUUUGGAAGAGUAAUACUGUUC-GCUUA-UCCAU-AUUUCCUCGUUCUGAGGAAGCCUU-UUGGAUAAAUUUAGAAGGACAACCUUUGUUUUAAAGGU-ACACCUUCGCU----UUUA------GAGCAGUGAGGAUCUUAUGAGUUGAGCUUUUGUUAUUUGGGAUUUA-------UUUCCCAGAUA--UCCGUACAAUA-GUUCGUAGUAAAGAUCCUCACAAUU
AADM01000033.1/32334-32068 AACCAAAACUUCUAGUCAGGAUGUUUUC-CAUUCC--ACAAGGGAU---ACAUGAAUC-AACGAAAGUGUCUGUUAAAGUUUUGGGAGAUUAAUACUGCUC-GCGUUCUUCUU-UAGCAUCCGUUUUGGAUGCACCUU-GAGGA---A-CAAGGUGGGUAAUUUUCGUUUUGAAGAU-AUGCCACCGAC---UUAUA------GAGCAGAGAGGCACCUAUGAGUUGAGUU-CAGG-ACUACGGUUUU--------UGACUG-CGGA--UACUUCCUGG--ACUCGUAGUAAGGAGCCUCACAACU
AAZN01000385.1/5032-4764   CACCAAAACUCUUUGUCAGGAGGUAUUUACUUGCAUUUUUUUGCAA---AA--UA-UC-CAUAAAUGCGUCUGUUACAGUUUUGGAAGAUCAAUAUUACUC-GCCUU-UUACU-CUUCUUUCGUUUUGAAGGAAAUAUGAGUGAA--A-UCAGAAGGACAAUCGUCGUUUUGAUGAU-AUACCUUCGCC--UCUUUA------GAGUAAGGACGAUCUUCAGAGUUGAGUCUUUGAU-CUU---AAUU--------UUUUUU-AAGA--CUAAUUCAAAGUACUCGUAGUAUAGAACGUCACAAUU
CR382123.1/1672568-1672301 UACCAAAAUUCUUUGUCAGGGUGUUUCU-GCGUACAUUCUAGUACA---ACUUAC-ACAUACAGAAGGGCCUGUUACAGUUUUGGAAGAGCAAUACUACCC-ACCCU-CGAUC-UAUCCAUCGUUUUGAUGGAGUCAU-GGUUGAAAC-CUAGUUGAACAAUCUUCGUUUUGAGGAU-AUAUCAGCGCUUUUAUUUC------GGGUACGGAGGAACUUAAGAGUUGAGCUUUGGAUC---------U--------GAAAAG-AAUU--AUUAUGCCAUG-GCUCGUAGUAAAGAACCUCACAUCA
AACF01000127.1/3251-2957   CACCAAAACUCUUUGUCAGGAUGUUUUU-GCUUGUUUUUUCGAAAGGAAAGACCA-UU-CACAAAAUCGUCUGUUAAAGUUUUGGAAGAUUGAUACUGUUCGCCUUA-UCCAUUCCAUCUUCGUUUUGAAGAUACUUUUUUGGAUAAU-UUUAGAAAUUC-CUUUCGUUUUGAAAGUUUUAUUUUUAAU----CUUAAUUUUAGAGCAGGGAGGAUCAUUAGAGUUGAGCAUUAUUUUGUUGAAGUUUCAUCAAGAAGCUUC-AAUCAUUUCGUAUAAUUUGCUCGUAGUAUUGAACCUCACAUUU
AACE03000009.1/21840-22105 CACCAAAACUCUUUGUCAGGGCGUUUUC--UAUUCCACCGAGAAUA--CAAUUCA-UC-AACGAAAAGGUCUGUUACAGUUUUGGAAGAUUAAUACCACUC-GCCUU-CUACU-UUUCUCCCGUUCUGGGAGAACUUG-GGUAGAAAC---AGGUGGGUAACCACCGUUUUGGUGGU-AUGCCACCGCU----UUUA------GAGUGAGGAGGAUCUUCAGAGUUAAGCUUUGGAUG-----GGUACA-------CCCCUU-CAAG--AUAAUUCCAUU-GCUUGUAGUAAUGAACCUCACAUUA
AE016815.5/616060-615812   UGCCAAAACUCUUUGUCAGGGCGCCUCU-C--UCC--UCACGGA--------UCA-AC-UACGGAGGUGCCUGUUACAGUUUUGGAAGAAUAAUACCGUUC-GCCGC-CCGCG--GUCUCCCGUUCUGGGAGAGCUUU-CCCGGGCA---UAGAUGGGUAACCCCGUUUU--GGGGU-AUGCCGUCGCU-----CUA------GAACGCGGAGGAUCUUAUGAGUUGAGCAUGGCCAUCGU-----------------AAAG-ACCC--AAUUAUGCCAUUGCUCGUAGUAAAGAACCUCACAUCC
#=GC SS_cons               ::<<<<<-----------<<<<<<<<<<.-<<<<<______>>>>>...------.--.--->>>>>>>>>>-------->>>>>,,,,,,,,,,((((((.,,<<<.<<<<<.-<<<<<<<_____>>>>>>>----.>>>>>>>>,.,,,<<<<<---<<<<<<<___>>>>>>>.--->>>>>,,,....,,,,......))))))-<<<<-<<<<------<<<<<--<<<<--<<<<<<<___........__>>>>.>>>-..----->>>>--->>>>>----->>>>->>>>::::::
#=GC RF                    uACCAAAaCUuUUUGUCAgGgcgcuUcu.cuguccuUUuuaggaca...AauUuA.UC.uACagAagcgcCuGUUAcaGUUUUGGAAGAuUAAUAcuGcuC.gCuuc.ucccc.ucuccccCGUUuUGggggagcuUu.ggggagaaa.uuAGgaGGauAAccuucgUUUugaaggU.AUACCucCgcU....UUUA......GagCaggGaGGAuCuuauGAGUuGAGcuUugguUaccuggGguUU........uucCcc.agga..uucaUaccauuUgCUCgUAGUAaaGaaCCuCACAauu
//
# STOCKHOLM 1.0

#=GF AC   RF01264
#=GF ID   snR83
#=GF DE   Small nucleolar RNA snR83
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   75.00
#=GF TC   75.20
#=GF NC   70.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00023
#=GF DR   snornadb; snR83;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300038;
#=GF RN   [1]
#=GF RM   15306656
#=GF RT   Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the
#=GF RT   Saccharomyces cerevisiae genome.
#=GF RA   Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM
#=GF RL   Nucleic Acids Res. 2004;32:4281-4296.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


Z49808.1/21552-21857       ACCCAAAAACAUCAAGAAAAGCCUUUCAAUAAAUUGCUCUUCUCUUGGCGAAAGAAAGCGGG----GG--GCAAAAAGAAUCACGGGACUUAUGUUUCGGGAUCUCUUUG------UUU------CUUCUUUUUUUCCCGGAGAAUAAUUUUUUAGGACCAAUUACCGUAGUUGCGACUACAACAAUUGUUGUUCAUACCCCCACGAUUUACUUUUUGAAAACUAGUUUUUGGAAUAAUAAUGUUGUAAAAUUUCCCUUUUUCCACCCCGAUUUGUAUUUUAUUUUUCGUUACAAAAUUGGGACUAAUAUUAAGGGCGACAGUU
AABY01000043.1/27193-26893 ACCCAAAAACAUCAAGAAAAGCCUUUCAAUAAAUUGCUUUUUUCUUGGCGAAAGAAAGCAGC----GG--UAAAGAGGGAGCUCGGGACUUAUGAUCCGGG-UCUCUUUG------UUC------CUUUUUUUUUUCCCAGAAAAUAA-UUUUUAGGACCAAUUACCGUAGUUGCGACUACAACAAUUGUUGUUCAUACCCCCACGAUUUACUUUUUGAAAACUAGUUUUUGGAAUAAUAAUGU---AAAAUUUCCCUUUUUCCACCCCAAUUUGUAUUUAAUUUUUCGUUACAAAAUUGGGACUAAUAUUAAGGGCGACAGUU
AACH01000838.1/496-192     ACCCAAAAACAUCAAGAAAAGCCUUUCAUUAAAUUGCUUUUCUCUUGGCGAGAGAGAGAGGU----GGCGACAAGA-GGGCUCCGGGACUUAUGUUUCGGAGUCUUUUUU---CUUUCG------CUUCUUUUUUUCCCGGAGAAC-ACCUUUCAGGACCAAUUACCGUAGUUGCGACUACAACAAUUGUUGUUCAUACCCCCACGAUUUACUUUUUGAAAACUAGUUUUUGGAAUAAUAAUGUUGU-AAAAUUCCCUUUUUCCACCCCAAUUUGUAUUUUA---UUCGUUACAAAAUUGGGACUAAUAUUAAGGGCGACAGUU
AACI02000694.1/1595-1913   ACCCAAAAACAUCAAGAAAAGCCUUUCAAUAAAUUGCUUUUUUCUUGGCGGAAAAGAGGGAAAAAUGGUGGGGAGAAGGGUCCCGGAACUUAUGUUUCAGGCCCUUCUUUUUCCUUUUUUUUUUACUUUUUUCC-UCCCGGAAAAUAAUUUUUCAGGACCAAUUACCGUAGUUGCGACUACACCAAUUGUUGUUCAUACCCCUACGAUUUACUUUUUGAAAACUAGUUUUUGGGAUAAUAAAGUUGU-AAAAUUCCCUUUUUCCACCCCAAUUUGUAUUUCA---UUCGUUACAAAAUUGGGACUAACAUUAAGGGCGACAGUU
AACA01000157.1/9531-9834   ACCCAAAAACAUCAAGAAAAGCCUUUCAAUAAAUUGCUUUUUUCUUGGCGAGGAGGAGAGGGAA--GG--UGAGAAUGGGGCCUGAGACUUCGGUUGCGGGUUCUCUUUUUUUCUUUCU------CUUUUUUUU-UCCCGGAAAAUAACUUUUCAGGACCGAUUACCGUAGUUGCGACUACACCAAUUGUUGUUCACACCCCCACGA-----UUUUUGAAAACUAGUUUUUGGCAUAAUAACGUU---UAGAUUUCCCUUUUCCACCCUAAUUUGUAUUUAAUUGUUCGUUACAAAAUUGGGACU-AUAUUAGGGGCGACAUUU
#=GC SS_cons               ::((((((((--------------((((((((((((,,,<<<<<<-<<-<<<<<<<<<<<<-....--..---<<<-<<<<<<<<<<<<____>>>>>>>>>>>>->>>-...------......>>>>>>>>>>>>>>>>>>>>,,,,,,,,,,<<<<<<<<<---<<<<<____>>>>>--->>>>>-->>>>,,,,,,,,,)))))))----)))))-----))))))))--------------.------<<<<<-------<<<<<<<<<<<_____________>>>->>>>>>>>--------->>>>>::::::::
#=GC RF                    ACCCaaaaaCAUCAAGAAAAGCCUuuCaauaaauuGCUUuucuCcUGGCGagggagagagGa....GG..uaAagaagGggcccGggaCUUauGuccCgggccCuuucuu...cUUUuu......CcucucucccuCCCgGagaaUAAuUUUUcAGgaCCaauuACCGuaGuUGCGaCuaCAaCaauuGUUGuuCAuACCCCcACgauuuaCUUUuuGaaAACUAGuuuuuGGaAUAAUAAuGUUGU.aAAaUUcCCuuUUUCCACCCcaauuuGuaUUUuAUUuUUCGUuaCAaaauugGGACUAAuAUUaaGGgCGACAgUU
//
# STOCKHOLM 1.0

#=GF AC   RF01265
#=GF ID   snR42
#=GF DE   Small nucleolar RNA snR42
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Published; PMID:9106664; Wilkinson A
#=GF GA   61.00
#=GF TC   62.30
#=GF NC   60.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00032
#=GF DR   snornadb; snR42;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300022;
#=GF RN   [1]
#=GF RM   9848653
#=GF RT   Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative
#=GF RT   RNA-binding protein, are present together with Gar1p in all H
#=GF RT   BOX/ACA-motif snoRNPs and constitute a common bipartite structure.
#=GF RA   Watkins NJ, Gottschalk A, Neubauer G, Kastner B, Fabrizio P, Mann M,
#=GF RA   Luhrmann R
#=GF RL   RNA. 1998;4:1549-1568.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


Z28287.1/412-62            AUAAC-AAUUUGUGAUGCUUUAGGGAGCCUAUUGUUUGAUGGUUUAUAGGAGCCGGAUUUGUCUUUU--UGACUAAUUUUCAACCUAUUCUUACUUCCAAAACUGUUGCAAUGGCUCUCGUUUUUUUUAAAUUUUUCUCUUUUCUCUUCUUUGGCAUAGUUUAUUUUUA-AUAAAUUAUUUC-AGGGUGAGAUAG-AGAAAGGAUAAUGAGUAUCGUAGAUAAAUCUUCGGUUCCGAAUAGUGUAACUGUUGGUGCUGAGGUAAUCCAUCUUUAAAACCAUCGCCGUUAGAGGUUGCUUCUGA-UAUUUUCGGUUAAGCGACCCAUGAAAUGGUGAUGACCUGAGGUAUGGAACAUCU
AABY01000005.1/88923-89269 AUACA-AAUUUGUGAUGCUUUAGGGGGCCUAUUGUUCGGCGGUUUAUAGGAGCCAGGUUUGUCUUUU---GACGAACCUUUAACCUAUUUUUACUUCCAAAACCGUUACAAUGGCUUUCUUUUAUUAAAA---UUUUUCUUUUCUUUUCUUUGGCUUAGUUUAUUUUUA-AUAAGUUAUUUC-AGGUGAAGAUAG-AAGAAGGAUAAAGAGUAUCGUAGAUAAAUCUUCGGUUCCGAAUAGUCUAACUAUUGGUAUUGAGGUAAUCCAUCUUUAAAACCAUCGCCGUUAGAGGUUGCUUCUGA-UGUUUUCGGUUAAGCGACCCAUGAAAUGGUGAUGACCUGAGGUAUGGAACAUCU
AACG02000132.1/12491-12835 AACAA-AAUUUGUGAUGCUUAAGGGGGGCUAUUGUUCGGCGGUUUAUAGGAGCCAGAUUUGUCUUUU--GGGCAGAUCUCCAACCUAUUCUUACUUCCAAAACCGUUGCGAUGGCUUUCCAUUA--------GAUUUUCCUUUCUUUUCCUCGGUUUAGUUUAUUUUAU-AUAAGUUACUUCGAGGAAGGAAAAG-AAAAAGGAUAACGAGUGUCGUAGAUAAAUCUUCGGUUCCGAAUAGUCUGACUAUUGGUAUUGAGGUAAUCCAUCUUUAAAACCAUUGCCGUUAGAGGUUGCUUCCGGUUAUAUCCGGUUAAGCGACCCAUGAAAUGGUGAUGACCUGAGGUAUGGAACAUCU
AACH01000061.1/2082-2427   UAAAA-AACUUGUGAUGCUCUUGGG-GUCCAUUGUUU-ACGGUUGAUAGAAGCCAGUUUUGUCAUUU--UGAUGAAAUUUCAUCCUAUCCUUAGUUCCAAAACCGCUCCAAUGACUUCCUUUUUAUUGA----UUUUUCCUUUUCUUUCCUUGGUUUAGUUUAUUUAUG-AUAAGUUAUUGC-AAGAAAGGAUAGGAAAAAGACUGAUGAGUGUCGUAGAUAAAUCUUCGAUUCCGAGUAGUCUGACUAUUGGUAUCGAGGUAAUCCAUCUUUAAAACCAUCGCCGUUAGAGGUUGCUUCUGA-UUCAUUCGGUUAAGCGACCCAUGAAAUGGUGAUGACCUGAGGUAUGGAACAUCU
AACI02000222.1/11469-11118 AUAACAAAUUUGUGAUACUUCAGGGGGCCUAUUGUUUCGCGGUUUAUAGAAGCCAGAUUUGCCUUUUUUUGACAGACCUCCAAUCUAUUAGUACUUUCAAAUCCGUUGCAAUGGCU-UCCUUUUCAUUGGAUUUUCCUCUUUU---UCCUUUGGUUUAGUUUAUUUUUAUAUAAGUUAUCCCAAGGAGGAGAGAG-GAAGAGAAUGAUGAGUGUCGUAGAUAAAUCUUCGGUUCCGAAUAGUCUGACUAUUGGUAUUGAGGGAAUCCAUCUUUAAAACCAUCGCCGUUAGAGGUUGCUUCCGG-UUUAUUCGGUUAAGCGACCCAUGAAAUGGUGAUGACCUAAAGUAUGGAACAUCU
#=GC SS_cons               :::::.:::::::(((((((,,<<<<<<<-<<<<<--<<<<<<<<<<<<<----<<<<<-<<<____.._>>>->>>>>---->>>>>----------->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,..,<<<<<----<<<<--<<<<<<-<<<<<<<<<_____.>>>>>>>>>->>.>>>>->>>>-->.>>>>,,,,,,,,))))))),,,,,,,,,,<<<<<<<-<<-<<<<<_____>>>>>>>->>>>>>>,,,<<<<<<<-------<<<<<<<<<<---<<<<<<<<<<<<._____>>>>-->>>>>>>>----->>>>>>>>>>------>>->>>>>::::::
#=GC RF                    auaAa.AAuUUGUGacgCucuaGgggGcCuauuGcUuggcGGuuuauaGgAGCCagguuUGuCuUUU..uGaCaaaccuucAacCuauucuUAcUUcCAaaaCCgccgCaauGgCcccCuuUUuuuuuaa..uuuucuCuUUucccUucccuGguguagcuuauUUuua.auaaguuacucC.agggagggauAg.gaaaAGaaUaAugaGcguCGUAGAUAAAUCuuCgguUCCGaauaGUcUgACuauuGGUaccGagGuAAuCCauCcUUAAAACCaucgCCguuAGAGGuuGCuuCcGg.UuuaUcCgGUUaaGCgaCCCAUGAaauGGugauGACCUgAgGUauGGaACAUCU
//
# STOCKHOLM 1.0

#=GF AC   RF01266
#=GF ID   snR45
#=GF DE   Small nucleolar RNA snR45
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   80.00
#=GF TC   120.50
#=GF NC   71.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34 -Z 549862.597050 CM SEQDB
#=GF DR   snornadb; snR45;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300076;
#=GF RN   [1]
#=GF RM   8797828
#=GF RT   The RNA world of the nucleolus: two major families of small RNAs defined
#=GF RT   by different box elements with related functions.
#=GF RA   Balakin AG, Smith L, Fournier MJ
#=GF RL   Cell. 1996;86:823-834.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


U56646.1/2-172               AUGA-CCUUCCAAGUUUUUAAAAGAAUAC-GAUGAUAUUAUUUGCG-UU---UCAAA--UCGAACAAUUCUUC---UCGGAGCGAU-----------------CUGAGGUUUUAAUGGAGAUAGCGGUUCCUGCGCAACCCAU-UG--AUCUUGUUACAU--------UCUUAAGAAUGA-------CAAGGACGC-U-U--U-UAUAA---AAUUCUGAUUCUU
AACF01000005.1/27414-27234   AUGA-CCUUCCAAGUUU-UAAAAGAAGAG-GAUGAUAUUAUUUGCG-UCA--UUUAA--UCGAACAAUUCUUC---UCAGGG---------UAU-UCUUACC-CUGAGGUUUUAAUGGAGAAAGCGGUUCCUGCGCAGAAAAU-UG--AUCUUGUUACAU--------UCGAAAGAAUGAUU-----CAAGGACGC-U-CAAU-UAGAA---AAUUCUGAUUCUU
AADM01000252.1/7157-7341     AUGA-CCUUCCAAGUUUUAUAAAGAAGAC-GAUGAGCUUAUUUGCG-UUAU-UUCAG--UCGAACAAUUCUUC---UCGUGCGGGCGCUCGC---GCCUGC--GUGAGGUUUUAAUGGAGAGUGUGGUUCCUGCGCAGCCCUU-UA--AUCUUGUUACAU--------UC-UAUGAAUGA-------CAAGGACAC-U-U--UAUAGAA---AAUUCUGAUUCUU
AAZN01000360.1/46023-45830   AUGAACCUUCCAAGUUU-UAAAAAGAGUGCGAUGAUACUAUUUGC-AUUUA-UUAAA--UCGAACAAUUCUUC---UCGGUGGACUAGAUAAUAUCUAAUUUACUGAGGUUUUAAUGGAGAAUGCGGUUCCUAUGCAGCCAAUAUA--AUCUUGUUACAU--------UCAAUUGAAUGA-------C-AGGACGC-U-A--A-UAUUAUGAAAUUCUGAUUCUU
CR382122.1/953555-953368     AUGA-CCUUCCAAGUUU-UAAAAGAAGAC-GAUGAUACUAUUUGCGCUUUU-UUAAU--UCUUACAAUUCUUUCG-UGGAUGGGAAU----UAU-UUUCUGU-UCAUGGUUUUAAUGGAGAAUGUGGUGCCCUCGCAAGCCUUAUA--AUCUUGUUACAU--------UCUUUGAAUGAU-------UUGGGACACUU-U--U-UAUAA---AAUUCUGAUUCUU
AACE03000002.2/254936-254755 AUGA-CCUUCCAAGUUUUAUAAAGAAUAG-GAUGAUAUUAUUUGCG-UU---UUAAAAGUCGAACAAUUCUUC---UCGACGCCUUGUGCG------------UUGAGGUUUUAAUGGAGAGUGUGGUUCCUGCGCAGACCAA-UAUAAUCUUGUUACAU--------UCUUU-GAAUGA-------CAAGGACAC-UAUACU-UAGAA---AAUUCUGAUUCUU
CR380955.2/1056254-1056064   AUGA-CCUUCCAAGUUU-AUUAAGAAGAC-GAUGAAAUUAUUUGCG-UGAAUCCUAU--UCGAACAAUUCUUC---UUGCGA---------U---CCUAUC--GUGAGGUUUUAAUGGAGAAAGCGGUACCAACGCAGACCUU-AU--UUCUUGUUACAUCCCUAGUUUCUUUCGAGGAGCUAGUUUUCUGGACGC-U-A--C-UAGAA---AAUUCUGAUUCUU
AE016819.5/990019-990191     AUGA-CCUUCCAAGUUUUAUAAAGAAGUG-GAUGAUAUGAUUUGCG-U-A--GCAAC--UCGAACAAUUCCUCGCCUGUGAUC-----AGG------------CUGAGGUUUUAAUGGAGAAAGUGGUGCCCGCGCA-GCAAA-UA--AUCUUGUUACAU--------UCUUU-GAAUGC-------CUGGGACAC-U-UG-C-UAUAA---AAUUCUGAUUCUU
#=GC SS_cons                 ::::.::::::::::::.:::::::::::.::::::::::::::::.::::.:::::..::::::::::::::...:::::::::::....:...::::::..::::::::::::::::::::::::::::::::::::::::.::..::::::::::::........::::::::::::.......:::::::::.:.:..:.:::::...:::::::::::::
#=GC RF                      AUGA.CCUUCCAAGUUU.uuaAAGaAgag.GAUGAuauUAUUUGCG.Uuau.uuaAa..UCGaACAAUUCUUC...Ucggggggaug....u...ucuuuc..cUGaGGUUUUAAUGGAGAauGuGGUuCCugCGCAGaCcau.ua..aUCUUGUUACAU........UCuuuuGAauga.......caaGGACgC.U.u..u.UAgaA...AAUUCUGAUUCUU
//
# STOCKHOLM 1.0

#=GF AC   RF01267
#=GF ID   snR37
#=GF DE   Small nucleolar RNA snR37
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   47.00
#=GF TC   48.50
#=GF NC   44.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00041
#=GF DR   snornadb; snR37;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300035;
#=GF RN   [1]
#=GF RM   15306656
#=GF RT   Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the
#=GF RT   Saccharomyces cerevisiae genome.
#=GF RA   Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM
#=GF RL   Nucleic Acids Res. 2004;32:4281-4296.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   9


Z49379.1/1742-1357           AACAUCAGUAGUGGUUAAUACUAUCUUUAGAUAAUAUUAAUUUCA---UUAUACCAUAGAAACCUAAAGAUUAGGUUAUUUUCGUUCUUCAUGUUAUGGAGUGUGA-GUGAU--GAGGAGCUU--------------GCUCUUUUAAGCUCAUAUUACGUAAUAAGUUAAUACUGGAG-CGA-GAAUAAUUUAAAUCAUUUCAUCAUAACCCAUAGCUGAAUGAACUUUGACUACUCCUAAACAAAGUAGU-AACAAUUUUCAUUUCGUUUCC--GGUUUCUUAGAUCGAAUAUUAUUCUGAGGAAA---------------UUCCCUGAU--UACAU--AUC---AGGGA-AAGGUU-CGCGUUUU-UAGAGAAUUGCGUAAU-GCGAUUUGAAAGUUUAAA--UUCCUAAGCGACUCUUCUUCAUGAUAAGACAGUU
AACI02000103.1/13708-13323   AACAUCAGUAGUGGUUAAUACUAUCUUUAGAUAAUAUUAAUUUCA---UUAUACCAUAGAAACCUAAAGAUUAAAUUAUUUUUGUUCUUCAUGUUAUGAAAUAUGA-GUUAU--GAAGAGCUU--------------GCUCUUUUGACCUCAUAUUAAGUAAUAAGUUAAUACUGGAA-CGA-GAAUUAUUCAAAUCAUUUCAUCAUAACCCAUAGCUGAAUGAAUUUUGACUACUCCUAAACAAAGUAGU-UACAAUUUUCAUUUCGUUUCC--GGUUUCUUAGAUCAAACAUUAUUCUGAGGAAG---------------UUCUCUGAU--UAUUA--AUC---AGAGA-AAGGUU-CGCGUUUU-UAGAGAAUUGCAUAAU-GCAGUUUGAGAGUUUAAA--UUCCUAUGCGACUCUUCUUCAUGAUAAGACAGUU
AABZ01000143.1/19792-19408   AACAUCAGUAGUGGUUAAUACUAUCUUUAGAUAAUAUUAAUUUCA---UUAUACCAUAGAAACCUAAAGAUUGAAUUAUUUUUGUUCUUCAUGUUAUG-GGUACGA-AUGAU--GAGGGGCUU--------------GCUCUUUUGAAUCCGUAUCACAUAAUAAGUUAAUACUGGAA-CGA-GAAUAAUUUAAAUCAUUUCAUCAUAACCCAUAGCUGAAUGAAUUUUGACUACUCCUAAACAAAGUAGC-UACAUUUUUCAUUUCGUUUCC--GGUUUCUUAGAUCAAAUAUUAUUCUGAAGGAG---------------UUCUCUAAU--CAAAA--GUU---AGGGA-AAGGUU-CGCGUUUU-UAGAGGAUUGUGUAAA-GCAAUUUGUGAGUUUAAA--AUCUUAGGCGACUCUUCUUCAUGAUAAGACAGUU
AACG02000202.1/2769-3153     AACAUCAGUAGUGGUUAAUACUAUCUUUUGAUAAUAUUAAUUUCA---UUAUACCAUAGAAACCUAAAGAUUGAAUAAUUUUUGUUCUUCAUGUUAUACAACUUGG-GCAAU--GAAGAGCUU--------------GCUCUUUUGCGUCCAUUUUGUUUAAUAAGUUAAUACUGGAA-CAA-GAAUAAUUUAAAUCAUUUCAU-ACAACCCAUAGCUGAAUGAAUUUUGACCACUCCUAAACAAAGUAGC-UACAAUUUUCAUUUCGUUUCC--GGUUUCUUAGAUCAAAUAUUAUUCUGAAGAAG---------------UUCCCUGAU--UACAA--AUC---AGGGA-AAGGUU-CGCGUUUU-UAGAGAAUUGCAUAAU-GCAAUUUGAGAGUUUAAA--UUCCGGUGCGACUCUUCUUCAUGAUAAGACAGUU
AACA01000601.1/346-4         AACAUCAGUAGUGGUUAAUACUAUCUUUUGAUAAUAUUAAUUUCA---UUAUACCAUAGAAACCUAAAGAUUGAAUAAUUUUUGUUCUUCAUGUUAUACAACUUGG-GCAAU--GAAGAGCUU--------------GCUCUUUUGCGUCCAUUUUGUUUAAUAAGUUAAUACUGGAA-CAA-GAAUAAUUUAAAUCAUUUCAU-ACAACCCAUAGCUGAAUGAAUUUUGACCACUCCUAAACAAAGUAGC-UACAAUUUUCAUUUCGUUUUCCGGUUUUCUUAGAUCAAAUAUUAUUUUUGAAGAAGGU------------UUCCCUGAU--UACAA--AUC---AGGGA-AAGG---UUCGCG----------------------------------------UUUUAGAGAA-UU--------GCAUAAUGCAUUU
AAZN01000183.1/45229-45595   AUCAUCAGUAGUGGUUAAUACUAUCUCAAGAUAAUAUUAAUUACA---AUUUUUUAUAGAAACCUAAAGUUUUGAUCAUUUGUGUUCUUA-AGUUAGGA---------------UACCUCUUC--------------GGGGGUAU------------UCUGAUUAGUUAAUACUGGAA-CUCUGAGUGAUUG-AUUCAUUACAU-AUAACCCAUAGCUGAGUGGCAUCUGACAGACCCUAAACAAGUCUGG-CACAGAUAUCAUUUCGUUUCC--GGUUUCUUAGAUCAUAAUCUCCUAUGAGGAAGG--------------UCCUCGAAUAGUCAAACUAUU---CGAGG-AAAGAUACAUGUUUAUCAGAGGAUUGUAUAAU-GCAAUCUGAGAGUUUGUA--AUCAGUCGUGUCUCUUCUUCAUGGUAGGACAAUU
AADM01000081.1/84372-83996   AUCAUCAGUAGUGGUUAAUACUAUCUCAAGAUAAUAUUAAUUACA--AUUUUUUUAUAGAAACCGAUG-UUUCAAUCACCUGUGUAUUUAA----AAGUGGGGUUUGUGGCU--UUGGUUUUC--------------GGACCAAAGUUGGGGCUUUGCUUA---AGUUAAUAUUGGUA-CGU--GGUGGUUGA----UUCAAGCAAUAACCCAUAGCUGAAUGGGCUUUGACCACCUCCAAACAAGGUGGC-CACAAAGUCCAUUUCGUUUCC--GGUUUCUUAGAUUAACGUCUGUCAUGAGGGAG---------------UAUGAACUC--UUUAA--GAG---UUCAU-AAGUGC-AUGUUUUU-CAGAGGAGCGUGUAAU-GCGCUCUGAGAGUUUGAAAGAUUCUGUUGUGCCCUCCUUCAUGUCAGUACAUUU
AACF01000014.1/34168-33753   AUCAUCAGUGGCGGUUAAUACUAUCUCAAGAUAAUAUUAAU--UA---CUAUAACAUAGAAACCUAGCGGUUCGAUCAUUUGUAUCCUCAUGACAGAG-GUUGGGA-GUUCUUAGAGAAGUUUUUGAUUCCAUCAUGGCUUUUUCUUCCUUUCAAUCUUUUGUUAGUUAAUACUGGGAUUAU-GAAUAAUUGAAACCAUUUCA--AUAACCCAUAGCUGAAUGAAUUUUGACUAUCUCCAAACAAGAUCGGGCACAAUUUUCAUUUCGUUUCC--GGUUUCUUAGAUUAUCAUCUAUUAUGAUGGGGGCAUUCUUUUUGGGACG-UCUAAG--GACGA--UUUCAGGGAAU-GAAGAG-CACGUUUA-CAGAGGAUUGUAUAAU-GCGAUCUGAGAGUUUGAA--UUCUACUGUGACUCCCUAUUAUGAUAGGACAUUU
AACE03000004.1/410643-410260 AUCAUCAGUAGUGGUUAAUACUAUCUCAAGAUAAUAUUAAUUACAAUUUUUUUCCAUAGAAACCUAAUGUUUCGGUUAUCUCGAUUCUUCACA-GCCA-GGUUUUG-AUGG---CUUUCAUUA--------------UUGAGGGUUUAUCGGUACC-UGGCUUGAGUUAAUACUGGAA-UUU-GAGUGACUG-AUUCUAUUUUU-CAACCCAAUAGCUGAAUGGAUUUUGACCACCCCCAAACAGGGUGGC-UACAAUUUCCAUUUCGUUUCC--GGUUUCUUAGAUCAUAAUCUGUUAUGAAGGAG----------------CGAUCCUC--UUUUU--GGG---GUUCGAAUUGC--AUGUUUCU-CAGAGGGUUGCGUAAUGGCAAUCUGAGAGUUUGGG-AUAUCUGCUGUGCUCUUCUUCAUGUCAGGACAUUU
#=GC SS_cons                 :::::::<<<<<<<<<<<<<-<<<<____>>>>->>>>>>>-->>...>>>>,,,,,[[[[[[[,,,,((((((((((((((((((((,,,<<<<<<<-<<<<<<<.<<---..<<<<<<___.............._>>>>>>--->>>>>>>>>->>>>>>><<<____>>>)))).))).)))))))))-)))),,,,,,,.,,,,,,,,,,,,,<<<<<<<--<<<<<<<<<_________>>>>>>.-->>>-->>>>>>>,,,,,,,..]]]]]]]-----------(((((-((((((((...............<<<<<<<<<.._____..>>>...>>>>>.>,<<<-.<<<<<-<<.<<<<<<<<<<<_____.>>>>>>>----->>>>>>..----->>>>>>>>))))))))-))))):::::::
#=GC RF                      AuCAUCAguaguGgUUAAUACUAUCUuaAGAUAAUAUUAAuUuCa...cuauaccAUAGAAAcCUAaaGguucaaucAuuuucGuuCuUaAcauuacgaggugcgg.gcgaU..caggcguUu..............GcgccugugugcccgcaccacguaaugAGUUAAUACUgGaa.Cga.gaaUgauugAaacCaUUucaU.AuAACCcAUAGCUgAaUGgauUuUGgCcacccCuAAACAAggugGc.uACAauUucCAuUuCGUUUCC..GgUUUCUUAGAUcAaaaucUgucauGagGgaG...............ucccccgac..uauaA..guc...ggggg.aAggcu.cgcccUuu.cagaggauuGcaUAAU.gCaaucuGAGAGuuugaa..uUcuugggcggccCucCcuCaUgacAggACAuUU
//
# STOCKHOLM 1.0

#=GF AC   RF01268
#=GF ID   SCARNA2
#=GF PI   snoU2-25
#=GF DE   Small Cajal body-specific RNA 2
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Published; PMID:15556860; Wilkinson A
#=GF GA   48.00
#=GF TC   48.60
#=GF NC   46.50
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; mgU2-25/61;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15556860
#=GF RT   Guide RNAs with 5' caps and novel box C/D snoRNA-like domains for
#=GF RT   modification of snRNAs in metazoa.
#=GF RA   Tycowski KT, Aab A, Steitz JA
#=GF RL   Curr Biol. 2004;14:1985-1995.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   20


BC071822.1/1-420             GUUUUAGGGAGGGAGAGCGGCCUGGGUCCUGGGU-GU-UGUGUGCGGAGCUG-UGGCGUCGCGUG--UGAGG-CGCGUGC----AGGGUGAG--UG--UGAG--UG--GACGCGUGA-------------GUGUG---UGAGUGU-----GCGCGCUUGGAGCGUGUUAGGCG--AGUGCGUGCGCCCACCCCUGCGCCCCUCC-UCCCGCUUACACUUUGAUCUUAUUUGAUCGGAUCGUGACCCCAGCCCCGCCGGGCCGACCCGAAAUGAAAAGCUCUCCUCCUGCGAAGCCC-----C---C---U---C---GGGGCGCU-GUGCAGCGAGGCC-CCUUAGGCGGCGGCCACGCUGUGGU----CCCCGAGGUCCCGGAGCUGGCCCUGCG-----------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGCUUGUCCCC-------------------GGCCACUG-AUUA--UCGAGGCGAUUCUGAUCUGG
AANU01202714.1/13473-13896   GUUUUAGGGAGGGUGAGUGGCCUGGAGCAUGGGU-GU-CGUGUGCGGAGCUG-UGGUGUCGCGUG--GGAGG-CGCGUGC----UGGCUGAG--UG--UGAG--UG--GACGCGUGA-------------GUGUG---UGAGUGU-----GCGCGCUUGGAGCGUGUUAGGCG--AGUGCGUGCGCCCACCCCUGCGCCCCUCC-UCCCGCUUACACUUUGAUCUUAUUUGAUCGGGUCGUGACCCUAGUCCCGCCGGUCCGACCCGAAAUGAAAAGCUCUCCUCCUGCGAAGCCC-----CCCAC---U---C---GAGGCGCCUGUGCAGAGAGGCC-CCUUAGGCGGCGGCAACGCUGCGGU----CCCCGAGGUCCUGGAGCUGGCCCUGCG-----------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGCUUGUCCCG-------------------GGCCAGUG-AUUA--UCGAGGCGAUUCUGAUCUGG
AAPY01722125.1/1839-1419     CAGUACGGGCGGGAGAUCGGCGUUGGGCUAGGGU-UU-UGUGUG--GUUCCG-UGGUGUCGCGUG--GAAGG-CGCGUGC----GAGCCGAG--AG--UGAG--UGGGAGCGCGAAU-------------GUGUGGCUUGAGUGU-----GCGGGCGUGGGGCGUGCAAGGCG--AGCGCGUGUGCCCACC-CUGAGCCCCUCC-CGCCGCCUACACCUUGAUCUUAUUUGAUUGGGUCGUGACUCCAGCCCCGCCGAGCCGACCCGAAAUGAGAAGCUCUCCUCCUGUGAAGCCC-----CCUUC---C---U---GGGGCGCU-GUGCAGCGAGGCC-UCUUGGGCGGCGGCCACGCCGUGGU----CCCCGGGGUCCUGA-----GUCCUUCG-----------GGGCCCGGUUGCUCGGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGCUUGUCCCG-------------------GGCCACUG-AUUA--UCGAGGCGAUUCUGAUCUGA
AAFC03017669.1/42418-42829   CUGGAAGUGAGGUUGCUGUAAAUUGCUGUGUGGU-GU-UGUGUGUGUUG--G-GGGGGUGGGGGG--GGGUG-CGCGUGU----AGGCCGAG--UGUGUGAG--UG--GAUGCGUGA-------------AUGUC---UGAGUGG-----GUGCGU-----GAAUGUGUGC-----GUGCGUGCGCUCGCCCAUGCACCCCUCC-CCCGGCCUACACGUUGAUCUUAUUUGAUCGGGUUGGGACUCCAGCCCCGCCGGUCCGACCCGAAAUGAAAAGCUUCCCUCCUGCGAAGCCCU---UC---C---U---C---GGGGCGCU-GUGCAGCGAGGCC-CCUUGGGCGGUGGCAACGCCGUGGC----CCCGGAGGUUCCGAG--CGGUCCUGUG-----------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGCUUGUCCCG-------------------CGCCAUUG-AUUA--UCGAGGCGAUUCUGAUCUGA
ABDC01616183.1/786-373       ACACCCGGCAGGGAGAGUGGCCUGGGGCGAGG-U-GG-UGUGCGUGGUGCCA-CGGUGU--CGUG--GAAGG-CACGCGU----AGGCCGAG--UG--UGAG--UG--GGUGCGCAA-------------GUGGG---UGCGCGA-----AUGCGC--GGGGCGUGCGAGGUG--AGUGUGUGCGCCCGCCCCUGCGCCCCUCC-CCCUGCCUACAACUUGAUCUUAUUUGAUCGGGUAGUGGCCCCAGCCU-GCCCGGCAGACCCGAGAUGAAAAGCUCUCCUCCUGCGAAGCCCC---UC---U---U---C---GGAGCACU-GUGCAGCUAGGCC-CCUUGGAGGGCGGCAACGCCCGGGC----CUCUGAGGUCCUGGAGCUGUCC-UGCG------------GGCC-CAGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGAUG--------AGGCU--G--GGCUUAUCCCG-------------------GGCCACUG-AUUA--UCGAGGCGAUUCUGAUUUGA
AAIY01801369.1/760-356       CCUCCUUAGCGGGAGAGUGGCGUGGGGUCUGGUU-UG-GGUCU-----------UGUGUCUCGUG--GAAGG-CGUGUG------UGGCCCG--CG--UGUG--UG--CGUGUGUCU-------------GUGUG---UGAGUGG-----GCGCGUGUGGGGAGUGCCAGACG--AGUGUAUGAGCCCGCCCCUGCGCCCCUCU-CCCCACCUACACCUUGAUCUUAUUUGAUCGGGUCC-GACCCCAGCCCCGCCGGGCCAACCCGAAAUGAAAUGAUCCCCUCCUGCGAAGCCC-----U---C-------C---GCGGCGCU-GUGCAGCGAGGCC-UGUUGGGCGGCGGCAACGCUGUGGU----CCCCGAGGUCCCGGAGCUGGUCCGAC------------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGACC--G--GGCUUGUCCUG-------------------UGUCGCUG-AUUA--UCGAGGCGAUUCUGAUCUGA
CAAA01147445.1/22509-22096   CCUCGCGAGUGGGAGUGCGGCUGGGGCUGUGGAU-GUCUGUGUGUGGUAUUG-UGU---GACGUG--AAUGG-UGCCUUU----GGGCUGAA--UG--CGAGUAUG--GAUAUUGGA-------------GUGUG---UGUGCGA-----GCG-ACUGGGAG-GUGCAAGGCG--AGUGUGUGUACCCCCCCU----CCCCUCC-CCUCGCCUACACCUUGAUCUUAUUUGAUCGGGUCGUGACCCCCGCCCCGCCGGGCCGCCCCGAAAUGAAAAGCAGCCCUCCUGCGAAGCCC-----C---C---U---CGGUGGGGCGCU-GUGCAGCGAGGCC-CUCUGGGCGGUGGCGGCGUCGCGGU----UCCCGGGGUUCCGGGAUCGGUCCUGC------------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGUCCGU-CCC-------------------AGCCGCUG-AUUA--CCGAG-CGAUUCUGAUCUGA
AAYZ01035671.1/1663-2066     GUGUGAGUGUCCGUGUGUGUCC---GUGCAGCGC-GC-GUGGCCGAGGUGUG-AGUGUCCGUGUG--UG----UCCGUGC----AGCGCGCG--UG--GCCG--AG--G-------U-----------------G---UGAGUGU-----CCGUGUGUGGGGCGUGCGAGGCG---GUGAGUGCGCCCGCCCCUG-CGCCCUCC-CGCCGCCUGCACUUUGAUCUUAUUUGAUCGGGCCGAGACCCCCG-----CCGCGCCGGCCCGAGAUGAAAAGCUUCCCUCCUGCGAAGCCCUGCUUC---C---G---C---GGGGCGCU-GUGCAGCGAGGCCCCCCCGGGCGGCGGCCGCGCCGCGGU----CCCCGAGGCCCCCGGGCCGGUCCCACG-----------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCU--CCGGGCUUGGCCCG-------------------GGCCGAUG-AUUA--CCGAGGCGAUUCUGAUCUGA
AACN010346987.1/16-443       CCUUCCCGGAGGGAGAGCGGCCUGGGGCGGCGGU-GC-UGUGUGUGGUGCUG-CGAUGU-GCGUG--GAAGG-CGCGUGG----AAGGCGCG--UG--GAAG---G--CGCGUGUGGGCUGAGUGAGUGGGCGCG---CGAGUGUGGUGGGUCCACGUGGGGCGUGCAAGGCGAGCGUGUGUGCGC-CGUCCCUGAGCCCCUCC-CCCCGUCUACACCUUGAUCUUAUUUGAUCGGGUUGUGA-CCCAGCCCCGCCGGGCCGGCCCGAGAUGAAAAGCUC-CCUCCUGCGAAGCCCC--CUC---C---G---C---GGGGCGCU-GUGCGGCGAGGCC-CG------CG-GGCGGCG--GCAG-----CACCGCGGCCCCGGCGCUGGUCUGACG-----------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGCCCGUCCCG-------------------CGCCGCUG-AUUA--UCGAGGCGAUUCUGAUCUGA
AAQQ01318379.1/8514-8113     CCUCACGGGAGGGAGAGCGGCCUGGGCUGAGGGG-AC-UGUGUGUUGUGUGGAAGGUGC--------------------G----UGUGGGCC--CA--GU-----G--AGCGAGUGG-------------ACGCU---CGAGUGU-----GUGUGCGUGGAGCGUGCAAGGCG--AGUGCGUGUGC-CCCACCUGCGCCCCUCC-CCCCGCCUACACCUUGAUCUUAUUUGAUCGGGUCGUGACCCCAGCCCCGCCGGGCCGCCCCGAAAUGAAAAGCUCUCCUCCUGCGAAGCCCC--CUC---C---U---C---UGGGCGCU-GUGCAGUGAGGCC-CUUUGGGCGGCGGCAGCGCCGCGGU----CCCUGAGGUCCCGGAGCUGGUCCUAU------------GGGCC-CGGUGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGCCUGUCCCG-------------------GGCCAGUG-AUUA--UCGAGGCGAUUCUGAUCUGA
AAFR03000204.1/16494-16050   GGGCAGGGGCGCGGGUUCUGCAUACCGGUUGCUU-GG-UGUGCGUGAGGCGG-CCGAGUUACGUGCGGAAGGACGCGUGG----AAGGCGAU--UG--AGUG--UG--UGUGUGAGUGCAAGGCCAGAGUGCCAG---UGUGUGU-----GCAAGGCGAGCGCAUGUCCGUGU--GCCGAGCCGGCCCUCC-CUAAACCUCUCC-CCCC-CCUACACGCUGAUCUUAUUUGAUCGGGUCGCG-CUCCUGCCCCGCCGGCCUGACCCGAGAUGAGAAGCUCCCCUCCCGCGAAGCCC----CG---G---U---C---GGGGCGCU-GUGCGGCGAGGCC--UAUGCGAACAGGCGGCG--GCGGCCGCUCCCGGGUUCCCCGGAGCCAGCCCUUCGCGGGCCUGGCCGGGCC-GGGCGCUCAGAAGUGAUGAGUUGAUCAGAUAGACG--------AGGCG--G--GGCUUGU-CCC-------------------UGCCCUUG-AGUA--UCGAGGCGAUUCUGAUCUGA
AAGV020430906.1/177-557      CUUUAGGGGAGGGAGCGCGGCCUGGGGUUCGGCU-GU--GUCUGUGGGGC----GGUGUCGCGUG--GAAGG-UGCAUGU-----GAGCC-G--AG--UGCG--UG--AGCG---GA--------------CGCG---UGUGUAU-----GUGUGCUUGGGGCGUGCAAGGCG--AGUGCGUGCGCCUCCUCCUGCGCCCCUCCCUCCCGCCUACACCUUGAUCUUAUUUGAUCCGGUCGUGAUCCCAGCCCCGCCGGGCCGACCCGAAAUGAAAAGCUGUCCUCCUGCGAAGCCC-----C---U---UC-CC---GGGGCGCU-GUGCAGCGAGGCC-UUUUGGGCGGUGGC-AAGCCGCGGU----CCCCGAGGCCCUGGACUCGGUCGGACG-----------GGACC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------A--------------GGC-------------------------------------------CGGGCUUGUCCUGA
AAWR02017117.1/118086-117666 GCUUUACGGAGGGAAAGCGGCCUGGGGUCGGGGA-GU--GUGUAUUGUGCUG-UGGUGUUGUGUG--GAAGG-CGCGUGC----UGGCCGAGCGUG--UGAG--UG--GACGGGCGC-------------AUGUG---UGAGUG-------CGAGCGUGGGGCGUGCAAGGCG--AGUGCGCGUGCCCGCCCCUGCGCCCUUCC-CCCCGCCUACACCUUGAUCUUAUUUGAUCGGGUUGUGACCCCAGCCCUGCCGGGCCGACCCGAAAUGAGAAGCUCCCCUCCUGCGAAGCCCA--CUC---C---U---C---GGGGCGCU-GUGCAGCGAGGCC-CCCUAGGCGGCGGCAUCGCCGCGGC----CCUGAAGGUCCCGGAGCCGGUCCUACG-----------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGCCC--G--GGCUUGUCCCA-------------------GGCCGCUG-AUUA--UCGAG-CGAUUCUGAUCUGA
AAPE02024784.1/7391-6995     CCUCACGGGAGGGAGCGCGGCCUGGGGUGCGGGU-GC-UGUGAGUGGUACUG-CGGUGUCGCGUG--GAUGG-CGCGUGC----GGGCCGAG--UG--UGUG--UG--U----GGGU-------------GGAUG---UGA---------GCGUGCGUGGGGCGUGCAAGGCG--AGUGCGUGACGCC--CCCUACGGCCCUCC-CCCCGUCUACACCUUGAUCUUAUUUGAUCGGGUUGUGACCCCAGCCC-GCCGGGCCGGCCCGAGAUGAAAAGCUCCCCUCCUGCGAAGCCC-----G---C---U---C---CGGGCGCU-GUGCAGCGAGGCC-CU-UGGGUGGCGGCGGCGCCGCGGU----CCCGGAGCC----------GAUCUGCG-----------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGCUUGU-CCC-------------------GGCCGCUG-AUUA--UCGAGGCGAUUCUGAUCUGA
AABR05090867.1/129988-129573 CCUCGCGAGUGGGAGCGCGGCUGGGGUGGUGGGUAGU-UUUGGGUUGUGUUG-U-GUGCUGCGUG--UGGUG-CAUGUGG----GCCGAGUG--CG--AGUA--CG--GAUGUGCGA-------------GUGUG---UGCGCG-------CGGGUCUGCAGCAUGGAAGGCG--AGUGUG--UGUCCUCC-CCACGCCCCUCC-CCUCGCCUACACCUUGAUCUUAUUUGAUCGGGUCGUGACCCCCGCCCCGCCGGGCCGCCCCGAAAUGAAAAGCAGCCCUCCUGCGAAGCCC-----C---C---UGGGU---GGGGCGCU-GUGCAGUGAGGCC-CUCUGGGCGGUGGCGACGCCGCGGU----UCCCGAGGUUCCCGGAUCGGUCCUGC------------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGUCCGU-CCC-------------------AGCCGCUG-AUUA--CCGAGGCGAUUCUGAUCUGA
AAQR03022577.1/18708-18284   GCUUAUGGGAGGGAGAGCAGCCAGGGGCGAAGUU-GUGUGUGUGUGGUGCUG-CGGUGUCGCGUG--GAAAG-CGCGUGU----GGGGCGAG--UG--UGAG--UG--UGCGCGCGA-------------AUCUAA-UUGAGUGU-----GCGCGCGUGGGGCGUGCUAGGUG--AGUGUGUGCGCCCGCCC-UGUGCCUCUUC-CUACACCUACACUUUGAUCUUAUUUGAUCGGGUUGUGGCCCCAGCCCCGCCGGGCAGACCCGAAAUGAAAAGCUCUCCUCCUGCGAAGCCU-----C---CUUUU---C---GGGGCGCU-GUGCAGCGAGGCC-CUUUGGGCGGCGGCAACGCCGCGGU----CUCCGAGGUCCCGGAGUCGGUCCUGCG-----------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGAUCGUCCCG-------------------GGCCACUG-AUUA--UCGAGGCGAUUCUGAUCUGA
AAGU03029536.1/144291-144707 GCUUCUUUACGGGAGAGAGGCAUGGGG--UGAGG-UU-UGAAUGGAGUUAUG-CUGUGUCGCGUG--AAAGG-CGCGUGCGUGUCGAGUG----UG--UGAG--UG--GAUGCGCGA-------------GU--G---CUAGUGG-----GCGCGCGUGGAGAGUGCAAGAGG--AGUGCGUGCACCCGCUCCUGCGCCCCUCU-UCCCGCCUACACCUUGAUCUUAUUUGAUCGGGUCGUGACCCCAGCCCCGCCGGGCCAACCCGAAAUGAAAAGAUCCCCUCCUGCGAAGCC------C---C---U---C---GGGGCGCU-GUGCGGCGAGGCC-CUUUGGGCGGCGGUAGCGCUGCGGU----CCCCGAGGUCCCGGAGCCGGUCCGAGG-----------GGGCC-CGGCGCUCAGAAAUGAUGAACUGAUCAGAUAGACG--------AGGCU--G--GGCUUGUCCCG-------------------GGCCGCUG-AUUA--UCGAGGCGAUUCUGAUCUGA
BK005568.1/1-420             GUUUUAGGGAGGGAGAGCGGCCUGGGUCCUGGGU-GU-UGUGUGCGGAGCUG-UGGCGUCGCGUG--UGAGG-CGCGUGC----AGGGUGAG--UG--UGAG--UG--GACGCGUGA-------------GUGUG---UGAGUGU-----GCGCGCUUGGAGCGUGUUAGGCG--AGUGCGUGCGCCCACCCCUGCGCCCCUCC-UCCCGCUUACACUUUGAUCUUAUUUGAUCGGAUCGUGACCCCAGCCCCGCCGGGCCGACCCGAAAUGAAAAGCUCUCCUCCUGCGAAGCCC-----C---C---U---C---GGGGCGCU-GUGCAGCGAGGCC-CCUUAGGCGGCGGCCACGCUGUGGU----CCCCGAGGUCCCGGAGCUGGCCCUGCG-----------GGGCC-CGGCGCUCAGAAGUGAUGAAUUGAUCAGAUAGACG--------AGGCC--G--GGCUUGUCCCC-------------------GGCCACUG-AUUA--UCGAGGCGAUUCUGAUCUGG
AF357344.1/1-60              ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAUUGAUCAGAUAGACG--------AGGCC--G--GGUCCGU-CCC-------------------AGCCGCUG-AUUA--CCGAG-CGAUUCUGA-----
AB221039.1/69829-69396       AUUUACCGGAGGGAGAGCGGCCAGGGGUGAGGUU-GG-AGUGUGUCGUGAUG-AGGUGUUGCGUG--GAAGG-CACAUGC----GGGCCAAA--UG--UGUGAAU----GGACGCGU-------------GA-------AUGUGA-----GUGCGCAUAGUGCAUACAAGGCG--AGGGCGUGUGCCCGCCCGGG--UCCCUCC-CCGC-----CGCCUUGGUCUUAUUUGAUGGGGUUGUGACUCCAGCCCCGCGGGACCGACCCGAAAUGAAAAGCUUAUCUCCUGCGAAGCCUU---GU---C---U---U---GGGGCGCU-GUGCGGCGAGGCC-CAAUGGGCGGUGGCGAUGCCGAGGU----CC--AGGA-------GCCGAGCCUAUG-----------GGGGC-UGGCGCUCAGAAGUGAUGAAUUGAUCAAAUAGACGAGGCCGGGAAAUAAAG--UUUUAAAAAACAAACAAACAAAAUAAAAAAUAUUUAUGGAAGACUUAGAGUCUACUCAUUCCUGA
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::.::.::::::::::::::.:(((((<<<<<<.._____.>>>>>>,....,,,,,,,,..,,..,,,,..,<..-<<<<____.............>>>>-...>,,<<<-.....-<<<<<-<<____________>>..->>>>>-->>>,,,,,,,,))))),,,,,.,,,,,,,,,,,,,,,,,,,,,,<<<--<<<<-<<<-<--<<<-<<___>>->>>>>>>->>>>----->>>,,,,,,,,,,,,,,,,,,,,....,<...<...<...<...<<<<-<<<.--<<-<<<-<<<<.<<______>>->>>>->>>->>>>>....>>>>>>>>,,,,,,,<<<<<<<<____...........>>>->.>>>>,,,<<<<------<<<<<<------------........-<<<<..-..<<______>>-...................>>>>----.----..------>>>>>>--->>>>:
#=GC RF                      auuuaaggGaGGGAGaGcGGCcuGGGguuuGggU.Gu.uGUGuGUgGugcuG.uggcgccgcGcG..gAAGG.CgCgugu....agggcgag..UG..uGaG..Ug..ggcgcGuGa.............gcgcG...uGaGugu.....GcgcgcgcgGaGCgUGcaAGgcg..AgcgcgUGcgCCCgCCCcUgcgccCCUCC.CCcCGCCUACACcUUGAUCUUAUUuGAUCGGGucgUGACcCCaGCCCCGCCGGgCcgaCCCGAAAUGAaAAGCUcuCCUCCUGCGAAGCCC....uc...c...u...c...gGGGCgCu.GUgCaGCgAgGCC.CcuUGGGcgGuGGCcacGCcGcgGc....CCCcgagguCCcGGaGccgGcCCuacG...........GGgCC.cggCGCUCAGaAGUGAUGAaUuGAUCAGAUAGACG........AGGCc..G..GGcUuGUcCCg...................gGCCacUG.AuUA..UCGAGGCgAuUCUGAuCUGA
//
# STOCKHOLM 1.0

#=GF AC   RF01269
#=GF ID   snR80
#=GF DE   Small nucleolar RNA snR80
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   40.20
#=GF NC   39.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF CL   CL00033
#=GF DR   snornadb; snR80;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15306656
#=GF RT   Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the
#=GF RT   Saccharomyces cerevisiae genome.
#=GF RA   Schattner P, Decatur WA, Davis CA, Ares M Jr, Fournier MJ, Lowe TM
#=GF RL   Nucleic Acids Res. 2004;32:4281-4296.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


U18795.1/49843-49668       GAACGUUUGACAACACUCUGGGACCAAGUUUCGAUGGUUAU-UUUUUUA-UUUCCAUCGAUGUCUUUCACUGUACUUAGUUCCAAUUUAUAUUGCAAACAAGAUU-AAUU-UAGGCGAUUACUCACUAAGAUAUACCUAUUUCUACUAUGGUUAUAUUAGUCCAUUUCAUA---GCCUUACAU
AABZ01000047.1/10323-10499 GCACGUUUGACAACACUCUGGGACCAAGUUUCGAUAGCUAU-UCUUUUA-UUUCUAUCGAUAUUUUUCACUGUACUUAGUUCCAAUUUAUAUUGCAAACAAGAUU-AAUUUUAGGCGAUUACUCACUAAGAUAUACCAAUUUCUACUAUGGUUAUAUUAGUCCAUUUCAUA---GCCUUACAU
AABY01000108.1/9971-10148  GAACGUUUGACAACACUCUGGGACCAAGUUUCGAUGAUAAUAUUUCUUA-UUUCCAUCGAUACCAUUCACUGUACUUAGUUCCAAUUUAUAUUGCAAACAAGAUUGAUUU-UAGGCGAUUACUCACUAAGAUAUACCUAUUUCUACUAUGGUUAUAUUAGUCCAUUUCAUA---GCCUUACAU
AACI02000833.1/1493-1320   GAACGUUUGACAACACUCUGGGACCAAGUUUCGAUAGUUAU-UUAUAAC----UCAUCGAUACCUUUCACUGUACUUAGUUCCAAUUUAAAUUGCAAACAAGAUU-AAUUUUAGGCGAUUACUCACUAAGAUAUACCUAUUUCUACCAUGGUUAUAUUAGUCCAUUUCAUA---GCCUUACAU
AACA01000046.1/28759-28583 GAACGUUUGACAUCACUCUGGGACCAAGUUUUGAUGGAGAC-UCUUUGAGUUUCUAUCAAUACCUUUCACUGUACUUAGUUCCAAUUUAUAUUGCAAACAAGAUU-AAUUUUAGGCGACUACUCACUAAGAUAUACCU-UUUCUACCAUGGUUAUAUUAGUCCAUUUCACA---GCCUUAAAU
AACF01000146.1/19937-20104 UAAAGUUUGACGACACUCUGGUGCCAAGUUUUGA----UUA-UCUUUGA-UUU---UCAAUUUAUUACGCUGUACUUGGUUCCUAUUUUGGUUUCAAACAAGAUU-UACU---GACUUUUACUCACUAAGAUA-ACCUACAUCU-CCAUGGUUAUAUUGGUCCAUCUUUCAAUCGUCAUACAU
#=GC SS_cons               ::::::<<<---------<<<<<<-<<<<-<<<<<<<____._______.___>>>>>>>------------->>>>->>>>>>---------->>>--------.----.-<<<<---------<<<<-<<<-<<<____________>>>>>>->>>>-----------...>>>>:::::
#=GC RF                    gAAcGUuuGACAACACUCuGGgaCCaaGuUucGaugguuau.UuUUUuA.UUUccauCgaUaucUUuCACUGUaCuuAGucCCaAUUUauAUUgCaaACAAGAUU.aAUU.UaGGCgaUUACUCACuaaGauaUaCCUAUuUCUACuAUGGuuauAuuaGUCCAUUUcauA...GCCuUAcAU
//
# STOCKHOLM 1.0

#=GF AC   RF01270
#=GF ID   snR84
#=GF DE   Small nucleolar RNA snR84
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   109.00
#=GF TC   129.60
#=GF NC   62.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snornadb; snR84;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12853629
#=GF RT   Computational identification of non-coding RNAs in Saccharomyces
#=GF RT   cerevisiae by comparative genomics.
#=GF RA   McCutcheon JP, Eddy SR
#=GF RL   Nucleic Acids Res. 2003;31:4119-4128.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


U33057.1/55298-54749       AUUGCACAACUUAAGUUUGUCGAGGAUCA-UUUUUUUGAACUGAAUCAUGCUCUUUUUA-AGUGCUUUGAAACCCUCGAUGAAUGUGUCAAUGUGCAAAGAUAAACCAUUGUUCUCUGUUGAUCAGUGACUU-AAUGUUUGCUUUGGAGAAUGAUAUUUUCCCUUUCCUAUAUUUGACUUUUGUUCUAAAAGUUAUUUGGAGAGAAAAGGCAUGAUUGAGGUUGCGACU---UU----UUCGUUUUUGCUUUUGCAUGGAUAAUUCAUCCAUGCACAUCUCAC--UUUAUUGGACCUUCAAGAUUGGUUUCCC--------AU--GUAAUUUA---AUUUUCUCUCCUCUACAUUUAAUAUGUUCUAUAUUAAUUAAUACCAAUUGAGUU-GUGCGUACUUCAUUGCAGAUAUUUUA-CCAGACCUGUCUGAGUUUUUCGUUCAAGUUUGGUUGAA--AUCGGCUUGAGGUAUAUGAA-CGUGGUUGGGAUAU-GGAG------AUU---------------------GGGAGAUCAAAGAAGCGAAAAUACCUGAGACAGUUUUUU-UAAAAAAGAAGCUAAGGAACAUGACUCAAAGAGACACAUUA
AABZ01000102.1/5093-4533   AUUGCACAACUUAAGUUUGUCGAGGAUCG-UUUUUUUAAACUGAAUCUUGCUCUUUUUU-GGCGC-UUGAAACCCUCGAUGAAUGUGUCAAUGUGCAAAGAUAAAAUAUUGUUCUCUGUUGAUCAGUGAUUUUGGC-UUUGCUUUGGAGAAGUAUCUUUUCCCUUUCCCAUAAUUGACUUUUGUCCUAAAAGUUGUUCGGAGAGAAUAAGCAUAGUUGAAGUUGCGACU---UUUUAUUUUUUUUUUGCUUUUGCAUGGAUACCAUAUCUAUGCACGUCUCAUG-UUUAUUGGACCUUCAACAUUGGUUUUUCCUUC-UGUUU--UGAGGUUA---AUAUUUUUUUCUCUACUUUUGAUAUGUCACAUAUUA----AUACCGAUUAUGUUCUUAAUUUCCUCAUCGCUGUUGUUUUAAUUCGACUCAUUUGAGUUCUUCAUUUGUGUUUGGUUGGAUAUUCAGUUUGAGGUAAAC-AA-CAUAGUUGGUAUGU-GCAGGAAAUGAUUGAAAAUCACAUGAACAUCUGGGUGAUCGUACAGAAGUGAAAAUACCUGAGGCAGUUUUGUACAAAAAAGAAGCUA---------------------------
AACG02000122.1/7707-7140   AUUGCACAACUUAAGUUUGUCGGGGAUCAUUUUUUUUAAACUGAAUCUUGCCCUUUUCUAAGUGU-UUGAAACCUUCGAUGAAUGUGUCAAUGUGCAAAGAUAGACUGUUGUUCUCUGUUGAUAAGUGAUUUUGGUAUAUGCUUUGGAAA---UUUUUUUCCCUUUCCUA---UUGACUUUUGUUUUAAAAGUCGUUUGGAAAGUAUAGGCAUGAUUAAAAUUGCGACUAUUUUUUAAUUGCUUUUCGCUUUUGCAUGCAUAUUAUAUGCAUGCACUCCUCAUGUUUUAUCAGACCUUCGAGAUUGGUUUUUCCAUG-UUUCU--GUUUUUUC---AUAUCAUUUCCCCUCCUUUUAAUAUGUCCUAUAUUA----ACACCAAUUGUUUU-GUACGUGUUGCAUUUCCCAUCAUG-AGUCAGUCUAGUCAGAGUUCUUCUUUCAAGUUUGGUUCGG--UUGGGCUUGAGACACAC-AG-CAUGGUUGGUGCGCGGGAGGGGAUGAUUGAGAAU-AUACGGAAAUC---GAAAGACCAUGGAAGCGAAGAUACCUGAGAUAGUUUUGC-UGAAAAAGAAGCUA-------------CAAAAGCUUGAUUC
AAEG01000088.1/36121-36653 AUUGCACAACUUAAGUUUGUCGAGGAUCAUUUUUUUUGAACUGAAUCAUGCUCUUUUUA-AGUGCUUUGAAACCCUCGAUGAAUGUGUCAAUGUGCAAAGAUAAACUAUUGUUCUCUGUUGAUCAGUGACUU-AAUGUUUGCUUUGGAGAAUGAUAUUUUCCCUUUCCUAUAUUUGACUUUUGUUCUAAAAGUUAUUUGGAAAGAAAAGGCAUGAUUGAGGUUGCGACU---UU----UUCGUUUUUGCUUUUGCAUGGAUAAUUCAUCCAUGCACAUCUCAC--UUUAUUGGACCUUCAAGAUUGGUUUCCC--------AU--GUAAUUUA---AUUUU-CUUCCUCUACAUUUAAUAUGUUCUAUAUUA----AUACCAAUUGAGUU-GUGCGUACUUCAUUGCAGAUAUUUUA-CCAGACCUGUCUGAGUUUUUCGUUCAAGUUUGGUUGAA--AUCGGCUUGAGGUAUAUGAA-CAUGGUUGGGAUAU-GGAG------AUU---------------------GGGAGAUCAAAGAAGCGAAAAUACCUGAGACAGUUUUUU-UAAAAAAGAAGCUA-------------CAGGAACAUGACUC
AABY01000065.1/22048-22610 AUUGCACAACUUAAGUUUGUCGAGGAUCA-AUUUUUUGAACUGAAUCUUGCUCUUUUCA-AGUGC-UUGAAACCCUCGAUGAAUGUGUCAAUGUGCAAAGAUAAACUAU---UCUCUUUUGACCAGUGAUUU-GAUAUUUGCCUUGGAGAAUAAUAUUUUCCCUUUCCUGUAAUUAACUUUUGUUCUAAAGGUUAUUUGGAGAGAAUAGGCAUGAUUGAAGUUGCGACU---UU-UUUUUGUUUUUUGCUUUUGCAUGG-UACUUGAUCCAUGCACUUCUCAU--UUUAUUGGACUUUCAAGAUUGGUUUCCCUCGU-GUUUUAAUUUUUGUU---AAAUUUUUCCCUCUACUUUUAAUAUGUCCUAUAUUA----AUACCGGUUAUGUU-GUACGUGUUUCAUUGCUGAUCUUUUA-CUAGACUCGUCUGAGUUCUUCGUUCAAGUUUGGUUGAU--UUCGGCUUGAGGUACAU-GA-CAUGGUCGGCAUGU-GGAGGAAAUGAUGGAAAGUUACAUGGAUUUU---GGGAGAUCAUAGAAGAGAAAAUAUUUGAGACAGUUUUGU-ACGAAAAGAAGCUA-------------UAAACAUGACUCAG
AACI02000054.1/8192-7621   AUUGCACAACUUAAGUUUGUCGGGGAUCAUUUUUUUUAAACUGAAUCUUGCCCUUUUUUAGGUGC-UUGAAACCCUCGAUGAAUGUGUCAAUGUGCAAAGAUAAACCGUUAUUCUCUGUUGAUAAGUGAUUUUGAUACUUGCCUUGGAAA----UUUUUUCCCUUUCCUAUAAUCAACUUUUGUUUUAAAAGUUGUUCGGAAAGAAUAGGCACAAUUAAAAUUGCGGCUUUCUUCCUAAGUUUUUAGGCUUUUGCAUCGACACUUC-UCUAUGCACUUCCCUCG-UUUAUUGGACUUUCAAAACUGGCUUUCCCUUCAUGUUU--UGUUUUUCUUUAUGUUGUUUCCUCUACUUUUAAUGUGUUCUAUGUUA----AUACCGAUUGUAAU-GUACAUGUUUCAUUGUUGA--CCUUAAGCAAGUUUGUCUGAGUUUUUUUUUCAAGUUUACUUAAG--UUCGCUUUGAGAUAUAUAAUAUAUGGUUGGCAUGU-GGAGGGGAUGCUUGAAACU-GCACAAACAUG---GGAGGGUCAUUGGAGUGGAGAUACCUGGGAGAGUUUUUU-UACAAAAGAAGCUA-------------AAAAACACAAUUCA
#=GC SS_cons               ::::::::::::::(((--((((((,<<<.<<<____>>>->>>,<<--<<-<<_____.>>->>.-->>,,,))))))--))),,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,(--((((((((---(((((,<<<<<<<___>>>>>>><<<<<<------<<<<<<<<<___>>>>>>>>>--->>>>>>,,,)))))--))))))))--),,,,...,,,,,,,,,,[[[[[[[[[[[<<<<<<<<_____>>>>>>>>,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,(((((((((----.(((((..--------...--(((-((((((((,,,,,<<<<<<<___>>>>>>>....,<<<<<<<<<<<<<.----<<<<<<<<--<<<<<---<<<<<<<<<<<-<<--<<<<___>>>>-->>->>>>>>>>>>>..->>>>>->>>>>>>>--.>>.>>>>>>>>>>>,,,.))))))))-)))-------.----)))))--...))))))))),]]]]]]]]]]],,,,,,,,,,<<<<<<__._______>>>>>>:.............::::::::::::::
#=GC RF                    AUUGCACAACUUAAguuUGuCGaGGAuCa.uuuUUUUaaaCuGaAuCuUGCuCuUUUuu.aGUGC.UUGaAACCCuCGaUGaauGUGUCAAUGUGCAAAGAUAAAcuaUUgUUCUCUGUUGAUcAGUGacuuugauaUUuGCcuUGGaaaauaaUauuuuCCCuuuCCUAUAaUcgaCuuuugUUcuaaaaGucgUUuGGaaaGAAuagGCaUgauuaaaguUGCGACU...UUuuaauuuuuuuucgCuuuuGCauggauAcUuuauccauGCACuUCUCAuG.UUUAUUGGACcUUCAAgAUuGgucuccCcuuu.ugucc..uuuuuuUa...AUaucuuuccCuCuACuUUuaauaugUuccauauua....AugCCgauuauguu.gUacgugccuCaUUgccgaUaucucaaccagacucGUccGagUUuuuCgUUCgAguuugguugag..uucggcUuGaggcacAu.aa.cauggucGGcaUgU.gGaGggaaUgauuGAaAaU.acAuggacaUu...GggagacCauagaaGcgaaaaUAccUGAGAcaGuuuuuU.uaaAAAAgaagCuA.............aAAaaaauaaauua
//
# STOCKHOLM 1.0

#=GF AC   RF01271
#=GF ID   snR30
#=GF DE   Small nucleolar RNA snR30
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Published; PMID:14749391; Wilkinson A
#=GF GA   80.00
#=GF TC   101.50
#=GF NC   51.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00078
#=GF DR   snornadb; snR30;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   7744794
#=GF RT   Isolation and characterization of the small nucleolar ribonucleoprotein
#=GF RT   particle snR30 from Saccharomyces cerevisiae.
#=GF RA   Lubben B, Fabrizio P, Kastner B, Luhrmann R
#=GF RL   J Biol Chem. 1995;270:11549-11554.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


X07673.1/425-1032          AACCAUAGUCUCGUGCUAGUUCGGUACUAUACAGGGAAGGGAAGUCACUCGCAUACGUGUGUGUGCAUUUCUUGCUAUUGCUGCUUAGCUUCUCUAAA-ACACUGGGCUA-CGUUUUUCAACGCUCGAGAGGCAGAGUCUCAAGGAGCCUCCAAUGGGCCUCACGUAUU-CA--UCUAGAUGGCGCUUCGGACAACGGCAUCACAUAAGAGAUGCAGCUCCUGACUUCUCCUCUGAUCUUCGUGAUCAGAGUUUU-GAGUCGUCAGACUACGAGCAGUUUCUCUUAGUCGUUGCAUCGGGUGCUGUUGCCUU-AAGCAUGUGUAUAUGGGGUUCGGGGGCUGUUGCCAUGAUAUAUAUGGAUGAGACAGAAGUGGCCCCGUUGACGAGUUUAACUUAGAUUAAGUAGGACGCAUGAUCUUGAGCUCUUUUCCUAUACUUUGUCCUAUGGCCAGCUUUCUCCUUAUUACGAAGAGAUUGCGGGAUGUGGGUGCAGAGUGGGAAAAUCUGAGUUCGGUCAUCUUUGUUGUUCGUCCUACCGCAGUAUAUUCCUAAACACUAUGAAAUGACCCUAGUU-GGUCCAUGAUCAUUUGGGUAAAACCAUACUGCAGACAUCU
AABY01000047.1/17961-17352 AACCAUAGUCUCGUGCUAGUUCGGUACUAUACAGGGAAGGGAAGUCACUCGCAUACGUGUGUGUGCACUUCUUGCUAUUGCUGCUUAGCUUCUCUAAA-ACACUGGGCUAGCG-UUUUCAACGCUCGAGAGGCAGAGUCUCAAGGAGCCCCCAAUGGGCCUCACGUAUU-CACAUCUAGAUGGCGCUUCGGACAACGGCAUCACAUAAGGGAUGCAGCUCCUGACUUCUCCUCUGAUCUUCGUGACCAGGGUUUU-GAGUCGUCGGACAACGGGCAGUUUCUCUUAGUCGUUGCGUCGGGUGCUGUUGCUUU-AACGAUGUGUACGAGAGGUUCGGGGGCUGUUGCCAUGAUAUAUAUGGAUGAGACAGAAGUAGCCCCGUUGACGAGUUUAACUUAGAUCAAGUAGGAUGCAUGACCUUGAGCUCUUUUCCUAUACUUUGUCCUAUGUCCGGCUUUCUCCUUAUUACGAAGAGAUUGCAUGAUGAAGGUGCAGAGUGGGAAAAUCUGAGUUCGGUCGUCUUUGUUGUUCGUCCUACCGCAGUAUAUUCCUAAACACUAUGAAAUGACCCUAGUU-GGUCCAUGAUCAUUUGGGUAAAACCAUACUGCAGAUAUCU
AACH01000215.1/7327-6713   AACCAUAGACUCGUGCUAGUUCAGUACUAUACAGGGAAGGGAAGUCACGCGCAUACGUGUGUGUGCAUUUCUUGCUAUUGCUGCUUAGCUUCUCUAAAAACACUGGGCUAGCGUUUUUCAGCGCUCGAGAGGCAAAGUCUCAAGGAGUCCCCAAUGGGCCUCACGUAUUUCACAUCUAGAUGGCAUUUUGGACAUCGGCACUAAAUAAGAGAUUCAGCUCCUGACUUCUCCUCUGGUCUUCAUGAACAGGGUUUUUGAGUCGUCGGAUCAUGGGCGGUUUCUCUUAGUCGUUGCACCGGGUGCCAUUGUCUU-AACGUUGUGUGCGGGUGGUUCGGGGGCUGUUGCCAUGAUUUAUAUGGAUGAGACAGAAGUAGCCCCGUUGACGAGUUUAACUUAGAUCAAGUAGGAUGCAUGAUCUUGAGCUCUUUUCCUAUACUUUGUUCCAUGCUCUGCUUUCUCCUUAUUACGAAGAGAUGGCAGGACGUGUGUGCCGAGUGGGAAAAUCUGAGUUCGGUCAUCUUCGUUGUUCAUCCUACCGCAGUAUAUUCCUAAACACUAUGAAAUGACCCUAGUUUGGUCCAUGAUCAUUUGGGUAAAACCAUACUGCAGACAUCU
AACI02000330.1/3807-4421   AACCAUAGUCUCGUGCUAGUUCGGUACUAUACAGGGAAGGGAAGUCACGCGCAUACGUGUGUGUGCACUUCUUGCUAUUGCUGCUUAGCUUCUCUAAAAACACUGGGCUAGCGUUUUUCAGCGCUCGAGAGGCAGAGUCUCAAGGAGCCCUCAAUGGGCCUCACGUAUUUCACGUCUAGAUGGCGCUUCGGACAUCGGCAUUAUAUGAGGGAUUCGGCUCCCAACUUCUCCUCUGGUCUUCGUGACCGGGGUUUUUGAGUCGUUGGGUCAUGGGUUGUUUCUCUCAGUCGUUGCAUCGGGCGUCGUUGCCUU-AACGAUGUGUGCGAGAGGUUCGGGGGCUGUUGCCAUGAUUUAUAUGGAUGAGACAGAAGUGGCCCCGUUGACGAGUUUAACUUAGAUCAAGUAGGAUGCAUGAUCUUGAGCUCUUUUCCUAUACUUUGUCCCAUGCCCGGCUUUCUCCUUAUUACGAAGAGAUAGCAGGAUGUGGGUGCAAAGUGGGAAAAUCUGAGUUCGGUCAUCUUUGUUGUUCAUCCUACCGCAGUAUAUUCCUAAACACUAUGAAAUGGCCCUAGUUUGGUCGAUGAUCAUUUGGGUAAAACCAUACUGCAGACAUCU
AACA01000009.1/17253-17860 AACCAUAGUCUCGUGCUAGUUCGGUACCAUACAGGAAAGGGAAGACACGCACAUACGUGUGUGUGCGCUUCUUGCUAUUGUUGCUUAGCUUUCCUAAA-ACACUGGGCUAGCGUUUCUCAACGCUCGAGAGGCAGAGUCUCAAGGAGCCCCCAGUGGGCCCCAUGCAUC---CAUCUAGAUGGCACUUCGGACAGUGGCACUAUAUAGGGGAUUCGGCUUCCAACUUCUCCUCCGGCCUUCGCGGCCGGGGUUUU-GAGUCGUUGGAUCACGGGCCGUUUCCCUUAGUCGUUGUCUUGGGUGUUGUUGCCUUUAACGAUGUGUGCGAGGGGUUCGGGGGCUGUUGCCAUGAUUUAUAUGGAUGAGACAGAAGUAGCCCCGUUGACGAGUC-AACUUAGAUCAAGUAGGAUGCAUGAUCUUGAGCUCUUUUCCUAUACUUUCUCCCACACCGGGCUUUCUCCUUAUUACGAAGAGAGAGCAAGGCGCGAGGGC-GAGUGGGAAAAUCUGAGUUCGGUCAUCUUUGUUGU-CAUCCUACUGCAGUAUAUUCCUAAACACUAUGAAACGGCCCUAGUUUGGUCAAUGAUCAUUUGGGUAAAACCAUACUGCAGACAUCU
#=GC SS_cons               ::::::::<<<<<<<-<<<<_____>>>>>>>->>>>,,,,{{{{-{{-{{{{-{{{,<<<<-----------<<<<________>>>>---------.>>>>,[[[[[[,,<<<<<<<_______>>>>>>>,,,((((((,,,<<<<<<<---<<<<<<<--<<<<-.----------------<<-<<-<<<<<<<<<<<<-<<<<<<<--<-<<<<<<<<<--<<<<<<<<<<<_____>>>>>>>>----.>>>-->>>>>----->>>>->-->>>>>>>>>---------->>>>>>>>>>>>--.>>------>>>>-->>>>>>>>>>>>>>,,,,<<<<<_____>>>>>,)))))),,,,,]]]]]]}}}}}-}}-}}---}}}},,,,,,,<<<<<<<<--<<<<--<<<<<<<<<<<<<<--<<<<<<<<<<<<<-<<-<<--<<<<___________>>>>-->>->>->>>>>>->>>>>>>>>>>>>>--->>>>>>>>>>>----------->>>>>>>>,<<<<<<<----------<<<---<<<<<<-<-<-<______>->->->>>>>>->>>------>>>>>>>::::::::
#=GC RF                    AACCAUAGucuCGugCuaGuUCgGUaCuauaCAGggaAGGGaaGuCaCgCGCaUaCGUGuGuGUGCauUUCUUGCuaUUGcUGCUuaGCUUcuCUAAA.aCaCUGGGCuaGCGcuucuCAaCGCUCGagaggCAgAGuCuCaAGGaGcCccCAaUGggCCcCAcGcauu.cAcaUCUAGAUGGCacuucGGACagcggCaccacAugaGgGaUuCaGCccCcgaCUUCuCCcCcGguCUUCguGacCgGgGUUUU.GaGUCGucgGAucAuggGCaGUUuCcCucaguCGUUGcaucGgguGccgcuGCCUU.aacgaUGUgugCgaGgGGuuCGggGgCuGUUGCCaugAUuUAuauGGAuGaGaCAGAAGuaGCCCCGuuGACGAGuuUAaCuuAGAUcAAGuaGGacGCAuGacCUuGagCuCuuuuCCuAUaCucugucccgcgcccgGCUUuCuCCUUAUUACGAAGaGauaGCAggacgcgggugcagaGugGGaaaaUCUGaGuuCgguCaUCUUuGUUGUUCguCCuaCcGCaGuauAUUCCUAAACaCuAUGaaauGaCCCuAGUUUGGUCaaUGAuCauuuGgGuAAAACCauaCuGCAGAcAUCU
//
# STOCKHOLM 1.0

#=GF AC   RF01272
#=GF ID   snR86
#=GF DE   Small nucleolar RNA snR86
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   120.00
#=GF TC   126.70
#=GF NC   104.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00037
#=GF DR   snornadb; snR86;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Saccharomyces_cerevisiae300031;
#=GF RN   [1]
#=GF RM   15923376
#=GF RT   The complete set of H/ACA snoRNAs that guide rRNA pseudouridylations in
#=GF RT   Saccharomyces cerevisiae.
#=GF RA   Torchet C, Badis G, Devaux F, Costanzo G, Werner M, Jacquier A
#=GF RL   RNA. 2005;11:928-938.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


Z48756.1/13768-12765         UAACCAUUGAUGAAAUUCUAUUGAAUGUCCCCAAUUUUCGGAAAAGGACUGCACCGAAAUAUUUCAAUCAAAAUCAUUU-AUCGUUUUGUUUAGCUAU--UUU-UUUCUCAAAUUAUCACUCUUUUCUUCCUUUUUCAUUCUCU-CAAUUGUUCUUUUUAUUUGAGGAAAUUUGAUUGUAUUGCAUAUACAACUAUGCGAUGCACUUUGUUCAUUUUAACUUUGGAUA-UAUGUGCCUUGCUAUGAACGCGUUCAU-UUUUA-AGUGACCGGACCCUAAAAUAUUCAGGUAGCAUGA-CGGAAGCUAUGAAUUAAUCCUGGUGGAGGGGUGUGUUCAGUUUGAGGGAGGAUGAUAAAA-UGGAACGGAGAUUGCAAGGAGACGUAGAAAAUAAAGUAGGAGCAAAUGGAUUUUCUGCUUGGCGGUAUAGCACGUUUGAGUUUUUCAGUCGUGUCUAUGUUCAGGUUUAUGAUAUGCUGUGGUUGAUUCUGUUGAUU-CACACGUUUCGCUUCCAUAUAGUGUGUUAACGGAAACUCCAUGUUAAGGUUUAUUAUAAGAAAAUUUUUUGAAUUUGUUCUUUUUAUAUUGGUUUACU--CUCCUCGUGAUUUCUU--UUCUUU-----UUUUAUCGUCAUCCUCUCUGAAUGUAUUUAUUACGCAUG--GCUUUUAUUCAUUGCUUUCUAACUGUGAUGG--GAGUUUUUUUC---UUGUUGCAUAAAUGAACGUGGGCGAGGUUUU-UAUUUUCAAACUUGGUGUACUAUAGUGCAAUGCGUUGUUAAUUGUAAUAC--GAUGUUUCUUCGAUAAAAGGAGCGGAGGGAGAAGGUGAAAUUACGAAGGAAAGAAAGAGAUGAGAAAUCAAGAAUGAAGCAAGACAUUGAUU-GAUAUGGUUGUUUUCGGUGCAUGUUUG-AUUACUAAAAGUUGGGGC-AUUCGAUGGUUUACAGAAGUCAUAAAUUCAAAUAUCCCGUUUAAUCGCUCAUCUAUUAAAAUCAAUAGUAGAAUGUAGUUUCAUACCCGGGAGAAAUUC
AABY01000081.1/5507-6509     UAACCAUUGAUGAAAUUCUGUUGAGUGUCCCCAAUUUUCGGAAAAGAAUUGCAUAGGCGUUGUUCAAUCAAG-UCAUUU-AUUGUUUUGUUUCGCUAUAUUUU-CUUUUCAAAUUGUCAUUCUUUUUCUUCUGUUUUGUUCU---CAAUUCUUCUUCU-GUUUGAGGAAAUUUGAUUAUAUUGCAUGUCCAGCUAUGCGAUGCACUUUGUUCAUUUUAACUUUGGAUA-UAUGCGCCUCGCUAUGAACAUGUUCAU-UUUUGUAGUGACCAGA---UAGGGGAUUCCAAUAGCAUGA-UGAAGGCUGAGGAUUAAUUCUAGUGGAGGGAUAUAUUUAGCUCAGACGAGGAUGAGAAAAAUGGAGUGGAGAUUACAAGGAGAGGUAAGAAAUAAAAAAGGAACGGAUGGGUUUUCUGCUUGGCUGUAUAGCAUGUUUGAGUUUUUCAGUUGUGUCUAUGUUCAAGUUUAUGAUAUGCUGUGGUUGGUUCUGUUGAUUUCACACGUUUUACUUCCAUAUAGUGUGUUGACGGAAACUCCGCGUUAAGGUUUAUUAUAAGGAAAUUUU--GAAUUUGUUCUUUUUAUGUUGUUUUACC--CUCUUUGCAAUUUUUUCCUUCUUU-----UUUUAUCCUCAUCUUUUCUGAAUGCAUCUAUUACACAUGCGGUUUUAAUUCACUGUUUUUUAAUUGCAAUGG--GAGUUUUCUUUGUGUUGUUGCAUGAUUGGACGUGGGCAAGGUUUC-UAUUUUCAAACUUGGUGCACUGUGGUGCAAUGCAUUGUUGCUUGCAAUACAUGAUGUUGCUUUGGCUAGAGAAGUGGAGGGGG-----GGAAAUACGAAGGAAAGAAAGA--UAAGAAAUCAA-AAUGGAGCAAGACAUUGAUUAGAUACAAUUAUGUUAUGUGCAUAUUUG-AUUACUAGAAGUUGGAGAGAUUCGACGGUUUACAGAAGUCAUAAAUUUAAAUAUCCCGUUUAAUCGCUCAUCUAUUAAAAUUGAUAGUAGAAUGUAGUUUCAUACCCGGGAGAAAUUU
AABZ01000413.1/1491-521      UAAUCAUUGAUGGAAUUCUAUUGGGUAUCCCCGAUUUUUAGGAAAAAAUUUCUUAGACAUAGU-CAAUAAAGAUCAUUU-UUUGUUCUGUUU---------------CUCAAAGUGUCUUUCUUUUUUCCCUU------------CAAAUCUUCAUCU-AUUCAAAGAAACUUGUAUAUAUUGCAU-UUCGGUUAUGCGAUGCACUUUGUUCAUUUUAACUUUGGAUC-AAUAUACCUCACCAUGAACAUGUUCUU-UUCUA--AUGACCAAA--UAAAGAUGUUCUAGUAUAGUGA-CGAAGGUCAUGAAUGAGCGCCGAGGGAGGGAUAUAUUCGGGC--AACGAGGAUGGAAAAA-UGGAAUGAAUACUUCAUGGAGGCGUAGGAAAUAAAAUAGGGAUAAGUGGGUUUUCUGCUUGACUGUAUAGCAUGAUUGAGUUUUUCAGUCGUGUCUAUGUUCAAGUUUAUGGUAUUCUGUGGUUGAUUCUGUUGAUUUCACACGUUUCACUUCCAUAUAGUGUGUCAACCGAAACUCUACGUGAAGGUUUACUAUAAGAAAAAUUU--CAAUUUGUUUUUAUUCUAUUG-UUUACU--CUCCGUGAUAUUUUUU--CUCUUU-----UAUUGUCCUUGUCUUUUCUGGAUAUAUCCUUUGCACAUU--GGUUUUAUUCAUUGUUUUCUAAUUAUGCUGG--GAGUCUUUUUG----UGUUGUAAGGAUUGGCGUGGGCGGGGCUUCAUUCUUCCAAACUUGGUGUACUAUGGUGCAGUGCGUUAUUGCUUGCAGUGA-UGAAGUUGCUUCGAGUACUUAAAUGGAGAGGA--GACGGAAAUAUUAAGGAAGAAAUGA-AUGAGAAAUGAA-AAUGUACAAAGACUUUGAUCAAGUAUGGUUUUGUUUUAUGCAUAUUUUUAUUACUAGAAGUUGGGGAGAUUUGAUGGUUUACAGAAGUCAUAAAUUCAAAUAUCCCGUUUAAUCGCUCAUCUAUUAAAGUUAAUAGUAGAAUGUAGUUUCAUACCCGGGAGAAAUUU
AACI02000062.1/9726-10739    UAAUCAUUGAUGAAAUUCUGUUGAGUAUCCCAAGCUUUUGGAUAUGGAUU-CAUAAGCAUGGC-CAACUGAGAUCAUUUUACUGUUUUGUCUCGCUAUAUUUU-UUUUUCAAAUUGUCAUUCUUUUUUUCUUUUUUUUCUUUUUACUCUAACUCUUCU-ACUUGUGGAAA-UUGAUUCUAUUGUAUAUCCAGAUGUAUGAUGCACCUU-UUCAUUUUAACUUUGGGUAAUGUUUGUCUCACUAUUAACAUGUUCAU-CUUUGCAAUGAUGGAA--UAGAAAAAUUCAGGUGGCAUGAUCUGAAGGUACGAGUGAGCUCCGAUGGGGGGACGUGCUUAGAAGGGGCAAGGACGAGGGAAGAGAAAUGAAGGUUUCAAGGAGAUAUAAUAGAUAAAAUGGGAGCGGAUGG--UUUCCGCUUGGCUGUAUAGCAUAAUUGAGUUUUUCAAUCAUGUCUAUGUUCAGGUUUAUGAUAUGCUGUGGCUGAUUCUGUUGAUUUCACACGUUUCACUUCCAUAUAAUGUGUUGAUGGAAACUCCACGUUAAGGCUUAUCAUAGGAAAUUAAUU-GAACUCGUUCCCUUUUUUAUUUUUUAUUGUCUUUUCCUGAUACUUUCAUUUUUUCGACUUUUUAUGCUUAUCUUUCCUAAGCACAUCUU---CACAUG-AGCGCUCAUCCG-UAUUUUCUAUUCACGUUAACAGAGUUUUUUUA-CGUUGUUGCAUGAUUGGGCAUGGGCGAGGCUUCAUUAUUCCAAACUUGGUGAAUUGUGGUGCAAUUCAUUGCUGGUCACAAUGCAUGACGUUUGUUUGGUUAGAAAAGCGAAGGAGA--AAGGAAGAUACUGGGGGAAAGAAAG-AUGAGAAAUCAA-AAUGGAACAAUAUUUUAAUA-GGUCUGGCAAUGUUUUGUGUAUAAUUCUAUUCCUAGAAGUUUAGGAGAUCCGAUGGUUUACAGAAGUCAUAAAUUCAAAUAUCCCGUUUAAUCGCUCAUCUAUUAAAAUUAAUAGUAGAAUGUAGUUUCAUACCCGGGAGAAAUUU
AACG02000005.1/115181-116180 UAACCAUUGAUGGAAUUCUAUUGAGUACCCCUAGCUUUUGAAAAGGAAUU-CGUGAGCAUGGC-CGUUUAGGAUCUCUUUAUUUUUUUGUUUUGCUAUAGUUCAUUUUUCAAAUCGUCAUUAUUUUUUCUUUUUUUUUUCUUU--UGACUCUCCUUUU-GCUUGAAGAAAUCUGAGGACAUUGUAUAUCCAAUUAGGUGAUACA-UUUAUUCAUUUUAACUUUGAAGC-AAUCUGUCUUACUAUUAACAUGUUUAUAUUUUGCAUUAGCCGGA---UAAAAUACUUCGAUGACAUGG-UAGAGAGGAUGAAUGAUCUCGAGUCGGGGAACGUAUUUACUU-AGGUCGGGAUGCGAGAGGAAAGAUAAAGAUUUUAUGGAGAUUUAAGAGAUAAGGUGAGUGGGGUCUUUUUUUCCGCUUGGCUGUAUAGCGUGAUUGAGUUUUUCAGUCGUGUCUAUGUUCAAGUUCAUGAUAUUCUGUGGUUGAUUUUGUUAAUUUCACACGUUUCACUACCAUACAGUGUGUUGACAGAAACUCCGCGUUAAGGUUUAUUAUAGGAAAUUUUU--CGACUC-CUCUUUUCCUAUUU-UUUAUUG-UCUUUUGUGACGUUUUUAUUUUUUUU-CUUAUUAUCCUCCUCCUUUCUAAGUAUUUCUUU--UACUUG-GGUUUUCAUUUG-UGCUUUUAAUUUAUGUUGUU-GAGGUAUUUUG-CGCUUUUGCAUGGAUGGACAUGGGUGAGACUUUAUUAUUUCAAACUUGGUGAAU----AUGUGCUGCCUUGUUGGUUGCAAUGUGUGAUGUUUAUUCAUGUAGGGGAGUGGAGGAGGA-AUGGAAAAUAGGAAAGAGUUGGUGG--UGGGGAGUUUG-AAUGGAACAAAAAAAU-AUUGGGUCUGGCCAUGU---AAAUGUGUUUU-AUUAUUAGGAGUUGGAGGCAUUCGAUGGUUUACAGAAGUCAUAGAAAUAAAUAUCCCGUCUAAUCGCUCAUCUAUUAAAAUUAAUAGUAGAAUGCAGUUUCAUAUCCGGGAGAAAUUC
#=GC SS_cons                 :::::::[[[[------[[[[[[[[[-[[[[[[[[[[[[[[----[[[[--[[[[[[[[[[[[.--[[[---[[[[---.---[[[[[[[[[[[---------.[[[[[[[---------[[[[[[[[[[[[[[---[[[[[-..----[[[[[[[[-.--[[[[[[[[[[-------[[[[[[[----[[[[-[[[[[-[[[[[[--[[-[[[[-----[[[[[[--.-----[[[[[[[[-----[[[[[[[[[.---[[[[[[[[[----..--[[[[[[[[[---[[-[[[[[.-[[[[[[-[[[[[[[[[<<<<___>>>>((((((((((((---(((-((((((((-------((((-(((((---(((((((--((((--((((-((-((((((((((---((((((<<<<<<---<<<<<<<<<<<<<<<___>>>>>>>>>>->>>>>->>>>>>,<<<<<<<-<<<<<<<--<-<<<<<<<<<---<<<<<________________>>>>>>>>>>>>>>->->>>>----->>>->>>>>>>))))))----..--))))))))))-))-))))---))))-..)))))))-----)))))-))))--.....--))))))))-)))---)))))))))))),,,,,,,,,,.,,,,]]]]]]]]]-]]]]]]---]]]]]-]]-..]]]-]]]]]]-.-]]]]]]]]]---]]]]]]]]]]]]]]]]]--------]]]]]]---]]]]-]]---]]]]]]-]]]]]-]]]]--]]]]]]]------]]]]]]]]]]----------]]]]]]]]..---]]]]]---]]]]]]]]]]]]]].-]]]]]]]----.--]]]]]]]]]]]--]]]]--]]]---]]]]]]]-]]]]]---]]]]-.----]]]]]]]]]]]]]]-]]]]]]]]]---------]]]]------------<<<<<--<<---<<<<<<<<<<<<_______>>>>>>->>>->>>---->>-->>>>>:::::::
#=GC RF                      UAAuCAUuGauGaAAUUCuguuGaguacCcCcaacuuuugGAAAagaauUgCacagacauggc.CAaccAAGaucaUUU.AUUgucuuguuccgCUAUAuUUu.uuucuCaAAuUGUCAUucuuuuuucccuucUUuuuucuu..caAuccccCuucU.auucgaagaaacUUGAuuacauuGcaUAUcCagcUacGcgAuGCaCcUUguUCauuUUAACuuuGgaua.uAUuUgcCucgCcAUgAACacGuucau.UUUugcagcggccggA..uuaagagacucagguagcguga.ugaaagcugcGaaugagccCcggugGggggaugugcucaGuuuggacgaGgaugagAaAAguggaaUgaagaUUucaaggaGAuguaagAaauaAaauggGagcgaguggauuuuCcgCuuGgCuGuauaGCacgauuGagUUUuuCagucguGUCuaugUuCaaGuUuaugauaUgCuGuGGUUGAuuccGuugaUUUCaCaCGUUUcACUuCCAUAUAGuGuGucaaCggaaACUCCaCGUuAAgGcUuaucauagGaaaauuuU..gAacucgcuCccuuuauauuguUuuacU..CuccuugugAUuucuucauucuUU.....UuuuaucCucauccUUUCugagcacauccuUUacACAUg.gGuucucauuCgcUgcuuucuAaucacguugg..gaguucucuua.cgcugcugcauGaauggaCguGgGcgaGgcUUuAUuuUucCaaaCUUgguGuacUaUgGuGCaaugCguUgcuGaUugCaaugcaUGAuguuucuucgauuAgagaAGuggaGgggg..aauggaaaUAcgaagggaaaaaaga.AuGagaaaUcAA.AAuggaacaagacauugauuagguaUGgccauguUcuguGuAUauuuu.AUUACuagaaguugGgGggauuCgacgGUUUACAGAAguCaUAAAuuuAAAUAuCCCGUUuaAUCgCuCauCuauuaAAAUUAAuaguaGAauGUaGuUUCAuacCCGGGaGAAAUUu
//
# STOCKHOLM 1.0

#=GF AC   RF01273
#=GF ID   sR34
#=GF DE   Small nucleolar RNA sR34
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   40.00
#=GF TC   63.00
#=GF NC   35.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11359559
#=GF RT   A guided tour: small RNA function in Archaea.
#=GF RA   Dennis PP, Omer A, Lowe T
#=GF RL   Mol Microbiol. 2001;40:509-519.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AE009950.1/1849547-1849600 ACCGAUGAGGAGCGUUAGCCACGCUGAA-GAUGAUGACAAGAGGGUUAGCCGAGG
AJ248288.1/255929-255876   GCCGAUGAGGACCGUUAGCCACGCUGAG-GAUGAUGAUAAGAGGGUUAGCCGAGG
AP006878.1/1226898-1226844 GCCGAUGACGAGCGUUAGCCACGCUGACUGAUGAGGAAAAGAGGGUUAGCCGAGG
BA000001.2/1732053-1732000 GCCGAUGAGGAUCGUUAGCCACGCUGAG-GAUGAUGAUAAGAGGGUUAGCCGAGG
#=GC SS_cons               :::::::::::::<<<<<<<---<<___.__________>>-->>>>>>>:::::
#=GC RF                    GCCGAUGAgGAgCGUUAGCCACGCUGAg.GAUGAUGAuAAGAGGGUUAGCCGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01274
#=GF ID   sR45
#=GF DE   Small nucleolar RNA sR45
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   40.00
#=GF TC   43.00
#=GF NC   33.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AE009950.1/1891933-1891879 CGGGAUGAGGAAGCCGAGGACACCUGA----UGGA------UGAUGACUCUUCGCUUCGCCGACC
AJ248283.1/64245-64299     CGGGAUGAGGAAGCCGAGGACACCUGA----AUUG------UGAUGAAUCUUCGCUUCGCCGACC
AP006878.1/1103625-1103571 AGGCGUGAUGACGCCGAGGACACCUGA----GCGG------UGAUGACUCUUCGCUUCGCUGACC
BA000001.2/55211-55265     CGGGAUGAGGAAGCCGAGGACACCUGA----AGGA------UGAUGACUCUUCGCUUCGCCGACC
CP000855.1/482396-482336   AGAAAUGAUGAGGCCGAGGACACCCGA----GCGGAGGCGAUGAGGAAUCUUCGCUUCGCUGAUU
CP002952.1/1906488-1906546 AGCCAUGAUGAGGCCGAGGACACCCGACGAAAGGA------UGAGGAAUCUUCGCUUCGCUGAGG
CP002372.1/782536-782476   GUGGAUGAUGAUGCCGAGGACACCCGA----GCAGAGGCAAUGAGGACUCUUCGCUUCGCUGACU
#=GC SS_cons               :::::<<--<<<<<-<<<<<<<_____....____......>>----->>>>>>>>>>-->>:::
#=GC RF                    aGggAUgAuGAaGCCGAGGACACCuGA....acGg......UGAuGAaUCUUCGCuUCGCcGAcc
//
# STOCKHOLM 1.0

#=GF AC   RF01275
#=GF ID   sR22
#=GF DE   Small nucleolar RNA sR22
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   74.30
#=GF NC   34.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11359559
#=GF RT   A guided tour: small RNA function in Archaea.
#=GF RA   Dennis PP, Omer A, Lowe T
#=GF RL   Mol Microbiol. 2001;40:509-519.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


BA000001.2/56302-56359     UCCGAUGAUGGGAACAGGGUAGCUGCCGA-GUUGAUGAGGAAGCCGUUCCAGACUGAGG
AJ248283.1/65334-65391     CCCGAUGAUGCCAACAGGGUAGCUGCCGA-GGCGAUGAGGAAGCCGUUCCAGACUGAGG
AP006878.1/1826866-1826924 ACCGAUGAUGGCAACAGGGUAGCUACCGAAGUUGAUGUGGAAGCCGUUCCAGUCUGAGG
AE009950.1/1889551-1889494 CCCGAUGAUGGGAACAGGGUAGCUGCCGA-GCUGAUGAGGAAGCCGUUCCAGACUGAGG
CP002372.1/1369559-1369615 GCCGAUGAUGGCAACAGGGUAGCUGCCGA--UUGAUGACGAAGCCGUUCCAGUCUGAGG
CP001398.1/331325-331381   ACCGAUGAUGGCAACAGGGUAGCUACCGA-GC-GAUGAGGAAGCCGUUCCAGUCUGAGG
#=GC SS_cons               :((-------(-(((,,<<<____>>>,,.<<<________>>>,)))-)-------))
#=GC RF                    aCCGAUGAUGGcAACAGGGuAGCUgCCGA.GcuGAUGAGGAagCCGUUCCAGuCUGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01276
#=GF ID   sR53
#=GF DE   Small nucleolar RNA sR53
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   49.00
#=GF TC   49.70
#=GF NC   48.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.77 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AE009950.1/1130394-1130451 GCCGAUGAUGAUGGUGGGCACUCGCCGA-UUGGUGAGG-UAAGGGGCGAGGAGACAGAGG
AJ248286.2/134883-134942   CCCGAUGACGAAGGUGGGCACUCUCCGACUUGAUGAGGAUGUGGGGCGAGGAGCCAGAGG
BA000001.2/1047513-1047572 GCCGAUGACGAAGGUGGGCACUCUCCGAUUUGAUGAGGAUGUGGGGCGAGGAGCCAGAGG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    gCCGAUGAcGAaGGUGGGCACUCuCCGAuUUGaUGAGGAUGuGGGGCGAGGAGcCAGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01277
#=GF ID   snoU54
#=GF DE   Small nucleolar RNA U54
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.60
#=GF NC   34.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00008
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=HUM30058;
#=GF DR   snoRNABase; U54;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   8674114
#=GF RT   Site-specific ribose methylation of preribosomal RNA: a novel function for
#=GF RT   small nucleolar RNAs.
#=GF RA   Kiss-Laszlo Z, Henry Y, Bachellerie JP, Caizergues-Ferrer M, Kiss T
#=GF RL   Cell. 1996;85:1077-1088.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   28


X96653.1/1-67                UGGCGAUGAGGAG-GU-ACCUAUUGUG-UUGAGUAAC-GGUGAUA-AU--U-U--UAUACGCUAUUCUGAGCCGAUU
AANU01108424.1/10337-10271   UGGCGAUGAGGAG-GU-ACCUACUGUG-UUGAAUAAC-GGUGAUA-GU--U-U--UAUACGCUAUUCUGAGCCAGUA
AAPY01773330.1/1468-1535     UGGCGAUGAGGAG-AUAACCUACUAUG-UUGAAUUAU-GGUGAUA-AU--U-U--UAUACGCUAUUCUGAGCCAGCU
AAQQ01210439.1/939-872       UGGCGAUGAGGAG-AU-ACCUACCGUG-UUGAAUUAU-GGUGAUAGUU--U-U--UAUACGCUAUUCUGAGCCAACU
AAHY01033119.1/946-1013      CGGCGAUGAGGAG-AU-ACCAACCGUA-UUGAGUUAU-AGUGAUA-UU--UCU--UAUACGCUAUUCUGAGCCGAUA
AANG01411219.1/1592-1526     UGGCGAUGAGGAG-AC-AAGAAGUGUG-UUGAGUUAU-GAUGAUC-GU--U-U--UAUACGCUAUUCUGAGCCAGCA
ABDC01369815.1/393-330       UGGCGAUGAGGAG-AU----UACUGUG-UUGAAUUAU-AGUGAUA-GU--U-U--UAUACGCUAUUCUGAGCCAGCA
AAFC03081308.1/29388-29454   UGGCGGUGAGGAG-AG-AAUUGCUGUG-UUGACUUAC-GGUGAUC-GU--C-U--UAUACGCUAUUCUGAGCCCGAG
AAYZ01097424.1/2681-2617     UGGCGAUGAGGAA-AU-ACCUGUAUUG-A--AUGCAC-GGUGAUA-AC--U-U--CAUACGCUAUUCUGAGCCGGCA
AANN01785293.1/168-99        UGGCGAUGAGGAAAUU-AACUACUGUG-UUGAAUCAC-GAUGAUA-GUUGU-G--UAUACGCUAUUCUGAGCCAGCG
DQ915206.1/172-236           UGGCGCUGAGGAG-AG-AAUUGC--UG-UUGAACUAC-AGUGAUA-GU--U-U--UAUACGCUAUUCUGAGCCAGCA
AAIY01264552.1/146-213       UGGCAAUGAGGAG-AG-AUCUAU-GUG-UUGAAUGAU-GGUGAUG-UU--U-UAUUGUACGCUAUUCUGAGCCAGCA
AAPN01137617.1/5310-5243     UGGCUAUGAAGAU-AA-AAUCAUGCAGAUUGAAGUUC-CGUGAUU-GU--U-U--UAUACGCUAUUCUGAGCCAACG
AAFR03011690.1/58281-58348   UGGCAAUGAUGAUGAA-AUUUAAGCAG-UUGAAUUUC-GGUGAUU-GU--C-U--CAUACGCUAUUCUGAGCCAGCU
CAAK05058725.1/14911-14843   UGGCUAUGAGGAU-AA-AAUUGUAUGA-ACGACUUAAACAUGAGU-UA--UAU--CAUACGCUAUUCUGAGCCCUUU
AAKN02044913.1/57316-57382   UGGCGAUGAGGAG-AC-UCCUAUUGUG-UUGAAUUAC-AAUGAUA-GG--U-U--UAUACGCUAUUCUGAGCCAGCA
AAWR02029913.1/50466-50532   UGGCGAUGAGGAG-AG-AAUUACUGUG-UUGAAUUAC-GGUGAUA-GU--U-U--UAUACGCUAUUCUGAGCCAGCA
AC129839.5/222599-222666     CGGCGAUGAGGAG-AU-ACCUACUGUG-UUGAAUUAU-GGUGAUA-UU--UCU--UAUACGCUAUUCUGAGCCGAUA
JN899119.1/2-64              UGGCGCUGAGGAG-AG-AAUUGC--UG-UUGAACUAC-AGUGAUA-GU--U-U--UAUACGCUAUUCUGAGCCAG--
EU094081.1/3-69              UGGCUAUGAAGAU-AA-AAUCAUGCAGAUUGAAGUUC-CGUGAUU-GU--U-U--UAUACGCUAUUCUGAGCCAAC-
AAWZ02021600.1/33004-33070   UGGCAAUGAGGAC-AA-AAAGUGUUAA-CUGAACUAC-CAUGAUU-AG--U-G--AAUACGCUAUUCUGAGCCAACA
AADN03002793.1/87922-87856   UGGCUAUGAGGAU-AA-ACUCUUAAAC-CUGAAUUGC-AGUGAUC-AU--U-U--UAUACGCUAUUCUGAGCCAACA
AAPE02009540.1/33397-33332   UGGCGAUGAGGAG-AC-GAUUGCU-CG-UUGAUCGGC-GGUGAUA-GU--U-C--UGUACGCUAUUCUGAGCCGGCG
AAEX03015802.1/155734-155668 UGGCGAUGAGGAG-AC-CAUUACUGUG-UUGAAUAAU-GAUGAUA-GU--U-C--UAUACGCUAUUCUGAGCCAGCA
AAQR03196802.1/212-278       UGGCGAUGAGGAG-AU-AUCUACUAUG-UGAAAUUAC-AGUGAUA-GU--U-U--UAUACGCUAUUCUGAGCCAGCA
AAGW02047266.1/23273-23338   UGGCGAUGAGGAG-AU-AC-AACUGUG-UUGAAUUAU-GGUGAUA-AC--U-U--AAUACGCUAUUCUGAGCCAGCU
AAGU03078707.1/79687-79751   UGGCAGUGAGGA---A-AAUCUAGGUG-UUGAAUUAU-GGUGAUA-GU--C-U--UAUACGCUAUUCUGAGCCAGCA
AB061842.1/1832-1898         UGGCGAUGAGGAG-GU-ACCUAUUGUG-UUGAGUAAC-GGUGAUA-AU--U-U--UAUACGCUAUUCUGAGCCAGCA
#=GC SS_cons                 :<<<_________.__.__________._________._______.__.._._.._______________>>>::::
#=GC RF                      UGGCgAUGAGGAg.Au.AauUacuguG.UUGAAUUAc.gGUGAUa.gU..U.U..UAUACGCUAUUCUGAGCCAgCa
//
# STOCKHOLM 1.0

#=GF AC   RF01278
#=GF ID   SNORD109A
#=GF PI   SNORD109B
#=GF DE   Small nucleolar RNA SNORD109A
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.40
#=GF NC   34.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00069
#=GF DR   snoRNABase; HBII-438A;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Homo_sapiens300793;
#=GF RN   [1]
#=GF RM   11726556
#=GF RT   The IC-SNURF-SNRPN transcript serves as a host for multiple small
#=GF RT   nucleolar RNA species and as an antisense RNA for UBE3A.
#=GF RA   Runte M, Huttenhofer A, Gross S, Kiefmann M, Horsthemke B, Buiting K
#=GF RL   Hum Mol Genet. 2001;10:2687-2700.
#=GF CC   Humans have two copies of the SNORD109 gene, SNORD109A and SNORD109B.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AY055808.1/1-67            GGAUCGAUGAUGAGAAUAAUUGUCUGAGGAUGCUGAGGGAC-------UCAUUCCAGAUGUCAAUCUGAGGUCC
ABDC01550852.1/596-662     GGAUCGAUGAUGAGCAAAAUUAUCUGAGGACGGUGAAGGAC-------ACACUGCAGAUGUCAAUCUGAGGUCC
AANN01347476.1/737-809     GGAUCGAUGAUGAGAA-AACUGUCUGAGGAUGCUGAGAGACAAAACAAGCACUGCAGAUGUCAAUCUGAGGUCC
AAKN02054628.1/68053-68119 GGAUCGAUGAUGAGAAAACUUGUCUGAGGACGCUGAGGGAC-------UAAUUACAGAUGGCAAUCUGAGGUCC
AAGV020383062.1/766-700    UGAUCAAUGAUGAGCAUAAUUGUCUGAGGAUGCUGAGGGAC-------UCAUUCUAGAUGUCAAUCUGAGGUCC
AAGU03082774.1/64065-64131 GGGUCAAUGAUGAACAUAAAUGUCCGAGGAUGCUGAGUGAC-------UCAUUGCAGAUGUCAAUCUGAGAUCC
AAEX03002194.1/58792-58726 GGAUCAAUGAUGAUCACAAUUGUCUGAGGAUGCUGAGGGAC-------UCAUUCCAGAUGUCAAUCUGAGGUCC
#=GC SS_cons               <<<<<____________________________________......._____________________>>>>>
#=GC RF                    GGAuCgAUGAUGAgaAuAAuUGUCUGAGGAUGCUGAGgGAC.......uCAuUgCAGAUGUCAAUCUGAGgUCC
//
# STOCKHOLM 1.0

#=GF AC   RF01279
#=GF ID   snoR53Y
#=GF DE   Small nucleolar RNA snoR53Y
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   43.00
#=GF TC   44.40
#=GF NC   40.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00080
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300082;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AC069159.8/55796-55870     AUUCCCUAUGAUGG--U-----------AA-----UAACCAUGCUAAUACUGAUG---UCUUGUGACUGAAUCAAAGUUAU---------GUGUCUGAGGGAAUU
AC172870.1/115241-115165   AUUCCCUAUGAUGGCUU-----------AA-----CAACCAUGCUAAUGCUGAUU---UCUUGUGACCGAAACAACGUUAA---------AUGACUGAGGGAAUA
AJ532521.1/2-78            GUUCCCAGUGAUGG--UUUAA-------AU-----UAACCAUGCUAAUACUGAUG---UCCAUUGACG--AGUAAAAGUGU---------UUUACUGAGGGAACC
AC167403.2/76385-76309     GUUCCCAAUGAUGU--U-----------ACUUU--UAACCAUGCUAAUGCUGAUUA--CAUGAUUAUC--UUUAAUAUCAA---------UAUACUGAGGGAACA
AARH01017162.1/10398-10481 GUUCCCAGUGAUGC--UUAAAU------AU-----GAACCAUGCUAAUGCUGAUCA--UUGGAUGACUGAAACUCUUUCUCAAU------CUUGCUGAGGGAACA
AASG02008443.1/3486-3392   GUUCCCAGUGAUGU--UGAAUUAUAUAUAU-----AUACCAUGCUAAUUCUGAUCAUGUUUUGUGACAGAAACCUCUUUCUCUUAUA---UUUGCUGAGGGAACA
AM460399.2/62494-62583     GUUCCCUAUGAUGG--U-----------UUGGAUUCAACCAUGCUAAUUCUGAUCA--UUCUGUGAUUGAAGCAUUUUUCUUUUUCCUAAUUUUCUGAGGGAACU
#=GC SS_cons               <<<<<_________.._...........__....._____________________..__________________________......_________>>>>>:
#=GC RF                    GUUCCCaaUGAUGg..U...........Au.....uAACCAUGCUAAUuCUGAUcA..UuuugUGAcuGAAaCaauuUUauuuU......uUUaCUGAGGGAACa
//
# STOCKHOLM 1.0

#=GF AC   RF01280
#=GF ID   snoR14
#=GF DE   Small nucleolar RNA snoR14
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; Wilkinson A
#=GF SS   Predicted; Wilkinson A
#=GF GA   40.00
#=GF TC   43.00
#=GF NC   37.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00076
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AC005314.3/54045-54126       UCGAGGUGACGAUAGAAAUUCACAGGUCUGUCAAUCCACUGA-------UAU-------A-------UGUGAUGUAAUUGUGU---UCUCGACAGGUUCUGAUCGA
AASG02003152.1/15450-15361   GCGAGGUGACGAUAGAAAUUCAUUGGUCUGUCAAUCCACUGAAUAAACAUAA-------C-------UUUGAUGUUACUAUGAA--UCCCGACAGGUUCUGAUCGC
AP004489.1/54837-54753       GCGAGGUGACGAUAUCACUUCAAUGGUAUGUCAAUUCACUGA-------UAC-------UAU-----CGUGAUGUAUUCAUGAA--UCCCGACAGGUUCUGAUCGC
AARH01008371.1/237066-236979 GCGAGGUGAAGAUAGAAAUUCAU--GUCUGUCAAUCCACUGA-------CUU-------AGUAACUGUGUGAUGUUAUCUUGAA--UCCCGACAGGUUCUGAUCGC
AC146791.12/24606-24523      GCGAGGUGAUGAUA-AAAUUCAUUUGUCUGUCAAUCCUCUGA-------UAU-------UC------UUUGAUGUUAUUUAUGAA-UCCCGACAGGUUCUGAUCGC
AM480118.2/5459-5549         GCGAGGUGACGAUAGAA-UUCAUUGGUCUGUCAAUCCACUGA-------UAUCAACAUCA-------GAUGAUGUUAAACAAUGAAUCCCGACAGGUUCUGAUCGC
AJ532488.1/8-96              GCGAGGUGAUGAUGAAUGUAUGAAUGUCUGUCAAUCCCCUGA-------UGUCAC----AA------AGUGAUGACUCCUCAUACAUCCCGACAGGCUCUGAUCGC
#=GC SS_cons                 <<<<______________________________________.......___.......__......_________________..________________>>>>
#=GC RF                      GCGAGGUGAcGAUAgAAaUUCAuugGUCUGUCAAUCCaCUGA.......Uau.......aa......ugUGAUGUuauuuugaA..UCCCGACAGGUUCUGAUCGC
//
# STOCKHOLM 1.0

#=GF AC   RF01281
#=GF ID   snoR35
#=GF DE   Small nucleolar RNA snoR35
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   44.50
#=GF NC   35.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00053
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300065;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   12


AK229253.1/328-248         CAGCAUGAUGAAAAACUGGAGACGCUGCCCCAGACUGACCGGAGAAAGAAGAAGUAAACGUCCUCCCUGAACCGUCUGACA
AARH01007112.1/21213-21133 CACUGUGAUGAAAAACAGGAGAUGCUGCACCAGACUGACCAGAGAAGGAUGUAGCAAAAGAUCGUCCCGUGGUAUCUGGAA
AASG02002680.1/896-816     CAGAAUGAUGGAAAACAGGAGAUGCCGCACCAGACUGUCCAGAGAAAGAUGUAGCAAAAGAACGCCCAGUAUUGUCUGGAA
AC144343.8/39743-39666     CAGUGUGCUGAUAAAUCGGGGAGGCUGCACCAGACUGACUAGAAAAUGAAG---UAAAAGUCCGCCCAGCACCGUCUGGAA
BT014600.1/289-209         CAGAGUGAUGAUAGAGAGGGGAAGCUGCACCAGAUUGAGGAGGGAAAGAAGAAGGAAAUGAGCGACCAGUGUUGUCGGAAG
AM442339.2/2631-2551       CACUGUGAUGAAAAACAGGAGAUGCUGCACCAGAUUGAGCUGAAAAAGAUGUCGCAAAAGAUCUCCCAUUGCUAUCUUGAA
ABIM01023851.1/6505-6425   CAGUGUGAUGGAAAACUGGGGAGGCUGCACCAGACUGACCAGAGAAAGAAGUGGCAAAAGAUCUUCCAGUGCUGUCUGGUA
BABK01020497.1/265-345     CAGAGUGAUGAAAAACUGGGGAGGCUACACCCGACUGACCAGAGAAAGACGUCGCAAAAGACCGCCCCGUACCAUCUGGAA
EU956683.1/317-240         CUGAGUGAUGAAAA---CCUGGAAGUGAUCCAGAUUGACCAGAAAACGAUGAUGUAAAUGGCCUUCCUGUGGAAUCUCUAA
ABXC01006227.1/37823-37746 CUGAGUGAUGAAAA---CCCGGAAGUGAUCCAGAUUGACCGGAAAAGGAUGAUGUAAAUGGCCUUCCUGUUGAAUCUCUAA
AK099785.1/381-301         CAGAGUGAUGGAACGCCCCUGGAACUGAUCCAGAUUGACCAGAAAAGGAUGCUGUAAACGGUCUUCCAGAUGAGUCUUGAA
AAAA02007495.1/60835-60755 CAGAGUGAUGGAAACCCCCUGGAACUGAUCCAGAUUGACCAGAAAAGGACCCUGUAAACGGUCUUCCAGUUGAGUCUUGAA
#=GC SS_cons               ::::::::::::::::::::<_________>-------<-<<<_______________________________>>>->::
#=GC RF                    CAGaGUGAUGAAAAAcaggaGAaGCUGcaCCAGAuUGAcCaGAaAAaGAuGuuGuAAAaGauCuuCCaGUacugUCuggAA
//
# STOCKHOLM 1.0

#=GF AC   RF01283
#=GF ID   snoU30
#=GF DE   Small nucleolar RNA U30
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; Wilkinson A
#=GF SS   Predicted; Wilkinson A
#=GF GA   45.00
#=GF TC   48.30
#=GF NC   41.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00052
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AP000603.1/65098-65183     UGCAGUGAUGAUGGGUAUA----A-AUCUCGUUAAUCUGA-AUUUUUGUUAAUGAAGAUACUUACUUCCCAACCAUUCAUUAAUAU-CUGAGC
AARH01002519.1/12521-12439 UGCUGUGAUGAUGAGACUAU---A-AUCUCGUUAAUCUGA-UUUAACCA---UGAGGAAAAACCCUC-UGAUCCAUUCUUCACUGU-CUGAGC
AASG02002801.1/14167-14078 UGCUGUGAUGAUGAGAUAAAAAUA-AUCUCGUUAAUCUGAUACCUAUCAUUAUGAGGACAAAUCCUC--UUUCCAUUCUUUAGUUUUCUGAGC
AM475808.2/15755-15675     UGCUGUGAUGAAGGUUAAA----AGAUCUCGUUAAUCUGA-AGAUUCAU---UGAGGAUACUUUCUU---AUCCAUUCAAUACAUU-CUGAGC
AC189369.2/56941-56854     UGCAGUGAUGAUGGAUUUAUGU-A-AUCUCGUUAAUCUGA-AAUAUU--UAUUGAGGAUAAAUACUUCCCAACCAUUCAUUCAAAUACUGAGC
#=GC SS_cons               :<<_________________..._._______________.__________________________.__________________.____>>
#=GC RF                    UGCuGUGAUGAUGgguuuAu...A.AUCUCGUUAAUCUGA.AuuuuuaaUaaUGAGGAuAaaUaCUu.cuAuCCAUUCaUUAauuU.CUGAGC
//
# STOCKHOLM 1.0

#=GF AC   RF01284
#=GF ID   snoR8a
#=GF DE   Small nucleolar RNA snoR8a
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   36.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AP000371.1/18814-18902     AAGAGUGCUAUGAUUGUAAAAGUAAUUCCUCGUACUGAA-AGC-----CAAU-GGCUUGAAAGACUCACAUUACUACCCAUAGAAUAUGAGCACUC
AM473368.1/38877-38965     UUGGUUGCGAUGAUUAU--AAGAAAUUCCUCGUACUGAA-UGCUAUAGCCAU-GGCAUGACAGACGC--CUUAACACCCAUAGAAUAUGAGCA-CC
AASG02000856.1/5230-5141   CUGGUUGCGAUGAUUAUGACA--AAUUCCUCGUUCUGAA-UGCUAUAGCCAU-GGCAUGACAGACUCCUAUUAC-ACCCAUAGAAUAUGAGCA-CC
AARH01006031.1/44112-44025 UUGGCUGUGAUGAUUAUAAAA---AUUCAUCGUUCUGAA-UGCUAUAGCCAU-GGCUUGACAGACU--CAUUUACACCCAUAGAAUAUGAGCA-CC
AACV01015078.1/173-87      UGUGGUGCAGUGAUUAUAAAA-UCAUUCCUCGUCCUGAU-GGG-----AGAUCUGCGUGAUCGACUCCUAUA--CACCCAUAGAAUCUGAGCACCA
CR955012.2/87183-87265     UUUACUGAAUUAAACGUAUCA--------GAGAACUGAA-UGCCAUUGCCAU-GGCAUGACAGACACGAAUA--CACUCAUAGAAUAUGAGCA-UA
AC189633.2/52174-52263     GAUGAUGCGAUGAUUGUAAAAGUAAUUCCUCGUACUGAAUAGC-----CACUAGGCUUUGUAGACUCACAUUAC-ACCCAUAGAAUAUGAGCAUCU
#=GC SS_cons               ::<<-<<______________._________________.____________.______________________________________>>.>>
#=GC RF                    uugGuUGcgaUGAUUaUAAAA.uAAUUCCUCGUaCUGAA.uGCuAUaGCcAU.GGCaUGAcAGACuCauAUuAcCACCCAUAGAAUAUGAGCA.Cc
//
# STOCKHOLM 1.0

#=GF AC   RF01285
#=GF ID   snoU31b
#=GF DE   Small nucleolar RNA U31b
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; Wilkinson A
#=GF SS   Predicted; Wilkinson A
#=GF GA   37.00
#=GF TC   37.80
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300157;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AC068667.6/51178-51267     GAAAGUGAUGAUAAG-GAAUUGUCGCCCCAGGCUUAAUCUGCAUCCAUUACGAUGGUUGUAACAUGGUGAUUGACUAUCUCU---GUCUGAUUC
AC150706.4/101697-101776   GGAUGUGAUGAUA-G-UAAUUGUCGCCCCAGUCUUAAUUUGCACCAAU-------GGUGUAAUAUGGUGACUGAC--ACUUU---AUCUGAUCC
AASG02001667.1/15770-15853 GGAAAUGAUGAUAAG-UA-CUGUCGCCCCAGUCUUA-----CUUGCAUAUAAAUAGAUGCAAGUUGGUGAUUGACUUUUAUU---AUCUGAUUC
AARH01004696.1/63929-64010 GAAAAUGAUGAUACU-UG-UUGUCGCCCCAGUCUUA-----CUUGCAUUUUGA--GGUGCAGGAUGGUGAUUGACAUUCCUU---GUCUGAUUC
AM455011.2/13557-13476     GGAUAUGAUGAUA---GUUUUGUCGCCCCAGUCUUA-CCUGCAUCUCUU-----GAUGCYGAGAUGGUGAUCGACSUUUUAU---AUCUGAUUC
AACV01008043.1/13929-14014 GAGGAUGAUGAUGUGAUAUUUGUCGCCCCAGUCUUA---UGAUCCGCUGUAAU-CGCGGAUGUGUGGUGAUUGAC-AUGUAA---AUCUGACUC
AAAA02011143.1/20357-20442 GAGCGUGAUGAUAUGAUAUUUGUCGCCCCAGUCUUA---GGAUCCGGAU-----UCCGGGCCAGUGCUGAUUGACAUGUUAUCAGAUCUGACUC
#=GC SS_cons               <<<____________.____________________...______________.____________________________...______>>>
#=GC RF                    GaaaaUGAUGAUAuG.UAuUUGUCGCCCCAGUCUUA...uGcuuccaUuuaaa.uguuGuaauaUGGUGAUUGACauuuUaU...AUCUGAuuC
//
# STOCKHOLM 1.0

#=GF AC   RF01286
#=GF ID   snoR26
#=GF DE   Small nucleolar RNA snoR26
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   47.00
#=GF TC   49.00
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300050;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


AC189510.1/85438-85343       GGAGCAUCAGUGAUGAAUUCCAUGAAAAAAUUGUUAUCCUUGCACUUUGA--UUGC-UA--GUGAAGAUAAAAUUGGGGUU-UUCGAUUUCUGAGAUUGCUC
AASG02005916.1/15106-15013   UGGGCAUCGGUGAUGAG-UUGAUACAAAAAUCGUUAUCCUUGCACUUUGA--UUUG-CA--GUGAAGAAAACUACGGGGUU-UUAUGUCUCUGAGAU-GCUC
AC170860.16/132109-132198    CGAGCAUCAGUGAUGAG-CAAUUCCAA----UGUUAUCCUUGCACUUUGA--UUAC-CA--GUGAAGAAGCUAAUGGGGAA-UGGUUACUCUGAGAU-GCUC
AARH01003024.1/1771-1862     CGAGCAUCAGUGAUGAG-U---UAGCCAAAUCGUUAUCCUUGCACUUUGA--UUUUACA--GUGAAGAAAAUCAUGGGGAC-AGAUUUCUCUGAGAU-GCUC
AM469240.1/1369-1459         UAAGCAUCGAUGAUGAC-UUACUU---CCUUUGUUAUCCUUGCACUAUGA--UUGC-UA--GUGAUGAAACUUAUAGGGAC-AGUUCAAUCUGAGAU-GCUC
AC093919.2/7338-7433         AGAGCAUCGGUGAUGU--UACAUCCAUCUAAACUCAUCCUUGCACUAUGAGGUCAC-CG--GUGAAGAAAAAAUUGGGGGAAUAUGUAGUCUGAGAU-GCUC
AAAA02017378.1/5560-5655     AGAGCAUUGGUGAUGU--UACAUCCAUCUAAACUCAUCCUUGCACUAUGA--GGUC-AACGGUGAAGAAAAAAUUGGGGGAAUAUGUAGUCUGAGAU-GCUC
CP002685.1/15890473-15890380 AGAGCAUCGGUGAUGAA-UCCAUGAAAAAAUUGUUAUCCUUGCACUUUGA--UUGC-UA--GUGAAGAAACAAAUGGGGUU-UUCGAUGUCUGAGAU-GCUC
#=GC SS_cons                 :<<<<<<<_________.________________________________..____.__..____________________.____________>>>.>>>>
#=GC RF                      aGAGCAUCgGUGAUGaa.UacaUacAaaaAuugUUAUCCUUGCACUuUGA..Uuuc.uA..GUGAAGAAAaaaaUGGGGau.uuuuuauUCUGAGAU.GCUC
//
# STOCKHOLM 1.0

#=GF AC   RF01287
#=GF ID   snoR27
#=GF DE   Small nucleolar RNA snoR27
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   41.00
#=GF TC   42.00
#=GF NC   40.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00079
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300051;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AC189510.1/85284-85187       AUUGGAUCAAUGAUU--UAAGUUAAUUAAACUGCGUUAUCUAUCUGCAAUUCUCCUCUUUCUAGGAGUUUGAAGAAAACCAU-A-AAAACCUGAGAUCCAGU
AARH01030264.1/984-1074      UGUGGAUCAAUGAUG--UUAUUGAUU-UUACUGCGUUAUCUUCCUGCA----UCUAAC---AAUGAAAUGAAGAUAAAUGUUUU-ACACCCUGAGAUCCAUU
AC170860.16/132308-132397    UAUGGAUCGGUGAUGUUUAUUUUAAA----CUGCGUUAUCUAUCCG--AAUCUUCCCA---AAGGAAUUGAAGAUAA--CCAUA-UAUUGCUGAGAUCCAUU
AASG02005916.1/14672-14579   AUUGGAUCGAUGAUG--UUCAUUAUG--AACUGCGUUAUCUAUCUG-AAACUUCCUUA---UUGGAAUUGAAGAAGUCUAUAAACACAUUCUGAGAUCUUGU
FN595991.1/7929227-7929136   AU-GGAUCAAUGAU---GUUACUAUG-AAACUGCGCUAUCUAUCUG-AAACAUCUUAA---UAGAAUUUGAAGAUAACGGAAUA-ACAUCGUGAAAUCCAAU
CP002685.1/15890327-15890231 AUUGGAUCGAUGAUUGAUUAGUUAAA-AUACUGCGUUAUCUUUCUGCAAAUCUCCUAU---AAGGAUUUGAAGACAAAUCAUGA-AAAACCUGAGAUCCAAU
#=GC SS_cons                 <<<<<<<________.._________._______________________________..._______________________.__________>>>>>>>
#=GC RF                      auuGGAUCaAUGAUg..UuaaUUAuu.aaACUGCGUUAUCUaUCUGCAAAucUCcuaa...uAGGAaUUGAAGAuAAaucauuA.AaAucCUGAGAUCCaau
//
# STOCKHOLM 1.0

#=GF AC   RF01288
#=GF ID   snoR31
#=GF DE   Small nucleolar RNA snoR31
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   44.90
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AB023044.1/29891-29990     UAGAUAAUGAUGAAGCAAAAUUAAUCUAAUCCAACACUUGAUCUGAGAGAUACUAUGUGCAUCUCCAAGUGAAGUUACAACUGUUAGCUUCUGAAUCUAA
AM435377.2/7052-7143       UAGAUUGGGAUGAAGCAACAGUACAUUAAUCCAACACUUGAUCUGAG-------AUAUUUAUAUCCAAGUGAUGUUA-AAUUCUAUGCUUCUGAAUCUAU
AASG02005463.1/7246-7155   CGGAUGGGGAUGAAGCAAUAUUUAAAUAAUCCAACACUUGAUCUGAG-------ACUUUAAUAGUCAAGUGAUGUUAACAUUAUCA-CUUCUGAAUCCGC
CT963106.2/109102-109018   UAGAUAAGGAUGAAGCAAUAU--AUAUAAUCCAACACUUGAUCUGAU--------UUUGUGAUGCCAAAUAUAUUUAUUAU-----GUUUCUGAAUCUAC
AJ310377.1/1427-1330       UGGAUUGUGAGGAGGUAAUUGAUGCAUAAUCCAACACUUGAUCAGAGGACGGCUUCUGUC--GUCCAUGUGACGUUACACAUCUUUGCAUCUGAAUCCAA
AAAA02011059.1/20813-20716 UGGAUUGUGAGGAGGUAAUUGAUGCAUAAUCCAACACUUGAUCAGAGGAUGGCUUUUGUC--GUCCAUAUGACGUUACACAUCUCUGCAUCUGAAUCCAG
#=GC SS_cons               :<<<___________________________________________________________________________________________>>>::
#=GC RF                    UgGAUuguGAuGAAGcAAuauuuauaUAAUCCAACACUUGAUCuGAGgauggCUaUuuuuAuauCCAagUGAuGUUAcaauUcUuuGCuUCUGAAUCcAa
//
# STOCKHOLM 1.0

#=GF AC   RF01289
#=GF ID   snoR17
#=GF DE   Small nucleolar RNA snoR17
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   66.70
#=GF NC   42.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AC011765.6/41033-40924 CAUAGUGAUGAAUUAUAUCACAAUUGUCACUACCUCUGAGGCAUAUUCUUGAUUCGUUUUUUUUUUUUAGAUUUUGGUUUCUAUCACCUUACUUCUUUAGGAGCCUGAUG
AC189574.2/21687-21784 UAUAGUGAUGAAUAUAAUCACAAUUGUCACUACCUCUGAGGCACAUUUUAUUUUCGUUUUGUAUCU---GACCCUGGUGAUUG-CAUCUAAGAACGGUGAUA--------
#=GC SS_cons           :::<<<<<<________________>>>>>>------------------------------------------------<<<<______________>>>>:::::::::
#=GC RF                uAUAGUGAuGAAUuauAUCACAAUUgUCACUACCUCUGAGGCAuAUUuUuuaUUCGUUUUuUuUuUUUAGAuuuUGGUuacuaUCAuCUuAcuuCuuuaguAGCCUGAUG
//
# STOCKHOLM 1.0

#=GF AC   RF01290
#=GF ID   SNORD10
#=GF PI   snoU6-77
#=GF DE   Small nucleolar RNA SNORD10
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.60
#=GF NC   34.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=XEN30041;
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=XEN30042;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   11387227
#=GF RT   RNomics: an experimental approach that identifies 201 candidates for
#=GF RT   novel, small, non-messenger RNAs in mouse.
#=GF RA   Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H,
#=GF RA   Bachellerie JP, Brosius J
#=GF RL   EMBO J. 2001;20:2943-2953.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   22


AF084536.1/1-141           AGUU-AGUGAUGAAAUCCCAUGCGUGUCAUCUGACUUC--CACGUCUCGCUCUGCCUU-CGCUCUG-CGCUG-U-CUGCGUUCUG-----CAGCUUGGG---U-UU------------GGCUAGGG--CA--G-AG-GAUUCUGGGAA-AUGAUCAGACCCGUUUAUCUGAAAACU
BAAF04088825.1/1745-1607   GUAU-GAUGAUGAAAUC-CAUGCGUGUCAACUGACUCU-----GUCCGUCUCAGCUGU-GGCGUUG-CUCUG-GGCGGCGUUCUG-----CUGGCCGAGAU-U-UU------------CGUGACAG--CU--G-AG--ACCCAGAGAC-AUGAUCACAACUCAUGGUCCUGAAUAC
AANH01007266.1/45004-45142 UGUAUAAUGAUGAUAAC-CAUGCGUGUCAGCUGACUCU-----GUAAACCUCUGCUGU-GUUGUUG-CACUGGU-CGGCGUUUUGU----CAGCCUGAG---UAUU------------CAGCACAG--CA--G-GG--CUACAGAGAC-AUGAUCAUACUUCACU-UCUGAAUACA
AAFR03049834.1/2493-2629   GCUC-UGUGAUGAUCCCCCAUGCGUGUCAUCUGAGCUC--AGCUUC---CCCUGAUCU-CUCAGUU-CCAAG-U-GGGUGUUUUG-----CCCUCUGGU---C-UCUG----------GGCUGG----CA--G-UG-GCUUCUGGGCACAUGAUCAUAAU--UUAACCCUGAGAGC
CAAE01009839.1/7361-7221   UGUAUUGGGAUGAAACC-CAUGCGUGUCAACUGAGUCU----CUAAAUCUCUUGUCGU-GGUGUCGACCCAG-C-UGGCGUUUUG-----CAAGCUUGA---C-UC------------GACAGCGAAGCA--A-GG--CCUUAGAGAA-AUGAUCAGGACUGACUUUCUGAAUGCA
CR848032.12/112696-112834  GUUU-UGUGAUGAUCCC-CAUGCGUGUCAACUGAUCCC--AGACUC----CCUGCAGU-GCUCAAU-GUCUGAU-GAGCGUUUUG-----CUCAACAGUGCAU-UU------------UGAGCCUG--UA--G-G---ACUCUGGGAACUUGAUCUUAACUUUUAAAUCUGAAAAC
AAYZ01465370.1/2554-2693   GCUC-UGUGAUGAACCC-CAUGCGUGUCAUCUGAGCCA----UGGAUUCCCUUGUCAC-CUCA--G-CCCAG-G-GAGUGUUCUACUUCCCAGGCUGUU---G-UC------------UGCCCUGU--CG--G-GG-AGUCCUGGCAA-AGGAUCAAACAUCAUA-CCCUGAGAGC
ABDC01224936.1/675-816     GCUC-UGUGAUGAACCC-CAUGCGUGUCAUCUGAGCCU--GGCUU----CCCUGCCA---UCUCAG-CCCAG-GGUAGUGUUCUA-----CUUCCCAGG---G-CUGUUGUCU-----GGCU-UGG--CA--G-GGAGGUCCUGGGCAAAGGAUCAGUCUCUGUAUUCUGA-GAGC
AAIY01730976.1/597-737     GCUC-UGUGAUGAACCC-CAUGCGUGUCAUCUGAGCCC--AGAUUC---C-CUG--UU-GUCUCAG-CCCUGGUGUGGUGUUCUAC----UUCCCAGAGCU-G-UU------------GUCUGACC--CA--GUAG-GAGUCUGGACAAAGGGAUCUAUCUUUCCAUUCUGAGAGC
AB011595.1/3767-3910       GCUC-UGUGAUGAACCC-CAUGCGUGUCAUCUGAGCCU--GGCUU----CCCUGUUGUUACCUUAG-CCCAG-G-UAGUGUUCUA-----CUUACCAGG---G-CUUUUGCC------UGGCUUAU--CA--G-GGAAGCUUUGGGCAAAGGAUCAGUCCUUGUAUUCUGA-GAGC
AAQQ01303584.1/533-675     GCUC-UAUGAUGAACCC-CAUGCGUGUCAUCUGAGCCU-----GGC---UUCCCUGUC-AUCUUAG-CCCAG-G-UAGUGUUCUA-----CUUCCUAGG---G-CUGCUGCUGUCU--GGCUUCCA--GG--G-AG-GUCCCAGGCAA-AGGAUCAGUCCUUGUAUUCUGA-GAGC
AAFC03127912.1/39293-39153 GCUC-UGUGAUGAACUC-CAUGCGUGUCAUCUGAGCCU--GGCUU----CCCUGUCAU-CUCA--G-CCCAG-G-UAGUGUUCUA-----CUUCCCAAG---G-CUGUUGUCU-----GGCCUGGA--AA--G-GG-GAUCCCAGGCAAAGGAUCAACCUUUGUAUUCUGA-GAGC
AALT01663743.1/11854-11714 GCUC-UGUGAUGAAUCC-CAUGCGUGUCAUCUGAGCCU--GAAAU----CCCUG--AG-GUCUCUG-CCCGG-G-UAGUGUUCUA-----CUUCCUAGG---G-UUAGUGUC------UAACCUUG--CAAGG-GG-UCUUCAGGCAG-AGGAUCAGUCUUUGUAUUCUGA-GAGC
AANG01159366.1/697-841     GCUC-UGUGAUGAA-CC-CAUGCGUGUCAUCUGAGCCU--GGCUUGGCUCCCC-UGUC-UUCUCGG-CCCGG-G-GAGUGUUCUA-----CUUCCCAGG---C-CUGUCGCCUG----GCCUGGCA--UG--G-GG-GUCCCAGGCAA-AGGAUCAGCUUUUGUA-UUCUGAGAGC
AANU01204612.1/11802-11660 GCUC-UGUGAUGGAGCC-CAUGCGUGUCAUCUGAGCCUCUGGCUU----CCCUGCCAG-UGCA--G-CCCAG-G-CAGUGUCCUA-----CUUCCCAGG---G-CUGUUUUC------UGGCUUGG--CG--G-GAACGUCCUGGGCAAAGGAUCAGUCUUUGUACUCUGA-GAGC
AAWR02013397.1/70518-70658 GCUC-UGUGAUGAACCC-CAUGCGUGUCAUCUGAGCCU--GGCUU----CCCUGUCUU-CUCA--G-CCCAG-G-UAGUGUUCUA-----CUUCCCAGG---G-CUGUUGUC------UGGCCUGG--CA--G-GGGGCUCCUGGGCAAAGGAUCAGUCUUUGUAUUCUGA-GAGC
AAHX01064586.1/44814-44955 GCUC-UGUGAUGAACCC-CAUGCGUGUCAUCUGAGCCU--GGCUU----CCCUGUUAA--CCUUAG-CCCAG-G-UAGUGUUCUA-----CUUACCAGG---G-CUUUUGCA------UGACCUAU--CA--G-GGAAGCCGAGGGCAAAGGAUCAGUCCUUGCAUUCUGA-GAGC
AAGU03065673.1/52028-52165 GCUC-UGUGAUGAACCC-CAUGCGUGUCAUCUGAGCCU--GGCAU----CCCUGUUG---CCUCAG-CCCAG-G-UAGUGUUCUA-----CUUUCCAGG---G-CUGUUGUCU-----GACU-UGG--CA--G-GG--GUCAGGGCAA-AGGAUCAAUCUUUACGUUCUGA-GAGC
AAQR03080653.1/4620-4482   GCUC-UGUGAUGAACCU-CAUGCGUGUCAUCUGAGCCU--GGCUU----CCCUGUCA---UCUCAG-CCCAG-G-UAGUGUUCUA-----CUUCCCGGG---G-CUUGUUU-------GGCU-UGG--CA--G-GGAGGUCCUGGGCAAAGGAUCAGUUUCUGUCUUCUGA-GAGC
CAAB02010156.1/39947-40087 UGUAUAGUGAUGAAACC-CAUGCGUGUCAACUGAUUCU----CUAAAACUCCUGCUGU-GCUGGUG-ACCAGGC-CGGCGUUUUG-----CUGGCUUGA---C-UCAA----------CAGUGCGG--CA--U-GG--CCUUGGAGGA-AUGAUCAGCAUUGACUUUCUGAAUACA
AK303222.1/647-788         GCUC-UGUGAUGGAGCC-CAUGCGUGUCAUCUGAGCCU----CUGGCUUCCCUGCCA---GUGCAG-CCCUG-G-CAGUGUCCUA-----CUUCCCAGG---G-CUGUUGUC------UGCC-UGG--CG--G-GAAGGUCCUGGGCAAAGGAUCAGUCUUUGUA-CUCUGAGAGC
AAPE02052145.1/47956-48094 GCUC-UAUGAUGAACCC-CAUGCGUGUCAUCUGAGCCU-----------GGCUUCCCU-GUCUCAG-CCCAG-G-UAGUGUUCUA-----CUUCCCAGG---G-CUAUUGUCUGGCCUGGCAAGGG--GG--G-----UCCCUGGCAA-AGGAUCAAAAUUUGAAUUCUGA-GAGC
#=GC SS_cons               <<<<.------------.--------------------..------...<<<<<<<<<._______._____._.__________....._________..._.____..........____>>>>..>>..>.>>.-----------.----------------------->>>>
#=GC RF                    GcUc.UGUGAUGAAcCC.CAUGCGUGUCAUCUGAgCCU..gGcuUa...ccCugccgu.guCuuaG.CCCaG.g.uaGUGUUCUa.....CUucCuaGG...g.uUgu..........ugcuacgg..ca..G.gg.gauuCuGGgaA.AgGAUCAgacuUugUauUCUgAAgAgC
//
# STOCKHOLM 1.0

#=GF AC   RF01291
#=GF ID   SNORD97
#=GF PI   snoU97
#=GF DE   Small nucleolar RNA SNORD97
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   47.50
#=GF NC   41.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=HUM30113;
#=GF DR   snoRNABase; U97;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   14602913
#=GF RT   Identification of 13 novel human modification guide RNAs.
#=GF RA   Vitali P, Royo H, Seitz H, Bachellerie JP, Huttenhofer A, Cavaille J
#=GF RL   Nucleic Acids Res. 2003;31:6543-6551.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   20


AY349597.1/1-142           UUGCCCGAUGAUUAUA---AA-AAGACGCGUUAUUAAGAGGACUU-UAUGCUG-----------------------------------GAGUUCU-UGA-------C----GUU-UUU--CUCUC--------------------------------------------------U-UU-U-CUAUACUU-C-UUU-UUCUUUCUUUGAAUGUCCAGCGUCCUGUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AANU01215512.1/34559-34417 UUGCCCGAUGAUUAUA---AA-AAGACGCGUUAUUAAGAGGACUU-AAUGCUG-----------------------------------GAGUUCU-UUA-------C----AUU-UUU--CUCUC--------------------------------------------------U-UU-U-CUGUACUU-AAUUU-UUCUUUCUUUGAAUGUCCAGCAUCCUGUGAGUGAAGAUUAUGAGAUAUGAGGGCAA
AACN010220664.1/1841-1699  UUGCCCGAUGAUUAUA---AAUAAGACGCGUUAUUAAGAGGACUU-AAUGCUG-----------------------------------GAGUUCU-UUA-------U----CUU-CUU--CUUUC--------------------------------------------------U-UU-U-CUGUACUU-C-UUU-UUCUUUCUUUGGAUGUCCAGCGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AAQQ01150653.1/4431-4289   UUGCCCGAUGAUUAUA---AA-AAGACGCGUUAUUAAGAGGACUU--AUGCUG-----------------------------------GAGUUCU-UUU-------C----UUU-UUU-UCUCUC--------------------------------------------------U-UU-UUCUGUCUUU-C-UUU-UUCUUUCUUUGAAUGUCCAGCGUCCUGUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AAPY01630084.1/2313-2174   UUGCCCGAUGAUUAUA---AA-AAGACGCGUUAUUAAGAGGACUU--AUGCUG-----------------------------------GAAUUCU-UUA-------C-----UU-UUU--CUUUC--------------------------------------------------U-UU-U-CUGUACUA-C-UGU-UUCUUUCUUUGGAUAUCCAGCGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AAFC03029483.1/5215-5064   UUGCCCGAUGAUUAUAAAAAA-AAGACGCAUUAUUAAGAGGACUU-AAUGCUG-----------------------------------GAAUUCU-UUAUCUUUACC----UUC-UUU--CUCUC--------------------------------------------------U-UU-U-CUGUACUA-C-UUU-UUCUUUCUUUGAAUGUCCAGCGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AALT01145109.1/7525-7385   UUGCCCGAUGAUUAUA---AA-AAGACGCGUUAUUAAGAGGACUU-AAUGCUG-----------------------------------GAAUUCU-UUA-------A----CCU-UCU--UUCUC--------------------------------------------------UCUU-U-CUGUACUU-C-UAU-UUCUUUCUUUGGA-GUCCAGCGUCCUAUGAGCGACGAUUAUGAGAUAUGA-GGCAA
AAFR03017658.1/25792-25647 UUGCCCAAUGAUUAUA---GA-AAGACGCGUUAUUAUGAGGACUU-UAUGCUG-----------------------------------GAAUUCU-UUA-------CCCUUUUU-UUU--CCCCC--------------------------------------------------U-AU-G-CUUUACUU-U-UCUCCUCUUUCUAUGGAUGUCCAGCGUCCUGUGAGC-AAGAUUAUGAGAUAUGAGGGCAA
AAIY01344330.1/434-574     CUGCCCGAUGAUUAUA---AA-AAGAUGCG---UUAAGAGGACUU--AUGCUG-----------------------------------GAGUUCU-UUA---AAACC----UCU-CUU--CUCUC--------------------------------------------------U-UU-U-CUGU-UUA-C-UAU-UUCUUUCUUUAGAUGUCCAGUGUCCUAUGAGCGAUGAUUAUGAGAUAUGAGGGCAA
AANN01327606.1/2604-2456   UUGCCCGAUGAUUAUA---AA-AAGACGCGCA---AAGAGGACAU-AACGCUG-----------------------------------GAGUUCU-UUA-------C----CUU-CUU--UUCUC---------------------------------------AUUUCUUCCUUU-UU-U-CUACACUU-C-UGU-UUCUUUCUUUGAA-GUCCAGUGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AAYZ01166701.1/3347-3192   UUGCCCGAUGAUUAUA---AA-AAGAUGCG---UUAAAAGGACU--UAUGCUG--------------GAUUCUUUUUUUUUCCCUUUUUUGUUUU-UAC-------U----CUU-UCU--CUUAC--------------------------------------------------U-UU-U-CUAUAC-----UUU-UUCUUUCUUUGAAUGUCCAGCGUCCUGUGAACGAAGAUUAUGAGAUAUGAGGGCAA
CAAA01084202.1/39331-39498 UUGCCCGAUGAUUAUA---AA-AAGACGCC----AAAGAGGACUU-AAAGCUGGAAUUCUUUUUCCUUUUAUUCUCUCCUCUACUCUUAUGUCUU-CAA-------C----UUC-UUU--UCUAC--------------------------------------------------U-UU-U-CUCU-------GCU-UUUUCUCUCUGGAUGUCCAGCGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AAWR02018352.1/52642-52501 UUGCCCGAUGAUUAUA---AA-AAGACGCGUUAUUAAGAGGACUU-AAUGCUG-----------------------------------GAGUCUU-CAC-------C----UUC-CUC--UUCUC--------------------------------------------------U-UU-U-CUCUACUU-C-UUU-UUCUUUCUUUGGAUAUCCAGCGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AAHX01007875.1/18703-18890 UUGCCCGAUGAUUAUA---AA-AAGACGCG----AAAGAGGACUU-GAAGCUG-----------------------------------GAAUUCU-UUU-------C----CUU-UUA--UUCUCUUCUCUACUCUUUGUCUUUAACUUCUCCUCUACUUUAAUUUUCUCUGCUUC-UU-U-UUCUCUGC-C-UUU-UCCUCUCUCUGGAUGUCCAGCGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AAGV020383719.1/3429-3289  UUGCCCAAUGAUUAUA---AA-AAGACGCGUUAUUAAGAGGACUU--AUGCUG-----------------------------------GAGUUCU-UUA-------C----CUC-UUU--CUUUC--------------------------------------------------U-UU-C-UUUCUGUA-C-UUU-UUCUUUCUUUGGAUGUCCAGCGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAG
AAKN02045488.1/10982-10840 CUGCCCGAUGAUUAUA---AA-AAGACGCGUUAUUAAGAGGACUU--AUGCUG-----------------------------------GAGUUCUUUUU-------C----UUU-UCU--CUCUU--------------------------------------------------U-UUUU-CUGUACUA-C-UUU-UUCUUUCUUUGGAUGUCCAGCGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AADN03004403.1/5456-5616   UUGCCCAGUGAUUAUA---GC-AAGACGCGUUAUUAUGAGGACUU--AUGCUG-----------------------------------GAACUCU-UCC-------U----ACU-UCU--CUUCC---------------------------UCCUCCUACUUUGCCCCUUCCUCU-UU-C-ACCUUAUU-C-CUC-ACUUUCCCUAGGGUAUCCAGCGUCCUGUGAGC-AAGAC--UGAGAUAUGAGGGCAA
AAPE02019433.1/6211-6351   UUGCCCGAUGAUUAUA---AA-AAGACGCGUU----AGAGGACUUAAAUGCUG-----------------------------------GAAUUCU-UCA-------U----CUU-CUUUCUUCCU--------------------------------------------------U-UU-U-CUGUACUA-C-UUU-UUCUAUCUUUAUAUGUCCAGCGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AAGU03044252.1/6143-6284   UUGCCCGAUGAUUAUA---AA-AAGACGCGUUAUUAAGAGGACUU--AAGCUG-----------------------------------GAGUUCU-UUA-------C----CUCAUUU--CUCUC--------------------------------------------------U-UU-U-CUGCACUU-C-UUU-UUCUUUCUUUGGAUGUCCAGCGUCCUAUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
AAGW02007855.1/5886-6026   UUGCCCGAUGAUUAUA---AA-AAGACGCGUUA--AAGAGGACUU-AAUGCUG-----------------------------------GAGUUCU-UUA-------U----CUU-UUC--CUCUC--------------------------------------------------U-UU-U-UCUGUACUUC-UUU-UUCUGUCUUUGGAUGUCCAGCGUCCUGUGAGCGAAGAUUAUGAGAUAUGAGGGCAA
#=GC SS_cons               <<<<<<----------...--.----------------<<<<<<<._______...................................>>>>>>>.---.......-....---.---..-----..................................................-.--.-.--------.-.---.-------------------------------------------------->>>>>>
#=GC RF                    uUGCCCGAUGAUUAUA...AA.AAGACGCgUUAUuAAGAGgacuu.aAuGCUG...................................gaguuCU.Uua.......c....uUU.UUU..cUcuC..................................................U.UU.U.cUuUacuu.c.UuU.UUcUuUCUuUGgAUGUCCAGCGUCCUaUGAGCGAAGAUUAUGAGAUAUGAGGGCAa
//
# STOCKHOLM 1.0

#=GF AC   RF01292
#=GF ID   snoR2
#=GF DE   Small nucleolar RNA snoR2/U65
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   45.10
#=GF NC   42.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00042
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300185;
#=GF RN   [1]
#=GF RM   9664033
#=GF RT   Localization and processing from a polycistronic precursor of novel
#=GF RT   snoRNAs in maize.
#=GF RA   Shaw PJ, Beven AF, Leader DJ, Brown JW
#=GF RL   J Cell Sci. 1998;111:2121-2128.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   11


AC007233.7/16823-16971     UGUCCGAUGCCACGUCGACGGUAGCU-------UUAGGGCAAUGAUCCUCGAUGCUAC-AUUGGACAUAAACAAA-----U--------GUACGU------GUUUCGCUUACUGAUAGGAACCUGUGGAUCUUGAAUUGAUUUACGAUCUA-CGGAGCC--AUUUCGGCGAUUACAUUU
DQ108823.1/379-527         UGUCCGAUGCCACGUCGACGGUAGCU-------UUAGGGCAAUGAUCCUCGAUGCUAC-AUUGGACAUAAACAAA-----U--------GUACGU------GUUUCGCUUACUGAUAGGAACCUGUGGAUCUUGAAUUGAUUUACGAUCUA-CGGAGCC--AUUUCGGCGAUUACAUUU
Y11049.1/506-650           GGCCUGAUGCCACGUCUCUGGUAGCU-------ACAU-GCUUUGACCAGAGAUGCUAUGAUCAGGCCGAUACAAA-----A--------GU---C------GUUUCACAUGUUGAUAGGAACCUG-GGGAC-GGCUUCUCCAUCUGUCCCA-CAGAGCC-GGUUUCUGUGAUCACAUUC
AARH01014343.1/1683-1829   GGUCCGAUGCCACGUUGCUGGUAGCCA------AAAUGGCGUUGACCGGCAAUGCUAUGAUUGGACCGAAACAAA-----U---------UCCAU------GUUUCGCUUGCUGAUAGGAAUCUGUGGAUCCUAUUCUGUU----GAUCCA-UGGAGCC-GUUUUCGGCGAUUACAUUU
AM460179.2/5268-5416       GGUCCGAUGCCACGUCGCCGGUAGCC-------AUU-GGCGAUGACCGGCGAUGCUAUGAUUGGACCGAUAUCAA-----U--------CUA--U------GUUUCGCAUGCUGAUAGGAACCUGUGGAUCAGGUUUAUGCCGUUGAUCUA-CGGAGCCGAUUUUUUGCGAUUACAUUU
AASG02011273.1/6035-5889   GGUCCAAUGCCACGUCGCCGGUAGCC-------AUGAGGCGUUGACCGGCGAUGCUAUGAUUGGACCUAAAUCAA-----U--------UU-CUU------GUUUCGCUGCCUGAUAGGAAUCUGUGGAUCUGAUUUCUUU---UGAUUCA-UGGAGCC-GAUUUCGGCGAUUACAUUC
AJ489967.1/1-152           GGCCUGAUGCCACGUCACUGUUAGCC--------ACGAGCAUUGAGCUGUGAUGCUAUGAUCAGGCCGAGACAAAGCUGAU--------UCUGGC------GUCUCACAAGUUGAUAGGAACCUGGGGACUGCUGUUCCAU---CGGUCCA-CAGAGCC-GGUUUCUGUGACUACAUUU
AY013245.2/56757-56907     GGCCUGAUGCCACGUCACCUGUAGCU-------AU--GGCUUUGACCGGUGAUGCUUUGAUUAGGCCAAAACCGA-----G--------UUGGUUUCGGACGUUUCACAUGUUUAUAGGAACCUG-GGACUGCAUCUCCAU---CGGUCUA-CAGAGCC-GGUUUCUGUGAUUACAUUU
AC140849.8/90491-90328     GGUCUGAUGCCACGUCUUUGAUAGCUACAUAUAUUUGAGCUCUGAUCAAAGAUGCUAUGAUUGGACCAAAAUCAA-----GAGUGUUAAUCAUUU------GUUUCGCAUUCUGAUAGGAAUCUGCUGAUCUUAUAUAUA---AUGAUCCUGCAGAGCC-GAUUUGUGCGAUUACAUUU
AAAA02007032.1/12923-12773 GGCCUGAUGCCACGUCACCUGCAGCU---------ACGGCUUUGACCGGUGAUGCUUUGAUUAGGCCAAAACAGA-----G--------UUGGUUUCCUACGUUUCACAUGUUGAUAGGAACCUG-GGACUGCAUCUCCAU---CGGUCUA-CAGAGCC-CGUUUCUGUCAUUACAUUU
CP002685.1/7520754-7520902 UGUCCGAUGCCACGUCGACGGUAGCUAU-----UUUUGGCAAUGAUCCUCGAUGCUAC-AUUGGACAUAGACAAA-----U--------GUACGU------GUUUCGCUUACUGAUAGGAACCUGUGGAUCUUGAUUCUAU--ACGAUCUC-CGGAGCC--AUUUCGGCGAUUACAUUU
#=GC SS_cons               :<<<<<<<<---<<<<<<-<<<-<<<.......____>>>---->>>->>>>>>--->->>>>>>>---------.....-........------......---<<<<<--------<<---<<<-<<<<<__________..__>>>>>-.>>>-->>.------>>>>>::::::::
#=GC RF                    gGcCcgAUgCCACgUCgcuGguAGCc.......auaugGCuuUGacCagcGAuGCUAcGAUcgGgCcaAaAcaAA.....u........uuauuU......GUUUCgCaugcUGAUAGGAAcCuGugGaccuuauuUcuaU..augguCca.CaGAGCC.gaUUUcuGcGAUUACAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01293
#=GF ID   ACA59
#=GF DE   Small nucleolar RNA ACA59
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   43.00
#=GF TC   44.90
#=GF NC   40.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   snoRNABase; ACA59;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15199136
#=GF RT   Human box H/ACA pseudouridylation guide RNA machinery.
#=GF RA   Kiss AM, Jady BE, Bertrand E, Kiss T
#=GF RL   Mol Cell Biol. 2004;24:5797-5807.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AL031296.1/85969-86120     GCCCAGGGUAUGUU---------------CACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACAGCU
AANU01225121.1/438-603     GCCCAGGGUAUGUUUAUGGGGUGAUGCUGCCCGGGGUGAUGCUGCCCUCCAAGCUGGCCCAUGGGUGACUGUGGGAAUGUUA-CUGCCUCACAACAUUUGUGCCUCAGUUACUCAUAGAUGUAGUGAGGGUGACAAUACUUACUCUCGUUGGUGAUAAGGAACAGCU
AAWR02037329.1/29294-29150 GCUCAGUGUGGGUU---------------AACCGGGUGAUGCUGCCCUCCUGGCUCUACCACUAAUGACCCUGGGCAGGGUC----CUCGACACCACU---GCCUCGGUUACCCAUCGGUGCAGUGCGGGUAGUAGUACCAAUGCUAAUUAGUUGUGAGGACCAACU
#=GC SS_cons               :<<<<<<<<-----...............----<<<<______>>>>-------------------->>>>>>>>-------.-----((((,<<<<<<<<<___________>>>>>>>>>,,,,<<<<<<<______>>>>>>>,,,,,))))::::::::::::
#=GC RF                    GCcCaggGuauGUU...............caCgGGGcGAUGCUgCCCUCCuaGCUggcCCAugggUGaCccuGgGaAuguUa.CUGCcccaCAaCacuuguGCCUCaGUUACcCauagguGuAGUGaGgGuggcAaUACccaCcCucgUUgGuggUaAGGAaCAgCU
//
# STOCKHOLM 1.0

#=GF AC   RF01294
#=GF ID   snoU89
#=GF DE   Small nucleolar RNA U89
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; Wilkinson A
#=GF SS   Predicted; Wilkinson A
#=GF GA   44.00
#=GF TC   44.10
#=GF NC   43.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00082
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=HUM30104;
#=GF DR   snoRNABase; U89;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   16


U47924.1/179615-179346       CAGGCUGAUGAGAC-UAAGGCGAAUGCGA-CUCCGUGCUCUCUGGCCC--UU--GGCUCCUU------------GUUG--GGGGUGGGGACUACAGAUGAGAUCUGAAAUCUUAGUGGUAGUACCUGAGCCAUGACUCCCCACUGUAAGGCCAGAUCAAUAGCAUUGGU--GGCCUUGCCUUCAUUUCUGG--UGCUGCC--CCUAGUUCCUGGCAGCAG---CCUGCAGGGAGGCCCACAGGUGGGGUCCACGGUAGGGCUG-GGCACAA--GC--CACCU-GAGCGCA-A-----CCUUGGAUCUGACA
ABDC01214908.1/3322-3055     CCGGCUGAUGAGAC-UAAGGCGAAUGCGA-CUCCGUGCUGUCUGGCCC--UU--GGCUCCUU------------GUUGCAGGGGU---GGAUAUAGACGGGAUCUGAAGUCUUAGUGGGGGUACCCGAGGC-UGGCUCCCCACUGUAAGGCCAGAUCAACAGCACUACU--GGCCUUGCCUCUAUUUGUGC--UGCUGCC--CGGAGUUCCUGACAGCAG---CCUGCAGGAAGGCCCACAGGUGGGGCCCAGGGUAGGGCUG-GGCACGA--GC--UAUCU-GAGCGCA-A-----CCUUGGAUCUGACA
AANG01081019.1/12170-11909   CCGGCUGAUGAGAC-UAAGGCGAAUGCGA-CUCUGUGCUCU---GUCC--UU--GGCUC---------------CCUG--GGGAUGGAGGUUUUGAAUGGGGUCUGAAAUCUUAGAGA-GGUGCCUGAGGCCUGGCUCCUCACUGUAAGG-CAGAUCAAUAGCACUGCU--GGCCUUGCCUCCAUUUCUGC--UGCUGCC--UCCAGUUCCUGGCAGCUG---CCUGCAGGGGGGCCCACAGAUGGGGACCAAAGUGGGACUA-GGCACGA--GC--UAUCU-GAGCGCA-A-----CCUUGGAUCUGACA
AAQQ01201252.1/668-932       CUGGCUGAUGAGAA-UAAGGCGAAUGUGA-UUUUGUGCUCUCUGACCC--UU--GGCUCCUG------------G-----GGGGCUAGG--UACAGAUGGGAUCUGAAAUCUUGGUGGGGAAACCUGAGUCCUGGCUCCCUGCCGUAAGGCCAGAUCAAGAGCACUGCU--GGCCUUGCCCUCAUGUCUGU--UGCUGCC--CCAAGUUCCUGGCAGUAG---CCUACAGGGAGGCCCACAGGUAGGGGCCAAAGAUGGGAUG-GGCACCA--GC--CAUGU-GAGCACA-A-----CCUUGGAUCUGACA
AACN010210013.1/211-475      CCGGCUGAUGACAC-UAAGGCGAAUGCGA-CUCUGUG-CUUUCUGGCC--CU--UGG--CUC------------CCUG--GGGUUGGGGGUUUUGAAUGGGAUCUGAAAUCUUAGUGG-GGUGCCCGAGGCCUGGCUCCUCACUAUAAGG-CAGAUCCAUAGCAAUGCC--GGCCUUGUCUCCACUUCUGC--UGCUGCC--UCCAGUUCCUGGCAGCCG---CCUGCAUGGGGGCCUACAGGUGGGGACCAAUAUGGGACUG-GGCACGA--GC--UAUCU-GAGCGCA-A-----CCUUAGAUCUGACA
AANN01670580.1/6889-6629     CUGACUGAUGAGAC-UAAGGCGAAUGCGA-CUCCAUGCUCUUCUGUCC--UU--G---------------------UG--GGGGCGGGGGUU-CAAGUGGCAUCUGAAAUCUUAGUGAGGGUCCCUGAAACCUGACUCCUUGCUGUAAGG-CAGAUGGAUAGCAUAGCU--GGCCUAGCCUGCUUUGUGGC--UGCUGCC--CCCAGUUCCUGGCAGCUG---UCUGCAGG-GGGCCCACAUGUGGGAACCAGAGCAGGAGCA-GGCAUGAGAGC--CACCUGGAGCGCA-A-----CCUUGGAUCUGACA
AAFC03061782.1/50090-50334   CUGGCUGAUGAGACUUAAGGCGAAUGCGA-C-CCGU--------GCCC--UU--CGACCCCU---------------G--GGGGCGGGGGUUCCGAGUGGGAUCUGAGAGCUUGGUGG-GGCACCUGAGGGCUGGCUCUCCGCCAUGAGG-CAGAUCAACAGCGCAGCU--GGCCUUGCCUCCACGUCCAC--UGCUGCC--UCCAGUUCCCGGCAGCUG---CCUGCAGGGAGGCCGACAGGUGGGG--C----------UG-GGCACGA--GC--CACGU-GAGCGCA-A-----CCUUGGAUCUGACA
AC002397.1/182589-182319     CCGGUUGAUGAGAC-CAAGGCGAAUGCGA-CUU-GGCCUACUGACUCU--UU--CUUGGCUUGGGAAUGGGGGUUGGG--GGGGGGGGGACAACUGGUGAGAUCUGAAAUCUUGGUGGGGGUACCUAAGGCCUGACUCCCUGCUGUAAGGCCAGAUCAAUAGCACUACU--GGCCUUGCCCUCAUGUCA-----GCUGCC--ACACAGUACUGGCAGCAU---CCUGUAGGGAGGCCCACAGGGGGUAGCCAACAUGUGAGUA-G-----C------CAUGU-GAGCGCA-A-----CCUUGAAUCUGACA
AAFR03037717.1/4116-3836     CUGGGUGAUGACUC-CAAGGCGAAUGCGACCUCCGUGCCUUCUGGCUC--CUGGCUCCCAGG------------GAGG--GGGGCAGUUAUGCUCUUAGAGGUCUGAAAUCUUGGUAG-GGAGCCAGAGGCCUGGACCCCUGCUGUAAAGCCAGACCCACAGAAUUGCUCAGGCC---CCUGGGUUUCCAGU-GGCUGCC--UCUAGACUCUGGCAGCUCUACCCAGCAGG--GGCCCACAGGUGGGGUCAGGGUGGAAGCAGAGGCAUUG--GCUGCGGUU-GAGCACA-ACAAACCCCUAGAUCUGACA
AAWR02029201.1/13597-13334   CUGGCUGAUGAGAC-UAAGGCGAAUGCGA-CUCCGUGCUCUC--UAUC--CU--UGG-CUUC------------CUGG--GGGUGGAGGUUUUGAAUGGA-AUCUGAAAUCUUAGUGG-GGUACCUGAGGCCUGGCUCCUCACUGUAAUG-CAGAUCAACAGCACUGCU--GGCCUUGCCUCUGUUUCUGC--UGCUACC--UCCAGUGACUGGCAGCUG---CCUGGAGGAGGGCCCACAGGUGGGGACCAAAGUAGGACUA-GGCACGA--GG--CAGCU-GAGCGCA-A-----CCUUGGAUCUGACA
AAKN02051612.1/143279-143544 CCGGCUGAUGAGAC-CAAGGCGAAUGUGA-UAC-GUGCUCUCUGCCCC--UU--GGCUUCUG------------GGCU--GGGUGC-----UGCAGAUGGGAUCUGGAAUCUUGGUGGGGACUCCUGAGGCCUGACUCCCCCUAGUAAGACUGGAGCCACAGCACUGCA--GGCCUCUCGUUGCUAUUGAGGCUGCUGCUGCCCUGGCCUCCAGCAGCAG---CAUGCAGGGAGGCCCACAGGUGGGACUU-UGGGUGGGAUG-GGCAGAA--GC--CAUGU-GAGCUCA-------CCUUGGAUCUGACG
AAHX01032846.1/20885-20625   CCGGUUGAUGAGAC-UAAGGCGAAUGCGA-CUUGGCCUACUGACUCUUGGCU--UGGGGGUG------------GUGG--GAGGACAGGACAACUAGUGAGAUCUGGAAUCUUGGCAGGGGCGCCAGAGGCCUGACUCCCUGCUGUAAGGCCAGAUCAAUAGCACUGCU--GGCCUCACCU--CUGUCAGC--UGCCACC--ACA--GCGCUGGCAGCAU---CCUGUAGGGAGGCCCACAGGAGGAG-CCA---AAGU-GUG-AGUA-----GC--CAUGU-GAGCGCAGA-----CCUCGAAUCUGACA
AAGV020207083.1/24-291       CCGGCUGAUGACAC-UAAGGCGAAUGCGA-CUCCGUGCUCUAU-GACC--CU--UGGUUCC-------------CUGG--GGAAUGAGGGUUAGGGAUGGGAUCUGAAAUCUUAGUGGGGGUACCUGAGACCUGGCUCCCCACUGUAAGGCCAGAUCAAUAGCACUGCU--GGCCUUGCCUCCAUUGCUGC--UGCUGUC--CCCAGUUCCCAGCAGCUG---CCUGCAGGGGGGCCCACACGUGGGAACCAAAGUAAGGCUA-AGCACGG--GC--CAUCU-GAGCGCA-A-----CCUUGAAUCUGACA
AAPE02007016.1/29674-29424   CUGGCUGAUGAAAC-UAAGGCGAAUGCGA-UUCCGUGCUCUCUGG------------GGGGG----------------------UGGAGUUCUCAAAUGGGAUCUGAAAUCUUAGUGG-GGUACCUGAGCU-UGGCUCCUCGCUGUAAAG-CAGAUCAAUAGCACUGCU--GGCCUUACCUCCAUUUCUGC--UGCUGCC--UCUAGUUCCUGGCAGCUG---CCUAUAGGGGGGCCCACAGGUGAGGACCAAAGUAAGACUA-GGCACGA--GC--CACCU-GAGCGCA-A-----CCUUGGAUCUGACA
AAQR03127805.1/1777-2030     CUGGCUGAUGAGAC-UAAGGCGAAUGCGA-CUC--UGCUUUCUGCCCC--UU--GGUUCCUU------------GUCA--GGGGUGGGG-----------GAUCUGAAAUCUUAGUGGGGGUACCUGAGGC-UGGCUCCCCACUGUAAAGCCAGAUCAAUAGCACA-CU--GGCCUCACCUCUGAUUCUGC--UGCUGCC--CCCAGUUCCUGGCAGCAG---UCUGCAGGGAGGCCUACAAGUGGGGCCCAAAGUAGGGCUA-G-CAUGA--GA--CAUCU-GAGCGUA-A-----CCUUGGAUCUGACA
AAGU03036160.1/24146-23890   CCAGCUGAUGAGAC-UAAGGCGAAUGCGA-CUCCAUGCCUGCUGACCU--UU--GGCUCCCG------------GGGG--AGGGUGG-------------GAUCUGAAAUCUUAGUGGGAGUGCCUAAGGCCUGGCUACCCACUGUAAGGCCAGAUCAAUAGCACUGCU--GGCCUUGCCUCUAUUUCUGC--UGCUGUC--CUCAGUUCCUGGCAGCUG---CGUGCAGGGGGGCCCACAGGUGGGGACCAAAGUAGGGUGA-GGCAUGA--AC--CAUCU-GAGCGCA-A-----CCUUGAAUCUGACA
#=GC SS_cons                 :::{---------{.{{{{{----{{{{-.{{{,,,[[[[[[[[<<<<..<<..<<<_____............>>>>..>>>>>,,(((((,,,,,,,,<<<<<<------<<<<<<-<<<____________>>>-->>>>>>------>>>>>>,,,,,,,,,,,,..<<<<<<-<<<--------<<..<<<<<<<..__________>>>>>>>-...>>--->>>>>>>>>,,,,,,,,,))))),]]]-]]]]],,.<<<____..>>..>,,,,.}}}}}}}.-.....}}}}}}------}:
#=GC RF                      CuGGcUGAUGAgAc.caaGGCGAAUGcGA.CuccGUgcccucccgccc..cu..cgcuccuu............gcgg..ggggcgggGcccacaaauGgGaUCuGAAAUCUugGcgGGggcaCCuGAGgCCUGgcuCCCcgCcgUAAgGCCaGAuCaAuAGCAcUGCU..GGCCucgCCuucaUuUcugg..uGCuGCC..uCuAGuucCUGGCaGCag...ccUGcaGGgaGGCCcACAGGUGGgggCcAggguagggcua.GGCAuga..GC..CAucU.gaGCgCA.A.....CCuuggAUCUGACA
//
# STOCKHOLM 1.0

#=GF AC   RF01295
#=GF ID   SCARNA7
#=GF PI   snoU90
#=GF DE   Small Cajal body-specific RNA 7
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; Wilkinson A
#=GF SS   Predicted; Wilkinson A
#=GF GA   65.00
#=GF TC   67.90
#=GF NC   51.20
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=HUM30105;
#=GF DR   snoRNABase; U90;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   12032087
#=GF RT   Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation
#=GF RT   and pseudouridylation guide RNAs.
#=GF RA   Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T
#=GF RL   EMBO J. 2002;21:2746-2756.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   18


AY077740.1/1-330             UGGAAAUGAUGAAAUAGAGAUAAUUGGGUG---UUGAAUGU------------U-G-UAUGACUGGAAAUUUUUAAUAUG-UAUAUUAUGUAAUU---CUUAUAAGUUUA-----------GUGUUUUAUAGGUACUUAAUA----GAGA--------------------GUGUGUAUGCAUGUG------UGUGU----------G----------------CU---UG-UGGUGGCUAUGG-AAAGGGGGCACUGACUG--GUGAUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAG-AAAUAACAUGGGUUGUUGAUUACAACAUUGCCAAUGAUUAUA-ACCCAAGAACAGCUCAC-CUAACUAGCCUGGCACCCUAAAAUCUCUAACAGGUUCAUUA--------A-A-A-UGGUCCUGUGAUCUGAUCCAA
ABDC01204998.1/1831-1486     UGGAAAUGAUGAAAUAGAGAUAUUUGGGUU---UUGAAUGU------------C-A-UGUGACUGGAAGUUUUAAAUAUG-UAUGUUUAGUAAUU---CUUCUAAGUUAA------------UAUUCUAUAGACACUUAGUA----CAGU--------------------GUGUGUGUGUGUGUG------UGUGU----------GUGUGUGCGCGCGCUUGCU---UG-UGGUGGCUAUGG-AAAGGGGGCACUGACUG--GUGAUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAG-ACAUAACAUGGGUUGUUGAUUACAACAUUGCCGAUGAUUAUA-ACCCAAGAACAGCUCAC-CUAAGUAGCCCAGCACCCUAAAAUCUCUAACAGGUCCAUUA--------A-ACA-UGGUCCCGUGAUCUGAUCCAA
AAPY01269291.1/652-330       UGGAAAUGAUGAAAUAGAGAUAAUUGGGUG---UUGAAUGU------------U-G-UGUGAUUGGAAAU-UUUAUUAUA-UAUA-----UAAUA---AUUCUAACUUUA-----------CUAUUUUAUA-GAACUUUAAA----UAGA--------------------GUGGGG-UGUGUGUG------UGUGU----------G----------------UG---UG-UGGUGGCUAUGG-AAAGGGGGCACUGACUG--GUGCUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAG-AAAUAACGUGGGUUUUUGACUACAACAUUGCCUAUGAUUAUA-GCCCCAAAACAGCUCAC-CUAACUAGCCCAGCACCCUAAAAUCUCUAACAGGUUCAUUA--------A-ACA-UGGUCCUGUGAUCUGAUCUGA
AAHX01017701.1/10820-11146   UGGAAAUGAUGAAAUAGAGAUAUCUGGGUG---UCGAAUGU------------U-GCUAUGAGUGGACAGUUUUAAUACA-UGUA----GUAAUU---CUCCUA-GUUUA-----------CUGUUUCCUUGGUACUUAUUAGUGUGAGU--------------------GCGUGCAUGCAUGUG------UGUGU----------G----------------UG---UG-UGGUGGCUAUG--AAAGGGGGCACUGAAUG--GUGAUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAG-AAAUAACAUGGGUUGUUGAUAACAACAUCGCCAAUGAUUAUA-ACCCAAAAACAGCUCAC-CUAAGUAGCCCAGCACCCUAAACUCUCUAACAGGAUCAUUA--------A-A----UGUCCUGUGAUCUGAUCCAA
AANN01532242.1/2725-3039     UGGAAAUGAUGAAAUAGAGAUAAUUGGGUG---UUGAAUGU------------U-G-UAUGAUUGAAAAUUCUUAAUAUG-UAAGUUUAAU--UU---UUUAUAA-----------------------AUACGUACGUGUGU----GUGU--------------------GUGUGUGUGUGUGUG------UGUGU----------A----------------CU---UG-UGAAGGCUAUGG-AAAGGGGGCACUGACUG--GUGAUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAC-AGAUAA-AUGGGUUGUUGA-UACAGCAUUGCCAGUGAUUAUA-ACCCAAGAACAGCUCAC-CUAAGUAGCCUAACACCCUAAGAUCUCUAACAGGUUCAUUA--------AGU-A-UGUUCCUGUGAUCUGAUCCAA
AANG01279938.1/4123-3780     UGGAAAUGAUGAAAUAGAGAUAAUUGGGUG---UUGAAUGU------------U-G-UGUGAUUGGAAACUUUUCAUAUG-UAAGUUAAGUAAUUAAGCUUAAUAUUUUAUAGAUAAUAGAGUGUGUGUGUGUGCCAUUUGU----GUGU--------------------GUGUGUGUGUGUGUG------CGUGC----------A----------------CU---CA-UGGAGGCUAUUG-AAAGGGGGCACUGACUG--GUGAUGCUGAUAUUGGAGUGCAUCUGAGGCAGUUGUAA-AAAUA-CAUGGGUUGUUGAUUACAACGUUGCCGAUGAUUAUA-ACCCAAGAACAGCUCAC-CUAAGUAGCCUAGCACCCUAAAAUCUCUAACAGGUUCAUCA--------A-ACA-UGGCCCUGUGAUCUGAUCCAA
AAYZ01477408.1/1346-1001     UGGAAAUGAUGAAAUAGAGGUAACAGGGUG---UUGAGUGUAUGUAUCGUGAAU-G-UAUGAGUGGAACUUGUUAGUAUU-AAUGUUAAGUAAUU---CUUCUAAGUUUA-----------GAGUUUUAUAGAUACUUCCUA----GAGA--------------------GUGUGUGUGCCUGUG------UGCGU----------G----------------CU---CA-UGGCGGCUAGGGCAAAGGGGGCGCUGAGUGUGGUGGUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAG-AAAUCACAGGGGUUAUUGAUUACAACAUUGCCAAUGAUUAUG-ACCCCAAAACAGCUCAC-CUAACUAGCCUUACACCCUAAAGUCUCUAACAGGUUCAUCA-------GA-C-A-UGAACCUGUAAUCUGAUCCAA
AAIY01552916.1/4711-5031     UGGAAAUGAUGAAAUAGAGAGAAAUGGGUG---UUGAGUGU------------U-G-UAUGAUUGAAGUUUUUUAAUUAG-UGUUUUAAGUAAUU---AGUCUAAAUUUA-----------AUAUUUUCU------GUAAUA----GUGU--------------------AUGCGUGUAUUUGUG------UGUGU----------G----------------CU---UG-A--AGGCUAUGG-AAAGGGGGCACUGACUG--GUGGUGCUGAGAUUGGAGUGCAUCUGAGGCUGUUGUAG-CAAUA-CAAGGG-UGCUGAUUACAACAUUGCCAAUGAUUAUA-ACCCAAAAAGAGCUCAC-CUGCCUAGCCAAGCACCCUAACAUCUCUAACAGGUUCAUUA--------A-A-CCUGGACCUGUGAUCUGAUCCAA
AAFC03009457.1/139378-139700 UGGAAAUGAUGAAAUAGAGAUAAUUGGGUG---UUAAAUGU------------U-G-UAUGAUUAGAAAAUUUUAAUAUC-UAAGUAAUCU-----------UAAGUUUA-----------AUAUUUUUUAACUGAUAGUGU----GUGUAU------------------GUGCGUGUGCAUGUG------UGUGU----------G----------------CU---UG-UGGAGGCUAUGA-AAAGGGGGCACUGACUG--GUGAUGCUGAUACUGGAGUGCAUCUGAGGCUGUUGUAG-AAGUG-CAUGGGUUGUUGAUUACAACAUUGCCUAUGAUUAUA-GCCCAGGAGCAGCUCAC-CU-AGUAGCCUAGCACCUUAAAAUCUCUGACAGGUUCACUG--------A-A-CGUGGUCCUGUGAUCUGAUCCAA
AC119847.12/95090-94748      UGGAAAUGAUGAAAUAGAGAUAUUUGGGUG---UUGAAUGU------------U-GCUGUGAGUGGAAAAUUUUAAUACA-UGUA----GUAAUU---CUCCUA-GUUUA-----------AUGUUUCAUUGAUAGUUACUA----GUGUAAGUGUGUGCAUGUAUGUCUGUGUGUGUGUGUGUG------UGUGU----------G----------------UG---UG-UGGUGGCUAUG--AAAGGGGGCACUGAAUG--GUGAUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAG-AAAUAACAUGGGUUGUUGAUAACAACGUUGCCGAUGAUUAAA-ACCCAAAAACAGCUCAC-CUAAGUAGCCCAGCACCCUAAACUCUCUAACAGGAUUAUUA--------A-A-C-A--UCCUGUGAUCUGAUCCAA
AAFR03046986.1/52054-52366   UGGAAAUGAUGAAACAGAGAUAACAGGGUGCAUUUGAAUGG------------U-G-UGUGAUUGGAGCAUUUUAAAAUU-UAAAUUAAGUAAAU---AUUAAAAUGGGG-----------GGGG---------------------GUGU--------------------AUGUGUGUGUGCGUG------GGUUU----------A----------------AG---UA-UAAAGGCUAAGG-AAAGGGAGCCCUGACAG--AUAAUGCAGAUAUCGGAGUGCAUCUGAGGCGGUUGUAA-AAAUA-CAAGAG-UGUUUAUUACAACUUUGCCAGUGAUUACA-AUUUGGAAACGGCUCAC-CUACCU-GCCUGACACCCUAUAAUCUCUAACAGGUUCAUAA--------A-U-G-UGGACCUGUAAUCUGAUCCAU
AAWR02042163.1/35190-34869   UGGAAAUGAUGAAAUAGAGAUAAUUGGGUG---UUGAAUGU------------U-G-UGUGAGUGGAAAUUUUGAAUACG-UAAGUUAAGUAAUU---AAUA----------------------UUUUAUAGGUACUUAGUA----GAGA--------------------GUGUGUGUGCAUGUG------UGUGU----------G----------------CUGCUCC-UGCUGGCUAUGG-GAAGGGGGCGCUGACUG--GUGAUGCUGAUACUGGAGUGCAUCUGAGGCUGUUGUAG-AAAUU-CAUGGGUUGUUGAUUACAACAUUGCCGAUGAUUAUA-ACCCAAGAACAGCUCAC-CUAAGUAGCCUAGCACCCUAAAAUCUCUGACAGGUUCAUUA--------A-ACA-UGCUCCUGUGAUCUGAUCCAG
AAKN02013691.1/1241-914      UGGAAAUGAUGAAAUAGAGAUAGUUGGGUG---UUGAAUGU------------U-G-UAUGACUGGAAAUUUUAGUAAUC-U---GUAAGUAAUU---CUU-UCAGUUGA-----------GUAUUUUGUAGUUAGUUAAUA----GAGU--------------------GUGUGCGCGUGUGUG------UGUGU----------A----------------UG---CGCUUGUGGCUAUGG-AAAGGGGGCACUGAAUG--GUGAUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAGAAAAUAACAUGGGUUCUUGAUUACAACAUUGCCAAUGAUUAUU-ACCCAAGAACAGCUCAC-CUAAGUAGCCUAGCACCCUAAAAUCUCUAACAGGUUCAUUG--------A-U-G-UGGUCCUGUGAUCUGAUCCAA
AAWZ02004566.1/4157-3827     UGUAUGUGUUGUGUGUGUGUAAAUUUGAUU---UUGAACAG------------U-A-AAUGCU-----AUUUUCAAUGGGAAAUUUUAUUUUAAA---CGGGAAAGUAGC-----------ACGGGUGGGUGGGGUGU--------GUGU--------------------GUGCUCAUGCAUGUG------UGUAA----------AA---------------GC---UC-UGUAUGAUGCAA-AUUAUGGGUACUGAAAAA-AAGCUGCUGAUUUCGGAGUGCAUCUGAGGCUGUUGC----AAAACCAUAGGGUCUUGACUGCAACAUUGCCAAUGAUUAGAGACCCAAGUUAAACUCAUAGUUUGCAUCAAGGUGUUUUUAAACCUCUGACAGGUUCAUUUUGUCAUGCA-A-A-GGAACCUGUGAUCUGAUCUAA
AAQR03113699.1/21331-21009   UGGAAAUGAUGAAAUAGAGAUAAUUGGGUG---UUGAAUGU------------U-G-UGUGGCUGGAAGUUUUUAAUAUG-UAUGUUUAGUAGUU---UUU----CAUUA-----------AUAUUUAAUAGGUACU--AGA----GAUA--------------------GUGUGUGUGCAUGUG------UGUGU----------------------------U---UG-UGGCGGCUAUGC-CAAGGGGGCACUGACGG--GUGAUGCUGACAUUGGAGUGCAUCUGAGGCUGUUGUAG-ACGUAACAUGGGUCAUUGAUUACAACAUUGCCAAUGAUUAUA-ACCCAAGAACAGCUCAC-CUAAUUAGCCGAACACCCUAAAAUCUCUAACAGGUUCAUGA--------A-ACA-UGGUCCUGUGAUCUGAUCCAA
AAPE02045386.1/34396-34731   UGGAAAUGAUGAAAUAAAGAUAAUCGGGUG---UUGAAUGU------------U-G-UAUGAAUGGAAAUUUUUAAUAUG-UAAGUUAAGUAAUG-------UAAGUUUA-----------AUAUUUUAUAGAUAAUUAAUA----GAAA--------------------GCGUGUGUGCGUGUG------UGUGUGUGUGUGUGCG----------------CU---CG-UGGAGGCUAUGG-AAAGGGGGCACUGACUG--GUGAUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAG-AAACA-UAUGGGUUGUUGAUUACAACAUUGCUGAUGAUUAUG-ACCCAAAAACAGCUCAC-CUAAGUAGCCUAACACCCUAAAAUCUUUAACAGGUUCAUUA--------A-A-UGUGUUCCUGUGAUCUGAUCCAA
AAEX03017331.1/258948-258623 UGGAAAUGAUGAAAUAGAGAUAAUUGGGUG---UUGAGUGU------------U-G-UGUGAUUGGAAAAUUUUAACAUG-UGAGUUAAGUAAUU--------AAGCUUA-----------AUAUUUUAUAGAUACUUAAUA----GAAU--------------------GUGUGUGUGUUUGUGUU----UGUGU----------G----------------CU---CA-UGGAGGCUAUUG--AAGGGGGCACUGACUG--GUGAUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAG-AAAUA-CACGGGUUGUUGAUUACAACGUUGCCGAUGAUUAUA-ACCCAAGAACAGCUCAC-CUAAGUAGCCUAGCACCCUAAAAUCUCUAACAGGUUCAUUA--------A-ACA-UGGUCCUGUGAUCUGAUCCAA
AAGW02014762.1/48919-49252   UGGAAAUGAUGAAAUAGAGAUAAUUGGGUG---UUGAAUGU-------------UG-UAUGACUGGAAAUUAUUAGUAUU-AAUGUUAAGAAAUU------AUAAGUUUA-----------AUGUUUUAUGGAUACUUACUA----GAGU--------------------GUGUGUGUGUGUGUGAGCAUGUGUGU----------G----------------CU---UA-UGGUGGCUAUGG-AAAGGGGGCACUGAGUG--GUGAUGCUGAUAUUGGAGUGCAUCUGAGGCUGUUGUAG-AAAUAACAUGGGUUGUUGAUUACAACAUUGCCGAUGAUUAUG-ACCCAAAAACAGCUCAC-CUAAGUAGCCUAACACCCUAAAAUCUCUGACAGGUUCAUUA--------A-ACA-UGGUCCUGUGAUCUGAUCCAA
#=GC SS_cons                 <<<<--------------------------...--------............-.-.-----------------------.--------------...------------...........---------------------....----....................---------------......-----..........-................--...--.------------.-----------------..------------------------------<<<<<<<<.-<<<<<<____>>>>>>-->>>>>>>>---------------.-----------------.-----------------------------------------........-.-.-.---------------->>>>:
#=GC RF                      UGGAAAUGAUGAAAUAGAGAUAAUUGGGUG...UUGAAUGU............U.G.UaUGAuUGGAAauUUUuAAUAug.UAugUUAAgUAAUu...cuuauAAgUUuA...........augUUUuaUaGauacuUaauA....GaGu....................GUGUGUGUGugUGUG......UGUGU..........g................cu...Ug.UGgaGGCUAuGg.AAAGGGGGCACUGAcUG..GUGaUGCUGAUAUUGGAGUGCAUCUGAGGCuGUUGuag.AAacaaCAUGGGuuguUGAuuaCAACaUUGCCaAUGAUUAuA.ACCCAAaAAcAGCUCAC.CUAAgUAGCCuagCACCCUAAAAUCUCUAACAGGUUCAUUA........A.A.a.UGguCCUGUGAUCUGAUCCAA
//
# STOCKHOLM 1.0

#=GF AC   RF01296
#=GF ID   snoU85
#=GF DE   Small nucleolar RNA U85
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; Locarna; Wilkinson A
#=GF SS   Predicted; Locarna; Wilkinson A
#=GF GA   41.00
#=GF TC   42.00
#=GF NC   40.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00082
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=HUM30099;
#=GF DR   snoRNABase; U85;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19633723
#=GF RT   Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed
#=GF RT   upon viral infection.
#=GF RA   Glazov EA, Kongsuwan K, Assavalapsakul W, Horwood PF, Mitter N, Mahony TJ
#=GF RL   PLoS One. 2009;4:e6349.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   21


AF308283.1/1-330               GCCACAUGA-UGAUAU--------CA----AGGCUGU---UGUGAUUCAGUUGGUUUGGCUAAG-CCCAGGGACCUU--UGGCCUGUUA---AAGGUCUGUAAUCUUGGUGGGCGAUACAGAGUUAUGU-GUGUUCACUGUAAGGGCAGACCAACAAGAAC---UUUUUCCUACUUUUGA-GC-----UACCUCUUUUUAAUAGGGGUGAUUCUUCC-AGUUGCUGGAGAGAAA-UUGUGGUAACUGGAGUGAGAGAGUAGGAACAG----GG-CAUGUUCAGGG----UAU--CAGGGCCAAGGGUCCUA--AAGGACUUAGCUUGUGUUAUGGCCACUGAGAGAUGAAACACAGAUCUUUGGUAAUCUGA-UGGCU
AF308282.1/1-316               UGCCCAUGA-UGAAAUA--UUCGACAUCGGAGUUUGCGCAUUGGCGACAAGACCUAAGGCUCAG-ACUCUAGCAAAU--C--UAGUUUC---AUCCGUUGUAAUCUUUGCUGCU-GCACUCCAGAAUUU-GCAGUGGCCGUAAGGCCAGCGGGACACCAAC--------AGCCAGGGAUC-AA-----GA----------------------CUAUU-AUCUGUCAUUGAGUCC-UA--GACAGAUAGUUUAGUCUCUGGUUUACAGAACACC-CAAAUGGAAAU----GAA--ACACGCGCUUUUGUCGACCCAGGAGCCAGUUAGGUCUAAGCUGUUUGUCAUGGUGACGAC--GUCUUUAGUAAUCUGAGCGCAA
AACN010346788.1/508-835        GCCAUGUGA-UGAUAU--------CA----AGGCUGU---GGUGAUUCAGUUGGUUUGGCUAAG-CCUGGGGACCUU--U-GACCUAUU---AAGGUCUGUAAUCUUGGUGGGCAAUACAGAGUUAUGU-GUGUUCGCUGUAAGGGCAGACCAACAAGAAA---UAUUUCCUACUUUUGA-AC-----UACCUCUCUUUAAUAAGAGGGUU-CUUCC-AGUUGCCAGAGAGAAA-CUAGGGUAGCUGGAGUGAGAGAGUGGGGACAG----GG-CAUGUUCAGGG----UAA--AGAGAUCAGGGGUCCCA--AAGGAUUUAGCUUGUGUUGUGGCCACUGAGAGAUGAAACACAGAUCUUUGGUAAUCUGA-UGGCU
AAQQ01201317.1/367-42          GCCACAUGA-UGAUAU--------CA----AGGCUGU---UGUGAUUCAGUUGGUUUGGCUAAG-CCUGGGAACCUU--UGACCUAUUA----UGGUCUGUAAUCUUGGUGGGUGAUACAGAGUUAUGU-GCAUUCACUGUAAGGGCAGACCAACAAGAAC---UUUCUCCUACUUUUGA-AC-----CACCUCUUUUUAAUAGGGGUGAUUCUUCC-AGUUGCCAGAGAGAAA-UUGUGGUAACUGGAGU--GAGGGUAGAAACAG----GG-CAUGUUUGAGA----UAU--CAGGGUCAGGGGUUUCA--AAGGACUUAGCUAUA-UUUUGACCACUGAGAGAUGAAACACAGAUCUUUGGUAAUCUGA-UGGCU
AAPY01657622.1/489-161         GCCAGGUGA-UGAUAC--------CC----AGGCUGC---UGUGACUCGGCUGGUCGGGCCGAG-CCCAGGGACCUC--UGACCCGUUG---A-GGUCUGUAAUCUUGGUGGGUGAUACAGAGUGGUGU-GCAUUCGCUGUAAGGGCAGACCAACAAGAAU---GUUGUCCUACUUUUGA-AC-----UACUUCUCUUUAACGUAAGAGAUUCUCCC-AGUUGCCAGGAAGGAA-UUGCGGUAACUGGAGUGAGAAGGUGGGAACAG----GG-CAUGUUCUGGG----UCU--CAGGAUCAGGGGUCCCU--AAGGACUCAGCCGGCGUGGUGGCCACCGAGAGAUGAGGCACAGAUCUUUGGUAAUCUGA-UGGCG
AASV01051783.1/978-664         UGCCCAUGA-UGAAAUA--UUCGACAUCGGAGUUUGCGCAUUUGCGACCAGACCUAAGGCUCAG-ACUCUAGCAAAU--C--UAGUUUC---AUCCGUUGUAAUCUUUGCUGCU-GCACUCCAGACUUU-GCAGUGGCCGUAAGGCCAGCGGGACACCAAC--------AGCCAGAGAUC-AA-----GA----------------------CUAUU-AUCUGUCCUUAAGUCC-UA--GACAGGUAGUUUAGUCUCUGGCUUACAGAACAUC-CAAAUGA-AUU----GAA--ACACGCGCUAUUGUCGACCCAGGAGCCACUUAGGUCUAAGCUAUAUGCCGUGGUGACGAC--GUCUUUAGUAAUCUGAGCGCAA
AAIY01414456.1/795-471         GCCAUAUGA-UGAUAU--------CA----AGGCUGU---UGUGAUUCAG-UGGGUUGACUAAG-UCCAGGGACCUG--UGGCC-CUUCAUGAAGGUCUGUAAUCUUGGUGGGCGAUACAGAGUUGUGU-GCGUUCGCUGUAAGGGCAGACCAACAAGAAG---UUGACCCUACUUUUGA-GC-----UCCCUCCUU---AAUGGGGGGAUUCUUCC-AGUUGCCAG---GAGA-AAAUGGUAACUAAAGCUAGAGAGUAGGGACAA----GG-CAGGUUGAGGU----GAU--GCGGGUCAGGGCUCCCA--AAGGACAUAGUCUGUAUUGUGACCACUGAGAGAUGAAACACAUAUCUUUGGUAAUCUGA-UGGCU
AAPQ01006440.1/1134796-1134481 UGCCCAUGA-UGACAUA--UUCGACAUCGGAGUUUGCGCAUUGGCGACCGGACCUAAGGCUCAG-ACUUUAGCAAAU--U--UAGUUUC---AUCCGUUGUAAUCUUUGCUGCU-GCACUCCAGAAUUG-GCAGUAGCCGUAAGGCCAGCGGGACACCACA--------UGCCAGGUAUC-AA-----GA----------------------CUAUU-AUCUGUCCUUAAGUCC-UA--GACAGAUAGUUUAGUUUCUGGCUUACAGAACACC-CAACUAGAAAU----GAA--ACACGCACUAUUGUCGACCCAGGAGCCACUUAGGUCCAAGCUAUUUGCCAUGGUGACGAC--GUCUUUAGUAAUCUGAAUGCAA
AAHY01057252.1/13385-13061     GCCAUGUGA-UGAUAU--------CA----AGGCUGU---UGUGAUUCAGUUGGUUUAGCUAAG-UCCAGGGACCUC--UGACCUAUUC---A-GGUCUGUAAUCUUGGUGGUCGAUACAGAGUAAUGU-GCGUUCACUGUAAGGGCGGACCGACAAAAAA-----UUUCCUACUCUUUAAAU-----UACCUCACUCCAGUCGGGGUGAUUC-UCC-AGCUGCCAGGGAGGAA-UUGUGGUAACUGGAAU--GAAAGUAGGAACAG-----U-CUUAUAUUCGA----GGUGCCAGGGUCAGUGGUCUCA--AAGGACUUAGCU-GUGUCAUGGCCACUGAGAGAUGACACACAGAUCUUUGGUAAUCUGA-UGGCU
AAFC03072403.1/28719-28398     GCCAUGUGA-UGAUAU--------CA----AGGCUGU---GGUGAAUCAGUUGGUUUGGCUAAG-CCC-GGGACCUC--UGACCUACUA-----GGUCUGUAAUCUUGGUGGGCGAUACAGAGCAAUGU-GUGUUCACUGUAAGGGCAGACCGACAAUA-----UUCUUCCUACUUGUGG-GC-----UGCCUCUCUUCAAUGGAGGCUGUUCUUCC-CGUUGCCAGAGAGAAC-AUGGGGUAACG--AGUAAGAGAGUAGGGAUAG----GG-CAUGCUCGGGA----CAU--CAGGGUCAGGUGUCCA---GAGGACUUAGCCUGUGCUGUGGCCACUGAGAGAUGAAACACAGAUCUUUGGUAAUCUGA-UGGCU
AAEU02002383.1/4909-4594       UGCCCAUGA-UGACAUA--UUCGACAUCGGAGUUUGCGCAUUUGCGACCGGACCUAAGGCUCAG-ACUCCAGCAAAU--U--UUGUUUC---AUCCGUUGUAAUCUUUGCUGCU-GCCCUCCAGAAUUG-GCAGUGGCCGUAAGGCCAGCGGAACACCAAA--------AGCCAGGUAUC-AA-----GA----------------------CUAUU-GUCUGUCCUUAAGUCC-UA--GACAGAUAGUUUAGUUUCUGGCUUACAGAACACC-AAAAUAAAAAU----GAA--ACACGCACUUUUGUUGACCCAGGAGCUACUUAGGGCUAAGCUAUUUGCCAUGGUGACGAC--GUCUUUAGUAAUCUGAAUGCAA
AAHX01032861.1/49736-49409     GCCAUGUGA-UGAUAU--------CA----AGGCUGU---UGUGAUUCAGUUGGUUUGGCUAAG-UCCAGGGACCUC--UGACCUAUUU----UGGUCUGUAAUCUUGGUGGUCGAUACAAAGUAAUGU-GCGUUCACUGUAAGGGCGGACCAACAAAAAU-----UUUCCUACUUUUUG-AACCACCUCACUCCAUCCAGUUGGGGUGAUUC-UCU-AGCUGCCAGGGAGGAA-UUGUGGUAACUGGA--AUGAAAGUAGGAAUAG----GU-UAUAUUCGAGA----UGC--CAGGGUUGGGAGUCUCA--AAGGACUUAGCU-GCGUCAUGGCCACUGAGAGAUGACACACAGAUCUUUGGUAAUCUGA-UGGCU
AALT01242224.1/2656-2975       GCCAUGUGA-UGAUAU--------CA----AGGCUGU---GGUGAUUCAGCUGGUUUGGCUCAG-UCUGGGGACCUU--UGACUCG--------GGUCUGUAAUCUUGGUGGACAAUACCGAGCU-UGU-GUGUUCGCUGUAAGGGCAGACCAAUAGAUAA----UCUCCCUACUUUCGA-AC-----GACGUCUCUUUCACAGAGGCGGCCCUGCC-AGUGGCCAGAGAGAAAACU--GGUGACUGGUGUCAAGGAGUAGGGACAG----GG-CGUUUUCCGGG----CAC--CGGGGUCGGGGCUCCCG--AGAGACUUGGCCUGUGCUGUGGCCGCUGGA--GAUGAACACAGAUCUUUGGUAAUCUGA-UGGCU
AAFR03037692.1/52518-52844     GCCAUAUGA-UGAUAU--------CA----AGGCUAU---UGUUACUUGGCUGGUCUUACUAAG-CCCUAGGACCCUGACUUUCCA-UC---UAGGUCUGUAAUCUUGGUGGGCAAUACAGAGCUGUGU-UUGUUUGCUGUAAGGGCAGACCAACAGGAAG----UUCUGCCUCUCUUAC-UCU----UAUCUCUCCCUAAGUGGAGUG---AUUUU-GGCUGCCACUGAAAGA-UCCUGGUAGCUAGAGCAGUGCAGAGGUAACAGGACAAG-C----CUAGAG----UAU--UGAAGUCAAGGACCCUA--GAAGGCUUAGCAUGUGAUAUAGCCGCCAAGAGAU-GAGCACAGAUCUUUGGUAAUCUGA-UGGCU
ABDC01189027.1/2314-1992       UGAGCAAGAGUGAGAC--------CC----UGUCUCUACUAAAAAUAAAGAGAAAUUAGCUGGA-CAAUUAAAAAUA--U-AUA---GA---AAGGUCUGUAAUCUUGGUGGGCAAUACAGAGUUAUGU-GUGUUCACUCUAAGGGCAGACCAACAAGAAC---UUUUUCCUACUUUUUA-GC-----CACCUCUUUUUAAUAGGAGUGAUUCUUCC-AGUUGCCAGGGAGAAA-UUGUGGUAACUGGAGUGAGAAAGUGGGAACAG----GG-CAUGUUAAAAG---------AAAAAAAAGAUUUUAUA--UAUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGU----GUGUGUGUGUAUAAAA-UUUAG
AADE01001581.1/17544-17844     GCUGCUUGA-GGCAACUGCUGUGACA----AGACUCAAAAUCGCAGACUUU------------A-GCUAUU--------C--CUGUUUC---AUCCGUUGUAAUCUUAGCUGCU-ACGUUGGAGCAUGUUGUAGAGGCUGUAAGGCCAACGGAACAUCAAC--------AGCCAUAGAGC-UA-----GACUGCUGUCUG------------UCGUC-AAGUUCAAGGCAGACA-GUUUAGAGCUGGGCUAAU---AUUCUUUCCAUAUAAUGAAACGCUAAAAA----GUU--AUUGUCGAC-----CCACACAGCAGUUGCUAAGGCUUGAGCUAGAAGCCACAUUGACGAC--GUCUUUAGUAAUCUGA-UAGAC
AAKN02051621.1/81967-81639     GCCAUGUGA-UGAUAC--------CA----AGGCUGU---UGUGAUUCAGUCGGUCUGAGUAAG--CCCGGGAACCU--G-GACCUGUU---ACGGUCUGUAAUCUUGGUGGGUGAUACAGAGUUAUGU-GCAUCCACUGUAAGGCCAGACCAACAAAAAC---UUUUUCCUACUUUCAA-AU-----CACUUCUCUUUCGUAGGGGUGAUCCUUCC-AGUUGCCAGGGAGAAA-UUGUGCUAACUGGAAU--GAGAGUAGAAACAG----GG-CAUGUUCCACGUUUCGAU--GGGGGUCAAGGUUCUCC--AAGGACUUAGCUCUC-UUAUGGCCACUGAGAGAUGAAACAUAGAUCUUUGGUAAUCUGA-UGGCU
AAWR02029181.1/9652-9978       GCCACAUGA-UGAUAU--------CA----AGGCUGU---GGUGAUUCAGUUGGUUUGGCUAAG-CCCGGGGACCUU--UGACCUG-UU---AAGGUCUGUAAUCUUGGUGGGCAAUACAGAGUUAUGU-GUGUUCGCUGUAAGGGCAGACCAACAAGAAA---UUCUUCCUACUUUUGA-AC-----UACCUCUCUUUAGUAGAGGUGAUUUUUCC-AGUUGCCAGGGAGAAC-UUCUGGUAACUGGAGUGAGAGAGUGGGGACAG----GG-CAUG-UCAGAG----UA---UGGGGUCAGGGGUCCCA--AAGGACUUAGCUUGUCUUGUGGCCACUGAGAGAUGAAACACAGAUCUUUGGUAAUCUGA-UGGCU
AAGW02051568.1/94965-95295     GCCACAUGA-UGAUAU--------CA----AGGCUGU---UGUGAUUCAGUUGGUCUGGCUAAG-CCCUGGGACCUU--UGACA-UCUU---AAGGUCUGUAAUCUUGGUGGGCGAUACAGAGUAGUGU-GCGUUCGCUGUAAGGGCAGACCAACACAAACUACUGUUUCCUACUUUUGA-GC-----UGCCUCUCUUGAAUAGAGGUCAAUCUUCC-AGUUGCCAGGGAGAAU-UG--GGUAACUGGAGUGAGAGAGCAGGAACAGAGCACG----UUCGGGUU----GUC--AGGAGUCAGAGGUCCCA--AAGGACUUAGCUUAUAGCAUGGCCACUGAGAGAUGAAACACAGAUCUUUGGUAAUCUGA-UGGCU
AAPE02007000.1/9230-9557       GCCACAUGA-UGAUAU--------CA----AGGCUUU---GGUGAUUCAGUUGGUUUGGCUAAG-CCCAGGGACCUU--UGACCUAUUA-----GGUCUGUAAUCUUGGUGGGCAAUACAGAGUUAUGU-GUGUUCACUGUAAGGGCAGACCAACAAGAAA---UUCUUCCUGCUUUUGA-AC-----UAUCUCUCUUUCAUGGAGAUAUUUCUUCCCAGUUGCCAGGAAGAAA-UUGUGGUAACUGGAGUGAGUAGGGAGG-ACAA----GG-CAUGUUCAUGG----UAU--CAGGGUCAAGGGUCCCA--AAGGACUUAGCUGGUGUUGUGGCCACUGAGAAAUGAAACACAGAUCUUUGGUAAUCUGA-UGGCU
AAQR03127883.1/27346-27022     GCCACAUGA-UGAUAU--------CA----AGGCUGU---UGUGAUUCAGUUGGUUUGGCUAAGUCCAAGG-AUCUC--UGACCUA-UU---AAGGUCUGUAAUCUUGGUGGGCAAUACAGAGUUAUGU-AUGUUCACUGUAAGGGCAGACCAACAAGAAC---UUUUUCCUACUUUUGA-GC-----UACCUCUUUUUAAUAGGGGUGUU-CUUCC-AGUUGCCAGGAAGAAA-CAGUGGUAACUGGAGUCAAAGAGUAGGAACAG----GG-CAUGUUCAAGG---------UAUGGUCAAGGGUUCUA--AAGGACUUAGCUUAUGUUAUGGCCACUGAGAGAUGAAACACAGAUCUUUGGUAAUCUGA-UGGCU
#=GC SS_cons                   (((------.------........--....-------...-((--(((((-((----------(.(-----(((((-..-----((-((...,,<<<<----------<<-<<<-<<____________.>>>>>->>---------->>>>,,,,,,,,,....,,,,<<<<<<<<<--.<<.....--------------------------<<<.-<<-<<<--<<_____.>>-->>>->>->>>>>-->>>>>>>>>,,,,,....<<._____>>,,,,....))-..))-------)))))---..---------------))------)))))))-------))--------------------.-))):
#=GC RF                        gcCacaUGA.UGAuAU........CA....AGgCUGu...UguGAguCaguuggUuUGGCUaAg.cCuaggGacccu..UGacccuUuc...AugguCUGUAAUCUUgGcGGccaacACaGAGuuAUGU.guggUcgCUGUAAGGgCAGaccAACAagAAc....UUUUccuacuuucga.ac.....uACcUCUcUUUaAuaGgGGuGaUUCUucc.AguUgCCAGugAGaaA.cagUGGuAacUggaguaagaaaguaggaACAG....gc.CAugUgcaaag....gau..agggGucAgggguCCcA..aAGGAcUUAGcuuGugcUauGgccacuGacAgAuuaAacACAGAUCUUUGGUAAUCUGA.UGgcu
//
# STOCKHOLM 1.0

#=GF AC   RF01297
#=GF ID   sR40
#=GF DE   Small nucleolar RNA sR40
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   97.40
#=GF NC   39.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AJ248287.2/136133-136073 GGCCAUGAGGACAGGCGGGUUUGCUGACCUCGGGGCGUGAUGAACCUUUGGAGCCCCGAGG
BA000001.2/597272-597332 GGCCAUGAGGAUAGGCGGGUUUGCUGACCUCGGGGCGUGAUGAACCUUUGGAGCCCCGAGG
#=GC SS_cons             :<<<_________>>>-----------<<<<<<<<<________________>>>>>>>>>
#=GC RF                  GGCCAUGAGGAuAGGCGGGUUUGCUGACCUCGGGGCGUGAUGAACCUUUGGAGCCCCGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01298
#=GF ID   snoU25
#=GF PI   snoU35
#=GF DE   Small nucleolar RNA U25
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   98.40
#=GF NC   35.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=XEN30021;
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=XEN30022;
#=GF DR   URL; http://snoopy.med.miyazaki-u.ac.jp/view.cgi?id=XEN30023;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   8962077
#=GF RT   A small nucleolar RNA requirement for site-specific ribose methylation of
#=GF RT   rRNA in Xenopus.
#=GF RA   Tycowski KT, Smith CM, Shu MD, Steitz JA
#=GF RL   Proc Natl Acad Sci U S A. 1996;93:14480-14485.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


U72853.1/1-69 UGCCAAUGAUGAGACCAAUCACAGACCUGUUCUGAAAGCAAUGAGGACAGCUUACUAUCUCUGAGGCCC
U72855.1/1-69 UGCCAAUGACGAGAUCAAUCACAGACCUGUUCUGAAAGCAAUGAGGACAGCUUACUAUCUCUGAGGCCC
U72854.1/1-69 UGCCAAUGAUGAGAUCAAUCACAGACCUGUUCUGAAAGCAAUGAGGACAGCUUACUAUCUCUGAGGCCC
#=GC SS_cons  :<<<----------------------<<<<<<____________>>>>>>-------------->>>::
#=GC RF       UGCCAAUGAuGAGAuCAAUCACAGACCUGUuCUGAAAGCAAUGAGgACAGCUUACUAUCUCUGAGGCCC
//
# STOCKHOLM 1.0

#=GF AC   RF01299
#=GF ID   SNORD2
#=GF PI   snR39B
#=GF DE   Small nucleolar RNA SNORD2
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.30
#=GF NC   36.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00072
#=GF DR   snoRNABase; snR39B;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Xenopus_tropicalis300118;
#=GF RN   [1]
#=GF RM   14960365
#=GF RT   Identification of a novel box C/D snoRNA from mouse nucleolar cDNA
#=GF RT   library.
#=GF RA   Zhou H, Zhao J, Yu CH, Luo QJ, Chen YQ, Xiao Y, Qu LH
#=GF RL   Gene. 2004;327:99-105.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   17


DQ351284.1/1267-1335         AAGUGAAAUGAUGGC-AAUCAUCUUUCGGGACUGA--CCUGAAAUGAAGAG-----------A----AU-ACUC--AUUG--CUGAUCACUU
X56953.1/2429-2497           AAGUGAAAUGAUGGCAAAUCAUCUUUCGGGACUGA--CCUGAAAUGAAGAG-----------A----AU-ACUC---UUG--CUGAUCACUU
AAPY01267864.1/1108-1174     AAGUGAAAUGAUGGC-AAUCAUCUUUCGGGACUGA--CCUGAAAUGAAGA-----------------AU-ACAU--UUUG--CUGAUCACUU
AALT01545687.1/2663-2595     AUGUGAAAUAUGGGC-UAUCAUCUUUCAAUACUGA--CUUGAAAUAUAGAG-----------A----AU-ACUC--AUUG--CUAGUCAUAU
AAVX01303330.1/1255-1187     GAGUGAAAUGAUGCU-UACCAUCUUUCGGGACUGA--CCUGAUAUGGAGAU-----------A----CA-UUAC--UUUA--CUGAUCACUC
AC149532.2/77133-77062       AAGUGAGAUGAUGGCAUACCAUCUUUCGGGACUGA--GUUGAUGUGAAGAG-----------U----UU-UUCUGUUUUG--CUGAUCACUU
CT027646.21/1398-1468        GUAUGAAGUGAUGGC--AUCAUCUUUCGGGACUGA--CCUGUUAUGGAGAU-----------A----AUCACUA--AUUUAACUGAUCAUAC
AANH01005452.1/10481-10410   GAGUGAUAUGAUGGCAUACCAUCUUUCGGGACUGACUCUUGUGAUGAUUUU-----------C----UU-GUAU--CUUA--CUGAUCACUU
CAAE01014542.1/132095-132022 CAGCGAUAUGAUGGCAUACCAUCUUUCGGGACUGA--CUUUUACAGUGGAG-----------AUGUUUU-ACCC--UUAA--CUGAUCGCUC
AAPN01382707.1/593-513       GAGUGACGUGAUGGCAUACCAUCUUUCGGGACUGA--CCUGAGAUGGAGAUGGAAAAAAAAAA----GU-AAAG--UCUG--CUGAUCACUU
AAPE02045174.1/15499-15431   AACUGAAACUAAGAC-AAUCGUCUUUGAGAACUGA--UCUGAAAUGAAGAG-----------A----GU-ACUC--AUUG--CUGAUCACUU
AADN03005882.1/213168-213237 AAGUGAUGUGAUGGUACACCAUCUUUCGGGGCUGA--CCUGAAAUGGAGAG-----------A----AC-UUGU--AAUG--CUGAUCACUU
AAGW02051643.1/30841-30774   AAAUGAAAUGAUGGC-AAUCAUCUUUCAGGACUGA--CCUGAAAUG-ACAG-----------A----AU-ACUC--AUUG--CUGAUCACUU
CAAB02007481.1/269022-269095 GAGUGAUAUGAUGGCACACCAUCUUUCGGGACUGACUCUUGCAAUGGAGAGCC---------U----AU-AACC--UUCA--CUGAUCACUU
AAQR03118660.1/1847-1915     UGGUGAGAUGAUGAC-AAUUAUCUUUCAGGACUGA--CCUGAAAUGAAGAG-----------A----AU-ACUC--AUUG--CUGAUCACUU
AAWZ02024796.1/55347-55276   AAGUGAGAUGAUGGUAUACCAUCUUUCGGGACUGA--CCUGAAAUGGAGAA-----------A----AA-UGUGUAACUG--CUGAUCACUU
AAEX03009404.1/121432-121500 UAGUGAAAUGAUGGC-AGUCAUCUUUUGGGAUUGA--CCUGAAAUGAAGAG-----------A----GU-ACUC--AUUG--CUGAUCGCUU
#=GC SS_cons                 <<<<<<_____________________________..______________..........._....__.____..____..____>>>>>>
#=GC RF                      gaGUGAaAUGAUGGCAuAcCAUCUUUCGGGACUGA..CcUGAaAUGaAGAg...........A....aU.Acuc..aUUg..CUGAUCACuc
//
# STOCKHOLM 1.0

#=GF AC   RF01300
#=GF ID   snoU49
#=GF DE   Small nucleolar RNA U49
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   35.00
#=GF TC   37.10
#=GF NC   33.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00062
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300176;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


DQ108823.1/109-181 UCCCGAUGAAGAAGCAAUCCCAUA-GAUAGGAAGUGCCGUAUGACACUUUACACAACAACGGACUGAACGACGA
AJ300655.1/3-68    ACCCGAUGAAGAAGCAAUCCCAAAAGAUAGGAAGUGCCGUAUGACACUUUACACAACAGCUAGCGU--------
AJ320263.1/4-65    UCCCAGUGAGGAUUCUAUGAC----CAUAGGAAGUGCCGUAUGACACUUUAAACAGCAGCUGCUUU--------
AJ489964.1/2-63    UCCCGGUGA----GGAAUCUAAGACCAUAGGAAGUGCCGUAUGACACUUUAAACAGCAGCUGCUUU--------
AJ310377.1/962-901 UCCCAGUGAGGAUUCUAUGAC----CAUAGGAAGUGCCGUAUGACACUUUAAACAGCAGCUGCUUU--------
#=GC SS_cons       :::::::::::::<<---------.-----<<<<<<________>>>>>>-------->>::::::........
#=GC RF            UCCCgaUGAaGAaGcaAUccCAuA.cAUAGGAAGUGCCGUAUGACACUUUAaACAaCAgCUGcuUU........
//
# STOCKHOLM 1.0

#=GF AC   RF01301
#=GF ID   snoR4a
#=GF DE   Small nucleolar RNA snoR4a
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   58.50
#=GF NC   35.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300074;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AC068667.6/42916-42992 GGAUAUGAUGAAAUGGCAAUAAUGUUUUGUGACACCCAGUCUGAUCUUCGUGAUUGAUUUGCCAUAUUUUCUGAUCC
AC068667.6/51308-51384 GGAUAUGACGAAAUGGCAAUAAUGUUUUGUGACACCCAGUCUGAUCUUCGUGAUUGAUCUGCCAUAUUUUCUGAUCC
#=GC SS_cons           <<<----------<<<<<_________________________________________>>>>>---------->>>
#=GC RF                GGaUAUGAuGAAAUGGCaAUAAUGUUUUGUGACACCCAGUCUGAUCUUCGUGAUUGAUuuGCCAUAUUUUCUGAuCC
//
# STOCKHOLM 1.0

#=GF AC   RF01302
#=GF ID   snoU36a
#=GF DE   SnoRNA U36a
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   46.20
#=GF NC   43.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.59 -Z 549862.597050 CM SEQDB
#=GF CL   CL00051
#=GF DR   URL; http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home;
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Arabidopsis_thaliana300168;
#=GF RN   [1]
#=GF RM   11780637
#=GF RT   Multiple snoRNA gene clusters from Arabidopsis.
#=GF RA   Brown JW, Clark GP, Leader DJ, Simpson CG, Lowe T
#=GF RL   RNA. 2001;7:1817-1832.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   15


DQ108835.1/292-381         UGGCAAUGAUUAUA----AACUUACCCGCGCUUCUGAGAUUAU--UCAAUGAAGUAGAUACGGUAA---AUACAUGGUUGAAUUUCUUAAUAUGAGCCA
DQ108711.1/301-390         UGGCAAUGAUUAUA----AACUUACCCGCGCUUCUGAGAUUAU--UCAAUGAAGCAGAUACGGUAA---AUACAUGGUUGAAUUUCUUAAUAUGAGCCA
AASG02001178.1/41441-41526 UGGCAAUGAUUAAA----GAUUUAUCCGCGCUUCUGAGAGAUA--UCAAUGAAGCAC--AAAAGAA---AU--AUGGUUGAAUUUCUUGAUAUGAGCCA
AARH01005974.1/498-589     UGGCGAUGAUUAAAAUGGAUUUUAUCCGCGCUUCUGAGAGAAA--UCAAUGAAGCAA--AAACAUA---AUUAAUGGUUGAAUUUCUUGAUAUGAGCCA
AY220676.1/4-88            UGGCAGUGAUUUGA----CA-UUACCCGCGCUUCUGAUAUAA---UCCGUGAAGCAAAGGG---AA---AAUAAUGGUUGAAUUCCUUAAUAUGAGCCA
CP000585.1/696645-696556   UGACGAUGAUGAUA----AAAAUAUCCGCGCUUCUGAUGAGUUCACGCUCGUGAGGUUAGACGAUA----U-UAUGGUUGAAUUUCUUCGGCUGAGUCA
AJ532539.1/3-90            UGGCAGUGAUUUGA----CAUUUACCCGCGCUUCUGAUUUAA---ACCGUGAAGUUAAGGG-AAAA---AAUAAUGGUUGAAUUUCUUAAUAUGAGCCU
AL161496.2/97232-97142     GGGCUAUGAUUACA----AAAUUAUCCGCGCUUCUGAGACUUAGUUCUAUGAAGUAUA-UACGAUA---AUCAAUGGUUGAAUUUCUUAAUAUGAGCCU
AM450298.1/4247-4334       UGGCAAUGAUUAUA----UG-UUAUCCGCGCUUCUGAGAGCAA--UCGAUGAAGCAUA-AAGGAAA---AAAAAUGGUUGAAUUUCUUAAUAUGAGCCA
AP004314.3/147764-147680   UGGCAGUGAUUUGA----CA-UUACCCGCGCUUCUGAUAUAA---UCCGUGAAGCAAAGGG---AA---AAUAAUGGUUGAAUUCCUUAAUAUGAGCCA
AACV01015141.1/22699-22615 UGGCAGUGAUUUGA----CA-UUACCCGCGCUUCUGAUAUAA---UCCGUGAAGCAAAGGG---AA---AAUAAUGGUUGAAUUCCUUAAUAUGAGCCA
AAAA02020760.1/6481-6394   UGGCAGUGAUUUGA----CAUUUACCCGCGCUUCUGAUUUAA---ACCGUGAAGUUAAGGG-AAAA---AAUAAUGGUUGAAUUUCUUAAUAUGAGCCU
EU410751.1/4-96            CGGUGAUGAGCAUG----AGUUUAUCCGCGCUUCUGAGGCCUU--GACCGGCCGUGCUGAUACUUACUCUUAUAUGGUUGAAUUUCUUCGCCUGAGCCC
AJ532537.1/4-89            UGGCAGUGAUUUGA----CA-UUACCCGCACUUCUGAUCUAA---UCCGUGAAGCAAAG--GGAAA---AAUAAUGGUUGAAUUUCUUAAUAUGAGCCG
AY220675.1/3-91            UGGCAGUGAUUUGA----CAUUUACCCGCGCUUCUGAUUUAA---ACCGUGAAGUUAAGGGAAAAA---AAUAAUGGUUGAAUUUCUUAAUAUGAGCCU
#=GC SS_cons               <<<<__________...._________________________.._____________________...__________________________>>>>
#=GC RF                    uGGCaAUGAUUauA....aAuUUAuCCGCGCUUCUGAgauaau..uccaUGAAGuaaagaaagaaA...AuuaAUGGUUGAAUUUCUUaAUAUGAGCCa
//
# STOCKHOLM 1.0

#=GF AC   RF01303
#=GF ID   sR49
#=GF DE   Small nucleolar RNA sR49
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   61.60
#=GF NC   34.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ248283.1/235441-235496 GGCGAUGAAGAACUGGAUCCGAGCUGAG-CUUAUGAUGAUGGAGGUUUAACCUGAGC
BA000001.2/220695-220750 GGCGAUGAAGAACUGGAUCCGAGCUGAU-CUCAUGAUGAAGGAGGUUUAACCUGAGC
AE009950.1/168854-168910 GGCGAUGAGGAGCUGGAUCCGAUCUGAUGUUUAUGAUGAGGGAGGUACAAGCUGAGC
#=GC SS_cons             :<<---<--<<<<<---<<<________.___________>>>>>>>>--->--->>
#=GC RF                  GGCGAUGAAgaaCUGGAUCCGAgCUGAu.cUUAUGAUGAaGGAGGuucAAcCUGAGC
//
# STOCKHOLM 1.0

#=GF AC   RF01304
#=GF ID   sR5
#=GF DE   Small nucleolar RNA sR5
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   40.00
#=GF TC   42.30
#=GF NC   39.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   11


BA000001.2/257161-257109   GUGAUGAUGAACGCCAUC-GAUACUGAGAU-----AUGAUGACCGGAU--UCCUGGCUGAU
AF195099.1/1-54            GAAAUGAUGAAUGGUCGACGGAACGGACCU-----AUGAAGAAUUGUU--GCCGGACUGAC
AJ248288.1/160716-160768   UAGAUGAUGAGCGCCAUC-GAUGCUGAGGA-----GUGAUGACCGGAU--UCCUGGCUGAU
L77117.1/441357-441413     UCGAUGAUGAGCAAUAAA--AAGCUGACUUA--AUAUGAUGAACCUUUCGGGGUAUCUGAG
AP006878.1/2002514-2002457 AAGGUGAUGAGCACUCUC-GAACCUGACGGGCAGGAUGAUGAGCGGAU--UCCUGGCUGAU
X98420.1/4632-4581         UUAGUGAUGAUGCCCUUC--AAUUUGAUUG-----AUGAUAAGGGCCC--GUGUUACUGAA
BA000023.2/1287805-1287754 UGGAUGAUGAAGCCCUUA--AAUAUGAUCG-----GUGAUAAAGGCCC--GUGUUACUGAU
CP000077.1/1126136-1126187 UGGAUGAUGAGGCCCUUU--CAAUAGAUUG-----GUGAUAAAGGCCC--GUGUUUCUGAU
AE009950.1/272692-272638   UGAAUGAUGAGCGCCAUCCGAUACUGAGGGC----AUGAUGACCGGAU--UCCUGGCUGAU
AE006641.1/820975-820924   UUGGUGAUGACGCCCUUC--AGUUUGAUUG-----AUGAUAAGGGCCC--GUGUUACUGAA
AF254841.1/1-50            --GAUGAUGAGCGCCAUC-GAUGCUGAGGA-----GUGAUGACCGGAU--UCCUGGCUGA-
#=GC SS_cons               ::::::::::::::::::.:::::::::::.....::::::::<<<__..__>>>::::::
#=GC RF                    UaGAUGAUGAgcgCCaUc.GAAaCUGAcug.....AUGAUGAacGgaU..GccUggCUGAu
//
# STOCKHOLM 1.0

#=GF AC   RF01305
#=GF ID   sR51
#=GF DE   Small nucleolar RNA sR51
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   38.00
#=GF TC   39.20
#=GF NC   35.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AJ248283.1/73088-73034     GUUGAUGAUGAA-CUCGCUUGUUGCUGAAGGGUGAUGAAGGGCAUACUGGCUGAUU
AP006878.1/1167429-1167375 GGCGAUGACGAACCUCACG-AUAGCUGAAGGGUGAUGAGGGGCAUACUGGCCGAGC
AE009950.1/1881800-1881853 UCCGAUGAUGAGUCUCGCUCG--GCUGAUAGAUGAUGUAGGGCAUACUGGCUGAGG
AF254835.1/2-56            GUUGAUGAUGAA-CUCGCUUGUUGCUGAAGGGUGAUGAAGGGCAUACUGGCUGAUU
#=GC SS_cons               <<<----<<<----<<<------<<<____>>>-->>>---->>>--->>>:::::
#=GC RF                    GccGAUGAuGAAuCuCgCUuGUuGCUGAAGGGUGAuGaAGGGCaUACUggCUGAgu
//
# STOCKHOLM 1.0

#=GF AC   RF01306
#=GF ID   sR52
#=GF DE   Small nucleolar RNA sR52
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   53.20
#=GF NC   41.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AE009950.1/1665032-1665089 GAAGAGGAUGAAAAAGAAG--AAAAGGCUGAAUAGAUGAUGAGAGGGGACCUCUCUGAUG
AJ248284.1/9864-9922       GGGGAGGAUGAAGAAAAAGUUCAAAGGCUGAA-AGGUGAUGAGAGGGGACCUCGCUGAUG
#=GC SS_cons               ::::::::::::::::::::::::::::::::.:::::::::<<<<___>>>>:::::::
#=GC RF                    GaaGAGGAUGAAaAAaAAGUUaAAAGGCUGAA.AGaUGAUGAGAGGGGACCUCuCUGAUG
//
# STOCKHOLM 1.0

#=GF AC   RF01307
#=GF ID   sR55
#=GF DE   Small nucleolar RNA sR55
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   35.00
#=GF TC   44.50
#=GF NC   33.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.20 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AE009950.1/1245431-1245494 ACCGAUGAAGAGUGUCAUCCCUGCUGAAA-CGGGGUCGAUGAUGAGGUA-UAGUCCCCACCUGAGG
AJ248286.2/3131-3195       ACCGAUGAUGAGUGUCAUCCCUGCUGAAAUCGGGGUCGAUGAUGACGUA-AAUUCCCCACCUGAGG
AP006878.1/1476852-1476910 ACCGAUGAGGAGUGUCAUCCCUCCUGAUGUCGAG----AUGAUGACAUU-A--UCCCCACCUGAGG
BA000001.2/939374-939311   ACCGAUGAUGUGUGUCAUCCCUGCUGAAA--GGGGUCGAUGAUGAUGUUUUGAUCCCCAUCUGAGG
#=GC SS_cons               :<<__________________________.___________________.______________>>
#=GC RF                    ACCGAUGAuGAGUGUCAUCCCUgCUGAAA.CGGGGUCGAUGAUGAcGUu.uaaUCCCCACCUGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01308
#=GF ID   sR58
#=GF DE   Small nucleolar RNA sR58
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   55.00
#=GF TC   71.10
#=GF NC   31.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AJ248284.1/234671-234725   CCCGAUGAUUGGAAACGGAGUGAGCUGAGGU-GUGAUGACCGACUUCCCGCUGAGG
BA000001.2/1413806-1413752 CCCGAUGAUUGGAAGUGGAGUGAGCUGAUGC-AUGAUGACCGACUUCCCUCUGAGG
AP006878.1/1257078-1257024 CCCGAUGAUUGGAAAGAGAGUGAGCUGAGAG-AUGAUGACCGACUUCUCGCUGAGG
D87814.1/94-148            UCCGAUGAUUGAAACGAGAGUGAGCUGAAAG-AUGAUGACCGACUUCUCGCUGAGG
AE009950.1/1495226-1495171 CCCGAUGAUUGAAAAUGGAGUGAGCUGAGUUAAUGAUGACCGACUUCCCACUGAGG
#=GC SS_cons               <<_____________________________.______________________>>
#=GC RF                    CCCGAUGAUUGgAAaugGAGUGAGCUGAgau.AUGAUGACCGACUUCcCgCUGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01309
#=GF ID   sR60
#=GF DE   Small nucleolar RNA sR60
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   63.00
#=GF NC   42.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AJ248285.1/31285-31339     CGGGAUGAGGAGUUCAGCCUAGGCUGAGGCGUGAUGAGGGAGUGACGGACUGACC
BA000001.2/1328880-1328826 CGGGAUGAGGAGUUCAGCCUAAGCUGAGACAUGAUGAGGGAGUGACGGACUGACC
AP006878.1/1626359-1626305 UGGGAUGAUGAGUUCAGCCUUGUCCGAGCUGUGACGAGGGAGUGACGGACUGACC
AE009950.1/1288175-1288229 CGGGAUGAGGAAUUCAGCCUAAGCUGAAGUAUGAUGAGGGAGUGACGGACUGACC
#=GC SS_cons               :<<__________________________________________________>>
#=GC RF                    CGGGAUGAGGAGUUCAGCCUAaGCUGAGguaUGAUGAGGGAGUGACGGACUGACC
//
# STOCKHOLM 1.0

#=GF AC   RF01310
#=GF ID   sR7
#=GF DE   Small nucleolar RNA sR7
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   37.00
#=GF TC   38.20
#=GF NC   33.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.26 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


BA000002.3/509234-509293   AAGUGUGAUGAUUUACUCCCGGACCGAGCAAUGCUGUGAGGACUACUUACCCGGCUGACA
AJ248285.1/47926-47870     AGGGAUGAUGAGCCUCCAUCCAA-GCUGAGCA--AGUGAUGAGUGCACAUCAGGCUGAAC
BA000001.2/1316443-1316499 CGGGAUGAUGAACCUCCAUCCCA-ACUGAAUA--AAUGAUGAAUGCACAUCAGGCUGACA
AE009950.1/1301535-1301479 UUCGAUGAUGAGCCUCCAUCCCAUGCUGAA-G--GGUGAUGAGUGCACAUCAGGCUGAGC
AF254831.1/3-59            AGGGAUGAUGAGCCUCCAUCCAA-GCUGAGCA--AGUGAUGAGUGCACAUCAGGCUGAAC
#=GC SS_cons               ::::::::::::::::::::::::::::::::..::::::::::::::::::::::::::
#=GC RF                    agGGAUGAUGAgCCUCCAUCCgAcgCUGAAaa..aGUGAUGAgUGCACAUCAGGCUGAca
//
# STOCKHOLM 1.0

#=GF AC   RF01312
#=GF ID   sR9
#=GF DE   Small nucleolar RNA sR9
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   36.00
#=GF TC   36.10
#=GF NC   33.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.54 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://lowelab.ucsc.edu/snoRNAdb/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


BA000002.3/171314-171247 GGGGAUGGUGAGGGGUGCGA-GCGCAGAGCCCCAG--GGGCGGUGAAGAAGGAUUAUAACAGCGUCUGACC
AF195103.1/6-60          ------------AAUAAUGAUGACUAACUCCAAUACUGACCAAUGAUGUCGUAACCC----GAAACUGAAU
AE006641.1/994550-994603 ------------UAGCGUGAUGAACCGUGUUUCAGCUGAUCUGUGACGAUAGCCCUU-----CGGCUGAGC
#=GC SS_cons             ............::<__________________________________________....________>:
#=GC RF                  ............aaguGuGAUGaaCAGaGCCucAGCUGauCaGUGAaGAaGGAucaU....GcGuCUGAcC
//
# STOCKHOLM 1.0

#=GF AC   RF01313
#=GF ID   AHBV_epsilon
#=GF PI   HHBV_epsilon
#=GF DE   Avian HBV RNA encapsidation signal epsilon
#=GF AU   Chen A
#=GF AU   Brown C
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Chen A, Brown C
#=GF SS   Published; PMID:17430968
#=GF GA   45.00
#=GF TC   46.50
#=GF NC   36.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00104
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0019079; viral genome replication;
#=GF RN   [1]
#=GF RM   9188560
#=GF RT   Sequence- and structure-specific determinants in the interaction between
#=GF RT   the RNA encapsidation signal and reverse transcriptase of avian hepatitis
#=GF RT   B viruses.
#=GF RA   Beck J, Nassal M
#=GF RL   J Virol. 1997;71:4971-4980.
#=GF RN   [2]
#=GF RM   17430968
#=GF RT   Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation
#=GF RT   signals.
#=GF RA   Girard FC, Ottink OM, Ampt KA, Tessari M, Wijmenga SS
#=GF RL   Nucleic Acids Res. 2007;35:2800-2811.
#=GF WK   Avian_HBV_RNA_encapsidation_signal_epsilon
#=GF SQ   10


X74623.1/2560-2616   UGCCAAGGUAUCUUUACGUCUACAUUGCUGUUGUCGUGUGUGACUGUACCUUUGGUA
AY250904.1/2560-2616 UGCCAAGGUAUCUUUACGUCUACAUUGCUGUUGUCGUGUGUGACUGUACCUUUGGUA
AY294029.1/2560-2616 UGCCAAGGUAUCUUUACGUCUACAUUGCUGUUGUCGUGUGUGACUGUACCUUUGGUA
AY536371.1/2566-2622 UGCCAAGGUAUCUUUACGUCUACAUUGCUGUUGUCGUGUUUGACUGUACCUUUGGUA
AY392760.1/2566-2622 UGCCAAGGUAUCUUUACGUCUACAUUGCUGUUGUCGUGUUUGACUGUACCUUUGGUA
AY521226.1/2566-2622 UGCCAAGGUAUCUUUACGUCUACAUUGCUGUUGUCGGCUUUGACUGUACCUUUGGUA
AY433937.1/2566-2622 UGCCAAGGUAUCUUUACGUCUACAUUGCUGUUGUCGGCUUUGACUGUACCUUUGGUA
M21953.1/2563-2619   UGCCAAGGUAUAUUUACGUCUACAUUGCUGUUGUCAAGUCUGACUGUACCUUUGGUA
M22056.1/2566-2622   UGCCAAGGUAUCUUUACGUCGACCUCGCUGUUGUUCCUUGUGACUGUACCUUUGGUA
AJ251934.1/2572-2628 UGCCAAGGUAUCUUUACGUCAACCUCGCUGUUGUUCCUUGUGACUGUACCUUUGGUA
#=GC SS_cons         <<<<<<<<<<<------<<<------<<____>>------->>>->>>>>->>>>>>
#=GC RF              UGCCAAGGUAUCUUUACGUCUACAUUGCUGUUGUCgugUuUGACUGUACCUUUGGUA
//
# STOCKHOLM 1.0

#=GF AC   RF01314
#=GF ID   mir-1227
#=GF DE   microRNA mir-1227
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   miRBase
#=GF SS   Published; PMID:17964270; Wilkinson A
#=GF GA   70.00
#=GF TC   72.90
#=GF NC   41.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   MIPF; MIPF0000454;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17964270
#=GF RT   Mammalian mirtron genes.
#=GF RA   Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC
#=GF RL   Mol Cell. 2007;28:328-336.
#=GF WK   MicroRNA
#=GF SQ   3


AC143896.2/45997-45910 GUGGGGCCAGGCGGUGGUGGGCACCGCUGGGGUGGGCACAGCAGCCAUGCAGAGCAGGCAGCUGACCCCGUGCCAUCCUCUUCCCCAG
AC138127.1/8944-8857   GUGGGGCCAGGCGGUGGUGGGCACUGCUGGGGUGGGCACAGCAGCCAUGCAGAGCGGGCAUUUGACCCCGUGCCACCCUUUUCCCCAG
AC206022.3/51292-51379 GUGGGGCCAGGCGGUGGUGGGCACUGCUGGGGUGGGCACAGCAGCCAUGCAGAGCAGGCAUUUGACCCCGUGCCACCCUUUUCCCCAG
#=GC SS_cons           :<<<<<---<<-<<<<<<<<<<<<<<<<---<<<<<<______>>>->>>-->>>>>----->>->>>--->>>>>>>>--->>>>>:
#=GC RF                GuGGGGCCAgGCGguGGcGGGCaCcGCuGGGGcgGGCACAGCAGCCAcgCAGaGCgGGCAuuuGACCCCGUgCCacCCcuUUCCCCaG
//
# STOCKHOLM 1.0

#=GF AC   RF01315
#=GF ID   CRISPR-DR2
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   36.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00014
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   19


AP008230.1/3154402-3154431 GUUUCAAUCCCUCAUAGGUAAGCUAACAAC
CP000679.1/62025-62054     GUUUCAAUCCCCAAAGGGAAGGCUACAAAC
CP000679.1/93287-93316     GUUUCAAUCCCCAAAGGGUAGGCUACAAAC
CP000141.1/1949543-1949572 GUUUCAAUCCCAGAUUGGUUCGAUUAAAAC
CP000716.1/360504-360533   AUUUCAAUUCCUCCAAGGUAAGGUAAAAAC
CP000141.1/1929243-1929272 GUUUCAAUCCCAGAAUGGUUCGAUUAAAAC
BA000043.1/355427-355398   GUUUCAAUCCCUCAUAGGUACGAUAAAAAC
CP000386.1/263210-263239   GUUUCAAUCCCUUAUAGGUAGGCUCAAAAC
CP000679.1/93158-93187     GUUUCAAUCCCCAAAGGGCAGGCUACAAAC
CP000568.1/717027-716998   GUUUCAAUUCCUCAUAGGUACGAUACAAAC
AARF01000280.1/1425-1454   GUUUCAAUUCCUUAUAGGUACGUUAGAAAC
AP009389.1/2004616-2004645 GUUUCAAUUCCUCAUAGGCAGGCUAAAAAC
CT573071.1/625535-625564   GUUUCAAUCCCUCAUAGGUAGAAUGAAAAC
CP000557.1/317462-317433   GUUUCAAUCUCUCAUAGGUACGAUACAAAC
CP000612.1/587612-587583   GUUUCAAUUCCUUAUAGGUAGGCUGAUAAC
CP000673.1/1722241-1722270 GUUUCAAUUCCUUAUAGGUAGUCUAAAAUC
CP000771.1/1024868-1024839 GUUUCAAUCCCUAAUAGGUAUGCUAAAAGC
CP000879.1/2085036-2085007 GUUUCCAUUCCUUAUAGGUAGGAUAAAAAG
CP001336.1/4172990-4173019 AUUUCAAUUCCUUAUAGGUAAGCUAACAAC
#=GC SS_cons               :<<<-----<<<___>>>-------->>>:
#=GC RF                    GUUUCAAUCCCUuAUAGGUAgGcUAAAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01316
#=GF ID   CRISPR-DR3
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   41.00
#=GF TC   41.20
#=GF NC   40.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   20


CP000673.1/2823144-2823173   AUUUAAAUACAAUCCUUGUUAAGGUUCAAC
CP000673.1/2825586-2825615   AUUUAAAUACAAUCCUUGUUAAAGUUCAAC
CP000728.1/2374103-2374132   AUUUAAAUACAUCUCAUGUUAAUGUUCAAC
CP000728.1/2376467-2376496   AUUUAAAUACAUCCUAUGUUAAUGUUCAAC
AE015927.1/1596015-1596044   AUUUAAAUACAACUCUUGUUAUUGUUCAAC
CP000728.1/2352762-2352791   AUUUAAAUACAUCUUAUGUUACUGUUCAAC
AE015927.1/1590005-1590034   AUUUAAAUACAUCCUAUGUUAAGGUUCAAC
CP000728.1/2521987-2521958   AUUUAAAUACAUCUUAUGUUAAUGUUCAAC
CP000673.1/3579827-3579856   AUUUAAAUACAAAUCUUGUUAAGUUUCAAC
CP000673.1/2835805-2835834   AUUUAAAUACAAUUCUUGUUAAGGUUCAAC
ABDY01000002.1/267925-267954 AUUUAAAUACAUACCAUGUUAAUGUUCAAC
CP000382.1/1866234-1866263   AUUUAAAUACAUCCCAUGUUAUUGUUCAAC
CP000727.1/2239349-2239378   AUUUAAAUACAUCCUAUGUUAUUGUUCAAU
CP000726.1/2253841-2253870   GUUUAAAUACAUCUCAUGUUAAUGUUCAAU
AM412317.1/2310339-2310368   GCUUAAAUACAUCUCAUGUUAAUGUUCAAC
ABDP01000013.1/120655-120684 UCUUAAAUACAUCCUAUGUUAAGGUUCAAC
ABDO02000004.1/251279-251308 AUUUAAAUACAUCUCAUGUCAAUGUUUAAC
ABDO02000004.1/254636-254665 AUUUAAAUACAUCUCAUGUUAUUAUUCAAC
CP000726.1/2256155-2256184   GCUUAAAUACAUCUUAUGUUACUGUUCAAC
ABAX03000005.1/109886-109915 AUUUCAAUACAACUCUUGUUAUUGUUUAUC
#=GC SS_cons                 ::::::::<<<<___>>>>:::::::::::
#=GC RF                      AUUUAAAUACAUCUCAUGUUAAUGUUCAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01317
#=GF ID   CRISPR-DR4
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.77 -Z 549862.597050 CM SEQDB
#=GF CL   CL00014
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   33


BX571865.1/44187-44214         GUGCACUGCCGUACAGGCAGCUUAGAAA
CR543861.1/2372998-2373025     CUUCACUACCGCACAGGUAGCUUAGAAA
CP000753.1/3865826-3865799     GUUCACCGCCGCACAGGCGGCUUAGAAA
CP000127.1/3128418-3128445     GUUCACCGCCGCACAGGCGGUUUAGAAA
AF530480.1/2088-2115           GUUCACUGCCGCAUAGGCAGCUUAGAAA
AANE01000001.1/559890-559863   GUUCACUGCCGAACAGGCAGCUUAGAAA
AAKV01000024.1/25336-25309     GUUCACUGCCGUAUAGGCAGCUAAGAAA
AE005174.2/1058490-1058517     RUUCACUGCCGUACAGGCAGCUUAGAAA
BX950851.1/4136202-4136229     GUUCACUGCCGUAUAGGCAGUUUAGAAA
CP000653.1/1535727-1535754     GUUCACUGCCGCACAGGCAGUUUAGAAA
BX936398.1/2964997-2964970     AUUCACUGCCGCACAGGCAGCUUAGAAA
AATN01000170.1/14109-14082     GUUCACUGCCAUAUAGGCAGCUUAGAAA
AACK01000014.1/16402-16429     CUUCACUGCCGUAUAGGCAGCUUAGAAA
AAOH01000006.1/219609-219636   GUUCACUGCCACACAGGCAGCUUAGAAA
CP000503.1/3947718-3947745     GUUCUCUGCCGCACAGGCAGCUUAGAAA
CP000542.1/1609263-1609236     GUUCACUGCCGGAUAGGCAGCUCAGAAA
CR628339.1/43303-43276         GUUCACUGCCGUACAGGCAGCUUAGAAG
CR378681.1/97619-97592         GUUCACUGCCGCACAGGCAGCUUAGAGA
CP000744.1/1205223-1205250     GUUAACUGCCGUGUAGGCAGCUAAGAAA
AASE01000005.1/56884-56911     GUUCACUGCCGGACAGGCAGCUUAGAAU
CP000308.1/2201251-2201224     GUUCACUGCUGCACAGGCAGCUUAGAAA
CP000720.1/3351663-3351636     GUUCACUGCCGCACAGGCAGCUUAUAUA
AAQW01000001.1/3290233-3290206 GUUCACUGCCGUAUAGGCAGCAAAAAAU
AAZW01000025.1/63827-63854     GUGUCCUGCCGCAUAGGCAGCUAAGAAA
CP000468.1/897888-897915       GUUCACUGCCGUACAGGCAGUCUUCAAA
AAQF01000183.1/1633-1660       GUUCACUGCCGGACAGGCAGCACAGAAA
AF316504.1/2339-2366           AUUCACUGCUGAACAAGCAGCUUAGAAA
CP000510.1/2545108-2545081     GUUUACUGCCGCACAGGCAGCUUAGGAA
CP000749.1/3991340-3991313     GUUCACCGCCGAACAGGCGGCUUAGGUU
AE004439.1/2082067-2082094     GUUAACUGCCGUAUAGGCAGCUUAGAAA
CP001157.1/550062-550089       CUUCACUGCCGUGUAGGCAGCUCAGAAA
CP000884.1/1357751-1357778     GUUCGCUGCCGCGUAGGCAGCUCAGAAA
CP000308.1/1471576-1471603     GUUCACUGUUGUACAGGCAGCUUAGAAG
#=GC SS_cons                   :::::<<<<<_____>>>>>::::::::
#=GC RF                        GUUCACUGCCGcACAGGCAGCUUAGAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01318
#=GF ID   CRISPR-DR5
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF CL   CL00015
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   12


CP000117.1/5766392-5766428 AUUGCAAUUAACUAAAAUCCCUAUCAGGGAUUGAAAC
CP000117.1/4823716-4823752 GUUGCAACACCACAUAAUCCCUAUUAGGGAUUGAAAC
CP000117.1/5229246-5229282 GUUUCUAUUAACACAAAUCCCUAUCAGGGAUUGAAAC
CP000117.1/1237074-1237110 GUUUUAAUUAACAAAAAUCCCUAUCAGGGAUUGAAAC
BA000019.2/3840701-3840737 GUUGCAACACCAUAUAAUCCCUAUUAGGGAUUGAAAC
CP000117.1/5229101-5229137 GUUUCUAUUAACACAAAUCCCUAUCAGGGAUUGAAAG
CP000117.1/2398703-2398667 GUUAAAACCCUCUAAAAUCCCUAUCAGGGAUUGAAAC
AAVU01000022.1/81169-81133 GUUACAAUUACCAAUAAUCCCUAUUAGGGAUUGAAAC
Z47161.1/118-82            GUUUAAACUUUAUAAAAUCCCUUUUAGGGAUUGAAAC
AAZV01000053.1/430-394     GUUGAAAUUCACCAAAAUCCCUUUGAGGGAUUGAAAC
AACY023784975.1/255-219    UUUCGGACAAAAUAAAAUCCCUUUUAGGGAUUUGAAC
CP001037.1/1228952-1228988 AUUGCAAUUUAUCAAAAUCCCUAUUAGGGAUUGAAAC
#=GC SS_cons               :::::::::::::::<<<<<<<___>>>>>>>:::::
#=GC RF                    GUUgcAAUUaAcuAAAAUCCCUAUuAGGGAUUGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01319
#=GF ID   CRISPR-DR6
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   39.40
#=GF NC   38.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   7


BA000001.2/1118970-1118941 GUUCCAAUAAGACUAAAAUAGAAUUGAAAG
BA000001.2/638821-638850   GUUCCAAUAAGACUAUAAGAGAAUUGAAAG
AP006878.1/835889-835918   GUUGCAAUAAGACUCUAAGAGAAUUGAAAG
BA000001.2/994690-994719   GUUCCAAUAAGACUAAAAUAGAAUUGAAAC
AJ248288.1/260196-260225   GUUCCAAUAAGACUAAAAUAGAAUUGAAAG
AE009950.1/698963-698992   GUUCCAAUAAGACUACAAAAGAAUUGAAAG
AE009950.1/698159-698188   GUUACAAUAAGACUAAAAUAGAAUUGAAAG
#=GC SS_cons               ::::<<<<______________>>>>::::
#=GC RF                    GUUCCAAUAAGACUAaAAuAGAAUUGAAAG
//
# STOCKHOLM 1.0

#=GF AC   RF01320
#=GF ID   CRISPR-DR7
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   36.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00015
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   10


AE010299.1/2381088-2381124 AUUCGCGAGCAAGAUCCACUAAAACAAGGAUUGAAAC
AE010299.1/2369655-2369691 AUUCGAGAGCAAGAUCCACUAAAACAAGGAUUGAAAC
AE008384.1/675413-675377   AUUCGCGAGCAAAAUCCAUUAAAACAAGGAUUGAAAC
AAWS01000020.1/72665-72629 CUUUCAGAGCAACAUCCAUUAAAACAAGGAUUGAAAC
CP000099.1/1665852-1665888 UAUCACGAAGAGUAUCCACUAAAACAAGGAUUGAAAC
ABBZ01003958.1/301-337     GCUUGCGAGCGAUAUCCACUACAACAAGGAUUGAAAC
CAAN02335272.1/2-38        GUCUGAAAGACUAAUCCACUACAACAAGGAUUGAAAC
ABBV01004124.1/127-91      GUUAAAGUAGAGUAUCCAUUAAAACAAGGAUUGAAAC
CP000743.1/1122352-1122388 GUCUAAAAGACACAUCCAUUAAAACAAGGAUGGAAAC
AACY020724281.1/153-117    AUCAAAAUGUAAAAUCCAUCAAAACAAGGAUUGAAAC
#=GC SS_cons               ::::::::::::<<<<<__________>>>>>:::::
#=GC RF                    gUUugAGAGcAAaAUCCAuUAAAACAAGGAUuGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01321
#=GF ID   CRISPR-DR8
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   39.50
#=GF NC   36.40
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   5


CP000492.1/2392221-2392257 GUUUCAAUCCCUCUUAAUACGUCAGGUCUUAAUCAAC
CP001101.1/1364064-1364028 GUCUCAAUCCCCUUUAUCCAAGCGGGUCUUCAUCUAC
CP000859.1/861183-861217   GUCGCAAUCCCCUCUAAC--AGCGGGUCUCUUCCUUC
CP001108.1/2174970-2175006 GUCUCAAUCCCCCUUACUCAAUCGGGUCUUCCUACAC
CP001101.1/1354261-1354225 GUCUCAAUCCCCUGUAGCUAAUCGGGUCUUCCUACAA
#=GC SS_cons               :::::<<-<<<--<<_____>>->>>>->::::::::
#=GC RF                    GUCUCAAUCCCCUcUAaccAAgCGGGUCUUcaUcuAC
//
# STOCKHOLM 1.0

#=GF AC   RF01322
#=GF ID   CRISPR-DR9
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.40
#=GF NC   44.60
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   7


CP000148.1/1195629-1195665 GUAGCGCCCGCCUACAUAGGCGGGCGAGGAUUGAAAC
AP006840.1/357447-357483   GUAGCACCCGGCCGCGAGGCCGGGUGAGGAUUGAAAC
AL954747.1/921600-921636   GUAGCGCCCGGUCACCAGACCGGGCGAGGAUUGAAAC
CP000267.1/4371048-4371084 GGAUCGCCCGGCAUUCAUGUCGGGCGCGGAUUGAAAC
CP000698.1/3158841-3158805 GAAGCGCCCGCCUUCAAUGGCGGGCGAGGAUUGAAAC
CP000450.1/1044889-1044853 GUAGCGCCCGGUCACCCGACUGGGCGAGGAUUGAAAC
CP001390.1/3767264-3767228 GUAGCGCCCGUCUGUAAAGGCGGGCGAGGAUUGAAAC
#=GC SS_cons               ::::<<<<<<<<<____>>>>>>>>>:::::::::::
#=GC RF                    GUAGCGCCCGgCcaCaAgGcCGGGCGAGGAUUGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01323
#=GF ID   CRISPR-DR10
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   39.80
#=GF NC   36.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   5


CP000686.1/3785723-3785687 GAAGCGACCACUGCCCCGCAAUGAAGGGGAUUGAAAC
CP000230.1/3525183-3525219 CUCGCAGCCCUUGCCCCGCUAUCGAGGGGACUGAAAC
CP000230.1/2668870-2668906 CUCGCAGCCUAUGCCCCGCCACCGAGGGGACUGAAAC
CP001364.1/4549202-4549238 CAGCAGAGCAUUGCCCCGCAAUGAAGGGGUUUGAAAC
CP000804.1/3452474-3452438 AAAAAAACAAAAGCCCCGCCAUGAAGGGGAUUGAAAC
#=GC SS_cons               :::::::::::<<<<<<________>>>>-->>::::
#=GC RF                    caagcAACCauUGCCCCGCaAUGAAGGGGAUUGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01324
#=GF ID   CRISPR-DR11
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   56.00
#=GF NC   35.40
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   5


AE009439.1/1328636-1328671 GUUUCAUUACCCGUAUUAUUGCGGGUUAAUUGCGAG
AE009439.1/1112486-1112521 GUUUCAUUACCCGUAUUAUUACGGGUUAAUUGCGAG
AE009439.1/1363323-1363358 GUUUCAUUACCCAUAUUAUUGCGGGUUAAUUGCGAG
AE009439.1/1362609-1362644 UAUUAUUUACCCAUAUUAUUACGGGUUAAUUGCGAG
AE009439.1/1297217-1297252 GUUUCAUUACCCGUGUUAUUACGGGUUAAUUGCGAG
#=GC SS_cons               ::::::::<<<<<<<____>>>>>>>::::::::::
#=GC RF                    GUUUCAUUACCCGuAUUAUUaCGGGUUAAUUGCGAG
//
# STOCKHOLM 1.0

#=GF AC   RF01325
#=GF ID   CRISPR-DR12
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.30
#=GF NC   36.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   5


CT573213.2/6037250-6037221 GUUGCGAUCCCUCCAGGGAUGAUCAGCGAC
CP000667.1/1140523-1140494 GUUGCGAUCCCUCCAGGGGUGAUGAGCGAC
CT573213.2/6604633-6604662 GUUGCUAUCCCUCUAGGGAUGAUCAGCGAC
CP000850.1/4224813-4224784 GUUGCGAUCCCUCCAGGCGUGAUAAGCAAC
CP000820.1/1655562-1655591 GUUGCGAUCCCCCCAGGGGUGAUCAGCGAC
#=GC SS_cons               <<<<<-<<<<<____>>>>>----->>>>>
#=GC RF                    GUUGCGAuCCCUCCAGGGgUGAUcAGCGAC
//
# STOCKHOLM 1.0

#=GF AC   RF01326
#=GF ID   CRISPR-DR13
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.10
#=GF NC   36.50
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   4


L77117.1/507952-507981   GUUAAAAUCAGACCGUUUCGGAAUGGAAAC
L77117.1/448-477         AUUAAAAUCAGACCGUUUCGGAAUGGAAAU
L77117.1/1049939-1049968 AUUAAAAUAAGACCGUUUCGGAAUGGAAAC
L77117.1/429543-429572   GUUAAAAUCAGACCGAUUCGGAAUGGAAAC
#=GC SS_cons             ::::::::::::<<<<<____>>>>>::::
#=GC RF                  aUUAAAAUCAGACCGuUUCGGAaUGGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01327
#=GF ID   CRISPR-DR14
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   45.30
#=GF NC   44.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00014
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF **   seedtax: Bacteria; Viruses
#=GF SQ   5


AM180355.1/3397589-3397617   AUUUACAUUCCAUAUAGUUAAUCUAAAAC
AM180355.1/3456730-3456758   AUUUACAUACCACUUAGUUAAUAUAAAAC
AM180355.1/2907861-2907889   AUUUACAUUCCAUAUAGUUAAUAUAAAAC
AAML04000013.1/111005-111033 CUUUACAUACCACAUAGUUGAUAUAAAAC
ABDQ01000003.1/138633-138661 AUUUACAUAUCACAUAGUUAAUAUAAAAC
#=GC SS_cons                 :::::::::::::::::::::::::::::
#=GC RF                      AUUUACAUaCCACAUAGUUAAUAUAAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01328
#=GF ID   CRISPR-DR17
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   42.00
#=GF TC   42.30
#=GF NC   40.40
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00014
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


CP000852.1/232643-232667   CUUUCUAAUCCCUUUUGGGAUUUUC
CP000852.1/370265-370289   CUUUCUAAUCCCUUUUGGGAUUUAC
CP000852.1/1700284-1700308 CUUUCUAAUCCCUCUUGGGAUUUUC
#=GC SS_cons               ::::::<<<<<<____>>>>>>:::
#=GC RF                    CUUUCUAAUCCCUUUUGGGAUUUuC
//
# STOCKHOLM 1.0

#=GF AC   RF01329
#=GF ID   CRISPR-DR15
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   36.00
#=GF TC   36.00
#=GF NC   35.60
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.87 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


CP000117.1/1622870-1622906 CUUUCAACCCGCCCCUAGCCGGGAUGGUCGUUGAAAC
CP000117.1/1622724-1622760 UUUUCAACCCACCCCUAGCCGGGAUGGUCGUUGAAAC
CP001037.1/6982878-6982914 CUUUCAACCCACCCAGUACCUGGAGGGUUGUUGCCAC
#=GC SS_cons               ::::<<<<<<--<<<_____>>>-->>-->>>>::::
#=GC RF                    CUUUCAACCCACCCcuagCCgGGAuGGUcGUUGaaAC
//
# STOCKHOLM 1.0

#=GF AC   RF01330
#=GF ID   CRISPR-DR16
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   6


CP000230.1/2716038-2716074 GUCUCCCGAGGCAGUAAUGCCUCGGCCUCAUUGAAAC
CP000230.1/2716111-2716147 GUCUCCCGAGGCAGUAAUGCCUCGGCCUCAUUGAAAC
CP000230.1/2716189-2716225 GUCUCCCGAGGCAGUAAUGCCUCGGCCUCAUUGAAAC
AE017180.1/77370-77406     GUAUUCCGGGGCCAUGAUGCCCCGGCCUCAUUGAAGC
AE017180.1/77442-77478     GUAUUCCGGGGCCAUGAUGCCCCGGCCUCAUUGAAGC
AE017180.1/77517-77553     GUAUUCCGGGGCCAUGAUGCCCCGGCCUCAUUGAAGC
#=GC SS_cons               :::::<<<<<<<______>>>>>>>::::::::::::
#=GC RF                    GUaUuCCGgGGCaaUaAUGCCcCGGCCUCAUUGAAaC
//
# STOCKHOLM 1.0

#=GF AC   RF01331
#=GF ID   CRISPR-DR18
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   56.50
#=GF NC   39.20
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   6


BA000019.2/447524-447560   GUUACUUACCAUCACUUCCCCGCAAGGGGAUGGAAAC
BA000019.2/447600-447636   GUUACUUACCAUCACUUCCCCGCAAGGGGAUGGAAAC
BA000019.2/447680-447716   GUUACUUACCAUCACUUCCCCGCAAGGGGAUGGAAAC
CP000804.1/2548856-2548892 GUGGAAAAACCCCAAAUCCCCGCCAGGGGAUUGAAAC
CP000804.1/2548778-2548814 GUGGAAAAACCCCAAAUCCCCGCCAGGGGAUUGAAAC
CP000804.1/2548478-2548514 GUGGAAAAACCCCAAAUCCCCGCCAGGGGAUUGAAAC
#=GC SS_cons               ::::::::::::::::<<<<<____>>>>>:::::::
#=GC RF                    GUuaauuAaCauCAauUCCCCGCaAGGGGAUuGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01332
#=GF ID   CRISPR-DR19
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   41.20
#=GF NC   38.30
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   4


CP000686.1/2323114-2323150 AUUUCGGCAAUUUCGACUCGUUGAAGAGUACUGAAAC
CP001337.1/699911-699875   CUUUCAAUACUUUCGGCUCACGGUAGAGCACUGAAAC
CP000804.1/4312467-4312502 UUUCCGAU-UUUUCGGCUCGCAGAAGAGCACUGAAAU
CP001364.1/3985384-3985420 CUUUCAACAAUUUCGGCUCACGGUAGAGCACUGAAAC
#=GC SS_cons               ::::::::::<<<<-<<<<______>>>>--->>>>:
#=GC RF                    cUUUCgAuAaUUUCGGCUCgCgGaAGAGCACUGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01333
#=GF ID   CRISPR-DR20
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   42.00
#=GF TC   44.10
#=GF NC   35.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


AM420293.1/5688772-5688807 CCGUCACCGACGCGCAGCG-UCGGUCCUCAUUGCGGC
AM420293.1/5697537-5697572 CUGUCACCGGCGCCAAGCG-UCGGUCCUCAUUGCGGC
CP000850.1/5064928-5064964 CCUUCACCGACCCAACGCGGUCGGUCUCCGUUGCGGG
#=GC SS_cons               :::::<<<<<<<<___>>>.>>>>>::::::::::::
#=GC RF                    CCgUCACCGaCGCaAaGCG.uCGGUCcUCAUUGCGGc
//
# STOCKHOLM 1.0

#=GF AC   RF01334
#=GF ID   CRISPR-DR21
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   50.00
#=GF NC   44.60
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP001364.1/731270-731306 UUUUCAAUCCCCUCGCGGGGAUUUUGGUUUUUUGAAG
CP001364.1/723288-723324 GUUUCAAUCCCCUCGCGGGGAUUUUGGUUUUUUGAAG
#=GC SS_cons             :::<<<<-<<<<____>>>>--->>>>::::::::::
#=GC RF                  uUUUCAAUCCCCUCGCGGGGAUUUUGGUUUUUUGAAG
//
# STOCKHOLM 1.0

#=GF AC   RF01335
#=GF ID   CRISPR-DR22
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   49.00
#=GF TC   49.20
#=GF NC   48.80
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   9


CP000419.1/1377759-1377794   GUUUUGGAACCAUUCGAAACAACACAGCUCUAAAAC
AL596173.1/159652-159687     GUUUUGUUAGCAUUCAAAAUAACAUAGCUCUAAAAC
AAFV01000057.1/1625-1660     GUUUUGGGACCAUUCAAAACAGCAUAGCUCUAAAAC
AADQ01000049.1/8488-8523     GAUUUGGUAGCAUUCAAAAUAACAUAGCUCUAAAAC
CP000024.1/1346659-1346694   GUUUUGAAACCAUUCGAAACAACACAGCGAGUUAAA
AE009949.1/853018-852983     GUUUUGGGACCAUUCAAAACAGCAUAGCAAGUUAAA
AADQ01000049.1/8224-8259     GUUUUGGUAGCAUUCGAAAUAACAUAGCUCUAAAAC
AE014133.2/1335038-1335073   GUGUUGGAAUCAUUCGAAACAACACAGCAAGUUAAA
AARP04000001.1/315365-315330 GUUUUGGUAGCAUUCAAAAUAACAUAGCUCUAAAAA
#=GC SS_cons                 <<<<<<<______>>>>>>>::::::::::::::::
#=GC RF                      GUUUuGGuAcCAUUCaAAACAACAUAGCUCUAAAAa
//
# STOCKHOLM 1.0

#=GF AC   RF01336
#=GF ID   CRISPR-DR23
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   48.90
#=GF NC   39.10
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


CP000113.1/8888031-8888066 GUGCUCAACGCCUUCCGGCAUCACGGCGAGCGGCAC
CP000113.1/8862320-8862355 GUGCUCAACGCCUUUCGGCAUCACGGCGAGCGGGAC
CP000113.1/8860814-8860849 ACGCUCAACGCCUUUCGGCAUCACGGCGAGCGGGAC
#=GC SS_cons               :<<<<---<<<<____________>>>>>>>>::::
#=GC RF                    GuGCUCAACGCCUUUCGGCAUCACGGCGAGCgGgAC
//
# STOCKHOLM 1.0

#=GF AC   RF01337
#=GF ID   CRISPR-DR24
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.90
#=GF NC   34.80
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   4


AY596293.1/36472-36501     GUUUCAGACGGACCCUUGGGCGGUUGAAGU
AY596293.1/50017-50046     GUUACAGACGGACCCUCGUGGGGUUGAAGC
CR936258.1/38286-38315     GUUUCAGACGAACCCUUGUGGGGUUGAAGC
AM180088.1/1383441-1383470 GUUUCAGAUGAACCCUUGUUGGGUUGAAGU
#=GC SS_cons               ::::::::::<<<<<_____>>>>>:::::
#=GC RF                    GUUUCAGACGaACCCUUGUGGGGUuGAAGu
//
# STOCKHOLM 1.0

#=GF AC   RF01338
#=GF ID   CRISPR-DR25
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   36.00
#=GF TC   36.40
#=GF NC   35.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00014
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   5


CP000077.1/1830035-1830011 CUUUCAAUCCCUUUUGGGAUUCAUC
BA000023.2/39769-39745     CUUUCAAUUCCUUUUGGGAUUCAUC
CP000077.1/1786560-1786584 CUUUCAAUCCCUUAUGGGAUUCUUC
BA000023.2/35736-35712     CUUUCAAUUCCUUUUGGGAUUCAUC
DQ831675.1/3421-3445       CUUUCAAUUCCUUUUGGGAUUAAUC
#=GC SS_cons               :::::<<<<<<____>>>>>>::::
#=GC RF                    CUUUCAAUuCCUUUUGGgAUUCAUC
//
# STOCKHOLM 1.0

#=GF AC   RF01339
#=GF ID   CRISPR-DR27
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.10
#=GF NC   34.50
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


CP000575.1/598118-598094 CUUUCAAUUCUUUCUAUGUUGUUAC
CP000575.1/351124-351100 CUUUCAAUUCUUUCUGUGUUGUUAC
CP000575.1/602999-603023 CUUUCAAUUCUUUCUGUGUUGCUAC
#=GC SS_cons             ::::<<<<_________>>>>::::
#=GC RF                  CUUUCAAUUCUUUCUGUGUUGUUAC
//
# STOCKHOLM 1.0

#=GF AC   RF01340
#=GF ID   CRISPR-DR29
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   39.70
#=GF NC   38.00
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000249.1/4015546-4015582 GCAGCGCCGGGCGUCCGCGCCCGGCGAGGUUCCCAAC
CP000249.1/4015617-4015653 GCAGCGCCGGGCGUCCGCGCCCGGCGAGGUUCCCAAC
#=GC SS_cons               ::::<<<<<<<<<____>>>>>>>>>:::::::::::
#=GC RF                    GCAGCGCCGGGCGUCCGCGCCCGGCGAGGUUCCCAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01341
#=GF ID   CRISPR-DR30
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   54.30
#=GF NC   34.00
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.8 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


CP000875.1/1607714-1607751 GUUUUAAUCCCCCAGAGAGGAUUCAGGUCUUUCGAAUA
CP000875.1/1607488-1607525 GUCCAGCCCUCCCAGAGAGGAUUCAGGUCUUUCGAAUU
CP000875.1/1605243-1605280 GCUUUUAUCCCCCAAAGAGGAUUCAGGUCUUUCGAAUC
#=GC SS_cons               ::::::::::::::<<<<<<_______>>>>>>:::::
#=GC RF                    GUUUuaAUCcCCCAGAGAGGAUUCAGGUCUUUCGAAUu
//
# STOCKHOLM 1.0

#=GF AC   RF01342
#=GF ID   CRISPR-DR32
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   48.00
#=GF TC   49.60
#=GF NC   42.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000875.1/3043293-3043329 AUUUCAAUCAACGCCCCGAGGAAGAGGGGAUUAAAAC
CP000876.1/135129-135165   GUAAGAAUCAUCGCCCCGACGAAGAGGGGUUUAAAAC
#=GC SS_cons               :::::::::::::<<<<________>>>>::::::::
#=GC RF                    aUuugAAUCAuCGCCCCGAgGAAGAGGGGuUUAAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01343
#=GF ID   CRISPR-DR33
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   39.30
#=GF NC   38.80
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


BA000022.2/2610662-2610698 CGUUUCCAAACCAUUGAUGCCGUAAAGCGUUUGGCGC
AE016823.1/1126696-1126660 ACUUACAAAAAUCGGGAUGCCGUUAGGCGUUGAGCAC
CP001221.1/3162259-3162295 UCUGAAUAUAACUUUGAUGCCGUUAGGCGUUGAGCAC
#=GC SS_cons               :::::::::::::::<<<<<<____>>>>>>::::::
#=GC RF                    ucUuacuAAAACuuuGAUGCCGUuAGGCGUUgAGCAC
//
# STOCKHOLM 1.0

#=GF AC   RF01344
#=GF ID   CRISPR-DR34
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   36.00
#=GF NC   34.60
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.00 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   5


AL157959.1/609469-609504   GUUGUAGCUCCCUUUCUCAUUUCGCAGUGCUACAAU
CP000746.1/436837-436802   GUUGUAGCUCCCUUUUUCAUUUCGCAGUGCUAUAAU
AE004969.1/81551-81586     GUUAUUGCUCCCGUUCUCAUUUCGCAGUGCUACAAU
CP000019.1/4783-4748       GUUUUAACUCCCUUUCUCAUUUCGCAAUGCUACAAU
AE004439.1/1319982-1320017 GUUGUAGUUCCCUCUCUCAUUUCGCAGUGCUACAAU
#=GC SS_cons               <<<<<<<<____________________>>>>>>>>
#=GC RF                    GUUgUAGCUCCCUUUCUCAUUUCGCAGUGCUAcAAU
//
# STOCKHOLM 1.0

#=GF AC   RF01345
#=GF ID   CRISPR-DR35
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.30
#=GF NC   34.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000450.1/2358073-2358038 GUCUCAAUCCCUUUGAAAUCAGGGCAUGGGUGUUUC
AL954747.1/140228-140263   GUCUCAAUCCCUUUGAAAUCAGGGCAUCGGUGUUUC
#=GC SS_cons               ::<<<<--<<<<________>>>>-->>>>::::::
#=GC RF                    GUCUcAAUCCCUUUGAAAUCAGGGCAUgGGUGUUUC
//
# STOCKHOLM 1.0

#=GF AC   RF01346
#=GF ID   CRISPR-DR36
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   38.00
#=GF TC   38.40
#=GF NC   37.30
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


AE017222.1/153333-153368 GUUGCAAGGGAUUGAACCCCGUAAGGGGAUUGCGAC
M33159.1/6325-6290       GUUGCAAGGGAUUGAGCCCCGUAAGGGGAUUGCGAC
AP008227.1/210807-210842 GUUGCAAGGGAUUGAGCCCCGUAAGGGGAUUGAUAC
#=GC SS_cons             ::::::::::::::<<<<<<____>>>>->>:::::
#=GC RF                  GUUGCAAGGGAUUGAgCCCCGUAAGGGGAuUGcgAC
//
# STOCKHOLM 1.0

#=GF AC   RF01347
#=GF ID   CRISPR-DR37
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   41.60
#=GF NC   35.00
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


BA000019.2/2179133-2179167 GUUUCCAUCCCCGUGAGGGGUAAGAGAUUAAAAAC
CP000117.1/4244596-4244630 GUUUCCAUCCCCGUGAGGGGUAAAGGAAUUAAAAC
AAXW01000070.1/13590-13624 GUUUCCAUCCCCGUGAGGGGAAUAAGUGUUUUGAA
#=GC SS_cons               :<<<----<<<<____>>>>---->>>::::::::
#=GC RF                    GuUuCCAUCCCCGUGAGGGGuAaAaGaaUUaaAAc
//
# STOCKHOLM 1.0

#=GF AC   RF01348
#=GF ID   CRISPR-DR38
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   44.00
#=GF TC   45.80
#=GF NC   42.10
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   5


CP000492.1/2383319-2383285 CUUUAUAUCUUAUUGCACUCAUAGAGGAUUGAAAC
AASE01000021.1/30301-30335 GAUCAUAUCUUAUUGCACUCAUAGAGGAUUGAUUA
CP001101.1/2492568-2492534 AACUAUAUCUAAUCGCACUCAUGGAGAAUUGAAAC
CP001110.1/2546719-2546753 CAUCAUAUCUUAUUGCACGCAUAGCGGAUUGAAAC
CP001097.1/1011761-1011795 CUUUAUAUCUAAUUGCACUCAUUGAGGAUUGAAAC
#=GC SS_cons               :::::::::::::::::<<<___>>>:::::::::
#=GC RF                    cAUUAUAUCUuAUUGCACUCAUaGAGGAUUGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01349
#=GF ID   CRISPR-DR40
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   42.00
#=GF TC   42.60
#=GF NC   41.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.5 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


ABDP01000018.1/9959-9988   GUUUAACUUCUACAUUAGAUGUAUUUAAAC
ABDP01000018.1/10281-10310 AUUUAACUUCUACAUUAUAUGUAUUUAAAC
ABDP01000018.1/11108-11137 GUUUAACUUCUAUAUUAGAUAUAUUUAAAC
#=GC SS_cons               :<<<<<----<<<<<___>>>>>->>>>>:
#=GC RF                    GUUUAACUUCUACAUUAgAUGUAUUUAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01350
#=GF ID   CRISPR-DR41
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   36.00
#=GF TC   36.20
#=GF NC   35.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


BA000001.2/152106-152078 CUUUCCACACUACUAAGUUCUACGGAAAC
AJ248284.1/175298-175326 CUUUCCACACUAUUUAGUUCUACGGAAAC
#=GC SS_cons             :<<<<<--<<<____>>>----->>>>>:
#=GC RF                  CUUUCCACACUAuUuAGUUCUACGGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01351
#=GF ID   CRISPR-DR42
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   41.60
#=GF NC   33.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.5 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


L77117.1/471658-471686   GUUUCCAUACAACAAUGUUCUUCUUAAAC
L77117.1/1177478-1177506 GUUUCCAUACAAUAUUGUUCUUCUUAAAC
DQ516721.1/34-62         GUUUCCAUACAAUACUGUUCUCCUUAAAC
#=GC SS_cons             :::::::::::::::::::::::::::::
#=GC RF                  GUUUCCAUACAAuAuUGUUCUuCUUAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01352
#=GF ID   CRISPR-DR43
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00014
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


CP000764.1/2136193-2136221 CUUUAUAUCCCACUACGUUCAGAUAAAAC
AAJM01000009.1/9302-9274   GUUUAUAUCCCACACAGUUCAGAUAAAAC
CP000764.1/2126031-2126059 CUUUCUAUUCCACUACGUUCAGAUAAAAC
#=GC SS_cons               :::::::::::::::::::::::::::::
#=GC RF                    cUUUaUAUcCCACuacGUUCAGAUAAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01353
#=GF ID   CRISPR-DR44
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.80
#=GF NC   34.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.8 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF **   seedtax: Bacteria; Archaea
#=GF SQ   3


AE017261.1/62530-62557     CUUCCAUACUAUCUAGUAAUUCUUAAAC
BA000011.4/122589-122616   CUUCCAUACUAACUAGUACAUCUUAAAC
AAXW01000052.1/29708-29681 CUUCAAUACUAUCUAGUAAUUCUAAUAG
#=GC SS_cons               ::::::<<<<____>>>>::::::::::
#=GC RF                    CUUCcAUACUAuCUAGUAAuUCUuAaAc
//
# STOCKHOLM 1.0

#=GF AC   RF01354
#=GF ID   CRISPR-DR45
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.10
#=GF NC   36.60
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


CP000561.1/1669259-1669282 CUUUCAAUCCUCUUCUUGAGAUUC
CP000660.1/1016099-1016076 CUUUCAAUCCUCUUUUUGAGAUUU
CP000660.1/999619-999596   CUUUCAAUCCUCUUUUUGAGAUUC
#=GC SS_cons               :<<<<<<________>>>>>>:::
#=GC RF                    CUUUCAAUCCUCUUUUUGAGAUUc
//
# STOCKHOLM 1.0

#=GF AC   RF01355
#=GF ID   CRISPR-DR26
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   39.30
#=GF NC   38.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   4


CP000504.1/990-1014        GUUUCUACUAUCUUUUGAUUUCUGG
CP000504.1/921-945         GUUUCUACUAUCUUUUGAUUUCUGG
CP000660.1/1039289-1039265 GUUUCAACUAUCUUUUGAUUUCGGC
AE009441.1/46203-46179     GUUUCAACUAUCUUUUGAUUUCUGG
#=GC SS_cons               :::::::::<<<____>>>::::::
#=GC RF                    GUUUCaACUAUCUUUUGAUUUCUGG
//
# STOCKHOLM 1.0

#=GF AC   RF01356
#=GF ID   CRISPR-DR28
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


CP000686.1/988082-988059 GGCAAAGCCCGCCUGCGCGGGCUA
CP000686.1/987926-987903 GGCAAAGCCCGCCUGCGCGGGCGA
CP000686.1/720650-720627 AGCGAAGCCCGCCUGCGCGGGCUA
#=GC SS_cons             :::::<<<<<<<____>>>>>>>:
#=GC RF                  GGCAAaGCCCGCCUGCGCGGGCuA
//
# STOCKHOLM 1.0

#=GF AC   RF01357
#=GF ID   CRISPR-DR31
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   35.60
#=GF NC   34.30
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


AP008227.1/239143-239107 GUUUCAAUCCUCUACGAGGCUAACGAGGUUUGCAACC
AP008227.1/228052-228088 GUUUCAAUCCUCUACGAGGCUGACGGGGUUUGCAACG
AE017222.1/204195-204159 GUAUCAAUCCUCUACGAGGCUAAAGAGGUUUGCAACC
#=GC SS_cons             <<<-<<<-<<<<____________>>>>->>>->>>:
#=GC RF                  GUuUCAAUCCuCUACGAGGCUAAcGaGGUUUGCaACc
//
# STOCKHOLM 1.0

#=GF AC   RF01358
#=GF ID   CRISPR-DR39
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   39.20
#=GF NC   38.30
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


L77117.1/352439-352469 AUUUCCAUUCCCCGAGGGAUCUGAUUUUACA
L77117.1/92501-92531   AUUUCCAUCCUCCAAGAGGUCUUAUUUUAAU
DQ516865.1/1968-1938   AUUUCCAUCCUCCAAGAGGUCUGAUUUUAAC
#=GC SS_cons           ::::::::<<<<___>>>>::::::::::::
#=GC RF                AUUUCCAUcCuCCAAGaGgUCUgAUUUUAau
//
# STOCKHOLM 1.0

#=GF AC   RF01359
#=GF ID   CRISPR-DR46
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   52.90
#=GF NC   43.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000875.1/3176591-3176628 AUUCAAAUAACCAAAAUCCUCGGAAGGGGAUUAAAACG
CP000875.1/1527845-1527808 CUUCAAAUAACCAAAAUCCUCGGAAUCGGAUUCAACAG
#=GC SS_cons               ::::::::::::::<<<<<<<____>>>>>>>::::::
#=GC RF                    aUUCAAAUAACCAAAAUCCccGGAAggGGAUUaAAaaG
//
# STOCKHOLM 1.0

#=GF AC   RF01360
#=GF ID   CRISPR-DR47
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   40.10
#=GF NC   36.00
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


AE000782.1/1694068-1694104 GUAAGAAAGGGAGGCUCCUGAAAAUGGAGAUUGAAAG
AE000782.1/1691005-1691041 AUAAGAAAGGGAGGCUCCUGAAAAUGGAGAUUGAAAG
#=GC SS_cons               ::::::::::::::<<<<_______>>>>::::::::
#=GC RF                    aUAAGAAAGGGAGGCUCCUGAAAAUGGAGAUUGAAAG
//
# STOCKHOLM 1.0

#=GF AC   RF01361
#=GF ID   CRISPR-DR48
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   60.60
#=GF NC   37.10
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


AE015924.1/2068868-2068904 GUCUUAAUAGCCUUACGGACUGUGUAUGUAUAGUGAG
AE015924.1/2068431-2068467 GUCUUAAUAGCCUUACAGACUGUGUAUGUAUAGUGAG
#=GC SS_cons               :::::::::::<<<<<--<<_______>>--->>>>>
#=GC RF                    GUCUUAAUAGCCUUACaGACUGUGUAUGUAUAGUGAG
//
# STOCKHOLM 1.0

#=GF AC   RF01362
#=GF ID   CRISPR-DR49
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   41.00
#=GF TC   41.00
#=GF NC   40.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


CR626927.1/4663161-4663207 GUUGUGAUUUGCUUUCAAAUUAGUAUCUUUGAACCAUUGGAAACAGC
CR626927.1/4661170-4661216 GUUAUGAUUUACUUUCAAAUUAGUAUCUUUGAACCAUUGGAAACAGC
AAXE02000104.1/43195-43149 GUUGUGAUUUACUUUCAUUUUAGUAUAUUUGAACCAUUAGAAACAAC
#=GC SS_cons               :::::::::::::<<<<<<________>>>>>>::::::::::::::
#=GC RF                    GUUGUGAUUUACUUUCAaaUUAGUAUcuuUGAACCAUUGGAAACAGC
//
# STOCKHOLM 1.0

#=GF AC   RF01363
#=GF ID   CRISPR-DR50
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   47.00
#=GF TC   48.10
#=GF NC   44.10
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


AM398681.1/1735485-1735530 GUUGGUAAUUAUAAGCUAAAAUACAAUUUUGAAAGCAAUUCACAAC
AAPR01000004.1/7933-7978   CCUGUGAAUUAUCACUAAAAAUACAAUUUUGAAAGCAAUUCACAAC
#=GC SS_cons               ::<<<<<<<<-----<<<<<______>>>>>----->>>>>>>>::
#=GC RF                    guUGugAAUUAUaAgcaAAAAUACAAUUUugAAAGCAAUUcaCAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01364
#=GF ID   CRISPR-DR51
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   51.90
#=GF NC   33.20
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


BX571661.1/139010-139046 GCAACACUUUAUAGCAAAUCCGCUUAGC-CUGUGAAAC
BX571661.1/137355-137318 GCAACACUUUAUAGCAAAUCCGUUCGAUGCCUUGAAAU
#=GC SS_cons             ::::<<<-----<<<______>>>------->>>::::
#=GC RF                  GCAACAcUUUAUAgCAAAUCCGcUuaauGCugUGAAAu
//
# STOCKHOLM 1.0

#=GF AC   RF01365
#=GF ID   CRISPR-DR52
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   50.00
#=GF TC   61.70
#=GF NC   35.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


AP004311.1/19865-19901 CUUUCCUUCUACUAAUCCCGGCGAUCGGGACUGAAAC
AP004311.1/17617-17653 CUUUCCUUCUACUAAUCCCGGCGAUCGGGACUGAAAC
#=GC SS_cons           ::::::::::::<<-<<<<<_____>>>>>->>::::
#=GC RF                CUUUCCUUCUACUAAUCCCGGCGAUCGGGACUGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01366
#=GF ID   CRISPR-DR53
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   51.00
#=GF NC   39.60
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CR522870.1/199064-199100 GCUUCAAUGUAGUCACCCCUUUCGAGGUGAUUGAUAC
CR522870.1/198212-198248 CCUUCAAUGUAGUCACCCCUUUCGAGGUGAUUGAUAC
#=GC SS_cons             :::::::::<<<<<<<<-<____>->>>>>>>>::::
#=GC RF                  gCUUCAAUGUAGUCACCCCUUUCGAGGUGAUUGAUAC
//
# STOCKHOLM 1.0

#=GF AC   RF01367
#=GF ID   CRISPR-DR54
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   39.20
#=GF NC   38.60
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


AE016827.1/1630952-1630988 GUUUCAAUCCCUUUAAGACAGGGCAAGGUCUUUCGAC
AE016827.1/1630091-1630127 GUUUCAAUCCCUUUAAGACAGGGCAAGGUCUUUCGAU
#=GC SS_cons               :::<<---<<<<_______>>>>--->>:::::::::
#=GC RF                    GUUUCAAUCCCUUUAAGACAGGGCAAGGUCUUUCGAu
//
# STOCKHOLM 1.0

#=GF AC   RF01368
#=GF ID   CRISPR-DR55
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   41.00
#=GF TC   42.40
#=GF NC   34.80
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CR628336.1/192328-192364 CCAAUAAUCCCUCAUCUAAAAAUCCAACCACUGAAAC
CR628336.1/192403-192439 CCAAUAAUCCCUCAUCUAAAAAUUUAACUAAUGAAAU
#=GC SS_cons             :::::::::::::::::::::::::::::::::::::
#=GC RF                  CCAAUAAUCCCUCAUCUAAAAAUuuAACuAaUGAAAu
//
# STOCKHOLM 1.0

#=GF AC   RF01369
#=GF ID   CRISPR-DR56
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   35.00
#=GF TC   36.00
#=GF NC   34.40
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CR936259.1/463-499         GUCGAGACGGACUGAAAACCCAGAACGGGAUUGAAAC
CR936257.1/1579504-1579540 GUCGAGACGGACUGAAAACCCAGAAUAGGAUUGAAAC
#=GC SS_cons               :<<<<--<<--<<<______>>>-->>--->>>>:::
#=GC RF                    GUCGAGAcgGACUGAAAACCCAGAAcgGGAUUGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01370
#=GF ID   CRISPR-DR57
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   39.00
#=GF TC   39.00
#=GF NC   38.60
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   3


CP000240.1/605231-605267   GUUUCCGUCCCCUUGCGGGGAAAAGGUAGGGAUCAAC
CP000239.1/130564-130600   AACCCCUUCCCCUUGCGGGGAAAAGGUAGGGAUCAAC
AAVW01000066.1/21673-21637 GUUUCCGUCCCCUUGCGGGGAAAUGGUUAUGAAAAAC
#=GC SS_cons               ::::<<-<<<<<____>>>>>--->>:::::::::::
#=GC RF                    GuUUCCgUCCCCUUGCGGGGAAAaGGUaGgGAucAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01371
#=GF ID   CRISPR-DR58
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   38.00
#=GF TC   39.00
#=GF NC   34.70
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000239.1/1860099-1860135 AGUUCCCCCUUCGUGGGGAUCCCUAGAAAUUGGAAAC
CP000240.1/159140-159176   AGUUCUCCCUUCGGGGGGAUCCCUAGAAAUUGGAAAC
#=GC SS_cons               :::<<<<<_____>>>>>:::::::::::::::::::
#=GC RF                    AGUUCcCcCUUCGgGgGGAUCCCUAGAAAUUGGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01373
#=GF ID   CRISPR-DR60
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   50.10
#=GF NC   39.80
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000254.1/2097878-2097914 GUUUCAAUCCCUAUCGGGUUUUCUUUUCCAUUGUGAC
CP000477.1/1699343-1699307 GUUUCAAUCCCUAUCGGGUUUUCUCACUCGUUGCGAC
#=GC SS_cons               ::::::::<<<____>>>:::::::::::::::::::
#=GC RF                    GUUUCAAUCCCUAUCGGGUUUUCUuuuuCaUUGuGAC
//
# STOCKHOLM 1.0

#=GF AC   RF01374
#=GF ID   CRISPR-DR61
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   38.00
#=GF TC   38.60
#=GF NC   36.80
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000608.1/1330120-1330084   CUAACAGUAGUUUACCAAAUAAUUCAGCAACUGAAAC
ABAH01000008.1/332898-332934 CUAACAGUAGUUUACCAAAUAAUUUAGCGACUGAAAC
#=GC SS_cons                 ::::<<<<-<<<_____________>>>->>>>::::
#=GC RF                      CUAACAGUAGUUUACCAAAUAAUUuAGCaACUGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01375
#=GF ID   CRISPR-DR62
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   55.80
#=GF NC   39.90
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000609.1/744870-744906 CUAAAAGAAUAACUUGCAAAAUAACAAGCAUUGAAAC
CP000609.1/745726-745762 CUAAAAGAAUAACUUGCAAAAUAACAAGCAUUACAAU
#=GC SS_cons             ::::::::::::<<<<________>>>>:::::::::
#=GC RF                  CUAAAAGAAUAACUUGCAAAAUAACAAGCAUUaaAAu
//
# STOCKHOLM 1.0

#=GF AC   RF01376
#=GF ID   CRISPR-DR63
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   37.00
#=GF TC   37.60
#=GF NC   36.50
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00015
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000612.1/1768527-1768563 GUCAAAACACAAAAUAAUUCCCUUUGGGAAUUGAAAC
CP000612.1/1768604-1768640 GUCAAAACACAAAAUAAUUCCCUUUGGGAAUUGAACC
#=GC SS_cons               ::::::::::::::<<<<<<<<___>>>>>>>>::::
#=GC RF                    GUCAAAACACAAAAUAAUUCCCUUUGGGAAUUGAAaC
//
# STOCKHOLM 1.0

#=GF AC   RF01377
#=GF ID   CRISPR-DR64
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   40.00
#=GF TC   61.10
#=GF NC   37.50
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00015
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000742.1/127571-127607 AUACGAAACGUUGAUCCAUCAAAACAAGGAUUGAGAC
CP000742.1/127644-127680 AUACGAAACGUUGAUCCAUCAAAACAAGGAUUGAGGC
#=GC SS_cons             :::::::::::::<<<<__________>>>>::::::
#=GC RF                  AUACGAAACGUUGAUCCAUCAAAACAAGGAUUGAGaC
//
# STOCKHOLM 1.0

#=GF AC   RF01378
#=GF ID   CRISPR-DR65
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   43.00
#=GF TC   55.40
#=GF NC   38.50
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   2


CP000742.1/270079-270115 GUUUCAAUGCUUGUUCUAAUGCAUUAUGCUCUUUUAC
CP000743.1/48442-48406   AUUUCAAAGCUUGUUUUAGUGCAUUAUGCUAUUUUAC
#=GC SS_cons             :::::<<-<<-<<<______>>>---->>-->>::::
#=GC RF                  aUUUCAAuGCUUGUUuUAaUGCAUUAUGCUaUUUUAC
//
# STOCKHOLM 1.0

#=GF AC   RF01379
#=GF ID   CRISPR-DR66
#=GF DE   CRISPR RNA direct repeat element
#=GF AU   Wilkinson A; 0000-0001-7406-0151
#=GF SE   Predicted; WAR; Wilkinson A
#=GF SS   Predicted; WAR; Wilkinson A
#=GF GA   45.00
#=GF TC   50.60
#=GF NC   37.60
#=GF TP   Gene; CRISPR;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00014
#=GF DR   URL; http://crispr.u-psud.fr/crispr/CRISPRHomePage.php;
#=GF DR   SO; 0001459; CRISPR;
#=GF DR   GO; 0006952; defense response;
#=GF RN   [1]
#=GF RM   17521438
#=GF RT   The CRISPRdb database and tools to display CRISPRs and to generate
#=GF RT   dictionaries of spacers and repeats.
#=GF RA   Grissa I, Vergnaud G, Pourcel C
#=GF RL   BMC Bioinformatics. 2007;8:172.
#=GF WK   CRISPR
#=GF SQ   4


AATN01002896.1/1464-1428   AGUUUAAUCCCUUGUAGGGAUUCUUUAUUUAUGGAAC
AATN01002896.1/1747-1712   GGUUUAAUCCCUUGUAGGGAUUC-UUAUUUAUGGAAC
CP000875.1/2850594-2850558 GUUUUAAUCCCUUGUAGGGAUUCUUUAUUUAUGGAAC
CP000875.1/2054143-2054179 GUUUUAAUCCCUUGUAAGGAUUCUUUAGUUAUGGAAC
#=GC SS_cons               :::::<<<<<<<___>>>>>>>:::::::::::::::
#=GC RF                    GuUUUAAUCCCUUGUAGGGAUUCUUUAUUUAUGGAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01380
#=GF ID   HIV-1_SD
#=GF DE   Human immunodeficiency virus type 1 major splice donor
#=GF AU   Chen A
#=GF AU   Brown C
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Chen A
#=GF SS   Published; PMID:18160437
#=GF GA   30.00
#=GF TC   30.20
#=GF NC   29.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.67 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0043484; regulation of RNA splicing;
#=GF RN   [1]
#=GF RM   18160437
#=GF RT   RNA structure modulates splicing efficiency at the human immunodeficiency
#=GF RT   virus type 1 major splice donor.
#=GF RA   Abbink TE, Berkhout B
#=GF RL   J Virol. 2008;82:3090-3098.
#=GF WK   Retroviral_Psi_packaging_element
#=GF SQ   22



EF545108.1/38-56   GGCGACYGGUGAGUACGCC
S69386.1/283-301   GGCGACUGGUGAGUACGCC
K03455.1/736-754   GGCGACUGGUGAGUACGCC
M17449.1/732-750   GGCGACUGGUGAGUACGCC
M38429.1/737-755   GGCGACUGGUGAGUACGCC
U63632.1/59-77     GGCGACUGGUGAGUACGCC
M38431.1/736-754   GGCGACUGGUGAGUACGCC
U26942.1/114-132   GGCGACUGGUGAGUACGCC
M13136.1/734-752   GGCGACUGGUGAGUACGCC
M17451.1/250-268   GGCGAACGGUGAGUACGCC
K03454.1/282-300   AGCGACUGGUGAGUACGCU
M22639.1/736-754   AGCGACCGGUGAGUACGCU
M62320.1/201-219   GGCGACUGGUGAGUACGCC
AY118157.1/282-300 GGCGACUGGUGAGUACGCA
AF286227.1/83-101  GGCGACUGGUGAGUACGCU
AY451080.1/30-48   AGCGACUGGUGAGUACGCC
AF190128.1/57-75   CGCGACUGGUGAGUACGCC
X52154.1/752-770   GGCGACUGGUGAGUACGCA
DQ373063.1/283-301 GGCGACUGGUGAGUACGCC
AY169968.1/277-295 GGCGACUGGUGAGUACGCA
DQ373064.1/281-299 GGCGACUGGUGAGUACGCC
AF465242.1/809-827 AGCGACCGGUGAGUACGCU
#=GC SS_cons       <<<<<<<____>>>->>>>
#=GC RF            GGCGACUGGUGAGUACGCC
//
# STOCKHOLM 1.0

#=GF AC   RF01381
#=GF ID   HIV-1_SL3
#=GF DE   HIV-1 stem-loop 3 Psi packaging signal
#=GF AU   Chen A
#=GF AU   Brown C
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Chen A
#=GF SS   Published; PMID:18713870
#=GF GA   33.00
#=GF TC   33.00
#=GF NC   32.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0019074; viral RNA genome packaging;
#=GF RN   [1]
#=GF RM   18713870
#=GF RT   MS3D structural elucidation of the HIV-1 packaging signal.
#=GF RA   Yu ET, Hawkins A, Eaton J, Fabris D
#=GF RL   Proc Natl Acad Sci U S A. 2008;105:12248-12253.
#=GF WK   Retroviral_Psi_packaging_element
#=GF SQ   19


X04415.1/323-345   UGACUAGCGG-AGGCUAGAAGGAG
S69386.1/310-332   UGACUAGCGG-AGGCUAGAAGGAG
K03454.1/309-331   UGACUAGCGG-AGGCUAGAAGGAG
M22639.1/763-785   UGACUAGCGG-AGGCUAGAAGGAG
M62320.1/230-252   UGACUAGCGG-AGGCUAGAAGGAG
K03455.1/763-785   UGACUAGCGG-AGGCUAGAAGGAG
M38429.1/763-785   UGACUAGCGG-AGGCUAGAAGGAG
AY451200.1/56-78   UGACUAGCGG-AGGUUAGAAGAAG
DQ054367.2/722-744 UGACUAGCAG-AGGCUAGAAGGGG
AY451087.1/57-79   UGACUAGCGG-AGGCUAGGAGAAG
EF178342.1/85-107  UGACUAGCGG-AGACUAGAAGAAA
AY456324.1/79-101  UGACUAGCGG-AGGCUAGAAGGGA
EF178429.1/87-109  UGACUAGCGG-AGGCUAUAAAGAG
AF197338.1/722-744 UGACUAGCAG-AGGCUAGAAGGAA
AF538302.1/786-808 UGACUAGCGG-AUGCUAGAAGAAA
AF042100.1/762-784 UGACUAGCGG-AGGCUAGAGGAGG
AY676590.1/82-104  UGACUAGCGG-AGGCUAGGGGGGG
DQ373064.1/307-330 UGACUAGCGGUAGGCUAGAAGGAG
AF465242.1/836-858 UGACUAGCGG-AGGCUAGAAGGAG
#=GC SS_cons       :::<<<<<__.__>>>>>::::::
#=GC RF            UGACUAGCGG.AGGCUAGAAGGAG
//
# STOCKHOLM 1.0

#=GF AC   RF01382
#=GF ID   HIV-1_SL4
#=GF DE   HIV-1 stem-loop 4 packaging signal
#=GF AU   Chen A
#=GF AU   Brown C
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Chen A
#=GF SS   Published; PMID:18713870
#=GF GA   31.00
#=GF TC   31.10
#=GF NC   30.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   18713870
#=GF RT   MS3D structural elucidation of the HIV-1 packaging signal.
#=GF RA   Yu ET, Hawkins A, Eaton J, Fabris D
#=GF RL   Proc Natl Acad Sci U S A. 2008;105:12248-12253.
#=GF WK   Retroviral_Psi_packaging_element
#=GF SQ   16


X04415.1/351-370     UGGGUGCGAGAGCGUCAGUA
K03454.1/337-356     UGGGUGCGAGAGCGUCAGUA
M22639.1/791-810     UGGGUGCGAGAGCGUCAGUA
M62320.1/258-277     UGGGUGCGAGAGCGUCAGUA
K03455.1/791-810     UGGGUGCGAGAGCGUCAGUA
M38429.1/791-810     UGGGUGCGAGAGCGUCAGUA
DQ396394.1/226-245   UGGGUGCGAGAGCGUCAAUA
AY169803.1/272-291   UGGGUGCGAGAGCGUCUGUG
AF418366.1/2-21      UGGGUGCGAGAGCGUCAGUU
AY134942.1/2-21      UGGGUGCGAGAGCGUCAGAA
EU047601.1/21-40     UAGGUGCGAGAGCGUCAGUA
AJ251056.1/3-22      AGGGUGCGAGAGCGUCAGUG
AY169805.1/239-258   UGGGUGCGAGUGCGUCAGUG
EF394357.1/353-372   UGGGUGCGAGAGCGUCAGUG
AF382828.1/9328-9347 UGGGUGCGAGAGCGUCUAUA
DQ373064.1/337-356   UGGGUGCGAGAGCGUCAAUC
#=GC SS_cons         ::<<<<<____>>>>>::::
#=GC RF              UGGGUGCGAGAGCGUCAGUA
//
# STOCKHOLM 1.0

#=GF AC   RF01383
#=GF ID   GRIK4_3p_UTR
#=GF DE   GRIK4 3 prime UTR element
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   38.00
#=GF TC   39.20
#=GF NC   37.60
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.72 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18824690
#=GF RT   A common variant in the 3'UTR of the GRIK4 glutamate receptor gene affects
#=GF RT   transcript abundance and protects against bipolar disorder.
#=GF RA   Pickard BS, Knight HM, Hamilton RS, Soares DC, Walker R, Boyd JK, Machell
#=GF RA   J, Maclean A, McGhee KA, Condie A, Porteous DJ, St Clair D, Davis I,
#=GF RA   Blackwood DH, Muir WJ
#=GF RL   Proc Natl Acad Sci U S A. 2008;105:14940-14945.
#=GF WK   GRIK4
#=GF SQ   8


AADC01102600.1/1773-1869     UAGUCCCGGAGGCCACAGGUACGCGCAGAGGCCGGGCGGGGCGGG-----AGGGGAGGGGCGGGGCGGGCGCUGCUGUCAGCCGCCAGCCGGAACUUGUACA
AADB02014399.1/719517-719598 UAGUCCCGGAGGCCACAGG-ACGCGCAGAGGCCGGG-------------------AGGGGCGGGGCGGGCGCUGCUGUCAGCCGCCAGCCGGAACUUGUACA
AP001929.5/104611-104706     UAGUCCCGGAGGCCACAGG-ACGCGCAGAGGCCGGGCGGGGCGGG-----AGGGGAGGGGCGGGGCGGGCGCUGCUGUCAGCCGCCAGCCGGAACUUGUACA
AAPY01307680.1/2250-2159     UAGCCCCGGCGGCCCCGGA--CACGUGGAGGCCAGGUGGGGAGG-------CGGGAGGGGCCGGGCCGGGGCCGCUGUCCGC-GCCAGCCCGGACUUGUACA
AANU01119004.1/4684-4608     UAGUCCCGGCGGCCACAGG-ACGCGCGGAGGC------------------------GGGGCGGGGCGGGCACUGCUGUCAGCCGCGAGCCGGGACUUGUACA
AB514210.1/18391-18491       UAGUCCCGGAGGCCACAGG-ACGCGCAGAGGCCGGGCGGGGCGGGAGGGGAGGGGCGGGGCGGGGCGAGCGCUGCUGUCAGCCGCCAGCCGGAACUUGUACA
AADA01131649.1/5135-5035     UAGUCCCGGAGGCCACAGG-ACGCGCAGAGGCCGGGCGGGGCGGGAGGGGAGGGGCGGGGCGGGGCGGGCGCUGCUGUCAGCCGCCAGCCGGAACUUGUACA
ABBA01031313.1/28753-28672   UAGUCCCGGAGGCCACAGG-ACGCGCAGAGGCCGGG-------------------AGGGGCGGGGCGGGCGCUGCUGUCAGCCGCCAGCCAGAACUUGUACA
#=GC SS_cons                 ::<<<<<---<<<<_____._________>>>>-----------.......----->>>>>:::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UAGcCCCGGaGGCCACAGG.ACGCGcaGAGGCCgGGcGGGGcGG.......gGGGaGGGgCgGGGCgGGcGCUGCUGUCAGCCGCcAGCCgGaACUUGUACA
//
# STOCKHOLM 1.0

#=GF AC   RF01384
#=GF ID   InvR
#=GF DE   Invasion gene-associated RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   PMID 17971080
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   101.80
#=GF NC   35.80
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17971080
#=GF RT   A small non-coding RNA of the invasion gene island (SPI-1) represses outer
#=GF RT   membrane protein synthesis from the Salmonella core genome.
#=GF RA   Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J
#=GF RL   Mol Microbiol. 2007;66:1174-1191.
#=GF WK   Invasion_gene_associated_RNA_(InvR)
#=GF SQ   4


Z17243.1/649-739           GUCACUUUUACGGUUGGCCAUUUGUCUCUUACGUUGCAUUUAUCAAUCUGCUUUUUGAUACAGCAGCACCUCGCUGCUGCUUUUUUAUUUG
Z17242.1/649-739           GUCACUUUUACGGUUGGCCAUUUGUCUCUUACGUUGCAUUUAUCAAUCUGCUUUUUGAUACAGCAGCACCUCGCUCGGUCUUUUUUUAUUU
CP001120.1/3019438-3019528 GUCACUUUUACGGUUGGCCAUUUGUCUCUUACGUUGCAUUUAUCAAUCUGCUUUUUGAUACAGCAGCACCUCGCUGCUGCUUUUUUUAUUG
CP000026.1/2859459-2859549 GUCACUUUUACGGUUGGCCAUUUGUCUCUUACGUUGCAUUUAUCAAUCUGCUUUUUGAUACAGCAGCACCUCGCUGCUGCUUUUUUUAUUU
#=GC SS_cons               :::::::::::(((,<<<_____>>>,,,,,,<<<<<---<<<<<<________>>>>>>-->>>>>))):::::::::::::::::::::
#=GC RF                    GUCACUUUUACGGuUGgCCAUUUGuCUCUUACGuuGCAUUuauCaaUCUGCUUUuuGauaCAGCagCaCCUCGCUgcugCUUUUUUuaUUu
//
# STOCKHOLM 1.0

#=GF AC   RF01385
#=GF ID   isrA
#=GF DE   isrA Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   51.00
#=GF TC   53.00
#=GF NC   49.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   10


ABEI01000010.1/57820-57936 AUCUUCACCGUCACGCUGCGCCCGGUCUCAAAUCCCGCUUCUUCCUGGCAGUCGCC------------GCUGGGGAU-UUGUGAGUAACAGGCGGUCAUGCAGGUUUCGCUGUUGAUGUGGCGGACGCUG
ABEL01000001.1/44634-44750 AUCUUCACAACAACGCUCGCCCCGGUCUCAAAUCCCGCUUCUUCCUGGCAGUCGCC------------GCUGGGGAU-UUGUGAGUAACAGGUGGUCAUGCAGGUUUCGCUGUUGAUGUGGCGGACGCUG
AE017220.1/332318-332446   AUCUUCACGGUGACGCCGCGCCCGGUCUUAAAUCCCGCUUCUUCCAGCCAGUCGCCCUUAAGGUGCAGGCUGGGGAU-UUGUGAGUAACAGGUGGUUAUACAGGUUUCGCUGUUGAUGUGGCGGACGCUG
AJ320483.1/34605-34733     AUCUUCACGGUGACGCCGUGCCCGGUCUCAAAUCCCGCUUCUUCCUGCCAGUCACCCUUAAGGUGCUGGCUGGGGAU-UUGUGAGUAACAGGCGGUCAUGCAGGUUUCGCUGUUGAUAUGGCGGACGCUG
CP000026.1/2566947-2566819 AUCUUCACGGUGACGCUGCGCCCGGUCUCAAAUCCCGCUUCUUCCUGCCAGUCACCCUUAAGGUGCUGGCUGGGGAU-UUGUGAGUAACAGGCGGUCAUGCAGGUUUCGCUGUUGAUAUGGCGGACGCUG
CP000266.1/661500-661372   AUCUUCACCGUGACACCCCGUCCGGUAUCAAAUCCGGCCUCUUUCAGCCAGUCGCCCUUAAGGUGCAGGCUG-GGAUGUUGUGAAUAAUACCGGGCUAUACCGGUUUUGCGGUCCUGGUGGCGGGCUCUG
ABEI01000010.1/55524-55652 AUCUUCACUGUCACGCUCGCGCCGGUAUCAAAUCCCGCUUCUGUCAGCCAGUCACCCUUGAGAUGCAGGCUGGGAAU-GCGUGAGUAAUAGGUGGUCAUGUGGGUUUUGCUGUUCUCGUGGCGGACGCUG
CP001138.1/319039-319167   AUCUUCACCGUCACGCUGCGCCCGGUCUCAAAUCCCGCUUCUUCCUGCCAGUCACCCUUAAGGUGCUGGCUGGGGAU-UUGUGAGUAACAGGUGGUUAUACAGGUUUCGCUGUUGAUGUGGCGGACGCUG
CP001144.1/341301-341429   AUCUUCACGGUGACGCCGCGCCCGGUCUUAAAUCCCGCUUCUUCCAGCCAGUCGCCCUUAAGAUGCAGGCUGGGGAU-UUGUGAGUAAUAGGUGGUCAUGUGGGUUUUGCUGUUGAUGUGGCGGACGCUG
CP001113.1/341502-341630   AUCUUCACGGUCACGCUGCGCCCGGUCUCAAAUCCCGCUUCUUCCUGCCAGUCACCCUUAAGGUGCUGGCUGGGGAU-AUGUGAGUAACUGGUGGUCAUGCAGGUUUCGCUGUUGAUGUGGCGGACGCUG
#=GC SS_cons               ::::::::::::::::::::::::::<-<<<<<<<<------------<<<<<<<<_____>>>>--->>>>>>>>>.>>>->------------------------<<<__________>>>:::::::
#=GC RF                    AUCUUCACgGUgACGCugcgcCCGGUcUcaaAUCCCGCUUCUUcCuGcCAGuCacCCUUAAGguGCaGgCUGGGGAU.uugUgAGUAAcAgguGGUcAUgcaGGUUUcGCUGUUgauGUGGCgGACGCUG
//
# STOCKHOLM 1.0

#=GF AC   RF01386
#=GF ID   isrB
#=GF DE   isrB Hfq binding RNA
#=GF AU   Barquist L; 0000-0003-4732-2667
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   35.00
#=GF TC   38.50
#=GF NC   34.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   3


AE006468.1/1104179-1104266 AACAGCACCCCGA-UAUAUCUGGUUGUUAGGUCCGGUUCGCUUUGGUCGGUUGGA--CCGGACAGGGCACGCCCGCUUCG-GUGGGCGUUUU
ABAN01000041.1/25481-25566 AAAAGCACCCCGA-UAUAUCAGGUUGUUGGGUCCGGUUCGCUUUGGUCGGU--GACACCGGAU-GGGCA-GCCCACUUAG-GUGGGCUUUUU
CP000822.1/1790855-1790768 AAUGGCACCUCGGUUUUACCAGGUAGAAAUGUCCGGUUCGCUUUGGUCGGU--GACGCCGGAC-GGGCAGGCCCACUUCGUGUGGGCUU-UU
#=GC SS_cons               :::::::::<<<<.____>>->>,,,,,,,<<<<<<<<<____________..>>->>>>>>>.----<<<<<<<<____.>>>>>>>>:::
#=GC RF                    AAuaGCACCcCGg.UaUAcCaGgUuGuuagGuCCGGcuCGCUUUGGUCGGU..GaCgCCGGaC.GGGCacGCCCaCUUcG.GuGGGCguUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01387
#=GF ID   isrC
#=GF DE   isrC Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   39.00
#=GF TC   39.70
#=GF NC   38.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   16


U31849.1/2304-2187           CUUAAUAAACAACAAAACCAAACGUACUUUCA-----GAUUUCAGGCUGGAAUGCGCACAGCUGAUUGUUGAUAAGGGCUACUCAUACCGACAGGCCAGUGAAGCGAUGAAUGUCGGUUCCAC
AF401292.1/92805-92927       CUUAAUGAACAAGAAAACCAAACGUACUUUCACCCCUGAAUUCAGGCUGGAAUGUGCACAGCUAAUUGUUGAUAAGGGCUACUCAUAUCGACAAGCCAGUGAAGCGAUGAAUGUCGGUUCUAC
BA000007.2/3875218-3875340   CUUAAUGAACAAGAAAACCAAACGUACUUUCACCCCUGAAUUCAGGCUGGAAUGUGCACAGCUAAUUGUUGAUAAGGGCUACUCAUAUCGACAAGCCAGUGAAGCGAUGAAUGUCGGUUCUAC
BA000007.2/4582371-4582493   CUUAAUGAACAAGAAAACCAAACGUACUUUCACCCCUGAAUUCAGGCUGGAAUGUGCACAGCUAAUUGUUGAUAAGGGCUACUCAUAUCGACAAGCCAGUGAAGCGAUGAAUGUCGGUUCUAC
AY857617.1/38394-38272       CUUAAUGAACAAGAAAACCAAACGAACCUUCACCCCUGAGUUCAGGCUGGAAUGUGCACAGCUGAUUGUUGAUAAGGGCUACUCAUAUCGACAGGCCAGUGAAGCGAUGAAUGUCGGUUCAAC
AACY022996748.1/137-259      CUUAAUGAACAAGAAAACUAAGCGUACUUUCACCCCCGAGUUCAGGAUGGAAUGUGCACAGCUGAUUGUUGAUAAGGGCUACUCCUAUCGACAAGCCAGUGAAGCGAUGAAUGUCGGUUCUAC
CP000247.1/4004836-4004714   CUUAAUGAACAAGAAAACAAAGCGUACCUUCUCUCCUGAGUUUAAGCAGGAAUGCGCCCAACUUAUCGUUGAUAAAGGUUACUCAUACCGGGAAGCCAGUGAAGCUAUGAGUGUUGGUUCCUC
AE014075.1/3452704-3452826   AUAAAACAACAAGAAAACAAAGCGUACCUUCUCUCCUGAGUUUAAUCUGGAAUGCGCCCAACUUAUCGUUGAUAAAGGUUACUCAUACCGGGAAGCUACUGAAGCUAUGAAUGUUGGUUUCUC
FM986651.1/55346-55468       CUUAAUGAACAAGAAAACCAAACGAACCUUCACCCCUGAGUUCAGGCUGGAAUGUGCACAGCUGAUUGUUGAUAAGGGCUACUCAUAUCGACAGGCCAGUGAAGCGAUGAAUGUCGGUUCAAC
FM986650.1/54257-54379       CUUAAUGAACAAGAAAACCAAACGAACCUUCACCCCUGAGUUCAGGCUGGAAUGUGCACAGCUGAUUGUUGAUAAGGGCUACUCAUAUCGACAGGCCAGUGAAGCGAUGAAUGUCGGUUCAAC
ABAK02000001.1/638809-638925 CUUAAUAAACAAAAAA-CCAAACGUUCUUUCA-----GAGUUCAGGCUGGAAUGCGCAUAGCUGAUUGUUGAUAAGGGCUACUCAUACAGACAGGCCAGUGAAGCGAUGAAUGUCGGUUCCAC
CP001138.1/1884236-1884119   CUUAAUAAACAAAAAAACCAAACGUACUUUCA-----GAGUUCAGGCUGGAAUGCGCAUAGCUGAUUGUUGAUAAGGGCUACUCAUACCGACAGGCCAGUGAAGCGAUGAAUGUCGGUUCCAC
AP009240.1/1492361-1492239   CUUAAUGAACAAGAAAACCAAACGAACCUUCACCCCUGAGUUCAGGCUGGAAUGUGCACAGCUGAUUGUUGAUAAGGGCUACUCAUAUCGACAGGCCAGUGAAGCGAUGAAUGUCGGUUCAAC
CU928163.2/283584-283462     CUUAAUGAACAAGAAAACCAAACGUACUUUCACCCCUGAAUUCAGGCUGGAAUGUGCACAGCUAAUUGUUGAUAAGGGCUACUCAUAUCGACAAGCCAGUGAAGCGAUGAAUGUCGGUUCUAC
CU928145.2/2991721-2991843   CUUAAUGAACAAGAAAACCAAACGAACCUUCACCCCUGAGUUCAGGCUGGAAUGUGCACAGCUGAUUGUUGAUAAGGGCUACUCAUAUCGACAGGCCAGUGAAGCGAUGAAUGUCGGUUCAAC
CP001919.1/40379-40257       CUUAAUGAACAAGAAAACCAAACGAACCUUCCCCCCUGAGUUCAGGCUGGAAUGUGCACAGCUGAUUGUUGAUAAGGGCUACUCAUAUCGACAGGCCAGUGAAGCGAUGAAUGUCGGUUCAAC
#=GC SS_cons                 ::::::((((,,,,,,,,,,,,,<<<<<<<<<--<<<<____>>>>->>>>>->>>>,,,<<<<-<<<<<<<<<-<<<___>>>->>>>>>>>>-->>>>,,,,<<<<____>>>>)))):::
#=GC RF                      cUUAAUgaaCAAgAAAACcAAaCGcgCuuuCaCcccuGAgUUCaggcuGgaaUGcgCacAgCugAuuguuGauaAGgGcUACuCAuauCgacaaGCcaGcGAAGCgauGAAUgucGGuucuaC
//
# STOCKHOLM 1.0

#=GF AC   RF01388
#=GF ID   isrD
#=GF DE   isrD Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   37.00
#=GF TC   38.30
#=GF NC   36.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   2


CP000026.1/1653079-1653129 UGCAUUUAUUUCAACAGAAACUCAGCGGCCACCGCGCAGGUGGCCUUUUUU
AM933173.1/1925685-1925735 UGCACUUAUUUCAACAGAAACUCAGCGGCCACCGCGCAGGUGGCCUUUUUU
#=GC SS_cons               :<<-----<<<<____>>>>---->><<<<<<<_____>>>>>>>::::::
#=GC RF                    UGCAuUUAUUUCAACAGAAACUCAGCGGCCACCGCGCAGGUGGCCUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01389
#=GF ID   isrF
#=GF DE   isrF Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   40.00
#=GF TC   45.10
#=GF NC   29.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   3


CP000026.1/1399939-1400207 ACAAUAGCCUCACUACCAUCAAGCGA-UA-CUGCUGCUUACGAGAAAC------AAGGGAUGCUGCGCACGCUGAUUAAAGUCACGUUCGGUUAUCCUGCGAUUUUUGACGAGGUUCGGCAGGAAUGCCAAAUCAACAAUGCGCAUGUUGUCGCCGGAUGUGGAUCCGGGUAUCAAAGCGUUUAUAGCCGUUGUCAGAGCUGCAGAACAUCAGUCAGAAAAAGCAGCGGACCAGGGUUCG------UGUGCAGGAUAAGCGGGUG-CAAAUCAACA----------GAAUUCGC
CP001144.1/1736669-1736962 AGAUUAUCCAGGAGAUACACGAAUUAAUUCUGGCGGGUGAAAUGGAAGUCGCCAAAAGGAUGCUGCGCACGCUGAUUAAAGUCACGUUCGCUUAUCCUGCGAUUUUUGACGAGGUUCGGCAGGAAUGCCAAAUCAACAAUGCGCAUGUUGUCGCCGGAUGUGGAUCCGGGUAUCAAAGCGUUUAUAGCCGUUGUCAGAGCUGCAGAACAUCAGUCAGAAAAAGCAGCGGACCAGGGUAAAACCCACUGAGCCAAAAACCUGCGCGACGAACCGGUCACAGUGGCCGGUUUUUUU
CP000857.1/2246703-2246992 AUAACGACCUGGACGCCGGCGAAUUA----UGGCGGGUGAAAUGGAAGUGGCCAAAGGGAUGCUGCGCACGCUGAUUAAAGUCACGUUCGGUUAUCCUGCGAUUUUUGACGAGGUUCGGCAGGAAUGCCAAAUCAACAAUGCGCAUGUUGUCGCCGGAUGUGGAUCCGGGUAUCAAAGCGUUUAUAGCCGUUGUCAGAGCUGCAGAACAUCAGUCAGAAAAAGCAGCGGACCAGGGUAAAACCCACUGAGCCAAAAACCUGCGCGACGAACCGGUCACAGUGGCCGGUUUUUUU
#=GC SS_cons               ::::::::::::::::::::::::::.::.::::[[[[,,,,,,,,,,,,,,,,,,((---(((((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<______>>>,,,,,,,,,,,<<<<---<<<---<<<<<<____>>>>>>---->>>->>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,)))))---)),<<<_____>>>,,,,,,,,,,,,]]]]-------<<<<<<<<<_____>>>>>>>>>::::
#=GC RF                    AuAauaaCCuggauaccaaCgAauuA.Ua.ugGCgggugAaauGgAAgUgGCCAAAgGGAUGCuGCGCACGCUGAUUAAAGUCACGUUCGgUUAUCCUGCGAUUUUUGACGAGGUUCGGCAGGAAUGCCAAAUCAACAAUgCGCAUGuuGUCGCCGGauGUGGauCCGGGUAUCaaAGCGuUUAUAGCCGUUGUCAGAGCUGCAGAACAUCAGUCAGAAAAAGCaGCGGACcAGGGUaaaACCCACUGaGCcaaAaacccGcGcGACaaacCGGcCACAGUGgCCGguuuUuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01390
#=GF ID   isrG
#=GF DE   isrG Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; ClustalW; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   100.00
#=GF TC   100.60
#=GF NC   99.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   5


AE017220.1/1118192-1117914 GUUUUGCGGCAUCUUCUGCUCUGGUGGCUGCUGCUCCGGCAGCAGUACUGCUUUGCGCCGCCAGUGAUGCGCUGGUAUCAGAUGCGGCGGCGUGAGUGGAUGCCUCCGAUGCUGAUGACGAGGCGGCUGUUGCGCUGGCCGCUGCUGUACUUGCUGACGUUGCUGCAUUUGUCUCAGAUGUUUUCGCUGCGGCUGCCGAUGCGGCUGCCGCCUUUUCCGACGCUGCCGCCGCAGUGGCUGACGCA------CCUGCAUCACCGGCACUGGAAGCCGCCUGCGUUU
AY034828.1/4205-4483       GUUUUGCGGCAUCUUCUGCUCUGGUGGCUGCUGCUCCGGCAGCAGUACUGCUUUGCGCCGCCAGUGAUGCGCUGGUAUCAGAUGCGGCGGCGUGAGUGGAUGCCUCCGAUGCUGAUGACGAGGCGGCUGUUGCGCUGGCCGCUGAUGUACUUGCUGACGUUGCUGCGUUUGUCUCAGAUGUUUUUGCUUCGGCUGCCGAUGCGGUUGCCGCCUUUUCCGACGCUGCCGCCGCAGUGGCUGACGCA------CCUGCAUCACCGGCACUGGAAGCCGCCUGCGUUU
ABAN01000002.1/24099-23821 GUUUUGCGGCAUCUUCUGCUCUGGUGGCUGCUGCUCCGGCAGCAGUACUGCUUUGCGCCGCCAGUGAUGCGCUGGUAUCAGAUGCGGCGGCGUGAUUGGAUGCCUCCGAUGCUGAUGACGAGGCGGCUGUUGCGCUGGCCGCUGCUGUACUUGCUGACGUUGCUGCGUUUGUCUCAGAUAUUUUUGCUGCGGCUGCCGAUGCGGUUGCCGCCUUUUCCGACGCUGCCGCCGCAGUGGCUGACGCA------CCUGCAUCACCGGCACUGGAGGCGGCCUGUGUUU
AE006468.1/2344732-2345013 GUUUCGCGGCCUCUUCGGCUCAGGUUGCCAAUUCUCCGGCUGCAGCUCUGCUUUGCGCUGCCAGUGAUGCGCUGGUAUCAGAUGCGGCGGCGUGGGUGGAUGCCUCCGAUGCUGAUGACUAGGCGGCUGCCGCCGUUCUGGCUGUGUCAGCCGACGCCGCGCUGGCUGAUGCCUCCCCGGCUUUUGUGGUCGCCGUACCUGCG-CUGCU--CUCCGCAGAUGCUGCGGAUGAAGCUGCCGACCAAAAUUCCCCUUGAAAACCAGCCUGUCAGGGCUGGUUUUUUU
CP001127.1/686959-686681   GUUUUGCGGCAUCUUCUGCUCUGGUGGCUGCUGCUCCGGCAGCAGUACUGCUUUGCGCCGCCAGUGAUGCGCUGGUAUCAGAUGCGGCGGCGUGAUUGGAUGCCUCCGAUGCUGAUGACGAGGCGGCUGUUGCGCUGGCUGCUGCUGUACUUGCUGACGUUGCUGCGUUUGUCUCAGAUAUUUUUGCUGCGGCUGCCGAUGCGGCUGCCGCCUUUUCCGACGCUGCCGCCGCAGUGGCUGACGCA------CCUGCAUCACCGGCACUGGAGGCCGCCUGCGUUU
#=GC SS_cons               :::::{{{{{-{{{--{{{{--{{{{[[[[[[[[--[[[[[[[,,,,,,,,,,,,,,,,<<<<<<<___>>>>>>><<<<<---<<<-<<<<<______>>>>>->>>--->>>>>((-((((((((-((((((-((((-(((((,<<____>>,,,,<<----<<<<<<<___>>>>>>>---->>,)))))-))))-))))))-))))))))-)),,,,]]]]]]]--]]]]]]]],,,,<<<......__>>>,,}}}}}}}}--}}}-}}}}}::::::::
#=GC RF                    GUUUugcggCauccUCuGCcCuGGugGCcgcugCUCCgGCaGCAGuaCUGCUUUGCGCcgCCaGuGAUGCgCuGGuauCaGAUGCGGCGGCguGagUGGauGCCUCCGAUGCuGauGaCgaGGcGGCUgccGCgccggcuGCcGcugcAcuugcuGaCGcugcugcgucuGuCUCagacgcUUUUgCugCgGCugccgacGCggcUGCCgCCucuuCcGAcGCuGCcGccGcagcgGCuGACgca......CCugcAucaCCgGCacuggagGccgccUgugUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01391
#=GF ID   isrH
#=GF DE   isrH Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; ClustalW; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   49.20
#=GF NC   38.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   6


CP000026.1/650686-650965     GGAGAUAUUCAGUUAUCCCCC-UCUUUAAAGGAGGCUGGUAACGCGUCGAUACAAGAGAUAUUGCUCUAUAAACAGUAACGUCGUUAUCUGUCAUGCCACCGAGGGUUAGCGGUCAUGGUUAACCAAAUAGGGCAGGUUAUUGCAAAGAGACAUCCGUGUUUAUACCCAAAAUAAUCCGUAGCCAACACAUAAGCAACUUGAAGUAUGAAGGGUAUAUGUCUGAUGGAAAAUCGGCCCUGGUGAGUAGAGUAAUGGCGCCGGAGGGGCUCCGGCGCUUUUU
ABEI01000001.1/306473-306194 GGGGAUAUUUAGUUAUCCCUC-UCUUUAAAGGGGGCUGGUAACGCGUCGAUAAAAGAGAUAUUGCUCUAUAAACAGUAACGUCGUUAUCUGUCAUGCCACCAUGGGUUAGCGGUCAUGGUUAACCAAAUAGGGCAGGUUAUUGCAAAGAGACAUCCGCGUUUAUACCCAAAAUAAUCCGUAGCCAACACAUAAGCAACUUGAAGUAUGAAGGGUAUAUGUCUGAUGGAAAAUCGUCCCUGGUGAGUAGGGUAAUAGCGCCGGAGGGACUCCGGCGCUUUUU
AE017220.1/2408863-2408584   GGAGAUAUUCAGUUAUCCCCC-UCUUUAAAGGAGGCUGGUAACGCGGCGAUACAAGAGAUAUUGCUCUAUAAACAGUAACGUCGUUAUCUGUCAUGCCACCGUGGGUUAGCGGUCAUGGUUAACCAAAUAGGGCAGGUUAUUGCAAAGAGACAUCCGCGUUUAUACCCAAAAUAAUCCGUAGCCAACACAUAAGCAACUUGAAGUAUGAAGGGUAUAUGUCUGAUGGAAAAUCGUCCCUGGUGAGUAGGGUAAUAGCGCCGGAGGGGCUCCGGCGCUUUUU
AE006468.1/2394582-2394303   GGGGAUAUUCAGUUAUCCCCC-UCUUUAAAGGUGGCUGGUAACGCGUCGAUACAAGAGAUAUUGCUCUAUAAACAGUAACGUCGUUAUCUGUCAUGCCACCGUGGGUUAGCGGUCAUGGUUAACCAAAUAGGGCAGGUUAUUGCAAAGAGACAUCCGCGUUUAUACCCAAAAUAAUCCGUAGCCAACACAUAAGCAACUUGAAGUAUGAAGGGUAUAUGUCUGAUGGAAAAUCGUCCCUGGUGAGUAGGGUAAUGGCGCCGGAGGGGCUCCGGCGCUUUUU
CP001127.1/2400359-2400080   GGAGAUAUUCAGUUAUCUCCC-UCUUUAAAGGAGGCUGGUAACGCGUCGAUACAAGAGAUAUUGCUCUAUAAACAGUAACGUCGUUAUCUGUCAUGCCACCGUGGGUUAGCGGUCAUGGUUAACCAAAUAGGGCAGGUUAUUGCAAAGAGACAUCCGCGUUUAUACCCAAAAUAAUCCGUAGCCAACACAUAAGCAACUUGAAGUAUGAAGGGUAUAUGUCUGAUGGAAAAUCGGUCCCGGUUAUCAGGGUAAUGGCGCCGGAGGGGCUCCGGCGCUUUUU
CP001138.1/2346066-2345786   GGGGAUAUUCAGUUAUCCCCCCUCUUUAAAGGGGGCUGGUAACGCGUCGAUACAAGAGAUAUUGCUCUAUAAACAGUAACGUCGUUAUCUGUCAUGCCACCGUGGGUUAGCGGUCAUGGUUAACCAAAUAGGGCAGGUUAUUGCAAAGAGACAUACGCGUUUAUACCCAAAAUAAUCCGUAGCCAACACAUAAGCAACUUGAAGUAUGAAGGGUAUAUGUCUGAUGGAAAAUCGGCCCUGGUGAGUAGGGUAAUGGCGCCGGAGGGGCUCCGGCGCUUUUU
#=GC SS_cons                 <<<<<<<______>>>>>>>,.<<<<<------<<<<<____>>->>>------>>>>>{{{{{{{{{{{,,<<<<<<<<___>>>>->>>>,,,,,[[[[[,,<<<<<<<_______>>>>>>>,,,,,(((--((((-((-((---(((((--------(((((((,,,,,,,,,,<<_____>>,<<<<--<_____>--->>>>,,))))))))))))--))-))))))--)))]]]]],}}}}}}}}}}}<<<<<<<<<___>>>>>>>>>:::::
#=GC RF                      GGgGauaUUcAGUuauCcCCC.uCucuAAAGGaGgCcGGUAACgCGcCGAUAcAagaGacauugCcCuacAAaCaGuaaCGUCGuuaUCuGuCAUGCcaCCguGGGuuagCGGUCAUGGcuaaCCAAAUAGGGCAGguuAuuGCaAAGaGaCaUcCGcGUUuauaCCCAAAAUAAUCCGuAGCCAaCACauaAGCAACUUGAAGuauGAAGGGuauauGuCuGAuGGaaaacCGuCCCcGGugAguaGgGcaaugGCGCCGGaGGGgCuCCGGCGCUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01392
#=GF ID   isrI
#=GF DE   isrI Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   45.00
#=GF TC   46.60
#=GF NC   43.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   30


ABEJ01000009.1/60520-60618   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
AB104436.1/3199-3297         UAUU-GUCGGUGUCUGGCAUCUGACAAGGGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCUGG-GCCGUUACAGCCACCAGUUUAAAUGAC
AF021817.1/2883-2785         -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
AL627269.1/34901-34999       -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
ABAO01000027.1/4186-4283     UAUU-GUCGGUGUCUGGCAUCUGCCAAGGGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GCCGUUACAACCACCAGCUUAG-AUAU
ABAO01000027.1/33813-33911   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
CP000026.1/1820880-1820782   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
AE017220.1/1158057-1158155   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUGU
AY144492.1/557-460           -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GUCGUUACAAUCACCAGCUUAG-AUAU
ABAN01000020.1/46731-46633   -AUGAGUAGGUGCCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
ABEL01000010.1/46545-46642   UAUU-GUCGGUGUCUGGCAUCUGACAAGGGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GCCGUUACAACCACCAGCUUAG-AUAU
ABEL01000010.1/109554-109652 -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
AF060858.1/7527-7429         -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUGU
AY144491.1/557-460           -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUUUCUGCCAUAACGGUGAAGCAGGAGUACUGUCGGG-GUCGUUACAAUCACCAGCUUAG-AUAU
AE014613.1/1892912-1892814   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
ABEJ01000008.1/1246-1344     UAUU-GUCGGUGUCUGGCAUCUGACAAGGGGAGAUGAUAUCUGCCAUAACGGCGAAGCAGAAGUACUUUCCGG-ACCGUUACAAUCACCAGUUUAAAUGAU
ABEI01000017.1/65512-65609   -AUGGGUAUGUGUCUGGCACCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GUCGUUACAAUCACCAGCUUAG-GUAU
ABAO01000067.1/1169-1071     UAUU-AUUGGUGUCUGGCAUCUGACGCAGGGCGAUGACAUUUGUCACAACGGAGAGGCUGAGAUUCUGGCGGG-ACCGUUAGAACCUCCAAUUUAAUACAU
FM200053.1/1816063-1815965   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
CP001138.1/1047001-1047098   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GUCGUUACAAUCACCAGCUUAG-AUAU
CP001113.1/1179781-1179879   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
CP001120.1/1119161-1119257   -AUU-GUCGGUGUCUGGCAUCUGACAAGGGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GCCGUUACAACCACCAGCUUAG-AUAU
AE006468.1/2761461-2761364   -AUU-AUUGGUGUCUGGCAUCUGACGCAGGGCGAUGACAUUUGUCACAACGGAGAGGCUGAGAUUCUGGCGGG-ACCGUUAGAACCUCCAAUUUAAUACAU
CP001113.1/1150121-1150217   -AUU-GUCGGUGUCUGGCAUCUGCCAAGGGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUACUGUCGGG-GCCGUUACAACCACCAGCUUAG-AUAU
CP001120.1/1182170-1182268   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
CP001127.1/1136117-1136215   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
AM933172.1/1055293-1055391   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGAAGUAAUAUCACCCGUGAAUAAUAAGAUUAUCCUUG-CUAU
CP001127.1/4328656-4328753   -AUU-GUCGGUGUCUGGCAUCUGACAAGGGGAGAUGAUAUCUGCCAUAACGGCGAAGCAGAAGUACUUUCCGG-ACCGUUACAAUCACCAGUUUAAAUGAU
CP001113.1/2761495-2761398   -AUU-AUUGGUGUCUGGCAUCUGACGCAGGGCGAUGACAUUUGUCACAACGGAGAGGCUGAGAUUCUGGCGGG-ACCGUUAGAACCUCCAAUUUAAUACAU
ABEH02000010.1/15225-15322   -AUGAGUAGGUGUCUGGCAUCUGACAAGAGGCGAUGAUAUCUGCCAUAACGGUGAAGCAGGAGUACUGUCGGG-GUCGUUACAAUCACCAGCUUAG-AUAU
#=GC SS_cons                 .:::::::<<<<<<---<-<<<______>>>->-->>>>>>-<<<_____>>>::::::::::::::::::::.::::::::::::::::::::::.::::
#=GC RF                      .AUgAGUaGgUgUCUGGCAuCuGACAAGaGgCGAUGAuAuCUgCCAUAACGGuGAAGCAGAAGUAaUaUCagg.GucguUAaaAacAccAucuUag.auAU
//
# STOCKHOLM 1.0

#=GF AC   RF01393
#=GF ID   isrJ
#=GF DE   isrJ Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; ClustalW; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   37.00
#=GF TC   37.40
#=GF NC   36.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   5


AE017220.1/1099138-1099216   UGUAAAUCUGAUAUCGUCGCCAUAGCUUCAAUCGUCGACCAAACAAAUUCAAGCCCUGCGGAUAACACCGCGGGGCUUU
ABEJ01000005.1/3900-3826     AGUAAAUCUGAUAUCGUCGCCAUAGCUUCAAUCGUCGACCAAACAAAUUCAAGCCUCGCCAUCG----UGCGGGGCUUU
ABAN01000002.1/901-979       UGUAAAUCUGAUAUCGUCGUCAUAGUUUCAAUCGUCGACCAAGCAAAUUCAAGCCCUGCGGAUAACACCGCGGGGCUUU
AAYU01000001.1/398535-398601 ACAAUUACCGCCAACGGUAACAAACUGA-----GUUAUCCAA---AAUCUGAGCCUCGCCAUCG----UGCGGGGUUUU
AE006468.1/2762031-2761957   UGUAAAUCUGAUAUCGUCGCCAUAGCUUCAAUCGUCGACCAAACAAAUUCAAGCCUCGCCAUCG----UGCGGGGUUUU
#=GC SS_cons                 :::::::::::::::<<<<-<____________>->>>>-----------<<<<<<<<<<____....>>>>>>>>>>:
#=GC RF                      ugUAAAUCUGAUAUCGucGcCAUAguuUCAAUCGUCgaCCAAACAAAUUcaAGCCccGCgaucg....cGCggGGCUuU
//
# STOCKHOLM 1.0

#=GF AC   RF01394
#=GF ID   isrK
#=GF DE   isrK Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; CMfinder; Infernal
#=GF SS   Predicted; CMfinder
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF **   seedtax: Bacteria; Viruses
#=GF SQ   52


CP000038.1/2936521-2936445     GCGCCAGCAAAAUCUGGCGUC-GGGAUUGGAACCCCG---GAUAGAGA-CCGCGACAGA------CACACGCCGCGA----GCGUGUUUUUU
CP000034.1/553852-553776       GCGCCAGCAAAAUCUGGCGUC-GGGAUUGGCGUCCCG---GAUGUUUA--CGGAGCGAUAU----GAGACGC-GCCC----GCGUCUUUUUU
AP008232.1/3106193-3106273     GCAUCUGGAAAUUCAGGUGCC-GGGAUUGGUCUCCCGCC-GAGAUUCA-CCGCGACAGAAU----GACACGCCGCGA----GCGUGUUUUUU
CP000468.1/2745196-2745271     GCACUGGCAAAAUCCAGUGCC-GGGAUUGGCGUCCCG---GAUUACUA-AAAGGCGCAU------UCACCGC-GCAA----GCGGUUUUUUU
CP000026.1/4467109-4467186     GCUGCCGCAAAAUCGGCAGCC-GGGAUUGGCGUCCCG---UUUACAAC-AUUGGCGACAC-----CGGACGCGCCUU----GCGUCUUUUUU
AE005174.2/318522-318599       GCUGUCGCAAAAUCGGCAGCC-GGAAUUGGCGUUCCG---UAUAACUU-AUUGGCGACAA-----UUGACGCCCCUU----GCGUCUUUUUU
AY626367.1/2706-2783           GCAGCCGCAAAAUCGGCUGCC-GGGAUUGGAACCCCG---GACAUUAC--AAGAGCGCA------CAACCGCGCUAU--AAGCGGUUUUUUU
CP000036.1/1140431-1140511     GCACCUGCAAAAUCAGGUGCC-GGGAUUGGAACCCCG---AAAUAUAA-CCAUACUGGCGACAC-GUGACGC-GUCU----GCGUCUUUUUU
AL627283.1/64614-64692         GCACCUGCAAAUUCAGGUGCC-GGGAUUAGCCUCCUG---AUUGACUU-CAUCGACGACACA---AAGGCGC-GUCU----GCGCUUUUUUU
CP000653.1/3381132-3381209     GCUGUCGCAAAAUCGGCAGCC-GGGCGUAGGAACCCGUG-UUUAACUA-UGGCGACAUC-------AGACGCGCCUU----GCGUCUUUUUU
AE014613.1/4674069-4674146     GCUGUCGCAAAAUCGGCAGCC-GGGCGUGGAAACCCGA--GUAAUCUA-ACGGCGACAC------CUGACGCGCCAU----GCGUCUUUUUU
DQ472459.1/652-575             GCUGCCGCAAAAUCGGCUGCC-GGGCGUAGGAACCCGA--GUUACUUA-UUGGCGACAC------CAGACGCGCCGU----GCGUCUUUUUU
M64113.1/5959-6036             GCUGUCGCAAAAUCGGCAGCC-GGGCGUAGGAACCCGUG-UAACUCGA-AGGCGACAUA-------UGACGCGCCAU----GCGUCUUUUUU
ABAN01000056.1/13099-13023     GCACCUUAUAAAGCGGGUGCC-GGGAUUGGCGUCCUG---GAAUUGUUAUCGGCGACAA------AUGACGC-GCCU----GCGUCUUUUUU
CP000243.1/942138-942064       GCACCUCAUAAAACGGGUGCC-GGGAUUGGAACCCCG---CUGAUCAA--CAAAGCGCA------CAACCGC-GCCA----GCGGUUUUUUU
AE017220.1/1315705-1315779     GUUGCUGUAAAUCCAGCAACC-GGGUUUAGCAGCCUG---GAACACAU--CACAGCGCA------CAACCGC-GCCU----GCGGUUUUUUU
CP000749.1/2732502-2732427     GCACUGGCAAAAUCCAGUGUC-GGGAUUGCAACCCCG---UUUUACAA-CAGCUGCCUAA-----AACACGCACC------GCGUGUUUUUU
ABCH01000029.1/41155-41234     GCACUGGCAAAAUCCAGUGCC-GAGUUUCGCAGCUCG---AAAAUACU-CAAGGCGCAUAGA---CGCCAGCUUCCU----GCUGGUUUUUU
ABAO01000085.1/1928-1852       GCACCUCAUAAAGCGGGUGCC-GGGCGUGGAAACCCG---GAAUUCAA-UAUAGAGCAC-------AACCGCGCUCA---UGCGGUUUUUUC
AAQW01000001.1/6009895-6009969 GCUGCCGCAAAUUCGGCAGCC-GGGAUUGGCGUCCCG---UGGAUUAG-----GCGGAC------ACACCGCCUUAA--GAGCGGUUUUUUU
CP000753.1/896118-896037       GCAUUGGCAAAAUCCAGUGCC-GGGAUUGAGACCCCG---CAAUAUCA-CAGGCGCAAUCAUGU-CGCCAGCCUAGU----GCUGGUUUUUU
AAYR01000002.1/390229-390303   GCAGCGGCAAAAUCCGUUGCU-GGGUUUAGCAGCCUG---AGACAAAA--CAGAGCGCA------CAACCGC-GCAG----GCGGUUACUAU
BA000007.2/2598473-2598547     GCACCUCAUAAAACGGGUGCC-GGGAUUCUCAACCCG---AUACAGAG--CAAAGCGCA------UAACCGC-GCUA----GCGGUUUUUUU
AE009952.1/4489427-4489353     GCAGCGGCAAAAUCCGUUGCC-GUGAUUAGCGUCCCG---GAAUUCAA-UAGAGUGCAC------GA-CCGC-ACAG----GCGGGUUCUCU
CP000266.1/771548-771624       GCACCUCAUAAAACGGGUGCC-GGGAUUGCUACCCCG---ACGAUGAC--UACUGCGCA------UAACCGCGCUCA---GGCGGUUUUUUU
AAMR01000038.1/33352-33272     GCACUGGCAAAAUCCAGUGUC-AGGAUUGGACCCCUGUUUGUUAACCA-AAGGCGCACAGA----CGCCAGC-UUUU----GCUGGUUUUUU
AE014073.1/1891448-1891524     GCACCUCAUAAAACGGGGGCC-GGGCGUGGAAACCCG---AACGUUAC--UGGAGCGCA------UAGCCGCGCUGA---AGCGGUUUUUUU
Z23100.1/1282-1358             GCACCUCAUAAAACGGGGGCC-GGGCGUGGAAACCCG---AACGUUAC-UCGAGCGCAU-------AGCCGCGCUGA---AGCGGUUUUUUU
AAZW01000012.1/43924-43843     GCACUGGCAAAAUCCAGUGUC-GGGAUUAGUCCCCCG---CAACAUAC-ACCCAAGGCGCAUAGACGCCAGC-UUUU----GCUGGUUUUUU
U88088.2/30625-30704           GUCGCUGUAAGUCCAGCGGCCUGGGAUUGGCGUCCCG---GAUUCAGA---GGCGGACA------CAACCGCCGUUUUCGAGCGGUUUUUUU
CP000891.1/933531-933450       GCAUUGGCAAAAUCCAAUGCC-GGGUUUCGCACCCCG---CAGUAUCA-CAGGCGCAAUCAUGU-CGCCAGCCUAGU----GCUGGUUUUUU
CP000468.1/5012357-5012433     GCACCUUAUAAAGCGGGUGCC-GGGCGUGGAAACCCG---GAAUUCAC--CAAAGCGCA------CAACCGCGCUCU---UGCGGUUUUUUU
CP000800.1/1448076-1448000     GCGUCAGCAAAAUCUGGCGUC-GGGAUUGGAACCCCG---GAUGUUUA--CGGAGCGAUAU----GAGACGC-GCCC----GCGUCUUUUUU
AE009952.1/2450357-2450283     ACACCUGCAAAAUCAGGUGUC-GGGAUUUGCACCCUG---GAUAUCAC--AACAACGCA------UAGCCGC-GUUU----GCGGUUUUUUU
ACID01000067.1/73516-73593     GCUGCCGCAAAAUCGGCAGCC-GGGCGUGAGAACCCGA--GCAAUCUA-ACGGCGACAU------AUGACGCGCCAU----GCGUCUUUUUU
CP000827.1/23442-23368         GCAGCCGCAAAAUCGGUUGCC-GGGUUUCGCAGCUCG---AACAUCAC--GGAAGCGCA------CGACCGC-GCCA----GCGGUUUUUUU
CP001157.1/3302585-3302667     GCUGCCGCCAAAUCGGCAGCCUGGGCUUGGCGGCCCG---GAUAAAAC-GGGCGGUCACA-----AAACCGCUGUAAAAAAGCGGUUUUUUU
CP001113.1/2762901-2762825     ACGCCAGCAAAAUCUGGCGUC-GGGAUUGGCGUCCCG---GAAUUUCA-CCGCGACAGA------GACACGCCGCGA----GCGUGUUUUUU
AAKB02000001.1/88057-87980     GCGUCAGCAAAAUCUGGCGUC-GGGAUUGGAACCCCG---GAUAUUCAACCGCGACAGA------CACACGCCGCGA----GCGUGUUUUUU
CP001144.1/2177648-2177572     GCACCUCAUAAAGCGGGUGCC-GGGAUUGGCGUCCUG---GAAUUGCAUACGGCGACAA------UGGGCGC-GUUA----GCGUCUUUUUU
CP001063.1/656925-657001       GCACCUCAUAAAACGGGUGCC-GGGAUUAGCACCCCG---AAAGUUAC-UCGAGCGCAU-------AACCGCGCUGA---AGCGGUUUUUUU
CP000946.1/1840734-1840806     GCGGCUGCAAAAUCAGGCGUC-GGGAUUGGCAUCCUG---UAAUACUU-CACUGACA---------ACACAA-UAUU----UUGUGUUGCGU
AAMJ02000008.1/84163-84086     GCACCUCAUAAAACGGGUGCC-GGGUUUCGCAGCCCG---GAAAUGUA--CGAGGCGACAC----AUGACGCGCCGA----GCGUCUUUUUU
AAJV02000004.1/34669-34595     GCGCCAGCAAAAUCUGGCGUC-GGGAUUGGCGUCCCG---GAUGAAAA-AGGCGACAAC-------AGACGC-GCCA----GCGUCUUUUUU
AE014613.1/2740919-2740996     GCUGCCGCAAAAUCGGCAGCC-GGGCGUGAGAACCCG---AGUAUGUUAUCGGCGACAU------AUGACGCGCCAU----GCGUCUUUUUU
CP001120.1/2560276-2560199     GUUGCCGCAAAAUCGGCAGCC-GGGCGUAGGAACCCGU--GUUAUCUG-AAGGCGAUAC------UACACGCGCCAG----GCGUGUUUUUU
CP001113.1/2885050-2885127     GCUGUCGCAAAAUCGGCAGCC-GGAAUUGGCGUUCCG---AAUAACUU--CAAGGCGACAC----GACACGCGCCAU----GCGUGUUUUUU
AB426055.1/6443-6517           GCACCUCAUAAAACGGGUGCC-GGGUUUCGCAGCCCG---CUGACAAA--CGUAGCGCA------CAACCGC-GCCA----GCGGUUUUUUU
AB426058.1/17859-17933         GCACCUCACAAAACGGGUGCC-GGGUUUCGCAGCCUG---CUGACUAC-ACAAGCGCAC-------AACCGC-GCCA----GCGGUUUUUUU
AALE02000005.1/109352-109275   GCUGCCGCAAAAUCGGCAGCC-GGGCGUGAGAACCCGU--GUAACUCA-AUGGCGACAC------AACACGCGCCAG----GCGUGUUUUUU
AALD02000013.1/100949-100872   GCUGCCGCAAAAUCGGCAGUC-GGGCGUAGGAACCCGU--GUUACUUA-UUGGCGACUC------AACACGCGCCAU----GCGUGUUUUUU
AALC02000033.1/29677-29751     GCAGCGGAAAAAUCUGCUGCC-GGGUUUGGAACCCCG---UAUUUCAA--CAGGGCGCA------UAACUGC-GUAA----GCGGUUAUUAU
#=GC SS_cons                   <<<<<<<______>>>>>>><.<<<<______>>>>>...--------.----------......-<<<<<<_____....>>>>>>:::::
#=GC RF                        GCacCcGCAAAAUCgGguGCC.GGGaUUGGcAuCCCG...gAaauuaa.acggggcaaa......cagcCGCggcuu....GCGgcuUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01395
#=GF ID   isrL
#=GF DE   isrL Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; MAFFT; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   35.00
#=GF TC   36.40
#=GF NC   34.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   4


AE017220.1/2856574-2856230 UUUGGCGACCUCUAUUUGUUCAUUCUGUGCGAGCAGUUUGCCGAUGGCUUCGCGAAUAGAAGGAUGCCAGUUAACGGCGCGAUUGACCGCGUCAUUGAGCGUCAGGUUGCCCGGCGCGGCGGCGCUGAGCGGCAACUCAGCGGCGGAGCCAUCCAGCGAAGGAAGCAUCUGGUCCGUUGCUAAUCCUUCGGAUGUAAUCAUUGGCGGCGCUUCUGCGCCCCGGGGCUGGUGAUGAAACAAAGCAAAUGCCAGUACGAUGGCGACAGGCGCGACUCUUCCCAUAGUUUAUCCCUUUUAAA---------UAUCACCGCUUGUUGCCCCGAACGUCGUGGCGUUCGGGGCUUUUUU
AACY020362060.1/625-978    CUUCGCCACGUCGAUUUGCUCGUUUUGCGAGAGCAGUUUGCCGAUGGAUUCACGAAUAGAAGGAUGCCAGCUCACGGCACGACUCACCGCGUCGUUGAGCGUCAGGCUACCGGGAGCGGCAGCGCUCAGCGGCAGAUCGGCAACCGCGCCGUCCAGCGAGGGAAGCAUCUGGCUAGUGGCCAGUCCUUCCGGCGUAAUAAUUUGCGGUUCAUCUUCGGCAUUCACCCGCAGGGUACAGAGCGUUAAUGCCAGCAGUAAGGCAACAGGCGCGACAUUUCUCAUAGAUUAUCCCUUACAAAAUACGGCAGCGACGACUGUUAUUGCCCCGGAUGUCAUCGCAUCCGGGGCUGUAGU
CP000026.1/2657202-2656858 UUUGGCGACCUCUAUUUGUUCAUUCUGUGCGAGCAGUUUGCCGACGGCUUCGCGAAUAGAAGGAUGCCAGCUAACGGCGUGAUUGACCGCGUCAUUAAGCGUCAGGUUGCCCGGCGCGGCGGCGCUGAGCGGCAACUCAGCGGCGGAGCCAUCCAGCGAAGGAAGCAUCUGGUCCGUUGCUAAUCCUUCGGAUGUAAUCAUUGGCGGCGCUUCUGCUCCCCGGGGCUGGUGAUGAAACAAAGCAAAUGCCAGUACGAUGGCGACAGGCGCGACUCUUCCCAUAGUUUAUCCCUUUUAAA---------UAUCACCGCUUGUUGCCCCGAACGUCGUGGCGUUCGGGGCUUUUUU
CP001113.1/2841555-2841211 UUUGGCGACCUCUAUUUGUUCAUUCUGUGCGAGCAGUUUGCCGACGGCUUCGCGAAUAGAAGGAUGCCAGUUAACGGCGCGAUUGACCGCGUCAUUGAGCGUCAGGUUGCCCGGCGCGGCGGCGCUGAGCGGCAACUCAGCGGCGGAGCCAUCCAGCGAAGGAAGCAUCUGGUCCGUUGCUAAUCCUUCGGAUGUGAUAAUUGGCAGCGAUUCUGCGCCCCGGGGCUGGUGAUGAAACAAAGCAAAUGCCAGUACGAUGGCGACAGGUGCGACUCUUCCCAUAGUUUAUCCCUUUUAAA---------UAUCACCGCUUGUUGCCCCGAACGUCGUGGCGUUCGGGGCUUUUUU
#=GC SS_cons               ::{-{{,{{-{{{,,,<<<<<_________>>>>><<<<<<-<<_____>>>>>>>>,[[[[[[[(((,<<<-<-<<<<<<______>>>>>>-->->>>,<<<<<<<<<<______>>>>>>->>>>,,))),,,,,<<<<<<<<-<<<<<<<______>>>------>>>>>>>>>>>>,]]]]]]]}}}-}},,<<<<<<-<<<<--<__________>-->>>>->>>>>>,,,,,,<<---<<<<________>>>>---->>}}-}---------------------------.........--------------<<<<<<<<<<<____>>>>>>>>>>>::::::
#=GC RF                    uUugGCgaCcuCgAUUuGcuCaUUcUGuGcGagCaguuuGcCGauGGcUuCgCgaauAGaaGGauGCCAGcuaaCGgCgcGAuUgACCgcGuCaUugagCGucaGGccgCCcGGcGCGGcggCGCugaGCGGCAacUCgGCggCgGagCCauCCAGCGAaGGaAGCAUCuGGcCcGccGCcAauCCuuCcGauGuAAucauugGCgGcgccUCUgCgcCccggggCcGgcgaugaaAcAaaGcaAAcGCCAGuAcgAuGGCgACAGgCGCGaCucUUCcCAUAGuUUAUCCCUUuuAAA.........uauCacCgcUUgUUGCCCCGgacGuCgUggCgucCGGGGCUuUuuU
//
# STOCKHOLM 1.0

#=GF AC   RF01396
#=GF ID   isrN
#=GF DE   isrN Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   44.00
#=GF TC   44.60
#=GF NC   43.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   17


Z83734.1/1448-1306           UAAUAACGG-GUUCGUCACGUGUGUUAUCCGGACGGUAAUGAUAAACCGUUCUGCUCAGGU--UCAG-GCUCCGGC-AGGCCUGACGGAUACUGAGUCCGAAUGCCGUUAUCAG-AUGAGUGACCAGCUCACGCUUAAAGGCUGGUUUU
ABEI01000013.1/92763-92621   CAAUAACGG-GUUCGUCACGCGUGGUAUCCGGAUGGUAAUGGUAAACCGUUCUGCUCAGGU--UCAG-ACUCCGGC-AGGCCUGACGGAUACUGAGUCCAAAUGUCGUUAUCAG-AUGAGUGACCAGCUCACGCUUAAAGGCUGGUUUU
ABAN01000021.1/58135-58003   UAAUAACGG-GUUCGUCACGUGUGUUAUCCGGAC----------AACCGUUCUGCUCAGGU--UCAG-GCUCCGGC-AGGCCUGACGGAUACUGAGUCCGAAUGCCGUUAUCAG-AUGAGUGACCAGCUCACGCUUAAAGGCUGGUUUU
AM236323.1/45422-45564       CAAUAACGG-GCUCGUCAGGCGUGGUAUCCGGGCGGUAAUGGUAAACCGUUCUGCUCAGGU--UCAG-ACUCCGGC-AGGCCUGACGGAUACUGAGUCCGAACGUCGUUAUCAG-AUGAGUAACCAGCUCACGCUUAAAGGCUAGUUUU
AJ132945.1/6323-6465         GGAUCACCG-GUUCAUCACGUCGUUUAUUCGGUUGAUAACGAAACACCGUCCUGCUCAGCG--AUAA-CGUCCUGC-AUGCCUGGCGUAUGCUCAUCGUAAACUGCGUGGUCAG-AUAGUUGACGAGCUCACGCUUUAUCGCUGGUUUU
AM286416.1/1148-1285         CUCUUACGG------AAGAGCGCGACACUCUGCGCGAAGAAGUUAACCGACUUAAUCAGGA--GAUA-CGUCCUGC-AUGCCUGGCGUAUGCUCAUCGUAAACUGCGUGGUCAG-AUAGUUGAUGAGCUCACGCUUUAUCGCUGGUUUU
AJ555214.1/7077-6937         CAAUAACGG-GUUCAUCACGCGUGGUAUCCGGGCGGUAAUGGUAAACCGUUCUGCUCAGGU--UCAG-ACUCCGGC-AGG-CUGACGGAUACUGAGUCCGAAUGUCGUUAUCAG-AUGAGUGACCAGU-CACGCUUAAAGGCUGAUUUU
CP000654.1/152139-152281     GGAUCACCG-GUUCAUCACGCCGGGUAUCAGGCUGAUAAAAAUAUACCGUCCUGCUCAGCG--AUAA-CGUCCUGC-AGGCCUGGCGUAAACUCAUGGCAAAAUGCGCCGUCAG-AUAGCGGACGAGUUCACGCUUUAUCGCUGGUUUU
ABAT01000003.1/86261-86394   CUACAAGCC------UUAAAACGGAAACCAAGACCAUAA---ACUUCUGUUUGGGUCAUUU--UAAC-AAAUGAUC-UCG-UUGGAGCCGUAGGAUCGCAAAUUGCGCGGUCAG-GUAAUUGACGAGCUCACGCUUUAUCGCUGGUUUU
AP006726.1/124365-124229     UUAUCGCCC-GAUCAUCCCGCCGGC--UCUGCC----AGUGGUAAACGGUUCUGCUCUGCA--UCAG-CAGUCCGC-AUCCCCGCCGGACACUGAUACGGUAAGCCUCCCGCAG-AAAAUGUACCGCCUGACGCUUCUGAGCCGGCCUC
ABCP01000010.1/78386-78244   CAAUCACCG-GUUCAUCCCGGGAGGUGUCCGGCCGAUACCGGUACACAGAGUCACUGAUGC--CAGC-GAUUCGGCAGGCUCUGC-GAAUGCUGACGCCGUGAGCCUGCUUAAG-GUAAUCCACCCGUUCUCGUCGAACGGCUGGCUUU
CR628337.1/907551-907693     CAAUGACAC-UUUCAUCAGAGCGACUAUCCGGUUUAUAGCGAUAAACCGAGUCGCUGAUAC--CUAC-AACUUUGC-AAGCGCGGCGUAAACUCACAGUAUGA-GCAUUGACUGCAUAAUCAACCAACUCCCGACGCACAGUUGGCUUC
ABEH02000004.1/255206-255064 AGAUCACCA-GUUCAUCUCGGCGUAUUUCGGCUUGGAGAAAAUAUACCGUCCUGCUCAGCG--AUAA-UGACCUCC-AUGCUUGACGUAAGUACAUGGCAAAUUGCACUGUCAG-AUAGUUGACGCUCUAGAAUUUUAUCAAUGAUUUU
AAMK02000003.1/142277-142135 UAAUCACCG-GCUCAUCACGUCGCGUAUCCGGCUGAUAACGAAAUACCGUCCUGCUCAGCG--ACAA-UGUCCUGC-AGGCCUGGCGUAAGCUCAUGGCAAACUGCGCGGUCAG-AUAGCUGACCAGCUCACGCUUUAUCGCUGGUUUU
CP000821.1/2382844-2382986   CAAUAACGG-GGUCAUCCCGGCACUUAUCAGGCUGAUAACGGUAUACCGAUGGACUGAUGCCAACAACGCGGCAGG-CAAGUCG---GAUACUGGUUUGAUGUACAUUGAGCAC-AUAAUCAACCAGUUCACGCCUGACCGCUGGCUUC
CP000970.1/3226881-3226739   CAAUAACGG-GGUCGUACCACGUGGUAUCCGGACGGUAAUGGGAAACCGUUCUGCUCUGGU--UCAG-ACUCCGGC-AGGCCUGAUGGACACUGAGUCCAAAUGUCGUUAUCUG-AUGAGUAACAAGCUCACGCUUACAGGCUGGUUUU
AAJU02000001.1/52687-52547   CGAAAACGACGGCCACAGACUAGGGCAUCAUGC--AUAA-AAUCGACAGACCAGCUCAGGU--UCAG-ACUCCGGC-AGGCCUGACGGAUACUGAGUUCGAACGUCGUUAUCAG-AUGAGUAACCAGCUCACGCUUAAAGGCUGGUUUU
#=GC SS_cons                 :::::::::.:::::::::::::::((((-((,,,,,,,,,,,,,,,,<-<<<<<---<<<..____.>>>--->>.>>>->,,<<<<________________>>>>,,))-).)))---<<<-<<<____________>>>->>>::
#=GC RF                      caAUaACgg.GuUCAUCacGccgGguAUCcGgcuGAUAAcGgUAaACcGUccuGcUCAggu..ucAa.acucCugC.aggCCUGgcGgAuaCUGAuugcAAAugcCgcuguCAG.AUaAUUgACcAGCUCACGCUUuAucGCUGGUuUU
//
# STOCKHOLM 1.0

#=GF AC   RF01397
#=GF ID   isrO
#=GF DE   isrO Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; ClustalW; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   42.00
#=GF TC   42.80
#=GF NC   38.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   6


AE014613.1/3046397-3046597   AUGCCCAAUCCAUUGAC-GCCGGAAAGGGUCCGUGUGGAUGAUGAUGCCGCGAAUAUCCGAUAUGCCAGCAUAAUAUCGAAUCACGGCACAAUAGCGCUCGUCUGCGUUCUGUCAGGGCCUGUUUUGGUAAUGCCUUUCUUUCUGUUAUGCGCUACGCUGAUCGUCUGAGUAUAUGGCCUGGC--CAUGCUGCCGGGUCAUUUU
CP000026.1/3016000-3016200   AUGCCCAAUCCAUUGAC-GCCGGAAAGGGGCCGCGCGGAUGAUGAUGCGCCGAAUAUCCGAUAUGCCAGCAUAAUAUCGACUCACGGCAUAAUGGCGCUCGUCUGCGUUCUGUCAGGGCCUGUUUUGGUAAUGCCUUUCUUUCUGUUAUGCGCUACGCUGAUCGUCUGAGUAUAUGGCCUGGC--CAUGCUGCCGGGUCAUUUU
ABEJ01000004.1/222903-223103 AUGCCCAAUCCAUUGAC-GCCGGAAAGGGUCCGCGCGGAUGAUGAUGCCGCGAAUAUCCGAUAUGCCAGCAUAAUAUCGACUCACGGCGCAAUGGCGCUCGUCUGCGUUCUGUCAGGGCCUGUUUUGGUAAUGCCUUUCUUUCUGUUAUGCGCUACGCUGAUCGUCUGAGUAUAUGGCCUGGC--CAUGCUGCUGGGUCAUUUU
CP000647.1/3636004-3636189   GCGCGCGGUCUGC-GGCAGGCAGAAA---UUCAUAUUUGCG-CCACGCGGC-------GCGGCGGCCUCUCCUCGCU------AUUGCGCGUUGCCGUUCACAGAGCUGCCUCCAGGGCUUGUUUUGGUAAUGCCUUUCUCCCAUUUAUGGGCUACCCUAGUGGCCUGAGUACAUGACCCGGCGGGUUUGUGCCGGGUCAUUUU
AE006468.1/3198380-3198580   AUGCCCAAUCCAUUGAC-GCCGGAAAGGGGCCGCGUGGAUGAUGAUGCCGCGAAUAUCCGAUAUGCCAGCAUAAUAUCGACUCACGGCACAAUGGCGCUCGUCUGCGUUCUGUCAGGGCCUGUUUUGGUAAUGCCUUUCUUUCUGUUAUGCGCUACGCUGAUCGUCUGAGUAUAUGGCCUGGC--CAUGCUGCCGGGUCAUUUU
CP001113.1/3181914-3182114   AUGCCCAAUCCAUUGAC-GCCGGAAAGGGUCCGCGCGGAUGAUGAUGCCGCGAAUAUCCGAUAUGCCAGCAUAAUAUCGACUCACGGCACAAUGGUGCUCGUCUGCGUUCUGUCAGGGCCUGUUUUGGUAAUGCCUUUCUUUCUGUUAUGCGCUACGCUGAUCGUCUGAGUAUAUGGCCUGGC--CAUGCUGCCGGGUCAUUUU
#=GC SS_cons                 ((((-((-------(((.<<<<<<<-<<<<<<<<<<<<<<<<<<-<<<<<-<<-----<<<<<<_________>>>>>>-->>->>>>>>>------->>>>>>>>>>------->>>>>>->>>>>>>,,,,,,,,,,,,,,,<<<<-<<<___>>>>>>>,)))))-))))<<<<<<<<<<..______>>>>>>>>>>:::
#=GC RF                      gugCcCaaUCcauUGgC.gcCggaaAgGGccCgcgcgggcGacgAcGCcgCGaAUAUCCGauauGCCagcauaauauCGAcuCAcgGCgcgaUGgcGcuCgcccgcgcuCuguCAGggCCcGuuucGguAAUGCCUUUCUuuCugucaUGcGCUACgCugaccGcCuGAGuacauGgCCcGGC..caUgcUGCCgGGcCauUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01398
#=GF ID   isrP
#=GF DE   isrP Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; ClustalW; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   45.10
#=GF NC   42.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   7


AL627279.1/174694-174547   GUUUGUCUAAUGACGCUGCGCUUAUCGGGUCGGUGCCGGAUUGGUAAUUCAUUGAUAUUUUUGCAUUCCUCUCCGAGGGCAAUAAGGCGAAUGUCAUAACUACAAUACGUUUUAACCAUUCAGGCGGAAGUUGGCUUCCGCCUGUUUU
AE017220.1/4241094-4241241 GUUUGUCUAAUGACGCUGCGCUUAUCGGGUCGGUGCUGGAUUGGUAAUUCAUUGAUAUUUUUGCAUUCCUCUUCGAGGGCAAUAAGGCGAAUGUCAUAACUACAAUACGUUUUAACCAUUCAGGCGGAAGUUGGCUUCCGCCUGUUUU
ABAN01000010.1/44102-43955 GUUUGUCUAAUGACGCUGCGCUUAUCGGGUCGGUGCUGGAUUGGUAAUUCAUUGAUAUUUUUGCAUUCCUCUUCGAGGGCGAUAAGGCGAAUGUCAUAACUACAAUACGUUUUAACCAUUCAGGCGGAAGUUAGCUUCCGCCUGUUUU
AM933173.1/3479703-3479556 GUUUGUCUAAUGACGCUGCGCUUAUCGGGUCGGUGCCGGAUUGGUAAUUCAUUGAUAUUUUUGCAUUCCUCUUCGAGGGCAAUAAGGCGAAUGUCAUAACUACAAUACGUUUUAACCAUUCAGGCGGAAGUUAGCUUCCGCCUGUUUU
CP001138.1/4233108-4233255 GUUUGUCUAAUGACGCUGCGUUUAUCGGGUCGGUGCCGGAUUGGUAAUCCAUUGAUAUUUUUGCAUUCCUCUUCGAGGGCAAUAAGGCGAAUGUCAUAACUACAAUACGUUUUAACCAUUCAGGCGGAAGUUGGCUUCCGCCUGUUUU
CP001127.1/4183799-4183946 GUUUGUCUAAUGACGCAGCGCUUAUCGGGUCGGUACCGGAUUGGUAAUCCAUUGAUAUUUUUACAUUCCUCUUCGAGGGCAAUAAGGUGGAUGUCGUAACUACAAUACGUUUUAACCAUUCAGGCGGAAGUUGGCUUCCGCCUGUUUU
CP000886.1/4248109-4248256 GUUUGUCUAAUGACGCUGCGCUUAUCGGGUCGGUGCCGGAUUGGUAAUUCAUUGAUAUUUUUGCAUUCCUCUUCGAGGGUAAUAAAGCGAAUGUCAUAACUACAAUACGUUUUAACCAUUCAGGCGGAAGUUAGCUUCCGCCUGUUUU
#=GC SS_cons               ((((((---((((((---(((((<<<<<-----<<<<_____>>>>----->>>>>,,,,<<<<---<<<<___>>>>>>>>,,)))))--))))))----))))-))------------<<<<<<<<<<____>>>>>>>>>>::::
#=GC RF                    GuuuGuCUAauGaCgCuGCGccuauCggGUCGGugCcGGAUUgGcaAUuCAccGauAUUUuugCAUUCCuCUuCGaGGGcaaUAaggCGAAcGuCauAACUaCaaUaCGUUUUAACCAUUCaGGCGGaaGUUaGCuuCCGCCuGUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01399
#=GF ID   isrQ
#=GF DE   isrQ Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; ClustalW; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   58.20
#=GF NC   34.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   6


ABEJ01000001.1/95266-95427 UCAUGUGAUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGGCAUGUCGUCCGGGCAUAAAGUCAUAUCGCCUGAACAGAGAACAUGUUACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGUCCAAAAAUACGUGGCGCUGAAAGGCGCAUUUUU
AL627284.1/6011-6172       UCAUGUGGUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGGCGUGUCGUCCGGGCAUAAAGUCAUAUCGCCUGCACAGAGAACAUGUCACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGCCCAAAAAUACGUGGCGCUGAAAGGCGCAUUUUU
AE017220.1/4670675-4670836 UCAUGUGAUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGGCGUGUCGCCCGGGCAUAAAGUCAUAUCGCCUGAACAGAGAACAUGUUACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGCUCAAAAAUACGUGGCGCUGAAAGGCACAUUUUU
ABAN01000009.1/29307-29147 UCAUGUGAUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGACGUGUCGUCCGGGCAUAAAGUCAUAUCGCCUGAACAGAGAACAUGUUACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGCCCAAAA-UACGUGGCGCUGAAAGGCGCAUUUUU
CP001138.1/4718718-4718879 UCAUGUGAUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGGCGUGUCGUCCGGGCAUAAAGUCAUAUCGCCUGAACAGAGAACAUGUUACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGCCCAAAAAUACGUGGCGCUGAAAGGCGCAUUUUU
AE006468.1/4762997-4763158 UCAUGUGAUCUAACGUAUCACGACUAAACGUAAGGGUAAAGCGGCUGGCGUAUCGUCCGGGCAUAAAGUCAUAUCGCCUGAACAGAUAACAUCUCACUGACUUUGAAACGCGAUUUUAUAAUUUGCUGCCCAAAAAUACGUGGCGCUGAAAGGCGCAUUUUU
#=GC SS_cons               :::<<<<<<<____>->>>>>>,,,,,(((((-((((<<<<<<<-<<<<<<<<--<<<<<<<<<<______>>>->>>>>---->>-->>>>>>>>>>>->>>>,,,,,<<<<_________>>>>,))))-----))))),<<<<<____>>>>>::::::
#=GC RF                    UCAcGuGauCUAACGUauCaCgACUAAaCGuaAGGGcaaaGCgGCuggcguguCGuCCgGGCauaAAGUCAuauCGCCcGaACAGagAacacgccaCcGACuuuGAAACGCgaUUUUAUAAUucGCUgCCCAAAAAuaCGuGGcGCcGAAAgGCgCAUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01400
#=GF ID   istR
#=GF DE   istR Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; CMfinder; Infernal
#=GF SS   Predicted; CMfinder
#=GF GA   45.00
#=GF TC   47.10
#=GF NC   38.80
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   15620655
#=GF RT   The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide.
#=GF RA   Vogel J, Argaman L, Wagner EG, Altuvia S
#=GF RL   Curr Biol. 2004;14:2271-2276.
#=GF WK   TisB-IstR_toxin-antitoxin_system
#=GF SQ   7


AP009048.1/3787168-3787297 CGUCAAAAUUCGUGCC-GAAAUUGCGCGUUCUGCGCGGAACACGUAUACUUUCAGUGUUGACAUAAUACAGUGUGCUUUGCGGUUACCAGCCGCAG--GCGACUGACGAAACCUCGCUCCGGCGGGGUUUUUU
CP000034.1/3891048-3890919 CGUCAAAAUUCGUGCC-GAAAUUGCGCGUUCUGCGCGGAACAGGUAUACUUUCAGUGUUGACAUAAUACAGUGUGCUUUGCGGUUACCAGCCGCAG--GCAGCUGACGAAACCUCGCUCCGGCGGGGUUUUUU
CP000647.1/4463903-4463773 AGAGAAAAACCG-ACCUUAAAUUGCGCGAACUGCAGCGAUCGCGUAUACUUUUGGCGUUGACGUAAUACAGUGUGCUU-GCGGCUACCACCUGUAACCAUGCUGAUAAAAACCUCGCUCCGGCGGGGUUUUUU
CP000653.1/26847-26977     CGUCAAAAUCCGUGCCUGAAAUUGCGCGUUCGUCGCCGAUCGCGUAUACUUCGUGCGUUGACGUAACACAGUGUGUUUUGCGGAAACCAACCGCAU--AACCCUGAAAAAACCUCGCUUCGGCGGGGUUUUUU
AL627280.1/122581-122710   CAUCAAAAUUCGCGCC-GAAAUUGCGCGUUCUGCACAGAACGCGUAUACUUCUGCUGUUGACAUAACACAGUGUGCUUCGCGGCUACCACCCGCAU--UACGCUGUAAGAACCUCGCUUCGGCGAGGUUUUUU
BA000007.2/4643722-4643593 CGUCAAAAUUCGUGCC-GAAAUUGCGCGUUUUGCGCGGAACACGUAUACUUUCUGUGUUGACAUAAUACAGUGUGCUUUGCGGUUACCAGCCGCGG--GCGGCUGACGAAACCUCGCUCCGGCGGGGUUUUUU
CU928145.2/4228267-4228138 CGUCAAAAUUCGUGCC-GAAAUUGCGCGUUCUGCGCGGAACACGUAUACUUUCAGUGUUGACAUAAUACAGUGUGCUUUGCGGUUACCAGCCGCAG--GCGGCUGAUGAAACCUCGCUCCGGCGGGGUUUUUU
#=GC SS_cons               :<<<<<----<<----.<<<--<<<<<<<<<<____>>>>>>>>>>--->>>--->>>>>>>,,,,,,<<<<-<<<<-<<<<<_______>>>>>>..>>>>>>>,<<<<<<<<<<<____>>>>>>>>>>>:
#=GC RF                    cGuCaaAAuuCgugCC.gaaAUugCgcGuuccgCgcggaaCgcGuaUACuucuagcGuuGaCaUAAuACaGcGcgccUuGCGGuuACCAgCCGCag..gcggCuGaaaaaaCCcCGCUcCGGCGgGGuuuuuU
//
# STOCKHOLM 1.0

#=GF AC   RF01401
#=GF ID   rseX
#=GF DE   rseX Hfq binding RNA
#=GF AU   Barquist L; 0000-0003-4732-2667
#=GF SE   Predicted; mafft; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   51.40
#=GF NC   45.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16513633
#=GF RT   Down-regulation of porins by a small RNA bypasses the essentiality of the
#=GF RT   regulated intramembrane proteolysis protease RseP in Escherichia coli.
#=GF RA   Douchin V, Bohn C, Bouloc P
#=GF RL   J Biol Chem. 2006 May 5;281(18):12253-9.
#=GF RN   [2]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [3]
#=GF RM   18399940
#=GF RT   Systematic deletion of Salmonella small RNA genes identifies CyaR, a
#=GF RT   conserved CRP-dependent riboregulator of OmpX synthesis.
#=GF RA   Papenfort K, Pfeiffer V, Lucchini S, Sonawane A, Hinton JC, Vogel J
#=GF RL   Mol Microbiol. 2008;68:890-906.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   12


U00096.2/2031673-2031762       UUUUUAUUAUUCUGUGUC-AUGAUGCUUCCGUUAUUAGCCUUUUAUCGUCUUGUUUAUA-UUUUUUGG-------G-CCGGCA-UGAU--GCCGGCUUUUUUU
ADUL01000065.1/419508-419598   UUUUUAUUUUUCUGUGUC-AUCAUGCCUCCGUUAUUAGCCUUUUAUCGUCUUGUUUAUAUUUUUUUUG-------G-CCGGCA-UGAU--GCCGGCUUUUUUU
AEHW01000009.1/678666-678577   UUUUUAGAUUUCUGUGUC-AUGAUAACCCCGUUAUUAGCCUUUUAUCGUCUUGUUUAUA-UUUUUUGG-------G-CCGGCA-UGAU--GCCGGCUUUUUUU
AEZL01000056.1/58439-58351     CUUUUAUUUUUCUGUGUC-AUGAUGCCUCCGUUAUUAGCCUUUUAUCGUCUUGUUUAUA--UUUUUGG-------G-CCGGCA-UGAU--GCCGGCUUUUUUU
ABKX01000010.1/117519-117606   UUUUUUGUUUUCUGUGUC-AUGAUACUUACGUUAUUAGCCUUUUAUCGUCUUAUUU-CA--UUUUUUG-------G-CCGGCA-UGAU--GCCGGCUUUUUUU
ADTS01000213.1/8514-8604       UUUUUAUUAUUCUGUGUC-AUGAUGCCUCCGUUAUUAGCCUUUUAUCGUCUUGUUUAUA-UUUUUUGG-------GCCCGCCG-GGGG--GCGGGCUUUUUUU
ABAK02000001.1/1456553-1456647 UUAUUAGCAUUAAGUGUC-AGAAUGAUUCGGUUAUUAGCCUUUUAUCAUUUAUUUUAUC-AUUACCCAC--AUU-A-CCGGCAUUUAU--GCCGGUUUUUUUU
AEJW01000167.1/545-457         UUUUUUGUUUUCUGUGUC-AUGAUAACUCCGUUAUUAGCCUUUUAUCGUCUUGUUUAUA--UUUUUGA-------G-CCGGCA-UGAA--GCCGGCUUUUUUU
CP000880.1/933210-933116       UUAUUGACAUUAAAUGUC-ACAAUGAUCCAGUUAUUAGCCUUCUAUCAUUUAUUUUACU-AUUACUCAC--AUU-G-CCGGCAUUUAU--GCCGGUUUUUUUA
FR877557.1/1977492-1977586     UUAUUGACAUUACAUGUC-AAAAUGAUCUGGUUAUUAGCCUUUUAUCAUUUAUUUUUCU-AUUACCCUC--AUU-G-CCGGCAGUGAU--GCCGGUUUUUUUU
FN543502.1/2145171-2145264     UUCU-GUUAAU-CAUGUC-AUUAUACUUUGGUUAUUAGCCUUACAUUAUUGAGAUACCCCUUUACUUU--UAUU-A-CCGGCAUCUGU--GCCGGUUUUUUUU
CU928158.2/1994605-1994703     UUUCACAUUUUGUAUG-CAAUGAUAGCCCGGUUAUUAGCCUUUUAUCAUCUACAAUCUG--UUACUACCCUAUUUA-CCGACAUUAAUUUGUCGGUUUUUUUU
#=GC SS_cons                   :::::::::::::<<---.<<<<<______>>>>>-->>--------------------.--------...---.<.<<<<<______..>>>>>>:::::::
#=GC RF                        UUuUUauuaUUauGUGUC.AugAUaauucgGUcaUUAGCCUUUUAUCaUcUagUUUaua.uUUauUua...AUU.g.CCGGCAuUgAU..GCCGGcUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01402
#=GF ID   STnc150
#=GF DE   STnc150 Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   60.00
#=GF TC   60.80
#=GF NC   51.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.98 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   17971080
#=GF RT   A small non-coding RNA of the invasion gene island (SPI-1) represses outer
#=GF RT   membrane protein synthesis from the Salmonella core genome.
#=GF RA   Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J
#=GF RL   Mol Microbiol. 2007;66:1174-1191.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   9


AL627271.1/218020-218286     CCUUUUAUUGAAAUAAUCCCCUGAUAAUAACAAUAAAUCUGGUAAGGCACUUUCAAAAAAUAGCCAAACCACACAUCAUAAAGAAAACCAC-CACAAUCAAAAUCGGUAACUAUCAGCUUUCAGGGG-GUCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGGACUACUAUUGCGGUCUGAAUUGAGGACGUUUUGAUAAAUU-----------AUUUUGAUAACCGUUCGAAUACUAAUAAUAAAUAUCCUCCGGCAUAGCCGGAGGUUUUUCUGAUG
AY633740.1/1971-1706         CUUUUUAUUAAAAAAUUCUCCUGAUAAUAACAAUAAAUCUGGUAAGGCACUUUCAAAAAAUAGCCAAAUCACACAUUAUUAAGAAAACCAC-UACAAUCAAAAUCGGUAACUAUCAGCUUUCAGGGGGGUCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGAACUACUAUUGCGGUCUGAAUUGAGGGAGUUUUGAUAAA-------------GUUUUGAUAACCGUUCGAAUACUAAUAAUAAAAACGGGGACGUUAAGUCCCCGUUUUUGUUUUUA
CP000026.1/1673567-1673844   CCUUUUAUUGAAAUAAUCCCCUGAUAAUAACAAUAAAUCUGGUAAGGCACUUUCAAAAAAUAGCCAAACCACACAUCAUAAAGAAAACCAC-CACAAUCAAAAUCGGUAACUAUCAGCUUUCAGGGGG-UCUCAGGUUAUCAUGACGAUCGGCGUAAAGGAUGGAUUACUAUUGCGGUCAGAAUUGAGGGAGUUUUGAUAAAUUUUUUUGAUAAAAUUUUGAUAACCGUUCGAAUGCUAAUAAUAAAAACGGGGACGUUAAGUCCCCGUUUUUGUUUUUA
CP001138.1/1888215-1888493   CCUUUUAUUGAAAUAUUAUCCUGAUAAUAACAACAAAUCUAAUAAGGCACUUUCAAAAAAUAGCCAAACCACCCAUCAUAAAGAAAACCACACACAAUCAAAAUCGGUAACUAUCAGCUUUCAACGGG-GCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGGAUUACUAUUGCGGUCAGAAUUGAGGAAGUUUUGAUAAAUUUUUUUGAUAAAAUUUUGAUAACCGUUCGAAUGCUAAUAAUAAAAACGGGGACGUUAAGUCCCCGUUUUUGUUUUUA
CP001144.1/2041074-2041352   CUUUUUAUUAAAAAAUUAUCCUGAUAAUAACAAUAAAUCUGGUAAGGCACUUUCAAAAAAUAGCCAAAUCACACAUUAUUAAGAAAACCAC-UACAAUCAAAAUCGGUAACUAUCAGCUUUCAGGGGGGUCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGAACUACUAUUGCGGUCUGAAUUGAGGGAGUUUUGAUAAAUUUUUUUGAUAAAGUUUUGAUAACCGUUCGAAUACUAAUAAUAAAAACGGGGACGUUAAGUCCCCGUUUUAGUUUUUA
ABEH02000010.1/181974-181708 CCUUUUAUUGAAAUAUUAUCCUGAUAAUAACAACAAAUCUGAUAAGGCACUUUCAAAAAAUAGCCAAACCACACAUCAUAAAGAAAACCAC-UACAAUCAAAAUCGGUAACUAUCAAUUUUCAGGGAA-UCUCAGGUUACCAUGACGAUCGGGGUAAAGGAUAGAUUACUAUUGCGGUCUGAAUUGAGGAAGUUUUGAUAAAUU-----------AUUUUGAUAACCGUUCGAAUGCUAAUAAUAAAAACGGGAACGUUAAGUCCCCGUUUUAGUUUUUA
ABAK02000001.1/634826-634549 CCUUUUAUUGAAAUAUUAUCCUGAUAAUAAAAACAAAUCUGAUAAGGCACUUUCAAAAAAUAGCCAAACCACACAUCAUAAAGAAAACCAC-CACAAUCAAAAUCGGUAACUAUCAACUUUCAGCGGG-GCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGGAUUACUAUUGCGGUCAGAAUUGAGGGAGUUUUGAUAAAUUUUUUUGAUAAAGUUUUGAUAACCGUUCGAAUGCUAAUAAUAAAAACGGGGACGUUAAGUCCCCGUUUUUGUUUUUA
CP001120.1/1330954-1330700   CUUUUUAUUAAAAAAUUAUCCUGAUAAUAACAAUAAAUCUGGUAAGGCACUUUCAAAAAAUAGCCAAAUCACACAUUAUUAAGAAAACCAC-UACAAUCAAAAUCGGUAACUAUCAGCUUUCAGGGGGGUCUCAGGUUAUCAUGACGAUCGGGGUAAAGGAUGAACUACUAUUGCGGUCUGAAUUGAGGGAG------------------------UUUUGAUAACCGUUCGAAUACUAAUAAUAAAUAUCCUCCGGCAUAGCCGGAGGUUUUUCAGAUG
CP001127.1/1289610-1289344   CCUUUUAUUGAAAUAUUAUCCUGAUAAUAACAACAAAUCUGAUAAGGCACUUUCAAAAAAUAGCCAAACCACACAUCAUAAAGAAAACCAC-UACAAUCAAAAUCGGUAACUAUCAAUUUUCAGGGAG-UCUCAGGUUACCAUGACGAUCGGGGUAAAGGAUGGAUUACUAUUGCGGUCUGAAUUGAGAGAGUUUUGAUAAAUU-----------AUUUUGAUAACCGUUCGAAUACUAAUAAUAAAAACGGGAACGUUAAGUCCCCGUUUUUAUUUUAA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::<<<______________>>>,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,<<<-<<_________________>>->>>---------------------------...........--------------------------<<<<<<<<<<<<-<<_____>>->>>>>>>>>>>>::::
#=GC RF                      CcUUUUAUUgAAAuAuUaUCCUGAUAAUAAcAAuAAAUCUGaUAAGGCACUUUCAAAAAAUAGCCAAAcCACACAUcAUaAAGAAAACCAC.uACAAUCAAAAUCGGUAACUAUCAgcUUUCAGgGgG.uCUCAGGUUAUCAUGACGAuCGGggUAAAGGAUGgAuUACUAuuGCGgUCuGAAUUGAGGgAGUUUUGAUAAAUU...........aUUUUGAUAACCGUUCGAAUaCUAAUaacaaaaacggggaCGUuaAGuCcccguuuuuguuuuUA
//
# STOCKHOLM 1.0

#=GF AC   RF01403
#=GF ID   STnc290
#=GF DE   STnc290 Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; ClustalW; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   67.30
#=GF NC   41.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   17971080
#=GF RT   A small non-coding RNA of the invasion gene island (SPI-1) represses outer
#=GF RT   membrane protein synthesis from the Salmonella core genome.
#=GF RA   Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J
#=GF RL   Mol Microbiol. 2007;66:1174-1191.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   6


CP000026.1/3012573-3012509 AUAAAAGAGUACCAAAAUGUCGUAUUCUGACAUGUUUACGAAGGGAGUACCGCUCCCUUCUUUUU
ABAN01000004.1/15088-15152 AUAAAAGAGUACCAAAAUGUCGUAUUCUGACAUGUUUACGAAGGGAGUACCGCUCCCUUCUUUUU
AE014613.1/3037123-3037059 AUAAAAGAGUACCAAAAUGUCGUAUUCUGACAUGGUUACGAAGGGAGUACCGCUCCCUUCUUUUU
AE017220.1/3153124-3153060 AUAAAAGAGUACCAAAAUGUCGUAUUCUGACAUGUUUACGAAGGGAGUACCGCUCCCUUCUUUUU
CP001127.1/3098499-3098435 AUAAAAGAGUACCAAAAUGUCGUAUUCUGACAUAUUUACGAAGGGAGUACCGCUCCCUUCUUUUU
CP001113.1/3178519-3178455 AUAAAAGAGUACCAAAAUGUCGUAUUCUGACAUGUUUACGAAGGGAGUACCGCUCCCUUCUUUUU
#=GC SS_cons               <<<--<<<<<<<_________>>>>>>>---->>>----<<<<<<<<_____>>>>>>>>:::::
#=GC RF                    auAAAAGAgUACCAAAAUGUCGUAuUCUGACAUguUUACGAAGGGAGUACCGCUCCCUUCUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01404
#=GF ID   PinT
#=GF PI   STnc440;
#=GF DE   PinT (STnc440) Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; CMfinder; Infernal
#=GF SS   Predicted; CMfinder
#=GF GA   60.00
#=GF TC   72.20
#=GF NC   33.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   17971080
#=GF RT   A small non-coding RNA of the invasion gene island (SPI-1) represses outer
#=GF RT   membrane protein synthesis from the Salmonella core genome.
#=GF RA   Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J
#=GF RL   Mol Microbiol. 2007;66:1174-1191.
#=GF RN   [3]
#=GF RM   26789254
#=GF RT   Dual RNA-seq unveils noncoding RNA functions in host-pathogen
#=GF RT   interactions.
#=GF RA   Westermann AJ, Forstner KU, Amman F, Barquist L, Chao Y, Schulte LN,
#=GF RA   Muller L, Reinhardt R, Stadler PF, Vogel J
#=GF RL   Nature. 2016;529:496-501.
#=GF WK   PinT_small_RNA
#=GF SQ   4


AE017220.1/4493746-4493821 AGUAACGGAUUACUUUGUGGUGUAGCGUAACGGUAAUUGUCCUCCUCAUAUUUGCGGCAGCGUAGUCUGCCGCUUU
CP000026.1/4311107-4311182 AGUAACGGAUUGCUUUGUGGUGUAGCGUAACGGUAAUUGUCCUCCUCAUAUUUGCGGCAGCGUAGUCUGCCGCUUU
CP000857.1/4489121-4489196 AGUAACGGAUUACUUUGUGGUGUAGCGUAACGGUAAUUGUCCUCCUCAUAUUUGCGGCAGCGUAGUCUGCCGCUUU
CP001138.1/4481325-4481400 AGUAACGGAUUACUUUGUGGUGUAGCGUAACGGUAAUUGUCCUCCUCAUAUUUGCGGCAGCGUAGUCUGCCGCUUU
#=GC SS_cons               ::::::<<<<<<<<_________________>>>>--->>>>-----------<<<<<<<______>>>>>>>:::
#=GC RF                    AGUAACGGauuaCuUUGUGGUGUAGCGUAACgGuaAUUguCCUCCUCAUAUUUGCGGCaGCGUAGUCuGCCGCUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01405
#=GF ID   STnc490
#=GF PI   STnc490k;
#=GF DE   STnc490 Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   56.00
#=GF TC   56.80
#=GF NC   55.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   76


AE014613.1/1746000-1745877   AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
ABEL01000013.1/45503-45626   AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
AL627266.1/195132-195255     AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
DQ077525.1/159-282           AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
AE014613.1/3012963-3012840   AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
CP000026.1/3882477-3882354   AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
AL627267.1/138113-138236     AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
CP000026.1/3012496-3012373   AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
ABAO01000002.1/1828-1951     AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
X91136.1/330-453             AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
ABAO01000010.1/100381-100258 AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
Z83734.1/2384-2261           AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
Y08755.1/90-213              AACCCCCUGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGUCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
CP000308.1/1021887-1022010   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AE014075.1/1239344-1239467   AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUGAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-ACUUUGCGGUCUGGCAACUGCAAGUGUCAAACAAGAAAUCAAAAG
DQ523609.1/3040-3163         AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUGAGGCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-ACCUUGCGGUCUGGCAACUGCAAGUGUCAAACAAGAAAUCAAAAG
AE014075.1/81944-82067       AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUGAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-ACUUUGCGGUCUGGCAACUGCAAGUGUCAAACAAGAAAUCAAAAG
CP000243.1/36021-36144       AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUGAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-ACCUUGCGGUCUGGCAACUGCAAGUGUCAAACAAGAAAUCAAAAG
CP000305.1/4400537-4400414   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
ABEL01000002.1/218485-218363 AACCCCCAGCCAGGCUGGG-G-UUCUGGAAAGCUUUCAGCCUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAAAAAUCAAAAG
CP000308.1/2451735-2451612   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
CP000668.1/1737900-1738023   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AE017042.1/1283001-1282878   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAYS01000002.1/249563-249440 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
DQ381420.1/134460-134337     AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUGAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-ACCUUGCGGUCUGGCAACUGCAAGUGUCAAACAAGAAAUCAAAAG
AF222258.1/50-173            AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUGAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-ACCUUGCGGUCUGGCAACUGCAAGUGUCAAACAAGAAAUCAAAAG
ABAT01000010.1/101607-101730 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAYR01000002.1/438845-438722 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
ABAT01000009.1/591-468       AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAYT01000004.1/236568-236691 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AM286415.1/1888472-1888595   AACCUCCAGCUAGGCUGGA-GGUUCCGUAAAGCUUUCAGCUUUGAGCCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-ACCUUGCGGUCUGGCAACUGCAAUGGUCAAACAAGAAAUCAAAAG
CP000305.1/496320-496197     AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
BX936398.1/736927-737050     AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AE017042.1/2974243-2974120   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
CP000720.1/2045958-2045835   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AL590842.1/3242646-3242769   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
CP000720.1/1944057-1944180   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
CP000668.1/2075044-2074921   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAYR01000004.1/182161-182038 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
ABCD01000001.1/694882-694759 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AJ698720.1/37535-37412       AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AL590842.1/300421-300544     AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AE009952.1/861638-861761     AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
CP000034.1/4186955-4187078   AACCCCCUGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUGAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-ACUUUGCGGUCUGGCAACUGCAAGAGUCAAACAAGAAAUCAAAAA
ABCD01000007.1/209365-209242 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
BX950851.1/2890491-2890368   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGCCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAACGUUCAACAAGAAAUCAAAAG
AAUB01000177.1/2340-2217     AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAYV01000002.1/356645-356522 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAYU01000009.1/102033-101910 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAYU01000006.1/84646-84523   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
BX936398.1/838160-838283     AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAYT01000001.1/782445-782568 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAYS01000006.1/192605-192728 AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAYV01000009.1/44685-44808   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AAUB01000188.1/4589-4712     AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AM286415.1/1478683-1478560   AACCUCCAGCUAGGCUGGA-GGUUCCGUAAAGCUUUCAGCUUUGAGCCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCCACUGCAAAUGUUCAACAAGAAAUCAAAAG
AE009952.1/4300688-4300565   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
U22457.1/992-1115            AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AJ238014.1/314-437           AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AJ430202.1/2387-2264         AACCCCCAGCUAGGCUGGG-GGUUCCGUAAAGCUUCCAGCUUUGGGGCGGAUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-ACCUUGCGGUCUGGCAACUGCAAUGGUCAAACAAGAAAUCAAAAG
AY150843.2/64946-65069       AACCUCCCGCUAGGCUGGA-GGUUCCGUAAAGCUUUCAGCUUUGAGCCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCCACUGCAAAUGUUCAACAAGAAAUCAAAAG
AJ238013.1/383-506           AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
Y09990.1/697-820             AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
X56834.1/10-133              AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
AAWP01000012.1/94396-94274   AACCCCCAGCUAGGCUGGG-GGUUCCGUAAAGCUUACAGCUAUAAGUCAGUUAUAUAA-CCCCUUUCAAUUUGAUAAAAAC-GUCUUGUGGUCUGGCAACUGCAAGAGUUAAUUAAG-AAUUGAAAG
CP000112.1/486984-487101     AACCCCCCGCUAGGCGGGG-GGGUCCGUAAAGCUUAAAGCUAUAGAGAUAUUAGUAAAACUCCUUUUGAUUUGCU-AAUUAAUCCCUGCGGUCUGGCAACUGCAGGU----GGCA---AAUCAAAAG
CP000668.1/3189373-3189251   AACCCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUU-CAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
FM200053.1/3008170-3008047   AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
AAYT01000019.1/52465-52345   ---CCCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
CP000970.1/3249833-3249712   AACCCCCAGCUAGGCUGGG-GG--CCGGAAAGCUUUCAGCUUUGAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-ACCUUGCGGUCUGGCAACUGCAAGUGUCAAACAAGAAAUCAAAAG
AAYT01000006.1/227345-227226 ----CCCAGCUAGGCUGGG-GGUUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
AF449498.2/941-820           AAACACCAGCCAGGCUGGUUGGUUCAGUUAAGCUUUCAGCUUCGAGAAUUUUAUGAAAG---CUAUUGAUUUGUU-AAAAU-AAAUCACAGUCUGGUGACUGCAAAAGUUAAACGAGAAAUCAAAAG
Y09991.1/620-743             AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUAAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-AUCUUGCGGUCUGGCAACUGCAAAAGUUCAACAAGAAAUCAAAAG
EU330199.1/32643-32766       AACCCCCAGCUAGGCUGGG-GGUUCCGGAAAGCUUUCAGCUUUGAGCCAGUUAUUAAAACCCCUUUUGAUUUGUU-AAAAC-ACCUUGCGGUCUGGCAACUGCAAGUGUCAAACAAGAAAUCAAAAG
CP000970.1/1108420-1108541   --UCCCCAGCCAGGCUGGG-GGUUCCGGAAAGCUUUCAGUUUUGAGCCAGUUAUUAAAACCUCUUUUGAUUUGUU-AAAAC-ACCUUGCGGUAUGGCAACAGCAAGUGUCAAACAAAAAAUCAAAAG
AAOS02000094.1/908-786       AACCCCCAGCUAGGCUGGG-G-UUCAGUAAAGCUUUCAGCUUUGGGUCAGUUAUAAAAACCCCUUUUGAUUUGUU-AAAAC-AGUUUGCGGUCUGGCAACUGCAAAUGUUCAACAAGAAAUCAAAAG
#=GC SS_cons                 <<<<<<<<<<___>>>>>>.>>>>,,,,<<<<<<___>>>>>>-------------------<<<<<<<<<<<<<.--<<<.-<<<<<<<<<______>>>>>>>>>>>>->>>>--->>>>>>>>>
#=GC RF                      aacCcCCaGCUAGGCuGGg.GguuCaGuaaaGCuUucaGCuuugaGucagUUAuaAAAACcCCuuuuGauuuGuu.AAaac.AccuuGCgGuCUGGcAaCcGCaaggguucaaCaAGAaauCaaaaG
//
# STOCKHOLM 1.0

#=GF AC   RF01406
#=GF ID   STnc500
#=GF DE   STnc500 Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   44.00
#=GF TC   44.90
#=GF NC   25.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   8


ABEJ01000009.1/99235-99518   AUAGUUCCUGCUCUUGAGGGCUGAUUGCGGCACAAAGCCUGCAAUAUCGAACAGAGUAGAGCCUAUCAAGUCUGCGGCAUGAAAAAAAGCGCGAUGUAAGUAAAGGAGGGGGAAUAUUUACAUCGCGUUGCCAACUUAUGACAGAACAUCACUGGAGAGUAAUCUGU-UGCUCUUACGGUGUUUAUAGCGCGCCAUUUGACGGAUGGUUUAUACUUGGCCCGGUAUUGUCGCCCCGGGCGUUGGCGUCACCGUGUGCUGUGUCGGUAUAGCGUGGUAUCAUGAAA
ABEL01000010.1/148270-148554 AUAGUUCCUGCUCUUGAGGGCUGAUUGCGGCACAAAGCCUGCAAUAUCGAACAGAGCAGAGCCUAUCAAGUCUGCGGCAUGAAAAAAAGCGCGAUGUAAGUAAAGGAGGGGGAAUAUUUACAUCGCGUUGCCAACUUAUGACAGAACAUCACUGGAGAGUAAUCUGUUUGCUCUUACGGUGUUUAUAGCGCGCCAUCUGACGGAUGGUUUAUAUCUGGCCCGGUAUUGUCGCCCCGGGCGUUGGCGUCACCGUGUGCUGUGUCGGUAUAGCGUGGUAUCAUGAAA
AE014613.1/1854565-1854281   AUAGUUCCUGCUCUUGAGGGCUGAUUGCGGCACAAAGCCUGCAAUAUCGAACAGAGCAGAGCCUAUCAAGUCUGCGGCAUGAAAAAAAGCGCGAUGUAAGUAAAGGAGGGGGAAUAUUUACAUCGCGUUGCCAACUUAUGACAGAACAUCACUGGAGAGUAAUCUGUUUGCUCUUACGGUGUUUAUAGCGCGCCAUCUGUCGGAUGGUUUAUAUCUGGCCCGGUAUUGUCGCCCCGCGCGUUGGCGUCACCGUGUGCUGUGUCGGUAUAGCGUGGUAUCAUGAAA
AE017220.1/1195456-1195740   AUAGUUCCUGCUCUUGAGGGCUGAUUGCGGCACAAAGCCUGCAAUAUCGAACAGAGCAGAGCCUAUCAAGUCUGCGGCAUGAAAAAAAGCGCGAUGUAAGUAAAGGAGGGGGAGUAUUUACAUCGCGUUGCCAACUUAUGACAGAACAUCACUGGAGAGUAAUCUGUUUGCUCUUACGGUGUUUAUAGCGCGCCAUCUGACGGAUGGUUUAUAUCUGGCCCGGUAUUGUCGCCCCGCGCGUUGGCGUCACCGUGUGCUGUGUCGGUAUAGCGUGGUAUCAUGAAA
CP000026.1/1782167-1781883   AUAGUUCCUGCUCUUGAGGGCUGAUUGCGGCAAAAAGCCUGCAAUAUCGAACAGAGCAGAGCCUAUCAAGUCUGCGGCAUGAAAAAAAGCGCGAUGUAAGUAAAGGAGGGGGAAUAUUUACAUCGCGUUGCCAACUUAUGACAGAACAUCACUGGAGAGUAAUCUGUUUGCUCUUACGGUGUUUAUAGCGCGCCAUCUGACGGAUGGUUUAUAUCUGGCCCGGUAUUGUCGCCCCGCGCGUUGGCGUCACCGUGUGCUGUGUCGGUAUAGCGUGGUAUCAUGAAA
AE006468.1/1216157-1216440   AUAGUUCCUGCUCUUGAGGGCUGAUUGCGGCACAAAGCCUGCAAUAUCGAACAGAGCAGAGCCUAUCAAGUCUGCGGCAUGAAAAAAAGCGCGAUGUAAGUAAAGGAGGGGGAAUAUUUACAUCGCGUUGCCAACUUAUGACAGAACAUCACUGGAGAGUAAUCUGU-UGCUCUUACGGUGUUUAUAGCGCGCCAUUUGACGGAUGGUUUAUACCUGGCCCGGUAUUGUCGCCCCGCGCGUUGGCGUCACCGUAUGCUGUGUCGGUAUAGCGUGGUAUCAUGAAA
CP001113.1/1218496-1218780   AUAGUUCCUGCUCUUGAGGGCUGAUUGCGGCACAAAGCCUGCAAUAUCGAACAGAGCAGAGCCUAUCAAGUCUGCGGCAUGAAAAAAAGCGCGAUGUAAGUAAAGGAGGGGGAAUAUUUACAUCGCGUUGCCAACUUAUGACAGAACAUCACUGGAGAGUAAUCUGUUUGCUCUUACGGUGUUUAUAGCGCGCCAUCUGACGGAUGGUUUAUAUCUGGCCCGGUAUUGUCGCCCCGCGCGUUGGCGUCACCGUGUGCUGUGUCGGUAUAGCGUGGUAUCAUGAAA
ABEH02000010.1/54557-54840   AUAGUUCCUGCUCUUGAGGGCUGAUUGCGGCACAAAGCCUGCAAUAUCGAACAGAGCAGAGCCUAUCAAGUCUGCGGCAUGAAAAAAAGCGCGAUGUAAGUAAAGGAGGGGGAAUAUUUACAUCGCGUUGCCAACUUAUGACAGAACAUCACUGGAGAGUAAUCUGU-UGCUCUUACGGUGUUUAUAGCGCGCCAUUUGACGGAUGGUUUAUACUUGGCCCGGUAUUGUCGCCCCGGGCGUUGGCGUCACCGUGUGCUGUGUCGGUAUAGCGUGGUAUCAUGAAA
#=GC SS_cons                 :::::::((((-((((((((((,<<<<<<<<_____>>>->>>>>,<<_____>>,,,,)))))-)))))---))))[[[[[,,,,,<<<<<<<<<<<<<<<____________>>>>>>>>>>>>>>>(((,,,,,,,,,,,<<<<<<<----<<<<<<<_______>>>>>>>-->>>>>>>,,,,,,,<<<<<<_____>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,))),]]]]]:::
#=GC RF                      AUAGUUCCuGCUCuuGagGGCuGauuGCGGCAcAAAGCCUGCaauAuCGAACAGaGcAGaGCCuAuCaaGUCUGCgGCauGaAAAAAagCGCGauGuaaguaAAGGAGGGGGAAuauuuaCauCGCGuugCCAACUUAUGACAgaaCauCACUGgaGaGuaAUCUGUUugCuCuuACGguGuuuAUAGCGCgCCaucUGACGgauGGuUUAUAucUGGCCCGGUAUUGUCGCCCCGcGCGUUGGCGUCACCGUGUGCUGUGUCGGUAUAGCGUGGuAuCauGAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01407
#=GF ID   STnc560
#=GF DE   STnc560 Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   55.00
#=GF TC   56.50
#=GF NC   54.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF CC   Original sequence was AE014075.1/1805202-1804553. Based upon sequence
#=GF CC   conservation this was trimmed to AE014075.1/1805101-1804887.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   12


AE005174.2/1939628-1939841   CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
AE014075.1/1805101-1804887   CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGUUUUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
CP000034.1/1455774-1455986   CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU--UUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
CP000266.1/1628757-1628544   CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
CP000036.1/1598345-1598558   CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUUCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
CP000038.1/1675303-1675516   CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAGGUGAUG
ABAN01000003.1/243628-243410 GCUUCAUUGAUAUUGACGGUGCUACAGUCGUUAGCGAUCCGUUAUCCUCGCAAGAAUUUGCCCGGUAGCGUAUAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUUACCGCUGGUGAACCGGCGGU-UUUUUUUGCCUGCCAUCCAGACAAAAGCGGCCCCUUGCGCAACGAUGCAGCAAGGGGCCGGCUCUGCGAGGGAUUAUCUCCGUUCAUUAAUCA
CP000468.1/1667136-1666923   CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
CP000970.1/1619937-1620150   CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAGUUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
AP009048.1/1624662-1624449   CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUUCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
FM180568.1/1719664-1719451   CAUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU-UUUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
AE005674.2/1592783-1592995   CUUUCAUUGAGAAAACUGAUGCUACUGU-GUCAACGAUCCGUUAUCAGUGCAGGAAAAUGCCUGUUAGCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUCACCGCCGGUUUACUGGCGGU--UUUUUUCGCCGUCAUAAAAAUC----AGGCCCCUUGUACACAACUGUAACAAGGGGCCGGUUAGGUGAGGGAUUAUCUCCGUUCAUUAGUCA
#=GC SS_cons                 :::::::::::::::::<<<<<____>>.>>>,,,,,,,<<<<<-<<<-<<<______>>>>>>->>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<____>>>>>>>>.---------------------<<....-<<<<<<<<<<<<<____>>>->>>>>>>>>>>>::::::::::::::::::::::::::::::::
#=GC RF                      caUUCAUUGAgAAAAcUGaugCUACuGu.guCAACGAUcCGuuaUCagUGCagGAAAAuGCcuGuuagCGUAAAAGCAAAACACAAAUCUAUCCAUGCAAGCAUUcaCCGCcgGUuuACcgGCGGu.UUUUUUUcgCcGUCAUAAAAAcc....AGGCCCCuuGuaCacAacuGuAaCaaGGGGCCggUUAgGUGAGGGAUUAUCUCCGUUCAUUAgUCA
//
# STOCKHOLM 1.0

#=GF AC   RF01408
#=GF ID   sraL
#=GF PI   ryjA
#=GF DE   sraL Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; ClustalW; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   39.00
#=GF TC   39.50
#=GF NC   37.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol. 2001;11:941-950.
#=GF RN   [3]
#=GF RM   11445539
#=GF RT   Identification of novel small RNAs using comparative genomics and
#=GF RT   microarrays.
#=GF RA   Wassarman KM, Repoila F, Rosenow C, Storz G, Gottesman S
#=GF RL   Genes Dev. 2001;15:1637-1651.
#=GF RN   [4]
#=GF RM   12762038
#=GF RT   Small RNA regulators of translation: mechanisms of action and approaches
#=GF RT   for identifying new small RNAs.
#=GF RA   Gottesman S, Storz G, Rosenow C, Majdalani N, Repoila F, Wassarman KM
#=GF RL   Cold Spring Harb Symp Quant Biol. 2001;66:353-362.
#=GF RN   [5]
#=GF RM   17982174
#=GF RT   Characterization of the role of ribonucleases in Salmonella small RNA
#=GF RT   decay.
#=GF RA   Viegas SC, Pfeiffer V, Sittka A, Silva IJ, Vogel J, Arraiano CM
#=GF RL   Nucleic Acids Res. 2007;35:7651-7664.
#=GF RN   [6]
#=GF RM   22336761
#=GF RT   Dynamics of Salmonella small RNA expression in non-growing bacteria
#=GF RT   located inside eukaryotic cells.
#=GF RA   Ortega AD, Gonzalo-Asensio J, Garcia-del Portillo F
#=GF RL   RNA Biol. 2012;9:469-488.
#=GF RN   [7]
#=GF RM   23893734
#=GF RT   An RpoS-dependent sRNA regulates the expression of a chaperone involved in
#=GF RT   protein folding.
#=GF RA   Silva IJ, Ortega AD, Viegas SC, Garcia-Del Portillo F, Arraiano CM
#=GF RL   RNA. 2013;19:1253-1265.
#=GF CC   The SraL RNA ('sra' for small RNA), discovered in E. coli,[2][3] and later
#=GF CC   in Salmonella Tiphimurium.[5][6] It is expressed only in stationary
#=GF CC   phase.[2] It may possibly play a role in Salmonella virulence.[5] The
#=GF CC   major stationary phase regulator RpoS is transcriptionally regulating SraL
#=GF CC   and directly binds to the sraL gene promoter. SraL down-regulates the
#=GF CC   expression of of the ribosome-associated chaperone Trigger Factor (TF),
#=GF CC   which is involved in the folding of the newly synthesised cystolic
#=GF CC   proteins.[7]
#=GF WK   SraL_RNA
#=GF SQ   6


AE014075.1/4830625-4830485   AUCAACACCAACCGGAACCUCCACCACG----UGCUCGA-A-UGAGGUGUGUUGACGUCGGGGGAAA-CCCUCCU-GUGUACCAGCGGGAUAGAGAGAAAGACAAAGAC--------CGGAAAACAAACUAAAGCGCCCUU--GUGGCGCUUUA-GUUUU
ABAO01000007.1/105121-104981 AUCAACACAAACCGGAACCUCCACCACG----UGCUCGAUA-UGAGGGGUGUUGACGUCGGGGGAAA-CCCUCCU-GUA-AUCAGCGGGAUAGAGCGAAAGACAAAGAC--------CGGAAA-CAAACUAAAGCGCCCUUA-GCGGCGCUUUA-GUUUU
CP000653.1/314792-314651     GUCAGCACAAACCGGAACCUCC-CCAAC----UGCUCGACA-UGAGGGGUGUUGAUGUCGGGGGAAA-CCCUCCC-GUGAACCAGCGGGAUAGAGAGAAAGACAAAGAC--------CGGGAA-UAAACUAAAGCGCCUUAGUCUGGCGCUUUA-GUUUU
CP000647.1/4886125-4885978   GUCGACGCAAACCGGAACCUCCAUCAACAGAUUGCGCAAUACUGAGGGACGUCGACGUCGGGGGAAA-CCCUCUC-GCGAACCAGCGAGAUAAUGCGAAAGACCAAGAC--------CGGAAAACAA-CUAAAGCGCCCAGUUGUGGCGCUUUA-GUUUU
AE017220.1/4439627-4439487   AUCAACACAAACCGGAACCUCCACCACG----UGCUCGAUA-UGAGGGGUGUUGACGUCGGGGGAAA-CCCUCCU-GUA-AUCAGCGGGAUAGAGCGAAAGACAAAGAC--------CGGAAA-CAAACUAAAGCGCCCUUA-GCGGCGCUUUA-GUUUU
X63534.1/2664-2530           GUUAGCACAAACCGGAA---CCUUGAAA----GA------G-----GGGUGCUGAUGCCGGGGGAAAACCCUCCUAGCCAGUGAGCAGGAUAA--CUAAAGGCCAGACCGAAAUUUUUGCAGU-AAAACAAAGGCGCCUAG----GGCGCUUUUUGUUUU
#=GC SS_cons                 :(((((((,,,,,<<_____>>,,,,,,....,,<<<<___.>>>>,,))))))),(((,<<<____.>>><<<<.<<______>>>>>>,,,,,,,,,,))),,,,,,........,,,,,,.,<<<<<<<<<<<<<____.__>>>>>>>>>.>>>>:
#=GC RF                      gucagCaCAAACCGGAACCUCCaucAaa....ugCuCgAua.cGaGGGGuGcugauGuCGGGGGAAA.CCCuCcc.GcaaaucAgCggGaUAaaGcgAAAGaCaAagaC........cGgAaa.caaaCuaaaGCGCCuuua.guGGCGCuuua.GuuuU
//
# STOCKHOLM 1.0

#=GF AC   RF01409
#=GF ID   STnc250
#=GF PI   ypfM_ORF
#=GF DE   STnc250 Hfq binding RNA
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   42.00
#=GF TC   42.20
#=GF NC   39.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF RN   [2]
#=GF RM   17971080
#=GF RT   A small non-coding RNA of the invasion gene island (SPI-1) represses outer
#=GF RT   membrane protein synthesis from the Salmonella core genome.
#=GF RA   Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J
#=GF RL   Mol Microbiol. 2007;66:1174-1191.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   3


AL627274.1/255987-255894     GAAGUCAUGCUUCGUAAAUAAAUGCCUGGAAGGCACCGCGCUCCCAUAGGGGAUAAGAAAAGGCGACUCAACGAAAGUCGCCUUUUUUGUGCCC
CP000026.1/453883-453976     GAAGUCAUGCUUCGUAAAUAAAUGCCUGGAAAGCACCGCGCUCCCAUAGAGGAUAAGAAAAGGCGACUCAACGAAAGUCGCCUUUUUUGUGCCC
ABEH02000006.1/327014-327107 GAAGUCAUGCUUCGUAAAUAAAUGACUGGAAGGCACCGCGCUCCCAUAGGGGAUAAGAAAAGGCGACUCAACGAAAGUCGCCUUUUUUGUGCCC
#=GC SS_cons                 <<<<_____>>>>,,,,,,,,,<<<<_____>>>>,,,,,,<<<<____>>>>,,<<<<<<<<<<<<<_______>>>>>>>>>>>>>::::::
#=GC RF                      GaaGUCAUGCuuCGUAAAUAAAuGccUGGAAggCaCCGCGCuCCcAUAGgGGaUAagaaaaGGCGaCuCAACGAAaGuCGCCuuuuuuGUGCCC
//
# STOCKHOLM 1.0

#=GF AC   RF01410
#=GF ID   BsrC
#=GF DE   BsrC
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; CMfinder; Infernal
#=GF SS   Predicted; CMfinder
#=GF GA   38.00
#=GF TC   38.30
#=GF NC   36.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18948176
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Bacillus
#=GF RT   subtilis.
#=GF RA   Saito S, Kakeshita H, Nakamura K
#=GF RL   Gene. 2008;428:1-10.
#=GF CC   The 301 nucleotide sequence from Kouji Nakamura has been trimmed to a
#=GF CC   highly conserved ~85 nucleotide long core to form this family.
#=GF WK   Bacillus_subtilis_BSR_sRNAs
#=GF SQ   29


U92976.1/1692-1779           -AU---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUCCAUCCUUACGGCUCC-UUGUCCGUGCCAG-UGUGAAUC-AGGAUACUAAAAAAAGUGA
CP000001.1/3008512-3008596   AUG---ACUU-AGAUAGUAUAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UUGUCCGUGCCAG-UGUGAAUC---AGGAUUGUAAAA-AUCA
AE016877.1/3618695-3618780   UAU---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UCGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAA-AUCA
BA000004.3/4072090-4072003   UAUU--ACCUGAAACAAUGAAAGCCCUA-CCU-CUCUUCCAUCCUUACGGCUCC-UUGACCGCGCCAG-UGUGAAUC---AGAUUUGUAAACAUUAA
CP000557.1/1567478-1567409   AUGA--AACAAAAACAAUGGAAGCCCUU-CCU-CUCAUCCAUCCUUGCCGCUCC-GAAGCGGCGCCAG-UGUGAAU---------------------
AP006627.1/1930070-1929989   ------AC--AAGACAACGAAAGCCCUU-CCU-CUCGAUCGUCCUUGCGGCUCC-GAGGCCGCGCCAG-UUUGAAUU---GCAUGUACAAAAAGUCU
CP000002.3/519159-519077     -AU---AC--AAGACAACGAAAGCCCUA-CCU-CUCAUUCGUCCUUGCGGCUCC-GAAGCCGCGCCAG-UGUGAAUU---GUGAAA-CAAAAAGUCU
AAOX01000003.1/167738-167825 UAU---ACCCAAAACAAUGAAAGCCCUG-CCU-CUCUUUCAUCCUUACGGCUCC-GUGUCCGUGCCAG-UGUGAAUC--AGGAUUUGCCAAAAACUU
CP000485.1/3480952-3481038   UAU---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UCGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUCAA
AAJM01000203.1/2188-2102     UAU---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UCGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUCAA
AE017355.1/3480821-3480907   UAU---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UCGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUCAA
AE017225.1/3410190-3410276   UAU---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UCGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUCAA
AAEK01000022.1/37026-36940   UAA---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UUGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUCAA
AE017194.1/3424855-3424941   UAA---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UCGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUCAA
AAXV01000004.1/141716-141802 UAU---ACCUAAAACAAUGAAACCCCUA-CCU-CUCUUUCAUCCUUAUGGCUCC-UUGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUCAG
BA000043.1/1667493-1667407   GAA---AACAAAAACAAUGGAAGCCCUG-CCU-CUCAUCCAUCCUUGCCGCUCC-GUGGCGGCGCCAG-UGUGAAUU---UGUCAAGCGGACAGCGG
ABCF01000001.1/182017-181928 UUG---CCCUAACACAAUGAAAGCCCUU-CCU-CUCGAUCAUCCUUAUGGCUCC-UUGGCCAUGCCAG-UGAGAAUUAGGGGGAAAUCUAACAAUAA
BA000028.3/2652274-2652187   UCU---ACUUAAG-CAAUGUAAGCCCUA-CCUGCUCUUACAUCCUUGCGACCCC-UUAGUCGCGCCAG-UGUGAAUA--AGCAUCUUCCCUAAAACA
AAAK03000003.1/35948-36036   UCU---CAUUUAAACGAUGUAUUCCCUAACCU-CUAAUACAUCCUUGUAACUCU-GAAGUUACGCCAGUUUUGAAUA---AAUUUCAUAAAAACAAA
AE016830.1/2406126-2406039   UUU---CAUUUAAGCGAUGUAUUCCCUA-CCU-CUAAUACAUCCUUGUAUCUCU-CUAGACACGCCAGUUUUGAAUA---AAAUCAUCAAAACAAUU
CP000764.1/1230550-1230471   UAU---ACUG-----GAUGAAAGCCCUA-CCU-CUCUCUCAUCAAUACGGUUCCUCUGACCGCUCC----UUGAUAC---ACUAGCAUGCGUAUCAC
CP001186.1/2978431-2978517   -AUU--ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UUGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUCAA
CP001022.1/2513680-2513765   AAC---ACCUGAAACGACGAAAGCCCUA-CCU-CUCUUUCGUUGUUACGGCUCC-UUGGCCGCGCCA--GCUGAAUC---AAGCGUUUUAGCAAGAA
CP000227.1/3394695-3394781   UAU---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UCGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUCAA
CP001177.1/3430881-3430966   UAU---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UCGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAA-AUCA
AE017355.1/1360036-1359957   UAU---ACUG-----GAUGAAAGCCCUA-CCU-CUCUCUCAUCAUUACGGUUCCACUGACCGCUCC----UUGAUUC---ACUAGUAUACCUAUAAA
AB001488.1/7558-7472         ---UGAACACAAGACAACGAAAGCCCUA-CCU-CUCAAUCGUCACUGCGGCUCC-GAAGCCGCGCCGG-UGUGAAUU---GUAAAACAAAAAAGUCU
ACMO01000186.1/753-839       UAU---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UUGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUUCA
CP001176.1/3670537-3670623   UAU---ACCUAAAACAAUGAAAGCCCUA-CCU-CUCUUUCAUCCUUACGGCUCC-UCGUCCGUGCCAG-UGUGAAUC---AGGAUUGCAAAAAUCAA
#=GC SS_cons                 :::...::::::::::::::::::::::.:::.:::::<<<--<<<<<<<<<__.__>>>>>>>-->>.-->>>:::...:::::::::::::::::
#=GC RF                      Uau...ACcuAAAACAAUGaAAGCCCUA.CCU.CUCuUuCaUCCUugCGGcuCC.uuggCCGcgCCAG.UguGaAUc...aggauugcaAAAAuuaa
//
# STOCKHOLM 1.0

#=GF AC   RF01411
#=GF ID   BsrF
#=GF DE   BsrF
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   50.00
#=GF TC   54.70
#=GF NC   31.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18948176
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Bacillus
#=GF RT   subtilis.
#=GF RA   Saito S, Kakeshita H, Nakamura K
#=GF RL   Gene. 2008;428:1-10.
#=GF WK   Bacillus_subtilis_BSR_sRNAs
#=GF SQ   11


AAER01000035.1/744583-744473 GCGAUGAGCUAAUUUACGUAAGACGAG-AGAUAUGCUUAAGU-GCUAAACACGCGAAUGUGGUCGCCUG-GUCU--CUCGCCGUAA--ACGCAUCAAGACGCCUGCUUU-------GCAGGCG-UC
AAOX01000006.1/156733-156625 GCGAUGAGCUAA-UUGAAUAAGCCGGC-GGGCGCUCCUUUAU-UGGAAAUGCACG-AUGUGG-CGUGCA-GCCU--GCCGCCUCAAU-ACGCA--AGACCCUCUGUUUC------AGGGGGUCUUU
ABCF01000001.1/108044-108150 GCGAUGAGCUGAAUUGUGUAAGUCGAG-GGACGAGCUUUCUAAGC--AACGUGCG-AUGUGG-CGCGCG-GUCU--CUCGCCUCAAU-ACGCA----GGCGCCUGUUUU----CGAACAGGCG--C
AE017194.1/4179039-4178929   GCGAUGAGCUAAUUUACGUAAGACGAG-AGAUAUGCUUAAGU-GCUAAACACGCGAAUGUGGUCGCCUG-GUCU--CUCGCCGUAA--ACGCAUCAAGACGCCUGUUUU-------GCAGGCG-UC
AE017355.1/4221260-4221151   GCGAUGAGCUAAUUUACGUAAGACGAG-AGAUAUGCUUAAGU-GCUAAACACGCGAAUGUGGUCGCCUG-GUCU--CUCGCCGUAA--ACGCAUCAAGACGCCUGCUU--------GCAGGCG-UC
CP000764.1/3188629-3188516   GCGAUGAGCUAAUUUACGUAAGACGAG-AGAUAUGCUUAAGU-GCUAAACACGCGGAUGUGGCCGCCUG-GUCU--CUCGCCGUAAA-ACGCAUCAAGACGCCUGCUAA-----UUUCAGGCG-UC
X58387.1/469-371             G----------AAUUGUGUAAGCCGAU-GUACAUGCCUUUACGGC---ACACACGAAUGUGG-CGUGUG-GUGC--AUCGCCUCAAU-ACGCA--AAGACGUUUGCCUU-----AGGCAAACG-UC
CP000903.1/4267303-4267194   GCGAUGAGCUAAUUUACGUAAGUCGAG-AGAUAUGCUUAAGU-GCUAAACAAGCGAAUGUGGUCGCCUG-GUCU--UUCGCCGUAA--ACGCAUCA-GACGCCUGCUUU-------GCAGGCG-UC
ACMT01000195.1/5719-5609     GCGAUGAGCUAAUUUACGUAAGACGAG-AGAUAUGCUUAAGU-GCUAAACACGCGAAUGUGGUCGCCUG-GUUU--CUCGCCGUAA--ACGCAUCAAGACGCCUGCUUU-------GCAGGCG-UC
AF027868.1/59089-59197       GCGAUGAGCUGAAUUGUGUAAGCCGAU-GUACAUGCCUUUACGGC---ACACACGAAUGUGG-CGUGUG-GUGC--AUCGCCUCAAU-ACGCA--AAGACGUUUGCCUU-----AGGCAAACG-UC
CP003056.1/3286648-3286530   GCGAUGAGCUGAAUUGCAUAAGCCGGCAAGGCAACCUUUUU--GG--AAUGCACA-AUGUGG-AGUGCAAGCCUUAGCCGCCGCAAGAAAGAUUGGAAAAAAGCGCCCCGGACCGGGCGCUUU-UU
#=GC SS_cons                 :::::::::::::(((((-----((((.((((,,<<______.>>,,,,<<-<<<_______.>>>->>.))))..))))-)))))-.---------<<<<<<<<<___.....__>>>>>>>.>>
#=GC RF                      GCGAUGAGCUaAaUUgcGUAAGaCGgg.aggcAugcuUuuau.gcuAAAcgcgCgAAUGUGG.cGcgcg.gccu..ccCGCCgcAAu.AcGcAUcAAGacgccuGcuuu.....aagCaggcg.uC
//
# STOCKHOLM 1.0

#=GF AC   RF01412
#=GF ID   BsrG
#=GF DE   BsrG
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR
#=GF GA   55.00
#=GF TC   55.40
#=GF NC   54.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0001896; autolysis;
#=GF DR   GO; 0090729; toxin activity;
#=GF RN   [1]
#=GF RM   18948176
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Bacillus
#=GF RT   subtilis.
#=GF RA   Saito S, Kakeshita H, Nakamura K
#=GF RL   Gene. 2008;428:1-10.
#=GF RN   [2]
#=GF RM   22229825
#=GF RT   BsrG/SR4 from Bacillus subtilis--the first temperature-dependent type I
#=GF RT   toxin-antitoxin system.
#=GF RA   Jahn N, Preis H, Wiedemann C, Brantl S
#=GF RL   Mol Microbiol. 2012;83:579-598.
#=GF RN   [3]
#=GF RM   26234942
#=GF RT   Against the mainstream: the membrane-associated type I toxin BsrG from
#=GF RT   Bacillus subtilis interferes with cell envelope biosynthesis without
#=GF RT   increasing membrane permeability.
#=GF RA   Jahn N, Brantl S, Strahl H
#=GF RL   Mol Microbiol. 2015;98:651-666.
#=GF RN   [4]
#=GF RM   23969414
#=GF RT   One antitoxin--two functions: SR4 controls toxin mRNA decay and
#=GF RT   translation.
#=GF RA   Jahn N, Brantl S
#=GF RL   Nucleic Acids Res. 2013;41:9870-9880.
#=GF RN   [5]
#=GF RM   26940229
#=GF RT   A multistress responsive type I toxin-antitoxin system: bsrE/SR5 from the
#=GF RT   B. subtilis chromosome.
#=GF RA   Muller P, Jahn N, Ring C, Maiwald C, Neubert R, Meissner C, Brantl S
#=GF RL   RNA Biol. 2016;13:511-523.
#=GF RN   [6]
#=GF RM   26565032
#=GF RT   In Vitro Characterization of the Type I Toxin-Antitoxin System bsrE/SR5
#=GF RT   from Bacillus subtilis.
#=GF RA   Meissner C, Jahn N, Brantl S
#=GF RL   J Biol Chem. 2016;291:560-571.
#=GF RN   [7]
#=GF RM   20525796
#=GF RT   Identification of regulatory RNAs in Bacillus subtilis.
#=GF RA   Irnov I, Sharma CM, Vogel J, Winkler WC
#=GF RL   Nucleic Acids Res. 2010;38:6637-6651.
#=GF CC   bsrE, bsrG and bsrH pair through intermolecular interactions with
#=GF CC   antisense sRNAs. They form type I toxin/antitoxin system that includes an
#=GF CC   mRNA encoding for a short, toxic peptide (bsrE, bsrG and bsrH) and an
#=GF CC   antitoxin that is comprised of an antisense RNA.[7] bsrG encodes a
#=GF CC   39-amino-acid toxin, and the 180 nucleotide antisense sRNA called SR4 acts
#=GF CC   as the antitoxin (they overlap by 123 nucleotides). SR4 interaction with
#=GF CC   the 3'UTR of bsrG RNA promotes bsrG degradation and inhibits its
#=GF CC   translation.[2][4] BsrG interferes with cell envelope biosynthesis, causes
#=GF CC   membrane invaginations and delocalisation of the cell wall synthesis and
#=GF CC   initiates autolysis.[3] bsrE RNA encodes 30 amino-acid toxin peptide. Its
#=GF CC   antitoxin gene, SR5 overlaps by 112 nucleotides at the 3' end of bsrE.[5]
#=GF CC   SR5 also overlaps bsrG from nucleotide 163 to 52 (Rfam overlap check). The
#=GF CC   antitoxin SR5 promotes bsrE degradation but unlike SR4 it does not
#=GF CC   directly inhibits toxin mRNA translation.[5][6]
#=GF WK   Bacillus_subtilis_BSR_sRNAs
#=GF SQ   6


AE017333.1/3485452-3485196 UAUAAAAAGCU---UUGCUCACUCAAGGGAAGUCUUGCUCAUCCCCU-UCUGAA-AGGGGGUGAUAAAA-AUGACAGCAUAUGAAACAAUCUCUUUAAUGAUUGCUUUUGGCAUGCUGAU---------UGCCAUGUUGUCAGAGAACAAA---------------------------GAAAAAUAGACCGCCCCUUGAGCCUGGAAAGUGAUAGGGAGUGGUCUAUUUUAGGUCAAU-CU-----GAGCAA-GCCCCUUCGA-AGGGCC--GGCUUUUUGUACA-AGCCGAAGUGUU-GG-AGCACUUCGG
AF027868.1/49816-50069     UACAGUAAGUU---UUGCUCACUCGAGGGA-GUCUUGCUCAUCCCCU-AAUGAA-AGGGG-UGAUGCU--AUGUCAACAUUCCAGGCAUUAAUGCUAAUGCUUGCAAUCGGGUCGUUUAUA------AUCGCCCUAUUGACGU---AUAUA--------------------------GAAAAAAUAGACCU-CCCUUGAGCCUCAGAACCUGAAGGGAUAGGCCUACCUAGAACC-ACAUC-----GAGCAA-GCCCUUU-G--AUGGGC--AACUUUUUGUACAGAGCCGGGGUGUU-GGUAGCACCUCGG
AP006627.1/3751669-3751418 AACAAUAGCAUA--ACGGUUACUCAAGGGU-GGUCGGCACA-CUCCC-AUGAAA-GGGGG-UGUUGCUGUAUGACAGUAUUUGAAGGAAUUUCCCUUAUGUUGACGUUUGGGCUUCUGAUC------GUUGCAAUGCUGUCAUUUCACAAC------------------------CACAAAAAAUAAUCCA-CCCUUGAGUU-------AGU--GGCUCAGGUGGAUUAUUCGUCCAA-UC-----GGCCG--AUCCCUU-GC-AGGGAUCCGAGCUAUUGUUUG-ACUGAAGGUGUG-AC-AGCACCUUCA
BA000004.3/369992-370242   CAAUAGAAUAGGAUUU-----CUCGAGGGU-GGUCGGCACACUCCCAAGUUGAAAGGGGG-UGGUGCUGUUUGACGGUAUUUGAAGCGUUGAUGUUUGC-CGUAGCGUUUGCGACUUUAAUC-----AUCGCGGUGCUGUCGUUUCAUGAA---------------------------AAAAAAUAAUCCA-CCCUUGAGUUAGCGGCUCAG-GUGGAUUCGUCUAUCCUAUGGCC--------------GA-UCCCCUU-G--GAGGGA-ACCGUUUUAUUGCAUGACCGUCGAUGUUACCGCAUCGGCGG
AARF01000097.1/2047-2290   GCAAUAG-------UGGCUUACGUGGGCGG-----UCGGCAUCACCU--CGGAA-AGGAGGUGAUGCU--AUGGAGACGUUUCAGGCUCUUCAAUUAAUGUUCUUAUUUGGAAUGUUUAUUCUAGCGCUUUUAACGUUUAUCCAGAAAAUG--------------------------AAAUAGAU-------CGCCCACGCUAAGGAAACGA----------UCUAUUUCGUUUGUAAACCUUAUUAAGCCGACCGCCUA-GUAGCGCGG------CUAUUGCCAGACCGUGGACGAU-ACCAGCGUCUGCG
AL009126.3/2273535-2273822 UACA-UAAAGU---UUGCUCACUCAAGGGA-GUCUUGCUCAUCCCCU--AUGAA-AGGGG-UGGGAAA--AUGACUGUUUACGAAUCAUUAAUGAUAAUGAUCAAUUUUGGCGGAUUGAUAUUAAAUACCGUCUUGUUGAUCUUCAAUAUAAUGAUGAUUGUAACGUCAAGCCAAAAGAAAAAAUAGACCUUCCCUUGAGUUUGGACACCUGAAGGGUUAGGCCUACGCAGAUUUGACAAC-----GAGCAA-GCCCUUU-G--AUGGGC--AGCUUU-UGUACAGAGCCAGGGUGCU-ACCAACACCCUGG
#=GC SS_cons               {{{{{-{{{-{...{{{{{{,[[[[[[[[-.[[[[,,,<<<-<<<<<.______.>>>>>.>>>,,,,..,,(((((((,,,,,,<<<__________>>>,,,,,,,,<<<<_________.....__>>>>,))))))),,,,,,,,,,..........................,,,,,,,,]]]]--.]]]]]]]],,,,,,,,,<<<._______________>>>,,,,,,,,,,.....}}}}}}.<<<<___.__.__>>>>..}-}}}-}}}}}-----<<<<<<<<<<.___>>>>>>>>>>
#=GC RF                    uacaauaagau...uuGcucACuCaaGGGa.GucuuGCuCAUCcCCu.auuGAA.aGGgG.UGaUGcu..AUGacagcaUuUgAAgCauUuauguUaAuGcUuauuuUUgGcgugUUuAUuc.....aUcgCcaugcuguCauuuaAuAua..........................aAAAAAAUagaCCa.CCCuuGaGuUugggaAucgg.AGGGauaGGUCUAUuccguuUcuAaAuC.....gagCaa.gccCcUU.Gu.auGggc..aacuuUuuguaCAgAgCcgggGuGcu.AcCagCaCcccgG
//
# STOCKHOLM 1.0

#=GF AC   RF01413
#=GF ID   miR-430
#=GF DE   microRNA miR-430
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   miRBase; Gardner PP
#=GF SS   Predicted; CMfinder; Gardner PP
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00096
#=GF DR   MIPF; MIPF0000003;
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15774722
#=GF RT   MicroRNAs regulate brain morphogenesis in zebrafish.
#=GF RA   Giraldez AJ, Cinalli RM, Glasner ME, Enright AJ, Thomson JM, Baskerville
#=GF RA   S, Hammond SM, Bartel DP, Schier AF
#=GF RL   Science. 2005;308:833-838.
#=GF WK   Mir-430_microRNA_precursor_family
#=GF SQ   46


BX088538.26/195245-195151  UUACCGUCAGGCUUUCACAA----GCCAGCCUCAAAGUUUGUUCU-CAAACU-UUAAGAAUCUAGUU--GGUAAG-UGCUAUUU-GUUGGGGUAGU--U-U-CAA-GUGA
BX088538.26/192490-192398  UUGAUAGAAACCAGUUGAGGUC--AACUCUAACUUUAG-----CAUCUUUCU-UUUAAGCAAAG--U--AGAAAG-UGCUAUCAAGUUGGGGUAGA--UGU--UUGCUGA
BX088538.26/190526-190438  CCACCAUU-GUCUCUAUCGG----UACCCUCACAAAAG-----CA-CUGACU-UUGAUGCUGUAUUU--GGUAAG-UGCUAUUU-GUUGGGGUAGU--UUU--AA-GUGA
AANH01007362.1/9092-9003   CCAGAUUUUGGCCAUUAGGAU---UACCCUUACAAAAA-----CA-CUGACU-UUGGUUCUCAAUAC--AGUAAG-UGCUUUUU-GUUGGGGUAGU--U-U--UG-CUGA
AANH01007366.1/6449-6361   CCAGAUUUGGUCAUUAGGAU----UACCCUUACAAAAA-----CA-CUGACU-UUGGUUCUCAAUAC--AGUAAG-UGCUUUUU-GUUGGGGUAGU--U-U--UG-CUGA
AANH01014755.1/1267-1355   CCUGAUUUGGUCUUCAUGGU----UACCCUUACAAAAA-----CA-CUGACU-UUGAUUCUCAAUAC--AGUAAG-UGCUUUUU-GUUGGGGUAGU--U-U--UG-CUGA
AANH01007361.1/2782-2693   UCCUUAUUUGGCCAUUAGGAU---UACCCUUACAAAAA-----CA-CUGACU-UUGGUUCUCAAUAC--AGUAAG-UGCUUUUU-GUUGGGGUAGU--U-U--UG-CUGA
AANH01014757.1/13117-13205 CCAGAUUUGGCCACUAGGAU----UACCCUUACAAAAA-----CA-CUGACU-UUAGUUCUCAACUC--AGUAAG-UGCUUUCU-GUUGGGGUAGU--U-U--UU-CUGA
AY064510.1/532-619         AUAACUUU-GUCACCAACAU----CACCCAAACACAAG-----CA-CUGACU-UGAGCUCUGAAUUC--AGUAAG-UGCUUCUU-GUUGGGGUAGU--G-U--UG-CUGA
BAAF04118514.1/7211-7298   GAAAAAUCAGACAUUCAGAU----GACCUUAACAUAGG-----CA-CUGACU-UGAAUUUCUU-UGC--AGUAAG-UGCUACAU-GUUGGGGUAGU--C-U--UU-GUGU
AY064509.1/705-798         ACAGUGUUUACCAGUCAGUAAUAUUCCCCUAACUUCAG-----CA-UUGACU-UGACUGUUGAAUUC--AGUAAG-UGCUACUU-GUUGGGGCAGU--UGA--AA-AUGA
AY064510.1/694-787         UUUCUGUUUACCAGUCAGUAAUAUUACCCUAACUUGAG-----CA-UUGACU-UGACUGUUGAAUUC--AGUAAG-UGCUACUU-GUUGAGGCAGU--UGA--AA-AUGA
CAAE01012407.1/28765-28674 AUUGGGCUAGUCACUUGAAGU---UACCCAAACACUGG-----CA-CUGACU-UGACAUUUUCAGAUACAGUAAG-UGCUACUU-GUUGGGGUAAU--U-U--UA-UUGA
BAAE01232573.1/595-508     GAAAAGUCAGACAUUCAGAU----GACCUUAACAAAGG-----CA-CUGAUU-UG-AGUUUGUUUGC--AAUAAG-UGCUACAU-GUUGGGGUAGU--C-U--UG-GUGU
AY064510.1/970-1056        AUAACUUU-GACACCAACAU----CACCCAAACACUAG-----CA-CUGACU-UGAGCUCUGAAUUC--AGUAAG-UGCUUCUU-GUG-GGGUAAU--G-U--UG-AUGA
BAAF04118514.1/2175-2262   UCGCUUUUGGACAUAAAGAU----GACCUUGACACAGG-----CA-CUGACU-UUUUCUUCUU-UGU--AGUAAG-UGCUACAU-GUUGGGGUAAU--U-U--UG-GUGU
BAAE01001321.1/729-644     UCGCUUUUGGACAUCAAGAU----GACCUUGACACAGG-----CA-CUGACU-CUUUCUUUUU---U--AGUAAG-UGCUACUU-GUUGGGGUAAU--U-U--UG-GUGU
CAAE01012407.1/27569-27479 AUUGGGCUAGUCACUGAAGU----UACCCAAACACUGG-----CA-CUGACU-UGACAUUUUCAGAUACAGUAAG-UGCUACUU-GUUGGGGUAAU--U-U--UA-UUGA
BAAE01001317.1/91-4        UCGCUUUUGGACAUCAAGAU----GACCUUGACACAGG-----CA-CUGACUCUUUCUUCUAUA--U--AGUAAG-UGCUACUU-GUUGGGGUAAU--U-U--UG-GUGU
CAAE01012407.1/25982-25893 AAAGUCUG-GUCAGUAACAU----GACCCAAACACUGG-----CA-CUGACU-UGACAUGUUCAGAUAGGGUAAG-UGCUACUU-GUUGGGGUAAU--U-U--UA-UUGA
CAAE01012407.1/37618-37528 AAAAGUCCGGUCAGUAACAU----GACCCAAACACUGG-----CA-CUGACU-UGACAUUUUCAGAUAGAGUAAG-UGCUACUU-GUUGGGGUAAU--U-U--UA-UUGA
CAAE01012407.1/31933-31844 AAAAGUCCGGUCAGUAACAU----GACCCAAACACUGG-----CA-CUGACU-UGACAUUUCAGAUA-GAGUAAG-UGCUACUU-GUUGGGGUAAU--U-U--UA-UUGA
AB095089.1/532-619         AUGACUUU-GUCAACAACAA----CACCCAAACACAAG-----CA-CUGACU-UGAGCUCUGAAUUC--AUUAAG-UGCUUCUU-GUUGGGGUA-A--UGU--UG-CUGA
BX088538.26/191757-191668  GCUACUAUUGUCACUAUCGG----UACCCUCACAAAGG-----CA-CUGACU-UGGAUGCUGUAAUU--GGUAAG-UGCUAUUU-GUUGGGGUAGU--UUC--AA-GUGA
AANH01007361.1/1221-1132   CCUGAUUUGGUCUUCAUGGU----UACCCUUACAAAAA-----CA-CUGACU-UUGUUUCUCAAAUA-CAGUAAG-UGCUUUUU-GUUGGGGUAGU--U-U--UG-CUGA
BAAF04118514.1/941-1028    AUGCUUUUGGACAUAAAGAU----GACCUUGACACAGG-----CA-CUGACU-CUUUCUUCUU-UGU--AGUAAG-UGCUACUU-GUUGGGGUAUU--U-U--UG-GUGU
AANH01007362.1/5180-5089   CCUGAUUUGGUCUUCAUGGAU---UACCCUUACAAAAA-----CAACUGACU-UUGGUUCUCAAUAC--AGUAAGUUGCUUUUU-GUUGGGGUAGU--U-U--UG-CUGA
BAAE01306502.1/271-354     UCGCUUUUGGACAUCAAAAU----GACCUUGACACAGG-----CA-CUGACU-CUGCUUUG-----U--AGUAAG-UGCUACUU-GUUGGGGUAAU--U-U--UG-GUGU
BAAE01232575.1/294-211     UCGCUUUUGGACAUCAAGAU----GACCUUGACACAGG-----CA-CUGACU------CUUCUUUGU--AGUAAG-UGCUACAU-GUUGGGGUAAU--U-U--UG-GUGU
AANH01014757.1/4511-4602   CUAGAUCUGGCGAUUUAGGAUUA-UCCCUUAACAACAA-----CA-CUGACU-UUGGUUCUCAAUAC--AGUAAG-UGCUUUUU-GUUGGGGUAGU--U-U--UG-CUGA
BX088538.26/186606-186514  AGAUAGAAAACCAGUUGACAUC--AACUCUAACUUUAG-----CAUCUUUCU-UUUAAGCAAAG--U--AGAAAG-UGCUAUCAAGUUGGGGUAGA--U-GUUUG-CUGA
AY064510.1/391-477         UUUUGGAAUCACGUUCAGAU----CACCUCAAAUGGAGA----CA-CUGAUG-AUUCUUGUGU---U--CAUAAG-UGCUUCUC-UUUGGGGUUGU--C-U--UG-GUUG
AB095087.1/352-440         UUUGUGAGAAUCAUUCUCAGAC--CACUUCAGAGGGAGC----CA-CUGGUG-AUUUUUGUGU---U--CAUAAG-UGCUUCUC-UUUGGGGUUGU--C-U--UG-GUUG
AAVX01519880.1/194-107     UGAACACUGAAGGCACACAU----CACCCAAACAGUAG-----CA-UUUUCC-UGUGUAUUUU-UCU--GCUAAG-UGCUACUG-GUUUGGGCAAU--G-U--UU-ACCU
AAVX01616752.1/71-158      UGGAAACUAAAGGCACAUAU----CACCCAAACAGUAG-----CA-UUUUCC-UGUGUAUUUU-UCU--GCAAAG-UGCUACUG-GUUUGGGCAAU--G-U--UU-ACCU
AAVX01559775.1/215-126     UGUAGAUUAAAGGCAAAUGU----UACCUGAACAGGAG-----CA-UUUUCU-AUUAUGUGUUUUUU--AGUAAG-UGCUACCUUGUUUGGGUGAC--A-U--UU-ACCU
AAVX01559775.1/358-273     UGUAGAUUGAAGGGACAUGU----CACCUAAACAGCAG-----CA-UUUUCU-GUUUGUUUUU---U--GGUAAG-UGCUAUCU-GUUUGGGCAAC--C-U--UU-UCCU
AAVX01282906.1/993-906     AGGACAGCAGAGGCACAUGU----AACCCAAACAGUAG-----CA-UUUUCC-UGUGUAUUUU-UUA--GAUAAG-UGCUACCU-GUUUGGGCAAC--G-U--UU-UCCU
BX088538.26/186864-186778  --AAUCUAAAGCACAUUAAG----AUCACUUCAAACAGGAG--CA-UUGAUU-UGUCCUUUGU---U--CAUAAG-UGCU-UCUCUUUGGGGUAGU--U-U--UA-AUAA
BX088538.26/191339-191247  UGAUAGAAAACCAGUUGACGUC--AACUCUAACUUUAG-----CAUCUUUCU-UUUAAGCAGAG--U--AGAAAG-UGCUAUCAAGUUGGGGUAGAUGU-U--UG-CUGA
CAAK05031383.1/3184-3096   CUACUGUU-GUCACUAUCGG----UGCCCUCACAAAGG-----CA-CUGACU-UGGAUGCUGCAUGU--GGUAAG-UGCUAUUU-GUUGGGGUAGU--UUC--AA-GUGA
CAAB02015703.1/6030-5941   UACUGGCAAGUCUUUAUUGU----UCCCUCAAAUUUAG-----CA-UUCACU-UGUCAUGUGAUAUC--AGUAAG-UGCUAUCU-GUUGGGGCGGC--UGU--AG-UUGA
CAAB02006813.1/486-396     UGAAUGUUAGUCACAAAAAU----UACCCAAACACGAG-----CA-CUGACU-UGGAAAUACUAAAUGCGGUAAG-UGCUACUU-GUUGGGGUACU--U-U--UA-CUGA
CAAB02006813.1/224-137     GGAGCAGAUCACACCCAGAA----GACCUCAAAUGGAAA----CA-CUGUUG-ACUAUCAUGU---U--CAAAAG-UGCUUCUC-UUUGGGGUUGU--C-U--UGAAUGU
CAAB02015703.1/5788-5699   AACAAGUUAUUCACAAAAAU----CACCCAAACACUGG-----CA-CUGACU-UGUAAUUAGUAAAUGGGGUAAG-UGCUAUUU-GUUGGGGUAGU----U--UA-GAGA
CAAB02006813.1/630-544     UGAGGUAGUCACACCCAGAA----AACCUCAAAUGGAAA----CA-CUGUUG-ACUAUCAUGU---U--CAAAAG-UGCUUCUC-UUUGGGGUUAU--C-U--UG-UUUG
#=GC SS_cons               :::::::::::<<<<-<-<-....-<<<<<-<<<--<<.....<<.<<-<<<.______________..>>>->>.>>>>--->.>>->>>>>---..-.>..>>.>>>:
#=GC RF                    uuaauuuuagacaccaagau....uaCCCuAACaaaAG.....CA.CUGaCu.UuuauuuUguAuuU..aGuAAG.UGCUAcUu.GUUgGGGuAGU..U.u..ug.gugA
//
# STOCKHOLM 1.0

#=GF AC   RF01414
#=GF ID   class_I_RNA
#=GF DE   Class I RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Gardner PP
#=GF SS   Published; PMID:15333696; Gardner PP
#=GF GA   45.00
#=GF TC   46.70
#=GF NC   42.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000990; class I RNA;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Söderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Dictyostelium_class_I_RNA
#=GF SQ   21


AAFI02000020.1/352240-352187   GUUGACCUUACAGCAAU-UCAUU---CU-----CUA-C-AUA---AAAAGAAAA------CCCCCUGUCAACUG
AAFI02000005.1/1972469-1972412 GUUGACCUUACAGCAAU-UCUCA---CAUU-UCCUUAC-AUU---CAAAGAAAA------CCUUC-GUCAACUG
AJ699383.2/1-58                GUUGACCUUACAGCAAA-UCUAA---CAUU-UCCUUAC-AUU---CAAAGAAAA------CCU-UUGUCAACUG
AAFI02000073.1/229626-229569   GUUGACCUUACAGCAAA-UCUAA---CAUU-UCCUUAC-AUU---CAAAGAAAA------ACUUC-GUCAACUG
AAFI02000056.1/94801-94858     GUUGACCUUACAGCAAA-UCCUG---CAGU-UCCUU-C-AUU---CUAAGAAAA------CCUUUCGCCAACUG
AAFI02000064.1/3698-3755       GUUGACCUUACAGCAAA-UCUUA---CAGU-UCCUU-C-AUU---CUAAGAAAA------CCUUCCGUCAACUG
AAFI02000073.1/231305-231359   GUUGACCUUACAGCAAA-UCUUA---CAAU----UU-C-AUC---CUAAGAAAA------AAUACAGUCAACUG
AJ699382.1/1-55                GUUGACCUUACAGCAAA-CCCUA---CAGU-CAUUU-C-AU------AAGAAAA------ACUACCGUCAACUG
AAFI02000063.1/197593-197647   GUUGAUCCUACAGCAAU-UCUAU---CA-----CUA-U-ACAU--ACAAAAGAA------ACCUUCGUCGACUC
AAFI02000023.1/1101542-1101487 GCUGACCUUACAGCAAU-UCUAU---CA-----CUC-U-ACAUU-CCAAAGAAA------UCCUUCGUCAGCUG
AAFI02000063.1/196801-196745   GUUGACCUUACAGCAAA-UCUAA---CA-UUUCCUUAC-A-----UUCAAAGAA------ACCUUCGUCAACUG
AAFI02000197.1/201320-201380   GUUGACCUUACAGCAA--UCUUAA--CAA---UUUUAUCACAUUAUAAAAAAAA------ACCUCAGUCAACUG
AAFI02000079.1/484303-484352   GUUGACCUCACAGCAA--UU------AACU-AGUUU-U-A-------AAGAAAC------CCCCUUGUCAACUG
AAFI02000023.1/1100345-1100294 GUUGACCUUACAGCAAA-UUAU----CA------UUCU-AC----AGGAAGAAA------ACCAUUGUCAACUG
AJ699389.1/1-65                GUUGACCUUACAGCAA--UCUAAU--CACAAAUUUU-U-ACU---UCACAAAAAAAAAACCCCUUCGUCAACUG
AAFI02000111.1/88660-88720     GUUGGCCUUACAGCAAAUUCUCA---CAA--AUUUU-U-ACUGAUUAAAAAAAA------CCCCUUGUCAACUG
AF310890.1/5089-5148           GUUGACCUUACAGCAAA-UCCUCU--CAA--AUUUU-U-ACUGA-UUAAAAAAA------CCCCUCGUCAACUG
AAFI02000197.1/204312-204370   GUUGACCUUACAGCAA--UCUUAA--CAAA-AUUUU-U-UCUGA-AUAAAAAAA------CCUAA-GUCAACUG
AJ699388.1/1-60                GUUGACCUUACAGCAA--UCCUAAAGCA---UUUUU-U-CUGAU-UAAAAAAAA------ACCAAAGUCAACUG
AAFI02000013.1/1022188-1022245 GUUGACCUUACAGCAAA-UCUUA---AAGC-UACUU-C-AUU---CUAAGAAAA------ACUCCUGUCAACUG
AAFI02000020.1/351880-351838   GUUGACCUUACAGCAAU-UC--------------UUCU-A---------AGAAA------CCCCCCGUCAACUG
#=GC SS_cons                   <<<<<<-----------.-----...----.--<<<.<.___...____>>>>-......------>>>>>>::
#=GC RF                        GUUGACCUUACAGCAAa.UCUuA...CAau.uuuUu.u.Acu...uaAAaaAaA......cCCuucGUCAACUG
//
# STOCKHOLM 1.0

#=GF AC   RF01415
#=GF ID   Flavivirus_SLIV
#=GF DE   Flavivirus 3'UTR stem loop IV
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:19064258
#=GF GA   62.00
#=GF TC   62.30
#=GF NC   60.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19064258
#=GF RT   A highly structured, nuclease-resistant, noncoding RNA produced by
#=GF RT   flaviviruses is required for pathogenicity.
#=GF RA   Pijlman GP, Funk A, Kondratieva N, Leung J, Torres S, van der Aa L, Liu
#=GF RA   WJ, Palmenberg AC, Shi PY, Hall RA, Khromykh AA
#=GF RL   Cell Host Microbe. 2008;4:579-591.
#=GF RN   [2]
#=GF RM   14696330
#=GF RT   5'- and 3'-noncoding regions in flavivirus RNA.
#=GF RA   Markoff L
#=GF RL   Adv Virus Res. 2003;59:177-228.
#=GF WK   Flavivirus
#=GF SQ   20


L24512.1/259-333       CCAAUGUCAGACCACGCCAUGGCGUGCCACUCUGC-GGAC-AGUGCAGUCUGCGACAGUGCCCCAGGAGGACUGGGU
DQ411032.1/10638-10712 CCAAUGUCAGACCACGCUACGGCGUGCCACUCUGC-GGAG-AGUGCAGUCUGCGAUAGUGCCCCAGGAGGACUGGGU
L48980.1/463-537       CCAAUGUCAGGCCACACCUGAGUGUGCCAUCCUGC-GGAG-GAUGCUGUCUGCGCCAGUGCCCCAGGAGGACUGGGA
AF221499.1/10614-10683 CCAACGUCAGGCCACAAAU--UUGUGCCACCCCGC-UGGG-GGUGCGGCCUG---CGCAGCCCCAGGAGGACUGGGU
AF075723.1/10614-10684 CCAACGUCAGGCCACAAAU--UUGUGCCACUCCGC-UGGGGAGUGCGGCCUG---CGCAGCCCCAGGGGGACUGGGU
AF306514.1/209-279     CCAACGUCAGGCCACAAUU--UUGUGCCAUUCCGC-UGGGGAGUGCGGCCUG---CGCACCCCCAGGAGGACUGGGU
AF208017.1/702-776     CCAGUGUCAGACCACACUUUAAUGUGCCACUCUGC-GGAG-AGUGCAGUCUGCGAUAGUGCCCCAGGUGGACUGGGU
AF297847.1/505-579     CCAGUGUCAGACCACGCCAUGGCGUGCCACUCUGC-GGAG-AGUGCAGUUUGUGACAGUGCCCCAGGAGGACUGGGU
AY765264.1/10602-10676 CAGUUGUCAGACCACACGCAAGUGUGCUACUCUGC-GAAG-AGUACUGUCUGCGUUAGAGCCCCAGGAGGACUGGGA
AB051292.1/10601-10671 CCAACGUCAGGCCACAAUU--CUGUGCCACUCCGC-UGGGGAGUGCGGCCUG---CGUAGCCCCAGGAGGACUGGGU
AF297858.1/519-593     CCAAUGUCAGACCACCCAUUGGCGUGCCACUCUGC-GGAG-AGUGCAGUCUGCGACAGUGCCCCAGGAGGACUGGGU
L48977.1/458-531       CCAGUGUCAGACCACACCUGA-UGUGCCACUCUGC-GGAG-AGUGCAGUCUCCGAUAGUGCCCCAGGUGGACUGGGU
DQ176636.2/10595-10669 CCAAUGUCAGACCACAUUUCGAUGUGCCACUCUGC-GGAG-AGUGCUGUCUGCGAUAGUGCCCCAGGUGGACUGGGU
AY303794.1/10614-10684 CCACCGUCAGGCCACAAAU--UUGUGCCACCCCGCUGGAG-GGUGCGGCCUG---CGCAGCCCCAGGAGGACUGGGU
AF196537.1/523-594     CCACCGUCAGACCACACCGAGGUGUGCCACUCAGC-GGAG-AGUGCGGUCUG---CGCAGCCCCAGGAGGACUGGGU
AF297857.1/485-559     CCAAUGUCAGACCACGCCAUGGCGUGCCACUCUGC-UGAG-AGUGCAGUUGACGACAGUGCCCCAGGAGGACUGGGU
L49311.1/478-551       CCAGUGUCAGACCACACUU-AGUGUGCCACUCUGC-GGAG-AGUGCAGCCUGCGCUAGUGCCCCAGGUGGACUGGGU
AF196535.1/535-609     CCAAUGUCAGACCACACUUUGGUGUGCCACUCUGC-GGAG-AGUGCAGUCUGUGAUAGUGCCCCAGGUGGACUGGGU
AY898809.1/10594-10661 CCCGUGUCAGGUCACA-----UUGUGCCACCUUGCCAGAA-GGUGCAACCUG---CGAGGCCCCAGGUGGACUGGGU
AY453412.1/10700-10767 CCCGUGUCAGGCCGC---AAA--GCGCCACUUCGC-CAAGGAGUGCAGCCUG---UAUGGCCCCAGGAGGACUGGGU
#=GC SS_cons           ::::((((((((<<<<<____>>>>>,<<<<____.____.>>>>,,)))))--)))----<<<<<_____>>>>>:
#=GC RF                CCAauGuCAGgCCACgcuuuagcGUGCCACuCuGC.gGAG.aGUGCaGcCUGcGaCaguGCCCCAGGaGGACUGGGU
//
# STOCKHOLM 1.0

#=GF AC   RF01416
#=GF ID   NrrF
#=GF DE   NrrF RNA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:17351036
#=GF GA   60.00
#=GF TC   67.40
#=GF NC   43.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0001263; regulation of translation, ncRNA-mediated;
#=GF RN   [1]
#=GF RM   19060140
#=GF RT   The Hfq-dependent small noncoding RNA NrrF directly mediates Fur-dependent
#=GF RT   positive regulation of succinate dehydrogenase in Neisseria meningitidis.
#=GF RA   Metruccio MM, Fantappie L, Serruto D, Muzzi A, Roncarati D, Donati C,
#=GF RA   Scarlato V, Delany I
#=GF RL   J Bacteriol. 2009;191:1330-1342.
#=GF RN   [2]
#=GF RM   17351036
#=GF RT   A novel fur- and iron-regulated small RNA, NrrF, is required for indirect
#=GF RT   fur-mediated regulation of the sdhA and sdhC genes in Neisseria
#=GF RT   meningitidis.
#=GF RA   Mellin JR, Goswami S, Grogan S, Tjaden B, Genco CA
#=GF RL   J Bacteriol. 2007;189:3686-3694.
#=GF RN   [3]
#=GF RM   28904860
#=GF RT   Regulation of Neisseria meningitidis cytochrome bc1 components by NrrF, a
#=GF RT   Fur-controlled small noncoding RNA.
#=GF RA   Pannekoek Y, Huis In 't Veld R, Schipper K, Bovenkerk S, Kramer G, Speijer
#=GF RA   D, van der Ende A
#=GF RL   FEBS Open Bio. 2017;7:1302-1315.
#=GF WK   NrrF_RNA
#=GF SQ   3


AL157959.1/333678-333520   CCACUCGGAAGCCGUCCGUUCCGAACCAUUAAACACCAUAUUUCCCCAUCA-UCACUUUCACACUUGGAGUCGGCAUAUACGAGACAUACAUUCCCUUUUUAUAUAUCAGAUACUCAAAACCGAAACGCCAAACCCACCUUCGCGGUGGGUUUGGCGUUU
AM421808.1/2107592-2107751 CCACUCGGAAGUCGUCCAUUCCGAACCAUUAAACACUGUAUUCCCUCACAAUUCACUUUCACACUUGGAGUCGGCAUAUACGAGACAUACAUUCCCUUUUUAUAUAUCAGAUACUCAAAACCGAAACGCCAAACCCACCUUCGCGGUGGGUUUGGCGUUU
AE004969.1/1976124-1975968 CCACUCGGAAGCCGUCCGUUCCGAACCAUUAAACACUGUAUUCCCUCACAAUUCACUUUCACACUUGGAGUCGGCAUAUACGAGACAUACAUUCCCUUUUUA---AUCAGAUACUCAAAACCGAAACGCCAAACCCACCCUAGCGGUGGGUUUGGCGUUU
#=GC SS_cons               ::::::<<<<---<<<<<<-<<<<-<<<_____________________________________>>>-->>>>----->>>->>>----->>>>----------------------------<<<<<<<<<<<<<<<<_____>>>>>>>>>>>>>>>>
#=GC RF                    CCACUCGGaaGcCGuCCguUCCGaACCaUUAAACACugUAUUcCCuCAcaAUUCACUUUCACACUuGGAGuCGGCAUAUacGAGaCAUACAuuCCCUUUUUAUAUAUCAGAUACUCAAAACCGaaaCGCCaaaCCCaCCuUcGCGGuGGGuuuGGCGuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01417
#=GF ID   RSV_RNA
#=GF DE   Retroviral 3'UTR stability element
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:19091866
#=GF GA   105.00
#=GF TC   106.00
#=GF NC   104.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0043487; regulation of RNA stability;
#=GF RN   [1]
#=GF RM   19091866
#=GF RT   Structural characterization of the Rous sarcoma virus RNA stability
#=GF RT   element.
#=GF RA   Weil JE, Hadjithomas M, Beemon KL
#=GF RL   J Virol. 2009;83:2119-2129.
#=GF RN   [2]
#=GF RM   16301601
#=GF RT   A 3' UTR sequence stabilizes termination codons in the unspliced RNA of
#=GF RT   Rous sarcoma virus.
#=GF RA   Weil JE, Beemon KL
#=GF RL   RNA. 2006;12:102-110.
#=GF WK   Rous_sarcoma_virus
#=GF SQ   8


V01197.1/2597-2885   UAGCGCUAACGCAA---UUAGUGGAAAAAGAAUUACAGUUAGGACAUAUAGAACCUUCACUUAGUUGUUGGAACACACCUGUCUUCGUGAUCCGGAAGGCUUCCGGGUCUUACCGCUUACUGCAUGAUUUGCGCGCUGUUAACGCCAAGCUUGUUCCUUUUGGGG-CCGUCCAACAGGGGGCGCCAGUUCUCUCCGCGCUCCCGCGUGGCUGGCCCCUGAUGGUCUUAGACCUCAAGGAUUGCUUCUUUUCUAUCCCUCUUGCGGAACAAGAUCGCGAAGCUUUUGCAUUUAC
DQ115805.1/2821-3109 UAGCGCUAACGCAA---UUAGUGGAAAAAGAAUUACAGUUAGGACAUAUAGAACCUUCACUUAGUUGUUGGAACACACCUGUCUUUGUGAUCCGGAAGGCUUCCGGGUCUUAUCGCUUAUUGCAUGACUUGCGCGCUGUUAACGCCCAGCUUGUUCCUUUUGGGGGCCG-CCAACAAGGGGCGCCAAUUCUCUCCGCGUUCCGGCGUGGCUGCCCCCUGAUGUUCUUAGACCUCAAGGGUUGCUUCUUUUUUAUUCCUCUUGCGGAACAAGAUCGCGAAGCUUUUGCAUUUAC
AF052428.1/2616-2904 UAGCGCUAACGCAA---UUAGUGGAAAAAGAAUUACAGUUAGGACAUAUAGAACCCUCACUUAGCUGUUGGAACACACCUGUCUUUGUGAUCCGGAAGGCUUCCGGGUCUUAUCGCUUAUUGCAUGACUUACGCGCUGUUAACGCCAAGCUUGUUCCUUUU-GGGGCUGUCCAACAGGGGGCGCCAGUUCUCUCCGCGCUCCCGCGUGGCUGGCCCCUGAUGGUUCUAGACCUCAAGGAUUGCUUCUUUUCUAUUCCUCUUGCGGAACAAGAUCGCGAGGCUUUUGCAUUUAC
Z46390.1/2821-3109   UAGCGCUAACGCAA---UUAGUGGAAAAAGAAUUACAGUUAGGACAUAUAGAACCUUCACUUAGUUGUUGGAACACACCUGUCUUUGUGAUCCGGAAGGCUUCUGGGUCUUAUCGUUUAUUGCAUGACUUGCGCGCUGUUAACGCCAAGCUUGUUCCUUUU-GGGGCCGUCCAACAGGGGGCGCCAGUUCUCUCCGCGCUCCCGGCUGGCUGGCCCCUGAUGGUCCUAGACCUCAAGGAUUGCUUUUUUUCUAUUCCUCUUGCGGAACAAGAUCGCGAAGCUUUUGCAUUUAC
DQ365814.1/2819-3107 UAGCGCUAACGCAA---UUAGUGGAAAAAGAAUUACAGUUAGGACAUAUAGAACCUUCACUUAGUUGUUGGAACACACCUGUCUUCGUGAUCCGGAAGGCUUCCGGGUCUUACCGCUUAUUGCAUGAUCUGCGCGCUGUUAAUGCCAAGCUUGUUCCCUUU-GGGGCCGUCCAACAGGGGGCGCCAGUUCUCUCUGCGCUCCCGCAUGGCUGGCCCCUAAUGGUCCUAGACCUUAAGGAUUGCUUCUUCUCUAUUCCUCUUGCGGAACAAGAUCGCGAAGCUUUUGCAUUCAC
D10652.1/2583-2871   UAGCGCUAACGCAA---UUAGUGGAAAAAGAAUUGCAGCUAGGACAUAUAGAACCUUCACUUAGUUGUUGGAACACACCUGUCUUUGUGAUCCGGAAGGCUUCCGGGUCUUAUCGCUUAUUGCAUGACUUGCGCGCUGUUAACGCUAAGCUUGUUCCUUUU-GGGGCCGUCCAACAGGGGGCGCCAGUUCUCUCCGCGCUCCCGCGUGGCUGGCCCCUGAUGGUCCUAGACCUCAAGGAUUGCUUCUUCUCUAUUCCUCUUGCGGAACAAGAUCGCGAAGCUUUUGCAUUUAC
AY350569.1/2597-2885 UAGCGCUAACGCAA---UUAGUGGAAAAAGAAUUACAGUUAGGACAUAUAGAACCUUCACUUAGUUGUUGGAACACUCCUGUCUUUGUGAUCCGGAAGGCUUCCGGGUCUUAUCGCUUAUUGCAUGACUUGCGCGCUGUUAACGCCAAGCUUGUUCCCUUU-GGAGCCGUCCAACAGGGGGCGCCAGUUCUCUCCGCGCUCCCGCGCGGCUGGCCCCUGAUGGUCCUAGACCUCAAGGACUGCUUCUUUUCUAUUCCUCUUGCGGAACAAGAUCGCGAAGCUUUUGCAUUUAC
AJ623290.1/2495-2786 UUGAUGCUUUGCAAACUUUAGUAGCCCGGGAGCUUCGCCUGGGUCACAUAGAGCCUUCGCUUAGUAGAUGGAACACUCCGGUGUUUGUAAUUCAGAAGAAAUCAGGGGCUUUUCGCUUGCUGCAUGACUUGCGCGCUGUCAAUUCUCAACUUAUACCCUUU-GGUGUGGUGCAACAGGGAGCACCUGUGUUAUCUGCGGUGCCGGAGGAAUGGGAAGUAACGGCCAUUGACUUGAAGGAUUGUUUUUUCUCAAUACCUCUAGCUGAGCAGGAUAGAGAAGCUUUCGCUUUUAC
#=GC SS_cons         ::::::::::(((-...--(((((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<--<<______>>-->>,,,,,,,,,,,,,,,,,<<<<<<<_______>>>>>>>,,,)))))---)))--------------------((----(((((((,,,,,.<<<<<<<-<<<---<<<<<<<<-<<____>>-->>>>>>>>--->>>->>>>>>>,<<<<<___________________________>>>>>,,,,,,,,,)))))))---)):::::::::::::::::
#=GC RF              UAGcgcUAAcGCaA...UUaGuGgAAAAAGAAUUaCAguUAGGACAUAUAGAACCUUCaCUUAGUuGuUGGAACACaCCuGUcUUUGUGaucCgGAAGgcuUCcGgguCUUAcCgCuUAuuGCAUGAcUUGCGCGCUGUUAAcgCcaAgCuUGuuCCuUUU.ggggccgUcCaACAgGgggCGCCagUucUcuCcGCGcucCcGcauGgcuggccccUgauggUCcUAGACcUcAAGGAUUGcUUcUUuUcuaucCCUCUuGCgGaaCAaGAUcGcGAAGCUUUUGCAUUUAC
//
# STOCKHOLM 1.0

#=GF AC   RF01418
#=GF ID   HIV_POL-1_SL
#=GF DE   HIV pol-1 stem loop
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:18974280
#=GF GA   54.00
#=GF TC   54.00
#=GF NC   53.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   18974280
#=GF RT   Evidence of a novel RNA secondary structure in the coding region of HIV-1
#=GF RT   pol gene.
#=GF RA   Wang Q, Barr I, Guo F, Lee C
#=GF RL   RNA. 2008;14:2478-2488.
#=GF WK   Structure_and_genome_of_HIV
#=GF SQ   29


AY169968.1/2046-2158 CAAGGGACAGUGUUGGUGGGACCAACACCUGUCAAUAUAAUUGGGAGAAAUAUUUUAACACAGAUAGGGUGCACACUGGUAUUCCCUAUCAGUUCAAUUGAAACUGUCCCAGU
X52154.1/2527-2639   GUAGGGACAGUAUUAGUAGGACCAACACCUGUAAAUAUAAUUGGAAGAAAUAUUUUGACACAAUUGGGUUGUACUCUAGUGUUCCCAAUUAGUUCAAUUGAAACUGUCCCAGU
DQ878451.1/214-326   AUAGGWUCAGURUUGGUAGGACCUACACCCGUCAACGUAAUUGGAAGAGGCUUGAUGACUCGGAUGGGCUGUACUUUAAAUUUUCCAAUUAGUCCUAUUAAAACUGUACCAGU
DQ878511.1/214-326   MKAACUACAGUAUUARUAGGACCUACACCUGUCAACGUARUUGGAAGGAAUCUGAUGACUCAGCUUGGUUGCACCUUAAAUUUCCCCAUUAGUCCUAUUGAAACUGUACCAGU
DQ672623.1/2268-2380 AUAGGUACAGUAUGAGUACGACCUACACCUGUCAACAUAGUNGAACGAAAUCUGUAGACUMGAAUGGUUUGCACUCUAAAUUUUCCCAUCAGUCCUAUUGAAACUGUACCAGU
DQ369152.1/214-326   AUAAGUACAGUAUUAGUGGGACCUACACCUGUCAGYGUAGUUGGAAGAAAUCUAAUGUCUCAACUUGGUUGCACUUUAAAUUUUCCYAUUAGUCCCAUUGAAACUGUACCAGU
DQ878674.1/214-326   GUAGGUUCUGUAUUAGUAGGACCUACCCCUGCCAACAUAAUUGGAAGAAAUGUGAUGACCCAGCUUGGCUUUACUUUAAAUUUUCCCAUUAGUCCUAUUGAAACAGURCCAGU
DQ017383.1/1970-2082 GUUGGUACAGUGUUAGUAGGACCAACACCUGUUAAUAUUAUAGGAAGAAACUUUUUAACACAGAUUGGCUGUACUCUAAAUUUUCCAUUAAGUCCUAUUAAAACUGUACCAGU
DQ878307.1/214-326   AUAGGUGAAGUGCUAGUAGGACCUACACCUUUYAAYGUAAUUGGAAGGAAUAUGAUGACUCAGAUUGGUUGUACUCUAAAUUUUCCYAUUAGUCCUAUUGACACUGUACCAGU
AF347286.1/214-326   GAAGGUACAGUAUUAAUAGGACNUACACCNGUCAACNUNAUAGGAAGAGAUNUGAUGACUCAGNUUUGUUGCACUUUAAAUUUUCCCAUUNGUCCUAUUGAAACUGUACCAGU
EF199601.1/214-326   GUAGGUACGGUAUUAGUGGGACCUACCCCUGUCGACAUAAUUGGAAGAAAUCUGUUGACUCGCCUUGGUUGCACUUUAAAUUUUCCAAUCGAUCCCGUUGAAACUGUACCAGU
DQ878079.1/214-326   AAAUGUACAGUAGUAAUAGGACCUACACCUGUCAACGUAGUUGGAAGAAAUCUGAUGACUCAAAUUGGUUGYACCUUAAAUUUUCCCAUUUGUCCUAUUAAAACUGUACCAGU
DQ373064.1/2021-2133 CUAGGUACAGUUUUAGUAGGACCCACACCAGUAAAUAUCAUAGGAAGGAACAUUUUAACUCAAAUUGGAUGUACUCUAAAUUUUCCUAUUAGCCCUAUUGAAACUGUACCAGU
AY771520.1/214-326   GUAGGUUCAGUGUUGAUAGGACCUACGCCUGUCAAYGUAAUUGGAAGAAAUAUAAUGACUCAGCUUGGUUGUACUUUAAAUUUUCCCAUUAGUCCUAUUGARACUGUACCAGU
DQ878094.1/214-326   AUAGGGUCAGUGUUAGUAGGACCGACACCUGCCAACGUAAUUGGAAGGAAURUACUGACUAAGAUUGGUUGUACGUUAAAUUUUCCAAUCAGUCCUAUUGAAACUGUACCAGU
DQ877823.1/214-326   AUAGGUUCAGUAUURGUAGGACCCACACCUGUCGAUGUAAUUGGAAGAAAUCUAAUGACUAAGCUUGGUUUCACUUUAAAUUUUCCCAUUAGUCCUAUUAAUACUGUACCAGU
AY366010.1/214-326   AUAAGUACAGURUUAGUAGGAGCUACMCCYGUCAAUGUAAUUGGGAGAAAUCUAAUGACUCAGAUUGGYUGYACUUUAAAUUUUCCUAUCAGUCCUAUUGAAACUGUACCAGU
AY857177.2/521-633   AUAGGUACAGUAUUAGUAGGACCUACMCCGGUCAACAUAAUUGGAAGAAAUCUGUUGACUCAGCUUGGUUGCMCUUUAAAUUUUCCCAUCAGUCCUAUUGAAMCUGUNNNNNN
AY995543.1/214-326   AUAAGUUCAGUGUUAAUAGGACCUACACCUGUCRACAUAAUUGGAAGARAUYUGAUGACUCAGAUUGGUUGCACUYUAAAUUUUCCCAUUKGUCCUAUKGAAACUGKACCAGK
EF449918.1/214-326   AUUGGUACRGUACUAGUAGGACCUACACCUGUCAACAUARUUGGAAGAGAUCUGUUGACUCAGCUUGGGUGUACACUAAAUUUUCCAAUUAGCCCCAUUAAAACUGUACCAGU
AF115393.1/1877-1989 ACAGGCACGGUAUUGGUGGGACCAACACCAGUGAAUAUAAUUGGCAGAAAUAUAUUGACACAAAUUGGCUGUACUUUAAAUUUUCCUAUAAGUCCCAUUGAAACAGUGCCAGU
AY787528.1/151-263   AUAGGUACAGUAUUAGUAGGACCCACACCUAUCAACAUAAUUGGAAGAAAUAUGUUGACUCAACUUGGAUGCACACUAAAUUUUNNNNNNAGUCCUAUUGAAACUGUGCCAGU
AF347260.1/127-239   ACGGGUACAGUAUUAAUANGACCNGCNCCUGUCAACAUAAUUGGAANANNUCUGAUGACUCAGAUNGGUUGCACCUUAAAUUUUCCCAUUAGUCCUAUUGAAACUGUACCAGU
AY855615.1/214-326   AUAGGUACAGUGUUGGUAGGACCUACGCCUGUCAACGUAGUUGGAAGAAAUAUAAUGACUAAKAUUGGUAGACCUCUAAAUUUUCCAAUUAGUCCUAUUGAAACUGWACCAGU
EF517447.1/184-296   GUAGGCACAGUGUUAGUAGGACCUACACCUGUCAACAUAAUUGGAAGGAACCUGUUGACUCGGAUUGGCUGUACUUUAAAUUUUCCMAUYWGUCCYAUUGAVACKGURCCAGU
EF517442.1/184-296   AUAGGUACAGUAUUAGUAGGACCGACACCUGCCGACAUAAUUGGACGAAAUAUGUUAACUCAGAUUGGUUGCACUCUAAAUUUCCMAAUYWGUCCYAUUGAVACKGURCCAGU
AY635695.1/505-617   AUAGGUACAGUAUUGGUNGGACCUACUCCUGCUGACAUAAUUGGACGAAAUAUGUUGACUAAGAUUGGUUGUACUUUAAAUUUCCCAAUUAGUCCUAUUGACGCUGUACCACC
AY771412.1/214-326   AUAGGUACAGUGUUGAUAGGACCUACACCURUCAACRUARUUGGAAGAAAUUUGAUGACUAAGMUUGGUUGCACUUUAAAUUUUCCCAUUAGUYCUAUUAACACUGUACCAGU
DQ869194.1/166-278   AUAGGKACAGUAUUAGUAGGACCUACMCCYGUCAACAUAAUUGGNCGAAAUAUGUUGACCCNGAUUGGNUGUACUUUVAAUUUUCCNAUCAGUCCUAUUGAAACUGKACCAGC
#=GC SS_cons         :::(((((((((((((((((((,,,,,,,,<<<<<<<<<___________>>>>>>>>>,,,<<<<<<________________>>>>>>,))))))))))))))))))):::
#=GC RF              aUAgGuaCaGUcucagUaGGaCCuACaCCUGucaacauaAUUGGAAGAAAuauguugaCucAgaUuGGuUGuACuuUAAAUUUUCCaAucAGuCCuAuugagACuGuaCcAGU
//
# STOCKHOLM 1.0

#=GF AC   RF01419
#=GF ID   IsrR
#=GF PI   lsrR
#=GF DE   Antisense RNA which regulates isiA expression
#=GF AU   Osuch I
#=GF SE   Predicted; MAFFT
#=GF SS   Predicted; PFOLD; Osuch I
#=GF GA   52.00
#=GF TC   52.00
#=GF NC   51.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16636284
#=GF RT   An internal antisense RNA regulates expression of the photosynthesis gene
#=GF RT   isiA.
#=GF RA   Duhring U, Axmann IM, Hess WR, Wilde A
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:7054-7058.
#=GF WK   Iron_stress_repressed_RNA
#=GF **   seedtax: Eukaryota; Bacteria; unclassified sequences
#=GF SQ   308


AM423539.2/7314-7144         AAUAACCAA-AUUUAAGA-CUUGGGGUAAACG---UCAAAUUAGUWAGUUAAUUUUCUUA----------UAUUAC----CC-CU----U-UG------GAACCCU---GG-------------U--------------------------C--AAUA----------AAUAAUAUCAAAUACUAA-AA-GAAA-AGAAUGUAUAU-CUAACAAGAUU-UAGU-GAA-----UACAA--AAUUAUGAUC-AUCUUA-UUUCUAUUUUUUUU
X97043.1/910-733             CGUACUCAA-ACAGGACG-GACAGGAUGGUGGCACCGGGGUU----GGUAACCACGCGCA----------CUUCAC-----------------------CAAUGGU---GG-------------AG---------UCGUAGACCCCA-UGGA--ACCG----------CAGCCA---GAUGACAAA-CA-GCAG-GGCUGCGUAAC-CUAAGGUGAGG-AGGU-GGU---GACCGAG--GAUGUUCCCC-AGUUUG-GCCGCGUCAUCCCA
AARH01011413.1/13675-13504   GGU-----A-AUUUGAUG-GAGAGAGAAAAAG---UAGUUUG----GUUGCUAUUGCUCU----------CAGCUU----CU-UU----U-AG------CCACUUU---UG-------------UU---------UCUUAA----------A--AGUA----------UAGAGCUUUGAAUAAUUG-AA-GAAA-AGCACCUAUAC-CUGGCAAGAUU-AUGU-GAA---CACCUAA--AAUUGUUGUC-AUUUUAAUUUCUAUCUUACCA
AM430133.2/11786-11596       AAUAAGCAA-AUGUGACA-CUUGAGCUAAGUU---CCAAGUU----GAUAAUUUUUCRUUUUCUU-----ACCUUUC--AUA-UC----U-UG------AAGUACA---GU-------------UG---------UCAAAUACACCU--CUG--AAUA----------AAGAACCACAAAUACUAGAGA-AACR-AACACCUAUAC-CUAACAAGAGU-AAGU-GAA----UUUUAA--AAUUGCAGUC-AUUUUA-UUUCUGUCUUUCCA
CP000239.1/2624256-2624432   UAUGCCCAACAGGUGGCC-AAAGGGGUUCCAG---UUGG--G----AGACACCAGGCGCA----------CCUCUC-----------------------CUGCCAC---CG-------------GG---------UCGAACAAGCCG-CCAA--ACAC----------CACUGCCUUGAGCACCAA-AA-GCCA-GGCUCCCAAUC-CCAGCAGCACC-AGGU-GGA---UCCCUAG--GAUGGUGGUC-AUCUUG-UUUUUGUCUUGCCA
X97043.1/2155-1978           CAUACUCAA-AAAUAACG-GAGAGAAUGGUGGCACCGGGGUU----AGAGACAAUGCGCA----------CAUCGC-----------------------CGAUGGU---GG-------------AA---------UCGUAAACGCCG-UGGA--AGCG----------AAUCCA---ACCGACGAA-GA-AGAU-UGCCCCCAAUC-CGAGCAGCAGC-AGGU-GAU---GACCCAG--AAUUAAGCCC-AGUUGC-UUGGGAUCAUCCCA
BA000045.2/2489488-2489287   CGUAGCCGA-AGAUGACC-GUCGGGUCGAGGG---UCGGAUU----GGUGACGGUGCGCA----------CCUGGCCGGCCC-AC----U-GG------UUGUUGU---UGUCGAAGAACCAGGGG---------UCGUAGAUGCCG-CCAA--ACCA----------GCAGGCCUUGGCCACCAG-CA-GGAA-GCAACCGAUCC-CAAGCAGGAUC-AGGU-GGA---UGCCCAG--GAUGGUGGUC-AUCUUG-UUCUUGUCUUUCCA
AM444593.1/967-773           AAUAACCAA-AUAUAACWACUUGGGCUAAGGG---UCAAGUU----GGUUAAUUUUCUUA----------CAUCYUC--CCCSUC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACGCCGACCAA--AWUA----------AAGAGCCUUGAAUACUA--GA-AGAA-AGCACCUAUACACUAACAAGAUU-AAGUAGAACUAACCCUAA--AAUUGUGGUCUAUUUUA-UUUCUAUCUUYCYA
AJ534947.1/502-328           CAUAGCCGA-AGAUAUCA-GCCGGGUUUAGGU---UGGG-------AGAUACGGUGUGCA----------CGGUAC-----------------------CCAGGGA---GG-------------CA---------UCAUACACGCCA-CCCC--AGAA----------CAUGGCCUUAGCCACAAA-UG-CUAA-GCAAAGGAUCC-CCAACAAUAGG-AGGU-GGU---GACCGAG--GAUGAGGCUG-AGUUGC-UUGGUAUCGCCCCA
AY835431.1/93748-93575       AUUUGUUGU-AAAUUAUU-ACUAACUUACGGG---GGCCUUU------------GACGAU----------CGACCC--------C----C-AA------CGGACCA---CG-------------GG---------UCAAAAAGACCG-CCGA--AAUA----------CAUUGCUUUCCAAACUAA-AA-GCCA-UGCACCAAAGC-CUAAAAUAACU-AAAU-GAA---UACCUAA--AAUUGUAGAC-AUUUUG-UUUUUAUCUUUCCA
AJ311688.1/541-367           GGUAGCCGU-AGAUCACC-CAGGGAUCGAGGG---UGGGCUG-------CACCAGGCGAA----------CGGUUU-----------------------GCUGGGU---GG-------------CA---------UCGUACAACCCG-CCCC--AGGU----------GGUGGCUUUGGCGACGAG-GA-GCAG-CGCCCCCGCCC-CCAAAAACAGU-AGGU-GAU---GACCGAG--AAUCAUUCCU-AAUUGG-GCCGGAUUUUCCCA
AP004950.1/14873-14693       AAUAACCAA-AUAUAAUA-GUUGGACUAA--G---UCAAAUU----GGUAAUUUUUCUUG----------CAUGUC-----C-CU----U-UG------GAGCCCA---GG-------------UA---------UCACAUAUACCC-CCAA--AAUA----------AAAAGCCUUGAAGACUAG-AA-GAAAAUCCCCCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAGUGUAGUC-AUUUUA-UUACG--CCCUGAG
CP000240.1/2372203-2372380   GGUAGGCAA-AGAUCCGC-AGCGGAUUGAGGG---UGGGAUC----CGCAACGAUCCGCA----------CGCGGC-----------------------CCAGGUU---GG-------------CA---------UCGUACAGCCCU-CCCC--AAAA----------GAGAGCCUUGGCCACCAG-CA-GCCA-UGCACCCAGCC-CCAGCAGCAGC-AGGU-GGA---UGCCGAG--GAUGGUGGUC-AUCUUG-UCGUCAUCUUCCCA
CP000239.1/2622597-2622774   GGUAGGCAA-AGAUCCGC-AGCGGAUUGAGGG---UGGGAUC----CGUAACUACGCGCA----------CGCGGC-----------------------CCAGUUG---AG-------------CA---------UCGUACAGCCCU-CCCC--AGAA----------GAGCGCUUUGGCCACCAG-CA-ACCA-GGCCCCCAGCC-CCAGCAGCAGC-AGGU-GGA---UCCCCAG--GAUGGUGGUC-AUCUUG-UCGUCGUCUUCCCA
AJ311687.1/555-378           GAUAGCCAU-AAAUCACA-AAGGGCUUAACAG---UGCCCUC----AGUAACUAGCCGUA----------CAUCAU-----------------------CAAUUCU---GC-------------UC---------CCGUAAAUUCCC-CCCC--AGAA----------CAUGCCUUUUCCCACCAG-CA-AUAA-AGCUCCUACAC-CCACAAACACA-ACAC-CCU---CCCCCAA--AAUUAAGCCC-AGCUGU-UUGGGCUCAUCCCA
DQ630521.1/24745-24575       GUUUAC--A-UCAUCUUU-UAAUGAUGGGAGG---CGGGUUG----------AAAAUUUA----------CCUCCU----------------G------GAGCCCA---AG-------------UA---------UCAUAUACACCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-AA-GCCA-AGCUCCAAAAC-CUAAAAUAAUU-AGGU-GGA---AACCUAA--AAUGCUUGUC-AUUUUG-UUCUUGUCUUUCCA
AASG02000597.1/43226-43418   AAUAACUGA-AAAUAACA-AUUGGACUAAAGG---UUAAGUA----G--UAAUUUUCUUA----------CAUCACC--UUC-CC----U-CCACCCCCGAGCCCA---GG-------------UA---------UCAUAUAUGCUC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUGC-CUAGCAAGAUU-AAGU-GAA---UAACUAAAAAAUUAUUAUC-AUUUUA-UUUCUAUUUUUUUA
AY552464.1/3103-2929         UGUAGCCUA-ACAAAGGA-AAAGGAUUGAGAG---UGGGACU-------CACAGUACGUA----------CUUCAC-----------------------CUAAAGU---AG-------------CA---------UCAAAAAUACCA-CCGA--AUAC----------AGUAGCUUUUAACACAAA-CA-AGAA-AGCACCUACUC-CUAAGAAAAUG-AGGU-GAU---GACCGAA--AAUAAAGGUU-AACUUG-UUGCCAUCAGACCA
AJ311691.1/541-367           GAUACCCGU-AAAUCACC-AAUGGGUCAAGCG---UGGGUUG-------CACCAGUCGCA----------CCGUUU-----------------------GAGUCGU---GG-------------CA---------UCAUAGAGGCCG-CCCC--AUGU----------GGUGGCUUUUAGGACUAG-CA-GCAG-CGCGCCCGCUC-CUAAAAACAGC-AAAU-GGU---GCCCUAA--GAUCAUCCCC-AAUUGC-UUGGGGUCGCCCCA
AY552464.1/1859-1685         GAUACCCAA-AGAUUGUA-AAUGGGUUAAGAG---UUGGGCU----AGUAACAGUUCUGA----------CCUCGC-----------------------CGAUGAC---AG-------------GG---------UCAUAGAUACCG----A--AGAA----------AACAGCCCAGAGGACUAA-AA-ACAA-GGCACCCAACC-CAAGAAGAAUU-AAGU-GGU---GACCAAG--GAUAAAACCU-AGACGU-UUACCAUCACCCCA
AASG02001249.1/17499-17692   AAUAACCGA-AAAUAACA-CUUGGGCUAAGGG---UUAAGUU----AGUAAUUUUUCUUACAUCUCC---CCCCCCC--CCC-CC----C-CG------GAGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAGCAAGAUU-AAGU-GAA---UACCUAU--AUAUAUAUAU-AUAUAU-AUAUAUAUAAGCCU
AB044481.1/354-187           GUU-----U-AAUUAAGU-UCUCACUUAAUUG---UGGC---------UGAAAAAUUUAC----------CACCGG-----------------------GCGCCCA---AG-------------UA---------UCGUAAACACCA-CCAA--AGUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-UGCACCUAGAC-CUAAAAUGAUU-AAGU-GGU---AACCUAA--AAUGUUUGUC-AUUUUG-UUUUUGUCUUUCCA
AADV02000296.1/863-689       GAUAGCCAA-AAAUGCGG-AUUGGGUCUAAAU---UUGGUUC-------AACAAUACGGA----------CUUCAC-----------------------CCACCAG---AG-------------GA---------UCAUAAAUUCCU-CCCC--AUUG----------GUUGGCUUUGAGGACCAG-AA-GGGC-UGCACCAAUGC-CUAAUAGGACU-AAGU-GAA---UCCCUAA--AAUACUGGUC-AUUUUU-UUGCCAUCUUGCCA
BA000019.2/4822586-4822763   GGUAGCUAA-AAAUAGUU-GCAAAGUUCCAAG---UCGGAUG----AGAAAUAACUCGCA----------CUUCUC-----------------------CUAAUGU---GG-------------GG---------UCGUAUAAGCCU-CCAA--AAAA----------GACGGCUUUGGCAACGAG-UA-AGCC-UGCUCCUAAAC-CUAGCAAAACU-AAAU-GUA---UGCCCAG--GAUAGUCGUC-AUUUUA-UUAGCAUCUUGCCA
M90639.1/768-597             UAAAACUAG-CUUUCACU------------AG---UUGG--A----GGCAAUGUGACUAA----------UUUUCAC--CUC-CA----G---------GAGCCCA---UG-------------UA---------UCAUAGAUUCCU-CCAA--AAUA----------CAUAGCUUUUAAAACUAA-UA-ACCA-AGCACCACAAC-CUAACAUGAUU-AAGU-GGU---AACCUAA--GAUAGAAGUC-AUUUUA-UUUUUAUCUUUCCA
CP000393.1/3826703-3826529   GAUAGCCGA-AAAUUCUG-ACAGGAUUUAGGU---UUGGCUG-------UACUAGUCGUA----------CCUUUU-----------------------CUACUAG---UG-------------GA---------UCAUAAAUACCG-CCUA--AAGC----------UGUUGCUUUUAUCACUAA-UA-GUGC-UGCUCCAAGUC-CUAACAACACU-AGAU-GGA---UACCUAG--AAUUGUUGUC-AUCUUA-UUGCCAUCUUCCCA
L26530.1/691-514             GAUAACCAU-AAAUAACC-AAAGGAUCUAAUG---UUGGCUG----ACUGACUAGGCGCA----------CCGUUU-----------------------GGGUGGU---GG-------------CG---------UCGUACAAUCCC-CCCC--AAUA----------CAUGGCUUUGCCUGCCAA-CA-GUAG-AGCUCCGGCCC-CCAGGAACAGG-AGAU-GAU---GACCCAA--AAUUAUCCCU-AGUUGC-UGGGGGUUUUCCCA
AB197035.2/120737-120551     AAUGACCGA-AUAUAACA-CCUGGACCCGCUG---UGAGAUU----CGUAAUUUCCCUUA----------CAUCCCC--ACC-AC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUGCACCU-CCGG--AAUA----------CGGAGCUUUGGACACCGA-UA-GAAG-GGCACCAAUAC-CCAGCAGGAUC-GGGU-GAA---UACCUGG--AAUGGUGGUC-AUUUUG-UUCCUAUCCCUCCG
AB158788.1/515-329           UAUAGUUAA-AUAUGAUA-ACAGGAGCUAUUG---UUGGGGA----UGCUACGCGAACUA----------CAUCUCC--ACC-AC----C-AG------CGGCCCA---GG-------------UA---------UCAUAAAUUCCA-CCGA--AGUA----------CAUAGCUUUCGCAACAAG-UA-GAUA-ACAUCCGCAAC-CUAAUAACACU-AGAU-GAA---AUCCCAA--GAUUGUUGCC-AUCUUA-UUUUUGUCACGCCA
M23639.1/790-613             GAUAACCAU-AAAUGACC-GCUGGAUUAAGCG---UCGGUUG----UGUUACCAAACGGA----------CUGUCU-----------------------GACUGGC---UG-------------CG---------UCGUAUAGGCCA-CCCC--AAGU----------UGUUGCCUUUGCCACCAG-CA-GCAA-UGCUCCAACCC-CGAGGAACAGC-AAGU-GGU---GUCCCAG--AAUGAGGCCU-AGUUGU-UUGGGAUCAUUCCA
AB158787.1/515-329           CAUAAUUAG-CUAUUAUU-AUAGGAUUUAGGG---UCGGUGC----UGUAACUCGAACUA----------CAUCUCC--ACC-UC----C-UG------CAGCCCA---GG-------------UA---------UCGUAAAUACCU-CCGA--AGUA----------AAGGGCCUUAGCAACAAG-UA-AAUA-ACAUCCAAAAC-CGAGAAGUAUU-AGAU-GAA---AACCUAG--AAUUGUUGUC-AUUUUA-UUUUUGUCACGCCA
AY876220.1/511-313           CGUAUCCAA-AAAUAAUA-AAUGGAUUGAUAG---UUGGGUU----AUCGAUAAAUCUAA----------CAUCACC--ACC-AC----C-AG------GUGCCCA---AG-------------UA---------UCAUAUAAACCA-AAACUAAAUACGUUACCUGGCAUAGCUCUGGCAGCAAA-UA-GUAA-UGCACCUAAGC-CAAGAAAAAUU-AAAU-GAA---UACCUAA--AAUAGAUGUC-AUUUUA-UUUUUGUCACGCCA
CP000393.1/3829197-3829020   GGUACCCGA-AGAUAGUU-UGUGGAUUCAGAG---UUGGUUC----AGUAAUCACUCGUA----------CAUUGG-----------------------CGAUCGC---CG-------------GA---------UCGUACAAACCA-CUAC--CAUA----------AACGGCUUUGACUACCAG-CA-UCAA-UGCUCCAAUCC-CUAGUAGUACU-AGAU-GAA---UGCCAAG--AAUAGUAGUC-AUUUUG-UUACCAUCAUUCCA
CP000393.1/3828100-3827923   AGUAGCCGA-AAAUGGUU-GUGGGGUUCAAAG---UUGGAUC----GUAAAUUACCCGCA----------CAUUCU-----------------------GAAUGAC---UG-------------GA---------UCGUAUAAUCCA-CCAU--AUGC----------CAUUGCUUUUGCUACAAG-CA-ACAA-AGCACCAAAUC-CCAACAAUACG-AGAU-GGA---UACCCAG--GAUAGUUGUC-AUUUUG-CCUGGAUCAUCCCA
AARH01003324.1/43325-43492   AAUAACCAA-AAAUAAUA---------------------CUU----GGUAAUUUUUCUUA----------UAUCUCC--CCC-CC----A---------GAGCCCA---GG-------------UA---------UCAUAUACACCC-CCAA--GAUA----------AAGAGCUCUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAGAUU-AAAU-GAA---UACCUAA--AAUUGUAAUA-AUUUUA-UUUCUAUCUUUCCA
AM778094.1/95027-95203       AAUAACCAA-AUAUAACA-CUUGGGCUAAGAG---UCAAGUU----GGUAAUUUUUGUAA----------CAUCUC---CCC-UC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACAUCU-CCAA--AAUA----------AAGAGUCUUGAAUACUAG-AA-G----------AAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUGGUU-AUUUUA-UUUAUAUCUUUCCA
AY876223.1/499-313           CAUAAUUAG-CUAUUAUU-AUAGGAUUUAGAG---UUGGUUU----UAUAACUUGAACUA----------CAUCUCC--ACC-UC----C-UG------CAGCCCA---GG-------------UA---------UCGUAAAUACCU-CCCA--AAUA----------AAGAGCCUUACCAACAAG-UA-AAUA-ACAUCCAAAAC-CGAGAAGUAUU-AGAU-GAA---AACCUAG--AAUUGUUGUC-AUUUUA-UUUUUGUCACGCCA
BA000039.2/1089797-1089620   GAUAGCCAU-AGAUGACA-AAGGGAUCCAACG---UGGGCUG----GGUUAUCAAGCGUA----------CCGUUU-----------------------GCAAAUU---GG-------------CA---------UCGUACAACCCA-CCCC--AGAU----------GGUUGCUUUGAGAACUAA-CA-GCAG-GGCACCGAACC-CCAAAAAGAGC-AGAU-GAU---GUCCCAA--AAUAAUGCCC-AGUUGU-UUUGGAUCAUCCCA
AASG02002677.1/23030-22834   AAUAACUGA-AAAUAACA-CUUGGGCUAAGGG---UUAAGUU----AGUAAUUUUUCUUACAUCCCCCCCCCCCUCC--UUC-CU----C-UG------GAGACCA---GG-------------UA---------UCAUAUACGCCC-CUAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUACCAAGAUU-AAGU-GAA---UACCUAA--AAUUGUUGUC-AUUUUA-UUUCUAUAUUUCCA
AACY021133897.1/1-184        ---AGCCGA-AGACCACA-CCCGGAUCGAGAG---UCGGAUU----GGUGAUCAGACGAA----------CAUCGCC--ACC-GC----C-GG------GUGCCCA---GG-------------UG---------UCGUAUACGCCA-CCAA--AGAA----------CAUGGCCUUGAAGACCAG-GA-GCAA-ACAGCCAACGC-CCAAGAGGAUU-AGGU-GAU---AGCCAAU--GAUGUUGGUC-AUUUGA-UUCUUGUCACGCCA
AJ582999.1/527-350           GAUAGCCAU-AGAUAACC-CAAGGAUCGAGGG---UUGGUUC----ACUAACGACUCGGA----------CAGCGC-----------------------CGAUAGU---UG-------------CG---------UCGUAUAAUCCC-CCCC--AGUA----------CAUAGCUUUGGCCACUAA-UA-AUAA-UGCAGCUAUAC-CUAAAAAGAGC-AGGU-GAU---GACCGAG--AAUAACUCCU-AAUUGU-CGGGGNUCGCUCCA
AARH01007846.1/112985-112801 AAUAACCAA-AAAUAACA-CUUUGACUAAGAG---UCAAGUU----GGUAAUUUGUCUUA----------CAUCUC-----C-UC----G-CA------GAGCCCA---UG-------------UA---------UCAUAUACACCA-CCAA--AAUAG---------AAGAGCUUUGAACACUAG-AA-GAAA-AACAUUUAUAC-CUAACAAGAUU-AAGU-GAA---UAUCUAA--AAUUAUUAUC-ACUUUA-UUUCUAUCUUUUCA
AACY021136096.1/554-371      GAUAUCCAA-GAAUAAUU-CGAGGGUCUAAUG---UUGGGUU-------GAUUAAUCUAA----------CUUCACC--UCC-AC----C-AG------GUGCCCA---UG-------------UA---------UCAUAAGCACCA-CCUAU-GAAA----------CACCAGUUUACAGACCAA-G--CAAG-UGCUCCAACAC-CAAGGACAAUA-AGAU-GAU---AUCCGAG--AAUGUUAGUC-AUCUGA-UUUUUAUCUCUCCA
AACY021969765.1/456-270      GGUAGCCGA-AGAUCACG-CCCGGGUCGAGGG---UCGGGUU----GGUGAUCAGGCGAA----------CGUCGCC--GCC-GC----C-AG------GGGCCCA---GG-------------UG---------UCGUAGACGCCG-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-CA-GCAG-GCAGCCGACUC-CCAGAAGAAUC-AGGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUCUUGUCGCGCCA
AACY021940540.1/50-233       GAUAACCAA-GAAUAAUA-CGAGGGUCUAAUG---UUGGAUU-------UAUAAGUCUAA----------CUUCACC--ACC-AC----C-AG------GGGCCCA---UG-------------UA---------UCAUAAGCUCCA-CCGA--UGAAG---------CACCAGUUUAGAGACCAA-G--CAAG-AGCACCUACUC-CAAGAACAAUA-AGAU-GAU---AUCCAAG--GAUAUUUGUC-AUCUGA-UUUUUAUCUCUCCA
AJ311684.2/544-367           GAUAGCCAU-AAAUCACG-GCUGGACUCAGGG---UAGGUUC----GGUCACCAGACGCA----------CGGUUU-----------------------GGGUGGC---AG-------------CA---------UCGUAUAAACCG-CCCC--AGUA----------CAUCGCUUUGGCGACUAA-CA-AUAA-GGCUCCUGCGC-CCAAAAAUAGC-AGGU-GAU---GGCCCAA--AAUGACGCCC-AAUUGU-UUCGGGUCGUCCCA
CP000110.1/1811437-1811251   GGUAGCCGA-AGAUCACG-CCCGGAUCGAGGG---UCGGGUU----AGUGAUCAUGCGGA----------CGUCACC--GCC-GC----C-GG------GGGCCCA---GG-------------UG---------UCGUAAACGCCG-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-CA-GCAG-GCAGCCGACGC-CCAGGAGAAUC-AGGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUCUUGUCACGCCA
AAVW01000010.1/1904-1727     GAUAGCCAA-AUAUCCGA-CCAGGGUUUAGAG---UUGGUUC----AGUAAUUACCCUUA----------CAUCUG-----------------------CUACAUC---AG-------------GG---------UCAUAAAGACCA-CCCC--AAAA----------CAGUGCUUUCGCCACCAA-UA-ACCA-AGCACCAAAAC-CCAAUAGCAAG-AGAU-GAA---UACCGAU--AAUGGUAGUC-AUUUUG-UCUUCAUCUUCCCA
Z72475.1/571-394             GAUAACCAU-AAAUAACU-GCUGGAUUGAGAG---UUGGGCC----UGUCACCAGGCGGA----------CGGUUC-----------------------CCGUUCC---CG-------------CA---------UCAUACAGUCCA-CCCC--AAUA----------CAUGGCUUUGCCAACUCG-CU-AUAA-GGCCCCUAAUC-CUAGAAAUAGC-AGAU-GAU---GUCCUAA--AAUCAACCCC-AACUGC-UUGGGAUCGUCCCA
L21858.1/896-719             GAUAGCCAU-AGAUAACA-AAGGGGUUGAGGG---UGGGAUG----GUUAACUACUCUGA----------CAACCU-----------------------GAGUUGU---UG-------------CG---------UCGUAUAGUCCU-CCCC--AAAA----------CAUAGCUUUUCCUACCAG-UA-AUAA-AGCUGCCAUGC-CUAAAAACAGG-AGGU-GAU---GCCCUAA--AAUCAAACCG-AGUUGU-UUCGGGUCGUUCCA
M88253.1/955-778             GAUACCCGU-AGAUCACC-GCCGGAUCGAGGG---UCGGCUC----UGUAACCAAGCGCA----------CGGUUU-----------------------GGGUCGC---UG-------------UG---------UCGUACAAACCG-CCAA--AGUA----------CAUCGCUUUCGCUACGAG-CA-AGAA-AGCACCCAGUC-CCAGCAACAGU-AAGU-GAU---GGCCCAA--AAUUAAACCC-AAUUGC-UUCGGGUCUUCCCA
AACY022673157.1/742-556      GGUAGCCGA-AGAUCACU-CCCGGAUCGAGGG---UCGGGUU----GGUGAUCAUGCGGA----------CAUCACC--GCC-GC----C-GG------GGGCCCA---UG-------------UG---------UCAUACACGCCG-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-CA-GAAG-GCAGCCGACGC-CCAGAAGGAUG-AGGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUCUUGUCACGCCA
AACY020889377.1/1-171        GAU------------------UGGGUUUAAUG---UUGGUGU----UGUAAUUAAACGAA----------CAUCACC--ACC-AC----C-AG------GCGCCCA---UG-------------UG---------UCAUAUACACCG-CCUA--AGUA----------CAUUGCUUUUACAACUAA-UA-AAAA-UGAACCAAGAC-CUAAAAGGCAU-AGGU-GAA---UUCCUAA--GAUAGUUGUC-AUUUUA-UUUUUAUCACGCCA
AACY020698291.1/240-423      GAUAUCCAA-AAAUGAUU-CUUGGAUCGAGUG---UUGGGUU-------GAUCAACCUAA----------CUUCUCC--UCC-AC----C-GG------GAGCCCA---AG-------------UG---------UCGUAUGCACCG-CCUA--UGUA----------CAUCCAAUUGAUGGACCA-UA-AAAG-AGCACCAACUC-CUAGAACAACC-AAAU-GAA---AACCAAG--AAUGUUGGUC-AUUUGA-UUUUUGUCUCUCCA
EF625817.1/84496-84311       AAUAACCAA-AUAUAACA-UUUGGGCUAAGAG---UCAAGUU----GGUAAUUUUUCUUA----------UAUCUAC--CCC-UC----C-G-------GAGCCUA---GG-------------UA---------UCAUAUACGACU-CCAA--AUUA----------AAGAGUCUUGAAUAUUAA-AG-GAAA-AACACCUAUAC-UUAACAAAAUU-AAAU-GAA---UACCCAA--AAUUAUGGUC-AUUUUA-UUUCUAUCUUUCCA
AAVW01000010.1/6331-6154     AGUAGCCAA-AAAUUGUC-AUCGGCUCCAAAU---UGGGAUU----ACUAAUCAGGCGAA----------CAUCAC-----------------------CAAAAUU---CG-------------GG---------UCAUAAACUCCG-CCAA--AAAA----------CAUCGCCUUUAGCACUAA-UA-GAAA-UGCACCCAAAC-CCAGAAAAAUC-AAGU-GAU---GACCUAA--AAUCAAACCC-AACUGC-UGAGGAUCAUUCCA
AJ311685.1/544-367           GAUAGCCAU-AAAUGACC-GCUGGAUUCAGGG---UGGGUUC----GGUUACCAGACGCA----------CGGUUU-----------------------GGGUGGC---GG-------------CA---------UCGUAUAAACCG-CCCC--AGUA----------CAUCGCUUUGGCGACUAG-CA-GUAA-GGCUCCUGCGC-CCAAAAAUAGC-AGGU-GAU---GGCCCAA--AAUCAGUCCC-AAUUGU-UUGGGGUCGUCCCA
BX569690.1/313391-313577     GAUAACCGA-AGAUCACG-CCCGGAUCGAGAG---UCGGGUU----GGUGAUCAUGCGGA----------CGUCACC--GCC-GC----C-GG------GGGCCCA---GG-------------UG---------UCGUAGACGCCA-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-CA-GCAG-GCAGCCGACGC-CCAGAAGGAUC-AAGU-GAU---AACCGAU--GAUGUUGGUC-AUCUGG-UUCUUGUCGCGCCA
CP000239.1/2366571-2366385   GGUAGCCGA-AGAUGACC-GCCGGGUUGAGCG---UGGGGUU----GGUGAUCACCCGCA----------CGUCGCC--ACC-CC----C-CG------GAGCCCA---GG-------------UG---------UCAUAGACGCCA-CCAA--ACCA----------CAUGGCCUUGGCCACCAA-CA-GGAA-AGCCCCCAACC-CCAACAGGAUG-AGGU-GGA---UCCCCAA--GAUGGUGGUC-AUCUUG-UUCUUGUCUUUCCA
CP000553.1/1315546-1315363   GAUAUCCAA-AAAUAAUU-CUUGGAUCGAGUG---UUGGGUU-------GAUCAACCUAA----------CUUCUCC--UCC-AC----C-UG------GAGCCCA---AG-------------UG---------UCGUAUGCACCA-CCUA--UAUA----------CAUCCAGUUAAUGGACCA-UA-GAAG-AGCUCCAACAC-CAAGAACAACC-AAAU-GAA---AACCAAG--AAUAUUGGUC-AUUUGG-UUUUUAUCUCUCCA
AACY023917498.1/775-592      GAUAUCCAA-GAAUAAUU-CGUGGGUCUAAAG---UUGGAUU-------AAUUAAUCUAA----------CUUCGCC--ACC-AC----C-AG------GUGCCCA---UG-------------UA---------UCAUAUGCACCG-CCUAU-GAAA----------CACCAGUUUACUGACCAA-G--CAAG-UGCUCCAACAC-CUAAAACAAUU-AGAU-GAU---AUCCAAG--GAUAUUAGUC-AUCUGA-UUUUUGUCUCUCCA
AAVW01000010.1/864-687       GAUAGCCAA-AAAUCACG-GUAGAAUUCCAGG---UAGGGUG----AGAAAUAACUCGCA----------CCUCAC-----------------------CCAAAUU---GG-------------CA---------UCAUACAAGCCG-CCAA--AAAA----------CAUAGACUUGGCAACCAG-UA-AGCC-AGCACCUAAAC-CCAGUAAUAUU-AAGU-GAA---UGCCCAA--AAUAGUUGUC-AUUUUG-UUGGCAUCCUCCCA
CP000111.1/1169482-1169299   GAUAACCAA-GAAUAACC-CUUGGAUCUAAUG---UUGGAUU-------GACUAAUCUGA----------CUUCACC--ACC-AC----C-AG------GUGCCCA---AG-------------UA---------UCAUAAGCACCA-CCAA--UGAA----------ACACCAGUUCACAGUCCA-UG-CUAA-UGCACCUACAC-CAAGAACACAC-AAAU-GAU---AACCAAG--AAUAUUGGUC-AUUUGA-UUUUUAUCUCUCCA
AACY021985367.1/611-797      GGUAGCCGA-AGAUCACU-CCCGGAUCCAGGG---UUGGAUU----GGUGAUCAUGCGGA----------CAUCACC--GCC-AC----C-GG------GUGCCCA---GG-------------UG---------UCAUAGACGCCG-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-CA-GCAG-GCAGCCGACGC-CUAGAAGAAUC-AGGU-GAU---AACCAAU--GAUAUUGGUC-AUCUGG-UUCUUGUCCCGCCA
AM778094.1/179256-179070     AUUAACUAA-AUAUAACA-UUUGAGCUAAGAG---UCAAGUU----GGUAAUUUUUCUUA----------UAUCUAC--CGC-UU----U-CG------GAGCCCA---GG-------------UA---------UCAUACACACCU-CCAA--AAUA----------AAGAGUCUUGAAUAUUAG-AA-GAAA-AACACCUAUAC-UUAACAAAAUU-AAAU-GAA---UACCCAA--AAUUAUGGUC-AUUUUA-UUUCUAUCUUUCCA
AADV02000027.1/29055-29232   GAUAGCCAU-AGAUCACU-AAGGGAUCUAAGG---UGGGUUG----GGUUACUAAACGAA----------CCGCCU-----------------------CUGUGGU---GG-------------AA---------UCGUAUAUACCG-CCCC--AGAA----------CAUCGCUUUUCCUACCAA-UA-GUAA-GGCAGCGACAC-CCAAGAAUAAG-AGAU-GAU---GGCCUAA--AAUAAUGCCA-AGUUUU-UUGGGAUCGUCCCA
CT971583.1/1514899-1514713   GAUAACCGA-AGAUCACG-CCAGGAUCCAGGG---UGGGAUU----GGUGAUCAGACGCA----------CAUCACC--ACC-GC----C-GG------GGGCCCA---GG-------------UG---------UCGUAGACGCCG-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-CA-GCAG-GCAGCCGACGC-CCAGAAGGAUC-AGGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUCUUGUCACGCCA
AY705210.1/782-592           AAUAACCAA-AUAUCACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUUUGA----------CAUCUCC--CCC-CCACCUU-GG------GUGCCCA---GG-------------UU---------UCAUAUAUGCCU-CCAA--AAUA----------CAGAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAAUAAAAUU-AAGU-GAA---CAUACAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
U38804.1/144840-145026       CAUAGCCAA-AUAUAACU-AAAGGAUUAAGAG---UAGGGUU----GCUCACAAACCUAA----------CAUCGCC--ACC-AC----C-UG------GUGCCCA---UG-------------UA---------UCAUAUACCCCU-CCAA--CAAA----------UAAAGACUUGAUUACUAA-UA-GAAA-UGCUCCAAUUC-CUAGUAAUACU-AAAU-GUA---UACCAAG--AAUUGUUGUC-AUCUUG-UUUUUAUCGCGCCA
AACY022034783.1/357-174      GAUAACCGA-GAAUAAUU-CUUGGAUCUAAGG---UUGGAUU-------AAUUAACCUAA----------CUUCACC--ACC-UC----C-AG------GUGCCCA---AG-------------UA---------UCAUAGGCUCCA-CCGAU-GAAA----------CACCAGUUUAGAGACCA--UG-CUAA-UGCCCCUACAC-CUAAAACAAUA-AGGU-GAU---AUCCGAG--GAUAUUAGUC-AUUUGA-UUCUUGUCUCUCCA
AM778096.1/110672-110487     AAUAACCAA-AUAUAACA-CUUGGGCUAAGAG---UCAAGUU----GGUAAUUUUUGUUA----------CAUCUC---CCC-UU----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACACCU-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAC-AACACUUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUAUGGUU-AUUUUA-UUUAUAUCUUUCCG
CP000240.1/887341-887527     AGUAGCCGA-AGAUCACA-GCGGGGUUCAAGG---UGGGGUU----GGUAAUUACCCGCA----------CAUCGCC--ACC-CC----C-UG------GAGCCCA---GG-------------UG---------UCAUAGACACCG-CCAA--ACCA----------CAUGGCCUUGGCCACCAA-UA-GGAA-AGCCCCCAACC-CCAACAGGAUC-AGGU-GGA---UCCCCAG--GAUGGUGGUC-AUCUUG-UUCUUGUCUUUCCA
AACY023613948.1/187-4        GAUAACCAA-GUAUUACU-CUUGGAUCUAGUG---UUGGGUU-------UACAAGUCUGA----------CUUCACC--ACC-AC----C-UG------GUGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUUACUGACCA--UG-CUAG-UGCACCUACAC-CCAGAACAAUC-AAAU-GAU---AUCCGAG--GAUAUUAGUC-AUCUGA-UUUUUGUCUCUCCA
U40144.1/1724-1538           GGUAACCGA-AGAGAACA-CUGGGGCUAAGGG---UGGGGUU----GGUGAUAACCCGAA----------CGCCGCC--GCC-AC----C-AG------GAACCCA---AG-------------GA---------UCAUAGAGUCCA-CCAA--AGAA----------CAUGGCUUUGAAGACAAA-CA-GGCU-UGCGCCAAUGC-CCAAAACGAUG-AGGU-GGA---AACCCAG--AAUAUUGGUC-AUCUGG-UUCUUAUCUUUCCA
AACY023403422.1/907-1089     AAUAACCAA-GAAUAACU-CUUGGAUCCAAAG---UUGGAUU-------AACAAGUCUUA----------CUUCACA--CCU-CC----A-G-------GUGCCCA---UG-------------UG---------UCAUAUGCACCA-CCAAU-AAAA----------CACCAGUUCACUGACCA--UG-CUAA-UGCACCUACAC-CUAAUACAAUC-AAAU-GAU---AACCAAG--AAUAUUUGUC-AUUUGA-UUUUUAUCUCUCCA
AACY023525685.1/1017-1203    GAUAGCCGA-AGAUCACA-CCCGGAUCGAGAG---UCGGGUU----AGUGAUCAGACGAA----------CAUCACC--GCC-GC----C-CG------GUGCCCA---GG-------------UG---------UCGUAGACGCCA-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-GA-GCAA-ACAGCCAACGC-CCAAGAGAAUA-AGGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGA-UUCUUGUCGCGCCA
AACY023522437.1/279-96       AAUAUCCAA-GAAUUAUU-CUAGGAUCUAAAG---UUGGAUU-------AAUUAAUCUAA----------CUUCACC--ACC-AC----C-AG------GUGCCCA---AG-------------UA---------UCAUAAGCUCCA-CCGAU-GAAA----------CACCAGUUUAGAGACCA--UG-CUAA-CGCCCCGACAC-CUAAAACAAUA-AGGU-GAU---AACCGAG--GAUAUUAGUC-AUUUGA-UUCUUGUCUCUCCA
AACY021330979.1/630-447      AAUAGCCAA-GAAUAACU-CUCGGAUCUAAAG---UUGGAUU-------GACUAGUCUGA----------CUUCACC--ACC-AC----C-AG------GUGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUUACUGACCA--UG-CUAG-UGCACCUACAC-CCAAAACAAUC-AAAU-GAU---AUCCAAG--GAUGUUUGUC-AUUUGG-UUUUUAUCUCUCCA
AACY022982591.1/603-420      AAUAACCAA-GAAUAACU-CUUGGAUCUAAAG---UUGGGUU-------AACAAGUCUGA----------CUUCACC--ACC-GC----C-UG------GUGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUAACUGACCA--UG-CUAA-CGCACCUACAC-CCAAAACAAUC-AAAU-GAU---AUCCAAG--GAUAUUUGUC-AUUUGG-UUUUUGUCUCUCCA
AJ311682.1/544-367           GAUAACCAA-AAAUGGUU-GCAGGAUUUAAAG---UAGGGUC----GGUAACGACACGGA----------CAUCUU-----------------------GGAUGUU---GA-------------CA---------UCGUAAAGUCCA-CCAA--AAAA----------CAUCGCUUUUCCUGCUAA-AA-GCAA-UGCACCUAUGC-CAAGAAAUAAU-AGAU-GAU---GACCCAG--GAUCAUGCCU-AAUUGC-UUGGGAUCGCCCCA
AANO01000002.1/64718-64532   GAUAACCGA-AGAUCACA-CCCGGAUCAAGGG---UGGGGUU----GGUGAUCAGGCGCA----------CGUCGCC--ACC-GC----C-AG------GUGCCCA---GG-------------UG---------UCGUAGACACCG-CCGA--AGAA----------CAUCGCCUUGAACACCAG-CA-GCAG-GCAACCCACAC-CCAGAAGGAUG-AGGU-GAU---AGCCGAU--GAUGUUGGUC-AUCUGG-UUCUUGUCGCGCCA
AACY023852583.1/568-382      GAUAACCGA-AGAUCACA-CCAGGAUCCAAGG---UUGGGUU----GGUGAUCAAACGAA----------CAUCACC--ACC-GC----C-AG------GUGCCCA---GG-------------UG---------UCGUAAACGCCA-CCGA--AGAA----------CAUGGCCUUGAACACCAG-CA-GCAG-GCAGCCGACGC-CAAGCAGGAUC-AAGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUCUUAUCGCGCCA
AACY020159117.1/712-895      GAUAACCAA-GAAUAACU-CUCGGAUCUAAAG---UUGGGUU-------UACAAGUCUGA----------CUUCACC--ACC-AC----C-UG------GUGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUGACUGACCA--UG-CUAA-CGCACCUACAC-CCAAAACAAUC-AAAU-GAU---AUCCAAG--GAUAUUUGUC-AUUUGA-UUUUUGUCUCUCCA
AY936348.1/4464-4650         AAAAACCAA-AUAUGAUA-CUUGGACUCAGGG---UCAAGUU----CGUAAUUUUUCUUA----------CAUCUC-----------------------CCCCUCC---AG-------------GGGCCCAAGUAUCAUAUACACCC-CCAA--AAUA----------AAGUGCUUUGAAGACUAA-AA-GAAA-AGCACCUAUAC-CUAAUAAUAUUAAGGU-GAU----ACCUAA--AAUAGUNNNC-ANUGUA-UUUCUAUCUUUCCA
AJ296146.1/583-406           AGUAGCUAA-AAAUAGUC-AUUGGAUCAAAAG---UUGGAUU----GGUAAUCAGGCGGA----------CAUUUU-----------------------CUAUAUG---AG-------------UG---------UCAUAUAUUCCG-CCAA--AAAA----------CAUGGCUUUUAGCACCAA-UA-AAAA-UGCACCAAAAC-CCAGAAUAAUC-AGGU-GAU---GUCCUAA--GAUCAAACCU-AGCUUU-UUAGGAUCAUUCCA
AATZ01000001.1/613782-613596 GAUAACCGA-AGAUCACG-CCAGGGUCGAGGG---UGGGGUU----CGUGAUCAAACGAA----------CGUCGCC--ACC-GC----C-GG------GGGCCCA---GG-------------UG---------UCGUAGACGCCG-CCGA--AAAA----------CAUGGCCUUAAAGACCAG-CA-GCAA-GCAGCCGACAC-CAAGAAGGAUC-AGGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUUUUGUCGCGCCA
AACY022527936.1/460-277      GAUAACCAA-GAAUAACU-CUUGGAUCUAAGG---UUGGGUU-------UACAAGUCUGA----------CUUCACC--ACC-AC----C-AG------GUGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-GAAA----------CACCAGUUUACUGACCA--UG-CUAG-UGCACCUACAC-CUAGAACAAUC-AAAU-GAU---AUCCGAG--GAUAUUUGUC-AUUUGA-UUUUUAUCUCUCCA
AY876218.1/499-313           CAUAGUUAA-AUAUUGCA-CCUGGAUUUAAGG---UUGGAUU----AGGUACAAGACGAA----------CAUCUCC--ACC-GC----C-AG------GUGCCCA---UG-------------UA---------UCGUAUAUACCU-CCAA--AGAA----------CAUCGCCUUGGCUACAAG-UA-AAAA-UGCCCCAAUUC-CAAGCAAUACU-AAGU-GUA---UCCCUAA--AAUCGUUGUC-AUUUUA-UUCUUAUCACGCCA
AANP01000004.1/315982-315796 GAUAACCGA-AGAUCACA-CCGGGAUCGAGGG---UGGGGUU----GGUGAUCAAGCGCA----------CGUCACC--ACC-GC----C-GG------GGGCCCA---GG-------------UG---------UCGUAGACGCCG-CCGA--AGAA----------CAUCGCCUUGAACACCAG-CA-GCAG-CGCACCGACGC-CAAGCAGGAUC-AAGU-GGU---AACCGAU--GAUGUUGGUC-AUCUGG-UUCUUAUCCCGCCA
AACY021296091.1/647-830      AAUAACCAA-GAAUAACU-CUCGGAUCCAAGG---UUGGGUU-------UACAAGUCUGA----------CUUCACC--ACC-AC----C-UG------GUGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUUACUGACCA--UG-CUAG-UGCACCUACAC-CUAAAACAAUC-AAAU-GAU---AUCCGAG--GAUAUUUGUC-AUUUGA-UUUUUAUCUCUCCA
AACY020164518.1/511-694      AAUAACCAA-GAAUGACU-CUUGGAUCUAGUG---UUGGGUU-------AACAAGUCUGA----------CCUCACC--ACC-AC----C-AG------GUGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUAACUGACCA--UG-CUAA-UGCACCUACAC-CCAAGACAAUC-AAAU-GAU---AUCCGAG--AAUAUUUGUC-AUUUGA-UUUUUAUCUCUCCA
AJ295840.2/571-394           GAUAGCCAA-AGAUGAUA-AAUGGAUUGAGAG---UAGGUUC----AGUAACUACCCGGA----------CGUCAU-----------------------GAAUUGU---GG-------------UG---------UCGUAUAGUCCA-CCCC--AGAA----------CAUCGCUUUUGCUACUAA-CA-ACAA-AGCGCCAGCAC-CUAAGAAAAGC-AGAU-GAU---GUCCUAA--GAUAAGACCA-AGUUUA-UUAGCAUCAUCCCA
AB158791.1/515-329           CAUAGUUGA-AGAUAGCA-CCUGGGUUUAGUG---UUGGGUU----UGUUACAACACGAA----------CGUCACC--ACC-AC----C-UG------GUGCCCA---UG-------------UA---------UCGUAAAGACCA-CCAA--GGAA----------CAUCGCUUUAGUUACAAG-AA-GGAA-UGAUCCAAUAC-CUAGAAGGAUA-AGGU-GAA---UCCCUAG--GAUUGUAGUC-AUCUUG-UUUUUAUCACGCCA
AAXW01000011.1/95089-94912   GAUAACCGU-AGAUAACU-AAGGGGUCUAAAG---UGGGUUG----AGUCACUAAACGAA----------CCGUUU-----------------------CAGUAGU---GG-------------AG---------UCGUACAACCCA-CCCC--AAUA----------CAUGGCUUUUCCCACUAA-UA-ACAA-UGCACCGAUGC-CUAAAAACAAG-AGGU-GAU---GACCUAA--AAUAAUACCC-AAUUUU-UUCGGGUCAUCCCA
CP000393.1/2534646-2534823   GAUAUCCAU-AUAUUACC-AAUGGAUCGAGAG---UGGGAUU----UGUUACUAAACGAA----------CUGUUU-----------------------GAGUUGU---CG-------------CA---------UCAUAAAGCCCA-UCGA--AAUA----------CAUAGCUUUUGCUGCUAA-UA-AUAA-AGCACCAAAUC-CUAAGAAAAGU-AGGU-GAU---GGCCUAA--GAUAAUACCU-AGCUUU-UUUGGAUCAUCCCA
AF239780.1/1566-1380         AAUAACUAA-AAAUAGUA-UUGGGGUUAAGGG---UCAUAUU----UGUUAUUUUUCUUA----------CAUCUCC--ACC-AC----C-CG------GAGCCCA---GG-------------UA---------UCAUAUAUACCU-CCAA--AAUA----------GAGAGCUUUUAGCACGAG-AA-GAAA-AGAACCAGCAC-CGAGUAAGAUG-AGAU-GAA---UACCCAA--AAUGGUAGUC-AUUUUA-UUUCUAUCCUUCCA
AAUA01000001.1/229102-228916 GAUAACCGA-AGAUCACA-CCGGGAUUCAGGG---UGGGGUU----GGUGAUUAGACGAA----------CAUCACC--ACC-AC----C-GG------GGGCCCA---AG-------------UG---------UCGUAGACGCCA-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-UA-GCAG-GCAUCCAACGC-CGAGAAGAAUC-AAGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUCUUGUCACGCCA
AACY020552557.1/3347-3530    GAUAACCAA-GAAUAACC-CUUGGAUCUAAAG---UUGGGUU-------AACAAGUCUAA----------CUUCUCC--ACC-AC----C-AG------GAGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUAACUGACCA--UG-CCAA-UGCACCUACAC-CAAGGACAAUC-AAAU-GAU---AUCCGAG--GAUAUUAGUC-AUUUGA-UUUUUGUCUCUCCA
AY876202.1/499-313           CAUAGCCAA-AAAUAACU-AAUGGAUUAAGAG---UUGGAUU----ACUCACGAAUCUAA----------CAUCACC--GCC-AC----C-UG------GUGCCCA---AG-------------UA---------UCAUAUACUCCA-CCAA--CAAA----------UAGAGCUUUGAUUACUAA-UA-AAAA-UGCUCCAAUAC-CUAGUAAUACU-AAAU-GUA---UGCCAAG--UAUUGUUGUC-AUCUUA-UUUUUAUCGCGCCA
AAOK01000004.1/203251-203065 GAUAACCGA-AGAUCACA-CCGGGAUCAAGCG---UUGGGUU----GGUGAUCAGACGUA----------CAUCACC--ACC-GC----C-CG------GAGCCCA---GG-------------UG---------UCGUAAACGCCG-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-CA-GCAG-GCAACCGACAC-CCAGAAGGAUC-AAGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUCUUGUCACGCCA
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AY741371.1/66479-66665       CAUAACCAA-AAAUGAUU-AAAGGGUUUAACG---UAGGAGC----UGAGAUAAUUCUAA----------CAUCUCC--ACC-AC----C-UG------GAGCCCA---CG-------------UA---------UCGUAAACACCA-CCAA--CGAA----------ACAAGCUUUGGCAACAAG-UA-GGAA-ACAACCAAUAC-CUAAUAAAAUU-AGGU-GGA---UUCCUAA--AAUUGUUGUC-AUUUUG-UUCUUAUCACGCCA
AY876214.1/499-313           CAUAUCCGA-UGAUUACA-ACAGGGUUUAAAG---UAGGAUU----AUCGAUAAUACGUA----------CAUCUCC--ACC-AC----C-UG------GAGCCCA---CG-------------UA---------UCAUAUAAACCA-CCUA--CAUA----------AAGAGCUUUAAUUACUAA-UA-AUAA-AGCUCCAAAUC-CUAGGAUUACU-AAAU-GAA---UACCUAG--AAUCGUAGUA-AUUUUA-UUCUUAUCACGCCA
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AY876208.1/499-313           CAUAAUUGA-AUAUCACU-UGAGGAUUUAAGG---UAGGGUU----AGAAAUAUAUCUAA----------CAUCUCC--UCC-AC----C-CG------GAGCCCA---UG-------------UA---------UCAUAAACACCG-CCAA--AGAA----------UAAAGAUUUGAACACUAA-UA-AGAA-GGCACCUACUC-CUAAAAGAAUC-GGGU-GAA---UUCCAAU--AAUUGUUGUC-AUUUUA-UUCUUAUCACGCCA
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AACY020459449.1/1080-1266    GAUAACCGA-AGAUCACA-CCGGGGUCGAGGG---UGGGGUU----CGUGAUCAAACGAA----------CGUCUCC--ACC-AC----C-UG------GAGCCCA---GG-------------UG---------UCAUAAACGCCA-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-GA-GCAG-GCAGCCCACAC-CCAAAAGGAUG-AGGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUUUUGUCGCGCCA
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AACY020865073.1/554-371      GAUAACCAA-GAAUAACC-CUUGGAUCUAAAG---UUGGAUU-------UACAAGUCUAA----------CUUCUCC--ACC-AC----C-AG------GUGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUCACUGACCA--UG-CUAA-UGCACCUACAC-CUAAAACAAUC-AAAU-GAU---AUCCAAG--GAUAUUAGUC-AUUUGA-UUCUUAUCUCUCCA
AY705208.1/760-574           AAUAACCAA-AUAUCACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUGA----------CAUCUC---CGC-CC----C-UG------GUGCCCA---GG-------------UA---------UCAUAUAUGCCU-CCAA--AAUA----------UAGAGCAUUGAGUACUAG-AAUAAAA-AGCACCUAUAC-CUAAUAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUUUAUCUUUCCA
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AJ311683.1/544-367           GAUACCCAU-AGAUGACA-AAGGGAUCGAGAG---UAGGACU----UGUUACUACGCGGA----------CAUCAU-----------------------GAAUUGC---GG-------------AG---------UCAUAUAGUCCU-CCGA--AAAA----------CAUCGCUUUUGCCACCAG-UA-AUAA-AGCACCUAAUC-CUAGAAAAAUC-AAGU-GAU---GUCCUAA--GAUUAAACCA-AGUUGU-UUCGGGUCGUUCCA
DQ069643.1/601-415           AAUAACCAA-AUAUAACA-CUUGGG-CUAGUG---UUAAGUU----GGUUAUUUUUCUUA----------CAUCUCC--CCC-CC----CCAG------GAGCCCA---GG-------------UG---------UCAUAUACACCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUCC-CUAACAAAAUU-AGAU-GAA---UACCUAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AASG02001643.1/33662-33473   AAUAACCGA-AAAUAAUA-CUUGGGCUAAGGG---UUAAGUU----AGUAAUUUUUCUUACAU-------CUCCCCC--CCC-CC----C-CG------GAGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAGCAAGAUU-AAGU-GAA---UACCUAA--AUUUGUUGUC-AUUUUA-UUUCUAUCUUUCCA
DQ366716.1/6989-6806         GAUAACCAA-GAAUAACU-CUUGGAUCUAAAG---UUGGGUU-------UACAAGUCUGA----------CUUCACC--ACC-AC----C-AG------GUGCCCA---CG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUUACUGACCA--UG-CUAA-UGCACCUACAC-CUAGUACAAUC-AAAU-GAU---AUCCAAG--GAUAUUUGUC-AUUUGA-UUUUUAUCUCUCCA
AJ311694.1/544-367           GAUAGCCAU-AGAUCACA-AAAGGAUUGAGAG---UUGGUUC----AGUUACAAGGCGAA----------CAUCAU-----------------------GAAUAUU---CG-------------UG---------UCAUAAAUUCCU-CCCC--AAAA----------CAUGGCUUUACCUACCAG-CA-AUAA-AGCUGCUACGC-CUAAAAACAAG-AGGU-GGU---GUCCUAA--GAUUAAACCC-AGUUGU-UUAGGAUCAUCCCA
DQ366718.1/24210-24393       GAUAACCAA-GAAUAACU-CUUGGAUCUAAAG---UUGGAUU-------AACAAGUCUGA----------CUUCACC--ACC-UC----C-AG------GCGCCCA---UG-------------UA---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUAACUGACCA--CG-CUAA-UGCACCUACAC-CUAAAACAAUC-AAAU-GAU---AUCCAAG--GAUAUUUGUC-AUUUGA-UUUUUAUCUCUCCA
AACY022678378.1/540-723      GAUAACCAA-GAAUAACU-CUUGGAUCUAGUG---UUGGGUU-------AACAAGUCUGA----------CUUCGCC--ACC-UC----C-AG------GUGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUUACUGACCA--UG-CUAG-UGCACCUACAC-CUAAAACAAUC-AAAU-GAU---AUCCAAG--AAUGUUUGUC-AUUUGA-UUUUUAUCUCUCCA
AACY020225090.1/429-612      GAUAACCAA-GGAUAAUU-CUAGGGUCGAGAG---UAGGAUU-------AACUAAUCUAA----------CUUCUCC--ACC-AC----C-AG------GUGCCCA---AG-------------UA---------UCAUAAGCUCCU-CCUC--CAAA----------CAUCCAGUUAGCUGUGAA-GA-AUAA-AGCACCAACAC-CUAAAACGAUU-AAGU-GAU---AACCAAG--GAUAUUGGUC-AUUUGG-UUUUUAUCUCUCCA
AACY021151713.1/364-178      GAUAACCAA-AGAUCACA-CCGGGAUCGAGGG---UGGGGUU----GGUGAUCAGACGCA----------CGUCACC--ACC-GC----C-GG------GGGCCCA---GG-------------UG---------UCGUAGACGCCA-CCGA--AGAA----------CAUCGCCUUAAACACCAG-CA-GCAG-CGCACCGACUC-CGAGAAGGAUC-AGGU-GGU---AGCCGAU--GAUGUUGGUC-AUCUGA-UUCUUAUCGCGCCA
AACY022579995.1/687-870      GAUAACCAA-AAAUUACC-CUUGGAUCCAAAG---UUGGAUU-------AAUAAGGCGAA----------CUUCUCC--GCC-AC----C-AG------GUGCCCA---AG-------------UA---------UCAUAUGCUCCA-CCAAU-AAAA----------CACCAGUUUACUGACCAA-G--CUAA-UGAACCUAUAC-CUAGAACUAUC-AAAU-GAU---AACCAAG--AAUGUUGGUC-AUCUGA-UUUUUAUCUCUCCA
AACY020480390.1/813-630      GAUAACCAA-GAAUGACU-CUUGGGUCUAAAG---UUGGGUU-------AACAAGUCUGA----------CUUCACC--ACC-UC----C-AG------GUGCCCA---AG-------------UG---------UCAUAUGCACCA-CCAAU-AAAA----------CACCAGUUUAUUGACCA--UG-CUAA-UGCACCUACAC-CUAAAACAAUC-AAAU-GAU---AGCCAAG--AAUGUUUGUC-AUUUGA-UUUUUAUCUCUCCA
AY705186.1/811-625           AAUACCCAA-ACAUCACG-CCUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUGA----------CAUCUCC--CCC-UC----C-GG------GUGCCCA---GG-------------UA---------UCAUAUACGCUU-CCAA--AAUA----------CAGAUCCUUGAGUACUAG-AA-GAAA-AGCACCUAUGC-CUAAUAAAAUU-AAGU-GAA---UCCCCAA--AAUCGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AACY020141787.1/783-966      GGUAACCAA-GUAUUACU-CUUGGAUCUAAUG---UAGGACU-------GACUAACCUAA----------CUUCUCC--ACC-AC----C-AG------GUGCCCA---UG-------------UA---------UCAUAAGCGCCU-CCGA--UGAA----------CAUCCAAUCAAAAACGAA-AA-AUAA-UGCACCAACGC-CUAAAACUAUU-AGGU-GAU---AACCCAA--AAUAUUAGUC-AUUUGA-UUCUUAUCUCUCCA
CP000552.1/1163838-1163655   GAUAACCAA-GGAUAACU-CUAGGAUCAAGUG---UUGGGUU-------GACAAGUCUUA----------CUUCUCC--UCC-UC----C-AG------GAGCCCA---UG-------------UA---------UCAUAAGCACCG-CCAAU-AAAA----------CACCAGUUUACUGACCAA-G--CUAA-UGCACCUACUC-CUAAAACAAUC-AAAU-GAU---AUCCAAG--AAUAUUGGUC-AUUUGA-UUUUUAUCUCUCCA
AACY021880462.1/651-834      GAUAACCCA-AAAUGACU-CUUGGGUCUAAAG---UUGGAUU-------AACAAGUCUGA----------CUUCACC--ACC-AC----C-AG------GAGCCCA---UG-------------UA---------UCAUAUGCACCA-CCAAU-AAAA----------CACCAGUUUAUUGACCAA-G--CUAA-UGCACCUACAC-CUAAAACAAUC-AGAU-GAU---AUCCGAG--GAUAUUUGUC-AUUUGA-UUUUUAUCUCUCCA
DQ864733.1/37438-37249       AAUAACCAA-AAAUAACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUAACA-------UCUCCCC--CCC-CC----C-CG------GAGCCCA---GG-------------UA---------UCAUACACGCCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAGAUU-AGGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AACY020050500.1/1276-1090    AGUAUCCGA-AAAUAACU-GAUGGGUCGUAAG---UUGGGUA----GCUAAUUACACGUA----------CAUCACC--ACC-AC----C-UG------GUGCCCA---CG-------------UG---------UCAUAAACUCCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-AA-GCCA-ACAACCAAGUC-CAAGAAUUACA-AGGU-GAA---UUCCUAA--AAUAGUAGUC-AUUUUG-UUCUUGUCUUUCCA
AY876216.1/394-208           CAUAACCGA-AAAUGAUU-AAAGGGUUUAAUG---UCGGAGC----UGUAAUAAUACGAA----------CAUCACC--ACC-AC----C-UG------GAGCCCA---UG-------------UA---------UCGUAUACUCCA-CCAA--CGAA----------ACAAGCUUUGGCAACAAG-UA-AAAA-ACAACCAAUAC-CUAAUAAAAUU-AGGU-GAA---UUCCUAA--AAUUGUUGUC-AUUUUG-UUCUUGUCACGCCA
AACY021388426.1/341-158      GAUAACCAA-GAAUAACU-CUUGGGUCUAAAG---UUGGAUU-------AACAAGUCUGA----------CUUCACC--ACC-AC----C-UG------GUGCCCA---UG-------------UG---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUUACUGACCA--UG-CUAG-AGCACCUACAC-CUAGAACAAUC-AAAU-GAU---AACCAAG--AAUGUUUGUC-AUUUGA-UUUUUAUCUCUCCA
CP000435.1/817015-817201     AAUAACCAA-AGAUCACA-CCUGGAUCAAGAG---UUGGAUU----CGUGAUCAAACGAA----------CAUCUCC--ACC-AC----C-UG------GGGCCCA---GG-------------UG---------UCGUAGACGCCG-CCAA--AGAA----------CAUGGCCUUAAAGACCAA-AA-GGAG-GCAGCCAACGC-CAAGAAGGAUC-AGGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUUUUAUCGCGCCA
AY876204.1/499-313           AGUAUCCAA-AGAUAAUG-GCUGGGUUUAAUG---UUGGAGU----UGAAACAAAUCUUA----------CAUCCCC--UCC-UC----C-UG------GAGCCCA---UG-------------UA---------UCAUACACACCA-CCUA--CAAA----------CAGAGCUUUAAUAACUAG-UA-AAAA-UGAUCCAAUAC-CGAGUAAAAUU-AAAU-GGA---UCCCCAA--AAUUGUGGUC-AUUUUG-UUUUUAUCUCUCCA
EF153940.1/1509-1323         AAUAACCAA-AUAACCUA-CUUGGGUUAAGGG---UCAAGUU----GGUAAUUCUUCUUA----------CAUCUCC--ACC-CC----C-GG------GUGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCUUUGAGGACCAG-GA-GAAA-GGCUCCUAUAC-CUAAGAGGAUC-AAGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AF137379.1/46146-45960       UGUAGCCAA-AAAUGACA-GCUGGACUGGUUG---UUGGAUU----AGUAAUCACGCGAA----------CAUCACC--GCC-GC----C-UG------GUGCCCA---UG-------------UG---------UCAUAAACGCCA-CCCA--AGUA----------ACGAGCUUUGAGAACCAA-CA-GCAA-AGCACCAAGUC-CAAGAAGCACA-AGGU-GAA---UUCCUAA--AAUGGUAGUC-AUUUUG-UUCUUAUCUUUCCA
AP008231.1/968997-969183     GGUAGCCGA-AGAUCACA-GCCGGGUUGAGGG---UUGGGUU----GGAGAUGAUGCGGA----------CAUCGCC--ACC-AC----C-CG------GCGCCCA---GG-------------UG---------UCAUAGACACCG-CCGA--AGAA----------CAUGGCCUUAAAGACCAG-CA-AGAA-GGCACCUAAGC-CCAGCAGAAUC-AGGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGA-UUCUUGUCUUUCCA
AY286123.1/11511-11697       AAUAACGAA-AGAUUAUA-GCUGGAUUUAGUG---UUGGAUU----UGAGACCAAUCGCA----------CAUCUCC--ACC-AC----C-UG------GUGCCCA---AG-------------UG---------UCAUACACACCU-GACA--GAAA----------CAUGGCUUUGAUUACUAA-UA-AAAA-CGCACCAAUAC-CUAGUAGAAUU-AAAU-GAA---UUCCCAA--GAUGGUGGUC-AUUUUA-UUUUUGUCUCUCCA
AF354643.1/1714-1531         GAUAACCAA-GUAUUACU-CUUGGAUCUAAAG---UUGG-------ACUAACCAAUCUAA----------CUUCUCC--UCC-AC----C-GG------GAGCCCA---UG-------------UG---------UCAUAAGCACCA-CCGA--UAAA----------CAUCCAAUCUGCGACGAA-AA-AUAA-AGCACCAACUC-CUAAAACUACU-AGGU-GAU---AACCCAA--UAUAUUAGUC-AUUUGG-UUUUUAUCUCUCCA
AACY021436835.1/668-854      CAUAACUGA-AGAUUACU-AAUGGGUUUAAUG---UAGGGUU----UUUAACAAGACGUA----------CAUCUCC--UCC-AC----C-UG------GAGCCCA---AG-------------UG---------UCAUAAACACCA-CCAA--CAUA----------CAUAGCUUUGGCUACUAA-UA-AAAA-CGCUCCAAUUC-CUAAUAAACAU-AAAU-GAA---UACCUAA--AAUUGUUGUC-AUUUUA-UUUUUGUCACGCCA
AACY020078041.1/1064-878     GAUAACCGA-AGAUCACA-CCAGGGCUGAGGG---UUGGGUU----GGUGAUCAGGCGAA----------CAUCGCC--ACC-AC----C-AG------GGGCCCA---GG-------------UG---------UCGUAAACACCG-CCGA--AGAA----------CAUGGCCUUGAAGACCAG-GA-GCAG-GGCACCAACGC-CAAGAAGGAUC-AGGU-GAU---AACCAAU--GAUGUUGGUC-AUCUGG-UUCUUAUCGCGCCA
AAVU01000074.1/448-262       GAUAACCGA-AGAUCACA-GCCGGGUUCAAUG---UGGGGUU----AUUGAUGACUCGGA----------CAUCUC-----------------------CACCACC---GGGCGCCCAAC----UA---------UCGUAGACACCG-CCAA--AGAA----------CAUGGCUUUAAACACCAG-CA-ACAG-CGCACCACAAC-CCAACAGGAUU-AAGU-GGU---AGCCGAU--GAUGUUGGUC-AUUUGG-UUCUUGUCUUUCCA
AF481844.1/506-320           GAUAACCAA-AGACGACA-GCAGGGCUAAGUG---UUAAGUU----AGUAAUCUUACGCA----------CUCCACC--CCC-UC----C-AG------GAGCCCA---UG-------------UA---------UCAUAAAUGCCG-CCAA--AAAA----------GACAGCUUUUCCUACAAG-UA-AGAG-AGCACCAGCUC-CUAGCAAAAGA-AGAU-GAA---UACCAAG--AAUGGUUGUC-AUCUUG-UUUUUAUCUUUCCA
AY673996.1/37840-37654       CAUAUCCAA-AUAUGAUA-GCUGGGUUUAAAG---UUGGGUU----AUUAAUUAAUCGUA----------CAUCUCC--UCC-AC----C-AG------GAGCCCA---UG-------------UG---------UCAUAUACUCCA-CCGA--AAAA----------UAAAGCUUUAAUCACAAG-UA-AAAA-CGACCCUAUGC-CUAGUAAUACA-AGAU-GUA---UACCAAG--AAUUGUUGUC-AUUUUA-UUUUUAUCUCUCCA
AY116657.1/1566-1380         AAUAACCAA-AUAUGAUA-CUUGGGCUAAGGG---UCAAGUU----AGUAAUUCUUCUUA----------CAUCUCC--CCC-CC----C-GG------GAGCCCA---AG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUAAGCACUAG-GA-GAAG-GGCGCCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUGGUGGUC-AUUUUA-UUUCUAUCUUUCCA
EF508371.1/16590-16776       CGUAUCCAA-UGAUUACU-ACAGGAUUUAAUG---UUGGGUU----GUCAAUGAUACGUA----------CAUCUCC--UCC-AC----C-UG------GAGCCCA---CG-------------UA---------UCGUAUAAACCA-CCAA--CAUA----------CAUAGCUUUUACUACUAG-UA-GUAA-AGCUCCAAAUC-CUAGUAUCACU-AGGU-GAA---UACCUAG--AAUAGUAGUA-AUUUUG-UUCUUAUCACGCCA
AY876211.1/499-313           UGUAUCCGA-AUAUAAUA-AGCGGAUUCAGUG---UAGGAUU----AUUAAUAAAUCUUA----------CAUCACC--UCC-AC----C-AG------GCGCCCA---UG-------------UA---------UCAUAAACACCG-CCAA--CAAA----------UAAAGCUUUUAUAACUAA-UA-AGAA-AGAACCUAUAC-CAAGUAGAAUU-AAAU-GAA---UUCCUAG--UAUAGUAGUC-AUUUUA-UUCUUAUCUCUCCA
AACY023410220.1/156-339      GAUAACCAA-AAAUUACC-CUUGGAUCCAAUG---UUGGGUU-------UAUAAGUCGGA----------CUUCUCC--UCC-AC----C-AG------GGGCCCA---AG-------------UA---------UCAUAUGCACCG-CCAAU-AAAA----------CACCAGUUUACUGACCAA-G--CUAA-UGCACCUACAC-CUAGAACUAUC-AAAU-GAU---AACCAAG--AAUAUUGGUC-AUUUGA-UUUUUAUCUCUCCA
AY876205.1/472-286           GGUAUCGAA-AGAUAAUC-GCUGGAUUUAAUG---UCGGAUU----AGAGAUCAAUCUUA----------CAUCUCC--ACC-AC----C-UG------GAGCCCA---UG-------------UA---------UCAUACACACCG-GAGA--UAAA----------CAUGGCUUUGAUCACUAG-AA-GGAA-AGCACCUACUC-CUAAAAGAAUU-AAAU-GAA---UUCCUAA--AAUGGUGGUC-AUUUUG-UUUUUAUCUCUCCA
AACY022173898.1/421-235      CAUAUCCAA-AAAUUACU-AAUGGAUUUAACG---UCGGGUU----UUUGAUUAAACGAA----------CAUCUCC--UCC-AC----C-UG------GAGCCCA---UG-------------UG---------UCAUAAACUCCA-CCUA--UGUA----------CAUUGCUUUUGCAACUAA-UA-AGAA-UGAUCCAAUUC-CUAGUAAACAU-AAGU-GAA---UACCUAA--AAUUGUUGUC-AUUUUA-UUUUUAUCACGCCA
AB086179.1/51677-51491       AAUACCCAA-AAAUAAUA-CUCGGACUAAGUG---UAAGAUU----UGUGAUUUCUCUUA----------CAUCUCC--ACC-AC----C-AG------GAACCCA---GG-------------UA---------UCGUAUACACCU-CCGA--AAAA----------UGAAGCCUUGAAUACCAG-GA-GAGA-AGCACCAAGAC-CUAGUAAAACA-AGAU-GAA---UACCUAG--AAUAGUAGUC-AUUUUA-UUCUUAUCUUUCCA
AACY023137906.1/312-495      GAUAACCAA-GAAUUACU-CUUGGAUCUAAGG---UUGGACU-------AACCAAUCUGA----------CUUCUCC--ACC-AC----C-GG------GGGCCCA---UG-------------UG---------UCAUAAGCACCA-CCAA--UAAA----------CAUCCAAUCAGCUACGAA-AA-AUAA-AGCACCAACUC-CUAAAACUAUU-AGGU-GAU---AACCCAA--UAUGUUAGUC-AUUUGG-UUCUUAUCUCUCCA
BA000019.2/4818079-4818256   AAUAACCGA-AAAUUAUG-CCUGGGUUAAGAG---UAGGGUU----AGUAAUCGAGCGUA----------CAUCUC-----------------------CCAAAUU---AG-------------UG---------UCAUAAAUGCCG-CCAA--AAAA----------CAUGGCUUUUAGCACUAG-UA-AGAA-UGCUCCUAAAC-CCAGAAUAAUU-AGGU-GAU---GUCCUAA--AAUCAAACUC-AAUUGU-UUAGGGUCAUUCCA
AY705196.1/827-641           AAUAGCCAA-AUAUCACG-CUUGGGCUAAGCG---UCAAGUU----GGUAANUUUUCUUA----------CAUCUC-----------------------CCCCUCC---GGGUGCCCAAG----CA---------UCAUAUACGCCU-CCAA--AAUA----------CAGAGAUUUGAGUACUAG-AA-GAAG-AGCACCUAGAC-CCAAUAAAAUU-AAGU-GAA---UACCCAA--GAUUGUAGUC-AUUUUA-UUUCGAUCUUUCCA
AF239796.1/1255-1069         AAAAACCAA-AAAUAGUG-UUGGGACUUAAAG---UAAGAUU----CGUUAUUUUUCUCA----------CAUCUCC--ACC-AC----C-AG------GAGCCCA---GG-------------UA---------UCAUAUAUACCG-CCAA--AAAA----------CAAAGCUUUUAGCACUAG-AA-GAAA-AGCGCCAGCCC-CUAGUAAAAUA-AGGU-GAA---UACCCAA--AAUAGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AY178864.1/32150-32336       GGUAACCAA-AGAUAAUA-UUGGGGUUUAGAG---UAAGAUU----CGUAAUUUCUCUUA----------CAUCUC-----------------------CGCCACC---GGGUGCCCAUG----UA---------UCAUACAACCCU-CCGA--AAUA----------GAGUGCUUUGAAAACCAG-UA-GGAA-AGCGCCGAAAC-CUAGUAAUAUU-AGAU-GAA---UACCGAG--AAUUGUAGUC-AUCUUA-UUUUUAUCCUUCCA
AY876217.1/499-313           CAUAGUUGA-AAAUAGCA-CCUGGGUUUAAAG---UAGGGUU----AGCUACAACACGUA----------CGUCUCC--ACC-AC----C-UG------GAGCCCA---AG-------------UA---------UCAUAAAGACCU-CCAA--AGAA----------CAUAGCCUUUAAAACAAG-AA-GGAA-AGCUCCAACUC-CUAAAAGGAUA-AGGU-GAA---UACCUAA--GAUAGUAGUC-AUCUUG-UUCUUAUCACGCCA
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AACY021756203.1/399-585      CGUAACCAA-AGAUAACA-CCUGGGUUUAAAG---UAGGGUU----AUCAAUGAUUCUUA----------CAUCACC--ACC-AC----C-UG------GUGCCCA---UG-------------UA---------UCGUAAAGACCG-CCAA--CAUA----------UAAAGCUUUAAUAACUAG-UA-AUAG-UGCUCCAAAUC-CUAGGAUAACU-AAGU-GAA---UACCAAG--AAUUGUAGUA-AUCUUG-UUCUUAUCUCUCCA
AY705203.1/827-641           AAUAACCAA-AUAUCACG-CUUGGGCUAAGGG---UAAAGUU----GGUAAUUCUUCUUA----------CAUCUC-----------------------CCCCUCC---GGGUGCCCAAG----UA---------UCAUAUACGCCU-UCAA--AAGA----------AAGAGCUUUGAGCACCAG-AA-GAAA-AGCACCUAGAC-CCAAUAAAAUU-AGGU-GAA---UACCCAA--GAUUGUAGUC-AUUUUA-UUUCGAUCUUUCCA
DQ308461.1/469-283           CAUAAGAAA-AAAUAACU-UGUGGAUUUAAUG---UUGGAUU----AGUAAUAUAUCUCA----------CAUCUCC--UCC-UC----C-UG------GCGCCCA---UG-------------UA---------UCAUAUACGCCA-CCAA--AGAA----------UAAGGCUUUAACAACCAA-UA-AAAA-UGAUCCAAUUC-CUAAUAGUACU-AAGU-GAA---UACCUAA--AAUUGUAGUC-AUUUUA-UUUUUAUCACGCCA
AAVW01000085.1/19826-20012   AAUAACCGA-AGAUUACA-GCAGGGUUUAAUG---UUGGGUU----AGUAAUAACACGAA----------CAUCACC--ACC-AC----C-AG------GGGCCCA---AG-------------UA---------UCGUACACACCG-CCAA--AGAA----------CAUUGCCUUCAGCACCAA-CA-GCAA-CGCACCACAUC-CCAGGAUGAUU-AGGU-GGA---AGCCGAU--GAUGUUGGUC-AUCUUG-UUCUUGUCUUUCCA
EF067920.1/13993-14179       CAUAACCAA-AAAUUACA-AUUGGGUUUAAUG---UAGGUGU----UGUAAUUAAACGAA----------CAUCGCC--ACC-AC----C-UG------GUGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--UGUA----------CAUUGCUUUAGCAACUAA-UA-AAAA-AGCACCACUAC-CUAAAAGACAU-AAAU-GAA---UCCCUAG--AAUAGUUGUC-AUCUUG-UUUUUAUCACGCCA
AF481839.1/506-320           GAUAACCAA-AUAUUGUA-CUAGGAUUCAGAG---UUAUAUU----AGUAAUUUUUCUAA----------CAUCUCC--UCC-UC----C-UG------GUGCCCA---AG-------------UA---------UCAUAAAGACCU-CCAA--ACCA----------GAUCGCUUUUGCCACUAA-UA-GUAA-UGCACCCGCAC-CUAAAAGAAUC-AAAU-GAA---UACCUAG--AAUAGUAGUC-AUUUUA-UUUUUGUCCUUCCA
AY876210.1/499-313           CGUAUCCAA-AAAUUACU-GAAGGGUUUAAAG---UUGGGUU----AUUAAUUAAUCUUA----------CAUCUCC--ACC-UC----C-UG------GUGCCCA---UG-------------UA---------UCAUAAACACCA-CCAA--AGAA----------AAGAGCUUUGAUAACUAA-UA-GAAA-AGAUCCUAUGC-CGAGAAGUAAU-AAAU-GAA---UGCCCAG--UAUAGUUGUC-AUCUUA-UUUUUAUCUCUCCA
AF528929.1/1566-1380         AAUAACCAA-AUAUAACA-CUUGGGCUGAGGG---UCAAGUU----GCUAAUUUUUCUUA----------CAUCUCC--CCC-CC----C-CG------GGGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGGGCCUUGAGUACUAG-AA-GAAA-GGCACCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUGGUAGUC-AUUUUA-UUUCUAUCUUUCCA
DQ897681.1/47242-47056       AAUAACCAA-AUAGAACA-CUUGGGCUAAGGG---UCAAAUU----AGUGAUUUUUCUGA----------CAUCUCC--CCC-CC----C-UG------GAGCCCA---GG-------------UA---------UCAUAUACACCC-CCAA--AAGA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCGCCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUG-UUUCUAUCUUUCCA
AY705211.1/813-627           AAUAACCAA-AUAUCACG-CUCGGGCUAAGGG---UCAAAUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-CC----C-GG------GUGCCCA---UG-------------UA---------UCAUAUACGCCU-CCAA--AAUA----------AAGGGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAAUAAGAUU-AGGU-GAA---UGCCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
BA000022.2/1348259-1348445   GAUAGCCGA-AGAUAAUC-GCCGGGUUGAGGG---UGGGGUU----AGUGAUCACCCGUA----------CGUCCCC--ACC-AC----C-GG------GGGCCCA---GG-------------UG---------UCGUAUACACCG-CCAA--AGAA----------CAUGGCUUUAAAGACCAG-UA-ACAG-AGCACCACAAC-CCAACAGGAUC-AAGU-GGU---AGCCAAU--GAUGUUGGUC-AUCUGG-UUUUUAUCUUUCCA
AY147671.1/1566-1380         AAUAACCAA-AUAUAACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUNUUA----------CAUCUCC--CCC-CC----C-AG------GGGCCCA---GG-------------UA---------UCAUAUACGCCC-CCNA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCNA--AAUUGUAGUC-AUUUUA-UUCCUAUCUUUCCA
CR954199.2/786-972           AGUAUCCGA-AAAUAACU-GAAGGGUCGUAAG---UUGGGUA----GCUAAUUACACGUA----------CAUCACC--ACC-AC----C-AG------GUGCCCA---UG-------------UA---------UCAUAAACUCCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-AA-GCCA-AGCACCAAUUC-CAAGAAGUACA-AGGU-GAA---UUCCUAA--AAUUGUUGUC-AUUUUG-UUCUUGUCUUUCCA
AY147642.1/1566-1380         AAUAACCAA-AAAUCACG-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUNUUA----------CAUCUCC--CCC-CC----C-CG------GGGCCCA---GG-------------UA---------UCGUAUACGCCU-CCAA--AAUA----------AAGAGCCUUGAGUACUAG-AA-GAAA-GGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCUAA--AAUUGUAGUC-AUUUUA-UUCCUAUCUUUCCA
AP004638.1/36026-36212       GAUAACCAA-AAAGAAUA-CUUGGACUAAGAG---UAAGGUU----UGUAAUUUUUCUUA----------CAUCCCC--ACC-UC----C-GG------GUGCCCA---UG-------------UG---------UCAUAGACACCG-CCAA--AGUA----------CACAGACUUUAAUACUAA-AA-GGAA-AGCACCAGCAC-CCAAUAGUAUU-AAAU-GAA---UACCUAG--AAUAGUGGUC-AUUUUA-CUCUUAUCCUUCCA
AF041468.1/14421-14607       CAUAACCAA-AUAUAACA-GCUGGAUUUAAAG---UUGGAUU----AUCAAUUAUUCUAA----------CAUCUCC--UCC-AC----C-UG------GAGCCCA---UG-------------UA---------UCGUAUAAACCA-CCAA--CAUA----------AAUAGCUUUUAUAACUAA-UA-AUAA-UGCACCAAACC-CAAGUAUUACU-AAAU-GAA---UACCUAG--AAUCGUAGUA-AUCUUA-UUUUUAUCACGCCA
EF153938.1/770-584           AAUAACCAA-AUAGAACA-CUAGGGCUAAGGG---UCAAAUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-CC----C-UG------GGGCCCA---GG-------------UA---------UCAUAUACACCU-CCAA--AAUA----------AAGAGCCUUAAGUACUAG-AA-GAAA-AGCACCCACAC-CUAACAAGAUU-AAGU-GAA---UGCCCAA--AAUGGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AF481848.1/506-320           GAUAACCAA-AUAUUGUA-CUAGGAUUGAGAG---UUAUAUU----AGUAAUUUUUCUAA----------CAUCUCC--UCC-UC----C-UG------GUGCCCA---AG-------------UG---------UCAUAAAGACCU-CCAA--ACCA----------AAUUGCUUUUGCAACUAA-UA-AAAA-UGCACCUGCAC-CUAGCAAAAUU-AAAU-GAA---UACCUAA--AAUAGUAGUC-AUCUUA-UUUUUGUCCUUCCA
AY465670.1/1566-1380         AAUAACCAA-AUAUGACA-CUUGGGCGAAGGG---UCAAGUU----GGUAAUUUUUNUUA----------CAUCUCC--CCC-CC----C-AG------GGGCCCA---GG-------------UA---------UCAUAUAUGCCC-CCAA--AAUA----------AACAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAGAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUGGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AF462407.1/1566-1380         AAUAACCAA-AUAUAACA-CUUGGGUUAAGUG---UUAUGUU----UGUAAUUUUUCUUA----------CAUCUCC--ACC-GC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACACCA-CCGA--AAUA----------CAAAGCCUUGAGCACUAG-GA-GGAA-AGCGCCAGCAC-CUAGCAAGAUU-AGGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUG-UUCCUAUCUUUCCA
AY705179.1/806-620           AAUAACCAA-AUAUCACG-UUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUGA----------CAUCUCC--UCC-CC----C-GG------GUGCCCA---GG-------------UA---------UCAUAUACGCCU-CCAA--AAUA----------CAGAGCCUUGAGUACUAG-AA-GAAA-AGCGCCUAUAC-CUAAUAAAAUU-AAGU-GAA---UCCCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AY958086.1/47888-48074       AAUAUCCAA-AUAUUACU-CCAGGGUUAAGAG---UGAUAUU----UGUGAUUUUUCUUA----------CAUCUCC--GCC-AC----C-AG------GUGCCCA---AG-------------UA---------UCAUACAAACCA-CCAA--AAUA----------UAGUGCUUUGAAUACAAG-CA-AAAA-UGCACCAGCAC-CUAAUAAAAUA-AGAU-GAA---UACCCAA--UAUGGUGGUC-AUCUUG-UUUUUAUCUUUCCA
EF506945.1/54725-54539       GGUAACCAA-AGAUAACA-GCUGGGCUAGUUG---UUGGAUU----UGUUAUAACACGAA----------CAUCUCC--ACC-GC----C-GG------GCGCCCA---AG-------------UA---------UCAUAAACCCCA-CCAA--AGUA----------AAGAGCUUUCCAAACAAG-GA-GCCA-AGCACCAAUAC-CUAAGAUUAUU-AAAU-GAA---UACCUAG--GAUAGUGGUC-AUUUUA-UUUUUAUCACGCCA
AY705207.1/813-627           AAUAACCAA-AUAUCACG-CUUGGGCUAAGAG---UCAAGUU----AGUAAUUUUUCUUA----------CAUCUC-----------------------CCCCUCC---GGGCGCCCAAG----UA---------UCAUAUACGCCU-CCGA--AAUA----------CCUAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAAUAAAAUU-AAGU-GAA---UACCCAA--GAUUGUAGUC-AUUUUA-UUUCGGUCUUUCCA
AY363056.1/538-352           AAUAACCAA-AGAUCACG-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-UC----C-GG------GUGCCCA---GG-------------UA---------UCAUAUACGCCU-CCAA--AAUA----------AAGAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAAUAAAACG-AGGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AF481849.1/506-320           AAUAACCAA-ACACAAUA-CUAGGGUUUAGAG---UAAGAUU----UACAAUUUUUCUUA----------CAUCUCC--ACC-AC----C-AG------GAGCCCA---AG-------------UA---------UCAUAUACACCA-CCAA--ACCA----------UAAAGCUUUGAACACUAA-UA-AAAA-UGCACCAGCAC-CCAAAAGGAUU-AAAU-GAA---UACCUAA--AAUGGUAGUC-AUUUUG-UUUUUAUCCUUCCA
AF481845.1/506-320           UGUAACCAA-AAAUAACG-GCUGGGCUAACAG---UUGGGUU----UGUAAUUAAACGUA----------CAUCACC--ACC-AC----C-UG------GGGCCCA---AG-------------UA---------UCAUAAACUCCA-CCAA--AAUA----------UAAUGCUUUCCAAACUAA-AA-GCCA-AGCUCCAAUUC-CAAGAAUAACA-AGAU-GUA---UUCCAAG--AAUAGUAGUC-AUUUUA-UUUUUAUCUUUCCA
AY705192.1/827-641           AAUACCCAA-AUAUCACA-CUUGGGCUGAGGG---UAAAGUU----GGUAAUCUUUCUGA----------CAUCCCC--CCC-UC----C-GG------GUGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------CAGAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAAUAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGCC-AUUUUA-UUUCUAUCUUUCCA
BA000039.2/1704142-1703956   GAUAGCCAA-AAAUUACC-CUUGGGUCAAGGG---UGGGGUU----GGUAAUGACGCGGA----------CAUCGCC--GCC-AC----C-GG------GUGCCCA---AG-------------UG---------UCGUAGAGGCCA-CCAA--AGAA----------CAUUGCUUUGGCCACCAA-AA-GUAA-AGCACCAAUAC-CGAGGACGAUC-AGGU-GGA---AACCGAG--GAUCGUCGUC-AUUUUG-UUUUUAUCUUUCCA
AY147645.1/1566-1380         AAUAACCAA-AUAUAACG-CCCGGGCUAAGGG---UCAAGUU----GGUUAUUUUUCUGA----------CAUCCCC--CCC-CC----C-AG------GGGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUAAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCUAA--AAUUGUAGUC-AUUUNA-UUUCUAUCUUUCCA
AF528934.1/1566-1380         AAUAACCAA-AUAUAAUA-CUUGGGCUAAGGG---UGACGUU----GGUAAUUUUUCUUA----------CAUCCCC--CCC-CC----C-UG------GAGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCGCCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AF528919.2/1566-1380         AAUAACCAA-AUAUAGUA-CCUGGAUUAAGCG---UAAGGUU----CGUAAUUUUUCUUA----------CAUCUCC--ACC-AC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUAUGCCA-CCAA--AAUA----------AAAAGCCUUGAACACUAG-GA-GAAA-GGCACCAGCAC-CUAGCAAGAUU-AGGU-GAA---UACCUAA--AAUUGUGGUC-AUUUUG-UUCCUAUCUUUCCA
AY147676.1/1566-1380         AAUAACCAA-AUAUAACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUNUUA----------CAUCCCC--CCC-CC----C-UG------GGGCCCA---GG-------------UA---------UCAUAUACACCU-CCAA--AAUA----------AAGAGCCUUAAGUACUAG-AA-GAAA-GGCACCUAUAC-CUAAUAAAAUU-AAGU-GAA---UACCCAA--AAUNGUGGUC-AUUUUA-UUUCUAUCUUUCCA
DQ317523.1/26456-26642       AAUAUCCAA-AUAUAAUA-CUUGGACUAAGGG---UCAAAUU----GGUUAUUUUUCUUA----------CAUCUCC--GCC-CC----C-CG------GAGCCCA---CG-------------UA---------UCAUAUAUACCU-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-CGCACCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AY465687.1/1566-1380         AAUAACCAA-AUAUAACG-CUUGGGCUAAGGG---UCAAGUU----GAUAAUUUUUCUUA----------CAUCUCC--GCC-CC----C-GG------GGGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUAAAUACGAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUGA-UUUCUAUCUUUCCA
CP000117.1/1530930-1530744   AAUAACCGA-AGAUUACA-GCUGGGUUCAGUG---UGGGAUU----AGUAAUUACACGUA----------CAUCACC--ACC-AC----C-AG------GGGCCCA---GG-------------UG---------UCAUAGACACCA-CCAA--AGAA----------CAUUGCUUUCAAUACCAA-CA-GCAA-CGCACCACAUC-CCAGGAUGAUC-AGGU-GGA---AGCCGAU--GAUAUUGGUC-AUCUUG-UUCUUAUCUUUCCA
AC145820.20/98759-98573      AAUAACCGA-AUAUAAUA-CUUGGACUAAGGG---UUAAGUU----UGUAAUUUUUCUUA----------CAUCUCC--CCC-UC----C-UG------GAGCCCA---GG-------------UA---------UCAUAUAUACCU-CCAA--AAUA----------AGAAGCCUUAAAUACUAG-AA-GAAA-AGCCCCUAUAC-CUAACAAUAUU-AAGU-GAA---UACCUAA--AAUAGUAGUC-AUUUUA-UUUCUGUCUUUCCA
AP002983.1/26804-26990       AAUAACCAA-AUAUAAUA-CUUGGACUAAGGG---UCAAAUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-CC----C-GG------GAGCCCA---AG-------------UA---------UCAUAUAUACCC-CCAA--AAUA----------AGAAGCCUUGAAUACUAG-AA-GAAA-AGCCCCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUGGUAGUC-AUUUUA-UUUCUAUCUUUCCA
DQ383815.1/34141-33955       AAUAACCAA-AUAUGAUA-CUUGGGCUAAGCG---UCAAGUU----GGUGAUUUUUCUUA----------CAUCUCC--UCC-UC----C-CG------GAGCCCA---AG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAGAC-CUAACAAGAUU-AAAU-GAA---UACCUAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AY147673.1/1566-1380         AAUAACCAA-AUAUAACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-CC----C-GG------GGGCCCA---GG-------------UA---------UCAUAUACNCCC-CCAA--AAUA----------AANAGCCUUGANUACUAN-AA-NAAA-ANCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUANUC-AUUUUA-UUUCUAUCUUUCCA
AF528920.1/1566-1380         AAUAACCAA-AUAUAAUA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--ACC-CC----C-AG------GGGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUGAGUACUAG-AA-GAAA-AGCACCCACGC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AY876219.1/499-313           CAUAUCCAA-AAAUAACU-AAUGGAUUUAGCG---UUGGGCU----AUUGAUAAAACGAA----------CAUCACC--ACC-AC----C-GG------GUGCCCA---AG-------------UA---------UCAUAAAUACCA-CCAA--CAAA----------CAUUGCUUUAAUUACUAA-UA-AGAA-UGAACCAAUUC-CUAACAAAACU-AAAU-GAA---UACCUAA--GAUUGUAGUC-AUUUUA-UUCUUAUCACGCCA
DQ069644.1/637-451           AAUAACCAA-AUAGAACA-CUUGGGUCAAGAG---UCAGGUU----CGUAAUUCUUCUUA----------CAUCUCC--ACC-AC----C-AG------GGGCCCA---GG-------------UA---------UCAUAUACACCU-CCAA--AAUA----------CAAAGCCUUGAGCACUAG-GA-GAAA-AGCACCAACAC-CUAGCAGGAUU-AGGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUG-UUCCUAUCUUUCCA
AF528943.1/1566-1380         AAUAACCAA-AUAUAGCA-CUUGAGUUAAGUG---UAAGGUU----CGUAAUUUUUCUUA----------CAUCUCC--ACC-GC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUAUGCCA-CCAA--AAUA----------UAAAGCCUUAAACACUAG-AA-GAAA-AGCACCGAUAC-CUAGCAAGAUU-AGGU-GAA---UACCUAA--AAUUGUGGUC-AUUUUG-UUCCUAUCUUUCCA
AY705177.1/827-641           AAUAACCAA-AUAUCACA-CUUGGGCUAAAGG---UCAAGUU----GGUAAUUUUUCUAA----------CAUCUCC--CCC-CC----C-CG------GGGCCCA---GG-------------UA---------UCAUAUACGCCU-CCAA--AAUA----------CAGAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAAUAAAAUU-AAGU-GAA---UGCCCAA--AAUGGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AY705204.1/827-641           AAUAACCAA-AUAUCACG-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUC-----------------------CCCCUCC---GGGUGCCCAAG----UA---------UCAUAUAUGCCU-CCAA--AAUA----------AAGAGCUUUGAGUACUAG-AA-GAAA-AGCACCUAGAC-CUAAUAAAAUU-AAAU-GAA---UACCCAG--GAUUGUAGUC-AUUUUA-UUUCGAUCUUUCCA
EF067921.1/53541-53355       CGUAACCGA-AAAUUACG-AUUGGAUUUAAUG---UUGGAGU----UGUAAUAUAACGAA----------CAUCACC--ACC-AC----C-CG------GUGCCCA---UG-------------UA---------UCGUAAACACCA-CCUA--AGUA----------CAUAGCUUUUGCAACUAA-UA-AUAA-UGCACCUAAAC-CUAAUAAACAU-AAGU-GAA---UACCUAA--AAUAGUAGUC-AUCUUA-UUUUUAUCACGCCA
AY147641.1/1566-1380         AAUAACCAA-AUAUAACC-UUUGGGCUAAGAG---UCAAGUU----AGUAAUUUUUCUGA----------CAUCCCC--CCC-CC----C-GG------GUGCCCA---GG-------------UA---------UCGUAUACGCCU-CCAA--AAUA----------AAGAGCCUUAAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
DQ851108.1/5527-5341         AAUAACCAA-AAAUAGUA-GCAGGACUAAUAG---UUGCGUC----AGUAAUUAAACGAA----------CGUCACC--ACC-UC----C-AG------GAGCCCA---AG-------------UA---------UCAUAAACACCA-CCGA--AAUA----------UGAAGCUUUUAAAACUAA-UA-ACCA-AGAUCCUAAUC-CUAAAAGGAUU-AAAU-GAA---UACCUAA--AAUAGUUGUC-AUUUUG-UUUUUGUCUUUCCA
AF022186.2/2628-2442         GAUAGCUAA-AAAUAAUU-GCUGGAUUUAAUG---UUGGAUU----AGUAAUGAAUCUAA----------UAUCUCC--UCC-CC----C-AG------GAGCCCA---UG-------------UA---------UCAUAAAUUCCA-CCUA--UAAA----------UAGUGCUUUAAUAACUAA-CA-AAAA-UGCUCCAAUAC-CUAGCAAUAUC-AAGU-GAA---UUCCUAG--UAUUGUUGUC-AUUUUA-UUUUUAUCUCUCCA
AY147658.1/1566-1380         AAUAACCGA-AUAUAACG-CUUGGACUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-CC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAUAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAAUAAAAUU-AGGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AADV02000249.1/1086-900      GAUAGCCGA-AAAUAAUU-GCGGGGUUCAAAG---UAGGAUU----AGUAAUCACACGCA----------CAUCUCC--GCC-AC----C-AG------GAGCCCA---AG-------------UG---------UCAUAGACACCG-CCAA--AGAA----------CAUGGCUUUGAACACCAA-CA-AUAG-CGCACCACCUC-CUAAGAGAAUG-AGGU-GAU---AACCAAU--AAUGUUGGUC-AUUUGG-UUCUUAUCUUUCCA
AY876226.1/499-313           AAUAACCAA-AGAUUACU-UGUGGAUUUAAGG---UGGGGUU----ACUUAUUACCCGCA----------CAUCUCC--GCC-GC----C-AG------GUGCCCA---AG-------------UA---------UCGUAAACACCA-CCAA--AAAA----------CAUUGCUUUAAAUACUAA-AA-GGAA-CGCACCGGUAC-CUAAUAGAAUU-AAAU-GGA---UACCAAU--AAUAGUGGUC-AUCUUG-UUUUUAUCUUUCCA
AY876221.1/469-283           CAUAACCAA-AAAUUACA-AUUGGGUUUAAUG---UUGGCGU----UGUAAUAUAACGAA----------CAUCGCC--ACC-AC----C-UG------GUGCCCA---UG-------------UA---------UCAUAAACACCA-CCUA--AGUA----------CAUAGCUUUUGCAACUAA-UA-AUAA-UGAUCCUAAAC-CUAAUAAACAU-AAGU-GAA---UACCUAA--AAUAGUAGUC-AUCUUA-UUUUUAUCACGCCA
AY465679.1/1566-1380         AAUAACCAA-AUAUAACG-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--GCC-UC----C-CG------GGGCCCA---GG-------------UA---------UCAUAUACGCCU-CCAA--AAUA----------AAGAGCUUUAAGUACUAN-AA-AAAA-AGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUCUUA-UUUCUAUCUUUCCA
AY147651.1/1566-1380         AAUAGCCAA-AUAUAACA-CUAGGGCUAAGAG---UCAAAUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-UC----C-CG------GGGCCCA---AG-------------UA---------UCAUAUAUGCCA-CCAA--AAUA----------AAGAGCUUUGAGUACUAG-AA-GAAA-AGCGCCUAGAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AY147652.1/1566-1380         AAUAACCAA-AUAUAAUA-CUUGGGCUAAGGG---UCAAGUU----AGUAAUUUUUCUUA----------CAUCCCC--CCC-UC----C-AG------GGGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AGGU-GAA---UACCUAA--AAUGGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AY147655.1/1566-1380         AAUAACCAA-AAAUAACG-CCCGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-CC----C-UG------GGGCCCA---GG-------------UA---------UCAUAUACCCCC-CCAA--AGUA----------AAGGGCCUUAAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
EF380351.1/37258-37072       AAUAACCAA-AUAUAACA-CUUGGACUAAGGG---UCAAAUU----UGUAAUUUUUCUUA----------CAUCUCC--CCC-CC----C-AG------GAGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUGAGUACUAG-AA-GAAA-AGCGCCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUCGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AAXW01000009.1/79515-79701   GAUAGCCGA-AGAUAAUU-GCGGGGUUAAGGG---UAGGGUU----AGUAAUCACACGCA----------CAUCUCC--GCC-AC----C-AG------GUGCCCA---AG-------------UG---------UCAUAGACACCA-CCAA--AGAA----------CAUGGCUUUGAACACGAG-UA-ACAG-CGCACCACAUC-CCAAGAUAAUG-AGGU-GAU---AACCAAU--AAUAUUGGUC-AUUUGG-UUCUUAUCUUUCCA
AF528926.1/1566-1380         AAUACCCAA-AUAUAACA-CUUGGACUAAGAG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-CC----C-CG------GAGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCUUUAAAUACUAA-CA-GAAA-GGCACCUAGAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUUGUUGUC-AUUUUA-UUUCUAUCUUUCCA
AY664839.1/1566-1380         AAUAACCAA-AUAUAACA-CUUGGGUUAAGAG---UUAGGUU----CGUAAUUUUUCUCA----------CAUCCCC--ACC-GC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACACCA-CCAA--GAUA----------CAAAGCCUUGAGCACUAG-UA-GAAA-AGCGCCAACAC-CUAGCAAUAUU-AGGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUG-UUCCUAUCUUUCCA
AC136521.2/141575-141389     AAUAACCAA-AUAUAACA-CCGGGGCUAAGGG---UCAAAUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-CC----C-AG------GAGCCCA---GG-------------UA---------UCAUAUAUAUCG-CCAA--AAUA----------AAGAGCUUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AGGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
Z67753.1/87948-88134         CAUAACCAA-AGAUUACG-AUUGGAUUUAAUG---UUGGCGU----UGUAAUUAAACGAA----------CGUCACC--ACC-AC----C-UG------GCGCCCA---UG-------------UA---------UCAUAAACACCA-CCUA--AGUA----------CAUUGCUUUAAUAACUAA-UA-AGAA-UGAACCAACAC-CUAAUAAACAU-AAAU-GAA---UACCUAA--AAUAGUAGUC-AUUUUA-UUUUUAUCACGCCA
AF123823.1/1561-1375         AAUAACCAA-AUAUAACA-CUUGGGCUAAGGG---UCAAGUU----AGUAAUUCUUCUUA----------CAUCUCC--CCC-CC----C-AG------GAGCCCA---GG-------------UA---------UCAUAUACGCCU-CCAA--AAUA----------AAGAGCCUUGAGCACUAG-GA-GAAA-AGCACCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AY876222.1/466-280           CGUAACCAA-AAAUUACA-AUUGGGUUUAAUG---UUGGUGU----UGUAAUAAAACGAA----------CAUCACC--ACC-AC----C-AG------GUGCCCA---UG-------------UA---------UCAUAUACACCA-CCUA--AAUA----------CAUUGCUUUGAUAACUAA-UA-AGAA-AGCACCACAAC-CUAAAAGACAU-AAGU-GAA---UACCUAA--GAUUGUUGUC-AUCUUA-UUUUUAUCACGCCA
AF239781.1/1566-1380         AAUAACCAA-AUAUAACA-CUUGGGCUAAGGG---UCAAGUU----AGUAAUUUUUCUUA----------CAUCUCC--CCC-UC----C-AG------GAGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAAA----------AAGAGCCUUAAAUACUAA-AA-GAAA-AGCACCGAUAC-CUAACAAGAUU-AAGU-GAA---UCCCCAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AY147667.1/1566-1380         AAUAACCAA-AUAUAACA-CUUGGGCUAAGGG---UCAAGUU----GUUAAUUUUUCUUA----------CAUCUCC--ACC-CC----C-GG------GGGCCCA---GG-------------UA---------UCAUAUACACCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-GGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCUAA--AAUNGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AJ506156.2/39473-39287       AAUAACCAA-AUAUAACA-CUUGGGCUAAGUG---UCAGGUU----GGUUAUUUUUCUUA----------CAUCUCC--GCC-AC----C-GG------GGGCCCA---GG-------------UA---------UCAUAUACGCCU-CCAA--AAUA----------AAGAGCCUUGAACACUAG-GA-GAAA-AGCGCCUACAC-CUAAUAAAAUU-AAGU-GAA---UACCCAA--AAUAGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AY147640.1/1566-1380         AAUAACCAA-AAAUAAUG-CUUGGGCUAAGGG---UCAAAUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-UC----C-GG------GAGCCCA---AG-------------UA---------UCAUAUAUGCCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AY147650.1/1566-1380         AAUAACCAA-AUAUGAUA-CUUGGGCUCAAGG---UCAAAUU----GGUAAUCUUUCUUA----------CAUCUCC--ACC-CC----C-GG------GAGCCCA---AG-------------UA---------UCAUAUAUACCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAAAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUGGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AJ316582.1/35870-35684       AAUAACCAA-AUAUGAUA-CUCGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-UC----C-UG------GAGCCCA---GG-------------UA---------UCAUAUACACCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCUAA--AAUUGUGGUC-AUUUUA-UUUCGAUCUUUCCA
AB112503.1/509-323           AAUAACCAA-AUACAAUA-CUUGGACUAAGGG---UCAAAUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-CC----C-CG------GAGCCCA---GG-------------UA---------UCAUAUACACCC-CCAA--AAUA----------AAGAGCCUUAAAUACUAG-AA-GAAA-AGCACCUACAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCGAUCUUUCCA
AY699173.1/1566-1380         AAUAACCAA-AUAUAACA-CUUGGGCUAAGAG---UUGGGUU----CGUAAUUUUUCUUA----------CAUCUCC--ACC-AC----C-AG------GGGCCCA---GG-------------UA---------UCAUAUACACCU-CCAA--AAUA----------CAAAGCCUUGAGCACUAG-AA-GAAA-AGCACCAACGC-CUAGCAAGAUU-AGGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUG-CUCCUAUCUUUCCA
AF239789.1/1567-1381         AAUAACCAA-AUAUAACA-CUUGGGCUAAGGG---UUAAGUU----GGUUAUUUUUCUUA----------CAUCUCC--CCC-CC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACGCCA-CCAA--AAUA----------AAGAGCUUUAAAUACUAG-AA-GAAA-AGCGCCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCGAG--AAUCGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AC189190.1/42758-42944       AAUAACCAA-AUAUAACA-CUUGGGCUAAGAG---UCAAGUU----UGUAAUUUUUCUUA----------CAUCCCC--CCC-UC----C-UG------GAGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------GAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUACAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUGGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AY147675.1/1566-1380         AAUAACCAA-AUAUAACA-CUUGGGCUAAGUG---UCAAAUU----GGUAAUUUUUCUUA----------CAUCCCC--CCC-CC----C-GG------GUGCCCA---GG-------------UA---------UCAUAUAUACCU-CCAA--AAUA----------AAGAGCCUUGAAUACUAA-AA-GAAA-AGCACCUAUAC-CUAAUAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AB001684.1/33956-34142       UGUAGCUAA-AGAUAACA-CCAGGACUUACUG---UUGGGUU----UGAAAUAAUACGAA----------CAUCACC--ACC-AC----C-AG------GAGCCCA---UG-------------UA---------UCAUAAAUUCCG-CCAA--AGUA----------CAUUGCCUUCCAAACUAA-AA-GCCA-AGCACCGAAUC-CUAGUACGAUA-AGAU-GAA---UACCUAA--AAUAGUAGUC-AUUUUA-UUUUUAUCUUUCCA
DQ196176.1/601-415           AGUAACCAA-AAACAACA-CCGAAGUUUGUAG---UUGGGUU----AGUAAUAAUUCUAA----------CGUCAC-----------------------CACCACC---CGGAGCCCAAG----UG---------UCAUAAAUACCA-CCAA--AGUA----------CAUAGCUUUUAAAACUAA-UA-ACCA-AGCACCACAAC-CUAACAUGAUU-AAGU-GGU---AACCUAA--AAUUGAUGUC-AUUUUA-UUUUUGUCUUUCCA
EF380353.1/34286-34100       AAUAACCAA-AUAUAACG-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-CC----C-UG------GGGCCCA---AG-------------UA---------UCGUAUACACCA-CCAA--AAUA----------AAGAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCUAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AY147657.1/1566-1380         AAUAGCCAA-AUAUAACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-CC----C-AG------GGGCCCA---GG-------------UA---------UCAUAUAUACCC-CCAA--AAUA----------AACGGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AAAU-GAA---UACCUAA--AAUGGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AF239793.1/1566-1380         AAUAACCAA-AUAUGACA-CUUGGAUUAAGUG---UCAGGUU----CGUAAUUUUUCUUA----------CAUCUCC--ACC-GC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACACCG-CCAA--AAUA----------AAAAGCCUUGAACACUGG-AA-GAAA-AGCACCAACAC-CUAACAAGAUU-AGGU-GAA---UACCUAA--AAUUGUGGUC-AUUUUG-UUCCUAUCUUUCCA
AY660566.1/54262-54448       AAUAACCAA-AUACAACA-CUUGGAUUAAGAG---UAAGAUU----UGUAAUUUUUCUUA----------CAUCUCC--ACC-AC----C-GG------GAGCCCA---CG-------------UA---------UCGUAUACACCU-CCAA--AAUA----------CAAAGCUUUGAGCACUGA-AA-GAAA-AGCACCAGCAC-CUAACAAGAUU-AAAU-GAA---UACCUAA--AAUUGUAGUC-AUUUUG-UUCUUAUCUUUCCA
AY664841.1/1566-1380         AAUAACCAA-AUAUAACA-CCUGGGUUAAGCG---UAAGAUU----CGUUAUUUUUCUUA----------CAUCUCC--ACC-GC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUAUGCCA-CCAA--AAUA----------CACAGCCUUGAAUACUAA-GA-GAAA-AGCACCAACAC-CUAGCAAGAUU-AGGU-GAA---UACCUAA--AAUUGUGGUC-AUUUUG-UUCCUAUCUUUCCA
DQ821119.1/40660-40846       AAUAACCGA-AUAUAACA-CUUGGACUAAGAG---UAAGGUU----CGUAAUCUUUCUUA----------CAUCCCC--ACC-UC----C-AG------GCGCCCA---UG-------------UA---------UCAUAUACACCU-CCAA--AAUA----------UAGAGCUUUGAACACUAA-UA-AAAA-AGCACCAGCAC-CUAACAGAAUU-AAGU-GAA---UACCUAA--AAUAGUGGUC-AUUUUG-UUCUUAUCUUUCCA
AY465665.1/1512-1326         AAUAACCAA-AUAUAACA-CCGGGGUUAAGGG---UCAAAUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-GC----C-UG------GGGCCCA---AG-------------UA---------UCAUAUAAGCCG-CCAA--AAUA----------GAGAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUUUAUCUUUCCA
AF239782.1/1536-1350         AAUAACCAA-AUAUAACA-CUUGGGCUAAGUG---UUAAGUU----GGUUAUUUUUCUUA----------CAUCUCC--ACC-CC----C-AG------GAGCCCA---GG-------------UA---------UCAUAUACUCCC-CCAA--AAUA----------AAGAGCCUUAAGUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AP008956.1/34089-33903       AAUAACCAA-AAAUAACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-CC----C-CG------GAGCCCA---GG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCUUUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAGCAAGAUU-AAGU-GAA---UACCUAA--AAUUGUUGUC-AUUUUA-UUUCUAUCUUUCCA
AF123817.1/1563-1377         AAUAACCAA-AUAUCACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-CC----C-AG------GAGCCCA---AG-------------UA---------UCAUAUACACCC-CCAA--AAUA----------AAGAGCUUUAAAUACUAA-AA-GAAA-AGCACCUAGAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUGGUGGUC-AUUUUA-UUUCUAUCUUUCCA
DQ422812.2/3560-3374         GGUAUCCAA-AAAUGGUU-GCAGGGUUUCCAG---UAGGAUU----UGUAAUAACUCUUA----------CAUCUC-----------------------CACCUCC---UGGUGCCCAAG----UA---------UCAUAAACACCG-CCAA--AAUA----------CAUAGCUUUUCCUACUAG-UA-GUAG-AGCACCAGCAC-CUAAAAGAAUA-AGAU-GAA---UACCAAG--AAUGGUAGUC-AUUUUA-UUUUUAUCUUUCCA
X13366.1/1942-1756           AAUAACCAA-AUAUAACA-CUGGGACUAAGGG---UCAAAUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-CC----C-AG------GGGCCCA---GG-------------UA---------UCAUAUACACCG-CCAA--AAUA----------AAGAGCCUUGAGUACUAG-AA-GAAA-AGCACCUAGAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUUGUAGUC-AUUUUA-UUUCGAUCUUUCCA
AF525948.2/1566-1380         AAUAACCAA-AUAUAGCC-ACUGGGUUAAGCG---UAAGGUU----CAUAAUUUUUCUUA----------CAUCUCC--ACC-GC----C-AG------GAGCCCA---GG-------------UA---------UCAUAUAUGCCA-CCAA--AAUA----------CAAAGCCUUGAAGACUAG-AA-GAAA-AGCACCAACAC-CUAGCAAAAUU-AAGU-GAA---UACCUAA--AAUUGUAGUC-AUUUUA-UUUCUAUCUUUCCA
AY465664.1/1566-1380         AAUAACCAA-AAAUGAUG-CUGGGGCUAAGAG---UUAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-AC----C-UG------GAGCCCA---GG-------------UA---------UCAUAUACACCU-CCAA--AAUA----------AACAGCUUUAAAUACCAG-AA-GAAA-AGCACCUAGAC-CUAACAAAAUU-AGGU-GAA---UGCCCAA--AAUUGUAGUC-AUUUUA-UUUCGAUCUUUCCA
AY465671.1/1565-1379         AAUAACCAA-AUAUCACA-CUAGGGUUAAGUG---UCAAAUU----GGUAAUCUUUCUUA----------CAUCUCC--UCC-AC----C-AG------GGGCCCA---GG-------------UA---------UCAUAUAUACCC-CCAA--AAUA----------AAGGGCUUUGAAUACUAA-AA-GAAA-AGCACCUAUAC-CUAACAAAAUU-AGGU-GAA---UACCUAA--AAUUGUAGUC-AUCUUA-UUUCUAUCUUUCCA
AF462401.1/1566-1380         AAUAGCCAA-AUAUAGCA-CUUGGGUUAAGAG---UCGGGUU----CGUAAUUUUUCUUA----------CAUCUCC--ACC-GC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACACCU-CCAA--AAUA----------CAAAGCCUUGAGCACUAG-AA-GAAA-AGCACCAACAC-CUAGCAAGAUU-AGGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUG-UUUCUAUCUUUCCA
AF123826.1/1564-1378         AAUAACCAA-AUAUAACA-CUUGGACUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-CC----C-GG------GAGCCCA---GG-------------UG---------UCAUAUACGCCU-CCAA--AAUA----------AAGAGCUUUGAAUACUAG-AA-GAAA-UGCACCUAUAC-CUAACAAAAUU-AAGU-GAA---UACCCAA--AAUAGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AF481843.1/506-320           AAUAGCCAA-AAAUAACA-GAAGCACUUGUAG---UUGGGUU----AGUAAUUAUACGAA----------CAUCUC-----------------------CACCACC---UGGUGCCCAAG----UA---------UCAUAAACACCU-CCAA--AAUA----------UAAUGCUUUCCAAACUAA-UA-GCCA-UGCUCCUAAUC-CUAAAAUAAUA-AGAU-GAU---AACCUAA--AAUAUUUGUC-AUUUUA-UUUUUGUCUUUAAA
AY664840.1/1566-1380         AAUAACCAA-AAAUAACA-CUUGGGUUAAGUG---UUAAGUU----CGUAAUUUUUCUUA----------CAUCUCC--ACC-GC----C-GG------GAGCCCA---AG-------------UA---------UCAUAUACACCG-CCAA--AAUA----------CAAAGCCUUGAGCACUAG-AA-GAAA-AGCACCAACAC-CUAGCAAGAUU-AGAU-GAA---UACCCAA--AAUUGUGGUC-AUUUUG-UUCCUAUCUUUCCA
AP005672.1/42864-43050       AAUAACCAA-AUAUAACA-CCAGGACUAAGAG---UAAGAUU----UGUAAUUUUUCUUA----------CGUCACC--UCC-UC----C-AG------GAGCCCA---AG-------------UA---------UCAUAUAUUCCG-CCAA--AAUA----------UAAGGCUUUAAAUACUAA-AA-GGAA-AGCGCCAGCAC-CUAAUAAAAUU-AAAU-GAA---UACCUAA--AAUAGUAGUC-AUUUUA-UUUUUAUCUUUCCA
AY876207.1/499-313           GAUAUCCAA-AAAUUAUU-AAUGGAUUUAAGG---UUGGAUU----AGUGAUAUAACGUA----------CAUCUCC--UCC-GC----C-CG------GAGCCCA---AG-------------UA---------UCAUAAACUCCA-CCUA--UAAA----------CAUUGCUUUUACUACUAG-UA-AAAA-CGCUCCAACCC-CCAAUAAAAUU-AAAU-GAA---UACCUAA--AAUUGUUGUC-AUUUUA-UUUUUAUCUCUCCA
AF166114.1/1991-1805         AAUAACCAA-AGAUAACU-GCUGGACUAAGUG---UUGGAUC----UGUAAUGAUUCUUA----------CAUCUCC--UCC-GC----C-UG------GAGCCCA---UG-------------UA---------UCAUAUACACCA-CCAA--AAUA----------GCAUGCUUUCCAUACUAA-UA-AAUA-UGCACCAACAC-CUAAAACAAUU-AAAU-GAA---UACCAAG--AAUAGUAGUC-AUUUUG-UUUUUGUCUUUCCA
DQ291132.1/126619-126433     AGUAACCAA-AGAUUACA-CCAGGGUUUGUAG---UUGGGUU----UGAAAUGAUACGAA----------CGUCACC--ACC-AC----C-GG------CAGCCCA---AG-------------UA---------UCGUAAACACCA-CCGA--AGUA----------CAUAGCUUUCCAAACUAA-UA-ACCA-AGCACCAAAAC-CUAAUAAGAUU-AAGU-GGA---UACCUAA--GAUAGUAGUC-AUUUUG-UUUUUAUCUUUCCA
AF481847.1/506-320           GAUAGCUAA-AUAUAACA-CUAGGAUUAAGAG---UUAGAUU----GGUAAUUUUUCUUA----------CAUCUCC--UCC-UC----C-CG------GUGCCCA---AG-------------UA---------UCAUAAAUACCU-CCAA--ACCA----------AAUUGCUUUUGCUACUAA-UA-AUAA-AGCACCUAGAC-CUAAUAAAAUU-AGAU-GAA---UACCUAA--AAUAGUGGUC-AUUUUG-UUUUUAUCUUUCCA
DQ396875.1/676-862           AGUAACCAA-AAACAACA-GCAGCAUUUGUAG---UUGGGUU----UGUAAUAAUACGAA----------CGUCUCC--ACC-UC----C-UG------GAGCCCA---UG-------------UA---------UCAUAAACACCA-CCAA--AAUA----------CAUAGCUUUCCAUACUAA-UA-ACCA-AGCUCCAAUAC-CUAACAUGAUA-AGGU-GGU---AACCUAA--GAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB044527.1/373-187           GGUAAUUAA-AAAUUACA-CCAGCAUUUGUUG---UUGGGUU----UGUAAUAACACGAA----------CGUCACC--ACC-AC----C-UG------GAGCCCA---AG-------------UG---------UCAUAAACACCG-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-UGCACCAAGAC-CUAGCAUGAUU-AGGU-GAU---AACCUAA--AAUGUUAGUC-AUUUUG-UUUUUAUCUUUCCA
U30821.1/99448-99262         UAUAACUAA-AAAUUACU-GUUGGGUUUAAUG---UUGGAUU----ACUAAUUACACGUA----------CAUCUCC--ACC-GC----C-UG------GUGCCCA---AG-------------UG---------UCAUAAACACCA-CCGA--AGAA----------CAUUGCUUUUAAUACUAA-AA-GUAA-AGCACCACUUC-CUAAAAGAAUU-AAAU-GAA---UACCAAU--AAUAGUAGUC-AUUUUA-UUUUUAUCUUUCCA
AB044525.1/373-187           GGUAGCCAA-AAAUAACG-GCUGCGUUUGUUG---UUGGGUU----UGUAAUAACACGGAUAUCUCCCC-CUCCAG-----------------------GGGCCCA---AG-------------UG---------UCGUAAACACCA-CCAA--AAUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUAAUU-AAGU-GGU---AACCUAA--AAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AY958085.1/116464-116278     GAUAGCCAA-AAAUAACA-CCAGGAUUUAAAG---UUAAAUU----UGUUAUUUUACGUA----------CAUCUCC--ACC-AC----C-AG------GUGCCCA---AG-------------UA---------UCAUAAACACCA-CCGA--ACCA----------UACAGCUUUAAACACUAG-UA-AGAA-AGCACCAAGUC-CUAAGAUAAUU-AAAU-GAA---UACCUAA--AAUGGUAGUC-AUUUUG-UUCUUAUCUUUCCA
CP000393.1/817039-816853     GAUAACCAA-AUAUAACA-GCAGGAUUCAAAG---UAGGGUU----AGUAAUUACUCGUA----------CAUCACC--GCC-AC----C-UG------GUGCCCA---AG-------------UA---------UCAUAGACACCA-CCCA--AGAA----------CACAGCUUUGAUUACUAA-UA-AGAA-UGCGCCCAAAC-CUAAUAUAAUU-AAGU-GGU---AGCCAAU--AAUAUUAGUC-AUCUGG-UUCUUAUCUUUCCA
AY876203.1/499-313           GAUAGCCAA-AAAUUACA-GCUGGAUUUAAAG---UAGGAUU----ACUAAUAAAACGUA----------CAUCGCC--ACC-AC----C-UG------GAGCCCA---UG-------------UA---------UCAUAUAUACCA-CCAC--UAAA----------UAAAGCUUUAAUAACAAG-UA-AAAA-UGCGCCUAUAC-CUAGAAGUAUU-AAAU-GAA---UACCUAA--UAUAGUUGUC-AUUUUA-UUUUUAUCUCUCCA
AB044530.1/373-187           GGUAACCGA-AGAUAACA-GCAGCGUUUGUAG---UUGGGUU----AGUAAUAACACGAA----------CGUCACC--ACC-AC----C-UG------GAGCCCA---AG-------------UG---------UCAUAAACACCA-CCGA--AGUA----------CAUUGCUUUCCAAACUAG-UA-ACCA-UGCACCUAAAC-CUAACAUAAUA-AGGU-GGU---AACCAAG--AAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AF481841.1/506-320           GAUAACCAA-AGAUAACU-CCUGGACUAACAG---UAAUAUU----AGUAAUUUUUCUUA----------CAUCACC--ACC-AC----C-AG------GUGCCCA---UG-------------UA---------UCAUAUACACCA-CCAA--ACCA----------UAUAGCUUUAGCUACUAA-UA-AUAA-AGCGCCAACAC-CUAAUAUAAUU-AAAU-GAA---UACCUAA--AAUAGUAGUC-AUUUUA-UUUUUAUCUUUCCA
X04465.1/40500-40314         AAUAACCAA-AGAUUACA-CCUGGACUAAGAG---UUAAAUU----UGUAAUUUUUCUUA----------CAUCUCC--ACC-AC----C-UG------GAGCCCA---UG-------------UA---------UCAUAAAUACCA-CCAA--AAUA----------UAAGGCUUUAAAUACUAA-AA-GAAA-AGCACCAGCAC-CUAACAAAAUU-AAAU-GAA---UACCUAA--AAUAGUAGUC-AUUUUG-UUUUUGUCUUUCCA
AF481837.1/506-320           GAUAGCCAA-AGAUAAUA-CUUGGAUCAUAUG---UAGGAUU----AGUUAUUACUCGAA----------CAUCUCC--UCC-AC----C-AG------GAGCCCA---AG-------------UA---------UCGUAAACACCU-CCAA--ACCA----------UACAGCUUUAGCUACUAA-UA-AUAA-UGCACCAAAGC-CUAGAAGAACU-AAAU-GAA---UACCUAA--AAUAGUAGUC-AUUUUG-UUUUUAUCUUUCCA
AB044522.1/373-187           GGUAACCAA-AAAUUACA-GCAGCGUUUGUUG---UUGGGUU----UGUAAUAACACGAA----------CGUCACC--ACC-CC----C-UG------GCGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--AAUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUGAUU-AGGU-GGU---AACCUAA--GAUAUUAGUC-AUCUUG-UUUUUGUCUUUCCA
AB086178.1/373-187           GAUAACCAA-AAAUUACA-GCUGCGUUUGUUG---UUGGGUU----AGUAAUUAUACGGAUGUCACCAC-CACCUG-----------------------GAGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-AGCGCCUAGUC-CUAAAAUGAUU-AGGU-GAU---AACCUAG--GAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB076171.2/473-287           GGUAACCAA-AAAUUACA-GCAGCAUUUGUUG---UUGGGUU----AGUAAUAACACGAA----------CGUCUCC--UCC-CC----C-UG------GUGCCCA---AG-------------UA---------UCGUAAACACCA-CCAA--AGUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-UGCACCUAAAC-CUAGAAUGAUU-AGGU-GGU---AACCUAA--AAUGUUUGUC-AUUUUG-UUUUUGUCUUUCCA
AB044480.1/373-187           GGUAACCAA-AAAUCACA-GCUGCAUUUGUUG---UUGGGUU----AGUAAUAACACGAAUGUCACCAC-CACCUG-----------------------GAGCCCA---UG-------------UG---------UCAUAAACACCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUGAUU-AGGU-GGU---AUCCUAA--AAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AF481846.1/506-320           AAUAACCAA-AAAUAACA-CUAGGAUUUAGUG---UUAAGUU----AGUAAUUUUUCUAA----------CAUCUCC--UCC-UC----C-UG------GAGCCCA---AG-------------UA---------UCGUAUACACCA-CCAA--AAUA----------AAGAGCUUUUAAUACUAA-UA-AAAA-AGCUCCUAAAC-CUAAUAAAAUA-AGAU-GAA---UUCCUAA--AAUAGUAGUC-AUCUUA-UUUUUAUCUUUCCA
AB044497.1/373-187           GGUAACCAA-AAAUUACA-GCUGCGUUUGUUG---UUGGGUU----AGUAAUAACACGAA----------CGUCACC--ACC-AC----C-AG------GAGCCCA---AG-------------UA---------UCGUAAACACCA-CCAA--AGUA----------UAAAGCUUUCCAAACAAG-UA-ACCA-UGCACCUAAAC-CUAAAAUGAUU-AGGU-GGU---AACCUAG--AAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB044504.1/373-187           GAUAACCAA-AAAUUACA-GCAGCAUUUGUUG---UUGGAUU----AGUAAUUACACGUA----------CGUCUC-----------------------CGCCGCC---GGGAGCCCAAG----UA---------UCAUAAAUACCG-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-GA-GCCA-CGCGCCUAGAC-CUAAAAUAAUU-AGGU-GAU---AACCUAA--AAUGUUAGUC-AUUUUG-UUUUUAUCUUUCCA
X62578.1/2940-2754           GAUAGCCAA-AAAUUACU-AAUGGAUUUAGGG---UUGGAUU----AUUGAUAUAACGUA----------CAUCACC--UCC-AC----C-AG------GUGCCCA---UG-------------UG---------UCAUAAACUCCC-CCAA--AAAA----------CAUAGCUUUUAUAACUAG-CA-AGAA-AGCUCCAAUUC-CUAAUAAAAUU-AAAU-GAA---UACCUAA--AAUAGUUGUC-AUUUUA-UUUUUAUCUCUCCA
AB044528.1/373-187           GGUAACCAA-AAAUAACA-GCAGCAUUUGUUG---UUGGGUU----AGUAAUAACACGAA----------CGUCACC--ACC-AC----C-UG------GAGCCCA---AG-------------UA---------UCGUAAACACCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-UGCACCUAAGC-CUAACAUGAUA-AGGU-GGU---AACCUAA--AAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB044505.1/373-187           GGUAACCAA-AGAUAACU-GCAGCAUUUGUUG---UUGGGUU----UGUAAUAACACGAA----------UGUCUCC--GCC-AC----C-UG------GCGCCCA---UG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAAUC-CUAAAAUAAUU-AGGU-GAU---AACCUAA--AAUAUUAGUC-AUUUUG-UUUUUAUCUUUCCA
AB044521.1/373-187           GGUAACCAA-AAAUAACA-GCAGCAUUUGUUG---UUGGAUU----AGUAAUAACACGAA----------CGUCAC-----------------------CACCACC---UGGUGCCCAAG----UA---------UCGUAAACACCA-CCAA--AGUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUGAUU-AGGU-GGU---AACCUAG--AAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB214423.1/373-187           GAUAACCAA-AAAUUACA-GCUGCGUUUGUUG---UUGGGUU----AGUAAUAACACGGAUGUCGCCGC-CACCUG-----------------------GAGCCCA---AG-------------UA---------UCAUAAACACCG-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUAAUU-AAAU-GGU---AACCUAA--GAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB044477.1/373-187           GGUAACCAA-AAAUAACA-GCAGCGUUUGUUG---UUGGAUU----AGUAAUAACACGAA----------CAUCACC--ACC-AC----C-AG------GCGCCCA---AG-------------UA---------UCAUAAACACCA-CCGA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-AGCCCCUAGAC-CUAAAAUGAUU-AAGU-GGU---AACCUAA--AAUGUUAGUC-AUCUUA-UUUUUAUCUUUCCA
AB044524.1/373-187           GGUAACCAA-AAAUUACA-GCAGCAUUUGUUG---UUGGAUU----AGUAAUAACACGAA----------CGUCUC-----------------------CACCGCC---CG-------------GGGCCCAAGUAUCGUAAACACCA-CCAA--AGUA----------CAUUGCUUUCCAAACUAG-UA-ACCA-UGCACCUAGAC-CUAAAAUGAUU-AAGU-GGU---AACCUAA--AAUGUUAGUC-AUUUUA-UUUUUGUCUUUCCA
AB214434.1/373-187           GAUAACCAA-AAAUUACA-GCUGCGUUGGUUG---UUGGAUU----AGUAAUGACACGAAUGUCACCAC-CACCUG-----------------------GAGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUAAUU-AAGU-GGU---AACCUAG--AAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB214418.1/373-187           GAUAGCCAA-AAAUCACA-GCCGCAUUUGUUG---UUGGGUU----AGUAAUAACACGAAUAUCUCCAC-CACCUG-----------------------GAGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAGAAUGAUU-AAGU-GGU---AACCUAG--AAUAUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB044529.1/373-187           AAUAACCAA-AGAUUACA-GCAGCGUUUGUUG---UUGGGUU----UGUAAUAAUACGAA----------CGUCAC-----------------------CACCACC---UGGUGCCCAAG----UA---------UCAUAAACACCA-CCAA--AAUA----------AAGAGCUUUUAAAACAAG-UA-ACCA-AGCCCCUAAAC-CUAACAUAAUA-AGGU-GAU---AACCUAA--AAUAUUAGUC-AUUUUG-UUUUUAUCUUUCCA
AB044508.1/373-187           GAUAACCAA-AGAUUACA-GCAGCAUUUGUUG---UUGGAUU----UGUAAUUACACGUA----------CAUCAC-----------------------CACCACC---CG-------------GGGCCCAAGUAUCGUAAAUACCU-CCAA--AAUA----------CAUAGCCUUCCAAACAAG-UA-ACCA-GGCACCAAGAC-CUAAAAUAAUU-AGGU-GAU---AACCUAA--AAUGUUAGUC-AUUUUG-UUUUUAUCUUUCCA
AB044509.1/373-187           GAUAACCAA-AGAUUACA-GCAGCACUUGUUG---UUGGAUU----UGUAAUAAUACGAA----------CAUCACC--GCC-UC----C-UG------GUGCCCA---AG-------------UA---------UCAUAAAUACCA-CCAA--AGUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUAAUU-AGGU-GAU---AACCUAA--AAUGUUUGUC-AUUUUG-UUUUUAUCUUUCCA
AB044501.1/373-187           GGUAACCAA-AAAUUACA-GCUGCAUUUGUUG---UUGGGUU----AGUAAUAACACGAA----------CGUCUC-----------------------CACCACC---GGGCGCCCAUG----UA---------UCGUAAACACCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGGC-CUAAAAUAAUU-AAAU-GGU---AACCUAA--AAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB044498.1/373-187           GGUAACCAA-AAAUUACA-GCAGCAUUUGUUG---UUGGAUU----AGUGAUAACACGUA----------CGUCUCC--ACC-GC----C-AG------GAGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUGAUU-AAGU-GAU---AACCUAA--GAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB214413.1/373-187           GAUAACCAA-AAAUUACC-GCUGCGUUUGUUG---UUGGGUU----AGUAAUCAUACGAAUGUCACCAC-CACCAG-----------------------GAGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAAAC-CUAAAAUGAUU-AGGU-GAU---AACCUAG--AAUAUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB044510.1/373-187           GGUAACCAA-AGAUAACC-GCUGCGUUUGUUG---UUGGGUU----UGUGAUAACACGAA----------CGUCGCC--ACC-AC----C-AG------GAGCCCA---UG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAAAC-CUAAAAUAAUU-AGGU-GAU---AACCUAA--AAUAUUUGUC-AUUUUG-UUUUUAUCUUUCCA
AB044499.1/373-187           GGUAACCAA-AAAUAACA-GCAGCAUUUGUUG---UUGGAUU----AGUAAUUACACGAA----------CGUCUCC--ACC-AC----C-UG------GAGCCCA---UG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUGAUU-AGGU-GAU---AACCUAA--AAUGUUAGUC-AUCUUG-UUUUUGUCUUUCCA
AB044496.1/373-187           GGUAACCAA-AAAUUACA-GCAGCAUUUGUUG---UUGGUUU----AGUAAUAACACGAA----------CGUCUCC--ACC-AC----C-UG------GAGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-UGCACCUAGAC-CUAAAAUAAUU-AGGU-GGU---AACCUAA--AAUAUUAGUC-AUUUUA-UUUUUGUCUUUCCA
AB044494.1/373-187           GAUAACCAA-AAAUUACA-GCUGCGUUUGUUG---UUGGGUU----AGUAAUAACACGAA----------CGUCACC--ACC-AC----C-AG------GAGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUAAUU-AGAU-GGU---AACCUAA--AAUGUUAGUC-AUUUUG-UUCUUGUCUUUCCA
AB044486.1/373-187           GAUAACCAA-AAAUUACA-GCAGCGUUUGUAG---UAGGGUU----AGUAAUAAUACGAA----------CAUCACC--ACC-AC----C-AG------GAGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--AGUA----------CAUAGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUAAUU-AAGU-GGU---AACCCAG--AAUGUUAGUC-AUUUUG-UUUUUGUCUUUCCA
AB044512.1/373-187           GAUAACCAA-AGAUUACA-GCAGCAUUUGUUG---UUGGGUU----AGUAAUAACACGUA----------CGUCACC--ACC-AC----C-UG------GAGCCCA---UG-------------UA---------UCGUAAAUACCA-CCAA--AGUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAGAC-CUAAAAUAAUU-AGGU-GAU---AACCUAA--AAUGUUAGUC-AUUUUG-UUUUUAUCUUUCCA
AB044520.1/373-187           GAUAACCAA-AAAUUACA-GCAGCAUUUGUUG---UUGGGUU----AGUAAUAACACGAAUAUCACCAC-CACCAG-----------------------GUGCCCA---AG-------------UA---------UCAUAAACACCA-CCAA--AAUA----------CAUUGCUUUCCAAACAAG-UA-ACCA-AGCACCUAAAC-CUAAAAUAAUU-AAGU-GGU---AACCUAA--AAUGUUAGUC-AUUUUG-UUUUUAUCUUUCCA
EU262890.1/30623-30809       AAUAACCAA-AUAGAAUA-CUUGGGCUAAGGG---UCAAGUU----AGUAAUUUUUCGUA----------CAUCUCC--CCC-UC----C-CG------GAGCCCA---GG-------------UA---------UCAUAUACGCCA-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAAAC-CUAACAAGAUU-AAGU-GAA---UACCUAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
CP001037.1/4582747-4582933   CAUAACCGA-AGAUAACU-GCUGGGUUCAAUG---UGGGAUU----GGUAAUAAUCCGAA----------CGUCACC--ACC-GC----C-UG------GUGCCCA---GG-------------UG---------UCAUACAACCCA-CCGA--AGAA----------CAUUGCUUUUGCUACCAA-UA-GCAG-CGCACCGAAUC-CCAAAAUAAUC-AGAU-GGA---AUCCGAU--GAUGUUGGUC-AUCUUG-UUCUUGUCUUUCCA
BX548175.1/1271393-1271207   CGUAUCCAA-AGAUCACG-CCUGGAUCAAGUG---UGGGGCU----GGUGAUUAAUCUCA----------CGUCGCC--ACC-AC----C-UG------GAGCCCA---GG-------------UG---------UCAUAGAUGCCG-CCAA--AGAA----------GCAGGCCUUGAGGAUCAG-AG-CAAG-AGCUCCCCAGC-CUAGAAAAAUC-AGGU-UGU---AACCAAG--AAUGUUGGUC-AUCUGA-UUUUUGUCUUUCCA
DQ424856.1/37749-37563       AAUAACCAA-AUAUAACA-CUUGGG-CUAAGGGU-CAA-GUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-UC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACGCCG-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
AM447437.2/1214-1028         AAUAACCAA-AUAUAACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------CAUCUCC--CCC-UC----C-GG------GAGCCCA---GG-------------UA---------UCAUAUACGCCG-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AGCACCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCCAA--AAUUGUGGUC-AUUUUA-UUUCUAUCUUUCCA
FN596039.1/7655-7475         AAUAACCAA-AUAUAACA-CUUGGGCUAAGGG---UCAAGUU----GGUAAUUUUUCUUA----------ACCCUC-----------------------CGGGAGCCCAGG-------------UA---------UCAUAUACGCCC-CCAA--AAUA----------AAGAGCCUUGAAUACUAG-AA-GAAA-AACACCUAUAC-CUAACAAGAUU-AAGU-GAA---UACCAAA--AAUUGUGGUC-AUUAUC-UUUCUAUCUUUCCA
FN596251.1/421135-420959     GUUGGGCAA-A----ACA-UAUGGUUGUUUGG---UUGGUUAAA--UGUUAUUAAUGAGA----------AUUCAUU----------------------GAGCUCG---AG-------------UA---------UCAUAUGCACCG-CCAA--AAUA----------AAAAGUCUUGAAUGCUAA-AA-GAAA-AGUACCUAUAC-CUAACAAGAUU-AAGA-GAA---UACCCAA--AAUUGUGGUU-AUUUUA-UUUUUAUCUUUCCA
#=GC SS_cons                 :::::::::.::::::::.:::::::::::::...:::::::....::::::::::::::..........:::::::..:::.::....:.::......:::::::...::.............::.........::::::::::::.::::..::::..........::::::::::::::::::.::.::::.:::::::::::.:::::::::::.:<<<.<<<...--<<<<<..__________.______.>>>>>>>>>>>:::
#=GC RF                      aAUAaCCAA.AaAUaACa.cuuGGauUaAggG...UuGGgUU....gGUaAUuauuCuuA..........CaUCuCC..aCC.aC....C.aG......GaGCcCA...gG.............UA.........UCAUAuAcaCCa.CCAA..AaUA..........cAuaGCuUUgaauACuAG.aA.gaAA.aGCACCuAuaC.CUAAaAaaAUU.Aagu.GAu...uAcccAa..AAUugUaGUC.AUUUUa.uUgguaUCuuuCCA
//
# STOCKHOLM 1.0

#=GF AC   RF01420
#=GF ID   snoR113
#=GF DE   Small nucleolar RNA snoR113
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   47.00
#=GF TC   47.70
#=GF NC   44.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AC020889.3/25746-25848       UGGCGAUGAUGAAAA----AAAGGCCGGACUUACGGCUACUACCACCGUGAAAGUGUGG---------UGGGUAGUAGAAUGAUGCUAAAGUAUCCAAAGGUUACAG---CUGAGCCUC
AM439246.2/30554-30644       UGGCUAUGAUGACAA----AAAGGCCGGACUUACAGCUGCUUCCAGUG---------GG---------UUGGUAGUAGAAUGAUG---AAGUUUUGCUAAGGUGAUU---CUGAGCCAG
AASG02004037.1/17014-16901   UGGCGAUGAUGACAAACAUAAAGGCCGGACUUACGGCUGCCACUGCUAAUAUAAUUUAGCUGGGUU--UUGGUAGUAGAUUGAUGAACCCACUUUUAUAAGGUUACU---CUGAGCCAG
AARH01006437.1/153808-153923 UGGCGAUGAUGAUAAA---AAAGGCCGGACUUACGGCUGCUACCAGAAAACUAAUUAAUUUUUCGUGGUCGGUAGUAGAUUGAUGAACUUCUCAUAUAAAGGUGUCUGUUCUGAGCCAC
AC150743.12/61371-61461      UGGCAAUGAUGAUA-----AAAGGCCGGUCUUACGGCUGCCAUUUACG---------UA---------UUGGUAGUAGAUUGAUU--ACUUUAAGGUUUAGGGUUUU---CUGAGCCAG
#=GC SS_cons                 :<<<___________....________________________________________........._______________________________________...____>>>::
#=GC RF                      UGGCgAUGAUGAuAA....AAAGGCCGGACUUACGGCUGCuACcaaugaaauAaUuuag.........UuGGUAGUAGAuUGAUGaaaauaUuuuauuAAGGUuuuU...CUGAGCCAg
//
# STOCKHOLM 1.0

#=GF AC   RF01421
#=GF ID   snoR114
#=GF DE   small nucleolar RNA snoR114
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   44.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   24


AC011807.4/8760-8847         AGGCUGUGAGGAA--ACUUGCG-CUUA---A-AUGAU-GGAUUUGGGUUCAUCACCAUCGUCUGAAAUAUUG-----ACGAGUUAGU---GCGCAUCUGAGCUU
AARH01005480.1/16910-16995   AAGCUAUGAGGAU--AUCUGUG-CUCA---U-GUGAU-G--AUAGGGUCUAUCACUACCGUCUGAUCUGCGG-----ACGAAUUCGA---GUGCAUCUGAGCUU
AM452399.2/5938-6029         GGGCAGUGACGAAAAAUUUGCG-CUAA---A-AUGUGAUGACUGGGUCUCAUCACCAUCGUCUGAUCUUUCGG----ACGAGAACUC---GCGCAUCCGAGCUC
AASG02007560.1/10700-10615   GAGCGAUGAUUAA--AUCUACA-CGCU---U-GUGAU-G--GUAGGGUCUAUCACUAUCUUCUGAUUUAAGG-----AAGAGAAUGG---GUGCGGCUGAGCUC
CR538722.1/118146-118232     UAGCUGUGAUGAA--AUUUGUGUCAAA---U-GUGUU-G---ACGGGUUCAUCACUAUCGUUUAACUUCGGUU----GCGAAAACUG---GCACAUCUGAGCUU
AASG02007560.1/3297-3211     GAGCAAUGAUUAA--GGCUGCA-CCCU---U-GUGAU-G--GUAGGGUCCGUCACUAUCUUCUGACUUUAAGG----AGGUAAAUAG---GUGCCUCUGAGCUC
AARH01016953.1/366-275       GAGCUGUGAGGAU--ACGAGUGCUUAU---U-GUGAU-G--AUAGGGUCUAUCACUACCGUCAGAUAUAUUCAUCGGACGAAAAGAA---GCGCUUCUGAGCUU
AARH01003570.1/220542-220631 GAGCUGUGAAGAA--AUUUGAA-CUCA---ACGUGAU-G--ACAGGGUCUAUAACUUUCGCCUGAUCCUCUUGGG--ACGAAAGCGA---GUGCUUCUGAGCUC
AARH01001139.1/126798-126714 GAGCAAUGAUGAA--AGCUGUG-CCGU---A-GCGAU-G--GUAGGGUCUAUCGCAAGCAUCUGAUCACCAG-----AUGA-UAUUG---GCUCUGCUGAGCUC
AASG02004085.1/19855-19768   AAGCUAUGAAGAA--AAAUGCGCUCUU---U-GUGAC-U--GUUGGGUCUGUCACACUCGCCUGAUCUUAGGA----GUGAUAUGAC---GCGCAUCUGAGCUC
AASG02004085.1/19161-19072   GAGCUAUGAGGAUA-UUUUGCA-CCUU---U-GUGAU-G--GUUGGGUCUAUCACUCUCAUCUGAUAUGGAG-----AUGAAAGCAGCAGGUUUAACUGAGCUC
AASG02001451.1/18100-18184   GAGCUAUGAGGAU---GAUACU-CUCC---U-GUGAU-G--GGUGGGUCUAUCACUUUCAUCUGAUUCACAG-----AUGAUAAUGA---GUGCUGCUGAGCUC
AARH01005987.1/8951-8861     GAGCGGUGAGGAC--ACCUGUGCUCCA---A-GUGAU-G--GUGGGGUCUAUCACUGCCGUCUGAUCUUUCAUUGG-AUGAAAGUGA---GCGCACCUGAGCUC
AC004665.3/80168-80256       UAGCUAUUAUGAA--AAUUGCG-CAUA---A-AUGAU-GGAUUUGGGUCCAUCAGAAUCGUUUGACAUAAAG-----ACGGGAUAGUU--GAGCAUCUAAGCUU
AASG02007560.1/2676-2591     GAGCGAUGAUUAA--GGCUGCA-CCCU---U-GUGAU-G--GUAGGGUCCGUCACUCUCUUCUGACUUAAGG-----AGGUAAAUAG---GUGCCUCUGAGCUC
AM452399.2/5306-5397         AGGCYGUGAYGAGUAAUUUGCG-CUGA---A-UUGUGAUGGCUGGGUCCCAUCACCAUCGUCUGAUCUUUCGG----ACGACAACUG---GCGCAUCUGAGCUC
AARH01006465.1/581033-581122 AAGCUGUGAGGAA--AUCUGUG-CUCA---UUGUGAU-G--AUAGGGUCUAUCACUACCGUCCGAUCUCCAUCCG--ACGACAAAGA---GUGCAUCUGAGCUU
AARH01008218.1/40726-40637   GAGCUGUGAUGAC--CUCUGUG-CUCA---ACGUGAU-G--AUAGGGUCUAUCACUACCGUCUGAUCAUCAUCGG--ACGAAAGCGA---GCGCAUCUGAGCUC
AC149637.11/88731-88817      AAGCUGUGAUGAU--AUUUGUGUCAAU---U-GUGGU-G---AUGGGUUCAUCACUAUAUUGCCUUUAGUGGC----UAAAAAACUG---GCACAUCUGAGCUU
AARH01005480.1/14753-14842   GAGCUGUGAGGAU--ACCAGUGCUUAU---U-GUGAU-G--AUAGGGUCUAUCACUACCGUCAGAUAUUCAUCGG--ACGAAAAGGA---GCGCAUCUGAGCUU
AAAA02017716.1/21797-21717   GAGUGAUGAGGAA--AU----G-CUCC---U-GUGAC-A--ACUGGGUUCGUCACAUUCAUCUGAUCUCAG------AUGUUUACGA---GCUAGUCUGAACUC
AM463322.1/16746-16655       GAGCAGUGAUGAGUAACAUGCG-CUAA---A-CUGUGAUGGCUGGGUCCCAUCACCAUCGUCAGAUCUUUCGG----ACGAGAACUU---GCGCAUCUGAGCUC
AM452399.2/3882-3973         GAGCAGUGAGGAUUGGUUUGCG-CUAA---A-CCGUGAUGGCUGGGUCUCAUCACCGACGUCUGAUGUAUCGG----ACGACAAUAC---GCGCAUCUGAGCUC
AM452399.2/2868-2960         GAGCAGUGACGAUUGAUUUGCG-CUAAACCU-GUGAU-GG-CUGGGUCUCAUCACCAACGUCUGAUGUAUCGG----ACGACAAUAC---GCGCAUCUGAGCUC
#=GC SS_cons                 <<<<_________.._______.____..._._____._..________________________________....__________...__________>>>>
#=GC RF                      gAGCugUGAuGAa..AuuUGcG.Cuaa...u.GUGAU.G..aUaGGGUCcAUCACuaUCgUCUGAUcUauaGg....AcGAaAAuga...GcGCAUCUGAGCUc
//
# STOCKHOLM 1.0

#=GF AC   RF01422
#=GF ID   snoR116
#=GF DE   small nucleolar RNA snoR116
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   47.00
#=GF TC   48.30
#=GF NC   39.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AC007202.3/26280-26365     CGGCGAUGAUGAUGAAACAAGAUUACCAUCAAACUUUGAGAGGU-----U----UUUCGCUCGUUGAUGUAAACUUC--UUUUUAUAAUCUGAGCCU
AM474843.1/11598-11685     AGGCAGCGAUGACGAGAAUCGUAUACCAUCAAACUAUGAAAGCU-----U----GGAAGCUUGUUGAUGCUAUCUAGAAUCAUUACUCUCUGAGCCU
AARH01003557.1/39889-39803 AGGCUGUGAUGAUGAAAAUUAUAUACCAUCAAACUAUGAGAGCUCAAAAU----GUGAGCUUGUUGAUGCCAUCUC------UUAUUCUCUGAGCCC
AASG02001221.1/38053-38137 GGGUAGUGAUGAAUAAA--AUCAUACCAUCAAACUAUGAAAGCU-----UAAGGAUAAGCUUUUUGAUGUUAACUAU--UUUU---AUUCUGAGCCC
AC189312.2/67390-67475     AGGCAGUGAUGAUGAAAAAAGAUUACCAUCAAACUUUGAGAGAU-----U----CACAGCUCGUUGAUGCAUACUUC--UUUAUAUUACCUGAGCCU
#=GC SS_cons               :<<<________________________________________....._...._______________________..______________>>>:
#=GC RF                    aGGCaGUGAUGAuGAAAAuaguaUACCAUCAAACUaUGAgAGcU.....U....auaAGCUuGUUGAUGcuAaCUuu..UUuUUAUuaUCUGAGCCu
//
# STOCKHOLM 1.0

#=GF AC   RF01423
#=GF ID   snoR117
#=GF DE   small nucleolar RNA snoR117
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   42.00
#=GF TC   43.60
#=GF NC   41.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AC007202.3/26176-26247       AGCCUGUGAUGU--UUGAGAUUGUCCGUACCAUCUGAG----UUUCUCCUUGACGA--------------UUACCUCCA-CUUUCUGAGGCUU
AP006084.1/89100-89169       GGCCUGUGAUGC--AUCAAUUUGUCCGUACCAUCUGAG----AUUUCUCUGAUCGA--------------UA--CUCCA-UUUUCUGAAUCUG
AARH01004368.1/118009-118095 AGCCUGUGAUGCA-UCAAAAUUGUCCGUACCAUCUGAG----AUCUUUCUGUAUCUUUGAUGACACACAAACUUGUAUA-GAUUCUGAGGCUU
AASG02001221.1/37908-37990   GGCCUGUGAUGGAAAAAUAAUUGUCCGUACCAUCUGAAGA--UAUCUGUCUUUUGAUGCAUCU-------CUUUACCUA-GAUUCUGAGGCCU
AC189312.2/67271-67350       GGUCUGUGAUGU--UUGAGAUUGUCCGUACCAUCUGAGAGUUUAUCUCGUUGAUGAGCUG----------UAUGCUCUU-GUUUCUGAGGCUU
AM460349.2/3821-3740         GGCCGGUGAUGCA-CAAGAAUUGUCCGUACCAUCUGAG----AUCUCUUUCCUUGAUGUGAGAU------UCAUCUCUAGCUUUCUGAGGCCU
#=GC SS_cons                 <<<<_________.________________________...._____________________......._________.________>>>>:
#=GC RF                      gGcCUGUGAUGcA.uuaaAAUUGUCCGUACCAUCUGAG....auUuUuuUuuaUGAUuuauga.......uuuucUCUA.guUUCUGAGgCcU
//
# STOCKHOLM 1.0

#=GF AC   RF01424
#=GF ID   snoR118
#=GF DE   small nucleolar RNA snoR118
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   44.00
#=GF TC   44.30
#=GF NC   41.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00071
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


AB026636.1/61895-61803       AAAGAUGAUG-AAUAUGCACUGGGCUCUGAGUUGUUGAUUGACA---UUCAACUUCUU-UUUGAUGCAUAA--U-GC-AGCCUAGAAAGCUUAAUCUGAUUU
AASG02000028.1/122020-121924 GAAGAUGAUG-AAAAUGCACUGGGCUCUGAGCAGGCUGUUGACAGCAGCUAUAGCUUA-UUUGAUGCACAAU-U-GC-AGCCUAGAAAGCUAUGUCUGAUCA
AARH01004350.1/130761-130670 GGAGAUGAUG-AAUAUGCACUGGGCUCUGAGCAAGCUGUUUA------UCAGCUGCUUAAUUGAUGCAUAA--UUGC-UGCCUAGAAAGCUAUGUCUGAUCU
AC159538.20/113729-113653    AUGAAUGAUG-AAUAAGCACUGGGCUCUGAGCAUAUAAUU---------------------UGAUGCACAU--U-GCUAGCCUAGAAAGCUAUAUCUGACUC
AM443762.2/1022-1091         AGAUAUGAUGAAAUGUGCACUGGGCUCUGAACAG-UGAUGGA---------------------------AA--U-GC-AGCCUAGAAAGCUAUAUCUGAUCU
AAAA02015409.1/2222-2309     AUGAAUGAUG-AA-AUGCACUGGGCUCCGAGCAGUGAAUUACGC---UGCGUUUUGAU-GGAUAUGCAU-------U-UGCCUAGAAAGCAUUGACUGAUAC
AACV01010897.1/7032-7119     AUGAAUGAUG-AA-AUGCACUGGGCUCCGAGCAGU-GAUUUACA--------CCGCGU-UUUGAUGGAUAUGCG-UU-UGCCUAGAAAGCAUUGUCUGACAC
AF461424.2/73524-73611       AUGAAUGAUG-AA-AUGCACUGGGCUCCGAGCAGUGAAUUAC---------GCUGCGU-UUUGAUGGAUAUGCG-UU-UGCCUAGAAAGCAUUGUCUGACAC
#=GC SS_cons                 ::::::::::.:::::::::::::::::::::::::::::::::....::::::::::.::::::::::::..:.::.::::::::::::::::::::::::
#=GC RF                      auggAUGAUG.AAuAUGCACUGGGCUCuGAGCAGuugaUUgaca....ucaucugcuU.uUUGAUGcAuAa..u.Gc.uGCCUAGAAAGCuaUGUCUGAucc
//
# STOCKHOLM 1.0

#=GF AC   RF01425
#=GF ID   snoR121
#=GF DE   small nucleolar RNA snoR121
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   50.00
#=GF TC   54.30
#=GF NC   42.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AB026653.1/15165-15249 AGCGGUGAAGAUAGAACAAAUUAUGUGACGG---AAGCCGUCACAGUCGUCCUGACCAACUGUGACGAUAGCAAGUGCCGUCUGAGCU
AC189218.2/6678-6765   AGCUGUGAAGAUAAAACAAUUAAAGUGACGGCUUAGCCCGUCGCUGUCGUCCUGACCAUCUGUGACGAUAGCAAGUGCCGUCUGAGCU
#=GC SS_cons           <<<__________________________________________________________________________________>>>
#=GC RF                AGCuGUGAAGAUAaAACAAuUaAaGUGACGGcUUAagCCGUCaCuGUCGUCCUGACCAuCUGUGACGAUAGCAAGUGCCGUCUGAGCU
//
# STOCKHOLM 1.0

#=GF AC   RF01426
#=GF ID   snoR126
#=GF DE   small nucleolar RNA snoR126
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   39.00
#=GF TC   39.20
#=GF NC   37.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AB018108.1/5630-5526     AGGCGGUGAUGACAAAAAA----CA---UUUCUCGAUGCUGAAACUUACUCGA-GAGACCAAAUCACUCUUGUAAUCUUUCGUGAUGCUUGUU-UUUAUGCGUGUCUGAGCCUA
CU179904.1/61661-61756   AGGCUGUGAUGAACAACAA----CA---UUUCUCGAAUCUGAUAAUUACAAAA-G----CAAAUUAUAUUUG-----CUUUUUGAUGACCGUG-UUUGUGCGUGUCUGAGCCUC
AAAA02010687.1/1542-1640 UGGCUGUGAUGACAAACAAACCUCG---UUUCUCGAUGCUGAGACUUGAUUUGUU----CAAGG---ACCAG-----AACUGUGCUGACCUUAAUUUGUGCGUGUCUGAGCCAC
BK004878.1/4907-4810     UGGCUGUGAGGACUAACUA----CUUUGUUUCUCGAUGCUG------ACUUGA-U----UCAAUCAAUCAAGGACCAAAAAAAUUUGAUGACC-UUUGUGCGUGUCUGAGCCAC
#=GC SS_cons             <<<<_______________....__..._________________________._....__________________________________._______________>>>>:
#=GC RF                  uGGCuGUGAuGAcaAAcAA....Ca...UUUCUCGAUGCUGAaAcUUAcUugA.u....cAAAucAuuCuaGuAauaaauugUgaUGAuugUu.UUUGUGCGUGUCUGAGCCac
//
# STOCKHOLM 1.0

#=GF AC   RF01427
#=GF ID   snoR127
#=GF DE   small nucleolar RNA snoR127
#=GF AU   Osuch I
#=GF SE   INFFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   37.00
#=GF TC   37.40
#=GF NC   36.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AC069556.4/36784-36921  CUGGAAUGAUGAUGCUUAGCCAAAUCAGAUAU----GUGCUCCAAGAGGCAUUUUUCUGUGGAACCUUGUUCAGC---AGAUGGUGUGCCUCUUGUUGUAGUGC--GUCUUAGACGAU-AUCACAGGGAAUGGU---UAUUGC-UGACCAGA
AC144541.12/54772-54621 CUGGAAUGAUGUGAAUUAGCCAAAUCAGACAUUAAUGUGCUCCAUAAGGCAACCGGCAUGAUCGAUCUGCUUGGAUCAUGUUGAUGACCCUCAUGUUGAAGCGCAUUUCUCUGAUGAUCAACAAAGAGAUUGGUUUCUUUUUCCUGACCAGA
AC189657.2/25905-25797  CUGGAGUGAUGAUGCUUAGCCAAAUCAGAUAU----GUGCUCCAAAAGGUACAU---------------------------------GCCUCUUGUUGAAGCGC--GUCUUGGACGAU-AUCACAGAGAAUGGU---UUUUGCCUGACCAGA
#=GC SS_cons            <<<<____________________________...._______________________________________...__________________________..____________._______________...__________>>>>:
#=GC RF                 CUGGAAUGAUGaugcUUAGCCAAAUCAGAuAU....GUGCUCCAaaAGGcAuuuuuCauuauaaauuUGuUuaGa...uGuUGaUGagCCUCuUGUUGaAGcGC..gUCUuuGAcGAU.AuCAcAGaGAaUGGU...UuUUgCCUGACCAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01428
#=GF ID   snoR128
#=GF DE   small nucleolar RNA snoR128
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   40.00
#=GF TC   40.90
#=GF NC   38.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AF317971.1/6-97              UUGCAAUGAUGAGAUCUU-AUAAUGAAAUUGAAAGUGUUU-------ACACUUCAUGA-ACGGUCGACAAAAUAGUCGAACCUGAGCGGUUAGCUGAGCAA
AM451544.1/694-602           UUGCAAUGAUGAG--UAU-AGGAACUUAUUGAAAGUGUCUCA-----AUACUUGAUGAGAUUGUCGACAACCUUGUCGAUCCUGAGCGGUUACCUGAGCAA
AASG02006843.1/13326-13243   UUGCUAUGAUGAG--UGG-UACAAACUAAUGAAAGUUUAUACAGCAAUUGCUUCUUGA-AA-------------UUUAAUCCUGAGCGGUUAUCUGAGCAA
AARH01002655.1/240508-240577 UUGCUAUGAUGAG--UAU-GAAAAGGUUAUGAGAGUUUUG--------------AUGA-AA-------------UUCAUUCCUGAGCGGUUAUCUGAGCAA
AC172879.2/81890-81794       UUGCAGUGAUGAUAACUUUAUGAUUACAAUGAAAGUGUUUUAAAA--ACGCUUAAUGA-ACGGUCGACAAAAU-GUCGAACCUGAGCGGUUAGCUGAGCAA
#=GC SS_cons                 :<<<_________..___._______________________.....___________.______________._______________________>>>:
#=GC RF                      UUGCaAUGAUGAG..uaU.aaaAaaauAaUGAAAGUgUuUua.....auaCUUaAUGA.AagGUCGACAAaaU.gUCgAuCCUGAGCGGUUAuCUGAGCAA
//
# STOCKHOLM 1.0

#=GF AC   RF01429
#=GF ID   snoR130
#=GF DE   small nucleolar RNA snoR130
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   40.00
#=GF TC   41.80
#=GF NC   38.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AC013483.7/59930-60049 UCCCAGUGAUGAACAUUUUAGUAAUCUGGAACGGUGAUAAAAUGGGGCUCCCUCUUGG--AUUAUUUCCGUGGAGGUUUUAGAGGAACCAUUGUUGAAGAUACUUGGCAACUUCUGAGGGUC
AC189454.2/18228-18110 UCCCAGUGAUGAAAGUUUUAGCAAUCUGGAACGGUGAGAAAAUGGGACUCCCUCUUUGGAAAUUUUCCCAUGGUGGUUA---AGGAACCAUUGUUGUAGAUUCUUGGCAACUUCUGAGGGUU
#=GC SS_cons           :<<<______________________________________________________.._________________________________________________________>>>::
#=GC RF                UCCCAGUGAUGAAaaUUUUAGuAAUCUGGAACGGUGAuAAAAUGGGaCUCCCUCUUuG..AuUuUUuCCaUGGuGGUUuUAGAGGAACCAUUGUUGuAGAUuCUUGGCAACUUCUGAGGGUu
//
# STOCKHOLM 1.0

#=GF AC   RF01430
#=GF ID   snoR134
#=GF DE   small nucleolar RNA snoR134
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   40.00
#=GF TC   40.50
#=GF NC   35.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


DQ108711.1/84-227        UCGCAGGA-GC-C--UCCCGGGCUAGUCUGAUAACUAAGGUACUUGAGGAACUAAGCCCCAAAGCUCCUGCUAGAUUAUUUUUGCCGUUU-GUGUUGCAGAUUUGCCUUAU------UCCUUAGGCUUU-UCUGUGUCAAAAAAGCGGCUAUAUCU
AARH01005974.1/108-255   CUGCACGAUGC-C--UCCCAGGCUUCGCUGAUUACAAA--CCCCUGAGGUAGAAAGUCCCAAAGCUCGUGCUAAAGCAUC--UGCCGUUUAGUGUUGCAGUUUAGCCUUUUGUACCUUUCCACGGCUUU-UCUGUGUCAAAUCAACGGCUACAUCU
AC151806.21/724-586      ACGCACGUUGCAA--CCCCGGGCUUCUCUGAAAUUUAA-----AGGAAGU-GAAAGCCCCAUUGCACGUGCUAAAUUGAU---GCCAUUC-GUGUUGCAGU-UCAUCUCGU---UAAUUCCACGAUUGA-UCUGUGUCAAAGUAAUGGCUACAUCG
AP003829.2/18223-18074   AUGCACGGUGC-UAACCCCGGGCUUGUCGGAUUGGAAU--CCUCUGAAGAAUGAAGCCCCAAUGCCUGUGCUAGAUCCACCAUGCCAUUCAGUGUUGCAGG---UCAUGAUGCUUCGAGCUCGUGAUUGGUCUGUGUCAGCGUAAUGGAUACAUUU
AAAA02020760.1/6696-6547 UUGCACGGUGC-UAACCCCGGGCUUGUCGGAUUCAAAU--CGCCUGAAGAAGGAAGCCCCAAUGCCUGUGCUAGAUCCACAAUACCAUUCAGUGUUGCAGG---UCUUGAUGCUUCGAGCAUGUGAUUGAUCUGUGUCAGCGUAAUGGAUACAUUU
#=GC SS_cons             ::<<<<<<-<<.-..----<<<<<<<<<<_________.._______>>>->>->>>>>---->>>>>>>>------------<<<<<<<--<<-<<<<<<.--<<<________________>>>---.>>>>>>->>--->>>>>>>:::::::
#=GC RF                  uuGCAcGgUGC.u..cCCCGGGCUucuCcGAUuauaAa..caccuGAgGaAgaAAGCCCCAAuGCcCgUGCUAgAuuaauuaUgCCguUcAGUGUugCAGg.UugccUuaUGcuucauuCuuaggcUuu.cCUGugUCAaaggAacGGcUAcAUcu
//
# STOCKHOLM 1.0

#=GF AC   RF01431
#=GF ID   snoR135
#=GF DE   small nucleolar RNA snoR135
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   45.40
#=GF NC   44.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AK229744.1/602-742         AAUGCAGAGAUUGUGUGUAUCGGCUUAGUGCG---AU--GUAAUGCGCUUUG--UA--CGAAAGAUUUCUCUGCGACAUUAA----UU---U-GGGGCAGAUGGGCAGUUGUGAUUCAA---UGU--CAAUUG----AAUAGCUCAACAAUCAUCUUCCCCACAAUU
AASG02004941.1/7144-6992   UGAGCAGGGAUUGUGUGUAUCGGCGUUGUGCUUUAAU--AAUAUGCGCAUUGAAUC--CGAAAGUGUUCCCUGCAAUAUAAAAAAUUC---A-GGGGAAGAUGGGCAGUUGUGUUUCAAGUUUGC--CAUUGA----AAUUUCUCAACAAUCAUCUUCCCCAUAUUU
AARH01009459.1/70100-69949 UAAGCAGGGAUUGUGUGUAUCGGCGCUGUGCU---AUAAUAAAUGCACUCUGAAUC--CGAAAGAGUUCCCUGCUAUAUUGA----UUUCUU-UGGGAAGAUGGGCAGUUGUGUUUCAU---UCU--CUUUUGUUGAAACUUUUCAACAAUCAUCUUCCCUACAUCA
EF533698.1/29127-29267     AGAGCGGGGAUUGUGUGUAUCGGUGUUGUGCU---ACAAUCAAUGCACUCU---UC--CGAAAGAGUUCCCUGCAAUAUUGU----CU---U-GAGAAAG-UGGGCAGUUGUGUUUUCA---UCU--UUUGUU----GAAAUCACAACAAUCAUUUUCCCUACAUCU
AP006458.4/149212-149071   CCUGCAGG-AUAGUGUGUAUCGGCCUAAUGCC---UUAUGCUAUGCAUUUUU--UG-CCGAAAGUGUUUCCUGCUAUAUCAA----UU---A-GAGGAAAGUGGGCAGUUG-GGUUAAG---CUU--AUUCUG----UUUUCUCCAACAAUCAUUUUCCUCUCAUUA
FN596494.1/3010183-3010330 GAAGCAGGGAUUGUGUGUAUCGGCGUUGUGCU---ACAAUUGAUGCGCGAUG--AAGCCGAAAGAGUUCCCUGCAAUAAUGA----UC---GAGGGGAAGGUGGGCAGUUGGGUUUCAU---CUCUACCAUUG----AAAUUCUCAACAAUCAUCUUCCCCACNNNN
#=GC SS_cons               :::<<<<<<<----<<<<<<____________..._______>>>>>>----..--..--------->>>>>>>--------....--...-.<<<<<<<<<<<---<<<<________...___..______...._______>>>>-->>>>>>>>>>>::::::
#=GC RF                    uaaGCaGGGAUUGUGuGuAUCGGCgUuGUGCu...AuAauuaAUgCaCuuUg..Ua..CGAAAGaGUUCCCuGCaAUAUuaA....Uu...u.ggGGaAGaUGgGCAGUUGuGuUUcAa...uuu..cuuuUg....aAuuucuCAACAAuCAuCUuCCccACAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01432
#=GF ID   snoR143
#=GF DE   small nucleolar RNA snoR143
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.50
#=GF NC   49.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AC079041.4/65653-65823 UUGCACUAUGUAUCGAAGGCUA-UGUCAAAUUACAGUGACAUAGUC---UUUAAUGCAAAAGUGCAGAAAGAGAGAGCUG---UUAAAUCAGCAA--GCGGCCAGACAACCGUCGGGAUAGAUCCACAGGUGAAGCGGAUUGAUUCCUCUGCUUUCAGCUACUAAAUCUAUCCUACAUAC
AC146468.1/16214-16379 CACCAGAAAUCAGUUAGUCCUACUUUCAUUUUAUGAUGGUAGGGUG---UUAAA---ACUGGUGCACAAAGAAAGUACUG---CUCUUGAAGCAGUGGCGGCCAGACAACCGUUGAGAUAGAUCCACAGAUGAA---CAACCUUUCUGUUGCUUGU--CUACUAAUUCUAUCUCACAUUA
AP009260.1/55179-55007 CUGCAC-ACGCAUA-AAGGCUA-UGCUUAAAUUUAUUGAAAUAGUGGAGUCUUGAGCGCUAGUGCAAAGAUGGAAUGCUGAGUUUAAACUCAGCG--GCGGCCAGACAACCGUUGAGAUGAAUCCACAGAUGGGUUCCAUUUACAGUGGUACUUGU--CUACUAAUUUCAUCUCAUAAUU
#=GC SS_cons           :<<<<<--<<<-<<<<<<<<<<.<<<<<________>>>>>>>>>>...>>>>>->>>--->>>>>--------------...------------..-----------------<<<<<<<<---------<<<<<<<__________>>>>>>>-..-------->>>>>>>>::::::
#=GC RF                cuGCAcaAcGcAuuuaaggCua.UgucaaauUauaaugacAuaGuc...uuaaaagCgcuagUGCaaAaAgagAgugCUG...uUaaauuagcag..GCGGCCAGACAACCGUuGgGAUgGAUCCACAGaUgaagcgcAuuuauucuggcgcuugu..CUACUAAuUCcAUCcCAcAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01433
#=GF ID   snoR137
#=GF DE   small nucleolar RNA snoR137
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   44.00
#=GF TC   44.10
#=GF NC   42.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AP000601.1/8208-8353     AUUGCUUCAUAAUGGUGAACUCUCU-UAGAUUAUAAAA-AGUGAGAGAUGUUCAAGUUUCCGGAGCAAAUAUUAA-------AC----UGGCCAGAAUUUAACAGCUCUGUGUUUAAAUUUUACUAUUUUCACAGUGUUACCUGUCUUCUGGUAUAUUU
AC189573.1/101276-101421 UUUGCUUCAUAAUGGUGAACUCUCU-UAGAUUAUAAAAAAGUGAGAGAUGUUCAAGUUUCCGGAGCAAAGAUCAA-------UU----UGGCCAGAAUUAAACAGCUCUGUGUUUUUCUCUU-CAAUGUUCACAGUGUUACCUGUCUUCUGGUAUAUUC
AARH01004246.1/3409-3552 GUUGCUUCCUACUGGUGAACUCUCC-C---UUGUAAUU-AGUGGGAGAAAUUCAUGUUUCCGAAGCAUAAAUUAAUUGAUGUAA----UUACCAGUAUUAAACAGCACGGUGCUUUGUUUCCA------GCACCGUGUUACCUGUCUCCUGGUACAUCC
AM482223.2/10561-10415   GUUGCUUCUUACUGGUGAACUCCCUCUAGAUCAUAA-----UGAGGGAUGUUCAUGUUUCCGAAGCAUACACCAA-------UCAUCUUUGCCAGUAUUAAACAGCGCCUGGGUGCUUAUCCUUAUUCACCACCGCGCUACCUGUCUCCUGGUACAUUU
#=GC SS_cons             ::<<<<<<-------<<<<<<<<<<.____________.____>>>>>->>>>>------->>>>>>--------.......--....--<<<<<<<------<<<-<<<<<__________________>>>>>->>>------->>>>>>>::::::
#=GC RF                  gUuGCuuCaUAaUGGuGaacuCuCu.uAGAUuAUAAaa.AGUGaGaGauguuCauGUUUCCGaaGCauAaAuuAA.......uu....UugCCaGgaUUAAACagCuCgguGuUuuuuuUuuacaaUuuuCaccGuGcuACCUGUCucCuGGuAuAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01434
#=GF ID   S_pombe_snR3
#=GF DE   small nucleolar RNA snR3
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   100.00
#=GF TC   128.30
#=GF NC   33.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00040
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ632000.1/1-167         ACCGUACUCGCUCAAGACAGUGCGAAUAGGAAGGUUUUUUA-CCCGCAUGGUAUUUUGCUAUGCAUUCGUAUUUGCUAUUCACUGAGCGUAUAUAAAUGAAUGGAUCUUUUAAGAGCUUGCUAACAAGAUAACCUACUUGUACGCGAGUGUCAGAAGGUCCACAUAUU
AATM01000018.1/5521-5685 ACCGUACCUGCUCAAGACAGUGCUGGUGGUGCGACUGUAUAGUUGCUACAGCAUUCUGCUGUGGAUCGCCAUCUGCUAUUCACUGAGCGGAGACGAAU--AUGAGCUUAUUAAGAGCUUGCUGCCAAUUUUACCGU-UUGUUAGCGAGUGUCAGAUGGCUCAAACAUC
CU329671.1/884332-884166 ACCGUACUCGCUCAAGACAGUGCGAAUAGGAAGGUUUUUUA-CCCGCAUGGUAUUUUGCUAUGCAUUCGUAUUUGCUAUUCACUGAGCGUAUAUAAAUGAAUGGAUCUUUUAAGAGCUUGCUAACAAGAUAACCUACUUGUACGCGAGUGUCAGAAGGUCCACAUAUU
#=GC SS_cons             ::::::::<<<<<<-------<<<<<<<-<<<---------.---<<<<<<<_____>>>>>>>->>>->>>>>>>------->>>>>>-------------<<<<<<<<<----<<<<<<--<<<<<________>>>>>-->>>>>>--->>>>>>>>>:::::::
#=GC RF                  ACCGUACucGCuCaAGACAGUGCggaugGggaGguUuUuUA.cccgcacaGcAUUuUgCugugcAuccgcauccGCUAUUCACuGaGCguAuAuaAAUGAAUGggccuuuuAAGAgCuuGCUaaCaaGaUaACCuaCuuGuaaGCgaGuGUCagaaggccCAaAuAUu
//
# STOCKHOLM 1.0

#=GF AC   RF01435
#=GF ID   S_pombe_snR5
#=GF DE   small nucleolar RNA snR5
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   80.00
#=GF TC   97.90
#=GF NC   39.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00038
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ632001.1/1-143           GCCAAUGGUCUCUUUUACCAAUUGCAGUCUGGCUUAAAGCAAUGAGGUUGUAAUUAAAUGGCUUGAGACCUAAAACAAACACCUUUUACAAUCCUUGUUUACUGGUUUUGAUAGUAAAUUCGGUUCGCUUGUGGUGUACAUUU
CU329671.1/2266169-2266027 GCCAAUGGUCUCUUUUACCAAUUGCAGUCUGGCUUAAAGCAAUGAGGUUGUAAUUAAAUGGCUUGAGACCUAGAACAAACACCUUUUACAAUCCUUGUUUACUGGUUUUGAUAGUAAAUUCGGUUCGCUUGUGGUGUACAUUA
AATM01000018.1/43683-43544 GCUUCAGGUCUCUUUUACCAAUUGCAGUCUGGCCAAAGGCAAUGAGGUUGUAAUUAAAUGGCUUGAGACCGAAAACGAUCCUCCGUUCUAAUCCUGACCAUCGAAUUUAUA---AUGGUCCGGUUCGCUUAAGGAGAACAUCU
#=GC SS_cons               ::::::<<<<<<-------<<<<<<<--<<-<<<___>>>---->>-->>>>>>>--------->>>>>>--------<<<<<---------<<<-<<<<<<<<_______>>>>>>>>->>>--------->>>>>::::::
#=GC RF                    GCcaauGGuCuCUUUUACCaauugCaGUCuGGCcuAAgGCAAUGaGGUuGuaauuAAAUGGCUUGaGaCCuAaAACaAaCccCuuUUacAAUCCguaccuaCuggUUUugAcaGuagguucGGUUCGCUUguGggGuACAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01436
#=GF ID   S_pombe_snR33
#=GF DE   small nucleolar RNA snR33
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   80.00
#=GF TC   91.20
#=GF NC   41.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00027
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ632003.1/1-145           CUGCAACUGCAAAUGGAAUAUU-UGAAAACUUAUUCUAAUAUUCCUAUA---UUGCUACUUCAUCAUGAAGUUGUUGCUAUAAAAAUUACUCUAGUUUGAGGGAGGGAACCCAAAUCGUGGUUUCUUCCUAUAGAAUGAGUGUACAAUU
CU329671.1/2448048-2447904 CUGCAACUGCAAAUGGAAUAUU-UGAAAACUUAUUCUAAUAUUCCUAUA---UUGCUACUUCAUCAUGAAGUUGUUGCUAUAAAAAUUACUCUAGUUUGAGGGAGGGAACCCAAAUCGUGGUUUCUUCCUAUAGAAUGAGUGUACAAUU
AATM01000129.1/62247-62100 AUGCGACGACUCCAAGAACGUCUUUUGCCUUGACCGGGGCGUUCUCAGGAGGGGGGCUUUCUAGUCCUUGGUAGUUGCUAGAAUGAAUGCACUAGUUUGAGGGAGGGAGUCU-CUCCAUGGCUUUUUCCUAUAGAAUGUGUUAACAUCU
#=GC SS_cons               ::<<<<<-<<<<--<<<<<<<<.______________>>>>>>>>----...>>>>----------------->>>>>---------<<<<<--------<<<<<<<<<<<________>>>>>>>>>>>------->>>>>:::::::
#=GC RF                    aUGCaACugCacaugGAAcguc.UgaaaauUuAuucugacgUUCcuAua...guGcuauUuuAuuaugaaGUuGUuGCUAuAAaaAucaCuCUAGUUUGAgGGAgggAgcCuAaauCgUGgcUucuUCCuAUAGAAUGaGuguACAauU
//
# STOCKHOLM 1.0

#=GF AC   RF01437
#=GF ID   S_pombe_snR10
#=GF DE   small nucleolar RNA snR10
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   50.00
#=GF TC   58.40
#=GF NC   40.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00031
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


CU329672.1/992602-992436 GAACAACGCUUAUUAUAACAGUCAAAAUAAAAGUGCUGCGGAUUCAAAACUUGAUGCAGUAAUAUAAAAGAUAAUUUGAACUGAAGACUAAAUUUAUAAAAAGAGACGAUUGGGUGAGAUGGUUUUCUUUUUUUAUGAUAAUCAUCUCAAUAAUUGUCACUACAUGA
AJ632002.1/1-167         GAACAACGCUUAUUAUAACAGUCAAAAUAAAAGUGCUGCGGAUUCAAAACUUGAUGCAGUAAUAUAAAAGAUAAUUUGAACUGAAGACUAAAUUUAUAAAAAGAGACGAUUGGGUGAGAUGGUUUUCUUUUUUUAUGAUAAUCAUCUCAAUAAUUGUCACUACAUGA
#=GC SS_cons             ::::::::::::::::::<<<<<<<<-------<<<<<<<---<<<_____>>>>>>>>>>------------->>>>->>>>---------------------<<<<<<------<<<<<<<<-<<_________>>->>>>>>>>----->>>>>>:::::::::
#=GC RF                  GAACAACGCUUAUUAUAACaGuCaaaAUAAAAGugCuGCgGAUuCaAAACUuGauGCaGuaAUAUAAAAGAUAAuuuGAaCuGAAGACUAAAUUUAUAAAAAGAGaCgauUGGGUGaGauGguuUuCUUUUUUUAUGaUaauCauCuCAAUAauuGuCACUACAUGA
//
# STOCKHOLM 1.0

#=GF AC   RF01438
#=GF ID   S_pombe_snR35
#=GF DE   small nucleolar RNA snR35
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00028
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AJ632004.1/1-172           AUCGUGCGGUUAUA-UACCGACGCCCACAAUUCGUGUUGCUCAC-UUUUCUUUUUCUUUUUCCAUGGAAUGGUUUGAGCGUCAUACGUGGGCCAGAGCCAUAUUGGACAUCUUAGUGCCCUUACAGGAAUAGUCAUAUUGAUACUUUUUCUGUGGGUCGGUAGUUCAGAUAGCU
AATM01000008.1/26054-26225 AUCGUGCGGUUUUAAUACCGAACGCCCACUCUCGUGUUGCUCACCUUUUCGUAUAAAUGGUUGGAAGGUUUUUUCGAGCGUCAACUGUGGGCCAGAGGUACAU-GAACGUCUUAGCACCCUUACAGUUGGAGUCCCAUCU-CCCUUCUUCUGUGGGUCGGUUGUUCAGAUAUCU
AJ577641.1/1-172           AUCGUGCGGUUAUA-UACCGACGCCCACAAUUCGUGUUGCUCAC-UUUUCUUUUUCUUUUUCCAUGGAAUGGUUUGAGCGUCAUACGUGGGCCAGAGCCAUAUUGGACAUCUUAGUGCCCUUACAGGAAUAGUCAUAUUGAUACUUUUUCUGUGGGUCGGUAGUUCAGAUAGCU
CU329671.1/2411190-2411361 AUCGUGCGGUUAUA-UACCGACGCCCACAAUUCGUGUUGCUCAC-UUUUCUUUUUCUUUUUCCAUGGAAUGGUUUGAGCGUCAUACGUGGGCCAGAGCCAUAUUGGACAUCUUAGUGCCCUUACAGGAAUAGUCAUAUUGAUACUUUUUCUGUGGGUCGGUAGUUCAGAUAGCU
#=GC SS_cons               ::::::::::::::.:::::::<<<<<<----------<<<<<-.--<<<<______________>>>>----->>>>>------->>>>>>----------<<<<<<------------<<<<<<<<<-<<___________>>->>>>>>>>>------->>>>>>::::::
#=GC RF                    AUCGUGCGGUUaUA.UACCGAcgcCCacaauUCGUGUUGCuCaC.UUuuCcUuUucuUuuUccaugGaaUggUUuGaGCGUCAuacguGGgcCAGAGccAuAuuGgaCaUCUUAGugCCCuuaCaGgaguaGUCauAUugAuaCuUcucCuGuggGUCGGUaGuuCagAUAgCU
//
# STOCKHOLM 1.0

#=GF AC   RF01439
#=GF ID   S_pombe_snR36
#=GF DE   small nucleolar RNA snR36
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   50.00
#=GF TC   58.40
#=GF NC   43.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00035
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AJ632005.1/1-164           UCUGUCUCCAUCAAACUCUCCUUAUAUUUUUUUAUGAUGAGGAUUGAGUUGAGAUUAGCGAUAUUUAAUUGUAUGGCUAAUUAAAUGAGACUAUAAAAAUCUGAGAUGCCGUUGAGUACGACUACUUCAAGGUGGAGUGGUUGUAAUUUAGUGCAUGUACAUAU
CU329671.1/1957449-1957286 UCUGUCUCCAUCAAACUCUCCUUAUAUUUUUUUAUGAUGAGGAUUGAGUUGAGAUUAGCGAUAUUUAAUUGUAUGGCUAAUUAAAUGAGACUAUAAAAAUCUGAGAUGCCGUUGAGUACGACUACUUCAAGGUGGAGUGGUUGUAAUUUAGUGCAUGUACAUAU
#=GC SS_cons               ::::::::::<<<<-<<<<<<<<<<___________>>>>>>>-->>>>>>><<<<<<<-<<<<______>>>>->>>>>>>-----------------------<<<<<-------<<<<<<<<<<<_____>>>>>>>>>>>------>->>>>::::::::
#=GC RF                    UCUGUCUCCAuCaaACuCuCCuuauAUUUUUUUAUGaugaGGaUUGaGuuGagauuaGCGauauUUAAUUguauGGCuaauuAAAUGAGACUAUAAAAAUCUGAGauGCCGUUGAGUaCgaCuaCuuCAAGGUGgaGugGuuGuAAUUUAGUGCauGUACAUAU
//
# STOCKHOLM 1.0

#=GF AC   RF01440
#=GF ID   S_pombe_snR42
#=GF DE   small nucleolar RNA snR42
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   90.00
#=GF TC   142.70
#=GF NC   34.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.69 -Z 549862.597050 CM SEQDB
#=GF CL   CL00032
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Â§Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ632006.1/1-208           AUCUCACAA--AAUAAUGAAUUACUGAUGUCAAAAAGUCUGCUCUCUUCUAACGCGGUUAUAAUAUAGAACCGUAUUAAUGGUUGCAGCUUUUUCCUCUUCAUGGAAUCGGUAUAGAUUAUGUCGGGGAGACCGACAGCAUAGCUUAAAACCAUCGUGAAGUCGUUGCUUC-GUGCCAUGGCUCGUGAUGACCGAAUGCUACGUACAGUUU
AATM01000125.1/1699-1489   AUCUCACAAAAAAUAAAGUCGCCAUGGUGUCGUUCCAACAGUUGAGUUUGUAGGACAAAUUUGGUCCUGCAGUUCGUGCUGAUAUGGUCGACUUCCUCUUGUGAGGAGUGGCGCAGAUCAAGCUGGGUUGACCAGCGUCAUAGCUUAAAACCAUCGUGAAGUCGUUGCUUUUGCAGAAUGGCUCGUGAUGACCGAAUGCUUCGUACAUUUU
CU329671.1/1917406-1917613 AUCUCACAA--AAUAAUGAAUUACUGAUGUCAAAAAGUCUGCUCUCUUCUAACGCGGUUAUAAUAUAGAACCGUAUUAAUGGUUGCAGCUUUUUCCUCUUCAUGGAAUCGGUAUAGAUUAUGUCGGGGAGACCGACAGCAUAGCUUAAAACCAUCGUGAAGUCGUUGCUUC-GUGCCAUGGCUCGUGAUGACCGAAUGCUACGUACAGUUU
#=GC SS_cons               :::::::::..:::::::::::::::<<<<<---------<<<-<--<<----<<<<<<_________>>>>>>------>>-->->>>-------------------->>>>>-----------------------<<-<<<<-------<<<<<<<<-<<<<<-<<___.__>>->>>>>>>>>>>>>------->>>>->>:::::::
#=GC RF                    AUCUCACAA..AAUAAuGaauuaaUGguguCaaaaaguCuGcucccUucuaAcgcgguuaUaauauagaaccguauUaaUgaUugcagCuuuUUCCUCUUcaugGaAucGgcacAGAUuAuGucGGGgaGACCgaCagCAuAGCUUAAAACCAUCguGAAGuCgUUgcUUc.GugcaAuGgCUCguGAUGACCGAAUGCUaCGuACAgUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01441
#=GF ID   S_pombe_snR46
#=GF DE   small nulceolar RNA snR46
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   60.00
#=GF TC   67.30
#=GF NC   43.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00021
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AJ632007.1/1-168           CCUUGGCCUUAUCGAAGCUUAUCUAGCUGCAAUUUACCAGUUAGAAAAGUCAAAAAUAGGCCUACAAAAUUGGCAAAUGCCGGUAACGAUUAUUUUUGCUUUGUUUCGCGAAAUCUUUAGUGAACGAAAAUCAAGGCUUAUAAUACAUUUUUAGAAAGUUGCACAUUU
CU329672.1/1718087-1717920 CCUUGGCCUUAUCGAAGCUUAUCUAGCUGCAAUUUACCAGUUAGAAAAGUCAAAAAUAGGCCUACAAAAUUGGCAAAUGCCGGUAACGAUUAUUUUUGCUUUGUUUCGCGAAAUCUUUAGUGAACGAAAAUCAAGGCUUAUAAUACAUUUUUAGAAAGUUGCACAUUU
#=GC SS_cons               ::::<<<<<--------<<<-<<<<<<<<________>>>>>>>>->>>-------->>>>>--------------------<<<<<-<<<<<----<<<<<<<<<<<-----<<______>>->>>>>-->>>>>>-->>>>>------------->>>>>::::::
#=GC RF                    CCUUGGCCuUAUCGAAGCuuAuCuagCuGCAAUUUACCaGuuaGaAaaGUCAAAAAUaGGCCUACAAAAUUGGCAAAUGCCGGuaaCGauuauUUUUGCuuuGuuuCGCGAAAuCUUUAGUGaACGaaaAUCaagGCUUauaauACAUUUUUAGAAAGuugCACAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01442
#=GF ID   S_pombe_snR90
#=GF DE   small nucleolar RNA snR90
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   80.00
#=GF TC   102.40
#=GF NC   40.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ632008.1/1-158           UUUGCACUAUUAAUCAGAAAUAGUUCAC-AGUUUAUGAGCGUAUUUCCUUCAUGCAGUGCAUAGAAUAAUGUUUUCAUACUCACUUUACCCUCAGGUGCUUCAAACUAACUUAGUUUGAUUUUUCGUUGCCUGCGGGCCAUACAUGUAUGAUAUAUUUC
CU329670.1/4937394-4937237 UUUGCACUAUUAAUCAGAAAUAGUUCAC-AGUUUAUGAGCGUAUUUCCUUCAUGCAGUGCAUAGAAUAAUGUUUUCAUACUCACUUUACCCUCAGGUGCUUCAAACUAACUUAGUUUGAUUUUUCGUUGCCUGCGGGCCAUACAUGUAUGAUAUAUUUC
AATM01000116.1/1900-2048   UAUGCACU-GUAAUCAGAAGCAGUCCACUUGUUUAUGGGCUUGCUUCCUUCAUGAAGUGCAGAGAUUAC--UUGUCAUUCACACUUUACCCGUUCGAGUUGGCGA----UU---UCUUCGUCGUUGUUUCGUUCGAGUCAUACAUGUCUGAUACAUUUC
#=GC SS_cons               ::<<<<<<-------<<<<<<<<<<<<_.______>>>>>->>>>>>>------->>>>>>---------------------------<<<-<<<<<<<-<<<<<<<<___>>>>>>>>------>->>>>>>->>>::::::::::::::::::::::
#=GC RF                    UuuGCaCuAuUAAUCaGaagcaGucCaC.aGUUUAuGggCgugcuuCcUUCAUGcaGuGCauAGAaUAaUGUUuUCAUaCuCACUUUACcCucagGcgcUgcagaCuaAcUuaGucugcuUuuUcgUugCcugCGgGcCAUACAUGUaUGAUAuAUUUC
//
# STOCKHOLM 1.0

#=GF AC   RF01443
#=GF ID   S_pombe_snR91
#=GF DE   small nucleolar RNA snR91
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   50.00
#=GF TC   71.20
#=GF NC   41.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


CU329670.1/3316609-3316466 ACGUUGCACUGCUGUUUUAUUUAGUGUUUGUAGGUUUUUUUCAUCCCAAAGACUUUACGGAGCAGCAGGAGAUUGAAUGAAAACUAAAAGGCAGUGGCUUGUUUUACUUUAUGAAGUUUACUGUAAGAGAAGUUUCCCACAUAU
AJ632009.1/1-144           ACGUUGCACUGCUGUUUUAUUUAAUGUUUGUAGGUUUUUUUCAUCCCAAAGACUUUACGGAGCAGCAGGAGAUUGAAUGAAAACUAAAAGGCAGUGGCUUGUUUUACUUUAUGAAGUUUACUGUAAGAGAAGUUUCCCACAUAU
#=GC SS_cons               ::::::::<<<<<<<<<--<--<<<-<<<<--<<__________>>>>>>->>>-->-->>>>>>>>>----------------------<<<----------------<<_______>>->>>::::::::::::::::::::
#=GC RF                    ACGUUGCACuGCuGuuuUAuUUaguGuuuGUAGGUUUUUUUCAUCCCaaaGacuUUaCGgagCaGCaGGAGAUUGAAUGAAAACUAAAAGgCaGUGGCUUGUUUUACUUuaUGAAGUUuaCuGuAAGAGAAGUUUCCCACAUAU
//
# STOCKHOLM 1.0

#=GF AC   RF01444
#=GF ID   S_pombe_snR92
#=GF DE   small nucleolar RNA snR92
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   80.00
#=GF TC   84.30
#=GF NC   38.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ632010.1/1-144           AAUCCAAAUAUUUUGCCUGCCAGCACUC--CAUAAUUUAGUUUAC--GAGUGGUGGUAUACUGUAAUACUUGGUAUACAAAGAGUCGACUCCACCCUGGAUUAACUUUUCCUUAUGUAUAUUCAGGACUA-AAUCAACGACUGACAAAC
CU329671.1/2121215-2121358 AAUCCAAAUAUUUUGCCUGCCAGCACUC--CAUAAUUUAGUUUAC--GAGUGGUGGUAUACUGUAAUACUUGGUAUACAAAGAGUCGACUCCACCCUGGAUUAACUUUUCCUUAUGUAUAUUCAGGACUA-AAUCAACGACUGACAAAC
AATM01000031.1/35647-35502 AAACCAGGUAUU--GCCUGCCGGCGUAUCCUAGCUCCUCGGAGCGUUAGACGUCGGUAUACUUGUAUACCGGGGAGAAGAAGCGUCGUCUCCACCCUCGUGAGCUGCAUCC-CACAGCGCUUGAGGACUAUAAUCACCGACCUACACUU
#=GC SS_cons               :::<<<<-<<<<--<--<<<<<-<<<<<..--<<<______>>>-..>>>>>->>>>>-->--->>>>->>>>---------<<<<<-------<<<<<<<--<<__________>>-->>>>>>>----.------>>>>>:::::::
#=GC RF                    AAuCCagauauuUUGCCugCCgGCgcuc..uAgcauuUaGuugcc..gagcGgcGGuaUACUguaauaCcuGGuAuAaaAAGgGuCGaCUCCACCCuggaguaccuuuUCCUuAuggaucuucaGGACUA.AAUCAaCGaCcgACAaau
//
# STOCKHOLM 1.0

#=GF AC   RF01445
#=GF ID   S_pombe_snR94
#=GF DE   small nucleolar RNA snR94
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   100.00
#=GF TC   159.20
#=GF NC   37.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ632012.1/1-210           UUAUUGCAACCUUCUAAUAACUUUAC-AUCUUCUUAUCCAAAGAAGAAGGGUUAGAAUGUACCGUGUUUUACGGAAGUUCCAUUCCCGUAGGGUUACAAUGUGUUGCUAGAAUAAACCGUAAGUCAUAGUACAUAUAGAGGCCAAUUCUGUA-AACUUUUUUAAAGUC----UAUGGAAAACCCUCUAUGUGUCUCCAAUAGAGAACGGACAUCUC
CU329672.1/923877-924086   UUAUUGCAACCUUCUAAUAACUUUAC-AUCUUCUUAUCCAAAGAAGAAGGGUUAGAAUGUACCGUGUUUUACGGAAGUUCCAUUCCCGUAGGGUUACAAUGUGUUGCUAGAAUAAACCGUAAGUCAUAGUACAUAUAGAGGCCAAUUCUGUA-AACUUUUUUAAAGUC----UAUGGAAAACCCUCUAUGUGUCUCCAAUAGAGAACGGACAUCUC
AATM01000113.1/13066-12855 AGCCUGCAAC-UACUAAUAGCUUCGUGGUCGCUUCUUCCAAAGCGGCAGGAGUGUCUUGCGUUGCGUUUUGCGACGGGGGCAUAUCUGCGGAGUUACA-UUUGUUGCUAGAAUAAG-CGUGAAUCAUAGUACACCGAGGGUCCACAUCUUCGUGUUGCUGUUCGCAGCAAUAUUCGGAUAACCCUCUCGGUGUCUCC-AUUGAGCACAAACAUUUU
#=GC SS_cons               :::::<<<<<---------<<<<<<<.---------------------<<<---<<<<---<<<<<___>>>>>-->>>>---->>>>>>>>>>-------->>>>>---------<<<<----------<<<<<<<<<<<----<<<<<<<.-<<<<_____>>>>-....>>>>>>>--->>>>>>>>>>>------------>>>>:::::::
#=GC RF                    uuauUGCaaCCUuCUAAUAaCuucgc.aUCuuuUuaUCCAAAGaaGaAgGguUagcauGuaccGcgUUUugCggaagugcCAUucCcgcggaGuUACAAUgUGuuGCUAGAAUAAaCcGuaAgUCAUAGUaCaccgaGaGgCCAauuCugua.aacgcUuUUagcguC....uacgGaaAACcCuCucgguGuCUCCAAUaGAGaaCgGACAUuUu
//
# STOCKHOLM 1.0

#=GF AC   RF01446
#=GF ID   S_pombe_snR95
#=GF DE   small nucleolar RNA snR95
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   60.00
#=GF TC   80.40
#=GF NC   34.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AB004535.1/423-644     UUUAACAACCAUGUUCACUUUCCACUUGAGAAGACACAAAAAUUGUCUUGUCGCUUUAGGAUAAUGUGUUGACUCGCAGGAACUAGUUGCAAUGAACGGCGAUUAAAUUGGUCUGUUUUUUUGUUGGUUAAGCAUGGUAGAUAACGUUUGUUCAAACAAUAGCUUAAAGUGACAUGGUUUUGCCUAUGUUUAUGGUAAAAGCAUCGAUAGAGCUGUACAUUU
AB004534.1/35594-35815 UUUAACAACCAUGUUCACUUUCCACUUGAGAAGACACAAAAAUUGUCUUGUCGCUUUAGGAUAAUGUGUUGACUCGCAGGAACUAGUUGCAAUGAACGGCGAUUAAAUUGGUCUGUUUUUUUGUUGGUUAAGCAUGGUAGAUAACGUUUGUUCAAACAAUAGCUUAAAGUGACAUGGUUUUGCCUAUGUUUAUGGUAAAAGCAUCGAUAGAGCUGUACAUUU
#=GC SS_cons           ::::::::<<<<<<<------<<<<--<<<<<<<<-<<<-<<<<<<<<--<-<<-<<<<-----<<<<______>>>>---->>>>-->>->-->-->>>>>>>--->>>>>>>-->>>>-->->>>--->>>>>>>---------------------<<<<<<<----<<<--<<-<<<<<<<_________>>>>>>>->>>>>--->>>>>>>::::::
#=GC RF                UUUAACAACCauGcuCACUUUCCaCUUgagaaGaCACaaAaaucGcCuUGuCGCUcuaGGAUAAuGcGUUGACUCgCaGGAACuagUUGCAaUGaACGgCgauuAAAuuGGuCuGUucucUUGUuGGUUAagCauGGUAGAUAACGUUUGUUCAAACAacaGCucAAAGcGaCAuGGuuuugCCUAUGUUUAUGGcaaaaGCauCgAUAgaGCuguACAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01447
#=GF ID   S_pombe_snR98
#=GF DE   small nucleolar RNA snR98
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   40.00
#=GF TC   41.30
#=GF NC   33.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AJ632016.1/1-212           AUGCCACAUACAUAGCACGAUUGGAGGCUUUGGAAUUUGAGUCUCGGUGAAUCAAAGUUCUUUGGUCUUGUGAAUCCACGUGCAACUAAAAGGAGUGCUAACAGUGACUUUUGGUACGCUGUGUAUAUGCAGAAAAAGAUAUUAGACACCAAUUAAGCCGGGACGAAAGCCUAAUUGGAUUGCUUUCGUCUGACUAUGCGUGUUUUACAUUU
CU329670.1/2330647-2330436 AUGCCACAUACAUAGCACGAUUGGAGGCUUUGGAAUUUGAGUCUCGGUGAAUCAAAGUUCUUUGGUCUUGUGAAUCCACGUGCAACUAAAAGGAGUGCUAACAGUGACUUUUGGUACGCUGUGUAUAUGCAGAAAAAGAUAUUAGACACCAAUUAAGCCGGGACGAAAGCCUAAUUGGAUUGCUUUCGUCUGACUAUGCGUGUUUUACAUUC
#=GC SS_cons               :(((---(((((((((---((--(((((-(((,,,<<<<<-<<_____>>->>>>>,<<<<<<<<<__________________>>>->>>>>>,,,,,,,)))-)-))))--))--)))))))))--)))------------<<<<<<<<----<<-<<<-<<<<<<<<___________>>>>>>>>>>>->>->>->>>>>>:::::::
#=GC RF                    AuGCCACauaCacaGCACGacUGgagGCUcuGGAAuuuGaGuCUCGGUGaAuCaaaGucCuuugGuCUUGUGAAUCCACGUGCAaCcAaaaGgaGUGCUAACagUGACcucUGguACGCuguGuauAUGCaGAAAAAGAUAUUagaCaCCaAUUAaGCCgGGaCGaaaGCCUAAUUGGAUUGCuuuCGuCcGACuAuGCGuGucuUACAUUu
//
# STOCKHOLM 1.0

#=GF AC   RF01448
#=GF ID   S_pombe_snR93
#=GF DE   small nucleolar RNA snR93
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   46.00
#=GF NC   40.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


CU329671.1/3172781-3172923 UUGCACUUUUUAACAAAAUUACCCGUGAGAUUAAUUGCGGUUGAACUUGUUUUUCGUGCUAGACUGAUGAUUCGCCCUUAUACAUAUUGGCUAACUUUCGGCUAAUCUUCACCGAAUUUAGUCAAGAAUUGGGUGGUACAAAU
AJ632011.1/1-143           UUGCACUUUUUAACAAAAUUACCCGUGAGAUUAAUUGCGGUUGAACUUGUUUUUCGUGCUAGACUGAUGAUUCGCCCUUAUACAUAUUGGCUAACUUUCGGCUAAUCUUCACCGAAUUUAGUCAAGAAUUGGGUGGUACAAAU
#=GC SS_cons               ::<<<<-----<<<<<--<<<-<<<--<______>-->>>->>>-->>>>>---->>>>------------<<<<<<-----------<<<<<<--<<<<<__________>>>>>->>>>>>------->>>>>>:::::::
#=GC RF                    UUGCaCUUUUUaaCaaAAuuaCCCGUGaGAUUAAuUGCGGUugaACuuGuuUUUCGuGCUAGACUGAUGAUuCgCCCUUAUACAUAUUGgCuaaCUuuCGGCUAAUCUUCACCGaaUuuaGuCAAGAAUUGGGuGgUACAAAU
//
# STOCKHOLM 1.0

#=GF AC   RF01449
#=GF ID   S_pombe_snR100
#=GF DE   small nucleolar RNA snR100
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   80.00
#=GF TC   99.50
#=GF NC   55.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


CU329671.1/3393616-3393802   UUUCUCCUCUUUCUGCCUAUCUGUUGUUCAUAAUCAACUGCGUAGUUCUGGUGAAGGAGUAAAUUAAACUGCC-----UCGCACCGCCGUACUCAUUUUUACCUCGAGUAUGGUGGCCGUGGAAUGGUGGUUUUUUAUGCAGUCGGGAAUGAAAGC-AGCUGUAAUUUCCUUGCAUAAUGAGCCUAAAUACCU
AATM01000023.1/268758-268938 UCUCUCCUCUUUCUGCCUGCCUGUUGUCCUUGAUCAGCUGAGCAGUUCUGGUGUAGGAGAAGAAUUAGCAGCCAUCCUUGUUCGUACCUUACCUCAUAUUAGCGAGCAGG-GGU------GGACCGU-----GUCUGCCGAGGCUCUUGGGGCUGUCUGUUCGUUGACUUCCUCUGGCUGCGGUUGACUACAA
AJ577640.1/1-187             UUUCUCCUCUUUCUGCCUAUCUGUUGUUCAUAAUCAACUGCGUAGUUCUGGUGAAGGAGUAAAUUAAACUGCC-----UCGCACCGCCGUACUCAUUUUUACCUCGAGUAUGGUGGCCGUGGAAUGGUGGUUUUUUAUGCAGUCGGGAAUGAAAGC-AGCUGUAAUUUCCUUGCAUAAUGAGCCUAAAUACCU
#=GC SS_cons                 <<<<<<<<---<<---<<<<--<<<<________>>>>--->>>>---->>--->>>>>->>>,,,,,,,<<<.....<<<<-<<<<<<<<<<<___________>>>>>>>>>>>-->>>>--->>><<<<<-<<<<<<<<--<<<<<<---<<_.__>>--->>>>>>>>>>>>>>->>>>>:::::::::
#=GC RF                      ucuCuCCuCUUuCUGCCugcCUGuuGUuCaUaAUCaaCUGagcaGUUCUGgUGaaGGaGuagauUaAaCugcC.....ucgCaCCaCCguacucauUuUUAcCuagaguacGGuGGCCGcggAauGgcGGcucUuuaugcaguCgggaauGaaagu.aGcuguaauuccccugcauaaUgagCCUaAaUACau
//
# STOCKHOLM 1.0

#=GF AC   RF01450
#=GF ID   S_pombe_snR96
#=GF DE   small nucleolar RNA snR96
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   100.00
#=GF TC   274.30
#=GF NC   33.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AJ632014.1/1-211           GCGGAAUCGUCAGCACUCGUUAAACAGGGAGUAAGAGGGAGUAAUAGAGUUGCCUGCAAGAGAAAACCUAGUUCAAACCUGCGAAAUUUGACGUGCAGUCAGUAGACGACGACCUGGCUGUAAACUAGCAUUUUUUACGAUUAAUUAGAAAGGUUAUUUGCUUUUUGAUUAAAUACGGAGAGUUUGGAUAACACAAGGGAUCGAAACAUUU
CU329670.1/1451437-1451227 GCGGAAUCGUCAGCACUCGUUAAACAGGGAGUAAGAGGGAGUAAUAGAGUUGCCUGCAAGAGUAAACCUAGUUCAAACCUGCGAAAUUUGACGUGCAGUCAGUAGACGACGACCUGGCUGUAAACUAGCAUUUUUUACGAUUAAUUAGAAAGGUUAUUUGCUUUUUGAUUAAAUACGGAGAGUUUGGAUAACACAAGGGAUCGAAACAUUU
#=GC SS_cons               <<<----<<<<<<---<<<-----<<<<-------<<<-<<________>>->>>---------------------->>>>>>>--->>>>>>>>>----------------<<<---<<<---<<<<-<<<<<<<----<<<<<<<<<<<<________>>>>>>>>>>>>---->>>>>>>>>>>--->>>--->>>::::::::::::
#=GC RF                    GCgGAAUCGuCagCACuCGUUAAACaGGGAGUAAGaGGGagUAAUAGAGuuGCCuGCAAGAGaAAACCUAGUUCAAACCuGCGaAAUuuGaCGuGCAGUCAGUAGACGACGACCuGGCuGuAAACuagCauuuuuuACGAuuaauuagaaaGGUUAUUUGCuuuuugauuaaAUACggagaguuugGAUAaCaCAAgGGAUCGAAACAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01451
#=GF ID   S_pombe_snR97
#=GF DE   small nucleolar RNA snR97
#=GF AU   Osuch I
#=GF SE   INFERNL
#=GF SS   Predicted; RNAalifold; Osuch I
#=GF GA   100.00
#=GF TC   192.80
#=GF NC   37.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ632015.1/1-148         AGGGUAAACUGUCGUUCCUUAAUACUUUUGUUACUUAUGCACCGAAUUCGACUAUUUCGCAUUCAUUAGUGAUAGACGUGAAUCAACAAAUCCAAGGGGUGUAGAUAGUUUAUAAUUUAUCUUGUAACGCAGUUUGUUUAUCACAUAC
X74615.1/3847-3701       AGGGUAAACUGUCGUUCCUUAAUACUUUUGUUACUUAUGCACCGAAUUCGACUAUUUCGCAUUCAUUAGUGAUAGACGUGAAUCAACAAAUCCAAGGGGUGUAGAUAGUUUAUAAUUUAUCUUGUAACGCAGUUUG-UUAUCACAUAC
CU329670.1/170709-170856 AGGGUAAACUGUCGUUCCUUAAUACUUUUGUUACUUAUGCACCGAAUUCGACUAUUUCGCAUUCAUUAGUGAUAGACGUGAAUCAACAAAUCCAAGGGGUGUAGAUAGUUUAUAAUUUAUCUUGUAACGCAGUUUGUUUAUCACAUAC
#=GC SS_cons             ::::::::::::::::::::::<<<-<<<<<<<<<-<<<<__________________>>>>----->>>>>>>>>->>>------------------<<<<<<<<<<________>>>>>>---->>>>::::::::::::::::::
#=GC RF                  AGGGUAAACUGUCGUUCCUUAAuaCUuuuguuaCuUauGCACCGAAUUCGACUAUUUCGCauUCAUUaGugauagaCGugAAUCAACAAAUCCAAGGGGuGuaGauagUUUAUAAUuuauCuUGUAaCgCAGUUUGUUUAUCACAUAC
//
# STOCKHOLM 1.0

#=GF AC   RF01452
#=GF ID   S_pombe_snR99
#=GF DE   small nucleolar RNA snR99
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   90.00
#=GF TC   167.60
#=GF NC   46.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15716270
#=GF RT   Identification and functional analysis of 20 Box H/ACA small nucleolar
#=GF RT   RNAs (snoRNAs) from Schizosaccharomyces pombe.
#=GF RA   Li SG, Zhou H, Luo YP, Zhang P, Qu LH
#=GF RL   J Biol Chem. 2005;280:16446-16455.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AATM01000002.1/50041-50225 CCAUCAUCAGUAGUGGUUUUAACUUACUUUGUUAUACAAGUAA-UUAAAAUCUAUCCCGGGGUCAAGUAUGAUGAUUGGAGCCGAAUGGCCUAGAAAAUGCAUCCGUUCCGUCCUCGGAGAU-GAUUGAGUAGCUGUCCCGGUCGGUGUCUCAGGU----GGGACAUUGUUGGG-UUGUUGUUCGCACAUAA
AATM01000025.1/2059-2243   CCAUCAUCAGUAGUGGUUUUAACUUACUUUGUUAUACAAGUAA-UUAAAAUCUAUCCCGGGGUCAAGUAUGAUGAUUGGAGCCGAAUGGCCUAGAAAAUGCAUCCGUUCCGUCCUCGGAGAU-GAUUGAGUAGCUGUCCCGGUCGGUGUCUCAGGU----GGGACAUUGUUGGG-UUGUUGUUCGCACAUAA
AJ577639.1/1-190           CCAUCAUCAGUA--GGUUUUAACUUACUUUGUUAUAUAAGUAAAGUAAAAUCAAUCCUGAAGUCAAGUAUGAUGGUUGGAGUCUCCGGACCAAGAAAAUGCAUCCGUUCCGUCUUCAGCGAAGAAUUGAGUGGCUUUCCCGGUCGUUGACUUUUUUCCAUGGGUCAAGGAUGGGAUUGUCUCCCAGACAUUU
AATM01000007.1/38232-38049 CCAUCAUCAGUAGCGGUUUUAACUUACUUUGUUAUAUAAGUAA-UUAAAAUCAAA-CUGUGGUCAAGUAUGAUGAUCGGAGCCGAAUGGCUUAGAAGAUGCAUCCGUUCCGUCCACAGAGAU-GACUGAGUAGCUGUCCCGGUCGACGUCUCAGGU----GGGACGUUGUUGGG-UUGUUGCUCGUACAUUU
AJ632017.1/1-190           CCAUCAUCAGUA--GGUUUUAACUUACUUUGUUAUAUAAGUAAAGUAAAAUCAAUCCUGAAGUCAAGUAUGAUGGUUGGAGUCUCCGGACCAAGAAAAUGCAUCCGUUCCGUCUUCAGCGAAAAAUUGAGUGGCUUUCCCGGUCGUUGACUUUUUUCCAUGGGUCAAGGAUGGGAUUGUCUCCCAGACAUUU
#=GC SS_cons               ::::::::::::::<<<<<<<<-<<<<<<________>>>>>>.>>>>>>>>,,,,<<<<<<-<------<<<<<<<---<<<____>>>------>>>->>>>------>->>>>>>----.------<<<<<---<<<<<-<<<<<<<<<____....>>>>>>>>>>>>>>.-->>>>>::::::::::
#=GC RF                    CCAUCAUCAGUAGuGguuuuaaCuuaCuuUGUUAUAuaaGuaa.uuaaaauCaAuCCcGggGUCAAGUAUGauGauuGGAGcCgaauGgCcuAGAAaauGCauCCGUUCCGUCccCgGaGAu.gAuUGAgcggCUgUCCCggUCgguGuCucaggU....ggGaCaccGcuGGG.UUGucgcuCguACAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01453
#=GF ID   RCNMV_TE_DR1
#=GF DE   3'TE-DR1 translation enhancer element
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:19577782
#=GF GA   80.00
#=GF TC   160.30
#=GF NC   60.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045975; positive regulation of translation, ncRNA-mediated;
#=GF RN   [1]
#=GF RM   17704138
#=GF RT   Hairpin structure within the 3'UTR of DNA polymerase beta mRNA acts as a
#=GF RT   post-transcriptional regulatory element and interacts with Hax-1.
#=GF RA   Sarnowska E, Grzybowska EA, Sobczak K, Konopinski R, Wilczynska A, Szwarc
#=GF RA   M, Sarnowski TJ, Krzyzosiak WJ, Siedlecki JA
#=GF RL   Nucleic Acids Res. 2007;35:5499-5510.
#=GF WK   Red_clover_necrotic_mosaic_virus_translation_enhancer_elements
#=GF SQ   3


AB034916.1/3596-3733 GAACUGGCAUCGGACCCUGGGAAACAGGCAUCUAGCGUAUUAAUAGGUCGCUAGAAGACGGGCAGGCUUCACCACUAGGUAACCUGCCGCCGAGAGGGAAAACCUCUGUGUGGUUGUGCGCACGUCGUUGUCGGAAGA
J04357.1/3596-3733   GAACCGGCAUCGGACCCUGGGAAACAGGUACCUAGCGUAUUAAUAGGUCGCUAGAAAUCGGGCGGGCUUCACCUUCGGGUAACCCGCCGUCGAGAGGGAAAACCUCUGUGUGGUUGUGCGCACGUCGUUGUCGGAAGA
L07884.1/3580-3717   GAACCGGUCUCGGACCCUGGUAAACAGGUACCUAGCGUAAUAGAAGGUCGCUAGAAAUCGGGUGGGCUUCACCUACGGGUAACCCACCGUCGAGAGGGAAAACCUCUGUGUGGUUGUGCGCACGUCGUUUCCUGAAGA
#=GC SS_cons         :::((((((-(((,,<<<<_____>>>>,,,<<<<<<-<<<____>>>>>>>>>,,,,,,<<<<<<-<<-<<<____>>>>>>>>>>>,,,,<<<<<_____>>>>><<<<<______>>>>>,)))-))))))::::
#=GC RF              GAACcGgcaUCGgACCCuGGgAAACaGGuAcCuaGCGUaccAauAgguCGCuaGAAauCGGGcgGGCuuCaCCuucgGGuaaCCcgCCGuCGaGaGGGAAAACCuCuGuGcGGUUGUGCgCaCGcCGUugcCgGAAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01454
#=GF ID   RCNMV_5UTR
#=GF DE   5'UTR enhancer element
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:19577782
#=GF GA   75.00
#=GF TC   136.00
#=GF NC   40.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045975; positive regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0043487; regulation of RNA stability;
#=GF RN   [1]
#=GF RM   19577782
#=GF RT   Host-dependent roles of the viral 5' untranslated region (UTR) in RNA
#=GF RT   stabilization and cap-independent translational enhancement mediated by
#=GF RT   the 3' UTR of Red clover necrotic mosaic virus RNA1.
#=GF RA   Sarawaneeyaruk S, Iwakawa HO, Mizumoto H, Murakami H, Kaido M, Mise K,
#=GF RA   Okuno T
#=GF RL   Virology. 2009 Aug; 391:(1)107-18
#=GF WK   Red_clover_necrotic_mosaic_virus_translation_enhancer_elements
#=GF SQ   3


L07884.1/1-120   U--AAACGUUUCACCGGUUUGUAAAUUGGAACUUCGUAGUUCGCCAGACGCCUUCUUCGUAUCAAGGAACUGGAAAUUGUACGGUGAGUCUGUCAUUUU-AUUUUCUACUUUUCGUACCAGUC
J04357.1/1-123   GACAAACGUUUUACCGGUUUGUAAAUAGGAGCACACAAGCUCGCUAGUCGCCCCCUUCGUAUCGGGGAUCUAGAGAUUAAACGGUAUACCUGUCAUUUUAAAUUUCUACUUUUCGUACCAGUC
AB034916.1/2-123 AACAAACGUUUUACCGGUUUGUAAAUUGGAAUUCUCGAAUUCGCCAGUCGCCUUCUUCGUAUCAAGGAUCUGGAAUUUGAACGGUAUCUUUAUCAUUUUAA-UUUCUACUUUUCGUACCAGUC
#=GC SS_cons     :<<<<<<_________>>>>>>,,,,,,<<<<______>>>>,<<<<---<<<<_________>>>>-->>>>---------<<<<<___________________________>>>>>::::
#=GC RF          aaCaaaCGUUUuACCGGuuuGuAAAUuGGagcucucaAgcuCGCcaGuCGCCccCUUCGUAUCggGGAuCugGAaaUUgaACGGuacaucUgUCAUUUUAAaUUUCUACUUUUCguaCCAGUC
//
# STOCKHOLM 1.0

#=GF AC   RF01455
#=GF ID   DPB
#=GF DE   Stem loopII regulatory element in POLB
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:17704138
#=GF GA   40.00
#=GF TC   41.00
#=GF NC   39.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0043487; regulation of RNA stability;
#=GF RN   [1]
#=GF RM   17704138
#=GF RT   Hairpin structure within the 3'UTR of DNA polymerase beta mRNA acts as a
#=GF RT   post-transcriptional regulatory element and interacts with Hax-1.
#=GF RA   Sarnowska E, Grzybowska EA, Sobczak K, Konopinski R, Wilczynska A, Szwarc
#=GF RA   M, Sarnowski TJ, Krzyzosiak WJ, Siedlecki JA
#=GF RL   Nucleic Acids Res. 2007;35:5499-5510.
#=GF WK   DNA_polymerase_beta
#=GF SQ   19


U38801.1/1036-1118         AUCCCACGAGGAGUCCUAAGUUAUUGCUUAACCUUUGCUAUGUAAGGGU--UGGGUG-UUUUAGGUGAUUGCCUCUUCUCUGUGCU
AC121835.2/151904-151989   AGCCCACUAGGAGUCCUAAUUUAUUUCUUAACCUUUGCUAUGUAAGGGUUUUUGGUGUUCUUAAGCGAUUGCUUCUUCUCUGUGCU
AANU01283619.1/6362-6277   AGCACAAUAGGAGUCUUAAUUUAUUUCUUAACCUUUGCUAUGUAAGGGUCUUUAGUGUUUUUAAAUGAUUGUUUCUUCUUCAUGCU
AF170802.6/30029-30114     AACCCAAUAGGAGUCUUAAUUUAUUUCUUAACCUUUGCUAUGUAAGGGUCUUUGGUGUUUUUAAAUGAUUGUUUCUUCUUCAUGCU
AAQQ01568546.1/667-582     AGCCCAAUAGGAGUCUUAAUUUAUUUCUUAACCUUUGCUAUGUAAGGGUCUUUGGUGUUUUUAAGUGAUUAUUUCUUCCCCAUGCU
AALT01363025.1/2640-2555   AGUCUGACAGGAGUCUUAAUUUAUUUCAUAAUCUUUACUGUGUAAGAGUCUUUGGAGUUUUUAAAUGAUUGCUUCUUCUUUACACA
AAYZ01133158.1/2444-2522   AG-CUGCCAGGAGUCUUAAUUUAUUCUGUAACCUUUGCUAUGUAAGGGUCUUUGGUG-UUUUAA-----UGACUGUUCUUUGUGCC
AACN010053099.1/2272-2187  AACUCAAUAGGAGUCUUAACUUAUUUCUUAACCUUUGCUAUGUAAGAGUCCCUGGUGUUUUUAAAUGAUUGUUUCUUCUUCUUGCU
AAPY01594407.1/10031-9946  AGUCCAAUAGGAGUCUUAAUUUAUUUCUUAACCUUUGCUACGUGAGGGUCUUGGGUGUUUUUAAAUCAUUGCUUCUUCUCAGGCGU
AANG01634187.1/5136-5051   AGCUCAACAGGAAUCUUGAUUUCCUUCUUAACCUUUGGUAUGUAAGGGUCUCUGGUGUUUUUAAAUGAUUGUUUCUUCUUCAUGCU
AANN01298359.1/1432-1348   ACAUAAAGAGGAGUCUUAAUUUAUUUCUUAACCUUUGCUAUGUAAGGGUCUUUGGUGUUUUUAA-UGAUUGCCUCUUCAUCCUUUA
AAFC03113714.1/4641-4726   AGCCCAAUCAGAGUCUUAAUUUAUUUCUUAAGCUUUGCUAUGUAAGGGUCUGUGGUGUUUUUAAGUAACUAUUUCUUCUUCAUGCC
AAGV020302119.1/560-475    AGCCCACGAGGAGUCUUAAUUUAUUUCUUAACCUUUGCUAUGUAAGGGUCUUUGGUGUUUUUAAAUAAUUGUUUCUUCUUCAUGCU
AAWR02023945.1/6081-5996   AGCCCCACAGGAGUCUUAAUUUAUUUCUUAACCUUUGCUAUGUAAGGGUCUUUGGUGUUUUCAAGUGGUUGUUUCUUCUUCAUGCU
AAGW02061658.1/6674-6589   ACAGCGCCAGGCGUCUUAAUUUAUUCCGUAACCUUUGCUAUGUAAGGGUCUUUGGUGUUUUUAAGUGACUGUUUCUUCUUCAUGCC
AAQR03169303.1/16906-16821 UGCCCACUAGAAAUCUUAAUUUAUUUCUUAACCUUUGCUAUGUAAGGGUCUUUGGUGUUUUUAAAUGAUUGUUUCUUCUUCAUGCU
AAGU03045098.1/8743-8658   AGCCCAGCAGGAGUCUUAAUUUAUUUCCUAACCUUUGCUAUGUAAGGGUCUUUAGUGUUUUUAAAUAAUUGUUUCUUCCUCAUGCU
AB050421.1/1721-1806       AGCACAAUAGGAGUCUUAAUUUAUUUCUUAACCUUUGCUAUGUAAGGGUCUUUAGUGUUUUUAAAUGAUUGUUUCUUCUUCAUGCU
AF491812.1/34307-34392     AACCCAAUAGGAGUCUUAAUUUAUUUCUUAACCUUUGCUAUGUAAGGGUCUUUGGUGUUUUUAAAUGAUUGUUUCUUCUUCAUGCU
#=GC SS_cons               ::::::::<<<<---<<<<-----<<----<<<<<<<<___>>>>>>>>---->>----->>>>----------->>>>:::::::
#=GC RF                    AgcccAauaGgAGUCuUaAUUUAUucCuUAACCuUUgCUAUGuAAgGGUCUUUggUGUUUUuAaaUgAUUGuUUCUuCuUcaUgCu
//
# STOCKHOLM 1.0

#=GF AC   RF01456
#=GF ID   VrrA
#=GF DE   Vibrio regulatory RNA of OmpA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:18681937
#=GF GA   50.00
#=GF TC   54.80
#=GF NC   42.50
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   19411843
#=GF RT   A novel sRNA that modulates virulence and environmental fitness of Vibrio
#=GF RT   cholerae.
#=GF RA   Song T, Wai SN
#=GF RL   RNA Biol. 2009;6:254-258.
#=GF RN   [2]
#=GF RM   25826569
#=GF RT   The VrrA sRNA controls a stationary phase survival factor Vrp of Vibrio
#=GF RT   cholerae.
#=GF RA   Sabharwal D, Song T, Papenfort K, Wai SN
#=GF RL   RNA Biol. 2015;12:186-196.
#=GF WK   Vibrio_regulatory_RNA_of_OmpA
#=GF SQ   11


AAWD01000052.1/15594-15733 GUGAUUGACAGAGCUUUGAGA-GUUUUACUGGCCGUCAAAUUUGGUUCUCGACCCGCUGUCACCAAUUACGCUGCUUUUUCCUUUUUAUUAACUCCUAUACUUGUGUACGCCCAAAGCCAGAUUGUUUUGGGCGUUUUUUU
AAND01000032.1/6374-6503   AG--AAAACAGAGUAUUUAGAUGUUUAACAGGCCGUCAAACUUGUUUCU-----CACUGUUUUCUUAAUUACUGCAUUUUCCU---UAUUAACUCCUAUACUUGUAUCCGCCCAAACCGCG-UUGGUUUGGGCUUUUUUUU
AAWG01000002.1/43318-43457 GUGAUUGACAGAGCUUUGAGA-GUUUUACUGGCCGUCAAAUUUGGUUCUCGACCCGCUGUCACCAAUUACGCUGCUUUUUCCUUUUUAUUAACUCCUAUACUUGUGUACGCCCAAAACCAGAUUGUUUUGGGCGUUUUUUU
AAUU01000047.1/9439-9300   GUGAUUGACAGAGCUUUGAGA-GUUUUACUGGCCGUCAAAUUUGGUUCUCGACCCGCUGUCACCAAUUACGCUGCUUUUUCCUUUUUAUUAACUCCUAUACUUGUGUACGCCCAAAACCAAAUUGUUUUGGGCGUUUUUUU
AATY01000002.1/96360-96221 GUGAUUGACAGAGCUUUGAGA-GUUUUACUGGCCGUCAAAUUUGGUUCUCGACCCGCUGUCACCAAUUACGCUGCUUUUUCCUUUUUAUUAACUCCUAUACUUGUGUACGCCCAAAAUCAGAUUGUUUUGGGCGUUUUUUU
AAUR01000002.1/90151-90289 GUGAUUGACAGAGCUUUGAGA-GUUUUACUGGCCGUCAAAUUUGGUUCUCGACCCGCUGUCACCAAUUACGCUGC-UUUUCCUUUUUAUUAACUCCUAUACUUGUGUACGCCCAAAACCAGAUUGUUUUGGGCGUUUUUUU
AAMR01000052.1/22638-22507 AG--AAAACAGAGUAUUUAGAAGUUUAACAGGCCGUCAAACUUGUUUCU---CUCCCUGCUUUCUUAAUUACUGCAUUUUCCU---UAUUAACUCCUAUACUUGUAUCCGCCCAAACCGCA-UUGGUUUGGGCUUUUUUUU
AAWF01000029.1/20514-20653 GUGAUUGACAGAGCUUUGAGA-GUUUUACUGGCCGUCAAAUUUGGUUCUCGACCCGCUGUCACCAAUUACGCUGCUUUUUCCUUUUUAUUAACUCCUAUACUUGUGUACGCCCAAAACCAGAUUGUUUUGGGCGUUUUUUU
D28504.1/1588-1457         GUAACAACUAGGGCAUUUAAA-GUUUCACUGGCCGUCAAACUUGUUU-----CAAUCUAAUU---GUUACGUUGCUGCUUUUUUCUUAUUAACUCCUAUGUUUGUAUCCGCCCAGUCAACUUUUCGGCUGGGCUUUUUUUC
AAKI02000049.1/13797-13936 GUGAUUGACAGAGCUUUGAGA-GUUUUACUGGCCGUCAAAUUUGGUUCUCGACCCGCUGUCACCAAUUACGCUGCUUUUUCCUUUUUAUUAACUCCUAUACUUGUGUACGCCCAAAACCAGAUUGUUUUGGGCGUUUUUUU
CP001485.1/1788549-1788410 GUGAUUGACAGAGCUUUGAGA-GUUUUACUGGCCGUCAAAUUUGGUUCUCGACCCGCUGUCACCAAUUACGCUGCUUUUUCCUUUUUAUUAACUCCUAUACUUGUGUACGCCCAAAGCCAGAUUGUUUUGGGCGUUUUUUU
#=GC SS_cons               <<<<<<<<<<<----<<<<<<.---------<<<<_______>>>>>>>>>>---->>>>>>--->>>>>-------------------------------------<<<<<<<<<<<______>>>>>>>>>>>::::::
#=GC RF                    GugauugacaGAGcuucGaGa.GUUUuACuGgcCgUCAAAuUuGguuCuCgaCccgCugucacCaaucaCgcUGCuuUUUccUUuUUAUUAACUCCUAUAcUUGUgUacGCCCaaacccagaUUgguuuGGGCguUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01457
#=GF ID   rli22
#=GF DE   Listeria sRNA rli22
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   116.90
#=GF NC   41.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00114
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0045947; negative regulation of translational initiation;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF RN   [2]
#=GF RM   27400116
#=GF RT   Two novel members of the LhrC family of small RNAs in Listeria
#=GF RT   monocytogenes with overlapping regulatory functions but distinctive
#=GF RT   expression profiles.
#=GF RA   Mollerup MS, Ross JA, Helfer AC, Meistrup K, Romby P, Kallipolitis BH
#=GF RL   RNA Biol. 2016;13:895-915.
#=GF CC   The UCCC motifs prevent ribosomal binding to oppA mRNA. 
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   6


AL591973.1/31997-32107       UAAUAUAGAACUUGUAAGCAAGGAAUACAAUUAGUUUUACUCCCUUUUUGCUAAUUGUAAACUUCCUUAAAAUCCUAAACUCCCUUUUUUGGACCGACUUGAUUGUCGGUC
AM263198.1/32814-32923       UAAUAUAGAACUUGUAAGCAAGGAACACAAUUAGUUUUACUCCCUUUUUGCUAAUUGUAGAAUUCCUUAAAAUCCUAAACUCCCUU-UUUGGACCGACUUGAUUGUCGGUC
AE017262.2/34076-34185       UAAUAUAGAACUUGUAAGCAAGGAAUACAAUUAGUUUUACUCCCUUUUUGCUAAUUGUAGAAUUCCUUAAAAUCCUAAACUCCCUU-UUUGGACCGACUUGAUUGUCGGUC
EU073162.1/361-470           UAAUAUAGAACUUGUAAGCAAGGAAUACAAUUAGUUUUACUCCCUUUUUGCUAAUUGUAGAAUUCCUUAAAAUCCUAAACUCCCUU-UUUGGACCGACUUGAUUGUCGGUC
CP002002.1/31999-32109       UAAUAUAGAACCUGUAAGCAAGGAAUACAAUUAGUUUUACUCCCUUUUUGCUAAUUGUAAACUUCCUUAAAAUCCUAAACUCCCUUUUUUGGACCGACUUGAUUGUCGGUC
AARN04000001.1/298123-298233 UAAUAUAGAACUUGUAAGCAAGGAAUACAAUUAGUUUUACUCCCUUUUUGCUAAUUGUAAACUUCCUUAAAAUCCUAAACUCCCUUUUUUGGAUCGACUUGAUUGUCGGUC
#=GC SS_cons                 :::::::::::::::::::<<<<<<<<<<<<<<<<______________>>>>>>>>>>--->>>>>>-----------------------<<<<<<<______>>>>>>>
#=GC RF                      UAAUAUAGAACUUGUAAGCaaGGaauaCaauuaGuUUUACUCCCUUUUUgCuaauuGuaaAauuCCuuAAAAUCCUAAACUCCCUUUUUUGGacCGaCUUGAUUGuCGguC
//
# STOCKHOLM 1.0

#=GF AC   RF01458
#=GF ID   rli23
#=GF DE   Listeria snRNA rli23
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   46.70
#=GF NC   42.80
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   7


AB261975.1/7738-7641     UAUUACAAUAUGAUUAGAGCGAUUAAGCUCAUUAUUGAUGUAAAAAGUUUCAGACUUUAGCGAGGAAUGGAAACUUUCUAUCGGGGCGUUAUCGGCGG
CP000255.1/68682-68585   UAUUACAAUGUGAUUAGAGUGAUUAAGCUCAUUAUUGAUGUAAAAAGUUUCAGACUUUAGCGAGGAAUGGAAACUUUCUAUCGGGGCGUUAUCGGCAG
CP000703.1/63982-64079   UAUUACAAUAUGAUUAGAGCUAUUAAGCUGAUUAUUGAUGUAAAGAGUUUCAGACUUUAGCGAGGAAUGGAAACUUUCUAUCGGGGCGUUAUCGGCAG
AM263198.1/671271-671368 GAUUUCAAUAUUAUUAGAACCUAAGUGUUCUUUAUAGAGGUAGAAUGUUUCAGACUUUAGUGAGAAAUGAAAUGAUUCUAUUGGAGCGUUAUCUAAGG
AL591976.1/215482-215385 GAUUACAAUAGAUUUAGCGUAUUUAUACGCUGUUUUAUGGUAGAAUGUUUCGCACUUUAGCGAGGAAUGGAAACAUUCUAUGGGAGCGUUGUCUGCGG
AL591973.1/172171-172268 GAUUACAAUAGAUUUAGCGUAUUUAUACGCUGUUUUAUGGUAGAAUGUUUCGCACUUUAGCGAGGAAUGGAAACAUUCUAUGGGAGCGUUGUCUGCGG
AL591974.1/157606-157509 GAUUACAAUAGAUUUAGCGUAUUUAUACGCUGUUUUAUGGUAGAAUGUUUCGCACUUUAGCGAGGAAUGGAAACAUUCUAUGGGAGCGUUGUCUGCGG
#=GC SS_cons             ::<<<<---<<<<--<<<<<______>>>>>>>>>---->>>>((((((((-((<<<____>>><<<<<____>>>>>,,))))))))))::::::::
#=GC RF                  gAuuaCAAUaugaUUaGcGcauuuAugCgCuucauugagGuaaaacGuuuCagaCuuUAGcgaGGaaugGAAAcauuCUAucGgagCguuaUCuGcgG
//
# STOCKHOLM 1.0

#=GF AC   RF01459
#=GF ID   rliE
#=GF DE   Listeria sRNA rliE
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR
#=GF GA   90.00
#=GF TC   119.50
#=GF NC   51.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.48 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17259222
#=GF RT   Identification of new noncoding RNAs in Listeria monocytogenes and
#=GF RT   prediction of mRNA targets.
#=GF RA   Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P
#=GF RL   Nucleic Acids Res. 2007;35:962-974.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   4


AL596169.1/38059-38283     UGAAUAAAAGAAAUAAAAAUAGAACUAUAGAUUAUUAGUAAAAAGUAAACCAUCCGCCACCUCCUAGUUGUUACAAACAGAAUAGCAAAGAAGAUUUAUUUUUGCACAUUGAUAAAAUGAUGUUUUCACUGGGUAGA-CUAACUAAAAAACACCUAUUUUCUACUAAGAGAAAAUAGGUGUUUUU-AUUUACUUUUAGCAUACGAAAA-UACUAUUUUAGUAGUUUGC
AL591979.1/174586-174808   UGAAUGAAAGACAUAAAUACCGCACUAUAAAUAGCUAAUAAAAAGUAAAUCAUCUGUCACCUCCUAGUUGUUAAAAACAGAAUAGCAGAGACGAAAUUUUUUUGCACAUAGCUAAAAUCACUUUUCCAUCUUCUAUUGCAUA-ACAAAAACACCUAUUUUCAUUAGUG-GAAAACAGGUGUUUUU-A-UAUAUUUUAUCUUCUGAAAA-UCCUUUUUUAGCUAUUUGU
AE017262.2/1564293-1564515 UGAAUGAACGACAUAAAUACUGCACUAUAAAUAGCUAAUAAAAAGUAAAUCAUCUGUCACCUCCUAGUUGUUAAAAACAGAAUAGCAGAGACGAAAUCUUUUUGCACAUAGCUAAAAUCACUUUUCCACCUUCUAUUGCAUA-ACAAAAACACCUAUUUUCAUUAGUG-GAAAACAGGUGUUUUU-A-UAUAUUUUAUCUUCUGAAAA-UCCUUUUUUAGCUAUUUGU
AARN04000022.1/18360-18579 UGAAUAAAAGACAUAAAUAUUACACUAUAAAUUAUUAAUAAAAAGUAAAUCAUCUGUCACCUCCUAGUUG-UAAAAAUAGAAUAGCAGAGUUAAAUUAUUUUUGCACAUAGCUAAAAUCGUUUUUUCACACUCUAGA-CAUA-GCAAAAA-CCCUAUUUUCCAUCUAA-GAAAAUAGG-GUUUUUUA-UAUAUUUUAGCCUCUGAAAAU-CCUUUUUUAGCUAUUUGU
#=GC SS_cons               ::::::::::::::::::::::::::[[[[[[[[[[[--[[[[[[,,,,,<<-<<<________>>>->>,,,,,,,((((,,,<<<<<<<_______>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,.,,<<<<<<<<<<-<<<<<_______.>>>>>->>>>>>>>>>.,.,,,,,,,,,,,,)))),,,,.,,]]]]]]]]]]]]]]]]]
#=GC RF                    UGAAUaAAaGAcAUAAAuAuugcACUauaaauagcuaaUaaaaaGUAAAuCaUCuguCACCUCCuaGUuGUUAaAAAcagaAUAGCagagaugAauUauuuuuGCACAUaGcUAAAAUcAuuUUUuCAcuuucUAua.CauA.acaaaaaCaCCuAuuuuCaauaaag.GaaaauaGGuGuuuuu.A.UauaUUUUAuCuucugAAAA.UcCuuuuuuagcuauuugu
//
# STOCKHOLM 1.0

#=GF AC   RF01460
#=GF ID   rliH
#=GF DE   Listeria sRNA rliH
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   151.70
#=GF NC   37.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17.56 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17259222
#=GF RT   Identification of new noncoding RNAs in Listeria monocytogenes and
#=GF RT   prediction of mRNA targets.
#=GF RA   Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P
#=GF RL   Nucleic Acids Res. 2007;35:962-974.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   3


AADQ01000003.1/73707-73279 CUUCCAGUCCACCAAACAUAUCACAUUUUUGGCAAAGGGAGCGAUAUUUGGGAUUGGAGCGAAUAAGUUGGCAAAAAGGAGUAAAGUUACAUAAUCUAGAAACUUCGGUACCGUGUAUAUCUACAACAACUGAGGCUAAACUGGUUGCGGCUGAGAACUCAUCCAUCACUUUUUCAAUGAGCAUUUCGUUGCUUUUGGACUGUAGUAACAUAGCUAUUCCCCUUUCGGCGAGACUUGGCGUGUUUCUGUCGUUCUUAGUAUAGCAUAUUUAUAAUGCGCUUACAUUUUCUUGCCAUGAAGAUAACAAUAUAUUGCUAAGAGUAAUUUCAUAAGAGAAUGCCCAAACCAUGCAUUACUGGAUGGCUUUUUGUCAUUAUUUUUUUUGAAGGCGCAAAAUUGUGUUAAAACACGAUUCGCGUCUUCUUUUUU
AL596167.1/168444-168872   CUUCCAACCCGCCAAACAUAUCACAUUUUUGGCAAAGCGAGCGAUAUUUUGGGUUAGAACGAAUGAGUUGGCAAAAAGGAGUAAAGUUACAUAAUCUUGAAACUUCGGUACCGUGUAUAUCUACAACAACUGAGGCUAGACUAGUAGCGGCUGAGAACUCAUCCAUGACUUUUUCAAGAAGCAUUUCAUUGCUUUUGGUUUGUAGUAACAUAGCUAUUCCCCUUUCGGCAAUACUUGGCGUGUUUCUGUCGUUCUUAGUAUAGCAUAUUUAUAAUGCGCUUACAUUUUCUUGCCAUGAAGAUAACAAUAUAUUGCUAAGACUAAUUUCAUAAGAGAAAGCCCAAACCAUGCUCUACUGGAUGGCUUUUUGUCGUUUAUUUUUUUGAAGGCGCAAAAUUGUGUUAAAACACGAUUCGCGUCUUCUUUUUU
AM263198.1/1123866-1124294 CUUCAAGGCCCCCAAACAUAUCACAUUUUUGACAAAGUGAGCGAUAUUUUGGGUUGGAACGAAUGAGUUGGCAAAAAGGAGUAAAGUUACAUAAUCUAGAAACUUCGGUACCGUGUAUAUCUACAACAACGGAGGCUAGACUCGUUGCGGCUGAAAACUCAUCCAUGACUUUUUCAAUGAGCAAUUCGUUGCUUUUGGACUGUAGUAACAUAGUUAUUCCCCUUUCGGCAAUACUUGGCGUGUUUCUGUCGUUCUUAGUAUAGCAUAUUUAUAAUGCGCUUACAUUUUCUUGCCAUGAAGAUAACAAUAUAUUGCUAAGACCAAUUUCAUAGUAAAAGCCCCAAACCAUGCAUGACUGGAUGGCUUUUUGUAUAUAAUUUUUUAAAAGGCGCAAAAUUGUGUUAAAACACGAUUCGCGUCUUCUUUUUU
#=GC SS_cons               ::::::::::::::::::::::::::{{{{{{{{{,,,[[[[[[[[---------[[[[[[--[[[[[--[[--[[[[[-[---[[[[[,,,,,<<<<<---<<<<<<<----<<<<____>>>>--->>>>>>>>>>>>,,,(((((<<-<<<____>>>->>,,,<<---<<<<<-<<<<<______>>>>>>>>>>-->>,))))),]]]]]---]-]]]]]--]]---]]]]]---]]]]]]]]]]]]]],,,<<<--<<<<_______>>>>--->>><<<<<<_______>>>>>>,,,,,,,,,}}}}}}}}},,,,,,,,,,,,,<<<<<<<<----<<<________>>>-->>>>>>>>,,,,,,,,,,,,,,,<<<<<<<<--<<<<<<<<____>>>>>>>>->>>>>>>>::::::
#=GC RF                    CUUCcAguCCaCCAAACAUAUCACAUuuuuggCaaAGuGagCGauaUUUuGGgUUggaaCgAAugaGuUGGCAAaaaGGAGUAAaguuaCAUAAucuaGAAACuuCgGuACCGuGuaUAUCuaCaACAaCcGagGCuagaCUaGuugCGGCuGagAACuCaUCCAUgaCUUUuuCaaugaGCauUUCgUuGCucuuGgacUGuAGuaaCAuagcuAUUCCCCuuuCGGCaAuaCucgGCGuGuuucuguCGuuCUUAGuaUAGCauAUUUAUAauGCGCUuaCauuuuCUUGCCAUGaagauAACAAUAUAuuGcuaagacuAAUUUCAUAagagaaggCCCAAACCaUGCauuACuGGAUGGccuucuGUcauUaaUUUUUUugaaGgCGCAAaauuGuGuUAAAaCaCgauuCGCGuCuucUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01461
#=GF ID   rli24
#=GF DE   Listeria sRNA rli22
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   100.00
#=GF TC   143.70
#=GF NC   48.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.73 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   6


AM263198.1/227004-227161   AGGACUGAGGGAUAUGCUUAGAAUGAGAAAAAUACUCGAAAAAAACAACCAAUCAAGAAUGAAGAUAAUAGGUUUUUCUUUAACGUUCGCGCAUAAUAAUUCCGCGUCUUUUCAAGGUUACGUUCGUUAAAAGUUAGGUCCUUCAAUCUUUCUUGAUU
AE017262.2/273433-273590   AGGACUGAGGGAUAUGCUUAGAAUGAAAAAUAUACUAGAAAAAAACAACCAAUCAAGACAGAAGAUAAUAGGUAUUUCUUUAACGUUCCUGCAUAGCCAACCGGUGUCUUUUCAAGGUAGCGUCCGUUAAAAGUUACGUCCUUCAAUCUUUCUUGAUU
AL591974.1/71029-71186     AGGACUGAGGGAUAUGCUUAGAAUGAAAGAUAUACUAGAAAAAAACAACCAAUCAAGACAGAAGAUAAUAGGUAUUUCUUUAACGUUCCUGCAUAGCUCACCGGUGUCUUUUCAAGGUAGCGUCCGUUAAAAGUUACGUCCUUCAAUCUUUCUUGAUU
AADQ01000025.1/29836-29679 AGGACUGAGGGAUAUGCUUGGAAUGAAAGAUAUGCUAGAAAAAAACAACCAAUCAAGACAGAAGAUAAUAGGUAUUUCUUUAACGUUCCUGCAUAGACAACCGGUGUCUUUUCAAGGUAGCGUCCGUUAAAAGUUAGGUCCUUCAAUCUUUCUUGAUU
CP001602.1/289096-289253   AGGACUGAGGGAUAUGCUUAGAAUGAAAGAUAUGCUAGAAAAAAACAACCAAUCAAGACAGAAGAUAAUAGGUAUUUCUUUAACGUUCCUGCAUAGACAACCGGUGUCUUUUCAAGGUAGCGUCCGUUAAAAGUUAGGUCCUUCAAUCUUUCUUGAUU
CP002004.1/272598-272755   AGGACUGAGGGAUAUGCUUAGAAUGAAAGAUAUACUAGAAAAAAACAACCAAUCAAGACAGAAGAUAAUAGGUAUUUCUUUAACGUUCCUGCAUAGACAACCGGUGUCUUUUCAAGGUAGCGUCCGUUAAAAGUUACGUCCUUCAAUCUUUCUUGAUU
#=GC SS_cons               <<<<.<<<<<<<<<<<<...<<<<<............<<.............>>......<<<<<...........>>>>>..>>>>>..>>>>.............<<<<<...<<......>>...>>>>>....>>>>>>>>.>>>>........
#=GC RF                    agGacuGagGGauauGCUUAGaauGAaAgAaAuAcUAGaAAAAAAcAAccAAuCAAGAaaaaaGaUAAUAGGUAuUuCuuuAACguuCguGCauAauaAacccGuGuCuuuucAAGgUAacGUcCGUUaaaaGUuAgguCCuuCaAuCuuUcUUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01462
#=GF ID   rli26
#=GF DE   Listeria sRNA rli26
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   100.00
#=GF TC   197.30
#=GF NC   41.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.42 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   5


AM263198.1/343359-343175     GAU---ACACCACAAAAGGGAGGUACAACAUGUUCAAAAUUUUUAGUUUCGUUUCAUUAAUACUUAGUAUGCUAAGUUUUAUGGGCUUACAAGUUUUAAAUGUUAUUCAAAAAAAUGUCAUAUUAUUAUCACUAUUAGAUAGCGAAGAAUUUAAUGACAUUCACUUUUUCGGGAGUUUAUUAGUAGUC
AADR01000001.1/47432-47615   AAAACUACAUCAUA----GGAGGUACAACAUGUACAAAAUUUUUAGUUUCGUUUCAUUAAUACUUAGUAUGCUAUGUUUUAUGGGCUUACAAGUUUUAAAUGUCAUUCAAAAAAAUGUCAUAUUAUUAUCACUAUUAGAUAGCGAAGAAUUUAAUGACAUUCACUUUUUCGGAAGUUUAUUGGUAAUA
AADQ01000030.1/20428-20241   GAUUCAACAUUAUAAAAGGGAGGUACAACAUGUACAAAAUUUUUAGUUUCGUUUCAUUAAUACUUAGUAUGCUAUGUUUUAUGGGAUUACAAGUUUUAAAUGUCAUUCAAAAAAAUGUCAUAUUAUUAUCACUAUUUGAUAGCCAAGAUUUUAACGACAUCCAUUUUUUCGGGAGUUUAUUAGUAGUA
AL591975.1/28707-28520       GAUUCAACAUUAUAAAAGGGAGGUACAACAUGUACAAAAUUUUUAGUUUCGUUUCAUUAAUACUUAGUAUGCUAUGUUUUAUGGGCUUACAAGUUUUAAAUGUCAUUCAAAAAAAUGUCAUAUUAUUAUCACUAUUUGAUAGCCAAGAUUUUAACGACAUCCAUUUUUUCGGGAGUUUAUUAGUAGUA
AARN04000004.1/121339-121526 GAUUCAACGCUAUAAAAGGGAGGUACAACAUGUACAAAAUUUUUAGUUUCGUUUCAUUAAUACUUAGUAUGCUAUGUUUUAUGGGCUUACAAGUUUUAAAUGUCAUUCAAAAAAAUGUCAUAUUAUUAUCACUAUUAGAUAGCGAAGAAUUUAAUGACAUUCACUUUUUCGGAAGUUUAUUAGUAAUA
#=GC SS_cons                 ::::::::{{{{,,,,,,[[[,<<<<_____>>>>,,,,,,,,,,,,,(((((,,,<<<<-<<<<-<<<-<<<__________>>>->>>>>>>->>>><<<-<<<<______>>>>->>>,,,,<<<<<_______>>>>>,,,,,,,,,,))))),,]]]<<<<<____>>>>>,,,,}}}}::::
#=GC RF                      gAuuCaACaccauAAAAGGgaGGuaCAACAUGuaCAAAAUUUUUAGUUuCguuUCAuuaaUaCuuAGuaUgCuAuGUUUUAUGgGcUuaCaaGuUuuaaauGUcauuCAAAAAaaugUCauAUUAuuauCACUAUUaGauagCgAAGAaUUUaacGaCAucCacucuUUCGggaguUUAUugguAgUa
//
# STOCKHOLM 1.0

#=GF AC   RF01463
#=GF ID   rli27
#=GF DE   Listeria sRNA rli27
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   55.00
#=GF TC   56.50
#=GF NC   41.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 38.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   3


AL591975.1/74831-74929   AUAAGUAUAUUUUAACGAUAUUAUCUAUCUAAAUUUACCACGAAUCUAGCCUAAAUUCAAUUAAAAAC-AAAUAGAAAAGCAAAAUUUCUCAUGACAAGA
AE017262.2/450059-450157 AUUAGUAUAUUUUACCGAUAUUAUCUAUCUAAAUUUACCAUGAAUCUAGCCUAAAUUCAAUUAAAAACAAA-UAGAAAAGCAAAAUUUCUCAUGAUAAGA
AARL02001074.1/230-132   ACAAGCAUAUUUUUAUGAUAUUAUCUAUCUAAAUUUACCAUGAAUCUAGCCUAAAUUCAAUUAAAAACAAA-UAGAAAAGCAAAAUUUCUCAUGACAAGA
#=GC SS_cons             ::::((,,,,,,,,,,<<<<_____>>>>,,,,,,,,,,,,<<<<_________>>>>,,,,,,,,,,,,,.,,,,,,,)):::::::::::::::::::
#=GC RF                  AuaAGcAUAUUUUaacGauaUUAUCuauCUAAAUUUACCAuGaauCUAGCCUAAauuCAAUUAAAAACAAA.UAGAAAAgCAAAAUUUCUCAUGAcAAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01464
#=GF ID   rliA
#=GF DE   Listeria sRNA rliA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   47.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17259222
#=GF RT   Identification of new noncoding RNAs in Listeria monocytogenes and
#=GF RT   prediction of mRNA targets.
#=GF RA   Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P
#=GF RL   Nucleic Acids Res. 2007;35:962-974.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   4


AADR01000009.1/6446-6222     ACGUGUUAUAAAAAUACGGUUUAUACACAUGGAAUUAUAGUUCUAUAUGAAAUAGGUUAUUUAUUAGAAGGAUUAAAUGGCUUAUU-UUAUUUUUUAAUGUAUAAAAUUAUGUAUAUGGACACAAGUUGUGUUAUUUUGAACAUAAAUUUAAGUGAAUCAAUUCUUAAUGUAUUGAUUUUCGUCUAAAAUAGGUCGUUCAUGACAAGAAUCGGACAUUUCAUUACA
AL591975.1/153584-153807     ACGUGU-AUAAAAAUACGGUUUAUACACGUGGGAUUAUGGUUCUAUAUGAAAUAGGUUAUUUAUUAGAAGGGUUAAAUGGCUUAUUUU-AUUUUUCAAUGUAUAAAAUUAUGUAUAUUGACACAAUUUGUGUUAUUUUGAACAUAAAUUUAAGUAAAUCAAUUCUUAAUGUAUUGAUUUUCGCCUAAAAUGGGUCGUUCAUGACAAGAAUCGGACAUUUCAUUACA
AARJ02000001.1/725829-725606 ACGUGU-AUAAAAAUACGGUUUAUACACGUGGGAUUAUGGUUCUAUAUGAAAUAGGUUAUUUAUUAGAAGGUUUAAAUGGCUUAUU-UUAUUUUUCGAUGUAUAAAAUUAUGUAUAUUGACACAAUUUGUGUUAUUUUGAACAUAAAUUUAAGUAAAUCAAUUCUUAAUGUAUUGAUUUUCGCCUAAAAUAGGUCGUUCAUGACAAGAAUCGGACAUUUCAUUACA
AARM02000265.1/981-758       AUAUGU-AUAAAAAUGCAUUUUAUACACAUGGGAUUUUAGUUCUAUUUGAAAUAGGUUAUUUAUUAGAACGAUUUAAUGGCUUAAU-UUAUUUUUCAAUGUAUAAAAUUAUGUAUAUUGACACAAUUUGUGUUAUUUUGAACAUGAAUUUAAGUAAAUCAAUUCUUAAUGUAUUGAUUUUCGCCUAAAAUAGGUCGUUCAUGACAAGAAUUGGACAUUUCAUUACA
#=GC SS_cons                 <<<<<<.<<<<<_______>>>>>>>>>>>[--[[--[[[[[[[((-((((,<<<<<<<<<______________>>>>>>>>>,,.,,,,,,,,,,,,,,,,,,,,<<<<<<-<<-<<<<<<_____>>>>>>--->>->>>>>>,))))-))<<<<<<<<-<_____>->>>>>>>>,,,,,,,,,,,,,<<<<____>>>>,]]]]]]]---]]--]::::::
#=GC RF                      acguGu.auaaaAAUaCgguuuauaCacguGGgauUaugguuCuauaugaaAuagGuuauuUAUUAGAAgGaUUaaauggCuuauU.UUAUUUUUcaAUGUAUAAAAuuauGuAuaUugaCaCAAuUUGuGuuaUUUugAaCauaaAuuuaAguaaauCaauUCUUAAUGUauuGauuuUCGcCUAAAAUaGGuCgUUCAuGaCAaGaaucgGACauUUCAUUACA
//
# STOCKHOLM 1.0

#=GF AC   RF01465
#=GF ID   rli31
#=GF DE   Listeria sRNA rli31
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   81.80
#=GF NC   62.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   3


AL596165.1/140809-140924 UAGAGAUUGUCAUUUGAAAUAAGCUAGUUAAGAAUAAAUCACUUCCCCCAUAGAAAUGUUCUUAACAGCUUAUUGCAAAUAAACACUCCUUUUAAGAUAGUUGUAGCACAGAAUUU
AM263198.1/560040-560154 UAGAGAUUGUUAUUUGAAAUAAGUUGGUUAAAAAUAAAUCACUUCCCCCAUAGAAAUAUUUUUAAUCACUUAAGACGAAUAAACACUCCU-UAAAUAUAGUUGUAGCACAGAAUUU
FM242711.1/601458-601572 UAGAGAUUGUCAUUUGAAAUAAGCUAAUUGAAAAUAAAUUACUUCCCCCAUAGAAAUAUUCUUAAUUGCUUAUUUCAAAUAAACACUCCU-UUAAGAUAGUUGUAGCACAGAAUUU
#=GC SS_cons             ::<<<--<<<-<<<<<-<<<<<<<-<<<<<<<<<<<--<<____________>>-->>>>>>>>>>>>>>>>>>->>>>>-->>>>>>::.:::::::::::::::::::::::::
#=GC RF                  UAGaGAUuGucauuuGAaauaaGcUgguuaagaauaAAucACUUCCCCCAUAgaAAuauucuuaaccgCuuauuaCaaauAAaCaCuCCU.UuAAgAUAGUUGUAGCACAGAAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01466
#=GF ID   rli34
#=GF DE   Listeria sRNA rli34
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold
#=GF GA   48.00
#=GF TC   48.30
#=GF NC   46.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   5


AL591976.1/163031-162948     UAGAUUUAUUCUUACACAGUAUGAGUAAUAUCUCCAUUUCAAUAAUAAAAUCUUACACAAUAUGAAGCAGUAUUCACUUUUUAU
FM242711.1/802853-802770     UAGAUUUAUUCUUACACAGUAUGGGUAAUAUCUCCAUUUCAAUAAUAAAAUCUUACACAAUAUGAAGCACUAUUCACUUUUUAU
AARU02000001.1/302730-302647 UAGAUUUAUUCUUACACAGUAUGAGUAAUAUCUCCAUUUCAAUAAUAAAAUCUUACACAAUAUGAAGCAAUAUUCACUUUUUAU
AARQ02000011.1/46979-46896   UAGAUUUAUUCUUACACAGUAUGAGUAACAUCUCCAUUUCAAUAAUAAAAUCUUACACAAUAUGAAGCAGUAUUCACUUUUUAU
AARN04000041.1/7000-6917     UGCAUUUAUUCUUACACAAUACGAGUAAUAUUAUGGUUUUCAUCACAAAACACCACACAUUUUGCGUCAUUAUUCACUAUUUAU
#=GC SS_cons                 :::::<<<<<<___________>>>>>>----------------------------------<<<<______>>>>::::::::
#=GC RF                      UAgAUUUAuuCUUACACAgUAUGagUAAUAUcuccAUUUcaAUaAUAAAAUcUUACACAaUaUGaagCAuUAuuCACUuUUUAU
//
# STOCKHOLM 1.0

#=GF AC   RF01467
#=GF ID   rli36
#=GF DE   Listeria sRNA rli36
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   52.00
#=GF NC   40.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   6


AL596166.1/150704-150621     AAAAUAGUAGUUAUUUCUUUAUAACGUUCAUAAAAGAAUAUCUAUUCAUUCCCACUUAGCUUCUGAUUCCCACAGAUCAAAAGC
AM263198.1/851747-851664     UAAAUAGUAGUUAUUUCUUUAUAGCGUUCCUUAAAGAAUAUCUAUUCAUUCCCACUUUGCUUCUGAUUCCCACAGAUCAAAAGC
AADQ01000002.1/102541-102624 UAAAUAGUAGUUAUUUCUUUAUAACUCUCAUAAGAGAAUAUCUAUUCAUUCCCACAUCGCUUCUGAUUCCCACAGAUCAAAAGC
AL591976.1/219527-219444     UAAAUAGUAGUUAUUUCUUUAUAACUCUCAUAAGAGAAUAUCUAUUCAUUCCCACAUCGCUUCUGAUUCCCACAGAUCAAAAGC
AE017262.2/859572-859489     UAAAUAGUAGUUAUUUCUUUAUAACUCUCAUAAGAGAAUAUCUAUUCAUUCCCACAUCGCUUCUGAUUCCCACAGAUCAAAAGC
FM242711.1/859984-859901     UAAAUAGUAGUUAUUUCUUUAUAACUCUCAUAAGAGAAUAUCUAUUCAUUCCCACAUCGCUUCUGAUUCCCACAGAUCAAAAGC
#=GC SS_cons                 :::::<<<<<-<<<<--<<<<<_______>>>>>-->>>>->>>>>------------<<<<-<<<<<______>>>>>->>>>
#=GC RF                      uAAAUaguaGUuauuUCcuuauAACucUCauaagAGaauaUCuauuCAUUCCCACaUcGCuuCuGauuCCCACAgauCaAaaGC
//
# STOCKHOLM 1.0

#=GF AC   RF01468
#=GF ID   rli32
#=GF DE   Listeria sRNA rli32
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold
#=GF GA   100.00
#=GF TC   109.50
#=GF NC   48.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   5


AL596165.1/143786-143638   GUGGAGGGCUUUUAUUUUUUCCCAAAAGAAAGC-AAGUAAUGUUAGAGCAAUAAUUCUAGUAUCCGAAUUAGUCUUAUCCCUUGGC-UCGCUCUAACGUUAUUACUCCCUAAUACUCCCUUUAACCGCAUCCCCCUGGUGCGGUUAUUUUU
AM263198.1/563016-562871   GAGGAGAGCUUUUAUUU---CCCAAAAGAAAGCAAAAUAAUGUUAAAGCAUUCAUUCU-GUAUCCGAAUUCGUCUUAUCCCUUGACGUUGCUUUAACAUUAU-UCUCCCUAAUACUCCCUUUAACCGCAUCCCCCUGGUGCGGUUAUAUUU
AADQ01000001.1/12801-12947 GUGGAGAGCUUUCAUUUU-UCCCAAGAGAAAGC-AAAUAAUGUUAGAGCAAUAAUUCUAGUAUCCGAAUUAGUCUUAUCCCUUGGC-UCGCUUUAAUAUUAUUUCUCCCUAAUACUCCC-UUAACCGCAUCCCCCUGGUGCGGUUAUUUUU
CP001175.1/2047013-2047158 GUGGAGAGCUUUUAUUUU-UCCCAAAAGAAAGC-AGGUAAUGUUAGAGCAAUAAUUCA-GUAUCCGAAUUAGUCUUAUCCCUUGGC-UCGCUUUAACAUUAUUACUCCCUAAUACUCCC-UUAACCGCAUCCCCCUGGUGCGGUUAUUUUU
AL591975.1/240750-240604   GUGGAGAGCUUUCAUUUU-UCCCAAGAGAAAGC-AAAUAAUGUUAGAGCAAUAAUUCCAGUAUCCGAAUUAGUCUUAUCCCUUGGC-UCGCUUUAAUAUUAUUUCUCCCUAAUACUCCC-UUAACCGCAUCCCCCUGGUGCGGUUAUUUUU
#=GC SS_cons               ::[[[[[<<<<<<-<<<_.____>>>->>>>>>.,((((((((((((((,,<<<<<<________>>>>>><<<_________>>>.,,))))))))))))))]]]]]-----------.-<<<<<<<<<<_____>>>>>>>>>>:::::
#=GC RF                    GuGGaGaGCuuucAuuuU.UCCCaaaAgaaaGC.AaauaauguuagaGCAauaauuCuAGUAUCCGaauuaGcCUUAUCCCUUGgC.UcGCucuaacauuauuuCuCCCUAAUACUCCC.UuaaCCGCacCCCCCUGguGCGGuuaUuUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01469
#=GF ID   rli33
#=GF DE   Listeria sRNA rli33
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   46.00
#=GF TC   47.80
#=GF NC   44.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 15 -Z 549862.597050 CM SEQDB
#=GF CL   CL00114
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0045947; negative regulation of translational initiation;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF RN   [2]
#=GF RM   27400116
#=GF RT   Two novel members of the LhrC family of small RNAs in Listeria
#=GF RT   monocytogenes with overlapping regulatory functions but distinctive
#=GF RT   expression profiles.
#=GF RA   Mollerup MS, Ross JA, Helfer AC, Meistrup K, Romby P, Kallipolitis BH
#=GF RL   RNA Biol. 2016;13:895-915.
#=GF CC   The UCCC motifs prevent ribosomal binding to oppA mRNA. 
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   3


AL591976.1/68326-68860   CCAUUACUUUUUCUCCCUUUUUUGUAGUGGGUUGUCUUUACUUACCUUAAACUCCCUUUUAUACUCUUUUGUGGUUGUGUAGCAACCCUUUGGAGUAUUUUUUUGGAAAAAAUGCUAAAUAUAAGAAAACUCCUCAAACAAGGGAAAGUUCGAGGAGUUCGGCAUUUACCAAUAUUUAUAAAUGCCACUGGGGAUUUUCUAAGUGAACAAAGAUAUGGAUGUUUGGGA-AAGCAUCCACUUUGAGAAUUUACCAUAGAUAGCUGGCGUUAAGUUGUAAUGUAGUAUAAAUCAUACAAUUCUUGUAGUACAUCAUAUAUAGCACUGAAUUACCAAAUUCCUGAUAAAUAAGGAAAGGGUGGAAUAAAAGUAUCUCAUCAGGUAUAUUUAAAUUACACGGUAGUUAAGGAGGUAACGAUAAGUUGAGUAAUUUUAACAUCAUGGGAUCUUUAAUGCUUAUAGCUGUUUUAGUUUUAGCAGUGUAUGUUAUUACCAAAGUUAUUAACAAAUUAAAAAAAUAAGUAGAGUUUAACUAAAA
AE017262.2/722820-723352 CCAUUACUUUUUCUCCCUUUUUUGUAGUGGGUUGUCUUUACUUACCUUAAACUCCCUUUUAUACU-UUUAGCGGUUGU-UAGCAGCCACUAAGAGUAUUUUUUUGUAAAAAACACUAAAUAAAUGAAAACUCCUCGAACAAGGGAAAGUUCGAGGAGUUCGGCAUUUACCAAUAUUUAUAAAUGCCACUGGGGAUUUUCUAAGUGAACAAAGAUAUGGAUGUUUGGGAAGAGCAUCCACUUGGAGAAUUUACCAUAGAUAGAUAGCGACAAGUUGUAAUGUAGUAUAAAUCAUACAAUUCUUGUAGUGCAUCAUAUAUAGCACUGAAUUAUUAAAUUCCUGAUAAAUAAGAAAAGACUGGAAUAAAAGUACCUCAUCAAGUAUAUUUAAUUUACGCGGGAGUUAAAGAGGUGAUAGAAGGUUGAGCAAUUUUAACAUCAUGGGAUCUUUAAUGCUUAUAGCUGUUUUAGUUUUAGCAGUGUAUGUUAUUACCAAAGUGAUUACCAAAUU-AAAAAAUAAGUAGAGUUUAACUAAAA
AARK02000088.1/2619-2088 CCAUUACUUUUUCUCCCUUUUUUGUAGUGGGUUGUCUUUACUUACCUUAAACUCCCUUUUAUACU-UUUAGCGGUUGU-UAGCAGCCACUAAGAGUAUUUUUUUGUAAAAAACACUAAAUAAAUGAAAACUCCUCGAACAAGGGAAAGUUCGAGGAGUUCGGCAUUUACCAAUAUUUAUAAAUGCCACUGGGGAUUUUCUAAGUGAACAAAGAUAUGGAUGUUUGGGA-GAGCAUCCACUUGGAGAAUUUACCAUAGAUAGAUAGCGACAAGUUGUAAUGUAGUAUAAAUCAUACAAUUCUUGUAGUGCAUCAUAUAUAGCACUGAAUUAUUAAAUUCCUGAUAAAUAAGAAAAGACUGGAAUAAAAGUACCUCAUCAAGUAUAUUUAAUUUACGCGGGAUUUAAAGAGGUGAUAGAAGGUUGAGCAAUUUUAACAUCAUGGGAUCUUUAAUGCUUAUAGCUGUUUUAGUUUUAGCAGUGUAUGUUAUUACCAAAGUGAUUACCAAAUU-AAAAAAUAAGUAGAGUUUAACUAAAA
#=GC SS_cons             :[[[[[[--[[[--[[----[[[[[-[[[[[[[-[[((((((((----(((-((((,,,,,<<<<.<---<-<<<<<_.___>>>>>->-->->>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<<<________>>>>>>>>>>>>,<<<<<<<<__________>>>>>>>>,,,))))-)))--)))))))),,,,,,,,<<<<<<<<<____.>>>>>>>>>,,,,]]-]]]]]]]-]]]]]------]-]--]]]--]]]]]]{{{{-{{{{{--{{{<<<<<-<<<-<<<_______>>>->>>-->>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,[[[,,<<<<-<<<<________>>>>->>>>,,,(((((-((((((((((-(((,,,,,,,,<<<<<<____>>>>>>,,,<<<<<__________>>>>>,)))-))))))))))----))))),,,,,,,,]]],,,,,,,,,,,,,,,,.,,,,,,,,,}}}--}}}}}}}}}:::
#=GC RF                  CCauuaCUUuuuCUCCCUUUuuuguAGuggguuGuCuuuaCuuaCCUUaaaCuCCCUUUUAuaCu.uUUagcGGcuGU.UAGCagCCacUaaGaGuaUUUUUUUGuAAAAAAcaCUAAAUAaAuGAAaaCuCCuCgaaCAAGGGAAAGuucGaGGaGuuCGGCauuuaCCAAUAUUUAuaaauGCCACUGGGgAuuuUCuaaGugaaCAAAGAUAuGGauGuucGGGA.gagCauCCaCUUgGaGaauuuaCCauagaUAGaUaGCGacaagUUGuaauGuaGuAuaaauCAuaCaauuCUuGuAgugCAUCAUAcauAgCaCUGaauuAuuAAAUUCCUGAUAAAUAAGaAAAGacuGGAAuaaaAguacCUCAUCAaguauAuuuaAuUuaCgCGggaguuaaagAgGugAuagaAgGuugagcAAUuuuaaCAUCauggGAUCUUUAAUGCuuauAgCuGuuuuagcucuAGCAGcGuaUGUUAUUACCaAAGUgAUUAcCAAAUU.AAAAAAUAAGuaGAguuuaaCuaAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01470
#=GF ID   rli38
#=GF DE   Listeria sRNA rli38
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   49.00
#=GF TC   49.20
#=GF NC   48.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   20


AL591977.1/262768-262917     ACAGAGUGGGAAUAGAAAGC-UAACAUAAUAAGAAUA-G-GAA-UAUCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGAUUU--UCAUUAAAAAUG--AUAUAUUUCC--CUACCA---CAAAUCCCUGUCAAG-AUG-AUG-CUUGACAGGGAUUUGUUU
AADR01000004.1/105341-105192 GCUGAGUGGGAGUAAAAAGC-UAACAUAAUAAGAAUA-G-GAA-UAUCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGAUUU--UCAUUAAAAAUG--AUAUGGUUUC--CUGCCA---CAAAUCCCUGUCAAG-AUG-AUG-CUUGACGGGGAUUUAUUU
AE017262.2/1132593-1132739   ACAGUAU---UAUAUUAAUU-UAGCUGUUAAAGUAUG-G-AAA-UACCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGGUUC--UCAUUAAAAAUG--AUAUAUUUCC--CUACCA---CAAAUCCCUGUCAAA-AUG-AUG-CUUGACAGGGAUUUGUUC
AARM02000208.1/1543-1692     UCCGAAUGGGAAUAAAAAAC-UAACAUACUAAAAAUU-G-GAA-UACCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGGUUU--UCAUUAAAAAUG--AUAUGGUUUC--CUACCA---CAAAUCCCUGUCAAG-AUG-AUG-CUUGACAGGGAUUUUUUU
FM242711.1/1125921-1126070   GUUGAGUGGGAGUAAAAAGC-UAACAUAAUAAGAAUA-G-GAA-UAUCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGAUUU--UCAUUAAAAAUG--AUAUGGUUUC--CUGCCA---CAAAUCCCUGUCAAG-AUG-AUG-CUUGACGGGGAUUUAUUU
AARI02001017.1/655-768       GUUGAGUGGGAAUAGAAAGC-UAACAUAAUAAGAAUA-G-GAA-UAUCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGAUUU--UCAUUAAAAAUG--AUAUGGUUUC--CUACC------------------------------------------ACAA
ACHK01000120.1/48426-48568   GUGGAGUGGGAAUAAAGAGC-CAACAUAAUAUGAAUG-GGGAA-UGCCGACAAAUCAAC-GUUUUUCA-ACU--------UUUGAAA-UGCU-UGUUUG--UCAUUGAAAAUG--AUAUGGUUCC--CUACCA---U-UUUCCCUACCAAA-A-------UUUGGUAGGGG--UCUUU
AAAK03000042.1/10371-10239   GUGGAGUGGGAAUAAGACGU-AAAUAUAAUAUGGAUG-GGGAA-UGCCGAUAAAUCAAC-GUUUUUCA-ACU--------UUUGAAA-UGCU-UGAUUU--UCAUUAAAAAUG--AUAUGGUUCC--CUACCA---UUUUU-----------CCU-ACC---------AAAAAAGGGC
ACIX01000266.1/4908-4755     ACAGGUA-GGAAUAAAGAGC-CAACAUGAUAUGAAUG-A-GAG-UGCCGUUAAAUCAAC-GUUUUUCA-ACU--------UACAAAA-UGCU-UGAAUU--UCAUUAAAAAUG--AUAUGGAUCCCCCUACCAAAAUAAAACCCUGCUGAG-AUG-AUA-CUUGGCAGGGAAUUUUUU
AARL02000856.1/384-530       GUUGAGUGGGAAUAGUAAGC-UAACAUAGUAAGUAUG-GAGAA-UGCAGAUAAAUCAAC-GUUUUUC-------------AACUAAA-UGCU-UGGUUA--UCAUUAAAUAUG--AUAUGCUUCC--CUACCA---UUUU-CCUUACCAAA-GUG-AAAUCUUGCUAAGAUGAAGCUA
ACNB01000009.1/7203-7351     AUUGAGUGGGAAUAAGACAU-UAAAUUAAUAAUAUUU-G-UGA-AGCCUAUCUUAAAGC-GUUUUUCA-ACU--------UGUUAAA-UGUU-UUAAAU--GCUUGAUUUAUG--AUAGUAUUCA--CCACCA---AAAGACCCCCCCAAGAUAU-AUUUCUUGGGGGG---UUAAUU
ACLO01000034.1/26824-26974   GUAGAGUGGGAAUAAAAUAU-AAACCUAAUUUAAA---G-UGA-CUUGAUUGAUUUAACAGCAUUUUG-AAUU-----GUUUUAAAA-CGCU-AAAAUC--UAAUUAAUUAU---AUUUGGUUCC--CCACCA---AAUA-CCCCACCAGA-AUUUCUU-UCUGGUGGGGAUUUUUUA
AAJM01000261.1/5712-5863     AUUGAGUGGGAAUAAAGAUA-UAACAUUGUUUAAAGU-G-AAAUUACUGUUCUAACAAC-GUUUUAGC-UAU--------UAUGUAA-UGGC-UGAAAA--CAAUUAAAUAUU--AACUUGUUUA--CCACCA---AAAACCCCACCAAUACAAC-AAG-UAUUGGUGGGGUUUUUAG
ABYO01000191.1/18041-17909   AUUGAAUGGGAAUAAAUAUA-UAAAAUGAUUUGAAUG-G-GAA-ACUCUAAAUUUCAAC--GUUUUUA-AAU--------GAUGAAAGUCAA-UGAAAU---CAAAUGAAUUGAUAUAUAGAUCC--CUGCCA---AAAUCC-----------UG-CCA---------AGGAUUUAUA
CP000056.1/799047-799191     CUUAAAUAAGAAGCAGAUAG-CAAUUUGAG----AGC-G-AAA-UCCCGAUUUAUCAGU-CUUUUAGA-GCUUAUAGCGAUUUGAAG-AAAC-UGAUAA--------AAU--G--AUUUGGUUUU--UUGCCA---AAAA-UCCUGCCAAA-AAA-AUC-UUUGGCAGGAUUUUUAUU
CP001348.1/2574349-2574222   AUUGAGUGGGAAUAAAAGUG-UAAGUUAAAUUGAUUG-GGGAA-AGCCUAUUUUGAA-G-GUUUUCCCCAUU--------UUUGUAA-GGUA-AUAAAA--UGGUUAGAAAU---AAAUAGUUCC--CCACCA---AAAACC---------------CA----------GAAUUGAGC
CP000407.1/961832-961683     GUUACUCUUAAAUAAGAGUCACAUCAUAAUUAGAUUGCG-GAA-UCCCUAUUUACCAG---UCUUUGA-GAG--------CGAUAAG-CGAU-UGAUAGAAACUGAUAAAUUG--AUUUGGUUUC--CUGCCA---AAAA-UCCUGCCAAA-AAU--UC-UUUGGCAGGAUUUUUGUU
CP001015.1/1258926-1258786   AAUAAGAGGCA-UA--------UACCAAUUAGAAUUC-G-GAA-UACUAUAGUAUCAGC-CUUUUAGA-AUCGUGAACACAUUUUAG-AAAC-UGAUAA--------AUU--A--AUUUAGUUUC--CUACCA---AAAA-CCCUACCAAA-AAU-UAA-UUUGGCAGGGUUUUUCUU
ACDZ02000009.1/22044-22191   AUUGAAUGGGAAUAGAUUAC-AAAUAUAAUUUGAAUG-G-AGA-AUCC--UAAUUUAACUGCGUUUCU-AGUU------GUUAUAAA-UGUUGUAAAUC--UAUUUAAUUCA---AUUAGGUUCC--CCACCA---AAAA-CCCCACCAAA-AUA---C-UUCGGUGGAGUCUUUUUA
AARN04000033.1/25262-25411   AUAGAGUGGGAACAAAAAGC-CAACAUAAUAAGUAUG-G-AAA-UACCAAUAAAUCAAC-GUUUUUCA-ACU--------UAUGAAA-UGCU-UGGUUC--UCAUUAAAAAUG--AUAUAUUUCC--CUACCA---CAAAUCCCUGUCAAG-AUG-AUG-CUUGACAGGGAUUUGUUU
#=GC SS_cons                 :::::::(((((,,,,,,,,.,,,,,,,,,,,,,,,,.,.,,,.,,,,,,,<<<<<<<-.<<-<<<<<.___........__>>>>>.->>>.>>>>>>..<<<<_____>>>..>,,,,,))))..)-----...-<<<<<<<<<<<<<<.___.___.>>>>>>>>>>>>>>::::
#=GC RF                      aUUGAgUGGgAAUAAaAauc.uAAcaUAAUauGAAUg.G.gAA.UaCCaAUauauCAaC.guUUUuca.AcU........UaugaAA.ugcu.UGauau..uCauUAAAaauG..aUaUgGUUcC..CUACCA...aAaacCCCugcCAag.Auu.Aua.cuUGgcaGGGguuUuuUu
//
# STOCKHOLM 1.0

#=GF AC   RF01471
#=GF ID   rliB
#=GF DE   Listeria sRNA rliB
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   40.00
#=GF TC   41.50
#=GF NC   37.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   4


AARQ02000018.1/17464-17103 AAGAAGAAAAGUUAGUGGGUUUUAGUUACUUAUUUUGAAAUGUAAAUAGCGCAACAGGUGCCAUAUACAAAC-UGCCUUUUUUUCGUUUUAGUUUACUUAUUGUGAAAUGUAAAUAUGUCCCAC-UGCUCAAUUUUUAACGGGACUCCAG-GUUUUAGUUACUUAUUAUGAAAUGUAAAUUUGGUUCCUUUGGAAAACAACAAUAACGUGUAGUAUUGUUUUAUUCAAUCAUUCAGAAUUGGUAAAUGCAGAAGCAGCAAAAUAACCAAAAGUAAUGACUUU----CGUUUUAAUUUCUUAAGAUGAAAUAUAAAU---GAAAACCUGUUAUACAUAGGAUUAUCUAUUUCCGUUAUAAUUAUUCCUUGCAA
AARU02000001.1/34131-34478 AAU-----------CCGCGUUUUAGUUACUUAUUUUGAAAUGUAAAU--CUAGAACAAAAGAAAAAUCA--U-GAGGGAUAUUUACGUUUUAGUUACUUAUUUUGAAAUGUAAAUGGUUUUGAAUGCUGGUGGUGAUAGUCCUAAUGAAG-GUUUUAGUUACUUAUUAUGAAAUGUAAAUUUGGUUCCUUUGGAAAACAACAAUAACGUGUAGUAUUGUUUUAUUCAAUCAUUCAGAAUUGGUAAAUGCAGAAGCAGCAAAAUAACCAAAAGUAAUGACUUU----CGUUUUAAUUUCUUAAGAUGAAAUAUAAAU---GAAAACCUGUUAUACAUAGGAUUAUCUAUUUCCGUUAUAAUUAUUCCUUGCAA
CP002002.1/524068-524429   AAGAGGAGAUUUUAGAUGUUUUUUGGUAGGUCGACAGAAAUAGCUCU--UU-GAGGUAAGAUGGGAGUAAGAAGAAAAGUUAGUGGGUUUUAGUUACUUAUUGUGAAAUGUAAAUUGCUCUCUUUUGUGUAAAGCACAUCAAGCAUGUAGCGUUUUAGUUACUUAUUGUGAAAUGUAAAUGCGAUUUUUGUC-AAAGGGACAGCGAUGGGUUACAA-GUUUUAGUUACUUAUUGUGAAAUGUAAAUUU----ACCACCAAAGUCCCUACACUCAAUACCACCAAAGCGUUUUAGUUACUUAUUGUGAAAUGUAAAUCGCUCUGACCUGUUCCUUGU-GCAACACUCGUUACAGUUUUAGUUACUUAUUGUGA
CP002003.1/543034-543393   AAGAAGAAAAGUUAGUGGGUUUUAGUUACUUAUUGUGAAAUGUAAAU--CGAUAAAAAAGAUAUUAGUAAUU-UAUUUGCAAUUUAGUUUUAGUUACUUAUUGUGAAAUGUAAAUUGCUCUCUUUUGUGUAAAGCACAUCAAGCAUGUAGCGUUUUAGUUACUUAUUGUGAAAUGUAAAUGCGAUUUUUGUC-AAAGGGACAGCGAUGGGUUACAA-GUUUUAGUUACUUAUUGUGAAAUGUAAAUUU----ACCACCAAAGUCCCUACACUCAAUACCACCAAAGCGUUUUAGUUACUUAUUGUGAAAUAUAAAU---GAAAACCUGUUAUACAUAGGAUUAUCUAUUUCCGUUAUAAUUAUUCCUUGCAA
#=GC SS_cons               ::::::::::::::::::<<<<<<<_________>>>>>>>------..-----------------------.-------------------------------((((((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<---<<<<<<<<___________>>>>>>>>-->>>>,,,,,,,,,,.,,,,,,,,,<<<<<<<<<<----.--<<<<<----<<<<<<<<<___________....______________________________________________>>>>>>>>>--->>>>>-...--->>>>>>>>>>,,,,,,,,,,,,,)))))):::::::::::::::::::::
#=GC RF                    AAgAaGAaAagUUAgugggUUUuaguUAcuUAuucugAAAuGuAaAU..cuagAaaaAAGauAuaAguAAau.uAaaugUuuuUuggUUUUAgUUACUUAUUgUGaAAugUAAAUugcUcUcuuUugUguAAaucAuAucaagcaUguAGCGUUUuAGUUACUUAUUaUgAAAUGUAAAugcGaUUuuUuUg.AAAagaACAguaAcGgGUcauAu.GUUUUAuUuAaUcAuccuGAAuUGuuAAuUu....AgCAgCAAAaUaaCuAaAauuAAUaaCuuuAAAGCGUUUUAaUUuCUUaggaUgAAAUaUAAAU...gAagACcUgUuacacAUAGgAuUAUccaUUuCcGUUaUAAUUAUUccUUGcAA
//
# STOCKHOLM 1.0

#=GF AC   RF01472
#=GF ID   rli40
#=GF DE   Listeria sRNA rli40
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   100.00
#=GF TC   207.10
#=GF NC   44.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17259222
#=GF RT   Identification of new noncoding RNAs in Listeria monocytogenes and
#=GF RT   prediction of mRNA targets.
#=GF RA   Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P
#=GF RL   Nucleic Acids Res. 2007;35:962-974.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   4


AL591978.1/115810-115547   GAAAUUAUUUUUAAUGUAAGUGAGGCGUCCUUAUGAAAAUUUCUAAACCAGCUUAUUUGGUUUUACUUGUUGUUGGCUUGGUUUUUGUUUUUCUAGGACUAUCUAAUAUAGGAAUCUCUAUUUUUUGGGAUUUUAGCGACUUAGAGAAUUUGAUGGUUGGUGGUUUGUUAAUCAUCAUUGGACUCAUCACACUUAGGAUUCGAUAUUCAUUUAAAAAAAGAGGAUAGAAAAAGCACUGCAAUUAUUGAUUGCAGUGCUUUUUCU
AL596168.1/16838-16576     GAAAUUAUUUUUAAUGUAAGUGAGGCGUCCUUAUGAAAAUAUCUAAACCGGCAUAUAUGGUUUUACUUGUUGUUGGCUUGGUUUUUGUUUUUUUGGGACUAUCUAAUAUCGGAAUUUCUAUUUUUUGGGACUUUAGCGACUUAGAAAAUAUGCUGGUUGGCUCUUUGCUAAUCAUCAUUGGGCUUAUUACACUUAGAGUUCGAUAUACAUUUAAAAAAAGAGGAUAGAA-AAGCACUGCAAAUUAUGAUUGCAGUGCUUUUCUA
AM263198.1/1260254-1259992 GGAAAUAUAUUUAAAGUAAGUGAGGCGUCCUUAUGAAAAUUUCUAAACCGGCAUAUAUGGUUUUGCUCGUUGUUGGCUUGGUUUUUGUUUUUUUAGGACUAUCUAAUAUCGGAAUUUCUAUUUUUUGGGAUUUUAGCGACUUAGAGAAUUUGAUGGUUGGUAGCUUAUUGAUCAUCAUUGGGCUCAUCACACUUAGAGUUCGGUAUUCAUUUAAAAAAAGAGAAUA-AAAAGGCACUGCAAUUUGAUUUUGCAGUGCUUUUUUA
AJ888460.1/14075-13815     GAAAUUAUUAUUA--GUAAGUGAGGCGUCCUUAUGAAAAUGUCUAAACCAGCAUAUAUCGUUUUGCUUGUUGUCGGCUUGGUUUUUGUUUUUUUAGGACUAUCUAACAUUGGGAUUUCGAUUUUCUGGGAUUUUAGUGAUUUAGAAAACUUGAUGGUUGGCUUAUUGUUAAUCAUUAUUGGGACAAUUACACUUAGAAUCCGCUAUUCGUUUAAAAAAAGAGGAUAGAA-AAGCACUGCAGUCAACUUUUGCAGUGCUUUUCUA
#=GC SS_cons               :::::[[[[[[[----[[[[[[[[,,<<<<<---<<<<<<<---<<<<<<<<--<<<-<<_____>>--->>>-->>->>>>>>->>>>>>>-->>>>>,,,,,,,,,,,,((((((,,<<<<<<<<<<__________>>>>>>>>>>,<<<<<<<<<<<_____>>>>>>>>>>>,,,,,,,,,,,,,,,,,,)))))),,,,]]]]]]]]------]]]]]]]<<<.<<<<<<<<<<<_______>>>>>>>>>>>->>>:
#=GC RF                    GaAAuuauccuuAAuGuaaguGagGCGuCCuUAUgaaaaugUCUaaaCCaGCaUauaUgGUUUUaCcuGUuguuGGCUuGGuuuUcguuuuuuUaGGaCUAUCUAAuAUuGGgauuuCuauuuucuggGAuUUUAGcGACuuagaaaauuuGauGguuggcuuuUUgcuaauCauCaUUGGgcuuAUuACACUUAgaaucCGaUAuuCauuuaAAAAAAgaggauagga.aaGCaCuGCaauuaauuuuuGCaGuGCuuUucca
//
# STOCKHOLM 1.0

#=GF AC   RF01473
#=GF ID   rli41
#=GF DE   Listeria sRNA rli41
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   55.00
#=GF TC   58.30
#=GF NC   35.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   6


AADQ01000044.1/10736-10242 UAGUAAGAUUUGAACUUGUGCUUUGAUUUAAGAGGAGGUAUUUUCUAUGACUAAAGUUAUUUUAACUAUUUUUGCAAUUAUUGUUCCCGCGUUUCUUGGAUUUAUACUUGCUUACCAAAUCUAUAAGAAAAAAACAGCCACUUAUAUGCCAUUAAAAAAUGAAUUUGUACACUGGGCUAAAUAAGCGCACAUUAAGGAGGAAAACAAAUUGAAAAAAACAGAAAGUGAAAAACCACUUGUCAUCAAAAUUGUUAUCAGCGUUCUCGUAGGUUUAUUUUUACUUAAUUUAAUGCCAUUUUUAGCGAUUUUCGGCUAAUUAUAUAUACUUAAAAAAGGCUUGAAGGUGCUUAUUUUUUAUGGUAUAUUGUAAAUUGUGUUGAAAUGAAUAGCAAUUUUUUAUGGUGAGACAAUUAAUGACAAAGAUGUCAGUUAAUGCUUUUUUUAUAAAAAGACUCCAGAGUGCCUAUUUAGAGGUGUUCUUGGGUCUUUUUUUGU
AL596168.1/18230-17738     UAGUAAGAUUUGUUCUUUUGUUUUGAUUUAAGAGGAGGUAUUUUCUAUGACUAAAGUUAUUUUAACUAUUAUCGCAAUUAUCGUUCCAGCAUUUCUUGGAUUUUUAUUUGCUUAUCAGAUUUAUAAGAAAAAAACUGCCACUUAUAUGCCACUAAAAAAUGAAUUUGUACACUGGGCAAAGUAAGCAUCUAAUAGGGAGGGAAUCAAGGUGAAAAAAACAGAAAGUGAAAAACCGCUUGUCAUCAAAAUUGUUAUUAGUGUUCUUGUUGGUUUAUUUUUACUUAAUUUAAUGCCAUUCUUAGCGAUCUUCGGUUAAUU-UUUUUACUUAAU-AGUGCUUGAAGCAGCUUAUUUUUUAUGGUAUAUUGUAAAUUGUGUUGAAAUGAAUAGCAAUUUUUUAUGGUGAGACAAUUAAUGACAGAGAUGUCAGUUAAUGCUUUUUUUAUAAAAAGACUCCAGAGUGCCGAUUUCGCGGUGUUCUUGGGUCUUUUUUUGU
AM263198.1/1261645-1261153 UAGUAAGUUCAGUUCAUGGGUUUUGAUUUAAGAGGAGGUAUUUUCUAUGACUAAAGUUAUUUUAACUAUUAUCGCAAUUAUUGUUCCAGCAUUUCUUGGAUUUUUAUUUGCUUAUCAGAUUUAUAAGAAAAAAACAGCCACUUAUAUGCCAUUAAAAAAUGAAUUUGUACAUUGGGCUAAGUAAGCACAAAUGAAGGAGGGAAACAAAAUGAAAAAAACAGAGAGUGAAAAGCCACUUGUUAUCAAAAUUGUUAUUAGUGUUUUAGUAGGUUUAUUUUUACUUAAUUUAAUGCCAUUUUUAGCCAUCUUUGGUUAAUU-UUUUUACUUAAAAG-UGCUUGAAGCAGGUUAUUUUUUAUGUUAUAUUGUAAAUUGUGUUGAAAUAAAUAGCAAUUUUUUAUGGUGAGACAAUUAAUGACAGUAAUGUCAGUUAAUGCUUUUUUUAUAAAAAGACUCCAGAGUGCCUUUUUUAUGGUGUUCUUGGGUCUUUUUUUGU
AL591978.1/117207-116713   UAGUAAGAUUUGAACUUGUGCUUUGAUUUAAGAGGAGGUAUUUUCUAUGACUAAAGUUAUUUUAACUAUUUUUGCAAUUAUUGUUCCCGCGUUUCUUGGAUUUAUACUUGCUUACCAAAUCUAUAAGAAAAAAACAGCCACUUAUAUGCCAUUAAAAAAUGAAUUUGUACACUGGGCUAAAUAAGCGCACAUUAAGGAGGAAAACAAAUUGAAAAAAACAGAAAGUGAAAAACCACUUGUCAUCAAAAUUGUUAUCAGCGUUCUCGUAGGUUUAUUUUUACUUAAUUUAAUGCCAUUUUUAGCGAUUUUCGGCUAAUUAUAUAUACUUAAAAAAGGCUUGAAGGUGCUUAUUUUUUAUGGUAUAUUGUAAAUUGUGUUGAAAUGAAUAGCAAUUUUUUAUGGUGAGACAAUUAAUGACAAAGAUGUCAGUUAAUGCUUUUUUUAUAAAAAGACUCCAGAGUGCCUAUUUAGAGGUGUUCUUGGGUCUUUUUUUGU
AE017262.2/1259510-1259017 UAGUAAGGUCUGAACAUGUGUUUUGAUUUAAGAGGAGGUAUUUUCUAUGACUAAAGUUAUUUUAACUAUUUUUGCAAUUAUCGUUCCUGCGUUUCUCGGAUUUAUACUUGCUUACCAAAUCUAUAAGAAAAAAACAGCCACUUAUAUGCCAUUAAAAAAUGAAUUUGUACAUUGGGCUAAAUAAGCGCACAUUAAGGAGGAAAACAAAUUGAAAAAAACAGAAAGUGAAAAACCACUUGUCAUCAAAAUUGUUAUCAGUGUUCUUGUAGGUUUAUUUCUACUUAAUUUAAUGCCAUUUUUAGCGAUUUUCGGCUAAUUAUUUAUACUUAAAAA-GGCUUGAAGGUGCUUAUUUUUUAUGGUAUAUUGUAAAUUGUGUUGAAAUGAAUAGCAAUUUUUUAUGGUGAGACAAUUAAUGACAAAGAUGUCAGUUAAUGCUUUUUUUAUAAAAAGACUCCAGAGUGCCUGUUUAGUGGUAUUCUUGGGUCUUUUUUUGC
AADR01000036.1/3819-4312   UAGUAAGGUCUGAACAUGUGUUUUGAUUUAAGAGGAGGUAUUUUCUAUGACUAAAGUUAUUUUAACUAUUUUUGCAAUUAUCGUUCCUGCGUUUCUCGGAUUUAUACUUGCUUACCAAAUCUAUAAGAAAAAAACAGCCACUUAUAUGCCAUUAAAAAAUGAAUUUGUACAUUGGGCUAAAUAAGCGCACAUUAAGGAGGAAAACAAAUUGAAAAAAACAGAAAGUGAAAAACCACUUGUCAUCAAAAUUGUUAUUAGUGUUCUUGUAGGUUUAUUUCUACUUAAUUUAAUGCCAUUUUUAGCGAUUUUCGGCUAAUUACUUAUACUUAAAAA-GGCUUGAAGGUGCUUAUUUUUUAUGGUAUAUUGUAAAUUGUGUUGAAAUGAAUAGCAAUUUUUUAUGGUGAGACAAUUAAUGACAAAGAUGUCAGUUAAUGCUUUUUUUAUAAAAAGACUCCAGAGUGCCUGUUUAGUGGUAUUCUUGGGUCUUUUUUUGC
#=GC SS_cons               ::{{{{{{,,,,,,,,,,,{{{{{,,,,((((-((--((-((((((<<<<<____>>>>>,,,,,,,,,,,,,<<<<-<<----<<<<<______>>>>>---->>->>>>,,,,,,,,,,,,,,))))))--))--))-)))),,,[[[[-[[[[[[[[,,,,,,,,,,,,,,,,<<<----<<<<<--------------------------------<<<<<<<______>>>>>->>---------------->>>>>---->>>(((((((((-((-((((((((((((((,,<<<<<________>>>>>,,,,,,,,,,,,,,,,,.<<<_____>>>,,,,,,,,,,,)))))))----)))))))-))-))))))))),,,,]]]]]]]]]]]]}}}}},<<<<<<<<<<____>>>>>->>>>>,,,,,}}}}}}<<<<<<<<<<-<<<<--<<<______>>>-->>>>->>>>>>>>>>::::
#=GC RF                    UAguaagaUuuGaaCaUguGuuuuGAUUuaaGAGGAGGuAuuuuCuaugaCUAAAGuuauUUUAACUAUUuUuGCaaUuaUuGUuCCcgCgUUUCugGGaUUUauacuuGCUUAcCAaAUcUAUAaGaaaaAAaCAGCCACuuaUAUgCCaUuaaaaaauGAAUUUGUACAuUGGGCuaAaUAagCgcAcAuuAAGGAGGaAAACAAAuUGAAAAAAACAGaaaGuGAAAAACCaCuuGuCAUCAAAAUUGUUAUuAgcGuucUuGuaGguucauuucUaCUuaauuuaaugcCauUUuuagCgAUuUUcGGcuaaUUAUuUaUACUUAAAAA.ggCUUGAAGccGcUUAUUUUUUauGguauAUUGuaaauugUGuUgaaaugaauAGCAauuuuuuauGGugagaCAauuaauGaCaaAgAuGuCaGuuaauGCUUUuuuuauaaaaaGaCuCCaGagUGCCgaUUUagcGGUguuCuUGgGuCuuuuuUUGu
//
# STOCKHOLM 1.0

#=GF AC   RF01474
#=GF ID   rli42
#=GF DE   Listeia sRNA rli42
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   147.90
#=GF NC   49.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   4


AM263198.1/1378553-1378383 UAACUGAAAUGCUUUAUGAGAGGAGUUUUCUUCCGCAAUGACUAAUAAAAAAGUAGUUCGCGUUGUCGUUAUCUUAAUGCUAAUCGCGAUUGUAUUAUCCAGCGUUUUAACCGGGGUAUUAAUGUUUUU-AUAGAUAUCCGAUGUCUGAGCCAAUAUGGUUCAGACUUUUUU
AL596168.1/188493-188323   UAUCUGAAAUGCUUUAUGAGAGGAGUUUUCUUCCGCAAUGACUAAUAAAAAAGUAGUUCGCGUUGUCGUUAUUUUAAUGUUAAUCGCGAUUGUAUUAUCCAGCGUUUUAACCGGGUUACUAAUGUUUUU-AUAGACAUCCGAGGUCUGAGCCAAUUUGGUUCAGGCUUUUUU
AL591978.1/239617-239447   UAUCUGAAAUGCUUUAUGAGAGGAGUUUUCUUCCGCAAUGACUAAUAAAAAAGUAGUUCGCGUUGUCGUUAUUUUAAUGUUAAUCGCGAUUGUAUUAUCAAGUGUUUUAACCGGGGUAUUAAUGUUUUU-AUAAAUAUCCAACGUCUGGGCCGAUUUGGUUCAGACUUUUUU
FM242711.1/1383323-1383154 UAUCUGAAAUGCUUUAUGAGAGGAGUUUUCUUCCGCA-UGACUAAUAAAAAAGUAGUUCGCGUUGUCGUUAUUUUAAUGCUAAUCGCGAUUGUAUUAUCCAGUGUUUUAACCGGGGUAUUAAUG-UUUUUAUAAAUAUCCGACGUCUGAGCCAAUUUGGUUCAGGCUUUUUU
#=GC SS_cons               ::::[[[[[[[[[--[[[[,,<<<<_____>>>>(((((<<<<<_________>>>>><<<<<<<-<<<<<___>>>>>->>>->>>>))))),]]]]--]]]]]]]]],,,,<<<<<<<-<<<____>.>>->>>>>>>,,,<<<<<<<<<_____>>>>>>>>>::::::
#=GC RF                    UAuCugaaacgCuUUaugaGAGGagUUUUCcuCCgCaaugaCuaAUAAAAAAGuaGucCGCGuugUCguuaUuUuaacGucaaUCGCGauuGcAucauCcaGcguuucaACCGGGguaucAaugUUUUc.auAgauacCCgAuGcCuGagCCaAUuUGGcuCaGgCUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01475
#=GF ID   rli45
#=GF DE   Listeria snRNA rli45
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold
#=GF GA   60.00
#=GF TC   89.80
#=GF NC   39.50
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   6


AADR01000003.1/142171-142094 UUACUAUUUGCGCAAGUUUUUACUUGUAUAGUUAUGCUUUAGCUCGUGACAAUUCCAGUAUGAAUGACACUGCAACAA
AM263198.1/2127523-2127600   UUACUAUUUGCGCAAGUUUUUAUUUAUAUAGCUAUGCGCUAGCUCGUGAUAAUUCAAGUAUGAAUGAUGAACCAACGA
AL596171.1/97397-97474       UUAGUAUUUGCGCAAGUUUUUACUUAUAUAGCUAUGCGCUAUCUCGUGAUAAUUCAAGUAUGAAUGAUAAACCGACUG
AL591982.1/53775-53852       UUACCAUUUGUGCUAGUUUUUACUUAUAUAGCUAUGCUUUAGCGCGCGACAAUUCAAGUAUGAACGACACAGCAACAA
AADQ01000011.1/3685-3762     UUACCAUUUGUGCUAGUUUUUACUUAUAUAGCUAUGCUUUAGCGCGCGACAAUUCAAGUAUGAACGACACAGCAACAA
AARL02000916.1/597-673       UUACUAUUUGCGCAAGUUUUUACUUAUAUAGUUAUGCUUUAGC-UGUGGUAAUUCCAGCAUGAAUGACACUGCAACAA
#=GC SS_cons                 :::::::((((((<<<<____>>>>,,,,,<<<<_____>>>>,,)))-)))::::::::::::::::::::::::::
#=GC RF                      UUAcuAUUUgcgCaAGUUUUUACUuAUAUAGcUAUGCuuUAgCuCGcgAcAAUUCaAGUAUGAAuGAcAcagCAACaA
//
# STOCKHOLM 1.0

#=GF AC   RF01476
#=GF ID   rliF
#=GF DE   Listeria sRNA rliF
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR
#=GF GA   60.00
#=GF TC   63.20
#=GF NC   52.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17259222
#=GF RT   Identification of new noncoding RNAs in Listeria monocytogenes and
#=GF RT   prediction of mRNA targets.
#=GF RA   Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P
#=GF RL   Nucleic Acids Res. 2007;35:962-974.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   5


AL591982.1/6292-6073         GAUGGGCAACCUAGUUUUUAUUUAAGGAGAAUUUGUUUAUUUAAAUCAAGGGCAAGCAAAAAUGUAAAAAAAGGGUAUACCCAAAAUAUACCCAAAACCAUCAUUGUAAAUACACUUUUUUCAAUGUAUAGCUAGGGUGGAUAUUAAUUGGUUGUGAAAAGAGUUG-CUUUUUAGUCAUGAUAGUAGCAUAUACUCGAGUAAGUUCUACAGAUUAAAAUUU
AADR01000024.1/29055-28843   GGGUGAUAAUUUCAUCUUCUCUU-UUUUGCUUUUAUAUUUUG----GUACAGCUGAUUCAUGUAAAAAA--AGGGUAUACCCAAAAUAUACACAAAACCAUCAGUGUAAAUGCAUUUUUUUCAAUGUAUAGUUAGGGUGGAUAUUAAAUGGUUGUGAAAAGAGUUG-CUUUUUAGUCAUGAUAGUAGCAUAUGCUCGAGUAAGUUCUACAGAUUAAAAUUU
AARQ02000010.1/106031-106250 UAAGGAUAGUUGUAUUUUUUAUUAUUUUGAAAUCAAUUGAGUACAUUUAGAGUGAGAACGAUUGUAUGAAUAGGGUAUACCCAAAAUAUACACGAAAGCAUCGUUGUAAAUACAUGAUUUUAGGUGUAUGAUUAGGGUGUAUAUUAAAUGGUUUUGAAAAGAGGUG-CUUUUUAGUCAUGAAAGUAGCAUAUGCUCGAGUAAGUUCUACAGAUCAAAAUUU
AADQ01000022.1/19284-19490   UAAGGAUAGUUGUAUUUUUUAUUAUUUUGAAAUCAAUUGAGUACAUUUAGAGUGAGAACGAUUGUAUGAAUAGGGUAUACCCAAAAUAUACACGAAAGCAUCGUUGUAA-------AUACAUGAU------UUUAGGUGUAUAUUAAAUGGUUUUGAAAAGAGGUG-CUUUUUAGUCAUGAAAGUAGCAUAUGCUCGAGUAAGUUCUACAGAUCAAAAUUU
CP002001.1/517488-517687     GGAUGAUAAUUUCAUCUUCUCUUUUUU-GAUUUUAUAUUUUG----GUACACCUAAUUAAUGUGAAAAU---GGGUAUAUCCAAAAUGUACACAAAACCGUUAUUGUGAAUACA-----------GGAUUUUCAA--UGUAUAUUAAAUAAUUUUGAAAAGAGGGGGCUUUUUAGUCACGAAAGCAGCAUAUGCUCAAGUAAGUUCUUCUAAUCAAAAUUU
#=GC SS_cons                 :<<<<<<______>>>>>>,,,,,,,,,,,,,,<<<<<<___________________>>>>>>,,,,,,,,<<<____>>>,,<<<<<<<<<___________________________________________>>>>>>>>>,,,,((((((((<<<<<<___.>>>>>>,,,,,,,,,,<<<<-<<-<<<____>>>->>->>>>,,,)))))))):
#=GC RF                      ggaggauAaUUuuaucuucuaUUauuuuGAauUcacuuguuuAaAUuuAgAgcuAguacaaguguAaaAAuAGGGUAUACCCAAAAUaUaCaCaAAAcCAUcaUUGUAAAUACAuuuUuuuuaAUGuAUagUUAgGGuGuAuAUUAAAUggUUuUGAAAAgAGguG.CUuUUUAGUCAUGAaAGuAGCAuAUgCUCGAGuAAgUUCUaCAGAUCAaAAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF01477
#=GF ID   rli43
#=GF DE   Listeria sRNA rli43
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   100.00
#=GF TC   191.80
#=GF NC   98.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   4


Y07640.1/1549-1802         UAAAUGGCGCGGGAUGGUAUACUAUACAAGCGUAUGGUUCAAAAAGAUACUUUGAAUUAAGAAGUACAAUAAAGUUAACUUCAUUAGACAAAAAGAAAAAACAAGGAAGAAUAGUACAUAGUUAUAAAUACU-UGGAGAGUGAGGUGUAAUAUGGGGGCAGCUGAUUUUUGGGGUUUCAUAUAUGUAGUUUCAAGAUUAGCCAUUGUUGCGGCAGUAGUUUACUUCUUAUACUUAUUGAGAAAAAUUGCAAAUAA
AADQ01000126.1/458-206     UAAAUGGCGCGGGAUGGUAUACUAUACAAGCGUAUGGUUCAAAAAGAUACUUUGAAUUAAGAAGUACAAUAAAGUUAACUUCAUUAGACAAAAAGAAAAAACAAGGAAGAAUAGUACAUAGUUAUA-AUACU-UGGAGAGUGAGGUGUAAUAUGGGGGCAGCUGAUUUUUGGGGUUUCAUAUAUGUAGUUUCAAGAUUAGCCAUUGUUGCGGCAGUAGUUUACUUCUUAUACUUAUUGAGAAAAAUUGCAAAUAA
AE017262.2/1841336-1841083 UACAUGGUCCGGGAUGGUAUACUAUACAAGCGUAUGGUUCAAAAAGAUACUUUGAAUUAAGAAGUACAAGAAAGUUAACUUCAUUAGACAAAAAGAAAAAACAGGCAAGAAUAGUACAUAGUUAUAAAUACUGUGGAGAGUGAGGUGUAAUAUGGGAGCAGCUGAUUUUUGGGGUUUCAUAUAUGUAGUUUCAAGA-UAGCUAUUGUUGCGGCAGUGGUUUACUUCUUAUACUUAUUGAGAAAAAUUGCAAAUAA
CP002002.1/2320764-2320510 UAAAUGGUGCGGGAUGGUAUACUAUACAAGCGUAUGGUUCAAAGAGAUACUUUGAAUUAAGAAGUACAAUAAAACUAUCUAAACUAGAUAAAAAGAAGAAAACAGCUUAUGUAGUACAUAAGUAUAAAUACUAUGGAGAGUGAGGUGCAAUAUGGGGGCAGCUGAUUUUUGGGGUUUCAUAUAUGUUGUUUCAAGAUUAGCCGUUGUUGCGGCAGUGGUUUACUUCUUAUAUUUAUUGAGAAAAAUUGCAAAUAA
#=GC SS_cons               ::::[[-[[[[[[[[[[[,,<<<<<<<____>>>>>>><<<<<_______>>>>>,,,,,((((((((--------((((((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<_______>>>>>><<<<<<-<<-<<<_________>>>->>->>>>>>))))))-------))))-)))),,,,,,,]]]]]]-]]]]]-]]<<<<<<<--<<<<<<_______>>>>>>>>>>>>>::::::
#=GC RF                    UAaAuGGcgCgggauGGuAUaCuauaCAAGCGuaugGuuCaaaaAGAUACuuuGaAUUAAGaaguaCaAuAAAguUaaCuccAuUAGAcAAAAAGAAaAAAcaaGgaagaaUAGUACacaguUAUAAAUacuguGgagaguGaGGuGcAAUAUGGGggCaGCuGauuuuugggGuuUCAUAUAuGuaGuuuCAAGAUUAgCCauuGuuGcgGCaGuaguuuACuuCuuaUAcUUAUugaGaaaaauugCAAAUAA
//
# STOCKHOLM 1.0

#=GF AC   RF01478
#=GF ID   rli47
#=GF DE   Listeria sRNA rli47
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold
#=GF GA   200.00
#=GF TC   413.00
#=GF NC   36.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   9


AM263198.1/2196592-2197100   UAUAUAUGUAAUACAACAAAC-AAUAAAAGGUGAUGCGAAUGACAAAAAUUUGGUGUACAAGCUGA-UUUUUUCUCAGCUUUGUCAUAUGCCGGC-AAACGUCUGGUGAAGGAUUUUAGUGUCAAAGGACAGAUGGUUAGCUUACAGGAGGAAGGCGAGGAGUAUACGCCGCGUCAGGGACUAUAUGCUAACUUAAGUUCUAGGGAGACGGAAUUUCGUUACGUCGCUCAUUUAUCAAUAU--UAUCAUCCUCACUACAUUGGUAAAUAAGCGAAUAAAGUAUCGUAUCAUUUAUGGCCACUAUUUAAACAAGUUACGGGCGCUCAUUUAUUCGCAAGUUUGAAUAUCUUGAGAAGUAAGUAGUAAGAUAAAUAAUUCGCCUACUUGUUUGAAAAUGCCUCACCGUUUUCCGAAUGUUGUAUGUUUAUUCAGAAACAUCCAGACAUGGUCCGGCCCAUCAGAUGAGUGGCAAGACAAGCUCAUCCGAAAAGAAAAACCUCGUGUGACGAAAUCG
AE017262.2/2215984-2216493   UAUAUAUAAAGUACAACGAACAAAUAAAAGGUGAUGCGAAUGAAACAAACUUGGUGUACAAGCUGAUUUUUUUCUCAGCUUUGUCAUAUGCCGGCAAAACGUCUGGUGAAGGAUUUUAGUGUC-AAGCAGCUACGGUUAGCUUACAGGAGGAAGGCGAGGAGUAUACGCCGCGUCAAGGACUUUACGCUAACUUA-GUUGUAGGAAGACGGAAUUUCGUUACGUCGCUCGUUUAUCAAUAU--UUUUAUCCUCACUACAUUGGUAAAUAAGCGAAUAAAGUAUCGUAUCAUUUAUGGCCACUAUUUAAGCAAGUUACGGGCGCUCAUUUAUUCGUAAGCUAGAAUAUCUUGAGAAGUAAGUAGCAAGACAAAGAAUUCGCCUACUUGUUUGAAAAUGCCUCACCGUUUUCCGAAUGUUGUAUGUUUAUUCAGAAACAUCCAGACAUGGUCCGGCCCAUCAGAUGAGUGGCAAGACAAGCUCAUCCGAAAAGAAAAACCCCGCGUGACGAAAUCG
AL596171.1/167376-167885     UAUAUAUAGAGUACAACGAAC-AAAAAAAGGUGAUGCGAAUGACAAAAACUUGGUGUACAAGCUGAUUUUUUUCUCAGCUUUGUCAUAUGCCGGCAAAACGUCUGGUGAAGGAUUUUAGUGUC-AAGCAACUAUGGUUAGUUUACAGGAGGAAGGCGAGGAGUAUACGCCGCGUCAAGGACUUUACGCUAACUUA-GUUGUAGGAAGACGGAAUUUCGUUACGUCGCUCGUUUAUCAAUAU-UUUUUAUCCUCACUACAUUGGUAAAUAAGCGAAUAAAGUAUCGUAUCAUUCAUGGCCACUAUUUAAGCAAGUUACGGGCGCUCAUUUAUUCGUAAGUUAGAAUAUCUUGAGAAGUAAGUAGCAAGACAAAGAAUUCGCCUACUUGUUUGAAAAUGCCUCACCGUUUUCCGAAUGUUGUAUGUUUAUUCAGAAACAUCCAGACAUGGUCCGGCCCAUCAGAUGAGUGGCAAGACAAGCUCAUCCGAAAAGAAAAACCCCGUGUGGCGAAUUUG
AL591982.1/126024-126532     UAUAUAUAUAGUACAACGAACAAAUAAAAGGUGAUGCGAAUGAAACAAACUUGGUGUACAAGCUGA-UUUUUUCUCAGCUUUGUCAUAUGCCGGC-AAACGUCUGGUGAAGGAUUUUAGUGUC-AAGCAACUACAGUUAGCUUACAGGAGGAAGGCGAGGAGUAUACGCCGCGUCAAGGACUUUACGCUAACUUA-GUUGUAGGAAGACGGAAUUUCGUUACGUCGCUCGUUUAUCAAUAUUUUUU-AUCCUCACUACAUUGGUAAAUAAGCGAAUAAAGUAUCGUAUCAUUCAUGGCCACUAUUUAAGCAAGUUACGGGCGCUCAUUUAUUCGUAAGUUAGAAUAUCUUGAGAAGUAAGUAGCAAGACAAAGAAUUCGCCUACUUGUUUGAAAAUGCCUCACCGUUUUCCGAAUGUUGUAUGUUUAUUCAGAAACAUCCAGACAUAGUCCGGCCCAUCAGAUGAGUGGCAAGACAAGCUCAUCCGAAAAGAAAAACCCCGCGUGACGAAAUCG
AARK02000013.1/18729-18220   UAUAUAUAAAGUACAACGAACAAAUAAAAGGUGAUGCGAAUGAAACAAACUUGGUGUACAAGCUGAUUUUUUUCUCAGCUUUGUCAUAUGCCGGCAAAACGUCUGGUGAAGGAUUUUAGUGUC-AAGCAGCUACGGUUAGCUUACAGGAGGAAGGCGAGGAGUAUACGCCGCGUCAAGGACUUUACGCUAACUUA-GUUGUAGGAAGACGGAAUUUCGUUACGUCGCUCGUUUAUCAAUAU--UUUUAUCCUCACUACAUUGGUAAAUAAGCGAAUAAAGUAUCGUAUCAUUUAUGGCCACUAUUUAUGCAAGUUACGGGCGCUCAUUUAUUCGUAAGCUAGAAUAUCUUGAGAAGUAAGUAGCAAGACAAAGAAUUCGCCUACUUGUUUGAAAAUGCCUCACCGUUUUCCGAAUGUUGUAUGUUUAUUCAGAAACAUCCAGACAUGGUCCGGCCCAUCAGAUGAGUGGCAAGACAAGCUCAUCCGAAAAGAAAAACCCCGCGUGACGAAAUCG
AARQ02000001.1/169323-168815 UAUAUAUAUAGUACAACGAACAAAUAAAAGGUGAUGCGAAUGAAACAAACUUGGUGUACAAGCUGA-UUUUUUCUCAGCUUUGUCAUAUGCCGGC-AAACGUCUGGUGAAGGAUUUUAGUGUC-AAGCAACUACAGUUAGCUUACAGGAGGAAGGCGAGGAGUAUACGCCGCGUCAAGGACUUUACGCUAACUUA-GUUGUAGGAAGACGGAAUUUCGUUACGUCGCUCGUUUAUCAAUAU-UUUUUAUCCUCACUACAUUGGUAAAUAAGCGAAUAAAGUAUCGUAUCAUUCAUGGCCACUAUUUAAGCAAGUUACGGGCGCUCAUUUAUUCGUAAGUUAGAAUAUCUUGAGAAGUAAGUAGCAAGACAAAGAAUUCGCCUACUUGUUUGAAAAUGCCUCACCGUUUUCCGAAUGUUGUAUGUUUAUUCAGAAACAUCCAGACAUAGUCCGGCCCAUCAGAUGAGUGGCAAGACAAGCUCAUCCGAAAAGAAAAACCCCGCGUGACGAAAUCG
AARM02000021.1/10235-10743   UAUAUAUAUAGUACAACGAACAAAUAAAAGGUGAUGCGAAUGAAACAAACUUGGUGUACAAGCUGA-UUUUUUCUCAGCUUUGUCAUAUGCCGGC-AAACGUCUGGUGAAGGAUUUUAGUGUC-AAGCAACUACAGUUAGCUUACAGGAGGAAGGCGAGGAGUAUACGCCGCGUCAAGGACUUUACGCUAACUUA-GUUGUAGGAAGACGGAAUUUCGUUACGUCGCUCGUUUAUCAAUAU-UUUUUAUCCUCACUACAUUGGUAAAUAAGCGAAUAAAGUAUCGUAUCAUUCAUGGCCACUAUUUAAGCAAGUUACGGGCGCUCAUUUAUUCGUAAGUUAGAAUAUCUUGAGAAGUAAGUAGCAAGACAAAGAAUUCGCCUACUUGUUUGAAAAUGCCUCACCGUUUUCCGAAUGUUGUAUGUUUAUUCAGAAACAUCCAGACAUAGUCCGGCCCAUCAGAUGAGUGGCAAGACAAGCUCAUCCGAAAAGAAAAACCCCGCGUGACGAAAUCG
CP002002.1/2183984-2184491   UAUAUAUAUAGUACAACGAACAAAUAAAAGGUGAUGCGAAUGAAACAAACUUGGUGUACAAGCUGA-UUUUUUCUCAGCUUUGUCAUAUGCCGGC-AAACGUCUGGUGAAGGAUUUUAGUGUC-AAGCAACUACAGUUAGCUUACAGGAGGAAGGCGAGGAGUAUACGCCGCGUCAAGGACUUUACGCUAACUUA-GUUGUAGGAAGACGGAAUUUCGUUACGUCGCUCGUUUAUCAAUAU--UUUUAUCCUCACUACAUUGGUAAAUAAGCGAAUAAAGUAUCGUAUCAUUCAUGGCCACUAUUUAAGCAAGUUACGGGCGCUCAUUUAUUCGUAAGUUAGAAUAUCUUGAGAAGUAAGUAGCAAGACAAAGAAUUCGCCUACUUGUUUGAAAAUGCCUCACCGUUUUCCGAAUGUUGUAUGUUUAUUCAGAAACAUCCAGACAUGGUCCGGCCCAUCAGAUGAGUGGCAAGACAAGCUCAUCCGAAAAGAAAAACCCCGCGUGACGAAAUCG
AARN04000036.1/7713-7209     UAUAUAUAUAGUACAA---ACAAAGAAAAGGUGAUGCGAAUGACUCAAACUUGGUGUACAAGCUGAUUUUUU-CUCAGCUUUGUCAUAUGCCGGC-AAACGUCUGGUGAAGGAUUUUAGUGUC-AAACAGCUACGGUUAGCUUACAGGAGGAAGGCGAGGAGUAUACGCCGCGUCAAGGACUUUACGCUAACUUA-GUUGUAGGAAGACGGAAUUUCGUUACGUCGCUCGUUUAUCAAUAU--UUUUAUCCUCGCUACAUUGGUAAAUAAGCGAAUAAAGUAUCGUAUCAUUCAUGGCCACUAUUUAAGCAAGUUACGGGCGCUCAUUUAUUCGUAAGUUAGAAUAUCUUGAGAAGUAAGUAGCAAGACAAGUAAUUCGCCUACUUGUUUGAAAAUGCCUCACCGUUUUCCGAUUGUUGUAUGUUUAUUCAGAAACAUCCAGACAUGGUCCGGCCCAUCAGAUGAGUGGCAAGACAAGCUCAUCCGAAAAGAAAAACCCCGCGUGACGAAUUCG
#=GC SS_cons                 ::::::::::::::::::::::::::::::{{-{{{{{------------{{{{{{--{,<<<<<<._______>>>>>>{{{{{---{{{{{-{.---{{{{{{{{{--{{{{{---{{{{{.,,<<<<<---<<<<<<<-<<-<<------<<<<-<<-<____>->>->>>>----->>->>->>>>>>>--.>>>>>,[[[[[[[[[,,,,,<<-<<<-<<<<<-<<<<<<<<<<__.._______________>>>>>>>>>>->>>>>----->>>->>,,,,,,,,,,(((-----(((((((((((---((((<<<-<<<<<<<<-<<<<_________>>>>->->>>>>>>>>>,,<<________>>)))))))))))))))---))),,,]]]]]]]]]<-<<<<<---<<______>>-->>>>>->,}}}}}}}}}}----}}}}}}}}}-}}}}}}-}}}}}}--}}-}}}}------------}}}}}-}}:::::::
#=GC RF                      UAUAUAUAuAgUACAAcgAACAAAuAAAAGGuGacGCGAAUGAaAcAAAcucGGuGUACAaGCuGa.UUUUUUCuCaGCuuuGuCAUAuGCCgGC.AAACguCuGguGAAGGaccUUAguGuC.AAgcaacuAcgGuuaGcUuaCaGGAGGAAGgCGAGGAGUAUACGCCGCGcCAAGGACuuuacgCuaaCcUA.guugcAGGaagaCGGAAUUUCGUuaCGuCGCuCguuuacCaauAU..UuUuAUCCUCACUACauuGguaaacAaGCGaAUAAAGuaUCGUAUCAUUcAUGGCCACUAuucaagCaaGuUACgGGCGCuCacuuacuCGcaaGuUAGAAUAUCuugAGAaguaaguaGCAAGacAAAgAAUuCGCCcaCuuGcuugaaAAUGCCUCACCGucuuCCGAauGuuGUAuGUUUAUUCaGAaaCauCCAGaCacgguCCGGCCCacCaGacGAGcGGCaAGaCaaGCUCaUCCgaAAAGAAAAACCcCGCguGaCGAAaUcG
//
# STOCKHOLM 1.0

#=GF AC   RF01479
#=GF ID   rli48
#=GF DE   Listeria sRNA rli48
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNaalfold
#=GF GA   100.00
#=GF TC   169.50
#=GF NC   52.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   3


AL596172.1/225721-225572   GACGUGAUAUACUUUUAAUAGAGGGAGGGGAGUUUCACCCCUCUG-AUUUAGCGGUUCUUGUCUUUAUCAUUCUUGUGUAUUGUUGUCAGCGCUACUACAAGAGUGAUAAUUUCAAGGACUGUUUUUAUUUCCUCUAAAACAUCUUUCACU
AL591982.1/261423-261274   GGCAUGUUAUA-AUUUAUUAGAGGGAGGGGAAUUCCACCCCUCUGAAUUUACUUGUCCUUGUUUUUAUCUUUCUUGCGUAAUGUUAUCAGCGCUACUGCAAGAGUGAUAAUUUCGAGGACUGUUUUUAUUUCCUCUAAAACAUCCUUCACU
CP002003.1/1286157-1286304 GACGUGAUAUA-CUUUUAUAGAGGGAGGGGAGUUUCACCCCUCUG--GUUACUUGUCCUUGUUUUUGUCUAUCUUGCGUAAUGUUAUCAGCGCUACUGCAAGAGUUACAAUUUCAAGGACUGUUUUUAUUUCCUCUAAGAUGUCUUUCACU
#=GC SS_cons               :::((((----.------((((((<<<<<<_______>>>>>>,,.,,,,,,,,<<<<<<<---<<<<<-<<<<<<<<<<-<<<_____>>>->>>->>>>>>>->>>>>--->>>>>>>,,,,,,,,,,,))))))---------)))):
#=GC RF                    GaCguGaUAUA.uUUUaauaGaGGGaGGGGAgUUuCACCCCuCUG.AuUUAcuuGucCuuGUuUuugucucuCuuGcGuaauGuUaUCAgCgCuaCUgCaaGagUgacaaUUUCaaGgaCUGUUUUUAUUUCCuCuaAaAcaUCuUuCacU
//
# STOCKHOLM 1.0

#=GF AC   RF01480
#=GF ID   rli52
#=GF DE   Listeria sRNA rli52
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   72.90
#=GF NC   49.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   6


AL596165.1/82988-82894     AGCUAUAAAUAAAUAUCCUUAUUCAGGAAUGUUACC-AACUUGGGCAUAACCUAGAUAAAUGGAGAAUUGGCUUUUUGGGCU-AUUUUUCGAUUUAU
AM263198.1/506759-506663   UCUUAUAAACAAAUAUCCUUAUUCAGGAAUGUUACCUAAUUUGGGCAUAACCUAGAUAAAACGAAAAUUGGCUUUUGGGGCUGUUUUUUCGAUUUAU
AADQ01000001.1/70381-70475 UCCUAUAAACAAAUAUCCUUAUUCAGGAAUGUUACC-AACUUGGGCAUAACCUAGAUAAAUGGAGAACUGGCUUUUUGGGCU-AGUUUUCAAUUUAU
AE017262.2/560498-560404   UCCUAUAAACAAAUAUCCUUAUUCAGGAAUGUUACC-AACUUGGGCAUAACCUAGAUAAAUGGAGAAUUGGCUUUUUGGGCU-AGUUUUCGAUUUAU
CP001175.1/2103647-2103741 UCCUAUAAACAAAUAUCCUUAUUCAGGAAUGUUACC-AACUUGGGCAUAACCUAGAUAAAUGGAGAAUUGGCUUUUUGGGCU-AGUUUUCGAUUUAU
AL591975.1/192421-192327   UCCUAUAAACAAAUAUCCUUAUUCAGGAAUGUUACC-AACUUGGGCAUAACCUAGAUAAAUGGAGAACUGGCUUUUUGGGCU-AGUUUUCAAUUUAU
#=GC SS_cons               :::::::::::::::<<<<_____>>>>,,,,,,,,.,,,<<<<<_____>>>>><<<<<<-<<<<<<<<<<<_____>>>>.>>>>>>>->>>>>>
#=GC RF                    uccUAUAAAcAAAUAuCCuUAUUCaGGaAUGUUACC.AAcuugGGCAUAACCuagauaaaugGagaacugGCuUUUuGgGCu.aguucuCgauuuau
//
# STOCKHOLM 1.0

#=GF AC   RF01481
#=GF ID   rli53
#=GF DE   Listeria sRNA rli53
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   74.80
#=GF NC   37.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   5


AL596166.1/244646-244818 ACGAAAAGGAGUGUUAUCUUAAGCCAAUGAAAUUCUAAUCCUGUAUUAUAUGAAAAAAUGAAGAAAGCUAUCCAAUUCUUGGGUAGAAACUAUUUUUUCGGACGGGAUUCGUAUGUUCAUUUCGCAUGAUAACUCUAGCUAUAGCCU---UUUUUGGCGUAGUUUCGCGGAUUCCU
AM263198.1/927833-928006 ACGAAAAGGAGUGUUAUCUUAAGCCAAUGAAAUUCUAAUCCUGUAUUAUAUGAAAAAAUGAAGAAAGCUAUCCAAUUUUUGGGUAGAAACUAUUUUUUCGGACGGGAUUCGUAUGUUCAUUUUGCAUGAUAACUCUAGCUAUAGGCUU--UUUUUGGCGUAGCUCCGCGGAUUCCU
AADQ01000002.1/6326-6154 AUGAAAAGGAGUGUUAUCUUAAGCCAAUGAAAUUCUAAUCCUGUAUUAUAUGAAAAAAUGAAGAAAGCUAUCCACUUCUCGGAUAGAAACUAUUUUUUCGGACGGGAUUCGUAUGUUCAUUUCGCAUGAUAACUCUUGCUAUAGGCC---UUUUUGGCGUAGCCCCGCGGAUUCCU
FM242711.1/956949-957123 ACGAAAAGGAGUGUUAUCUUAAGCCAAUGAAAUUCUAAUCCUGUAUUAUAUGAAAAAAUGAAGAAAGCUAUCCAAUUCUCGGAUAGAAACUAUUUUUUCGGACGGGAUUCGUAUGUUCAUUUCGCAUGAUAACUCUUGCUACAGG-CCUUUUUUUGGCGUAGCCUCGCGGAUUCCU
AL591977.1/65829-66001   AUGAAAAGGAGUGUUAUCUUAAGCCAAUGAAAUUCUAAUCCUGUAUUAUAUGAAAAAAUGAAGAAAGCUAUCCACUUCUCGGAUAGAAACUAUUUUUUCGGACGGGAUUCGUAUGUUCAUUUCGCAUGAUAACUCUUGCUAUAGGCC---UUUUUGGCGUAGCCCCGCGGAUUCCU
#=GC SS_cons             ::::::((((((<<<<<<----<<-<<<<<<---<-<<<<<<<<------<<<<<<<<<<-------<<<<<<_______>>>>>>---->>>>>>>>>>->>>>>>>>->---->>>>>>-->>-->>>>>>,,,,<<<<<-<<<_..._____>>>>>>>>,,,,,,,))))))
#=GC RF                  AuGAAAaGGaguGuuauCUUAAGCCaauGaaAUUCUaauCCcGuAUUAUAcGaaaaaaugAAGAAAGCuauCCAaUUcUuGGauaGAAACcauuuuuuCgGaCgGGauuCGUAUGuuCauuUcGCAUGauaaCUCUuGCuacAGccu...UUUUUggCguaGCuuCGCGGacuCCu
//
# STOCKHOLM 1.0

#=GF AC   RF01482
#=GF ID   AdoCbl_riboswitch
#=GF PI   rli55
#=GF DE   AdoCbl riboswitch
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:19246383
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00101
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045893; positive regulation of transcription, DNA-templated;
#=GF DR   GO; 0046336; ethanolamine catabolic process;
#=GF RN   [1]
#=GF RM   19246383
#=GF RT   Multiple posttranscriptional regulatory mechanisms partner to control
#=GF RT   ethanolamine utilization in Enterococcus faecalis.
#=GF RA   Fox KA, Ramesh A, Stearns JE, Bourgogne A, Reyes-Jara A, Winkler WC,
#=GF RA   Garsin DA
#=GF RL   Proc Natl Acad Sci U S A. 2009;106:4435-4440.
#=GF RN   [2]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF RN   [3]
#=GF RM   25146291
#=GF RT   Riboswitches. A riboswitch-containing sRNA controls gene expression by
#=GF RT   sequestration of a response regulator.
#=GF RA   DebRoy S, Gebbie M, Ramesh A, Goodson JR, Cruz MR, van Hoof A, Winkler WC,
#=GF RA   Garsin DA
#=GF RL   Science. 2014;345:937-940.
#=GF RN   [4]
#=GF RM   25794617
#=GF RT   Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and
#=GF RT   control expression of heavy metal transporters.
#=GF RA   Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker
#=GF RA   RR
#=GF RL   Mol Cell. 2015;57:1088-1098.
#=GF RN   [5]
#=GF RM   28483920
#=GF RT   Cobalamin riboswitches exhibit a broad range of ability to discriminate
#=GF RT   between methylcobalamin and adenosylcobalamin.
#=GF RA   Polaski JT, Webster SM, Johnson JE Jr, Batey RT
#=GF RL   J Biol Chem. 2017;292:11650-11658.
#=GF WK   Cobalamin_riboswitch
#=GF SQ   7


AM263198.1/1141155-1141305   AUUCGUUCAUACAAAC-A-AGUUAGAUAAUGGAAGUCUGGUGAAAAUCCAGCACGGUCCCGCCACUGUAAG-GAGU----UAGA-CACUC-UAAGUCAGGUCUUUUAUCUAGUUGUUUUAACUGGUUAUACUGCUUCGAGGC-AAAGCAUGUAUAAUUCUU
AL596167.1/185724-185873     AUUCGUUCAUACAAAC-A-GUUA-GAUACUGGAAGUCUGGUGAAAAUCCAGCACGGUCCCGCCACUGUAAG-GAGU----UAGA-CACUC-UAAGUCAGGUCUUUUAUCUAAUUGUUUUAACUGGUUAUACUGCUUCGAGGC-AAAGCAUGUAUAAUUCUU
CP000387.1/512706-512558     AAUUGAUUUUAGUACU-U-UUAA-GGAUAUGGAAGUCUGGUGUAAAUCCAGCGCGGUCCCGCCACUGUGAU-AAGC----UUUUCAGCUU-UAAGUCAGGUCUUUAUUCUUAAAUUUU--AGUAGAUUUCAUGCCUCGAUGU-AAGGUAGUGAUGUCAGUU
AL591978.1/38103-38252       AUUCGUUCAUACAAAC-A-GUUA-GAUACUGGAAGUCUGGUGAAAGUCCAGCACGGUCCCGCCACUGUAAG-GAGU----UAGA-CACUC-UAAGUCAGGUCUUUUAUCUAAUUGUUUUAACUGGUUAUACUGCUUCGAGGC-AAAGUAUGUAUAAUUCUU
ACAU01000031.1/82562-82413   AAACGAAUAUUUUAUG-A-AAAAUAUGAAUGGAAG-CCAGUGAGAAUCUGGCACGGUCCCGCCACUGUGAAGAAGC----AAGGUUGCUUUUAAGUCAGGUCUUUUCAUUUUUUCAUU--AUUGGGCAUGCUGUUUCGAGGC-AAAACA-GGAUGUUUCUU
AARF01000069.1/20924-20775   GCCACAAUAUAAAAGU-U-U-UA-GGCAAUGGAAGUUUGGUGCAAAUCCAACGCGGUCCCGCCACUGUGAU-AGACCGGAUACC-GGUCU-UAAGUCAGGUCUUUUGCCUAGAAACUUUGAGCAACCAA-CCGCUUCGAGGCGAAAGUG-G--UGGUUUAG
ABGD02000024.1/243122-242978 UCUUAAAAAUAUAUGAA-GCUUC-AGAUGAGGAAA-CGAGUGGGAAUCUCGUACGGUCACGCCACUGUGUA-GCGG----UUAU-ACCGC-AAAGUCAGGUCGUCAUCUGGAG-UCAUAUCCAUCGUUUG-AGCUUCGAGGG-AAAG---GGAGAUGGAUG
#=GC SS_cons                 :::::::::::::(((.(.((((.((((,,,,,,<-<<<<_______>>>>>,,<<<___>>>,<<<---<.-<<<....--<_.>>>>-.>---->>>,,,,,,))))))))))))------<<<<<<-<<<<<<______._>>>>>.>->>>>>>:::
#=GC RF                      auuugaauAUAuaagc.a.cuua.GgcaaUGGAAGUCuGGUGaaAAUCCaGCaCGGuCcCgCCACUGUgAg.agGc....Uagu.cgCcu.cAAGUCAGGUCUUUugcCuaagugcuUuaAcuggccaUacugCuUCGAGGc.AAaGca.ggAuggccuUu
//
# STOCKHOLM 1.0

#=GF AC   RF01483
#=GF ID   rli56
#=GF DE   Listeria sRNA rli56
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold
#=GF GA   47.00
#=GF TC   49.20
#=GF NC   41.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   6


AL596167.1/187481-187580   CGUGUGGAAUAAUAAAUAUAGCAGAGCAACGGGGCUCCCUCAAAAAUAUUGCACAAUAUUUUUAAGGGGCUCUUUCUAUUUUCUGGGAGAAUUUUUUCUC
AADQ01000003.1/54674-54575 CGUGUGGAAUUAUAAAUAUAGCAGAGCAACGGGGCUCCCUCAAAAAUAUUGCACAAUAUUUUUAAGGGGCUCUUUCUAUUUUCUUGGAGAAAUUUUUCUC
AM263198.1/1142912-1143011 CGUGUGGAAUAAUAAAUAUAGCAGAGCAACGGGGCUCCCUCAAAAAUAUUACACAAUAUUUUUAAGGGGCUCUUUCUAUUUUCUUGGAGAUAUUGUUCUC
AE017262.2/1178639-1178738 CGUGUGGAAUUAUAAAUAUAGCAGAGCAACGGGGCUCCCUCAAAAAUAUUGCACAAUAUUUUUAAGGGGCUCUUUCUAUUUUCUUGGAGAAUUUUUUCUC
AADR01000004.1/52118-52019 CGUGUGGAAUUAUAAAUAUAGCAGAGCAACGGGGCUCCCUCAAAAAUAUUGCACAAUAUUUUUAAGGGGCUCUUUCUAUUUUCUUGGAGAAUUUUUUCUC
AL591978.1/39859-39958     CGUGUGGAAUUAUAAAUAUAGCAGAGCAACGGGGCUCCCUCAAAAAUAUUGCACAAUAUUUUUAAGGGGCUCUUUCUAUUUUCUUGGAGAAAUUUUUCUC
#=GC SS_cons               :::((((((,,,,,,,,,,,<<___>>,,,<<<<<-<<<<-<<<<<<<<<____>>>>>>>>>->>>>>>>>>))))))-------<<<<<____>>>>>
#=GC RF                    CGUgugGaaUuAUAAAUAUAGCAGAGCAACgGgGCUCCCuCaaaaauauugCACaauauuuuuAaGGGGCcCcuuCcacUUUCUuGGaGaaaUUuuuCuC
//
# STOCKHOLM 1.0

#=GF AC   RF01484
#=GF ID   rli59
#=GF DE   Listeria sRNA rli59
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; cmfinder
#=GF GA   100.00
#=GF TC   150.80
#=GF NC   44.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   5


AADQ01000042.1/19077-18897 AACUAAUAACGUUGCAUAAUAAAACAAAGGAGGAAUGGACGAUGAAUAAUUAUAUGAAGACUUCAAACAAGGCAUUAUUGCGCUUAAAAAUAGAAUUUAUUUCACCGGACCAUUUCGCGAGCAAGGGAACUCUCCUUUAAUUUGGUUUUAUUUUAUACAAAGUGGUGACAAAUAAAUAUAU
AM263198.1/1680824-1680644 AACUAAUAACGUUGCAUAAUAAAACAAAGGAGGAAUGGACGAUGAAUAAUUAUAUUACGGCUUCAAACAAGACAUUAUUGCGCUUAAAAAUAGAAUUUAUCUCACCGGACCAUUUCAGGAACAAGGGAGCUCUCCUUUAAUUUGGUUUUAUUUUAUACAAAGUGGUGACAAAUAAUUAUAU
AL591980.1/52553-52373     AACUAAUAACGUUGCAUAAUAAAACAAAGGAGGAAUGGACGAUGAAUAAUUAUAUGAAGACUUCAAACAAGGCAUUAUUGCGCUUAAAAAUAGAAUUUAUUUCACCGGACCAUUUCGCGAGCAAGGGAACUCUCCUUUAAUUUGGUUUUAUUUUAUACAAAGUGGUGACAAAUAAAUAUAU
AE017262.2/1680252-1680072 AACUAAUAACGUUGCAUAAUAAAACAAAGGAGGAAUGGACGAUGAAUAAUUAUAUGAAGACUUCAAACAAGGCAUUAUUGCGCUUAAAAAUAGAAUUUAUUUCACCGGAUCAUUUCGCGAGGAAGGGAACUCUCCUUUAAUUUGGUUUUAUUUUAUACAAAGUGGUGACAAAUAAAUAUAU
AL596169.1/159182-159002   AACUAAUAUCGUUGCAUAAUAAAACAAAGGAGGAAUGGACGAUGAAUAAUUAUAUUACGACUUCAAACAUGGCAUUAUUGCGCUUAAAAAUAGAAUUUAUUUCACCGGACCAUUUCGCGAGCAUGGGAACUCUCCUUUAAGUUGGUUUUAUUUUAUACAAAGUGGUGACAAAUAAAUAUAU
#=GC SS_cons               ::::::::::((-----((((((((,,,,,,<<<<<<<-<<-<<<<-<<<<-<<<-------------<<<<<<____>>>->>>---->>>->>>>--->>>>->>-->>>>>>>,,,,,,<<<<<<____>>>>>>,,,,,,))))))))----))----<<____>>:::::::::::
#=GC RF                    AACUAAUAaCGuUGCAUaauaaaaCAAAGGAGgaauGGACGAuGaaUaauuAuaugAaGACUUCAAACaaGGCaUUAUuGCGCuuAAAAauaGaauuUAUuuCaCCGGACCauuuCgcGAgcaagGGaACUCuCCuuuAAuUUGGuuuuauuUUAUaCAAAGuGGUGACaAAUAAaUAUAU
//
# STOCKHOLM 1.0

#=GF AC   RF01485
#=GF ID   rli61
#=GF DE   Listeria sRNA rli61
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.40
#=GF NC   49.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   4


AL596171.1/217918-217813   CGUGAAAUAAAUCACAAACAAAUACCCCC-UUUAUUUGAUUGUGUGAAUUUCUCCUUUUGAUUGCGCUGUAAGAAGCCGUGGCAUUUAGCUACGGCUUUUUACGUUA
AL591982.1/175363-175258   CGUGAAAUAAAUCACAAACAAAUACCCCC-UUUAUUUGAUUGUGUGAAUUUCUCCUUUUGAUUGCGCUGUAAGAAGCCGUGGCAUUUUGCUACGGCUUUUUACGUUA
AE017262.2/2270477-2270372 CGUGAAAUAAAUCACAAACAAAUACCCCC-UUUAUUUGAUUGUGUGAAUUUCUCCUUUUGAUUGCGCUGUAAGAAGCCGUGGCAUUUUGCUACGGCUUUUUACGUUA
CP001175.1/359548-359653   CGUGAAAUAAAUCACAAACAAAUA-CCCCCUUUAUUUGAUUGUGUGAAUUUCUCCUUUUGAUUGCGCUGUAAGAAGCCGUGGCAUUUUGCUACGGCUUUUUACGUUA
#=GC SS_cons               :<-<<<<<----<<<<<-<<<<<<_____.__>>>>>>->>>>>--->>>>>->--------------<<<<<<<<<<<<<<<_____>>>>>>>>>>>>>>>::::
#=GC RF                    CGUGaaauAAAUCaCaaACaaauacCCCC.UUuauuuGAuuGuGUGAauuuCUCCUUUUGAUUGCGCUGuaagaaGCCGugGCAUUUuGCcaCGGCuucuuaCGUUA
//
# STOCKHOLM 1.0

#=GF AC   RF01486
#=GF ID   rli62
#=GF DE   Listeria sRNA rli62
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold
#=GF GA   83.00
#=GF TC   102.40
#=GF NC   82.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.97 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF **   seedtax: Bacteria; Viruses
#=GF SQ   2



AARP04000034.1/18168-18035 UACAAAAAUAAAUUUUAUAUUAAGGUCUGCACUUCACUUCUCGUUUAUAAUCUUAUGAUGACAUAGCAGGAGGUUGCUAUGU-UGCCUGGCAGAGGCUUUGUAUCUGAUCGUUGGUCUUGAUGGGAGACGCAUCU
AF042193.1/1242-1372       UGUCUUCCCAUAUUUAAUAUU---CUUUUCGUAGGGUCAUUUAAUCGUGUUCGCACGA-CGUAUAGUAGCAGGGUGCUAUAUGCCCCAGGAAGUGGGUUUAUAACUUACCGUUGGUCCCGAUGGGAGACGCAUCC
#=GC SS_cons               ::::::::::::::::::::::::::((((-(-(((,,,,,,,,<<<<<____>>>>>,,<<<<<<<<______>>>>>>>>.)))-)-)))),<<<----<<<<_____>>>>-->>><<<<<____>->>>>:
#=GC RF                    UauaaaaauAaAUUUuAUAUUAAGgUcugCauuggguuuuUuauucgugaUCucacgaUgacauaGcaGgAGGuugCuaugu.cccCaGGcagagggUUUauaaCUuAuCGuugGUcccGauGGGAGACGCauCu
//
# STOCKHOLM 1.0

#=GF AC   RF01487
#=GF ID   rliI
#=GF DE   Listeria sRNA rliI
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold
#=GF GA   45.00
#=GF TC   48.50
#=GF NC   38.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17259222
#=GF RT   Identification of new noncoding RNAs in Listeria monocytogenes and
#=GF RT   prediction of mRNA targets.
#=GF RA   Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P
#=GF RL   Nucleic Acids Res. 2007;35:962-974.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   5


AADR01000011.1/41253-41491 UAUUAAUGAAAAGAGGUGAGAUGACAUGUUUCUUUUGAAUGCGCGAACUAGUAUAGCUAAAUUUUUGUAUAUUGUCCGUGCAAUUUUUUCCGGUAUUGCAGUUACAUUGGCGAAGUCUGCCCAAAAAACUGUAUAACUAGAAAAAAUGAGAGAAGCAUGGAGUCACGCAAUCGGUUUGUAUAGUGCUAAAUUAGUAUUAUACUUAUAAUUGGCGUCGGGCGCUUGUCUGACGCUUUUUU
AM263198.1/2742760-2742522 UAUUAAUGAAAAGAGGUGAGAUGACAUGUUUCUUUUGAAUGCACGCAGUAGUAUAGCUAAGUUUUUAUAUAUUGUCCGUGCAAUUUUUUCCGGUAUUGCAGUUACAUUGGUGAAGUCUGCCCAAAAAACUGUAUAACGAGAAAAAAUGAGAGAAGCAUGGAGUCACGCAAUCGGUUUGUAUAGUGCUAAAUUGGUAUUAUACUUAUAAUGGGCGUCGGGCGCUUGUCUGACGCUUUUUU
AL596174.1/8221-7983       UAUUAAUGAAAAGAGGUGAGAUGACAUGUUUCUUUUGAAUGCGCGAACUAGUAUAGCUAAAUUUUUGUAUAUUGUCCGUGCAAUUUUUUCCGGUAUUGCAGUUACAUUGGUGAAGUCUGCCCAAAAAACUGUAUAACUAGAAAAAAUGAGAGAAGCAUGGAGUCACGCAAUCGGUUUGUAUAGUGCUAAAUUAGUAUUAUACUUAUAAUUGGCGUCGGGCGCUUGUCUGACGCUUUUUU
AADQ01000008.1/15420-15182 UAUUAAUGAAAAGAGGUGAGAUGACAUGUUUCUUUUGAAUGCGCGAACUAGUAUAGCUAAAUUUUUGUAUAUUGUCCGUGCAAUUUUUUCCGGUAUUGCAGUUACAUUGGCGAAGUCUGCCCAAAAAACUGUAUAACGAGAAAAAAUGAGAGAAGCAUGGAGUCACGCAAUCGGUUUGUAUAGUGCUAAAUUAGUAUUAUACUUAUAAUUGGCGUCGGGCGCUUGUCUGACGCUUUUUU
AL591984.1/123200-122962   UAUUAAUGAAAAGAGGUGAGAUGACAUGUUUCUUUUGAAUGCGCGAACUAGUAUAGCUAAAUUUUUGUAUAUUGUCCGUGCAAUUUUUUCCGGUAUUGCAGUUACAUUGGCGAAGUCUGCCCAAAAAACUGUAUAACGAGAAAAAAUGAGAGAAGCAUGGAGUCACGCAAUCGGUUUGUAUAGUGCUAAAUUAGUAUUAUACUUAUAAUUGGCGUCGGGCGCUUGUCUGACGCUUUUUU
#=GC SS_cons               :::::::(((--((-(((-(((--((((((((((((,,,<<<<<<-<<--<<<<<<________>>>>>>--->>->>>>>><<<<<<<<--<<--<<<<<<<-----<<<<_____>>>>----->>>>>>>-->>-->>>>>>>>))))))))))))--)))-)))--))--)))<<<<<<<<<<<___>>>>>>>>>>>,,,,<<--<<<<<<<<<<____>>>>>>>>>>-->>:
#=GC RF                    UAUUAAUgaaAAGaGGcGAGacGACauGcuuCucucGAAuGCgCGaacUAguacagcUAAaUUUcuguacAUUgucCGcGCaauuuuuuCcGGuAUugCaGuuAcAUUGGcgAAGUccgCCcAAAAaaCuGcaUAaCgAGaaaaaaugagaGaagCauGGAguCACgCAAuCGGuucGuauagugCuaAAUuaGcacuauaCUUAUaaUugGCGuCgGgCGcUUGcCcGaCGCcUUuuU
//
# STOCKHOLM 1.0

#=GF AC   RF01488
#=GF ID   rli49
#=GF DE   Listeria sRNA rli49
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   40.00
#=GF TC   46.20
#=GF NC   39.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   5


AL591983.1/265202-265364   UUUUUUUGAAACUAACAUCAUUUUCGUCUUAGUAAAGAUAAACUUACCAGUGUAAGUAUAGUCUUCUUUUGUGCGAAUUAGUGGCUCAUAAACUAAUUCCUCUACUCCAAAAGAUUCUAUCGUUUGCACGCCGUCCACAUUAAAAGUGUUCCCGCUUAAGAAA
AE017262.2/2608947-2609109 UUUUUUUGCAACUAACAUCAUUUUCGUCUUAGUAAAGAUAAACUUACCUGUAUUAGUAUAGCCUUCUUUUGUGCGGAUUAUUUGUUCAUACACUAUCUCCUCUACUUCAAGUGAUUCUAUUGUUUGCUCGCCGUCCACAUUAAAAGGGUUCCCACUUUAGAAA
AADR01000039.1/180-18      UUUUUUUGCAACUAACAUCAUUUUCGUCUUAGUAAAGAUAAACUUACCUGUAUUAGUAUAGCCUUCUUUUGUGCGGAUUAUUUGUUCAUACACUAUCUCCUCUACUUCAAGUGAUUCUAUUGUUUGCUCGCCGUCCACAUUAAAUGGGUUCCCACUUUAGAAA
AADQ01000033.1/22990-22828 UUUUUUUGAAACUAACAUCAUUUUCGUCUUAGUAAAGAUAAACUUACCAGUGUAAGUAUAGUCUUCUUUUGUGCGAAUUAGUGGCUCAUAAACUAAUUCCUCUACUCCAAAAGAUUCUAUCGUUUGCACGCCGUCCACAUUAAAAGUGUUCCCGCUUUAGAAA
AARM02000066.1/1554-1716   UUUUUUUGAAACUAACAUCAUUUUCGUCUUAGUAAAGAUAAACUUACCAGUGUAAGUAUAGUCUUCUUUUGUGCGAAUUAGUGGCUCAUAAACUAAUUCCUCUACUCCAAAAGAUUCUACCGUUUGCACGCCGUCCACAUUAAAAGUGUUCCCGCUUUAGAAA
#=GC SS_cons               ::::((((((<<<<<---<______>-->>>>><<<<<------<<<________>>>------>>>>>,,))))))-------------------------------------<<<<<--<<--<<<<________________>>>>---->>-->>>>>:
#=GC RF                    UUUUuuuGcaaCuaaCAUCAUUUUCGUCuuaGuaaaGaUAAACUuaCCaGUgUaAGuaUAGuCUuCuuuUGugCgaaUUAgUgGuUCAUAaACUAauUCCUCUACUuCAAaaGAuuCuaUuGuUUgCaCGCCGUCCACAUUAAAAGuGuUCCCaCUUuaGaaA
//
# STOCKHOLM 1.0

#=GF AC   RF01489
#=GF ID   sbrA
#=GF DE   Listeria sRNA sbrA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR
#=GF GA   45.00
#=GF TC   50.70
#=GF NC   37.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   6


AL591978.1/239363-239433   GUACAUCUAGAUCCAUACCCCUAAACUCCCUAGAUGUCUUGGGUAGUACUCUCGGGUGCUGCUCUUUUUUU
AM263198.1/1378300-1378370 GUACAUCUAGAUCCAUACCCCUAAACUCCCUAGAUGUCUUGGGUAGUACUUUCGGGUACUGCUCUUUUUUU
AE017262.2/1379081-1379151 GUACAUCUAGAUCCAUACCCCUAAACUCCCUAGAUGUCUUGGGUAGUACUUUCGGGUGCUGCUCUUUUUUU
ABCF01000017.1/44134-44066 AUACAUCUAGAUCCAUACCCCUAAACUCCCUAGAUGAA--GGAUAGCUCUUAUAUGGGCUAUCCUCUUUUU
AADR01000179.1/217-147     GUACAUCUAGAUCCAUACCCCUAAACUCCCUAGAUGUCUUGGGUAGUACUUUCGGGUGCUGCUCUUUUUUU
AARL02001293.1/414-344     GUACAUCUAGAUUCAUACCCCUAAACUCCCUAGAUGUCUUGGGUAGUACUUUCGGGUGCUGCUCUUUUUUU
#=GC SS_cons               :::<<<<<<_____________________>>>>>>----<<<<<<<<<<____>>>>>>>>>>:::::::
#=GC RF                    GUACAUCUAGAUCCAUACCCCUAAACUCCCUAGAUGUcUUGgGuAGcaCuUUcGgGugCUgCcCUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01490
#=GF ID   rli51
#=GF DE   Listeria snRNA rli51
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   48.00
#=GF TC   48.50
#=GF NC   46.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   9


AY168080.1/216-96    AUAUCCCAAAGUUUAAGCCACCUAUAGUUUC-UACUGC-AAAACGUAUAAU--UUAGUUCCCACAUAUACUAAAAAA--CGUGUCCUUAACUCUCUCUGUCAGAUUAGUUGUAGGUGGCUUAAACUU
AY510072.1/4036-4154 AUAUUA-AAAGUUUGAGUCACUUAUAGUUUCCUACUGCGAAAACAUAUAAU--UUAGUUCCCACCCAUACUAA-AAU--UGUGUCCUUAACUCUCUA--UUAAUUUGGCUAUACGUGGCUUAAUCUU
AY510073.1/4042-4162 AUAUUA-AAAGUUUAAGUCACUUAUAGUUUCCUACUGCGAAAACAUAUAAUUUUUAGUUCCCACCCAUACUAA-AAU--UGUGUCCUUA--GCUCUCUAUUAAUUUGGCUAUAGGUGGCUUAAUCUU
AY512490.1/3938-4058 AUAUCCCAAAGUUUAAGCCACCUAUAGUUUC-UACUGC-AAAACGUAUAAU--UUAGUUCCCACAUAUACUAAAAAA--CGUGUCCUUAACUCUCUCUGUCAGAUUAGUUGUAGGUGGCUUAAACUC
AY512446.2/3933-4053 AUAUCCCAAAGUUUAAGCCACCUAUAGUUUC-UACUGC-AAAACGUAUAAU--UUAGUUCCCACAUAUACUAAAAAA--CAUAUCCUUAACUCUCUCUGUCAGAUUAGUUGUAGGUGGCUUAAACUU
EU372052.1/3947-4067 AUAUCCCAAAGUUUAAGCCACCUAUAGUUUC-UACUGC-AAAACGUAUAAU--UUAGUUCCCACAUAUACUAAAAAA--CGUGUCCUUAACUCUCUCUGUCAGAUUAGUUGUAGGUGGCUUAAACUU
EU372053.1/3947-4067 AUAUCCCAAAGUUUAAGCCACCUAUAGUUUC-UACUGC-AAAACGUAUAAU--UUAGUUCCCACAUAUACUAA-AAAA-CGUGUCCUUAACUCUCUCUGUCAGAUUAGUUGUAGGUGGCUUAAACUU
FJ041145.1/3922-4042 AUAUCCCAAAGUUUAAGCCACCUAUAGUUUC-UACUGC-AAAACGUAUAAC--UUAGUUCCCACAUAUACUAA-AAA-ACGUGUCCUUAACUCUCUCUGUCAGAUUAGUUGUAGGUGGCUUAAACUU
EU372028.1/3954-4074 AUAUCCCAUAGUUUAAGCCACCUAUAGUUUC-UACUGC-AAAACGUAUAAU--UUAGUUCCCACAUAUGCUAAAAAA--CGUGUCCUUAACUCUCUCUGUCAGAUUAGUUGUAGGUGGCUUAAACUU
#=GC SS_cons         ::::::::(((-(((((((((((((((((,,.,,,<<_.____>><<<--<..<<<<<__________>>>>>-->-..->>>,,,,,,,,,,,,,,,,,,,,,,,)))))))))))))))))-)))
#=GC RF              AUAUccCAaaGUuuaaGcCaCcuacaguuUC.UACcGC.AAAACguauAAu..uuaGuUCCCACauAUaCuaaAAaa..cgugUCCUUAACuCUCUcUgUcAgaUUagcuguagGuGgCuuaaaCuu
//
# STOCKHOLM 1.0

#=GF AC   RF01491
#=GF ID   rli54
#=GF DE   Listeria sRNA rli54
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold
#=GF GA   80.00
#=GF TC   103.00
#=GF NC   36.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   5


AL591977.1/188584-189111   GUAUUAAUAAAAUUCUUGUUUUCGAGUAAAACAGAAAUAACAUUUUAAAUAAAAGGAAAGUUCCUGUUUUUUUAUGAAACAUUGUGAAAGAAUGAAAGUUUUUUCACAUACUCUCUUAAAACCCAUGUUUUCAAUGAGGAAUUUGUGGUAAUAACUGGAGAGGCUACGUAAUUAGUUAAUAGGAAUUUAGAAAAAAGCUUCCGGAAUCUGCUUCUUUCUAUAGAAUAACUUUUCUUUUUACUACGCUAUUAUAAUUAAUACACAAUCAGGAUGGCAGUUUUAAAAAAACCAU-CUAGUAAGGUAAAUGACCGGACGAGCGUUACAUAAAACGCAUACCUAACUAAUGAAGAAUUUGAAACUGUACAAUGUGAAUGACGAAAGGGUGGAUACGAAAUGGCUUCUAAAACAAAGAAGGCUAUUAUCGACGUAAAGAAACAAUUUGAGGCUGUUCAUAAACAAUUUGAAUUGGUUCAAAUUUUGAAUGAAAAAGGAGAAAUUGUUAAUCCAGAUUUAAUGCCGGAUUUAACA
AM263198.1/1043902-1044428 GUAUUAAUGAAAUUCUUGUUUUUUAGUAAAACAGAAUUAAC-UUUUAUUAAAAAGGAAAGUUCCUACAUUUUUAUGAAACAUUGUGAAAGAAUGAAAGUUUUUUCACAAUCUCUCUUAAAACCCAUGUUUUCAAUAAGGAUUUUGUGGUAAUAACUGGAGAGGCUGUGCAAUAAGUUGAUGGGAAUUUAGAAAAAAGCUUCCGGAAUUCGCUUCUUUCUAUAGAAUAACUUUUCUUUUUACUACGCUAUUAUAAUUAAUACACAAUCAGGAUGGCAGUUUUAGAUGAAUCAUUUUAGGAUGGUAAAUGACCGGACGAGCGUUACAUGAAACGCGUACCUGACUAAUGAAGAAUUU-AAACUGUACAAUGUGAAUGACGAAAGGGUGGAUACGAAAUGGCUUCUAAAACAAAGAAGGCUAUUAUCGACGUAAAGAAACAAUUUGAGGCUGUUCAUAAACAAUUUGAAUUGGUUCAAAUUUUGAAUGAAAAAGGAGAAAUCGUAAAUCCAGAUUUAAUGCCAGAUUUAACU
AE017262.2/1079194-1079721 GUAUUAAUAAAAUUCUUGUUUUUAAGUAAAACAGAAAUAAC-UUUUAACUAAAAGGAAAGUUCCUGAUUUUUUAUGAAACAUUGUGAAAGAAUGAAUAUUUUUUCACAAACUCUCUUAAAACCCAUGUUUUCAAUGAGGAUUUUGUGGUAAUAACUGGAGAGGCUACGUAAUUGGUUAAUAGGAAUUUAGAAAAAAGCUUCCGGAAUCUGCUUCUUUCUAUAGAAAGACUUUUCUUUUUACUACGCUAUUAUAAUUAAUACACAAUCAGGAUGGCAGUUUUAAAAGAAUCCAUUUAGAUGGGUAAAUGACCGGACGAGCGUUACAUAAAACGCAUACCUAACUAAUGAAGAAUUUGAAACUGUACAAUGUGAAUGACGAAAGGGUGGAUACGAAAUGGCUUCUAAAACAAAGAAGGCUAUUAUCGACGUAAAGAAACAAUUUGAGGCUGUUCAUAAACAAUUUGAAUUAGUUCAAAUUUUGAAUGAAAAAGGAGAAAUCGUUAAUCCAGAUUUAAUGCCGGAUUUAACU
AADR01000017.1/24753-25280 GUAUUAAUAAAAUUCUUGUUUUUAAGUAAAACAGAAAUAAC-UUUUAACUAAAAGGAAAGUUCCUGAUUUUUUAUGAAACAUUGUGAAAGAAUGAAUAUUUUUUCACAAACUCUCUUAAAACCCAUGUUUUCAAUGAGGAUUUUGUGGUAAUAACUGGAGAGGCUACGUAAUUGGUUAAUAGGAAUUUAGAAAAAAGCUUCCGGAAUCUGCUUCUUUCUAUAGAAUGACUUUUCUUUUUACUACGCUAUUAUAAUUAAUACACAAUCAGGAUGGCAGUUUUAAAAGAAUCCAUUUAGAUGGGUAAAUGACCGGACGAGCGUUACAUAAAACGCAUACCUAACUAAUGAAGAAUUUGAAACUGUACAAUGUGAAUGACGAAAGGGUGGAUACGAAAUGGCUUCUAAAACAAAGAAGGCUAUUAUCGACGUAAAGAAACAAUUUGAGGCUGUUCAUAAACAAUUUGAAUUAGUUCAAAUUUUGAAUGAAAAAGGAGAAAUCGUUAAUCCAGAUUUAAUGCCGGAUUUAACU
AL596167.1/96029-96557     GUAUUAAUAAAAUUCUUGUUUUUGAGUAAAACAGAAUUAACAUUUUAAAUAAAAGGAAAGUUCCUGUUUUUUUAUGAAACAUUGUGAAGGAAUGAAUGUUUUUUCACAAACUCUCUUAAAACCCAUGUUUUCAAUGAGGAUUUUGUGGUAAUAACUGGAGAGGCUGCGUAAUUAGUUGAUAGGAAUUUAGAAAAAAGCUUCCGGAAUCUGCUUCUUUCUAUAGAAUAACUUUUCUUUUUACUACGCUAUUAUAAUUAAUACACAAUCAGGAUGGCAGUUUUAAAAGAAUCCAUUUAGAUGGGUAAAUGACCGGACGAGCGUUACAUAAAACGCAUACCUAACUAAUGAAGAAUUUGAAACUGUACAAUGUGAAUGACGAAAGGGUGGAUACGAAAUGGCUUCUAAAACAAAGAAGGCUAUUAUCGACGUAAAGAAACAAUUUGAGGCUGUUCAUAAACAAUUUGAAUUAGUUCAAAUUCUAAAUGAAAAAGGAGAAAUCGUAAAUCCAGAUUUAAUGCCGGAUUUAACU
#=GC SS_cons               {{{{{{{{,,,,<<<<-<<<<<_____>>>>>>>>>,,,,,.,,,,,,,,[[[[[[[[[[[[-[[[,,(((((((--(((,<<<<<<<<<<<<____>>>>>>>>>>>>,<<<<<<------<<<<<--<<<_____>>>--->>>>>-------->>>>>>,,,,,,,,,,,,)))-))))))),,<<<<<<-<<<<___________>>>>->>>>>>]]]---]]]]]]]]]]]],,,,,,,,,,,,,,,}}}}}}}},,,,[[[[[-[[(((((((((((,,,<<<<<<____>>>>>>,,,,,,,,<<----<<<<<______>>>>>--->>,,,,,,,,,,,,,,))))))))))),,,<<<<--------------------<<<<<<<<<<<<<_______>>>>->>>>>>->>>>>>>,,,,,,,]]-]]]]](((,,<<<<<--<-<<<<<<<<____>>>>>>>>->-->>>>>,,,<<<___________>>>,,,,,,,,,)))::::::::::
#=GC RF                    GuauuaauaAAAuuCuUGuuuuuaAGUaaaaCaGaaaUAAC.UUUUAaauaaaaGgaaaGuuCCuguuuuuuuauGAaaCAuuGuGaaagaacGAAuguuuuuuCaCaaaCuCuCuUAAAACCCaugUUuuCAAUgAGgauUUuguGGUAAUAACUgGaGaGGCUacGuAAUuaGuuaauaggaaUUuaGaaaAaaGCUUCCGGAAUcuGCuuCuuuCuacaGAAuaaCuuuuCuuuuUACUACGCUAUUAUAauuaauaCACAAuCaggAuGgCaGuuucaaaagAacCcauuUAGaugGguAAAUGACCGGACGAGCGuuACAUaAaaCGCaUACCUaACUAAUGAAGAAuuugaaaCuGuACAauGuGAAUGACGAAAGGGUGGAUACGaaaugGCuuCuAAAACAAaGaaGGCuauuAuCGaCguAAAGAAACaAuuuGaGGCUGuuCauAAaCaauuuGaaUUaGuuCaaauuuugAauGaaAAAGGaGAAAUcGUuAAuCCAGAUUUAAUGCCgGAUUUAACu
//
# STOCKHOLM 1.0

#=GF AC   RF01492
#=GF ID   rli28
#=GF DE   Listeria sRNA rli28
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   44.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   1944809
#=GF RT   Muscarinic cholinergic control of vasopressin secretion from the acute
#=GF RT   hypothalamoneurohypophysial explant.
#=GF RA   Michels KM, Meeker RB, Hayward JN
#=GF RL   Neuroendocrinology. 1991;54:219-226.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   21


AL591984.1/64286-64098     UUUCUUAUGCUAUAAUAAAUUUAGUAGUAGUAAAGUGAAAAAGAUGGUGGCUAAAUCUC----CAGGAACGGGGGUGAUGCC--UCUUGGUUAUAGAAG-----GUUUUACUC-------CUA-GAAAGGA-----AUAG----CCGUGUCUGUGUAUGAAGCACUGACGUUUGCGGUGGUAUUUGCCACCCUCGUC-GUGAUGAU---UCUCGACUUUAA
AADR01000010.1/27194-27381 AAUAUUAUGUUAUAAUA-UAAAGGCAGUAGCAAAGUGAGAAAGAUGGUGGCUAAAUCCU----CAUUA--GGGGGUGAUGCC--UAUGCUUGAAUGUAU----AGUUUUACUC-------CUG-GAAAGGAG----CUAG----ACUUGUCUGUGUUUGAAGCACUUACGCUGAUGAUCGCUUUUGCGACAUUAGUC-GUGCUGAU---ACUAGGCUUUGA
AL591975.1/147394-147206   AUUAUUAUGAUAUAAUAAGAAAAGCAGUAGUAAAGUGAAAAAGAUGGUGGCUAAAUCUC----CAGGAACGGGGGUGAUGCC--UCUUGGUUAUAGAAG-----GUUUUACUC-------CUA-GAAAGGA-----AUAA----CCGUGUCCGUGUAUGAAGCACUGACGUUUGCGGUGGUAUUUGCCACCCUCGUC-GUGAUGAU---UCUCGACUUUAA
AL592102.1/74442-74629     AAUAUUAUGUUAUAAUA-UAAAGGCAGUAGCAAAGUGAGAAAGAUGGUGGCUAAAUCCU----CAUUA--GGGGGUGAUGCC--UAUGCUUGAAUGUAU----AGUUUUACUC-------CUG-GAAAGGAG----CUAG----ACUUGUCUGUGUUUGAAGCACUUACGCUGAUGAUCGCUUUUGCGACAUUAGUC-GUGCUGAU---ACUAGGCUUUGA
AL596173.1/248588-248772   UUUUGAAUGCUAUAAUAGUAAAUGCAGUAGCAAAGUGAAUA-GACGGUGGCUAAUCCUC----AGU---AGGGGAUGAUGCC--UAUGGUUUACA-AAG-----GUUUUACUC-------CUA-GAAAGGA-----AUAAA---GCAUGUCUGUAUUUGAAGCAAUGACUUUAAUGUUGGCUUUUGCCACAUUGGUU-GUGCUGAU---ACUAGACUUUAA
AF454824.1/105141-105322   UGAAGAAUUAUGUAU-AAUAACUUUUGCAGAAAAGUGAAAA-GAUAAUGGCUAAUCUCU----UGAAUAAAGGGGUGAUGCC--UAUGGUUCAUA---------GCUUUAUCU-------CUA-G-AUGUA-----GUAG----ACAUGUCUGGAUUCGAAAUAUUAUUGCUAAUGGUUGCAUUCGUAACGCUAGUU-UUGCUGGG---GAUAGACCGUAU
AE016830.1/3140576-3140392 GUACAAAUGUGUUAU--ACUACACAAGUAGGAA---GUUUAUGACGGUGGCAAUUUCUC----AAAAA-AAGGGGGACUGCCAAUGUUUUUGCUUGUUU-----GCUCUUUCC-------CUA-GAAAGGA-----AUAG----UAGUGACUGUCUUUGAAGCAUUGAUGCUUGCGAUUGCUUUCGCAACAUUAAUU-GUCAAAAU---CAGUAAUAAAAA
BX571856.1/2306297-2306117 GUGUGCAUGUUAUAAUAUUUAUUG----AGCAAGUUGGAUA-GAUGGUGGCUAAUCUCU----UAAUA-AAGGGGUGAUGCC--UAUGGUUAUAG---------UUGUUACUC-------CUA-GAAAGGA-----CUA-----GCAUGUCUGAUUUUGAAAUGCUGAUGAUUGUAUUAACAAUCAUUGGUUUAGUA-UUGAUUAGUACUCAAGACCAUAA
AF270261.1/1778-1602       CAAUCAAUGUUACAAUA-UAUUUG----AGCAA-GUUAGAUAGAUGGUGGCUAAUCUCA----UGAAA-AUGGGGUGAUGCC--UAUGGUUUUGG---------UUUCUACUC-------CAA-GAAAGGA-----AUA-----GCAUGACUGAUUAUGAAAUGCUAAUGAUUGUUCUUACAAUCAUUGGUCUAGUA-AUAAUGAG---CAAUAACCAAAA
AM263198.1/480402-480226   AAACUAAUGCUAUAAUAAUUCUUACA--AGCAAUGU--UUAUGGUGGUGGCUAGCCUUCUUUUUACUAAGCGAGGUGAUGCC--UAUGUGUUAUAUUUUUGUUAGGCUCUCU---------UA-GAAUGGA-----UAGA----UAAUGACCGUUUAUGAAGCACUGUC------------UUUUGC-ACUAUUAU---UAAACAG---UCAAAAUAACCA
U67965.1/2452-2272         GUGUGCAUGUUAUAAUAUUUAUUG----AGCAAGUUGGAUA-GAUGGUGGCUAAUCUCU----UAAUA-AAGGGGUGAUGCC--UAUGGUUAUAG---------UUGUUACUC-------CUA-GAAAGGA-----CUA-----GCAUGUCUGAUUUUGAAAUGCUUAUGGUUGUAUUAACAAUCAUUGGUUUAGUA-UUGAUUAGUACUCAAGACCAUAA
CP000003.1/1821490-1821678 GUCCCUAUGAUACAA---UAAACCUCGUAACAAAGU--AAAAAACGGUAGUCGUAGCCUUAU-GUCUGGA---GGUGGUGCU--UAUGUAUGUAAGUCA---CAGAA--ACCA-------AAA-GAAAGGAGACGACAAG----GUUUGUCAGUUUAUGAAACGCUUACUUUGAUGAUUGCUUUUGGUACUCUGAUA-GUAGCUAU---CAUGAAUAACAA
AF053140.1/302-125         AAUAUAUUGAUAUAA---UGAAAGUG--AGCAAGUUGGAUA-GAUUGCGGCUAGUCUCU----UGAAAAAAGGGAU---UCC--UAUGUUUAUAG--UU-----GGU--ACUU-------CUA-GGAAGGA-----CUA-----GCAUGUCUUAUUUCGAAAUGCUGAUGGUUGUAUUAACAAUUAUGAGUUUAGUC-UUAAUUAGUAAUCAAAACUCUGA
AY849557.2/50148-49963     UUCUUUUUGUUAUAAUAUUUAAAG----AGAAA-GUUUAUA-GCGGUUGGCUAAGUAUA----GAAAG--AGGGGUGAUGCC--UAUGAGUAUAG---------GUAUUUCCCUAUCAAACUA-GAAAGGC-----AAAAAU--UUUUGAGUGUCUCAGACAGCUUAACCUUGAUGAUUGCAUUUGCAAGUUUCAUU-GUUAUGUU---GCUCAAUCUCAU
AF343837.1/14016-13837     CUUUUUAUGCUAUAA---UAGAAUUGAUAGUAAAGU-UUAAUGACGGUGGCUAUCCAAU----CGAAAGUGA-GGUGGUGCG--UAUGAAC-------------GUACUUCCA-AAAUCUAUA-GAAAGGA-----GAAGCC--UUUUGUCCGUUUCGGAAAGUUUGCAACUAAUGCUUGCGUUUGGUGGGUUUAC----AUUGAC---CC-UAAUCACAA
AAAK03000014.1/3079-3261   UUAGAUAUGCUAUAAUAGUCAAGA---CAGUAAAGUUUGAA-GACGGUGGCGACUUCUG----GAAAGGUGG---UGGUGCU--UAUGAAUGUAA---------GUGCUAAAA------UCUAUGAAAGGA-----GUAAGCC-UUUUGUCCGCAUAUGAGACAAUUCAAACCAUUCUUGGUUUUGGUAUGUUUACC-AUUGCUUU---GAUUAGUUUGAU
AB033232.1/4817-4996       GUAAUUAUGGUAAUA---UGCAGAAGUGAGCAAGUUGGAUA-GAUGGUGGCUAUCUGAG----UAUAA--GGAGGUGGUGCC--UAUGGUGGCAUUACU-----GAA--AUCU-------UUA-GAAAGGA-----GACG----CCUAAUGAUUACAAUUAGUAC-CAUGUUGCAGUUUGGUUU-AUUCCUUAUUGCAUUGAUAGG---UCUAGUAAUCAA
U17233.3/14064-13884       UGUUUUAUGGUAUAA----UAGAGAAGUAGAAAAGU---UAUGACGGUGGCGACUCAAU----AGAAG-CGGAGGUGGUACG--UAUGAAUGUACUCAC-----AAA--AUCU-------GUU-GAAAGGA-----GUAGCC--UUUUGUCCGCAUAUGAGACAAUUCAAACCAUUUUAGGCUUUGGUAUGUUUACC-AUUGCGUU---AAUCGGUUUGAU
CP000408.1/1993609-1993425 UUAACUGUGCUAUAA---UAGUUUUUGCAGAAAAGU--AAA-GACGGUGGCUCUAAUUU----CUGAAAGGUAGGUGGUGUC--UAUGGGCAAAUCAUC-----AAA--AUCU------AACA-GAAAGGA-----GAAGCUAUCUUUGUCAACCUUUGAGGUCUUAACACUCAUGUUUGUAGCUGGUAACUUUGUU-AUCGCUCU---CG-UGAUGUUAG
AARK02000222.1/2339-2158   GUUUCAAUGCUAUAC----AAAAAGAGUAAGCAAGU--UUAUGGUGGUGGCUAGCUCUUUC--AACAAGAAAGGGUGAUGCC--UAUGAAUAUUUUUGU---UAGGAUUGCC---------UG-GAAAGGA-----UAAC----CCAUGACCGUUUAUGAAGCACUGUCUUUUGCAGUUGCUUUUGCAACCCUGGU----GUUGCU---AUUGAACAGUCA
AARJ02000030.1/56513-56698 UGAAGUAUGGUAUAA---UAAACGUUGCAAGCAAGU--UUAUGGUGGUGGCUAGCCUCUUCU-CAAAGAAAGAGGUGAUGCC--UAUGAUUUUUUUGUU----AGGCUCUCC---------UG-GAAAGGA-----UAUG----CAAUGACCGUUUAUGAAGCAUUGUCUUUCGCAAUCGCUUUUGCAACCCUUGUG-UUGCUCAU-AAGUAGU-CAAAA-
#=GC SS_cons               :::::::::::::::...::::::::::::::::::::::::::::(((((,,,,,,,,....,,,,,,,<<<<<<<<-<<_.._______________.....>>->>>>>>.......>>,.,,,,,,,.....,,,,....,,,,<<<-<<<<_____>>>>->>>,,,,,,,,,,,,,,,,)))))----<<<.<-<<____...>>->>>>:::::
#=GC RF                    uUaauUAUGuUAUAA...UaAaaguaGuAGcAAAGUGaauAuGAuGguggCUAauuuuu....uaaAAAaagGGGuGaUgCC..UAUGauUguauuuuu.....GuauUaCCC.......cuA.GAAAGGA.....auAG....ucuUgucugucuaUGAAagacUgacguUuaUGuUuGCuUUUGcuacuUUuguc.uUgaUgaU...ucUagacauuAA
//
# STOCKHOLM 1.0

#=GF AC   RF01493
#=GF ID   rli37
#=GF DE   Listeria sRNA rli37
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   90.00
#=GF TC   156.30
#=GF NC   44.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   4


AL596166.1/191514-191759   UUACCUUUAUCUCCAGUCUAUUUUUUUAUAAAUACUAAUGUU---AGGGAACGGGUGUGUGGCGCUCGUCAUGAAGAUAAACAAAAUUAUCGAAUAUAUUGUAGUAGCAAUCAUCGUUCUAGUGUGGACUUACUUCAUUGUCAUUAAAGAAAUUCUUCCUAAAAAUAUAGGAUUUAUUUCAUUAGUAAUUCUAUCAAUAGUUCUUUAUUUUAUAGGUAAAAGGUUGAAUGGGAAACAUAGCAGAUAAAA
AE017262.2/907513-907759   UUAACUUUAUCUACAGUCUAUUUUUUUAUAAAUACUAAUG--UUAAGGAUACGGGAGUGUGGCGCUCGUCAUGAAGAUAAACAAAAUUAUCGAAUAUAUUGUAGUAGCAAUCAUCGUUUUAGGUUGGACUUACUUCAUUGUUAUUAAAGAAAUUCUCCCUAAAAAUAUAGGAUUUAUUUCAUUAGUAAUUUUAUCAAUAAUUCUUUAUUUUGUAGGCAAAAGGUUGAAUGGGAAACAUAGCAGAUAAAA
AARK02000157.1/1874-1628   UUAACUUUAUCUACAGUCUAUUUUUUUAUAAAUACUAAGG--UUAAGGAUACGGGAGUGUGGCGCUCGUCAUGAAGAUAAACAAAAUUAUCGAAUAUAUUGUAGUAGCAAUCAUCGUUUUAGGUUGGACUUACUUCAUUGUUAUUAAAGAAAUUCUCCCUAAAAAUAUAGGAUUUAUUUCAUUAGUAAUUUUAUCAAUAAUUCUUUAUUUUGUAGGCAAAAGGUUGAAUGGGAAACAUAGCAGAUAAAA
AARN04000008.1/60526-60280 UUAACUUUAUCUACAGUCUAUUUUUUUAUAAAUACUAAUG--UUAGGGAUACGGGAGUGUGGCGCUCGUCAUGAAGAUAAACAAAAUUAUCGAAUAUAUUGUAGUAGCAGUCAUCGUUUUAGGGUGGACUUACCUCAUUGUCAUUAAAGAAAUUCUCCCUAAAAAUAUAGGAUUUAUUUCAUUAGUAAUUCUAUCAAUAGUUCUUUAUUUUGUAGGUAAAAGGUUGAAUGGGAAACAUAGCAGAUAAAA
#=GC SS_cons               ::::::::::::::::[[[[[[[--[[-[---[[[[,,,,..,,,,,,,,<<<<<-<_____>->>>>>,,,,,,,,,,,(((((((----((((-((((((((,,,,,,,,,,,<<<<______>>>>,,,,,,,,,,,,,<<<<<-<<<<<----<<<<______>>>>---->>>>>->>>>>,,,,)))-)))))))))---))))))),]]]]-]-]]--]]]]]]]:::::::::::::::::
#=GC RF                    UUAaCUUUAUCUaCAGuCuauuuUUuuAuAAAugCuAAuG..UUAaGGauaCGgGaGUGUGGCGCuCGuCAUGAAGAUAAacaaaauUAUCGaauAuauuGuagUAGCAaUCAUCGuucUAGguUggaCUUACuUCAUUGUuauuaaAGaaauUCUcCCuaAAAAUAuaGGAUUUauuuCAuuaguAAUUcuaUCaauaauuCUUUauuuuguAgGcaAaAggUUgaaugGgAAACAUAGCAGAUAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01494
#=GF ID   rliD
#=GF DE   Listeria sRNA rliD
#=GF AU   Osuch I
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   49.40
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17259222
#=GF RT   Identification of new noncoding RNAs in Listeria monocytogenes and
#=GF RT   prediction of mRNA targets.
#=GF RA   Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P
#=GF RL   Nucleic Acids Res. 2007;35:962-974.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   9


AM263198.1/1338370-1338045 CUGUUAAUGGGAAAAA--GUCUCCCGGACGUGGUUUUUUAGAACCUACUGCUGCAGUUAAAACGACCGUAUCACCGUAACGAAUUAAUGCUGCCCCACUUGCUUGUUUUGCUAAUUGACCUACUUCAACAGAUAAUGUUUUACCUGCCCAUUCUGUUGAAAACACUUGUUUUUCAGACAUAUUUUAAUCUCCUUUGAUUAGGA---AA--CACGAACCAGAAACUUUACCAUGCAUAAGAAUGUUCACGCACACUUUAGAUUUUCUAAAGCACACAUGAAUCCAAAAACCUGCUACAAAUAGCGAUUUU-CUGAAGCACGUUUUUGGAUUCAUG
AADR01000075.1/2128-2454   CUGUUAGUGGGAAAAA--GUCGCCUGGACGUGGUUUUUUAGAACCUACUGCUGCUGUUAAAACGACCGUAUCGCCGUAACGAAUUAAGGCUGCUCCACUUGCUUGUUUUGCUAAUUGACCUACUUCGACAGAUAAUGUCUUACCUGCCCAUUCUGUUGAAAAUACUUGUUUUUCAGACAUAUUUUAAUCUCCUUUGAUUAGGAAAAA---CACGAACCAGAAACUUUACCAUGCAUAAGAAUGUUCACGCACACUUUAGAUUUUCUAAAGCACACAUGAAUCCAAAAACCUGCUAAAAAUAGCGAUUUU--UGAAGCACGUUUUUGGAUUCAUG
AL591978.1/199529-199202   CAGUUAAUGGGAAAAA--GUCGCCUGGACGUGGUUUUUUAGAACCUACUGCGGCUGUUAAAACAACCGUAUCGCCGUAACGAAUUAAGGCUGCCCCACUUGCUUGUUUUGCUAAUUGACCUACUUCAACAGAUAAUGUUUUACCUGCCCACUCUGUUGAAAAUACUUGUUUUUCAGACAUAUUUUACUCUCCUUUGAUUAGGAAAAA---CACGAACCAGAAACUUUACCAUGCAUAAGAAUGUUCACGCACACUUUAGAUUGUCUAAAGCACACAUGAAUCCAAAAACCUGCUAAAAAUAGCAAAUUUU-UGAAGCACGUUUUUGGAUUCAUG
AL596168.1/148311-147985   CUGUUAAUGGGAAAAA--GUCGCCAGGACGUGGUUUUUUUGAACCAACUGCAGCUGUUAAAACGACAGUAUCGCCGUAACGAAUUAAGGCUGCUCCACUUGCUUGUUUUGCUAAUUGACCUACUUCGACAGAUAAUGUCUUACCUGCCCAUUCUGUUGAAAAUACUUGUUUUUCAGACAUAUUUUAAUCUCCUUUGAUUAGG-AAAA--ACACGAACCAGAAACUUUACCAUGCAUAAGAAUGUUCACGCACACUUUAGAUUUUCUAAAGCACACAUGAAUCCAAAAACCUGCUAAAAAUAGCGAUUUU--UGAAGCACGUUUUUGGAUUCAUG
AADQ01000013.1/8010-7683   CAGUUAAUGGGAAAAA--GUCGCCUGGACGUGGUUUUUUAGAACCUACUGCGGCUGUUAAAACAACCGUAUCGCCGUAACGAAUUAAGGCUGCCCCACUUGCUUGUUUUGCUAAUUGACCUACUUCAACAGAUAAUGUUUUACCUGCCCACUCUGUUGAAAAUACUUGUUUUUCAGACAUAUUUUACUCUCCUUUGAUUAGGAAAAA---CACGAACCAGAAACUUUACCAUGCAUAAGAAUGUUCACGCACACUUUAGAUUGUCUAAAGCACACAUGAAUCCAAAAACCUGCUAAAAAUAGCAAAUUUU-UGAAGCACGUUUUUGGAUUCAUG
FM242711.1/1343217-1342891 CUGUUAGUGGGAA-AAA-GUCGCCUGGACGUGGUUUUUUAGAACCUACUGCCGCUGUUAAAACGACCGUAUCGCCGUAACGAAUUAAGGCUGCUCCACUUGCUUGUUUUGCUAAUUGACCUACUUCGACAGAUAAUGUCUUACCUGCCCAUUCUGUUGAAAAUACUUGUUUUUCAGACAUAUUUUAAUCUCCUUUGAUUAGG-AAAA-A-CACGAACCAGAAACUUUACCAUGCAUAAGAAUGUUCACGCACACUUUAGAUUUUCUAAAGCACACAUGAAUCCAAAAACCUGCUAAAAAUAGCGAUUUU--UGAAGCACGUUUUUGGAUUCAUG
AE017262.2/1339221-1338895 CUGUUAGUGGGAAAAA--GUCGCCUGGACGUGGUUUUUUAGAACCUACUGCCGCUGUUAAAACGACCGUAUCGCCGUAACGAAUUAAGGCUGCUCCACUUGCUUGUUUUGCUAAUUGACCUACUUCGACAGAUAAUGUCUUACCUGCCCAUUCUGUUGAAAAUACUUGUUUUUCAGACAUAUUUUAAUCUCCUUUGAUUAGGAAAAA---CACGAACCAGAAACUUUACCAUGCAUAAGAAUGUUCACGCACACUUUAGAUUUUCUAAAGCACACAUGAAUCCAAAAACCUGCUAAAAAUAGCGAUUUU--UGAAGCACGUUUUUGGAUUCAUG
CP001175.1/1280631-1280955 CUGUUAAUGGGAA-AA-AGUCGCCUGGACGUGGUUUUUUAGAACCUACUGCCGCUGUUAAAACGACCGUAUCUCCGUAACGAAUUAAUGCUGCUCCACUUGCUUGUUUUGCUAAUUGACCUACUUCAACAGAUAAUGUUUUACCUGCCCAUUCUGUUGAAAACACUUGUUUUUCAGACAUAAUUUAAUCUCCUUUGUUUAGGAA--A---CACGAACCAGAAACUUUACCAUGCAUAAGAAUGUUCACGCACACUUUAGAUUUUCUAAAGCACACAUGAAUCCAAAAACCUGCUAAAAAUAGCGAUUUU--UGAAGCACGUUUUUGGAUUCAUG
CP002002.1/1318451-1318124 CAGUUAAUGGGAAAAA--GUCGCCUGGACGUGGUUUUUUAGAACCUACUGCGGCUGUUAAAACAACCGUAUCACCGUAACGAAUUAAGGCUGCCCCACUUGCUUGUUUUGCUAAUUGACCUACUUCAACAGAUAAUGUUUUACCUGCCCACUCUGUUGAAAAUACUUGUUUUUCAGACAUAUUUUACUCUCCUUUGAUUAGGAAAAA---CACGAACCAGAAACUUUACCAUGCAUAAGAAUGUUCACGCACACUUUAGAUUGUCUAAAGCACACAUGAAUCCAAAAACCUGCUAAAAAUAGCAAAUUUU-UGAAGCACGUUUUUGGAUUCAUG
#=GC SS_cons               ::{{{--{{{{{{[[[..[[---[[[[,(((<<<<<____>>>>>,,,<<<<<-<<<____>>>->>>>>,,,,,,,,))),,,,,,,,,,,,,,,,,,,,,,((((((-(((((--(,,,,,<<<<<<<<<----<<_______>>---->>>>>>>>>,,,,,,<<<<<___>>>>>,,,,,,,,,,,,,,)--)))))--))))...)),,,,]]]]--]]]]],,,,<<<______________>>>,,,,,,,,,,}}}}}}-}}}---<<<<<<<<<<<<<<<--<<<_______________..___>>>-->>>>>>>>>>>>>>>
#=GC RF                    CuGuuAaugGgaaaaa..GuCgCCuGGACGuGGuuuUUUAgaaCCuACugCgGCcGuUAAAaCgACcGuaUCgCCGUAaCGAAUUAAgGCUGCuCCACUUGCUuGuuuuGCuaauUGaCCUACuuCaaCaGaUAAUGuuUUACCUgCCCAuuCuGuuGaaAAuACUuGuuuUUCagaCaUAuUUUAaUCUCCUuUGauuaGGAaaaa...CaCGAACCaGAAaCuuuACCAuGCAUAAGAAUGUUCACGCaCACUUUAGAUuuuCuaAagCACACauGaauCCaaaaaCCUGCuAAAAAUAGCgAuUUU..UGAaGCACGuuuuuGGauuCauG
//
# STOCKHOLM 1.0

#=GF AC   RF01495
#=GF ID   ACAT
#=GF DE   Human acetyl-coA cholesterol acyltransferase mRNA
#=GF AU   Osuch I
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Published; PMID:18542101
#=GF GA   37.00
#=GF TC   37.20
#=GF NC   36.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0006446; regulation of translational initiation;
#=GF RN   [1]
#=GF RM   18542101
#=GF RT   RNA secondary structures located in the interchromosomal region of human
#=GF RT   ACAT1 chimeric mRNA are required to produce the 56-kDa isoform.
#=GF RA   Chen J, Zhao XN, Yang L, Hu GJ, Lu M, Xiong Y, Yang XY, Chang CC, Song BL,
#=GF RA   Chang TY, Li BL
#=GF RL   Cell Res. 2008;18:921-936.
#=GF WK   ACAT1_mRNA
#=GF SQ   8


AK300551.1/12-158          UAGCUUAGCAGGCG-A--------CGUUGCGGGCCC-UGGGCGCCAGGAGAGCUUCCCGGAGU-CGACCUUCCUGCUGGCUGCUCUG---UGACCGCUUCCCGGCUCUGCCCUCUUGGCCGAAGUGCCCGCUGC----CGGGCGCGGGCCUCAGGUCGAAUUGAC
ABSL01055675.1/4050-3904   UAGCUUAGCAGGCG-A--------CGUUGCGGGCCC-UGGGCGCCAGGAGAGCUUCCCGGAGU-CGACCUUCCUGCUGGCUGCUCUG---UGACCGCUUCCCGGCUCUGCCCUCUUGGCCGAAGUGCCCGCUGC----CGGGCGCGGGCCUCAGGUAACGGUGGU
AB168948.1/94-240          CCGCCCAGCAGGCG-A--------CGUUGCGGGCGC-UGGGCGCCAGGAGAGGUUCCCGGAGC-CGACCUUCCGGCUGGCCGCUCUG---UGACUGCUUCCCGGCUCUGCCCUCUUGGCUGAAGUCCCCGCUGC----CGGGCGCGGGCCUCAGACAAUACAAUG
ABGA01074421.1/3703-3849   UAGCUCAGCAGGCG-A--------CGUUGCGGGCCC-UGGGCGCCAGGAGAGCUUCCCGGAGU-CGACCUUACUACUGGGUGCUCUG---UGACCGUUUCCCGGCUCUGCUCUCUUGGCCGAAGUGCCCGCUGC----GGCGCGCGGGCCUCAGGUAACGGUGGU
L21934.2/1243-1399         UAGUUAAAUAGCUAUAUUUAUAUAUAUCCAGGGCACCCCGAAUUCGGGAGAGCUUCCCGGAGU-CGACCUUCCUGCUGGCUGCUCUG---UGACCGCUUCCCGGCUCUGCCCUCUUGGCCGAAGUGCCCGCUGC----CGGGCGCGGGCCUCAGACAAUACAAUG
AK290659.1/5-151           UAGCUUAGCAGGCG-A--------CGUUGCGGGCCC-UGGGCGCCAGGAGAGCUUCCCGGAGU-CGACCUUCCUGCUGGCUGCUCUG---UGACCGCUUCCCGGCUCUGCCCUCUUGGCCGAAGUGCCCGCUGC----CGGGCGCGGGCCUCAGACAAUACAAUG
AANU01240625.1/4118-3972   CCGCCCAGCAGGCG-A--------CGUUGCGGGCGC-UGGGCGCCAGGAGAGGUUCCCGGAGC-CGACCUUCCGGCUGGCCGCUCUG---UGACUGCUUCCCGGCUCUGCCCUCUUGGCUGAAGUCCCCGCUGC----CGGGCGCGGGCCUCAGGUAACGGUGGU
AAKN02002834.1/19056-18906 UUGAAGAGAGGUUG-G--------CGUUGCGGGCGC-AGGGCGACGGGACAUCUUCC-CGGGACCGACCUGUGUGCUGGU--CCCG-GAUUGACGGGUUUCCGACUCGUGUCUCUUGAUGGAGGCUCCCGGAGCCCGGCGGGCUUGGGCCUCAGUAUUAACAGAA
#=GC SS_cons               ::::::::::::<<._........>>,,,,,,,,,,.,,,,,,<<-<<<-<<<-<<-<<<<<-.<<-<<________>>->>>>>>>...->>-->>>>>>->>------------<<<<---<<<<<<<____....>>>>>>>->>>>:::::::::::::::
#=GC RF                    UaGcuuAGcAGgcG.A........CgUUgcGGGCaC.ugGGcGcCaGGAgAgCUUCCCgGaGu.CgACCUuccuGCUGGccGCuCuG...UGACcGcUUCCCGgCUCugccCUCUUGGccGAAGcgCCCGcuGC....CGGGcgCGggCCUCAGauaauacaguu
//
# STOCKHOLM 1.0

#=GF AC   RF01496
#=GF ID   Afu_182
#=GF DE   A. fumigatus sRNA Afu_182
#=GF AU   Osuch I
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; clustal_alifold;
#=GF GA   65.00
#=GF TC   69.40
#=GF NC   63.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Aspergillus_fumigatus_non-coding_RNAs
#=GF SQ   19


AP007157.1/2099511-2099708   ACAUGAACAACGCAAA----AUCAACAUUCU--UCAAAAAGCGUUC--CUACGAGGAUA----UCU-C-CUAU-------U----G----G-GGUGAU---GCCUAUGAAG---UACG---GAA-AUCGUCAUAAAGAAUGGAGAG-GAACUGC----AAACCGC--AGG-GUGUCGAUCUUGGGUGCAGUGUCUU-CUAGAACUCUUC-------GAGUUCAGUGGAAGGGAUUGCAAUGAUUGAUUCUACAC
AM270071.1/76243-76042       ACAUGAACAACGCAAA----AUCAACAUUCU--UCAAAAAGCGUUC--CUGCGAGGAUAUCUUUCC-C-UACU-------G----G----G-UCUGUAUA-GCCGAUGAAG---UACG---GAA-AUCGUCAUACAGAAUGGAGAG-AAACUGC----CUCUGGC--AGA-GUAUCGAUCUUGGGUGCAGUGUCUGACUUGAACUUAG----------GUUCGGUGGAAGGGACUGCAAUGAUUGAUUCUACAA
AAKD03000019.1/555127-554916 UCAUGAACAACGCAAAA--AAACAACAUUCU--UUCAAAAGCGUUC--CUACGAGGACCCCACUCA-U-CUUC-------U----U-------GAGAUGG-GCCUAUGAAG---UACG---GAA-AUCGUCAUAGAGAAUGGAGAG-GGAUUGC---UUUUCUGC--AUA-GGGCCGAUCUUGGGUGCAGUGCCUGACUUGAUCUCGUCUUC-GACGGGCUCGGUGGAAGGGACUGCAAUGAUUGGCUCUACAG
ABDB01000049.1/530293-530077 UCAUGAACAACGCAAAU---AACAACAUUCU--UUCAAAAGCGUUC--CUACGAGGAUUAUCCUCC-U-CUAC-------G----G----G-AGAGAUAG-GCCGAUGAAG---UACG---GAA-AUCGUCAUAUAGAAUGGAGAG-GGAUUGUGGGAUAUCCGC--AAA-GUGUCGAUCUUGGGUGCAGUGUCUGACUUGAUCUCGUCUAAUGGCGAGCUCGGUGGAAGGGACUGCAAUGAUUGGCUCUACAG
ABIT01002923.1/8233-8422     CCAUGAACAACGCAAAU---UUCAACAUUCU--ACA-------GUCCUCUCCUCGCAAAGGUUUCU-C-CUAA-------G----A----A-ACCCAUGA-UGUCAGGAAG---UAUGCAAGAU-AUACUUGUAUAGAAUGAAGAA-AAAA-UC----AUUAAGC--------UUCGAUCUUGGGUGCAGUGUCAUUCUUGAAUC---------------UUCGUGGAUGGGAUUGCAAUGAUUGAUGCUACAU
ABVF01000206.1/31008-30822   CCAUGAACAACGCAAAU---AAUCACAUUCC--ACCA--AGAUGUU--CUGCAA-AAGUUCUCUCG-A-GAAU-------U----C----AUGAUGACAG-GAUAUUCAAGUGACAUG---ACCUAUGUUUCUUGGGAAUGGAGAC-GGAA-------AACAAGA--------UUCGGUCUUGGGUGCAGUGUCAUUCA---A-----------------UUCAUGGAUGGGAUUGCAAUGAUUGAACCUACAA
AAJN01000152.1/53370-53565   UCAUGAACAACGCAAA----AUUAACAUUCU--UUCAAAAGCGUUC--CUGCGAGGCCCAUCUCCUUU-CUUC-------G----G----A-AUGGAAGAUACCAAUGAAG---UACG---GAA-AUCGUCAUAAAGAAUGGAGAG-AAACUGC----UUCGUGC--AGG-GUGUCGAUCUUGGGUGCAGUGCCUGACUGC-U-----------------CUUAUGGCAGGGACCGCAAUGAUUGAUUCUACAC
AARE01001672.1/3804-3993     CCAUGAACAACGCAAAAA-AACCAACAUUCU--ACUAAAAGCGUUC--CUACAAAGGAAGGGAUCU-A-AAAA-------G----A----U----UUUGU-UCCCAUGAGG---UAUG---GAA-AUCGUCAUAUAGAAUGGAGAUCGGAAUAU----UUUC-----------GUUGGUCUUGGGUGCAGUGCCAUUCCUGAUCU---------------UUCAUGAAUGGGAUUGCAAUGAUCGACGGGACAU
ABAR01000023.1/265876-265685 AUAUGAACAACGCAAAA--AAUCAACGUUCU-CUCUAAAAGCAUUC--UUGCGAGUAUCACCUCCC-CUCUAC-------G----GAGAGG-AGUGUGCA-UACCAUGAAG---UACA---GAA-AUCGUCUAUGGGAAUGGAGAA-AAAA-CC----A------------GUGUUGGUCUUGGGUGCAGUGUCUU-CCAGUCCA-----------------UAUGGGAGGGAUUGCAAUGAUCGAUUCUACAC
AACD01000077.1/117755-117949 ACAUGAACAACGCAAA----AUUCACAUUCU--UUCAAAAGCGUUC--CUACAAAGGAAACUAUCU-U-CUA---------------------GAUAGGG-ACCUAUGAAG---UACG---GAA-AUCGUCAUAUAGAAUGGAGAC-AGACUGC----AA--UGC--AGA-GUAUCGAUCUUGGGUGCAGUGUCUGCCUGGCCAUA--A--------GGCUCUAUGGGAGGGACUGCAAUGAUUGGUUCUACAG
AM920437.1/4515356-4515175   UCAUGAACAACGCAAAA---CU-CACAUUCUACUCAAAAAGCGUUC--CUACGAAGACU---------------------------------------UG-UCUGAUGAAG---UACG---GAA-AUCGU-AUAGAGAAUGGAGAC-CAAGUGC---CAACUGGC--AAAGGUGUCGAUCUUGGGUGCAGUGCCUG--CUGACCUCUG----------GUCAUGUAGUAGGGAUUGCAAUGAUUGAUUCUACAU
ABAS01000011.1/380437-380648 AUAUGAACAACGCAAAA--AACUAACAUUCU-CUCUAAAAGCAUUC--UUGCGAGUAUCUCCUUCC-C-UUCUUAUGAGGG----G----G-AGUGUGUA-UACCAUGAAG---UAUA---GAA-AUCGUCUAUGGGAAUGGAGAA-GAAUUUUU--CCUUGAGAAGAAA-GUGUUGGUCUUGGGUGCAGUGUCUU-CCAGUUUU-------------UUAUUAUGGGAGGGAUUGCAAUGAUCGAUUCUACAG
AAIW01000332.1/43559-43750   CCAUGAACAACGCAAAU---UUCAACAUUCU--ACA-------GUCCUCUCCUUUCAAAGGUUUCU---CUGG-------G----A----A-AUCCAUGA-UGUCAGGAAG---UAUA--CAAC-AUGCUUGUAUAGAAUGGAGAU-CAAA-UCA--CAAUCAGC--------UUCGAUCUUGGGUGCAGUGCCAUUCCUGAAGUCUC------------UUCGUGGAUGGGAUUGCAAUGAUUGAAUCUACAU
AAGI01000073.1/79925-79729   UAUUGAACAACGCAAAU--UUUCAACACUCA--CUAUAAAGCAUUU-UCUAUGGAGAGACCCGUCG-C-CCAU-------GUGGCG----G-UGUGAGGU-UUCCAUGAGA----AAG---AAA-ACCGUCAUGUGAAGUGGAGAC-GAGACAC----CAGU----------GGCUGAUCUUGGGUGCGGUUUCUU-------CGGCUC-------UUGAGCAAUGGAAGAGAGCGCAAUGAUUGGCCGUACAU
ABWI01000913.1/43537-43351   CCAUGAACAACGCAAAU--AAAUCACAUUCC--GUCAAAA--UGUU--CUGCAA-AAGUUCUUUCG-G-GGAU-------U---CA----U-GAUGCCAG-GACGUUCAAGUUACAUG---ACCUAUGUUUCUUGGGAAUGGAGAA-GGAA-GC----AAGA-----------UUCGGUCUUGGGUGCAGUGCCAUCC--------------------GCUUCAUGGAUGGGAUUGCAAUGAUUGAACCUACAG
AAGT01000591.1/35083-34897   GGAAGUACAACGCAUAC----AUCACAUUCG--CUAUAAAGCAUUU--UCGGUGAGAAACCCGUCA-U-CAUUC-----G-UGAUG----A-UGUGAGGU-UUCCACGAC----CUUG---AGA-AUCGUCAGUCGAAAUGGAGAG-AAAUUUG-------------------AUCGAUCUUGGGUGCGGCGCUUC-------CUUUU----------UCACUAUAGGAAGGGUCGCAAUGAUUGGCCAUACAU
ACIW01002324.1/21815-21623   CAUUGAACAACGCAAAAAAAUUGCACACU-C--ACGAAAAGCAUUU-UCUUUGGAGAGACCCGUCG-U-CUAC-------GG-ACG----G-UGUGAGGU-UUCCAUGAGA----ACG---AAA-ACCGUC-UGUGAAGUGGAGAG-GAAU-AC----UUUG-----------GCUGAUCUUGGGUGCGGUUUCUCCCUGCUUUU---------------GCAGUGGGAGAGAGCGCAAUGAUUGGUCGUACAU
AAXI01000415.1/230458-230646 CAUUGAACAACGCAAAAA-AUUGCACACU-C--ACGAAAAGCAUUU-UCUUUGGAGAGACCCAUCG-U-CUAC-------GG-ACG----G-UGUGAGGU-UUCCAUGAGA----ACG---AAA-ACCGUC-UGUGAAGUGGAGAA-----UAC----AAUG-----------GCUGAUCUUGGGUGCGGUUUCUCCCUGCUUUU---------------GCAAUGGGAGAGAGCGCAAUGAUCGGUCGUACAU
ABQE01000150.1/54766-54952   CCAUGAACAACGCAAAU--AAAUCACAUUCC--GUCA--AGAUGUU--CUGCAA-AAGUUCUUUCG-A-GGAU-------U----C----AUGAUGUCAG-GACGUUCAAGUUACAUG---ACCUAUGUUUCUUGGGAAUGGAGAA-GGAA-GU----AAGA-----------UUCGGUCUUGGGUGCAGUGCCUUCC--------------------GCUUCAUGGAUGGGAUUGCAAUGAUUGAACCUACAA
#=GC SS_cons                 :::::::::::::::::...:::::<<<<<<..----------<<<..<<<<______________._.____......._...._...._.________._________>...>>->...>>>.---------->>>>>>-----.-------....-------.......-<<<<<<<-----<<<<<<-<<<__________.............__________>>>->>>>>>-->>>>>>>:::::::
#=GC RF                      ucAUGAACAACGCAAAu...auuaACAuUCu..ucaAAAAGCauuc..cUgCgaagAaaucuuUCu.u.cuau.......g....g....a.aguGauga.uuCcAUGAAG...cAug...gaa.AUcgUCaUauaGAaUGGAGAa.gAAaUgc....aauaaGc.......ugucgaUCUUGGGUGCagUGcCuuuCuuGaucU.............guuuuaUGGaaGgGAcuGCAAUGAuugacucUACAu
//
# STOCKHOLM 1.0

#=GF AC   RF01497
#=GF ID   ALIL
#=GF DE   ALIL pseudoknot
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:18474594
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 2001126; positive regulation of translational frameshifting;
#=GF RN   [1]
#=GF RM   18474594
#=GF RT   Apical loop-internal loop RNA pseudoknots: a new type of stimulator of -1
#=GF RT   translational frameshifting in bacteria.
#=GF RA   Mazauric MH, Licznar P, Prere MF, Canal I, Fayet O
#=GF RL   J Biol Chem. 2008;283:20421-20432.
#=GF WK   ALIL_pseudoknot
#=GF SQ   26


AE014075.1/332349-332233     CGCUUAUUUUGCGAAGGCGGAGUUCGACCGCCUCUGGAAAAAAUGAUGCCACUGCUGGAUAAGCUGCGUGAGCAGUACGGGGUCGGACCGCUAUGCAGCGAA-CUGCAUAUUGCCCCG
AAJT02000099.1/10563-10679   CGCUUAUUUUGCGAAGGCGGAGUUCGACCGCCUCUGGAAAAAGUGAUGCCACUGCUGGAUAAGCUGCGUAAGCUGUACGGGGUCGGACCAGUAUGCAGUGAA-CUGCAUAUUGCCCCG
L04539.1/888-774             CGCUUAUUUUCCGAAGGCGGAGUUCGACCGCCUCUGGAAAAAAUGAUGCCACUGCUGGAUAAGCUGCGUGACA--UACGGGGUCGGACCGGUAUGCAGCGAA-CUGCAUAUUGCCCCG
AAMK02000010.1/18129-18244   CGCUUAUUUUGCGAAGUCGGAGUUCGACCGCCUCUUGAA-AAAUAAUGCCACUGCUGGAUAAGCUACGUGAGCAGUACGGGGUCGGACCGGUAUGCAGUGAA-CUGCAUAUUGCCCCG
CP000036.1/4424346-4424239   CGCUUAUUUUGCGAAGGCGGAGUUCGACCGCC---------AGUGAUGCCACUGCUGGAUAAGCUGCGUAAGCUGUACGGGGUCGGACCGGUAUGCAGUGAA-CUACAUAUUGCCCCG
AP009243.1/37009-36893       CGCGUAUUUUGCGAAGGCGGAGUUCGACCGCCUGUGGAAAAAAUAGCGCCUCUGGUGGAUACCCUGCGUGGUACGCACGGGGUCGGACCGGUAUGCCACGAGCUGGC-UGUCGCCCCG
AJ868433.1/46548-46664       AGCAUAUUUUGCCCAGGCGGCGCUCGACCGCCACUGCAAGAAAUAGCGUCGUUAAAGGUGCCGCUGAUGGAACAGCAUGGGGUCGAGCCGGUAUGUCAGGAA-CGGCAUAUUGCCCCG
AJ868434.1/46548-46664       AGCAUAUUUUGCCCAGGCGGCGCUCGACCGCCACUGCAAGAAAUAGCGUCGUUAAAGGUGCCGCUGAUGGAACAGCAUGGGGUCGAGCCGGUAUGUCAGGAA-CGGCAUAUUGCCCCG
CP000037.1/89930-89814       CGCUUAUUUUGCGAAGGCGGAGUUCGACCGCCUCUGGAAAAAGUGAUGCCACUGCUGGAUAAGCUGCGUAAGCUGUACGGGGUCGGACCGGUAUGCAGUGAA-CUACAUAUUGCCCCG
CP000058.1/1784287-1784171   AGCCUAUUUUGCCCAGGCGGAGCUCGACCGCCCAUUCAAACGAUGAAGACGUUUAUUGAUGAAAACCGCCAGUCUUACGGGGUCGAGCCGAUUUGCAAGGUG-UUGCCAAUCGCCCCG
AE008923.1/2830641-2830757   CGCGUAUUUCGCCAAGGCGGAACUCGACCGCCACCACAAGAAGUGAUGGGCUUCAUCGACGCACAACGCGAGCACUUCGGGGUCGAGUCGAUCUGCAAAGCC-UUGCAGGUUGCCCCG
CP000158.1/533933-533817     AGCGUAUUUUGCUCAGGCGGAGCUCGACCGCCGACCGAAGACAUGAUCGCGUUCAUUGACGACCAUCGCGAUGUUUAUGGGGUCGAGCCGAUCUGCAGGGUA-UUGCCGAUUGCCCCA
CP000490.1/980093-980209     AGCAUAUUUUGCGAUGGCGGAGCUCGACCGCCGGUCGAAGUGAUGGUGGGUUUCAUCGACGCGCACCGGGAUGCGCACGGGGUCGAGCCGAUCUGCGACGUG-CUGCCGAUCGCCCCG
AY297781.1/43697-43813       CGCUUUUUUCGCCCAGGCGGCGCUCGAUCGCGAACUGAAGAAGUAAACGCCUAUCUCGAUCAGCACCGGGAUCUGUACGGGGUCGAGCCGAUCUGCAAGGUA-UUGCAGGUCGCUCCG
AATQ01000017.1/4870-4754     UGCCUAUUUUGCCCAGGCGGAGCUCGACCGCCCACUGAAGCGAUGAUCGCCUUCAUCGAAGAGCACCGGAUGGACUUCGGGGUCGAGCCGAUCGGCAAGGUG-CUGCCGAUCGCCCCG
CP000512.1/2978371-2978255   GGCGUAUUUUGCCCAGGCGGAGCUCGACCGCCGGUUCAAGCCAUGACGGGGUUCAUCGACGAACACCGCGCCAGGUACGGAGUCGAGCCGAUCUGCAGGGUG-CUGCCGAUCGCUCCG
ABSH01000039.1/135074-134958 GGCGUAUUUUGCACAGGCGGAGCUCGACCGCCCGUUUCGCAAAUGAUGGAUUUCAUUGCGGAAAGCCGAGAGACACUUGGGGUCGAACCAAUCUGCAGGGCG-CUGCAGUUUGCCCCU
ACNX01000025.1/2183-2299     CGCAUAUUUUGCCCAGGCGGAGCUCGACCGCCGGUCCAGGACAUGAUCGCCUUCAUCGAAGAGAACCGUGAAGCCAUCGGGGUCGAGCCGAUCUGCAGGCAC-CUGCCGAUUGCCCCA
ABSK01000054.1/41228-41344   AGCUUUUUUCGCGGCGGCGGACCUCGACCGCCUAUGGAAGAGAUGAUCAUGUUCAUAGACGACCAUCGUGAGCAUCUUGGCGUCGAGGCGAUUUGCAAGGUU-UUGCCGAUCGCGCCA
AL954747.1/2771839-2771723   UGCUUUUUUCGCCCAGGCGGAGCUCGACCGCGUUCUGAAGAAGUAAACGCUUACAUUGACCAAUAUCGGAGUAUCUAUGGGGUCGAGCCAGUCUGCAAGGUG-UUGCAGGUUGCCCCU
CP000450.1/2568937-2568821   CGCUUUUUUCGCUCAGGCGGAGCUCGACCGCAAACUCAAAUCCUGAGAUCGUUCAUCGACCAGUACCGCGACGCCCAUGGGGUCGAGCCGAUCUGCAAGGUU-UUGCAGGUCGCCCCA
CP000009.1/716541-716657     UGCGUAUUUUGCCCAGGCGGAACUCGACCGCCGGUUCAGGCCAUGACGCGCUUCAUUGAUGAGCACCGGCAGACAUAUGGUGUCGGGUCAAUCUGCAAGAUC-CUGCCGAUUGCACCA
ABCT01000003.1/210244-210128 CGCUUUUUUCGCCCAGGCGGAACUCGACCGCCUCAAAAAGAAAUGAGGCGCUUCAUCGAUGAACACCGCCAAACCUUUGGGGUCGAGUCAAUCUGUAAGUCC-UUUCAGAUUGCCCCU
ABHC01000041.1/4824-4938     GGCCUAUUUUGCUCAGGCGGAGCUCGACCGCCACGGCAAAUGGUGAUGUCGUUCAUCGACACGCACCGCGAGGAACUGGGUAUCGAGCCGAUCUGCCGUGAACUGGCA-AUCG--CCC
ACOA01000003.1/586280-586164 AGCGUAUUUUGCUCAGGCGGAGCUCGACCGCCCGUUUCGGAAGUGAUCAGCUUUAUCAAAGAGCAUCGUGAUGUCUGCGGGGUCGAGCCGAUUUGUCGUGUU-UUGCAGAUUGCCCCU
AALV01000004.1/92706-92590   CGCAUAUUUCGCGGCGGCGGAGCUCGACCGCCCGUUCCGCAAAUGAUCGCGUUCAUCGACAAUCAUCGUGGCGUCUUUGGUGUCGGGCCGAUCUGCCGGGUC-UUGGGGAUCGCACCA
#=GC SS_cons                 :::::::::::::::<<<<<_______>>>>>---------------------------------------------<<<<<------<<-<<<<<<<____.>>>>>>>->>>>>>>
#=GC RF                      cGCuUAUUUUGCccAGGCGGAGCUCGACCGCCuauugAAgaaaUGAugucaUUcAUcGAuaAgCauCGugAgauguacGGgGUCGAGCCgaucuGcaggGua.cugCagaUcGCcCCg
//
# STOCKHOLM 1.0

#=GF AC   RF01498
#=GF ID   Afu_190
#=GF DE   A. fumigatus snoRNA Afu_190
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ABDB01000050.1/749589-749691 AUAUGAUGAGAUAUCAUAGCUGGCACCAGUCAGACGGGGUGGUUAUAAACCAUAUCCACUGUUGAUUAGCUCUGGUCCGGGAACGCUACCCGAGAUCCCUGAC
ABFO01000069.1/3951-4046     ACAUGAUGAAAAUCUUUCGCUGGCACCAGUC---CUAGAAAGACUUGUACUCUGUUUGCUGCGGACAACCCUUUGGCU----UCUAAAUGCCUCCUAUCUGAU
ABKH01000207.1/44184-44282   CUAUGAUGAGACUUCUUAGCUGGCACCAGUC---CUAGAAAGAUUUGUUCUCUGUUUGUUGCGGAUUAGCUUU-GCAAUGGCUUAUAUAGCCUUGUUUCUGAU
#=GC SS_cons                 :::::::::::::::::::::::::::::::...:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      aUAUGAUGAGAuuUcuUaGCUGGCACCAGUC...CuaGaaaGaUuUGuaCucUGUuuGCUGcgGAUuAgCUuUgGucugGGauCguaaugCcuuaUuuCUGAu
//
# STOCKHOLM 1.0

#=GF AC   RF01499
#=GF ID   Afu_191
#=GF DE   A. fumigatus snoRNA Afu_191
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   60.00
#=GF TC   70.40
#=GF NC   47.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


AM270162.1/34733-34641       CUUCCAUGAUGAAUUA---AUCAAGAAUUCUGCAAUCCUGACAAUCUC--CUACUUUU---UGUG---AGAUUGCAUGUUGAC----U----CUUCUACACUUGAUCUGACC
AACD01000017.1/202498-202407 CUUCAAUGAUGAUCAC---UUCAAGAAUUCUGCAAUUCCGACAAUCUC--CAGGCUUC---UGUG---AGAUUGCGUGUUGAC----C-----UACUACACUUGACCUGAUU
AP007169.1/1056814-1056914   UUUGCAUGAUGAUUAUUCCUUCGAGAAUUCUGCAAUUCGGACAAUCUCCUCAGUUUAC---UGUGGCGAGAUUGCAUGUUGAC----A----UUUCUACACUUGAUCUGACU
AM920431.1/1133479-1133568   ACUACGUGAUGAU--C---AUUAUGAAUU-UGCAAUCCUGACAACCAC--CUAUCACA---UGUG---AGGUUGUAUGUUGAC----U----CUUCUACACUUGAUCUGACC
ABKH01000223.1/23365-23271   UACAAAUGAUGAAAUA---AG--AGAAUUCUGCAAUACUGACAAUUUC--CAUUUAUCU--UGUG---AAAUUGACUGUUGAC----ACAA-UUCCUACACUUGAUCUGAUU
AATX01000368.1/131622-131526 CUUCAAUGAUGAACAA------AAGAAUUCUGCAAUACUGACAAUUUC--CUGCUCUGGCGUGUG---AAAUUGCAGGUUGACAAAUU----UUCCUACACUUGAUCUGAUU
ABBT01000237.1/263787-263882 ACCAACGGAUGAAUAA------GAGAAUUCUGCAAUACCGACAAUUUC--CAUUUUAUAU-UGUG---AAAUUGACUGUUGAC----ACAAAUUCCUACACUUGAUCUGAAC
#=GC SS_cons                 ::::::::::::::::...:::::::::::::::::::::::::::::..::::::::...::::...:::::::::::::::....:....::::::::::::::::::::
#=GC RF                      uuUaaaUGAUGAauaa...aucaAGAAUUCUGCAAUaCuGACAAUcUC..CaguUuuc...UGUG...AgAUUGcaUGUUGAC....u....uUuCUACACUUGAUCUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF01500
#=GF ID   Afu_198
#=GF DE   A. fumigatus snoRNA Afu_198
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   40.00
#=GF TC   40.80
#=GF NC   37.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AACD01000006.1/37257-37396   CACGAAACGCCAAAAUGAUGAGAACACUGUUCAAGAACCGAUAUUU---UUAGGAAGAGCCGGAAGAGGUAUGGCAGGGG---------ACUUGAAUAA-UAGAAGCUCC--UGCCGUCGGUGCUUAUAAUGGUUCUACUGAAUGGUGUUUCGCU
AM920430.1/196085-195955     AAACAGACUCUAUCAUGAUGAGAUUCGC--AUUAGAACCGGAAUUUUUAAUAGGAAGAGCCGGAAGAGGUAUGGCAGAGG-----------CUGAAA-----------GCCCUGUCGUCGAUGCUUAUAAUGGUUCUCCUGAGUAGAGUCUUUGG
ABKH01000411.1/150082-150224 CCCACAAACUUGACAUGAUGAGAUACAU--CCAAGAACCGAAUACAAUUUUAGGAAGAGCCGGAAGAGGUAUGACAUGCCGUCACUAUCAAACUCAA---UGGGGCCGCAAAUGCAACACGUCCCCAG-------CUGCAGAUUUGGAAAAAUUU
ABBS02000005.1/49246-49105   CCAACCAACUUUACAUGAUGAGAUACAA--UCAAGAACCAAAUAUAUU-UUAGGAAGAGCCGGAAGAGGUAUGGCAUGCCGUCACUAUUAAACCUCA---UGGUGCGACAGUUGCAUUACAUUCCCAG-------CAAAGGAUUGAGAUUUUCCU
AAIW01000463.1/1572-1714     CAUUCCGCAAUUACAUGAUGA----CCU--ACCACAACCCAUUACU---UUAGGAAGAGCCGGAAGAGGAAUGGCAGCCCAUCAACCCUUACAAACA---AGGGAAACUUCCAGGCAAAUAUGCACUGAGAAACCCGACAGAAGUGGCAAAAAUA
AM269966.1/51552-51701       CAACCUACACCUAUAUGAUGAGAAUUUUUUUCAUGAACCGG----UAUAUUAGGAAGAGCCGGAAGAGGAAUGGCAGGGA-CCCCUCUAAAAUAAAAAAGAAGGGUGUUCACUGUCGUCGAUGCUUAUAAUGGUUCUGCUGAGUGGUGUUUAAAA
#=GC SS_cons                 ::::::::::::::::::::::::::::..::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::...:::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      CaaacaAcacuuAcAUGAUGAGAuucau..uCaAGAACCgaauauuuU.UUAGGAAGAGCCGGAAGAGGuAUGGCAgggcguCacucuuaaauaaaA...ugGggcguccacUGccguagaUgCuuagAauGGuuCuaCuGAgUgGgguuuauuu
//
# STOCKHOLM 1.0

#=GF AC   RF01501
#=GF ID   Afu_199
#=GF DE   A. fimigatus snoRNA Afu_199
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   45.00
#=GF TC   50.40
#=GF NC   39.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AM921939.1/1-79            UCAAAUGACGAGAAAAUUAGCUCUAGAUCAGGAGUCGCUUCUGCGGCGGUGACGGAUAAAGUCAUGUAUUAUCUGAUGA
ABFN01002286.1/18465-18539 UGAGAAAAAUAUUUCAUUAGCUCUAGAUCAGGAGCUGCUCUCGCAGCGGUGAUAGACA----UGUAUAUUAUCUGAUUA
AM920436.1/2795267-2795192 UCGCAUGACGAGGAAA-UAGCUCUAGAUCAGGAGUCACUUUUGUGACAAUGACGGAUUAA--CAUGUAUUAUCUGAUUG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..:::::::::::::::::
#=GC RF                    UcagAuGAcgAguaaAUUAGCUCUAGAUCAGGAGucGCUuUuGcGGCGGUGAcGGAuaAA..caUGUAUUAUCUGAUua
//
# STOCKHOLM 1.0

#=GF AC   RF01502
#=GF ID   Fungi_SRP
#=GF PI   Afu_202; SRP_euk_arch; SCR1; Afu_202
#=GF DE   Fungal signal recognition particle RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19838050
#=GF SS   Published; PMID:19838050
#=GF GA   65.00
#=GF TC   65.60
#=GF NC   64.80
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.99 -Z 549862.597050 CM SEQDB
#=GF CL   CL00003
#=GF DR   URL; http://rnp.uthscsa.edu/rnp/SRPDB/SRPDB.html;
#=GF DR   SO; 0000590; SRP_RNA;
#=GF DR   GO; 0006617; SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition;
#=GF DR   GO; 0005786; signal recognition particle, endoplasmic reticulum targeting;
#=GF DR   GO; 0048501; signal recognition particle, plasma membrane targeting;
#=GF RN   [1]
#=GF RM   11839493
#=GF RT   Towards the structure of the mammalian signal recognition particle.
#=GF RA   Wild K, Weichenrieder O, Strub K, Sinning I, Cusack S
#=GF RL   Curr Opin Struct Biol 2002;12:72-81.
#=GF RN   [2]
#=GF RM   10678824
#=GF RT   Crystal structure of the ribonucleoprotein core of the signal recognition
#=GF RT   particle.
#=GF RA   Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA
#=GF RL   Science 2000;287:1232-1239.
#=GF RN   [3]
#=GF RM   11243816
#=GF RT   Structural and energetic analysis of RNA recognition by a universally
#=GF RT   conserved protein from the signal recognition particle.
#=GF RA   Batey RT, Sagar MB, Doudna JA
#=GF RL   J Mol Biol 2001;307:229-246.
#=GF RN   [4]
#=GF RM   12520023
#=GF RT   SRPDB: Signal Recognition Particle Database.
#=GF RA   Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T
#=GF RL   Nucleic Acids Res 2003;31:363-364.
#=GF RN   [5]
#=GF RM   12140321
#=GF RT   Prediction of signal recognition particle RNA genes.
#=GF RA   Regalia M, Rosenblad MA, Samuelsson T
#=GF RL   Nucleic Acids Res 2002;30:3368-3377.
#=GF RN   [6]
#=GF RM   19838050
#=GF RT   Kinship in the SRP RNA family.
#=GF RA   Rosenblad MA, Larsen N, Samuelsson T, Zwieb C
#=GF RL   RNA Biol. 2009;6:508-516.
#=GF WK   Signal_recognition_particle_RNA
#=GF SQ   50


AAIM02000151.1/16295-15999   -GAC-UGUAAUGGUCU------AACGGUGAA--------GGCGUUC----AAAC--CCGU-----------------------------------------------------------------------------------------------------------------U---CAACC-GCCCAUCCCAAU-A-----------------------------CUGUAGUACUUCG--GUAUCGCAG-----------CCCUCCGCC-------GCGC-CCCGCCCG--------------AACG-CU--GCGGU-----------------------------------------------------------------GGUCGCC-CACUCGUG-CAGGUAACU-CACGA-UGCUGGAACUUUGCGG-----------------CC--CUAAGCAC-----------------UGGAGAUGAC--CCUUGAGGGAGGUUUCACUCUGCAGAGAU--CUCUCCC-CCGU-CG-CGUGG----CGG-GUGGG-AAC-ACGUUAG-U----GCGGGGG---------------------------------GAUUUGGGAUGGCAAGUGGAUGAGAUGGAGCAGCCAACU-----------------------------------------------------------------------------------GUCUUU----UUU------
AAFU01000720.1/9717-9996     -GAC-UGUAAUGGUCAG----UUUGGUUUCG---------GAGGCA----CUUG--AUUUU----------------------------------------------------------------------------------------------------------------CU-CGCU-------GUUUCU---------------------------------ACUCCAUCCCCAUAAGAACCC----------------------CCCAGCG-GCGC-CCAGCACG--------------AAUC-UC--GCGGU-----------------------------------------------------------------GGCCACC-CACUCGCA-CGGGUAACC-UGCGA-UCGCUGCGU-----GU-----------------GGCCCUAAGCAA-----------------UGAAGAUGAC--ACUUGAGGGAGGUCUCACUCUGCAGAGGC--AUCUUCA-CCGU-CA-GAUGG----CGC-GCUGG-AUC-ACGAUCG-CUGGGGGCUUGGG-------------------------------GU-AGAGCGGC--GAGAUGGA---------GAUGUCGACU----------------------------------------------------------------------------------CCAAUUU-----UU------
AAFT01000084.1/73852-74124   UUGC-UGUGAUGGCAUU------UGGCAGAA-------GCGCGCUAAC---CGC-GCCCUUUGCGAUGCUUGU---------------------------------------------------------------------------------------UACAGGAGAAGUGU-----------CCGGUUCG------------------------------------------------------------------------------------AUCC-CUGCGUGG-------------GUUAU-CC--ACGG-------------------------------------------------------------------CGGAAG----CGGCU-UGAGUAAUC-AGCCUUCGA-CCGCCAG--------------------------CUAACA-------------------AGCAGGCUUAAACCCGGAGGGAAGCA--AUUCAGCACGGGG--ACCUGU--CCGU-GG-GGAGG----CGA-AACGG-AUG-GCACAUC-UUC-UGGC----U--------------------------------UUGGCAAGUAUUGUAUGGG-----------GCCUAGUG----------------------------------------------------------------------AUGCGACU-CCACAGGAUUU----UUU------
AAIH02000014.1/160337-160617 AAUC-UGUCAUGGAUAA----CCCAGUGGGA-----------GG-------UCA-GCCG----------------------------------------------------------------------------------------------------------------------CUAA---GAC-GAUAACCU-------------------------------UGCUUCGG-UUC--UCCACAC---------------CAGCGG--GACC-GGUGC-CUGGUACG--------------AAUC-CU--GGGGU--------------------------------------------------------------CGUCGUUGUA---CUCGUG-CGAGUAAUC-CACGAUCGC-UACA-ACGCG-----------------------CUAAGCAA-----------------UGGAGAUGAU--UCUUGAGGGAAGCA--AUUCUGCAGAGAC--AUCUCCA-CCCU-GG-GGUGG----CGUCGCCAG-AAU-ACACC-G-AC---CCGUUAC----------------------------------AGGGAAAUUGG-CUACU-------------UGGCUGG------------------------------------------------------------------------AC--------AACUACGUCUCUCUUCUUUUU
AP007169.1/992884-993155     AAUC-UGUCAUGGAUAA----CCCAGUGGGA-----------GG-------UCA-GCCG----------------------------------------------------------------------------------------------------------------------CUAA---GAC-GAUAACCU-------------------------------UGCUUCGG-UUC--UCCACAC---------------CAGCGG--GACC-GGUGC-CUGGUACG--------------AAUC-CU--GGGGU--------------------------------------------------------------CGUCGUUGUA---CUCGUG-CGAGUAAUC-UACGAUCGC-UACA-ACGCG-----------------------CUAAGCAA-----------------UGGAGAUGAU--UCUUGAGGGAAGCA--AUUCUGCAGAGAC--AUCUCCA-CCCU-GG-GGUGG----CGUCGCCAG-AAU-ACACC-G-AC---CCGUUAC----------------------------------AGGGAAAUUGG-CUACU-------------UGGCUGG------------------------------------------------------------------------AC--------AACUACAUCU-CU--------
U18916.2/67873-68301         AGGC-UGUAAUGGCUUU-----CUGGUGGGA-------UGGGAUACGU--UGA---GAAUUCUGGCCGAGGAACAAAUCCUUCCUCGCGGCUAGACACGGAUUGC-----------------------ACGCCCUUUGGGCAAGGGAUAGUUCUCUAUUCCGCACCGUGCCCUGUUGUGGC----AACCGUCUUUCCUCCGUCGU-------------AAAUUUGUCCUGGGCAGAGCUGUCUGCCCGGAGGCG---GGAGAGUCCGUUC-UGA--AGUGU-CCCGGCU-AUAAU---AAAUCGAUCU-UU-GCGGG-CA----------------------------------------------------------GCC-CGUU-GGC-AGGAGGCG-UGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAGG--------UAGUUCUGGGUC-CUUAGGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCGUCAGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UCA--GUCGGAUAAUUGUGC-----------------AAGUUGAUC--------------------------------------------------------------------------------------------------------------------------------------------
M20836.1/96-351              -CGC-UGUAAUGGC----------UUGGUCG--------AAGUGUUUA--GUAC-UCCCA-----------------------------------------------------------------------------------------------------------------A-UAGUGCAUGUUCGGUGGUCUC------------------------------------------------------------------------GGGUUCGAGUCUC-GCUUUCGA---------------UCC-CU--CGAUC-----------------------------------------------------------------UGCCACGUCUGUUCGA-AGAGUAGUCUUCGUG-GCA-ACUGGCA-------------------------GUUAAAC-------------------CGUGUAGUAC-CGAUGGAGGUUGGAA--ACAAUGCACAUCA--CUACCGG-GUCU-UG-GGCAG---UGCG-AUAGC-GAU-GGGAUUC---ACCU-----------------------------------------UCGCAGGAUGUGCAU--------------GGAAGUAU--------------------------------------------------------------------AAACACA-----ACGGUCG-------UU------
AAFM01000021.1/278347-278600 GUGC-UGUGAUGGCAU--------UUGGCAG--------AAGCGUACC--GAGC-GCGCA-----------------------------------------------------------------------------------------------------------------C-------UAUUUCGGCUUACCU------------------------------------------------------------------------AUCUUCGUGGGUC-CGGUUCGA---------------UCC-GC--GCGGU-----------------------------------------------------------------CAGAAUG-UCUCAAUU-CGAGUAAUC-AAUUGUGC--AGUUCUA-------------------------GCAGCGA-------------------GCGGCAGUAC-CACUGGAGGGAAGCA--AUUCAGCACAGUAAGCCGCCCG--UGCAGA-GGCGA---AGCG--GAAG-ACC-CAGCUGU-UUAAGG-----------------------------------------AGGACGGAAUAGUGAC------------UGGUAUGUCG------------------------------------------------------------------A--CUCCA-----C---UC--------UUUU----
ABKH01000392.1/23226-22890   UAGC-UGUGAUGGUCC------AAGUGGGAG--------ACCCGCUG---CAUC-CGCC-----------------------------------------------------------------------------------------------------------------------------GCGUGUCUGUG-G-----------------------------CUCUGGGGCCAUCUCAUCCCCGA-------------AA----CAGCGAGAGGUGC-CUGGUUCG--------------AAUCCCC--G-GGUCGCGGCAGACUCUCGGCCAAUGGAGCCGAGCCACACUCGGCUGUGUCGGCCGGGGGAGUCUCCUCCCCA-CA---CUCG-UGCGAGUAAUCCA-CGAUC---UGCUGUGGC---------------------GCGCUAAGCC------------------CUGGCCCGGA-CCCUCGAGGGAAGCG--AUUCUGCAGAGAACAGGCCC--CCCGGA---GAUGG----CGGCGCCAG-ACU-ACACC-C-UCGCUG-----------------------------------------CACAG-UGCCCAA----------------GGCGGACUGGCAGGUC----------------------------------------------------GACUUUUU----------------------------------
ABPO01001973.1/1696-1204     ------------------------------------------AUACGU--UGA---GAAUUCUGGCCGAGGAACAAAUCCUUCCUCGCGGCUAGACACGGAUUGC-----------------------ACGCCCUUUGGGCAAGGGAUAGUUCUCUAUUCCGCACCGUGCCCUGUUGUGGC----AACCGUCUUUCCUCCGUCGU-------------AAAUUUGUCCUGGGCAGAGCUGUCUGCCCGGAGGCG---GGAGAGUCCGUUC-UGA--AGUGU-CCCGGCU-AUAAU---AAAUCGAUCU-UU-GCGGG-CA----------------------------------------------------------GCC-CGUU-GGC-AGGAGGCG-UGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAGG--------UAGUUCUGGGUC-CUUAGGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCGUCAGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UCA--GUCGGAUAAUUGUGCAAGUUGAUCGCUUCGGCGGUUUAAUUUGGCGGU-----GCCAUCA--------GGAUUUACUCGCACAUUGUGGCCGUU--------------------------------------CCCUCGGGGAUGGAGUGUGUCCU----GAACCAUA------UUUUU---
ABFN01002269.1/2818-2493     -AGC-UGUCAUGGCCU-------AAUUGGAA---------GACUGUCU------------GCUC----------------------------------------------------------------------------------------------------------AACACCCGCAG---CCAACCCAU----------------------------------GAAUUCUGCUUAGUCAGAAA------------------GGAC--GAGACGGUGC-CUGGUUCG--------------AAU--CC-CGGAGUCGCGACCCGGGCGUGGUUUUAUU----------------UAAUGGACCGCGUCUUUUCUGGUUCUCCCACA----CUCGUG-CGAGCAAUC-CACGAACGG-CUGU-GGCGC--------------------G--CUAGGCAA-----------------UGGAGGCGAC--GCUUGAGGGAAGCA--AUUCUGCAGAGAC--ACCUCCA-CUCCGGG--AUGG----CGGCACCAG-AUC-ACAUCGG-CU---GUUCAC-------------------------------------UGUGGGUUGGCCGUGG-----------A---------------------------------------------------------------------------UUCUGGACG---GUCAACUUUU----UUUU-----
AAPO01000065.1/128485-128187 -GGC-UGUGAUGGCUUU----UAGUGGAA---------GUGUACUU----CU-----UG-----------------------------------------------------------------------------------------------------------------------CGC---ACUCUCAGAUUUGUUAAA-------------------UUGUGUAAAAGAUUCUCUUGAGUUUUUUC-----------GCU-GUGU---UCAAAGUGU-CCAGUUC---------------GAUC-CU-CGCGGU-------------------------------------------------------------UUGAAUUUUCU-UGACUACU-UGAGGAAUC-AGUACU-GU--CAGA-UUCU----------------------GCUAAUUAA-----------------UAGCACCACC--ACUGGAGGGAAGCA--AUUCAGCACAGU---AAUGCUAUCCGUGAC-GGAGG---CGAU-ACUGG-AUG-GCACAUU-GU----------UCCGUU----------------------AGUUAAUAGUCUGGGAAAGC---------------CUUAG------------------------------------------------------------------------UGUG-AC-----G-ACUCUAU----UUUU-----
AADM01000319.1/21426-21827   UCAC-UGUAACGGUCG------ACAGUGGAAC------U-GUAUUUUC--CGAG-AUU--UCUGACCUGGGUUCAAACCCUGCGGUCGGACGUGU--------------------------------------------UACGCUUUAAGCCUCUUUCGGGAGGUUGCUACACG-----------CUCAGUCUAACA----------------------------AU--------------------------------------CGAG---UCGACGUGC-CCUGGUAACAA-------AUCGAUCC--UUGCGGG---------------------------------------------------------------CAGU-CCAGG-GCGAGAUG-UGAGAAGUC-CGUCUUGUA-CCUGGUACGGCAAUGG--------UAGGCGAGGGUG-CUUAACGCUAACCCGUCUCUUGUGCUCCUAU-CGCUGAAGGGGAGUUUCAUCCAGCACAGCA--AGAGCAA-CCCGUGAUGGAGG-----CGACUGGG-AUU-ACAC-UU-GUC--CUCGUAUAAGGGAUU-----------------UAUCCCUUCGUUG---UGGGC-----G-----------UGAAUCUCAUCCUAUG------------------------------------------------------GAAUGUGAAGAUACU---AGAACC-CUG-------------
AAKD03000026.1/249785-250050 AAUC-UGUCAUGGAUAA----CCUAGUGGAA-----------GA-------CCC-GCCG----------------------------------------------------------------------------------------------------------------------CUAA---GUC-AGUAACCU-------------------------------UGCUGCGG-CAA--UUGCC------------------AGCGG--GAAA-GGUGC-CCGGUACG--------------AAUC-CU--GGGGU--------------------------------------------------------------CGUCGCUGUA---CUCGUG-CGAGUAAUC-CACGAU-GC-UACA-AGGCG-----------------------CUAAGCAA-----------------UGGAAGUGAU--UCUUGAGGGAAGCA--AUUCUGCAGAGAU--AUUUCCA-CCCU-GG-GAUGG----CGUCGCCGG-AUA-ACACC-U-AC---CCGUUAC----------------------------------AGGGAAAUUGG-CUGUC-------------UGGCUGG------------------------------------------------------------------------AC--------AACCGCAAU---U--------
CP000502.1/544949-544852     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUCAGUCUGUUA--CAUUCUA-------------------------GCAAUGA--------------------GUAGCACCAUCACUGGAGGGAAGCA--AUUCAGCACAGUA--UGUUACCCGUGGUGGAGGCGA---AACG--GACG-GCA-C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
AJ550803.2/101-623           AGGC-UGUAAUGGCUUU-----UCGGUGGGA-------UGGGAUACAU--UGG---GAAUUCUGGCCGAGGAACAAAUCCUUCCUCGCGGCUAGACACGGAUUGC------------------------ACGCCUUUCGGCAAGGGAUAGUUUUCUAUUCCGCACCGUGCCCUGUUGUGGC----AAUCGUCUUUCUCCCGUCGU------------CAAUUUGUCCCCGGGCAGAACUGUCUGCUCGGAGGCG---GGGGAGUCCUAUC-UGU--AGUGU-CCCGGCU-UUAAU---AAAUCGAUCU-UU-GCGGG-CA----------------------------------------------------------GCC-CGUU-GGC-AGGAGGCG-UGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAGG--------UAGUUGUGGGUCCCUUUGGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCGUCAGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UCA--GUCGGAUAAUCGUGCAAGUUGAUCGUUUCGGCGAUUCAAGUUGGCGGU-----GCCAUCA--------GGAUUUACUCGCACAUUGUGCCAUUC--------------------------------------CCUCGGGGAUGGUUGUGUGUUCU----GAACCACA------UUUUU---
M28116.1/247-765             AGGC-UGUAAUGGCUUU-----CUGGUGGGA-------UGGGAUACGU--UGA---GAAUUCUGGCCAGGAACAAAUCCUUCCUCGCGGCUAGACACGGAUUGC-------------------------ACGCCCUUUGGCAAGGGAUAGUUCUCUAUUCCGCACCGUGCCCUGUUGUGGC----AACCGUCUUUCCUCCGUCGU-------------AAAUUUGUCCUGGGCAGAGCUGUCUGCCCGGAGGCG---GGAGAGUCCGUUC-UGA--AGUGU-CCCGGCU-AUAAU---AAAUCGAUCU-UU-GCGGG-CA----------------------------------------------------------GCC-CGUU-GGC-AGGAGGCG-UGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAGG--------UAGUUCUGGGUC-CUUAGGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCGUCAG---AAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UCG-AGUCGGAUAAUUGUGCAAGUUGAUCGCUUCGGCGGUUUAAUUUGGCGGU-----GCCAUCA--------GGAUUUACUCGCACAUUGUGGCCGUU--------------------------------------CCCUCGGGGAUGGAGUGUGUCCU----GAACCAUA------UUUUU---
CR382127.1/176581-176314     UAGC-UGUAAUGGCAUU------UUGUCGGA-------GUGGUAAAU---CGUC-UUCUUGUUGUGCGUUCGAG-------------------------------------------------------------------------------------UCUUGGGCUCUGCAC-----------UUGGCCAU--------------------------------------------------------------------------------UUGGUUGU-CCUUUCCG--------------AAU--UC-UGCGGU---------------------------------------------------------------UGAUGGGCG-UCUCGGUC-UGAGUAAUC-GGCUUUGAGAUUUCCGU-------------------------UCUAAGA-------------------UUAACUGGGA-AACUUCAGUGGAGCA--AUCCAGCAGAGAU-CCAGUUG--CCGUGGG-UAUGG----CGG--UGGG-AUC-GCAACCA-A-G-UGGU---------------------------------------AUAU-GUUAU-------------------GGAAGAU---------------------------------------------------------------------AUUUACGA----UCACGAUU--------------
AJ564197.1/1-533             -AGC-UGUAAUGGCUCA-----AUGGUGGAAU------UGUACACCUU---GG---GAUUUCUGACUUUGGUUCAAUCCUCGCAGUCGGACGUAGGUUAGCAUGUCACGU-------------UUCGGCGUGGCAAGGGGUACUCACCUUCCCGUGGGGCUCCGCACUGCGCGUCGGCGAC----AACCGUCAUC-CUUCUCUCGCU---------UCCAGUUGCCGAGGCCGUCAAUCUUGGCGGUCUCAGAG--AGAGGGACUCGGGG-UUA-ACGUGU-CCCGGUU-AUUA------UCGA-UCU-UC-GCGGGGUU---------------------------------------------------------UGUU-UGCGCGUU-CGGGCACG-AGAGAAAUC-CGUGUUCCUGGGCGUGU--GGCAAAG--------UAGUUACGGGUUCCUUGUGG-----------GCCUCGCCUUGAC-CGCUGAAGGGGAGUUUCAUCCAGCACAGCG--AGGGCGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACUA---GUUCUCCGAGUAC------------------------------AAGUGCAGA---------CU----------GGGUUGGCCCUGUGCCAAUCUUAACGGGCGGUGUCGCUGAUAAUUACCCACCAGUAAAGGUACGUUGCUUGCAGCGUGGGGUGUAC---AAAACUAUUU----U--------
M20264.1/96-351              -CGC-UGUAAUGGC----------UUGGUCG--------AAGUGUUUA--GUAC-UCCCA-----------------------------------------------------------------------------------------------------------------A-UAGUGCAUGUUCGGUGGUCUC------------------------------------------------------------------------GGGUUCGAGUCUC-GCUUUCGA---------------UCC-CU--CGAUC-----------------------------------------------------------------UGCCACGUCUGUUCGA-AGAGUAGUCUUCGUG-GCA-ACUGGCA-------------------------GUUAAAC-------------------CGUGUAGUAC-CGAUGGAGGUUGGAA--ACAAUGCACAUCA--CUACCGG-GUCU-UG-GGCAG---UGCG-AUAGC-GAU-GGGAUUC---ACCU-----------------------------------------UCGCAGGAUGUGCAU--------------GGAAGUAU--------------------------------------------------------------------AAACACA-----ACGGUCG-------UU------
AAIW01000330.1/33747-33449   AGCU--GUCGU-GGCGCAACGGGAGACGGGCUGCUCUAACCCGCCGUC-CACCC-AUGCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUUCUGCUGAGUCAGAAC-------------------GCACUCGCCCGGUGC-CUGGUUCG--------------AAUC----CGCGAGUCGCGACCUUG----------------------------------------UUAAAGAGGUU----CUCCCG-CCCUCA-CGCGAGUAGUCCG-UGAAUUGGCGGCGGC-----------------------GCGCUAAGCA------------------AUGGAGGCGA-CCCUUGAGGGAAGCA--AUUCUGCAGAGACUCCU-CCA-CUCGCG---GAUGG----CGGCACCAG-AUC-ACACCGG-CGGUG------------------------------------------CAU---------------------------CGUGGGUG------------------------------------------------------------------GGCGACGGGAUCUGGCCUGUCGAC-UUUUUU----
CR382126.1/1162031-1162525   ACCC-UGUCGAAGGAGU-----GUGAUGCUUG------GAUAUGUGGC---UC---CGG-UUCGAAACCGCACAGUCACACCGGGUCUCUUUCAAAUGGAAGAGGUUUCACAAUG---GUAUCCCAAACAGGCGUGAAAUGUCUCGUAGUGGUUAUAUGCCAUUACCCGCUUUUCG-UGUCUGGCCGCCCGGUCUACGCGUUCAUUUAUUUGUGUAACUGCUUUGGACAGCUGGAUCUCGGUUCGGUUG-------------UC-ACGU-GGUCGACGUGUCCCAC-CGUUAC--------AAAAUUG-UU-GCGGGUUAU-------------------------------------------------------CCUUUGUGGUGGCU-CGGUCGCA-UGAGAAGUC-UGCGGUUCGAAGCCCAACUGGUAACGAUU--UAGCAUUUCAACUAAUACUUGAAG--------CUAGUUUAGUGUUUAACGUUGUAGGGGAGUCUCAUCCAGCACAACG-AACACUG--CCCGUGA-CGAGG-----UGGUGUGG-AUU-GCACGU---CC-CGUG-GUUAAGCAGUGC---------------GUGUGGGUUC--------------------------------------AGAG------------------------------------------------------------GCAGACAUACAC----UGUCCUUCAU---UUU------
AM921947.1/1-264             AAUC-UGUCAUGGAUAA----CCUAGUGGAA-----------GG-------CCU-GCCG----------------------------------------------------------------------------------------------------------------------CAAA---GUC-AGUAACCU----------------------------------UGCUG---CGGCAUUUG----------------CCAGCG--GGAAAGGUGC-CCGGUACG--------------AAUC-CU--GGGGU-------------------------------------------------------------CGUCGUUGUA----CUCGUG-CGAGUAAUC-CACGAU--G-CUA-CAAGGC--------------------G--CUAAGCAA-----------------UGGAAGUGAA--UCUUGAGGGAAGCA--AUUCUGCAGAGAC--ACUUCCA-CCCU-GG-GAUGG----CGUCGCCGG-AGG-ACACC-U-AC---CCGUUAC----------------------------------AGGGAAGUUGG-CUGUU-------------UGGCUGG--------------------------------------------------------------------ACAACCG-------CAA------------------
AJ550805.2/102-536           GAGC-UGUAAUGGCUUU------UGGUGGAA-------CCAGGUGUCC--CGAG--AGU-UCUGGUCUGGGUUCGAACCCUACGGCCAGACGUGGUUG--------------------------------------CAAUUAUACAACUCUUUGUGGGUUGGCGCCGCGCCCAAGCUC-------AACUGCACUU-------------------------------------CCUCGUAAGAGG---A--------------GCCGAGUU-UUAGACGUGU-CCCGGAU-UAU-------AUCGAUCU-UU-GCGGG-G-----------------------------------------------------------AGU-CCUG-GGC---GAGACA-UGAGAAGUC-UGUCUUC---GCU-UAGGUACGGCAAUGGUACCACACGACGCACCUUGCGUCGUUGUGUGGUUUUCGCAUGCUCCUUCCGCUG-AAGGGGAGUUUCAUCCAGCA-CAGC-AGGAGUCA-CCCGUGA-GGAGG----CGG-CCGGG-AUG-GCAC-UC--GU--CCUCGGUA--------------------------------U-----------------------------CAUUAAGCACGGCGGUGGGCUGGGAUUUCC-------------------------UCGGGGCAUUUAGCCUCUGUUGGACACCUUA--GGAACUACCA-------------
AL669999.1/52995-52714       CGAC-UGUAAUGGUCA--------AGGUGGG---------UUUGAA----GGCA--CUUGAU--------------------------------------------------------------------------------------------------------------UUUCUCAAUG-UCUCUA-UUCCAU------------------------------G--UCCAAAUCUGGAAG--------------------------CCCAGCGG-CGC-CCAGCACG--------------AACC-UU--GCGGU-----------------------------------------------------------------GGUCACC-CACUCGCA-CGGGUAGCC-UGCGACUU--GCUGCGC---GU-----------------GGCCCUAAGCAA-----------------UGAAGAUGAC--ACUUGAGAGAGGUUCCACUCUGCAGAGAC--AUCUUCA-CCGU-CA-GGUGG----CGC-GCUGG-AUU-ACGAUCG-CUGGGGGGU---U--------------------------------G-GGAUAGAG--CGUUGAGA---------UGGAGAUGUC----------------------------------------------------------------------GACU-------CCUAUUUU-------------
CU638743.1/2301930-2302215   CGGC-UGUAAUGGUCAU----AUUGGUUAAG---------GAGACG----CCUG--AAAA-----------------------------------------------------------------------------------------------------------------U---CUUC---UCCCGACUCCA-------------------------------GUCUCAUAUCCAUGAGAACUU----------------C-----CCCCGUG-GCGC-CCAGCGUG--------------AAUC-UU--GCGGU-----------------------------------------------------------------GGCCACC-CACUCGCA-CGGGUAACC-UGCGA-UGCUGCG--CC---GU-----------------GGCCCUAAGCAA-----------------UGAAGAUGAU--ACUUGAGGGAGGCUUCACUCUGCAGAGGC--AUCUUCA-CCGU-CC-GAUGG----CAG-GCUGG-AUC-ACGAUCG-UGGGGGGAAUGUGA-----------------------------GAU-GGAGCGGA--GAGGUGGG---------GAUGUCGACU----------------------------------------------------------------------------------CCGAUUU-----U-------
ABKI01000267.1/87812-87686   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CA---CUCG-UGCGAGUAAUCCA-CGAU----UGCUGUGGC---------------------GCGCUAAGCC------------------CUGGCCUGGA-CCCUCGAGGGAAGCG--AUUCUGCAGAGAACAGGCCC--CCCGGA---GAUGG----CGGCGCCAG-ACA-ACACC-CCUCGCUG-----------------------------------------CACA---------------------------------------------------------------------------------------------------------------------------------------
ABHV01000487.1/55395-55521   ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CA---CUCG-UGCGAGUAAUCCA-CGAU----UGCUGUGGC---------------------GCGCUAAGCC------------------CUGGCCUGGA-CCCUCGAGGGAAGCG--AUUCUGCAGAGAACAGGCCC--CCCGGA---GAUGG----CGGCGCCAG-ACA-ACACC-CCUCGCUG-----------------------------------------CACA---------------------------------------------------------------------------------------------------------------------------------------
M20837.1/130-397             UAGC-UGUAAUGGCAUU------UUGUCGGA-------GUGGUAAAU---CGUC-UUCUUGUUGUGCGUUCGAG-------------------------------------------------------------------------------------UCUUGGGCUCUGCAC-----------UUGGCCAU--------------------------------------------------------------------------------UUGGUUGU-CCUUUCCG--------------AAU--UC-UGCGGU---------------------------------------------------------------UGAUGGGCG-UCUCGGUC-UGAGUAAUC-GGCUUUGAGAUUUCCGU-------------------------UCUAAGA-------------------UUAACUGGGA-AACUUCAGUGGAGCA--AUCCAGCAGAGAU-CCAGUUG--CCGUGGG-UAUGG----CGG--UGGG-AUC-GCAACCA-A-G-UGGU---------------------------------------AUAU-GUUAU-------------------GGAAGAU---------------------------------------------------------------------AUUUACGA----UCACGAUU--------------
AJ550802.2/101-625           AGGC-UGUAAUGGCUUU-----CUGGUGGAA-------UGGGAUACGU--UGA---GAAUUUUGGCCGAGGAACAAAUCCUUCCUCACGGCCGGACACGGAUUGCA----------------------CGCCCUUUGGGCAAGGAGUAGAAUUUCUAUUUCGCGCCGUGCCCUGUUGUGGC----AACCGUCUUUCCCCCGUCGU-------------UGGUUUGUCCUGGGCAGAGCUGUCUGCCCGGAGGCG---GGGGAGUCCUAUC-UAA--AGUGU-CCCGGCU-UAAAUA--AAUCGA-UCU-UU-GCGGG-CA----------------------------------------------------------GCC-CAUU-GGC-AGGAGGCG-UGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAUG--------UAGUUCUGGGUCCCUUAGGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCAUCAGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UUA--GUGGGAUAAUCGUGCAAAUUUAUCGCUUCGGUGGUUUAAAUUGGCGGU-----ACCAUCA--------GGAUUUACUCUCACAUUGUGGUCAU---------------------------------------ACCUUCUGGUGUGAGUGUGUAUUC--CAAACCAUU------UUUUU---
ABBS02000167.1/47703-48016   -AGC-UGUCAUGGCCG--------AAGGGA----------GACCUCCC------------GCAU---------------------------------------------------------------------------------------------------------CCGCGAGGUGUG---UGUGGC-------------------------------------UUGGGGGUCACCUGAUCCCCCA-------------AACAGCG--GACUUGGUGC-CUGGUUCG--------------AAU--CG-CCGGGUCGCGAGAUUUUGUCCU------------------------------UCACGGGGCAACUUCUUCUCCCGCA----CUCGUG-CGAGUAGUC-CACGACCGG-CUGUCGGUGC--------------------G--CUAAGCCC-----------------UGGCCCGUAC--CCUCGAGGGAAGCG--AUUCUGCAGAGAC--CGGGCCC-CCCGGCG--AUGG----CGGCACCAG-AUC-ACACC-G-C----CGCUGCA---------------------------------C-----ACCCAC-CGCGC---------------UGAAUG-------------------------------------------------------------------GGAUGGUCG---ACUUUCUUUU----UUUU-----
AJ550804.2/101-633           AGGC-UGUAAUGGCUUU------UAGUGGAAC------CAAGUA-UUU--UG-G--GAUAUUUGGCCUGGGAACGAAACUUCCUUACGGUCAGACAUGGAUUGCACGUUUCGUC-----UUUGGCGGAACAAGGGGUUUUGCCAAGUUUUGGUAGGGUUCUGCGCCAUGCCCUGUUGCUUC----AACCGUCUUC-CUGAACCCGCCUGU--UAGGGCUUGUCUCGGCUGGUGUAGUUUUCUGUGCCAGUUGGAGGGUUUAGGGCUCUGA-GUUAACGUGU-CCCGGUU-UAACAAUCAAUCGA-UCU-UC-GCGGG-UU----------------------------------------------------------GCU-CGUU-GGC-AGACAGCG-CGAGAAAUC-CGUUGUUUCUGUCCGAUGCGGCAAUGU-------AAUCUGGUCAUG-UGAC----------------CUCGCCUUGACCGCCAUUAGGGGAGAUUCAUCCAGCGAUGGC-AAAGGCGA-CCCGUGAGAGAGG----CGA-CUGGG-AUG-GCACUGU-U-C-UUAGGGUUAACAA-----------------------GUACAAGUUCGGU----------U-----------UAUUAUGG-ACGGUGGAGUCUGGUAUUU-----------------------------CCUACCACAUGUUGGGUGUAAACUACUCUUAGGAACCACUAA--CU--------
X15220.1/254-348             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA--ACAAUGCACAUCA--CUACCGG-GUCU-UG-GGCAG---UGCG-AUAGC-GAU-GGGAUUC---ACCU-----------------------------------------UCGCAGGAUGUGCAU--------------GGAAGUAU--------------------------------------------------------------------AAACACA-----ACGGUCG-------UU------
AJ550801.2/101-624           AGGC-UGUAAUGGCUUU-----CUGGUGGGA-------UGGGAUACGU--UGG---GAAUUUUGGCCGAGGAACAAAUCCUUCCUCGCGGCCAGACACGGACUGC-----------------------ACGCCCUUUGGGCAAGGGAUGGUUCUCCAUCUCGCACCGUGCCCUGUUGUGGC----AACCGUCUUUUCUCCGUCGC-------------UAAUUUGUCCUGGGCAGAAAUGUCUGCUCGGAGGCG---GGGGAGUCCGGUC-UGA--AGUGU-CCCGGCU-AUAAUA--AAUCGA-UCU-UU-GCGGG-CA----------------------------------------------------------GCC-CGUU-GGC-AGGAGGCG-CGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAGG--------UAGUCCUGGGUCCCUUUGGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCGGCAGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UCA--GUCGGAUAAUCGUGCAAGUUGAUCGUUUCGGCGGUCUAAUUUGGCGGU-----GCCAUCA--------GGAUUUACUCGCACAUUGUGUUCGU---------------------------------------UCCCUCGGGGACGAGUGUGUAUCC--UGAACCACA------UUUUU---
ABDB01000012.1/250050-249778 -AAUCUGUCAUGGAUAA----CCUAGUGGAA-----------GG-------CCU-GCCG----------------------------------------------------------------------------------------------------------------------CUAA---GUC-AGUAACCU-------------------------------UGCUGCGG-CAU--UUGCC------------------AGCGG--GAAA-GGUGC-CCGGUACG--------------AAUC-CU--GGGGU--------------------------------------------------------------CGUCGUUGUA---CUCGUG-CGAGUAAUC-CACGAU-GC-UACA-AGGCG-----------------------CUAAGCAA-----------------UGGAAGUGAA--UCUUGAGGGAAGCA--AUUCUGCAGAGAC--ACUUCCA-CCCU-GG-GAUGG----CGUCGCCGG-AGG-ACACC-U-AC---CCGUUAC----------------------------------AGGGAAGUUGG-CUGUU-------------UGGCUGG------------------------------------------------------------------------AC--------AACCGCAAU---CUUCUUUU-
CR382138.2/1783896-1784154   AUGC-UGUGAUGGCGU--------AUGGCAG-------AAGCGCGCA---GAUU-GUGUA-----------------------------------------------------------------------------------------------------------------C-UUUUGAUUCUUUAUUACAGUU-----------------------------------------------------------------------------UAAGUGUC-CGGUUCGA---------------UCU-CU--GCGGU---------------------------------------------------------------C-GCAAACU-UGUGAAUU-UGAGUAAUCA-AUUCUUCA-AGUUUCA--------------------------GCAAUGA------------------GUGGCAAUAU-CGCUGGAGGGAAGCA--AUUCAGCACAGCA---CGCUAC-CCGU-AG-AGAGGCGAAGCG-GAUGGCACUUGGCUGG----CUUU-----------------------------------------GGUAAGGAGUUAUAA--------------GUAUCUUG--------------------------------------------------------------------UGUGUC-------GACUCCAA----UUUU-----
AAGT01000618.1/120774-120486 UGAC-UGUAACGGUCA--------UAAGCCC---------AAGACG----AGCC--CACA-----------------------------------------------------------------------------------------------------------------CUCCCAAUU-CUUCCA-CUCAAAAA---------------------------UCUCAAUCUAACGAUUGAAGCU----------------A-------CCAACAGUGC-CCAGUCCG--------------AACA-CC--GCGGU-----------------------------------------------------------------GACAGUC-CACUCGUG-CGGGAAACC-CACGA-UGCUGGUGUUGUC------------------------UUGAGCAA-----------------UGAAGAUGAU-UUCUUGAGGGAGGUUUCACUCUGCAGAGAG--CUCUUCA-CCUU-AG-UGUGG---CGGU-AUUGA-AUU-ACAUUUG-UUGUGUG-GU--U--------------------------------U-GGAGAGGG--GAUUUGGG---------UUGGGUCUCU--------------------------------------------------------------------ACUUUU-------GCAGUUUU-------------
AAGI01000146.1/295518-295256 -ACC-UGUAACGGGUCU-----UCACCAGAA-----------GG-------UGC-ACCG----------------------------------------------------------------------------------------------------------------------UCAU----CCACACUCACCUCCCU--------------------GCCACU---------------------------------------ACCCUUGCA-GGAGC-CCAGUUCG--------------AGUC-CU--GUGGU--------------------------------------------------------------GUCCACUCCA---CUCAUU-UAGGUAACU-AAUGAUG-C-UGGA-UGGAC-----------------------CUAAGCAA-----------------UGAAUACAAC-CAGACGAGGGAAGAA--AUUCUGCAGUCGG--GUAUUCA-CCAU-GG-GACGG----CGGCGCUGG-AUU-ACUCC-C-ACGAGGGU----UG-----------------------------GGGGGCAAGUGUGG-GC----------------UGGGGUA------------------------------------------------------------------------UC--------GACUGGUA----UUUU-----
CR380957.2/172768-173266     AGGC-UGUAAUGGCUAU-----UUAGUGGAA-------UUGUUCUCCU--UGG---GAA-UUUUGGUCUGGGUUCGAACCCUACGGCCAGACGCGGAGGCACGCCUUUAAUU---------AUUACACCGUUUCGGUGGGGGCAAAGGAGCAAGCUGGGCUCGCCCAGCCUGUUCC-UGC------ACCGUGA---CUUCCCGUG------------AACUGCAGUC--GUCUCCCCCCUGUGGGG-AAGGC------GAGCCACCCAG--GGA--CGUGU-CUCGGUU-CAUCCAACCAAUCGAUCC-UU-GCGGGCGUUC-----------------------------------------------------GUGGCC---CC-UGC-UGGCGCUG-UGAGUAAUC-CAGUGUCCU-CUAGGGCC-GGCAACGUAGCUACGGUCUACCCUCCCUAGGAGGGG---------GGCC-CACCUUCACCGCCGUUAGGGGAGUUUCAUCCAGCGAUGGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-UCGGG-AUG-GCACUGG-UCC-CGUGGUUACCUA--------------------------CCUGCAGUCGCGGUGGCAUUAUCCUG---CCCUUCAAU----GGGC-----------------------------------------------------------UUUGGGAUUAUCA----AGACCACAAU--UUU-------
CR382130.1/819164-819433     -AGC-UGUAAUGGCAUU------UUGUCGGA-------GUGGUAAAU---CGCC-UUCUUGUUGUGCGUUCGAG-------------------------------------------------------------------------------------UUCUGGACUCUGCAC-----------UGGGCUAC--------------------------------------------------------------------------------UUUGUUGU-CCUUUCCG--------------AAU--UC-UGCGGU---------------------------------------------------------------UGAUGGGCG-UCUCGGUC-UGAGUAAUC-GGCUUUGAGAUUUCCGU-------------------------UCUAAGA-------------------UUAACUGGGA-UACUUCAGUGGAGCA--AUCCAGCAGAGAU-CCAGUUG--CCGUGGG-UAUGG----CGG--UGGG-AUA-GCAACAA-A-G-UGGU---------------------------------------AUAU-GUUAU-------------------GGAAGGU---------------------------------------------------------------------AUUUGCAA----UCACGACUCU---C--------
AARE01000240.1/1572-1827     -AGC-UGUCAUGGCCU--------AAGGGAA---------AACUGUCCGU-------------------------------------------------------------------------------------------------------------------------------CCUA--------CGCUCUUCU--------------------------UUC--GU-GAGUUUA-UCUCACC----------------------GCGUCG-GGUGC-CUGGUUCG--------------AAUC-CG--CGAGU--------------------------------------------------------------CGCCAUCACA---CCCGUG-UAGGGAACUC-ACGGUCGC-UGUG-UGGCG-----------------------UUAAGCAA-----------------UGAGAAUGAU--ACUUCAGGGAAGCA--AUUCUGCAGAGGC--AUUUUCA-CU-CAUG-GAUGG----CGGUGCCAG-AAU-ACACU-A-GACGU---CGUA----------------------------------GAUUGCGCUGG-UCA----------------------------------------------------------------------------------------------GGUU------GACUCUUU----UUUU-----
BN001308.1/1058465-1058198   UAUC-UGUUAUGGAUAG----UCGAGUGGGA-------G----A-------UCA-GCCG----------------------------------------------------------------------------------------------------------------------CUAG----UC-GGUGACCU-------------------------------UGCUAAGGUCUUGGCC---------------------AGCGC--CGACUGGUGC-CCGGUACG--------------AAUC-CU--GGGGU--------------------------------------------------------------UGUCGAUGUA---CUCGUG-CGAGUAAUC-CACGAUCGC-UACA-CGGCA-----------------------UUAAGCAA-----------------UGGAAGUGAC--CCUUGAGGGAAGCA--AUUCUGCAGAGAC--ACUUCCA-CCCU-GG-GGUGG----CGUCAUCGG-AUU-ACACC-G-UC---GCGUUAC----------------------------------AGGGAACCUGG-CUGUA-------------UGGUUGG------------------------------------------------------------------------G--------CAACCACUU-----UUU-----
BN000251.1/1-520             AGGC-UGUAGUGGCUUU-----CUGGUGGGA-------UGGGAUACAU--UG--GGA-AUUCUGGCCGAGGAACAAAUCCUUCCUCGCGGCUAGACACGGAUUGCACGCCCUUUGGGCAAGGGGUGGUUUUCUACUCCGCACCGUGCCCUGUUGUGGCAACCGCCUUUUCCCUGUC--------G-----------UAAAU---------------------UUGUCCUGGGCAGAGCUGUCUGCCUGGAGGCA---GGGGAGUCCGGUC-UGA--AGUGU-CCCAGCU-AAAAU---AAAUCGAUCU-UU-GCGGGCA------------------------------------------------------------GCCCGUU-GGC-AGGAGGCG-UGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAGGUAGU-UCUGGGUCCC---UUA----GGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCGUCAGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UCA--GUCGGAUAAUCGUGC------------------AAGUUGAU-----------------C----------GU--UU----CGGCGGUUUAAUUUGGCGGUGCCAUCAGGAUUU--ACUCGCACAUUGUGCCAUUCCCUUGGGAAUGAGUGUAUUCU----GAACCAUUU-----UUU-----
BN000249.1/1-524             AGGC-UGUAAUGGCUUU-----CUGGUGGAA-------UGGGAUACGU--UGA---GAAUUUUGGCCGAGGAACAAAUCCUUCCUCACGGCCGGACACGGAUUGCA----------------------CGCCCUUUGGGCAAGGGGUAGAAUUUCUAUUUCGCGCCGUGCCCUGUUGUGGC----AACCGUCUUUCCCCCGUCGU-------------UGGUUUGUCCUGGGCAGAGCUGUCUGCCCGGAGGCG---GGGGAGUCCUAUC-UAA--AGUGU-CCCGGCU-UAAAUA--AAUCGA-UCU-UU-GCGGG-CA----------------------------------------------------------GCC-CAUU-GGC-AGGAGGCG-UGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAUG--------UAGUUCUGGGUCCCUUAGGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCGUCAGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UUA--GUAGGAUAAUCGUGCAAAUUUAUCGCUUCGGUGGUUUAAAUUGGCGGU-----ACCAUCA--------GGAUUUACUCUCACAUUGUGGUCAU---------------------------------------ACCUUCUGGUGUGAGUGUGUAUUC--UAAACCAUU------UUUU----
AE016819.5/770994-770615     -AGC-UGUGACGGCCUU-----UGGCCGGAA---------GGGACAUU----AG--CAAUCCCGGCUUGGUGAGGCGCUCCCGCGUUCGAACCUGCGGCCGGGC-------------------------AUGGUUGCGGAAAAGCGAGGUUGCCUAGCUCCUCGUGCGCCAUGAUACCAC-----ACUGGUCU-------------------------------------------UU------------------------------C--UGACGCGUGU-CCUGCUA-CUU-------AUCGAUUU-CU-GCGGGU-------------------------------------------------------------UUGC-CGUCGA-UGCUGACA-UGGGAAACC-UGUCGGUGG---GGCGUGCAGUAA-------------UGGCAGGGCGAAUGCC------------CGUCCGCUCAUA--CGCUGGAGGGGAGUUUCAUCCAGCACAGCG--CGAGCGG-CCCGUGG-GGAGG-----CGAGCAGG-AUG-GCACGUG-UUA--G------GCGCU------------------------UGCGC---GGACCUAUC-GUGGU-----------AUUGGAGCAU------------------------------------------------------------------UAUGUUCC------GACCGACU-----UUU-----
BK006939.2/441987-442507     AGGC-UGUAAUGGCUUU-----CUGGUGGGA-------UGGGAUACGU--UGA---GAAUUCUGGCCGAGGAACAAAUCCUUCCUCGCGGCUAGACACGGAUUGC-----------------------ACGCCCUUUGGGCAAGGGAUAGUUCUCUAUUCCGCACCGUGCCCUGUUGUGGC----AACCGUCUUUCCUCCGUCGU-------------AAAUUUGUCCUGGGCAGAGCUGUCUGCCCGGAGGCG---GGAGAGUCCGUUC-UGA--AGUGU-CCCGGCU-AUAAU---AAAUCGAUCU-UU-GCGGG-CA----------------------------------------------------------GCC-CGUU-GGC-AGGAGGCG-UGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAGG--------UAGUUCUGGGUC-CUUAGGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCGUCAGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UCA--GUCGGAUAAUUGUGCAAGUUGAUCGCUUCGGCGGUUUAAUUUGGCGGU-----GCCAUCA--------GGAUUUACUCGCACAUUGUGGCCGUU--------------------------------------CCCUCGGGGAUGGAGUGUGUCCU----GAACCAUA------UUUU----
AASO01002446.1/15135-14810   -AGC-UGUGAUGGCCU-------AAAUGGAA---------GACUGUCU------------GCUC----------------------------------------------------------------------------------------------------------AACACCCGCAG---CCAACCCAU----------------------------------GAAUUCUGCUUAGUCAGAAA------------------GGAC--GAGACGGUGC-CUGGUUCG--------------AAU--CC-CGGAGUCGCGACCCGGGCGUGGUCUUAUU----------------UAAUGGACCGCGUCUCUUCUGGUUCUCCCACA----CUCGUG-CGAGCAAUC-CACGAACGG-CUGU-GGCGC--------------------G--CUAGGCAA-----------------UGGAGGCGAC--ACUUGAGGGAAGCA--AUUCUGCAGAGAC--ACCUCCA-CUCCGGG--AUGG----CGGCACCAG-AUC-ACACCGG-CU---GUUCAC-------------------------------------UGUGGGUUGGCCGUGG-----------A---------------------------------------------------------------------------UUCUGGACG---GUCAACUUUU----UUUU-----
AAIL02000049.1/308591-308882 CGGC-UGUAAUGGUCAA-----ACGGUGAAG---------GCUCUC----GCAC-AAAGG-----------------------------------------------------------------------------------------------------------------C-CCGCC-------ACUCCCCA-------------------------------AUCCCACCCCCGUCAGAUCCCC---------------U-----CCGUUCG-ACGC-CCAGCCCG--------------AACG-CC--GCGGU-----------------------------------------------------------------GGCCGCC-CGCUCGUA-CAGGUAACU-UACGA-U---GUCGGAAACACUUUA----------CCGUGGCCCUAAGCAA-----------------UGGAGAUGAC--ACUUCAGGGAGGCUUCACUCUGCAGAGAA--CUCUCCC-CCGU-CG-CGUGG----CGG-GCUGG-AUU-ACGAUCG-CGGAGGGCGUGGG--------------------------------UUGGGGUGGU--GGGACGGA---------GAAUGCCAAC---------------------------------------------------------------------------------ACCUUUUU-------------
BN000250.1/1-523             AGGC-UGUAAUGGCUUU-----CUGGUGGGA-------UGGGAUACGU--UGG---GAAUUUUGGCCGAGGAACAAAUCCUUCCUCGCGGCCAGACACGGACUGC-----------------------ACGCCCUUUGGGCAAGGGAUGGUUCUCCAUCUCGCACCGUGCCCUGUUGUGGC----AACCGUCUUUUCUCCGUCGC-------------UAAUUUGUCCUGGGCAGAAAUGUCUGCUCGGAGGCG---GGGGAGUCCGGUC-UGA--AGUGU-CCCGGCU-AUAAU---AAAUCGAUCU-UU-GCGGG-CA----------------------------------------------------------GCC-CGUU-GGC-AGGAGGCG-CGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAGG--------UAGUCCUGGGUCCCUUUGGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCGGCAGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UCA--GUCGGAUAAUCGUGCAAGUUGAUCGUUUCGGCGGUCUAAUUUGGCGGU-----GCCAUCA--------GGAUUUACUCGCACAUUGUGUUCGU---------------------------------------UCCCUCGGGGACGAGUGUGUAUCC--UGAACCACA------UUUU----
BN000171.1/1-523             AGGC-UGUAAUGGCUUU-----CUGGUGGGA-------UGGGAUACGU--UGG---GAAUUUUGGCCGAGGAACAAAUCCUUCCUCGCGGCCAGACACGGACUGC-----------------------ACGCCCUUUGGGCAAGGGAUGGUUCUCCAUCUCGCACCGUGCCCUGUUGUGGC----AACCGUCUUUUCUCCGUCGC-------------UAAUUUGUCCUGGGCAGAAAUGUCUGCUCGGAGGCG---GGGGAGUCCGGUC-UGA--AGUGU-CCCGGCU-AUAAUA--AAUCGA-UCU-UU-GCGGG-CA----------------------------------------------------------GCC-CGUU-GGC-AGGAGGCG-CGAGGAAUC-CGUCUCUCU-GUCUGGUGCGGCAAGG--------UAGUCCUGGGUCCCUUUGGG-----------GCUCCACCUUCACCGCUGUUAGGGGAGUUUUAUCCAGCGGCAGC-AAAGGUGA-CCCGUGAUGGAGG----CGG-CCGGG-AUA-GCACAUA-UCA--GUCGGAUAAUCGUGCAAGUUGAUCGUUUCGGCGGUCUAAUUUGGCGGU-----GCCAUCA--------GGAUUUACUCGCACAUUGUGUUCGU---------------------------------------UCCCUCGGGGACGAGUGUGUAUCC--UGAACCACA------UUUU----
#=GC SS_cons                 <<<<._______>>>>-.....-[[[[[[[[.......--[[[[[[[-..[[[[..[[[-----..........................................................................................................----.-.[[[[....[[[[[[[[[[...............................,,,<<<<<<<____>>>>>>>,...............,.((((-.((((((((((.((((((((..............((((.((.(((((,,............................................................,<.<<<<<<<<.<<<<<<<<.-<<____>>.>>>>>>>>-.>>>>>>>>->....................,<<<___>>>,.................<<<<<<<---.<<<<<----<<<___.._>>>---->>>>>..>>>>>>>.))))))).))))-....))).))))).---.))))))).))).-)))),,,,................................,.]]]]]]]]]].]]]].............-]]]-]]]]-..................................................................-]]]]]]]-....-]]]]]]]].....::......
#=GC RF                      aaGC.UGUAAUGGCuuU.....auaguggaa.......uagggaacuU..agcc..cccuUcUG..........................................................................................................ccug.u.uggc....cccccccacc...............................ccugggcagauuugucugcccg...............u.cggcc.ugacagGUGu.CCcGgccG..............Aucc.uu.GcGGGUc............................................................uc.cccccgcc.cggucgcg.cGAGuAAUC.cgcgacugu.ggcgggggCg....................gcgcUAAguga.................ucgccuugAC.gcCUugAGGGgAGcu..AUcCAGCAgAGgc..aaggcga.CCCgUga.ggaGG....Cgg.cCgGG.AUu.gCACcug.uca.ugccggaUA................................u.gguggggggg.gcca.............agggaggcuc..................................................................Gaguucccu....gaaccacua.....UU......
//
# STOCKHOLM 1.0

#=GF AC   RF01503
#=GF ID   Afu_203
#=GF DE   A. fumigatus sRNA Afu_203
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   37.00
#=GF TC   37.10
#=GF NC   33.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Aspergillus_fumigatus_non-coding_RNAs
#=GF SQ   3


ABDB01000029.1/278235-278125 GACGAGGAUUAUAUAUAUUGCAUGGCUUUCGGACAACCAUGACGGUAACUCCAUACCUUUGGUAUGUUGUCAUGGCUGCAUGACGUACAUCGCAGGGGUAAUGAGUCGACC
AAHF01000002.1/294063-293953 GACGAGGAUUAUAUAUAUUGCAUGGCUUUCGGACAACCAUGACGGUAACUCCAUACCUUUGGUAUGUUGUCAUGGCUGCAUGACGUACAUCGCAGGGGUAAUGAGUCGACC
AAKE03000007.1/238870-238761 GACGGGGAUUAUAUAUUGCAUGAGUUUCUCGGACA-CCAUGACGGUAGCUUCAUACCUUUGGUAUGUUGUCAUGGCUGCAUGACGUACAUCGCAGGGGUAAUGAGUCGACC
#=GC SS_cons                 ::<<<<<--<<<_________>>>-->>>>>------------<<<-<<<<--<<<<<<<<<-<<<<<<<<<<<____>>>>>>>->>>>>->>>>>>>>-->>>>-->>>
#=GC RF                      GACGaggAUcauAUAUauugcauggcccuCGGACAACCAUGACGGuAaCucCAuaCCccuGGUauGucGuCauGGCUGCauGaCgUaCauCGCaggGGuaAUgaGuCGaCC
//
# STOCKHOLM 1.0

#=GF AC   RF01504
#=GF ID   Afu_254
#=GF DE   A. fumigatus sRNA Afu_254
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Mafft_alifold;
#=GF GA   60.00
#=GF TC   64.70
#=GF NC   57.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Aspergillus_fumigatus_non-coding_RNAs
#=GF SQ   6


ABBC01002008.1/1443-1591     UUACAAAGCAAAUACUUCUCUAAACAAUUUUAACUCUUUUUAAACGUUUUUACGUUCAAACUACCCAGUCAA-AAUGAAUCCCUGCUCC-U-----GCAACUGCUGCUCCGGCAACUGCAACAACUGCUCUUGCGGCUCCUGC--GGC---------GUACGUUGAC
AM921949.1/1-163             AUACUAAGCCUCAUAUCAACUGAACAGUCUAUCUUCUUCAAGGAACGCUUCGUUCACCAUCAACUCAAUCAA-AAUGACUCCCUGCUCC-GCAACACCUGCUCCUGCUCCAGCGACUGCAACGGCUGCUCCUGCUCCUCUUGC--GGUCACUAAAUGGCACAUCAAG
AAIW01000118.1/24548-24695   UUCCAAUCCAAAUACUUCUACCAACACAUUCAAC-CUUUUAACGUUUUUACGUUUCCAAACCACUCAAUCAA-CAUGUCUCCCUGCUCC-U-----GCAACUGCUGCUCCGGCAACUGCAACUCCUGCUCUUGCUCCAACUGC--AGC---------GUAAGUUGAC
ABKI01000021.1/23912-24064   UUCGAAAGUCUCAGAAUCC---AAAGAUAACGAAUUUUCUAAACAAAUUCACCACCAAAACCACCCAUUAAA-AAUGUCUCCCUGCUCC-U-----GCAACUGCUGCUCCGGCGACUGCAACUCCUGCAGCUGCAAAAGCUGC----UCUGUAAGUUGGACAUGACG
ACBT01000416.1/161909-161745 UAAUACAUUUAAAGGCAAUCCAAAAAUCUUACCGAAUUUCAAAACAAAUUCAUCACCCAUCUACCCAUCCAAAAAUGUCUCCCUGCAACUGCAACUGCUGUGCCGGCGACUGCAACUCCUGCAGCUGCACCAGCUGCUCUGUG--AGUUGAUAUAAAAACAAGGGUU
AAIH02000092.1/25468-25316   AUACCAAACUACUCUACGACU-------UUCAUUAUUUCGAACUAUCCAGUUCAUACCAAUCCCUCCACAAC-CAUGUCUCCCUGCAGC-U-----GCAACUGCUGCUCCGGCAACUGCAACUCCUGCUCUUGCAGCGACUGCAAGGUAUGCACCUACCACUUUACC
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::<<<<--.-.....<<<_____>>>--->>>>---<<<------<<____>>------>>>..::::::::::::::::::::::
#=GC RF                      UUAcaAAgcuAaaaauuauCuaAAaAauUUcaauucUUuuAAaaaaauUucauaucCcAaCcACuCAaUcAA.AAUGUCUCCCuGCucC.u.....GCaACUgCuGCUCCaGCaACUGCaACucCUGCuCcUGCugCuccuGC..gGUuugUAaaUaguAcaUuaac
//
# STOCKHOLM 1.0

#=GF AC   RF01505
#=GF ID   Afu_264
#=GF DE   A. fumigatus snoRNA Afu_264
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   40.00
#=GF TC   41.50
#=GF NC   39.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


ABFN01001674.1/1569-1669   UCACAUGAUGAUAAAUCCCAUUUUUCAAU---GUUUCUGGUACCUCUUAUGUCAGGGACGGGCAUUCCAUGCCUUGUCCCGAUGAUCUUAAUGGACUUCUGAUA
AM921924.1/1-103           CUACGUGAUGAUACAACACCUUUUUUACUUUAUUUUCUGGUACCUCUUAUGUCAGAAGCAGAUCCUUG-UGGUCUGUUUCAAUGAUCUUAAUGGACUUCUGACA
AM270126.1/44992-44895     UUACAGGAUGAAACACACCAUAUUUU--UUAUUUUUCUGGUACCUCUUAUGUCAGAGGUAG---GCUU-CGGUCUAUCUCGAUGAUCUAAAUGGACUUCUGAUA
AAJI01001332.1/9180-9080   CUUGCCAAUGAUGAUAUACACCAAAUACA--AUUUUCUGGUACCUCUUAUGUCAGGGGUGGAACCUAU-GGUUUCUCUCCAAUGAUCUAUAUGGACUUCUGAUU
ACBU01000792.1/38856-38958 CUUGCCAAUGAUGAUAUACACCAAUACAAUUAUUUUCUGGUACCUCUUAUGUCAGGGGUGGGACCUCU-GGUCUCACCCCGAUGAUCUAACUGGACUUCUGAUA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::
#=GC RF                    cUacauGAUGAUaaaauaCAuuuuUuaauUuaUUUUCUGGUACCUCUUAUGUCAGgGGugGgaccUuu.uGuuuuguccCGAUGAUCUaAAUGGACUUCUGAUA
//
# STOCKHOLM 1.0

#=GF AC   RF01506
#=GF ID   Afu_294
#=GF DE   A. fumigatus snoRNA Afu_294
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I;
#=GF GA   43.00
#=GF TC   43.80
#=GF NC   42.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   10


AAJN01000116.1/81248-81329   UCCUAUGAUGAUUUCU-UUAAU--CGCUGUGUUCUUACUGAACCC---CAUUGAAGAAA-AACCAUAUUUCACCUUGGAGAACUGAUCU
AAKD03000028.1/39409-39327   UUGUAUGAUGAAUAAA-AUAUU--CGCUGUGUUCUUACUGAAUAC--ACAUUGACGAAA-AAAAAUAUUUCACCUUGGAGAACUGACCC
AM270160.1/33725-33807       UUGCAUGAUGAAUUCU-UAAAU--CGCUGUGUUCUUACCGAACCA---CCUUGACGAAACAACAAAGAUUCACCUUGGAGAACUGAACU
ABAR01000017.1/60688-60770   UCUGAUGAACAACAAA-UAUUU--CGCUGUGUUCUUACCGAGUCUCGGCAUUGAAGA---AAAACUAUUUCACCUUGGAGAACUGAUCA
ABKH01000217.1/22805-22886   CCACUUGAUGAACUCU-UAUUUU-CGCUGUGUUCUUACCGAGUUUUUACUUUGAAGAUC-AAC----UAUCAUCUUGGAGAACUGAUCC
AAID01000591.1/8306-8389     UGCUCUGAUGAACCCA-AAUAUU-CGCUGUGUUCUUUCCGAGUCA--ACCUUUGACGAA-ACACAUAUUUCACCUUGGAGAACUGAGAU
AAGI01000154.1/96737-96661   UCACAUGAUGAACACAAUGAUU--CGCUGUGUUCUUACUGAACUA---CAUUGAAGA---AACA----AUCACCUUGGAGAACUGACAC
ABVF01000208.1/106308-106391 UUAUCUGAUGAGACAA-UGAUAUUCGCUGUGUUCUUUCCGAGUCAU-ACUUUGACGAUA-CACAUCAU--CACCUUGGAGACCUGAUCC
AM920431.1/1467327-1467246   UUGCAUGAUGAACCCC-AAUAUA-UGCUGUUCUAUCUCUGAACUA---UCAUGUCGAUA-AA-AUAUUUUCACCUUGGAGAACUGAUAU
ABBT01000237.1/603293-603214 UCAUCUGAUGAACUCA-UAUUU--CGCUGUGUUCUUACCGAGUCUUGACUUUGAGGACA-ACUAUCAU-----CUUGGAGAACUGAUGA
#=GC SS_cons                 ::::::::::::::::.:::::..:::::::::::::::::::::..::::::::::::.:::::::::::::::::::::::::::::
#=GC RF                      UuauaUGAUGAAcuCa.UauuU..CGCUGUGUUCUUaCcGAguca..ACaUUGaaGAuA.AAcAuuaUUUCACCUUGGAGAACUGAucu
//
# STOCKHOLM 1.0

#=GF AC   RF01507
#=GF ID   Afu_298
#=GF DE   A. fimigatus snoRNA Afu_298
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   40.00
#=GF TC   40.80
#=GF NC   38.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Aspergillus_fumigatus_non-coding_RNAs
#=GF SQ   3


AM921940.1/1-93            GCGGAUGAUUAUAU-UUUUUAACUCAGAGCCCCUGGA---GGGUGCCUUGAAGAUCAAAAACAAUGCAACAACAAACACUCUAAUUUUUUGAUGACG
AARE01007308.1/520-615     GCAAAUGAUUAUAUAUUUUUAACCCUGAACUUCGGUCAUCCGGACAAUUGAAGAUCAAAAA-AACGCAACAACUUACACUCUAAUUUUUUAAUGACG
AAIH02000363.1/27276-27186 GCGGAUGAUGAUAU-UUUUUAACUCGUAGUCACUGUU---GUG-GCGUUGAAGAUCAAAAACUA-GCAACAACAAACACUCUAAUUUUUUGCUGACC
#=GC SS_cons               ::::::::::::::.::::::::::::::::::::::...:::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GCggAUGAUuAUAU.UUUUUAACuCugAgccuCuGuu...ggGugcgUUGAAGAUCAAAAACaAcGCAACAACaaACACUCUAAUUUUUUgaUGACg
//
# STOCKHOLM 1.0

#=GF AC   RF01508
#=GF ID   BYDV_5_UTR
#=GF DE   Barley yellow dwarf virus 5'UTR
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:11389856
#=GF GA   75.00
#=GF TC   99.90
#=GF NC   32.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0003743; translation initiation factor activity;
#=GF DR   GO; 1904973; positive regulation of viral translation;
#=GF RN   [1]
#=GF RM   11389856
#=GF RT   Base-pairing between untranslated regions facilitates translation of
#=GF RT   uncapped, nonpolyadenylated viral RNA.
#=GF RA   Guo L, Allen EM, Miller WA
#=GF RL   Mol Cell. 2001;7:1103-1109.
#=GF WK   Barley_yellow_dwarf_virus_5'UTR
#=GF SQ   4


EF521838.1/1-149 -AGUGAAGAUUGACCAUCU-CACAAAAGCUGUUACGUGCUUGUAACACACUACACACUCGUUUUGUAUUCGAGAAGUAGU-UGCAACAACGGUCCCCUUAUUGCCUGACAA-GCUGAGGGCCACCCUUCUAUCCC-CACCGCCAUCAUGUUUUU
AY220739.1/1-150 UAGUGAAGAUUGACCAUCU-CACAAAAGCUGUUACGUGCUUGUAACACACUACACACUCGUUUUGUAAUCGAGAAGUAGU-UGCAAGAACGGUCCUCUCAUUGCCUGACUA-GCUGAGAGCCAUCCUUCUAUCCC-CACCGCCACCAUGUUCUU
EF521828.1/1-150 -AGUGAAGGUUGACCACCUACACAAAAA-GACUUUGUGCUUGAAGUCUACAGCUCACCUGUUUUGUAUUCAGGACGUUGUCUGCAACAACGGUCAACAGUACGCCCGACACCGUACUG--CCACCUCCCUAUCCCCCCCCGCCAACAUGCUUCU
AF235167.1/1-149 -NNUGAAGAUUGACCAUCU-CACAAAAGCUGUUACGCGCUUGUAACACACUACACACUCGUUUUGUAUUCGAGAAGUAGU-UGCAACAACGGUCCCCUUAUUGCCUGACAA-GCUGAGGGCCACCCUUCUAUCCC-CACCGCCACCAUGUUCUU
#=GC SS_cons     .:<<<<-<<<_____>>>>.>>>,,,,,,<<<<<<______>>>>>>,<<<<<---<<<<_________>>>>-->>>>>.,,,,,,,,,<<<-<<<<<<--<<_______.>>>>>>>>-->>>::::::::::.::::::::::::::::::
#=GC RF          .AguGaAGguUGACCacCu.CacAAAAgCugcuacGuGCUUguagcacaCuaCaCACccGUUUUGUAuUCggGAaGuaGu.UGCAAcAACGGuCCcCucauuGCCuGACaa.GCugaGgGCCaCCcuuCUAUCCC.CaCCGCCAuCAUGuUuuU
//
# STOCKHOLM 1.0

#=GF AC   RF01509
#=GF ID   Afu_300
#=GF DE   A. fumigatus snoRNA Afu_300
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   40.00
#=GF TC   44.70
#=GF NC   39.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   10


ABHV01000190.1/62758-62846     UAUGAUGAUCAUUUUCGUAUAA-----UAUACGCUGGAAAUUACCGGCUGAAACCCUUCGGGUCGUUGACGAUAUUAAAUGGCU-AUUUCUGAUU
AM921941.1/1-88                UCGCAUGAUGCUUUCGUAUUUU-----UAUACGCUGGAAAUUACCGACCGAGACC-UUCGGGUCGUCGACGAUAUCAAAUGGCU-AUUUCUGAUG
ACBU01001064.1/82545-82636     UCAUAUGAUGAUCAAUUUUUGUAU-AAUAUACGCUGGAAAUUACCGGCCGAGACC-UUCGGGUUGUUGACGAUAUAAAAUGGCU-AUUACUGAUU
AAIM02000027.1/316786-316700   UCUCGUGAUGAUCAUUUCUUUUAC-AAUAUACGCUGGAAAUUACCGGCUGAGUUC-U-----UCUUUGACGAUAUAAAAUGGCU-AUUUCUGAUU
ABAS01000006.1/940748-940659   UUUUAUGAUGAUCAUUUCGUAU---AAUAUACGCUGGAAAUUACCGGCUGAGGCU-CUCGGGUCUUUGAUUAUAUCUAAUGGCU-UUGACUGAUC
FQ790246.1/404277-404366       UGUGAUGAUGAUCAGUUUAUGC-U-UUUGCAUGCUGGAAAUUACCGACUGAAGUC-CUCGGGCUUUUGACGACA-AAAAAGGCU-GUUACUGAGC
AM270078.1/67935-67846         UUGCAUGAUGCUUCUUUUACAA---UAUAUACGCUGGAAAUUACCGACUGAGACC-UUCGGGUCAUCGACGAUAUAAAUUGGCU-AUUUCUGAUC
AM920437.1/1346411-1346502     UAUCAUGAUGAACGCGAUGUGUAUGAAAAUACGCUGGAAAUUACCGUCUCAGACC-UUCGGGUCGGUGAUGAUA-CAAAUGGCU-AUUUCUGAUC
AACU03000132.1/430891-430980   UCACCUGAUGAUCAAUUUUUUGCU-UCGGCAAAGUUGGAAUUACCGACUGAGAC---UCAUGUCGCUGAAGAAGCAAACUGGCU-GUUUCUGAUU
AAEC03000001.1/4388891-4388799 UAACAUGAUGAUUCUUUCUUUGUA-ACUAUACGCUGGAAAUUACCGACCGAGACC-UUCGGGUCUCUGACGAUACAAAAUGGCUGAUAUCUGAUU
#=GC SS_cons                   ::::::::::::::::::::::::.::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::.::::::::::
#=GC RF                        UcucaUGAUGAUcauuUuuUuuau.aauAUAcGCUGGAAAUUACCGaCUGAGaCC.UUCGGGUCguUGAcGAuAuaAAaUGGCU.aUUuCUGAUu
//
# STOCKHOLM 1.0

#=GF AC   RF01510
#=GF ID   MFR
#=GF DE   M. florum riboswitch
#=GF AU   Osuch I
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   INFERNAL
#=GF SS   Published; PMID:17911257
#=GF GA   50.00
#=GF TC   70.70
#=GF NC   37.40
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0032546; deoxyribonucleoside binding;
#=GF DR   GO; 0031554; regulation of DNA-templated transcription, termination;
#=GF RN   [1]
#=GF RM   17911257
#=GF RT   Guanine riboswitch variants from Mesoplasma florum selectively recognize
#=GF RT   2'-deoxyguanosine.
#=GF RA   Kim JN, Roth A, Breaker RR
#=GF RL   Proc Natl Acad Sci U S A. 2007;104:16092-16097.
#=GF WK   Mesoplasma_florum_riboswitch
#=GF SQ   3


AE017263.1/29965-30028   ACUUAUACAGGGUAGCAUAAUGGGCUACUGACCCCGCCAUGAAACCUAUUUCAUGACUAUAGGU
AE017263.1/668937-668875 ACUUAUACAGGGUAGCAUAAUGGGCUACUGA-ACCGCCCCGGGACCAAUCUCGGGACUAUAAGU
AE017263.1/31976-32038   ACUUAUACAUGAUAACAUAUCGGGUUGUCGA-CCUGCCUUAAGACCGAUCUUAAGACUAUAAGA
#=GC SS_cons             (((((((,,,<<<<<<_______>>>>>>,,.,,,,,<<<<<<<____>>>>>>>,,)))))))
#=GC RF                  aCuUAUACAggGuAGCAUAauGGGCUaCcGA.cCcGCCcuGaGACCaAUCuCagGACUAUAaGu
//
# STOCKHOLM 1.0

#=GF AC   RF01511
#=GF ID   Afu_304
#=GF DE   A. fumigatus snoRNA Afu_304
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   35.00
#=GF TC   35.20
#=GF NC   34.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AASO01002524.1/351-456       UAUUAUGAUGAAUAAGAGCUA--UAAGCUCGAUAUAAUCCCAGCUCGUCGAAUGUUCUCGUUU---AUUCUCACG-UUGAGGACAUCCUGAGAUGA-AGUCCAACCCUGAUAA
ABHV01000193.1/263095-263203 UUCUAUGAUGAACAAGAGCAAAAU--GCUCGAUAUAAUCCCAGCUCGUUGAAUGGUCUCAAUUUUAUAUCUCACG-UAGAGGCCAUGUUGAGAUGA-UAUUCUAUCCUGAUCC
AM921929.1/1-106             UCAUAUGAUGAAUAAGAGCUU--U--GCUCGAUAUAA-CCCAGCUCGUCGAACAGCCUCAUCUUUAAUUACAACG-CAGAGGCUGUCAUGAGAUCA-UGUCCUAUCUGAUUCA
ABAS01000006.1/78826-78932   CUAUAUGAUGAAUAAGAGCAU--UU-GCUCGAACAUAACCCAGCUCGUCGAACA-CCUCGUUUUUUUUUCUCACG-UUGAGGUUGUCUUGAGAUAA-AAACUCGUCUGAAACA
ACBU01000934.1/39509-39619   UACCAUGAUGAACAAGAGCACAAC--GCUCGAUAUAAUCCCAGCUCUUCGAAUGGCCUCGUUUUUAUAUCUCACGUUUGAGGCCAUAUUGAGAUUUGAAUCCAACCCUGAUAA
#=GC SS_cons                 :::::::::::::::::::::..:..:::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::.::::::::::::::::
#=GC RF                      UuaUAUGAUGAAuAAGAGCau..U..GCUCGAuauaAuCCCAGCUCGUCGAAuggcCUCgUUUUUauuUCUCACG.UuGAGGccgUcuUGAGAUga.aauCCuauCcugauca
//
# STOCKHOLM 1.0

#=GF AC   RF01512
#=GF ID   Afu_309
#=GF DE   A. fumigatus sRNA Afu_309
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   48.00
#=GF TC   49.20
#=GF NC   45.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Aspergillus_fumigatus_non-coding_RNAs
#=GF SQ   10


AM921953.1/1-318           ACCAAUUGAACAAACACGGAUCUGUGUCCAGCGAUCCUGAGCAUGGAAC-UGUUUCUCUUCACGGAGGGGCUGCUUCUGUGUCUCGGUUG--AUUGCUG-GACAGUUCGACGACUUAAGGAGCCAUUCCCUU----------GUGGAUGGU-UUUU----AUUUCCGGUCGACAGAUC-UCAGAUCGA-AUGCUGGCAUUAGGAU--UA--CU-UGGUCUUGAGCUCCC---GA---------UA--------GGUGAGCUCGGCUUGAGGGCCUAG-UA-GCCAGCGGCGUCAUAUUCCUGAUCCCUUUACC-----------------GAUUUGGCCGUCGGCUUGUGAGGUUAGGGAAAAACCAUGAC-UAGCCAACAUAU
AAIW01000350.1/3989-4323   UCCUCAACACAAACCACAGAUCUGUGUCCAGUAGUCCUGUUCCAGCUGC-UGGUCGUCCUUCGUGAUGGCUAGUAGCUGUGUUUCGGUUG--AUU-CUG-GACAGUUCGACGACCUAUGGAGCCAUCACUUU-----------CUUAUGAU-GUCA----AUUUCCGGUCGACAGAUC-UCAGAGCGAGAUACAGUGACCAGGAG--UUCACU-CUGCCUUGAGCUUCC---GU---------CA--------GGUGAGCUCGGUGAGAUGGCCUGG-U-UGCUGAAGACGCCAUAUUCCGUCUCCCUUUACCGAUGUGCCCCUUCUUGGGGCCAGGCCGUCGGCUGAUGAGGUUAGGGACUAACCAUGGC--AGCCAACAUCC
ABRJ01000032.1/26170-26452 CUCAUCACAACAAACCCAGAUCUGUGUCCAGCAGUCCUGAUCCAACCAG-AGU-----AUUCGU-----GCUCUGGUUGUGUUUCGGUUGUUAUUGCUG-GACAGCUCGACGAUUCAUGGAGCCAUCAAGGAUUA---CCCCUCAAAUGGU-GUCA----AUUUCCGGUCGACAGAUC-UCAGAGAGAACCUCAGCG-----GC---CCAGUU-UUUCCUUUUUUGCC---------------UU---------GUGUGAAAGGGAAUUUAACACU---CUGCCUUGAGC-------------UCCCUCCCCG------------------UUUCGACGGGCUGGUGAAUUCGGUAAGGU-------------GGCUGGGUUCC
AM920437.1/3101326-3101627 ACCAA-------ACACCGGAUCUGUGUCCAGAUUUCCUGUCCA--CGGA-CUCCAGUC-----UGACUGGUUUCUG---UGUGACGGUUG--AGAGCUG-GGCAUUUCGACGAGCUU-GGAGCCAUCAUUUU---------CGUGGAUGGC-CUUUA-CGGUUUCCGGUCGACAGAUC-UCAGAAUAA-GUGUCUGCGCCUUGUG--AU--GC-GGGUCUUGAGCUCCC---AC----------U--------GGUGAGCUCGGCUUGACAGCUUGG-U-GUCGGACGGCGUCAUAUUUCAUAUCUCUUUGCCG------------------AUUGGCCGUUGGCCGCUGAGGUUAGGGAAUAACCAUGAC-UUGCCAACAUAU
EU780991.1/1-296           A---------------CGGACCUGUGCCCAGCGCUCCUCUGCCGCCAGC-UCGU----GCUUGC----ACUUGUAGGC-AGCUAGGGUUG--AGUGCUGAGGCAGUUCGGCA-ACCAAGGAGCCAUCCAGGACUUUACGUUCUUCCAUGAU-GUCA----AUUUCCAUCCGACAGGUCACCAGA-A---GAACCGAACUCCGGUG--UGAACC-UC-----GUUCG-CC---GC---------AA--------GGCUUGAGCUUGGGGAGCGCCGGAUGAUGUAGGGGAAGUCAUAUUCCAAU-CCGUUCGCCG--------------------AGGACGUCGUCCUAUGAGGCUGGGG-GAAACCAUGACAAUUGCCACAUUU
BN001307.1/2431637-2431325 AUGAACAGAACACACACGGAUCUGUGUUCGGCGAUCCUGAUCG--CAGAAAGA-----GUUUAC-----UCUUCUG---UGUUUCGGUCG--AUUGCUG-GACAGUUCGACGACCAAAGGAGGCACCCAUUC--------UCUCGUUUGGU-GUCCAUUGUUUUCCGGUCGACAGAUC-UCAGAUUAA-AUGUCGGCAUUGGGUGGUUCACUU-UGGUCUUGAGCUCCC---UC---------AU--------GGUGAGCUCGGCUGGGGUUCCUGG-U-GUC-GACGGCGUCAUAUUCCUGUUCCCUUUGCC-----------------GAUUUGGCCGUCGGCUGAUGAGGUCAGGGAGAAACCAUGGC-UAGCCAACAUUC
FQ790321.1/369500-369214   AUCAA------AACACCAGAUUUGUGUCCAGCGUCCCUUUGCCA-------GAACUGCUUGUCAGCG---------AUGGUUUAAGGUUG--UAUGCUGAGGCAGUUCGAUCGUCUAUGGAGCCAUCAACCUACCA-AGGUAAUUUAUGAU-GUCA----AUAUCCGAUCGACAAAUC-UCAGAAUGAUCGGUCCUU------------AUGA-AA--C-UUGAGUCGC---UU---------CG--------GCUGAUUCGG--UGGAUGA--GU---GUACUGAAGACGUCAGAUUCCAAAUCUGUUUGCC--------------------UAGGCUGUUAGCCCUUGAGGUUGCGGAAUAACCCUCUC---GUCUACAUUU
AM270079.1/209972-209642   CAGAACAGAACACACACGGAUCUGUGUUCAGCGAUCCCGUUCAUGGAGG-GU--GCGGCUUCGGCUGUUAUUUCUUU-GUGUUUCGGUUG--AACGCUG-GACAGUUCGACGACUUAAGGAGCCAUUCAUCU---------UGUGGAUGGU-UUUUG--CACUUCCGGUCGACAGAUC-UCAGAUUAA-AGGUUGGCGCUGGGUG--UUCACUCGGGUCUUGAGCUCCCU-UGU---------UUUCGAACUUGGUGAGCUCGGCUGGAGUUCCUGG-UU-GCUGACGGCGUCAUAUUCCUACUCCCUUCACC-----------------GAAUUGGCCGUCGGUCACUGAGGUUAGGGAAAAACCAUGAC-CUGCCAACAUUA
AP007155.1/3180884-3180570 CUUUUUCGAACACACACGGAUCUGUGUCCAGCGAUCCUGAGCGUGGAGG-C---------UUG---------UCUUCUGCGUCUCGGUUG--AUUACUG-GACAGUUCGACGACUUAAGGAGCCAUCACAUU---------CAUGGAUGGUCGAUU----AUUUCCGGUCGACAGAUC-UCAGAUUAA-AGGUCGACAUUGGGUG--UUCGCUCUGGUCUUGAGCUCCCUUC--CUUUCGGGGUU--------GGUGAGCUCGGCUGGAGAGCCUGG-U-GCUCGGCGGCGUCAUAUUCCUACUCCCUUUACC-----------------GAUUUGGCCGUCGGCCCAUGAGGUUAGGGAAAAACCAUGGC-CAGCCAACAUAC
AASO01001520.1/4391-4721   ACCAA-------ACCACAGAUCUGUGCCCAGCAAUCCUGUUCGAGCGGU-CGACCAUCAUUCGUGGUGGUCUUCGGCUGUGUUUCGGUUG--AUU-CUG-GACAGUUCGACGACCUAUGGAGCCAUCACUAUUU-----AAAUUUCAUGGU-GUCA----AUUUCCGGUCGACAGAUC-UCAGAUUGAGAUGCAGCGGUCAGGAG--UACACU-CUGCCUUGAGCUCCC---AU---------UU--------GGUGAGCUCGGUGAGAUGGCCUGA-UAUGCUGAAGACGCCAUAUUCCACCUCCCUUCACCGAUACAUCCCUUUAUGGGAUUAGGCCGUCGGCUGAUGAGGUUAGGGAAAAACCAUGGC--AGCCAAC----
#=GC SS_cons               :::::::::::::::::((((((((<<<<<<-<<<<<<<<<<<<<<<<<.-<<<-<<<<____>>>>.>>>->>>>>>->>->>>>>-->..>>>->>>.>>>,,,,,,,<<<<<--<<<-<<<________........________>>>.->>>....------>>>>>))))))).),,,,,,,,.,,<<<---<<<<<<--..------.-<<<<--<<<<<<<<...__.........__........>>->>>>>>>>>>------>>>>>.>->>>,,,,<<<<<<<<--------<<<<<--<<<.................-----<<<<___>>>>----->>>->>>>>------>>>>>.-->>>:::::::
#=GC RF                    aucAauagAAcAaacaCaGAuCUGUGuCCAGCgcuCCugugCcagccgg.uggcccgccUUugggcg.gccUccggcuGgGUcacgGUUG..agcGCUG.GaCAGUUCGACGaccuAuGgAgcCAUCaauuu........ucuUuuAUGgu.guCa....AUUUCCgguCGACAGaUC.uCAGAuugA.augccgacaccggGuG..Uuaacu.ucgcCUUgagcuCCC...gu.........uu........GGUGagcucGgcggGAuagCccgg.uaggcuGaaGgCGcCAuAUUCCaauuCCcuUugCC.................GauUuGgCcGUCgGcCgaUGAGGcUagGGaaaAACCaUGgC.uaGcCaACAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01513
#=GF ID   Afu_335
#=GF DE   A. fumigatus snoRNA Afu_335
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   50.00
#=GF TC   56.30
#=GF NC   39.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


EU780959.1/1-95              CUUUAUGAUGAAC-CCCUGAUAGGGACAUCUUAUGCCAAACGCAAAUGAUGUGAAUUUGGGCUCGGUAUUUUAGUAGAUGCUUCGAG--UUUCUGAUC
ABBS02000011.1/58644-58737   CCCAAUGAUGAUCAUCCAGAUAGGGACAGCUUAUGCUAU--GCAUGUGAUGUUACC-UGGAAAGAGAAUUUUAGUAGAUGCCUCUUGU-UAUCUGAGC
AM921933.1/1-97              UCGAGUGAUGAUCUUCCUGAUAGGGACAUCUGAUGCAAAAAGCACAUGAUGCGAAC-AGGACAAGAGAUUUUAGUAGAUGCUUCUUGGAUAUCUGAAG
AM920431.1/2305920-2305824   UCGUAUGAUGACUUUCCCGAUAGGGACAUCUGAUGCAAAUUGCAUAUGAUGUUACC-AGGACAAGAGAUUUUAGUAGAUGCUUCUUGACUAUCUGAAA
ABHV01000074.1/132700-132607 UCCAAUGAUGAUUUUCCAGAUAGGGACAGCUUAUGCUAU--GCAAAUGAUGUCACC-UGGAAAGAGAAUUUUAGUAGAUGCCUCUUUU-GAUCUGAGG
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::.:::::::::
#=GC RF                      uCgaAUGAUGAucuUCCuGAUAGGGACAuCUuAUGCuAaauGCAuAUGAUGUuAcC.uGGacaggggAUUUUAGUAGAUGCuUCuuGu.UaUCUGAgg
//
# STOCKHOLM 1.0

#=GF AC   RF01514
#=GF ID   Afu_513
#=GF DE   A. fumigatus snoRNA Afu_513
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   48.00
#=GF TC   49.80
#=GF NC   42.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7


ABBT01000198.1/255535-255636 UUCCAGGAUGAA-UGGCACUGGGCUCCGACGGUGUUGA-UAUCACAA--CCCGGUUAUGA-UGGACAUGCC-CUUUGUGGCAGGCCUAGAAAACCUCGCCCACUGAUU
ABKH01000207.1/32612-32717   UUGCAGGAUGAA-UGGCACUGGGCUCCGACGGGCAUUG-AUACAGCAACCCGGUUUAUGAUUGGAUAUGCCAUAUUGUGGCAGGCCUAGAAAACCUCGCCCACUGAAU
ACBU01001064.1/82848-82950   UUCUAGGAUGAA-UGGCACUGGGCUCUGACGGUGUUGAUAUAACAA---CCCGGUUAUGA-UGGACAUGCCCUUUCGUGGCAGGCCUAGAAAACCUUGCCCACUGAUU
AM920437.1/1346631-1346733   UCCGAAGAUGAAACGGCACUGGGCUCCGACGGCGUUUA-AAAAAUG---UCCGGUCAUGA-UGGAUGCGCCUUUUUGCGGCAGGCCUAGAAAACCUCGCCCACUGAGA
AM921931.1/1-103             UUCGAUGAUGAAGCGGCACUGGGCUCCGACGGCGUCGA-AUAGACG---UCCGUUUGUGA-UGGAUAUGCCUCUUUGUGGCAGGCCUAGAAAACCUCGCCCACUGAUA
AAGI01000315.1/11653-11569   UACAAUGAUGAUACGGCACUGGGCUCCGA---------------------CAAUUCUUGA-CGGAUAUGCCUACCA-UGGCAGGCCUCAGAAACCUCGCCGACUGAUA
ABJE01000834.1/15159-15059   CAAUAUGAUGAAGCGGCACUGGGCUCCGA--GAGUACC-UAAUGGG---CUCGACCAUGA-GCGACACGCCUCUUUGCGGCAGGCCUAGAAAACCUCGCCCACUGAUU
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::.:::::::...:::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UucuAgGAUGAAgcGGCACUGGGCUCCGACGGuGuuga.auaaagg...cCcGuUuaUGA.uGGAuAuGCCuuuUuGuGGCAGGCCUAGAAAACCUCGCCCACUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF01515
#=GF ID   Afu_514
#=GF DE   A. fumigatus snoRNA Afu_514
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   39.00
#=GF TC   39.70
#=GF NC   32.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


ABVF01000102.1/235831-235936 UGCUAUGAUGUGGUAAUUUGCGGUUGAUCCGGCUUUUGUGAAUCUCCCGCCAGAGUAUUCUCAAGCAACUGUCGGGGUGAUAUUUA-AUUUCUUACAUAUUCUGAUU
ABIW01001098.1/7114-7219     UCCAAUGAUGCGGUAAUUUGCGGUUGAACCAUCCGCUGUGAAGCUCUCGCCUGGGUUUCUCAUACAGCGGUUAGAUAAUGAUAGCC-AUUUCUUACAUAUUCUGAAU
AM921937.1/1-105             UCACAUGAUGCGGUAAUUUGCGAUUGACACAGUGUCUGUGAA-CCCUCGCCGGGGUUCUUUCAAGCAGCACUGCCGCAUGAUAUUC-AUUUCUUACAUAUUCUGAUA
ABKI01000243.1/38567-38673   CAUAAUGAUGCGGUAAUUUGCGGUUGAUCCGUUCACUGUGAAGCUCCCGCCAGAGCUUCAAAUAGCAGUUUUCGGCUGUGAUAUUCAAUUUCUUACAUAUUCUGAAC
AAKE03000009.1/912863-912966 UCACAUGAUGCGGUAAUUUGCGAUUGACGCAGUGUCUGUGAA-CCCUCGCCGGGGUUCUUU-AAGCAGCGCUGCCGCAUGAUAUUC-AUUUCUUACAUAUUCUGAUA
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::
#=GC RF                      UccaAUGAUGCGGUAAUUUGCGGUUGAucCggucuCUGUGAAgCuCuCGCCgGgGUuuuuuaaAGCAgcuuUgggguauGauauUC.AUUUCUUACAUAUUCUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF01516
#=GF ID   v-snoRNA-1
#=GF DE   Human herpesvirus 1 small nucleolar RNA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   75.00
#=GF TC   85.10
#=GF NC   33.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19680535
#=GF RT   Expression and processing of a small nucleolar RNA from the Epstein-Barr
#=GF RT   virus genome.
#=GF RA   Hutzinger R, Feederle R, Mrazek J, Schiefermeier N, Balwierz PJ, Zavolan
#=GF RA   M, Polacek N, Delecluse HJ, Hüttenhofer A
#=GF RL   PLoS Pathog. 2009;5:e1000547.
#=GF WK   Epsteinâ€“Barr_virus_small_nucleolar_RNA_1
#=GF SQ   2


AY037858.1/148954-149018 UCCCGAUGAUGACACCCGCCGCGGCUGUCUGAGGCAGCUGAGGAAAUUGGUUGAGAUUCUGACGU
L06837.1/376-312         UCCCGAUGAUGAUGACAACCGCGGCUGUCUGAAGCGGCUGACGAAAUCGGUUGAGAUUCUGAUGA
#=GC SS_cons             :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  UCCCGAUGAUGAugaCagCCGCGGCUGUCUGAgGCgGCUGAgGAAAUuGGUUGAGAUUCUGAuGu
//
# STOCKHOLM 1.0

#=GF AC   RF01517
#=GF ID   iscRS
#=GF DE   iscR stability element
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:19407815
#=GF GA   40.00
#=GF TC   43.40
#=GF NC   35.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0075139; response to host iron concentration;
#=GF RN   [1]
#=GF RM   19407815
#=GF RT   Small RNA-induced differential degradation of the polycistronic mRNA
#=GF RT   iscRSUA.
#=GF RA   Desnoyers G, Morissette A, Prevost K, Masse E
#=GF RL   EMBO J. 2009;28:1551-1561.
#=GF WK   iscR_stability_element
#=GF SQ   4


AE014075.1/2929823-2929714 UAAAAAGAAUUCAGAAUCAGGCCGGAGUGUUUA-GCGCUCCGUAAACACGGUCGUACAUCCAGCCGGUAGCCUGGUUCCUUGCAUUGAGUGAUGUACGGAGUUUAUAGAGC
AL627275.1/89889-89782     AAAAAAGAAUUCAGAAUCAGGCCGGGACGCGGA-C-GUCCCGUCAACACGGUCGUACAUCCAGCCGGUUGCCUGAUUCCUUGCAUUGAGUGAUGUACGGAGUUUA-AGAGC
CP000647.1/3144905-3144796 UAAAGAGCUUUCAGAAUCAGGCCGGGAUGCUCCGACAUUCCGUGUACUCGGUCGUACAUCAAGCCGGUUGCCUGAUUCCUUGCAUUGAGUGAUGUACGGAGU-UUAAGAGC
AE014073.1/2640264-2640155 UAAAAAGAAUUCAGAAUCAGGCCGGAGUGCUAA-AUACUCCGUAAACACGGUCGUACAUCCAGCCGGUAGCCUGAUUCCUUGCAUUGAGUGAUGUACGGAGUUUAUAGAGC
#=GC SS_cons               :::::::[[[[[,(((((((((<<<<<<_____.__>>>>>>,,,<<-<<<____________>>>>>,))))))))),,<-<<<______>>>->,,]]]]]::::::::
#=GC RF                    uAAAaAGaauuCAGaauCaGGCCGGggcGcuua.acgccCCGUaaaCaCGGUCGUACAUCcAGCCGGuuGCCuGauuCCUuGCauUGAGUGauGUaCGGaguuUauAGAGC
//
# STOCKHOLM 1.0

#=GF AC   RF01518
#=GF ID   pRNA
#=GF DE   NoRC assoicated RNA, pRNA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:18600236
#=GF GA   34.00
#=GF TC   34.00
#=GF NC   33.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006338; chromatin remodeling;
#=GF RN   [1]
#=GF RM   18600236
#=GF RT   The structure of NoRC-associated RNA is crucial for targeting the
#=GF RT   chromatin remodelling complex NoRC to the nucleolus.
#=GF RA   Mayer C, Neubert M, Grummt I
#=GF RL   EMBO Rep. 2008;9:774-780.
#=GF WK   NoRC_associated_RNA
#=GF SQ   23


X01547.1/347-436           CGAUGGUGGCGUUUUUGGGGACAGGU------GUC-CGUGUCGCGCGUCGCCUGGGCCGGCG-GCGUGGUC-GGUGACGCGACC-----UCCCG---GCCC-CGGGGA
J00304.1/369-464           CGAUGGUGGCGUUUUUGGGGACAGGUGUCCGUGUC-CGUGUCGCGCGUCGCCUGGGCCGGCG-GCGUGGUC-GGUGACGCGACC-----UCCCG---GCCC-CGGGGG
AL353644.34/167218-167307  CGAUGGUGGCGUUUUUGGGGACAGGU------GUC-CGUGUCGCGCGUCGCCUGGGCCGGCG-GCGUGGUC-GGUGACGCGACC-----UCCCG---GCCC-CGGGGG
GU372691.1/2883-2969       GUUAUGGGGUCAUUUUUGGGCCACCU------CCC-CAG---GUAUGACUUCCAGGUAUUCU-CUGUGGCC-UGUCACUUUCCU-----CCCUG---UCUC-UUUUAU
AAHX01389274.1/503-589     UACAUGGGGACCUCUUGGGGACACGU------CAC-CGA---ACAUGACUUCCAGACGUUCC-GUGUGGCC-UGUCAUGUUUAU-----CCCUG---UGUC-UUUUAC
AAHX01101633.1/7738-7652   UCAUGG-GGACUUUUUUGGGACACCG------UAC-CAG---GCAUGACUUCCAGGUUUACC-AUGUGGCC-UGUGAAUUUCCU-----CCCUG---UCCCGUUAUUG
M14803.1/575-661           UGAUUGGGACAAUAUUUGGGGCAC--------UUCGCCGGUCCC--GACUUCCAGAAUUUCC-GUGUGGUC-UGUGAAUUUAU------CACCG---CUACACUGUCA
ABDC01495134.1/2742-2833   UCACUGGGGACGUGUUGGGGACGGGU------GGC-C-G--CAUCUGGGUUCGUGG-GGACC-GCGUGGUCAAGUGGCUCUUCCCCGGCCCCCU---CGCC-GUGUUU
ABDC01526153.1/1801-1893   GCACUGGGGACGUGUUGGGGACAGGU------GGC-C-G--CGUCUGGGUUCGUGGUGGUCG-GCGUGGUCAAGUGGCUCUUCCACGGCUCCCU---CGCC-GUGUUU
AAGV020521404.1/2049-2132  CUAUG-GGGUCGUCCUGUGGGCCAGU------GGC-CGC---AUGACGCUUCCGGGAGGUCG-GUGUGACC-AGCGGA--UUGU-----CCCUG---UGUC-AGGGCU
AAYZ01456726.1/287-374     CGAUGGCUGUGUUUUUGGGGACUUGU------GAC-CCGGGCCCCCAUCU---GAGGGGCGG-CUGUGUCC-CAUAGG--UUGU-----CCCUGUUGUCCC-CUGGAA
ABRP01366066.1/371-287     CGAUGGGGU-CGUGCUGGGGCCCGGU------GGC-CGAGCCUC--GUUUCCGAGGAGGCCG-CCGAGAUC-CGCGGA--UAAG-----CCCCG---CUGA-CGGGCG
ABRR01362537.1/599-684     UUAUGGGGGUAGGGCUGGGGGCAGGU------GGC-CGG---ACCGAGGUCCCGGGGCCCCCCCUGCAAAU-CGUGGA--CCCG-----ACCCG---UUUC-CGGGCG
L31782.1/406-491           CUCUAGGGCAGGGCUGGGGGACAAGU------GUC-CGG---AUGGGGGUUCCGGGGAUACCCCCACGUCC-UGUGGG--UGGG-----CCCCG---CUGC-UGGGCA
AAWR02043243.1/629-715     CGAUGGGGUCGUGCUUGGGGUCUGGU------GGC-CGUG--GCCGUGAUCCAGGGGUUCCCCUCGUGAUC-CGUGGG--UGGG-----CCCCG---UCUC-CGGGCG
ABGA01210943.1/3454-3366   CCAUGGUGGCCUUUUUGGGGACAGAU------GUC-CAGGUCGCACAUUU-CUGGGCCGGUG-GUGUGGUC-GGUGACUCGACA-----CCCCG---CCGC-CAGGCG
AADA01148175.1/12805-12893 CCAUGGUGGCCUUUUUGGAGAUAGAU------GUC-CAGAUCGCUCAUUU-CUGGGCUAGUG-GUGUGGUC-GGUGACUCGACA-----CCCUG---CCCC-CAGGCG
AANU01175373.1/12565-12652 CCAUGGUGGACU-UUUGGGAACAGGU------AUC-UGGGUCACGUGUUU-CUGAGUCGGUG-GCGUGGUU-CGUGACUCAACA-----CCCUG---CCCC-UAGGCA
AANU01147195.1/694-605     CGAUGGUGGCGAUUUUGGGGACAGAUGCCCGUGUCGCGGGUUCC-------CUGGGCCGGCG-GCGUGGUC-GGUGACUCGACC-----UCCUG---UCUC-CUGGGG
AADD01205172.1/14918-14830 UGAUGGUGGCGUUUUUGAGGACAGAU------GUC-CGUGUCUUG-GUUUCCUGGGCCAGCG-GCAUCGUC-GGUGACUCGAUC-----UCCUG---CCCC-CGGGGG
AADA01204110.1/119-30      CGAUGGUGGCGUUUUUGGGGACAGGU------GUC-CGUGUCGCGCGUUUCCUGGGCCGGCG-GCGUGGUC-GGUGACACGACC-----UCCUG---GCCC-CGGGGG
CABD02423207.1/498-587     CGAUGGUGGCGUUUUUGGGGACAGGU------GUC-CGUGUCGCGCGUUUCGUGGGCCGGCG-GUGUGGUC-GGUGACUCGACC-----UCUCG---GCCC-CGGGGG
AAGW02077987.1/6111-6028   GAUGGGUGG-CAUUUUGGGGACAAGU------GAC-CGGGUCCCCAAGCU---CAGAGGUGG-CUGUGUCC-AGUGCA--UCAG-----CCCUG---UGUC-CUCUCG
#=GC SS_cons               :::<-<-<<-<<-----<<<<-----......<<<.<<-<<<<<<<________________.>>>>>>>-.>>->>>------.....>>>>-...>>>>.>->:::
#=GC RF                    cgAuGGgGgcggUuUUGgGGaCAgGU......guC.CgGGuCgCgcGucUuCugGGcgguCG.gcGuGgUC.cGUGacUCUacu.....uCCcG...cccC.CugGcg
//
# STOCKHOLM 1.0

#=GF AC   RF01519
#=GF ID   CC0196
#=GF DE   Caulobacter sRNA CC0196
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   35.00
#=GF TC   35.40
#=GF NC   34.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18373523
#=GF RT   Small non-coding RNAs in Caulobacter crescentus.
#=GF RA   Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L
#=GF RL   Mol Microbiol. 2008;68:600-614.
#=GF WK   Caulobacter_crescentus
#=GF SQ   2


AE005673.1/1465670-1465727 UCUUUGAAGGCACCCACCAUCACUGACUUCCACAGCCCGGCCGCAAAGCCGGGCUGCU
CP001340.1/1491646-1491703 UCUUUGAAGGCACCCACCAUCACUGACUUCCACAGCCCGGCCGCAAAGCCGGGCUGCU
#=GC SS_cons               ::::::::::::::::::::::::::::::::<<<<<<<<<______>>>>>>>>>::
#=GC RF                    UCUUUGAAGGCACCCACCAUCACUGACUUCCACAGCCCGGCCGCAAAGCCGGGCUGCU
//
# STOCKHOLM 1.0

#=GF AC   RF01520
#=GF ID   CC0734
#=GF DE   caulobacter sRNA CC0734
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;Mafft_pfold;
#=GF GA   45.00
#=GF TC   53.00
#=GF NC   40.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18373523
#=GF RT   Small non-coding RNAs in Caulobacter crescentus.
#=GF RA   Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L
#=GF RL   Mol Microbiol. 2008;68:600-614.
#=GF WK   Caulobacter_crescentus
#=GF SQ   2


CP001340.1/708218-708312 GUAAGCAGUUGAUUUUUGUGAUAACCGUCAAAUCGACCACUUAGGGUCACCACUUAACGCUGUCCACAAACGGCCUGGCGACCACUUAAGGCUGU
AE005673.1/639907-640001 GUAGCCCUUUGAUUUUUCAGAACACUGCCAAAUCGACCAUUUGGGGUCACCACUCAACGCUGGCCACAAACGGCAUGGUGACCACUUAAGGCUGU
#=GC SS_cons             :::::::::<<<<<________________>>>>>---------<<<<<<<<------<<<<________>>>>->>>>>>>>::::::::::::
#=GC RF                  GUAagCauUuGauuUUUguGAuaACuGuCAaauCgACCAuUUaGGGuCaCCaCUuAACGCuGuCCACAAACgGCauGGuGaCCACUUAAGGCUGU
//
# STOCKHOLM 1.0

#=GF AC   RF01521
#=GF ID   CC1840
#=GF DE   caulobacter sRNA CC1840
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;Clustal_alifold;
#=GF GA   50.00
#=GF TC   60.40
#=GF NC   40.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18373523
#=GF RT   Small non-coding RNAs in Caulobacter crescentus.
#=GF RA   Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L
#=GF RL   Mol Microbiol. 2008;68:600-614.
#=GF WK   Caulobacter_crescentus
#=GF SQ   3


CP001340.1/2059942-2059848 GUCGAUCGGUCGCCGCGCCCAUCCGUCCCUCAAAGCGGCGAUCGGUUCUCAGG------CAAGUCCUGCGGAGACGCGCCGCCUCCCCC-AGGCGGCGCGUC
CP000927.1/2939844-2939751 UGCAACCGGCCGUCGCGCCAACCCGUCCCUCGAUGCGGCGAUCGGUU--CAGG------UUCGUCCUGCGGAGGCCCGCCGCUUUCCCUGAAGCGGCGGGUC
CP000747.1/1819643-1819544 AUCGGUCGGUCGCCGCGCUCUCCCGUCCCUCGAAGCGGCGGACGAUCCGGAUGGAACGACACGCCCAUCGGCGGCGCGCUG-CUCGCAA-GAGCGGCGCGCC
#=GC SS_cons               :::<<<<<<<<<<<<<__________________>>>>>>>>>>>>>------......-------------<<<<<<<<<<<<_____.>>>>>>>>>>>>
#=GC RF                    auCgacCGgcCGcCGCGCccacCCGUCCCUCgAaGCGgCGgcCGgucCucAgG......cacGuCCugCGGaGgCgCGCcGCcuccCcu.agGCgGCGcGcC
//
# STOCKHOLM 1.0

#=GF AC   RF01522
#=GF ID   TB10Cs1H1
#=GF DE   Trypanosomatid snoRNA TB10Cs1H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   45.00
#=GF TC   48.10
#=GF NC   38.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   TB10Cs1H1_snoRNA
#=GF SQ   4


AAHK01011372.1/313-243     CAUCCCCU-UUAAUAGCGAGCGGACCCUCAGUGCAUCACCGCGAGCCGCUCGUCUACACCGGGGGAGAGAGA
FN554973.1/1694836-1694906 CAUCCCCU-UUAAUAGCGAGUGGUCUUUGUGUGCAUCUCCGCAAACCACUCGUCUACACCGGGGGAAAGAUA
FR799010.1/957243-957312   CAUCCCUUGUUAAUAGCGAGCAGUCCAC--CUGCAUCCCCGCAAGCUGCUCGUCUACACCGGGGGAGAGAGA
FR796468.1/1551329-1551398 CAUCCCUUGUUAAUAGCGAGCAGUCCAC--CCGCAUCCCCGCAAGCUGCUCGUCUACACCGGGGGAGAGAAA
#=GC SS_cons               ::<<<<<<.------<<<<<<<<<____________________>>>>>>>>>------->>>>>>::::::
#=GC RF                    CAUCCCcu.UUAAUAgCGAGcgGcCcaugugUGCAUCuCCGCAAgCcgCUCGuCUACACCggGGGAgAGAgA
//
# STOCKHOLM 1.0

#=GF AC   RF01523
#=GF ID   TB10Cs1H2
#=GF DE   Trypanosomatid snoRNA TB10Cs1H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   69.60
#=GF NC   35.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18986541
#=GF RT   Psiscan: a computational approach to identify H/ACA-like and AGA-like
#=GF RT   non-coding RNA in trypanosomatid genomes.
#=GF RA   Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S,
#=GF RA   Unger R
#=GF RL   BMC Bioinformatics. 2008;9:471.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   5


AAHA01000001.1/1740119-1740181 AGCACUCAU-UUCAAGCUGCG--CGAGCAUAAGCGUGUUGCUC-CGUGGUCGGGUGACGUGCGAGAC
AAHK01011372.1/778-716         AGCACUCAU-UUCAAGCCGUC--CGAGCAAAAACGAGUUGCUC-UGCGGUCGGGUGACGUGCAAGAC
FR799573.1/931352-931418       AGCGCUCAUUUUCAAGCCGCACGCGGGCCUGUUGCUGGUGCCCCUGCGGUCGGGUGAUGCGCGAGAG
FR799010.1/957384-957450       AGCGCUCAUUUUCAAGCCGCACGCGGGCCUGCUGCUGGUGCCCCUGCGGUCGGGUGAUGCGCGAGAG
FN554973.1/1695830-1695892     AGCACUCAU-UUCAAGCUACG--CGAGCAUAAGCGUGUUGCUC-CGUGGUCGGGUGACGUGCGAGAC
#=GC SS_cons                   :<<<<<<<<.-----<<<<<<..-<<<<<_________>>>>>.>>>>>>--->>>>->>>>:::::
#=GC RF                        AGCgCUCAU.UUCAAGCcGCg..CGgGCaUaaucgUGuuGCcC.cGCgGUCGGGUGAcGcGCGAGAc
//
# STOCKHOLM 1.0

#=GF AC   RF01524
#=GF ID   TB10Cs1H3
#=GF DE   Trypanosomatid snoRNA TB10cs1H3
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   70.30
#=GF NC   47.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   5


AAHK01011372.1/538-464         CACGCGGGCAGGAACGUGGCAGGCCGCAGAGGGUUGCCAUUCAUUCCUCG--UGCGGUUCAACAACAUGGUCCAAGA
AAHA01000001.1/1729154-1729225 CU-GCUUGCAGGAACGUGGCAGGCCACCGAGGUC--ACACUCGUGCUUCG--CGUGGUUCAACAACAUGGUCCCAGA
FR799010.1/955856-955929       CCCCGUGGUCGGAACGUGGCAGGCCGCGGAGGGC--ACACCCAUCCCCCACACGCGGUUCAAC-ACAUGAUCCCAGA
FR796468.1/1551018-1551091     CUCCGUGGACGGAACGUGGCAGGCUGCGGAGGGC--ACACUCAUCCCUCAUACGCGGUUCAAC-ACAUGAUCCCAGA
FN554973.1/1694600-1694671     CU-GCUUGCAGGAACGUGGCAGGCCACCGAGGUC--ACACUCGUGCUUCG--CGUGGUUCAACAACAUGGUCCCAGA
#=GC SS_cons                   ::::::::::<<<-<<<<----<<<<<-<<<<<_..________>>>>>-..->>>>>------->>>>->>>::::
#=GC RF                        CuCgcugGcaGGAACgUGGCAGgCCGCaGaGGgc..ACAcUCaUcCCuCg..cGCGGuUCAACAACAuGgUCCcAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01525
#=GF ID   TB10Cs2H1
#=GF DE   Trypanosomatid snoRNA TB10Cs2H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   35.00
#=GF TC   43.10
#=GF NC   31.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   4


AAHK01016749.1/680-745     AGGCGUUGUCGGUUGGGUCAGUGG---CACGUGCUCUCCCUGUAACCCUAUCUCGCAGCCCCGAGAACA
FR796465.1/255542-255610   CGGCGUUGUCGGUUGGGCGUGACUCCUUGCACCUCGUAGGUACGACCCUAUCUCGCAACCCCCAGAUUC
FR799008.1/262789-262857   CGGUGUUGUCGGUUGGGCGUGACUCCUUGCACCUCGUAGGUACGACCCUAUCUCGCAACCCCCAGAUUC
FN554973.1/2671481-2671546 CGGCGUUGUCGGUUGGGCCAGUGG---CAAAUUUUAUCCCUGCAGCCCUAUCUCGCAACUCCUAGAACC
#=GC SS_cons               :<<-<<<<<-----<<<_______...__________________>>>------>>>>>->>:::::::
#=GC RF                    cGGCGuUGUCGGUUGGGCgaGugu...uaCAucUugUaggUaCaACCCUAUCUCGCAaCCCCcAGAauc
//
# STOCKHOLM 1.0

#=GF AC   RF01526
#=GF ID   ceN106
#=GF DE   C. elegans snoRNA ceN106
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   60.00
#=GF TC   78.80
#=GF NC   36.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.75 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948649.1/1-78 CGAUGAUGAUGAAGAAUUU--UUGAUAUGGUGUCAGGACCUCUGAGAGUUCCGUGA-UGAUGUUUAGAGUUCCUGAAUCUU
AM050290.1/2-78 CGAUGAUGAUGAAGAAUUU--UUGAUAUGGUGUCAGGACCUCUGAGAGUUCCGUGA-UGAUGUUUAGAGUUCCUGAAUC-U
DQ789444.1/1-78 -GACGGUGAUGAAGAAUUUUAUUGAUAUGGUGUCAGGACCUCUGAGAGUUCCGUGACUGAGGAUUAGAGUUCCUGAGUC--
#=GC SS_cons    :<<________________..___________________________________.____________________>>.:
#=GC RF         CGAuGaUGAUGAAGAAUUU..UUGAUAUGGUGUCAGGACCUCUGAGAGUUCCGUGA.UGAuGuUUAGAGUUCCUGAaUC.U
//
# STOCKHOLM 1.0

#=GF AC   RF01527
#=GF ID   CrfA
#=GF PI   CC3510
#=GF DE   Caulobacter sRNA CrfA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Clustal_alifold;
#=GF GA   38.00
#=GF TC   38.40
#=GF NC   36.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18373523
#=GF RT   Small non-coding RNAs in Caulobacter crescentus.
#=GF RA   Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L
#=GF RL   Mol Microbiol. 2008;68:600-614.
#=GF RN   [2]
#=GF RM   20601471
#=GF RT   CrfA, a small noncoding RNA regulator of adaptation to carbon starvation
#=GF RT   in Caulobacter crescentus.
#=GF RA   Landt SG, Lesley JA, Britos L, Shapiro L
#=GF RL   J Bacteriol. 2010;192:4763-4775.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


CP001340.1/3781500-3781365 GCAAGGACGAAACGAGCCCACCAGAGAGCUCCCGUUCUUCGGCGUUUCGGGGAGGAAACGCCCGCCUAGAUCGAAUGAUCGAGAAAAUAGCCAGCCCGUCGCGAUUAUCCCCCGCGGCGGGUUUGGUGUAUCUGGG
CP000927.1/5059023-5058889 GCAAGGAAGAAACGAGCCCA-AAGAGAGCUCCCUUCCUUCGGCGUUUCGGGGAGGAAACGCCCACCUAGAUCGAAUGAUCGAGAAAUAGCCGGACCCGUCGCGAUUAUCCCCCGCGGCGGGUUUGGUGUAUCUGGC
#=GC SS_cons               <-<<<<<<<----<<<<-<______>->>>>->>>>>>>><<<<<<<<______>>>>>>>>---(((((<<<<____>>>>,,,,,,<<<<<<<<<<<<<<<_________>>>>>>>>>>>>>>>,,,))))):
#=GC RF                    GcaaGgacGAAAcGaGCcCAcaAGAGAGCuCcCgucCuuCGGCGuuuCGGGGAGGaaaCGCCcacCcaGauCGaAUGAuCGaGAAAaagcCgggCCCGcCGCGAUUAUccccCGCGgCGGGcccGgcGUAuCugGg
//
# STOCKHOLM 1.0

#=GF AC   RF01528
#=GF ID   CC3513
#=GF DE   caulobacter sRNA CC3513
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Mafft_alifold;
#=GF GA   40.00
#=GF TC   42.20
#=GF NC   33.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18373523
#=GF RT   Small non-coding RNAs in Caulobacter crescentus.
#=GF RA   Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L
#=GF RL   Mol Microbiol. 2008;68:600-614.
#=GF WK   Caulobacter_crescentus
#=GF SQ   2


CP001340.1/3785285-3785457 AUCCGC--UAGGCGGGGCUCUGGCUGGGUACGCUCGGCUUUAGAGCGCGCGGACCCGGCCGAUCCCGCGAGGCGAGGUCGGAUGGUGGUGGUGGCCGUGAUGGUGCGGCGUGCGGGUCAUUGCGGGGGCGGUGUAGCGGAUGGCG-GCGGUGAGGGGAAGGGCUUCGUUCAAAGCC
CP000927.1/5062836-5063006 AUCCGCCUUGGGCGGGGCUCAGGCUGGG--CGUUCG---UUAGAGCGAACGGACCCGGCCGAUCCCGCGAGGCGAGGUCGGAUGAUGGUGGUGGCCGUGAUGAUGCGGCUGGCGGGUCAUUGUGGCGGGGCUAUAGCGGAUGAGGAGGGGUGGGGGAAGGGGCAGCAUCGGCAGAG
#=GC SS_cons               :<<<<<..___>>>>>((((,<<<<<<<<-<<<<<<_________>>>>>>->>>>>>>>,,<<<<-<<--<<---<<<-<---<<<<<<-<-<<<<--<<<<<-<<_____>>->>>>>-->>>>->>>>>>>-->->>>----.>>-->>->>>>,,)))):::::::::::::
#=GC RF                    AcCCGC..UaGGCGGgGCcCaGGCcGGGuACGcuCGgcuUUAGAGCGagCGGaCCCgGCCGAuCCCGCgAGgCGAGguCGGAUGguggcgGcGgCCgUGauGgcGCGGCuuGCGGgcCauUGcGGcGgcgccacAGCGGacGagG.GcGGcGaGGGaAaGgGCauCaUugaaAGag
//
# STOCKHOLM 1.0

#=GF AC   RF01529
#=GF ID   CC3552
#=GF DE   Cauldobacter sRNA CC3552
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold;
#=GF GA   50.00
#=GF TC   71.70
#=GF NC   40.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18373523
#=GF RT   Small non-coding RNAs in Caulobacter crescentus.
#=GF RA   Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L
#=GF RL   Mol Microbiol. 2008;68:600-614.
#=GF WK   Caulobacter_crescentus
#=GF SQ   2


ABRU01000059.1/74859-74754 GGAGGCGGCGACGCCCCCCCCGACUUGAGAUUGGCGAAAGCCAAUCUGUCGCCUCCGCGCCUCAUUCUCGAUGAUGCCACUUGAAGGCGGCCCGCAGGGGUCGCCU
CP001340.1/3830132-3830235 GAAGGCGGCGACGCCC--CCCGACUUGAGACUGGCGAAAGCCAGUCCGCCGCCUUCGCACCCCUUUGUUGAUGCGAACUCAGGCGGACCGGGUGACCGGACCGCCU
#=GC SS_cons               ((((((((((,<<_______>>,,,,,,<<<<<<<____>>>>>>>))))))))))----------------------------<<<<<<<<<____>>>>>>>>>
#=GC RF                    GgaGGCGgCgACGCCCccCCCGACUUGAGacuGGCGAAAGCCaguCcGcCGCCucCGCaCCuCaUUgUuGAUGauaaCaCuuGaaGgCggcccGaaggggccGcCu
//
# STOCKHOLM 1.0

#=GF AC   RF01530
#=GF ID   CC3664
#=GF DE   Caulobacter sRNA CC3664
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Clustal_alifold;
#=GF GA   60.00
#=GF TC   63.50
#=GF NC   46.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18373523
#=GF RT   Small non-coding RNAs in Caulobacter crescentus.
#=GF RA   Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L
#=GF RL   Mol Microbiol. 2008;68:600-614.
#=GF WK   Caulobacter_crescentus
#=GF SQ   2


AE005673.1/3920055-3920190 GUCGGCUGAUCGGAGACCCUGUGGUCCAGGAUCCUGAACAGCCCCCCCAGCCCCCCAGAUCAUGGGCCGGUCAGCCGACAAACCUAUAUCCCCUCCCCGAGAUGAGCCCGCGCGGACCACCCCCACCGCGCGGGCU
CP001340.1/3946037-3946172 GUCGGCUGAUCGGAGACCCUGUGGUCCAGGAUCCUGAACAGCCCCCCCAGCCCCCCAGAUCAUGGGCCGGUCAGCCGACAAACCUAUAUCCCCUCCCCGAGAUGAGCCCGCGCGGACCACCCCCACCGCGCGGGCU
#=GC SS_cons               <<<<<<<<<<<<<----<<<<<<<<<--<<---<<<___________>>>--->>-->>>>>>>>>>>>>>>>>>>>>>,,,,,,,<<<<-<______>->>>><<<<<<<<<<<__________>>>>>>>>>>>
#=GC RF                    GuCGGCuGacCGGAGAcCCcguGguCcAGGAUcCuGAAcAGccccccCaGcccCCcAGacCacgGGCCGguCaGCCGaCAAAccUAcauCcCcUccccGAGaugaGCCCGCGCGGAccAcccccACCGCGCGGGCu
//
# STOCKHOLM 1.0

#=GF AC   RF01531
#=GF ID   TB10Cs3H1
#=GF DE   Trypanosomatid snoRNA TB10Cs3H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   40.00
#=GF TC   44.10
#=GF NC   35.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   4


AAHK01023897.1/136-197     AGCGGUGUCGCUAUGCGUC-CCCGC----AGACAGUGCGGUGCGACGGUACGAAGCACGCGCGAGAG
FN554973.1/3774657-3774718 AGCAGUGUCGCUAUGCGUU-CCCGU----CAGUAAUACGGGCUAACGGUACGAAGCACGUGCGAGAG
FR796468.1/933944-934009   AGCAGUGUCGCUAUGCGU-CUCCGUCUCACCUCGGUGCGGAGCAACGGUACGAAACACGUGCGAGAC
FR799010.1/956343-956408   AGCAGUGUCGCUAUGCGU-CUCCACCUCACCCCGAUGCGGAGCAACGGUACGAAACACGUGCGAGAC
#=GC SS_cons               :<<<<<<----<<<-<<<<.<<<<<...._______>>>>>-->>>>>>>----->>>->>>:::::
#=GC RF                    AGCaGUGUCGCUAUGCGUc.cCCGc....caucaaUgCGGggcgACGGUACGAAaCACGuGCGAGAg
//
# STOCKHOLM 1.0

#=GF AC   RF01532
#=GF ID   TB10Cs3H2
#=GF DE   Trypanosomatid snoRNA TB10Cs3H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   45.00
#=GF TC   50.20
#=GF NC   34.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   6


AAHK01020514.1/750-683         UGUAUGCAGCCAC-UCCGGGCAGGACGACGCCG--GU-UUGGUGGCG-UGGAGUCCAAUCGGUGCGGCGAGAC
AAHA01000001.1/3813320-3813388 CGCCAGCAGCCGC-CCCGGGCAGGAUGGCGCCC--GUGUCCUUGGCG-UGACGUCUAAUCGGUGCGGCGAGAU
FR796465.1/103544-103472       UGCCGCCUGCACCUUCCGGGCAGGAUGCCGCCCUUGCGCCCUUGGCGACUGUGUCCAAUCGGUGGUGCGAGAU
FR799008.1/88022-87950         UGCUGCCUGCACCUUCCGGGCAGGAUGACGCCCUUGCGGCCUUGGCGACUGUGUCCAAUCGGUGGUGCGAGAU
FN554973.1/3774444-3774512     CGCUAGCAGCCGC-CCCGGGCAGGAUGGCGCCC--GUGUCCUUGGCG-UGACGUCUAAUCGGUGCGGCGAGAU
HE575323.1/3715102-3715168     UGUUCCCAGCCAC-ACCGGGCAGGAUGGCGCCC----GGUGAUGGCG-UCGCGUCCAAUCGGUGUGGCGAGAG
#=GC SS_cons                   ::::::::<<<<<.-<<-----<<<<<-<<<<_..________>>>>.--->>>>>---->>->>>>>:::::
#=GC RF                        UGcuagCaGCcgC.uCCGGGCAGGAugaCGCCC..GuGuccuUGGCG.uugcgUCCAAUCGGUGcgGCGAGAu
//
# STOCKHOLM 1.0

#=GF AC   RF01533
#=GF ID   TB10Cs4H3
#=GF DE   Trypanosomatid snoRNA TB10Cs4H3
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   45.00
#=GF TC   47.70
#=GF NC   37.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   3


AAHK01000005.1/22680-22614 GACGCCCCUCCAACCGCU--UCGCACCGUGCUGCCCCGUGCACUGCGGAGUGAUAUAUGUGG-CGGAGAU
FR796466.1/1224122-1224189 GACGUCACCCCAACCGCUGCUCAUACGUCGUUGCCCAUCGUAUAGCGG--UGAUAUUUGUGGACGGAGAU
FN554973.1/3266668-3266603 GACGCCCAUACAACCGCC--CCACACCGUGCUUUG-CAUGCAUUGUGGGGUGAUACAUGUGG-CGGAGAU
#=GC SS_cons               ::<<<<<--------<<<..<<<<<--<<<<________>>>>>>>>>>>>------->->>.>>:::::
#=GC RF                    GACGcCccucCAACCGCc..uCgcaCcguGcUgccCcuugCacugcGggGUGAUAUaUgUGg.CGGAGAU
//
# STOCKHOLM 1.0

#=GF AC   RF01534
#=GF ID   TB10Cs4H4
#=GF DE   Trypanosomatid snoRNA TB10Cs4H4
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   68.50
#=GF NC   45.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   2


AAHK01000100.1/7483-7548       GAGGAGAUCCGUAGCCACGGUGCCUUGCCUACUUCGUGGCGCACUGUGGGUGGUGAUUUUCCGAGA
AAHA01000001.1/3327281-3327219 GAGGAGGCCCGUAGCCACGGCAU---GCCUUUUUGGUGGUGCGUUGUGGGUGGUGGCUUUCCAAGA
#=GC SS_cons                   ::<<<<<<<-----<<<<<<<-<---<<<________>>>>->>>>>>>----->>>>->>>::::
#=GC RF                        GAGGAggcCCGUAGCCACggcacCUUgCCUauUUgGUGGcgCgcuGUGGGUGGUGgcuUUCCaAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01535
#=GF ID   TB10Cs5H2
#=GF DE   Trypanosomatid snoRNA TB10Cs5H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   40.00
#=GF TC   40.90
#=GF NC   34.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18986541
#=GF RT   Psiscan: a computational approach to identify H/ACA-like and AGA-like
#=GF RT   non-coding RNA in trypanosomatid genomes.
#=GF RA   Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S,
#=GF RA   Unger R
#=GF RL   BMC Bioinformatics. 2008;9:471.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   5


AAHK01001095.1/15481-15405     GGAGCAGGCAACGUCUGUAUUAUGUGGGAGU-UCGCUCGUUUUCCUCAUCUGCAU-UUGUACUGUAGAAGCCUGCAAGA
AAHA01000001.1/2180159-2180225 GGAGCAGACUACGUCUGUAAUAUGC--GGAACCAAC------CUU--CUCUGCAC--UUUACUGUAAAUGUCUGCGAGA
FR796468.1/2236646-2236568     GUAGCCGACGACGUCUGUGUGCUGCGCGAGAACGGCUUGUCGCUCUCCUGUGCGCUUUUCACUGUAAUAGUCGGCAAGA
FN554973.1/2138563-2138629     AGAGCAGACCACGUCUGUAAUAUGC--GGUACCAAC------CUU--CUCUGCAC--UUUACUGUAAAUGUCUGCGAGA
FR799573.1/2210403-2210325     GGAGCCGGCCACGUCUGUGUGCUGCGCGAGAACGGCCUAUCGCUCUCCUAUGCGCUUUUCACUGUAAGAGUCGGCAAGA
#=GC SS_cons                   :::<<<<<<-------<<<---<______________________________>-.--->>>------->>>>>>::::
#=GC RF                        GGAGCcGgCaACGUCUGUguuauGCGcGAgAaCagCuugUcgCUcUCcUcUGCaC.UUUcACUGUAAaaGcCgGCAAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01536
#=GF ID   TB10Cs5H3
#=GF DE   Trypanosomatid snoRNA TB10Cs5H3
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   45.00
#=GF TC   46.00
#=GF NC   40.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18986541
#=GF RT   Psiscan: a computational approach to identify H/ACA-like and AGA-like
#=GF RT   non-coding RNA in trypanosomatid genomes.
#=GF RA   Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S,
#=GF RA   Unger R
#=GF RL   BMC Bioinformatics. 2008;9:471.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   7


AAHK01000300.1/41988-42062     AAACGGGAACUCUCUGGAUGCAUUUUCCGGCUACUUAUUUCUCCGGGUGCCACUCCUCAUCUUUUCCCGAAGAGG
AAHA01000001.1/2180510-2180579 GAACGGUAACUCUCUGGAAACU---CAUCCCCUCUUUUC--UGUAGAUGUGUUUCCUCAUCGGUUCCCGGAGAAA
FR799010.1/2243945-2243878     AAACGACAACUCUCUGGGUUCC---UCGAGUACUUUC---AUCUCAGUG-UAAUCCUCAUCAGUUGUUGGAGAGA
FR796468.1/2237480-2237410     AAACUACAACUCUCUGGAUCCC---UUGGGCCAUUUCUCGUUCCCAGUG-CGAUCCUCAUCAGUUGUCGAAGAAG
FR796468.1/2238206-2238139     GAACUACAACUCUCUGGAUUCC---UCGAGUCGUUCAAU--UCUC-GUG-CAAUCCUCAUCGGUUGUCGAAGAGA
FR799573.1/2211219-2211149     AAACUACAACUCUCUGGAUCCC---UUGGGCCAUUUCUCCUUCCCAGUG-CGAUCCUCAUCAGUUGUCGAAGAAG
FN554973.1/2138913-2138982     UAACGGUAACUCUCUGGAAACU---CAUCCCCUCUUUUC--UGUAGAUGUGUUUCCUCAUCGGUUCCCGGAGAAA
#=GC SS_cons                   :::<<<<<<<-----<<<----...--<<__________.___>>----.--->>>------>>>>>>>::::::
#=GC RF                        aAACggcAACUCUCUGGAUuCc...UcggGCcauUUuUc.uUcccgGUG.caaUCCUCAUCaGUUgccGaAGAaa
//
# STOCKHOLM 1.0

#=GF AC   RF01537
#=GF ID   TB11Cs2H1
#=GF DE   Trypanosomatid snoRNA TB11Cs2H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   40.00
#=GF TC   43.90
#=GF NC   37.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   7


HE575324.1/2850424-2850494 CAAGCUCUUAUUAGUAGUGCGUGCGCCACAAAAGC-AAGAGGCGCCAU-GCACGAAACUGAGGAGCGAGAGUU
HE573027.1/2943773-2943842 AAAGCUCUUU-AUGUAGUGCGCGUGCCACAAAACC-AGCAGGCAGUGU-GCACGAAACUGGAGAGCCAGAUAC
Z50171.1/232-303           AAAGCUCUUUUAUGUAGUGUGCGUACCACGAAAGU-AGCAGGUACUGCGACACGAAACUGGAGAGCGAGACUC
AF177033.1/1-70            ACAGCCCUUA-CUGUAGUGCGCGUGCCGCAAACCA-CCUAGGCACCGU-GCAUGAAACUGGAGGGCGAGAGAC
FR796401.1/453256-453325   GACGCGCUCA-CUGUAGUGCGCGUGCCGCAAGACC-CACAGGCACCGU-GCAUGAAACUGGAGCGCUAGAUGG
FR798979.1/436576-436646   GGUGCGCUUA-CUGUAGUGCGCGUGCCGCAAGACCCCACAGGCACCGU-GCAUGAAACUGGAGCGCUAGAUUG
AF545070.1/422-492         AAAGCUCUUUUUUGUAGUGCGCUCGUCGCUAAACC-AACAGACGCGGU-GCACGAAACUGGAGAGCAAGAGAU
#=GC SS_cons               :::<<<<<<-.-----<<<<<<<<<<<________.____>>>>->>>.>>>>------->>>>>>:::::::
#=GC RF                    aAAGCuCUua.uUGUAGUGCgCguGCCgCaAAAcc.aacAGGCaCcGu.GCACGAAACUGgAGaGCgAGAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01538
#=GF ID   TB11Cs3H1
#=GF DE   Trypanosomatid snoRNA TB11Cs3H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   58.20
#=GF NC   49.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.48 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   4


AAHK01000353.1/1536-1608   AAGGCUCUCGUUGAACAAUCCCACCGGUGAGUGUAUACAUUCGGUCUCCUGCGUGGACCUGAGAGAGCCAAGA
FN554974.1/2738555-2738626 AAGGCCCUCA-UGAACAAUCCCACCGGUGAGUGUACUCAUUUAGUCUCGUGCGUGGACCUAGGAGCGCCAAGA
HE575324.1/2852896-2852967 AAGGCUCUCA-CGAACAAUCCCACUGGUGAGUGUAUCUUCUUAGUCUCCUACGUGGACCUAAGAGUGCCUAGA
FR796432.1/1554771-1554842 CCGGCUCUCA-CGAACAAUCCCGCCCGGAGUUUACCGUACUUGAUCUCUUGCGCGGACCUACGGGUGCCCAGA
#=GC SS_cons               ::<<<-<<<-.---------<<<<<<--<<<<<____>>>>>------->>->>>>------>>>->>>::::
#=GC RF                    AAGGCUCuCA.uGAACAAUCCCaCCgGugaguguAuucacucaGUCUCuuGCGuGGACCUAaGaGuGCCaAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01539
#=GF ID   TB11Cs4H1
#=GF DE   Trypanosomatid snoRNA TB11Cs4H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   45.00
#=GF TC   46.20
#=GF NC   43.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   5


AAHK01031442.1/205-276   ACAUCUUGCCCUGUCUGGCGCCCUGUCUGUGCAAACGGUUGGUGGCGG-GCCCGCCCGAAAGCGCAAGAGAGA
FR799002.1/383424-383494 GCAUCUUGAUCUGUCUGGCA-CCUGUCUUUACA-CCUGUCAGUGACAGAGCCCGCCCGAAAGCUCAAGAGAGA
FR796423.1/375700-375630 UCAUCUUGACCUGUCUGGCA-CCUGUCUUUACA-CCUGUCAGUGACAGAACACGCCCGAAAGUUCAAGAGAGA
FN554974.1/453914-453844 AAAUCUUACCCUGUCUAGCUGCCUGUCAGUAUA-C-UUUCGGUGACGGUAUUGGCUCGAAAGUGUAAGAGAGA
EF100612.1/5-76          CCGUCUUGCCCUGUCUGGCGCCCUGUCUGCGCACGCGGUCAGUGACGG-GUGCGCCCGAAAGCGCAAGAGAGA
#=GC SS_cons             :::<<<<<<-------<<<---<<<<<______._________>>>>>----->>>------->>>>>>::::
#=GC RF                  acAUCUUGcCCUGUCUGGCacCCuGuCUgUaCA.cCuGUCaGUGaCgGagcucGCCCGAAAGcgCAAGAGAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01540
#=GF ID   TB11Cs4H2
#=GF DE   Trypanosomatid snoRNA TB11Cs4H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   55.30
#=GF NC   37.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   6


AAHK01025874.1/529-592   AAGGUGCGUCUUGAGACCCACCGCCCCGU-GACGCUGGGCGCUUGGGUGCAUCGGCGCCCCGAGA
FR796423.1/378278-378215 ACGGAGUGCAUUGAGUCCCACCGCUCCCC-ACCAGUACGCGCGUGGGAGCAUCAACUCUCCUAGA
FR796459.1/382440-382377 ACGGAGUGCAUUGAGUCCUACCGCUCCCC-ACCAGUAAGCGGGUGGGAGCAUCAACUCUCCUAGA
FN554974.1/454562-454500 GAGGUAUGCAUUGAGACCCACUGCCU-U-CAUAUGUAGGCGAGUGGGAGCAUCAGCAUCCCGAGA
FR799002.1/383101-383165 AAGGAGUGCAUUGAGUCCUACCGCUCCCCCACUACUGAGCGCGUGGGAGCAUCAACUCUCCGAGA
AY028385.2/414-477       AAGGCGCGCUUUGAGACCCACCGCCUCGC-AGCAGUGGGCGCGUGGGUGCAUCAGCGCCCCGAGA
#=GC SS_cons             ::<<<<-<-------<<<<<<<<<<<___.______>>>>>->>>>>>------->->>>>::::
#=GC RF                  AAGGaGUGCaUUGAGuCCCACCGCccCcC.AccagUggGCGcGUGGGaGCAUCAgCuCuCCGAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01541
#=GF ID   TB11Cs4H3
#=GF DE   Trypanosomatid snoRNA TB11Cs4H3
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   40.00
#=GF TC   40.60
#=GF NC   39.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   3


AAHB01000003.1/140391-140316 AGCGCAGCAUCCCUUGGGCCAGUGGCAACCAUUUAAUGCCGUGGGGAUGUGGCCCCUGUCCUGUUGCGCGAGAGCC
EF100612.1/333-406           AGCGCAACAUCCCUUGGGCCGGCGGCCUGCUGUUGGUGCCGCGCG--UGGCGCCCCUGUCCGAUUGUGCGAGAGUU
AAHK01014327.1/904-977       AGCGCAACAACCCUUGGGCCGGUGGCGCACUGUCGGUGCCGCGCG--UGGCGCCCCCUGUCGGUUGCGCGAGAGUU
#=GC SS_cons                 :<<<<<<<<------<<<<<_________________________..___>>>>>------>>>>>>>>:::::::
#=GC RF                      AGCGCAaCauCCCUUGGGCcgGUGGCauaCugUUggUGCCGcGcG..UGggGCCCCUgucCuGuUGCGCGAGAGuu
//
# STOCKHOLM 1.0

#=GF AC   RF01542
#=GF ID   TB11Cs5H1
#=GF DE   Trypanosomatid snoRNA TB11Cs5H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   45.00
#=GF TC   48.30
#=GF NC   32.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   2


AAHK01000645.1/2940-3009     AAGCACACACCAACCAGCCCCU-UCAGUGUUCUGGAAUACAUGCUGGUGGCCAAAGUGCGGUGCGAGAAAU
AAHB01000009.1/736763-736693 CAACACCCACCAACCAGCCCCUUUCUGUGCGGUAGCUUGCACAAUGGUGGCCAAAGUGUGGUGUGAGAUUU
#=GC SS_cons                 ::<<<<<<<<------<<<<<-----<<<<________>>>>--->>->>>---->>>->>>>>:::::::
#=GC RF                      aAgCACcCACCAACCAGCCCCUUUCugUGcugUaGauUgCAcaaUGGUGGCCAAAGUGugGUGcGAGAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF01543
#=GF ID   TB11Cs5H2
#=GF DE   Trypanosomatid snoRNA TB11Cs5H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   47.00
#=GF TC   47.10
#=GF NC   46.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18986541
#=GF RT   Psiscan: a computational approach to identify H/ACA-like and AGA-like
#=GF RT   non-coding RNA in trypanosomatid genomes.
#=GF RA   Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S,
#=GF RA   Unger R
#=GF RL   BMC Bioinformatics. 2008;9:471.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   5


FR796426.1/380009-380073   ACGCUGCAUCAGUACAGCGACAUCAUCUU-----UCCGAGUGGUGAUGCCUGCUGGCGAUGCCAGCAAGA
FN554974.1/4230305-4230238 AAGCAGCAUCAGUACAGCGGUGGUAUCGCUAAG-GCACCAUGAUGCUUUCCGCUGGCGAUGU-GGCGAGA
HE575324.1/4513176-4513109 AAGCAGCAUCAGUACAGCGGAGGUGCCCCAUUG-GCUCCAUGGCGCGUUCCGCUGGCGAUGC-GGCGAGA
AAHK01000645.1/3393-3461   AAGCAGCAUCAGUACAGCGGUGGCUCCACUAAAUACGCUAUGGUGCCAUUCGCUGGCGAUGU-GGCGAGA
FR799582.1/371343-371407   ACGCUGCAUCAGUACAGCGACAUCACCUU-----ACCGAGUGGUGAUGCCUGCUGGCGAUGCCAGCAAGA
#=GC SS_cons               ::<<-<<<<-----<<<<<--<<<<<<______._______>>>>>>--->>>>>--->>>>.->>::::
#=GC RF                    AaGCaGCAUCAGUACAGCGguggcacCucuaag.aCucaaUGgugccuuCCGCUGGCGAUGC.gGCgAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01544
#=GF ID   TB11Cs5H3
#=GF DE   Trypanosomatid snoRNA TB11Cs5H3
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   52.10
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18986541
#=GF RT   Psiscan: a computational approach to identify H/ACA-like and AGA-like
#=GF RT   non-coding RNA in trypanosomatid genomes.
#=GF RA   Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S,
#=GF RA   Unger R
#=GF RL   BMC Bioinformatics. 2008;9:471.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   5


AAHK01000038.1/50201-50138 AGGCCGGUUCGAAGGCCC-------UUCAUUC--AAUUGCUAU-GAGUGGGC-G----UGGUUCAAAGACUGGCCGAGA
FN554974.1/4230133-4230068 AGGUCAGUUCGAAGGCCCAGUA---CUUGUAC--CAUUG-UAA-GUGCAA--UG----UGGUUCAAAAGCUGACCAAGA
FR799005.1/554913-554981   AGCACAGUUCGAAGG-CCGUCAUUCUUUGUAUAACAUGU-AGA-AUGCAA--U-----CGGUUCAAAAUCUCUGCUAGA
FR796426.1/563108-563177   CGCACAGUUCGAAGG-CCGUCAUCCCCUGUACUACAUCU-UAGGGUGCUU--U-----CGGUUCAAAGGCUGUGCCAGA
FR796462.1/549991-550059   AGCAUAAUUCGAAGG-CCGUCA---UUCCUAC--UAUCC-CUU-GUGGAA--UGUAAUCGGUUCAAACAUUGUGCCAGA
#=GC SS_cons               :<<<<<<<<------.<<<-<<...-<<<<<<.._____.___.>>>>>>..>>....>>>------>>>>>>>>::::
#=GC RF                    AGcacAGuuCGAAGG.CCGUcA...UucgUaC..cAUuu.uau.GuGcga..Ug....CGGUUCAAAaaCUgugCuAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01545
#=GF ID   TB3Cs2H1
#=GF DE   Trypanosomatid snoRNA TB3Cs2H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   60.00
#=GF TC   62.50
#=GF NC   33.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18986541
#=GF RT   Psiscan: a computational approach to identify H/ACA-like and AGA-like
#=GF RT   non-coding RNA in trypanosomatid genomes.
#=GF RA   Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S,
#=GF RA   Unger R
#=GF RL   BMC Bioinformatics. 2008;9:471.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   2


AAHK01000562.1/23818-23886 AAUGAGGGACUAAGAGCUGCGGUAUUCGGUGUUUAUCCGUGCCUUCCACAGUGUCAUUGCCCUCAGAGA
AC096673.14/26249-26183    AAUGAGGGUCUAAGAGCUGGGGAC--CGGAACCUUUCCAUGUUCUUCCCAGUGUCAUUGCCCUCAGAGA
#=GC SS_cons               ::<<<<<<<------<<<<<<<<_____________________>>>>>>>>------>>>>>>>::::
#=GC RF                    AAUGAGGGcCUAAGAgCUGgGgaaUUCGGuauuUaUCCaUGuuuucCcCAGuGUCAUUgCCCUCAGAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01546
#=GF ID   TB6Cs1H1
#=GF DE   Trypanosomatid snoRNA TB6Cs1H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   40.00
#=GF TC   63.20
#=GF NC   36.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   6


AAHK01012838.1/375-440   CGGCCAGCGAAAACACAGGCGCCGUG-CUUGC-AACGAUCACUUCGCCUGCACCUGUGCUGCCCCAGA
AC013353.9/110996-110931 AGGCUAGCGAAAACACAGGCGUUUUG-CUUAC-GUCAAUCACUGCGUCUGCACCUGUGCUACCCGAGA
AAHK01012125.1/639-574   CGGCCAGCGAAAACACAGGCGCCGUG-CUUGC-AACGAUCACCUCGCCUGCACCUGUGCUGCCCCAGA
FR796458.1/633590-633657 AGGUCAGCGAAAACACAGUCGAAGUGGUAUUGACCCCGUCAUUUCGCCUGCACCUGUGCUGUCCGAGA
FR799579.1/612347-612414 AGGUCAGCGAAAACACAGUCGAAGCGGUAUUGACCCCGUCAUUUCGCCUGCACCUGUGCUGUCCGAGA
HE575319.1/404948-404883 AGGUCAGCGAAAACACAGGCGUUUUG-UUUAC-AUGGGUCACUGCGUCUGCACCUGUGCUGUCCGAGA
#=GC SS_cons             :<<-<<<<<------<<<<<<<--<<._____.______>>-->>>>>>>------>>>>>->>::::
#=GC RF                  aGGuCAGCGAAAACACAGgCGcuguG.uuUac.auCgaUCacUgCGcCUGCACCUGUGCUGuCCgAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01547
#=GF ID   TB6Cs1H3
#=GF DE   Trypanosomatid snoRNA TB6Cs1H3
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   40.00
#=GF TC   44.10
#=GF NC   32.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   5


AAHK01000712.1/945-879   ACCGCGGGUUGCACCGUUGUGGAGCACAAACAUUCAUUGCACCAACGGCGGACUUGCCCUCGGGAGA
AC013353.9/109432-109370 ACCGCGGGUUGCACCGUUGCGGGACACG----CUGAUUGUCCAUGUGACGGACUUGCCUGUGGAAGA
AC013353.9/111577-111515 ACCGCGGGUUGCACCGUUGCGGGACACG----CUGAUUGUCCAUGUGACGGACUUGCCUGUGGGAGA
FR798998.1/766101-766038 ACCAGGAGUAGCACCGUUGCGGAACACGG---CCCAUUGAUCUAUCGGCGGACUUGCUCUUGGGAGA
FR799613.1/641192-641255 ACCAGGAGUAGCACCGUUGCGGAACACGA---CCCAUUGAUCUAUCGGCGGACUUGCUCUUGGGAGA
#=GC SS_cons             :<<<<<<<------<<<<<--<<<<<___..._____>>>>>--->>>>>------>>>>>>>::::
#=GC RF                  ACCgcGGGUuGCACCGuUGCGGggCACGa...CucAUUGccCuauCGgCGGACUUGCCCgcGGGAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01548
#=GF ID   TB6Cs1H4
#=GF DE   Trypanosomatid snoRNA TB6Cs1H4
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   60.00
#=GF TC   70.90
#=GF NC   34.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   4


AAHK01030140.1/350-422   CCCCUCAACGUUAGAGGUCCCUUGGUGGCU---GUAU-CUAUCGAUGUCGCUUCACAGGAUACCCAUUGAGGCUAGA
AC013353.9/110422-110350 CACCUCAUUAUUAAAGGUCCCUUGGCGACU---GUAC-UUAUCGAUGCCGCUCCACAGGAUACCCAUUGAGGUUAGA
FR798998.1/765999-765924 CGCCGCG-CAUUCAAGGUCCCUUGGCGGCGAUUAUAUACCCUCGAUGCUGCUUCACAGGAUACCCAGCGUGGCCAGA
FR799579.1/615388-615463 CGCCGCG-CAUUCAAGGUCCCUUGGCGGCGAUUAUAUACCCUCGGUGCUGCUUCACAGGAUACCCAGCGUGGCCAGA
#=GC SS_cons             :<<<<<<---------<<<<----<<<<<_...____.________>>>>>------>>>>------>>>>>>::::
#=GC RF                  CgCCuCgucAUUaAAGgUCCCUUGGcggCu...aUAU.cuaUCGAUGccgCUUCACAGGAuACCCAucGaGGcuAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01549
#=GF ID   TB8Cs2H1
#=GF DE   Trypanosomatid snoRNA TB8Cs2H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   40.00
#=GF TC   41.20
#=GF NC   33.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   6


AAHK01028594.1/483-419     ACC-UGCACUUCGCUCGUCUCGCUCCCUUCCUCGUGAGCGUGUGGACGAUGGAUGGUGA-AGGGAGA
AC099045.21/121306-121367  ACC-UCCGCUUCGCUCGUGGCAUUCUUC---CAGUGAGCGCACUUACGAUGGAUGGUGG-AGGAAGA
FR799615.1/552183-552122   GCAGUUCGCAUCG-UCGUCGCAAAAGCAGCGCAGCGGUCG---UGAUGGUGGGUGGUGG-AGGAAGA
FR796432.1/1078115-1078052 ACC-UGCACUUCGCUCGUCCCGCUCGCGUGUCGAUGAGUG--GUGCCGAUGGAUGGUGUGAGGGAGA
HE575323.1/1787813-1787874 ACC-UCCGCUUCGCUCGUUGAACUCUUU---CUGUGAGUAUAUCUCCGAUGAACGGUGG-AGGAAGA
FN554971.1/400160-400221   ACC-UCCGCUUCGCUCGUGGCAUUCUUC---CAGUGAGUGCGCUUACGAUGGAUGGUGG-AGGAAGA
#=GC SS_cons               :<<.<<<<<-----<<<<<<<<<<<__________>>>>>--->>>>>>------>>>>.>>>::::
#=GC RF                    ACC.UcCgCUUCGCUCGucgCgcuCucuucuCaGUGagcGuaucgaCGAUGGAUGGuGg.AGGAAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01550
#=GF ID   TB8Cs3H1
#=GF DE   Trypanosomatid snoRNA TB8Cs3H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   45.00
#=GF TC   56.00
#=GF NC   31.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   7


AAHK01022453.1/206-268 AUGGGGUACGAAUGCGCCUGGUGGUGACUGCUCACCUUUGCGUGGGAAACGCCUCAAAGAAGC
AC159420.1/7886-7948   AUGAGGUUCGAAUGCGCCUGACGGUUUUUGUCCGACGUGGUGUGGGAAACGCCUCAAAGAAGU
FR796455.1/43976-44038 AUGGGGUUCGAAUGCGCUGGUCGAAACCGGUUUGCCCUAGCGUGGGAAACGCCCCAAAGAUCC
FR798998.1/39703-39765 AUGAGGCUCGAAUGCGCUGGUCAAGACUGGUUUGCCCGAGCGUGGGAAACGCCCCAAAGAGGU
FR796419.1/39405-39467 AUGGGGUUCGAAUGCGCUGGUCGAAACCGGUUUGCCCUAGCGUGGGAAACGCCCCAAAGAGCC
FR799576.1/39265-39327 AUGGGGUUCGAAUGCGCUGGCCGAAACCGGUUUGCCCUAGCGUGGGAAACGCCCCAAAGAUCC
AF050095.1/519-581     AUGGGGUUCGAAUGCGCCCGGUGACGCUGGUUCGCCAUGGCGUGGGAAACGCCCCAAAGAGUG
#=GC SS_cons           :<<<<<<------<<<<<<<-<<<_______>>>->>->>>>>------->>>>>>:::::::
#=GC RF                AUGgGGuUCGAAUGCGCcgGucgaaacugGUucgCCcUgGCGUGGGAAACgCCcCAAAGAagc
//
# STOCKHOLM 1.0

#=GF AC   RF01551
#=GF ID   TB8Cs4H2
#=GF DE   Trypanosomatid snoRNA TB8Cs4H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   56.30
#=GF NC   34.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18986541
#=GF RT   Psiscan: a computational approach to identify H/ACA-like and AGA-like
#=GF RT   non-coding RNA in trypanosomatid genomes.
#=GF RA   Myslyuk I, Doniger T, Horesh Y, Hury A, Hoffer R, Ziporen Y, Michaeli S,
#=GF RA   Unger R
#=GF RL   BMC Bioinformatics. 2008;9:471.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   2


AAHK01000232.1/46030-46097 ACCCGAGGGCCAUCGUCGGACGCCCCCG--CCUGCC-CAAUCGGGCUGCUCCGAAACAACACCCUCGCAGA
AC099045.21/83563-83632    AAACGAGGGACAUCGUCGGGGG-CUCUGAUUCAACUUCUGUGGGGCCAAACCGAAACAACACCUUCGAAGA
#=GC SS_cons               :::<<<<<<------<<<<--<.<<<<______________>>>>->--->>>>------->>>>>>::::
#=GC RF                    AaaCGAgGGaCAUCGUCGGagg.CcCuGAUuCaaCuUCuaUgGgGCcaaaCCGAAACAACACCcUCGaAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01552
#=GF ID   TB9Cs1H2
#=GF DE   Trypanosomatid snoRNA TB9Cs1H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   35.00
#=GF TC   42.00
#=GF NC   32.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   5


AAHK01002462.1/4028-3959 CACGGGGCAAUCCGAGGUGCCCGUGCGCUGU---------------GCUCUGCCGCGGUGGUGCCUUCUGGUAGUCCCGGAGAUG-
FR796458.1/633802-633887 AACGGGGCAAUCCGAGGUGCACGUGGCUUGCGCCCGCUCGCGGGACUCUGUGCCGUGGUGCGACCUUCUGGUAGCGCCGGAGAGCC
FN554972.1/374434-374365 CACGGGGCAAUCCGAGGUCAGUGAGC-----UUCA----------CUUCGUGCCGCAUGA-UGCCUUCUGGUGGCUCCGGAGAAGC
FR798998.1/764012-763927 AACGGGGCAAUCCGAGGUGCACGUGGCUUGCGCCCGCUCGCGGGGCUCGGUGCCGUGGUGCGACCUUCUGGUAGCACCGGAGAGCC
FR796422.1/673006-673091 AACGGGGCAAUCCGAGGUGCACGUGGCUUGCGCCCGCUCGCGGGACUGUGUGCCGUGGUGCGACCUUCUGGUAGCGCCGGAGAGCC
#=GC SS_cons             ::<<<-<<------<<<______________________________________________>>>------->>->>>:::::::
#=GC RF                  aACGGGGCAAUCCGAGGUgcacGUGgcuUGcgcCcGCUCGCGGGaCUcuGUGCCGuGGuGcgaCCUUCUGGUAGCuCCGGAGAgcC
//
# STOCKHOLM 1.0

#=GF AC   RF01553
#=GF ID   TB9Cs1H3
#=GF DE   Trypanosomatid snoRNA TB9Cs1H3
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   35.00
#=GF TC   35.80
#=GF NC   32.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   3


AAGZ01000003.1/383585-383520 UGAGAACGCGCUAUUAGCUCCCAACGG-GUAUGACUGCUUCCACUUGGGUUCCUGAGGCGUGUGAGA
FR798998.1/756193-756129     UGCCAACGCGCUAUU-GCUUCCGCUGCGGCGUGCCGAUGCGC-AGCGGGAUCCUGAGGUGCGUGAGA
FR796458.1/633683-633747     UGCCAACGCACUAUU-GCUCCCGCUGCUGCGUGUCGAUGAGC-AGCGGGUUCCUGAGGUGCGUGAGA
#=GC SS_cons                 :::::<<<<<<<---.---<<<<___________________.__>>>>------->>>>>>>::::
#=GC RF                      UGccAACGCgCUAUU.GCUCCCGcuGcuGcgUGaCgaugugC.agCGGGuUCCUGAGGcGCGUGAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01554
#=GF ID   TB9Cs2H1
#=GF DE   Trypanosomatid snoRNA TB9Cs2H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   45.00
#=GF TC   70.40
#=GF NC   33.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   4


AAHK01026543.1/41-107          GGACCACAUUGGAGUUGUGUCCUGGACCCG--CUGCGUUGUCCUUG-CUGCACACUCACGUGGUCCGAGA
AAGZ01000003.1/1401153-1401084 GGCCCACAUUGGAGUUGUGUCUUGGGCUAACAUUUCUGUGUCCUUGUUUGCACACUCACGUGGUCCGAGA
FR796431.1/1679987-1680052     GGCCCACAUUGGAGUUGUGUCCUGGCCCCA----GCAGUGGCCCUGUCUGCACACUCGCGUGGGCCAAGA
FR799009.1/1586401-1586466     GGCCCACAUUGGAGUUGUGUCUUGGCCGCA----GCGGUGGCCCUGCCUGCACACUCACGUGGGCCAAGA
#=GC SS_cons                   <<<<<<<---------<<<<---<<<<___.._______>>>>------>>>>------>>>>>>>::::
#=GC RF                        GGcCCACAUUGGAGUUGUGuCuUGGcCucA..uUgCggUGgCCuUGucUgCACACUCACGUGGgCCaAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01555
#=GF ID   TB9Cs3H1
#=GF DE   Trypanosomatid snoRNA TB9Cs3H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   45.00
#=GF TC   53.10
#=GF NC   33.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   6


AAHK01028073.1/619-688     CGCACAAUUU-ACACGGACCCGCCCUGGUGUUCUAC-CUUGGUGCCGGUGGU-GUCCGCCAGUGUUGUGCAAG
FN554972.1/1586904-1586972 AGCACAAUUU-ACACGGAUUCACCCUGACU-UAUAU-UUUAAUGCCGGUGUU-AUCCGCCAGUGUUGUGCCAG
FR796467.1/1323966-1323900 AGCCGAAUUAAACACGGAUCUGCG-AGAC---GUAC-UUCAGCUUUCGUGAG-AUCCGCCAGUGUUUUGCAAG
FR796401.1/450597-450665   AGUACGAUUAAACACGGACGCGCCGCUGC---AUACGCUUGGUGCUGGCGCC-GUCCGCCAGUGUCGUACGAG
FR799009.1/1240278-1240212 CGCAGAAUUAAACACGGAUCAACU-UGAC---CUAC-UUCAGUGUCAGUGGA-AUCCGCCAGUGUUUUGCAAG
AY495452.1/299-366         AGCACGAUAU-ACACGGAUACACCUUGGC---GAUA-CUCGGUGCCGGUGUCGAUCCGCCAGUGUCGUGCGAG
#=GC SS_cons               :<<<<<<<-------<<<<--<<---<<<...____.______>>>->>---.>>>>------>>>>>>>:::
#=GC RF                    AGCAcgAUUaAACACGGAuccaCcuuggc...aUAc.uUuaGUgccgGuGuu.aUCCGCCAGUGUcgUGCaAG
//
# STOCKHOLM 1.0

#=GF AC   RF01556
#=GF ID   TB9Cs3H2
#=GF DE   Trypanosomatid snoRNA TB9Cs3H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   51.10
#=GF NC   35.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   3


AAHK01028073.1/132-194     AGUGCCCUCAGGUAAUGUGGUGGUUGCGA-UCCCGUCAGCACCGCAGGUUCAAGAGGCACGAGA
FN554972.1/1587207-1587268 AGUGCCCUCAGGUAUUGUGGUGUUUGUU--GCUUAUCGCCAUCACAGGUUCAAGAGGCACAAGA
FR799592.1/451726-451789   AGUGCCGUCAGGUAAAGUGACGAUGGUGUGUCCCAUCCGCGCCACUGGUUCAGGCGGCACGAGA
#=GC SS_cons               :<<<<<--------<<<<<<<<----<__.____>---->>>>>>>>-------->>>>>::::
#=GC RF                    AGUGCCcUCAGGUAauGuGguGaUuGugu.uCccaUCagCacCaCagGUUCAAGaGGCACgAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01557
#=GF ID   TB9Cs4H1
#=GF DE   Trypanosomatid snoRNA TB9Cs4H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   40.00
#=GF TC   47.90
#=GF NC   33.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   4


AAHK01023180.1/143-203     UGAGGUCGA-AGUGUACCCCGCGUGCCCA--CCAAUGGCGUAU---CGGGGAAUGGAACCGACCGAG
FR799008.1/635706-635771   CGAGGUCUU-UGUGUACCCCGUGCGUCCCCACUUGUGACGCACACAUGGGGAAUGGACAGGACCGAG
FN554972.1/1641980-1642041 UAAGGUUGCCUGUGUACCUCAUGCGUCUC--UUUGUGGUGUUG---UGGGGAAUGAAGGCGACCGAG
FR799620.1/567236-567301   CGAGGUCUUC-GUGUACCCCGUGCGCCCCCACUCGUGGCGCACACAUGGGGAAUGGUCAAGACCGAG
#=GC SS_cons               :::<<<<<<-------<<<<<--<<<<__.._____>>>>---...>>>>>------->>>>>>:::
#=GC RF                    uGAGGUCguCuGUGUACCCCgUGCGcCCc..CUuGUGgCGuAc...cGGGGAAUGGAaacGACCGAG
//
# STOCKHOLM 1.0

#=GF AC   RF01558
#=GF ID   TB9Cs4H2
#=GF DE   Trypanosomatid snoRNA TB9Cs4H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   51.10
#=GF NC   38.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   5


AAHK01023180.1/366-436         AGGCCCUCCAGCUACCACGUGAAGCGUAUACUC--UCAGUCUUUGCGGA-GGUCGUUCUACUGGGCCAAGAGGC
AAGZ01000003.1/1698082-1698152 AGGCCCGCCAGCUACCACGUGGAGUGUAUACUC--UCUAUCUCUACGAC-GGUCGUUCUACCGGGCCAAGAAGC
FR799009.1/1588669-1588741     CGUCCCACCAGCUACCACGCGGAGUGUAUACCCCUUCAGUCUUCGCGGGCGGUCGUUUU-CUGGGCCAAGAUGC
FN554972.1/1645844-1645914     AGGCCCGCCAGCUACCACGUGGAGUGUAUACUC--UCUAUCUCUACGAC-GGUCGUUCUACCGGGCCAAGAAGC
FR796467.1/1658932-1659004     CGUCCCACCAGCUACCACGCGGAGUGCAUACCCUUUCAGUCUUCGCGGUCGGUCGUUUU-CUGGGCCAAGAUGC
#=GC SS_cons                   :<<<<<<------<<<-<<<<<<<_________.._____>>>>>>>--.>>>-------->>>>>>:::::::
#=GC RF                        aGgCCCgCCAGCUACCACGcggAGUGUAUACuC..UCagUCUccgCGgu.GGUCGUUcUACcGGGcCAAGAuGC
//
# STOCKHOLM 1.0

#=GF AC   RF01559
#=GF ID   DdR1
#=GF DE   Dictyostelium snoRNA DdR1
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   70.00
#=GF TC   80.80
#=GF NC   43.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.91 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ698945.1/1-66              UGAAUGAUGAAACAAACAGACCUGAUCUGA---------AC-AGUCAAUGUUGACCAAAACUAAGAAGUUCUGACU
AAFI02000040.1/500089-500154 UGAAUGAUGAAACAAACAGACCUGAUCUGA---------AC-AGUCAAUGUUGACCAAAACUAAGAAGUUCUGACU
ADID01000667.1/28045-28120   AAUAUGAUGAAAAAAACAGACCUGUACUGACAUUGCAAAACAAAACAGUGAGGAAUAAAUCUAAGAAGUUCUGACA
#=GC SS_cons                 ::::::::::::::::::::::::::::::.........::.::::::::::::::::::::::::::::::::::
#=GC RF                      ugaAUGAUGAAAcAAACAGACCUGauCUGA.........AC.AguCAgUGuuGAccAAAaCUAAGAAGUUCUGACu
//
# STOCKHOLM 1.0

#=GF AC   RF01560
#=GF ID   DdR10
#=GF DE   Dictyostelium snoRNA DdR10
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   48.00
#=GF TC   49.90
#=GF NC   43.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 40.08 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AJ699371.1/1-81                UUAAUGAUGAUACACAAAA---UC-AUAUGUCAAUUCCUUUAACAUGAAAUAG-AA--UGAUUAUAACGAUUUUCCAUUUAACUGACG
AAFI02000013.1/120819-120899   UUAAUGAUGAUACACAAAA---UC-AUAUGUCAAUUCCUUUAACAUGAAAUAG-AA--UGAUUAUAACGAUUUUCCAUUUAACUGACA
ADID01000479.1/7580-7497       UUAAUGAUGAUUAAAAAAA---UCUAUAUGUCAAUUCCUUUAACCUGAAAAAA-AAGCUGAUUAUAAAGAUUUUCCAUAAUUCUGACA
ADHC01000026.1/1640476-1640556 GAGAUGAUGAUAGAAAAAAAAAUC-UAUAGUCAAUUCCUUUAACAUGAAACAGCUA--UGAUU--AAUGAU--UCAAUAUAUCUGACU
#=GC SS_cons                   :::::::::::::::::::...::.::::::::::::::::::::::::::::.::..::::::::::::::::::::::::::::::
#=GC RF                        uuaAUGAUGAUacAaAAAA...UC.auauGUCAAUUCCUUUAACaUGAAAuAG.aA..UGAUUAUAAcGAUUUUCcAUauauCUGACa
//
# STOCKHOLM 1.0

#=GF AC   RF01561
#=GF ID   DdR11
#=GF DE   Dictyostelium snoRNA DdR11
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   65.00
#=GF TC   80.70
#=GF NC   40.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.03 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AAFI02000019.1/388135-388060 UUAAUGAUGUAUUCCUCAGCUCACACCGACCACGAUGACGACAAAAAACUUUGUUCCUUAUUUUUAUUGUCUGACA
AJ699372.1/1-75              UCAAUGAUGUAUUCCUCAGCUCACACCGACCACGAUGACGACAAAAAACUUUGUUCCUUAUUUUUA-UGUCUGACA
ADID01000600.1/18555-18482   UUAAUGAUGUAUUC-ACAGCUCACACCAACCACGAUGACGACAAACAAACUUGUUCCUUGAU-AUAUUGGCUGAAU
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UuAAUGAUGUAUUCCuCAGCUCACACCGACCACGAUGACGACAAAaAAcuUUGUUCCUUauUUuUAUUGuCUGAca
//
# STOCKHOLM 1.0

#=GF AC   RF01562
#=GF ID   DdR12
#=GF DE   D. discoideum snoRNA DdR12
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   70.00
#=GF TC   110.10
#=GF NC   37.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AJ699373.1/1-75              UAAGUGAUGAGAUUUAUUUCAUGUGUUUCAGAUGAUUACAUCCUGAUUAUAACCUAUGACGAAAAUUGACUGAUU
AAFI02000109.1/111070-110996 UAAGUGAUGAGAUUUAUUUCAUGUGUUUCAGAUGAUUACAUCCUGAUUAUAACCUAUGACGAAAAUUGACUGAUU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UAAGUGAUGAGAUUUAUUUCAUGUGUUUCAGAUGAUUACAUCCUGAUUAUAACCUAUGACGAAAAUUGACUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01563
#=GF ID   DdR13
#=GF DE   Dictyostelium snoRNA DdR13
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   65.00
#=GF TC   88.90
#=GF NC   32.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.91 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ699374.1/1-80              GGAAUGAUGAUUGACAACCGCCCCAGUCUGCAAUCUUAAUGAUGA--UUCGGAUUUACAAGACACGCCAGUUUUGCUUCUGA
AAFI02000040.1/499806-499884 UGAAUGAUGAUAUAUCACCGCCCCAGUCA-UAAUUUUUGUGCUGA--UUCGGAUUUACAGAACACGCCAGUUUUGCUUCUGA
ADID01000667.1/27682-27758   UGUAUGAUGAUACAC-ACCGCCCCAGUCUGCAACAUCAUUGCUGACAUACGGAU----AAAACACGCCAGUUUUGCUACUGA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::..:::::::::::::::::::::::::::::::::::
#=GC RF                      uGaAUGAUGAUauAcaACCGCCCCAGUCuGcAAuuUuauUGcUGA..UuCGGAUUUACAaaACACGCCAGUUUUGCUuCUGA
//
# STOCKHOLM 1.0

#=GF AC   RF01564
#=GF ID   DdR14
#=GF DE   D. discoideum snoRNA DdR14
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   80.00
#=GF TC   95.10
#=GF NC   37.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AAFI02000039.1/102443-102507 AUUAUCCUAUACUUUAGAACCCAUAGUGAAAUGAUUUUACAACCUUCUUUAGAAGACGUCUGAUU
AJ699375.1/1-65              AUUAUCCUAUACUUUAGAACCCAUAGUGAAAUGAUUUUACAACCUUCUUUAGAAGACGUCUGAUU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      AUUAUCCUAUACUUUAGAACCCAUAGUGAAAUGAUUUUACAACCUUCUUUAGAAGACGUCUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01565
#=GF ID   DdR15
#=GF DE   Dictyostelium snoRNA DdR15
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   70.00
#=GF TC   118.00
#=GF NC   40.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.57 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ699376.1/1-113           UAGCUGAUGAAAACCUAGAUGACGAGUCAUAAUUCUCUACAAGGUUCACUUAUUUGAUUAGGUUUCCUAAUACAA--ACGUUUACCUUGUCUGUUGAUGAUCUUUGGCCCUGAUU
AAFI02000049.1/53505-53617 UAGCUGAUGAAAACCUAGAUGACGAGUCAUAAUUCUCUACAAGGUUCACUUAUUUGAUUAGGUUUCCUAAUACAA--ACGUUUACCUUGUCUGUUGAUGAUCUUUGGCCCUGAUU
ADID01000659.1/13005-13117 UAGAUGAUGAAAACUUAGAUGACGAGUCAUAAUUUUCUACGAGGG--AUUAAUUCUUUUAGGUUUUCUAGGAGAAUUAAUUUUCCCUUGAUAGUUGAUGAUUUUGGCGCCUGAUU
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..::::::::::::::::::::::::::::::::::::::
#=GC RF                    UAGcUGAUGAAAACcUAGAUGACGAGUCAUAAUUcUCUACaAGGuUCAcUuAUUugaUUAGGUUUcCUAauAcAA..AcgUUUaCCUUGucuGUUGAUGAUcUUuGgcCCUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01566
#=GF ID   DdR16
#=GF DE   Dictyostelium snoRNA DdR16
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   70.00
#=GF TC   73.80
#=GF NC   40.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.02 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AJ699377.1/1-78            AAUAUGAUG-AAGUAU--UCAAACUCAGCU--CUAUGAAAUCUGUGAUUACUCAAUUUGAUUUCUCACGACAGUCUUCUGACA
AAFI02000135.1/6224-6148   AAUAUGAUG-AAGUAA--UUCAACUCAGCU--CUAUGAAAUCUGUGAUUACUCAAU-UGAUUUCUCACGACAGUCUUCUGACA
ADID01000101.1/93885-93964 UUUAUGAUGGAAGUAAAUCUAUACUCAGCU--CUAUGAUCUCUGUGAUUACUCAAU-AGUUUUCUCACGACAGUCUUCUGACA
AEYA01001051.1/51140-51068 CUUAUGAUG-A--CAA--UUUAAUCCAGCUCACUCUGAAAACUGUGAUGAG-CA-UUUUAU---UCACGACAGUCUUCUGACA
#=GC SS_cons               :::::::::.::::::..::::::::::::..:::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    auUAUGAUG.AAGUAa..UUaaACUCAGCU..CUaUGAaauCUGUGAUuAcUCAAUUuGaUUUCUCACGACAGUCUUCUGACA
//
# STOCKHOLM 1.0

#=GF AC   RF01567
#=GF ID   DdR17
#=GF DE   D. discoideum snoRNA DdR17
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   80.00
#=GF TC   101.20
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AAFI02000013.1/1197997-1198066 UAAAUGAUGAUCAAAAUAUAUUUGCUAUUCUUAGUUAUUUAUCAAUCAUGCUGAAUGGAAAUUUCUGAUU
AJ699378.1/1-70                UAAAUGAUGAUCAAAAUAUAUUUGCUAUUCUUAGUUAUUUAUCAAUCAUGCUGAAUGGAAAUUUCUGAUU
#=GC SS_cons                   ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                        UAAAUGAUGAUCAAAAUAUAUUUGCUAUUCUUAGUUAUUUAUCAAUCAUGCUGAAUGGAAAUUUCUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01568
#=GF ID   DdR18
#=GF DE   Dictyostelium snoRNA DdR18
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:15333696
#=GF GA   80.00
#=GF TC   125.70
#=GF NC   37.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.82 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AAFI02000024.1/236827-236973 ACUCAACAGCCUGCCUCCGUUUUGU-GUUUGGUUCUUUU-AU----ACCAAAUAAACA-AGUUUUAUGGCAAGAAGCUCAUAAUAAACAUACAUGUGCCUUUAAUCAAUCUGUAAUCUGUUCUAUUACACGAUUUUCAUGCAGUCACAACAACU
AJ699379.1/1-147             ACUCAACAGCCUGCCUCCGUUUUGU-GUUUGGUUCUUUU-AU----ACCAAAUAAACA-AGUUUUAUGGCAAGAAGCUCAUAAUAAACAUACAUGUGCCUUUAAUCAAUCUGUAAUCUGUUCUAUUACACGAUUUUCAUGCAGUCACAACAACG
ADID01000307.1/8024-7880     AAUUUUGAGCGUA---CCGUGGGGGGAUUGGGUUCUUUUUAUACCAAUCUAAUAAUAAACCUGUUU---UAAUAUGCUCAAAGAAAAAAU---GGUGCCUUUAAUCAAUCGGUAAUCUGUUCUAUUACUGGAUUUUCAUGCAGUCACUACAUUC
#=GC SS_cons                 :::::::<<<-<<<<-----<<<<<.<<<<<<<______.__....>>>>>>>-->>>.>>------>>>>---->>>---------------<<<<-<<-<<---<<<<<<<<<<_______>>>>>>->>>>---->>->>->>>>::::::
#=GC RF                      AaUcaacaGCcugCCUCCGUggugu.auuuGguUCUUUU.AU....acCaaauAAaca.ccUuUUaUGGcaAgAaGCuCAuAauAAAaAUAcAuGuGCCuUuaAUCaauCuGuaauCUGUUCUauuaCacGauuUUCAugCaGUCaCaACAacu
//
# STOCKHOLM 1.0

#=GF AC   RF01569
#=GF ID   DdR2
#=GF DE   Dictyostelium snoRNA DdR2
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;
#=GF GA   80.00
#=GF TC   101.50
#=GF NC   42.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.74 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ698946.1/1-83            UAGAUGAUGAUUUCUUUCCCCGUCCGACACGACUGUGAUUGACAAGAUAAGAUUUAAUUUUUAAUUAAGCCAAAAAC-UCUGAU
AJ703792.1/1-82            -AAAUGAUGAUUUCUUUCCCCGUCCGACACGACUGUGAUUGACAAGAUAAGAUUUAAUAUUUUAUUAAGCCAAAAAC-UCUGAU
ADID01000090.1/48191-48274 AUUAUGAUGAUUCCUUUCCCCGUCUUACUCGACUAUGCUUGAAAACAUAAGGUUUACUAUUAAUUCUAGCCAAAAACAUCUGAU
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::
#=GC RF                    uauAUGAUGAUUuCUUUCCCCGUCcgACaCGACUGUGaUUGAcAAgAUAAGaUUUAaUaUUuaaUuaAGCCAAAAAC.UCUGAU
//
# STOCKHOLM 1.0

#=GF AC   RF01570
#=GF ID   Dictyostelium_SRP
#=GF PI   DdR20
#=GF DE   Dictyostelium signal recognition particle
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:15333696
#=GF GA   90.00
#=GF TC   249.10
#=GF NC   63.60
#=GF TP   Gene; snRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17.33 -Z 549862.597050 CM SEQDB
#=GF CL   CL00003
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Signal_recognition_particle_RNA
#=GF SQ   3


AJ699381.1/1-278               AUGCAGGAUUGGGUAGCGGCAACCUGUAA-UCA-----AGCGAUGCAUUCGAGGCGAGGACG--AGAGCAUUGUUAGGACCUUUGGGACAAGCGACGCAUAC-AGUUGAUCCACACUAACGUUGGUGUCGACAUACUAUCAGUCUCUAAGGAUU-GAAAGUAAGUUGAUAAUGACCAAGUCAAGGUCCAGGCUGGCAACAGAGCAGACAGAGCGAGGCACAUCGAUGGGUAGCGAGGAAAGUCGACUUAAAGUCGUCCAAAGGAAAUAACAAUGUAAACU-CGAACAAA
AAFI02000003.1/1572065-1571783 AUGCAGGAUUUAGUUGCGAUUAUCUAUAA-CCUCUUGCUGAGGUGCGUUAGAGGAGAGGAUG--AGAGCAUUGUUAAGACCAUUGGGGAAAACGACGCAUAG-AGUUGAUCCACACUUACGUUGGUGUCGACAUACCUUGAGUCCAUAAGGAUU-GAAAGUAAGUUGAUAAUGACCGAGUCAAGGUCCAGGCUGGCAACAGAGCAGACAGAGCGAGGCACAUCGAUGGGAAGCGAGGAAAGUCGACUUAAAGUUGUCCAAAGGAAAUAACAAUGUAAACU-CAGACAAA
ADID01000417.1/32900-33182     AUCCAUGGCUGGGU-GUUAUAACCUGUAAUCCAAAAGAAGCCUUGGGAGUA-----AGGAUGGGGGAGGUUGGUCAGAGUUAAUGGAAAAAACACAGCAUAAAAGAUGAUCCACUGUUACAGCGGGGUCAACAUCCACAGAGUCCGUAUGGAUUACUGCGAAGGUUGAUAAUGACAGAUCCUAGGUACAGGCUAGCAAUAGAGCACACAAAGAAAUGCGCCUCGUCGGGAGUGGGGGAAAGUCAUCCUAAAUGUGUCCAAAGAUAAUGAUUAGCUAAACUUCAGACAAA
#=GC SS_cons                   <<<<<-<<<<<<<<_______>>>>-->>.>>----------->>>>><<<___>>>---((..((-(((((((((---(((((((-----(((((---((-.(((((((((---(((-(((((((<<<<<<-<<<<-<<<<<<<____>>>>>.>>->>>>->>>>>>,,<<-<<--<<<---<<<----<<<____>>>---->>>->>->-->>>>,)))))))--)))---)))---))))))))--))))))))))))---)))))))))---)).))::::::
#=GC RF                        acgCagGguuggGuaGcgauaaCccgUaa.cCaaaaGaaGcguuGcguucgAGGcgaGGAcG..aGAgcauugucaggacccuuGGgaaAAaCgccGCAuaa.aGucGauCCACacuuACgucGggguCgaCAucCcuugaguCcaUAagGauu.caagGgaaGucGauAAuGACcgAgucaAGGucCAGGCugGCAAcaGAGCAgaCAgaGcgAgGCaCcuCgacGGGaagcGaGGaAAGuCgaCuuaAAggcGuCCaagggaAAugacaauguAAACu.CggACAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01571
#=GF ID   DdR35
#=GF DE   D. discoideum class II sRNA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:15333696
#=GF GA   60.00
#=GF TC   91.10
#=GF NC   38.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Dictyostelium_class_II_RNA
#=GF SQ   3


AJ699396.1/1-59              AAGCUCGCCUUACAGCAAUUACUCUGA-UUUUUCUCCAAAAAAAAAACCUUCGCGAGUUG
AF482392.1/336-394           AAGCUCGCCUUACAGCAAUUACUCUGA-UUUUUCUCCAAAAAAAAAACCUUCGCGAGUUG
AAFI02000031.1/281317-281258 AAGCUCGCCUUACAGCAAUUACUCUGAAUUUUUCUCCAAAAAAAAACCCUUCGCGAGUUG
#=GC SS_cons                 :(((((((,,,,<<<________>>>,.<<<<<________>>>>>,,,,,,))))))):
#=GC RF                      AAgCUCGCCUUACAGCAAUUACUCUGA.UUUUUCUCCAAAAAAAAAaCCUUCGCGAGuUG
//
# STOCKHOLM 1.0

#=GF AC   RF01572
#=GF ID   DdR4
#=GF DE   Dictyostelium snoRNA DdR4
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   70.00
#=GF TC   122.60
#=GF NC   38.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.68 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ703793.1/1-106             UAAGUGAUGAUAACCCAAAUAGAAAUUUUUUUUUGAUUCCUUUCGAUUCUCUGUUCUAGAGCGUUGGGGGAUACUCUGUGAUUCUAUAUUCAUAGUUACUCUGAUA
AAFI02000024.1/237109-237214 UAAGUGAUGAUAACCCAAAUAGAAAUUUUUUUUUGAUUCCUUUCGAUUCUCUGUUCUAGAGCGUUGGGGGAUACUCUGUGAUUCUAUAUUCAUAGUUACUCUGAUU
ADID01000307.1/7372-7267     CGAAUGAUGAUAACCUAAAUAAUAAUCUCUUGCUGAUUCCUUUUGAUAUUCCGUUCUGGAAUAUUGGGGGAUACUCUGUGACUCUUUAUUCAUAGUUACUCUGACU
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      uaAgUGAUGAUAACCcAAAUAgaAAUuUuUUuuUGAUUCCUUUcGAUucUCuGUUCUaGAgcgUUGGGGGAUACUCUGUGAuUCUaUAUUCAUAGUUACUCUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF01573
#=GF ID   DdR5
#=GF DE   Dictyostelium snoRNA DdR5
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;
#=GF GA   70.00
#=GF TC   107.30
#=GF NC   39.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.08 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AJ703794.1/1-81            UCUAUGAUGAGUAUCGGACACUUUUGAACUUAAUUGAAAACGAAACACGAUUU-UUUGCGUUAUCUAAAUUUUCCUCUGA-CA
AAFI02000135.1/5897-5817   UCUAUGAUGAGUAUCGGACACUUUUGAACUUAAUUGAAAACGAAACACGAUUU-UUUGCGUUAUCUAAAUUUUCCUCUGA-CA
ADID01000101.1/94473-94555 UCUAUGAUGAGUAUCGGACACUUUUGAACUUAUUUGAAAACAAAACACGAUUUUUUUGCGUUAUCUAAUAUUUUCACUGAACA
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::.::
#=GC RF                    UCUAUGAUGAGUAUCGGACACUUUUGAACUUAaUUGAAAACgAAACACGAUUU.UUUGCGUUAUCUAAauUUUcCuCUGA.CA
//
# STOCKHOLM 1.0

#=GF AC   RF01574
#=GF ID   DdR6
#=GF DE   Dictyostelium snoRNA DdR6
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   90.00
#=GF TC   103.00
#=GF NC   37.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.47 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3



ADID01000140.1/43579-43495   UCAAUGAUGAUAUAAUUUAUCCCUGUCUUAGC-UUUCUGUCAUGCUGAAAAAU-CAUGGUAGCCUGUGGUAAGG-CUUUUACCUGACA
AJ699367.1/1-86              UUAAUGAUGAAAUAAUUUAUCCCUGUCUUAGUAUUUCUGUCUUGCUGAGAAAAU--UGUUGGCCUGUGGUAAGGUCUUUAACCUGACA
AAFI02000019.1/530860-530775 UUAAUGAUGAAAUAAUUUAUCCCUGUCUUAGUAUUUCUGUCUUGCUGAGAAAAU--UGUUGGCCUGUGGUAAGGUCUUUAACCUGACA
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::..::::::::::::::::::::::::::::::::
#=GC RF                      UuAAUGAUGAaAUAAUUUAUCCCUGUCUUAGuAUUUCUGUCuUGCUGAgAAAau..UGuUgGCCUGUGGUAAGGUCUUUaACCUGACA
//
# STOCKHOLM 1.0

#=GF AC   RF01575
#=GF ID   DdR7
#=GF DE   Dictyostelium snoRNA Dd7
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   80.00
#=GF TC   109.90
#=GF NC   34.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.31 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3



ADID01000475.1/21144-21245 AGUAUGAUGAUAGGUUGCACAUUAUCUGAUCGUCUUUUGAGCUCGCUUUAAGUAGUAGGCUUUGAAAUCAAUUGAUCCAGGGCUUAGGCCCCCCUCUGACUA
AJ699368.1/1-98            UGAAUGAUGAUUGGUUGCACAUUAUCUGAUCGUCUGUUGAGCUCGCGUUCAUUCGUAGGCUUUGAAAUUAACCGUCCGUG----UUCGCACAAAUCUGACCA
AAFI02000129.1/52136-52039 UGAAUGAUGAUUGGUUGCACAUUAUCUGAUCGUCUGUUGAGCUCGCGUUCAUUCGUAGGCUUUGAAAUUAACCGUCCGUG----UUCGCACAAAUCUGACCA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::....::::::::::::::::::
#=GC RF                    uGaAUGAUGAUuGGUUGCACAUUAUCUGAUCGUCUgUUGAGCUCGCgUUcAuUcGUAGGCUUUGAAAUuAAccGucCguG....UucGCaCaaaUCUGACcA
//
# STOCKHOLM 1.0

#=GF AC   RF01576
#=GF ID   DdR8
#=GF DE   D. discoideum snoRNA DdR8
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   80.00
#=GF TC   123.80
#=GF NC   33.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15333696
#=GF RT   Novel non-coding RNAs in Dictyostelium discoideum and their expression
#=GF RT   during development.
#=GF RA   Aspegren A, Hinas A, Larsson P, Larsson A, Soderbom F
#=GF RL   Nucleic Acids Res. 2004;32:4646-4656.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AJ699369.1/1-88              CCAGUGAUGAACGUAAUUUGCGUAUGAACUAGCAGACAUCAUUUGUGUUCUCGUCUCUAGCUUUGAUCGAUCAUUUAUUGUCUCUGAG
AAFI02000085.1/500501-500414 CCAGUGAUGAACGUAAUUUGCGUAUGAACUAGCAGACAUCAUUUGUGUUCUCGUCUCUAGCUUUGAUCGAUCAUUUAUUGUCUCUGAG
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      CCAGUGAUGAACGUAAUUUGCGUAUGAACUAGCAGACAUCAUUUGUGUUCUCGUCUCUAGCUUUGAUCGAUCAUUUAUUGUCUCUGAG
//
# STOCKHOLM 1.0

#=GF AC   RF01577
#=GF ID   RNase_P
#=GF DE   Plasmodium RNase_P
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:17901154
#=GF GA   100.00
#=GF TC   155.90
#=GF NC   91.80
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00002
#=GF DR   SO; 0000374; ribozyme;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Ribonuclease_P
#=GF SQ   2


AE001362.1/767014-766389 UAUGCAAUGAGUUUAAGCUCAAAACAUCCUGCAAAUAUACAUACACAAAAUGAAAGAAAGAAAUAAAAAAGAAAAAAGAAAAAAUGGAAAAAUAGGUCACAUAUUUGUAUGUUUCUUGUUUUUCCAUUUUUUUUUUUUUUUUUUUUUUUCCUUUUUCUUUCUCCUAAUUUGUGUAAUUUUUAUAAAAACAGGAAGGAAGGUCUGAGAUGCUGCAUUUAAAGAAUAGAAAAGAAAAGUCAAUGAAUUUUAAUUUUUUUUUUUUUUUUUUUUAUAAUUCUUAUGAAUUAAAAAGAAAGAAAAAAAAAGUUAUAACAUUCGUUGUUACUUUUUAUUUCACAUAUAUAUAUAUAUAUAUAUUCUUUAAUAAAAUUUUUGAGAGAAAAUGUAUUGAACAAAUAUUAAUUAGUUACCAGAAAUAUCAAUCAUAUAUUUAAAAUUUCGUAAGAAGUUUUGUGUAUGGUUUUGAAAAAGCUAAUAAGCAAGUAUACAUUGGUGAGUUCGAUUUUUGAGGUUUUUCUUUAUUCCUACAUCUCAUAUAUCAAUAUUUUUUUUAUAAUUAUAUAUUAUACGAGGUGAUAAUAAGAAAAAUAACUUAAUUCAGACUACUCCUAAAUUCAUUGCUGCAA
ABGV01007094.1/642-28    UAUGCAAUGAGUUUAAGCUCAAAACAUCCUGCAAAUAUACAUACACAAAAUGAAAGAAAGAAAUAAAAAAGAAAAAAGAAAAAAUGGAAAAAUAGGUCACAUAUUUGUAUGUUUCUUGUUUUUCCAUUUUUUUUUUUUUUUUUUUUUUUCCUUUUUCUUUCUCCUAAUUUGUGUAAUUUUUAUAAAAACAGGAAGGAAGGUCUGAGAUGCUGCAUUUAAAGAAUAGAAAAGAAAAGUCAAUGAAUUUUAAUUUUUU---------UUUUUAUAAUUCUUAUGAAUUAAAAAGAAAGAAAAAAAAAGUUAUAACAUUCGUUGUUACUUUUUAUUUCACAUAUAUAUA--UAUAUAUAUUCUUUAAUAAAAUUUUUGAGAGAAAAAGUAUUGAACAAAUAUUAAUUAGUUACCAGAAAUAUCAAUCAUAUAUUUAAAAUUUCGUAAGAAGUUUUGUGUAUGGUUUUGAAAAAGCUAAUAAGCAAGUAUACAUUGGUGAGUUCGAUUUUUGAGGUUUUUCUUUAUUCCUACAUCUCAUAUAUCAAUAUUUUUUUUAUAAUUAUAUAUUAUACGAGGUGAUAAUAAGAAAAAUAACUUAAUUCAGACUACUCCUAACUUCAUUGCUGCAA
#=GC SS_cons             :::{{{{{{{{{{{{,,[[[[[[[,,<<<<<----------<<<<<<<________________________________________________________________________________________________________________________>>>>>>>------------->>>>>,,,,AAA,AAAAA(((((((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,<<<<<<____>>>>>>,,,,,,,,,,,,,,<<<-<<<<<<---------------<<<<<<<--<<<<<<<<____>>>>>>>>>>>>>>>---------->>>>>>>>>))-))))),,,,,,,,,,,,,,,,,]]]]]]]<<<<<<<_________________________________________________________________>>>>>>>,,,,,,,aaaaaaaa,,,,,}}}}}}}}}}}}:::::
#=GC RF                  UAUGCaauGaguuuaAGCuCaaaaCAuCCuGCAAAUAUACAuaCaCaaAAUGAAAGAAAGAAAUAAAAAAGAAAAAAGAAAAAAUGGAAAAAUAGGUCACAUAUUUGUAUGUUUCUUGUUUUUCCAUUUUUUUUUUUUUUUUUUUUUUUCCUUUUUCUUUCUCCUAAUuuGuGuaAUUUUUAUAAAAACaGGaAGGAAGGUCUGAGaugCuGCAUUUAAAGAAUAGAAAAGAAAAGUCAAUGAAUUUUAAUUUUUUUUUUUUUUUUUUUUAUAAUUCUUAUGAAUUAAAAAGAAAGAAAAAAAAAGUUAUAACAUUCGUUGUUACUUUUUAUUUCACauauauauAUAUauauauauUCUUUAAUAAAauuuuuGAGAgaaaauGUAUUGAACAAAUAuuaAuuaGuuACCAGAAAUAUCAAUCauauauUUaaaauuuCGUAAGaaguuuuguguauGGUUUUGAAAAagCuaauaaGCAaGuauACAUUGGUGAGUUCGAUuuuuGaGguuuuuCUUUAUUCCUACAUCUCAUAUAUCAAUAUUUUUUUUAUAAUUAUAUAUUAUACGAGGUGAUAAUAAGaaaaauAACUUAAUUCAGACUACUCCuaaauuCauuGCUGCAA
//
# STOCKHOLM 1.0

#=GF AC   RF01578
#=GF ID   RUF1
#=GF DE   Plasmodium RNA of unkown function RUF1
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   70.00
#=GF TC   87.60
#=GF NC   43.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Plasmodium_RUF1_RNA
#=GF SQ   3


ABHA01002293.1/730-967     UGGUUAAAUUACACUCAACGAUUUAAUUUUUUUUUUUGAAUAUUUUAUCGUUAUUUAUUUUUUAACCUAAAUUAAGUUAUCAUUCAAUUUUUUAUUUUCCAAAAAUAAAAAUUGUAUUGAUAUUUCUCUUCAUAUUCCCGGUAUUUUCAACGCCCAUAAUAGGGCAGCUUCUUGUUAAGUAGUGUUGAUUUUGCCGUAACAAAACGGCGAGGAGACAAAUAUAAAUGAAAUAAAAAAU---------------------------
AANS01001205.1/23509-23246 UGGUUAAAUUACACUCAACGAUUUAAUUUUUUUUUUUGAAUAUUUUAUCGUUAUUUAUUUUUUAACCUAAAUUAAGUUAUCAUUCAAUUUUUUAUUUUCCAAAAAUAAAAAUUGUAUUGAUAUUUCUCUUCAUAUUCCCGGUAUUUUCAACGCCCAUAAUAGGGCAGCUUCUUGUUAAGUAGUGUUGAUUUUGCCGUAACAAAACGGAGAGGA-ACAAAUAUAAAUGAAAUAAAAAAUAUGUAAAAAUAAAUGAAUAUUAUAUGG
AASM01000666.1/1920-1657   UGCUUAAAUUACACUCCACGAUUUAAUUUUUUUUUCUGAAUAUUUUAUCGUUAUUUAUUUUUUAACCUAAAUUAAGUUAUCAUUCAAUUUUUUAUUUUCCAAAAAUAAAAAUUGUAUUGAUAUUUCUCUUCAUAUUCCCGGUAUUUUCAACGCCCAUAAUAGGGCAGCUUCUUGUUAAGUAGUGUUGAUUUUGCCGUAACAAAACGGAGAGGA-ACAAAUAUAAAUGAAAUAAAAAAUAUGUAAAAAUAAAUGAAUAUUAUAUGG
#=GC SS_cons               :<<<<<<<--------<<<<<<--<<<-<<<______>>>->>>-->>>>>>-------->>>>>>>---------------{{{{,,<<<<<<<<<_____>>>>>>>>>[[[[[[[-----[[[[[[[[,,,,,,,,((((---(((((<<<<______>>>>,<<<-<<_____>>->>>)))))---))))<<______>>]]]]]]]].---]]]]]]],}}}}::::::::::::::::::::::::::::::::::::
#=GC RF                    UGguuaaaUUACACUCaaCGauUUaauUuuuUUUUuUgaaUauuUUauCGuuAUUUAUUUuuuaacCUAAAUUAAGUUAUCAuuCaAUuuuuuauuuUCCAAaaauaaaaauuguauuGAUAUuuCuCuuCAUAUUCCCGGuaUUUuCaaCGCCCAUAAUAGGGCAgCuUCuUGUUAaGUaGuGuuGaUUUugCCGuAACAAAaCGgaGaGga.ACAaauauaaAuGaaAUAAAAAAUAUGUAAAAAUAAAUGAAUAUUAUAUGG
//
# STOCKHOLM 1.0

#=GF AC   RF01579
#=GF ID   RUF2
#=GF DE   Plasmodium RNA of unknown function RUF2
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   90.00
#=GF TC   110.70
#=GF NC   52.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Plasmodium_RUF2_RNA
#=GF SQ   3


AABL01001458.1/5179-5331 UUAUUUAAAUAUUUAUUUAAGUAUUUAUU-UAAAUGUUUAUUUAAAUAUUUUUAAACA--------AAUAAUAACGUCAAACUUGUUCAUACAACAAAUGUAUAUACGGUGGCUUUUUAAAUU-UUGAUUUUAAAAGUGUCAAUCCAUAUAUAUCACAGACCU
CAAJ01001233.1/1534-1687 UUCAUUGAACAUUUCGAAGGGCUAUUAUG-AAAAUAUUUAUUUAAAUAUUUUUAAACA--------AAUAAUAGCAUCAAAUUUGUUCAUAAAACAAAUGUAUAUACGGUGGCUUUUUAAAUUUUUAAUUUUAAAAGUGUCAAUCCAUAUAUAUCACAGCACC
AM910986.1/47547-47704   ACCAUUGAACGAUUCGAAGAGUUAUUAUUGUGAAUAUUUUUUUC-----CAAAAAAUAUGUCCAAAAAUAUUAGCUUCAAAUCUGUUCAUAUAACAAAUGUAUAUACGGUGGCUUUUUAAAUUUUUAAUUUUAGAAAUGUCAAUCCAUAUAUAUCACAGAGAA
#=GC SS_cons             :::::<<<<<<---------<<<<<<<<<.----<<<<<<____________>>>>>>........>>>>>>>>>-------->>>>>>----------<<<<<<<-<<<<<<<<<<<<<<________>>>>>>>>->>>>-->>->>>>>>>:::::::::
#=GC RF                  uucaUugaacauUUcgaagaGcuauuauu.uaAAuguuuaUUUaAAUAUuuuuaaaca........aauaauagCuUCAAAuuuguucaUAuAACAAAUguauauaCGGuGgCcuuuuaaaUUUUUaAUuuuaaaagUGuCaAUCCAuauauauCACAGaacu
//
# STOCKHOLM 1.0

#=GF AC   RF01580
#=GF ID   RUF3
#=GF DE   Plasmodium RNA of unkown function RU6-F3
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   80.00
#=GF TC   117.80
#=GF NC   64.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Plasmodium_RUF6_RNA
#=GF SQ   3


ABGT01001025.1/1494-1680 AAUAUUUAUGUUUAU--AUUUAUAUUUAUGUUUAUAUUUAUGUUUAUGUUUAUGUCCAUAUGUUUGCAAUCUA-UUCACUUACUAUUAAACCAUAUUAUUAAGG-AAUUAGUAAACUAAACGA-UUGCUAUAAUAAUUAUGACAAUUUUG-UUUAAUUAUUAAAAUUAUUAUUCUUUUUUUUGAUUAAUUUUA
ABGY01007749.1/135-323   CAUAUUUAUGUUCUACACCUCACACUUAUGUUUAUAUUUAUGUUUAUGUUUAUGUCCAUAUGUUUGCAAUCUA-UUCACUUACUAUUAAACCAUAUUAUUAAGG-AAUUAGUAAACUAAACGA-UUGCUAUAAUAAUUAUGACAAUUUUG-UUUAAUUAUUAAAAUUAUUAUUCUUUUUUUUGAUUAAUUUUA
ABHA01000372.1/1354-1542 AAUAUUUAUGUUUAU--AUUUAUAUUUAUGUUUAUAUUUAUGUUUAUGUUUAUGUCCAUAUGUUUGCAAUCUAUUUCACUUACUAUUAAACCAUAUUAUUAAGGGAAUUAGUAAACUAAACGAAUUGCUAUAAUAAUUAUGACAAUUUUGGUUUAAUUAUUAAAAUUAUUUAUUCCUUUUUUUUUGA--UUAA
#=GC SS_cons             ::::::::((((((,..,,,,,,,,,<<<<--<<<<--<<<____>>>-->>>>-->>>><<<<-<<<<----.-----<<<<<<-----<<-<<____>>->>.--->>>>>>---------.>>>>--->>>>,,))-))))------.-<<<<<<<--<<<<__________>>>>-->>>>>>>:::::
#=GC RF                  aAUAUUUAuGuuuau..auUuAuAuUuauGUUuauaUUuauGUUUaugUUuaugUCCauauguuUGCaaUCUA.UUCACuuaCuaUUAAACCAuaUUAUuaAGG.AAUuaGuaaACUAAACGA.uuGCUAUaauaAUuaUgaCaAUUUUG.UuuaaucaUUaaaaUUAUUauUcuuuuuUUugauuaaUUUuA
//
# STOCKHOLM 1.0

#=GF AC   RF01581
#=GF ID   RUF6-5
#=GF DE   Plasmodium RNA of unknown function RUF6-5
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   70.00
#=GF TC   71.80
#=GF NC   67.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Plasmodium_RUF6_RNA
#=GF SQ   20


ABGT01004244.1/715-869     AGCUGCCCC-AGUAGCCCAGUCGUUA-GGUAUGUAACCUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-AUAA-GAAAAGUUGCAAAUCGAGCUGCUGA---GU-UACCCGGAGGGGGGUGGCGCAAUUUUUUUAUACAAUU-UUAUAU
ABGW01008373.1/13-167      AGCUGCUCC-AGUAGCCCACUCGUUA-GGUAUGUUGCCUUCCCCUGUGAGAACGUGGGUUCG-CUCCGCUGGCCGGCAAUUGC-AUAG-GAAAAGUUGCAGAUCGGGCUGUUGG---GU-UACCCGGAGGGGGGGGGCGCAUUUUUUUUAUAAAAUUUUUAUAU
ACBR01000475.1/12622-12777 AGCUGCCCC-AGUAGCCCAGUCGUUA-GGUAUGUAACCUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-CUGA-GAAAAGUUGCAGACCGAGCUGCUGA---GU-UACCCGGAGGGGGGUGGCGCAAUUUUUUUAUAAAAUUUUUAUAU
ABGT01000824.1/1318-1164   AGCUGCCUC-AGUAGCCCAAUCGUUA-GGUAUGUUGCCUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-AUAG-GAAAAGUUGCAAAUCGAGCUGUUGG---GU-UACCCGGAGGGGGGCGGCGCAAUUUUAAAAAUUUUUU-UUUUUU
ABGX01005580.1/687-844     AGUUGUCCC-AAUGAUCCAGUGGGAA-GGUAUGUAAGUUUUCUUUGAAGUGACACAGGUUCGAUUCCGCGUCCUUGAGUUUCU-GAGAUAAAAAGUUGCAGGCCAAGAUACUGAAGAUU-CGUUCGGA-AUGGGCAACACCAUUUUUUUUA-UUUUUUCAAUAU
ACBS01000019.1/58018-58173 AGCUGCCUC-AGUAGCCCAGUGGUUA-GGUAUGUAAUCUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-CUGA-GAAAAGUUACAGACCGAGCUACUGA---GU-UACCCGGAGGGGGGCGGCGCAAUUUUUUUAUAAAAUUUUUAUAU
ABGY01001380.1/1691-1846   AGCUGCCCC-AGUAGCCCAGUCGUUA-GGUAUGUAACCUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-CUGA-GAAAAGUUGCAGACCGAGCUGCUGA---GU-UACCCGGAGGGGGGUGGCGCAAUUUUUUUAUAAAAUUUUUAUAU
AASM01003368.1/261-419     AGUUGUCCC-AAUGAUCCAGUGGGAA-GGUAUGUAAGUUUUCUUUGAAGUGACACAGGUUCGAUUCCGCGUCCUUGAGUUUCU-GAGAUAAAAAGUUGCAGGCCAAGAUACUGAAGAUU-CGUUCGGA-AUGGGCAACACCAUUUUUUUUAUUUUUUCCAAAAU
AL844503.1/961289-961443   AGCUGCCCC-AGUAGCCCAGUCGUUA-GGUAUGUAGC-UUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-CUGA-GAAAAGUUGCAGACCGAGCUACUGA---GUUUACUCGGAGGGGGGUGGCGCAAUUUUUUUAUAAAAUU-UUUUAU
AL844503.1/595408-595562   AGCUGCCUC-AGUAGCCCAGUCGUUA-GGUAGGUAACUUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCAACAAUUUC-AUAA-GAAAAGUUGCAAAUCGAGCUGCUGA---GU-UACCCGGAGGGGGGUGGCGCAAUUUUUUUAUACAAUU-UUAUAU
ABHA01007567.1/575-726     AGCUGCCUC-AGUAGCCCAGUCGUUA-GGUAUGUAGC-UUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-AUAA-GAAAAGUUGCAAAUCGAGCUGCUGA---GU-UACCCGGAGGGGGGUGGCGCAAUUUUUUU---UAUUUUUUAUAU
ACBR01000078.1/12898-13053 AGCUGCCUC-AGUAGCCCAGUGGUUA-GGUAUGUAGCUUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-AUAA-GAAAAGUUGCAGAUCGAGCUGCUGA---GU-UACUCGGAGGGGGGCAGCGCAAUUUUUUUUUAUUUUUUAUAUAA
AANS01000752.1/3132-2977   AGCUGCCUC-AGUAGCCCAGUCGUUA-GGUAUGUAACCUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-AUAA-GAAAAGUUGCAGAUCGAGCUGCUGA---GU-UACCCGGAGGGGGGUGGCGCAAUUUUUUUAUAAAAUUUUUAUAU
ABGS01008741.1/1138-981    AGUUGUCCC-AAUGAUCCAGUGGGAA-GGUAUGUAAGUUUUCUUUGAAGUGACACAGGUUCGAUUCCGCGUCCUUGAGUUUCU-GAGAUAAAAAGUUGCAGGCCAAGAUACUGAAGAUU-CGUUCGGA-AUGGGCAACACCAUUUUUUUUA-UUUUUUCAAUAU
ABGV01006609.1/1102-945    AGCUGCCCCCAGUAGCCCAGUCGUUAGGGUAUGUAGC-UUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUCCCUGA-GAAAAGUUGCAAACCGAGCUGCUGA---GU-UACCCGGAGGGGGGCGGCGCAAUUUUUUUAUAAAAUUUUUAUAU
ABGV01004280.1/2140-1985   AGCUGCCUC-AGUAGCCCAAUCGUUA-GGUAUGUUGCCUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-AUAG-GAAAAGUUGCAGAUCGAGCUGUUGG---GU-UACCCGGAGGGGGGCGGCGCAAUUUUUUUAUAAAAUUUUUAUAU
AL844507.2/428756-428601   AGCUGCCUC-AGUAGCCCAGUCGUUA-GGUAUGUAACCUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-AUAA-GAAAAGUUGCAGAUCGAGCUGCUGA---GU-UACCCGGAGGGGGGUGGCGCAAUUUUUUUAUAAAAUUUUUAUAU
AL844503.1/564354-564509   AGCUGCCCC-AGUAGCCCAGUCGUUA-GGUAUGUAACCUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-CUGA-GAAAAGUUGCAGACCGAGCUGCUGA---GU-UACCCGGAGGGGGGUGGCGCAAUUUUUUUUAUUUUUUAUAUAAU
AE014188.3/1715969-1715815 AGCUGCCUC-AGUAGCCCAGUCGUUA-GGUAUGUAACUUUUCCUUGUGAGAACGUUGGUUCGACUCCGCUUGCCGACAAUUUC-AUAA-GAAAAGUUGCAAAUCGAGCUGCUGA---GU-UACCCGGAGGGGGGUGGCGCAAUUUUUUUAUACAAUU-UUAUAU
GQ282350.1/11-150          -GUUGUCCC-AAUGAUCCAGUGGGAA-GGUAUGUAAGUUUUCUUUGAAGUGACACAGGUUCGAUUCCGCGUCCUUGAGUUUCU-GAGAUAAAAAGUUGCAGGCCAAGAUACUGAAGAUU-CGUUCGGA-AUGGGCAACACCAUUUU------------------
#=GC SS_cons               :((((((((.,<<<<<-<<<<-<<<-.<<<-<<<<<<-<<<-<<<<<<<<<--<<<<<<-<<____>>--->>>>>>-->>>>.>>>>.>->>>>>>>>>->>>->>>->>>>-...>>.>>><<___>>))))))))::::::::::::::::::::::::::
#=GC RF                    AGccgcCcc.AGuggcCCagccgcuA.GguAuGuaacuuuuCcuuguGggaACgccGGcUCGAcUCCGCuUgCCggcaauccC.acaa.gAaaaguugCagacCgagcUgcuGA...gu.caCcCGGAGgggGgcggCgCaAUUUUUUUauauaaUUuuuAUAU
//
# STOCKHOLM 1.0

#=GF AC   RF01582
#=GF ID   RUF4
#=GF DE   RNA of unknown function RUF4
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   55.00
#=GF TC   55.40
#=GF NC   53.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Plasmodium_RUF4_RNA
#=GF SQ   2


ABHA01003077.1/889-1165  AUUUAUAUUUAUUUAUUUGUAGUCCCUUUUUGAAGGGAAAGAAAUUAUGUAUACACCUCAUGUGUAUAUAGACAAUUUUUUUUCCCAUAUAUUCACUUGUAAAAAGGGUAAAUAAAUUUUAUAAUUUAAUCACAUGUGUAUUUUUAUUUUAUUUAUAAGUUUUUUAUGAAUAAAAUUAGUAGUAAAUAUACAUGCUUCGUGCGAUAAAGACAUUUAAAAAAGAGAUGAACCAAAAAAUCUUCAUAAGCGAUAUAUACGUUAGAUAUGUAAUAGACAU
AE014187.2/982251-982525 AUUUAUAUUUAUUUAUUUGUAGUCCCUUUUUGAAGGGAAAGAAAUUAUGUAUACACCUCAUGUGUAUAUAGACAAUUUUUUUUCCCAUAUAUUCACUUGUAAAAAGGGUAAAUAAAUUUUAUAAUUUAAUCACAUGUGUAUUUUUAUUUUAUUUAUAAGUUUUUUAUGAAUAAAAUUAGUAGUA-AUAUACAUGCUUCGUGCGAUAAAGACAUUUAA-AAAGAAAUGAACAAAAAAAUGUGCAUAUGUAAUAUAUAUGUUAUAUAUGUAAUACAUAU
#=GC SS_cons             ::(((((---(((((((((----(((((((,,,,<<<<<<<<<<---<<<<<<<<<_____>>>>>>>>>------>>>>>>>>>>,<<<<______>>>>))))))))))))))))--))))),,,,(((,,<<<<<<<<<---<<<<<<<<<<<<<<___>>>>>>>>>>>>>>------->->>>>>>>><<_____>>))),,,,,<<<<<_______>>>>>,,,,,,,,,,<<<-<<<<<<<<<<______>>>>>>>>>>---->>>:::
#=GC RF                  AUuuauaUUUauuuauuugUAGUCCCuuuuUGAAGGGaaagaaaUUAuguauaCaCCUCAUGuGuauacaGACAAUuuucuuuCCCAuacaUUCACUuguaaaaaGGGcaaauaaauUUuauaaUUUAauCACauGuguauuUUUauuuuauucauaagUUUcuuaugaauaaaauUAGUAGUaAauacaCauGCUUCGUGCGauAAAGACaucuAAAAAAGagauGAACaAAAAAAuguuCauaugcgacAUAUAugucgcauauGUAAUacauAU
//
# STOCKHOLM 1.0

#=GF AC   RF01583
#=GF ID   snoR01
#=GF DE   small nucleolar RNA snoR01
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   55.00
#=GF TC   63.10
#=GF NC   46.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AM910986.1/47208-47291   CAAAUGAUGAGA-AUACCUUGUUGAAAGAUUUUGAUUUUAUAAUCAAAUGAUUGUUUA-AUCCUCUAAGAAGAUCUGAUACCUUUU
CAAJ01001233.1/1131-1214 UAAAUGAUGAUAAUUAUAUUUUUAAAAGAUUUUGAUUAAU-AAUCAAAUGUUUAAUAACU-CCUCUAAGAAGUUCUGAUUAUUUAA
ABGS01001071.1/1216-1134 UGAAUGAUGAGAAAUACAUUAGCAAAUGAUUUUGAUUUUA-AAUCAAAUGAUUGAUUA-A-CCUCUAAGAAGUUCUGAAUAUUUAU
#=GC SS_cons             ::<<____________________________________._________________._._____________________>>::
#=GC RF                  uAAAUGAUGAgAAaUAcaUUauUaAAaGAUUUUGAUUuua.AAUCAAAUGaUUgaUuA.a.CCUCUAAGAAGuUCUGAuuauUUau
//
# STOCKHOLM 1.0

#=GF AC   RF01584
#=GF ID   snoR03
#=GF DE   small nucleolar RNA snoR03
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   116.20
#=GF NC   52.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


ABGY01000889.1/1819-1978 CUUCAUAUAUAUUCCAUUUGUGUUCCAUGUGUU---UAUAUAAAUGAACUACGUGGGUCAAAAAAUGGAUAAAGAAAAUUAAGGAGAUAUAUUACUUUAUUUCAUUUUUUGUUGUUUUAUUAAUACAUAAAAAAAAAUAGUAUAUUUCUUCAACAACAUAUAA
CAAJ01002653.1/9780-9629 UUUAAUAUAG-UUCCAUUUGUGUUUCAUAAGCUAAGUAUACAAAAUAGC-UCGUGAGUCAAAAAAUGGAUAAAAAAAUUGC-AGAAAUAAA--A-AAUAUAUCAAUUUUU-AUGAUUUAUUUAUGCAUAAA----AAUAAUUUAGUUCUUCAACAACACAUUG
#=GC SS_cons             ::::::::::::<<<<<<<-<<-<<<<<<<<<<...__________>>>->>>>>>>->>-->>>>>>>-------------((((((((((((,,,,,,,,<<________>>,<<<<<______>>>>>,,,,,,))))))))))))::::::::::::::
#=GC RF                  uUUaAUAUAuAUuCCauuuGuGUucCauguGcu...UAUAuAAAuuagCUacguGggUCaAAaaauGGaUAAAaAAAaUuaAaGaaauauacuacuuUAUuUCauUUUUUGuuGuuuuauUaAUaCauaaaAAAAAAuaguauauuuCuUCAACAACAuAUaa
//
# STOCKHOLM 1.0

#=GF AC   RF01585
#=GF ID   snoR07
#=GF DE   small nucleolar RNA snoR07
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   44.00
#=GF TC   46.90
#=GF NC   39.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AANS01001575.1/3964-3877 UUAAAAUGAUGAAUAACUUUUGAGCGAUGGGCGGACUGAAAAAAGUGAGAGAACUUUU--AUUUGUAGAAAAUCGCAUAAUCUGAUAAGA
AASM01001991.1/91-2      UUAAAAUGAUGAAUAACUUUUGAGCGAUGGGCGGACUGAAAAAAGUGAGAGACCCCCCCAACUUGUAGAAAAUCGCAUAAUCUGAUAAGA
CAAJ01004367.1/269-353   UUAAAAUGAUGAAUAACUUUUGAGCGAUGGGCGGACUGAAUAAAAGUCGA-AACUUUA--AU--GUAGAAAAUCGCUGAAACUGAUAAGA
CAAI01002062.1/861-777   UUAAAAUGAUGAAUAACUUUUGAGCGAUGGGCGGACUGAAUGAA---AGUCUAAACUU--GAAUGUAGAAAAUCGCUGAAACUGAUAAGA
#=GC SS_cons             <<<_______________________________________________________.._________________________>>>::
#=GC RF                  UUAAAAUGAUGAAUAACUUUUGAGCGAUGGGCGGACUGAAuAAAgugAGagaacuuUu..AuuUGUAGAAAAUCGCuuAAaCUGAUAAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01586
#=GF ID   snoR09
#=GF DE   small nucleolar RNA snoR09
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   50.00
#=GF TC   68.10
#=GF NC   42.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AABL01000190.1/3903-3814   UUUAAAUGAUGAAAUCGUACGCUUGGCAUCUGAAAAAUUUGCUAAUUUUGAAGAUAACUUUUUUAACCAGUUAUCCCUAUCUGAUAUAAA
ACBS01001329.1/10278-10195 UUUAAAUGAUGAAAACGUACGCUUGGCAUCUGAAUAAUUU-----AUUUGAAGAUAAAUU-UUUAAUCAGUUAUCCCUAUCUGAUAAAAA
ABGV01006213.1/122-39      UUUAAAUGAGGAAAACGUACGCUUGGCACCUGAAUAAUUU-----AUUUGAAGAUAAAUU-UUUAAUCAGUUAUCCCUAUCUGAUAAAAA
#=GC SS_cons               <<<_____________________________________....._______________.__________________________>>>
#=GC RF                    UUUAAAUGAuGAAAaCGUACGCUUGGCAuCUGAAuAAUUU.....aUUUGAAGAUAAaUU.UUUAAuCAGUUAUCCCUAUCUGAUAaAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01587
#=GF ID   snoR10
#=GF DE   small nucleolar RNA snoR10
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   65.00
#=GF TC   83.10
#=GF NC   41.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AABL01000190.1/4648-4579 UUUAUAUGAUGAUUAGUCCU-UGUCUAAA--------UAAAAAAAAUGAAGACAAUAGUACUGCCCCAAACUGAUUAAA
ABGW01006943.1/417-341   UUUAUAUGAUGAUUAGUC-U-UGUCUGAAUAUUUAAUUUUAAAAAAUGAAGACAAUAGUACUGCCCCAAACUGAUUAAA
AM910991.1/281397-281326 UUAACAUGAUGAUUAGUU-UUUGUCUAAAU------UUACAAAUAAUGAUGACAAUUGUACUGCCCCAAACUGAUUAAA
CAAJ01001585.1/2541-2470 UUUAUAUGAUGAUUAGUC-U-UGUCUGAAUAAUAA-----AAAAAAUGAAGACAAUUGUACUGCCCCAAACUGAUUAAA
#=GC SS_cons             <<<<______________._.______________._______________________________________>>>>
#=GC RF                  UUuAUAUGAUGAUUAGUc.U.UGUCUaAAUAuUuA.UUauAAAaAAUGAaGACAAUuGUACUGCCCCAAACUGAUUaAA
//
# STOCKHOLM 1.0

#=GF AC   RF01588
#=GF ID   snoR13
#=GF DE   small nucleolar RNA snoR13
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   60.00
#=GF TC   77.90
#=GF NC   38.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


ACBS01000723.1/11593-11697 UUUUGAAUGAGGAAAAAAGUUCUCAAAUGUUCGCAGUUGAGAGUUUUUAGUAAAAA-GCUCAAUGAAUUUUUAUU--GUAGCCUUCACUUAGAUGUCUGACAAUAAAA
ABGW01001570.1/334-439     UUGUGAAUGAUGAAAAAAGUUCUCAAAUGUUCGCAGUUGAGAGUUUUUAGAAAAAAAGCUCAAUGAAUUUUUAUU--GUAGCCCUCACUUAGAUGUCUGACACAAGAA
AM910991.1/1216709-1216813 UGUUGAAUGAUGACAAAUAUUCUCAAAUGUUCGCAGUUGAGAGUUCCAUUAGAACA-ACUCGAUGAAUUGUCUUU--GUAGCCUUCACUUAGAUGUCUGACUCCAGAG
CAAJ01004906.1/5093-4994   UUGUGAAUGAUGAUAAAAUUUCUCAA-UGUUCGCAGUUGAGAGUU------AAACA-ACUCUAUGAAGUUUUUUCACGUAGCCUUCACUUAGAUGUCUGACACAAAAA
#=GC SS_cons               <<<<____________________________________________________.__________________..___________________________>>>>
#=GC RF                    uucUGAAUGAuGAaAAAaaUUCUCAAAUGUUCGCAGUUGAGAGUUuuuagaAAAaA.aCUCaAUGAAuUuUUuUU..GUAGCCUUCACUUAGAUGUCUGACacaAgaa
//
# STOCKHOLM 1.0

#=GF AC   RF01589
#=GF ID   plasmodium_snoR11
#=GF DE   small nucleolar RNA snoR11
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   161.30
#=GF NC   58.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


ABGU01000965.1/1561-1359 UAAGAGCAAUUUUAUUAUGUUAAGAUUAUAUAUUGUACAUUUCAAGUACAUAUAUAUAUAUCUACAUAUAUAAAAAUAUAUAAAAAAAAA-AAUAAUAAAUAAUAUAAUUGCUUAAAAA---AAAAAACUUGAAGUUAGCACGAUAAUCAGGGCAUAAGAUGUUAUAAAUUGUGAGCAUCCUAUGCAGUACAAGUUUGUGCACAAUU
ACBS01001330.1/862-656   UAAGAGCAAUUUUAUUAUGUUAAGAUUAUAUAUUGUACAUUUCAAGUACAUAUAUAUAUAUCUACAUAUAUAAAAAUAUAAAAAAAAAAAUUAUAAAUAAAUAUAUAUUUGCUUAAAAAAAAAAAAAACUUGAAGUUAGCACGAUAAUCAGGGCAUAAGAUGUUAUAAAUUGUGAGCAUCCUAUGCAGUACAAGUUUGUGCACAAUU
#=GC SS_cons             :::((((((((-((((((,,,,<<<<<<<<<<<<<<<<_______>>>>>->>>>>>>->>>>,,<<<<<<____>>>>>>,,,,,,,,,,,,,,,,,,))))))-))))))))------------------------<<<<<<--------<<<<<-<<<<<<__________>>>>>>->>>>>--------->>>>>>::::::
#=GC RF                  UAAgaGCaauuUuauuauGUUAaGauuauauauuGuaCAUUUCAAGuaCaUauauauaUauCuACauauauAAAAauauauAAAAAAAAAuaAUAAaaAauaauaUaauuGCuuAAAAAAAAAAAAAACUUGAAGUUAGCaCgaUAAUCAGGGCauaAGauGuuAUAAAUUGUGagCauCCuauGCAGUACAAGUuuGuGCACAAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01590
#=GF ID   plasmodium_snoR14
#=GF DE   small nucleolar RNA snoR14
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   90.00
#=GF TC   114.60
#=GF NC   46.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.15 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4



CAAI01004629.1/216-91      UUUGAAUGAUGAAG-UAUUUACU--ACUGAUUUAGGGCCAAAAUUU----AAUUUUUU-UGUUAAAAAAAAAUUAAACUUGUAAUAUGCAUUAUUACACUAAAAAAUGAUGGCUUAAUCUUCUCACUGACAAAA
ABHA01001532.1/667-541     UUUGAAUGAUGAAA-AAUAUGCUGUCCUGAUUUAGGGCCAGAGGUUUCCUAUAUUUUU-UUUUCUUUUGGAAAAAGAAUGGUAACCUAUAUAAU-----CUUAAGAUGAUGGCUUAAUCUUCUCACUGACAAAG
ACBS01000373.1/22837-22710 UUUGAAUGAUGAAA-AAUAUGCUGUCCUGAUUUAGGGCCAAAGGUUUCCUAUAUUUUUUUUUUCUUUUGAAAAAAGAAUGGUAACCUAUAUAAU-----CUUAAGAUGAUGGCUUAAUCUUCUCACUGACAAAA
ABGX01004004.1/953-826     UUUGAAUGAUGAAAAAAUAUGCUGUCCUGAUUUAGGGCCAAAGGUUUCCUAUAUUUUU-UUUUCUUUUGAAAAAAGAAUGGUAACCUAUAUAAU-----CUUAAGAUGAUGGCUUAAUCUUCUCACUGACAAAA
#=GC SS_cons               <<<___________.___________________________________________.___________________________________....._______________________________>>>:
#=GC RF                    UUUGAAUGAUGAAa.aAUaUgCUGUcCUGAUUUAGGGCCAAAggUUUCCUAuaUUUUU.UuUUcuuuugAAAaaAgAaUgGUAAccUauAUaAU.....cuuAAgAUGAUGGCUUAAUCUUCUCACUGACAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01591
#=GF ID   snoR15
#=GF DE   small nucleolar RNA snoR15
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:17901154
#=GF GA   50.00
#=GF TC   50.70
#=GF NC   45.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4



AM910996.2/1733707-1733590 ACAACGUGAUGAUAAAAGAAAACGGCGAUGCUUUUACUC-GUGC----UCCUUUUAGCUAUCUACAAGGG----GCUA-----CAUGA-AGCGAAAUGAGCGACAAA--AGCGAGUAGUUUUCAAUCUGAUAAAA
ABGY01002306.1/259-129     UUUAUAUGAUGAGAAAAUUAAAUGGCGAUAUUGUAAUUU-AUUAUACUUACUUUUAAUUCUUUGAAAGUAUGUAUAUA-AAAUAAUGA-AGUG-AAUGAGCGUCAAAAAAAUGAGUAGUUUUCAAUCUGAUAAAA
AASM01000120.1/2889-2759   UUUAUAUGAUGAGAAAAUUAAAUGGCGAUAUUGUAAUUU-AUUAUACUUACUUUUAAUUCUUUGAAAGUAUGUAUAUA-AAAUAAUGA-AGUG-AAUGAGCGUCAAAAAAAUGAGUAGUUUUCAAUCUGAUAAAA
ABGZ01005962.1/1153-1020   CUCAUAUGAUGAGGAAAUUAAACGGCGAUAUUGUACUUUCAUUAUCCCUACUUCUUAAUCUCUGAAAGUAUGUAUAUAAAAAUAAUGAAAGUG-AAUGAGGGCCAAAAAAAUGAGUAGUUCUCAAUCUGAUAAAA
#=GC SS_cons               :::<------<-------------<<--<<<<---<<<<.--<<<<<-<<<<<<<<<____>>>>>>>>>->>>>>--.>>>>-----.>>>>.----->>------------------------->--->::::
#=GC RF                    uuuauaUGAUGAgAAAAuuAAAuGgCGAugcugUaauuu.aUuauaCuuaCuuucaguUcUcugaaaGuaUGuauaUA.aaauaAUGA.agcg.AAUGAGcGuCAAAAAAauGAGUAGUUuUCAAUCUGAuAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01592
#=GF ID   plasmodium_snoR17
#=GF DE   small nucleolar RNA snoR17
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   51.00
#=GF TC   51.20
#=GF NC   50.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 36.87 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5



CAAI01002424.1/3270-3195 UUUUUUAUGAUG-AAAAAAA-----AAUAUCUGAUUCUAAGUUGAUGAUA-UCUUAUAUCAUUUCACCAAGAUCUCUGAAAAA
CAAJ01001830.1/5076-5001 UUUUUUAUGAUG-AAACAAAC-----AAAGCUGAUAACAAGUUGAUGACAGC-UUAUAUCAUUUCACCAAGAUCUCUGAAAAA
ABGX01001459.1/817-896   UUUUUUAUGAUG-AAAAUAAAAAAGAAAAGCUGAUAAAAAGUUGAUGAUU-U-UUAUGCUAUUUCACCAAGAUCUCUGAAAAA
ABGV01003715.1/582-661   UUUUUUAUGAUG-AAAAUAAAAAAGAAAAGCUGAUAAAAAGUUGAUGAUU-U-UUAUGCUAUUUCACCAAGAUCUCUGACAAA
ABGZ01002434.1/1056-1135 UUUUUUAUGAUGGAAAAUAAAAAAGAAAGCUUGAU-CAAAGUUGAUGAUU-U-UUAUGCUAUUUCACCAAAAUCUCGGAAGAA
#=GC SS_cons             :<<<<_______._____________________________________._.__________________________>>>>
#=GC RF                  UUUuuUAUGAUG.AAAAuAAaAAAGAAAAgCUGAUaaaAAGUUGAUGAUu.U.UUAUgcuAUUUCACCAAGAUCUCUGAaaAA
//
# STOCKHOLM 1.0

#=GF AC   RF01593
#=GF ID   plasmodium_snoR16
#=GF DE   small nucleolar RNA snoR16
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   70.00
#=GF TC   78.70
#=GF NC   40.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.70 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3



AM910996.2/156798-156669   UUUACGAAUGAUGAAUUGUAAAAAUACGAUGUACUCUCGAGUCCUGAGUAGAAACAUUGAACUCAAACAUUGCUCAGUUGAGCGUGAGUUUAAGAUGAAGUAAACUUUGGAAUCUGACGAAAAAAAUUUU
ACBS01001318.1/13764-13639 AAACCACAUGAUGAAAAUAAUUGAUACGAUGAACUUGCGAGUCCUGAGUAUAA---CUGAACUCAACAAUUACUCAGUUGAGCGUAGGUUUGAUAUGAAAUUAAAA-UAAAUUCUGAAAUUAAAUUCUCU
ABGZ01003381.1/1888-1763   AAACCACAUGAUGAAAAUAAUUGAUACGAUGAACUUGCGAGUCCUGAGUAUAA---CUGAGCUCAACAAGUACUCAGGUGAGCGUAGGUUUGAUAUGAAAUUAAAA-UAAAUUCUGAAAUUAAAUUCUCU
#=GC SS_cons               :<<__________________________________________________...__________________________________________________._________________>>::::
#=GC RF                    aaacCacAUGAUGAAaauaAuugAUACGAUGaACUugCGAGUCCUGAGUAuAA...cUGAaCUCAAcaAuUaCUCAGuUGAGCGUagGUUUgAuAUGAAaUuAAaa.UaaAuUCUGAaauuAAAuucUcU
//
# STOCKHOLM 1.0

#=GF AC   RF01594
#=GF ID   snoR18
#=GF DE   small nucleolar RNA snoR18
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   55.00
#=GF TC   61.30
#=GF NC   41.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.32 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3



CAAJ01009251.1/10-101      UAUAAGGUUAUUAUGAUGAUU-CAAUGAUAGGACAGAAAAAAUAUU--UGUUGAUAAACAAUAUAGCCGAUAAUUAAUAAUUUCUGAACACCUUU
ABGS01009239.1/169-258     UAUAAAGUCA-UAUGAUGAUUACAAUGAUAGGCCUGAUUAAAUUUUCAUGUUGAUAAAUUUUAUAGCCGAUAAUAUAAAUAUGCUGA----UUUC
AANS01000868.1/16293-16382 UAUAAAGUCA-UAUGAUGAUUACAAUGAUAGGACUGAAUAAAUUUUCAUGUUGAUAAAUUUAAUAGCCGAUAAUAUAAAUAUGCUGA----UUUC
#=GC SS_cons               :::<<<____.____________________________________________________________________________....>>>:
#=GC RF                    UAUAAgGUcA.UAUGAUGAUUACAAUGAUAGGaCuGAauAAAUuUUCAUGUUGAUAAAuuuuAUAGCCGAUAAUauAaAuaUgCUGA....cUUc
//
# STOCKHOLM 1.0

#=GF AC   RF01595
#=GF ID   snoR19
#=GF DE   small nucleolar RNA snoR19
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   60.00
#=GF TC   92.00
#=GF NC   43.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AM910994.1/759659-759754 AAAAAUGAUGAUUCUAUGCGCAG--AAAUAAAAAUCAAAGUCGUACUACU--AUGUAGAAUGAUGAUACUU----GAUGUCAUCCUUGAACUGAUUUUUUUUUU
ABGV01006154.1/1319-1218 UAAAAUGAUGAUAUUAUAUAUGG--GCGCACAUUUAAAUUUCAUACUACUAAAUGUAGAAUGAUGAAAAUUAUAGGUUGUCAUCCUUGAUCUGAUUAUUUUUUA
ABGU01007392.1/389-288   UAAAAUGAUGAUAUUAUAUAUGG--GCGCACAUUUAAAUUUCAUACUACUAAAUGUAGAAUGAUGAAAAUUAUAGGAUGUCAUCCUUGAUCUGAUUAUUUUUUA
CAAJ01003293.1/4693-4790 AAAAAUGAUGAUAAUAAAUUAAGCGCAACUAAAUUUUUUGUCAUACUACU--AUGUAGAAUGCUGAUAAAG----GAUGUCAUCCUUGAACUGAUUUUUUUUAU
#=GC SS_cons             :<<<<__________________.._________________________..___________________....______________________>>>>:::
#=GC RF                  aAAAAUGAUGAUauUAuAUauaG..aaacaaAauUaaauuUCAUACUACU..AUGUAGAAUGaUGAuAAuu....GAUGUCAUCCUUGAaCUGAUUuUUUUUuu
//
# STOCKHOLM 1.0

#=GF AC   RF01596
#=GF ID   plasmodium_snoR20
#=GF DE   small nucleolar RNA snoR20
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   45.00
#=GF TC   48.70
#=GF NC   39.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AANS01000679.1/2648-2727 UAUUACAUGAUGAAUAAGCUUCUACGAAUCACGACGGUCUUCUGAC--AUUAUCAAUGGAGAUGGUAGAACGUUCUGAUCUC
CAAJ01009473.1/1004-1085 AUAUACAUGAUGAUUAAGUUUCUACGAAUCACGACGGUCUUCUGACGUAUAAUAGAUGGAGAUGGUAGAACGUUCUGACCAU
#=GC SS_cons             ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  uuuUACAUGAUGAuUAAGuUUCUACGAAUCACGACGGUCUUCUGACGUAUuAUagAUGGAGAUGGUAGAACGUUCUGAuCuu
//
# STOCKHOLM 1.0

#=GF AC   RF01597
#=GF ID   snoR22
#=GF DE   small nucleolar RNA snoR22
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   50.00
#=GF TC   50.40
#=GF NC   42.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ABGU01005326.1/920-838   UUUUUAUGAUGAUACAAUUCCAAAAAUGCAAGUAGGGACAUGAGAAUAUUAUAAAUAUGUUCGUCUUCUAUUAUCUGAAAAAA
CAAI01002564.1/5984-5906 UUUUAAUGAUGAUAAAAUUUGUCAAAUGCAAGUAGGGACAUGAGAAUA---UAAAUAUGUUCGUUA-UUGUUAUCUGAAAAAA
ABHA01002982.1/1386-1304 UUUUUAUGAUGAUACAAUUCCAAAAAUGCAAGUAGGGACAUGAGAAUAUUAUAAAUAUGUUCGACUUCUAUUAUCUGAAAAAA
#=GC SS_cons             <<<<___________________________________________________________________________>>>>
#=GC RF                  UUUUuAUGAUGAUAcAAUUccaaAAAUGCAAGUAGGGACAUGAGAAUAUUAUAAAUAUGUUCGucuUcUaUUAUCUGAAAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01598
#=GF ID   snoR23
#=GF DE   small nucleolar RNA snoR23
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   70.00
#=GF TC   70.50
#=GF NC   57.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 37.05 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3



AM910995.1/1210650-1210732 UGUGUAUGAUGAGAAAAAA-AAAAAAAUUUAACUUUCGUUCUUCUGCAUUUAACGAAAUGAUGAUGAAUUGUAC-UCUGACACGG
ABGW01004497.1/1342-1258   UGUAUAAGAUGAAUAAAAAAAAAAUUAUUUAACUUUCGUUCUUCUGCAUCUUUUGAAGUGAAGAUAAAUUUUAUAUCUGAUACAA
ACBS01000744.1/2382-2299   UGUAUAUGAUGAAUAAAAA-AAAAUUAUUUAACUUUCGUUCUUCUGCAUCUUUUGAAGUGAAGAUAAAUUUUAUAUCUGAUACAA
#=GC SS_cons               <<<________________._____________________________________________________________>>>:
#=GC RF                    uGUaUAuGAUGAauAAAAA.AAAAuuAUUUAACUUUCGUUCUUCUGCAUcUuuuGAAgUGAaGAUaAAUUuUAuAUCUGAuACaa
//
# STOCKHOLM 1.0

#=GF AC   RF01599
#=GF ID   plasmodium_snoR24
#=GF DE   small nucleolar RNA snoR24
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   55.00
#=GF TC   63.30
#=GF NC   45.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4



AABL01002187.1/2652-2576 UUUUUAUGAUGAUAU------AAAAAUU--UUUGGGUAAUUUACGUCUGAAAAUU-UUGAUGAACAAAAAUGUA--UAUCUGAAAAAA
AM910995.1/424185-424272 AUUCUAUGAUGAACAACACUAAAAAAUAUCUUUGGGUAAUUUACGUCUGAAAUUCUCUGAUGAAUAUUCCAGACUAGAUCUGACGAAU
AASM01002319.1/1903-1824 CUUUAAUGAUGACUGA--AUAAAUAAUA--UGUGGGUAAAUUACGUCUGAAAAUUAUUGAUGAUUAUUAUAGU----AUCUGAAAAAA
ACBS01000744.1/2752-2673 UUUUAAUGAUGACUGA--AUAAAUAAUA--UGUGGGUAAUUUACGUCUGAAAAUUAUUGAUGAUUAUUAUAGU----AUCUGAAAAAA
#=GC SS_cons             :<<<____________..__________..____________________________________________..________>>>:
#=GC RF                  uUUuuAUGAUGAuuaA..aUAAAaAAUA..UuUGGGUAAUUUACGUCUGAAAaUUaUUGAUGAaUAUUauAGua..uAUCUGAaaAAa
//
# STOCKHOLM 1.0

#=GF AC   RF01600
#=GF ID   snoR25
#=GF DE   small nucleolar RNA snoR25
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   50.00
#=GF TC   61.90
#=GF NC   45.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


CAAJ01001824.1/1127-1059 UUUUAAUGAUGAAAUAUACAGACCUGACUUGAAAAUAAAAUUUGAGAAU--GCAUAACGCUCCUGAACAAA
ABGV01005517.1/794-725   UUUUAAUGAUGAGAAAAACAGACCUGAUUUGAAAA-AUAAUUUGAGAAUAAUUAUAACCCUCCCUGAAAAA
GQ282330.1/1-68          UUUUAAUGAUGAGAAAAACAGACCUGAUUUGAAAA-AUAAUUUGAGAAUAAUUAUAACGCUCCUGA--AAA
AE014187.2/974016-973947 UUUUAAUGAUGAGAAAAACAGACCUGAUUUGAAAA-AUAAUUUGAGAAUAAUUAUAACGCUCCUGAAAAAA
#=GC SS_cons             <<<<_______________________________.______________________________>>>>:
#=GC RF                  UUuUAAUGAUGAgAaAaACAGACCUGAUUUGAAAA.AuAAUUUGAGAAUAAuUAUAACgCUCCUgAAaAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01601
#=GF ID   plasmodium_snoR26
#=GF DE   small nucleolar RNA snoR26
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   50.00
#=GF TC   52.70
#=GF NC   44.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ACBS01000745.1/1206-1058 -------------AUGUUAACAAUAAUUCAUGAUGUAAAAAUGUUAUCCAGUGAUGUUUUUAUUAGAGGCUAAAAAAAAAUGUUUAUGCAAUGAUAAAACGAGUUAAGCAUUUUUUUUUAAGUUGCCGACUCACCUGACAUUGGAACAACCAAAAUUAUUGU
ABGS01008962.1/448-289   AAGGCCUUAAAAAAGGUUAACAAUAAUUCCGGGUGUAAAAAUGUUAUG--GGGAUGUUUUUAUUAAAGGCUAAAAAAAAAGGUUUAUGCAAUGAAAAAACAAGUUAAGCAUUUUUUUUUAAGUUGCCGACCCACCUGACUUUGGAACAACCAAAAUUAUUGU
ABHA01007249.1/1009-850  UAUGCCUUAAUAAAUGUUAACAAUAAUUCAUGAUGUAAAAAUGUUAUG--AGGAUGUUUUUAUUAGAGGCUAAAAAAAAAUGUUUAUGCAAUGAUAAAACGAGUUAAGCAUUUUUUUUUAAGUUGCCGACUCACCUGACAUUGGAACAACCAAAAUUAUUGU
#=GC SS_cons             ::::::::::::::::::::<<<<<<<<____________________.._______________________________________________________________________________________________________>>>>>>>>:
#=GC RF                  aAuGCCUUAAaAAAuGUUAACaauaauuCauGaUGUAAAAAUGUUAUg..ggGAUGUUUUUAUUAgAGGCUAAAAAAAAAuGUUUAUGCAAUGAuAAAACgAGUUAAGCAUUUUUUUUUAAGUUGCCGACuCACCUGACaUUGGAACAACCAAaauuauuGU
//
# STOCKHOLM 1.0

#=GF AC   RF01602
#=GF ID   plasmodium_snoR27
#=GF DE   small nucleolar RNA snoR27
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   59.30
#=GF NC   42.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


CAAJ01000274.1/402-548   UAUGCUGAUUUAGCCACAGUGGCAUUUUUCAUUAUU-UAAUACUUUUGGUGCCAUCUGCUAGAAAUCAGCUACAACAAAUUCAU-AAUUUUAGGAACCAUUAAAAAAAUU-AUUAAUUUUUUCUAUU---GGGCCAUAU-UUAUGAGUACAACA
AANS01000720.1/390-531   AAUGCUGAUUUA-CCACAGUGGCAACUAAU----UU-UUCUUCAUUUACUGUUUACUGCCAGAAAUCAGCUAAAUCGAUUUCAU-AAUUUUAGGAACCAUAGAAAAAAUU-GAGAAUUUUUUUUUGU---GGGCCGUAU-UUAUGAAUACAAAU
ACBS01000746.1/2236-2383 AAUGCUGAUUUA-CCACAGUGGCAACUAAU----UUUUUCUUCAUUUACUGUUUACUGCCAGA-AUCAGCUAAAUCGAUUUCAUUAAUUUUAGGAACCAUAGAAAAAAUUGGAGAAUUUUUUUUUUUGUGGGGCCGUAUUUUAUGAAUACAAAU
CAAI01000969.1/1122-981  UAUGCUGAUUUAGCCACAGUGACAUUUACA----U--AUAUAUUUUUGAUGUCAUCUGCUAGAAAUCAGCUAAAACAAAUUCAU-AAUUUUAGGAACCAUUAAAAAAAUU-GUUAAUUUUUUCUAUU---GGGCCAUAU-UUAUGAAUACAAUA
#=GC SS_cons             :::<<<<<<<<-----<<<<<<<<______....__.____________>>>>->>>>---->>>>>>>>---------<<<<<.-------<<--<---<<<<<<<<<<.___>>>>>>>>>>---...>-->>----.-->>>>>:::::::
#=GC RF                  uAUGCuGauuuAGCCACaGuggCauuUaau....UU.uuaUacuUUUaauGccaaCuGCuAGaaauCaGCUAaAaCaAauuCau.AAUUUUAGGAACCAUagaaaaaauu.guuaauuuuuucuauU...GGGCCaUAU.UUauGaaUACAAaa
//
# STOCKHOLM 1.0

#=GF AC   RF01603
#=GF ID   snoR29
#=GF DE   small nucleolar RNA snoR29
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   50.00
#=GF TC   51.50
#=GF NC   44.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ABHA01003077.1/169-252   CAAAAAUGAUGACAACCU-UUCAUAAUAU-AAAGCCUUUCGGGUCUGA-AGAGCAUUAUGAUGAUAAAAAAAAAAAAAACUGAUUUU
ABGY01002358.1/1180-1264 AAAAAAUGAUGACAACCUUUUCAUAAUAU-AAAGCCUUUCGGGUCUGA-AGAGCAUUAUGAUGAUAAAAAAAAAAAAAACUGAUUUU
AABL01002376.1/9610-9528 AAAAAAUGAUGAAACCAU-UUAUGAUUAUCAAAGCCUUUCGGGUCUGAGAGUAAACUAUGAUGAUUAUAA---GUAAAGCUGAUUUU
#=GC SS_cons             ::<<<<____________.__________.__________________.__________________________________>>>>
#=GC RF                  aAAAAAUGAUGAcAaCcU.UUcauAaUAU.AAAGCCUUUCGGGUCUGA.AGagcAuUAUGAUGAUaAaAAAAAaaAAAaCUGAUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01604
#=GF ID   plasmodium_snoR28
#=GF DE   small nucleolar RNA snoR28
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   63.00
#=GF TC   74.00
#=GF NC   41.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ABGT01006737.1/707-786   UAUAUAAUGAUGAAAACUUCAAGGAAGUGCCGUCCGAAAAAAAAAAUGUUGACGAUAAUUAAUUAAUCUGAACAUAAUUA
CAAI01000969.1/797-720   AUUAUAAUGAUGAAAAUAUCCAGGAAGUGCCGUCUGAUUC--UUUUUGUUGACGAUAAUUAAAAAUUCUGACCAUAAUUA
AE014187.2/979708-979785 UAUAUAAUGAUGAAAACUUCAAGGAAGUGCCGUCCGAAUA--UUUAUGUUGACGAUAAUUAAUUAAUCUGAACAUAAUUA
#=GC SS_cons             ::::<<<<________________________________..__________________________________>>>>
#=GC RF                  uaUAUAAUGAUGAAAAcuUCaAGGAAGUGCCGUCcGAaua..uuuaUGUUGACGAUAAUUAAuuAaUCUGAaCAUAAUUA
//
# STOCKHOLM 1.0

#=GF AC   RF01605
#=GF ID   plasmodium_snoR30
#=GF DE   small nucleolar RNA snoR30
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   43.00
#=GF TC   43.40
#=GF NC   40.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ABHA01003077.1/735-808 UUUUAAUGAUGAUAUGAAG--AACUUGGUCUGUGUUACUGAAAUAAUAUAGAGAUGAAAAAAAA---ACGACUGAAAAA
CAAJ01004442.1/633-711 UUUUAAUGAUGAUACAAACACACCUUGGUUCGUGUUACUGAACUAACAUUGAGAUGAAAAACUGUGUGACACUGAAAAA
GQ282335.1/1-74        UUUUAAUGAUGAUAUGAAG--AACUUGGUCUGUGUUACUGAAAUAAUAUAGAGAUGAAAAAAAA---ACGACUGAAAAA
#=GC SS_cons           :<<<_______________..___________________________________________..._________>>>
#=GC RF                UUUUAAUGAUGAUAugAAg..AaCUUGGUcuGUGUUACUGAAaUAAuAUaGAGAUGAAAAAaaa...acgACUGAAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01606
#=GF ID   plasmodium_snoR31
#=GF DE   small nucleolar RNA snoR31
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   60.00
#=GF TC   61.60
#=GF NC   53.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ABGV01002952.1/1394-1538 GUUAUAUAUUAAUUUAUUGUGUAAUCCCUAGCGGGCAAGAUUUUUUCAAAGAAUGAAAAAGAUCGUAAUC-GUCUAGGUAAUAAAAAUUUAAAAAAAAAAAAAUGUUGUAAGUUUUUAGUU-UUGCAAUAUAUUUUUUUUUUAAUAC
ABGU01005259.1/2-144     GUUAUAUAUUAAUUUAUUGUGUUAUCCCUAGCGGGCAAGAUUUUUUCAAAGAAAGAAAAAGAUCGUAAUC-GUCUAGGUAAUAAAAAUUUAAAAAAAAAAAAAUGUUGUAAGAC-UUAGUU-UUGCCCC-CCUCCUUUUUUUAAUAC
AABL01002376.1/8273-8130 UCGUUAUUAUAAUAUA-UGUAUAAUUCCUAGCGGGCAAGAUUUUUUCAAAAAAUGAAAAAUAUCAUAAUCAGUCUAGGUAACAAAAAUUAAAAA--GAAAAAUUAUUGUAAUUUUAAAAUUAUUACAAUGGUUUUUUUUUUGCACAA
#=GC SS_cons             ::::::::::::::::::::::::::<<<<<<<<----<<<<<<<<<_______>>>>>>->>>---->>.>->>>>>-------------<<<<<<<<<<-<<<<<<<<<__________.>>>>>>>>>->>>>>>>>>>:::::
#=GC RF                  guuaUAUauUAAUuUAUUGUgUaAUcCCuaGCGgGCAAGauuuuuuCAAAgAAuGaaaaagauCgUAAuC.GUCuaGGUAAuAAAAAUUuAaaaaaaaaaaAgcguuGcaaguuUuuAgUU.uugCaacgcuuuuuuuuuuuaAuAc
//
# STOCKHOLM 1.0

#=GF AC   RF01607
#=GF ID   ceN100
#=GF DE   C. elegans snoRNA ceN100
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   105.50
#=GF NC   66.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948644.1/1-132           AAACGAGGUCCAGAGUCACCUUUUCAGCA--AAAUGCAGUUAGGGUGCUAGGAUUUCUCGAAAAUGAAAU-UGGUCGUAUUAUGCAAGUAGGGCUUGCUUUUGCGCUCCCCGACUUCACCUCAUUCCCAAACAUU
AM051045.1/1-130           --ACGAGGUCCAGAGUCACCUUUUCAGCA--AAAUGCAGUUAGGGUGCUAGGAUUUCUCGAAAAUGAAAU-UGGUCGUAUUAUGCAAGUAGGGCUUGCUUUUGCGCUCCCCGACUUCACCUCAUUCCCAAACAUU
AAGD02011775.1/10125-10258 AAACGAGGUCCAGAGUCACCAUUUCGGAUUGAUUUUCUGAUUUGGUGCUAGGAUUUCUCGAAAAUAAAAUUUGGUCGUAUUAUGCAAGUAGGGCUUGCU-AUGCGCUCCCCUCCUUCACCUCAUUCCCAUACAAU
DQ789524.1/1-130           AUACGAGGUCCAGAGUCACCUCUGAGAAU--AUGUAUCUCUUCGGUGCUAGGAUUGCUCGAAAAUGAAUU-AGGUACU-UUAUGCAAACAGUUCUUGCGU-UAUGCUCAUCUGUUUCACCUCCGUUUCUGACAAA
#=GC SS_cons               :::<<<<<<<<--<<-<<<<<<--<-<<_..____>>->-->>>>>>>>->>>>-->>>>----------.<<<--<<----<<-<<<<-<<<---<<______>>-->>>->>>>>>---->>-->>>::::::
#=GC RF                    AaACGaGguCCAGaGUCaCCcuUucagcu..AuaUgcaguUagGGuGCuAGGauUuCuCGAAAAUgAAaU.uGGUcguAUUAuGCaagcAGggCUUGCuUuUgcGCUCccCugcuuCaCCUCacUcCCaaACAau
//
# STOCKHOLM 1.0

#=GF AC   RF01608
#=GF ID   ceN102
#=GF DE   Caenorhabditis snoRNA ceN80
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   52.40
#=GF NC   39.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948646.1/1-142           UAUCCAUGUUUACUACUACUUUUCAUCUCUUUUUCACUGAAAUGUCGAGUAUUUUUGCGAUGCAUGGUAAAGAAAU-------CAAGGUGACCAGGUUUCUUUUCAAUUUUCCCCCAU----AAUUGAAGAGUUACAAUGCCAUCUGACAAGG
AAGD02009255.1/32794-32653 AUCCCAUGUUUACUACUACUUGCUACCUCUAUA-AUUUGAGAUUUCGAGUAUUUUUGCGAUGCAUGGAAAAUAAAAG----ACUAAAAUGGCCAGGUUUCUUUUCAUA--UUCCAAAU----UGAUGAAAAGUUACAAUGUCAUUUCACAAAA
DQ789505.1/1-143           AAACCAUGUUUACUACUACUUGUCACCUCUCC--CCUUGAGAUUUCGAGUAUUUUUGCGAUGCAUGGAAAAUGAAAUUUCAAAAAAUCUGACCAGGUUUCUUUCUA----ACCCUUAU----AGCUAGAAAGUUACAAUGUUAGUUGACAAUU
ABLE03020925.1/355-491     CAUCCAUGUUUACUACUACUUG--AUCUCUGUUUUUGGAGUUUUUCGAGUAUU-UUGCGAUGCAUGGGAGAGAAA---------AUUGUGACCAGGUUUCUU--CAAAUUUCCCAAUUUCGGACUUGA--AGUUACAAUGUCAUUGUACAAUA
#=GC SS_cons               :::<<<<<<-------<<<<<<-----<<_________>>----->>>>>>---------->>>>>>---------.......--<<<<<<<---<<--<<<<<<<<___________....__>>>>>>>>-->>--->>>>>>>:::::::
#=GC RF                    aauCCaUGuUUACUACUaCUugucAuCuCUuuuUuuuuGagaUuUcgAGuAUUUUUGCGAUgCAuGGaAAAuAAAa.......uAaggUGaCCAGGUUUCUuuccaaaUUucCCaaaU....aauuggaaAGUUACAAUGuCAccuuACAAua
//
# STOCKHOLM 1.0

#=GF AC   RF01609
#=GF ID   ceN103
#=GF DE   Caenorhabditis snoRNA ceN103
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   55.00
#=GF TC   60.50
#=GF NC   42.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948605.1/1-109             UACCCCAUGAUGUAUCAAUUUAGCUAAUUGUGAG----CUACUUCGCUCUCGAGAUUU----UGUCUUGAAGUGUG-AGUCGUAUUGAACGAAC-U-UUGUCGAAGCUGAUCUGAGGGAG
CAAC02000457.1/320111-319995 UUCCCCAUGAUGUCAAAACUUAGCUAAUUGUGAGUCGUCUAAUAUUCUAAAAAGCAUUGCCUUGUU-UGGAAUUUA-GCUGAUACUGAACUAAUAU-UCGUCGAAGCUGAUCUGAGGGAC
DQ789513.1/1-115             U-CCCCAUGAUGUCAAAACUUAGCUAAUUGUGAGUCGUCUAAUAUUCUAAAAAGCAUUGCCUUGUU-UGGAAUUUA-GCUGAUACUGAACUAAUAU-UCGUCGAAGCUGAUCUGAGGGA-
ABEG02000404.1/2440-2549     UUCCCAAUGAUGUCAAAACUUAGCUAAUUGUGAG----CUGCUUCAUUU-UAAGAAAC----UGUCUUAGAAUAAGAAAUAGCACUGAACAAAU-AAUCGUCGAAGCUGAUCUGAGGGAA
#=GC SS_cons                 ::<<<_____________________________....____________________....______________._________________._.__________________>>>::
#=GC RF                      UuCCCcAUGAUGUcaaAAcUUAGCUAAUUGUGAG....CUAaUuuucUaaaAAGaauU....UGUuUUggAAUuua.aaUaaUAcUGAACuAAU.u.UcGUCGAAGCUGAUCUGAGGGAa
//
# STOCKHOLM 1.0

#=GF AC   RF01610
#=GF ID   ceN104
#=GF DE   Caenorhabditis snoRNA ceN104
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   65.00
#=GF TC   80.10
#=GF NC   37.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AY948647.1/1-169         CUGCAAUG-UU--CUCA--GUGCAUCCUUUGGUUCUCCGAGCCGAAAGAAGUCACUAGCUGAAAAAGAGUUUAUACUCUGAUCACAC-------------------------------------AGUAA-CAUUGCAAUAAAAGCUUAGCUCGAGAUGCGUGUGCCGUUCUGCUUUU-AAUGCGAUCUGGUUCCUUUUCUCCUCGGGACAAUU
AY948716.1/2-197         AAGCAGUU-CU--CC-A--A--CAGAAAUAUGUG---CAUGAAGUGAUGGUUUGGGUAAC----CAUUUCAUCUUUUCAUGUCAUAUAUCUCCUGCCUCUCACGGUUUCAUCUGUGAGAAGCUUCAAAG-AACUGCAAUAGAAGUCUAGCUCGAGAUGCGUGUGCCGGUUUGCUUUU-AAUGCAAUAUGGUUCCUUUUCUCCUCGGGACAGUU
DQ789490.1/2-146         GUGCAGUUUCU--CU-C--AU----GGUUU-------UCGACUGCUGACCGUAAAUUUU-------CCGGUCAGAGGUCGUUAG--------------------------------------------AGAACUGCUAUAUAAGCCUAGCUCGAGAUGCGUGUGCUGGUUUGCUUCC-AAUGCGAACUGGUUCCUUUUCUCCUCGGGACAAUU
ABEG02009257.1/8953-8799 CAGUUCUU-CU--CU-G--GAGCAAUGAAAAUUUCUCCUAACUGCUGGCAAUCAAAUUU-------GUUGCCAGAAGUUGCUCA--------------------------------------------G-AACUGCUAUAUGAGUCUAGCUCGAGAUGCGUGUGCCGGAUUGCUUUUCAAUGCGAUCUGGUUCCUUUUCUCCUCGGGACAAUU
ABEG02009257.1/8495-8339 AUGCAGUU-UUUCCU-GGAAAGCUAUGAGAAUAGCU-CAAGCUGCUGGCACU-AGUUUU-------ACCGCCAGAAGUUGUUCU--------------------------------------------A-AACUGCUAAAUGAGCCUAGCUCGAGAUGCGUGUGCUGGGUUGCUUCUCAAUGCGAUCUGGUUCCUUUUCUCCUCGGGACAAUU
#=GC SS_cons             ::((((((.,,..,,.,..,<<-<<<____>>>->>.,,<<<<-<<<<<___________...._____>>>>>->>>>,,,,,,,,.....................................,,,,,.))))))-------------<<<<<<--<-----<<<<<<<<<<____.___>>>>>>>>>>------->-->>>>>>::::::
#=GC RF                  auGCagUu.cU..Cu.a..aaGCaccaauaggugCu.CaggcuGcgggcauUuAauUuuu....aAuuugcccgaagccguUcauAu.....................................aaaAa.aAcuGCaAUAuaAGucUAGCuCGAGAUGCGUGUgCcggguuGCUUuU.AAUGCgaccugGuUCCUUUUCUCCUCGgGACAAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01611
#=GF ID   ceN108
#=GF DE   Caenorhabditis snoRNA ceN108
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   50.00
#=GF TC   53.10
#=GF NC   44.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


DQ789422.1/5-79            GUGCAAUGACUGACUUGGAUAAGUUUCGGCUGAAACGUCACACUUGAUGCCAACUUUUAAGAAUUUGCUGAGCAC
AY948650.1/1-70            GUGCGAUGAAUGACUUGGAUAAGUUUCGGCUGAAACUUG----GUGAUGCCAACUUUUUAAAA-CUGCUGAGCAC
AAGD02000330.1/39067-38998 GUGCGAUGACUGAUUUGGAUAAGUUUCGGCUGAUAAUUA----UUGAUGCCAACUUUUGAAUA-UUGCUGAGCAC
#=GC SS_cons               <<<<___________________________________....____________________._______>>>>
#=GC RF                    GUGCgAUGAcUGAcUUGGAUAAGUUUCGGCUGAaAcuUa....uUGAUGCCAACUUUUaAaaA.uUGCUGAGCAC
//
# STOCKHOLM 1.0

#=GF AC   RF01612
#=GF ID   ceN105
#=GF DE   Nematode snoRNA ceN105
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   55.00
#=GF TC   56.50
#=GF NC   53.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948648.1/1-141           GAUUGUCGUGAAUCUUGAUCGGCGUGUUUAUUUUACCCGCGUUGAUUGUAAAGGCCGACAUAUAUCAAAAUUUGACAUUAAUGCUGGAAGUUUCUGAAAUAGUUCC----------AUUUUUCUUCCAAUUAU-UUCAAAUGUCAAACAAAC
DQ789506.1/1-149           GAUUGUCGUGAAUCUUGGUCGAUGGGCUUAUUUUACCCCCAUUGAUUGUAAAGGCCGACAUAUACCAGUUUCGACGGUUACUUACAGGAACAGCCUGAACAUUUUGAUUUUUGAAGGUU--UUUUCUG-UAAGCUUGUAAUUGCUGUCGAAC
ABEG02000343.1/11795-11924 UUUUGUCGUGAAUCUUGAUCGACGAAUUGAGUUUACCUGCGUUGAUUGUAAAGGCCGACAUAUAUAAAACA-UGACACUACUGUUCGUACUUGUUU----AGUACC---------------UGUUCGGAUCAUCUGAAAGUUUC--UCAGAU
#=GC SS_cons               :::<<<<<-<-----<<<<<<<<<<<--<<___>>-->>>>>>>>>>>------>>>>>>----------<<<<<<<<<<<<<-<<<<<<-------<<<______..........>>>..->>>>>>-->>>->--->>>>>>>>>:::::
#=GC RF                    gaUuGuCGUGAAUCUugauCgacGgGuUuauUUuaCCCcCguuGauugUAAAGGCCGaCaUAUAucAaauccggccauuacugucgGgaguugcuuaaacAgUucc..........guu..UcucCcgAUcagCuuaaaauggccggCaaAc
//
# STOCKHOLM 1.0

#=GF AC   RF01613
#=GF ID   ceN109
#=GF DE   Nematode snoRNA ceN109
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   52.00
#=GF TC   53.60
#=GF NC   48.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948651.1/1-67          GCGCAAUGAAUGUUUAACCAUCUUUCGGCUGAAUCCA----UGAUGCCAAUUUUCAAAAUACUGAGCGCAU
DQ789419.1/8-78          GCGCGAUGAAGGUUUAACCAUCUUUCGGCUGACGAAACGACUGAUGCUAGCAUUUUCUAUACUGAGCGCGU
ABLE03023867.1/3997-4063 GCGCGAUGAAGGUUUAACCAUCUUUCGGCUGAGUUCA----UGAUGCCAGAAUUUUCUAUACUGAGCGCUU
#=GC SS_cons             <<<__________________________________...._________________________>>>::
#=GC RF                  GCGCgAUGAAgGUUUAACCAUCUUUCGGCUGAauucA....UGAUGCcAguaUUUucuAUACUGAGCGCaU
//
# STOCKHOLM 1.0

#=GF AC   RF01614
#=GF ID   ceN110
#=GF DE   Caenorhabditis snoRNA ceN110
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   51.20
#=GF NC   44.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948712.1/1-127 AUGCAGAUGUCCAUUACGAAAAGGCUCUUUACCUUUUGACGUUUAGUUAAAUUUGCGAAAUAAAAUUGAUGUCUCGAAGACAUGUGCUUCAUAUUUUGAUGCUCAUGUUCAAGAUCAGCAAACAAAC
AM051026.1/1-124 --GCAGAUGUCCAUUACGCGAAUGC-CUGUGCUUUUCGACGUUUAGUUUAGUCUGCAAGAUAGAAUUGAUGUCUCGAAGACAGGUACAUCAGCUUUUAGAGUUCCUGUUCAAGAUCAGCAAACAAAC
AY948652.1/1-126 GAGCAGAUGUCCAUUACGCGAAUGC-CUGUGCUUUUCGACGUUUAGUUUAGUCUGCAAGAUAGAAUUGAUGUCUCGAAGACAGGUACAUCAGCUUUUAGAGUUCCUGUUCAAGAUCAGCAAACAAAC
#=GC SS_cons     ::<<<<<<-------<<<<<<<___.________>>>>->>>-------->>>>>>---------<<<--<<<<-<<--<<<<<-<<_____________>>->>>>>>>->>>>--->>>::::::
#=GC RF          auGCagacGUCCAUUaCGcgaauGC.CUgUgCuUuucgACGuUUAGUUuAgucuGCaAgAUAgAAuuGAUguCuCGaAGaCagGUgCaUCAgcUUUUagaGcUCcuGuuCAaGauCAGCaaACAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01615
#=GF ID   ceN111
#=GF DE   Nematode snoRNA ceN111
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   43.00
#=GF TC   43.60
#=GF NC   42.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


DQ789435.1/1-69          AAGCCAUGAUGAUUUUAUAGUUCAGCUAAUCUACG-GAUUUGAUGAUAAAUUUCGCCCCUAUCAGAGCUU-
AY948653.1/1-70          AAGCAGUGAUGAUUUUAUAGUUCAGCUUAUCUUCG-GAUUUGAUGAGAAAUUUCGCCCCUAUCAGAGCUUU
ABLE03025354.1/1587-1657 AAGCUAUGAAGAUUUUAUAGUUCAGCUUACCCCAGCGGAUUGAUGAUAAAUUUCGCCCCUAUCUGAGCUUU
#=GC SS_cons             <<<________________________________._______________________________>>>:
#=GC RF                  AAGCuAUGAuGAUUUUAUAGUUCAGCUuAuCuucG.GauUUGAUGAuAAAUUUCGCCCCUAUCaGAGCUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01617
#=GF ID   ceN113
#=GF DE   Caenorhabditis snoRNA ceN113
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   40.00
#=GF TC   40.10
#=GF NC   37.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AY948654.1/1-131           UGGCUAAUGAUGUUCUCUGCGAAAUACACAACUUACUACAAACUGAUCUUAUUUGAAUUGAGGGUUACUGUAGCUACUACUGUAGCUACCGUAAUCCUCACAGUGUGAACUUAAAUUAAAGACUGAAGCUU
ABLE03030381.1/11339-11443 UGGCUGGUGAUGCUC---GCGAAUUAUACAACUUACUACAACCUGAUCUUAUUUGAAAGGUUCUAUACAGUACCUACUCC----------------------GUGUGAACUGAAAUU-ACGACUGAAGCUG
#=GC SS_cons               ::<<<_________________________________________________________________________________________________________________________>>>::
#=GC RF                    UGGCUaaUGAUGuUCUCUGCGAAaUAuACAACUUACUACAAaCUGAUCUUAUUUGAAuuGauguuUACuGUAgCUACUaCUGUAGCUACCGUAAUCCUCACAGUGUGAACUuAAAUUAAaGACUGAAGCUu
//
# STOCKHOLM 1.0

#=GF AC   RF01618
#=GF ID   ceN114
#=GF DE   Nematode snoRNA ceN114
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   44.00
#=GF TC   44.30
#=GF NC   39.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


DQ789446.1/1-61            GUGCAAGGAUGAA-AAGAACUCUCUCACUGAUAGAUGAUGUCUUCCUACAUUAUCAGAGCAC-
AY948655.1/1-63            GUGCAAGGAUGAAAAAGAACUCUCUCACUGAUAGAUGAUGUCUUCCUACAUUAUCAGAGCACU
ABLE03028744.1/13391-13453 GUGCAAGGAUGAAAAAGAACUCUCUCACUGAUACGUGAUGUCUUCCUACAUUAUCAGAGCACU
#=GC SS_cons               <<<________________________________________________________>>>:
#=GC RF                    GUGCAAGGAUGAAAAAGAACUCUCUCACUGAUAgaUGAUGUCUUCCUACAUUAUCAGAGCACU
//
# STOCKHOLM 1.0

#=GF AC   RF01619
#=GF ID   ceN115
#=GF DE   C. elegans sRNA ceN115
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   44.00
#=GF TC   45.90
#=GF NC   42.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Caenorhabditis_elegans_small_RNAs
#=GF SQ   2


Z80218.1/3076-3234 CAGUUCUCCAAGACGGACGGAGCUUUCGAGUUUCGUGCUACGGCACGUCUCUCGGAGAGCCAAGACAAAUCCAAGUCAAAAACCAACAAACCAAAUAAAUGACUUAACAAAAUGCUCCCCGUCUUUAAAUUUUGGAAAAGGGUCCCAAUAGGGACCCGG
AY948611.1/1-159   CAGUUCUCCAAGACGGACGGAGCUUUCGAGUUUCGUGCUACGGCACGUCUCUCGGAGAGCCAAGACAAAUCCAAGUCAAAAACCAACAAACCAAAUAAAUGACUUAACAAAAUGCUCCCCGUCUUUAAAUUUUGGAAAAGGGUCCCAAUAGGGACCCGG
#=GC SS_cons       ::::::((((((((((--(((((<<<<<<<---<<<<<____>>>>>--->>>>>>>,,,,,,,,,,,,,,,<<<<<<_____________________>>>>>>,,,,,,,,)))))))))))--------))))---<<<<<<<____>>>>>>>::
#=GC RF            CAGUUCuCCaaGaCGGACGGaGCcucCGaGUUUCGuGCUACGGCaCGUCUCuCGgagAGCCAAGACAAAUCCaaGuCaAAAACCAACAAACCAAAUAAAuGaCuuAACAAAAUGCuCCCCGuCuUUAAAUUUuGGaAAAGGGuCCCAAUAGGGaCCCGG
//
# STOCKHOLM 1.0

#=GF AC   RF01620
#=GF ID   ceN125
#=GF DE   Nematode snoRNA ceN125
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   60.00
#=GF TC   65.90
#=GF NC   35.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948601.1/1-137         CUCACCCACGGCAACAAAUUCCAAUUGUGUGUAA--CAUUCAAUGCAAUUGAGCCGACGCCGUGGGAAAUCACUUUCGUGGAACCAUUUGAUCCCACGCUCGUU-ACU--GUUAAUGAUUGUGGUUUGCACGUGGUUUACAA
DQ789470.1/1-139         C-CACCCAAGGCAACAAAUUCCAAUCGUGUGAUCUUCUCGCAACACGAUUGAGCCGACGCCUUGGGAAAGCAUUGUCUUUG-ACCAUUUGAUCCCACUCUCGCU-ACUCAAUUGGUGAUUGUGGUUUGCACAUGGUCCACAC
AM051030.1/1-135         --CACCCACGGCAACAAAUUCCAAUUGUGUGUAA--CAUUCAAUGCAAUUGAGCCGACGCCGUGGGAAAUCACUUUCGUGGAACCAUUUGAUCCCACGCUCGUU-ACU--GUUAAUGAUUGUGGUUUGCACGUGGUUUACAA
ABLE03021230.1/1176-1046 CCCACCCAUGGCAACAAAUUCCAGUCGCGUGUUU---UGUCAACGCGAUUGAGCCGACGCCAUGGGAAAUCAAAUGC------CCAUUUGAUCCCACUUUCGGCGAUU--UUCGCCGACUGUGGUUUGCACGUGGUCCACAG
#=GC SS_cons             :.::((((((((,,,,,,,,,<<<<<<<<<____..______>>>>>>>>>,<____>))))))))--------------<.<<<<<-<<<--<<<<--<<<<<.___..___>>>>>-->>>>-->->>->>>>>->::::
#=GC RF                  C.CACCCacGGCAACAAAUUCCaaucGcguGuua..CuuuCAacgCgauuGAGCCGACGCCguGGGAAAuCAuuuuCgUgg.aCCacUuGaUCCCaCucuCgcc.AcU..aUuggcGauUGuGGUUuGCaCguGGuucACAa
//
# STOCKHOLM 1.0

#=GF AC   RF01621
#=GF ID   ceN126
#=GF DE   Caenorhabditis snoRNA ceN126
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   150.40
#=GF NC   48.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


DQ789472.1/2-132         AAGCAGUCGUUCAGUGACGCAAGCGAUUUUUCA-AUGCGUUUGUGCCUAAUCUUUGACUGCAAGAGAAUCAUUGUCAUAGUCAAGCGGUCCGCUAUCUGUGUAGCAUUCUGUUCAAGAUUUGACUUACAUUU
AY948664.1/1-130         AAGCAGUCGUUCAGUGGCGCAAGCGAUUUUCCC-AUGCGCUUGUGCCUAAUCUUUGACUGCGAGAUAAA-AAUGUCAGAGUCAAGCGGUCCGCUAUCUGUGUAGCAUUCUGUUCAAGAUUUGACUGAUAUUU
ABLE03031933.1/4816-4685 AUGCAGUCGUUCAGUGGCGCUGGCGAUUUUCUCAAUGCGCCUGUGCCUAAUCUUUGACUGCGAUAUCAUUGUUGUCAUAGUCAAGCGGUCCGCUACCAGUGUAGCAUUCUGUUCAAGAUUUGACUUAUAUUU
#=GC SS_cons             ::<<<<<<<------<<<<<<<<<<________.___>>>>>>>>>>------->>>>>>>------------<<<<-<<<<-<<<<<---<<<<<____>>>>>--->>>>>--->>>>>>>>::::::::
#=GC RF                  AaGCaGuCgUUCAGUGgCgCaggCGAUUUUccc.AUGCGccuGuGcCUAAUCUUuGaCuGCgAgAuaAuuauUGuCauaguCAagCgGUCCGCuacCuGUguaGCAUUCuGuuCAAGauuuGaCUuAuAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01622
#=GF ID   ceN22
#=GF DE   Nematode snoRNA ceN22
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   45.00
#=GF TC   47.90
#=GF NC   36.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AY948615.1/1-76            AUUGCAGACCGGUGAUGAAACUGUUCUAGGAAGUGCCGUCUUAGAAACAAUGAUUAUGAAUUGGACGCUGAGGUCA
ABEG02003613.1/24170-24244 AUUGCAGGCCGGUGAUGAAACUGU-CUAGGAAGUGCCGUCUUAGAAACAAUGAUUAUACAUUGGACGCUGAGGCCA
#=GC SS_cons               ::::::<<<<_____________________________________________________________>>>>:
#=GC RF                    AUUGCAGgCCGGUGAUGAAACUGUUCUAGGAAGUGCCGUCUUAGAAACAAUGAUUAUaaAUUGGACGCUGAGGcCA
//
# STOCKHOLM 1.0

#=GF AC   RF01623
#=GF ID   ceN23-1
#=GF DE   Caenorhabditis sRNA ceN23-1
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; cmfinder;
#=GF GA   40.00
#=GF TC   72.50
#=GF NC   36.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Caenorhabditis_elegans_small_RNAs
#=GF SQ   3


AY948616.1/1-100               AUCUACCUUACUCGAAA-ACCCGCAUAUGAAGACCACUAAAUGACGAAUCCUAAUAACCCAAUGGGUUUCAUUGCGGAUAUGAGGCAUUUGUCUGAGCGGA
AAGD02011396.1/24298-24397     CCCUACCUUACUCGAAA-ACCCGUCGAUGAAGACCACUAAAUGACGAAUCCUAAUAACCCAAUGGGUUUCAUUGCGGAUAUGAGGCAUUUGUCUGAGCGGG
CAAC02000575.1/1203610-1203510 GCCUACCUUACUCGAAAUACCCGUCGAUGAAGACUACUAAAUGACGAAUCCUAAUAAACCAAUGGUUUUCAUUGCGGAUAUGAGGCAUUUGUCUGAGCGGG
#=GC SS_cons                   :::::::::::::::::.::<<<<------------------<<<<<<<<<<-<<<-<<<<<<<<___>>>>>>->>->>>->>>->>>>>>>--->>>>:
#=GC RF                        acCUACCUUACUCGAAA.ACCCGccgAUGAAGACcACUAAAUGaCgaauCCuAauaAcCCaauGggUUuCauuGCGgAuauGaGGCauuuGuCUGAgCGGg
//
# STOCKHOLM 1.0

#=GF AC   RF01624
#=GF ID   ceN27
#=GF DE   Nematode snoRNA ceN27
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   38.00
#=GF TC   38.10
#=GF NC   35.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


ABEG02003244.1/3220-3299 GACUUUUACAAUCCUAUGAUGAGAGUUUGCGACUAGGGCGGUCAUACAUAAUCAUGGUGAUUCUAGUCAUUCUGAUGGUA
FO080432.1/18063-18142   CACUUGUUACAUCCAAUGAUGAGAGUUUGCGACUAGGGCGGUCUUACACAAUCAUGGUGAUUCUAGUCAUUCUGAUGGUA
#=GC SS_cons             ::::::::::::<<<____________________________________________________________>>>::
#=GC RF                  gACUUuUuaaAUCCaAUGAUGAGAGUUUGCGACUAGGGCGGUCuUACAuAAUCAUGGUGAUUCUAGUCAUUCUGAuGGUA
//
# STOCKHOLM 1.0

#=GF AC   RF01625
#=GF ID   ceN28
#=GF DE   Caenorhabditis snoRNA ceN28
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   70.00
#=GF TC   104.50
#=GF NC   47.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948623.1/1-88              CACGUCUGGUGAGGAUGAAAACAGGACAGGUUUCGCUAAAAUAUUA-CCGAAUGCCAAUAUGUCGAGACACCUUGGCUGUCUGAGGACG
CAAC02000575.1/854533-854445 UACGUCUGGUGAGGAUAGAAAAAGGACAGGUUUCGCUAAAAUACUAGCCGAACGCCAACAUGUAGAGACACCUUGGCUGUCUGAGGACG
DQ789436.1/1-87              --CGUCUGGUGAGGAUAGAAAAAGGACAGGUUUCGCUAAAAUACUAGCCGAACGCCAACAUGUAGAGACACCUUGGCUGUCUGAGGACG
ABLE03009837.1/7795-7881     UGCGUCUGGUGAGGAUAGAAAAAGGACAGGUUUCGCUAAAAU-UAG-CAGAACGAGAACAUGUCGAGAUACCUUGGCUGUCUGAGGACG
#=GC SS_cons                 ::<<<<________________________________________.______________________________________>>>>
#=GC RF                      uaCGUCUGGUGAGGAUAgAAAaAGGACAGGUUUCGCUAAAAUAuuA.CcGAAcGccAAcAUGUaGAGAcACCUUGGCUGUCUGAGGACG
//
# STOCKHOLM 1.0

#=GF AC   RF01626
#=GF ID   ceN30
#=GF DE   Caenorhabditis snoRNA ceN30
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   65.00
#=GF TC   90.70
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


DQ789421.1/3-75          GGCUGUGAAGAUCACUAUUCCCAACGCUUGGAAUGAAAAUUACUGAUUAUAAUCCAAUCCUUUUCUGAGCCAA
AY948671.1/1-73          GGCUGUGACGAUUACUAUUCCCAACGCUUGGAAUGAACCAAAGUGAUUAUUAACCAAUCCUUUUCUGAGCCAA
AM051016.1/3-74          GGCUGUGACGAUUACUAUUCCCAACGCUUGGAAUGAACCAAAGUGAUUAUUAACCAAUCCUUUUCUGAGCCA-
ABLE03029083.1/8900-8971 GGCUGUGAAGAACAAUAUUCCCAACGCUUGGAAUGAAACAAAGUGAUUAUU-UCCAAUCCUUAUCUGAGCCCA
#=GC SS_cons             <<<_________________________________________________________________>>>::
#=GC RF                  GGCUGUGAaGAuuAcUAUUCCCAACGCUUGGAAUGAAacAAAgUGAUUAUuAuCCAAUCCUUuUCUGAGCCAA
//
# STOCKHOLM 1.0

#=GF AC   RF01627
#=GF ID   ceN36-1
#=GF DE   Nematode snoRNA ceN36-1
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   48.00
#=GF TC   49.20
#=GF NC   42.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


DQ789475.1/2-133         CAUCGCUCUCCAGCUCCAUGC-AGACGUAAG-AAAGUCAGUGUGGCGUUUUCAUGAGCGGAAAUUGUACACUGUUCCAUAAAACAAUUGUUACACUCUUUAUGAGAGAACGAUCACCUAAUGGUUCAAACAUUU
AY948673.1/1-130         CAUCGCUCUCCAGCUCCAUGC-CGAUGUAAA-AAAGUCAGUGUGGCGUUUUCAUGAGCGGAAAUUAU-CACUGUUCCAAAAAACAAUUGCUAGUCUCC-UGUGAGCUAAUGAUCACCUGAUGGUUCAGACACUU
AY948674.1/1-129         -AUCGCUCUCCAGCUCCAUGC-AGACGUGAA-AAAGUCGGUGUGGCGUUUUCAUGAGCGGAAAUUAA-CAUUGUUCCAAAAAACAAUUGCUAGUCUCC-UGUGAGCUAAUGAUCACCUGAUGGUUCAAACACUU
ABLE03021145.1/2158-2290 CAUCGCUCUCCAGCUCCAUGCUAGACGUACAUUCAGUCAGUGUGGCGUUACAAUGAGCGGAAAUUGU-CACUGUUCCUAAAAACAAUUGCUAGUCUCUGUAUGAGCUAAUGAUCACCUGGUGGUUCAGACAUUU
ABEG02002611.1/2974-3102 UAUCGCUCUCCAGCUCCAUAC-UAACGUAA--GAAGUCAGUGUGGCGUUUUCACGAGCGGAAAUUGU-CACUGUUCCAAAAAACAAUUGCUAGUCUCC-UGUGAGCUAAUGAUCACCUGAUGGUUCAGACAGAU
#=GC SS_cons             ::<<<<<<---<<<-<<<<<<.--<<_____.___>>-->>>>>>->>>----->>>>>>-------.-----------------<<<<-<<<-<<<_.___>>>>>>->>>>:::::::::::::::::::::
#=GC RF                  cAuCGCuCUCCagCUCCaugC.agacGUAaa.aaAguCAGuguGGCGuuuUcAUGaGCGgAAAUUgu.CAcUGUUCCaAAAAACAauugcuaguCuCu.UgUGaGcuaAcgauCACCUgAUGGUUCAgACAuuU
//
# STOCKHOLM 1.0

#=GF AC   RF01628
#=GF ID   ceN38
#=GF DE   Caenorhabditis snoRNA ceN38
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   50.70
#=GF NC   35.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948675.1/1-137           ACGCGUCAUUUUCAUCCAAUUGGCAACGUG-AUUCU-AAUGUUGGCGAUUCAGCGUAUU---UCUGACGCAAAAUUGAUAACUUCUCCAUUGACGUCUAGUCAGACUAAACUGGCUCGGAUACAAUUAGGGAGUUUACACUU
DQ789469.1/2-141           ACGCGUC-UUUUCAUCCAAUUGUCAAUGUGUAAUCC-AAUGUUGAUGAUUCAGCGAAUUCAUUCAGACGCAAUACUGACAACUUCUCCAUUGACAUCUAGUCAGACUAAACUGGCUUGGAUACAAUUAGGAAGUUUACAUUU
AAGD02006733.1/29859-29995 ACGCGUCUUAUUCAUCCAAUCUUCAACGUG-AAACACAAUGUUGGGGAUUCAGCGUAUU---UCGGACGCAAAACUGACAACUUCUCCAUUGACGUCUAGUUAGCUUUCACUACC-UGGAUACAAUUAGGAAGUUGACAAUU
#=GC SS_cons               ::<<<<<<---------<<<<<<<<<<<<_._____._>>>>>>>>>>>>---------...-->>>>>>---------<<<<<<<--<<<<--<<<<<<<<<<______>>>>>->>>>>->>>>-->>>>>>>:::::::
#=GC RF                    ACGCGuCcUuUUCAUCCaaucgcCaacguG.AauCu.AauguuGgcgauuCAGCGuAUU...UCgGaCGCAAaAcUGAcaaCuuCuCCauuGACguCuaGccaGacUaaACuggCUugGacACaauUAgGaaGuuuACAuUU
//
# STOCKHOLM 1.0

#=GF AC   RF01629
#=GF ID   ceN39
#=GF DE   Nematode snoRNA ceN39
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   35.00
#=GF TC   36.60
#=GF NC   33.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948676.1/1-131       AUGGCGGAUAGGAACCAGGUCAUGUUUGUACGUGAUUUGGGCCGACAUCCCCGCCGAAAUAGUCCU-GCGAAGAUCUAAGGUCGCUUCUGGAUGGAUUUGCCACCGGGUGCACACCAUCUUCGUGCACAAUU
DQ789464.1/2-132       UAGGCGGAUAGGAACCAGGUCAUGUUUGUAUGUGAUUUGGGCCGACAUCCCCGCCGAAAGAAAUUC-GUGAAGAUCUAAGGUCGCUUCUGGAUGGAUUUGCCACCGGGUGCACACCAUCUUCAUGUACAAUU
AM051048.1/1-129       --GGCGGAUAGGAACCAGGUCAUGUUUGUACGUGAUUUGGGCCGACAUCCCCGCCGAAAUAGUCCU-GCGAAGAUCUAAGGUCGCUUCUGGAUGGAUUUGCCACCGGGUGCACACCAUCUUCGUGCACAAUU
ABLE03016317.1/858-727 UAGGCGGUUAGGAACCAGUUCAUGUCUGUACGUGAUUUGGGCCGACAUCCCCGCCAAAAUGGAACUCUUGAAGAUUUAAGGUCGCUUCUGAAUGGAUUUGCCAUCAGGUGCACACCAUCUUCACGUACACUU
#=GC SS_cons           ::<<<<<---<<--<<<<<<<<<<<____>>>>>>>>>>>->>------->>>>>-----------.<<<<<<<<----<<<-<<-<<<<<-<<<_____>>>>>>>>->>-->>>>>>>>>>>::::::::
#=GC RF                uaGGCGGaUAGGAACCagguCacGuuUGUaCguGaccuGGGCCGACAUCCCCGCCgAAAuagaucu.gcGaaGaucUAAGGuCGCUcCcGgAuGGAUUUGCCacCgGgUGCACaCCauCuuCgcGuACAaUU
//
# STOCKHOLM 1.0

#=GF AC   RF01630
#=GF ID   ceN40
#=GF DE   Nematode snoRNA ceN40
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   35.00
#=GF TC   35.10
#=GF NC   32.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.75 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948677.1/1-122           CAGCGGUGAUCGAUGACUUGUGCAGUGGCCGAGGCGAUCGGAUUGUGAUGUCGCCUGAA-AAGGCGG-GACCCAACGUCGCGCCUUUCGCCAGAAGAUGGAAAU--AUGCGCAACGUCUGAGCUGA
DQ789544.1/1-118           ---CGGUGAUCGAUGACUUGUGCAGUGGCCGAGGCGAUCGGAUUGUGAUGUCGCCUGAA-AAGGCGG-GACCCAACGUCGCGCCUUUCGCCAGAAGAUGGAAAU--AUGCGCAACGUCUGAGCUG-
DQ789456.1/1-123           GGGCGAUGAUCGAAAUCUUGUGCAGCGGCCGAGGCGUUUGUGCUG-GACGUGGCCUGAAUAAGGCUGUAACCCAACGUUCCGCCUUUCGCCAGAAGAUGGAUGC-UUUGCGCAAUGUCUGAGCC-U
ABEG02001388.1/25733-25610 UGGCGAUGAUAGAAAUCUUGUGCAACGGCCGAGGCGAUCGGAUUGCGACGUCGCCUGAG-AAGGCGG-GACCCAACGUCGCGCCUUUCGCCAGACGAUGGAUACUCUUGCACAGUGUCUGAGCUCC
#=GC SS_cons               :<<<_______________________________________________________._______.____________________________________.________________>>>::
#=GC RF                    ugGCGaUGAUcGAaauCUUGUGCAguGGCCGAGGCGaUcGgAuUGuGAuGUcGCCUGAA.AAGGCgG.gACCCAACGUcgCGCCUUUCGCCAGAaGAUGGAuAu.uuUGCgCAAuGUCUGAGCcgu
//
# STOCKHOLM 1.0

#=GF AC   RF01631
#=GF ID   ceN41
#=GF DE   Caenorhabditis snoRNA ceN41
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   50.30
#=GF NC   39.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948678.1/1-137         AUGCACCUUGCACUCUACGCCUUUCCUUUCAAUGGG-UUGGUAUGAUUUAAUAAGGAUGCAAGAGAAUAGUACGGGAAGUUCGAAGACUUGCGGAUUUGCUUCCACGGCUCCGCGAGUUCAUAACUGUCACCACAAUU
DQ789485.1/2-135         CAGCACCUU-CACUCUU---CUAUCAUUCCUGUGUGAAUGCCUAGAUUUAUUAAGGAUGCAAGAGAGAAGAACGGGAAGUUCGAAGACUUGCGGCAAGUUUCUCACGACUCCGCGAGUUCAAAACUAUCACCACAUUU
ABLE03013179.1/5502-5636 UGGCACCUUGCACUCUACGCCUUUCCUUUCAAUGGG-CUGGUAUGAUUUAUGAAGGAUGCGAGAGCGAA-ACUGGGAAGUUCGAAGACUCGUG-AAUGGCUUUUACGGCUCCACGAGUUCGAAACUAUCACCACAAUU
#=GC SS_cons             ::<<<<<<<------<<--<<---<<<______>>>.-->>-->>------->>>>->>>-------------<<<<<<<<----<<<<<<<<<----<<<_____>>>->>>>>>>>>--->>>>->>->>::::::
#=GC RF                  uaGCaCCuuGCACUCuaCGCCUuUCcuUuCaaUggG.uUGGuaugAUUUAuuaaGGAuGCaAGAGagaAGaacGGGaaGuuCGAAgaCucGcGGaauggcuuucACggcUCCgCgaGuuCaaaaCuauCACCACAaUU
//
# STOCKHOLM 1.0

#=GF AC   RF01632
#=GF ID   ceN42
#=GF DE   Caenorhabditis snoRNA ceN42
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   42.00
#=GF TC   44.20
#=GF NC   39.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948679.1/1-131             AUUCCUUCUUAUCCUGCACUCAGUUUGUUCAUUGACUGUGGAGCCUGGAAAUGGAGGAGAAAGUAAAUUUGAUGAUUACUAAUACUUCGCUGUCUUUAGAGGACGCGGAGAUUGUGAGACUUGAAACAUUU
AAGD02000374.1/11494-11623   AUUCCUUCUUAUCCUGCACUCAGUUUGUUGAUUGGCUGUGGAGCCUGGAAAUGGAGGAUAAAUGAUAUUGAAGGAGUGCUAUUACUU-GACGUCUUCUGAGGAUGUGGAGAUAGUGUGAAUUUGAACAAUU
CAAC02000450.1/951386-951258 AUUCCUUCAUAUCCUGCACGCAGUU-AUUCGAUGGCUGUGGAGCCUGGAAACGGAGGAUAGAUAAGUUUAAAUGAAUACUAAUGCUU-GGUGUCUUCUGAAGACACCGAGAUUGUGUGAAUUUGAACAUCA
#=GC SS_cons                 ::<<<<<<---<<<-<<-<-<<<<<________>>>>>->-->>-->>>--->>>>>>---------<<<<<---<<<<-----<<<.<-<<<<<_____>>>>>>->>>--->>>>--->>>>>::::::
#=GC RF                      AUuCCuuCuUAuCCUGCACuCaGcuUgUUcauUggCuGUGGAGCCUGGaAAuGgaGGauAaAuaAaaucgaauGAguaCUAaUaCuu.GacGuCcUcuGAgGaCgCggaGAUuGugcGAauucgaACAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01633
#=GF ID   ceN43
#=GF DE   Caenorhabditis snoRNA ceN43
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   71.70
#=GF NC   37.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948680.1/1-129         UGCCCGGUCUUUGCCCCGGAUCAACUUUAAUAGUUAUGACGGUUUCCGACUCGGGAAAAUAGAUUCUUGCAUAACGACGGAAAUUUCAGAGUUUGUUCUGAAUGUCUCCAGUCGAUGUGCAAUACAAUU
DQ789471.1/2-129         AGCCCGGUCUUUGCCCCGGAUCAACUUGAAUAGUUAUGACGGUUUCCGACCAGGGAAAAUAGAUUCUUGUACGUAGA-GGUGAUUUCAGACUACGUUCCGAAUGUCUCUUGUCUACGUACAAUACAUUU
AM051039.1/1-128         -GCCCGGUCUUUGCCCCGGAUCAACUUUAAUAGUUAUGACGGUUUCCGACUCGGGAAAAUAGAUUCUUGCAUAACGACGGAAAUUUCAGAGUUUGUUCUGAAUGUCUCCAGUCGAUGUGCAAUACAAUU
ABEG02003473.1/3428-3556 UGCCCGGUCUUUGCCCCGGAUCAACUAAAAUAGUUAUGACGGUUUCCGACACGGGAAAAUGGAAUAUUGCACGACGACAGAAAUUUCAGACCUCGCUCCGAAUGACUCUUGUCGAUGUGCAAAACAUUU
#=GC SS_cons             ::<<<<<<<------<<<----<<<<_____>>>>---->>>----->>>->>>>-----------<<<<<<<-<<<<<<<---<<<-<<______>>->>>---->>>->>>>->>>>>>>:::::::
#=GC RF                  uGCCCgGuCUUUGCCCCGGAUCaaCuuuAAUaGuuAUGACGGUUUCCGaCucGGGAAAAUaGAuUcuuGcacgacGaCgGaaAUuuCAGacuuuGuuCuGaaUGuCuCcuGuCgAcgugCaauACAuUU
//
# STOCKHOLM 1.0

#=GF AC   RF01634
#=GF ID   ceN44
#=GF DE   Caenorhabditis snoRNA ceN44
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   70.00
#=GF TC   88.80
#=GF NC   35.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


DQ789442.1/1-71        -GACCAUGAUAGGAUAACCUAGAGUCUCUGAACCAUUUCGUGUUUGCACAAACAAUGCUCUUUGUCUGAGUC--
Z48717.1/2830-2757     CGACAAUGAUAGGAUAACCUAGAGUCUCUGAACCAUUUCGUGUUUGCAAAAACAAUGCUCCUUGUCUGAGUCAG
AEKS01002425.1/291-364 GGACUAUGAUAGGAUAACCUAGAGUCUCUGAACCAUUUCGUGUUUGUACAAACAAUGCUCUUUGUCUGAGUCAG
#=GC SS_cons           :<<<_________________________________________________________________>>>::
#=GC RF                gGACuAUGAUAGGAUAACCUAGAGUCUCUGAACCAUUUCGUGUUUGcAcAAACAAUGCUCuUUGUCUGAGUCAG
//
# STOCKHOLM 1.0

#=GF AC   RF01635
#=GF ID   ceN45
#=GF DE   Caenorhabditis snoRNA ceN45
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   60.00
#=GF TC   90.20
#=GF NC   47.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948682.1/1-127         GUGGGGCACAGAGUUGCAGUUGAUUGAAACUAAAUCAUGUGCGCUAAGUUGUCCCGAAAGUAUC--UUUGGAUUUCUACAAAACAGUGUUCCUUCUUUAGGAUGCUGAUCCGUAGAGAUCUGAACAAAU
AM051058.1/1-124         ---GGGCACAGAGUUGCAGUUGAUUGAAACUAAAUCAUGUGCGCUAAGUUGUCCCGAAAGUAUC--UUUGGAUUUCUACAAAACAGUGUUCCUUCUUUAGGAUGCUGAUCCGUAGAGAUCUGAACAAAU
DQ789500.1/1-127         GGGGGGCACAGAGUUGCAAGUGAUUGAAACUAAAUCAUCUGCGCUAAGUUGUCCCGAAAUGGUG-UUUCGGAUUUUAAGAAAAUGAUGCUUGCUUCAUGAAGUGUCGUUGAUAU-CUAUUCGAACAAUU
ABEG02006882.1/6227-6355 CUGGGGCACAGAGUUGCAGUUGAUUGAAACUAAAUCAUGUGCGCUAAGUUGUCCCGAAAUCAUCGUUUCGGAUUAUAAGAAGGCAGUGUUACUCCUCUAGGACACUGUUGAUAUGAUAUUCGUACAAUU
#=GC SS_cons             ::<<<<<<<--<<<-<<<--<<<<<_______>>>>>-->>>>>>-->->>>>>>---------.---<<<<<<<<<<<----<<<<<<<<________>>>>>>>>---->>>>>>>>>>>:::::::
#=GC RF                  guGGGgCaCAGaGuUGCaguuGauuGAAACUAaauCaUguGCgCuAAGUuGuCCCGAAAuuaUc.UUUcggaucucuacAAaacgGcgucccuucuuUaggacgCcguUgaguagagauccgaACAAuU
//
# STOCKHOLM 1.0

#=GF AC   RF01636
#=GF ID   ceN46
#=GF DE   Caenorhabditis snoRNA ceN46
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   90.90
#=GF NC   31.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948683.1/1-125           CUUGCACGACUGCAACCUGCUUUCGGAACUUUACCGUCUGCGGUACUUGUAGUGCUAUAUGAGCGUGGGCCCUCCGUGUGCGUGUAAUUUAAUUGAACUAGCACUCCGUUGGUCACCGGAUAAUU
DQ789462.1/1-120           -----ACGACUGCAACCUGCUUUCGAUACAUUAUCGUCUGCGGUACUUGUAGUGCUAAAUGAAUGUGGGCCCUCCGUGUGCGUGUGAACUAAUUGAACUAGCACUCCGUUGGUCACCGAACAAUC
ABEG02006684.1/26041-25917 CUUGCACGACUGCAACCUGCUUUCGGAGCUUUUCCGUCUGCGGUACUUGUAGUGCUAAAUGAGCGUGGGCCCUCCGUGUGCGUGUAACUUCAUUGAACUAGCACUCCGUUGGUCACCGGACAAUU
#=GC SS_cons               ::::::::<<<<<<<-<<<<---<<<<<___>>>>>--->>>>--->>>>>>>----------<<--<<<<--<-<-<<<<--<<___________>>-->>>>->->-->>>>-->>:::::::
#=GC RF                    cUUGcACGaCugCaaCCuGCUUUCGgcaCuUugcCGUCUGCgGUACuuGuaGuGCUAaAUGAgcGUGGgCCCUCCGUGuGCGUGuaAuuUaAUUGAaCUAGCaCUCCGUUGGuCACCggAcAAUu
//
# STOCKHOLM 1.0

#=GF AC   RF01637
#=GF ID   ceN47
#=GF DE   Nematode snoRNA ceN47
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;Osuch I;
#=GF GA   35.00
#=GF TC   35.70
#=GF NC   34.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AY948630.1/1-155             ACGUAAAUGAAGAAAUACCAUCCUUGCUCUGCGA--GUCGUUGAGC--AAUCACUUGAGAACUCUGA-UGA-GGUAUUGUAGCAUCGGGUUACGGUAG-CCGAGUCAGUUGAUUCUCAUCAUGUGGCACUUCGACGGUGAACAGUUAUGGCCUCUGAUACGU
AAGD02001042.1/12284-12133   AUGUGCGUGAAGAAAUACCAUCCUUGCUCUGCGA--GGCGAUGGAC--ACACACUCGAGAACCCUGC-GGA-GGUACCGUAGCAACGGGUUACAGUAA-CCGAAGCAGUCGAUUCUC---UAGUGGUUCUUCGCCGGUGAACAGUUAUGGCCUCUGACACAU
CAAC02000522.1/191093-190937 CGUUAAAUGAAGAAAUACCAUCCUUGCUCUGCGAUGGCCGUCAAAC--AUACACUUGAGAAUUCUGUGUGAGGGUACUGUAGCAUCGGGUUACUGUACACCAAUCCAGACGAUUCUC---AGGUGGUUUGACGCCGGUGAACAGCUAUGGCCUCUGAUAACG
DQ789432.1/2-154             U---AAAUGAAGAAAUACCAUCCUUGCUCUGCGAUGGCCGUCGAACACAUACACUUGAGAAUUCUGAGUGAGGGUACUGUAGCAUCGGGUUACUGUACACCAAUCCAGACGAUUCUC---AGGUGGUUCGACGCCGGUGAACAGCUAUGGCCUCUGAU---A
DQ789547.1/1-149             U---AAAUGAAGAAAUACCAUCCUUGCUCUGCGA--GUCGUUGAGC--AAUCACUUGAGAACUCUGA-UGA-GGUAUUGUAGCAUCGGGUUACGGUAG-CCGAGUCAGUUGAUUCUCAUCAUGUGGCACUUCGACGGUGAACAGUUAUGGCCUCUGAU---A
ABLE03021199.1/11625-11773   UCGUAAAUGAUGAGAAAACAUCCUUGCUCUGCGA--GUCGUUUGGC--AAAUUGUUUUUCUGGAAAU-UGG-AAAUUUUAAACAUCGGGUUUA------UUAUUUCACUUGAUUCGGAAACUCAUG-GCUUCGACGGUGAACAGCGUUGGCCUCUGAUACGU
#=GC SS_cons                 :<<<______________________________..__________..___________________.___.__________________________.___________________________________________________________>>>:
#=GC RF                      ucgUAAAUGAAGAAAUAcCAUCCUUGCUCUGCGA..GuCGUUgaaC..AaACAcUUGAGAAuucUGu.UGA.GGUAuUGUAGCAUCGGGUUAcuGUAa.CCaAuuCAguuGAUUCUcAuaaugUGGuuCuuCGaCGGUGAACAGuUAUGGCCUCUGAUAcgu
//
# STOCKHOLM 1.0

#=GF AC   RF01638
#=GF ID   ceN48
#=GF DE   Caenorhabditis snoRNA ceN48
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   112.20
#=GF NC   68.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AY948684.1/1-125           AUGCACACAGAAAGUCGAGAUUGCCGGCUUCAAAGGCUUUAUCGUUGAUUACGUGUGCUAUAACAACGCCAUAGGUAUCAUUCUUCGUCUUCUUAGGCGCGGAACAUCUAAAUAUGGCUACAUUU
AAGD02002937.1/70069-70193 AUGCACACUGAAAGUCGAGACAGCCGACUUCAAAGGCUUUUUCGUUGAUUAUGUGUGCCAUACCAACGCCAUAGGUAUCAUUCUUCGUCUUAUUAGACGCGGAACAUCUAAAUAUGGCUACAAAC
DQ789460.1/2-126           CCGCACGCUGAAAGUCGAGUGAGCCUGCUCCAAAGGCUCUUUCGUUGAUUAUGUGUGCCAGAACAACGCCAUAGGUAUCAUUCUUCGUCUUCUUAGGCGCGGAACAUCUAAAUAUGGCUACAGUU
AM051029.1/1-120           --GCACACAGAAAGUCGAGAUUGCCGGCUUCAAAGGCUUUAUCGUUGAUUACGUGUGCUAUAACAACGCCAUAGGUAUCAUUCUUCGUCUUCUUAGGCGCGGAACAUCUAAAUAUGGCUACA---
ABEG02001053.1/4687-4809   CCGCACACAGAAAGUCGAGGAGGCCUG--ACAAAGGCUUUUUCGUUGAUUACGUGUGCUAUAACAAUGCCAUAGGUAUCAUUCUUCGUCUUCUUAGGCGCGGAACAUCUAAAUAUGGCUACAAAC
#=GC SS_cons               ::<<<<<<-------<<<<<-<<<<_________>>>>->>>>>-------->>>>>>---------<<<<<<--<<---<<<<-<<<<<____>>>>>->>>>---->>-->>>>>>:::::::
#=GC RF                    auGCaCaCaGAAAGUCGagaugGCCggCUuCAAAGGCcuucuCGUUGAUUAuGuGuGCuAuAaCAAcGCCauaGGuaUCAuuCuUCGcCuUcUUaGgCGCgGaaCAUCuaAAuauGGCUACAaau
//
# STOCKHOLM 1.0

#=GF AC   RF01639
#=GF ID   ceN49
#=GF DE   Caenorhabditis snoRNA ceN49
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   65.00
#=GF TC   66.90
#=GF NC   36.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


DQ789461.1/2-136         UCCGCCUCUCUACCAAACACUCGUAAGUACUAUUUAUUGCGAGUGCAUGGAAGAGGCGAAUAGAGAACGGAACGUUGUCCACCCCUUCAAUCAUC-AUCAAAUUGGAUUGCGGGCACUUUACCACGGUCGACAUUU
AAGD02001955.1/2837-2971 UACGCCUCUCUACCAAACACUUACAAGUUCUGUUUAUUGUGAGUGCAUGGAAGAGGCGAAUAGAAAACGGAACGAUGUCCACCCCUUCAAUCAUCAGAA-AAUUGGAUUGCGGGCACUUUACCUCGGUCGACAGUU
AY948685.1/1-134         ACCGCCUCUCUACCAAACACUUGCAAGUUCUGUUUAUUGCAAGUGCAUGGAAGAGGCGAAUAGAAAACGGAAUGAUGUCCACUCCUUCGAUUAUC-GUU-CAUUGGAUUGCGGGCACUUUACCUCGUUCGACAUUU
#=GC SS_cons             ::<<<<<<<---<<<--<<<<<<<<<__________>>>>>>>>>-->>>->>>>>>>-----------<<-<<<-<<-----<<<-<<<<<___.___._____>>>>>->>>------>>->>>->>:::::::
#=GC RF                  ucCGCCuCuCUACCaAACaCucgcaaGUuCUgUUUAuugcgaGuGCAuGGAaGaGGCGAAUAGAaAACGGaAcGaUGuCCACcCCuUCaaucAUC.guu.aAUUGgauuGCgGGCACUUUaCCuCgguCGACAuUU
//
# STOCKHOLM 1.0

#=GF AC   RF01640
#=GF ID   ceN51
#=GF DE   Caenorhabditis snoRNA ceN51
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   65.00
#=GF TC   65.90
#=GF NC   31.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948687.1/1-139           CACCGCGUGAGUACUGGCUGUUUGUGUCUCCG-CCAUUGCCAAUCAGCUGUCAUUAACCACGCAAUACCGUACAGAGGUGCUAAAUUACCGU--GAAAACCACUUUAAAAAUUGGUCACUCGGAGGAGGCACCUCAACAUUU
DQ789466.1/1-138           ----GCGUGAGUACUGGCUGUUUGUGUCUCCAUCCAUUGCCAAUCAGCUGUCAUUAACCACGCAAGACUGUAACGGAGUGCUAAAUUACCGUGUGAAUACCAUAACAAAGAUUGGUCACUCGGAGGAGGCGCUUCCACAUUU
AAGD02000343.1/14342-14202 CACUGCGUGAGUACUGGCUGUUUGUGUCUCCA-CCAUUGCCAAUCAGCUGUCAUUAACCACGCUAAACUGAAAUGGAGUGCUAAAUUACCGUGUGAAUACCAUAACCAAGAUUGGUCACUCGGAGGAGGCACUUCCACAUUU
#=GC SS_cons               ::::<<<<<-<<<<-<<<<<-<<<-<<_____._____>>>>>->>>>>>>----->>>>>>>-----------<<<<<<<<---<<-<<<-<<<<---<<<__________>>>>>>>->>>>>-->>>>>>>>:::::::
#=GC RF                    cAcuGCGuGAGuaCUgGCuGUuuGUGcCUCCa.CCAUUgCCaaUCaGCcGuCAUUAaCCaCGCaAaACuGuAauGggGuGCcAAAcuACCGUGuGaAuACCauaacaAAgAUuGGuCaCUCGGagGAgGCaCccCcACAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01641
#=GF ID   ceN53
#=GF DE   Caenorhabditis snoRNA ceN53
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   50.00
#=GF TC   50.90
#=GF NC   46.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AAGD02006818.1/4023-4095 CGGCAGUGAUCGAAUUAUCA-UGAGCCAAUCCUUUUCUGAACACUGUGAGGAUUCAUAUGAUAGGUCUGAGCCA
DQ789515.1/1-74          UGGCAAUGAUUGAAUUAUCAUUGAGCCAAUCCUUUUCUGAACUCCAUGAGGAUGGAAAUGAUAGGUCUGAGCCA
AY948688.1/1-74          UGGCAAUGAUCGAAUUAUCAUUGAGCCAAUCCUUUUCUGAAUUCUGUGAGGAUGUAAAUGAUAGGUCUGAGCCA
#=GC SS_cons             <<<<__________________________________________________________________>>>>
#=GC RF                  uGGCAaUGAUcGAAUUAUCAUUGAGCCAAUCCUUUUCUGAAcuCugUGAGGAUguAaAUGAUAGGUCUGAGCCa
//
# STOCKHOLM 1.0

#=GF AC   RF01642
#=GF ID   ceN54
#=GF DE   Caenorhabditis snoRNA ceN54
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   60.00
#=GF TC   62.00
#=GF NC   39.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


DQ789510.1/3-70            GUUUGUGAUGACUGCAUACGGAUCACUGGGCUCUGAAUAUUCAUGAAACGAUAAUAUCCGUUCUGAUA
AY948689.1/1-68            GUUUGUGAUGACUGCAUACGGAUCACUGGGCUCUGAAUCUCUAUGAACCGAUAAUAUCCGUUCUGAUA
ABLE03004509.1/13480-13547 GUGUGUGAUGACUAUUUACGGAUCACUGGGCUCUGAAUAUUCAUGAAUCGAUAAUAUCCGUUCUGAUA
#=GC SS_cons               :::<<_____________________________________________________________>>
#=GC RF                    GUuUGUGAUGACUgcaUACGGAUCACUGGGCUCUGAAUaUucAUGAAuCGAUAAUAUCCGUUCUGAUA
//
# STOCKHOLM 1.0

#=GF AC   RF01643
#=GF ID   ceN56
#=GF DE   Caenorhabditis sRNA ceN56
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; cmfinder;
#=GF GA   60.00
#=GF TC   69.50
#=GF NC   59.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Caenorhabditis_elegans_small_RNAs
#=GF SQ   4


AY948634.1/1-125           UUCCCCGUGAUUACAA-ACAUUGCUGAAACCUGCCCACCCGAAAGCUUCGAGAU----UGGCGUGGGGGCC-GAUCGAGGAAAA-GCUGACAACGGUGGGAACCAUGAUACAGAUUAUGAGAGAUGAGGGAU
DQ789508.1/1-124           --CCGUAUGAUUACAA-ACUUCGCUGAUACCUGCCCACCCGAAAGCUCAGAGAC---UAGGAGUGGGGUCCCGGUUGAGGACGGCGCUGACAACGGUGGGAACCAUGAUACAGAUUAUGAGAGAUGAUGG--
ABEG02001682.1/16197-16326 UUCCCACUGAUUACAA-ACUUCGCUGAUACCUGCCCACCCGAAAGUCUCGAGAUCGCCUGGAGUGGGGUCCGGAUUGAGGACAG-GCUGACAACGGUGGGAACCAUGAUACAGAUUAUGAGAGAUGAGGGAU
ABLE03025124.1/2292-2171   CGCCCAAUGAUAUCAACACCUCGCUGAUUCCUGCCCACCCGAAGGUCUCGAG--------GCGAGUGGGGU-CGUCGAGGAAAG-GCCGACAACGGUGGGAACCAUGAUACUGAUUAUGAGAGAUGAGGGCU
#=GC SS_cons               :((((,,,,,,,,,,,.,,,,,,,,,,,,,,,,<<<<<<----<<<<<<--<<<....-<<<______>>>.->>>-->>--->.>>>------>>>>>>,,,<<<<<<____>>>>>>,,,,,,,,)))):
#=GC RF                    ugCCcaaUGAUuaCAA.ACuUcGCUGAuaCCUGCCCaCCCGAAgGccccGAgac....uGgcGuGgGGgcC.ggucGAggAaag.gCcGACAACGGuGGGAACCaugauACaGauuauGAGAGAUGAgGGcU
//
# STOCKHOLM 1.0

#=GF AC   RF01644
#=GF ID   ceN59
#=GF DE   Caenorhabditis snoRNA ceN59
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   50.00
#=GF TC   76.30
#=GF NC   41.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948692.1/1-136         CACGGCCAGUUUGAGUUGAUUCGCUCUUUCGCAAUAGAGCUUUGAGUCAAAUUACUGUCCGGAAAUUAUAGAGAUGAAGCUCAUUUGGAGCAAUAA-------CAAUUGUUGAAGCUCCGAAAAUGAUGCUCUUCCCACAAUU
DQ789501.1/2-142         CACGGGCAGUUUGAGUUGAUUCGCUCUUUAUUGAUGGAGCUU-GGGUCAAAUUACUGUCCGAAAAUGAUAGAGAAGAAGAUCUAAUCAAUUUGAAUUGUCUUCCUUAUGAAG-AUGAUUUAUCAAUAGUCUCUUCCCACACUU
ABEG02008766.1/7402-7267 CACGGGCAGUUUGAGUUGAUUCGCUCUUUUAAAGUAGAGCUU-GGGUCAAAUUACUGUCCGAAAAUUAUAGAGAGG-AGCUCAUGUAUAGAUUGAAA----U-UGUUUGGAAAACUUUCAACCACAUAGCUCUUCCCACAGUU
#=GC SS_cons             ::<<<<<<<<-----<<<<<<<<<<<<________>>>>>--.>>>>>>>--->>>>>>>>-----------<<-<-<<<_________________...._._________________________>>>->>>::::::::
#=GC RF                  CACGGgCaGUUUGAGUUGaucCGCUCuUUuauaaUaGAGCUU.GgguCAAAUUACuGuCCGaAAAUuAUAGAGaagAaGcUCauaUaaAguuaaAau....U.cauuUGaagAAuuuucaAucAuaaagCuCuuCCCACAaUU
//
# STOCKHOLM 1.0

#=GF AC   RF01645
#=GF ID   ceN58
#=GF DE   Nematode snoRNA ceN58
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   60.00
#=GF TC   61.10
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948691.1/1-139           CUGCGUCUCUCCAACCCGGACAACUCGCAACUUGUUGCAAUGGUCAGUUCGACUGUUAGAGACGCUAAAUAAGAAAAUUGGCGGAUUCGCUAACGUCG-CGUCCCAUGACCGGAGUUUGAAAGUAGGCCGCUGAACAAUU
DQ789463.1/2-141           CCGCGUCUCUCCAACCCGGACAACUCGCAACAUGUUGCAAUGGUCUGUUCGACUGUUAGAGACGCUAGAUAAGAAAAUUGGUGGAUUCGCUAACACCGCCGUCCUAUGACCGGAGUUUGAUAGUAGGCCGCUGAACACUU
ABEG02008024.1/16011-16149 CUGCGUCUCUCCAACCCGGACCUAUCGCAACGUGUUGCCUUGGUUGGUUCGACUGUUAGAGACGCUAGAUGAGAAACUUGGCGUUUUCGCUAACACCG-CAUCCUAUGAUCGGAGUUUGAUAGUAGGUCGCUGAACACUU
#=GC SS_cons               ::<<<<<<<<--<<<-<<<<<<--<<<<<<____>>>>--->>-->>>>>>--->>>>>>>>>>>---------------<<<<-<--<<<<<<-<<<.-<<<____>>>>>>->>>---->>>-->>>>>:::::::::
#=GC RF                    CuGCGuCuCuCCaaCCCGgaCcacuCGCaaCaUGuuGCaaUGgUcgGuuCGACUGuuaGaGaCGCUAgAUaAGAAAaUUGGcGgauUCgCuaaCacCG.CguCCuAUGacCGgAGuuUGAuaGuAGgcCgCUGAACAcUU
//
# STOCKHOLM 1.0

#=GF AC   RF01646
#=GF ID   ceN63
#=GF DE   Caenorhabditis snoRNA ceN63
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   65.00
#=GF TC   85.50
#=GF NC   42.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


DQ789409.1/1-64            G---UCAGUGAAGAUAAUACUUACCGCCCCAGGCAUAAUGUUUGUGAUGAUUGGUUUAUUCCGAGAC--
AY948696.1/1-69            GUUGUCAGUGACGAUAUUACUUACCGCCCCAGGCAUAGUGUUUGUGAUGAUUGGUUUAUUCCGAGACUU
CAAC02000514.1/91985-92053 GUUGUCAGUGAAGAUAAUACUUACCGCCCCAGGCAUAAUGUUUGUGAUGAUUGGUUUAUUCCGAGACUU
#=GC SS_cons               :::<<<__________________________________________________________>>>::
#=GC RF                    GUUGUCAGUGAaGAUAaUACUUACCGCCCCAGGCAUAaUGUUUGUGAUGAUUGGUUUAUUCCGAGACUU
//
# STOCKHOLM 1.0

#=GF AC   RF01647
#=GF ID   ceN61
#=GF DE   Caenorhabditis snoRNA ceN61
#=GF AU   Osuch I
#=GF SE   INFNERAL
#=GF SS   Predicted; Osuch I
#=GF GA   60.00
#=GF TC   63.70
#=GF NC   50.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948694.1/1-76          CCGUCGAUGACGACCAAGAGUUAUCCCUGUCUGAAUGAUUGUGAGGACAAAAGACUAUGGUAACACUCCGAGACUA
DQ789403.1/1-72          --GUCAAUGACGAAUAGAAGUUAUCCCUGUCUGAAUGAUUGUGACGACAAACAACUAUGGUAACACUCCGAGAC--
DQ789529.1/1-72          --GUCGAUGACGACCAAGAGUUAUCCCUGUCUGAAUGAUUGUGAGGACAAAAGACUAUGGUAACACUCCGAGAC--
ABEG02005220.1/7600-7525 UCGUCGAUGACGACCAGAAGUUAUCCCUGUCUGAAUGAUUGUGAGGAAAAAAGACUAUGGUAACACUCCGAGACUA
#=GC SS_cons             ::<<<__________________________________________________________________>>>::
#=GC RF                  uCGUCgAUGACGAccAaaAGUUAUCCCUGUCUGAAUGAUUGUGAgGAcAAAAgACUAUGGUAACACUCCGAGACUA
//
# STOCKHOLM 1.0

#=GF AC   RF01648
#=GF ID   ceN65
#=GF DE   Caenorhabditis snoRNA ceN65
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   48.00
#=GF TC   48.20
#=GF NC   43.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


CAAC02000457.1/1091310-1091374 AAGCGAUGACGAAUGAUAUCUGCUCUAAUGAGUCUGAAUCCCCAUGUUGAGAUCUUAUCUGAGCU
AY948697.1/1-65                AAGCGAUGACGAUUGAUAUCUGCUCUAAUGAGUCUGAAUUACCAUGUUGAGAUCUUGUCUGAGCU
DQ789516.1/1-64                -AGCGAUGACGAAUGAUAUCUGCUCUAAUGAGUCUGAAUCCCCAUGUUGAGAUCUUAUCUGAGCU
#=GC SS_cons                   :<<<__________________________________________________________>>>
#=GC RF                        AAGCGAUGACGAaUGAUAUCUGCUCUAAUGAGUCUGAAUccCCAUGUUGAGAUCUUaUCUGAGCU
//
# STOCKHOLM 1.0

#=GF AC   RF01649
#=GF ID   ceN67
#=GF DE   Caenorhabditis snoRNA ceN67
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   70.00
#=GF TC   73.40
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948698.1/1-134           GCCCCCAUUAUCUUUCCAUCAAAUGAUUUAGGACGUCAUUGAUGGCUUAGAAUGGGGAAAAUUGAAUCGGUAGAAUGUGAUUUGUGAGUUGUUCACUGACACGUGGCAACUCGUAUUCGCUACUUCCUACAUUU
DQ789502.1/2-131           AAUCCCAUUAUCUUUCCAUCAGCCGAUUU-UGAAGUCACUGAUGGCUUAGAAUGGGAGAUAUUGUCA-GGUCGAAUCUGAUAAAUGAUUCAUAAGCCCUAGUUUGUUGCAUCAU-UUCAUU-CUACCGACAAAC
ABLE03014686.1/14601-14472 AAUCCCGUUAUCUUUCCAACAGCUGACUC-CUACGUCAUUGUUGGCUUAAUAUGGGUGAAAUUGACU-GGAUGAUUCUGAAAUAGGGUUAUGUUGCUGAAAAUUGACAAACCGC-UUCACU-CGUUCUACAUUU
#=GC SS_cons               ::<<<<<<<------<<<<<<<-<<<<__.____>>>>>>>>>>>----->>>>>>>----------.<<-<<---<<<<----<<<<<<<-<<<<______>>>>>>>>>>>-.->>>>-.>>->>:::::::
#=GC RF                    aacCCCaUuAUCUUUCCAuCAgcuGAcUu.ugAcgUCacUGaUGGCUUAgaAuGGGggAaAUUGacu.GGucGAaUguGAuauacGguucguccgcugaaauguggcgaacCgu.UUCacU.CguCCuACAuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01650
#=GF ID   ceN68
#=GF DE   Caenorhabditis snoRNA ceN48
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   157.90
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AY948699.1/1-121       GUGCCGGAUUUAAACACUUCUGAGUUGCUCACAUGCUCAGAAGAACAAGGUUCGGAAAAUUAGUGAUCAUUUGAUGUGCUGAACUCCAAAGAGUCAAAACUGAGUUGGUGAUCGUACAUUU
FO080159.1/19595-19715 GUGCCGGAUUUAAACACUUCUGAGUUGCUCACAUGCUCAGAAGAACAAGGUUCGGAAAAUUAGUGAUCAUUUGAUGUGCUGAACUCCAAAGAGUCAAAACUGAGUUGGUGAUCGUACAUUU
#=GC SS_cons           ::::<<<<<<<-----<<<<<<<<<_________>>>>>>>>>---->>>>>>>------------<<<<<----<<--<<<-<<<____>>>>>>-->>------>>>>>::::::::::
#=GC RF                GUGCCGgauuuAAACACuuCuGaGuUGCUCACAUgCuCaGaaGAACAagguuCGGAAAAUUAGUGAuCauuUGAUGuGCuGaACuCCAAAGaGuCaAAaCUGAGUUgguGaUCGUACAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01651
#=GF ID   ceN69
#=GF DE   Caenorhabditis snoRNA ceN69
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   45.00
#=GF TC   47.20
#=GF NC   34.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AY948700.1/1-107       GACAGGAUGAUGAGUCACUCGCUGAGUGACAAUAAGCCGAGUGUUAGCGGUUUUUAUGUAAUCGUGAUGAUCAUUCCCUCAAAAGCGAUAAUUGUGAACUGACUGUC
DQ789509.1/1-106       GACAGGAUGAUGAGUCACUCGCUGAGUGACAAUAAGCCGAGUGUUAGCGGUUUUUC-ACAACCGUGAUGAUCAUUCCCUCAAAAGCGAUACAUGUGGUCUGACUGUC
AB125759.1/1-105       -ACAGGAUGAUGAGUCACUCGCUGAGUGACAAUAAGCCGAGUGUUAGCGGUUUUUAUGUAAUCGUGAUGAUCAUUCCCUCAAAAGCGAUAAUUGUGAACUGACUGU-
ABEG02012096.1/730-834 GACAGAAUGAUGAGUCGCUCUAAGAGUGACAAUAAGCCGAGUGUUAGCGGUUUU--CGUAACCGUGAUGAUCAUUCCCUCAAAAGCGAUCUAUGUGGUCUGACUGUC
#=GC SS_cons           <<<<<_________________________________________________________________________________________________>>>>>
#=GC RF                GaCaGgAUGAUGAGUCACUCgcuGAGUGACAAUAAGCCGAGUGUUAGCGGUUUUUauguAAuCGUGAUGAUCAUUCCCUCAAAAGCGAUaaaUGUGauCUGACuGuC
//
# STOCKHOLM 1.0

#=GF AC   RF01652
#=GF ID   ceN70
#=GF DE   Caenorhabditis snoRNA ceN70
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   65.00
#=GF TC   70.70
#=GF NC   46.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AY948701.1/1-71          GCGCGAUGAACUCUUUACCAUCUUUCGGGGCAUAACACUCUUGAUGAUAACAUACCCAUUUGCUGAGCGCU
DQ789437.1/1-70          GCGCGGUGAAUUCAUUACCAUCUUUCGGGGCAUAUCAAUCCUGAUGAUAACAUAACCAUAUGCUGAGCGC-
ABLE03019911.1/4913-4980 GCGCGAUGAAAUCUUUACCAUCUUUCGGGGCAUAACACACUUGAUGAUAACAUACC---UUGCUGAGCGCU
#=GC SS_cons             <<<________________________________________________________________>>>:
#=GC RF                  GCGCGaUGAAuUCuUUACCAUCUUUCGGGGCAUAaCAcuCuUGAUGAUAACAUAcCCAUuUGCUGAGCGCU
//
# STOCKHOLM 1.0

#=GF AC   RF01653
#=GF ID   ceN80
#=GF DE   Caenorhabditis snoRNA ceN80
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   111.90
#=GF NC   63.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AY948703.1/1-131           CAGCAUCGAAAAUGGACGGACUUUCCCGAUGGAUCGUUUCGUAUAAUUUUGGUGCAAAAUAGUAGAGAGACGCAGUGUUACUCUUCCUUACGUUACCUGUAUCUGGAGAGUGUCAAGCGUUUCCCACAUUU
DQ789483.1/3-133           GUGCAUCAGAAAGGGACGGGGUUUCCAGUUGGAUUGAUCCGUAUAAUUUUGAUGCGAAAGCAUAGAGAGGUGCAGUGUUACUCUUCAUCACGGAUUUUGUGAACGGAGAGUGUCAAGCGCUUCCCACAAUU
DQ789473.1/5-135           UUGCAUCGAAAAGGGACGGGGUUUCCUACUGGAUUGUUCCGUAUAAUUUUGGUGCGAAAGCAUAGAGAGCCGCAGUGUUACUCUUCAUCACAGAUUUUGUGAACGGAGAGUGUCAAGCGGUUCCCACAUUC
AY948702.1/1-131           UUGCAUUGAAAAGGGACGGGCUAUCUUUAUGGAUUGUUUCGUAUAAUUUUGAUGCGAGAUAAUAGAGAGGCGCACUGUUACUCUUCAUCACUUUUUCUGUGAACGGAGAGUGUCAAGCGCUUCCCACAAUU
ABEG02002099.1/19118-18988 AAGCAUUGAAAAGGGACGGUUUUUCUAAUUAGAACAUUCCGUAUAAUUUUGGUGCAAUAGCAUAGAGAGCCGCAGUGUUACUCUUCUUUACAAAUCCUGUAUCUGGAGAGUGUCAAGCGGUUCCCACAAUC
#=GC SS_cons               ::<<<<<<<<<----<<<<<---<<<____>>>---->>>>>---->>>>>>>>>---------<-<<<<<<<--<<-<<<<<<<<--<<<<_____>>>>--->>>>>>>>->>->>>>>>>->::::::
#=GC RF                    uuGCaccgaaaAgGGaCGgguUuuCcuauUgGauuguccCGuAUAAuuuugguGCgAaAgaAUAGAGaggcGCAguGUuaCuCuuCaUcaCguauuccGugaauGgaGaGugUCaAGCgcuuCCCACAaUu
//
# STOCKHOLM 1.0

#=GF AC   RF01654
#=GF ID   ceN82
#=GF DE   Caenorhabditis snoRNA ceN82
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   98.70
#=GF NC   47.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AY948705.1/1-134           ACGCUCUUCAAAAGCACUGGUUAUCGGACUCAGACUUGUCCAUGCCAGCCGUCAAAA-UGAGCAAUAUGAAAUAUCCUGUUUUUGGGUGAGGUGUAACUGUAUUUAGAUUAGAUCUCAAUAACACGAUGACAGUU
DQ789482.1/2-135           AUGCUCUUUAAAAGCACUGGUUAUAGGACUCUGACUUGUCCAUGCCAGCCGUCAAAA-UGAGCUAUAUAGAAUAUCUUGUUUUUGGGUGAGGUGUAAUUGUAUUUAGAUUAGAUCUCAAUAACACGAUGACAAUU
AAGD02002634.1/3105-2972   UUGCUCUUCAAAAGCACUGGUUUUAGGAUCCAUUAUUAUCCAAGCCAGCCGUCAAAACUGAGCUAUAAAAAUUAUCUUGUUUUUGGGUGAGGCGUAU-UCAAAUCAGAAUGUGUCUCAAUAACACGAUGACAAUC
DQ789492.1/2-135           UUGCUCUUCAAAAGCACUGGUUUUAGGAUCCAUUAUUAUCCAAGCCAGCCGUUAAAACUGAGCUAUAAAAAAAAUCUUGUUUUUGGGUGAGGUGUAU-UCAAGUCAGAAUGGAUCUCAAUAACACGAUGACAAUU
AY948709.1/1-134           AUGCUCUUCAAAAGCACUGGUUUUAGGAUCCACUAUUAUCCAAGCCAGCCGUCAAAACUGAGCUAUAAGAAUUAUCUUGUUUUUGGGUGAGGUGUAU-UCAAUUCAGAAUGCGUCUCAAUAACACGAUGACAAUU
ABEG02000948.1/35135-35268 AUGCUCUUCAAAAGCACUGGUUAUAGGAUCCAUUAUUAUCCAAGCCAGCCGUCAAAACUGAGCUAUAAGAAUUAUCUUGUUUUUGGGUGAGGUGCA-UUCAAUUCAGAAUGGGUCUCAAUAACACGAUGACAAUU
#=GC SS_cons               ::<<<<-------<<-<<<<<----<<<<________>>>>-->>>>>-->>------->>>>-------------------<<<<-<<<<<<-<<<<<_______>>>>>->>>>>>---->->>>::::::::
#=GC RF                    aUGCuCUUcAAAAgCACuGGuUaUAGGaccCAuuaUUguCCAagCCaGCCGucAAAAcUGaGCuAUAaaAAauAUCUUGUUUuuGGGuGaGgcGcauuucaAuUcAgaauggguCuCaAUAACACgaUGACAAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01655
#=GF ID   ceN84
#=GF DE   Caenorhabditis snoRNA ceN84
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   81.90
#=GF NC   55.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


DQ789480.1/2-131           AUGCCACAGUGUCUGGGCAAAGUAGGCUGUUUUUAAUAGUACUAACUUAAUCCACUGAUGGCUAUAGGAAAG-C-AUUGUGUAAUCCCCGA-ACACC-UCUGUGGUGUAUUGGAUUCAUGACAUUGCGACAAUU
AY948707.1/1-129           UUGCCUCAGUGUCUGGGCAAAGCAGACUGUUUUUAAUAGUACUGACUUAAUCCACUGAUGGCUAUAGAAAAA-C-AUUGUGUAAUCCCCGA-ACACC-U-UGUGGUGUAUUGGAUUCAUGACAUUGUGACAAUU
DQ789488.1/2-110           AUGCCACAAUGUCUGGGCAAGGUGUCCUGCACC-CGCUUGAUCAACCUAAUCCAUUGAUGGCUAUAUAAAAU-UCAUUGAUUAAUCC------------CUGU----------CGAGUUGAAUUAGA-ACUCUU
DQ789520.1/2-133           UUGCCACAAUGUCUGGGCAAGGUGCCCUGCACC-CGCUUGAGCAACCUAAUCCAUUGAUGGCUAUAUAAAAUUC-AUUGAGUAAUCCCUGUUGAGUUAUAUAGAACUUUCCAGUUUCAUAUCAUUGAUACAAUU
ABEG02005632.1/13365-13236 CCGCCACAGUGUCUGGGCAAAGUAGGCUGUUUUUAAUAGUACUAACUUAAUCCACUGAUGGCUAUAUAGAAG-C-AUUGUGUAAUCCCCGA-GCACC-UCUGUGGUGUAUUGGAUUCAUGACAUUGCGACAAGU
#=GC SS_cons               ::<<<-<<<<----<<<--<<<<<<<<<<<_____>>>>>->>>->>>-->>>>>>>-->>>----------.<.-<-<<<<-----<<<<.<<<<<._____>>>>>->>>>------->>>>->->::::::
#=GC RF                    uUGCCACaguGUCUGGgCAagGuggccugcuuuUagcaggAccaACcuAAuCCacuGAUGGCUAUAuAAAAu.c.AuUguguAAUCCCcgg.acgcc.UcUguggcguaccgGauucaUgacauugagACaauU
//
# STOCKHOLM 1.0

#=GF AC   RF01656
#=GF ID   ceN72-3_ceN74-2
#=GF PI   ceN72-3
#=GF DE   Nematode sRNA ceN72-3_ceN74-2
#=GF AU   Osuch I
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR;
#=GF GA   38.00
#=GF TC   38.20
#=GF NC   37.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF RN   [2]
#=GF RM   25908866
#=GF RT   Non-coding stem-bulge RNAs are required for cell proliferation and
#=GF RT   embryonic development in C. elegans.
#=GF RA   Kowalski MP, Baylis HA, Krude T
#=GF RL   J Cell Sci. 2015;128:2118-2129.
#=GF WK   Caenorhabditis_elegans_small_RNAs
#=GF SQ   13


AY948638.1/1-132               CACAUCGGUCCGGAGUUGAUGGGUUACCC------A------G-U-CAUUCUUCUGCUUGCAGGAGAGC--CCGGUGUC------CUUGU---GAUGCCA-----------AACC---CGUGUU-CCU-A-ACAGAAUACAAACCCUUCCCAUCGACACCAACUUGACCGU-UG-U-
AY948637.1/1-133               CACAUCGGUCCGGAGUUGAUGGGUUACCAG-----A------U-U-AAUUCUUCUGCUUGCAGGAGAGC--CCGGUGUC------CUUGU---GAUGCCA-----------AACC---CGUGUU-CCU-A-ACAGAAUACAACCCCUUCCCAUCGACACCAACUUGACCGU-UG-U-
AC084593.1/10924-11064         UGUCACGGUCCGGCGUUGAUGGGUUAUCAC-----U------C-G-UAAUCUUCUGCUUGCAGGAGG-C--CCGUUCUUCAGGCAUCUGUCUGUUGAACA-----------ACCC---CGCGUU-CCU-C-ACGGUUCGCACCCCCUUCCCAUCAGCACCAACUUGACCGU-UA-U-
AC084533.1/19141-19276         CA---CGGUCCGGCGUUGAUGGGUUAUCAG-----U------C-G-AAAUCUUCUGCUUGCAGGAGA-A--CCGUUCUUCAGACAUCUGUCUGUGGAACA-----------ACCC---CGCGUU-CCU-C-ACGGUUCGCAACCCCUUCCCAUCAACACCAACUUGACCGA----U-
ABEG02001147.1/23044-23186     CAC-UCGGUCCGGAGUUGAUGGGUUAUCUA-----U------G-AAUCUUCUUCUGCUUGCAGAAGGAA--CC--CGUU------CUUCA---GAUGUAAGUCUGUUGAACACCC---CGCAAC-CCUCA-AAAAGUUGCAACCCGAUCCCAUCAACACCAACUUGACCGU-UG-U-
ABEG02008175.1/12257-12109     CACUUCGGUCCGGAGUUGAUGGGUUAUCAUUCUGA-AUUGUUU-A-CUCUCUUCUGCUUGCAGGAGAACCCCCGGUUUC------AUUGC---GAAACCA-----------AAACUCUCGCAUU-CUC-AUUAAGAGUGCAAAACCUUCCCAUCAACACCAACUCGACCGU-UG-U-
ABEG02001159.1/32125-31982     CACUUCGGUCCGGAGUUGAUGGGUUAUCUA-----C------GAA-UCUUCUUCUGCUUGCAGAGGAAA--CC--CGUU------CUUCA---GAUGCAAGUCUGUUGAACACCC---CGCAGCCUUC-A-AACAGUUGCAAACCCUUCCCAUCAACACCAACUUGACCGU-UG-U-
AY948640.1/1-78                -GUAUCGGUCCGGCGUCAGUGGGUUAUCAA-----G------U--------------UUG--------C--CU----CC------CUUCG---GG----A-----------AU-------------------UU--------------CUCAUCGGCACCAACUUGACCGU-UG-CU
ABEG02001764.1/101375-101451   -GCAUCGGUCCGGAGUCAGUGGGUUAUCGG-----U------U-C-UUUC----CCCUUGGG----GA-------------------------------A---------------------------------------------UUUCCCAUCGGCACCAACUCGACCGU-UG-UU
AY948639.1/1-79                -GUCUCGGUCCGGCGUCAGUGGGUUAUCGU-----A------U-U-UC--------------------U--CU----CC------CUUCG---GG---G-----------------------------------------A---AUUUCCCAUCGGCAUCAACUUGACCGU-UG-CG
CAAC02000474.1/1542122-1542198 A-CCUCGGUCCGGCAUCUUUGGGUUAUCUU-----A--------------------------------U--AGGAUCUC------U-UCG---GGGAUCA------------------------------------------------UCCAUUGAUACUAACUUGACCGU-UGAA-
ABEG02010311.1/614-545         CGG-ACGGUCCGGAGUCAGUGGGUUAUCCA-----A------A-A-UU----------UG-----------------------------A--------------------------------------------------A--ACCCUCCCAUUGACACCAACUUGACCGUUUG-U-
CAAC02000474.1/1664399-1664320 C-UGUCGGUCCGGCGUCAGUGGGUUAUCGU-----G------A-U-UC---------UUU----------------CCC--------UCC---GGG---------------------------------------------GAAAUUUCCCAUCGACACCACCUUGACCGU-UGUU-
#=GC SS_cons                   :(((-(((((-((-(((((((((,,,,,,,.....,......,.,.,,<<<<<<<<____>>>>>>>>,..,,..<<<<......_____...>>>>,,,...........,,,,...,<<<<<.<__._.___>>>>>>,,,,,,,,)))))))))-))-----)))))-.)).).
#=GC RF                        cacaUCGGUCCGGaGucgaUGGGUUAUCau.....u......u.a.uuuuCucCuGCUUGCaGgaGaaa..Cc..cccc......uUUcu...ggggucA...........AacC...CGcgcc.cuu.a.aaagggcgCAaacccUUCCCAucgaCACCAACUUGACCGU.ug.u.
//
# STOCKHOLM 1.0

#=GF AC   RF01658
#=GF ID   ceN81
#=GF DE   Caenorhabditis snoRNA ceN81
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   56.70
#=GF NC   43.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.35 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


DQ789486.1/2-127 ACCGAAGAGUAGUCAUUUGUAUAUGUUUCUUAUAUGUACAGAGUUACACUCUUCGAAUAUCAGUGCUUCUUCUCGUUGGAGUUGUUUGAUUUAUGAGCAAUUACCUCUAUUCUGAAAGCAACAAUU
AY948704.1/1-126 GUCGAAGAGUAGUCAUUUGUAUACGUGAUACACUUAUACAGAGUUACACUUUUCGUAUAUAAGUGCUUCUUCUCGUUGGAGUUGUUUAUUUAAUGAGCAAUUACCUCUAAACUGAAAGCAACAAUU
AM051042.1/1-124 --CGAAGAGUAGUCAUUUGUAUACGUGAUACACUUAUACAGAGUUACACUUUUCGUAUAUAAGUGCUUCUUCUCGUUGGAGUUGUUUAUUUAAUGAGCAAUUACCUCUAAACUGAAAGCAACAAUU
#=GC SS_cons     ::<<<<<<<<-<<--<<<<<<<<-<<_____>>->>>>>>>>--->>>>>>>>>>--------<<<<<--<<---<<<<<<<<<<<<<_____>>>>>>>---->>>>>>--->>>>>>>::::::
#=GC RF          auCGaagaGuAGuCAuuuGuauacgugauacacuuauaCagaGUUaCaCucuuCGuAUAUaAGuGCuuCUuCUCGuugGaGuuGuuuauUUaAugagCaaUUACCuCuaaaCUGaaaGCaACAAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01659
#=GF ID   ceN86
#=GF DE   Caenorhabditis snoRNA ceN86
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   40.00
#=GF TC   41.00
#=GF NC   34.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


DQ789465.1/2-125 UGGCAGCGUUGUUUGAGAGUUUACUCCCGUGAGGAAGCAUCUAUUUAUCGCUGCGAGAUAAAAUAUGUCCUUUAUUCCCGCUCCUGAAUUUUGUUUCUUGCGCGAUGAUGCGGCCAUGACAAUU
AY948708.1/1-122 CUGCAACUAUUCAAGAGAUUUGCCUCCCGUGGGGCA--CGCCUUUUUUCGUUGCGAAAUAAAACAUGUCCUUUAUUCCCGCUCCUGGAUUGUGUUUCUUGCGCGAUGAUAUGGCUAUGACAAUU
#=GC SS_cons     ::<<<-------<<<<<---<<<<<<____>>>>>>----->>>>>----->>>---------<<<<-<<--<<<<--<<<-<--<<<______>>>-->->>>-->>>>->>->>>>::::::
#=GC RF          uuGCaaCuuUuuaagagAuUugcCuCCCGUGaGgcaGcauCcuuuuaUCGuuGCGAaAUAAAAcaugUCCUUuauuCCCGCUCCUGaaUUuUGUuuCUUGCGCGAUgauauGGCcaugACAAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01660
#=GF ID   ceN88
#=GF DE   Nematode snoRNA ceN88
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   40.00
#=GF TC   41.30
#=GF NC   34.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AY948710.1/1-140             UUUCUCUCGUCUUGGCGCUUCCACUGGUGAAUGUGGUUGUGUAUGUUACGAGAGACAAAGUAGCGCCUA-ACGGCUUUCGGAUCUCCUUCGGUGUUUGUCUUGAAUUUCGACAAAUGUCAUCCUCUGGGUUCGAGACAAUU
DQ789495.1/2-142             UAUCUCUCGUCUUGGCGCUUCCACUGGUGAAUGUGGUUGUGUAUGUUACGAGAGGAAAAGUAGUGUCUUUUAGACUUUCGGAUCUCCUUCGGUGUUUGCCUUGAAUUUCGGCAAAUGUCAUCCUCUGGGUUCGAGACAAUU
AAGD02001053.1/226532-226393 CACCUCUCGUCUUGGCGCUUCCACUGGUGAAUGUGGUUGUGUAUGUUACGAGAGGAAAAGUAGUGCCUC-GCGGCUUUCGGAUCUCCUUCGGUGUUGGUCUUGAAUUUCGACCAAUGUCAUCCUCUGGGUUCGAGACACUU
AY948717.1/1-139             CG-CUCCUAUCUUGGCGCUUCCAUUGGUGAAUAUGGCUGUGUAUGUUAUAGGAGAGAUAGUAGUGCCUU-UUGGCUUUCGGAUCUCCUUCGGUGUUUGUCUUGCAUCUCGACAAAUGUCAUCCUCUGGGUUCGAGACAAUU
DQ789494.1/1-141             UUCCUCCUAUCUUGGCGCUUCCACUGGUGAAUGUGGCUGUGUAUGUUAUAGGAGAAAAAGUAGUGUCUUCUGGACUUUCGGAUCUCCUUCGGUGUUUGUCUUGCAUCUCGACAAAUGUCAUCCUCUGGGUUCGAGACAUUC
ABEG02011470.1/1482-1343     UUGCUCCUAUCUUGGCGCUUCCAUUGGUGAAUAUGGCUGUGUAUGUUAUAGGAGGAAAAGUAGUGUCUU-UAGACUUUCGGAUCUCCUUCGGUGUUUGUCUUGAAUCUCGACAAAUGUCAUCCUCUGGGUUCGAGACAAUA
#=GC SS_cons                 ::<<<<<<<<----<<<<--<<<<________>>>>-->>>>----->>>>>>>>,,,,,,,,,<<<__.__>>>-<<<<<<<<<-----<<--<<<<<<_________>>>>>>-->>------->>>>>>>>>::::::
#=GC RF                      uucCuCccguCUUGgCgCUUCCacUGGUGAAUguGGuUGuGuAUGUUacggGaGgaAAAGUAGUGcCUu.uaGgCUuuCGgauCuCCUUCGgUGuuuGuCUUGaAUuUCGaCaaaUGuCAUCCUCUgGguuCGagACAaUu
//
# STOCKHOLM 1.0

#=GF AC   RF01661
#=GF ID   ceN92
#=GF DE   Caenorhabditis snoRNA ceN92
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   53.00
#=GF NC   43.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


DQ789487.1/2-127           CAGCACAUA------AAUACGGAGAAUUUCGAAGUCGAUAUUUUCUAGUCGUAGUGUGCGAUAUAAACCGUUCUACUGCCACACGGGUACUGGCCUUGAAGCUGUAUCGGUUCCAAAGUUGUUCGAACAAUU
AY948714.1/1-132           UUGCACCUACCAAUUAUAUCGGAAGAUUUUGAAGUCAUAGUUUUCCUAUCGUAGUGUGCAAUAAAAACCGUUCUACUGCCACACGGGUACUGGCCUUGAAGCUGUAUCGGUUCCAAAGUUGUUCGAACAAUU
AAGD02001344.1/30481-30356 UGGCACAUA------AACACGGAGGAUUUUGAAGUCAUAUUUUUCUAGUCGUAGUGUGCUAUAAAAACCGUUCUUCUGCCACACGGGUACUGGCCUACAAGCUGUAUCGGUUCCAAAGUUGUUCGAACAAUU
DQ789476.1/9-130           UGUUAUCUA------GAA--AUCAUAAGUUGUAGUUACUUUGUGAUACAAAU-AGGUGGUAUAAUGAUUGUUCCUCUGCCACACGUGUACUGGCUU-UAUGCUGUAUGAGUUCCAAAGAUCUACGAACAAUU
#=GC SS_cons               :<<<<<<<-......-----<<<<<<<<-<<____>>->>>>>>>>------->>>>>>>--------------<<<-----<<-<<<<<-<<<______>>>>>>>>->>----->>>:::::::::::::
#=GC RF                    UggcacccA......aaaaCggaagacuUuGaAGUCauagucuuccaaucgUAgggugccAUAAaaAccGUUCuaCUGCCACaCGggUaCUgGCcUuuAaGCuGuAucgGuUCCAAAGuUgUuCGAACAAUU
//
# STOCKHOLM 1.0

#=GF AC   RF01662
#=GF ID   ceN89
#=GF DE   Caenorhabditis snoRNA ceN89
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   48.00
#=GF TC   49.00
#=GF NC   36.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


CAAC02000486.1/298980-299055 UCGCGAUGAGGAAAUUCAUCAC--ACACACACUCCGAAUUUUCGUGUAGAGAAUUAUUAAGAACGGAUAUCUGAGCGC
AY948711.1/1-78              GCGCGAUGAGGAUUGAUAACACAUACACACACUCUGAAGUUAUGUGAAGAGAUAAUUGAAGAACGGAUAUCUGAGCGC
DQ789512.1/1-74              -CGCGAUGAGGAAAUUCAUCAC--ACACACACUCCGAAUUUUCGUGUAGAGAAUUAUUAAGAACGGAUAUCUGAGCG-
ABLE03009035.1/16633-16558   GCGCGAUGAGGAAGAAUAUCACAUACACACACUCCGAA-UUCUGUGAGGAGAUAAUU-AAGAACGGAUAUCUGAGCGC
#=GC SS_cons                 <<<<______________________________________________________________________>>>>
#=GC RF                      gCGCGAUGAGGAaauauAuCACAUACACACACUCcGAAuUUuuGUGaAGAGAuaauUuAAGAACGGAUAUCUGAGCGc
//
# STOCKHOLM 1.0

#=GF AC   RF01663
#=GF ID   ceN93
#=GF DE   Caenorhabditis sRNA ceN93
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR;
#=GF GA   60.00
#=GF TC   62.40
#=GF NC   46.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Caenorhabditis_elegans_small_RNAs
#=GF SQ   4


AY948715.1/1-131           UUUCCAUUAAGUAGUCCCGUACG--U-UGAAAUUUUCACGUACGGUUUGGACAAUAUGGAGAAAU-GA-AUGUUACUCUUUUUGCAAUGACGCUGAAACAUAUUUUCGCUUUGUUAGCCAUAAGUUUAAAACAAUU
AAGD02000325.1/17694-17561 UUUCCAUUCAGUAGUCCCGGACGAAU-UUAAAACAUAACGUACGGUUUGGACAUAAUGGAGAAAUAGA-ACAUUACUCUUUUUGCAGCGAAGCUGAAAACUAUUUUCGUUUUGCUAGCCAUAAGUGUAAAACAAUU
DQ789474.1/2-133           UUCCCAUUCAGUAGUCCCGGACG--AAUUAGAAUUUAGCGUACGGUUUGGACAUAAUGGGGAAAU-GG-ACUUUACUCUUUUUGCAGCGAAGUUGAUCCUUAUGAUCUCUUUGCUAGCCAUAAGUUUAAUACAAUG
ABEG02007532.1/10743-10875 AUUCCAUUCAGUAGUCCCGGACG--AAUUAGAAUUUAACGUACGGUUUGGACAUAAUGGAGAAAU-AAAAUAUUGCUCUUUUUGCAGCGGAGCUGAACUUUAUGUUCUCUUUGCUAGCCAUAAGUGUAAAACAAUA
#=GC SS_cons               <<<<<<<<--<<-<--<<<-<<<..-.<<<_____>>>>>>->>>-->-->>-->>>>>>>>---.--.---<<<<-<<<---<<<<<<<<<<-<<<<_____>>>>>>>>>>>>->>--->>>->>>>:::::::
#=GC RF                    uuuCCauucAGuAgUCCCGgaCG..u.uuaaAauuuaaCGuACGGUUuGGaCAuaauGGagaAAU.ga.AuauuacUCuuUUUGCagcgaaGcUGaacuuUAUguuCgCuuugcuAGCCAUaaGUguaaaACAAUu
//
# STOCKHOLM 1.0

#=GF AC   RF01664
#=GF ID   ceN101
#=GF DE   Caenorhabditis snoRNA ceN101
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   70.00
#=GF TC   87.50
#=GF NC   43.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AM286188.1/1-127 AUCCUCGCUUAUAAGCCGGGGGACUAGCCU-UUGCUGAGUUCACUAGUAAAACGCGAGGAAAAUUAUAGAGACAUCCAGACACCGAUUAUGUUGUGAUAUAUUCGGUCACUUCGUAUGUCCCACAGUU
DQ789479.1/4-131 UACCUCACUUAUAAGCCGGGGGACUAGCUUUAUGUUGUGUUCACUAGUAAAAUGUGAGGUAGAGUAUAGAGACAGCCAGACACCGAGAAUGUUUUGAUGUUUUCGGUCACUUUGUGUGUCCCACAUUU
DQ789525.1/3-129 AUCCUCGCUUAUAAGCCGGGGGACUAGCCU-UUGCUGAGUUCACUAGUAAAACGCGAGGAAAAUUAUAGAGACAUCCAGACACCGAUUAUGUUGUGAUAUAUUCGGUCACUUCGUAUGUCCCACAGUU
AY948645.1/1-128 AACCUCUCUUAUAAGCCGGGGGACUAGCAUUUUGUUAAGUUCACUAGUAAAAUGAGAGGUAAAGCAUAGAGACAACCAGACACCGAGAAUGUUUUGAUGUUUUCGGUCACUUUGUGUGUCCCACAAAU
#=GC SS_cons     :<<<<<<<------<<--<-<<<<<<<<_____>>>>->>>>->-->>----->>>>>>>--------<-<<<<<-<<<<-<<<<<<<<<<<____>>>>>>>>>>>--->>>>->>>>>->::::::
#=GC RF          auCCuCgCUUAUAAgCCGGGGgaCcagCuUuuUGcugaGuuCACUAGuAAAAuGcGaGGaAaAuuAUAGAGaCauCCggaCaCCGaguauguUuUGauauacuCGGuCACuucGUauGuCCCACAauU
//
# STOCKHOLM 1.0

#=GF AC   RF01665
#=GF ID   P13
#=GF DE   Pseudomonas sRNA P13
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   70.00
#=GF TC   99.20
#=GF NC   35.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   2


CP000744.1/2512491-2512566 UGUGCCGCACUGACCGCUCGUCAGCUCGUCGCGGAUGCUUUACCAUGGUGACUUCGCGCCGGAUCAGCUCCGGCGU
AE004091.2/3106994-3106919 CCGGGCGAACUGACCGCUCGUCAGCUCGCCGCGGAUGCUUUACCAUGGGCGCUUCGCGCCGGAUCAGCUCCGGCGU
#=GC SS_cons               :::<<<<<-<<<<<_____>>>>>->>>>><<<<<<<<<<______>>>>>->>>>><<<<<<_____>>>>>>::
#=GC RF                    uguGgCGaACuGaCCGCUCGuCaGCuCGcCGCGgaugcuuUACCAUgggcaCuuCGCGCCGGaUCAGCuCCGGCGU
//
# STOCKHOLM 1.0

#=GF AC   RF01666
#=GF ID   rox2
#=GF DE   Drosophila rox2 ncRNA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:18039876
#=GF GA   55.00
#=GF TC   56.90
#=GF NC   47.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0046536; dosage compensation complex;
#=GF RN   [1]
#=GF RM   18039876
#=GF RT   An evolutionarily conserved domain of roX2 RNA is sufficient for induction
#=GF RT   of H4-Lys16 acetylation on the Drosophila X chromosome.
#=GF RA   Park SW, Kang YIe, Sypula JG, Choi J, Oh H, Park Y
#=GF RL   Genetics. 2007;177:1429-1437.
#=GF WK   Drosophila_roX_RNA
#=GF SQ   4


AE014298.4/11474057-11474127 AAAAGACGUGUAAAAUGUUGC-AAAUUAAGCAAAUAUAUAUGCAUAUAUGGGUAACGUUUUACGCGCCUUAA
AAQB01006867.1/48644-48573   AAAAGGCAUGUAAAAUGUUGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAUGGUAACGUUAUACGCGCCUUAA
AAKO01003448.1/902-972       AAAAGACGUGUAAAAUGUUGC-AAAUUGAGCAAAUAUAUAUGCAUAUAUGGGUAAUGUUUUACGCGCCUUAA
AASV01031043.1/115-45        AAAAGACGUGUAAAAUGUUGC-AAAUUAAGCAAAUAUAUAUGCAUAUAUGGGUAAUGUUUUACGCGCCUUAA
#=GC SS_cons                 ::<<<-<<<<<<<<<<<<<<<._____________________________>>>>>>>>>>>>>>>->>>::
#=GC RF                      AAAAGACGuGUAaAAuGUUgC.AAAuuAAgcAAAuAuAuAugcAuAuAugGGuAACgUUuUACgCGCCUUAA
//
# STOCKHOLM 1.0

#=GF AC   RF01667
#=GF ID   rox1
#=GF DE   Drosophila rox1 ncRNA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:18039876
#=GF GA   58.00
#=GF TC   59.20
#=GF NC   52.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0046536; dosage compensation complex;
#=GF RN   [1]
#=GF RM   18039876
#=GF RT   An evolutionarily conserved domain of roX2 RNA is sufficient for induction
#=GF RT   of H4-Lys16 acetylation on the Drosophila X chromosome.
#=GF RA   Park SW, Kang YIe, Sypula JG, Choi J, Oh H, Park Y
#=GF RL   Genetics. 2007;177:1429-1437.
#=GF WK   Drosophila_roX_RNA
#=GF SQ   3


AAST01032201.1/702-760   UUCGUGUUUCGGAAAACGCUCUAAAAGGCGCAAUUUUAAAUCGUUUUCCGAAAUGGGAA
U85980.1/3421-3479       UUCGUGUUUCGGAAAACGCAUUAAAAGGCGUAAUUUUAAAUCGUUUUCCGAAAUGGGAA
AAEU02000625.1/2414-2356 UUCGUGUUUCGGAAAACGCACUAAAAGGCGUAGUUUUGAAUCGUUUUCCGAAAUGGGAA
#=GC SS_cons             <<<-<<<<<<<<<<<<<<--<<<<<<_______>>>>>>-->>>>>>>>>>>>>>->>>
#=GC RF                  UUCGugUUUCGGAAAACGCauuAAAAGGCGuAaUUUUaaAUCGUUUUCCGAAAugGGAA
//
# STOCKHOLM 1.0

#=GF AC   RF01668
#=GF ID   P10
#=GF DE   Pseudomonas sRNA P10
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   37.00
#=GF TC   37.50
#=GF NC   36.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   8


AE004091.2/1807682-1807753 CGUUUCCGAUCCCACCGCUUGUCCG-CUCCCCGGGCACGGCAGCAAUCCCAUCGGCGUCGGUUCC-GCCGACGU
CP000680.1/88354-88425     CCUCGGCGAUCCCACCGCCUGCCCG-AUUCCCGGCCACGGCACCAACCCGAUCGCCGCCGGCUCG-CCCGACGU
AE016853.1/6176263-6176192 CGUCACCGACCCCACGGCUUGCCCG-CUCCCCGGCCACGGCACCAAUCCUAUCGUUGCUGGCUCC-AGCAACGU
AAKV01000055.1/239-311     CCUGGGCGAUCCGACCGCGUGUCCCGCUGCCGGGCCACGGCAGCAACCCGAUCGUCGGCGGCUCG-CCCGACGU
ABZR01000282.1/1582-1653   ACUUGGCGACUUGCAUGCCUGCCCG-AUUCCGGGCCACGGCAUCACGCCCAUUGU-GACGGCUUCAAGCGAUGU
CP000094.2/4669909-4669838 CGUCACCGACCCAACCGGCUGCCCA-CUGCCUGGUCAUGGCAACAACCCGAUCGUCUCCGGCUCG-CCGGACGU
CP000094.2/3667993-3667922 AAUCACUGAUCCAACCUCUUGCCCG-AUGCCCGGGCAUGGCCCGAAGGCCAUCGCCUCAGGAUCC-CCCGACGU
CP000094.2/6264513-6264442 CGUAUCCGACCCCACCGCUUGCCCG-CUCCCCGGCCACGGCACCAACCCGAUCGCCGCCGGUUCC-GGCGACGU
#=GC SS_cons               ::::::((,,,,,,,,<<<<<-<<<._____>>>->>->>>,,,,,,,,,,<<<<<<_______>.>>>>>)):
#=GC RF                    cgUcacCGAuCCaACcGCcUGCCCg.cUuCCcGGcCACgGCAcCAAcCCgAUCGccgcCGGcUCc.ggCGACGU
//
# STOCKHOLM 1.0

#=GF AC   RF01669
#=GF ID   P14
#=GF DE   Pseudomonas sRNA P14
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   45.00
#=GF TC   46.60
#=GF NC   38.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   4


AE004091.2/3206733-3206877 CUGGAUAUUUUUUGAACAAACGACACUCCAACUACU-GCUAAAGUCGGGGGGACUAAAAAAAAAGUUGCUCGGCUUGCGCUUGGUCAGUUUACUUACUACAAGUAAUGGGUAGUAUGUA-GCCGGCUAAUUUCCCCGGCUGGGGAGA
CP000712.1/3852783-3852927 CUGCACAUUUUUUUCACAGACAC-GUCGCAAAUCUU-GUCGGCGCGGAGUCAAGCAACAUUUUUUUUGCAGUUCUUGCGCUCUGUCAGUUUACUUACUACAAGUAAUGGGUACUAUGUACGCCGGCCAGUUUCUCUUUCCUGAGAGA
CP000076.1/4971318-4971462 CUGAAUAUUUUUUAUACAACCCGCUAAAAAGUUGCUCGAAAAAGAAACAGCGCCUAGAAUUUUUUUUGCU--UCUUGCGCUACGUCAGUUUACUUACUACAAGUAAUGGGUAGUAUGUACGCCGGCUAUUUCCUCACUCUGAGGUGA
CP000744.1/2357512-2357368 CUGGAUGUUUUUUGAACAAAACACUCUCCAACUACU-GCUAAAGUCGAGGAGGCUAAAAAAAAAGUUGCUCGGCUUGCGCUUGGUCAGUUUACUUACUACAAGUAAUGGGUAGUAUGUA-GCCGGCUAAUUUCCCCGGCUGGGGAGA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::.<<--<<<<<<-<<<<<<<________>>>>>>>>>>>>>-->>,,,<<<-<<-<<<-<<<<<<-<____>-->>>>>>->>>->>->>>,,,<<<<<<______>>>>>>
#=GC RF                    CUGaAuAUUUUUUaaACAAacaaCuuuacAAuUacU.GcuAaaGccgaggcgacuAAaAuuuuaguugcccggCuuGCgCUuuGuCAGuUUACUUACUACAAGUAAUGGGUAGUAUGUACgCCGgCuAaUuuCcCuuuCugGgGagA
//
# STOCKHOLM 1.0

#=GF AC   RF01670
#=GF ID   P17
#=GF DE   Pseudomonas sRNA P17
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   45.00
#=GF TC   46.90
#=GF NC   39.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   3


CP000438.1/1869507-1869788 GCAAGGAACUGGUCGCCCGGUCCAGCGACUUUCUCGAUGGGCAACUGGACUUCCGCGGACAACUGGCGGUGCGCAGCCACCUGCUCAUGUGCGGGCAUUGCCGGCGCUUCAUCCGCCAGAUGCGCCUGACCCAGGCGACCGUGCGCCAUCUGCCGGAAGGGCAGGGGCCGGAACUCGACCGCCUGGCCGCGCAUCUCUCCGAGUUGCGCAAGGACGCCGCGCGGCGCUGAGCCGGGGUACCCUCGACACCAAGCCGCCGCCCGCGAUUCGUGGGCGGCGGCU
CP000744.1/1873510-1873789 GCAAGGAACUGGUCGCCCGGUCCAGCGACUUUCUCGAUGGGCAACUGGACUUCCGUGGACGACUGGCGGUACGUAGCCAUCUGCUCAUGUGUCGGCAUUGCCGGCGCUUCAUCCGGCAGAUGCGCCUGACCCAGGCGACCGUGCGCCGCCUGCCCGAAGGACAGAGCCCGGAACUCGACAGGCUGGCCGCGCACCUCGUCGAACUGCGCAAGGACGCCGCGCGGCGCUGAGCCCGGCCGCCAAGGAAA--AAGCCGCCGCCCGUGAAUCGCGGGUGGCGGCU
AE004091.2/3677716-3677435 GCAAGGAACUGGUCGCCCGGUCCAGCGACUUUCUCGAUGGGCAACUGGACUUCCGUGGACAACUGGCGGUGCGCAGCCACCUGCUCAUGUGCCGGCAUUGCCGGCGCUUCAUCCGCCAGAUGCGCCUGACCCAGGCGACCGUGCGCCAUCUGCCGGAAGGGCAGGGGCCGGAACUCGACCGUCUGGCCGCGCAUCUCUCCGAAUUGCGCAAGGACGCCGCGCGGCGCUGAGCCGGGGUACCCUCGACACCAAGCCGCCGCCCGCGAUUCGUGGGCGGCGGCU
#=GC SS_cons               ::::::::::{{{--{{{{{--{{{{{,,,,,,[[[-[[[[[[,,,<<____>>(((--((-(((((((,,,<<<<____>>>>,,,,<<<<<<<<___>>>>>>>>,,,,,)))))))-))))),]]-]]]]--]]][[[[[[(((,,<<<<<____>>->>><<<<-<________>->>>>))),<<<<<--<<___>>-->>>>>,,,,,,,,,]]]]]]}}}}}--}}}}}--}}}----------<<<<<<<<<<<<<<___>>>>>>>>>>>>>>
#=GC RF                    GcAAGGAAcUGGucGCCcGGUcCaGCGAcUUUcuCGAuGGGCaAcUGGAcUUCCGcGGACgACuGgCGGUgcGcaGccAuCugCUcAUGcGccGGCAUUGCCggCgCUUcAUCCGcCaGAcGCgCcuGACCCaGGCGaCCGcGCGCCauCuGCCgGAAGGgCaGgGgCcGGAAcUcGACaGcCcGGCcGCGCaucuCuucGaauuGCGCAAGGAcGccGCgCGGCGCuGAGCCgGGguaCCaucGAaAccAaGCCGCCgCCCgcGAuUCgcGGGcGGCGGCu
//
# STOCKHOLM 1.0

#=GF AC   RF01671
#=GF ID   P18
#=GF DE   Pseudomonas sRNA P18
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   60.00
#=GF TC   73.20
#=GF NC   52.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   4


CT573326.1/1362999-1363133 GGCGGCGUGCUGCUCAGCCCGUUUCUGAUCUACGUGUUGAUGGCGCUGUUGCUCACCGGCGUGCUGCGCCUGGUGGUCCAGGCCACCCCCCUGGGGCGCUGGAUCUGGCAUGAAGCGCUGUUCGACGCGGCGUUG
CP000949.1/1289266-1289400 GGCGGCGUGCUGCUCAGCCCUUUUCUGAUCUACGUGUUGAUGGCUCUGGUGCUUACCGGUUUGUUGCGCUUUGUCGUGCAAGCAACGCCAUUGGGGCGCUGGAUCUGGCAUGAAGCGCUGUUCGACACAGCGCUG
AE004091.2/3703156-3703022 GGCGGCGUCUACCUCAGCCCGCUGUUCGUCUAUGCCCUGCUGGCGCUGGCGGCCACCGCCGCGCUGCGGGUGCUGAUCCAGAAAACGCCGUUGCGUCGCUGGGUCUGGCACGAGGCGCUGUUCGACUGCGCCCUG
CP000076.1/5312266-5312132 GGCGGGGUGCUGCUCAGCCCGUUCCUGAUUUAUGUGGUGCUGGCGCUGGUGCUGACCGGUGCCCUGCGGAUGCUGGUGCGGGUAACCGGGCUGGGCCGCUGGAUCUGGCACGAAGCACUGUUCGAUUGUGCCCUG
#=GC SS_cons               :<<<<<<<<<<<<<<<<<<<<<<_______________>>>>>->>>>>->>----->>>>>>>>>>((,,,,,<<<-<<<_________>>>->>><<<<<<<<--<<<________>>>-->>>>>>>>))::
#=GC RF                    GGCgGcgcgccgCcCaGcCCguuucUgaUcUAuGuguUgauGGCgCuGguGcuuACCggcgcgCuGCGguUgcUGgugCagguaACgccgcuGggcCGCcggguCUGgCauGAaGCgCuGuUCGacccgGCcCUG
//
# STOCKHOLM 1.0

#=GF AC   RF01672
#=GF ID   P2
#=GF DE   Psudomonas sRNA P2
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   80.00
#=GF TC   163.30
#=GF NC   38.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   7


AE004091.2/356478-356615     CUGCGUAAACCUGUUGUCCCGGAGGAAGUGGCUGGAAAGCGAACUGCGCGAAGCGGGUCCGGCCGGCGCUGGCCGGCACCCGCAACUCGGCGCCCAGAGGCACUAAGCGCGGGGGGCGUAUGCUAGCAUGUUCUCCCU
FM209186.1/349447-349584     CUGCGUAAACCUGUUGUCCCGGAGGAAGUGGCUGGAAAGCGAACUGCGCGAAGCGGGUCCGGCCGGCGCUGGCCGGCACCCGCAACUCGGCGCCCAGAGGCACUAAGCGCGGGGGGCGUAUGCUAGCAUGUUCUCCCU
AAKW01000055.1/47805-47942   CUGCGUAAACCUGUUGUCCCGGAGGAAGUGGCUGGAAAGCGAACUGCGCGAAGCGGGUCCGGCCGGCGCUGGCCGGCACCCGCAACUCGGCGCCCAGAGGCACUAAGCGCGGGGGGCGUAUGCUAGCAUGUUCUCCCU
CP000438.1/370626-370763     CUGCGUAAACCUGUUGUCCCGGAGGAAGUGGCUGGAAAGCGAACUGCGCGAAGCGGGUCCGGCCGGCGCUGGCCGGCACCCGCAACUCGGCGCCCAGAGGCACUAAGCGCGGGGGGCGUAUGCUAGCAUGUUCUCCCU
CP000744.1/419239-419376     CUGCGUAAACCUGUUGUCCCGGAGGAAGUGGCUGGAAAGCGAACUGCGCGAAGCGGGUCCGGCCGGCGCUGGCCGGCUCCCGCGAGUCGGCGCCCGGAGGCACUAAGCGCGGGGGGCGUAUGCUAGCAUGUUCUCCCU
AAKV01000079.1/32921-32784   CUGCGUAAACCUGUUGUCCCGGAGGAAGUGGCUGGAAAGCGAACUGCGCGAAGCGGGUCCGGCCGGCGCUGGCCGGCACCCGCAACUCGGCGCCCAGAGGCACUAAGCGCGGGGGGCGUAUGCUAGCAUGUUCUCCCU
AAQW01000001.1/344636-344773 CUGCGUAAACCUGUUGUCCCGGAGGAAGUGGCUGGAAAGCGAACUGCGCGAAGCGGGUCCGGCCGGCGCUGGCCGGCACCCGCAACUCGGCGCCCAGAGGCACUAAGCGCGGGGGGCGUAUGCUAGCAUGUUCUCCCU
#=GC SS_cons                 ::((((------((-((((-((,,,,<<<-<<<____>>>-->>><<<<<<-<<<<<<<<<<<<<____>>>>>>>->>>>>>--->>->>>>))-)-)))))---))))<<<<<<--<<<<____>>>>-->>>>>>
#=GC RF                      cUGcGcAAAccUGuUGccccGGAGGAaGuGGcuGGAAagCGAaCuGcGcGaAGcGGGuccGGccgGcGccggCCggcaCCCgCaAcuCGgCgCCCagAggCaCUAAgCgCgGGGgGcGcauGcUAGCaugUUCcCCCc
//
# STOCKHOLM 1.0

#=GF AC   RF01673
#=GF ID   PhrS
#=GF PI   P20
#=GF DE   PhrS
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Predicted; WAR; cmfinder;
#=GF GA   37.00
#=GF TC   38.10
#=GF NC   35.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0009372; quorum sensing;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF RN   [2]
#=GF RM   21375594
#=GF RT   The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa
#=GF RT   quinolone signal.
#=GF RA   Sonnleitner E, Gonzalez N, Sorger-Domenigg T, Heeb S, Richter AS, Backofen
#=GF RA   R, Williams P, Huttenhofer A, Haas D, Blasi U
#=GF RL   Mol Microbiol. 2011;80:868-885.
#=GF RN   [3]
#=GF RM   18832323
#=GF RT   Detection of small RNAs in Pseudomonas aeruginosa by RNomics and
#=GF RT   structure-based bioinformatic tools.
#=GF RA   Sonnleitner E, Sorger-Domenigg T, Madej MJ, Findeiss S, Hackermuller J,
#=GF RA   Huttenhofer A, Stadler PF, Blasi U, Moll I
#=GF RL   Microbiology. 2008;154:3175-3187.
#=GF WK   PhrS
#=GF SQ   13


CP002496.1/1822393-1822605 AUCGAGCAACACCCAACCGGCAA----CUGGAGGCCAU-CAA---CAUGUUCAUCGACGAAGUGGUUCUCGCAGGGAUUCUUACAGUAGGCCUCAUGGUCGCUUUCUUCGGUGGGGUCGGUUACUUCAUCUGGAAGGAUUCCCAUAGCCGCAAAG---GCUGAUCCUC-CCGGA-UACACAGAGCACGCAAGGCACUUA-GGGCGACUU-CGGUCGCCCGUUUUUUUU
CP000712.1/1333472-1333680 AUCGGACAACGGCAAACGAAU---------GGGGAGGC-CAG---CAUGUUCUUCGACAACGUGGUUAUCGCCGGUGUGGUAACGGUCGGGCUGAUGGUCGCCUUCUUUGCCGGUCUGGGCAUUUUCAUCUGGAAGGACUCGAACAAGCGCAAGCCGCGCUGA-CCUU-CCGGG-UACAC-GAGCACGCAAGGCAUUUA-GGGCGACUU-CGGUCGCCCAUUUUUUUU
CT573326.1/1360595-1360804 AUCGGAUGACGGCACACCAAG---------GGAGGGGC-CGA---CAUGUUCUUCGACAACGUGGUUAUCGCCGGUGUGGUAACGGUCGGGCUGAUGUUGGCGUUCUUCGCCGGUCUGGGAAUUUUCAUCUGGAAGGAUUCGAACAAGCGCAAGCAGCGCUGAUCCUU-CCCGA-UUCAC-GAGCACGCAAGGCAUUUA-GGGCGACUU-CGGUCGCCCAUUUUUUUG
CP000949.1/1286938-1287146 AUCGGACAACGGCAAACGAAU---------CGGGAGGC-CAA---CAUGUUCUUCGACAAUGUGGUUAUCGCUGGUGUGGUAACGGUCGGGUUGAUGUUCGCGUUCUUUGCCGGUCUGGGCAUUUUCAUCUGGAAGGACUCGAACAAGCGCAAGCCGCGCUGA-CCUU-CCAGG-UUCAC-GGGCACGCAAGGCAUUUA-GGGCGACUU-CGGUCGCCCAUUUUUUUU
CP000076.1/1485736-1485944 --------AUCGCAACAGGGCAA----GAGCAGGAGGC-CAG--UCAUGUUUUUCGACAAUGUGGUGAUCGCCGGAGUGCUGACUGUCGGCCUCAUGGUUCUGUUUUUCGCAGGGUUUGGAUUCUUUAUCUGGAAAGACGCGAAUAAGCGCAAGAAGCCUUAAGUCUU-UCCAG-GGCAACGAGCACGCAAGGCAUUUU-GGGCAACUU-CGGUUGCCCUUUUUUUUG
CP000514.1/1289787-1289982 -----AUCAAGUUUUACAGGUA--------CAGGAGACAUAG--CCAUGUAUAUGGACGCAGUUGUAAUCGCCGGAAUCGCCACAGUAUUGCUGAUGAUUGGCUUCUUCGUCGGAGUCGGCAUCUUCGUCAUGAAGGAUCAGAAGAGUCAU-----------GCUGCU-AAAGG-CGGAAAGAACCACCAGGGUGGUCA-UGGCAGCUGACGAACAGACAGCUUU---
CP000438.1/1841702-1841914 AUCGAGCAACACCCAACCGGCAA----CUGGAGGCCAU-CAA---CAUGUUCAUCGACGAAGUGGUUCUCGCAGGGAUUCUUACGGUAGGCCUCAUGGUCGCUUUCUUCGGUGGGGUCGGUUACUUCAUCUGGAAGGAUUCCCAUAGCCGCAAAG---GCUGAUCCUC-CCGGA-UACACAGAGCACGCAAGGCACUUA-GGGCGACUU-CGGUCGCCCGUUUUUUUG
CP002585.1/1555466-1555684 UUGAACCCAUCGCAACAGGGGCAA---GACCAGGAGGC-CAG--UCAUGUUUUUCGAUAAUGUGGUGUUUGCCGGGGUGUUGACGGUCGGCCUCAUGGUCGUGUUUUUCGCAGGCUUUGGAUUAUUCAUCUGGAAAGACGCGCACAAGCGGAAAAAACCGUAGGUCUUUCCGGC-UACAACGAGCACGCAAGGCAUUUU-GGGCGACUU-CGGUCGCCCUUUUUUUUG
AM181176.4/1498156-1498373 UUAGCCCUAUCGCAACAGGGCAA----GUGCAGGAGGC-CGG--UCAUGUUUAUCGAUAAUGUGGUAUUUGCCGGAGUGCUGACUGUGAGCCUCAUGGUGAUGUUUUUUGUAGGGUUUGGAAUUUUUAUCUGGAAAGACGCGAACAAGCGUAAAAAACCAUAGGUUUU-UCCGGGUUACAUGAGCACGCAAGGCAUUUU-GGGCGACUU-CGGUCGCCCUUUUUUUGC
CP001978.1/1579474-1579663 GUUUAAUCAAGUUAAUUGCCGG--------AAGGAGAAACAA---AAUGUAUAUGGACGCCGUUGUGAUCGCAGGUAUUGCCACUGUACUGCUGAUGCUUGGCUUUUUUGUUGGUGUUGGCAUCUUCGUGAUGAAAGAUCAGAAGGAGCAC-----------GGACAC-CAGGA-UAGAA-A----AGAAGGGAAGCAC-GGAC--AUA-AG-----CCGGUUUGACG
CP001157.1/3127108-3126901 AUCGAAGA-GAGCAACGGUG----------AAGAGUGC-CAG--CCAUGUUGGUCGAUGAAGUGGUAGUGGCGGGGACGGCAGUCGCGGGAUUGAUAUUCGUUUUCACCGGUGGGAUCGGUUAUUUCAUCUGGAAGGACGCACGGAAAUACAAAUAACGA--AGUCCU-UCGGA-UUCCA-GAGCACGCAAGGCACUUUCGGGCGACGU-UAGUCGCCCUUUUUUUUU
CP000304.1/3199247-3199041 AUCGAA---CAGCGAAUCAGGU-------UUCGGAGGU-AGGUCUCAUGUUUGUCGAUAAUGUGGUGCUCGCAGGGGUGGUCACGGUCGGCCUGAUGGUCGCCUUCCUCGGAGGCUUCGGAUAUUUCAUCUGGAAGGACGCGCA------CAAGAAGCGCUGAGUUCUUCCAGA-UUCAAAGAGCACGCAAGGCAUUUA--GGCGACCUAUGGUCGCC-UUUUUUUUG
CP002727.1/1679465-1679679 AACGUAGCGCCAUACCCGAGCAGCAGGUGCAAGGAGG--CAG---CAUGUUCCUAGAUGUGGUGGUUCUCGCCGGUAUCGGCACCGUUGGGCUGAUGAUUCUGUUUGGUAUCGGGUUCACGUAUUUCGUCUGGAAGGAUGCGAGCAAGAAAAAGCCGCACUGA--UCG-CCGGA-CUCAC-GAGCACGCAAGGCAUU-G-GGGCGACUU-CGGUCGCCCUUUUUUUCG
#=GC SS_cons               :::::::::((((,,,,,,,,,.......,,,,,,,,,.,,,...,,,,,,,,,,,,,,,,<<<_____>>>,,,,,,,,,,,,,,,,<<<<____>>>>,,,,,,,,,)))),,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,.,,,,,,,,<<-<____>>>,,,,,.<<<<<<<__.__>>>>>>>:::::::::
#=GC RF                    aUcGaAuaAcggCaAacgaGua.......gaAGGAGGc.CAG...CAUGUUuaUcGAcgauGUgGUuaUcGCcGGuaUgguaACuGUaggcCUGAUGgucGugUUcUUcGccgGguUcGGauuuUUCAUCUGGAAGGAugCGAAcAAgCacAAaaagCgcUgAgucuU.cCgGa.UucAaaGAGCACGCAAGGCAuUUa.GGGCGACUU.cGGUCGCCCuUUUUUUUg
//
# STOCKHOLM 1.0

#=GF AC   RF01674
#=GF ID   P27
#=GF DE   Pseudomonas sRNA P27
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   50.00
#=GF TC   107.80
#=GF NC   49.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   4


AE004091.2/4781786-4781978 CGGGUUUACUCCUGGAUGUUACCGUUUCGUCCAGCCGGGGCCGGACGUCGUUUUGGUGUCUGAUUCGGUAACCGAAUCGGGAGCACCAUCUGCGUAGGCUUGUGGUUUAAGGCUUGCGCCACCUACGGUCUUGGAUAGCCCCCGCCAGGCAGGGACCCCAAUACCUGUGCAGCG--GGCAGAACCCGCUGCACGA
CP000949.1/5244591-5244779 CGGGUUUACUCCUGGUUUUUACCGUUUCAUCUGGCCGAAGCCGGAUGUCGUUUUGGUGUCUGAUUCGGUAA-CGAAUCGGGAGCACCAUCUGCGUAGGCUUGAGGUUUAAGACUUGCGCCGCCUACGGUCUUGGAUAGCCCCCGCCAGGCAGGGACCCCAAU---UUUGCUGAU--GGCGCGACGGAUCGCGCCA
AE016853.1/677321-677128   GGGUUUAACUCCUGCUUGUUACCGUUUCAUCCGACCGGAGUCAGAUGUCGUUUUGGUGUCUGAUUCGGUAA-GGAACCGGGAGCACCAUCUGCGUAGGCUUGAGGUUUAAGACUUGCGUCGCCUACGGUCUUGGAUAGCCCCCGCCAGGCAGGGACCCCAAUCUUUAAAACGGAGCGGCAAACAACGCCGCGCCA
CP000712.1/551550-551361   CGGGUUUACUCCUGGUUUUUACCGUUUCAUCUGGCCGAGGCCGGAUGUCGUUUUGGUGUCUGAUUCGGUAA-CGAAUCGGGAGCACCAUCUGCGUGGGCUGAUAUUUUAAGGCUUGCGCCGCCUACGGUCUUGGAUAGCCCCCGCCAGGCAGGGACCCCAAUU--UUUGCUGGC--GGCGCGACUGGUCGCGCCG
#=GC SS_cons               :((((((---((((,,,,,,,,<<---<<<<<<<<____>>>>>>>>->>,,,<<<<<<<<<<<<<_____._>>>>>>>-->>>>>>,,,<<<--<<<<----<<<<<<<<<<____________>>>>>>>>>>>>>>-->>>))))---))))))----------------..<<<<<<______>>>>>>:
#=GC RF                    cGGguucACUCCuGguUuUUACCGUUUCguCcGgCCGaaGcCgGacGUCGUUUuGGuGuCuGauuCGGUAA.cGaauCgGGAgCaCCaUCUGCGUaGGCuugagguuuaaGaCuUGCGcCgCCUACgGuCuuggacaGCCCCCGCCaGGCAGggacCCCAAUuuuUuugcuGau..gGcgcgacucgucgcgCca
//
# STOCKHOLM 1.0

#=GF AC   RF01675
#=GF ID   CrcZ
#=GF PI   P29
#=GF DE   Pseudomonas sRNA CrcZ
#=GF AU   Burge S; 0000-0002-2506-927X
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   95.00
#=GF TC   107.80
#=GF NC   88.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0045013; carbon catabolite repression of transcription;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF RN   [2]
#=GF RM   17462015
#=GF RT   The Pseudomonas putida Crc global regulator is an RNA binding protein that
#=GF RT   inhibits translation of the AlkS transcriptional regulator.
#=GF RA   Moreno R, Ruiz-Manzano A, Yuste L, Rojo F
#=GF RL   Mol Microbiol. 2007;64:665-675.
#=GF RN   [3]
#=GF RM   20080802
#=GF RT   Small RNA as global regulator of carbon catabolite repression in
#=GF RT   Pseudomonas aeruginosa.
#=GF RA   Sonnleitner E, Abdou L, Haas D
#=GF RL   Proc Natl Acad Sci U S A. 2009;106:21866-21871.
#=GF WK   CrcZ
#=GF SQ   19


CP000438.1/5580520-5580923   ACAACAACAAUAACAAGCAA--C--GACG-AAGAC-AAUAAAAACAACACGUAACGACUCCAGCACAACAAAAACAA-AAUCG-C-GGAGGCGCAGCUAACUGAUUCUUUUGGAGAGGAGUUGCUGUCGGG--A-CC-------------CGUC--CCGCAGCCAGUCGGAAGAAGAAU-AA-AACUGCC-UCGA-GGCAG-CGCACAGACUG-G-UUGGAUCGC------U--------CG-----ACGAUCAUGGCAGCAUCAGCGACCAAAGCAAUCCGUUUGCUAUUGAACUCCCAGCCUGGGAGAUAUCCCUGAAGCGACUGGCUCAAGGGACG-GGUCGACAAACAAAAACAACAAGCCCG----AAAUCA-UAAUAA--A--AACAAAGCACGC--ACCUA-CUUGGGGGGGAGCUUCGGCUCCCCCAGUAGCUUC-----ACCCCUCCCUCCGUUUUCCCCGUUUUU
CP000076.1/4546202-4546607   AUAACAAGAAUAAAAAGCAG--C-----A-AACCU-AAUAAAAAUAAGACGUAACGACUCUGAGAUAACAAAAACAA-CACGG-C-AGAGACGCAGCUAACAGAUUUUUUUGGAGAGGAUGCACUGUGCAG--GAGGG--CUUGCAAGAGCCAC--CCGCAACCGGUCAGA-GAACAAU-AA-AACUACC-CUGA-GGUAG-CUCCCGAACUG-G-UUGGAUCGC------C-------CUG-----GCGAC-ACA-UUGAAUCAGCGCUCAAAAAAAUACGUUUGCUCUUGA--UCCCGGAU--GGGGAUCGCCAA-AAACAGCAG--UAAAGGGCAA-CGGUUGCCAAAAACAACAAUAGACCGC----CCCUCAAUAAUAA--AAAAAGAGCACGCAACGACAAA-AUUAAAGGGGAGCUUCGGCUCCCCU--UUGUGCU-----UUCU-GCGAUCCCUCUUUGCUGCCCAU
AM181176.4/4288010-4288409   AUAACAAGAAUAAAAAGCAC--C-------AAGCCUAAUAAAAAUAAGACGAAACGACUCUGACAUAACAAAAACAA-CACGG-C-AGAGACGCAGCUAACAGAUUUUUUUGGAGAAGAUGUGCUUCGCAG--G-GUA--CGGCGUGCCGAAAC--CCGCAACCGGUUAGA-GAAAAAU-AA-AACUACC-U-CA-GGUAG-CUACC-CACUG-G-UUGGAUCGA------U--------A------ACGAA-GAAGCAG-AUCAGCGCUCAAAAAAAUACGUUUGCUCUUGA--CCCCGAAU--GGGGGUCGCCCA-AAACAGCGG--UAAAGGGUAA-CGGUUGCCAAAAACAACAAUAGACCGC----CCCUCAAUAAUAA--AAAAAGAGCACGCAACGACA-A-AUUAAAGGGGACCCUCGGGUCCCCU--UUGUGCU-----UUCU-GCGUUUCGUUCAUGUGUUGAUU
AACY022997144.1/409-23       ACAAAAACAAUAACAAGCUU--U--GUAC-AAGAC-AAUAAAAAUAAGACGAAUCGACUCACGCAUAACAAAAACAA-CACGG-C-GGAGGCGCAGCUAACUGAUUCUUUUGGAGAGGCGUUGCAUUUGGG--G-CU-------------UGCC--CCGCAACCAGGCCGA-GAACAACAAA-AACUGCC-CUAA-GGCAG-AGCCUGAACUG-G-UUGGAUCG-------U--------AG-----AUCA-----GCAA-CACAGCGACCAAAGCAAUCCGUUUGCUCUUGG--CUCCUGAUU-GGGAGUGUCAUGAAGGAAG----CUUCGUGGCGA-GGGCGAUCAACAAAAACAAGAAGCCCG----ACAUCAAUAAUAA--A--AAUAGAGCACGC--AACUA-CUUCUGGGGGAGCUUCGGCUCCCCUUGUAGUUU---------CCGGGAUUUGACCUUCAAACGCUU
CP000680.1/3959213-3959603   ACAACAACAAUAACAAGCAA--U--GCCC-CACAC-AAUAAGAACAAGACGUAACGACUCCAGAACAACAAAAACAA-CAAGGAC-GGAGGCGCAGCUAACUGAUUCUUUUGGAGAGGAGUUGCCGCAAGG--G-GUU--CU--------GCCC--CUGCAACCAGACCGA-GAACAAC-AA-AACUGCC-UUCA-GGCAG-CACCCGAACUG-G-UUGAUUA------------------------------AUGGCAGCAUCAGCGUCCAAAGAAAUCCGUUUGCUAUUGGCUCCCCACUCUAGGGAGCACCCGGUGAGCCACGGCGAGCCGGGAAG-GGCCAAACAACAAGAACAACAGGCCCU----CAAUAA-CAACAA--A--AACAAAGCACGC--ACCAA-CUUGGGGGGGAGCUUCGGCUCCCCCAGUAGCUUC-----CGC---UCCACGG--AUCCCCGCCUGC
AY210414.1/5-400             ACAAGACCAAUAACAAGCAA--U--GCAA-AAGAC-AAUAAAAAUAAGACGAAUCGACUCACGCACAAUAAAAACAA-GACGG-CGAGAGGCGCAGCUAACUGAUUCUUUUGGAGAGGCGUUGUAUUUGGG--G-CU-------------UGCC--CCACAACCAGGCCGA-GAACAAU-AAAAACUGUC-UCAA-GACAGGUGCCUGAACUG-G-UUGGAUCGA------U--------UG--------AUCACUGCAA-CACAGCGACCAAAGCAAUCCGUUUGCUCUUGG--CUCCCGAUUGGGAGG-GUCACAAAGGAAAAAA--CCUUGUGGCGUGGGCACUCAACAAAAACAAGAAGCCCG----AAACCAAUAAUAA--A--AAUAGAGCACGU--AACUA-AUUCUGGGGGAGCUUCGGCUCCCCUUGUGGUUUC--------UGUCGUUCCGCCUCCCCGCAGCCU
CP001157.1/452815-452416     ACAACAAAAAUAAAAAACGG--U-------AUCUC-AAGAACAACAAUACGAAACGACUCUGACAUAACAAGAACAAGCACGG-C-AGAGACGGCGCAAACUGAUUUUUUUGGAGAGGAUUCGCGCUCCUG--G-GGU---------CUAGGCC--CCGCAGCCGGACAGA-GAACAAU-AA-AACUACC-UCGA-GGUAG-CGCCCGGACUG-G-UUGGAUCAC------U--------UG-----GUGAUCAUCGCGAUAUCGGCGAUCAAAGAAAUACGUUUGCUCUUGG--CCCCGGCU---GGGGCCGACU-GAAGCA-CUUUCUUCAGAGUGG-CGGUCGACAAAAACAACAACAGAUCGA----GCA----CAAGAA--G--AACAAAGCACAAAGUCG-A-UUUCGAGGGGAGCUCAGGCUCCCCUCUGUGCUUCGAGCGAUCCCCCUUUCCGGAAAACCCGGCUCA
ABZR01000507.1/797-1199      ACAAAAAUAAAAACACGCAG--C-------AACCC-AAUAAAAACAACACGUACCGGCUCUGACAUAACAAGAACAA-CACGGAC-AGAGGCGUAGCUAACAGAUUUUUUUGAAGUGGACA-GCUUUUCUG--A-ACAGCUUGCCUGGCAAGUCGUUCGCAGUCAGACAGA-GAACAAU-AA-AACUGCC-CCAA-GGCAG-CUCCCGUACUG-A-CUGGAUC--------A--------AC-----ACGAUGAAAGUGGCCUCAGCGCUCAAAAAAAUACGUUUGCUCUUGA--UCCAGCUU--GUGGGUCGCUCAAAAAAGA-UG--UGAAGGGUCA--GGUCACCAAAAACAACAACAGACCUC----CCGACA-AACAAA--A--AAGAGCAUAGAGAUAC-AC-CUUGAAGGGGAGCCCAGGCUCCCCU--UCGUGCU-----UUCUGGCGUUUGCCUGGCGCCGAUGUC
CP000075.1/941123-940737     ACAAGAAGAACAACAAGCAGUAC--GACA-CCCAC-AAUAAAAACAAUACGAAUCGACUCACGCAUAACAAGAACAA-UACGG-C-GGAGGCGCAGCUAACUGAUUCUUUUGGAGAGGAGUUGUAUUUGGG--G-CU-------------UGCC--CCGCAACCAGGCCGA-GAACAACAAA-AACUACC-CUUA-GGUAG-CGCCUGAACUG-G-UUGGAUCGA----------------------AUGAUCAUUGCAA-CGCAGCGACCAAAGCAAUCCGUUUGCUCUUGA--CUCCCGACUGGGAGGUUUCACAGACGCAGGUC--UCGU--GAAU-GGGCACUCAACAAAAACAAGAAGCCCA----GGCAGA-AAACAA--U--AAUAAAGAGC----ACACA-CUUU-GGGGGAGCUUCGGCUCCCCCAGUAGCUUC-----CCC------GCCUUGAUCCGCGCCAUC
CP000949.1/2173887-2173503   ACAACAACAACAAAAAA-----U--GCGA-CACCC-AAUAAAAACAACAUGUAACGGCUCUGACAUAACAAGAACAA-CACGG-C-AGAGGCGUAGCAAGCAGAUUUUUUUGGAGUAGACACGCUUUUCAG--G-GGU-----------UCGCC--CCGCGGUCUGGCACA-GAACAAU-AA-AACUACC-UUAA-GGUAG-CGG-CAGUCAGCA-UCGGAUCCU------C---------------AGGAUGAAAGCAG-GUCAGCGCUCAAAAAAAUACGUUUGCUCUUGA--CCCCGGUU--GGGGGUCACCCGCAA-CA--------CCAAGGCA-GGCCUACAAA-AACAACAA-AAGGCCA----GCCUCAAUAAUAA--G--AAAAGAGCAGGCAACAACG-CUUUGAGGGGAGCUUCGGCUCCCCU--CAGUGCU-----UCCUGCCCUCCUCCUCCUGCUGUUUCU
CP000712.1/5102230-5102624   ACAAAAACAAUAACAAGCAC--U--GAAA-UCUAG-AAUAAGAACAAGACGAAACGGCUCACGCACAAUAAAAACAA-GAUGG-C-GGAGGCGCAGCUAACUGAUUCUUUUGGAGAGGAUGCGUGUUUGGG--G-CU-------------UGCC--CCACAACCAGGCAGA-GAACAACAAA-AACUGCACUAAA-AGCAG-CGCCUGAACUG-G-UUGGAUCGA------C--------AG-----AU---CAACGUGUCAUCAGCGGCCAAAGCAAUCCGUUUGCUCUUUA--CCCCCGGUUUGGGGGUCGUCCACAAGCUUCGAGAUUUGUGGGCA-GGGCACUCAACAAAAACAAGAAGCCCA----GCAAAA-AAACAA--U--AAGA--GCACGC--AACGA-CUUCUUGGGGAGCUUAGGCUCCCCUUGUCG---U-----UUCUACCCUUCUGGCAGGCAUCCUGCU
AE016853.1/1046951-1046563   ACAAGAAAAACAACAAGCAG--UACGACA-CCCAU-AACAAGAACAAUACGAAUCGACUCACGCAUAACAAGAACAA-CACGG-C-GGAGGCGCAGCUAACUGAUUCUUUUGGAGAGGAGUUGUAUUUGGG--G-CU-------------UGCC--CCGCAACCAGGCCGA-GAACAAU-AAAAACUACC-CUUA-GGUAG-CGCCUGAACUG-G-UUGGAUCGA----------------------AUGAUCAUUGCAA-CGCAGCGACCAAAGCAAUCCGUUUGCUCUUGA--CUCCCGACUGGGAGGGUUCA--CAGACAAAAGUCUCGUG--AAU-GGGCACUCAACAAAAACAAGAAGCCCG----UACAGA-AAAUAA--A--AAUAAAGAGC----ACACA-CUUU-GGGGGAGCUUCGGCUCCCCCAGUAGCUUC-----CAGA----CCCUAUCUGCGCCGUAGUG
CP000058.1/1024980-1024589   ACAAGAAAAACAACAAGCAGUAC--GACA-CCCAU-AAUAAAAACAACACGAAUCGACUCACGCAUAACAAGAACAA-CACGG-C-GGAGGCGCAGCUAACUGAUUCUUUUGGAGAGGAGUUGUAUUUGGG--G-CU-------------UGCC--CCGCAACCAGGCCGA-GAACAACAAA-AACUACC-CUUA-GGUAG-AGCCUGAACUG-G-UUGGAUCGA----------------------AUGAUCAUUGCAA-CGCAGCGACCAAAGCAAUCCGUUUGCUCUUGA--CUCCCGAUUGGGAGGUUUCACAGA--CGAAGG--UCUCGUGAAU-GGGCACUCAACAAAAACAAGAAGCCCA----UACAGA-AAACAA--U--AAUAAAGAGC----ACACA-CUUU-GGGGGAGCUUCGGCUCCCCCAGUAGCUUC-----CCCAG-CGUUAAUACGCGCCAUCGUUU
CT573326.1/5029853-5030248   ACAAGAACAAUAACAAGCAC--U--GCAA-CUCAG-AAUAAGAACAAGACGAAACGGCUCACGCACAAUAAAAACAA-GACGG-C-GGAGGCGCAGCUAACUGAUUCUUUUGGAGAGGAGUUGUGUUUGGG--G-CU-------------UGCC--CCACGAUCAGGCAGA-GAACAACAAA-AACUGCACUCAAAAGCAG-CACCUGAACUG-A-UUGGAUCGA------A--------AG-----AUCAGCAUC--AU-CUCGGCGACCAAAGCAAUCCGUUUGCUCUUCA--CCCCAGGUUUUGGGGUCGUUCACAAGCUUCGAGAUUUGUGGACA-GGGCACUCAACAAAAACAAGAAGCCCA----GCAGAA-AAAUAA--U--AAGAGCACACAA----CGA-CUUGGUGGGGAGCUUCGGCUCCCCAUGUCGUUU--------CUCCCCCUCCCGCAUCACCGUCCAC
CP000926.1/2668609-2668225   ACAACAACAAAAAAAAUGUG--A-------CACCC-AAUAAAAACAACAGGUAACGGCUCUGACAUAACAAGAACAA-CACGG-C-AGAGGCGUAGCAAGCAGAUUUUUUUGGAGUCGACACGCUUUUCAG--G-GG-----------UACGCC--CCGCGGUCUGGCACA-GAACAAU-AA-AACUACC-UCAA-GGUAG-CAG-CAGCCAG-GUUCGGAUCAG---------------CC-----AUGAUGAAAGCAG-GUCAGCGCUCAAAAAAAUACGUUUGCUCUUGA--CCCCGCAU--GGGGGUCGCCCGCAA---------CACCAGGACA-AGC-CGACAAAAACAACAAUAG-GCCG----GUCCCAAUAAUAA--A--AAAAGAGCAGGCAACAACG-CUUUGAGGGGAGCUUCGGCUCCCCU--CAGUGCU-----UCCUGCCCUCUUCCUCCUUCUGCUUCU
ABSM01000002.1/220033-220450 ACAACAAGAAUAA-AAGCAC--G--CAGC-ACACC-AAUAAAAACAAUACGUACCGGCUCUGACAUAACAAGAACAA-CACGGAC-AGAGACGUAGCUAACAGAUUUUUUUGAAGUGGAUA-GCUUUUCUG--A-ACCACUUGCCCUGCAAGUCGUUUGCAGCCAGACAGA-GAACAAU-AA-AACUGCC-CUGA-GGCAG-CUCCGGAACUG-G-UUGAAUCGU------UGC---GAUAGAAAGCACGAUGAAAGUGACAUCAGCGCUCAAAAAAAUACGUUUGCUCUUGG--UCC-AGCCUCU-GGACCGCUCAAAAAAGA-UG--UGAAGGGUCA--GGUCGCCAAAAACAACAACAGGCCUC----CCGAAA-AACAAA--A--AAGAGCAUAGAG--ACAUACCUUGAAGGGGAGCCCAGGCUCCCCU--UCGUGCU-----UUCCGACGUUUGCUUUUGCCUGCUCAA
CP000304.1/3565446-3565836   ACAACAACAAUAACAAGCAG--A--UCC----CAC-AAUAAGAACAAGACGUAACGGCUCCAGCAAAACAACGACAA-GAAGG-C-GGAGGCGCAGCUAACUGAUUCUUUUGGAGAGGACAUGCCA-CGGG--G-UU-------------CGCC--CCACGACCAGGCCGA-GAACAACAAA-AACUGCA-UCGA--GCAG-GCCCUGCACUG-G-UUGGAUC------------------G-----AAGAUCAAGGCAACGUCAGCGACCAAAGAAAUCCGUUUGCUAUUGG--CUCCCACUGUGGGAGCGUUCCCGACGGCCACGGCCCGAAGGACA-GGCGAAC-AACAAGAACAGCAACGCCUGAGAAGACCAAUAACAAUAA--AUAAGCACGCGA--CAUUA-UUCAGAGGGGAGCUUCGGCUCCCCU--CAGUGCU-----AUCUGGCUCCGCGGUUUCC------UU
CP000094.2/4135995-4136383   AUAACAAGAAUAAAAAGCAG--C-------AAACC-AAUAAAAAUAAGACGUACCGACUCUGACAUAACAAAAACAA-CACGG-C-AGAGACGCAGCUAACAGAUUUUUUUGGAGAAGGUGUGCUUUUCAG--G-GUG--UUCCUCGGAAUGAC--CCGCAACCGGGCAGA-GAACAAU-AA-AACUACC-UUCA-GGUAG-CUCCCGAAUCG-G-UUGGAUCGC------U--------AG-----ACGAG-AAAGCAG-AUCAGCGCUCAAAAAAAUACGUUUGCUCUUGA--CCCCGGAU--GGGGGUCGCCAAAAAACAGCGG--UAAAGGGCCA-CGGUUGCCAAAAACAACAACAGACCGC----CCCUCAAUAAUAA--A--AAGAGCACGCGACGACAAA-AUUAAAGGGGAGCUUCGGCUCCCCU--UUGUGCU-----GUCUGGCGUUCUG--------------
AEAF01000363.1/420-840       ACAACAAAAACAAGAAACGA--A--GCGGCAAACC-AAUAAAAACAAGACGUAACGGCUCUGACAUAACAAGAACAA-AACGGAC-AGAGGCGCAGCUAACAGAUUUUUUUGGAGUGGAUAAGCUUUACAGGGA-CCU--UUCGGUGAAAGGCC--UCGCGACCGGACAGA-GAACAAU-AA-AACUACC-UUCA-GGUAG-CUUCCGAACCG-G-UGGGAUCACGAUGUU-GUGAAGACAG-----GUGAUUAAAGCGA-GUCAGCGCUCAAAAAAAUACGUUUGCUCUUGA--CCCCGGAU--GGGGGUCGCUCAACAACG-CUG--UAAAGGGAC--UGGCCAUCAACAACAAUAACAGGCCGC----CCUACAACAAUAA--A--AAGAGCAGGUAA--AACAC-AUUGGAGGAGAGCUACGGCUCUCCU--UUGUGUU-----UUUCGUCCCCAGGAAGCUGCAGCGUAG
#=GC SS_cons                 ::::::::::::::::::::..:..::::.:::::.::::::::::::::::::<<-<<<<________________._____._.>>>>->>,,,,,,,,,,,,,,<<<<<---------<<<-------..-.---...........-----..---<<<<<<<-----.-------.--.--<<<<<.____.>>>>>.-------->>>.>.>>>------......-........--.....-------------.---->>>-->>>>>,,,,,,,,,,,,,,,,,<..<<<<_______>>>>>,,,,,,,,,,,,,,,,..,,,,((((((.<<<<__________________>>>>,....,,,,,,.,,,,,,..,..,,,,<<<<----..-----.----<<<<<<<<<____>>>>>>>>..>->>>>,.....,,,))))))::::::::::::::::::
#=GC RF                      ACAAcAAaAAuAAcAAGCAg..u..gaaa.aacac.AAUAAaAACAAgACGuAaCGaCUCugaCAuAACAAaAACAA.cAcGG.C.aGAGGCGcAGCUAACuGAUUuuUUUGGAGaGGAuucGCuuUucgG..G.cuu...........auGcC..CCGCaaCCaGgCaGA.GAACAAU.AA.AACUgCC.uuaA.GGcAG.cucCuGaACuG.G.uuGGAUCga......u........aG.....AuGAUcAaaGCaa.aUCAGCgauCAAAaaAAUaCGUUUGCUCUUGg..CcCCggaUUuGGGgGccgcccaaAAacaacug..UaaaggGccg.gGgcaauCAAcAAaAACAAcAagcCca....acaucA.uAAuAA..a..AAgAgcgcacaa..AcauA.cUUuggGGGGAGCUUcGGCUCCCCc..cagcgcu.....uuCcggCccucuguuuuuccugcuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01676
#=GF ID   P31
#=GF DE   Pseudomonas sRNA P31
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; cmfinder;
#=GF GA   40.00
#=GF TC   43.00
#=GF NC   39.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   4


CP000075.1/4988190-4988269 AGAAGACCUCCCGUAAAUAAAACCUGAAAGGGCGAUCGCAGGCUGCAAAAAAGCGGAAUGACGUAGUUAC--GUCACCCCGC
CP000926.1/5281621-5281702 AGAAGACCUCCCGUAAAUCAAGCAUGAAAGGGCGAUCGCAGGUUGCAAAAAAGCGGAGUGACGUAUGGACACGUCACCCCGC
AE004091.2/5344903-5344981 AGAAGACCUCCCGUAAAUCAAGCCUGACUGGUCG--CGCAGG-UGUAAAAAAGCGGGAUGACACCGUGAAGAGUCAUCCCGC
CT573326.1/810183-810102   AGAAGACCUCCCGUAAAUCAAGCCUGAAAGGGCGAUCGCAGGUUGCAAAAAAGCGGAAUGACGUAUGGACACGUCACCCCGC
#=GC SS_cons               ::::<-<<<------------<<<<____>>>>------>>>->--------<<<<--<<<<<<______>>>>>>-->>>>
#=GC RF                    AGAAgACCUCCCGUAAAUcAAGccuGAaagggCGAUCGCAGGuuGcAAAAAAGCGGAAUGaCgcauugAcgcGuCAcCCCGC
//
# STOCKHOLM 1.0

#=GF AC   RF01677
#=GF ID   P35
#=GF DE   Pseudomonas sRNA P35
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   70.00
#=GF TC   89.40
#=GF NC   41.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   2


CP000438.1/5149434-5149373 GCCGGUGGAACGAGCGGCCCUCCGUCUGCGCGUCCCUUCCUGGGGUUCGCAGGCGGAGGGCU
AE004091.2/4985843-4985782 GCCGGCGGAACGAGCGGCCCUCCGUCUGCGCGUCCCUUCCUGGGGUUCGCAGGCGGAGGGCU
#=GC SS_cons               <<<<______>>->><<<<<<<<<<<<<<<--<<<<_____>>>>-->>>>>>>>>>>>>>>
#=GC RF                    GCCGGuGGAACGAGCgGCCCUCCGuCUGCGCGuCCCUUCCUGGGgUUCGCAGgCGGAGGGCu
//
# STOCKHOLM 1.0

#=GF AC   RF01678
#=GF ID   P37
#=GF DE   Pseudomonas sRNA P37
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   91.10
#=GF NC   43.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   2


AE004091.2/5672363-5672302 CGACCUGCCGUCGCCUCUUGACGAAACUCGCUAGUCGUUAGCAUGACCGGCGGGUUUCGUCU
CP000438.1/5943765-5943704 CGACCUGUCGUCGCCUCUUGACGAAACUCGCUAGUCGUUAGCAUGACUGGUGGGUUUCGUCU
#=GC SS_cons               <<<<_____>>>>------<<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>>:
#=GC RF                    CGACCUGuCGUCGCCUCUUGACGAAACuCgCuaGUCgUUAGCAuGACugGcGgGUUUCGUCU
//
# STOCKHOLM 1.0

#=GF AC   RF01679
#=GF ID   P36
#=GF DE   Pseudomonas sRNA P36
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   36.00
#=GF TC   37.10
#=GF NC   34.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   2


AE004091.2/5308433-5308493 CAACCUGUUACCGCGGACGUACCGCGUAACAGAAACCGGGUUCAUCGGUAACGGGAACCCG
CP000744.1/5610507-5610567 CAACCUGUUACCGCGGACGUGCCGCGUAACAGAAACCGGGUUCAUCGGUAACGGGAACCCG
#=GC SS_cons               ::::<<<<<<<-<<<<_____>>>>>>>>>>>----<<<<<<<-<<<____>>>>>>>>>>
#=GC RF                    CAACCUGUUACCGCGGACGUaCCGCGUAACAGAAACCGGGUUCAuCGGUAACGgGAACCCG
//
# STOCKHOLM 1.0

#=GF AC   RF01680
#=GF ID   P5
#=GF DE   Pseudomonas sRNA P5
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Mafta_alifold;
#=GF GA   60.00
#=GF TC   101.40
#=GF NC   34.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF RN   [2]
#=GF RM   18405392
#=GF RT   Genome-wide search reveals a novel GacA-regulated small RNA in Pseudomonas
#=GF RT   species.
#=GF RA   Gonzalez N, Heeb S, Valverde C, Kay E, Reimmann C, Junier T, Haas D
#=GF RL   BMC Genomics. 2008;9:167.
#=GF CC   Identified as IgRs 491 in [2].
#=GF WK   Pseudomonas_sRNA
#=GF SQ   2


AE004091.2/912791-912861   GGUCUGCUCUUCUUCUUCCCGGGCACACCAGCCGCAGCGAAAUUCGCGGCCGAGCUGUCUGUGCCGCUCGU
CP000744.1/4813718-4813648 GGUCUGCUCUUCUUGUUCCCGGGCACACCAGCCGCAGCGAAAGGGGCGGCCGAGCUGUCUGUGCCGCGCGU
#=GC SS_cons               <<<-<<<<<___________>>>>>->>>,<<<<<__________>>>>><<<<<-<<____>>->>>>>:
#=GC RF                    GGUCUGCuCUUCUUgUUCCCGgGCACACCAGCCGCAGCGAAAuugGCGGCCGaGCUGuCUGUgCCGCuCGU
//
# STOCKHOLM 1.0

#=GF AC   RF01681
#=GF ID   P4
#=GF DE   Pseudomonas sRNA P4
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   37.00
#=GF TC   37.30
#=GF NC   35.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   2


CP000744.1/4962754-4962967 GAAGAAUCUCCUUUCAUCGUGGUGUUGGUACGUUGAG-AAGUCGUCUUGCAUGAGGCGGCGCCGUGCUUGCCGGGCUUUGCAUCCCUAGCCGGUCGAAGGGGCCGCUGGGGUUAAAACUCGCAAGUUCCGGUGACAGAUCGGGGAAAAAAUCUCGGGAGCAUCGAAUUGUUUUCAGGCCCUUUCCUCGGGUGUUCGAAGGCUCUGCGCCGGGCGU
AE004091.2/747469-747255   GAAGAAUCUCCUUUCAUCGUGGUGUUGGUACGUUGAGGAAGUCGUCUUGCAUGAGGCGGCGCCGUGCUUGCCGGGCUUUGCAUCCCUAGCCGGUCGAAGGGGCCGCUGGGGAUAAAACUCGCAAGUUCCGGUGACAGAUCGGGGAAAAAAUCUCGGGAGCAUCGAAUUGUUUUCGCAGCCUUUCCUCGGGUGUUCGCAGGCUCUGCGCCGGGCCU
#=GC SS_cons               ::::::::::::<<<<-<<<<_______>>>>->>>>---[[[<<<<<____>>>>>(((((-(-((((<<<<<--<<<<<<<<<<<<<<-<<<<_____>>>>>>>>>>>>>------->>>>>-->>>>><<<<--<<<<<<<<<---<<<-<--<<<<______>>>>-->>>>--->>>>>>>>>->>>>,,,))))-)-))))),]]]::
#=GC RF                    GAAGAAUcUccUcuCaUCGugGUGUUGGcaCGUuGaggAAGcCGcCucGcAUgaGgCGGCGCcGUGCcugCCGGGccuuGCauCCCcaGCcGGcCGAAGGGgCCGCugGGGauAAAAcUcGCaagUUCCGGcgaCaGAcCGgGGaaaAAAccccGGGagCaUcGAAUuGcuUUCggggccuuuCCcCGgGuGuccGaagGCUCUGCGCCGGgCgU
//
# STOCKHOLM 1.0

#=GF AC   RF01682
#=GF ID   P8
#=GF DE   Pseudomonas sRNA P8
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   60.00
#=GF TC   105.40
#=GF NC   35.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   2


AE004091.2/1117532-1117609 GAGGCUUCGGCGAAAAUUUGUGCACAAAUGGAAAGCAGCUUGUCAAGGGUUGAGAGCGUUAGGCUCUAAACGCUUGAU
CP000744.1/4483389-4483312 GGUGCCGCGGCGAAAAUUUGUGCACAAAUGGAAAGCAGCUUGUCAAGGGCUGAGAGCGAUAGGCUCUAAACGCUUGAU
#=GC SS_cons               :<<<<----<<----<<<<<____>>>>>----->>->>>><<<<<<-<<<-<<<<<_____>>>>>->>>->>>>>>
#=GC RF                    GagGCuuCGGCGAAAauuuGUGCACaaauGGAAAGCAGCcuguCaaGGGuuGaGaGCGaUAGGCuCuAaaCGCuuGau
//
# STOCKHOLM 1.0

#=GF AC   RF01683
#=GF ID   P6
#=GF DE   Pseudomonas sRNA P6
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   51.60
#=GF NC   44.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   3


CP000744.1/4747485-4747994 UCGAAGGGGAUAGCAUCGAUUGGCAGGAGAAAUAGAACCUUGCCCAGGCCGCCGACGGAUAUGCGUGUU-CACCGGCUCUUGCGCAGGGACGCCUUCUCGUGGAAAGGGCGCCAGCUGGGGUGAGCGGCAUUCUAGCGACAGGCCGGAAGUGGUUAUUUCUUCAAUGCGACAACUAAUUAUAAAAGCACCGAAGAGGGCUUUCGGCGAUAUUGACAGGCAGCUGCAUUUGUGCCCGGAAAGCGCGAAGUGUAAUCAAUGAGUAAAGCAAAUCUCAAGCCAUAAAUUGGUAAUUCCUUCUUCUUCAACGGUUUGGACGAGCCGACUCGCUUCGCCUGCUACCCCGUGUCGCACCCUCACGGUGCGUGGCGUUUCCUCUCGCCCCAAUUAUGCGCAGGCGCGCAUCACCGAAGUGUUACCGCCCACGCAUUCCC-GCGCGCGCCCAUUCGGCACGCCCUCCUCCUCGACCCGCGCCAAAUGAAAGACCCCGCGCAGCUCGCACCGCGCGGGGUC
AF012537.1/624-115         UCGAAGGGGAUGGCAUCGAUUGGCAGGAGAAAUAGAACCUUGCCCAGGCUGCCGACGGAUAUGCGUGAUCCACCGGCUCUUGCGCAUGG-CGCCUUCUCGUGGACAGGGCGCCAGCUGGGGUGAGCGGCAUUCUAGCGACAGGCCGAAAGUGGUUAUUUCUUCAAUGCGACAACUAAUUAUAAAAGCACCGAAGAGGGCAUUCGGCGAUAUUGACAGGCAGCGACAUUUGUGCCCGGAAAGCGCGAAGUGUAAUCAAUGAGUAAAGCAAAUCUCAAGCCAUAAAUUGCCAAUUCCUUCUCCUUCAAUGGCUUGCCCGCUACGACUCGCCUCGACUGCUACCCCGUGUCGCACCUUGGCUGUGCGUGGCGUUUCCUCUCGCCCCAAUUAUGCGCAGGCGCGCAUCACCGAAGUGUUACCGCCGCCCCAUUCCCGGCGCGAGCCCAUUCGAAACGCCCUCCUCCUCGGCCCGCGCCAAAUGAAAGAC-CCGCGCGGCUCGCACCGCGCGGGGUC
AE004091.2/972154-971645   UCGAAGGGGAUGGCAUCGAUUGGCAGGAGAAAUAGAACCUUGCCCAGGCUGCCGACGGAUAUGCGUGAU-CACCGGCUCUUGCGCAUGG-CGCCUUCUCGUGGACAGGGCGCCAGCUGGGGUGAGCGGCAUUCUAGCGACAGGCCGAAAGUGGUUAUUUCUUCAAUGCGACAACUAAUUAUAAAAGCACCGAAGAGGGCAUUCGGCGAUAUUGACAGGCAGCGACAUUUGUGCCCGGAAAGCGCGAAGUGUAAUCAAUGAGUAAAGCAAAUCUCAAGCCAUAAAUUGCCAAUUCCUUCUCCUUCAAUGGCUUGCCCGCUACGACUCGCCUCGACUGCUACCCCGUGUCGCACCUUGGCUGUGCGUGGCGUUUCCUCUCGCCCCAAUUAUGCGCAGGCGCGCAUCACCGAAGUGUUACCGCCGCCCCAUUCCCGGCGCGAGCCCAUUCGAAACGCCCUCCUCCUCGGCCCGCGCCAAAUGAAAGACCCCGCGCGGCUCGCACCGCGCGGGGUC
#=GC SS_cons               {{{{-{{{{{-{{{-{{{{,,<<<<<<-<________>>>>>>>,,{{{{{{,,,{{{--{{{{<<<__.>>>,,{{-{{{{{{{{{<<.<<<<<<-<<___>>->>>>>>>>,,,[[[[[[[[[-[[-------[[-[[,,<<<<<<-<<-----<<<<<<<--<<<_________________>>>-->>>>>>>>>->>>>>>(((((-(---(((((((<<<<<<<<<<_______>>>>->>>>>>,,,,,,,<<<<--<<<------<<<<<<<<________________________>>>>>>>>--->>>--->>>>,,,,))-)))))---)-)))))<<<<_______>>>>]]-]]----]]-]]]]]]]]],,,}}}}}}}}}-}}}}}}--}}},,,,,,,,,,<<<<_________>>>>}}}-}}},,,}}}}---}}}-}}}}}-}}}}----------------<<<<<<<<<<<<______>>>>>>>>>>>>
#=GC RF                    cCGaAGgGGaUgGCAuCGaUUGGCagGAGAAAUAGAACCcuGCCCAGGCcGCCGACGGAUauGCGuGaU.CaCCGGCUCcuGCGCauGG.CGCCcuCuCGUGGaaagGGCGCCAGCuGGGGcGaGCGGCAUUCUAGCGaCAGGCCGaaAGcGGUUAccuCuuCAAuGCGACAACUAAUUAUAAAAGCaCCGaaGagggCauuCGGCGacacUGACAgGCaGCgaCacuuGcGCCCGGAAAGCgCGaaguGuAAUCAAUGaGuAAagCAAAUCUCaagCCguAAAUUGccAAUUCCUUCUcCUUCAacGGcuuGcaCGcuaCGaCuCGCcUcGaCuGCcACCCCguguCGCaCCuUggCuGuGCGuGGCGUUUCCUCuCgCCCCaAUUauGCGCagGCGCGCauCACCGAAGUGUUACCGCcgaCcCAUUCCcgGCGCgaGCCCAUuCGaaACGCcCuCCcCCuCGgCCCGCGCCAAAUGAAAGaCcCCGCGCgGCUCGCACcGCGCGGgGuC
//
# STOCKHOLM 1.0

#=GF AC   RF01684
#=GF ID   mascRNA-menRNA
#=GF DE   MALAT1-associated small cytoplasmic RNA/MEN beta RNA
#=GF AU   Marz M
#=GF AU   Stadler PF; 0000-0002-5016-5191
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Marz M, Stadler PF
#=GF SS   Published; PMID:19041754;
#=GF GA   42.00
#=GF TC   42.20
#=GF NC   41.70
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   19041754
#=GF RT   3' end processing of a long nuclear-retained noncoding RNA yields a
#=GF RT   tRNA-like cytoplasmic RNA.
#=GF RA   Wilusz JE, Freier SM, Spector DL
#=GF RL   Cell. 2008;135:919-932.
#=GF RN   [2]
#=GF RM   19106332
#=GF RT   MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon
#=GF RT   muscle differentiation and are essential components of paraspeckles.
#=GF RA   Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL
#=GF RL   Genome Res. 2009;19:347-359.
#=GF RN   [3]
#=GF RM   12970751
#=GF RT   MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and
#=GF RT   survival in early-stage non-small cell lung cancer.
#=GF RA   Ji P, Diederichs S, Wang W, Böing S, Metzger R, Schneider PM, Tidow N,
#=GF RA   Brandt B, Buerger H, Bulk E, Thomas M, Berdel WE, Serve H, Müller-Tidow C
#=GF RL   Oncogene. 2003;22:8031-8041.
#=GF CC   The seed alignment for this family was obtained from the following
#=GF CC   publication: Marz M, Stadler PF. Homology Search for Small Structured
#=GF CC   ncRNAs. Handbook of RNA biochemistry. 2010;1:1-1. There is no PMID
#=GF CC   available for this book chapter so only the authors have been referenced
#=GF CC   above.
#=GF WK   MALAT1-associated_small_cytoplasmic_RNA
#=GF SQ   53


AAVX01392965.1/352-296       GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACGGGGU--UCAAAUCCCUGUGGUAUC
ABRR01392295.1/3256-3200     GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACAGGGU--UCAAAUCCCUGUGGCAUC
ABRP01112166.1/967-912       GAUGCUGGUGGUUGGCACUCCUGG-UUU--CAGGACGGGGU--UCAAAUCCGUGUGGCGUC
AAGV020417859.1/1926-1870    GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACGGGGU--UCAAAUCCCUGUGGCGUC
ABQO010154554.1/12820-12764  GAUACUGGUGGUUGGCACUCCUGG-GCU-CCAGGACGGGGU--UCAAAUCCCUGCGGUAUC
AANU01213847.1/880-824       GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACGGGGU--UCAAAUCCCUGCGGCAUC
AAGW02079994.1/2665-2609     GAUGCUGGUGGUUGGCACUCCUGG-AUU-CCAGGACGGGGU--UCAAAUCCCUGCGGCGUC
FJ209302.1/1-57              GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACGGGGU--UCAAAUCCCUGCGGCGUC
AAYZ01386528.1/546-602       GAUGCUGGUGGUUUGGACUCCUGG-UCU-CCAGGACAGGGU--UCAAAUCCCUGCGGCGUC
AANG01068091.1/251-307       GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACAGGGU--UCAAAUCCCUGCGGCGUC
FJ209303.1/1-57              GACGCUGGUGGCUGGCACUCCUGG-UUU-CCAGGACGGGGU--UCAAGUCCCUGCGGUGUC
AAWZ02033013.1/100428-100484 GACGCUGGUGGUUGGCACUCCUGG-CUU-CCGGGACGGGGU--UCAAGUCCCUGCGGUGUC
AAWZ02012849.1/20624-20568   GACGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGAUGGGGU--UCAAGUCCCUGCGGCGUC
AAWZ02003190.1/48926-48870   GACACUGGUGGUUGGCGCUCCUGG-CUU-CCAGGACGGGGU--UCAAGUCCCUGCGGCGUC
AAWZ02023558.1/2948-3004     GACGCUGGUGGUUGGCGCUCCUGG-UUU-CCAGGACGGGGU--UCAAGUCCCUGCGGCGUC
CAAB02008122.1/13078-13135   GACCCCGGUGGU-GGCACUCCUGACGUCGUCGGGACAGGGU--UCGAUCCCCUGCGGUGUC
CAAE01015008.1/734729-734672 GACCCCGGUGGU-GGCACUCCUGACGCUGUCAGGACAGGGU--UCGAUCCCCUGCGGUGUC
AANH01006626.1/48422-48365   GACUCCGGUGGU-GGCACUCCUGACUCUGUCAGGACGGGGU--UCAAUCCCCUGCGGUGUC
BAAF04021703.1/269-212       GACUCCGGUGGU-GGCACUCCUGUUUUACUCAGGACGGGGU--UCAAUUCCCUGCGGUGUC
CR383676.21/53723-53778      GACCCUGGUGGA-GGCACUCCUGA-UUC-UCAGGACGGGGU--UCAACUCCCUGCGGCGUC
AAEX03011638.1/69024-68967   GACGCUGGUGGU-GGCACGCCCAGCACUGCUGGGCCAGGGU--UCAAGUCCCUGUGGCGUC
ABDC01368197.1/3766-3823     GGCGCUGGUGGU-GGCACACCCAGCAUUGCUGGGCCAGGGU--UCAAGUCCCUGCGGCGUC
ABRP01112170.1/2219-2162     GGCGCUGGUGGU-GGCACACCCAGCACUGCUGGGCCAGGGU--UCGAGUCCCUGCGGCGUC
ABRP01358695.1/1145-1202     GGCGCUGGUGGU-GGCACACCCAGCACUGCUGGGCCAGGGU--UCGAGUCCCUGCGGCGUC
AAKN02038533.1/52991-53047   GGCGCUAGUGGU-GGCACGUCCA-CGCUGCUGGGCCGGGGU--UCAAGUCCCCGUGGCGCC
AANU01213855.1/9774-9717     GGCACUGGUGGU-GGCACGUCCAGCACGGCUGGGCCGGGGU--UCGAGUCCCCGCAGUGUC
AP000769.5/11415-11472       GGCGCUGGUGGU-GGCACGUCCAGCACGGCUGGGCCGGGGU--UCGAGUCCCCGCAGUGUU
AP000944.4/186375-186432     GGCGCUGGUGGU-GGCACGUCCAGCACGGCUGGGCCGGGGU--UCGAGUCCCCGCAGUGUU
AAYZ01096777.1/140-195       GGCGCUGGUUGU-GGCAC-UCCAGCAAGGCUGGG-CGGGGU--UCGAGUCCCCGAGGCGCC
AAWR02037820.1/24718-24775   GGCGCUGGUGGC-GGCACACCCAGCACUGCUGGGCCGGGGU--UCAAGUCCCCGUGGCGUC
AAPY01608506.1/875-818       GGUGCUGGUGGU-GGCACACCCAGCACUGCUGGGCCGGGGU--UCAAGUCCCCGCAGCAUC
ABRO01149254.1/16633-16689   GGUGCUGGUGGU-GGCACGCACA-CACUGCUGGGCCGGGGU--UCGAGUCCCCGCAGCACC
AANN01095771.1/1642-1585     CGCGCUGGUGUG-GGCACGCCUGGCACUGCUGGGCCGGGGU--UCGAGUCCCCGCGGCGUC
AALT01088474.1/420-477       GGCGCUGGUGGU-GGCACGCCUGGCACUGCCGGGCCGGGGU--UCGAGUCCCCGCGGCCCC
ABRR01601793.1/466-523       GGCGCUGGUGGU-GGCACGCCUAGCACUGCUGGGCCAGGGU--UCGAGUCCCUGCAUCGUC
AAFC03127117.1/16809-16752   GGCGCUGGUGGU-GGCACGCCUGGCACUGCUGGGCUGGGGU--UCGAGUCCCUGCAGCGUC
AC142098.2/109996-109941     GGCACUGGUGGC-GGCACGCCCG-CACCU-CGGGCCAGGGU--UCGAGUCCCUGCAGUACC
AAHX01009291.1/23050-22998   GGCACUGGUGAU-GGCACGCCCG----UG-UGGGCCGGGGU--UCGAGUCCCCGCAGUACC
ABQO010835126.1/468-519      GGCACUGGCGGU-GGCGCGCCC---AGU---GGGCCGGGGU--UCGAGUCCCCGUGGUGUC
ABRN01286761.1/4358-4301     GGCACUGGUGGU-GGCACGCCUGGUACUGCUGGGCCAGGGU--UCAAGUCCCUGCAGUGUC
ABRQ01073706.1/2005-1948     GGUGCUGGUGGU-GGCACGCCUUGUAGCGCAGGGUCGGGGU--UCGAGUCCCCGUGGCGCC
AAQQ01417558.1/2448-2506     AUUGUUGGUGGUUGGCACUCCUGG-CUU-CCAGGACGGGGUGAUACACACUUAGCCGAGAU
ABRQ01073700.1/1033-977      GAUGCUGGUGGUUGGCACUCCUGC-UUG-CCAGGAUGGGGU--UCAAGUCCCUACAGUGUC
ABRO01149261.1/3153-3209     GAUGCUGGUGGUUGGCACUCCUGG-UUC-CCAGGAUGGGGU--UCAAGUCCCCGCGGUGUC
AAPY01121102.1/562-506       GAUGCUGGUGGUUGGCACUCCUGG-UUC-ACAGGAUGGGGU--UCAAAUCCCUACGGCAUC
AAPE02043328.1/32649-32705   GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACGGGGU--UCGAGUCCCUGUGGCGUC
AAWR02037822.1/6847-6903     GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACGGGGU--UCGAAUCCCUGCGGCGUC
AAHX01009290.1/8975-8919     GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACGGGGU--UCAAGUCCCUGCGGCGUC
BK001411.1/7277-7333         GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACGGGGU--UCAAAUCCCUGCGGUGUC
AAEX03011638.1/19026-18969   GAUGCUGGUGGUUGGCACUCCUGGAUUU-CCAGGACAGGGU--UCAAAUCCUUGCAGUGUC
AAPN01356548.1/4743-4799     GAUGCUGGUGGUUGGCACUCCUGG-GUU-CCAGGACAGGGU--UCAAAUCCCUGCAGUGUC
AAKN02038533.1/93476-93532   GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACGGGGU--UCAAAUCCCUGCAGUGUC
AALT01463641.1/1777-1833     GAUGCUGGUGGUUGGCACUCCUGG-UUU-CCAGGACAGGGU--UCAAGUCCCUGCGGUGUC
#=GC SS_cons                 (((((((<<<__.__>>><<<<<<.___.>>>>>><<<<<_..______>>>>>)))))))
#=GC RF                      GacgCuGGUGGU.GGCACuCCuGG.uuU.CCaGGaCgGGGU..UCaAgUCCCcGCgGcguC
//
# STOCKHOLM 1.0

#=GF AC   RF01685
#=GF ID   6S-Flavo
#=GF DE   6S-Flavo RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   85.00
#=GF TC   85.30
#=GF NC   84.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.40 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   6S_/_SsrS_RNA
#=GF SQ   82


AACY020447591.1/2625-2518    ACUCAACGC-UA-AUUUAA-UUCGAAGAGGUGAGUUUUGGGUG-CACAAGCAA-GCC-----G---------------UUCUAA---------A-CGGAUCCUU-AAACACGCA-GGUAGCCUCAAACA-UGUU--UAAUUCGAGUUU
AACY023367443.1/977-1083     ACUCAACGAGUA--UUAAA-UUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUAGA-----------AUAGAUCCUU-GAAUAUUUG-AUUAGCCUUAAUCC-UGUU--UUUUAGGAGUUU
AACY020213873.1/1014-911     ACUCAACAC-UA-AUUU-UAUUAAAAAAGGUGAGUC-UGUUUGCUA-GAGCGU-GCC-----UGAAG----------------------------AGGAUUAUC-GAAUAUUCA-GUUAGCCUUAAACC-UGUA--UAAACAGAGUUU
AACY021690114.1/503-396      ACUCAAC---GAGUUAUUAAUUAAGAGUGGUGAGUUUCAAUUG-UAAAAGCAA-GCU-----G----U----------CUUGA-----------ACAGAUCCUU-GAUCAGUUGUGU-AGCUACAAACC-UGGU--UUUAUGGAGUUU
AACY023872386.1/757-863      ACUCAACGC-UA-AUCA-A-UUAAGAAGGGUGAGUUUAGAUUGUUA-AAUCGU-GCU-----G----A----------UUUAU-----------UCAGAUUUUU-GAUCAGUCUUGU-AGCCCUAAACC-UGUU--AAAAUGGAGUUU
AACY023901853.1/19-122       ACUCAACGC-GA-AUUU-U-UUAUAAAGGGUGAGUCAUUUCUGCUA-AAGCAC-GCCUAAUU----------------------------------GGAUCCUU-GAUCAGUAU-GUUAGCUCUAAUCU-UGUU-UUAAUGAGAGUUU
AACY021047594.1/669-776      ACUCAACGAGUU-AUUA-A-UUAAGAGUGGUGAGUUUCAAUUG-UAAAAGCAA-GCU-----G----U----------CUUGA-----------ACAGAUCCUU-GAUCAGUUGUGA-AGCCACAAACC-UGAU--UUUUAGGAGUUU
AACY020510232.1/565-668      ACUCAACAC-UA-UUUUUU-UUAAAAAAGGUGAGUC-UGUAUGCUA-GAGCGC-GCC-----CUAAG----------------------------GGGAUUUUC-GAAUAUUCA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY020434657.1/1413-1515    ACUCAACAC-UA--UUUUU-UUAAAAAAGGUGAGUC-UGUAUGCUA-GAGCGC-GCC-----CUAAG----------------------------GGGAUUUUC-GAAUAUUCA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY020267703.1/1008-1112    ACUCAAC---GA-GUAUUAAUUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CCUGA-----------AUAGAUCCUU-GAAUGUUUA-AUUAGCCUUAAUCC-UGUU--UUU-AGGAGUUU
AACY020008268.1/1470-1576    ACUCAAC---GA-GUAUUAAUUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUUCG----------AAUAGAUCCUU-GAAUGUUUA-AUUAGCCUUAAUCC-UGUU--UAUUAGGAGUUU
AACY020016197.1/794-902      ACUCAAC---GAGCUUUUAAUUCAGAGAGGUGAGUUUCAUUUG-UAAAAGCAA-GCU-----G----U----------CAUUG----------AACAGAUCCUU-GAUCAAUUGUGU-AGCCUCAAACU-UGAU--UUUUAGGAGUUU
AANA01000001.1/543738-543632 ACUCAACAC-UA--UUC-UAUUAUGAAGGAUGAGUCUUAACUACUA-AAGCAA-GCC-----A----C----------CUUGA-----------GUGGAUCCUU-GAACAGUUA-GUUAGUCCUAUAUA-UGUC-AUU-AUGGAGUUU
ABCO01000011.1/67885-68005   ACUCAACAC-UA-AUUCUU-UUAAAAAGGGUGAGUUAAAGUUG-UAAAAG-AAUGCC-----G----CUAG----AACCUUG-GUUC---UCGGGCGGACCCUU-GAUCAGCUU-GGGAGCCCUAAACU-UUUU--UAAAUGGAGUUU
AACY021874420.1/579-471      ACUCAAC---GAGCUUUUAAUUAGAAGAGGUGAGUUUCAUUUG-UAAAAGCAA-GCU-----G----U----------CUUUG----------AGCAGAUCCUU-GAUCAAUUGUGU-AGCCUCAAACU-UGAU--UUUUUGGAGUUU
AACY020499922.1/3516-3625    ACUCAACAC-UA-AUUCAA-UUAAAAGAGGUGAGUUUAAGUUG-CAAAAGCAA-GCC-----G----C----------CACCG----------AGUGGAUCCUU-GAACAAUUU-GGUAGCCUCAAACC-UGUU-UAUUUCAGAGUUU
AACY023638381.1/630-524      ACUCAACGAGUA--UUAAA-UUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUUGA-----------AUAGAUCCUU-GAAUAUUUA-AUUAGCCUUAAUCC-UGUU--UUUUAGAAGUUU
AACY022946535.1/33-141       ACUCAAC---GAGCUUUUAAUUCAGAGAGGUGAGUUUCAGUUG-UAAAAGCAA-GCU-----G----U----------CUUGU----------AACAGAUCCUU-GACCAAUUGUGU-AGCCUCAAACU-UGAU--UUUUAGGAGUUU
AACY022878811.1/859-756      ACUCAACGC-AA-AUCU-U-UUAUAAAAGGUGAGUCAAUAUUGUUA-AAGCGU-GCC---------------------UUUAC-------------GGAUACUU-GAUCAGUAU-GUUAGCCUUAAUCU-UGUA-UUAAUAGGGGUUU
AACY022797658.1/99-201       ACUCAACAC-UA--UUUUU-UUAAAAAAGGUGAGUC-UGUAUGCUA-GAGCGC-GCC-----CUAAC----------------------------GGGAUUUUC-GAAUAUACA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY021349943.1/102-211      ACUCAAC---GAGCUUUUAAUUCAGAGAGGUGAGUUUCAGUUG-UAAAAGCAA-GCU-----G----U----------CUUUUG---------AACAGAUCCUU-GAUCAAUUGUGU-AGCCUCAAACU-UGAU--UUUUAGGAGUUU
AACY023575949.1/699-596      ACUCAACAC-UA-UUUUUU-UUAAAAAAGGUGAGUC-UGUAUGCUA-GAGCGC-GCC-----CUAAG----------------------------GGGAUUUUC-GAAUAUUCA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY020277320.1/1990-1886    ACUCAACGC-UA-AUAA-A-UUAAAAAGAGUGAGUC-UAGAUCCUA-GAGCGU-GCC-----U----U----------UUUU------------AAGGAUUAUC-GAAUAUUUA-GUUAGCUCUAAACU-UG-U-AUAAAUGGAGUUU
AACY020948886.1/318-212      ACUCAAC---GAAAUUU-U-UAAUAAUGGGUAAGUCCGUUUGG-UAAAAGCAA-GCU-----U----U----------CAUGA-----------AAAGAUCCUU-GAUCCAAAG-GUUAGCCCAAAUCC-UGUU-UAUAUAGGAGUUU
AACY023596667.1/803-909      ACUCAACGC-GA-AUUUUU-UUAUAAAGGGUGAGUCUAUUCUGCUA-AAGCAA-GCC---------------------UUAAUA---------G--GGAUCCUU-GAUCAGUUA-GUUAGCUCUAAACU-UGUU-AAUACAAGAGUUU
AACY020631901.1/326-429      ACUCAACAC-UA-UUUUUU-UUAAAAAAGGUGAGUC-UGUAUGCUA-GAGCGC-GCC-----CUCAG----------------------------GGGAUUUUC-GAAUAUUCA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY022582938.1/199-92       ACUCAACGAAGA--UUAAA-UUCAAAGAGGUGAGUCACUAUUG-UAAAAGCAU-GCU-----G----C----------CUAGA-----------GCAGAUCCUU-GAUCAAUGG-GGUAGCCUCAAACC-UGUU--UAUAUGGAGUUU
AACY022077491.1/360-464      ACUCAACGC-GA-AUUUUU-UUAUAAAGGGUGAGUCAUUUCUGCUA-AAGCAC-GCCUAAUU----------------------------------GGAUCCUU-GAUCAGUAU-GUUAGCUCUAAUCU-UGUU-UUAAUGAGAGUUU
AACY020328983.1/1095-989     ACUCAACGC-GA-AUUUUU-UUAUAAAGGGUGAGUCUAUUCUGCUA-AAGCAA-GCC---------------------UUAAUA---------G--GGAUCCUU-GAUCAGUUA-GUUAGCUCUAAACU-UGUU-AAUACAAGAGUUU
AACY023486059.1/1017-911     ACUCAAC---GAAAUUU-U-UAAUAAAGGGUGAGUCCUUUUGG-UAAAAGCAU-GCU-----U----U----------CUUGA-----------AAAGACCCUU-GAUCCAAAG-GUUAGCCUAAAUCC-UGUU-UAUAUGGGAGUUU
AACY020543799.1/1137-1244    ACUCAAC---GA-GCUUUAAUUAGAAGAGGUGAGUUAUAAUUG-UAAAAGCAA-GCU-----G----C----------CUUGA-----------GCAGAUCCUU-GAUCAGUUAUGU-AGCCUCAAACC-UGUU-UAUUUAGGAGUUU
AACY020447051.1/547-443      ACUCAAC---GA-GUAUUAAUUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUUGA-----------AUAGAUCCUU-GAAUGUUUA-AUUAGCCUUAAUCC-UGUU--UUU-GGGAGUUU
AACY023159522.1/455-349      ACUCAACGAGUAUACAA---UUAAAAAAGGUGAGUA-CAAGUGUUA-AAGCAA-GCU-----A----U----------CUAGA-----------AUAGAUCCUU-GAUCAUUUG-AUUAGCCUUAAUCC-UGUU--UAAAAGGAGUUU
AAOG01000003.1/188107-187981 ACUCAAC---GA-GUAUCUAUUAUAAAGGAUAAGUCUCAGUUGCUA-AAGCAA-GCC-----A----UAGAAUUCGAAUUUA-UUCUUUUUCAGGUGGAUCCUU-GAUCAGCUA-GUUAGUCCUAAACC-UG-U-AAUAAUGGAGUUU
AACY020192006.1/201-95       ACUCAACGAGUA--UUAAA-UUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUUGA-----------AUAGAUCCUU-GAAUAUUUA-AUUAGCCUUAAUCC-UGUU--UUUUAGGAGUUU
AACY020386012.1/1647-1751    ACUCAAC---GA-GUAUUAAUUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUAGA-----------AUAGAUCCUU-GAAUAUUUA-AUUAGCCUUAAUCC-UGUU--UUU-UGGAGUUU
AACY020431015.1/4238-4344    ACUCAACGAGUAUACAA---UUAAAAAAGGUGAGUA-CAAGUGUUA-AAGCAU-GCU-----A----U----------CUAGA-----------AUAGAUCCUU-GAUCAUUUG-AUUAGCCUUAAUCC-UGUU--UAAAAGGAGUUU
AANC01000006.1/17405-17297   ACUCAACAC-UAUAUUC-U-UUAAGAGGGAUGAGUCUGAGUUG-UAAAAGCGC-GCC-----G----U----------CUUUG----------AACGGAUUCUU-GAUCAGCUC-GUUAGUCCUAUGAU-UUAU--UUUAAGGAGUUU
AACY023452605.1/1026-918     ACUCAAC---GAGCUUUUAAUUCAGAGAGGUGAGUUUCAUUUG-UAAAAGCAA-GCU-----G----U----------CUUGU----------AACAGAUCCUU-GAUCAAUUGUGU-AGCCUCAAACU-UGAU--UUUUAGGAGUUU
AACY024105008.1/150-43       ACUCAACGC-UA-AUUA-A-UUAUAAAGGGUGAGUUUAGGUUGCUA-AAUCGU-GCU-----G----A---------AAUUU-----------UUCAGAUUUUU-GAUCAGUCUUGU-AGCCCUAAUCC-UGUU--AAACUGGAGUUU
AM398681.1/1319608-1319714   ACUCAACAC-UA-ACAA-A-UUAAAAUGAGCAAAUCAUCGUUACUAUAGC-AA-GCC-----A----A----------UUUAG----------UUUGGAA-GCUUGAACAACGA-GUUAACUCAAAACU-UGUC-AAUC-CG-AGUUU
AACY022359968.1/171-62       ACUCAACAC-UA-AUUCAA-UUAAAAGAGGUGAGUUUAAGUUG-CAAAAGCAA-GCC-----G----C----------CUUCG----------AGCGGAUCCUU-GAACAAUUU-GGUAGCCUCAAACC-UGUU-UAUUUCAGGGUUU
AACY020332875.1/756-650      ACUCAACGAGUA--UUAAA-UUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUAGA-----------AUAGAUCCUU-GAAUAUUUG-AUUAGCCUUAAUCC-UGUU--UUUUAGGAGUUU
AACY020548926.1/1148-1045    ACUCAACAC-UA-AUAA-A-UUAAAAAGAGUGAGUC-UAAAUGCUA-GAGCGU-GCC-----U---------------UUUUU------------AGGAUUUUC-GAAUAUUUA-GUUAGCUCUAAACU-UG-U-AUAAAUAGAGUUU
AACY023871604.1/1063-1165    ACUCAACAC-UA--UUUUU-UUAAAAAAGGUGAGUC-UGUGUGCUA-GAGCGC-GCC-----CUAAG----------------------------GGGAUUUUC-GAAUAUUCA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY021484564.1/600-708      ACUCAAC---GAAGUUUACAUUAAAAGAGGUGAUUUGCCGUUG-UAAGAGCAA-GCU-----G---------------UUUUGU---------A-CAGAUCCUC-GAUCAGUGG-GGUAGCCUCAAACCUGUCU-AAUUAAG-GGUUU
AACY020234078.1/918-1023     ACUCAAC---GAAAUUU---UAAUAAAGGGUAAGUCCGUUUGG-UAAAAGCAA-GCU-----U----U----------UCUGA-----------AAAGAUCCUU-GAUCCAAAG-GUUAGCCCAAAUCC-UGUU-UACAUAGGAGUUU
AACY023737341.1/1224-1118    ACUCAACGAGUAUACAA---UUAAAAAAGGUAAGUU-CAAGUGUUA-AAGCAA-GCU-----A----U----------CUAGA-----------AUAGAUCCUU-GAUCAUUUG-AUUAGCCUUAAUCC-UGUU--UAAAAGGAGUUU
AACY022937137.1/491-387      ACUCAAC---GA-GUAUUAAUUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUUGA-----------AUAGAUCCUU-GAAUGUUUA-AUUAGCCUUAAUCC-UGUU--UUU-AGGAGUUU
AAPD01000002.1/349281-349171 ACUCAACACAUA-AUUC-U-UUAAAAAAGGUGAGUCGUGGUUG-UAAAAGCAA-GCC-----G----GA--------CCUAGGA---------GCCGGAUCCUU-GAUCAAUCA-GUUAACCUUAAACUU---U-AUUUAAGGAGUUC
AACY020444574.1/981-1087     ACUCAACGAGUA--UUAAA-UUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUUGA-----------AUAGAUCCUU-GAAUAUUUG-AUUAGCCUUAAUCC-UGUU--UUUUAGGAGUUU
AACY020130858.1/2237-2131    ACUCAACGAGUA--UUAAA-UUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUUGA-----------AUAGAUCCUU-GAAUAUUUA-AUUAGCCUUAAUCC-UGUU--UUUUAGGAGUUU
AACY020266888.1/1479-1375    ACUCAAC---GA-GUAUUAAUUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUUGA-----------AUAGAUCCUU-GAAUGUUUA-AUUAGCCUUAAUCC-UGUU--UUU-AGGAGUUU
AACY023266825.1/372-266      ACUCAAC---GA-GUAUUAAUUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUUCG----------AAUAGAUCCUU-GAAUGUUUA-AUUAGCCUUAAUCC-UGUU--UAUUAGGAGUUU
AACY023265141.1/15-123       ACUCAAC---GAGCUUUUAAUUCAGAGAGGUGAGUUUCAGUUG-UAAAAGCAA-GCU-----G----C----------CUUGU----------AGCAGAUCCUU-GACCAAUUGUGU-AGCUUCAAACU-UGAU--UUUUAGGAGUUU
AACY020489887.1/2667-2558    ACUCAAC---GAGCUUUUAAUUCGGAGAGGUGAGUUUCAUUUG-UAAAAGCAA-GCU-----G----U----------CUUGU----------AACAGAUCCUU-GAUCAAUUGUGU-AGCCUCAAACU-UGAU-UUUUUAGGAGUUU
AAPR01000008.1/9568-9681     ACUCAACAU-UU-ACUA-U-UUAAAAAGGGUGAGUUUCAGUUGCUA-AAGCAA-GCC-----G----CC-------ACUUCG-GU------GCAGCGGAUCCUU-GAUCAGCUG-GGUAUCCCUAAACC-UGUU--UACACGGAGUUU
AACY023385857.1/744-847      ACUCAACAC-UA-UUUUAA-UUAAAAAAGGUAAGUC-UGUUUGCUA-GAGCGU-GCC-----UGAAA----------------------------AGGAUUGUC-GAAUAUUCA-GUUAGCCUUAAACC-UGUA--UAAACAGAGUUU
AACY021018287.1/183-287      ACUCAAC---GA-GUAUUAAUUAAGAAAGGUGAGUU-UAAAUGCUA-AAGCAA-GCU-----A----U----------CUUGA-----------AUAGAUCCUU-GAAUAUUUA-AUUAGCCUUAAUCC-UGUU--UUU-AGGAGUUU
AACY020507234.1/1071-1178    ACUCAACGC-GA-AUUA-A-UUAAAAAGAGUGAGUC-CAAGCCCUA-GAGCGU-GCC-----C----U---------AAUCUU----------UUGGGAUUUUC-GAAUGCUUG-GUUAGCUUUAAUCU-UGUA--UAAAUGGAGUUU
AACY020556599.1/3535-3641    ACUCAACGC-UA-AUCA-A-UUAAGAAGGGUGAGUUUAGAUUGUUA-AAUCGU-GCU-----G----A----------UUUAC-----------UCAGAUUUUU-GAUCAGUCUUGU-AGCCCUAAACC-UGUU--AAAAUGGAGUUU
AACY023212115.1/1316-1423    ACUCAACGC-UA-AUUUAA-UUCGAAGAGGUGAGUUUUGGGUG-CACAAGCAA-GCC-----G----U----------UUUAU-----------ACGGACCCUU-AAACACACA-GGUAGCCUCAAACA-UGUU--UAACUCGAGUUU
AACY023587494.1/499-603      ACUCAACGC-GA-AUUUUU-UUAUAAAGGGUGAGUCAUUUCUGCUA-AAGCAC-GCCUAAUU----------------------------------GGAUCCUU-GAUCAGUAU-GUUAGCUCUAAUCU-UGUU-UUAAUGAGAGUUU
AACY023598841.1/337-229      ACUCAACGA-GC-UUUAAU-UUAAGAGAGGUGAGUUAUGACUG-UAAAAGCAU-GCU-----G----C----------CUUGA-----------GCAGAUCCUU-GAUCAGUUGUGU-AGCCUCAUACC-UGUU-UAUUUAGGAGUUU
AACY024022377.1/517-409      ACUCAAC---GAGCUUUUAAUUCAGAGAGGUGAGUUUCCUUUG-UAAAAGCAU-GCU-----A----C----------CCUUG----------AGUAGACCCUU-GAGCAUUGGUGU-AGCCUCAAACU-UGAU--UUUUAGGAGUUU
AACY020332158.1/137-240      ACUCAACAC-UA-UUAAAU-UUAAAAAAGGUGAGUC-UGUGUGCUA-GAGCGC-GCC-----CUCAG----------------------------GGGAUUUUC-GAAUAUUCA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY023578674.1/733-835      ACUCAACAC-UA--UUUUU-UUAAAAAAGGUGAGUC-UGUAUGCUA-GAGCGC-GCC-----CUAAG----------------------------GGGAUUUUC-GAAUAUUCA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY023876911.1/708-600      ACUCAAC---GAGCUUUUAAUUAUGAGAGGUGAGUUUCAUUUG-UAAAAGCAA-GCU-----G----U----------CUUAG----------AACAGAUCCUU-GAUCAAUUGUGU-AGCCUCAAACU-UGAU--UUUUAGGAGUUU
AACY023283640.1/586-483      ACUCAACAC-GA-AUUU-U-UUAUAAUGGGUGAGUCAUUACUGCUA-AAGCGC-GCC-----A----U-------------------------UAUGGAUACUU-GAUCAGUAU-GUUAGCCUAAAUCU-UGUU-UUAAUAAGAGUUU
AACY020157838.1/468-571      ACUCAACAC-UA-UUUUUU-UUAAAAAAGGUGAGUC-UGUAUGCUA-GAGCGC-GCC-----CUAAG----------------------------GGGAUUUUC-GAAUAUAUA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY023277178.1/593-486      ACUCAAC---GAGCUUUUAAUUCAGAGAGGUGAGUUUCUUUUG-CAAAAGCAA-GCU-----G----C----------CUUGA-----------GCAGAUCCUU-GACCAUAGGUGU-AGCCUCAAACU-UGAU--UUUUAGGAGUUU
AACY020065208.1/172-280      ACUCAAC---GAGCUUUUAAUUCAGAGAGGUGAGUUUCAGUUG-UAAAAGCAA-GCU-----G----C----------CUUGU----------AGCAGAUCCUU-GACCAAUUGUGU-AGCCUCAAACU-UGAU--UUUUAGGAGUUU
AACY021863342.1/483-586      ACUCAACAC-UA-UUUUUU-UUAAAAAAGGUGAGUC-UGUAUGCUA-GAGCGC-GCC-----CUCAG----------------------------GGGAUUUUC-GAAUAUUCA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY020810601.1/9-112        ACUCAACAC-UA-UUUUUU-UUAAAAAAGGUGAGUC-UGUAUGCUA-GAGCGC-GCC-----CUAAG----------------------------GGGAUUUUC-GAAUAUUCA-GUUAGCCUUAAACU-UGUA--UAACAGGAGUUU
AACY023530069.1/157-263      ACUCAACGC-UA-AUCA-A-UUAAGAAGGGUGAGUUUAGAUUGUUA-AAUCGU-GCU-----G----A----------UUUAC-----------UCAGAUUUUU-GAUCAGUCUUGU-AGCCCUAAACC-UGUU--AAAAUGGAGUUU
AACY020241607.1/715-607      ACUCAACGA-GC-UUUAAU-UUAAGAGAGGUGAGUUAUGACUG-UAAAAGCAU-GCU-----G----C----------CUUGA-----------GCAGAUCCUU-GAUCAGUUGUGU-AGCCUCAUACC-UGUU-UAUUUAGGAGUUU
AACY023573129.1/494-389      ACUCAACGC-UA-AUAA-A-UUAAAAAGAGUGAGUC-UAGAUCCUA-GAGCGU-GCC-----U----U----------UUUUU-----------AAGGAUUAUC-GAAUAUUUA-GUUAGCUCUAAACU-UGUA--UAAAUGGAGUUU
AACY023611324.1/371-268      ACUCAACGC-GA-AUUUUU-UUAUAAAGGGUGAGUCUUUUCUGCUA-AAGCAU-GCC-----AG-UA----------------------------UGGAUCCUU-GAUCAGUUA-GUUAGCCUUAAUCU-UGUU--UUAUGAGAGUUU
CP002046.1/1491650-1491760   ACUUAACAA-UC-AAUUAU-UUGAAAAGGGUAAGUUUUAAUUGUAA-AAACAA-GCC-----G----U----------CUUAG----------AACGGAAGUUU-GAUCAGUUA-UGUAGCCCUAAACU-UUAUUAUUUAUGAAGUUU
FQ032835.1/12857-12735       ACUCAACAG-UU-AUUU-U-UUAUAAAGAGUGACUCUAAGUUGUAA-AAGCAC-GCC-----G----UUAC---UAGACUUGUUCUA--GGUAGACGGAACCUU-GAUCAGCUU-UAUAGCUCUAAUCC-UUAC--UAUUAGGAGUUU
CP002157.1/2325242-2325350   ACUCAACAU-UA-AUUUGU-UUAAAAAGGGUGAGUUUAGAUUGUAA-AAGCAG-GCC-----U----U----------CUCGAU---------AAAGGAUCCUU-GAUCAGUCU-GGUAACCCUAAACC-UGUU--UUC-UGGAGUUU
CP001712.1/1852705-1852812   ACUCAACAU-UA-CUUUAA-UUAGAAAGGGUGAGUUUAGGUUGUAA-AAGCAA-GCC-----U----U----------CUUUG----------AAAGGAUCCUU-GAGCAAUCU-GUUAGCCCUAAACC-UGUU--UAU-AGGAGUUU
#=GC SS_cons                 :::::::::.::.::::::.::::::<<<<<------<<<<<----.<<<---.-<<.....<....<.........._____.........._>>>>--->>>.---->>>>>.---->>>>>:::::.::::..::::::::::::
#=GC RF                      ACUCAACac.uA.aUUuuu.UUAaAAggGGuGAGUuucggcuGcUA.aAgCAa.GCc.....g....c..........cUUga..........agcgGAUccUu.GAuCagccg.GUUAgCCccAAaCu.UGuU..UuauaGGAGUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01686
#=GF ID   Acido-1
#=GF DE   Acido-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   59.40
#=GF NC   48.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Acido-1_RNA_motif
#=GF SQ   4


CP000473.1/3480719-3480784 AAUGGCCCCGAGC-UGGGUA---CUCGGGGCCUGCACUCAGAGGGU-GGCGGUGGGAGGGGACUCACCGCC
CP000473.1/3481695-3481760 AAUGGCCCCGAGC-UGGGUA---CUCGGGGCCUGCACUCAGAGGGU-GGCGGUGGGAGGGGACUCACCGCC
CP000360.1/235844-235785   GGAGCAGCGAA---GAA-------UUAGUUGCGAAACUGAUUGACU-GACGGCGGGAGAGAUCCCGCCGUU
CP000473.1/3413964-3414030 AAAGGGUCCG--CCUGGGUAGUA--CGGACCCUGCACUCAGAGGGUUGGCGGCGGGAGGGGUCUCGCCGCC
#=GC SS_cons               :::<<<<<<<<._.______....>>>>>>>>--------------.<<<<<<<<<______>>>>>>>>>
#=GC RF                    AAaGgccCcGA.C.uGGGUA....UCgGggcCuGcACUcAgaGGgU.GGCGGcGgGAGGGGuCcCgCCGCC
//
# STOCKHOLM 1.0

#=GF AC   RF01687
#=GF ID   Acido-Lenti-1
#=GF DE   Acido-Lenti-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   36.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Acido-Lenti-1_RNA_motif
#=GF SQ   87


ABEF01025289.1/1108-1063     CCCAGGGCUUACGCCCUAGGCUAUUUCACGUCGCCCCUCCGGGGCU
ABEF01020663.1/164-119       CCCAAGGCUCACGCCCUGGGCUAUUACACGUCGCUCCUUCAGAGCU
ABCK01000016.1/15957-15912   CCCAAGGCUCACGCCUUGGGCUUUAUUAUUUCAUGCCUUCAGCAUU
ABCK01000007.1/85099-85054   UCUAGUUCUCACGAACUAGGCUAAGUUAUGGCGUGCUUUCAGCACU
ABCK01000006.1/115823-115868 GCUAGUUCUCACGAACUAGGCUAAGUUAUGGCGUGCUUUCAGCACU
ABCK01000004.1/95064-95109   CCUAGUUCUCACGAACUAGGCUUAGUUAUGGCGUGCCUUCAGCACU
ABCK01000007.1/84866-84821   UCUAGCUCUCACGAGCUAGGCUAAAUCAUGGCGUGCUUUCAGCACU
CP000360.1/1267162-1267117   CCCAGCGCUCACGCGCUGGGCUACCAACUGGCGCCACUACGUGGCU
ABCK01000020.1/21790-21835   CCUAGCUCUCACGAGCUAGGCUAAUUUAUACCGUGCUUUCAGCACU
AACY023821681.1/1048-1003    CCUAGGGCUUACGCCCUAGGCUAAUAAAGUUCGCCCCUUCAGGGCU
CP000360.1/2657849-2657804   CCCACCACUCACGUGGUGGGCUAUCUCGUUCCGAGCCUGUGGCACU
ABCK01000012.1/104879-104834 CCUAGCACUUUCGUGCCAGGCUGUACUAUAUCGUCCCUUUGGGACU
ABCK01000007.1/4868-4823     CCUAGCUCUCACAAGCUAGGCUGUGUUAUGUCGUACCUUUGGUACU
ABCK01000002.1/237476-237521 CCUAGCUCUCACGAGCCAGGCUGAACUAUACCGUACUCUCGGUACU
ABCK01000006.1/85512-85557   CCUGGCACUUCCGUGCCAGGCUAAUGUAUGUCGUGCUUUCAGCACU
ABCK01000002.1/270461-270416 ACUAGCACUGACGUGCUAGGCUGAGUUAUGCCGUACCUUCGGUACU
AACY020305437.1/490-535      CCUAGGGCUUACGCCCUAGGCUAAUAAAGUUCGCCCCUUCAGGGCU
AACY023821681.1/559-514      CCUAGGGCUUACGCCCUAGGCUAAUAAAGUUCGCCCCUUCAGGGCU
AAFX01117144.1/99-54         CCCAGCGUUGAAACGCUGGGCUAUUCUCGGGUGUCCCUACGGGACG
ABCK01000001.1/416706-416661 CCUAGCACUUGCGUGCCAGGCUGAGUUAUGCCGUGCUUUCAGCACU
ABCK01000029.1/8929-8884     CGUGUGGCUAACGCCACACGCUAAUAUCUAUCGGUGCUCUGCACCU
CP000360.1/5623899-5623854   CCCUCCACUCACGUGGCGGGCUAUUUCAUUGCGUCGCUACGCGACU
ABCK01000001.1/225878-225923 CCUAGCUCUCACGAGCCAGGCUAUGUUAAGCCGUCCCUUCGGGACU
ABCK01000001.1/431760-431715 CCUAGCACUUUCGUGCCAGGCUGAGUUAUGCCGUGCUUUCAGCACU
ABCK01000012.1/53466-53511   CCUAGCACUUGCGUGCUAGGCUGAGUUAUGUCGUCCCCUUGGGACU
ABCK01000001.1/416558-416513 CCUAGCACUGCCGUGCCAGGCUGAGUUAUGCCGUGCUUUCAGCACU
AACY020309501.1/2525-2480    CCUAGGGCUUACGCCCUAGGCUAAUAAGGUACGGGCCUUCAGCCCU
CP000360.1/4339116-4339161   CCCACCGCUUACGCGGUGGGCCAUUGCAUGGCGUCGCUGCGCGACU
ABCK01000005.1/168430-168475 CCCAAGGCUCACGCCUUGGGCUUUAUUUUGUCAUGCCUUCAGCAUU
ABCK01000020.1/22700-22745   CCUAGCUCUCACGAGCUAGGCUAAUUUAUACCGUGCUUUCAGCACU
ABCK01000006.1/14425-14470   CCUAGCUCUGGCGAGCCAGGCUAAGUUAUGUCGUGCCUUCAGCACU
AACY020525177.1/1636-1681    CCUAGGGCUUACGCCCUAGGCUAAUAAGGUACGGGCCUUCAGCCCU
CP000360.1/5475883-5475928   CCCACCUCUUACGAGGUGGGCUAUUGCAUUUCGUCGCUUCGCGACU
ABCK01000006.1/107180-107225 CCUAGCACUCCCGUGCUAGGCUAAUGUAUGUCGUGCCUUCAGCACU
CP000360.1/2094937-2094982   CCCACCACUCUCGUGGUGGGCUUAUUUAUUGCGUCGCUGCGCGACU
AACY021466345.1/654-698      CCAGGGAUUUC-AUCCCUGGCUAAUAUAUUUCGUGCUUUCAGCACU
AAFX01127360.1/81-36         CCCAGCGAUGAAUCGCUGGGCUAUUUUCGAGCGUCCCGGCGGGACG
BX294154.1/174227-174182     CCUUGGGUUGAAACCCAAGGCUGCCAGAUUCCGUCGCUCCGCGACU
AAGA01022342.1/568-523       CCCAGCGAUGAAUCGCUGGGCUAUUGUCCAACGACCCGCCGGGUCG
AAFX01104218.1/182-227       CCCACGGCUGACGCUGUGGGCUACUCUGUGACGCCGCUACGCGGCU
ABCK01000002.1/270653-270608 ACUAGCACUGACGUGCUAGGCUGAGUUAUGCCGUACCUUCGGUACU
ABCK01000006.1/14204-14249   CCUAGCUCUGGCGAGCCAGGCUAAGUUAUGUCGUGCCUUCAGCACU
ABCK01000002.1/210449-210494 CCUAGCUCUCACGAGCCAGGCUGAACUAUACCGUACCUUCGGUACU
ABCK01000012.1/106309-106264 CCUAGCACUGUCGUGCCAGGCUGUACUAUACCGUCCCUUUGGGACU
ABCK01000029.1/14774-14819   CCUAGUUCUGACGAACUAGGCUGAUCUAUACCGUUCCUUCAGAACU
ABCK01000001.1/226073-226118 CCUAGCUCUCACGAGCCAGGCUAUGUUAAGCCGUCCCUUCGGGACU
ABCK01000002.1/212552-212597 CCUAGCUCUCACGAGCCAGGCUGAACUAUACCGUACCUUCGGUACU
AACY020311120.1/4637-4592    CCUAGGGCUUACGCCCUAGGCUAAUAAGUAGCGCGCCUACAGCGCU
ABCK01000020.1/22585-22630   CCUAGCUCUCACGAGCUAGGCUAAUUUAUACCGUGCUUUCAGCACU
ABCK01000006.1/85251-85296   CCUAGCACUUCCGUGCUAGGCUAAUGUAUGUCGUGCUUUCAGCACU
ABCK01000001.1/419681-419636 CCUAGCACUUCCGUGCCAGGCUGAGUUAUGCCGUCCCAUUGGGACU
ABCK01000001.1/246515-246470 CCUAGCUCUCACGAGCUAGGCUAAUUUAUACCGUGCUUUCAGAACU
CP000698.1/3835061-3835106   CCGUGGGAUGAAUCCCACGGCUAACAUCAAGCGCCCCGACGGGGCU
ABCK01000006.1/14314-14359   CCUAGCUCUGGCGAGCCAGGCUAAGUUAUGUCGUGCUUUCAGCACU
ABCK01000016.1/16196-16151   CCCAAGGCUCACGCCUUGGGCUUUAUUAUUUCAUGCCUUCAGCAUU
ABCK01000001.1/226211-226256 CCUAGCUCUGACGAGCUAGGCUAAGUUAAUACGUACUUACAGCACU
BX294154.1/187945-187900     CCUCGGGUUGAAACCCGAGGCUGACAAAUUUCACCGCUCCGCGGUU
ABCK01000026.1/37913-37958   CGUGUGGCUCACGCCACACGCUACAUUAUGUCGGGCUUCCAGCCCU
CP000360.1/5238069-5238024   CUCGCUUCGGAAGUGGUGGGCUAUUGCAUCGCGUGCCUUCGGCACU
ABCK01000005.1/275464-275419 CCUAGCUCUCACGAGCCAGGCUAGCGUAUGCCGUACCUUAGGUACU
CP000360.1/4968491-4968536   CCCACCGCUUACGCGGUGGGCUAUUACGUGGCGUCGCUUCGCGACU
AACY022263854.1/185-140      CCUAGGGCUUACGCCCUAGGCUAAUAAAGUACGGGCCUUCAGCCCU
ABCK01000020.1/22470-22515   CCUAGCUCUCACGAGCUAGGCUAAUUUAUACCGUGCUUUCAGCACU
CP000360.1/133300-133255     CCCACCACUCACGUGGUGGGCUAUUUCAUUCCGUCGCUGCGCAACU
ABCK01000001.1/416780-416735 CCUAGCACUUGCGUGCCAGGCUGAGUUAUGCCGUGCUUUCAGCACU
ABCK01000026.1/37713-37758   CGUGUGGCUCACGCCACACGCUACAUUAUGUCGGGCUUCUAGCCCU
ABCK01000002.1/270845-270800 ACUAGCACUGACGUGCUAGGCUGAGUUAUGCCGUACCUUCGGUACU
ABCK01000010.1/121151-121196 CCUAGCCCUUACGGGCCAGGCUAAAUUAUGCCGUGCUUUUAGCACU
CP000360.1/3571283-3571238   CCCACCUCUUACGAGGUGGGCUAUUUUCUUGCGUGCCUUCGGGACU
ABCK01000016.1/16051-16096   CCUAGUUCUGACGAACCAGGCUCAGUUAUGCCGUGCUUUCAGCACG
ABCK01000010.1/120473-120518 CCUAGCCCUUACGGGCCAGGCUAAAUUAUGCCGUGCUUUCAGCACU
AACY020300607.1/593-638      CCUAGGGCUUACGCCCUAGGCUAUUAAAGUACGCACCUACAGCGCU
ABCK01000001.1/417523-417478 CCUAGCACUGCCGUGCCAGGCUGAGUUAUGGCGUGCUUUCAGCACU
ABCK01000001.1/416632-416587 CCUGGCACUGCCGUGCCAGGCUGAGUUAUGCCGUGCUUUCAGCACU
ABCK01000016.1/16291-16336   CCUAGUUCUGACGAAUUAGGCUCAGCUAUGCCGUGCUUUCAGCACU
ABCK01000001.1/246374-246329 CCUAGCUCUCACGAGCUAGGCUAAUUUAUGCCGUUCCUUCAGAACU
ABCK01000006.1/103015-103060 CCUAGCACUUCCGUGCCAGGUUAAUGUAUGGCGUGCCUUCGGCACU
CP000360.1/3022749-3022704   CCCACCGCUUACGCGGUGGGCUAUUUCAUUCCGUCGCUGCGCGACU
ABCK01000002.1/237916-237961 CCUAGCUCUCACGAGCCAGGCUGAACUAUACCGUACUCUCGGUACU
AAGA01022342.1/675-720       CCCAGCAGUGAACUGCUGGGCUACUAUCAGAUGUCCCUUCGGGACA
ABCK01000080.1/409-454       CCUAGCACUUACGUGCCAGGCUGAGCUAUGCCGUGCUUUCAGCACU
ABCK01000002.1/217312-217357 CCUAGCUCUCACGAGCCAGGCUGAACUAUAACGUACCUUCGGUACU
ABCK01000006.1/178011-178056 CCUAGCUCUCACGAGCUCGGCUAAUUUAUACCGUGCUUUCAGCACU
AAFX01099936.1/271-316       CAGUGGGCUGAAGCCCACUGCUAUUAUAUUCCGCCGCUGCGCGGCU
ABCK01000010.1/120955-121000 CCUAGCCCUUACGGGCCAGGCUAAAUUAUGCCGUGCUUUCAGCACU
ABCK01000001.1/431565-431520 CCUAGCACUUUCGUGCCAGGCUGAGUUAUGCCGUGCUUUCAGCACU
ABCK01000001.1/226142-226187 CCUAGCUCUCACGAGCCAGGCUAUGUUAAGCCGUCCCUUCGGGACU
#=GC SS_cons                 <<<<<<<<____>>>>>>>>------------<<<<<___>>>>>:
#=GC RF                      CCUAGCgCUgACGcGCUAGGCUAauuUAUgcCGUgCCUUCGGcACU
//
# STOCKHOLM 1.0

#=GF AC   RF01688
#=GF ID   Actino-pnp
#=GF DE   Actino-pnp RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   43.00
#=GF TC   43.00
#=GF NC   42.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Actino-pnp_RNA_motif
#=GF SQ   77


AACY023426552.1/759-700    AUUGGUCCUCGGUAGUGGU-UUCCGG-G--------------------CAGUUAUA---------------------CCCGUGA-ACUUCGAUCGAAGAU-CC-AU
AACY020708686.1/419-480    CGUGGUCCUCGGUAGUGGUUCA-CAC-A----A-C-------------UUUUCU-----------------G---U-UGUG-UGUGCUUCGAUCGAUGAU-CA-UC
AACY023352938.1/798-727    GAUGGUCCUCGGUAGUGGU-UUCCGC-GAA--C-A-------------GAUAUAAGUAUUUG---------U---G-CGCGUGA-ACUUCGAUCGAAGAC-UC-UU
AACY020665672.1/306-242    AUUGGUCCUCGGUGGUGGC-UUACGG-A----U-U--U-U--------UACA-----------------AGA---ACGCCGUGG-GCUUCGAUCGAAGAU-CC-AU
CP000850.1/1544689-1544762 ACCGGUCUCCGGUAGUGGCCCC-CGG-G----CAU--CCGGC------AGCAC--------------GCCGACCCG-CCCG-GGCGCUUCGAUCGAAGAC-CG-GC
CP000667.1/1548720-1548793 ACCGGUCUCCGGUAGUGGCCUC-CGG-GCAUCC-G--GCAUC------UCGCC--------------GAUCC---G-CCCG-GGCGCUUCGAUCGAAGAC-CG-GC
CP000431.1/7150693-7150751 GUCGGUCUUCGGUAGUGGU-CUUCCG-G----A-C-------------ACG--------------------G---U-CCGGGGG-ACUUCGAUCGACGGC-CG-CC
AL583920.1/13687-13757     GGCGGUCUUCGGUAGUGGCUGU-CGG-G----C-U----CUCCG----GAUC-------------UGGAGCA---G-GUCG-GCCGCUUCGAUCGAUGGC-CG-UA
AACY020163669.1/593-531    AUUGGUCCUCGGUAGUGGU-UUCCGGGG----U-U--U----------UACA------------------AG---A-CCCGUGA-ACUUCGAUCGAAGAU-CC-AU
CP000384.1/2248687-2248748 GGCGGUCUUCGGUAGUGGCUGC-CGG-U----G-A--C----------GCGA------------------GU---C-CCCG-GCCGCUUCGAUCGACGGC-CG-UA
CP000656.1/4277016-4276958 CGCGGUCUUCGGUAGUGGC-UGCCGG-A----G---------------AGAGA----------------------C-UCCGACA-GCUUCGAUCGACGGC-CG-UC
AACY023292770.1/648-584    GAUGGUCCUCGGUAGUGGU-UUCCGC-G----C---------------UUGAAUACUU-----------------G-CGCGUGA-ACUUCGAUCGAAGAU-UCAUU
AACY020924984.1/409-479    UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A--G-UUUG-----UUAAU-------------UAAAUU---U-GCCGUGA-ACUUCGAUCGAUGAU-CC-AA
AACY020053120.1/1600-1521  AAUGGUCCUCGGUAGUGGU-UUCCGC-G----CACGACAUCCUU----ACU--------------AAGGAAACAAGUCGCGUGA-ACUUCGAUCGAAGAUUCA-UU
AACY020571544.1/471-413    UGGGGUCCUCGGUAGUGGC-UCUCGGAU----A---------------UUUA-----------------------U-GCCGACG-GCUUCGAUCGAUGAU-CU-CC
AACY021246509.1/305-247    AUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A-------------UGA--------------------U---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU
CP000820.1/1413476-1413546 GCCGGUCCUCGGUCGUGGC-CGCCGG-GA---C-G--A-GCGCC----GUC--------------GGUGC-C---G-CCCGGAG-ACUUCGACUGAGCAC-CG-GC
AACY021521465.1/225-297    AAUGGUCCUCGGUAGUGGC-UCACGA-A----A-UGCUGAUU------CAGAA--------------AAUAA---U-UUCGUGG-ACUUCGAUCGAAGAU-UCAUU
CP000481.1/1705830-1705770 GCCGGUCCUCGGUCGUGGU-CU-CCG-GG---A-G--C----------GCAA------------------GC---U-GCGG-AG-GCUUCCAUCGAAGAC-CG-GC
AE016822.1/918955-919031   GCUGGUCCUCGGUGGUGGU-AUCCGG-A----U-G----CG-UUCGCCGUCA---------GGC-AAUCGGC---A-GCCGUGU-AUUUCUACUGAUGGC-CA-GA
AL939124.1/278624-278683   GCCGGUCCUCGGUAGUGGCCCC-CGG-G----G-G-------------CAGA-------------------U---C-CCCG-GGUGCUUCGAUCGAAGAC-CG-GC
AACY023439687.1/1346-1402  ACUGGUCCUCGGUGGUGGC-UUACGG----------------------AUGAUUG-----------------------CCGUGG-GCUUCGAUCGAAGAU-CC-AU
AACY023300562.1/827-768    UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A-------------ACGU-------------------U---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU
AE017283.1/1592080-1592022 AUGGGUCCUCGGUAGUGGC-CACCGG-G----G---------------CGCGA----------------------U-CCCGGCG-GCUUCGAUCGAAGAC-CG-GU
AAGP01000012.1/38273-38199 UUCGGUCCUCGGUAGUGGC-UUCCGG-AAGA-G-C--ACGCAU-----GCGC--------------AUGCUGA--U-UCCGUGG-GCCCCGAUCGAUGAC-CG-GC
AACY023309503.1/1286-1224  AAUGGUCCUCGGUAGUGGU-UUCCGC-A----C-A-------------AAUUAA-----------------U---G-UGCGUGA-ACUUCGAUCGAAGAU-UCAUU
CP000511.1/2507941-2507999 CGCGGUCUUCGGUAGUGGC-UGCCGG-A----G---------------AGACA----------------------C-UCCGGCA-GCUUCGAUCGACGGC-CG-UC
BX248343.1/231827-231757   GGCGGUCCUCGGUAGUGGCUGC-CGG-G----C-U----CUCCG----GAUC-------------UGGGGCA---G-GUCG-GCCGCUUCGAUCGAUGGC-CG-UA
AACY023326738.1/962-904    GUCGGUCCUCGGUAGUGAA-GUUCGG-C----U-C-------------GAU--------------------G---A-GCCGCGC-UUCUCGAUCGAAGAU-CG-AC
AACY022754660.1/110-50     UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-U-------------CGGAU------------------A---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU
AACY024006489.1/767-823    AUUGGUCCUCGGUGGUGGC-UUCCGG-A--------------------AUAAA------------------------UCCGUGA-GCUUCGAUCGAAGAU-CC-AU
AE016958.1/3223271-3223201 GGCGGUCUUCGGUAGUGGCUGC-CGG-G----C-U----CUCCG----GAUC-------------UGGAGCA---G-GUCG-GCCGCUUCGAUCGAUGGC-CG-UA
AACY023441057.1/1068-995   CAUGGUCUCCGGUAGUGGU-UUUCAG-A----U-AAUUAGAUUU----AAU--------------AAAUC-U---A-UCUGAGA-ACUUCGAUCGUAGAUUCA-UU
AACY020790955.1/80-142     AUUGGUCCUCGGUAGUGGU-UUCCGGGG----U-U--U----------UACA------------------AG---A-CCCGUGA-ACUUCGAUCGAAGAU-CC-AU
CP000509.1/3377420-3377345 CUCGGUCCUCGGUAGUGGC-UCUCAGCA----U-C-----CGGCCGGCUCU----------GCCG--CGCAG---A-UCUGCGG-GCCUCGAUCGAAGAC-CG-GC
CP000854.1/2339435-2339506 GGCGGUCUUCGGUAGUGGCUGC-CGG-G----CAC--C-CCG------GAUC---------------UGGGGAAAG-UCCG-GCCGCUUCGAUCGACGGC-CG-UA
CP000249.1/4254111-4254042 GCCGGUCCUCGGUCGUGGU-CGCCGG-GA---U-G--G--GU------ACGG---------------GCACCGG-A-CCCGGGG-ACUUCGACUGAGCAC-CG-GC
AACY023436648.1/995-922    CAUGGUCUCCGGUAGUGGU-UUUCAG-A----U-AAUUAGAUCU----AAU--------------AAAUC-U---A-UCUGAGA-ACUUCGAUCGUAGAUUCA-UU
BX842580.1/319742-319672   GGCGGUCCUCGGUAGUGGCUGC-CGG-G----C-U----CUCCG----GAUC-------------UGGGGCA---G-GUCG-GCCGCUUCGAUCGAUGGC-CG-UA
AP006618.1/4102358-4102295 GUCGGUCUUCGGUAGUGGCCUCUCGA-G----U-G--G----------ACAU------------------CC---G-CCCGUCGGGCUUCGAUCGAUGAC-CG-CC
AACY023313868.1/759-819    UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A--A----------CGA-------------------UU---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU
AACY023437808.1/532-468    AUUGGUCCUCGGUGGUGGC-UUACGG-A----U-U--U-U--------UACA-----------------AGA---ACGCCGUGG-GCUUCGAUCGAAGAU-CC-AU
AACY023308296.1/1399-1470  AUCGGUCCUCGGUUGUGGC-UUCCGG-G----CCU--A-AAUU-----UUUU--------------AAUU-AAAU--CCCGUGG-GCUUCCAUCGAAGAU-CC-GU
AACY023341077.1/765-703    AAUGGUCCUCGGUAGUGGU-UUCCGC-A----C-A-------------AAUUAA-----------------U---G-UGCGUGA-ACUUCGAUCGAAGAU-UCAUU
AACY020051675.1/2004-2064  UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A--A----------CGA-------------------UU---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU
AACY020529213.1/353-293    GUCGGUCCUCGGUAGUGGC-UUCCGG-G----C-A-------------GAUGA------------------U---G-CCCGUGG-GCCUCGAUCGAAGAC-CG-GC
AACY023353825.1/1157-1215  GUCGGUCCUCGGUAGUGAA-GUUCGG-C----U-C-------------AAU--------------------G---A-GCCGCGC-UUCUCGAUCGAAGAU-CG-AC
AACY020470050.1/941-881    UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A--A----------CGA-------------------UU---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU
AACY020174452.1/327-265    AUUGGUCCUCGGUAGUGGU-UUCCGGGG----U-U--U----------UACA------------------AG---A-CCCGUGA-ACUUCGAUCGAAGAU-CC-AU
AACY020946272.1/515-457    ACUGGUCCUCGGUGGUGGC-UUACGG-A----G-A-------------UGA--------------------U---C-UCCGUGG-GCUUCGAUCGAAGAU-CC-AU
CP000454.1/1593772-1593848 CGCGGUCCUCGGUAGUGAU-UCCCGG-GAA--C-G----GCUUCG---AAGAA-----------UGAAGCCC---GGCCCGUGG-GUCUCGAUCGAUGAC-CG-GG
CP000474.1/1715342-1715414 CGCGGUCCUCGGUAGUGAU-UCCCGG-GAA--A-C--C-AUC------UGUGAC-------------GAUGA---UGCCCGUGG-AUCUCGAUCGAUGAC-CG-GG
CT573213.2/6238131-6238064 GCCGGUCCUCGGUCGUGGU-CGCCGG-G----A-GCGG-GC-------UUC-----------------GUCC---UCCCCGGGG-GCUUCGACUGAGCAC-CG-GC
AACY023331383.1/842-771    AUCGGUCCUCGGUUGUGGC-UCCCGG-GCCAAA-U--U-UA-------UUAAUU--------------UAAA---U-CCCGUGG-GCUUCCAUCGAAGAU-CC-GU
AM420293.1/6641639-6641570 GCCGGUCCUCGGUAGUGGC-UCCCGG-GCG--G-A--C-CUC------GCAG---------------GAGGU---U-CCCGAGG-GCUUCGAUCGAUGGC-CG-GC
AACY020057517.1/1019-1083  UUUGGUCCUCGGUGGUGGC-UUACGG------A-U--U-U--------AAACAA---------------GAA---U-GCCGUUG-GCUUCGAUCGAAGAU-CC-AU
AACY023344935.1/1046-983   UUCGGUCCUCGGUAGUGAU-GUCCGG-A----A-A--A----------AAGUUC----------------UU---U-UCCGUGC-GUCUCGAUCGAUGAC-CG-GG
AACY023336117.1/1190-1249  AAUGGUCCUCGGUAGUGGU-UUCCGG-A----U-G-------------AUU--------------------C---A-UCCGUGA-ACUUCGAUCGAAGAUACA-UU
CP000750.2/752310-752240   ACCGGUCCUCGGUAGUGGC-CUCCGG-A----A-G--C----------AGCACGACCACCA---------GC---U-UCCGUGG-GCCUCGAUCGAAGGC-CG-GG
CP000479.1/3804947-3804877 GGCGGUCUUCGGUAGUGGCUGC-CGG-G----C-U----CUCCG----GAUC-------------UGGAGCA---G-GUCG-GCCGCUUCGAUCGAUGGC-CG-UA
AACY023306957.1/1382-1311  AAUGGUCCUCGGUAGUGGU-UUCCGG-AG---A-U--U-U-CU-----UUCGU-------------AGAAAAG--U-UCCGUGA-ACUUCGAUCGAAGAU-UC-AU
BA000030.3/3089217-3089156 GCCGGUCCUCGGUAGUGGCCCC-CGG-G----G---------------GAAGUGAG-------------------C-CCCG-GGUGCUUCGAUCGAAGAC-CG-GC
AACY022757199.1/365-309    GCUGGUCCUCGGUGGUGGC-UUACGGAU--------------------GAUU-------------------------GCCGUGG-GCUUCGAUCGAAGAU-CC-AU
AACY023297464.1/53-112     UUUGGUCCUCGGUAGUGGU-UUCCGG-A----A-A-------------ACGU-------------------U---U-UCCGUGA-ACUUCGAUCGAAGAU-CC-AU
AACY023333656.1/840-769    AUCGGUCCUCGGUUGUGGC-UUCCGG-GCC--U-A--A-AUU------CUUU---------------AAUUUA--AUCCCGUGG-GCUUCCAUCGAAGAU-CC-GU
CP000088.1/925836-925906   GCCGGUCUUCGGUAGUGGU-UCUCCG-AC---A-CG-C-CC-------GCACCA--------------GGGG---UCUCGGGGA-ACUUCGAUCGAUGGC-CG-GC
AACY023311107.1/673-600    UAUGGUCCUCGGUAGUGGU-UUCCAG-A----U-G--U-AUGCA----CCAGA------------UGUAUAU---A-GCUGUGA-ACUUCGAUCGAAGAUUCA-UU
AACY023312886.1/602-542    AAUGGUCCUCGGUAGUGGU-UUCCAG-A----U-G-------------UUUG-------------------C---A-UCUGUGA-ACUUCGAUCGAAGAU-UCAUU
AACY023445683.1/836-893    AAUGGUCUCCGGUAGUGGU-UUACGA-A--------------------AUUGA------------------------UUCGUGA-ACUUCGAUCGUAGAUUCA-UU
AACY020469612.1/870-946    AAUGGUCCUCGGUAGUGGU-UUCCGC-AGA--G-C--G-CGA------UUAAAUUCGC---------UUGCG---U-UGCGUGA-ACUUCGAUCGAAGAUUCA-UU
AACY023308618.1/1250-1184  AAUGGUCCUCGGUAGUGGU-UUCCGC-A----A-G--G-C--------GCCAAA---------------GUU---U-UGCGUGA-ACUUCAAUCGACGAUUCA-UU
AACY020164649.1/1734-1676  ACUGGUCCUCGGUGGUGGC-UUACGG----------------------AUAACGAUG---------------------CCGUUG-GCUUCGAUCGAAGAU-CC-AU
CP000480.1/2735853-2735921 GGCGGUCUUCGGUAGUGGC-UGCCGG-GA---A-UCCA-AA-------CAGG----------------UUUA---U-CCCGACA-GCUUCGAUCGACGGC-CG-UA
AACY023314755.1/1127-1062  AAUGGUCCUCGGUAGUGGU-UUCCGCAA----G-AC-G-C--------UUUC-----------------GUU---C-UGCGUGA-ACUUCGAUCGACGAU-UC-AU
AACY023816550.1/761-687    GUCGGUCCUCGGUAGUGGC-CCUCGAAGGGAUU-C----GCGC-----CCA---------------GCGC-GAG-AACCCGGGG-GCCUCGAUCGAAGAC-CG-CC
AACY020554846.1/2493-2429  AUUGGUCCUCGGUGGUGGC-UUACGG-A----U-U--U-U--------UACA-----------------AGA---ACGCCGUGG-GCUUCGAUCGAAGAU-CC-AU
AACY023344307.1/624-697    AAUGGUCCUCGGUAGUGGU-UUCCAG-A----U-G----CAAGCA---CUAGA-----------UGUUUGGC---A-UCUGUGA-ACUUCGAUCGAAGAU-UC-AU
#=GC SS_cons               <<<<<<<--<<<<---<<<.<<-<<<.<....<.<.._.__.......____................___>...>.>>>>->>.>>>--->>>>-->>>.>>.>>
#=GC RF                    accGGUCCUCGGUAGUGGc.uccCGG.g....c.c..u.au.......aaua................auag...g.cCCGUga.gCUUCGAUCGAaGAC.Cg.gu
//
# STOCKHOLM 1.0

#=GF AC   RF01689
#=GF ID   AdoCbl-variant
#=GF DE   AdoCbl variant RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00101
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF RN   [2]
#=GF RM   28483920
#=GF RT   Cobalamin riboswitches exhibit a broad range of ability to discriminate
#=GF RT   between methylcobalamin and adenosylcobalamin.
#=GF RA   Polaski JT, Webster SM, Johnson JE Jr, Batey RT
#=GF RL   J Biol Chem. 2017;292:11650-11658.
#=GF WK   Cobalamin_riboswitch
#=GF SQ   144


ABEF01043191.1/931-798    CAUACUACAGGAGUAG-UGGGAAA-UAAUGUGUA-----AAUCAUUGGCUGUACUCGCAACGGU----------AAAAAAA----------------GCCCGGAAACCACAUAAAGU-AUACCACUGUUGGAUGAAGACCGAGAAAAGUC--A-C--G-UUCCAC-AAUUUUCAU
ABEF01008614.1/1-139      -UACUGAAA-GUAUUG-UGGGAAA-UAAUGUGUA-----AAUCAUUGACCGUUCCUGCGCUGGUA-AGAA----UAAAN-----------UUUUA--GUCCAGACACCAC-CAGUAU-AGCCCUCUGUCGAAUGACGACCAGGAAAAGUC--U-A--G-UUCUAC-AAUGAAAAA
ABEF01048062.1/1373-1515  AUACUGAAAUACAUGG-UGGGAAA-CAAUGUGGA-----AAUCAUUAACUGUUCCUGCAACGGUAAGAAC----AAGA------------GUUUAA-GUCCGGGCACCGCCUAGUAU-AGACCCCUGUUGAAUGAAGACCAGGAAAUGUC--U-A--G-UUCUAC-AAUGAAAAA
AACY021783667.1/387-517   UAGCUGAAAUGCAUGG-UGGGAAAUUCGUGUGAA-----AGUCAUGAGCUGUACCCGCAACCGU----------AUA--------------------GUCGGAGCGCCACCCAGUUA-AGUCCGCUGUUGAAUGAUGGCCGGGAACAGUC--U-A--G-UUCUAC-AAUGAAAAA
AACY024096041.1/425-555   UGACUGAAAUGCAUGG-UGGGAAAUCUGUGUGAA-----ACUCAUAGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUUA-AGUCCGCUGUUGAAUGAUGGCCAGGAAAAGUC--U-A--G-UUCUGC-AAUGAAAAA
AACY023165784.1/469-599   AAGCUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUUCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGCUA-AGUCCUCUGUUGAGCGAAGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUGAAAAA
AACY023870645.1/164-34    AUACUGAAAAGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUCCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGUCCGCUGUUGAAUGAUGGCCAGGAGGUGUC--U-A--A-UUCUAC-AAUUUAAAA
AACY021413889.1/650-519   GUAUCGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUUCCUGCAAAGGU----------UAAA-------------------GUCCUAGCGCCACCCGAUAU-AGUCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUGC-AAUUUAAAU
AACY023022368.1/358-488   AUACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAA-AGUCCGCUGUUGAAUGAGGGCCAGGGAGAGUC--U-A--G-UUCUACUAAUAUCUA-
AACY020138480.1/1015-884  AUACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUUCCUGCAACGGU----------UAUA-------------------GUCCGAGCGCCACCCAGUAU-AGUCCGCUGUUGAACAAUGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUUAAAUU
AACY023114032.1/602-472   UAACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUCUUCCUGGAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUUA-AGCCCUUUGCUGAACGAAGGCCAGGAAAAGUC--U-A--G-UUCUAU-AAUGAAAAA
AACY021858808.1/134-265   AUACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUUCCUGCAACGGU----------AAUA-------------------GUCCGAGCGCCACCCAGUAG-AGUCCGAUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--A-UUCUAC-AAUGAAUAA
AACY020496120.1/188-58    AUGUCGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCGAUGA-AGCCCUUUGUUGGAUGAAGGCCAGGGAAAGUC--U-A--G-UUCUAC-AAUGAAAAA
AACY020633803.1/429-559   GUGCUGAAAUGCAUGG-UGGGAAAUUAAUGUGAA-----AUUCAUUGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAA-AGUCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--A-UUCUUCUAAUUAUUA-
AACY021762656.1/83-213    GUACUGAAAUGCAUGG-UGGGAAAUCAGUGUGGA-----AUUCACUGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGUCCGCUGUUGAACGAGGGCCAGGAAUAGUC--U-A--G-UUCUGC-AAUAUUUAA
AACY023108236.1/475-603   GUACUGAAG--UUUGG-UGGGGAAUCAGUGUGAA-----AUUCAUUGGCUCUACCUGGAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGUCCGCUGUUGAAUGAUGGCCAGGGAAAGUC--U-A--A-UUCUAC-AAUUUUAAU
AACY023652229.1/711-851   AUACCGAAAU-UUAGG-UGGGGAA-CAAUGUGAA-----AUUCAUUGGCUGUUCCUGCAACGGUGUGAACG---AA-A------------GUUUAA-GUCCGAGCGCCACCCGGUAU-AGUCCGCUGUUGAACGAA-GCCAGGAAAAGUC--U-A--G-UUCUGC-AAUGCAAAA
AACY022516968.1/418-295   AUAUUG--------GUCUGGGAAAUAAGUGUGAA-----AUUCAUUUGCUGUUCCUGCAACGGU----------UAAA-------------------GUCCGAAUGCCAACCAAUAA-AGUCCGCUGU-GAAUGAUGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUGAAAAA
AACY021909721.1/309-440   UUGCCGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCACUGGCUGUUCCUGCAACGGU----------UAAA-------------------GUCCGAGCGCCACCCGGUAA-AGCCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--A-UUCUAC-AAUGUAAAA
AACY022630724.1/579-709   AUAUUGAAAUGCAUGG-UGGGAAAUCUAAGUGUA-----AUUCUUAGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGUCCGCUGUUGAACGAGGGCCAGGGAAAGUC--U-A--G-UUCUACUAAUAAUAA-
AACY023369206.1/771-916   AAGUUGAA-U-CUUGG-UGGGGAA-UAAUGUGAA-----AAUCAUUAACUGUUCCUGCAACGGUAAUAAC-UU-AAUA---------AAUGUUAAA-GUCCGAGUGCCGCCCAACUU-AGUCCUUUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUAC-GAUGAAAAA
AACY021644072.1/454-572   GUGCUAAAAG-CAUAG-UGGGAAAGUGACGUGAA-----AUUCGUCCACAUUACUUGAUAAGGU----------CAUA-------------------GUCCGAAUGCCACCUAGCAC-AGAA----------C--AGAGCAAGGAGACUC--GAAUGG----UAA-GAUUGAUUA
AACY023991155.1/473-604   GUGUUGAAAUGCAUGG-UGGGUAAUCAAUGUGAA-----AUUCGUUGGCUGUUCCUGCAACGGU----------UAUA-------------------GUCCGAGCGCCACCCAACAU-AGUCCGAC-UAGAAUGAAGGCCAGGAAAAGUC--U-A--A-UUCUGUUAACGGCAAA
AACY023374844.1/1359-1486 GUAUUGAAU--CUUGG-UGGGGAA-UAAUGUGAA-----AAUCAUUAGCUGUUCCUGCAACGGU----------AA-A-------------------GUCCGAGUGCCGCCCAAUAU-AGUCCGCUGUUGAAUGAUGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUUUUAAU
AACY021026116.1/737-595   GUACUGAAUAAGUGAG-UGGGGAA-UAAUGUGUG-----AAUCAUUAACUGUUCCUGCAACGGUAAAAC-----CUAAAA-----------GUUAA-GUCCGAGCGCCACCCAGUAU-AGCCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUGC-AAUUAAAAA
AACY020572665.1/147-19    GUACUGAAU--CUUGA-CGGGGAAUUAGUGCGAA-----AUUCACUUGCUGUUCCUGCAACCGU-----------AUA-------------------GUCGGAGUGCCGUCCAGUAU-AGUCCGCUGUUGAGCGAUGGCCAGGAAAAGCC--U-A--G-UUCUGC-AAUUUAAUU
AACY020700152.1/351-479   AUACUGAAU--CGUGU-UGGGGAAGCAAGGUGAA-----AUACCAUGGCUCUACCAGGAACCGU-----------AUA-------------------GUCGGAGUGCCAACCAGUAU-AGUCCGCUGUCGAAUGAAGGCCUGGGAAAGUC--U-A--A-UUCUAC-AAUGUAAAG
AACY021675760.1/326-183   AUGCUGCAAUGUAUGG-UGGGAAAUUAAUGUGUA-----AUUCAUUAGCUGUUCCUGCAACGGUAAUAAC----AU-UU-----------GUUUAA-GUCCGAGAGCCACCCAGCAU-AGACCCCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUGAAAAA
AACY023752846.1/868-993   UAAAUAAGUUUAUAUG-UGAUGAAGUAGAGUGAA-----AUUCUCUCACUGU-CGCGCAACGGU----------UAAA-------------------GUCCGAAC-UCACGUAUAAG-CUAAAGACGUAGCU--AGGCUCGCGGAA-AGC--U-A----AGCAGU-UACUCAAAA
AACY021350931.1/557-442   GGCCUAAAAG-CGUAG-UGGGAAAGUGACGUGAA-----AUUCGUCCAGAUUACUUGAUACGGU----------UAUA-------------------CUCCGAAUGCCACCUAGGCC------------AUACAACGAGCAAGGAGACUC--A-A--CAU------GAUAAGAUU
AACY020649872.1/608-492   UUCCUAAAAG-CAUAG-UGGGAAAGAGACGUGUA-----AUUCGUCCACAUUACUUGAUACGGU----------GAUA-------------------GUCCGAAUGCCACCUAGGAAUAGA-----------U--AGAGCAAGGAGACUCAAUGA--A----UAA-AGUAACU--
AACY023906339.1/379-251   GUGUUGAAA--CUUGG-UGGGGAAUCAGUGCGUA-----AUUCAUUGGCUCUACCUGGAACCGU----------AA-A-------------------GUCGGAGUACCACCCAACAU-AGCCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUAC-UAUUAAAAA
AACY023681118.1/924-793   CAACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUUCCUGCAACGGU----------AA-AA------------------GUCCGAGCGCCACCCAGUUA-AGUCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--A-UUCUAC-AAUGAAAAA
AACY023147184.1/534-406   AUACUGAAG--UUUGG-UGGGGAAUCAGUGUGAA-----AUUCAUUGGCUCUACCUGGAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGUCCGUUGUUGAAUGAAGGCCAGGGAAAGUC--U-A--G-UUCUACUAAUAAUAA-
AACY020983335.1/747-877   AUGUUGAAAUGUAUGG-UGGGAAAUCAAUGUGAA-----ACUCAUUGGCUGUUCCUGCAACGGU----------AA-AA------------------GUCCGAGCACCACCCAACAU-AGUCCGUUGUCGAAUGAA-GCCAGGAGAAGUC--U-A--A-UUCUGC-AAUGAAAAA
AACY024085015.1/673-814   AUACUGAAGU-UUAGG-UGGGGAA-CAAUGUGAG-----AUUCAUUGACUGUUCCUGCAACGGUGUGAAC----GAAA------------GUUUAA-GUCCGAGCGCCACCCAGUAU-AGCCCGCUGUUGAACGAAGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUGCAAAA
AACY022588215.1/51-179    CUGCUGAAU--CUUAG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGUGCCACUCAGUAA-AGUCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUUAAAAA
AACY022463201.1/577-448   GCAUUGAAU--CGUGA-UGGGAAAUUAAUGUGAA-----AAUCAUUAGCUGUGCCUGCAACGGU----------UAAA-------------------GUCCGAGUGCCAUCCAAUGU-AGUCCGCUGUUGAAUGAGGGCCAGGGAAAGUC--U-A--A-UUCUAC-AAUUUUAAU
AACY020423335.1/2472-2603 ACACUGAAAUGCUUGG-UGGGAAAUCAAAGUGAA-----AUUCUUUGGCUGUACCUGCAAUCGU----------GAAA-------------------GUCGGAGCGCCACCCAGUGC-AGUCCUUUGUCGAAUGAUGGCCAGGAAAAGUC--U-A--A-UUCUGC-AAUGAAAAA
AACY021169004.1/468-599   AUACUGAAA-GCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUUCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGUCCGCUGUCGAAUACGAGCCAGGAAGAGCU--U-AUUA-UUCUAC-AAUGAAAAA
AACY022398892.1/265-395   AUGUUGAAAUGCAUGG-UGGGAAAUCAGUGUGAG-----AUUCAUUGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCGCCCAACAU-AGUCCGCUGUUGAAUGAUGACCAGGGAAAGUC--U-A--A-UUCUAC-AAUGAAAAA
AACY021388442.1/364-226   AUACUGAAU--CAUGG-UGGGGAA-CAAUGUGAA-----AUUCAUUGACUGUUCCUGCAACGGUAAAAGU----AAA-------------AUUGA--GUCCGAGUGCCACCCAGUAA-AGUCCGCUGUCGAGUGAAGGCCAGGAAAAGUC--U-A--A-CUCUGC-AAUAUUAAA
AACY023548791.1/614-484   UCGUCGAAAUGCAUGG-UGGGGAAUCAGUGUGAA-----AUUCGCUGGCUGUUCCUGCAACCGU----------AU-A-------------------GUCGGAGCGCCACCCGAUAA-AGUCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUUUAAAA
AACY023126394.1/172-299   UAGCUGAAA--GUUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUGCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGCUA-AGUCCGCUGU-GAAUGAGGGCCAGGGAAAGUC--U-A--G-UUCUAC-AAUGAAAAA
AACY020285976.1/1664-1524 GUACUGAAGU-UUAGG-UGGGGAA-CAAUGUGCA-----AAUCAUUGACUAUCCCUGUAACGGUAAGAAU----UA-C------------AUUCAA-GUCCGAGCGCCACCCAGUAU-AGUCCGCUGUUGAAUGAUGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUUUUAAU
AACY020090121.1/1319-1189 AUACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUUCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCGGUAU-AGACCCCUGUCGAAUGAUGGCCAGGAAAAGCC--U-A--G-UUCUGC-AAAAUAGCA
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AACY021570976.1/760-634   AUAUUGAU----AUGG-UGGGGAAUCAGUGUGAA-----AUACAUUGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAAUAU-AGUCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUGC-AAUGAAAAA
AACY023326434.1/328-197   AUAGUAAAUAAUUUAG-UAGGAAAACAGCGCGAA-----AUUUGUUGGCUAUACCUGCAACCGU----------UAAA-------------------GUCGGAGAGCCACCCAGUAU-AGCCCAGUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-CUCUGC-AACUAAUUU
AACY020861911.1/106-235   GGACUGAAU--CAUGG-UGGGGAAUUAAUGUGAA-----AUUCAUUAGCUGUUCCUGCAACGGU----------UAAA-------------------GUCCGAGUGCCACCCAGUAA-AGUCCGGUGUUGAACGAAGGCCAGGAAAAGUC--U-A--G-UUCUGC-AAUUAAAGU
AACY022355432.1/165-24    GUGCUGAAAUGCAUGG-UGGGAAA-CAAUGUGUA-----AAUCAUUGACUGUUCCUGCAACGGUAAAAAC----GAAA------------GUUUA--GUCCGAGCGCCACCCAGCAU-AGCCCGCUGUUGAACGAUGAUCAGGAAAAAUC--U-A--G-UUCUAC-AAUGAAAAG
AACY020016467.1/57-194    UAACUCUCAC-GAGGU-UGGGAAA-GUCAGUGAAUACAUAAUCUGACACUGCCCCCGCAACGGUGA--------ACAACA-----------------GUCCGAAUGCCAACGAGGUG-AGACC--------AACAUUAGCGGUGGUGCUAUGAAAAUUAUCUUAAUCAUAUAAAA
AACY022416029.1/255-113   AUACUGAAAUGCAUGG-UGGGGAA-CAAUGUGAA-----AUUCAUUGACUGUUCCUGCAACGGUGUGAAC----AU-AA-----------GUUUGA-GUCCGAGCGCCACCCAGUAU-AGCCCGCUGUUGAACGAAGGCCAGGAAAAGUC--U-A--G-UUCUGC-AAUGUAAAA
AACY022113209.1/484-354   GUAUUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCGCUGGCUGUUCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGUCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUUAGAAA
AACY022575647.1/592-722   AUACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAA-AGUCCGCUGUUGAAUGAUGGCCAGGAAAAGUC--U-A--G-UUCUGC-GAUGAAAAA
AACY023664897.1/19-147    AUGCUGAAU--CUUGG-UGGGGAAUCAAUGUGUA-----AAUCGUUGACUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGUGCCACCCAGCA--AGUCCGUUGAUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUUCUAAUAUUUUA
AACY024040712.1/28-158    AUACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUCCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGCCCGCUGUUGAACGAAGGCCAGGAAAAGUC--U-A--G-UUCUGC-AAUGCAAAA
AACY023995715.1/131-1     AUACUGAAAAGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUUCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGACCCCUGUCGAAUGAUGGCCAGGAAAAGCC--U-A--A-UUCUAC-AAUACUUAA
AACY023625703.1/312-182   AUACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUUCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCGGUAU-AGUCCGCUGUUGAAUGAUGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUGAGAAA
AACY020440875.1/1972-1839 GUACUGAAU--CGUGA-UGGGGAA-UAAUGUGAA-----AUUCAUUAGCUGUACCUGCAACGGU----------GAAAAAAAA--------------GUCCGAGUGCCAUCCAGUAU-AGUCCGCUGUUGAGUGAAGGCCAGGAAAAGUC--U-A--G-CUCUACGAUUAUUAA-
AACY022354164.1/308-178   GUACUGAAACGCAUGG-UGGGGAAUAAAUGUGAA-----AUUCAUUUGCUGUUCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGUCCGCUGUUGAACGAAGGCCAGGAAAAGUC--U-A--G-UUCUGC-AAUUAAAUU
AACY020191282.1/590-462   GUAUUGAAU--CAUGG-UGGGGAAUUAAUGAGAA-----UUUCAUUUGCUGUUCCUGCAACCGU----------AA-A-------------------GUCGGAGUGCCACCCAAUAU-AGUCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUUUUUAA
AACY023664534.1/643-515   UUGCUGAAU--CAUGG-UGGGGAAUCAGUGUGAA-----AUUCAUUGGCUCUUCCUGGAACCGU----------AA-A-------------------GUCGGAGUACCACCCAGUAA-AGUCCGCUGUUGAAUGAUGGCCAGGAAAAGUC--U-A--G-UUCUAC-AAUUAAAAA
AACY021097151.1/299-429   GUGUUGAAUAAGUGAG-UGGGGAAUCAGUGUGAA-----AUUCAUUGGCUGUGCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAACAU-AGUCCGCUGUUGAAUGAUGGCCAGGAAAAGCC--U-A--G-UUCUGC-AAUUUUUAA
AACY022116441.1/1-131     AUACCGAAAUGCUUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCGGUAA-AGUCCGCUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--A-UUCUGC-AAUGAAAAA
AACY023884527.1/589-719   AUACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUACCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAA-AGACCGUUGUCGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUAC-UAUUUUAAA
AACY020928737.1/777-647   AUACUGAAAUGCAUGG-UGGGAAAUCAGUGUGAA-----AUUCAUUGGCUGUUCCUGCAACCGU----------AA-A-------------------GUCGGAGCGCCACCCAGUAU-AGCCCGUUGUUGAAUGAAGGCCAGGAAAAGUC--U-A--G-UUCUAU-AAUUUAAAA
#=GC SS_cons              ((((((----.---((.(((,,,,,<<<<<____.....___>>>>>AA<<<_BBB>>>,<<<_..........____...................aa>>>,,,,))))))))))).-----------<<<<--<<<<_bbb____>>>..>.-..>.>>>:::.:::::::::
#=GC RF                   auacugAAau.caugG.uGGGAAAucaguGUGAA.....AUUCacugaCuguaCcUgcaACgGU..........aAaA...................GUCcGAgcGCCaCccaguau.AGuCCgcUGUuGaacgAaGgcCAGGAAAAguC..u.A..g.uuCUAc.AAUuaaAAa
//
# STOCKHOLM 1.0

#=GF AC   RF01690
#=GF ID   Bacillaceae-1
#=GF DE   Bacillaceae-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   35.00
#=GF TC   35.30
#=GF NC   34.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Bacillaceae-1_RNA_motif
#=GF SQ   95


AL009126.3/3774322-3774256   AUAAAAGG-AACGGCG-GCUAA-AUGCUUAGGCGUCCUGCCUAA---ACACCGCCGUCA-UCACAUCCUGUAA-A
D88802.1/21456-21390         AUAAAUGG-AUCACAG-GUUAA-GUC-CACCGCAUCCCGCGGUG---ACACCUGUGUGACCUGCAUCGUGCAG-G
D26185.1/73415-73349         AUAAAUGG-AUCACAG-GUUAA-GUU-CACCGCAUCCUGCGGCG---ACACCUGUGUGACCUGCGUCGUGCAG-G
AB031215.1/4515-4578         GGAAAAGG-A-ACCAC-GCUAA-GGGC-GUGACAUCGUGUCAC---AACGCCUGGU--ACCUACAUCCUGUAG-G
AAOX01000020.1/14455-14389   CCUUAAGG-AACGCAG-ACUAA-AAAC-GCCACGUCCUGCUGC---AACGUCUGCAUGACCCCCAUCCUGGGG-G
CP000560.1/98703-98768       AACAUAGG-AACACCU-GCUAA-AUGC-GCCACUUCCUGUGGC---AACGCAUGUGU-UAGCAUGUCCUAUGC-G
CP000813.1/555169-555235     AGGAAAUG-AUCACAU-GCUAA-GUUC-GCUACAUCGUGUAGC---AACGCAUGUGUGAUAUGCAUCCUGCAUA-
AAOX01000032.1/33782-33716   CCUUAAGG-AACGCAG-ACUAA-GAAC-GCCACGUCCUGUGGC---AACGUCUGCAUAACCCCCAUCCUGGGG-G
ABFU01000134.1/1560-1495     CAAAAAUG-AACUUCU-ACUAA-GUUC-GCCACGUCCUGUGGU---AACGUAGAAGUCA-GCGCGUCGUGCGC-A
CP000002.3/925587-925653     AAUAAGUG-AACGCUG-GCUAA-AUAC-GCCACAUCGUGUGGC---AACGCCUGCAUGACCCACAUCCUGUGG-G
Z82044.1/10237-10171         AUAAAUGG-AUCACAG-GUUAA-GUU-CACCGCAUCCUGCGGCG---ACACCUGUGUGACCUGCGUCGUGCAG-G
ABFU01000135.1/2040-2106     GUAAAAUG-AACGUCG-AUUAA-GUUC-GCUACGUCCUGUAGC---AACAUCGACAUCAUGCACAUCAUGUGC-A
CP000002.3/920927-920861     AGUAAUGG-AGCGCAG-AUUAA-GUUC-GUCACAUCCUGUGAC---AACAUCUGCAUGACCUGCAUCGUGCAG-G
CP000813.1/2738313-2738247   AGGAGAUG-AUCACAU-GCUAA-GUUC-GCUACAUCGUGUAGC---AACGCAUGUGUGAUAUGCAUCCUGCAUA-
X55332.1/771-705             AUAAAUGG-AUCACAG-GUUAA-GUU-CACCGCAUCCUGCGGCG---ACACCUGUGUGACCUGCGUCGUGCAG-G
AAOX01000006.1/139439-139373 GAUUAAGG-AACGCAG-GCUAA-AGAC-GCCACGUCCUGUGGC---AACGCCUGCAUGACCCGCGUCCUGCGG-G
AAOX01000016.1/19511-19445   CCUUAAGG-AACGCAG-ACUAA-GAAC-GCCACGUCCUGUGGC---AACAUCUGCAUGACCAGCUUCCUGGGG-G
AAOX01000009.1/76759-76693   GAUAAAGG-AACGCGU-ACUAA-GAAC-GCCACGUCCUGUGGC---AACGUCCGCAUGACCCACAUCCUGUGG-G
AAOX01000011.1/44591-44525   AAUUAAGG-AACGCAG-GCUAA-AGGC-GCCACGUCCUGUGGC---AGCGCCUGCAUGACCCGCGUCCUGCGG-G
CP000813.1/9503-9569         AGGAAAUG-AUCACAU-GCUAA-GUUC-GCUACAUCGUGUAGC---AACGCAUGUGUGAUAUGCAUCCUGCAUA-
ABFU01000013.1/842-907       CAAAAAUG-AACUUCU-ACUAA-GUUC-GCCACGUCAUGUGGC---AACGUAGAAGUCA-GCGCGUCGUGCGC-A
AAOX01000014.1/110652-110586 AAUCAAGG-AACGCAG-GCUAA-AACC-GCCACGUCCUGUGGC---AACGCCUGCAUGACCCGCAUCCUGCGG-G
AAOX01000004.1/108233-108299 -GCCUUGGUCACGCAG-ACUAA-GAAC-GCCACGUCCUGUGGC---AACGUCUGCAUGACCCCCAUCCGGGGG-A
AAOX01000016.1/93298-93232   CAACGAGG-AACGCAG-GCUAA-GGGC-GCCACGUCCUGUGGC---AACGCCUGCAUGACCCGCAUACUGCGG-G
AE017333.1/711979-712045     GAGGAAGG-AUCGGCG-GCUAACCGCC-CAGGCGUCCUGCCUG---AACGCCGCCGU-CAUCACCUCCUGUGAA-
AAOX01000009.1/145067-145001 CAUUAAGG-AGCGCAG-ACUAA-GAAC-GCCACGUCCUGUGGC---AACGUCUGCAUGACCCACAUCCUGUGG-G
CP000002.3/2767401-2767337   --GAAAGG-AGACUCG-GCUAA-GGUCUUUCGCGUCCUGCGAAA--AACGCCG-GUC-ACCUUCGUCCUGGUGU-
AAOX01000020.1/52596-52530   ACUUAAGG-AACGCAG-ACUAA-GAAC-GGCACGUCCUGUGGC---AACGUCUGCAUGACCCCCAUCCUGGGG-G
AE017333.1/920778-920712     AGUAAUGG-AGCGCAG-AUUAA-GUUC-GUCACAUCCUGUGAC---AACAUCUGCAUGACCUGCAUCGUGCAG-G
AL009126.3/319012-319078     CGAAGUGG-AUCAACG-GCUAA-AUUCUCAGGCGUCCUGCCUAA---ACGCCGUCGU-CAUCACAUCCUGUGAA-
AE017333.1/39281-39347       AGGCAAGG-AAACUCG-GCUAA-AGGCCCUCACAUCCUGUGAGG--AACGCCCAGU--ACCUUCGUCCUGAAG-G
AAOX01000014.1/92801-92867   ACUAAAGG-AACGCAG-ACUAA-GAAC-GCCACGUCCUGUGGC---AACGUCUGCAUGACCCCCAUCUUGGGG-G
AAOX01000033.1/19237-19171   UGUCAAGG-AACGCAG-ACUAA-AAAC-GCCACGUCCUGUGGC---AACGUCUGCAUGACCCGCGUCCUGCGG-G
X00007.1/494-428             AUAAAUGG-AUCACAG-GUUAA-GUU-CACCGCAUCCUGCGGCG---ACACCUGUGUGACCUGCGUCGUGCAG-G
CP000002.3/3080604-3080669   CUGACUGG-UUGCCCG-GCUA--GACCUUUCACGUCCUGUGAAA--AACGCCCAGU--ACCUUCCUCCUGAAG-G
AAOX01000004.1/234474-234540 CCCUAAGG-AACGCAG-ACUAA-GAAC-GCCACGUCCUGUUGC---AACGUCUGCAUGACCCGCAUCCUGGGG-C
AAOX01000004.1/227007-227073 CCUUAAGG-AACGCAG-ACUAG-GAAU-GCCGCAUCCUGUGGC---AACGUCUGCAUGGCCAGCUUCCUGGGG-G
AAOX01000015.1/33444-33377   AUUAGAGG-AACGCAGGGCUAA-AACC-GCCACGUCCUGUGGC---AACGCCUGCAUGAACCGCGUCCUGCGG-G
CP000002.3/616707-616773     AGGCAAGG-AAACUCG-GCUAA-AGGCCCUCACAUCCUGUGAGG--AACGCCCAGU--ACCUUCGUCCUGAAG-G
AAOX01000004.1/240854-240920 CCUAAAGG-AACGCAG-ACUAA-GAAC-GCCACGUCCUGUGGC---AACGUCUGCAUGACCCCCAUCCUGGGG-G
AAOX01000014.1/110839-110773 AAUCAAGG-AACGCAG-GCUAA-AACC-GCCACGUCCUGUGGC---AACGCCUGCAUGACCCGCAUCCUGCGG-G
CP000813.1/531946-532012     AGGAAAUG-AUCACAU-GCUAA-GUUC-GCUACAUCGUGUAGC---AACGCAUGUGUGAUAUGCAUCCUGCAUA-
ABFU01000131.1/643-708       CAAAAAUG-AACUUCU-ACUAA-GUUC-GCCACGUCCUGUGGU---AACGUAGAAGUCA-GCGCGUCGUGCGC-A
AAOX01000001.1/33520-33454   GAUUAAGG-AUCGCGG-ACUAA-AAAC-GCCACGUCCUGUGGC---AACGUCCGCAUGACCCGCAUCCUGCGG-G
BA000028.3/3404930-3404863   CAGGGGGG-ACCUUCU-GCUAA-AAUCGCCCACGUCCUGUGGGC--AACGCAGAAAU-CACCACAUCCUGUGG-A
AAOX01000001.1/32371-32305   UAUCGAGG-AACGCGG-ACUAA-GUAC-GCCACGUCGUAUGGC---AACGUCCUCAUGACCCGCUUCCUGCGG-G
AAOX01000026.1/47929-47995   CCUUAAGA-AACGCAG-ACUAA-GAAC-GCCACGUCCUGUGGC---AACGUCUGCAUGGCUCCCAUGCUGGAG-C
CP000813.1/138237-138303     AGGAUGUG-AUCACAU-GCUAA-GUUC-GCUACAUCGUGUAGC---AACGCAUGUGUGAUAUGCAUCCUGCAUA-
BA000028.3/423489-423422     ACAGAAGG-ACCUUCU-GCUAA-AAUCGCCCACGUCCUGUGGGC--AACGCAGAAAU-CACCACAUCCUGUGG-G
AAOX01000016.1/10629-10563   AACUAAGG-AACGCAG-ACUAA-AAAC-GCCACGUCCUGUGGC---AACGUCUGCAUGACCCACAUCCUGUGG-G
ABRX01000010.1/918-852       AGGAAAUG-AUCACAU-GCUAA-GUUC-GCUACAUCGUGUAGC---AACGCAUGUGUGAUAUGCAUCCUGCAUA-
AAOX01000027.1/25525-25460   AAUAGAGG-AACGCGG-ACUAA-GAGC-GCCACGUCCUGUGGC---AACGUCCGCAUGACCCGCAU-CUGUGG-G
AB000617.1/32101-32167       CGAAGUGG-AUCAACG-GCUAA-AUUCUCAGGCGUCCUGCCUAA---ACGCCGUCGU-CAUCACAUCCUGUGAA-
AAOX01000016.1/93112-93046   UAUCGCCG-AGCGCAG-GCUAA-GGGC-GCCAAGUCCUGUGGC---AACGCCUGCAUGACCUGCAUCCUGUGG-G
AAOX01000017.1/72416-72482   AAUAAAGG-AACGCGG-ACUAA-GAAC-GCCACGUCCUGUGGC---AACGUCCGCAUGACCCGCAUCCUGCGG-G
AE017333.1/34404-34338       AAUAAUGG-AGCGCAG-AUUAA-GUUC-GUCACAUCCUGUGAC---AACAUCUGCAUGACCUGCAUCGUGCAG-G
AF478063.1/204-272           AGCGCCGU-AAUUUCG-CCUAAAGGCAGCCCGCGUCCUGCGGGC--AACGGCGAAAU-AUCGCCAUCCUGGCG-A
AAOX01000018.1/15801-15737   CACUAAGG-AACGCAG-ACUAA---AA-ACCACGUACUGCGGC---AACGUCUGCAUAACCCACAUCCCGUGG-C
AAOX01000022.1/85956-85890   CUUUAAGG-AACGAAG-ACUAA-GAAC-GCCGCGUCCUGUGGC---AACAUCUGCAUGACCAGCUUCCUGGGG-G
AB001488.1/47895-47961       CGAAGUGG-AUCAACG-GCUAA-AUUCUCAGGCGUCCUGCCUAA---ACGCCGUCGU-CAUCACAUCCUGUGAA-
CP000002.3/611992-611926     AAUAAUGG-AGCGCAG-AUUAA-GUUC-GUCACAUCCUGUGAC---AACAUCUGCAUGACCUGCAUCGUGCAG-G
AE017333.1/176409-176472     AUGCAAGG-AAGGCAU-GCUAA-AAGC-GCAACGUCCUGUUGC---AACGCAUGCAC-UUGUACGUCCUGUA---
K00637.1/489-423             AUAAAUGG-AUCACAG-GUUAA-GUU-CACCGCAUCCUGCGGCG---ACACCUGUGUGACCUGCGUCGUGCAG-G
X04167.1/78-144              AGGUAAGG-AAACUCC-GCUAA-GGGCUCUCACAUCCUGUGAGA--AACGCCCAGU--ACCUUCAUCCUGAAG-G
CP000002.3/163014-163080     AGGCAAGG-AAACUCG-GCUAA-AGGCCCUCACAUCCUGUGAGG--AACGCCCAGU--ACCUUCGUCCUGAAG-G
AP006627.1/1440503-1440567   AGCUAAGG-AUCUUCG-GUUAA-GGUC-GCGACGUCCUGUCGC---AACACCGAAGC-CAACACAUCC-GUGUG-
AAOX01000070.1/3409-3475     CACUAAGG-AACGCAG-GCUAA-GUAC-GCCACGUCCUGUGGC---AGCGCCUGCAUGGCCCACUUCCUGUGG-G
AAOX01000019.1/82190-82124   AAUCAAGG-AACACAG-GCUAA-GAGC-GCCACGUCCUGUGGC---AACGCCUGCAUGACCCGCGUCCUGCGG-G
ABFU01000002.1/740-674       UAAAAAUG-AACGUCG-AUUAA-GUUC-GCUACGUCCUGUAGU---AACAUCGACAUCAUGCACAUCAUGUGC-A
AAOX01000050.1/9503-9437     CCUUAAGG-AACGCAG-ACUAA-GAAC-GCCACGUCCUGUGGC---AACGUCUGCAUGACCAGCUUCCUGGGG-G
BA000004.3/561399-561462     GGAAAAGG-A-ACCAC-GCUAA-GGGC-GUGACAUCGUGUCAC---AACGCCUGGU--ACCUACAUCUUGUAG-G
CP000002.3/926189-926254     UUUAAAGG-AAGGCAU-GCUAA-GAUC-GCAACGUCCUGCUGC---AACGCAUGCAC-UUGUAGGUCCUGUAC-U
BA000028.3/675233-675300     AAAUAAGG-AAGUUCG-UUUAA-AACCGUUCACGUCCUGUGAAC--AACACCGAACG-ACCUACAUCCUGUAG-G
AE017333.1/800647-800712     GAGGAAGG-AUCGGCG-GCUAA-CCGC-CAGGCGUCCUGCCUG---AACGCCGCCGU-AAUCACCUCCUGUGAA-
AE017333.1/611798-611732     AAUAAUGG-AGCGCAG-AUUAA-GUUC-GUCACAUCCUGUGAC---AACAUCUGCAUGACCUGCAUCGUGCAG-G
AE017333.1/99862-99928       AGGCAAGG-AAACUCG-GCUAA-AGGCCCUCACAUCCUGUGAGG--AACGCCCAGU--ACCUUCGUCCUGAAG-G
ABRX01000002.1/133-67        AGGAAAUG-AUCACAU-GCUAA-GUUC-GCUACAUCGUGUAGC---AACGCAUGUGUGAUAUGCAUCCUGCAUA-
EU157946.1/358-425           AGGCUCGU-AAUUUCG-CCUAAAGGCAGCCCGCGUCCUGCGGGC--AACGGCGAAAU-AUCGCCAUCGUGGCG--
AAOX01000009.1/75104-75038   CACUAAGG-AACGCAG-ACUAA-GAAC-GCCACGUCCUGUGGC---AACGUCUGCAUGACCCACAUCCUGUGG-G
CP000002.3/1210076-1210142   GGAGAAGG-AUCGGCG-GCUAAUCGCC-CAGGCGUCCUGCCUG---AACGCCGCCGU-CGUCACUUCCUGUGAA-
AAOX01000017.1/99694-99760   AAUUAAGG-AACGCAG-GCUAA-AAAC-GCCACGUCCUGUGGC---AACGCCUGCAUGACCCGCGUCCUGCGG-G
BA000028.3/2452262-2452329   AAAAGGAG-ACUUUCU-GCUAA-AAUCGCCCAUGUCCUGUGGCU--AAAGCAAAAAUCA-CCACAUCCUGUGG-A
CP000002.3/3118594-3118528   AGGCAAGG-AAACUCG-GCUAA-AGGCCCUCACAUCCUGUGAGG--AACGCCCAGU--ACCUUCGUCCUGAAG-G
AAOX01000041.1/673-607       AAUAAAGG-AACGCAG-GCUAA-AGAC-GCCACGUCCUGUGGC---AACGCCUGCAUGACCCGCAUCCUGCGG-G
CP000002.3/2767466-2767402   --UGAAAA-GGACUCG-GCUAA-GGGCUUUCACAUCCUGUGAAA--AAAGCCGAGU--ACCUUCGUCCUGGUGU-
AE017333.1/57839-57905       GAGGAAUG-ACCGCAU-GCUAA-GAGC-GAGGCGUCCUGCCUC--AGGCGCAUGCAU-UUGUACGUCCUGUAC-U
CP000002.3/3243766-3243832   GAGGAAGG-AUCGGCG-GCUAACCGCC-CAGGCAUCCUGCCUG---AACGCCGCCGUCA-UCACCUUCUGUGA-A
AAOX01000026.1/29664-29729   AAUUAAGG-AACGCAG-GCUAAAAACG--CCACGUCCUGUGG----AACGCCUGCAUGACCCGCGUCCUGCGG-G
AL009126.3/9815-9749         AUAAAUGG-AUCACAG-GUUAA-GUU-CACCGCAUCCUGCGGCG---ACACCUGUGUGACCUGCGUCGUGCAG-G
BA000028.3/2350186-2350119   AAAUAAGG-AAGUUCG-UUUAA-AACCGUUCACGUCCUGUGAAC--AACACCGAACG-ACCUACAUCCUGUAG-G
AAOX01000048.1/12-78         UAUAAAGG-AACGCAG-ACUAA-AAAC-GCCACAUCCUGCGGC---AGCGUCUGCAUGACCCGAAUCCUGUGG-G
ABFU01000133.1/2038-2104     UAAAAAUG-AACGUCG-AUUAA-GUUU-GCUACGUCCUGUAGC---AACAUCGACAUCAUGUGCAAAGUGAGC-U
AE017333.1/14582-14648       AGGCAAGG-AAACUCG-GCUAA-AGGCCCUCACAUCCUGUGAGG--AACGCCCAGU--ACCUUCGUCCUGAAG-G
CP000813.1/905312-905381     AGGAAAUG-AUCACAU-GCUAA-GU-UCGCUACAUCGUGUAGCGACAACGCAUGUGUGAUAUGCAUCCUGCAUA-
X04164.1/339-273             AUAAAUGG-AUCACAG-GUUAA-GUU-CACCGCAUCCUGCGGCG---ACACCUGUGUGACCUGCGUCGUGCAG-G
#=GC SS_cons                 ::::::::.::<<<<<.<<---.----.<<<<<_____>>>>>...--->>>>>>>---<<<<<_____>>>>.>
#=GC RF                      aauaAAGG.AacgcaG.GCUAA.GauC.gccaCGUCCUGuggc...AACGCCugcgUGAcccgCaUCCUGcgg.g
//
# STOCKHOLM 1.0

#=GF AC   RF01691
#=GF ID   Bacillus-plasmid
#=GF DE   Bacillus-plasmid RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   31.00
#=GF TC   31.30
#=GF NC   30.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Bacillus-plasmid_RNA_motif
#=GF SQ   31


BABE01000260.1/3320-3379     GCAGUCAACGG-UACCGG----------A--GGCG-----GUCUGUGCCGAGGAU-AAGGAGUUGACGG-CUAAACCACU
BABE01002635.1/459-518       GCAGUCAACGG-UACCGG----------AG-GCGG-----UUUGUGC-CGAGGAU-AAGGAGUUGACGG-CUAAACCACU
ABDM02000063.1/126031-126093 UUAGUCAACGGCUAGCGG----------ACAACCG-----UAAGGGAGGGGCAUU-AAGGAGUUGACUA-AAUAACACCU
AF200347.3/3074-3134         GCUGUCAAUGG-UAGCGG----------AC-GAGC-----GUAGCGUGGGAGCAU-AAGGAAUUGACAG-CUCUAAACCA
AF440277.1/2644-2584         GCUGUCAAUGG-UAGCGG----------AC-GAGC-----AAAGCGUGGGAGCAU-AAGGAAUUGACAG-CUCUAAACCA
AF438419.1/149-209           GCUGUCAAUGG-UAGCGG----------AC-GAGC-----GUAGCGUGGGAGCAU-AAGGAAUUGACAG-CUCUAAACCA
AB024514.1/1928-1989         GUAGUCAACGG-UACCGG----------AACGACC-----AACGGGAGCGAGGAU-AAGGAGUUGACUAGCUA-ACUAAA
AB243053.1/5968-6023         UGAGUCAACGG-UAACCG-------------GACC-----GUAGGGAGG---AUU-AAGGAGUUGACUC-GCUCAGCGCC
ABDM02000052.1/278-352       UGUGUCAACGG-UAAGCGGACAGAUCGAAGCGAUAGC---GAAGAGAAGGAGCAUUAAGGAGUUGAUAC-ACUCACAAUG
X56204.1/6441-6496           UUUGUCAACGG-UAAGCG-------------GACC-----GAAGGGAGC---AUU-AAGGAGUUGACAA-ACUCAUGACA
AY230134.1/376-432           UGAGUCAACGG-UAAGCG-------------GAACG----AAAGUGAGC---AUU-AAGGAGUUGACUC-AUUCACUACA
AJ871638.1/3291-3366         UCUGUCAACGG-UAAGCGGACAGAAUGAA--GCUGUAAGCGAAAUGAAGGAGCAUUAAGGAGUUGACAG-ACUUACUAUG
CP000764.1/2388712-2388646   UGUGUCAACGG-UACCGG----------ACUGAACCCGUAAGGGUGAGGGAGGAU-AAGGAGUUGACAC-ACUCACUAUG
U32379.1/5173-5228           UGAGUCAACGG-UAACCG-------------GACC-----GUAGGGAGG---AUU-AAGGAGUUGACUC-GCUCAGCGCC
CP000418.1/332-272           GCUGUCAAUGG-UAGCGG----------AC-GAGC-----AAAGCGUGGGAGCAU-AAGGAAUUGACAG-CUCUAAACCA
U67921.1/5075-5141           AGUGUCAACGG-UACCGG----------ACCGAAC-CCGAAAGGGGCGGGAGGAU-AAGGAGUGGACACGUGCAUCGGAU
AJ243967.1/594-660           UGUGUCAACGG-UACCGG----------ACCGAACCCGUAAGGGGGUGGGAGGAU-AAGGAGUUGACAC-ACUCACUAUG
AF036712.1/104-159           UGAGUCAACGG-UAAGCG-------------GAAC-----GAAGUGAGC---AUU-AAGGAGUUGACUC-AUUCACUACA
AF091592.1/6989-7044         UGAGUCAACGG-UAACCG-------------GACC-----GUAGGGAGG---AUU-AAGGAGUUGACUC-GCUCAGCGCC
CP000423.1/360213-360153     GCUGUCAAUGG-UAGCGG----------AC-GAGC-----GUAGCGUGGGAGCAU-AAGGAAUUGACAG-CUCUAAACCA
AAJM01000209.1/3338-3283     UUUGUCAACGG-UAAGCG-------------GACC-----GAAGGGAGC---AUU-AAGGAGUUGACAA-ACUCAUGACA
U32380.1/6354-6409           UGAGUCAACGG-UAACCG-------------GACC-----GUAGGGAGG---AUU-AAGGAGUUGACUC-GCUCAGUGCU
AB167898.1/7457-7397         GCUGUCAAUGG-UAGCGG----------AC-GAGC-----AAAGCGUGGGAGCAU-AAGGAAUUGACAG-CUCUAAACCA
AJ871637.1/120-192           UAUGUCAACGG-UAAGCGGACGAACGAAGCAAAGC-----GAAGUGAAGGAGCAUUAAGGAGUUGACAU-AUUUACCACA
J04240.1/65-124              AAUGUCAACGG-UACCGG----------ACUGAGC-----UU-GCGAGGGAGGAU-AAGGAGUUGACAU-UUU-GCUGUC
AJ272266.1/3044-3110         UGUGUCAACGG-UACCGG----------ACCGAACCCGUAAGGGGGCGGGAGGAU-AAGGAGUUGACAC-ACUCACUAUG
CP000041.1/1986-2052         UGUGUCAACGG-UACCGG----------ACCGAACCCGAAAGGGUGCGGGAGGAU-AAGGAGUUGACAC-ACUUACUAUG
AB001488.1/69116-69169       UGUGUCAACGG-UACCGG----------AA-------------CGAAGUGAGGAU-AAGGAGUUGACAU-AUUCAGCGCU
AY096005.1/3083-3036         GCUGUCAAUGG-UAGCGU-----------------------------GAGAGCAU-AAGGAAUUAACAG-CUUUUAACUA
ABCZ02000102.1/1783-1717     CGUGUCAACGA-UACCGG----------ACCGAGCCCGAAAGGGAUAGGGAGGAU-AAGGAGUUGAUAC-GUCCACUACA
U32378.1/5114-5169           UGAGUCAACGG-UAAGCG-------------GAAC-----GAAGUGAGC---AUU-AAGGAGUUGACUC-AUUCACGACA
#=GC SS_cons                 <<<<<<<<<__.______..........__.____....._______________._____>>>>>>>>.>:::::::::
#=GC RF                      uguGUCAACGG.UAaCGG..........AC.GAaC.....gaAGgGAGGGAGgAU.AAGGAGUUGACac.auUcAcuaca
//
# STOCKHOLM 1.0

#=GF AC   RF01692
#=GF ID   Bacteroid-trp
#=GF DE   Bacteroidete tryptophan peptide leader RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   49.00
#=GF TC   49.10
#=GF NC   48.70
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 37.90 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0046500; S-adenosylmethionine metabolic process;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Bacteroid-trp_RNA_motif
#=GF SQ   35


BABB01000545.1/1746-1604     CCAAAAUAAAAACAGAUUUUAUGAAUAGAAUCA-UGGUA-A---AUACAUAUUGGUGGC--GU-UUC-UUACAACUAAACAAGUCGUAAGGGAACCA-GACC---AU-GUA----UAU-AUACCUG-ACAUUCUAAUAAGGAUAUUC----AAACU-GAAGGCCUGUC
BAAU01000768.1/936-1077      CCAAAAUAAAAACAGAUUUUAUGAAUAGAAUCA-UGGUA-A---AUACAUAUUGGUGGC--GU-UUC-UUACAACUAAACAAGUCGUAAGGGAA-CCAGACC---AU-GUA----UAU-AUACCUG-ACAUUCU-AAAAGGAUAUUC----AAACU-GAAGGCCUGUC
BABB01001584.1/2460-2322     GGUCAAAAAUAAAAAAGAUAAUGAAAACAAUGU-UCGUA-A---AUACAUAUUGGUGGUG-GCAUCCGUUACAACUCCGGCAGUCGUAAGGGAG-CAGUGCUC--GU-AUGUAUAUAU-GUACA------AUAU-AGAUAUAUA-----------AAAGAGCCCUGUC
BABA01003390.1/487-628       CGAUAAAACAAAAAAAGUCAAUGAAAACAAUGU-UAGUA-A---AUACAUAUUGGUGGUG-GCACCCGUUACAACUCCGACAGUCGUAAGGGAG-CAGCGCUC--GU-AUG----UAU-AUAUG-----------UAAUAUAUAGUAAAAAACAAAAAGAGCCCUGUC
AP006841.1/3050356-3050502   CCGUUAAAUAACAAUUAGCAAUGAUGACAAUGC-AAGUA-A---AUACAUAUUGGUGGUG-GCGCCCGUUACAACUCCGACAGUCGUAAGGGAG-CAGCGCUC--GU-AUG----UAU-AUACC------UCAUUAAAGAUAUAACAGAAUUUAGAAAGAGCCCUGUC
BABD01002850.1/1611-1480     CCGUAAUAACAACAAAAGUCAUGAGAACAAUUA-UAGUA-A---AUACAUAUUGGUGGUGGCGCUCU-UUACAACUCAUAAGGUCGUAAGGAAC-CAGUCCUC-----AUG----UAU-AUACU-----AUCAU----GAUAUA----------AUAAAAGGUCUGUC
BABB01001973.1/2743-2604     CGUAAUAACAAAACAGAGUCAUGAGAACAUUCG-UAGUA-A---AUACAUAUUGGUGGUGGCGCUCCG-UACAACUCAAAAGGUCGUAAGGAAC-GAAGACUC--GU-AUG----UAU-AUAUAAACACUACAU-AAAGAUAU------------AAAGAGGUCUGUC
CP000383.1/3762321-3762447   UCCCCCAUAUCUUUGUAACCAUGAAAACAAUUA-CAGGA-A---CUAAACAAUUGUGGUG-GUGCGU----GAACUAAUC-AGUUC---GUGAA-CA-UGCUG--CU-GU---------GUCCU-----GUUUGAAAAUAUAUCA--------AAAAAGAGGCUUGCU
AANA01000002.1/232794-232908 AUUUUUACCUUUGUAACAUAAUGAAAAACAGUA-UA----A---ACAUAUCUUGGUGGUG-GAACUC----UCUUAACUAAUAAGU---GAGUU-UA-UACCU-----GUA----UGU-A---A-----------AAAUAUAUU-----------AAAAAGGCUUAUC
AACY020232167.1/1417-1534    UCGUUGCUAUAUUUGAAGUGAUUAUGAAUUUAA-AAUUA-A---UUACUAAUUGGUGGCA-AU-CGC----UUAAUUUUC-AUUAG---GUCGA-UAACUCU---UU-UAGU--UUACAGUAAA------UAAU----------------------AAAAGGCUUGUU
CP000140.1/693567-693428     -CGUAAUAACAAAACAGAGUCAUGAGAACAUUCGUAGUA-A---AUACAUAUUGGUGGUGGCGCUUCG-UACAACUCAAAAGGUCGUAAGGAAC-GAAGACUC--GU-AUG----UAU-AUAUAAACACUACAU-AAAGAUAU------------AAAGAGGUCUGUC
CU207366.1/2785164-2785282   UCAUCUCUAUCUUUGAAGUCAUGUUUAAAAUGA-AAAAA-A---AUAACUGGUGGUGGAA-UAACUU------ACGUCAAACUUCGU--GAGCU-A--AACUG--CU-AUU----UUCAAUAUA--------------GAAAUU-----------AAAAAGGCUUGUU
AAWS01000005.1/77275-77138   UUGCUUUGAAUAUGAAUGAAAAAAGUUUACAUA-UUACA-A---G---AUGUUGGUGGUGG---CAC---AAAAGAGAAC-UCUCUUCUGUGAA-UAGCCCCG--UU-GUA----UAC-GUGUAAA-ACUUUAUUACAUAAAGAUAU-----AAGCAAAAAGGCUUCC
AM398681.1/621441-621313     UUUGAACUUUAAUUAAGAACAUGAACACAUUUU-UAAAC-A---AUACUUGGUGGUGGA--AUAAUUU-----ACGUCAAACGUCGUGAACUAA-UC-CUCUA--UA-UUG----UAU-UUUUA------AAACUCAAAAUAUA-----------AAAAAGGCUUGUC
CP000139.1/5029321-5029462   CCAAAAUAAAAACAGAUUUUAUGAAUAGAAUCA-UGGUA-A---AUACAUAUUGGUGGC--GU-UUC-UUACAACUAAACAAGUCGUAAGGGAA-CCAGACC---AU-GUA----UAU-AUACCUG-ACAUUCU-AAAAGGAUAUUC----AAACU-GAAGGCCUGUC
AACY020813116.1/689-564      UUACACUUCAAAACAAACAAAUGAACACAAUUU-UAAAU-C---AUA---CUUGGUGGUGGAACUUC----AAGAUUUCA-AUCUUCGUGAAGU-AAACCCUU--AG--------UAU-AUUUA------AUUUAAAAUAUUUA-----------AAAAAGGCUUGUC
AACY020986511.1/530-635      UAUAUUUGAUCUGAAAUGAAAAACACAAAACAA-UA---UA------CUUGGUGGUGGAA-CUAUCG------AUAUCCAAUGUCGUGA---AA-C--CCCUA--GU-GUG----UAAAA---A------AUAC-----------------------AAAGGCUUGUC
AAPR01000002.1/281378-281492 UUAUUCUUAUGUUUGCAAGAUGCUUAAAACAAA-UAACAAA---U--CUUGGUGGUGGUC-UUUAUU------ACGUCAAACGUCGUG-ACUUA-GA-UCCUG--CU-AUG----UAA-AUAUA------UCAU-----------------------AAAGGCUUGUC
AAOG01000004.1/65950-65830   UCUACCCUACUUUUGUACUCGACAUGAAAAAUA-AUACA-A---ACAAAACUUGGUGGUGG-AACUC----UCUUAAUUCAUAAGU---GAGAU-GAAUCCUAUAUG-UUU----AUA-ACAUA-----------AUA-----A-----------AAAAAGGCUUAUC
AAVM02000001.1/509313-509169 CCAUUAAAUAACAAAUGACAAUGAGAACUAUAU-UAGUA-A---AUACAUAUUGGUGGUG-GCGUCCGUUACAACUCCGACAGUCGUAAGGGAG-CAGCGCUC--GU-AUG----UAU-AUACC------UCAUUAAAGAUAUAACAG--AUUUGAAAGAGCCCUGUC
ABCO01000006.1/190508-190390 UUAUUAUAUUUGAAACAUAAUUAUGCAAACAAC-AAACA-AU-CUUACUUGGUGGUGGAA-UAACUC----UCGACAAAA-AUCGU---GAGCU-AAGCACUA--UU-UGG----UAU-AUAUC------AUAC----------------------AAAAGGCUUGUC
AAYH02000042.1/71718-71577   CGAUAAAACAAAAAAAGUCAAUGAAAACAAUGU-UAGUA-A---AUACAUAUUGGUGGUG-GCACCCGUUACAACUCCGACAGUCGUAAGGGAG-CAGCGCUC--GU-AUG----UAU-AUAUG-----------UAAUAUAUAGUAAAAAACAAAAAGAGCCCUGUC
AACY023257297.1/1028-1145    UCGUUGCUAUAUUUGAAAUGAUUAUGAAUUUAA-AAUUA-A---AUACUAAUUGGUGGCAG-U-CAC----UUAAUUUUC-AUUAA---GUCGA-UAACUCU---UU-UAGU--UUAUAGUAAA------UAAU----------------------AAAAGGCUUGUU
ACGA01000075.1/100947-100803 CCAUAAAAUUACAAAAGACAAUGAGAACAAUGU-UAGUA-A---AUACAUAUUGGUGGUG-GCACCCGUUACAACUCCGACAGUCGUAAGGGAG-CAGUGCUC--GU-AUG----UAU-AUACC------UCAUUAAAGAUAUAACAG--AUUUGAAAGAGCCCUGUC
AAXX01000005.1/34839-34711   UGCAACAUACAAUUAAGAAAAUGAUUUCAAUUU-UAAAC-A---AUACUUGGUGGUGGUC-UAACUU------ACGUCGAACUUCGUGAGCGA---A-UCCUG--CUAUAG----UAUCAUUUAAA-ACC-----AAAUACAUA-----------GAAAAGGCUUGUC
AACY023631135.1/379-262      UCGUUGCUAUAUUUGAAGUGAUUAUGAAUUUAA-AAUUA-A---AUACUAAUUGGUGGCA-AU-CGC----UUAAUUUUC-AUUAA---GUCGA-UAACUCU---UU-UAGU--UUAUAGUAAA------UAAU----------------------AAAAGGCUUGUU
AE015928.1/657806-657662     CCGAUAAAUAACAAAAGACAAUGAGAACAAUGU-UAGUA-A---AUACAUAUUGGUGGUG-GCGCCCGUUACAACUCCGACAGUCGUAAGGGAG-CAGUGCUC--GU-AUG----UAU-AUACC------UCAUUAAAGAUAUAACAA--AUUUGAAAGAGCCCUGUC
AACY023223091.1/227-342      AUAUAUUUGACAAUAAGAAUAUGAAAACAAUAA-AUACA-A---AUACUUGGUGGUGGAAA-ACCUU------ACGUCAAACUUCGU--GAGCUAAAGCACUA--UUGGUA----UAA-AUAUA-----C--------------------------AAAAGGCUUGUC
CR626927.1/3113186-3113332   CCGUUAAAUAACAAUUAGCAAUGAUGACAAUGC-AAGUA-A---AUACAUAUUGGUGGUG-GCGCCCGUUACAACUCCGACAGUCGUAAGGGAG-CAGCGCUC--GU-AUG----UAU-AUACC------UCAUUAAAGAUAUAACAGAAUUUAGAAAGAGCCCUGUC
AANC01000011.1/62856-62973   ------UUAUCUUUGAUGCUCAAAUUAUGAAAAACAAAACA---GUAAAUACU--UGGUG-GUGGAUCUCGCAACAGUAA-UGUCGUGAAACAA-C--CU--U--GU-AUU----UAAAAUUUA-----------AAUAACUG--------------AAAGGCCUGUC
CP000685.1/5912047-5912172   -UGUCACAUCAAAAUAAAGAAAUGAGAACAAUA-AUGAACA---AUACUUGGUGGUGGAA-CAAUUU------ACGUCAAACGUCGUGAACGA---AGCUUCC--UA-UGG----UAU-UUUCA------AAACUAUAAAUAU-------------AAAAGGCUUGUC
AAXE02000021.1/155182-155313 CCGUAAUAACAACAAAAGUCAUGAGAACAAUUA-UAGUA-A---AUACAUAUUGGUGGUGGCGCUCU-UUACAACUCAUAAGGUCGUAAGGAAC-CAGUCCUC-----AUG----UAU-AUACU-----AUCAU----GAUAUA----------AUAAAAGGUCUGUC
AAGA01016891.1/820-699       ACGUUUCUAUAUUUGCAACAAUGUUUAAAAUAA-CUGUA-C---AUACUUGGUGGUGGAA-UAACUU------ACGUCAAACGUCGU--GAGCU-AGCUACUA--GU-UUG----UAUAAUCUA-----------AUAUAUAA-------------AAAAGGCUUGUC
CP002157.1/43940-44056       UCAUUUCUAUAUUUGAGGCAAUGAAAAACAGAA-CAAAU-A---AUACAUGGUGGUGGAG-UAACUU------ACGAAAAACGUCGU--GAGCA-AAGCAUCA--UU-GUA---GUAA-AACUA----------------UAU-------------AAAAGGCUUGUC
CP002046.1/1429092-1428971   UAUAAUCCUGAGUAUAUUUGGCGCAUAUUAUGA-AAGCA-AACAAUACAUCUUGGUGGU--GGAACAACUCUAGACAAUA-GUCGUGAG----C-CA-CGCUU--AGUAUG----UAA-AUACA------AUAC----------------------CAAAAGCCUGUC
#=GC SS_cons                 :::::::::::::::::::::::::::::::::.::<<<.-...<<<<<<<<-<<<<---.<<-<<<....<-<<<_____>>>->--->>>->.>-->>>>-..>>.>>>....>>>.->>>:......::::.:::::::::...........:::::::::::::
#=GC RF                      ucauaauuauAauaaAaauaAUGAaaAaAAUuA.uAguA.A...aUACauauUGGuGGUG.guaccC....cAAcuucaAAagUCgUAAGggAa.cAgCaCUa..au.auG....UAu.AUacA......uuAU.AAAuAUAUA...........AAAAAGGCuUGUC
//
# STOCKHOLM 1.0

#=GF AC   RF01693
#=GF ID   Bacteroidales-1
#=GF DE   Bacteroidales-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   60.00
#=GF TC   66.00
#=GF NC   59.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Bacteroidales-1_RNA_motif
#=GF SQ   41


BABD01027605.1/926-751       AGGGUUACCCCACGUGUG-CGAGGGGAA-CUGACGAGUAC--AUCAAACCCCGA-ACA-AGCUC-GGUUCGC-AAGGGCGG--CCGC------CCC---UUUC---GGAU---AAGCUAA-GCCACGUCGG-AUCA-CAAA-GGUGACAAAGCACUCAAAUCCGG---UCA-CACGGAGUUGGU-ACAUAUCAACAGUGCGGCUUUUACA
BAAY01005444.1/242-57        GGUUGUUCCGGUUUGAUC-GGGAUACUC-AUCAAAAUAAA--ACGAA--ACCGAGG-A-AGUUUCUCUUGUU-AAUGGCGGG-CCACAUAAAACCC---UUAU---GGGACUAAGCUGUAUAGC-CGGUGG-AUUA-CAAA-GAC-GGAGAGCUCUCAAAUCCUA---UUAGCUCGGAGUUUCAUCACAUGAGUGGGGCAAGCCCUUUUC
BAAX01000158.1/508-314       GGUCGUUUCGGUUAGAUU-GGGAUACUC-AUCACAUUACAAAUUAUGAAACCGAGA-A-GACUUCUCUUGCC-UAUGGCGGG-CCACAAUAAGCCGGACUUCG-UUCGGU-GAAGCUGCAAAGC-CGGUGG-AUUA-CAAA-AGCGGG-GGGCUCUCAAACUUAUUGCUAAGUUCGGAGUUUCA-UCACAUCAUCGG-GCGACCCUUUUC
BAAX01010365.1/733-913       CGCCAC----GUUCGAUC-GGGAUACUC-AUCAAUAAAAA--AAUCGAAACCGAGAAG--ACUUCUUUUGCC-AAUGGCGGG-CCAUAUAAAACC----UCAGU---GGACUAAGCUGCAAAGC-CGGUGG-AUUA-CAAA-GGCGGA-GAGCUCUCAAAUCUUG---UAUACUCGGAGUUUCA-UCACAUCAC-UGGGCGUCCCUUUUU
BAAX01004754.1/420-598       GACCGUAUCGGUUAGAUC-GGGAUACUC-AUCAAUAAAAA--AACGAAAACCGAGAUG--AUUUCUAUUGCU-AAUGGCGGG-CCACAU----UCC---UUCG---GGAU---AGCUGUAGAGC-CGGUGG-AUUA-CAAA-GGC-GUAGAACUCUCAAAUCUUA---UUAGCUCGGAGUUUCA-UCACAUCA-CGAUGCGGUCUUUUAG
BABA01004120.1/1238-1415     AGCCGCACUUGUUCGAUU-GGGAAACUC-AUCAGUUUAU----UUUAAUUCCGAGACAUAGCUCUUGUCGCC-AAUGGCGGG-CCGCG-----CCC---UUCG---GGGU---AUGCUUA-GCA-CGGCGG-AUUA-CAAA-GGUGGCAAAGCACUCAAAUCCUG---UCA-UACGGAGUUUGU-UCACAUCUACAGUGCGGCUUUUUCA
BABD01027604.1/632-810       AGCCGCACUUGUUCGAUU-GGGAAACUC-AUCAGUUUAUU--UUAAU--UCCGAGACAUAGCUCUUGUCGCC-AAUGGCGGG-CCGCA-----CCC---UUCG---GGGU---AUGCUUA-GCA-CGGCGG-AUUA-CAAC-GGUGGCAAAGCACUCAAAUCCUG---UCC-UACGGAGUUUGUUCCUAUUCUACCGUGCGGCUUUUUCC
BABD01016942.1/749-930       AGCCGCACAUGUGCGAUU-GGGAAACUC-AUUCAGUUUAU--UUUAUU-UCCGAGACAAAGCUCUUGUCGUC-AAUGGCGAG-CCGAA-----ACC---UUCGA--GGGC---AUGCUUC-ACAACGGCGGUAUUAACAAG-GAUGGCAAAGAACUCAAUUCCUG---UCA-UAACGAGUUUGU-CCUAUUCUAC-GUGCGGUUUCUUUA
BABD01000999.1/665-840       AGCCGCACUUGCAGAAUC-GGGAAACUC-AUCAAAUUAU---AAGAAAUACCGAGA-ACAGCUUCAUCUUCC-AAUGGCGGG-CCAC------GCC---UUCG---GGU----AGCAUUUAUGC-CGGUGG-AUUA-CAAA-GGGGGA-GAGCACUCAAAUCAUG---UUU-AUCGGAGUUUCG-UCACGCCUCUGGUGCGGCUUUCCUU
BABG01004849.1/451-627       AGCCGCAUUAGUUGGAUU-GGGAAACUC-AUCAAACUAA---UCUGAAAACCGAGACAUAGCUUCAUCUUCC-AAUGGCGGG-CCAC------GCC---UUCG---GGU----AGCAUUUAUGC-CGGUGG-AUUA-CAAA-GGAGGA-GAGCACUCAAAACCUG---UCA-UUCGGAGUUUCA-UCGCAUCACUGGUGCGGCUUCAUUA
BAAU01004407.1/862-686       AGCCGCAUUAGUUGGAUU-GGGAAACUC-AUCAAACUAA---UCUGAAAACCGAGACAUAGCUUCAUCUUCC-AAUGGCGGG-CCAC------GCC---UUCG---GGU----AGCAUUUAUGC-CGGUGG-AUUA-CAAA-GGAGGA-GAGCACUCAAAACCUG---UCA-UUCGGAGUUUCA-UCGCAUCACUGGUGCGGCUUCAUUA
BAAX01034787.1/345-169       AGCCGCAUUAGUUGGAUU-GGGAAACUC-AUCAAACUAA---UCUGAAAACCGAGACAUAGCUUCAUCUUCC-AAUGGCGGG-CCAC------GCC---UUCG---GGU----AGCAUUUAUGC-CGGUGG-AUUA-CAAA-GGAGGA-GAGCACUCAAAACCUG---UCA-UUCGGAGUUUCA-UCGCAUCACUGGUGCGGCUUCAUUA
BAAY01001699.1/365-541       AGCCGCAUUAGUUGGAUU-GGGAAACUC-AUCAAACUAA---UCUGAAAACCGAGACAUAGCUUCAUCUUCC-AAUGGCGGG-CCAC------GCC---UUCG---GGU----AGCAUUUAUGC-CGGUGG-AUUA-CAAA-GGAGGA-GAGCACUCAAAACCUG---UCA-UUCGGAGUUUCA-UCGCAUCACUGGUGCGGCUUCAUUA
BABA01025825.1/358-177       AGCCGCAUUGAUUGGAUC-GGGAUACUCUAUCUAUUUUU---AUGAUAUACCGCGACU-AGCUUCGCUUCUCUAUGG-CGGGCCUACG-----CCC---UUCG---GGGU---UACUCUUGAGU-CGGUGG-AUUA-CUUAGUAGUAGGUAGUACUCNUAUCAGU---CUA-UACGGAGUUUCA-UCACAUUAACCGUGCGGCGUUCUUA
BABB01013913.1/442-618       AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAUUAA----ACUGAAAACCGAGACA-AGCUUCGCUUCUC-AAUGGCGGG-CCACA-----UCC---UUCG---GGAU---AACUUUAUAGU-CGGUGG-AUUA-CAAA-GAGGA-CGGGCACUCAAAUCAUG---UCA-UUCGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUUUAA
BAAZ01000710.1/2540-2717     AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAACUAUU--AUGAAAUACCGAGACA-AGCUUCGCUUCUC-GAUGGCGGG-CCACG-----CCC---UUCG---GGGU---AACUUUG-AGU-CGGUGG-AUUA-CAAA-GAGGA-CGAGCGCUCAAAUCAUG---UCA-UUCGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUUUUA
BABA01003411.1/651-828       AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAACUAUU--AUGAAAUACCGAGACA-AGCUUCGCUUCUC-GAUGGCGGG-CCACG-----CCC---UUCG---GGGU---AACUUUG-AGU-CGGUGG-AUUA-CAAA-GAGGA-CGAGCGCUCAAAUCAUG---UCA-UUCGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUUUUA
BAAY01021114.1/550-727       AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAUUUUU---AUGAAAUACCGAGACA-AGCUUCAGUUCUU-AAUGGCGGG-GCACG-----CCU---UUCG---GGGU---AACUCUUGAGU-CGGUGG-AUUA-CAAA-GAGGAC-GAGCACUCCCAUCAUG---UCG-UACCGAGUUUCA-UCACCUCAUCGGUGCGGAGUUUCUA
BAAZ01019253.1/445-268       AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAUUUUU---AUGAAAUACCGAGACA-AGCU-UCGCUUCUCAAUGGCGGG-CCACG-----CCC---UUCG---GGGU---AACUCUUGAGU-CGGUGG-AUUA-CAAAGAGGAG--GAGCACUCAAAUCAUG---UCA-UACGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUCUAU
BABG01009248.1/549-726       AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAUUUUU---AUGAAAUACCGAGACA-AGCU-UCGCUUCUCAAUGGCGGG-CCACG-----CCC---UUCG---GGGU---AACUCUUGAGU-CGGUGG-AUUA-CAAAGAGGAG--GAGCACUCAAAUCAUG---UCA-UACGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUCUAU
BABD01001370.1/2435-2258     AGCCGCAUAGAUUGGAUC-GGGAAACUC-AUCAAUUCUA---AUGAAAUACCGAGACA-AGCUUCAGUUCUC-AAUGGCGGG-CCACG-----CCC---UUCG---GGGU---AACUCUUGAGU-CGGUGG-AUUA-CAAA-GAGGAC-GAGCACUCAAAUCAUG---UCA-UACGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUCUAU
BAAU01008698.1/740-563       AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAUUCUA---AUGAAAUACCGAGACA-AGCUUCAGUUCUC-AAUGGCGGG-CCACG-----CCC---UUCG---GGGU---AACUCUUGAGU-CGGUGG-AUUA-CAAA-GAGGAC-GAGCACUCAAAUCAUG---UCA-UACGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUCUAU
BABB01001469.1/28-205        AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAUUCUA---AUGAAAUACCGAGACA-AGCUUCAGUUCUC-AAUGGCGGG-CCACG-----CCC---UUCG---GGGU---AACUCUUGAGU-CGGUGG-AUUA-CAAA-GAGGAC-GAGCACUCAAAUCAUG---UCA-UACGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUCUAU
AE015924.1/2190292-2190123   AGCCGCACUGU-UAGAUCGGGGAAACUC-AUCAUAACAA------CUAUUCCGAGG-ACAAUU-UCAUCGCU-GAUGGCGGG-CCGC------ACC---UUCG---GGU-----UGCUUU-GCA-CAGCGG-AUUA-CAAA-GGUGGUGGAAUCCUCAAAUCUUG---UCU-UUCGGAGUUU-A-CGCUAUCCGCAGUGCGGCUUUUCAU
ABYH01000068.1/291-468       AGCCGCACAUGUUCGAUU-GGGAAACUC-AUCAGUUUA----UUUUAAUUCCGAGACACAGCUCUUGUCGUC-AAUGGCGGG-CCGCA-----CCC---UUCG---GGGC---AUGCUUA-GCA-CGGCGG-AUUA-CAAA-GAUGGCAAAGCACUCAAAUCCUG---UCA-UACGGAGUUUGU-UCAUAUCUACGGUGCGGCUUUCUUU
AAXF02000045.1/146907-147084 AGCCGUAUCGACUGGAUC-GGGAAACUC-UUCAAAUUAAU--CUGAUGCACCGAGA-A-AGCUUCGUUCUUC-AAUGGCGGG-CCACA-----UCC---UUCG---GGAC---AGCUUUA-AGC-CGGUGG-AUUA-CAAA-GAGGG-CGAGCGCUCAAAUCUUG---UUCUAUCAGAGUUUCA-UCACAUCGUCGAUGCGGCUUUUUUU
ABIY02000127.1/14645-14470   AGCCGCACUUGCAGAAUC-GGGAAACUC-AUCAAAUUAU---AAGAAAUACCGAGA-ACAGCUUCAUCUUCC-AAUGGCGGG-CCAC------GCC---UUCG---GGU----AGCAUUUAUGC-CGGUGG-AUUA-CAAA-GGGGGA-GAGCACUCAAAUCAUG---UUU-AUCGGAGUUUCG-UCACGCCUCUGGUGCGGCUUUUCUU
AAXE02000021.1/125990-125813 AGCCGCACAUGUUCGAUU-GGGAAACUC-AUCAGUUUA----UUUUAAUUCCGAGACACAGCUCUUGUCGUC-AAUGGCGGG-CCGCA-----CCC---UUCG---GGGC---AUGCUUA-GCA-CGGCGG-AUUA-CAAA-GAUGGCAAAGCACUCAAAUCCUG---UCA-UACGGAGUUUGU-UCAUAUCUACGGUGCGGCUUUCUUU
AE015928.1/512928-513105     AGCCGUAUCGACUGGAUC-GGGAAACUC-UUCAAAUUAAU--CUGAUGCACCGAGA-A-AGCUUCGUUCUUC-AAUGGCGGG-CCACA-----UCC---UUCG---GGAC---AGCUUUA-AGC-CGGUGG-AUUA-CAAA-GAGGG-CGAGCGCUCAAAUCUUG---UUCUAUCAGAGUUUCA-UCACAUCGUCGAUGCGGCUUUUUUA
BAAX01004326.1/2389-2212     AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAUUUUU---AUGAAAUACCGAGACA-AGCU-UCGCUUCUCAAUGGCGGG-CCACG-----CCC---UUCG---GGGU---AACUCUUGAGU-CGGUGG-AUUA-CAAAGAGGAG--GAGCACUCAAAUCAUG---UCA-UACGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUCUAU
ABQC02000016.1/77157-77332   AGCCGUACUUGCAGAAUC-GGGAAACUC-AUCAAAUCUA---AAGAAAUACCGAGACA-AGCUUCUACUUCC-AAUGGCGGG-CCAC------GCC---UUCG---GGU----AGCAUUUAUGC-CGGUGG-AUUA-CAAA-GGAGG-GGAGCACUCAAAACCUG---UCA-UUCGGAGUUUCG-UCACGCCUCGGGUACGGCUUCUCCU
CP000139.1/4991729-4991553   AGCCGCAUUAGUUGGAUU-GGGAAACUC-AUCAAACUAA---UCUGAAAACCGAGACAUAGCUUCAUCUUCC-AAUGGCGGG-CCAC------GCC---UUCG---GGU----AGCAUUUAUGC-CGGUGG-AUUA-CAAA-GGAGGA-GAGCACUCAAAACCUG---UCA-UUCGGAGUUUCA-UCGCAUCACUGGUGCGGCUUCAUUA
ABVO01000025.1/18262-18439   AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAUUUUU---AUGAAAUACCGAGACA-AGCUUCAGUUCUU-AAUGGCGGG-CCACG-----CCC---UUCG---GGGU---AACUCUUGAGU-CGGUGG-AUUA-CAAA-GAGGAC-GAGCACUCAAAUCAUG---UCA-UACGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUCUAU
CP000140.1/788079-788256     AGCCGCACUUGUUCGAUU-GGGAAACUC-AUCAGUUUAU----UUUAAUUCCGAGACAUAGCUCUUGUCGCC-AAUGGCGGG-CCGCG-----CCC---UUCG---GGGU---AUGCUUA-GCA-CGGCGG-AUUA-CAAA-GGUGGCAAAGCACUCAAAUCCUG---UCA-UACGGAGUUUGU-UCAUAUCUACAGUGCGGCUUUUUCA
ABJL02000008.1/781990-781813 AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAACUAUU--AUGAAAUACCGAGACA-AGCUUCGCUUCUC-GAUGGCGGG-CCACG-----CCC---UUCG---GGGU---AACUUUG-AGU-CGGUGG-AUUA-CAAA-GAGGA-CGAGCGCUCAAAUCAUG---UCA-UUCGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUUUUA
AAVM02000004.1/418226-418403 AGCCGUAUCGACUGGAUC-GGGAAACUC-UUCAAAUUAAU--CUGAUAUACCGAGA-A-AGCUUCGAUCUUC-AAUGGCGGG-CCACA-----UCC---UUCG---GGAC---AGCUUUA-AGC-CGGUGG-AUUA-CAAA-GGGGA-CGGGCACUCAAAUCUUG---UUCUAUCAGAGUUUCA-UCACAUCGUCGGUACGGCUUUUUUA
AP009380.1/146751-146582     AGCCGCACUGU-UAGAUCGGGGAAACUC-AUCAUAACAA------CUAUUCCGAGG-ACAAUU-UCAUCGCU-GAUGGCGGG-CCGC------ACC---UUCG---GGU-----UGCUUU-GCA-CAGCGG-AUUA-CAAA-GGUGGUGGAAUCCUCAAAUCUUG---UCU-UUCGGAGUUU-A-CGCUAUCCGCAGUGCGGCUUUUCAU
AP006841.1/1960011-1960187   AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAUUAA----ACUGAAAACCGAGACA-AGCUUCGCUUCUC-AAUGGCGGG-CCACA-----UCC---UUCG---GGAU---AACUUUAUAGU-CGGUGG-AUUA-CAAA-GAGGA-CGGGCACUCAAAUCAUG---UCA-UUCGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUUUAA
ABWZ01000013.1/484277-484453 AGCCGCAUUAGUUGGAUU-GGGAAACUC-AUCAAACUAA---UCUGAAAACCGAGACAUAGCUUCAUCUUCC-AAUGGCGGG-CCAC------GCC---UUCG---GGU----AGCAUUUAUGC-CGGUGG-AUUA-CAAA-GGAGGA-GAGCACUCAAAACCUG---UCA-UUCGGAGUUUCA-UCGCAUCACUGGUGCGGCUUCAUUA
ABFZ02000019.1/401830-402007 AGCCGCAUUGAUUGGAUC-GGGAAACUC-AUCAAUUCUA---AUGAAAUACCGAGACA-AGCUUCAGUUCUC-AAUGGCGGG-CCACG-----CCU---UUCG---GGGU---AACUCUUGAGU-CGGUGG-AUUA-CAAA-GAGGAC-GAGCACUCAAAUCAUG---UCA-UACGGAGUUUCA-UCACAUCAUCGGUGCGGCUUUCUAU
ABXI02000044.1/6713-6890     AGCCGUAUCGACUGGAUC-GGGAAACUC-UUCAAAUUAAU--CUGAUGCACCGAGA-A-AGCUUCGUUCUUC-AAUGGCGGG-CCACA-----UCC---UUCG---GGAC---AGCUUUA-AGC-CGGUGG-AUUA-CAAA-GAGGA-CGAGCGCUCAAAUCUUG---UUCUAUCAGAGUUUCA-UCACAUCGUCGGUACGGCUUUCUUA
#=GC SS_cons                 ::::::::::::::::::.:::::::::.::::::::::...::::::::::::::::.:(((-((((((((.--((-----.((((,.....<<<...____...>>>,...,<<<____>>>.,,)))).----.))--.)))))))))))::::::::::::...:::.::::::::::::.:::::::::::::::::::::::::
#=GC RF                      AGcCGcAuuggUUgGAUc.GGGAaACUC.AUCAaauuaa...auuaaAuaCCGAGACA.AgCUUccgccccc.AAuGGCGGG.CCaca.....cCC...UUCG...GGgu...AgcuuUaaagc.CGguGG.AUUA.CaAA.gggggcggAGcaCUCAAAUCuUG...UcA.uuCGGAGUUUcA.UCacAUCauCgGUGCGGCUUUuUua
//
# STOCKHOLM 1.0

#=GF AC   RF01694
#=GF ID   Bacteroides-1
#=GF DE   Bacteroides-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   43.00
#=GF TC   43.50
#=GF NC   40.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Bacteroides-1_RNA_motif
#=GF SQ   40


BABD01000872.1/1354-1286       AUGCAGACG---CUUAA---AACACUUGGAUGUAUGUGAAUAUGUGUAAGU---GUUAC--CUG----UUC--------CAGAAG----UGGAAAA
BAAV01015564.1/659-744         AUGCAAAUCA-CCUGAUAAAGCUUCUUAUGGGUAUGCGAAUAUAGAUCAGUCA-AGCAAG-AUAUGCCUCCCC-GGCAUUACA------GGUAAGA
BAAV01015564.1/424-504         GUGCAAAUC-GCCUGAUG--GCUGCUUGUAGGUAUGCGAAUAUAUAUGAGUC--AGUGAA--UAUGCCUCCCC-GGCA-UA-AC-----AGGAAGA
BABG01016634.1/466-385         AUGCUAAUCGACCUGAA---GCUGUUUAUGAGUAUGCGAAUAUACGUAAAU---GGUAC--UUAUGCCUCCCC-GGCA-UAGACA----GGAAAGA
BABB01010445.1/346-262         AUGCAAAUCGGCCUGAA---GCGCUUUAUGCCUAUGGGAAUAUCCAUAAUAGU-CGCACCG-UAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
BABA01000991.1/1142-1226       AUGCAAAUCGGCCUGAA---GCGCUUUAUGCCUAUGGGAAUAUCCAUAAUAGU-CGCACCG-UAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
BAAZ01000465.1/2353-2434       UUGCAAAUCAGCCUGAU---GCUGUUUAUGUAUAUGUGAAUAUCCGUAACU---AGUAC--UUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
BABD01020940.1/232-313         GUGCAAAUCAGCCUGAA---GCUGUUUAUGUAUAUGUGAAUAUCCGUAACU---AGUAC--GUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
BABG01021432.1/589-670         GUGCAAAUCAGCCUGAA---GCUGUUUAUGUAUAUGUGAAUAUCCGUAACU---AGUAC--GUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
BAAU01022191.1/354-273         GUGCAAAUCAGCCUGAA---GCUGUUUAUGUAUAUGUGAAUAUCCGUAACU---AGUAC--GUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
BABD01004454.1/837-918         AUGCAAAUCGGCCUGAC---GCUGCUUAUGUAUAUGUGAAUAUCCGUAAUU---AGUAC--AUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
BABB01007489.1/586-505         AUGCAAAUCGGCCUGAU---GCUGCUUAUGUAUAUGUGAAUAUCCGUAAUU---AGUAC--AUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
BAAU01022945.1/559-640         AUGCAAAUCGGCCUGAC---GCUGCUUAUGUAUAUGUGAAUAUCCGUAAUU---AGUAC--AUAUGCCUCCCC-GGCA-UAGACU----GGUNAGA
BAAY01000403.1/207-288         AUGCAAAUCAGCCUGAA---GCUGCUUAUGUGUAUGUGAAUAUCCAUAAUU---AGUAC--GUAUGCCUCCCC-GGCA-UAGACA----GGUACGA
BAAX01008592.1/313-232         GUGCAAAUCGGCCUGAA---GCCAUUUAUGUAUAUGUGAAUAUCCAUACUC---GGUAC--AUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
BABB01000399.1/1462-1380       AUGCAAAUAA-CCUGAA---CCCCUUCUGGGAUAUGUGAAU--ACCUGAUUGNCGGUAG--UUAUGUUACUCAAAACA-UAGAGC----AGGCUAA
BAAU01002748.1/674-588         AUGCAAAUA-ACCUGAAACC-CCUCUUGGA--UAUGUGAAUAC--CUGAUUGGCGGUAG--UUAUGUUACUCAAAACA-UAGAGCAGGCUAAAAAA
BAAV01002879.1/654-568         AUGCAAAUA-ACCUGAAACC-CCUCUUGGA--UAUGUGAAUAC--CUGAUUGGCGGUAG--UUAUGUUACUCAAAACA-UAGAGCAGGCUAAAAAA
BABA01008930.1/1160-1074       AUGCAAAUA-ACCUGAAACC-CCUCUUGGA--UAUGUGAAUAC--CUGAUUGGCGGUAG--UUAUGUUACUCAAAACA-UAGAGCAGGCUAAAAAA
BABG01024910.1/369-455         AUGCAAAUA-ACCUGAAACC-CCUCUUGGA--UAUGUGAAUAC--CUGAUUGGCGGUAG--UUAUGUUACUCAAAACA-UAGAGCAGGCUAAAAAA
AAVM02000001.1/1013664-1013584 AUGCAAGUCGACCUGAA---GCUGUUUGUGAGUAUGUGAAUAUACAUGGAU---AGUAC--UUAUACCUCCCC-GGUA-UAGAC-----AGGGAGA
AAVM02000011.1/71894-71814     AUGCAAAUC-GCCUGAUG--ACUACUUGUAGGUAUGCGAGUAUAUAUGAGUC--GGUGAA--UAUGCCUCCCC-GGCA-UA-AC-----AGGUAGA
AAXF02000043.1/119625-119709   GUGCAAAUC-GCCUGAUAAAGCUUCUUGUGUGUAUGCGAAUAUAGAUAAGUCA-AGCAAGG-UAUGCCUCCCC-GGCA-UG-AC-----AGGAAGA
CR626927.1/3042077-3041996     AUGCAAAUCGGCCUGAA---GCUGUUUAUGUGUAUGUGAAUAUCCAUAAUU---AGUAC--UUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
ABZZ01000088.1/2180-2261       AUGCUAAUCGACCUGAA---GCUGUUUAUGAGUAUGCGAAUAUACGUAGAU---AGUAC--UUAUGCCUCCCC-GGCA-UAGACA----GGAAAGA
AAXF02000043.1/119356-119436   AUGCAAAUC-GCCUGAUG--GCUACUUGUAGGUAUGCGAAUAUAUAUAGGCU--AGUGAA--UAUGCCUCCCC-GGCA-UA-AC-----AGGAAGA
AAYH02000045.1/87516-87435     GUGCAAAUCAGCCUGAA---GCUGUUUAUGUAUAUGUGAAUAUCCGUAACU---AGUAC--GUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
CP000139.1/4788592-4788510     AUGCAAAUA-ACCUGAAACC-CCUCUUGGA--UAUGUGAAUAC--CUGAUUGGCGGUAG--UUAUGUUACUCAAAACA-UAGAGCAGGCUAA----
ABIY02000058.1/8754-8822       AUGCAGACG---CUUAA---AACACUUGGAUGUAUGUGAAUAUGUGUAAGU---GUUAC--CUG----UUC--------CAGAAG----UGGAAAA
ABVO01000039.1/26199-26280     AUGCAAAUCAGCCUGAA---GCUGCUUAUGUGUAUGUGAAUAUCCAUAAUU---AGUAC--GUAUGCCUCCCC-GGCA-UAGACA----GGUACGA
AP006841.1/3456921-3457005     AUGCAAAUCGGCCUGAA---GCGCUUUAUGCCUAUGGGAAUAUCCAUAAUAGU-CGCACCG-UAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
EU064611.1/183-264             AUGCAAAUCGGCCUGAU---GCUGCUUAUGUAUAUGUGAAUAUCCGUAAUU---AGUAC--AUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
AP006841.1/2980257-2980176     AUGCAAAUCGGCCUGAA---GCUGUUUAUGUGUAUGUGAAUAUCCAUAAUU---AGUAC--UUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
ABJL02000008.1/538328-538247   UUGCAAAUCAGCCUGAU---GCUGUUUAUGUAUAUGUGAAUAUCCGUAACU---AGUAC--UUAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
CR626927.1/3358325-3358409     AUGCAAAUCGGCCUGAA---GCGCUUUAUGCCUAUGGGAAUAUCCAUAAUAGU-CGCACCG-UAUGCCUCCCC-GGCA-UAGACA----GGUAAGA
AE015928.1/2410987-2410907     GUGCAAAUC-GCCUGAUG--ACUGCUUGUAGGUAUGCGAAUAUAUAUGAGUC--AGUGAA--UAUGCCUCCCC-GGCA-UA-AC-----AGGAAGA
ABWZ01000015.1/81732-81814     AUGCAAAUA-ACCUGAAACC-CCUCUUGGA--UAUGUGAAUAC--CUGAUUGGCGGUAG--UUAUGUUACUCAAAACA-UAGAGCAGGCUAA----
AE015928.1/2410752-2410667     AUGCAAAUC-GCCUGAUAAAGCUUCUUAUGGGUAUGCGAAUAUAGAUAAGUCA-AGCAAG-GUAUGCCUCCCC-GGCAUUACA------GGUAAGA
AE015928.1/768695-768775       AUGCUAAUCAGCUUGA----UCUGUUUGUGAGUAUGUGAAUAUGAGUAAAU---GGUAC--UUAUGCCUCUCC-GGCA-UAGACA----GGUAUGA
AAVM02000011.1/62850-62766     AUGCAAAUC-GCCUGAUAAAGCUUCUUAUGGGUAUGUGAAUAUAGAUAAGUCA-AGCAAGA-UAUGCCUCCCC-GGCA-UA-AC-----AGGAAGA
#=GC SS_cons                   :::::::::::::::::...<<<--<<<<<-<<<<____>>>>->>>>>---..>>>--..<<<<<<<_____.>>>>.>>>:::....:::::::
#=GC RF                        AUGCAAAUcagCCUGAa...gCcucUuaugugUAUGUGAAUAuacauaAuUg..gGcAc..cUAUGCCUCCCc.GGCA.UAgAca....gGuAAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01695
#=GF ID   C4
#=GF DE   C4 antisense RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   45.00
#=GF TC   45.00
#=GF NC   44.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   C4_antisense_RNA
#=GF **   seedtax: other sequences; Bacteria; Viruses; unclassified sequences
#=GF SQ   456


BAAW01000646.1/4186-4274       CUCAAUG-GCG-GG-UC--GAGC--GG-GGGCGUC-GCAA--GACGC-GCCGGU---AUCCAGUAUG----------ACCGGUAAGGCU-A-ACUCC--GCU---C----GA-UUC-U-GC-CACCCGC
BAAW01012961.1/630-545         CUCAAUG-GUG-G--CU--GGGC--GG-GGGCACC-GUAA--GGUGC-GCCGGU---UGCCUGUAAC----------GCCGGUAGUUCC-A-ACCCC--GUU---C----AG--UC-C-AC-CACCAU-
BABF01001575.1/2753-2840       GAUUAUG-GUG-GG-CU--GGGC--GG-GGGCACC-GAAA--GGUGC-GCCGGU---CUCCGUUGAC----------GCCGGUUACGCC-A-ACCCC--GUC---C----AG--UU-C-AC-CACCAGU
BABF01001366.1/2134-2221       AAUUAUG-GUG-GG-CU--GGAC--GG-GGGCACC-GAAA--GGUGC-GCCGGU---UUCCGAUAAC----------GCCGGUUACGCC-A-ACCCC--GUU---C----AG--UU-C-AC-CACCAGC
BAAW01005016.1/464-551         AAUAAUG-GUG-GC-UC--GAGU--GG-GGCAGUC-UUCG--GACUG-GCCGGU---AUUCUGUGAA----------GCCGGUACUGCA-A-ACCCU--GUU---C----GG--GU-C-AC-CACCAAU
BAAX01008057.1/541-455         GAUAAUG-GCA-GU-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GC-GGU---UUCCAAUAAG----------GCCGGUUACGCC-A-ACCCC--GUU---C----GG--GC-U-GC-CACCAGU
BAAW01000581.1/4187-4100       GAUAAUG-GCA-GU-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---UUCCAAUAAG----------GCCGGUUACGCC-A-ACCCC--GUU---C----GG--GC-U-GC-CACCAGU
AAHR02000018.1/20965-20874     UUCUAUG-GUC-GG-GCCUUGGU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UCCCUUGGAC----------GCCGGUC-UGUC-A-ACCCU--GCC---AU-GUGC--CC-G-GC-CACCCCG
AAZJ01000012.1/9811-9897       CUCAAUG-GUA-GC-GU--GUAG--CG-GUAAAGG-UUCG-CCCUUU-GCUGUG---UUCCAAUUGU----------CGCGGUU-UUCG-A-GACCG--UUA---C----AC--GU-U-AC-CGCCAA-
AM286415.1/4498927-4498841     AGCAAUG-GUG-GG-CU--GGAC--GG-GGGCAUC-GAAA--GAUGC-GCCGGG---UUCUCUGUUG----------ACCGGUC-UGCU-A-ACCCC--GUU---C----AG--UC-C-AC-CACCCAA
AAKB02000001.1/4257494-4257407 AAUUAUG-GUG-GG-GC--GUAC--GG-GGCCGAC-UUCG--GUCGG-GCCGGG---UUCUAUGUUU----------GCCGGUAGUCUC-A-ACCCU--GUA---C----GU--CU-C-GC-CACCCCG
AE015451.1/4856630-4856545     CGAUAUG-ACG-GU-UG--UGCG--UG-GGAGGCC-UUCG--GGCCU-GCCGGG---UUUGCCAUAC---------CCCUGGUC-UUCC-A-CCCCG--CGU---A----CA--AC-U-GU-CACCC--
AP008232.1/2663915-2664000     CUCUAUG-GUG-GA-CU--GGAU--GG-GGCAGCC-GAAA--GACUG-GCCGGU---UGGUUGUAU------------CCGGUAACGCU-A-ACUCC--AUU---C----AU--UU-C-AC-CACCAAU
CP000521.1/1581044-1581128     CGUAGCG-GUA-GGACG--GGAG--AG-GGACACC-CUCG--GGUGU-GCUGGU---UUAUCUUAC------------CCAGUC-CGCG-A-ACCCU--UUC---U----CG-UUC-U-GC-CACCA--
AE015451.1/2038016-2037928     UGUCAUG-GCA-GU-CG--UACG--CG-GGCAGAC-UUCG--GUCUG-GCCGAG---CUUUGUAGCUC--------CCUCGGUU-UCUC-A-CCCCG--UGU---A----CG--AC-U-GC-CGCCCUG
AP008232.1/2901789-2901873     ---AAUG-GUG-GC-UC--AGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGA---UUCCAGAUUG----------ACCGGUAGUCUC-A-ACCCC--GUC---U----GG--GC-U-GC-CACCAAU
CP000800.1/1447230-1447147     AAUUAUU-GUG-GG-GC--GCAU--GG-GGGAGCU-GAAA--AGCUC-GUCGG------UCGGUUUC-----------CCGGUAGUUCC-A-ACCCU--GUG---C----GU--CU-C-AC-CACCCGA
AE015451.1/1420040-1419951     GUUUAUG-GCG-GC-UG--UACG--UG-GGGCAC-CUUCG-U-GUGC-GCCGAG---UUACUCCGGGA-------UCCUCGGUC-UGUC-A-ACCCA--UGU---A----CA--GC-U-GC-CACCCUC
U63086.1/3647-3560             AAUUAUG-GUG-GC-UC--AGAU--GG-GGCCAAC-UUCG--GUUGG-GCCGGU---UUCUUCUUGU----------ACCGGUGUUGAG-A-ACCCU--GUC---U----GG--GC-U-AC-CACCCCU
CP000521.1/872109-872195       CGUUGCG-GUA-GGACG--AGUG--AG-GGACACC-UUCG--GGUGU-GCUGAU---UUCUUACUA------------UCAGUC-UGCU-A-ACCCU--UGC---U----CG-UUC-U-GC-CACCAUA
CP000521.1/2778777-2778689     CGUAGCG-GUA-GGACG--GGAG--AG-GGACACC-UACG--GGUGU-GCUGGU---UAUAUCUUUC----------ACCAGUC-UGCU-A-ACCCU--UUC---U----CG-UUC-U-GC-CACCAUA
CP000058.1/4631607-4631691     CUUUAUG-GUG-GC-CG--UGCG--CA-UGGCGUC-UUCG--GAUGC-ACCGGG---UGCCAGCAG------------CCGGUC-UACC-A-ACUUG--CAC---A----CG--GC-C-GC-CACCUUA
AP008233.1/50694-50779         AUCAAUG-GUG-GG-CU--GGAC--AG-GGGAACU-GAAA--GGUUC-GCCGUU---AGCUUUGGC------------ACGGUAGUAUC-A-CCCCU--GUU---C----AG--UU-C-AC-CACCAGC
AP008232.1/1935487-1935401     AAUAAUG-GUG-GG-CU--GGAU--GG-GGGAGCC-GCAA--GGCUC-GCCGG----GUCCUUCUUA----------GCCGGUAGUCUC-A-ACCCU--GUU---C----AG--CU-C-GC-CACCAAU
ABEW01000015.1/43415-43331     AAUUAUG-GUG-GGGCG--UGAU--GG-GGAGGC--CUCG---GCCU-GCUGG----UUUCAUGUAC----------GCCAGUC-UGUC-A-ACCCU--GUC---A----CG-UCC-U-GC-CACCCU-
CP000075.1/5651663-5651744     CUUUAUG-GUG-GC-CG--UGCG--UG-GGGCGUC-UUCG--GAUGC-ACCGG----UUCCUAAUC-----------ACCGGGC-UACU-A--CCUG--CGU---G----CG--GC-C-GC-CACCU--
X51522.1/8507-8420             GUCAAUG-GUA-GC-UC--AGGC--GG-GGCAGCC-UCCG--GGCUG-GCCGGU---AUCCUGUGAA----------GCCGGUAUUCUC-A-CCCCC--GUC---U----GG--GC-U-AU-CGCCAUC
CP000614.1/463132-463042       UUCUAUG-GUC-GG-GC-CUGAU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UUCCUUUGAC----------GCCGGUU-CGCC-A-ACCCU--GUC---AU-GUGC--CC-G-GC-CACCCCA
CU914168.1/2037810-2037723     UUUUAUG-GCG-GG-CC--GGGC--GG-GGCCAGC-UUCG--GCUGG-GCCGGU---UGCCUGUAGG-----------CCGGUU-UUCC-A-CCCCC--GCCGUCU----GG--CC-C-GC-CACCCC-
CT573326.1/2592733-2592818     UUUCAUG-GCG-GC-UG--UACG--UGUGGGCAC--CUCG-U-GUGC-GCCGAG---UGCCAACGUC-----------UCGGUC-UGUC-A-ACCCG--CGU---A----CA--GC-U-GC-CACCCUC
AATN01000261.1/8052-7963       CUCUUUG-GUA-GU-GU--GCGU--GG-GGAGACC-UUCG--GGUCU-GCCGGUU-UUGCCUUGUGU---------UGCCGGUC-UGCG-A-ACCCC--GCG---C----AU--GC-U-GC-CACCAAU
CT573326.1/3854037-3854123     CUCUAUG-GCG-GC-UG--UGCA--UG-GGGCACG-CUUG--CGUGC-GCCGGU---UUUUGUGUCC----------GCCGGUC-UGUC-A-ACCUA--UGC---A----UA--GC-U-GC-CACCUAC
AAKB02000001.1/3919264-3919351 AAUUAUG-GUG-GG-CU--GGGC--AG-GGGAGCC-GAAA--GGCUC-GCCGGU---CUCCGUUGAC----------GCCGGUAGUGCA-A-ACCCU--GUU---C----AG--UC-C-GC-CACCAGC
CP001111.1/4249221-4249309     GGCUAUG-GCG-GG-CG--GGGC--GU-GGGGGC--CUUG-U-GCCC-GCCGGUUUCUUCCUAAUAG----------CCCGGUU-UUCG-A-GCCAC--GCU---C----UG--CC-C-GC-CACCUUU
AP008232.1/1527580-1527499     AACAAUG-GUG-GC-UC--AGGU--GG-GGGAGCC-GUAUAAGGCUC-GCCGG---------GGUAC----------ACCGGUAUUGCG-A-ACCCC--GCU---U----GG--GC-U-AC-CACCA--
CP000034.1/1757441-1757528     AUCAAUG-GUG-GG-CU--GUAU--GG-GGCCGAC-UUCA--GUCGG-GCUGGU---UCCCUUGAUU----------GCCAGUUGUAGC-A-ACCCU--GUA---C----AG--UC-C-AC-CGCCAGC
CP000949.1/3737714-3737803     UUCAAUG-GCG-GC-UG--UGUG--UG-GGGCACG-CUUG--CGUGC-GCCGGAA-CUUCCUAUGUC---------CGCCGGUC-UGUC-A-ACCUG--CAC---A----CA--GC-U-GC-CACCCAA
AE016853.1/6094972-6094888     UGCUAUG-GCG-AC-UG--UGCG--CU-UGGCACC-UUCG--GGUGC-GCCGG----UUCUUAGCUC----------ACCGGUC-UACU-A-ACUUG--CGU---A----CA--GU-U-GC-CGCCUU-
AE014613.1/4519523-4519609     CUCAAUG-GUG-GG-CC--GGGC--GG-GGGCGCU-GCAA--AGCGC-GCCGG----UGUCGAUGAG----------GCCGGUAAGGCU-A-ACCCC--GUC---C----GG-UUC-C-AC-CACCAU-
CP000949.1/232971-232881       CGUUAUG-GCG-GC-CG--UGCG--CG-GGCAGGC-UUAC--GUCUG-GCCGAG---UUUUGCCUUUGU------UCCUCGGUU-UCUC-A-CCCUG--CGU---A----CG--GC-U-GC-CACCCAC
CU459141.1/902172-902258       CUCUGCG-GCG-GAACG--GGAG--GG-GGACACC-UUUG--GGUGU-GCUGG------CCUCGUUU---------GACCAGUC-UGUC-A-ACCCU--CUU---U----CG-UUC-U-GC-CACCAUA
CP000712.1/770187-770275       UGUCAUG-GCG-GC-UG--UGUG--UG-GGCAGGC-UUCG--GCCUG-GCCGGG--UUUCCAAGUUU----------CCCGGUAUUCCU-A-CCCCG--CAC---A----CA--GC-U-GC-CACCCAA
AE006468.1/2762765-2762682     AAUUAUG-GUG-GG-GC--GUAU--GG-GGGAGCC-GAAA--GGCUC-GCCGG------UCGGUGAU-----------CUGGUUACGCC-A-ACCCU--GUA---C----GU--CU-C-AC-CACCCAA
CP000949.1/2235872-2235786     UGUUAUG-GUG-GU-UG--UACG--UGCGGGCACC-CUCU--GGUGC-GCCGAG---UGCCAACGUC-----------UCGGUC-UGUC-A-ACCCG--CGU---A----CA--GC-U-GC-CACCUCA
L31763.1/1866-1948             ---UAUG-GCA-GC-AU--ACGU--GG-GAGAACC-GAAA--GGUUC-GCCGU----UUCUUUCGU-----------AGCGGUAGUUCC-A-AUCUC--GCG---U----AU--GC-U-GU-CGCCCUC
AJ868434.1/21311-21396         AUCAAUG-GUG-GG-CU--GGAC--AG-GGGAACU-GAAA--GGUUC-GCCGUU---AGCUUUGGC------------ACGGUAGUAUC-A-CCCCU--GUU---C----AG--UU-C-AC-CACCAGC
CP001068.1/1318896-1318982     CUUCAUG-GCG-GG-CC--GGGC--GG-UGAGACC-UUCG--GGUCU-GCCGG----UUUCUAGAUG----------GCCGGUC-UGCU-A-ACGCC--GUCG-UC---AGG--CC-C-GC-CACCC--
AE015451.1/2302915-2302823     UCUAAUG-GCG-GC-CG--UACG--UG-GGCAGGC-UUCG--GCCUG-GCCGAGUCAUUGCGUAUUUC-------UCCUCGGUU-UCUC-A-CCCCG--CGU---A----CG--GC-U-GC-CACCCUC
AJ868435.1/1478-1562           AUCUAUG-GUG-GG-CU--GGAU--GG-GGGAGCC-GAGA--GGCUC-GCCGUU---UACUUGUAU------------CCGGUUGUUAG-A-ACCCU--GUU---C----GG--CU-C-AC-CACCAA-
CP000712.1/4999895-4999981     CUUUAUG-GCA-GC-UG--U-CA--UG-GGGCAC--CUCG-U-GUGC-GCCGG------CUUUUGGUUCU---GUUCACCGGUC-UGUC-A-ACCCA--UGU---A----CA--GC-U-GC-CGCCU--
ABFF01000008.1/134074-133992   AAUUAUG-GUG-GG-CU--GUGU--GG-GGGCACC-GAAA--GGUGC-GCCGG------UUGGUUUC-----------CCGGUUACGCC-A-ACCCU--GCA---C----AG--UU-C-AC-CACCAG-
CP000949.1/5572111-5572024     CUCCAUG-GCG-GU-CG--UGCG--CG-GGCAGGC-UUCG--GUCUG-GCCGGGG-UUACCGUAUGU----------CCCGGG--UCUC-A-CCCCG--UGC---A----CG--AC-U-GC-CACCCAA
FM200053.1/4462479-4462566     UGUAAUG-GUG-GC-UC--AGGC--GG-GGGCUUC-UCAC--GAAGC-GCCGGU---UUCCAAUGUU----------GCCGGUUACGCC-A-ACCCC--GUC---U----GG--GC-U-AC-CACCAGU
AB426055.1/6553-6640           AAUUAUG-GUG-GG-GC--GUAC--GG-GGCCGAC-UUCG--GUCGG-GCCGGG---UUCUGCGUUU----------GCCGGUACUGCG-A-ACCUC--GUA---C----GU--CU-C-GC-CACCCAC
CP000949.1/4994192-4994108     GUCUAUG-GCG-GU-GC--UGCG--CG-GGACACC-UGAU--GGUGU-GCUGGA---UUCCUUUCGC----------UCCAGUC-GGCC-A-ACCCG--CGU---A----CC--GC-C-GC-CACCC--
ABEW01000002.1/653315-653228   GAUAAUG-GUA-GU-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---AUCCUUGAAG----------GCCGGUUACGCC-A-ACCCC--GUU---C----GG--GC-U-GC-CACCAGU
AE009952.1/3599632-3599718     AACAAUG-GUG-GG-CU--GGAC--GG-GGGCAUC-GAAA--GAUGC-GCCGGG---UUCUCUGUUG----------ACCGGUC-UGCU-A-ACCCC--GUU---C----AG--UC-C-AC-CACCCAA
ABEH02000007.1/298126-298209   AAUUAUG-GUG-GG-GC--GUAU--GG-GGGAGCC-GAAA--GGCUC-GCCGG------UCGGUGAU-----------CCGGUUACGCC-A-ACCCU--GUA---C----GU--CU-C-AU-CACCCAA
AE015451.1/81574-81663         GUCCAUG-GCG-GC-UG--UUCG--CA-GGAGGC--UUCG-U-GCCU-GCUGGG---UUUUAGAUCUCC------CACCCGGUU-UACC-A-CCCUG--CGU---A----CA--GC-U-GC-CACCCAU
CP000949.1/3459349-3459439     UUCAAUG-GCG-GC-UG--UACG--UGCGGGCACG-CUUG--CGUGC-GCCGGAA-CUUGCAUAGUC---------CGCCGGUC-UGUC-A-ACCCA--UGU---A----CA--GC-U-GC-CACCCUU
AAKB02000001.1/3718805-3718718 AAUUAUG-GUG-GG-GC--GUGC--GG-GGCAGUC-GCAA--GACUG-GCCGGG---UUCCGUGAUG----------ACCGGUUGUAGC-A-ACCCU--GUA---C----GU--CU-C-AC-CACCCAU
CP000521.1/3419053-3418968     CGUAGCG-GUA-GGACG--GAAG--UG-GGACACU-UUCG--AGUGU-GCUGG------CCUCUGAG----------ACCAGUC-UGUC-A-ACCCA--CUU---U----CG-UUC-U-GC-CACCAUA
CP000680.1/1667390-1667307     --CUAUG-GCG-GG-CC--GUGU--GA-GGCGGGC-UUCG--GCCCG-GCCGGU---UCCCUUGGUU----------CCCGGUU-UACC-A-CCCUU--GCA---C----GG--UC-C-GC-CUCCAU-
U82619.2/27704-27791           AGUUAUG-GUG-GG-CU--GGGC--GG-GGGCAUC-GAAA--GAUGC-GCCGGU---UUCCUUGAUC----------ACCGGUUACGCC-A-ACCCC--GUU---C----AG--UU-C-AC-CACCAGC
AACY022261932.1/205-288        GGCUAUG-GCG-GG-CG--GGGC--GU-GGGGGU--CCUG-U-ACCC-GCCGGU---UCCCAACAU------------CCGGUU-UUCG-A-GCCAC--GCU---C----UG--CC-C-GC-CACCUUU
CP000671.1/965902-965987       CCCAAUG-AUG-AA-CU--GUUU--AG-GAGGAUC-GAAA--GAUCC-GCCGUU---UUGCUCUAAG----------UACGGUACUGCG-A-AUCCU--AUU---C----AG--UU-C-AU-CACCA--
AAJX02000031.1/41435-41522     AAUUAUG-GUG-GG-GC--GUGC--AG-GGCCAAC-UUCG--GUUGG-GCCGGG---UUCUAUGUUG----------ACCGGUAUUUCC-A-CCCCU--GUA---C----GU--CU-C-AC-CACCUAU
CP000270.1/4245368-4245279     UUCAAUG-GGC-GG-GC-CGUGG--UG-GGGAGCC-GAAA--GGCUC-GCCGGU---AUGUUUUUGG----------CCCGGUC-UGCU-A-ACCCG--CUA---CG--UGC--CC-G-CU-CACCCUC
CP000949.1/3736610-3736700     UUCUAUG-GUG-GC-UG--UGCG--UG-GGGCACG-CUUG--CGUGC-GCCGG----AACUUUGCUUAU-----UCCGCCGGUC-UGUC-A-ACCCA--CGU---A----CA--GC-U-GC-CACCCUU
AAUJ02000001.1/2357971-2357889 CUUUACG-GUG-GG-CC--GUGU--GG-GGACACCCGCGA-GGGUGU-GCCGG------UCCUACUG-----------CCGGUC-GACC-A-ACCCU--GCA---C----GG--UC-C-AC-CACCU--
CP000712.1/3625062-3625148     AGUUAUG-GCA-GC-UG--UGCG--UG-GGGCAC-CUUCG-U-GUGC-GCCGGG---AUUCUCAGUGC--------CCCCGGUC-UGUC-A-ACCCA--CAA---A----CA--GC-U-GC-CACCC--
AJ564013.1/23719-23806         AAUUAUG-GCA-GU-CC--AGGC--GG-AGCAGCU-UUCG--AGCUG-GCCGGU---AUCCGUUGGG----------GCCGGUAUUCCU-A-CCUCC--GUU---U----GG--GC-U-GC-CACCCCA
CP000712.1/1439621-1439537     CUUAAUG-GCA-GC-UG--UGCA--UG-GGGCACA-UUCG--UGUGC-GCCGG----GUCCUUGGGU----------ACCGGUC-UGUC-A-ACCCA--UGU---A----UA--GC-U-GC-CUCCAU-
CP000058.1/1124857-1124771     CGUUAUG-GCG-GG-UU--GCGC--AG-GAGCACC-CUCG--GGUGC-GCCGGU---CUCCUUGUAC----------GCCGGUC-CGCC-A-AUCCU--GUG---C----AA--UC-C-GC-CACCCUA
CP001111.1/2228925-2229010     AGCUAUG-GCG-GG-CG--GUGC--GU-GGAGGC--CUUG-C-GCCU-GCCCGG---UCAUCCACAC----------ACGGGGU-UUCG-A-ACCAU--GCA---C----CG--UC-C-GC-CACCUUU
CP000672.1/169172-169257       CCCAAUG-AUG-AA-CU--GUUU--AG-GAGGAUC-GAAA--GAUCC-GCCGUU---UACUCUAAUC----------AACGGUACUGCG-A-AUCCU--AUU---C----AG--UU-C-AU-CACCA--
AACY023997402.1/172-261        AAUUAUG-GCG-GC-UG--UGCG--UA-GGGCGCC-UUCG--GGCGC-GCCGGG---UUUGUGUGGGA-------UUACCGGUC-UACU-A-ACCUG--CGC---A----CA--GC-U-GC-CACCCAA
CP000521.1/871633-871716       UAUUAUG-GCG-AAAUG--AAAG--AA-GGACGC--CUCG-U-GUGU-GCUGGG---UACUCAAAG------------CCAGUC-UGUU-A-ACCUU--CUU---U----CG-UUU-C-GC-CGCCA--
CT573326.1/3960618-3960708     CUCGAUG-GCG-GC-UG--UACG--UGCGGGCACG-CUCG--CGUGC-GCCGG----AACUUUGCUUAU-----UCCGCCGGUC-UGUC-A-ACCCG--CGU---A----CA--GC-U-GC-CACCCU-
CP000308.1/654903-654816       GUCAAUG-GUG-GC-CC--AGGC--GG-GGGCUCC-GAAA--GGAGC-GCCGGU---UUCCAAGAAG----------UCCGGUAACGCU-A-ACUCC--GUC---U----GG--GC-U-AC-CACCCAA
CP001120.1/2560118-2560031     UAUUAUG-GUA-GU-CC--AGGC--GG-GGCAGCU-UUCG--GGCUG-GCCGGU---AUCCUUCAGA----------GCCGGUAUUCCU-A-CCCCC--GUC---U----GG--GC-U-AC-CACCCAU
CP001063.1/3805636-3805723     AUCAAUG-GUG-GC-GU--UAGU--GG-GGCUACG-UUCG--CGUAG-GCCGGU---UUCCUUUGUG----------UCCGGUAUUUCC-A-CCCCU--GCU---A----AC--GU-C-AC-CGCCAUU
ABBR01001020.1/7221-7131       AUCUAUGGGCG-GG-UG-AUGGC--AG-GGAGACC-UUCG--GGUCU-GCCGGU---UUCCUAUGGG-----------CCGGUU-CGCC-A-ACCUU--GUC---AU--UCG--CC-C-GCUCACCCCA
AE008924.1/1645-1553           UUCUAUG-GUG-GG-CG--GUGC--GC-GGAGGCU-GCAA--GGCCU-GCCGGU---UAUCGCUCUUUUC----CUAUCCGGUUUUGAU-A-GCCGC--GUA---C----CG--UC-C-AC-CACCUU-
CP000827.1/23340-23253         AUCAAUG-GUG-GG-GC--GUGC--AG-GGGAGCC-GAAA--GGCUC-GCCGGG---UUCUUUCGUG----------ACCGGUACUGCG-A-ACCUU--GUA---C----GU--CU-C-AC-CACCCCG
AACY020214859.1/3101-3015      UUCUAUG-GUG-GA-CC--GUGU--GG-GGCAGGC-UUUU--GCCUG-GCCGGU---UCCCUCGGAC----------GCCGGUU-UGUC-A-CCCCC--GCA---C----GG--UC-C-GC-CACCCAU
AAMK02000026.1/15471-15558     AAUUAUG-GCG-GG-GC--GUAC--GG-GGCCGAC-UUCG--GUCGG-GCCGGG---UUCUAUGUUU----------GCCGGUACUGCG-A-ACCUC--GUA---C----GU--CU-C-GC-CACCCAC
CP000436.1/565968-566054       CUCAAUG-GUA-GA-GC--GUAA--AG-GGCAACCGCUUG-CGGUUG-GCUAUG---UUCCUUUGUA----------CGUAGUU-UCCU-A-CCCCU--UUA---C----GC--UU-U-AC-CGCCC--
CP000949.1/645079-645163       GCCAAUG-GUG-GC-UG--CGUG--CU-GGAGAUC-UUCG--GAUCU-GCCGGU---UUUCGUCUGU-----------CCGGUC-UUGC-AGACCUG--CAC---G----UA--GC-C-GC-CACCC--
AL590842.1/2369225-2369312     AACAAUG-GUG-GG-GC--GUAC--GG-GGGAGCU-GAAA--GGCUC-GCCGGG---UGUUGUUGUG----------ACCGGUAGUGCA-A-ACCUC--GUA---C----GU--CU-C-AC-CACCCAA
AAMR01000038.1/33213-33129     AAUUAUG-GUG-AG-CU--GGGC--GA-GGCAGC--UUUA-U-GCUG-GUCGC----UUCCUUUGGU-----------GCGAUAGGUCC-A-ACCUU--GCU---C----AG--UU-C-AC-CACCCAA
AATO01001785.1/1808-1889       --CUAUG-GGC-GGGCC--GUGU--GG-GGAGACC-UUCG--GGUCU-GCCGG------CCCUCUG-----------ACCGGUU-CGCC-A-ACCCC--GCA---C----GGUUCC-G-CC-CACCC--
CP000949.1/4352039-4352126     CUUCAUG-GCA-GC-UG--UACA--UG-GGGCAC-CUUCG-U-GUGC-GCCGGG---UUCCUUGGGU---------CACCGGUC-UGUC-A-ACCCG--UGU---A----UA--GC-U-GC-CUCCAUU
AJ298298.1/9612-9699           AAUUAUG-GUG-GG-CU--GGGC--AG-GGGAGCC-GAAA--GGCUC-GCCGGU---UUCCUUGAGC----------GCCGGUAGUUCC-A-ACCCU--GUU---C----AG--UC-C-GC-CACCAGC
AAKY01000125.1/82257-82346     AUCAAUG-GGU-GG-GCGACGGU--GG-GGAGGC--UUCG---GCCU-GCCGGU---UCCCUUGGAC----------GCCGGUC-UGCA-A-ACCCU--GCC---GU-CUGC--CC-G-CC-CACCCCA
CP000521.1/3904932-3904848     CUCUAUG-GUA-GGGCG--GAAG--GG-GGACGCG-UUCG--CGCGU-GCUGG------UCGCUAGG-----------UCAGUC-UGCU-A-ACCCU--CUU---U----CG-UUC-U-AC-CACCCUA
AE015451.1/759603-759688       UGUAAUG-GCG-GC-UG--UGCG--UG-GGAGACC-UUCG--GGUCU-GCCGAG---UUCCUUUUCC-----------UCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GC-CACCCUA
AACY023484293.1/1191-1104      UGUUAUG-GCG-GC-CG--UGUG--UG-GGCAGGC-UUCG--GCCUG-GCCGGG---UUCCAAGUUU----------CCCGGUAUUCCU-A-CCCCA--CGC---A----CG--GC-U-GC-CACCCAA
CP000057.2/1577676-1577591     CCCAAUG-AUG-AA-CU--GUUU--AG-GAGGAUC-GAAA--GAUCC-GCCGUU---UUGCUCUAAG----------UACGGUACUGCG-A-AUCCU--AUU---C----AG--UU-C-AU-CACCA--
CP000884.1/416056-415973       UUU--CG-GCG-GG-GC--UGUG--CA-GGACCUCCGCAA-GGGGGU-GCCGG----CUCCUUUGC------------CCGGCC-CGCC-A-ACCUG--CAC---A----GC--CC-U-GC-CACCCGU
CP001113.1/4718071-4718158     GAUAAUG-GUG-GU-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---UUCCAAUAAG----------GCCGGUAUUCCU-A-CCCCC--GUU---C----GG--GU-C-AC-CACCCAU
CP001068.1/3798621-3798710     UUUCAUG-GCG-GG-CC--GGGC--GG-UGAGACC-UUCG--GGUCU-GCCGGU---AGCUGGGAUAG--------GGCCGGUC-UGCU-A-ACGCC--GUCG-UC---AGG--CC-C-GC-CACCC--
AAKB02000001.1/87954-87870     AAUAAUG-GUG-GG-GC--GUAU--GG-GGGAGCU-GAAA--GGCUC-GCCGG----UUGGUUGAU------------CCGGUAGUUCC-A-ACCCU--GUA---C----GU--CU-C-AC-CACCCAA
CP000753.1/896014-895930       UUCUAUG-GUG-AG-CU--GGGC--GG-GGCAACC-UUCG--GGUUG-GCCGC----UUCCUGUGAU-----------GCGGUAGUCUC-A-ACCCC--GUU---C----AG--CU-C-AU-CACCAC-
AB285204.1/36578-36665         AAUUAUG-GUG-GG-GC--GUAC--AG-GGGCAUC-GCAA--GAUGC-GCCGGU---AAGGGUAGCC----------GCCGGUAACGCC-A-ACUCU--GUA---C----GU--CU-C-AC-CACCUCU
CP001052.1/3805115-3805024     UUCUAUG-GGC-GG-GCUGUGGU--GG-AGGAGCC-GCAA--GGCUC-GCCGGA---UUGUUUCAAG----------CCCGGUC-UGUC-A-ACUUC--GCU---AC-AUGC--CC-G-CU-CACCCUC
CP000672.1/760122-760036       CUCAAUG-GUA-GC-GC--GUAA--UG-GGCAACC-CUUAGCGGUUG-GCUGCU---UUCCUGUAAA----------GGCAGUU-UGUC-A-CCCCG--UUA---C----GU--GC-U-AC-CGCCC--
CP000266.1/771649-771736       GAUUAUG-GUG-GG-GC--GUGC--AG-GGCAGCC-GCAA--GGCUG-GCCGGU---UUCGGUAGUC----------ACCGGUUGUAGC-A-ACCCU--GUG---C----GU--CU-C-AC-CACCCAU
AE014073.1/1891549-1891636     AAUUAUG-GUG-GG-AU--GUGC--AG-GGCAGUC-GCAA--GACUG-GCCGGG---UUCUGGAGUG----------ACCGGUAUUUCC-A-CCCCU--GUA---C----GU--CU-C-AC-CACCCUU
FJ184280.1/16551-16635         AUUUAUG-GCG-GG-CU--GUGU--GG-GGGAGCC-GAAA--GGCUC-GCCGG----AUGUUUCGA------------CCGGUAGUGCU-A-ACCCC--GCA---C----AG--UU-C-GC-CACCACG
CP000949.1/4811936-4811849     UUUUAUG-GCA-GC-UG--UGCG--CG-UGCAGGC-UUAG--GCCUG-ACCGUG--GUGACUCCAAC-----------ACGGGCUUCUC-A-CCUCG--CGC---A----CG--GC-U-GC-CACCCCA
CP000020.2/2237983-2237900     AAUUAUG-GUG-GG-CU--GAGU--GA-GAGCAC--UUCG---GUGC-GCCGU----AUCCUUGGA-----------AGCGGUAUGACU-A-AUCUU--GCU---C----AG--UU-C-GC-CACCCAA
ABBH01000753.1/1638-1728       UUCAAUG-GUC-GG-GCCUUGGU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---GUCCUCGGGU----------UCCGGUC-UUCC-A-ACCCU--GCC---AU-GUGC--CC-G-GC-CACCCC-
AATN01000014.1/4394-4308       CUCUAUG-CGG-GA-CU--GUGC--GG-GGCAGCC-UUCG--GGCUG-GCCGG----UACUCUGUAG-----------CCGGUUUUUCU-A-CCCCC--GUA---C----AG-CUC-C-CG-CACCUAA
CP000712.1/5795249-5795332     CGUUAUG-GCA-GU-UG--UGCG--CG-UGAGGCC-GUUU--GGCCU-ACCGGC---UUGCCUUCUC----------CCCGGUU-UUCC-A-CCCCG--CGC---A----CA--AC-U-GC-CGCC---
CP000800.1/1447971-1447889     AUUUAUG-GCG-GG-CU--GUGU--GG-GGGAGCC-GAAA--GGCUC-GCCGGU---UUCCGUAC-------------CCGGUAGUUCC-A-ACCCC--GCA---C----AG--UU-C-GC-CACCA--
AAKB02000001.1/956526-956439   GAUAAUG-GUG-GU-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---UUCCUUGAAG----------GCCGGUAUUCCU-A-CCCCC--GUC---C----GG--GC-U-AC-CACCCAU
AP008232.1/2086052-2085968     AUCAAUG-GUG-GC-UC--AGGU--GG-GGGAACC-GAAA--GGUUC-GCCGG----UUGGUUUAU------------CCGGUUGUGAC-A-ACCCU--GUC---U----GG--GC-U-AC-CACCAAU
AE017220.1/1315804-1315890     AAUUAUG-GUG-GC-UU--GGGU--AG-GGGAGCC-GAAA--GGCUC-GCCGGG---UUCUGUGAUG----------ACCGGUC-UGCU-A-ACCCU--GCU---C----AG--GU-C-AC-CACCAGU
CT573326.1/910398-910306       CUCUAUG-GCG-GC-UG--UGUG--UG-GGGCAC--CUCG-U-GUGC-GCCGGG---UUUUUUGGCUUUU---UCCUGCCGGUC-UGUC-A-ACCCA--UGC---A----CA--GC-U-GC-CACCCUC
AAZF01000002.1/232050-231964   CUCAAUG-GUA-GC-GU--GUAG--CG-GUAAAGG-UUCG-CCCUUU-GCUGUG---UUCCAAUUGU----------CGCAGUU-UUCG-A-GACCG--UUA---C----AC--GU-U-AC-CGCCAA-
CT573326.1/1493171-1493083     UUAUAUG-GCG-GC-UG--UAUG--UG-GGGCAC--UUCG-U-GUGC-GCCGGG---GUUUUGCUCUUG-----CUGACCGGUC-UGUC-A-ACCCA--UGU---A----CA--GC-U-GC-CACCC--
AP008232.1/2897417-2897333     ---AAUG-GUG-GC-UC--AGGC--GG-GGCAGCC-UAAG--GGCUG-GCCGGG---UUCCGAUACG----------ACCGGUAGUCUC-A-ACCCC--GUC---U----GG--GC-U-GC-CACCAAU
AAJV02000026.1/43700-43787     AAUUAUG-GUG-GG-GC--GUAU--GG-GGCCGAC-UUCG--GUCGG-GCCGGG---UUCUUUGCUA----------GCCGGUUGUGGA-A-ACCCU--GUA---C----GU--CU-C-AC-CACCCCG
CP000949.1/2235498-2235414     CGUUAUG-GCG-GC-UG--UGCG--UG-GGGCACC-UUCG--GGUGC-GCCGGG---UGCCUGACGU----------CCCGGUC-GGCU-A-ACCCG--CGU---A----CA--GC-U-GC-CACCC--
AACY022015598.1/415-329        UUUUAUG-GUG-GC-UG--UGCG--CA-GGGCACC-UUCG--GGUGC-GCCGGA--UUUACCUUGUG----------GCCGGUC-GACU-A-ACCUG--CGU---A----CA--GC-C-GC-CACCCA-
ABBD01000499.1/2644-2554       AUCAAUG-GGU-GG-GCCGUGGC--GG-GGAGACG-CUUG--CGUCU-GCCGGU---UUCCUGUAGG-----------CCGGUU-CGCC-A-ACCCU--GUC---AC-GUGC--CC-G-CC-CACCCCA
CP000949.1/761865-761777       CGUAAUG-GCG-GC-CC--UGCG--UG-GGCAGAC-CUCG--GUCUG-GCCGGA--UUUCCCAUGUU---------UACCGGUU-UCUC-A-CCCCA--CGC---A----UG--GC-U-GC-CACCCAA
AY374448.1/32623-32536         AAUUAUG-GUG-GC-UC--AGGC--AG-GGCAGCU-UUCG--GGCUG-GCCGGU---AGCUGAUUGG----------GCCGGUAUUCCU-A-CCCUU--GUC---U----GG--GU-C-AC-CACCAAC
CP001144.1/2177547-2177460     AAUUAUG-GUG-GG-CU--GGGU--GG-GGGCACC-GAAA--GGUGC-GCCGGU---UUCCGUAUGC----------GCCGGUUACGCC-A-ACCCU--GCU---C----AG--UU-C-AC-CACCAGC
CR522871.1/46573-46654         UUCUAGG-GCG-GG-CU--AUA---UGUGGGAGC--UUCG---GCUC-GCUGG----UUCCGGUGA------------CCAGCC-UACC-A-ACCCA---UA---U----AG-UCC-C-GC-CCUUUUU
ABCH01000029.1/41299-41379     GCCAAUG-GUG-GG-CU--GGAC--GA-GGCAGC--UUCG---GCUG-GCCGU----UUCCUUGAGU-----------ACGGUACUGCG-A-ACCUC--GUU---C----AG--UU-C-AU-CACC---
CP000572.1/114154-114063       UUCAAUG-GUC-GG-GCCUUGGU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UUCCUUGGAC----------GCCGGUU-CGCC-A-ACCCU--GUC---AU-GUGC--CC-G-GC-CACCCCA
CP000026.1/4467249-4467336     UGUAAUG-GUG-GC-UC--AGGC--GG-GGGCUUC-UCAC--GAAGC-GCCGGU---UUCCAAUGUU----------GCCGGUUACGCC-A-ACCCC--GUC---U----GG--GC-U-AC-CACCAGU
CP000521.1/98547-98462         CUUUGCG-GUA-GGACG--GGAG--GG-GGACGC--CCCG-C-GCGU-GCUGG----UUCUACGAGU-----------CCAGUC-UGUC-A-ACCCC--CUU---U----CG-UUC-U-AC-CACCCUA
AACY020973416.1/501-587        CUCAAUG-GUG-GC-UG--UACG--CA-GGGCACU-UUCG--GGUGC-GCCGGU---UUCGUUGAUC---------CGCCGGUC-UACU-A-ACCUG--CAU---A----CA--GC-C-GC-CACCCA-
CP000304.1/813410-813328       CUUUAUG-GGC-GG-GC--CGUG--CG-GGGCAUC-UUCG--GAUGC-GCCGG------CCCUCAG-----------ACCGGUA-CGCC-A-ACCCG--UGC---G----GU--CU-G-CU-CACCCAA
CP000513.1/1080812-1080727     UGUUAUG-GCA-GU-GU--GCGU--GG-GAGAACC-GCAA--GGUUC-GCCGU----UUCUUUCGU-----------AGCGGUAGUCUC-A-AUCCU--GCG---U----AC--AC-U-GU-CGCCCUC
CT573326.1/3518484-3518397     UGUCAUG-GCG-GC-UG--UGUG--UG-GGCAGGC-UUCG--GCCUG-GCCGGG---UUCCAAGUUU----------CCCGGUAUUCCU-A-CCCCA--CGC---A----CA--GC-U-GC-CACCCAA
AP008232.1/3106295-3106377     CUCAAUG-GUG-GG-CU--GGAU--GG-GGGAGCC-GAAA--GGCUC-GCCGG------AAGGUGAA----------CCCGGUAAGACC-A-ACUCC--GUU---C----AG--UU-C-GC-CACCC--
CP000783.1/2971361-2971274     UGUAAUG-GUG-GC-UC--AGGC--GG-GGCUGAC-UUCG--GUCAG-GCCGGU---AUCCGUUAGA----------GCCGGUAUUUCC-A-CCCCC--GUC---U----GG--GC-U-AC-CACCAGU
CU928161.2/566114-566201       AAUUAUG-GUG-GG-GC--GUGC--AG-GGGCAUC-GAAA--GAUGC-GCCGGG---GUCAUGUGCG----------ACCGGUUACGCC-A-ACCCU--GUA---C----GU--CU-C-AC-CACCUCU
CP000626.1/1033991-1033907     CAUUAUG-GUG-GG-CU--GGGC--AG-GGGCGC--UUCG---GCGC-GCCGUG---UUCCGAUAG-----------AGCGGUAGUACU-A-ACCUU--GUC---C----AG--UU-C-AC-CACCCAU
CP000712.1/93169-93257         GUCUAUG-GUG-GC-UG--UGCG--UG-GGAGGCU-UUCG--AGCCU-GCCUGG---AUUGGAAAAUG--------CCCGGGUC-UACC-A-CCUCG--CGU---A----CA--GU-C-GC-CACCCAU
CP000036.1/4221428-4221341     GUCAAUG-GUA-GC-UC--AGGC--GG-GGCAGCC-UCCG--GGCUG-GCCGGU---AUCCUGUGAA----------GCCGGUAUUCUC-A-CCCCC--GUC---U----GG--GC-U-AU-CGCCAUC
CP000529.1/1018953-1018867     GUUUUUG-GCG-GC-UC--GAA---UG-GGAGAGC-GCAA--GCUCU-GCCGGU---UUCCGCAAGGAU------GUCCCGGUU-CGUC-A-ACCCG---UU---C----GA--GC-U-GC-CGCCC--
CP000076.1/1157583-1157668     UGCAAUG-GCG-GC-UG--UGCG--UG-GGAGGG--CUCG-U-CCCU-GCCGGG---UUCCUGUAUC----------UCCGGUU-UACC-A-ACCUG--CGC---A----CG--GC-U-GC-CACCCAU
DQ126339.2/20363-20278         UAUUAUG-GUG-GG-CU--GUGU--GG-GGGCACC-GAAA--GGUGC-GCCGG----GUCCUUUUAG-----------CCGGUUACGCC-A-ACCCU--GCA---C----AG--UU-C-AC-CACCAAC
BX571870.1/266739-266822       CUCUAUG-GCG-GU-UC--AGGC--AG-GGGAGGU-UAAC--ACCUC-GCCGG------AAAUGAAC----------GCCGGUC-UGCA-A-ACCCU--GUU---U----GA--AU-C-GC-CACCACC
CP000926.1/2758723-2758809     UUUUAUG-GCG-GC-UG--UGCG--UA-GGGCGC-CUCCG-U-GCGC-GCCGGU---UUCCUUGAUU----------CCCGGUC-UACC-A-ACCUG--CGU---A----CA--GC-C-GU-CACCACU
AACY021510274.1/194-280        UUUGAUG-GUG-GC-UG--UGCG--UA-GGGCAUC-UUCG--GGUGC-GCCGGC--UUUGCGUUGUU---------CCCCGGUC-UACU-A-ACCUG--CGC---A----CA--GC-U-GC-CACCC--
CP000800.1/1422976-1422889     GAUUAUG-GUG-GG-AC--GUGC--AG-GGCAGCC-GCAA--GGCUG-GCCGGG---UUCGUUAGUG----------ACCGGUAUUUCC-A-CCCCU--GUA---C----GU--CU-C-AC-CACCCUU
AE014613.1/2741095-2741182     GUCAAUG-GUA-GC-UC--AGGC--GG-GGCAGCC-UCCG--GGCUG-GCCGGU---UUCCGAUAAC----------GCCGGUAUUCUC-A-CCCCC--GUC---U----GG--GC-U-AU-CGCCAUC
AF157835.1/28158-28072         AUCAAUG-GUG-GG-CU--GGAU--GG-GGGAGCC-GAAA--GGCUC-GCUGG----GUCCUUGUUA----------GCCGGUAGUCUC-A-ACCCU--GUU---C----AG--UU-C-AC-CGCCAAU
AACY023455698.1/1534-1447      UGUUAUG-GCG-GU-UC--GGGC--GA-GGGCCUC-GAAA--GGGGC-GCUGGG---UUCCGUAGUG----------ACCAGUUACGCC-A-ACCUU--GUC---C----GG--GC-U-GC-CACCAGU
CP001068.1/3611015-3610928     UUCAAGG-GCG-GG-CC--GGGU--GG-GGAGACC-UUCG--GGUCU-GCCGGU---GCUCCAGAGA----------ACCGGUU-CGCU-A-CCCCC--GCCGUCU----GG--CC-C-GC-CACCC--
AAKB02000001.1/3918608-3918695 AAUUAUG-GUG-GG-CU--GGGC--AG-GGGAGCC-GAAA--GGCUC-GCCGGU---UUCCUUGAUC----------GCCGGUAGUUCC-A-ACCCU--GUU---C----AG--UC-C-GC-CACCAGC
CP000946.1/1150557-1150470     GUCAAUG-GUA-GC-UC--AGGC--GG-GGCAGCC-UCCG--GGCUG-GCCGGU---UUCCGAUAAC----------GCCGGUAUUCUC-A-CCCCC--GUC---U----GG--GC-U-AU-CGCCAUC
CR543861.1/3357993-3358079     CUUUGCG-GUA-GAACG--GGAG--GG-GGACGCG-UCCG--CGCGU-GCUGG----UUCUGUAUGU-----------CCAGUC-UGUC-A-ACCCU--CUU---U----CG-UUC-U-GC-CACCAUA
CP000712.1/1545409-1545496     UUCAAUG-GUG-GC-UG--UGCG--UG-GGGCGCC-UUCG--GGUGC-GCCGGG---UUUCUCAAUUU--------GACCGGUC-UGUC-A-ACCCG--UGC---A----CA--GC-U-GC-CACCCU-
AACY023588064.1/172-86         GUUUAUG-ACG-GC-UG--UGCG--CG-GGAGACC-UUAG--GGUCU-GCCGGU---UUUCUCUACU----------GCCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GU-CACCCAU
AJ560763.1/6364-6280           GUCAAUG-AUG-AA-CU--GGUU--GA-GGGAUC--GAAA---GAUC-GCCGUU---UACACCGUGU----------UACGGUA-CGCC-A-ACCUU--GAU---C----AG--UU-C-AU-CACCAGU
AP008234.1/16189-16105         AUCUAUG-GUG-GG-CU--GGAU--GG-GGGAGCC-GAGA--GGCUC-GCCGUU---UACUUGUAU------------CCGGUUGUUAG-A-ACCCU--GUU---C----GG--CU-C-AC-CACCAA-
AATN01000346.1/4921-5003       AGUUAUG-GGC-GG-UC--GUG---UG-GGGCAUC-UUCG--GGUGC-GCCGG----UUCCUAUUC------------CCGGUC-UUCC-A-ACCCG---CA---C----GG-CCU-G-CC-CUCCCCG
CP000075.1/363735-363830       GUUUAUG-GCG-GC-UU--UGCG--UG-GGGCACC-UUCG--GGUGC-GCCGGU---UGCUUGCGCUUGUU--CCACACCGGUC-UGCU-A-ACCCG--CGU--CA----AA--GU-C-GC-CACCCUU
CP000949.1/97824-97912         GUCUAUG-GCG-GC-UG--UGCG--CG-GGAGGCU-UUCG--AGCCU-GCCUGG---AUUGGAAAAUG--------CCCGGGUC-UACC-A-CCUCG--CGG---A----CA--GU-C-GC-CACCCAA
CP000958.1/2782600-2782509     UUCUAUG-GUC-GG-GCCUUGGU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UCCCUUGGAC----------GCCGGUU-CGCC-A-ACCCU--GCC---UU-GUGC--CC-G-GC-CACCCCA
AACY022740819.1/172-86         CGCUAUG-GUG-GC-UG--UGCG--CG-GGAUACC-UUCG--GGUAU-GCCGGU---UUCCUUAAUC----------UCCGGUC-CGCG-A-ACCUG--CGC---A----CA--GC-U-GC-CACCCUC
CP000266.1/2768141-2768228     AAUUAUG-GUG-GG-GC--GUGC--AG-GGGCAUC-GCAA--GAUGC-GCCGGG---UUCUAUGUUG----------ACCGGUUACGCC-A-ACCCU--GUA---C----GU--CU-C-AC-CACCUCU
AAZE01000005.1/1255-1340       CCCAAUG-AUG-AA-CU--GUUU--AG-GAGGAUC-GAAA--GAUCC-GCCGUU---UUGCUCUAAG----------UACGGUACUGCG-A-AUCCU--AUU---C----AG--UU-C-AU-CACCA--
AF009672.1/1403-1489           CUCUAUG-GUA-GGGCG--GAAG--GG-GGACGCG-CUUG--CGCGU-GCUGGU---UUCUUUGUUU----------GCCAGUC-UGUC-A-ACCCU--CUU---U----CG-UUC-U-AC-CACCC--
ABBD01000806.1/5334-5425       UUCAACG-GUC-GG-GCCUUGGC--GG-GGGUGCC-CUCG--GGCAC-GCCGGU---UUCCGUUUUC----------GCCGGUA-CGCC-A-ACCCU--GUC---AU-GUGC--CC-G-GC-CACCCCA
CP000282.1/342124-342208       UGCUAUG-GUG-GG-CU--GUAU--GG-GGCACCC-UUAG--GGGUG-GCCGC----UUCCUUGUGU-----------GCGGUAGUCUC-A-ACCCU--GUG---C----AG--CC-C-AU-CACCAU-
CP000949.1/4993676-4993591     UGUAAUG-GCG-GC-UG--UGCG--UG-GGAGACC-CUCG--GGUCU-GCCGGG---UUCCUUUUCC-----------UCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GC-CACCCUA
AACY020355503.1/7049-6960      UUCAAUG-GGC-GG-GC-CGUGG--UG-GGGAGCC-GCAA--GGCUC-GCCGGU---UUGUUUUCGA----------CCCGGUC-UGCU-A-ACCCG--CUU---CG--UGC--CC-G-CU-CACCCUU
CP000616.1/633610-633518       UUCUAUG-GGC-GG-GCCUGGGU--GG-GGAGACC-UUCG--GGUCU-GCCGGU---GUUCAUUAGC---------CGCCGGUU-CGCC-A-ACCCC--GCU---CU-GCGC--CC-G-CU-CACCCCG
CT573326.1/3291941-3291852     CGUUAUG-GCA-GC-UG--UGCG--UG-GGGCAC--CUCG-U-GUGC-GCCGGU---UUCUGGUCUUGU------UCACCGGUC-UGUC-A-ACCCA--UGU---A----CA--GC-U-GC-CACCUUC
CP000075.1/5828644-5828559     CUCUAUG-GCG-GC-UG--UGCG-UGA-GGGCACU-UUCG--GGUGC-GCCGG------UCUUAGCU----------CCCGGUC-GACU-A-ACCUU-UCGC---A----CA--GC-U-GC-CACCUCA
CP000949.1/4567808-4567894     CGUCAUG-GCA-GU-UG--UGCG--CG-GGAGGC-CGCAA-A-GCCU-ACCGGG---UUUACUCGUA----------GCCUGGA-UUCC-A-CACCG--CGU---A----CA--AC-U-GC-CACCCAU
AACY022950291.1/288-376        AGUUAUG-GCG-GC-UG--UGCG--CU-GGAGACC-UUCG-GGGUCU-GCCGGG---UUUCCUUUGC----------CCCGGUC-UUGC-ACACCUG--CGU---A----CA--GC-U-GC-CACCCUC
AP008232.1/1233127-1233043     CUCAAUG-GUG-GA-CU--GGAU--AG-GGCUACC-GAAA--GGUAG-GCCGG------ACGGUGAA----------CCCGGUAGUAUC-A-ACCCU--GUU---C----AG--UU-C-AC-CACCAAU
AAJX02000004.1/60275-60362     AAUUAUG-GUG-GG-GC--GUAC--AG-GGGCAUC-GCAA--GAUGC-GCCGGU---AAGGGUAGCC----------GCCGGUAACGCC-A-ACUCU--GUA---C----GU--CU-C-AC-CACCUCU
CT573326.1/619442-619529       AGUCAUG-GCA-GC-UG--UGCG--CG-UGCAGGC-UUCG--GCCUG-GCCGUG---GUGUUCGGGA----------CACGGUCUUCUC-A-CCUCG--CGC---A----CG--GC-U-GC-CACCCAC
AL646052.1/3705084-3704998     UUCUAUG-GCG-GG-CC--GGGU--GA-GGAGACC-UUCG--GGUCU-GCCGG----UUUCUUGGAG----------GCCGGUU-CGCC-A-GCCUC--GCCG-UC----GG-GCC-C-GC-CACCU--
AACY020312264.1/460-372        CUUGAUG-GUG-GC-UG--UGCG--CA-GGGCGUC-CUCG--GGCGC-GCCGGC---UUUGUGUGUUU--------CCCCGGUC-UACU-A-ACCUG--UGC---A----CA--GC-U-GC-CACCCUU
AACY021328634.1/148-66         UUUCAUG-GUG-GC-UG--UGCG--CG-GGAGACC-UUCG--GGUCU-GCCGG----UUCCAUUC-------------CCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GC-CACCCAA
AATN01001375.1/3013-2929       GUCUAUG-UGG-GA-CU--GUGC--GG-GGCAGCC-UUCG--GGCUG-GCCGG----UUCGUAUGCU-----------CCGGUAUUUCC-A-CCCCC--GUA---C----AG---C-U-CC-CGCCCUU
AE015451.1/5989252-5989335     CGUUAUG-GCA-GU-UG--UGCG--CG-UGAGGCC-GUUU--GGCCU-ACCGGC---UUGCCUUCUC----------ACCGGUU-UUCC-A-CCCCG--CGC---A----CA--AC-U-GC-CGCC---
ABWV01000003.1/33677-33592     CCCAAUG-AUG-AA-CU--GUUU--AG-GAGGAUC-GAAA--GAUCC-GCCGUU---UUGCUCUAAG----------UACGGUACUGCG-A-AUCCU--AUU---C----AG--UU-C-AU-CACCA--
CP000521.1/2055349-2055265     CGUAGCG-GUA-GGACG--GGAG--AG-GGACACC-UUUG--GGUGU-GCUGG----AGUCUUAA-------------CCAGUC-UGCG-A-ACCCU--CUU---U----CG-UUC-U-GC-CACCAUA
CU914168.1/3177813-3177725     GUGCAUC-GCG-GG-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGG----UUUCUACGUU----------GCCGGUU-UUCG-A-CCCCC--GCUGUCU----GG--CC-C-GC-CACCCCU
AAKB02000001.1/4316512-4316599 AAUUAUG-GUG-GG-CU--GGGC--AG-GGGAGCC-GAAA--GGCUC-GCCGGU---UUCCUUGAUC----------GCCGGUAGUGCA-A-ACCCU--GUU---C----AG--UC-C-GC-CACCAGC
AP008233.1/13096-13181         AACAAUG-GUG-GC-UC--AGGC--GG-GGCACCC-GUAA--GGGUG-GCCGGU---AUCCAAGGAA----------GCCGGUU-UCUC-A-CUCCU--GUC---U----GG--GC-U-AC-CACCUC-
CP001113.1/2762799-2762716     AAUUAUG-GUG-GG-GC--GUAU--GG-GGGAGCC-GAAA--GGCUC-GCCGG------UCGGUGAU-----------CCGGUUACGCC-A-ACCCU--GUA---C----GU--CU-C-AC-CACCCAA
CP001164.1/2702471-2702389     AAUUAUG-GUG-GG-CU--GUGU--GG-GGGCGGA-GAGA--UCCGC-GCCGG------UCGGUUUC-----------CCGGUUACGCC-A-ACCCU--GCA---C----AG--UU-C-AC-CACCAG-
CT573326.1/427349-427440       UGUUAUG-GCA-GC-UG--UGCG--CG-GGCAGGC-UUU---GCCUG-GCCGGA---AUGUAGCCUCCAA---CUUCGCCGGU--UCUC-A-CCCCG--CGC---A----UG--GC-U-GC-CACCCAU
CP000521.1/2365091-2365008     UGUUAUG-GUG-GG-UU--AGGC--GG-AAGUGC--UUCG---GCAC-GCUAG----ACCCUUGAG-----------ACUAGUAAGACC-A-AUUCC--GUU---U----AA--CC-U-GC-CACCCUA
AAKB02000001.1/3306985-3306902 CAUUAUG-GCG-GG-CU--GGC---GG-GGGCGC--UUCG---GCGC-GCCGGU---UUCCUCUAAC----------GCCGGUAUUGCA-A-ACCUC---GU---C----AG--UU-C-GC-CACCCAU
CP000949.1/4793577-4793664     AGUUAUG-GCG-GC-CG--UGCG--UG-GGCAGAC-UUCG--GUCUG-GCCGGG---GCCCUUCUUG----------CCCGGUAUUCCU-A-CCCCA--CGC---A----UA--GC-U-GC-CACCCAA
CU928162.2/2571954-2572041     AUCAAUG-GUG-GG-CU--GUAC--GG-GGGCGGA-GCAA--UCCGC-GCCGGU---UUCUUCAGUG----------UCCGGUAAGGCU-A-ACCCU--GUA---C----AG--UC-C-GC-CACCAGC
CP001172.1/278092-278175       CGUAGCG-GUA-GGGCG--AGGG--AG-GGACGC--CUUG-U-GCGU-GCUGA----UUCUUGUGUG-----------UCAGUC-UGUC-A-ACCUU--CUC---U----CG-UUC-U-AC-CACCA--
CT573326.1/791092-791007       UGUAAUG-GCG-GC-UG--UGCG--UG-GGAGACC-UUCG--GGUCU-GCCGGG---UUCCUUUUCC-----------UCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GC-CACCCUA
CT573326.1/4670418-4670332     UGCUAUG-GCA-GC-CG--UGCG--CG-GGCAGG--UUCG-U-CCUG-ACCGGU--UUUCCUUCGUG----------GCCGGGU-UCUC-A-CUCCG--CGC---A----UG--GC-U-GC-CACCCAA
CP000783.1/596095-596008       AAUUAUG-GUG-GC-UC--AGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---UUCCAAUAAG----------GCCGGUAUUCCU-A-CCCCC--GUC---U----GG--GC-U-AC-CACCCUU
AM286415.1/2104229-2104144     AGAAAUG-GUG-AG-CU--GGGC--GG-GGGCAUC-GUAA--GGUGC-GCCAG----UUUUUGGGUG----------ACUGGUC-UGUC-A-ACCCC--AUC---C----AG--CU-C-AG-CACCUAC
AAUU01000060.1/5711-5630       AAUUAUG-GUG-GG-CU--GGGC--GA-GGCAGC--UUCA---GCUG-GCCGU----UUCCAAGGUU-----------GUGGUAGGACU-A-ACCUC--GUU---U----AG--UU-C-AC-CACCA--
AACY022036859.1/446-363        AAUAAUG-GUG-GC-UC--AGGC--GG-GGGCUUC-GUAA--GAAGC-GCCGG----UUCGUAUGUC-----------CCGGUGACGCU-A-ACCCC--GUC---U----GG--GC-U-AC-CACCC--
CP000468.1/2745296-2745380     UAUUAUG-GUG-GG-CU--GUGU--GG-GGGCACC-GAAA--GGUGC-GCCGGG---UCCUUUUAG------------CCGGUUACGCC-A-ACCCU--GCA---C----AG--UU-C-AC-CACCAA-
AE004091.2/1348513-1348430     CUUCAUG-GCG-GA-UC--GCGU--GG-GGAGACC-CUCG-UGGUCU-GCCGG----UUCCGUUUC------------CCGGUC-UGUC-A-ACCCU--GCG---C----GA--UC-CUGC-CUCCA--
CT573326.1/28932-29019         GUCUAUG-GCG-GC-UG--UGCG--CG-GGAGGCU-UUCG--AGCCU-GCCGG----GUCUGGUACCU--------CCCCGGUU-UACC-A-CCCCG--UGU---A----CA--GC-U-GC-CACCCAU
AP008232.1/444749-444836       UAUAAUG-GUG-GGACG--UAAC--GG-GGGAGCC-UUCG--GGCUC-GCCGG----CUUCAUCUUCU-------UCACCGGUA-UGCU-A-ACCCC--GAU---A----CG-UCU-C-GC-CACC---
CP000076.1/6960256-6960341     AUCUAUG-GCG-GC-UG--UGCG--UA-GGGCACC-UUCG--GGUGC-GCCGG----UUCCUUUAGC-----------CCGGUC-UUCC-ACACCUG--CGC---A----CG--GC-U-GC-CACCCUC
CP000034.1/2215306-2215222     AUUUAUG-GUG-GG-CU--GUGU--GG-GGGAGCC-GAAA--GGCUC-GCCGGU---UUCCGUAC-------------CCGGUAGUCUC-A-ACCCU--GCA---C----AG--CU-C-GC-CACCAGA
CP000076.1/2447607-2447522     UGUUAUG-GCG-GC-UG--UGUG--CG-GGACACC-UUCG--GGUGU-GCCGG----UGUCGUUGUA----------GCCGGUC-GGCC-A-ACCCU--CGC---A----CA--GC-U-GC-CACCCUC
CP000926.1/1232976-1232891     CGUCAUG-GCA-GU-UG--UGCG--CG-GAAGGC-CGCAA-A-GCCU-ACCGGG---UUUGCUCGUA----------GCCUGGA-UUCC-A-CACCG--CGU---A----CA--AU-U-GC-CACCCU-
AATN01000261.1/4595-4680       GUCUAUG-UGG-GA-CU--GUAC--GA-GGCAACC-UUCG--GGUUG-GCCGG----UGCUUGGUAG-----------CCGGUUGUUGC-A-ACCUC--GUA---C----AG-CUC-C-CG-CACCUC-
AM260480.1/532510-532418       GUUUUUG-GCG-GG-CC--GGGC--GG-GGCAGCC-GAAA--GGCUG-GCCGGA---UUACUCUGUGA-------AGACCGGUU-UGGU-A-CCCCC--GCUGUCU----GG--CC-C-GC-CACCCUU
CP000076.1/4859973-4859886     UGUUAUG-GCG-GC-CG--UGCG--CG-GGAGAUC-UUCG--GAUCU-GCCGGG---GUUCUGGUAA----------CUCGGUC-UUGC-ACACCCG--CGU---A----CG--GC-U-GC-CACCUUA
CT573326.1/5667972-5667886     CUCCAUG-GCA-GC-CG--CACG--CG-GGCAGGC-UUCG--GCCUG-GUCGGG--UUUCCUAUUGG----------CCCGGG--UCUC-ACCCCCG--CGU---G----UU--GC-U-GC-CACCAU-
CP000744.1/373488-373402       AGUUAUG-GCG-GC-UG--UGCG--CG-GGGCACC-UUCG--GGUGC-GCCGGG---UUCCUUUGUC----------CCCGGUC-UGCU-A-ACCCG--CGU---A----CA--GC-U-GC-CUCCCAU
CP000076.1/6137446-6137360     CUUAAUG-GUG-GGCUG--UGCG--CG-GGACACC-UUCG--GGUGU-GCCGGG---UGCCUUCUUC-----------CCGGUU-GACC-A-ACCUG--UGC---A----CA-GUC-C-GC-CACCCA-
CP000946.1/1840817-1840905     CUCAAUG-GUG-GGAUC--GGGC--GG-GGGCGUC-GUAA--GACGC-GCCGG----UGUCAGUGAG----------GCCGGUAAUGCC-A-ACUCC--GUC---C----GG-UUU-C-AC-CACCCGU
ABFH02000001.1/1900935-1901022 CUCAAUG-GUG-GG-CC--GGGC--GG-GGGCGCU-GCAA--AGCGC-GCCGG----UGUCGAUGAG----------GCCGGUAAGGUC-A-ACCCC--GUC---C----GG-UUC-C-AC-CACCCGC
CT573326.1/980078-980164       CUUCAUG-GCA-GC-CG--UGUU--CG-GGCAGAC-CUCU-GGUCUG-GCCGGG---UUUCAUGUCC-----------UCGGUU-UCUC-A-CCCCG--UAC---A----CG--GU-U-GC-CACCCAA
L31763.1/8697-8777             ---UAUG-GCA-GC-AU--ACGU--GG-GAGAACC-GAAA--GGUUC-GCCGU----UCCUUGUGU-----------AGCGGUAAGGUC-A-AUCCU--GCG---U----AU--GC-U-GU-CGCCC--
CP000521.1/1469454-1469538     CGUAGCG-GUA-GGACG--GAGG--UG-GGACGC--CUUG-U-GCGU-GCCGG----UUUCUAGAUG----------ACUGGUC-UGUC-A-ACCCG--CCU---U----CG-UUC-U-AC-CACCA--
CT573326.1/5708208-5708293     CGUAAUG-GCA-GU-UG--UAUG--CG-GGAGGCC-UCU---GGCCU-ACCGGG---UGACCUUCUU----------UCCGGAU-UUCC-A-CCCCG--UGU---A----CA--AC-U-GC-CGCCCUC
AAKB02000001.1/4317534-4317620 AAUUAUG-GUG-GG-GC--GUGC--AG-GGCCAAC-UUCG--GUUGG-GCCGGG---UUCUUUGGUG----------ACCGGUU-UCUC-ACCCC-U--GUA---C----GU--CU-C-AC-CACCUAU
CP000521.1/1492888-1492976     CUUUCUG-GUA-GA-GU--GAAA-AGG-GGAUAUC-UUUU-GGAUGU-GCCAG----UUUCUAGAUG----------UCUGGUC-UGCU-A-ACCCU-UCUU---C----AC--UC-U-AU-CAUUGUC
AE016825.1/675562-675477       UUCUAUG-GCG-GGCCG--UGGU--GG-GGAUACC-UACG--GGUAU-GCCGG----UUCCUUACUG-----------CCGGUU-CGCC-A-ACCCU--GCC---A----UGCGCC-C-GC-CACCC--
BX571965.1/1334602-1334513     UUCUAUG-GGU-GG-GCCAUGGC--GG-GGGAGCG-CUCG--CGCUC-GCCGG----UGCCAACGUU-----------CCGGUC-UGUC-A-ACCCU--GUC---AU-GUGC--CC-G-CC-CACCCCA
AJ868436.1/1478-1562           AUCUAUG-GUG-GG-CU--GGAU--GG-GGGAGCC-GAGA--GGCUC-GCCGUU---UACUUGUAU------------CCGGUUGUUAG-A-ACCCU--GUU---C----GG--CU-C-AC-CACCAA-
CP000644.1/3150898-3150985     CGUUAUG-GCG-GU-UC--GGGU--GA-GGGCCCC-GCAA--GGGGC-GCUGGA---CUCCAAGGUC----------UCCAGUUACGCC-A-ACCUC--GUC---C----GG--GC-U-GC-CACCAGA
AACY020847254.1/17-105         UACUUUG-GCG-GG-CC--GGAU--GG-UGAGACC-UCCG--GGUCU-ACCGGU---UUCCUUGGG-----------ACCGGGU-CGCU-A-ACACC--AUCG-UC---AGG--CC-C-GC-CACCCUC
CP000949.1/5447594-5447505     UGUUAUG-GCG-GU-CG--UACG--CG-GGCAGAC-UUCG--GUCUG-GCCGAG---CUUUGUAGCUC--------CCUCGGUUUUCUC-A-CCCCG--CGU---A----UG--AC-U-GC-CACCUAG
ABAN01000056.1/12998-12911     AAUUAUG-GUG-GG-CU--GGGU--AG-GGGCACC-GAAA--GGUGC-GCCGGU---UUCCGAUAAC----------GCCGGUUACGCC-A-ACCCU--GCU---C----AG--UU-C-AC-CACCAGU
Z23101.1/937-1024              GAUUAUG-GUG-GG-GC--GUGC--AG-GGCAGCC-GCAA--GGCUG-GCCGGU---UUCGGUAGUC----------ACCGGUUGUAGC-A-ACCCU--GUG---C----GU--CU-C-AC-CACCCAU
AAMJ02000035.1/3716-3799       AUUUAUG-GUG-GG-CU--GUGU--GG-GGGAGUU-GAGA--GACUC-GCCGG----AUGUUUCGA------------CCGGUUACGCC-A-ACCCU--GCA---C----AG--UU-C-AC-CACCCA-
AP008232.1/3395263-3395347     AUCAAUG-GUG-GG-CU--GGAU--GG-GGCAGCC-GUCA--GGCUG-GCCGG------AUGACAAU----------CCCGGUACUGCG-A-ACCCU--GUU---C----AG--UU-C-AC-CACCAGU
CP001111.1/1890579-1890487     CUUCCUG-GCG-GG-CG--GUGC--GU-GGGGGCC-CUCG--GGCCC-ACCGG------UCUAUGGUGCUAUUUCAUCCCGGU--UUGC-A-GCCAC--GCA---U----CG--UC-C-GC-CACCUCU
AATO01009354.1/30-113          AGUUUCG-GGC-GG-GC--CGUG--CG-GGAGACC-UUCG--GGUCU-GCCGG----UUCCUGUAU------------CCGGUU-CGCC-A-ACCCG--CAC---G----GU-UCC-G-CC-CACCCG-
AL646052.1/3475955-3475871     AAGCGCC-GCG-GG-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---UUCUACGUUU-----------CCGGUU-UGUC-A-CCCCC--GCCGUCU----GG--CC-C-GC---CCC--
AACY021637507.1/420-335        UGUAAUG-GCG-GC-UG--UGCG--UG-GGAGACC-UUCG--GGUCU-GCCGAG---UUCCUUUUCC-----------UCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GC-CACCCUA
CP000949.1/4843174-4843087     UUUCAUG-GCA-GC-CG--UGCG--UG-UGCGGGC-UUCG--GUCCGGGCCGCG---GUUCCUGGAC-----------GCGGUCUUCUC-A-CCUCG--CGU---A----CG--GC-U-GC-CACCCAA
ABFG01000007.1/330034-330119   UAUUAUG-GUG-GGGCG--UAAC--GG-GGGAGCG-UUCG--CGCUC-GCCGG----UUCCGUUGAU----------GCCGGUC-UGCU-A-ACCCU--GUU---A----CG-UCU-C-AC-CACCC--
CP000038.1/1984424-1984511     CAUUAUG-GUG-GG-GC--GUGC--AG-GGGCGGA-GAAA--UCCGC-GCCGGG---UUUUGUGAUG----------ACCGGUUACGCC-A-ACCCU--GUA---C----GU--CU-C-AC-CACCUCC
AP008232.1/1814121-1814038     CUCAAUG-GUG-GG-CU--GGAU--GG-UGGAGCC-GAAA--GGCUC-ACCGG------UUGGUUAC----------UCCGGUA-CGCG-A-ACUCC--GUC---C----AG--CU-C-GC-CACCCUC
CP000103.1/68166-68083         UUUUACG-GGC-GG-GU--CGUG--UG-GGGAGCC-UUCG--GGCUC-GCCGG----UUCCUUUGU------------CCGGUA-CGCC-A-ACUCG--CAC---G----AU-UCC-G-CC-CACCCG-
CP000058.1/5451361-5451443     UUUUAUG-GUG-GU-CG--UGCG--UG-GGGCAUC-UUCG--GAUGC-ACCGGG---GUUCCUGGA------------CCGGGC-UACU-A--CCUG--CGC---A----UG--AU-C-AC-CACCCU-
CU914168.1/48873-48786         UUCCAUG-GCG-GG-CC--GGGU--GA-GGAGACC-UUCG--GGUCU-GCCGG----UUUCUUGGAG----------GCCGGUU-CGCC-A-GCCUC--ACCG-UC----GG-GCC-C-GC-CACCUC-
CP000546.1/1333874-1333783     AUCAAUG-GGU-GG-GCCUUGGC--AG-GGAGACC-UUCG--GGUCU-GCCGGU---UGCCUCCUAU----------GCCGGUU-CGCC-A-ACCCU--GCC---UU-GUGC--CC-G-CC-CGCCCAU
CP000521.1/1060224-1060139     CGUUGCG-GUA-GGACG--GGAG--GG-GGACGCG-CUCG--CGCGU-GCUGG------UCUGUAUA----------CCCAGUC-UGUC-A-ACCCC--UUC---U----CG-UUC-U-AC-CACCCUA
AE008922.1/3556259-3556339     UUCUAUG-GCG-GG-CG--GUG---CGUGGAGGGC-UUCG--GCCCU-GCCGG----UUCCGUUUGU-----------CCGGUC-UGCC-A-ACCCG---CA---C----CG--UC-C-GC-CACC---
CP000090.1/2423671-2423759     UUCUAUG-GCG-GG-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGG----UACCUUGUGC----------GCCGGUU-UUCG-A-CCCCC--GCUG-UC----GG-GCC-C-GC-CACCCCU
ABBM01000179.1/20561-20652     UUCAACG-GUC-GG-GCCUUGGC--GG-GGGUGCC-CUCG--GGCAC-GCCGGU---UUCCGUUUUC----------GCCGGUA-CGCC-A-ACCCU--GUC---AU-GUGC--CC-G-GC-CACCCCA
AE009952.1/2450258-2450171     AACAAUG-GUG-GG-GC--GUAC--GG-GGGAGCU-GAAA--GGCUC-GCCGGG---UGUUGUUGUG----------ACCGGUAGUGCA-A-ACCUC--GUA---C----GU--CU-C-AC-CACCCAA
AAMM02000028.1/49678-49767     AUCAAUG-GGU-GG-GCGACGGU--GG-GGAGGC--UUCG---GCCU-GCCGGU---UCCCUUGGAC----------GCCGGUC-UGCA-A-ACCCU--GCC---GU-CUGC--CC-G-CC-CACCCCA
AACY021190852.1/472-555        CUUUAUG-GCA-GC-UG--UGCG--CG-GGAGACC-UUCG--GGUCU-GCCGG----AACUCGGUC------------CCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GU-CACCCAU
CP000712.1/4379908-4379996     UGUCAUG-GCA-GU-CG--UACG--CG-GGCAGAC-UUCG--GUCUG-GCCGAGC-CUUGUAGCUCC----------CUCGGUU-UCUC-A-CCCCG--UGU---A----CG--AC-U-GC-CACCCUG
CP001063.1/714668-714581       AUCAAUG-GUG-GG-CU--GUAU--GG-GGCUGAC-UUCG--GUCAG-GCUGGU---CUCCUUUUGC----------GCCAGUUGUGGU-A-ACCCU--GUA---C----AG--UC-C-AC-CGCCAGC
CP000058.1/5617115-5617032     CUUUAUG-GCG-GC-UG--UGCG--CGAGGGCACC-UUUG--GGUGC-GCCGG------UCUUAGCU----------CCCGGUC-GACU-A-ACCUU--CGC---A----CA--GC-U-GC-CACCUC-
EU871626.1/6976-7063           GUCAAUG-GUA-GC-UC--AGGC--GG-GGCAGCC-UCCG--GGCUG-GCCGGU---AUCCUGUGAA----------GCCGGUAUUUCC-A-CCCCC--GUC---U----GG--GC-U-AU-CGCCAUC
CT573326.1/4960291-4960206     UGCCAUG-GCG-GC-UG--UGCG--CG-GGAGACC-UUCG--GGUCU-GCCGGG---UUCCAAGUUC-----------CCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GC-CACCCAU
AACY022552370.1/497-410        AUUUAUG-GCG-GG-CC--GUGU--GA-GGCAGGC-UUCG--GCCUG-GCCGGC---GUCCUUCGUG---------GGUCGGUC-UACC-A-CCCUU--GCA---C----GG--UC-C-GC-CUCCAUA
CP000863.1/1529352-1529265     UUUGAUG-GAG-GAACG--GGAG--UG-GGACACC-CUUG--GGUGU-GCUGG----UUUCUUAGGU----------AUCAGUC-UGCU-A-ACCCU--CUU---U----CG-UUU-C-GC-CACCAUA
AM260480.1/273927-274013       -UCCAUG-GGC-GG-GCCAUGGC--GG-GGGAGCC-CUCG--GGCUC-GCCGG----CUCCUUCUC-----------ACCGGUC-UGCU-A-ACCCU--GCC---UU-GCGC--CC-G-CC-CGCCC--
BX571861.1/290384-290469       AGUAAUG-GUG-GU-UC--AGGC--GG-GGGAGGC-UUCG--GCCUU-GCCGGA---AGGUAGCUA------------CCGGUACUGUG-A-ACCCU--GUC---U----GA--AU-C-AC-CAUCAUC
CT573326.1/4355591-4355676     CCUCAUG-GCG-GC-AG--UACG--UG-GGGCAC--CUCG-U-GUGC-GCCGGG---UCUCGGAGUC----------CUCGGUC-UGUC-A-ACCCA--CGU---A----CC--GC-U-GC-CACCCUC
CP000653.1/3381272-3381359     UGUAAUG-GUG-GC-UC--AGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---UCUCAUAGUU----------ACCGGUAUUCCU-A-CCCCC--GUC---U----GG--GC-U-AC-CACCCAU
AACY022978821.1/658-747        AUCAAGG-GCG-GG-CC--GGGC--GG-GGAGACC-UUCG--GGUCU-GCCGGU---GCUCCAGAGA----------GCCGGUU-UGCU-A-CCCCC--GCCG-UC---AGG--CC-C-GC-CACCCGU
CT573326.1/5582506-5582595     CUCUAUG-GCG-GC-UG--UGCG--UGCGGGCACG-CUUG--CGUGC-GCCGGA---AUUUUACGAUUU------UCGCCGGUC-UGUC-A-ACCCA--CGC---A----CA--GC-U-GC-CACCC--
CP001408.1/11522-11431         UUCAAUG-GUC-GG-GCCUUGGU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UUCCUUGGAC----------GCCGGUU-CGCC-A-ACCCU--GUC---AU-GUGC--CC-G-GC-CACCCCA
AACY022724003.1/39-129         CUUUAUG-GCG-GC-UG--UGCG--CG-GGAGACC-UUCG--GGUCU-GCCGG------CCUUUGCUUUA---UUUCACCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GC-CACCCAU
CP000034.1/553748-553664       AUUUAUG-GCG-GG-CU--GUGU--GG-GGGAGCC-GAAA--GGCUC-GCCGGU---UUCCGUAC-------------CCGGUUACGCC-A-ACCCU--GCA---C----AG--UU-C-GC-CACCAGU
CP001172.1/3057352-3057269     CAUUAUG-GUA-GGGUG--AAAG--UGGGGACGC-CUCUG-U-GCGU-ACUGG----UUCUUGAG-------------UCAGUC-UGCU-A-CUCCA--CUU---U----UG-UCC-U-GU-CACCA--
CP000618.1/216892-216802       UUCAAUG-GGC-GG-GCCUGGGU--GG-GGCGACC-UUCG--GGUCG-GCCGGU---UUCUUUGGUU-----------CCGGUU-CGCC-A-ACCCU--GCC---UU-GCGC--CC-G-CU-CACCCCA
AASA01000084.1/6161-6256       GUCUAUG-GUA-GC-GU--GUAG--CG-GGCAAGG-UUCG-CCCUUG-GCUGUU---UUUGGUUCGCCGU---UUGUAGCAGUUUUCUC-A-CCCCG--UUA---C----AC--GC-U-AU-CGCCCUG
CP000076.1/5731958-5732043     UUUUAUG-GUG-GC-UG--UGCG--UG-GGAGACC-UUCG--GGUCU-GCCGGG---UUCCUUUUCC-----------CCGGUU-CGCC-A-ACCUG--CGC---A----CA--GC-U-GC-CACCCUA
CP000749.1/652730-652647       CGUUAUG-GUG-GU-UG-UGCGU--GG-GGAGAC--UUCG---GUCU-GCCAGG---UACCUUGUG-----------ACUGGUC-UGCU-A-ACCCU--GCG---U---GCA--GC-C-AC-CACCC--
CR543861.1/2750060-2750143     CUCUGCG-GUA-GAACG--GGAG--GG-GGACACC-UUCG--GGUGU-GCUGA----UUCUUAGGU------------UCAGUC-UGCU-A-ACCCC--CUU---U----CG-UUC-U-GC-CACCA--
AP008232.1/1663464-1663548     AAUUAUG-GUG-GGGCG--UAAC--GG-GGGAGCG-CUUG--CGCUC-GCCGGG---UUCUGUGUGG-----------CCGGUC-UGUC-A-ACCCU--GUU---A----CG-UCU-C-GC-CUCC---
CP000749.1/619642-619558       CUUUAUG-GUG-GC-UG-UGUGU--GG-GGAGAC--UUCG---GUCU-GCCAGC---UUUCGUUUUG----------ACUGGUC-UGCU-A-ACCCU--GUA---C---GCA--GC-C-AC-CACCU--
CP000151.1/2729355-2729271     UUCUAUG-GGU-GG-CG-CGAGU--GG-AGAGGC--UUCG---GCCU-GCCGGG---UUCCGUAUGC----------CCCGGUC-UGUC-A-ACUUC--GCU---CG--UUG--CC-G-CC-CACC---
Z23100.1/1383-1470             AAUUAUG-GUG-GG-AU--GUGC--AG-GGCAGUC-GCAA--GACUG-GCCGGG---UUCUCGAGUG----------ACCGGUAUUUCC-A-CCCCU--GUA---C----GU--CU-C-AC-CACCCUU
CP000891.1/933427-933345       UACUAUG-GUG-AG-CU--GGGU--GG-GGCAACC-UUCG--GGUUG-GCCGU------UCCUGUG------------ACGGUAGUGCG-A-ACCCU--GCU---C----AG--CU-C-AU-CACCAAU
CP000720.1/1069976-1069890     AACAAUG-GUG-GG-CU--GGAC--GG-GGGCAUC-GAAA--GAUGC-GCCGGG---UUCUCUGUUG----------ACCGGUC-UGCU-A-ACCCC--GUU---C----AG--UC-C-AC-CACCCAA
CU928164.2/2071448-2071364     CAUUAUG-GCG-GGGCG--UAAC--GG-GGGAGC-CUUUG-U-GCUC-GCUGG----UUUCCAGAUG----------ACCAGUC-UGCU-A-ACCCU--GUU---A----CG-UCU-C-GC-CACC---
AAZF01000003.1/38900-38815     CCCAAUG-AUG-AA-CU--GUUU--AG-GAGGAUC-GAAA--GAUCC-GCCGUU---UUGCUCUAAG----------UACGGUACUGCG-A-AUCCU--AUU---C----AG--UU-C-AU-CACCA--
FM209186.1/4492488-4492571     CUUCAUG-GCG-GA-UC--GCGU--GG-GGAGACC-CUCG-UGGUCU-GCCGG----UUCCGUUUC------------CCGGUC-UGUC-A-ACCCU--GCG---C----GA--UC-CUGC-CUCCA--
AB426058.1/17969-18056         AAUUAUG-GCG-GG-GC--GUAC--GG-GGCCGAC-UUCG--GUCGG-GCCGGG---UUCUUGUGUA----------GCCGGUACUGCG-A-ACCUC--GUA---C----GU--CU-C-GC-CACCCAC
AAZG01000002.1/114094-114177   CUCAAUG-GUA-GA-GC--GUAA--UG-AGCCGUC-UAU---GACGG-GCUGUC---UUCCUGUGAU----------GGCAGUU-UUCC-A-CCUUG--CUA---C----GC--UC-U-AC-CGCCC--
CP000124.1/323597-323506       UUCAAUG-GUC-GG-GCCUUGGU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UUCCUUGGAC----------GCCGGUU-CGCC-A-ACCCU--GUC---AU-GUGC--CC-G-GC-CACCCCA
CR522870.1/446698-446777       CUUUUGG-GUG-AC-UG--UGU----G-GGAGACC-UUCG--GGUCU-GCCGA----UUCCGUUUG-----------AUCGGUC-GUCC-A-ACCC----GC---A----UA--GU-C-GC-CCUUUU-
AAKY01000047.1/15905-15993     -UUUAUG-GGC-GG-GCGGUGGU--AG-GGAGACC-CUCG--GGUCU-GCCGGA---AUCCUCUAGA----------UCCGGUU-CGCC-A-ACCUU--GUC---AU-UCGC--CU-G-CC-CACCC--
CP000010.1/2633521-2633430     AUCAAUG-GGU-GG-GCCUUGGC--AG-GGAGACC-UUCG--GGUCU-GCCGGU---UGCCUCCUAU----------GCCGGUU-CGCC-A-ACCCU--GCC---UU-GUGC--CC-G-CC-CGCCCAU
AACY022315142.1/421-335        AGUCGCG-GCG-GC-UA--UGCG--CG-GGCACGU-UUCG--ACGUG-GCUGAG---AUCCCUGGGU---------ACUCGGU--UCCU-A-CCCCG--CGU---A----UG--GC-U-GC-CACCCAU
CP001063.1/657026-657113       AAUUAUG-GUG-AG-GC--GUGC--GG-GGCAGCC-GCAA--GGCUG-GCCGGG---UUCUCGAGUG----------ACCGGUAGUGCU-A-ACCCU--GUG---C----GU--CU-C-AC-CACCCAU
CP000871.1/112302-112211       UUCUAUG-GGC-GG-GCCAAGGC--GG-GGAGAC-CUUCG-A-GUCU-GCCGGU---UUCUUUGAUU----------UCCGGUU-CGCC-A-ACCCU--GCC---UU-GUGC--CC-G-CU-CACCCCA
AACY023484211.1/916-1003       UUUUAUG-GUG-GC-CA--UGCG--CA-GGGCGCU-UUCG--AGCGC-GCCGGUU-UUUCCAUGUGU----------GCCGGUC-UACC-A-ACCUU--CGU--AA----UG--GC-C-AC-CACCC--
AL646052.1/2052344-2052257     UUCUUUG-GCG-GG-CC--GGGC--GG-GGAGACC-UUCG--GGUCU-GCCGG----UUCCGUUGUU-----------CCGGUU-CGCC-A-ACCCC--GCCGUCU----GG--CC-C-GC-CACCCCU
AACY024037253.1/508-421        UUUUAUG-CCU-GG-GC--GUAG--UG-GGAGUCC-GCAA--GGACU-GCCGGG---UUCCGUGGAU----------ACCGGUU-GGCU-A-ACCUG--CUA---C---UGC--CC-A-GG-CACCCGU
AY536429.1/22188-22101         AUCUAUG-GUA-GC-UC--AGGC--GG-GGCAGGC-AUUA--GCCUG-GCCGGU---UUCCGAUGAC----------GCCGGUAUUCCU-A-CCCCC--GUC---U----GG--GC-U-AU-CACCAAU
CT573326.1/2692820-2692908     UGUCAUG-GCG-GC-UG--CGUA--UG-GGAGGCC-UUUG--GGCCU-GCCGGU---UUUCUCUUUUG--------CGCCGGUC-UUGC-AGACCUG--UAC---G----UA--GC-U-GC-CACCCU-
AE004439.1/2002795-2002883     CUCAAUG-GUA-GC-GU--GCGA--UU-GGCAACG-UUUAAUCGUUG-GCUGUG---UUCCGUAUGU----------CGCAGUU-UUCC-A-CCCAG--UCG---C----AC--GU-U-AC-CGCCCUA
AAKB02000001.1/98353-98440     AAUUAUG-GUG-GG-AU--GUGC--AG-GGCAGUC-GCAA--GACUG-GCCGGG---UUCUCGAGUG----------ACCGGUAUUUCC-A-CCCCU--GUA---C----GU--CU-C-AC-CACCCUU
CP000243.1/942027-941938       AAUUAUG-GUG-GG-GC--GUAC--GG-GGCCGAC-UUCG--GUCGG-GCCGGGU-UUUCUUUGUUG----------ACCGGUAGUUCC-A-ACCCU--GUA---C----GU--CU-C-AC-CACCCCG
AE016853.1/447442-447360       UUUUAUG-GUG-GU-CG--UGCG--CG-GGGCAUC-UUCG--GAUGC-ACCGGG---GUUCCUGGA------------CCGGGC-UACU-A--CCUG--CGC---A----UG--AC-C-AC-CACCCU-
AE015451.1/5149014-5148927     UUCAAUG-GUG-GC-UG--UGCG--UG-GGGCGCC-UUCG--GGUGC-GCCGGG---UUUCUCAAUUU--------GACCGGUC-UGUC-A-ACCCG--UGC---A----CA--GC-U-GC-CACCCU-
AAJU02000058.1/222-135         AAUUAUG-GUG-GG-CU--GGAC--GG-GGGCACU-GAAA--GGUGC-GCCGGU---UUCCGAUAAC----------GCCGGUUACGCC-A-ACCCC--GUU---C----AG--UU-C-AC-CACCAGC
CP000468.1/5012458-5012545     AAUUAUG-GUG-GG-GC--GUGC--AG-GGCCAAC-UUCG--GUUGG-GCCGGG---UUCUUUGGUG----------ACCGGUAUUUCC-A-CCCCU--GUA---C----GU--CU-C-AC-CACCAAU
ACCE01000003.1/349714-349626   UUUUAUG-GGU-GG-GCGUGGGU--GG-GGAGACC-UUCG--GGUCU-GCCGGU---AUCCAGAGAC----------GCCGGUU-CGCC-A-ACCCC--GCU---CA-CUGC--CC-G-CC-CACC---
CP000447.1/1972071-1971987     UACUAUG-GUG-GG-CU--GGGU--GA-GGCAGCC-AUUU--GGCUG-GCCGC----UUCCUUGAU------------GCGGUAGUUCG-A-ACCUU--GCU---C----AG--CU-C-AU-CACCCAA
AATN01000014.1/29392-29478     GUCUAUG-UGG-GA-CU--GUGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---UACUCUUUA------------CCGGUAGUUCC-A-ACCUC--GCA---C----AG-CUC-C-CG-CUCCUCU
CP001164.1/322547-322634       GAUAAUG-GUA-GU-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---UUCCAAUAAG----------GCCGGUUACGCC-A-ACCCC--GUU---C----GG--GC-U-GC-CACCAGU
CP001182.1/2226180-2226096     CGUAGCG-GUA-GGACG--GGAG--UG-GGACACC-UUCG--GGUGU-GCUGG----AGUCUUAC-------------CCAGUC-CGUC-A-ACCUG--CUU---C----CG-UUC-U-GC-CACCAUA
AACY022076807.1/19-106         UUUUAUG-GUG-GC-UG--UGCG--CG-GGGCGCU-UUCG--AGUGC-GCCGGG---UGCCUAACGU----------CCCGGUC-UUCC-ACACCUG--CGU---A----CA--GC-C-GC-CACCCAU
CP001408.1/1102534-1102623     AUCAAUG-GGU-GG-GCGACGGU--GG-GGAGGC--UUCG---GCCU-GCCGGU---UCCCUUGGAC----------GCCGGUC-UUCC-A-ACCCU--GCU---GU-CUGC--CC-G-CC-CACCCCA
CP000926.1/4104649-4104558     CUCAAUG-GCG-GC-UG--UGCG--UGUGGGCACG-UUCG--CGUGC-GCCGGU--CUUUCUUUCUUU-------CCACCGGUC-UGUC-A-ACCCG--CGC---A----UA--GC-U-GC-CACCCAA
AAAL02000013.1/8678-8770       AUUUACG-GUG-GG-GC--AGUC--AG-GAAGACC-GCAA--GGUCU-GCCGG----UUCAUGCGCAAGCU-CCGUUCCCGGUU-UGCC-A-AUCCU--GCC---U----GU--CC-C-AU-CACCA--
CP001157.1/4107394-4107480     UGUCAUG-GCG-GC-UG--UGCG--UG-GGAGGGC-UUCG--GCCCU-GCCGGG---UCCCGUUUGC----------CCCGGUC-CGCG-A-ACCCG--CGC---A----CA--GU-C-GC-CACCAGU
AE015451.1/2858046-2857965     AGUUAUG-GCA-GC-UG--UGCG--UG-GGUUAC-CUUCG-U-GUGU-GCAGGG---AUUCUCAGUGC--------CCCCGGUC-UGUC-A-ACCCA--CAA---A----CA--GC-U-GC--------
AE015451.1/335774-335862       CGCCAUG-GUG-GU-CG--UACG--UG-GGCAGAC-CUCG--GUCUG-GCCGGG--CUUCCUUAUUC---------ACUCGGUU-UCUC-A-CCCUG--CGU---A----CG--GC-U-GC-CGCCCCA
AAZW01000012.1/43784-43701     UAUUAUG-GUG-GG-CU--GGGC--GA-GGCAGC--UUCG---GCUG-GCCGU----AACCUUGGG-----------AGCGGUAGGACU-A-ACCUU--GUU---C----AG--CU-C-AC-CACCCGA
CU928161.2/565251-565338       AAUUAUG-GUG-GG-CU--GGGU--GG-GGGCACC-GAAA--GGUGC-GCCGGU---UUCCGUAUGC----------GCCGGUUACGCC-A-ACCCU--GCU---C----AG--UU-C-AC-CACCAGC
ABBG01000072.1/36101-36192     UUCUAUG-GUC-GG-GCCUUGGU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UCCCUUGGAC----------GCCGGUU-CGCC-A-ACCCU--GCC---UU-GUGC--CC-G-GC-CACCCCA
CP000076.1/1753283-1753198     CUUCAUG-GCG-GC-UG--UGCG--UG-GGAGAUCCUUUU-GGGUCU-GCCGGC---UUAUCUGGUG-----------CCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GC-CACCU--
AACY020565495.1/24069-24161    UUCUAUG-GGC-GG-GCCUGGGU--GG-GGAGACC-UUCG--GGUCU-GCCGGU---GUUCAUUAGC---------CGCCGGUU-CGCC-A-ACCCC--GCU---CU-GCGC--CC-G-CU-CACCCCG
CP000680.1/3776559-3776646     AUUUAUG-GCG-GG-CC--GUGU--GA-GGCAGGC-UUUU--GCCUG-GCCGGC--CUUCCUUCGUG---------GGUCGGUC-UACC-A-CCCUU--GCA---C----GG--UC-C-GC-CUCCAU-
CP000521.1/590336-590422       CGUUGCG-GUA-GGACG--AGUG--AG-GGACACC-UUUG--GGUGU-GCUGA----UUCUUUACU-----------AUCAGUC-UGCG-A-ACCCU--UGC---U----CG-UUC-U-GC-CACCAUA
CP000800.1/2210954-2210869     AUUUAUG-GUG-GG-GC--GUGU--AG-GGGAGUC-GAAA--GGCUC-GCCGGG---UCCUUUUAG------------CCGGUAGUGCA-A-ACCCU--GCA---U----GU--CU-C-AC-CACCCAA
CP000949.1/5384635-5384551     ---UAUG-ACG-GC-UG--UACG--CG-GGAGGUC-UUCG--GGCCU-GCCGGG---UUAACCAUGC----------ACCGGUCUUUCC-A-CCCCG--UGU---A----CA--GC-U-GU-CACCCUA
CP001068.1/10238-10326         CUUUAUG-GCA-GG-CC--GGGU--GG-GGAGACC-UUCG--GGUCU-GCCGGU---UUUCUUUGGG---------GACCGGUU-CGCC-A-GCCCC--GCCG-UC----GG-GCC-U-GC-CACCC--
AP008229.1/1727613-1727532     CUUUAUG-GCG-GG-CG--GUA---CGUGGGGGGC-UUCG--GCCCC-GCCGG----UCCCUGAGU------------CCGGUA-GACC-A-ACCCG---UG---C----CG--UC-C-GC-CACCCC-
BX571965.1/98311-98220         UUCAAUG-GUC-GG-GCCUUGGU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UUCCUUGGAC----------GCCGGUU-CGCC-A-ACCCU--GUC---AU-GUGC--CC-G-GC-CACCCCA
CT573326.1/3966788-3966882     UUUAAUG-GUG-GC-UG--UACG--UGUGGGCACG-CUUG--CGUGC-GCCGG----AACUUUUGUGUGAU-UUACCGCCGGUC-UGUC-A-ACCCA--CGU---A----CA--GC-U-GC-CACCCU-
AASA01000084.1/6623-6711       GUCUAUG-GUA-GC-GU--GUAG--CG-GGCAAGGUUUCG-CCCUUG-ACUGCU---UACCUGAUGU----------UGCAGUU-UUCC-A-CCCCG--UUA---C----AC--GC-U-AU-CGCCCUA
CP000926.1/94425-94514         GUCCAUG-GCG-GC-UG--UUCG--CA-GGAGGC--UUCG-U-GCCU-GCUGGG---UUUUAGAUCUCU------CACCCGGUU-UACC-A-CCCUG--CGU---A----CA--GC-U-GC-CACCCAU
AAWD01000002.1/57743-57826     CAUUAUG-GUG-GG-CU--GGGC--AG-GGGCGC--UUCG---GCGC-GCCGC----UUCCUUGAGU-----------GCGGUAGUACU-A-ACCUU--GUU---C----AG--UU-C-AC-CACCCAU
CP000058.1/369048-369143       GUUUAUG-GCG-GC-UU--UGCG--UG-GGGCACC-UUCG--GGUGC-GCCGGU---UGCUUGCGCUUGUU--CCACACCGGUC-UGCU-A-ACCCG--CGU--CA----AA--GU-C-GC-CACCCUU
CT573326.1/1026431-1026518     UUUCAUG-GCA-GC-CG--UGCG--UG-GGCGGAC-UUUG--GUCCG-ACCGCG---UUUCUGUGUC----------CGCGGACUUCUC-A-CCUCG--CGC---A----CG--GC-U-GC-CACCCAC
CT573326.1/2115228-2115143     UUCAAUG-GUG-GC-UG--UGCG--UG-GGGCGCA-CUCG--UGCGA-GCCGGU---UUCCUUGAUU----------CCCGGUU-GACC-A-ACCCG--CGU---A----CA--GC-C-GU-CGCCAU-
CP000949.1/762778-762687       UGCUAUG-GCA-GC-CG-CAACG--CG-GGCAGGC-UUCG--GCCUG-GCUGGC---UUAUGCCGAUCU------UUGCCGGUC-UCUC-A-CCCCG--CGU---U----CG--GC-U-GC-CACCUUA
ABBP01000530.1/16827-16739     UUUUAUG-GGU-GG-GCGUGGGU--GG-GGAGACC-UUCG--GGUCU-GCCGGU---AUCCAGAGAC----------GCCGGUU-CGCC-A-ACCCC--GCU---CA-CUGC--CC-G-CC-CACC---
CP000958.1/1408535-1408626     AUCAACG-GGU-GG-GCCUGGGU--GG-GGAGACC-UUCG--GGUCU-GCCGGU---UGCCUCCAUU----------GCCGGUU-CGCC-A-ACCCC--GCU---CA-GUGC--CC-G-CC-CACCCCA
CP001068.1/3750478-3750390     UACUUUG-GCG-GG-CC--GGAU--GG-UGAGACC-UUCG--GGUCU-ACCGGU---UUCCUUGGG-----------ACCGGGU-CGCU-A-ACACC--AUCG-UC---AGG--CC-C-GC-CACCCUC
CP000438.1/4286083-4286166     CUUCAUG-GCG-GA-UC--GCGU--GG-GGAGACC-CUCG-UGGUCU-GCCGG----UUCCGUUUC------------CCGGUC-UGUC-A-ACCCU--GCG---C----GA--UC-CUGC-CUCCA--
CP001172.1/1339654-1339738     CUUUAUG-GUG-AG-GC--UAGG--AG-GGGCACG-CUUG--CGUGC-GCUGGU---UUCCUUUUGU----------ACCAGUC-UGUC-A-ACCCU--UCU---A----GU--CU-U-GC-CACCA--
CP000970.1/4088325-4088412     GUCAAUG-GUA-GC-UC--AGGC--GG-GGCAGCC-UCCG--GGCUG-GCCGGU---UUCCGAUAAC----------GCCGGUAUUCUC-A-CCCCC--GUC---U----GG--GC-U-AU-CGCCAUC
AAUJ02000001.1/2349362-2349446 CUUUACG-GUG-GG-CC--GUGU--GG-GGACACCCGCGA-GGGUGU-GCCGG----UUCCUACGG------------CCGGUC-CGCC-A-ACCCU--GCA---C----GG--UC-C-AU-CACCUC-
CP000826.1/638142-638057       AACAAUG-GUG-GC-UC--GGGU--GG-UGCUUCC-UUCG--GGAAG-GCCGGG---AUCCGUUGGG----------GCCGGUA-CGCU-A-ACACU--GCU---C----GA--GC-U-AC-CACCCC-
CP000038.1/2936419-2936336     AAUUAUG-GUG-GG-GC--GCAU--GG-GGGAGCU-GAAA--AGCUC-GCCGG------UCGGUUUC-----------CCGGUAGUUCC-A-ACCCU--GUG---C----GU--CU-C-AC-CACCCGA
AAJX02000034.1/25727-25814     AAUUAUG-GCG-GG-GC--GUAC--GG-GGCCGAC-UUCG--GUCGG-GCCGGG---UUCUUGUGUA----------GCCGGUACUGCG-A-ACCUC--GUA---C----GU--CU-C-GC-CACCCAC
CP000075.1/4827916-4828000     GUUUAUG-GUG-GC-CG--UGCG--CU-UGGCGUC-UUCG--GACGC-ACCGGC---UUGCCUGGUC----------ACCGGUC-UACC-A-ACCUG--CGU---A----CG--GC-C-GC-CACCC--
CP000949.1/572002-572090       CUUUAUG-GCA-GC-UG--UGCA--UG-GGGCAC--UUCG-U-GUGC-GCCGGG---UUUUGGUUUGC-------CUACCGGUC-UGUC-A-ACCCA--UGU---A----CA--GC-U-GC-CACCCUC
AE016825.1/4158872-4158962     UUCUAUG-GGC-UG-GCCAUGGC--AG-GAGCGUG-CUUG--CACGC-GCCGGU---CACCUUGAGU----------CCCGGUC-CGCC-A-AUCCU--GCC---AUUGUGC--CA-G-CC-CACCC--
CP000926.1/5921653-5921739     CGUCAUG-GCA-GU-UG--CACG--CG-GGAGGCC-GUAU--GGCCU-GCCGGG---GUUCCGAUAG----------CCCGGCU-UUCC-A-CCCCG--CGU---G----CA--GC-C-GC-CACCCUU
CR543861.1/920344-920258       CUUUGCG-GUA-GAACG--GAAG--GG-GGACGCG-UCCG--CGCGU-GCUGG----UUCUAGAUGU-----------CCAGUC-UGUC-A-ACCCU--CUU---U----CG-UUC-U-GC-CACCAUA
AL646052.1/1663851-1663938     UUCAAUG-GCG-GG-UC-GAGGU--GG-GGACACC-UUCG--GGUGU-GCCGG----UUCCUGGUAG-----------CCGGUC-GGCC-A-ACCCC--GCU---UU--CGG--UC-C-GC-CGCCCGU
CT573326.1/5194676-5194589     CGUUAUGGGCG-GA-GC--CGUG--UGUGGGAGCC-UUCG--GGCUC-ACCGG------ACCUUCUG----------ACCGGCAACGCC-A-ACCCG--CAC---G----GC--UC-C-GUCCACCCAU
ACDJ01000040.1/5832-5919       GUCAAUG-GUG-GGUCG--GGGC--GU-GGGAGCC-UUAC--GGCUC-GCCAGU---CGUCAUUAG------------CUGGUACUGCA-A-ACCAU--GUU---C----CG-AUU-C-AC-CACCAAA
ABEL01000004.1/418202-418115   UAUUAUG-GUA-GU-CC--AGGC--GG-GGCAGCU-UUCG--GGCUG-GCCGGU---AUCCUUCAGA----------GCCGGUAUUCCU-A-CCCCC--GUC---U----GG--GC-U-AC-CACCCAU
CT573326.1/1922676-1922764     UUCAAUG-GCG-GC-UA--UGCG-UUG-GGAGACC-UUCG--GGUCU-GCCGGG---UUCCUGUAUC----------CUCGGUC-UUGC-A-CCCCU-GCGC---A----UA--GC-U-GC-CACCUAU
M16568.1/170-255               AAUUAUG-GUG-GGGCG--UGAU--GG-GGAGGC--UUCG---GCCU-GCUGG----UUUCACUAAC----------GCCAGUC-UGUC-A-ACCCU--GUC---A----CG-UCC-U-GC-CACCUGU
AM933172.1/2049639-2049552     AAUUAUG-GUG-GG-GC--GUGC--AG-GGCCAGU-UUCG--GCUGG-GCCGGG---UUCUAUGUUG----------ACCGGUAUUUCC-A-CCCCU--GUA---C----GU--CU-C-AC-CACCUAU
AACY020886687.1/713-793        UUUUAUG-GCG-GG-CG--GUA---CGCGGGGGGC-UUCG--GCCCC-GCCGG------CCCUUGG-----------ACCGGUA-GACC-A-ACCCG---UG---C----CG--UC-C-GC-CACCCC-
AL590842.1/969600-969686       AACAAUG-GUG-GG-CU--GGAC--GG-GGGCAUC-GAAA--GAUGC-GCCGGG---UUCUCUGUUG----------ACCGGUC-UGCU-A-ACCCC--GUU---C----AG--UC-C-AC-CACCCAA
AL646052.1/1013264-1013352     UUUUAUG-GCG-GG-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---GGCCUCCUUU----------GCCGGUU-UUCC-A-CCCCC--GCUG-UC---AGG--CC-C-GC-CACCCC-
ABBO01000018.1/1738-1645       UUCAAUG-GCG-GG-CCUUGGCUGAGG-GGACACC-UUCG--GGUGU-GCCGGU---UUCCUUUUGC----------GCCGGUC-CGCG-A-ACCCCAAAGC---CU-UGCG--CC-U-GC-CACCA--
CT573326.1/1180765-1180854     CGUUAUG-GCA-GC-UG--UGCG--UG-GGGCAC--CUCG-U-GUGC-GCCGGU---UUCUGGUCUUGU------UCACCGGUC-UGUC-A-ACCCA--UGU---G----CA--GC-U-GC-CACCUUC
CP000712.1/1788565-1788652     AUUUUUG-GCG-GC-UG--UGCG--CG-GGAGGUA-UUCG--UACCU-GCCGGGU-CUACCGUGUGC-----------CUGGUC-UUCC-A-CCCCG--CGU---A----CA--GU-U-GC-CACCCUA
AM286415.1/1858079-1857993     AGCAAUG-GUG-AG-CU--GGGC--GG-GGGCAUC-GCAA--GAUGC-GCCGGG---UUCUUCGAUG----------ACCGGUC-UGUC-A-ACCCC--GCC---C----AG--UU-C-AC-CACCCAU
AP008232.1/2063246-2063161     CUCAAUG-GUG-GG-CU--GGAU--AG-GGCAGCC-GCAA--GGCUG-GCCGG------AUGGUGAU----------CCCGGUAGUUCCUA-ACCCU--GUU---C----AG--CU-C-GC-CACCAAU
CP001157.1/3302690-3302774     CGUUAUG-GGC-GG-GC--CGUG--UGUGGGGGCC-UUAC--GGCCC-GCCGG----UUCCCGUUU------------CCGGUC-CGCC-A-ACCCG--CAC---G----GU-UCC-G-CU-CACCCA-
CP000863.1/1348202-1348290     CUCUGCG-GCG-GAACG--GGAG--GG-GGACAUC-UUCG--GAUGU-GCUGAU---UUUUGGGUAA----------AUCAGUC-UGCU-A-ACCCC--UUU---U----CG-UUU-C-GC-CACCAUA
CP000076.1/3142100-3142011     UUUCAUG-GCG-GC-UG--UACG--CG-GGAGAUC-CUCG--GAUCU-GCCGAU---UAUUGUGGGAU-------GAGUCGGCU-CGCC-A-ACCCG--CGU---A----UA--GC-U-GC-CACCUAU
CT573326.1/2652833-2652926     CGCAAUG-GUG-GC-UA--CGUG--CG-GGUGACC-UCUU--GGUCA-GCCGGG---UUUUCGCCUCGUA---AUGCCCCGGUC-UUGC-AGGCCCG--UAC---G----UA--GC-U-GC-CACCCU-
AAJV02000004.1/34572-34487     CUCAAUG-GUG-GG-CU--GUGU--GG-GGGCGGA-GCGA--UCCGC-GCCGG----UUCCUUUUUC-----------CCGGUUACGCC-A-ACCCU--GCA---C----AG--UU-C-AC-CACCAUA
CP000653.1/4152361-4152449     UCCAAUG-GUG-GG-CC--GAGC--GG-GGGCGUC-GCAA--GACGC-GCCGGU---AUCCGAAGAG----------GCCGGUAAGGCU-A-ACCCU--GUU---C----GG-UUC-C-AC-CGCCAGC
AACY020562497.1/1153-1062      UUCUAUG-GGC-GG-GCCUUGGU--GG-GGAGACC-UUAG--GGUCU-GCCGGC---UGCUUGUGUG----------ACCGGUU-CGCC-A-ACCCU--GCC---GU-GCGC--CC-G-CU-CACCUCA
CP000863.1/1208992-1209076     CUCUACG-GCG-GAACG--GGAG--GG-GGACACC-UUCG--GGUGU-GCUGGG---UUUUUUCGG------------CCAGUC-UGCU-A-ACCCC--CUU---U----CG-UUC-U-GC-CACCU--
CT573326.1/2996471-2996385     CUCAAUG-GUG-GC-UG--UGCG--UA-GGGCACG-UUCG--CGUGC-GCCGGU---CUUCUCAGUUC--------CUCCGGUC-UGUC-A-ACCUA--CGC---A----CA--GC-U-GC-CACCC--
AAKB02000001.1/3919920-3920007 AAUUAUG-GUG-GG-GC--GUGC--AG-GGGCAUC-GCAA--GAUGC-GCCGGG---UUCUAUGUUG----------ACCGGUUACGCC-A-ACCCU--GUA---C----GU--CU-C-AC-CACCUCU
CP000949.1/1561229-1561317     UGUAAUG-GCG-GC-UG--UACC--CG-GAAGGC--CUCG-U-GCCU-ACCGAG---UUUUCCUGAAUG------CACUCGGGU-UUCC-A-CUCCG--UGU---A----CA--GC-U-GC-CACCCU-
CP000949.1/3436701-3436796     UUUUAUG-GUG-GC-UG--UGCG--UGUGGGCACG-CUUG--CGUGC-GCCGGAGCUUUUCGUGAUUUU-----ACCGCCGGUC-UGUC-A-ACCCA--CGU---A----CA--GC-U-GC-CACCCCA
CP001113.1/2885196-2885283     GAUAAUG-GUA-GU-CC--GGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---UUCCUUGAAG----------GCCGGUUACGCC-A-ACCCC--GUU---C----GG--GC-U-GC-CACCAGU
CP000949.1/4245697-4245612     UGCCAUG-GCG-GC-UG--UGCG--UG-GGAGGCC-UUCG--GGUCU-GCCGGG---UUCCAAGUUC-----------CCGGUU-CGCC-A-ACCUG--CGU---A----CA--GC-U-GC-CACCCUC
CP000075.1/4545144-4545229     UGCUAUG-GCG-GC-UG--UGCG--UC-GGAGACC-UUCG--GGUCU-GCCGGU---UUCCUGGAU-----------ACCGGUU-CGUC-A-ACCUU--CGC---A----CA--GC-U-GC-CACCCAU
AE003849.1/2387378-2387297     GUCUAUG-GCG-GG-UG--GCGU--GG-AGAGACU-UUCG--AGUCU-ACCGG------UCCUGGGG-----------UCGGUC-UUCU-A-ACUCC--GCG---U----CG--UC-C-GC-CUCCAU-
AE014613.1/4674209-4674296     AGUAAUG-GUG-GC-UC--AGGC--GG-GGCCGAC-UUCG--GUCGG-GCCGGU---AUCCGUUAGA----------GCCGGUAUUUCC-A-CCCCC--GUC---U----GG--GC-U-AC-CACCACU
AP008232.1/1219801-1219714     AAUAAUG-GCGUGA-UG--UAAC--GG-GGGAGCC-GUAA--GGCUC-GCCGGA---UUUCUCUUUG----------ACCGGUC-UGUC-A-ACCCU--GUU---A----CG--UCUC-GC-CACCCU-
CP000036.1/1140537-1140623     AAUUAUG-GUG-GG-CU--GGGC--GG-GGGCACC-GUAA--GGUGC-GCCGG----UUCCAGUAUG----------GCCGGUAGUUCC-A-ACCUC--GUU---C----AG--UC-C-AC-CACCCAU
CP000058.1/2874551-2874467     UGUUAUG-GCG-GC-UG--UGCG--UC-GGAGACU-CCAG--GGUCU-GCCGGC---GUUGUGAGGU----------GCCGGUU-CGCU-A-ACCUU--CGC---A----CA--GC-C-GC-CACCC--
CP000949.1/760030-759945       CGUUUUG-GCA-GC-UG--UGCA--UG-GGGCAC--CUCG-C-GUGC-GCCGGU---UUUGGUCUGUU--------CACCGGUC-UGUC-A-ACCCA--UGU---A----CA--GC-U-GC-CGCCU--
AACY020187178.1/1583-1668      GGCUAUG-GCG-GG-CG--GUGC--GUUGGGGGCG-UUCG--CGCCC-GCCGG------CUUGAGGCC-------AACCCGGA--UUCG-A-ACCAC--GUA---C----CG--CC-C-GC-CACCUU-
CT573326.1/4962315-4962229     CGUCAUG-GCG-GU-GG--UGCG--CG-GGACACC-UUCG--GGUGU-GCCGGG---CCCCUUUCGU----------CCCGGUC-GGCC-A-ACCCG--CGU---A----CU--GC-U-GC-CACCUAA
CT573326.1/793129-793043       UUCCAUG-GCA-GC-CG--UGUG--CG-GGCAGGC-UUCG--GUCUG-ACCGGG---UUUCUUGUGC----------CCCGGAU-UCUC-A-CCCUG--UUC---A----CG--GC-U-GC-CACCCUU
AE016853.1/3480015-3480104     CGCUAUG-GCG-GC-UG--UGUG--CG-GGAGACC-UUCG--GGUCU-GCCGGGGUUUGUCUUUUUG----------CCCGGUU-CGCC-A-ACCCU--CGC---A----CA--GC-U-GC-CACCCAU
AE015451.1/2855914-2855828     UUUCAUG-GCG-GC-UG--UACG--UGUGGGCACC-CUGU--GGUGC-GCCGAG---UGCCAACGUC-----------UCGGUC-UGUC-A-ACCCG--CGU---A----CA--GC-U-GC-CACCAUC
AAKB02000001.1/377030-376945   CAUUAUG-GCG-GGGCG--UAAC--GG-GGGAGC-CUUUG-C-GCUC-GCUGGU---UUCCCAAUUU----------GCCAGUC-UGCU-A-ACCCU--GUU---A----CG-UCU-C-GC-CACC---
CP000949.1/4994063-4993975     UGUCAUG-GCG-GC-UG--UGUG--UG-GGCAGGC-UUCG--GCCUG-GCCGGG--UUUCCAAGUUC----------CCCGGUAUUCCU-A-CCCCA--UAC---A----AA--GC-U-GC-CACCCCC
CU928161.2/4962469-4962556     AAUUAUG-GUG-GG-GC--GUGC--AG-GGCCAAC-UUCG--GUUGG-GCCGGG---UUCUUUGGUG----------ACCGGUAUUUCC-A-CCCCU--GUA---C----GU--CU-C-AC-CACCAAU
ABBH01000502.1/7145-7238       UUCAAUG-GCG-GG-CCUUGGCUGAGG-GGACACC-UUCG--GGUGU-GCCGGU---UUCCUUUUGC----------GCCGGUC-CGCG-A-ACCCCAAAGC---CU-UGCG--CC-U-GC-CACCA--
CP000521.1/1493304-1493388     CUCUGCG-GUG-GAACG--GGAG--GG-GGACACC-UUCG--GGUGU-GCUGA----UCUUUUGGCU----------AUCAGUC-UGUC-A-ACCUU--CUC---U----CG-UUU-C-AC-CACC---
DQ017661.1/98772-98685         AUCUAUG-GUA-GC-UC--AGGC--GG-GGCAGGC-AUUA--GCCUG-GCCGGU---UUCCGAUGAC----------GCCGGUAUUCCU-A-CCCCC--GUC---U----GG--GC-U-AU-CACCAAU
CP000653.1/1205701-1205615     GAUCAUG-GCG-GC-GC--UGGU--GG-AGCAGC-CGAAA-A-GCUG-GCCGU----UUUUAUCGUG----------UACGGUAUUCCU-A-CCUCC--GUC---A----GC--GC-U-AC-CAUCCCU
AE017220.1/1315152-1315239     AAUUAUG-GUG-GG-GC--GUGC--AG-GGCCAGU-UUCG--GCUGG-GCCGGG---UUCUAUGUUG----------ACCGGUAUUUCC-A-CCCCU--GUA---C----GU--CU-C-AC-CACCUAU
CP000712.1/339637-339726       CGUAAUG-GCG-AC-UG--UGCG--CG-GGCAGAC-CUUG--GUCUG-GCCGAG--CUUCCUACGUUC--------ACUCGGUU-UCUC-A-CCUCG--UGC---A----CG--GU-U-GC-CGCCUUU
CP000436.1/1602795-1602876     GUCAAUG-AUG-GG-CU--GAUU--GA-GGGAUC--GAAA---GAUC-GCCGUU--CAUCCGUGUU------------ACGGUA-CGCC-A-ACCUU--GAU---C----AG--UU-C-AU-CACCA--
CP001111.1/2522440-2522526     GGCUAUG-GCG-GG-CG--GUGC--GU-GGGGGCU-UCCG--GGCCC-GCCGGA--CUGACAUCAAC-----------CCGGUG-UUCG-A-ACCAC--GUA---C----CG--CC-C-GC-CACUUUU
CP000521.1/871520-871603       CACUAUG-GUA-GGACG--AGAG--GG-AGACGC-CUUAG-U-GCGU-ACUGA----AUCCUUGGG------------GCAGUC-UGUC-A-ACUUC--CUU---U----CG-UUC-U-AC-UGCCA--
AE015451.1/5390633-5390719     GUUCAUG-GCG-GU-UG--UGCA--UG-GGGCACG-CUUG--CGUGC-GCCGGU---UUCUGUGUUC----------GCCGGUC-UGUC-A-ACCCA--UGC---A----CA--GC-U-GC-CACCAUU
CP000947.1/1874605-1874691     CUCAAUG-GUA-GA-GC--GUAA--AG-GGCAACCGCUUG-CGGUUG-GCUAUG---UUCCUUUGUA----------CGUAGUU-UCUC-A-CCCCU--UUA---C----GC--UU-U-AC-CGCCC--
ABBF01000782.1/19995-20086     UUCUAUG-GUC-GG-GCCUUGGU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UCCCUUGGAC----------GCCGGUU-CGCC-A-ACCCU--GCC---UU-GUGC--CC-G-GC-CACCCCA
AAJW02000006.1/162043-162130   AAUUAUG-GCG-GG-GC--GUAC--GG-GGCCGAC-UUCG--GUCGG-GCCGGG---UUCUUGUGUA----------GCCGGUACUGCG-A-ACCUC--GUA---C----GU--CU-C-GC-CACCCAC
ABBO01000209.1/19106-19197     UUCAAUG-GUC-GG-GCCUUGGC--GG-GGGUGCC-UUCG--GGCAC-GCCGGU---UUCCUUUUGC----------GCCGGUU-CGCC-A-ACCCU--GUC---AU-GUGC--CC-G-GC-CACCCCA
CP000270.1/915998-916090       UGCAAUG-GGC-GG-GCCGUGAU--AG-GGAGACC-UUCG--GGUCU-GCUGGU---UUGGUUUGGU----------GCCAGUC-UGUC-A-ACCUU--GUC---ACUGUGC--CC-G-CU-CACCACC
CP001157.1/1684908-1684822     UGUCAUG-GCG-GC-UG--UGCG--CG-GGAGACC-GAAA--GGUCU-GCCGGG---UUCCGUGUGU----------CCCGGUU-CGCC-A-ACCUG--CGC---A----CA--GU-C-GC-CUCCAAU
CP000863.1/2410295-2410211     CUCUGCG-GCG-GAACG--GGAG--GG-GGACACC-UUCG--GGUGU-GCUGGA---UUCUUUGGCU-----------CCAGUC-UGCU-A-ACCCU--CUU---U----CG-UUU-C-GC-CACC---
AAMJ02000007.1/122662-122749   AAUUAUG-GUG-AG-GC--GUGC--GG-GGCAGCC-GCAA--GGCUG-GCCGGG---UUCUCGAGUG----------ACCGGUAGUGCU-A-ACCCU--GUG---C----GU--CU-C-AC-CACCCAU
CP000513.1/824732-824817       UGUUAUG-GCG-GC-AU--ACGU--AG-GAGAACC-GCAA--GGUUC-GCCGU----UUCUUUCGU-----------AGCGGCAAGGCU-A-AUCCU--GCG---U----AU--GC-U-GU-CGCCCUC
CP000020.2/2238674-2238589     AAUUAUG-GUG-GG-CC--GAGU--GA-GGCCGA--UUCG-U-UCGG-GCCGUU---UUCCUUGUGU----------CGCGGUAGUAUC-A-ACCUU--GCU---C----GG--UU-C-GC-CACCAA-
CP001052.1/1150520-1150612     UGCAAUG-GGC-GG-GCCGUGAU--GG-GGAGACC-UUUU-GGGUCU-GCUGG----UUUGGUUUGG----------GCCAGUC-UGUC-A-ACCUU--GUC---ACUGUGC--CC-G-CU-CACCACC
CP000529.1/380216-380131       AGUUUUG-GCG-GC-UC--GGA---UG-GGGGAGC-CUCG--GCUCC-GCCGGU---UUUCGCAAGAG-------UGCCCGGUA-GACC-A-ACCCG---UU---C----GA--GC-U-GC-CGCCC--
AE015451.1/1995754-1995667     GCUUAUG-GCG-GC-UG--UACG--UGCGGGCCC-CCUCA-U-GUGU-GCCGAG---UGCCAACAAU----------CUCGGUC-UGUC-A-ACCCA--AGU---A----CA--AC-U-GC-CACCCUC
CP000949.1/2826683-2826599     ---UAUG-GCG-GC-UG--UACG--UGCGGGCAC-CUUCG-U-GUGC-GCCGAG---UGCCAACAAU----------CUCGGUC-UGUC-A-ACCCG--CGU---A----CA--GC-U-GC-CACCCUC
CP000076.1/5946544-5946629     CGUUAUG-GCG-GG-UU--GCGU--GG-GAGAACC-UUCG--GGUUC-GCCGG----UUCCUUGAUU----------CCCGGUC-CGCC-A-AUCCU--GCG---C----AA--UC-C-GC-CACCCUG
AAYX01000007.1/10966-11055     UUCUAUG-GGU-GG-GCCAUGGU--GG-GGGAGCG-CUUG--CGCUC-GCCGG----UGCCAACGUU-----------CCGGUC-UGUC-A-ACCCU--GUC---AU-GUGC--CC-G-CC-CACCCCA
AB027308.1/563-650             AUCUAUG-GUA-GA-UC--AGGC--GG-GGCAGGC-AUUA--GCCUG-GCCGGU---UUCCGAUGAC----------GCCGGUAUUCCU-A-CCCCC--GUC---U----GG--GC-U-AU-CACCAAU
CP000570.1/98244-98153         UUCAAUG-GUC-GG-GCCUUGGU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UUCCUUGGAC----------GCCGGUU-CGCC-A-ACCCU--GUC---AU-GUGC--CC-G-GC-CACCCCA
AACY020902803.1/274-191        CGUUAUG-GCA-GU-UG--UACG--CG-GGAGAUC-UUCG--GAUCU-ACCGG------ACUCCGUC-----------ACGGUC-UUGC-ACACCCG--CGU---A----CU--GC-U-GC-CACCCUA
AAZF01000005.1/72866-72949     CUCAAUG-GUA-GA-GC--GUAA--UG-AGCCGUC-UAU---GACGG-GCUGUC---UUCCUGUGAU----------GGCAGUU-UUCC-A-CCUUG--CUA---C----GC--UC-U-AC-CGCCC--
AP008232.1/4059279-4059192     UAUAAUGGUGA-GG-CG--UAAC--GA-GGGAGC--CUCUGC-GCUC-GCCGGG---UUCUCUGAC-----------ACCGGUC-UACU-A-ACCUC--GAU---A----CG--UC-U-CUCCACCCCG
ACID01000067.1/73692-73779     GUCAAUG-GUA-GC-UC--AGGC--GG-GGCAGCC-UCCG--GGCUG-GCCGGU---AUCCGUUAGA----------GCCGGUAUUCUC-A-CCCCC--GUC---U----GG--GC-U-AU-CGCCAUC
CP001111.1/440130-440046       UUCUAUG-GCG-GG-CG--GUG---CGUGGGGAUC-UUCG--GAUCC-GCCGG------UCUGGUACA--------UACCGGUU-UUCG-A-GCCCG---CA---C----CG--UC-C-GC-CACCUUU
AE003849.1/1588569-1588477     GUUUAUG-GUG-GG-GC--AGUC--AG-GAAGACC-GCAA--GGUCU-GCCGGU---UUAUGCGCAAGCUC--CUUUCCCGGUU-CGCU-A-AUCCU--GCC---U----GU--CC-C-AU-CACCA--
AAQW01000001.1/6009993-6010074 ---UAUG-GGC-GG-GC--CGUG--UG-GGGCUGC-GCAA--GCAGC-GCCGG----UUCCUAAUC------------CCGGUA-CGCC-A-ACCUG--CAC---G----GU-UCC-G-CC-CACCCUG
CT573326.1/4896084-4896172     UCUUAUG-GCG-GC-UG--UGCG--UG-GGGCAC--UUCG-U-GUGC-GCCGGG---UUUUGGGAUGC-------CUACCGGUC-UGUC-A-ACCCA--UGU---A----CA--GC-U-GC-CACCUUC
FN543502.1/3869686-3869599     AAUUAUG-GUG-AG-GC--GUAU--GG-GGCCGAC-UUCG--GUCGG-GCCGGG---UUCUUUGGUU----------GCCGGUAGUUCC-A-ACCCU--GUA---C----GU--CU-C-AC-CACCCCG
FN649414.1/341376-341463       AUCAAUG-GUG-GC-UC--AGGC--GG-GGGCUUC-UUCG--GAAGC-GCCGGU---AUCCUUCAGA----------GCCGGUUACGCC-A-ACCCU--GUC---U----GG--GC-U-AC-CACCAGC
CP002729.1/3009644-3009727     AAUUAUG-GUG-GG-CU--GGGC--AG-GGGUCC--GAAA---GGAC-GCCGG----UACCACUUAG----------GCCGGUA-CGCC-A-ACCUU--GUC---C----AG--UU-C-AC-CACCAGU
CP002276.1/954141-954228       UCCAAUG-AUG-AA-CU--GUUU--AG-GAGGAUC-GAAA--GAUCC-GCCGUU---UUGCUCUAAG----------UACGGUACUGCG-A-AUCCU--AUU---C----AG--UU-C-AU-CACCAAC
CP002290.1/108489-108577       GUCUAUG-GUG-GC-UG--UGCG--UG-GGAGGCU-UUCG--AGCCU-GCCUGG---AUUGGAAAAUG--------CCCGGGUC-UACC-A-CCUCG--CGU---A----CA--GU-C-GC-CACCCAU
AE005174.2/2673794-2673881     AAUUAUG-GCG-GG-GC--GUAC--GG-GGCCGAC-UUCG--GUCGG-GCCGGA---UUCUUUGCUC----------UCCGGUGUUGAG-A-ACCCU--GUA---C----GU--CU-C-GC-CAGCCCG
CP002277.1/983980-983892       UCCAAUG-AUG-AG-CU--GAAU--GA-GGGGAUC-GAAA--GAUCC-GCCGUU---UUGCUCUUAA---------GUACGGUACUGCG-A-ACCUC--GUU---C----AG--UU-C-AU-CACCAAC
CP002599.1/3607439-3607349     UUCUAUG-GUC-GG-GC-CUGAU--GG-GGGUGCG-UUCG--CGCAC-GCCGGU---UUCCUUUGAC----------GCCGGUU-CGCC-A-ACCCU--GUC---AU-GUGC--CC-G-GC-CACCCCA
CP001363.1/1300831-1300916     AUUUAUG-GUG-GG-CU--GUGU--GA-GGGCUUC-UUAG--GAAGC-GCCGGG---UUUGAGUAG------------CCGGUAAGACC-A-ACCUU--GCA---C----AG--UU-C-AC-CACCCGU
CP001671.1/365416-365503       AAUUAUG-GUG-GG-CU--GGAC--AG-GGCAGCC-GAAA--GGCUG-GCCGGU---UUCCUUGUAC----------GCCGGUACUGCG-A-ACUCU--GUU---C----AG--UC-C-AC-CACCAGC
CU928162.2/3259953-3259866     AACAAUG-GUG-GG-CU--GUAU--GG-AACUUCC-UUCG--GGAAG-GCUGGU---UUCCUCUAAC----------ACCAGUAAGGCC-A-AUUCC--GUA---C----AG--UC-C-AC-CGCCAGC
CP001383.1/1480110-1480023     AAUUAUG-GUG-GG-AU--GUGC--AG-GGCAGUC-GCAA--GACUG-GCCGGG---UUCUCGAGUG----------ACCGGUAUUUCC-A-CCCCU--GUA---C----GU--CU-C-AC-CACCCUU
AALC02000033.1/29776-29863     AUCAAUG-GUG-AG-CU--GGGC--AG-GGGCAUC-GCAA--GAUGC-GCCGGA---UUCUCUGUUG----------ACCGGUAGUUCC-A-ACCUU--GCU---C----AG--UU-C-AC-CACCCAU
AALC02000019.1/4774-4687       AGCAAUG-GUG-GC-UC--AGGC--GG-GGCAGCU-UUCG--GGCUG-GCCGGU---UUCCAAGGUU----------GCCGGUAUUCCU-A-CCCCC--GUC---U----GG--GC-U-AC-CACCCAU
AALE02000005.1/109212-109128   AGCAAUG-GUG-GC-UC--AGGC--GG-GGCAGCU-UUCG--GGCUG-GCCGGU---AUCCAUUGAG----------GCCGGUU-UCUC-A-CCCCC--GUC---U----GG--GC-U-AC-CACCC--
AALD02000013.1/100809-100722   AGCAAUG-GUG-GC-CC--AGGC--GG-GGCAGCC-UUCG--GGCUG-GCCGGU---UUCCAAUAAG----------GCCGGUAUUCCU-A-CCCCC--GUC---U----GG--GC-U-AC-CACCCAU
AALF02000007.1/2845-2758       AGAAACG-GUG-AA-CU--GGGU--GG-GGGCAUC-GCAA--GAUGC-GCCGGG---UUCUUUGGUA----------ACCGGUAGUUCC-A-ACCUC--GCU---C----AG--UU-C-AC-CACCCAU
CP001644.1/3289607-3289519     UUUUAUG-GCG-GG-CC--GGGC--GG-GGCCAGC-UUCG--GCUGG-GCCGGU---UUCCUGUAG-----------GCCGGUU-UCUC-A-CCCCC--GCUGUCU----GG--CC-C-GC-CACCCUC
CP000094.2/1747486-1747401     CGUUAUG-GCG-GC-UG--UAUG--CG-GGAGACC-UUCG--GGUCU-ACCGGG---GUGCCUGAGA-----------CCGGUU-CGCU-A-ACCUG--CGU---A----CA--GC-U-GC-CACCCUU
#=GC SS_cons                   :::::((.(((.((.((..((((..((.((<<<<<.____..>>>>>.<<<<<_...__________.........._>>>>>,.,,,,.,.,))))..)))...)....))..)).).)).)):::::
#=GC RF                        uuuuAUG.Gcg.Gg.cc..ggcc..gG.GGgggcC.uUcG..Ggccc.GCCGGu...UUcCuuuuuu..........aCCGGUc.UgCC.A.ACCCc..ggc...c....gg..cC.c.gC.CACCcuu
//
# STOCKHOLM 1.0

#=GF AC   RF01696
#=GF ID   Chlorobi-1
#=GF DE   Chlorobi-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   52.50
#=GF NC   38.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Chlorobi-1_RNA_motif
#=GF SQ   15


CP000607.1/1489337-1489270 GAAAUACCUCACGCCCGUGGGGUUGAGCAGAUGUAAUGGGGGACAUCUGCUCAC--AAAAAAAAGCGGCU
CP000096.1/1700120-1700054 GAAACUCCUCACGCCCGUGAGGUGGAACAGGUGUAAUGGGGGACACCUGUUCA---UAAAAAAAGCGGCC
CP001108.1/1747881-1747814 GAAUUGCCUCACGCCAGUGGGGUAGAGCAGCUGGAAUGGGGGCCAGCUGCUCAA--CAAAAAAAGCGACC
CP000607.1/970580-970645   GAAAUUCCUCACGCCAGUGAGGUUGAGUUGGUGUAAUGGGGGACACCAACUC----UCAGAGAGACGGCU
CP001097.1/1886329-1886262 GAAACUCCUCACGCCCGUGGGGAAGAGCAGGUGGAAUGGGGGCCAUCUGUUCAA--GAAAAAAGGAGGUC
CP001108.1/1748207-1748138 AAAUUACCUCACGCCAGUGGGGUAGAGUAGCUGGAAUGGGGGCCAGCUGCUCACUUUAAAAAAAGCGACC
CP000607.1/146066-146001   AAAAAGCCUCAUGCAAAUGAGGUGGAGCAUGCGUAAUGGGGGACGCAUGCUC----ACCAGAAAACGGCC
CP001097.1/1886042-1885975 GAAAUUCCUCACGCCCGUGGGGAAGAACAGGUGGAAUGGGGGCCAUCUGUUCAA--GAAAAAAGGAGGUC
CP000096.1/1700346-1700281 GAAACUCCUCACGCCCGUGGGGUGGAGCAGGUGUAAUGGGGGACACCUGUUC----GAAAAAAAGCGGCU
CP001108.1/973622-973555   AUCAUGCCUCACGCCCGUGAGGUAGAGUAGGAGGAAUGGGGGCCUCCUGCUCAC--UGUUUAAAGCGGCC
CP001101.1/895163-895229   GUAAUGCCUCACGCCCGUGGGGUAGGACAGGUGUAAUGGGGGACACCUGUUCAC--ACUAAAAGCGUCC-
CP001108.1/2025902-2025839 AUAAUACUUCGCGCAAGUGAAGU-GUGUAGGUCU-GUGGGGGAUUUCUGCAC----GGGUAAAAGCAGCA
CP000096.1/1700572-1700507 GAAACUCCUCACGCCCGUGGGGUGGAGCAGGUGUAAUGGGGGACACCUGUUC----GAAAAAAAGCGGCU
CP001097.1/1885760-1885693 GAAAUUCCUCACGCCAGUGAGGAAGAACAGGUGGAAUGGGGGCCAUCUGUUCAC--AAAAAAAAGCGGCU
CP001101.1/1871474-1871409 UUUCAGCCUCACGCCCGUGGGGUUGGGCAGGCGUAAUGGGGGACACCUGCUC----GAAGAAAAGCGGUC
#=GC SS_cons               ::::<<<<<<<<____>>>>>>>><<<<<<<<<<________>>>>>>>>>>:...::::::::::::::
#=GC RF                    gAAAuaCCuCACGCCaGUGaGGuaGaGCAGguGuAAUGGGGGaCacCUGCuCA...aaaaAAAAGCGGCc
//
# STOCKHOLM 1.0

#=GF AC   RF01697
#=GF ID   Chlorobi-RRM
#=GF DE   Chlorobi-RRM RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   45.00
#=GF TC   46.60
#=GF NC   43.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Chlorobi-RRM_RNA_motif
#=GF SQ   18


AE006470.1/1802605-1802684 AAACUUUCUGGACAACGGUUGGGCCAGA-G--GCU-UUCAAGU-GAUU-U-GUGCUUUUG-AUU-AUUUGGC-AGCUUUUCUCUUU-CUAU
CP000096.1/1162497-1162569 AAA---UCAG-CCAAUGGUUGG--CUGAUCGCGCUAU-CAAGU-AAUU-G-GUGCUUU-G-GUU-ACUUGCC---UG-CUCUCUUU-UUAU
CP000492.1/1452008-1452080 AUG---UCAG-UCAAUGGUUGA--CUGAUC--GCUAUUCAGGU-AAUU-U-GUGCUUU-G-GUU-ACUUGUC-GGUA--UCUCUUU-UUUU
CP000607.1/178328-178256   AAA---UCAU-CCAAUGGUUGG--CUGAUC--GCUG-ACAGGU-UAU-GU-GUGCUUU--GGUU-ACCUGUUGAGCGUUUCUUUUUUC---
CP001108.1/1344490-1344426 AA----CCAC-AGAAUGGUU-----UGG-C--GCU-UUCAGGU-GAUU-U-GUGCUCUUG-AUU-AUUUGUA-AGCG------UAUAGUAU
CP000492.1/3066282-3066355 AAU---UUAG-CCAGUGGUUGG--CUGAUC--GCGAUUCAAAU-AAUU-U-GUGCUUU-G-GUU-AUUUGCU-UGCG--UCUCUAUUCUAU
CP001097.1/100693-100622   AA----UUAG-CCAAUGGUUGG--CUGAUC--GCG-UUCAAAU-AAUU-U-GUGCCUU-G-GUU-GUUUGCA-UGCG--UUUCUUUUCUAU
AASE01000008.1/61479-61554 AAG---CAAGACCAACGGUUGG-UCUGAAA--ACU-UUCAAGU-GAUU-U-GUGCUUUUG-GUU-AUUUGAC-AGUG--UCUCUUUUUGAU
CP000108.1/2033621-2033693 AA----UUAG-UCAAUGGUUGA--CUGAUUC-GCUACUCAAGU-AAUU-U-GUGCGUU-G-GUU-ACUUGAC-GGUA--UCUCUUU-UUCU
CP000607.1/1000654-1000582 AAU---UCAG-CCAAUGGUUGG--UUGAGA--AGUGUGCGGGU-AAUU-G-GUGCUAU-G-GUU-AUCUGCA-AGA--CUAUCUUU-UUAU
CP001101.1/1507528-1507452 AAUCG-UUAG-CCAAUGGUUGG--UUGAUC--GCUG-UCCGAU-GAUU-U-GUGCUUUUG-AUU-GUUUGAU-GGCGUUUCUCUCU-UUAU
CP001101.1/100323-100249   -ACA--UCAG-CCAAUGGUUGG--CUGAUC--GCUAU-CGGAU-AAC-GU-GUGCUUUU-GGUU-AUUUGAC-AGCGGUUCUCUUU-CUAU
AE006470.1/127930-127857   ---CAUUUAG-CCAGUGGUUGG--CUGAUC--GCU-UGCGAGAAAAC-AG-GUGCUUU--GGUUAUCUCGU--GGCG--UUUCUUUUUUAU
CP001108.1/134270-134199   A-----UUAG-UCAAUGGUUGA--CUGACC--GCA-UUCAAAU-AAUU-UUGUGCUUUUG-GUU-GUUUGUC-UGCG--CUUCUUU-CUAU
CP001110.1/1458931-1459003 AAU---UCAG-UCAAUGGUUGG--CUGAUC--GCUAUUCAAGU-AAUU-U-GUGCUUU-G-GUU-ACUUGCC-GGUA--UCUCUCC-CUAU
CP000096.1/94199-94127     AAA---CCAG-CCAAUGGUUGG--CUGGUC--GCU-UACAGGU-AAUU-U-GUGCCUU-G-GUU-AUCUGCAGAGCG--CCUCUUU-CUAU
AASE01000039.1/9214-9286   AAA---UCAG-CCAAUGGUUGG--CUGAUC--GCUAUGCAAGU-AAUU-U-GUGCUUU-G-GUU-ACUUGCC-GGCG--UCUCUUU-CUAU
CP001110.1/2187184-2187256 AAA---UCAG-UCAAUGGUUGA--CUGAUC--GCUAUUCAAGU-AAUU-U-GUGCUUU-G-GUU-ACUUGAC-GGUA--UCUCUUU-CUAU
#=GC SS_cons               :::...<<<<.<<<<___>>>>..>>>>-<..<<<--<<<<<<.<<<<._._______.>.>>>.>>>>>>-.>>>>..:::::::.::::
#=GC RF                    AAa...ucAG.cCAAUGGUUGg..CUgaUc..gCuaUuCaagu.aAuU.U.GUGCUUU.G.gUu.acuuGac.aGcg..UcUCUUU.uUAU
//
# STOCKHOLM 1.0

#=GF AC   RF01698
#=GF ID   Chloroflexi-1
#=GF DE   Chloroflexi-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   80.00
#=GF TC   96.20
#=GF NC   37.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Chloroflexi-1_RNA_motif
#=GF SQ   3


CP001337.1/880748-880664 CGUCCGGUGGAUUGCGACGGGCAGGAAGGCAGGCAUUGGCCGGCCUUCCUGCCCGCUUUCGGUUGCCGCUGACGGGAACACGUCA
CP001337.1/822346-822429 CGUCCCGUCGGCUGCGGCGGGCAGCACGGCCGACAUUGGCCGGCCG-GUUGCCCGCCUUCGUUUGUUGAUGACCGAAACGCAACA
CP001337.1/830453-830536 CGUCCCGUGGGAUGCGGCGGGCAGCACGGCCGACAUUGGCCGGCCG-GUUGCCCGCCUUCGUUUGUUGAUGACCGAAACGCAACA
#=GC SS_cons             :::::::::::::::<<<<<<<<<<-<<<<<<________>>>>>>.>>>>>>>>>>-<<<<<____>>>>>:::::::::::::
#=GC RF                  CGUCCcGUgGguUGCGgCGGGCagcAcGGCcGaCAUUGGCCgGCCg.gcuGCCCGcCUuCgguUGuugcuGaCcGaAACgCaaCA
//
# STOCKHOLM 1.0

#=GF AC   RF01699
#=GF ID   Clostridiales-1
#=GF DE   Clostridiales-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   48.00
#=GF TC   48.10
#=GF NC   47.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Clostridiales-1_RNA_motif
#=GF SQ   194


BABB01000778.1/1764-1911     ----AUCGUAGACA-A----UGAG-GA------AAAUAAAAAAUCAGAGGCAAGC-UCGCUUGCCUCUGAU-UUUUUAUUU-----GA-CGAA--UGU--CCGG-AUAU-GAGCAA---G-AAGC-AC------------CU-AA-------------GU-GC-GGA---UUGCGA------AUA-UACGG------A-GGCU-GGU-------------GUAA------------GCCAG-CCG----UGUCUA-CGAU----
BAAV01034327.1/142-292       ------UGUAAGC--AA------U-GA-----GCCAUGCAAGCUGAAA--UGUGC-UUGCACAGAUUUCAG-CUUAUAUGGC----GA-A-----UGUCAAUAA-U----GAACAAC--G-AAGG-UC------------GG--A-------------GA-CCGGGA--GUUGUGA----------AUUAU------C-AAGG-CUCGGGAGU-AGC---GA-A----GCUACGGAGAGAC-UUG-----GCUUA-CA------
BAAV01001515.1/1917-1759     ------AUAAAGCC-UG---GUCU-CA-----AAG-CGUAUAAAUGAUG-CAAGC-UUGCUUGAAAAAAUU-UGUACGCUUU----AG-AGAC-GCUA--AUGG-ACAU-GAGCAA---G-AAGC-AC------------GG-UA-------------GU-GC-GGA---UUGCGA------AUG-UACAU------A-GGAU-UGCGGGAGU-------GAAA-------GCGUAGCAAU-CCGUA--GGCUUU-AU------
BAAV01002929.1/1019-863      ------UAUAACACCAG--AUUCA-AA-------AAA-AGACUGCGU--UCAUGC-UUGCAUGAAAACGCA-GUCUUUUU------UA-UGAAU-CGC--CAAA-AUAU-GAGAAA---A-UAGC-CC------------GA-UA-------------GG-GU-GGU---UUUCGA------AUA-UUUUGU-----A-GAAU-UGCGAGAGU-UC----GA-A-----GAACGUAGCAAU-UC-----GUGUUA-UA------
BAAU01003785.1/137-308       --------AAACGUCAG--GGGCA--------AAGUACAGGAAGCCGUU-CGGGC-UUGCACGAGAAGGCU-UCCUGCCAUU-------UGCCC-CG---CCUAAUGCC-GAAAAC---G-UAAU-AAAAAGUU------GUAAACAU----AACUUUUU-AUGGGA---CUUUGA------GGU-AUGGG----------AU-UACGGGAAU-UGC---GA-A----GCAAUGGAGUAAUCAG----GAGGUAG---------
BAAY01014504.1/21-201        ------UAUGACUUUAG--GGUCA-AA------AGGUAU-CAUC-GAU-GCACGC-UUGCAUGCAAUUCGA-UGUAUACCU-----UAGUGACC-CGC--ACUA-CACC-GAGAAA---G-UAAC-AGUUUGCUGC----AGGGAC----GCAGAAAAUUAGC-GGA---CUUCGA------GGU-GUAGU------C-AGAU-UAUGGAAAU-GC----GU-A-----GCAUGGAGCAAU-CUGAUU-AA-UCA-UA------
BAAU01003080.1/9-185         ------UGAUUAA--AG--GGUCA-AA------AGGUAU-CAUCGAU--GCAUGC-UUGCAUGCAAUUCGA-UGUAUACCU-----UAGUGACC-UGC--ACUA-CACC-GAGAAA---G-UAGC-AAUUUACUAUGC--GA--A---GC-UAGUAAAUUAGC-GGA---UUUCGA------GGU-GGAGU------C-AGAU-UACGGGAAU-GC----GG-A-----GCAUGGAGUAAU-CUGA----UUAAU-CA------
BAAU01005865.1/1412-1225     AUAAUAUGAUUAA--AG---GGUC-AA-----AAGGUAU-CAUC-GAUG-CAUGC-UUGCAUGCAAUUCGA-UGUAUACCUU----AGUGACC--CGC--ACUA-CACU-GAGAAA---G-UAGC-AAUUUACUAUGC--GA--A---GC-UAGUAAAUUAGC-GGA---UUUCGA------GGU-GGAGU------C-AGAU-UACGGGAAU-GC----GG-A-----GCAUGGAGUAAU-CUGA----UUAAU-CAUA-AAU
BABG01004091.1/375-562       AUUUUGUGAUUAA--AG---GGUC-AA-----AAGGUAU-CAUC-GAUG-CAUGC-UUGCAUGCAAUUCGA-UGUAUACCUU----AUUGACC--CGC--ACUA-CACC-GAGAAA---G-UAGC-AAUUUGCUGCG---GG-GA----CGUAGCAAAUUAGC-GGA---UUUCGA------GGU-GGAGU------C-AGAU-UACGGGAAU-GC----GU-A-----GCAUGUAGUAAU-CUGA----UUAAU-CAUA-AAU
BAAV01002036.1/1046-870      ------UGAUUAA--AG---GGUC-AA-----AAGGUAU-CAUC-GAU-GCAUGC-UUGCAUGCAAUUCGA-UGUAUACCUU----AUUGACC--CGC--ACUA-CACC-GAGAAA---G-UAGC-AAUUUGCUGCG---GG-GA----CGCAGAAAAUUAGC-GGA---UUUCGA------GGU-GUAGU------C-AGAU-UACGGGAAU-GC----GU-A-----GCAUGUAGUAAU-CUGA----UUAAU-CA------
BABB01002899.1/2303-2116     --AUUUUGUGAUUAAA-----GGG-UC--AAACG-GUAU-CAUC-GAU-GCAUGC-UUGCAUGCAAUUCGA-UGUAUGCCUUAUU-GA-CCCG--CAC--UACA-CC---GAGAAA---G-UAGC-AAUUUGCUGCG---GG-GA----CGUAGCAAAUUAGC-GGA---UUUCGA--------G-GUGGAG-----UCAGAU-UACGGGAAU-GC----GU-A-----GCAUGUAGUAAU-CUGA--UUAAUCA-UA-AAU--
BAAX01023897.1/957-790       ------AGGUUAA--G----GGUC-AA------AGGGUCGAAAGCGCGGUCAGGC-UUGCAUGAUAAGGCU-UUUGAACUU-----GU-GACC--CGC---UAA-ACAU-GAGGAA---G-UAGC-GAUUUGC-------G--UA--------GCAAAUCAGCGGGA---UUCCGA------AAG-UUUAC------A-GAAU-UGCGUGAGC-AGC---UU------GCUGCGAAGCAAU-UCG-----UUGACACA------
BABD01004363.1/554-380       --UUUUUGAUUAC--AG-----UG-UA--C-AAGUCCAGUCAUCCACC--UGUGC-UUGCACAAAGGUGGA-UGACUGGACUUAG-GA-CA----CGCC-CCAA-GAAU-GAGCAU---A-AAGU-GAAGC---------GA-AA----------GCUUC-AC-GAU---AUGCGA------AUG-CUUGGG-----AAGGAU-UGCGGGAGU-GC----GA-A-----GCACGUAGCAAU-CCG-----GAAAG-CAAAAA--
BAAV01016969.1/686-523       ------UAAUGCCU-----GAGUC-AA-----AAGGGCUA--ACCCCACAUGAAC-UUGCUCAUAAGUGGU-AAAAGACCUU----AG-GACCCGCGC--CC---AUAU-GAGCAAAAAG-CGGG-AA------------GACUA-------------UC-CCACGA--UAUGCGA------AUGUU--GGU-----A-GAAUCAA----AGUUGGG---GU-G----CCCCUGAAAUUAUAUA-----AAGUAC-UA------
BAAX01018853.1/543-708       -----AUGAUACA--AG---GGUC-AA--------AAGGUCAUGCGUUU-CAUGC-UUGCAUGAAAAAGCA-UGA-CUU-------AUUGACC--CGC--AAAA-CACC-GAANA----G-UAGC-CAUUUUUC------G--UA-------GAAAAAUGAGC-GGA----UUUGA------GGU-GUUUUU-----A-GGAU-UGCGAGGGC-AU----GA-A-----AUGCGAAGCAAU-CCCG----UGUAU-CAU-----
BAAU01028694.1/160-335       ------UGUAAGCCAAG---GGAA-CA-----AAAGUGCAGGUGCUGU-UCGUGC-UUGCACGAUAAGGCA-UCUGAC-UUU----GG-UUCC--CGCC-AAAA-ACAU-GAAGAA---G-AAGC-GAUUUGC-------A--UC--------GCAAAUCUGC-GGA---UUCUGA------AUG-UUUUU------A-GAAU-UGCGGGAGC-AGC---GU-A----GCUGCGGAGCAAU-UCGU--UGGCUUACCA------
BAAZ01005512.1/486-314       -----GUAAGCCAA-G----GGAA-CA-----AAAGUGCAGGUGCUGU-UCGUGC-UUGCACGAUAAGGCA-UCUGAC-UUU----GG-UUCC--CGCC-AAAA-ACAU-GAAGAA---G-AAGC-GAUUUGC-------AU--U--------GCAAAUCUGC-GGA---UUCUGA------AUG-UUUUU------A-GAAU-UGCGGGAGC-AGC---GU-A----GCUGCGUAGCAAU-UCG----UUGGCU-UAC-----
BABE01004765.1/1080-911      ------UGAUAUC--AGG--GGUCAAA-----AGG-UCAAAAAGUC-GUUCGUGC-UUGCACGAUAAGAC--UUUUGAACUG----GG-GACC--CGC--CAA--CCAU-GAGAAA---G-UAGC-GAUUUAC-------G--CA--------GUAAAUCAGC-GGA---UUUCGA------AUG--UUUG------A-GAAU-UGUGGGAGC-UGC---UU-G----NCAGCGGAGCAAU-UCGUG---GAUAU-CA------
BABA01009489.1/308-486       -UGAG-UGAUACU--AG---GGUCGAA------AAG-UCACAAGCUGAU-CAUGC-UUGCAUGAAGAGGCU-UGUGACCUU-----GA-GACC--UGU--UAAA-ACAU-GAGGAU---G-CAGC-GAUUUUC-------AA--G--------GAAAAUCAGC-GA----AUCCGA------AUG-UUUUU------A-GAAU-UGCGAGAGU-UGC---GU-A----GCAACGAAGCAAU-UCGUA---AGUAU-CAAUUCAU
BAAZ01027624.1/869-703       ------UGAUACU--AG---GGCA-AA------AGCUCCAAAAGCCGUU-CGUGC--UGCACGAUAAAGCU-U--UGAGCU-----NG-GGAC-CCGC--AAAA-ACAU-GAGGAU---G-CAGC-GAUUUUC-------AA--A--------GAAAAUCAGC-GA----AUCCGA------AUG-UUUUU------A-GAAU-UGCGAAAGU-UGC---AU-A----GCAACGGAGCAAU-UCGUG---GGUAU-CG------
BAAV01006167.1/863-1032      ------UGAUACC--AG---GGUC-AA------AAGCUCCAAAAGCCGUUCGUGC-UUGCACGAUUAGGUU-UUUGAGCUU-----GG-GACC--CGC--AAAA-ACAU-GAGGAU---G-CAGC-GAUUUUC-------AA--G--------GAAAAUC-AG-CGA---AUCCGA------AUG-UUUUU------A-GAAU-UGCGAAAGU-UGC---AU-A----GCAACGGAGCAAU-UCGUG---GAUAU-CA------
BABD01002878.1/1413-1244     ------UGAUACU--AG---GGUC-AA----AAGCUCCAAAAGCCGU--UCGUGC-UUGCACGAUAAGGGU-UUU--GAGCUU---GG-GACC--CGC--AAAA-ACAU-GAGGAU---G-CAGC-GAUUUUC-------AA--G--------GAAAAUC-AG-CGA---AUCCGA------AUG-UUUUU------A-GAAU-UGCGAAAGU-UGC---AU-A----GCAACGGAGCAAU-UCGUG---GGUAU-CA------
BAAY01020707.1/871-700       ------UGAUACU--AG---GGUC-AA---AAGCUCCAAAAAGCCGU--UCGUGC-UUGCACGAUAAGGGU-UU--UG-AGCUU--GG-GACC--CGCA-AAAA-ACAU-GAGGAU---G-CAGC-GAUUUUC-------AA--A--------GAAAAUCAGC-GA----AUCCGA------AUG-UUUUU------A-GAAU-UGCGAAAGU-UGC---AU-C----GCAACGGAGCAAU-UCGUG---GGUAU-CA------
BABG01005618.1/356-523       ------UGAUACCC-GG----GUCAAA--AGG----UCUAAACCCAC--AUAAGC-UCGCUCAUAGGUGG----AUGAAAAACCU-UGGAACC--CGC--CCCA-AUAU-GAGCAUAAAAGCAGG-AU------------GA-UA-------------AU-CC-CACGAUAUGCUA------AUA-UUGGGU-----A-GGUU-UGUUGGAGU-GC----GU-A-----GCACGUAACAAU-CCGCA---GGUAU-CA------
BAAV01006120.1/617-787       -----AAGAUGCC--AG--GGUCA-AA------AGCCUGAAA-CCACGA-UGUGC-UUGCACAGGAGUGGU-UUUAUGGCU-----UAAUGACC-CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGAGC---------GU-AA----------GCUUC-AC-GAU---AUGCGA------AUA-UUGGAU-----A-GAAU-UGUGGGAGU-AC----GA-A-----GUACGGAACAAU-UCGUAU--GGCAU-CUU-----
BAAY01008255.1/580-413       ------UGAUACC--AG--AGUCA-AA-----AGGUC-UAAACCAAC--AUGAGC-UUGCUCAUAAGUGGG-UGAAUGACCU----UA-UG-CUGCGC--CCCA-AUAU-GAGCAUAAAAGUGGG-AU------------GA-UA-------------AUCCCGUGA--UGUGCAA------AUA-UUGGGG-----A-GGAU-UGUGGGAGU-GC----GC-A-----GCACGAAACAAU-CCAAA---UACAU-CG------
BABG01000170.1/596-450       ------UGAUACC--AG---GGUC-AA-----AAGGUCUAAACCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACAUU----GG-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-AU------------GA-UA-------------AUCCCAUGA--UAUGCGA------AUAUUUGGG------A-GAAU--------------------AU--------------AUAUUACA---UAUUU-CA------
BABG01013486.1/1030-1197     ------UGAUACC--AG---GGUC-AA----AAGGUCUGAGCCC-AC--AUGAGC-UCGCUCAUAGGUNGG-GGAAAGACCUU---GG-GAAC--CGN--CCCA-AUAU-GAGCAU-A-A-AAGU-GGGAU---------GA-UG----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----C-AGAU-UGUGGGAGU-GC----GUAU------CACGGAACAAU-CCGGUA---GUGU-CA------
BABG01029695.1/208-75        ------UGAUACC--AG---GGUC-AA----AAGGUCUA-AACCCAC--AUGAGC-UUGCUCAUAGGUGGG-UGAAAGACCUU---GG-GACC--CGC--CACG-AUAU-GC-------G------------------------A-------------------------------------AUA-UUGGG------G-GAAU-UGUGGGAGU-GC----UU-A-----GCACGGAACAAU-UCGCA---GGUAU-UA------
BAAU01002076.1/1922-1755     ------UGAUACC--AG--GGUCA-AA-----AGGUCU-AAACCCAC--AUGAGC-UCGCUCAUAUGUGGG-UGAAAGACCU----UG-GGACC-CGC--CCCA-AUAU-GAGCAU---A-AAAG-UGUGAU--------GA-UA---------AUCCCA--U-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAACAAU-CCGUA---GGUAU-CA------
BABG01002268.1/1271-1104     ------UGAUACC--AG--GGUCA-AA-----AGGUCUAA-ACCCAC--AUGAGC-UUGCUCAUAGGUGGG-UGAAAGACCU----UG-GGACC-CGC--CCCG-AUAU-GAGCAUAA-A-AGUG-GGAU----------GA-UA-----------AUCC-CA-UGA--UAUGCGA------AUA-UUGGGG-----A-GAAU-UGCGGGAGU-GC----GU-A-----GCACGGAGUAAU-UCGUA---GGUAU-CA------
BABG01000453.1/2218-2049     ------UGAUACC--AG-----GG-GC--AAAAGGUCUAA-ACCC-AC-AUGAGC-UCGCUCAUAGGUGGG-UGAAAGACCUUGU-GA-CC----CACUCCCUG-AUAU-GAGCAU-A-A-AAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGG-----A-GAAU-UGUGGGAGU-GC----GU-A-----GCACGGAACAAU-UCGUA---GGUAU-CA------
BAAZ01002221.1/1348-1515     ------AGAUGCC--AG--GGUCA-AA-----AGGUCU-AAGCCCAC--AUGAGC-UUGCUCAUAGGUGGG-UGAAAGACCU----UA-GAACC-CGC--CCUG-CUAU-GAGCAU-A-A-AAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
BAAU01024958.1/207-374       ------AGAUGCC--AG--GGUCA-AA-----AGGUCU-AAUCCCAC--AUGAGC-UUGCUCAUAAGUGGG-UGAAAGACCU----UG-GGACC-CGC--CCCA-AUAU-GAGCAU-A-A-AAGU-GGGAU---------GA-CA----------AUCCC-GC-GAU---AUGUGA------AUA-UUGGGU-----A-GAAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-UCGUA---GGCAU-CA------
BABG01002811.1/1092-925      ------UGAUACC--AG--GGUCA-AA-----AGGUCU-AAACCC-AC-AUGAGC-UUGCUCAUAGGUGGG-UGAAAGACCU----UG-GGACC-CGC--CCCG-AUAU-GAGCAU-A-A-AAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGG-----A-GAAU-UGUGGGAGU-GC----GU-A-----GCACGGAACAAU-UCGUA---GGUAU-CA------
BABG01000343.1/2063-1896     ------UGAUACC--AG--GGUCA-AA-----AGGUCU-AAACCC-AC-AUGAGC-UUGCUCAUAGGUGGG-UGAAAGACCU----UG-GGACC-CGC--CCCG-AUAU-GAGCAU-A-A-AAGU-GGGAU---------UA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGG-----A-GAAU-UGUGGGAGU-GC----GU-A-----GCACUGAGCAAU-UCGUA---GGUAU-CA------
BABG01000353.1/3907-4074     ------UGAUACC--AG--GGUCA-AA-----AGGUCUAAACCC-AC--AUGAGC-UUGCUCAUAGGUGGG-GGAAAGACCU----UG-GGACC-CGC--CCCG-AUAU-GAGCAU-A-A-AAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGG-----A-GAAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-UCGUA---GGUAU-CA------
BAAU01001385.1/1948-2124     --AUUAUGAUACC--AGG--GUCA-AA-----AGGUCU-AAACCC-ACA-UGAGC-UUGCUCAUAGGUGGG-UGAAUGACCU----UG-GGAC-CCGC--CCCA-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------GUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GUAU-UGUGGGAGU-GC----GU-A-----GCACGGAACAAU-CCGUAG--GGUAU-CAUAGU--
BABG01021235.1/944-778       ------UGAUUCC--AG--GGUCA-AA------AGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAUGUGGG-GAAAGACUU-----UA-GGACC-CGC--CCCG-AUAU-GAGCAU-A-A-AAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAG-UGUGGGAGU-GC----GU-A-----GCACGAAGCAAU-CCGUA---GGUAU-CA------
BABG01006456.1/435-583       ------UGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGGU-----------------GCUAU--------------GUGCCAGU---GGCA--CA------
BABG01003277.1/999-1150      --------AGAUACCAG---GGUC-AA----AAGGUAUA-AAUCCAC--AUGAGC-UUGCUCAUAGGUGGG-UGAAAGACCUU---GG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGG-----A-GA---------AGU-------GUCA-------AUAUA------UAUAA-GUUGUUU---------
BABA01019112.1/596-425       ------CGAUACC--A-----GGUCAAA--AAGGUCAUGAAUACGAUC--CAAGC-UCGCUUGCAGGAGA--AUUCUAGAACUU-GGA-ACC---CGCCU-AAA-ACAU-GAGUAA---G-AAGC-CAU--GUU-----CGG-AA-------GAUGAAUGAGC-GGA---UUACGA------AUG-UGUUC------A-GAAU-GGCGAGAGA-GC----AA-A-----GCACGUAGCAAU-UC------GGUAU-CA------
BAAY01010317.1/1179-1351     ------UGAUACC--AG--GGGAC-AA-----AGUUUGGAAGACCGAC-GCAAGC-UUGCUUGCAGGAGGA-CUUGCAAAAU----UG-GGACC-CGC--CAAAAACAU-GAGUAA---G-AAGC-CAUUUUU-------GU-UA--------AAAAAUGAGC-GGA---UUACGA------AUG-UUUUCU-----A-GGAU-UGCGGGAGC-AC----AC-A-----GUGCGGAGCAAU-CGA-----CGAAU-CA------
BAAZ01003651.1/1125-947      --AUGAUGAUGCC--AG---GGGC-AA----AAGAGUGGAAAUCCGGAA-CAGGC-UUGCCAGCAGGAGGA-UUUUUGGACUU---GG-GACC--UGCU-AAAA-ACAU-GAGUAA---G-AAGC-CAGUAUUU------AAAGAA------AAAUA---AGC-GGA---UUAGGG------AUG-UUUUU------A-GAAU-UGCGGAAGU-GC----AA-A-----GCAUACAGCAAU-UC------GGUAU-CAUC-U--
BAAU01002871.1/989-818       ------AGAUAUC--AG---GGUC-AA----AAGGUCUAAAAUCCGACG-AGGGC-UUGCUUGAAGGAGGA-UUUUUGAACUU---GG-GACC--CGCC-AAAA-ACAU-GAGUAA---G-GAGC-CAUUUUUU------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------A-GAAU-UGCGGGAGU-GC----AA-A-----GCACGUAGCAAU-UC------GGUAU-CA------
BABG01026309.1/776-604       ------UGAUACC--AG---GGUC-AA----AAGGUCUAAAAUCCGAUG-AGGGC-UUGCAUGAAGGAGGA-UUAUUGAACUU---GG-GACC--CGCC-UAAA-ACAU-GAGUAA---G-GAGC-CAUUUUUU------GA--A-------GAUAAAUGAGC-GGA---UUACGA------AUG-UUUUA------A-GAAU-UGCGGGAGUUGC----AA-A-----GCACGUAGCAAU-UC------GGUAU-CA------
BAAU01018938.1/559-388       ------UGAUAUC--AG---GGUC-AA----AAGGUCGGAAAUCCGACG-CAAGC-UUGCUUGCAGGAGGA-UUUUUGAAUUU---GG-GACC--CGCC-AAAA-ACAU-GAGUAA---G-GAGC-CAUUUUUU------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------G-GAAU-UGCGGGUGU-GC----AA-A-----GCACGCAGCAAU-UC------GGUAU-CA------
BABG01019443.1/442-271       ------UGAUACC--AG---AGUC-AA----AAGGCCGAAAAUCCGA-UGCAAGC-UUGCUUGCAGUAGGA-UUUUUGAACUU---GG-GACC--CGAC-AAAA-ACAU-GAGUAA---G-AAGC-CAUUUUUU------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------A-GAAU-UGCGGGAGU-GC----AA-A-----GCACGUAGCAAU-UC------GGUAU-CA------
BABG01006738.1/1128-957      ------UGAUACC--AG---AGUC-AA----AAGGCCGAAAAUCC-GAUGCAAGC-UUGCUUGCAGGAGGA-UUUUUGAACUU---GG-GACC--CGAU-AAAA-ACAU-GAGUAA---G-GAGC-CAUUUUUU------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------A-GAAU-UGCGGGAGU-GC----AA-A-----GCACGUAGCAAU-UC------GGUAU-CA------
BABB01006594.1/1215-1043     ------UGAUACC--AA----GGUCAA----AAGGUCAUAAAUCC-GAUGCAAGC-UUGCUUGCAGGAGGA-UUUUUGAACUU---GGAAUC---CGCCAAAAA-GCAU-GAGUAA---G-AAGC-CAUUUUUU------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------A-GAAU-UGCGAGAGU-GC----AA-A-----GCACGUAGCAAU-UC------GGUAU-CA------
BAAU01010790.1/206-35        ------UGAUACC--AG---GGUC-AA----AAGUUCAGAAAUCC-AAUGCAAGC-UUGCUUGCAGGAGGA-UUUUUGAACUU---GG-GACC--CGCC-AAAA-ACAU-GAGUAA---G-AAGC-CAUUUUGG------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------A-GAAU-UGCGGAAGU-GC----AA-A-----GCACGUAGCAAU-UC------GGUGU-CA------
BAAX01004650.1/1582-1753     ------UGAUACC--AG---GGUC-AA----AAGGUCAUAAAUCC-GAUGCAAGC-UUGCUUGCAGGAGGA-UUUUUGAACUU---GG-GACC--CGCC-AAAA-ACAU-GAGUAA---G-AAGC-CAUUUUUU------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------A-GAAU-UGCGAGAGU-GC----AA-A-----GCACGUAGCAAU-UC------GGUAU-CA------
BABB01010898.1/183-12        ------UGAUACC--AG---GGUC-AA----AAGGUCAUAAAUCC-GAUGCAAGC-UUGCUUGCAGGAGGA-UUUUUGAACUU---GG-GACC--CGCC-AAAA-ACAU-GAGUAA---G-AAGC-CAUUUUUU------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------A-GAAU-UGCGAGAGU-GC----AA-A-----GCACGUAGCAAU-UC------GGUAU-CA------
BAAX01029733.1/904-738       ------UG-UACN--AG---GGUC-AA-----AGGUCGGGAGUCCGA--GCCAAC-UGGCUUGCAGGAGGA-UUG-GGACCU----UG-GACC--CGCC-AAAA-ACAU-GAGUAA---G-AANC-CAUUUUUN------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------A-GUAU-UACGGAAGU-GC----AA-A-----GCACGUAGCAAU-UC------GGUAU-CA------
BAAX01029732.1/509-679       ------UG-UACC--AG---GGUC-AA----AAGGUCGGGAGUCC-GAUGCAAAC-UUGCUUGCAGGAGGA-UUUGUGACCUU---GG-GACC--CGCC-AAAA-ACAU-GAGUAA---G-AAGC-CAUUUUUU------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------A-GUAU-UACGGAAGU-GC----AA-A-----GCACGUAGCAAU-UC------GGUAU-CA------
BABG01034003.1/219-392       ------CGAUGUACCAG---GGUC-AA----AAGGUCGGGAGUCC-GAUGCAAAC-UUGCUUGCAGGAGGA-UUUGUGACCUU---GG-GACC--CGCC-AAAA-ACAU-GAGUAA---G-AAGC-CAUUUUUU------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUU------A-GUAU-UACGGAAGU-GC----AA-A-----GCACGUAGCANU-UC----GGU--AU-CA------
BABA01033985.1/198-26        ------UGAUACC--AG---GGUC-AA----AAGGUUGGAAAUCU-GAUGCAAGC-UUGCUUGCAUGAAGA-UUUUUAAUCUU---GG-GACC--CGCC-AAAA-ACAU-GAGUAA---G-AAGC-CAUUUUUC------GC--A-------GAAAAAUGAGC-GGA---UUGCGA------AUG-UUUUUG-----A-GGAU-UGUGAGAGC-AC----GC-A-----GUGCGGAGCAAU-CC------GGUAU-CA------
BAAU01012045.1/8-179         ------UGAUACC--AG---GGUC-AA----AAGGUCCGAAAUCCGCU-GCAAGC-UUGCUUGCAAGAGGA-UUUUUGACCUU---GG-GACC--CGCC-AAAA-ACAU-GAAUAA---G-CAGC-CAUUUUUC-------A-UA-------GAAAAAUGAGC-GGA---UUAUGA------AUG-UUUUU------A-GGAU-UGUGAGAAC-AC----GC-A-----GUGCGAAACAAU-CC------GGUAU-CA------
BAAX01011900.1/516-344       ------AGAUACC--AG----GGU-CA---AAAGGUCAGAAGUUCGAC-GCAAGC-UUGCCUGCAGGAGAA-UUUUUGACCUUG--GG-ACC---CGCCA-AAA-ACAU-GAGUAA---G-UAGC-CAUUUUUC------AA--A-------GAAAAAUGAGC-GAA---UUACGA------AUG-UUUUCG-----A-AGAU-UGCGGGAGC-AU----AU-A-----GUGCGGAGCAAU-CU------GGUAU-CA------
BABA01008401.1/371-199       ------UGAUACC--AG---GGUC-AA----AAGGUCAGAAGUUCGAC-GCAAGC-UUGCUUGCAGGAGAA-UUUUUGACCUU---GG-GACC--CGCC-AAAA-ACAU-GAGUAA---G-UAGC-CAUUUUUC------AA--A-------GAAAAAUGAGC-GAA---UUACGA------AUG-UUUUUA-----A-GAAU-UGCGGGAGC-AC----GC-A-----GUGCAGAGCAAU-UC------GGUAU-CA------
BAAV01014729.1/399-571       ------UGAUACC--AG--GGUCA-AA-----AGGUCAGAAAGCCGAC-GCAAGC-UUGCUUGCAAGAGGU-UUUUUGAACU----CU-UGACC-CGCC-AAAA-ACAU-GAGUAA---G-UAGC-CAUUUUUC------AA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUUG-----A-AGAU-UGCGAGAGU-GC----AA-A-----GCACGUAGCAAU-CU------GGUAU-CA------
BABG01028078.1/59-230        ------UGAAGCUU------GUCGUCAAA----GGUCAUAAAGCCGAU-GCAAGC-UUGCUUGCAAGAGGU-UUU-UGAAC-----UCUUGACC-CGCC-AAAA-AUAU-GAGUAA---G-UAGC-CAUUUUUC------AA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUUG-----A-AGAU-UGCGAGAGU-GC----AA-A-----GCACGUAGCAAU-CU------GGUAU-CA------
BAAU01021894.1/499-327       ------UGAUACC--AG-----GG-UC--AAAAGGUCAGAAAGCCGAUG-CAAGC-UUGCUUGCAAGAGGA-UUUUUGACCUCUU-GA-CC----CGCC-AAAA-ACAU-GAGUAA---G-UAGC-CAUUUUUC------AA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUUG-----A-GGAU-UGCGAGAGU-GC----AA-A-----GCACGUAGCAAU-CU------GGUAU-CA------
BAAU01019454.1/338-511       ------AUGAUACC-AG-----GG-UC--AAAAGGUCA-GAAAGCUGAUGCAAGC-UUGCUUGCAAGAGGA-UUUUUGACCUUUU-GA-CC----CGACA-AAA-ACAU-GAGUAA---G-UAGC-CAUUUUUC------AA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUAUG-----A-GGAU-UGCGAGAGU-GC----AA-A-----GCACGUAGCAAU-CU-----GGUAUC-A-------
BAAU01006425.1/310-139       ------UGAUACC--AG---GGGA-----UAAAAGUCAGAAGUCUGAC-GCAAGC-UUGCUUGCAGGAAGA-CUUCUGACCUUUA----UCCC--CGC--CAAA-ACAU-GAGUAA---G-UAGC-CAUUUUAC------GA--A-------GAAAAAUGAGC-GGA---UUACGA------AUG-UUUUG------A-GGAU-UGUGAGAGC-AC----GAAA-----GUGCGGAACAAU-CC------GGUAU-CA------
BABG01019422.1/349-526       ------UGUCAUAC-AG---GGAA-UC----AAGGAGAAAAAAUCAACG-CAAGC-UUGCUUGCAGGGGAU-UUUUUCUCUUU---GA-UUCC--CGC--ACAA-ACAU-GAACAA---G-CAGC-CAUUUUUC------GU-AA-------GAAAAAUGAGC-GGA---UUAUGA------AUG-UUUGUG-----GAGAAU-CGCGGGAGC-AC----GA-A-----GUGCGGAGCGAU-UCUG---GUAUGA-CA------
BAAU01004259.1/2023-1862     ------CA-------UAAG------CA----GAGGAGAGCAAGGCGAGAUCGUGC-AUGCACGAAAAAGCU-UUUAUAUUACC---GAC-----CCGC--CCAA-ACAU-GAGAAA---G-AAGC-GAUUUAC-------GA--A--------GUAAAUCAGC-GGA---AUUCGA------AUG-UUUGC------A-GAAU-UGCGGGAGC-AGC---GA-A----GCUGCGGAGCAAU-UCGCAG--------UG------
BABG01022086.1/338-167       ------UAUUAUC--AAAA---GU-A----GAGGGACGAAGAGCCGUU--CGUGC-UAGCACGAAAAAGGC-UUUAUGUAUUUU--CG-AC---CCG---CCAA-ACAU-GAGAAA---G-GAGC-GAUUUAC-------AA--A--------GUAAAUCAGC-GGA---AUUCGA------AUG-UUUGG------A-GAAU-UGAGGGAGC-AGC---AA-A----GCUGCGGAGCAAU-UCGUA---GGUAU-UA------
BABG01022086.1/599-773       ------UUAUCAAAA--------G-UA--GAGGG-ACGAAGAGCCGUU--CGUGC-UACCACGAAAAAGGC-UUUAUGUAUUCUC-GA-C-----CCG--UCCA-ACAU-GAGACA---G-GAGA-GAAUU---------ACAAAGUA-------AACUC-GC-GGA---AUUCGA------AUGUUUGGAG-----A---AUUGGGGGGAGC-AGC---AA-A----GCUGCGGAGCUAUUAGUAAGUAUUGAU-CA------
BAAU01025016.1/257-80        ------UGAUGUA--AG---UGUC-AA----AAGUAUAAAAAGACGUU--UCUGC-UUGCAGAAUAAGACU-UUUUUA--CUU---GG-GACA--CGC--UAAA-CACC-GAAAAC---GCAAUA-AAAUGUCGU-----GAAU-------ACGGCAUUU-UA-UGAAA-GUUUGA------GGU-GUUUA------A-GGAU-UGCGUGAAU-UGC---AU-A----GCAAUGUAGCAAU-CCUGA---UAUAU-CA------
BAAU01001327.1/473-650       ------UGAUGUA--AG---UGUC-AA----AAGUAUAA-AAAGUCGUU-UCUGC-UUGCAGAAAAAGACU-UUUUUA--CUU---GG-GACA--UGC--UAAA-CACC-GAAAAC---GGAAUA-AAAUGUCGU-----GAAU-------ACGGCAUUU-UA-UGAAA-GUUUGA------GGU-GUUUA------A-GGAU-UGCGUGAAU-UGC---AU-A----GCAAUGUAGCAAU-CCUGA---UACAU-CA------
BABB01016599.1/587-763       ------UGAUGCA--AG--UGUCA-AA-------AGUAUAAAUUGCGU-UUGUGC-UUGCACAAUAAGNCA-UUUAUACU------UAUUGACA-CGCCGAACA-AC---GAGAAC---GGAAAU-AAAUGGUG-----UGAACA-------CACCAUUUUAU-GGGGA-GU-CGA--------GGGUGUCG-----AGGGAUGUGA---AAUUGC----GUNA-----GCAUGAAGCAAU-CUGGA---UGCAU-CA------
BABD01030819.1/530-707       ------UGAUGUA--AG--UGUCU-CA------AGUAUAAAUUGC--GUUUGUGC-UCGCGCAAAUUAGCC-CUUUAUACU-----UUUUGACA-CGC--CGAA-CACC-GA-------AAACGA-AAUAUAAUGGUGUGUA-CA---CGCCCUUUUAUU-UCGUGUUC-------------GGU-GUUCG------A-GGAU-AGCGGGAAUUGC----GU-AU----GCCUGGAGCAAU-CCGGU---UACAU-CA------
BABA01021654.1/738-917       -----AUGAUGUA--AG---UGUC-AA-----AAGUAUAAAUUGC--GUUUGUGC-UCGCACAAAUAAGCA-AUUUGUACUU----AUUGACA--CGC--CGAA-CACC-GAAAAC---G-AAAUCACAUGGUGU-----GAAC-------AUGCCAUUUUAUGGGA---GUCUGA------GGU-GUUCG------A-CGAU-UGCGCGGAU-UGC---AU-A----GCAUUGGAGCAUC-CGGU----UCCUU-CGU-----
BAAU01001711.1/3615-3436     ------UGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UCGCACAAAUAAGCA-AUUUAUACU-----UAUUGACA-CACC-GAAC-ACCU-CAAACU---CCCAUA-AAAUGGUGU-----GAAC-------ACGCCAUUU-UAUGGG---AGUUUG------AGG-UGUUCG-----A-GGAU-UGCGGGAAU-UGC---AU-A----GCAAUGGAGCAAU-CCGGU---UACAU-CA------
BAAU01018515.1/135-314       ------UGAUGUA--AG--UGUCA-GAAU-----UAUAGGAUAGCGUAA-UGUGC-UCGCACAAAUAAGCA-AUAAUACU------UAUAGACA-CGC--CGAA-CACC-GAAAAC---G-AAAU-AAAAUGGAGU----GA-AC-----AUGCCAUUAU-AUGGGA---GUAAGA------GGU-GUACG------A-GGAU-AGCGGGAAU-UGC---AU-A----GCAAAGGAGCAAU-CCGGU---AACAU-CA------
BABA01021655.1/915-740       ------GGAGGAA--AG---GUCA-AA------AGUA-AAAUGGCGU---UGUGC-UCGCACAAAUAAGCA-AUUGGUACU-----GAGUGAC-ACGC--CGAA-CUCC-GUAAAC---G-AAAU-AAAAUGGG------GUGAACAG----GCCAUUUU-AUGGGA---GUNUGA------GGU-GUUCG------A-GGAU-UGCGGGAAU-UGC---AU-A----GCAAUGGAGCAAU-CCGGU---UACAU-CA------
BABG01001408.1/592-769       ------UGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UUGCACAAAUAAGCA-AUUUAUACU-----UAUUGACA-CGCC-GAACAAC---GAGAAC---G-GAAU-AAAAUGGUGU----GAAC------GCACCAUUUU-AUGGGA---GUUCGA-------GG-UGUUCG-----A-GGAU-UGUG-GAAU-UGC---GU-A----GCAAUGGAACAAU-CCGGG---UACAU-CA------
BABG01003064.1/575-752       ------UGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UUGCACAAAUAAGCA-AUUUAUACU-----UAUUGACA-CGC--CGAA-CAAC-GAGAAC---G-GAAU-AAAAUGGUGU----GA-AC-----ACACCAUUUU-AUGGGA---GUUCGA------GGU-GUUCG------A-GGAU-UGCGA-AAU-UGC---GU-A----GCAAUGAAGCAAU-CCGGG---UACAU-CA------
BAAV01013666.1/622-801       ------UGAUGUA--AG--UGUCA-AA-----AAGUAUAAAUUG-CGUU-UGUGC-UCGCACAAAUAAGCA-AUUUAUACUU----UU-UGACA-CGC--CGAA-CACC-GAAAAC---G-GAAU-AAAAUGGUGU----GAAC------ACACCAUUUU-AUGGGA---GUUUGA------GGU-GUUCG------A-GGAU-UGCGGGAAU-UGC---AU-A----GCAAUGGAGCAAU-CCGGU---UACAU-CA------
BAAX01013747.1/612-800       -UAUUAUGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UUGCACAAAUAAGCA-AUUUAUACU-----UAUUGACA-CGC--CGAA-CACC-GAAAAC---G-GAAU-AAAAUGGUGU----GAAU------ACGCCAUUUU-AUGGGA---GUUUGA------GGU-GUUCG------A-GGAU-UGCGGGAAU-UGC---AU-A----GCAAUGGAGCAAU-CCGUA---GGUAU-CAUAAUA-
BABG01026309.1/567-389       ------UGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UCGCACAAAUAAGCA-AGCUGUACU-----UAUUGACA-CGC--CGAA-CACC-GAAAAC---G-AAAU-AAAAUGGUGU----GAAC------AUGCCAUUUU-AUGGGA---GUUUGA------GGU-GUUCG------A-GGAU-UGCGGGAAU-UGC---AU-A----GCAAUGGAGCAAU-CCGGU---UACAU-CA------
BABG01009698.1/320-498       ------UGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UCGCACAAAUAAGCA-AUUUAUACU-----UAUUGACA-CGC--CGAA-CACC-GAAAAC---G-GAAU-AAAAUGGUGU----GAAU------ACGCCAUUUU-AUGGGA---GUUUGA------GGU-GUUCG------A-GGAU-UGCGGGAAU-UGC---AU-A----GCAAUGGAGCAAU-CCGGU---UACAU-CA------
BAAU01018414.1/172-350       ------UGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UCGCACAAAUAAGCA-AUUUAUACU-----UAUUGACA-CGC--CGAA-CACU-GAAAAC---G-AAAU-AAAAUGGUGU----GAAC------ACGCCAUUUU-AUGGGA---GUUUGA------GGU-GUUCG------A-GGAU-UGUGGGAAU-UGC---AU-A----GCAAUGGAGCAAU-CCGGU---UACAU-CA------
BABD01009573.1/298-120       ------UGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UCGCACAAAUAAGCA-AUUUAUACU-----UAUUGACA-CGC--CGAA-CACC-GAAAAC---G-AAAU-AAAAUGGUGU----GAAC------ACGCCAUUUU-AUGGGA---GUUUGA------GGU-GUUCG------A-GGAU-UGCGGGAAU-UGC---AU-A----GCAAUGGAGCAAU-CCGGU---UACAU-CA------
BABG01004235.1/1830-1652     ------UGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UCGCACAAAUAAGCA-AUUUAUACU-----UAUUGACA-CGC--CGAA-CACC-GAAAAC---G-AAAU-AAAAUGGUGU----GAAC------ACGCCAUUUU-AUGGGA---GUUUGA------GGU-GUUCG------A-GGAU-UGCGGGAAU-UGC---AU-A----GCAAUGGAGCAAU-CCGGU---UACAU-CA------
BAAU01019504.1/336-499       ------UGUA-UA--AGC-UCCCG-GA----CAGCGGCUGGGCGACU-GGUAAGC-UUGCUUGCCGAGACG-CACAGACAUUG---GA-CGGGG-CA---ACAG-GUAU-GAGCAC---G-CAGG-C------------AUA-UGC-------------G-CC-GGA---GUGCGA------AUG-CCUGUC-----G-GGAU-UGCGGGAGU-GC----GA-U-----GCACGGGGCAAU-CCGC---AGGUUA-UA------
BABG01032637.1/818-657       ------GUGAAAGU------GUUG-CC----AGGUGGUUA-GGUGGAUUGUGUAU-UUGCAUGCCAGGAAA-CAUAAACAUUU---GG-CAGC--CAG--GCCG-GUAUUAAGUAA---G-CAGG-GC------------AA-CA-------------GC-CC-GGA---UCAUGA------AUA-GUGGAG-----G-CAGU-UGUGGGAGU-GCC---AA-C----GGUAC-AUACAGC-UG-----ACUUUC-AU------
BABB01014983.1/514-357       ------CGAAAAGG------GU-G-UC----AGGGGGAUG--ACAGAAUGCGUGC-UCGCACGCAAGGAGU-UUCAAACAUUU---GA-CAAC--CAA--GCCGGGCAU-GAGUAA---G-CAGA-GC------------GA-AA-------------GC-CC-GGA---UUACGA------AUG-CCGGCG-----G-AGAU-UGCGGGAGC-AC----GC-A-----GUGCGGAGCAAU-CU-----CCUUU--CG------
BAAX01013085.1/392-234       ------UGAAAGC-------GUUG-UC---AAGCGGUUAGACAUU--CUGCGUGC-CUGCACGCAGUGAA--GAAUAGGCAUUU--GA-CGAC--CAA--GCCG-GUAU-G-GUAA---G-CAGG-GC------------GA-UA-------------GC-CC-GGA---UUACGA------AUG-CUGGCG-----G-UAGC-UGCGGGAGU-GCC---GA-A----GCCACGGAGCAGC-UG------GCUUU-CA------
BABG01015553.1/646-811       ------UAUGAAAGU-----CCCA-GA----CGGCAGCCAAGAAUGAGC-CAUGCUUUGCAUGAGCGAAUU-CUUGGAUAUCG---GA-UGGG--CUA--GACC-GUAU-GAGUAA---G-UAGG-GC------------GA-UA-------------GC-CC-GGA---UUACGA------AUG-CGGUCG-----G-CAGC-UGUGGGAGC-GCC---UAUA----GGCGCGGAACAGC-UG----ACUUUCA-UA------
BABA01025769.1/311-472       -----AUGAAAGU-------CCCG-GA----CGGCAGCCGCGAAUGAGC-UAUGC-UUGCAUGAGCGAAUU-CACGGGUAUCG---GA-CGGG--CAA--GCCG-GUAU-GAGCAA---G-GAGC-GC------------GA-UA-------------GC-GC-GGA---UUGCGA------AUG-CUGGCG-----A-CGAU-UGCGUGAGC-ACC---AA-A----GGUGCGGAGCAAU-CG------GCUUU-CAU-----
BAAZ01006092.1/658-819       -----AUGAAAGU-------CCCG-GA----CGGCAGCCGCGAAUGAGC-CAUGC-UUGCAUGAGCGAAUU-CACGGGUAUCG---GA-CGGG--CAA--GCCG-GUAU-GAGCAA---G-GAGC-GC------------GA-UA-------------GC-GC-GGA---UUGCGA------AUG-CUGGCG-----A-CGAU-UGCGGGAGC-ACC---AA-A----GGUGCGGAGCAAU-CG------GCUUU-CAU-----
BABA01017275.1/327-488       -----AUGAAAGU-------CCCG-GA----CGGCAGCCGCGAAUGAGC-CAUGC-UUGCAUGAGCGAAUU-CACGGGUAUCG---GA-CGGG--CAA--GCCG-GUAU-GAGCAA---G-GAGC-GC------------GA-UA-------------GC-GC-GGA---UUGCGA------AUG-CUGGCG-----A-CGAU-UGCGGGAGC-ACC---AA-A----GGUGCGGAGCAAU-CG------GCUUU-CAU-----
BABG01006513.1/1158-997      -----AUGAAAGU-------CCCG-GA----CGGCAGCCGCGAAUGAGC-CAUGC-UUGCAUGAGCGAAUU-CACGGGUAUCG---GA-CGGG--CAA--GCCG-GUAU-GAGCAA---G-GAGC-GC------------GA-UA-------------GC-GC-GGA---UUGCGA------AUG-CUGGCG-----A-CGAU-UGCGGGAGC-ACC---AA-A----GGUGCGGAGCAAU-CG------GCUUU-CAU-----
BABG01006599.1/897-736       -----AUGAAAGU-------CCCG-GA----CGGCAGCCGCGAAUGAGC-CAUGC-UUGCAUGAGCGAAUU-CACGGGUAUCG---GA-CGGG--CAA--GCCG-GUAU-GAGCAA---G-GAGC-GC------------GA-UA-------------GC-GC-GGA---UUGCGA------AUG-CUGGCG-----A-CGAU-UGCGGGAGC-ACC---AA-A----GGUGCGGAGCAAU-CG------GCUUU-CAU-----
BAAU01013082.1/887-727       -----AUGAAAGU-------CCCG-GA----CGGCAGCCGCGAAUGAGC-CAUGC-UUGCAUGAGCGAAUU-CACGGGUAUCG---GA-CGG---CAA--GCCG-GUAU-GAGCAA---G-GAGC-GC------------GA-UA-------------GC-GC-GGA---UUGCGA------AUG-CUGGCG-----A-CGAU-UGCGGGAGC-ACC---AA-A----GGUGCGGAGCAAU-CG------GCUUU-CAU-----
BAAU01013081.1/474-635       -----AUGAAAGU-------CCCG-GA----CGGCAGCCGCGAAUGAGC-CAUGC-UUGCAUGAGCGAAUU-CACGGGGAUCG---GA-CGGG--CAA--GCCG-GUAU-GAGCAA---G-GAGC-GC------------GA-UA-------------GC-GC-GGA---UUGCGA------AUG-CUGGCG-----A-CGAU-UGCGGGAGC-ACC---AA-A----GGUGCGGAGCAAU-CG------GCUUU-CAU-----
BABG01034775.1/591-754       ------UAUGAAAGU-----CCCG-GA----CGGCAGCCGCGAAUGAGC-CAUGC-UUGCAUGAGCGAAUU-CACGGGUAUCG---GA-CGGG--CAA--GCAG-GUAU-GAGCAA---A-GAGC-GC------------GA-UA-------------GC-GC-GGA---UUGCGA------AUG-CUGGCG-----A-CGAU-UGCGGGAGC-ACC---AA-A----GGUGCGGAGCAAU-CG----GCUUUCA-UG------
BAAU01019179.1/574-738       ------UAUGAAAGU-----CCCG-GA----CGGCAGCCGCGAAUGAGC-CAUGC-UUGCAUGAGCGAAUC-CACGGGUAUCG---GA-CGGG--CAA--GCCG-GUAU-GAGCAA---G-GAGC-GC------------GA-UA-------------GC-GC-GGA---UUGCGA------AUG-CUGGCG-----A-CAAU-AGCGGGAGC-ACC---AA-A----GGUGCGGAGCAAU-CG----GCUUUCAUUG------
BAAU01026019.1/748-585       ------UAUGAUAUU-----CCCG-GA----CGGCAUCCGCGAAUGAGC-CAUGC-AUGCAUGAGCGAACU-CACGGGCAUCG---GU-CGGG--CAA--GCCG-GUAU-GAGCAA---G---GA-GC----------UCGA-UA-------------GC-UC-GGA---UUGCGA------AUG-CUGGCG-----A-CGAU-UGCGGGAUC-ACC---AA-A----GGUGCGGAGCAAU-CG----UCUUUCA-UG------
BABG01018910.1/823-983       ------UGAAAGU-------CCCG-GA---CGGCAGCCG-CGAAUGAGC-CAUGC-UUGCAUGAGCGAAUU-C-ACGGGUAUCG--GA-CGGG--CAA--GCCG-GUAU-GAGCAA---G-GAGC-GC------------GA-UA-------------AC-GCCGAA---UUGCG-------AUG-CUGGCG-----G-CCAA-UGCGGGAGC-CAC---AA-A----GGGGCGGAGCAAU-CG------GCUUUCCA------
BAAU01018222.1/959-800       ------UGAAAGU-------CCCG-GA---CGCAAGCCG-GAAUUGAGC-CAUGC-UUGCUUGAGCGA-UU-UCACGGGUAUCG---A-CGG---CAAA-GCCC-GUAU-GAGCAA---G-GAGC-GC------------GA-UA-------------GC-GC-GGA----UGCGA-----AAUG-CUGGCG-----A-CGAU-UGCGGGAGC-ACC---AA-A----GGUGCGGAGCAAU-CG------GCUUU-CAU-----
BAAU01026020.1/410-570       ------UGAAAGU-------CCCG-GA---CGGAAACCGCGAAUAAGC-C-AUGC-UUGCAUAGAGCGAAU-UCACAGGCAUCG--AA-CGGG--CAA--ACCG-GUAU-GAGCAA---A-GAAC-GC------------GA-UA-------------GC-GC-GAA---UAGCGA------AUG-CAGGCA-----A-CGAU-AGCGGGAGC-ACC---AA-A----GGUACAGAGCAAU-CG------GAUAA-CA------
BABG01008432.1/584-749       ----UGGGAUAUUA-AG--AUUUG-CA------AUAAAG-CCCAGACC-GACUGC-UUGCAGGCGAGGCUG-GGACUUUAU----UAG-CAAAU-CAA--ACAC-ACAU-GAGCAU---G-UAGG-AC------------GA-UA-------------GU-CC-GGA---AUGCGA------AUG-UGUGUC-----A-CGGA-UCCGAGAGC-AC----GA-A-----GUGCGGAGGAGC-CGUGU--UAAUA--CCCG----
BABG01026909.1/932-754       -GUCUUUGGUGAAU-AG---UCGG-UCA----AA-GCAUAGGCGGGAC-GACUGC-UUGCAGGCAGGAACG-CCUAUGCAUU---AGA-CGGA--CAA--ACAG-ACAU-GAGCAA---G-UAGG-GC------------GA-CA-------------GC-CC-GGA---AUGCGAAUGCGAAUG-GCUGUA-----G--CGG-UUCGAGAGU-GC----GA-A-----GCACGGAGAAACGCGUG---AUUCAC-CAAAGAU-
BAAZ01010534.1/457-622       -----AUAUAAUAAU-----UCCG-UC----AUGCAAAUAAGCAGCGAGG-CUGC-UUGCAGACGGAGCUG-CUUAUUUAUAU---GA-CGGA--UAA--ACAG-ACAU-AAGCAU---G-AAGG-AC------------GA-UA-------------GU-CC-GGA---AUGCGC------AUG-GCUGUU-----A-CGAU-UUCGGGAGU-UC----GA-A-----GAACGGAGAAAU-CGUG--AUUAUUA-UAU-----
BABG01021957.1/675-835       ------GUAUAAUA-AG-----CU-CACC---CAUA-AAAUCCUGCG-UGACUGC-UUGCAGGCAAAGCAG-GAUUUCUAUG---AGG-GGAG--CAA--ACAG-ACAU-GAGCAA---G-AAGG-AC------------GA-UA-------------GC-CC-GGA---UUGCGA------AUG-UCUGUG-----A-CGAU-UUCGAGAGU-GC----GU-A-----GCACGAAAAAAU-CG-----UGUUAUUAU------
BABG01021956.1/564-404       ------GUAUAAUA-AG-----CU-CACC---CAUA-AAAUCCUGCG-UGACUGC-UUGCAGGCAAAGCAG-GAUUUCUAUG---AGG-GGAG--CAA--ACAG-ACAU-GAGCAA---G-AAGG-AC------------GA-UA-------------GC-CC-GGA---UUGCGA------AUG-UCUGUG-----A-CGAU-UUCGAGAGU-GC----GU-A-----GCACGAAGAAAU-CG-----UGUUAUUAU------
BABA01014690.1/426-585       ------UAUAAUA--AA---CUCA-CC-----CAUAGAAAGUCCAC-AUGACUGC-UUGCAGGCAAGGUGU-ACUUUCUAUG---AGG-GGAG--UAA--ACAG-ACAU-GAACAA---G-UAGG-AC------------GG-UA-------------GU-CC-GGA---UUGUGA------AUG-UCUGUU-----A-CGAU-UUCGAGAGU-GC----GAUA-----GCACGGAGAAAU-CG------UAUUA-UA------
BABG01032678.1/440-280       ------CAGAUGA--AG--CUCAC-CC------AUAGAAAGCAUGAGC-GACUGC-UUGCAGGCGGCGAAG-GCUUUCUAU-----GAGGGGAG-CAA--ACGA-ACAU-GAGCAA---G-AAGG-AC------------GA-UA-------------GU-CC-GGA---UUGCGA------AUG-GUCGUU-----A-CGAU-UUCGAGAGU-GC----GU-A-----GCACGGAGAAAU-CGA-----UUAAGAUA------
BABG01005904.1/388-548       ------GACAUAAG-A-----CUC-----AACCAUAGAAAACAUCCGUGA-CUGC-UUGCAGGUAAAGGAU-GUUUUCUAU-GUU-GG-GAG---UAA--AACA-AUAU-GAGUAU---G-AAGG-AC------------GA-CA-------------GU-CC-GGA---AUACGA------AUA-UUGGUU-----G-CAAU-UUCGAGAGU-GC----GC-A-----GCACAUAGAAAU-UG-----CUUAUGAUA------
BAAZ01018676.1/282-125       ------AACAU----AG----CUC-A---UCC-AUAGGAAACAGACGU-GACUGC-UAGCAGGCAGCGGAU-GUUUCCUAUGAGA-G--GAG---CGG--ACAA-ACAU-GAGUAU---G-CAGG-AC------------GA-UA-------------GU-CC-GGA---AUACGA------AUG-UUUGUU-----A-CGAU-UUCGAGAGU-GC----GC-A-----GCACGGAGAAAA-CGUAU-----AUG-UU------
ABOU02000026.1/37629-37796   ------UGAUGCU--AG--GGUCA-AA------AGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCU-----UU-UGACC-CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000050.1/152044-151877 ------UGAUACC--AG--GGUCA-AA------AGGUCUGACACCAC--GUGUGC-UCGCACACUAGUGGUAGAAUGACCU-----UG-UGACC-CGC--CCCA-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCACGA--UAUGCGA------AUC-UUGGGU-----A-GGAU-UGUGGGAGC-AC----GU-A-----GUGCGUAACAAU-CCGUA---GGUAU-CA------
ABOU02000032.1/102267-102100 ------UGAUGCC--AG--GGUCA-AA------AGGUCUGACACCAC--GUGUGC-UCGCACACUAGUGGUAGAAUGACCU-----UG-UGACC-CGC--CCCA-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCACGA--UAUGCGA------AUG-UUGGGU-----A-GGAU-UGUGGGAGC-AC----GU-A-----GUGCGUAACAAU-CCGUA---GGUAU-CA------
ABOU02000006.1/26217-26050   ------AGAUACC--AG--GGUCA-CA------AGGUCUGACACCAC--GUGUAC-UCGCACACUAGUGGUAAAAUGACCU-----UG-UGACC-CGC--CCCA-AUAU-GAGCAUAAAAGCGGG-GC------------GU-AA-------------GCACUACGA--UAUGCGA------AUG-UUGGGU-----A-GGAU-UGUGGGAGC-AC----AU-A-----GUGCGUAACAAU-CCGUA---GGUAU-CA------
ABOU02000050.1/30313-30480   ------UGAUACC--AG--GGUCA-AA------AGGUCUGACACCAU--GUGUGC-UCGCACACUAGUGGUAGAAUGACCU-----UG-UGACC-CGC--CCCA-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUG-UUGGGU-----A-GGAU-UGUGGGAGC-AC----GU-A-----GUGUGUAACAAU-CCGUA---GGUAU-CA------
ABOU02000020.1/7403-7236     ------AGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUAUUCGGU------A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000015.1/694-861       ------UGAUGUC--AG---GGUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
ABOU02000036.1/12225-12058   ------AGAUGCC--AA---GGUC-AA-----AAGGUCUAAGCCCACA--UGAGC-UUGCUCACAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAUAAAA-GUGGAAU------------GA-UA-------------AUCCCACGA--UAUGCGA------AUA-UUGAGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
AAQL01002944.1/686-515       ------UGAUACC--AG----GAU-CA---AAAGUUCGGAAAUCUGAC-GCAAGC-UUGCUUGCACAAAGA-UUUAUGAACUU--GGA-AUC---CGCCA--AA-ACAU-GAGUAA---G-UAGC-CAUUUUU------CGA-AG--------AAAAAUGAGC-GGA---UUACGA------AUG-UUUUUG-----A-GGAU-UGCGGGAGU-AC----AA-A-----GUACGGAGCAAU-CC------GGUAU-CA------
ABOU02000034.1/55546-55713   ------UGAUACC--AG---GGUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACC--CGC--CCCA-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCACGA--UAUGCGA------AUG-UUGGGU-----A-GGAU-UGUGGGAGC-AC----GU-A-----GUGCGUAACAAU-CCGUA---GGUAU-CA------
ABOU02000037.1/8075-7919     ------AGAUGUCA-----GGGUC-AA-----AAGGUCUGAAACCAC--GUGUAC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACCCGCCCCG-----AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-G----------C-GGGU-------AGU-GC----GU-A-----GCACGAAACAAU-CCGU---UGGCAU-CA------
AAQL01001492.1/2869-2692     ------UGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UUGCACAAAUAAGCA-AUUUAUACU-----UAUUGACA-CGCC-GAACAAC---GAGAAC---G-GAAU-AAAAUGGUGU----GAAC------ACACCAUUUU-AUGGGA---GUUCGA-------GG-UGUUCG-----A-GGAU-UGCGA-AAU-UGC---GU-A----GCAAUGAAGCAAU-CCGGG---UACGU-CA------
ABOU02000047.1/13649-13478   ------UGAUGCC--AG---GGUC-AA----AAGUUACUAAGCCCACC-AUGAGC-UUGCUCAUAGGUGGG-UGAAAGACCUU---AG-GACC--CGC--CCCG-ACUAUGAGCAUAAAAGUAGGGAU------------GA-UA-------------AUCCCACGA--UAUGCGA-------AGAUUGGGU-----A-GGAU-UGUUGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000049.1/54819-54986   ------UGAUGUC--AG---GGUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GCCC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCAGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
ABOU02000035.1/2399-2566     ------UGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GAUC--UAC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACAGAGCAAU-CCGUA---GGCAU-CA------
AAXA02000006.1/32226-32385   ------UAUAAA---AGU-AUUAU-CA------AUAGAUAGCUUGGAG-GCAUGU-UUACAUGCAUUACAG-GCUAUCUAU-----UAGAUAAUCUGA--GCUG--CAU-GAACAA---G-AAGG-GC------------GA-AA-------------GC-CC-GGA---UUGUGA------AUG--UGGC------AGCAGA-UGCGGGAGU-GC----AA-A-----GCACGGAGCAUC-UGGA----UUUUA-UA------
ABOU02000052.1/12141-11974   ------UGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-AACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000007.1/34416-34583   ------UGAUGCC--AG--GGUCA-AA------AGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCU-----UU-UGACC-CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000034.1/13978-13811   ------UGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAUAAAA-AUGGGGC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUA---GGCAU-CA------
AAVL02000035.1/139817-139954 ------UGAUUAC--AA---CGUC-AA----AAAGUC-UUAUCCCGCU--UGUGC-UUGCACAAUAAAGGG-AUAAUGACUUU---GA-GACG--CGC--CC---ACAA-CA-------U-GC-----------------GAAUA-------------------------------------UUGAG--GGG-----AAGGAU-UGUGGGACU-GC----GA-A-----GCACGCAACAAU-CCGU----GUAAU-CA------
ABOU02000029.1/251-83        ------UGAUGCC--AG---GGUCAAA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
AAVL02000037.1/174692-174858 --------ACUCACCAA--CCCCC-GG-----AAC-UUUCAAGGCACC--UGUGC-UUGCACAAAGGUGCC-UUGAAAAGUU----UC-GGGGG-UGC--CUUA-UUAU-GAGCAUAAAA-GGGCGAC------------GA--A-------------GUCGCACGA--UAUGCGA------AUA-AUAAGG-----ACAGAU-UGCGGGAGC-GG----GA-A-----GCGCGUAGCAAU-CUGA--GGUGAGU---------
AAQL01000723.1/772-931       ------UGAAAGU-------CCUG-AA----CGGCAGCCAUGAAUGAGU-CAUGC-UUGCAUGAACGAAUU-CAUGGAUAUCG---GG-CAGG--CUA--AACU-GUAU-GAGUAA---G-CAGG-GC------------AA-UC-------------GC-CC-GGA---UUACGA------AUG-CAGUUG-----G-CAGU-UACGUGAGU-GCC---AU-A----GGCACGGAGUAAC-UG------ACUUU-CA------
AAVL02000036.1/99484-99318   --------AGCUUACAG---CGUA-GA----AAAGUCUU-ACUGCACC--UGUGC-UUGCACAAAGGUGCA-GAAAAGACUUU---GA-GACG--CGCC-CCGA-ACAU-GAGCAAAAAAGCGAA-GC------------GA--A-------------GC-UG-AGUGAUAUGCGA------AUG-UACGGG-----AAGGAU-UGUGUGAGU-GC----GA-A-----GCACGUAGCAAU-CCG---GUAAGCU---------
ABOU02000032.1/95004-94837   ------AGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GAAC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000046.1/32106-32273   ------AGAUGUC--AG---GGUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACC--CGC--CCAG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
ABEY02000023.1/60157-59998   ------UGAAAGU-------CCUG-AA----CGGCAGCCAUGAAUGAGU-CAUGC-UUGCAUGAACGAAUU-CAUGGAUAUCG---GG-CAGG--CUA--AACU-GUAU-GAGUAA---G-CAGG-GC------------AA-UC-------------GC-CC-GGA---UUACGA------AUG-CAGUUG-----G-CAGU-UACGUGAGU-GCC---AU-A----GGCACGGAGUAAC-UG------ACUUU-CA------
ABOU02000042.1/30676-30843   ------AGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-AACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
AAVL02000035.1/75876-75709   ------UAUUAUAC-AG---UGUC-AA-----AAGGUCUUAGCCCACC--UGUGC-UUGCACAAAGGUGGGAAAAUGACCUU----GA-GACA--CGC--UCCG-AUAU-GAGCAUAAAA-GGGAAGC------------GU-AA-------------GCUUCACGA--UAUGCGA------AUAAUCGGGG-----A-GGAU-UGCGGGAGU-GC----GA-A-----GUGCGGAGCAAU-CC-----GUAUAA-UA------
ABOU02000010.1/11853-12020   ------UGAUACC--AG--GGUCA-AA------AGGUCUGACACCAC--GUGUGC-UCGCACACUAGUGGUAGAAUGACCU-----UG-UGACC-CGC--CCCA-AUAU-GAGCAUAAAA-GUGGCAC------------GU-AA-------------GCACCACGA--UAUGCGA------AUG-UUGGGU-----A-GGAU-UGUGGGAGC-AC----GU-A-----GUGCGUAACAAU-CCGUA---GGUAU-CA------
AAQL01009672.1/669-843       ------UGAUAUC--AG---GGUC-AA-----AAGGUCAGAAAGUCGU-UCGUGC-UUGCACGAUAAGACU-UUG-GAGCUU----GG-GACU--CG---UCAA-ACAU-GAGAAA---G-UAGC-AAUUUAC-------GU--A--------GUAAAUCAGA-GGA---UUUCGA------AUG-UUUGAGUAUUGACAGGC-CAG----AG-UCAGGAAA-AUUUUUGACU---CUGGC-CU------GCUAUAUA------
ABEY02000008.1/42145-41983   ------AGAAAGC-------CCCA-GA----CGGCGAACAUGCAGCGU-UCAUGC-UUGCAUGAAACGCUG-CAUGUUCAUCG---GA-UGGG--CAG--AUAU-UCAU-GAGCAU---G-UAUG-CC------------GA-UA-------------GG-CA-GGA---AUGCGA------AUG-AAUGU------G-CGAU-UACGAGAGC-CAC---GA-A----GUGGCGAAGUAAU-CGUAAG--GCUUU-CU------
ABOU02000053.1/15696-15863   ------AGAUGUC--AG---GGUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
ABOU02000034.1/1573-1406     ------AGAUACC--AG--GGUCA-AA------AGGUCUGACACCAC--GUGUGC-UCGCACACGAGUGGUAGAAUGACCU-----UG-UGACC-CGC--CCCA-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCACUA--UAUGCGA------AUG-UUGGGU-----A-GAAU-UGUGGGAGC-AC----GU-A-----GUGCGUAACAAU-CCGUA---GGUAU-CA------
ABOU02000028.1/138359-138192 ------AGAUGUU--AG---GAUC-AA-----AAGGGUUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GCCC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-UA------
ABOU02000053.1/313-480       ------UGAUGCC--A---GGGUCAAA------AGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCU-----UA-GGCCC-CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
AAYW02000007.1/152558-152719 ------UGAAUAAC-----CCCGG-CA-----AGCAAUUACACAGCAU-GCCUGC-UAGCAGGCAAAGCUG-UGUAAUUAUU----UG-CCGGG-CAA--ACAG-ACAU-GAGCAU---G-AAGG-AC------------GA-AA-------------GU-CC-GGA---AAGCGA------AUG-GCUGAG-----G-CGAU-UUCGGGAGU-UC----GA-A-----GAACGGAGAAAU-CGUA---GUUAUU-CA------
ABOU02000027.1/54252-54086   ------UGAUACU--AG---GGUG-AA----AAGGUAUG-AAUCCAU--AUGAGC-CUGCUCAUAAGUGGA-UAAAAGACCUU---UG-AACC--CGU--CCCA-AUCU-GAGCAUAAAA-UGGA-AU------------UG-UA-------------AU-CC-UGAGAUAUGCGA------AUA-GUGGG------AUGGAU-UAUGGGAGU-GC----GU-A-----GCACCGAACAAU-CCAUA---GGUAU-CA------
ABOU02000045.1/33335-33167   ------AGAUGCC--AG---GGGC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUAUUCGGU------A-GGAU-UGUGGGAGU-GC----CGUA-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000036.1/901-734       ------UGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GU-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000026.1/49611-49444   ------UGAUGCC--AG---UGGC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAAACCUU----AG-GACC--CGC--CCCG-AUAU-GAACAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGUGA------AGA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000026.1/3951-3784     ------UGAUGCC--AG---GGUC-AA----AAGGUCU--AAGCCCAC-AUGAGC-UUGCUCAUAGGUGGA-UGAAAGACCUU---AG-GACC--CGC--CUCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCAUGAAACAAU-CCGUA---GGCAU-CA------
ABOU02000033.1/1730-1897     ------AGAUACC--AG--GGUCA-AA------AGGUCUGACACCACA--UGUGC-UCGCACACUAGUGGUAGAAUGACUU-----UG-UGACC-CGC--CCCA-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCACGA--UAUGCGA------AUG-UUGGGU-----A-GGAU-UGUGGGAGC-AC----GU-A-----GUGCGUAACAAU-CCGUA---GGUAU-CA------
AAVL02000027.1/21462-21630   ------UGAUUAC--AG-----UG-GA--UCAAAGUCAGCAGCCCACU--UGUGC-UUGCACAAGAGUGGG-GUGAUGACCUUGA-GA-CA----CGC--CCCCAACAU-GAGCAU---AAAAGU-GUAGC---------GC-AA----------GCUAC-AC-GAU---AUGCGA------AUGCUGGGGG-----A-GGAU-UGCGGGAGU-GC----GA-A-----GCACGUAGCAAU-CCG-----GUAAU-CA------
AAXA02000010.1/9926-9759     ------UGAUGCC--AG---GGUC-AA----AAGGUCUA-AAUCCAC--AUGAGC-UUGCUCAUAAGUGGA-UGAAAGAUCUU---GG-GACC--CGC--CCCA-AUAU-GAGCCU---AGAAGU-GGGAU---------GA-CA----------AUCCC-AC-GAU---AUGCGA------AUAAUUGGG------A-GGAU-UGUGAGAGU-GC----AA-A-----GCACGGAACAAU-CCGUA---GGCAU-CA------
ABGC03000035.1/101575-101752 ------UGAUGUA--AG--UGUCA-AA------AGUAUAAAUUGC--GUUUGUGC-UUGCACAAAUAAGCA-AUUUAUACU-----UAUUGACA-CGC--CGAA-CAAC-GAGAAC---G-GAAU-AAAAUGGUGU----GA-AC-----ACACCAUUUU-AUGGGA---GUUCGA------GGU-GUUCG------A-GGAU-UGCGA-AAU-UGC---GU-A----GCAAUGAAGCAAU-CCGGG---UACAU-CA------
ABOU02000056.1/160-327       ------UGAUGCC--AG---GGUC-AA----AAGGUCU--AAGCCCAC-AUGAGC-UUGCUCAUAGGUGGA-UGAAAGACCUU---AG-GACC--CGC--UCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000035.1/23673-23840   ------UGAUGCC--AG---GGUC-GA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GAGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGAAGU-GC----GU-A-----GCACGGAGCAAU-CCGCA---GGCAU-CA------
AAQL01000629.1/688-862       ------UAAAGCCC-AG----UCG-CC------AUGUAAGAACGC-UGUGUGAGC-UUGCUCACAUAUGCG-UUCCUACAU-----GCGCGA---CGCUAACCC-GUAU-GAGCAA-A-ACAGGG-ACCGAGC------CAA-AA-------GCGAGGGA-CC-GAU---UUGCGA------AUG-CGGGU------A-GGAU-UGCGGGAAU-GC----GUCA-----GCAUGGAGCAAU-CCG---UGGGCUU-UA------
ABEY02000023.1/72091-71928   ------UACAAUAAU----CCCAU-CA-----AGCAGAAAAGUGGACGA-ACUGC-UUGCAACAUCGGGCA-CUUUUCUAUU----UG-AUGGG-UAA--ACAG-UCAU-AAGCAC---G-CAGG-AC------------GA-UA-------------GU-CC-GGA---GUGCGC------AUG-GCUGGC-----A-CGAU-UUCGAGAGU-UC----GA-A-----GAACGAAGAAAU-CGUG--AUUAUUG-UA------
AAVO02000012.1/105629-105795 --------GAACACCAG---GGUU-AA-----AAACUGCAAAAGACGU-UCGUGC-UUGCACGAUAAGGCU-UUUG-AGUUU----GG-AACC--CGC---CAA-AUAU-GAGAAA---G-UAGC-GAUUUAC-------GA-UA--------GUAAAUCAGC-GGA---UUUCGA------AUA-UUUGC------A-GGAG-UGUGGGAGU-AGC---UU------GCUACGGAACACU-CCGU--GGUAC-----------
ABOU02000048.1/174081-174247 ------AGAUGCC--AG---GGGC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGUUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-UCGCAUAUCG-UGGG-AU------------GA-UA-------------AUCCCACGA--UAUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000039.1/74302-74135   ------AGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAU--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GGCC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000049.1/14048-14215   ------UGAUGUC--AG---GGUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAAAAUGACCUU----GA-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------ACGCCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
ABAX03000010.1/68909-68756   ------UGAUACC--AG---GGUC-AA-----AAGGGUA---UGCGUU-UCAUGC-UUGUAUGAAAAAGCA----GGGCUUU----GG-GACC--CAU--AAAA--CAU-GAGAAA---G-CAGC-CC------------GAUUA-------------GG-GC-GGA---UUUCGA------AUG--UUUUU-----A-GGAU-UGUGGGAGC-AC----AA-A-----GUGCGGAACAAU-CCGCA---GGUAU-CU------
ABOU02000050.1/140438-140271 ------UGAUACC--AG--GGGCA-AA------AGGUCUGACACCAC--GUGUGC-UCGCACACCAGUGGUAGAAUGACCU-----UG-UGACC-UGC--CCCA-AUAU-GAGCAUAAAAGUAGG-GC------------GU-AA-------------GCACCACGA--UAUGCGA------AUG-UUGGGU-----A-GGAU-UGUGGGGGC-AC----GU-A-----GUGCGUAACAAU-CCGCA---GGUAU-CA------
ABOU02000031.1/28256-28423   ------UGAUGUC--AG---GGUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCACGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
ABOU02000032.1/41539-41372   ------UGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-AACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGC-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000048.1/41861-41694   ------CGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
AAVL02000023.1/56132-55966   ------CGAUUGCAU----UGUCC-AA------AGGUCUUUUCUCACC--UUUGC-UUGCACAAUGAUGGGAAAAUGACCU-----UG-GGACA-CGC--CCGG-AUAU-GAACAUAAAG-GUGAAGC------------GU-AA-------------GCUUCGCGA--UAUGCAA------AUA-UCAGGG-----A-GGAU-UGCGGGAGU-GC----GU-A-----ACACGUAACAAU-CC----GUGCAAU-CA------
ABOU02000028.1/127880-127713 ------UGAUGUC--AG---GGGC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
ABEY02000022.1/37900-37738   ------CGCGUUAU-AA--UCCCG-UC----AAGCGCGC---ACAUGC-GAGAGC-UUGCUCGCGGCAUGU---AGCGCAUUU---GA-CGGGA-UGA--CGCG-ACAU-GAACAC---G-AAGG-CC------------GA-UA-------------GG-UC-GGA---GUGUGA------AUG-CCGCGC-----A-GAAA-UGCGGGAGC-AC----GA-A-----GUGCGAAGCAAU-UCUGUG-UUAACG-CG------
ABOU02000028.1/3639-3806     ------UGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AGA-UUGGGU-----A-GGAC-UGUGGAAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000017.1/92862-93029   ------UGAUGUC--AG---GCUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
AAVL02000037.1/286875-287041 --------AUAUUACAG---UGUC-AA-----AAGGUCU-UUUCCACC--UGUGC-UUGCACAAAGGUGGAAAAAUGACCUU----GG-GACA--CGC--CCACAAUAU-GAGCAA---AAAAGU-GGAGC---------GU-AA----------GCUUC-AC-GAU---AUGCGA------AUAUUGUGGU-----A-GGAU-UGUGGGAGU-GC----GA-A-----GCACGUAACAAU-CCG---GUAAUAA---------
ABOU02000020.1/5236-5069     ------AGAUGUC--AG---GGGC-AA----AAGGUCUAA--GCCCACA-UGAGC-UUGCACACUGGUGGU-AGAAUGACCUU---GA-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGGGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
ABOU02000050.1/2046-1878     ------UGAUACC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGGGGC------------GU-AA-------------GCACCACGA--UAUGCGA------AUG-UUGGGU-----A-GGAU-UGUGGGAGC-AC----GU-A-----GUGCGUAACAAU-CCGUA---GGUAU-CA------
ABOU02000047.1/5367-5200     ------UGAUGCC--AG---GGUC-AA----AAGGUCUA-AGCCCAC--AUGAGC-UUGCUCAUAGGUUGG-CGAAAGACCUU---AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GU----GU-A-----GCACGGAGCAAU-CCGCA---GGCAU-CA------
ABOU02000036.1/26948-26781   ------UGAUACC--AG--GGUCA-AA------AGGUCUGACACCAC--GUGUGC-UCGCACACGAGUGGUAGAAUGACCU-----UG-UGACC-CGC--CCCA-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCACGA--UAUGCGA------AUG-UUGGGU-----A-GGAU-UGUGGGAGC-AC----GU-A-----GUGCGUAACAAU-CCGUA---GGUAU-CA------
ABOU02000034.1/8847-8680     ------AGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUAUUCGGU------A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000037.1/173-6         ------AGAUGUC--AG---GGUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUU---GGCAU-CA------
ABOU02000035.1/71253-71086   ------AGAUGUC--AG---GGUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GG-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UCUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
AAXA02000013.1/250273-250440 ------AGAUGCC--AG---GGGC-AA----AAGGUCUA-AAUCCAC--AUGAGC-UUGCUCAUAAGUGGA-UGAAAGACCUU---GG-GCCC--CGC--CCCA-AUAU-GAGCCUAAAAGUAGG-AU------------GA-CA-------------AUCCCACGA--UAUGCGA------AUA-AUGGGG-----A-GGAU-UGUGGAAGU-GC----AA-C-----GCACGGAACAAU-CCGUA---GGCAU-CA------
ABOU02000055.1/90388-90555   ------UGAUGUC--AG---GGUC-AA-----AAGGUCUGACACCAC--GUGUGC-CUGCACACUGGUGGUAGAAUGACCUU----GA-GGCC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
AAVO02000013.1/48190-48022   ------UGAUACC--AG--GGGCA-AA------AAUUUCAAAUGAUGU-UCGUGC-UUGCACGAUAAAGCA-UUUGAAUUU-----GG-GGACC------UCCAAACAU-GAGGAA---G-UAGC-GAUUUAC--------A-UA--------GUAAAUCAGC-GGA---UUCCGA------AUG-UUUGA------A-GGAU-UGUGGGAGC-AG----UUUA-----CUGCGGAACAAU-CCGUA---AGUAU-CA------
AAVL02000031.1/48980-49147   ------CGCUUAC--AG--UGUAC-AA------GUCCAGUCAUCCACC--UGUGC-UUGCACAAAGGUGGA-UGACUGGAC-----UUAGGACA-CGCC-CCAA-GAAU-GAGCAU---AAAAGU-GAAGC---------GA-AA----------GCUUC-AC-GAU---AUGCGA------AUG-CUUGGG-----AAGGAU-UGCGGGAGU-GC----GA-A-----GCACGUAGCAAU-CCG-----GUAAG-CA------
ABOU02000023.1/2814-2981     ------UGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUAGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUAGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000049.1/30234-30401   ------UGAUGUC--AG---GGUC-AA-----AAGGUCUGAAACCAC--GUGUGC-UUGCACACUGGUGGUAGAAUGACCUU----GA-GACC--CGC--CCCG-AUAU-GAGCAUAAAAGUGGG-GC------------GU-AA-------------GCACCAUGA--UAUGCGA------AUA-GCGGGU-----A-GAAU-UGUGGGAGU-GC----GU-A-----GCACGAAACAAU-CCGUU---GGCAU-CA------
ABOU02000028.1/88980-89147   ------UGAUGCC--A---GGGUCAAA------AGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCU-----UA-GGCCC-CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000029.1/8103-7936     ------AGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-GACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-GC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
ABOU02000051.1/49001-48834   ------UGAUGCC--AG---GGUC-AA-----AAGGUCUAAGCCCAC--AUGAGC-UUGCUCAUAGGUGGGUGAAAGACCUU----AG-AACC--CGC--CCCG-AUAU-GAGCAU---AAAAGU-GGGAU---------GA-UA----------AUCCC-AC-GAU---AUGCGA------AUA-UUGGGU-----A-GGAU-UGUGGGAGU-UC----GU-A-----GCACGGAGCAAU-CCGUA---GGCAU-CA------
#=GC SS_cons                 ......(((((((..,,...<<<<.--.....<<<<<<<<<<<<<<<<.<<<<<_.___>>>>>->>>>>>.>>>>>>>>>>....--.>>>>..,,,..<<<<.<<<<.--<<<<...-.--<<.<<<<<.........__.__..........>>>>>.>>.---...>>>>--......>>>.>>>>>,.....,.<<<<.<<<----<<.<<....__._.....>>>>--->>>>>.>>,,....))))).))......
#=GC RF                      ......uGaugcc..AG...ggcc.aA.....aaggucuaaacccccu.gcguGC.UUGCacgcaaggggg.uuuagaccuu....ga.ggcc..CGc..ccca.acaU.GAGcAu...G.aAGc.gcuuu.........GA.uA..........aaagc.gC.GGA...aUgCGA......Aug.uugggg.....A.ggau.uGcGGGAGu.gc....gu.A.....gcaCGgAgCaau.ccGu....ggcau.Ca......
//
# STOCKHOLM 1.0

#=GF AC   RF01700
#=GF ID   Collinsella-1
#=GF DE   Collinsella-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   35.00
#=GF TC   37.90
#=GF NC   32.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Collinsella-1_RNA_motif
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   6


BAAV01020360.1/623-820       GGCAGCUCGCAGGAGUGCGGACUGUC------GUCUGA-UUGUUUGAGG-GUGCCAGAUGUAAAUAAUCGGUGGAGCGGCUGCAAAAG-----------------------------AGCCGUCUCGCUGGGUAAAAUCAGGAU---GUGCCGCGGAACCCGC--UCCUCAGCUAGUCACACUUCGGAAGCGCGGGCAACGC--AGGUAUUAUCGUUCUAAAGGGCCGGCUGCAA-CCGGCCC
AM263037.1/4029-4216         AGCGACAUGAG-----------GCCAUCUGCG------------CUCAU-GUGCUGAAUCCAAU----CGUUC--------GGUGGUUUAGGUUCUGUACCCAUUCCAUGGCGGCGG--------GAACGGGUAUAAUCGAAAUCGAAAGAAGCGGACCCCGCGCAGGU-GGCUA-----ACC-AGAUA-CGCGGGCGAUGCGGAUUU--UCA-GUUGCAAAGGCCGGGCUGCACUCCCGGCC
AAQL01011519.1/1637-1441     GGCAGCUCUCASGAGUGCGGGCUGCC------GUCUGA-UUGUUUGAGG-GUGCCAGAUGUAAAUAAACAGUGGAGCGGCUGCAAAAG-----------------------------AGCCUCCUCACUGGGUAAAAUCAGGUU---GUGCCGCGGAACCCGC--UCCUCAGCUAGUCACACUUCGGAAGCGCGGGCAACGC--AGGUAUUAU-CGUCUAAAGGGCCGGCUGCAA-CCGGCCC
AAVN02000005.1/150266-150458 AACGGUAC--GGGACAGUGCGCAGUA------GUGCGAGCUGUCC--GUCGUGGUAGAUCUAAAUAAACGGUGGGACGGCUGCAAAAG-----------------------------AGCCGCCCCACCGGGCAAAAUCAAGGU---GUGCCGCGGAACCCGC--UCCUCAGUCGGUCA-ACUUUGGAAGCUCGGGCAACGC--AGGUGUUAA-UGUCUAAAGGGCCGG-GGCAA-CCGGCCC
AAQK01009958.1/721-525       GGCAGCUCUCAGGAGUGCGGGCUGCC------GUCUGA-UUGUUUGAGG-GUGCCAGAUGUAAAUAAACAGUGGAGCGGCUGCAAAAG-----------------------------AGCCUCCUCACUGGGUAAAAUCAGGUU---GUGCCGCGGAACCCGC--UCCUCAGCUAGUCACACUUCGGAAGCGCGGGCAACGC--AGGUAUUAU-CGUCUAAAGGGCCGGCUGCAA-CCGGCCC
AAQK01004081.1/545-363       CGC--CGC-C-GCAC-GGUGCCUUCG------GGCACCCUUGGU-G-GCAG-GCGUA----AAA-AAACGGUGGAGCGGCUGCAAAAG-----------------------------AGCCGCCCCACCGGGUAAAAUCAGAAAUGAAAGAAGCGGACCCCGCGCAGGU-GGCUA-----ACC-GGUUA-CGCGGGCGAUGCGGAUUU--CAG-GUUCAAAGGCCGGGGCUGCAA-CCCCGGC
#=GC SS_cons                 <<<<-<<<<<<<<---<<<<<<____......>>>>>>.--->>>>>>>.>>>>>,,,,,,,,,,,,,<<<<<<-<<<<<<_______.............................>>>>>>->>>>>>,,,,,,,,,,,,,,...<<<<<<<<---<<<<<..<<____________.______>>--->>>>>--->>>..->>>>>,,,.,,,,,,,,<<<<<<<______.>>>>>>>
#=GC RF                      ggCagCgcgcgggAgugcgggCugca......Gcccgc.uUGcccgcgc.GuGccaaAUcuAAaUAAACgguggAgcGGCuGcaaaag.............................aGCCgcCccaccGGGUAaAAUCaaaaU...gugccGCgGAaCCCGc..ucgUCaGCUAGUCA.ACuUaGgaAGCgCGGGCaAcGC..AgguacUaa.guUcuAAAGGgcgGGCUGCAa.CCcgcCC
//
# STOCKHOLM 1.0

#=GF AC   RF01701
#=GF ID   Cyano-1
#=GF DE   Cyano-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   41.00
#=GF TC   41.10
#=GF NC   40.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.40 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Yfr2
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   265


AACY020150049.1/2734-2667    UUGUGUGU--AGGAGA--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAGAUCAAUUUAAAA
AACY020276306.1/1163-1099    GAAUGUGUA-AGGGGG--------------AACGC----CUC-ACGGG--GUGGAAACAAGGUCACAC-UCCCGAGAG--ACGUUUUGGA
CP000551.1/950815-950748     UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY023996426.1/346-279      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY021689719.1/88-157       GAUUGUGUGAAGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUGUAAAUCAAUUUUUAA
BA000019.2/3740217-3740143   UUGUGUGUG-AGGAGC-AAGUUAAAAAUAAAAAGCGU--CU----GGG--GUGGAAACACGGCAACAC-UCCC---AGGCGCUUU-UUAA
CP000806.1/4333822-4333760   GAGAGCUUA-AAGAGU--------------AAAGCAC--UU----GGU--GUCGAAACAAGGCAAGAC-UUCC---AGGUGCUUUUCUCA
AACY022402615.1/111-44       AUGUGUGU--AGGAGG--------------AAUUGAU--CUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUUUUAAA
AACY021987453.1/787-720      UUGUGUGU--AGGAGG--------------AAUUAGU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAAAUAAAUUAAUUUUAAA
AACY020315515.1/115-182      ACGUGUGA--AGGAGU--------------GGUUUUA--UUA-AAAAA--GUGGAAACAAGGAAACAC-UUUAUUUAGUAAAACCUUAAA
CP000095.2/386958-387022     CAUUUUGUG-AGGAGU-UG-----------AGAUCCU--CC----GUA--GUGGAAACAAGGAAACAC-UUAC---GCCUGAUCUCACGA
AACY021095475.1/781-714      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUUAA
AACY023483591.1/1389-1322    CUGUGUGU--AGGAGA--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY023992293.1/359-424      --AUGUGUGUAGGAG---------------GAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAA-
AACY021317291.1/525-594      UGGCGUGUGAAGGAGU--------------AGUUCUA--CUU-UAUCA--GUGGAAACAAGGAAACAC-UUGAUUAAGUAGAACCAAUAA
AACY020128055.1/1112-1050    CAAUGUGUG-AGGAAA--------------ACGCC----UC--ACGGG--GUGGAAACAAGGUCACAC-UCCC---GAGGGACGUUUUGG
CP000435.1/785499-785563     UGAUUUGUG-AGGAGG--------------GCUUC----UUC-ACGGA--GUGGAAACUAGGAAACAC-GUCCAACUA--GAAGCCGAGA
CT971583.1/2191549-2191619   AUUCGUGUG-AGGAGU-GCU----------AAGCGCC--UCU-UCAGG--GUCGAAACAAGGACAGAC-UCCUGC-AACGCGCUUCACUU
AAVU01000009.1/97263-97206   AGGUCUGU--AGAAGA--------------AGUGC----UU----GGG--GUCGAAACACGGCCAGAC-UCCC---AG--GUACUUUUUC
CP001287.1/3572549-3572613   GUAAGAGUG-AUAUGA--------------AAAAG----CCU-UUGGA--GUCGAAACAUGGCAAGAC-GCCCAGAGG--CUUUUCAUUU
AACY022816974.1/444-377      GUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUUUUAAA
AACY021543993.1/684-620      CGGUAUGUG-AGGAGU-UG-----------AGAUCCU--CC----GUA--GUGGAAACAAGGAAACAC-UUAC---GCCUGAUCUCACGA
AACY023138387.1/700-769      UCGUGUGUGAAGGAGU--------------GGUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUAGUAAAACCAUAAA
AACY024093113.1/1400-1464    UCAUUUGUG-AGGAGG--------------GCUUC-U--UC--ACGGA--GUGGAAACAAGGCAACAC-GCCCAAAGA--GAAGCCGAGA
AACY021257245.1/511-579      UUGUGUGU--AGGAGG-------------AAUUGAUU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAAAUAAAUUCAAUUUUAA
AACY022065759.1/70-10        UCAUGUGUG-AGGGA---------------AAACUUC--AC----GGG--UUGGAAACAAGGACACAC-CCCC---GUGAGGUUU-CGGA
AACY022571874.1/310-243      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY020234471.1/890-953      GCCUAAGUG-AGGAGA--------------AAAGC----UC--ACGGG--GUGGAAACAAGGAAACAC-GCCGAGUGA--GUUUUUUAAA
CP000110.1/1389620-1389683   GGAUAUGUG-AGGA----------------AAACGCU--UC--ACAGG--GUGGAAACAAGGACACAC-UCCUAA-GAGUCGUUU-UGAA
AACY020357699.1/880-813      UCUCGUGUG-AGGAGU-GC-----------AGACGCU--AC--UCAGG--GUCGAAACAAGGACAGAC-UCCUGAGGU--UGUCUGAAUU
CP000554.1/356821-356885     UCAUUUGUG-AGGAGG--------------ACUUC----UCC-UCGGA--GUGGAAACAAGGAAACAC-GCCCAAAGA--GAAGUCUUGA
CP000825.1/982248-982181     CUGUGUGU--AGGAGG--------------AAUUGGU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGUUAUAAAUCAAUUUUAAA
AACY020078093.1/106-173      AGGUGUGU--AGGAGG--------------AAUUGGU--UUA-AUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUUUUAAA
AACY020541267.1/1187-1251    GGGUUUGUG-AGGAA---------------AAACGCC--UC--ACAGG--GUGGAAACAAGGACACAC-UCCUGC-GAGCCGUUU-UGGA
AACY023508876.1/308-375      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY020160454.1/749-682      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UCGAUAUAAAUCAAUUUUUAA
AACY021431087.1/186-119      AUCUGUGUG-AAGGAG--------------UGGUUUU--UUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUAGGAAACCAUAAA-
AACY023413985.1/295-229      CUGUGUGU--AGGAGU--------------GGUUUUA--CUG-AAACA--GUGGAAACAAGGGAACAC-UUGAUUUAGU-AAACCAUAAA
AACY020380635.1/918-986      GUAUGUGCG-AGGAGU-GCAG---------AGCAUCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGUGUUCCACU
AACY021325932.1/691-760      AUAAGUGUGAAGGAGU--------------GGUUUUA--CUA-AAACA--GUGGAAACAAGGAAACAC-UAGAUUUAGUAAAACCUAGAG
BX569695.1/152883-152951     GAAUGUGUG-AGGAGU-GCUG---------AACGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGUGUUCCACU
AAXW01000004.1/185218-185280 GAGAGAGCU-AGUAGA--------------AAAGCAC--UU----GGG--GUCGAAACACGGCAAGAC-UCCC---AGGUGCUUUUCUCA
BA000019.2/3740423-3740349   UUGUGUGUG-AGGAGC-AAGUUAAAAAUAAAAAGCGU--CU----GGG--GUGGAAACACGGCAACAC-UCCC---AGGCGCUUU-UUUA
AACY020954375.1/623-690      GAGUGUGU--AGGAGG--------------AAUCGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAUUCGAUUUUAAA
AACY021520000.1/142-211      AAGUGUGUGAAGGAGC--------------GGUUUUA--CGG-AAUCA--GUGGAAACAAGGAAACAC-UUUAUUUCGUGAAUCCACGAA
CP000097.1/2054658-2054726   UAGGGUGUG-AGGAGU-GCAA---------AACACCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGUGUUCCACA
AACY023389774.1/796-729      CUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY022748562.1/190-123      UUGUGUGU--AGGAGG--------------AAUUGGU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY020576553.1/3-65         GGGUUUGUG-AGGAAA--------------ACGCCUC--AC----AGG--GUGGAAACAAGGACACAC-UCCU---GCGAGCCGUUUUGA
AACY023869238.1/444-376      AUUUGUGUG-AGGAGU-GCUG---------AACGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGUGUUCCUCU
CP000435.1/1138022-1138086   GAAAUCGUG-AGGAAG--------------ACUUC----UUC-GCGGA--GUGGAAACUAGGCAACAC-GCCCAAAGA--GAAGUCGAGA
AACY020220392.1/706-639      CUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
CP000552.1/45910-45978       GAGUGUGU--AGGAGA--------------GAUUUAU--CUAAAAAAA--GUGGAAACAAGGAAACAC-UCAAUUUAGAUAAAUCAAUAA
AACY023398564.1/398-331      UUGUGUGU--AGGAGA--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY020147429.1/1363-1432    AAAAGUGUGAAGGAGU--------------GGUUUUA--CUA-AAACA--AUGGAAACAAGGAAACAU-UUGAUUUAGUAAAACUUAGAA
BA000022.2/2730521-2730587   AGGUGUGUG-AGGAGU-AAGUU--------GAAGCCC--CC----GGA--GUCGAAACAAGGAAAGAC-GCCCAG-GG--GCUUUUUCU-
AACY022745118.1/849-916      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUUAA
CP000576.1/133115-133048     AUGUGUGU--AGGAGA--------------GGUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUCAUUUAGUAAAACCAGAAA
AACY023580922.1/763-700      GAGUGUGU--AGGAGA--------------AAGUG----AUU-UUUCG--GUGGAAACAUGGAAACAC-UUGAUUAAU--CAUUUUGAAA
AACY022560642.1/734-666      AUUUGUGUG-AGGAGU-GCUG---------AACGCCUCUAC----AGG--GUCGAAACAAGGACAGAC-UCCU---GUAUGUGUUCCUCU
AACY020729705.1/114-182      AUUUGUGUG-AGGAGU-GCUG---------AGCGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAAUGUGCUCCUCU
AATZ01000003.1/191809-191743 UACCUUGUG-AGGAAA--------------AAAUCCU--UC--ACAGG--GUGGAAACAAGGACACAC-UCCUGA-GAUUGAUUUCGUAA
AACY023379843.1/1267-1334    UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AAUA01000003.1/154002-153938 UCGUUCGUG-AGGAGA-UA-----------AAGCUUC--UC----GGG--GUGGAAACAAGGUCACAC-UCCU---GAGCAGCUUUCGGA
AAOK01000003.1/24359-24290   AUUUGUGUG-AGGAGC--------------UCAGCAG--UUUCACAGA--GUCGAAACAAGGAAAGAC-UUCUUUGAAUUGCUGACCCUG
AACY023503794.1/1502-1435    UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUUAAUUUUUAA
AACY023467326.1/485-417      UCGAGUGUGAAGGAGU--------------GGUUUAU--CU--AAACA--GUGGAAACAGGGAAACAC-UUGAUUUAGUUAAACCAGAAU
AADV02000078.1/6931-6871     GAGAAUGUG-AAGAGA--------------AAAGC----AC----UGA-GGUCGAAACAAGGCAAGAC-UUCAA--GU--GCUUUUCUUG
AACY020555356.1/89-157       AUUUGUGUG-AGGAGU-GCCG---------AACGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAAUGUGUUCCUCU
AACY023591125.1/679-615      AUGUGUGU--AGGAGU--------------AAGCA----GUAAAUUAA--GUGGAAACAUGGAAACAC-UUAAUAUAC--UGCUUUUAAA
BX548174.1/346826-346893     AGGUGUGU--AGGAGA--------------GGUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUAGUUAAACCAAGGA
BX569692.1/86136-86196       AUGGAAGUG-AGGA-A--------------AAAUCUA--AC----GGG--UUGGAAACAAGGACACAA-CCCC---GUGAGGUUU-CGGA
AACY021704362.1/132-65       UUGUGUGU--AGGAGG--------------AAUUGAU--UU--AUUUUA-GUGGAAACAAGGAAACAC-UAAAAUUAAAUCAGUUUUUAA
AACY021315144.1/556-623      GUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY020846405.1/740-673      UUGUGUGU--AGGAGG--------------AAUUGUU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY023370801.1/203-270      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY022969765.1/115-47       AGAUGUGUG-AGGAGU-GCUG---------UACGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAAUGCAUACCACC
CP000095.2/382482-382546     UUAUAUGUG-AGGAGU-UG-----------AGAUCCU--CC----GCA--GUGGAAACAAGGAAACAC-UUGC---GACUGAUCUCACAA
CP000828.1/407448-407375     CACUGUGUG-AGGAGCGAACU---------AAAAAAG--GGC-AUCAA--GACGAAACACGGCCAGUC-GUUGAUGCCCUUUUUUGCAUU
AAUA01000001.1/379823-379889 UUUCUUGUG-AGGAGU-UG-----------AACUCCUCUGU----GGA--GUGGAAACAAGGCAACAC-GUCC---ACACGAGUUCACGA
AACY023992381.1/371-440      AAAUGUGUGAAGGAGU--------------AGUUUUA--CUG-AAUCA--GUGGAAACAAGGAAACAC-UUGAUUUGGUAAAACUAUAAA
AANO01000044.1/1123-1054     AUCUGUGUG-AGGAGU-GCUG---------AACGCCUCUUC----AGG--GUCGAAACAAGGACAGACUCCCU---GAACGUGUUCCUCA
AACY022308197.1/474-544      AAGUGUGUGAAGGAGU--------------GGUUUUA--UCUGAAGCA--GUGGAAACAAGGAAACAC-UUGAUUUGGUAAAACUAUAAA
CP000117.1/4756822-4756897   UUGUGUGUG-AGGAGC-AAGUUAAAAAUAAAAAGCGC--CU----GGG--GUGGAAACACGGCAACAC-UCCC---AGGCGCUUUUUAAU
AACY023511526.1/1250-1317    UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
BA000019.2/3740057-3739982   AGUUGUGUG-AGGAGC-AAGUUGAAACUAAAAAGCAU--CU----GGG--GUGGAAACACGGCAACAC-UCCC---AGAUGCUUUUUAAU
AACY023811577.1/1142-1073    UAUUGUGUG-AGGAGU-GCCG---------AGCGCCU--CU--UCAGG--GUCGAAACAAGGACAGAC-UCCUGCAAC--GCGUUCCACU
AACY021216492.1/381-314      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY021691404.1/256-323      UUGUGUGU--AGGAGU--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
CP000553.1/53519-53454       AUACCUGUG-AGAAGU-UG-----------AGAUCCU--GC----GCA--UUGGAAACAAGGAAACAACUUGU---GCCUGAUCUUCAAA
AACY021138311.1/349-282      AUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUUAA
AACY020214504.1/1621-1554    UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAGAUCAAUUUUAAA
AACY020081738.1/987-1054     AUGUGUGU--AGGAGG--------------AACUGAU--UAA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUUCUAAUCAGUUUUAAA
CP000097.1/1422400-1422465   UAGCUCGUG-AGGAAA--------------AAAUCCU--UC--AAAGG--GUGGAAACAAGGACACAC-UCCUGA-GAUUGAUUU-CGAA
CP000110.1/2274186-2274254   UCUUGUGUG-AGGAGU-GCUG---------AACGCUACUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGUGUUCCUCU
AACY020543120.1/2060-2124    GAAGUCGUG-AGGAA---------------AAACGCC--UC--ACGGG--GUGGAAACAAGGUCACAC-UCCCGA-GAGACGUUU-UGGA
BX548175.1/2205028-2204960   AACAUCGUG-AGGGGU-GCGAAUC------AACAG-U--UC----AGG--GUCGAAACAAGGCAAGAC-UCCU---GAUUCUGUCCCACC
AACY020749022.1/336-272      CCAGUUGUG-AGGAGU-UG-----------AGAUCCU--CC----GCA--GUGUAAACAAGGAAACAC-UUGC---GCCCGAUCUUCAAA
AP009552.1/3189581-3189508   AAUUGUGUG-AGGAGUGAGAAG--------AAAGCAAAGUCC-UUGGG--GUCGAAACACGGCAAGAC-UCCC---GAGGGCUUUUCCAU
AACY022254776.1/700-633      UUGUGUGU--AGGAGG--------------AAUUG-A--UUAAUCUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUUCUCGA
AACY021168187.1/502-566      GGAUCUGUG-AGGAA---------------AAACGCC--UC--ACAGG--GUGGAAACAAGGACACAC-UCCUGC-GAGCCGUUU-UGGA
BX548174.1/654509-654576     AUGUGUGU--AGGAGA--------------AGUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGGUUUAGUAAAACUAUAUA
AACY021654136.1/450-517      AAGUGUGA--AGGAGU--------------GGUUUUA--CUU-AAUCA--GUGGAAACAAGGAAACAC-UUAAUUUAGUAAAACCAAUAA
AACY021633646.1/734-802      UUAUGUGUGAAGGAGU-G------------GUUUU----CUA-AAAUG--GUGGAAACAAGGAAACAC-UUAUAUUAGCAAAAACCAUUA
AACY020158054.1/210-277      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUUAA
AANO01000001.1/236655-236586 UCUUGUGUG-AGGAGUGCA-----------GAACGCUCUCCU---GGG--GUCGAAACGAGGACAGAC-UCCCG--GCAUCGUUCCACCU
CP000554.1/2447837-2447769   AACAUUGUG-AGGGGU-GCGAAUC------AACAG-U--UC----AGG--GUCGAAACAAGGAAAGAC-UCCU---GAAUCUGUCCCACC
AACY020243925.1/850-917      AUGUGUGU--AGGAGU--------------GGUUUUA--CUG-AAUCA--GUGGAAACAAGGAUACAC-UUGAUUCAAUAAGACCUUAAA
AACY022141642.1/329-396      AGGUGUGU--AGGAGA--------------GGUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUAGUUAAACCAAGGA
CP000435.1/1487818-1487754   GGUCGUGUG-AGGAGG--------------GCUUC----UUC-ACGGA--GUGGAAACAAGGCAACAC-GCCCUACGA--GAAGCCGAGA
AACY024084384.1/77-10        AUAUGUGU--AGGAGU--------------GGAUUUA--CUG-AAGCA--GUGGAAACAAGGAAACAC-UUGUUUUGGUAGAACCAUAAA
AACY022777151.1/226-294      CAAAGUGUG-AGGAGU-GCCG---------AACGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGUGUUCCUCU
AACY022960539.1/504-571      AUGUGUGU--AGGAGG--------------AAUUGAU--UUU-UUUCA--GUGGAAACAAGGAAACAC-UUGAAUUAAAUUAAUUUUUAA
CP000111.1/1173349-1173281   CAAGUGUGA-AGGAGU--------------GGUUUUAC-UC--AAGCA--GUGGGAACAAGGAAACAC-UUGGUUAGGUAAAACCAGAAA
AACY020221960.1/785-852      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUUAAUUUUUAA
AP008231.1/483196-483267     GGGCGAGUG-AGGAGU------GAACGCUCAGAACAA--CU----CCAAGGUCGAAACACGGAAAGACCUUGG---AGUUGUUCUUUG--
AACY020087340.1/667-600      AAGUGUGC--AGGAGU--------------GGUUUUA--CUG-AAGCA--GUGGAAACAAGGAAACAC-UUGAUUUGGUAGAACCGUAAA
CP000110.1/534384-534444     GUGGCAGUG-AGGA----------------AAAACCUU-GC----GGG--UUGGAAACAAGGACACAA-CCCC---GCGAGUUUU-CGAA
AACY021502744.1/632-699      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-CUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY020208029.1/1057-1124    UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCGAUUUUAAA
AACY020355416.1/2374-2435    UCAUGUGUG-AGGA-A--------------AAACUUC--AC----GGG--UUGGAAACAAGGACACAA-CCCC---GUGAGAUUUUCGGA
BX548174.1/972178-972111     --UUGUGUGUAGGAGA--------------GGUUU-U--AUUAAAUCA--GUGGAAACAAGGAAACAC-UCGAUUUAUUAGAACCAAUUU
AACY022003043.1/283-219      GAAGUCGUG-AGGAA---------------AAACGCC--UC--ACGGG--GUGGAAACAAGGUCACAC-UCCCGA-GAGACGUUU-AGGA
AACY020352918.1/899-839      AUGUAAGUG-AGGA-A--------------AAACCUA--AC----GGG--UUGGAAACAAGGACACAA-CCCC---GUGAGGUUUCGGA-
AAOK01000007.1/27940-27870   GUGAGUGUG-AGGAGUGCU-----------AAGCGCCUCUUC---AGG--GUCGAAACAAGGACAGAC-UCCUGC-AACGCGUUUCACUU
AACY022726725.1/589-656      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUUUUAAA
AANP01000001.1/504528-504459 AAUCGUGUG-AGGAGU-GCCG---------AGCGCCU--CU--UCAGG--GUCGAAACAAGGACAGAC-UCCUGCAAC--GCGUUCCACU
AACY023385722.1/1424-1491    UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY021676918.1/403-336      UUGUGUGU--AGGAGA--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAGAUCAAUUUAAAA
BX548175.1/1667396-1667332   UCGUUUGUG-AGGAGG--------------ACUUC----UCC-UCGGA--GUGGAAACAAGGAAACAC-GCCCAAAGA--GAAGUCUUGA
AACY020439943.1/1686-1617    AUACGUGUGAAGGAGU--------------GGUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUAGUAAAACCUUUAA
AACY022714742.1/605-673      UUUUGUGUG-AGGAGU-GCCG---------AACGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGUGUUCCUCU
CP000097.1/1540528-1540466   CAUGAGGUG-AGGAUA--------------AAAAC----UU--ACGGG--GUGGAAACAAGGCCACAC-UCCCACUGA--GUUUU-CGGA
AACY020116240.1/716-783      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUUUUAAA
AACY020372967.1/245-178      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AATZ01000002.1/532918-532850 AUCUGUGUG-AGGAGU-GCUG---------AACGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGUGUUCCUCA
AACY020702184.1/174-238      GGGAUUGUG-AGGGA---------------AAACGCC--UC--ACGGG--GUGGAAACAAGGUCACAC-ACCCGA-GAGACGUUU-UGGA
AAXW01000069.1/22055-21992   GAGAGAGUA-AUGUAA--------------GAAAG----CAC-UUGGG--GUCGAAACACGGCAAGAC-UCCCAGGUG--UUUUCUAUU-
AADV02000005.1/52634-52696   GAGUGAGUU-AGUAGA--------------AAAACAC--UU----GGG--GUCGAAACACGGCAAGAC-UCCC---GGGUGUUUUUCUCA
AACY020569195.1/535-602      AUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
CP000435.1/1026369-1026433   UCAAAAGUG-AGGAGG--------------GCUUC----UUC-ACGGA--GUGGAAACUAGGUAACAC-GCCCAAAGA--GAAGCCGAGA
ABSE01000014.1/50433-50504   UGGGGUGUG-AGGAGU-GC-----------GGAACGUC-UCU-UCAGG--GUCGAAACGAGGACAGAC-UCCCGAAGAUCGUUCCAACGU
CP000111.1/952144-952077     AUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUUUUAAA
CP000435.1/2394765-2394834   CAUGACGUG-AGGAGU-GCUUUAC------GCCUCUU--UC----AGG--GUCGAAACAAGGAAAGAC-UCCU---GAAUGAGUUCUUCU
AACY022710478.1/720-787      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUGUGAAUCAAUUUUAAA
AACY023860816.1/1286-1350    GAAUAUGUG-AGGGA---------------AAACGCC--UC--ACGGG--GUGGAAACAAGGUCACAC-UCCCGA-GAGACGUUU-UGGA
AACY020118974.1/1162-1095    UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY021521267.1/495-432      AAUCUCGUG-AGGAGA--------------AAAGC----UC--ACGUG--GUGGAAACAAGGACACAC-UCACGUUGA--ACUUUCAGAA
AACY022739590.1/61-128       AUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUUAA
AACY021162595.1/581-511      ACUUGUGUG-AGGAGUGCU-----------AAGCGCCUCUUC---UGG--GUCGAAACAAGGACAGAC-UCCAGC-AACGCGUUUCACUU
AACY022203762.1/23-92        UAUUGUGUG-AGGAGU-GCCG---------AGCGCCU--CU--UCAGG--GUCGAAACAAGGACAGAC-UCCUGCAAC--GCGUUCCACU
AACY020313721.1/3625-3693    UCCUGUGUG-AGGAGU-GCUG---------AACGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGUGUUCCUCU
AACY021609961.1/124-57       UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGUUGUAAAUCAAUUUUAAA
AE017126.1/1298860-1298930   UAUAUUGUG-AGGAGU-U------------GAGAUUUA-GCG-AAGGA--GUCGAAACUAGGAAAGAC-UUCCUAAGCCAAUCUCAAAUA
AACY021389859.1/353-284      AUAUGUGUGAAGGAGU--------------GGUUUUA--UUA-AAAUA--GUGGAAACAAGGAAACAC-UUGAUUUAGUAAAGCCAAAAG
AACY023486067.1/927-860      AUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY020762549.1/469-402      GGCUGUGUG-AGGAGUGCA-----------AGCGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAAUGUGCCCACUU
AACY020132987.1/2089-2022    AUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAGAUCAAUUUAUUA
CP000553.1/1037361-1037424   UAAUUUGUG-AGGAGU-AG-----------AGAUCCUCCGCA--------GUGGAAACAAGGAAACAC-UCA----GCCUGAUCUCACGA
AACY021891503.1/641-574      AUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY022693590.1/211-278      AUGUGUGU--AGGAGC--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUUAAUUUUUAA
BX569692.1/82335-82394       CCGAAAGUG-AGGAAA-AA-----------AUCUC----AC----GGG--UUGGAAACAAGGACACAA-CCCC---GU--GCGGU-UUCG
CT971583.1/901908-901843     AUUUGUGUG-AGGAAC-CG-----------GCAACCCC-AA----AGA--GUCGAAACAAGGUCAGAC-GUCU---UUGUGUUGCCGGCC
CP000552.1/977450-977385     UUGUGUGU--AGGAG---------------AGUUUUA--UUA-AAUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAUAAAAUU-AUUC
AACY022160529.1/638-705      UUGUGUGU--AGGAGG--------------AAUUGAU--UUU-UUUCA--GUGGAAACAAGGAAACAC-UUGAGAUAAAUCAAUUUUAAA
AACY020126105.1/87-20        UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUUUUAAA
AACY023516764.1/456-524      CUUCGUGUG-AGGAGUGCA-----------AAGCGUC--UCU-UCUGG--GUCGAAACAAGGACAGAC-UCCA---GCAACGCGUCUCAC
AACY021152381.1/572-511      UUGGAAGUG-AGGA-A--------------AAACCUC--GC----GGG--UUGGAAACAAGGACACAA-CCCC---GUGCGGUUUAGGAA
AACY021871929.1/236-303      AUGUGUGU--AGGAGG--------------AAUUGAU--UUA-CUCCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUUUUAAA
CP000095.2/983401-983465     UAAUUUGUG-AGGAGU-AG-----------AGAUCCU--CC----GCA--GUGGAAACAAGGAAACAC-UUGC---GCCUGAUCUCACGA
BA000039.2/599896-599961     AAGUGUGUG-AGGAGC-GAACCAGUUA---AGGGC----AC----CGA--GACGAAACACGGCCAGUC-GUCG---GU--GCUCUUU---
AACY023494626.1/598-665      AUGUGUGU--AGGAGG--------------AACUGAU--CUA-CUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAGUUUUAAA
AACY020225600.1/975-909      GUCCGCGUG-AGGAAA--------------AAACG----CCACACGGA--GUGGAAACAAGGACACAC--UCCCUAGAAGCGUUUUAGAG
CP000806.1/3842870-3842932   GAGAGAGUU-AGUAGG--------------AAAGCAC--UU----GGG--GUCGAAACACGGCAAGAC-UCCC---AGGUGCUUUUCUCA
AACY021130542.1/414-347      CUGUGUGU--AGGAGG--------------AAUUGAU--UUG-UUUCA--GUGGAAACAAGGUAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY023419487.1/832-765      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY021206527.1/452-519      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGUUAUAAAUCAAUUUUAAA
AACY020454526.1/1522-1585    CAAUACGUG-AGGAAA--------------AAAAC----UC--ACGGG--GUGGAAACAAGGUCACAC-UCCCGCUGA--GUUUUCGGAA
AACY020474987.1/1736-1672    GAAAGUGUG-AGGAA---------------AAACGCCAAAC----GGG--GUGGAAACAAGGUCACAC-UCCCGG-GAGACGUUU-UGGA
AACY020344237.1/1345-1283    UCGGGAGUG-AGGAAA--------------AAAGCUA--AC----GGG--UUGGAAACAAGGACACAA-CCCC---GUGAGUUUUCGAAG
AACY024024913.1/260-197      AAGUGUGU--AGGAGA--------------AGAUGAU--UUU---UCA--GUGGAAACAUGGAAACAC-UUGAU--UACUCAUCUUAAAA
BA000019.2/3744859-3744787   AAUAGUGUG-AGGAGC-AAGUUGAAAUUA-AGAGCGC--UU----AGA--GUGGAAACACGGUAACAC-UUCU---GAGCGCUUU-UUA-
AACY021940173.1/556-489      AUGUGUGA--AGGAGA--------------GGUUUUU--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUAGUAAAACCAAUAA
CP000553.1/401851-401915     UCUGCUGUG-AGGAGU-U------------GAGAUCCU-CA----GUA--GUGGAAACAAGGAAACAC-UUACGCCUG--AUCUCACGA-
CP000117.1/4756984-4757059   UUGUGUGUG-AGGAGC-AAGUUAAAAAUAAAAAGCAU--CU----GGG--GUGGAAACACGGCAACAC-UCCC---AGGUGCUUUUUAGU
AACY021214834.1/400-467      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY020653435.1/692-759      AUGUGUGU--AGGAGG--------------AAUUG-A--UUCAUUUCA--GUGGAAACAAGGAAACAC-UUGAUGUAAAUCAAUUUUAUA
AACY022927705.1/528-596      ACUUGUGUG-AGGAGU-GCUG---------AGCGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAAUGUGUUCCUCU
AACY020630165.1/61-124       UUACUUGUG-AGGAGA--------------AACGC----UC--ACGGG--GUGGAAACAAGGACACAC-CCCCGCAGA--GUUUUCGAAG
CP000878.1/1238813-1238882   GAAAACGUG-AGGAGU-U------------GAGAUUC--ACU-AAGGA--GUCGAAACUAGGAAAGAC-UUCCUUGUUGAAUCUCAAAGA
AACY021411319.1/364-297      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGGCAUAAAUCAAUUUUAAA
AACY020244504.1/994-1064     CGAAGUGUG-AGGAGUGGA-----------AAACGCU--UCU-UCCGG--GUCGAAACAAGGACAGAC-UCCGGUCGUG-CGUUUCACUU
AACY022102368.1/629-696      AUGUGUGU--AGGAGA--------------GGUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUCAUUUAGUGAAACCAGAAA
AACY021030468.1/364-296      AAAUGUGUG-AGGAGU-GCUG---------UACGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAAUGCUUACCACC
AACY020383402.1/473-541      CAUGGUGUG-AGGAGU-GCUG---------AAUGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGCGUUCCACU
AACY020681922.1/250-313      AAAUUUGUG-AGGAGA--------------AAAGC----UC--ACGUG--GUGGAAACAAGGACACAC-UCACGUUGA--ACUUUCAGAA
AACY021587609.1/290-223      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY021039175.1/655-724      UUACGUGUGAAGGAGU--------------GGUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUAGUAAAACCUCUAA
AACY021990372.1/396-463      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY022533641.1/75-142       UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY023472650.1/1609-1542    UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGACUUAAAUCAAUUUUAAA
AACY023136525.1/270-203      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY021821683.1/357-421      AUGACCGUG-AGGAGU-UG-----------AGAUACU--CC----GCA--GUGGAAACAAGGAAACAC-UUGC---GACUGAUCUCACAA
CP000240.1/729361-729297     UGAGGAGUG-AAGAGA--------------AGAAG----CCU-CUGGG--GUCGAAACACGGACAGAC-GCCCAGGGG--UUUUUUCAUG
AACY021779742.1/204-138      UUGUGUGU--AGGAGG--------------AAUUGAU--UU--AUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUUUUUUA
CP000435.1/979499-979563     UCAUCCGUG-AGGAGG--------------GCUUC----UUC-ACGGA--GUGGAAACAAGGAAACAC-GUCCAACGA--GAAGCCGAGA
AACY021174268.1/622-556      UCUCGUGUG-AGGAGUGCG-----------GACGCUUC-UC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAGUUCGUCCGAUU
AACY020719504.1/365-434      UAACGUGUGAAGGAGU--------------GGUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUAGUAAAACUAGAAA
AACY023732078.1/355-289      AUAGAUGUG-AGGAGU-UG-----------GGAUC----CUC-CAGCA--GUGGAAACAAGGAAACAC-UCGCUUAAA--GAUCCACUAA
CP000095.2/44898-44834       AUAACUGUG-AAGAGU-UG-----------AGAUCCU--GC----GCA--GUGGAAACAAGGAAACAC-UUGU---GCCUGAUCUUAAAA
CP001291.1/1097567-1097639   UGUGGUGUG-AGGAAA-AAGU---------AGAGAAA--CGU-UUGGG--GUCGAAACACGGACAGAC-UCCCGAACGUUUUUCUCAUUU
AACY024065475.1/500-567      GUGUGUGU--AGGAGG--------------AAUUGAU--UUA-CUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY023418274.1/844-913      AAAUGUGUGAAGAAGU--------------AGAUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUGGUAAAUCCAUAAA
BX548174.1/383387-383453     UUGUGUGU--AGGAGA--------------GUUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUCGGU-AAAACCAGAA
AACY020393837.1/387-320      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY021543986.1/450-514      UAACUCGUG-AGGAGU-UG-----------AGAUCCU--CC----GCA--GUGGAAACAAGGAAACAC-UUGC---GACUGAUCUCACAA
AACY021920112.1/142-75       UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY023392962.1/1340-1407    AUGUGUGU--AGGAGG--------------AAUAGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUCUAAA
CP000435.1/997952-998016     UCACUUGUG-AGGAGG--------------GCUUC-U--UC--GCGGA--GUGGAAACUAGGCAACAC-GCCCAACGA--GAAGCCGAGA
BA000039.2/1092076-1092149   GACUUAGUG-AGGAGU-GAUUCGCAAAC--AAAAGUC--CU----AGG--GUCGAAACACGGCAAGAC-UCCU---AGGGCUUUUUAUUU
AACY020362163.1/470-402      GAAUGUGUG-AGGAGU-GCUG---------AACGCCUCUUC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAACGUGUUCCACU
AACY023486972.1/1286-1350    UGUCUUGUG-AGGAA---------------AAACGCC--UC--ACGGG--GUGGAAACAAGGUCACAC-UCCCGA-GAGACGUUU-UGGA
AACY021117314.1/253-186      AAAAGU-AG-AGGAGU--------------UGUUUUA--UUG-AAUUA--GUGGAAACAAGGAAACAC-UUUAUUCAAUAAAACUAAAAA
AACY021892181.1/234-167      UAGUGUGU--AGGAGA--------------GGUUUUA--AUU-AAGCA--GUGGAAACAAGGAAACAC-UUGUUUAAUUAAAACCAAUAU
AACY021287398.1/584-519      GAGGUUGUG-AGGAA---------------AAACGCG--CUC-AGGGG--GUGGAAACAAGGUCACAC-UCCCAAAAGA-CGUUU-UGGA
AACY021238100.1/83-150       UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
CP000435.1/1490305-1490241   AACUUUGUG-AGGAGA--------------GCUUC----UUC-UUGAA--AUGGAAACGAGGCGACAC-GUCCUAAAA--GAAGCCGAGA
BA000022.2/1558977-1558901   UUGUGUGUG-AGGAGU-AA---GAUUAAUAAGGAAGCAGCC--GGAGG--GUCGAAACAUGGCAAGAC-UCCUUGCGGACUUCCUUA---
AACY022095129.1/135-68       GUUUAUGUG-AGGA-A--------------AAAUCGC--UUC-ACGGG--GUGGAAACAAGGAAACAU-UCCCGAGAAGCGUUUUUGGAA
CP000239.1/383657-383721     UGAGGAGUG-AAGA----------------GAAGAAG--CCU-CUGGG--GUCGAAACACGGACAGAC-GCCCAGAGGUUUUUUC-AUG-
CP000435.1/772842-772778     UCAUUUGUG-AGGAAG--------------GCUUC-U--UC--ACGGA--GUGGAAACUAGGCAACAC-GCCCAACGA--GAAGCCGAGA
AACY023499622.1/1040-1109    ACGUGUGUGAAGGAGU--------------GGUUUAU--CUG---AAACAGUGGAAACAAGGAAACAC-UUUAUUUAGUUAAACCAUAAU
CP000576.1/949300-949233     UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGUAACAC-UUGAUGUAAAUUAAUUUUAAA
AACY020131256.1/2739-2807    GUGUGUGU--AGGAGG--------------AAUUAAU--UUU-AAUCAA-GUGGAAACUAGGAAACAC-UUGAUCUAGAUUAAUUUAAAA
AACY020691863.1/165-232      --GAGUGUGUAGGAGA--------------GGUUUUU--CUU-AAACA--GUGGACACGAGGAAACAC-UUGAUUAAGUAAAACUUAGAA
AACY023497110.1/1115-1182    AAGUGUGA--AGGAGU--------------GGUUUUA--CUU-AAGCA--GUGGAAACAAGGAAACAC-UUGUUUUAGUAAAAUCAUUAA
AACY020533745.1/1614-1545    AAUUGUGUG-AGGAGU-GCCG---------AGCGCCU--CU--UCAGG--GUCGAAACAAGGACAGAC-UCCUGCAAC--GCGUUCCACU
AACY022291016.1/307-374      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAGUUUUAAA
BA000022.2/3398354-3398286   ACAGGUGUG-AGGAAA-UUAGA--------AAAACAU--CU----GGA--GUCGAAACAAGGAAAGAC-GCCCC--AGGUGUUUUUUUAU
AACY021707697.1/409-342      UUGUGUGU--AGGAGA--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGUUGUAAAUCAAUUUAAAA
AACY022670896.1/316-249      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY022127596.1/673-604      AUGUGUGUGAAGGAGU--------------GGUUUUA--CUA-AUAUA--GUGGAAACAAGGAAACAC-UAGAUUUAGUAAAACCCAAAG
AACY021169804.1/544-475      AGAUGUGUGAAGGAGU--------------GGCUUUA--CUA-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUAGUAAUACCAAGAA
CP001037.1/7794370-7794295   UUGUGUGUG-AGGAGC-AAGUUAAAAGUAAAAAGCGU--UU----GGG--GUGGAAACACGGCAACAC-UCCC---AAGCGCUUUUUAAU
AACY020483279.1/1407-1338    GUAUGUGUGAAGGAGU--------------GGUUUUA--CUG-AAACA--GUGGAAACAAGGAAACAC-UUGAUUUAGUAAAACCUUAAU
AACY020157215.1/696-627      AUAUGUGUGAAGGAGU--------------GGUUUUA--UUA-AAUCA--GUGGGAACAAGGAAACAC-AUGAUUUAAUAAAAUCAUCAA
AACY023936622.1/770-706      UGUCGUGUG-AGGAAA--------------AACGC----CUC-ACGGG--GUGGAAACAAGGUCACAC-UCCCGAGAA--GCGUUUUGAA
AP009552.1/3427434-3427352   UAUCGUGUG-AGGAGUAUAAGUUCAGCAUAAGAGGAA--CCU-UUGGG--GUCGAAACACGGCAAGAC-UCCCAGAGGUUCUUCUUUUUC
AE017126.1/556707-556642     UGAGAUGUG-AGGAGA--------------AAGCU----UCUCUAAAA--GUGGAAACUAGGAAACAC-UUUUUAGGA--AGCUAAAAAA
AACY023423049.1/37-106       UGUUGUGUG-AGGAGUGAA-----------GAGCAUC--UCU-UCAGG--GUCGAAACAAGGACAGAC-UCCUG--GAUGUGUUCCGCUU
AACY023220809.1/650-584      UAAAUUGUG-AGGAAA--------------AAAUCCU--UC--ACAGG--GUGGAAACAAGGACACAC-UCCUGA-GAUUGAUUUCGAAA
AACY022794573.1/344-413      AUAUGUGUGAAGGAGU--------------GGUUUUA--CUG-AAGCA--GUGGAAACAAGGGAACAC-UUGAUUUGGUAAGACCAUAAA
CT978603.1/2048577-2048642   UUUCGUGUG-AGGAGU-GCG----------GACGCUUC-UC----AGG--GUCGAAACAAGGACAGAC-UCCU---GAGCUCGUC-CGAU
AACY022318658.1/442-509      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUAAAA
AACY020242363.1/719-656      AAUUUGGUG-AGGAGA--------------AAAGC----UC--ACGUG--GUGGAAACAAGGACACAC-UCACGUUGA--ACUUUUUGAA
AACY020480287.1/557-624      UUGUGUGU--AGGAGG--------------AAUUG-A--UUCAUUUCA--GUGGAAACAAGGAAACAC-UUGAUUUAAAUCAAUCUCAAA
AACY021601408.1/194-130      GAAUCUGUG-AGGAA---------------AAACGCC--UC--ACGGG--GUGGAAACAAGGUCACAC-UCCCGA-GAGACGUUU-UGGA
AACY021374053.1/374-307      CUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUUUAAA
AACY023193703.1/132-199      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCA--GUGGAAACAAGGAAACAC-UUGAUAUAAAUCAAUUCUAAA
AACY020642683.1/192-123      GAAGGUGUGAAGGAGU--------------GGUUCUA--CUG-AAAGA--GUGGAAACGAGGAAACAC-UUGAUUUGGUAAAACCAUGAA
AACY021298016.1/403-336      UUGUGUGU--AGGAGG--------------AAUUGAU--UUA-UUUCG--GUGGAAACAAGGAAACAC-UUGAUUUAAAUUAAUUUUAAA
CP000553.1/397455-397519     UUAUUUGUG-AGGAGU-UG-----------AGAUCCU--CC----GCA--GUGGAAACAAGGAAACAC-UUGC---GCCUGAUCUCACAA
CP002198.1/5651097-5651024   UGUGGUGUG-AGGAAAAAAGU---------AGAGAAG--UGC-UUGGG--GUCGAAACACGGAAAGAC-UCCCAGGCACUUUUCUCAUUU
CP001701.1/2720734-2720670   GUAAGAGUG-AUAUGA--------------AAAAG----CCU-UUGGA--GUCGAAACAUGGCAAGAC-GCCCAGAGG--CUUUUCAUUU
CP002198.1/5246061-5246134   UUCGGUGUG-AGGAGA-AAUGU--------AGAAAAG--CGU-UUGGG--GUCGAAACACGGCAAGAC-UCCCAGGCGCUUUUCUCAUUA
#=GC SS_cons                 :::::::::.:::::<..............<<<<<--..<<-.--<<<..<<<____________>>>.->>>--->>-->>>>>>::::
#=GC RF                      uugUGUGUG.AGGAGu..............aguucau..uca.auggg..GUGGAAACAAGGAAACAC.UcccuuugaaugaacuauaaA
//
# STOCKHOLM 1.0

#=GF AC   RF01702
#=GF ID   Cyano-2
#=GF DE   Cyano-2 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   42.40
#=GF NC   35.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Cyano-2_RNA_motif
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   57


AACY020962023.1/228-436    AGCAGC-ACGGGAGA-GCGACCCGUUAGCUGGCAGACAAUC-CAGUCCCCAUCC----CAC---GGCAACUGUG----GAUGGGACUG-GC-UUU----CUGC--------GC----UCUUCAGAUCUCUGAAAAGAGUUGGU-GCAUUCGCACUAAAUCUUUGUAUUGCGACGAACUUG-UUUGUAGCGGAU-ACCGCAUCGCUCGGGGGGAA----CGCUG----UUCUCCUCGCGGU-UCCGUCGCCCCA
CP000110.1/1587566-1587776 AGCAGC-ACGGG--A-GCGACCCGUUGGCUGGCAGACAAUC-CAGUCCC-AGCAC---AC----GGCAAG-CGU----GAUGGGGUUG-GC-UUU----GUGCU---UAUCCCCG--UCUUCCAAUAACGGGAAAGACUUAAU-GCAUCGCACCGAAAUACAUAAUGCCUCGUCAACGUU-AUGGA-ACGGCA-ACUGCAUCGCUCGGGGAGAA----UGCUG----UUCUCCUCGCGGU-UCCGUCGCCCCA
AACY021287395.1/727-523    GGCAGUACCGGGAGA-CUGACCCG-UAGCUAGCAGACAAUUC-AGUCCC-AGUAC---UC----GGCAAG-CGU----GAUGGGGCUU-GC-UUU----CAGC--------GC----UCUUCAGAUCUCUGAAAAGAGUCGGU-GCAUU--CAUUAAAGCUACGUAAUGCGACGAUCUUG-UUUGCAGCUGAU-ACCGCAUCGCUCGGGGAGAA----CGUCG----UUCUCCUCGAGGG-UCCGUGGCCCCA
AACY020080451.1/2335-2132  GGCAGUACCGGGAGG-GCGACCUGGUAACUGGCAGAAAUAGC-UCCCUU-GGCA----CG----AGCGAU---U----GCCAGGGGGA-GC-UUU----CUGC--------GC----UCUUCAAAUCUCUGAACAGAGUUAGU-GCAUUUGCUACAAGCCCGUGUAUCGCGGCGAGCUUG-UUCAU-GCGGAU-ACCGCAUCGCUCGGGGAGAA----CAGCG----UUCUCCUCGCGGU-UCCGUCGCCUAA
AACY020704875.1/621-398    AGCAGCACCGAGAGAGGCGACUCGGGAGCUGGCAGAAACCAGUCCCUAA-GGCC----UC----AGAAGA---C----UCCUUAGGGA-GUGUUU----UUGC-GCCUUCAUAUCGUCUUCCACUAACAAGAAAGAUUCCGUA-GUCUGCAGCUUGAAUCGAGAUCAUUCGUCAGGCUUG--GAAU-GCGGA--GUCGAAUCGCUCGGGAAACGUCGGCGCGACCGAUGUUUCUCUCGGC-UCCGCGGUCAGU
AACY020087787.1/1393-1187  AGCAGUACGGGGAGA-GCGACCCUGAUGCUGGCAGAAGAGU--UUCCCC-GUUG----AG----A-AGAU---C----AGCGGGGAAA-UC-UCU----CUGUG---CCUGAA----AGGUCUGAAAGCUUUAGACAUUCAGU-GCAUCAGGCACAAAUCAAUGUGCCGUCGCGAGCAUA-UUUAC-GCGGAA-ACCGCAUCGCUCGGGCAGGA----CCUGU----UUCUCCUCGCGGU-UCCGUGGCUCCA
AACY023859177.1/448-245    GGCAGCACCGGGAGA-GCGACCUGGUAGCUGGCAGAAAUAGC-UCCCUU-GGCA----CG----AGCGAU---U----GCCAUGGGGA-GU-UUU----CUGC--------GC----UCUUCAAAUCUCUGAAAAGAGUUAGU-GCAUUUGCGACAAGCGCCUGUAUAGCGGCGAACUUG-UUUAA-GCGGAU-ACCGCAUCGCUCGGGGCGAA----CAUGU----UUCUCCUCGCGGU-UCCGUAGUCCCG
AACY022144301.1/293-79     AGCAGC-ACGGGAGA-GCGACCCGUG-GCUGGCAGACAAUCCAGCCCCC-AUCC----CAC---GGCAACUGUG----GAUAGGGGCUGGC-UUU----CUGCG---CUUAACCCCGUCUUCAAAUAAAGGGAAAGAUUCAGU-GCAUUGCACUUGAUUGCACAACUUCUCGCCAGCGUU-AGGGA-ACGG---ACCGCAUCGCUCGGGGCGAA----CAUCU----UUCUCCUCGCGGU-UCCGUAGUCCCG
AACY023860816.1/629-425    GGCAGCACCGGGAGA-GCGACCUGGUAGCUGGCAGACAAAGC-CCCCAU-GGCA----CG----AGCGAU---U----GUCAUGGGGA-GC-UUU----CUGC--------GU----UCUUCAGAUCUCCGAAAAGAGUUGGU-GCAUUCGCACUAAAGCUGUGUAUUGCGACGAACUUG-UUUGCAGCGGAU-ACCGCAUCGCUCGGGGAGAA----CGGCG----UUCUCCUCGCGGU-UCCGUGGUCCCG
AACY020828517.1/466-667    GACGGCCUCAGUAGA-GCGAUCUGAGAGCUGGCAGAACCCC-UGUCUCC-CGCG----UG----AGCGAU---C----GCGGGGGACA-CC-GUU----CUGU--------------GCAACGGAAACCUGAAAAGAGUCAGU-GCAUAUGACGCACAGCCCUGUAUCGGAACGAGCUUG-UGAAG-GCAGAC-ACCGCAUCGCUCGGGAAGAG----CA-AG----CUCUUCUCGCGGUCUCUGCAGUCCCU
AACY023864898.1/528-698    -------------------------------AUAGUCAUGUC-ACCCUU-GGCA----CG----AGCGAU---U----GUCAGGGGUA-GC-UUU----CUGC--------GC----UUUUCAAAAAUCGGAAGAAAUUUGUA-CCUUUUGAGACGAAGGUUUGUAUACCGAGGAACGUG-UUUAA-GCGGAU-ACCGCAUCGCUCGGGGA-------CGUCG----UUCUCCUCGCGGU-UCCGUGGCCUCA
AACY023866064.1/421-205    AGCAGC-ACGGGAGA-GCGACCCGUUAGCUGGCAGAUAAUCCAGUCCUU-AUCC----CAC---GGCAUCUG-G----GACGAGGGCUGGC-UUU----CUGCG---CUUAAUCCCGUCUUCCAAUAAUGGGAAAGUUUCAGU-GCAUCGCACCGAAGUGCAUAACGCUUCACCAAGAUU-GUGGA-ACGGCA-ACCGCAUCGCUCGGGGAGAA----CGCAG----UUCUCCUCGCGGU-UCCGUCGUUCCA
BX569690.1/23572-23372     GACGGCCUCGGAAGA-GCGAUCCGAGAGCUGGCAGAACCCC-UGUCUCC-UGCG----UG----AACGAU---C----GCGGGAGACA-AC-CUU----CUGU--------------GCAACGGAAUGCUGAAAAGAGUCAGU-GCAUACGACGCAUGGCUCCGUAUCAGGAGGAGCUUG-UGUGU-GCAGAC-ACCGCAUCGCUCGGGAAGAG----CA-AG----CUCUUCUCGCGGU-UCUGUAGUCCUU
BX569692.1/5509-5287       AGCAGCACCGAGAGA-GCGACUCGGGAGCUGGCAGAAACCA--GUCCCU-AUGGCCUCAG----AAGACU---C----CUUAGGGACA-G--UUU----UUGC-GCCUUCAUAUCGUCUUCCACUAACAAGAAAGAUUCCGUA-GUCUGCAGCUUGAAUCGAGAUCAUUCGUCAGGCUUG--GAAU-GCGGA--GUCGAAUCGCUCGGGAAACGUCGGCGCGACCGAUGUCUCUCUCGGC-UCCGCGGUCAGU
CP000110.1/1429118-1429312 AGCAGCACGGGGAGA-GCGACCCUGGGGCUGGCAGACGAGU--UUCCCC-GUUG----AG----AGGGAU---C----AAUGGGGAAC-CC-UCU----CUCU------UAAA----GCUGUAGAAAUUCAGUGCAUCAGGCG-CAAAUCAGUGUGAC----------GUGGCGAACGUG-UUUAU-GCGGAU-AUCGCAUCGCUCGGGGAGGA----CUCGC----UUCUCCUCGCGGU-UCCGUGGCUCCA
AACY020344237.1/289-488    GACGGCCUCAGUAGA-GCGAUCUGAGAGCUGGCAGAACAC---GUCUCC-UGCG----UG----AGCGAU---C----GCGGGGGACA-AC-GUU----CUGU--------------GCAACGGAAUCCUGAAAAGAGUCAGU-GCAAACGACGCAUAGCUCUGUAUCACUACGAGCUUG-UGCAU-GCAGAC-ACCGCAUCGCUCGGGAGGAG----CA-AG----CUCUUCUCGCGGUCUCUGCAGUCCUU
AACY020723165.1/385-184    GACGGCCUCGGAAGA-GCGAUCCGAGAGCUGGCAGAACCCC-UGUCUCC-UGCG----UG----AGCGAU---C----GUGGGAGACA-CA-GUU----CUGU--------------GCAACGGA-UUCCGAAAAGACUUGGU-GGGUUCGCCAAGAAGCUUU-UAGCGCGGCGAAUUUG-GUUGU-CCCGAUGGUGGCAUCGCUUGGGAGGGA----CAGCG----UCCUUCUCGCGACCUCAGCAGCCCCC
CP000110.1/535123-534921   GACGACCUCGGAAGA-GCGAUCCGAGUGUUGGCAGAACCCC-UGUCUCC-UGCG----UG----AGCGAU---C----GCGGGAGACA-CC-GUU----CUGU--------------GCAACGGAAUUCUGAAGACACUUGGU-GUGUUCGUAGGGAAACUACGUAACACGGCGAACGUA-UGUUC-ACCGAU-GCCGCAUCGCUCGGGAAGGA----CAGAG----UUCUUCUCGCGGCCUCAGUAGCCUCC
AACY023862766.1/764-569    GGCAGUGCCGGGAGA-GCGACCCGGUAUCUGGCGGAAGA---GUCCUCU-GUUG----AG----AGCGAU---C----AACAGAGGAC----UUU----UCUU--------------AAUACUGAAAUCUGAAUUUAAGUAGU-GCAUAUGGACGGUUUGCCUGUGCACUCAGGAACGUA-UUCAG-GUGGAU-ACCGCAUCGCUCGGGGAGGA----CAAGU----UCCUCCUCGCGGUUCCCGUCUUU---
AACY020541253.1/628-424    GGCAGC-ACGGGAGA-GCGACCCGUCGGCUGGCAGUCAAAGCAACCCUU-GGCA----CG----AGCGAU---U----GUCAGGGGCG-GC-UUU----CUGC--------GC----UUUUCAGAAAUCGGAAGAAAUUUGUA-CCUUUUGAGACGAAGGUGUGUAUACCGACGAACUUGCUUUCA-GCGGAU-ACCGCAUCGCUCGGGGAGAA----CGCUG----UUCUCCUCGCGGU-UCCGUCGCCCCA
BX569692.1/83980-83778     GGCAGCACCGGGAGA-GCGACCCGGCAGCUGGCAGAUAAAGC-CUCCUU-GGCA----CG----AGCGAU---U----ACCAGGGAGA-GC-UUU----CUGC--------GA----UCUUUAGAUGUCUUAAAACACAUGGA-GUAUUUGACUCAAAGGUAUGUGCCGUUGCGAGCUUU-GUUAU-ACGUA--AUCGCAUCGCUCGGGGCAAA----CAUCG----UUUUCCUCGCGGU-UCCGUGGUCCCA
AACY021402715.1/576-377    GACAGCCUUGGGAGA-GCGACCCAUGAGCUGGCAGAACCCU--GUCUCC-UGCG----UG----AGCGAU---C----GCGGGAGACA-UC-GUU----CUGU--------------GGAACAGAA-CCCGAAGAGACUUGGU-GGGUUUGCAGCGAAGCUCUGUGUCAGGCCGAACUUG-UACAU-ACAGUC-ACCGCAUCGCUCGGGAAGAG----CA-AG----CUCUUCCCGCGGUUUCUGUGGUCCUU
AACY020499990.1/1754-1551  GGCAGC-ACGGGAGA-GCGACCUGUUGGCUGGCAGUCAAAGCAACCCUU-GGCA----CG----AGCGAU---U----GUCAGGGGUA-GC-UUU----CUGC--------GC----UUUUCAAAAAUCGGAAGAAUUUUGUA-CCUUUUGAGACGAAGGUUUGUAUACCGAGGAACGUG-UUUAA-ACGGAU-ACCGCAUCGCUCGAGAAGAA----CAUCG----UUCUUCUCGCGGU-UCCGUGGUCCCG
AACY021993227.1/240-37     GGCAGCACCGGGAGA-GCGACCUGGUGGCUGGCAGAAAUAGC-UCCCUU-GGCA----UC----AGCGAU---U----GCCAGGGGGA-GC-UUU----CUGC--------GC----UCUUCAGAUCUCUGAAAAGAGUUGGU-GCAUUUGCAGCAAGGCCUUGUAUCGCGGCGAACUUG-UUCAA-GUGCGA-ACCGCAUCGCUCGGGGAGAA----CAGCG----UUCUCCUCGCGGU-UCCGCCGCCCCA
AACY021195981.1/214-11     GACGGCCUCGGAAGA-GCGAUCCGAGAGCUGGCAGAACCCC-UGUCUCC-UGCG----UG----AGCGAU---C----GUGGGAGACA-CC-GUU----CUGU--------------GCAACGGAAUCCUGAAAAGACUUGGC-GCGUUCGCCGAGAAGUUCAGUAGCGCGGCGAACUUG-GUCGU-ACCGACGGUCGCAUCGCUCGGGAAGAA----CAGCG----UUCUUCUCGCGGCCUCAGUAGCCCCC
AACY021681433.1/249-449    GACGGUCACGGGAGA-GCGAUCCGAGGGCCGGCAGAACCCC--GUCUCC-CGUG----CG----AGCGAU---C----GCGGGAGACA-AC-GUU----CUGC--------------GCUGUUUAAAUCUGAAGAAAACUAGU-GCGUAUGGCCCAUCUGGGAACGGGUGAACGAGCUUU-ACCUU-UCAGUU-UCCGCAUCGCUCGGGAAGGG----CA-AC----CUCUUCUCGCGGUCUCCGCAGUCCUU
AACY020355415.1/3116-2919  GGCAGCCUCGGUAGA-GCGAUCCGAGAGCUGACAGAACAC---GUCUCC-UGCG----UG----AGCGAU---C----GCGGGAGACA-CC-GUU----CUGU----------------GCCAUAAACCUGAAAAGAGUUAGU-GCAUUUGAUGCACAGCUCUAUAUCAGUACGAGCUUG-UGAAU-GCAGAC-ACCGCAUCGCUCGGGGAGAA----CAGCG----UUCUCCUCGCGGU-UCCGCCGCCCCA
AACY023177878.1/234-437    GACGGCCUCAGUAGA-GCGAUCUGAGAGCUGGCAGAACCCG-UGUCUCC-UGCG----UG----AGCGAU---C----GUAGGAGACA-CC-GUU----CUGU--------------GCUAUAGAAUCCUGAAAAGACUUGGU-GCGUUCGCCAAAAAGUUCAGUGGUGCGGCGAACUUG-GUUGU-ACCGAUGGUCGCAUCGCUCGGGAAGGA----CAGCG----UUCUUCUCGCGGCCUCAGUAGCCCCC
AACY020474042.1/48-252     GGCAGUACCGGGAGA-GCGACCUGGUAACUGGCAGAAAUAGC-UCCCUU-GGCA----CG----AGCGAU---U----GCCAGGGGGA-GC-UUU----CUGC--------GC----UCUUCAGAUCUCUGAAAAGAGUUGGU-GCAUUCGCGCUAAAGCCUUGUAUAGCGACGAACUUG-UUUUCAGCGGAU-ACCGCAUCGCUCGGGGAGAA----CGUCG----UUCUCCUCGCGGU-UCUGUGGCCUCA
AACY020073648.1/525-327    AGCAGCACGGGGAGA-GCGACCCUGGGGCUGGCAGACGAGU--UUCCCC-GUUG----AG----AGCGAU---C----AAUGGGGGAA-CC-UCU----CUGU----------------GUCUAAAAGCUGUAGAAAUUCAGU-GCAUCAGGCGCAAAUCAGUGUGACGUGAUGAACGUG-UUUAU-GCGGAU-ACCGCAUCGCUCGGGGAGGA----CUCGC----UUCUCCUCGCGGU-UCCGUGGCUCCA
AACY022815789.1/321-525    GGCAGCACUGGGAGA-GCGACCUGGUAGCUGGCAGAUAUAGCCCCCCUU-GGCA----UG----AGCGAU---U----GCCAUGGGGA-GC-UUU----CUGC--------GC----UCUUCAAAUCUCUGAAAAGAGUUAGU-GCAUUUGCUACAAGCCCGUGUAUCGCCGCGAGCUUG-UUCAU-GCGGAU-ACCGCAUCGCUCGAGGAGAA----CAGCG----UUCUCCUCGCGGU-UCCGUGGCCCCA
AACY022973485.1/694-493    GACGGCCUCAGUAGA-GCGAUCUGAGAGCUGGCAGAACCCC-UGUCUCC-CGCG----UG----AGCGAU---C----GCGGGGGACA-CC-GUU----CUGU--------------GCAACGGAAACCUGAAAAGAGUCAGU-GCAUAUGACGCACAGCCCUGUAUCGGAACGAGCUUG-UGAAG-GCAGAC-ACCGCAUCGCUCGGGAAGAG----CA-AG----CUCUUCUCGCGGUCUCUGCAGUCCCU
CP000110.1/913565-913767   GUCGGCUUCGGAAGA-GCGAUCCGAUAGCUGGCAGAACCCC-UGUCUCC-UGCG----UG----AGCGAU---C----GCGGGAGGCA-CC-GUU----CUGU--------------GCAACGGAAUUCCGAAGAAAGUUGGU-GCGUUCGUGGAGAAACAAAGUAGCGCAGCGAACUUG-UAAUC-ACCGAU-GCCGCAUCGCUCGGGAAGGA----CAGAG----UUCUUCUCGCGGCCUCAGUAGCCUCC
AACY023868281.1/1073-860   AGCAGC-ACGGGAGA-GCGACCCGUG-GCUGGCAGACAAUCCAGCCCCC-AUCC----CAC---GGCAACUGUG----GAUGGGGCUG-GC-UUU----CUGCG---CUUAACCCCGUCUUCCAAUAUCGGGAAAGAUUCAGU-GCAUUGCACUUGAUUGCACAACUGCUCGCCAACGUU-CGGGA-ACGGA---CCGCAUCGCUCGGGGCGAA----CAUCU----UUCUCCUCGCGGC-UCCGUAGUCCCG
AACY020964560.1/47-244     GGCAGCCUCGGUAGA-GCGAUCCGAGAGCUGACAGAGC---CUGUCUCC-UGCG----UG----AGCGAU---C----GCGGGAGACA-CU-GUU----CUGU----------------GUCACAAACCUGAAAAGAGUUAGU-GCUUUUGUUGCGCAGCUCCGUAUCGGGACGAGCUUG-CAUUU-GCAGAC-ACCGCAUCGCUCGGGAAGAG----CA-AG----CUCUUCUCGCGGUCUCUGUAGCCCUU
CP000110.1/1291073-1290872 GGCAGC-ACGGGAGA-GCGACCCGUCAGCUGGCAGUCAAGGC-ACCCUU-GGCA----UG----AGCGAU--------GUCAGGGGUU-GC-UUU----CUGC--------GC----UUAUCAAAAAUCUGAAGACAUUUGGU-GCAUUUGCGUAAGAGGUUUGUAACGCGCCGAACGUG-UUUAA-GCGGAU-ACUGCAUCGCUUGGGGAGGA----CUAGU----UCCUCCUCGCAGU-UCCGUGGCCCCA
AACY023866666.1/1417-1219  AGCAGCACGGGGAGA-GCGACCCUGGGGCUGGCAGACGAGU--UUCCCC-GUUG----AG----AGCGAU---C----AAUGGGGGAA-CC-UCU----CUGU----------------GUCUAAAAGCUGUAGAAAUUCAGU-GCAUCAGGCGCAAAUCAGUGUGACGUGACGAACGUG-UUUAU-GCGGAU-ACCGCAUCGCUCGGGGAGGA----CUCGC----UUCUCCUCGCGGU-UCCGUGGCUCCA
AACY022777272.1/634-419    GGCAGC-ACGGGAGA-GCGACCCGUUAGCUGGCAGACAAUCCAGGCCCC-AUCC----CAC---GGCAACUGUG----GAUGGGGCCUGGC-UUU----CUGCG---CUUAACCCCGUCUUCCAAUAACGGGAAAGAUUCAGU-GCAUUGCACUUGAUUGCAGAACGCCUCGGCAGCGUU-AUGGA-GCGGA---CCGCAUCGCUCGGGGCGAA----CAAGC----UUCUCCUCGCGGC-UCCGUAGUCCCG
AACY021967263.1/333-130    GGCAGCACCGGGAGA-GCGACCUGGUGGCUGGCAGAAAUAGC-UCCCUU-GGCA----CG----AGCGAU---U----GCCAGGGGGA-GC-UUU----CUGC--------AC----UCUUCAGAUCUCUGAAAAGAGUUGGU-GCAUUUGCGACAAGCACUUGUAUCGCAGCGAGCUUG-UUCAU-GCGGAU-ACCGCAUCGCUCGGGGAGAA----CAGCG----UUCUCCUCGCGGU-UCCGUCGCCCCA
AACY022976157.1/525-322    GACGGCCUCAGUAGA-GCGAUCUGAGAGCUGGCAGAACCCC-UGUCUCC-UGCG----UG----UGCGAU---C----GCGGGGGACA-CC-GUU----UUGU--------------GCAACGGAAUCCUGAAAAGACUUGGU-GCGUUCGCCGAGAAGUUCAGUAGCGCAGCGAAUUUG-GUUGU-ACCUACGGUCGCAUCGCUCGGGAAGGA----CAGCG----UUCUUCUCGCGGCCUCAGUAGCCCCC
BX569694.1/107903-107700   GACGGCCUCAGUAGA-GCGAUCUGAGAGCUGGCAGAACCCC-UGUCUCC-UGCG----UG----AGCGAU---C----GUAGGAGACA-CC-GUU----CUGU--------------GCUUCGGAAUCCUGAAAAGACUUGGU-GCGUUCGCCAAAAAGUUCAGUGGUGCGGCGAACUUG-GUUGU-ACCGAUGGUCGCAUCGCUCGGGAAGGA----CAGCG----UUCUUCUCGCGGCCUCAGUAGCCCCC
AACY020318689.1/1145-942   GGCAGC-ACGGGAGA-GCGACCCGUUGGCUGGCAGUCAAAGCGACCCUU-GGCA----CG----AGCGAU---U----GUCAGGGGUG-GC-UUU----CUGC--------GC----UUUUCAAAAAUCGGAAGAAAUUUGUA-CCUUUUGAGACAAAGGUUUGUAUGCCGAGGAACUUG-UUUAA-GCGGAU-ACCGCAUCGCUCGGGGAGAA----CGUCG----UUCUCCUCGCGGU-UCCGUGGCCUCA
AACY020355416.1/3083-2880  GACGGCCUCAGUAGA-GCGAUCUGAGAGCUGGCAGAACCCC-UGUCUCC-UGCG----UG----AGCGAU---C----GCGGGGGACA-CC-GUU----UUGU--------------GCAACGGAAUCCUGAAAAGACUUGGU-GCGUUCGCCGAGAAGUUCAGUAGCGCAGCGAAUUUG-GUUGU-ACCGACGGUCGCAUCGCUCGGGAAGGA----CAGCG----UUCUUCUCGCGGCCUCAGUAGCCCCC
AACY020355416.1/332-135    GGCAGCCUCGGUAGA-GCGAUCCGAGAGCUGACAGAACAC---GUCUCC-UGCG----UG----AGCGAU---C----GCGGGAGACA-CC-GUU----CUGU----------------ACCAUAAACCUGAAAAGAGUUAGU-GCAUUUGAUGCACAGCUCUAUAUCAGUACGAGCUUG-UGAAU-GCAGAU-ACCGCAUCGCUCGGGGAGAA----CAGCG----UUCUCCUCGCGGU-UCCGCCGCCCAC
AACY023379744.1/1010-1208  AGCAGCACGGGGAGA-GCGACCCUGGGGCUGGCAGACGAGU--UUCCCC-GUUG----AG----AGCGCU---C----AAUGGGGGAA-CC-UCU----CUGU----------------GUCUUAAAGCUGUAGACAUUCAGU-GCAUCAGGCGCAAAUCAGUGUGACGUGACGAACGUG-UUUAU-ACGGAU-ACCGCAUCGCUCGGGGAGGA----CUCGC----UUCUCCUCGCGGU-UCCGUGGCUCCA
AACY021507139.1/426-212    AGCAGC-ACGGGAGA-GCGACCCGUUUGCUGGCAGACAAUCCAGUCCCC-AUCG----CAC---GGCAA----CUGUGGAUGGGGCUG-GC-UUU----CUGCG---CUUAACCCCGUCUUCCAAUAACGGUAAAGAUUCAGU-GCAUUGCACUUGAUUGCAGAACUCGUCGGCAGCGUU-AUGGA-ACGG---ACCGCAUCGCUCAGGGCGAA----CAAGU----UUCUCCUCGCGGU-UCCGUAGUCCCG
AACY021178095.1/424-221    GGCAGUACCGGGAGA-GCGACCUGGUAACUGGCAGAAAUAGC-UCCCUU-GGCA----CG----AGCGAU---U----GCCAGGGGGA-GC-UUU----CUGC--------GC----UCUUCAGAUCUCUGAAAAGAGUUAGU-GCAUUUGCAACAAGCACGUGUAUCGCGGCGAGCUUG-AUCAG-GCGGAU-ACCGCAUCGCUCGGGGAGAA----CAGCG----UUCUCCUCGCGGU-UCCGUCGCCCCA
AACY021113176.1/653-453    GACGGCCUUGGAAGA-GCGAUCCGAGAGCCGGCAGAACCAA-UGUCUCC-CACG----CG----AGCGAU---C----GUGGGAGACA-AA-GUU----CUGU--------------GUAAAUGAAUUCUGAAGAGACUUGGU-GCAAUUGCCAGCAAGUACUGGUUCGGACCGAGCUUG-UUGAA-GCAGAC-ACUGCAUCGCUCGGGAAGAG----CA-AG----CUCUUCUCGCAGU-UCUGUAGUCCUU
AACY021747145.1/553-751    AGCAGCACGGGGAGA-GCGACCCUGGGGUUGGCAGACGAGU--UUCCCC-GUUG----AG----AGCGAU---C----AAUGGGGGAA-CC-UCU----CUGU----------------GUCUAAAAGCUGUAGACAUUCAGU-GCAUCGGGCACAAAUCAGUGUGACGAAGCGAACGUG-UUUAU-GCGGAU-ACCGCAUCGCUCGGGGAGGA----CUCGC----UUCUCCUUGCGGC-UCCGUGGCUCCA
AACY022979180.1/595-818    AGCAGCACCGAAAGAGGCGACUGGGGAGCUGGCAGAAACC--AGUCCCU-AAGGCCUCAG----AAGACU---C----CUUAGGGACUGUU-UUUGCGCCUUC--------AUAUCGUCUUCCACUAACAAGAAAGAUUCCGUAGUCUGCAGCUUAAAUCGAGAUCAUUAGUCAGGCUUG--GAAU-GCGGA--GUCGAAUCGCUCGGGAAACGUCGGCGCGACCGUUGUCUCUCUCGGC-UCCGCGGUCAGU
AACY024091896.1/264-485    AGCGGCACCGAGAGA-GCAACUCGGGAGCUGGUAGAAACC--AGUCCCU-ACGG----CGUCCUAAGGGU---C----CGUAGGGACU-GU-UUUGCGCCUUC----AUGUCG----UCUUCCGAUAACAAGAAAGAUUCCGU--AGUUUGCAGCUUGUAUCGAGAUCGUUCGUCAGGCU-UUAAGAGCGGA--GUCGAAUCGCUCGGGAGACAUUGGCGAGACCGAUGUCACUCUCGGC-UCCGCAGUCAGC
BX569692.1/86859-86657     GACGGCCUCAGUAGA-GCGAUCUGAGAGCUGGCAGAACCCCCUGUCUCC-CGCG----UG----AGCGAU---C----GCGGGGGACA-CC-GUU----CUGU--------------GCAACGGAAUGCUGAAAAGAGUCAGU-GCAUACGACGCAUGGCUCCGUAUCAGGAGGAGCUUG-UGUGU-GCAGAC-ACCGCAUCGCUCGGGAAGAG----CA-AG----CUCUUCUCGCGGUCUCUGCAGUCCUU
AACY021350119.1/504-716    CGCAGCAGCACGAGA-GCGACCCAUUUGCUGGCAGACAAUCCAGUCUCA-UUAC----AA----GGCAAA--CG----UGAUGGGGCU-GU-UUU----CUGCG---CUUAACCCCGUCUUCCAAUAAUUGGAAAAAUGCAGU-GCAUUGCACUUGAUUGCACAACUCCUCGUCAGCGUU-AGGGA-ACGG---ACUGCAUUGCUCGGGGCGAA----CAUCG----UUCUCCUCGCGGU-UCCGUAGUCCCG
AACY022978784.1/214-12     GGCAGCACCGGGAGA-GCGACCCGGCAGCUGGCAGAUAAAGC-CUCCUU-GGCA----CG----AGCGAU---U----GCCAGGGAGA-GC-UUU----CUGC--------GC----UCUUUAGAUGUCUUAAAAUAUAUGGU-GUAUUUGAUUCAAAAGUAUGUGCCGUUGCGAGCUUU-AUUUU-ACGUA--AUCGCAUCGCUCGGGGCGAA----CAUCG----UUUUCCUCGCGGU-UCCGUGGUCCCA
AACY020360436.1/280-502    AGCAGCACCGAGAGA-GCGACUCGGGAGCUGGCAGAAACC--AGUCCCU-AUGGCCUCAG----AAGACU---C----CUUAGGGACU-G--UUU----UUGCGCCUUCAUAU----CGUCUUCCACUAACAAGAAAGAUUCC-GUAGUCUGCAGCUUGAUUCGAGAUCAUUCGUCAGGCUUGAAAUGCGGA--GUCGAAUCGCUCGGGAAACGUCGGCGCGACUGAUGUCUCUCUCGGC-UCCGCGGUCAGU
AACY024059966.1/6-207      GGCAGCCUCGGGAGA-GCGACCCAAGAGCUGACAGAAC---CCGUCUCC-UGCG----UG----GGCGAU---C----GUGGGAGACG-GC-GUU----UUGU--------------GAAAUGGAAUCCUGAAAAGACUUGGU-GCGUUCGCCGAGAAGCUCAGUAGCGCGGCAAACUUG-GUUGU-ACCGAUGGUCGCAUCGCUCGGGAAGAA----CCGCG----UUCUUCUCGCGGCCUCAGUAGCCCCC
AACY020316257.1/2428-2644  AGCAGC-ACGGGAGA-GCGACCCGUUAGCUGGCAGACAAUCCAGUCCUC-AUCC----CAC---GGCAUCUG-G----GACGAGGGCUGGC-UUU----CUGCG---CUUAAUCCCGUCUUCCAAUAACGGGAAAGUUUCAGU-GCAUCGCACCGAAGUGCAUAACGCUUCACCAAGCUU-UUGGA-ACGGCA-ACCGCAUCGCUCGGGGAGAA----CGCUG----UUCUCCUCGCGGU-UCCGUCGCCCCA
#=GC SS_cons               ::<<<<<<<<<<___.____>>>>>>->>>><<<<<<<---.<<<<<<<.<<<<....__....______...>....>>>>>>>>>>.--.>>>....>>>>........--....--------------------------.------------------------------------.-----.<<<<<-.<<<<<-------<<<<<<<<...._____....>>>>>>>>>>>>>.>>>>>:::::::
#=GC RF                    aGCAGCcccGGgAGA.GCGAcCCgggAGCUGGcAGAaaacc.uguCccc.ggcg....uG....AGcgAU...c....gccgggGaca.gC.uuU....CUgC........ac....ucUuCagAaauCuGaAAAgAuUuaGU.GcaUuugacuuaAaucuauguaucgugaCgAaCuUg.uuuau.gCgGAu.gCCGCAUCGCUCGGGgaGaa....Caugg....uuCucCUCGCGGc.UCcGcaGuCcca
//
# STOCKHOLM 1.0

#=GF AC   RF01703
#=GF ID   Dictyoglomi-1
#=GF DE   Dictyoglomi-1 RNA
#=GF AU   Yang J
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   150.00
#=GF TC   220.90
#=GF NC   68.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Dictyoglomi-1_RNA_motif
#=GF SQ   4


CP001146.1/1770511-1770277 UGCUACAGGCGUCAAGGGGUCCGAAAGGUACUCC-UGA-UGUACCUUGGC----ACUGAGUAAAGUCUUGGGUACC-UAGGGAAAGGUGAAGGAGCUAGACUCCUUACCAAGUACUUAGGGGGUGGAGAGUAGUAGGAGUGUUGGAGAAGCCCGGUGCUCCUAUGAAAUCUGGAAAAUCCUGAGGCUGAAAGGU----GAGAAGGUACAAGGAGGCUUCCAAGUAGGGUCUGUUGAGCCUGUGGCA
CP001146.1/383960-384195   UGCCACAGGCAUCAAGGGGUCCGAAAGG--CUCCCUGA-UGUGCCU-GACUGGGACUGAGUAAGUCUCAGGG--GC-CAAGGAAAGGU-AAGGAGUAAAA-UCCUUACUAAGUACUUGGAGGCCAGAAGGUAACAGGGGUAUUGGAAAAGCCCGGUACCUCUGUGAAAUCUGGUAAAACCCUGGGAUGAGAGGUCUCGGGA-GGGUGCAAGGGAGAAGCUGAGUAGGGUCCGUUGAGCCUGUGGCA
CP001251.1/100291-100057   UGCCACAGGCGUCAAGGGGUCCAAAAGGUACUCC-UGA-UGUACCUUGGC----ACUGAGUAAAGUCUUGGGUAGC-UGGGGAAAAGUGGAGGAGCAAGACUCCUUACUGAGUACUUAGGGUUUAGAGAGUAGUAGGGGUGUUGGAGAAACCUGGUACUCCUACGAAAUCUGAAAAAUCCUGAGGCUGAAAGGU----GAGAGGGUACAGGGGAGUUUCCAAGUAGGAUCUGUUGAGCCUGUGGCA
CP001251.1/520396-520631   UGCCACAGGCAUCAAGGGGUCCGAAAGG--CUCC-UGAGUGCACUU-GGCUGGGACUAAGUAAGUCCCGGAG--GCUCAAGGAAAGGU-AAGGGGUAAAAACCCUUACUAAGUACUUGAGAUCUAGAAAGUAACAGGGGUAUUGAUAAAGCUCGGUACCUCUGUGAAAUCUGGAAGAA-UCUGGGAUGAAAGGUCUCAGAG--GGUGCAAGGGAGAGGCUGAGUAGGGUCCGUUGAGCCUGUGGCA
#=GC SS_cons               ((((((((((-((((-((--((----((..((((.(--.(((((((.--((((((((------(((((((((..,<.<<<<----<<<.<<<<<_______>>>>>>>>----->>>>>,,<<<<<<-----<<<<<<<<<<<<<______>>>>>>>>>>>>>---->>>>>>,,,,)))))))))----))))))))--.)))))))-)))))---))-----))--))-))))))))))))))
#=GC RF                    uGCcaCaGGCauCaaGgGGUCCgAAAgG..CucC.cGA.uGcaCcc.GgCcgggaCcgAGUAAggcccgggG..gc.cagGGAAAgGu.aaGGgGuaAaAacCCuuaCcaAGUACcugggguccaGaaaGUAgcaGggGugccGgaaAAgCcCggcaCccCugcGAAAuCuggaAaAaCcccgggccGAaAgGucccgGag.ggGugCaagGgaGauuCcaAGUAGGgUCcGuuGaGCCuGugGCa
//
# STOCKHOLM 1.0

#=GF AC   RF01704
#=GF ID   Downstream-peptide
#=GF DE   Downstream peptide RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   32.00
#=GF TC   32.00
#=GF NC   31.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Downstream-peptide_motif
#=GF **   seedtax: Bacteria; Viruses; unclassified sequences
#=GF SQ   627


AACY023852401.1/427-367        UUACGUUCAUCUAC----------------------UUAAUC-------------------------------GUAGACGCAU-CAAUACAUCA-UUCAUGGAACGG-GGGAUGGUG
AACY020105649.1/520-461        AAACGUUCAUCUCG----------------------UUUUA--------------------------------CGGGCCGCAU-UAAGAUUGAA-GCCAAGGAACGG-GGACUUCAG
AACY021486203.1/224-276        GUCCGUUCAUCUC-----------------------UUCG----------------------------------GAGACGCAU-GAUAACCUAG---CAUGGAACGGGG---CUAGG
DQ366726.1/9273-9330           UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021585725.1/501-447        GUCCGUUCAUCC------------------------UUAAUU---------------------------------GGACGCAU-GUC--AGCUA-GCCAUGGAACGG-GGGCUAGGU
AACY023378822.1/71-126         GUCCGUUCAUCGC-----------------------UUUAU---------------------------------GCGACGCAU-GUC--AUCUA-GUCAUGGAACGG-GGGCUAGGU
AACY020145739.1/221-168        GUCCGUUCAUCCC-----------------------GCAA----------------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
CP000576.1/381532-381475       UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
CP000551.1/1075404-1075342     UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020110964.1/763-824        AAACGUUCAACUUGC---------------------AUAUA-------------------------------GCAAGCCGCAG-AUCGACUUAA-GCCAUGGAACGG-GGACUUGAG
AACY024016529.1/48-109         AAACGUUCAACUUGC---------------------GAUAA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020634737.1/366-305        GAUCGUUCACUUCGC---------------------AUCGC-------------------------------GCGAAGCGCAG-UUCGCCUCAG-GCCAUGGAACGG-GGACCUGAG
AACY023385431.1/1395-1340      GUCCGUUCAUCGC-----------------------UUUAU---------------------------------GCGACGCA---UGUAAUCAA-GUCAUGGAACGG-GGGCUUGGU
AACY022747294.1/181-124        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022706290.1/738-792        GUCCGUUCAUCC------------------------CUAAUGA--------------------------------GGACGCA---UGAAAUCCA-AGCAUGGAACGGGGC-UUGGG-
AACY021033246.1/109-171        GUCCGUUCAUCCC-----------------------GAAAGAAAAAGUA-------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
CP000111.1/621613-621552       AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY022751299.1/99-37          GUCCGUUCAUCCC-----------------------GAAAGAAAAAGUA-------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
CP000111.1/1396332-1396270     AAUCGUCCGAUCUG----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020683847.1/486-429        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY020569629.1/829-768        AAACGUUCAACUUGC---------------------CUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020137992.1/297-242        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCAU-GAUAAGAGAA-U--AGGGAACGGG---AUUCUC
AACY022212537.1/198-136        GUCCGUUCAUCCC-----------------------GAAAGAAAAAGUA-------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
AACY022814147.1/553-610        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020530472.1/843-906        AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AACY021714628.1/682-744        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY022558914.1/87-146         AAACGUUCACUUCGU---------------------CUCG--------------------------------ACGAAGCGCAG--ACAAGCCAG-GCCAUGGAACGG-GGACCUGGA
AACY023562070.1/560-501        AAACGUUCACCCCCU---------------------CUUG--------------------------------AGGGGGCGCAG--AUGCUCCAA-GCCAUGAAACGG-GGACUUGGA
CP000111.1/1134894-1134832     UAACGUUCAUCCAAG---------------------UUUAUAUUU---------------------------CU-GGACGCA---UGAUAUGGG-AGUAGGGAACGGGAU-UCUCAU
CP000110.1/518912-518973       AAACGUUCACUUCGCU--------------------ACAC-------------------------------AGCGAAGCGCAG-UUCGACUCAG-GGCAUGGAACGG-G-GCCUGAG
AACY020215429.1/1492-1438      GUCCGUUCAUCCU-----------------------GCAA----------------------------------AGGACGCAU-GACAACCUAA--GCAUGGAACGGGGC--UUAGG
AACY021870564.1/31-88          UUUCGUUCACCCUU----------------------AUUU---------------------------------GAGGGCGCAG-UUCGUGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023937843.1/555-612        AAGCGUUCACCUCG----------------------UUCG---------------------------------CGAGGCGCAU--UUCUGUCAG-GCCAUGGAACGG-GGACCUGGC
AACY020913601.1/631-685        GUCCGUUCAUCCC-----------------------UUAU----------------------------------GGGACGCA---UGCAAUCAG-AUCAUGGAACGG-GGGUCUGAU
AACY020855123.1/326-386        AAACGUUCACCUCGC---------------------UUCU--------------------------------GUGGGGCGCAG-CUCAACCCAA-GCCAUGGAACGG-GGGCUUGGA
CP000551.1/634086-634025       AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY022418303.1/550-612        UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020594948.1/437-495        AUACGUUCAUCCUAG---------------------UUAU--------------------------------CUUGGACGCA---UGAAAUGGA-AAUAGGGAACGGGAU-UUCCAU
AACY020349425.1/1803-1864      GCACGUUGAGCCCC----------------------AUCCAUC------------------------------GGGGCUGCAG-UCAGACCCGC-GUCAGGCAACGG-GGACGCGGG
AACY022984807.1/821-764        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
CP000825.1/1406723-1406661     AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022993341.1/611-554        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAUAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY023859177.1/1129-1187      CAACGUUCACCUCGC---------------------UUAU--------------------------------GCGAGGCGCAG-AUC--ACCAG-GCCAAGGAACGG-GGACCUGGA
AACY023381404.1/1391-1329      UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
CP000553.1/1478715-1478655     AAUCGUCCGAUCUGC---------------------CUAU--------------------------------GUAGACCGCAG-UUCGACUCAA-GCCAAAGGACGG-GGACUUGGG
AACY021489233.1/577-632        AUUCGUUCACCC------------------------UUAACU---------------------------------GGGCGCAG-UCCGAGCUAU-ACCAUGGAACGG-GGG-AUAGC
AACY021446557.1/389-451        AAUCGUCCGAUCUA----------------------CCAUCCGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAAAGGACGG-GGAUUUGAG
CP000576.1/1338899-1338837     AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY021939782.1/317-378        AAACGUUCAACUUGCU--------------------CAU--------------------------------AGCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
CP000553.1/1087010-1086948     AAACGUUCAACUCGC---------------------UACAUU------------------------------GCGAGCCGCAU-CUCGAUUUAA-GCCAAGGAACGG-GGACUUAAA
CP000576.1/632920-632859       AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021889827.1/495-432        AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AACY022979095.1/129-193        AGACGUUCACCUUGCC--------------------UCCCUC-----------------------------GGCAAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
BX548174.1/627956-627894       AAACGUUCAACUUGUA--------------------AUAA-------------------------------UGCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUGGG
CP000551.1/1365468-1365406     AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022711762.1/97-154         UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
CP000554.1/1495940-1496001     AAACGUUCACCCUGA---------------------UCAUU-------------------------------GCAGGGCGCAG-UUCGAGCCAA-GCCAUGGAACGG-GGACUUGGA
AACY022684009.1/789-846        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
BX548174.1/395850-395793       UUUCGUUCACCUUC----------------------UUUA---------------------------------GAAGGCGCAG-UUCGAGUCAU-ACCAGGGAACGG-GGG-AUGGC
AACY020718464.1/542-487        GUCCGUUCAUCCAU----------------------UUU----------------------------------AUGGACGCA---UGAAACCAC-AUCAUGGAACGG-GGGUGUGGU
CP000097.1/2177551-2177613     CAACGUUCACUUCGC---------------------UACGGC------------------------------GCGAAGCGCAU-CACACCUCAG-GCCAUGGAACGG-GGACCUGGG
AACY020158701.1/488-553        GUCCGUUCAUCUCUAC--GU----------------AUUA---------------------------ACAAGUAGAGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY020314628.1/1415-1357      CAACGUUCACCUCGC---------------------UCCU--------------------------------GCGAGGCGCAG-AUC--ACCAG-GCCAAGGAACGG-GGACCUGGA
AACY023423714.1/574-512        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY023504924.1/366-304        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022447031.1/23-81          GUCCGUUCAUUCUUC---------------------UUAG--------------------------------GAAGAACGCA---UGAAACCAC-AUCAUGGAACGG-GGGUGUGGU
AACY022725076.1/162-105        AACCGUUCAUCCU-----------------------AUUUA---------------------------------AGGACGCAG-UUCGAGCUAU-UCCAGGGAACGG-GGGUAUAGC
AACY020215017.1/3528-3590      GUCCGUUCAUCCC-----------------------GAAAGAAAAAGUA-------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY022928932.1/106-157        GUACGUUCACCC------------------------UUCG-----------------------------------GGGCGCAU-AUCUA-CCAU--GCAUGGAACGGGGC--AUGGA
CT978603.1/1340859-1340915     UCACGUUGAUCCC-----------------------UAAG----------------------------------GGGAUGCAG-CUCGAUUCCA-GUCAGGCAACGG-GGGCUGGAA
AACY022815645.1/60-8           GUCCGUUCAUCCC-----------------------AAUA----------------------------------GGGACGCAU-GACAACCUAG---CAUGGAACGGGG---CUAGG
CP000110.1/1391085-1391144     UCACGUUGAGCCU-----------------------CAUCCAC-------------------------------AGGCCGCAG-UCAGUUCCAC-GCCAGGCAACGG-GGGUGUGGG
AACY023413235.1/360-299        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY022590022.1/377-315        UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY021943446.1/23-85          AAACGUUCAACUCGC---------------------UACCUU------------------------------GCGAGCCGCAU-CUCGAUUUAA-GCCAAGGAACGG-GGACUUAAA
AACY020454357.1/553-606        UUACGUUGAGCC------------------------ACAA-----------------------------------GGCUGCAG--UAAAUGCUU-ACCAGGCAACGG-GGGUAAGUU
AACY022057923.1/105-48         UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-CCCAUGGAACGG-GG-GAUGGC
AACY023511542.1/252-195        UUUCGUUCACCCUC----------------------UUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
ACNY01000002.1/278641-278580   GAUCGUUCACUUCGC---------------------AUCGC-------------------------------GCGAAGCGCAG-UUCGCCUCAG-GCCAUGGAACGG-GGACCUGAG
AACY023461790.1/1468-1530      GUCCGUUCAUCCC-----------------------GAAAGAAAAAGUA-------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
CP000552.1/662192-662132       AAACGUUCAACUUGC---------------------GCAU--------------------------------GCAAGCCGCAG-AUCGAUCUAA-GCCAUGGAACGG-GGACUUAGG
AACY020243648.1/1664-1606      GUACGUUCAUCCUAG---------------------UUGU--------------------------------CUUGGACGCA---UGAAAUGGA-AAUAGGGAACGGGAU-UUCCAU
AACY023380677.1/572-629        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020557147.1/1694-1747      GUCCGUUCAUCCC-----------------------UUCG----------------------------------GGGACGCA--UGAGAACUAA--GCAUGGAACGGGGC--UUAGU
AACY023999305.1/204-142        GUCCGUUCAUCCC-----------------------GAAAGAAAAAGUA-------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY023938474.1/1158-1220      UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020185798.1/645-707        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020303260.1/268-331        AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AACY023405649.1/602-658        UUUCGUUCACCCUC----------------------UUU----------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020091254.1/530-468        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAG-GCCAUAGGACGG-GGACUUGAG
AACY022176631.1/885-830        AUUCGUUCACCCA-----------------------GAAC----------------------------------UGGGCGCAG-UCCGAGCUAU-ACCAAGGAACGG-GGG-AUAGC
AACY021767147.1/746-803        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
BX548174.1/817330-817389       UAACGUUCAUCC---UA-------------------GUAA------------------------------UAUCUGGACGCAU-GAC--AUGGA-AAUAGGGAACGGGAU-UUCCAU
CP000554.1/984332-984275       AACCGUUGGCCCC-----------------------CUUCC---------------------------------GGGGCGCAG-UCAGACUUAA-GCCAGGCAACGG-GGGCUUAAG
AACY023924099.1/993-941        GCACGUUCACCC------------------------UUUG-----------------------------------GGGCGCAG---GCAAUCUA-ACCAUGGAACGG-GGGUUAGGU
CP000097.1/973366-973307       CCACGUUGAGCUUC----------------------CAAUC--------------------------------GAAGCUGCAG-UCAGACCCAU-GCCAAGCAACGG-GGGCGUGGG
AACY023383882.1/1059-1002      UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022234759.1/276-219        UUUCGUUCACCCUC----------------------AAUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022360476.1/826-764        CAACGUUCACUUCGCU--------------------ACAC-------------------------------AGCGGAGCGCAG-UUCGACCGGC-GCCAUGGAACGG-GGACGCCGG
AACY022802873.1/608-549        AAACGUUCAUCUCG----------------------UUUAA--------------------------------CGAGCCGCAU-UAAGAUUGAA-GCCAAGGAACGG-GGACUUCAG
ACDW01000004.1/718908-718851   UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021712026.1/693-750        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021623887.1/206-149        UUUCGUUCACCCUC----------------------ACUA---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022818175.1/184-246        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022977679.1/606-668        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022916502.1/831-768        AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AANO01000069.1/694-756         CAACGUUCACUUUGC---------------------UGAUAC------------------------------GCAAAGCGCAU-CACACCUCAG-GCCAUGGAACGG-GGACCUGGG
AACY022394159.1/235-290        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCAU-GAUUAGAGAA-U--AGGGAACGGG---AUUCUC
AACY022035041.1/176-230        GUCCGUUCAUCCC-----------------------UUCG----------------------------------GGGACGCA---UGAAUCCUA-GGCAUGGAACGGGGU-CUAGGU
AACY020396045.1/947-1009       GUCCGUUCAUCCC-----------------------GAAAGAAAAAGUA-------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY022005844.1/458-401        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY022706192.1/94-32          AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
CP000095.2/1035098-1035036     AAACGUUCAACUCGC---------------------UACAUU------------------------------GCGAGCCGCAU-UUCGAUUUAA-GCCAAGGAACGG-GGACUUAAA
CP000095.2/1444215-1444155     AAUCGUCCGAUCUGC---------------------UUAC--------------------------------GUAGACCGCAG-UUCGACUCAA-GCCAAAGGACGG-GGACUUGAG
AACY021519823.1/138-195        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020219155.1/890-952        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
CP000095.2/1536467-1536524     AGACGUUCAGCUC-----------------------UAUU---------------------------------CGAGUCGCAG-UUAGAUUCAA-GCCAUGGAACGG-GGACUUGAA
AACY022721247.1/660-716        GUCCGUUCAUUCCC----------------------UAAC---------------------------------GGGAACGCA---UGAAACCAC-AUCAUGGAACGG-GGGUGUGGU
AACY023602099.1/832-888        GAACGUUGGCCCC-----------------------AGUG----------------------------------GGGGCGCAG-UUCGAUCUCA-AACAGGCAACGGGGU-UUGAGA
AACY020217963.1/776-714        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY021203536.1/641-580        AAACGUUCACUUCGCU--------------------ACAC-------------------------------AGUGAAGCGCAG-UUCGACUCAG-GGCAUGGAACGG-GG-CCUGAG
CP000553.1/397281-397219       AAACGUUCAACUCAUC--------------------AAAU-------------------------------GAUGAGCCGCAG-UUUGACUCAA-GCCAAGGAACGG-GGACUUGAG
BX569695.1/264389-264453       AGACGUUCACCUCGCC--------------------AGCCUC-----------------------------GGCAAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY023416457.1/1187-1131      GUCCGUUCAUCCUG----------------------AUUA---------------------------------UAGGACGCA---UGAAACCUG-AUCAUGGAACGG-GGGUCAGGU
AACY022685122.1/141-79         AAGCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GUCAUAGGACGG-GGACUUGAG
AACY020543559.1/538-477        UCACGUUCACCUCGU---------------------CUUCG-------------------------------GCGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY021483025.1/393-449        GUCCGUUCAUUCUC----------------------UUAU---------------------------------GAGAACGCA---UGAAACCAC-AUCAUGGAACGG-GGGUGUGGU
AACY023941631.1/69-9           AAGCGUUCACCUC-----------------------ACUUAUUC------------------------------GAGGCGCAG-CUCGAUCCAA-GCCAUGGAACGG-GGGCUUGGG
AACY023488045.1/608-551        UUUCGUUCACCCUC----------------------UUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020820181.1/221-164        AACCGUUCAUCAU-----------------------AUUUA---------------------------------AGGAUGCAG-UUCGAGGUAU-UCCAAGGAACGG-GGGGAUAGC
AACY020112953.1/1475-1414      AAACGUUCAACUUGCU--------------------UAU--------------------------------AGCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
CP000097.1/937913-937973       AGACGUUGAGCUUGG---------------------CAUG--------------------------------CUGAGCUGCAG-UUUGAAUUCA-UCCAGGCAACGG-GGGAUGGGU
AACY022449092.1/423-363        CAACGUUCACCUCUC---------------------CUUGC-------------------------------GGGAGGCGCAG--ACAAGCCAG-GCCAUGGAACGG-GGACCUGGA
AACY020146634.1/373-430        UUUCGUUCACCCUC----------------------UUCU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023414958.1/299-361        AAUCGUCCGAUCUA----------------------CCUUUUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAAAGGACGG-GGACUUGAG
AACY022743658.1/827-770        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021152154.1/3-79           UUACGUUCAUCCAUACAUAACCU-------------AAUAAC----------------------AGGU--UGUAUGGACGCAU-CAAUACAUUA-UUCAGGGAACGG-GGGAUGGUG
AACY023958584.1/325-268        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021653733.1/569-515        GUACGUUCAUCCC-----------------------UUCA----------------------------------GGGACGCAU-AACUUGCCUG--GCAUGGAACGGGGC--CAGGG
CP000552.1/426597-426540       UUUCGUUCACCCA-----------------------UAAUAU--------------------------------UGGGCGCAG-UUCGAGUCAU-ACCAGGGAACGG-GGG-AUGAC
AACY023103770.1/544-490        UUCCGUUCAUCCC-----------------------ACAA----------------------------------GGGACGCAU-GUUUGCAUAG--GUAUGGAACGGGAC--CUAUG
AACY023466595.1/966-907        AAACGUUCACCCCCU---------------------CUUG--------------------------------AGGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
AACY020626333.1/763-708        AUUCGUUCACUC--C---------------------UAAU--------------------------------G--GAGCGCAG-UCCGAGCUAU-ACCAUGGAACGG-GGG-AUAGC
AACY023493572.1/1152-1099      GUCCGUUCAUCCC-----------------------UUAU----------------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
AACY021398198.1/428-485        UUUCGUUCACCUUC----------------------AUCU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
CP000553.1/1573052-1573109     UGACGUUCAGCUC-----------------------UAUU---------------------------------CGAGUCGCAG-UUAGAUUCAA-GCCAUGGAACGG-GGACUUGAA
AACY021848892.1/469-530        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY022751365.1/203-146        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022466179.1/663-602        AAACGUUCAACUUGC---------------------GUUCA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021485586.1/446-503        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023139246.1/705-767        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UAAGAUUCAA-GCCAUAGGACGG-GGACUUGAG
AACY023957296.1/326-269        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021755234.1/783-721        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022116976.1/80-23          CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY022733664.1/506-441        GUCCGUUCAUCCCUAC--GU----------------AUCA---------------------------ACAAGUAGGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY021709640.1/779-841        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022793035.1/483-545        AAUCGUCCGAUCUA-CG-------------------AUC-------------------------------UGUUAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022683133.1/938-882        UUUCGUUCACC-UC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020200073.1/494-551        AACCGUUCAUCCU-----------------------AUUUA---------------------------------AGGACGCAG-UUCGAGCUAU-UCCAGGGAACGG-GGGUAUAGC
AACY021031530.1/418-479        CAACGUUCACCUCGUC--------------------ACA--------------------------------GGCGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020558859.1/409-356        GUCCGUUCAUCCC-----------------------GCAA----------------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY020867268.1/192-135        UUUCGUUCACCCUC----------------------GCUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
CP000435.1/2112063-2112005     AAACGUUGGUCCCC----------------------AGUA---------------------------------GGGGACGCAG-UCCGAUCUCA-AACAAGCAACGGGGU-UUGAGG
AACY023122558.1/251-195        UUUCGUUCACCCUC----------------------UUU----------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022682055.1/501-439        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020543122.1/725-785        UAACGUUCACCUCUU---------------------UUCG--------------------------------GAGAGGCGCAG-UUCGAUUCAG-GCCAAGGAACGG-GGACCUGAA
AACY022155008.1/760-702        AAGCGUUCACCCCU----------------------UUCGA--------------------------------AGGGGCGCAG--ACACUCCAA-GCCACGGAACGG-GGACUUGGA
AACY020205048.1/821-769        GUCCGUUCAUCC------------------------UUCG-----------------------------------GGACGCA---UGACACCAA-AGCAUGGAACGGGGC-UUUGGU
AACY021746337.1/127-189        CAACGUUCACUUCAUC--------------------CUUG-------------------------------GGUGAAGCGCAG-UACGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY023855862.1/42-101         AAAUGUUCACCCCCU---------------------CUUG--------------------------------AGGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
AACY021175404.1/406-344        AAUCGUCCGAUCUA----------------------CCAUUUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY023163906.1/449-511        AUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY022350944.1/833-894        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020118932.1/682-626        GUCCGUUCAUCCCC----------------------CCUU---------------------------------GGGGACGCA---UGACUCCUA-AGCAUGGAACGGGGC-UUAGGU
AACY022436312.1/741-803        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020135773.1/509-454        GUCCGUUCAUCGC-----------------------UUUAU---------------------------------GCGACGCAU-GUC--AUCUA-GUCAUGGAACGG-GGGCUAGGU
AACY022013859.1/261-322        AAGCGUUCAACUUGC---------------------AUAUA-------------------------------GCAAGCUGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020116663.1/636-579        CAACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCAU-GAC--AUGAG-AAUAGGGAAAGGGAU-UCUCAU
AACY023484494.1/816-877        UCACGUUCAUCUCAUC--------------------UCC--------------------------------GGCGAGGCGCAA-UUCGACUCAA-GCCAUGGAAUGG-UGACCUGAG
AACY023139080.1/632-577        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCAU-GAUAAGAGAA-U--AGGGAACGGG---AUUCUC
AACY023800545.1/1362-1299      AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AACY020131598.1/1013-1068      GUCCGUUCAUCGC-----------------------UUUAU---------------------------------GCGACGCAU-GUC--AUCUA-GUCAUGGAACGG-GGGCUAGGU
AACY020527401.1/1924-1868      UCACGUUGAGCCC-----------------------CUUA----------------------------------GGGCUGCAG-UUCGUUCCAC-GCCAGGCAACGG-GGGCGUGGG
AACY020568474.1/454-511        UUUCGUUCACCCUC----------------------AGUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022076031.1/253-192        GAUCGUUCACUUCGC---------------------AUCGC-------------------------------GCGGAGCGCAG-UUCGCCUCAG-GCCAUGGAACGG-GGACCUGAG
AACY024015920.1/449-392        AACCGUUCAUCCU-----------------------AUUUA---------------------------------AGGACGCAG-UUCGAGCUAU-UCCAGGGAACGG-GGGUAUAGC
AACY021892372.1/627-570        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
BX548175.1/1082118-1082175     AACCGUUGGCCCCG----------------------UUC----------------------------------CGGGGCGCAG-UCAGACUUAA-GCCAGGCAACGG-GGGCUUAAG
AACY023406090.1/129-68         AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAAGGAACGG-GGACUUAAG
AACY022966659.1/685-742        UUUCGUUCACCCUC----------------------UUUA---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAGGGAACGG-GGG-AUGGC
AACY022024447.1/714-652        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGGG
AACY023410383.1/1196-1255      AAUCGUUCACUUCG----------------------UUACGG-------------------------------CGGAGCGCAG--GCAAGCCAG-GCCAUGGAACGG-GGACCUGGA
AACY021448444.1/565-627        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AAOK01000003.1/2958-2897       ACACGUUCACCUCAC---------------------UCCUG-------------------------------GUGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020478311.1/756-808        GUCCGUUCAUCUC-----------------------UUCG----------------------------------GAGACGCAU-GACAACCUAG---CAUGGAACGGGG---CUAGG
AACY021567067.1/287-349        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020875815.1/692-631        CAUCGUUCACCUCGUC--------------------CCU--------------------------------GGCGAGGCGCAG-UACGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY023991880.1/791-845        GUCCGUUCAUCC------------------------CUAAUGA--------------------------------GGACGCA---UGAAAUCCA-AGCAUGGAACGGGGC-UUGGG-
AACY022923740.1/553-494        AAACGUUCACCCCCU---------------------CUUG--------------------------------AGGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
AACY023382864.1/366-304        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022678904.1/329-273        UUUCGUUCACCCUC----------------------UUU----------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023989052.1/676-738        AUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY021220275.1/163-106        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AATZ01000001.1/347865-347805   AUACGUUGAGCUUGG---------------------GAUA--------------------------------CUGAGCUGCAG-UCUGAAUUCA-UCCAGGCAACGG-GGGAUGGGU
CP000110.1/1932912-1932853     AAACGUUCACCCCUG---------------------CUUG--------------------------------CGGGGGCGCAG--ACGCUCCAA-GCCACGGAACGG-GGACUUGGG
AACY020529250.1/448-504        UCACGUUGAGCCC-----------------------CUUA----------------------------------GGGCUGCAG-UUCGUUCCAC-GCCAGGCAACGG-GGGCGUGGG
AACY021061891.1/686-624        GUCCGUUCAUCCC-----------------------GAAAGAAAAAGUA-------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
AACY021509228.1/725-663        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGGG
AACY022320013.1/540-486        GUACGUUCAUCCC-----------------------AUUU----------------------------------GGGACGCA---UGCUGCCUA-ACCAUGGAACGG-GGGUUAGGU
AACY020406884.1/980-922        GUCCGUUCAUCCCU----------------------UUCAAUC------------------------------AGGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
AACY020770731.1/455-512        UUUCGUUCACCCUC----------------------AAUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020773438.1/17-69          GUCCGUUCAUCUC-----------------------UUCG----------------------------------GAGACGCAU-GACAACCUAG---CAUGGAACGGGG---CUAGG
AACY022579616.1/474-419        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCAU-GAUAAGAGAA-U--AGGGAACGGG---AUUCUC
AACY023503045.1/208-147        AAACGUUCAACUUGCU--------------------UAU--------------------------------AGCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY023856379.1/52-113         UCACGUUCACCUCGU---------------------CUUCG-------------------------------GCGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020299582.1/1393-1330      AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAAUGG-GGACCUGGA
AACY022610843.1/201-137        UAACGUUCACCUUGUA--------------------UCACUUG----------------------------UGCGAGGCGCAU--AAAUGACUG-GCCACGGAACGG-GGACCAGUG
AACY024097856.1/1456-1395      AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY022331919.1/774-830        UUUCGUUCACCCUC----------------------UCU----------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020355098.1/1369-1429      UCACGUUGAGCUUCG---------------------AUCU--------------------------------CGGAGCUGCAG-UCAGACCCAC-GCCAGGCAACGG-GGGCAUGGG
AACY020761921.1/73-14          UCACGUUGAGCCU-----------------------CAUCAAC-------------------------------AGGCCGCAG-UCAGAUCCGC-GCCAGGCAACGG-GGGCGUGGG
AACY020076899.1/2281-2220      AAACGUUCACUUCGCU--------------------ACAC-------------------------------AGCGAAGCGCAG-UUCGACUCAG-GGCAUGGAACGG-G-GCCUGAG
AACY021153216.1/140-83         UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021303692.1/242-181        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY023480124.1/1153-1215      UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020117131.1/550-607        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAUAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY020097280.1/1976-2032      GUCCGUUCAUCCU-----------------------UUAAUU--------------------------------AGGACGCA---UGAAUUCAC-AGCAUGGAACGGGGC-UGUGAU
AACY021909707.1/651-590        AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GGCAUGGAACGG-GGACUUAAG
AAUA01000001.1/589598-589524   CGACGUUCACUCCGCGGCCCAC--------------AGAUC------------------------GUGAGUC-CGGAGCGCAG-UUCGUUUCAG-GCCAUGGAACGG-GGGCUUGAG
AACY023179717.1/496-435        GCACGUUGAGUCCCG---------------------UCCAU-------------------------------CGGGGCUGCAG-UCAGACCCGC-GUCAGGCAACGG-GGACGCGGG
AACY022711720.1/688-741        GUCCGUUCAUCUC-----------------------UUCG----------------------------------GAGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY023136505.1/41-98          UUUCGUUCACCCUC----------------------UUUU---------------------------------GAGGGCGCAG-UUCGUGUCAU-ACCAUGGAACGG-GGG-AUGGC
CP000553.1/1135171-1135114     AUACGUUCGCCUCA----------------------ACUCA--------------------------------UGGGGUGCA---UCAAAUGGA-AGUAGGGAACGGGAU-UUCCAG
AACY021880003.1/342-400        CAACGUUCACCUUGC---------------------UUCU--------------------------------GCAAGGCGCAG-AUC--ACCAG-GCCAAGGAACGG-GGACCUGGA
AACY022343895.1/568-629        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAAGGAACGG-GGACUUAAG
AACY022820161.1/384-323        AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020523392.1/1030-974       UCACGUUGAGCCC-----------------------CUUG----------------------------------GGGCUGCAG-UUCGUUCCAC-GCCAGGCAACGG-GGGCGUGGG
AE017126.1/924002-923944       AAACGUUCAACUCU----------------------UAUU---------------------------------AGAGCCGCAG-UUCGACUCAA-GCCAUGGAACGG-GGACUUGAG
AACY020315366.1/1466-1527      CGACGUUCACCUCGCU--------------------UCC--------------------------------AGCGGGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020007771.1/1442-1390      UUACGUUCAUCC------------------------GUUA-----------------------------------GGACGCA---UGCCACCUG-AUCAUGGAACGG-GGGUCAGGU
AACY021113534.1/244-301        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AAOK01000003.1/23492-23438     GCACGUUGAGCC------------------------GCAA-----------------------------------GGCUGCAG-UUCGCUCCGC-ACCAAGCAACGG-GGGUGUGGA
AAUA01000003.1/375474-375414   GCACGUUGGGCCC-----------------------CAUUCCGU------------------------------GGGCUGCAG-AUCGAUCCAC-GCCAAGCAACGG-GGACGUGGA
AACY022731378.1/545-483        UCACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY022095702.1/458-406        GUCCGUUCAUCCC-----------------------CUUG----------------------------------GGGACGCAU-GAUAACCUAG---CAUGGAACGGGG---CUAGG
AACY024000929.1/900-961        AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY023496785.1/858-796        AAUCGUCCGAUCUA----------------------CCAUUUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY023405912.1/254-316        AAUCGUCCGAUCUA-C--------------------CAUUA------------------------------GUUAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY023420777.1/27-88          AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUCAA-GCCAUGGAACGG-GGACUUAAG
AACY023156751.1/638-581        CAACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCAU-GAC--AUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY020142909.1/127-62         GUCCGUUCAUCCCUAC--GU----------------AUCA---------------------------ACAAGUAGGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY020124945.1/1418-1479      AAACGUUCAACUUGC---------------------AUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020705787.1/270-331        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AANP01000002.1/393072-393016   UCACGUUGAGCCC-----------------------CUCG----------------------------------GGGCUGCAG-UUCGUUCCAC-GCCAGGCAACGG-GGGCGUGGG
AACY022514146.1/646-591        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCAU-UAUAAGAGAA-U--AGGGAACGGG---AUUCUC
AACY022374463.1/18-79          AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021943823.1/876-938        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGGC
AACY021215600.1/344-406        UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020160893.1/184-122        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGUCUCAA-GCCAUAGGACGG-GGACUUGAG
AACY021290041.1/74-12          AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020631192.1/758-819        UCACGUUCACCUCACC--------------------UCC--------------------------------GGUGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-UGACCUGAG
AACY020243126.1/334-273        CAUCGUUCACCUCGUC--------------------CCU--------------------------------GGCGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY022742625.1/478-424        GUCCGUUCAUCGC-----------------------UUAU----------------------------------GCGACGCAU-GUC--AUCUA-GUCAUGGAACGG-GGACUAGGU
BX548175.1/599397-599336       AAACGUUCACCCUGA---------------------UCAUU-------------------------------GCAGGGCGCAG-UUCGAGCCAA-GCCAUGGAACGG-GGACUUGGA
AACY020948555.1/827-771        GUCCGUUCAUCCAU----------------------UUUU---------------------------------AUGGACGCAU-GAAAACCUAG-GC-AUGGAACGG--GGCUUAGG
AACY020297199.1/1067-1130      AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
CP000097.1/1411351-1411410     CAACGUUCACCUCAC---------------------AUUU--------------------------------GUGAGGCGCAG--ACAACCCAG-GCCAAGGAACGG-GGACCUGGA
AACY020358273.1/706-763        AAACGUUCACCCUG----------------------AUA----------------------------------CAGGGCGCAG-UGGUUCGCAG-GUCAUGGAACGG-GGGCCUGUU
AACY023498231.1/603-660        UUUCGUUCACCCUC----------------------GUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021218032.1/747-693        GUCCGUUCAUCCU-----------------------GCAA----------------------------------AGGACGCAU-GACAACCUAA--GCAUGGAACGGGGC--UUAGG
AACY020607772.1/440-499        AAACGUUCACCCUCU---------------------CUUG--------------------------------AGGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
AACY020157988.1/3201-3258      AAACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCAU-GAC--AUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY021165643.1/315-376        AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUGA-GCCAUGGAACGG-GGACUUAAG
AACY021522549.1/363-310        GUCCGUUCAUCCC-----------------------GAUA----------------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY024054811.1/687-748        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020306399.1/159-222        AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AACY021156446.1/432-494        GUCCGUUCAUCCC-----------------------GAAAGAAAAAGUA-------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY021648818.1/263-207        UCACGUUGAGCCC-----------------------CUUA----------------------------------GGGCUGCAG-UUCGUUCCAC-GCCAGGCAACGG-GGGCGUGGG
AACY020227903.1/1474-1416      GUACGUUCAUCCUAG---------------------UUAU--------------------------------CUUGGACGCA---UGAAAUGGA-AAUAGGGAACGGGAU-UUCCAU
AACY023499715.1/547-609        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
BX569692.1/299116-299176       UUACGUUGAGCUUC----------------------UUCAAU-------------------------------GAAGCUGCAG-UCAGACCCAC-GCCAGGCAACGG-GGGCAUGGG
AACY022092498.1/763-706        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023474577.1/21-82          AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020357144.1/944-883        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY023389253.1/682-630        GCACGUUUAUCC------------------------UUUC-----------------------------------GGACGCA---UGAAGCUCA-AUCAGGAAACGG-GGAUUGAGU
CT971583.1/901002-900948       ACACGUUGAGCC------------------------UUCG-----------------------------------GGCUGCAG-UUCGUUUCAC-ACCAAGCAACGG-GGGUGUGAA
AACY020934955.1/275-332        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020339639.1/1483-1424      GUCCGUUCAUCCC-----------------------UUUAGUAC------------------------------GGGACGCAU--GACACCUAA-GCCAUGGAACGG-GGGCUUGGG
ABVN01031734.1/163-104         GCACGUUGAGCUUC----------------------CAAUC--------------------------------GAAGCUGCAG-UCAGACCCAU-GCCAAGCAACGG-GGGCGUGGG
AACY022307030.1/63-117         ACACGUUGAGCCC-----------------------ACCA----------------------------------GGGCUGCA---CACAAACCA-ACCAAGCAACGG-GGGUUGGGU
AACY021019598.1/799-738        CGACGUUCACCUCGCU--------------------UCC--------------------------------AGCGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020999811.1/807-868        AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021791818.1/701-647        GUCCGUUCAUCUC-----------------------UUCG----------------------------------GAGACGCA---UGAAACCUG-AUCAUGGAACGG-GGGUCAGGU
AACY021912921.1/925-986        CGACGUUCACCUCGCU--------------------UCC--------------------------------AGCGAGGCGCAG-UUCGACUCAU-GCCAUGGAACGG-GGACCUGAG
AACY021365180.1/177-234        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAUAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY022122895.1/629-567        UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020458900.1/1490-1549      GUACGUUGGCCCGGC---------------------AGUA--------------------------------GUCGGGCGCAG-UCAGAACCGA-GCCACGCAACGG-GGGC-CGGU
AACY023852689.1/1236-1294      CAACGUUCACCCC-----------------------UUUCGUU-------------------------------GGGGCGCAG--ACACUCCAA-GCCACGGAACGG-GGACUUGGA
CP000095.2/382308-382246       AAACGUUCAACUCAUC--------------------AAAU-------------------------------GAUGAGCCGCAG-UUUGACUCAG-GCCAAGGAACGG-GGACUUGAG
AACY022090289.1/515-462        GUCCGUUCAUCCC-----------------------GCAA----------------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
CP000825.1/663461-663400       AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUGAG
AACY023410201.1/1139-1191      GUCCGUUCAUCUC-----------------------UUCG----------------------------------GAGACGCAU-GACAACCUAG---CAUGGAACGGGG---CUAGG
AACY020315903.1/1908-1847      GAUCGUUCACUUCGC---------------------AUCGC-------------------------------GCGAAGCGCAG-UUCGCCUCAG-GCCAUGGAACGG-GGACCUGAG
AACY022817460.1/389-447        AGUCGUUCAUCCU-----------------------AAUUAA--------------------------------AGGACGCAG-ACCGAGCUAU-UCCAGGGAACGG-GGGUUUAGC
AACY021270736.1/266-328        AAUCGUCCGAUCUA----------------------CUAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020104385.1/1119-1065      GUCCGUUCAUCCU-----------------------UAAC----------------------------------AGGACGCAU-GAUCACCAAG--GCAUGGAACGGGGU--CUUGG
AACY021543986.1/277-215        AAACGUUCAACUCAUU--------------------AAAU-------------------------------GAUGAGCCGCAG-UUUGACUCAA-GCCAAGGAACGG-GGACUUGAG
AACY022715021.1/396-450        GUCCGUUCAUCC------------------------CUAAUGA--------------------------------GGACGCA---UGAAAUCCA-AGCAUGGAACGGGGC-UUGGG-
AACY020098782.1/762-705        UUUCGUUCACCCUC----------------------AAUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022553156.1/90-150         AAACGUUCAACUUGC---------------------UUUA--------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY022554157.1/607-548        AAGCGUUGGCUCCC----------------------UCUUC--------------------------------GGGAGUGCAG-UUCGAUUCAG-GCCAAGCAACGG-GGACCUGAG
AACY023425845.1/76-17          AAACGUUCAUCUCG----------------------UUUUA--------------------------------CGAGCCGCAU-UAAGAUUGAA-GCCAGGGAACGG-GGACUUCAG
AACY023533360.1/824-876        GUCCGUUCAUCC------------------------UUCG-----------------------------------GGACGCA---UGAGAUCUG-ACCAUGGAACGG-GGGUCAGGU
AACY022973486.1/844-903        CAACGUUCACCUCAC---------------------UUCU--------------------------------GUGAGGCGCAG-AUCAA-CCAG-GCCAAGGAACGG-GGACCUGGA
AY939843.1/19588-19642         GUCCGUUCAUCCC-----------------------UUAC----------------------------------GGGACGCA---UGACUCCUA-AGCAUGGAACGGGGC-UUAGGU
AACY021806590.1/388-449        AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021573850.1/25-78          GUACGUUCAUCCC-----------------------AUU-----------------------------------GGGACGCA---UGCUGCCUA-ACCAUGGAACGG-GGGUUAGGU
AACY020747426.1/360-303        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021085807.1/701-639        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY021821683.1/183-121        AAACGUUCAACUCAUU--------------------AAAU-------------------------------GAUGAGCCGCAG-UUUGACUCAA-GCCAAGGAACGG-GGACUUGAG
AACY023989628.1/899-961        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020476280.1/1756-1817      AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY022548211.1/168-223        AUUCGUUCACCC------------------------UAUAUU---------------------------------GGGCGCAG-UCCGAGCUAU-ACCAUGGAACGG-GGG-AUAGC
AACY020871116.1/140-78         AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020157863.1/1332-1270      UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020092540.1/1425-1368      CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY020135377.1/1102-1155      GUCCGUUCAUCCU-----------------------AAUU----------------------------------AGGACGCA---UGAAAUCCA-AGCAUGGAACGGGGC-UUGGG-
AACY020084175.1/901-962        AAACGUUCAACUUGC---------------------AUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUGAG
AACY021121964.1/699-753        GUCCGUUCAUCCC-----------------------UUCG----------------------------------GGGACGCA---UGACACCAC-AGCAUGGAACGGGGU-UGUGGU
AACY021690712.1/862-916        GUCCGUUCAUCCU-----------------------UAAC----------------------------------GGGACGCAU-GAUCACCACA--GCAUGGAACGGGGU--UGUGG
AACY022485538.1/490-427        AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AACY020830453.1/384-443        AAACGUUCACCCCUG---------------------UGCG--------------------------------CAGGGGCGCAG--ACACUCCAA-GCCACGGAACGG-GGACUUGGA
AACY023381402.1/1332-1271      AAACGUUCAACUUGC---------------------CUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
DQ366713.1/22577-22639         AAUCGUCCGAUCUA-CU-------------------AUU-------------------------------AGAUAGACCGCAG-UACGAAUCAA-GCCAUAGGACGG-GGACUUGAU
AACY022242270.1/458-398        GCACGUUGAGCUUC----------------------UUCAAU-------------------------------GAAGCUGCAG-UCAGGCCCAC-GCCAGGCAACGG-GGGCAUGGG
AACY020316432.1/1025-1086      GAUCGUUCACUUCGC---------------------AUCGC-------------------------------GCGAAGCGCAG-UUCGCCUCAG-GCCAUGGAACGG-GGACCUGAG
AACY023383716.1/603-543        CAUCGUUGGCCUGC----------------------CAUUU--------------------------------GUAGGUGCAG-UUCGAUCCGGAGUCAUGCAACGG-GGACCCGGA
AACY022698961.1/426-488        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
CP000110.1/738974-739032       UGACGUUCACCCCU----------------------CAACUC-------------------------------AGGGGCGCAG-AUC--ACCAG-GCCAAGGAACGG-GGACCUGGA
AACY020219735.1/1610-1553      UUUCGUUCACCCUC----------------------AAUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020315450.1/781-723        CAACGUUCACCUCGC---------------------UUCU--------------------------------GCGAGGCGCAG-AUC--ACCAG-GCCAAGGAACGG-GGAGCUGGA
FJ869294.1/419-358             GCACGUUCACCUCAC---------------------CACUG-------------------------------GCGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020215108.1/805-859        GUCCGUUCAUCCC-----------------------UUAC----------------------------------GGGACGCA---UGACUCCUA-AGCAUGGAACGGGGC-UUAGGU
AACY021821135.1/447-506        AAACGUUCAUCUCG----------------------UUUUA--------------------------------CGAGCCGCAU-UAAGAUUGAA-GCCAAGGAACGG-GGACUUCAG
AACY023459118.1/417-476        AAACGUUCACCCCCU---------------------CUUG--------------------------------AGGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
AACY020727255.1/724-662        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020731433.1/637-694        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020401397.1/573-627        GUCCGUUCAUCCC-----------------------UAAC----------------------------------GGGACGCAU-GAUCACCACA--GCAUGGAACGGGGU--UGUGG
AACY021399886.1/406-468        AAUCGUCCGAUCUA----------------------CCAUUUGA-----------------------------UAGACCGCAG-UAAGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY021452063.1/397-458        AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021741662.1/168-229        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021781943.1/554-492        AAUCGUCCGAUCUA----------------------GCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGGG
AACY023815915.1/952-1015       AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
CP000553.1/1071068-1071010     ACACGUUCAGCU------------------------GAAAACAA-------------------------------AGCUGCAG-UAAGACUCGA-GACAUGGAACGGGGU-CUUGGG
AACY022100278.1/128-71         AUUCGUUCACUCUU----------------------ACUA---------------------------------AAGAGCGCAG-UUCGAGCUAU-ACCAUGGAACGG-GGG-AUAGC
AACY020095771.1/1522-1467      GUCCGUUCAUCGC-----------------------UUUAU---------------------------------GCGACGCAU-GUC--AUCUA-GUCAUGGAACGG-GGGCUAGGU
AACY020816292.1/578-516        AAACGUUCACCUUGUU--------------------GCUU-------------------------------AACAAGGCGCAG-CACGACUCAG-GCCAUGGAACGG-GGGCUUGGG
AACY022853809.1/468-413        UGACGUUGAGCCC-----------------------ACUAC---------------------------------GGGCUGCA---UAAAUUCCG-GCCAGGCAACGG-GGGCCGGUU
AACY022309134.1/672-610        AAUCGUCCGAUCUACC--------------------AUUU-------------------------------GAUAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY021356460.1/648-702        GUCCGUUCAUCGC-----------------------UUAU----------------------------------GCGACGCAU-GUC--AUCUA-GUCAUGGAACGG-GGGCUAGGU
AACY020641854.1/530-473        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023848065.1/1065-1124      UCACGUUGAGCCU-----------------------CUUCAAC-------------------------------AGGCAGCAG-UCAGAUCCAC-GCCAGGCAACGG-GGGCGUGGA
AACY020152379.1/1872-1933      AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
CP000097.1/1170507-1170566     AAACGUUCACCUUGC---------------------AUCC--------------------------------GCAAGGCGCAG--UCAAGCCAG-GCCACGGAACGG-GGACCUGGA
AACY020758892.1/34-95          AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020313637.1/368-310        CAACGUUCACCCCU----------------------UCCAA--------------------------------AGGGGCGCAG--ACACUCCAA-GCCACGGAACGG-GGACUUGGA
AACY020003603.1/874-821        GUCCGUUCAUCC------------------------UUCG-----------------------------------GGACGCA---UGACACCAUAAGCAUGGAACGGGGCUUAUGG-
AACY020296667.1/462-399        AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AATZ01000003.1/210964-210907   GAACGUUCGCCCCU----------------------CUA----------------------------------AGGGGUGCAG-UCCGACUUGG-GUCAAGGAACGG-GGACCCGAG
AACY022212085.1/127-73         GUCCGUUCAUCCU-----------------------UAAC----------------------------------AGGACGCAU-GAUCACCAAG--GCAUGGAACGGGGU--CUUGG
AACY020081083.1/235-296        AAACGUUCAACUUGC---------------------AUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021915618.1/324-381        GUCCGUUCAUCCAU----------------------UUUUC--------------------------------AUGGACGCA---UGAAACCUA-AGCAUGGAACGGGGC-UUAGGU
AACY023505966.1/588-526        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGGCUUGAG
AACY020146640.1/1245-1306      AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY022814849.1/375-313        UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
BX569695.1/221762-221821       UAGCGUUGACCCGG----------------------AUCUU--------------------------------CCGGAUGCAG-UUCGUUCCGG-GCCAUGCAACGG-GGGCCAGGA
AACY023498460.1/1046-1108      UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY021143341.1/785-837        GUCCGUUCAUCC------------------------UACG-----------------------------------GGACGCA---UGAAACCUA-AGCAUGGAACGGGGC-UUAGGU
AACY020600843.1/442-380        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY023852496.1/181-240        UCACGUUGAGCCU-----------------------CAUCAAC-------------------------------AGGCCGCAG-UCAGAUCCAC-GCCAGGCAACGG-GGGCGUGGG
AACY020769520.1/379-440        AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020736346.1/227-289        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY023362883.1/949-889        AAACGUUCAACUUGC---------------------GUUA--------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021449889.1/230-284        UUACGUUCAUCC------------------------UAUCUU---------------------------------GGACGCA---UGAAAUGGA-AAUAGGGAACGGGAU-UUCCAU
AACY023861106.1/98-159         AAACGUUCACUUCGCU--------------------ACAC-------------------------------AGCGAAGCGCAG-UUCGACUCAG-GGCAUGGAACGG-G-GCCUGAG
AACY023936644.1/788-733        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCAU-GAUAAGAGAA-U--AGGGAACGGG---AUUCUC
AACY021123074.1/566-504        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
BX569694.1/114198-114257       AAUCGUUCACUCCGU---------------------UAUC--------------------------------GCGGAGCGCAG--UCAAGCCAG-GCCAUGGAACGG-GGACCUGGA
AACY020124600.1/441-379        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY023238914.1/644-586        GGACGUUGGUCCCC----------------------CAUA---------------------------------GGGGACGCAG-UUCGAUCUCA-AACAAGCAACGGGGU-UUGAGA
AACY020456247.1/1560-1613      GUCCGUUCAUCC------------------------UUCG-----------------------------------GGACGCA---UGACACCAUAAGCAUGGAACGGGGCUUAUGG-
AACY020438503.1/293-355        AAACGUUCAACUUGUA--------------------AUAA-------------------------------UGCAAGCCGCAA-AUCGACUCAA-GCCAUGGAACGG-GGACUUGAG
AACY021669382.1/466-404        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UUCGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY021917001.1/582-525        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020727887.1/215-271        UUUCGUUCACCCUC----------------------ACU----------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023870022.1/758-817        AAACGUUCACCCCCU---------------------CUUG--------------------------------AGGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
AACY022546697.1/343-404        UCACGUUCACCUCGU---------------------UUUCA-------------------------------GCGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020132550.1/2130-2191      GUCCGUUCAUCCC-----------------------GAAAGAAAAAGUA-------------------------GGGACGCAU-GACAACCUAG---CAUGGAACGGGG---CUAGG
AACY021590011.1/378-435        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY023236864.1/364-311        GUCCGUUCAUCC------------------------UUCG-----------------------------------GGACGCA---UGACACCAUAAGCAUGGAACGGGGCUUAUGG-
AACY023148838.1/683-738        GUCCGUUCAUCGC-----------------------UUUAU---------------------------------GCGACGCAU-GUC--AUCUA-GUCAUGGAACGG-GGGCUAGGU
AACY023194591.1/562-614        GUUCGUUCACCC------------------------UUAU-----------------------------------GGGCGCA--UAACACCUAG-AGCAUGGAACGGGGC--CUAGG
AACY020218796.1/3638-3700      GUCCGUUCAUCCC-----------------------GAAAGAAAAAAUA-------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
AACY021786368.1/377-315        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY022743645.1/569-626        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
CP000111.1/391792-391735       UUUCGUUCACCCUC----------------------UCUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AATZ01000001.1/222184-222243   ACACGUUCACCUUG----------------------CAUCCA-------------------------------CAAGGCGCAG--UCAAGCCAG-GCCACGGAACGG-GGACCUGGA
AACY020596405.1/175-234        CAACGUUCACCUCU----------------------UUCGA--------------------------------AGAGGCGCAG-UUCGAUUCAG-GCCAAGGAACGG-GGACCUGAA
AACY023498998.1/432-371        AAACGUUCAACUUGC---------------------AUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021901675.1/534-478        UUUCGUUCACCCUC----------------------UUU----------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023377816.1/742-804        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY021959806.1/190-250        ACACGUUCACCUCUU---------------------UUCG--------------------------------GAGAGGCGCAG-UUCGAUUCAG-GCCAAGGAACGG-GGACCUGAA
AACY020735122.1/92-29          AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AACY023988768.1/554-497        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
AE017126.1/398283-398223       AAACGUUCACCCUGA---------------------UACU--------------------------------UCAGGGCGCAG-ACCCAAUAAG-GCCACGGAACGG-GGACCUUAC
AACY020555995.1/3324-3384      ACACGUUCACCUCUU---------------------UUCG--------------------------------GAGAGGCGCAG-UUCGAUUCAG-GCCAAGGAACGG-GGACCUGAA
AACY021376241.1/491-429        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022093997.1/182-127        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCAU-GAUAAGAGAA-U--AGGGAACGGG---AUUCUC
AACY021088879.1/151-98         GUCCGUUCAUCCC-----------------------GAUA----------------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
CP000435.1/778927-778986       CAACGUUCACCUCAC---------------------UUCU--------------------------------GUGAGGCGCAG--ACUCGCCAG-GCCACGGAACGG-GGACCUGGA
AACY022725376.1/816-754        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020146676.1/1439-1380      AAACGUUCAUCUCG----------------------UUUUU--------------------------------CGAGCCGCAU-UAAGAUUGAA-GCCAAGGAACGG-GGACUUCAG
AACY020380457.1/1284-1225      AAACGUUCAUCUCG----------------------UUUUA--------------------------------CGAGCCGCAU-UAAGAUUGAA-GCCAAGGAACGG-GGACUUCAG
AACY020125731.1/386-448        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY023129621.1/721-778        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAUAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY023155983.1/590-647        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023943892.1/264-207        GAACGUUGGCCCC-----------------------GCCAA---------------------------------GGGGUGCAG-UCAGUCCCGC-GCCAGGCAACGG-GGACGCGGG
CP000095.2/1083243-1083186     AUACGUUCGCCUCA----------------------ACUCA--------------------------------UGGGGUGCA---UCAAAUGGA-AGUAGGGAACGGGAU-UUCCAG
AACY020368675.1/1346-1406      AAGCGUUCACCUC-----------------------ACUUAUUC------------------------------GAGGCGCAG-CUCGAUCCAA-GCCAUGGAACGG-GGGCUUGGG
AACY020494967.1/635-578        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020110786.1/1031-1093      AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
BX569692.1/330721-330782       CAGCGUUCACUUCGC---------------------AUUCC-------------------------------GCGGAGCGCAG-CUCGACUCAG-GCCAUGGAACGG-GGGUCUGGG
AACY023516959.1/358-303        UUUCGUUCACCC------------------------UUAACU---------------------------------GGGCGCAG-UUCGAGCUAU-ACCAAGGAACGG-GGG-AUAGC
AACY020103457.1/2102-2155      GUCCGUUCAUCCU-----------------------AAUU----------------------------------AGGACGCA--UGAGAUCCAA--GCAUGGAACGGGGC--UUGGG
AACY021471759.1/316-262        GUCCGUUCAUCCC-----------------------UUAC----------------------------------GGGACGCA---UGACACCAC-AGCAUGGAACGGGGU-UGUGGU
AATZ01000001.1/53754-53694     AAACGUUGAACCGAU---------------------AGUU--------------------------------GUCGGUUGCAG-UUAGAGCCAG-GUCACGCAACGG-GGUCCUGGU
AACY022127252.1/75-136         AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020522066.1/2224-2280      UCACGUUGAGCCC-----------------------CUUG----------------------------------GGGCUGCAG-UUCGUUCCAC-GCCAGGCAACGG-GGGCGUGGG
AACY021754047.1/655-596        AAACGUUCACCCCCU---------------------CUUG--------------------------------AGGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
AACY020044163.1/355-301        GUCCGUUCAUUCC-----------------------GCAA----------------------------------GGAACGCA---UGACGGUCU-ACCAUGGAACGG-GGGUAGACU
AACY020213622.1/1965-1908      UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023558700.1/768-707        AAACGUUCACUUCGCU--------------------ACAC-------------------------------AGCGAAGCGCAG-UUCGACUCAG-GGCAUGGAACGG-G-GCCUGAG
AAUA01000003.1/77229-77287     ACACGUUGGCCACG----------------------AGUG---------------------------------UGUGGCGCAG-UUCGAUCUCA-AGCAAGCAACGGGGC-UUGAGA
AACY020114592.1/2035-2090      GUCCGUUCAUCCC-----------------------UAAC----------------------------------GGGACGCA--UGAUCACCAA-GGCAUGGAACGGGGU-CUUGGU
AACY022268926.1/465-407        AAACGUUCACCUCG----------------------CCCAG--------------------------------CGAGGCGCAG-AUCGACUCAG-GCCAUGGAACGG-GGG-CUGAG
AACY022164825.1/422-484        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UAGGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020142518.1/1568-1625      UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022359289.1/409-470        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY023862748.1/448-509        GAUCGUUCACUUCGC---------------------AUCGC-------------------------------GCGAAGCGCAG-UUCGCCUCAG-GCCAUGGAACGG-GGACCUGAG
CP000095.2/1019126-1019068     ACACGUUCAGCU------------------------GAAAACAA-------------------------------AGCUGCAG-UAAGACUCGA-GACAUGGAACGGGGU-CUUGGG
AACY022351946.1/260-208        GUCCGUUCAUCUC-----------------------UUCG----------------------------------GAGACGCAU-GACAACCUAG---CAUGGAACGGGG---CUAGG
AACY021419510.1/412-349        AGACGUUCACCCUGCU--------------------UUUUA------------------------------AGCAGGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGGG
AACY020835342.1/267-206        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY023383737.1/1189-1127      UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020822122.1/27-79          GUCCGUUCAUCC------------------------UUCG-----------------------------------GGACGCA---UGAGAUCUG-ACCAUGGAACGG-GGGUCAGGU
AACY020828527.1/587-645        AAACGUUCACCCCU----------------------GUUUC--------------------------------GGGGGCGCAG--ACACUCCAA-GCCACGGAACGG-GGACUUGGA
AACY022811576.1/261-199        UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY023848834.1/767-826        AAGCGUUCACCCCCU---------------------CUGG--------------------------------AGGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
AACY022147687.1/518-580        AAUCGUCCGAUCUA----------------------CCGUUUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAAAGGACGG-GGACUUGAG
AACY021024425.1/720-782        UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
CP000576.1/1086706-1086644     UAACGUUCAUCCAAG---------------------UUUAUAUCU---------------------------CU-GGACGCA---UGCAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020091003.1/1614-1559      GUCCGUUCAUCCUG----------------------AUA----------------------------------UGGGACGCA---UGCAAUCAA-GUCAUGGAACGG-GGACUUGGU
AACY021886743.1/236-176        AAACGUUCAACUCGC---------------------GAAG--------------------------------GCGAGCCGCAA-GUCGACUUGA-GCCAUGGAACGG-GGACUUAAG
AACY022821404.1/413-474        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY023926329.1/417-477        GCACGUUCACCUCUU---------------------UCCG--------------------------------GAGAGGCGCAG-UUCGAUUCAG-GCCAAGGAACGG-GGACCUGAA
AACY023617861.1/327-276        GUCCGUUCAUCC------------------------UUCG-----------------------------------GGACGCA--UGAGAUCCAA--GCAUGGAACGGGGC--UUGGG
AACY022178947.1/106-49         UUUCGUUCACCCUC----------------------AUAU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020422577.1/653-601        GUCCGUUCAUCCC-----------------------UUCG----------------------------------GGGACGCAU-GAUAACCUAG---CAUGGAACGGGG---CUAGG
AACY022163005.1/242-304        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY022381872.1/274-331        GUCCGUUCAACCUU----------------------CUUUG--------------------------------AAGGUCGCA---UGAAACCAC-AGCAUGGAACGGGGU-UGUGGU
AACY020135089.1/1271-1214      UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022350248.1/138-191        UAACGUUGAACC------------------------CUAUGA---------------------------------GGUUGCAA--UAAAACCGA--CCAUGCAACGGGGG--UCGGU
AACY021090753.1/356-414        GUCCGUUCAUCCCU----------------------UUCAAUC------------------------------AGGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
AACY020217100.1/1518-1576      AACCGUUCAUCCU-----------------------AAUUUA--------------------------------AGGACGCAG-UUCGAGCUAU-UCCAGGGAACGG-GGGUAUAGC
AATZ01000003.1/202513-202454   CAACGUUCACCUCAC---------------------AUUU--------------------------------GUGAGGCGCAG--ACAACCCAG-GCCAAGGAACGG-GGACCUGGA
AACY020093347.1/1463-1402      AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020217607.1/1834-1776      CAACGUUCACCCCU----------------------UUUGA--------------------------------AGGGGCGCAG--ACACUCCAA-GCCACGGAACGG-GGACUUGGA
AACY024004044.1/481-534        GUCCGUUCAUCCC-----------------------GCAA----------------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY021134408.1/279-217        AAUCGUCCGAUCUA----------------------CCAACUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY023849344.1/1362-1303      UCACGUUGAGCCU-----------------------CAUCAAC-------------------------------AGGCCGCAG-UCAGACCCGC-GCCAGGCAACGG-GGGCGUGGG
AACY022969230.1/793-734        AAUCGUUCACUCCGU---------------------UAUC--------------------------------GCGGAGCGCAG--UCAAGCCAG-GCCAUGGAACGG-GGACCUGGA
AACY022682222.1/443-381        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY023375461.1/388-443        GUCCGUUCAUUCCC----------------------AGU----------------------------------GGGAACGCA---UGAAACCAC-AUCAUGGAACGG-GGGUGUGGU
AACY023482557.1/228-281        AUACGUUCACUCCC----------------------AUU----------------------------------GGGAGCGCAU-GCAUUCUAGU-G--AUGGAACGGG---CACUAG
CP000435.1/1642629-1642569     CAUCGUUCACCUCGU---------------------UUUU--------------------------------GCGAGGCGCAG-AUCGGCCCAA-GCCAAGGAACGG-GGACUUGGG
AACY022696781.1/141-198        GUCCGUUCAUCCAU----------------------UUUUC--------------------------------AUGGACGCA---UGAAACCUA-AGCAUGGAACGGGGC-UUAGGU
AACY021706386.1/734-795        AAACGUUCAACUUGC---------------------GAAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY023508450.1/885-828        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAGGGAACGG-GGG-AUGGC
AACY021022913.1/977-915        AAUCGUCCGAUCUA----------------------CCAUUUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY021474861.1/89-147         ACACGUUCAGCU------------------------AAAUUUCA-------------------------------AGCUGCAG-UAAGACUCGA-GACAUGGAACGGGGU-CUUGAG
AACY020083605.1/1352-1290      AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
CP000110.1/1025849-1025788     CCACGUUCACCUCGU---------------------CUUCG-------------------------------GCGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020600928.1/242-181        UCACGUUCACCUCGU---------------------UUUCA-------------------------------GCGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY023004636.1/181-120        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
CP000110.1/532787-532847       AAACGUUCACCUCGC---------------------UUCU--------------------------------GUGGGGCGCAG-CUCAAUCCAA-GCCAUGGAACGG-GGGCUUGGA
AACY023620289.1/540-488        GUCCGUUCAUCC------------------------UUCG-----------------------------------GGACGCAU-GAUCACCACA--GCAUGGAACGGGGU--UGUGG
AAUA01000003.1/162424-162364   CAACGUUCACCCCGC---------------------CCAU--------------------------------GCGGGGCGCAG-CUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
BX569692.1/82486-82545         AAACGUUCACCCCUC---------------------UUUC--------------------------------GGGGGGCGCAG--ACACUCCAA-GCCACGGAACGG-GGACUUGGA
AACY020456471.1/2763-2819      GUCCGUUCAUCCC-----------------------GCAA----------------------------------GGGACGCA--UGACAUGAGGUGACAUGGAACGGGGU-CCCUCA
AACY021562483.1/105-44         AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020593180.1/87-149         AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY021612733.1/82-139         GUCCGUUCAUCGCU----------------------AAUUU--------------------------------AGCGACGCA---UGCAACCUA-GCCAUGGAACGG-GGGUUAGGU
AACY020116683.1/1265-1319      GUCCGUUCAUCGC-----------------------UUAU----------------------------------GCGACGCA---UGUAAUCAA-GUCAUGGAACGG-GGGCUUGGU
AACY020650148.1/708-647        CAGCGUUCACUUCGC---------------------AUUCC-------------------------------GCGGAGCGCAG-CUCGACUCAG-GCCAUGGAACGG-GGGUCUGGG
AACY020493813.1/2062-2004      UUUCGUUCACCUUC----------------------AUUAU--------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGAC
AACY020494069.1/613-561        GUCCGUUCAUCCC-----------------------GAUA----------------------------------GGGACGCAU-GACAACCUAG---CAUGGAACGGGG---CUAGG
AACY023649577.1/772-830        AUACGUUCAUCCUAG---------------------UUAU--------------------------------CUUGGACGCA---UGAAAUGGA-AAUAGGGAACGGGAU-UUCCAU
AACY020226045.1/1513-1452      CAUCGUUCACCUCGUC--------------------CCU--------------------------------GGCGAGGCGCAG-UACGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY023867226.1/852-906        GUACGUUCAUCCC-----------------------AUUC----------------------------------GGGACGCA---UGCUGCCUA-ACCAUGGAACGG-GGGUUAGGU
AACY020475540.1/1850-1911      UCACGUUCACCUCGUC--------------------UUU--------------------------------GGCGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020948351.1/138-81         UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021040601.1/73-129         UUUCGUUCACCCUC----------------------UUU----------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AAUA01000001.1/1150407-1150468 GAUCGUUCACUUCGU---------------------AUCGC-------------------------------ACGAAGCGCAG-UUCGCCUCAG-GCCAUGGAACGG-GGACCUGAG
AACY021135726.1/297-237        ACACGUUCACCUCUU---------------------UUCG--------------------------------GAGAGGCGCAG-UUCGAUUCAG-GCCAAGGAACGG-GGACCUGAA
AACY020372119.1/841-777        AGACGUUCACCUUGCUU-------------------CUUG------------------------------AAGCAAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020143429.1/1760-1820      AAACGUUCACCCCC----------------------CUCUUGC------------------------------GGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
AACY022290720.1/130-69         AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCUGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021315556.1/303-357        GUCCGUUCAUCCUA------------------------AU---------------------------------UAGGACGCA---UGAAAUCUG-AUCAUGGAACGG-GGAUCAGAU
AACY022493650.1/604-550        GUCCGUUCAUCCC-----------------------AAGU----------------------------------GGGACGCA---UGACGCUCU-ACCAUGGAACGG-GGGUAGAGU
AACY020251219.1/1590-1651      CAUCGUUCACCUCGUC--------------------CCU--------------------------------GGCGAGGCGCAG-UACGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY020657909.1/95-33          AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
CP000552.1/378828-378767       UUACGUUCAUCC-UAA--------------------UUGAAU-----------------------------UUACGGACGCAU-GAC--AUGGA-AAUAGGGAACGGGAU-UUCCAU
CP000110.1/2439513-2439574     GAUCGUUCACUUCGC---------------------AUCAC-------------------------------GCGAAGCGCAG-UUCGCCUCAG-GCCAUGGAACGG-GGACCUGAG
AACY021432045.1/868-929        CUACGUUCAGUCAGCA--------------------CUCG-------------------------------UGUUGACCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGA-
AACY023997045.1/774-720        GUCCGUUCAUCCC-----------------------UUAC----------------------------------GGGACGCA---UGACUCCUA-AGCAUGGAACGGGGC-UUAGGU
AACY021645078.1/666-720        GUCCGUUCAUCCC-----------------------UUCG----------------------------------GGGACGCA---UGACUCCUA-AGCAUGGAACGGGGC-UUAGGU
AACY020352101.1/1112-1048      AGACGUUCACCUUGCC--------------------UCCCUC-----------------------------GGCAAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY023410946.1/80-23          CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAUAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY022741063.1/398-337        GAUCGUUCACUUCGC---------------------AUCGC-------------------------------GCGAAGCGCAG-UUCGCCUCAG-GCCAUGGAACGG-GGACCUGAG
AACY021855367.1/94-153         AAACGUUCAUCUCG----------------------UUUUU--------------------------------CGAGCCGCAU-UAAGAUUGAA-GCCAAGGAACGG-GGACUUCAG
AACY021439574.1/271-328        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
CT978603.1/1727489-1727429     GCACGUUCACCUCGC---------------------UCCG--------------------------------GUGAGGCGCAG-UUCGAUCCAG-GCCAUGGAACGG-GGACCUGGA
AACY023850043.1/1175-1116      UCACGUUGAGCCU-----------------------CAUCAAC-------------------------------AGGCCGCAG-UCAGAUCCGC-GCCAGGCAACGG-GGGCGUGGG
AACY020215626.1/402-455        GUCCGUUCAUCCC-----------------------GCAA----------------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
AACY020220459.1/904-966        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY021321565.1/41-103         AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY021507954.1/290-347        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020607949.1/872-815        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020149141.1/2049-1987      UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY024101750.1/823-888        GUCCGUUCAUCCCUAC--GU----------------AUCA---------------------------ACAAGUAGGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGA
AACY020321851.1/1303-1243      ACACGUUCACCUCUU---------------------UUCG--------------------------------GAGAGGCGCAG-UUCGAUUCAG-GCCAAGGAACGG-GGACCUGAA
AACY022811775.1/600-658        AGUCGUUCAUCCU-----------------------AAUUAA--------------------------------AGGACGCAG-UUCGAGCUAU-UCCAGGGAACGG-GGGUAUAGC
AACY022062813.1/946-885        AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AAUA01000001.1/260927-260989   CAACGUUCACCUCCC---------------------UUUGCC------------------------------GGGAGGCGCAG-UUCGAUUCAG-GCCAUGGAACGG-GGACCUGAA
CT978603.1/1019340-1019397     UCACGUUGGCCCC-----------------------GGCAA---------------------------------GGGGUGCAG-UCAGACCCGC-GCCAGGCAACGG-GGACGCGGG
AACY023361774.1/1167-1108      AAACGUUCAUCUCG----------------------UUUUU--------------------------------CGAGCCGCAU-UAAGAUUGAA-GCCAAGGAACGG-GGACUUCAG
AACY020363747.1/1464-1521      AGCCGUUCACCCUG----------------------GUU----------------------------------CAGGGCGCAG-UGGUUCUCAG-GUCAAGGAACGGGGA-CCUGUU
AACY022447983.1/152-214        AAACGUUCAACUUGC---------------------AUUUAC------------------------------GCAAGCCGCAG-AUCGACUUAA-GCCAAGGAACGG-GGACUUAAG
AACY023231803.1/344-400        GUCCGUUCAUCCC-----------------------GCAA----------------------------------GGGACGCA--UGACAUGAGGUGACAUGGAACGGGGU-CCCUCA
AACY021881643.1/581-643        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGCCUCAG-GCCAUAGGACGG-GGACUUGAG
AACY020541148.1/700-640        AAACGUUCACCCCCU---------------------CUUGC-------------------------------GGGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
CP000551.1/407110-407052       UUUCGUUCACCCUC----------------------AUUUG--------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020162733.1/317-378        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY023928200.1/423-478        AUUCGUUCACUC--C---------------------AAAA--------------------------------G--GAGCGCAG-UCCGAGCUAU-ACCAUGGAACGG-GGG-AUAGC
AACY023821394.1/1146-1083      AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AACY022542130.1/197-135        AAUCGUCCGAUCUA----------------------CUAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020087445.1/899-846        GUCCGUUCAUCCC-----------------------UUAC----------------------------------GGGACGCA--UGACAACUAA--GCAUGGAACGGGGC--UUAGU
AACY022455268.1/733-794        CAGCGUUCACUUCGC---------------------AUUCC-------------------------------GCGGAGCGCAG-CUCGACUCAG-GCCAUGGAACGG-GGGUCUGGG
AACY020872306.1/436-498        UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020136717.1/1025-1082      CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAUAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY020111227.1/64-126         AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY021791783.1/522-576        AUUCGUUCACCC------------------------UAAUA----------------------------------GGGCGCAG-UCCGAGCUAU-ACCAUGGAACGG-GGG-AUAGC
AACY023482404.1/203-255        GUCCGUUCAUCCC-----------------------AAAU----------------------------------GGGACGCAU-GACAACCUAG---CAUGGAACGGGG---CUAGG
CP000878.1/1063065-1063005     AAGCGUUCACCUUC----------------------UUAUUC-------------------------------GAAGGCGCAG-UUCGACUCAA-GCCAUGGAACGG-GGACUUGGG
AACY023995738.1/181-124        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY023861007.1/1140-1081      AAACGUUCACCCCCU---------------------CUUG--------------------------------AGGGGGCGCAG--AUGCUCCAA-GCCAUGGAACGG-GGACUUGGA
AACY022699591.1/267-210        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY020302472.1/1556-1619      AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AACY021228313.1/423-475        AUACGUUCACCUC-----------------------UUAC----------------------------------GAGGCGCA---UAACAACAA--GCUUGGAACGGGGC--UUGUU
AACY022250052.1/587-641        GUCCGUUCAUCCU-----------------------UAAC----------------------------------GGGACGCAU-GAUCACCACA--GCAUGGAACGGGGU--UGUGG
AACY021282448.1/620-558        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY023670106.1/669-727        AUACGUUCAGCU------------------------CAAUUUAA-------------------------------AGCUGCAG-UAAGACUCGA-GACAUGGAACGGGGU-CUUGGG
AACY021596955.1/479-426        GUCCGUUCAUCCC-----------------------AAUA----------------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
AACY020344237.1/796-738        CAACGUUCACCUUG----------------------CUUCUA-------------------------------CAAGGCGCAG-AUC--ACCAG-GCCAAGGAACGG-GGACCUGGA
AACY022454084.1/391-324        AAUCGUCCGAUCUACCA-------------------UUUCAUU---------------------------UGAUAGACCGCAG-UAGGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY020495036.1/1265-1322      UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020633531.1/266-327        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY023510952.1/10-72          AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGGCUUGAG
AACY021239559.1/282-219        AAGCGUUCACUCCAC-C-------------------ACUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
BX548174.1/350508-350446       AAUCGUCCGAUCUA-C--------------------CACUA------------------------------GAUAGACCGCAG-UACGACUCAA-GCCAAAGGACGG-GGACUUGAG
AACY020437876.1/1860-1803      UCACGUUGAUCCCC----------------------ACA----------------------------------GGGGAUGCAG-CUCGAUUCCA-GUCAGGCAACGG-GGGCUGGAG
AACY021184437.1/629-569        AAACGUUCACUUCGC---------------------UUUU--------------------------------GCGGGGCGCAG-CUCGAUCCAA-GCCAUGGAACGG-GGGCUUGGG
CP000110.1/2424541-2424485     CUGCGUUCACCCUG----------------------AAC----------------------------------UAGGGCGCAU-CUACA-ACGA-GUCAGGGAACGG-GGGCUCGUC
BX569690.1/30462-30521         AAGCGUUCACCUC-----------------------ACUUUUC-------------------------------GAGGCGCAG-CUCGAUCCAA-GCCAUGGAACGG-GGGCUUGGG
AACY020607057.1/241-303        AAACGUUCAACUCGUU--------------------GCAU-------------------------------AGCGAGCCGCAU-CUCGAUUUAA-GCCAAGGAACGG-GGACUUAAA
AACY023145361.1/80-23          CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAUAUGAG-AAUAGGGAACGGGAU-UCUCAU
CP000576.1/1058156-1058213     CAACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY020366972.1/1869-1930      UCACGUUCACCUCACC--------------------UCC--------------------------------GGUGAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY023848195.1/1188-1132      GGACGUUCACCUCU----------------------AUCUU--------------------------------GGAGGCGCA---ACCAACUGA-UCCACGGAACGG-GGG-ACAGU
AACY020306852.1/423-367        UCACGUUGAGCCC-----------------------CUUA----------------------------------GGGCUGCAG-UUCGUUCCAC-GCCAGGCAACGG-GGGCGUGGG
AACY020218401.1/1749-1687      AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022727901.1/367-305        UUACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY021516817.1/217-160        UUUCGUUCACCCUC----------------------AAUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY022857668.1/684-629        UGACGUUGAGCCC-----------------------ACUAC---------------------------------GGGCUGCA---UAAAUUCCG-GCCAGGCAACGG-GGGCCGGUU
AACY020114711.1/845-783        AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
CP000878.1/390849-390787       AAGCGUUCACCCUG----------------------UUUCAAC------------------------------CAGGGCGCAAAUUAGAACCAG-GCCAUGGAACGG-GGACCUGGU
AACY020214524.1/1265-1330      GUCCGUUCAUCCCUAC--------------------GCAUCAACAA-------------------------GUAGGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
AACY020126626.1/975-1029       GUCCGUUCAUCCU-----------------------UAAC----------------------------------GGGACGCAU-GAUCACCACA--GCAUGGAACGGGGU--UGUGG
AACY022467976.1/131-75         UCACGUUGAGCCC-----------------------CUUA----------------------------------GGGCUGCAG-UUCGUUCCAC-GCCAGGCAACGG-GGGCGUGGG
AACY023469870.1/595-540        GUCCGUUCAUCCCU-----------------------UCG---------------------------------GGGGACGCA---UGAAACCAC-AUCAUGGAACGG-GGGUGUGGU
AACY022822164.1/628-566        AAUCGUCCGAUCUA----------------------CCAUUAGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY023863339.1/763-701        UUACGUUCACUUCGUU--------------------GUCC-------------------------------AACGAAGCGCAG-UCCGACUCAG-GCCAUGGAACGG-GGACCUGAG
AACY021843998.1/733-794        AAACGUUCAACUUGC---------------------GUAUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY021195976.1/208-149        AAGCGUUCACCUC-----------------------ACUUUUC-------------------------------GAGGCGCAG-CUCGAUCCAA-GCCAUGGAACGG-GGGCUUGGG
AACY022729736.1/904-840        AGACGUUCAUCUUGCC--------------------AGCCUC-----------------------------GGCAAGGCGCAG-UUCGACUCAG-GCCAUGGAACGG-GGACGUGAG
AACY023493009.1/130-183        GUCCGUUCAUCCC-----------------------GCAA----------------------------------GGGACGCA--UGACACCCAA--GCAUGGAACGGGGC--UUGGU
AACY020970097.1/597-651        GUACGUUCAUCCC-----------------------AUUU----------------------------------GGGACGCA---UGCUGCCUA-ACCAUGGAACGG-GGGUUAGGU
AACY024062697.1/147-204        CUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAAAUGAG-AAUAGGGAACGGGAU-UCUCAU
AACY020368020.1/129-67         AAUCGUCCGAUCUA----------------------CCAUCUGA-----------------------------UAGACCGCAG-UACGACUCGA-GCCAUAGGACGG-GGACUUGAG
AACY021140337.1/758-701        AUACGUUCGCCUCA----------------------ACUCA--------------------------------UGGGGUGCA---UCAAAUGGA-AGUAGGGAACGGGAU-UUCCAG
AACY020543120.1/324-382        CAACGUUCACCUCGC---------------------UUCU--------------------------------GCGAGGCGCAG-AUC--ACCAG-GCCAAGGAACGG-GGACCUGGA
AACY021485224.1/131-75         UCACGUUGAGCCC-----------------------CUUA----------------------------------GGGCUGCAG-UUCGUUCCAC-GCCAGGCAACGG-GGGCGUGGG
AACY021236678.1/571-628        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY021525487.1/571-514        UUUCGUUCACCCUU----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
BX569690.1/27660-27600         CAACGUUCACCUCUC---------------------CUCGC-------------------------------GGGAGGCGCAG--ACAAGCCAG-GCCAUGGAACGG-GGACCUGGA
AACY021187365.1/42-96          GAACGUUCACCGGU----------------------UCAC---------------------------------ACCGGCGCAC-UUC--UUCAG--GCAGGGAACGGGGC--CUGAG
AACY021659580.1/765-703        UAACGUUCAUCCA-AG--------------------UUUAUAU----------------------------CUCUGGACGCA---UGAAAUGGG-AGUAGGGAACGGGAU-UCUCAU
AACY020526506.1/1349-1286      AAGCGUUCACUCCAC-C-------------------CCUU------------------------------GCGUGGAGCGCAG-UUCGAUCCAG-GCCAAGGAACGG-GGACCUGGA
AACY020344007.1/558-613        UAACGUUCACCCC-----------------------GCAAG---------------------------------GGGACGCAU--GUUA-CUAG-CUCAUGGAACGG-GGAGCUAGA
AACY022727367.1/320-263        UUACGUUCAUCCAA----------------------UUUAU--------------------------------UUGGACGCA---UGAUAUGAG-AAUAGGGAACGGGAU-UCUCAU
CP000097.1/995827-995767       UCACGUUGAACCGAC---------------------AGCC--------------------------------GUCGGUUGCAG-UUAGAGCCAG-GUCACGCAACGG-GGUCCUGGU
AACY021248787.1/511-454        UUUCGUUCACCCUC----------------------AUUU---------------------------------GAGGGCGCAG-UUCGAGUCAU-ACCAUGGAACGG-GGG-AUGGC
AACY020211817.1/1232-1294      UAACGUUCAUCCAAG---------------------UUUAUAUC----------------------------UUUGGACGCA---UGAAAUGGG-AUUAGGGAACGG-GAUUCUCAU
AACY022041124.1/184-123        AAACGUUCAACUUGC---------------------GUUUA-------------------------------GCAAGCCGCAA-AUCGACUUAA-GCCAUGGAACGG-GGACUUAAG
AACY020090277.1/1076-1138      AAUCGUCCGAUCUA----------------------CCAUUAGA-----------------------------UAGACCGCAG-UACGACUCAA-GCCAUAGGACGG-GGACUUGAG
AACY022156705.1/826-918        --ACGUUCAUCCCA-----GAGCCAGC-UCGAAGCAUUCU---------UGCCAUCGAUAACUGGCUCGCCAUAGGGACGCAG---CAACCUAA--CGAUGGAACGGGCG--UUAGG
AACY023452725.1/1148-1063      GUACGUUCAUCG-CAUUCGCCUACCAGG--------ACAAGUUA---------------CC-AGUA-GUGAAUGACGACGCAG---GCAACCUA-CUCAUGGAACGG-GGGGUAGGU
#=GC SS_cons                   :::AAAAA:<<<<<......................____................................_>>>>>-----.-----<<<<<.<<<___aaaaa_.>>->>>>>>
#=GC RF                        auACGUUCAuCCcc......................uUuu................................uggGGaCGCAG.UucgAcccaa.gcCAUGGAACGG.Ggacuuggg
//
# STOCKHOLM 1.0

#=GF AC   RF01705
#=GF ID   Flavo-1
#=GF DE   Flavo-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   42.00
#=GF TC   42.00
#=GF NC   41.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.05 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Flavo-1_RNA_motif
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   201


AM398681.1/1935873-1935792     UUCUAGCC-------CUGAUAGUAGU-GGAAAUCC--UUUUUUC-----UGG--CU------------------------------------CCUUU-------------------------------------------AGCCAG--GAA---AAAGAUU-GCAACGGAUAGCAGGAAAUAGC
AACY022969018.1/529-462        UAAUAGCC-------CUGAUGGGAAU-GGCAUCC--UCC--CAA------------------------------------------------CUUGA---------------------------------------------------UUG---GGA-GAU-AGAAUGGACAGCAGGAAAAAGG
CP000685.1/2288233-2288156     CCCUAGCC-------CCGAUAGUAGU-GGAAAUCC-UUU--UGU-----GCC--G-------------------------------------GGGUU--------------------------------------------CGGC---ACA---AAAGAUU-GCAACGAAUAGCGGGAUUAGCU
AACY021615962.1/586-507        ------UU-GCGUUAAGGAUUGAAGU-GGCAUCCU-UUU--UUU-----GCU----------------------------------------GCCACAUAU-----------------------------------------GGC---AAA---AAAAGAU-AUAACUGAAAGCCUGACCUAUA
AACY020056867.1/1414-1334      ------UU-GCGUUAAGGAUGGAAGU-GGAAAUCC-UUU--UUA-----UUU--UU------------------------------------UCUUU-------------------------------------------AAAAA---UAA---AAAGAUUGUGAACGGACAGCCUGCCCAUGC
AAXX01000002.1/108484-108388   CCCUAGCC-------CAGAUAGAAGA-GAAAAUCC-UUU--UUAUA---CCU------GA--CAG-GUUUUC---------------------------------------------------------GAAAACCUGCA--AGGCA-UAA---AAAGAUU-GAAACGGAUAGCUGGAUAAAGC
CP000685.1/2164515-2164593     CCUUAGCC-------CUGAUAGAAGU-GGAAAUCC-UUU--UGU------------------------------------------------GAAGCUUUAGCGGA------------------------------------------ACA---AAAGAUU-GAAACGGAUAGCAGGAAUAGCU
CP000685.1/30089-30168         CCCUAGCC-------CCGAUAGAAGC-GGAAAUCC-UUU--UUG-----UGG--CG------------------------------------GGGUU-------------------------------------------CGCCA---CAA---AAAGAUU-GAAGCGGAUAGCGGGAUUUAGC
AM398681.1/1213634-1213560     ---UUCUC-GCGUGAGUGAUUGAGGC-GUUAUCC---UU--UUU-----UG-----------------------------------------AGGAA----------------------------------------------CG---AAA---AAAAGAU-AUAGCCGAAAGCACGACCCAGC
AM398681.1/1008767-1008846     UUCUAGCC-------CCGAUAGUAGU-GAAAAUCC-UUU--UUC-----UGG--CU------------------------------------CCUUU-------------------------------------------AGCCA---GGA---AAAGAUU-GUAACGGAUAGCGGGAAUAGCU
AACY020037845.1/1519-1445      ------CC-GCGCUAAGGAUGGACGU-GGAAAUCC-UUU--UUU-----GGG----------------------------------------AGCGG---------------------------------------------CCC---AAA---AAAGAUU-GCAGC-CACAGCCUGACCAAGC
AM398681.1/1035242-1035316     ---AUUUU-GCGUUAGGGAUAGCAGC-GAAAAUC---CU--CCC-----GAU----------------------------------------UUUUC---------------------------------------------UUC---GGG-----AGAUU-GUAGCGUAUAGCCCGACCCUUU
AATO01014758.1/41-120          AACUAGCC-------CCGAUUGCAGC-GACAUCC--UUU--UUG------------------------------------------------UGAGGAGGAACGACGAG---------------------------------------CAA---AAA-GAU-ACAGCGGAAAGCGGGAAAUAGC
AAPR01000007.1/184845-184929   AGUCGCUC-GCGUUAGGGAUAGAAGC-GGCAUCCC-UCA--UUG-----CCG--AU------------------------------------AGGU--------------------------------------------AUCGG---AAA---UGAGGAU-AUAGCAUAUAGCCCGACGCUUU
AM398681.1/2808043-2808124     UUUUAGCC-------CCGAUAAUAGU-GGAAAUCC--UU--UUUG----UUU----------------------------------------UUUUCUUU------------------------------------------AAA---AAACAAAAAGAUU-GUAACGGAUAGCGGGAAUAGCU
AACY023335274.1/673-598        UUAUAGCC-------CCGGUAGUAGC-GGCGUCC--UGU--UGU-----GGC--G-------------------------------------GGUUU--------------------------------------------CGCC---ACA---ACA-GAU-AGAGCAAAUAACGGGACAAAUC
AM398681.1/2214869-2215012     UUUUAGCC-------CAGAUGGAAAC-GGAAAUCC--UU--UUGCGGGAAAA--UU--GU--AUU-UUUUAU-UGCCUAAAA-AG-AGC---GACCAAAGGAA---------GCUCCUUUU-UGGGCUUAUAAAAAA-ACAAUUUUACAAA---AAAGAUU-GUAGUGUACAGCUGGAUUGGCU
AAGA01020195.1/147-76          GUCUAGCC-------CAGAUUGAAAC-GACAUCC--UUU--UUU----------AU------------------------------------UUUUC-------------------------------------------AU------AAA---AAA-GAU-AUAGUGGAAAGCUGGAAAUAGC
AM398681.1/2287165-2287240     UUUUAGCC-------CUGAUGGAAGC-GAAAAUCC-UGU--UUC-----GUU----------------------------------------UUUUGG--------------------------------------------AAC---GAA---ACAGAUU-GUAGCG-ACAGCAGGAAAAUGG
AM398681.1/2670156-2670237     UUUUAGCC-------CUGAUAGCAGU-GGAAAUCC-UUU--UCUUU---UUU----------------------------------------UCCUUU--------------------------------------------AGA---AAAAGAAAAGAUU-GCAACGGAUAGCAGGAAUAGCU
AAGA01000221.1/2489-2410       ---UAUUU-GCGUGAAGGAUUGUAGU-GACAUCCU-UUU--UAA-----UUU----------------------------------------UGAU----------------------------------------------AAAAA-UUG---AAAAGAU-AUAACGAAAAGCCUGACCUUUA
AM398681.1/1248668-1248760     GGCUAGCC-------CCGAUUGCAGC-GGAAAUCC-UAU--UAU-----AGU--UG--UC--AGG-U-------------------------UUUUUU------------------------------------ACCUGACAGCU---AUA---AUAGAUU-GAAGCGAAAAGCGGGAAUUUUG
AATN01003474.1/279-358         UUUUAGCC-------CCGAUUGUAAC-GGAAAUCC-UUU--UUA-----AUU--UU------------------------------------UCUUU-------------------------------------------AAAAU---UAN---AAAAAUU-GUAGUGGAAAGCGGGAAAUAGC
AACY020637118.1/538-435        CUCUAGCC-------CGGAUAAUAGU-GGAAAUCC-UUU--UUU-----GUU-----------------AGUAUAAAAACCC---AUCG---ACUG----------------CGAUCAGGG-U-------------------GACAC-AAA---AAAGAUU-GCAACGGAUAGCCGGAUUAGCU
AACY020611296.1/253-175        AUU---UC-GCGUGAGGGAUUGCAGC-GGAAAUCC-UUU-----------------------------------------------------GUGGAACGAAGUGGAGC---------------------------------------------AAAGAUU-GCAGCGGAAUGCCCGACCAAGU
AACY023344773.1/472-396        ------CC-GCGAAAGGGAUAGCAGC-GGCAUCCU-UUU--GU-------------------------------------------------GAAGCGAAAGCGGA-------------------------------------------AC---AAAAGAU-AGAGCGAAUAGCCCGACCCAAG
AM398681.1/2174176-2174099     UUCUAGCC-------CAGAUGGAAAC-GGCAUCCU-UUU--UCU-----UGC--U-------------------------------------CCUUU--------------------------------------------AGCA---AGG---AAAAGAU-AGAGUGUACAGCUGGAAAUAGC
AM398681.1/1590815-1590896     ------CC-GCGUGAGGGAUAGCAGC-GGAAAUCC-UUU--UUU--UGAGGC----------------------------------------UUUUC---------------------------------------------GCCGAUAAA---AAAGAUU-GUAGCGCAUAGCCCGACCCGAC
AACY020920919.1/140-69         GUCUAGCC-------CCGAUAGCAGC-GGCAUCC--UUU--UGG------------------------------------------------ACUAUAGG------------------------------------------------CCA---AAAAGAU-AAAGCGAAUAGCGGGACAAAAU
AM398681.1/1446748-1446827     ------UU-GCGUUAGGGAUUGAAGU-GGAAAUCC-UUU--UUG-----AGG--CU------------------------------------UUUUU-------------------------------------------UGCCU---CAA---AAAGAUU-GUAACGUAAAGCCCGACCCUUG
CP000685.1/1625353-1625432     UUUUAGCC-------CCGAUAGAAGU-GGAAAUCC-UUU--UGCUU---UUU----------------------------------------UCUUU---------------------------------------------AAAAA-GGA---AAAGAUU-GCAGCGAAUAGCGGGAUCAGCU
AM398681.1/501028-501102       ---UUUUU-GCGUGAGGGAUUGAGGC-GGUAUCCU-UUU--UU-------------------------------------------------GAGGCACGA------------------------------------------------AA---AAAAGAU-AUAGCCGAAAGCCCGACCCCGC
AAGA01008778.1/401-330         ------UU-GCGUUAGGGAUUGAAGU-GGAAAUCC-UUU--UUA------------------------------------------------UUUUUCA-------------------------------------------------UAA---AAAGAUU-GUAGCGUAAAGCCCGACCUUUU
AM398681.1/197892-197971       UCCUAGCC-------CCGAUUGCAAC-GGAAAUCC-UUU--UUC-----UUG--CU------------------------------------UCUUU-------------------------------------------AGCAA---GGA---AAAGAUU-GAAGUGUAAAGCGGGAAAUAGC
AAXX01000001.1/707496-707593   UAAUAGCC-------CCGAUGGAAGU-GGAAAUCU-UUU--UUUU----CCU--UGCUUC--GAC-UU------------------------CGCUC------------------------------------AACUUGACAAGGU--AAA---AAAAAUU-GUAACGGACAGCGGGACUGAGA
AM398681.1/1920625-1920557     UUUUAGCC-------CUGAUGGAAGU-GGAAAUCC-UUG--CC-------------------------------------------------UUUUUU---------------------------------------------------GG---CAAGAUU-GUAACGUACAGCAGGAAUAAUG
AAGA01008631.1/782-851         ------CU-GCGUUAGCGAUAGAAAC-GGCAUCC--UUU--UGC------------------------------------------------UUUUUCU-------------------------------------------------GCA---AAA-GAU-AUAAUGGAUAGCGCGACCGGNU
AM398681.1/746192-746081       UUUUAGCC-------CUGAUGGAAGC-GGAAAUCC-UUU--UUU-----UUG-----------------UGCGUAUGAGUGC-CUCGUG---UUUU----------------UACGGGGCA-CUCAUACGCA----------CAA---AAA---AAAGAUU-GUAGC-AACAGCAGGAAUAUGG
AACY020833911.1/208-285        UCCUAGCC-------CAGAUAGGAAC-GGUAUCCU-UUU--UAU-----UUU----------------------------------------UCUUU---------------------------------------------AAAAA-AUA---AAAAGAU-AAAGUGGAUAGCUGGAAAUAGC
CP000685.1/3263136-3263057     CCCUAGCC-------CCGAUAGAAGC-GGAAAUCC-UUU--UUG-----UGG--CG------------------------------------GGGUU-------------------------------------------UGCCA---CAA---AAAGAUU-GAAGCGGAUAGCGAGAUUUAGC
AACY023455489.1/874-765        AACUAGCC-------CAGAUAGGAAC-GGCAUCCU-UUU--UAU-----UGU--UU---------------------UAGGG-ACAUGC---CCUUC---------------GACUGUGCU-UAGGGUGAUA--------AAACA---AUA---AAAAGAU-AGAGUGGAUAGCUGGAAAUAGC
AACY023332939.1/874-798        ------CC-GCGAAAGGGAUAGCAGC-GGCAUCCU-UUU--GU-------------------------------------------------GAAGCGAAAGCGGA-------------------------------------------AC---AAAAGAU-CCAGCGAAUAGCCCGACCCAAG
AM398681.1/2047222-2047145     UUUUAGCC-------CUGAUGGUAAC-GGCAUCC--UUU--UGC-----UUU--UU------------------------------------UCUUU-------------------------------------------AGAAA---GCA---AAA-GAU-AGAGUGAACAGCAGGAAUAGCU
AACY023449132.1/1228-1320      CUCUAGCC-------CGGAUUGGAAU-GACAUCCU-UUU--UUC-----AUU----------------------------GC-CAUGGG---UUUUAA--------------CCCUCGGC----------------------AAU---GAA---AAAAGAU-AUAAUGGAAAGCCGGACACAGC
AACY023343637.1/919-987        CCCUAGCC-------CAGAUAGUAAU-GGAAAUCC------CAC-----GCU----------------------------------------UUUG----------------------------------------------GGC---GUG------GAUU-GCAAUGGAUAGCUGGAAAUAGC
AM398681.1/774374-774469       UUUUAGCC-------CUGAUAGUAGU-GGAAAUCC-UAA--CAA-----AAA-------------------------AAAAC-AACUAU---GAUA----------------AUAGUUGUU-U-------------------UUU---UUG---UUAGAUU-GUAACGAAUAGCAGGAACGAAG
AATN01007049.1/497-418         ------UU-GCGUUAGGGAUUGCAGU-GAAAAUCC-UUU--UAU-----UUU--UU------------------------------------UCUUU-------------------------------------------AAAAA---AUA---AAAGAUU-GUAACGGAAAGCCCGACCUCGU
AM398681.1/1392373-1392452     UAAUAGCC-------CUGAUAGAAGU-GGAAAUCC-UUU--UGU-----UUU--UU------------------------------------CCUUU-------------------------------------------AAAAA---ACA---AAAGAUU-GUAACAAAUAGCAGGAAAUAGC
CP000685.1/2573472-2573547     UCCUAGCC-------CUGAUGGAAGC-GGCAUCCU-UUU--GCG-----CCG----------------------------------------GGGUU---------------------------------------------CGG---CGU---AAAAGAU-AUAGCGGACAGCAGGAAAUAGC
AM398681.1/1895555-1895473     ---GGUUU-GCGUGAGGGAUUGCAGU-GGAAAUC---CU--UUUUU---GAG----------------------------------------GUUUUU--------------------------------------------CUCCG-AAAAAAAGA--UU-GUAACGGAAAGCCCGACCCGAU
AM398681.1/2408210-2408133     UUUUAGCC-------CUGAUGGUAGC-GGCAUCCU-UUU--UCU-----UGC--U-------------------------------------CCUUU--------------------------------------------AGCA---AGG---AAAAGAU-AUAGCGUACAGCAGGAAAUGGC
AAGA01022321.1/338-409         GUCUAGCC-------CUGAUUGAAAC-GACAUCC--UUU--UUU----------AU------------------------------------UUUUC-------------------------------------------AU------AAA---AAA-GAU-AUAGUGGAAAGCAGGAAAUAGC
CP000685.1/506429-506508       CCCUAGCC-------CCGAUAGAAGC-GGAAAUCC-UUU--UUG-----UGG--CG------------------------------------GGGUU-------------------------------------------CGCCA---CAA---AAAGAUU-GAAGCGGAUAGCGGGAUUUAGC
AAGA01007071.1/800-721         ------UU-GCGUUAGCGAUAGUAAU-GACAUCCU-UUU--UUU-----GCU----------------------------------------GCCAUAUAU-----------------------------------------GGC---AAA---AAAAGAU-AUAAUGGAUAGCGCGACCCUUG
CP000685.1/5783002-5782927     GUCUAGCC-------CUGAUGGAAGC-GGCAUCCU-UUU--GUG-----GCG----------------------------------------GUGUU---------------------------------------------CGC---CGC---AAAAGAU-AUAGCAGACAGCAGGUUUCAGC
AACY023736844.1/55-1           ---------------GGGACCGAAGC-GGAAAUCC-UUU--CUC------------------------------------------------AAUUU---------------------------------------------------GAG---AAAGAUU-GCAGCGUAGGGCCCG-------
AM398681.1/2053796-2053715     ACAAUGCC-GCGUAAGGGAUAGUAGU-GGAAAUCC--UU--UUU-----G------------------------------------------AGAGGA---------------------------------------------AC---GAACAAAAAGAUU-GUAACGAAUAGCCCGACCCGCU
AM398681.1/2333989-2334068     UUUUAGCC-------CAGAUAAGAGU-GGAAAUCC-UUU--UAU-----UUU--UU------------------------------------CCUUC-------------------------------------------AAAAA---AUA---AAAGAUU-GAAACGUAUAGCUGGAAUUGCU
AAPD01000003.1/306499-306573   AUAGAACU-GCGUUAAGGAUUGUAAC-GGCAUCC---UU--UUG--------------------------------------------------CGA---------------------------------------------------UGGAGCAAAAGAU-AUAGUGAAAAGCCUGACCCGAU
AM398681.1/1726586-1726667     ------CC-GCGUGAGGGAUAGCAGC-GGAAAUCC-UUU--UUU--UGAGGC----------------------------------------UUUUC---------------------------------------------GCCGAUAAA---AAAGAUU-GUAGCGCAUAGCCCGACCCGAC
CP000685.1/4084547-4084621     CAAUAGCC-------CCGAUCGAAGU-GAUAUCCU-UUU--CAU-----GCU----------------------------------------UCUUU---------------------------------------------AGC---AGG---AAA-GAU-AUAACGAAGAGCGGGACUAAAG
AM398681.1/557267-557188       GCUUAGCC-------CCGAUAGAAGU-GGAAAUCC-UUU--UGU-----UUU--UU------------------------------------UCUUU-------------------------------------------AAAAA---ACA---AAAGAUU-GGAACGGAUAGCGGGAAUGGCU
AM398681.1/2078980-2079061     CCCUAGCC-------CCGAUAGAAGU-GGAAAUCC-UUU--UUU-----GGC--GA------------------------------------UUUUUCU-----------------------------------------UCGCC---AAA---AAAGAUU-GGAACGUAUAGCGGGAAAUAGC
AM398681.1/554571-554650       UUUUAGCC-------CCGAUUGCAGU-GGAAAUCC--UUUUUUGAG----GC----------------------------------------UUUUC---------------------------------------------GC----CGAUAAAAAGAUU-GUAACGGAAAGCGGGAAAUAGC
AM398681.1/715409-715482       CCCUAGCC-------CUGAUUGUAGU-GAAAAUCC-UUU--UUU------------------------------------------------GAGGCACGA-----------------------------------------------AAA---AAAGAUU-GAAACGUAAAGCAGGAAAAAGC
AAGA01016516.1/507-429         GU-------GCGUUAGCGAUUGAUAC-GGUAUCCU-UUU--UUGUG---CGC----------------------------------------GCUUAU--------------------------------------------GCG---CAA---AAAAGAU-AUAGUGGAAAGCGCGACUCUUG
AM398681.1/1628589-1628684     AUUUAGCC-------CUGAUGGAAGU-GAAAAUCC-UUU--AUA-----UGU----------------------------CA-UACAGG---UUUUUAGAA-----------CCUGUAUG----------------------ACA---UAU---AAAGAUU-GUAACGUACAGCAGGAAAAUGG
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AM398681.1/861460-861379       AAAUAGCC-------CUGAUAGAGGC-GAUAUCCU-UUU--UGU--AGAGCC----------------------------------------UUUUC---------------------------------------------GGCGAAACA---AAAAGAU-AAAGCCGAAAGCAGGAUAAAGC
AM398681.1/253670-253741       CCCUAGCC-------CUGAUAGUAGU-GGAAAUCC-UCG--CCA------------------------------------------------UUUUUCU-------------------------------------------------UGG---CGAGAUU-GUAACGGAUAGCAGGAUUGGCU
AM398681.1/2110216-2110300     ---AUUUU-GCGUUAGGGAUAGAAAC-GGAAAUCC--UU--UUUU----GAG----------------------------------------GCUUU---------------------------------------------UUUGCCGAUAAAAAAGAUU-GAAGUGUAUAGCCCGACCCUUG
AM398681.1/1105092-1105174     ---GUUUU-GCGUUAGGGAUUGUAGU-GGAAAUCC-UUU--UGU-----UUU--UU------------------------------------CCUUU-------------------------------------------AAAAA---ACA---AAAGAUU-GCAACGGAAAGCCCGCUCGAAC
AM398681.1/679787-679868       GUUUAGCC-------CAGAUGGCAGU-GGAAAUCC-UUU--UCU-----UUU--UU------------------------------------UUCUUU------------------------------------------AAAAAA--AGA---AAAGAUU-GUAACGUACAGCUGGAAAUAGC
CP000685.1/4125942-4126020     CUAUAGCC-------CUGAUAGAAGC-GGUAUCCU-UUU--UCU-----UGC--U-------------------------------------UCUUU--------------------------------------------AGCA---AGA---AAAAGAUACAAGCGGAUAGCAGGAAAUUGC
AM398681.1/1414124-1414055     AUAUAGCC-------CUGAUGGA-GU-GAAAAUCC-UUG--CCA------------------------------------------------UUUUUCU-------------------------------------------------UGG---CAAGAUU-GUAGCGA-GAGCAGGAAAUUAG
CP000685.1/4304111-4304188     UUCUAGCC-------CCGAUAGCAGU-GGAAAUCC-UUU--UGCA----CCG----------------------------------------GGGUU---------------------------------------------CGGC--GCA---AAAGAUU-GCAACGUAUAACGGAAAGAGCU
AM398681.1/1383710-1383784     ---UGUUU-GCGUGAGGGAUUGAGGC-GGUAUCCU--UU--UUU------------------------------------------------GAGGCACG------------------------------------------------AAA---AAAAGAU-AUAGCCGAAAGCCCGACUUGAG
AAGA01012270.1/463-391         ------UU-GCGUUAGGGAUUGUAAC-GAAAAUCC-UUU--UUC------------------------------------------------UUUUUUCA------------------------------------------------GAA---AAAGAUU-GUAGUGAAAAGCCCGACCCGAU
CP000685.1/3049569-3049492     CCCUAGCC-------CUGAUAGCAGC-GGCAUCCU-UUU--UGU-----UUU----------------------------------------UUCUU---------------------------------------------UAAAA-ACA---AAAAGAU-AUAGCGGAUAGCAGGAAAUAGC
AM398681.1/499344-499263       CUUUAGCC-------CCGAUGGAAGG-GAAAAUCC-UUU--AUGGAA--GUC----------------------------------------UUUUUU--------------------------------------------GACGA-CAU---AAAGAUUUGGAAU-GACAGCGGGAAACCAA
AAGA01005650.1/868-941         CUGUAAUA-------AGGAUUGCAGC-GGUAUCCU-UUU--UUU------------------------------------------------GAGGAACGA-----------------------------------------------AAA---AAAAGAU-UUAGCGUAAAGCCUGAUUACUU
AM398681.1/496580-496509       UUUUAGCC-------CAGAUAGCAGU-GAAAAUCC-UCG--CCA------------------------------------------------UUUUUCU-------------------------------------------------UGG---CGAGAUU-GCAACGGAUAGCUGGAUUAGCU
AM398681.1/609953-610031       CCCUAGCC-------CUGAUAGCAAC-GGAAAUCC-UUU--UUU-----GAG----------------------------------------GUUUU---------------------------------------------UAC---CGAAAAAAAGAUU-GUAGUGAAUAGCAGGAAAUAGC
AM398681.1/1545638-1545717     UUUUAACC-------CCGGUUGUAGC-GGAAAUCC-UUU--GCU-----UUU--UU------------------------------------UCUUU-------------------------------------------AGAAA---AGC---AAAGAUU-GAAGUGCAAAACGGGAAUAUGG
AACY023343756.1/768-839        UUUUAGCC-------CUGAUGGAAGU-GAAAAUCC-UAC--CGA------------------------------------------------AUUUUCA-------------------------------------------------UCG---GUAGAUU-GUAACGGACAGCAGGAAUAAAC
AAFZ01020400.1/659-542         GCUUAGCC-------CCGAUUGAAGU-GGCAUCCU-UUUUAAUUGUCAGUUC--GA------------------------GU-GAAUUU---GUGAAGAAUGAGU-------AAAUUUGUA-------------------UCGAGAACAAAUUAAAAAGAU-AUAACGGAAAGCGGGAAUUAGC
AM398681.1/730679-730599       CCCUAGCC-------CAGAUGGAAGG-GAAAAUCC-UUU--UCU-----UUU--UU------------------------------------UUCUUUA-----------------------------------------AAAAA---AGA---AAAGAUU-GGAAU-GACAGCUGGAAAUAGC
CP000685.1/5269445-5269368     CUCCAGCC-------CCGAUUGCAGC-GGAAAUCCGUUUCUGCC-----G------------------------------------------GGGUC-----------------------------------------------C---GGCACAAAAGAUU-ACAGCGCAAAGCGGGAGAGGCU
AM398681.1/1246430-1246349     UUUUAGCC-------CAGAUAGCAGU-GAAAAUCC-UUU--UGC-----UUU--UU--U---------------------------------UCUUU------------------------------------------AGAAAA---GCA---AAAGAUU-GUAACGUAUAGCUGGAUUAGCU
AM398681.1/570785-570704       ------CC-GCGUGAGGGAUAGCAGC-GGAAAUCC-UUU--UUU--UGAGGC----------------------------------------UUUUC---------------------------------------------GCCGAUAAA---AAAGAUU-GUAGCGCAUAGCCCGACCCGAC
AAGA01007791.1/724-655         ------UU-GCGUUAGCGAUAGUAAC-GGCAUCCU-UUU--GCU------------------------------------------------UCUUC---------------------------------------------------UGC---AAAAGAU-AUAGUGGAAAGCGCAAUCCAGU
AM398681.1/2036769-2036665     UUCUAGCC-------CCGAUUGAAGC-GAAAAUCC-UGU--CAU-----UGC-----UAAAAAAA-UA------------------------UUGCUGUUUUAUUGUUU------------------------UGUUUCU--GCA---AUG---ACAGAUU-GUAGUGUAAAGCGGGAGAAUGU
AACY022394829.1/754-679        ACAUAGAA-------GCGAUAGCAGC-GGCAUCCU-UUU--UUGU----CCU----------------------------------------GAUA----------------------------------------------AGG---UAA---AAAAGAU-AUAGCGAAUAGCGCGACCCGAA
AM398681.1/2118876-2118797     GUUUAGCC-------CUGAUAGUAGU-GGAAAUCC-UUU--UCU-----UUU--UU------------------------------------UCUUU-------------------------------------------AAAAA---AGA---AAAGAUU-GUAACGGAUAGCAGGAAAUAGC
AM398681.1/1039046-1038965     ------CC-GCGUGAGGGAUAGCAGC-GGAAAUCC-UUU--UUU--UGAGGC----------------------------------------UUUUC---------------------------------------------GCCGAUAAA---AAAGAUU-GUAGCGCAUAGCCCGACCCGAC
AM398681.1/1308986-1309129     UAUUAGCC-------CCGAUUGCAGU-GGAAAGC---UU--UUUGAAAUCUC--GU--------U-ACAUUUUUUCUUGCUA-AAAAAG---AGCGACGGUAGGAGCUC---CUUUUUUUG-CUUAGAAAAAAGUAA---ACGAGAGGAAA---AAA-CUU-GUAACGAAAAGCGGGAAAUAGC
AM398681.1/796790-796871       CCCUAGCC-------CAGAUUGCAGU-GGAAAUCC-UUU--UUG-----UUU--UU------------------------------------UUCUUU------------------------------------------AAAAAA--CAA---AAAGAUU-GUAACGAAAAGCUGGAAAUAGC
AM398681.1/229911-229990       UUUUAGCC-------CCGAUUGCAAC-GGAAAUCC-UUU--UUG-----UUU--UU------------------------------------UCUUU-------------------------------------------AAAAA---CAA---AAAGAUU-GAAGUGUAAAGCGGGAAUAGCU
CU207366.1/2681845-2681951     ---AAUUU-GCGUUAGGGAUUGAAGC-GGCAUCCU-UUU--UUGAA---GUG--CU--GA---GC-CC------------------------AGAGCCUGUCGAA----------------------------GGGUCGAAGCACA--CAA---AAAAGAU-AUAGCGGAAAGCCCGACCAUCG
AM398681.1/790061-790132       CUUUAGCC-------CUGAUGGAAGU-GGAAAUCC-UCG--CCA------------------------------------------------UUUUUCU-------------------------------------------------UGG---CGAGAUU-GUAACGUACAGCAGGUAUAUGA
CP000685.1/143366-143445       UUCCAGCC-------CUGAUGGAAGC-GGAAAUCC-UUU--UGC-----UUU--UU------------------------------------CCUUU-------------------------------------------AAAAA---GCA---AAAGAUU-GCAGCGUACAGCAGGAACCAAU
AM398681.1/970882-970805       CCCUAGCC-------CUGAUUGUAGC-GAUAUCC--UUU--UUCUU---GCU----------------------------------------CCUUU---------------------------------------------AGCAA-GGA---AAA-GAU-AUAGCGAAAAGCAGGAAAUAGC
AATN01001724.1/670-588         GACUAGCC-------CUGAUUGUAGU-GAAAAUAG--AAAAUGC-----UUC--CA------------------------------------UUGUU-------------------------------------------UGGAA---GCAUUUUU-UAUU-GUAACGGAAAGCAGGAAUAAGG
CP000685.1/6019588-6019666     AUCUAACC-------CCGACAGGAUC-GAUAUCCU-UUG--CCU-----GGC----------------------------------------UUUUUUUA------------------------------------------GAC---AGG---UAAAGAU-AAAGAGUAUGGCGGGAACAAAU
AM398681.1/563089-563169       UUAUAGCC-------CUGAUUGUAAU-GGAAAUCC-UUU--UGC-----UUU--UU------------------------------------CUUUU-------------------------------------------AAAAAA--GCA---AAAGAUU-GCAAUGGAAAGCAGGAAUAGGG
AM398681.1/1187860-1187781     UUUUAGCC-------CCGAUAGUAGU-GGAAAUCC-UUU--UUUGA---GGU----------------------------------------UUUUC---------------------------------------------UCCGA-AAA---AAAGAUU-GUAACGGAUAGCGGGAAAUAGC
AM398681.1/77564-77485         CCCUAGCC-------CCGAUAGUAGU-GAAAAUCC-UUU--UUUGA---GGC----------------------------------------UUUUC---------------------------------------------GCCGA-AAA---AAAGAUU-GAAACGAAUAGCGGGAUUAGCU
AM398681.1/1200485-1200417     UUGUAGCC-------CCGAUCGAAGU-GAAAAUC--UCU--CGC------------------------------------------------UUUUUU--------------------------------------------------GCG---AGA-AUU-GUAACGCAGAGCGGGAAUAAUC
AACY023346451.1/1301-1383      ------UC-GCGUUAAGGAUUGAAGU-GGAAAUCC-UUU--UGAAA---GCUGAGC------------------------------------UUGC--------------------------------------------GAAGC---UCA---AAAGAUU-GAAGCAAAAAGCCUGACCCGCA
AACY021471998.1/307-395        UUCUAGCC-------CAGAUAGGAGU-GAAAAUCC-UUG--UUCCAAUGCGA--GG------------------------------------UGUUG-------------------------------------------CCUCGAAUGGAG--CAAGAUU-GCAACGGAUAGCUGGAAAGCGC
AAFZ01019740.1/299-229         ------CU-GCGUUAGGGAUUGAAGC-GAUAUCCU-UUU--UUG------------------------------------------------UUUUUA--------------------------------------------------UAA---AAAAGAU-UUAGCGAAAAGCCCGACCACGC
AM398681.1/1406269-1406338     UUUUAGCC-------CUGAUGGAAGU-GGAAAUCC-UUG--CC-------------------------------------------------UUUUUUU--------------------------------------------------GG---CAAGAUU-GCAACGUACAGCAGGAAUACUG
AM398681.1/47864-47783         CCCUAGCC-------CUGAUAGUAGU-GGAAAUCC-UUU--UCU-----UUU--UU------------------------------------UUCUUU------------------------------------------AGAAAA--AGA---AAAGAUU-GCAACGAAUAGCAGGAAAUAGC
AM398681.1/1534455-1534380     GAAUAGCC-------CUGAUAGAGGC-GAUA--GC-UCU--CGU-----UGA----------------------------------------GUUUUUU-------------------------------------------UCGAA-ACG---AGAC--U-AAAGCCGAUAGCAGGAAUUGCG
AM398681.1/1910757-1910674     CCCUAGCC-------CAGAUAGUAGU-GGAAAUCC--UU-UUGUG----UUC--GC------------------------------------AAAAAAA-----------------------------------------GCGAAC--ACA---AAAGAUU-GAAGCGAAUAGCUGGAAAUAGC
AM398681.1/2032864-2032933     AAAUAGCC-------CUGAUGGA-GU-GAAAAUCC-UCG--CCA------------------------------------------------UUUUUCU-------------------------------------------------UGG---CGAGAUU-GUAAUGA-CAGCAGGAUUAUGG
AM398681.1/2778208-2778065     UUUUAGCC-------CAGAUAGUAAC-GGAAAGCC-UUU--UGA-----GAA--GAAAGGCUUAU-UUUUCUUGAUAAAAAA-C-AAC----GACCAACGGAA----------GUUCGUUU-UUUGUUUAGAAAAAUUGCUUUUC---UGAUUAAAAGCUU-GUAGUGUAUAGCUGGAAAUGGC
AAFX01012497.1/673-756         CCCUAGCC-------CUGAUGGUAGC-GGCAUCC--UUU--UGU-----UUU--GC------------------------------------GCCGGAAGGAA-------------------------------------GCAAA---ACA---AAA-GAU-ACAGCGGACAGCAGGAAGAAGC
AM398681.1/2367514-2367443     GUUUAGCC-------CCGAUAGUAGU-GGAAAUCC-UCG--CCA------------------------------------------------UUUUUCU-------------------------------------------------UGG---CGAGAUU-GCAACGGAUAGCGGGAAAUAGC
CP000685.1/2303534-2303455     CCCUAGCC-------CCGAUAGAAGC-GGAAAUCC-UUU--UUG-----UGG--CG------------------------------------GGGUU-------------------------------------------CGCCA---CAA---AAAGAUU-GAAGAGGAUAGCGGGAUUUAGC
AM398681.1/1244341-1244422     ------CC-GCGUGAGGGAUAGCAGC-GGAAAUCC-UUU--UUU--UGAGGC----------------------------------------UUUUC---------------------------------------------GCCGAUAAA---AAAGAUU-GUAGCGCAUAGCCCGACCCGAC
AACY022246563.1/1-77           -CCUAGCC-------CCGAUAGAAGC-AGAAAUCC-UUC--CGC-----GCC--G-------------------------------------GGGUU--------------------------------------------CGGC---GCA---GAAGAUU-GGAGCGGAUAGCGGGAUCAGCU
AACY023351369.1/1312-1229      ------CU-GCGUUAAGGAUUGUAGU-GAAAAUCC-UUU--UGCUC---GCUGAGC------------------------------------UUGUC-------------------------------------------GAAGC---GCA---AAAGAUU-GAAACGGAAAGCCUGGCCGAAG
AACY021676707.1/861-755        UUUUAGCC-------CCGAUUGAAGU-GGAAAUCC-UUU--ACU-----GUUUUUGGAAAAAGCC-CU------------------------UCGACUGCGCUC-----------------------------AGGGUGACAAAC---AGU---AAAGAUU-GUAACGCAAAGCGGGAAAAUGG
AM398681.1/1377002-1377143     UUUUAGCC-------CAGAUAGAAAU-GGAAAGC---UU--UUGCAGUUGGC----------UUG-UAUUUUUUCUUGACAC-GAAAG-AGCGACCAACGGAA------GCUCCUUUUGUG-GCUUUGAAAAAAACAG----GCCUACAAA---AAA-CUU-GGAAUGUAUAGCUGGAAUGGCU
AM398681.1/909081-909000       CCCUAGCC-------CUGAUUGCAGC-GAAAAUCC-UUU--UUG-----UUU--UU------------------------------------UCCUUU------------------------------------------AAAAAA--CAA---AAAGAUU-GUAGCGAAAAGCAGGAUUAGCU
CP000685.1/2946722-2946641     ACCUAGCC-------CCGAUAGAAGU-AGAAAUCC-UUU--UUU-----GUU--UU--U---------------------------------UCUUU------------------------------------------AAAAAC---AAA---AAAGAUU-GUAAGGAAUAGCGGGAUUAGCU
AACY021064219.1/580-505        UCAUAGCC-------UCGAUUGCAGC-GGCAUCC--UUU--UGU------------------------------------------------GAAGCAAAGCGGA-------------------------------------------ACA---AAA-GAU-ACAGCGGAAAGCGGGAAAAAGC
AM398681.1/2364097-2364027     UUUUAGCC-------CUGAUGGAUGU-GAAAAUCC-UCG--CCA------------------------------------------------UUUUUCU-------------------------------------------------UGG---CGAGAUU-GAAAC-GACAGCAGGUAUAUGG
AACY020190544.1/1398-1306      UAAUAGCC-------CGGAUUGCAGU-GAAAAUCC-UUU--UUUU----AAU--AC--C---------------------------------GUAGUGCCAACGAA---------------------------------GGAAUUU--AAA---AAAGAUU-GCAACGUAAAGCCGGAAAUAGC
AM398681.1/1939445-1939549     UUGUAGCC-------CCGAUAGUAGU-GGAAAUCC-UUU--UUU-----UUG----------------------UUUGAGUU-CU-CGC---UUUUUUU-------------GCGAGGAAC-UUAAG---------------CAA---AAA---AAAGAUU-GAAACGGAUAGCGGGAGGUUUG
AAGA01000521.1/2119-2033       GAUUAGCCUGCGUUAGCGGUUGUAGU-GGCAUCCU-UUU--UUU-----GCU----------------------------------------GCCACAUAU-----------------------------------------GGC---AAA---AAAAGAU-AUAACGGAAGACGCGACCCUUG
AAFZ01001332.1/514-624         ------UC-GCGUUAAGGAUAGUAGU-GGAAAUCC-UUU--UUA-----UGUCAGU-------------------UCGAGUG-AAUUUG---CUUUG---------------CAAAUUUGUAUCGAGA------------ACACA---UAA---AAAGAUU-GAAACGGAUAGCCUGUUUAAAC
AAGA01006339.1/175-246         ------UU-GCGUUAAGGAUUGCAGC-GACAUCCU-UUU--UUG------------------------------------------------UUUUUCU-------------------------------------------------CAA---AAAAGAU-ACAGCGAAAAGCCUGACUUUAC
AM398681.1/704714-704643       UGAUAGCC-------ACGAUUGAAGU-GAAAAUCC-UCG--CCA------------------------------------------------UUUUUCU-------------------------------------------------UGG---CGAGAUU-GAAACGGAAAGCGGGAAAAUGG
AATN01007431.1/187-265         GUUUAGCC-------CUGAUUGAAGU-GGAAAUCC-UUU--UUU-----UGA--GU------------------------------------GAUA--------------------------------------------ACUCA---AAA---AAAGAUU-GCAACGAAAAGCAGGAAAAUGG
CP000685.1/4306293-4306370     CACUAGCC-------CCGAUGGCAGU-GGAAAUCC-UUU--UGU-----GCC--G-------------------------------------GUGUU--------------------------------------------CGGC---ACA---AAAGAUU-GAAGCGAACAGCGGGAAAAAGC
AM398681.1/285771-285842       AAAUAGCC-------CCGAUAGUAGU-GAAAAUCC-UCG--CCA------------------------------------------------UUUUUCU-------------------------------------------------UGG---CGAGAUU-GCAACGGAUAGCGGGAACGUAA
AM398681.1/310503-310574       GUUUAGCC-------CCGAUUGUAGC-CGAUAUCC-UUU--GU-------------------------------------------------GAGGUACGA------------------------------------------------AC---AAAGAUA-AAGGCGAAAAGCGGGAAAAUGG
AAOG01000002.1/549859-549739   AUUUGCAU-GCGUUAGGGAUUGCAAU-GAUAUCCU-UUU--GCU-----GUGAAUU------CGG-AUC--------CAUCU----------GCAAAGA-------------------AGA-UGCAAAUUUAGA-UCGAAAACAC---AGC---AAAAGAU-AAAACGAAAAGCCCGCUCGAAC
AANA01000002.1/151471-151560   GUUUAGCC-------CUGAUUGUAAU-GGCAUCCU-UUUAAGGU-----AAA--------------------------------CAGAU---GAAA----------------AUCUGC------------------------UUU---AUCUAAAAA-GAU-AAAAUGGAAAGCAGGAAAUAGC
CP000685.1/5605119-5605044     CCCUAGCC-------CUGAUGGAAGC-GGCAUCCU-UUUAUCGC------------------------------------------------GCCGCG--------------------------------------------------GCGGAUAAAAGAU-ACAGCGGACAGCAGGAACAGCU
ABCO01000011.1/43084-43011     ------UU-GUGUUAGGGAUUGAUGC-GGCAUCC--UUU--UUU-----GCU----------------------------------------UUUUC---------------------------------------------UGC---AAA---AAA-GAU-AUAGCGGAAAGCCCGGUUAUUU
AM398681.1/1550751-1550672     UUUUAGCC-------CUGAUAGCAGU-GGAAAUCC-UUU--UCUUU---UUU----------------------------------------CCUUU---------------------------------------------AAAAA-AGA---AAAGAUU-GCAACGAAUAGCAGGAAUAGCU
AM398681.1/2004068-2003989     UGAUAGCC-------CAGAUAGUAGU-GAAAAUCC-UUU--UGU-----UUU--UU------------------------------------UCUUU-------------------------------------------AAAAA---ACA---AAAGAUU-GUAACGGAUAGCUGGAAAUAGC
AM398681.1/380759-380680       UUUUAGCC-------CUGAUAGCAGU-GGAAAUCC-UUU--UGUUU---UUU----------------------------------------CCUUU---------------------------------------------AAAAA-ACA---AAAGAUU-GCAACGGAUAGCAGGAUUAGCU
AM398681.1/1509239-1509334     AGCUAGCC-------CUGAUGGAAGU-GGAAAUCC-UUU--AUA-----CAC----------UAA-ACAGGUUU------------------UUAA-------------------------------AAACCUGUUUA----GUG---UAU---AAAGAUU-GUAAC-GACAGCAGGAAUAUGG
AAGA01004019.1/141-212         GUCUAGCC-------CAGAUUGAAAU-GACAUCCU-UUU--UUC------------------------------------------------UUUUUCA-------------------------------------------------GAA---AAAAGAU-AUAAUGGAAAGCUGGAAAAAGC
CP000685.1/5193557-5193632     UCCUAGCC-------CCGAUCGAAAU-GUUAUCUU-UUU--GUG-----GUG----------------------------------------GGGUU---------------------------------------------CAC---CAC---AAAAAAU-AUAAUGCAGAGCGGGACAAAUG
AANC01000009.1/127964-127876   UUUUAGCC-------CUGAUUGCAGC-GGCAUCCU-UUUUAAUGG----UUGA-GC--C---------------------------------UAAA-------------------------------------------GGCGAAAG-CAUUAAAAA-GAU-ACAGCGGAAAGCAGGAAAUAGC
AM398681.1/1526942-1527028     AUGCCCCU-GCGUGAGGGAUUGAAGU-GAAAAUCC--UU-UUUUGA---GGC----------------------------------------UUUUC---------------------------------------------GCCGAUGAA---AAAGAUU-GUAACGGAAAGCCCGACCCGAG
AAFX01083668.1/596-525         ------UU-GCGCGAGGGAUGGCAGC-GGCAUCCU-UUU-----------------------------------------------------GUGAGGAACGAGC-------------------------------------------------AAAAGAU-ACAGCGAACAGCCCGACCCUUG
AACY022785771.1/549-625        ------UU-GCGUGAGGGAUUGGAGU-GGAAAUCC-UUU--UGC-----UUU----------------------------------------UGAAA---------------------------------------------AAAA--GCA---AAAGAUU-GCAACGGAAAGCCCGGCCCUCU
AE017226.1/1611636-1611767     CUCGGACA-------GCGAUUGAAGC-AGAAAUCC-UUU--UUGCGGUGUGU--UUAAG---CAAAAA---GCAAG-CUCUGACC-------GGAG--------------------GGAAG-AGCCUUGCCUGUGAAGACAAAUGCAGCAA---AAAGAUU-GGAGCGGAAAGCGCGGUGUUCA
AAXX01000001.1/681187-681276   GAAUAGCC-------CCGAUGGAAGU-GGAAAUCC-UGU--UAU-----UGU--GA--GA--UUG-C-------------------------CUC---------------------------------------GCAAGCUCGCA---AUG---ACAGAUU-AUAACGGACAGCGGAACUGAGA
CP000685.1/2274636-2274717     AAAAGUCU-GCGUAAGGGAUAGAAGC-GGCAUCC---UUUUAUG-----UUG----------------------------------------GGGUU---------------------------------------------CAC---CAU---AAAAGAU-AGAGUGGAUAGCCCGACCCGAA
AACY020783078.1/362-278        ------UU-GCGUUAAGGAUGGAAGU-GGAAAUCC-UUU--UUA-----GGC--GC--C---------------------------------AUUUUUA----------------------------------------GGCGUC---UAA---AAAGAUUGAGAGCGUACAGCCUGACCUUGU
AAPD01000009.1/100600-100698   ---AUAUU-GCGUUAAGGAUAGUAGU-GAAAAUCC-UUU--UUGU----GGU--UU--UU--UUC-GC------------------------UUUC-------------------------------------GCGAAAACUGCCUU-CAA---AAAGAUU-GCAACGGAUAGCCUGUUAAAAC
CP000685.1/3138939-3138862     UUUUAGCC-------CCGAUAGCAGC-GGAAAUCC--UUC-UGC------------------------------------------------GCCGGUGUUCG---------------------------------------------GCACA-AAAGAUU-GCAGCGGAUAGCAGGAAAAAGC
AANA01000001.1/2098709-2098633 -GCUGAGC-GCGUUAAGGAUUGUAGU-GACAUCC---UU--UU-U----UGU----------------------------------------UUUUC---------------------------------------------ACA----AA---AAA-GAU-AUAAUGUAAAGCCUGACCUUUA
AM398681.1/1193056-1193135     GCCUAGCC-------CUGAUAGAAGU-GAAAAUCC-UUU--UUG-----UUU--UU------------------------------------CCUUU-------------------------------------------AAAAA---CAA---AAAGAUU-GCAACGAAUAGCAGGAAAUUGC
CP000685.1/4794620-4794545     UGCUAGCC-------CUGAUUGUAAC-GACAUCCU-UUU--GUG-----GUG----------------------------------------GGGUU---------------------------------------------CAC---CAC---AAAAGAU-AUAGUGAAAAGCAGGAAUCAGC
AAGA01010696.1/631-712         ------UU-GCGUUAAGGAUAGCAAU-GGAAAUCC-UUU--UUU-----UGC--UG------------------------------------CCAUAAA-----------------------------------------CGGCA---AAA---AAAGAGU-GUAAUGUAUAGCCUGUUAAAAC
AACY023353804.1/1191-1266      UUCUAGCC-------CUGAUGGAAGC-GACAUCCU-UUU--AAC-----GCU----------------------------------------UCCCA---------------------------------------------AGC---GUU---AAAAGAU-AAAGCGUACAGCAGGACCAAAA
AM398681.1/1170893-1170815     AUUUAGCC-------CCGAUUGAAGCUUGUAUCCU-UUU--GGC-----UCA----------------------------------------UUUUUCU-------------------------------------------UGA---GCC---AAAAGAU-ACUGCGAAAAGCGGGAUUAUGG
AACY023345814.1/199-289        AA-------GCGUUAAGGAUAGUAGC-GGCAUCCU-UUU--UUU-----GGC--UA------------------------------------CCCACAAUAAUAGUUU--------------------------------UGGCC---AAA---AAAAGAU-AUAGCGAAUAGCCUGCCCGAUA
AAXX01000001.1/665852-665786   CUUUAACC-------CCGAUAGAAAU-GAAAAUCC--AA--UGC------------------------------------------------GCUA----------------------------------------------------GCA---UU-GAUU-GUAAUGGAUAGCGGGAAAAUGG
AAFX01075099.1/446-369         UUCUAGCC-------CUGAUAGUAGA-GAAAAUCC-UUU--UGUG----CCG----------------------------------------GGGUU---------------------------------------------CGGU--ACA---AAAGAUU-GUAACGGAUAGCAGGAAACAGC
AAXX01000003.1/127063-126966   UAAUAGCC-------CAGAUGGAAGU-GGAAAUCU-UUU--UUUA----CCU--UG--UU--------------------------------UCGACUUCGCUCAACUU-----------------------------GACAAGGU--AAA---AAAAAUU-GUAACGGACAGCGGGACUAAAA
AM398681.1/2705148-2705079     UUUUAGCC-------CUGAUGGA-GU-GAAAAUCC-UUG--CCA------------------------------------------------UUUUUCU-------------------------------------------------UGG---CAAGAUU-GUAGCGA-GAGCAGGAAUAGGG
AAXX01000001.1/83759-83835     UUUUAGAC-------CCGAUAGAAGC-GACAUCC--UUU--AUU-----GCU--UU------------------------------------UUUU--------------------------------------------AAUGC---AAU---AAA-GAU-AUAGCGCAUAGCGGGACCACUA
CP000685.1/3128289-3128364     ACUUAGCC-------CCGAUAGAAGC-GGCAUCCU-UUU--AUG-----GCG----------------------------------------UUGUU---------------------------------------------CGC---CAU---AAAAGAU-ACAGCGGAGAGCGGGAAACAGC
AANA01000001.1/7555-7625       GUUUAGCC-------CUGAUUGAAAC-GAUAUCCU-UUU--UUG-----U------------------------------------------UUUU------------------------------------------------A---CAA---AAAAGAU-UAAGUGUAAAGCAGGAAAUUGC
AM398681.1/304427-304506       CCCUAGCC-------CUGAUAGUAGU-GGAAAUCC-UUU--UUUGA---GGC----------------------------------------UUUUC---------------------------------------------GCCGA-AAA---AAAGAUU-GUAACGGAUAGCAGGAAAUAGC
AAGA01000787.1/233-154         ------UU-GCGUUAGCGAUUGAAAU-GACAUCCU-UUU--UUU-----GCU----------------------------------------GCCAUAUAU-----------------------------------------GGC---AAA---AAAAGAU-AUAAUGGAAAGCGCGACCCUUG
AATN01004274.1/852-927         GGUUAGCC-------CCGAUUGCAGC-GGCAUCCU-UUU--GCG-----GAA----------------------------------------CGAAG---------------------------------------------UGC---AGC---AAAAGAU-ACAGCGGAAAGCGGGACAGAAU
AM398681.1/2223908-2223831     CUCUAGCC-------CUGAUGGUAGC-GGCAUCCU-UUU--UCU-----UGC--U-------------------------------------CCUUU--------------------------------------------AGCA---AGG---AAAAGAU-AUAGCGGACAGCAGGAUUGGCU
AM398681.1/615293-615371       ---GUUUU-GCGUUAGGGAUUGAGGC-GGUAUCCU-UUU--UCU-----GG-----------------------------------------UUUUUCU--------------------------------------------CC---AGA---AAAAGAU-AUAGCCGAAAGCCCGACCCGAC
AM398681.1/265405-265326       UUUUAGCC-------CCGAUAGCAAC-GGAAAUCC-UUU--UUC-----UUU--CU------------------------------------UUUUC-------------------------------------------AGAAA---GAA---AAAGAUU-GGAGUGAAUAGCGGGAAAAUGG
AM398681.1/1068344-1068426     ---UUUUU-GCGUUAAGGAUUGUAGU-GAAAAUCC-UUU--UUG-----GCG--A-------------------------------------UUUUUCU------------------------------------------UCGC---CAA---AAAGAUU-GUAACGGAAAGCCUGACCCCGA
AATN01006259.1/511-433         UUUUAGCC-------CUGAUUGCAGC-GGUAUCUU-UUU--AUU-----UUU--UU------------------------------------CUUU--------------------------------------------AAAAA---AAU---AAAAAAU-AUAGCGGAAAGCAGGAAUAUGG
AAGA01013740.1/576-648         ------CU-GCGUUAGGGAUUGUAGU-GGCAUCCU-UUU--UUG------------------------------------------------UCUUUUUU------------------------------------------------CAA---AAAAGAU-AUAACGGAAAGCCCGACCCUUG
AAGA01021647.1/467-387         GU-------GCGUUAGGGAUAGAAAC-GGUAUCCU-UUU--UUU-----GCU----------------------------------------GCCAUAUAU-----------------------------------------GGC---AAA---AAAAGAUUUUAGUGGAUAGCCCGACCCUUG
AM398681.1/1832426-1832503     UUCUAGCC-------CUGACAGUAGC-GGCAUCC--UUU--UUC-----UUU--UU------------------------------------UCUUU-------------------------------------------AAAAA---GGA---AAA-GAU-AUAGCGGAUGGCAGGAUUAGCU
AACY020620609.1/690-615        UUCUAGCC-------CUGAUGGAAGC-GACAUCCU-UUU--AAC-----GCU----------------------------------------UCCCA---------------------------------------------AGC---GUU---AAAAGAU-ACAGCGUACAGCAGGACCCAAC
CP000685.1/1737234-1737153     CAUUAGCC-------CCGAUUGAAGA-GGAAAUUA-UUUUGCUU-----UUU----------------------------------------UCUUU---------------------------------------------AAAA--AAGCAAAAUGAUU-GCAACGAAAAGCGGGAACUAUU
AACY021992490.1/438-338        GUCUAGCC-------CCGAUGGGAAC-GGUAUCCU-UUUUUAGG-----AUU--GGCCUG--AGC-AUU-----------------------UGCG------------------------------------AAGGCACAUCAAU---CCUGAAAAA-GAU-ACAGUGGACAGCGGGAAACACC
AM398681.1/689704-689625       CCCUAGCC-------CCGAUUGAAAC-GGAAAUCC-UUU--UUA-----UUU--UU------------------------------------CCUUU-------------------------------------------AAAAA---UAA---AAAGAUU-GCAGUGUAAAGCGGGAAAUAGC
AM398681.1/2504159-2504240     ------CC-GCGUGAGGGAUAGCAGC-GGAAAUCC-UUU--UUU--UGAGGC----------------------------------------UUUUC---------------------------------------------GCCGAUAAA---AAAGAUU-GUAGCGCAUAGCCCGACCCGAC
AM398681.1/1728075-1727998     CCCUAGCC-------CCGAUAGUAGU-GAAAAUCC--UU--UUUGA---GGC----------------------------------------UUUUC---------------------------------------------GCCG--AAA---AAAGAUU-GCAACGGAUAGCGGGAUUGGCU
AM398681.1/2008367-2008445     CUCUAGCC-------CUGAUAGCAGU-GAAAAUCC-UUU--UUU-----GAG----------------------------------------GUUUU---------------------------------------------UUC---CGAAAAAAAGAUU-GUAACGGAUAGCAGGAAAUAGC
AAGA01025318.1/237-140         ------CU-GCGUUAGCGGUUGAAGU-GGCAUCCU-UUU--UAU-----UUG--UC-U----CCU-C-------------------------GAGCGCAGUCGA------------------------------GAGGUUGACAA---AUA---AAAAGAU-AUAACGGAAAACGCGACCCUUG
CP000685.1/2008746-2008669     GUGUAGCC-------CCGAUAGAAGU-GGAAAUCC-UUU--UGUA----CCG----------------------------------------GGGUU---------------------------------------------CGGU--ACA---AAAGAUU-GAAACGGAUAGCGGGACCUCAG
AAOG01000001.1/717586-717518   GUUGAGCC-------CUGAUUGAAGU-GACAUCUU-UUU--UG-------------------------------------------------CUUUUC---------------------------------------------------CA---AAAAGAU-AUAGCGGAAAGCAGGAAAUAGC
AM398681.1/633751-633658       UUUUCUCU-GCGUGAGGGAUUGAAGU-GGAGCUCU-UUU--UUU-----GUU--UG--GC--------------------------------GUUUUUUA--------------------------------------GCCAAAU---AAA---AAAAAGCGGGAACGAAAAGCCCGACCCGUA
CP000383.1/1783674-1783753     UCACCGGC-GCGUUAGGGGUAGGAGC-GGAAAUCC-UUUUU--------UGU----------------------------------------UUUUC---------------------------------------------ACAAA-------AAAGGUU-GGAGCGGAUAGCCCGGCGCCAG
AAFY01026635.1/558-632         ------CU-GCGUUAGGGAUUGGAAC-GGCAUCC--UUU--UUU-----UUG----------------------------------------CAUUU---------------------------------------------CAA---AAA---AAAAGAU-AUAGUGAAAAGCCCGACCCCUU
AAFY01026313.1/278-352         ------CU-GCGUUAGGGAUUGGAAC-GGCAUCC--UUU--UUU-----UUG----------------------------------------CAUUU---------------------------------------------CAG---AAA---AAAAGAU-AUAGUGAAAAGCCCGACCCCUU
AM398681.1/102392-102471       UUUUAGCC-------CCGAUUGUAGU-GAAAAUCC-UUU--UCU-----UUU--UU------------------------------------UCUUU-------------------------------------------AAAAA---AGA---AAAGAUU-GAAGCGUAAAGCGGGCGAAUGA
AACY023331481.1/1068-1161      ------CC-GCGUUAGGGAUAGCAGC-GGCAUCCU-UUU--UAA-----AAG----------GAG-ACU-----------------------GAGGAACUCGA-----------------------------AGUCAC----CGU---UUA---AAAAGAU-AGAGCGCAUAGCCCGACCUGAA
AM398681.1/1132910-1132995     AUCGAGCU-GCGUUAGGGAUAGUAGC-GAAAAUCC-UUU--UUAGA---GGC----------------------------------------UUUUC---------------------------------------------GCCGA-UAA---AAAGAUU-GUAGCGAAUAGCCCGACCCUUG
#=GC SS_cons                   ::::::::.......<<<-<<---<<.---<<<<-.-<<..<<<.....<<<........................................_____.............................................>>>...>>>...>>->>>>.--->>--->>->>>::::::::
#=GC RF                        uuuUAGCC.......ccGAUuGaAGc.GGAAauCC.UUU..uuu.....ggc........................................uuuuu.............................................gcc...aaa...AAAGauU.GuAgCGgAaAGCggGAauaagu
//
# STOCKHOLM 1.0

#=GF AC   RF01706
#=GF ID   Gut-1
#=GF DE   Gut-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   50.20
#=GF NC   49.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Gut-1_RNA_motif
#=GF SQ   38


BAAY01013587.1/1155-1074 CUUUGGUAAUGACCG-CAAG----------------CGGUCAUUACA-----------GUGAAAUUAGC----CGUUG-----GCGAGUGAAAUCUGACUU-U-----GUCAGGUGAAAUUGCCC
BABA01021652.1/1029-1103 CUGUUUUAUUCG----ACUGACCG---------------CGAGUGAU----------------AUUGCC----UUUCG-----GACAGUGAAAUGAUGCCU-U-----GCUUCGUGAUAUUGCCU
BAAZ01025322.1/207-137   CAGUUAUAUUCGCC--UGUC-----------------GACGAGUGAU----------------AUUG------CCGUG-------CAGUGAUAUUCGGUCA-U-----ACCGAGUGAUAUUGCCU
BAAZ01000095.1/996-1085  AAAGGAAGUGCGCC--UCUGUUAUAUUCGCCUGAC--GGCGAGCGAU----------------AUUGUC----CUUUG-----GACAGUGAUAUUAUGCUU-C-----GCAUCGUGAUAUUGCCU
BAAZ01000085.1/2840-2766 CAGUUAUAUUCGC---CUGACA----------------GCGAGUGAA----------------AUUGUC----CUUCG-----GACAGUGAUAGGAUACUU-C-----GCAUCGUGAUAUUGCCU
BAAZ01000322.1/194-268   CAAUUAUAUUCGCC--UGAC-----------------GGCGAGUGAU----------------AUUGUC----CUUUG-----GACAGUGAUAUUAUGCUU-C-----GCAUCGUGAUAUUGCCU
BAAZ01000187.1/6811-6737 CAGUUAUAUUCGCC--UGAC-----------------GGCGAGUGAU----------------AUUGUC----CUUCG-----GACAGUGAUAUUAUGCUU-C-----GCAUCGUGAUAUUGCCU
BAAZ01023714.1/541-467   CAGUGAAAUUCGCCG----U----------------UGGCGAGUGAA----------------AUCUGA----CUUUG-----UCAGGUGAAAUCGUCCUGUC-----GGACGGUGAAAUUGCCC
BAAZ01023713.1/569-643   CAAUGUCAUUCGCCG----U----------------UGGCGAGUGAC----------------AUCUGA----CUUUG-----UCAGGUGAAAUCGUCCUGUC-----GGACGGUGAAAUUGCCC
BAAV01002358.1/574-499   CAGUGAAAUUUGCCC-UUGU----------------GGGCAAGUGAA----------------AUACGC----CUGCG-----GCGUGUGAAAUGCGA-UAAC------UCGCGUGAAAUGUUCG
BAAY01000359.1/865-937   CAAUUAAAUUAAUCC-UUGC----------------GGAUUAGUGAA----------------AUAUUC----UUUCA-----GAAUAUGAAAUUGC--UU-A-------GCAAUGAAAUACGCC
BAAV01000249.1/935-1007  CAUUUAAAUUAAUCC-UUGC----------------GGAUUAGUGAA----------------AUAUUC----UUUCA-----GAAUAUGAAAUUGC--UU-A-------GCAAUGAAAUACGCC
BAAZ01000840.1/447-370   CAACGAAAUAAAUCCCUU-C---------------GGAAUUUGUGAA----------------AUUGCC----CUUCG-----GGCAGUGAAAUGUUGCUG-C-----GCAACGUGAAAUACCUG
BAAZ01000059.1/8055-8130 AGUAUAAUCU-ACCC-UUGC----------------GGGUGAGGGAA----------------AUACCG----CUCCG-----CGGUGUGAUAUACGCCUC-C-----GGCAUGUGAGAUCGCUG
BAAZ01000224.1/3117-3043 CAACGAAAUAAAUCC-UGUC----------------GGAUUUGUGAA----------------AUGCG-----CUUCG------CGCGUGAAAUAUGGCUU-C-----GCCAAGUGAAAUGCCUG
BAAV01000831.1/176-100   CAACGAAAUAAAUCUCUUUC---------------GGGAUUUGUGAA----------------AUGCC-----CUGCG------GGCGUGAAAUACGCCUG-C-----AGCGUGUGAAAUCGCUG
BAAV01005774.1/722-647   CAACGAAAUAAAUCCCUU-C---------------GGGAUUUGUGAA----------------AUGCC-----CUGCG------GGCGUGAAAUACGCCUG-C-----GGCGCAUGAAAUCGCUG
BAAZ01000130.1/2480-2404 CAACGAAAUCCACCC-UUUC----------------GGGUGGGUGAA----------------AUACUG----CUUCG-----CGGUGUGAUAUACGCCUG-C-----GGUGUGUGAAAUCGCUG
BAAZ01000130.1/2240-2164 CAACGAAAUCCACCC-UUUC----------------GGGUGGGUGAA----------------AUACCG----CUUCG-----CGGUGUGAUAUACGCCUG-C-----GGCGUGUGAAAUCGCUG
BABA01009772.1/249-173   CAACGAAAUCCACCC-UUUC----------------GGGUGGGUGAA----------------AUACCG----CUUCG-----CGGUGUGAUAUACGCCUG-C-----GGUGUGUGAAAUCGCUG
BAAZ01000130.1/2720-2644 CAACGAAAUCCACCC-UUUC----------------GGGUGGGUGAA----------------AUACCG----CUUCG-----CGGUGUGAUAUACGCCUG-C-----GGCGUGUGAAAUUGCUG
BABA01009772.1/489-413   CAACGAAAUCCACCC-UUUC----------------GGGUGGGUGAA----------------AUACCG----CUUCG-----CGGUGUGAUAUACGCCUG-C-----GGCGUGUGAAAUUGCUG
BAAZ01000130.1/2960-2884 CAACGAAAUCCACCC-UUUC----------------GGGUGGGUGAA----------------AUACCG----CUUCG-----CGGUGCGAUAUACGCCUG-C-----GGCGUGUGAAAUUGCUG
BAAX01002128.1/1051-1127 CAACUAAAUCCACCC-UUGC----------------GGGUGGGUGAA----------------ACAUUG----CUUCG-----CAAUAUGAAAUACGCUUU-C-----AGCGUAUGAAACCGCUG
BAAV01000542.1/1906-1830 CAACUAAAUCCACCC-UUGC----------------GGGUGGGUGAA----------------AUAUUG----CUUCG-----CAAUAUGAAAUACGCUUU-C-----AGCGUAUGAAAUCGCUG
BAAY01000031.1/2665-2589 CAACUAAAUCCACCC-UUGC----------------GGGUGGGUGAA----------------AUAUUG----CUUCG-----CAAUAUGAAAUACGCUUU-C-----AGCGUAUGAAAUCGCUG
BAAV01000007.1/9765-9689 CAACUAAAUCCACCC-UUGC----------------GGGUGGGUGAA----------------AUAUUG----CUUCG-----CAAUAUGAAAUACGCUUU-C-----AGCGUAUGAAAUCGCUG
BAAY01000734.1/1413-1489 CAACUAAAUCCACCC-UUGC----------------GGGUGGGUGAA----------------ACAUUG----CUUCG-----CAAUAUGAAAUACGCUUU-C-----AGCGUAUGAAAUCGCUG
BAAY01000985.1/3257-3333 CAACUAAAUCCACCC-UUGC----------------GGGUGGGUGAA----------------ACAUUG----CUUCG-----CAAUAUGAAAUACGCUUU-C-----AGCGUAUGAAAUCGCUG
BAAY01000139.1/5333-5257 CAACUAAAUCCACCC-UUGC----------------GGGUGGGUGAA----------------ACAUUG----CUUCG-----CAAUAUGAAAUACGCUUU-C-----AGCGUAUGAAAUCGCUG
BAAV01000478.1/3780-3704 CAACUAAAUCCACCC-UUGC----------------GGGUGGGUGAA----------------ACAUUG----CUUCG-----CAAUAUGAAAUACGCUUU-C-----AGCGUAUGAAAUCACUG
BAAU01007736.1/751-678   CAAUGAAAUCCGUCC--UGC----------------GGACGGGUGAA----------------AUCCUG----CCGUG-----CAGGAUGCAAUACGC-GC-C------GCGUGUGAAAUCGCUG
BAAV01002358.1/807-713   CAGUGAAAUUCGUUCCUA-C---------------GGAACGAGUGAAAUAUCUUCGAUGUGAAAUAUUUG---CCUCG----CAAAUGUGAGAUAUGCCUG-C-----GGCAUAUGAAG-GAACG
BAAU01005691.1/934-861   CAAUGAAAUUCGUUUCUC-U---------------GGAACGAGUGAA----------------AUAU------CUUAG-------AUGUGAAAUAUGCCUG-C-----GGCAUAUGAAAACAGGU
BAAV01001911.1/1505-1595 AAGUGAAAUAUCUCGCUG-C---------------GCUCGAUGUGAA----------------AUAAUUUGCGCGA-G-CGCAAAUUGUGAAAUAUUGCUCCUGCGUCGCAAUGUGAAAUAAAAU
BAAV01002358.1/1261-1351 AAGUGAAAUAUCCCGCCGAU---------------GCGGGAUGUGAA---------------AAUGUUUGC--CUUNGC--GCAAACGUGAAAUAUUGCUCCUUCGUCGCAAUGUGAAAUGAAAU
AAQL01009370.1/2866-2792 UAGUGAAAUAAAUCC-UUAC----------------GGAUUUGUGAA----------------AUACG-----CUUUG------CGUGUGAAAUAUUCAUU-C-----UGAAUGUGAAAUGCCUA
AAQL01009359.1/1511-1592 CUUUGGUAAUGACCGCAA-----------------GCGGUCAUUACA-----------GUGGAAUUCGC----CGUUG-----GCGAGUGAAAUCUGACUU-U-----GUCAGGUGAAAUCGUCC
#=GC SS_cons             :::::::<<<<<<<<.____................>>>>>>>>,,,................<<<<<<...._____.....>>>>>>,,,<<<<<<<__._.....>>>>>>>::::::::::
#=GC RF                  CAaUGAAAUucgcCc.Uuuc................gGgcgaGUGAA................AUauuc....CUUcG.....gaauGUGAaAuauggCUu.C.....GccaugUGAAAUugccu
//
# STOCKHOLM 1.0

#=GF AC   RF01707
#=GF ID   JUMPstart
#=GF DE   JUMPstart RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   35.00
#=GF TC   35.20
#=GF NC   34.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   JUMPstart_RNA_motif
#=GF SQ   128


CP001127.1/4368291-4368328   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
FM180568.1/2257697-2257659   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
AAOJ01000002.1/773534-773497 AAGCACAUGAGGAGCUA-UAACCUUAGGGCGGUAGCAUU
CP000826.1/3180995-3180958   UAGCGCAUUGGGAGCUG-UAACUCAAGGGCGGUAGCGUG
U00096.2/2135484-2135446     CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
AL627273.1/85681-85643       CAGUGCACUGGUAGCUGAUGAACCAGGGGCGGUAGCGUG
CP000447.1/3427572-3427535   GGGCAUAUUGGAAGCCG-UAAUCCAUGGGCGGUAGCGUG
CP000507.1/2730356-2730319   GGGCACGUUGGAAGCCA-AAAUCCAUGGGCGGUAGCGUG
CU928161.2/4014266-4014228   CAGUAUUCAGGUAGCUGUUGAGCCUGGGGCGGUAGCGUG
CP000886.1/4403693-4403730   AAGCGUAUUGGUAGCAG-UAAGCCAAGGGCGGUAGCGUU
CP001120.1/4473688-4473725   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
CP000446.1/1523017-1523054   GGGCAAUAUAGAGGCCG-CAAUCUAUGGGCGGUAGCGUG
CP000026.1/4232657-4232694   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
CP000444.1/1598550-1598587   GGGCAAUAUAGAGGCCG-CAAUCUAUGGGCGGUAGCGUG
CP000886.1/867107-867145     CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
CU928163.2/2436269-2436231   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
EU296420.1/988-1026          CAGUGUACUGGUAGCUGUGGAGCCAGGGGCGGUAGCGUG
AE014613.1/867247-867285     CAGUGCACUGGUAGCUGAUGAACCAGGGGCGGUAGCGUG
CP000886.1/842962-843000     CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
BX950851.1/1980483-1980520   CAGCGCUUUGAUAGCUG-UGAGUCAAGGGCGGUAGCGUU
CP000462.1/3246313-3246279   CA-CA--CUGGGAGCUG-UAACUCAGGGGCGGUAGCUAU
EU294167.1/1024-1062         CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
CP001127.1/2200235-2200197   CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
AE006468.1/4477737-4477774   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
CU928145.2/2367959-2367921   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
U52666.1/243-281             CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
CP000946.1/1755756-1755794   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
AF078736.1/530-568           UAGUGCACUGGUAGCUGUUAAGCCAGGGGCGGUAGCUUG
CP000462.1/3999712-3999749   CAGCAGACUGGAGGCUG-AAAUUCAGGGGCGGUAGCCUU
CP000653.1/2879815-2879778   CAGUGGAUUGGUAACUG-AAAGCCAAGGGCGGUAGCGUG
CP000039.1/193310-193347     CAGCGCUUUGGGAGCUG-AAACUCAAGGGCGGUAGCGUA
CP000644.1/1482254-1482291   CAGCGAACUGGGGGCUG-UAACUCAGGGGCGGUAGCCAA
BX950851.1/1606683-1606720   CAGUGCAUUGGUAGCUA-UGAGCCAAGGGCGGUAGCGUG
EU294175.1/1025-1063         CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
CR378671.1/333618-333581     CAGCAUAUUGGGAGCUG-CAACCUAAGGGCGGUAGCGUG
CP000247.1/2175301-2175263   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
CP000462.1/1556882-1556845   UAGCAGGCUGGAGGCUG-UAAUCCACGGUCGGUAGCGUG
L14842.1/650-688             CAGUGCACUGGUAGCUGUUAAGCCAGGGGCGGUAGCGUG
CU928164.2/4323135-4323097   CAGUAUUCAGGUAGCUGUUGAGCCUGGGGCGGUAGCGUG
CP000970.1/4046236-4046198   CAGUAUUCAGGUAGCUGUUGAGCCUGGGGCGGUAGCGUG
CP000447.1/1634047-1634084   CAGCAAUCUAGAAGCUG-UAAUCUAGUGGCGGUAGCGUG
CP000970.1/1018107-1018145   CAGUGUAUUGGUAGCUAAAAAGCCACGGGCGGUAGCGUG
EU294164.1/1024-1062         CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
AE014299.1/3334245-3334208   GGGCAAUAUAGAGGCCG-CAAUCUAUGGGCGGUAGCGUG
CU928163.2/4267493-4267455   CAGUAUUCAGGUAGCUGUUGAGCCUGGGGCGGUAGCGUG
EU294169.1/1024-1062         CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
CP000462.1/4001368-4001405   CAGCAAGCUCGAGGCUG-GAAUUCAGGGGCGGUAGCGUU
CP000644.1/4144866-4144902   CAGCAUACAGGGAGCUG-AAACCC-CGUGCGGUAGCUAU
CP000243.1/2275109-2275071   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
CP000462.1/4017751-4017788   CAGCAGACUGGAGGCUG-AAAUUCAGGGGCGGUAGCCAU
FM200053.1/859896-859934     CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
CU928145.2/4183237-4183199   CAGUAUUCAGGUAGCUGUUGAGCCUGGGGCGGUAGCGUG
FM200053.1/4228344-4228381   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
CP000644.1/3822863-3822900   CAGCAGACUGGAGGCUG-UAAUUCAGGUGCGGUAGCUAU
CP000802.1/3837796-3837758   CAGUAUUCAGGUAGCUGUUGAGCCUGGGGCGGUAGCGUG
CP000644.1/1330418-1330381   GAGCAUAUUGGAAGCUG-UCAUCCAAGGGCGGUAGCGUA
CAAU01003370.1/3544-3506     CAGUGCACUGGUAGCUGAUGAACCAGGGGCGGUAGCGUG
CU928162.2/4242379-4242341   CAGUAUUCAGGUAGCUGUUGAGCCUGGGGCGGUAGCGUG
CP001063.1/1072629-1072667   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
CP000857.1/1702017-1702055   CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
CP001164.1/4655178-4655140   CAGUAUUCAGGUAGCUGUUGAGCCUGGGGCGGUAGCGUG
CP000857.1/4407689-4407726   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
AM286415.1/3358260-3358223   CAGUGUAUUGGUAGCUG-UGAGCCAAGGGCGGUAGCGUG
CU928161.2/2134532-2134494   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
CP000644.1/3828635-3828672   CAGCACACUGGAGGCUG-AAAUUCAGGGGCGGUAGCCAU
CP000468.1/4099539-4099501   CAGUAUUCAGGUAGCUGUUGAGCCUGGGGCGGUAGCGUG
AM933173.1/4312866-4312903   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
CP000644.1/1331858-1331821   GAGCAUAUUGGAAGCUG-UAAUCCACGGGCGGCAGCGUG
AF285969.1/1064-1102         CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
AM933173.1/2174336-2174298   CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
CAAQ01001590.1/136-174       CAGUGCACUGGUAGCUGAUGAACCAGGGGCGGUAGCGUG
AF060869.1/2004-2041         AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
CU928162.2/2346476-2346438   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
EU296408.1/1024-1062         CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
AE006468.1/2178692-2178654   CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
CP000462.1/1408724-1408687   GAGCAUAUUGGAAGCUG-UAAUCCACGAGCGGUAGCGUG
CP000036.1/908336-908298     CAGUGUAUUGGUGGCUAAAAAGCCAGGGGCGGUAGCGUG
AP009048.1/2139597-2139559   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
DQ868766.1/1024-1062         CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
AP008232.1/1611345-1611382   UAGCGCAUUGGUAGCUA-CGAACCAAGGGCGGUAGCGUG
AE014075.1/2424993-2424955   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
CP000266.1/2120667-2120629   CAGUGCACUGGUAGCUGUUAAGCCAGGGGCGGUAGCGUG
CP000783.1/1124151-1124188   CAGUAGAUUGGUAACUG-AAAGCCAAGGGCGGUAGCGUG
AJ576316.1/825-862           AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
AE017333.1/4124432-4124394   AAGCACAGCGGCAGCAAAUAAGCCGCGGGCGGUGGUGUC
DQ371800.1/314-352           CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
CP001113.1/4468905-4468942   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
AAPH01000003.1/46145-46182   CAGCAUAUUGGGAGCUG-CAACCUAAGGGCGGUAGCAUG
CP000462.1/2238472-2238435   CAGCAAUCUGGGGGCUG-UAACCCAGGGGCGGUAGCUAU
EU274663.1/168-205           CAGCAAACUGGGGGCUG-UAACUCAGGGGCGGUAGCUAU
EU118168.1/916-954           CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
CP000462.1/3395992-3396029   GAGCGCAUUGGAAGCUG-UAAUCUAGGGGCGGCAGCGUG
EU296407.1/1024-1062         CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
CP001144.1/2310345-2310307   CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
DQ069297.1/1024-1062         CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
ABEW01000009.1/78780-78817   AAGCGUAUUGGUAGCAG-UAAGCCAAGGGCGGUAGCGUU
X56793.1/3987-4025           CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
AM933172.1/4334958-4334995   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
EU296422.1/1025-1063         CAGUGCACUGGUAGCUGUUAAGCCAGGGGCGGUAGCGUG
AM933172.1/2183328-2183290   CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
CP000948.1/2226492-2226454   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
CP000644.1/3267272-3267309   GAGCAUUUUGGAAGCUG-UAAUCCACGGGCGGUAGCGUG
CP001138.1/2136558-2136520   CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
EU296418.1/1024-1062         CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
EU294163.1/1024-1062         CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
CP000946.1/1781475-1781513   CAGUGCUCUGGUAGCUGUAAAGCCAGGGGCGGUAGCGUG
CP000783.1/1149747-1149785   UAGUGCACUGGUAGCUAUUGAGCCAGGGGCGGUAGCAUU
AY730593.1/1118-1156         CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
AE017220.1/4412354-4412391   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
CU928158.2/2178898-2178860   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
CP000644.1/2746012-2746048   CAGCACUCGGGGAGCUG-UAACCCA-GUGCGGUAGCUAU
AE005174.2/2883049-2883011   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
CP000462.1/3268141-3268104   CAGCAAACUGGGGGCUG-UAACUCAGGGGCGGUAGCUAU
CP000826.1/1725327-1725364   CAGUACAUUGGUAGCUG-AAAGCCAGGGGCGGUAGCGUG
CAAS01000602.1/1454-1492     CAGUGCACUGGUAGCUGAUGAACCAGGGGCGGUAGCGUG
CP000247.1/3912685-3912647   CAGUAUUCAGGUAGCUGUUGAGCCUGGGGCGGUAGCGUG
CP001138.1/4397367-4397404   AAGCGUAUUGGUAGCAG-GAAGCCAAGGGCGGUAGCGUU
BX936398.1/1198616-1198653   CAGUGCAUUGGUAGCUG-UAAGCCAAGGGCGGUAGCGUG
CP001113.1/2190132-2190094   CAGUGCACUGGUAGCUGAUGAGCCAGGGGCGGUAGCGUG
AM849474.2/468-505           CAGUGCAUUGGUAGCUG-UAAGCCAAGGGCGGUAGCGUG
AAOJ01000005.1/28893-28856   AAGCACUUUGGGAGCUU-UAACCUAAGGGCGGUAGCGUA
FN649414.1/2372203-2372165   CAGUGUAUUGGUAGCUAAAAAGCCAGGGGCGGUAGCGUG
AALD02000001.1/93983-93946   CAGUGCAUUGGCUGCUG-UGAGCCAAGGGCGGUAGCGUU
AALC02000011.1/546-509       CAGUGCAUUGGCUACUG-UAAGCCAAGGGCGGUAGCAUG
AALE02000006.1/195385-195422 CAGUACAUUGGUAGCUG-UAAGCCAAGGGCGGUAGCGUG
AALF02000002.1/85615-85652   CAGCGCAUUGGUUGCUG-UAAGCCAAGGGCGGUAGCAUA
FP929040.1/4175198-4175235   CAGUGGAUUGGUAACUG-AAAGCCAAGGGCGGUAGCGUG
AALD02000001.1/114588-114551 CAGUGCAUUGGUUACUG-CAAGCCAAGGGCGGUAGCAUU
#=GC SS_cons                 :::::::<<<<<_____.___>>>>>:::::::::::::
#=GC RF                      CAGCGcAcUGGuAGCUG.UAAgCCAgGGGCGGUAGCGUG
//
# STOCKHOLM 1.0

#=GF AC   RF01708
#=GF ID   L17DE
#=GF DE   L17 ribosomal protein downstream element
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   37.00
#=GF TC   37.20
#=GF NC   36.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   L17DE_RNA_motif
#=GF SQ   52


CP000023.1/1696818-1696743   UGAGUGUUAUGAUGAUGGAAUAG-CUUA--G--------------------------------------------CUUUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUGGGC-AAGA----UGCCCAGCGG
CP000056.1/78525-78602       UGAGUGUUAUGAUGAUGGAGUAAUCGAGA-G-------------------------------------------AUUAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA--UUUU----UCCUAGCGG
FM211187.1/205769-205840     -GAGUGUUAUGAUGAUGGAGU----CUUGU-----------------------------------------------GCUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA-UUUCG---GUCCUAGCGG
AE016830.1/212775-212844     AGAGUGUUAUGAUGUUGGAG-----GCGA-------------------------------------------------CUCC--GAGUCUAGCUCU-GCUUUC-CCUGCUAAA-GAUGG---CUUUAGCAGG
AADR01000037.1/21840-21767   GGAGUGUCAUGAU-AUGGAG-----ACUUCG-------------------------------------------UG--UUCC--UUGUCUAGCUCUGUGUUUC-CUAGUCUAC--UUAAU--CGUAGGCUAG
FM177140.1/2597596-2597526   -GAGCGUUACGAUGAUGGCAGG---CCCAGU--------------------------------------------UCCUGCU--UAGUCUAGCUU---------GAGAGCACCGGGCAA-C-CGGUUGUCUC
ACBD01000026.1/62237-62310   AGAGUGUUAUGAUGUUGGAAG----AUAUU-----------------------------------------------UUUCC--GAGUCUAGCUCAGCGCUGCUCCUCAAGCG--AAUAU---CGCUUGGGG
CP001175.1/2915652-2915727   GGAGUGUCAUGAU-AUGGAGAC---UUCGU----------------------------------------------GUUUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-CUUAAUC-GUAGGCUAGG
CP000259.1/78847-78924       UGAGUGUUAUGAUGAUGGAGUAAUCGAGA-G-------------------------------------------AUUAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA--UUUU----UCCUAGCGG
AE009949.1/79130-79207       UGAGUGUUAUGAUGAUGGAGUAAUCGAGA-G-------------------------------------------AUUAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA--UUUU----UCCUAGCGG
FM242711.1/2658157-2658082   GGAGUGUCAUGAU-AUGGAGAC---UUCGU----------------------------------------------GUUUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-CUUAAUC-GUAGGCUAGG
AM263198.1/2597533-2597458   GGAGUGUCAUGAU-AUGGAGAC---UUCGU----------------------------------------------GUUUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-UUUAACC-GUAGACUAGG
AE005176.1/2151650-2151528   UGAGUGUUAUGAUGUUGGCGGG--GGUUUCUGUGGGUGCAUGUGUUGAGUUGUGAUUGACUCUCUUUCGCAUCAGCCUUGCUUAUAGUCUAGCUCU--GUCUG-AUUAGAUUA--AAUUU--CUAAUCUAGU
CP000033.3/304248-304302     UAAGCGUAAAGAUGAUGGC------GUAA--------------------------------------------------GCU--UAGUCUAGCUUA--------GAUGAU-----UAAGA------AUCAUC
CP000114.1/90353-90424       -GAGUGUUAUGAUGAUGGAAUC---AAUC-----------------------------------------------GAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUGAGA-AUUA----UUCUCAGCGG
CP000829.1/79251-79328       UGAGUGUUAUGAUGAUGGAGUAAUCGAGA-G-------------------------------------------AUUAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA--UUUU----UCCUAGCGG
CP000024.1/1697442-1697367   UGAGUGUUAUGAUGAUGGAAUAG-CUUA--G--------------------------------------------CUUUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUGGGC-AAGA----UGCCCAGCGG
AE009948.1/90643-90714       -GAGUGUUAUGAUGAUGGAAUC---AAUC-----------------------------------------------GAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUGAGA-AUUA----UUCUCAGCGG
ABAE01000002.1/97263-97335   UGAGUGUUAUGAUGAUGGAGU----CUUGC-----------------------------------------------GCUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA--UUUCG--GUCCUAGCGG
AE014074.1/79240-79317       UGAGUGUUAUGAUGAUGGAGUAAUCGAGA-G-------------------------------------------AUUAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA--UUUU----UCCUAGCGG
CP000387.1/122640-122714     -GAGUGUUAUGAUGAUGGAAUAG-AAUC--U--------------------------------------------CUAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA--UUCUU---UCCUAGCGG
CP000936.1/298088-298159     -GAGUGUUAUGAUGAUGGAGU----CUUGU-----------------------------------------------GCUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA-UUUCG---GUCCUAGCGG
AADQ01000051.1/6006-5931     GGAGUGUCAUGAUAUGGGGA-----CUUCGU-------------------------------------------GU--UUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-UUUAAUC-AUAGGCUAGG
AAFA03000012.1/44855-44782   UGAGUGUUAUGAUGAUGGAAUC---CUAUUC--------------------------------------------UGAUUCU--UAGUCUAGCUC-UGGUCU--ACCGCUGAG--CUUAU---CUCAGCGG-
CP000408.1/87129-87202       UGAGUGUUAUGAUGAUGGAAUC---CUAUUC--------------------------------------------UGAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUGAG---CUUGU----CUCAGCGG
CP000920.1/236794-236865     -GAGUGUUAUGAUGAUGGAGU----CUUGU-----------------------------------------------GCUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA-UUUCG---GUCCUAGCGG
CP000407.1/87133-87206       UGAGUGUUAUGAUGAUGGAAUC---CUAUUC--------------------------------------------UGAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUGAG---CUUGU----CUCAGCGG
AM295007.1/79773-79850       UGAGUGUUAUGAUGAUGGAGUAAUCGAGA-G-------------------------------------------AUUAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA--UUUU----UCCUAGCGG
AE017262.2/2640188-2640113   GGAGUGUCAUGAU-AUGGAGAC---UUCGU----------------------------------------------GUUUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-CUUAAUC-GUAGGCUAGG
CP000921.1/242144-242215     -GAGUGUUAUGAUGAUGGAGU----CUUGU-----------------------------------------------GCUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA-UUUCG---GUCCUAGCGG
AARY02000048.1/3323-3248     GGAGUGUCAUGAUAUGGGGA-----CUUCGU-------------------------------------------GU--UUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-UUUAAUC-AUAGGCUAGG
CP000918.1/249020-249091     -GAGUGUUAUGAUGAUGGAGU----CUUGU-----------------------------------------------GCUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA-UUUCG---GUCCUAGCGG
AL596173.1/172594-172519     GGAGUGUCAUGAU-AUGGAGAC---UUCGU----------------------------------------------GUUUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-UUUAAUC-GUAGGCUAGG
CR936503.1/1723553-1723485   AGGGCGUUAUGAUGAUGGCA-----UUUAU---------------------------------------------U--UGCC--AAGUCUAGUCCU-----AAGGUUAUGUU---AGCACCAC-AGCAUAAC
AARJ02000003.1/333791-333866 GGAGUGUCAUGAU-AUGGAGAC---UUCGU----------------------------------------------GUUUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-CUUAAUC-GUAGGCUAGG
AARL02000440.1/344-269       GGAGUGUCAUGAUAUGGGGA-----CUUCGU-------------------------------------------GU--UUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-CUUAAUC-GUAGGCUAGG
AARK02000043.1/3050-3125     GGAGUGUCAUGAU-AUGGAGAC---UUCGU----------------------------------------------GUUUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-CUUAAUC-GUAGGCUAGG
CP000419.1/1755085-1755008   UGAGUGUUAUGAUGAUGGAAUAG-CUUA--G--------------------------------------------CUUUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUGGGC-GCAAGA--UGCCCAGCGG
BA000034.2/73239-73316       UGAGUGUUAUGAUGAUGGAGUAAUCGAGA-G-------------------------------------------AUUAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUAGGA--UUUU----UCCUAGCGG
AE017198.1/395992-396043     UAAGCGUGAUGAUGGUGGC------UUUU--------------------------------------------------GCC--UAGUCUAGCUUA--------GAUG-U-----UAA--------AUCAUC
CP000413.1/346685-346736     UAAGCGUGAUGAUGGUGGC------UUUU--------------------------------------------------GCC--UAGUCUAGCUUA--------GAUG-U-----UAA--------AUCAUC
CP000422.1/1379186-1379131   -GGGUGUUACGAUGUUGGA------GAAA--------------------------------------------------UCC--UAGUCUAGCCC------ACGGCGAGU-----UUUUA------ACUUGC
AL766843.1/90859-90930       -GAGUGUUAUGAUGAUGGAAUC---AAUC-----------------------------------------------GAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUGAGA-AUUA----UUCUCAGCGG
AAJQ01000070.1/1744-1815     -GAGUGUUAUGAUGAUGGAAUC---AAUC-----------------------------------------------GAUUCU--UAGUCUAGCUC-UGGUCUA-CCGCUGAGA-AUUA----UUCUCAGCGG
AM406671.1/2310910-2310792   UGAGUGUUAUGAUGUUGGCGGG--GGUUUCUGUGGGUGCAUGUGUUGAGUUGUGAUUGACUCUCUUUCGCAUCAGCCUUGCUUAUAGUCUAGCUC--UGUCU--GAUUAGA----UUAAAU-U--UCUAAUC
CP001602.1/250247-250322     GGAGUGUCAUGAUAUGGGGA-----CUUCGU-------------------------------------------GU--UUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-UUUAAUC-AUAGGCUAGG
CP002222.1/921534-921612     CGGGCGUUAUGAUGGUGGCUACU-GGCAAAA-------------------------------------------UAGUAGCU--AAGUCUAGUUCG----GAA-GUUAUUUAU-GGUUAGA-CAUAGAUGGC
CP001834.1/2379663-2379545   UGAGUGUUAUGAUGUUGGCGGG--GGUUUCUGUGGGUGCAUGUGUUGAGUUGUGAUUGACUCUCUUUCGCAUCAGCCUUGCUUAUAGUCUAGCUC--UGUCU--GAUUAGA----UUAAAU-U--UCUAAUC
CP002002.1/2654597-2654522   GGAGUGUCAUGAUAUGGGGA-----CUUCGU-------------------------------------------GU--UUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-UUUAAUC-AUAGGCUAGG
AP010655.1/1842242-1842170   UGAGUGUUAUGAUGUUGGAAUU--AUAA-----------------------------------------------UAAUUCU--UAGUCUAGCUC-UGGUCUACCACUAGGAG--AGG-----CUCCUAGUG
CP001604.1/250247-250322     GGAGUGUCAUGAUAUGGGGA-----CUUCGU-------------------------------------------GU--UUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-UUUAAUC-AUAGGCUAGG
AL591983.1/296650-296575     GGAGUGUCAUGAU-AUGGGGAC---UUCGU----------------------------------------------GUUUCC--UUGUCUAGCUCUGUGUUU--CCUAGUCUA-UUUAAUC-AUAGGCUAGG
#=GC SS_cons                 :<<<<-----<<<---<<<<<<...______............................................_>>>>>>..-->>>-->>>>..------.<<<<<<<<<.._____.._>>>>>>>>>
#=GC RF                      uGAGUGUUAUGAUGaUgGcggg...gUuuuu............................................uccugCu..UAGUCUAGCUC..uGUcUa.gcucgggga..uUaau..uuccccgagc
//
# STOCKHOLM 1.0

#=GF AC   RF01709
#=GF ID   Lacto-rpoB
#=GF DE   Lacto-rpoB RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   40.70
#=GF NC   39.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Lacto-rpoB_RNA_motif
#=GF SQ   31


AE005176.1/1864719-1864661   GUUUGUCAGCAAAAUCUGUGGGAUAUAUUGUCCCCAUAGG-CUUU--GUAAGCAACGAAACA
CP000387.1/174628-174686     AUUUGUCG-UGUGCUUUAUUUGAAAUAUUGUCCAAAUAGAAGCUU--ACAGCAGUUAAAUCA
CP000419.1/1720910-1720853   AUUUGUCG-UCUUAUUUGAUUGAAAUAUUGUCCAAUCAAG-AGAU--ACAGCAGUUAAAUCA
CP000017.1/93919-93976       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
CP000056.1/93407-93464       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
AE007317.1/1751875-1751818   AUUUGUCG-UAGGUUUUGUCUGAAAUAUUGUCCAGACAAG-GCUC--ACAGCAGUUAAAUCU
AM406671.1/1970359-1970301   GUUUGUCAGCAAAAUCUGUGGGAUAUAUUGUCCCCAUAGG-CUUU--GUAAGCAACGAAACA
CP000407.1/110341-110398     AUUUGUCG-UGUGUCUUGUUUGAAAUAUUGUCCAAACAAG-GCUU--GCAGCAGUUAAAUCA
FM177140.1/2635349-2635292   UUUGGACA-GGCUGUCAGGACGAUCUAUUGUCCGUUCUGG-CUAA--UGAAAAAGCAAAAAC
CP000425.1/1876302-1876244   GUUUGUCAGCAAAAUCUGUGGGAUAUAUUGUCCCCAUAGG-CUUU--GUAAGCAACGAAACA
AE009948.1/179028-179085     AUUUGUCG-UCUGUCUAGGUUGAAAUAUUGUCCGACCUAG-AUAU--ACAGCAGUUAAAUCA
BA000034.2/88129-88186       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
CP000259.1/93729-93786       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
CP000233.1/234847-234900     AAUUGAUU----GUUUGUUAUGAUAUAUUGUCCAUAGCAG-ACUU---GAUAAAAGCAAAAA
AE004092.1/93363-93420       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
FM211187.1/1927843-1927786   AUUUGUCG-UAGGUUUUGUCUGAAAUAUUGUCCAGACAAG-GCUC--ACAGCAGUUAAAUCU
CP000408.1/110247-110304     AUUUGUCG-UGUGUCUUGUUUGAAAUAUUGUCCAAACAAG-GCUU--GCAGCAGUUAAAUCA
AE009949.1/94021-94078       AUUUGUCG-UCCAAUCUAGCUGAAAUAUUGUCCAGUUAGG-AAGA--ACAGCAGUUAAAUCA
CP000705.1/1544739-1544681   UGAGUUCA-UUUGAACCUGGUGAUCUAUUGUCCAUCAGAU-UCUGC-AUAAAAGCCAAAGAC
ACHL01000156.1/7622-7564     GAUGAAGA-AAAGGCAGAAACGAAAUAUUGUCCGUUUCGG-CUUUAA-UAUAAGGAAACAAA
CP000918.1/1874948-1874891   AUUUGUCG-UAGGUUUUGUCUGAAAUAUUGUCCAGACAAG-GCUC--ACAGCAGUUAAAUCU
AL766844.1/35933-35990       AUUUGUCG-UCUGUCUAGGUUGAAAUAUUGUCCGACCUAG-AUAU--ACAGCAGUUAAAUCA
CP000023.1/1667715-1667658   AUUUGUCG-UCUUAUUUGAUUGAAAUAUUGUCCAAUCAAG-AGAU--ACAGCAGUUAAAUCA
AE016830.1/3112617-3112562   AAGUGACG-A--AGCAGGAGCGAAAUAUUGUCCGUUCCGG-UUUU--UUAUAGGAAAACAAA
CP000114.1/188955-189012     AUUUGUCG-UCUGUCUAGGUUGAAAUAUUGUCCGACCUAG-AUAU--ACAGCAGUUAAAUCA
CP000920.1/1824936-1824879   AUUUGUCG-UAGGUUUUGUCUGAAAUAUUGUCCAGACAAG-GCUC--ACAGCAGUUAAAUCU
CR936503.1/1751463-1751404   GUAGAAAA-AUUUAUUGUGCUGAUCUAUUGUCCAGCACGG-UAUUCAUGAAAAGCAAAAAUA
CP000416.1/1660516-1660460   AACUGAAA-UUGAACGU-GCCGAUAUAUUGUCCGGUGACG-UUUG--UUAUAAGAAGCCAAA
AAPZ02000001.1/635020-634962 UGAGUUCA-UUUGAACCUGGUGAUCUAUUGUCCAUCGGAUUCUGC--AUAAAAGCCAAAGAC
CP000936.1/1942796-1942739   AUUUGUCG-UAGGUUUUGUCUGAAAUAUUGUCCAGACAAG-GCUC--ACAGCAGUUAAAUCU
AP010655.1/195434-195491     AUUUGUCG-UUUGCUUUGGUUGAAAUAUUGUCCAAACAAA-GCUC--ACAGCAGUUAAAUCA
#=GC SS_cons                 :::::::<.<--<<<<<<<<<<__________>>>>>>>>.>>--..>>:::::::::::::
#=GC RF                      AUUUGUCg.uaugaUuugucUGAAAUAUUGUCCAgacaaG.ucUu..acAgaAGuuAAAaCA
//
# STOCKHOLM 1.0

#=GF AC   RF01710
#=GF ID   Lacto-usp
#=GF DE   Lacto-usp RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   53.30
#=GF NC   34.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Lacto-usp_RNA_motif
#=GF SQ   6


AE017198.1/846317-846228   GAUCAAACU-AAAG-ACGUUGGAAUUUAUGAAUAACAUCUGAAUCGGAAUACUAGCUUGUCCUAGGAUCCAUAUUCACUGCGACAUAGAUUC
CR954253.1/608889-608801   GAUCAAACU-UAAGGACGUGGUGGCCUGUCAGUAACUACUGAAUCGGAAUGCUGCUCA--CGCAGAAUCCAUAUUCACUGCGCGACGGGCCG
CP000412.1/603031-602943   GAUCAAACU-UAAGGACGUGGUGGCCUGUCAGUAACUACUGAAUCGGAAUGCUGCUCA--CGCAGAAUCCAUAUUCACUGCGCGACGGGCCA
CP000033.3/767168-767078   GAUCAAACUAUAAG-ACGUGGUGGUUGGCAAAUAACUACCGAAUCGGAAUACUGCCUUGUUGCAGGAUCCAUAUUCGCUGCGAUGCUGACCG
CP000413.1/1232606-1232695 GAUCAAACU-AAAG-ACGUUGGAAUUUAUGAAUAACAUCUGAAUCGGAAUACUAGUCUGAUCUAGGAUCCAUAUUCACUGCGACAUAGAUUC
AE016830.1/1051896-1051978 CAUGAGUUUACAAAGUGGUC--GAGCCUUGAUUAAAAAA-CUAUUGUUAUACGUGCGUU-UUGUGAAAACAUAU-----GAGAUAAUGUUCA
#=GC SS_cons               :::::::::.::::::::::::<<<<<<<<---------<<<<<-<<<---<<<<____._>>>>-->>>-->>>>>------>>>>>>>>:
#=GC RF                    gAUcAAAcU.uAAGGAcGUuGuGgcccgugAaUAAcaacuGAAUcGgaAUACugguuug.uccaGaAucCAUAUUCaCUGcGAcacgggcCa
//
# STOCKHOLM 1.0

#=GF AC   RF01711
#=GF ID   Lnt
#=GF DE   Lnt RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   55.00
#=GF TC   61.10
#=GF NC   47.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Lnt_RNA_motif
#=GF SQ   10


CP001101.1/905954-906014   CAGGAAAU---UU-U---------UUG-C-UGGUAAUUCCUGUUAAAUAACAGCUUGAAACAAAUUUAAAUAAUAA
CP000607.1/1481205-1481140 CAGGAGUCGGGAACU-------UCUU--U-CGCAUACUCCUGUUAAAUAACAGCUUGAAAGAAAUUUAAAGAAUAU
CP000096.1/1687310-1687245 CAGGGGCCCGUUU-U-------AC-UGAA-AGCCUACCCCUGUUAAAUAACAGCUUGAAAUAAAUUUAAAGAAUAA
AASE01000007.1/53638-53577 CAGGAAAA----U-U---------UUGAGCAGUCCAUUCCUGUUAAAUAACAGCUUAGAAUAAAUUUAAAGAAUAA
CP001110.1/1091010-1091073 CAGGAAAA---AAUU-------UCAUGG--AGAUUAUUCCUGUUAAGUAACAGAGUGGAAGAAAUUUAAAGAAUAA
CP001108.1/1737722-1737663 CAGGAAAU---UU-U---------UUG-C-UGGCAAUUCCUGUUGAAU-ACAGCUUGAAACAAAUUUAAAGAAUAA
CP000108.1/1796390-1796458 CAGGGAAA---AA-ACUUUCUCAC-CGA--AACCAUUCCUUGUUUGGUAACAGCUUUCUAUAAAUCUAAAGAAUUA
AE006470.1/1404024-1403967 CAGGAAAA----A-C-------AC-UGG---GUUGCUUCCUGUUA--UAACAACUUGAAACAAAUUUAAAGAAUAA
CP000492.1/2186687-2186628 CAGGAAAU----A-C--------CAUGA---GUUGAUUCCUGUUAAAUAACAGCUUGAAAUAAAUUUAAAGAAUAA
CP001097.1/1874171-1874112 CAGGAA------A-U-------ACACGG--AGAUGAUUCCUGUUAAAUAACAGAUUGUUAUAAAUUUAAAGAAUAA
#=GC SS_cons               <<<<<<__...__._.......______..______>>>>>>::::::::::::::::::::::::::::::::::
#=GC RF                    CAGGaAAa...aa.u.......aCuUGA..aGuuaAUuCCUGUUAAAUAACAGCUUGaAAuAAAUUUAAAGAAUAA
//
# STOCKHOLM 1.0

#=GF AC   RF01712
#=GF ID   Methylobacterium-1
#=GF DE   Methylobacterium-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   43.30
#=GF NC   36.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Methylobacterium-1_RNA_motif
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   34


ABEF01010507.1/763-658     AAAGUUGGAUUAAUUGGUGACUAAA-GAUU-CCCA-ACAAGACGGGGGAG----A-AAUU-A--CCCCCACACGAUAUUCAAGAUCACUGCA-UCGGUAGAAUA-U-CGUGACCGAAGGU
ABEF01000929.1/382-280     AAAGUUGGAU--G-GGGUCACUAAA-CAUU-UCCA-GCAGGACGAGGGAG----A-AAUUUA--CCCUCACACGAUAUGAA-AAUCA-UCCAAUCGGUUUCAUA-U-CGUGACCGUAGUU
ABEF01013431.1/35-137      AAAGUUGGAU--AUGGGUGGUUAAA-CAUU-UCCA-GCAGGACGGGGGAG----A-AAUC-A--CCCCCACACGGUAUGAA-AAUCA-UCCAAUCGGUUUCAUA-U-CGUGACCGUAGUU
ABEF01039662.1/104-207     AAAGUUGGAU--AUGGGUGGUUAAA-CAUU-UCCA-GCAGGACGAGGGAG----G-AUUUUA--CCCUCACACGAUAUGAC-CAUCA-UCCAAUCGGUUUCAUA-U-CGUGACCGUAGUU
AACY021222670.1/59-162     AAAGUUGAAU--AUGGGUUCUAAAA-UAUU-CUCA-ACAGGACGAGGGAG----A-AAUA-A--CCCUCAAAUGAUAUGGAUAGUGAUUGCA-UCUGCUCCAUA-U-UGUUACCGAAGUU
AACY023405062.1/1217-1321  AAAGUCGGA---AUGGGUGUUGAAA-GAUU-ACCG-ACAAGAUGAGGGAA----ACACGCAA--CCCUCGUUCGAUGCGGGUAAUUAUUCCA-ACAGUUCCGCA-U-CGAUGCCGCUGCU
AACY023283424.1/196-95     AAAGUUGGA---AUUGGUGUCUAAA-GAUU-ACCA-ACAAGACGAAGGAA----U-UAUC-A--CCUUCAAGCGAUGCAGG-CAUCA-UUCAGUCGGUUAUGCA-U-CGCUACCGUAGUU
AACY023518733.1/758-860    AAAGUUGGAUGGG---GUGUCGAAA-GAUU-UCCA-ACAGGACGAGGGAG----A-AUUA-A--CCCUCAAGUGAUGCAGGUAAUUA-UCCAAUCAGUUCUGCA-U-UGCUACCGUAGUU
AACY023842588.1/681-568    AAAGGUGAAACGCCA-CUGUGUCAAAUAAUUCUCA-CCAGGAUGGGGGCUCUGUUUACCUGCAACCCUCGGCCACAAUGAA-UGUUGUUCUA-CGAGCUACAUU-G-UGGUACCGCUGCU
AACY023975293.1/371-471    AAGACUAA----AACGGUAGCAAAU-AUUG--UUA-GUAAGACGGGGGAG----A-AAUA-A--CCCCCAUAGAAUAUAAAAGGUAA-UCACAUCUGCAUUAUA-U-UCUAACCGAAGGU
AACY024016669.1/719-820    AAAGUUGGA---CUUGGUGUCUAAA-GAUU-ACCA-ACAAGACGAAGGAA----U-UAUC-A--CCUUCAAGCGAUGCAGG-UAUCA-UCUAGUCGGUUAUGCA-U-CGCUACCGUAGUU
AACY023229177.1/664-563    CAAGUUGGA---AUG-GUGUUUAAA-UAUU-CCCA-ACAGGACAAGGGAG----A-ACUU-A--CCCUUACAGAAUAUGAU-GGUAAAUGUA-UCUGCAUCAUAAU-UCUGACCCUAGUU
AACY020711569.1/62-163     CAAGUUGGA---AUG-GUUCUAAAA-UAUU-CCCA-ACAGGACGAGGGAG----A-AAUA-A--CCCUCAAAGGGUCUGGAUUGUAAUUGUA-UCUGCACCAGA-C-ACUUACCGAAGUU
AACY022912620.1/112-215    AAAGACAGAA--AAAGGUGUUGAAAAAUUA-UCUG-UCAGGAUUCAGGUG----A-AAUAUA--CCUG-UGGUGGGGGAGA-UGCUA-UCCGACAUGCACUCUC-U-CGCUCCCGUAGUU
AACY021673151.1/567-668    AAAGUUGGA---ACCGGUGUCUAAA-GAUU-GCCA-ACAAGACAAAGGAA----U-UAUC-A--CCUUCAAGCGAUGCAGG-CAUUA-UCCAGUCGGUAAUGUA-U-CGCUACCGCAGUU
AACY023024298.1/507-607    AAAGUUGGA---CUGGGUGAUUAAA-CAUU-ACCA-ACAGGACGAGGGAG----U-AUUUUA--CCUUCACACGAUAUGUC-UAUCA-UUCAAUCGGUUUCAUA-U-CGUGACCGUAG--
AACY021497895.1/642-541    CAAGUUAGA---AUG-GUGUUAAAA-UAUU-CCCA-AUAGGACAAGGGAG----A-AAUA-A--CCCUUACAGAAUAUGAA-AUUUAUCUUCAUCAGAUUCAUA-U-UCUGACCGAAGUU
AACY020143093.1/563-664    CAAGC-AGA---AAUGGUGUUAAAAUAUUA-UCUA-GCAGGAUAAGGG------A-AAGUUA--CCCUUAAAGAAUAUGAA-AUUUAUCUUCAUCAGAUUCAUA-U-UCUUACCGAAGUU
AACY021683184.1/672-770    ---GUUGGA---AUG-GUGUUAAAA-UAUU-CCCA-GCAGGACAAGGGAG----A-AAUA-A--CCCUUACAGAUUAUGAU-AGUAA-ACAUAUCUGCAUCAUAUA-UCUGACCGAAGUU
AACY020036283.1/1055-1158  AAAGACAGAA--AUCGGUGCCUAAG-AAUUAUCUG-UCAGGAUUCAGGUG----A-AAAAUA--CCUG-UGGUGGGAGAGA-UGCUA-UCUGACAUGCACUCUC-U-UGCUCCCGUAGUU
AACY023611012.1/235-337    CAAGUUGAAA--AAUGGUGUCUAAA-UAUU-AUCA-GCAGGACGAGGGAG----A-UAUA-A--CCCUCACAAGAUGCAGA-AUUUA-UCCUCACAGAUUUGUA-U-CUUGACCGUAGUU
AACY021532984.1/176-283    AAAGUUGGA---CUGGGAGACAAAA-UAUU-CCCA-ACAGGACGAGGGAACGUCA-CAAUUA--CCCUCGAGCGUUAAGGACUGUGAUUGUA-UCUGCACCUUA-U-CGUUACCGUAGUU
AACY022519618.1/576-680    AAAGAUGGA---AGGGGUAUUCAAA-GAUU-UCCACUCAGGACGAGGGAA----G-AAUUAA--CCCUCAAACGAUUAGGACUGUGAUUGCA-UCUACACCUAG-U-CGUUACCGUAGUU
AACY020968185.1/720-823    AAAGUUGGAC--AGGGGUGACUAAA-CAUU-UCCA-ACAGGACGAGGGAG----U-AUUUUA--CCCUCACACGAUAUGAC-CAUCA-UCCAAUCGGUUUCAUA-U-CGUGACCGCAGUU
AACY023842409.1/527-424    AAGGGUGAAC--G-GGGCGUCUAAA-CAUU-AUCA-UCACGACGGUGGAA----A-CAUU-A--CCACCAAACGUCUGGGGUCGUUG-UCCAAUGAGCGCCCAG-AUCGUUACCGUAGAU
AACY023211906.1/672-568    AAAGUCGGA---AUGGGUGUGUAAA-GAUU-UCUG-ACAGGAAGAGGGAA----ACAAGCAA--CCCUCGUUCGGUGCGGGUAAUCAUUCCA-ACGGUUCCGCA-U-UGAUGCCGCUGCU
AACY022630472.1/230-333    AAAGACAGAA--AUCGGUGCCUAAG-AAUUAUCUG-UCAGGAUUCAGGUG----A-AAAAUA--CCUG-UGGUGGGAGAGA-UGCUA-UCCGACAUGCACUCUC-U-UGCUCCCGUAGUU
AACY020077010.1/1561-1458  AAAGUUGGAA--AUGGGUGCCUUAA-GGUU-UCCA-ACAGGACGA---AUAAGAUCUAACCC-----UCAAGUGAUACAAGUAAUCA-UUCAGUCGGUUCUGUA-U-CUCCACCUUAGUU
AACY023286650.1/775-673    AAAGUUGGAUGGG---GUGUCUAAA-GAUU-UCCA-ACAGGACGAGGGAG----A-UUUA-A--CCCUCAAGUGAUGCAGGUAAUUA-UCCAAUCAGUUCUGCA-U-UGCUACCGUAGUU
AACY021073165.1/567-670    AAAGUUGGAU--AUGGGUGCAUAAA-GAUU-CCCA-ACAGGACGAGGGAG----A-AGUA-A--CCCUCAAGUGAUACAGGUAAUCA-UCCAGUCGGUUCUGUA-U-CGCUACCGUAGUU
AACY023263926.1/1147-1250  AAAGACAGAA--AUCGGUGCUUAAG-AAUUAUCUG-UCAGGAUUCAGGUG----A-AAAAUA--CCUG-UGGUGGGAGAGA-UGCUA-UCCGACAUGCACUCUC-U-UGCUCCCGUAGUU
AACY020456029.1/1712-1609  AAAGACAGAA--ACCGGUGGUUAAA-AAUUAUCUG-UCAGGAUUCAGGUG----A-AAUAUA--CCUG-UGGCAAGAGAGA-UGUUA-UCUGACUGACCCUCUC-U-UGCUCCCGUAGUU
AACY021104292.1/534-431    AAAGUUGGAU--AUGGGUGAAUAAA-CAUU-ACCA-GCAGGACGAAGGAA----C-AUUUUA--CCUUCACACGAUAUGUC-UAUCA-UGCAAUCGGUUUCAUA-U-CGUGACCGUAGUU
CP000943.1/3127751-3127842 UAAGGUCC-------AACGACA----------GGA-UCAUGAUGAGGGAA----UGUGUU-A--CCCUCACGCUGCUGGGA-UGUCG-GCUUCAUGGCUUCCAGAG-AGCGACCGUUGUA
#=GC SS_cons               :::<<<<<<-..<<<__________.>>>-.>>>>.>>,,,,,<<<<<__...._.______..>>>>>-<<<<<<<<<<-.<<<<_._______>>>>>>>>>.>.>>>>:::::::::
#=GC RF                    AAAGuugGaa..aucGGUGuuuAAA.gauU.uCca.aCAgGAcGaGGGAg....a.aauuuA..CCCuCacgcgauacgga.ugucA.Uccaaucggcaccgua.u.cgcgACCGuAGUU
//
# STOCKHOLM 1.0

#=GF AC   RF01713
#=GF ID   Moco-II
#=GF DE   Moco-II RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   35.00
#=GF TC   42.20
#=GF NC   30.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Moco-II_RNA_motif
#=GF SQ   7


CP000142.2/278681-278728   U---GCGCUAAUUUCGGCCUCUGCCCAGAGUGCAGACCCAACGAAACCCGC
CP000142.2/186813-186856   U---GCGCUUAUUUCGUCCUCCGUACU----ACGGACCCAACGAAACCCGC
CP000142.2/189530-189575   U---GCGCUCAUUUCGUCCUCCAUCGCCG--AUGGACUCAACGAAACCCGC
CP000116.1/2557036-2556993 U---GUAGCCAUCGGGCCGUCCGCUUA----GCGGACGGCGCCGAUUCCGG
CP000482.1/1659585-1659542 ----GCGCUCACUUCGUCCUCUGCCCCG---GCAGACCACACGAAACCCGC
CP000698.1/1183100-1183148 UCAGGCGCUUACUUCGUCCUCUGCCAAAG--GCAGACUUAACGAAACCCGC
CP000482.1/1639928-1639883 U---GCGCCCACUUCGUCCUCUGUACAGA--GCAGACCCAACGAAACCCGC
#=GC SS_cons               :...:::::::::<<<<--<<<<<_____..>>>>>---->>>>:::::::
#=GC RF                    U...GCGCUcAUUUCGuCCUCcGCccAgg..GCgGACccAaCGAAACCCGC
//
# STOCKHOLM 1.0

#=GF AC   RF01714
#=GF ID   Ocean-V
#=GF DE   Ocean-V RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   75.00
#=GF TC   86.30
#=GF NC   53.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Ocean-V_RNA_motif
#=GF SQ   3


ABEF01002814.1/681-753 AUAUUUUAUGACUUCAUUCAAUUGAAGUCCUCAAAGUGAGUACGUCGUAAGAUCGAAGCGCUGACGGAAAACU
ABEF01002040.1/258-187 ACUCUUUUUGGUUUCAUUCAGUUGAAACCCUCA-AGCGAGUACGCCGUAAGACGCAAGCGCAGGCGGAAAACU
ABEF01025170.1/751-680 ACUCUUUUUGAUUUCAUUCAGUUGAAAUCCUCA-CGCAAGUACGCCGUAAGACGCAAGCACAGGCGGAAAGCU
#=GC SS_cons           :::::::::<<<<<<<______>>>>>>>----.--------<<<<________________>>>>:::::::
#=GC RF                AcucUUUuUGgcUUCAUUCAgUUGAAgcCCUCA.aGcgAGUACGcCGUAAGAcgcAAGCgCaGgCGGAAAACU
//
# STOCKHOLM 1.0

#=GF AC   RF01715
#=GF ID   Pedo-repair
#=GF DE   Pedo-repair RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   150.00
#=GF TC   192.50
#=GF NC   46.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Pedo-repair_RNA_motif
#=GF SQ   6


ABCM01000001.1/430655-430865 AACGAAACUUUGC-ACGACAGACCUCGGAAAUCUCAACAAGCAAA-GUAUGG-AUUGAUAGACGGCCCGAUUUCUGUAACUUUACC-CAGAAAUAUGGGCGUCUUCCGUGCUGCUUGUUGGGGAACUUAGGUUCUC-UCCUCUCCGAGGAGGUGUCGU-GCGUGCGGGAGGCGACCAUAUUUUAUUG-UUCCCUCCUGCUAUUAGGAUCAUUGCUUUA
ABCM01000009.1/161544-161756 AACGAAACUUUGCAUCAGUAGGCCUAGUAAACCAGAACAAGCAAA-GUAUGG-AUUGAUAGACGGCCCAAUUUCUGUAACUUUACC-CAGAAAUAUGGGCGUCUUCCGUGCUGCUUGUUCGGGAACUUCGGUUCCU-ACCCAUACUAGGGGGUACUGAUGCGUGCGGGAGGCGACCAUAUUUUAUUG-UUCCCUCCUGCUAUUAGGAUCAUUGCUUUA
ABCM01000036.1/10445-10236   AACGAAACUUUGCAACGAUAGACCUCGGAAAUCUCUGCAAGCAAA-GUAUGG-AUUGAUAGACUGUUCGAUUUCUGUAACUUUAUCUCAGAA-UAUGGGCGUCUUCCGUGCUGCUUGCUGGAGAACU-CUGUUCUC-UCCCUGCCGAGGGGGUAUCGUUGCGUGCGGGAGGCGACCAUAUUUU-UUGUUCCUUUCCUGU--AUUGGAUCAUUGCUUUA
ABCM01000014.1/11514-11305   AACGAAACUUUGC-ACAGUAGACCUAGUAAACCUCAGUAAGCAAA-GUAUGG-AUUGAUAGACAGCCCGAUUUCUGUACCUUUACC-CAGAAAUAUGGGCGUCUUCCGUGCUGCUUACUGGAGAACU-CUGUUCUC-GCCUUUACUAGGAGGUGCUGU-GCGUGCGGGAGGCGACCAUAUUUCAUUG-UUCCCUCCUGCUUAUAGGAUCAUUGCUUUA
ABCM01000003.1/261261-261464 AACGAUACUUUGC-AGGACAGACCUCGGAAAUCUUAGCAAGCAAAGC-AC-G-GUGAUAGAGU-GCCCGAUUUCUGUAUAUUUGUG-CAGAAAUAUGGGCGUUCUCCGUAG-GCUUGCUAGAGGGUUUCGGCUCUU-ACCUCUCCGAGGGGGUGUUCU-GCAUGCGGGGAGCGACCAUAUUUC-UUGCUUCCCUCUUUU----AGAAUCAUUGCUUUA
ABCM01000010.1/52472-52680   AACGAUACUUUGCAAAAACAGACGUCGGAAAUCUAAACAGGCAAAGC-GCGGUGAAAAUGAAU-GCCCGGUUUCUGUAUAUUUGUG-CGGAAAUAUGGGCGUUCUCCGUAG-GCCUGUUAGAGAGUUUCGGCUCUCGUCCCCUCCGACGGGGUGUUUUUGCAUGCGGGGAGCGCCCAUAUUUC-UUGCUUUCCUCUUUU----AGAAUCAUUGCUUUA
#=GC SS_cons                 :::::::::::(((((((((--((((((,,,,,,<<<<<<<<--<.<<<<<<.<-----<<<<-<<<<<<<<<<<<__________.>>>>>>>->>>>>>>>>>>>>>>>>>>>>>>>><<<<<<____>>>>>>.,AAA,,))))))aaa)))))))))--<<<<<<<<-<<-<<______._>>->>->>>>>>>>..:::::::::::::::::
#=GC RF                      AACGAaACUUUGCaacggcaGACcucGgAAAuCucagcaaGCAAa.gcacGG.auugAuggacaGccCgauuuCuGUAacUUUauc.CaGaaauAuGggCguccuCCgugcuGCuugcugggGagcUUcggcuCcc.uCCuuucCgagGgGGugccguuGCgUgcggGagGCgaCCaUAUUUu.UuGcuccCcuCcugc..aUAGgAUCAUUGCUUUA
//
# STOCKHOLM 1.0

#=GF AC   RF01716
#=GF ID   PhotoRC-I
#=GF DE   PhotoRC-I RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   45.00
#=GF TC   52.00
#=GF NC   39.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   PhotoRC_RNA_motifs
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   65


AACY023623377.1/287-246        UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCCUCG-GAGAC
AACY020357826.1/692-649        AGGCAGGGCAUCCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
BX569694.1/85338-85295         AGGCAGGGCACACCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY020002466.1/34-75          AGGCAGGACUUCU--GUCCUUUCUUAAACC-GUCCCCUCG-GGGGC
AACY020555888.1/1588-1547      UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCCUCG-GAGAC
AACY023381520.1/1204-1161      AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY020230102.1/641-682        UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCCUCG-GAGAC
AANP01000006.1/165195-165236   UGGCAGGGCAUCCCUGCCCUUCCGU-AACU--GCUCUUCG-GAGUU
AACY023856811.1/682-725        AGGCAGGGCUUUCCUGCCCUUCCUUAAAUC-GUUCCUUCG-GGAAC
AACY020358569.1/853-811        AGGCAGGGCCCCCU-GCCCUUCCUUAAACC-GUCCCUUCG-GGGGC
AAUA01000001.1/704108-704066   CGGCAGGGCUUCCU-GCCCUUCCGU-AACCCGUCUCUUCG-GAGAC
AACY023836901.1/556-515        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
BX569694.1/302425-302468       AGGCAGGGCACACCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY020238074.1/633-592        UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCCUCG-GAGAC
AACY022984900.1/632-589        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAGC
AACY020529854.1/1240-1199      UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY022410753.1/109-66         AGGCAGGGCUUUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY020523621.1/456-415        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY022923429.1/153-110        AGGCAGGGCUUUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY022976215.1/127-170        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY023834750.1/421-380        CGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCCUCG-GAGCU
CP000110.1/311054-311011       AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGGAC
AACY022383745.1/671-628        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY023810594.1/196-237        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY023869287.1/634-676        AGGCAGGGCUACCU-GCUCUUCCUUAAACC-GUCCCUUCG-GGGGC
AACY020489273.1/1935-1892      AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
CP000110.1/510580-510623       AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGGAC
AACY022913798.1/22-63          CGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY023829657.1/1220-1179      CGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY023841191.1/1433-1392      UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
CP000435.1/2093117-2093075     CGGCAGGGCAUCCU-GCCCUUCCGU-AACC-GUCUCCUUGUGAGAC
AACY020970686.1/333-290        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
CT971583.1/1915281-1915241     UGGCAGGGCAUCCU-GCCCUUCCGU-AACC--GCUCUUCG-GAGCA
AACY022150842.1/460-501        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY020529150.1/730-771        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY020363125.1/1324-1281      AGGCAGGGCGUCCCUGCCCUUCCUUAAAUC-GUUCCUUCG-GGAAC
AAOK01000001.1/197766-197807   UGGCAGGGCAUUCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCC
AACY021570204.1/746-787        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AACY023816053.1/812-853        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
CP000435.1/372998-372956       CGGCAGGGCAUCCU-GCCCUUCCGU-AACC-GUCUCCUUGUGAGAC
AACY021375498.1/405-363        AGGCAGGGCUACCU-GCCCUUCCUUAAACC-GUCCCUUCG-GGGGC
AANP01000005.1/140760-140801   UGGCAGGGCAUCCCUGCCCUUCCGU-AACU--GCUCUUCG-GAGCU
AACY021170829.1/357-400        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
CP000097.1/1945369-1945412     AGGCAGGGAUUCCUGUCCCUUCCAUAAACC-GUCCCCUCG-GGGGC
AACY023021307.1/72-115         AGGCAGGGCGUCCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY022012151.1/406-363        AGGCAGGGCAUCCCUGCCCUUCCUUAAACC-GUCCCUUCG-GGGGC
AACY021975488.1/320-279        UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCUUCG-GAGAC
AACY023861064.1/1393-1436      AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY022150667.1/535-576        UGGCAGGGCUUCCU-GCCCUUCCGU-AACC-GUCUCCUCG-GAGAC
AAUA01000004.1/159482-159440   CGGCAGGGCUUCCU-GCCCUUCCGU-AACCCGUCUCUUCG-GAGAC
AACY022192565.1/241-199        AGGCAGGGCUACCU-GCUCUUCCUUAAACC-GUCCCUUCG-GGGGC
ACNY01000005.1/1126774-1126731 AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY020542254.1/1310-1353      AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY021083976.1/176-133        AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY023406904.1/1134-1177      AGGCAGGGCUUUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AAOK01000002.1/170526-170567   UGGCAGGGCAUUCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCC
CP000097.1/1741889-1741846     AGGCAGGGAUUCCUGUCCCUUCCAUAAACC-GUCCCCUCG-GGGGC
AACY022905865.1/478-437        UGGCAGGGCAUCCCUGCCCUUCCGU-AACC--GCUCUUCG-GAGCU
AATZ01000004.1/136676-136719   AGGCAGGGAUUCCUGUCCCUUCCAUAAACC-GUCCCCUCG-GGGGC
AACY023521750.1/1115-1073      AGGCAGGGCUACCU-GCUCUUCCUUAAACC-GUCCCUUCG-GGGGC
AACY023988443.1/35-78          AGGCAGGGCACACCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AACY023863310.1/1225-1182      AGGCAGGGCUCUCCUGCCCUUCCUUAAACC-GUUCCUUCG-GGAAC
AF156980.1/155-195             UGGCAGGGCAUCCU-GCCCUUCCGU-AACC--GCUCUUCG-GAGCA
AATZ01000002.1/657722-657679   AGGCAGGGAUUCCUGUCCCUUCCAUAAACC-GUCCCCUCG-GGGGC
AACY022125101.1/820-863        AGGCAGGGCAUCCCUGCCCUUCCUUAAACC-GUCCCUUCG-GGGAU
#=GC SS_cons                   :<<-<<<<<______>>>>>->>-------.<<<<<____.>>>>>
#=GC RF                        aGGCAGGGCuUCCCUGCCCUUCCuUAAACC.GuCCCUUCG.GGGaC
//
# STOCKHOLM 1.0

#=GF AC   RF01717
#=GF ID   PhotoRC-II
#=GF DE   PhotoRC-II RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   PhotoRC_RNA_motifs
#=GF SQ   445


AACY022793910.1/307-403   CAUCCAAU---GCAAA-CUGCUUUUA---------------------ACCGAGACCUA---U-A--GGCAG-GAU-AAUACU--U-CGUCUCUCAU---A-UCCAGUA-GCGAGGGGU--UGCUGGAAAUAAGUUUCGCA-
AACY022804648.1/571-479   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023124067.1/177-271   CACCAAUU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCACU
AACY023716334.1/821-909   GGACAUAC----UUUA-AUCCC--C-------------------CUAACCAAGACCAC--------GGGGU-UAU-A-------A-UGUCU-UCUU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUACCGUAUCGC
AACY023920504.1/982-1077  UCAUCAAU---GUUUG-CUCCC---G------------------CUAACCGAGACCUA---U----GGGAG-GGU-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUAGUAUCGC
AACY020142352.1/919-825   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY022017387.1/749-845   CCUCUGAG---AACAA-CUGCU-UUA---------------------ACCGAGACCUA---U-G--AGCAG-UAU-A--AGCA-UUAGUCUCUCAU---AUCCAUCAG-UGAAGGG-A--UUGGUGGAAAUAUAGUUUCGC
AACY023929284.1/914-1007  UACCGAA-----GUUU-UUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAA-GUA-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUAGUUUCGC
AACY020552511.1/2066-2164 AUCCAAUG----CACA-ACUGC-UCU------------------UAAACCGAGACCUAU--A-G--GCAGU-AUA-A--UAC--CUCGUCUCUAAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAAAGUAUCGC
AACY020328712.1/39-133    UAACCGUU---GUGAA-CACCCCGUA--------------------AACCGAGACCUC---U-A--GGGUG-UCU-A--AAU--CACGUCUCUAAU---A-UCCUGUC-U-UAGGG-U--GACAGGAA-AUAGUAACUCCA
AACY023708834.1/794-881   UGACAUUA----UAAU-CCCCC---U--------------------AACCGAGAUC-----A----UGGGG---U-AAUAAU-----AUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUCCGUAUCG
AACY022692203.1/168-262   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY020225241.1/1153-1249 UAGUGGUA--CAUUCU-CUCCC----------------------CAAACCGAGACCUA---U-A--GGGAG-AAU-A--AAU--UAUGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUUAAUAUCG
AACY021797428.1/608-510   CCCUGUUG----CACA-ACUGC-UCU------------------UAAACCGAGACCUAU--A-G--GCAGU-CUA-A--UAC--CUCGUCUCUAAU---A-UCCAGAA-GGGAAGGGAU-UUCUGGAA-AUAUAGUAUCAC
AACY021822626.1/694-599   CCUCCUUU----GAAG-ACUGC-UCU------------------CAAACCAAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUUUUAU-----CCAGUAG-U-GAGGG-A--UUACUGGAAAUAAGUUUCGCA
AACY020214670.1/1578-1485 UAAGACA-----UUCU-CUCCC----------------------CAAACCGAGACCUA---C-A--GGGAG-AAU-A--AAU--UACGUCUCUCAU---A-UCCACCA-UUAAAGGGAC-UGGUGGAA-AUAUUAAUAUCG
AACY023475852.1/636-724   -GCUCAUC--GUAUCA-UCCCC--CU--------------------AACCAAGACC-----A-U--GGGGU-UAU-A-------A-UGUCU-UCUU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUACCGUAUCGC
AACY022342374.1/717-812   -UACCUUA--UAUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GGU-A--AAU--UACGUCUUUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAAAGUAUCGC
AACY023923076.1/240-335   --UCAUCAA-AGUUUG-CUCCC--GC------------------U-AACCGAGACCUAU-------GGGAG-GGU-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUAGUUUCGC
AACY022180667.1/475-573   AUAAACUU---ACACA-CUGCU---C------------------CCAACCGAGACCUAC--GUA--GGCAG-UAUAA--UACA-U-CGUCUCUCAU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY020234178.1/863-955   UUUCUA------UGUG-CUCCC--CG------------------CAAACCGAGACCUA---U-A--GGGAG-GUU-A--AAC--G-AGUCUCUCAU---ACCUUUUCC-U-GAGGG-U--GGAAAAGGAAUAUUUAAUUCA
AACY020907537.1/492-396   GAACAUAU--AUUCUG-CUCCC--CU------------------UCAACCAAGACCUAU--A----GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022224056.1/667-762   -CCUCCUC---UGAAGACUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACC--U-CGUCU-UC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023239128.1/1153-1248 UAACUGUU---CUUAA-CACCC--CU------------------CAAACCAAGACCUCU--A----GGGUG-UAU-A--AAC--A-CGUCUUUCAU---A-UCCUUGC-CUUAGGG-UG-GCGAGGAA-AUAGUAACUCCA
AACY020122437.1/1969-1875 UACCAAUU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCACU
AACY023417859.1/928-1023  -UACCUUA--UAUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GGU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY021146200.1/880-794   UUGCUCAC----AUAA-UCCCU----------------------CUAACCGAGAUCA---------CGGGG-GUU-A---------CAUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUUAUAUCGC
AACY022594866.1/682-587   UAACUGUU---UGUAA-CACCC--CU------------------CAAACCAAGACCUAU--A----GGGUG-UCU-A--AAC--A-CGUCUUUCAU---AUCCUAGAC-U-UAGGG-U--GUCUGGGAAAUAGUAACUCCA
AACY020634157.1/482-579   UAACAGUU----GUUC-CUCUU-UCA---------------------ACCGAGACCUA---U-G--GGGAG-GUU-A--AACA-U-AGUCUCUCAUCUUA-CCUUCAC-UUGAGGG-UG-GUGAAGGAAAUCGGUAAAUUG
AACY021021950.1/400-307   UACCGAA-----GUUU-UUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAA-GUA-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAAAGUAUCGC
AACY020480001.1/357-452   -UACCUUA--UAUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GGU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY020115700.1/501-594   -CACCUCA--UAUGUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY022770840.1/111-202   UAACAA----GUUCCU-CUUCC--UA---------------------ACCGAGACCUA---U-G--GGGAG-GUU-A--AACA-C-AGUCUCUCAU---A-UCCCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
AACY020216953.1/816-912   ACCCAUUG----UGCA-ACUGC-UCU------------------CAAACCAAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUUUC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020107854.1/1099-1199 UCACCCUGA-GUACAA-CUGCUCUUA--------------------AACCGAGACCUA---U-A--GGCAG-UAU-A--AGUA-UUAGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY021199287.1/407-312   --UCAUCAG-UGUUUG-CUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAGGGUA-A--AAU--A-CGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAAAGUAUCGC
AACY021705995.1/572-477   UAACACAU---AUUUG-CUCCC--CU------------------UCAACCAAGACCUAU--A----GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY020214802.1/148-239   UCAUAU------UCUG-CUCCC--GC------------------UUAACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCU
AACY020205504.1/2313-2406 UACCACAU---UCUUG-CUCCC---G------------------CUAACCAAGACCUA---U----GGGAG-GAU-A--AAU--UACGUCU-UUAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY021514883.1/887-790   UAAUCUUA----CACA-CUGCUCCCA---------------------ACCGAGACCUA---U-GUAGGCAG-UAUAA--UACA-U-CGUCUCUCAU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY020098520.1/483-575   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCU
AACY021459371.1/670-754   UCACAUAU----AUUC-CCUCU------------------------AACCGAGAUCA---------UGGGG-GUU-A---------CAUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAAUCGUAUCG
AACY023861468.1/1427-1523 UAACUUGG---UGUAA-CACGCCUUA----------------------CCGAGACUAAA--C-A--GCGUG-UCUAA--AAAA-C-AGUCUCUCAU---ACCUCAGGC-G-GAGGG-U--GUCUGAGGAAUAAUCUAACUU
AACY023734147.1/466-381   UCAUCAUA----UAUU-CCCUC---U--------------------AACCGAGAUC-----A-C--GGGGG--UU-A---------CAUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUCCGUAUCG
AACY021356776.1/721-623   UCACCUUUUCUAUGUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAAAGUAUCGC
AACY022594455.1/257-162   UUACUGUU---CGUAA-CACCCCU-U------------------C-AACCAAGACCUAU--A----GGGUG-UCU-A--AAA--A-CGUCUUUCAU---A-CCUGUGU-CUAAGGG-UG-AUACAGGA-AUAGUAAAACCA
AACY022818170.1/323-418   UUACCAUU---GUUUG-CUCCC---G------------------CUAACCAAGACCUA---U----GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUAGUUUCGC
AACY021840524.1/491-398   UACCACAA---UCUUG-CUCCC--GU------------------U-AACCAAGACCU----A-U--GGGAG-GAU-A--AAU--UACGUCU-UAAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023435099.1/169-78    UAACAA----GUUCCU-CUUCC--UA---------------------ACCGAGACCUA---U-G--GGGAG-GUU-A--AACA-C-AGUCUCUCAU---A-UCCCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
AACY020200453.1/161-60    UAACCCAUC-GUACAA-CUGCU--CC------------------C-AACCAAGACCUUU--GUA--GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGGAAAUAAGUUUCGCA
AACY023528958.1/263-155   UAACGUAA--CACCAU-CUUGG---AGAACCGGACUAAUACUCCU--ACCGAGAC-UA---U----CCAAG---U-A--AAA--UACGUCUCUCAU---A-CCUGUCU-CUGAGGG-UG-AGACAGGA-AUACUAUAACUU
AACY023539113.1/755-655   UAACCGUGC-GUACAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCGAAAGUAAAGGGAU--UUUCGGAAAUAAGUUUCGCU-
AACY023488110.1/332-239   UGAUCAUA---UUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UAAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020771543.1/607-513   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUAGUAUCGC
AACY022948636.1/252-155   AAUCUUUU---GUAAA-CUCCC--CG------------------UAAACCGAGACCUC---U-A--GGGAG-UAU-A--AAUG-CACGUCUCUAAU---A-CCCACAC-UGGAGGG-UG-GUGUGGGA-AUAUCAUAACCG
AACY020343018.1/838-746   UAAUUCUU----GUAG-CACCCCUUA--------------------AACCAAGACCUA---U-A--GGGUG-CAU-A--AAA--A-CGUCUUUCAU---A-UCCUCGC-U-AAGGG-U--GCGAGGAA-AUAGUAACUCCA
AACY021751545.1/556-648   UAACACAU----UUCA-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UGCUGGAA-AUAAGUUUCGCA
AACY020781986.1/301-397   UUGAUCAG---AUUUG-CUCCC--GU------------------UUAACCGAGACCU----A-U--GGGAG-GAU-A--AAA--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAAAGUAUCGC
AACY020214560.1/763-670   UAACACAU---AUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY020127084.1/700-605   CCUCCUUU----GAAG-ACUGC-UCU------------------CAAACCAAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUUUUAU-----CCAGUAG-U-GAGGG-A--UUACUGGAAAUAAGUUUCGCA
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AACY020184022.1/2592-2685 UAACGA-----CUGUG-CUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAG-GGU-A--AAU--CACGUCUCUCAU---A-UCCACAC-UAGAGGG-UG-GUGUGGGUGAGAUUUAUAAAU
AACY020216550.1/801-899   AUCCAAUG----CACA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUCUCAU---AUCCGACAG-UGAAGGG-A--UUGUCGGAAAUAAGUAUCGCU
AACY023380453.1/1183-1275 UAACACAU----UUCA-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UAAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023860341.1/1220-1316 UGAUCAUA---UUCUG-CUCCCCUUA--------------------AACCAAGACCUC---U-A--GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAAUAUCGCA
AACY020212970.1/394-297   CAUCCAUU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-CUA-A--UAC--UUCGUCUCUCAU---A-UCCUGUA-GCGAGGGGU--UACAGGAAAUAAGUUUCGCA-
AACY023654246.1/702-798   UUGCUCAU---AUAUU-UCCCC--UG---------------------ACCAAGACUAAA--C----GGGGU-UAU----AAU--U-AGUCU-UCAUCAUG-CCUAUAGAUGCAAGGGUA-CUAUAGGAAAUCAAGUUCUGC
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AACY023553929.1/181-99    UUACAACA--CACACG-CUCCC--CG------------------UAAACCAAGACCUA---U-A--GGGAG-GAU-A--AAU--UACGUCUUU---------------UCUUACCCUUC--------AUAUACCCGUACUU
AACY020183006.1/682-774   UAACAUU----GUCCA-CACCC--GC------------------U-AACCGAGACCUA-----U--GGGUG-UAU-A--AAU--UACGUCUCUCAU---A-UCCCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
AACY020739733.1/475-380   UCACUUUC----CAAA-CACCC--CU------------------CAAACCGAGACCUAU--A----GGGUG-UAU-A--AAU--CACGUCUCUCAU---A-CCAGCCC-UGGAGGG-UA-GGGUUGGA-AUAUUUUACCUA
AACY022490730.1/249-163   UUGCUCAC----AUAA-UCCCU----------------------CUAACCGAGAUCA---------CGGGG-GUU-A---------CAUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUUAUAUCGC
AACY020862294.1/398-493   ACACCAUU---GUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY023400829.1/763-857   CAACAC------CUAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022109084.1/416-326   UAACAUA-------CC-CACGC----------------------CUCACCAGGACUAAA--C-A--GCGUG-GUA-A--AACA-ACAGUCCUUCAU---A-CCUCUGC-U-UAGGG-U--GCAGAGGA-AUAGUAACUCCA
AACY020506831.1/1718-1823 UAACACAA----CAUC-UUGGA----GAACCGGACUAAUACUCCU--ACCGAGAC-UA--------UCCAA-GUA-A--AAU--A-CGUCUCUCAU---A-CCUGGCC-UGGAGGG-UA-GGUCAGGA-AUACUAUAACUU
AACY020153485.1/629-724   UACCUUAU---AUGUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAAAGUAUCGC
AACY024002773.1/359-453   UCACCAUA----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY022345084.1/518-610   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCU
AACY020177026.1/651-540   UGACAGUU----GUUC-UUGCU----GAAACGGGACGAUAACUCCUUACCGAGAC-UA--------UGCAA-GUA-A--AAU--A-CGUCUCUUAUGCUACCUUUCUC-UUGAGGG-UA-GAGAAAGG-AAAUCAAGUAAA
AACY020489559.1/941-848   UAACACAU---UUCAG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020883826.1/213-306   UAACACAU---AACUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022715299.1/53-147    UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY020456986.1/3902-3997 UAACUGUU---CUUAA-CACCC--CU------------------CAAACCAAGACCUCU--A----GGGUG-UCU-A--AAC--A-CGUCUUUCAU---AUCCCAGAC-U-UAGGG-U--GUCUGGGAAAUAGUAACUCCA
AACY024005900.1/761-670   UAACAA----GUUCCU-CUUCC--UA---------------------ACCGAGACCUA---U-G--GGGAG-GUU-A--AACA-C-AGUCUCUCAU---A-UCCCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
AACY020165724.1/228-137   UAACGA----GUUCCU-CUUCC--UA---------------------ACCGAGACCUA---U-G--GGGAG-GUU-A--AACA-C-AGUCUCUCAU---A-UCCCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
AACY020138775.1/1659-1754 CAACACC-----GACA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY021652828.1/429-334   AAAAUGUU---CUGGA-CACCCCGUA--------------------AACCAAGACCUC---U-A--GGGUG-UAU-A--AAU--A-CGUCUUUCAU---A-CCCACGC-CCGAGGG-UG-GUGUGGGA-AUAGUAAAACCG
AACY020434003.1/1374-1279 GAUAAUUA---AAAUA-CUCCC----------------------CAAACCGAGACCUA---C-A--GGGAG-AAU-A--AAU--UACGUCUCUCAU---AUCCGUAAG-UGAAGGG-A--UUUACGGAAAUAUAAGUUUCG
AACY023483806.1/1623-1721 UUUCAACA--CCAUAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020541678.1/815-720   UAUCGUUA----CAAA-CUCUC--CG------------------CAAACCGAGACCUC---U-A--GGGAG-UAU-A--AAU--CACGUCUCUAAU---A-CCUGACC-UGGAGGG-UA-GGUCAGGA-AUAUUCUACCUA
AACY021444878.1/162-64    UAACCCUG--CGUAAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCUGUA-GCGAGGGGU--UACAGGAA-AUAAGUUUCGCA
AACY023420221.1/1163-1258 CAACACUU---UCCUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAAAGUAUCGC
AACY022141534.1/419-325   AUCCGUUG---GACCA-CACCC--CG------------------CAAACCGAGACCUC---U-A--GGGUG-UCU-A--AAA--CACGUCUCUUAU---A-UCCUGUC-U-AAGGG-U--GACAGGAA-AUAGUAACUCCA
AACY023935879.1/1400-1493 UAACGUUU----UUUU-GUCGCCUUA----------------------CCAAGACUAAA--C-A--GCGAC-AUU-A--AAUA-ACAGUCUUUCAU---A-CCUCUAC-U-AAGGG-U--GUAGAGGA-AUAGUAACUCCA
AACY023495939.1/1272-1180 UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY023991214.1/160-258   CUCCCUUG---UAGAA-CUGCUCUUA--------------------AACCGAGACCUA---U-A--GGCAG-UCU-AAUACU--U-CGUCUCUCAU---AUCCGAAAG-UGAAGGG-A--UUUUCGGAAAUAAGUAUCGCA
AACY023459804.1/993-898   UGACGU------ACAA-CUGCUCUUA--------------------AACCGAGACCUA---U-A--GGCAG-UAUAA--AAC--CUCGUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUAGUAUCGC
AACY021261407.1/202-107   -CAUCCAA--UGCAAA-CUGCU---U------------------U-AACCGAGACCUGU--G----AGCAG-UAU-A--AGCAAU-AGUCUCUCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAA-AUAAGUUUCGCA
AACY020923311.1/215-307   UAUCAAUA----UCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCG-UCAU---A-UCCAGUA-GUGAGGG-AG-UACUGGAAAUAAGUUUCGCA-
AACY020328935.1/2109-2189 ---------------A-CACGC--CU------------------C--ACCGAGAC-UAAACA----GCGUG-UUU-A--AAAAAU-AGUCUCUAAU---A-CCUCAGG-CGGAGGG-UG-UCUGAGGA-AUAUUCUA----
AACY023481124.1/597-499   UCCCUCAG---UAGAA-CUGCUCUUA--------------------AACCGAGACCUA---U-A--GGCAG-UAU-AAUACU--U-CGUCUCUCAU---AUCCGAAAG-UGAAGGG-A--UUUUCGGAAAUAAGUAUCGCA
AACY022470867.1/570-665   UAACAAGU----CUUC-ACACC-CCU------------------CAAACCAAGACCUCU--A-G--GGUGU-AUA-A--AAA----CGUCUUUCAU---A-UCCUUGC-CUUAGGG-UG-GCGAGGAA-AUAGUAAAACCA
AACY020331758.1/975-882   UCACUA------AUCA-CUCCC--CU------------------CCAACCAAGACCUAU--A----GGGAG-UAU-A--AAU--UACGUCUUUCAU---A-UCCGAAA-GUGAGGGAU--UUUCGGAA-AUAAGUUUCGCA
AACY021863626.1/795-700   UCACCCAU---UUUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY020154769.1/1380-1477 UAACCCUU--GCUACA-AGUGC-UCU------------------CAAACCAAGACCUAU--A-G--GCACU-AUA-A--UAC--UUCGUCUUUUAU-----CCAGUAG-U-GAGGG-A--UUACUGGAAAUAAGUUUCACA
AACY020493838.1/1722-1625 CAUCCAGU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-CUA-A--UAC--UUCGUCUCUCAU---A-UCCUGUA-GCGAGGGGU--UACAGGAAAUAAGUUUCGCA-
AACY023466118.1/1409-1313 ----AAAGC-GACAUCUUGACC-CCU------------------CAAACCGAGACCUAU--A-G--GGUCA--UU-A--AAC--UACGUCUCUAAU---A-CCUUCAC-CUGAGGG-UG-GUGAAGGA-AUACUUAACACA
AACY023484917.1/848-751   CAUCCAUU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-CUA-A--UAC--UUCGUCUCUCAU---A-UCCUGUA-GCGAGGGGU--UACAGGAAAUAAGUUUCGCA-
AACY022815598.1/365-457   UAUCAGUG----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCGA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY023512790.1/1405-1310 UAACACAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCGUUAAG-UGAAGGG-A--UUUAACGAAAUAUAGUAUCGC
AACY020254233.1/393-297   CCUCACUA---UCCAA-CACGC----------------------CUCACCAAGACUAAA--C-A--GCGUG-UAU-A--AACA-AUAGUCUUUAAU---ACCUCAGGC-G-GAGGG-U--GUCUGAGGAAUAUUCUAACUU
AACY023503994.1/1166-1259 UAACACAU---UACAG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020068528.1/441-550   UCACUUUUU-CUAUCC-UUGGA----GCAACGGGUCUAAUCACCUU-ACCGAGAC-UA--------UCCAA-GUA-A--AAU--A-CGUCUCUCAU---A-CCUCUGG-UGGAGGG-UG-CCAGAGGA-AUACUUCAUACA
AACY022768281.1/706-612   UAACAUU---GUCUUC-CUGCC--GU------------------UUGACCGAGAC-UA--------GGCAGGGUU-ACCAAU--C-CGUCUCUCAU---A-UCCCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
AACY023419504.1/1141-1047 AUCCGUUG---GACCA-CACCC----------------------CAAACCGAGACCUA---U-A--GGGUG-UCU-A--AAU--CACGUCUCUCAU---ACCUCCAGC-U-GAGGG-U--GCUGGAGGAAUAGUAAAACCA
AACY020206528.1/791-884   CACUAAUU---AUUUG-CUCCC---G------------------CUAACCAAGACCUA---U----GGGAG-GAU-A--AAU--UACGUCU-UAAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCACU
AACY022925814.1/56-151    ACACCAUU---GUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY024100673.1/648-745   CAUCCAAU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-CUA-A--UAC--UUCGUCUCUCAU---A-UCCUGUA-GCGAGGGGU--UACAGGAAAUAAGUUUCGCA-
AACY020184022.1/3994-4087 UCUCAUAA---ACACC-UUGCC-CCA----------------------CCAGGAC-UAA--U-G--GGCAA-GUA-A--AAU--C-CGUCCUUCAU---A-UCUGCGA-UGGAGGG-UG-UCGCAGAACAUAACUGUAACU
AACY022769557.1/606-512   UAAUAUU---GUCUUC-CUGCC--GU------------------UUGACCGAGAC-UA--------GGCAG-GAUUACCAAU--C-CGUCUCUCAU---A-UCCCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
AACY021364709.1/428-331   UAUCAAAC---GCACA-CUGCU--CG------------------CAAACCGAGACCUA---U-A--GGCAG-UAUAA--UACA-U-CGUCUCUCAU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY023486714.1/1380-1473 UAACACAA---UACAG-CUCCC---G------------------CUAACCAAGACCUA---U----GGGAG-GAU-A--AAU--UACGUCU-UAAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY021726107.1/190-93    UUCAACAC---CAUAA-CUGCU--CC------------------C-AACCAAGACCUCU--GUA--GGCAG-UAU-AAUACU--U-CGUCUUUC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022196968.1/503-409   ---CAAUUC-AAUCUU-GCUCC--CG------------------CUAACCGAGACCUA---U-G--GGAG--AAU-A--AAU--UACGUCUCUAAU---A-CCUUCAC-CUGAGGG-UG-GUGAAGGA-AUAUUUAAUUCA
AACY020328953.1/2114-2209 UAAUCCUU----GUAA-CACGC-CUG---------------------ACCGAGACUAAA--C-A--GCGUG-UAU-A--AACA-ACAGUCUCUCAU---A-CCAACUC-UGGAGGG-UA-GAGUUGGA-AUAUUUUACCUA
AACY020139214.1/1396-1490 UAACACAU---UUCAG-CUCCC--GC------------------UUAACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGUAA-GUGAGGGAU--UUACAGGA-AUAAGUUUCGCA
AACY022719080.1/203-297   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY022565375.1/42-136    UAACACAU--AUCUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCGUAA-GUGAGGGAU--UUACGGAA-AUAUGUUUCGCA
AACY023233086.1/917-1012  UAACGCUU---CUUAA-CACUC--CU------------------CAAACCAAGACCUAU--A----GGGUG-UCU-A--AAC--A-CGUCUUUCAU---A-UCCUUGC-CUUAGGG-UG-GCGAGGAA-AUAGUAAAACCA
AACY022658321.1/555-662   AAACUUUU----GUGA-CUUGC---UGAAACGGGACUAAUCUCCUC-ACCGAGGC-UA---A----GCAAG---U-A--AAA--UACGCCUCUCAU---AUCCUUACC-U-GAGGG-U--GGUAAGGAAAUAAGUACCUCC
AACY023729224.1/1534-1622 -GCUCAUC---GUAUC-AUCCC--C-------------------CAAACCAAGACCAA--------GGGGU-UAU-A-------A-UGUCUUUU-U---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUCGUAUCGC
AACY021524041.1/364-458   CAACAC------CUAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020593363.1/473-567   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY023999425.1/204-301   CAUCCAGU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-CUA-A--UAC--UUCGUCUCUCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAAAUAAGUUUCGCA-
AACY020125448.1/662-754   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCU
AACY020604424.1/19-113    UAAUGUGU--UGUGAA-CACCC--CA------------------UAAACCGAGACCUC---U-A--GGGUG-UAU-A--AAC--A-CGUCUCUCAU---A-UCCUCUC-U-AAGGG-U--GAGAGGAG-AUAGUAACUCCA
AACY020541110.1/980-885   UAUCGUUA----CAAA-CUCUC--CG------------------CAAACCGAGACCUC---U-A--GGGAG-UAU-A--AAU--CACGUCUCUAAU---A-CCUGACC-UGGAGGG-UA-GGUCAGGA-AUAUUCUACCUA
AACY021019750.1/558-465   UAAGGCA-----UUUU-CUCCC-CUA---------------------ACCGAGACCUA---U-A--GGGAG-AAU-A--AAU--UACGUCUCUCAU---A-UCCACCA-UUAAAGGGAC-UGGUGGAA-AUAUUAAUAUCG
AACY021788358.1/711-618   UAACACAU---UUCAG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGUAA-GUGAGGGAU--UUACAGGA-AUAAGUUUCGCA
AACY020273112.1/689-603   ---UCAUC---AUAUC-AUCCC--C-------------------CUAACCAAGACCAC--------GGGGU-UAU-A-------A-UGUCU-UCUU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUCGUAUCGC
AACY020113996.1/1469-1564 CCUCCUUU----GAAG-ACUGC-UCU------------------CAAACCAAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUUUUAU-----CCAGUAG-U-GAGGG-A--UUACUGGAAAUAAGUUUCGCA
AACY020340005.1/2082-1990 UAACAUA-------CC-CACGCCUUA----------------------CCAGGACUAAA--C-A--GCGUG-GUA-A--AACA-ACAGUCCUUCAU---A-CCCACGA-UGGAGGG-UG-UCGUGGGA-AUAUUUUAUUCG
AACY021952587.1/229-324   GAACAUAU--AUUCUG-CUCCC--GU------------------UUAACCAAGACCU----A-U--GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020540908.1/831-923   UAACAUA-------CC-CACGCCUUA----------------------CCAGGACUAAA--C-A--GCGUG-GUA-A--AACA-ACAGUCCUUCAU---A-CCCACAC-UGGAGGG-UG-GUGUGGGA-AUACUACUACCG
AACY020332783.1/1228-1323 UCAAUAUU---ACAUA-CUCCC--CU------------------UCAACCAAGACCUAU--A----GGGAG-UCU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023855625.1/789-882   ----ACUCA-UUGUAA-ACACG-CCU------------------C--ACCAAGAC-UAAACA-G--CGUGU-CUA-AACAAC----AGUCUUUCAU---A-CCUUGCC-U-UAGGG-U--GGCAAGGA-AUAGUAACUCCA
AACY023416394.1/1534-1440 GAACACAU---UACUG-CUCCC--GC------------------UUAACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY022727697.1/663-755   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCU
AACY021840888.1/199-105   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-AAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY021720533.1/195-287   GUACGUUA----CAUU-CUCCU----------------------CAAACCGAGACCUAU-------AGGGA-AUU-A--AAA--CACGUCUCUAAU---A-CCAACCC-UGGAGGG-UA-GGGUUGGA-AUACUUAUAUCA
AACY021691325.1/300-195   UCACCUUU----UCUC-UUGGA----GACCCGGACUAACACUCCU-A-CCGAGAC-UA--------UCCAA-GUA-A--AAU--A-CGUCUCUCAU---A-CCAACUC-UGGAGGG-UA-GAGUUGGA-AUACUAUACUCA
AACY020326543.1/320-223   UUACAUGU--CUCACC-CACGC----------------------CUCACCAGGACUAAA--C-A--GCGUG-GUA-A--AACA-AGAGUCCUUCAU---A-CCCACUC-UGGAGGG-UA-GAGUGGGA-AUACUAUACCCA
AACY020944351.1/778-871   UAACACAU---UUCAG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGUAA-GUGAGGGAU--UUACAGGA-AUAAGUUUCGCA
AACY024112006.1/155-58    ACACUUCG---UCCUA-CUCCC--CG------------------CAAACCGAGACCUC---U-A--GGGAG-UCU-A--AACG-CACGUCUCUAAU---A-CCUACGC-CUGAGGG-UG-GUGUAGGA-AUAUUCUAUCCG
AACY020216207.1/910-812   UAACACAA--UAUUCG-CUCCCCCUC--------------------AACCGAGACCUA---U-A--GGGAG-GAU-A--AAU--UACGUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUUAAUAUCG
AACY023210938.1/548-641   UAACGGUUC-GUAACA-CUCCC----------------------CAAACCAAGACCUA---U-A--GGGUG-UAU-A--AAA--A-CGUCUUUAAU---A-CCUCUGC-C-UAGGG-C--GCAGAGGA-AUAGUAAAACCA
AACY020003728.1/1075-980  UAACUGUU---CUUAA-CACCC--CU------------------CAAACCAAGACCUCU--A----GGGUG-UCU-A--AAC--A-CGUCUUUCAU---AUCCCAGAC-U-UAGGG-U--GUCUGGGAAAUAGUAACUCCA
AACY020738172.1/407-502   ACACCGAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY020206835.1/1949-2041 UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCU
AACY022807090.1/853-759   UAACAU------CGCC-ACUGC-UCU------------------CAAACCAAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUUUC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020217555.1/1529-1625 ACCCAUUG----UGCA-ACUGC-UCU------------------CAAACCAAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUUUC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020458534.1/1085-1179 AAUCAUUU----GUAA-CACCCCCCA--------------------AACCAAGACCUA---U-A--GGGUG-UAU-A--AAA--A-CGUCUUUCAU---AUCCCGGAC-U-UAGGG-U--GUCUGGGAAAUAGUAACUCCA
AACY020215065.1/2612-2705 U--CGUCAA-UAUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023420966.1/1266-1360 UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY021830790.1/479-386   UAACACAA---UACAG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020136505.1/924-832   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCU
AACY023921301.1/1161-1066 -UUCAUCU--CAGUUU-UUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAA-GUA-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAAAGUAUCGC
AACY023933052.1/1207-1304 UAAUGUGUU-GCAAAC-ACGCC-----------------------UCACCAAGAC-UAA--A-C--AGCGU-GUCUA--AACA-ACAGUCUUUCAU---A-CCUCAGA-UGGAGGG-UG-UCUGAGGA-AUAUUAAUACCG
AACY023696318.1/573-657   UCAUCUUA---AUAUA-CCCCU------------------------AACCGAGACCA---------CGGGG-----A-------AAAGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUACCAGUAUCG
AACY020973467.1/880-786   GAACAUAU---AUUUG-CUCCC--GU------------------UUAACCAAGACCU----A-U--GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023930995.1/1224-1332 AAUCUGUU--GUAAAC-UUGGA----GAAACGGGUCUAAUCACCUU-ACCGAGAC-UA--------UCCAA-GUA-A--AAU--A-CGUCUCUCAU---A-CCUGUGA-CGGAGGG-UG-UCGCAGGA-AUAAUAAUACUA
AACY024026143.1/67-160    GAUCAUA-----UUCA-CUCCCCGUA--------------------AACCGAGACCUA---U-A--GGGAG-GAU-A--AAU--UACGUCUCUCAU---A-CCCACAG-UGAAGGG-A--UUGUGGGA-AUAUAAGUUUCG
AACY022802203.1/187-93    ACACCAAU---AUUUG-CUCCC---G------------------CUAACCAAGACCUA---U----GGGAG-GAU-A--AAU--UACGUCU-UUAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY023448773.1/737-833   UCACCAUC----CAAA-CACGC-CUG---------------------ACCGAGACUAAA--C-A--GCGUG-UCU-A--AACA-AUAGUCUCUCAU---A-CCAACUC-UGGAGGGGUA-GAGUUGGA-AUAUUUUACCUA
AACY020142980.1/1379-1478 CAACAUAU---UCCUA-CUGCU---C------------------CCAACCGAGACCUAC--GUA--GGCAG-UAU-AAUACU--U-CGUCUCUCAU---AUCCGAAAG-UGAAGGG-A--UUUUCGGAAAUAAGUAUCGCA
AACY020491718.1/850-753   UAUCAAAC----GCAC-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUCUCAU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY020216716.1/723-817   UAACACAU--AUUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020129088.1/798-701   CAUCCAGU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-CUA-A--UAC--UUCGUCUCUCAU---A-UCCUGUA-GCGAGGGGU--UACAGGAAAUAAGUUUCGCA-
AACY020691323.1/394-303   UAACAA----GUUCCU-CUUCC--UA---------------------ACCGAGACCUA---U-G--GGGAG-GUU-A--AACA-C-AGUCUCUCAU---A-UCCCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
AACY022509971.1/485-390   -UACCUUA--UAUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GGU-A--AAU--UACGUCUUUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAAAGUAUCGC
AACY023362766.1/1078-1186 AAUCUCUU--GUAAAC-UUGGA----GAAACGGGUCUAAUCACCUU-ACCGAGGC-UA--------UCCAA-GUA-A--AAU--A-CGCCUCUCAU---A-CCUGUGG-CGGAGGG-UG-UCACAGGA-AUAUUAAUACUA
AACY020894010.1/406-313   CAACAC------CUAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023854054.1/879-977   GAACGUUGU-CUCACC-CACGC----------------------CUCACCAAGACUAAA--C-A--GCGUG-GUA-A--AAUA-AUAGUCUUUCAU---A-CCUACAU-CGGAGGG-UG-AUGUAGGA-AUAUCUUACUCG
AACY022798634.1/727-632   UGAUCAUA---UUCUG-CUCCCCUUA--------------------AACCAAGACCUA---U-A--GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020337501.1/583-678   GCACAUUC--GUCUAA-CACCCCGUA--------------------AACCGAGACCUC---U-A--GGGUG-UCU-A--AAU--CACGUCUCUCAU---A-CCUUGUC-U-AAGGG-U--GGCAAGGA-AUAGUAACUCCA
AACY020110951.1/1060-1153 UAACACAU---UUCAG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGUAA-GUGAGGGAU--UUACAGGA-AUAAGUUUCGCA
AACY021093162.1/280-185   -UAUCGUGA-CACUUG-UCGGC--UU---------------------ACCGAGAC-UCA--A-C--GUCGACAAU-A--AACA-UUAGUCUCUCAU---A-CCUCUCC-UUCAGGG-U--GGAGAGGA-AUAUUCUUUUCG
AACY022481264.1/374-286   UCCCAAUA--CAAAUC-UUGCC-----------------------CUACCGAGAC-UA--------GGCAA-GUA-A--AAU--C-CGUCUCUAAU---A-UCUUCUC-U--AGGGGU--GAGAAGAA-AUAAUAAACUCG
AACY023651945.1/411-324   UGACCUAC---UAUUC-CCCCU------------------------AACCGAGAUCA---------UGGGG-UUA-A--AAU-----AUCUCUCAU---AUCCGCCAG-UAAAGGG-A--UUGGUGGAAAUAAUCGUAUCG
AACY020217779.1/2318-2414 UGAUCAUA---UUCUG-CUCCCCGUA--------------------AACCAAGACCUC---U-A--GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAAUAUCGCA
AACY021776305.1/175-77    AACCCAUU--GUGCAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022735578.1/719-624   ACACCAUU---GUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY023453041.1/804-709   UCACUUUC----CAAA-CACCC--CU------------------CAAACCGAGACCUAU--A----GGGUG-UAU-A--AAU--CACGUCUCUCAU---A-CCCGACC-UGGAGGG-UA-GGUUGGGA-AUAUUUUACUCG
AACY023436991.1/741-834   UAACAAUU---GUCCU-CUUCC--UA---------------------ACCGAGACCUA---U-G--GGGAG-GUU-A--AACA-C-AGUCUCUCAU---A-UCCCCGC-U-AAGGGGU--GCGGGGAGCAUAGUAACUCCA
AACY021304347.1/102-6     UAACACAU---AUUUG-CUCCC--GC------------------UUAACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UAAU---A-UCGUUAAGUGAAGGGAU--UUAACGAAAAUAUAGUAUCGC
AACY024015778.1/826-734   CAUCAGUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAAAUAAGUUUCGCA-
AACY020169160.1/1058-952  UAACAUA-----GUUC-AUGGA----GAAACGGGAC-UCAUCUCCUUACCGAGAC-UA--------UCCAU-GUA-A--AAU--A-UGUCUCUCAU---A-UCCACAC-UGGAGGG-UG-GUGUGGAGCAUACUGAUACCA
AACY020248103.1/919-825   UAACACAU---AUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCACCA-GUGAGGGAU--UGGUGGAA-AUAUGUUUCGCA
AACY020487753.1/1012-1106 UCACCAUA----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY022622029.1/235-320   UUUCUCUA----CUAC-UUGCCGUUA----------------------CCGAGAC------U-A--GGCAG-GAC----AAU--C-CGUCUCUAAU---A-UCCUGAU-U--AGGG-C--UUCAGGAAAUAACUUAAUAC-
AACY021575021.1/634-540   CAACAC------CUAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY021002284.1/227-323   UAAUCAUU---UGUAA-CACGC----------------------CUCACCGGGACUAAA--C-A--GCGUG-UCUAA--AAAA-C-AGUCUCUAAU---A-UCCACUC-GCAAGGG-UA-GAGUGGAG-AUACUACUACCU
AACY022735139.1/761-666   UAACACAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCGUUAAG-UGAAGGG-A--UUUAACGAAAUAUAGUAUCGC
AACY022469240.1/151-233   UCACAU------AAUC-CCUCU------------------------AACCGAGAUCA---------CGGGG-GUU-A---------CAUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUUAUAUCGC
AACY024093090.1/9-104     UAACCAUU---UGUAA-CACCCCUUA--------------------AACCAAGACCUC---U-A--GGGUG-UCU-A--AAC--A-CGUCUUUCAU---A-UCCUUGC-CUUAGGG-UG-GCGAGGAA-AUAGUAAAACCA
AACY023491532.1/1169-1264 UAACACAU---AUUUG-CUCCC--CU------------------UCAACCAAGACCUAU--A----GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY020213240.1/1294-1389 UAACACAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCGUUAAG-UGAAGGG-A--UUUAACGAAAUAUAGUAUCGC
AACY020144177.1/1073-1169 ACCCAUUG----UGCA-ACUGC-UCU------------------CAAACCAAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUUUC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020203700.1/129-224   UAACACAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-AAU-A--AAU--UACGUCUUUCAU---A-UCGUUAA-GUGAAGG-GA-UUGAUGGAAAUAUAGUAUCGC
AACY020218091.1/691-783   UAUCAGUG----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY020203369.1/754-660   UAACACAU--AUUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020085804.1/5-100     UGACGU------ACAA-CUGCUCUUA--------------------AACCGAGACCUA---U-A--GGCAG-UAUAA--AAC--CUCGUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUAGUAUCGC
AACY020139044.1/1089-1186 CAUCCAGU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-AUA-A--AAC--UUCGUCUCUCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAAAUAAGUUUCGCA-
AACY021466897.1/361-269   CACCGUUG---GACCA-CACCC----------------------CAAACCGAGACCUA---U-A--GGGUG-UCU-A--AAU--CACGUCUCUCAU---A-CCUCAGC-U-AAGGG-U--GCUGAGGA-AUAGUAACUCCA
AACY020476512.1/908-1002  GAACACAU---UACUG-CUCCC--GC------------------UUAACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY020143056.1/1841-1747 UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY022694327.1/699-793   UCACCAUU----CUUG-CACCC---G------------------UUAACCGAGACCUA---U----GGGUG-GUU-A--AAU--UACGUCUCUCAU---AUCCAGUAG-UGAAGGG-A--UUACUGGAAAUAUAGUUUCGC
AACY020092358.1/1404-1309 CACCCAUU---GCAAA-CUGCU-UUA---------------------ACCGAGACCUG---U-G--AGCAG-UAUAAGCAAU----AGUCUCUCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAAAUAAGUUUCGCA-
AACY020335852.1/802-706   UUACGUUG---UACCA-CACGCCUUA----------------------CCGAGACUAAA--C-A--GCGUG-UUUAA--AAAA-C-AGUCUCUCAU---ACCUCAGGC-G-GAGGG-U--GUCUGAGGAAUAUUCUAACUU
AACY022940112.1/339-243   UAACUUGG---UGUAA-CACGCCUUA----------------------CCGAGACUAAA--C-A--GCGUG-UCUAA--AAAA-C-AGUCUCUCAU---ACCUCAGGC-G-GAGGG-U--GUCUGAGGAAUAAUCUAACUU
AACY021689927.1/555-461   UCACCAU-----CCAU-CACGCCUUA----------------------CCAGGACUAAA--C-A--GCGUG-ACU-A--AACA-ACAGUCCUUCAU---A-CCCACUC-UGGAGGG-UA-GAGUGGGA-AUACUAUACUCA
AACY021234892.1/315-415   UAACCCUGC-GUACAA-CUGCUCUUA--------------------AACCGAGACCUA---U-A--GGCAG-UCU-AAUACU--U-CGUCUCUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAAGUUUCG
AACY020684859.1/666-570   CAUCCAAU---GCAAA-CUGCUUUUA---------------------ACCGAGACCUA---U-A--GGCAG-GAU-AAUACU--U-CGUCUCUCAU---A-UCCAGUA-GCGAGGGGU--UGCUGGAAAUAAGUUUCGCA-
AACY021390108.1/143-48    CAUCCAUU---GCAAA-CUGCU--CU------------------CAAACCAAGACCUAC--A----GGCAG-UAU-AAUACU--U-CGUCUUU--U---A-UCCAGUA-GCGAGGGGU--UACUGGAA-AUAAGUUUCGCA
AACY020129998.1/2142-2237 -UACCUUA--UAUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GGU-A--AAU--UACGUCUUUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAAAGUAUCGC
AACY022569000.1/312-219   UAACACAA---UACAA-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UAAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022723243.1/277-182   ACACCAUU---GUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY023178247.1/107-202   UAACACAU---AUUUG-CUCCC--GC------------------UUAACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UAAU---AUCGUUAAG-UGAAGGG-A--UUUAACGAAAUAUAGUAUCGC
AACY020156426.1/2089-1997 UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCU
AACY022811130.1/694-786   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY022689748.1/507-415   UCACCAU-----AAUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAAAUAAGUUUCGCA-
AACY020590093.1/591-683   UCACUA------AUCA-CUCCC--CU------------------CCAACCAAGACCUAU--A----GGGAG-UAU-A--AAU--UACGUCU-UCAU---A-UCCGUAA-GUGAGGGAU--UUACGGAAAUAAGUUUCGCA-
AACY021143513.1/343-436   UAAGGCA-----UUUU-CUCCC-CUA---------------------ACCGAGACCUA---U-A--GGGAG-AAU-A--AAU--UACGUCUCUCAU---A-UCCACCA-UUAAAGGGAC-UGGUGGAA-AUAUUAAUAUCG
AACY020322392.1/1157-1253 ACACAUAU---AUCUG-CUCCCCUUA--------------------AACCAAGACCUA---U-A--GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCGAAA-GUGAGGGAU--UUUCGGAA-AUAAGUUUCGCA
AACY022817358.1/255-350   ACACCAUU---GUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY020171165.1/1310-1401 UAACGUUG----GACA-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-UAU-A--AGA--A-CGUCUCUCAU---A-UCCCGCU-U-GAGGG-U--GGCGGGAACAUAGUAACACCA
AACY023735672.1/1148-1059 CCUCAUUU---UUAUC-AUCCC--C-------------------CUAACCAAGACCAC--------GGGGU-UAU-A-------A-UGUCU-UCUU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUCCGUAUCG
AACY023373273.1/994-900   UCACCAUU----UUUA-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY021813748.1/131-36    UCACUUUC----CAAA-CACGC--CU------------------U--ACCGAGAC-UAAACA----GCGUG-UCA-A--AAAAAC-AGUCUCUCAU---A-CCUCAGG-CGGAGGG-UG-UCUGAGGA-AUAUUUUACCUA
AACY023886477.1/836-931   UAACACCA----CCUA-CUCCCCCUA--------------------AACCAAGACCUA---U-A--GGGAG-UAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022814665.1/445-538   UUUCUA------UGUG-CACCC--GC------------------UUAACCGAGACCUAU-------GGGUG-GUU-A--AAU--UACGUCUCUAAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY023480279.1/475-380   UCACUUUC----CAAA-CACGCCUUA----------------------CCGAGACUAAA--C-A--GCGUG-UCUAA--AAAA-C-AGUCUCUCAU---ACCUCAGGC-G-GAGGG-U--GUCUGAGGAAUAUUUUACCUA
AACY022269382.1/217-309   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY021224911.1/473-385   -CCUCAUC---UGUUU-AUCCC--C-------------------CUAACCAAGACCAC--------GGGGU-UAU-A-------A-UGUCU-UCUU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUCGUAUCGC
AACY023429956.1/532-624   UAACGUUG----CUCA-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-UAU-A--AAG--UACGUCUCUCAU---A-UCCUGCC-U-GAGGG-U--GGCGGGAGCAUAGUAUCACCA
AACY020175982.1/2282-2376 UAACAUU---GUUAAA-CUCCCAUUA---------------------ACCGAGACCUA---U-G--GGGAG-UAU-A--AAU--UACGUCUCUCAU---A-UCCCGCC-U-GAGGG-U--GGCGGGAGCAUAGUAACUCCA
AACY023483556.1/1398-1491 UAACACAU---AUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY022213373.1/507-411   UUAGUGAG---UUGAA-CACCC--CU------------------UCAACCGAGACCUAU--A----GGGUG-UCU-A--AAU--CACGUCUCUCAU---ACCUUUCUC-U-GAGGG-U--GAGAAAGGAAUAUUUUACCGA
AACY021902398.1/152-245   CAACAC------CUAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY021708592.1/352-256   UAACUUGG---UGUAA-CACGCCUUA----------------------CCGAGACUAAA--C-A--GCGUG-UCUAA--AAAA-C-AGUCUCUCAU---ACCUCAGGC-G-GAGGG-U--GUCUGAGGAAUAUUCUAACUC
AACY021980752.1/603-510   UCUCAUAA---ACACC-UUGCC-CCA----------------------CCAGGAC-UAA--U-G--GGCAA-GUA-A--AAU--C-CGUCCUUCAU---A-UCUGCGA-UGGAGGG-UG-UCGCAGAGCAUAACUGUAUUA
AACY023135879.1/269-362   ACACAUAU---AUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GCGAGGGAU--UACUGGAAAUAAGUUUCGCA-
AACY021304186.1/636-541   UAACACAU---AUUUG-CUCCC--CU------------------UCAACCAAGACCUAU--A----GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY022942077.1/665-572   UACCGAA-----GUUU-UUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAA-GUA-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUAGUAUCGC
AACY023340531.1/617-725   UAACUUUU---GUGAC-UUGCU----GAAAAGGGACUAAAACUCCUCACCGAGGC-UA--------AGCAA-GUA-A--AAU--A-CGCCUCUCAU---AUCUCAGUC-U-GAGGG-U--GACUGAGAAAUAAGUACCUCC
AACY022158370.1/896-799   CAUCCAGU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-CUA-A--UAC--UUCGUCUCUCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAAAUAAGUUUCGCA-
AACY020120326.1/649-747   CUCCCUUG---UAGAA-CUGCUCCUA--------------------AACCGAGACCUA---U-A--GGCAG-UAU-AAUACU--U-CGUCUCUCAU---AUCCGAAAG-UGAAGGG-A--UUUUCGGAAAUAAGUAUCGCA
AACY021732350.1/406-308   CAUCCAAU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-AUA-A--UAC--CUCGUCUCUAAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAAAGUAUCGC
AACY022946302.1/491-584   UAACACAU---AUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCGAAA-GUGAGGGAU--UUUCGGAA-AUAAGUUUCGCA
AACY023490019.1/1089-1181 UAACACAU----UUCA-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY021771087.1/721-627   CAACACC-----AUAA-CUCCU--CG------------------CAAACCGAGACCUA---U-A--GGGAG-UAUAA--AACA-U-CGUCUCUU-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020210957.1/561-653   UAACACAU----UUCA-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022819017.1/317-223   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-AAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY021282207.1/613-519   UACCAAUU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCACU
AACY021611641.1/726-626   UCACCCUGA-GUACAA-CUGCUCUUA--------------------AACCGAGACCUA---U-A--GGCAG-UAU-A--AGUA-UUAGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY021269056.1/269-176   UAACACAU---AACUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022811730.1/141-238   CAUCCAGU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-CUA-A--UAC--UUCGUCUCUCAU---A-UCCUGUA-GCGAGGGGU--UACAGGAAAUAAGUUUCGCA-
AACY020342881.1/1016-922  UAAUCUUU---UGUAA-CUCCC--CU------------------CCAACCGAGACCUAU--A----GGGAG-UAU-A--AAG--CACGUCUCUCAU---A-CCUUGCC-U-AAGGG-U--GGCAAGGA-AUAGUAACUCCA
AACY022717573.1/427-519   UCACCAU-----AAUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAAAUAAGUUUCGCA-
AACY023375452.1/998-1092  UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GGU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY023374731.1/903-1001  UCACCUUUUCUAUGUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAAAGUAUCGC
AACY023926080.1/612-705   UCACCA------AUCA-CUCCC--CU------------------CCAACCAAGACCUAU--A----GGGAG-UAU-A--AAU--UACGUCUUUCAU---A-UCCGAAA-GUGAGGGAU--UUUCGGAAAUAAGUUUUCGC-
AACY020493561.1/487-393   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY020673357.1/443-537   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY020215129.1/673-766   UAAGGCA-----UUUU-CUCCC----------------------UAAACCGAGACCUA---C-A--GGGAG-AAU-A--AAU--UACGUCUCUCAU---A-UCCACCA-UUAAAGGGAC-UGGUGGAA-AUAUUAAUAUCG
AACY020562160.1/3808-3717 UUGCACAA---------CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY021968994.1/275-181   UCACCAUU----UUUA-CACCC---G------------------UUAACCGAGACCUA---U----GGGGG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY020259217.1/272-177   UCACCAUC----CAAA-CACGC--CU------------------U--ACCGAGAC-UAAACA----GCGUG-UUU-A--AAAAAC-AGUCUCUCAU---A-CCCGACC-UGGAGGG-UA-GGUUGGGA-AUAUUUUACCGA
AACY023403495.1/1065-972  CUCCGAAU---AUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020012833.1/1261-1356 UAACUGUU---CGUAA-CACCC--CU------------------CAAACCAAGACCUAU--A----GGGUG-UCU-A--AAC--A-CGUCUUUCAU---A-UCCUUGC-CUUAGGG-UG-GCGAGGAA-AUAGUAACUCCA
AACY020202133.1/408-488   -----------------CUCCC---G------------------CUAACCAAGACCUA---U----GGGAG-GAU-A--AAU--UACGUCU-UAAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022796127.1/224-319   UAACACAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAAAGUAUCGC
AACY024096831.1/744-839   UCACUUUC----CAAA-CACUC--CU------------------CAAACCGAGACCUAU--A----GGGUG-UAU-A--AAU--CACGUCUCUCAU---A-CCAACUC-UGGAGGG-UA-GAGUUGGA-AUAUUUUACCUA
AACY020329768.1/311-406   UCACAAUA----CUUA-CUCCCCUUA--------------------AACCAAGACCUA---U-A--GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCU
AACY022248603.1/264-357   UUACUGUU----CGUA-ACACC-CCU------------------CAAACCAAGACCUCU--A-G--GGUGU-CUA-A--AAA----CGUCUUUAAU---A-CCUCUGC-C-UAGGG-C--GCAGAGGA-AUAGUAACUCCA
AACY023886486.1/1018-1113 UCACAAUA----CCUA-CUCCCCUUA--------------------AACCAAGACCUA---U-A--GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCGAAA-GUGAGGGAU--UUUCGGAAAUAAGUUUCGCU-
AACY020121181.1/1077-983  UACCAAUU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCACU
AACY022731190.1/527-435   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY022003701.1/439-344   UAAUCUCU---UGUAA-CACUCCGUA--------------------AACCGAGACCUC---U-A--GGGUG-UAU-A--AAC--A-CGUCUCUAAU---ACCUCAGGC-G-GAGGG-U--GUCUGAGGAAUAUUCAUACUA
AACY020678195.1/49-141    CAUCAGUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAAAUAAGUUUCGCA-
AACY020330447.1/1551-1647 ACACAUAU---AUCUG-CUCCCCUUA--------------------AACCAAGACCUA---U-A--GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCGAAA-GUGAGGGAU--UUUCGGAA-AUAAGUUUCGCA
AACY020087980.1/1207-1305 CAUCCAAU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUCUAAU---AUCCACUAG-UGAAGGG-A--UUGGUGGAAAUAAAGUAUCGC
AACY023445816.1/57-151    UAACAUUG----UCUU-CCUGCCGUU------------------UG-ACCGAGAC-U----A-G--GCAGG-GUU-ACCAAU--C-CGUCUCUCAU---A-UUUCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
AACY022715614.1/2-98      CCUCCUAU----GCAA-ACUGC-UCU------------------UAAACCAAGACCUAC--A-G--GCAGU-AUA-A--UAC--UUCGUCUUUC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY021335216.1/143-47    AAAUGCUU---CUGGA-CACCC--CU------------------CAAACCAAGACCUAU--A----GGGUG-UAU-A--AAC--CACGUCUUUCAU---A-CCUAAGC-CUGAGGG-UG-GCUUAGGA-AUAGUAAAACCG
AACY023907961.1/344-437   UACCGAA-----GUUU-UUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAA-GUA-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUAAUAUCGC
AACY020263255.1/728-633   UUAAGUUG---UACAA-CACCC--UG------------------UAAACCGAGACCUC---U-A--GGGUG-UCU-A--AAC--A-CGUCUCUAAU---ACCUCAGGC-G-GAGGG-U--GUCUGAGGAAUAUUCAUACUA
AACY024015518.1/143-234   UCAUAU------UCUG-CUCCC--GC------------------UUAACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UAAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023338535.1/835-742   UUACGUUUC-CUUUAC-ACUUC--UC-------------------AAACCGGGAUCAA---G-A--GAAGC-----A--AAG----CAUCCCUCAU---A-UCCACGA-UGGAGGG-UG-UCGUGGAGUAUACUGUACCAA
AACY023671521.1/700-616   CAUCACAU----AUUC-CCUCU------------------------AACCGAGAUCA---------CGGGG-GUU-A---------CAUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUCCGUAUCG
AACY020326651.1/232-127   UAACGUAA----CACC-UUGGA----GAACCGGACUAACACUCCU--ACCGAGAC-UA--------UCCAA-GUA-A--AAU--A-CGUCUCUCAU---A-CCUGGCC-UGGAGGG-UA-GGUCAGGA-AUACUAUAACUU
AACY022817846.1/222-315   UAAGGCA-----UUUU-CUCCC-CUA---------------------ACCGAGACCUA---U-A--GGGAG-AAU-A--AAU--UACGUCUCUCAU---A-UCCACCA-UUAAAGGGAC-UGGUGGAA-AUAUUAAUAUCG
AACY021985922.1/304-207   CAUCCAUU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-CUA-A--UAC--UUCGUCUCUCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAAAUAAGUUUCGCA-
AACY020264461.1/366-273   ----ACUCA-UUGUAA-ACACG-CCU------------------C--ACCAAGAC-UAAACA-G--CGUGU-CUA-AACAAC----AGUCUUUCAU---A-CCUUGCC-U-UAGGG-U--GGCAAGGA-AUAGUAACUCCA
AACY020003678.1/742-837   UAACUGUU---CUUAA-CACCCCGUA--------------------AACCAAGACCUC---U-A--GGGUG-UCU-A--AAC--A-CGUCUUUCAU---A-UCCUUGC-CUUAGGG-UG-GCGAGGAG-AUAGUAAAACCA
AACY020086453.1/796-891   UAACACAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCGUUAAG-UGAAGGG-A--UUUAACGAAAUAUAGUAUCGC
AACY021531785.1/355-449   AUCCGUUG---GACCA-CACCC----------------------CAAACCGAGACCUA---U-A--GGGUG-UCU-A--AAU--CACGUCUCUCAU---ACCUCCAGC-U-GAGGG-U--GCUGGAGGAAUAGUAAAACCA
AACY022328136.1/232-330   CAUCCAAU----GCAA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-AUA-A--UAC--CUCGUCUCUAAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAAAGUAUCGC
AACY020117957.1/102-196   UAACACAU---UUCAG-CUCCC--GC------------------UUAACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGUAA-GUGAGGGAU--UUACAGGA-AUAAGUUUCGCA
AACY020457716.1/1556-1647 UUAUACUU-------A-CUCCCCUUA--------------------AACCAAGACCUA---U-A--GGGAG-UAU-A--AAA--A-CGUCUUUCAU---ACCUGUGUC-U-AAGGG-U--GAUACAGGAAUAGUAAAACCA
AACY024113264.1/1185-1091 -UCGCCCA---AGUUU-UUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAA-GUA-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUAGUUUCGC
AACY024015401.1/134-40    GAACACAU---AACUG-CUCCC--GC------------------UUAACCAAGACCUA-----U--GGGAG-GAU-A--AAU--UACGUCU-UAAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020331451.1/1434-1528 UAACACAU---AUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCGAAA-GUGAGGGAU--UUUCGGAAAUAAGUUUCGCU-
AACY020004210.1/333-238   UAACUGUU---UGUAA-CACCC--CU------------------CAAACCAAGACCUAU--A----GGGUG-UCU-A--AAC--A-CGUCUUUCAU---AUCCUAGAC-U-UAGGG-U--GUCUGGGAAAUAGUAACUCCA
AACY020214003.1/102-200   AUAAACUU---ACACA-CUGCU---C------------------CCAACCGAGACCUAC--GUA--GGCAG-UAUAA--UACA-U-CGUCUCUCAU---A-UCCAGUA-GCGAGGGGU--UGCUGGAAAUAAGUUUCGCA-
AACY022191797.1/485-389   CAACUUGG---UGUAA-CACGCCUUA----------------------CCGAGACUAAA--C-A--GCGUG-UUUAA--AAAA-C-AGUCUCUCAU---A-CCCACGA-UGGAGGG-UG-UCGUGGGA-AUACUAAUACCG
AACY020086867.1/586-680   UAACACAU---UUCAG-CUCCC--GC------------------UUAACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGUAA-GUGAGGGAU--UUACAGGA-AUAAGUUUCGCA
AACY022943287.1/573-478   ACACAUAU---AUCUG-CUCCCCUUA--------------------AACCAAGACCUA---U-A--GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCGUAA-GUGAGGGAU--UUACGGAA-AUAUGUUUCGCA
AACY020554127.1/2321-2415 CAACAC------CUAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020185404.1/1850-1755 AAACACAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCGUUAAG-UGAAGGG-A--UUUAACGAAAUAUAGUAUCGC
AACY021249318.1/449-544   CCUCCUUU----GAAG-ACUGC-UCU------------------CAAACCAAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUUUUAU-----CCAGUAG-U-GAGGG-A--UUACUGGAAAUAAGUUUCGCA
AACY020462684.1/568-663   UAACUGUU---CGUAA-CACUC--CU------------------CAAACCAAGACCUCU--A----GGGUG-UAU-A--AAC--A-CGUCUUUAAU---A-UCCUUGC-CUUAGGG-UG-GCGAGGAG-AUAGUAAAACCA
AACY022696757.1/726-626   UCACCCUGA-GUACAA-CUGCUCUUA--------------------AACCGAGACCUA---U-A--GGCAG-UAU-A--AGUA-UUAGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY020031178.1/1208-1303 UAACAAGU---CGUAA-CACCC--CU------------------CAAACCAAGACCUAU--A----GGGUG-UCU-A--AAC--A-CGUCUUUCAU---A-UCCUUGC-CUUAGGG-UG-GCGAGGAA-AUAGUAAAACCA
AACY020094761.1/1232-1325 CUCCGAAU---AUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022807956.1/441-521   UCACUUAU----UUUG-CUCCC---G------------------CUAACCGAGACCUA---U----GGGAG-GAU-A--AAU--UACGUCUCUC--------------GUACUACCCUUC-------AUAUACAACGUACU
AACY021141130.1/741-830   UACCACAU---UCUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUU----
AACY020320791.1/1148-1237 UCCCCAUC--AGUUUA-UCCCC--CU--------------------AACCAAGACC-----A-U--GGGGU-UAU-A-------A-UGUCU-UCUU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUACCGUAUCGC
AACY023993124.1/941-846   --ACACCUA-UAAAUC-UUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAA-GUA-A--AAU--UACGUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUACAGUAUCGC
AACY021639959.1/721-627   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY023875288.1/954-1042  UCAUCUUA---AUAUA-CCCCU------------------------AACCGAGAC-UAA-------ACGGG-GAU-A-----A-C-AGUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAACAGUACCG
AACY021896458.1/422-515   UAACACAU---UUCAG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGUAA-GUGAGGGAU--UUACAGGA-AUAAGUUUCGCA
AACY021174230.1/232-134   UCCCUCAG---UAGAA-CUGCUCUUA--------------------AACCGAGACCUA---U-A--GGCAG-UAU-AAUACU--U-CGUCUCUCAU---AUCCGAAAG-UGAAGGG-A--UUUUCGGAAAUAAGUAUCGCA
AACY022216119.1/883-789   UCACUAAU--UAUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCACU
AACY020170823.1/743-652   UAACAA----GUUCCU-CUUCC--UA---------------------ACCGAGACCUA---U-G--GGGAG-GUU-A--AACA-C-AGUCUCUCAU---A-UCCCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
AACY020182108.1/1-91      UA---GUU----CCCU-CUUCC--UA---------------------ACCGAGACCUA---U-G--GGGAG-GUU-A--AACA-C-AGUCUCUCAU---A-UCCACAC-UGGAGGG-UG-GUGUGGAGCAUACUUGUAACU
AACY020083061.1/666-764   AUCCAAUG----CACA-ACUGC-UCU------------------CAAACCGAGACCUAU--A-G--GCAGU-AUA-A--UAC--UUCGUCUCUCAU---AUCCGACAG-UGAAGGG-A--UUGUCGGAAAUAAGUAUCGCU
AACY021336192.1/664-759   ACACCAUU---GUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY022851071.1/664-762   UAACCCUGC-GUAAAA-CUGCU---U------------------U-AACCGAGACCUAU--G----AGCAG-UAU-A--AGCAAU-AGUCUCUCAU---AUCCGAAAG-UGAAGGG-A--UUUUCGGAAAUAAGUUUCGCA
AACY023478430.1/1474-1379 ACACCAAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAAAGUAUCGC
AACY020202678.1/724-627   UAUCAAAC---CCACA-CUCCU--CG------------------CAAACCGAGACCUA---U-A--GGGAG-UAU-AAUACU--U-CGUCUCUAAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022665721.1/717-812   UCACUAUC----CAAA-CACGC--CU------------------C--ACCGAGAC-UAAACA----GCGUG-UCU-A--AAAAAC-AGUCUCUCAU---A-CCUCAGG-CGGAGGG-UG-UCUGAGGA-AUAUUUUACCUA
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AACY020088812.1/315-220   ACACCAAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
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AACY023930183.1/577-483   UAACAGU-----UGAA-CACCC--CU------------------UCAACCGAGACCUAU--A----GGGUG-UCU-A--AAU--UACGUCUCUCAU---ACCUUUCUC-U-GAGGG-U--GAGAAAGGAAUAUUUUACCGA
AACY022088609.1/921-821   UAACCCUGC-GUACAA-CUGCUCUUA--------------------AACCGAGACCUA---U-A--GGCAG-UCU-AAUACU--U-CGUCUCUCAU---AUCCAUCAG-UGAAGAG-A--UUGAUGGAAAUAUAAGUUUCG
AACY020142778.1/482-388   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY023463929.1/945-1041  CAACACC-----GUCA-CUGCUCCCA---------------------ACCAAGACCUC---U-GUAGGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
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AACY023356087.1/419-324   AAACCUUCC-UGGACA-CUCCC----------------------CAAACCAAGACCUA---U-A--GGGUG-UAU-A--AAA--A-CGUCUUUCAU---AUCUCAAUC-U-UAGGG-U--GAUUGAGAAAUAGUAAAACCA
AACY020474578.1/633-537   UAACGAUA---UACUA-CUCCC--UG------------------UAAACCGAGACCUC---U-A--GGGAG-UCU-A--AAU--UACGUCUCUAAU---A-CCUUCGC-CUGAGGG-UG-GUGAAGGA-AUAUUUACUUCA
AACY022675729.1/794-701   AAUCCGUU---GUACA-CACCC--CG------------------CAAACCAAGACCUC---U-A--GGGUG-UAU-A--AAA--A-CGUCUUUCAU---A-UCCUCUC-U-AAGGG-U--GAGAGGAA-AUAGUAACUCCA
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AACY022586543.1/527-432   GAACAUAU---AUUUG-CUCCC--CU------------------UCAACCAAGACCUAU--A----GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020217428.1/518-423   ACACCAUU---GUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY020553249.1/1392-1297 ACACCAUU---GUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY020102819.1/658-742   CCUCACUU---UUUUG-CUCCU--UU--------------------AACCGAGACCUUUA-A-A--GGGAG-GAUAA--AAC--UUCGUCUCUC--------------GUACUACCCUUC-------AUAUACAACGUACU
AACY023507804.1/489-397   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY022699853.1/447-354   UAACACAU---UUCAG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGUAA-GUGAGGGAU--UUACAGGA-AUAAGUUUCGCA
AACY020554255.1/2964-2872 UAUCAGUG----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY023457159.1/1411-1315 -AACCGAC---ACAUU-UGACC-CCU------------------UCAACCGAGACCUAU--A-G--GGUCA--UU-A--AAC--UACGUCUCUAAU---ACCUCUACC-U-GAGGG-U--GGUAGAGGAAUACUAACUUCA
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AACY022803877.1/705-613   UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY020209582.1/3058-3152 UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY023362403.1/1392-1298 UAACAGU-----UGAA-CACGC----------------------CUCACCGAGACUAAA--C-A--GCGUG-UCUAA--AAAA-C-AGUCUCUCAU---A-CCAACUC-UGGAGGG-UA-GAGUUGGA-AUAUUUUACCUA
AACY022724898.1/102-7     UUACCAUU---GUUUG-CUCCC---G------------------CUAACCAAGACCUA---U----GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY020552257.1/3152-3247 UCACCAUC----CACA-CACCC--CU------------------CAAACCGAGACCUAU--A----GGGUG-UAU-A--AAU--CACGUCUCUCAU---A-CCAACCC-UGGAGGG-UA-GGGUUGGA-AUAUUUUACUCA
AACY023470184.1/968-1064  --CCUCUG--AGACAA-CUGCU--CU------------------UAAACCGAGACCU----A-C--AGCAG-UCUAA--AAC--UUCGUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUAGUAUCGC
AACY021188973.1/159-252   UACCGAU-----GUUU-UUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAA-GUA-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAAAGUAUCGC
AACY020477480.1/431-524   ACACAUAU---AUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GCGAGGGAU--UACUGGAAAUAAGUUUCGCA-
AACY020120495.1/644-558   UCAUCAUA----UCUU-CCCCC---U--------------------AACCAAGACC-----A----CGGGGUUAU-A-------A-UGUCU-UCUU---A-UCCACUAUUGAAGGGAU--UAGUGGAA-AUACUGUAUCGU
AACY022381781.1/688-788   CACCCUUGC-UACAAA-CUGCU--CG------------------CAAACCGAGACCUA---C-A--GGCAG-UAU-AAUAAU--U-CGUCUCUCAU---A-UCCAGAA-GGGAAGGGAU-UUCUGGAA-AUAUAGUAUCGC
AACY022691014.1/281-191   UCACCAUA----CAUC-UUCCUGCUA---------------------ACCAAGAC------U-G--AGGAA-GUA-A--AAC--A-CGUCU-UCUU---GUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAACAGUAUCG
AACY023425505.1/336-238   UCACCUUUUCUAUGUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAAAGUAUCGC
AACY020325905.1/498-595   UUUCGUUA--CAUACC-CACGCCUUA----------------------CCAGGACUAAA--C-A--GCGUG-GUA-A--AACA-ACAGUCCUUCAU---A-CCUACAU-CGGAGGG-UG-AUGUAGGA-AUAUUUUAUCUG
AACY021240804.1/592-684   UAACACAU----UUCA-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023208719.1/1052-1147 UAACAAGU---CGUAA-CACCC--CU------------------CAAACCAAGACCUCU--A----GGGUG-UAU-A--AAC--A-CGUCUUUCAU---AUCUCUAUC-U-UAGGG-U--GAUAGAGAAAUAGUAACUCCA
AACY021204902.1/639-732   ACACAUAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GCGAGGGGU--UACUGGAAAUAAGUUUCGCA-
AACY020209329.1/1554-1459 UAACACAU---AUUUG-CUCCC--GC------------------UUAACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UAAU---AUCGUUAAG-UGAAGGG-A--UUUAACGAAAUAUAGUAUCGC
AACY022626449.1/39-134    UAACUGUU---UGUAA-CACCC--CU------------------CAAACCAAGACCUAU--A----GGGUG-UCU-A--AAC--A-CGUCUUUCAU---AUCCCAGAC-U-UAGGG-U--GUCUGGGAAAUAGUAACUCCA
AACY020205115.1/1092-997  CAACACC-----GCCA-CUGCUCUUA--------------------AACCAAGACCUA---U-A--GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-CCUGUAA-GUGAGGGAU--UUACAGGAAUAAGUUUCGCA-
AACY022792218.1/463-556   UAAGGCA-----UUUU-CUCCC----------------------CAAACCGAGACCUA---U-A--GGGAG-AAU-A--AAU--UACGUCUCUCAU---A-UCCACCA-UUAAAGGGAC-UGGUGGAA-AUAUUAAUAUCG
AACY020168622.1/998-907   UAACAA----GUUCCU-CUUCC--UA---------------------ACCGAGACCUA---U-G--GGGAG-GUU-A--AACA-C-AGUCUCUCAU---A-UCCCGCU-U-GAGGG-U--GGCGGGAACAUAGUAUCUCCA
AACY023464248.1/984-1076  UAUCAAUA----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY023393968.1/1120-1025 UAACACAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCGUUAAG-UGAAGGG-A--UUUAACGAAAUAUAGUAUCGC
AACY021060717.1/230-135   UCACCAUC----CACA-CACGC--CU------------------U--ACCAGGAC-UAAACA----GCGUG-GCU-A--AAAAAC-AGUCCUUCAU---A-CCUGAUC-UGGAGGG-UA-GAUCAGGA-AUACUAUACUCA
AACY021946085.1/659-754   ACACCAAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY020648992.1/267-172   --UCAUCAG-UGUUUG-CUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAGGGUA-A--AAU--A-CGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAAAGUAUCGC
AACY021240311.1/563-659   AGACAUAU----ACCU-CUCCCCUUA--------------------AACCGAGACCUA---U-A--GGGAG-UUU-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUAGUUUCGC
AACY020111732.1/272-349   ---UCACU---UAUUA-CUCCC---G------------------CUAACCGAGACCUA---U----GGGAG-AAU-A--AAU--UACGUCUCU---------------UUUUUACCCUUC-------AUAUACCGCACUUA
AACY020338014.1/927-1024  UCACAGUAC-GUUACA-UUCUCCUUA--------------------AACCGAGACCUA---U-A--GGGAA-UUC-A--AAC--A-CGUCUCUCAU---A-CCAACCC-UGGAGGG-UA-GGGUUGGA-AUACUAUACUCA
AACY021022586.1/387-292   UAACUGUU---CUUAA-CACCC--CU------------------CAAACCAAGACCUCU--A----GGGUG-UAU-A--AAC--A-CGUCUUUCAU---A-UCCUUGC-CUUAGGG-UG-GCGAGGAA-AUAGUAACUCCA
AACY023547889.1/114-28    UUGCUCAC----AUCU-UCCCU--CU--------------------AACCGAGAUC-----A----AGGGG-GUU-A---------CAUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAACUGUAUCA
AACY021996135.1/759-665   UACCAAUU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCACU
AACY023374072.1/549-643   UCACCAUU----CUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GGU-A--AAU--UACGUCUCUCAU---AUCCACUAG-UGAAGGG-A--UUAGUGGAAAUAUAGUAUCGC
AACY021894329.1/701-607   UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-AAU-A--AAU--UACGUCUCUCAU---AUCCUGUAG-UGAAGGG-A--UUACAGGAAAUAUAGUAUCGC
AACY020106504.1/1213-1116 UAUCAAAC---CCACA-CUCCU--CG------------------CAAACCGAGACCUA---U-A--GGGAG-UAU-AAUACU--U-CGUCUCUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY022379488.1/1-95      CUCCUUUG----AAGA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUUAU-----CCAGUAG-U-GAGGG-A--UUACUGGAAAUAAGUUUCGCA
AACY022262515.1/447-545   ACCCUAAG----UACA-ACUGC-UCU------------------UAAACCGAGACCUAU--A-G--GCAGU-AUA-A--UAC--CUCGUCUCUAAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUAGUAUCGC
AACY022811153.1/686-591   GAACAUAU---AUUUG-CUCCC--CU------------------UCAACCAAGACCUAU--A----GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020215007.1/2005-1907 ACCCAUUG---UGCAA-CUGCUCUCA--------------------AACCAAGACCUAU--U-A--GGCAG-UAU-AAUACU--U-CGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023896978.1/24-118    UAACACAU--AUCUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCGAAA-GUGAGGGAU--UUUCGGAA-AUAAGUUUCGCU
AACY023201590.1/1042-947  UAACUGUU---UGUAA-CACCC--CU------------------CAAACCAAGACCUAU--A----GGGUG-UCU-A--AAC--A-CGUCUUUCAU---AUCCCAGAC-U-UAGGG-U--GUCUGGGAAAUAGUAACUCCA
AACY023043092.1/288-193   AAUCGUUC---GAACA-CUCCC--CA------------------CAAACCGAGACCU----CAA--GGGAG-AAU-A--AAU--A-CGUCUCUCAU---A-CCUGCAC-UGGAGGG-UG-GUGCAGGA-AUACUAAAACUA
AACY020149617.1/67-160    -AUCCUAA--UAUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUAGCU
AACY022553660.1/486-393   UCACCA------AUCA-CUCCC--CU------------------CCAACCAAGACCUAU--A----GGGAG-UAU-A--AAU--UACGUCUUUCAU---A-UCCAGUA-GUGAGGGAU--UGCUGGAA-AUAAGUUUCGCU
AACY023477202.1/647-555   UAUCAGUG----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY020642959.1/523-428   UCACCAUC----CAAA-CACGC-CUG---------------------ACCGAGACUAAA--C-A--GCGUG-UCU-A--AACA-ACAGUCUCUCAU---A-CCAACUC-UGGAGGG-UA-GAGUUGGA-AUAUUUUACCUA
AACY023887037.1/412-315   CUCCUGAG----UACA-ACUGC-UCU------------------UAAACCGAGACCUAU--A-G--GCAGU-AUA-A--AAC--UUCGUCUCUCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAAAUAAGUUAUCGC-
AACY020131158.1/1074-1168 GAACACAU---UACUG-CUCCC--GU------------------UUAACCAAGACCU----A-U--GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY023489517.1/383-291   UAUCAGUG----UUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-CCUGCAA-GUGAGGGAU--UUGCAGGA-AUAAGUUUCGCA
AACY024011867.1/310-402   UGACUA------CAAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUUAU-----CCAGUAG-U-GAGGG-A--UUACUGGAAAUAAAUAUCGCU
AACY022807554.1/456-549   UAACACAU---UUCAG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020700392.1/582-489   CAACAC------CUAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUC-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY023891700.1/39-135    UCACCUUUU-CAUUCU-GUCGC----------------------CUCACCAAGACUAAA--C-A--GCGAC-AUU-A--AAUA-ACAGUCUUUCAU---A-CCUCUGC-U-UAGGG-U--GCAGAGGA-AUAGUAACUCCA
AACY022879865.1/121-30    -GACCCCU--UUUUAC-UUCCC--UU---------------------ACCAAGACUUA---A-C--GGGGU-UAU----AAU--U-AGUCU-UCUU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUACUGUAUCGU
AACY022552544.1/453-358   GAACAUAU---AUUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY023492156.1/1380-1285 ACACCAAU---AUUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY023395387.1/764-861   UAUCAAAC---GCACA-CUGCU--CG------------------CAAACCGAGACCUA---U-A--GGCAG-UAUAA--UACA-U-CGUCUCUCAU---A-UCCUGUA-GUGAGGGAU--UACAGGAA-AUAAGUUUCGCA
AACY020490393.1/480-385   UCACCAAC----CACA-CACGCCUUA----------------------CCGAGACUUAA--C-A--GCGUG-UCUAA--AAAA-C-AGUCUCUCAU---A-CCCGACC-UGGAGGG-UA-GGUUGGGA-AUAUUUUACCGA
AACY023425336.1/1007-914  UAACACAU---AACUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020253837.1/281-358   CAACACUU---CUUUC-GACCC---G------------------CUAACCGAGACCUA---U----GGGUC-GUU-A--AAU--UACGUCUCU---------------AUCUUACUC----------ACAUAACAUCGCAC
AACY020780247.1/79-1      ---------------A-CACGC--CU------------------U--ACCAGGAC-UAAACA----GCGUG-UCU-A--AAAAAC-AGUCCUUCAU---A-CCUGAUC-UGGAGGG-UA-GAUCAGGA-AUACUA------
AACY020114285.1/245-344   CAACAUAU----UCCU-ACUGC-UCU-------------------CAACCGAGACCUCUAUA-G--GCAGU-CUA-A--UAC--UUCGUCUCUCAU---AUCCGAAAG-UGAAGGG-A--UUUUCGGAAAUAAGUAUCGCA
AACY022946473.1/6-86      -----------------CUCCC---G------------------UUAACCGAGACCUA---U----GGGAG-GGU-A--AAA--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAAAGUAUC--
AACY020633864.1/535-631   UAACGUUUC-UUAAGA-CUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAG-GAU-A--AAU--UACGUCUCUCAU---A-CCCACAC-UGGAGGG-UG-GUGUGGGA-AUAAUGUAUCAU
AACY021150359.1/314-222   UAACACAU----UUCA-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCU-UCAU---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCA
AACY020952027.1/260-166   UAACACAU--AUCUUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUU-AU---A-UCCGUAA-GUGAGGGAU--UUACGGAA-AUAUGUUUCGCA
AACY021887816.1/490-385   UCACCACU----CUUC-UUGGA----GACCGGGCCUAAUACGCCU--ACCGAGAC-UA--------UCCAA-GUA-A--AAU--A-CGUCUCUCAU---A-CCAACCC-UGGAGGG-UA-GGGUUGGA-AUACUAUACUCU
AACY022214008.1/522-615   UAACGCUU----CAAA-CACCC--CG------------------CAAACCGAGACCUC---U-A--GGGUG-UCU-A--AAU--UACGUCUCUCAU---A-UCCUGUC-U-AAGGG-U--GACAGGAA-AUAGUAACUCCA
AACY023923575.1/589-683   -UCGCCCA---AGUUU-UUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAA-GUA-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAUAGUUUCGC
AACY020487365.1/1860-1766 UCACCAUU----UUUG-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-GAU-A--AAU--UACGUCUCUCAU---AUCCAUCAG-UGAAGGG-A--UUGAUGGAAAUAUAGUAUCGC
AACY020596340.1/268-360   CAACAC------UUAA-CUGCU--CU------------------CAAACCAAGACCUAU--A----GGCAG-UAU-AAUACU--U-CGUCUUUUAU-----CCAGUAG-U-GAGGG-A--UUACUGGAAAUAAGUUUCGCA
AACY020211432.1/845-943   CAACAUAU----UCCC-ACUGC-UCU-------------------CAACCGAGACCUCUAUA-G--GCAGU-AUA-A--UAC--UUCGUCUCUCAU---A-CCUGUAA-GUGAGGGAU--UUACAGGAAUAAGUUUCGCA-
AACY020109483.1/1604-1510 UAACUGAA--UAUCUG-CUCCC--GC------------------U-AACCAAGACCUAU-------GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCU
AACY023916157.1/409-315   UCACCCCA----GUUU-UUCCC--GU------------------U-AACCGAGACCU----A-U--GGGAA-GUA-A--AAU--UACGUCUCUCAU---AUCCACCAG-UGAAGGG-A--UUGGUGGAAAUAAAGUAUCGC
AACY022698737.1/629-722   UUAUCAAU---AUUUG-CUCCC---G------------------CUAACCAAGACCUA---U----GGGAG-GAU-A--AAU--UACGUCUUUU-U---A-UCCAGUA-GUGAGGGAU--UACUGGAA-AUAAGUUUCGCU
AACY020166069.1/934-841   UAACAUA---GUUAAA-CACCC--GU------------------U-AACCGAGACCU----A-U--GGGUG-UAU-A--AAU--CACGUCUCUCAU---A-UCCCCGC-U-AAGGG-U--GCGGGGAGCAUAGUAUCUCCA
#=GC SS_cons              ::::::::...:::::.<<<<<..-<.................._.____________...>....>>>>>.---.-..---..------------...-.<<<<<<<._______._..>>>>>>>::::::::::::::
#=GC RF                   UaACauuu...uuuua.cuccc..uu..................u.AACCgAGACCUA...a....gggag.gaU.A..AAU..uaCGUCUCUCAU...A.CCcgcac.uggAGGG.U..gugcgGGAAAUAauuuuucca
//
# STOCKHOLM 1.0

#=GF AC   RF01718
#=GF ID   Polynucleobacter-1
#=GF DE   Polynucleobacter-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   37.00
#=GF TC   38.80
#=GF NC   31.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Polynucleobacter-1_RNA_motif
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   16


AACY020164468.1/385-250    GACUCGCACAGGUC--UAUUUCUUGUGCCC-UGGAC----CAGGACCUCG--GG-UCG-CUGGGA-UGGAAAUCUCUC--GCCGUUAAGAGUGCUCA--ACCACUACCC-GAAA---GGAUGAA-GAUCGCU-ACUAAGC----CCUGCGAUUUGGU-UGUUU
AACY020875110.1/558-692    GACUCGCACAGGUC--AAUUUCAUGUGCC--UAGAGACAACCGGA--UAA-----UAA-CGGGGA-CGGAAGCCUCACC-GCGCUAGUGAGCACUCA--AUCAGUAUCCUUAAC--AGGACCAC-GAUCGCA----AAUU----GCCGCGGUUUGAU-UGUUU
AACY023337941.1/911-775    GGCUAGCACAGGCU--AAAAUCGUGUGCGU-UGGAC----CUGACUCUAUG-GA-GGA-CAGGGA-UGCAAGACUCUGC-GCUGUACAGAGCACUCA--ACUACUAUCCUUAAC--AGGACGAA-GAUCGCA----AAUG----GCCGCGGUUUAGU-UGUUU
AACY020722792.1/610-753    GGCUUGUGUCGCCAAUAUACUUAGACACCCAUAAAAC---CAGGCACUAGG-GUUGCG-CUGGGGAAGGAACUUCCGU--GCAGUAGCGGAGACUUGUUGCCACUAUCCUUGAC--AGGACGCA-AUUC--ACGGUAUGAAAC------GAAUUGGCAC-UAG
AACY023444331.1/997-859    GGCUAGUGCAGGCC--AAUAUCGUGCACUGACGACAA---CGGGAUCCAUGUGA-UCG-CCGGGA-CCAAAGACUCC---GCCGC-AGGAGCGCUCA--ACCACUAUCC-UUUACC-GGACGAA-GGUCGCA----AGUG--UGCCUGCGGCUUGGU-UGUUU
CP000655.1/2130772-2130906 GGGCAGUGACACCCAGUCGUUAUGUCACCC-UAAAG----CUGGACUUAG--AG-UCA-CAGUCA-UGGAAAUUCUGG--GCAGUAGCAGAGACUUGCAGUCACUAACC-AAUA---GGAUGCC-GUUGG-AUGUUGCUAC-------CCAACUGACUCA---
AACY023426681.1/1153-1018  GGCUUGCACAGGCC--AAAAUCGUGUGCCC-UAGAC----CUGGAUCUCG--GA-UCA-CAGGGA-UGGAAGACUCACC-GCGCUAGUGAGCACUCA--GCAACUAUCC-UUGACC-GGACGAC-GAUCGCU----AAUU----GCCGCGGUUUUGC-UGUUU
AACY023837279.1/563-421    AGCCCCCACCGGCA--GAGAUAUGGUGGACUUGGAC----CUGGCACAGCA-GUGGCG-CAGGGAAAUGAAUGUCCGU--UUGACGGCGGAGACUCGU-GUCACUACC--UUCG----GAUGCA-GAUCAGAUAUGCCUA--AUGAACUGAUUUGACACGUUU
AACY023810512.1/1108-1250  AGCCCCCACCGGCG--AAGAUAUGGUGGACUUGGAC----CUGGCACAGCA-GUAGCG-CAGGGAAAUGAAUGUCCGU--UUGACGGCGGAGACUCGU-GUCACUACC--UUCG----GAUGCA-GAUCAGAUAUGCCUA--AUGAACUGAUUUGACACGUUU
AACY020171637.1/2433-2295  GGCUAGUGCAGGCC--AAUAUCGUGCGCUGACGACAA---CGGGAUCCAUGUGA-UCA-CCGGGA-CCAUAGACUCC---GCCGC-AGGAGCGCUCA--ACCACUAUCC-UUUACC-GGACGAA-GGUCGCA----AGUG--UGCCUGCGGCUUGGU-UGUUU
AACY020175642.1/1328-1469  GGCUUGUGUCAGCCG-GUUAACAGACACCCAUAAAAC---CUGGCACUUGG-GUUGCA-CAGGGGACGGAAAUUCCGAC-GCAGUAGCGGAGACUUGUUGCCACUAUCCUUGAC--AGGACGCA-AUUC--AUGGUAUGAAAA------GAAUUGGCACG---
AACY023297456.1/141-279    GAGCAGCGAUACUCACUCGUUAUAUCGCCC-UAAAC----CUGGACAUUGG-UGUUCG-CAGGGA-UGGAAAUUCUGAA-GCAGUAGCAGAGACUUGUAGUCACCAUCCUUUAC--AGGACGCU-AUUAG-AGUUGCUUA--------CUAAUUGACACA---
AACY020621676.1/475-342    AGCUGGCACAGGCUGUAAUAUCGUGUGCCC-UAGAC----CUGGUA-GCAA--U-ACA-CAGGGA-CGGAAGCCUUCUC-GCUACAAGAAGCACUCA--AUCACUACCC-GCAA---GGAUGCA-GAUAGCA----AAC-----GCCGCUAUUUGAU-UGUUU
AACY022246450.1/351-501    GCCGCGCACAGGCG--ACCAUUACGUGCCCUUAAAC----CCUGGUCUACUUGAAUCACAGGGGA-UGGAAGUUCCGACAUUAGCAACGGAGAUAUAG-UUCACUACC--CCACCA--GAUGAGUUAUGGGAUAUGCCUUCAUACAACCCAUUUGAACUAUAG
AACY021449047.1/488-350    GAGCAGCGAUACUCAUUUGUUAUAUCGCCC-UAAAC----CUGGACAUUGG-UGUUCU-CAGGGA-UGGAAAUUCUGAA-GCAGUAGCAGAGACUUGUAGUCACUAUCCUUCAC--AGGACGCU-AUUAG-AGUUGCUUA--------CUAAUUGACACA---
AACY020053583.1/1248-1119  GAGCAGUGACACUCAGUCGUUAUGUCACCC-UAAAA----CUGGACUUAG--AG-UCA-CAGGGA-CGGAAAUUCUGG--GCGGUAGCAGAGACUUUA-UUCACUAUCCUUUAC--AGGACG---------CCAUUAGCCUUGC---------UGACUAAUAU
#=GC SS_cons               :::::<<<<<____.._______>>>>>,,.,,,,,....<<<<<<<____.>>.>>-.>>>,,,.,,,,,,,<<<<__._______>>>>----(((.(((,,,,,<<.____...>>,,,,,.<<<<<<_________.._.___>>>>>>,)))))):::
#=GC RF                    GgCuaGcgccGGCc..aauaUcuggcgCcC.UAaAc....CuGGaccUagg.gg.uCa.CaGGGA.uGGAAguucCgac.GCaGUAgcGgagACUcgu.guCACUAuCC.Uuac...GGAcGaa.gaucGcAuaUuaaUa..u.gcagCgauuUGacacgUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01719
#=GF ID   Pseudomon-1
#=GF DE   Pseudomon-1/ErsA RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   60.00
#=GF TC   80.80
#=GF NC   49.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0046677; response to antibiotic;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0045975; positive regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0042710; biofilm formation;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF RN   [2]
#=GF RM   25186153
#=GF RT   Post-transcriptional regulation of the virulence-associated enzyme AlgC by
#=GF RT   the sigma(22) -dependent small RNA ErsA of Pseudomonas aeruginosa.
#=GF RA   Ferrara S, Carloni S, Fulco R, Falcone M, Macchi R, Bertoni G
#=GF RL   Environ Microbiol. 2015;17:199-214.
#=GF RN   [3]
#=GF RM   22590564
#=GF RT   Comparative profiling of Pseudomonas aeruginosa strains reveals
#=GF RT   differential expression of novel unique and conserved small RNAs.
#=GF RA   Ferrara S, Brugnoli M, De Bonis A, Righetti F, Delvillani F, Deho G,
#=GF RA   Horner D, Briani F, Bertoni G
#=GF RL   PLoS One. 2012;7:e36553.
#=GF RN   [4]
#=GF RM   28976035
#=GF RT   Probing the sRNA regulatory landscape of P. aeruginosa:
#=GF RT   post-transcriptional control of determinants of pathogenicity and
#=GF RT   antibiotic susceptibility.
#=GF RA   Zhang YF, Han K, Chandler CE, Tjaden B, Ernst RK, Lory S
#=GF RL   Mol Microbiol. 2017;106:919-937.
#=GF RN   [5]
#=GF RM   29497413
#=GF RT   The Small RNA ErsA of Pseudomonas aeruginosa Contributes to Biofilm
#=GF RT   Development and Motility through Post-transcriptional Modulation of AmrZ.
#=GF RA   Falcone M, Ferrara S, Rossi E, Johansen HK, Molin S, Bertoni G
#=GF RL   Front Microbiol. 2018;9:238.
#=GF CC   Functions to regulate the AlgC enzyme.[2] Based on this information, the
#=GF CC   new name ErsA for the RNA was adopted. Negatively regulates major porin
#=GF CC   oprD expression responsible for uptake of carbapenem antibiotics, by base
#=GF CC   pairing with oprD 5'UTR (leading to increased bacterial resistance to
#=GF CC   meropenem)[4].Positively regulates amrZ mRNA and contributes to biofilm
#=GF CC   formation and motility.[5]
#=GF WK   Pseudomon-1_RNA_motif
#=GF SQ   19


AAKW01000050.1/2192-2078       AUGCUCCUUUGCAGUGUUUAGUGUUGGCAGAU--UCCUGGACCCCGCCCUAGCGGUCCGGA-CUUGAACCCCGA-ACUUC-CCCUCCC-CAUACGAAGCUCGGGGUUUUUUUU-GCCUGGAA
CP000949.1/5662721-5662606     AUGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUA-UCU-GGACCCCGCCCUAGCGGUCCGGA-CUUGGACCCCGA-ACUUCCCCCUCCC-CAUACGAAGUCCGGGGUUUUUUUU-GCCCGAAA
CP000926.1/142830-142945       AUGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUA-UCU-GGACCCCGCCCUAGCGGUCCGGA-CUUGGACCCCGA-ACUUCCCCCUCCC-CAUACGAAGUCCGGGGUUUUUUUU-GCCCGGAA
CP000075.1/287565-287450       GUGCUCCUA-GUUGUGUUAAGUGUUGGCAGUUA-UCC-AGAUCCCACCCUAA-GGUCUGGACCUUAAGCCCCGGAACUUCCCCCUCCC-CAUGCGAAGUCCGGGGUCUUUUUU-GCCUGCGA
CP000438.1/6456548-6456433     AUGCUCCUUUGCAGUGUUUAGUGUUGGCAGAU--UCCUGGACCCCGCCCUAGCGGUCCGGA-CUUGAACCCCGA-ACUUCCCCCUCCC-CAUACGAAGCUCGGGGUUUUUUUU-GCCUGGAA
FM209186.1/6519552-6519437     AUGCUCCUUUGCAGUGUUUAGUGUUGGCAGAU--UCCUGGACCCCGCCCUAGCGGUCCGGA-CUUGAACCCCGA-ACUUCCCCCUCCC-CAUACGAAGCUCGGGGUUUUUUUU-GCCUGGAA
AE004091.2/6183637-6183522     AUGCUCCUUUGCAGUGUUUAGUGUUGGCAGAU--UCCUGGACCCCGCCCUAGCGGUCCGGA-CUUGAACCCCGA-ACUUCCCCCUCCC-CAUACGAAGCUCGGGGUUUUUUUU-GCCUGGAA
CT573326.1/74508-74623         AUGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUA-UCU-GGACCCCGCCCUAGCGGUCCGGA-CUUGAACCCCGA-ACUUCCCCCUCCC-CAUAUGAAGUCCGGGGUUUUUUUU-GCCCGGAA
CP000680.1/155482-155598       AUGCUCCUUUGUUGUGUUAAGCGUUGGCAGACA-UCU-GAACCCCGCCCUAGCGGUUCAGACCUUAAACCCCGA-ACUUCUCCCUCCC-CAUACGAAGCUCGGGGUUUUUUUU-GCCCAAAA
CP001157.1/65000-64890         AUGCUCCUU-GUUGUGUUAAGUGUUGGCAGAUA-UUC-GGACU---CUUCGG-GGUCCGGA-GUUGAACCCCGG-GCUUCUUCCUCCCCCACACGAAGUCCGGG--UUUUUUUUGCCCGGAA
CP000076.1/81738-81854         AUGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUA-UCU-GGACCCCGCCCUAGCGGUCUAGAACUUGAACCCCGA-ACUUCCCCCUCCC-CAUACGAAGUCCGGGGUUUUUUUU-GCCUGAAA
AE016853.1/373116-372999       GUGCUCUUAAGUUGUGUUAAGUGUUGGCAGUUAUUCC-GGACCCCACCCUAA-GGUCCGGACCUUAAGCCCCGGUACUUC-CCCUCCC-CAUGUGAAGUCCGGGGUCUUUUUUUGCCUGCGA
CP000712.1/144034-144149       AUGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUA-UCU-GGACCCCGCCCUAGCGGUCCGGA-CUUGGACCCCGA-ACUUCCCCCUCCC-CAUACGAAGUCCGGGGUUUUUUUU-GCCCGGAA
AAQW01000001.1/6411526-6411411 AUGCUCCUUUGCAGUGUUUAGUGUUGGCAGAU--UCCUGGACCCCGCCCUAGCGGUCCGGA-CUUGAACCCCGA-ACUUCCCCCUCCC-CAUACGAAGCUCGGGGUUUUUUUU-GCCUGGAA
CP000304.1/135860-135973       AUGCUCCUU-GUUGUGUUAAGUGUUGGCAGAUC-UCU-GGACCCCGCCCUAGCGGUCCGGA-UUCGA-CCUCGA-ACUUCCCCCUCCC-CCAAUGAAGUUCGAGGUUUUUUUU-GCCUGGAG
CP000744.1/6507817-6507702     AUGCUCCUUUGCAGUGUUUAGUGUUGGCAGAU--UCCUGGACCCCGCCCUAGCGGUCCGGA-CUUGAACCCCGA-ACUUCCCCCUCCC-CAUACGAAGCUCGGGGUUUUUUUU-GCCUGGAA
AE015451.1/130441-130556       AUGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUA-UCU-GGACCCCGCCCUAGCGGUCCGGA-CUUGGACCCCGA-ACUUCCCCCUCCC-CAUACGAAGUCCGGGGUUUUUUUU-GCCCGGAA
CP000058.1/299668-299553       GUGCUCCUA-GUUGUGUUAAGUGUUGGCAGUUA-UCC-AGAUCCCACCCUAA-GGUCUGGACCUUAAGCCCCGGAACUUCCCCCUCCC-CAUGCGAAGUCCGGGGUCUUUUUU-GCCUGCGA
CP000094.2/60881-60764         AUGCUCCUAUGUUGUGUUAAGUGUUGGCAGAUA-UCU-GAACCCCGCCCUAGCGGUUCGGAACUUAAACCCCGGAACUUCUCCCUCCC-CAUAUGAAGUCCGGGGCUUUUUUU-GCCUGCGA
#=GC SS_cons                   :::::::::::::::::::::::::::::::::.<<<.<<<<<__________>>>>>>>>.---<<<<<<<<<.<<<<<________._____>>>>>>>>>>>->>>::::.::::::::
#=GC RF                        AUGCUCCUauGuuGUGUUaAGUGUUGGCAGAUA.uCc.GGaCCCCgCCCUAGCGGuCCgGa.cUUgaaCCCCGg.aCuuCcCCCUCCC.CAUAcGaaGucCGGGGUuuuUUUU.GCCuGgAA
//
# STOCKHOLM 1.0

#=GF AC   RF01720
#=GF ID   Pseudomon-Rho
#=GF DE   Pseudomon-Rho RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   45.00
#=GF TC   48.00
#=GF NC   40.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Pseudomon-Rho_RNA_motif
#=GF SQ   16


AE015451.1/5948619-5948520 UUCGGC-CUCGCACUG----CUUUUC---CAGUGCCCUCUACAUGCCGUCGCCGA-AGCA--UC--CCUAAUUCGAAUCAGUA-CGCGA-UCCUG-UCGCCAUC-CAGCGGCGCGGC
CP000680.1/316056-316157   UUCGGC-CUCGCUGCA----UUUCCUUA-UGCAGCCCUCUGCAUGCCGUCGCCGA-UUCAU-UC--C--UACUCGAACUCGUU-CGCGA-UCCUG-UCGCCUUCUCUGCGGCGCGGC
CP001157.1/4815671-4815563 UUCGGCUCUCGCAGCGAAUCUAUCUUUAUCGCUGUCCUCCGUCAGUCGUCGCCGA-CGCACCUC-----UUUUAGAACAAGUACAGCGA-UCCGA-UCGCCUUCCCUGCGGCGCGGC
CP000058.1/330473-330572   UUCGGC-CCCGCAACG---GCUUCUC---CGUUGCCCCCUGCUAGCCGUCGCCGA-CGC---UCU-CCU--UUCGAUUUAGUA-CGCGA-UCCUG-UCGCCUUUUCUGCGGCGCGGC
CP000076.1/6800498-6800398 UUCGGC-CCCGCACUG---GUUUCUC---CAUUGCCCCCUGCAAGCCGUCGCCGA-CGC---UCUCC--UUUUCGAAUUAGUA-CGCGA-UCCUG-UCGCCUUCUCUGCGGCGCGGC
CP000744.1/6182387-6182288 UUCGGG-CUCGCGACG---UUUUUUC---CGUCGCCUUCUGCAUGCCG-UCCCGGACGCACUUC--C--UACUCGAACUUUCU-AGCGC-UCCUG-UCGCC-CC-UUGCGACACGGC
CP000949.1/5563696-5563597 UUCGGC-CUCGCACUG----UUUCUC---CAGUGCCCCCUGCACGCCGUCGCCGA-CGCACU----CCUAAUUAGAAUCUGUG-CGCGA-UCCUA-UCGCCUUC-UAGCGGCGCGGC
CP000304.1/602149-602251   UUCGGC-CACGCGACG----CUUUCUUC-CGUCGCCCUCUGCAUGCCGUCGCCGA-CGCACUUCAGCCUCAU----AAAGCAC-AACGAACCUCGUUCGUC-UC-CUGCUGCGCGGC
AM181176.4/6458453-6458354 UUCGGC-CCCGCACUG---GUUUCUC---CACUGCCCCCUGCAAGCCGUCGCCGA-CGCAU-UC--C--UUUUCG-AUUAGUA-CGCGA-UCCUG-UCGCCUUCUCUGCGGCGCGGC
CP000712.1/5757664-5757565 UUCGGC-CUCGCACUG----CUUUUC---CAGUGCCCUCUACAUGCCGUCGCCGA-AGCA--UC--CCUAAUUCGAAUCAGUA-CGCGA-UCCUG-UCGCCAUC-CAGCGGCGCGGC
AE016853.1/5963068-5962969 UUCGGC-CCCGCAACG---GCUUCUC---CGUUGCCCCCUGCUAGCCGUCGCCGA-CGC---UCU-CCU--UUCGAUUUAGUA-CGCGA-UCCUG-UCGCCUUUUCUGCGGCGCGGC
AE004091.2/5900281-5900181 UUCGGG-UUCGCGACG---UUUUUUC---CGUCGCCUUCUGCAUGCCG-UCCCGGACGCACUUC--C--UACUCGAACUUUCU-AGCGC-UCCUG-UCGCCCCC-UUGCGACACGGC
CT573326.1/5652749-5652649 UUCGGC-CUCGCACUG---ACCCUUU---CAGUGCCCUCUGCACGCCGUCGCCGA-AGCA--UC--CCUAAUUCGAAUCAGUA-CGCGA-UCUUG-UCGCCAUC-UAGCGGCGCGGC
CP000075.1/320164-320263   UUCGGC-CCCGCAACG---GCUUCUC---CGUUGCCCCCUGCUAGCCGUCGCCGA-CGC---UCU-CCU--UUCGAUUUAGUA-CGCGA-UCCUG-UCGCCUUUUCUGCGGCGCGGC
CP000926.1/5894889-5894790 UUCGGC-CUCGCACUG----CUUUUC---CAGUGCCCUCUACACGCCGUCGCCGA-AGCA--UC--CCUAAUUCGAAUCAGUA-CGCGA-UCCUG-UCGCCAUC-UAGCGGCGCGGC
CP000094.2/6124613-6124513 UUCGGC-CCCGCACUG---GUUUCUC---CACUGCCCCCUGCUAGCCGUCGCCGA-CGCAC-UC--C--UUUUCGAAUAAGUA-CGCGA-UCCUG-UCGCCUUCUCCGCGGCGCGGC
#=GC SS_cons               ::::::.:::<<<<<<..._______...>>>>>>---------<<<<-<<<<<-.-----.--..-----------------.-<<<<.<___>.>>>>----.--->>>>>>>>>
#=GC RF                    UUCGGc.CuCGCggcG...uuUUuUc...CgccGCCCuCUGCauGCCGUCGCcGA.cGCAc.UC..CCUuaUUcGAAuuagua.cGCGa.cCCug.uCGCCuUC.cuGCgGCGCGGC
//
# STOCKHOLM 1.0

#=GF AC   RF01721
#=GF ID   Pseudomon-groES
#=GF DE   Pseudomon-groES RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   50.70
#=GF NC   35.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.91 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Pseudomon-groES_RNA_motif
#=GF SQ   18


CP000075.1/4857654-4857544 GUA-UGGGUCACCGCAAGGUUUCUGGCCUGAA--GGCCAGACCGUA-UUCUGCGGUUCG-CGCGU-CGAACCGUAA-CCGGC-AAGUCCGGAUUU----AAACCGGCCGGUGCACU-----CACCGGA
CP000744.1/5112607-5112494 GUA-ACGGUCACCGCAAGGUCCCUGCC-AUACG--GGCAGGCUGUC-UUACGCGGCUCG-CGCGU-CGAGUCGCAACCCGGC-AACGCCGGCUUCAAC-AAACCCGCCGGA-CUUCGA----UCCGGC
AE004091.2/4917616-4917502 GUA-ACGGUCACCGCAAGGUCCCUGCC-ACAAG--GGCAGGCUGUC-UUACGCGGCUCG-CGCGU-CGAGUCGCAACCCGGC-AACGCCGGCUUCAACAAAACCCGCCGGA-CUUCGA----UCCGGC
D26376.1/164-278           GUA-ACGGUCACCGCAAGGUCCCUGCC-ACAAG--GGCAGGCUGUC-UUACGCGGCUCG-CGCGU-CGAGUCGCAACCCGGC-AACGCCGGCUUCAACAAAACCCGCCGGA-CUUCGA----UCCGGC
CP000926.1/5023691-5023573 GUAUGUGGUCACCGCAAGGUUUCUGGCGGCAA--CGCCAGACAUUACACAGGUGGUUCGCCCAUUGCGGGCCACCUCCCGGC-AACGCCGGACAGCAU-CAACCCGCCGGUGUCGA-----UACCGGC
CP000712.1/4882595-4882478 GUAUGUGGUCACCGCAAGGUUUCUGGUGGCAA--CACCAGACAUUACACAGGUGGUUCGCUCACAGCGGGCCACCC-CCGGC-AACGCCGGACAGCAUCAAAACCGCCGGU-GUCGA-----ACCGGC
CP000304.1/3389964-3389849 GUA-GCGGACACCGCAAGGUCGCUGUCGUGUU--CGACAGUCCGUC-UUCUGCGGCUCG-CACUG-CGGGCCGCAA-CCGGC-ACAGCCGGAUUUGCC-CAACCCGCCGAUGAAGGGU---CAUCGGC
AE015451.1/1549106-1549223 GUAUGUGGUCACCGCAAGGUUUCUGGUGGCAA--CACCAGACAUUACACAGGUGGUUCGCUCACAGCGGGCCACCC-CCGGC-AACGCCGGACAGCAUCAAAACCGCCGGU-GUCGA-----ACCGGC
FM209186.1/5251323-5251209 GUA-ACGGUCACCGCAAGGUCCCUGCC-ACAAG--GGCAGGCUGUC-UUACGCGGCUCG-CGCGU-CGAGUCGCAACCCGGC-AACGCCGGCUUCAACAAAACCCGCCGGA-CUUCGA----UCCGGC
CP000949.1/1064702-1064819 GUAUGUGGUCACCGCAAGGUUUCUGGUGGCAA--CACCAGACAAUACACAGGUGGUUCGCCCGUCGCGGGCCACCC-CCGGC-AACGCCGGACAGCAU-CAACCCGCCGGUGUCGA-----CACCGGC
CP000438.1/5081170-5081056 GUA-ACGGUCACCGCAAGGUCCCUGCC-ACAAG--GGCAGGCUGUC-UUACGCGGCUCG-CGCGU-CGAGUCGCAACCCGGC-AACGCCGGCUUCAACAAAACCCGCCGGA-CUUCGA----UCCGGC
CP000076.1/5584544-5584432 GUA-ACGGUCACCGCAAGGUUUCUGGUGCUGA--CACCAGACAGAC-UUCCGCGGCUCG-CUUGU-CGAGCCGCAC-CCGGC-AAAGCCGGAUUUGCU--AACCCGCCGGU-AUCGAC----ACCGGC
CT573326.1/4773909-4773793 GUA-GUGGUCACCGCAAGGUUUCCGGUGAGUU--CACCGGGCAUGACACACGGGGUUCGCUGAAGGCGGGCCCUGA-CCGGC-AACGCCGGACCGAAU-CAACCCGCCGGUGCUGA-----CACCGGC
CP001157.1/1312101-1312213 CUA-GCGGUCACCGCAAGGUUCCUGUC-GGAC---GACAGGCUAUC-UUCUGCGGUCCCGCACUGC-GGGCCGCAA-CCGGC-AAUGCCGGCUUUUAC-UAACGGGCCGAUGAUGG-----CAUCGGU
CP000058.1/4661390-4661280 GUA-UGGGUCACCGCAAGGUUUCUGGC-AUGAAG-GCCAGACCGUA-UUCUGCGGUUCG-CGCGU-CGAACCGUAA-CCGGC-AAGUCCGGAUUU----AAACCGGCCGGUGCACU-----CACCGGA
AE016853.1/4940472-4940362 GUA-UGGGUCACCGCAAGGUUUCUGGC-CUGAAC-GCCAGACCGUA-UUCUGCGGUUCG-CGCGU-CGAACCGUAA-CCGGC-AAGUCCGGAUCC----GUAGCGGCUGGCGCAUU-----CGCCGGA
CP000680.1/4070023-4070138 GUA-GCAGUCACCGCAAGGUGCCUGCC-CCUGA--GGCAGUCCGAC-UUUCGCGGUGCG-CCCAG-CGUGCCGCGC-CCGGC-CUCGCCGGAUUUUAC-AAACCCGCCGAC-CAAGCAAGA-GUCGGC
CP000094.2/5078998-5078885 GUA-UCGGUCACCGAAAGGUUUCCGGU-AUUUGA-ACCGGACAGAC-UUCCGCGGUUCG-CUCGA-CGAGCCGCAA-CCGGCGCAGGCCGGAUUCGUU-AAACCCGCCGG--GACUACA----CCGGC
#=GC SS_cons               :::.::::::<<<____>>>,<<<<<<.____...>>>>>>,,,,,.,,,<<<<<<<<<._____.>>>>>>>>>,.<<<<_.____>>>>,,,,,,,.,,,,,,<<<<<<._____.....>>>>>>
#=GC RF                    GUA.gcGGUCACCGCAAGGUucCuGgc.auaa...gcCaGgCagua.uUacGcGGcuCG.Cgcgu.CGagCCgCga.CCGGC.AAcGCCGGaUuuaau.aAAcCcgCCGGu.cuuua.....aCCGGc
//
# STOCKHOLM 1.0

#=GF AC   RF01722
#=GF ID   Pyrobac-1
#=GF DE   Pyrobac-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   41.20
#=GF NC   35.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF RN   [2]
#=GF RM   22282340
#=GF RT   Discovery of Pyrobaculum small RNA families with atypical pseudouridine
#=GF RT   guide RNA features.
#=GF RA   Bernick DL, Dennis PP, Hochsmann M, Lowe TM
#=GF RL   RNA. 2012;18:402-411.
#=GF CC   The motif has been shown by [2] to be part of sRNA202 and sRNA203
#=GF CC   canonical and noncanonical pseudouridine guide RNA (H/ACA RNA). 
#=GF WK   Pyrobac-1_RNA_motif
#=GF SQ   8


CP000561.1/138640-138702   ACUGCCGGGACUACGCCGGGCAAGGCCGGC-GCCGU-GCCGCGCUGUGACCCCGGCGGGGCGCCU
CP000504.1/1105103-1105165 ACUGCCGGGACUACGCCGGAUAAGAGCGGC-UAUAU-GCCGCGCUGUGAAUCCGGCGGGGUUUUA
CP000504.1/1584379-1584438 AAAUUCUAGAU--GGGCUACAGAGAGCCGC-UUAC--GCGGCACUGUGAUGUAGCCUGACGGUGU
CP000561.1/482784-482726   ACG-CCGCGAC--GGGCUGUCGAGAGCCGC-GUCU--GCGGCGCUGUGAGACGGCCUGACGGCGU
AE009441.1/587219-587280   UGUGCCGGGACUACGCCGGGUGAGAGCGGC-GUGU--GCCGCCCUGUGAAUCCGGCGGGGUGCCU
CP000660.1/634088-634027   ACA-CAGCGAC--AGGCUGUUGAGAGCCGCCUCAGAGGCGGCGCUGUGAGACGGCCUGACGGUGU
CP000660.1/650735-650674   AGCGCCGGGACUACGCCGGGUGAGAGCGGC-UGGC--GCCGCACUGUGGGCCCGGCGGGGUGCCU
AE009441.1/1080081-1080140 ACAACCGCGAC--GGGCUGUGGAGAGCCGC-GCCC--GCGGCGCCGUGAAACAGCCUGACGGUGU
#=GC SS_cons               ::::::::::<..<<<<<<<<----<<<<<.____..>>>>>------->>>>>>>>>:::::::
#=GC RF                    AcagCCGgGAC..cGgCgGguGAGAGCgGC.uuac..GCcGCgCUGUGAacCcGcCgGaggGugU
//
# STOCKHOLM 1.0

#=GF AC   RF01723
#=GF ID   Rhizobiales-2
#=GF DE   Rhizobiales-2 RNA
#=GF AU   Corbino K
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   43.60
#=GF NC   37.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Rhizobiales-2_RNA_motif
#=GF SQ   15


CP000301.1/1899601-1899703 GGGAGCGGACAUCC-CUCCCCAACGAUGCCGUAUUC-GGCGCGAGCGCC-CAUCCACCC-A-GCGCC-AAUA-UGGCUC---GACCCGCCCGGUUGUCCCCCCCGGGCGGGUC
CP000283.1/2153720-2153823 GGGAGCGGAAAGCCCCUCCCCAACGAGGCUGUAUUC-GGCGCGAGCGCC-CAUCCACCCCA-GCGCCA-AUA-UGGCUU---GACCCGCCCGGUUGUCCCC-CCGGGCGGGUC
CP000494.1/3149215-3149317 GGGAGCGGUGAUCC-CUCUCCCCAAA-GCUAUAUAA-GGCGCGAGCGCC-CAUCCACCCCAAGCGCCC-AUA-UGGCU---CGAGCCGUCCGGUUGUCCCC-CCGGACGGCUC
CP001096.1/2195886-2195989 GGGAGCGGAAACCACCUCCCUAAUGAGGCCAGUC---GGCGCGAGCGCC-CAUCCACCCCU-GCGCU--GAUAUGGCUUU-UGACCCGCCCGGUUGUCCCC-CCGGGCGGGUC
CP000250.1/641631-641545   UCCACACG------CGUGGAGUU-GCG----UCC---GGCACGGGCGCCUCAUCCACCCCC-GUGUC--GGA-----GCA--GACCCGCCCGGUCGUCCC--CCGGGCGGGUC
BA000040.2/86174-86270     CUGAGGCCGAU----CUCACGUGGAUCCU-GCGUCC-GACACGGGCGCCUCAUCCACCCC--GUGUC--GUG-C----CCCGACCCCGCCCGGCUGUCCCC-CCGGGCGGGGU
AAMY01000022.1/71516-71421 GGGAGGCA-----AACUCCCCG--AG-GCUAUAU-CAGGCGCGAGCGCC-CAUCCACCCCA-GCGCCC-AUA-UGGCUU---GACCCGUCCGGUUGUCCCC-CCGGACGGGUC
CP000250.1/4059694-4059591 GGGAGCGGAAAGCCCCUCCCCAAAGAGGCUGUAUUC-GGCGCGAGCGCC-CAUCCACCCCA-GCGCC-AAUA-CGGCUU---GACCCGCCCGGCUGUCCCC-CCGGGCGGGUC
BX572598.1/302205-302308   GGGAGCGGAAACCACCUCCCUAACGAGGCCAGUC---GGCGCGAGCGCC-CAUCCACCCCU-GCGCU--GAUAUGGCUUU-UGACCCGCCCGGUUGUCCCC-CCGGGCGGGUC
BA000040.2/3362455-3362556 GGGAGCGGUCAUCC-CUCCCCAUC-A-GUCAUAU-CAGGCGCGAGCGCC-CAUCCACCCCAAGCGCCC-AUA-UGGCU---CGACCCGUCCGGUUGUCCCC-CCGGACGGGUC
CP000463.1/2056469-2056569 GGGAGCGCAAACCA-CUCCCCAUC-G-GCUGUAUUC-GGCGCGAGCGCC-CAUCCACCCAA-GCGCC-AAUA-UGGCU---UGACCCGCCCGGCUGUCCCC-CCGGGCGGGUC
CP000463.1/126470-126561   AUCGCCGCCCAACCCGUGGAGUCGCG------UCC--GGCACGGGCGCCUCAUCCACCCC--GUGUC--GAAC--------CGACCCGCCCGGCUGUCCCC-CCGGGCGGGUU
CP000319.1/2918364-2918268 GGGAGCCAAAA----CUCCCCA--AA-GCUAUAU-CAGGCGCGAGCGCC-CAUCCACCCCA-GCGCCC-AUA-UGGCUU---GACCCGCCCGGUUGUCCCC-CCGGGCGGGUC
CU234118.1/2873967-2874068 GGGAGCGGUGAUCCCCUCCCCAU--A-GCUAUAU-CAGGCGCGAGCGCC-CAUCCACCCCAAGCGCCC-AUA-UGGCU---CGAGCCGUCCGGUUGUCCCC-CCGGACGGCUC
CP000115.1/2442749-2442653 GGGAGGCCA----AACUCCCCG--AG-GCUAUAU-CAGGCGCGAGCGCC-CAUCCACCCCA-GCGCCC-AUA-UGGCUU---GACCCGUCCGGUUGUCCCC-CCGGACGGGUC
#=GC SS_cons               <<<<<__________>>>>>,,,,<<-<<<<<<<--.<<<<<_______.___________.>>>>>..>>>.>>>>>>..-<<<<<<<<<<<________.>>>>>>>>>>>
#=GC RF                    gggagcggaaAuCaccuccccauagagGccgugcuc.GgCgCGaGCGCC.CAUCCACCCCa.GcGcC..gca.cggCuc..uGacCCGcCCGGuUGUCCCC.CCGGgCGGguC
//
# STOCKHOLM 1.0

#=GF AC   RF01724
#=GF ID   SAM-Chlorobi
#=GF DE   SAM-Chlorobi RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   35.00
#=GF TC   47.80
#=GF NC   32.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   SAM-Chlorobi_RNA_motif
#=GF SQ   9


CP000492.1/1051404-1051321 CGGCAUCCCCAUUACCUAUGGACACGGUGCC-CCGGA--CU--CA-------GA--AA---UA---ACUU--UU-UG-A-G-UCUU-CCGGGAAAGAUUUU-CCGUGUCC-AG
CP000096.1/776880-776786   AGGCAUCCCCAUUACCUAUGGACACGGUGCCG-CAGGCUCA--CUCCCU-CUGG--AA---UUCA-GUUU--CCAAG-U-GACCUGCCGG--AAAGGUUUU-CCGUGUCC-AG
CP001097.1/1777504-1777592 CGGCAUCCCCAUUACCUAUGGACACGGUGCCG-CAGG--CU--CU---U-CCGG--AAA-AUUC--UUUU--CC-GG-A-U-CCUGCAGG--AAAAAUUUU-CCGUGUCC-AG
CP001110.1/2180242-2180331 CGACAUCCCCAUUACCUAUGGACACGGUGUCG-CAGG--CU--CUCA-A-CAGG--GGUUGUU----UCC--CC-AG-G-G-UCUGCUGG--AA--GUUUUUCCGUGUCCCAG
CP001101.1/1771524-1771611 CGGCAUCCCCAUUACCUAUGGACACGGUGCCG-AAAG--CUU-CC-------GG--CC--GAUC--G-GU--UCAGGAAUG-CUU-GUAUUCA-GGGUUUU-CCGUGUCC-AC
AE006470.1/705942-705855   CGGCAUCCCCAUUACCUAUGGACACGGUGCCA-AAAG--CU--CUCU-UGC-GG--GA--GUU---G-UC--CCCGG-A-G-CUUG-CCG--AAAGGUUUC-CCGUGUCC-CG
AASE01000037.1/8265-8178   UGACACUCCCAUUACCUAUGGACACGGUGUCA-CAAG--CU--CUCA-A-C-AG--GG--GUUCU-G-CC--CU-CG-A-G-CUUGCCGG--AA--GUUUUUCCGUGUCC-AG
CP001108.1/886484-886396   AGGCAUCCCCAUUACCUAUGGACACGGUGCCG-CAAU--CU--CC-------GGAAGA--GAUC--GUUCGACC-GGAA-G-AUUGUUGUC-G--GGUUUU-CCGUGUCC-AU
CP000607.1/1264526-1264615 CAGCAUCACCAUUAUCUAUGGACACGGUGCUG-CAGA--CCUUCU-------GG--AAG-GAACAUGGUU--CC-AG-G-G-UCUGUCGG--AAAGGUUUU-CCGUGUCC-AG
#=GC SS_cons               <<<<<<<-<<<<_____>>>>---->>>>>>>.<<<<..<<..<<...-.-.<<..<<..____..__>>..>>.>>.>.>.>>>>::::..:::::::::.::::::::.::
#=GC RF                    cGGCAuCCCCAUUACCUAUGGACACGgUGCCg.cagg..Cu..Cc...u.C.GG..gg..GuuC..gucc..CC.gG.a.G.ccuguugg..AAAGGUUUU.CCGUGUCC.Ag
//
# STOCKHOLM 1.0

#=GF AC   RF01725
#=GF ID   SAM-I-IV-variant
#=GF DE   SAM-I/IV variant riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.80
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.35 -Z 549862.597050 CM SEQDB
#=GF CL   CL00012
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0046500; S-adenosylmethionine metabolic process;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   SAM_riboswitch_(S_box_leader)
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   437


ABEF01007799.1/1141-1268       CACCAGCAUCAGGAGCGACCC--------AUUA------------GGGU-CCGGCA-ACC-U-AGC--A--ACGGAGA----UA-GCUA--AGGUGCCUU-G-A-GA--GUG-A------------ACAA------------------UCAUUC-------UCGAUGUGCGGGUUC--------CAGUU------------------------GAGCCCGAAACAGAAA-CUCCGACGG
BAAX01001997.1/1769-1874       UCGAAACAUCAAGAG-CAGUA--------UUAA------------U-CU-GCACCA-ACC-G-AGC-----ACGACA--------GCCA--CGGUGGU----------------------------CAAGAUAC-----------------------------GAUGUGGAAAU----------AAGUUUA------------------------AUUUCAAAAA-UAAGUCUUUAUGA
ABEF01026777.1/1438-1540       AACCAGCAUCAAGAGCAGGGU--------UGAC------------GCCC-UCGCCA-ACC-U-GCCC----UGUCC--------GGGCA--AGGUGGUU----------CC--C------------GAAA------------------G-GG-----------GAUGCGGCC------------ACAA-----------------------------GGCAA---CAAAGCGGGCCCAU
AACY020331037.1/853-942        GCUUUGCAUAAAGAG-AG-----------GGAAGC-------------C-UCAGCA-ACC-U-AGA-----AUGCCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUUAC----------------------------AACAA----AAAAUGGCUUUUU
AACY020251371.1/791-877        AAGUUGCAUAGAGAG-AGGAA------------------------UUCC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAUUGGCGUUC
AACY020473630.1/833-747        UGAAUGCAUAGAGAG-AGGAA------------------------UUCC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY020357342.1/559-467        AAUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY020554034.1/791-702        GUUUUGCAUAAAGAG-AGG----------GAAG--------------CC-UCAGCA-ACC-U-AGA-----UUGCCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUUAC----------------------------AACAA----AAAAUGGCUUUUU
AACY023471425.1/1443-1530      UAAAUGCAUAGAGAG-AGGAA------------------------UUCC-UCAGCA-ACC-U-AG------AUGCCAA--------CUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA----AAAAUGGCGUUCC
AACY021769818.1/232-138        CAUUGUCAUCAAGAGUUGGG---------AUGACA-----------CCC-ACACCA-ACC-U-GCU-----UACCG---------AGCA--AGGUGGUC---------------------------AAAC---------------------------------GAUGUGGCC------------UUAG-----------------------------GGCAA-CCAAUCGCGUGUCA--
AACY022292471.1/307-208        AUUAAGCAUCAGGAGUGAAUA--------AGAAAU----------UAUU-CUGCCA-ACC-U-GCUU----UGAGGA-------AAGUA--AGGUGGA----------------------------GUAG---------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
AACY020250700.1/987-1093       GAAUAUCAUUAAGAGUUCCGUGA------AAG-----------UCACGG-AUGCCA-ACC-G-AUCC----UUCGCA-------GGGCA--CGGUGGAA----------------------------AAAAAA------------------------------GAUGAGAGG------------CUCGCA---------------------------CCUAAAAACAAAUAGCGAAUC-
AACY020289175.1/1718-1630      AAAAAGCAUGGAGAG-AGGUU-----------A------------AGCC-UCAGCA-ACC-U-AGA----AAGCUA---------ACUA--AGGUGCUU---------------------------UAAG---------------------------------UAUGUGGUU------------UGA------------------------------AACAA-----AAAAUAGCUUUU
AACY020436349.1/1266-1356      AAGAUGCAUUAGGAAAGGGG---------UUA--------------UCC-CUGCCA-ACC-U-GCA-----UACCG---------UGCGA-AGGUGGUA----------------------------AUA---------------------------------UAUGCGGCC------------AAAA-----------------------------GGCAAAAA----UUAGGUCUCA
AACY022194140.1/224-333        -----UCAUCAGGAGAGGUUUC-------UUACUU---------GAAAC-CCACCA-ACC-G-AAC-----UUAAAA--------GUUA--CGGUGGUUAGU-U-----CCA-U-------------UAA------------------ACGG---------GAGAUGUGCCUU-----------GAAA----------------------------AAGGAAAAA-UAGAACCGCCU--
AACY020691912.1/807-704        UCGCUACAUCACGAG-CGACC--------AACU------------GGUC--CGGCA-ACC-G-GGA-----------A-------UCCA--CGGUGCCAA-G-------UCA-C------------UUCG------------------GUGA----------CGAUGUGGCCCC----------GCAA---------------------------GGGGCAA-CGGACCCGUGACUC--
AACY020553512.1/101-193        AUUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAU
CP000873.1/467570-467678       ACCGCACAUCCAGAG-UUGGG--------GCGACG----------CCCA-ACGCCA-ACC-U-GCC-----GUUCCG--------GGCA--AGGUGGUAC-U-------CCC-C------------GAAA------------------GGGA----------GGAUGUGGCCG-----------AAC-----------------------------CGGCAA---UUAUACGGAUGAAG
AACY020784198.1/120-213        AGAAAGCAUCAAGAA--CACA--------UAAU------------UGUG--UACCA-ACC-G-ACC-----UUCCGA--------GGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGCGGGAC-----------AAUC----------------------------GUUCAAAA---GUUUCGGAAAUC
AACY020281887.1/114-202        UAUUUGCAUAUAGAG-AGG----------GAAA--------------CC-UCAGCA-ACC-U-AGA-----AUGCCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UUAC-----------------------------AACAA----AAAAUGGCUUUUU
AACY023696825.1/714-806        AAUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY023507554.1/1049-1148      AUUAAGCAUCAGGAGUGAAUA--------AGAAAU----------UAUU-CUGCCA-ACC-U-GCUU----UGAGGA-------AAGUA--AGGUGGA----------------------------GUAG---------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
AACY020176386.1/887-1007       AUCCUGUAUGUAGAG-UGCCUCU------CGAU----------AGGGGC--CACCAGACC-G-AGCAACU-CCACA-----AGUAGCCA--CGGUGGUU---------------------AGAAUCGCAA--------GAUUC--------------------CAUACGUAGG-----------AGACAA--------------------------CCUAAAAAA--UGGAGGUGCCC-
AACY020430151.1/744-648        AAAAAGCAUCAAGAGCAGAG---------UUAAGU-----------CUC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAC--------------------------AAAU---------------------------------GAUGCGGUU------------GUUC-----------------------------AACAA---AUAAUGGAGAUAAA
AACY022771515.1/120-17         GCGCUACAUCACGAG-CGACC--------AAAC------------GGUC--CGGCA-ACC-G-GGA---------------A---UCCA--CGGUGCCAA-G-------UCA-C------------UUCG------------------GUGA----------CGAUGUGGCCCC----------GCAA---------------------------GGGGCAA-CGGAUCGCAUGGUG--
AACY020114415.1/340-432        UUAAAACAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY021536907.1/438-344        UCAAAAUAUCACGAGAAGGGU--------UUGC------------AUCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUAUGGC-------------GUUCA-----------------------------GCAAA---CAUAGGAGAAUAG
AACY022508868.1/93-196         UUAUAACAUCAAGACAAGGGC--------CGAC------------GCCC-UGACCA-ACC-U-GCC-----CCCCG---------GGCA--AGGUGGACG-C-G----------------------AAAG-------------------------------CGGAUGUGGCCUAA---------AGU---------------------------UUAGGCAA----CCAAGCGGGAGUA
AACY021479654.1/475-585        AAUCAGCAUCUAGAAACACCUC-------GCAA-----------GAGGU-GUGGCA-ACC-G-AGCC----CACCA--------GGCCA--CGGUGCCU----------CCC-A------------ACAAA-----------------UGGG-----------GAUGCGGCGC-----------GACGA---------------------------GCGCAAAA---GAACUGGUGCUC
AACY023698657.1/321-413        AAUAAGCAUAUAGAG-AAGGU--------AAAG------------ACCU--CAGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY020556356.1/9293-9389      AAACUACAUUUUGAG-AGGGA--------GUAA------------UCCC--UGCCA-ACC-U-GCA-----AUAACC--------UGCGA-AGGUGGU---------------A------------ACUU------------------U--------------AAUGUGGCUUA----------A------------------------------UAAGCAAAAAAA---GGUUCUUUC
AACY020173786.1/742-856        CGACGACAUCACGAGCGACCC--------UCAC------------GGGU-CCGGCA-ACC-G-GG------AUCG-----------CCACUCGGUGCCAU-C-U-CG--CC---------------GCGA--------------------GGCG-------GGGAUGUGGUCCCGC--------GACG-------------------------GCGGGACAA-GGAGGUGACAUGGC--
AACY023398704.1/1264-1169      AAAAAUCAUCAAGAG-UGAGA--------UUAGGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAA---------------------------------GAUGAGGUU------------AAUC-----------------------------AACAA---GUAUAGGAGUGUUA
AACY020554374.1/5481-5389      AUUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY023713997.1/222-314        UAGGAACAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUUG-U------------------------------------------------------------AGAUGUGGCA------------GUAA-----------------------------UGCAA---CUAAGUAGUCGUAU
AACY021580150.1/451-351        CCUCAGCAUUAAGAG-AGGGC--------UGAC------------GCCC--CGCCA-ACC-U-GCA-----GCUG----------UGCA--AGGUGGUC----------UCC-C------------GCCA------------------GGGA-----------AAUGUGGCC------------UUCAA----------------------------GGCAA-CAACAGCGUCGGCC--
AACY020744244.1/368-464        UUUAUGCAUUAAGAGCAGGA---------UUAAUU-----------UCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGUA--AGGUGGAAA--------------------------AAAU---------------------------------GAUGCGGUU------------AACC-----------------------------AACAA---CUAUAGGAGCUAAA
AACY020106543.1/2258-2159      AUUAAGCAUCAGGAGUGAAUA--------AGAAAU----------UAUU-CUGCCA-ACC-U-GCUU----UGAGGA-------AAGUA--AGGUGGA----------------------------GUAG---------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
AACY023366624.1/990-898        ACAGUGCAUCAAGAA-CGC----------AAU---------------GC-GUACCA-ACC-G-ACA-----CACUCGA-------UGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGCGGAGA-----------ACAAC---------------------------UCUCAA--AUUAAUCGAGUAAU-
AACY022380554.1/353-444        GUAUAGCAUCAAGAA-CGC----------AAU---------------GC-GUACCA-ACC-G-ACA-----CACUCGA-------UGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGUGGAGA-----------UAUU----------------------------UCUCAA-AGAUUCGAGUAAUC--
AACY021048897.1/409-545        CUUUGGCAUCCAGAGUCCCACGC-----GACCU----CUUGAAGCGUGG-GCGGCA-ACC-G-GGUC----AAGCGC-------GAUCA--CGGUGCCGA-G---GUCAGCC-C------------UUCU------------------GGGG----------UGAUGCGGC-ACGCAAGGC---CAU---------------------GCCUUGUGCAGCAA-CAUCAGCGCUC-----
AACY022728072.1/92-211         ACAGUACAUCAAGAGUUGUUCA-------UUAA-----------UGAAC-ACGGCA-ACC-U-GGG-----AUUGACA-------CCCA--AGGUGCCA--C-U-AG--CC---------------GAAG--------------------GGUU-------AGGAUGGGGUUUAGC--------CGAAA------------------------GCUAAGCAA-AAAAGUGUGAGAAA--
AACY020588692.1/445-537        UAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY020048217.1/3548-3456      AAUAUACAUUAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAACUAGUCAAAA
AACY023738170.1/418-505        GUUUUGCAUAAAGAG-AGG----------AAAU--------------CC-UCAGCA-ACC-U-AG------AUACCAA--------CUA--AGGUGCUA----------------------------UUU---------------------------------GAUGUGGUU------------UUAC-----------------------------AACAA----AAAAUGGUAUUUC
AACY020148119.1/839-753        UGAGUGCAUAUAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY020516216.1/1635-1543      AGUAAGCAUAUUGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY023587568.1/603-501        ACCCAUCAUUAAGAG-AGGAC--------UGAC------------GUCC--CGCCA-ACC-U-GCC-----UUUUCC--------GGCA--AGGUGGUA----------GCC-U------------UAGUU-----------------AGGC-----------GAUGAGACC------------CUUG-----------------------------GGUAA---CUAAUGGAUCAUCA
AACY023449939.1/987-888        AUUAAGCAUCAGGAGUGAAUA--------AGAAAU----------UAUU-CUGCCA-ACC-U-GCUU----UGAGGA-------AAGUA--AGGUGGA----------------------------GUAG---------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
AAFX01070226.1/249-124         CGAAGACAUCCCGAGUGGCCUCGUC----UGGU--------GACGAGGC-GCAGCA-ACC-U-GCC-----AACGACC-------GGCA--AGGUGCUUG-U-------GCG-C------------AGCG------------------GCGC----------AGAUGUGGCCACGCAA------GG-------------------------UUGCGAGGCAA--CGAACAGUCGCCCC-
AACY022632962.1/263-367        UCCGGACAUCAAGAGUAGGGC--------UGAC------------GCCC-UCACCA-ACC-U-GCC------GACCC--------GGCA--AGGUGGUG----------UCC-C------------AAAA------------------GGGA-----------GAUGUGGCC------------AAGGAC---------------------------GGCAA---CUAAGGGGUCCAAC
AACY020251371.1/2025-2117      AAGAAGCAUAUAGAGAAGGUU----------UA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUA----------------------------AUA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAUUAGUCAAAC
AACY023315004.1/1135-1237      CAGAUUCAUCAAGAG-AGGGC--------UGAC------------GCCC--CGCCA-ACC-U-GCU------GUUUG--------AGCA--AGGUGGUUA---------UUC-C------------GUAA------------------GGAA-----------GAUGUGGCU------------UAUUC----------------------------AGCAA---CCUCAAGCGUCACC
CP000959.1/1018491-1018388     AUCAAGCAUCCAGAG-UCGGG--------UUU-------------CCCG-ACGCCA-ACC-U-GCC-----CUCCCG--------GGCA--AGGUGGAC----------GCC-C-------------UCG------------------AGGC-----------GAUGCGGCCG-----------AUUGA---------------------------CGGCAA---CGAAACGGGAGCAG
AACY020409173.1/538-450        AAAAAGCAUGGAGAG-AGGUU----------AA------------AACC-UCAGCA-ACC-U-AGA----AAGCUA---------ACUA--AGGUGCUU----------------------------AAA---------------------------------UAUGUGGUU------------UGU------------------------------AACAA-----AAAACAGCUUUC
AACY020929092.1/724-820        AAAGUUCAUCAAGAG-UGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAA--------------------------AAAU---------------------------------GAUGUGGUU------------AAUC-----------------------------AACAAA---UAAUGGAGAUGCA
AACY023621099.1/135-40         UAUAAGCAUCAAGAGCGAGA---------UUAAUU-----------UCU-CCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAGU---------------------------------GAUGCGGUU------------AUUC-----------------------------AACAA---UUAAAGGAGUAGAA
AACY023403796.1/1244-1130      UGACAGCAUCAGGAGAGAUUUCU------AAAA----------AGAAAU-CCACCA-ACC-G-AGC-----UUAAAA--------GCUA--CGGUGGUUAGU-U-----CCA-U-------------UAA------------------ACGG---------AAGAUGUGCCUC-----------AAUA----------------------------GAGGAA-AAAUGGAACCGCCU--
AACY021710656.1/616-530        UGAGUGCAUAUAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY020505932.1/3030-3122      UAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY023898889.1/1101-1196      UUCUGGCAUCUAGAGCGAGA---------UUAAAU-----------UCU-CCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGCGGUU------------AACC-----------------------------AACAAA---UAAAGGAGUUAAA
AACY020101119.1/425-514        GCGCUACAUCAAGA---AUAC--------UUAAUU----------GUAU---ACCA-ACC-G---------GACGAUA----------A--CGGUGGUU---------------------------UAGC---------------------------------GAUGUGGGC------------AUCACA---------------------------GUCAAAA---UCGAUUCUCAUA
AACY022924688.1/248-340        AAGAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY020491193.1/1967-2053      UAAAUGCAUAGAGAG-AGG----------AAUU--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY020494659.1/3034-2942      UUAUGACAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUUG-U------------------------------------------------------------AGAUGUGGCA------------GUAA-----------------------------UGCAA---CCAAGUAGUCGUAC
AACY021344802.1/341-455        UUAUCUCAUCAUGAGCGGUUU--------CUCU-CAC--------AAAC-CCGCCA-ACC-G-AGC-----CUAAAA--------GCCA--CGGUGGUCA-G-U-UCCGCU----------------AAA--------------------AGGA-------AUGAUGUGCCUU-----------UUAU----------------------------UAGGAAAAA-GUGGAACCGCC--
AAOW01000005.1/152632-152735   AUUUAACAUCAAGAGUAGGGC--------UGAC------------GUCC-UCACCA-ACC-U-GCC-----AACCUG--------GGCA--AGGUGGUU------------------------GCUAUAA--------AGC----------------------GAUGUGGUCG-----------AUUC----------------------------CGACAA---CGAAUCAGGUAGAC
AACY020433596.1/2634-2542      UAAUAACAUAAAGAGAAGGUU----------AA------------GGCC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUUG-U------------------------------------------------------------AGAUGUGGCA------------GUAA-----------------------------UGCAA---CCAAGUAGUCGUAU
AACY020272341.1/1114-976       UCCAAGCAUCAGGAGUGGCCUUGC-----GAAA---------GCGGGGU-CCGGCA-ACC-U-GGUU----UGGAGA-------AGCCA--AGGUGCCUU-G-GAUG--CUG-U-------GACAGAAUU--------CUGUU-----ACGGUG------ACCGAUGUGCGAAUGU--------UU---------------------------ACAUUCGAA-CAGAAUUUCUCUCG--
AACY021231107.1/205-108        ACAAUGUAUUAAGAG-UGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUACGGUUU-----------UUAU----------------------------UAACAA---CAAAUGGAGGUUCA
AACY020892474.1/179-271        AAUAUACAUAAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GGAA-----------------------------UGCAA---CUAAAUAGUCAAAA
CP000709.1/441133-441241       ACCGCACAUCCAGAG-UUGGG--------GCGACG----------CCCA-ACGCCA-ACC-U-GCC-----GUUCCG--------GGCA--AGGUGGUAC-U-------CCC-C------------GAAA------------------GGGA----------GGAUGUGGCCG-----------AAC-----------------------------CGGCAA---UUAUACGGAUGAAG
AACY020098227.1/1332-1240      CAUAAGCAUCAAGA---ACAC--------UAAUU-----------GUGU---ACCA-ACC-G-AUC-----UUCCGA--------GACA--CGGUGGUU----------------------------UAG---------------------------------AAUGCGGGAC-----------AAUC----------------------------GUUCAAAA---GAUUCGGAAAUC
AACY021071265.1/759-845        UAAUUGCAUAGAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAUUGGCGUUC
AACY020477250.1/717-631        UAAAUGCAUAGAGAG-AGGAA------------------------UUCC-UCAGCA-ACC-U-AGU-----UGCCA---------ACCA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY020293165.1/279-372        AUCUUGCAUCCCGA---ACCC--------UUUAGU----------GGGU---GCCA-ACC-G-AGC-----AGAGAA--------GCCA--CGGUGGCA---------------------------AAAC---------------------------------GAUGCGGGCAU----------U------------------------------AUGCCAA-AACAUAUUCCGAGA--
AACY020492046.1/519-605        UAAAUGCAUAGAGAG-AGGAU------------------------UUCC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCUUUC
AAEW02000015.1/42526-42659     ACCAUGCAUUAAGAGAGGCGUGGCGGC--AUGA------GCCAA-GCGC-CCGGCA-ACC-U-G-------ACAAC-----------CA--AGGUGCCA--G-C----AUGU-U-UUGUG-AACA-CGG----------UGUUUGCAAAACA---------GCGAUGCGCCCC-----------GUAA----------------------------GGGGAA-AGUUGACCUACCGU--
AACY020208399.1/1640-1726      UGAGUGCAUAUAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY020068969.1/866-767        AUUAAGCAUCAGGAG-UGAAUAA------GUAA----------UUAUUC--UGCCA-ACC-U-GCUU----UGAGGA-------AAGUA--AGGUGGAU----------------------------UAA---------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
AACY024064010.1/1047-955       GUAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY020561147.1/40418-40521    AUCAAGCAUCCAGAG-UCGGA--------UUC-------------UCCG-ACGCCA-ACC-U-GCC-----CUCCCG--------GGCA--AGGUGGAC----------GCC-U-------------CCA------------------AGGC-----------GAUGCGGCCG-----------AUUUA---------------------------CGGCAA---CGAAACGGGAGCAG
AACY020181329.1/1342-1222      AUCCUGUAUGUAGAG-UGCCUCU------CGAU----------AGGGGC--CACCAAACC-G-AGCAACU-CCACA-----AGUAGCCA--CGGUGGUUA---------------------GAAUCGCAA--------GAUUC--------------------CAUAUGUAGG-----------AGACAA--------------------------CCUAAAAAA--UGGAGGUGCCC-
AACY023505660.1/626-720        AAGAUACAUCAAGAG-UGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC------ACUCC--------GGCA--AGGUGGAA---------------------------AAAA---------------------------------GAUGUGGUU------------AACC-----------------------------AACAA---UUAAAGGAGUUAAA
AACY020243063.1/177-88         GUUUUGCAUAAAGAG-AGG----------GAAG--------------CC-UCAGCA-ACC-U-AGA-----UUGCCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUUAC----------------------------AACAA----AAAAUGGCUUUUU
AACY020181346.1/9550-9431      UAGAGGUAUGAGGAU-UGCCUCACU----AACCCCAA----GGUGAGGC--UGCCA-ACC-G-AGC-----ACAU----------GCCA--CGGUGGCC--G---AA--UCU-U-------------AAU------------------GAGAUU--------CCAUACGUUGG-----------AUUAA---------------------------CCAGAAAAAGGAG-CCCUGUG--
AACY020800775.1/440-319        AUUUUGUAUGUAGAG-UGCCUCU------CGAU----------AGAGGC--CACCAGACC-G-AGCAACU-CCAAAC----AGUAGCCA--CGGUGGUUA---------------------GAAUCGCAA--------GAUUC--------------------CAUACGUAGG-----------AGACAA--------------------------CCUAAAAAA--UGGAGGUGCCC-
AACY023494623.1/1058-962       AAAUAACAUUUCGAG-AGGGA--------GCAA------------UCCC--UGCCA-ACC-U-GCA-----UUAACC--------UGCGA-AGGUGGUAA--------------------------CUUU---------------------------------AAUGUGGCUU-----------AUU-----------------------------AAGCAAAAAAA---GGUUUCUCC
AACY022669929.1/401-309        AAUAAGCAUAUAGAG-AAGGU--------UUAG------------ACCU--CGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAG
AACY021621762.1/356-449        ACUGAGCAUCAGGAG-UGGGC--------GCAA------------GCCC--CGCCA-ACC-U-GCUU-----ACCC--------AAGCA--AGGUGGUU--CGA----------------------------------------------------------GAAUGUGGCC------------GUAA-----------------------------GGCAA---CCAAGUGGGUUCUC
AACY020175566.1/301-414        CGACGACAUCAGGAGCGACCC--------UCAC------------GGGU-CCGGCA-ACC-G-GG------AUCG-----------CCACUCGGUGCCU--U-C-CG--CC---------------UCAC--------------------GGCG-------GAGAUGUGGUCCCGC--------GAGC-------------------------GCGGGACAA-GGAGGUGACAUGGC--
AACY022940092.1/322-421        AUCAAGCAUCAGGAGUGAAUAA-------GAAA-----------UUAUU-CUGCCA-ACC-U-GCUU----AGAGGA-------AAGUA--AGGUGGA----------------------------GUAG---------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
AACY020408240.1/227-137        AAGGUGCAUUAAGAAAGGGG---------UUA--------------UCC-CUGCCA-ACC-U-GCA-----UACCG---------UGCGA-AGGUGGUA----------------------------AUA---------------------------------UAUGCGGCC------------AAAA-----------------------------GGCAAAA----GUUAGGUCUCA
AACY023068576.1/606-514        AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GGAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY022117635.1/301-399        CCGCAACAUUAAGAG-AGGGC--------UGAC------------GCCC--CGCCA-ACC-U-GCA-----GCUG----------UGCA--AGGUGGUA----------CCC-C-------------GAA------------------AGGG-----------AAUGUGGCC------------UUAA-----------------------------GGCAA-CGACAGCGUCAGCC--
AACY023099908.1/98-208         UACAUGCAUCAAGAUAGGUCUUU--------UU-U--------AAAGAC-CUGCCA-ACC-G-AGC-----UUCAAA--------GCCA--CGAUGGUA--------AGUUC-C-------------AAC----AAAA----------GGAA-----------GAUGUGUCC------------GUAAA----------------------------GGAAA-AAACGAUCAACC----
AACY023669787.1/612-524        AAAAAGCAUGGAGAG-AGG----------UAAAAU------------CC-UCAGCA-ACC-U-AGA----AAGCUA---------ACUA--AGGUGCUU----------------------------AAA---------------------------------UAUGUGGUU------------UAU------------------------------AACAA-----AAAAUAGCUUUU
AACY020477924.1/1643-1551      UAGGAACAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAU
AACY022504339.1/418-316        AAUGAUCAUUAAGAG-AGGAC--------UGAC------------GUCC--CGCCA-ACC-U-GCC-----UUAUCC--------GGUA--AGGUGGUAA---------CCU-C------------AUAU------------------GAGG-----------GAUGAGACC------------UAAG-----------------------------GGUAA---CCAAAGGAUCAUUG
AACY021272089.1/454-550        ACAAAACAUCAAGAA-AGAGUG-------AUGA-----------CACUC-UUACCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGUUU--------------------------AAAC---------------------------------GAUGUGGCU------------UUC------------------------------AGCAA---CUAAAGGAGGUAAU
AACY020375700.1/1515-1609      AAUAUAUAUCAUGAGAAGGA---------UUUAUU-----------UCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAA---------------------------------GAUAUGGC-------------GUUCA-----------------------------GCAAA---UAAUGGAGGUGUG
AACY022269084.1/174-77         UAAUUGUAUCAAGAGCAGAG---------UUAAUU-----------CUC-UCUCCA-ACC-U-GCUAG---CUU---------CUAGCA--AGGUGGAAC--------------------------AAAU---------------------------------GAUACGGC-U-----------AUUC----------------------------ACGCAA----CUAAAAGGAGAUC
AACY022902937.1/198-306        UUCAAUCAUCCCGAGCGAUUCGGUC----CCACAA------GCCCGAAU-CCACCA-ACC-U-GUCC----AAGGC--------GGAUA--AGGUGGUUC--------------------------UCAU---------------------------------GAUGAGCCC------------GUUCU----------------------------GGGAA-GCCGUCCACGCACG--
CP000699.1/636052-635945       AUGCAGCAUCAAGAGUUGGGC--------CGGC------------GCCCAACGCCA-ACC-U-GCC-----GAUCCG--------GGCA--AGGUGGCG--C-------UCC-C------------GCGA------------------GGGG----------GGAUGUGGCCG-----------AUC-----------------------------CGGCAA---CCAAGCGGACCAAG
AACY020132046.1/1210-1087      AAACAACAUCAGGAGUGGUUUCA------UAUU----------UGAAAC-CCGCCA-ACC-G-AGCCCAGAUAAA-----UCAAGGCUA--CGGUGGUU------UGAUCCUU--------------AA------------------ACGGUA----------GAUGUGCCUA-----------GGAAAA--------------------------UAGGAA-ACAUAGUAAGCCGC--
AACY023286370.1/297-205        CUUAUACAUUAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAACUAGUCAAAA
AACY023872706.1/1205-1109      AUUUUACAUCUAUAGAGAAGG--------GUGA------------CCUU--CACCA-ACC-A-GCC-----AGACUU--------GGCAA-CGGUGGUU---------------------------CAAC---------------------------------GAUGUGGCUU-----------UUG-----------------------------AAGCAA---CAAUAAAGUCAGAU
AACY020548058.1/648-734        UAAAUGCAUAGAGAG-AGG----------AAAU--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGU-------------GAU-------------------------------ACAA--CAAAAAAUGGCGUUC
AACY020184636.1/1250-1336      UAAAUGCAUAGAGAG-AGG----------GAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY021425142.1/531-429        UAUAAUCAUUCAGAG-AGGAC--------UGAC------------GUCC--UGCCA-ACC-U-GCA-----UUUUCC--------GGCA--AGGUGGUUA-C-C-----UC---------------AUUU--------------------GA---------GGGAUGAGACC------------GUAG-----------------------------GGUAA---CCAAAGGAUCAUUG
AACY023996159.1/385-293        AAUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY020760933.1/589-481        AAGGAACAUUAAGAGAGGUCCA-------AUAU-----------UGGGC-CCGGCA-ACC-U-AGG-----ACGGACA-------CCCA--AGGUGCUU----------CCC-A------------GAAA------------------UGGG-----------GAUGUGGUAC-----------GAAA----------------------------GUACAA--GUAAUUGUCCACAC-
AACY020471545.1/1557-1444      GUAGUACAUCACGAG-CGACC--------AACA------------GGUC--CGGCA-ACC-G-GG------AUUUC----------CCA--CGGUGCCA--U-U-UC--GC---------------GAAAU-------------------GCGA-------AAGAUGUGGCUACGCC-------AACA------------------------GGCGUAGCAA-CGGGCUGGCUCAGU--
AACY020758038.1/271-176        AUCUAGCAUCAGGAG-UGAGC--------GAAA------------GCUC--CGCCA-ACC-U-GCC-----CUCCCA--------GGCA--AGGUGGCGCAG-------------------------------------------------------------AAUGUGGCCUC----------AUU----------------------------GAGGCAA---UCAACUGGGAUUCA
AACY023841578.1/259-157        CCCAAGCAUCAAGAGAGGGGC--------CCUC------------GCCC-CCACCA-ACC-U-GCC-----CAACCC--------GGCA--AGGUGGUCG---------UCC-U--------------UC------------------GGGA-----------GAUGUGGCCG-----------AUC-----------------------------CGGCAA---CAAACGGGU-GCAG
AACY022716110.1/377-469        AAGAGGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY020515115.1/1918-2010      ACUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGGCUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAUUAGUCAAAA
AACY020340651.1/1065-973       GAGAAGCAUUUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GCAA-----------------------------UGCAA---CUAAGUAGUCAAAG
AACY023512723.1/650-561        UUUCAACAUCAAGA---AUAC--------UUAAAU----------GUAU---ACCA-ACC-G-A-------ACGA------------UAG-CGGUGGUU---------------------------UAGU---------------------------------GAUGUGGGC------------AUCCAA---------------------------GUCAAAA---UCGAUUCUCAUA
AACY023996530.1/508-416        UUAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY020495019.1/245-331        UGAGUGCAUAUAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY023014452.1/536-447        AAGAUGCAUUAAGAAAGGGGU-----------U------------AUCC-CUGCCA-ACC-U-GCA-----UACCG---------UGCGA-AGGUGGUA----------------------------AUA---------------------------------UAUGCGGCC------------AAAA-----------------------------GGCAAAAA-----UAGGUCUCA
AACY022006392.1/340-429        GGGUCGCAUCAAGA---ACGC--------UAAG------------GCGU---ACCA-ACC-G-ACA-----GCUCGU--------UGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGCGGGGA-----------UCU-----------------------------UCCCAAACAAA----CGAGAAAU
AACY021125113.1/499-592        AUUAUUCAUCAAGAGUAAGA---------UUAAUU-----------UCU-UCUCCA-ACC-U-GCC-----AGCUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGAGGC-------------AAUCA-----------------------------GCAA----UAUAGGAGAAAGG
AACY020098447.1/1122-1000      UUUUAUCAUCAGGAGUGGUUUCA------UAA-----------UGAAAC-CCGCCA-ACC-G-AGCUUAGAAAAA-----UCAAAGUUA--CGGUGGUU------UGAUCC---------------UUAAAC------------------GGUA---------GAUGUGCCUA-----------GGAAAA--------------------------UAGGAA-ACAUGAUUAGCCGC--
AACY020327880.1/953-857        AUAGAGCAUUAAGAGCAGGG---------UUAAAU-----------CCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAA--------------------------AAAU---------------------------------GAUGCGGUU------------AACC-----------------------------AACAAA---CAUAGGAGUACAA
AACY020411818.1/3750-3838      AAAAAGCAUGGAGAG-AGG----------GUAAAA------------CC-UCAGCA-ACC-U-AGA----AAGCUA---------ACUA--AGGUGCUU----------------------------AAA---------------------------------UAUGUGGUU------------UAU------------------------------AACAA-----AAAAUAGCUCUC
AACY020317023.1/234-331        ACACAACAUGAAGAGUAACU---------GAAUUA-----------GGU-UCACCA-ACC-U-GCA-----AA------------UGUA--AGGUGGUU----------UCC-U--------------CA------------------AGGG-----------CAUGUGACC------------GUAA-----------------------------GGUAA-UAUACAUGCCUCCU--
AACY020414565.1/1377-1469      UAAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY020532609.1/3243-3139      ACUCAGCAUCAAGAGAAGGGC--------CUCG------------GCCC-GCACCA-ACC-U-GCC----AACACCC--------GGCA--AGGUGGUCG-C-C---------C------------GAAA------------------G------------GGGAUGCGGCC------------AAACC----------------------------GGCAA---CUAAAGGGCAGGCC
AACY020029910.1/1636-1728      GAUAUACAUAUAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAACUAGUCAAAA
AACY022543694.1/437-345        CAUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAG
AACY022869497.1/434-342        UUGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAA
AACY020492046.1/1757-1849      AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY020031148.1/475-383        GAUAUACAUAUAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAACUAGUCAAAA
AACY023655795.1/998-903        AUUGAACAUCAAGAG-UGGGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAGC---------------------------------GAUGUGGUU------------AACC-----------------------------AACAA---CUAAAGGAGAAAAA
AACY022879010.1/492-584        AAGAAGCAUGUAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY023493356.1/1222-1127      GGUUUGAAUCUAGAGCAGGA---------UUAAAU-----------UCC-UCUCCA-ACC-U-GCC-----CUCUCC--------GGCA--AGGUGGAA---------------------------AAGU---------------------------------GAUUCGGUU------------AACC-----------------------------AACAAA---UAAAGGAGUUAAA
AACY023286370.1/1537-1449      AUUAUGCAUGAAGAG-AGG----------GCAA--------------CC-UCAGCA-ACC-UAGA-----AAGCAAA----------CAA-AGGUGCUA-----------------------------AA---------------------------------GAUGCGGUUU-----------UUU-----------------------------AAACAA----AAAAUAUGCUUAU
AACY020444019.1/956-835        CGUCGUUAUCAAGAGCGGCGCAC------AUUC----------GUGUGC-CCAGCA-ACC-U-GGG-----GUGGACA-------CCCA--AGGUGCUUU-C-C-UA--C-----------------UUU---------------------GUA-------GGGAUAUGGCGACGGCU------CUA------------------------AGUCGGCGCAA--CAAAGUGUCCCAUG-
AACY020490313.1/636-544        UAGGAACAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUUG-U------------------------------------------------------------AGAUGUGGCA------------GUAA-----------------------------UGCAA---CUAAUUAGUCGUAC
AACY023572833.1/528-430        AUCCUGUAUCAAGAGCAGAG---------UUAAUU-----------CUC-UCUCCA-ACC-U-GCUA----ACUUC--------UAGCA--AGGUGGAAC--------------------------AAAU---------------------------------GAUACGGC-U-----------AUUC----------------------------ACGCAA---CUAAAAGGAGAUCA
AACY022364730.1/503-404        AUUAAGCAUCAGGAG-UGAAUAA------GUAA----------UUAUUC--UGCCA-ACC-U-GCUU----AGAGGA-------AAGUA--AGGUGGAGUAG-------------------------------------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
CP000533.1/31707-31598         GUUCAACAUCAGGAGUUGGACA-------GUAG-----------UGUCC-ACGCCA-ACC-U-GCC-----UACUCG--------GGCA--AGGUGGU----------------------------AUCGCUUAUGCA-------------------------GAUGGGGCCUU----------UAAAC--------------------------AAGGUAA---CCAAACGAGUCCCU
AACY022756908.1/132-29         GCGCUACAUCACGAG-CGACC--------AUAC------------GGUC--CGGCA-ACC-G-GGA-----------A-------UCCA--CGGUGCCAA-G-------UCA-C------------UUCG------------------GUGA----------CGAUGUGGCCCC----------GCAA---------------------------GGGGCAA-CGGAUCGCAUGGUG--
AACY022689574.1/326-418        AAGGAACAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY022809384.1/289-381        AUUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY020290243.1/3798-3706      AUUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGGCUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAUUAGUCAAAA
AACY020219775.1/1020-1116      CAUCAACAUCAAGAGAAAGA---------UUGGGU-----------UCU-UCUCCA-ACC-U-GCU-----AACUCA--------GGCA--AGGUGGAAU--------------------------AAAA---------------------------------GAUGUGGUU------------AACC-----------------------------AACAA---UUAAAUGAGGUAAU
AACY020401066.1/1365-1271      UAUGUAUAUCAUGAGAAGGA---------UUUAUU-----------UCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAA---------------------------------GAUAUGGC-------------GUUCG-----------------------------GCAAA---UAAAGGAGGAAAG
AACY022955029.1/106-192        UAAAUGCAUAGAGAG-AGGAA------------------------UUCC-UCAGCA-ACC-U-AGU-----UGCCA---------ACCA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY023730967.1/1126-1215      UAAAAGCAUUAAGAGAGGGUA----------AU------------UACC-UCAGCA-ACC-U-GGA----AGGCU----------ACCA--AGGUGCUA---------------------------AGAA---------------------------------GAUGUGGCU------------UUA------------------------------AGCAA-----AAAAGAGCCAAU
AACY020838872.1/555-460        UUAAUGUAUCAAGAGAAGGA---------UUAAAU-----------UCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGUA--AGGUGGAA---------------------------AAAA---------------------------------GAUGCGGUU------------AACC-----------------------------AACAA---UUAAAGGAGUUAAA
CP000360.1/5414708-5414585     UUCCAGCAUCAGGAGUGUCCUGGC-----CGCUUUAA-----GCCAGGU-CCGGCA-ACC-G-AGC-----UUUGGAGAC-----GCUA--CGGUGCCAC-G-A-------------------GUCGCAA--------GAC--------------------UCAAUGUGCGGAC----------GAAA---------------------------GUCCGAAAGGAUGUCUCCCGA---
AACY020495403.1/2582-2676      UAUGUAUAUCAUGAGAAGGA---------UUUAUU-----------UCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAA---------------------------------GAUAUGGC-------------GUUCG-----------------------------GCAAA---UAAAGGAGGAAAG
AACY021913758.1/688-597        GUUUAGCAUCAAGA---ACGC--------UUAU------------GCGU---ACCA-ACC-G-ACA-----CGCUCGU-------UGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGCGGGG------------CUCCU----------------------------CCCAAAAAAA---CGAGAAAUC
AACY020195299.1/11-103         AAUGAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------CAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY023064355.1/203-105        GAACAACAUCUAUAGAGAAGC--------UUAU------------GCUU--CACCA-ACC-U-GCCA----AGAUC--------UGGCAA-AGGUGGUU---------------------------CAAC---------------------------------GAUGUGGCU------------UUAAUU---------------------------AGCAA---CAAUAAGAUCGUAG
AACY023328494.1/1231-1341      AUCCAACAUCAAGAGUGACUC--------AGCAAU----------GAGU-ACAGCA-ACC-G-AGCC----AGCCA--------GGCCG--CGGUGCUU----------CCC--------------GCCA-------------------GGG-----------GAUGUGAUG---------CACGAAA-----------------GUG---------UAUAAAAA--CUUCUGGCCCU-
AACY023384040.1/1454-1362      UUAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY023968756.1/852-755        UAUCAUCAUCAGGA--CGGGA--------GAAA------------UCCC---ACCA-ACC-G-AGC-----UU-AG---------GCCA--CGGUGGUU----------UGU-C------------AAGU------------------GACA-----------GAUGAGCAGC-----------AAU-----------------------------GCUGAAAA----UAUCUGAAACC
AACY022418261.1/564-678        AUGUAUCAUCAGGAGCGGUUUCA------GGAA----------AGAAAC-CCACCA-ACC-G-AGC-----CUCAAA--------GCUA--CGGUGGUUAGU-U-----CCA-U-------------UAA------------------ACGG---------GAGAUGUGCCUU-----------GAAA----------------------------AAGGAAAAA-UGGAGCCGCCU--
AACY021029522.1/357-450        AUCUUGCAUCCCGA---ACCC--------UUUAGU----------GGGU---GCCA-ACC-G-AGC-----AGAGAA--------GCCA--CGGUGGCA---------------------------AAAC---------------------------------GAUGCGGGCAU----------U------------------------------AUGCCAA-AACAUAUUCCGAGA--
AACY020465783.1/343-252        ACAGUGCAUGAAGAG-AGG----------GAAA--------------CC-UCAGCA-ACC-UAGA-----AAGCAAA----------CAA-AGGUGCUU----------------------------CAA----------------------------------AUGCGGUUUU----------UUA----------------------------UAGACAA---AAAAAUAUGCUAUU
AACY020097780.1/583-491        AAUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAC
AACY020495310.1/1138-1046      AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY023483956.1/181-273        CAUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAG
AACY023164875.1/482-386        AAAAAGCAUCAAGAGCAGAG---------UUAAGU-----------CUC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAC--------------------------AAAU---------------------------------GAUGCGGUU------------GUUC-----------------------------AACAA---AUAAUGGAGAUAAA
AACY022012118.1/281-394        AUUCAACAUCAGGAGCGGUUUCA------AAAC----------UGUAAC-CCGCCA-ACC-G-ACC-----CAAAUG--------GGCA--CGGUGGU-------UAGAUCC-U-------------UAA------------------GCGGUA---------GAUGUGCCUU-----------UGAU----------------------------UAGGAAA-UCUUAAAAGCUGC--
AACY020498997.1/1130-1217      UAAUUGCAUAAAGAG-AGG----------GAAA--------------CC-UCAGCA-ACC-U-AGU------UGCCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AAAU-----------------------------AACAA----AAAAUGGCUUCUU
AACY020277418.1/1687-1600      AAAAAGCAUGGAGAGAGG-----------UAAAGC-------------C-UCAGCA-ACC-U-AGA----AAGCUA---------ACUA--AGGUGCUU----------------------------UAA---------------------------------UAUGUGGUU------------UAA------------------------------AACAA-----AAAAUAGCUUUU
AACY020084959.1/695-784        GCGUCACAUCAAGA---AUAC--------UUAAGU----------GUAU---ACCA-ACC-G---------GACGAUA----------A--CGGUGGUU---------------------------UAGC---------------------------------GAUGUGGGC------------AUCACA---------------------------GUCAAAA---UCGAUUCUCAUA
AACY024060958.1/479-571        AGUAGACAUAAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY020146386.1/1428-1520      GAGGAACAUAAAGAG-AAGGU--------AAAG------------ACCU--CGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAGA-----------------------------UGCAA---CUAAGUAGUCAAAA
AACY023656688.1/97-2           AAUAUGCAUUAAGAGUGAGA---------UUAAUU-----------UCU-CCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAGU---------------------------------GAUGCGGUU------------AUUC-----------------------------AACAA---UAAAGGAGUAGAAA
AACY021071260.1/590-498        AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
CP000759.1/851733-851842       ACAUCACAUCAAGAG-UUGGG--------GAGACG----------CCCA-ACGCCA-ACC-U-GCC-----UCUCCG--------GGCA--AGGUGGUA------CU--CUC-U------------GUAA------------------AGAGAG---------GAUGUGGCC------------AAACC----------------------------GGCAA---AUAUACGGACAAAG
AACY021667883.1/657-543        UGUCAUCAUCAGGAGUGAUCUUU--------AAGU--------AAAGAU-CCACCA-ACC-G-AGC-----CUAAAA--------GCUA--CGGUGGUUAGU-U-----CCA-U-------------UAA------------------ACGG---------AGGAUGUGCCUU-----------GAAG----------------------------AAGGAA-AAAGUGGAACCGCC--
AACY021285989.1/46-140         AAUAUAUAUCAUGAGAAGGA---------UUUAUU-----------UCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAA---------------------------------GAUAUGGC-------------GUUCA-----------------------------GCAAA---UAAAGGAGGUAUG
AACY023441040.1/452-343        AAUCAGCAUCUAGAAGCACCUC-------GAAA-----------GAGGU-GUGGCA-ACC-G-AGCC----CACCA--------GGCCA--CGGUGCCU----------CCC-A------------ACAA------------------CGGG-----------GAUGCGGCGC-----------GACGA---------------------------GCGCAAAA---GAACUGGUGCUC
AACY023871234.1/221-126        AUCGAACAUCAAGAG-UGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------UAAA---------------------------------GAUGUGGUU------------AAUC-----------------------------AACAAA---UAUAGGAGUAAAC
AACY020516175.1/1516-1608      AGUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY021320796.1/390-273        UAAAGGCAUUACGAGUGGUCUGGU-----UAAA---------ACUAGAU-CCGGCA-ACC-U-GGG----AGGACA---------CCCA--AGGUGCCCG-C-U-----------------CAUCCGCAA--------GGAAG------------------AGGAUGUGGCCU-----------GAAA----------------------------GGGCAA----CAAAGUGUCCGGU
AACY023285819.1/1291-1383      UGUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAG
AACY023113558.1/484-580        AAAAAGCAUCAAGAGCAGAG---------UUAAGU-----------CUC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAC--------------------------AAAU---------------------------------GAUGCGGUU------------GUUC-----------------------------AACAA---AUAAUGGAGAUAAA
AACY022004743.1/542-637        ACCCUGUAUCUUGAGCAGGA---------UUUAAU-----------UCC-UCUCCA-ACC-U-GCC-----UACUCC--------GGCA--AGGUGGAA---------------------------AAAC---------------------------------GAUACGGUU------------AAUC-----------------------------AACAA---UUAAAGGAGAGAAA
AACY023720466.1/280-394        UUGCGUUAUCAAGAGCGGUGCAC------UUCC----------GUGCAC-CCGGCA-ACC-U-GGG-----GUGGACA-------CCCA--AGGUGCUUU-C-C-UA--C-----------------UUU---------------------GUA-------GGGAUAUGGCUGA----------GG-----------------------------UCUACGA-CCAAAGCAACAAAGUG
AACY023630570.1/819-723        UAUUGGUAUCAAGAGCGGGA---------UUAAAU-----------UCU-CCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAA--------------------------AAAU---------------------------------GAUGCGGUU------------AACC-----------------------------AACAA---CCAAAGGAGUCUAA
AACY020145665.1/933-841        ACUAGACAUAAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY020253539.1/634-726        AUUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAUUAGUCAAAA
AACY020183603.1/425-534        AACCAGCAUCUAGAAACACCUC-------GAAA-----------GAGGU-GUGGCA-ACC-G-AGC-----CCACCAG-------GCCA--CGGUGCCU----------CCC-G------------ACAA------------------CGGG-----------GAUGCGGCGC-----------GACGA---------------------------GCGCAAAA--GAACUGGUGCUC-
AACY021642302.1/326-240        UGAAUGCAUAGAGAG-AGGAA------------------------UUCC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY020117021.1/502-410        UAAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAGA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY023618809.1/135-43         UUAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCCCGGA-------------------------------------------------------------AAUGUGGCA------------GUGA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY022004864.1/199-318        UAGAGGUAUGAGGAUUGCCUCGCUA----ACCCGA------AGGUGAGG-CUGCCA-ACC-G-AGC-----ACGU----------GCCA--CGGUGGCC--G-A-AU--CUU-A---------------A------------------UGAGAU-------UCCAUAUGUUGG-----------AUUAA---------------------------CCAAAA-AAA-GGAGCCCUAUG-
AACY023370451.1/640-734        GCCAUGCAUCCAGAGUAGGAG--------CUAG------------CUCC-UCGCCA-ACC-U-GCA-----ACUCCAA-------AGCA--AGGUGGCC---------------------------AAAU---------------------------------GAUGCGGC-------------AAUC------------------------------GCAA---CCAAUUGGAGAACA
AACY020315257.1/171-263        UUACGACAUCAAGAA-CGCAU------------------------AUGC-GUACCA-ACC-G-ACU-----AUCUCGA-------AGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGUGGGUA-----------GCUC----------------------------UACCAA-AAAUUCGAGCAAUC--
AACY023285819.1/50-138         UAUUUGCAUAAAGAG-AGG----------GAAA--------------CC-UCAGCA-ACC-U-AGA-----AUGCCA--------ACCA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UUAC-----------------------------AACAA----AAAAUGGUAAUUA
AACY020806376.1/43-140         GCUCUGCAUCAAGAG-CCGAC----------UU------------GUCG-GCGCCA-ACC-U-GCC-----UCCCCG--------GGCA--AGGUGGCUAGC-G----------------------AAAG-------------------------------CGGAUGCGGCC------------UUGA-----------------------------GGCAA---CCAAGC-GGGAGCA
AACY020587818.1/348-440        CAUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAG
AACY023404581.1/902-810        UAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAGA-----------------------------UGCAA---CUAAGUAGUCAAAA
AACY020099146.1/973-881        UCUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAUA
AACY020281887.1/1346-1438      CAUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------CAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAUUAGUCGAAG
AACY020641585.1/375-271        GAUGAGCAUCAAGAG-CGU--CGUCGGGAUGG-----UCCCGAC---AC--CACCA-ACC-G-G-------UCCUC-----------CAUCCGGUGGUU----------CCC-A-------------UCU------------------UGGG-----------GAUGCGGCCC-----------UUA-----------------------------GGGCAAA-------GGAGGCCAU
AACY021235322.1/323-221        ACCACGCAUUAAGAG-AGGAC--------UGAU------------GUCC--CGCCA-ACC-U-GCG-----UGUUCC--------AGCA--AGGUGGUU----------GCC-U------------UAAUU-----------------AGGC-----------GAUGAGACC------------UAAG-----------------------------GGUAA---CCAACGGGUCAUCA
AACY023418101.1/1085-1180      UUUUUGUAUCUUGAGCAGGAU--------UUAA------------UUCC-UCUCCA-ACC-U-GCC-----UACUCC--------GGCA--AGGUGGAA---------------------------AAAC---------------------------------GAUACGGUU------------AAUC-----------------------------AACAA---UUUAAGGAGAAAAA
AACY020430580.1/2307-2395      AAAAUGCAUGGAGAG--AGGA--------CAAA------------UCCU--CAGCA-ACC-U-AG----AGAGCUA---------ACUA--AGGUGCUU----------------------------AAA---------------------------------UAUGUGGUU------------UAU------------------------------AACAA-----AAAAUAGCUUUC
AE017224.1/745625-745733       ACCGCACAUCCAGAG-UUGGG--------GCGACG----------CCCA-ACGCCA-ACC-U-GCC-----GUUCCG--------GGCA--AGGUGGUAC-U-------CCC-C------------GAAA------------------GGGA----------GGAUGUUGCCG-----------AAC-----------------------------CGGCAA---UUAUACGGAUGAAG
CP000248.1/722861-722994       CCCCAACAUCGAGAG--UUGGGG------UGACGC--------UCC-AA--CGCCA-ACC-U-GCC-----GUUCCG--------GGCA--AGGUGGUAC-C-C-GA--UCC-G-CAAGG-CGGC-CCCG---------GCCGAAUUGCGAAAG-------GGGAUGUGGCCG-----------AUC-----------------------------CGGCAA---CCAAACGGACACGG
AACY023474639.1/280-367        UAAAUGCAUAGAGAG-AGGAA------------------------UUCC-UCAGCA-ACC-U-AG------AUGCCAA--------CUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA----AAAAUGGCGUUCC
AACY020490715.1/511-419        AUAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-AGA-----UGACUA--------UCCA--AGGUGCUC----------------------------AGA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY021211837.1/282-374        UCUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GGA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY020050185.1/855-953        AUUAAGCAUCAGGAG-UGAAUAA------GCAA----------UUAUUC--UGCCA-ACC-U-GCU-----UGAGGAA-------AGUA--AGGUGGAA----------------------------UAC---------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
AACY021824918.1/619-528        UAUUAGCAUCAAGAA-CGC----------UUA---------------GC-GUACCA-ACC-G-ACU-----AUUUCGA-------AGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGUGGGUA-----------GCUC----------------------------UGCCAA-AUUUUCGAGCAAUC--
AACY023374497.1/754-846        ACUUUGCAUCAAGAA-CGC----------AAU---------------GC-GUACCA-ACC-G-ACA-----UACUCGA-------UGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGCGGAGA-----------AUAAC---------------------------UCUCAAA---UUUUCGAGUAAUC
AACY023933995.1/1174-1268      CCAGUGUAUCAAGAGUGAGA---------UUAAAU-----------UCU-CCUCCA-ACC-U-GCC-----CACUCC--------GGUA--AGGUGGAA---------------------------AAAC---------------------------------GAUACGGCA------------AUC------------------------------UGCAA---UACAAGGAGGAAAC
CP000533.1/62361-62468         GCUCAUCAUUAAGAGAUGGGU--------UGAC------------GCCC-ACACCA-ACC-U-GCC-----AUUCGG--------GGCA--AGGUGGUU----------UGC-U------------UUCA------------------AGCA-----------GAUGUGGCUC-----------CUCGAA--------------------------GAGCAA---CCAAGCCGGCAGCG
AACY020146386.1/192-278        UAAAUGCAUAGAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----AGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AAAC-----------------------------AACAA-----AAAUUGGCGUUC
AACY020195427.1/941-1036       UAUCAGCAUCAAGAGUAGGA---------UUAAAU-----------UCC-UCUCCA-ACC-U-GCC------ACUCC--------GGCA--AGGUGGAAA--------------------------AAAU---------------------------------GAUGUGGUU------------AACC-----------------------------AACAA---CUAAAGGAGUUAAA
AACY021970555.1/127-221        UUUGUACAUCAAGAG-UGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC------ACUCC--------GGCA--AGGUGGAA---------------------------AAAA---------------------------------GAUGUGGUU------------AACC-----------------------------AACAA---UUAAAGGAGUUAAA
AACY021623362.1/963-874        GCGCUACAUCAAGA---AUAC--------UUAAGU----------GUAU---ACCA-ACC-G-A-------ACGA------------UAA-CGGUGGUU---------------------------UAAC---------------------------------GAUGUGGGC------------AUCCUA---------------------------GUCAAA-GUCGAUUCUCAUA--
AACY022325607.1/259-357        AUAGUACAUCAGGAGUGAAUAA-------GAAA-----------UUAUU-CCGCCA-ACC-U-GCU-----UGAGGA--------AGUA--AGGUGGCA----------------------------GAG---------------------------------AAUGUGGUC------------UUAAUU---------------------------GACAA--UUUGGUUCCUCGUU-
AACY023427826.1/25-137         CUUCAGCAUCACGAG-UGACCGG------GAAA----------CCGGUC--CGGCA-ACC-G-GGG-----UUGG----------UCCA--CGGUGCCAG-C-U-CA--AUC-G------------GCAA------------------CGGUUG-------GGGAUGUGGCGG-----------GAAA----------------------------CCGCAA-----CGGGCCCGGUCC
AACY020342180.1/1693-1601      GAGAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GCAA-----------------------------UGCAA---CUAAGUAGUCAAAG
AACY020160892.1/861-956        AAUGUGUAUCUAGAGCAGGA---------UUAAAU-----------UCC-UCUCCA-ACC-U-GCC-----UACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGCGGUU------------AACC-----------------------------AACAA---UUAAUGGAGUUAUA
AACY020443119.1/958-870        GGUUUGCAUAAAGAG-AGG----------GAAU--------------CC-UCAGCA-ACC-U-AGA-----UUACCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UAAC-----------------------------GACAA----AAAAUGGUAUUUU
AACY023449668.1/862-748        AAUUAUCAUCAGGAGUGAUCUUU--------AAGU--------AAAGAU-CCACCA-ACC-G-AGC-----CUAAAA--------GCUA--CGGUGGUUAGU-U-----CCA-U-------------UAA------------------ACGG---------AGGAUGUGCCUU-----------GAAA----------------------------AAGGAA-AAAGUGGAACCGCC--
AACY023089372.1/160-256        GAGAAGCAUUAAGAGCAGAG---------UUAAGC-----------CUC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAC--------------------------AAAU---------------------------------GAUGCGGUU------------GUUC-----------------------------AACAA---AUAAUGGAGAUAAA
AACY021754793.1/61-153         AUAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUC----------------------------GGA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAACA
AACY023360051.1/671-573        AUAAUGCAUCAAGAG-UGGAUAA------UAAA----------UUAUUC--CGCCA-ACC-U-GCU-----UGAGGA--------AGUA--AGGUGGCA----------------------------GAG---------------------------------AAUGUGGUC------------UUAAUU---------------------------GACAA--UUAGGUUCCUCGUU-
AACY023913045.1/570-665        CAAUAGCAUCAAGAGCAGGA---------UUAAAU-----------UCC-UCUCCA-ACC-U-GCC------ACUCC--------GGCA--AGGUGGAAA--------------------------AAAU---------------------------------GAUGUGGUU------------AACC-----------------------------AACAA---CUAAAGGAGUUAAA
AACY023273183.1/156-55         UCCACGCAUUAAGA--CUUGG--------GAGA------------CCAA---GCCA-ACC-U-GCC-----GGUCCA--------GGCA--AGGUGGUUA-C-G---------A------------GAAA------------------U------------CGGAUGUGAGCU-----------AUUUCA--------------------------AGCUAA----CAAAUGGACUCUC
AACY020104876.1/245-370        AGUUAAUAUCAAGAGCAGUUC--------AUAUUUAA--------GAAC-UCACCA-ACC-GGGCUCAGA-UCAA------UCAGAG-AAUCGGUGGUAU-U-A-----GCC-U-------------UAA------------------UCGC---------UAGAUGUGCCCA-----------GGAAAA--------------------------UGGGAAA-UGUAAAGCCGCAAUU
AACY020188276.1/838-930        AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY023700707.1/1037-950       UAGUUGCAUAAAGAG-AGG----------GAAA--------------CC-UCAGCA-ACC-U-AGU------UGCCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UAAC-----------------------------AGCAA----AAAAUGGCAUCCC
AACY023108908.1/316-224        AGUAGACAUAAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY023737247.1/614-523        AAGAUGCAUUAAGAAAGGGGU-----------U------------AUCC-CUGCCA-ACC-U-GCA-----UACCG---------UGCGA-AGGUGGUA----------------------------AUA---------------------------------UAUGCGGCC------------AAAAA----------------------------GGCAAAAA----UUAGGUCUCA
AACY021860279.1/473-572        AUUAAGCAUCAGGAGUGAAUA--------AGAAAU----------UAUU-CUGCCA-ACC-U-GCUU----UGAGGA-------AAGUA--AGGUGGA----------------------------GUAG---------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
AACY023370035.1/1421-1515      AAUGCGUAUCUAGAGCAGGA---------UUAAAU-----------UCC-UCUCCA-ACC-U-GCC------ACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGCGGUU------------AACC-----------------------------AACAA---UUAAUGGAGUUAUA
AACY021424810.1/386-491        AAGAUACAUGAAGAG-AGGAC--------UGAC------------GUCC--CGCCA-ACC-U-GCU-----AGAUCC--------GGCA--AGGUGGUUU-C-C-----UUU-U-------------UUA------------------AAAA---------GGCAUGUGACC------------UUCG-----------------------------GGUAA---CAAUGGGGUCCAUG
AACY020505932.1/1795-1882      UAAAUGCAUAGAGAG-AG-----------GGAUAC-------------C-UCAGCA-ACC-U-AG------AUGCCAA--------CUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA----AAAAUGGCGUUCC
AACY023537168.1/911-823        GGUUUGCAUAAAGAG-AGG----------AAAU--------------CC-UCAGCA-ACC-U-AGA-----AUACCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UUAC-----------------------------AACAA----AAGAUGGUAUUUC
AACY023909420.1/125-3          AUAAAGCAUCAGGAGCGGUUUCA------AGU-----------UGAAAC-CCGCCA-ACC-G-AACUUAGAAAAA-----UCAAAGUUA--CGGUGGUU------UGAUCCU-U--------------AA------------------ACGGUA---------GAUGUGCCUA-----------GGAAAA--------------------------UAGGAA-ACAUGAUUAGCCGC--
AACY020249953.1/1780-1874      GUCGAAUAUCACGAGAAGGAU--------UUAU------------AUCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUAUGGC-------------GUUCA-----------------------------GCAA---UCAUAGGAGGAAAU
AACY020048217.1/4787-4698      AUCUUGCAUGAAGAG-AGG----------GUAA--------------CC-UCAGCA-ACC-UAGA-----AAGCAAA----------CAA-AGGUGCUA-----------------------------GA---------------------------------GAUGCGGUUUU----------UU-----------------------------AAAACAA----AAAAUAUGCUACC
AAFX01125835.1/348-230         UUGGUGCAUCCAGAGCGGCUCGCC-----CGACGC-------GGUGAGC-CCGGCA-ACC-U-GCC-----CGGACC--------GGCA--AGGUGCUU----------------------CGCGCAAACCCA-----GCGCA--------------------GAUGUGGCCC-----------AUAG----------------------------CGGCAA---CACGAGGUCCAGCC
AM421808.1/441618-441728       GCGCUGCAUUAAGAGUUGGGA-----------A------------UUCC-AUGCCA-ACC-U-GCUUUUC-AAAAG-----GAAAAGUA--AGGUGGAC----------GGU-U------------GAAA------------------AGCC-----------GAUGUGGCUC-----------ACCA----------------------------GAGCAA-UCCAAACCCGCUUGA-
AACY023277031.1/313-409        AGGAUUCAUCAAGAG-UGGGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAC--------------------------AAGU---------------------------------GAUGAGGUU------------AACC-----------------------------AACAA---CUAAUGGAGUUACA
AACY020517867.1/661-753        AGUAAGCAUAUUGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY023474639.1/1515-1607      AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACCGU-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAA-
AACY020151691.1/305-217        AAAAAGCAUGGAGAG--AGGU--------CAAA------------ACCU--CAGCA-ACC-U-AGA----AAGCUA---------ACUA--AGGUGCUU----------------------------AAA---------------------------------UAUGUGGUU------------UAU------------------------------AACAA-----AAAAUAGCUUUC
AACY024062246.1/396-491        GAUAUUCAUCAAGAGUGAGA---------UUAAAU-----------UCU-CCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGGGGUU------------AAUC-----------------------------AACAA---UUAAAGGAGUAAGA
AACY022716812.1/476-599        UAAUAUCAUCAGGAGCGGUUUCG------UAUU----------UGAAAC-CCACCA-ACC-G-AGCCCAG-AUAAAU----CAUGGUCA--CGGUGGU-------UAGAGCC-U-------------UAA------------------ACGCUA---------GAUGCGCCCA-----------GGAAAA--------------------------UGGGAA-ACAUGAUUAGCCGC--
AACY022857067.1/564-478        UGAGUGCAUAUAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY022335763.1/106-11         AAAUUGUAUCAAGAGCAGGA---------UUUAAU-----------UCC-UCUCCA-ACC-U-ACC-----UACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGCGGUU------------AAUC-----------------------------AACAA---UUAAUGGAGGUAAC
AACY020212291.1/117-209        ACUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY022092685.1/448-536        AAAAAGCAUGGAGAGAGGGU---------AAA--------------ACC-UCAGCA-ACC-U-AGA----UAGCUA---------ACUA--AGGUGCUU----------------------------AAA---------------------------------UAUGUGGUU------------UAU------------------------------AACAA-----AAAAUAGCUUUU
AACY020516175.1/278-365        AAAAAGCAUGGAGAGAGG-----------UAAAGC-------------C-UCAGCA-ACC-U-AGA----AAGCUA---------ACUA--AGGUGCUU----------------------------UAA---------------------------------UAUGUGGUU------------UAU------------------------------AACAA-----AAAAUAGCUUUU
AACY020475741.1/547-639        GUUUUGCAUCAAGA---ACGC--------UAAU------------GCGU---ACCA-ACC-G-ACA-----CGCUCGU-------UGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGCGGGUA-----------GCUC----------------------------UACCAAA--CAAAUCGAGCUAA-
AACY020353810.1/1121-1029      UUUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCCU----------------------------AAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAA
AAOA01000009.1/175160-175267   AAGGGGCAUCAAGAG-GGG----------UUCGU-------------CC-CCACCA-ACC-G-CCC-----ACUCC---------GGGAA-CGGUGGUU---------------------------AAUC---------------------------------GAUGCGCCAUAGGCCCUGC--UGC--------------------GCAGG---UAUGGAA---CAAAAAGGAGAUAU
AACY021228520.1/864-751        UGAUAACAUCAGGAGAGAUUUCU--------AAGU--------AGAAAU-CCACCA-ACC-G-AGC-----UAAAA---------GCUA--CGGUGGUUAGU-U-----CCA-U-------------UAA------------------ACGG---------AGGAUGUGCCUU-----------GAAA----------------------------AAGGAA-AAAGUGGAACCGCC--
CP000459.1/271286-271389       AUCAAGCAUCCAGAG-UCGGG--------UUU-------------CCCG-ACGCCA-ACC-U-GCC-----CUCCCG--------GGCA--AGGUGGAC----------GCC-C-------------UCG------------------AGGC-----------GAUGCGGCCG-----------AUUGA---------------------------CGGCAA---CGAAACGGGAGCAG
AACY023455732.1/308-395        UAAAUGCAUAAAGAG-AG-----------GGAUAC-------------C-UCAGCA-ACC-U-AGU------UGCCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA----AAAAUGGCGUUCC
AAGA01001063.1/1368-1271       AUAAAUUAUCAAGAA--UCUC--------AAUAAAAG--------GAGA--UAGCA-ACC-U-GCA-----AUAACA--------AGCA--AGGUGCUA---------------------------AAUA---------------------------------GAUAAGCCAA-----------GUAA----------------------------UUGGAACAAA----UGUUAAAUC
AACY020259813.1/1669-1756      UAGUUGCAUAAAGAG-AAG----------GAAA--------------CU-UCAGCA-ACC-U-AGU------AGCCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AAAU-----------------------------AACAA----AAAAUGGCUUCUU
AACY023410360.1/1196-1313      UAAUAUCAUCAGGAGUGGUUUCG------UAGU----------UGAAAC-CCGCCA-ACC-G-UGCCCAG-AUAAAU----CAGGGAAG--CGGUGGU-------UAGAGCC-U-------------UAA------------------ACGCUA---------GAUGUGCCU---------------------------------------------AGGAAAA-UAGGAAACACAAAG
AACY021255928.1/715-620        UAAUCACAUCAAGAG-AGGGU--------GAAA------------GCCC--CGCCA-ACC-A-GCC-----UAAUCG--------GGCAA-CGGUGGUC---------------------------UUAA---------------------------------GAUGCGACCC-----------UUA-----------------------------GGGUAA---CAAUUCGAUUAAGG
AACY020492511.1/566-474        CAUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAG
AACY020700407.1/737-642        AAUUUGCAUCAAGAG-UGAGA--------UUAAUU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAGU---------------------------------GAUGCGGUU------------AUUC-----------------------------AACAA---UUAAAGGAGUAGAA
AACY021067675.1/98-221         UAUCAACAUCAGGAGUGGUUUCA------UAGU----------UGAAAC-CCACCA-ACC-GAGCCU----AGAUAAAUC----AGGGAUCCGGUGGU-------UAGACCU-C-------------UAA------------------AUGGUA---------GAUGUGCCCA-----------GGAAAA--------------------------UGGGAAA-CAUAAUAAGCCAC--
AACY021918427.1/327-240        UAAAUGCAUAGAGAG-AG-----------GGAUAC-------------C-UCAGCA-ACC-U-AG------AUGCCAA--------CUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA----AAAAUGGCGUUCC
AACY022859046.1/406-504        GCAAUACAUCAUGAG-UGAAUAA------GAAA----------UUAUUC--CGCCA-ACC-U-GCU-----UGAGGA--------AGUA--AGGUGGCA----------------------------GAG---------------------------------AAUGUGGUC------------UUAAUU---------------------------GACAA--UUAGGUUCCUCGUU-
AACY023408551.1/1374-1279      AAUUAGUAUCAAGAGCAGAG---------UUAAGU-----------CUC-UCUCCA-ACC-U-GCC-----AACUCC--------GGUA--AGGUGGAAA--------------------------AAUU---------------------------------GAUGCGGCA------------UUC------------------------------UGCAA---UACAAGGAGAAAGA
AACY023567589.1/257-349        ACUUUGCAUCAAGAA-CGC----------AAU---------------GC-GUACCA-ACC-G-ACA-----UACUCGA-------UGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGCGGAGA-----------AUAAC---------------------------UCUCAAA---UUUUCGAGUAAUC
AACY020047005.1/1120-1212      GAGGAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------AAUGUGGCA------------GCAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY023073430.1/619-524        UGCCAACAUCAAGAGAAGAGU---------AAA------------ACUC-UCGCCA-ACC-U-GCU------GCUCC--------AGUA--AGGUGGUA--------------C------------AAAA------------------A--------------GAUGAGGUC------------AUUC-----------------------------GACAA---UGAUAGGAGUGUCA
AACY021750064.1/438-530        AUUAGACAUAAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
CP000113.1/1123541-1123419     GCGCAGCAUCAAGAGCGGCCGCCGC----CUCGC-------GCGGUGGC-CCGACA-ACC-U-GGAG----UCGGAC-------CUCCA--AGGUGUCC---------------------------AAAC---------------------------------GAUGCGGUUCGAGGAGC----AGGG---------------------GCUCCCCGAGCAA-UCCAAGCGUCCGAA--
AACY023438706.1/681-781        CACCAUCAUCAAGAA-UGCAG--------AAGAACA---------CUGC-AUACCA-ACC-G-AGC-----AGCCAA--------GCAG--CGGUGGUC---------------------------AAUC---------------------------------GAUGAGGACC-----------AAAAA---------------------------CGUCAA-AAAAAUGGAAAUCA--
AACY023453966.1/898-811        UAAAUGCAUAGAGAG-AG-----------GGAUAC-------------C-UCAGCA-ACC-U-AG------AUGCCAA--------CUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA----AAAAUGGCGUUCC
AACY023562779.1/750-661        ACACUACAUCAAGA---AUAC--------UUAAAU----------GUAU---ACCA-ACC-G-A-------ACGA------------UAG-CGGUGGUU---------------------------AAGC---------------------------------GAUGUGGGC------------AUCACA---------------------------GUCAAAA---UCGAUUCUCAUA
AACY023110182.1/387-483        AAGUGGUAUCAAGAGCAGAG---------UUAAGU-----------CUC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAC--------------------------AAAU---------------------------------GAUGCGGUU------------GUUC-----------------------------AACAA---UUAAAGGAGAUAAA
AACY020114069.1/1282-1374      CGUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------AAA---------------------------------GAUGUGGCA------------AAAU-----------------------------UGCAA---CUAAGUAGUCAAAA
AACY020277418.1/449-357        AGUAAGCAUAUUGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY020347367.1/1189-1095      UACAGAUAUCAAGAGCAGGA---------UUAAAU-----------UCC-UCUCCA-ACC-U-GCC-----CUCUCU--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUAUGGCU------------UUC------------------------------AGCAA-CUAAAGGAGGAAAA--
AACY020597859.1/342-437        CAAUUGCAUCAGGAA-UCCCA----------AA------------UGGG--UACCA-ACC-G-AGAG----AACAUA-------CUCCA--CGGUGGUA---------------------------AAAC---------------------------------GAUGCGGACC-----------GGAA----------------------------GGUCAA-AAUAAAAGUAAUCU--
AACY022787147.1/309-190        GAAUUGCAUUUAGAGCGGUC-GGAGUCG-UAG------UG-CUCUUGGC-CCGGCA-ACC-U-GGG-----UUCGCC--------CCCA--AGGUGCUU----------GCA-C------------ACGAU-----------------GUGC-----------GAUGCGGUCGG----------AUAC---------------------------CCGGCAA--ACCGGCGCCGAUUC-
AAOA01000016.1/47143-47251     CGACUGCAUCAAGAG-GGGC---------AUA--------------GCC-CCACCA-ACC-G-CCC-----ACUCC---------GGGAA-CGGUGGUCC--------------------------AAAU---------------------------------GAUGCGCCAAUGGCUCUGC--AUU--------------------GCAGA--CA-UGGAA---CAUAAAGGAGACCU
AACY020515115.1/670-757        UAAUUGCAUAAAGAG-AGG----------AAAG--------------CC-UCAGCA-ACC-U-AGU------UGCCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UAAC-----------------------------AGCAA----AAAAUGGCAUCAC
AACY022543696.1/466-554        GGUUUGCAUAAAGAG-AGG----------AAAU--------------CC-UCAGCA-ACC-U-AGA-----AUACCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UUAC-----------------------------AACAA----AAAAUGGUAUUUC
AACY021762775.1/443-351        CAUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAG
AACY024079331.1/447-570        AGUUAACAUCAGGAGUGGUUUCG------UAGU----------UGAAAC-CCGCCA-ACC-G-AGCCCAG-AUAAAU----CAUGGUCA--CGGUGGU-------UAGAGCC-U-------------UAA------------------ACGCUA---------GAUGUGCCUA-----------GGAAAA--------------------------UAGGAA-ACAUAAAGCCGCCU--
AACY024005133.1/481-378        GCGCUACAUCACGAG-CGACC--------AUAC------------GGUC--CGGCA-ACC-G-GGA-----------A-------UCCA--CGGUGCCAA-G-------UCA-C------------UUCG------------------GUGA----------CGAUGUGGCCCC----------GCAA---------------------------GGGGCAA-CGGAUCGCAUGGUG--
AACY020167686.1/1628-1731      GCGCUACAUCACGAG-CGACC--------AUAC------------GGUC--CGGCA-ACC-G-GGA-----------A-------UCCA--CGGUGCCAA-G-------UCA-C------------UUCG------------------GUGA----------CGAUGUGGCCCC----------GCAA---------------------------GGGGCAA-CGGAUCGCAUGGCG--
AACY020430580.1/3543-3635      AAUAUACAUUAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY020691148.1/68-191         AAACAUCAUCAGGAGUGGUUUCA------UAGU----------UGAAAC-CCGCCA-ACC-GAGCCCAGA-UAAA------UCAGGG-AAGCGGUGGU-------UAGAGCC-U-------------UAA------------------ACGCUA---------GAUGUGCCUA-----------GGAAAA--------------------------UAGGAA-ACACAAAGCCGCCU--
AACY020289175.1/479-387        AGUAAGCAUAUUGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY023933740.1/780-878        AAAAAGCAUCAGGAGUGAAUAA-------GAAA-----------UUAUU-CUGCCA-ACC-U-GCU-----UGAGGAA-------AGUA--AGGUGGAA----------------------------UAC---------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
AACY024004693.1/41-150         AACCAGCAUCUAGAAACACCUC-------GCAA-----------GAGGU-GUGGCA-ACC-G-AGC-----CCACCAG-------GCCA--CGGUGCCU----------CCC-A------------ACAA------------------CGGG-----------GAUGCGGCGC-----------GACGA---------------------------GCGCAAAA--GAACUGGUGCUC-
AACY021201900.1/462-346        GAAGUACAUCAAGAGAGGCUCA-------AAUU-----------UGGGU-CCGGCA-ACC-U-GGG-----AUGGACA-------CCCA--AGGUGCUCG-C-U-UG--CCU-AG---------------------------------UAGGUG-------AGGAUGCGGUUUC----------GGAA---------------------------GAAACAA--UGAAGUGUCCGGCG-
AACY020280463.1/1762-1661      AUCACACAUGAAGAG-AGGAC--------UGAC------------GUCC--CGCCA-ACC-U-GCC-----CGGACC--------GGCA--AGGUGGUU----------CCC-C------------UCCC------------------GGGG-----------CAUGCGACC------------AAAG-----------------------------GGUAA---CCAAGUGUCCAUGA
CP000529.1/4203375-4203271     AGACAACAUCAAGAC-UGGAU--------AGAAAU----------AUUC-AGACCA-ACC-U-GCC-----AACUCG--------GGCA--AGGUGGUUA-----GC-------------------GAAA----------------------GCA--------GAUGGGGCUU-----------CUCG----------------------------AAGCAA---CCAAACGAGCCAUU
AACY022721140.1/632-540        UAAGAACAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------AAAA-----------------------------UGCAA---CUAAGUAGUCAAAU
AACY024102763.1/297-205        GAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------AAUGUGGCA------------GCAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY020554743.1/6070-6188      UAAAGGUAUGAGGAUUGCCUCACUA----ACCCCA------AGGUGAGG-CUGCCA-ACC-G-AGC-----ACGU----------GCCA--CGGUGGCC--G-A-AU--CUU-A---------------A------------------UGAGAU-------UCCAUAUGUUGG-----------AUUAA---------------------------CCAAAA-AAGGAGCC---CUAUG
AACY020374006.1/456-551        AUCGAACAUCAAGAG-UGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAGU---------------------------------GAUGUGGUU------------AAUC-----------------------------AACAAA---UAAAGGAGAAAAA
AACY020516796.1/1643-1520      AGAUUACAUCAGGAGUGGUCUCA------GUAA----------UGAAAC-CCACCA-ACC-G-AACCCAG-AUAAAU----CGAGGUUA--CGGUGGUU------UGAUCCU-U--------------AA------------------ACGGUA---------GAUGUGCCCA-----------GGAAGA--------------------------UGGGAA-ACAUGAUUAGCCGC--
AACY020719763.1/201-82         AAAGAACAUUAAGAGAAGUUUGGU-----GAAA---------ACUAAGC-UCAGCA-ACC-U-GGG-----AAAGGCA-------CCCA--AGGUGCUU----------------------CCAGUAUUU--------ACUGG--------------------GAUGAGGCCCGAU--------AGA--------------------------AUUGGGCAA--CAAAGUGUCUGAGU-
AACY020099425.1/760-666        AAGAUACAUCAAGAGCAGGA---------UUAAGU-----------UCC-UCUCCA-ACC-U-GCC------ACUCC--------GGCA--AGGUGGAA---------------------------AAAA---------------------------------GAUGUGGUU------------AACC-----------------------------AACAA---UUAAAGGAGUUAAA
AACY021738328.1/622-497        GGGCGUCAUCAAGAAGUGCCGUGCC----UCGUC-------GGCCCGGC-AUGCCA-ACC-U-GAU-----CCGAAG--------UUCA--AGGUGGUU----------UCU-C---------UGGCCUU--------CCA-------GAGA-----------GAUGCGCGUCGG---------AAGAA-------------------------CCGACGAACAAA---CCUUCGACUC
AACY020487706.1/863-955        AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY023407370.1/1041-1133      UUAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY023357773.1/1559-1467      CAUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAG
AACY023767351.1/867-762        UCCCAGCAUCCAGAG-AGGCCA-------UGG------------UGGCC-UCGCCA-ACC-U-GCU-----CCUCC---------AGCA--AGGUGGCA----------UCC-C-------------GAUCAA---------------GGGA-----------GAUGCGGCCC-----------GACA----------------------------GGGCAA----CGAAAGGAGAUCC
AACY022849402.1/732-640        AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GCAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY021297719.1/563-471        GAGAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GCAA-----------------------------UGCAA---CUAAGUAGUCAAAG
AACY023396022.1/1219-1097      GAUUAACAUCAGGAGUGGUUUC--------UAAUU---------GAAAC-CCACCA-ACC-G-AGCAAAG-AUAAAU----CAAUGUUA--CGGUGGUU------UGAUCCU-U--------------AA------------------ACGGUA---------GAUGUGCCCA-----------GGAAAA--------------------------UGGGAA-ACAUGAUUAGCCGC--
AAXX01000006.1/136094-135999   AUUAAGCAUCAAGAU-AAUCC--------AUUG------------GGUU--AGCCA-ACC-G-AUC-----AACUCAC-------GACA--CGGUGGCU----------------------------UAG---------------------------------UAUGCGGAAC-----------AGUC----------------------------GUUCAA--AUGUGUUGAGAAAU-
AACY020038799.1/723-820        AAAUAUCAUCAGGA--CGGGA--------GUAA------------UCCC---ACCA-ACC-G-AGC-----UU-AA---------GCCA--CGGUGGUU----------UGU-C------------AAGU------------------GACA-----------GAUGAGCAGC-----------AAA-----------------------------GCUGAAA----CUAUCUGAAGCC
AACY023097597.1/645-755        GAAUUACAUCAAGAG-AGAGC--------GAAA------------GCUC--CACCA-ACC-A-GCC-----UAAUCG--------GGCAA-CGGUGGUU---------------------------CAAC---------------------------------GAUGAGACC------------GAAAAAGAAAUACUUAAGUA-------------GGUAA---CAAUACGAUUGAGC
AACY022873516.1/143-57         UUAUUGCAUAGAGAG-AGG----------GAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY022730775.1/680-588        UAGAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GCAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY020031148.1/1716-1625      ACAGUGCAUGAAGAG-AGG----------GAAA--------------CC-UCAGCA-ACC-UAGA-----AAGCAAA----------CAA-AGGUGCUU----------------------------CAA----------------------------------AUGCGGUUUU----------UUA----------------------------UAGACAA---AAAAAUAUGCUAUU
AACY023502001.1/877-771        AUCAAGCAUCAAGAGAAGAACUA------AUACUCAA------UGGUUC-UCGCCA-ACC-U-GCU----AAACCU---------GGUA--AGGUGGU----------------------------CGAGUAAAA----------------------------GAUGUGGCU------------UCGC-----------------------------AGCAA----UUAAGAGGUCAAU
AACY020472258.1/364-477        GUAGUACAUCACGAG-CGACC--------AACU------------GGUC--CGGCA-ACC-G-GG------AUUUC----------CCA--CGGUGCCA--U-U-UC--GC---------------GAAAU-------------------GCGA-------AAGAUGUGGUUACGCC-------AGCA------------------------GGCGUAGCAA-CGGGCUGGCUCAGU--
AACY024080065.1/279-371        UAAGAACAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAU
AACY020360095.1/3049-2955      AAGAUACAUCAAGAGCAGGA---------UUAAGU-----------UCC-UCUCCA-ACC-U-GCC------ACUCC--------GGCA--AGGUGGAA---------------------------AAAA---------------------------------GAUGUGGUU------------AACC-----------------------------AACAA---UUAAAGGAGUUAAA
AAUW01000010.1/69484-69362     CGCCAUCAUCAAGAGAAGGGC--------UGGC------------GCCC-UCGCCA-ACC-U-GCC-----GUCCG---------GGCA--AGGUGGUU----------UCC-G-------------CAA------------------CAGG-----------GAUGCGGCCGGUCAGACCCUCUACC-----------------GA-GGUUU-UCCGGCAA----CGAAGCGGUUAAU
AACY023449041.1/987-1079       CAUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAG
AACY020088771.1/512-625        ACUAAUCAUCAGGAGAGGUUUCA------UAAC----------UGAAGC-CCACCA-ACC-G-ACCC----AAAU---------GGGCA--CGGUGGUU------CGAUCCU-U--------------GA------------------ACGGUA---------GAUGCGCCUU-----------UAAA----------------------------AAGGAAA-UCACAAAGCCGCC--
AACY020192706.1/264-356        AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY021025521.1/348-253        UUACUGCAUCAAGAGUAGAG---------UUUAGU-----------CUC-UCUCCA-ACC-U-GCC-----CACUCC--------GGUA--AGGUGGAAA--------------------------AAGU---------------------------------GAUGCGGCA------------UUC------------------------------UGCAA---UACAAGGAGGAAGA
AACY020087873.1/1258-1347      GCGCAACAUCAAGA---AUAC--------UUAAUU----------GUAU---ACCA-ACC-G-A-------ACGA------------UAA-CGGUGGUU---------------------------AAAC---------------------------------GAUGUGGGC------------AUCCUA---------------------------GUCAAA-GUCGAUUCUCAUA--
AACY021493053.1/911-781        GAUGUUCAUCAGGAGAGGUCUGA------GCAA----------UCAGAC-CCGGCA-ACC-U-GGG-----CGGAAGC-------CCCA--AGGUGCCUC-C-C-AA--UCG-A------------GCCU------------------UCGGGUCUGAAAGGGGAUGUGGUCAG----------CAAUAA-------------------------CUGGCAA---CGAAACUUCCUGGA
AACY022288712.1/729-852        AUAGUACAUCAGGAGUGGUUUCA------GUAU----------UGAAAC-CCGCCA-ACC-G-AACCCAGAUAAA-----UCAAGGUUA--CGGUGGUU------UGAUCCU-U--------------AA------------------ACGGUA---------GAUGUGCCCA-----------GGAAGA--------------------------UGGGAA-ACAUGAUUAGCCGC--
AACY021240446.1/353-242        CAAUUACAUCAAGAG-AGAGC--------GUAA------------GCUC--CACCA-ACC-A-GCC-----UAAUCG--------GGCAA-CGGUGGUU---------------------------CAAC---------------------------------GAUGAGACC------------GAAAGAGGAAUAACUUAAGUA------------GGUAA---CAAUACGAUUGGGC
AACY020694102.1/167-72         ACCUUGUAUCUUGAGCAGGA---------UUUAGU-----------UCC-UCUCCA-ACC-U-GCC-----UACUCC--------GGCA--AGGUGGAA---------------------------AAAC---------------------------------GAUACGGUU------------AAUC-----------------------------AACAA---UUAAAGGAGAGAAA
AE004969.1/118224-118334       GCGCUGCAUUAAGAGUUGGGA-----------A------------UUCC-AUGCCA-ACC-U-GCUUUUC-AAACG-----GAAAGGUA--AGGUGGAC----------GGU-U------------GAAA------------------AACC-----------GAUGUGGCUC-----------GCCG----------------------------GAGCAA-UCCAAACCCGCUUGA-
AACY023115370.1/503-620        AGUUAACAUCAGGAGUGGUUUCA------UAGU----------UGAAAC-CCGCCA-ACC-G-AGCCCAGAUAAA-----UCAUGGUUA--CGGUGGU-------UAGAGCC-U-------------UAA------------------ACGCUA---------GAUGUGCC-------------UA--------------------------------GGAA-AAUAGGAAACAUAAAG
AACY020490313.1/1868-1779      AUUUUGCAUAAAGAG-AGG----------GAAG--------------CC-UCAGCA-ACC-U-AGA-----UUGCCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUUAC----------------------------AACAA----AAAAUGGCUUUUG
AACY020308756.1/717-624        AUCUUGCAUCCCGA---ACCC--------UUUAGU----------GGGU---GCCA-ACC-G-AGC-----AGAGAA--------GCCA--CGGUGGCA---------------------------AAAC---------------------------------GAUGCGGGCAU----------U------------------------------AUGCCAA-AACAUAUUCCGAGA--
AACY020553208.1/6570-6666      CUAAUACAUCAAGAG-AGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAA--------------------------AAAU---------------------------------GAUGUGGUU------------AACC-----------------------------AACAAA---CAUAGGAGUACAA
AACY020064609.1/1218-1313      UAAGAGCAUCAGGAGUGGGA---------CUUGU------------UCC-CCGCCA-ACC-U-GCU-----UACCGA--------AGCA--AGGUGGUU---------------------------AGAG---------------------------------UAUGUGGCC------------UAAAC----------------------------GGCAA---CCAAAUCGGACUCU
AACY023894002.1/606-508        AGACAACAUUAAGAG-AGGGC--------UGAC------------GCCC--CGCCA-ACC-U-GCA-----GCUG----------UGCA--AGGUGGUA----------CCC-C-------------GAA------------------AGGG-----------AAUGUGGCC------------UAAA-----------------------------GGCAA-CGACAGCGUCAGCC--
AL157959.1/650530-650640       GUGCUGCAUUAAGAGUUGGGA-----------A------------UUCC-AUGCCA-ACC-U-GCUUUUC-AAAUG-----GAAAGGUA--AGGUGGAC----------GGU-U------------GAAA------------------AACC-----------GAUGUGGCUC-----------ACCA----------------------------GAGCAA-UCCAAACCCGCUUGA-
AACY021707435.1/476-571        AAUAUACAUCAAGAG-CGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGAGGUU------------UAUC-----------------------------AACAAA---UAAAGGAGUUAAA
AACY020114069.1/41-129         AGUUUGCAUAAAGAG-AGG----------AAAU--------------CC-UCAGCA-ACC-U-AGA-----UUACCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UAAC-----------------------------GACAA----AAAAUGGUAUUUU
AACY020501706.1/2164-2069      GAUAUACAUCAAGAGCGAGA---------UUAAAU-----------UCU-CCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGUGGUU------------AACC-----------------------------AACAA---AUAAAGGAGUUAAA
AACY023384145.1/1243-1358      GUCAAUCAUCAGGAGAGAUUAC-------AAUAAA---------GUAAU-CCACCA-ACC-G-ACC-----CAAAAG--------GGCA--CGGUGGUU------UGAUCCU-U--------------AA------------------ACGGUA---------GAUGUGCCUC-----------AGAA----------------------------GAGGAA-UCUUAAAGCCGCCUGA
AACY023360781.1/549-463        UUAAUGCAUAGAGAG-AGG----------AAUU--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY023280010.1/509-603        ACAUUACAUUUUGAGAGGGUU----------AA------------AACC-CUGCCA-ACC-U-GCA-----UAACCU--------UGCGA-AGGUGGUA---------------------------UUAU---------------------------------GAUGUGGCU------------UAUA-----------------------------AGCAAAAAAA---AGGUCCUUU
AACY020434678.1/7044-7134      AAGAUGCAUUGAGAAAGGGAU-----------U------------AUCC-CUGCCA-ACC-U-GCA-----UACCG---------UGCGA-AGGUGGUA----------------------------AUA---------------------------------UAUGCGGCC------------AAAA-----------------------------GGCAAAAA----UUCGGUCUCA
AACY021717596.1/367-461        ACCUAGCAUCAAGAGAAGAGU--------UGU-------------ACUC-UCUCCA-ACC-U-GCC-----CAAUCC--------GGCA--AGGUGGAAA--------------------------AAAU---------------------------------GAUGUGGC-------------AUUCA-----------------------------GCAAA---UAUAGGAGAUCGC
AACY020483405.1/90-1           UUGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCA---
AACY020582823.1/269-371        AGUCAGCAUUUAGAG-AGGGC--------UGACGC----------GCCC--CGCCA-ACC-U-GC------AGCUUGA--------GCA--AGGUGGUUA---------CCU-C------------GCAA------------------GAGG-----------GAUGUGGCCU-----------GAU-----------------------------AGGCAA-----CGUCGAGCGUUG
AACY020551483.1/2636-2539      UUAUUGCAUCGAGAGUAGGAC--------GAAA------------GUCC-UCGCCA-ACC-U-GCU-----UACCCA--------AGCA--AGGUGGUC---------------------------CAAU---------------------------------AAUGUGGCC------------CUUACA---------------------------GGCAA---CCAAAUGGGAAUCC
AACY024050872.1/154-249        AUCGUACAUCAAGAG-UGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAGA---------------------------------GAUGUGGUU------------AAUC-----------------------------AACAA---CUAAAGGAGAAAAA
AACY020788491.1/56-148         AUAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY023060821.1/255-369        GUGUAACAUCAGGAGCGGUUUCU------AAGU----------AGAAAC-CCACCA-ACC-G-AGC-----CUCAAA--------GCUA--CGGUGGUCAGU-U-----CCA-U-------------UAA------------------ACGG---------AAGAUGUGCCUU-----------GAAA----------------------------GAGGAAAAA-UGGAACCGCCU--
AACY020080953.1/3577-3485      CAUAAGCAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAG
AACY020166778.1/510-399        GGUAUGCAUCUAGAAGUCACUUG------GCGA----------CAAGUG-AUGGCA-ACC-G-AGCC----CACCA--------GGCCA--CGGUGCCU----------CGC-U------------GUAA------------------CGGG-----------GAUGCGGCGC-----------GACGA---------------------------GCGCAAAA---GAACUGGUGCUC
AACY023409075.1/925-1017       GUAUUGCAUAAUGAA--CGUU--------UUUA------------AACG--UACCA-ACC-G-ACA-----UCUCAU--------UGCA--CGGUGGUUUUG-------------------------------------------------------------AAUGUGGGUG-----------UCUC----------------------------UGCCAAAA----UUAUGAGAAAU
AACY023900834.1/994-1089       UUCUGGCAUCUAGAGCGAGA---------UUAAAU-----------UCU-CCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGCGGUU------------AACC-----------------------------AACAAA---UAAAGGAGUUAAA
AACY020411818.1/4986-5078      AACAUACAUAAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AANA01000001.1/1651504-1651599 UGGCAGUAUCAGGAA-CGCAA--------GAA-------------UUGC-GUACCA-ACC-G-AGC-----AAAAAA--------GCUA--CGGUGGUU----------------------------UAG---------------------------------UAUACGGACA-----------GUUC----------------------------UGUCAAAA-UAAAUGAACAUCC-
AACY020439129.1/2510-2602      AUGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAA
AACY020225991.1/1900-1814      UUAUUGCAUAGAGAG-AGG----------GAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UUAC-----------------------------AACAA-----AAAAUGGCGUUC
ABCR01000016.1/10470-10573     AUCGCACAUCAAGAGUGAGGC--------CUGU------------GCCU-CUACCA-ACC-U-GCC-----CUUCCC--------GGCA--AGGUGGUG----------UCC-G------------AACA------------------AGGA-----------GAUGUGGCC------------AUGAC----------------------------GGCAA----CCAAGGGGAUCAU
AACY023522594.1/207-113        GUUGAAUAUCACGAGAAGGAU--------UUAU------------AUCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUAUGGC-------------GUUCA-----------------------------GCAAA---CAUAGGAGGAAAA
AACY024112069.1/477-563        UGAGUGCAUAUAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY023473445.1/207-306        AUUAAGCAUCAGGAGUGAAUA--------AGAAAU----------UAUU-CUGCCA-ACC-U-GCUU----UGAGGA-------AAGUA--AGGUGGA----------------------------GUAG---------------------------------GAUGUGGUC------------UUAAU----------------------------GACAA--UUAAGUUCCUCAUC-
AACY021918035.1/709-603        AUCUUUCAUCAAGAGCUGGGC--------CGAC------------GCCC-ACGCCA-ACC-U-GCCC----CGCCC--------GGGCA--AGGUGGAU------------------------CGCGAAA--------GCG----------------------GAUGUGGCUUC----------UAAC---------------------------GAAGCAA---CCAAGCGGGUCAAG
AACY020029910.1/395-486        ACAGUGCAUGAAGAG-AGG----------GAAA--------------CC-UCAGCA-ACC-UAGA-----AAGCAAA----------CAA-AGGUGCUU----------------------------CAA----------------------------------AUGCGGUUUU----------UUA----------------------------UAGACAA---AAAAAUAUGCUAUU
AACY023781615.1/453-361        AAUAUACAUAAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAGAA
AACY021933713.1/55-142         UGAGUGCAUAUAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA----AAAAAUGGCGUUC
AACY022832886.1/280-194        UGAGUGCAUAUAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY023367397.1/199-322        AAUCAUCAUCAGGAGUGGUUUCA------UGAU----------UGAAAC-CCGCCA-ACC-G-AGCCUAG-AUAAAU----CAAGGUCG--CGGUGGU-------UAGAGCC-U-------------UAA------------------ACGCUA---------GAUGUGCCCA-----------GGAAAA--------------------------UGGGAA-ACAUGAUUAGCCGC--
AACY023511498.1/688-780        GAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------AAUGUGGCA------------GCAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY021849718.1/721-830        UUUAUACAUCAGGAA--GGUC--------UAUAU-----------GACC--UGCCA-ACC-G-ACUC----UGGGU--------GAGCA--CGGUGGUU------UGAAUCC-U-------------UAA------------------ACGGUA---------GAUGUGCCUU-----------GAAA----------------------------AAGGAAA--CCUAGAAGCCACC-
AACY023402647.1/1053-958       AGCAAGCAUCUUGAGUGAGA---------UUAAAU-----------UCU-CCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAGU---------------------------------GAUGCGGUU------------AACC-----------------------------AACAA---UUAAAGGAGUAAAA
AACY020086339.1/403-491        AAAAAGCAUGGAGAG-AGGUU----------AA------------AACC-UCAGCA-ACC-U-AGA----AAGCUA---------ACUA--AGGUGCUU----------------------------AGA---------------------------------UAUGUGGUU------------UGU------------------------------AACAA-----AAAACAGCUUUC
AACY020495019.1/1481-1573      GAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------AAUGUGGCA------------GCAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY020375381.1/1502-1407      AUUUUGCAUCUUGAG-AGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-ACC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGUGGUU------------AACC-----------------------------AACAAA---UAAAGGAGUUAAA
AACY022184932.1/558-464        AUAGAGUAUCAAGAGUAGAGU---------GAA------------ACUC-UCGCCA-ACC-U-GCCU----ACCC---------GGGCA--AGGUGGUA---------------------------AAAA---------------------------------GAUGCGGCU------------AACC-----------------------------GGCAA---CCAAACGGGGACCC
AACY021652149.1/718-804        UAAAUGCAUAGAGAG-AGGAA------------------------UUCC-UCAGCA-ACC-U-AGU-----CGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AACAA-----AAAAUGGCGUUC
AACY023677285.1/918-830        AAAAAGCAUGGAGAG-AGGUU----------AA------------AACC-UCAGCA-ACC-U-AGA----AAGCUA---------ACUA--AGGUGCUU----------------------------GAA---------------------------------UAUGUGGUU------------UGU------------------------------AACAA-----AAAAUAGCUUUC
AACY020439832.1/1023-928       AUUGGACAUCAAGAG-UGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAGU---------------------------------GAUGUGGUU------------AAUC-----------------------------AACAAA---UAAAGGAGUAAAA
AACY021520391.1/331-423        AAUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY023484057.1/321-433        UAAUAACAUCAGGAGCAGUUUC-------UUUAUU---------GAAAC-UCGCCA-ACC-GAGUC-----AGUAA---------GACA-GCGGUGGUU------UGAUCCA-U--------------AA------------------AUGGUA---------GAUGUGCCC------------AAAA-----------------------------GGGAA-ACAUAUAAAGCCAC--
AACY023468294.1/539-447        AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY020076934.1/2446-2554      AAGGAACAUUAAGAGAGGUCCA-------AUAA-----------UGGAC-CCGGCA-ACC-U-AGG-----ACGGACA-------CCCA--AGGUGCUU----------CCC-A------------GAAA------------------UGGG-----------GAUGUGGUAC-----------GAAA----------------------------GUACAA--GUAAUUGUCCACAC-
AACY023296326.1/566-470        AGGAUUCAUCAAGAGUGAGA---------UUAGAU-----------UCU-CCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAA--------------------------AAAU---------------------------------GAUGUGGUU------------AAUC-----------------------------AACAA---CUAAAGGAGUUAUA
AACY020270417.1/535-630        GACAUGCAUCAAGAGUAGAG---------UUAAGU-----------CUC-UCUCCA-ACC-U-GCC------ACUCC--------GGCA--AGGUGGAAA--------------------------AAAA---------------------------------GAUGUGGUU------------AACC-----------------------------AACAAA---UAAUGGAGUUAAA
AACY021322626.1/690-782        GUACUGCAUUAAGAA-CGUU---------AUA--------------GAC-GUACCA-ACC-G-ACAA----ACUCA--------UUGCA--CGGUGGU----------------------------UUUG---------------------------------AAUGCGGGUG-----------UCUC----------------------------UACCAAAA----UAAUGAGAAAU
AACY023009993.1/839-749        AAGGUGCAUUAAGAAAGGGG---------UUA--------------UCC-CUGCCA-ACC-U-GCA-----UACCG---------UGCGA-AGGUGGUA----------------------------GUA---------------------------------UAUGCGGCC------------AAAA-----------------------------GGCAAAAA----UUAGGUCUCA
AACY022990670.1/572-668        GUCAGGUAUCAAGAGUAGGA---------UUAAAU-----------UCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAAA--------------------------AAGU---------------------------------GAUACGGUU------------GUUC-----------------------------AACAA---AAAUAGGAGUAACU
AACY023993811.1/239-147        UAAAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY022468102.1/350-442        UUAAAACAUCAUGAG-AGA----------UUAAAU------------UC-UCACCA-ACC-U-GCU-----GACUCC--------AGCA--AGGUGGUA---------------------------AAAA---------------------------------GAUGUGGUU------------AACC-----------------------------AACAA---CUAAAGGAGUUAAA
AACY024079110.1/778-875        CCAAUACAUCAAGAG-AGAGA--------UUAAGU----------UCUC--CUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA--------------A------------AAAA------------------U--------------GAUGUGGUU------------AACC-----------------------------AACAAA---CAUUGGAGUACAA
AACY021960338.1/597-712        UUAUAACAUCAGGAGCGGUUUC-------AUAGCA---------GAAAC-CCGCCA-ACC-G-ACCC----AUGU---------GGGCA--CGGUGGUU------UGAUCCU-U--------------AA------------------ACGGUA---------GAUGUGCCUC-----------ACAA----------------------------GAGGAA-UCUUAAAGCCGCCUGA
AACY020136271.1/828-741        GGUUUGCAUAAAGAG-AGG----------GAAU--------------CC-UCAGCA-ACC-UAGAU-----UACCA---------AUUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UAAC-----------------------------GACAA-----AAAAUGGUAUUU
AACY022455332.1/194-102        AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUA----------------------------GAA---------------------------------AAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY023908039.1/555-463        UUGAAACAUAUAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUCG-U------------------------------------------------------------AAAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAUUAGUCAAAA
AAKX01000119.1/136189-136086   AUCAAGCAUCCAGAG-UCGGG--------UUU-------------CCCG-ACGCCA-ACC-U-GCC-----CUCCCG--------GGCA--AGGUGGAC----------GCC-C-------------UCG------------------AGGC-----------GAUGCGGCCG-----------AUUGA---------------------------CGGCAA---CGAAACGGGAGCAG
AACY020492511.1/1806-1718      GGUUUGCAUAUAGAG-AGG----------AAAU--------------CC-UCAGCA-ACC-U-AGA-----AUACCA--------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------UUAC-----------------------------AACAA----AAAAUGGUAUUUC
AACY022492595.1/463-580        AGUUAACAUCAGGAGUGGUUUCA------UAGU----------UGAAAC-CCGCCA-ACC-G-AGCCCAG-AUAAAU----CAUGGUCA--CGGUGGU-------UAGAGCC-U-------------UAA------------------ACGCUA---------GAUGUGCC-------------UA--------------------------------GGAA-AAUAGGAAACAUAAAG
AACY022741470.1/512-415        AUCAUACAUCUAUAGAGAAGG--------GUAA------------CCUU--CACCA-ACC-A-GCCA----AGACU--------UGGCAA-CGGUGGUU---------------------------CAAC---------------------------------GAUGUGGCUU-----------UUG-----------------------------AAGCAA---CAAUAAAGUCAGAU
AACY023705900.1/919-1025       UAACAACAUUAAGAGAGGUCA--------UUAG------------UGGC-CCGGCA-ACC-U-AGG-----AUGGACA-------CCCA--AGGUGCUU----------CCC-A------------GAAA------------------UGGG-----------GAUGUGGUAC-----------GAAA----------------------------GUACAA--GUAAUUGUCCCAAC-
AACY020423913.1/3046-3139      GUUGAGCAUCAAGA---ACGC--------UAAU------------GCGU---ACCA-ACC-G-ACA-----CGCUCGU-------UGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGUGGGUG-----------GCUC----------------------------UACCAAA--CUAAUCGAGCUUUC
AACY021823955.1/284-382        AUCCUGUAUCAAGAGCAGAG---------UUAAUU-----------CUC-UCUCCA-ACC-U-GCUA----ACUUC--------UAGCA--AGGUGGAAC--------------------------AAAU---------------------------------GAUACGGC-U-----------AUUC----------------------------ACGCAA---CUAAAAGGAGAUCA
AACY022718741.1/342-435        ACAUAGCAUCAAGAGUAGGA---------CUUGU------------UCC-UCACCA-ACC-U-GCA-----ACUCCAA-------AGCA--AGGUGGUC---------------------------AAUA---------------------------------GAUGCGGC-------------AAUC------------------------------GCAAA---CAAUUGGAGAACA
AACY023311957.1/783-659        CCCUCACAUCACGAGUGGCUCGG------UUUU----------CCGGGC-UCGGCA-ACC-U-GGG-----GCGAACA-------CCCA--AGGUGCCAA-C-C-CA--CC----------------UUU--------------------GGUG-------GGGAUGCGGCUUCCACC------UUCC-----------------------GGUGUCGGCAA--CAACCAGUUCGAGG-
AACY022762621.1/313-199        CGACGACAUCAAGAGCGACCC--------UCAC------------GGGU-CCGGCA-ACC-G-GG------AUCG-----------CCACUCGGUGCCAU-C-C-----CGC-C------------UCGC------------------GGCG---------GGGAUGUGGUCCCGC--------ACUC-------------------------GCGGGACAA-GGAGGUGACAUGGC--
CP000152.1/3090724-3090621     GUCAAGCAUCCAGAG-UCGGA--------UUC-------------UCCG-ACGCCA-ACC-U-GCC-----CUCCCG--------GGCA--AGGUGGAC----------GCC-U-------------CUG------------------AGGC-----------GAUGCGGCCG-----------AUUUA---------------------------CGGCAA---CGAAACGGGAGCAG
AACY020498997.1/2371-2463      AUUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGGCUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAUUAGUCAAAA
AACY020086339.1/1639-1731      AGUAGACAUAAAGAGAAGGUU----------AA------------GACC-UCAGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAAUAGUCAAAA
AACY021123789.1/139-44         UUAAAGUAUCAAGAGAAGGA---------UUAAAU-----------UCC-UCUCCA-ACC-U-GCC-----AACUCC--------GGUA--AGGUGGAA---------------------------AAAA---------------------------------GAUACGGUU------------AACC-----------------------------AACAA---UUAAAGGAGCAAUA
AACY023457680.1/173-265        AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGGCUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY023861419.1/882-790        AUUAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----AGACUA--------UCCA--AGGUGCCU----------------------------GAA---------------------------------GAUGUGGCA------------GAGA-----------------------------UGCAA---CUAAAUAGUCAAAA
CP000692.1/3559-3450           CUUCAGCAUCAAGAGUUGGGC--------CGAC------------GCCCAGCGCCA-ACC-U-GCU------UCCCG--------AGCA--AGGUGGCU--U-U-CU--UCC-U---------------U------------------CGGAAG-------AAGAUGUGGCCG-----------GUC-----------------------------CGGCAA---CUAAACGGGACAAG
AACY020858903.1/521-623        ACGUUGCAUGAAGAG-AGGGC--------AGAC------------GCCC--CGCCA-ACC-U-GCC-----UGACAC--------GGCA--AGGUGGUUU-C-C-UU-------------------GAAA----------------------AA-------GGCAUGAGACC------------AUAG-----------------------------UGUAAA---CACAGUGUCCAUG
AACY020331588.1/716-808        UUGAAACAUACAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUAG-U------------------------------------------------------------AAAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAUUAGUCAAAA
AACY020514730.1/2517-2605      AUUGUGCAUGAAGAG-AGG----------GUAA--------------CC-UCAGCA-ACC-UAGA-----AAGCAAA----------CAA-AGGUGCUA-----------------------------AA---------------------------------GAUGCGGUUU-----------UUU-----------------------------AAACAA----AAAAUAUGCUAUU
AACY022059262.1/134-223        AAAAAGCAUCAAGA---ACGC--------GAAU------------GCGU---ACCA-ACC-G-ACA-----GCUCGU--------UGCA--CGGUGGUU----------------------------UAG---------------------------------AAUGCGGGG------------GUCCU----------------------------CCCAAA----UUAACGAGAAAU
AACY023400827.1/1711-1619      CAAGCACAUCGAGAGCGGA----------CUAAAU------------UC-CCACCA-ACC-C-GCA-----UACUCA--------AGCA--AGGUGGUU----------------------------CAG---------------------------------CAUGUGGCC------------AAAU-----------------------------GGCAA---UCAACUGGGUAUCU
AACY023729720.1/424-336        AAAAAGCAUGGAGAG--AGGU--------AGAA------------GCCU--CAGCA-ACC-U-AGA----AAGCUA---------ACUA--AGGUGCUU----------------------------AAG---------------------------------UAUGUGGUU------------UAU------------------------------AACAA-----AAAAUAGCUUUU
AACY023908770.1/692-806        UUACAUCAUCAGGAGCGAUUUCU------UACG----------AGAAAU-CCACCA-ACC-G-AGC-----UUAAAA--------GCUA--CGGUGGUUAGU-U-----CCA-U-------------UAA------------------ACGG---------AAGAUGUGCCUU-----------GAAA----------------------------AAGGAA-AAAGUGGAACCGCC--
AACY022640834.1/583-487        AGGAAACAUCAAGAA-AGAGUG-------AUGA-----------CACUC-UUACCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGUUU--------------------------AAAC---------------------------------GAUGUGGCU------------UUC------------------------------AGCAA---CUAAAGGAGGUAAU
AACY020546191.1/1354-1440      UGAGUGCAUAUAGAG-AGG----------AAUA--------------CC-UCAGCA-ACC-U-AGU-----UGCCA---------ACUA--AGGUGCUU----------------------------UUU---------------------------------GAUGUGGUU------------AUAC-----------------------------AGCAA-----AAAAUGGCGUUC
AACY022825914.1/237-332        AGUGUUCAUCAAGAGUGGGA---------UUUAGU-----------UCU-CCUCCA-ACC-U-GCC-----AACUCC--------GGCA--AGGUGGAA---------------------------AAAU---------------------------------GAUGUGGUU------------AACC-----------------------------AACAAA---UAAAGGAGUUAAA
AACY023455354.1/428-520        AAGAAGCAUAAAGAGAAGGUU----------AA------------GACC-UCGGCA-ACC-U-GGA-----UGACUA--------UCCA--AGGUGCUU----------------------------GAA---------------------------------GAUGUGGCA------------GAAA-----------------------------UGCAA---CUAAGUAGUCAAAC
AACY023254477.1/1093-1197      UUCGGACAUCAAGAGUAGGGC--------UGAC------------GCCC-UCGCCA-ACC-U-GCC------UACCC--------GGCA--AGGUGGUG----------CUC-C------------GAAA------------------GGAG-----------GAUGUGGCC------------AUAGAC---------------------------GGCAA---CUAAAGGGUCUAAG
AACY020911503.1/589-700        CAAAAUCAUCAGGAGCGAUUUCC------AGAU----------GGAAAU-CCACCA-ACC-G-GCCC----AAUU---------GGGAA--CGGUGGUUA-----GG--UCA-A-------------AUA------------------AUGACA---------GAUGUGCCC------------UUUA-----------------------------GGGAA-ACUCUGAACCGCCU--
CP002046.1/2215703-2215606     CUUAAUUAUCAAGAA--UCUC--------AAAGA-----------GAGA--UAGCA-ACC-U-GCA-----AUAACG--------AGCA--AGGUGCUAA--------------------------AAUA---------------------------------GAUAAGCCAA-----------AUUCAA--------------------------UUGGAAAAAA----UGUUAAUUC
CP001712.1/639245-639336       UUCCUGCAUCAGGA---ACGC--------UAAGGC----------GCGU---ACCA-ACC-G-AGC-----AUAAAA--------GCCA--CGGUGGUU----------------------------CAG---------------------------------AAUGCGGAC------------GGUC-----------------------------GUCAAAAAAA-UAAUUCCUU--
AE002098.2/1888986-1888876     GUGCUGCAUUAAGAGUUGGGA-----------A------------UUCC-AUGCCA-ACC-U-GCUUUUC-AAAAG-----GAAAAGUA--AGGUGGAC----------GGU-U------------GAAA------------------AGCC-----------GAUGUGGCUC-----------ACCA----------------------------GAGCAA-UCCAAACCCGCUUGA-
#=GC SS_cons                   :::::(((((,,,,<-<<<<<........____............>>>>.>><<<-.-<<.<.<<<.....AAAAAA........>>>-..>>>->>>,...........................,,,,.................................)))))-<<<<...........____............................>>>>::...:::::aaaaaa:::
#=GC RF                        aaaaagCAUcAAGAGugGgcc........uuaa............ggcC.cCgcCA.ACC.u.ggc.....aaauca........gccA..aGGUGgcu...........................aaaa.................................gAUGcGgccg...........aaaa............................cggcAA...caaaaugguuaaau
//
# STOCKHOLM 1.0

#=GF AC   RF01726
#=GF ID   SAM-II_long_loops
#=GF DE   SAM-II long loop
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   44.00
#=GF TC   44.70
#=GF NC   41.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   SAM-II_riboswitch
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   126


BAAY01000229.1/4860-4801       AAA-ACAGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAG--------------------------AAAAAAAUG-CUAAAAAAUACAUU
BABA01032719.1/684-625         AAA-ACAGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAG--------------------------AAAAAAAUG-CUAAAAAAUACAUU
BABD01010212.1/361-302         AAA-ACAGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAG--------------------------AAAAAAAUG-CUAAAAAAUACAUU
BABD01004898.1/734-675         AAA-ACAGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAG--------------------------AAAAAAAUG-CUAAAAAAUACAUU
BAAU01003527.1/70-11           CGAUA-UGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACACAUCCU
BAAV01005021.1/856-915         CGAUA-UGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACACAUCCU
BABD01000682.1/2075-2016       CGAUA-UGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACACAUCCU
BAAX01034998.1/534-475         CGAUA-UGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACACAUCCU
BABA01000840.1/862-921         CGAUA-UGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACACAUCCU
BAAY01003005.1/1818-1877       CGAUA-UGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACACAUCCU
BABG01001786.1/1819-1878       UGAAA-UGUGGAAAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACAACAUUC
AM398681.1/321748-321688       AAUCG-AGAGGAAAAAUUUGAACU-------------------GAUUGCA-A-CCUCGUU-------------------------AAAAAAAUG-CUAAAGCAGAAAUU
AAPD01000001.1/935844-935772   CAAUU-AGGGGAAAGAUUUGGCU--------------------GCUUGCG-A-CCUCGUUUUCAUGUUCG------------AAAACAUAAACG-CUAAAACAGUGUAC
AACY020226321.1/506-565        UUAAA-CGAGGAUCGAUUUGUCU--------------------GAUUGCA-A-CCUCUAU-------------------------AAAAAAGUG-CUAAAGCAGUAGCU
AACY022850478.1/878-818        ACAAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGUGUUG
AAXE02000111.1/39496-39555     AUUGA-UGUGGAUAGAUUUGUAUU-------------------GCUUGCA-A-CCACAGG--------------------------AAAAAAUG-CUAAAAACAAGCCC
AACY021292300.1/273-332        CAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY023943407.1/647-587        AUAAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGUAUUG
AACY021228766.1/856-797        AUAAA-CGAGGAUCGAUUUGACU--------------------GAUUGCA-A-CCUCUUU-------------------------AAAAAAGUG-CUAAAGCAGAUGCU
AACY023971441.1/142-202        UUAAA-CGAGGAAGGAUUUGACU--------------------GAUUGCACA-CCUCGAU-------------------------AAAAAAUUG-CUAAACCAGAGUUG
AACY023024880.1/159-218        UGUUA-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCAUA-------------------------AAAAAAAUG-CUAAAGCAGUGUUG
AACY020348523.1/304-245        UAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY020987302.1/866-808        GUAUA-UGAGGAAAAAUUUGACU--------------------GAUUGCA-A-CCUCAAG--------------------------AAAAAAUG-CUAAAAUUGAUUUU
AACY023951743.1/60-119         ACAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY023795149.1/997-939        CCGCC-AGUGGAAAAAUUUGACU--------------------GAUUGCA-A-CCACCUU--------------------------AAAAAAUG-CUAAAGCAGUUCCC
CP000139.1/1599296-1599355     AAA-ACAGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAG--------------------------AAAAAAAUG-CUAAAAAAUACAUU
AACY021173370.1/137-194        AAAUA-GGUGGAGUGAUUUGACU--------------------GCUUGCA-A-CCACAUU---------------------------AAAAAAG-CUAAAAUUUGUCCU
CU207366.1/366446-366372       ACUGA-AAGGGAUAGAUUUGACU--------------------GAUUGCA-A-CCCU-AAUACUUAUAAAAGGUAUUUU---------AAAAUG-CUAAAGCAGAAUGU
AACY021513568.1/618-677        AUAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUCA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
ACGA01000041.1/74606-74547     GAAAG-UGUGGACAGAUUUGAGUA-------------------GCUUGCA-A-CCACGGA--------------------------AAAAAAUG-CUAAAACACGUCUG
AACY021330987.1/297-240        UCUUA-AGUGGAUAAAUUUGGCC--------------------GAUUGCA-A-CCACUCC---------------------------AAAAAUG-CUAAAAACAGGAAC
AACY022589258.1/489-429        UAGAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGUGUUG
AAVM02000002.1/266706-266765   GAAAG-UGUGGACAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACACGACUC
AACY023713394.1/744-803        GAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCAUU-------------------------AAAAAAUUG-CUAAAGCAGUAUUU
AACY022144381.1/603-662        AACAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY020258321.1/992-932        AUUAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGUGUUG
AACY020258861.1/1566-1507      AUAAA-AGAGGAAAGAUUUGACU--------------------GAUUGCA-A-CCUCUCA-------------------------AAAAAAGUG-CUAAAACAGCUUUA
CR626927.1/69593-69652         UGAAA-UGUGGAAAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACAACAUUC
AACY023403142.1/1259-1199      UUAAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGUAUUG
AACY023235685.1/470-410        AUUAA-CGAGGAAGGAUUUGACU--------------------GAUUGCAGA-CCUCGCA-------------------------AAAAAAAUG-CUAAAACAGAAUUG
AANC01000003.1/237275-237201   AA--A-AGAGGAAAGAUUUGACU--------------------GAUUGCA-A-CCUCUUAUGCUGAAACAUCGGCGU--------AAAAAAAUG-CUAAAGGCAGUACU
AACY020538121.1/2684-2742      CCGCC-AGUGGAAAAAUUUGACU--------------------GAUUGCA-A-CCACCUU--------------------------AAAAAAUG-CUAAAGCAGUUCCC
AACY023643543.1/630-571        UUGUU-AGAGGAACGAUUUGACU--------------------GAUUGCA-A-CCUCUUU-------------------------AAAAAAGUG-CUAAAGCAGUAGCU
AACY022040351.1/329-388        UAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCAUU-------------------------AAAAAAUUG-CUAAAGCAGUAUUU
AACY023628503.1/749-690        AGAAU-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUCA-------------------------AAAAAAUUG-CUAAAACAGUAAUU
AACY024041675.1/840-782        AACAC-GGUGGAUAAAUUUGACU--------------------GAUUGCA-A-CCACUUA--------------------------AAAAAAAG-CUAAAGCAGUAUUA
AACY020012966.1/2002-2058      UAACU-AGUGGAAUGAUUUGAAU--------------------GCUUGCA-A-CCACCAA----------------------------AAAAAG-CUAAAACGAACUUA
AP009380.1/2055065-2055124     AUCAG-CGUGGAAGGAUUUGUAAU-------------------GCUUGCA-A-CCACGAG--------------------------AAAAAAUG-CUAAAACAUUUCUU
AACY023745073.1/891-950        UUGUU-AGAGGAUCGAUUUGACU--------------------GAUUGCA-A-CCUCUUU-------------------------AAAAAAGUG-CUAAAGCAGAGCUU
AACY020046896.1/683-743        AAUAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGUGUUG
AACY021498341.1/375-434        UUAAA-CGAGGAUCGAUUUGUCU--------------------GAUUGCA-A-CCUCUAU-------------------------AAAAAAGUG-CUAAAGCAGUUGCU
AACY020924815.1/303-365        UUAAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-AACCUCGAA-----------------------AAAAAAAAUUG-CUAAAGCAGUGUUG
AACY022934602.1/688-629        CAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY023491905.1/399-458        CACUC-AGAGGAACGAUUUGACU--------------------GAUUGCA-A-CCUCUUU-------------------------AAAAAAGUG-CUAAAGCAGUAGCU
AACY021213112.1/176-235        CAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY023616082.1/79-20          CAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY021715294.1/721-663        AUAAU-CGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUAA--------------------------AAAAAAUG-CUAAAGCAGUGUUG
AACY020009875.1/3178-3120      GGGGC-AGUGGAAGGAUUUGACU--------------------GCUUGCA-A-CCACGAU--------------------------AAAAAAUG-CUAAAUACAGCACA
AACY020027165.1/1329-1270      CUAAC-AGAGGAAUGAUUUGACU--------------------GAUUGCA-A-CCUCUAA-------------------------AAAAAAUUG-CUAAAGCAGUAUUU
AACY021992465.1/118-177        GGAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCAUU-------------------------AAAAAAUUG-CUAAAGCAGUAUUU
AACY020071365.1/1598-1540      GAGUU-UGUGGACAGAUUUGGCC--------------------UAUUGCA-A-CCACAAA--------------------------AAAAAAUG-CUAAAAACGUUUCA
AE015928.1/4108976-4109035     GAAAG-UGUGGACAGAUUUGAGCA-------------------GCUUGCA-A-CCACGGA--------------------------AAAAAAUG-CUAAAACACGUCUU
AACY021828173.1/306-365        CUAAU-AGAGGAUAAAUUUGAUCU-------------------GAUUGCA-A-CCUCAUA--------------------------AAAAAAAG-CUAAAGCAGUAAUU
AACY022708930.1/363-422        CAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY021719197.1/354-295        GCAAA-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUCA-------------------------AAAAAAGUG-CUAAAACAGCUUUA
AACY020149886.1/877-936        CUAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
ABCM01000030.1/26135-26215     AUUAA-AGUGGACUGAUUUGCGAUGCUAUGUCAAAAAUAGCGGGAUUGCA-A-CCACGUA------------------------AAAAAAAGUG-CUAAUGUUUCUACA
AACY023969146.1/37-96          AAUAU-AGAGGACAAAUUUGAUCU-------------------GAUUGCA-A-CCUCAUU--------------------------AAAAAAAG-CUAAAGCAGUAUAU
AACY020065925.1/602-660        UGUAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA--------------------------AAAAAAUG-CUAAAGCAGUGUUG
AACY023563425.1/759-817        AUAAU-CGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUAA--------------------------AAAAAAUG-CUAAAGCAGUGUUG
EU060946.1/37-96               CGAUA-UGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACACAUCCU
AACY020435334.1/143-202        GCAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCAUU-------------------------AAAAAAUUG-CUAAAGCAGUAUUU
AACY020159503.1/993-933        AAUAA-CGAGGAAGGAUUUGUCU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGAAUUG
AE015924.1/1994578-1994637     AUCAG-CGUGGAAGGAUUUGUAAU-------------------GCUUGCA-A-CCACGAG--------------------------AAAAAAUG-CUAAAACAUUUCUU
AACY023634238.1/717-776        UUAUU-AGAGGAUCGAUUUGACU--------------------GAUUGCA-A-CCUCUUU-------------------------AAAAAAGUG-CUAAAGCAGAAGCU
AACY023698643.1/1374-1315      UAAUU-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCAUA-------------------------AAAAAAUUG-CUAAAGCAGUGUUG
AACY023372826.1/421-361        ACGAA-CGAGGAAAAAUUUGACCU-------------------GAUUGCA-A-CCUCUAU-------------------------AAAAAAAUG-CUAAAACAGUAUUU
AACY021576146.1/97-156         UUAUU-AGAGGAACGAUUUGACU--------------------GAUUGCA-A-CCUCUUU-------------------------AAAAAAGUG-CUAAAGCAGAUGCU
AACY023934990.1/1181-1240      CAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY022383234.1/424-483        GAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUCA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AAMZ01000003.1/48269-48210     AAUAA-CGAGGACAGAUUUGACU--------------------GCUUGCA-A-CCUCAAA--------------------------AAAAAAUGGCUAAAAUCAAACAC
AANA01000001.1/1408910-1408969 AAUUA--GAGGAAAAAUUUGAACU-------------------GAUUGCA-A-CCUCAUU-------------------------AAAAAAAUG-CUAAAGCAGUAAUU
AACY021913000.1/878-819        UUAAC-AGAGGAUAAAUUUGUUCU-------------------GAUUGCA-A-CCUCAAA--------------------------AAAAAAAG-CUAAAGCAGUAAAU
AACY023767453.1/1015-958       UAACA-AGUGGACAAAUUUGGCU--------------------GAUUGCA-A-CCACUCC---------------------------AAAAAUG-CUAAAACAGGAAUG
AACY020011721.1/593-534        UUAAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-G-CCUCGAU-------------------------AAAAAAUUG-CUAAAACAGUGUUG
AACY020489309.1/2946-2886      AGUAA-CGAGGAAGGAUUUGUCU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGAAUUG
AACY020021759.1/671-611        GAAUG-CGUGGAAGGAUUUGACU--------------------GCUUGCA-A-CCACUAG------------------------AAAAAAAAUG-CUAAAUACAGCACA
AACY020115125.1/839-898        GAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
BAAV01002129.1/648-707         AAA-ACAGUGGAGAGAUUUGAGUA-------------------GCUUGCA-A-CCACAG--------------------------AAAAAAAUG-CUAAAAAAUACAUU
AACY023569644.1/754-695        UUGUU-AGAGGAACGAUUUGACU--------------------GAUUGCA-A-CCUCUCU-------------------------AAAAAAGUG-CUAAAGCAGUAGCU
AACY021898092.1/283-225        AGAUU-UGUGGAGAGAUUUGGCC--------------------UAUUGCA-A-CCACCAA--------------------------AAAAAAUG-CUAAAAAAGUUUCA
AACY020976473.1/382-323        AUUUC-AGAGGAAAAAUUUGAACU-------------------GAUUGCA-A-CCUCGUU--------------------------AAAAAAUG-CUAAAGCAGGAAUU
AACY020479744.1/588-647        CACUC-AGAGGAACGAUUUGACU--------------------GAUUGCA-A-CCUCUUU-------------------------AAAAAAGUG-CUAAAGCAGUAGCU
AACY023242166.1/491-431        AUUAA-CGAGGAAGGAUUUGACU--------------------GAUUGCAGA-CCUCGCA-------------------------AAAAAAAUG-CUAAAACAGAAUUG
AACY023608701.1/684-743        UUAUU-AGAGGAACGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAGUG-CUAAAGCAGUAGCU
AAXX01000001.1/754085-754145   AACAA-AGAGGAAAAAUUUGAACU-------------------GAUUGCA-A-CCUCAUU-------------------------AAAAAAAUG-CUAAAGCAGUAUUC
AACY023025519.1/730-671        CCCUC-AGAGGAACGAUUUGACU--------------------GAUUGCA-A-CCUCUUU-------------------------AAAAAAGUG-CUAAAGCAGUAGCU
AP006841.1/64060-64119         UGAAA-UGUGGAAAGAUUUGAGUA-------------------GCUUGCA-A-CCACAGA--------------------------AAAAAAUG-CUAAAACAACAUUC
AACY021387527.1/312-255        AAAUA-GGUGGAGUGAUUUGACU--------------------GCUUGCA-A-CCACAUU---------------------------AAAAAAG-CUAAAAUUUGUCCU
AACY024036108.1/92-33          UUAUU-AGAGGAACGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAGUG-CUAAAGCAGUAGCU
AACY022928259.1/329-269        ACAAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGUGUUG
AACY022192745.1/838-781        GUAUU-AGUGGAGUGAUUUGACU--------------------GCUUGCA-A-CCAC-CA--------------------------AAAAAAAG-CUAAAUUUGAUGUC
AACY020050544.1/274-215        CAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY020262906.1/1161-1220      GAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUCA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY020448488.1/380-438        UCCAA-AGAGGA-CGAUUUGACU--------------------GAUUGCA-A-CCUCUCG-------------------------AAAAAAGUG-CUAAAAUGUAUGCC
AACY022283545.1/615-674        UUGUU-UGAGGAUCGAUUUGACU--------------------GAUUGCA-A-CCUCUUU-------------------------AAAAAAAUG-CUAAAGCAGACAUU
AACY020923398.1/499-558        UAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY023778830.1/696-636        ACAAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGUGUUG
AACY020013445.1/795-736        UUAUU-AGAGGAACGAUUUGACU--------------------GAUUGCA-A-CCUCUUU-------------------------AAAAAAGUG-CUAAAGCAGAUGCU
AACY021816178.1/148-206        AUAAU-CGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA--------------------------AAAAAAUG-CUAAAGCAGUGUUG
AACY020026171.1/2307-2366      CCCAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUCA-------------------------AAAAAACUG-CUAAAACAGCUUGC
AACY021616887.1/276-335        CAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUCA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY021864797.1/383-441        UAUUA-AGUGGACAAAUUUGACU--------------------GAUUGCA-A-CCACUCC--------------------------UAAAAAUG-CUAAAACGGGAUAA
AACY020050713.1/281-221        ACAAA-CGAGGAAGGAUUUGACU--------------------GAUUGCA-AACCUCGAA-------------------------AAAAAAAUG-CUAAAGCAGUGUUG
AAPR01000008.1/157663-157721   UGCAU-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUUUU--------------------------AAAAUG-CUAAAGCAGUUUCA
ABVV01000001.1/132708-132768   UUAAA-CGAGGAAGGAUUUGACU--------------------GAUUGCACA-CCUCGAU-------------------------AAAAAAAUG-CUAAACCAGAGUUG
AACY023377901.1/249-307        GAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA--------------------------AAAAAUUG-CUAAAGCAGUAAUU
AACY020386810.1/38-97          UAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY023954900.1/309-250        CAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY023370070.1/230-289        GAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
AACY020315669.1/1646-1587      UAAAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUUA-------------------------AAAAAAUUG-CUAAAGCAGUAAUU
CP000140.1/2817240-2817181     AUUGA-CGUGGAUAGAUUUGUAUU-------------------GCUUGCA-A-CCACGGG--------------------------AAAAAAUG-CUAAAAACAUAUCC
AACY020448805.1/1119-1178      CCCAC-AGAGGAAGGAUUUGACU--------------------GAUUGCA-A-CCUCUCA-------------------------AAAAAACUG-CUAAAACAGCUUGC
ABYH01000277.1/7168-7109       AUUGA-UGUGGAUAGAUUUGUAUU-------------------GCUUGCA-A-CCACAGG--------------------------AAAAAAUG-CUAAAAACAAGCCC
CP001712.1/3498502-3498423     UUUCC-AGAGGACAGAUUUGACU--------------------GAUUGCA-A-CCUCUGAUCCGGAAUUGAGCCGGACCACC-----AAAAAUG-CUAAAGCAGUUUGC
CP002157.1/243781-243711       CAUCA-AGAGGAAAGAUUUGACU--------------------GAUUGCA-A-CCUCGAAGUUCUCAACUUC--------------AUAAAAUG-CUAAAGCAGUACCU
#=GC SS_cons                   :::::.<<<<<----<<<_____....................>>>AAAA.-.>>>>>::.........................:::::::aa.a:a:::::::::::
#=GC RF                        auuaa.aGaGGAaaGAUUUGAcU....................GAUUGCA.A.CCuCuuA.........................AAAAAAAUG.CUAAAGCAguuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01727
#=GF ID   SAM-SAH
#=GF DE   SAM/SAH riboswitch
#=GF AU   Yang J
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   43.10
#=GF NC   30.60
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.56 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0046500; S-adenosylmethionine metabolic process;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   SAM-SAH_riboswitch
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   53


CP000578.1/343169-343120     CAA-CCGUCACAACGGCUUCCUGGCGUGAC-GG--GGUUAACCCCAACGGAGCA
CP000377.1/211359-211407     AUG-CCGCCACAACGGCUUCCUGGCGUGGC-GG--AUCUCAUCC-AAUGGAGCA
AACY020589009.1/251-203      ACG-UCGUCACAACGGCUUCCUGGCGUGAC-GA--UACACAUCU-AAUGGAGCA
AACY023759949.1/393-346      UAU-UGCACGCAACGGCUUCCUGACGCGUG-AG--UUGUAAUU--AUCGGAGCA
AACY020526688.1/2154-2202    CUC-CUGUCACAACGGCUUCCUGGCGUGGCGGG--CAACAUCC--AAUGGAGCA
CP000032.1/9372-9422         GAC-CUGCCACAACGGCUUCCUGGCGUGGCGAG--GGAAACCUUCAAUGGAGCA
CP000144.1/688624-688575     CAA-CCGUCACAACGGCUUCCUGGCGUGAC-GG--GGUUAACCCCAACGGAGCA
AACY020245805.1/1080-1127    UCC-UACACGCAACGGCUUCCUGACGCGUGAGG--UGUAAUC---AUUGGAGCA
AACY021643013.1/428-383      UGG---CACGCAACGGCUUCCUGACGCGUG-----AGAUUGAAUUAUUGGAGCA
ABSK01000009.1/52599-52551   UUU-UAUCCACAACGGCUUCCUGAAGUGGA-UC--GACAUUUAA-ACUGGAGCA
ABIE01000005.1/70619-70571   UUA-CUGCCACAACGGCUUCCUGGCGUGGC-AG--GCUAAACCC-AACGGAGCA
AACY020522644.1/2673-2625    AUC-UCGCCACAACGGCUUCCUGACGUGGC-GG--CAGAACCCU-AAUGGAGCA
AACY022220959.1/246-198      GUG-CUGUCACAACGGCUUCCUGGCGUGGC-GG--CGAAAACCU-AAUGGAGCA
AACY023829178.1/189-238      GCG-CUGCCACAACGGCUUCCUGGCGUGGC-GG--UCUGACAGUCAAUGGAGCA
AAFY01026626.1/203-251       GAA-UUGCUACAACGGCUUCCUGACGUGGC-GA--UCUAUAUGA-ACUGGAGCA
AACY023873338.1/90-135       UAG---CACGCAACGGCUUCCUGACGCGUG-----AGCUUUAAUUAUCGGAGCA
AACY021789724.1/224-271      UGA-UGCACGCAACGGCUUCCUGACGCGUGAGA--UUAAAUU---AUUGGAGCA
AATR01000003.1/91067-91114   UAA-GGCUUACAACGGCUACCUGAAGUAAG-UU--GACAUAAA--AACGGAGCA
ABXS01000051.1/24818-24865   AAU-CUGCCACAACGGCUUCCUGACGUGGCUAU--UUAAUCU---AUUGGAGCA
AACY022370156.1/216-170      UCC-UAGCUGCAACGGCUUCCUGGCGCAGCUUA--CAUUUU----AUUGGAGCA
CP000264.1/678143-678190     ACU-CCUCCACAACGGCUUCCUGACGUGGG-GG--AUUAUUUG--AAUGGAGCA
AACY020081998.1/989-1034     AGA---CACGCAACGGCUUCCUGACGCGUG-----AAAUUAAAUUAUUGGAGCA
CP000662.1/776419-776468     CAA-CCGUCACAACGGCUUCCUGGCGUGGC-GG--GGAUAACCCCAACGGAGCA
AACY020253271.1/246-293      AAU-UGCACGCAACGGCUUCCUGACGCGUG-AG--UUUUAAUU--AUCGGAGCA
ABXE01000008.1/209807-209759 AGA-CUGCCACAACGGCUUCCUGACGUGGU-GG--AAAAAUCUU-ACUGGAGCA
CP000489.1/1874599-1874647   UGA-CCGCCACAACGGCUUCCUGGCGUGGC-GG--CGUCAUUUC-AACGGAGCA
ABCR01000003.1/393478-393430 AAC-CCGUCACAACGGCUUCCUGGCGUGAC-GG--CUGACAUAC-AAUGGAGCA
AACY020145469.1/1022-977     UGG---CACGCAACGGCUUCCUGACGCGUG-----AGAUAAAAUUAUUGGAGCA
AACY022262901.1/198-151      ACA-UGUACGCAACGGCUUCCUGGCGCGUG-AA--CCGUAAUU--AUUGGAGCA
AACY020064664.1/1378-1332    UCC-UAGCUGCAACGGCUUCCUGGCGCAGCUUA--CAUUUU----AUUGGAGCA
AACY022514310.1/232-279      AAU-GUUCUACAACGGCUUCCUGACGUAGG-GC--AAUUCUUU--UUUGGAGCA
ABXF01000008.1/119484-119533 UAC-CUGCCACAACGGCUUCCUGGCGUGGCGGG--CUGAACCUC-AAUGGAGCA
AACY022603193.1/622-575      UGA-AACUUAUAACGGCUACCUGAAGUAAG-UU--UUUUUAUA--AACGGAGCA
AACY020255086.1/785-738      UAU-UGCACGCAACGGCUUCCUGACGCGUG-AG--UUUUAAUU--AUCGGAGCA
CP000362.1/3781791-3781742   AGC-GAACCACAACGGCUUCCUGACGUGGU-UC--UUCAUUGGCGAUUGGAGCG
AACY020308077.1/1017-1066    GCG-CUGCCACAACGGCUUCCUGGCGUGGC-GG--UCUGACAGUCAAUGGAGCA
ABIF01000007.1/192066-192114 UUA-CUGCCACAACGGCUUCCUGGCGUGGC-AG--GCUAAACCC-AACGGAGCA
AAYC01000001.1/142050-142098 UA-CCUGUCACAACGGCUUCCUGGCGUGACGAGG--UGACCUC--AGUGGAGCA
AAFZ01022139.1/317-268       AUG-CCGCCCCAACGGCUUCCUGACGGGGC-GG--AUUCACUUUAAAUGGAGCA
ABID01000011.1/17084-17036   AGA-GCAUCACAACGGCUUCCUGACGUGGU-GC--GUAAUUUUU-AUUGGAGCA
AACY020223500.1/3303-3256    UAU-UGCACGCAACGGCUUCCUGACGCGUG-AG--UUUUAAUU--AUCGGAGCA
AACY021040428.1/508-461      UAU-UGCACGCAACGGCUUCCUGACGCGUG-AG--UUUUAAUU--AUCGGAGCA
CP000830.1/1046963-1046915   CCG-ACGCUGCAACGGCUUCCUGGCGCAGCGGU--CGCUAUUC--AAUGGAGCA
AACY020533904.1/2663-2615    GCG-ACCCCACAACGGCUUCCUGGCGUGGG-GA--CACACACAU-AAUGGAGCA
ABXM01000011.1/241752-241702 UUA-CUGCCACAACGGCUUCCUGGCGUGGCAGG--CUGAACCCCCAACGGAGCA
AAYA01000008.1/121966-121918 ACC-CCGUCACAACGGCUUCCUGGCGUGAC-GG--AGAAACCCG-AAUGGAGCA
AAYB01000002.1/503668-503715 AUU-CUGUCACAACGGCUUCCUGACGUGGC-AG--AGAUUUUU--AAUGGAGCA
AATQ01000051.1/20133-20085   UCC-CCGUCACAACGGCUUCCUGGCGUGAC-GG--CUGGUACCC-AAUGGAGCA
AAXZ01000012.1/36217-36265   UGU-CCCCCUCAACGGCUUCCUGACGAGGCGGG--CUUAACAA--AACGGAGCA
AACY020525991.1/1534-1483    CCG-CUGUCACAACGGCUUCCUGGCGUGGC-GGCUAAACCAUUUUAUCGGAGCA
ABSH01000031.1/84911-84863   ACU-CGUCCGCAACGGCUUCCUGACGCGGAUCG--ACAUUUAA--ACUGGAGCA
AACY021083615.1/454-500      CCG-UAGCUGCAACGGCUUCCUGGCGCAGCUUA--CAUUUU----AUUGGAGCA
CP002623.1/543970-544019     AGC-GAACCACAACGGCUUCCUGACGUGGU-UC--UUCAUUGGCGAUUGGAGCG
#=GC SS_cons                 :::.<<<<<<<--<<<____>>>-->>>>>.>>..:::::::::.:::::::::
#=GC RF                      uaa.ccgcCACAACGGCUUCCUGACGUGgc.gg..uuuaaauuu.AaUGGAGCA
//
# STOCKHOLM 1.0

#=GF AC   RF01728
#=GF ID   STAXI
#=GF DE   STAXI RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   38.00
#=GF TC   38.20
#=GF NC   37.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   STAXI_RNA_motif
#=GF SQ   30


CP000826.1/4584247-4584093     UGUCGUU-UUCG--GACGACCAUCCAAUGUCUCAGCACUCUGUGA-GAGGCGCC-UUCG----GGUGAGUGCCAU--CCAAUGUUUCAUGUGACCUGUGA-GAAAC--GCC--UUCG------GGU-GGUCGC-----AAUAUCCUC-GUAGCCUGGAAGAUGAU----GCC----CAUGU-----GGC----GGU-ACCUC
FM211060.1/31054-30895         UGUUGUU-UUCG--GACAACGG-CCAAUGUCAGACGAGUCUGAGA-CUGACGCC-UUUG----GGUGACUCGUC---AUAAAACCAUU-GUAACCUGAGAGAUGGU--GCC--UUUG------GGC-GG-UAC-------ACCCGUUUAUCCUUUGAAA-ACGGGU---AUCACUGAUUA--CAGUGAU---GAAGGUGCAU
CP000720.1/4172667-4172518     CGUUGU--UUUGA--GCAACAUGCCAAUGUCCUGGCGAUUUGAAA-GGGACGCC-UUCG----GGUAAUCGCAUG--CCAAUGUCACC-UUAACCUGAGAGGUGAC--GCC--UUCG------GGC-GG-UA-------CCCCCGUU-AACCUUUGAGA-AUGGG----GAU----CGCA------AUC----AAGUCGCGA
AE005174.2/1087216-1087367     UGUCGC--UUUU---GCGACCAGCCAAUGUUCCAGCAGUCUGAGA-GGGACGCC-UUCG----GGUGACUGCCAG--CCAAUGUUUCA-GCAAUCUGAGA-GAAAC--GCC--UUCG------GGU-GAUUGC-----AAUAUCCUC-GUAGCCUGAAAGAGGAU----GCC----UUUAU-----GGU----GG-UACAUC
CAAU01003246.1/549-710         UGGUGCA-UUAGC-UGCACCCA-CCAAUGCCCCGGUGAUCUGAGA-GGGGCGCC-UUCG----GGUGAUUGCAUA--CCAAUGUCACC-GUAGCCUGAGAGGUGGC--GCC--UUCG------GGU-GG-UAC-------AGCCCUUUAAUCUUUGGAA-ACGGC---UGUCGUG-UACUUC-UGCGACG---AAGAUAUUU
ABFH02000001.1/1901911-1902034 UGCUGUC-GUU---GACAGCGC-CCAACGCUUCA-CAACCUGAAA-GAAGCGCCUGUUAUCAGGACGGUUG-AUCCAUUUACCGGUGCAGACCUCUGCAAACACCG-GGUUGCAGAACAUCGCGACGGAGGUC---------------------------------------------------------------------
AL627283.1/65689-65812         UGCUGUC-GUC---GACAGCGC-CCAACGCUUCA-CAACCUGAAA-GAAGCGCCUGUUAUCAGGACGGUUG-AUCCGUUUACCGGUGCAGACCUCUGCAAACACCG-GGUCGCAGAACAUCGCGACGGAGGCC---------------------------------------------------------------------
BX950851.1/650861-651015       UGUCGU--CUCUG--ACGACCA-CCAAUGAUCUUUCAGUCUGUGA-GGAUCGCC-UUCG----GGUGACUGAAUC-----ACUUUUCC-AAAGCCUGCAAGGAAAAGGGCGU-GAUUAAGAAGCGC-GGU--------AAAUCUGCC-AUCCUUUGAGA-GCAGAU---GUC----ACCA------GGU----AG-UUUGAA
AL627282.1/224334-224495       UGGUGCA-UUAGC-UGCACCCA-CCAAUGCCCCGGUGAUCUGAGA-GGGGCGCC-UUCG----GGUGAUUGCAUA--CCAAUGUCACC-GUAGCCUGAGAGGUGGC--GCC--UUCG------GGU-GG-UAC-------AGCCCUUUAAUCUUUGGAA-ACGGC---UGUCGUG-UACUUC-UGCGACG---AAGAUAUUU
BA000007.2/1399050-1399201     UGUCGC--UUUU---GCGACCAGCCAAUGUUCCAGCAGUCUGAGA-GGGACGCC-UUCG----GGUGACUGCCAG--CCAAUGUUUCA-GCAAUCUGAGA-GAAAC--GCC--UUCG------GGU-GAUUGC-----AAUAUCCUC-GUAGCCUGAAAGAGGAU----GCC----UUUAU-----GGU----GG-UACAUC
CP000720.1/4214684-4214528     UGUUGU--CGAUG--ACAACUG-CCAAUGUUCCAGUGAAUUGAGA-GGAACGCC-UUCG----GGUAAUCACAUG--CCAAUGCCAUC-AUGACCUGUGAGAUGGC--GCU--UUCG------GGC-GGUUAA--CCCAAAUCUGUC-AACCUUUGCAA-ACAGA----GACC---UUCG-----GGUU----AAGGCAGAC
AM286415.1/3774300-3774141     UGUUGC--AUCGC--GCAACAUGCCAAUGUCCUGGUGAUUUGAGA-GGGACGCC-UUCG----GGUAAUCGCAUG--CCAAUGUCACC-UUAGCCUGAGAGGUGAC--GCC--UUCG------GGC-GG-UA--------CCCUCGUUAACCUUUGAAAAUGGGG-AUCGCAA---CAGAG----UUGCGGU-AAGGUCUCU
AE014613.1/4445927-4446088     UGGUGCA-UUAGC-UGCACCCA-CCAAUGCCCCGGUGAUCUGAGA-GGGGCGCC-UUCG----GGUGAUUGCAUA--CCAAUGUCACC-GUAGCCUGAGAGGUGGC--GCC--UUCG------GGU-GG-UAC-------AGCCCUUUAAUCUUUGGAA-ACGGC---UGUCGUG-UACUUC-UGCGACG---AAGAUAUUU
CP000826.1/437613-437767       UGUCGUU-UUCG--GACGACCAUCCAAUGUCUCAGCACUCUGUGA-GAGGCGCC-UUCG----GGUGAGUGCCAU--CCAAUGUUUCAUGUGACCUGUGA-GAAAC--GCC--UUCG------GGU-GGUCAC-----AAUAUCCUC-GUAGCCUGAAAGAGGAU----GCC----CAUGU-----GGC----GGUACCUC-
BX950851.1/602159-602313       CGUCAU--CUCUG--AUGACCA-CCAAUGAUCUAUCAGUCUGUGA-AGAUCGCC-UUCG----GGUGACUGAAUC-----ACUUUUCC-AAAGCCUGCAAGGAAAAGGGCGU-GAUUAAGAAACGC-GGC--------AAAUUUGCC-AUCCUUUGAGA-GCAAAU---GUC----AUCA------GGU----AA-UUUAAA
AM286415.1/3772495-3772339     CGUUGU--CUAUG--ACAACUG-CCAAUGUUCCGGUGACUUGAGA-GGAACGCC-UUCG----GGUAAUCACCUG--CCAAUGCCAUC-AUGACCUGAGAGAUGGC--GCU--UUCG------AGC-GGUUAA--CUUAAAUCUGUC-AACCUUUGCAA-ACAGA---GACC----UUCG------GGUU---AAGGCCUAC
BX950851.1/648593-648750       CAUCGUCCACUC-GGACGAUCA-CCAAUGAUCUUUCAGUCUGUGA-GGAUCGCC-UUCG----GGUGACUGAAUC-----ACUUUUCC-AGAGCCUGUAAGGAAAAGGGCGU-GAUUAAGAAGCGC-GGU--------AAAUCUGCC-AUCCUUUGAGA-GCAGAU---GUC----ACCA------GGU----AG-UUUAAA
CP000826.1/440732-440887       UGUUGUC-UUCG--GACAACCAGCUAAUGCUUCAGCACUCUGUGA-GAAGCGCC-UUCG----GGUGAGUGCCAA--CCAAAGUUUCA-GCGGUCUGUGA-GAAAC--ACC--UUCG------GGU-GACUGCA----AAUAGCCUC-GUAGCCUGCAAGAGGCA----GCC----CAUGU-----GGC----GGUAACUCC
CP000826.1/366915-367070       CGUUGUC-UUCG--GACAACCAGCCAAUGCUUCAGCACUCUGUGA-GAAGUGCC-UUCG----GGUGAGUGCCAA--CCAAAGUUUCA-GCAGUCUGUGA-GAAAC--GCC--UUCG------GGU-GACUGCC----AAUAGCCUU-GUAGCCUGAAAGAGGAA----GCC----CAUGU-----GGC----GGUAACUCC
AJ627388.1/93867-94022         UGUUGUC-UUU---GACAACGG-CCAAUGUUCCCGUGAUUUGAGA-GGAACGCU-UUCG----GGUAAUCACAUG--CCAAUGCCAUC-AUGACCUGUGAGAUGGC--GCU--UUCG------GGC-GG-UAC-ACCUAAAUCUGUU-AACCUUUGCAA-ACAGA---GACC----UUCG------GGUU---AAG-GCUCA
BX571862.1/297443-297600       UAUCGC--GUAA---GCGAUCG-UUAAUGUUCCCGUAGUCUGAGA-GGAACGCC-UUCG----GGUGACUGAUC---UCAAUGCCAUC-AUAGCCUGAGAGAUGGC--GUC--UUCG------GAC-GGCA--------AAUCCGUUUAUCCUUUGAAA-ACGGGU---AUCACUAACAA--UAGUGAU---GAAGGUGCAA
CP000826.1/4581610-4581456     UGUUGUC-CUUG--GACAACCAGCUAAUGCUUCAGCACUCUGUGA-GAAGCGCC-UUUG----GGUGAGUGCCAG--CCAAAGUUUAA-GCGGUCUGUGA-GAAAC--GCC--UUCG------GGU-GACUGCA----AAUAACCUC-UUAGCCUGAAAGAGGCA----GCC----CAUGU-----GGC----GGU-AACUC
CP000886.1/4564505-4564663     CGUUGCG-UUGUA-UGCAACAUGCCAAUGCCUCGGCGAUCUGAGA-GAGGCGCC-UUCG----GGUGAUCGCCAUG-CCAAUGCCACC-GUGACCUGAGAGGUGGC--GCC--UUCG------GGC-GGU--------AACUUCGUUUACCCUUUGAAA-ACGAAG---AUCG---CAUA-----CAGUUU--GAAUCUGGC
CP000886.1/4503610-4503764     CGUUGUC-AUC---GACAACUG-CCAAUGCCCUGGUGAUUUGAGA-AGGGCGCC-UUCG----GGUAAUCACAUG--CCAAUGCCACAUAAAACCUGAGA-GUGGC--GCC--UUCG------GGU-GGU--------AAACCUGUUUAACCUCUGAGA-ACAGGU---ACUC---CUGGC----GAGUU---GAGGUCCAU
AE014613.1/4520498-4520621     UGCUGUC-GUC---GACAGCGC-CCAACGCUUCA-CAACCUGAAA-GAAGCGCCUGUUAUCAGGACGGUUG-AUCCGUUUACCGGUGCAGACCUCUGCAAACACCG-GGUCGCAGAACAUCGCGACGGAGGCC---------------------------------------------------------------------
AM286415.1/3821315-3821159     UGUUGU--CUACG--ACAACUG-CCAAUGUUCCGGUGACUUGAGA-GGAACGCC-UUCG----GGUAAUCACCUG--CCAAUGCCAUC-AUGACCUGAGAGAUGAC--GCU--UUCG------AGC-GGUCAA--CCUAAAUCUGUC-AACCUUUGCAA-ACAGA---GACC----UUCG------GGUU---AAGGCCUAU
CP000886.1/4566669-4566826     CGUUGU--CUCUG--ACAACUG-CCAAUGCCUGAGUGAUUUGAGA-CAGGCGCC-UUCG----GGUAAUCACAUG--CCAAUGCCAUC-AUAACCUGAGAGAUGGC--GCU--UUCG------GGC-GGUUC------AAACCUGUUUAACCUUUGCAA-ACAGG--AACCUG---AUUA-----CAGGUU--AAGGUCCUU
CAAY01001733.1/729-852         UGCUGUC-GUC---GACAGCGC-CCAACGCUUCA-CAACCUGAAA-GAAGCGCCUGUUAUCAGGACGGUUG-AUCCGUUUACCGGUGCAGACCUCUGCAAACACCG-GGUCGCAGAACAUCGCGACGGAGGCC---------------------------------------------------------------------
AALF02000047.1/30023-29916     CGUUGUC-UUC---GACAACAC-CCGAUGCUGCCAUGACCUGUAAGGUAGCACU-GUAC----AGUGGUCAA---A-CCCCAGUUGCC-UGGACCUGAAAUGCAAC--ACU--UUUAG-----AGU-GGUAAC---------------------------------------------------------------------
AALF02000025.1/1014-908        CGUUGUC-AUC---GACAACAC-CCUAUGCAUUCAUGCUCUGUAAGGAUGCGCC-GAAA----GGUGAGCAA---G-CCCGAGUUGCC-CAGACCUGAAAUGCAAC--ACU--UUAG------AGC-GGUAAC---------------------------------------------------------------------
#=GC SS_cons                   :<<<<<<.____..>>>>>>,,.,,,,,,,,,,,<<<<<<-----.-----<<<.____....>>>>>>>>>,,,..,,,,,,,,,,,.<<<<<<-----------..<<<..____......>>>.>>>>>>......,,,,,,,,.<<<<<<-----.-----....<<<....____......>>>....>>>>>>:::
#=GC RF                        UGuUGuc.uUcu..gaCAaCca.CCAAUGcUucagcgauCUGAGA.GgagCGCC.UUcG....GGUGaucgcaUg..cCaAuguuucC.gucgCCUGagAggaaac..GCc..UUcg......gGC.GGcgac......AauccgUu.guccuuUGaAA.Acgga....gcc....uuua......ggc....aaggacuau
//
# STOCKHOLM 1.0

#=GF AC   RF01729
#=GF ID   Termite-flg
#=GF DE   Termite-flg RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   43.90
#=GF NC   34.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Termite-flg_RNA_motif
#=GF SQ   13


ABDH01006538.1/207-311   AAUUGCUUCGUACCGUCU-UCGG---A--AACACCCUGUACUAUAGGCGCGAACUGGU-CAGGGUUUU------CCGGCUGUACGGUACGACUCGGGCAAAGGAUUGCUCGGGUAUUU
ABDH01005516.1/187-291   AAUUGCUUCGUACCGUCU-UCGG---A--AACACCCUGUGCUAUAGGCGCGAACUGGU-CAGGGUUUU------CCGGCUGUGUGGUAUGGCUCGGGCAAAGGAUUGCUCGGGUAUUU
ABDH01031000.1/179-73    GGCCGUUUCGUUCCGUUCGGCGGCUAAUUUU-UGGGGGAGG---AGGCGCGAAA--CCGCCCCCA-AAAA-A--CCGCUUUCGCGGGACGGCUCCGGCA-UGGAUGGCCGGAGCAAGU
ABDH01011841.1/172-278   GGCCAUUUCGUUCCGUACGGCGGCAUAU-UU-UGGGGGAGG---AGGCGCGAAA--CCGCCCCCA-GAGGAA--CCGCUUUCGCGGGACGGUCCCGGCA-CGGAUGUUCGGGACAAGU
ABDH01019639.1/580-474   GGCCGUUUCGUUCCGUAUGGCGGCCUAU-UU-UGGGGGAGG---AGGCGCGAAA--CCGCCCCCAGGAGA-A--CCGCUUUCGCGGGAUGGUUACGGCA-UGGAUAGCCGUGACAAGU
ABDH01040472.1/816-922   GGCCGUUUCGUUCCGUACGGCGGCCUAU-UU-UGGGGGAGG---AGGCGCGAAA--CCGCCCCCAGGAGA-A--CCGCUUUCGCGGGACGGUCCCGGCA-UGGAUGGCCGGGACAAGA
ABDH01025479.1/472-571   GAACGUUUCGUUCCGUAC-GCGGGA-AUAAA-GGUCGG-UU-----GCGCGA----AA-CCGUCU-UUGA-AAACCGCCCC-GCGGGACGACUCCGGCA-AGGAUUGCCGGUGUAAGC
ABDH01004069.1/90-191    GGCCGUUUCGUUCCGUAU-GCGGGA-AUAAG-AGGCGG-UU-----GCGCGA----AA-UCGUCUGCUGA-AAACCGCUCCCGCGGAACGGCUCCGGCA-AGGAUAGCCGGAGCAAGC
ABDH01009620.1/89-189    AACCGUUUCGUUCUGUAU-GCG-GAUAAAGA-AAAUGG-UU-----GCGCGA----AA-CCAUUU-UUGGCAGA-CGCUUCCACGGGACGGCUCCGGCA-CGGAUGGCCGGGGUAAAU
ABDH01005032.1/522-422   AAUCGUUUCGUUCUGUAA-GCG-GAUAAAGA-AAACGG------CGGCGCGAAA-----CCGUUU-UUGGCAGA-CGCUCCCGCGGGACGGCUCCGGCA-CGGAUGGCCGGAGUAAAU
ABDH01040089.1/2908-2808 AAUCGUUUCGUUCUGUUU-GCGGCAGAC-AG-GAACGG------CGGCGCGAAA-----CCGCUC-CUGA-AUACCGCUACCGCGGAACGGCUCCGGCA-AGGAUAGCCGGGGUAAAG
ABDH01022490.1/329-430   AAUCGUUUCGUUCUGUUU-GCGGCUUAUUGG-AG-CGG------CGGCGCGAAA-----CCGUCU-CCUCUACUCCGCGUCCGCGGAACGGCUCCGGCA-AGGAUAGCUGGGGCAAGC
ABDH01011825.1/35-136    AAUCGUUUUGUUCUGUUU-GCGGAUUAUCAG-AG-CGG------CGGCGCGAAA-----CCGUCU-CUUGUAAGCCGCAUCCGCGGAACAGCCUCGGCA-AGGAUAGCCGGGGUAAGC
#=GC SS_cons             ::::::::<<<<<<<<--.<<<<-----.<<.<<<<<<-<<...__________..>>.>>>>>>.>>--.-..>>>>---->>>>>>>><<<<<<<<_.______>>>>>>>>::::
#=GC RF                  aaucGUUUCGucCcGuau.gCGGcauAu.gg.gggcgGagc...aGGCGCGAAa..gc.Ccgccc.ccga.A..CCGcuuucgCgGgaCGgccccGGCA.aGGAUaGCCggggcAagu
//
# STOCKHOLM 1.0

#=GF AC   RF01730
#=GF ID   Termite-leu
#=GF DE   Termite-leu RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   51.00
#=GF TC   51.00
#=GF NC   50.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Termite-leu_RNA_motif
#=GF SQ   20


ABDH01034349.1/657-580   GACGAAAGGGCGCGA--------------UAAA----------------UCGCGCCCUUUCAUAGAU--------AGUUCGGGG-----GCUAAA-----CCCCCGAACUUCAGUCAAAAU-------CAAAG
ABDH01039360.1/692-617   CGAAAGGGGGCGCG---------------UAAA-----------------CGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUAAA-----CCCCGCAUUUUCAAUCAAAAU-------CAAAG
ABDH01040491.1/1714-1789 AACGAAAGGGCGCG---------------UAAA-----------------CGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUAAA-----CCCCGCAUUUUCAAUCAAAGG-------CAAAA
ABDH01041047.1/7614-7689 GACGAAAGGGCGCG---------------UAAA-----------------CGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUAAA-----CCCCGCAUUUUCAGUCAAAGG-------CAAAG
ABDH01040822.1/1467-1392 GACGAAAGGGCGCG---------------UAAA-----------------CGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUAAA-----CCCCGCAUUUUCAGUCAAAAA-------CAAAG
ABDH01024454.1/562-639   GACGAAAGGGCGCGA--------------UAAA----------------UCGCGCCCUUUCAUAGAU--------AUAUGCGGG-----GCUAAA-----CCCCGCAUAUUCAGUCAAAGU-------CAAAG
ABDH01040894.1/1192-1117 GACGAAAGGGCGCG---------------UAAA-----------------CGCGCCCUUUCAUAGAU--------AUAUGCGGG-----GCUAAA-----CCCCGCAUAUUCAAUCAAAGU-------CAAAA
ABDH01004321.1/335-412   GACGAAAGGGCGCGA--------------UAAA----------------UCGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUGAA-----CCCCGCAUUUUCAGUCAAAAU-------CAAAG
ABDH01040812.1/1997-2072 GACGAAAGGGCGCG---------------UAAA-----------------CGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUAAA-----CCCCGCAUUUUCAAUCAAAAG-------CAAAG
ABDH01040182.1/3096-3021 GACGAAAGGGCGCG---------------UAAA-----------------CGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUAAA-----CCCCGCAUUUUCAGUCAAAGU-------CAAAG
ABDH01040994.1/213-138   GACGAAAGGGCGCG---------------UAAA-----------------CGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUAAA-----CCCCGCAUUUUCAGUCAAAGU-------CAAAG
ABDH01016605.1/80-155    GACGAAAGGGCGCG---------------UAAA-----------------CGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUAAA-----CCCCGCAUUUUCAGUCAAAGU-------CAAAG
ABDH01015524.1/202-125   GACGAAAGGGCGCGA--------------UAAA----------------UCGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUAAA-----CCCCGCAUUUUCAAUCAAAGU-------CAAAG
ABDH01041052.1/3073-3148 GACGAAAGGGCGCG---------------UAAA-----------------CGCGCCCUUUCAUAGAU--------AAAUGCGGG-----GCUAAA-----CCCCGCAUUUUCAAUCAAAAU-------CAAAG
ABDH01044059.1/83-186    AUCAGCCGGUAAGGC--GCGGUUCCUUCCCUGUGGAAGG--CCAGCG--GCUUUACCGGAUUUCUCAAGCGCUCCCUAAGGGG------UUAA--------C-CCCUUAGGAUACAUAGA--------GGAGG
ABDH01037712.1/11-126    ACGAG--GGUAG-GGCACGGGA-UUCCU-UUUU-AGGAAAAUC-UGCAGCCUUUACCGGGUUUCUCA--------AGUUUCGGAAUGA-GAAAAC-CCAUUCAGGGGAUUGAAGUAUAGGAGUACAUAGGAAA
ABDH01021984.1/236-127   AGUAGCCGGUAAGGGCACGGAG-UUCCU-UUUU-AGGAAAAUC-UGCAGCCUUUACCGGGUUUCUCA--------AGUUCUGGAGUGGGGAAAAC-CCAUUCACAGGAUUGGUAUAUA----------GGAGG
ABDH01040673.1/4423-4312 AUUAGCCGGUAAAGGCACGGAG-UUCCU-UUUU-AGGAAAAUC-UGCAGCCUUUACCGGGUUUCUCA--------AGUUCCGGAGUGG-AAAAAGACCACUUACGGGAUUGAAGUAUAUA--------GGAGG
ABDH01022123.1/160-273   AUUAGCCGGUAAUGGCACGGAG-UUCCU-UUUU-AGGAAAAUC-UGCAGCCUUUACCGGGUUUCUCA--------AGUUCUGGAGUGG-AAAAAGACCACUUACGGGAUUGGAGUAUAAAAU------GGAGG
ABDH01039021.1/112-223   AUCAGCCGGUAAUGGCACAGAA-UUCCU-UUUU-AGGAAAAUC-UGCAGCC-UUACCGGAUUUCUCA--------AGUUCCGGAGUGG-AAAAAGACCACUUACGGGAUUGAAGUAUUUAU-------GGAGG
#=GC SS_cons             :::::<<<<<<<<<<..<<<<-.<<<<<.____.>>>>>..>>.>>-..>>>>>>>>>>-----<<-........<<<<<<<<<.....______.....>>->>>>>>>>>:::::::::.......:::::
#=GC RF                  aucAgccGGucgcGg..ccGga.ccccc.Uuuu.ggggg..cC.ggc..cCgcgaCCgguuuUcuca........agaugcGGg.....gaaAAa.....cCaCgcaucugaAgUauAaAu.......ggAaG
//
# STOCKHOLM 1.0

#=GF AC   RF01731
#=GF ID   TwoAYGGAY
#=GF DE   TwoAYGGAY RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   43.00
#=GF TC   43.00
#=GF NC   42.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00106
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   TwoAYGGAY_RNA_motif
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   210


BAAZ01005038.1/287-455       UGCAAACUAUGC----AC-AUA-AUAAAAGCAUU-GAGCAAAGUCACUACCUAAGUGUACG-CGC-GUCCACGGACGGACGCGCGAGCUG-UC--UCGUGC-AUGGAU-GC-ACGUU-GACAGCGUAACG-----AGAACUUAAACAGCCUUCCACGCUCAAUGCUUAUUAU--UAU-GUAGCGUAGUUUGUA
BAAX01027538.1/775-609       UAUAAGA-GAAUU-G-UG-AUA-UUACCAGUGUU--CCGCCCC-UAUAA-ACA--GCAAUG-ACC-AGACACG-AGGUCUGGUCAAGCGA-AUA-CUGAGGCA-GGAUGCC-GAA--UAUGAGCGUGUGCGU---CCACCGCCACAACACUCCCU-CGGAAACACCCGGUAA--UAUCCAAUUGUCUUAUCCG
BAAW01000251.1/9337-9272     --------------------------------------------------------GGACU-GAC-CGCCA-GGACGGUGGUCAGAGGAU-CGG-UCGAGACAGGGACGUC-GAGU-CCGGCCCGGUCC----------------------------------------------------------------
BAAU01025327.1/674-835       ACUUGAAAGCUGGUUGUG-CAA-UUCUUA-----UAUUUCCCUCUAGUAUACC--GAUAUG-CGC-GUACACGGAUGUACGCGCAAGUAA-GG--GCGCGCCAAGGAUGGC-GCGU--CCGAACGGU-UAGU---CCAUUCCCAUAUCAAUUUG--AAGU------CUAGAG--AUGCCACCACUUCUUGUGC
BAAU01012842.1/247-79        CUUGAAAGCUGAU-UGUG-AUA-GUUCUUAGAUA-UUCCAUUCAAUUUA-UCA--GCAACG-AUU-UGACACGGAUGUCAAAUCGAGCGA-A-A-ACGCAACA-GGACGUU-GCG--UAUGAGCGGUUGCGU---UCGUAGCAAAAACUUAUAA--GGAAUAUCU-UAGAAA--UAUCCAAUCAGCUUUCUGG
BAAY01006061.1/789-955       CUUGAAAGCUGUU-UGUG-AUA-GUUCUUAAACU-UUCCCUUCAACCCA--CA--GCAGCG-AUU-UGACACGGAUGUCAAAUCGAGCGA-A-A-ACGAAACA-GGACGUU-UCG--UAUGAGCGGCUGCGU---CCACAGAAAAGCAUCUGC---GGAAAGUUU-UAGAAA--UAUCCAGACAGCUUUCUGG
BAAU01018933.1/896-731       CUGAAAAGCUGAU-GAAG-AAA-GUUCUUAAACU-UCCCCUAAGACUA---CA--GCA-CG-GAU-UGACAAGGAGGUCAAAUCGAGCGA-AU--ACGCAACAC-GACGUU-GCGU--AUGAGCGUAUACGU---CCGUAUAAAAGACAUAGAC--GGAAAGUUU-UAGAAA--GAUCCAAUCAGCUUUCUGG
BAAU01010825.1/211-45        CUUGAAAGCUGAU-UGAG-AUA-GUUCUUAAACU-UUCCCUAAAAACUA--CA--GCAACG-AUU-UGACAAGGAGGUCAAAUCGAGCGA-AA--ACGCAACAC-GACGUU-GCGU--AUGAGCGUUUACGU---CCGUAUAAAAACAUAGAC---GGAAAGUUU-UAGAAA--UAUCCAAUCAGCUUUCUCG
BAAZ01011936.1/179-13        UAUGUUUGCAACC-U-UG-AAA-GAACUU-AGUG-UUCUAUUAAGUCAU--CA--GGGAUG-UUU-GUACACG-AUGUUCAAACAAGUCG-CCG-UUGAGCCAUGGACGGC-GAAU-CGGCGACGAUCCCGU---ACGUUAGAAAAGAGUAUAUU-AGA-CACU--UAGUAC--UUUCUGACGAUUCACCCGG
BABA01001199.1/531-366       UAUGUU-UGGAAC-U-UA-GAA-GUACUU-GAUG-UUCUGUAAAUAUC---CA--GCAAUG-UUU-GAACACG-AUGUUCAAACAAGCCG-UCG-UUGAGCCAUGGACGGC-GAAU-CGACGGCGGUUGCGU---ACGAUAUUAUUGUGUAUAUC-AGAACAUU--UAGUAC--UUCUUAGUUUCAAUACAUC
BABD01029348.1/766-601       UAUGUU-UGAAAC-U-UA-GAA-GUGCUU-AAUG-UUCUGUA-UUACAU--UA--GCAAUG-UUU-GAACACG-AUGUUCAAACAAGCCG-CCA-CUGAGCCAUGGAUGGC-GAAU-UGGCGGCGGUUGCGU---ACGGUAAAAUACCGUAGAUC-AGAACAUU--UAGCAC--UUUUUAGUUUCAAUACAUC
BABA01008647.1/531-365       UAUGUU-UGAAUC-C-UA-GAA-GUUCUU-AAUG-UUCUGUAAUUAUAC--UA--GCCAUG-UUU-GAACACG-AUGUUCAAACAAGCCG-CCA-CUGAGCCAUGGAUGGC-GAAU-UGGCGGCGGUGGCGU---AUUAUAUCAAUAUAUAAAUC-AGAACAUU--UAGAAC--UUCUUAGAUUCAAUACAUU
BAAU01005978.1/405-243       UGAAAGCUGAUUG-U-GC-AGU-UUCUUA-UACU-UUCCAUUCGUAAU---CA--GUAACG-AUU-UGACACGGAUGUCAAAUCGAGCGA-AUA--CGCAACAC-GAUGUU-GCG--CAUGAGCGGUUACGU---CCAUAUAGAAAAACUAUGA--GGAAAGUA--UUAGAA--AAU-GCCAAUUAGUUUUCU
BAAU01001958.1/671-504       CUUGAAAGUCGGU-UGAG-CUA-UUUCUUAUACU-UUCCAUCUAAAAC---CA--GAUAGG-CGG-GUACAAGGAUGUACCUGCCAGUGA-G-A-CCGCGCCAAGGACGGC-GCGU-U-CGAACGGUAUCGU---CCAAUAACAAAGCAUCUAU--GGAAAGUAU-UAGAAA--UAACCAACCAACUUUCUGG
BAAU01003657.1/644-477       CUUGAAAGCUGAU-UGUG-CUG-UUUCUUAUACU-UUCCCUCUAUAUA---CA--GAUAGG-CGG-GUACAAGGAUGUACCCGCCAGUGA-GG--CCGUGCCAAGGAGGGC-ACGU--CCGAACGAUAUUGU---CCGGUAACAAUACCAAUAA--GGAAAGUAU-UAGAAA--CAGCCAAUCUGCUUUCUGG
BAAU01005466.1/843-675       CUUGAAAGUCAGU-UGUG-AUA-UUUCUU-AUAC-UUUCCUUUAAUUCU-CCA--GAUAUG-CGG-GUACAAGGAUGUACCCGCAAGUGA-GG--UCGCGCCACGGAUGGC-GCGU--CCGAACGGUAUCGU---CCGAUAACAUAUCUUAUAUG-GAAAGUAU--UAGAAA--UAUCCAACUGGCUUUCUGG
BAAU01021915.1/521-357       GAAAGUCUGCCCC-U-GC-UAA-UUCUUA-UACU-UUCCCUAAAUAUU---CA--GAUAGG-AGG-GUACAAGGAUGUACCCGACAGUGA-GG--UCACGCCAAGGAGGGC-GUGU--CCGAACGGUAUCGU---CCGGUUACAAAACCUAUAC--GGAAAGUA--UUAGAA--GUAGCUGGGGUAACUUUCU
BAAU01002859.1/30-193        UGAAAGUCUGUUG-U-AC-UGU-UUCUUA-UGCU-UUCCCUAGAUAUC---CA--GAUAGG-CGG-GUACACGGAUGUACCCGCCAGUGA-G-A-CCACGCCAAGGACGGC-GUGU-U-CGAACGGUAUCGU---CCGGUAAAAACAUCUAUAU--GGAAAGUA--UUAGAA--ACA-GUAAACAGGCUUUCU
BAAU01005978.1/732-895       UGAAAGUUGAUUG-U-GC-UGU-UUCUUA-UACU-UUCCUUCUUCAUA---CA--GAUAUG-CGG-GUACAAGGAUGUACCCGCAAGUGA-GG--CCGCGCCAAGGACGGC-GCGU--CCGAACGGUAUCGU---CCGUAUUCAAUAUCUAUAU--GGAAAGUA--UUAGAA--ACA-ACCAAUCAGCUUUCU
BAAU01027214.1/624-783       UUUGUUUGAGGCU-U-AC------UCUUA-GACU-UUUCUUUAGUAAUC--CA--GCUAUC-CAC-AGACAUGGAUGUCUGUGGAAGUCA-GAU-AUGGAACAAGGAGGUU-CCGU-AUCUGACGGUAGCGG---UCAUAAUCAUAACCUAUAU--GAAAAGUC--UUAGAA------AUAUCCACUUAAAUC
BABG01023967.1/528-365       UGAAGUUCAAUCG-U-GC-UGA-CUCUUA-GACU-UUUCUUUUGCUUU---CA--GCUAGC-UUC-GUACAUGGAUGUACGAAGCAAUGA-GG--CCGCGCCACGGACGGC-GCGU--CCGAAUGGUAGCGU---CACCUAUAACUACCUAUAU--GAAAAGUC--UUAGAG--UCA-GUCGAUUGAAGCUUC
BABG01000271.1/2224-2061     UGAAGUUCAAUCG-U-GC-UGA-CUCUUA-GACU-UUUCUUUCGCUCC---CA--GCCAGC-UUC-GUACAUGGAUGUACGAAGCAAUGA-GG--CCGCGCCACGGACGGC-GCGU--CCGAAUGGUAGCGU---CACCUAUAAUUACCUAUAU--GAAAAGUC--UUAGAG--ACA-GCCGAUUGAAGCUUC
BABG01000436.1/2508-2345     UGAAGUUCAAUCG-U-GC-UGA-AUCUUA-GACU-UUUCUUUCGCUUU---CA--GCUAGC-UUC-GUACAUGGAUGUACGAAGCAAUGA-GG--CCGCGCCACGGACGGC-GCGU--CCGAAUGGUAGCGU---CACUUAUAACUACCUAUAU--GAAAAGUC--UUAGAG--ACA-GCCGAUUGAAGCUUC
BABG01005079.1/1103-1266     UGAAGUUCAAUCG-U-GC-UGA-CUCUUA-GACU-UUUCUUUCGCUCC---CA--GCUAGC-UUC-GUACAUGGAUGUACGAAGCAAUGA-GG--CCGCGCCACGGACGGU-GCGU--CCGAAUGGUAGCGU---CACCUAUAACUACCUAUAU--GAAAAGUC--UUAGAG--ACA-GCCGAUUGAAGCUUC
BABG01000221.1/4934-4771     UGAAGUUCAAUCG-U-GC-UGA-CUCUUA-GACU-UUUCUUUCGCUCC---CA--GCUAGC-UUC-GUACAUGGAUGUACGAAGCAAUGA-GG--CCGCACCACGGACGGC-GCGU--CCGAAUGGUAGCGU---CACCUAUAACUACCUAUAU--GAAAAGUC--UUAGAG--ACA-GCCGAUUGAAGCUUC
BABG01000508.1/3021-2858     UGAAGUUCAAUCG-U-GC-UGA-CUCUUA-GACU-UUUCUUUCGCUUC---CA--GCUAGC-UUC-GUACAUGGAUGUACGAAGCAAUGA-GG--CCGCGCCACGGACGGC-GCGU--CCGAAUGGUAGCGU---CACCUAUAACUACCUAUAU--GAAAAGUC--UUAGAG--ACA-GCCGAUUGAAGCUUC
BABG01030864.1/800-634       GGAGGUUCAAUCG-U-GC-AGA-CUCUUA-GACU-UGGUCUUAGCGUAC-CCA--GCUAGC-AUC-GUACAUGGAUGAACGAACAAGGAG-GC--CGCGGCCACGGACGGC-GCGU--CCGAAUGGGAGCGU---CACGUAGAACUACGGAUAAU-GAAAAGUC--UUAGAG--ACA-GCCGAUGGAAGCUUC
BAAU01025988.1/467-305       GAAGUUA-AACUG-U-GC-UGA-GUCUUA-GACU-UUUCCUAUACAUC---CA--GCCAGC-UUC-GUACAAGGAUGUACGAAGCAACUA-AG--CCGCGCCACGGAUGGC-GCGU--CUGAGUGGUGGCGU---CCAUUAUCAAUAUAUAUAU--GAAAAGUC--UUAGAG--UCA-GCCGGUUAAAGCUUC
BABG01000900.1/2303-2139     UGAAGUUUGAUUG-U-GA-UAG-UUCUUA-GUCU-UUCCCUUUAUCCAC--CA--GCUAGC-UUC-GUACAUGGAUGUACGAAGCAGCGA-AG--CCGCGCCAUGGACGGC-GCGU--CUGAGCGGUAGCGU---CAGUUACCAUAAUUUAUAU--GGAAAGGC--UUAGAA--AUA-UCCAAUCAAAGCUUC
BABG01034670.1/387-221       UUGAAGUUCAAUC-G-UG-CUG-ACUCUU-AGAC-UUUUUCUUAGCGAC-CCA--GCUAGC-UUC-GUACAUGGAUGUACGAAGCAAUGA-GG--CCGCGCCACGGACGGC-GCGU--CCGAAUGGUAGCGU---CACCUAUAACUACCUAUAUG-AAAAGUCU--UAGAGU--CAGCC-GAUUGAAGCUUCU
BABG01000393.1/2168-2002     UUGAAGUUCAAUC-G-UG-CUG-ACUCUU-AGAC-UUUUUCUUAGCGAC-CCA--GCUAGC-UUC-GUACAUGGAUGUACGAAGCAAUGA-GG--CCGCGCCACGGACGGC-GCGU--CCGAAUGGUAGCGU---CACCUAUAACUACCUAUAUG-AAAAGUCU--UAGAGA--CAGCC-GAUUGAAGCUUCU
BABG01000236.1/4066-3900     UUGAAGUUCAAUC-G-UG-CUG-ACUCUU-AGAC-UUUUUCUUAGCUAC-CCA--GCUAGC-UUC-GUACAUGGAUGUACGAAGCAAUGA-GGC--CGCGCCACGGACGGC-GCG--GCCGAAUGGUAGCGU---CACCUAUAACUACCUAUAUG-AAAAGUCU--UAGAAA--CAGCC-GAUUGAAGCUUCU
BAAU01005512.1/763-597       UGAAGUUUAAUUG-A-GA-UAU-UUGUUA-GACU-UUUCCUUAAUACCA--CA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUUU-GAU-AUGGGACAAGGAUGUC-CCGU-AUCAAACGGUAGCGU---ACAUACCCACUACCUAUAC--GAAAAGUC--UUAGAA--AUA-UCCGAUUAAAGCUUC
BABG01000690.1/1558-1724     UGAAGUUCAAUUG-U-GA-UAG-UUCUUAGACUU-UUCCUUAACUACC---CA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACACGGAUGUC-ACAU-AUCGAACGGUAGCGG---CAGUAGUCACAACCUAUA---AGAAAAGUC-UUAGAA--AUA-UCCAAUUGAAACUUC
BABG01000393.1/2416-2582     UGAAGUUCAAUUG-U-GA-UAG-UUCUUAGACGU-UUCCUUAACUACC---CA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACACGGAUGUC-CCGU-AUCGAACGGUAGCGG---CAGUAGUCACAACCUAUA---AGAAAAGUC-UUAGAA--AUA-UCCAAUUGAAACUUC
BABG01014358.1/541-707       UGAAGUUCAAUUG-U-GA-UAG-UUCUUAGACUU-UUCCUUAACUACC---CA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACACGGAUGUC-CUGU-AUCGAACGGUAGCGG---CAGUAGUCACAACCUAUA---AGAAAAGUC-UUAGAA--AUA-UCCAAUUGAAACUUC
BABG01016197.1/197-363       UGAAGUUCAAUUG-U-GA-UAG-UUCUUAGACUU-UUCCUUAACUACC---CA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACACGGAUGUC-CUGU-AUCGAACGGUAGCGG---CAGUAGUCACAACCUAUA---AGAAAAGUC-UUAGAA--AUA-UCCAAUUGAAACUUC
BABG01000271.1/2472-2638     UGAAGUUCAAUUG-U-GA-UAG-UUCUUAGACUU-UUCCUUAACUACU---CA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---CAGUAGUCACAACCUAUA---AGAAAAGUC-UUAGAA--AUA-UCCAAUUGAAACUUC
BABG01001478.1/2351-2518     UGAAGUUCAAUUG-U-GA-UAG-UUCUUA-GACU-UUUCCUUAACCCCC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---CAGUAGUCACAACCUAUAA--GAAAAGUC--UUAGAA--AUA-UCCAAUUGAAACUUC
BAAU01027214.1/514-349       UGAAGUUCAAUUG-U-GA-UAG-UUCUUA-GGCU-UUUCCUUAAUACAC--CA--GCUAUC-CAC-AGACACGGAUGUCUGUUGAAGUGA-GAU-AUGGGACA-GGACGUC-CCGU-AUCGAACGGUAGCGG---UCGAUGUUAUUACCUAUAU--GAAAAGCC--UUAGAA--AUA-UCCAAUUGAAGCUUC
BABG01006543.1/58-224        UGAAGUUCAAUUG-U-GA-UAG-UUCUUA-GACU-UUUCCUUAACUCCC--CA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUUC-GAU-AUGGGACACGGAUGUC-CCGU-AUCGAACGGUAGCG----GCAGUAGUCACAACCUAUAU-GAAAAGUC--UUAGAA--AUA-UCCAAUUGAAACUUC
BAAX01012202.1/62-228        UGAAGUUCAAUUG-U-GA-UAG-UUCUUA-GACU-UUUCCUUCACUCAC--CA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACACGGAUGUC-CCGU-AUCGAGCGGUAGCG----GCAGUAGUCACAACCUAUAA-GAAAAGUC--UUAGAA--AUA-UCCAAUUGAAACUUC
BABG01000704.1/141-1         -----------------G-AUA-GUUCUUAGACU-UUUCCUUAACUACC--CA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACACGGAUGUC-ACAU-AUCGAACGGUAGCGG---CAGUAGUCACAACGGAUAA--GAAAAGUCU-UAGAAA--UAUCC--------------
BABG01000436.1/2753-2925     UUGAAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUCUUUCUCUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---GAACUACCAUUACGUAUAUGAAAACCUGCAUUAGCAG-GACU-UGUUGAUGGGAGCUU
BABG01030578.1/419-590       CAUGAAUUUCAAU-UGUG-AUA-GUUCUU-AGAC-UUAUCUUUCUCUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGAAUUCGAACGGUAACGG---AAACUACCAUAACGUAUAUG-AAACGUCU--UACAAC--UAUCCAUUUGAAGCUUCUG
BABG01000752.1/502-671       UUGGAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUCCUUAACUAC-UCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---CAGUAGUCACAACCUAUAAG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAACUUCUG
BABG01000982.1/2748-2608     -----------------G-AUA-GUUCUU-AGAC-UUUUCCUUAACUAC-UCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACACGGAUGUC-CCGU-AUCGAACGGUAGCGG---CAGUAGUCACAAGCUAUAAG-AAAAGUCU--UAGAAA--UAUCC--------------
BABG01026739.1/558-388       CUUGAAGUCCAAU-UGUG-AUA-GUUCUU-AGAC-UUUUCCUCAACUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUUC-GAU-AUGGGACACGGAUGUC-CCGU-AUCGAACGGUAGCGG---CAACUACCGUUACCUAUAUG-AAAAGUCU--CAGAAA--UAUCCAAUUGGAGCUUCUG
BABG01000222.1/98-267        UUGAAGUUCAAUC-G-UG-AUA-GUUCUU-AGAC-UUUUUCUAGGCUAC-CCA--GCUAUC-CAC-AGACACGGAUGCCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGAUAGCGG---CAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAGCCAUAAUAAACU
BABG01002686.1/791-622       UUGAAGUUCAAUU-G-UG-AUA-AUUCUU-AGAC-UUUUCCUUAACUAC-UCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACACGGAUGUC-CCAU-AUCGAACGGUAGCGG---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAACUUCUG
BABG01009970.1/135-304       UUGAAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUCUUUCUCUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACACGGAUGUC-CCGU-AUCGAACGGUAGCGA---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAACUUCUG
BABG01000900.1/2431-2600     UUGAAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUUCUUAGCUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAGCCAUAAUAAACU
BABG01002620.1/1696-1527     UUGAAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUUCUUAGCUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAGCUUCUG
BABG01000236.1/4311-4480     UUGAAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUCCUUAACUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAGCUUCUG
BABG01001970.1/2862-2722     -----------------G-AUA-GUUCUU-AGAC-UUUUCCUUAACUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCC--------------
BABG01005381.1/998-829       UUGAAGUUUAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUCUUUCUCUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAGCUUCUG
BABG01000272.1/136-305       UUGAAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUCUUUCUCUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUUGAACGGUAGCGG---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAGCUUCUG
BABG01000704.1/846-1015      UUGAAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUCUUUCUCUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAGCUUCUG
BABG01000732.1/2801-2632     UUGAAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUCUUUCUCUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAGCUUCUG
BAAU01001873.1/176-7         UUGAAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUCUUUCUCUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAUGGAUGUC-CCGU-AUCGAACGGUAGCGG---AAACUACCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAGCUUCUG
BABG01005079.1/856-687       UUGAAGUUCAAUU-G-UG-AUA-GUUCUU-AGAC-UUUUCCUUAACUAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACACGGAUGUC-CUAU-AUCGAACGGUAGCGG---AAACUAUCAUUACGUAUAUG-AAAAGUCU--UAGAAA--UAUCCAGCCAUAAUAAACU
BAAU01024793.1/91-230        -----------------G-AUA-GUUCUU-AGAC-UUUUCUUUAAUAAC-CCA--GCUAUC-CAC-AGACACGGAUGUCUGUGGAAGUGA-GAU-AUGGGACA-GGACGUC-CCGU-AUCGAACGGUAGCGG---CAACUGCCGCCACAUAUAUG-AAAAGUCU--UAGAAA--UAUCC--------------
BAAU01025327.1/250-81        UUGAAGUUUAAUU-G-AG-AUA-GUUCUU-AGAC-UUUUCAUUAGUUAC-CCA--GCUAUC-CAC-AGACAAGGAUGUCUGUGGAAGUGA-GAU-AUGGGACAAGGAUGUC-CCGU-AUCGAACGGUAGCGG---CAGCUGCCAGUACAUACAUG-AAAAGUCU--UAGAAA--UAUCCAAUUGAAGCUUCUG
BABG01034670.1/631-803       CUUGAAGUCUAAU-UGUG-AUA-GUCCCU-AGAC-UUUUCUUUCUCUAA-CCA--GCUAUC-CACCAGACACGGAUGUCUGUGGAAGUGAAAAU-AUGGGACCUGGAUGUC-CCGU-AUCCAACCGCAGCGG---ACACUACCAUUACGUAUAUC-AAAAGUCU--UAGAAA--UAUCCAAUCGAAGCCUCCU
BAAU01001873.1/419-587       CUUGAAGUUUGAU-UGUG-AUA-GUUCUU-AGUC-UUUCCAUUAGUAAA-CCA--GCUAGC-UUC-GUACAAGGAUGUACGAAGCAGCGA-AG--CCGUGCCAAGGAGGGC-ACGU--CUGAGCGGUAGCGU---CAGUUACCAUAAUUUAUAUG-UAAAGACU--UAGAAA--UAUCCAAUCAAAUCUUCUG
BABG01000690.1/1307-1140     UUGAAGUUUAAUU-G-UG-AUA-GUUCUU-AGUC-UUUCCCUUAGUCAA-CCA--GCUAGC-UUC-GUACACGGAUGUACGAAGCAGCGA-AG--CCGCGCCAUGGACGGC-GCGU--CUGAGCGGUAGCGU---CAGUUAUCAUAGUUUAUAUG-GAAAGACU--UAGAAA--UAUCCAAUCAAAGCUUCUG
BABG01000098.1/5643-5475     CUUGAAGUUUGAU-UGUG-GUA-GUUCUU-AGUC-UUUCCCUUAGCCAA-CAA--GCUAGC-UUC-GUACACGGAUGUACGAAGCAGCGA-AG--CCGCGCCAUGGACGGC-GCGU--CUGAGCGGUAGCGU---CAGUUACCAUAGUUUACAUG-GAAAGACU--UAGAAC--UAUCCAAUCAAAGCUUCUG
BABG01015786.1/315-483       CUUGAAGUUUGAU-UGUG-AUA-GUUCUU-AGUC-UUUCCCUUAGCCAA-UCA--GCUAGC-UUC-GUACACGGAUGUACGAAGCAGCGA-AG--UCGCGCCAUGGACGGC-GCGU--CUGAGCGGUAGCGU---CAGUUAUCAUAGUUUACAAG-GAAAGACU--UAGAAA--UAUCCAAUCAAAGCUUCUG
BABG01000704.1/651-483       CUUGAAGUUUGAU-UGUG-AUA-GUUCUU-AGUC-UUUCCCUUAGUCAA-CCA--GCUAGC-UUC-GUACACGGAUGUACGAAGCAGCGA-AG--CCGCGCCAUGGACGGC-GCGU--CUGAGCGGUAGCGU---CAGUUAUCAUAGUUUAUAUG-GAAAGACU--UAGAAA--UAUCCAAUCAAAGCUUCUG
BABG01002686.1/1035-1203     CUUGAAGUUUGAU-UGUG-AUA-GUUCUU-AGUC-UUUCCCUUAGUCAA-CCA--GCUAGC-UUC-GUACACGGAUGUACGAAGCAGCGA-AG--CCGCGCCAUGGACGGC-GCGU--CUGAGCGGUAGCGU---CAGUUAUCAUAGUUUAUAUG-GAAAGACU--UAGAAA--UAUCCAAUCAAAGCUUCUG
BABG01001970.1/3125-3293     CUUGAAGUUUGAU-UGUG-AUA-GUUCUU-AGUC-UUUCCCUUCGCCAA-CCA--GCAAGC-UUC-GUACACGGAUGUACGAAGCAGCGA-AG--CCGCGCCAUGGACGGC-GCGU--CUGAGCGGUAGCGU---CAGUUACCAUAGUUUAUAUG-GAAAGACU--UAGAAA--UAUCCAAUCAAAGCUUCUG
BABG01002029.1/55-223        CUUGAAGUUUGAU-UGUG-AUA-GUUCUU-AGUC-UUUCUCUUAGCCAA-CCA--GCUAGC-UUC-GUACACGGAUGUACGAAGCAGCGA-AG--CCGCGCCAUGGACGGC-GCGU--CUGAGCGGUAGCGU---CAGUUACCAUAGUUUAUAUG-GAAAGACU--UAGAAA--UAUCCAAUCAAAGCUUCUG
BABB01000035.1/5490-5654     UACGC-AGUAACU-U-AG-AGU-AUGUUU-GAAA-UCACUUCUAUACA---UA--GCAACG-CUC-GUACACGGAUAUAUGAGUGAGUCC-AUA-CUAAACUAC-GAUGGC-AAA--UAUUGACGGUGGCGU---ACUACUAUCUCAACCUAUAU-GUGAUUUC--UUACAU--ACUCUUGGUUACGGAGUAA
BAAY01004664.1/626-790       UACGU-AGUGACU-U-AG-AGU-AUGUUU-GAAA-UCACUUCUAUGCA---UA--GCAACG-CUC-GUACACGGAUGUACGAGCGAGUCC-AUA-UUGAGCCAC-GAUGGC-GAA--UAUGGACGGUUGCGU---ACUACUGUCUCAACCCAUAU-GUGAUUUC--UUACAU--ACUCUUAGUUGCGGAGUAA
BABB01000035.1/5824-5988     UACGU-AGUGACU-U-AG-AGU-AUGUUU-GAAA-UCACUUCUAUGCA---UA--GCAACG-CUC-GUACACGGAUGUACGAGCGAGUCC-AUA-UUGAGCCAC-GAUGGC-GAA--UAUGGACGGUUGCGU---ACUACUGUCUCAACCCAUAU-GUGAUUUC--UUACAU--ACUCUUAGUUGCGGAGUAA
BABB01000035.1/6159-6323     UACGU-AGUGACU-U-AG-AGU-AUGUUU-GAAA-UCACUUCUAUGCA---UA--GCAACG-CUC-GUACACGGAUGUACGAGCGAGUCC-AUA-UUGAGCCAC-GAUGGC-GAA--UAUGGACGGUUGCGU---ACUACUGUCUCAACCCAUAU-GUGAUUUC--UUACAU--ACUCUUAGUUGCGGAGUAA
BABG01033689.1/201-365       UACGC-AGUAACU-U-AG-AGU-AUGUAU-GAAA-UCACUUCAACACA---UA--GCAACG-CUC-GUACACGGAUGUACGAGCGAGUCC-AUA-CUGAGCCAC-GAUAGC-GAU--UAUGGACGGUUGCGU---ACUAUUGUCUCAACCUGUAU-GUGAUUUC--UUACAU--ACUCUUAGUUGCGGAGUAU
BABG01033688.1/603-439       UACGC-AGUAACU-U-AG-AGU-AUGUUU-GAAA-UCACCUCAACACU---UA--GCAACG-CUC-GUACUCGGAUGUACGAGCGAGUCC-AUA-CUGAGCCAC-GAUGGC-AAA--UAUGGACGGUUGCGU---ACUAUUGUCUCAACCUAUAU-GUGAUUUC--UUACAU--ACUCUUGGUUACGGAGUAA
BABB01000035.1/6534-6698     UACGC-AGCAACU-U-AG-AGU-AUGUUU-UAAA-UCACUUCAACACA---UA--GCAACG-CUC-GUACACGGAUGUACGAGCGAGUCC-AUA-CUGAGCCAC-GAUGGC-GAA--UAUGGACGGUUGCGU---ACUACUGUCUCAACCUAUAU-GUGAUUUC--UUACAU--ACUCUUAGUUACGGAGUAA
BAAY01004664.1/1001-1165     UACGC-AGUAACU-U-AG-AGU-AUGUUU-GAAA-UCACUUCAACACU---UA--GCAACG-CUC-GUACACGGAUGUACGAGCGAGUCC-AUA-CUGAGCCAC-GAUGGC-GAA--UAUGGACGGUUGCGU---ACUACUGUCUCAACCUAUAU-GUGAUUUC--UUACAU--ACUCUUAGUUACGGAGUAA
BABD01000901.1/293-129       UACGC-AGUAACU-U-AG-AGU-AUGUUU-GAAA-UCACUUAAACACA---UA--GCAACG-CUC-GUACACGGAUGUACGAGCGAGUCC-AUA-CUUAGCCAC-GAUGGC-GAA--UUUGGACGGUGGCGU---ACUACUGUCUCAACCUAUAU-GUGAUUUC--UUACAU--ACUCUUAGUUGCAGAGUAA
BAAV01016980.1/240-405       UAUGG-AGCUGCC-U-AG-AGA-CUGUUA-AAAU-UAUGUACACAGCC---CA--GCAACG-CAC-GCACAUGGACGUGCGGGCGAGGCG-UU---AGCGCCAUGGACGGC-GCUA--AAAGCCGGUUGCGU--CAUGGUCUAAGCAAUCCCUAAUCAUAAUUU--UUACAG--UGUCUUGGCAGCGUAAUCA
BAAY01025688.1/25-193        GUACCAAGCGGCC-U-AG-GGA-UUGUUG-GAAU-UGUGUUUGCAAUC---CA--GCAACG-CCC-GUGCACGGAAGCACGGGCGAGACG-UUA-CCGCGCCAUGGACGGC-GCGU-AAAAGUCGGUUGCGU--CCUACCUGUCACAACCUGUAU-CACAAUUC--UUACAA--GCCCUUAGCCGCGUAGUAU
BAAU01014849.1/675-838       UAUGG-AGAUAUU-U-AG-AGU-CUGUUGGAAUU-AUGUCACAACA-----CA--GCAAUG-UCC-GUGCAUGGACGCACGGGACAGGCG-UU---AGCGCCACGGACGGC-GCUA--AAAGCCGGGUGCGU---CCUAUAGCCAAAACCUGAAA-UCAU-AUUCCNUACAG--AGUCUUAAUAUCGAAAUAC
BABB01001311.1/954-792       UAUGG-AGAUAUU-U-AG-AGU-CUGUU--GGAA-UUAUGUCAAAACA---CA--GCAAUG-UCC-GUGCAUGGACGCACGGACAAGGCG-UU---AGCGCCACGGACGGC-GCUA--AAAGCCGGUUGCGU---CCUAUAGCCAAAACCUAAAUCAUAAUUCC--U-ACAG--AGUCUUAAUAUCGAAAUAC
BABG01001480.1/1057-1219     UAUGG-AGAUAUU-U-AG-AGU-CUGUU--GGAA-UUAUGUCACAACA---CA--GCAAUG-UCC-GUGCAUGGACGCACGGACAAGGCG-UU---AGCGCCACGGACGGC-GCUA--AAAGCCGGUUGCGU---CCUAUAGCCAAAACCUAAAUCAUAAUUCC--U-ACAG--AGUCUUAAUAUCGAAAUAC
BAAU01014848.1/872-709       UAUGG-AGAUAUU-U-AG-AGU-CUGUU-GAAAU-UAUGUCAC-AACA---CA--GCAAUG-UCC-GUGCAUGGACGCACGGACAAGGCG-UU---AGCGCCACGGACGGC-GCUA--AAGCCCGGUUGCGU---CCUAUAGCCAAAACCUGAAAUCAU-AUUUCCU-ACAG--AGUCUUAAUAUCGAAAUAC
BABG01027172.1/434-599       UACGA-AGCAGCU-U-AG-AAG-CAGUUA--GAA-UUAUUUCCACAUA---CA--ACAAUG-CCC-CAGCAUGGACGCUGGGGCAAGGUG-UU--AUGAGCCAUGGACGGC-GCAU-AAAAGCCGGUUGUGU--CAUGGUCUAAACACACUAAAUCAUAAUUC---UUACUG--CUUCUUAGCUGCGUAGUAC
BAAY01029070.1/262-101       UUACGAAGCAGCU-U-AG-ACG-CAGUUAGAAGU-AUGUCCA--CCUA---CA--ACAAUG-CCC-CAGCAUGGACGCUGGGGCAAGGCG-UU--AUGUGCCAUGGACGGC-ACAU-AAAAGCCGGUUGUGU---CAUGGUCUAACACACUAA---UCAUAUUC--U-GCAA--GCU-UCAGCCUAGUCCUUC
BAAU01017280.1/548-713       UACGA-AGCAGCU-U-AG-AAG-CAGUUAGAAUU-AUGUCCA--UAUA---CN--ACAAUG-CCC-CAGCAUGGACGCUGGGGCAAGGCG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUGUGU---CAUGGUCUAAACACACUAAA-UCAUAAUUC-UUACUG--CUUCUUAGCUGCGUAGUAC
BABB01000615.1/1519-1684     UACGA-AGCAGCU-U-AG-AAG-CAGUUAGAAUU-AUGUCCACC-UA----CA--ACAAUG-CCC-CAGCAUGGACGCUGGGGCAAGGCG-UU--AUGUGCCAUGGACGGC-ACAU-AAAAGCCAGUUGUGU---CAUGGUCUAAACACCCUAAA-UCAUAAUUC-UUACUG--CUUCUUAGCUGCGUAGUAC
BABB01001694.1/1795-1629     ACGCUACGCUGUU-U-AG-AUG-CUGUA-GAAUU-AUGCUUCA-CAAA---UA--GAAAUG-CCC-CACCAUGGACGGUGGGGCAAGGCG-UU--ACGCACCACGGACGGU-GCGU-AAAAGCCGGUUUCGU---CAUUCUGUGAAACUCUAUAU-GCAUAAUUCAU-ACAG--CAUCUUAACUGCAAAGCGU
BABG01003660.1/430-264       ACGCUACGCUGUU-U-AG-AUG-CUGUA-GAAUU-AUGCUUCA-CAAA---UA--GAAAUG-CCC-CACCAUGGACGGUGGGGCAAGGCG-UU--ACGCACCACGGACGGU-GCGU-AAAAGCCGGUUUCGU---CAUUCUGUGAAACUCUAUAU-GCAUAAUUCAU-ACAG--CAUCUUAACUGCAAAGCGU
BABD01004484.1/414-248       UAGCGGAGCUAUU-U-AG-AGU-CUGUU-AAAUU-AUGCUUUGAAGCA---CA--GAAAUG-CCG-AGGCAUGGAAGCCGAGGCAAGGAG-AUA-UCGAGCC-CGGACGGC-GAG--UAUCGACGGUUUCGU---CAGGCAUAGAAGUAUUUACU-GCAUAAUUUAU-ACAG--AGUCUUAAUAGCGCAGUGU
BABB01000759.1/2789-2955     UAGCGGAGCUAUU-U-AG-AGU-CUGUU-AAAUU-AUGCUUUGAAGCA---CA--GAAAUG-CCG-AGGCAUGGACGCCGAGGCAAGGAG-AUA-UCGAGCC-CGGACGGC-GAG--UAUCGACGGUUUCGU---CAGGCAUAGAAGUACUUACU-GCAUAAUUUAU-ACAG--AGUCUUAAUAGCACAGCGU
BABB01012412.1/295-129       UAGCGGAGCUAUU-U-AG-AGU-CUGUU-AAAUU-AUGCUUUGAAGCA---CA--GAAAUG-CCG-AGGCAUGGACGCCGAGGCAAGGAG-AUA-UCGAGCC-CGGACGGC-GAG--UAUCGACGGUUUCGU---CAGGCAUAGAAGUACUUACU-GCAUAAUUUAU-ACAG--AGUCUUAAUAGCACAGCGU
BABB01000218.1/10258-10425   UAGCGAAGCUGUU-U-AG-AGU-CUGUA-GAAUU-AUGCUUCGAUACA---CA--GAAAUG-CAC-CGGCAGGGACGCCGGGGCAAGGAG-CUA-UCGAGCCAUGGAGGGC-GAG--UAGCGACGGUUUCGU---CAGCCGGAGAAAAUCUAUAA-GCAUAAUUC-GUACAG--AAUCUUAACAGCGCAGCGU
BAAV01011582.1/1247-1090     ----------GUU-U-AG-AGU-CUGUA-GAAUU-AUGCUUCUAUACA---CA--GAAAUG-CAC-CGGCAGGGACGCCGGGGCAAGGAG-CUA-UCGAGCCAUGGAGGGC-GAG--UAGCGACGGUUUCGU---CAGCAAAAGAAAGUCUAUAA-GCAUAAUUC-GUACAG--AAUCUUAAAAGCGCAGCGU
BAAY01014418.1/579-411       UAGCGGAGCUGUU-U-AG-UGG-CUGUA-GAAUU-AUGCAUAGAAACA---CA--GAAAUG-CCC-GGCCAUGGAAGGCAGGGCAAGGAG-AAA-UCGAGCCAUGGAGGGC-GAG--UUUCGACGGUUUCGU---CGAGCAUAGAAAAUGUAAAAAGCAUAAUUC-GUACAG--CCACUUAACAGCAAAGCGU
BABB01012429.1/422-254       UAGCGAAGCGCCU-U-GG-AUA-UUGUAGAAGUU-AAGUCAUGAAACG---CU--GAUACG-CAA-AUGCAUGGACGCAGUGGCGAGGAG-AC--ACGGGCCUCAGAUGAC-UCGU--UUCGGCGGAUUCGU---CAAGAAUUGACCGCCUUCAG-GCAGAAUUUCGAGCAG--AAUAUUAGCCGUGCAGCGU
BABD01008410.1/4-171         UAGCGGAGUCACU-U-AG-AUA-CUGUAGAAUUA-UGCUUCA--CACG---CA--AAAAUG-CCC-CGCCAUGGACGGCGGGGCAAGGCG-UU--AUGCGCCACGGAUGGC-GCAU-AAAAGCCGGUUUUGU---CAAGCAUAGAAAACAUAAAA-AGCAUAAUUCGUACAG--UAUCUUAGUGAUGCAGCGU
BABB01000982.1/9-177         UAGCGAAGCUGCC-U-AG-AUA-CUGUUGAAUUA-UGCACACGAUACA---CA--GAAAUG-AGU-UCCCACGGAUGGGAGCUCAAGGAG-A-A-CCGCGCCACGGACGGC-GCGU-U-UCGACGGUUUCGU---CAAGCAUAGAUACCCUAUAA-AGCAUAAUUCCUACAG--UAUCUUGGCAGUGCAGCGU
BAAV01009409.1/543-375       UAGCGGAGCUGCC-U-AG-AUA-CUGUUGAAUUA-UGCACACUAUACA---CA--GAAAUG-AGC-UCCCACGGAUGGGAGCUCAAGGAG-A-A-CCGCGCCACGGACGGC-GCGU-U-UCGACGGUUUCGU---CGGGUAUCGUAAAUCUUUAA-GGCAUAAUUCCUACAG--UAUCUUGGCUGCGUAGCGU
BAAV01021692.1/208-376       UAGCGAAGCUGCC-U-AG-AUA-CUGUUGAAUUA-UGCACACGAUACA---CA--GAAAUG-CCC-UGCCACGGAUGGCAGGGCAAGGAG-A-A-CCGCGCCACGGACGGC-GCGU-U-UCGACGGUUUCGU---CGAGCAUCGUAAAUCUUUAA-GGCAUAAUUCCUACAG--UAUCUUGGCAGUACAGCGU
BAAY01014083.1/441-609       UAGCGAAGCUGCC-U-AC-AUA-CUGUCGAAUUA-UGCACACGAUACA---CA--GAAAUA-AAC-UGCCACGGAUGGCAGUUCGUGGAG--AA-UCGCGCCACGGACGGC-GCG--UUGCGACGGUUGCGC---CGGGAAUAGAUACCCGAUAA-AGCAUAAUUCCUACAG--UAUCUAGGUCGUGCAGCGU
BABD01026585.1/392-224       UAGCUAAGCCGCU-U-AGUAUA-CUGUAGGAUUA-UGCACAUGAAGCA---CA--GUUAUG-ACU-UGCCAUGGAGGGCAAGUCUAGGUG-UA--CCGCGCCACGGAAGGC-GCGU--UUAGACGGUUUCGU---CAAGCAUAGAAGCGCACAAA--GCAUAAUCCGUACAG--UAUCUUAGCGGCAUAGCGU
BABG01025746.1/314-481       UAGCGAAGCCGCU-U-AG-AUA-CUGUAGGAUUA-UGCACAUGAAGCA---CA--GAAAUG-ACU-UGCCAUGGAGGGCAAGUCAAGGAG-A-A-CCGCGCCACGGAAGGC-GUGU-U-UCGACGGUUUCGU---CAAGCAUAGAAGCGUAAAA--AGCAUAAUCCGUACAG--UAUCUUAGCGGCAAAGCGU
BABB01000066.1/9671-9504     UAGCGAAGCCGCU-U-AG-AUA-CUGUAGGAUUA-UGCACAUGAAGCA---CA--GAAAUG-ACU-UGCCAUGGAGGGCAAGUCAAGGAG-A-A-CCGCGCCACGGAAGGC-GCGU-U-UCGACGGUUUCGU---CAAGCAUAGAAGCGCAAAA--AGCAUAAUCCGUACAG--UAUCUUAGCGGCAAAGCGU
BABG01011318.1/737-576       ------UGCGUUA-U-UG-AAC-CAGUU--AAUU-UUGGCACGCUGUAC-UUG---AAAUG-CAC-CGGCAUGGACGCCGGGGCAAGGCG-UU--AUGUGCCAUGGACGGC-ACAU-AAAAGCCGGUUUAGU---CGAGCAUAGAAAAACUAUGA-GCAUAAUUC-GUACAG--CCUCUUAACAGCGUAGCGU
BABB01010186.1/350-180       UAGCGCAGCCUCU-U-AG-AUA-CUAUAGAAAUU-AUGCCCAU-GAAAC-ACA--GAAAUG-UCC-UGCCAUGGACGGCAGGACAAGGUG-UU--AUGCGCCAUGGAUGGC-GCAU-AAAAGCCGGUUUCGU---CAAGCAUAGAACAACUACAA-GCAUAAUUUCGUACAG--UAUCUUAGAGACGUAGCGU
BAAV01001293.1/234-67        UAGCGAAGCUGUU-U-AG-AGU-CUGUA-GAAUU-AUGCCCUGAUAAC---CA--GAAAUG-CAC-CGGCAUGGACGCCGGGGCAAGGCG-UU--AUGUGCCAUGGACGGC-ACAU-AAAAGCCGGUUUCGU---UGAGCAUAGAAAACCUUCGA-GCAUAAUUC-GUACAG--CCUCUUAACCGCGUAGCGU
BABD01036649.1/946-792       ---------GGUU-U-AG-AUA-CUGUA-GAAAU-UAUGCCCAUGAGAC-ACA--GAAACG-CCC-CGCCAUG-ACGCAGGGGCGAGGAG-AC--CCGCGCCAUGGACGGC-GCGU--UUCGACGGUUUCGUCAAAGUAUAGAAAAAACUUCCAGCCAUAAUUUUGGUACAG--UAUUCUAACC---------
BABB01000222.1/7557-7727     UAGCGAAGCUGCU-U-AG-AGA-CUGUAGAAUUA-UGCCCAAGAAAAA---CA--GAAAUG-CCC-GGCCAUGGACGGCCGGGCAAGGCG-UU--AUGCGCCAUGGAAGGC-GCAU-AAAAGCCGGUUUCGU---CAAGCAUAGAACCACCCCAA-GGCAUAAUUCGUACAG-CUCUCUUAGCAGCGUAGCGU
BABB01000066.1/11493-11661   UAGCGAAGCUGUU-U-AG-AUA-CUGUAGGAUUA-UGCCCGUGAAGCA---CA--GAAAUC-CGC-AGCCAUGGACGGCUGGGGAAGGCG-UU--AUGCGCCACGGACGGC-GCAU-AAAAGCCGGUUUCGU---CGAGCAUUGAAAACCCAAA--AGCAUAAUCCGUACAG--UAUCUUAACAGCGCAGCGU
BABB01000043.1/4826-4994     UAGCGAAGCUGUU-U-AG-AUA-CUGUAGAAUUA-UGCACAUGAAACA---CA--GAAAUG-CCC-AGCCAUGGAUGGCUGGGCAAGGUG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUUCGU---CAAGUAUAGAAACACUAUA--AGCAUAAUUCGUACAG--AAUCUUAACAGCAAAGCGU
BABD01000800.1/2312-2144     UAGCGAAGCUGUU-U-AG-AUA-CUGUAGAAUUA-UGCACAUGAAACA---CA--GAAAUG-CCC-AGCCAUGGAUGGCUGGGCAAGGUG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUUCGU---CAAGCAUAGAAACACUAUA--AGCAUAAUUCGUACAG--AAUCUUAACAGCAAAGCGU
BAAY01002367.1/1949-1782     UAGCGAAGCUGUU-U-AG-AUA-CUGUA-GGAUU-AUGUUUAAAUACG---CA--GAACUG-CCC-AGCCAUGGACGCCGGGGCAAGGCG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUUCGU---CAAGCAUAGAAAACCAAAAG-GCAUAAUUCCU-ACAG--AUUCUUAAUGGCGUAGCGU
BABD01001878.1/2188-2332     -----------UU-U-AG-AAU-CUGUU-GAAUU-AUGCUUCACAAC----CA--GAAAUG-CAC-CGGCAUGGACGCCGGGGCAAGGUG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUUCGU---CAAGCAUAGAAAACCAAAAG-GCAUAAUUCCU-ACAG--AUUCUUAA-----------
BAAY01018278.1/527-698       UUACGAAGUGACU-U-AA-AUA-UCGUUAAAAUU-AUGCCAUGAAACA---CA--GAAGUGACCC-UGACAUGGAAGGCAGGACAAGGCG-UA--AUGCGCCAUGGACGGA-GCAU-AAAAGCCGGUUUCGU---CAAGCAUAGAAAACAUAAAA-GCAUAAUUC-UAACAAUUAAUCUUAAAACAAGUAAGA
BABB01000120.1/4140-4308     UACGA-AGUGACU-U-AG-AUA-UUGUUAGAAUU-AUGCCAUGAAACA---CA--GAAAUG-CCC-UGCCAUGGACGGCAGGGCAAGGCG-UU--AUGCGCCACGGACGGC-GCAU-AAAAGCCGGUUUCGU---CAAGCAUAGAAAAUCUUAAA-GCAUAAUUC-UUACAA-UUAUCUUAGCCACGUAGUUU
BABG01008261.1/622-790       UACGA-AGUGACU-U-AG-AUA-UUGUUAGAAUU-AUGCCAUGAAACA---CA--GAAAUG-CCC-UGCCAUGGAAGGCAGGGCAAGGUG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUUCGU---CAAGCAUAGAAAACCCUAAA-GCAUAAUUC-UUACAA-UUAUCUUAGUCACGUAGUUU
BABD01011793.1/129-1         ------------------------UGUUAGAAUU-AUGCCAUGAAACA---CA--GAAAUG-CCC-UGCCAUGGAAGGCAGGGCAAGGCG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUUCGU---CAAGCAUAGAAAACAUUAAA-GCAUAAUUC-UUACA----------------------
BAAV01008811.1/615-783       UACGA-AGUGACC-U-AG-AUUUCUGUUAGAAUU-AUGCCAUGAAACA---CA--GAAAUG-CCC-UGCCAUGGAAGGCAGGGCAAGGCG-UU--AUGCGCCACGGACGGC-GCAU-AAAAGCCGGUUUCGU---CAAGCAUAGAAAACCUUAAA-GCAUAAUUC-UUACAG--AAUCUUGGCCACGUAGUAC
BABD01016812.1/730-558       UAGCGAAGCGGCU-U-AG-AUA-CUGUAGAAAUUUAUGCCAUGAAACA---CA--GAAAUG-CCC-AGCCAUGGUCGGCUGGUCAAGGCG-UUU-AUGCGCCAUGGACGGC-GCAUUUAAAGCCGGUUUCGU---CAAGCAUAGAAAGACUGUAA-GCAUAAUUUCGUACAG--AAUCUUAGCCGCGCAGCGU
BABB01000628.1/3990-4158     UAGAGAAGUUGCU-U-AG-AGU-CUGUCAGAAUU-AUGCUUAGAGGAG---CA--GAAAUG-CCC-GGCCAUGGACGGCUGGGCAAGGCG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUUCGU---CUGUCAUAGAAAGAUUAAAA-GCAUAAUUC-CUACAG--ACUCUUAGCAGCGUAGCGU
BABG01023578.1/628-797       UAGCGCAGUGGCU-U-AG-AUA-CUGUAGAAUUA-UGCCCAUGAAACG---CA--GAAAUG-CCC-CGGCAUGGACGCCGGGGCAAUGUG-AAA-CCGCGCCAUGGACGGC-GCG--UAUCGACGGUUUCGU---CAAGCCUAGAAAAUCUACAA-AGCAUAAUUCGUACAG--UACCUUAGCUGCGUAGCGU
BAAU01014784.1/416-585       UANGCGCGUGGCU-U-AG-AUA-CUGUAGAAUUA-UGCACAUGAAACG---CA--GAAAUG-CCC-CGGCAUGGACGCCGGGGCAAGGAG-AAA-CCGCGCCAUGGACGGC-GCG--UUUCGACUGUUUCGU---CAAGCAUAGAAAAUCUAAGA-AGCAUAAUUCGUACAG--UACCUUAGCUGCGUAGCGU
BABB01000738.1/4375-4544     UAACGAAGCUGCU-U-AG-UGU-CUGUAGAAUUA-UGCGCAUGAAACG---CA--GAAACU-CAC-CUGCAUGGACGCAGGUGAGAGGAG-AAG-ACGCGCCAUGGACGGC-GCG--UUUCGACGUUUUCGU---CAAGCAUAGAAGCCCUUCAA-AGCAUAAUUCGUACAG--ACACUUUGCAGCGCAGUGU
BABD01036650.1/491-660       UAGCGAAGAGGUU-U-AG-AUA-CUGUAGAAAUU-AUGCCCAU-GAGAC-ACA--GAAACG-CCC-CGGCAUGGACGCAGGGGCGAGGAG-A-A-CCGCGCCAUGGACGGC-GCGU-U-UCGACGGUUUCGU---CAAGUAUAGAANAACCUCAN-GCAUAAUUUCGUACAG--UAUCUUAGCCACGUAGCGU
BAAV01030986.1/399-567       UAGCGCAGUGGGU-U-AG-AAA-CUGUAGAAAUU-AUGCCACAAAGCA---CA--GAAACG-CCC-CUGCAAGGACGCGGGGGCGAGGAG-A-A-CCGCGCCACGGACGGC-GCGU-U-UCGACGGUUUCGU---CAAGCAUAGAAACCCUUCAA-GCAUAAUUUCGUACAG--UAUCUUACCCACGAAGCGU
BABG01019423.1/456-362       --------------------------------------------AACG---CA--GAAACG-CUC-CUGCAUGGACGCAGGAGCGAGGAG-AA--CCGCGCCAUGGACGGC-GCGU--UUCGACGGUUUCGU---CAAGCAUAGAAACCCUAAAA--------------------------------------
BABB01000639.1/4945-5113     UAGCGAAGCGGCU-U-AG-AUA-CUGUAGAAAUU-AUGCCAUGAAACA---CA--GAAACG-CUC-CUGCAUGGACGCAGGGGCGAGGAG-A-A-CCGCGCCACGGAUGGC-GCGU-U-UCGACGGUUUCGU---CAAGCAUAGAAACCCUUCAA-GCAUAAUUUCGUACAG--AAUCUUAGCCGCGCAGCGU
BABB01001805.1/359-528       UAGCGAAGUGGCU-U-AG-AUA-CUGUAGAAAUU-AUGCCCAUGAAGCG--CA--GAAACA-CCC-CUGCAUGGACGCAGGGGUGAGGAG-A-A-CCGCGCCACGGACGGC-GCGU-U-UCGACGGUUUCGU---CAAGCAUAGAAACCCAUCAA-GCAUAAUUUCGUACAG--AAUCUUAGCCACGUAGCGU
BAAV01024931.1/129-298       UAGCGAAGUGGCU-U-AG-AUA-CUGUAGAAAUU-AUGCCCAUGAAGUG--CA--GAAACA-CCC-CUGCAUGGACGCAGGGGUGAGGAG-A-A-CCGCGCCACGGACGGC-GCGU-U-UCGACGGUUUCGU---CAAGCAUAGAAACCCAUCAG-GCAUAAUUUCGUACAG--AAUCUUAGCCACGUAGCGU
BABB01018585.1/578-742       UAGCGAAGUGGUU-U-AG-AUA-CUGUA-GAAAA-UAUGCCCAUGAGAC-ACA--GAAACG-CCC-CGGCAUGGAUGCAGGGGCGAGGAG-AAA--CGCGCCAUGGACGGC-GCGU-UUUCGACGGUUUCGU---CAAGUAUAGAAAACCCUCAG-CAUAAAUUC-GUACAG--UAUCUUAGCCAC-----GU
BABB01000031.1/589-760       UAGCGAAGCUGCC-U-AG-AUA-CUGUAGAAAUU-AUGCCCAU-GAAAC-GCA--GAAAUG-CCC-CGCCAAGGACGGCGGGGCAAGGAU-UAU-AUGCGCCAUGGACGGC-GCAU-AUAAUCCGGUUUCGU---CAAUCAUAGAAACCCUAAAA-GCAUAAUUUCGUACAG--AAUCUUGGCAGCGAAGCGU
BABG01001700.1/1701-1529     UAGCGAAGCUGCC-U-AG-AUA-CUGUAGAAAUU-AUGCCUAU-GAAAC-GCA--GAAAUG-CCC-CGCCAAGGACGGCGGGGCAAGGAU-UAU-AUGCGCCAUGGACGGC-GCAU-AUAAUCCGGUUUCGU---CAAGCAUAGAAACCCUAAAAAGCAUAAUUUCGUACAG--AAUCUUGGCUGCGAAGCGU
BAAY01006880.1/32-203        UAGCGAAGCUGCC-U-AG-AUA-CUGUAGAAAUU-AUGCCCAUGAAACG--CA--GAAAUG-CCC-CGCCAAGGAUGGCGGGGCAAGGAU-UAU-AUGCGCCAUGGACGGC-GCAU-AUAAUCCGGUUUCGU---CAAGCAUAGAAACCCUAAAA-GCAUAAUUUCGUAUAG--AAUCUUGGCUGCGAAGCGU
BAAU01016443.1/70-136        --------------------------------------------------------AAAUG-CCC-CGCCAAGGACGGCGGGGCAAGGAU-UAU-AUGCGCCAUGGACAGC-GCAU-AUAAACUAUAUU----------------------------------------------------------------
BAAV01012556.1/776-710       --------------------------------------------------------AAAUG-CCC-CGCCAAGGACGGCGGGGCAAGGAU-UAU-AUGCGCCAUGGACAGC-GCAU-AUAAACUAUAUU----------------------------------------------------------------
BABG01018343.1/594-502       ---------------------------------------------------CA--GGAAUG-GCC-AGCGAUGGAAGGCAGGGCAAGGGG-UU--AUGGGCCAUGGACGGC-GCAGCAAAGCCCGGGUUCGG---AGAGCAUAGAAAACCAUACA--------------------------------------
BABB01008784.1/236-405       UAGCGAAGCUGCU-U-AG-AUA-CUGUCGAAUUA-UGCACAUGCUACA---CA--GAAAUG-CCG-AGGCAUGGACGCCGAGGCAAGGAG-AAA-UCGAGCCAUGGAUGGC-GAG--UUUCUACGUUUUCGU---CAUCCUAUGAAAACCAACAA-AGCAUAAUUUGCACAG--AAUCUUGGCUGCGUAGGGG
BAAU01006263.1/1601-1770     UAGCGAAGCUGCU-U-AG-AUA-CUGUCGAAUUA-UGCACAUGCUACA---CA--GAAAUG-CCG-AGGCAUGGACGUCGAGGCAAGGAG-AAA-UCGAGCCAUGGAUGGC-GAG--UUUCGACGGUUUCGU---CAUCCUAUGAAAACCUACAA-AGCAUAAUUUGCACAG--UAUCUUGGCUGCGCAGCGU
BAAV01012488.1/890-721       UAGCGAAGCUGCU-U-AG-AUA-CUGUCGAAUUA-UGCACAUGCUACA---CA--GAAAUG-CCG-AGGCAUGGACGCCGAGGCAAGGAG-AAA-UCGAGCCAUGGAUGGC-GAG--UUUCGACGGUUUCGU---CAUCCUAUGAAAACCUACAA-AGCAUAAUUUGCACAG--UAUCUNGGCUGCGCAGCGU
BABB01011528.1/151-320       UAGCGAAGCUGCU-U-AU-AUA-CUGUCGAAUUG-GGGGGAUGCUACG---AA--GAAUUG-CCG-AGGCAUGGACGCCGAGGCGAGGAG-AAA-UCGAGCCAUGGAUGGC-GAG--UUUCGACGUUUUCGU---CAUCCUAUGAAAACCUACAA-AGCAUAAUUUGCACAG--UAUCUUGGCUGCGCAGCGU
BABB01000321.1/5277-5446     UAGCGGAGCUGCU-U-AG-AUA-CUGUUGAAUUA-UGCCCAAGAGAAC---CA--GAAAUG-CAC-CGGCAUGGAAGCCGGGGCAAGGAG-CUA-UCGAGCCAUGGAGGGC-GAG--UAGCGACGGUUUCGU---CUGGCAUAGAAAAACUAUAA-GGCAUAAUUCUUACAG--UAUCUUGGCAGCAAAGCGU
BABD01000536.1/5186-5325     CUAGA--GUCUGU-U-AGAAUU-AUGUCA--------------AAACA---CA--GCAAUG-CUC-CGACACG-ACGUCGGGGCAAGGCG-UUA-CCGCGCCAUGGACGGC-GCGU-AAAAGCCGGUUGCGU---CAAGCAUAGAAAACCUUU-------------AAGCAU--AAUCUUACAGACGAA----
BABB01001613.1/799-965       UACGA-AGCUGCU-U-AG-AGU-CUGUA-GAAUU-GCAUACGAAAAAC---CA--ACAACG-CCC-AUGCAUGGACGCAUGGGCGAGGUG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUGUGU---CAAAAAGCCACAACCGGCAU-AUGCAAUUC-GUACAG--ACACUUAGCAGCGUAGUUC
BABG01000872.1/465-630       UACGA-AGCUGCU-U-AG-AGU-CUGUA--GAAU-UGCAUACGAAAAC---CA--ACAACG-CCC-AUGCAUGGACGCAUGGGCGAGGUG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUGUGU---CAAAAAGCCACAACUGGCAUAUGCAAUUC--GUACAG--ACACUUAGCAGCGUAGUUC
BAAY01007451.1/25-190        AUUCGUA-UCGCU-U-AG-AGU-CUGAA--GAAU-UGCAUACGAAAAC---CA--ACAACG-CCC-AUGCAUGGAUAAAUGGGCGAGGUG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUGUGU---CAAAAAGCCACAACCGGCAUAUGCAAUUC--GUACAG--ACACUUAGCAGCGUAGUCC
BABG01025117.1/31-202        UNAAGGAGACGCG-CGNU-ACG-UAGCAG-AUCU-UCCCGGGGUGAUUCGUCA--ACAACG-CGC-AUGCAUGGACGCAUGGGCGAGGUG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUGUGU---CAAAAAGCCACAACCGGCAU-AUGCAAUUC-GUACAG--ACACUUAGCAGCGUAGUCC
BABB01000925.1/486-653       AAGAAGAGUGGAA-G-AAAAUA-CUGCAG-GA----GCACCUGACACAAAUAG--GCUUCU-UCC-A-GCAUGGACGCAUGGGCGAGGCG-UU--AUGCGCCAUGGACGGC-GCAU-AAAAGCCGGUUGUGU---CAAAAAGCCACAACCGGCAUAUGCAAUUC--GUACAG--ACACUUAGCAGCGUAGUUC
ABEF01021936.1/751-686       -------------------------------------------------------GGGUA--CCC-CGGCAUGGAUGCCGGGG-UAGCCG-CGA-CACGGCCAUGGAUGGC-CGA--UCGCGGCGGGCCC---------------------------------------------------------------
BAAV01011978.1/813-978       CGGCGGAGACUGU-G-AG-AUU-UUCUU-GGAAA-GUGGCUGGACCUC---AG--GGGCAA-CGC-GAACACG-AUGUUCGCGUUAGCCG-AUA--AGUGCCAUGGAUGGC-AACG-UAAAGGCGGCCCCGU---CAUGGUGAGAAGCACUUGG--CCACUUUCCUUUAGAA--AAUCC-ACAGUUGUAGCUA
BAAX01016096.1/604-769       CGGCGGAGACUGU-G-AG-AUU-UUCUU-GGAAA-GUGGUCGAGCCGC---AG--GGGCAA-CGC-GAACACG-AUGUUCGCGUUAGCCG-GU--AGGCGACAUGGAUGGCAGCGU--AAAGGCGGCCCCGU---CAUGAUGAGAAGCACUUCG--CCACUUUCCUUUAGAA--AAUCC-ACAGUUGUAGCUA
BABG01022683.1/528-364       UGUCGGAGGAUGUAU-GAUAUC-UUCUAGUAAAG-UG---GAGAAAGA---CA--GGGGGAAAGC-GGACACG-AUGUACGUGUCAGCCGAUUG-UCGA--CAUGGAUGU--GGAU-CGUAGGCGGCCCGGU---CAUGACGAGAUACUACUCAU---CACUUUUAGUAGAA--AAU-UCACAUCCGGAGACC
BABG01010186.1/991-843       ---------GGUG-G-UG-AUA-UUUUCU-CGAA-AAGUGUUGAUAGAC-AGG--GGGA-A-AGC-GGACACG-AUGUCCGCGUCAGCCG-AU--CCGCGCCAUGGAUGGC-GCGU--GUAGGCGACCCCGU---CAUGAUUAGAACCACUGUAUCACUUUUCA--UUAGAA--AAUUCACACC---------
BAAX01032386.1/191-337       ---------GGUG-G-UG-AUA-UUUUCU-CGAA-AAGUGUAGAAAAA---CA--GGGUGG-AGC-GAACAGG-ACGUUCGCGACAGGCG--GA-CGUUGCCAUGGAUGGC-AAC--UGGAGCCGUGCCCGU---GCGGUUUAGAACCGCUACUC-ACUUUUCG--UCAGAA--AAUUCCCACC---------
BABD01036144.1/678-842       UGUCGGAGUAUGU-U-GA-UAU-UUUCUAGAANA-GUG--CUGAAAGA---CC--GGGGGAAAGC-GGACACG-AUGUCCGCGUCAGCCU-AC--AGUCGACAUGGAUGUC-GACU--GUAGGCGGGCCUGU---CAUGACGAGAACUACUCAU---CACUUUUCGUAGAAN--AUUCCCACCUGGAGACGCG
BABA01026201.1/110-272       UGUCGGAGGAUGU-U-GA-UAU-UUUCUAGAAAA-GUGCUGAAAGACA---GG--GGGA-A-AGC-GGACACG-AUGUCCGCGUCAGCCG-AUU-GUC-GACAUGGAUGUC-GAC--UGUAGGCGGCCCCGU---CAUGACGAGAACCACUCA---UCACUUUUCGUAGAAA--AU--UCACAUCUGGAGACC
BABG01018589.1/701-539       CGUCGGAGGAUGU-U-GA-UAU-UUUCUAGAAAA-GUGCUGAAAGACA---GG--GGGA-A-AGC-GGACACG-AUGUCCGCGUCAGCCG-AUU-GUC-GACAUGGAUGUC-GAC--UGUAGGCGACCCCGU---CAUGACGAGAACUACUCA---UCACUUUUCGUAGAAA--AU--UCACAUCCGGAGACC
BABA01015165.1/783-945       UGUCGGAGGAUGU-U-GA-UAU-UUUCUAGAAAA-GUGCUGAAAGGCA---GG--GGGA-A-AGC-GGACACG-AUGUCCGCGUCAGCCG-AUU-GUC-GACAUGGAUGUC-GAC--UGUAGGCGGCCCCGU---CAUGACGAGAACUACUUA---UCACUUUUCGUAGAAA--AU--UCACAUCCGGAGACC
BAAX01033270.1/298-136       UGUCGGAGGAUGU-U-GA-UAU-UUUCUAGAAAA-GUGCUGAAAGGCA---GG--GGGA-A-AGC-GGACACG-AUGUCCGCGUCAGCCG-AUU-GUC-GACAUGGAUGUC-GAC--UGUAGGCGGCCCCGU---CAUGACGAGAACUACUCA---UCACUUUUCGUAGAAA--AU--UCACAUCCGGAGACC
BABG01004015.1/650-812       UGUCGGAGGAUGU-U-GA-UAU-UUUCUAGAAAA-GUGCUGAAAGACA---GG--GGGA-A-AGC-GGACACG-AUGUCCGCGUCAGCCG-AUU-GUC-GACAUGGAUGUC-GAC--UGUAGGCGGCCCCGU---CAUGACGAGAACUACUCA---UCACUUUUCGUAGAAA--AU--UCACAUCCGGAGACC
BABG01005149.1/1125-964      UGUCGGAGGAUGU-UGAU----AUUUCUAGAAAA-GUG--CUGAAAGG---CA--GGGGGAAAGC-GGACACG-AUGUCCGCGUCAGCCG-AU--UGUCGACAUGGAUGUC-GACU--GUAGGCGGCCCCGU---CAUGACGAGAACUACGCAU---CACUUUUCGUAGAAAAU----UUACAUCCGGAGACC
BABG01028760.1/763-600       GGUCGGAGCGUGU-UGAU-AUU-UUCUUA-AGCA-GUGGUGAGCCAU----CA--GGGUGG-AGC-AAACACG-AUGUUUGCGACAGGCG-GC--CGGCGACAUGGAUGUC-GCC--AAGAGCCGUGCCCGU---UCGGAUGAGAUACACUUUAU-CCACUGCU--UUAGAA--AAU-UCACACUCGGAGACC
BABG01012947.1/690-527       UGUCGGAGCGUGU-U-GA-UAU-UUUCUU-AAGC-AGUGGUGAGUCAU---CA--GGGUGG-AGC-AAACACG-AUGUUUGCGACAGGCG-GC--CGGCGACAUGGAUGUC-GCCU-AG-AGCCGUGCCCGU---UCGAAUGAGAUACACUUUAUCCACUGCUU--UAGAAA--AU--UCACACUCGGAGACC
BABG01005904.1/1457-1294     UAUCGGACGGUGG-U-GA-UAU-UUUCU-CGAAA-AGUGCUGAAAAU----CA--GGGUGG-AGC-GAACAGG-ACGUUCGCGACAGGCG--GA-CGUUGCCAUGGAUGGC-AAC--UGGAGCCGUGCCCGU---GCGGAUUAGAACCGAUAUCU-CACUUUUCGUCAGAAA--AU--UCCCACCGGGAGACC
BAAX01016096.1/154-8         --------GGUGU-U-GA-UAU-UUUCUUGAAAA-GUG--CUGAAAGA---CA--GGGUGG-AGC-GAACAGG-ACGUUCGCGACAGGCG--GA-CGUUGCCAUGGAUGGC-AAC--UGGAGCCGUGCCCGU---ACGGAUUAGAACCACUAUAU--CACUUUUCGUAGAAA--AU--UCACACC--------
BAAX01017353.1/47-216        UUUGGGAGAAAAU-U-AG-AAA-A-UCUUGGUAU-GCCUGCCUACACA---CA--GUGAUG-UUC-UGCCACGGAUGGCAGAACAAGGCA-GCA-UCGAGUCAUGGAUGAC-UCGU-UGUUGCCGUUCACGU---CACUCCGCGAAAAUCUAAUUCAGGCAUACC-UAGACU--UUUCUUAUUUUCGGACAAC
BAAZ01022944.1/390-224       UAUGUUUGAGCCU-U-AG-AAU-UACUUA-AUGU-UCUUUCUUCUUGU---AA--GCAAUA-CCU-GAACACG-AUGUUCAGGUAAGCAG-CCA-CUGAGCCAUGGAUGGC-GAAU-UGGCUGCGGUUGCGU---AUUUUGAGAAUAUGUUUGUU-AAGAACAU--UUAGUA--AUUCUUAGGUUCAAUACAU
CP000510.1/3672869-3673034   CUACGAAAAUUUC-C-GU-ACGUUUUUCU-----UCCUCAAUCAAUUCCUUUA--GCA-AG-UGG-AAACAUGGAUGUUUCUGCUAAGUU-CGGCUCUGCACAUGGAUGUG-CUGU-CCGGACUGG-UGCGU---UAAAAAGGAAUUUAUUUAGU-AAGA------UAAAAAAACGUCUCGGAACGGCAUUCU
CP000507.1/4244752-4244914   UACGCAUCCCCCU-U-CCGAAG-UUGCCG-----GAGGAAAAUGUCUUCAAUA--GCAAG--CUC-CGUCAGGGACGACGGAG-CAGGCA-CCG-UUGAGCCAUGGAUGGU-GAGU-CGGUGCCGGUUGCGU---GCAUUGAAGGCAUUUUACGC-AGGG------UAACAA--CUUCGGUGGGGCGCCCUUU
CP000510.1/1228464-1228624   UAGGCAAUUUCCG-U----ACGUUUUUCU-----UGCUCAAUCAAUCUCUUUA--GCA-AG-UGG-AAACAUGGAUGUUUCCACUAAGUU-CGGCUCUGCACAUGGAUG---CUGU-CCGGACUGG-UGCGU---UAAAAAGAAAUUUAUUUAGU-AAGA------UAAAAAAACGUC-CCGGACGGCACUCU
AP009389.1/96011-96076       -------------------------------------------------------GAG-GG-UGC-GGACAGGGAAGUCCGCACCAGCCC-GAA-CCGAGCCA-GGAUGGU-GAGU-UGAGGGCGG-CUC---------------------------------------------------------------
AAGA01007355.1/352-440       ----------------------------------------------------A--GUAAUG--UC-GCGCAUGGAUGCGCGCCCAAGCCA-UG--CUUGUACAUGGAUGUA-CUAU--CAUGGCGUUUACGU---UCACAACAAUUAAUUAUUUG--------------------------------------
AAQK01002832.1/794-627       UAGCGAAGCUGUU-U-AG-AGU-CUGUA-GAAUU-AUGCUUCGAUACA---CA--GAAAUG-CAC-CGGCAGGGACGCCGGGGCAAGGAG-CUA-UCGAGCCAUGGAGGGC-GAG--UAGCGACGGUUUCGU---CAGCUGGAGAAAAUCUAUAA-GCAUAAUUC-GUACAG--AAUCUUAACAGCGCAGCGU
AP009389.1/444630-444476     UUGCGUAGCGUCG-U-UAGGUG-AACUU--GGCGAAACUGAGGUUGCGG--AA--UUGGGG-CGC-GGACA-GGACGUCCGCGCCAGCCC-UCA-CCGAGCCA-GGACGGU-GAGU-UGAGGGCGGCCCAAU---UCCGCCCGA------------AGUGAGCC--AUAGUU--CACC--CGACGCGAAGCAU
AAOH01000004.1/570569-570658 ----------------------------------------------------A--GCCAUG--UA-UUUCAUGGAUGAAAUA-CAAGGUG-AAG-CUUGGCCAUGGAUGGC-CUAU-CUUCACCGUUGGCGU---UCACAUCAAUCGAUUAUUUG--------------------------------------
CP000510.1/4230005-4230169   ---CUAGGCAAUU-U-CC-GUACGUUUUU--CUU-GUCUGAGAAAUCACUUUA--GCA-AA-GGA-AAUCAUGGAUGAUUUCAUUAGGCU-CGGCUCUGCACAUGGAUGUG-CUGU-CCGAGCCGG-UGCGU--------UAAGAAGUUAUUGAGCAGACAAGAAUAAAAAACGUCUCGGAACGGCAUUCU--
AP009389.1/2855527-2855462   -------------------------------------------------------GGG-GG-UGC-GGACAGGGAUGUCCGCACCAGCCC-GAA-CCGAACCA-GGACGGU-GAGU-UGAGGGCGG-CCC---------------------------------------------------------------
AAQK01003545.1/346-511       UAUGG-AGCUGCC-U-AG-AGA-CUGUUA-AAAU-UAUGUACACAGCC---CA--GCAACG-CAC-GCACAUGGACGUGCGGGCGAGGCG-UU---AGCGCCAUGGACGGC-GCUA--AAAGCCGGUUGCGU--CAUGGUCUAAGCAAUCCCUAAUCAUAAUUU--UUACAG--UGUCUUGGCAGCGUAAUCA
CP000510.1/3670339-3670176   UACGGAAAUUUCC---GU-ACG-UUUU---UCUU-GAUCAAUCAAUUCCUUUA--GCA-AA-GGA-AAUCAGGGAUGAUUUCAUUAGGCU-UGGUUCUGCACAUGGAUGUG-CUGU-CCAAGCCGG-UGCGU---UAAAAAGGGAUUUAUU-----UAUCAAGA--UAAAAAAACGUCUCGGACGGCACUCU-
AAQL01005167.1/1809-1645     UACGC-AGCAACU-U-AG-AGU-AUGUUU-GAAA-UCACUUCAACACA---UA--GCGACG-CUC-GUACACGGAUGUACGAGCGAGUCC-AUA-CUGAGCCAC-GAUGGC-GAA--UAUCGGCGGUGGCGU---ACUGCUUUCUCAACCUAUAU-GUGAUUUC--UUACAU--ACUAUUAGUUGUGGAAUAA
AP009389.1/2842660-2842505   UUGCGUAGCGUCG-U-UAGGUG-AACUU--GGCGAAACUGAGGUUGCGGAAUU--GGG-GG-CGC-GGACA-GGACGUCCGCGCCAGCCC-UCA-CCGGGCCA-GGACGGU-GAGU-UGAGGGCGG-CCC-----AAUUCCGCCCGA---------AGUGAGCC--GUAGUU--CACC--CGACGCGAAGCAU
AAQL01005167.1/1366-1202     UACGC-AGCAACU-U-AG-AGU-AUGUUU-GAAA-UCACUUCUAUACA---UA--GCAACG-CUC-GUACAUGGAUGUACGAGCGAGUCC-AUA-CUGAUCCAC-AAUGGC-GAA--UAUGGACGGUUGCGU---ACUAUUGUCUCAACCUAUAU-GUGAUUUC--UUACAU--ACUCUUGGUUACGAAGUAA
AACY021824455.1/791-625      CACUCCAAUUCCC-C-GU-GAU-CACAC-CUGAA-ACUGAGUUAAUGAU--GA--GUAAUU--UA-CAGCAUGGAUGCUGUA-CAAAGCG-UAG-CUUGGCCAUGGAUGGC-CUAU-CUACGCUGGUUACGU---UCACAUCAUUAACGUAAGUUGAAGAUACAG---UGAG--AUCCUCGGGUGCGCCGUGG
CR954246.1/2620603-2620680   -------------------------------------------------------GUAAUA--UC-GCGCAUGGAUGCGCGA-UAAGGCG-AAA-CUAGGCCAUGGAUGGC-CUAU-CUUCGCCGUUUACGU---UCACAUCAA-------------------------------------------------
CP000510.1/1227322-1227152   CGGCUAGGCAAUU-U-CC-GUA-CGUUUUUCUUG-UGCUGAACAAACACUUUA--GCA-AG-AGA-AAACAUGGAUGUUUUCUCUAACCU-CAG-CCAGUACAGGGAUGUA-AUGU-CUGAGGUGG-UGCGUAAAAAAGUGGUUGGGCAGUGCA--AGAAUAA---AAAACG--UGUCGGAACGGCAUUCUUU
AATE01001808.1/286-452       UUGCGAAGGCGGA-UGAG-AUU-UUCUUG-AUAU-UCCGUCAUCAAUA---CA--GAAAUU-GCG-GGACAAGGAUGUCCCGCAAAGCCCGUGG-CUGAGCCA-GGAUGGC-UCAU-UGAGGGCGGUUUCGU---CCGUCGCCGCAACCUUGC---CGGAAUAU--UUAGAA--AAUCCAUCAGCCGCAGUCA
CP000510.1/4227970-4227804   CUACGAAAAUUUC-C-GU-ACG-UUUUU-CUUGU-GCUGAACAAGUGCU-UUA--GCA-AG-AGA-AAACAUGGAUGUUUUCUCUAACCU-CAG-CCAGUACAGGGACGUA-AUGU-CUGAGGUGG-UGCGU---------UAAAAAGCGGUUGGGCAGUGCAAGAAUAAAAAACGUCUCGGAACGGCACUUU
CP000510.1/1237521-1237683   UAGGAAAUUUCCG---AC-CGU-UUUUAU-----UGCUCAAUCAAUCUCUUUA--GCA-AG-UGG-AAACAUGGAUGUUUCCACUAAGUU-CGGCUCUGCACAUGGAUGUG-CUGU-CCGGACUGG-UGCGU---UAAAAAGAGAUUUAUUUAGU-AAGA------UAAAAAA-ACGUCCCGGACGGCAUUCU
AAQL01010319.1/70-235        UUUGGGAGAAAAU-U-AG-UAA-AUCUUA-GUCU-GGCUGUUCAUGUA---UA--GUGUUU-UGC-UGCCAUGGACGGCAGCAAAAGUCU-UAA-G---CCCAUGGAUGGG-GUAU-UUAAGACGUACACGU---CACUCCAUCGUAACCGAACUCAGGCAGAC--UUAGAU--UUUCUUAUUUUCGUACAAC
AAQK01009172.1/640-806       UUUGGGAGAAAAU-U-AG-UAA-AUCUUA-GUCU-GGCUGUUCAUGUA---UA--GUGUUU-UGC-UGCCAUGGACGGCAGCAAAAGUCU-UAA---GCCCCAUGGAUGGG-GUAU-UUAAGACGUACACGU---CACUCCAUCGUAACCGAACUCAGGCAGAC--UUAGAU--UUUCUUAUUUUCGUACAAC
AACY021793539.1/663-497      CACUCCAAUUCCC-C-GU-GAU-CACACC-UGAAACUUAGUUAAUGAU---GA--GUAAUU--UA-CAGCAUGGAUGCUGUA-CAAAGCG-UAG-CUUGGCCAUGGAUGGC-CUAU-CUACGCUGGUUACGU---UUACAUCAUUAACGUAAGUU-GAAGAUAA--AGUGUG--AUCCUCGGGUGCGCCGUGG
AAGA01000950.1/618-692       -------------------------------------------------------GUAAU--UAA-UUGCAUGGAUGCAAUUA-AAGGCG-UGA-CUUCGCCAUGGACGGC-GAAU-ACACGGCGGUUACGU---UCAUAU----------------------------------------------------
AAVS01000041.1/17899-17733   UACUCCAAUUCCC-C-GU-GAU-CACAC-CUGAA-ACUCAGUUAAUGAU--GA--GUAAUU--UA-CAGCACGGAUGCUGUA-CAAAGCG-UAG-CUUGGCCAUGGAUGGC-CUAU-CUACGCUGGUUACGU---UCACAUCAUUAACGUAAGUUGAAGAUACAG---UGUG--AUCCUCGGGUGCGCCGUGG
FP929050.1/1811263-1811094   UUUGGAAGAAAAU-U-AG-AAA-A-UCUUGGUGU-GCCUGUCUACACA---UA--GUGAUG-UUC-UGCCACGGAUGGCAGAACAAGGCA-GCA-UCGAGUCAUGGAUGAC-UCGU-UGUUGCCGGUCACGU---CACUCCGAGAAAAUCUAAACCAGGCAUACC-UAGACU--UUUCUUAUUUUCGUACAAC
FP929049.1/2414402-2414571   UUUGGGAGGAAAU-U-AG-AGG-UUCUUA-GUGC-CCUUGUCACAAAA---CA--GCGUUU-UGC-UGCCACGGAUGGCAGCAAAAAUCC-CCG-UCGAGCCAUGGAAGGC-UCGUCCGGGGAUGCACGCGU---CACUCUGCCACAACCCAGAUCAAGGGCAC--UUAGAA--CCUCUUAUUUCCGUACAAC
FP929049.1/1700873-1700706   UUUGGGAGAAAAU-U-AG-GCA-AUCUUAGUCUG-CCUGUCCGUAACA---CA--GUGUUG-UGC-UGCCAUGGACGGCAGCACAAGUCU-UAA--UGUGCC-CGGAUGGC-ACAU-UUAAGACACACACGU---CACUCUGCCACAAUCUGAAC-CAGGCAGCC-UUAGAU--UGUCUUAUUUUCGGACAAC
FP929049.1/139863-139696     UUUGGGAGAAAAU-U-AG-AAA-AUCUUA-GUAU-GCCUGUUAAUGCA---UA--GUGUUU-UGC-UGCCAUGGAUGGCAGCAAAAGUCU-UAA--CGUCCCAUGGACGGG-ACGU-UUAAGACGUACACGU---CACUCCUGGAAAAUCUAAAUCAGGCAUAC--UUAGUU--UUUCUUAUUUUCGGACAGC
FP929049.1/2742443-2742276   CUUGGGAGAAAAU-U-AG-AAA-AUCUUA-GUAU-GCCUGUAAAUACA---CA--GUGUUG-UGC-UGCCACGGAUGGCAGCGCAAGUCU-UAA--CGUGCCAUGGAGGGC-ACGU-UUAAGACGUACACGU---CACUUUGAAAGAGCAUAAAGCAGGCAUAC--UUAGUU--UUUCUUAUUUUCGGACAAU
FP929049.1/1556322-1556490   UUUGGGAGAAAAU-U-AG-AAA-GUCUUUGUAUG-CCUGUUCACAAUA---CA--GUGUUG-UGC-UGCCACGGACGGCAGCACAAGUCU-UAA--UGUGCC-CGGAUGGC-ACAU-UUAAGACGCACACGU---CACUCCGGCAUAAAACUAAAUCAGGCAUAC-UUAGAC--UUUCUUAUUUUCGGACAAC
ABYJ02000055.1/41634-41802   UUUGGAAGAAAAU-U-AG-AAA-AUCUUA-GCCU-GCCUGUCUAUUCA---CA--GUGAUG-UUC-UGCCACGGAUGGCAGAACAAGGCU--UC-ACGAGCCAUGGAAGGC-UCGUUGAACGCCGUUCACGU---CACUCUGAGAAAAUCUGACUCAGGCAAGC--UUAGAU--UUUGUUAUUUUCGUACAAC
FP929049.1/3640970-3641137   UUUGGAAGGAAAU-U-AG-AAA-CUCUUAGGAUG-CCUGUUCGCAACA---UA--GUGUUG-UGC-UGCCAUGGACGGCAGCACAAGUCC-UAA--UGUGCC-CGGAUGGC-GCAU-UUAGGACGUACACGU---CACUCCGCCCCAACCUGAAU-CAGGCAUGC-UUAGAG--UUUCUUAUUUUCGGACAAC
FP929050.1/3816299-3816467   UUUGGGAGAAAAU-U-AG-AAA-AACUUG-GUCU-GCCUGUAGUUACA---CA--GUGAUG-UUC-UGCCACGGAUGGCAGAACAAGGCU--UC-ACGAGCCAAGGAUGGC-UCGUUGAACGCCGGUCACGU---CACUCCGCCAUAACCUAAAUCAGGCAGAC--CUAGCU--UUUCUUAUUUUCGUACAAC
ABYJ02000038.1/41440-41607   UUUGGGAGAAAAU-U-AG-AAA-GUCUUUGUAUG-CCUGUUCACAAUA---CA--GUGUUG-UGC-UGCCACGGACGGCAGCACAAGUCU-UAA--UGUGCC-CGGAUGGC-ACAU-UUAAGACGCACACGU---CACUCCGCCACAAUAUAAAU-CAGGCAUAC-UUAGAC--UUUCUUAUUUUCGUACAAC
FP929049.1/52935-53103       UUUGGUAGAAAAU-U-AG-AAA-AUCUUA-GUAU-GUCUGUCUAUUCA---CA--GUGAUG-UUC-UGCCAUGGAUGGCAGAACAAGGCA-GCA-UCGAGUCAGGGAUGAC-UCGU-UGCUGCCGUUCACGU---CACUUUGAAAAAAUCUAAUUCAGGCAUAC--UUAGUU--UUUCUUAUUUUCGGACAUC
FP929050.1/3137508-3137342   UUUGGUAGAAAAU-U-AG-AAA-AACUUA-GUAU-GCCUGUUAACACA---CA--GUGUUG-UGC-CGCCACGGACGGCAGCCCAAGUCC-UAA--UGUGCC-CGGAUGGC-ACAU-UUAGGACGCACACGU---CACUCCGCCACACACCCCCGCAGGCAUAC--UUAGCU--UUUCUUAUUUUCGGACAUC
FP929050.1/3642761-3642592   UUUGGGAGAAAAU-U-AG-AAA-AUCUUA-GUGU-GUCUAUAGGUACA---CA--GUGAUG-UUC-UGCCACGGAUGGCAGAACAAGGCA-GCA-UCGAGUCAUGGAUGAC-UCGU-UGUUGCCGGUCACGU---CACUCCGAGAAAAUCUAACCCAGACACAC--UUAGACU-UUUCUUAUUUUCGUACAAC
#=GC SS_cons                 :::::::((((((.-.((.(((.((((--.((((.((((---------...--..(((,<<.<<<.<<<<______>>>>>>>>>,<<<<.<<<.----<<<______>>>.----.>>>>>>>,,,)))--...--------------------.))))))))..--))))..)))-)))))))):::::::
#=GC RF                      UauggaAgcagcu.U.ag.aua.cUcuUu.aauu.uucccuuuAaacA...CA..GcaAug.ccC.ggaCAuGGAUGuccGggcaAGccg.uaa.acGcGCCAUGGAuGGC.GCGU.uuacggCGGUugCGU...CAaguauaaAaAcccuuaau.ggaaaauu..UuagAg..uauCcuagcugcGuAguuu
//
# STOCKHOLM 1.0

#=GF AC   RF01732
#=GF ID   asd
#=GF DE   MarS sRNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   54.20
#=GF NC   42.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0048027; mRNA 5'-UTR binding;
#=GF DR   GO; 0045975; positive regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0009405; pathogenesis;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF RN   [2]
#=GF RM   28947755
#=GF RT   The Regulatory Small RNA MarS Supports Virulence of Streptococcus
#=GF RT   pyogenes.
#=GF RA   Pappesch R, Warnke P, Mikkat S, Normann J, Wisniewska-Kucper A, Huschka F,
#=GF RA   Wittmann M, Khani A, Schwengers O, Oehmcke-Hecht S, Hain T, Kreikemeyer B,
#=GF RA   Patenge N
#=GF RL   Sci Rep. 2017;7:12241.
#=GF RN   [3]
#=GF RM   19888332
#=GF RT   A genome-wide analysis of small regulatory RNAs in the human pathogen
#=GF RT   group A Streptococcus.
#=GF RA   Perez N, Trevino J, Liu Z, Ho SC, Babitzke P, Sumby P
#=GF RL   PLoS One. 2009;4:e7668.
#=GF CC   Interacts with the 5'UTR of the mga transcript (the multiple virulence
#=GF CC   gene regulator gene) and was renamed MarS for mag-activating regulatory
#=GF CC   sRNA. In MarS deletion strains expression of mga and several Mga-activated
#=GF CC   genes is reduced. This down-regulation of virulence factors leads to
#=GF CC   increased susceptibility of the deletion strain to phagocytosis, reduced
#=GF CC   adherence to human keratinocytes. However, the lack of MarS increased
#=GF CC   bacterial dissemination and tolerance towards oxidative stress.[2] Called
#=GF CC   SR914400 in [3].
#=GF WK   Asd_RNA_motif
#=GF SQ   31


BA000034.2/1038560-1038410   AUGCGAUGAGUCGAUU--GUGACUGCAAAGUCACUUUUGC--GCA-GGGGAGGUCAU-----------------------UAA-GGCGGGAAGCC---GACUUUGAUAAUCUGUGUGAACCAUUUUAUCACAAUCUUAUUUA-UUAAGAAUGCCCCUU---GGAUUGAGA--UAU--UCUCAAUCCUUUUU
AE007317.1/905038-905180     AUGCGAUGAGUCGAUAG-GUAGUCUUCGGACUACUAUUGA--GCAUAAGGAGGUCA------------------------UAA-CGCAGGA-GCG---GACCUUGAUGAGUUGUGUGAACCUGCUCAUCA------CAU----GAAG--AUGCCUCUUA--GUCCCUAGUCUAGC-GACU-GGGAUUUUUA
AAFA03000003.1/43666-43815   AUGCGAUGAGCCGAGUA-GUGAC--UUU-GUCACUUUCGAC-GCU-AGGGAGGUCU-UCA-----UUUAAU------UGA-AA-CGCAGGA-GCG---GACCUUGAAUAGUUGUGUGAACCUUCUAUUCU------CAUCG--GAAACGAUGCCCU-----GGCCCACC--UUUAU--GGUGGGCCUUUUU
CP000829.1/950516-950366     AUGCGAUGAGUCGAUU--GUGACUGCAAAGUCACUUUUGC--GCA-GGGGAGGUCAU-----------------------UAA-GGCGGGAAGCC---GACUUUGAUAAUCUGUGUGAACCAUUUUAUCACAAUCUUAUUUA-UUAAGAAUGCCCCUU---GGAUUGAGA--UAU--UCUCAAUCCUUUUU
CP000919.1/911676-911818     AUGCGAUGAGUCGAUAG-GUAGUCUUCGGGCUACUAUUGA--GCAUAAGGAGGUCA------------------------UAA-CGCAGGA-GCG---GACCUUGAUGAGUUGUGUGAACCUGCUCAUCA------CAU----GAAG--AUGCCUCUUA--AUCCCUAGUCUAGC-GAUUGGGGAUUUUU-
CP000419.1/1185932-1185782   AUGCGAUGAGUCGAUU--GGCUC-UUUA-GAGCCUUUUGC--GC-UGAGGAGGU---CAA-----CAUUAAA-----UUGUAA-CGCAGGA-GCG---GACCUUGAGUAGUUGUGUGAACCUGCUACUCU------CAUC---GAAA-GAUGCCUCUUA--UCCCUUGCC-GUUU--GGUAGGGGAUUUUU
FM211187.1/908905-909047     AUGCGAUGAGUCGAUAG-GUAGUCUUCGGGCUACUAUUGA--GCAUAAGGAGGUCA------------------------UAA-CGCAGGA-GCG---GACCUUGAUGAGUUGUGUGAACCUGCUCAUCA------CAU----GAAG--AUGCCUCUUA--AUCCCUAGUCUAGC-GAUUGGGGAUUUUU-
CP000387.1/1221575-1221437   GUGCGAUGAGUCGAUA--UGCAGAUUUU-CUGCAAAUUGAA-GCA-UGGGAGGUCA------------------------UAA-CGCAGGA-GCG---GACCUUGAUCAGUUGUGUGAACCUGCUGAUCA------CAC----AAAA--GUGCCCUUA---UCCCCAGUC-UACG--GAUUGGGGAUUUUU
ABAA01000002.1/167881-168023 AUGCGAUGAGUCGAUAG-GUAGUCUUCGGACUACUAUUGA--GCAUAAGGAGGUCA------------------------UAA-CGCAGGA-GCG---GAUCUUGAUGAGUUGUGUGAACCUGCUCAUCA------CAU----GAAG--AUGCCUCUUA--GUCCCUAGUCUAGC-GACU-GGGAUUUUUA
CP000024.1/1150990-1150840   AUGCGAUGAGUCGAUU--GGCUC-UUUA-GAGCCUUUUGC--GC-UGAGGAGGU---CAA-----CAUUAAA-----UUGUAA-CGCAGGA-GCG---GACCUUGAGUAGUUGUGUGAACCUGCUACUCU------CAUC---GAAA-GAUGCCUCUUA--UCCCUUGCC-GUUU--GGUAGGGGAUUUUU
CP000260.1/989456-989306     AUGCGAUGAGUCGAUU--GUGACUGCAAAGUCACUUUUGC--GCA-GGGGAGGUCAU-----------------------UAA-GGCGGGAAGCC---GACUUUGAUAAUCUGUGUGAACCAUUUUAUCACAAUCUUAUUUA-UUAAGAAUGCCCCUU---GGAUUGAGA--UAU--UCUCAAUCCUUUUU
AAJR01000023.1/31271-31407   AUGCGAUGAGUCGAUAU-GUGGU--UUU-ACCACUAUUGC--GC--AGGGAGAUUA------------------------UAAACGCAGGA-GCG---GAUCUUGAUAAGUUGUGUGAACCUUCUUAUCA------CACUU--GAAAAGGUGCCCUUAGC-UUACUA----CUAC-----UUGUAAUUCAU
CP000425.1/1641549-1641391   AUGCGAUGAGUCGAAUAAUUCUACUUUUGUAGAAUUUCGAA-GC-UAAGGAGUGC--UGGGAAAUUGA----GUUUUCCG----CGCAGGAAGCGUGAGUAUUUGUCAAAAUGUGUGAACCUUUUUGACA------CACU-U-UU---AGUGCCUUAAAAAGCCCUU----GUAA-----AAGGGCUUUUU
CP000918.1/969596-969738     AUGCGAUGAGUCGAUAG-GUAGUCUUCGGACUACUAUUGA--GCAUAAGGAGGUCA------------------------UAA-CGCAGGA-GCG---GACCUUGAUGAGUUGUGUGAACCUGCUCAUCA------CAU----GAAG--AUGCCUCUUA--GUCCCUAGUCUAGC-GACU-GGGAUUUUUA
AAJP01000010.1/35943-36079   AUGCGAUGAGUCGAUAU-GUGGU--UUU-ACCACUAUUGC--GC--AGGGAGAUUA------------------------UAAACGCAGGA-GCG---GAUCUUGAUAAGUUGUGUGAACCUUCUUAUCA------CACUU--GAAAAGGUGCCCUUAGC-UUACUA----CUAC-----UUGUAAUUUCU
AM406671.1/839782-839941     AUGCGAUGAGUCGAAUAAUUCUACUUUUGUAGAAUUUCGAA-GC-UAAGGAGUGC--UGGGAAAUUGA----GUUUUCCG----CGCAGGAAGCGUGAGCAUUUGUCAAAAUGUGUGAACCUUUUUGACA------CACU-U-UU---AGUGCCUUAAAA-AGCCCUU---GUAA----AAGGGCUUUUUU
CP000261.1/946984-946834     AUGCGAUGAGUCGAUU--GUGACUGCAAAGUCACUUUUGC--GCA-GGGGAGGUCAU-----------------------UAA-GGCGGGAAGCC---GACUUUGAUAAUCUGUGUGAACCAUUUUAUCACAAUCUUAUUUA-UUAAGAAUGCCCCUU---GGAUUGAGA--UAU--UCUCAAUCCUUUUU
CP000262.1/1020618-1020468   AUGCGAUGAGUCGAUU--GUGACUGCAAAGUCACUUUUGC--GCA-GGGGAGGUCAU-----------------------UAA-GGCGGGAAGCC---GACUUUGAUAAUCUGUGUGAACCAUUUUAUCACAAUCUUAUUUA-UUAAGAAUGCCCCUU---GGAUUGAGA--UAU--UCUCAAUCCUUUUU
AE005176.1/1668839-1668682   AUGCGAUGAGUCGAAUAAUUCUACUUU-GUAGAAUUUCGAA-GC-UAAGGAAUAC--UGGGAAAUUGG----GUUUUCCG----CGCAGGAAGCGUGAGUAUUUGUCAAAUUGUGUGAACCUUUUUGACA------CACU-U-UU---AGUGCCUUUAAAAGCCCUC----GAAA-----GAGGGCUUUUU
CP000407.1/684117-684266     CUUGGUUGAC--AAGUU-GAGUUCUUUCCCACUCCCUUCGACGC-UAGGGAGGUCU-UCA-----UUUAAU------UGA-AA-CGCAGGA-GCG---GACCUUGAAUAGUUGUGUGAACCUUCUAUUCU------CAUCG--GAAACGAUGCCCUUG---CCCACC----UUUAU----GGUGGGCUUUU
CP000114.1/1119613-1119477   AUGCGAUGAGUUGAUAU-GUGGU--UUU-ACCACUAUUGC--GC--AGGGAGAUUA------------------------UGAACGCAGGA-GCG---GAUCUUGAUAAGUUGUGUGAACCUUCUUAUCA------CACUU--GAAAAGGUGCCCUUAGC-UUACUA----CUAC-----UUGUAAUUCCU
ABAD01000016.1/11693-11835   AUGCGAUGAGUCGAUAG-GUAGUCUUCGGGCUACUAUUGA--GCAUAAGGAGGUCA------------------------UAA-CGCAGGA-GCG---GACCUUGAUGAGUUGUGUGAACCUGCUCAUCA------CAU----GAAG--AUGCCUCUUA--AUCCCUAGUCUAGC-GAUUGGGGAUUUUU-
AE009948.1/1063292-1063156   AUGCGAUGAGUCGAUAU-GUGGU--UUU-ACCACUAUUGC--GC--AGGGAGAUUA------------------------UAAACGCAGGA-GCG---GAUCUUGAUAAGUUGUGUGAACCUUCUUGUCA------CACUU--GAAAAGGUGCCCUUAGC-UUACUA----CUAC-----UUGUAAUUUCU
AE009949.1/972072-971922     AUGCGAUGAGUCGAUU--GUGACUGCAAAGUCACUUUUGC--GCA-GGGGAGGUCAU-----------------------UAA-UGCGGGAAGCC---GACUUUGAUAAUCUGUGUGAACCAUUUUAUCACAAUCUUAUUUA-UUAAGAAUGCCCCUU---GGAUUGAGA--UAU--UCUCAAUCCUUUUU
CP000920.1/934330-934472     AUGCGAUGAGUCGAUAG-GUAGUCUUCGGACUACUAUUGA--GCAUAAGGAGGUCA------------------------UAA-CGCAGGA-GCG---GACCUUGAUGAGUUGUGUGAACCUGCUCAUCA------CAU----GAAG--AUGCCUCUUA--GUCCCUAGUCUAGC-GACU-GGGAUUUUUA
J02667.1/46-182              AUGCGAUGAGUCGAUU--GUGGU-UUAU-ACCACAUACG----C-UAAGGAGAUCA------------------------UAA-UGCAGGA-GCA---GAUCUUGGCAAGUUGUGUGAACCUGCUUGCCA------CACUUAAUCAAAAGUGCCUUUU---CCCUUGU---AAUA----ACAAGGGCUUUU
ABFS01000002.1/115091-115233 AUGCGAUGAGUCGAUAG-GUAGUCUUCGGGCUACUAUUGA--GCAUAAGGAGGUCA------------------------UAA-CGCAGGA-GCG---GACCUUGAUGAGUUGUGUGAACCUGCUCAUCA------CAU----GAAG--AUGCCUCUUA--GUCCCUAGUCUAGC-GACU-GGGAUUUUUA
AE005672.3/956780-956922     AUGCGAUGAGUCGAUAG-GUAGUCUUCGGACUACUAUUGA--GCAUGAGGAGGUCA------------------------UAA-CGCAGGA-GCG---GACCUUGAUGAGUUGUGUGAACCUGCUCAUCA------CAU----GAAG--AUGCCUCUUA--GUCCCUAGUCUAGC-GACU-GGGAUUUUUA
AJ421083.1/209-345           AUGCGAUGAGUCGAUAU-GUGGU--UUU-ACCACUAUUGC--GC--AGGGAGAUUA------------------------UAAACGCAGGA-GCG---GAUCUUGAUAAGUUGUGUGAACCUUCUUGUCA------CACUU--GAAAAGGUGCCCUUAGC-UUACUA----CUAC-----UUGUAAUUUCU
CP000003.1/919140-918990     AUGCGAUGAGUCGAUU--GUGACUGCAAAGUCACUUUUGC--GCA-GGGGAGGUCAU-----------------------UAA-GGCGGGAAGCC---GACUUUGAUAAUCUGUGUGAACCAUUUUAUCACAAUCUUAUUUA-UUAAGAAUGCCCCUU---GGAUUGAGA--UAU--UCUCAAUCCUUUUU
CP000023.1/1153119-1152969   AUGCGAUGAGUCGAUU--GGCUC-UUUA-GAGCCUUUUGC--GC-UGAGGAGGU---CAA-----CAUUAAA-----UUGUAA-CGCAGGA-GCG---GACCUUGAGUAGUUGUGUGAACCUGCUGCUCU------CAUC---GAAA-GAUGCCUCUUA--UCCCUUGCC--GUUU-GGUAGGGGAUUUUU
#=GC SS_cons                 :::::::::::<<<<<-.<<<<<<____>>>>>>>>>>>,..,,.,((((<<<<--........................---.<<<____.>>>...->>>><<<<<<<<___________>>>>>>>>......<<<<...____.>>>>)))),,,..<<<<<<<<<.____..>>>>>>>>>:::::
#=GC RF                      AUGCGAUGAGUCgagga.guggccuUuuggccacccucGa..GC.UggGGAgguCA........................UAA.cGCAGGA.GCg...GaccUuGacgAgcUGUGUGAACCUgcUcguCa......cAcc...uaAA.ggUgCCccUua..gccccgggc.uuau..gcccggggcUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01733
#=GF ID   atoC
#=GF DE   atoC RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   58.20
#=GF NC   40.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   AtoC_RNA_motif
#=GF SQ   8


CP001124.1/4343880-4343790 GGUAUAAUGUGAAUAGAU-----AACAGAGUUGCGGAGGAUC-AAAGGAUCCUCCU--UCCCCUAGCCGACUUGCCCUCCUAGUCGCUAGGGUUUUUUU
CP000698.1/4839082-4838991 GGUAUACUAUAAUCA-AAG----AUAAGAGUUGC-GAGGAUC-GAAAGAUCCUCAUUAUGCCCUAGCUGACUUGCCCUCCUAGUCACUAGGGUGUUUUU
AE017180.1/3694623-3694713 GCUAUAGUUUACUUAGA------AAAAGAGUUGC-GAGGGUC-GAGAGAUCCUCAUUAUGCCCUAGUCGACUUUCCCUCCUAGUCGCUAGGGUGUUUUU
CP001390.1/620844-620935   GUUAAACUAUAAUCA-AAG----AUAAGAGUUGC-GAGGGUC-GUGAGAUCCUCAUUAUGCCCUAGCUGACUUGCCCUCCUAGUCACUAGGGUGUUUUU
CP000482.1/292999-292905   GCUAUACUAAAAAUAGAUAGACGAACAGA-UUGC-GAGGUUCCACGCGAACCUCAU-GUGCCCUGG-UAAUUUUCCCUCCUAGUUGCCAGGGUGUUUUU
CP001089.1/351026-350937   AGUACACUAUUAGUAGAGA----AUAUGU-UUGC-GAGCCCCCUCGGGGGUCUCAU--CGCCCUCG-UUGCCGCCCCUCCUGGUGACGGGGGCUUUUUU
CP000148.1/67665-67752     GGUAUACUAUAAGUG-A--------AAGAAUUGC-GAGGGUC-GCAAGGCCCUCAUUAUGCCCUAGUUGACUUUCCCUCCUAGUCGCUAGGGUGUUUUU
AE017180.1/1810322-1810409 GAAUACGGCGAAGAGGAUG----AAGAGUAGUGU-GCUGGUG-CAAUUGUAAGCAUUAUGGGGGGCCUGCCGAUGU-----CGGAGGCCCCUUUUUUAG
#=GC SS_cons               :::::::::::::::::::....:::::::::::.<<<<<<<.____>>>>>>>-----<<<<<<<-<<<<<_________>>>>>>>>>>>>::::::
#=GC RF                    GgUAuAcUauAAguAGAug....AaaAGaaUUGC.GaGgguc.aaaagaccCuCAUUAUgcccugGCcgaCuuuCCCUCCUaGucgCcaggguuUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01734
#=GF ID   Fluoride
#=GF PI   crcB;
#=GF DE   Fluoride riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   31.00
#=GF TC   31.00
#=GF NC   30.80
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.09 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF DR   GO; 1902617; response to fluoride;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF RN   [2]
#=GF RM   22194412
#=GF RT   Widespread genetic switches and toxicity resistance proteins for fluoride.
#=GF RA   Baker JL, Sudarsan N, Weinberg Z, Roth A, Stockbridge RB, Breaker RR
#=GF RL   Science. 2012;335:233-235.
#=GF RN   [3]
#=GF RM   28719589
#=GF RT   An excited state underlies gene regulation of a transcriptional
#=GF RT   riboswitch.
#=GF RA   Zhao B, Guffy SL, Williams B, Zhang Q
#=GF RL   Nat Chem Biol. 2017;13:968-974.
#=GF CC   Previously known as crcB RNA.
#=GF WK   CrcB_RNA_motif
#=GF SQ   287


BAAV01024370.1/684-614       UCAGNNAUCGGGAAUGAU-GUUCUCCCC------------UGGGA-----------------------------------------------------------------UUCCAAAA--CCGC----------------------UGUUUC----------------------------------------------------GCUGAUGACGUCUGCUUUUUU
BABE01001448.1/1961-1891     GUCCGUGACGGCGAUGGA-UCC-CGCCU------------GGC----------------CGAU-------------------------------------------------GCCGAA--CUGCC---------------------GAUCU----------------------------------------------------GGCUGAUGGUUCCUGCCCCGUC
BAAV01007000.1/1090-1152     CUUUGCACCGGCUAUGGG-AUU-AGCCUU--------------------------------------------------------------------------------------UAA--CCGCCC--------------------UUCG----------------------------------------------------GAGCUGAUGAUCCCUACAAUUUG
BABC01000066.1/7792-7723     CUGGGAUUCGGCGAUGGG-ACC-CGCCU------------GAA----------------CUUGU------------------------------------------------UUCGAA--CCGC----------------------ACACU-----------------------------------------------------GCUGAUAGUUCCUACACACGA
BABE01006493.1/378-447       UAAGGAACCGGCGAUGGA-ACC-CGCCU------------GAA----------------CUCGU------------------------------------------------UUCGAA--CCGC----------------------ACACU-----------------------------------------------------GCUGAUAGUUCCUACACACGA
BABB01014491.1/724-793       UGGAGAACCGGCGAUGGG-ACC-CGCCU------------GAA----------------CUUGU------------------------------------------------UUCGAA--CCGC----------------------ACACU-----------------------------------------------------GCUGAUAGUUCCUACACACGA
BABE01000053.1/15068-15137   UGGAGAACCGGCGAUGGG-ACC-CGCCU------------GAA----------------CUUGU------------------------------------------------UUCGAA--CCGC----------------------ACACU-----------------------------------------------------GCUGAUAGUUCCUACACACGA
BABF01001201.1/3795-3726     UGGAGAACCGGCGAUGGG-ACC-CGCCU------------GAA----------------CUUGU------------------------------------------------UUCGAA--CCGC----------------------ACACU-----------------------------------------------------GCUGAUAGUUCCUACACACGA
BAAY01017851.1/254-182       UAGCUGGCAGGGAAUGAA-GUUCUCCCC------------AGGC---------------AGU-------------------------------------------------GCCUAAA--CCGCU---------------------AUUAC----------------------------------------------------AGCUGAUGACUUCUGUUGUUUA
BABB01015950.1/548-449       AAUAUUACUGGGAAUGAG-GUU-CUCCCA-----------GGAACGAGA----------UAGAAAUAGCUAAAUC-------------------------------UUUCGUUCAUAA--CCGCUU--------------------GAUUAUA-------------------------------------------------AAGCUGAUGACUUCUGCAAAGCG
BABF01003476.1/1904-1985     CUGUUACCCGGGAAUGAG-GUC-UCCCA------------UGGUAGUGU----------AAU--------------------------------------------AU-UUACCAGAA--CCGCU---------------------UAUGAC---------------------------------------------------AGCUGAUGGCUUCUGCAUUGUG
BAAV01013884.1/268-196       AAUAUCAAAGGGAAUGAA-GUACUCCCU------------UGG----------------GAAA-------------------------------------------------CCUAAA--CUGCUU--------------------AUUC----------------------------------------------------AAGCUGAUGACUUCUACGAUUUU
BABG01014606.1/762-690       CGAAUGAGAGGGAAUGAA-GUUCUCCCU------------AGG----------------GAAA-------------------------------------------------CCAGAA--CUGCUG--------------------AAUA----------------------------------------------------UAGCUGAUGACUUCUACGAUUAU
BAAZ01021286.1/777-699       AGAAUAAACGGGAAUGAA-GUU-CUCCCG-----------AAGUAA-------------CCAGA---------------------------------------------UUACUUGAA--CCGCU---------------------UUAAA----------------------------------------------------AGCUGAUGACUUCUGCGACGAA
BAAV01021889.1/203-131       GAAACAAAUGGGAAUGAAUGUC-UCCCC------------GGGA---------------UCA-------------------------------------------------UCCCGAA--CCGCU---------------------UAUUA----------------------------------------------------AGCUGAUGACUUCUGUGAUAAC
BABG01014343.1/547-474       AUCCAGAACGGGAAUGAG-GUUCUCCCA------------CGAU---------------UUUUG-----------------------------------------------AUCGAAA--CCGCC---------------------AAAA-----------------------------------------------------GGCUGAUGACUUCUGUGCAUGG
BABG01003409.1/431-358       AAAGAAAAAGGGAAUGAA-GUUCUCCCU------------CGAA---------------GAGA------------------------------------------------UUCGAAA--CCGCU---------------------UAUUA----------------------------------------------------AGCUGAUGACUUCUGUGUAAUG
BABC01003766.1/468-402       AAGUGAAUAGGUGAUGGU-GUU-CGCCUU--------------------------------------------------------------------------------------UAA--AUGCUA--------------------ACGAAAGA------------------------------------------------UAGCUAAUGACGCCUACUAAAGU
BABF01015109.1/43-109        AAGUGAAUAGGUGAUGGU-GUU-CGCCUU--------------------------------------------------------------------------------------UAA--AUGCUA--------------------ACGAAAGA------------------------------------------------UAGCUAAUGACGCCUACUAAAGU
BAAW01000138.1/2195-2134     AGCCUCACAGGGGAUGGC-AUUCCCCCUU--------------------------------------------------------------------------------------GAA--CCGCC---------------------AUGU-----------------------------------------------------GGCUAAUGAUGCCUGCUUUUUA
CP000254.1/1236994-1237053   AAUCCUGCCGGUGAUGAG-AUC-CACCGU--------------------------------------------------------------------------------------AAA--CCGC----------------------CCGCU-----------------------------------------------------GCUAAUGACUUCUACCCGGAA
CP000822.1/1484941-1485003   UUUUUUACAGGAGAUGGC-AUU-CCUCCUCA------------------------------------------------------------------------------------UAA--CCGCC---------------------CUCU-----------------------------------------------------GGCUGAUGAUGCCUGCACAUUC
CP000759.1/989075-989138     GUACAUGAUGGGAAUGGG-GUUCUCCCG---------------------------------------------------------------------------------------AAA--CUGCCA--------------------GCAAU---------------------------------------------------UGGCUGAUGACUCCUGCUUGAAU
CP000854.1/4256142-4256216   ACUAGCAGCGGCGAUGGG-GCU-CGCCA------------GGAAG--------------CUCGA----------------------------------------------CUUCUGAA--CCGCC---------------------AGCC-----------------------------------------------------GGCUGAUGGCACCUGCGAACAA
CP000885.1/3806199-3806127   CUUACUGACGGGAAUGAA-GUU-CUCCCA-----------AGGU---------------UUU-------------------------------------------------ACCUAAA--CUGCU---------------------UAUAA----------------------------------------------------AGCUGAUGACUUCUGUGAAUUA
AE004091.2/4914637-4914575   UUGCCGACAGGAGAUGGC-AUUCCUCCUU--------------------------------------------------------------------------------------CAA--CCGCCC--------------------CUG-----------------------------------------------------GGGCUGAUGAUGCCUACGCAUGA
CP000360.1/3066978-3066906   CAACUUCAUGGCGAUGGA-GUU-CGCCC---------------------------------------------------------------------------------------UAA--CCGC-CGCAGC---------------CACGUU---------------------------------------------GCUGCGUGCUGAUAACUCCUGCCGACAC
CP000125.1/1222860-1222794   GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
CP000545.1/1653068-1653134   GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
BX950851.1/1468958-1468853   CACUAAAGCGGAGAUGAC-AUUCCUCCC------------UACC---------------CUAACGCCGCCAAAAAUGCUGGCAGCCUGAAGUACAA---------------GGUACAA--CCGCC---------------------ACCC-----------------------------------------------------GGCUGAUGAUGUCUACGUCCAC
CP000270.1/1757402-1757341   UGCUGCGCUGGAGAUGGC-AUU-CUCCUU--------------------------------------------------------------------------------------UAA--CCGCC---------------------CUUAU----------------------------------------------------GGCUGAUGAUGCCUGCUCGCCC
AAVO02000004.1/13914-13993   AAAUAUAAAGGGAAUGAG-GUU-CUCCCU-----------AAGUAA-------------UAAAA---------------------------------------------UUACUUAAA--CCGCUU--------------------AUGA----------------------------------------------------AAGCUGAUGACUUCUGCGAGUAA
CP000547.1/225172-225238     GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
AAFX01080011.1/664-577       UUUGGGCGCGGUGAUGGA-GUU-CACCA------------UCUACUA------------CAAA---------------------------------------------UA-UGGAAAA--CCGUCCAACU----------------UCUUU-----------------------------------------------AGCCGGACUAAUAACUCCUACCUAUAA
CP000227.1/4763720-4763779   AUAAUUAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
CP000923.1/40525-40583       AUACCAUAAGGCGAUGGA-GCU-CGCCA---------------------------------------------------------------------------------------UAA--AUGCG---------------------GAA------------------------------------------------------CGCUGAUGGCUCCUAUUAGGAG
CP000557.1/2739339-2739277   AACAUACUAGGCGAUGGG-GUU-CGCCA---------------------------------------------------------------------------------------UAA--CCACCG--------------------GCUUC---------------------------------------------------CUGCUGAUGACUCCUGCUGCGUU
AADL01000991.1/122-193       UGUAGUCCGUGGAAUGGC-GUU-UCCACUAAUUC---------------------------------------------------------------------------------AAA--CCGCCGGCU-----------------GA---------------------------------------------------AGCUGGCUGAUGACGCCUGCUUGAAA
ABQR01000024.1/52165-52090   UGUUUACAGGGGAAUGAG-GUU-CUCCCU-----------UAGU---------------GUCAU-----------------------------------------------ACUAAAA--CCGCUU--------------------AUUU----------------------------------------------------AAGCUGAUGACUUCUGUGUGAUU
CP001139.1/34842-34908       CCAAAUACGGGUGAUGGA-UUUCCACCUU--------------------------------------------------------------------------------------UAA--CCGCUCU-------------------AUUUU--------------------------------------------------AGAGAUAAUGAUUCCUACUAUAGC
CP000744.1/5109630-5109568   UAGCCGGCAGGAGAUGGC-AUUCCUCCUU--------------------------------------------------------------------------------------CAA--CCGCCC--------------------CUG-----------------------------------------------------GGGCUGAUGAUGCCUACGCAUGA
CP000481.1/804142-804061     CCUGAUGACGGCGAUGGA-GUC-CGCCU------------GACCGGUGU----------GAUCG------------------------------------------ACACCGG-CGAA--GUGUC---------------------ACCU-----------------------------------------------------GGCUGAUGGCUCCUACCUCCCA
CP000525.1/1388196-1388262   GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
CP000975.1/1993796-1993891   GAAAUCCCUGGCAAUGGA-GUU-UGCCG------------UCCCGCCGGU---------UCGAAGU---------------------------------------ACU--UGGGAAAA--CCUCCUUUC-----------------UUGAAAA----------------------------------------------GAAAGGCUGAUAACUCCUACUUCAAC
FM177140.1/2571522-2571586   AGAAGAACAGGCGAUGAU-GUU-CGCCG---------------------------------------------------------------------------------------CAA--AUGAUUG-------------------UGUAG--------------------------------------------------CAAUCUGAUGACGUCUACUGAAAC
AE010299.1/4831358-4831427   UGUAACAAUGGUGAUGAG-GUC-CACCC------------UGAU---------------AAUU------------------------------------------------GUCAAAA--CCGC----------------------UUAU------------------------------------------------------GCUGAUGACUUCUACACAACU
ABQQ01000001.1/79958-80027   UAAGGAACCGGCGAUGGA-ACC-CGCCU------------GAA----------------CUCGU------------------------------------------------UUCGAA--CCGC----------------------ACACU-----------------------------------------------------GCUGAUAGUUCCUAUACACGA
ABYT01000096.1/44476-44400   AAUCUUUUUGGGAAUGAA-GUU-CUCCCU-----------UAGU---------------UUAAA-----------------------------------------------ACUAAAA--CCGCUU--------------------UUUAU---------------------------------------------------AGGCUGAUGACUUCUGUGUUUUU
CP000004.1/152206-152146     CCUGGACAAGGGGAUGGG-GUU-CCCCUG--------------------------------------------------------------------------------------AAA--CCGCC---------------------GCAA-----------------------------------------------------GGCUGAUGACUCCUCUGUGCCG
CU695240.1/565243-565309     CCGGCUUGCGGAGAUGGC-AUACCUCCCU--------------------------------------------------------------------------------------UAA--CCGCCGA-------------------UCACC--------------------------------------------------UCGGCUGAUGAUGCCUACAAGUUC
ABQC02000019.1/404312-404380 UCGAAUCAAGGGAAUGGG-ACU-UCCCU-------------------------------GUGAU---------------------------------------------------AAA--CCGCUA--------------------AUGAAG--------------------------------------------------UAGCUGAUAGUUCCUACCGGAGC
CU468135.1/2891609-2891537   GUAUCACAAGGUGAUGGU-GCUCCACCU-------------------------------UUCC----------------------------------------------------CAA--CCGCCCUGA-----------------UUUUU------------------------------------------------UC-GGGCUGAUGACGCCUGAUAAAAC
ABLC01000083.1/20871-20937   GUUGGCCGUGGAGAUGGC-AUUCCUCCCU--------------------------------------------------------------------------------------UAA--CUGCCGA-------------------UUCGU--------------------------------------------------UCGGCUGAUGAUGCCUACACACCC
FM954972.2/699217-699134     UAGCCAUCAGGUGAUGGG-GUUCCACCU------------AAGC---------------UUUU------------------------------------------------GCUUCAA--CCGC--CCGUUC--------------UUUU----------------------------------------------GAACCGU-GCUAAUGACUCCUACAGAAUC
ABVY01000154.1/6708-6604     UACUAAAGCGGAGAUGAC-AUUCCUCCC------------UACCCU-------------CGCGCAGCCAAAACGCUGACAGCCUUAAAAAC------------------AGGGUACAA--CCGCC---------------------ACUC-----------------------------------------------------GGCUAAUGAUGUCUACGUCCAC
AE017198.1/798633-798695     AUUUAAUAUGGUGAUGGU-GUU-CACCA-------------------------------AUU-----------------------------------------------------UAA--CCGAU---------------------UAAU-----------------------------------------------------AUCUGACGACGCCUACUUUCUU
CP000884.1/3908908-3908971   CUGCACGAUGGGAAUGGA-GCU-UCCCG---------------------------------------------------------------------------------------AAA--CCUCCCU-------------------GCGA---------------------------------------------------AGGGCUGAUGGCUCCUGCCUUGGU
CP000697.1/351714-351653     GGCCGCGCCGGCGAUGGG-GUU-CGCCGU--------------------------------------------------------------------------------------GAA--CCGCCC--------------------GCG-----------------------------------------------------GGGCUGAUGACUCCUGUUUCGAU
AAFX01005291.1/667-735       ACGUCGCGUGGUGGUGGA-GUC-CACCU---------------------------------------------------------------------------------------GAA--CCGCCGCUC-----------------UGACU------------------------------------------------GGACGGCCAAUGACUCCUACGCAUAG
AP008230.1/2441450-2441510   AAUCAGAUAGGCGAUGGA-GUU-CGCCUU--------------------------------------------------------------------------------------UAA--CCGCC---------------------GCUU-----------------------------------------------------GGCUAAUGACUCCUGCCGGUUA
AAAK03000106.1/3476-3542     AGUGAAUAGGUGUAUGGU-GUUCGCCUU---------------------------------------------------------------------------------------UAA--AUGCUA--------------------ACGAAAGA------------------------------------------------UAGCUAAUGACGCCUACUAAAGU
CP000903.1/4869306-4869365   AUAAUCAUAGGUGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--CCGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
CP000678.1/1167738-1167808   UAAUAACUUGGUGAUGGG-GUU-CACCA------------GAAA---------------CUUAU-----------------------------------------------UUUCAAA--CCGC----------------------AAUU------------------------------------------------------GCUGAUAACUCCUAUGUUAUA
CP000682.1/1397941-1398019   UAGGUUACUGGGGAUGGC-GUC-CCCCA------------GGG----------------CUUGUU-----------------------------------------------CCCGAA--CCGCCU--------------------GAUACAUGA-----------------------------------------------AGGCUGAUGACGCCUAUCUCUUG
FM177140.1/2570801-2570747   AAAUUAAAUGGCGAUGGU-GUU-CGCCUA--------------------------------------------------------------------------------------UA---CG------------------------CAAGU-------------------------------------------------------UGAUGACACCUACCUUGAG
CP000863.1/439864-439930     CUAAAACAGGGAGAUGGC-AUUCCUCCCUUGAA----------------------------------------------------------------------------------AAA--CCGCC---------------------GUAUU----------------------------------------------------GGCUAAUGAUGCCUACGUUACC
AM920689.1/2646740-2646665   GGCCAUCUCGGAGAUGGC-GUUCCUCCGCGCUGUACCAU----------------------------------------------------------------------------CAA--CCGUAGC-------------------GAUC---------------------------------------------------GCUACUGAUGACGCCUACAAGAAC
CP000812.1/982299-982238     AAUAAGCCUGGUGAUGGA-GUC-CACCGU--------------------------------------------------------------------------------------UAU--UUGCC---------------------UUAAA----------------------------------------------------GGCUGAUGACUCCUACUUGAAU
CP001001.1/4759637-4759698   CGUCCCGAUGGGGAUGGA-GUU-CCCCG---------------------------------------------------------------------------------------AAA--CCGCCC--------------------GUCA----------------------------------------------------GGGCUGAUGACUCCUACCGCGAA
CP000011.2/224010-224076     GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
CP000250.1/3360939-3360999   AACGGCGAUGGGGAUGGA-GUC-CCCCGA--------------------------------------------------------------------------------------CAA--CCGCC---------------------GCGA-----------------------------------------------------GGCUGAUGACUCCUACCGGGCG
CP000423.1/2429871-2429817   AAAUUAAAUGGCGAUGGU-GUU-CGCCUA--------------------------------------------------------------------------------------UA---CG------------------------CAAGU-------------------------------------------------------UGAUGACACCUACCUUGAG
ABYW01000007.1/311285-311355 UAAUAACUUGGUGAUGGG-GUU-CACCA------------GAAA---------------CUUAU-----------------------------------------------UUUCAAA--CCGC----------------------AAUU------------------------------------------------------GCUGAUAACUCCUAUGUUAUA
CR543861.1/406046-406112     CGACAGAUAGGAGAUGAC-AUUCCUCCUCGCAA----------------------------------------------------------------------------------AAA--CCGCC---------------------GUUCU----------------------------------------------------GGCUAAUGAUGUCUACGUUACC
CP000780.1/914945-915010     UCUGUCAGGGGCGAUGAA-GUC-CGCCG---------------------------------------------------------------------------------------UAA--CCGCCUUAC-----------------CCUAA---------------------------------------------------AGGCUGAUGACUUCUGUUUUAUG
CP000100.1/2263916-2263989   UACAAGCAGGGUGAUGGA-GCU-CACCU---------------------------------------------------------------------------------------CAA--CCGCGCACUCGG--------------CAUGGC--------------------------------------------CCGAU--CGCUGAUGGCUCCUACAGUUCU
BABD01000872.1/1124-1056     CAAAGUCAGGGGAAUGGG-ACU-UCCCU-------------------------------GUUAU---------------------------------------------------AAA--CCGCUA--------------------AUAAAG--------------------------------------------------UAGCUGAUAGUUCCUGCCGGAGU
CP000438.1/5078189-5078127   UUGCCGACAGGAGAUGGC-AUUCCUCCUU--------------------------------------------------------------------------------------CAA--CCGCCC--------------------CUG-----------------------------------------------------GGGCUGAUGAUGCCUACGCAUGA
CP000967.1/2767544-2767620   UCGGGAUUCGGAGAUGGC-GUUCCUCCGCGCAGUUCCAUC---------------------------------------------------------------------------AAA--CCGUAGC-------------------GAUU---------------------------------------------------GCUACUGAUGACGCCUACAAGAAC
AM039952.1/2350991-2351059   GGCCGCACAGGAGAUGGC-AUUCCUCCUC--------------------------------------------------------------------------------------GAA--CCGCACGCA-----------------CCC--------------------------------------------------UGCGCGCUGAUGAUGCCUGCCCACCC
CP001176.1/5025071-5025130   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
L39876.1/4762-4825           UGCUGCAACGGCGAGGGA-GUC-CGCCGAA-------------------------------------------------------------------------------------CAA--AUGCCA--------------------AUGA----------------------------------------------------UGGCUGAUGACUCCUACAAAUAU
AE005176.1/1105212-1105286   AUAAAUGAUGGGUAUGGU-GCACACCCG---------------------------------------------------------------------------------------AAA--CCGCUUUAAGA---------------AUAAAA---------------------------------------------UCUUAAAACUAAUGGCGCCUACAAACAA
AE014295.3/925740-925809     UGGAGAACCGGCGAUGGA-ACC-CGCCU------------GAA----------------CUCGU------------------------------------------------UUCGAA--CCGC----------------------ACACU-----------------------------------------------------GCUGAUAGUUCCUACACACGA
AE008691.1/1847557-1847497   AAUAUUUAAGGUGAUGAA-GCC-CACCU---------------------------------------------------------------------------------------UAA--UUGCC---------------------GUAAA----------------------------------------------------GGCUGAUGGCUUCUACGAAGAU
AAPH01000002.1/303167-303249 AUUAUGACGGGAGAUGAU-GAUCCUCCUU--------------------------------------------------------------------------------------UAA--CUGCCUUA------------------CUGAAGUUUACCCUUCUUA-----------------------------------UAAGGAUGAUGACGUCUAACAACAU
AE016879.1/4823733-4823792   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
AAMR01000022.1/13784-13701   UAGCCAUCAGGUGAUGGG-GUUCCACCU------------AAGC---------------UUUU------------------------------------------------GCUUCAA--CCGC-CCGUUC---------------UUUC-----------------------------------------------GAACAGUGCUAAUGACUCCUACAGAAUC
AP009049.1/304406-304465     AAAUAAUAAGGUGAUGGA-GUU-CACCA---------------------------------------------------------------------------------------UAA--CCGCA---------------------GAAA-----------------------------------------------------UGCUUAUGACUCCUACAAAUAA
CP000485.1/4850198-4850257   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
ACIZ01000090.1/22576-22630   GAAUUAAAUGGCGAUGGU-GUU-CGCCUAUACG----------------------------------------------------------------------------------UAA--GU------------------------------------------------------------------------------------UGAUGACACCUACCUUGUA
CP000325.1/3045327-3045401   ACUAGCAGCGGCGAUGGG-GCU-CGCCA------------GGAAG--------------CUCGA----------------------------------------------CUUCUGAA--CCGCC---------------------AGCC-----------------------------------------------------GGCUGAUGGCACCUGCGAACAA
CP001034.1/285558-285483     GGAUUUGACGGCGAUGGA-GCU-CGCCA------------GGA----------------UUAAAU-----------------------------------------------UCCAAA--CUGCUUU-------------------CUUA---------------------------------------------------GAAGCUAAUGGCUCCUACCCUAUC
CP000724.1/4518368-4518305   AUGCUCAUAGGCGAUGGA-GUU-CGCCAU--------------------------------------------------------------------------------------UAA--CCACUG--------------------GAUAA---------------------------------------------------CAGUUAAUGACUCCUGCGAAACA
AAXB02000001.1/235634-235709 CUUUUAGAAGGGAAUGAA-GUU-CUCCCU-----------UAGUG--------------AUCA-----------------------------------------------UACUAGAA--CCGCU---------------------UAUAA----------------------------------------------------AGCUGAUGACUUCUGCGAAUAA
AAOU01000011.1/78540-78473   AUUAUGGCGGGAGAUGAU-GUUCCUCCUU--------------------------------------------------------------------------------------AAA--CCGCCUU-------------------UCAAUC-------------------------------------------------AAGGAUAAUGACGUCUAACAACAU
CP000423.1/2430592-2430656   AGAAGAACAGGCGAUGAU-GUU-CGCCG---------------------------------------------------------------------------------------CAA--AUGAUUG-------------------UGUAG--------------------------------------------------CAAUCUGAUGACGUCUACUGAAAC
ABBJ01001663.1/1415-1349     GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
CP000009.1/2355903-2355981   GAGGCAGAAGGCAAUGGA-UUC-UGCCU------------GACCG--------------UUCC-----------------------------------------------CGGUCGAA--CCGCUUC-------------------AUCCG--------------------------------------------------GAAGCUGAUGAUUCCUGUCCCUCG
CP000853.1/1242223-1242295   AUUUCUAUAGGGAAUGAA-GUU-CUCCCU-----------UGGC---------------AAUA------------------------------------------------GCCUAAA--CCGCA---------------------AAUA-----------------------------------------------------UGCUGAUGACUUCUGCGAAAAU
AAQL01009062.1/467-395       AGGCAGAAAGGGAAUGAA-GUUCUCCCC------------CGAU---------------UUUU------------------------------------------------AUCGAAA--CCGC----------------------CAAUGA----------------------------------------------------GCUGAUGACUUCUGUGCAAUG
AAZP01000053.1/29998-29932   GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
AE016825.1/2613318-2613254   UUCUAUUGCGGAGAUGGC-AUUCCUCCCG--------------------------------------------------------------------------------------UAA--CCACCC--------------------CUAGA---------------------------------------------------GGGUUGAUGAUGCCUACGGUAUU
CP000855.1/737518-737592     GGCUUUUCGGGCGAUGGC-GUC-CGCCCG------------GGC---------------UUCGA-----------------------------------------------GCC-GAA--CCGCCC--------------------GUUUU---------------------------------------------------GGGCUGAUGACGCCUGUUCUCUG
AM406671.1/1450312-1450238   AAUAAUGAUGGGUAUGGU-GCACACCCG---------------------------------------------------------------------------------------AAA--CCGCUUUAAGA---------------AUAAAA---------------------------------------------UCUUAAAACUAAUGGCGCCUACAAACAA
CP001146.1/51886-51949       AUCACAAGUGGCGAUGGA-GUC-CGCCAUA-------------------------------------------------------------------------------------UAA--UUGCC---------------------GAUAAA---------------------------------------------------GGCUGAUGACUCCUACUUAUGU
AAQK01000307.1/4537-4610     UAAUAACUUGGUGAUGGG-GUU-CACCA------------GAAA---------------CUUAU-----------------------------------------------UUUCAAA--CCGCA---------------------AAAAU----------------------------------------------------UGCUGAUAACUCCUAUGUUAUA
AL590842.1/2918233-2918170   UCAAGAUCUGGAGAUGAC-ACGCCUCCA---------------------------------------------------------------------------------------UAA--CCGCC---------------------CUAACAA--------------------------------------------------GGCUAAUGAUGUCUACGUGACC
AE015928.1/5995735-5995673   CUUUGCACCGGCUAUGGG-AUU-AGCCUU--------------------------------------------------------------------------------------UAA--CCGCCC--------------------UUUG----------------------------------------------------GAGCUGAUGAUCCCUACAAUUUG
AAFX01053991.1/352-284       AACGAUAACGGCGAUGGG-GUU-CGCCAGUC------------------------------------------------------------------------------------AAA--CCACUCGC------------------GGCG--------------------------------------------------GCGAGUUGAUGACCCCUACUUCGAG
AP009256.1/922963-923040     CUGGACUGCGGUGAUGGG-ACU-CGCCU------------GAAGCC-------------GUUACA--------------------------------------------GGCUUCGAA--CCGC----------------------AAACCC----------------------------------------------------GCUGAUGGUUCCUACGACAUA
CP001283.1/4890016-4890075   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
AE016830.1/2384514-2384445   UAGCAACAUGGUGAUGGU-GUU-CACCAC--------------------------------------------------------------------------------------GAA--CUAUUUAUU-----------------GGACG------------------------------------------------AAUAAAUUAAUGACGCCUACCAAACG
ABXA01000043.1/134014-134086 AUAUUAGAAGGGAAUGAA-GUU-CUCCCU-----------UAGA---------------AAAA------------------------------------------------UCUAAAA--CCGCA---------------------UUUA-----------------------------------------------------UGCUGAUGACUUCUGUAACUAU
BA000001.2/1278365-1278285   GGUUCCUUGGGCGAUGGC-GCC-CGCCCG-----------GGGC---------------UUCGA-----------------------------------------------GCCCGAA--CCGCCUCCC-----------------GUU--------------------------------------------------GGGAGGCUGAUGGCGCCUAUUCUGUA
CP001177.1/4829881-4829940   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
FM178380.1/1142244-1142180   GGCGUACAAGGUGAUGGG-GUGCCACCUACU------------------------------------------------------------------------------------UAA--CCGCC---------------------AAUUU----------------------------------------------------GGCUGAUGACUCCUACAGUAAA
AAVL02000037.1/287218-287292 UAAAUAAAAGGGAAUGAG-GUUCUCCCU------------CGAU---------------UUA-------------------------------------------------AUCGAAA--CCGCUU--------------------AUAAC---------------------------------------------------AAGCUGAUGACUUCUGUGCAAUA
ABHH01000009.1/50257-50182   UACCAUUUUGGGAAUGAAUGUC-UCCCU------------UAGC---------------AUACU-----------------------------------------------GCUUAAA--CCGCUU--------------------AUUA----------------------------------------------------AAGCUGAUGACUUCUGCGCAUAG
CP000254.1/1244505-1244443   GUAAACCAGGGUGAUGGG-GUU-CACCUG--------------------------------------------------------------------------------------UAA--CCGCUU--------------------UUUC----------------------------------------------------CAGCUGAUGACUCCUCUUCCUGU
AE016853.1/5215709-5215637   CGGCGCAUUGGAGAUGGC-AUUCCUCCAUUAAC----------------------------------------------------------------------------------AAA--CCGCUGC-------------------GCCCGUA------------------------------------------------GCAGCUGAUGAUGCCUACAGAAAC
ABVX01000036.1/35509-35405   UACUAAAGCGGAGAUGAC-AUUCCUCCC------------UACCCU-------------CGCGCAGCCAAAACGCUGACAGCCUUAAAAAC------------------AGGGUACAA--CCGCC---------------------ACUC-----------------------------------------------------GGCUAAUGAUGUCUACGUCCAC
AACY023333559.1/192-117      AAUAGUGGCGGGAAUGAA-GUGCUCCCU------------UCAU---------------AUGAU-----------------------------------------------AUGAAAA--CCGCA---------------------AACACG---------------------------------------------------UGCUGAUGACUUCUACGAUUUU
AM889285.1/3856660-3856597   CGUCCGGUCGGAGAUGGA-GUA-CCUCCGUA------------------------------------------------------------------------------------UAA--CCGCCC--------------------CCA-----------------------------------------------------GGGCUGAUGACUCCUGCUCGCAU
CP001337.1/1659433-1659494   UAGCUCAUAGGUGAUAAG-GCU-CACCGUU-------------------------------------------------------------------------------------GAA--CUGCCCG--------------------------------------------------------------------------CGGGCUGAUGGCCUCUACAGAAGU
CP000789.1/3337036-3337110   AAUGGGCACGGUGAUGGG-GUGCCACCG------------GAAUC--------------GAAA-----------------------------------------------GAUUCGAA--CCGCU---------------------UUAA-----------------------------------------------------AGCUAAUGACUCCUACAGAAAC
BAAY01001852.1/271-348       CUGGACUGCGGUGAUGGG-ACU-CGCCU------------GAAGCC-------------GUUACA--------------------------------------------GGCUUCGAA--CCGC----------------------AAACCC----------------------------------------------------GCUGAUGGUUCCUACGACAUA
CP000826.1/1310091-1310029   UCGAACGACGGAGAUGAC-AUUCCUCCU---------------------------------------------------------------------------------------UAA--CCGCCU--------------------UCAC----------------------------------------------------GGGCUGAUGAUGUCUACGUAACC
ACGY01000069.1/12451-12387   AGAAGAACAGGCGAUGAU-GUU-CGCCG---------------------------------------------------------------------------------------CAA--AUGAUUG-------------------UGUAG--------------------------------------------------CAAUCUGAUGACGUCUACUGAAAC
CP000481.1/805841-805902     ACUGAACGCGGCGAUGAA-GCC-CGCCGA--------------------------------------------------------------------------------------CAA-UGCGCCG--------------------CC------------------------------------------------------CGGCUGAUGGCUUCUACCGAGUU
ABBQ01000905.1/4347-4281     GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
ACCE01000005.1/360072-360138 GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
CP001215.1/4826181-4826240   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
ABJD02000101.1/724041-724112 CUAACAAAAGGAGAUGGC-AUUCCUCCUGUUUAA---------------------------------------------------------------------------------AAA--CCGUCC--------------------AAAUAAA-------------------------------------------------GGGCUGAUGAUGCCUGCGUUCAC
CP000605.1/969434-969503     UGGAGAACCGGCGAUGGG-ACC-CGCCU------------GAA----------------CUUGU------------------------------------------------UUCGAA--CCGC----------------------ACACU-----------------------------------------------------GCUGAUAGUUCCUACACACGA
CP001078.1/1342444-1342385   UAUAUAUUAGGUGAUGGA-GUU-CGCCUU--------------------------------------------------------------------------------------UAA--ACGC----------------------GUAAU-----------------------------------------------------GCUAAUGACUCCUACAAAAAA
CP000141.1/1888854-1888795   AAAUUUAAUGGCGAUGGG-GCU-CGCCU----------------------------------------------------------------------------------------AA---CGCUC--------------------AUCU----------------------------------------------------GAGCUAAUAGCUCCUACCGAAAG
CP000650.1/81552-81622       UUGCGGCGAGGUGAUGGC-GUUCCACCUUACC-----------------------------------------------------------------------------------CAA--CCGCUUC-------------------CCCUGA-------------------------------------------------GAAGCUGAUGACGCCUGAUAUUAC
AE009950.1/1333263-1333185   GUUCUUUGGGGUGAUGGC-G-C-CGCCCG-----------GGGC---------------UUCGA-----------------------------------------------GCC-GAA--CCGCCUCCC-----------------GUU--------------------------------------------------GGGAGGCUGAUGGCGCCUAUUCUGUA
AE005176.1/274025-274097     AUAGUAGAUGGGUAUGGU-GCACACCCG---------------------------------------------------------------------------------------AAA--CCGUUUCAAGA---------------AAUAG-----------------------------------------------CUUGAAUCUAAUGGCGCCUACAAAGCA
CP001407.1/4853207-4853266   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
ABSD01000048.1/169379-169321 CAUUUAUAAGGUGAUGGG-GCC-CACC----------------------------------------------------------------------------------------AAA--CCGCC---------------------GCAA-----------------------------------------------------GGCUGAUGGCUCCUUUUGAAAA
CP000957.1/84698-84619       UUUAGCGAUGGUGAUGGA-GCU-CACCG---------------------------------------------------------------------------------------AAA--CCGCCCAGG-----------------AUUUUUCUUAAUUGCA-------------------------------------CCUCGGCUAAUGGCUCCUACGCUUCC
AM743169.1/1735698-1735635   GACCGCGAUGGGGAUGGG-GCUCCCCCGA--------------------------------------------------------------------------------------UAA--CCGCCU--------------------GAGA----------------------------------------------------AGGCUGAUGGCUCCUGCCAGGAC
CP001132.1/2508708-2508771   AAAACGUGUGGCGAUGGA-GUC-CGCCCAA-------------------------------------------------------------------------------------UAA--CCGCCU--------------------UUAU----------------------------------------------------AGGCUGAUGACUGCUACUGAUCC
CP000780.1/914829-914764     UUUUUUAACGGCGAUGAA-GUC-CGCCUC--------------------------------------------------------------------------------------CAA--CCGCCAC-------------------GUAUC--------------------------------------------------GUGACUGAUGACUUCUACCGGGGA
CP000822.1/1490183-1490109   AGUUCACAAGGUGAUGGU-GUUCCACCU-------------------------------UUCC----------------------------------------------------CAA--CCGCCGGUUC----------------GCUC------------------------------------------------GAAUCGGAUGAUGACGCCUGAUAUACA
ABYN01000048.1/132548-132614 UAGGGCAAAGGAGAUGGC-AUUCCUCCUGUAAC----------------------------------------------------------------------------------AAA--CCGCC---------------------AUUGU----------------------------------------------------GGCUAAUGAUGCCUACGUUACU
CP001189.1/2909225-2909147   GUCGGCGCAGGCAAUGGA-UUUCUGCCU------------GACC---------------GUCCG-----------------------------------------------GGUCGAA--CCGCCUC-------------------UUUCG--------------------------------------------------GGGGCUGAUGAUUCCUACCCACCG
ABOX02000009.1/3464-3546     AUAUGCAUUGGCAAUGGG-GUU-UGCCU------------UCUCG--------------GUCAA----------------------------------------------CGAGAGAA--CCGC-CUGA-----------------UUAUU------------------------------------------------UCGGUGCUGAUAACUCCUAUUGGUAC
CP000478.1/3591388-3591322   UUGAAUUGCGGCGAUGAA-GUU-CGCCCU--------------------------------------------------------------------------------------GAA--CCGCCCC-------------------GGGCCA-------------------------------------------------GGGGAUGAUGACUUCUACUUCGAA
ABGC03000023.1/52156-52229   AAAGAAAAAGGGAAUGAA-GUUCUCCCU------------CGAA---------------GAGA------------------------------------------------UUCGAAA--CCGCU---------------------UAUUA----------------------------------------------------AGCUGAUGACUUCUGUGCGAUG
ABQV01000049.1/12339-12285   AAAUUAAAUGGCGAUGGU-GUU-CGCCUA--------------------------------------------------------------------------------------UA---CG------------------------CAAGU-------------------------------------------------------UGAUGACACCUACCUUGAG
CP000924.1/2271016-2270957   AUACCAUAAGGUGAUGGA-GCU-CGCCA---------------------------------------------------------------------------------------UAA--AUGCG---------------------GAAA-----------------------------------------------------CGCUGAUGGCUCCUAUUAGGAG
CP001598.1/4823759-4823818   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
CR378667.1/326415-326332     AUUAUGACGGGAGAUGAU-GUUCCUCCUU--------------------------------------------------------------------------------------UAA--CUGCCUUA--CUGAAG----------UUUACC----------------------------------------CUUCUUAAUAAGGAUGAUGACGUCUAACAACAU
AM889285.1/3849897-3849819   GUCGGCGCAGGCAAUGGA-UUUCUGCCU------------GACC---------------GUCCG-----------------------------------------------GGUCGAA--CCGCCUC-------------------UUUCG--------------------------------------------------GGGGCUGAUGAUUCCUACCCACCG
AANC01000009.1/2226-2162     UCAAUCACAGGCAAUGAG-GUC-UGCCUC--------------------------------------------------------------------------------------AAA--CCGCUU--------------------CUUAGC--------------------------------------------------AAGCUGAUGACUUCUACUUAACC
ACKA01000027.1/241427-241361 GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
BA000043.1/2726409-2726347   AAUCGAAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--CCGCCG--------------------GCUUC---------------------------------------------------CGGCUGAUGACUCCUGCUGCAAA
CP000568.1/234427-234485     UGAAUAAAAGGUGAUGGA-GUU-CACCU---------------------------------------------------------------------------------------GAA--AUGC----------------------GUAAU-----------------------------------------------------GCUGAUGACUCCUACAGGAAU
CP001052.1/1800329-1800268   UUGCGCGCUGGAGAUGGC-AUU-CUCCCU--------------------------------------------------------------------------------------UAA--CCGCC---------------------CUCGU----------------------------------------------------GGCUGAUGAUGCCUGCUUCGUC
CP001130.1/523442-523357     CAGGUUUAAGGAGAUGGC-GUU-CUCCU------------UGAUGCU------------CAUAAA-------------------------------------------AGCAUCAAAA--CCGCCU--------------------CACAUAUA------------------------------------------------AGGCUAAUAACGCCUACCUGCUC
AP009389.1/615295-615357     AUAUUUUCUGGCGAUGGG-GCU-CGCCU---------------------------------------------------------------------------------------UAAUUUUGCU---------------------GAAAA----------------------------------------------------AGCUGAUAGCUCCUACCCGUAA
ABXU01000089.1/23581-23642   GAAGGUCAAGGGGAUGGA-GUC-CCCCAU--------------------------------------------------------------------------------------GAA--CCGCA---------------------UGUUU----------------------------------------------------UGCUGAUGACUCCUGCCGGACC
AE000666.1/688929-688867     CAUCCUGCAGGUGAUGGA-GUC-CACCUU--------------------------------------------------------------------------------------UAA--CCGCUU--------------------UUUC----------------------------------------------------UGGCUGAUGACUCCUGCAUAAUA
AE009952.1/1314365-1314302   UCAAGAUCUGGAGAUGAC-ACGCCUCCA---------------------------------------------------------------------------------------UAA--CCGCC---------------------CUAACAA--------------------------------------------------GGCUAAUGAUGUCUACGUGACC
CP000413.1/283109-283169     AAUUGAAUAGGCGAUGAC-GGU-CGCCAU--------------------------------------------------------------------------------------UAA--ACGA----------------------GCAAAA----------------------------------------------------UCUAAUGACGUCUACUAUUUA
CP000004.1/152384-152449     UCCCGACAAGGGGAUGGA-GCUCCCCCUU--------------------------------------------------------------------------------------CAA--CCGCCCU-------------------CGCA---------------------------------------------------AGGGCUGAUGGCUCCUACCGCGAC
CP000822.1/1409469-1409541   CCUGUGCAGGGUGAUGGC-GUUCCACCUU------------------------------AUUC----------------------------------------------------CAA--CCGCCU--------------------CGUUUCAGU-----------------------------------------------AGGCUGAUGACGCCUGAUAUGAC
CP000413.1/1279279-1279217   AUUAUAAUAGGUGAUGGC-GUU-CACCA-------------------------------AUU-----------------------------------------------------UAA--CCGAU---------------------UAAG-----------------------------------------------------AUCUGACGACGCCUACUUUCUU
CP000230.1/293075-293134     GACGAUACUGGGAAUGGG-GUC-UCCCG---------------------------------------------------------------------------------------AAA--CCGCC---------------------GAAA-----------------------------------------------------GGCUGAUGACUCCUACCGCGUA
AP008232.1/1344619-1344556   CUUUCCCCAGGAGAUGAA-AUUACUCUUUA-------------------------------------------------------------------------------------UAA--CCGCC---------------------GCUCU----------------------------------------------------GGCUGAUGAUGUCUACGUUCAU
CP000943.1/4458865-4458926   UGGCGGUCUGGGGGUGGA-GUU-CCCCA---------------------------------------------------------------------------------------UAA--CCGCCC--------------------ACCC----------------------------------------------------GGGCCGAUGACUCCUACCGCGUG
ABYS02000004.1/646163-646241 CUUACCGGUGGCGAUGGG-ACU-CGCCUG-----------GGG---CCU----------GCA--------------------------------------------AGGAUUCCCGAA--CCGC----------------------AAUUCC----------------------------------------------------GCUGAUGGUUCCUAUUGACGC
ABSD01000048.1/33401-33462   UCUGCUUCGGGUGAUGGC-GUC-CACCCC--------------------------------------------------------------------------------------GAA--ACGCC---------------------CGCGU----------------------------------------------------GGCUGAUGACGCCUUUUCGCAU
CU459141.1/3434387-3434321   UUAAAACAGGGAGAUGGC-AUUCCUCCCUUGAA----------------------------------------------------------------------------------AAA--CCGCC---------------------GUAUU----------------------------------------------------GGCUAAUGAUGCCUACGUUACC
CP000254.1/1238338-1238398   UGUCAUACUGGUGAUGGA-GUU-CACCA---------------------------------------------------------------------------------------AAA--CCGCC---------------------GUUCG----------------------------------------------------GGCUGAUAACUCCUACAGGAUG
BA000040.2/2887392-2887315   CGCACAGAUGGGGAUGGA-GUC-CCCCGA--------------------------------------------------------------------------------------CAA--CCGCCCG--GCGGU------------AGGUG-------------------------------------------ACCGUGAUGGGCUGAUGACUCCUGCUUGAGG
ABYL01000251.1/1837-1776     UUCGCGGCUGGAGAUCGC-AUU-CUCCAU--------------------------------------------------------------------------------------UAA--CCGCCCC-------------------U------------------------------------------------------GGGGCUGAUGAUGCCUGCUACGCC
CP001069.1/247334-247411     CCCCGUUGUGGAGAUGGC-AUGCCUCCCU--------------------------------------------------------------------------------------UAA--CCGCCGGUUAGCG-------------CGUAA--------------------------------------------CGAU-ACCGGCUGAUGAUGCCUACAAGUUC
BA000019.2/2723228-2723309   AUUACUAAUGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------AAA--CCGCUAUUCUAG--------------UCAAAAAAUUAAU-------------------------------------CUAGAA-GGCUGAUGACUCCUACUUUUCU
ABVL01000003.1/298778-298860 GCCCGUAACGGCAAUGGA-UUUCUGCCG------------CCCGA--------------GUGA-----------------------------------------------UCGGGGAA--CCGCUUGGU-----------------AACG-------------------------------------------------GCCAGGCUGAUGAUUCCUGUUUUCAC
FM209186.1/5248344-5248282   UUGCCGACAGGAGAUGGC-AUUCCUCCUU--------------------------------------------------------------------------------------CAA--CCGCCC--------------------CUG-----------------------------------------------------GGGCUGAUGAUGCCUACGCAUGA
AE013598.1/2682944-2683020   UCGGGAUUCGGAGAUGGC-GUUCCUCCGCGCAGUUCCAUC---------------------------------------------------------------------------AAA--CCGUAGC-------------------GAUU---------------------------------------------------GCUACUGAUGACGCCUACAAGAAC
AAQL01004413.1/1469-1396     AAAGAGAAAGGGAAUGAA-GUUCUCCCU------------CGAA---------------GAGA------------------------------------------------UUCGAAA--CCGCU---------------------UAUUA----------------------------------------------------AGCUGAUGACUUCUGUGUAAUG
ABCM01000001.1/151944-151879 UUGCCUAAGGGAAAUGGU-GUCCUUCCAAUU------------------------------------------------------------------------------------UAA--CCGCUU--------------------UUAG----------------------------------------------------AAGCUGAUGGCGCCUGCAAUGAU
AAWO01000020.1/7863-7793     AGGAAGACAGGCGAUGGG-GUU-CGCCA---------------------------------------------------------------------------------------AAA--CCGCCCCGG-----------------AGAACAG----------------------------------------------CGGGAGCUGAUGACCCCUACUCCAUU
CP000764.1/3708919-3708978   AAUGAAUACGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------CAA--CCGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGGAU
AE008691.1/1840761-1840702   UGCAUAAAAAGUGAUGGA-ACC-CACUU---------------------------------------------------------------------------------------UAA--CCGCC---------------------GAAA-----------------------------------------------------GGCUGAUGGUUCCUACUUGUGA
CU468230.2/2879674-2879608   UUAAAACAGGGAGAUGGC-AUUCCUCCCUUGAA----------------------------------------------------------------------------------AAA--CCGCC---------------------GUAUU----------------------------------------------------GGCUAAUGAUGCCUACGUUACC
AAHW02000001.1/301150-301084 GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
AJ248285.1/89834-89914       GUUCUCUUGGGCGAUGGC-GCC-CGCCCG-----------GGGC---------------UUCGA-----------------------------------------------GCCCGAA--CCGCCUCCC-----------------AUG--------------------------------------------------GGGAGGCUGAUGGCGCCUAUUCUUGA
AAMY01000002.1/145285-145345 GAAAUCGAUGGGGAUGGA-GUU-CCCCGA--------------------------------------------------------------------------------------UAC--CCGCC---------------------GCAA-----------------------------------------------------GGCUGAUGACUCCUACCGGGCG
ABSD01000050.1/82708-82766   CAUUUAUAAGGUGAUGGG-GCC-CACC----------------------------------------------------------------------------------------AAA--CCGCC---------------------GCAA-----------------------------------------------------GGCUGAUGGCUCCUUUUGAAAA
AAFX01041918.1/509-577       AAGUCCGAAGGCGGUGGA-GUC-CGCCA---------------------------------------------------------------------------------------CAA--CCGUCAUG------------------CGCCUGC-----------------------------------------------CGUGGCCAAUGACUCCUGCGGGGUU
AE006641.1/885812-885728     AAUGAAGUAGGGGAUGGC-GUC-CCCCU------------GGGG---------------AUAA------------------------------------------------CCCCGAA--CCGCCUC-------------------UUGAUUAAUGAUA------------------------------------------GGGGCUGAUGACGCCUACUUCACC
ABCH01000002.1/2875-2939     UGCAACCAAGGUGAUGGG-GUUCCACCUACU------------------------------------------------------------------------------------UAA--CCGCC---------------------AAAUC----------------------------------------------------GGCUGAUGACUCCUACAGUUUC
CP000099.1/4790369-4790299   UAUCCUAUAGGUGAUGAA-GUC-CGCCA------------AGAU---------------UUACA-----------------------------------------------GUCUAAA--CCGC----------------------UUAU------------------------------------------------------GCUGAUGACUUCUACAUUAAU
CP001364.1/429603-429664     AAUCGAUUGGGUGAUGAG-GCU-CACCCU--------------------------------------------------------------------------------------CAA--CUGCC---------------------AUUAC----------------------------------------------------GGCUGAUAGCCUCUACAGGGAA
ABGR01000008.1/95568-95493   AUUGGGGUUGGUGAUGGG-GUGCCACCG------------GAAUC--------------GAAU-----------------------------------------------GAUUCAAA--CCGCU---------------------UGUAU----------------------------------------------------AGCUGAUGACUCCUACAGAGAC
AE017355.1/4836662-4836721   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
CP000668.1/3010272-3010335   UCAAGAUCUGGAGAUGAC-ACGCCUCCA---------------------------------------------------------------------------------------UAA--CCGCC---------------------CUAACAA--------------------------------------------------GGCUAAUGAUGUCUACGUGACC
AAWP01000027.1/44793-44868   AAUGCACACGGUGAUGGG-GUGCCACCA------------GAAUC--------------GAAA-----------------------------------------------GAUUCAAA--CCGCU---------------------UUUAC----------------------------------------------------AGCUGAUGACUCCUACAGAAAC
AE008923.1/2352963-2353030   GGCCGCACAGGAGAUGGC-AUUCCUCCUC--------------------------------------------------------------------------------------GAA--CCGCACGC------------------ACCC--------------------------------------------------GCGCGCUGAUGAUGCCUGCCCACCC
AACY020346117.1/2623-2561    UUGCGCGCUGGAGAUGGC-AUU-CUCCAU--------------------------------------------------------------------------------------UAA--CCGCC---------------------CUUGAU---------------------------------------------------GGCUGAUGAUGCCUGCUUCGCC
ABCM01000022.1/54798-54866   UUGCAAUACGGAAAUGGU-GUCCUUCCGAUU------------------------------------------------------------------------------------CAA--CCGCUUU-------------------UUUCA--------------------------------------------------AAAGCUGAUGGCGCCUACAAUAGA
AAFX01046182.1/76-12         AACCCCAAGGGAAAUGGU-GUC-UUCCCUGCAC----------------------------------------------------------------------------------AAA--CCGCU---------------------UGAA-----------------------------------------------------AGCUGAUGACGCCUUCAAAUCG
AAQL01000312.1/1879-1949     UAAUAACUUGGUGAUGGG-GUU-CACCA------------GAAA---------------CUUAU-----------------------------------------------UUUCAAA--CCGC----------------------AAUU------------------------------------------------------GCUGAUAACUCCUAGGUUAUA
AAEW02000001.1/156146-156076 CAUGUUAACGGGAAUGGA-GUUCUCCCGG--------------------------------------------------------------------------------------UAA--CCGCCUG-------------------UCGAUUUUU----------------------------------------------CAGGCUGAUGACUCCUGUAUGAGG
ABCC02000039.1/237860-237932 AUAAGUACCGGGAAUGAA-GUU-CUCCCU-----------UAGU---------------CUG-------------------------------------------------ACUAGAA--CCGCU---------------------UAUAA----------------------------------------------------AGCUGAUGACUUCUGCAUUAUG
CP001186.1/4973458-4973517   AUAAUCAGAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--CUGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
ABBM01000878.1/872-806       GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
CP001111.1/1611287-1611224   GGCGACGAUGGGGAUGGG-GCUCCCCCGA--------------------------------------------------------------------------------------UAA--CCGCCU--------------------GAGA----------------------------------------------------AGGCUGAUGGCUCCUGCCAAGAC
CP000679.1/782565-782643     GAAUAUAGAGGCGAUGGA-GUU-CGCCUU--------------------------------------------------------------------------------------AAA--UUGCCACAAG----------------AAUGAAAAAUAC----------------------------------------CUUGUGGCUGAUAACUCCUGUCCGUAU
AL954747.1/1838968-1838902   AUAAUAAUUGGAGAUGGC-AUUCCUCCAU--------------------------------------------------------------------------------------UAA--CCGCCGC-------------------AAUCU--------------------------------------------------GUGGCUGAUGAUGCCUACGACUGG
CP000358.2/504027-504091     AGCAACACAGGCGAUGGC-AUG-CGCCUU--------------------------------------------------------------------------------------GAA--CCGCC---------------------CCGCGUCC-------------------------------------------------GGCUGAUUAUGCCUACCUUCCC
CP000319.1/1049491-1049431   CUGGAAACAGGGAAUGGU-GUC-UCCCUU--------------------------------------------------------------------------------------UCA--CCGCC---------------------GACU-----------------------------------------------------GGCUGAUGACUCCUGCUGACUG
CP000975.1/1995740-1995815   CUCUUAUUGGGCGAUGGG-GCU-CGCCGACCGU----------------------------------------------------------------------------------UAA--CCGCCGUUCUU---------------UUCA-----------------------------------------------AAGAA-GGCUGAUAGCUCCUACCUCUAA
AAXG02000029.1/31858-31932   GUGAAUCAGGGGAAUGAA-GUG-CUCCCC-----------GGGGC--------------GUG------------------------------------------------GCCCCGAA--CCGCG---------------------UUUGA----------------------------------------------------CGCUGAUGACUUCUGCAUUUUG
ABLD01000041.1/16968-17073   UUGCGUGCUGGAGAUGGC-AUU-CUCCA------------AUGGGUGUCCGGCGUGCGCUUCAACACAC---------------------------GCGCUCGCGCGA-ACCCAUUAA--CCGC----------------------CUCGU-----------------------------------------------------GCUGAUGAUGCCUGCUUCCCC
AADL01001839.1/2172-2233     UUCAAGAAAGGCUAUGAC-GUU-AGCCUU--------------------------------------------------------------------------------------UAA--GCGCC---------------------CUCCG----------------------------------------------------GGCUGAUAACGUCUGAUCUUUA
CP000884.1/1926512-1926446   GCAGCGCAAAGAGAUGGC-GUGCCUCUA---------------------------------------------------------------------------------------AAA--CCGCCGCAC-----------------UA---------------------------------------------------GUGCGGCUGAUGACGCCUACAGAACC
AAPS01000002.1/29498-29423   AAUGGGUUCGGUGAUGGG-GUACCACCG------------GAAUC--------------GAAA-----------------------------------------------GAUUCGAA--CCGCU---------------------GUUAA----------------------------------------------------AGCUAAUGACUCCUACAGAAAC
CP000115.1/166253-166313     GAAAUCGAUGGGGAUGGA-GUC-CCCCGA--------------------------------------------------------------------------------------UAA--CCGCC---------------------GCAA-----------------------------------------------------GGCUGAUGACUCCUACCGGGCG
AM406671.1/272338-272410     AUAAUAGAUGGGUAUGGU-GCACACCCG---------------------------------------------------------------------------------------AAA--CCGUUUCAAG----------------AAAUAA----------------------------------------------CUUGAAUCUAAUGGCGCCUACAAAGCA
AADL01002490.1/18401-18475   AUGACGAGGGGUGAUGGA-GUC-CACCU---------------------------------------------------------------------------------------GAA--CGGCCCUUUCUU--------------UCAUA---------------------------------------------AGGAAAGGGAUGAUGACUCCUGUGAGAGA
CU914166.1/1142118-1142184   CCGGCUUGCGGAGAUGGC-AUACCUCCCU--------------------------------------------------------------------------------------UAA--CCGCCGA-------------------UCACC--------------------------------------------------UCGGCUGAUGAUGCCUACAAGUUC
AL646052.1/1941892-1941826   CCGGCCUGCGGAGAUGGC-AUGCCUCCCU--------------------------------------------------------------------------------------UAA--CCGCCGA-------------------UCCCA--------------------------------------------------UCGGCUGAUGAUGCCUACAGGUUC
ABLC01000046.1/24103-24037   GUCACGCGUGGAGAUGGC-AUUCCUCCUU--------------------------------------------------------------------------------------UAA--CCGCCGA-------------------UUCGC--------------------------------------------------UCGGCUGAUGAUGCCUACGUGCCC
CP000702.1/1794817-1794880   AACCCAACGGGCGAUGAG-GCC-CGCCC---------------------------------------------------------------------------------------AAA--CUGCCCU-------------------GAAG---------------------------------------------------AGGGCUGAUGGCCUCUACUGGCUU
ABXP01000064.1/2857-2798     UGCAUAAAAAGUGAUGGA-ACC-CACUU---------------------------------------------------------------------------------------UAA--CCGCC---------------------GAAA-----------------------------------------------------GGCUGAUGGUUCCUACUUGUGA
CP001130.1/516815-516883     UAACCACAAGGAGAUGGC-GUU-CUCCUU--------------------------------------------------------------------------------------UAA--GCGCCUCCU-----------------UCAA-------------------------------------------------AAGAGGCUGAUAACGCCUACAAGCUC
CU458896.1/2498027-2498099   UUCGUCAGGCGCGAUGGA-UCU-CGCCA------------GGG----------------CUUGU------------------------------------------------CCCGAA--CCGCC---------------------ACUGAC---------------------------------------------------GGCUGAUAGUUCCUGUGUUGAU
CP000021.2/1258800-1258735   AUACGUAAAGGUGAUGGG-GUUCCACCUACU------------------------------------------------------------------------------------UAA--CCGCCA--------------------AUGU----------------------------------------------------UGGCUGAUGACUCCUACAGAAUA
ABXP01000064.1/9651-9591     AAUAUUUAAGGUGAUGAA-GCC-CACCU---------------------------------------------------------------------------------------UAA--UUGCC---------------------GUAAA----------------------------------------------------GGCUGAUGGCUUCUACGAAGAU
CP001196.1/1408427-1408488   AUUGUUGAUGGGGAUGGA-GUUCCCCCGA--------------------------------------------------------------------------------------UAA--CCGCC---------------------GCAA-----------------------------------------------------GGCUGAUGACUCCUACCGGACG
CP000117.1/118149-118230     GUUACUAAUGGCGAUGGA-GUU-CGCCC---------------------------------------------------------------------------------------AAA--CCGCUAUUCUAG--------------UCAAAAAAUAAAU-------------------------------------CUAGAA-GGCUGAUGACUCCUACUACUCU
CP001043.1/2012557-2012617   GCGCGCGCCGGAGAUGGC-AUU-CUCCU---------------------------------------------------------------------------------------UAA--CCGCC---------------------CUCGU----------------------------------------------------GGCUGAUGAUGCCUGCUUCGCC
CP000240.1/171311-171206     CCGGCAACCGGCGAUGGA-GUU-CGCCG---------------------------------------------------------------------------------------CAA--CCGCCUCA-CUU--------------GGAAUUUUUCUAUAGAGGAAGAGGGUUCUAACCUCAA-------------AAGCUGAGGCUGAUGACUCCUACACUUCU
CP000859.1/3573766-3573832   AGAAACGAUGGGGAUGGG-GUC-CCCCGA--------------------------------------------------------------------------------------CAA--CCGCC---------------------GCACUGGACA-----------------------------------------------GGCUGAUGACUCCUGCCGAUAC
CP000930.2/1203106-1203045   AAGGGAAUACGCGAUGGA-GUU-CGCGGU--------------------------------------------------------------------------------------AAA----GCCG--------------------UUUUG---------------------------------------------------CGGAUGAUGACUCCUACUCGAUU
AP006878.1/440492-440567     UUCAGCGCGGGCGAUGGC-GUC-CGCCCG-----------GGGC---------------UUCGA-----------------------------------------------GCCCGAA--CCGCUC--------------------GAAA----------------------------------------------------GGGCUGAUGACGCCUGUUCUACU
AAWL01000036.1/2586-2647     UAAGUUUGCGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--GUCCGC--------------------AUAA----------------------------------------------------GCGGUAAUGACUCCUACCAGGAC
AAHO01000134.1/6134-6200     GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
AP006620.1/61342-61253       GAGUCCGCAGGCGAUGGA-UCUCCGCCG------------AGACGACC-----------GACCUAUG----------------------------------------GGCCGUCUGAA--CCGCCCC-------------------GGUCC--------------------------------------------------GGGGCUGAUGGUUCCUUCCCCACG
ACNB01000166.1/6496-6555     AUAAUCAGAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--CUGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
ABEY02000020.1/92291-92375   AUUAUAAAAGGGAAUGAG-GUU-CUCCUC-----------UGG----------------AAAACCUGAAUGGGCA------------------------------A------CCUAAA--CUGCU---------------------AAUAU----------------------------------------------------AGCUGAUGACUUCUACGAUUAU
CP000950.1/3331346-3331409   UCAAGAUCUGGAGAUGAC-ACGCCUCCA---------------------------------------------------------------------------------------UAA--CCGCC---------------------CUAACAA--------------------------------------------------GGCUAAUGAUGUCUACGUGACC
CP000697.1/677221-677283     UCCGAUGCCGGUGAUGGA-GUU-CACCGUG-------------------------------------------------------------------------------------UAA--CCGCCC--------------------GUG-----------------------------------------------------GGGCCGAUGACUCCUGUUCAUAU
AF359557.1/22906-22967       AUCUGCACAGGAGAUGGC-AUU-CCUCCUUG------------------------------------------------------------------------------------AAA--CCGC----------------------CUCGU-----------------------------------------------------GCUGAUGAUGCCUACGUAAAC
CP001133.1/1365444-1365379   AUACGUAAAGGUGAUGGG-GUUCCACCUACU------------------------------------------------------------------------------------UAA--CCGCCA--------------------AUGU----------------------------------------------------UGGCUGAUGACUCCUACAGAAUA
AE016877.1/4975681-4975742   AUAAUCCUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACG-----------------------CGCUGCUUAU-------------------------------------------------CUUAUGACUCCUACCAGUAU
ABXW01000051.1/16406-16474   GUCUUGUUAGGAGAUGGC-AUUCCUCCUA------------------------------GUU-----------------------------------------------------UAA--CCGUCC--------------------UUUUGU--------------------------------------------------GGACUGAUGAUGCCUACGUAAAC
CP000319.1/237736-237676     GACAUCGAUGGGGAUGGA-GUU-CCCCGA--------------------------------------------------------------------------------------UAC--CCGCC---------------------GCAA-----------------------------------------------------GGCUGAUGACUCCUACCGGGCG
CP000239.1/520035-519935     CCGGCAACGGGCGAUGGG-GUU-CGCCG---------------------------------------------------------------------------------------CAA--CCGCCUCAGGC---AGAUCCUAGGGAUAAAGUU------------------------------UCUCUAAGACUUAGAGCUGGGGCUGAUGACUCCUACUCUUCU
AE000782.1/1391410-1391471   AUCGGUAUGGGUGAUGGC-GUC-CACCUU--------------------------------------------------------------------------------------CAA--CCGCC---------------------GCUAA----------------------------------------------------GGCUGAUGACGCCUGUUCUCAG
ABBP01001115.1/6777-6711     GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
BAAZ01017612.1/714-637       CUGGACUGCGGUGAUGGG-ACU-CGCCU------------GAAGCC-------------GUUACA--------------------------------------------GGCUUCGAA--CCGC----------------------AAACCC----------------------------------------------------GCUGAUGGUUCCUACGACAUA
ACAN01000070.1/46719-46650   UAGCAACAUGGUGAUGGU-GUU-CACCAC--------------------------------------------------------------------------------------GAA--CUAUUUAUU-----------------GGACG------------------------------------------------AAUAAAUUAAUGACGCCUACCAAACG
ABSD01000051.1/73291-73230   UCUGCUUCGGGUGAUGGC-GUC-CACCCC--------------------------------------------------------------------------------------GAA--ACGCC---------------------CGCGU----------------------------------------------------GGCUGAUGACGCCUUUUCGCAU
CP001052.1/4147651-4147580   GAAGCUUUCGGAGAUGGC-AUUCCUCCCG--------------------------------------------------------------------------------------UAA--CCGCCCUGC-----------------AUUCCC-----------------------------------------------GCAGAGCUGAUGAUGCCUACGAGUUC
AAHS03000001.1/321518-321584 GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
AAIR02000026.1/4415-4481     GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
AADL01000572.1/2844-2904     CCGGCGGAUGGCGAUGGG-GUU-CGCCU----------------------------------------------------------------------------------------AAU-CCCGC---------------------AUUUC----------------------------------------------------GGGUGAUGACUCCUACCAUGGG
CP000020.2/35443-35510       CCAAAUACGGGUGAUGGA-UUUCCACCUU--------------------------------------------------------------------------------------UAA--CCGCUCUA------------------UUUU--------------------------------------------------UAGAGAUAAUGAUUCCUACUAUAGC
AAKV01000114.1/24659-24721   UUGCCGACAGGAGAUGGC-AUUCCUCCUU--------------------------------------------------------------------------------------CAA--CCGCCC--------------------CUG-----------------------------------------------------GGGCUGAUGAUGCCUACGCAUGA
CP000517.1/1061364-1061422   AACUAAAUAGGUGAUGAC-GUU-CACCAU--------------------------------------------------------------------------------------UAA--CCGA----------------------GAGA------------------------------------------------------UCUAAUGACGGCUACUUUAUC
CT573326.1/3719897-3719836   CGUGGCCCAGGAGAUGGC-AUUCCUCCUU--------------------------------------------------------------------------------------GAA--CCGC----------------------CUCAGC----------------------------------------------------GCUGAUGAUGCCUACGCAACC
AP008971.1/1641037-1640963   AUAGAUUUGGGGAAUGAA-GUG-CUCCCU-----------UGUUA--------------U--------------------------------------------------UAACUAAA--ACGCAA--------------------AAAUU---------------------------------------------------UUGCUGAUGACUUCUGUUUUUUA
AL954747.1/1756266-1756341   UGAAGAUAAGGAGAUGGU-GUUCCUCCUUUUGAAG--------------------------------------------------------------------------------AAA--CCGCAGCCG-----------------UUUAG------------------------------------------------CG-CUGCUGAUGACGCCUACAGGACC
CP001147.1/1737215-1737284   UUUAAAAAAGGCGAUGGA-GUU-CGCCUG--------------------------------------------------------------------------------------UAA--GUGCCUCUG-----------------AUUUU------------------------------------------------CAGGGGCUGAUAACUCCUACCUUAAA
ABVK02000003.1/30981-31043   UGCCCUUAGGGCGAUGGA-GUC-CGCCU---------------------------------------------------------------------------------------UAA--CCGCCC--------------------GCUUC---------------------------------------------------GGGCUGAUGACUCCUACCGGGUU
AE017225.1/4825068-4825127   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
AAZW01000073.1/10424-10341   UAGCCAUCAGGUGAUGGG-GUUCCACCU------------AAGC---------------UUUU------------------------------------------------GCUUCAA--CCGC--CCGUUC--------------UUUU----------------------------------------------GAACCGU-GCUAAUGGCUCCUACAGAAUC
AE017334.2/4823859-4823918   AUAAUCAUAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--ACGCU---------------------GCUU-----------------------------------------------------AGCUAAUGACUCCUACCAGUAU
ABBF01000636.1/6946-6880     GCGGCGACCGGAGAUGGC-AUGCCUCCGUA-------------------------------------------------------------------------------------CAA--CCGCCGG-------------------CGAG---------------------------------------------------CCGGCUGAUGAUGCCUACGCGUUC
CP002952.1/944770-944695     AGGGGGACGGGCGAUGGC-GUC-CGCCCG-----------GGGC---------------UUCGA-----------------------------------------------GCCCGAA--CCGCCC--------------------GCUC----------------------------------------------------GGGCUGAUGACGCCUGUUCUACC
CP001793.1/4378898-4378958   AUUGAAUGAGGCGAUGGA-GUU-CGCCA---------------------------------------------------------------------------------------UAA--CCGCU---------------------UCCAU----------------------------------------------------AGCUAAUGACUCCUACCAGAGG
FP929050.1/1488806-1488733   GUAUGAAACGGGAAUGAG-GUUCUCCCA------------CGA----------------UUAAU------------------------------------------------UCGAAA--CCGCUA--------------------AAUU----------------------------------------------------UAGCUGAUGACUUCUGUGUAGAC
AE008692.2/542148-542071     UAUAGACAAGGUAAUGGA-AUC-UACCU------------GAUCC--------------UUUCUAU--------------------------------------------GGAUCGAA--CCGCC---------------------CUUUA----------------------------------------------------GGCUGAUGACUCCUGCUCAAAC
CP002372.1/388527-388452     GUUUAGUCGGGCGAUGGC-GUC-CGCCC------------GGGC---------------UUCGA-----------------------------------------------GCCCGAA--CCGCCC--------------------GUUAA---------------------------------------------------GGGCUGAUGACGCCUGUUCUACC
ABXV02000011.1/470942-470875 AUUUAUUUGGGAGAUGGC-AUUCCUCCUACCC-----------------------------------------------------------------------------------AAA--CCGUCC--------------------AUAUU---------------------------------------------------GGACUGAUGAUGCCUACGUAAAC
AALF02000002.1/247760-247698 GCAAGAUCUGGAGAUGAC-AUUCCUCCA---------------------------------------------------------------------------------------UAA--CCGCC---------------------CUUCAA---------------------------------------------------GGCUGAUGAUGUCUACGUAACC
CP002222.1/1678154-1678089   AAGUUAAUCGGCGAUGAC-GUU-CGCCA-------------------------------CAUAA---------------------------------------------------UAA--UUGAU---------------------AAUCA----------------------------------------------------AUUUGAUGACGUCUACUGUUUG
CP001656.1/4006535-4006595   AGUGAAUAAGGCGAUGGA-GUU-CGCCAU--------------------------------------------------------------------------------------UAA--CCGCC---------------------UGCG-----------------------------------------------------GGCUAAUGACUCCUACCAAUGU
CP001638.1/886398-886457     AGAGUAAUAGGCGAUGGA-GUU-CGCU----------------------------------------------------------------------------------------AAA--CUAUC---------------------GUUCG----------------------------------------------------GGCUGAUGACUCCUACCAGUAA
#=GC SS_cons                 :::::::::::::::<<<.<<<.-----.......................................................................................---..--<<<<...................._____...................................................>>>>---->>>>>>:::::::::
#=GC RF                      uuggcaaccGGaGAUGGc.GUU.CuCCg.......................................................................................cAA..CCGCCu....................auaau...................................................aGGCUGAUGACgCCUACuuuuac
//
# STOCKHOLM 1.0

#=GF AC   RF01735
#=GF ID   epsC
#=GF DE   epsC RNA
#=GF AU   Yang J
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   57.70
#=GF NC   33.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Eps-Associated_RNA_element
#=GF SQ   30


ACNG01000079.1/252537-252424 UGGUGAUGUCUCC-UGACCGCUAUCAAUGGAGGCACUCGAUUAUGCUGUGGGUUG---U----GAAA--------A-----CAACCUUAGAUGCCA---GUCGUCAAAAGUGUAAUGUGAGGGAGGGUUAGAUGCCCA
CP000813.1/3064659-3064548   AGGUGAUGUCUCC-UAAUCUUUAACAAUGGAGGCACUCGAUCCUGCUGUGGG-CA---U----GACA--------A-----UG-CCUUAGAUGCUC---GUCAUCAAUAGUGGGAUGUGAGGACGGGUUUGAUGCCCA
Z71928.1/3784-3900           AGGUGAUGUCUCC-UGACCUGUAUCAAUGGAGGCACUCGGCUCUGCUGUGGG-CA---GC---UGAAGUU----GC-----UG-CCUUAGAUGCUG---GUCGUCGCUGGCGGGGCGUGAGGAUGGGUUAAAUGCCCA
AE017355.1/5012340-5012216   UGGUGAUGUCUCC-UAACCGUUAUCAACGGAGGCACUCGGUCGUGCUGUGGG-UA---GAAAUUUUU----AUUUCGAACCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGACGUGAGGAUGGGUUAGAUGCCCA
CP001177.1/5041753-5041629   UGGUGAUGUCUCC-UAACCGUUAUCAACGGAGGCACUCGGUCGUGCUGUGGG-UA---GAAAUUUUU----AUUUCGAACCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGACGUGAGGAUGGGUUGGAUGCCCA
ABFU01000061.1/6074-6193     AGGUAAUGUCUCCUCUACCUUUAUCAAGGGAGGCACUCGGUCAUGCUGUGGGUCU---U----UAGGAUU-----A-----AGACCUUAGACACGAA-AGUUGUCGAUGGUGGGAUGUGAGGGUGGGUUAAAUGCCCA
ABDL02000017.1/36572-36696   UGGUGAUGUCUCC-UAACCGUUAUCAACGGAGGCACUCGGUUGUGCUGUGGG-UA---GAAAUUUUU----AUUUCGAACCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGGCGUGAGGUUGGGUUAGAUGCCCA
ABDA02000004.1/319655-319532 GGGUGAUGUCUCC-UAACCUUUAUCAAUGGGGGCACUCGGUCGUGCUGUGGG-UA---GAAA-UUUUA----UUUCGUGCCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGGCGUGAGGUUGGGUUAGAUGCCCA
CP000903.1/5040395-5040271   UGGUGAUGUCUCC-UAACCGGUAUCAACGGGGGCACUCGGUCGUGCUGUGGG-UA---GAAAUUUUU----AUUUCGAACCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGGCGUGAGGAUGGGUUAGAUGCCCA
CP000485.1/5036733-5036609   UGGUGAUGUCUCC-UAACCGUUAUCAACGGAGGCACUCGGUCGUGCUGUGGG-UA---GAAAUUUUU----AUUUCGAACCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGGCGUGAGGAUGGGUUAGAUGCCCA
CP000903.1/3464620-3464507   UGGUGAUGUCUCC-UUACCGCUAUCAACGGAGGCACUCGAUUAUGCUGUGGGUUG---U----GAAA--------A-----CAACCUUAGAUGCGA---GUCAUCAAGAGUGUAAUGUGAGGGAGGGUUAGAUGCCCC
ABRX01000002.1/446041-445929 AGGUGAUGUCUCC-UAAUCUUUAACAAUGGAGGCACUCGAUCCUGCUGUGGGCAU--------GACCA-------------AUGCCUUAGAUGCUC---GUCAUCAAUAGUGGGAUGUGAGGACGGGUUUGAUGCCCA
ABDM02000010.1/36823-36946   UGGUGAUGUCUCC-UAACCGUUAUCAACGGGGGCACUCGGUCGUGCUGUGGG-UA---GAAA-UUUUA----UUUCAUGCCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGACGUGAGGAUGGGUUGGAUGCCCA
ABVH01000011.1/99992-99868   CGGUGAUGUCUCC-UUACCGUUAUCAACGGAGGCACUCGGCCAUGCCGUGGG-UG---GGGACGAUGACG-GUCCUAU---CA-CCUUAGACGCUC---GUCGUCGAGGGUGUGGCGUGAGGGCGGGUUAGAUGCCCG
CP000560.1/3285925-3285809   AGGUGAUGUCUCC-UUACCUUUAUCAACGGAGGCACUCGGCUCUGCUGUGGG-CG---GCG--CUUUU-----CGC-----CG-CCUUAGAUGCUG---GUCGUCGGUGGCGGGGUGUGAGGACGGGUUAAAUGCCCA
AAOX01000001.1/153591-153706 CGGUGAUGUCUCC-UCGCCGUUAUCCAAGGGGGCACUCGGCCAUUCUGUGGG------AUC--AGG-------GAUCUUUU---CCUUAGACGCUU---GUCGUCAUUGGAGUGGUGUGAGGGCGGGUUGGAUGCCCU
AAJM01000088.1/3912-4034     UGGUGAUGUCUCC-UAACCGUUAUCAACGGAGGCACUCGGUCGUGCUGUGGG-UA---GAAA-UUAUA----UUUC-AACCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGGCGUGAGGAUGGGUUGGAUGCCCA
AE017333.1/3521372-3521256   AGGUGAUGUCUCC-UUGCCUUUACCGAUGGAGGCACUCGGCUCUACCGUGGG-CA---GAC--UACCU-----GUC-----UG-CCUUAGACGCAA---GUCGUCGAUGGCGGGGCGUGAGGACGGGUUAAAUGCCCA
AE017194.1/4986228-4986105   UGGUGAUGUCUCC-UAACCGUUAUCAACGGAGGCACUCGGUCGUGCUGUGGG-UA---G-AAAUUUUA---UUU-CAUGCCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGACGUGAGGAUGGGUUAGAUGCCCA
CP000557.1/3376553-3376429   CGGUGAUGUCUCC-UUACCGUUAUCAAUGGAGGCACUCGGCCAUGCCGUGGG-UGGGGAC---GAUGACG----GUCCUAUCA-CCUUAGACGCCC---GUCGUCGAGGGUGUGGCGUGAGGGCGGGUUAGAUGCCCG
CP001186.1/5148287-5148163   UGGUGAUGUCUCC-UAACCGUUAUCAAUGGGGGCACUCGGUCGUGCUGUGGG-UA---GAAAUUUUU----AUUUCGCACCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGACGUGAGGAUGGGUUAGAUGCCCA
AP006627.1/3853484-3853372   CGGUUACGCCUUCUUUACCGUUAUCAAGGAAGGUACUCGGCCAUGCUAAGGG--A---A----GCAUUA------U-----U--CCUUAGGCGCAU---GUCGCCGCCAGCAUGGUGUGAGGGGAGGUUCGAUGCCUC
BA000004.3/3844415-3844295   AGGUAAUGUCUCC-UUACCUUUAUCGACGGAGGCACUCGGCCAUGUUGUGGGUCG---U-C--AAUCAGC---G-A-----UGACCUUAGACGCGUC-CGUUGUCAUUGAUGUGGCGUGAGGUGAGGUUCAAUGCCUC
AE016877.1/5186485-5186361   UGGUGAUGUCUCC-UAACCGUUAUCAAAGGAGGCACUCGGUCGUGCUGUGGG-UA---GAAAUUUUU----AUUUCGAACCUA-CCUUAGACGCUU---GUCGUCGGGAGUAUGACGUGAGGAUGGGUUAGAUGCCCA
BA000043.1/3368754-3368630   CGGUGAUGUCUCC-UUACCGUUAUCAACGGAGGCACUCGGCCAUGCCGUGGG-UGGGGAC---GAUGACG----GUCCCGGCA-CCUUAGACGCCC---GUCGUCGAGGGUGUGGCGUGAGGGCGGGUUAGAUGCCCG
CP002472.1/365227-365338     CGGGUAUGUCUCU-CAUCCGUUAUCGUGCGAGGCACUCGGCCAUGCUGUGGGUGU--------GUGU--------------GCACCUUAGACGCCU---GUCGUCAAGAGUGUGGUGUGAGGGCGGGUUAGAUGCCCG
CP001656.1/474472-474585     AGGUCAAGUCUGCUGCACCUUUAUCACUGCAGGCACUCGGUCACGCUGUGGGUUU---------AAUAGC-----------AAACCUUAGGCAUU----AUUGCCAAGGGUGUGAUGUGAGGAGGGGUUAAAUGCCCC
CP001793.1/6013260-6013140   AGGUAAUGCCUACUGAACCUCUACCACCGUAGGCACUCGAUUAUGCUGUGGG------CAUCCGUCAAACAGGAUG--------GCUUAGACGUUC---AUCGUCGAUGGCGUAAAGUGAGGAAGGGUUAGAUGCCCU
CP001791.1/3286630-3286514   AGGUGAUUUCUCCUGCACCUUUAUCAAUGGAGGAACUCGACUUUGCUGUGGGUCC---C--------AAA-----G-----GGACCUUAGGUGCAGACAGUUACCGGCGGUGAAGUGUGAGGUGAGGUUGGAUGCCUU
CP001638.1/3298415-3298291   CGGUGAUGUCUCC-UUACCGUUAUCAAUGGAGGCACUCGGCCAUGCCGUGGGUGG---G-GACGAUGACG-GUC-CUG---CCACCUUAGACGCUA---GUCGUCGAGGGUGUGGUGUGAGGGCGGGUUAGAUGCCCG
#=GC SS_cons                 AAAA::<<<<<<<.__aaaa________>>>>>>>((((((((((((,,<<<.<<...<<<.._____.....>>>.....>>.>>>,,<<<<___...__>>>>,,,))))))))-)))),,<<<<<_____>>>>>
#=GC RF                      aGGUgAuGuCucC.uaACCuuUAUCAAuGgaGgCaCuCggccgcgCcGUgGG.cg...gcg..uauua.....cgc.....cg.CCuUAGacGCuu...GUCguCgaugGcgcggcGuGaGGacGGGuUagAUgCCCg
//
# STOCKHOLM 1.0

#=GF AC   RF01736
#=GF ID   flg-Rhizobiales
#=GF DE   flg-Rhizobiales RNA
#=GF AU   Corbino K
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   55.00
#=GF TC   71.40
#=GF NC   33.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Flg-Rhizobiales_RNA_motif
#=GF SQ   13


CP000319.1/1569053-1568914   CGAA-CCG--CAGGCUUGGGAGAGCCG-UGGGGUUCG---AAAAC-GAUC-CGGCG---GCGGCCUGGGAGGGCCUUCA-CGCG-GGUC----CUC---AAGGGGAGAAC--CACCGAUGGAGAAUACGCUCCUCAUCGGACUGUCGCGGCAGAUGAUGCUCG
BX572605.1/213149-213287     UGAG-CCG--CGCGCUUGGGAGAGCGCCUGCGGUUCG-----CAC-GAUC-CG-CCAC-C-GGUCUGGGAGGGCU-UGGCGGCG-GGUC---AUU----CAAGGGAGAAC--CACCGAUGGAGAAUGCUCUUCUCGUCGGACUGUCACGGCAGGUCGUGCUCG
AAMY01000006.1/139562-139419 CGAA-CCGGA-AGGCUUGGGAGAGCCU-CAAGGUUCG---AUCAA-UCCGGUG-UGAC---GGCCUGGGAGGGCCUUCUUCACA-CGGAUUCAC-----AAGGGGAGAAC--CACCGAUGGAGAAUGCCCUCCUCAUCGGACUGUCGCGGCAAAUGAUGCUCG
CP000115.1/1232441-1232299   GAA--CCGGA-AGGCUUGGGAGAGCCU-GAAGG-UUC----CGAUCGAUC-CGGUGCGGGCGGCUUGGGAGAGCCUUCCUCACG-GAUC----CUC---AAGGGGAGAAC--CACCGAUGGAGAACACCCUCCUCAUCGGACUGUCGCGGCAGAUGAUGCUCG
CP000463.1/1727246-1727103   GCA--GCG--CGGGCUUGGGAGAGCCGCCGGGC-UGC---ACAAC-AACC--GGGACC-GGCCUUUGGGAGAGGG-ACGUU-CGCGGUUCGGAU-----CAGGGGAGAUCAUGGCCGAUGGAGAAUGCCCAGCUCAUCGGACUAUCACGGCAGGUGACGUUGG
CP000301.1/1644277-1644136   UGAA-GCG---CGGCUUGGGAGAGCUUUAGCGCUUCG----CGGC-AACCACG-GA-C-GGCCUUUGGGAGAGGG-GC-GUGCGCGGUUCAGAC-----AAGGGGAGAUC--GGCCGAUGGAGAAUGCACUCCUCAUCGGACUGUCGCGGCAGAUGACGUUGG
CP000250.1/4321689-4321823   CGAG-CCG---CUGCUUGGGAGAGC---GCCGGUUCG----AGGC-GAUC-CG-CGGAA--GGUCUGGGAGGACC--GGGGGCG-GAUC----CGA---GAAGGGAGAAC--CACCGAUGCAGAAUACGCUUCUGGUCGGCUUGUCGCGGCAGGUCGUGCUCG
CP000283.1/1900071-1899939   GAA--CCA--C-UGCUUGGGAGAGC----GUGG-UUC---ACGGC-GAUC-CG-CGA-GA-GGUCUGGGAGGACC--GGGCGCG-GGUC----CUU---AAAGGGAGAAC--CACCGAUGCAGAAUACGCUUCUGGUCGGCUUGUCGCGGCAGGUCGUGCUCG
CP001096.1/4748751-4748889   UGAG-CCG--CGCGCUUGGGAGAGCGCCUGCGGUUCG-----CAC-GAUC-CG-CCAC-C-GGUCUGGGAGGGCU-UGGCGGCG-GGUC---AUU----CAAGGGAGAAC--CACCGAUGGAGAAUGCUCUUCUCGUCGGACUGUCACGGCAGGUCGUGCUCG
CU234118.1/5227487-5227637   CGAACCCG--CCGGCUUGGGAGAGCUG-AAAGGUUCGGAGAAGA--CCCGGUCG-AGACC-GCCUUGGGAGAGGC-GCCGCGGA-CGGG-AUUCGUUAAGAGGGGAGAUC--GACCGGUGGAGAAUGCGCUUCUCAUCGGAUUGUCGCGGCAGAUGGUGCUGG
CP001196.1/1375948-1375814   GAA--CCG--UCCGCUUGGGAGAGCG--AACGG-UUU---AACG--GACCACC-AUCG---GCUUUGGGAGAGGC---CGGUCGCGGUU----UUGC--AAGGGGAGAUC--U-GCGAUGGAGAACACGAGUCUCGUCGCGCUAUCGCGCCAGAUGACGCUUG
BA000040.2/6396344-6396490   GAGACCCG--GGGGUUUGGGAGAACCU-GACGGUCUCGUUCACGG-GGUC-CG-CCAA-GGCGCUUGGGAGAGCG-AGGAGGCA-GAUCUCACU-----CAGGGGAGAUC--UUCCGAUGCAGAACGCGCUUCUGAUCGGCUUGUCACGGCAGAUGACGUUGG
CP000494.1/5726916-5727065   CGAACCCG--CCGGCUUGGGAGAGCUG-AACGGUUCA-GGAAGAC-CCGCU---GGACGCCGCCUUGGGAGAGGC-ACCGAA--AGCGGUAUUCGUUAAAAGGGGAGAUC--GACCGGUGGAGAAUGCGCUUCUCAUCGGAUUGUCGCGGCAGAUGGUGCUGG
#=GC SS_cons                 <<<<.<<<..<<<<<<<____>>>>>>.->>>>>>>>...,,,,,.<<<<.<<.----.-.<<<<<____>>>>>.------>>.>>>>.------...-----------..--<<<<<-<<<<<_____>>>>>>>>>>:::::::::::::::::::::::
#=GC RF                      cgaa.cCg..ccgGCUuGGGAgAGCcg.agcGguucg...Aagac.gacc.cg.uaaa.g.ggccuGGGAgggcc.ucguugcg.gguc.auacuu...aAGGGGAGAuC..uaCCGauGgAGaaUgCgCuuCUcauCGGacUGUCgCGGCAGaUgauGcUcG
//
# STOCKHOLM 1.0

#=GF AC   RF01737
#=GF ID   flpD
#=GF DE   flpD RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   45.10
#=GF NC   33.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   FlpD_RNA_motif
#=GF SQ   8


BX950229.1/1636889-1636843 UCAUGUGACGAACAACCCGAAGGCUAAGGCCAGGGGA-GUUCUGAUGA
CP000609.1/1662793-1662839 UCAUAUGACGAGCAACCCGAAGGUUUAGACCAGGGAA-GUUCUGAUGA
CP000742.1/1013956-1013910 UCAGGUGACAAACGACCCGAAGGUAGAUACCAGGGGA-GUUUUGAUGA
AE009439.1/172713-172667   CCGGAUGAUGGCCCGGGGGAACCCUAACGGGACCCCG-GGCCGGACGG
CP000743.1/1282979-1283025 ACAGAUGAUGCACUAUCCGAAGGCUUA-GCCAGGGUAUGUGUUGAUGU
CP000745.1/931385-931339   UCAUAUGACGAACAACCCGAAGGUUAAAACCAGGGAA-GUUCUGAUGA
CP000867.1/925551-925597   UCAUAUGACGAGCAACCCGAAGGCUAAAGCCAGGGAA-GUUCUGAUGA
L77117.1/1131452-1131497   CCAGAUGAGGCACCACUCGAAGGC-AAUGCCAAAGUG-GUGCUGAUGG
#=GC SS_cons               <<<<-----<<<<--<<<---<<<____>>>->>>--.>>>>-->>>>
#=GC RF                    uCAGAUGAcGaaCaACCCGAAGGCUAAuGCCAGGGaA.GuuCUGAUGa
//
# STOCKHOLM 1.0

#=GF AC   RF01738
#=GF ID   gabT
#=GF DE   gabT RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   45.00
#=GF TC   49.30
#=GF NC   42.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   GabT_RNA_motif
#=GF SQ   17


CP000744.1/354519-354583   GGCGGG--CCUGCAAGUCCCGAGACAGUCGAUCAUCGUAUGCUGC-CUUGGGGAGCUUCCUU--CCCGCC
FM209186.1/294056-294120   GGCGGG--CCUGCAAGUCCCGAGGCAGUCGAUCAUCGCAUGCUGC-CUUGGGGAGCUUCCUU--CCCGCC
CP000926.1/277381-277441   GGUGGC--CAGG--GCGUUUGCGGCAGUCGAUCAACGAAUACUGUUCGCGAGCAC--UCCCA--GCC-CC
AE016853.1/327286-327345   GGCGG---CCUG--AAGGCUGCAGCAGUCGAUCAUCGUAUGCUGU-UGCAGUUGA--UCCAGC--CCGCU
AF299291.1/591-652         GGUGGC--CAGG--GCGUUCACGACAGUCGAUCAACGAAUACUGUUCGCGAGCAC--UCCCA--GCCGCC
CP000304.1/847701-847762   GAACGC--UCCG--GAUGGUGCGGCAGUCGAUCAUCGUAUGCUGC-CGCGCCCGC-UUCCUG--GCGUUC
CP000949.1/5521043-5520982 GGUGGC--CAGG--GCGUUCACGGCAGUCGAUCAACGAAUACUGUUCGCGAGCAC--UCCCA--GCCACC
CP000438.1/315247-315311   GGCGGG--CCUGCAAGUCCCGAGGCAGUCGAUCAUCGCAUGCUGC-CUUGGGGAGCUUCCUU--CCCGCC
CP000058.1/106095-106036   GGUGG---CCUG--AAGGCUGCAGCAGUCGAUCAUCGUAUGCUGC-CGCAGUUGA--UCCGGU--CCGCU
CP000076.1/220742-220801   GGUGG-CCCGGG-ACCG-CUCCGACAGUCGAUCAUCGCAUGCUGU-CGCAGGCGCU-UCC-----CCGCC
CP000680.1/239262-239322   AGUCCC--UUGC--G-GCCCGGUUCAGUCGAUCAUCGCAUGCUGA-ACCGACCA---CUCGCCGGGGACG
CT573326.1/199162-199223   GGUGGC--CAGG--GCAGGCGUGACAGUCGAUCAACGAAUACUGUGCACGUUUGCG-UCC-A--GCCACC
AE015451.1/264770-264831   GGUGGC--CAGG--GCGUUCACGACAGUCGAUCAACGAAUACUGUUCGCGAGCAC--UCCCA--GCCGCC
AM181176.4/205139-205200   AGUGGC--CGGG--AAAGCUGUGGCAGUCGAUCAUCGCAUGCUGC-CGUAGUUGCC-UCCCC--GCCACG
CP000075.1/99873-99814     GGUGG---CCUG--AAGGCUGCAGCAGUCGAUCAUCGUAUGCUGC-CGCAGUUGA--UCCGGU--CCGCU
AE004091.2/301106-301170   GGCGGG--CCUGCAAGUCCCGAGGCAGUCGAUCAUCGCAUGCUGC-CUUGGGGAGCUUCCUU--CCCGCC
CP000094.2/226838-226898   UGCGG-C-CGGG--AACGCCGUGGCAGUCGAUCAUCGCAUGCUGC-CACCGCCGA-UUCCUC---CCGCU
#=GC SS_cons               <<<<<<..----..--<<<<<<<<<<<<<<_____>>--->>>>>.>>>>>>>--..-----..>>>>>>
#=GC RF                    gGcGGc..CcgG..aagcccgcGgCAGUCGAUCAUCGcAUGCUGc.Cgcgggcac..UCCua..gCCgCc
//
# STOCKHOLM 1.0

#=GF AC   RF01739
#=GF ID   glnA
#=GF DE   Glutamine riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   36.00
#=GF TC   36.10
#=GF NC   35.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0070406; glutamine binding;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF RN   [2]
#=GF RM   21282981
#=GF RT   Bacterial aptamers that selectively bind glutamine.
#=GF RA   Ames TD, Breaker RR
#=GF RL   RNA Biol. 2011;8:82-89.
#=GF CC   Previously known as glnA RNA.
#=GF WK   GlnA_RNA_motif
#=GF **   seedtax: Bacteria; Viruses; unclassified sequences
#=GF SQ   956


AACY023629992.1/266-216      AUCGUUCAUCCU---------------------------UAAG--------------------------------------------------------------------------GGGACGG-AAGUAGUC--------------------GCA-A----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY021446275.1/546-496      AACGUUCAACCU---------------------------UUU---------------------------------------------------------------------------AGGUCGG-AAGUAGGU--------------------AUG-AC---------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY020096225.1/379-325      AUCGUUCAAUCUGU-------------------------UAAG------------------------------------------------------------------------ACAGAUCGG-AAGUAGG---------------------AUU-AAG---------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY020374393.1/1155-1100    AUCGUUCAAUUUGCC------------------------U-AA-----------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY022479074.1/704-652      AUCGUUCAACUC---------------------------AUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023448407.1/161-213      AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY020454040.1/772-835      UACGUUCAUCUCAACA-----------------------CAU-----------------------------------------------------------------------UGUUGGGACGC-AAGUAGUCUG------------------AGA-AAG------------------------------------------------------------------------------------------------CAGAUGAAGGAACGGGAA
AACY023910677.1/99-149       AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGG---------------------GUA-AAA---------------------------------------------------------------------------------------------------CCGAAGGAACGCCGC
AACY023256552.1/1488-1436    CACGUUCAUCUU---------------------------UUAAUU------------------------------------------------------------------------AAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020889107.1/472-419      AUCGUUCAUCCUC--------------------------UUA--------------------------------------------------------------------------GAGGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AADV02000064.1/2221-2140     AUCGUUCAUCUCU--------------------------ACAUUGCCAUAAACAAAGACAAUUA----------------------------------------------------AGAGACGG-AAGUAGGC--------------------UGUGAAUAAGUU---------------------------------------------------------------------------------------------GCCGAAGGAACGCUUU
AACY024098432.1/677-625      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
CP001291.1/2301537-2301596   AUCGUUCAUCCUUC-------------------------UAGUUUU---------------------------------------------------------------------GGAGGACGG-AAGUAGGGA-------------------AAA-A---------------------------------------------------------------------------------------------------UCCCGAAGGAACGCGCU
AACY023583366.1/744-690      CACGUUCAUCACCU-------------------------UUUA------------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020126282.1/48-101       AUCGUUCAACUUC--------------------------AUUGC------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY021286276.1/276-222      CUCGUUCAUCUUC--------------------------GCAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGUA-------------------AUG-G---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY020065980.1/2452-2400    UUCGUUCAUCCC---------------------------GAAA--------------------------------------------------------------------------GGGACGG-AAGUAGGUG-------------------AUA-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
CP001344.1/2330090-2330186   AUCGUUCAUCUCUCC------------------------AAUUAAUCCGACUUUGACAACCGGGAUGGACCUCUUACAGGUG--------------------------------GGAGAGACGG-AAGUAAGG--------------------AUAAU----------------------------------------------------------------------------------------------------CCUGAAGGAACGCGCC
AACY020697594.1/342-285      AUCGUUCACCUCAU-------------------------AAAUUGA---------------------------------------------------------------------GUGAGACGG-AAGUAGGU--------------------UAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAGU
AACY023615516.1/805-855      AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY021920004.1/496-547      AUCGUUCAACCC---------------------------UUAAU-------------------------------------------------------------------------GGGUCGG-AAGUAGGC--------------------AUC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY022706645.1/449-509      UACGUUCAUCCUAAUUU----------------------AAUC---------------------------------------------------------------------AAAUUAGGACGG-AAGUAGUC--------------------GUG-A----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY020280405.1/1415-1365    UACGUUCAACC----------------------------UUUAU--------------------------------------------------------------------------GGUCGG-AAGUAAGC--------------------UUGAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUU
AACY020273812.1/1347-1407    AUCGUUCAAUUCUCA------------------------UUAAUUUU-------------------------------------------------------------------UGAGGAUCGG-AAGUAGGU--------------------UUA-U----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020439894.1/2209-2267    AUCGUUCAUCUCAUU------------------------UAAUG----------------------------------------------------------------------AGUGAGACGG-AAGUAGGU--------------------UGAAA----------------------------------------------------------------------------------------------------GCCGAAGGAACGCUGU
AACY023581058.1/940-990      AUCGUUCAACCC---------------------------AUUU--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------UGC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAA
AACY021104451.1/221-174      UACGUUCAUCC----------------------------UCAG---------------------------------------------------------------------------GGACGG-AAGUAGC---------------------ACAAA-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACU
AACY022220894.1/505-453      UUCGUUCAUCUC---------------------------GUAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCGCU
AACY023651030.1/1094-1040    UACGUUCAUCAUGU-------------------------UUAA------------------------------------------------------------------------GCAUGACGG-AAGUAGGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY022943789.1/314-366      AUCGUUCAACUC---------------------------UUUUU-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCUGACGGAACGCAUG
CP001291.1/4627294-4627352   AUCGUUCAUCUCU--------------------------AUUCAAGC---------------------------------------------------------------------AGAGACGG-AAGUAGGGA-------------------AAG-U---------------------------------------------------------------------------------------------------UCCCGAAGGAACGCGCC
AACY023585828.1/575-523      AUCGUUCAUCUC---------------------------GAAU--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UGCCGAAGGAACGCACC
AACY021334105.1/438-378      AUCGUUCAAUUUAAAUG----------------------GAAA---------------------------------------------------------------------CAUUUAGAUCGG-AAGUAGAC--------------------AUU-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022841699.1/33-83        AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020273812.1/1271-1334    AUCGUUCAUCUUUAAAAA---------------------UUUAU-------------------------------------------------------------------UUUUUAAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023563711.1/719-665      AUCGUUCAUCCUUA-------------------------CUUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY020369453.1/479-531      AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY021448544.1/508-458      UUCGUUCAUCU----------------------------AUUCAC-------------------------------------------------------------------------AGACGG-AAGUAGGA--------------------AUU-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY021624958.1/932-883      UACGUUCAACC----------------------------UUAU---------------------------------------------------------------------------GGUCGG-AAGUAAGC--------------------UUG-UA---------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAA
AACY021990430.1/189-136      AUCGUUCAAUCUGC-------------------------UUAG------------------------------------------------------------------------GCAGAUCGG-AAGUAGG---------------------GUAAA-----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023596340.1/925-870      AUCGUUCAAUUUGCC------------------------U-AA-----------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020635629.1/100-48       AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY021091523.1/279-332      AUCGUUCAAUCUGC-------------------------UAUA------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------AAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023101112.1/473-526      AUCGUUCAAUCUGC-------------------------UUAG------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------AAA------------------------------------------------------------------------------------------------------ACUGAAGGAACGCGGA
AACY021808171.1/254-201      AUCGUUCAAUCUGU-------------------------AAUU------------------------------------------------------------------------ACAGAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY021997040.1/811-758      AUCGUUCAACUUC--------------------------AAAAU------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020413443.1/1222-1165    AUCGUUCAUUCAC--------------------------UUAAUU-----------------------------------------------------------------------GUGAACGG-AAGUAAGUGU------------------AGU----------------------------------------------------------------------------------------------------ACGCUGAAGGAACGCAUC
AACY021167380.1/201-255      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY022945028.1/276-335      AUCGUUCAUCCUUU-------------------------GUG-------------------------------------------------------------------------AAAGGACGG-AAGUAGGU--------------------AAAAAAUCAA-----------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY023404441.1/943-992      AACGUUCAACC----------------------------UUAU---------------------------------------------------------------------------GGUCGG-AAGUAAGC--------------------UUG-UA---------------------------------------------------------------------------------------------------GCUGAAGGAACGUAUU
AACY022102949.1/942-890      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023054784.1/777-837      AACGUUCAUCUUAGUUU----------------------AUUC---------------------------------------------------------------------AAAUUAGGACGG-AAGUAGUC--------------------GUA-A----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY021804470.1/751-808      AUCGUUCAACCUCUU------------------------UUAAG----------------------------------------------------------------------AAGAGGUCGG-AAGUAGGU--------------------UUU-U----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023632309.1/56-6         ACCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY021531642.1/147-98       AUCGUUCAUCUCC--------------------------CUAG-------------------------------------------------------------------------GGAGACGC-AA--AAGU--------------------CUG------------------------------------------------------------------------------------------------------ACUGAAGGAACGGAAA
ABLZ01115713.1/5-56          CACGUUCAUCCC---------------------------UAUU--------------------------------------------------------------------------GGGACGG-AAGUAGGC--------------------AUAGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUU
AACY020353363.1/977-1031     AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020151967.1/2109-2053    AUCGUUCAAUUUGCU------------------------GAAA-----------------------------------------------------------------------AGUAAAUCGG-AAGUAGG---------------------GUA-AAA---------------------------------------------------------------------------------------------------CUGAAGGAACGCGGA
AACY020469105.1/599-649      ACCGUUCAACUC---------------------------UUAU--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY020013751.1/1778-1725    AUCGUUCAUCCU---------------------------UUCUU-------------------------------------------------------------------------GGGACGG-AAGUAGGUA-------------------AUA-G---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY020353363.1/909-964      UACGUUCAUCAUUC-------------------------UUUUU-----------------------------------------------------------------------GAAUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022420381.1/85-30        AUCGUUCAAUCUGU-------------------------AAAUU-----------------------------------------------------------------------ACAGAUCGA-AAGUAAGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY022800866.1/545-492      AUCGUUCAUCCU---------------------------UUUAG-------------------------------------------------------------------------AGGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY022227654.1/290-337      UACGUUCAUCCC---------------------------ACU---------------------------------------------------------------------------GGGACGG-AAGUAGC---------------------ACA-A-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACU
AACY023856333.1/582-634      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY020556514.1/1195-1142    AACGUUCAUCCU---------------------------UUCUU-------------------------------------------------------------------------GGGACGG-AAGUAGGUA-------------------AUA-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY023256552.1/1428-1374    AUCGUUCAAUUCUU-------------------------GUUA------------------------------------------------------------------------AAGAAUCGG-AAGUAGGG--------------------GUG-A----------------------------------------------------------------------------------------------------CCCAAAGGAACGCGGA
AACY020369125.1/2096-1954    AACGUUCAUCUUAUU------------------------UUUAU----------------------------------------------------------------------AAUAAGACGG-AAGUAGGAAGAUA---------------GGAAAACCUCUUUCUUUUUCAAAGAAAGGCAAGCAAGUACCGCUUAGGUUUAAUUAUCAUAGGCGGGAACGAGACCGAA---------------------UAUCUGCCGAAGGAACGCGUU
AACY020365577.1/386-334      AACGUUCAUCUUU--------------------------AAUA-------------------------------------------------------------------------AAAGACGG-AAGUAGGU--------------------UAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY023635669.1/546-599      AUCGUUCAAUCUGC-------------------------AAUA------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------AAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023048471.1/328-273      AUCGUUCAACCUAU-------------------------UAUU------------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------CAAAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY023856333.1/647-701      AUCGUUCAACCUAU-------------------------UUU-------------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------CAUAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY021814745.1/474-524      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023928750.1/299-245      AUCGUUCAAUCUAC-------------------------UAU-------------------------------------------------------------------------GUAGAUCGG-AAGUAAGC--------------------UUCUU----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020152915.1/1984-1930    AUCGUUCAAUCUGA-------------------------AUAU------------------------------------------------------------------------UCAGAUCGG-AAGUAGGU--------------------UAA-U----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGGA
AACY022486863.1/771-716      UACGUUCAUCACUC-------------------------UUUAA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020348126.1/16-72        AUCGUUCAACCUAU-------------------------UUUAA-----------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------CUAAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020392098.1/1276-1328    AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------AUA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020466052.1/1039-901     AUCGUUCAUUCAAUGCUCU--------------------UUUUU------------------------------------------------------------------AGUGCAUUGAACGG-AAGUAGGAAGAUA---------------GGAAAACCUCUUUCUGCACGAUGUGUAGAAAGGCUAGCUAGUACCUUUUAUAGGGAACGAGACCGAA---------------------------------UAUCUACCGAAGGAACGCGUU
AACY020497055.1/1213-1265    AUCGUUCAUCUUC--------------------------GUAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAC
AACY020142594.1/4369-4319    AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCCGC
AACY023123681.1/544-598      AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020399442.1/4403-4350    UACGUUCAUCCU---------------------------UAAC--------------------------------------------------------------------------AGGACGG-AAGUAGGCA-------------------CAUAA---------------------------------------------------------------------------------------------------UGCCGAAGGAACGCAUU
AACY021760230.1/315-257      AUCGUUCAAUUUAAG------------------------AUUUU----------------------------------------------------------------------CUUAAAUCGG-AAGUAGGU--------------------CUUGG----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUG
AACY020228028.1/1238-1290    AUCGUUCAUCUUC--------------------------GUAA-------------------------------------------------------------------------GAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY020059928.1/1227-1277    ACCGUUCAACUC---------------------------AUAU--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------AAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY021837236.1/468-417      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020557518.1/854-804      AUCGUUCAUCCC---------------------------UAGU--------------------------------------------------------------------------GGGACGG-AAGUAAGU--------------------GAA-U----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGGC
AACY020508420.1/937-987      AACGUUCAACCA---------------------------U-UA--------------------------------------------------------------------------UGGUCGG-AAGUAGGU--------------------UUGAA----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUU
AACY023216978.1/797-746      AUCGUUCAUCCC---------------------------UUAGG-------------------------------------------------------------------------GGGACGG-AAGUAGUC--------------------GCA-A----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY020592216.1/308-243      GUCGUUCAUCCGGUGA-----------------------UUGAU---------------------------------------------------------------------UCACUGGACGC-AAGUAAGC--------------------CGUUAUUGUU-----------------------------------------------------------------------------------------------GCUGAAGGAACGGGAA
AACY023651030.1/1027-974     AUCGUUCAAUCUGC-------------------------UUAA------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY021278176.1/388-442      UACGUUCAUCCA---------------------------GUAU--------------------------------------------------------------------------UGGACGG-AAGUAGUCAA------------------ACA-A--------------------------------------------------------------------------------------------------GUGACGAAGGAACGCCGA
AACY020135087.1/1559-1611    AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCGUU
AACY023868432.1/218-272      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY021041201.1/645-697      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023668649.1/575-624      AUCGUUCAACCCU--------------------------U----------------------------------------------------------------------------AGGGUCGG-AAGUAAGC--------------------UAG-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020564829.1/2327-2380    AUCGUUCAACUUC--------------------------AUUAC------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GGA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY022828902.1/661-611      AACGUUUAUCC----------------------------UGAAAC-------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------GAA-U----------------------------------------------------------------------------------------------------GCUGAAGAAACGCACU
AACY023484124.1/850-800      AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020763994.1/168-217      UACGUUCAUC-----------------------------AUAUA---------------------------------------------------------------------------GACGG-AAGUACCCA-------------------AUC-U---------------------------------------------------------------------------------------------------UGGGGAAGGAACGCACU
AACY020766012.1/704-649      AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCAAAACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
CP001344.1/4727152-4727068   AUCGUUCAUCUCCA-------------------------ACCGUGACUGACUGUCCAAUUGACCUCAGUCC--------------------------------------------UGGAGACGG-AAGUAGGGA-------------------GUC-A---------------------------------------------------------------------------------------------------UCCCGAAGGAACGCGCC
AACY021757996.1/786-841      UACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020558260.1/221-140      AUCGUUCAUCUUUUGCACU--------------------AACUU------------------------------------------------------------------AAUGCAAAAGACGG-AAGUAGGAAGAUAG--------------GAA-AACCU------------------------------------------------------------------------------------------CUUUCUUCCCAAGGGAGGAAAG
AACY021551130.1/700-647      AACGUUCAUCUUU--------------------------UAAUA------------------------------------------------------------------------AAAGACGG-AAGUAGGU--------------------UAG-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUU
AACY020223595.1/743-690      AUCGUUCAACUUC--------------------------AAAUU------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GUA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY023718955.1/294-346      UACGUUCAUCAUG--------------------------UUUA-------------------------------------------------------------------------CAUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY021171418.1/103-54       AUCGUUCAACC----------------------------AUUAA--------------------------------------------------------------------------GGUCGG-AAGUAGGC--------------------AAU-C----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY022563169.1/306-361      AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCAAAACGG-AAGUAAAC--------------------GUA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY023693896.1/653-707      AUCGUUCAACUC---------------------------UUAAU-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AAAAAUA--------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY020596620.1/75-130       CACGUUCAUCACUC-------------------------UUUUG-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022997040.1/716-663      AUCGUUCAAUCUGC-------------------------UUAG------------------------------------------------------------------------GCAGAUCGG-AAGUAGG---------------------GAA-AA----------------------------------------------------------------------------------------------------CUGAAGGAACGCGGA
AACY021138991.1/467-522      UACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GAGUGACGG-AAGUAGAU--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020334651.1/828-778      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020329574.1/76-132       AUCGUUCAUCUUUAU------------------------GAGA-----------------------------------------------------------------------AUAAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY022008610.1/340-287      AUCGUUCAUCCUC--------------------------UUA--------------------------------------------------------------------------GAGGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY023527417.1/187-137      AUCGUUCAUCUC---------------------------UUUG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY023939311.1/121-171      AUCGUUCAACCC---------------------------CUUU--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------AAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACG
AACY021281822.1/314-365      UUCGUUCAUCUA---------------------------UC----------------------------------------------------------------------------UAGACGG-AAGUAAGGCU------------------UUU----------------------------------------------------------------------------------------------------AGCCUGAAGGAACGCAUU
AACY021146080.1/302-254      AACGUUCACCC----------------------------GUAA---------------------------------------------------------------------------GGGCGG-AAGUAAGC--------------------GAU-C----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY022082177.1/731-784      UACGUUCAUCAUG--------------------------UUUUA------------------------------------------------------------------------CAUGACGG-AAGUAGGC--------------------AAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY022976997.1/276-329      AUCGUUCAAUCUGU-------------------------GAAA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY022061262.1/212-268      AUCGUUCAAUCCUU-------------------------GUUUAG----------------------------------------------------------------------GAGGAUCGG-AAGUAGGG--------------------GUG-A----------------------------------------------------------------------------------------------------CCCAAAGGAACGCGGA
AACY022625265.1/384-331      AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUAA------------------UGG----------------------------------------------------------------------------------------------------UUACCGAAGGAACGCACC
AACY020240095.1/3750-3802    UUCGUUCAUCCC---------------------------GAAA--------------------------------------------------------------------------GGGACGG-AAGUAGGUG-------------------AUA-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY023143063.1/136-83       AACGUUCAUCUUU--------------------------UAAUA------------------------------------------------------------------------AAAGACGG-AAGUAGGU--------------------UAG-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUU
AACY022082177.1/797-850      AUCGUUCAAUCUGU-------------------------GAGA------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------UAU------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY022976997.1/210-263      UACGUUCAUCAUG--------------------------UUUGA------------------------------------------------------------------------CAUGACGG-AAGUAGGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY021190992.1/188-242      AUCGUUCAAUUUGC-------------------------AGCUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023150189.1/558-508      AUCGUUCAUCUC---------------------------UUUG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCCGC
AACY023048471.1/393-341      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY020315878.1/979-931      UACGUUCAGGC----------------------------AUCAG--------------------------------------------------------------------------GCCCGG-AAGUAGC---------------------AUACA-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACC
AACY023594769.1/609-662      AUCGUUCAUCCU---------------------------UUCAU-------------------------------------------------------------------------AGGACGG-AAGUAAGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY023527417.1/239-189      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020287182.1/522-470      UUCGUUCAUCCC---------------------------GCAA--------------------------------------------------------------------------GGGACGG-AAGUAGGUG-------------------AUA-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY020330816.1/316-370      AUCGUUCAUCCUUA-------------------------CAUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY021720846.1/116-59       AUCGUUCAAUCUGU-------------------------GUGUAA----------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAAUA----------------------------------------------------------------------------------------------------GUCGAAGGAACGCGGA
BX548175.1/1564016-1564091   AACGUUGAGCU---AGGUCAUCG----------------CAUCGU-------------------------------------------------------------CGUUGAUCCAUCAGCCGG-AAGUAGCCCU------------------CCG-C--------------------------------------------------------------------------------------------------AAGGCGAAGCAACGCUCC
AACY023503840.1/1160-1212    AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY020200469.1/970-918      UUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUG-------------------AUA-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
ABYK01000008.1/24464-24568   AUCGUUCAUCUCCCCCA-CCCGUUAACU--CAACUGG--CCGUUUGU---------------------------------------------CCAGUUAUUGGUUAACGUUCUGAGGAAGACGG-AAGUAGGG--------------------ACCCAUG--------------------------------------------------------------------------------------------------CCCGAAGGAACGCGCC
AACY023485267.1/460-513      AUCGUUUAUCC----------------------------UGAAAC-------------------------------------------------------------------------GGACGG-AAGUAAACC-------------------AUCAA---------------------------------------------------------------------------------------------------GGUUGAAGAAACGCUCU
AACY020428904.1/56-108       AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020290039.1/916-970      AUCGUUCAUCCUA--------------------------UUCU-------------------------------------------------------------------------UGGGACGG-AAGUAAGUA-------------------AUA-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY021614818.1/456-399      AUCGUUCAUUCAC--------------------------UUAAUU-----------------------------------------------------------------------GUGAACGG-AAGUAAGUGU------------------AGU----------------------------------------------------------------------------------------------------ACGCUGAAGGAACGCAUC
AACY023219984.1/1097-1045    AUCGUUCAUCUU---------------------------UAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY020517659.1/979-1031     AUCGUUCAUCCU---------------------------UUCAC-------------------------------------------------------------------------AGGACGG-AAGUAGUC--------------------UAAAU----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY023867165.1/1312-1259    CACGUUCAUCAUG--------------------------UUUAA------------------------------------------------------------------------CAUGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY020414671.1/2603-2498    GUCGUUUAUCUCAUAA-----------------------GUAUCUUCCAGUAUCUCCUUAAAGCGCAUAGCAAUAAUUGGUUCAAAACCA-----------------------UUGUGAGACGC-AAGUAAGC--------------------GGA-A----------------------------------------------------------------------------------------------------GCUGAAGAAACGGAGU
AACY023206567.1/1414-1476    UACGUUCAUCUCAAC------------------------ACAUC----------------------------------------------------------------------GUUGAGACGC-AAGUAAGCA-------------------AGUUAAG-------------------------------------------------------------------------------------------------UGCUGAAGGAACGGGAA
AACY020250855.1/439-389      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023733388.1/1260-1316    AUCGUUCAAUCUAUU------------------------U-AU-----------------------------------------------------------------------AAUAGAUCGG-AAGUAAGC--------------------AUCAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAGA
AACY023629456.1/59-114       AUCGUUCAAUUUGCC------------------------U-AA-----------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020284050.1/747-799      UUCGUUCAUCCC---------------------------GAAA--------------------------------------------------------------------------GGGACGG-AAGUAGGUG-------------------AUA-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY022607344.1/286-339      AUCGUUCAUCCU---------------------------UUCUU-------------------------------------------------------------------------GGGACGG-AAGUAGGUA-------------------AUA-G---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY023647930.1/323-375      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY020385429.1/505-455      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020505512.1/1073-1023    AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAG-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020066766.1/2162-2111    AACGUUCAUCC----------------------------AUAUA--------------------------------------------------------------------------GGACGG-AAGUAGAC--------------------UAC-UCA--------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUU
AACY023850522.1/1345-1290    AUCGUUCAAUUUGCC------------------------AAA------------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023076791.1/480-417      UUCGUUCAUUCACU-CUA---------------------AAUG--------------------------------------------------------------------UAGCAGUGAACGG-AAGUAGUCA-------------------AUU-G---------------------------------------------------------------------------------------------------UGACGAAGGAACGCAUC
AACY020962165.1/175-117      AUCGUUCAAUUUAAA------------------------UUUA-----------------------------------------------------------------------UUUAAAUCGG-AAGUAGAUC-------------------UAA-C---------------------------------------------------------------------------------------------------GAUCGAAGGAACGCAUG
AACY023195267.1/1363-1313    CACGUUCAUCCU-----------------------------AA--------------------------------------------------------------------------GGGACGG-AAGUAGGC--------------------UGA-AAA--------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY020473249.1/101-156      AACGUUCAAUCUAU-------------------------UUAAA-----------------------------------------------------------------------GUAGAUCGG-AAGUAAGC--------------------UUA-U----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGU
AACY021577843.1/473-532      AUCGUUCAAUUUAAG------------------------GUUAU----------------------------------------------------------------------CUUAAAUCGG-AAGUAAGUC-------------------UUU-U---------------------------------------------------------------------------------------------------GACUGAAGGAACGCAUG
AACY020990484.1/907-856      AUCGUUCAACUC---------------------------UUUAA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY023110175.1/103-47       AUCGUUCAUCUUUAU------------------------GUAA-----------------------------------------------------------------------AUAAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY020223595.1/812-762      AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGUC
AACY023734044.1/988-934      AUCGUUCAUCCUA--------------------------UUCU-------------------------------------------------------------------------UGGGACGG-AAGUAAGU--------------------AAUGAC---------------------------------------------------------------------------------------------------ACUGAAGGAACGCAUC
AACY020318127.1/532-580      AACGUUCACCC----------------------------GAAA---------------------------------------------------------------------------GGGCGG-AAGUAGGC--------------------GGU-C----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY020134078.1/141-91       AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY023364796.1/691-744      UACGUUCAUCAUG--------------------------UUUUA------------------------------------------------------------------------CAUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY021674813.1/801-750      UACGUUCAUCCU---------------------------AAU---------------------------------------------------------------------------AGGACGG-AAGUAAGC--------------------AAU-AAA--------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY021012785.1/619-669      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAA
AACY020117051.1/1198-1249    AACGUUCAACC----------------------------UUUUUU-------------------------------------------------------------------------GGUCGG-AAGUAGGU--------------------UUG-AA---------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
CP000806.1/2393902-2393983   GUCGUUCAUCUCUACAUUGU-------------------UAGGAAAAAAC-----------------------------------------------------------GCAGUGAAGGGACGG-AAGUAGGC--------------------UUGCAAUCUAGA---------------------------------------------------------------------------------------------GCCGAAGGAACGCUCA
AACY024067319.1/594-648      AUCGUUCAAUCUGU-------------------------AUGA------------------------------------------------------------------------ACAGAUCGG-AAGUAGG---------------------UUA-AAC---------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY020880957.1/394-444      AACGUUUAUCC----------------------------UGAAAC-------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------GAA-U----------------------------------------------------------------------------------------------------GCUGAAGAAACGCACU
AACY021182484.1/448-394      AUCGUUCAACUC---------------------------AUUGU-------------------------------------------------------------------------GAGUCGG-AAGUAAGUAC------------------AUA----------------------------------------------------------------------------------------------------GUACUGAAGGAACGCAUG
AACY020450414.1/979-851      CACGUUCAUCUGGC-------------------------ACGAGUAAAAGUAG--------------------------------------------------------------GUCAGACGG-AAGUAGGCAGAU----------------AAAAAUACAUCUCUUCAAAAAGAGAGGUUCGCAUCAAGCGUCCGCUUGUUGCAUUAAACA-----------------------------------------AUCUACCGAAGGAACGCAUU
AACY021091523.1/213-266      UACGUUCAUCAUG--------------------------UUUUA------------------------------------------------------------------------CAUGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY022263612.1/518-567      CUCGUUCAUCCU---------------------------AAA---------------------------------------------------------------------------AGGACGG-AAGUAGGC--------------------UUU-U----------------------------------------------------------------------------------------------------GCCGAAGGAACGCACC
AACY023535011.1/418-359      AUCGUUCAAUUUAAGA-----------------------GAUA----------------------------------------------------------------------UCUUAAAUCGG-AAGUAAGUC-------------------AUU-----------------------------------------------------------------------------------------------------GACUGAAGGAACGCAUG
AACY022460121.1/377-327      UUCGUUCAUCU----------------------------AUUCAC-------------------------------------------------------------------------AGACGG-AAGUAGGA--------------------AUU-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY023620377.1/162-110      AUCGUUCAUCUUC--------------------------GUAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY022008610.1/398-344      AUCGUUCAUCCCA--------------------------UUCU-------------------------------------------------------------------------UGGGACGG-AAGUAGUC--------------------AAU-UUA--------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY022710041.1/208-77       AUCGUUCAUUCCUUGC-----------------------UACAUUUUGAU---------------------------------------------------------------GCAAGGAACGG-AAGUAGGAAGAUA---------------GGAAAACCUCUUUCUUUUUAAAGAAAGGCAAGCAAGUACCGAUAAGGGAACGAGACCGAA----------------------------------------UAUCUACCGAAGGAACGCGUU
AACY020280406.1/573-635      AUCGUUCAUCUC---------------------------ACUUAAUG----------------------------------------------------------------------GAGGCGG-AAGUAGGUAA------------------CGGGAGAA-----------------------------------------------------------------------------------------------UUAAUAAAGGAACGCAAC
AACY020000274.1/383-329      AUCGUUUAUCC----------------------------UGAAAC-------------------------------------------------------------------------GGACGG-AAGUAAACCA------------------UUU-A--------------------------------------------------------------------------------------------------AGGUUGAAGAAACGCUCU
AACY020074155.1/1580-1526    AUCGUUCAAUCUGC-------------------------UUAG------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCGGA
AACY023900896.1/472-527      UACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GAGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023039004.1/333-281      AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCC
AACY020443845.1/3289-3345    AUCGUUCAACCUAU-------------------------UUUAU-----------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------GAUAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020507360.1/1227-1177    AUCGUUCAUCC----------------------------AAUUAC-------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------AGC-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCGCU
AACY020557797.1/2401-2458    AUCGUUCAUUCAC--------------------------UUAAUU-----------------------------------------------------------------------GUGAACGG-AAGUAAGUGU------------------AGU----------------------------------------------------------------------------------------------------ACGCUGAAGGAACGCAUC
AACY021541586.1/301-246      AUCGUUCAUUUUGA-------------------------AUAUU-----------------------------------------------------------------------UCAAAACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY020387692.1/419-478      AUCGUUCAUCUCAUUU-----------------------G-CU----------------------------------------------------------------------GAAUGAGACGG-AAGUAGGUU-------------------AGA-G---------------------------------------------------------------------------------------------------GACCGAAGGAACGCAGU
AACY020065980.1/2516-2453    AUCGUUCAUUCACU-CUA---------------------AAUG--------------------------------------------------------------------UAGCAGUGAACGG-AAGUAGUCA-------------------AUU-G---------------------------------------------------------------------------------------------------UGACGAAGGAACGCAUC
AACY020116233.1/50-104       AUCGUUCAAUUUGC-------------------------AGCUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023162460.1/756-811      AUCGUUCAUUUUGA-------------------------GUAUC-----------------------------------------------------------------------UCAAAACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY020034953.1/1566-1629    UACGUUCAUUCACU-CUA---------------------AAUG--------------------------------------------------------------------UAGCAGUGAACGG-AAGUAGUCA-------------------AUU-G---------------------------------------------------------------------------------------------------UGACGAAGGAACGCAUC
AACY023099954.1/186-238      AUCGUUCAUCUUC--------------------------GAGA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAC
AACY022839264.1/329-384      AUCGUUCAAUCUAA-------------------------CUAGU-----------------------------------------------------------------------UUAGAUCGG-AAGUAGGC--------------------CAC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY023895541.1/302-248      AUCGUUCAUCCC---------------------------CUUAUU------------------------------------------------------------------------GGGACGG-AAGUAGUC--------------------AAU-UUA--------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY020564601.1/2625-2575    AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAA
AACY023615516.1/753-803      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020151967.1/68-14        AUCGUUCAAUUUGC-------------------------AUUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAUGC-----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023939311.1/55-108       AUCGUUCAACUC---------------------------UUAUUU------------------------------------------------------------------------GAGUCGG-AAGUAGAC--------------------AGUUU----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023721140.1/113-50       AUCGUUCAUUCACU-CUA---------------------AAUG--------------------------------------------------------------------UAGCAGUGAACGG-AAGUAGUCA-------------------AUU-G---------------------------------------------------------------------------------------------------UGAUGAAGGAACGCAUC
AACY022240520.1/660-720      AACGUUCAUCCUAGUUU----------------------AUUC---------------------------------------------------------------------AAAUUAGGACGG-AAGUAGUC--------------------GCA-A----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY020507668.1/980-1038     AUCGUUCAAUCUAUUA-----------------------UAAA----------------------------------------------------------------------UAAUAGAUCGG-AAGUAAGC--------------------UUA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAGA
AACY020443307.1/1821-1873    AUCGUUCAUCUCU--------------------------GAAA-------------------------------------------------------------------------AGAGACGG-AAGUAAGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCC
AACY023563711.1/646-594      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY020284050.1/683-746      AUCGUUCAUUCACU-CUA---------------------AAUG--------------------------------------------------------------------UAGCAGUGAACGG-AAGUAGUCA-------------------AUU-G---------------------------------------------------------------------------------------------------UGACGAAGGAACGCAUC
AACY020264949.1/673-617      AUCGUUCAACCUAU-------------------------CUAAA-----------------------------------------------------------------------GUAGGUCGG-AAGUAAGC--------------------UAACU----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY022786883.1/600-481      UACGUUCAUUUUGCGG-----------------------UCAG----------------------------------------------------------------------CCGCAAAACGG-AAGUAGGAGGAUA-AUCAAUAUUUCCU-UGUGGUAAGGGAAUUCAGCAUCCCGGAC----------------------------------------------------------GGGAUCAAUUGAGAUAUCUACCGAAGGAACGCGUU
AACY020047278.1/646-693      UACGUUCAUCC----------------------------UACG---------------------------------------------------------------------------GGACGG-AAGUAGC---------------------ACUAA-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACU
AACY020324288.1/1156-1104    AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY022331149.1/333-275      AUCGUUCAUCUCAU-------------------------UUGAU-----------------------------------------------------------------------AUGAGACGG-AAGUAAGUU-------------------UUCUU---------------------------------------------------------------------------------------------------AACUGAAGGAACGCUGU
AACY022023721.1/254-304      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY022403129.1/191-246      AUCGUUCAAUUUGUC------------------------UUGA-----------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023949594.1/699-644      UACGUUCAUCAUUC-------------------------UCUUU-----------------------------------------------------------------------GAAUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023410640.1/1099-1154    AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCGAAACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY021620531.1/481-431      AACGUUCAACUC---------------------------AUUA--------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------GAA-U----------------------------------------------------------------------------------------------------GCCGAAGGAACGCACC
AACY022716167.1/549-491      AUCGUUCAUCCU---------------------------UAUUUU------------------------------------------------------------------------GGGACGG-AAGUAGGU--------------------AAAAAAUCAA-----------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY023545052.1/325-271      CACGUUCAUCACU--------------------------UUAUAC-----------------------------------------------------------------------GGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022726119.1/235-287      AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------AUA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020742811.1/338-286      AUCGUUCAUCUC---------------------------GUAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UGCCGAAGGAACGCACC
AACY023408594.1/650-704      AUCGUUCAAUCUGU-------------------------AUUU------------------------------------------------------------------------ACAGAUCGG-AAGUAAGC--------------------CAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY020507668.1/916-967      AUCGUUCAACUC---------------------------GAAA--------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------GUAAA----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY022751187.1/436-488      AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY021276613.1/459-397      AUCGUUCAUCUUUAGAAA---------------------UUUA--------------------------------------------------------------------UUUUUAAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY021294965.1/804-854      AUCGUUCAACCC---------------------------UUUU--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------UUC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAA
AACY022841699.1/102-155      AUCGUUCAACUUC--------------------------AAUAC------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY022496080.1/546-596      AACGUUUAUCC----------------------------UGAAAC-------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------GAA-U----------------------------------------------------------------------------------------------------GCUGAAGAAACGCACU
AACY020502525.1/286-234      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY021868731.1/93-143       AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAA
AACY020783410.1/858-804      AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY022295381.1/480-426      AUCGUUCAAUUUGC-------------------------AGCUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY022614279.1/125-171      GUCGUUCAUCC----------------------------AUAA---------------------------------------------------------------------------GGACGG-AAGUAGG---------------------GAA-A-----------------------------------------------------------------------------------------------------CCGAAGGAACGCAUC
AACY023750866.1/339-287      AUCGUUCAUCUC---------------------------GCGA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-G---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY023374828.1/921-977      UGCGUUGAUCCU---------------------------UUUGU-------------------------------------------------------------------------AGGACGC-AAGUAACUCU------------------CUAGG--------------------------------------------------------------------------------------------------AGAGUGAAGCAACGGGAA
AACY023410640.1/1166-1220    AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY020289447.1/869-815      UACGUUCAUCACCU-------------------------UACA------------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023401421.1/1357-1303    AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020424567.1/1235-1287    AUCGUUCAUCUUC--------------------------GAGA-------------------------------------------------------------------------GAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY020505512.1/1004-951     AUCGUUCAACUUC--------------------------ACUAC------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020078007.1/1062-1010    AUCGUUCAUCCC---------------------------UUUUUU------------------------------------------------------------------------GGGACGG-AAGUAGAC--------------------AAA-U----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023536350.1/519-464      AUCGUUCAAUCUGAA------------------------UUAA-----------------------------------------------------------------------UUCAGAUCGG-AAGUAGGU--------------------AAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY021884274.1/460-511      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020428429.1/939-889      AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020330959.1/663-618      AUCGUUCAUCCC---------------------------AAU---------------------------------------------------------------------------GGGACGC-AAGUAAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CU--CGGAACGGAUU
AACY020214857.1/1668-1621    UACGUUCAUCCC---------------------------ACA---------------------------------------------------------------------------GGGACGG-AAGUAGC---------------------GAA-A-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACU
AACY020210502.1/370-316      AUCGUUCAAUUUGC-------------------------AGCUC-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023987148.1/226-171      AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCAAAACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY020400000.1/898-951      AUCGUUCAACUUC--------------------------AUUAC------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY021255706.1/321-272      ACCGUUUAACUC---------------------------GAAA--------------------------------------------------------------------------GAGUCGG-AAGUAGG---------------------GAAAA-----------------------------------------------------------------------------------------------------CCGAAGAAACGCACU
AACY020228028.1/1309-1361    AUCGUUCAUCUUC--------------------------GUAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAC
AACY021884274.1/388-440      AUCGUUCAACUUC--------------------------UCAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY021486302.1/170-226      AUCGUUCAACUUAC-------------------------UCAUUU----------------------------------------------------------------------GUAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY022479074.1/639-585      AUCGUUCAACCUAU-------------------------UUU-------------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------CUAAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY021939941.1/248-307      AUCGUUCAAUUUAGG------------------------AUUUU----------------------------------------------------------------------CCUAGAUCGG-AAGUAAGUC-------------------GAA-A---------------------------------------------------------------------------------------------------GGCUGAAGGAACGCAUG
AACY020016022.1/137-85       AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
CP000828.1/2595141-2595223   AUCGUUCAUCCCUUAACU---------------------CGUCUUUAACUCUAUUCUUAGU--------------------------------------------------AGUCAAGGGACGG-AAGUAGAGC-------------------CUU-C---------------------------------------------------------------------------------------------------GCUCGAAGGAACGCGCC
AAUA01000001.1/657594-657669 AACGUUGAGCU---CGGUCGAC-----------------CUUUCGC-------------------------------------------------------------GUCGACCCGCAAGCCGG-AAGUAGCC--------------------CAUCCGCAA------------------------------------------------------------------------------------------------GGCGAAGCAACGCUCC
AACY021624876.1/183-229      AACGUUCAUCCC---------------------------GAAA--------------------------------------------------------------------------GGGACGC-AAGUA-----------------------AGCCGA------------------------------------------------------------------------------------------------------CACGGAACGGAUU
AACY020065288.1/1626-1680    AUCGUUCAUCCU---------------------------UUUCUU------------------------------------------------------------------------GGGACGG-AAGUAGGUA-------------------AUA-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY023867165.1/1246-1192    AUCGUUCAAUCUGC-------------------------AGAA------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------AUU-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY021037897.1/96-150       UGCGUUGAUCCU---------------------------UUUGUU------------------------------------------------------------------------AGGACGC-AAGUAAGGC-------------------UGA-G---------------------------------------------------------------------------------------------------GCCUGAAGCAACGGGAC
AACY024097173.1/330-381      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020216610.1/530-480      ACCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020884354.1/284-231      AUCGUUCAACUC---------------------------ACUAA-------------------------------------------------------------------------GAGUCGG-AAGUACCC--------------------AUU-AUA--------------------------------------------------------------------------------------------------GGGGAAGGAACGCACU
AACY023733388.1/1195-1247    AUCGUUCAACUC---------------------------GAAA--------------------------------------------------------------------------GAGUCGG-AAGUAAGCU-------------------AAA-U---------------------------------------------------------------------------------------------------GGCUGAAGGAACGCAUG
AACY020389036.1/1135-1187    AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY021390959.1/865-918      UUCGUUCAUCUC---------------------------UUCGA-------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCACU
AACY023981442.1/894-840      AUCGUUCAUCCU---------------------------UUUCUU------------------------------------------------------------------------GGGACGG-AAGUAAGUA-------------------AUA-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY020315100.1/860-808      AUCGUUCAUCUUC--------------------------GUAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAC
CP000806.1/2707245-2707170   AUCGUUCAUCCUUUC------------------------CAGCAGACAUUCAUCAACAAU------------------------------------------------------GGAGGGACGG-AAGUAAGGA-------------------UUU-U---------------------------------------------------------------------------------------------------UCCUGAAGGAACGCGCC
AACY021585159.1/62-3         AUCGUUCAUCUCAUU------------------------UAAGGC---------------------------------------------------------------------AGUGGGACGG-AAGUAAGU--------------------AAAAC----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGUG
AACY021097822.1/333-388      CACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GAGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020505432.1/55-105       AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023164810.1/326-379      AUCGUUCAACCUUU-------------------------UUU-------------------------------------------------------------------------AAAGGUCGG-AAGUAAGC--------------------ACU-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020986353.1/419-367      AUCGUUCAACUC---------------------------UUAU--------------------------------------------------------------------------GAGUCGG-AAGUAGGCA-------------------AAU-A---------------------------------------------------------------------------------------------------UGCUGAAGGAACGCAUG
AACY021524998.1/714-771      AUCGUUCAUUCAC--------------------------UUAAUU-----------------------------------------------------------------------GUGAACGG-AAGUAAGUGU------------------AGU----------------------------------------------------------------------------------------------------ACGCUGAAGGAACGCAUC
AACY023516001.1/608-548      AUCGUUCAAUUUAAG------------------------GUUUUA---------------------------------------------------------------------CUUAAAUCGG-AAGUAAGUC-------------------UUU-U---------------------------------------------------------------------------------------------------GACUGAAGGAACGCAUG
AACY021958614.1/234-287      UGCGUUGAACCU---------------------------UUUGU-------------------------------------------------------------------------AGGUCGC-AAGUAAGCC-------------------AGA-G---------------------------------------------------------------------------------------------------GGCUGAAGCAACGGGAA
AACY024111564.1/274-220      AUCGUUCAAUUUGC-------------------------AACUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAUAC-----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023299976.1/711-659      AUCGUUCAUCUU---------------------------UGAAAU------------------------------------------------------------------------AAGACGG-AAGUAAGC--------------------GUA-U----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY023282293.1/702-755      AUCGUUCAAUAUGC-------------------------AUAU------------------------------------------------------------------------GCAUAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023606304.1/83-30        AUCGUUCAUCUC---------------------------GAAAA-------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UGCCGAAGGAACGCACC
AACY023683577.1/382-436      AUCGUUCAAUCUGC-------------------------AGAA------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------UUU-U----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY022336911.1/581-639      AUCGUUCAAUCUAAG------------------------UAUUU----------------------------------------------------------------------CUUAGAUCGG-AAGUAGGU--------------------CUGUG----------------------------------------------------------------------------------------------------ACUGAAGGAACGCAUG
ABRV01000019.1/87833-87915   UUCGUUCAUCUCGA-------------------------UCCCCUCAAGGUAGUAGU----------------------------------------------------------UCGAGACGG-AAGUAAGG-ACAGC--------------AGUUCCC--------------------------------------------------------------------------------------------GCUGACCCUGAAGGAACGCGUU
AACY024085939.1/719-772      UACGUUCAUCAUGU-------------------------UUU-------------------------------------------------------------------------ACAUGACGG-AAGUAGGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY022515796.1/623-568      UACGUUCAUCAUUC-------------------------UUAUU-----------------------------------------------------------------------GAAUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020050352.1/2916-2863    AUCGUUCAUCUUC--------------------------UAAUA------------------------------------------------------------------------GAAGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGUG
AACY022726119.1/307-358      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY023503565.1/582-531      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAU
AACY020338589.1/314-367      AUCGUUCAACUUU--------------------------AAUAG------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY021423025.1/251-305      UACGUUCAUCACU--------------------------UUAAUU-----------------------------------------------------------------------AGUGACGG-AAGUAGAC--------------------AAU-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022951168.1/216-163      AUCGUUCAUCUUC--------------------------UUAUG------------------------------------------------------------------------GAAGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGUG
AACY020142594.1/4421-4371    AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAA
AACY020938992.1/607-661      AUCGUUCAAUCUG--------------------------UUAAUU-----------------------------------------------------------------------CAGAUCGG-AAGUAAGU--------------------UCA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGGA
AACY020830136.1/544-598      AUCGUUCAAUCUGU-------------------------UUAU------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------UAA-U----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGGA
AACY023165583.1/299-359      AUCGUUCAAUUUAGGA-----------------------UUAU----------------------------------------------------------------------UCCUGAAUCGG-AAGUAAGUC-------------------AAA-A---------------------------------------------------------------------------------------------------GACUGAAGGAACGCAUG
AACY022210576.1/622-539      AUCGUUCACCC----------------------------GAAA---------------------------------------------------------------------------GGGCGG-AAGUACCCUAUUUUCUGUACAUAAUUCUAUGCU--------------------------------------------------------------------------------GGAAAUAU------GGGGUAGGGGAAGGAACGCACC
AACY022161803.1/831-883      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAC
AACY023750866.1/393-343      AUCGUUCAUCCU---------------------------UAAG--------------------------------------------------------------------------GGGACGG-AAGUAGUC--------------------GCA-A----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY022326751.1/308-254      CACGUUCAUCACCU-------------------------AAUC------------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020223595.1/864-814      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY022183545.1/793-745      UUCGUUCAUCCUC--------------------------GCAA-------------------------------------------------------------------------GAGGACGC-AA--AAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CUGAAGGAACGGGAA
AACY020382879.1/340-288      AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020215859.1/650-598      AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020237494.1/318-391      AUCGUUGGGCUC---GGGCCUG-----------------CUCUUA--------------------------------------------------------------CAGACCUCUUCAGCCGG-AAGUAGCCAC------------------CCG-C--------------------------------------------------------------------------------------------------GUGGCGAAGCAACGCUCC
AACY021990430.1/255-202      UACGUUCAUCAUG--------------------------UUUAU------------------------------------------------------------------------CAUGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023245794.1/363-311      CACGUUCAUCUU---------------------------UUAAUU------------------------------------------------------------------------AAGACGG-AAGUAGAU--------------------GUA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022298437.1/866-814      AUCGUUCAACCC---------------------------UGCAGU------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------UUC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAU
AACY021090368.1/351-270      AUCGUUCAUCUUUUGCACU--------------------AACUU------------------------------------------------------------------AAUGCAAAAGACGG-AAGUAGGAAGAUAG--------------GAA-AACCU------------------------------------------------------------------------------------------CUUUCUUCCCAAGGGAGGAAAG
AACY020369453.1/551-602      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY023093815.1/433-490      AUCGUUCAUUCAC--------------------------UUAAUU-----------------------------------------------------------------------GUGAACGG-AAGUAAGUGU------------------AGU----------------------------------------------------------------------------------------------------ACGCUGAAGGAACGCAUC
AACY023138288.1/674-734      AUCGUUCAUCUCU--------------------------UAGUUUU----------------------------------------------------------------------AGAGACGG-AAGUAGACCU------------------UAAAA--------------------------------------------------------------------------------------------------AAGUCGAAGGAACGCAUG
AACY020134078.1/210-160      AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY022751482.1/205-156      AUCGUUCAACC----------------------------AUAU---------------------------------------------------------------------------GGUCGG-AAGUAGGU--------------------UUGAC----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
CP000240.1/2191743-2191662   AUCGUUCACCUCUGCA-----------------------GUUGGCUCACCAGUGGCCUGGAGCUG------------------------------------------------UGCAGAGACGG-AAGUAGGG--------------------GUCUU----------------------------------------------------------------------------------------------------CCCGAAGGAACGCGCC
AACY020564829.1/2206-2256    AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020555684.1/2430-2484    AUCGUUCAUCCUUA-------------------------CUUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY023638748.1/479-529      AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY022842103.1/630-686      AUCGUUCAAUCUAU-------------------------UUUAU-----------------------------------------------------------------------AUAGAUCGG-AAGUAAGC--------------------ACAAU----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY021066889.1/690-635      UACGUUCAUCAUUC-------------------------UUUUA-----------------------------------------------------------------------GAGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
CP000239.1/931758-931667     AUCGUUCAUCCUCUCGCCUGCUGUUUGGCUU--------AUCGUG-----------------------------------------------------GAGCAAGACGGCA-GCCGGAGGACGG-AAGUAGGGA-------------------GCU-A---------------------------------------------------------------------------------------------------UCCCGAAGGAACGCGCC
AACY020212356.1/1530-1480    AUCGUUCAACCA---------------------------UUA---------------------------------------------------------------------------UGGUCGG-AAGUAGGU--------------------UUG-AA---------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY020555885.1/2641-2591    AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023969055.1/754-807      AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUAA------------------UGG----------------------------------------------------------------------------------------------------UUACCGAAGGAACGCACC
AACY023520018.1/1297-1358    UACGUUCAUCU----------------------------UAACUUAU-----------------------------------------------------------------------AGACGG-AAGUAGACUAUU----------------GCA-AC-----------------------------------------------------------------------------------------------GAUAGUUGAAGGAACGCAUU
AACY021577843.1/545-598      UUCGUUCAACUCU--------------------------UAAUA------------------------------------------------------------------------AGAGUCGG-AAGUAGGC--------------------AAC-U----------------------------------------------------------------------------------------------------GCCGAAGGAACGCUUA
AACY023638748.1/427-477      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023848865.1/1281-1326    AUCGUUCAUCCC---------------------------AAU---------------------------------------------------------------------------GGGACGC-AAGUAAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CU--CGGAACGGAUU
AACY023091009.1/203-149      AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY021376510.1/251-199      AUCGUUCAUCUAU--------------------------UCAU-------------------------------------------------------------------------AUAGACGG-AAGUAGGC--------------------AGA-C----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACU
AACY021190992.1/121-175      CACGUUCAUCACCU-------------------------UUUA------------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY021541586.1/234-180      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------CGA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY020416756.1/1664-1720    AUCGUUCAUCUUUAU------------------------GUAA-----------------------------------------------------------------------AUAAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY022163341.1/297-351      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY021528051.1/874-824      AACGUUCAACCA---------------------------UUG---------------------------------------------------------------------------UGGUCGG-AAGUAGGU--------------------UUG-AA---------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY022086925.1/534-588      CACGUUCAUCGC---------------------------CCUAAAAA----------------------------------------------------------------------GCGACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY020332580.1/786-655      AUCGUUCAUUCAGUGCCCU--------------------AUUUU------------------------------------------------------------------AGUGCAUUGAACGG-AAGUAGG-AAAAC---------------CUGAAAACCUCUAUCUGAAAAGAUAGGUAAGCAAGUACCCGCUAGGGGAACGAGACCGAAA---------------------------------------GUUUUACCGAAGGAACGCGUU
AACY020027094.1/410-362      UACGUUCAGGC----------------------------AUCA---------------------------------------------------------------------------GCCCGG-AAGUAGGA--------------------GUU-A----------------------------------------------------------------------------------------------------UCCGAAGGAACGCACC
AACY024118785.1/615-567      AUCGUUCAUCC----------------------------CAAAA--------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------AAU------------------------------------------------------------------------------------------------------GCCGAAGGAACGCACC
AACY021251278.1/319-370      AUCGUUCAACUC---------------------------GAAA--------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUUA----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023992491.1/721-776      UACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GAGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022839954.1/548-490      CUCGUUCAUUCAGAA------------------------GAAA-----------------------------------------------------------------------UUCUGAACGG-AAGUAGGU--------------------AAUGAC---------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY023143293.1/261-206      AUCGUUCAAUUUGCC------------------------UUCA-----------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY024097173.1/258-310      AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCACC
AACY020212401.1/327-379      AUCGUUCAUCUUU--------------------------GAAA-------------------------------------------------------------------------AAAGACGG-AAGUAGGC--------------------AAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCGAG
AACY020542192.1/2127-2180    AUCGUUCAUCCU---------------------------UUCAU-------------------------------------------------------------------------AGGACGG-AAGUAAGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY022220894.1/563-509      UUCGUUCAUCUA---------------------------UC----------------------------------------------------------------------------UAGACGG-AAGUAGGAU-------------------UAAAAUUU------------------------------------------------------------------------------------------------AUCCGAAGGAACGCAUU
AACY023143293.1/328-273      CACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023214669.1/1588-1637    AACGUUCAUCCC---------------------------ACU---------------------------------------------------------------------------GGGACGG-AAGUAAGC--------------------AUA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCUUC
AACY020264949.1/738-686      AUCGUUCAACUCA--------------------------GUU--------------------------------------------------------------------------UGAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023513220.1/642-593      AUCGUUCAUCC----------------------------AUUAC--------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------AAC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY021623722.1/358-413      AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCAAAACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY022860823.1/392-347      AUCGUUCAUCCC---------------------------AAU---------------------------------------------------------------------------GGGACGC-AAGUAAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CU--CGGAACGGAUU
AACY022594555.1/253-201      AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY023581040.1/405-452      AUCGUUGGACU----------------------------AAA----------------------------------------------------------------------------AGUCGG-AAGUAAGC--------------------AAU-C----------------------------------------------------------------------------------------------------GCUGAAGCAACGCACU
AACY020232172.1/1639-1584    AUCGUUCAAUUUGCC------------------------UAU------------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UUA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY022138576.1/234-180      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY020157868.1/334-389      AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCGAAACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY022800866.1/603-549      AUCGUUCAUCCCA--------------------------UUAU-------------------------------------------------------------------------UGGGACGG-AAGUAGUC--------------------AAU-UUA--------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY020290181.1/1346-1409    AUCGUUCAUUCACU-CUA---------------------AAUG--------------------------------------------------------------------UAGCAGUGAACGG-AAGUAGUCA-------------------AUU-G---------------------------------------------------------------------------------------------------UGAUGAAGGAACGCAUC
AACY023530723.1/1280-1330    AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY021902385.1/65-5         UACGUUCAUCCCCU-------------------------AACAU-----------------------------------------------------------------------AGGGGACGC-AAGUACUCUA------------------CGAAU--------------------------------------------------------------------------------------------------GAGAGGAAGGAACGGGAA
AACY024076916.1/215-268      AUCGUUCAAUCUGC-------------------------UUAG------------------------------------------------------------------------GCAGAUCGG-AAGUAGG---------------------GAA-AA----------------------------------------------------------------------------------------------------CUGAAGGAACGCGGA
AACY023583366.1/677-623      AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY022023258.1/386-328      UCCGUUCAUCUAUAUU-----------------------UAAA----------------------------------------------------------------------GAUAUAGACGG-AAGUAGUC--------------------GUA-A----------------------------------------------------------------------------------------------------GGCGAAGGAACGCAUU
AACY022849373.1/614-667      AUCGUUCAAUCUGC-------------------------AAUA------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------AAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023947774.1/543-595      UACGUUCAUCCU---------------------------UAU---------------------------------------------------------------------------GGGACGG-AAGUAGGGGA------------------UUA----------------------------------------------------------------------------------------------------UCCCCGAAGGAACGCAUA
AACY022907826.1/642-567      AACGUUGAGCU---UGACAGGUG----------------UUCCG--------------------------------------------------------------CAUCUGUCGUUCAGCCGG-AAGUAGCC--------------------CCUCCGCAA------------------------------------------------------------------------------------------------GGCGAAGCAACGCUCC
AACY020530594.1/1891-1816    AACGUUGAGCU---UGACAGGUG----------------UUCCG--------------------------------------------------------------CAUCUGUCGUUCAGCCGG-AAGUAGCC--------------------CCUCCGCAA------------------------------------------------------------------------------------------------GGCGAAGCAACGCUCC
AACY022001680.1/619-567      AUCGUUCAUCUC---------------------------UCAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-G---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY020498371.1/1365-1313    AUCGUUCAUCUC---------------------------GUAA--------------------------------------------------------------------------AAGACGG-AAGUAGGGA-------------------AUG-A---------------------------------------------------------------------------------------------------UGCCGAAGGAACGCACC
AACY022086925.1/601-655      AUCGUUCAAUCUGC-------------------------AAAA------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------UUU-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY022486863.1/703-648      AUCGUUCAAUUUGCC------------------------U-AA-----------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY021241723.1/233-283      ACCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020290181.1/1410-1462    UUCGUUCAUCCC---------------------------GUAA--------------------------------------------------------------------------GGGACGG-AAGUAGGUG-------------------AUA-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY023364796.1/757-810      AUCGUUCAAUCUGU-------------------------UAUU------------------------------------------------------------------------ACAGAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY022670969.1/894-949      AUCGUUCAAUCCUU-------------------------GUUUAA----------------------------------------------------------------------GAGGAUCGG-AAGUAGGG--------------------CAA------------------------------------------------------------------------------------------------------CCCAAAGGAACGCGGA
AACY022039567.1/365-417      CACGUUCAUCCC---------------------------UACA--------------------------------------------------------------------------GGGACGG-AAGUAAGC--------------------CAU-AGU--------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAU
AACY023682620.1/511-569      AUCGUUCAAUUUAAA------------------------UUUA-----------------------------------------------------------------------UUUAAAUCGG-AAGUAGAUC-------------------UAA-C---------------------------------------------------------------------------------------------------GAUCGAAGGAACGCAUG
AACY023503840.1/1225-1280    AUCGUUCAACCUAU-------------------------UAUU------------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------CAAAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
CP000240.1/2902190-2902288   AUCGUUCAUCCUCUCGC-GUGCUG---------------GGCGGCUCGUUAAUGUAGGUAGAGCGA---------------------------------------CAUCACGGCCAGAGGACGG-AAGUAGGGA-------------------GAU-A---------------------------------------------------------------------------------------------------UCCCGAAGGAACGCGCC
AACY020428011.1/1689-1638    AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020445308.1/1001-1059    GACGUUCAUUUUAGUA-----------------------GCAA----------------------------------------------------------------------UACUAAAACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023928750.1/364-312      AUCGUUCAACUC---------------------------AAUAU-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUU-GU---------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY023408594.1/583-638      AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCAAAACGG-AAGUAAAC--------------------AUA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY020986353.1/354-296      AUCGUUCAAUCUAAU------------------------UUAU-----------------------------------------------------------------------AUUAGAUCGG-AAGUAGGCA-------------------AAU-A---------------------------------------------------------------------------------------------------UGCUGAAGGAACGCAGA
AACY024067319.1/527-581      UACGUUCAUCGC---------------------------CUUAAAAA----------------------------------------------------------------------GCGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020240685.1/377-327      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023596340.1/993-938      CACGUUCAUCAUCC-------------------------UUAUG-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022061262.1/150-204      UACGUUCAUCUUU--------------------------UUAAAU-----------------------------------------------------------------------AAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020795282.1/440-570      AUCGUUCAUUCAGUGCCCU--------------------UUUUU------------------------------------------------------------------AGUGCAUUGAACGG-AAGUAGG-AAAAC---------------CUGAAAACCUCUAUCUGAAAAGAUAGGUAAGCAAGUACCCGUAAGGGGAACGAGACCGAAA---------------------------------------GUUU-ACCGAAGGAACGCGUU
AACY020563764.1/2605-2549    AUCGUUCAUCUUUAU------------------------GAAA-----------------------------------------------------------------------AUAAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY023682620.1/582-634      AUCGUUCAACCU---------------------------UUAAUU------------------------------------------------------------------------AGGUCGG-AAGUAAGC--------------------AAC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020419699.1/403-465      AUCGUUCAUCUUUAAAAA---------------------UUUA--------------------------------------------------------------------UUUUUAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY020514091.1/890-942      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY022736085.1/436-381      UUCGUUCAUCUUAC-------------------------CCU-------------------------------------------------------------------------GUAAGACGG-AAGUAGACA-------------------UUC-U---------------------------------------------------------------------------------------------------UGUCGAAGGAACGCAUA
AACY020900317.1/189-142      AUCGUUCAUCCCC--------------------------AAG--------------------------------------------------------------------------GGGGACGC-AAAU------------------------GCCGACU-----------------------------------------------------------------------------------------------------GAAGGAACGGGUC
AACY021182484.1/381-326      AUCGUUCAAUCUAA-------------------------CUUGU-----------------------------------------------------------------------UUAGAUCGG-AAGUAAGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020388700.1/1617-1565    AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY022301935.1/380-330      AACGUUCAACCU---------------------------UUA---------------------------------------------------------------------------AGGUCGG-AAGUAGGU--------------------UUGAA----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY023545356.1/501-555      AUCGUUCAAUUUGCC------------------------UUA------------------------------------------------------------------------GGCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY021097822.1/401-456      AUCGUUCAAUCUGAA------------------------UUAA-----------------------------------------------------------------------UUCAGAUCGG-AAGUAGGU--------------------AAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY021601485.1/472-420      AUCGUUCAUCUA---------------------------UUCA--------------------------------------------------------------------------UAGACGG-AAGUAGGU--------------------AAU-ACA--------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY020402636.1/1170-1228    AUCGUUCAUCUCAU-------------------------UUAAA-----------------------------------------------------------------------AUGAGACGG-AAGUAAGUU-------------------UUCUU---------------------------------------------------------------------------------------------------AACUGAAGGAACGCUGU
AACY023879838.1/286-227      AUCGUUCAAUUUAAG------------------------UUAGU----------------------------------------------------------------------CUUAAAUCGG-AAGUAGGUC-------------------UUU-U---------------------------------------------------------------------------------------------------GACUGAAGGAACGCAUG
AACY021868731.1/145-195      AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCCGC
AACY023385492.1/1411-1460    UACGUUCAGCC----------------------------UUAU---------------------------------------------------------------------------GGUCGG-AAGUAAGC--------------------UUGUA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAA
AACY020236614.1/928-978      AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGUC
AACY022627048.1/204-153      AUCGUUCAACCC---------------------------UUUUU-------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------UUA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAA
AACY020389036.1/1200-1255    AUCGUUCAACCUAU-------------------------UAUA------------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------CAAAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020338589.1/193-243      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY024021276.1/438-490      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY020382879.1/268-217      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020428429.1/991-941      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020563270.1/1088-1036    AUCGUUCAUCUUC--------------------------GAGA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAC
AACY022149997.1/171-120      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY022563169.1/373-427      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAAGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY020514091.1/817-871      AUCGUUCAUCCUUA-------------------------CUUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY020414407.1/995-1052     AUCGUUCAUCUCAUU------------------------AAUUG----------------------------------------------------------------------AGUGAGACGG-AAGUAGG---------------------UAA-GAU---------------------------------------------------------------------------------------------------CCGAAGGAACGCAGU
AACY020160526.1/997-1046     AUCGUUCAUCC----------------------------AUUAC--------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------AAC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AAVU01000006.1/147500-147393 AACGUUCAUCUCUCUGAUCUGGA-GA--ACGCUGAUCUAGGUA-----------------------------------------------UAG-UCAGGAAAAUCAUCGAGAUAGGAGAGACGG-AAGUAGGGAA------------------AUCAUCA------------------------------------------------------------------------------------------------UUCCCGAAGGAACGCGCC
AACY020424567.1/1306-1358    AUCGUUCAUCUUC--------------------------GAGA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY020455148.1/219-271      AUCGUUCAUCCC---------------------------UUUA--------------------------------------------------------------------------GGGUCGG-AAGUAUGC--------------------UAU-AAU--------------------------------------------------------------------------------------------------GCAGAAGGAACGCAUC
AACY023165583.1/372-427      UUCGUUCAACCCUU-------------------------AUAAC-----------------------------------------------------------------------AAGGGUCGG-AAGUAGGC--------------------ACC-U----------------------------------------------------------------------------------------------------GCCGAAGGAACGCUUU
AACY023410968.1/256-309      AUCGUUCAUCUCG--------------------------CUUAU------------------------------------------------------------------------UGAGACGG-AAGUAAGU--------------------UUU-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCAGA
AACY022860373.1/42-94        AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY020263130.1/153-99       AUCGUUUAUCC----------------------------UGAAAC-------------------------------------------------------------------------GGACGG-AAGUAAACCA------------------CCA-A--------------------------------------------------------------------------------------------------UGGUUGAAGAAACGCUCU
AACY023401421.1/1425-1370    UACGUUCAUCAUUC-------------------------UUAUU-----------------------------------------------------------------------GAAUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY021112096.1/9-58         AUCGUUCAACCC---------------------------AUAU--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------AUC------------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020348046.1/34-87        AUCGUUCAACUUC--------------------------AAUAA------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020091056.1/1924-1870    AUCGUUCAAUUUGC-------------------------AGCUC-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY020830136.1/470-531      UACGUUCAUCGCUAGUU----------------------UAAAU--------------------------------------------------------------------AAUAAGCGACGG-AAGUAGGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023551536.1/1020-1079    AUCGUUCAAUUUGAGA-----------------------CUUU----------------------------------------------------------------------UCUCAAAUCGG-AAGUAGGU--------------------UUUUA----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUG
AACY020287182.1/586-523      AUCGUUCAUUCACU-CUA---------------------AAUG--------------------------------------------------------------------UAGCAGUGAACGG-AAGUAGUCA-------------------AUU-G---------------------------------------------------------------------------------------------------UGACGAAGGAACGCAUC
AACY022780679.1/330-280      AACGUUCAACCA---------------------------UUA---------------------------------------------------------------------------UGGUCGG-AAGUAGGU--------------------UUG-AA---------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUC
AACY023603220.1/907-959      AUCGUUCAUCUUC--------------------------GUAA-------------------------------------------------------------------------GAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY020289447.1/802-747      AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGGU--------------------UCA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY021258419.1/501-453      AUCGUUGGACU----------------------------AUUA---------------------------------------------------------------------------AGUCGG-AAGUAGGC--------------------AUA-A----------------------------------------------------------------------------------------------------GCCGAAGCAACGCACC
AACY021769560.1/20-70        AUCGUUCAUCCC---------------------------UGUG--------------------------------------------------------------------------GGGACGG-AAGUAGUC--------------------GCA-A----------------------------------------------------------------------------------------------------GAUGAAGGAACGCAUU
AACY022138576.1/301-246      AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCAAAACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
CP000806.1/1043231-1043292   AUCGUUCAUCUGUUG------------------------UCAC-----------------------------------------------------------------------CAACAGACGG-AAGUAGGGA-------------------AUCAAUA-------------------------------------------------------------------------------------------------UCCCGAAGGAACGCGCC
AACY022253413.1/728-782      AUCGUUCAUCUUC--------------------------UUAUAU-----------------------------------------------------------------------GAAGACGG-AAGUAGAC--------------------GGA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
CP000828.1/3254265-3254355   AUCGUUCAUCUUGCAUCGCUUGUCUGUUUGAUU------CCU------------------------------------------------------GAUCAA--AGGUGAGUCA-GCAAGACGG-AAGUAAGG--------------------CAU-UUA--------------------------------------------------------------------------------------------------CCUGAAGGAACGCGCC
AACY021294965.1/733-791      AUCGUUCAAUUUAAG------------------------AUUUU----------------------------------------------------------------------CUUAGAUCGG-AAGUAGGU--------------------CUUUG----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUG
AACY022276201.1/156-211      UACGUUGAUAGUC--------------------------UGUU-------------------------------------------------------------------------GACUACGC-AAGUAAGCC-------------------AGAAG---------------------------------------------------------------------------------------------------GGCUGAAGCAACGGGAA
AACY022023258.1/327-273      AUCGUUCAUCUC---------------------------AUUU--------------------------------------------------------------------------GAGACGG-AAGUAGGUAA------------------UGG-U--------------------------------------------------------------------------------------------------UUACCGAAGGAACGCGUU
AACY021726409.1/435-381      AACGUUCAAUCUA--------------------------UAUUUU-----------------------------------------------------------------------UAGAUCGG-AAGUAAGC--------------------UUA-U----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGU
AACY020889107.1/530-476      AUCGUUCAUCCCA--------------------------CUCA-------------------------------------------------------------------------UGGGACGG-AAGUAGUC--------------------AAU-UUA--------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY020481299.1/727-783      AUCGUUCAACCUAU-------------------------UUUAU-----------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------GAUAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY023929012.1/60-113       AUCGUUCAUCUAU--------------------------UCAA-------------------------------------------------------------------------AUAGACGG-AAGUACCU--------------------AUCAA----------------------------------------------------------------------------------------------------GGGGAAGGAACGCACU
ABYK01000024.1/20386-20477   AUCGUUCAUCUCUUUUCGCUCU-----------------AAGGGUUUUCUAGCCCUAAUGUUC--------------------------------------------AGAG-GAGGGGAGACGG-AAGUAGGGA-------------------GUA-A---------------------------------------------------------------------------------------------------UCCCGAAGGAACGCGCC
AACY020233904.1/1236-1180    AUCGUUCAACCUAUC------------------------UAA------------------------------------------------------------------------GAUAGGUCGG-AAGUAAGC--------------------UAACU----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY024065093.1/27-81        AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUUGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023528798.1/471-421      AACGUUUAUCC----------------------------UGAAAC-------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------GAA-U----------------------------------------------------------------------------------------------------GCUGAAGAAACGCACU
AACY020234329.1/321-269      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY020481299.1/662-714      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023165440.1/778-719      AUCGUUCAUCUCU--------------------------UAGUUUU----------------------------------------------------------------------AGAGACGG-AAGUAGACCU------------------UAA-A--------------------------------------------------------------------------------------------------AAGUCGAAGGAACGCAUG
AACY020416756.1/1739-1791    AUCGUUCAUCUUC--------------------------GAGA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAC
AACY020091056.1/1992-1937    CACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GAGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020078853.1/246-296      AUCGUUCAUCCU---------------------------UAAG--------------------------------------------------------------------------GGGACGG-AAGUAAUC--------------------GUA-A----------------------------------------------------------------------------------------------------GAUGAAGGAACGCAUU
AACY022252054.1/65-115       AUCGUUCAACCC---------------------------UAAU--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------AGC-C----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
ABRS01000006.1/124108-124201 AUCGUUCAUCUCUCUAGACAUC-----------------AGUCAGUUAGCAAUUAGCCGUGAAG-------------------------------------------GAUGAUUAGGGAGACGG-AAGUAGGG--------------------GCA-ACU--------------------------------------------------------------------------------------------------CCCGAAGGAACGCGCC
AACY020564829.1/2258-2308    AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY023521111.1/1206-1153    AACGUUCAUCCC---------------------------GUUAG-------------------------------------------------------------------------GGGACGG-AAGUAAGC--------------------AAUCAA---------------------------------------------------------------------------------------------------GCUGAAGGAACGCACU
AACY020445308.1/1072-1126    AUCGUUCAAUCUGU-------------------------UAAA------------------------------------------------------------------------ACAGAUCGG-AAGUAAG---------------------GUA-AAA---------------------------------------------------------------------------------------------------CUGAAGGAACGCGGA
AACY022147633.1/208-257      AUCGUUCAUCCU---------------------------AAA---------------------------------------------------------------------------AGGACGG-AAGUAAGC--------------------AUC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY020164575.1/1649-1600    GACGUUCAUCAC---------------------------AAAU--------------------------------------------------------------------------GUGACGG-AAGUACC---------------------AAUGA-----------------------------------------------------------------------------------------------------GGGAAGGAACGCACC
AACY023148198.1/241-109      AUCGUUCAUUCCCUGCAU---------------------CAUUUUA-----------------------------------------------------------------AUGCAAGGAACGG-AAGUAGGAAGAUA---------------GGAAAACCUCUUUCUUUUUUAAAGAAAGGCAAGCAAGUACCGAUAAGGGAACGAGACCGAA---------------------------------------UAUCUACCGAAGGAACGCGUU
AACY021276613.1/384-324      AUCGUUCAAUUCUCA------------------------UAAAUAUU-------------------------------------------------------------------UGAGAAUCGG-AAGUAGGU--------------------UUA-U----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
CP000393.1/4678876-4678823   AGCGUUCAUCUUC--------------------------UCA--------------------------------------------------------------------------GAAGACGG-AAGUAAGGA-------------------AAC-A---------------------------------------------------------------------------------------------------UCCUGAAGGAAUUUACC
AACY021760230.1/244-194      AUCGUUCAACCC---------------------------UUUU--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------UUC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUA
AACY022986758.1/530-584      AUCGUUCAACUC---------------------------AUUGU-------------------------------------------------------------------------GAGUCGG-AAGUAGGUAC------------------AUU----------------------------------------------------------------------------------------------------GUACUGAAGGAACGCAUG
AACY023880517.1/846-898      AACGUUCAUCCU---------------------------AAAA--------------------------------------------------------------------------AGGACGG-AAGUAGGCA-------------------UAU-A---------------------------------------------------------------------------------------------------UGCCGAAGGAACGCACC
AACY020155181.1/1032-1082    UACGUUCAACC----------------------------UUUAU--------------------------------------------------------------------------GGUCGG-AAGUAAGC--------------------UUGAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAU
AACY020394557.1/1190-1239    AUCGUUCAUCUC---------------------------UUA---------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCCAC
AACY020509663.1/287-237      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY022521969.1/251-194      AUCGUUCAACCUAU-------------------------AUAA------------------------------------------------------------------------GUAGGUCGG-AAGUAAGC--------------------UAAUACU--------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY022420381.1/152-97       AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCAAAACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAAA
AACY023484124.1/781-728      AUCGUUCAACUUCA-------------------------AUA-------------------------------------------------------------------------UGAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020331357.1/1285-1339    AUCGUUCAUCCUUA-------------------------CAUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY021939941.1/320-374      UUCGUUCAACCCUA-------------------------UUAA------------------------------------------------------------------------UGGGGUCGG-AAGUAGGC--------------------AUC-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCCUU
AACY022706645.1/510-562      AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCGUU
AACY021898535.1/514-566      AUCGUUCAACUC---------------------------AAUUU-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023535011.1/346-296      AUCGUUCAACCC---------------------------AUGU--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------UUC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAA
AACY023461508.1/100-163      AUCGUUCAUUCACU-CUA---------------------AAUG--------------------------------------------------------------------UAGCAGUGAACGG-AAGUAGUCA-------------------AUU-C---------------------------------------------------------------------------------------------------UGACGAAGGAACGCAUC
AACY023881567.1/1213-1266    UACGUUCAUCACCU-------------------------UUU-------------------------------------------------------------------------AGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023598562.1/165-113      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY020477826.1/1858-1912    CACGUUCAUCACCU-------------------------GACU------------------------------------------------------------------------AGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022839954.1/609-552      UUCGUUCAUC-----------------------------UUAACU--------------------------------------------------------------------------GACGG-AAGUAGAAUA------------------CUGCAAGGG----------------------------------------------------------------------------------------------UAUUCGAAGGAACGCAUU
AACY020232024.1/305-357      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
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AACY022448527.1/404-342      AUCGUUCAUCUUUAGAAA---------------------UUUA--------------------------------------------------------------------UUUUUAAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY023616234.1/174-226      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY022378028.1/248-301      UUCGUUCAUCUC---------------------------UUUUG-------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-G---------------------------------------------------------------------------------------------------UGCCGAAGGAACGCACU
AACY021233376.1/200-252      AUCGUUCAUCUAU--------------------------UCAU-------------------------------------------------------------------------AUAGACGG-AAGUAGGC--------------------AGA-C----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACU
AACY020315100.1/933-879      AUCGUUCAUCCUUA-------------------------CUUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY023585828.1/635-579      AUCGUUCAUCC----------------------------ACUAG--------------------------------------------------------------------------GGACGG-AAGUAAGUGU------------------AUAAUAA------------------------------------------------------------------------------------------------ACACUGAAGGAACGCAUU
AACY023353218.1/988-1038     CACGUUCAACUC---------------------------AUUA--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GUA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY023693896.1/589-639      CACGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGAC--------------------GAU-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020250641.1/1754-1709    AUCGUUCAUCCC---------------------------AAU---------------------------------------------------------------------------GGGACGC-AAGUAAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CU--CGGAACGGAUU
AACY022326751.1/241-187      AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023635669.1/480-533      CACGUUCAUCAUG--------------------------UUUUA------------------------------------------------------------------------CAUGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY023928625.1/934-881      AUCGUUCAACUC---------------------------ACUAA-------------------------------------------------------------------------GAGUCGG-AAGUACCC--------------------AUC-AUA--------------------------------------------------------------------------------------------------GGGGAAGGAACGCACU
AACY022667721.1/375-321      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UGC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY020363512.1/1284-1340    AUCGUUCAAUCUAAU------------------------UAUU-----------------------------------------------------------------------AUUAGAUCGG-AAGUAAGC--------------------UAA-G----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAGA
AACY020443434.1/284-409      UACGUUCAUCUUAAUC-----------------------UGCA----------------------------------------------------------------------GGUUAAGACGG-AAGUAGGGAGAUA---------------GGAAAACCUCUUUCUUUGAUCAAAGAAAGGCAAGCUAGUACCGAAAGGGAACGAGACCGAA---------------------------------------UAUCUACCGAAGGAACGCGUU
AACY024021276.1/365-419      AUCGUUCAUCCUUA-------------------------CUUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY022183448.1/579-633      AUCGUUCAUCUUUG-------------------------CUUG------------------------------------------------------------------------CAAAGACGG-AAGUAGAC--------------------AAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY022978235.1/284-233      AUCGUUCAACUC---------------------------AAUU--------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUAU----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY023255025.1/888-839      CACGUUCAUCCU---------------------------AUUAU-------------------------------------------------------------------------AGGACGG-AAGUAGC---------------------AAU-A-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACU
AACY023109972.1/190-245      CACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022196254.1/126-68       AUCGUUCAAUUUAAG------------------------AUUUU----------------------------------------------------------------------CUUAAAUCGG-AAGUAGGU--------------------CUUUG----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUG
AACY022977491.1/56-114       AUCGUUCAAUUUAAA------------------------UUUA-----------------------------------------------------------------------UUUAAAUCGG-AAGUAGAUC-------------------UAA-C---------------------------------------------------------------------------------------------------GAUCGAAGGAACGCAUG
AACY022559745.1/837-787      AUCGUUCAACUC---------------------------AUUA--------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------GAU-U----------------------------------------------------------------------------------------------------GCCGAAGGAACGCACC
AACY021844398.1/504-458      AUCGUUCAUCCC---------------------------AAAA--------------------------------------------------------------------------GGGACGC-AAGUAAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CU--CGGAACGGAUU
AP008231.1/1705656-1705712   AUCGUUGGCCCAG--------------------------UUUAU------------------------------------------------------------------------CUGGGUGG-AAGUAAGGUC------------------UUU----------------------------------------------------------------------------------------------------GGCCUGAAGCAACGCGCC
AACY023477415.1/486-438      UACGUUCAUCCUC--------------------------GCAA-------------------------------------------------------------------------GAGGACGC-AA--AAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CUGAAGGAACGGAUG
AACY023249604.1/301-248      AUCGUUCAUCCU---------------------------UUCUU-------------------------------------------------------------------------GGGACGG-AAGUAAGUA-------------------AUA-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY020134078.1/262-212      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020133097.1/1416-1466    AUCGUUCAUCCC---------------------------CUAG--------------------------------------------------------------------------GGGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
BA000022.2/458952-458891     AUCGUUCAUCUUCU-------------------------CUUUUUGA--------------------------------------------------------------------AGAAGACGG-AAGUAGGGA-------------------UAU-AU--------------------------------------------------------------------------------------------------UCCUGAAGGAACGCGCC
AACY021804600.1/576-692      UACGUUCAUCAUAUA------------------------GCAA-----------------------------------------------------------------------UAUAUGACGG-AAGUAAG-CAAC----------------CUGAAAACCUCUUACAUUUGUAAGGCAAGCAAGUACCGAAAGGGAACGAGACCGAAA--------------------------------------------GUUGACUGAAGGAACGCGUU
AACY020096225.1/446-392      UACGUUCAUCAUCC-------------------------GUUU------------------------------------------------------------------------GGAUGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY021768549.1/729-784      UACGUUCAUCAUUC-------------------------ACUUU-----------------------------------------------------------------------GAAUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020039026.1/3657-3709    AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY022499355.1/321-269      AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY021363006.1/402-353      UACGUUCAACC----------------------------UUAU---------------------------------------------------------------------------GGUCGG-AAGUAAGC--------------------UUGUA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAU
AACY023900896.1/540-595      AUCGUUCAAUCUGAA------------------------UUAA-----------------------------------------------------------------------UUCAGAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023615516.1/874-927      AUCGUUCAACUUC--------------------------AUUAC------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020388700.1/1545-1494    AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY023484124.1/902-852      AUCGUUCAACUC---------------------------UGAG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY022842103.1/565-617      AUCGUUCAACUCU--------------------------UUAU-------------------------------------------------------------------------AGAGUCGG-AAGUAGGC--------------------AAU-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY022404797.1/184-240      AUCGUUCAACUUAUU------------------------AUAC-----------------------------------------------------------------------AAUAAGUCGG-AAGUAAGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY023268770.1/563-512      AUCGUUUAUCCC---------------------------AUUUU-------------------------------------------------------------------------GGGACGG-AAGUAGGC--------------------AAU-C----------------------------------------------------------------------------------------------------GCCGAAGAAACGCACC
AACY020042403.1/1204-1151    AUCGUUCAAUAUGC-------------------------AAAU------------------------------------------------------------------------GCAUAUCGG-AAGUAGGU--------------------AAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020428011.1/1761-1709    AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY021334105.1/365-315      AUCGUUCAACCC---------------------------AAAU--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------AUC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY022978235.1/220-164      AUCGUUCAAUCUAU-------------------------UUUUA-----------------------------------------------------------------------AUAGAUCGG-AAGUAAGC--------------------ACCAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY021861345.1/60-113       AACGUUCAUCCC---------------------------AUAAG-------------------------------------------------------------------------GGGACGG-AAGUAAGCA-------------------AUC-A---------------------------------------------------------------------------------------------------UGCUGAAGGAACGCACU
AACY022135883.1/600-541      AUCGUUCAUCUCAUU------------------------UAAUG----------------------------------------------------------------------AAUGAGACGG-AAGUAGGU--------------------UUAGUU---------------------------------------------------------------------------------------------------ACUGAAGGAACGCGGU
AACY020443307.1/1766-1818    AUCGUUCAUCUCU--------------------------AUUA-------------------------------------------------------------------------GGAGACGG-AAGUAGAC--------------------AAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCU
AACY023689073.1/1342-1284    AUCGUUCAUCUCAUU------------------------UAAUG----------------------------------------------------------------------AGUGAGACGG-AAGUAGGU--------------------UGAAA----------------------------------------------------------------------------------------------------GCCGAAGGAACGCUGU
AACY020151967.1/2177-2122    UACGUUCAUCACUC-------------------------UUAUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY021702671.1/742-687      AUCGUUCAAUCUGU-------------------------AUAA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAAUA----------------------------------------------------------------------------------------------------GCCGAAGGAACGCGGA
AACY021302428.1/187-138      CACGUUCAUCCU---------------------------AUCA--------------------------------------------------------------------------AGGACGG-AAGUAGC---------------------AUAAC-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACC
AACY023879838.1/214-163      AUCGUUCAACCC---------------------------UUUUU-------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------UUC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAA
AADV02000026.1/14400-14340   AUCGUUCAUCUGCUG------------------------CUAU-----------------------------------------------------------------------CAGCAGACGG-AAGUAGGGA-------------------AAA-AUA-------------------------------------------------------------------------------------------------UCCCGAAGGAACGCGCC
AACY022448527.1/329-269      AUCGUUCAAUUCUCA------------------------UUAUUUUU-------------------------------------------------------------------UGAGAAUCGG-AAGUAGGU--------------------UUA-U----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020482819.1/233-180      AUCGUUCAUCUUCU-------------------------ACU-------------------------------------------------------------------------AGAAGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCGUG
AACY021451918.1/661-712      AACGUUCAUCCU---------------------------AAAA--------------------------------------------------------------------------AGGACGG-AAGUAGGC--------------------AAUAU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCACC
AACY022691753.1/662-610      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY022242696.1/765-815      CACGUUCAUCCU---------------------------UAAC--------------------------------------------------------------------------AGGACGG-AAGUAGGC--------------------UUA-U----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUU
AACY022800930.1/463-412      UACGUUCAUCCC---------------------------UCCG--------------------------------------------------------------------------GGGACGC-AAGUAGGA--------------------CAGAG----------------------------------------------------------------------------------------------------UCCGAAGGAACGGGAG
AACY023174288.1/756-811      AUCGUUCAUCCUAA-------------------------CUAA------------------------------------------------------------------------UAAGGACGG-AAGUAAGC--------------------UUCAU----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020106880.1/29-81        AUCGUUCAUCUUU--------------------------GAAA-------------------------------------------------------------------------AAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCGAG
AACY021423025.1/318-373      AUCGUUCAAUUUGC-------------------------UUUAA-----------------------------------------------------------------------GCAAAUCGG-AAGUAGGU--------------------UUU-U----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020210349.1/1880-1826    AUCGUUCAACUC---------------------------GUAGU-------------------------------------------------------------------------GAGUCGG-AAGUAGGUAC------------------AUU----------------------------------------------------------------------------------------------------GUACCGAAGGAACGCAUG
AACY023549608.1/451-399      AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------AAUGAA---------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUC
AACY020234329.1/394-340      AUCGUUCAUCCUUA-------------------------CUUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY023407327.1/810-760      AUCGUUCAUCC----------------------------AUUUAC-------------------------------------------------------------------------GGACGG-AAGUAAGC--------------------AAC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY021390959.1/810-861      AACGUUCAUCUA---------------------------UC----------------------------------------------------------------------------UAGACGG-AAGUAAGGCU------------------UCU----------------------------------------------------------------------------------------------------AGCCUGAAGGAACGCAUU
AACY021347722.1/342-294      UUCGUUCAUCUCC--------------------------UACG-------------------------------------------------------------------------GGAGACGC-AA--AAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CUGAAGGAACGGGAA
AACY020034973.1/2040-1979    UACGUUCAUCUCCUA------------------------ACAC-----------------------------------------------------------------------UAGGAGACGC-AAGUACCUCA------------------CGAAU--------------------------------------------------------------------------------------------------GGAGGGAAGGAACGGGAA
AACY020132250.1/2937-2987    AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAA
AACY020157868.1/401-455      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY023545052.1/258-203      AUCGUUCAAUUUGCC------------------------UUA------------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UUA-U----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY021890349.1/593-642      AUCGUUUAUCC----------------------------UAUAC--------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------AUU-U----------------------------------------------------------------------------------------------------GCCGAAGAAACGCACC
AACY022378028.1/193-244      UUCGUUCAUCUA---------------------------UC----------------------------------------------------------------------------UAGACGG-AAGUAAAGCU------------------UUU----------------------------------------------------------------------------------------------------GGCUUGAAGGAACGCGUU
AACY020399464.1/855-915      AUCGUUCAAUUCUCA------------------------UAAAUAUU-------------------------------------------------------------------UGAGAAUCGG-AAGUAGGU--------------------UUA-U----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY021953087.1/881-823      AUCGUUCAUC-----------------------------GUUAUUUGGG----------------------------------------------------------------------GACGG-AAGUAGG---------------------UAAAAAAUCAAA----------------------------------------------------------------------------------------------CCGAAGGAACGCAUC
AACY022957008.1/763-713      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY022120080.1/17-69        AUCGUUCAUCUUC--------------------------UAAA-------------------------------------------------------------------------GAAGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGC
AACY020210349.1/1813-1757    AUCGUUCAAUCUAAU------------------------GUUG-----------------------------------------------------------------------AUUAGAUCGG-AAGUAAGC--------------------UCC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020210502.1/438-383      CACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY021451657.1/180-230      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020192141.1/2094-2039    AUCGUUCAAUUUGCC------------------------UUA------------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UUA-U----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020502525.1/359-305      AUCGUUCAUCCUUA-------------------------CAUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY020215975.1/332-285      UUCGUUCAGGC----------------------------ACUG---------------------------------------------------------------------------GCCCGG-AAGUAGC---------------------AUACA-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACC
AACY023937387.1/1535-1585    AACGUUCAACCA---------------------------UUA---------------------------------------------------------------------------UGGUCGG-AAGUAGGU--------------------UUG-AA---------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUC
AACY023536350.1/587-532      CACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GAGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020399464.1/780-842      AUCGUUCAUCUUUAAAAA---------------------UUUA--------------------------------------------------------------------UUUUUAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY021885836.1/326-273      UUCGUUCAUCUC---------------------------UUUAA-------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UGCCGAAGGAACGCACU
AACY021946484.1/524-582      AUCGUUCAAUUUAAG------------------------UUUUU----------------------------------------------------------------------CUUAAAUCGG-AAGUAAGU--------------------CUUUG----------------------------------------------------------------------------------------------------ACUGAAGGAACGCAUG
AACY022283709.1/46-98        AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020235333.1/134-79       AUCGUUCAAUUUGUC------------------------UUU------------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UUA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020766012.1/637-583      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY023899502.1/1274-1328    AUCGUUCAUCCUUA-------------------------CUUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY022336911.1/652-702      AUCGUUCAACCC---------------------------UGAA--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------UUC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAA
AACY023520018.1/1362-1418    UUCGUUCAUCAGAG-------------------------AAGA------------------------------------------------------------------------CCCUGACGG-AAGUAGGU--------------------AAUGAC---------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY020456021.1/49-101       AUCGUUCAUCUC---------------------------GAGA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UGCCGAAGGAACGCACC
AACY023065314.1/381-329      AUCGUUCAUCUUC--------------------------GAGA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAC
AACY022102949.1/877-822      AUCGUUCAACCUAU-------------------------UUUC------------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------CAUAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCUCA
AACY023007897.1/839-894      CACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY021241356.1/534-486      AUCGUUCAGCCA---------------------------UGA---------------------------------------------------------------------------UGGCCGG-AAGUAGGU--------------------AAU------------------------------------------------------------------------------------------------------ACCGAAGGAACGCACC
AACY023736167.1/1195-1245    AUCGUUCAACCC---------------------------GCAU--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------UGA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAA
AACY020419699.1/478-538      AUCGUUCAAUUCUCA------------------------UUAAUAUU-------------------------------------------------------------------UGAGGAUCGG-AAGUAGGU--------------------UUA-U----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020346740.1/174-231      AUCGUUCAUCUCAU-------------------------AAUUUGA---------------------------------------------------------------------GUGAGACGG-AAGUAGG---------------------GUA-AAA---------------------------------------------------------------------------------------------------CCGAAGGAACGCAGU
AACY024076743.1/893-788      GUCGUUUAUCUCAUAA-----------------------GUAUUUUCCAGUAUCUCCUUAAGGCGCACAGCAAAAAUUGGUUCAAAACCA-----------------------UUGUGAGACGC-AAGUAAGC--------------------GGA-A----------------------------------------------------------------------------------------------------GCUGAAGAAACGGAGU
AACY024104261.1/967-915      AUCGUUCAUCUUC--------------------------GUAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAC
AACY023448407.1/107-157      AACGUUCAUCCC---------------------------UUAG--------------------------------------------------------------------------GGGACGG-AAGUAGUC--------------------AUA-A----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY020094250.1/485-531      AUCGUUCAGUCCC--------------------------AUAA-------------------------------------------------------------------------GGGACCGC-AAGUA-----------------------AGCCGA------------------------------------------------------------------------------------------------------CACGGAACGGA--
AACY020476800.1/1958-1908    AUCGUUCAUCCC---------------------------CUAG--------------------------------------------------------------------------GGGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020042403.1/1270-1217    CACGUUCAUCAUG--------------------------UUUUA------------------------------------------------------------------------CAUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022668466.1/390-444      AUCGUUCAAUUUGC-------------------------AGCUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023104284.1/766-826      AUCGUUCAAUUUAGGA-----------------------UUAU----------------------------------------------------------------------UCCUGAAUCGG-AAGUAAGUC-------------------AAA-A---------------------------------------------------------------------------------------------------GACUGAAGGAACGCAUG
AACY024103490.1/687-737      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023204119.1/495-442      AUCGUUCAUCCC---------------------------UUAUA-------------------------------------------------------------------------GGGUCGG-AAGUAUGC--------------------UAU-AAU--------------------------------------------------------------------------------------------------GCAGAAGGAACGCAUC
AACY023015051.1/670-527      AUCGUUCAUCUUAUUU-----------------------UAUU----------------------------------------------------------------------AAAUAGGACGG-AAGUAGGAAG------------------AUAGGAAAACCUCUUUCUUUUUUAAAGAAAGGCUAGCAAGUACCGCUUGGGUUAAUUUAUCUUAGGCGGGAACGAGACCGAAUAU------------------CUGCCGAAGGAACGCGUU
AACY021720846.1/185-129      UUCGUUCAUUUUGA-------------------------UUAUUU----------------------------------------------------------------------UCAAAACGG-AAGUAGAC--------------------AUA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCGUG
AACY020505512.1/1125-1075    AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023949594.1/631-577      AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020135087.1/1498-1558    UACGUUCAUCCUAAUUU----------------------AAUC---------------------------------------------------------------------AAAUUAGGACGG-AAGUAGUC--------------------GUG-A----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY020331357.1/1358-1410    AUCGUUCAUCUUC--------------------------GGAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGAC
AACY022617765.1/678-626      AUCGUUCAUCCC---------------------------UUUA--------------------------------------------------------------------------GGGUCGG-AAGUAUGCA-------------------UUA-A---------------------------------------------------------------------------------------------------UGCAGAAGGAACGCAUC
AAXW01000008.1/84668-84587   GUCGUUCAUCUCUACAUUGU-------------------UACGAGAAAAC-----------------------------------------------------------ACAGUGAAGGGACGG-AAGUAGGCUU------------------GUAUCAUG-----------------------------------------------------------------------------------------------AAGCCGAAGGAACGCUCA
AACY023647930.1/388-442      AUCGUUCAACCUA--------------------------UUAUU------------------------------------------------------------------------UAGGUCGG-AAGUAAGC--------------------CAAAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY023099954.1/111-167      AUCGUUCAUCUUUAU------------------------GUAA-----------------------------------------------------------------------AUAAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY021623722.1/425-479      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY021267397.1/434-486      GUCGUUCAUCUC---------------------------AAAU--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------AAU-AUA--------------------------------------------------------------------------------------------------ACCGAAGGAACGCACU
AACY023745558.1/335-391      UUCGUUCAUCUA---------------------------UC----------------------------------------------------------------------------UAGACGG-AAGUAAGUCUU-----------------UAA-UUU-----------------------------------------------------------------------------------------------AAGACUGAAGGAACGCAUU
AACY021138991.1/535-589      AUCGUUCAAUUUGC-------------------------CAUAA-----------------------------------------------------------------------GCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023501516.1/463-414      UACGUUCAGCC----------------------------UUAU---------------------------------------------------------------------------GGUCGG-AAGUAAGC--------------------UUGUA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAA
AACY023870187.1/312-365      AUCGUUCAUCCUC--------------------------UUA--------------------------------------------------------------------------GAGGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY020338589.1/245-295      AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY021391528.1/593-646      UACGUUCAUCUUAC-------------------------AAA-------------------------------------------------------------------------GUAAGACGG-AAGUAAGC--------------------GAA-U----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY020396882.1/757-816      AUCGUUCAAUUUAGGU-----------------------UUUA----------------------------------------------------------------------ACUUAAAUCGG-AAGUAGAU--------------------CUUUG----------------------------------------------------------------------------------------------------AUCGAAGGAACGCAUG
AJ630128.1/142359-142415     AUCGUUCAUUCGCUAUU----------------------CGCA---------------------------------------------------------------------AAUAGCGAACGC-AA--AAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CUGAAGGAACGGGAC
AACY020428429.1/870-817      AUCGUUCAACUUC--------------------------AAUAC------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY024021050.1/441-384      CUCGUUCAUUCUCA-------------------------UAGAC-----------------------------------------------------------------------UGAGAACGG-AAGUAGGU--------------------AAUGAC---------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY021396263.1/541-596      UACGUUCAUCAUUC-------------------------UUAUU-----------------------------------------------------------------------GAAUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020039042.1/482-534      AUCGUUCAUCUC---------------------------GCAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY020425839.1/427-482      AUCGUUCAACCUAU-------------------------AUAU------------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------UAUAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020141842.1/1386-1335    AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020396882.1/829-878      AUCGUUCAACCC---------------------------UUUU--------------------------------------------------------------------------GGGUCGG-AAGUAGGC--------------------AAA------------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY022997040.1/784-729      UACGUUCAUCAUGU-------------------------GUUUA-----------------------------------------------------------------------ACAUGACGG-AAGUAGGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY020266601.1/1180-1128    AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY021281822.1/369-422      CUCGUUCAUCUC---------------------------UUUAA-------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UGCCGAAGGAACGCACU
AACY021669684.1/506-562      AUCGUUCAACUC---------------------------AUUGU-------------------------------------------------------------------------GAGUCGG-AAGUAGGCAU------------------UACUA--------------------------------------------------------------------------------------------------GUGCUGAAGGAACGCAUG
AACY023503565.1/654-602      AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY021978343.1/929-873      AUCGUUCAAUCUGU-------------------------UGAAU-----------------------------------------------------------------------GCAGAUCGG-AAGUAGGA--------------------UAA-AA---------------------------------------------------------------------------------------------------UCUGAAGGAACGCGGA
AACY020473531.1/2284-2334    AUCGUUCAACUC---------------------------AAAU--------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------ACA-U----------------------------------------------------------------------------------------------------GCCGAAGGAACGCACC
AACY021804470.1/673-738      AUCGUUCAUCUUGUAAGU---------------------UUUCUAA-----------------------------------------------------------------GCUUAUUGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023184960.1/517-567      AACGUUCAACC----------------------------AUUUA--------------------------------------------------------------------------GGUCGG-AAGUAGGU--------------------UUG-AA---------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUC
AACY020001711.1/3605-3667    UACGUUCAUCUCAACA-----------------------CAU-----------------------------------------------------------------------UGUUGGGACGC-AAGUAAGCA-------------------AGUUAAG-------------------------------------------------------------------------------------------------UGCUGAAGGAACGGGAA
AACY023516001.1/535-484      UUCGUUCAACCC---------------------------CAAAA-------------------------------------------------------------------------GGGUCGG-AAGUAGGC--------------------AUC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCUUA
AACY022521969.1/316-264      AUCGUUCAACUC---------------------------AAUUU-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023629992.1/212-160      AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY020236614.1/876-926      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY024036082.1/501-556      UACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020101836.1/1327-1222    GUCGUUUAUCUCAUAA-----------------------GUAUCUUCUAGUAUCUCCUUAUGGCGCAUAGCAAUAAUUGGUUCAAAACCA-----------------------UUGUGAGACGC-AAGUAAGC--------------------GGA-A----------------------------------------------------------------------------------------------------GCUGAAGAAACGGAGU
AACY020141842.1/1458-1406    AUCGUUCAACUUC--------------------------UUAG-------------------------------------------------------------------------GAAGUCGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY020428904.1/128-179      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY023550809.1/726-595      AUCGUUCAUUCAGUGCUCU--------------------UUUUU------------------------------------------------------------------AGUGCAUUGAACGG-AAGUAGG-AAAAC---------------CUGAAAACCUCUAUCUGAAAAGAUAGGUAAGCAAGUACCCAUAAGGGGAACGAGACCGAAA---------------------------------------GUUUUACCGAAGGAACGCGUU
AACY020232024.1/232-286      AUCGUUCAUCCUUA-------------------------CUUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY022466684.1/260-381      UUCGUUCAUCUUAUA------------------------UUUUA----------------------------------------------------------------------UAUAAGACGG-AAGUAGG-AAAC----------------CUGAAAACCUCUUUCUAUUCAGAAAGGCAAGCAAGUACCCGCAAGGGGAACGAGACCGAAA----------------------------------------GUUUACCGAAGGAACGCUAU
AACY021808171.1/320-267      UACGUUCAUCAUG--------------------------UUUUA------------------------------------------------------------------------CAUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020394557.1/1138-1188    AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020362314.1/1080-1026    AUCGUUCAAUCUGU-------------------------UUUU------------------------------------------------------------------------ACAGAUCGG-AAGUAAGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY022404797.1/122-172      AUCGUUCAUCUC---------------------------CAAG--------------------------------------------------------------------------GAGACGG-AAGUAGAC--------------------UUA-G----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020209947.1/299-354      AUCGUUCAAUUUGCC------------------------CUUA-----------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020208065.1/308-212      AACGUUCAUCUCACU------------------------UGUU-----------------------------------------------------------------------AGUGAGACGG-AAGUAGGAAGAU----------------AGGAGCUUGAAAGCUCCGCUGCGAGUAAAUUGCUAA-----------------------------------------------------------------AUCUGCCGAAGGAACGCGUU
AACY023081145.1/227-278      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY023165440.1/662-610      UUCGUUCAACCUA--------------------------GAAA-------------------------------------------------------------------------UAGGUCGG-AAGUAGG---------------------GUA-AUA---------------------------------------------------------------------------------------------------CCGAAGGAACGCGCC
AACY020123372.1/1977-2040    UUCGUUCAUUCACU-CUA---------------------AAUG--------------------------------------------------------------------UAGCAGUGAACGG-AAGUAGUCA-------------------AUU-G---------------------------------------------------------------------------------------------------UGACGAAGGAACGCAUC
AACY023910677.1/47-97        AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAA
AACY023579103.1/822-764      AUCGUUCAUCCUU--------------------------AUUGA------------------------------------------------------------------------AAGGACGG-AAGUAGGU--------------------AAA-AAUCAA-----------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY023109972.1/258-312      AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023150189.1/610-560      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAA
AACY020237209.1/884-811      AUCGUUGGGCUC---GGGCCUG-----------------CUCUUA--------------------------------------------------------------CAGACCUCUUCAGCCGG-AAGUAGCCAC------------------CCG-C--------------------------------------------------------------------------------------------------GUGGCGAAGCAACGCUCC
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AACY020214273.1/1267-1172    AUCGUUCAUUCUCG-------------------------CAA-------------------------------------------------------------------------CGAGAACGG-AAGUAAGAAAC-----------------CUGAAAACCUCUCACUUUCUGUGAGGCUAGUUAACCGAAA--------------------------------------------------------------GUUUCCGAAGGAACGCAUG
AACY020151967.1/136-81       CACGUUCAUCACUC-------------------------UUAUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023616234.1/101-155      AUCGUUCAUCCUUA-------------------------CUUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY021883244.1/45-103       CACGUUCAUUUGCUAUU----------------------UGCA---------------------------------------------------------------------AAUAGCAAACGG-AAGUAGG---------------------GAU-A-----------------------------------------------------------------------------------------------------CCGAAGGAACGCGAA
AACY021946484.1/595-645      AUCGUUCAACCC---------------------------AUUU--------------------------------------------------------------------------GGGUCGG-AAGUAAGC--------------------UGA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAA
AACY020938992.1/540-595      AUCGUUCAUUUUGA-------------------------GUAUC-----------------------------------------------------------------------UCAAAACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY023091009.1/272-216      CACGUUCAUCACU--------------------------AUUUUUUG---------------------------------------------------------------------AGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023987148.1/159-105      AUCGUUCAAUCUGU-------------------------AUUA------------------------------------------------------------------------ACAGAUCGG-AAGUAGGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGA
AACY023530723.1/1332-1382    AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------GAG-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCCAC
AACY021402648.1/672-624      AACGUUCACCC----------------------------GAAA---------------------------------------------------------------------------GGGCGG-AAGUAGGC--------------------AAU-C----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY023581064.1/358-408      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY020061925.1/1003-1053    AUCGUUCAUCCC---------------------------UAGA--------------------------------------------------------------------------GGGACGG-AAGUAGUC--------------------GCA-A----------------------------------------------------------------------------------------------------GAUGAAGGAACGCAUU
AACY022670969.1/833-886      UACGUUCAUCUUU--------------------------UUAAAU-----------------------------------------------------------------------AAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAA-GAACGCAUG
AACY024019205.1/1314-1364    AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023545356.1/434-488      CACGUUCAUCACC--------------------------UUUUAU-----------------------------------------------------------------------GGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020070556.1/2461-2516    AUCGUUCAACCUAU-------------------------UACU------------------------------------------------------------------------AUAGGUCGG-AAGUAAGC--------------------CAAAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020078007.1/998-944      AUCGUUCAAUCCUU-------------------------UUU-------------------------------------------------------------------------AGGGGUCGG-AAGUAGGU--------------------AUC-AU---------------------------------------------------------------------------------------------------ACUGAAGGAACGCGGA
AACY021702671.1/811-755      UUCGUUCAUUUUG--------------------------AUUAAUUU---------------------------------------------------------------------CAAAACGG-AAGUAGAC--------------------AUA-U----------------------------------------------------------------------------------------------------GUCGAAGGAACGCGUG
AACY023359536.1/288-339      UACGUUCAUCCC---------------------------UUUU--------------------------------------------------------------------------GGGACGC-AAGUAAGC--------------------CAGAG----------------------------------------------------------------------------------------------------GCUGAAGGAACGGGAA
AACY020458048.1/622-572      UACGUUCAUCCU---------------------------ACAAA-------------------------------------------------------------------------AGGACGG-AAGUAGCA--------------------CUA------------------------------------------------------------------------------------------------------UGCGAAGGAACGCACU
AACY020235333.1/201-147      CACGUUCAUCACCU-------------------------AGUU------------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY021769560.1/74-126       AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-G---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY023950991.1/720-674      UACGUUCAUCC----------------------------AAUG---------------------------------------------------------------------------GGACGG-AAGUAGG---------------------GAA-A-----------------------------------------------------------------------------------------------------CCGAAGGAACGCACU
AACY020203238.1/1485-1532    UACGUUCAUCCC---------------------------ACA---------------------------------------------------------------------------GGGACGG-AAGUAGC---------------------GAA-A-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACU
AACY023655704.1/781-728      AACGUUCAAUCUAU-------------------------AUU-------------------------------------------------------------------------AUAGAUCGG-AAGUAAGC--------------------UUA-U----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGU
AACY022977491.1/127-179      AUCGUUCAACCUU--------------------------UGUA-------------------------------------------------------------------------AAGGUCGG-AAGUAAGC--------------------UAC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGUA
AACY024072980.1/170-229      AUCGUUCAUCUUAUU------------------------GAUUA----------------------------------------------------------------------AGUGAGACGG-AAGUAGGU--------------------UAGGGA---------------------------------------------------------------------------------------------------ACCGAAGGAACGCUGU
AACY020596620.1/143-197      AUCGUUCAAUUUGC-------------------------AGCUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGG---------------------UAU-AC----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023593735.1/2-55         AUCGUUC-AUCUGU-------------------------UUAG------------------------------------------------------------------------ACAGAUCGG-AAGUAGG---------------------AUA-AUA---------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY023136147.1/412-467      AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCAAAACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY020376888.1/119-175      UUCGUUCAUUUUGA-------------------------UUAAUU----------------------------------------------------------------------UCAAGACGG-AAGUAGAC--------------------AUA-U----------------------------------------------------------------------------------------------------GUCGAAGGAACGCGUG
AACY020411127.1/1629-1524    GUCGUUUAUCUCAUAA-----------------------AUAUCUUCUAGUAUCUCCUUAUGGCGCAUAGCAAUAAUUGGUUCAAAACCA-----------------------UUGUGAGACGC-AAGUAAGC--------------------GGA-A----------------------------------------------------------------------------------------------------GCUGAAGAAACGGAGU
AACY020428281.1/2388-2331    AUCGUUCAUUCAC--------------------------UUAAUU-----------------------------------------------------------------------GUGGACGG-AAGUAAGUGU------------------AGU----------------------------------------------------------------------------------------------------ACGCUGAAGGAACGCAUC
AACY023653930.1/113-164      AUCGUUCAACUC---------------------------AAUU--------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUAU----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY020032680.1/219-166      AUCGUUCAUCCU---------------------------UUCUU-------------------------------------------------------------------------GGGACGG-AAGUAGGUA-------------------AUA-G---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY020517659.1/1035-1087    AUCGUUCAUCUC---------------------------GCAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY023736167.1/1122-1182    AUCGUUCAAUUUAAGAA----------------------UUU----------------------------------------------------------------------UUCUUAAAUCGG-AAGUAAGU--------------------CAUUG----------------------------------------------------------------------------------------------------ACUGAAGGAACGCAUG
AACY022295381.1/548-493      CACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023245794.1/303-250      AUCGUUCAAUCCUU-------------------------CUA-------------------------------------------------------------------------AAGGAUCGG-AAGUAGGG--------------------GUG-A----------------------------------------------------------------------------------------------------CCUUAAGGAACGCGGA
AACY020388886.1/849-901      AUCGUUCAACCUU--------------------------UUUA-------------------------------------------------------------------------AAGGUCGG-AAGUAAGC--------------------UAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY021192611.1/379-425      AUCGUUCAUCC----------------------------UAAA---------------------------------------------------------------------------GGACGG-AAGUAGG---------------------CUA-G-----------------------------------------------------------------------------------------------------CCGAAGGAACGCACU
AACY020209947.1/232-287      CACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY023594419.1/724-679      AUCGUUCAUCCC---------------------------AAU---------------------------------------------------------------------------GGGACGC-AAGUAAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CU--CGGAACGGAUU
AACY021278176.1/444-507      CUCGUUCAUUCACU-CUA---------------------AAUG--------------------------------------------------------------------UAGCAGUGAACGG-AAGUAGGA--------------------AAUUAA---------------------------------------------------------------------------------------------------UCCGAAGGAACGCAUC
AACY022138270.1/399-345      AUCGUUCAAUCUGU-------------------------UUAU------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------UAA-U----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGGA
AACY023219984.1/1151-1101    AUCGUUCAUCCC---------------------------UGUG--------------------------------------------------------------------------GGGACGG-AAGUAGUC--------------------GCA-A----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY022169908.1/95-147       UACGUUCAUCCU---------------------------CACU--------------------------------------------------------------------------AGGACGG-AAGUAGGCG-------------------AAA-A---------------------------------------------------------------------------------------------------CGCUGAAGGAACGCACC
AACY022069665.1/540-490      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY021885836.1/381-330      UUCGUUCAUCUA---------------------------UC----------------------------------------------------------------------------UAGACGG-AAGUAGAGCU------------------UUU----------------------------------------------------------------------------------------------------AGCUUGAAGGAACGCAUU
AACY020074155.1/1646-1593    UACGUUCAUCAUG--------------------------UUUAU------------------------------------------------------------------------CAUGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY020329574.1/151-203      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGAC
AACY020557063.1/1854-1800    CACGUUCAUCACUC-------------------------UUAG------------------------------------------------------------------------GAGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020332481.1/755-808      AUCGUUUAUCC----------------------------UGAAAC-------------------------------------------------------------------------GGACGG-AAGUAAACC-------------------ACAAA---------------------------------------------------------------------------------------------------GGUUGAAGAAACGCUCU
AACY023484401.1/885-837      AACGUUCACCC----------------------------GAAA---------------------------------------------------------------------------GGGCGG-AAGUAAGC--------------------AAU-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCACC
AACY020039026.1/3602-3653    AUCGUUCAUCCC---------------------------GCGAG-------------------------------------------------------------------------GGGACGG-AAGUAGUC--------------------GCA-A----------------------------------------------------------------------------------------------------GAUGAAGGAACGCAUU
AACY023899502.1/1347-1399    AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY022839264.1/262-316      AUCGUUCAACUC---------------------------AUAGU-------------------------------------------------------------------------GAGUCGG-AAGUAAGUAC------------------GUU----------------------------------------------------------------------------------------------------GUACUGAAGGAACGCAUG
AACY020555885.1/2520-2467    AUCGUUCAACUUC--------------------------AAUAC------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY022167379.1/379-429      AACGUUCAUCCU---------------------------UAAG--------------------------------------------------------------------------GGGACGG-AAGUAGUC--------------------GAA-A----------------------------------------------------------------------------------------------------GACGAAGGAACGCAUU
AACY024061969.1/570-623      AACGUUCAUCUU---------------------------UUGAUAU-----------------------------------------------------------------------AAGACGG-AAGUAGGU--------------------GAU-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUU
AACY021505351.1/797-748      -ACGUUCAACCA---------------------------UUA---------------------------------------------------------------------------UGGUCGG-AAGUAGGU--------------------UUG-AA---------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY023718955.1/359-412      AUCGUUCAAUCUGU-------------------------UUUU------------------------------------------------------------------------ACAGAUCGG-AAGUAGGU--------------------AAU------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AANP01000006.1/217608-217533 AACGUUGAGCU---UGAUGGGUGC---------------UCC---------------------------------------------------------------GCAUCUGUCGUUCAGCCGG-AAGUAGCC--------------------CCUCCGCAA------------------------------------------------------------------------------------------------GGCGAAGCAACGCUCC
AACY023216978.1/742-690      AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY022360960.1/703-755      AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAGGU--------------------GAA-A----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGAC
AACY023367856.1/758-708      ACCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY022515796.1/555-501      AUCGUUCAAUUUGC-------------------------AGUUU-----------------------------------------------------------------------GCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY022849373.1/548-601      CACGUUCAUCAUG--------------------------UUUUA------------------------------------------------------------------------CAUGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY020411502.1/323-380      AUCGUUCAUCUCAUU------------------------AAUUG----------------------------------------------------------------------AGUGAGACGG-AAGUAGG---------------------UAA-GAU---------------------------------------------------------------------------------------------------CCGAAGGAACGCAGU
AACY020907559.1/603-660      AUCGUUCAUCUCAU-------------------------AAUUUGA---------------------------------------------------------------------GUGAGACGG-AAGUAGGU--------------------AAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAGU
AACY020016584.1/1235-1297    UACGUUCAUCUCAAC------------------------ACAUA----------------------------------------------------------------------GUUGGGACGC-AAGUAAGCA-------------------AUAACAG-------------------------------------------------------------------------------------------------UGCUGAAGGAACGGGAA
AACY023581058.1/868-927      AUCGUUCAAUUUAAGA-----------------------GUUU----------------------------------------------------------------------UCUUAAAUCGG-AAGUAAGUC-------------------AUU-----------------------------------------------------------------------------------------------------GACUGAAGGAACGCAUG
AACY020389322.1/915-772      AUCGUUCAUCUUAUUU-----------------------UAUU----------------------------------------------------------------------AAAUAAGACGG-AAGUAGGAAG------------------AUAGGAAAACCUCUUUCUUUUUUAAAGAAAGGCUAGCAAGUACCGCUUGGGUUAAUUUAUCUUAGGCGGGAACGAGACCGAAUAU------------------CUGCCGAAGGAACGCGUU
AACY022625265.1/442-388      UACGUUCAGCC----------------------------GAGA---------------------------------------------------------------------------GGCCGG-AAGUAGACU-------------------UCAUUAUU------------------------------------------------------------------------------------------------AGUCGAAGGAACGCAUU
AACY020233904.1/1301-1249    AUCGUUCAACUC---------------------------AUUUU-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY022352167.1/319-188      AUCGUUCAUUCAGUGCCCU--------------------UUUUU------------------------------------------------------------------AGUGCAUUGAACGG-AAGUAGG-AAAAC---------------CUGAAAACCUCUAUCUGAAAAGAUAGGUAAGCAAGUACCCGUAAGGAGAACGAGACCGAAA---------------------------------------GUUUUACCGAAGGAACGCGUU
AACY023969055.1/699-750      CACGUUCAUCC----------------------------ACUUA--------------------------------------------------------------------------GGACGG-AAGUAGAC--------------------UAC-UCA--------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUU
AACY022167379.1/433-485      AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
CP001344.1/1229538-1229443   AUCGUUCAUCUCUCUAGCAACUUA---------------CCUCUGUACUUACCUCUGUAUAGU------------------------------------------UAGGCAUCUGGAGAGACGG-AAGUAGGG--------------------GUUUC----------------------------------------------------------------------------------------------------CCCGAAGGAACGCGCC
AACY020229567.1/124-51       AUCGUUGGGCUC---GGGCCUG-----------------CUCUUA--------------------------------------------------------------CAGACCUCUUCAGCCGG-AAGUAGCCAC------------------CCG-C--------------------------------------------------------------------------------------------------GUGGCGAAGCAACGCUCC
AACY022834373.1/568-624      UACGUUCAUCUCAA-------------------------CACAU-----------------------------------------------------------------------UUGAGACGC-AAGUAGGG--------------------CUGAG----------------------------------------------------------------------------------------------------CCUGAAGGAACGGGAA
AACY020411740.1/25-75        ACCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023199264.1/943-993      GACGUUCAUCC----------------------------AACA---------------------------------------------------------------------------GGACGG-AAGUAGAC--------------------UAC-UCA--------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUU
AACY020035461.1/1291-1345    AUCGUUCAUCCU---------------------------UUUCUU------------------------------------------------------------------------GGGACGG-AAGUAAGUA-------------------AUA-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY023257588.1/1100-1154    AUCGUUCAUCCU---------------------------UUUCUU------------------------------------------------------------------------GGGACGG-AAGUAGGUA-------------------AUA-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY024036082.1/568-622      AUCGUUCAAUUUGCC------------------------UUA------------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020363512.1/1217-1271    AUCGUUCAACUC---------------------------AUUGU-------------------------------------------------------------------------GAGUCGG-AAGUAGGUAC------------------AUU----------------------------------------------------------------------------------------------------GUGCUGAAGGAACGCAUG
AACY020376888.1/188-242      AUCGUUCAAUCUGU-------------------------AUUAA-----------------------------------------------------------------------ACAGAUCGG-AAGUAGG---------------------GAA-AA----------------------------------------------------------------------------------------------------CCGAAGGAACGCGGA
AACY020529410.1/5650-5725    AACGUUGAGCU---UGACAGGUG----------------UUCCG--------------------------------------------------------------CAUCUGUCGUUCAGCCGG-AAGUAGCC--------------------CCUCCGCAA------------------------------------------------------------------------------------------------GGCGAAGCAACGCUCC
AACY023101112.1/405-460      UACGUUCAUCAUGU-------------------------UUUUA-----------------------------------------------------------------------ACAUGACGG-AAGUAGGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCAUG
AACY023868432.1/151-206      AUCGUUCAUUUUGA-------------------------AUAAU-----------------------------------------------------------------------UCAAAACGG-AAGUAAAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCAUG
AACY020562190.1/8543-8595    AUCGUUCAUCUUC--------------------------GAAA-------------------------------------------------------------------------GAAGACGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGGC
AACY022499355.1/249-198      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY020188747.1/1165-1120    AUCGUUCAUCCC---------------------------AAU---------------------------------------------------------------------------GGGACGC-AAGUAAG---------------------CCG-A-----------------------------------------------------------------------------------------------------CU--CGGAACGGAUU
AACY020123372.1/2041-2093    UUCGUUCAUCCC---------------------------GAAA--------------------------------------------------------------------------GGGACGG-AAGUAGGUG-------------------AUA-A---------------------------------------------------------------------------------------------------UACCGAAGGAACGCAUC
AACY020471289.1/1134-1183    AUCGUUCAUCC----------------------------CAAAA--------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------AUU-A----------------------------------------------------------------------------------------------------GCCGAAGGAACGCACC
AACY020324288.1/1229-1175    AUCGUUCAUCCUUA-------------------------CUUG------------------------------------------------------------------------UAAGGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY022240520.1/721-773      AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUA-------------------AUG-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCGUU
AACY020912192.1/748-800      AUCGUUCAACUC---------------------------UUUUA-------------------------------------------------------------------------GAGUCGG-AAGUAGGC--------------------AUUGU----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAUG
AACY022161803.1/756-812      AUCGUUCAUCUUUAU------------------------GUAA-----------------------------------------------------------------------AUAAAGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUUGAAGGAACGCGCC
AACY020147734.1/1525-1476    AUCGUUCAUCC----------------------------AUUAC--------------------------------------------------------------------------GGACGG-AAGUAGGC--------------------ACC-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCU
AACY023668649.1/502-562      AUCGUUCAAUUUAAUC-----------------------AUUU----------------------------------------------------------------------GGUUAAAUCGG-AAGUAGAUC-------------------UUU-U---------------------------------------------------------------------------------------------------GAUCGAAGGAACGCAUG
AACY023638748.1/548-601      AUCGUUCAACUUC--------------------------AAUAC------------------------------------------------------------------------GAAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAAC
AACY023207139.1/1222-1275    UACGUUCAUCCUAC-------------------------AGU-------------------------------------------------------------------------GUAGGACGG-AAGUAGAC--------------------GUA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCACC
AACY023523806.1/411-541      AUCGUUCAUUCAGUGCCCU--------------------UUUUU------------------------------------------------------------------AGUGCAUUGAACGG-AAGUAGG-AAAAC---------------CUGAAAACCUCUAUCUGAAAAGAUAGGCAAGCAAGUACCUGUAAGGGGAACGAGACCGAAA---------------------------------------GUUU-ACCGAAGGAACGCGUU
AACY020494819.1/354-304      AUCGUUCAACCA---------------------------UUA---------------------------------------------------------------------------UGGUCGG-AAGUAGGU--------------------UUG-AA---------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
BA000039.2/1753204-1753120   AUCGUUCAUCUUCGCUAGAGCGCACCUGA----------AAAC---------------------------------------------------------UUGGGUGAGC---AGCGAAGACGG-AAGUAGGG--------------------CAGUUGU--------------------------------------------------------------------------------------------------CCCGAAGGAACGCGCC
AACY020158276.1/1001-941     AUCGUUCAUCCUUA-------------------------UUUU------------------------------------------------------------------------UGGGGACGG-AAGUAGGU--------------------AAAAAAUCAA-----------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY023719768.1/8-61         AUCGUUCAAUCUGC-------------------------ACAA------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY022714989.1/200-142      AUCGUUCAUCCUU--------------------------GUUU-------------------------------------------------------------------------GGGGACGG-AAGUAGGU--------------------AAAAAAUCAA-----------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY021843513.1/630-685      UACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GUA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022251786.1/814-760      AUCGUUCAAUCUGU-------------------------UUAU------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------UAA-U----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGGA
AACY022623996.1/664-617      AACGUUCAGGC----------------------------GUCAA--------------------------------------------------------------------------GCCCGG-AAGUAGC---------------------AUU-A-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACU
AACY020630404.1/110-50       AUCGUUCAAUUUAAGAA----------------------UU-----------------------------------------------------------------------UUCUUAAAUCGG-AAGUAGGUC-------------------AUU-U---------------------------------------------------------------------------------------------------GACUGAAGGAACGCAUG
AACY021251278.1/383-440      AUCGUUCAAUCUAUU------------------------UUCU-----------------------------------------------------------------------AAUAGAUCGG-AAGUAAGC--------------------AACAA----------------------------------------------------------------------------------------------------GCUGAAGGAACGCAGU
AACY020400000.1/777-827      AUCGUUCAACUC---------------------------UUCG--------------------------------------------------------------------------GAGUCGG-AAGUAAGC--------------------GAA-A----------------------------------------------------------------------------------------------------GCUGAAGGAACGCGCA
AACY020400000.1/829-879      AUCGUUCAUCUC---------------------------UUAG--------------------------------------------------------------------------GAGACGG-AAGUAGGU--------------------UAA-A----------------------------------------------------------------------------------------------------ACCGAAGGAACGCGCC
AACY023461508.1/164-216      UUCGUUCAUCCC---------------------------GAAA--------------------------------------------------------------------------GGGACGG-AAGUAGGU--------------------GAU-CAU--------------------------------------------------------------------------------------------------ACCGAAGGAACGCAUC
AACY020479336.1/53-3         AACGUUCAUCCC---------------------------UUUA--------------------------------------------------------------------------GGGACGG-AAGUAGAC--------------------UAA-U----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY021669684.1/575-629      AUCGUUCAAUCUAC-------------------------AUU-------------------------------------------------------------------------GUAGAUCGG-AAGUAAGU--------------------UUAAA----------------------------------------------------------------------------------------------------ACUGAAGGAACGCGCA
AACY020570891.1/242-187      UACGUUCAUCACUC-------------------------UUUUA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY022668466.1/322-377      CACGUUCAUCACCC-------------------------UUUUA-----------------------------------------------------------------------GGUUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY021539475.1/694-640      AUCGUUCAUCCU---------------------------UUUCUU------------------------------------------------------------------------GGGACGG-AAGUAGGUA-------------------AUA-A---------------------------------------------------------------------------------------------------UACUGAAGGAACGCAUC
AACY020557063.1/1787-1732    AUCGUUCAAUCUGAA------------------------UUAA-----------------------------------------------------------------------UUCAGAUCGG-AAGUAGGU--------------------AAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020977974.1/529-472      UGCGUUGAUCCC---------------------------GGAAU-------------------------------------------------------------------------GGGACGC-AAGUAGGCC-------------------ACAUUUGG------------------------------------------------------------------------------------------------GGCCGAAGCAACGGAAA
AACY021920004.1/423-483      AUCGUUCAAUUUAAAUG----------------------GAAA---------------------------------------------------------------------CAUUUAGAUCGG-AAGUAGAC--------------------AAU-U----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY024085939.1/785-838      AUCGUUCAAUCUGU-------------------------UAAA------------------------------------------------------------------------GCAGAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY020192141.1/120-65       CACGUUCAUCACCU-------------------------UUACA-----------------------------------------------------------------------GGGUGACGG-AAGUAGAC--------------------GAA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
AACY020066766.1/2107-2054    AUCGUUCAUCUC---------------------------GAAA--------------------------------------------------------------------------GAGACGG-AAGUAGGUAA------------------UGG----------------------------------------------------------------------------------------------------UUACCGAAGGAACGCACC
AACY020570891.1/175-121      AUCGUUCAAUUUGCC------------------------AUA------------------------------------------------------------------------GGCAAAUCGG-AAGUAGGU--------------------UAA------------------------------------------------------------------------------------------------------ACCGAAGGAACGCGGA
AACY023980157.1/761-710      AACGUUCAUCUUUU-------------------------UUU-------------------------------------------------------------------------AAAAGACGG-AAGUAGC---------------------GAA-A-----------------------------------------------------------------------------------------------------GCGAAGGAACGCACC
AACY020803240.1/308-256      AUCGUUCAACUC---------------------------AAUA--------------------------------------------------------------------------GAGUCGG-AAGUACCC--------------------AUC-AUA--------------------------------------------------------------------------------------------------GGGGAAGGAACGCACU
AACY021286276.1/327-277      CUCGUUCAUCCC---------------------------GCAA--------------------------------------------------------------------------GGGACGG-AAGUAGGC--------------------UAA-G----------------------------------------------------------------------------------------------------GCUGAAGGAACGUACC
AACY020494598.1/250-300      AACGUUCAACCA---------------------------UUA---------------------------------------------------------------------------UGGUCGG-AAGUAGGU--------------------UUG-AA---------------------------------------------------------------------------------------------------ACCGAAGGAACGCGUC
AACY021876887.1/486-432      CACGUUCAUCACUC-------------------------AUUU------------------------------------------------------------------------GAGUGACGG-AAGUAGAC--------------------GCA-A----------------------------------------------------------------------------------------------------GUCGAAGGAACGCAUG
CP002198.1/3653058-3653002   AUCGUUCAUCUCUG-------------------------GAAU------------------------------------------------------------------------CAGAGACGG-AAGUAGGGA-------------------AAC-C---------------------------------------------------------------------------------------------------UCCCGAAGGAACGCGCC
CP002198.1/1274053-1274110   AUCGUUCAUCUCU--------------------------UUAUACC----------------------------------------------------------------------AGAGACGG-AAGUAGGGA-------------------AAG-U---------------------------------------------------------------------------------------------------UCCCGAAGGAACGCGCC
#=GC SS_cons                 ::(((((,<<<<<<<........................_____......................................................................>>>>>>>,,,.,,,,,<<<<..................._____...................................................................................................>>>>,,,,)))))::::
#=GC RF                      AUCGUUCAuCucccc........................uuuuu......................................................................ggggaGaCGG.AAGUAGGca...................auaaa...................................................................................................ugCCGAAGGAACGCguu
//
# STOCKHOLM 1.0

#=GF AC   RF01740
#=GF ID   gyrA
#=GF DE   gyrA RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   45.00
#=GF TC   51.10
#=GF NC   33.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   GyrA_RNA_motif
#=GF SQ   18


AE016853.1/1913388-1913472 UCGUAAGUCGCUGCCCUGCAA-AUGC-UGGCAGCGGCGAGCUUCGU--AUACCCC-GAAUGG-GUU-UGCGAGGU-UUCACCAGAAAAAGGAA
CP000075.1/4990467-4990380 ACGUGAGUUGGGUCCGGGCCUGUAUG--GGGCUCAACGAGUUUGGU--GCGGCUCAGGAGAG-CCUUCGCCGAACGUCCUCAAGAGUGCGGAA
AE016853.1/5075507-5075421 ACGUGAGUUGGGUCCGGGCCUGUAUG--GGGCUCAACGAGUUUGGCUGG-GCUCAGGA--GG-GUCUUGCCAAACGUCCUCAAGAGUGCGGAA
AE015451.1/1970972-1971057 UCGUAAGUCGUCGCACC-CUU-AUGCGCUGCGGCGGCGAGCUUCGUUCG-GCCCUUGA-UGGAGCU--GCGAAGU-UUCACCAGAAAAAGGAA
CP000926.1/1515672-1515757 UCGUAAGUCGUCGCACC-CAU-AUGCGCUGCGGCGGCGAGCUUCGUUCG-GCCCUUGA-UGGAGC--UGCGAAGU-UUCACCAGAAAAAGGAA
CP000075.1/4333410-4333326 UCGUAAGUCGCUGCCCCGCAC-AUGC-UGGCAGCGGCGAGCUUCGU--AUACCCC-GAAUGG-GUU-UGCGAGGU-UUCACCAGAAAAAGGAA
CP000076.1/956664-956750   ACGUGAGUUGGGUCCGGGCCUGUAUU-GGGGCUCAGCGAGUUUGGCAGA-GCUCAGGA--GG-GU-UUGCCGGACGUCCUUAAGAGUGCAAAG
CP000680.1/2034231-2034317 UCGUGAGUCGUUGAU-GGCUUGAAGC-UAUC-GCGACGUGCUCCAUGGC-GUUCCAGGAAGA-AUGACGCGGAGU-UUCACCAGAAAAAGGAA
L29417.1/169-253           UAGUGAGUUGGCGC--UGCUC-GGGC-AUGCGCCGACCUACUUCGUUUG-CCUCAGGAUCGA-GGC-GGCGAAGU-UCCACCAGAAAAAGGAA
CP000058.1/4214931-4214847 UCGUAAGUCGCUGCCCUGCAC-AUGC-UGGCAGCGGCGAGCUUCGU--AUACCCC-GAAUGG-GUU-UGCGAGGU-UUCACCAGAAAAAGGAA
CP000076.1/5017949-5017863 UCGUAAGUCGGUGCAUGGCACUAGGC-CUGCAGCGGCGAGCUUCGUU-C-GUCCCAUA-UGG-AUGUGACGAAGU-UUCACCAGAAAAAGGAA
CP000058.1/4794981-4794894 ACGUGAGUUGGGUCCAGGGCCUGUAUG-GGGCUCAACGAGUUUGGCAGG-GUUCAGGA--GG-GUCUUGCCGAACGUCCUCAAGAGUGCGGAA
CT573326.1/1558985-1559071 UCGUAUGUCGUCGCUUCCCUUCACGC--AGCGGCGGCGAGCUUCGUU-C-GUCCUACGAGGG-ACCAGGCGAAGU-UUCACCAGAAAAAGGAA
CP000949.1/1498124-1498209 UCGUAAGUCGUCGCACC-CUU-AUGCGCUGCGGCGGCGAGCUUCGUUCG-GCCCUUGA-UGGAGCU--GCGAAGU-UUCACCAGAAAAAGGAA
CP000712.1/4452264-4452179 UCGUAAGUCGUCGCACC-CUU-AUGCGCUGCGGCGGCGAGCUUCGUUCG-GCCCUUGA-UGGAGCU--GCGAAGU-UUCACCAGAAAAAGGAA
CP000744.1/1991443-1991527 UAGUGAGUUGGCGC--UGCUC-GGGC-AUGCGCCGACCUACUUCGUUUG-CCUCAGGAACGA-GGC-GGCGAAGU-UCCACCAGAAAAAGGAA
CP000094.2/897043-897130   ACGUGAGUUGGGUCCGGGCCUGUAUU-GGGGCUCAACGAGUUUGGCGAA-GCUCAGGA--GGGGU-UUGCCGAACGUCCUCAAGAGUAUGAAG
CP000094.2/4610446-4610360 UCGUAAGUCGGCGCAUGGCACUCGGC-CUGCAUCGACGAGCUUCGU-GC-GUCCCCUA-UGG-AUAUGGCGAAGU-UUCACCAGAAAAAGGAA
#=GC SS_cons               ::::::<<<<<<<<<--<<_____>>.->>>>>>>>><<<<<<<<<<<<.<<<<____._>>.>>>>>>>>>>>>.>>:::::::::::::::
#=GC RF                    uCGUgAGucGccgCcuggcuugaugc.ugGcggCgaCgAgcuucGuggg.gccCaaGA.uGg.gccccgCgaagc.UcCaCcAGAAaAaGGAA
//
# STOCKHOLM 1.0

#=GF AC   RF01741
#=GF ID   hopC
#=GF DE   hopC RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   44.70
#=GF NC   35.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   HopC_RNA_motif
#=GF SQ   4


CP000241.1/931504-931564   UUACAAGCUCUGAUGUAACUAAAUCC-CAA-AUUUAAUCUCAAUCAAGGAGCAUCCCAUUGAU
AM260522.1/1116631-1116693 CCAUAAGCCCUGAUGUAACUUAAACCACAAAUUUAAACUUCAAUCAAGGAGCAUCCCAUUGAC
AE001439.1/931454-931513   UUACAAGCUCUGAUGUAACUGAAUCC-CA--AUUUAAUCUCAAUCAAGGAGCAUCCCAUUGAU
AE000511.1/965107-965166   UUACAAGCUCUGAUGUAACUAAAUCC-CA--AUUUAAUCUCAAUCAAGGAGCAUCCCAUUGAU
#=GC SS_cons               ::::::<<<<<<<<-----<<<<<__.___.>>>>>------>>>-->>>>>:::::::::::
#=GC RF                    UUAcAAGCuCUGAUGUAACUaAAuCC.CAA.aUUuAAUcUCAAUCAAGGaGCAUCCCAUUGAU
//
# STOCKHOLM 1.0

#=GF AC   RF01742
#=GF ID   lactis-plasmid
#=GF DE   lactis-plasmid RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   70.00
#=GF TC   73.30
#=GF NC   53.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Lactis-plasmid_RNA_motif
#=GF SQ   14


AF378372.1/1907-1800   CCAAAAAUAAAAAG-AAUCGUCUGAAACGAGGAA-CAAACUAAAAUGUAAAUUUUAGG-UG-UGACCGAGUGGAAGAUGAUUACUUUUUACCGUAAGUGUAUAUCCACUUAC
AF036485.2/39289-39184 CCAAAAAUAAAAAU-AGUCAUCUGAAACGAACAA-AAA-UAAAAUUGG-AAAUUUUAGCUU-UU-GUGAGUGAAAGAUGAAUUAUUUUUACUGUACUUGUGUACACAAGUAC
AF116286.2/6041-6146   CCAAAAAUAAAAAG-AUUCGUCUGAAACGAACAA-AAA-UAAAAUUGG-AAAUUUUAGGUU-UU-GUGAGUGAAAGAUGAAUACUUUUUACUGUACUUGGGUACCCAAGUGC
AF380336.1/2486-2593   CCAAAAAUAAAAAG-AAUCGUCUGAAACGAGGAACAAA-CUAAAAUGUAAAUUUUAG--UUGUUACCGAGUGGAAGAUGAUUACUUUUUACCCUAUGUGUAUACACACAUAG
U44843.1/3235-3340     CCAAAAAUAAAAAU-AUUCGUCUGAAACGAACAA-AAA-UAAAAUUGG-AAAUUUUAGGUU-UU-GUGAGUGAAAGAUGAAUACUUUUUACUGUAAGUGUAGCCACACUUGC
AF247159.1/3083-3188   CCAAAAAUAAAAAG-AUUCGUCUGAAACGAACAA-AAA-UAAAAUUGG-AAAUUUUAGGUU-UU-GUGAGUGAAAGAUGAAUACUUUUUACUGUACUUGGGUACCCAAGUGC
AF243383.1/6908-7013   CCAAAAAUAAAAAU-AGUCAUCUGAAACGAACAA-AAA-UAAAAUUGG-AAAUUUUAGGUU-UU-GUGAGUGAAAGAUGAAUUAUUUUUACUGUAAGUGUGUACACACUUGC
AJ272077.1/2304-2198   CCAAAAACAAAAACUAAUCAUCUGAAA-GAGC-GGCAAUCUAAAAUUA-CAUUUUAGGUUGUUUAGCUC--GUCAGAUGAUUAGUUUUUACCCUAAGUGGGUACCCACUUAG
AF409136.1/6099-5994   CCAAAAAUAAAAAU-AUUCGUCUGAAACAAACAA-AAA-UAAAAUUGG-AAAUUUUAGGUU-UU-GUGAAUGAAAGAUGAAUUAUUUUUACUGUAAGUGUAGCCACACUUGC
AY849557.2/22275-22170 CCAAAAAUAAAAAU-AUUCGUCUGAAACGAACAA-AAA-UAAAAUUGG-AAAUUUUAGGUU-UU-GUGAGUGAAAGAUGAAUACUUUUUACUGUAAGUGUGUACACACUUAC
CP000428.1/26010-25905 CCAAAAAUAAAAAG-AUUCGUCUGAAACGAACAA-AAA-UAAAAUUGG-AAAUUUUAGGUU-UU-GUGAGUGAAAGAUGAAUUAUUUUUACUGCACUUGGGUACCCAAGUGC
AF036485.2/4166-4061   CCAAAAAUAAAAAU-AUUCGUCUGAAACGAACAA-AAA-UAAAAUUGG-AAAUUUUAGGUU-UU-GUGAGUGAAAGAUGAAUACUUUUUACUGUACUUGGGUACCCAAGUAC
CP000427.1/3486-3591   CCAAAAAUAAAAAG-AUUCGUCUGAAACGAACAA-AAA-UAAAAUUGG-AAAUUUUAGGUU-UU-GUGAGUGAAAGAUGAAUACUUUUUACUGUACUUGGGUACCCAAGUGC
U26594.2/245-352       CCAAAAAUAAAAAG-AAUCGUCUGAAACGAGGAACAAA-CUAAAAUGUAAAUUUUAG--UUGUUACCGAGUGGAAGAUGAAUACUUUUUAACCUAUGUGUAUACACACAUAG
#=GC SS_cons           :::::::<<<<<<<.<<<<<<<<---<<--<<<<.<<-.<<<<<<<__._>>>>>>>-->>.>>.>>-->>--->>>>>>>>->>>>>>>--<<<<<<<<____>>>>>>>>
#=GC RF                CCAAAAAuaaaaag.auuCguCuGAAaCGAgcaa.aaA.caaaauugg.AaauuuugGguu.uu.gcgAGuGaAaGacGaauacuuuuuacuguacguGgguACcCacguac
//
# STOCKHOLM 1.0

#=GF AC   RF01743
#=GF ID   leu-phe_leader
#=GF DE   leu/phe leader RNA from Lactococcus
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   70.00
#=GF TC   74.30
#=GF NC   45.30
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Lactis-leu-phe_leader_RNA_motif
#=GF SQ   9


AE005176.1/1239635-1239796 AAUGUAAAUUAACAAAAAAGAGGAACUUGAAAUGACAUACACACAAU---UUUC-----AUUGUUGUUGAUCAAGGUGGACCUACAUUAGCUUU-UGUGGCUAA-AAUAUGUGGGUCCUGUUUGGCGAUA---GUCAUU-UCGAGGACCGAG-AGACGUCCUCAC-GGGCGUCUUUUU
CP000425.1/808768-808614   AAU---AAG-----AAAACGAGGUCCAAAA-AUGACUAAUACACAAGCUUCUCUU--AACUUGUUGUUG---AAGGAGGGCUCACACUAGCUAAUUU-AGCUA--AAUGUGUGAGUCCUCUUUGGCGUUA---GUCAUUGACGAGGAUGAAG-AGACGUCCUCA--GGACGUCUUUUU
CP000425.1/1233390-1233230 AAUGUAAAUUAACAAAAAAGAGGAACUUGAAAUGACAUACACACAAU---UUUC-----AUUGUUGUUGAUCAAGGUGGACCUACAUUAGCU--UUUCGGCUAA-AAUAUGUAGGUCCUAUUUGACAACA---GUCAUU-UCGAGGACCAUG-AGACGUCCUCAG-GGGCGUCUUUUU
AE005176.1/1281659-1281495 AAU---AAUAUUAAAUAUCGAGGUUCCAAAAUGAUUAACAACUUUAAAAAAUUUUAUUUUUUCUUUAUG------AAUGAUCCACAUUAGUU---UUUGGCUAAUAAAAUGUGGGUCCUCUUUGAUGUUCGUUAAUCAUCUAGGGGAUAAAGAAGACGUCCCCUG-GGACGUCUUUUU
AM406671.1/1258179-1258019 AAUGUAAAUUAACAAAAAAGAGGAACUUGAAAUGACAUACACACAAU---UUUC-----AUUGUUGUUGAUCAAGGUGGACCUACAUUAGCU--UUUCGGCUAA-AAUAUGUAGGUCCUAUUUGACAACA---GUCAUU-UCGAGGACCAUG-AGACGUCCUCAG-GGGCGUCUUUUU
AM406671.1/1728588-1728748 AAU---AA-UUAAAAAAACGAGGUCCAAUAAAUGACUUAUUUACAAGCUUCUCUU--AACUUGUUGUUG---AAGGAGGGCUCACACUAGCUAAUUUAAGCUA--AAUGUGUGAGUCCUCUUUGACGUUU---GUCAUUAACGAGGACGAAG-AGACGUCCUCA--GGACGUCUUUUU
AM406671.1/1198427-1198591 AUU---AAUAUAAAAUAUUGAGGUUCCAAGAUGAUUAACAACAGUAAAAAAUUUUAUUUUUUCUUUAUA------AAUGAUCCACAUUAGUU---UU-GGCUAAUAAAAUGUGGGUCCUCUUUGAUGUUCGUUAAUCAUCUAGGGGAUAAAGAAGACGUCCUCUGGGGACGUCUUUUU
CP000425.1/1276225-1276061 AUU---AAUAUAAAAUAUUGAGGUUCCAAGAUGAUUAACAACAGUAAAAAAUUUUAUUUUUUCUUUAUA------AAUGAUCCACAUUAGUU---UU-GGCUAAUAAAAUGUGGGUCCUCUUUGAUGUUCGUUAAUCAUCUAGGGGAUAAAGAAGACGUCCUCUGGGGACGUCUUUUU
AE005176.1/820178-820018   AAU---AA-UUAAAAAAACGAGGUCCAAUAAAUGACUUAUUUACAAGCUUCUCUU--AACUUGUUGUUG---AAGGAGGGCUCACACUAGCUAAUUUAAGCUA--AAUGUGUGAGUCCUCUUUGACGUUU---GUCAUUAACGAGGACGAAG-AGACGUCCUCA--GGACGUCUUUUU
#=GC SS_cons               :::...::::::::::::::::::::::::((((((,,,,,,<<<<<-<<_____..>>>>>>>,,,,,...,,,,,<<-<<<<<<<<<<<<..____>>>>>-.--->>>>>>>->>,,,,,,,,,,,,...))))))---<<<<<<<___.___>>>>>>>::.::::::::::::
#=GC RF                    AAU...AAUuuAaAAaAauGAGGuuCuaaAAaggacauauAcacaAgauuuUuuU..aacUuguUguUG...AAGgagGacccACAuUAGcu..UUUuggCUAA.AAuaUGUgggUCcUcUUUGAcGuUa...guccuUaucGaGGAcgAAG.AGAcgUCCuCag.GGaCGUCUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01744
#=GF ID   livK
#=GF DE   livK RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   65.00
#=GF TC   78.00
#=GF NC   34.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.99 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   LivK_RNA_motif
#=GF SQ   8


AE016853.1/2667662-2667745 AGGGUCCCUUGCCACACGCCCAUUCUCGGCAGGUGUGGAAGGC-CCCUCGCAUGACUGGUCCUGACACUGUC-GUCACGCCAGCCC
CP000075.1/2563385-2563468 AGGGUCUCUUGCCACACGCCCAUUCUCGGCAGGUGUGGAAGGC-CCCUCGCACGACUGGUCCUGACACUGCC-GUCACGCCAGCCC
CP000058.1/3459167-3459084 AGGGUCCCUUGCCAUACGCCCACUCUCGGCAGGUGUGGAAGGU-CCCUCGCACGACUGGUCCUGACACUGCC-GUCACGCCAGCCC
CP000075.1/2563011-2562928 CCAGCUGUUUGCCCUACGCCCCUCUU-GGCAAGUAGGGAGACACCUCGCGUACGACUGGAUCGGACGCAGUU-GUCCCGCCAGAUU
CP000075.1/2565410-2565491 GCGGAAGGUUGCCAUACGCCCUGACCCGGCAGGUAUGGAA-CA-CCGCGUGGCGACCGGCGUGGACAACGAC-GUCC-UCCGGAUC
CP000058.1/3457138-3457057 GCGGACGCUUGCCAUACGCCCUGAACCGGCAGGUAUGGAA-CA-CCGCGUGGCGACCGGCAUGGACAACGGC-GUCC-UCCGGAUC
AE016853.1/2667241-2667158 CCAGCUGUUUGCCCUACGCCCCCUU--GGCAAGUAGGGAGACACCUCGCGUACGACUGGAUCGGACACAGUUUGUCCCGCCAGAUU
AE016853.1/2669688-2669769 GUGGACGCUUGCCAUACGCCCUGACCCGGCAGGUAUGGAA-CA-CCGCGUGGCGACCGGCAUGGACAACGGC-GUCC-UCCGGAUC
#=GC SS_cons               <<<<--<<<<-<<<<<<<<<_______>>>-->>>>>>>>>>-.>>>>-----<<<<<<---<<<<______.>>>>-->>>>->>
#=GC RF                    ggGGucgcuUGCCauACGCCCuuucuCGGCAgGUauGGAagca.CCcccguaCGaCcGGuucgGACAcuGuc.GUCcCgCCgGauC
//
# STOCKHOLM 1.0

#=GF AC   RF01745
#=GF ID   manA
#=GF DE   manA RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   33.00
#=GF TC   33.10
#=GF NC   32.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   ManA_RNA_motif
#=GF **   seedtax: Bacteria; Viruses; unclassified sequences
#=GF SQ   189


AACY020215820.1/97-281       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY021715400.1/446-237      GAAGG-------GCUUAUAAU--------------CCUUCC-U---GUGGGUG-ACUCGAAAUA-----ACCUG---UCGUGAG---------CGGGUUAAGGU-A-UGC-AGAU--C--------------------------CCU-GUGGUGGGGCUGGCAGAGUCC-----AAUC----------GGAUGA-GCCA-AA-AGACA-AAUACCA--AGUCUA--AUCU--GUAGU------UCGAAGUAGGUAAUCCAU-GA-ACUG--------------------AUGUUCACGCCGAAAAGUU-GGAGGUAU-UCAGUAA-UCCUCCCCCAC-GCCA
AACY020207351.1/1118-924     ---CGAAG----GACG----------------CUUUGCUUACA---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUUC----------GCAA---------------GAACAG-AACUACU---GAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-CCCAACCUCCC-ACCC
AACY023389895.1/1202-994     GUUG--------GACG--------------------CAACAUA---GGGAGUG-ACUGAAUUAAACUU-GCUGGC--A-AUAG---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCAGGAUGCCUCUU---GAGA--------AAGAAGCGACCUG-AACUAUC---UUACCA---GAUGG--GACU--CAUGC-AACGCAGUAAAA------AUUAC-UAAG-----A-----------------GUAGCAAUGCCCUGCGUUU-GUAAGCAU-ACUCAAA-UCUUACCUCCC-ACUU
AACY023527836.1/1180-1397    ----UUAGGU--GACG--------------GCCUAACUGUA-G---GGAUGUGCGUUGAAUAACAUCUUCGUC----C-AC-U-----------GAUGUAAAAC-G-GCG-UGUC--A--------------------------CAG-GUGGAGCUGAGGCCACCCUUCUG---GUAA--------CAGUAGGG-AGCCACAUCACUC--AAUCCA--GAGUGG--GACA--CG-GC-AG---GGAGGGAACGAAUGCCAA-UA-ACUG-GA-----------------GUGAG--UACCCCAAACUU-GUAGGUAAUCCAGAG--UCCUACCAUCC-CCCG
AACY020206600.1/439-252      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GGAA---------------UGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY021648734.1/613-429      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY022061139.1/626-441      GUUG--------GACG--------------------CAACA-U---GGGUGUG-ACUGAACAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUAU--------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAC-UCCAACCACCC-UCCU
AAOU01000012.1/1214-1408     CUUUAGAC----GACG----------------GUUUGAAGC-G---GGGAGUGCAGAGAAUAA------UAGU----AAUCAGCG---------ACUAUAAUCU-G-GCU-UAUC--A--------------------------CGG-GUUGUGCCGACCUAACUU-GCG----GUGA---------CGUUAAGUUAGGACAUCGCC----GACAU---GGCGG--GAUU--AAGGUUCGAUGAG---------------A-U---CGG-AGCUGA------------------------CUCAUUGUUGUAGGUAU-UCCAAAG-UCCUACCUCCC-ACCU
AACY021006766.1/544-742      GUUGACCU----GACG----------------AGGUUAACA-C---GGGAGUG-ACUGAAUAA------CCCUGUU-GGAAUUA-------GGCGGGGUAAUGU-A-AAU-GGUU--A--------------------------GAG-GUGGUACUCGCCUUCCC---------UAAA--------------GGAAGUG-AACC--C---GAACCAA--G--GG--AACC--AUUGU-UGUUAUGUA---CUAAUUUUCG------CAC-UA-----------------GCGA---UUCCCAUAACUU-GAGAGUAA-AAUGUAA-UCUCUCCUCCC-CCCU
AACY021925052.1/214-26       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GCAA---------------UGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY021544909.1/483-669      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUACC-----------GCAG----------------GGUAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-UA-ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020240867.1/163-355      GACG--------GUCA--------------------CCUUGCA---GGGAGUG-ACUGAAUAAU-CUU-UCUGGC--AUAU-A---------GCUGGAUAAGGU-G-AUG-AGAU--A--------------------------CAG-GUGGUGCUG-CUGUGG----------UUUU---------------CCACAG-AACCGAC---AAACCA---GUCGG--AUCU--CAGGC-AAGGAUGUAAAA------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUCCUUU-GUUGGUAAUACAGAAA-CCCAACCUCCC-ACUU
AACY023995876.1/9-193        GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AACAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY022707325.1/115-305      GUUGA------UCAC--------------------UCAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUUU-U---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------GAG-GUGGUGCUCGCUGUUG----------GGAA---------------CAACAG-AACU-AC---AAACCAA--GU-AG--GUCU--CAUGC-AAAGACGU----------AUUUC-UAAACUG-UA-----------------GAAA---UGCCCGUCUUUU-GUAGGUAC-ACAGGAA-UCCUACCUCCC-ACCU
AACY020215580.1/1977-1793    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACC-----------GCAG----------------GGUAG-AACCGAC---CUACCA---GUCGG--GUCU--CAGGC-AACAACGUU---------UUUAC-U--GCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAU-UCCAACCUCCC-UCUU
AACY022799775.1/698-513      GUUG--------GACG--------------------CAACA-U---GGGUGUG-ACUGAACAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUAU--------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAC-UCCAACCACCC-UCCU
AACY020491127.1/104-294      GUAAG-------GACG-------------------CUUACGUC---GGGUGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGUCC----------GCAG---------------GGGCAG-AACCGAU----GACCA---AUCGG--GUCU--CAGGC-AGAGGAGU----------AAUUC-UAAACUG-UA-----------------GAAA---UGCCCUUCUCUU-GUUGGUAU-ACAGGAA-UCCAACCACCC-UCUU
AACY020134449.1/1404-1586    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAC------------GAAA-----------------GUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCCU
AACY020213261.1/1131-1317    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAGGACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020095693.1/50-237       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-GGUC--A--------------------------GAG-GUGGUGCUCGCUGUCC----------GCAG---------------GGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY022808284.1/597-409      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUUC----------GCAA---------------GGACAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCCU
AACY023482594.1/832-645      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUUC----------GCAA---------------GGACAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-UGUAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUACUU-GUUGGUAU-ACAGGAA-CCCAACCUCCC-UCUU
AACY020482322.1/269-458      GUC--------UGACGAGAUU----------------GAUC------GGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-A-CUA-GGAC--A--------------------------CAG-GUGGUGCUG-CUGGCA----------GAAA---------------UGUCAG-AAUCGAC---UUACCA---GUCGG--GUCU--UAGGU-AGAGAAG-----------UUUUC-UUAACUG-UA-----------------GAAA---UGCCCUUCUCUU-GUUGGUAU-ACAGUAG-UCCAACCUCCA-CCCU
AACY022177928.1/761-576      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACC-----------GAGA----------------GGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUGACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUCGGUAC-ACAGGAA-UCCGACCUCCC-UCUU
AACY020130804.1/777-969      UGUUG-------GACG-------------------CAACAACU---GGGUGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUA-CGAC--A--------------------------CAG-GUGGUGCUG-CUCCUAG---------GGAA--------------CUAGGAG-AAUCGAC---UUACCA---GUCGG--GUUG--UAGGC-AGAGAUG-----------AUUUC-UAAACUG-UA-----------------GAAA---UGCCCAUCUCUU-GUUGGUAU-ACAGGAC-UCCAACCACCC-UCCU
AACY021401878.1/467-649      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUCC------------GAAA-----------------GGAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AACAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020110904.1/1362-1549    GUGCU-------GAUC-------------------AACACAUC---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CACC------------GAAA-----------------GGUG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AGAGAUGU----------UUUUC-UAAACUG-UA-----------------GAAA---UGCCCAUCUCUU-GUUGGUAU-ACAGGAU-UCCAACCUCCC-CCUU
AACY022717813.1/217-402      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACC-----------GAGA----------------GGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY021430125.1/656-472      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023424185.1/746-931      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACC-----------GAGA----------------GGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AACAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020185578.1/726-913      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY021130090.1/376-592      ----GGAGG---GACG---------------CCAAACGACA-----GGAGAUG-ACUGAACAAC-----CCUUA---UGUGGUCCACCG--C-UGGGGUAUAGU-UGAGUAGGAC--A--------------------------GGCUGUGGUGGCCGC-CCUGAUUAACCA--GAGA-------UGG--GAGCAGGUG-AAUCC----GAAACCAAA---GGA--GUCC-GAAAGA-UCACGGGUAUAACUUAGC----------AGU-AA-----------------GUGUA--GACCCCCGUGUU-GUGGGUAU-AACUGAAGUCCCACUCUCC-ACCC
AACY020220196.1/1033-1220    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-UGUAACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUACUU-GUUGGUAU-ACAGGAA-CCCAACCUCCC-UCCU
AACY020112293.1/1931-1744    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUGACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020700616.1/542-373      AAGGAAG----UAGCU-----------------CUUCCUUAUC---GGGUAUG-GCCGAAUAA------GUCCG---CCA-------------CGGACUAAGGC-ACAGGGCACGCAAA---------------------------------------CCAAGAACC-------GACU------------GGU-GGAGG-AA----------------------UGCGUG-ACUGGU-AACGCGU------------CUAC----ACUG-UA-----------------GUGG---CAUAACGCGUUU-GGAGGUAU-ACAGCAAGGCCUCCUACCC-ACCU
AACY023878348.1/850-1018     ----UGCCU---CGAUCA-------------AGGUAUGACU-----GACGGUG-ACUGAAUAA------GGCG----UUAUGC-----------UGCCUAAAGU-A-AAC-AGU--------------------------------------------CCUAGGUGAACGGCC-AAGC------GGCU--CUGACUAGGU---------------------------ACU--GUGGU-AGAGUGU---------------C-CUGCCUAGCAUAGUAU----------------------ACACUCUU-ACAGGUAAUAAAGUAAAUCCUGUCCGUC-AACU
AACY020333800.1/1867-1677    GUAAG-------GACG-------------------CUUACAUC---GGGAGUG-ACUGAAUAAA-CUU-GCUGGC--AUAC-G---------UCUAGUUAAGGU-G-AUG-AGUU--A--------------------------GAG-GUGGUGCUCGCUGCUG----------GGAA---------------CAGUAG-AACU-AC---AAACCAA--GU-AG--AACU--CAGGU-CUGAUGGU----------CUUUC-UA-ACUG-UA-----------------GAAA---UGCCCCAUCAGU-GUUGGAAC-ACAGAAA-CCCAACCUCCC-UCUU
AACY020192296.1/1145-1333    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GCAA---------------UGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AAUAACGUA---------UUUAC-UA-UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023675901.1/516-707      ---------------GGGUAACUCUGAAAU------CCCAUCUUG------UG-GCUGAAUCAAUCUAAACUC----AGA--------------GAGAUAAAGC-A-AUA-GCAC--A--------------------------GAG-GUUAUACUCACUUUGACGUAGA----CUAACCA------UCUAUG-AGGAG-AAUCAAC-----GUAACU-GUUGG--GUGU--UAGGU-AC----------------------AAGGGCAAAAAAAUCUGAGUCGAGA------------------GUU-GUUGGUAA-UCGCUAA-UCCAAC------AUCC
AACY020095509.1/287-489      --UAGUU-----GACG-----------------GACUAGUA-C---GGUAGUG-ACGGAAAG-------CCCC----UCCUCC-----------GGGGCAACGU-G-CAA-UAUU--C--------------------------CCU-GUCGUGGGG---CAAUCACACCUA--GAGA-------UAGGAGUCGUUGUA-AAGG--ACACUAACGA--GU--CU--AAUA--UUGGC-GGUUUCGGUAAU------UCUGC-AAUUAUG-UA-----------------GGGG---GACAGGAAACUU-CCGGGUAU-ACAUUAG-CCCCGGCUACC-ACCA
AACY020136550.1/901-719      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAC------------GAAA-----------------GUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020217323.1/1051-858     UGUUG-------GACG-------------------CAACAACU---GGGUGUG-ACUGAAUAAU-CUU-ACUGGC--AUAU-A---------GCUAGAUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUCCUAG---------GGAA--------------CUAGGAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AGAGACGU----------UUUUC-UAAACUG-UA-----------------GAAA---UGCCCGUCUCUU-GUUGGUAU-ACAGGAC-UCCAACCACCC-UCCU
AACY020774201.1/512-698      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-UGUAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUACUU-GUUGGUAU-ACAGGAA-CCCAACCUCCC-UCCU
AACY020114877.1/97-280       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAC------------GAAA-----------------GUAG-AACUGAC--UCAACCA---GUCAG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023270407.1/595-781      GCUC--------GACG--------------------GAGCGACAAAGGGUAUG-ACGGAAUAAA--CU-GCUGU---CGCG------------GCAGUUAACGU-G-CAAUGCUC-------------------------------------------AUUGGC---AGGACUUACC------AAGUCUGGGGGCCGAU---------------------------GAGG-GUUGGC-UC-AAAGUAGGGUUUUGACUUGA-AAACUCA-AGCUGUGACCCCAAAAC------------------GAU-GGAGGUAA-AUGAGAA-UCCUCCUACCC-AUUA
AACY023373358.1/1536-1344    GUGCCU------GAUC------------------A-GCACAUC---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-CGAC--A--------------------------GGG-GUGGUGCCCGCUGCUG----------GGAA---------------CAGUAG-AAUCGA----AAACCAA---UCGG--GUCG--UAGGC-AAAGGUGU----------AUUUC-UAAACUG-UA-----------------GAAA---UGCCCGCCUUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020438888.1/737-920      GUCU--------GACG--------------------AGACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAC------------GAAA-----------------GUAG-AACCGAU--UCAACCG---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY023503740.1/923-737      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAGGACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY022819827.1/26-216       GUUG--------GACG--------------------CAACAACU--GGGUGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-CGAC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GGAA---------------UGGCAG-AACU-AC---AAACCAA--GU-AG--GUCG--UAGGC-AGAGUGGU----------AAUUC-UAAACUG-UA-----------------GAAA---UGCCCUGCUCUU-GUUGGUAU-ACAGGAU-UCCAACCACCC-UCCU
AACY020218785.1/265-455      GUUG--------GACG--------------------CAACACU---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-UGAU--A--------------------------CAG-GUGGUGCUG-CUGCUUC---------GGAA--------------GAAGUAG-AACCGAU---CAACCA---AUCGG--AUCA--CAGGC-AGAGAUG-----------AUUUC-UAAACUG-UA-----------------GAAA---UGCCCAUCUCUU-GUUGGUAU-ACAGGAA-CCCAACCUCCC-CUCU
AACY023861074.1/1114-918     GGUGACU-----GAUC-----------------A-UCACCAUC---GGGAGUG-ACUGAAUAA------CCCUGUU-GGAAUUU-------GGCGGGGUAAUGU-A-AAU-GGUU--A--------------------------GAG-GUGGUACUCGCCUUCCC---------UAAA--------------GGAAGUG-AACC--C---GAACCAA--G--GG--AACC--AUUGU-UGUUAUGCA---CAAAUAUUCG------CUU-UA-----------------GCGA---UUCCCAUAACAU-GAGGGUAC-GAAGUAU-UCCCUCCUCCC-ACAC
AACY022099112.1/480-288      GGUGACU-----GAUC-----------------A-UCACCAUA---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGCAAAGGACGUAU--------UUUAC----ACUG-UA-----------------GUAA---UGCCCGUCCUUUUGUUGGUAU-ACAGUAA-UCCAACCUCCC-ACCC
AACY021848889.1/398-208      ---UGACU----GAUC----------------A-UCGGGUA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGAU-----------GCGA----------------GUCAG-AACCGAC---CAACCA---GUCGG--GUCU--CAGGCAAGGAAUGUAU--------UUUAC----ACUG-UA-----------------GUAA---UGCCCAUUCCUUUGUUGGUAU-ACAGUAA-UCCAACCUCCC-CCCU
AACY021572652.1/228-44       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY021701017.1/849-656      ---GGAUC----GACG----------------GAUCUGACA-C---GGGAGUG-ACUGAAUAAU-CUU-UCUGGC--AUAU-G---------GCUGGAUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUCC------------GAAA-----------------GGAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AGAGGCG-AAAA------CUUAC-UU-ACUG-UA-----------------GUAA---UGCCCUCCUCUU-GUUGGUAAUACAGGAA-UCCAACCUCCCCACCC
AACY023911245.1/654-471      GUUG--------GACG--------------------CAACGUU---GGGAGUG-ACUGAAUAAU-CUU-UCUGGC--AAAC-----------GCUGGAUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUUC------------GAGA-----------------GAAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AAGAACGUAU--------UUUAC----UCUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAU-ACAGUAA-UCCAACCUCCC-UUUU
AACY020092686.1/688-881      ---GAGUU----GACG----------------AACUCAGCA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUUU-U---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------GAG-GUGGUGCUCGCUGUUG----------GGAA---------------CAACAG-AACU-AC---AAACCAA--GU-AG--GUCU--CAUGC-AAAGACGU----------AUUUC-UAAACUG-UA-----------------GAAA---UGCCCGUCUUUU-GUAGGUAC-ACAGGAA-UCCUACCUCCC-ACCU
AACY023908345.1/175-367      -G-AGUAAC---GACG---------------GUUACA-UC------GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGAUGCUG-CUGCUC----------GUAA---------------GAGUAG-AAUCGAC---CAAUCA---AUCGG--GUCU--CAGGC-AGAGAAG-----------UUUUC-UAAUCUG-UA-----------------GAAA---UGCCCUUCUCUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-CCUU
AACY020276929.1/339-537      GUUGAAUC----GACG----------------GGUUCAAC--G---GGGAGUG-ACUGAAUAAA-CUU-UCUGGC--AUAU-A---------GCUGGUUAAGGU-G-ACG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACUC----------GCAA---------------GAGUAG-AAUCGAU---UUACCA---AUCGG--GUCU--CAGGC-AAGGACGUAAAA------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAAUACAGAAA-CCCAACCUCCC-ACAC
AACY023944427.1/316-499      GUCU--------GACG--------------------AGACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAC------------GAAA-----------------GUAG-AACCGAU--UCAACCG---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY022174812.1/728-926      AGAGAACU----GAUC----------------A-UUCUCUAUA---GGGUAUG-CCAGAAUAA------CAGAUGUGGUCAUG-------CAC-UCUGUAAUGGUGAAGUAAGUC--A--------------------------GGG-GUGGUGCCCGCUGUG-----------GAAG----------------CACAG-AACU--C---UAACCAA--G--AG--GACUGAAAAGAAUGAGGAUCACUA-------UUAC-U----AC-UA-----------------GUGA---GACCAUCUUCAUUGAGGGUAU-AGUAAAA-UCCCUCUACCC-AACC
AACY022698323.1/322-137      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACC-----------GAGA----------------GGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AACAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCCU
AACY020132116.1/923-738      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU--UCAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY023489024.1/243-431      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUUC----------GCAA---------------GGACAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023255719.1/1156-957     GUUCUC------GACG------------------GAGAACACC----GAGUUG-GCUGAAUAAU-CCU-UUUCCU--A---AA---------AGGGGAUAAAGC-U-AAC-AACU--A--------------------------GGUUAUAGUGACCACUCAAUGAUCC-----GAAU----------GGAUUG-AGAG-AACUAUC---GUAACU---GAUAG--AGUU--GUUGA-AUAUGUGAUAA--------UAGA-A---UUG-UA-----------------UUUA---AGG-CACAUAUU-GGAGGUAAUACAAUAA-UCCUUCACUC--ACCU
AACY023514947.1/316-131      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUAU--------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020546570.1/1436-1623    GUAAG-------GACG-------------------CUUACAUC---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUUC------------UUCG-----------------GAAG-AAUCGAC---UUACCA---GUCGG--GUCU--UAGGC-AGAGACGU----------UUUUC-UAAUCUG-UA-----------------GAAA---UGCCCGUCUCUU-GUUGGUAU-ACAGGAU-UCCAACCUCCC-UCUC
AACY020093225.1/691-504      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUGACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY023654870.1/902-704      GUUGAAUC----GACG----------------GGUUCAACG-----GGGAGUG-ACUGAAUAAA-CUU-UCUGGC--AUAU-A---------GCUGGUUAAGGU-G-ACG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACUC----------GCAA---------------GAGUAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AAGGACGUAAAA------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAAUACAGAAA-CCCAACCUCCC-ACCC
AACY022146823.1/204-20       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGAU-----------GCGA----------------GUCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAACAGGUA---------UUUAC-A--ACUG-UA-----------------GUAA---UGCCCCUGUUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020134738.1/3011-3198    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUGACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCCU
AACY020197861.1/1709-1522    GUAAG-------GACG-------------------CUUACGUC---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUCU-A---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGC------------GAAA-----------------GCAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AGAGGUGU----------UUUUC-UAAACUG-UA-----------------GAAA---UGCCCGCCUCUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023647721.1/467-665      AGAGAACU----GAUC----------------A-UUCUCUAUA---GGGUAUG-CCAGAAUAA------CAGAUGUGGUCAUG-------CAC-UCUGUAAUGGUGAAGUAAGUC--A--------------------------GGG-GUGGUGCCCGCUGUG-----------GAAG----------------CACAG-AACU--C---UAACCAA--G--AG--GACUGAAAAGAAUGAGGAUCACUA-------UUAC-U----AC-UA-----------------GUGA---GACCAUCUUCAUUGAGGGUAU-AGUAAAA-UCCCUCUACCC-ACCC
AACY022825751.1/761-950      ----------------GGUAAUACCGAACU------CCCACUUUA------UG-ACCGAAUAAA-CUAAACUC----AGA--------------GAGUUAAGGU-A-AUG-GCAC--A--------------------------GAG-GUUGUACUCACU--UUGACGAUG---ACUAA------CCAUCAUUGAGGAG-AACUUUC-----GUAACU-GAAAG--GUGU--UAGGUA---CAAGGGAGAAAAAAU----------CUGAG-----------------------------CUUGAAGUUGUAGGUAA-UCGUUAA-UCCUAC------AUCC
AACY020246166.1/1374-1182    GUGCCU------GAUC------------------A-GCACAUC---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-CGAC--A--------------------------GAG-GUGGUGCUCGCUGCUG----------GGAA---------------CAGUAG-AACU-AC---AAACCAA--GU-AG--GUCG--UAGGC-UGAGUGGU----------AAUUC-UAAACUG-UA-----------------GAAA---UGCCCUGCUCUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-ACAU
AACY022807862.1/457-268      GUAAG-------GACG-------------------CUUACACU---GGGUGUG-ACUGAAUAAA-CUU-ACUGGC--AUCU-A---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAUC-----------UUCG----------------GAUAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AGAGGUGU----------UUUUC-UAAACUG-UA-----------------GAAA---UGCCCGCCUCUU-GUUGGUAU-ACAGGAA-UCCAACCACCC-UCCU
AACY022467117.1/242-58       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023905966.1/704-512      GUAAC-------GACG-------------------GUUACAUC---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-CGAC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GGAA---------------UGGCAG-AACUACU---GAACCA---AGUAG--GUCG--UAGGC-AGAGAAGU----------UUUUC-UAAUCUG-UA-----------------GAAA---UGCCCUUCUCUU-GUUGGUAU-ACAGGAU-UCCAACCUCCC-UCUU
AACY023513855.1/409-595      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-UGUAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUACUU-GUUGGUAU-ACAGGAA-CCCAACCUCCC-UCCU
AACY022664387.1/392-207      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACC-----------GCAG----------------GGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUGACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUCGGUAC-ACAGGAA-UCCGACCUCCC-UCCU
AACY024049533.1/564-366      GGUGACU-----GAUC-----------------A-UCACCAUC---GGGAGUG-ACGGAAUAA------CCCUGUU-GGAAUUU-------GGCGGGGUAACGU-A-AAU-GGUU--A--------------------------GAG-GUGGUGCUCGCUGCUGGG--------UCCG-------------UCCUGGAG-AACC--C---AUACCAA--G--GG--AACC--AUUGU-UGUUAUGCA---CAAAUAUUCG------CUU-UA-----------------GCGA---UUCCCAUAACAU-GAGGGUAC-GAAGUAU-UCCCUCCUCCC-ACUC
AACY020200113.1/2457-2272    GUUG--------GACG--------------------CAACA-U---GGGUGUG-ACUGAACAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUAU--------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAC-UCCAACCACCC-UCCU
AACY020864144.1/547-362      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUAU--------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020114483.1/353-538      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAUC-----------GAGA----------------GGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCCU
AACY023385673.1/583-399      GUUG--------GACG--------------------CAACAUU---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUA-CAAC--A--------------------------CAG-GUGGUGCUG-CUGC------------GAAA-----------------GCAG-AAUCGAC---UUACCA---GUCGG--GUUG--UAGGC-AGAGAUGA----------UUUUC-UA-ACUG-UA-----------------GAAA---UGCCCAUCUCUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-ACCU
AACY022566045.1/204-22       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUUC------------GAAA-----------------GAAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020213897.1/488-302      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUACC-----------GCAG----------------GGUAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY022818928.1/571-381      GUUG--------GACG--------------------CAACAACU--GGGUGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-CGAC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GGAA---------------UGGCAG-AACU-AC---AUACCAA--GU-AG--GUCG--UAGGC-AGAGUGGU----------AAUUC-UAAACUG-UA-----------------GAAA---UGCCCUGCUCUU-GUUGGUAU-ACAGGAU-UCCAACCACCC-UCCU
AACY023201299.1/682-492      ----------------GGUAAAACCAAAAU------CCCACUUUA------UG-GCUGAAAAAAUCUAUUCUC----AGA--------------GAGAUAAAGC-A-AUA-ACAU--A--------------------------GAG-GUUGUACUCGAUUCUACGAUGAU---UAACC-------AUCAUUUAAGAAU-AACUAUC-----GUAACU-GGUAG--AUGU--UAGGU-A-----------------------UGAAGUAAUAAAAUCUGUGCUAAAAG------------------UU-GUAGGUAA-UCGCAAA-UCCUAC------AUCC
AACY020821457.1/539-727      GUC--------UGACGAGAUU----------------GAUC------GGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-A-CUA-GGAC--A--------------------------CAG-GUGGUGCUG-CUGGCA----------GGAA---------------UGUCAG-AAUCGAC---UUACCG---GUCGG--GUCU--UAGGU-AGAGAAG-----------UAUUC-UA-ACUG-UA-----------------GAAA---UGCCCUUCUCUU-GUUGGUAU-ACAGUAA-UCCAACCUCCA-CCCU
AACY022017605.1/364-182      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUUC------------GAAA-----------------GAAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AACAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY022744932.1/757-573      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY021458751.1/609-422      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCC----------GCAG---------------GGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023422649.1/622-438      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020216686.1/371-558      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCCU
AACY022740041.1/509-319      UGGUCU------GACG------------------AGAUUAAU----CGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-A-CUA-GGAC--A--------------------------CAG-GUGGUGCUG-CUGGCA----------GUCA---------------UGUCAG-AAUCGAC---UUACCA---GUCGG--GUCU--UAGGU-AGAGAAG-----------UUUUC-UU-ACUG-UA-----------------GAAA---UGCCCUUCUCUU-GUUGGUAU-ACAGUAU-UCCAACCUCCA-CCCU
AACY020559926.1/1138-953     GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAUC-----------GAGA----------------GGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUGACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCCU
AAOJ01000001.1/468857-469050 -UUUAGGC----GACG----------------GCUUGAAGC-G---GGGAGUGCAGAGAAUAA------UAGU----AUUCAGCG---------ACUAUAAUCU-G-GCU-UAUC--A--------------------------CGG-GUUGUGCCGACCUAACUU-GCG----GUGA---------CGUUAAGUUAGGACAUCGCC----GACAU---GGCGG--GAUU--AAGGUUCAAUGAG---------------A-U---CGG-AGCUGA------------------------CUCAUUGUUGUAGGUAU-UCCAAAG-UCCUACCUCCC-ACCU
AACY020138107.1/1524-1710    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUACC-----------GCAG----------------GGUAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-UA-ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020209638.1/622-440      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUUC------------GAGA-----------------GAAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCCU
AACY020793376.1/417-232      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUAU--------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAU-UCCAACCUCCC-UCUU
AACY023403182.1/1367-1554    GUUG--------GACG--------------------CAACGUUA--GGGAGUG-ACUGAAUAAU-CUU-UCUGGC--AAAC-----------GCUGGAUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CACC------------GAGA-----------------GGUG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AAGGACGUAAAA------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-CCCU
AACY020119574.1/1151-1336    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU--UCAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY023404546.1/1320-1505    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-GGUC--A--------------------------GAG-GUGGUGCUCGCUACC-----------GCAG----------------GGUAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020983822.1/578-390      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GCAA---------------UGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AAUAACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020495829.1/1869-2055    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-UGUAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUACUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020133026.1/411-599      GACG--------AACU--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUUU-U---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------GAG-GUGGUGCUCGCUGUUG----------GGAA---------------CAACAG-AACU-AC---AAACCAA--GU-AG--GUCU--CAUGC-AAAGACGU----------AUUUC-UAAACUG-UA-----------------GAAA---UGCCCGUCUUUU-GUAGGUAC-ACAGGAA-UCCUACCUCCC-ACCU
AACY023486741.1/47-233       GUUG--------GACG--------------------CAACA-U---GGGUGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUC-----------GCAA----------------GACAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AAUAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCACCC-UCCU
AACY021921369.1/361-542      AAUGGGA----UAGCU-----------------UCCCGUUAUA---GUGAGUG-GCUGAAUAA------AUCC----UACCCAAC---------GGAUUAAGGC-A-CACAAACC--UG---------------------------------------CUCCAACGGUC-----AAGU----------GACUGA-GGAGGU-------------------------GGUG-AGUGGUAAGCGAUUACAAAU------UAAC-U-ACUUAGGUA----------------GUUG---GG--AGUCGCUUUGGGGGUCAACCAAGAA-UCCCCCCUCGC-ACCC
AACY021690547.1/447-259      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGGCA----------GGAA---------------UGUCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AAUAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020085891.1/1079-893     GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AACAAUGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUCGGUAU-ACAGGAA-UCCGACCUCCC-UCUU
AACY020104611.1/632-822      GUAAG-------GACG-------------------CUUACGUU---GGGUGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGUCC----------GCAG---------------GGGCAG-AACCGAU----GACCA---AUCGG--GUCU--CAGGC-AGAGGAGU----------AAUUC-UAAACUG-UA-----------------GAAA---UGCCCUCCUCUU-GUUGGUAU-ACAGGAA-UCCAACCACCC-UCUU
AACY021252372.1/471-283      GUCG--------GACG--------------------CGACG-U---GGGAGUG-ACCGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GGAA---------------UGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AAUAACGUAU--------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UUUC
AACY023424190.1/589-774      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCCU
AACY020478716.1/1676-1489    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCC----------GCAG---------------GGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AAGGACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAU-ACAGAAA-CCCAACCUCCC-UCUU
AACY021062003.1/574-387      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCU----------GCAA---------------UGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020552995.1/2337-2520    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUUC------------GAGA-----------------GAAG-AACCGAC--UCAACCA---GUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020815807.1/293-105      GUAAC-------GACG-------------------GUUACAUC---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAUC-----------GAAA----------------GAUAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AGAGAUGU----------UUUUC-UA-ACUG-UA-----------------GAAA---UGCCCGUCUCUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023375566.1/756-564      GUGCCU------GAUC------------------A-GCACAUC---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-CGAC--A--------------------------GGG-GUGGUGCCCGCUGCUG----------GGAA---------------CAGUAG-AAUCGA----AAACCAA---UCGG--GUCG--UAGGC-UGAGGUGU----------AUUUC-UAAACUG-UA-----------------GAAA---UGCCCGCCUCUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY022844081.1/355-157      AGAGAACU----GAUC----------------A-UUCUCUAUA---GGGUAUG-CCAGAAUAA------CAGAUGUGGUCAUG-------CAC-UCUGUAAUGGUGAAGUAAGUC--A--------------------------GGG-GUGGUGCCCGCUGUG-----------GAAG----------------CACAG-AACU--C---UAACCAA--G--AG--GACUGAAAAGAAUGAGGAUCACUA-------UUAC-U----AC-UA-----------------GUGA---GACCAUCUUCAUUGAGGGUAU-AGUAAAA-UCCCUCUACCC-AACC
AACY020479078.1/954-1136     GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAC------------GAAA-----------------GUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AACAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCCU
AACY021955282.1/244-57       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUGACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020132762.1/1813-1626    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUGACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020495590.1/3659-3845    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-UGUAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUACUU-GUUGGUAU-ACAGGAA-CCCAACCUCCC-UCCU
AACY022010950.1/470-652      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUUC------------GAAA-----------------GAAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCCU
AACY020938789.1/94-289       --UGAUCU----GACG----------------AGGUUGACA-U---GGGUGUG-ACAGAACAA------UCCUGUU-GGAAAUA-------GGCGGGAUAAUGU-A-UAG-ACUC--A--------------------------GAG-GUGGUGCUCGCAAUCC----------CUAAA--------------GGAUUG-AACU--C---UGACCAA--G--AG--GUGU--CUAGU-UAAUCGGUA---UUAAAUUUCG------CUU-UA-----------------GCGA---UUCCCCGAUUAU-GUUGGUAU-GAAGUAA-UCCAAUCACCC-ACCC
AACY023208588.1/538-331      GAAGG-------GCUUAUAAU--------------CCUUCC-U---GUGGGUG-ACCGAAUAAG-CCU-GUC-----GUGAGCG-----------GGCUAAAGU-A-UGC-AGAU--C--------------------------CCU-GUGGUAGGGUUGGUAGAGUUC-----AAUC----------GAAUGA-GCCA-AAU-GAC--AAUACCAU--GUCUA--GUCU--GUAGU--UUGAAGUAGGUACACAA-UGA-----ACUGAUGU-----------------UCA---CGCCGAAAAAUU-GGAGGUAU-ACAGUAG-UCCUUCCCCAC-AUCU
AACY022239896.1/292-108      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY022817295.1/709-898      GUC--------UGACGAGAUU----------------GAUC------GGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-A-CUA-GGAC--A--------------------------CAG-GUGGUGCUG-CUGGCA----------GUCA---------------UGUCAG-AAUCGAC---UAACCA---GUCGG--GUCU--UAGGU-AGAGAAG-----------UUUUC-UUAACUG-UA-----------------GAAA---UGCCCUUCUCUU-GUUGGUAU-ACAGUAU-UCCAACCUCCA-CCCU
AACY022796308.1/461-646      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUAU--------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY021967473.1/403-602      GAAGG-------GCUUAUAAU--------------CCUUCC-U---GUGGGUG-ACUGAAAUA------ACCUGUU-GUG-----------AGCGGGUUAAGGU-A-UAC-GAUU-----------------------------CUCUGUGGUGGAG-UACCGAUGGGC-----AAAU----------GUCUGA-GGUA----GGAU---UUCCCA---AUCC---AAUU--GUAGU-AC--GAGUAGGCACAUAAUGAA------CUA-AU-----------------GUUC---ACACCGAAAGUU-GGGAGUAU-GUAGUAG-UCUCCCCCCAC-ACCU
AACY022949245.1/85-270       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-GGUC--A--------------------------GAG-GUGGUGCUCGCUACC-----------GCAG----------------GGUAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020320373.1/466-660      ---CGAAG----GACG----------------CUUUGCUUACA---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUUC----------GCAA---------------GAACAG-AACUACU---GAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-CCCAACCUCCC-ACCC
AACY023500890.1/1007-1191    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020334510.1/1232-1428    GGUGACU-----GAUC-----------------A-UCACCAUC---GGGAGUG-ACUGAACAA------CCCUGUU-GGAAUUA-------GGCGGGGUAAAGU-A-AAU-GGUU--A--------------------------GAG-GUGGUACUCGCCUUCCC---------UAAA--------------GGAAGUG-AACC--C---GCACCAA--G--GG--AACC--AUUGU-UGUUAUGUA---CUAAUUUUCG------CUU-UA-----------------GCGA---UUCCCAUAACUU-GAGGGUAU-GAAGUAU-UCCCUCCUCUC-ACUC
AACY023200164.1/1390-1179    GGAGAUU-----GAUC-----------------A-UCUCCAUA---GGGUAUG-GCUGAAUAA--CUG-UUGUG---GUCAUCA---------CGCAGUAAGGCUGAAGUAGAAC--A--------------------------GGCUGUGGUGGCCGCCAAGGAAUACCGG--GAGA-------CCGG-AGUCUUGUG-AAUC---C-UUAACCG--G---GA--GUUC-GAAAAGAUCAGAGG-----------UUUAC-UAAGCAU-UA-----------------GUGA---GACCCCUCUGUU-GAAGGUAU-AAUGUAA-UCCUUCUACCC-ACCU
AACY023545229.1/224-28       GGAACCU-----GAUC-----------------A-GUUCCAUA---GGGUGUG-ACUGAAUAA------CUCUGUU-GGAAUUA-------GGCGGAGUAAUGU-A-AAU-GGUU--A--------------------------GAG-GUGGUACUCGCCUUCCC---------UAAA--------------GGAAGUG-AACC--C---GAACCAA--G--GG--AACC--AUUGU-UGUUAUGUA---CUAAUUUUCG------CUU-UA-----------------GCGA---UUCCCAUAACUU-GAGGGUAC-GAAGUAG-UCCCUCCACCC-AACC
AACY020128968.1/699-884      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACC-----------GAGA----------------GGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AACAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY022345091.1/580-388      ---GGGUU----GACG----------------AACCUGACA-U---GGGAGUG-ACUGAAUAAU-CUU-UCUGGC--AUAU-A---------GCUGGAUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGC------------GAAA-----------------GCAG-AAUCGUC---UUACCA---GACGG--GUCU--CAGGC-AAGGACGUAAAA------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAAUACAGGAA-UCCAACCUCCC-ACCC
AACY022749271.1/244-60       GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCCU
AACY022205174.1/65-262       ---UUCUC----GACG----------------GAGAGUCCAUA---GGGUGUG-ACCGAAUAAC-----CCUUGU--GGAGGC---------ACGGGGUAAGGU-AUAUUAGGAC--A--------------------------GGG-GUGGUGCCCGCUGUG-----------CUUG----------------CAUAG-AAUC--C--GAUACCAA--G--GA--GUCC-GAAAGU-CUGGAAGUCC--UCAUAUUACAC-----CUA-CAA----------------GUGU---AUCCCUUUCAGU-GAAGGUAUAGUAGAA--CCCUUUCACCC-ACUA
AACY023529990.1/202-395      ---GGGU----UGAUC-----------------ACCUAACA-C---GGAAGUG-ACUGAAGAA------CCCUGUU-GGAAUUA-------GGCGGGGUAAAGU-A-UUG-AGUU--A--------------------------GAG-GUGGUGCUCGCUG-AC----------AUU----------------GUGCAG-AACC-CU---UUACCA---AG-GG--AACU--CAAGU-UGUAAUG---AACCUUACAUCGC----ACAC-UA-----------------GCGA---UUCCCGUUACUU-GAGGGUAA-AAUGAAU-UCCCUCCUUCC-ACAC
AACY023417680.1/378-566      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GCAA---------------UGACAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AAUAACGUA---------UUUAC-UA-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023415502.1/565-378      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-GGUC--A--------------------------GAG-GUGGUGCUCGCUGUCC----------GCAG---------------GGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023662090.1/967-1167     GUUGAGGC----GACG----------------GUCUUGACA-C---GGGAGUG-ACUGAAUAAA-CUU-GCUGGC--AUAA-G---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GAGUAG-AACCGAC---CUACCA---GUCGG--GUCU--CAGAU-AGUACAGUAAAAA-----UCUAC-UC-AAU---------------------GUAGCAAUGCCCUGUACUU-GUUGGUAA-ACAUGAA-CCCAACCUCCC-ACCC
AACY022940138.1/171-365      ---GAUUC----GACG----------------GAAUUGACA-C---GGGUGUG-ACAGAACAA------CCCUGUU-GGAAAUA-------GGCGGGGUAAUGU-A-UAG-ACUC--A--------------------------GAG-GUGGUGCUCGCAAUCC----------CUAAA--------------GGAUUG-AACU--C---UGACCAA--G--AG--GUGU--CUAGU-UAACCAGUA---UUAAAUUUCG------CUU-UA-----------------GCGA---UUCCCUGGUUAU-GUUGGUAU-GAAGUAA-UCCAAUCACCC-UCCC
AACY020142946.1/468-285      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAC------------GAAA-----------------GUAG-AACCGAU--UCAACCA---AUCGG--GUCU--CAGGC-AACAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020124586.1/1202-1387    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCCU
AACY020490446.1/1141-1333    GUGCCU------GAUC------------------A-GCACAUU---GGGUGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-CGAC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GGAA---------------UGGCAG-AACU-AC---AAACCAA--GU-AG--GUCG--UAGGC-AGAGUGGU----------AAUUC-UAAACUG-UA-----------------GAAA---UGCCCUGCUCUU-GUUGGUAU-ACAGGAU-UCCAACCACCC-UCCC
AACY020342776.1/999-1196     ---UUCUC----GACG----------------GAGAGUCCAUA---GGGUGUG-ACCGAAUAAC-----CCUUGU--GGAGGC---------ACGGGGUAAGGU-AUAUUAGGAC--A--------------------------GGG-GUGGUGCCCGCUGUG-----------CUUG----------------CACAG-AAUC--C--GAUACCAA--G--GA--GUCC-GAAAGU-CUGGAAGUCC--UCAUAUUACAC-----CUA-CAA----------------GUGU---AUCCCUUCCAGU-GAAGGUAUAGUAGAA--CCCUUUCACCC-ACUA
AACY020127425.1/675-857      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUUC------------GAAA-----------------GAAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY022486287.1/566-382      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023720909.1/681-485      --UGGAGC----GACG----------------GUUCUGACA-C---GGAAGUG-ACUGAAGAAC-CCU-GUUGGA--AUUA-G---------GCGGGGUAAAGU-A-UUG-AGUC--A--------------------------GGC-GUGGUGGCCGCUGCUA----------GGAA---------------UAGUAG-AACC--C---CGACCAA--G--GG--GACU--CAAGU-UGUAACG-AA--CCUACUAUCGC----ACAC-UA-----------------GCGA---UUCCCGUUACUU-GAGGGUAA-AAUGAAU-UCCCUUCUUCC-ACCC
AACY022179318.1/340-155      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUAU--------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY023915754.1/634-444      GUAAG-------GACG-------------------CUUACAUC---GGGAGUG-ACUGAAUAAA-CUU-GCUGGC--AUAC-G---------UCUAGUUAAGGU-G-AUG-AGUU--A--------------------------GAG-GUGGUGCUCGCUGCUG----------GGAA---------------CAGUAG-AACU-AC---AAACCAA--GU-AG--AGCU--CAGGU-CUGAUGGU----------CUUUC-UA-ACUG-UA-----------------GAAA---UGCCCCAUCAGU-GUUGGAAU-ACAGAAA-CCCAACCUCCC-UCUU
AACY024035515.1/611-799      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACCGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GGAA---------------UGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AAUAACGUAU--------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCCU
AACY021374401.1/351-166      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCCU
AACY020108195.1/542-726      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020127680.1/3203-3020    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACC-----------GCAG----------------GGUAG-AACCGAC---CUACCA---GUCGG--GUCU--CAGGC-AAGA-CGUU---------UUUAC----ACUG-UA-----------------GUAUA--UGCUCGUUCUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY020204639.1/597-409      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUUC----------GCAA---------------GGACAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-UU-UCUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCCU
AACY023897464.1/348-543      ---GGGGGC---GACG---------------GUUCUCUUAC-A---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUUU-U---------GCUAGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUUG----------GCAA---------------CGACAG-AAUCGUC---UUACCA---GACGG--GACU--CAGGC-AGGCAAGU----------CUUUC-UA-ACUG-UA-----------------GAAA---UGCCCUUGUCUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-ACCC
AACY022717616.1/595-778      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUUC------------GAGA-----------------GAAG-AACCGAC--UCAACCA---GUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020114377.1/2649-2834    GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU--UCAACCA---AUCGG--GUCU--CAGGC-AACAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY022040587.1/15-201       -UGCCU------GAUC------------------A-GCACAUU---GGGUGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUA-CAAC--A--------------------------CAG-GUGGUGCUG-CUCC------------GAAA-----------------GGAG-AAUCGAC---UUACCA---GUCGG--GUUG--UAGGC-AGAGAUG-----------AUUUC-UAAACUG-UA-----------------GAAA---UGCCCAUCUCUU-GUUGGUAU-ACAGGAU-UCCAACCACCC-UCCC
AACY022498088.1/117-300      GUUG--------GACG--------------------CAACAUA---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAC------------GAAA-----------------GUAG-AACCGAC---CUACCA---GUCGG--GUCU--CAGGC-AAGAACGUU---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-CCCU
AACY022245593.1/557-752      ----GGU------UCGCU---------------ACCUGAUA-C---GGGAGUG-ACUGAAUAAG-CUU-GCUGGC--AUAA-G---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GAGUAG-AACCGAC---CUACCA---GUCGG--GUCU--CAGAU-AGUACAGUAAAAA-----UCUAC-UC-AAU---------------------GUAGCAAUGCCCUGUACUU-GUUGGUAA-ACAUGAA-CCCAACCUCCC-ACCA
AACY022749285.1/445-262      UACUCGAC----GACG----------------GUUGAGUAA-A---GGGAAUG-ACUGAAUAAU-----CCUCUG--ACAU-----------UGGGGAUAAGGU-G-CUG-CUGC-------------------------------------------GUUGCUAUAU-GCG--AAGACCAAA--CGCUAGGGGGUAAC---------------------------GUGG--UAGAC-UAAGGGC-----------UACAC-UGAACUG-UACC---------------GUGU---CACUGUCCUUAU-GUGAGUAAUGCAGAAA-UCUCACUUCCC-ACUA
AACY021571292.1/762-571      GUCGG----ACCGAUCAA-----------------CCGACA-U---GGAAGUG-ACUGAAUAA------CCCUGUU-GGAAUUA-------GGCGGGGUAAUGU-A-GAC-AGUU--A--------------------------GGG-GUGGUGCCCGCUAC------------UUCG-----------------GUAG-AACU--A---UUACCAA--U--AG--AACU--GUUGU-UGUUAUGUA---CUAAUUUUCG------CAC-UA-----------------GCGA---UUCCCAUAGCAU-GAGGGUAA-AAUGUAU-UCCCUCCUUCC-ACCC
AACY022558238.1/193-7        GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-UGUAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUACUU-GUUGGUAU-ACAGGAA-CCCAACCUCCC-UCCU
AACY020124002.1/1166-980     GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-UGUAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUACUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY022378599.1/522-717      ---GAGUU----GACG----------------AACCCAACA-C---GGGAGUG-ACUGAACAAA-CUU-GCUGGC--AUAA-G---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CACGUU----------G-AA---------------AACGUG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGAC-AGUAAGGUAAAAA-----UCUAC-U--AAU---------------------GUAGCAAUGCCCCUUACUU-GUUGGUAC-ACAUUAU-UCCAACCUCCC-ACAC
AACY021533087.1/482-295      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY023905797.1/1021-836     GUAAC-------GACG-------------------GUUACGUC---GGGAGUG-ACUGAAUAAU-CUU-UCUGGC--AAAC-----------GCUGGAUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUUC------------GAGA-----------------GAAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AAGAACGUAU--------UUUAC----UCUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UUUU
AACY021475308.1/358-157      GUUGGG-CC---GACG---------------GGUUCCAACA-C---GGGAGUG-ACUGAAUUAAACUU-GCUGGC--A-AUAG---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUACUCGCUUUCC----------UUCG---------------GGAUAG-AACCAUC---CUACCA---GAUGG--GACU--CAUGC-AACGCAGUAAAA-------UUAC-UA-AGAG-UA-----------------GCAA---UGCCCUGCGUUU-GUAAGCAU-ACUCAAA-UCUUACCUCCC-UCAU
AACY023492788.1/472-658      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-UGUAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUACUU-GUUGGUAU-ACAGGAA-CCCAACCUCCC-UCCU
AACY023718593.1/892-705      GUUG--------GACG--------------------CAACGCA---GGGAGUG-ACUGAAUAAU-CUU-UCUGGC--A-AA-C---------GCUGGAUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CACC------------GAAA-----------------GGUG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AGAGAUGUAAAA------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUCUCUU-GUUGGUAC-ACAGAAA-CCCAACCUCCUCACAC
AACY023423879.1/188-372      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY021349141.1/279-465      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCUC----------GCAA---------------GGGUAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-UGUAACGUA---------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUACUU-GUUGGUAU-ACAGGAA-UCCAACCUCCC-UCUU
AACY021190420.1/572-380      GUAAG-------GACG-------------------CUUACGUC---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-AGAU--A--------------------------CAG-GUGGUGCUG-CUUCUAG---------GGAA--------------CUAGAAG-AAUCGAC---UUACCA---GUCGG--AUCU--CAGGC-AGAGAUGA----------UUUUC-UA-ACUG-UA-----------------GAAA---UGCCCAUCUCUU-GUUGGUAC-ACAGGAG-UCCAACCUCCC-UCUU
AACY023389124.1/348-161      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGUC--A--------------------------GAG-GUGGUGCUCGCUGUCC----------GCAG---------------GGGCAG-AACUACU---CAACCA---AGUAG--GACU--CAGGC-AACAACGUA---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUGUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY023545418.1/840-1025     GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUGACGUA---------UUUAC-UU-ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCCU
AACY023891661.1/657-850      GUGCCU------GAUC------------------A-GCACACU---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUA-CAUU--A--------------------------GAG-GUGGUGCUCGCUGUCA----------GCAA---------------UGACAG-AACUACU---CAACCA---AGUAG--AAUG--UAGGC-AGAGAAGU----------UUUUC-UAAUCUG-UA-----------------GAAA---UGCCCUUCUCUU-GUUGGUAU-ACAGGAU-UCCAACCUCCC-UCUU
AACY022372313.1/231-416      GUUG--------GACG--------------------CAACA-U---GGGUGUG-ACUGAACAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU---CAACCA---AUCGG--GUCU--CAGGC-AAUAACGUAU--------UUUAC-U--UCUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAU-ACAGGAC-UCCAACCACCC-UCCU
AACY021105468.1/464-279      GUUG--------GACG--------------------CAACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-U---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGCA-----------GCGA----------------UGCAG-AACCGAU--UCAACCA---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
AACY020395162.1/2008-2196    GUGCCU------GAUC------------------A-GCACAUC---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--AUAU-A---------GCUGGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUGC------------GAAA-----------------GCAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AGAGGAGU----------UUUUC-UAAACUG-UA-----------------GAAA---UGCCCUCCUCUU-GUCGGUAC-ACAGGAA-UCCGACCUCCC-UCUU
AACY023326212.1/1275-1445    GCUUC-------GACG-------------------GAAGAGCUG--GAGUAUG-GCUGAAUAA------UCUG----AUAGUUGUAUGGG----CAGAUAAAGC-A-CUA-GAG-----GGCGUAACGGCUGGGUGUAACCCAA-----------------------------------------------------------------------------------CUC--UAGGU-GUGCU--GAUUA-------GCGGG----CUU-GAC---------------UCCGU-AACAAAUAGGCACU-GGUGGUAA-AAAGCAU-CCCACCUACUC-ACCU
AY940168.2/164830-165013     GUCU--------GACG--------------------AGACA-U---GGGAGUG-ACUGAAUAAA-CUU-ACUGGC--A-AC-C---------GCUAGUUAAGGU-G-AUG-AGAC--A--------------------------CAG-GUGGUGCUG-CUAC------------GAAA-----------------GUAG-AACCGAU--UCAACCG---AUCGG--GUCU--CAGGC-AAUAACGUU---------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUAUUU-GUUGGUAC-ACAGGAA-UCCAACCUCCC-UCUU
GU071092.1/144844-145040     UGAAUC------GACG------------------GGUUCAACG---GGGAGUG-ACUGAAUAAA-CUU-UCUGGC--AUAU-A---------GCUGGUUAAGGU-G-ACG-AGAC--A--------------------------CAG-GUGGUGCUG-CUACUC----------GCAA---------------GAGUAG-AAUCGAC---UUACCA---GUCGG--GUCU--CAGGC-AAGGACGUAAAA------UUUAC-U--ACUG-UA-----------------GUAA---UGCCCGUUCUUU-GUUGGUAAUACAGAAA-CCCAACCUCCC-ACCC
#=GC SS_cons                 <<<<<.......____..................._>>>>>--...{{{{[,,.<<--------..--.<<<<<...____._..........>>>>>---->>.,.,((.(((,..,..........................<<<._BBBB_>>>.<<<<<<..........____..............>>>>>>,.,,<<<<<...__bbbb...>>>>>..))))..)],,,.<<<<<<<---........-<<<<._.._AAA.A_.................>>>>...---->>>>>>>,.<<<<<___.aaaa___._>>>>>}}}}:.::::
#=GC RF                      ccuuc.......GACG...................ugaagguu...GgggaUG.aCUGAAUAAA..UU.ccucG...auAu.u..........CgaggUAAgGu.a.acg.ccuC..A..........................gaG.GUGGUGCuc.cccccc..........gaaa..............ggggggG.AAccgac...uaACCA...gucgg..aggu..guGGu.agggacguAa........Uucgc.U..aCUg.uA.................gcga...ugCCcgucccuU.GuuGGUAu.AcAGuAA.UCCaaCcucCC.ACCu
//
# STOCKHOLM 1.0

#=GF AC   RF01746
#=GF ID   mraW
#=GF DE   mraW RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   50.20
#=GF NC   49.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.08 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   MraW_RNA_motif
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   45


BABE01001411.1/1117-1012     ---GUGAUCGCGUGAUCCG---CGGCUCCGGUCCGACCGG----GCCC---CCUGACACAACUUCCCCUGUGCCAGG--UGGU----UCAG--CCGGAACGGAACCC---CGGACCACGGGUCGUCGACA
AACY020485544.1/125-13       ---GAUUUUUCGUUUGGCUUGA-GGCCUCUCUCUGCAAAU----AGUGUCCACCGACUUU-CUUCCCCGAAGCCGGAAGCAAU----GUUU--GCAGAGAGGGACC-UC-GGUUAAACGCAAAAAAACCG
AACY020531684.1/1492-1395    ---UUCUGAUCUGUCGGUU---CGACUCCCUCCCGU--------CGGC---CCUGAGACACCUUCCCCGGUCCCAGG--UCUC----------ACGGAGGGGAAUCA---GACCGACAGGCCGGAUCGAA
AACY023330346.1/1371-1266    ---CAAUUGAUGCUGCUUU---UGGCCUCUGGCCGU-UGACUCG-----AUCCUGGCGCACCUUCCCCGGUGCCAGGC------UCUCCA---ACGGCCAGGGACUA---AAGGCAGUAACAAGAUCUGA
AE016958.1/2107071-2106968   ---GCAUGCCCGUGCAACG---UGGCCUCUGCCCGA---A---CCGAC---CCUGGCGUA-CUUCCCCAACGCCAGG--UUCGUGCCU-----UCGGACAGGGACCU---CGAUGCAGGGGCAGCUCGCC
CP000479.1/2329935-2330038   ---GCAUGCCCGUGCAACG---UGGCCUCUGCCCGA---A---CCGAC---CCUGGCGUA-CUUCCCCAACGCCAGG--UUCGUGCCU-----UCGGACAGGGACCU---CGAUGCAGGGGCAGCUCGCC
AM420293.1/6587882-6587766   ---UCGCGACCGGGUGUCGUGA-GGCCUCGGUCCGCUCGGCUAUCGCA-CGCCUGGUGCACCUUCCCCGGCAUCAGG---ACGCGAC--GG--GCGGGCGGGGACC-UGACGGAACCCGGUCUCUGGGGG
AACY023802001.1/1325-1228    ---UUCUGAUCUGUCGAUU---CGACUCCCUCCCGU--------CGGC---CCUGAGACACCUUCCCCGGUCCCAGG--UCUC----------ACGGAGGGGAAUCA---GAUCGACAGGCCGGAUCGAA
AACY020527137.1/3936-4043    ---UGACCCACCUGCGGUG---AGGCCCCCACCCGC---U--GGGCGC-CCCCUGGCACUCCUUCCCCGGUGCCAGG--ACGCGCAAA-----GCGGGCGGGGACCU---GACCGGGACGGUGACUAUCG
CP000474.1/1859969-1860072   ---UUGAAUGGGAUCUCCAGCC-GCCC---------AUCGAACUGUC--UUCCUGGCUCACCUUCCCCUGAGCCAGGC-CGGCGGAACGAUA-G--------GCGC-GGAUGGGGAUCCGAUUCAAGAAU
BX842579.1/4584-4481         ---GCAAACCCGUGCACCG---UGGUCUCUGCCCGA---A---GCGAC---CCUGGCGUA-CUUCCCCAACGCCAGG--UUCGUGUCU-----UCGGACAGGGACCU---CGGUGCAGGGGCGGCGCCUG
AM711867.1/2111756-2111656   ---UUCUGACCCCGGCCCC---UGACUCCCAGCCGUCCGA-----CGC---CCUGCCGCA-CUUCCCCGGCGGCAGG----------UCGGG-ACGGAUGGGGAUCA---GGAGCCGCGGACAGGACAGC
AACY020303111.1/2459-2361    ---UUUCUAGCUCGCAUUG---CAAGCUCUUGCCGAUUCG------------CUGACAAC-CUUCCCCUUUGCCAG---AUAU----CGAA--UCGGACAGGGCUCG---GGAUGCGAGAUAGAACAUCC
BX927154.1/172046-171941     ---GCAGGGAGCGCGUGUA---UGGACUCUGCUCGAGGAG---U-GGC---UCUGGUGUA-CUUCCCCGACAUCAGA---UCG-AGACUUU--UCGAGUGGGGCCC----UGUACGCACUCCGUGAUUUG
AACY023339844.1/882-987      ---CAAAUGAUGUUGCCUG---UGGCCUCUGGCCGU-UGGCU--AGAU---CCUGGCGCACCUUCCCCGGUGCCAGG--CUCU----CCA---ACGGCCAGGGACUA---GAGGCAGCAGCAAGAUCUGA
CP000854.1/3907758-3907655   ---GCAUGUCCGUGCACCG---UGGUCUCUGCCCGA---A---CCGAC---CCUGGCGUA-CUUCCCCAACGCCAGG--UUCGUGCCU-----UCGGACAGGGACCU---CGGCGCAGGGGCAUUGCGCC
AP006618.1/1911134-1911235   ---CGAGCGAGUGCCGCG----CGGUCUCUGCCCGGACG----CGGAC---CCUGGCGUA-CUUCCCCGACGCCAGG--UGCC-G----GU--UCGGACAGGGACCA----CGGGGCAUUCGCCUCCGGU
AE017283.1/823520-823625     ---GUGAUCUCGCGGUCCG---CGGGUCCGGGCCGACCGG----GCCC---CCUGACACAACUUCCCCUGUGCCAGG--UGGU----UCAG--CCGGAACGGAACCU---CGGAUCACGGGUCAUCGACA
CP000580.1/3436786-3436691   ---GCCC---GUGCAGCG----UGGCCUCUGUCCGAACCG------GC---CCUGGCGUA-CUUCCCCGACGCCAGG--UC------CGCC--UCGGACAGGGACC----UCGCUGCAGGGGCGUACAGC
AACY021504095.1/507-605      ---UUUCUAGCUCGCAUUG---CAAGCUCUUGCCGAUUCG------------CUGACAAC-CUUCCCCUUUGUCAG---ACAU----CGGA--UCGGACAGGGCUCG---GGAUGCGAGAUGGACACUCC
CP000384.1/3463004-3462909   ---GCCC---GUGCAGCG----UGGCCUCUGUCCGAACCG------GC---CCUGGCGUA-CUUCCCCGACGCCAGG--UC------CGCC--UCGGACAGGGACC----UCGCUGCAGGGGCGUACAGC
FM211192.1/1071563-1071669   ---GCAU---GCUCCCGCAUCGUGGUCUCUGUCCGAAGGC---ACGAC---CCUGGCGUA-CUUCCCCAACGCCAGG--GUCG-U--GCCU--UCGGACAGAGACCACGAUGCGGGGAUAUUUGCGU---
CP000750.2/3783753-3783867   ---UACCGACCGUCGACCG---CGGCCUCCAGCCGCCCCGUCCCCGGU---CCUGACGCCACUUCCCCGGCGCCAGG--GCCGGGGGCGCGA-GCGGAUGGGGACCG---CGACCGACGGUCGGCUCGCG
AACY021275604.1/288-181      ---UGACCCACCUGCGGUG---AGGCCCCCACCCGC---U--GGGCGC-CCCCUGGCACUCCUUCCCCGGUGCCAGG--ACGCGCAAA-----GCGGGCGGGGACCU---GACCGGGACGGUGACCUUCG
AACY020533382.1/84-181       ---UUCUGAUCUGUCGGUU---CGACUCCCUCCCGU--------CGGC---CCUGAGACACCUUCCCCGGUCCCAGG--UCUC----------ACGGAGGGGAAUCA---GACCGACAGGCCGGAUCGCA
AAMN01000002.1/113267-113369 ---GAUCCACCCCGGCUCC---CGGCCUCCAGCCGA-------CUGGG-CUCCCGACACGACUUCCCCCGUGCCGGGC-CCCG-G--------ACGGAUGGGGACCA---GGAGCCGGGGAACGGAUCAC
BX248358.1/253065-252957     ---AUGCGGAGUAUACGCA---UGAACUCUGACUGGACGC---CGUGC---UCUGGUGUA-CUUCCCCGAUAUCAGA--GCAU-GGAGCGUA-CCAGUCAGGGCUC----UGUGUAGACCCCGCCUUUAC
CP000431.1/1168667-1168567   ---CCCGCGAAUGCCGCGA----GGCCUCUGUCCGA---C---GGAAC---CCUGACGCA-CUUCCCCAGCGCCAGG--UUUU-CAUU-----UCGGGCAGGGACC----UCGAAGCAUUCGCCACGGCA
CP000454.1/1740203-1740305   ---UUGUAUGAGAUCUCCAGCC----GCCCAUCCGAACGU---UG-----UCCUGGCUCA-CUUCCCCGGAGCCAGG-----C-GG-ACGU--CCGGAUAGGC-GC-GGAUGGGGAUCUGGUUCAAGAAA
AE016822.1/1598755-1598652   ---GUUCUAGCGCCUGGCGCCG-GACUCCCAGCCAU-------CCCGA---CCUGACACCACUUCCCCGGUGUCAGG--UCGG-G--------AUGGAUGGGGAUC-GGACGCCAGGGGCCGGACCGGAG
AACY020525946.1/1769-1876    ---UGACCCACCUGCGGUG---AGGCCCCCACCCGC---U--GGGCGC-CCCCUGGCACUCCUUCCCCGGUGCCAGG--ACGCGCAAA-----GCGGGCGGGGACCU---GACCGGGACGGUGACCUUCG
AACY020762416.1/463-356      UGUGACA---UAGGCGGUG---AGGCCUCCUCCCGCUGGG---CACCC---CCUGGCACCCCUUCCCCGGUGCCAGG--AAGU-G----CAAGGCGGGCGGGGACCU---GACCGACCUAGUCCCUUUCA
AP009044.1/2259341-2259236   ---GCAGGGAGCGCGUGUA---UGGACUCUGCUCGAGGAG---U-GGC---UCUGGUGUA-CUUCCCCGACAUCAGA---UCG-AGACUUU--UCGAGUGGGGCCC----UGUACGCACUCCGUGAUUUG
CP000656.1/3149681-3149784   ---GCAGGCCCGUGCAGUG---UGGCCUCUGUCCGA---A---CCGGC---CCUGACGUA-CUUCCCCGACGUCAGG--UUCGCGACC-----UCGGACAGGGACCU---CACUGCAGGGGCCGCCCCGA
BA000035.2/2185285-2185181   ---GCAUGGAGCGCGUGUA---AGGACUCUGCUCGAGGAG---UCAGC---UCUGGUGUA-CUUCCCCGACAUCAGA--UC-G-ACACC----UCGAGUGGGGCCC----UGUACGCACUCCGUGAUUGA
AACY021154577.1/173-76       ---UUCUGAUCUGUCGGUU---CGACUCCCUCCCGU--------CGGC---CCUGAGACACCUUCCCCGGUCCCAGG--UCUC----------ACGGAGGGGAAUCA---GACCGACAGGCCGGAUCGAA
AACY020292930.1/1705-1587    UAGGUGC---GUCGCGAUG---AGGCCUCCCCCCGCGUGG--CAGGUGGCUCCUGGCAUCACUUCCCCGAUGCCGGGCACACCGGAUCCACACGCGGGAGGGGACCU---GAUCGAGACGCCAUGAACCG
AACY020310070.1/3981-4079    ---UUUCUAACUCGCAUUG---CAAGCUCUUGCCGAUUCG------------CUGACAAC-CUUCCCCUUUGUCAG---AUAA----CGGA--UCGGACAGGGCUCG---GGAUGCGAGAUGGACACUCC
CP000511.1/3758649-3758546   ---GCAGGCCCGUGCAGUG---CGGCCUCUGCCCGA---A---CCGGC---CCUGACGUA-CUUCCCCGACGUCAGG--UCCGCACCC-----UCGGACAGGGACCU---CACUGCAGGGGCCGCCCCGA
CR931997.1/884904-885017     ---AAACGGAGUGUGCGCAGGCCCUUACCUGCGUGGACGA--CGCGGA-AUCUUGACGUA-CUUCCCCAAUGUCAAG--CCCG-CAC------CCACGCAGGUGAGGCCCUGUACGCACUCCUUUAGCUU
AACY020060518.1/687-788      ---UGUGAUCCCGUGUUCG---AGACUCCCGUCCGUUUGC-----------CCUGUGACACCUUCCCCGGUUCCAGG---UCU----GCCAC-ACGGAAGGGAAUCU---CGAAUCCGGGUCGCUAGAGG
AACY020523275.1/458-556      ---UUUCUAGCUCGCAUUG---CAAGCUCUUGCCGAUUCG------------CUGACAAC-CUUCCCCUUUGUCAG---ACAU----CGGA--UCGGACAGGGCUCG---GGAUGCGAGAUGGACACUCC
AACY020523748.1/2428-2525    ---UUCUGAUCUGUCGGUU---CGACUCCCUCCCGU--------CGGC---CCUGAGACACCUUCCCCGGUCCCAGG--UCUC----------ACGGAGGGGAAUCA---GACCGACAGGCCGGAUCGAA
AACY020524352.1/2839-2937    ---UUUCUAGCUCGCAUUG---CAAGCUCUUGCCGAUUCG------------CUGACAAC-CUUCCCCUUUGUCAG---ACAU----CGGA--UCGGACAGGGCUCG---GGAUGCGAGAUGGACACUCC
FR878060.1/2418763-2418660   ---GCAAACCCGUGCACCG---UGGUCUCUGCCCGA---A---GCGAC---CCUGGCGUA-CUUCCCCAACGCCAGG--UUCGUGUCU-----UCGGACAGGGACCU---CGGUGCAGGGGCGGCGCCUG
#=GC SS_cons                 ...:::::::::<<<<<<<...-<<-<<<<<<<<<<<<<<...<<<<<...<<<<<<<<_.________>>>>>>>>..>>>>.>-.>>>>..>>>>>>>>>>->>-...>>>>>>>:::::::::::::
#=GC RF                      ...uuauuaacuccccccg...uGgccuCcgcCCGcccgg...cgggc...CCUGgcgca.CUUCCCCggcgcCAGG..gccc.ga.ccgg..gCGGgcgGggAcCu...cggggggaggccgaaacuca
//
# STOCKHOLM 1.0

#=GF AC   RF01747
#=GF ID   msiK
#=GF DE   msiK RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   33.00
#=GF TC   34.60
#=GF NC   29.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   MsiK_RNA_motif
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   120


BAAY01007686.1/255-195       AAAGAA-----AUCCCUUUACAACGGAUCGUGAGGCACGUACCUGCCUCUGAAAGGAU--GACAAAUC
AACY023308612.1/1044-986     GGCCAUCA-----CCUUCAUCCACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU
BX248355.1/160867-160810     CACUUUAU----UUCUUCUACU-CGGAUCGUUCGGCACGUACCUGCCGAUA-AAGAA---UGGAGUU-
AACY020556781.1/1408-1350    CGAACA-----UCGCUCUUACUUCGGAUCGUCCGGCACGUUCCUGCCGGUGAGAG-GA--ACCACCA-
AACY023290927.1/440-498      GGCCAUCA-----CCUUCAUCCUCGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU
AACY023803192.1/795-737      GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA
AACY023828838.1/892-834      GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY020296654.1/3720-3776    GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY023817491.1/7-64         UGUUGGAUG-----CUUUCACCACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY023314832.1/131-189      CGUGAGAC-----CUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGAAGAAG----GAGUGCUA
AACY022653449.1/402-460      GCGCGGCA-----UCCAUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGGA----GAAAAUAA
AACY021215036.1/138-80       UGGA-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA---
AM849034.1/2895497-2895439   GCAUCACA-----UCCAUCACCACGGAUCGUCGGGCACGUACCUGCCCGUGAAGGA----GAACACCG
AACY020059319.1/116-58       UGGA-----CUUGCUUCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAGAGA---
CP000667.1/4785498-4785555   CGGCCCGC-----UCUUUCACU-CGGAUCGUCCGGCACGUUCCUGCCGGUGAAAGG----AAGCACCC
AACY022515996.1/291-233      GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY023808612.1/943-1001     GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGU-AAGAGA---GGAAAAA-
AE014295.3/1661060-1661118   GAACAA-----AUCCCUUUACAACGGAUCGUGAGGCACGUACCUGCCUCUGAAAGGAU--UAGUAA--
AACY020309138.1/212-270      GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY020711540.1/892-834      GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA
AACY020801666.1/396-454      UGGC-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGUGCAU---
AACY023816586.1/1430-1488    GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA
AE017283.1/439778-439720     GUCACCGA-----UUUUCCACAACGGAUCGUCGGGCACGUACCUGCCCGUGGAAAG----GAACAACG
CP001341.1/953078-953020     AAACAUGAA----CCAUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAA-GG----GAUUGAUA
AAMN01000005.1/40921-40863   GGGUUU-----UUCCCUUUACAACGGAUCGUCCGGCACGUUCCUGCCGGUGAAGG-AA--GGCAAUG-
AACY020530366.1/1402-1460    GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY020523976.1/2197-2141    GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY023442678.1/506-448      CCCA-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAGGAA---
AACY023841016.1/464-520      GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY021171437.1/836-780      GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY021496387.1/154-96       GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY020303265.1/68-126       GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY020599560.1/709-651      UGGA-----CUUGCUUCAUCCAACGGAUGGUCGGGCACGUACUUGCCCCGAGAAGG-AAGAGAAA---
AACY020064545.1/673-730      AAGAGGC----AC-UCGUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAGU--AGAAA---
AACY020470988.1/2403-2346    ACGAGGC----ACUC-AUCACGAAGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAGU--AGAAA---
AACY023319023.1/289-231      GGCCAUCA-----CCUUCAUCCACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU
AACY023331894.1/236-178      GGCCAUCA-----CCUUCAUCCACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU
AACY023355258.1/868-926      AAAUCGUU----UCCAUUCACUACGGAUCGUCCGGCACGUACCUGCCGGUGAA-GGA---GAAAACA-
AACY020170145.1/1281-1223    AGGAUGA-----CCUAUCUCCAACGGAUCGUCCGGCACGUACCUGCCGGGAGA-GGG---AGCUAACG
AACY023323829.1/260-317      GGCUAACG-----CCUUACCCU-CGGAACGUCGGGCACGUACCUGCCCGGAUAAGG----AAGAAAUA
AACY023430589.1/1577-1636    -CCGUGAGA---CCUUCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGA-GAAGG---AGUAAACA
AACY020169821.1/1024-1081    UGGUCGCAA-----UACUUCCAAAGGAUCGUCGGGCACGUACCUGCCCGGAAGGA-----GAAAAAAU
AACY020177699.1/315-373      UGGA-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA---
AACY020051425.1/729-671      UGGA-----CUUGCUUCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAGAGA---
AACY023443860.1/741-683      CGUGAGAC-----CUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGAAGAGG----GAGUAAUA
AACY020058740.1/867-924      AAGAGGC----AC-UCGUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAGU--AGAAA---
AACY023834223.1/295-237      GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY022769167.1/65-123       GGGA-----CUUACUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAGAAA---
AACY023291338.1/1308-1251    GCCAUAAC-----CUUCAUCCU-CGGAUCGUCGGGCACGUACCAGCCCGGAUAAGG----AAGUCUUC
AP009256.1/2026471-2026413   ACAAAA-----AUCCCUUUACAACGGAUCGUGAGGCACGUACCUGCCUCUGAAAGGAU--GACAAA--
AACY023838183.1/673-731      GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY023836095.1/167-109      GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA
AACY021127318.1/81-23        GGGC-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA---
AACY023352948.1/821-764      AGCGAUCA----C-CUAUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAG---AAACAA--
AACY023256209.1/29-86        ACGAGGC----ACUC-AUCACGAAGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAGU--AGAAA---
AACY020538448.1/527-469      CUCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY023318012.1/501-443      GGCCAUCA-----CCUUCAUCCACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGAAAU
AACY022901723.1/625-567      GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA
AE016822.1/1880494-1880552   CCACAUCA-----UCCAUCACUACGGAUCGUCCGGCACGUACCUGCCGGUGAAGGA----GAACACGA
AACY023844945.1/1161-1219    GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY021052297.1/178-120      GGAGUAAC-----CUCCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGAAGGAG----AGCUAGAA
AACY021345393.1/154-96       GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY020554771.1/6628-6686    UGGA-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA---
AACY020176623.1/1738-1796    AAAAAGAC-----CUUCAUCCAACGGAACGUCGGGCACGUACCUGCCCGGAAGAAG----GAGUAAAA
AACY023795141.1/1172-1114    GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY020619186.1/175-233      CUCG-----CUUACUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA---
ABMI01052056.1/105-49        GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY023836412.1/551-495      GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY023792959.1/1429-1476    ---------------UUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY023294700.1/958-1016     CAGUA----ACU-CUUCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGAGAAGG-AGUAAGUA---
AACY022775623.1/200-141      GCUGGCG-----CCUUUAUCCAACGGAUCGUCGGGCUCGUACCUGCCCGGUUAAGGG---AGUUACUU
AACY020468017.1/554-613      -CCGUGAGA---CCUUCAUCCAACGGAUCGUCGGGCACGUACCUGCCCGGA-GAAGG---AGUAAACA
AACY023982826.1/13-71        GACCAUCA-----CCUUCAUCCACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU
AACY023340538.1/662-720      GCUCAUCA-----CCUUCACCUACGGAUCGUCGAGCACGUACCUGCUCGGAGAAGG----AGAAAUUC
AACY020296024.1/375-317      CGAACA-----UCUCUCUUACUUCGGAUCGUCCGGCACGUUCCUGCCGGUGAGAG-GA--ACCACCU-
AACY023434470.1/1454-1512    UGGA-----CUUACUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGAAAAA---
U12007.1/36-95               -CACCACCA---CCUUCCUACAACGGAUCGUCCGGCACGUUCCUGCCGGUAG-AAGG---GGGCCCUU
AACY023331001.1/307-249      UGUGAGAC-----CUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGAAGAGG----GAGAAAUA
BA000030.3/4887082-4887138   UGGACACCA-----CCUUUACU-CGGAUCGUCCGGCACGUUCCUGCCGGUGAAGG-----GGGCCCCU
AACY020525511.1/587-645      GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY020011956.1/378-436      GGGUGGGU----UCCAUUCACAAAGGAUCGUCCGGCACGUACCUGCCGGUGAA-GGA---GAAAAUC-
AAOB01000005.1/162025-162083 GAUCGCUG----UCCAUUCACUAAGGAUCGUCCGGCACGUACCUGCCGGUGAA-GGA---GAAAAAU-
AACY020307023.1/1756-1814    GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGU-AAGAGA---GGAAAAA-
AACY023801115.1/426-484      GGCUGUCGA----CUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAG----AGGAAAAA
CP000750.2/1372523-1372582   -UGAAGACC---CCAUUCCACAACGGAUCGUCCGGCACGUACCUGCCGGUGGAA-GG---ACACACGA
CP000605.1/1702669-1702727   GAACAAAU-----CCCUUUACAACGGAUCGUGAGGCACGUACCUGCCUCUGAAAGG----AUUAGUAA
AACY023315685.1/655-597      GGUUAGCA-----CCUUCAUCCUCGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAAUUAC
CP000850.1/5276815-5276872   CGGUCCGU-----UCUUUCACU-CGGAUCGUCCGGCACGUUCCUGCCGGUGAAAGG----AAGCACCC
AACY023818985.1/972-916      GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY023293856.1/1006-1063    ACCAGCAC-----CUUCAUCCU-CGGACCGUCGGGCACGUACCUGCCCGGAUAAGG----AAAUGUAA
AACY020165622.1/5444-5502    CCAC-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGUGAAA---
AACY023826769.1/1080-1024    GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY020533395.1/706-648      GGCUGUCG----UCUCUUCACGACGGAUCGUCCGGCACGUACCUGCCGGU-AAGAGA---GGAAAAA-
AACY023292971.1/264-205      CAGUGAGA----CCUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGA-GAAGG---AGUAAUUA
AP006618.1/5869874-5869931   UGCCGACA-----CCCUGUACU-CGGAUCGUCCGGCACGUUCCUGCCGGUGAAGGG----AAGUAUCU
AACY020524589.1/159-101      GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY020296610.1/2203-2147    GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY020172986.1/652-594      CGUGAGAC-----CUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGAAGAGG----GAGUAAUA
CP000474.1/988504-988446     GAAAAUGAA----CCAUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAA-GG----GAUUGAUA
AACY020174331.1/171-229      GUGUAGGG----CUCUAUCACUACGGAUCGUCCGGCACGUACCUGCCGGUGA-GGAG---AAAAAAU-
AACY020176753.1/132-74       UGGC-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGUGCAU---
AACY023806029.1/782-838      GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY023822562.1/1011-1067    CCGUCG------UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-GGAGA---GGAAAAA-
AACY023799473.1/826-768      GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAAA-
AACY022641081.1/812-869      CCACCUUU-----CUUCUUACAACGGAUCGUCCGGCACGUUCCUGCCGGUGA-GAG----GACUUGUC
AACY021867778.1/709-766      GGCUGUCG----UCUCUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUG-AGAGA---GGAAAA--
AAQK01003194.1/85-143        ACAAAA-----AUCCCUUUACAACGGAUCGUGAGGCACGUACCUGCCUCUGAAAGGAU--GACAAA--
AY842007.1/445-387           UUCACUG----UUUCUCACACUACGGAUCGUUCGGCACGUACCUGCCGAUG-GAGGAG--AUUCUG--
AACY023826784.1/354-298      GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY020467656.1/1124-1066    GGCCAUCA-----CCUUCAUCCUCGGACCGUCGGGCACGUACCUGCCCGGAGAAGG----AGAGCAAU
CP000431.1/4502789-4502731   CGGCACAC----CCCUAACACU-CGGAUCGUCCGGCACGUUCCUGCCGGUGG-AGGG---AUUCAUUU
AACY023309530.1/927-871      -GGCCAGCA-----CUUAAUCCUCGGAUCGUCGGGCACGUACCUGCCCGGAUAAG-----GAAAGUGA
CP001601.1/1416488-1416546   UUCACUG----UUUCUCACACUACGGAUCGUUCGGCACGUACCUGCCGAUG-GAGGAG--AUUCUG--
AACY021516186.1/700-758      UGGC-----CUUGCUUCAUCCAACGGACCGUCGGGCACGUACCUGCCCGGAGAAGG-AAGUGCAU---
AAYI02000004.1/407474-407531 CCACGG------UCACCCCACUACGGAUCGUCCGGCACGUACCUGCCGGUGGGAAGG---AAAACUC-
AACY023307698.1/644-701      GCUGUCC-----UCUAUUCACUACGGAUCGUCCGGCACGUACCUGCCGGUGAA-GGA---GAUACAC-
AACY020294371.1/1956-2012    GUUGGAUG------CUUUCACAACGGAUCGUCCGGCACGUACCUGCCGGUGAAGG-----AGAUAAAA
AACY022762350.1/772-830      CGUGAGAC-----CUUCAUCCAACGGAUCGUCGGGUACGUACCUACCCGGAAGAGG----GAGAAAUA
AACY023224611.1/1289-1232    GACGAACA----C-CCAUCACAAUGGAUCGUCCGGCACGUACCUGCCGGUGAAGGAG---AAGAUC--
CP000509.1/1122407-1122464   CCGUGCUCA----CC-UUUACGACGGAUCGUCCGGCACGUACCUGCCGGUGAA-GG----AGUUGUUC
#=GC SS_cons                 ::::::::....:<<<<<<<-----------<<<<<<______>>>>>>>>>>>>>....::::::::
#=GC RF                      ggcuauca....uCcuuucaCAACGGAUCGUCcGGCACGUACCUGCCgGugaaagG....AgaaAaaa
//
# STOCKHOLM 1.0

#=GF AC   RF01748
#=GF ID   nuoG
#=GF DE   nuoG RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   33.00
#=GF TC   33.20
#=GF NC   32.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.40 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   NuoG_RNA_motif
#=GF SQ   31


BX950851.1/3380818-3380775     GAAUUUUUGAUUAGC-GCCUGUG-------------------GUAA-------------------------------------CACGGGCCAUUAUGGAAG
CP000266.1/2400881-2400839     GAAUU-UCGAUUAAC-GCUCGGU-------------------CCCUG------------------------------------ACCGAGAAAA-CUGGAAG
CP000822.1/489807-489849       -GUCAUUCGAUUAAC-GCUUAGU-------------------CCCUG------------------------------------ACUAAGCCAA-CUGGAAG
L25055.1/3109-3151             GAAUU-UCGAUUAACGCUCAGUC-------------------UCU--------------------------------------GACUGAGAAAACUGGAAG
AL590842.1/2865144-2865102     GAAUUUUUGAUUAAC-GCCUGCC-------------------GUAA-------------------------------------GGUGGGUCAU-UUGGAAG
CP000653.1/3066128-3066087     GAAUU-UUGAUUAAC-GCUCGGA-------------------UUUA-------------------------------------UUCGAGCCAA-CUGGAAG
ABXW01000062.1/94927-94967     GUAUUUAUGUUUAAC-GCCUGC--------------------UAAC--------------------------------------GCGGGCCUU-UGGGAAG
ABJD02000101.1/1598670-1598628 GUAUUUUUGAUUAAC-GCCUGCU-------------------GUUG-------------------------------------AGCGGGCCUU-UGGGAAG
CP001164.1/3167747-3167705     GAAUU-UCGAUUAACGCUCAGUC-------------------UCU--------------------------------------GACUGAGAAAACUGGAAG
CP000034.1/2279970-2279928     GAAUU-UCGAUUAAC-UCUCAGU-------------------CUCUG------------------------------------ACUGAGAAAA-CUGGAAG
U00096.2/2398237-2398195       GAAUU-UCGAUUAACGCUCAGUC-------------------UCU--------------------------------------GACUGAGAAAACUGGAAG
CP000468.1/2505047-2505005     GAAUU-UCGAUUAACGCUCAGUC-------------------UCU--------------------------------------GACUGAGAAAACUGGAAG
CP000247.1/2431502-2431460     GAAUU-UCGAUUAACGCUCAGUC-------------------UCU--------------------------------------GACUGAGAAAACUGGAAG
BX936398.1/3056609-3056567     GAAUUUUUGAUUAAC-GCCUGCC-------------------GUAA-------------------------------------GGUGGGUCAU-UUGGAAG
AM286415.1/1502345-1502387     GAAUUUUUGAUUAAC-GCUUGCC-------------------UUAU-------------------------------------GGCAAGCCAC-UUGGAAG
ABVX01000005.1/121832-121789   GAAUUUUUGAUUAGC-GCUCGUG-------------------GUAA-------------------------------------CACGGGCCAUUAUGGAAG
ABVY01000005.1/55699-55656     GAAUUUUUGAUUAGC-GCUCGUG-------------------GUAA-------------------------------------CACGGGCCAUUAUGGAAG
CP000308.1/2292180-2292138     GAAUUUUUGAUUAAC-GCCUGCC-------------------GUAA-------------------------------------GGUGGGUCAU-UUGGAAG
CP000970.1/2487091-2487049     GAAUU-UCGAUUAACGCUCAGUC-------------------UCU--------------------------------------GACUGAGAAAACUGGAAG
CU928158.2/901378-901420       GAAUU-UCGAUUAACGCUCAGUC-------------------UCU--------------------------------------GACUGAGAAAACUGGAAG
CP000783.1/903670-903711       GCAUU-UUGAUUAAC-GCCUGGC-------------------UCGC-------------------------------------GCCAGGCCAA-CUGGAAG
CP000826.1/3658544-3658502     GAAUUUUUGAUUAAC-GCCUGCC-------------------GCAA-------------------------------------GGCAGGCCAC-UUGGAAG
X68301.1/5226-5268             GAAUU-UCGAUUAACGCUCAGUC-------------------UCU--------------------------------------GACUGAGAAAACUGGAAG
AP008232.1/2743668-2743627     GCAUUUUUGAUUAAC-GCCCGCC-------------------GUU--------------------------------------GGCGGGCCUC-ACCUGAG
BX571869.1/128187-128145       GAAUUUUUGAUUAAC-ACUUGCU-------------------GAAA-------------------------------------AGCAGGUCAU-UUGGAAG
ABXV02000040.1/97420-97380     GUAUUUAUGAUUAAC-GCCUGC--------------------UAAC--------------------------------------GCGGGCCUU-UGGGAAG
CP001383.1/2447286-2447244     GAAUU-UCGAUUAAC-GCUCGGU-------------------CCCUG------------------------------------ACCGAGAAAA-CUGGAAG
ABWM02000010.1/129715-129674   GAAUU-UUGAUUAAC-GCUCGAA-------------------GCAA-------------------------------------UUCGAGCCAA-CUGGAAG
AALF02000033.1/35251-35166     GAUUUUUUGAUUAAC-GCUUGUAAACGAACCGUUUUAAGGUCGUCGUAACA-------------GACAAUAAACGUGUUCAAAUACAAGUCAC-UUGGAAG
AALD02000035.1/8938-9024       GAAUUUUUGAUUAAC-GCUUGUAAAACGAAC-CGUUU-----CAAGGUCGCCGUAACAGCCAAU-----AAACGUGUUCAA-UUACAAGCCAC-UUGGAAG
AALC02000034.1/31511-31427     GAAUUUUUGAUUAAC-GCUUGUAAAUGAACCGCCUUAAUGUCGUCGUGCA--------------GACAUUAAAUCGGCUUAUGCACAAGUCAC-UUGGAAG
#=GC SS_cons                   :::::::::::::::.<<<<<<<..................._____....................................>>>>>>>:::.:::::::
#=GC RF                        GAAUUUUUGAUUAAC.gCUuGUc...................guagG....................................gACaAGcCAc.UUGGAAG
//
# STOCKHOLM 1.0

#=GF AC   RF01749
#=GF ID   pan
#=GF DE   pan motif
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   36.20
#=GF TC   36.30
#=GF NC   36.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.77 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Pan_RNA_motif
#=GF SQ   74


AP008230.1/495034-495118       UGGGCAGUAUC---AUUC-----GAACUGCACCUUUUCGUAAGAACCA-UUCAAUAUUACA-------------------------------------------CU-GCCUGUAGCC--AAUAC-----GGACCGGGACAGAGGG
CP000148.1/1843118-1843197     GACCCGCAAC----GCU-------G-GCGGAGUCGAAAAUCUGUUCAC-GACAAAUUGAUA-------------------------------------------CU-GCCUGGAUUC--GUAC------GAACCGGGACGGAUGG
EF191494.1/1477-1386           UGGGCAGUAUCG--CCUG----CGAACUGCACCUAUUAUUAAAAUAGA-UAGACAUUGCAGCAGU---------------------------------------CU-GCCUUGAUCC--AAAAAA----GGACUGGGACAGAGGG
AM180355.1/1753012-1752923     UGGAUGGUAUCUU-GUUAU--AAGAACUAUACUUUAAAUGUUUUUAAU-UAUUUUGUCUUAUG-----------------------------------------UA-ACUCAUAUCC--UCA-------GGAAUGAGAUUAGAAA
AP008230.1/226528-226558       --------------------------------------------------------------------------------------------------------CC-GCUUGGAUCA--UUA-------UGACCGAGACGGAGAA
CP000557.1/2247695-2247598     AGGGCAGUAUCUUUGUCGA-AAAGAACUGCACCGCGCCGGCAAAAUGA-AUGAAUAAAGAUAAU----------------------------------------CU-GCCUUGAUCCUUGCAG----AAGGACUGGGACAGAGGG
AAML04000010.1/512346-512257   UGGAUGGUAUCUU-GUUAU--AAGAACUAUACUUUAAAUGUUUUUAAU-UAUUUUGUCUUAUG-----------------------------------------UA-ACUCAUAUCC--UCA-------GGAAUGAGAUUAGAAA
AL591981.1/224238-224152       UGGAUGAUACC---UUUACC---GGAUCAUACUAACGCUACUAAAAAA-AUAUGUUUU----------------------------------------------UU-GCCUUGAUUAAAGUAA----UUUAACAGGGACGAAAAG
AP006627.1/2188202-2188112     AGGGCUGUAUCU--GCU-----AGAACGGCACCCAAAAGAGGUAUGGG-AUUGUAACGUAACGAAAGC------------------------------------UU-GCCUGGAUCU--UUCGG-----AGACCGGGACAUAG--
CP000142.2/2140848-2140761     GGCCCGGAAC----AUGA------G-CCGGAGCCAAAAGAUCGCCGCC-UCGUUCAGCCAAGACUUAUA-----------------------------------CC-GCCUGGAUCC--AUC-------GGACCGGGACGGAAGG
AP009049.1/620310-620391       UGGGUAGUAUC---GUUUU----GAGCUGCACCAUAAGUGUUGAUAAA-UUAUUCUU-----------------------------------------------CU-GCUCAUAUCA--AUUUU-----UGAAAGAGACAGGAUG
CP000612.1/1959508-1959602     CGGGUAGUAUCC--UAAUGC---GAACUGCACCUGGUUAUGGUAGACA-AGGCUAAAAAUAAGGUGUUUU----------------------------------CC-GCUUGGAGCC--AAU-------GGACCGAGACGGGGGG
AE016879.1/1471453-1471549     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGCAAU-ACGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP000698.1/2436108-2436193     GGACCGUAAC----AU--------GUGCGGAUCCAAUGCGUUUCACGA-GUAAACACAAUUAAAUA--------------------------------------CC-GCCAGGAUUC--CAUGU-----GAACCGGGACGGGAGG
AAWL01000012.1/11046-10947     AGGGUGGCAUC---AUCAC----GAGCCACACCUAACAAGUUAAGUUU-AUGAAUUUAAUAGUAUGUGUCUUACC-----------------------------CC-GCUUAGAGCCC-AAA------GGGACUGAGACGGAAGG
CP001177.1/1576904-1577000     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGCAAU-ACGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
AE017262.2/1958220-1958134     UGGAUGAUACC---UUUACC---GGAUCAUACUAAUGCUACUAAAAAA-AUAUGUUUU----------------------------------------------UU-GCCUUGAUUAAAGUAA----UUUAACAGGGACGAAAAG
CP000923.1/444299-444210       GUGGUGGUAUCU--UCAU----AGAACCACACACUUCAUAAAAAUUCA-AUAGGGCUCAUUUCGGCC-------------------------------------CC-GCCAGGAUC---ACAA-------GACCGGGACGGGAGA
AM412317.1/507696-507607       UGGGUAGUAUCC--AAUAU---GGAACUGCACCUGAUUGUUUUUAUUU-CUAAAUUUGUAUAAAAAC--------------------------------------U-GCUCACAUC---AAUAA------AAUUAAGACA-AAAU
BA000043.1/2224448-2224346     AGGGCAGUAUCUUUCGCAA-GAAGAACUGCACCGAGGCCGACAGCACG-AAUAGGUGAAGGAAAUGAU------------------------------------CU-GCCUUGAUCCUUUUUUG---AAGGACUAGGACAGAGGG
CP000727.1/492861-492772       UGGGUAGUAUCC--AAUAU---GGAACUGCACCUGAUUGUUUUUAUUU-CUAAAUUUGUAUAAAAAC--------------------------------------U-GCUCACAUC---AAUAA------AAUUAAGACA-AAAU
AE017194.1/1625746-1625842     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAUGCAAU-ACGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP001598.1/1471476-1471572     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGCAAU-ACGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP001186.1/1464230-1464326     UGGGCAGUAUC---AGAGU----GAACUGCACCAUGAUUCGAAGUAAU-AUGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP001215.1/2767627-2767531     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGCAAU-ACGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP000027.1/736022-736109       UGCCACCGACC---UUAACC---GGCGGUGAGCUUUCGGGUGCUUUAA-AUUAAAUAUCUCC------------------------------------------CC-GCUUGGAUCG--GAAAA-----CGGCCGAGACGGUAAA
CP000560.1/2160220-2160132     UGGGCAGUAUC---AUAAU----GAACUGCACCCGAUCAGCAGAACAG-AGAUUACGAAAAGU-----------------------------------------CU-GCCUUGAUCC--AAAAAA----GGACUGGGACAGAGGG
FM242711.1/1965103-1965017     UGGAUGAUACC---UUUACC---GGAUCAUACUAAUGCUACUAAAAAA-AUAUGUUUU----------------------------------------------UU-GCCUUGAUUAAAGUAA----UUUAACAGGGACGAAAAG
AAEK01000008.1/121285-121188   UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGCAAU-ACGAAAAAAUAAUAACUUGGAUU--------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP001283.1/1539215-1539311     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGCAAU-ACAAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP001581.1/547039-546950       UGGGUAGUAUCC--AAUAU---GGAACUGCACCUGAUUGUUUUUAUUU-CUAAAUUUGUAUAAAAAC--------------------------------------U-GCUCACAUC---AAUAA------AAUUAAGACA-AAAU
AE017355.1/1495897-1495993     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGCAAU-ACAAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
AARK02000071.1/2224-2138       UGGAUGAUACC---UUUACC---GGAUCAUACUAAUGCUACUAAAAAA-AUAUGUUUU----------------------------------------------UU-GCCUUGAUUAAAGUAA----UUUAACAGGGACGAAAAG
AAXV01000082.1/1922-1833       AGGGCAGUAUC---CAUUGU---GAACGGCACCUUCAAAACGUAAGAU-CUCAUACUAACAAAUAU--------------------------------------CU-GCCUUGAUC---UAUAU------GACAGGGACGGAAGA
AAOX01000023.1/58833-58746     UGGGCAGUAUCA--UAA-----UGAACUGCACCUUUCUAUCUUUUUAU-AUUGAAUAGUUU-------------------------------------------CU-GCCUAGAUCCA-GCAUA----UGGACCGGGACAGAGGG
AE016830.1/1807268-1807187     UGGAUGAUAUUU--GAA-----AAAACCAUACUGUAUGUUUGAUUUAA-UUUUUAUUUUU--------------------------------------------AA-GCUCAUAUC---GUAA-------GAAUGGGACUUGUAG
CP000001.1/1506507-1506603     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGCAAU-ACGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
ACOM01000005.1/1073198-1073280 UGGGUAGUAUCU--UAU-----GGAGCUAUACCAGACUUUUUUCAUUA-GAAUAUACUUA--------------------------------------------CA-ACUCAUAUC---UAUGC------GAAUGAGAUUGAAAU
AAAK03000022.1/21023-21104     UGGAUGAUAUUU--GAA-----AAAACCAUACUGUAUAUUUGAUUUAA-UUUUUAUUUUU--------------------------------------------AA-GCUCAUAUC---GUAA-------GAAUGGGACUUGUAG
AE017180.1/1868704-1868781     GGCCCGCAAC----CCA-------G-GUGGAGCCGUCAUCCUUUUUUU-CGGAUAUA-----------------------------------------------CU-GCCUGGAUUCA-CGAC-----UGAACCGGGACGGAAGG
CP000764.1/1369573-1369667     UGGGCAGUAUC---GAAAU----GAACUGCACCGUUAUUCCAAGCAGG-GAACAAUAAUAAUUUGGAUU-----------------------------------CU-GCCUUGAUCCA-AUAA-----UGGACUGGGACAGAGGG
CP000485.1/1530923-1531019     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGCAAU-ACAAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP001336.1/421223-421307       UGGGCAGUAUC---AUUC-----GAACUGCACCUUUUCGUAAGAACCA-UUCAAUAUUACA-------------------------------------------CU-GCCUGUAGCC--AAUAC-----GGACCGGGACAGAGGG
CP001176.1/1520549-1520645     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGUCAU-ACGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
AM263198.1/1952862-1952776     UGGAUGAUACC---CUUACC---GGAUCAUACUAAUGCUACUACCAAA-AAUAUGUUU----------------------------------------------UU-GCCUUGAUUAAAGCCA----UUUAACAGGGACGAAAAG
CP001089.1/993374-993468       UGACAGCCACCC--GUUU----GGGGGCUGAUCAGUAGCUGUAGUACC-AUAGAAAGACAUA------------------------------------------CC-GCCCGGAUUUGUUGUUCUGUACAAACCGGGACGGACGG
CP000903.1/1511194-1511291     UGGGCAGUAUC---AAAGC----GAACUGCACCAUUAUUUUACGCAGU-AUGAAAAAAUAAUAAUUUGGAUU--------------------------------CU-GCCUUGAUCCA-AUAA-----UGGACUGGGACAGAGGG
CP000232.1/135673-135762       CGGGCGCUACCA--CCUG----UGGAGCGCACCGGAGGCUACUUUAAA-UUUAAUUACAUCCAGG---------------------------------------CC-GCUUGGAUCU--CCAG------GGACCGAGACGGGUGC
AE001437.1/3049173-3049265     CGGGGAGUAUCUAUAUUU--AUAGAACUUCACCUAUAGUUUUUUUAUU-ACAUAUUGUACACAAACU-------------------------------------C--GCCCAUAUC---GAGA-------GAGUGGGACUGAAAU
AE016877.1/1488675-1488771     UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGUCAU-ACGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP000728.1/519010-518921       UGGGUAGUAUCC--AAUAU---GGAACUGCACCUGAUUGUUUUUAUUU-CUAAAUUUGUAUAAAAAC--------------------------------------U-GCUCACAUC---AAUAA------AAUUAAGACA-AAAU
AAJM01000082.1/9999-9903       UGGGCAGUAUC---AGAGU----GAACUGCACCAUGAUUCGAAGUAAU-AUGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP000612.1/168083-168168       CGGGUAGUAUCCC-UAG----GGGAACUGCACCUUUUUCCUGACAAAU-AAAAUAUUUUG--------------------------------------------CC-GCUUGGAGCC--GAAG------GGACCGAGACGGGGGG
ABCF01000055.1/10245-10154     AGGGCAGUAUCG--AUGA----CGAACUGCACCACUUUCGUAUAACUG-AAUAAAGACAGUAAAUUU-------------------------------------CU-GCCUUGAUCC--AUAU------GGACAGGGACGGAGGG
CP000382.1/189304-189393       UGGGUAGUAUCU--AUGG----AGAGCUACACCUAAUUGUUAUAUUAA-AAGAUAAUAUUUUUAAUCGUU-------------------------------------GCUCAUAUC---GUCAG------GAAUGAGAC--UUUU
CP000679.1/2883401-2883291     AAGGUGGCAUCGACAAGAAUGUCGAGCCAUACUAUAUCCAUUUAGGUU-AUCUUCUGUUUAAAAAAUUAAAUAGAAAG--------------------------CU-GCCCUGAUUUU-UAAA-----AGAACAGGGACUGCUAA
AARF01000121.1/6916-7046       GAGGCGGUAUCC--AAUAUC---GAACUGCACUCUUACAAGAUCUUCA-UUUAUAACGUUUUUAACAUGAACCAUAUUGUUAGCUUAACGGAUGAUGACGGAUUCU-GCUCUGAGCC--UGGAG-----GGACCGAGACAGAAGG
BA000004.3/1757772-1757872     UGGGCGGUAUCC--AAUUC---GGAACGGCACCAUCUGACGAACGUUG-UUUAAAUUGGAUGAUUACAAAUGAG------------------------------CU-GCCUUGAUCC--AAAAA-----GGACUAGGACAGAGGG
ACLV01000036.1/134544-134640   UGGGCAGUAUC---AGAGC----GAACUGCACCAUGAUUCGAAGUCAU-ACGAAAAAUAAUAACUUGGAUU---------------------------------CU-GCCUUGAUCC--AAUAAC----GGACUGGGACAGAGGG
CP000688.1/714742-714829       UGCCACCGACCG--UAAC----CGGCGGUGAGCGCUUAGAGACUUCAA-AUUAAAUAGAUCC------------------------------------------CC-GCUUGGAUCG--UAAAA-----CGGCCGAGACGGUAAA
CP001022.1/1742788-1742696     AGGAUGAUAGCC--ACUU----GGAGUCAUACCGGUUAGAGGCUUAUA-UUCAUAUUGUUUAUUUGA-------------------------------------CU-GCCUUGAUCC--UACUC-----GGACAGGGACAGAAGG
AAXB02000027.1/5609-5713       GAGACGGUAUCUGUCCCUG-ACAGAACCAUACUCAGAACUGAAGCACU-GGAAUCUCAUAAUUUUCAACAAAAAU-----------------------------GA-GCUUAUAUUU--UCAG------GAAAUAAGACUCAGGA
AP009389.1/221041-221141       AGGGCGGUAUCCG-GGCG---CGGAACCGCACCGUAAAAAAGCGUUUU-UUUGACAACCUGGUAUUUUUUGGAA------------------------------CC-GCUUGGAGCC--GGAA------GGACCGAGACGGGAGG
CP000141.1/2132748-2132660     UUGAGGACACC---GUUAU----GGGUCCUACAGAGUCGAUUUAUUUU-UUAAAAAAUCAAUAUGA--------------------------------------CC-GCUUGGAUCC--AGA-------GGACCGAGACGGGAGU
CP000721.1/3038116-3038029     UGGGUAGUAUC---GAAAAA---GAGUUACACCAAAUUUUUUAGCAUU-AAUUAUAUAUAAUA-----------------------------------------CA-ACUCAUAUC---UAUAAU-----GAAUGAGAUUGAAAU
CP000002.3/2325639-2325550     UGGGCAGUAUCC--UCUG----GGAACUGCACCUGGAAAGCAUGCAAC-UUAUAAAAAAACAGU----------------------------------------CU-GCCUUGAUCC--AAAAA-----GGACUGGGACAGAGGG
AJ965256.1/635641-635728       UGCCACCGACCG--UAAC----CGGCGGUGAGCGCUUAGAGACUUUAA-AUUAAAUAGAUCC------------------------------------------CC-GCUUGGAUCG--UAAAA-----CGGCCGAGACGGUAAA
AADR01000086.1/2839-2925       UGGAUGAUACC---UUUACC---GGAUCAUACUAAUGCUACUAAAAAA-A-UAUGUUU----------------------------------------------UUUGCCUUGAUUAAAGUAA----UUUAACAGGGACGAAAAG
AL596170.1/241651-241565       UGGAUGAUACC---UUUACC---GGAUCAUACUAACGCUACUUACAAA-AAUUUGUUUU---------------------------------------------UU-GCCUUGAUUAA-UUCAU----UUAACAGGGACGAAAAG
AARR02000005.1/105709-105623   UGGAUGAUACC---UUUACC---GGAUCAUACUAAUGCUACUAAAAAA-AUAUGUUUU----------------------------------------------UU-GCCUUGAUUAAAGUAA----UUUAACAGGGACGAAAAG
CP002001.1/1975922-1975836     UGGAUGAUACC---UUUACC---GGAUCAUACUAACGCUACUAAAAAA-AUAUGUUUU----------------------------------------------UU-GCCUUGAUUAAAGUAA----UUUAACAGGGACGAAAAG
CP003056.1/3189389-3189477     UGGGUAGUAUCU--AUUUC---GGAACUAUACCAAUUCAGCUUUUUAU-ACAAAAUAGAUU-------------------------------------------CU-GCCUUGAUCC--UUAAAC----GGACGGGGACAGAGGG
CP002002.1/1933749-1933663     UGGAUGAUACC---UUUACC---GGAUCAUACUAACGCUACUAAAAAAAUAUGUUUU-----------------------------------------------UU-GCCUUGAUUAAAGUAA----UUUAACAGGGACGAAAAG
AARN04000030.1/20419-20333     UGGAUGAUACC---UUUACU---GGAUCAUACUAACGCUACUAAAAAA-AUAUGUUUU----------------------------------------------UU-GCCUUGAUUAAAGUAA----UUUAACAGGGACGAAAAG
#=GC SS_cons                   <<<<<<<<-<<_.._____....>>>>>>>->>>--------------.------------------.....................................<<.<<<<<<-<<<.._____.....>>>>>>>>->>>::::
#=GC RF                        uGGGcgGUAUCc..aauau....GAACcgCACCauuacuagauauaaa.aUuAaauuuuuuuaaaua.....................................Cu.GCcugGAUCc..uaaAa.....gGACcggGACaGAaGG
//
# STOCKHOLM 1.0

#=GF AC   RF01750
#=GF ID   ZMP-ZTP
#=GF PI   pfl;
#=GF DE   ZMP/ZTP riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   39.00
#=GF TC   39.00
#=GF NC   38.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.95 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 1900371; regulation of purine nucleotide biosynthetic process;
#=GF DR   GO; 0006730; one-carbon metabolic process;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF RN   [2]
#=GF RM   26280533
#=GF RT   Recognition of the bacterial alarmone ZMP through long-distance
#=GF RT   association of two RNA subdomains.
#=GF RA   Jones CP, Ferre-D'Amare AR
#=GF RL   Nat Struct Mol Biol. 2015;22:679-685.
#=GF RN   [3]
#=GF RM   25616067
#=GF RT   An ancient riboswitch class in bacteria regulates purine biosynthesis and
#=GF RT   one-carbon metabolism.
#=GF RA   Kim PB, Nelson JW, Breaker RR
#=GF RL   Mol Cell. 2015;57:317-328.
#=GF CC   Previously known as pfl RNA. ZMP is also known as AICAR.
#=GF WK   Pfl_RNA_motif
#=GF SQ   182


BAAV01000055.1/2897-2982       UGAGUUUUCUGCGACUGACGGAUUAU-------------------------------------------------------------------------------------------UGCAG-A--------------------------------------------------------------------GC----A-CUGCA-A-GGGAACAGAAAAACUCUUUUU------------------------------------------------------------------CAGCCGACCGUCUGGGCACACCUG
BAAU01012305.1/993-909         UGAGUUUUCUGCGACUGACGGAUUAU-------------------------------------------------------------------------------------------UGCAG-A--------------------------------------------------------------------GC----A-CUGCA-A-GGGAACAGAAAAACUCUUUU-------------------------------------------------------------------CAGCCGACCGUCUGGGCACACCUG
BABG01015168.1/550-636         AGCUGACCCUUCUGCUGACGGAUCU--------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------GC----A-CCACA-G-UGCAGAAGGGGAGAGAAGCUUUA----------------------------------------------------------------AUGCCGACCGUCUGGGCAGCCUUG
BAAU01017791.1/392-305         AACGGGUUUGCCUGCUGACGGAACGU-------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------GC----A-CCACA-G-UGCAGACAAAACCGGGUUUUGUU----------------------------------------------------------------ACGCCGACCGUCUGGGCAGCCUUG
BAAY01004625.1/493-580         AACGGGUUUGCCUGCUGACGGAACGU-------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------GC----A-CCACA-G-UGCAGACAAAACCGGGUUUUGUU----------------------------------------------------------------ACGCCGACCGUCUGGGCAGCCUUG
BAAU01002505.1/255-341         AGACCGUAUCUCUGCUGACGGAACCU-------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------GC----A-CCACA-G-UGCAGGGAUGGCGGGAGAGUCA-----------------------------------------------------------------AUGCCGACCGUCUGGGCAGCCUUG
BAAX01023463.1/777-691         AGACCGCAUCCCUGCUGACGAAACCU-------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------GC----A-CCACA-G-UGCAGGGGUGCUGGGGAUGUCA-----------------------------------------------------------------AUGCCGACCGUCUGGGCAGCCUUG
BAAU01027299.1/88-174          AGACCGCAUCCCUGCUGACGGAACCU-------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------GC----A-CCACA-G-UGCAGGGGUGCUGGGGAUGUCA-----------------------------------------------------------------AUGCCGACCGUCUGGGCAGCCUUG
BABF01003966.1/1020-1104       UCAGCGUGUCGUGACUGGCGAACA---------------------------------------------------------------------------------------------GGUGG-G--------------------------------------------------------------------CC----A-CCACC-G-GGGAGCGACGCGUCGGCAUCGA-----------------------------------------------------------------UAGCCGCCCGCCUGGGCUAGAGGC
BAAY01025330.1/152-59          CGCAAGGCCGCUGACCGACGGGAUAU-------------------------------------------------------------------------------------------UGUGG-G--------------------------------------------------------------------GCUU--A-CCACA-G-GGGACGCGGCGUUAUCACUUGCCUUUU------------------------------------------------------------AAGCCGACCGUCUGGGCUGCAUAC
BABA01016569.1/75-168          CGCAAGGCCGCUGACCGACGGGAUAU-------------------------------------------------------------------------------------------UGUGG-G--------------------------------------------------------------------GCUU--A-CCACA-G-GGGACGCGGCGUUAUCACUUGCCUUUU------------------------------------------------------------AAGCCGACCGUCUGGGCUGCAUAC
BAAX01001391.1/197-281         GAAAGCACAGGCAACUGACGGAAC----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GCAC--A-CCAC--AUGGGAGCCU--GCUGUAAUACGAA----------------------------------------------------------------CUGUCGACCGUCUGGGCAAACCUG
BAAX01000081.1/4230-4146       AGAUCCGUACAGGACUGACGGAAUCAA-------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GUC---A-CCAC--G-UGAACUGUACGGACCCUUUC-------------------------------------------------------------------AUGCCGACCGUCUGGGCAAGAGUA
ABEF01039966.1/1068-1153       UGACCCCGAUACGACUGGCGGAGAGA--------------------------------------------------------------------------------------------GUGG-G--------------------------------------------------------------------UA----A-CCAC--GAGGGAGUAUCGGGGCCAGCGAGA-----------------------------------------------------------------UCGCCGACCGCCUGGGCACUGACA
BAAV01020765.1/806-725         AAAAAGAUCCGUGACUGACGGUUUUU--------------------------------------------------------------------------------------------GUGG-G--------------------------------------------------------------------GC----A-CCAC-CA-GGGAGCGGAUUCUUAAAA---------------------------------------------------------------------AGGCCGACCGUCUGGGCAGCAUCU
BAAY01013765.1/896-1010        CAGAUUCCCUGCAACUGACGGACACA-------------------------------------------------------------------------------------------GGUGG-A--------------------------------------------------------------------GCGCAAA-CCACC-G-GGGAGCAGGGAGUUCCGUAAUC-----------------AGAUGCACCGUGAA---GUGUAUCU---------CA------------AUGCCGACCGUCUGGGCAGUGUCG
ABEF01017404.1/1032-947        GAUUCCUGGUGUAACUGGCGGAUU---------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------AACGA-A-CCACA-G-GGGAGCACCGGGAAAUGAAA-------------------------------------------------------------------UAGUCGACCGCCUGGGCUGAGCAA
BABE01005334.1/246-164         AAGGUCUUCGGUGACUGACGGAAU---------------------------------------------------------------------------------------------UGUGG-G--------------------------------------------------------------------ACUA--A-CCACA-A-GGGAGCCGGAGAUUUGAU---------------------------------------------------------------------GAGUCGACCGUCUGGGCAGUAUUU
BAAY01012400.1/201-108         UUUAAGCCAUGCGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-U--------------------------------------------------------------------GGA---A-CCAC--G-UGGAGCAUGGCC----------------------------GGGUGCCUGCG-----GGCGUCCC---------UC------------UUGCCGACCGUCUGGGCGCACUCA
BABF01008002.1/701-620         AACAACAUACAAUGCUGACGGAUUA---------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUUA--A-CCAC--G-UGUAUUGUAUGCGAAGAA---------------------------------------------------------------------ACGCCGACCGUCUGGGCAGAAGAU
BABA01021702.1/659-750         AAACGACCAUACGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GCA---A-CCAC--A-UGGAGUGUGGCC-----------------------------GGACGUAAACC----GCGUCC-----------UC------------UUGCCGACCGUCUGGGCACACUGA
BAAY01000038.1/8293-8388       UAGGCGCCGUGUAACUGACGGAAA----------------------------------GCCCAUUU--------GGGC-----------------------------------A---GGCAG-G--------------------------------------------------------------------CUAA--A-CUGCC-G-GGGAACGCGGCGUAUAAA---------------------------------------------------------------------AAGCCGACCGUCUGGGCAGCCUCU
BAAV01000327.1/435-340         UAGGCGCCGUGCAACUGACGGAAA----------------------------------GCCCAUUU--------GGGC-----------------------------------A---GGCAG-G--------------------------------------------------------------------CUAA--A-CUGCC-G-GGGAACGCGGCGUAUAAA---------------------------------------------------------------------AAGCCGACCGUCUGGGCAGCCUCU
BABG01000244.1/657-739         AUGAGGUCAUAUGACUGACGGAGCAC--------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUCA--A-CCAC--AUGGGAGUAUGAUCAUUAA----------------------------------------------------------------------UCGCCGGCCGUCUGGGCAAUCUUG
BABD01005042.1/856-936         AGGCAGUUAUACGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AAUG--A-CCAC--A-GGGAGUAUAGCGUGAGAAG--------------------------------------------------------------------AGGCCGACCGUCUGGGCAGAAGAA
BAAV01011945.1/1060-974        CAUUAGUUAUAUGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUUG--A-CCAC--A-GGGAGUAUAAUAAAUCAAAAUGAAG--------------------------------------------------------------AAGCCGACCGUCUGGGCAAAGAAG
BAAX01007901.1/363-439         AGACAGUUAUAUGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------UA----A-CCAC--A-UGGAGUAUAACAGUUGA----------------------------------------------------------------------UUGCCGACCGUCUGGGCGCACAUU
BABG01000490.1/211-374         UAUAAGCUGUACAACUGGCGGAAA-----GCAUAUAUAGAAUAUCAGAUA-GAGCAUUCAGCAUGGU-------GUUGAA-GUAUGUAUCAUUGCAUUGAAGUAAGUAUAUGUG----GUGGGA--------------------------------------------------------------------UU----ACCCAC--A-GGGAGUACAGUAAUAAUAUGUUUAU--------------------------------------------------------------CAGCCGACCGCCUGGGCAACCCUG
BAAX01006362.1/459-383         UAGACGCUGUGCAACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------UG----A-CCAC--A-GGGAGCACAGGGAAGAA----------------------------------------------------------------------GAGCCGACCGUCUGGGCACAGCCU
BABG01005810.1/129-214         AAGACACCGCGGAACUGACGGAAUGAU-------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUCG--A-CCAC--G-UGAACCGCGGAUGAUCUGAU-------------------------------------------------------------------UGGCCGACCGUCUGGGCAGGGAAA
BAAY01015723.1/323-408         AAGGAUAGGAAGAACUGACGGAUUCU--------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUUG--A-CCAC--G-UGAACUUCCUAUUUCGAAAAC------------------------------------------------------------------AAGCCGACCGUCUGGGCAGGGAAA
BABA01029967.1/180-94          ACACCUCUUCGCCACUGGCAGAUAA---------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------CAAA--A-CCAC-AG-GGCGGCGCAGGGGAUUGGGUUU-----------------------------------------------------------------ACGCCGGCUGCCUGGGCAACAUGG
BAAW01014873.1/349-270         UAGGCACCAUGUGACUGGCGCUGAA--------------------------------------------------------------------------------------------GACAG-A--------------------------------------------------------------------AU----A-CUGUC-G-GGGAGCAUGGUCGACG-----------------------------------------------------------------------UCGCCGCGCGCCUGGGCAUUACCG
BAAW01002219.1/737-658         UCGUCACCAUGUGACUGGCGUUUUA--------------------------------------------------------------------------------------------GACAG-G--------------------------------------------------------------------UC----A-CUGUC-G-GGGAGCAUGGUUGCCG-----------------------------------------------------------------------CCGCCGCGCGCCUGGGCAUCACUU
AAQK01001363.1/401-486         CAUUAGUUAUAUGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUUG--A-CCAC--A-GGGAGUAUAAUAAAUCAAAUGAAG---------------------------------------------------------------AAGCCGACCGUCUGGGCAAAGAAG
AACY022905908.1/566-649        UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGAAGCAGAU------------------------------------------------------------------UGGCCGUACGCCUGGGCCACCUGC
BA000030.3/4242005-4241916     CCGACGGGCCGUGACUGGCGCGCUGG-------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------ACCG--A-CCAUC-G-GGGAGCGGCCUGAAUGCGAAUGU----------------------------------------------------------------GUGCCGUGCGCCUGGGCCGAACGU
CP000673.1/3903782-3903862     AAUGUGUUGUAUGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------UUCA--A-CCAC--A-GGGAGUACAGCGUUUUGGA--------------------------------------------------------------------AAGCCGACCGUCUGGGCAUGAUGC
AE001437.1/2562148-2562228     AGAAAAUCAUGCAACUGGCGGAA-----------------------------------------------------------------------------------------------AUGG-A--------------------------------------------------------------------GUUC--A-CCAU--A-GGGAGCAUGAUUAAUAUAA--------------------------------------------------------------------GAAUCGACCGCCUGGGUAAAUUAA
CP000270.1/613445-613553       UCAUCCCUGCGUGACUGGCGAUA-----------------------------GAA-CCGGUUCAAAC-------AACCGGAUUC-----------------------------AA--GGUGG-A--------------------------------------------------------------------GCAA--C-CCACC-G-UGAAGCGCAGGGUGCCGUU--------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUG
CP000721.1/4111764-4111685     UAGAGGUUAUACGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUAA--A-CCAC--A-UGAAGUAUAACAAGUAAU---------------------------------------------------------------------AAGCCGACCGUCUGGGCAAAAGUC
AAQL01005444.1/915-834         CAGAAGCUGCAUGACUGGCGGAAA----------------------------------------------------------------------------------------------GUAGGA--------------------------------------------------------------------UU----ACCUAC--A-GGGAGUGCAGUGAAGUGAG--------------------------------------------------------------------AAGCCGACCGCCUGGGCAGCCUGA
AAMN01000004.1/194357-194435   CUCACGGGUGACGACUGGCGCA-----------------------------------------------------------------------------------------------GGUGG-A--------------------------------------------------------------------CC----A-CCACC-G-GGGAGUCACAUGGGACAC---------------------------------------------------------------------GCAUCGCCCGCCUGGGUGCACCCG
AM711867.1/2838330-2838247     CGGACCCGUCGCGACUGGCGUUCG---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACUCACACGGUUGG------------------------------------------------------------------UGGCCGUACGCCUGGGCCACGACG
ABBI01001009.1/7408-7308       UAGUCCCUGCGUGACUGGCGAUAC---------------------------------GACCUUUCU--------GGGUC----------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCAGGGCGUCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CP000927.1/5164264-5164343     GCCCGUUCGCGUGACUGGCGCUAGU--------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------GA----A-CCAUC-G-GGGAGCGCGAACCACA-----------------------------------------------------------------------UCGCCGCGCGCCUGGGCUCCUCGA
AAWL01000017.1/16393-16312     GACAGGAUACAGGACUGGCGGAUUA---------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AGCA--A-CCAC--G-UGGACUGUAUCCGAAGAA---------------------------------------------------------------------AAGCCGACCGCCUGGGCAAAAAUU
AATO01015318.1/246-81          AGCGGGGCACGCAACUGGCGAUA-------------------------GGC-GCGCAAGUCCCACC--------GGGCU-GCGCUGCU-------------------------GAC--GUGG-AGACCC----------GCAAAAACAAGCCGUUUUUUGC-------------------------------AA----A-CCAC-UG-GGGAGCGUGCCGCG--------------------CGGAACAAGGCAGCGU------UUGCC-----CCG----CCGCGAU-------CCGUCGUUCGCCUGGGCAGCCCUU
CP000614.1/815126-815226       UCACCCCUGCGUGACUGGCGAUA---------------------------------GAACCCUUC---------GGGUUC---------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CP000667.1/2367924-2367834     CCCUCGGGCCGUGACUGGCGCGAUCUGG-----------------------------------------------------------------------------------------GAUGG-A--------------------------------------------------------------------GC----A-CCAUC-G-GGGAACGGCCCAUCACGAGGACGC---------------------------------------------------------------ACGCCGAGCGCCUGGGCCUCCACA
CP001096.1/33229-33147         CACGCCUCGCGCGACUGGCGACGUUAG------------------------------------------------------------------------------------------GAUGG-A--------------------------------------------------------------------GC----A-CCAUC-G-GGAAGCGCGGGACGUAU----------------------------------------------------------------------CUGCCGCGCGCCUGGGCAUAGCUU
CP001348.1/2599825-2599904     AAACUGUCAUACAACUGGCGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GAUU--A-CCAC--AUGGGAGUAUGACUUUAAU----------------------------------------------------------------------AAGCCGGCCGCCUGGGCAUCAUAA
AACY024109839.1/883-800        UGAUGCCAUCGCAACUGGCGUGAA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGAAGCAGAU------------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
CP000721.1/1211931-1212029     UAUUAGUCAUAUGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GUU---A-CCAC--A-UGAAGUAUGACUA---------------------------GGCAUAUUAUCUU---AUAUGCC----------ACAAA---------AAGCCGACCGUCUGGGCAAAAAAA
CP000726.1/3402727-3402637     AAUAAAUCAUAUGACUGGCGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUUA--A-CCAC--A-GGGAGUAUGAUUUAGAAAUUUAAGUUAGA----------------------------------------------------------AUGUCGACCGCCUGGGCAAUAAAA
AP009385.1/718103-718202       UCACCCCUGCGUGACUGGCGAUA----------------------------------GAACCCUCG--------GGUUC----------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCAGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CU234118.1/352539-352459       CGGCUCUCGCGCGACUGGCGACUUUG-------------------------------------------------------------------------------------------GAUGG-A--------------------------------------------------------------------GC----A-CCAUC-G-GGGAGCGCGGGAUCGA-----------------------------------------------------------------------CCGCCGUGCGCCUGGGCAACUGAA
CP000850.1/78653-78732         CUCGGGCAGCGCGACUGGCGAG-----------------------------------------------------------------------------------------------GGUGG-U--------------------------------------------------------------------GA----A-CCACC-G-GGGAGCGCUGAUGGCUGGA--------------------------------------------------------------------GCAUCGCCCGCCUGGGUGCUUCUC
CP000875.1/3502313-3502228     GCAUGAAUCGGUGACUGGCGAUACACAAA----------------------------------------------------------------------------------------CGUGG-G--------------------------------------------------------------------CA----A-CCACG-G-GGGAGCCGAUUUGCGCAG---------------------------------------------------------------------AUGCCGCUCGCCUGGGCAAAGGGC
AACY020353424.1/798-906        UCAUCCCUGCGUGACUGGCGAUA-----------------------------GAA-CCGGUUCAAAC-------AAUCGGAUUC-----------------------------AA--GGUGG-A--------------------------------------------------------------------ACAA--C-CCACC-G-UGAAGCGCGGGGUGCCGUU--------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCUGUG
AACY023075686.1/109-271        ACCGUUCGGCGUGACUGGCGGAGC---------------------------------GCAGGCAAUUAC-----CCUGU---------------------------------------GUGG-ACUGCAUCCUGGAUCUGUCGUGGUUAGUUU-CCCCGGCA-AUCCAUUGCCGCAUUAGCGCAAAGCGUUCCCUA--A-CCAC--G-GGUAGCGUUGAACUGAA----------------------------------------------------------------------CCGCCGACCGCCUGGGCACGCCCG
AACY020521775.1/559-642        UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
AACY022405903.1/398-315        UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
CP000090.1/861611-861511       UCCACCUUGCGCGACUGGCGAUGUCA--------------------------------------------------------------------------------------------GUGG-G--------------------------------------------------------------------UACU--A-CCAC--GAGGAAGCGCAAGUUCUCU-------------------------GGCGUGAAGUUCAGACGC---------------------------CUGCCGCUCGCCUGGGCAGCGAAU
CP001408.1/3257848-3257748     UAGUCCCUGCGUGACUGGCGAUAC---------------------------------GACCUUUCG--------GGGUC----------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCAGGGCGUCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CP000727.1/3299834-3299744     AAUAAAUCAUAUGACUGGCGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUUA--A-CCAC--A-GGGAGUAUGAUUUAGAAAUUUAAGUUAGA----------------------------------------------------------AUGUCGACCGCCUGGGCAAUAAAA
AE001437.1/1127408-1127485     UAAGAAUCGUAUAACCGGCGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUA---A-CCAC--A-GGGAGUACGAUUUUAAA----------------------------------------------------------------------AAGCCGACCGCCUGGGCAAAAAGA
CP000151.1/810912-811012       UCACCCCCGCGUGACUGGCGAUA---------------------------------GAACCCUUC---------GGGUUC---------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
AACY021675814.1/503-420        UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGAAGCAGAU------------------------------------------------------------------UGGCCGUACGCCUGGGCCACCUGC
CP000728.1/3519944-3519854     AAUAAAUCAUAUGACUGGCGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GUUA--A-CCAC--A-GGGAAUAUGAUUUAGAAAUUUAAGUUAGA----------------------------------------------------------AUGUCGACCGCCUGGGCAAUAAAA
ABBG01000261.1/19106-19005     UAUCCCCUGCGUGACUGGCGAUAA---------------------------------GACCUUUCG--------GGGUC----------------------------------AAA-GGUGG-A--------------------------------------------------------------------GCGU--C-CCACC-G-UGAAGCGCAGGGCGUCGCUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CP000086.1/1555456-1555556     UACCCCCUGCGUGACUGGCGAUAC---------------------------------GACCUUUCG--------GGGUC----------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGUCGCUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
AP006627.1/3516508-3516431     GAAUCUGUAUGUGACUGGCGCGAA----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------UA----A-CCAC--AAGGGAGCAUACGGAUCA-----------------------------------------------------------------------AAGCCGUGCGCCUGGGCAAAGGAA
AACY021007951.1/190-107        UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
AAQL01002083.1/670-587         AAGCAGUUGUACGACUGGCGGAAAA---------------------------------------------------------------------------------------------GCAGGG--------------------------------------------------------------------UU----ACCUGU--G-GGGAGUACAAC-GUUAUCCUG------------------------------------------------------------------AUGCCGACCGCCUGGGCGACCGCU
AACY020990021.1/376-489        AUGCAAGCGCAUGACUGGCGAUGAAA-------------------------------------------------------------------------------------------GGUGG-A--------------------------------------------------------------------AG----A-CCACC-G-GGAAGUGCGCAG------------------GGUUUGAG-UGCAUCCAAGGA-----UGG-UGUGAGUCAGCCCA-------------AAGCCGCUCGCCUGGGCACUUUGA
AACX01000007.1/312508-312608   UACCCCCUGCGUGACUGGCGAUAC---------------------------------GACCUUUCG--------GGGUC----------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGUCGCUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
AAKY01000114.1/32845-32745     UCACCCCUGCGUGACUGGCGAUA---------------------------------GAACCCUUC---------GGGUUC---------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCAGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CP000512.1/3298357-3298515     CGAGGGGUACGCGACUGGCGAUA-------------------------GGC-GCGGUGCAUCCGCGAAGGCG--GA--CGCCGCCGCU-------------------------GAC--GUGG-AAACCG------------GCAGGCACUUUCACCUGC---------------------------------GA----A-CCAC-UG-GGAAGCGUGCCGCA---------------------------CGGGCUGCAA-----GGCCCG-----------UUGUGUU-------CCGCCGUUCGCCUGGGCAGCCCUU
ABED02000029.1/984986-984900   AGACCGCAUCCCUGCUGACGGAACCU-------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------GC----A-CCACA-G-UGCAGGGGUGCUGGGGAUGUCA-----------------------------------------------------------------AUGCCGACCGUCUGGGCAGCCUUG
BA000040.2/6500011-6499926     GUCCUAUCGCGCGACUGGCGAGCUAA-------------------------------------------------------------------------------------------CGUGG-A--------------------------------------------------------------------AUCG--A-CCACG-G-UGAAGCGCGAAGGGUUCCG--------------------------------------------------------------------ACGCCGAUCGCCUGGGCAACCAAU
ABCC02000037.1/46406-46317     GGUAGGGCGUGUGACUGGCGGAUA----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GCA---A-CCAC--A-GGGAGCACGCAGUACCAUGAACUAUUUU-----------------------------------------------------------GAGCCGACCGCCUGGGCACGCAUG
AACY023312929.1/255-91         UACAGGGUACGCAACUGGCGAUA-------------------------GGA---GCCUGGCAUUCGCAAACUUCUGCGAGCCAACUCU-------------------------GAC--GUGG-AAAU------------GGGUGGGCUUGUU--CCCUUCC-------------------------------UCA---A-CCAC-UG-GGGAGCGUGCAC---------------------------CUUGUACUGGUGUUUG-GGUUCAAG---------GUUU----------CAGCCGUUCGCCUGGGCAGCCCAU
CP000570.1/3132286-3132186     UAGUCCCUGCGUGACUGGCGAUAC---------------------------------GACCUUUCG--------GGGUC----------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCAGGGCGUCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CP000774.1/674390-674303       UAUCCUCCGCGCGACUGGCGAAAUCA-------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGCGGAGACUGGUCUUUC----------------------------------------------------------------GAGCCGAUCGCCUGGGCAGCACUU
CP000958.1/862927-863027       UCACCCCUGCGUGACUGGCGAUA---------------------------------GAACCCUCA---------GGGUUC---------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
BA000030.3/688247-688162       GGUGUGGGCCGUGACUGGCGCUGA---------------------------------------------------------------------------------------------GGUGG-A--------------------------------------------------------------------GC----A-CCACC-G-GGGAGCGGUCUGACGAGACGUCG----------------------------------------------------------------UUGCCGUGCGCCUGGGCGAGUGGU
AACY020525716.1/1032-1115      UGACGCCAUCGCAACUGGCGUGAA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGACGCAGAU------------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
CP000269.1/2768093-2767971     UUCGUCUCACGUGACUGGCGAAUC----------------------CGAC-UGGUUUUCCUGCUGUUU-----AUAGGUAAAUUACGUCG-----------------------UAA-GGUGGGC--------------------------------------------------------------------UU----ACCCACC-G-UGAAGCGUGAGAUUUCA----------------------------------------------------------------------UUGCCGUGCGCCUGGGUAGCCCGA
CP001025.1/786181-786281       UCACCCCUGCGUGACUGGCGAUA---------------------------------GAACCCUUC---------GGGUUC---------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
AAQK01000738.1/824-909         CAUUAGUUAUAUGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUUG--A-CCAC--A-GGGAGUAUAAUAAAUCAAAUGAAG---------------------------------------------------------------AAGCCGACCGUCUGGGCAAAGAAG
AARF01000447.1/2648-2568       GAGCCCCGGUGUAACUGGCGACAG----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GCGA--A-CCAC--AUGGAAGCACCGGGGAAUA----------------------------------------------------------------------CGGCCGGUCGCCUGGGCAAAGAGC
AACY020548403.1/122563-122663  UCACCCCCGCGUGACUGGCGAUA---------------------------------GAACCCUUC---------GGGUUC---------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CU207211.1/2356811-2356707     UUCGUCUCACGUAACUGGCGAAUC-------------------------------CGAC-CGAUCACAC-----CGUGUCG--------------------------------UAA-GGUGG-G--------------------------------------------------------------------CCUA--U-CCACC-G-UGAAGCGUGAGAUUUUA----------------------------------------------------------------------UUGCCGUGCGCCUGGGUAGCCCGA
CP001052.1/844994-845102       UCAUCCCUGCGUGACUGGCGAUA-----------------------------GAA-CCGGUUCAAAC-------AACCGGAUUC-----------------------------AA--GGUGG-A--------------------------------------------------------------------GCAA--C-CCACC-G-UGAAGCGCAGGGUGCCGUU--------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUG
AACY021101856.1/474-633        AGCGGGGUACGCAACUGGCGAUA-------------------GGC-GUGGUCCAGGAAGGUUGAAA--------AACC-----GGGCCACCGCU-------------------GAC--GUGG-AAACCAG----------CAGAUGCUUGC---CGUCUG--------------------------------UGA---A-CCAC-UG-GGGAGCGUACCGCC----------------------------CAGGCUGA------GCCUG------------AAGCGUU-------CCGCCGUUCGCCUGGGCAGCCCUU
AP009049.1/1156093-1156015     AAGGAAUCGUAUAACCGGCGGCA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUUA--A-CCAC--A-AGGAGUACGAUUUUUAA----------------------------------------------------------------------AAGCCGACCGCCUGGGCAAUCAAA
AACY023502772.1/158-61         AGCGAUCCACACAACUGGCGACAA---------------------------------AAGGCUGA---------GCCUU----------------------------------AA--GAUGG-A--------------------------------------------------------------------UGAA--A-CCAUC-G-GGGAGUGUGAAAAGAACC---------------------------------------------------------------------UAGCCGCUCGCCUGGGCAUAGACA
AAQK01007158.1/471-387         AAGUACUUUUGUAACUGACGGAAUACAA------------------------------------------------------------------------------------------GAUG-G--------------------------------------------------------------------GG----A-CAUC--G-UGGAGCAAAAGUAUGAAAAU-------------------------------------------------------------------GAGCCGACCGUCUGGGCAGUGUUU
CP000612.1/48258-48175         CUACAGUUGCAUGACUGGCGGAUUUU-------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------GC----A-CCACA-A-AGGAUUGUAACUGUUUUUU--------------------------------------------------------------------AAGCCGACCGCCUGGGCAAUACAC
AAQL01000770.1/335-416         GUUAAGUUAUACGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUAA--A-CCAC--A-GGGAGUAUAAUCGUGUAAAA-------------------------------------------------------------------GAGUCGACCGUCUGGGCUAAGAAU
AAQK01002083.1/535-449         CAGUAGUGCUGUGACUGACGGGUAUA-------------------------------------------------------------------------------------------CGCGG-G--------------------------------------------------------------------CA----A-CCGCG-G-GGGAGCAGCGCGAACAUACUCA-----------------------------------------------------------------GUGCCGACCGUCUGGGCAAGCCGU
AAXB02000001.1/5878-5961       AGAAGAUCUGAUGACUGACGGAUAA--------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------GU----A-CCACA-G-GGGAAUCAGAUACUUGGUAA-------------------------------------------------------------------GAGCCGACCGUCUGGGCAGCAUUU
ABAX03000024.1/304792-304708   CAUAAGUCAUAUGACUGACGGACAA---------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GUUU--A-CCAC--A-GGAAGUAUGACAACGAAUUUU------------------------------------------------------------------UAGCCGACCGUCUGGGCACCCUGC
AE016822.1/1921306-1921208     GGCCUUCGUCGCGACUGGCGCUCA---------------------------------------------------------------------------------------------GAUGG-U--------------------------------------------------------------------C-----A-CCAUC-G-GGGAGCGACGACGG--------------------------UACCUCGAACGAA---CG-GGUG----------GAUU----------CGGCCGCGCGCCUGGGUCGAUAGC
CP000539.1/1721986-1721827     AGCAGGGCACGCAACUGGCGAUA-------------------------GGC-GCGGAGGUCUUCCG--------GGACA-CCGCCGCU-------------------------GAC--GUGG-ACACCG---------GCAGGAAACAGCGU--UUUUCUGC------------------------------AA----A-CCAC-UG-GGGAGCGUGCCGC-------------------------GCGGCAGGCACCA-----GCC--CCGC--------AGCGAU--------CCGUCGUUCGCCUGGGCAGCCCUU
ACOM01000001.1/496623-496702   UAUAGGUUAUACAACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUAA--A-CCAC--A-UGAAGUAUAACAAGUAAU---------------------------------------------------------------------AAGCCGACCGUCUGGGCAAAAGUC
CP000267.1/2925225-2925356     CGGGUGGCACGCGACUGGCGAUA-------------------------GGC-UCUCA-ACCCGGCAA-------GGGCGUGAGACGCU-------------------------GAA--GUGG-G--------------------------------------------------------------------AAC---A-CCAC--GGGGGAGCGUGCCGCA---------------------------UUGCCAAUG------UGGCAA-----------CUGUGUU-------UAGCCGUUCGCCUGGGCAGCCCUG
AACY023798967.1/1144-1061      UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGAAGCAGAU------------------------------------------------------------------UGGCCGUACGCCUGGGCCACCUGC
AACY022292946.1/74-157         UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
AAQK01001691.1/259-341         AUAGAAUCUGAUUACUGACGGAGAAA-------------------------------------------------------------------------------------------UGUGG-G--------------------------------------------------------------------AU----A-CCACA-G-GGGAAUCAGAUUUGCAGG---------------------------------------------------------------------AUGCCGACCGUCUGGGCAACAUUU
AACY024046541.1/1198-1115      UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGAAGCAGAU------------------------------------------------------------------UGGCCGUACGCCUGGGCCACCUGC
CP001043.1/2749838-2749724     UCACCCCUGCGUGACUGGCGAUA-------------------------GAACCC--AAUGCUGUCA--------AGCGUGGCGGGUUC-------------------------AA--GGUGG-A--------------------------------------------------------------------GCGU--C-CCACC-G-UGAAGCGCAGGGUGCCGUU--------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCAUG
AACY024110163.1/611-528        UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGAAGCAGAU------------------------------------------------------------------UGGCCGUACGCCUGGGCCACCUGC
AACY020310666.1/1673-1756      UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGAAGCAGAU------------------------------------------------------------------UGGCCGUACGCCUGGGCCACCUGC
AACY020539641.1/41-124         UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGAAGCAGAU------------------------------------------------------------------UGGCCGUACGCCUGGGCCACCUGC
CP001068.1/718457-718329       UCCACCUUGCGCGACUGGCGAAUCC----------------------------UGAAGCCGCUUCA--------GCGGCUUCG------------------------------ACAU-GUGG-G--------------------------------------------------------------------CAGCG-A-CCAC--GAGGAAGCGCAAGGUUUCU------------------------GGCGUCAUGCACAACGGCGC--------------------------CUGCCGCUCGCCUGGGCAGCGAAU
CP001098.1/2532894-2532806     AAAGGGUCAUACGACUGGCGGUAUUA-------------------------------------------------------------------------------------------UAUGG-A--------------------------------------------------------------------AUUA--A-CCAUA-G-GGGAGUAUGACCGAUACUGGAA-----------------------------------------------------------------UAGCCGACCGCCUGGGCAGAUAGA
CP000378.1/359253-359353       UCACCCCUGCGUGACUGGCGAUA---------------------------------GAACCCUCA---------GGGUUC---------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
AL939121.1/191211-191300       ACCCCGGGCCGUGACUGGCGCGCUGG-------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------ACGA--A-CCAUC-G-GGAAGCGGCCCCGGAAACACCGA----------------------------------------------------------------GAGCCGUGCGCCUGGGCCAUCCGU
AACY021099823.1/580-497        UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGAAGCAGAU------------------------------------------------------------------UGGCCGUACGCCUGGGCCACCUGC
CP000750.2/2906133-2906236     GACCGUGGCCGCGACUGGCGCAG----------------------------------------------------------------------------------------------GGUGG-G--------------------------------------------------------------------UC----A-CCACC-G-GGGAGCGGCCACGG---------------------------GCACCCGCA------GGG-GC-----------GUCCGCCGUUCACGGGGUCGUCCGCCUGGGCCUCGCGU
CP000142.2/3231175-3231262     AAGGUCUCCCGUAACUGGCGUCUCGA-------------------------------------------------------------------------------------------GGUGG-A--------------------------------------------------------------------UC----A-CCACC-G-GGGAGCGGGGCCAAAAGACCUUA----------------------------------------------------------------CAGCCGUACGCCUGGGCCCCCUUU
CP000458.1/907214-907314       UCACCCCUGCGUGACUGGCGAUA---------------------------------GAACCCUCA---------GGGUUC---------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CP000352.1/2912877-2912979     UCCACCUUGCGCGACUGGCGAAGUCA--------------------------------------------------------------------------------------------GUGG-G--------------------------------------------------------------------UACU--A-CCAC--GAGGAAGCGCAAGUUCAUU------------------------GGGCGUGAUAUUCG-AUGCGC-------------------------CUGCCGCUCGCCUGGGCAGCGAAU
AACY023845234.1/1152-1235      UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
AACY021685826.1/176-92         GGUCAAAAGCGCGACUGGCGUUAGGUA------------------------------------------------------------------------------------------AGUGG-G--------------------------------------------------------------------AA----A-CCACU-G-GGAAGCGCUGAAGCAUCAA--------------------------------------------------------------------AAAUCGCACGCCUGGGUUUUUGUC
ABBH01000544.1/39713-39813     UACCCCCUGCGUGACUGGCGAUAC---------------------------------GACCUUUCG--------GGGUC----------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGUCGCUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CU914168.1/2467319-2467448     UCCACCUUGCGCAACUGGCGAAUC--------------------------CUGGG-GCUGCCGCC---------GGCAGUACCCGG---------------------------CA---GUGG-G--------------------------------------------------------------------CAUUG-A-CCAC--GAGGAAGCGCAAGGUCUCU------------------------GGCGUCAUGCACAACGACGC--------------------------CUGCCGCUCGCCUGGGCAGCGAAU
AACY021818080.1/421-338        UGAUGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGACGCAGAU------------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
CP001581.1/3668607-3668517     AAUAAAUCAUAUGACUGGCGGAA-----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUUA--A-CCAC--A-GGGAGUAUGAUUUAGAAAUUUAAGUUAGA----------------------------------------------------------AUGUCGACCGCCUGGGCAAUAAAA
ABGC03000034.1/58026-58108     AUAAGGUCAUAUAACUGACGGAGCAC--------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUUA--A-CCAC--AUGGAAGUAUGAUCAUUAA----------------------------------------------------------------------UCGCCGACCGUCUGGGCAAUCUGU
AACY023809027.1/335-252        UGACGCCAUCGCAACUGGCGUGAA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACACAGACGCAGAU------------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
CP000850.1/2571296-2571207     UCCUCGGGCCGGGACUGGCGCGGUUGG------------------------------------------------------------------------------------------GAUGG-A--------------------------------------------------------------------GC----A-CCAUC-G-GGGAACGGCCCGUGACGAGGACGC---------------------------------------------------------------ACGCCGGGCGCCUGGGCCUCCACA
CP000868.1/2806670-2806571     UCACCCCUGCGUGACUGGCGAUA----------------------------------GAACCCUCG--------GGUUC----------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCAGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
ABAW02000024.1/334916-334999   UAGAUGUUAUAUGACUGACGGAUAAA--------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AAUG--A-CCAC--A-GGAAGUAUAAUGUUGAUAA--------------------------------------------------------------------AAGCCGACCGUCUGGGCAGAAAAG
AACY020038179.1/1074-1209      AGUUUUGCACGCGACUGGCGAUA--------------------GGCU-GGCG-GCUUUAGAAACAAA-------UUC-AAAGCUUGCCCGGCU--------------------GAC--GUGG-A--------------------------------------------------------------------AU----A-CCAC-UG-GGAAGCGUGC-------------------------------CGCACUGUUUAACU-GGUGCGUU-----------------------CAGCCGUUCGCCUGGGCAGCCCUG
AACY023807203.1/1083-1000      UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
CP001340.1/32806-32887         CCGCGUUCGCGCGACUGGCGUUCG----------------------------------------------------------------------------------------------GAGGGA--------------------------------------------------------------------AAUG--ACCCUC--G-GGAAGCGUGGACUUUCA----------------------------------------------------------------------GAGCCGUUCGCCUGGGCGCCUAAC
CP000927.1/52674-52595         CGCCGUCCGCGUGACUGGCGAUCA---------------------------------------------------------------------------------------------CAGGG-A--------------------------------------------------------------------GC----A-CCCUG-A-GGGAGCGCGGACGUCAU----------------------------------------------------------------------GAGCCGUUCGCCUGGGCGCCCCAC
AAFX01055788.1/246-86          ACCGCGGUACGCAACUGGCGAUA------------------------------GGCG-CGGCCCACCGAGCG--GCCGGCGCC------------------------------GA--CGUGG-ACAUCAGCACAGG-GGCUGCCUGAAG-----CGGGCAGCCGAUUGU-----------------------UCC---A-CCACG-G-GGAAGCGUGCCGC------------------------------CGGGGUCU-----UCCG-------------GUGUU---------CAGCCGUUCGCCUGGGCAGCCCUU
AACY020107892.1/280-377        AGCGUCGCACACAACUGGCGACAA---------------------------------GAGGCUUA---------GCCUU----------------------------------AA--GAUGG-A--------------------------------------------------------------------UGAA--A-CCAUC-G-GGGAGUGUGAAAAGAAUA---------------------------------------------------------------------UAGCCGCUCGCCUGGGCAUAUACA
CP000249.1/708324-708410       GCCCGGAGUCGUGACUGGCGCAUCGA-------------------------------------------------------------------------------------------GGUGG-A--------------------------------------------------------------------ACUG--A-CCACC-G-GGGAGCGA--UCGAGCGGAACG-----------------------------------------------------------------GUGCCGCGCGCCUGGGCACCCCCG
AAVO02000004.1/47771-47851     CAACGACUGCAUGACUGGCGGAA-----------------------------------------------------------------------------------------------GUAG-G--------------------------------------------------------------------AUGA--A-CUAC--A-GGGAGUGCAGUAAGUGAAC--------------------------------------------------------------------GUGCCGACCGCCUGGGCAGCCUGG
AACY020992384.1/614-461        AACGGGGUACGCGACUGGCGAUA-------------------------GGC-GCUGCAUUUAGCCAA-------UGGAUGCAGCCGCU-------------------------GAC--GUGG-AAACCAG----------CAAGAACCUAC---UUCUUG--------------------------------UGA---A-CCAC-UG-GGAAGCGUGCCGCA----------------------------GGGGCCCU------GCCCC------------GUGCGUU-------CAGCCGUUCGCCUGGGCAGCCCUU
CP000774.1/1504618-1504701     GCUGCCUUGCGUGACUGGCGAGAAGG-------------------------------------------------------------------------------------------GGUGG-A--------------------------------------------------------------------GCCA--A-CCACC-G-UGGAGCGCGAGGCAAUC----------------------------------------------------------------------GCGCCGCUCGCCUGGGCACCCUUU
CP000316.1/3034848-3034979     AGGGAGGUGCGCGACUGGCGAUA--------------------------GGUAUCA-UGGUCUUGCC-------GGCCAUUGAUGCU--------------------------GAC--GUGG-G--------------------------------------------------------------------GAC---A-CCAC-UG-GGAAGCGCACCGCUCAAAGCCGUUUGGCCACAGCGUU--------------------------------------------------CAGCCGUUCGCCUGGGCAGCCCUU
AACY023813097.1/490-407        UGAUGCCAUCGCAACUGGCGUGAA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
BA000040.2/625249-625331       GCUCGCUCGCGCGACUGGCGACCUUG-------------------------------------------------------------------------------------------GAUGG-A--------------------------------------------------------------------GC----A-CCAUC-G-GGAAGCGCGGGACUUAAG---------------------------------------------------------------------ACGCCGCGCGCCUGGGCAUAGACA
CP000463.1/30517-30436         CCUCGCUCGCGCGACUGGCGACCUUG-------------------------------------------------------------------------------------------GAUGG-A--------------------------------------------------------------------GC----A-CCAUC-G-GGAAGCGCGGGCCAUAU----------------------------------------------------------------------CUGCCGCGCGCCUGGGCAUCGUAU
AAOX01000008.1/65010-65093     UAAAGGCGCAGUGACUGACGACGAUA--------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AGAA--A-CCAC--AGUGGAGCUGCGUGCAUAUA---------------------------------------------------------------------UAGCCGGUCGUCUGGGCAGCCAGC
AAXG02000001.1/53805-53882     AGUGCGCUAUAUGACUGACGGAA-----------------------------------------------------------------------------------------------GUGG-G--------------------------------------------------------------------UUG---A-CCAC--A-UGGAGUAUAGCGGACAU----------------------------------------------------------------------GAGCCGACCGUCUGGGCACGCUGC
CP000494.1/329370-329290       CGGCUCUCGCGCGACUGGCGACUUUG-------------------------------------------------------------------------------------------GAUGG-A--------------------------------------------------------------------GC----A-CCAUC-G-GGGAGCGCGGGGUGGA-----------------------------------------------------------------------UCGCCGUGCGCCUGGGCAAAUUGA
AAQL01010485.1/981-899         AUGAGGUCAUAUGACUGACGGAGCAC--------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AUCA--A-CCAC--AUGGGAGUAUGAUCAUUAA----------------------------------------------------------------------UCGCCGGCCGUCUGGGCAAUCUUG
CP000820.1/2987702-2987614     GCGAAGGGUCGUGACUGGCGCGCUCG-------------------------------------------------------------------------------------------GGUGG-A--------------------------------------------------------------------AGCA--A-CCACC-G-GGAAGCGACGAAGCUGCUGGCG-----------------------------------------------------------------GCGCCGUGCGCCUGGGUGCCUCCG
AE005673.1/88947-89027         CCGCGUUCGCGUGACUGGCGCUAGU--------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------GA----A-CCAUC-G-GGGAGCGUGGACAUCAU----------------------------------------------------------------------AAGCCGCGCGCCUGGGCUCCCUUU
AAFZ01025325.1/141-230         UUACCCUGCCGUGACUGGCGAGUUUUUG-----------------------------------------------------------------------------------------CGUGG-A--------------------------------------------------------------------ACUA--A-CCACG-G-GGAAGCGGCAGGGGGCUGCAC------------------------------------------------------------------CUGCCGAUCGCCUGGGCGCUUUUC
CP000885.1/835881-835983       AUUACAAUGUACGACUGGCGGAAA--------------------------------CUGUAGGAGA--------CUACAG--------------------------------------GUGGGG--------------------------------------------------------------------AUA---ACCCAC--A-GGGAGUACAUUUAAUAACAAUAA----------------------------------------------------------------GAGCCGACCGCCUGGGCCACCACC
AACY020523850.1/190-107        UGAUGCCAUCGCAACUGGCGUGAA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
CP000440.1/762627-762727       UCACCCCUGCGUGACUGGCGAUA---------------------------------GAACCCUUC---------GGGUUC---------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCGGGGCGCCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
CP000529.1/3062025-3062156     AGCGCGGUGCGCGACUGGCGAUA--------------------------GGCC-UCAUGGUUUCAC--------AACUCUGAAGGCC--------------------------GA--CGUGG-G--------------------------------------------------------------------AC----A-CCACG-G-GGAAGCGCACCGUUUGA--------------------------GGUCAUCU-----GGCC-------------AAAAAGCGUU----CAGCCGUUCGCCUGGGCAGCCCUU
AACY020296783.1/43-126         UGAUGCCAUCGCAACUGGCGUGAA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
AL646052.1/778049-777920       UCCACCUUGCGCAACUGGCGAAUC--------------------------CUGGG-GCUGCCGCC---------GGCAGUACCCGG---------------------------CA---GUGG-G--------------------------------------------------------------------CGUUG-A-CCAC--GAGGAAGCGCAAGGUCUCU------------------------GGCGUCAUGCACAACGACGC--------------------------CUGCCGCUCGCCUGGGCAGCGAAU
AACY024109386.1/572-489        UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
AAVL02000036.1/176021-175941   UAUAUUCCAUAUGACUGGCGGAUUA---------------------------------------------------------------------------------------------GUGGGA--------------------------------------------------------------------UU----ACCCAC--A-GGGAGUAUGGAUGCACG----------------------------------------------------------------------UAGUCGACCGCCUGGGCAACCCUC
CP000359.1/539910-539993       GAGCGGGUGG-UGACUGGCGCUGAAC--------------------------------------------------------------------------------------------GUGG-G--------------------------------------------------------------------CCA---A-CCAC--G-GGGAAGCCAUCCGCAUUGCUG------------------------------------------------------------------UGAUCGCGCGCCUGGGUCGGACGC
AAUJ02000001.1/1536455-1536301 GCGGGUGUACGCAACUGGCGAUA------------------------------GGCG-CAGAGUUU--------UCUGCCGCU------------------------------GAC--GUGG-AAACCGG----------CAGACUGCAA----GGUCUG--------------------------------UGA---A-CCAC-CG-GGGAGCGUACCGCC----------------------CAGAGCCGCAGCGA------CUGCAGC-CUG------CAAGCGUUU-----CAGCCGUUCGCCUGGGCAGCCCUU
AARF01000325.1/402-322         GAGCCCCGGUGUAACUGGCGACAG----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GCGA--A-CCAC--AUGGAAGCACCGGGGAAUA----------------------------------------------------------------------CGGCCGGUCGCCUGGGCAAAGAGC
ABCF01000005.1/78206-78117     GACAAAAGCAGUAACUGGCGAAAAC--------------------------------------------------------------------------------------------UGUGG-A--------------------------------------------------------------------ACCA--A-CCACA-A-GGGAGCUGCUUUUCUUACGCUUAA---------------------------------------------------------------UAGCCGUUCGCCUGGGCUGAGGCU
AACY021145871.1/594-676        CUGAUGCUACGCAACUGGCGUAAU---------------------------------------------------------------------------------------------GAUGG-A--------------------------------------------------------------------UA----A-CCAUC-G-GGGAGCGUAAGGAAGCGUGC-------------------------------------------------------------------UGGCCGUACGCCUGGGCUGACACG
CT573213.2/1191460-1191545     GCUGGGAGUCGCGACUGGCGCACAGA-------------------------------------------------------------------------------------------GGUGG-A--------------------------------------------------------------------ACUG--A-CCACC-G-GGGAGCGAUGAGCGGGUCG--------------------------------------------------------------------GUGCCGUGCGCCUGGGUGCCUCCG
CP000572.1/3148595-3148495     UAGUCCCUGCGUGACUGGCGAUAC---------------------------------GACCUUUCG--------GGGUC----------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGCAGGGCGUCGUUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
ABBM01000487.1/14069-13969     UACCCCCUGCGUGACUGGCGAUAC---------------------------------GGCCUUUCG--------GGGUC----------------------------------AA--GGUGG-A--------------------------------------------------------------------GCAU--C-CCACC-G-UGAAGCGUAGGGCGUCGCUU-------------------------------------------------------------------UUGCCGUUCGCCUGGGCAGCCGUU
AACY020539987.1/444-527        UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
AACY021513409.1/321-238        UGACGCCAUCGCAACUGGCGUGUA---------------------------------------------------------------------------------------------GAUGG-G--------------------------------------------------------------------UC----A-CCAUC-G-GGGAGCGACA-CAGACGCAGAU-----------------------------------------------------------------UGGCCGAACGCCUGGGCCACCUGC
AAYI02000004.1/189562-189478   UAAGCGUGUCGUGACUGGCGAACA---------------------------------------------------------------------------------------------GGUGG-G--------------------------------------------------------------------CC----A-CCACC-G-GGGAGCGACGCGUCGGCAUCGA-----------------------------------------------------------------UAGCCGCCCGCCUGGGCUAGAGGC
AAYI02000004.1/2328470-2328386 GGGAGACGCCGCGACUGGCGAG-----------------------------------------------------------------------------------------------GGUGG-A--------------------------------------------------------------------UG----A-CCACC-G-GGGAGCGGCCGCAUUUCCCGCGAG---------------------------------------------------------------GCGUCGCCCGCCUGGGCGCCUGGG
ABAX03000018.1/2486-2565       UGAAAGCUGUGCGACUGGCGGAUA----------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------GAA---A-CCAC--G-GGGAGCACGGCAGCAGAA---------------------------------------------------------------------AUGCCGGCCGCCUGGGCAACUUUU
AAVO02000015.1/35242-35324     AAAGUCUCUGGUAACUGGCGGAGUA---------------------------------------------------------------------------------------------GUGG-A--------------------------------------------------------------------AAUC--A-CCAC--AUGGGAAUCAGAGAUUUGCA---------------------------------------------------------------------GAGCCGACCGUCUGGGCAGUAUUU
AE000513.1/880781-880696       CUGCGGAAGG-UGACUGGCGCGAAAAC-------------------------------------------------------------------------------------------GUGG-G--------------------------------------------------------------------AAG---A-CCAC--G-GGGAAGCCUUCUGGCAUAGCAA-----------------------------------------------------------------AGACCGUGCGCCUGGGUCGGACGC
CP000667.1/2571803-2571720     UGGAAACGAUGCGACUGGCGGCACCGAG-----------------------------------------------------------------------------------------GAUGG-A--------------------------------------------------------------------ACG---A-CCAUC-G-GGGAGC-UCGUCGCGGA----------------------------------------------------------------------GGGUCGACCGCCUGGGCCUUUCCG
CP001644.1/756294-756165       UCCACCUUGCGCGACUGGCGAAUCC---------------------------UGAAGCUGCUUUG---------AGCGGCUUCG-----------------------------ACAU-GUGG-G--------------------------------------------------------------------CAGCG-A-CCAC--GAGGAAGCGCAAGGUUUCU------------------------GGCGUCAUGCACAACGGCGC--------------------------CUGCCGCUCGCCUGGGCAGCGAAU
#=GC SS_cons                   ::((((((((((,,,,,,,,,,,,..................................,<<<___.........>>>,,.......................................<<<<._....................................................................___..._.>>>>..,.,,,,))))))))))---......................................................................<<<<<_________>>>>>:::::
#=GC RF                        aaccccccgcgcgACUGGCGaaaa..................................cggcuua.........gccgu.......................................GUGG.A....................................................................ucu...A.CCAC..G.GGgAgcgcgggggguaa......................................................................cuGCCGauCGCCUGGGCagcccuu
//
# STOCKHOLM 1.0

#=GF AC   RF01751
#=GF ID   potC
#=GF DE   potC RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   44.00
#=GF TC   45.30
#=GF NC   41.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   PotC_RNA_motif
#=GF SQ   136


AACY020741309.1/734-806   AUGAUUGUGCUCAGAUCUU--UUCUCCU----UCAGGAUCUUUACCCUUUCCUAAGCA-ACA-AG---UUUUGGGCACA-AAAAA
AACY020326390.1/565-493   AUGAUUGUGCUCAGAUCUU--UUCUCCU----UCAGGAUCUUUACCCUUUCCUAAGCA-UUA-AG---GUUUGGGCACA-AAAAA
AACY023723108.1/723-792   GACGGGGUGCUCGCAAUCU--UUCUCCA----UUAGGAUUCUUACCCUUUCCUAAU-C-----UGA--UCGUGAGCACC-UUAAA
AACY020258941.1/1404-1336 UAGAUGGUGCCCACG-UCA--CUCUCCC-----UAGGAUCUUUACCCUUUCCUA-G-A-AAU-UG---UCGUGGGCAUU-AAAAA
AACY022314716.1/323-392   UAGACGGUGCCCACG-UCA--CUCUCCU----CUAGGAUCUUUACCCUUUCCUAGA-A-GU--CG---UCGUGGGCAUU-AAAAA
AACY020265186.1/1566-1635 UAGACGGUGCCCACG-UCA--CUCUCCU----CUAGGAUCUUUACCCUUUCCUAGA-A-GU--CG---UCGUGGGCAUU-AAAAA
AACY020341197.1/2373-2442 UAGCCGGUGCCCACG-UCA--CUCUCCU----UUAGGAUAUUUACCCUUUCCUAAA-A-AU--UG---UCGUGGGCAUU-AAAAA
AACY023705969.1/397-328   UAGACGGUGCCCACG-UCA--CUCUCCU----CUAGGAUCUUUACCCUUUCCUAGA-A-AC--UG---UCGUGGGCAUU-AAAAA
AACY021742173.1/363-294   UAGACAGUGCCCACG-UCA--CUCUCCU----CUAGGAUCUUUACCCUUUCCUAGA-A-AU--UG---UCGUGGGCAUU-AAAAA
AACY023104983.1/407-341   UAUAUAGUGCUCAUA-ACC--UUCCCAA----UUAGAUGAUUUACCCC-AUCUAAU-A-----UG---UUAUGAGCACU-UAUAA
AACY022978203.1/419-491   UUUAUAAUGCCCACGAU-CUGUUGAAUU----UUAGGAUUUUUACCCUUUCCUAAACA-AUUA-----UUGUGGGCAUU-GACAA
AACY022881389.1/801-733   UAGACGGUGCCCACG-UCA--CUCUCCC-----UAGGAUCUUUACCCUUUCCUA-G-A-AAC-UG---UCGUGGGCAUU-AAAAA
AACY023891533.1/365-430   AAUAAAAUGCUCACAGUUA---------AUAAUUAGGAUUUUUACCCUUUCCUAAU-A-----AA---CUGUGAGCAUU-CAAUA
AACY023730877.1/1294-1226 AUGAUUGUGCUCAAA-UCU--UUCUCC------UAGGAUCUUUACCCUUUCCUA-AUA-AUU-AG---UUUUGGGCACA-AAAAA
AACY023783618.1/1144-1213 UAGACAGUGCCCACG-UCA--CUCUCCU----CUAGGAUCUUUACCCUUUCCUAGA-A-GU--CG---UCGUGGGCAUU-AAAAA
AACY023856989.1/191-122   UAGACGGUGCCCACG-UCA--CUCUCCU----CUAGGAUCUUUACCCUUUCCUAGA-A-AU--UG---UCGUGGGCAUU-AAAUU
AACY022209000.1/647-715   UAAAUGGUGCCCACG-UCA--CUCUCCC-----UAGGAUCUUUACCCUUUCCUA-G-A-AAC-UG---UCGUGGGCAUU-AAAAA
AACY021291153.1/390-460   UAGACGGUGCCCACG-UCA--CUCUCCU----UUAGGAUCUUUACCCUUUCCUAAA-A-AUU-UG---UCGUGGGCAUU-AAAAA
AACY022371993.1/73-4      UAAACAGUGCCCACG-UCA--CUCUCCU----UUAGGAUCUUUACCCUUUCCUAAA-A-AU--UG---UCGUGGGCAUU-AAAAA
AACY023722526.1/1099-1030 UAGACGGUGCCCACG-UCA--CUCUCCU----CUAGGAUCUUUACCCUUUCCUAGA-A-AU--UG---UCGUGGGCAUU-AAAAU
AACY020417845.1/1545-1614 UAGAUGGUGCCCACG-UCA--CUCUCCU----UUAGGAUCUUUACCCUUUCCUAAA-A-AU--UG---UCGUGGGCAUU-AAAAA
AACY022930639.1/574-505   AAAAUUGUGCUCAUUAUCU--CUCUCCA-----UAGGAUUUUUACCCUUUCCUA-U----U--AGCGAUAUUGGGCACA-AACAA
AACY020291070.1/2171-2103 UAGAUGGUGCCCACG-UCA--CUCUCCC-----UAGGAUCUUUACCCUUUCCUA-G-A-AAC-UG---UCGUGGGCAUU-AAAAA
AACY020232142.1/1598-1530 UAGACGGUGCCCACG-UCA--CUCUCCC-----UAGGAUCUUUACCCUUUCCUA-G-A-AAC-UG---UCGUGGGCAUU-AAAAA
AACY021976805.1/39-106    AUGAUUGUGCUCAAA-UCU--UUCUCC------UAGGAUCUUUACCCUUUCCUAA--U-AUU-AG---UUUUGGGCACA-AAAAA
AACY020255219.1/303-236   UAGAUGGUGCCCACG--CA--CUCUCCC-----UAGGAUCUUUACCCUUUCCUA-G-A-AAC-UG---UCGUGGGCACU-AAAAA
AACY023596628.1/763-831   UAGACGGUGCCCACG-UCA--CUCUCCC-----UAGGAUCUUUACCCUUUCCUA-G-A-AAC-UG---UCGUGGGCAUU-AAAAA
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AACY023553826.1/369-300   AGAUAUGUGCUCACG-UCA--CUCUCCU----CUAGGAUAUUUACCCUUUCCUAGA-A-AU--UG---UCGUGGGCACU-AAAAA
AACY021118191.1/102-34    UAGAUGGUGCCCACG-UCA--CUCUCCC-----UAGGAUCUUUACCCUUUCCUA-GAA-AA--UG---UCGUGGGCAUU-AAAAA
AACY021879943.1/689-617   UAGACGGUGCCCACG-UCA--CUCUCCU----UUAGGAUCUUUACCCUUUCCUAAAAAUAAU-UG---UCGUGGGCAUU-AAAAA
AACY023901039.1/445-514   AAGAAUGUGCUCACU-UUC-UUUCUCCA----UUAGGAUCUUUACCCUUUCCUAAUUU-----GA---UUGUGGGCACU-CUUAA
AACY022595046.1/418-349   ACAAUUGUGCCUAUA-AUC--CUCUCUU----CUAGGAUUCUUACCCUUUCCUUAAAAA----GA---UUAUAGGCAUA-AAAAA
AACY023451810.1/761-830   UAGACGGUGCCCACG-UCA--CUCUCCU----CUAGGAUCUUUACCCUUUCCUAGA-A-GU--CG---UCGUGGGCAUU-AAAAA
AACY023230060.1/756-820   AUGAUUGUGCUCAUA-G----CUCUUCG-----AAAGGUAUUUACCCUACC----UAAUUUAA-----CUAUGAGCACU-AAAAA
AACY020503162.1/2658-2590 AAGAUUGUGCUCAAA-UCU--UUCUCCU-----UAGGAUCUUUACCCUUUCCUA-A-A-CUU-AG---UUUUGAGCACU-AAAAA
#=GC SS_cons              :::::<<<<<<<<<<.-<<..-------....-<<<<<___________>>>>>--.-.--..>>...->>>>>>>>>>.:::::
#=GC RF                   aagAuugUGCcCAcg.UCa..cUCUCCu....uUAGGAUcUUUACCCUUUCCUAaa.A.au..uG...UcgUGgGCAca.AAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01752
#=GF ID   psaA
#=GF DE   psaA RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   52.10
#=GF NC   38.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   PsaA_RNA_motif
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   31


AACY020449412.1/941-1133     UCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUGA-----AGACAAGGGGUUUCG-GC-CUUU-UG-AAC--GCACUGAUGCCCU--GACGCUG-CUUCAUUACGGAG-CUGUGUC--CGGGGCC--CCGGUGGAU--UUCG--AUCCG-CCGGAGGGGUGGCCCUCCACCUCGACUCCAGUCCCUCGAGGAACGACUCGAUGA
AACY023990482.1/660-468      UCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUG--A---AGCCAAGGGGUUUCG-GC-CUUU-U-GAA--UGCACUGACGCCCU--GACGCUG-CUUCAUUGUGGAG-CUGUGUC--CGGGGCC--CCGGUGGAU--UUCG--AUCCG-CCGGAGGGGUGGCCCUCCACCUCGACUCCAGUCCCUCGAGGAACGACUCGAUGA
AACY022973181.1/620-429      CCUAUGCUUCCGCCAGCGGUCCCCUUUUU-GGGGCCC-CA-GCUUCAGUGC-----AGCAAAGGGGUUUCG-GCUCCCAA--GC----GGUCUGACGCCCUGUCACGGUU---UCCCUGCGG---AGCUGUGCCCGGGGCC--CCGACGGAU--UCCG--GUCCG-UCGCAGGGGUGGCCCUCCACCUCGAUACCCGUCCCUCGAGGAACGACUCGAUGA
AACY020539721.1/694-890      UCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-AAUGCUCCAGUGA-----GAGUCAGGGAUUUCU-GU-UCCU-GGCAA---CCACUGGCGCCCGGGUGCGGUGACGC---UCU-GCUGAGCUGUGCCCGGGGCC--CCGGCGAGCC-AUUC-GGUUUG-CCGGAGGGGUGGCCCACCACCUCGAU-CCCGUCCCUCGAGGAACGACUCGAUGA
AACY020494075.1/1015-823     CCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUGC-----AGACAAGGGGUUUCG-AC-CCCUUUGCC----GUACUGACGCCCG--AACGCCG-AUUCCUUGCGAAU-CCUUGUU--CGGGGCC--CCGAUUGGC--UUCG--GCCCU-UCGGAGGGGUGGCCCACCACCUCGAAACCCGUCCCUCGAGGAACGACUCGAUGA
AACY023990411.1/165-356      CCUAUGCUUCCGCCAGCGGUCCCCUCCUU-GGGGCCC-CA-GCUUCAGUGC-----AGACAAGGGGUUUCG-AC-CCUU---UCCC--UUACUGACGCCCU--AAUGCAG-AUUCCUUGCGAAU-CCGUGUU--CGGGGCC--CCGAUUGGC--UUCG--GCCCG-UCGGAGGGGUGGCCCACCACCUCGAAACCCGUCCCUCGAGGAACGACUCGAUGA
AACY024062603.1/140-333      CCUAUGCUUCCGCAAGAGGUCCCCUUGUC-GGGGCCC-AA-GCACCAGUUC-----GUACAAGAGGUUUCG-GC-CUCC--G-AUC--GAGCUGGCGCCCGGCGGUUCCG-UCUCUAU--GAGG-C-GAGCUGUCAGGGCC--CC-GACAGGC-UCAG-GCCUAU-CGGAAGGGGUGUCCCAUCACCUCGAUCCCGUCCCCUCGAGGAACGACUCGAUGA
AACY023855819.1/413-222      CCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUGC-----AGACAAGGGGUUUCG-AC-CUCU-UGCU----GUACUGACGCCCG--AACACCG-AUUCCUUGUGAAU-CCUUGUU--CGGGGCC--CCGAUUGGC--UUCG--GCCCU-UCGGAGGGGUGGCCCACCACCUCGAAACCCGUCCCUCGAGGAACGACUCGAUGA
CP000110.1/340021-340213     CCUAUGCUUCCGCCAGCGGUCCCCUCUUA-GGGGCCC-CA-GCUUCAGUGC-----AGACAAGGGGUUUCG-AC-CCCU-U-UGCC--GUACUGACGCCCG--AAUGCUG-AUUCCUUGUGAAU-CCGUGUU--CGGGGCC--CCGAUUGGC--UUCG--GCCCG-UCGGAGGGGUGGCCCACCACCUCGAAACCCGUCCCUCGAGGAACGACUCGAUGA
AAOK01000002.1/133205-133012 CCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-AGCGCUCCAGUGG-----U-CGUCAGGGGUUUGCGCCCCUG-GCG-----CCAUUGGCGCCCGGACGUGGUGACGC-UCU---GCGGAGCUGCGUUCGUGGCC--CCGGUGAAC--AUUU--GUUCA-UCGGAGGGGUGGCCCACCACCUCGAU-CCCGUCCCUCGAGGAACGACUCGAUGA
AACY020239904.1/6072-5880    CCUAUGCUUCCCGCAGCGGUCCCCUCUUU-GGGGCCC-UA-GCUCCAGUGA-----G-AGUCAGGGUUCAUUGC-UCUGAACG-----CCACUGGCGCCCGGCCACGGUGAAGC-UU----GCUGAUCCGCGCCCGGGGCC--CCGGUAAUCC-CAU--GGAUUU-CCGGAGGGGUGUCCCACCACCUCGAU-CCCGUCCCUCGAGGAACGACUCGAUGA
BX569694.1/270245-270053     UCUAUGCUUCCGCCAGUGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUGA-----AGUCAAGGGGUUUCG-GC-CUUU-UGAAC---GCACUGAUUCCCU--GACGCUG-CUUCAUUGCGGAG-CUGCGUC--CGGGGCC--CCGGUGGAU--UUCG--AUCCG-CCGGAGGGGUGGCCCUCCACCUCGACUCCAGUCCCUCGAGGAACGACUCGAUGA
AACY023865411.1/787-979      CCUAUGCUCUACGCAGCGGUCUCCUCUUU-GGGGCCC-UA-GCCUCAGUAC-----A-GCAAAGGAGUUC--CGACUCU-UGCGCA--GUGCUGUCGCCCG--GAUCAUG-CACCCUUGUGGAG-CGUGGCC--CGGGGCC--CCAGCGGAC--CUCG--GUUCG-CUGGAGGGGUGGCCCUCCACCUCGAAUCCCGUCCCUCGAGGAACGACUCGAUGA
AACY022060962.1/274-465      CCUAUGCUUCCGCCAGCGGUCCCCUUUUU-GGGGCCC-CA-GCUUCAGUGC-----UGCCAAGGGGUUUCG-GCUCCCAA--GC----GGACUGACGCCCUGUCACGGUU---CCCCCGCGG---AGCUGUGCCCGGGGCC--CCGGCGGAU--UCCG--GUCCG-UCGGAGGGGUGGCCCUCCACCUCGAUACCCGUCCCUCGAGGAACGACUCGAUGA
AACY020541355.1/1376-1184    CCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUGC-----AGACAAGGGGUUUCG-AC-CUCUUCGCC----GUACUGACGCCCG--AACACCG-AUUCCUUGCGAAU-CCUUGUU--CGGGGCC--CCGAUUGGC--UUCG--GCCCU-UCGGAGGGGUGGCCCACCACCUCGAAACCCGUCCCUCGAGGAACGACUCGAUGA
AAUA01000004.1/189443-189638 UCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCCUAAAGCUCCAGUGG-U---GG-UAAGGGGUUUCG-GCUUC---UGAAA--ACCACUGGCGCCCGGAUGCGGCAAGGC-CAU---GCCGAGCUGCGACCGGGGCC--CCGAUGAAC--UCCG--GUUCG-UCGGAGGGGUGGCCCUCCACCUCGAU-CCCGUCCCUCGAGGAACGACUCGAUGA
AACY022140395.1/66-257       CCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUGC-----AGACAAGGGGUUUCG-AC-CUCU-UGCC----GUACUGACGCCCG--AACGCCG-AUUCCUUGCGAAU-CCUUGUU--CGGGGCC--CCGAUUGGC--UUCG--GCCCU-UCGGAGGGGUGGCCCACCACCUCGAAACCCGUCCCUCGAGGAACGACUCGAUGA
AACY023852721.1/182-374      CCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUGC-----AGACAAGGGGUUUCG-ACCUCCUC---GCU--GUGCUGGCGCCCG--AACUCUG-AUUCCUUGCGAAU-CCGUGUU--CGGGGCC--CCGAUUGGC--UUCG--GCCCU-UCGGAGGGGUGGCCCACCACCUCGAAACCCGUCCCUCGAGGAACGACUCGAUGA
CP000435.1/402382-402566     UCUAUGCUCAAAUCAGCGGUCCCCUCUUU-GGGGCCC-AAAGCACCAGU-------GACGGUCAGGGUUU--UC-CUGGUCUGA------GCUGGCGCCCG-----GCUAAAGCCUUCG-GGCUAUGGC-----CGGGGCC--CCGGCGAACU-GUCC-GGUUCU-CCGGAGGGGUGGCCCUCCACCUCGAU-CCCGUCCCUCGAGGAACGACUCGAUGA
CP000097.1/1900065-1899872   CCUAUGCUUUUUUCAGCGGUCCCCUCUUUUGGGGCCC-UA-GCUUCAGUGC-----AGUAAAGGGGUUUCG-GCUUCCU-UUAAA---GCAUUGACGCCCGGCCAUG--G-CUCCCUUGCGGAG-C--UGUGUUCGGGGCC--CCGACGAGC--UUCG--GUUCG-UCGGAGGGGUGGCCCACCACCUCGAU-CCCGUCCCUCGAGGAACGACUCGAUGA
AACY021504741.1/55-247       CCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUGC-----AGUCAAGGGGUUUCG-GC-CAUU-UGAAC---GCACUGACGCCCU--GAUGCAG-CUCCUAUACGGAG-CUCCGUC--CCGGGCC--CCGGUGGAU--UUCU--GUCCG-CCAAAGGGGUGGCCCUCCACCUCGACUCCAGUCCCUCGAGGAACGACUCGAUGA
CP000554.1/2066948-2066752   UUUAUGCUUCUCGAAGCGGUCCCCUUGUA-GGGGCCC-AUAGCUCCAGUGU-----G-AGUCUGAGUUUCG-ACUUUUG-ACUU----GUGCUGGCGCCCGGUAUCAGCA-CCACUUCG-GUGG-UGGUGUCUCCGGGGCC--CCGGCAAGCC-CUUG-GGCCUG-UCGAAGGGGUGGCCCUCCACCUCGAU-CCCGUCCCUCGAGGAACCUCUCGAUGA
AACY024089783.1/576-384      UCUAUGCUUCCGCGAGAGGUCCCCUCUUU-GGGGCCC-CAAGCACCAGUUG-----GUGAAAG-GGCUUAG-GCCCGCUCUUC-----CAGCUGGCGCCCGGCGGUUCAG-GCGCUU---GCGU-CUGUGCCAUCGGGGCC--CCGACGGGC---UAC--GCCUG-UCGGAGGGGUGGCCCACCACCUCGAUCCCGUCCCCUCGAGGAACGACUCGAUGA
AANP01000005.1/107675-107479 UCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-AAUGCUCCAGUGA-----GAGUCAGGGGUUUCU-GU-UCCU-GGCAA---CCACUGGCGCCCGGGUGCGGUGACGC---UCU-GCUGAGCUGUGCCCGGGGCC--CCGGCGAGCC-AUUC-GGUUUG-UCGGAGGGGUGGCCCACCACCUCGAU-CCCGUCCCUCGAGGAACGACUCGAUGA
AATZ01000002.1/703831-704023 CCUAUGCUUUUUUCAGCGGUCCCCUCUUU-GGGGCCC-CU-GCUUCAGUGC-----AGUAAAGGGGUUUCG-GCUUCCU-UUAAG---GCAUUGACGCCCGGCCACG---ACUCCCUUGCGGAGC---UGUGCUCGGGGCC--CCGACGAGC--UUCG--GUUCG-CCGGAGGGGUGGCCCACCACCUCGAU-CCCGUCCCUCGAGGAACGACUCGAUGA
CT971583.1/414736-414928     CCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-AGCGCUCCAGUGG-----C-CGACAGGGGUUUCGCU-CCUG-UCG-----CCAUUGGCGCCCGGUCGUGGUGACGC-UUC---GCGGAGCUGCGUCCGGGGCC--CCGGUGAAC--AUCU--GUUUA-UCGGAGGGGUGGCCCACCACCUCGAU-CCCGUCCCUCGAGGAACGACUCGAUGA
AACY020857496.1/508-325      --------UCCGCCAGCGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUGC-----AGGCAAGGGGUUUCG-AC-CCCU-UGCC----GUACUGACGCCCG--AAUCCUG-AUUCCUUGCGAAU-CCGUGUU--CGGGGCC--CCGAUUGGC--UUCG--GCCCG-UCGGAGGGGUGGCCCACCACCUCGAAACCCGUCCCUCGAGGAACGACUCGAUGA
BX548175.1/1864565-1864369   UUUAUGCUGCUUGAAGCGGUCCCCUUGUA-GGGGCCC-AUAGCUCCAGUGU-----G-AGUCUGAGUUUCG-ACUUUCG-ACUU----GUGCUGGCGCCCGGUAUCAGCA-CCACUUCG-GUGG-UGGUGUCUCCGGGGCC--CCGGCAAGCC-CAUG-GGCCUG-UCGAAGGGGUGGACCUCCACCUCGAU-CCCGUCCCUCGAGGAACCUCUCGAUGA
AACY023800530.1/428-232      UCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-AAUGCUCCAGUGA-----GAGUCAGGGAUUUCU-GU-UCCU-GGCAA---CCACUGGCGCCCGGGUGCGGUGAUGC---UCU-GCUGAGCUGUGCCCGGGGCC--CCGGCGAGCC-AUUC-GGUUUG-CCGGAGGGGUGGCCCACCACCUCGAU-CCCGUCCCUCGAGGAACGACUCGAUGA
AANO01000001.1/318481-318691 CUUAUACUUCCGCCAGCGGUCCCCUCAUC-GGGGCCC-CA-GCUCCAGUGCUGGCAGCGGCUUUCGGUCUUUUCCGAA--GCCACUCCGCACUGGUGCCCAU-GGUUCCAAGGAUCUCG-AUCCACGGAACC-GUGAGGCCCACCGGCCUGGCCUUUCGGCCCGGUCCGGAGGGGUGGACCUCCACCUCGAC-UCCGUCCCUCGAGGAACGUCUCGAUGA
AACY023856959.1/244-53       CCUAUGCUUCCGCCAGCGGUCCCCUCUUU-GGGGCCC-CA-GCUUCAGUGC-----AGACAAGGGGUUUCG-AC-CUCU-UGCU----GUACUGACGCCCG--AACACCG-AUUCCUUGUGAAU-CCUUGUU--CGGGGCC--CCGAUUGGC--UUCG--GCCUU-UCGGAGGGGUGGCCCACCACCUCGAAACCCGUCCCUCGAGGAACGACUCGAUGA
#=GC SS_cons                 :::::::::::::::::[[[[[[[[[[,,.(((((((.,,.<<-<<<<<<<.....--<<<<<<<<<____.>>.>>>>.>>>--...>>>>>>>->>,<<<.<<<<<<<.<<<<_____>>>>.>>>>>>>.>>>)))))..))<<<<<<<..____..>>>>>.>>]]]]]]]--]]]-----<<<<<<__________>>>>>>:::::::::::::
#=GC RF                      ccUAUGCUUccgccAGcGGuCCCCuccUu.GGGGCCC.aA.GCucCaGugc.....agggggggggcUUcg.gc.cccc.cccaa...gcaCuGgcGCCCgg.ggcgccg.cgccuuuguggcg.cggcgcc.ccGGGGCC..CCGgcgggc..uuug..gcccg.cCggaGGGGUGgCCCaCCACCuCGauaCCcGUCCCuCGaGGAACGACUCGAUGA
//
# STOCKHOLM 1.0

#=GF AC   RF01753
#=GF ID   psbNH
#=GF DE   psbNH RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   45.00
#=GF TC   47.00
#=GF NC   31.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   PsbNH_RNA_motif
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   39


AACY020226160.1/210-268      GGGUGAAGUUCAGUCCCGAUACUGUAAGGGUCCUGGCCCU-GAUA-AGGGCCGAUCCUGUC
CP000110.1/272727-272670     GGGUGGUUUGAUGUCUCGAUACUGUAGGGGC--CGACUCCGGUUC-GGGGUUGAUCCUGUC
AACY021771740.1/261-204      GGGUGGUUUGAAGUCUCGAUACUGUAGGGGC--CGACUCCGGUUC-GGGGUUGAUCCUGUC
AACY022999858.1/763-706      GGGUGAAUUGAAGUCUGGAUACUGUAGGGGC--CGAUUCCGUUUC-GGGGUCGGUCCUGUC
AACY023860024.1/1426-1368    GGGUGAAGUUCAGUCCCGAUACUGUAGGGGUCCCGGCCCU-GAUC-AGGGCCGAUCCUGUC
AACY020543121.1/1394-1451    GGGUGGUUUGAAGUCUCGAUACUGUAGGGGC--CGACUCCGGUUC-GGGGUUGAUCCUGUC
AACY020233379.1/1256-1198    GGGUGAAGUUCAGUCCCGAUACUGUAGGGGUCCCGGCCCU-GAUC-AGGGCCGAUCCUGUC
ACNY01000001.1/204437-204494 GGGUGGUUUGAAGUCUCGAUACUGUAGGGGC--CGACUCCGGUUC-GGGGUUGAUCCUGUC
AACY020543417.1/1564-1621    GGGUGGUUUGAAGUCUAGAUACUGUAGGGGC--CGACUCCGGUUC-GGGGUUGAUCCUGUC
CT971583.1/340673-340616     GGGUGAAGUUCAGUCCGGAUACUCUAGGGGUCCCGGCCC-GGAUG--AGGCCGAUCCUGUC
AACY020315631.1/1394-1337    GGGUGUUGAAAAGUCCAGAUACUGUAGGGGC--CAGCUCCGGUUC-GGGGCUGAUCCUGUC
BX569689.1/271369-271312     GGGUGAAUUGAAGUCUAGAUACUGUAGGGGC--CGAUUCCGUUUC-GGGGUCGGUCCUGUC
CP000554.1/2161522-2161580   GAUGGUGAUUAAGCAUGCCUACUGUAAUGGUCAUAGUCCG-CAUA-CGGACUAAUCCUGUC
BX548175.1/1943364-1943422   GAUGGUGAUUAAGCAUGCCUACUGUAAUGGUCAUAGUCCG-CAUA-CGGACUAAUCCUGUC
AACY022223136.1/380-437      GGGUGGUUUGAAGUCUCGAUACUGUAGGGGC--CGACUCCGGUAC-GGGGUUGAUCCUGUC
AACY020540927.1/743-800      GGGUGGUUUGAAGUCUCGAUACUGUAGGGGC--CGACUCCGGUUC-GGGGUUGAUCCUGUC
AACY024114286.1/266-323      GGGUGGAUUGAAGUCUGGAUACUGUAGGGGC--CAACUCCAGUUC-GGGGUUGGUCCUGUC
CP000097.1/1985986-1986043   GGGUUAAAGGAAGUGCGGAUACUGUAGGGGC--CAGCUCCGGUUA-GGGGCUGGUCCUGCC
AACY020542616.1/2468-2411    GGGUUGUUUGAAGUCUCGAUACUGUAGGGGC--CGACUCCGGUUC-GGGGUUGAUCCUGUC
CP000435.1/322025-321967     GGGUUGAAUUAAGUCUCGAUACUGUAGGGGCUCCGACCC-AUAUAG-GGGUCGAUCCUGUG
AATZ01000002.1/616384-616327 GGGUUAAAGGAAGUGCCGAUACUGUAGGGGC--CAGCUCCGGUUA-GGGGCUGGUCCUGCC
AACY023184528.1/275-332      GGGUAAAUUGAAGUCUAGAUACUGUAAGUGC--CGAUUCCGUUUC-GGGGUCGGUCCUGUC
AACY021990769.1/633-690      GGGUGGAUUGAAGUCUGGAUACUGUAGGGGC--CAACUCCAGUUC-GGGGUUGGUCCUGUC
AACY022195604.1/689-746      GGGUGAGGUUCAGUCUGGAUACUGUAGGGGCCACGGCCC-AGAAC--GGGUCGAACCUGUC
AAOK01000002.1/214718-214775 GGGUGGAGUUCAGUCCCGAUACUCUAGGGGUCCCGGCCC-GGAAG--AGGCCGAUCCUGUC
AACY020117009.1/1236-1293    GGGUGAAUUGAAGUCUGGAUACUGUAGGGGC--CGAUUCCGUUUC-GGGGUCGGUCCUGUC
AACY020528150.1/1029-972     GGGUGAGGUUCGGUCUGGAUACUGUAGGGGCCAUGGCCCGGAA---CGGGUCGAACCUGUC
AACY020639821.1/275-332      GGGUGGUUUGAAGUCUCGAUACUGUAGGGGC--CGACUCCGGUUC-GGGGUUGAUCCUGUC
AACY020241192.1/1261-1319    GGGUGAAGUUCAGUCCCGAUACUGUAGGGGUCCCGGCCCU-GAUC-AGGGCCGAUCCUGUC
AACY020530644.1/2012-2069    GGGUGAGGUUCAGUCUGGAUACUGUAGGGGCCACGGCCCGGAA---CGGGUCGAACCUGUC
AACY021272084.1/482-540      GGGUGAAGUUCAGUUCCGAUACUGUAAGGGUCCCGGCCCU-GAAG-AGGGCCGAUCCUGUC
AACY023423749.1/759-702      GGGUGGUUUGAAGUCUCGAUACUGUAGGGGC--CGACUCCGAUUC-GGGGUUGAUCCUGUC
AACY021984717.1/346-289      GGGUGAGGUUCAGUCUGGAUACUGUAGGGGCCAUGGCCCGGAA---CGGGUCGAACCUGUC
AACY024047947.1/76-19        GGGUGAGGUUCGGUCUGGAUACUGUAGGGGCCAUGGCCCGGAA---CGGGUCGAACCUGUC
AAUA01000004.1/95600-95543   GGUUCAGGUUCGGUCUGGAUACUGUAGGGGUCCUGGUCC-UGAUA--AGGCCGAACCUGUC
AACY021843345.1/466-523      GGGUGGUUUGAAGUCUCGAUACUGUAGGGGC--CGACUCCGGUUC-GGGGUUGAUCCUGUC
AACY021883368.1/186-243      GGGUGGUUUGAAGUCUCGAUACUGUAGGGGU--CGACUCCAGUUC-GGAGUUGAUCCUGUC
AANP01000005.1/188511-188568 GGGUGAGGUUCAGUCUGGAUACUGUAGGGGCCAUGGCCCGGAA---CGGGUCGAACCUGUC
AACY020532422.1/4804-4747    GGGUGAGGUUCAGUCUGGAUACUGUAGGGGCCACGGCCCGGAA---CGGGUCGAACCUGUC
#=GC SS_cons                 ::::::::::::::::::::::::::<<<<<--<<<<<<<_____.>>>>>>>>>>>>:::
#=GC RF                      GGGUGaauUuAAGUCUgGAUACUGUAGGGGuCaCggCCCcGgaUc.gGGGccGaUCCUGUC
//
# STOCKHOLM 1.0

#=GF AC   RF01754
#=GF ID   radC
#=GF DE   radC RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   42.50
#=GF NC   39.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   RadC_RNA_motif
#=GF SQ   130


AF440523.1/104338-104193       AUGCUGGCCCCAUG-C---CUGCUGACGUC-GUCAGC--GACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-GGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCUU--CCGCGAGCGGCC-ACCAG---CCU----CUGGU-GGCGGAUGC
AAUJ02000001.1/68610-68462     CCACAUCGGAAAUG-C---CUGCCGACGUC-GUCGGC--GACAUGCCC--AGGUAGCCC-CGGUCUUCAAGGCUAC-GGCGCAG---UCCG------CUGCGCU--GAC--CACA------ACCCCGUUCGC----CUC-GCAUCC-UGGCCGCGAACGAUC-ACCGC---UGCC---GCGGU-GAUGGAUGC
AE008923.1/2619655-2619805     ACGCUCACCGCAUG-C---CUGCCGAAAGAUUUCGGC--GACAUGC-C--AGGCAACCUCCGGUCUUCGAGGUUGC--GCGCGG---CCCGCAAA--CUGCGU---GAC--CGAA-------CCAGUUCGCU-----UC-GCAUCC-UUCGCGCGAACGGCC-GCCGG---UUUUC--CCGGU-GGCGGAUGC
CP000712.1/3312138-3312275     UGAGCUGCAC-----A---CCGCUGUCGUU-GACAGC--A-----CCC--AGGUAGCCA-GGACCUUCAAGGCUAC--GCCCG----UUU--------CGGGUG--GUU--CUCC------CCCAAAGUGCG----ACUCGCGCUCGGCAGCUCGCACGGUC-ACCGU---CCCA---UCGGU-GAUGAGCGC
CP001281.2/1090214-1090069     AUCCUCACGCCAUGCG---UUGCUGAAAGUCGUCAGC--GGCAUGCCC--UGGCAGUCU-CGGUCUUCAAGACUGC-AACGCGG---UUCG------CCGCGUC--GAC--CGAU-------CCAGUCCGCU-----UC-GCAUCGCCCACCGCGGACGCUC-GCCGG---C------CUGGC-GACGA-UGC
CP000050.1/2470043-2469891     AUCCUUUCCCCAUG-U---UCGUCGGCGUU-GCCGAC--A-CAUGCCC--AGGCAGCCG-AGACCUUCAAGGCUGCAAGUGCGG---GAAA------CCGCACA--GGU--CGUUUCAU--UCCAAGGACGC----GUCCGCGUCCAUCAACGCCACCCACA-AGGGA---CCUC---UCCCU-UGCG--GGC
CP000949.1/3637927-3638064     UGAGCUGCAC-----A---CCGCUGUCGUU-GACAGC--A-----CCC--AGGUAGCCA-GGACCUUCAAGGCUAC--GCCCG----UUU--------CGGGUG--GUU--CUCC------CCCAAAGUGCG----ACUCGCGCUCGGCAGCUCGCACGGUC-ACCGU---CCCA---UCGGU-GAUGAGCGC
CP001281.2/1081156-1081001     AGGCUGACGCCUUGCC---CCGCCGACUGACGUCGGC--AGCAC-CCC--AGGCAGCCA-AGAUCUUCAAGGCUGC-GGCGCGA---UCCG------UCGCGCU--GGU--CGUU-----GUCCUGCUCGACGCCUCGGCGCGUCA-CUUCCUCAACCCUCA-AGGGA---UUUCC--UCCCU-UGCAG-GGC
CP000555.1/2516445-2516590     AGCUCACCCUCAUGCG---UUGCUGACCGUCGUCAGC--GGCAUGCCC--UGGCAGUCU-CGGUCUUCAAGACUGC-AACGCGG---UUCG------CCGCGUU--GAC--CGAU-------CCAGUCCGCU-----UC-GCAUCGCCCACCGCGGACGCUC-GCCGG---C------CUGGC-GACGA-UGC
CP001339.1/2976117-2976263     GGCUACUUCCCAUG-U---CCGUCGGCGUU-GCCGAC--AACAUGCCC--AGGUAGCCA-AGACCUUCAAGGCUAC-GGUGCGU---UGCG------ACGCACU--GGU--UGUU------CUCUUUGCCAA----GAC-GCUCACGG--GCGUUCCCUUCC-AUCCC---CUU----GGGGC-AGUGACUGC
CP000050.1/2466860-2466713     AUGCUGCCCCCAUG-C---CUGCUGACGUU-GUCAGC--AACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-GGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCAU--CUGCGAGCGACC-ACCGG---CCUGU--CCGGU-GGCGGAUGC
CP001339.1/3002033-3002179     AGAUACCCGAGAUG-C---CUGCUGACAAC-GUCAGC--GACAUGCCC--AGGUAGCCG-CGAUCUUCAAGGCUGC-GGCGCGGU--UUCG-----ACCGCGUU--GAU--CGUU-------CCAGUUCGCA-----CC-GCAUCC-CACGCGCGAACAUCC-AUCGU---UU-----UCGAU-GGAGGAUGC
AE003849.1/1689983-1689846     AUUCUCCCUCC-UGCA---UUGCCGAUGU--AUCGGC--AGCA-GCCC----GCAGCCA--GGGUGUCAAGGCUGC-CGCGGG----UUCCA------CCCGUGCCACC--CA---------CCAGUUCGCC-----UCGGCAUCU-CACCGGCGAACGCUG-CCC-----ACCG-----GGG-CAUCGAUGC
AE008923.1/2605044-2605188     UUGCGCCUCC---GAU---UCGCCG--U-----CGGCAUUUC---CCC--A-GCAGCCA-UGACCUACCAGGCUGC-GGUGCGG---CUCG------CCGCACA--GGU--CAUC-------CCUCAUCGGGCGCGUCCUGCGUCCUUCCACGCCAACCCAC-AAGGGAUCUUCCU--CCCUU-GCG---GGC
AM039952.1/2727007-2726872     AAGCUGCCCGCAUG-U---UCGCUGAU-UC-GUCAGC--A-CAUGCCA----GCAGCCA--GGG-UUCCAGGCUGC-CGCGGG----UCUCU------CCCGCGU-UGC--CCA--------CCAGUCCGCA-----UC-GCAUCA-GGUCUGCGGACGCGC-GUCCC---C------GUGAC-GUCGA-UGC
AAKW01000073.1/72757-72610     AUGAUGAGCGCGUGAU---CUGCUGACGUU-GUCAGC--GACAUGCCCC-AUGCAGCUC-GGAUCCGAAGUGCUGC-AGCAC-----AGCCCAGC----GUGUU--GAU--CCAA------CCCAAGACCGU-----AUAGCUUCUGGUAGCACGGUCGGUC-GGCCU----------CGGUC-GAUAGAAGC
FM209186.1/2848562-2848414     CCACAUCCGAAAUG-C---CUGCCGACGUU-GUCGGC--GACAUGCCC--AGGUAGCCCUCGGUCUUGAAGGCUAC-GGCGCGG---CUCG------CCGCGCU--GAC--CGCU------ACCCGUUCGCU----UUC-GCAUCC-UGGCCGCGAACAAUC-ACCGC---CGC----GCGGU-GAUGGAUGC
CP000075.1/1658497-1658347     AUUCUCAAGACAUGUA---CCGCUGACGUU-GUCAGC--AACAUGCCC--GGGUAGUCA-GGAUC-UCACGACUAC-GAUGCG----UCCCA------CGCAUU--GAU--CCCU------CCCAAAGUUCG----CAAAGCUUCCGGAGGCGCGAACGAUC-GGUGU---UUCAA--ACGCC-GAUGGAUGC
CP000512.1/531393-531251       CUAUCGACCGCAGGUC---GCGGAGGACUUCUCCUCC-----CUUCCC--AGGCAGCCA-UGAUCUUCAAGGCUGC-GGCGC-----GCUG--------GCGCC--GAU--CACA-------CCAGUCCGCU-----CC-GCAUCCGAAACGGUGGACGCCC-AGCGC---GAAA---GCGCU-GGUGGAUGC
CP000270.1/3604961-3605108     CUACCGCCGAAAUG-C---CUGCCGACGUU-GUCGGC--GACAUGCCC--AGGUAGUCCUCGGUCUUCAAGGCUAC-GGCGCGG---UUGC------CCGCGCU--GAC--CGAU------ACCCGUUCGCU-----CC-GCAUCC-UGGCCGCGAACAAUC-ACCGC---UGC----GCGGU-GGUGGAUGC
AAQW01000001.1/6030570-6030704 GGGAGUCGCA-----A---GAGCUGUCGAU-GACAGC--A-----CCC--AGGUGGCCC-GAACCUUAAAGGUCAC-GCCGC-----UCCC--------GCGGU--GGU--UCACCC----GCAAGUACGAU-----UC-GCGUCCGGCAGCUCGUACGGUC-AC---UACCCAU------GU-GAUGGAUGC
CP000774.1/3635395-3635546     AUUCUUGCCCCAUG-U---UCGUCGGCGUU-CCCGAC--A-CAUGCCC--AGGCAGCCA-AGACCUUCAAGGCUGCAAGCACGG---GAAG------CCGUGCU--GGU--CGAUGUUU--UCCACGGACGU----ACC-GCGUCCAUCCACACCACCCACA-AGGGA---CCUC---UCCCU-UGCG--GGC
CP000539.1/1499393-1499248     UCCUUGCGCC-AUGU----UCGUCGGCGUU-GCCGAC---ACAUGCCC--AGGCAGCCG-AGACCUUCGAGGCUGCAAGCGCGG---GAAA------CCGUGCU--GGU--CGUU------UCUUCCUACGG-----AC-GCUCCGCGUCCAUCCACCCACA-AGGGA---CCUC---UCCCU-UGCG--GGC
ABFH02000001.1/1099005-1098868 AUUCUCCCUCC-UGCA---UUGCCGACGUA--UCGGC--AGCA-GCCC----GCAGCCA--GGGUGUCAAGGCUGC-CGUGGG----UUCCC------CCCGCGCCACC--CG---------CCAGUUCGCC-----UCGGCAUCU-CACCGGCGAACGCUG-CCC-----ACCG-----GGG-CAUCGAUGC
CP000438.1/5292565-5292700     --AAUUCGAA-UUGGC---UCGCUGUCGUU-GACAGC--GCC--UCCC--AAGGAGCCA-GGGUU--UAAGGCUCC-GGCGC-----GCAA--------GCGCU--AAC--CCAC------CCAAGACCGCC-----ACAGCACUCGGCAGCGCGGUCG--C-AUCAC---GCAA---GUGAU-GGAG--UGC
AAHW02000025.1/23298-23445     AUGUUUAUUCCGUACG---CGGUCGAUCUU--UCGAC--CU-GUGCCC--AGGCAGCCGAUGGUCUUCAAGGCUGC-GCUGCGU---GUCA------UCGCAGU--GAC--UCAUCG-----CCAGUCCGCU-----UC-GCAUCGCUUGCCGCGGACGCUC-AUCCG---CAC----CGGAU-GACGA-UGC
AM902716.1/1370935-1371077     AGUCUUGCGGCAUGUG---UUGCUGAUCCCGAUCAGC--ACCAUGCCA----GCAGCCA--GGUCUUCA-GGCUGC-GCCGUGG---AACGA-----CCACGUA--GAC--CGAU-------CCAGUCCGCU-----UC-GCAUCG-UUUUCGCGGACGCAC-GCC--ACAGCC------GGC-GUCGA-UGC
ABBN01001396.1/97405-97260     GGCUCAAGACCAUGUU---CCGCUGAC-UC-GUCAGC--AACAUGCCC--AGGUAGCCA-UGAUCUUCAAGGCUAC-GGCGCGGUG-UUCU----CACCACGUU--GAU--CG---------CCCGUUCACA----UAAGGCAUCCAU---GGCGAACAUCC-AUCAG---CC-----CUGAU-GGAGA-UGC
AM902716.1/1375792-1375941     ACGCUACCGCCAUGUU---GCGCUGACUCCGGUCAGC--AACAUGCCC--AGGUAGCCA-CGGUCUUCAAGGCUAC-GACGCGG--UUCCGU-----CCGCGU---GAU--CACA-------CCAGUUCGCA----CUCGGCAUCCCA--GCGCGAACGACC-GUCGA---GCAA---UCGAC-GGUGA-UGC
CP000539.1/2364053-2363900     ACGCUGGCCGCAUG-U---UCGCUGGCGUU-GCCGGC--AGCAUGCCC--AGGCAGUCG-AGACCUUCAAGACUGC-GGCGCGG---UUCG------CCGUGCU--GGU--UGCU------UCGUUCUCCGGGCGCACCCGCGUCCAUCCACCUCACCCUCA-AGGGAC--AGACC--UCCCU-UGC---GGG
AE003849.1/1678879-1678735     AUGCUACCCCCAUG-C---CUGCUGACGUU-GUCAGC--GACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-CGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCAU--CCGCGAGCGGCC-ACCAG---UC-----CUGGU-GGCGGAUGC
CP000076.1/5411071-5411217     AUUAUUGAACCGUGAU---CUGCUGACGUC-GUCAGC--AACAUGCCCC-AUGCAGCUC-GGAUCCGUAACGCUGC-AGCACG----UUAAU------CGUGU---GAU--CCUC------CUCAAGGUCGU-----UCAGCUUCUGGUAGCACGACCGGUC-GAC-----UAUCC----GUC-GAUAGAAGC
CP000270.1/3572546-3572683     AUUCUUCCUCC-UGCA---UUGCCGACGU--GUCGGC--AGCA-GCCA----GCAGCCG--GGGUGUCCAGGCUGC-CGUGGG----UUCUA------CCCGCGCCACC--CA---------CCAGUUCGCC-----UCGGCAUCU-CACCGGCGAACGCUG-CCC-----ACCG-----GGG-CAUCGAUGC
CP000539.1/1332744-1332597     CCACAUCGGAAAUG-C---CUGCCGACGUU-GUCGGC--GACAUGCCC--AGGUAGCCC-CGGUCUUCAAGGCUAC-GGCGCAG---UCCA------CUGCGCU--GAC--CGAA------ACCCGUUCGCC-----UC-GCAUCC-UGGCCGCGAACGGUC-ACUGC---AAUC---GCGGU-GAUGGAUGC
AAUJ02000001.1/104590-104445   AUGCUGACCCCAUG-C---CUGCUGACGUU-GUCAGC--GACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-GGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCAU--CCGCGAGCGGCC-ACCAG---CCU----CUGGU-GGCGGAUGC
CP000555.1/2560890-2561040     AUUCCCCAGACAUG-C---CCGCCGGCGUU-GCCGGU--GACAUGCCC--AGGUAGCCAUCGAUCUUCAAGGCUGC-GGCGCGG---CUCGU-----CCGCGUU--GAU--CGAA------ACCCGUUCGCA-----UC-GCAUCCCUUGACGCGAACGGCC-ACCGC---AUCC---GCGGU-GGUGGAUGC
AM902716.1/4524050-4523902     CCACUACGGAAAUG-C---CUGCCGACGUC-GUCGGC--GACAUGCCC--AGGUAGCCCGCGGUCAUUGAGGCUAC-GGCGCAG---CACG------CUGCGCU--GAC--CGCU------ACCCGUUCGCC-----CC-GCAUCC-UGGCCGCGAACGAUC-ACCGC---UGCU---GCGGU-GAUGGAUGC
CU207211.1/1993906-1994045     AAGCUGCCUGCAUGUG---UCGCUGA-UCCG-UCAGC--ACCAUGCCA----GCAGCCA--GGGUUUCCAGGCUGC---CGCGGA--UUCUC----UCCGCG--CCACC--CG---------CCAGUCCGCC----AUC-GCAUCG-AGUCUGCGGACGCGC-GUC--CUCGU-------GAC-GCCGA-UGC
AE003849.1/1681828-1681680     UCCUGCCCCCCAUG-U---UCGUCGGCGUU-GCCGAC--A-CAUGCCC--AGGCAGCCG-AGACCUUCGAGGCUGCAAGCACGG---GAAG------CCGUGCU--GGU--CGUU------UCUUCCUAUGG-----AC-GCACCGCGUCCAUCCACCCACA-AGGGA---CCUC---UCCCU-UGCGGGCGG
CP000270.1/3576431-3576582     AUCCUUGCCCCAUG-U---UCGUCGGCGUU-GCCGAC--A-CAUGCCC--AGACAGCCG-AGACCUUCAAGGCUGCAAGUGCGG---GAAA------CCGUGCU--GGU--CUUU-------UUUCUUAUCGGACGUUCCGCGUCCAUCCACGCCACCCACA-AGGGA---UCUC---UCCCU-UGCG--GGC
AE008923.1/2603319-2603458     AUGCUGCGCGCAUGUG---UUGCUGACGUC-GUCAGC--GCCAUGCCA----GCAGCCG-GGAUCCCUG-GGCUGC-CGCGGGA---UACG------UCCCGCGC-GAU--CCA--------CCAGUCCGCU-----UC-GCAUCGGU--CCGCGGACGAGC-GCC-----UUUCU----GGC-GCCGA-UGC
CP000438.1/5288768-5288916     AUGAUGAACGCGUGAU---CUGCUGACGUU-GUCAGC--GACAUGCCCCCAUGCAGCUC-GGAUCCGAAAUGCUGC-AGCACAG---CCCA------CCGUGUU--GAU--CCAA------CCCAAGACCGC----AUA-GCUUCUGGUAGCGC----GGUC-GGUCG---GCCU---CGGUC-GAUAGAAGC
CP000774.1/3637020-3637165     AUGCUGACCCCAUG-C---CUGCUGACGCU-GUCAGC--GACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-GGCGCAGU--UUCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCAU--CCGCGAGCGGCC-ACCAG---UCC----CUGGU-GGCGGAUGC
AM902716.1/1148088-1148234     CCACAUCGAAAAUG-C---CUGCCGACGUC-GUCGGC--GACAUGCCC--AGGUAGCCC-CGGUCUUCAAGGCUAC-GGCGCAG---UCCG------CUGCGCU--GAC--CGCA------ACCGUUCGCC------UC-GCAUCC-UGGUCGCGAACGAUC-ACCGC---UGCC---GCGGU-GGUGGAUGC
AM039952.1/2618952-2618813     AAGCUGCCCGCAUGUG---UCGCUGA-UCCG-UCAGC--ACCAUGCCA----GCAGCCA--GGGUUUCCAGGCUGC-CGCGGAG---UUU-------CUCCGCGCUACC--CG---------CCAGUCCGCC----AUC-GCAUCG-AGUCUGCGGACGCGC-GUC--CUCGU-------GAU-GCCGG-UGC
AAQW01000001.1/3510184-3510323 AAGCUGCCUGCAUGUG---UCGCUGA-UCCG-UCAGC--ACCAUGCCA----GCAGCCA--GGGUUUCCAGGCUGC---CGCGGA--UUCUC----UCCGCG--CCACC--CG---------CCAGUCCGCC----AUC-GCAUCG-AGUCUGCGGACGCGC-GUC--CUCGU-------GAC-GCCGA-UGC
CP000076.1/5414185-5414317     --AUUCCGGA-UUGGU---UCGCUGUCGUC-GACAGC--GCC--UCCA--AAGGAGC--CAGGGUUUCAA-GCUCC-GGCG------CGUCG--------CGCU--AAC--CCAC------CCAAGAUCGCU-----UA-GCACUCGGUAGCGCGAUCA--C-AUCAC---CUA----GUGAU-GGAG--UGC
AM920689.1/2821286-2821433     AUGCUGCCCCCAUG-C---CUGCUGACGUU-GUCAGC--AACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-GGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCAU--CUGCGAGCGACC-ACCGG---CCUGU--UCGGU-GGCGGAUGC
AM039952.1/2722273-2722129     AUGCUGACCCCAUG-C---CUGCUGACGUU-GUCAGC--GACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-CGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCAU--CCGCGAGCGGCC-ACCAG---UC-----CUGGU-GGCGGAUGC
CP001281.2/1079638-1079490     CGCUUCCGGCCAUGUU---CCGCUGACGUCCGUCAGC--GACAUGCCC--AGGCAGCCA-CGAUCUUCAAGGCUGC-GACGCGGU--UCCG-----ACCGCGUU--GAU--CACC-------CCAGUUCGCA-----CCGGCAUCCAU--GCGCGAACGGCC-AUCGG---UUC----UCGAU-GGCGA-UGC
AY273869.1/67627-67492         --AAUUCGAA-UUGGC---UCGCUGUCGUU-GACAGC--GCC--UCCC--AAGGAGCCA-GGGUU--UAAGGCUCC-GGCGC-----GCAA--------GCGCU--AAC--CCAC------CCAAGACCGCC-----ACAGCACUCGGCAGCGCGGUCG--C-AUCAC---GCAA---GUGAU-GGAG--UGC
CU207211.1/1996181-1996326     AUGCUGACCCCAUG-C---CUGCUGACGUU-GUCAGC--GACAUGC-C--AGGCAAUCAUCGGUCUUCGAGGUUGC-GGCGCAGU--UUCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCAU--ACGCGAGCGGCC-ACCAG---UCU----CUGGU-GGUGGAUGC
AAKV01000112.1/75975-75825     UUCUUUGCACCGUGAG---CUGCUGACGUU-GUCGGCA-AUCCUCCCC--CAGUAGUCA-UGAUCUGAAAGACUAC-GACACGG---AUUU------CCGUGUA--GAU--CGAA------CCCAAGAUCGC----ACCAGCUUCCGGUAGCGCGAUCAAUC-AGCCC---AC-----AGGUU-GAUGGAAGC
AM039952.1/2602146-2601999     AUGCUGCCCCCAUG-C---CUGCUGACGUU-GUCAGC--AACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-GGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGUUCGCA-----CC-GCAUCCAU--CUGCGAGCGACC-ACCGG---CCUGU--UCGGU-GGCGGAUGC
AE008923.1/2668338-2668489     AUCCUGCGGCGCAG-GCAGCGGGGACGUUUGCGUCUC--CACUUCCCA--GCACAGCCG-CGGUCUUCGAGGCUGU-GGCGCGG---GCCA------CCGCGUC--GAU--CGCU-------CCCGUCCGCA-----CC-GCAUCCGACACCGCGGACGCCC-AGCGC---CCAG---GCGCU-GGAGGAUGC
CP000539.1/1497620-1497476     AUGCUGACCCCAUG-C---CUGCUGACGUU-GUCAGC--GACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-CGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCAU--CCGCGAGCGGCC-ACCAG---UC-----CUGGU-GGCGGAUGC
AM902716.1/1519640-1519785     AUGCUGCCCCCAUG-C---CUGCUGACGUU-GUCAGC--GACAUGC-C--AGGCAACCAUCGGUCAUCGAGGUUGC-GGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCGU--CCGCGAGCGGCC-ACCAG---UCU----CUGGU-GGCGGAUGC
AAQW01000001.1/962101-961954   AUGAUGAGCGCGUGAU---CUGCUGACGUU-GUCAGC--GACAUGCCCC-AUGCAGCUC-GGAUCCGAAGUGCUGC-AGCACAG---CCCA------CCGUGUU--GAU--CCAA------CCCAAGACCGC-----AUAGCUUCUGGUAGCGCGGUCGGUC-GGCCU----------CGGUC-GAUAGAAGC
CP000539.1/1463970-1463823     CCACAUCCGAAAUG-C---CUGCCGACGUU-GUCGGC--GACAUGCCC--AGGUAGCCC-CGGUCUUCAAGGCUAC-GGCGCAG---UCCA------CUGCGCU--GAC--CGAA------ACCCGUUCGCC-----UC-GCAUCC-UGGCCGCGAACGGUC-ACUGC---AAUC---GCGGU-GAUGGAUGC
AAKW01000063.1/23023-22892     AGAUGCAAGCGCUGCU-----------GA----------GGCAGCCGA--AUGUGGCCAGAAACCUGAAAGGUCAC-GCCGC-----AACC--------GCGGU--GGU--UCAACC----CCCAAGUACGA----UUC-GCAUCCGGCAGCUCGUACGGUC-AC---UACCCAU------GU-GAUGGAUGC
EF611301.1/64524-64375         UCCUUUACCCCGUGAG---CUGCUGACGUU-GUCGGCA-ACCCUCCCC--CAGUAGUCA-UGAUCUGAAAGACUAC-GACACGG---ACUU------CCGUGUA--GAU--CGAA------CCCAAGAUCGC----ACCAGCUUCCGGUAGCGCGAUCAAUC-AACCA---C------AGGUU-GAUGGAAGC
AF440523.1/73006-72859         CCACAUCGGAAAUG-C---CUGCCGACGUC-GUCGGC--GACAUGCCC--AGGUAGCCC-CGGUCUUCAAGGCUAC-GGCGCAG---UCCG------CUGCGCU--GAC--CGCA------ACCCGUUCGCC-----UC-GCAUCC-UGGCCGCGAACGAUC-ACCGC---CACC---GCGGU-GAUGGAUGC
CR555306.1/1513825-1513675     AUUCCCCAGAUAUG-C---CCGCCGGCGUU-GCCGGU--GACAUGCCC--AGGUAGCCAUCGAUCUUCAAGGCUGC-GGCGCGG---CUUGU-----CCGCGUU--GAU--CGAC------ACCCGUUCGCA-----UC-GCAUCCCUUGACGCGAACAGCC-ACUGC---AUCC---GCGGU-GGUGGAUGC
CP000949.1/5450160-5450296     CGGGAGUCGC----AA---GAGCUGUCGAU-GACAGC--AC----CCC--AGGUGACCC-GAACCUUGGAGGUCAC-GCCGC-----UCCC--------GCGGU--GGU--UCACCC----GCAAGUACGAU-----UC-GCGUCCGGCAGCUCGUACGGUC-AC---UACCCAU------GU-GAUGGAUGC
CP000744.1/4614401-4614549     AUGAUGAACGCGUGAU---CUGCUGACGUU-GUCAGC--GACAUGCCCCCAUGCAGCUC-GGAUCCGAAAUGCUGC-AGCACAG---CCCA------CCGUGUU--GAU--CCAA------CCCAAGACCGC----AUA-GCUUCUGGUAGCGC----GGUC-GGUCG---GCCU---CGGUC-GAUAGAAGC
CP000050.1/2444672-2444524     CCACCACCGAAAUG-C---CUGCCGACGUU-GUCGGC--GACAUGCCC--AGGUAGCCUGCGGUCCUUGAGGCUAC-GGCGCAG---CCCG------CUGCGCU--GAC--CGCU------ACCCGUUCGCC-----UC-GCAUCC-UGGCCGCGAACGAUC-ACCGC---AGCC---GCGGU-GGUGGAUGC
CP000539.1/2362535-2362387     CGCUUCCGCCCAUGUU---CCGCUGACGUCCGUCAGC--GACAUGCCC--AGGCAGCCA-CGAUCUUCAAGGCUGC-GAUGCGGU--UCCG-----ACCGCGUU--GAU--CACC-------CCAGUUCGCA-----CCGGCAUCCAU--GCGCGAACGGCC-AUCGG---UUC----UCGAU-GGCGA-UGC
AY257538.1/44287-44422         --AAUUCGAA-UUGGC---UCGCUGUCGUU-GACAGC--GCC--UCCC--AAGGAGCCA-GGGUU--UAAGGCUCC-GGCGC-----GCAA--------GCGCU--AAC--CCAC------CCAAGACCGCC-----ACAGCACUCGGCAGCGCGGUCG--C-AUCAC---GCAA---GUGAU-GGAG--UGC
CP000450.1/107737-107590       ACCCUUACCCCAUG-A---UUGCUGACGUU-GUCAGC--GACAUGC-C--GGGCAACCAUUGGUCUUUAAGGUUGC-GGCGCGAC--ACCU-----GCCGCGU---GAC--CACA-------CCAGUUCGCA-----CC-GCAUCCAC--GCGCGAACGACU-GCCAG---UUUUU-UCUGGU-GGUGA-UGC
AM902716.1/1116746-1116892     AUGCUUGCCCCAUG-U---UCGUCGGCGUU-GCCGGC--A-CAUGCCC--AGGCAGUCG-AGACCUUCGAGGCUGCAAGCGCGG---GAAG------CCGCGCU--GGU--CGUU------UCUUCCUCCGG-----AC-GUACCGCGUCCAUCCACCCACA-AGGGA---CCUU---UCCCU-UGCG--GGA
AM039952.1/2724046-2723901     UCCUUGCGCC-AUGU----UCGUCGGCGUU-GCCGAC---ACAUGCCC--AGGCAGCCG-AGACCUUCGAGGCUGCAAGCGCGG---GAAA------CCGUGCU--GGU--CGUU------UCUUCCUACGG-----AC-GCUCCGCGUCCAUCCACCCACA-AGGGA---CCUC---UCCCU-UGCG--GGC
CP000512.1/593292-593146       ACGCUCCACGCAUG-C---CUGCUGACUGAAGUCAGC--GACAUGC-C--AGGCAACCUUUGGUCUUCGAGGUUGC--GCGCAGCC-GCCA----GGCUGCGU---GAC--CGAG-------CCAGUUCGCA-----UC-GCAUCCUC--GCGCGAACGGCC-ACUGG---ACC----CCGGU-GGCGA-UGC
CP000712.1/5156415-5156550     ---AAGGUUC------AAAGCGCUGCCUUA-GGCAGCAC------CCC--AGAUGACCA-GAGCCUUCAAGGUCAU-GCCGC-----UAAC--------CCGGU--GGU--UCAU------CCCAAAGUGCG----AUUCGCGCCCGGAGGCUCGCACGGUC-AUUCG---CC-----AGAAU-GAUGGACGC
AM039952.1/2727905-2727768     AUUCUCCCUCC-UGCA---UUGCCGAUGGU--UCGGC--AGCA-GCCC----GCAGCCA-GGGUG-UCAAGGCUGC-CGCGGG----UUCCA------CCCGCGC-CAC--CCA--------CCAGUUCGCC-----UCGGCAUCU-CACCGGCGAACGCUG-CCC-----ACCG-----GGG-CAUCGAUGC
CP000539.1/2365997-2365852     AUCCUCACGCCAUGCG---UUGCUGACAGUCGUCAGC--GGCAUGCCC--UGGCAGUCU-CGGUCUUCAAGACUGC-AACGCGG---UUCG------CCGCGUC--GAC--CGAU-------CCAGUCCGCU-----UC-GCAUCGCCCACCGCGGACGCUC-GCCGG---C------CUGGC-GACGA-UGC
CR555306.1/1470276-1470128     CGCUUCCUGCCAUGUU---CCGCUGACUCCCGUCAGC--AGCAUGCCC--AGGUAGCCA-CGAUCUUCAAGGCUAC-GACGCGGU--UCCG-----ACCGCGUU--GAU--CACC-------CCAGUUCGCA-----CCGGCAUCCAC--GCUCGAACGCCC-AUCGG---UUU----CCGAU-GGCGA-UGC
AAKW01000073.1/71679-71530     UCCUUUACCCCGUGAG---CUGCUGACGUU-GUCGGCA-ACCCUCCCC--CAGUAGUCA-UGAUCUGAAAGACUAC-GACACGG---ACUU------CCGUGUA--GAU--CGAA------CCCAAGAUCGC----ACCAGCUUCCGGUAGCGCGAUCAAUC-AACCA---C------AGGUU-GAUGGAAGC
AAUJ02000001.1/106760-106609   AUGCUUACCCCAUG-U---CCGUCGGCGCU-GCCGAC--A-CAUGCCC--AGGCAGUCG-AGACCUUCGAGGCUGCAAGCACGG---GAAA------CCGUGCU--GGU--CGUUUCUU--CCUACGGACCU----ACC-GCGUCCAUCCACGCCACCCACA-AGGGA---CCUC---UCCCU-UGCG--GGC
CP001339.1/2968251-2968397     ACCUACACCCCAUG-C---GCGCUGACCUCCGUCAGC--ACCAUGCCC--AGGCAGCUU-CGGUCUUCAAAGCUGC-GGCGCGG---UUCUU-----CCGCGUU--GAC--CGAU-------CCAGUCCGCU-----UC-GCAUCG-CUCCUGCGGACGAUC-GCCAU---GUC----CUGGC-GACGA-UGC
AAKV01000112.1/77053-76905     AUGAUGAACGAGUGAU---CUGCUGACGUU-GUCAGC--GACAUGCCCCCAUGCAGCUC-GGAUCCGAAAUGCUGC-AGCACAG---CCCA------CCGUGUU--GAU--CCAA------CCCAAGACCGC-----AUAGCUUCUGGUAGCGCGGUCGGUC-GGCCU----------CGGUC-GAUAGAAGC
AM902716.1/1113738-1113874     AAGCUGUCCGCGUG-U---UCGCUGAU-UC-GUCAGC--A-CAUGCCA----GCAGCCA--GGGUUUCA-GGCUGC-CGCGGGG---UUCU------CUCCGCGCAACC--CA---------CCAGUCCGCA-----UC-GCAUCC-AUUGCGCGGACGCGC-GUU-----CCCAA----GAC-GCUGA-UGC
CP000352.1/2536533-2536678     AUGCUGGCCCCAUG-C---CUGCUGACGUC-GUCAGC--GACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-GGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCUU--CCGCGAGCGGCC-ACCAG---CCU----CUGGU-GGCGGAUGC
CP000884.1/4572348-4572496     CCACUACGGAAAUG-C---CUGCCGACGUC-GUCGGC--GACAUGCCC--AGGUAGCCCGCGGUCAUUGAGGCUAC-GGCGCAG---CACG------CUGCGCU--GAC--CGCU------ACCCGUUCGCC-----CC-GCAUCC-UGGCCGCGAACGAUC-ACCGC---UGCU---GCGGU-GAUGGAUGC
CP000744.1/4617910-4618045     --AAUUCGAA-UUGGC---UCGCUGUCGUU-GACAGC--GCC--UCCC--AAGGAGCCA-GGGUU--UAAGGCUCC-GGCGC-----GCAA--------GCGCU--AAC--CCAC------CCAAGACCGCC-----ACAGCACUCGGCAGCGCGGUCG--C-AUCAC---GCAA---GUGAU-GGAG--UGC
CP001616.1/2634709-2634843     UGGCAUCCGC--UG-----UUGCCGACAUU-GUCGGC--UUCG--CCA----GCAGCCA--G-GGUUUCAGGCUGC-CGUGGAG---CUUG------CUCCAUG--CCA--CCCG-------CCAGUUCGCC----GUC-GCAUCG-CUCGGGCGAACGCUG-CCC--AUGC--------GGG-CAUCGAUGC
CP000774.1/3633128-3633268     AAGCUGCCCGCAUGUG---UCGCUGAU-UC-GUCAGC--ACCAUGCCA----GCAGCCA--GAGUUUCCAGGCUGC---CGCGGA--UUCUU----UCCGCG--CUACC--CG---------CCAGUCCGCC----AUC-GCAUCG-AGUCUGCGGACGCGC-GUCAC---CC-----GUGAC-GCCGA-UGC
CU207211.1/2030494-2030641     CCGCCACCGAAAUG-C---CUGCCGACGUU-GUCGGC--GACAUGCCC--AGGUAGCCCGCGGUCCUUGAGGCUAC-GGCGCAG---UCUU------CUGCGCU--GAC--CGCU------CCCCGUUCGCU-----CC-GCAUCC-UGGCCGCGAACAAUC-ACCUC---UGC----GUGGU-GGUGGAUGC
AAMM02000010.1/119452-119305   ACGCUUGGCCCAUGUU---CCGCUG-CUCC-GUCAGC--GACAUGCCC--AGGUCUCCA-CGAUCUUCAAGGCGAC-GCCGGAG---GUUUCCA---CUCCGUU--GAU--CGAU-------CCCGUUCGCU----UUCGGCAUCCAC--GCGCGAACGACC-AUCGG---UU-----UCGAU-GGUGA-UGC
CP000539.1/1502364-1502228     AAGCUGUCCGCAUG-U---UCGCUGAU-UC-GUCAGC--A-CAUGCCA----GCAGCCA--GGGUUUCA-GGCUGC-CGCGGGG---UUCU------CUCCGCGCAACC--CA---------CCAGUCCGCA-----UC-GCAUCC-AUUGCGCGGACGCGC-GUC-----CCCAA----GAC-GCUGA-UGC
ABBN01001396.1/102254-102109   AUGGUGCGUCCGUA-C---AUGGUCGAUCCCUCGACC--G--GUGCCC--AGGCAGCCGAUGGUCUUCAAGGCUGC-GCUGCGA---GUCA------UCGCAGU--GAC--UGCG-------CCAGUCCGCU-----UC-GCAUCGCUCGCCGCGGACGCUC-AUCCC---CAC----CGGAU-GACGA-UGC
CR555306.1/1477955-1477810     AUGCUGCUGCCAUGCG---CUGCUGACAGCCGUCAGC--ACCAUGCCC--UGGCAGCUC-CGGUCUUCAAGGCUGC-AACGCGG---UUCG------CCGCGUG--GAU--CGAA-------CCAGUCCGCU-----UC-GCAUCGCCCGCCGCGGACGAGC-GUC-----UUCAC----GAC-GCCGG-UGC
CP000050.1/2474704-2474565     AAGCUGCCCGCAUGUG---UCGCUGA-UCCG-UCAGC--ACCAUGCCA----GCAGCCA--GGGUUUCCAGGCUGC-CGCGGAG---UUU-------CUCCGCGCUACC--CG---------CCAGUCCGCC----AUC-GCAUCG-AGUCUGCGGACGCGC-GUC--CUCGU-------GAU-GCCGG-UGC
CR555306.1/1434850-1434698     GACCCCCAGACAUG-C---CCGCCG-CGUCCGUCGGC--GACAUGCCC--AGGUAGCUCUCGAUCUUCAAGGCUAC-GGCGCGG---CGCGA-----CCGCGCU--GAU--CGAA------ACCCCCGUUCG----CUUCGCAUCGCUUGCCGCGAACAGCC-ACCGU---ACAA---GCGGU-GGCGGAUGC
AAUJ02000001.1/109762-109626   AAGCUGCCCGCAUG-C---UCGCUGAU-UC-GUCAGC--A-CAUGCCA----GCAGCCA--GGGUUUCA-GGCUGC-CGCGGGG---UUCU------CCCCGCGCAACC--CA---------CCAGUCCGCA-----UC-GCAUCC-AUUGCGCGGACGCGC-GUC-----GCCAA----GAC-GCUGA-UGC
CP000774.1/3663513-3663661     CGACCACCGAAAUG-C---CUGCCGACGUU-GUCGGC--GACAUGCCC--AGGUAGCCUGCGGUCCUUGAGGCUAC-GGCGCAG---UCCU------CUGCGCU--GAU--CGCU------ACCCGUUCGCC-----UC-GCAUCC-UGGCCGCGAACGAUC-ACCGC---ACCC---GCGGU-GGUGGAUGC
AAKV01000112.1/59821-59674     UCCUUUGAGCCGUGAG---CUGCUGACGUU-GUCGGC--AUCCCUCCA----GUAGCCG-UGAUCUGCGAGGCUAC-AGCACGG---AUUA------CCGUGUA--GAU--CACUCC-----CUAGGUCGCA-----CCAGCUUCCGGAAGCGCGAUCAAUCGACC-----AUCA-----GGUUGAUGGAAGC
AY273869.1/70169-70019         --UCCUUUACCACG-UGAGCUGCUGACGUU-GUCGGCA-ACCCUCCCC--CAGUAGUCA-UGAUCUGAAAGACUAC-GACACGG---ACUU------CCGUGUA--GAU--CGAA------CCCAAGAUCGC----ACCAGCUUCCGGUAGCGCGAUCAAUC-AACCC---AC-----AGGUU-GAUGGAAGC
CP000555.1/2530285-2530433     CGCUUCCGGCCAUGUU---CCGCUGACGUCCGUCAGC--GACAUGCCC--AGGCAGCCA-CGAUCUUCAAGGCUGC-GACGCGGU--UCCG-----ACCGCGUU--GAU--CACU-------CCAGUUCGCA-----CCGGCAUCCAA--GCGCGAACGGCC-AUCGG---UUC----UCGAU-GGCGA-UGC
AAMM02000010.1/124116-123970   AUGGUGCAUCCGUACG---CGGUCGAUCCC-CUCGAC--CU-GUGCCC--AGGCAGCCGAUGGUCUUCAAGGCUGC-GCUGCGU---GUCA------UCGCAGU--GAC--UGCG-------CCAGUCCGCU-----UC-GCAUCGCUCGCCGCGGACGCUC-AUCCC---CAC----CGGAU-GACGA-UGC
CP000075.1/1657819-1657666     AUUCUGAAGCCAUGUA---CCGCUGACGUU-GUCAGC--AACAUGCCCG-AGGUAGUCU--GGAUUUCAUGACUAC-GAUGCG----UUUUU------CGCAUU--AAU--CCAA------CCCCCAGUUCG----CAAAGCAUUCGGAAGCGCGAACGGUUGAUCAG---UUUAU--CUGGUUGAUGGAUGC
CP000712.1/3339390-3339527     CCACUUGUGC----AA---UCGCUGGUUUU-UCCGGC--AU----CCC--AGGUAGCCA-UAACCUUUGAGGCUAC-GUCAC-----GCAU--------GUGAU--GGU--UACC-------CCGAAAUGCG----AUUCGCGUUCGGCAGCUCGCAUGGUC-ACCGU---UCC----CCGGU-GAUGAACGC
AM902716.1/1373516-1373669     AACCUGACGACAUG-U---UUGCUGGCGUU-GCCGGC--UGCAUGCCC--AGGCAGUCG-AGACCUUCAAGACUGC-GGUGC-----CUCGUU------GCACU--GGU--UGGUCUGUUCUACCGGCGCAU-----UCCGCGCCA-AUCACUCAACCCACA-AGGGA---CGCCC--UCCCU-UGUGGCGGG
CP000512.1/598085-597946       AUGCUGGAUGCAUGUG---UAGCUGACGCC-GUCAGC--GCCAUGCCA----GCAGCCU-GGAUC-UCAGGGCUGC-CGCGGGA---CACG------UCCUGCGC-GAU--CCA--------CCAGUCCGCU-----UC-GCAUCGGU--CCGCGGACGAGC-GCC--CUCGU-------GGC-GUCGA-UGC
AM902716.1/1118341-1118486     AUGCUGACCCCAUG-C---CUGCUGACGUU-GUCAGC--GACAUGC-C--AGGCGACCAUCGGUCUUCGAGGUUGC-GGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCAU--CCGCGAGCGGCC-ACCAG---CCU----CUGGU-GGCGGAUGC
AAHW02000025.1/26964-27111     AAGCUUCGCGCAUGUU---CCGCUG-CUUC-GUCAGC--GACAUGCCC--AGGUCGCCA-CGAUCUUCAAGGCGAC-GCCGGAG---AUUUCCA---CUCCGUU--GAU--CGAG-------CCCGUUCGCU----UUCGGCAUCCAC--GCGCGAACAACC-AUCGG---CC-----UCGAU-GGUGA-UGU
EF611301.1/61988-61853         --AAUUCGAA-UUGGC---UCGCUGUCGUU-GACAGC--GCC--UCCC--AAGGAGCCA-GGGUU--UAAGGCUCC-GGCGC-----GCAA--------GCGCU--AAC--CCAC------CCAAGACCGCC-----ACAGCACUCGGCAGCGCGGUCG--C-AUCAC---GCAA---GUGAU-GGAG--UGC
CP000450.1/108863-108710       AUCCUUAAAACAUG-U---UCGCUGGCGUA-GCUGGC--AGCAU-CCC--AGGCAGUCA-AGGCCAUCAAGACUGC-GGCGAAC---CUACA-----GUUCGCU--GGC--UGAU------CUCAUCUCCGG-----AC-GCUCAUCGUCCAUUCCAACCCC-AAGGGACCAUUCAUCCCUAU-GGGGGUGA-
CP000744.1/4615660-4615809     UUCUUUGCACCGUGAG---CUGCUGACGUU-GUCGGCA-AUCCUCCCC--CAGUAGUCA-UGAUCUGAAAGACUAC-GACACGG---AUUU------CCGUGUA--GAU--CGAA------CCCAAGAUCGC----ACCAGCUUCCGGUAGCGCGAUCAAUC-AACC------ACA---GGUU-GAUGGAAGC
AM039952.1/2694905-2694758     CCACAUCCGAAAUG-C---CUGCCGACGUU-GUCGGC--GACAUGCCC--AGGUAGCCCUCGGUCUUGGAGGCUAC-GGCUCGG---CUUG------CCGCGCU--GAC--CGCU------ACCCGUUCGCU-----UC-GCAUCC-UGGCUGCGAACAAUC-ACCGC---UGC----GCGGU-GGUGGAUGC
CP001339.1/2972753-2972901     UGCUUGCGGCCAUGUU---CCGCUGAU--CCGUCAGC--GACAUGCCC--AGGUAGCCA-CGGUCUUCGAGGCUAC-GACGCGGU--UCCG-----ACCACGU---GAC--CGAU-------CCAGUUCGCA-----CCAGCAUCC-CAUGCGCGAACGUUC-GCCCC---UCCC---AGGGU-GAUGGAUGC
CP000539.1/2312741-2312591     AUUCCCCAGACAUG-C---CCGCCGGCGUU-GCCGGU--GACAUGCCC--AGGUAGCCAUCGAUCUUCAAGGCUGC-GGCGCGG---CUCGU-----CCGCGUU--GAU--CGAA------ACCCGUUCGCA-----UC-GCAUCCCUUGACGCGAACAGCC-ACCGC---ACCU---GCGGU-GGUGGAUGC
CP000949.1/3676296-3676402     ---------------------------------------------CCC--AGGUGGCCU-CAACCUUCAAGGCCAC-GUCAC-----UCCC--------GUGAU--GGU--UGUC-------CCAAGGGCGA-----UUAGCGUUCGGUGGCUCGCCCGGUU-GCCGC---UCCC---GCGGU-GAUGAGCGC
CP000352.1/2530420-2530571     AUGCUUGCCCCAUG-U---UCGUCGGCGUU-GCCGGC--A-CAUGCCC--AGGCAGUCG-AGACCUUCGAGGCUGCAAGCGCGG---GAAA------CCGUGCU--GGU--CGUUUCUU--CCUACGGACCU----ACC-GCGUCCAUCCACGCCACCCACA-AGGGA---CCUC---UCCCU-UGCG--GGC
DQ515909.1/20554-20704         AUUCCCCAGACAUG-C---CCGCCGGCGUU-GCCGGU--GACAUGCCC--AGGUAGCCAUCGAUCUUCAAGGCUGC-GGCGCGG---CUCGU-----CCGCGUU--GAU--CGAA------ACCCGUUCGCA-----UC-GCAUCCCUUGACGCGAACAGCC-ACCGC---AUCC---GCGGU-GGUGGAUGC
CP000450.1/78726-78571         AAACGACUGAAUUG-U---CCGCCGUCCCA-GACGGU--AACAAGCCC--AGGUAGCCCGCGAUCUUAAAGGCUAC-GGCGUGGC--GUAU-----GCCGCGUU--GAUUGCGCA------CCCCCGUUCCG----CACCGCAUCC-CCUGCGCGGAUACCC-ACCUG---ACACG--AAGGU-GGUGGAUGC
AJ617740.1/88819-88684         AAGCUGCCCGCAUG-U---UCGCUGAU-UC-GUCAGC--A-CAUGCCA----GCAGCCA--GGGUUUCA-GGCUGC-CGCGGG----UCUCU------CCCGCGUUGCC--CA---------CCAGUCCGCA-----UC-GCAUCA-AGUCUGCGGACGCGC-GUCCC---C------GUGAC-GUCGA-UGC
AM902716.1/4559739-4559594     AUGCUGAGCCCAUG-C---CUGCUGACGUU-GUCAGC--GACAUGC-C--AGGCAACCAUCGGUCUUCGAGGUUGC-GGCGCAGU--UCCC-----ACUGCGU---GAC--CGAG-------CCAGCUCGCA-----CC-GCAUCCAU--CCGCGAGCGGCC-ACCAG---UCU----CUGGU-GGUGGAUGC
CP000076.1/5412448-5412599     UAUUUUCAACCAUGUA---CCGCUGACGUU-GUCAGC--AACAUGCCC--UAGUAGUCA-CGAUCUGUGAGACUAC-GACACGA---AAAU------UCGUGUU--GAU--CAGA------CCCAAGACCGC-----CCAGCUUCCGGUAGUGCGGUUGAUC-AGUCA---AUAAU--UGACU-GAUGGAAGC
AM902716.1/4560875-4560729     AUCUUUACCCCAUG-U---UCGUCGGCGUU-GCCGAC--A-CAUGCCC--AGGCAGCCA-AGACCUUCAAGGCUGCAAGCGCGG---GAAA------CCGUGCU--GGU--UGUU------UCUUUCUACGG-----AC-GCAUCGCGCCCAUCCACCCACA-AGGGA---CCUC---UCCCU-UGCG--GGC
AE003849.1/1689085-1688948     AAGCUGCCCACAUG-U---UCGCUGAUUCCGAUCAGC--A-CAUGCCA----GCAGCCA--GGG-UUCCAGGCUGC-CGCGGG----UCUCU------CCCGCGUUGCC--CA---------CCAGUCCGCA-----UC-GCAUCA-AUUCCGCGGACGCGC-GUCCC---C------GUGAC-GUCGA-UGC
AM902716.1/4563132-4562996     AAGCUGCCCGCAUG-U---UCGCUGAU-UC-GUCAGC--A-CAUGCCA----GCAGCCA-UGGG-UUCCAGGCUGC-CGUGGG----UUCUU------CCCGCGUAACC--CG---------CCAGUCCGUA-----UC-GCAUCA-AGUCUGCGGACACGC-GUCCC---C------GUGAC-GCCGA-UGC
CP000512.1/595771-595624       ACGCUUCGGCUAUG-C---CUGCCGACAGAUGUCGGC--GACAUGCCC---GGCAACCACCGGUCUUCGAGGUUGC--GCGCAGC--GCCCC----GCUGCGU---GGC--CGGA-------CCAGUUCGCU-----UC-GCAUCACU--UCGCGAACGGCC-UCCGG---UUCC---ACGGG-GGCGCAUGC
CP000094.2/873551-873694       CAAUUGGCGCACGG-A---UCGCUGUCGUU-GACAGC--U-CCAGCCC--AGAUAGCCA-GAACCUUUAAGGCUAU-GCCAC-----UUGC--------GUGGU--GGU--UCUC-------CCAAAGUGCG----AUUAGCAUCCGGCGGCUCGCACGGUC-ACUCC---CCA----AGAGU-GAUGGAUGC
CP001644.1/716928-717076       CAUCGAAGGAAAUG-C---CUGCCGAGUCU-CUCGGC--GACAUGCCC--AGGUAGCCA-CGAUCUUCAAGGCUAC-GACGCGG---CUUGG-----CCGCGCU--GAU--CGAC-------CCCGUUCGCU-----GC-GCAUCCCUGGACGCGAACAGCC-ACUGC---GCAU---GCGGU-GGCGGAUGC
CP001644.1/695091-695241       ACGCUUCCCGCAUGUU---CCGCUGACACCCGUCAGC--AGCAUGCCC--AGGUAGCCA-CGAUCUUCAAGGCUAC-GGCGCGGU--UCCG-----ACCGCGUU--GAU--CACA-------CCAGUUCGCU-----CCGGCAUCCCA--GCGCGAACGGCC-AUCGG---UUCUC--CCGAU-GGUGA-UGC
CP001644.1/697672-697826       AGGCUACGCCCAUG-U---CCGUCGGCGUU-GCCGAC--AACAUGCCC--AGGUAGCCC-AGACCUUCAAGGCUAC-GGUGCGU---UGCG------ACGCAC---GGU--CUGAAUUUUCUCCACGACGCU----CACCGCGUUUUCUUCCAUCCCCCUGG-GGCAG---UGA----CUGCC-CUCGCCGGU
CP000094.2/3444997-3445139     UACAAAGGGCGUGG-U---UCGCUGUCGUU-GACAAC----CCAGCCC--AGGUAGCUU-GAACCUUCAAGGCUAC-GCCAC-----GUUC--------GUGGU--GGU--UUAC-------CCAAGUGCGA-----UCAGCGUUCGGAAGCUCGCGCGGUU-ACCGC---UUCA---GCGGU-GAUGAAUGC
CP000094.2/3469195-3469339     AACCCGAGGUACGG-A---UCGCUGUUAUC-GACAGC--A-CUUUCCC--AGGUAGCCA-GAACCUUCAAGGCUAC-GUUAC-----UUCG--------AUGAU--GGU--UCUC------CCCAAGUGCGA-----UUAGCGUUCGGUGGCUCGCACGGUG-ACCGU---UGCU---ACGGU-GAUGAACGC
CP001644.1/689922-690061       UGCUUUGCGGCACGUG---UUGCUGACCUG-AUCAGC---ACAUGCCA----GCAGCCU--GGGUCUUUCGGCUGC-CGCGGGA---AUCC------UCUCGUGCGACC--CA---------CCAGUCCGCU-----UC-GCAUCGACCACCGCGGACGGGC-GUU-----UCAC-----AAC-GCCGA-UGU
CP001644.1/692605-692765       ACGCUGAUUGCAUG-U---UCGCUGGCGUU-GCCGGCA-AGCAUGCCC--AGGCAGUCG-AGACCUUCGAGACUGC-GGUGCGG---UUCG------CCGUGCU--GGU--UGUUUUUC--CUUCCCCGGGCGCAUGUC-GCGUCCAUCCACCUCACCCCCA-AGGGAUACACC----UCCCU-UGCGGGCGG
#=GC SS_cons                   ::::::::::<<<<.<...--<<<<<<___.>>>>>>..>->>>>,,,..,,<<<<<<_.__________>>>>>>.<<<<<<<...____......>>>>>>>..---..----......-----------.....--.------------<<<----<<<.<<<<<...____...>>>>>.>>>--->>>
#=GC RF                        AugcUucccccauG.u...ccGCuGacgUu.guCaGC..aaCaugCCC..AGGcAGCCa.aGauCUUCAAGGCUgC.ggCGcGG...uuca......CCgCGcu..GaU..Cgau......cCCAguuCGcu.....uC.GCaUCcguuagCGCgaaCGccc.accgc...uccc...gcggu.gggGGAuGC
//
# STOCKHOLM 1.0

#=GF AC   RF01755
#=GF ID   rmf
#=GF DE   rmf RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   45.00
#=GF TC   48.30
#=GF NC   32.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   RMF_RNA_motif
#=GF SQ   16


CP000438.1/2155099-2154971 UUGGUUAGAACUCCAGUUAAUC-C-GCCCACCGCAACGGU-GUC-G-GGCG---AGGGUCGUCACGCCGGCAACGACCCC-UUUCGGCGAAAGC--UUCGCCAGGCCUCCCCUG-GGGGCCAACGGGACAUAA--CAGUCAAC
AE016853.1/2557709-2557579 UUGGUUAGAAAUC-AACUCAGG-U-CAUUUCCGCAAUGGUUAUG-G-CAUCA--AGGCCCGCCACGCCGGCAGCGGGCCC-CAACGGCAGAAGAC-UCUGCCCGACCCCACCAC-GGGGUCUCAGGGAUAUUA--CAGUCAAC
AE004091.2/3414255-3414382 UUGGUUAGAACUCCAGUUAAUC-C-GCC-ACCGCAACGGU-GUC-G-GGCG---AGGGUCGUCACGCCGGCAACGACCCC-UUUCGGCGAAAGC--UUCGCCAGGCCUCCCCUG-GGGGCCAACGGGACAUAA--CAGUCAAC
CP001157.1/1881137-1881012 UUGGAUAGAAAUCGA--UCAGUCC-CCC-GCCGCAACGGU-GGG-GGGA-----GAAACCGCGACGCCGGCAGCGGUUUC--GUCGGCAGCCAAG-GCCGCCAGGUCUCGCCAU-GAGGCCAAUGGGACAUAA--CAGUCAAC
CP000744.1/2140830-2140703 UUGGUUAGAACUCCAGUUAAUC-C-GUC-ACCGCAACGGU-GUC-G-GGCG---AGGGUCGUCACGCCGGCAACGACCCC-UUUCGGCGAAAGC--UUCGCCAGGCCUCCCCUG-GGGGCCAACGGGACAUAA--CAGUCAAC
CP000949.1/1789746-1789617 UUCGUUAGAACUG-GUCUUAGGCCGCUU---CGCAACG---AAGUGGCACUUUCA-GCCCGCCACGCCGGCAGCGGGCGCAAACCGGCAGAAAGACUCUGCCCGGCCUCGGA---GAGGCCGACGGGACAUUA--CAGUCAAC
CP000076.1/2087729-2087597 UUGGUUAGAACUC-AACACAGGUU-GGC-GCCGCAACGGU-GUC-AACAUCAA-A-GCUCGCGACGCCGGCAGCGAGCAC-CAACGGCAGAAGCAAUCUGCCCGACCU-CAACGA-AGGUCGACGGGACAUAAAGCAGUCAAC
CT573326.1/1832021-1831892 UUCGUUAGAACUG-GCCUUAGGUC-GUC--UCGCAACGG--GGC-GGCACCUUCA-GCCCGCCACGCCGGCAGCGGGCGCACACCGGCAGAACGAUUCUGCCCGGCCUCGGA---GAGGCCGACGGGACAUUA--CAGUCAAC
CP000075.1/2459729-2459599 UUGGUUAGAAAUC-GUCUCAGGUC-AUC-GCUGCAAUGGU-GAU-GGCAUCA--AGGCCCGCGACGCCGGCAGCGGGCCC-CAACGGCAGAAGAU-UCUGCCCGACCUCAACAC-GGGGUCUCAGGGAUAUUA--CAGUCAAC
CP000926.1/1814897-1814768 UUCGUUAGAACUG-GUCUUAGGCCGCAU---CGCAACG---AGGCGGCACCUUCA-GCUCGCCACGCCGGCAGCGAGCGCAAACCGGCAGAAAGACUCUGCCCGGCCUCGGA---GAGGCCGACGGGACAUUA--CAGUCAAC
CP000712.1/4073813-4073942 UUCGAUAGAACUG-GUCUUAGG-C-CGC-UUCGCAACGAG-GCG-G-CACUUUCA-GCUCGCCACGCCGGCAGCGAGCGCAAACCGGCAGAACGACUCUGCCCGGCCUCGGA---GAGGCCGACGGGACAUUA--CAGUCAAC
CP000058.1/2438030-2437900 UUGGUUAGAAAUC-GUCUCAGG-U-CAUCUCUGCAACGGUUAUG-A-CAUCAA-G-GCCCGCGACGCCGGCAGCGGGCAC-CAACGGCAGAAGAU-UCUGCCCGACCUCAUCAA-GGGGUCUCAGGGAUAUUA--CAGUCAAC
AE015451.1/2388767-2388638 UUCGAUAGAACUG-GUCUCAGG-C-CGC-UUCGCAACGAG-GCG-G-CACUUUCA-GCUCGCCACGCCGGCAGCGAGCGCAAACCGGCAGAACGACUCUGCCCGGCCUCGGA---GAGGCCGACGGGACAUUA--CAGUCAAC
CP000680.1/3334674-3334807 UUCGUUAGAACACUACCUAAGG-CUUUC-GCUGCAAUGGC-GAAGG-CACAGA-AGGUUCGCCACGCCGGCAGCGGACCUUCGCAGGCAGAUACG-UCUGCCAGGCCUUGCCAC-AAGGCCAACGGGACAUAA--CAGUCAAC
CP000304.1/2608193-2608318 UGGGUUAGAACUC-ACCUCAGGCC-GUC-AUCGCAAGGAU-GUC-GGCG-----AGGCGCGCCACGCCGGCAGCGCGCCUCAAUCGGCAG-UCUAU-CUGCCCGGUCUCGCCAU-GAGGCCACAGGAACAC----CAGUCAAC
CP000094.2/1989142-1989010 UUGGUUAGAACUG-GACACAGGUU-GAC-GUCGCAACGGC-GUC-AACACCUU--GGCUCGCCACGCCGGCAGCGAGCCGCCAACGGCAGAGUUUUUCUGCCAGACCUCAGUU--GAGGUCGACGCGACAAAAA-CAGUCAAC
#=GC SS_cons               :::::::::::::.:::::::<<<.<<<.<<<_____>>>.>>>.>>>,,,,,.,<<<<<<<__________>>>>>>>,.,,,,<<<<<<____.>>>>>>,<<<<<<_____.>>>>>>::::::::::::..::::::::
#=GC RF                    UUgGUUAGAAcUc.aucUcAGgcc.gcc.gccGCAAcggc.ggc.ggcAcuuu.AGGccCGCcACGCCGGCAGCGggCCc.cauCGGCaGaaaaa.uCuGCCaGGCCuCaccau.GaGGCCaacGGGAcAUaA..CAGUCAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01756
#=GF ID   rne-II
#=GF DE   rne-II RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   58.30
#=GF NC   40.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Rne-II_RNA_motif
#=GF SQ   16


CP000712.1/4270107-4270479 AUACGUGCAGGGUGGAGAUGCACAGCCCUCGGACCGUGUAGCACCGCGUCCGGCCACCAGCCCACUGA-CGGUUGG-UGAGCGGAUAAGGUCCU-------------GAACA-GAUGCCCUCCG---GGCGUCCACGGCUGA-CGGU-UGAUUCCUCCUCCUGACUGAGUGCACAAGGCCCGCUUGGUUGAUUCGGAUACCUAUUCGAAGCCACCGGGGCCUUGUUGGC------------ACCGCAGCAAACAGGACGCGUC-GUCGCGACAACGGCAGGCUGGGCAA------CCGGCUGGUGCCGAACGUCGCUCGACACGGGGGUGGCCCGG----CCACCCUU---UGCGCACCUUGGCACCGACCAUGAGACGUCGUGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
AE004091.2/3332603-3332870 ACAUGUGUAGGGUGGAGAUGUACGGCUGUUGGACUGCGU-------------------------------------------------------AGCUUCUAGCUUGAUCCA-GACG--CAUU-UUU--CGUCCGCCUCCGA-CAGC-CGAUUCCUCCUCCUGACUCAAGUGCUUCUGAA-------------------------------------------------------------AC-ACAGGAAGCAGGAGACGUA-GUCGCGGAC-CG---GCA---CCCAG--------UGC-----CGAGCGCCGCUGGACACGGGAAUGGCCCG-----CCAUUCCUGAAUACGCGCCCGAGCACCGACCGUGAGA-GUCGUGUGUGCCGAUCGCCGUUUCCGGUAGCCCCGGAAACC-A
CT573326.1/1679634-1679264 AUACGUGCAGGGUGGAGAUGCACAGCCCUCGGACCGUGUGGCACUGCGUCC-CCCACCGCCCCAGUGAUCGGGCGACGGAC-GGACAAGGUCCU-------------GAACA-GACGCCCUUGC---GGCGUCCACGGACGAUCGGU-UGAUUCCUCCUCCUGACUGAGUGCACCAGGCCCGUUCGAUUGAUUCGGAUGACAUUCGAAAAGCUCGACAGGUCUUUUGGC------------ACCGC--AAAACAGGACGCGUC-GUCGCGACCACGGCAGGCUGGGCAA------CCGGCUGGUGCCGAACGUCGCCAGACACGGGGGUGGCCCG-----CCACCCUU---UGCGCACCUUGGCACCGAUCAUGAAAAAUCGCGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
CP000926.1/1667321-1666950 AUACGUGCAGGGUGGAGAUGCACAGCCCUCGGACCGUGUAGCACCGCGUCCGGCCACCAGCCCACUCA-CGGCUGG-CGAGCGGAUAAGGUCCU-------------GAACA-GAUGCCUCCG----GGCGUCCACGGCUGA-CGGU-UGAUUCCUCCUCCUGACUGAGUGCACAAGGCCCGCUUGGUUGAUUCGGAUACCUAUUCGAAGCCACCGGGGCCUUGUUGGC------------ACCGCAGCAAACAGGACGCGUC-GUCGCGACAACGGCAGGCUGGGCAA------CCGGCUGGUGCCGAACGUCGCUCGACACGGGGGUGGCCCGG----CCACCCUU---UGCGCACCUUGGCACCGACCAUGAGACGUCGUGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
CP000438.1/2236725-2236458 ACAUGUGUAGGGUGGAGAUGUACGGCUGUUGGACUGCGU-------------------------------------------------------AGCUUCUAGCUUGAUCCA-GACG--CAUU-UUU--CGUCCGCCUCCGA-CAGC-CGAUUCCUCCUCCUGACUCAAGUGCUUCUGAA-------------------------------------------------------------AC-ACAGGAAGCAGGAGACGUA-GUCGCGGAC-CG---GCA---CCCAG--------UGC-----CGAGCGCCGCUGGACACGGGAAUGGCCCG-----CCAUUCCUGAAUACGCGCCCGAGCACCGACCGUGAGA-GUCGUGUGUGCCGAUCGCCGUUUCCGGUAGCCCCGGAAACC-A
CP000076.1/1992152-1991866 AUACGUGUAGGGUGGAGAUGCACAACCGUCGGACUGUGU-------------------------------------------------------AGCAUUAGGCUUUAUCAA-GACG--CUUCAUCU--CGUCCACAGUCGC-CGGU-UGAUUCCUCCUCCUGACAGACUUUUGCUUAAGCGGUGCCUUAGUC------------------------------------------------ACCACAGCAAGCAGGACGCGUAAGUCGCGACUUCGUUC------UUAGUUACCC--------GGACGAACCUCGCUAGACACUCGAGUGGUCAA-----CCACUCCU---GACGCACCU-GACACCGACCGUGAGAAGUCGUGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
AE015451.1/2150898-2150526 AUACGUGCAGGGUGGAGAUGCACAGCCCUCGGACCGUGUAGCACCGCGUCCGGCCACCAGCCCACUGA-CGGCUGG-UGAGCGGAUAAGGUCCU-------------GAACA-GAUGCCCUCCG---GGCGUCCACGGCUGA-CGGU-UGAUUCCUCCUCCUGACUGAGUGCACAAGGCCCGCUUGGUUGAUUCGGAUACCUAUUCGAAGCCACCGGGGCCUUGUUGGC------------ACCGCAGCAAACAGGACGCGUC-GUCGCGACAACGGCAGGCUGGGCAA------CCGGCUGGUGCCGAACGUCGCUCGACACGGGGGUGGCCCGG----CCACCCUU---UGCGCACCUUGGCACCGACCAUGAGACGUCGUGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
CP000058.1/1897287-1896999 AUACGUGUAGGGUGGAGACGCACAACCAUCGGACUGUGU-------------------------------------------------------AGCACAAGGCUUGUUCUA-GACG--CUUCAUCU--CGUCCGCUACCGA-UGGU-CGAUUCCUCCUCCUGACAAAGCUUUUGCUGAAAAGGGUGUCUUAUGCC---------------------------------------------ACCACAGCAAGCAGGAAACGUC-GUCGCGAC--CCUA-CGCCC-CCUCU------GGGCG----AGGA-CCUCGCUAGACACUGGAGUG-UCCAAC----CACUCCU---GACGUGCCCUGACACCGACCGUGAGAAGUCGUGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
CP000949.1/1675457-1675072 AUACGUGCAGGGUGGAGAUGCACAGCCCUCGGACCGUGUAGCACCGCGUCCGGCCACCGGCCCAGUGAAUGGCCGG-CGAGCGGAUAAGGUCCU-------------GAACA-GAUGCCCCAUG---GGCGUCCACGGCUGA-CGGU-UGAUUCCUCCUCCUGACUGAGUGCACGAGGCCUGCUGGGUUGAUUCGGAUAUCGAUUCGGAUAUCUCUGCAGAUACCGCAGGGGCCUCUUGGCACCGCAGCAAACAGGACGCGUC-GUCGCGACAACGGCAGGCUGGGAAA------CCGGCUGGUGCCGAACGUUGCUCGACACGGGGGUGGCCCGG----CCACCCUU---UGCGCACCUUGGCACCGACCAUGAGAAGUCGUGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
CP001157.1/1465433-1465164 AUACGUGCAGGGUGGAGAUGCACAACCAUCGGAUUGCGU-------------------------------------------------------AGCUGCAAGCUUUCAUCCAGACGC-ACAAG----GCGUCCGCUGCCGA-UGCU-UGAUUCCUCCUCCUGAUUGAUUGCUUUCUGCC-------------------------------------------------------------ACAACAGUAAGCAGGAGACGUA-GUCGCGACUCUGGC-------CACCA--------------GCCAAAUGUUGCUUGACACGGGAACGGACGACAA--CCUUUCCUG--AACGGCCCCUGUCACCGACCGCGAGA-GUCGUGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
CP000744.1/2242576-2242309 ACAUGUGUAGGGUGGAGAUGUACGGCUGUUGGACUGCGU-------------------------------------------------------AGCUUCUAGCUUGAUCCA-GACG--CAUU-UUU--CGUCCGCCUCCGA-CAGU-CGAUUCCUCCUCCUGACUCAAGUGCUUCUGA--------------------------------------------------------------AACACAGGAAGCAGGAGACGUA-GUCGCGGAC-CGGCA------UCCGA-------------UGCCGAGCGCCGCUGGACACGGGAAUGGCCCG-----CCAUUCCUGAAUACGCGCCCGAACACCGACCGUGAGA-GUCGUGUGUGCCGAUCGCCGUUUCCGGUAGCCCCGGAAACC-A
CP000680.1/1785155-1784883 AUACGUGUAGGGUGGAGAUGUACAACUGUCGGACUGCGU-------------------------------------------------------AGCAUAUCGCUUGAUCAAAGACG--CCUCAUCU--CGUCCGCUACCGC-CAGU-UGAUUCCUCCUCCUGACUGAGUGCUUUCUGUC-------------------------------------------------------------ACCACAGCAAGCAGGAGACGUCCGUCGCGACC-GC-A-GCC---UCUGAU-------GGCAG---GC--CGUCGCUCGACAGUGGAACG-AUUUACGAC-CGUUUCU---GACGCGCCU-GACACCGACCCUGAGA-GUCGUGUGUGCCUAACGUGGCUUCCGCUAGCCCCGGAACCC-A
AE016853.1/4346971-4347259 AUACGUGUAGGGUGGAGACGCACAACCAUCGGACUGUGU-------------------------------------------------------AGCACAAGGCUUGUUUUA-GACG--CUUCAUCU--CGUCCGCUACCGA-UGGU-CGAUUCCUCCUCCUGACAAAGCUUUUGCUGAAAAGGGUGUCUUAUGCC---------------------------------------------ACCACAGCAAGCAGGAAACGUC-GUCGCGAC--CCUC-CGCCC-CCUCU------GGGCG----AGGA-CCUCGCUAGACACUGGAGUGGCCAA-----CCACUCCU---GACGCGCCCUGACACCGACCGUGAGAAGUCGUGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
CP000304.1/2848416-2848682 AUGCGUGUUGGGUGGAGAUGCACAGCAU-CGGAUUGCGU-------------------------------------------------------AGCAAAG-GCUU-UCACA-GACG--CUCCAUUC--CGUCCGCUACCG--AUGCCUGAUUCCUCCUCCCGAACCAUUGCUUCUGUU--------------------------------------------------------------CCGACAGCAAGCAGGAGACGUC-GUCGCGACGCCG---GCC---CAUUU--------GGC-----CGCACAUCGCUGGACACUGGAGUG-CCUUACAAC-CAUUCCU---GACUCACCU-GACACCGACCGCGAGA-GUCGUGUGUGCCGAACGCCGUUUCCGGAUGCCACGGAAACCGA
CP000075.1/1845898-1845610 AUACGUGUAGGGUGGAGACGCACAACCAUCGGACUGUGU-------------------------------------------------------AGCACAAGGCUUGUUCUA-GACG--CUUCAUCU--CGUCCGCUACCGA-UGGU-CGAUUCCUCCUCCUGACAAAGCUUUUGCUGAAAGGGGUGUCUUAUGCC---------------------------------------------ACCACAGCAAGCAGGAAACGUC-GUCGCGAC--CCUC-CGCCC-CCUCU------GGGCG----AGGA-CCUCGCUAGACACUGGAGUG-UCCAAC----CACUCCU---GACGUGCCCUGACACCGACCGUGAGAAGUCGUGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
CP000094.2/4701518-4701785 AUACGUGUAGGGUGGAGAUGCACAACCGCUGGACUGUGU-------------------------------------------------------AGCAACAGGCUUUAUCAA-GACG--CUUCAUCU--CGUCCACAGCCAC-CGGU-UGAUUCCUCCUCCUGACUGAGUGCUUAAGUA--------------------------------------------------------------GCCACAGCAAGCAGGACGCGUACGUCGCGAUAACGGCC------CAAUU-------------GGCCGGACAUCGCUGGACACGGGAAUGGCCAA-----CCACUCCC---GACGCACCU-GACACCGACCGUGAGAAGUCGUGUGUGCCGAACGCCGUUUCCGGCAGCC-CGGAAACCGA
#=GC SS_cons               :::::::::::::((((-----((((((((((---(((,.......................................................<<<_____>>>,,,,,,,.<<<<..________..>>>>)))--)))).)))).))----))))<<<<<_________________________________.............................................___________>>>>>,,((((.<<<<<<<---<<<<<<<<<<._____......>>>>>..>>>>>---->>>>-->>>,,,<<<<<<<_____....>>>>>>>,...)))),,,,,,,<<<<<<<<________>>>>->>>>,,,,,,,,,,<<<<<<<______.>>>>>>>:::
#=GC RF                    AUACGUGuAGGGUGGAGAUGcACggCcgucGGACuGcGU.......................................................aGCauaaaGCuUgauacA.GAcG..cuuuaUuu..CgUCCgCugCCga.cgGc.cGAUUCCUCCUCCuGAcugAgugcuuuaugaccguuuggUugauUcgg.............................................ACcaCAGcAAgCaGGAcaCGuc.GUCGCGacaacggcaggccg.ucaau......cggcc..ugccgAACguCGCUaGACACggGgguGGcCcga....CCaccCcU...gaCGcaCCuuGaCACCGACCaUGAGAaGUCGUGUGuGCCGAACGCCGuUUCCGGcAGCC.CGGAAaCCGA
//
# STOCKHOLM 1.0

#=GF AC   RF01757
#=GF ID   sbcD
#=GF DE   sbcD RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   41.90
#=GF NC   39.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   SbcD_RNA_motif
#=GF SQ   6


CP000618.1/92362-92499     CCUGC-GUCGGAAUGGCACUUCCGAAAAU-GGGCUGUAGCGCAGCGUGACCAUGCUGUGCGAGGACGACCUAACGUCCUCUCU-AUGAGCC------GACC------GGCUCCCU-GAGCACCACGUCCCCGGAAGGGACGUGGUGCUU--GGGUC
ABLK01000025.1/8990-8853   CCUGC-GUCGGAAUGGCAUUUCCGAAAAU-GGGCUGUAGCGCAGCGUGACCAUGCUGUGCGAGGACGACCUAACGUCCUCUAU-AUGAGCC------GACC------GGCUCCCU-GAGCACCACGUCCCCGGAAGGGACGUGGUGCUU--GGGUC
CP001068.1/1712737-1712884 CCUGCGGU-GGACGAAA--GUCC-UAAAU-GGGUUGUUGUGCGGCGUGAACAUGCUGCACGAGAACGACUUUACGUUCUCCCCCCUGAGCGAAGUGCAUUGGCACGACGCUCCCUGU-GAGCCACGCCCCCGAAAGGGGCGUGGCA--GCAGGUUU
AY305378.1/312212-312058   CCUGCGGCCGAACCUGUGGGUUCGCGAAAUGGGUUGCUGUGCAGCGUGACCAUGCUGCACGAGGACGACUUUACGUCCUCAGCAUCGAGCAGCGCGCAAUUGUGCGCCGCUCCCUG-AGUGCCACGCCCCCGGAAGGGGCGUGGCAUUGCAGGUUC
CP001028.1/294183-294046   CCUGC-GGCGGAGUGGUAUUUCCGAAAAU-GGGCUGUUGCGCGGCGUGACCAUGCUGCGCGAGGACGACCUAACGUCCUCGAU-AUGAGCC------GACC------GGCUCCCU-GAGCGCCACGUCCCCAGAAGGGACGUGGCGCUU--GGGUC
CP000355.2/74841-74687     CCUGCGGCCGAACCUGUGGGUUCGCGAAAAGGGUUGUUGUGCAGCGUGACCAUGCUGCACGAGGGCGACUUUACGUCCUCAACAUUGAGCCGCGCGCACUAGUGCGCCGCUCCCCG-AGUGCCACGCCCCCGGAAGGGGCGUGGCAGUUCGGGUUC
#=GC SS_cons               ::::::::<<<<<______>>>>>,,,,,.,,,,,(((<<<<<<<<<____>>>>>>>>><<<<<<<______>>>>>>>))),,,<<<<<--<<<<____>>>>-->>>>><<<<<<<<<<<<<<<<<<_____>>>>>>>>>>>>>>>>>>:::
#=GC RF                    CCUGCGGuCGgacuuguaugucCGaaAAu.GGGuUgccGcGCaGCguGAcCauGCuGCgCGaGGaCGACuUuACGuCCuCggcaauGaGCggaGcgcaauugcgCGacGCuCCCcGgagcgCCaCGcCCCCggAAGGGgCGuGGcgcucCgGGuUc
//
# STOCKHOLM 1.0

#=GF AC   RF01758
#=GF ID   sucA-II
#=GF DE   sucA-II RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   70.00
#=GF TC   132.90
#=GF NC   63.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   SucA-II_RNA_motif
#=GF SQ   17


AE016853.1/2419253-2419470 CUGCGGCGCAG-G-CUUCAA-CCGGCGCCGUAGUUUUA--A--CCUGAGC-A-GU-AGCUCGCAAAGCU-GCC--GCUCUU-A-UUUUGAAGAAAUGA-GACCAGCAGGGGCA-UCCGGGCUGGUACCCGGA--CUAUCUGCGUGAUCCCU-GGUGACUU---GAUACAGU--CG--CUGCACA--CG-ACUAUUUCAGGAUU--GCUCUGGUG-UCUUCGCC-GGUGG-UG-UCCCCUUACCGAGGGUGACCA
CP001157.1/3081299-3081086 CUGCGGCGUCG-GAAGCGAUUCCGGCGUCGUAGCCAAAGAUGGAUC-------CGCAGCUCAUGAAGCCGCG-------CU--CCUAUGAAGAAUU--UGACUAGCAGGGGCA-UCCGGGCAA-CGCUCGGA--CUAUCUGUGGGAUCCGU-AGUGGCUUUA--CCAAAGU--CG--CUGCUCCA-UG-ACUUUGGAACGACCAUGUGC-GGC--UCG-CGCC-GAUGG-UA-UCCCCUCAA-GAGGGUGACCA
CT573326.1/3928150-3927934 CCGAGGUGCGG-GCGCUGA-GUCCGCACUGCGG--UAA--AA-CCCGAGC-AAGG--GCCCACAAAGC--CCGC-GCUCAUUACCUAUGAAGAUAUGA-GACCAGCAGGGGCU-UCCGGGCUGGUACCCGGA--AAAUCAGCAGGAUCC-A-GGUGGCGU---GGUUCAGU--C-G-CUGUGUUCG-G-ACUUUUCCAGGUUU--GCUGUGGC--UCU-CGCC-GAUC--AG-UCCCCUAACCGAGGGUGACCA
CP000076.1/1921629-1921848 CCACGGCGCGG--GCUUCAAC-CCGCGUCAUGGCUCUA--A--CCUGAGC---AGCAGCUCACAAAGUGGCU---GCUCUAUA-UUUUGAAGAAAUGA-GACAAGCAGGGGCA-UCCGGGCUGGUACCCGGA--CUAUCAGCGUGAUCCUA-AGUGGCUU---GUUUUGGU--C-G-CUGCAUUCG-G-ACUUCUGCAAGCUU--GCUC-GGUG-UCGUCGCC-GGUGG-UGUUCCCCUAACCGAGGGUGACCA
CP000075.1/2329440-2329657 CUACGGCGCAG-G-CUUCAA-CCGGCGCCGUAGUUUUA--A--CCUGAGC-A-GU-AGCUCGCAAAGCU-GCG--GCUCUU-A-UUUUGAAGAAAUGA-GACCAGCAGGGGCA-UCCGGGCUGGUACCCGGA--CUAUCUGCGUGAUCCCU-GGUGACUU---GAUACAGU--CG--CUGCACA--CG-ACUAUUUCAGGAUU--GCUCUGGUG-UCUUCGCC-GGUGG-UG-UCCCCUUACCGAGGGUGACCA
CP000438.1/3919482-3919269 CUGUGGCGCCG-GAGUUCU-UCCGGCGUCGCAG--CAACUAAGC--GGGC---CA-AGCUCACAAAGCCAUG---GCCCAG-A-UUUGAAAAAUAU---GACCAGCAGGGGCA-UCCGGGCUGGUACCCGGA--CUAUCUGCGGGAUCUGUAGUGGCCAUACCGAU--GUCG-CUGCCUG------AG-GAC-U-UCG-GAGC--CUUCAAGGU-UU--CGCCAGGUGGUUG-UCCCCUUACCGAGGGUGACCU
CP000680.1/2769676-2769456 CUGCAUUACCG-GCUCCG--GUCGGUAAUGCAG--CAA--AAGCCAGAGC---CGCAGCCCACAAAGCCGCG---GCUCAU-A-CUCGAAAAAUAUGACGACCAGCAGGGGCA-UCCGGGCUGGUACCCGGA--CUAUCUGCGGGAACCCAAGUGGCUUG---AUCCGAGU--CG--CAGCAAGA-UG-ACUUUGAUUGGAGC--CAUGCGGUAUUCA-CGCC-GGUGG-UG-UCCCCUUACCGAGGGUGACCA
FM209186.1/4144158-4143945 CUGUGGCGCCG-GAGUUCU-UCCGGCGUCGCAG--CAACUAAGC--GGGC---CA-AGCUCACAAAGCCAUG---GCCCAG-A-UUUGAAAAAUAU---GACCAGCAGGGGCA-UCCGGGCUGGUACCCGGA--CUAUCUGCGGGAUCUGUAGUGGCCAUACCGAU--GUCG-CUGCCUG------AG-GAC-U-UCG-GAGC--CUUCAAGGU-UU--CGCCAGGUGGUUG-UCCCCUUACCGAGGGUGACCU
AE004091.2/1724027-1724240 CUGUGGCGCCG-GAGUUCU-UCCGGCGUCGCAG--CAACUAAGC--GGGC---CA-AGCUCACAAAGCCAUG---GCCCAG-A-UUUGAAAAAUAU---GACCAGCAGGGGCA-UCCGGGCUGGUACCCGGA--CUAUCUGCGGGAUCUGUAGUGGCCAUACCGAU--GUCG-CUGCCUG------AG-GAC-U-UCG-GAGC--CUUCAAGGU-UU--CGCCAGGUGGUUG-UCCCCUUACCGAGGGUGACCU
CP000712.1/1868297-1868514 CCGAGGUGCGG-GUGGUGA-GCCCGCACUGAGG--UAA--AA-CCCGAAC-AAGG--GCCCACAAAGC--CCGC-GUUCAUUACCUAUGAAGAUAUGA-GACCAGCAGGGGCUUUCCGGGCUGGUACCCGGAA--AAUCAGCAGGAUCC-A-GGUGGCGU---GGUUCAGU--C-G-CUGUUUUCG-G-ACUUUUCCAGGUUU--GCUGUGGC--UCU-CGCC-GAUC--AG-UCCCCUAAUCGAGGGUGACCA
CP000926.1/4187312-4187095 CCGAGGUGCGG-GUGGUGA-GCCCGCACUGAGG--UAA--AA-CCCGAAC-AAGG--GCCCACAAAGC--CCGC-GUUCAUUACCUAUGAAGAUAUGA-GACCAGCAGGGGCUUUCCGGGCUGGUACCCGGAA--AAUCAGCAGGAUCC-A-AGUGGCGU---GGUUCAGU--C-G-CUGUUUUCG-G-ACUUUUCCAGGUUU--GCUGUGGC--UCU-CGCC-GAUC--AG-UCCCCUAAUCGAGGGUGACCA
CP000304.1/2022862-2023085 CUGCGGCGCCGAAGUCGAAGCUCGGCGCCGUAGUUUUAG-UAG---GAAUC--CC-AGCUCACAAAGCC-GG--GAUUUC--A-CUCUGAAAAUUUGAUGACCAGCAGGAGCA-UCCGGGUUG-UGCCCGGGAACUAUCUGCGCGGUCCGU-AGUGGCUUUA-CCUG-AGUCGCUG-CUUC-----AGAACU-UGGGAAG-UCAUGCUGCGGUUUCCA-CGCU-GGUGG-UG-UCUCCUUAUCGAAGGUGACCA
CP000949.1/3875508-3875291 CCGAGGUGCGG-GUGGUGA-ACCCGCACUGAGG--UAA--AA-CCUGAGC-AAGG--GCCCACAAAGC--CCGC-GCUCGAUACCUAUGAAGAUAUGA-GACCAGCAGGGGCUUUCCGGGCUGGUACCCGGAA--AAUCAGCAGGAUCC--AAGUGGCGU---GGUUCAGU--C-G-CUGUGUUCG-G-ACUUUUCCAGGUUU--GCUGUGGC--UCU-CGCC-GAUC--AG-UCCCCUAACCGAGGGUGACCA
AE015451.1/4735854-4735637 CCGAGGUGCGG-GUGGUGA-GCCCGCACUGAGG--UAA--AA-CCCGAAC-AAGG--GCCCACAAAGC--CCGC-GUUCAUUACCUAUGAAGAUAUGA-GACCAGCAGGGGCUUUCCGGGCUGGUACCCGGAA--AAUCAGCAGGAUCC-A-AGUGGCGU---GGUUCAGU--C-G-CUGUUUUCG-G-ACUUUUCCAGGUUU--GCUGUGGC--UCU-CGCC-GAUC--AG-UCCCCUAAUCGAGGGUGACCA
CP000058.1/2325229-2325446 CUGCGGCGCAG-G-CUUCAA-CCGGCGCCGUAGUUUUA--A--CCUGAGC-A-GU-AGCUCGCAAAGCU-GCC--GCUCUU-A-UUUUGAAGAAAUGA-GACCAGCAGGGGCA-UCCGGGCUGGUACCCGGA--CUAUCUGCGUGAUCCCU-GGUGACUU---GAUACAGU--CG--CUGCACA--CG-ACUAUUUCAGGAUU--GCUCUGGUG-UCUUCGCC-GGUGG-UG-UCCCCUUACCGAGGGUGACCA
CP000744.1/3824583-3824370 CUGUGGCGCCG-GAGUUCU-UCCGGCGUCGCAG--CAACUAAGC--GGGC---CA-AGCUCACAAAGCCAUG---GCCCAG-A-UUUGAAAAAUAU---GACCAGCAGGGGCA-UCCGGGCUGGUACCCGGA--CUAUCUGCGGGAUCUGUAGUGGCCAUACCGAU--GUCG-CUGCCUG------AG-GAC-U-UCG-GAGC--CUUCAAGGU-UU--CGCCAGGUGGUUG-UCCCCUUACCGAGGGUGACCU
CP000094.2/1802825-1803041 CUUAGGCGCGG--GCUUCAAC-CCGCGCCAUGG--CUAU-AA-CCAGAGC-A-GC--AGCCAUAAGCU--GCG--GCUCUU-A-UUUUGAAGAAAUGA-GACAAGCAGGGGCA-UCCGGGCUGGUACCCGGA--CUAUCAGUGUGAUCCUA-AGUGGCUU---GUUUUGGU--C-G-CUGCAUUCG-G-ACUUCUGCAAGCUU--GCUC-GGUG-UCGGCACC-GAUGG-UGUUCCCCUAACCGAGGGUGACCA
#=GC SS_cons               <<<<<<<<<<<.<<_____.>>>>>>>>>>>>>..,,,..,,,,,,<<<<...<<.-<<<_____>>>-.>>...>>>>--.-.--------------.-------(((((((.<<<<<<______>>>>>>..<<<<<-<<<-<<<<<--.<<<<<<<<...<<---<<<..<<_.________.>>.>>>--->>>>>->>..>>>-->>>-.>>-.>>>-.>>>>>.)).-))))):::::::::::::::
#=GC RF                    CcgcGgcGCcG.Gguuuaa.cCCgGCgcCgcgG..uaA..AAGccuGaGC...gg.AGCuCAcAAaGCc.cc...GCuCau.A.uUuugAAgAuAUGA.GACcAGCaGGGGCa.uCCGGGCUGGUACCCGGa..CcauCuGcGgGacCcgu.gggggCcu...ggUuuggu..CgG.CUGcauuc.cG.accuUuccagGacc..ccccugGgu.uCu.CgCC.GaugG.uG.UCCCCuuAcCGAGGGUGACCA
//
# STOCKHOLM 1.0

#=GF AC   RF01759
#=GF ID   sucC
#=GF DE   sucC RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   50.00
#=GF TC   61.90
#=GF NC   41.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   SucC_RNA_motif
#=GF SQ   18


AM181176.4/1990066-1990136     GUCACAGGUGGCGCGGCACUCA--UAAUGAGCGCAGCGCCGAA-UGCGCAGUACCUA-ACGAA-GACGGU-AAAAAG
AE015451.1/4729904-4729836     GUCACAGGUGGUGCGGCGCCA-CUGA--UGGCGCAGCGCCGAA--GCGCAGUACCUA-ACGAA-GACGGU-AAAAAG
CP000949.1/3869575-3869507     GUCACAGGUGGUGCGGCGCCA-GUAA--UGGCGCAGCGCCGAA--GCGCAGUACCUA-ACGAA-GACGGU-AAAAAG
CP000058.1/2331289-2331357     GUCACAGGUGGUGCGGCACG--CUGA---CGUGCAGCACCGAA-UGCGCAGUACCUAAACGAA-GACGGU-AAUAAG
AF128399.1/418-488             GUCACAGGUGGUGGGGCGC---CACGA---GCGCUCCGCCGAAAUGCGCAAUACCUAGACGAAUAACGGUAGACAAG
CP000438.1/3913400-3913330     GUCACAGGUGGUGGGGUGC---CACGA---GCGCUCCGCCGAAAUGCGCAAUACCUAGACGAAUAACGGUAGACAAG
CP000076.1/1927644-1927715     GUCACAGGUGGUGCGGCACUCAAUCU-UGAGCGCAGCGCCGAA-UGCGCAGUACCUA-ACGAA-GACGGU-AAAAAG
AE016853.1/2425315-2425383     GUCACAGGUGGUGCGGCACG--CUGA---CGUGCAGCACCGAA-UGCGCAGUACCUAAACGAA-GACGGU-AAUAAG
CP000680.1/2763649-2763581     GUCACAGGUGGCGCGGUAU---CACAA---GUACAGCGCCGAA-UGCGCAAUACCUAAACGAA-GACGGUAGACAAG
CP000744.1/3818499-3818429     GUCACAGGUGGUGGGGCGC---CACGA---GCGCUCCACCGAAAUGCGCAAUACCUAGACGAAUAACGGUAGACAAG
AAXY01000001.1/309539-309608   AUGAUCCGCAGUGCGGGGUC--GCUCA--GGCCCCGCGCUGAG-AGCGCAGUAACAAAACAAG-GACGGU-AAGCCA
CP000712.1/1874247-1874315     GUCACAGGUGGUGCGGCGCCA-CUGA--UGGCGCAGCGCCGAA--GCGCAGUACCUA-ACGAA-GACGGU-AAAAAG
AE004091.2/1730109-1730179     GUCACAGGUGGUGGGGCGC---CACGA---GCGCUCCGCCGAAAUGCGCAAUACCUAGACGAAUAACGGUAGACAAG
CP000926.1/4181364-4181296     GUCACAGGUGGUGCGGCGCCA-GUAA--UGGCGCAGCGCCGAA--GCGCAGUACCUA-ACGAA-GACGGU-AAAAAG
CP000075.1/2335517-2335585     GUCACAGGUGGUGCGGCACG--CUGA---CGUGCAGCACCGAA-UGCGCAGUACCUAAACGAA-GACGGU-AAUAAG
CT573326.1/3922206-3922138     GUCACAGGUGGUGCGGCGCCA-GUAA--UGGCGCAGCGCCGAA--GCGCAGUACCUA-ACGAA-GACGGU-AAAAAG
AAQW01000001.1/2290395-2290465 GUCACAGGUGGUGGGGCGC---CACGA---GCGCUCCGCCGAAAUGCGCAAUACCUAGACGAAUAACGGUAGACAAG
CP000094.2/1808806-1808876     GUCACAGGUGGCGCGGCACUC-AUAAA-GAGCGCAGCGCCGAA-UGCGCAGUACCUA-ACGAA-GACGGU-AAAAAG
#=GC SS_cons                   ::::::::<<<<<<-<<<<<.._____..>>>>>->>>>>>::.:::::::::::::::::::.::::::.::::::
#=GC RF                        GUCACAGGuGGuGcGGcGCc..cuuaA..gGCgCagCgCCgAA.UGCGCAGUACCUAaACGAA.GACGGU.AAaAAG
//
# STOCKHOLM 1.0

#=GF AC   RF01760
#=GF ID   traJ-II
#=GF DE   traJ-II RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   40.00
#=GF TC   40.60
#=GF NC   38.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   TraJ-II_RNA_motif
#=GF **   seedtax: other sequences; Bacteria; unclassified sequences
#=GF SQ   47


CP001012.1/26926-26824     GGGCAGGAUA-UGUGAAGUAGG-CCCACCG-GAAA-UC-CGGUGUUCCUUCUUCACUU-UCCC-UUAUUCGCACCUU-CGGUACUCAACGGGA----AUCCUGCUCUGCGAGGCU
CP000301.1/3949352-3949248 GAUUUCGGCA-UUCGGAACGGG-GCCCCAU-UGAA-GA-AAAGGAGCC-AUUCCGGUA-AUCC-UGAGU-UGGGAUU-AUCCCAUUUUGGGAUACUUGCUGAAAUCCGUGGGGUG
EF079106.1/90966-90864     GGGCAGGAUG-UGCGAAGUUAG-CUAACCG-GCGG-GC-CGGUUAUCUAUCUUCGCUG-UCCC-UUAUUCGCGCCUG-CGGCACUCAACGGGC----AUCCUGCUCUGCGAGGCU
AATN01002910.1/431-532     GGGCAGGAUA-UGUGAAGUAGG-CCCACCC-GCAA-GC-GGGUCGUCCUUCUUCACGAAGCCC-UUAUUCGCA-CUG-CG-UGCUCAACGGAC----AUCCUGCUCUGCGAGGCA
AATO01014663.1/426-326     GGGCAGGAUA-GGUGAAGUAGG-CCCACCC-GCAA-GC-GGCUUGUCCUUCUUCACUGCGCCU--UAUUCGCA-CUG-CG-UGCUCAACGGGC----GUCCUGCUCUGCGAGGCC
CR555308.1/58535-58432     GGGCAGGAUG-GGCGAAGUUAG-CUAACCAGCGGA--GCCGGUUAUCUACCUUCGCUA-ACCC-UUAUUCGCGCCGG-GGGCGCUCAACGGGC----AUCCUGCUCUGCGAGGUU
AATO01000064.1/3040-3141   GGGCAGGAUA-UGUGAAGUAGG-CCCACCC-GCAG-GC-GGGUCGUCCUUCUUCACGAAGCCC-UUAUUCGCA-CUG-CG-UGCUCAACGGAC----AUCCUGCUCUGCGAGGCA
AAJT02000036.1/37600-37697 CGGCAGGAUG-UGUGUUGUAC--CGGUACGGGCAA-GCCCGCACCA-GUCCAACACCG-CCCC-UUACUCACC--UA-C--GGUUCGACGG--C---AUCCUGCUCUGCGAGGCU
DQ065837.1/46261-46159     GGGCAGGAUA-GGUGAAGUUAG-CUAACCG-GAAA-GC-CGGUUAUCUAUCUUCACUAUCCCC-UUAUUCGCA-CUU-CG-UGCUCAACGGGGA---AUCCUGCUCUGCGAGGCU
CP000019.1/2725-2621       GGGCAAGAUA-UGUAAAGUUGGCCUUAUUUUAUGAAAUAAAAUAAAUCCACUUUACU--CGGAUGUAUUCGCC--AU-A--GGCUCAAAUCCUAU--AUCUUGUCCUUCAGAGUU
CP000802.1/2661881-2661783 GGGCAGGACA-UGUAAAGUGGG-CCCACCG---CU-A--CGGUGUUCCAACUUUACCA-CUCC-CUAUUCGCCGCAU-CGCGGCUCAAGGG--C---GUCCUGCUCUGCGAGGCU
CP000514.1/1924450-1924346 GGGCAGGAUA-GGUGAAGUUAG-CUAACCGGCGGA--GCCGAUUAACUAUCUUCACUU-CCCC-UUAUUCGCCCCGG-AGGCGCUCAACGGGUA---AUCCUGCUCUGCGAGGCU
CP000894.1/6849-6746       GGGCAGGAUA-GGUGAUGUAGUCCUACAAUGGUAA-ACCAUUGCAGACUUCAUCACUU-UGAC-UUAUUCGCUCCCUUCGGGGCUCAACG-------UUCCUGCUCUGCGAGGCA
CP000539.1/2704928-2704828 GGGCAGGAUA-UGUGAAGUAGG-CCCACCG-GCAA-GC-CGGUUGUCCUUCUUCACUG-UCCC-UUAUUCGCGC-GG-G-GCGCUCAACGGGC----AUCCUGCUCUGCGAGGCU
AM286415.1/1319525-1319423 GGGCAAGAUA-GGUGAAGUUAG-CUAACCA-GCAA-GC-UGGUUAUCAAUCUUCACUC-UCCC-UUAUUCGCACCUU-CGGCGCUCAACGGGG----AUCUUGCUCUGCGAGGCA
AATO01000111.1/3894-3995   GGGCAGGAUA-UGUGAAGUAGG-CCCACCC-GCAG-GC-GGGUUGUCCUUCUUCACGAAGCCC-UUAUUCGCA-CUA-CG-UGCUCAACGGAC----AUCCUGCUCUGGGGGUGU
AM778842.1/22315-22211     GGGCAGGAUG-UGUGAAGUAGG-CCCACCAUGCAA-GCAUGGUGAUCCU-CUUCACUU-CCCC-UUAUUCGCGCCUG-CGGCGCUCAACGGGGC---AUCCUGCCCUGCGGGGCC
AB237782.1/39467-39364     GGGCAAGAUG-GGCGAAGUUAG-CUAACCG-GCAA-GC-CGGUUAUCUAUCUUCGCUU-CCCC-UUAUUCGCGCCGG-UGGCACUCAACGGGGC---AUCUUGCUCUGCGAGGCA
AATO01000068.1/16563-16663 GGGCAGGAUA-GGUGAAGUAGG-CCCACCC-GCAA-GC-GGCUUGUCCUUCUUCACUGCGCCU--UAUUCGCA-CUG-CG-UGCUCAACGGGC----GUCCUGCUCUGCGAGGCC
CP000541.1/55378-55480     GGGCAGGAUA-GGCGAAGUUAG-CUAACCG-GCGA-GC-CGGUUAUCUAUCUUCGCUG-UCCC-UUAUUCGCGCCUG-CGGCACUCAACGGGC----AUCCUGCUCUGCGAGGCG
AE014292.2/351801-351898   CGGCAAGAUG-UGUGUUGUAC--CGGUACGGGCAA-GCCCGCACCA-GUCCAACACCG-CCCC-UUACUCACC--UG-C--GGUUCGACGG--C---AUCUUGCUCUGCGAGGCU
AB231906.2/16811-16708     GGGCAGGAUG-UGCGAAGUUAG-CUAACCGGGCGA-GC-CGGUUAUCUAUCUUCGCUG-UCCC-UUAUUCGCGCCUG-CGGCACUCAACGGGC----AUCCUGCUCUGCGAGGCG
AATO01006181.1/93-193      GGGCAGGAUA-GGUGAAGUAGG-CCCACCC-GCAA-GC-GGCUGGUCCUGCUUCACGGCGACU--UAUUCGCA-CUG-CG-UGCUCAACGGGC----GUCCUGCUCUGCGAGGCC
CP000718.1/50565-50463     GGGCAAGAUA-GGUGAAGUUAG-CUAACCG-GCAA-GC-CGGUUAUCUAUCUUCACUC-UCCC-UUAUUCGCGCCUC-CGGCACUCAAUGGGA----AUCUUGCUCUGCGAGGCU
ACKA01000056.1/36240-36140 GGGCAGGAUA-GGUGAAGUUAG-CUAACCG-GCAA-GC-CGGCUAACUAUCUUCACUC-CCC--UUAUUCGCGCCGU-CGGCGCUCAAC-GGGC---AUCCUGCUCUGCGAGGC-
U55819.1/7294-7191         GGGCAGGAUA-GGUGAAGUAGG-CCCACCC-GCGA-GC-GGGUGUUCCUUCUUCACUG-UCCC-UUAUUCGCACCUGGCGGUGCUCAACGGGA----AUCCUGCUCUGCGAGGCU
AB084167.1/1746-1843       GGGCAAGACA-GGUGAAGUAGG-CCCACCA-GCAA-GC-UGGUGAUCCUUCUUCACGUCUUGC-CUAUUCGCC--UACC--GGCUCAAGGUGA----GUUU--CCGAAUCGGAA-
CP000675.2/637692-637591   GGGCAAGAUA-GGUGAAGUUAG-CUAACCA-GCAA-GC-UGGCUAUCAAUCUUCACAA-ACCU--UAUUCGCACCUU-CGGUGCUCAACGGGU----AUCUUGCUUUUUGAGAUC
AJ431260.1/72113-72011     GGGCAGGAUA-GGCGAAGUUAG-CUAACCG-GCAA-GC-CGGUUAUCUAUCUUCGCUG-UCCC-UUAUUCGCGCCUG-CGGCACUCAACGGGC----AUCCUGCUCUGCGAGGCG
X54458.1/4722-4619         GGGCAGGAUG-UGUGAAGUUAG-CUAACCG-GCGA-GC-CGGUUAUCUAUCUUCACUG-UCCC-UUAUUCGCGCCGG-GGGCGCUCAACGGGUC---AUCCUGCUCUGCGAGGCA
AATO01001338.1/1541-1617   --------UA-UGUGAAGUAGG-CCCACCC-GCAG-GC-GGGUCGUCCUUCUUCACGAAGCCC-UUAUUCGCAC-UG-C-GUGCUCAACGGGG----A-----------------
AACY020355487.1/1834-1731  GGGCAGGAUG-GGUGAUGUAGUCCUACAAUGGUAA-ACCAUUGCAGACUUCAUCACUU-UGAC-UUAUUCGCUCCCUUCGGGGCUCAACG-------UUCCUGCUCUGCGAGGCC
CP000521.1/788981-789083   GGGCAGGAUG-GGUGAAGUUAG-CUAACCG-GCAA-GC-CGGUUAUCUAUCUUCACUG-UCCC-UUAUUCGCGCCGG-GGGCACUCAACGGGA----AUCCUGCCCUGCGGGGCU
CR628336.1/68995-68919     --------UA-UGUGAAGUUAG-CUAACCA-GCAA-GC-UGGUUACCAAACUUCACGA-GUCU--UAUUCUCACCUU-CGGUGCUCAACGGAA----A-----------------
AAKK02000007.1/48960-48861 GGGCAGGAUA-GGUGAAGUAGG-C-CCACCAACAA-GUUGAUGGUUCCUAUUUCACUC-GUCCUUUAUUCGCACCUU-CGG-GCUCAACGGUCC-----CCUGCUCUACGAG---
CP000231.1/12307-12404     GGGCAGGAUG-UGUGUUGUAC--CGGUACGGGCAA-GCCCGCACCA-GUCCAACACCG-CCCC-UUACUCACC--UG-G--GGUUCGACGG--C---AUCCUGCUCUGCGAGGCU
BX572606.1/138193-138089   GAUUUCGGCA-UGUGGAACGGG-GCCCCAU-UGAA-GA-AAAGGAGCC-AUUCCGGUA-AUCC-UGAGU-UGGGAUU-AUCCCAUUUUGGGAUACUUGCUGAUAUCCGUGGGGUG
CP000522.1/12579-12479     AGGCAAGAUG-UGUAAUGUUAU-AUAACAUGGCAAGCCUUGGUUAUAUAA-AUUACC--CGAC-UUAUUCGCU--UU-C--AGCUCAACGUGGC---AUCUUGUCCUGCGGAGCU
BX571965.1/3882620-3882519 GGGCAGGAUG-UGUGAAGUAGU-CCCACCG-GCAA-GC-CGGCGUUCCUACUUCACU--UUCC-UUAUUCGCACCUU-CGGUGCUCAACGGAA----AUCCUGCUCUGCGAGGCA
AATO01001339.1/2043-2117   ----------AUGUGAAGUAGG-CCCACCC-GCAA-GC-GGGUCGUCCUUCUUCACGAAGCCC-UUAUUCGCAC-UG-C-GUGCUCAACGGGG----------------------
AATO01001736.1/260-360     GGGCAGGAUA-GGUGAAGUAGG-CCCACCC-GCAA-GC-GGCUUGUCCUUCUUCACGGCGCCU--UAUUCGCA-CUG-CG-UGCUCAACGGGC----GUCCUGCUCUGCGAGGCC
CP000451.1/49656-49755     AGGCAAGAUG-UGUAAUG-UAG-UCCUACAUGCUACGCAUUUUG-GCUAACAUUACCU-UCAC-UUAUUCGCC--UU-U--GGCUCAACGUUA----AUCUUGCUCUGCGAGGCC
K00832.1/110-7             GGGCAGGAUA-GGUGAAGUAGG-CCCACCC-GCGA-GC-GGGUGUUCCUUCUUCACUG-UCCC-UUAUUCGCACCUGGCGGUGCUCAACGGGA----AUCCUGCUCUGCGAGGCU
CP000675.2/204445-204345   GGGCAAGAUA-GGUGAAGUUAG-CUAACCA-GCAA-GC-UGGCUAUCAAACUUCACA--AGCC-UUAUUCGCACCUA-CGGUGCUCAACGG--U---AUCUUGCUUUUUGAGAUC
CP000438.1/1312525-1312628 GGGCAGGAUG-UGUGAAGUAGG-CCCACCC-GCAA-GC-GGGUUGUCCUUCUUCACGU-CCCC-UUAUUCGCGCCGG-GGGCGCUCAACGGGGC---AUCCUGCUCUGCGAGGCU
AATO01004256.1/272-372     GGGCAGGAUA-GGUGAAGUAGG-CCCACCC-GCAA-GC-GGCUUGUCCUUCUUCACGGCGCCU--UAUUCGCA-CUG-GG-UGCUCAACGGGC----GUCUUGCUCUGCGAGGCC
L36668.1/237-134           GGGCAGGAUA-GGUGAAGUAGG-CCCACCC-GCGA-GC-GGGUGUUCCUUCUUCACUG-UCCC-UUAUUCGCACCUGGCGGUGCUCAACGGGA----AUCCUGCUCUGCGAGGCU
#=GC SS_cons               (((((((((,.,<<<<<<-<<<.--<<<<<.<___._>.>>>>>-->>>->>>>>>,,.<<<<.------<<<<<__._>>>>>----->>>>,...))))))))):::::::::
#=GC RF                    GgGcagGauA.uGuGaaGUagG.cucaccg.gcAA.Gc.cggugauCcuuCuuCaCua.cccC.UUAUUCgcgccUu.cggcgcUCAAcGggga...auCcugCuCUGcGaGGcu
//
# STOCKHOLM 1.0

#=GF AC   RF01761
#=GF ID   wcaG
#=GF DE   wcaG RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   42.00
#=GF TC   42.10
#=GF NC   40.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   WcaG_RNA_motif
#=GF **   seedtax: Viruses; unclassified sequences
#=GF SQ   118


AACY021406512.1/454-355   CUGUGUCCUGG-AAUG---A-CAUUAAA--------CUUACCCUGGUGCGGAUGG-GAUAU--CUC-------UC-CCGCC--UGG-UUUCUUAUUU--CCA---GUCA--AAG-AAUAAGUGGU-GGAUCCAAUU
AACY023469040.1/185-282   UCUAAUUUCUUGCUUU---A-C--UUUA--------AAGCAAGUGGUGCGGAUGGAGGUAA------------CUCCCGCU--CUG-UUUCUUACUU--CAG---GUAA--AAG-AGUAAGUGGC-GUGCAUGUAA
AACY020324371.1/52-147    UUUGGUUUCUUGCU-U---C-C--UAA---------AAGCAAGUGGUGCGGAUGG-GAUUA---UC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AACAAGUGGC-GUGCAUGUAA
AACY020752344.1/390-290   UCUGGUUUCUUGCU-UUU-C-CA-UCAAA-------AAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUUA--AAG-AAUUGGUGGC-GAGCAACCUG
AACY020568242.1/264-167   UAUACCCCGUUGGA-U---AAGGGUUA---------AGCCAACUGGUGCGGA------CAUCU----------------GCAAAGG-UUUCUUGUUUUUCCUUACGUCUAAAAG-AACAAGUGGC-GAGCCUGCAA
AACY023433109.1/137-234   AAGAGUUUCCAGUU-U---CUU--UCAA--------AAACUGGUGGUGCGGA------ACAUCUGC---------------AACGG-UUUCCUAUUUUUCCGUUCGUCUCAAAG-AAUAGGUGGC-GAGCCUGAGU
AACY023547826.1/1166-1069 UUUGGUUUCUUGCUUU---C-C--CAAA--------GAGCAAGUGGUGCGGAUGGAGGAAA------------CUCCCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AAUAAGUGGC-GUGCAUGGCA
AACY020459569.1/734-637   AAGAGACUCGG-UAAG---UCGUAUAAA--------CUAGCCCUGGUGCGGAUGG-GUUAC------------UC-CCGCU--CUG-UUUCUUACUU--CAG---GUUA--AAG-AGUAAGUGGC-GUGCAUGACA
AACY020324138.1/1766-1666 UAAAGUUUCCUGCU-U---CUA--UCAA--------AAGCAGGUGGUGCGGAUGG-GGUUUUAUAC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AACAAGUGGC-GUGCAUGGUA
AACY020665448.1/671-574   AUGAGUUUACGGCA-U---CUC--UCAA--------AUGACGUUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUCA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY023529106.1/239-334   UCUGGUUUCUUGCU-U---C-C--UAA---------AAGCAAGUGGUGCGGAUGGAGGAAA------------CUCCCGUC--CUG-UUUCUUACUU--CAG---GAUA--AAA-AGUAAGUGGC-GUGCAUGGCA
AACY023934810.1/336-436   UAAAGUUUCCUGCU-U---CUA--UCAA--------AAGCAGGUGGUGCGGAUGG-GGUUUUAUAC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AACAAGUGGC-GUGCAUGGUA
AACY020171514.1/1767-1863 CGAAGUCCUGG-AAUG---ACU--UGAAU-------CUUACCCUGGUGCGGAUGG-GGCAA------------CC-CCGCC--CAG-UUUCUUGCUU--CUG---GAUA--AAG-AGCAAGUGGC-GAGCCUGAAG
AACY020176707.1/31-128    UUUGGUUUCUUGCUUC---C-A--UAAA--------GAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GCCA--AAG-AAUUGGUGGC-GAGCCUGAAU
AACY022763676.1/152-249   AUGAGUUUACUGCC-U---CUC--UCAA--------GGGCAGUUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUUA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY020487672.1/475-573   UUGAGUUUCUUGCU-U---CUC--CCAA--------AAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUA---AAG-AGCAAGUGGC-GUGCAUGAAG
AACY020339333.1/547-645   UUGAGUUUCUUGCU-U---CUC--CCAA--------AAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUA---AAG-AGCAAGUGGC-GUGCAUGAAA
AACY020340892.1/670-571   GAUGGUUUCUUGCUUU---ACC--UAA---------GAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUAA--AAG-AGUAAGUGGC-GUGCAUGAAA
AACY020174582.1/308-207   UCUGGUUUCUUGCU-UUUUC-CA-UAAAA-------AAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUUA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY020340941.1/516-608   AAUGGUUUCUUACU-U---C-C--UAA---------AAGUAAGUGGUGCGGAUGG-GAUU-------------UC-CUGCC--UGG-UUUCUAAUUU--CCA---GUUA--AAA-AAUUAGUGGC-GAGCCUGCAA
AACY020338817.1/1719-1622 CAUGGUUUCCUGCUUC---C----UCAAA-------GAGCAGGUGGUGCGGAUGGAG-UUUA--C---------UCCCGCC--UGG-UUUCUUGUUU--CCA---GUCA--AAG-AACAAGUGGC-GAGCCUAGGG
AACY022874153.1/651-557   CACGUCUCGGGACG-A---CGC--UAAAC-------UCG-CCCUGGUCGGGAUGGGUUUA----AC-------GACCCCUC--GGG-UUUCCUAGUU--CCU---------AAA-ACUAGGUGGU-GGAGUCAUAU
AACY020340614.1/593-690   AAUACCCCGUAGGA-U---AAGGGUUA---------AGCCUGCUGGUGCGGAUGG-GAUC----UU-------UC-CCGCC--UGU-UUUGUUUGUU--UCA---GUAA--AAA-ACAAGCACCC-CAUAAAUAAU
AACY024102834.1/487-392   UCGGGUUUCUUGCU-U---C-C--UAA---------AAGUAAGUGGUGCGGAUGG-GAUA----AC-------UC-CCGCC--UGG-UUUCUAUGUU--CCA---GUCA--AAA-AUGUAGUGGUGGAGUCAAUUA
AACY020486676.1/450-555   UGGUGCCCGCAAGAUAAGGCACAAUAAAAA------UUCUUGCUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUCA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY020335869.1/2449-2354 UUUAGUUUCCUUGU-U---C----UUAA--------AAUAAGGUGGUGCGGAUGG-GAUUA---UC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AACAAGUGGC-GUGCAUGUAA
AACY021154134.1/427-527   UUUGGUUUCUUGCU-UUU-C-CA-UUAAA-------AAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCUUGCCU--CCA---GUUA--AAG-GGCAAGUGGC-GAGCCUGAGU
AACY023436498.1/646-743   UUUGGUUUCUUGCUUC---C-A--UAAA--------GAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUCA--AAG-AAUUGGUGGC-GAGCCUGAAU
AACY020521214.1/641-548   CAGUCUCGGGAUGACU---C----UAAA--------AGCGCCCUGGUGCGGGUGG---AUGUUG------------CCGCU--UGG-UUUGUGUGUU--CCA---GUCA--AAG-ACACUCUGGU-AAAUCCCCUU
AACY023931175.1/1535-1436 AAAGAGUCGG--UA-U---CUCGAUAAA--------CUAGCCCUGGUCGGGAUGG-GUUGA---CC-------CC-CCUCCGCUGG-UUUCUUGCUU--CCA---GUCA--AAG-AGCAAGUGGC-GCGGCAUGAU
AACY023933048.1/1193-1295 AUGGGUUUCUUGCU-U---C-C--UAA---------AAGCAAGUGGUGCGGAUGGAGUAAU------------GCUCCCGCUUGAGAUUUAGUUAUUA-CUCAACAUAA--AAA-AUAACUUGGC-GUGCAUGAUC
AACY021847009.1/372-471   UAGAGUUUCUUGCU-U---CUC--UCAA--------GAGCAAGUGGUGCGGAUGG-GGUU-UAUAC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AAUAAGUGGC-GUGCAUGGCA
AACY021240789.1/185-86    UGAGGUUUCUUGCUUC---UCC--UAA---------GAGCAAGUGGUGCGGAUGGGGUUUA---UA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GACA--AAG-AGCAAGUGGC-GUGCAUGAAA
AACY020006358.1/1315-1216 GAUGGUUUCUUGCUUU---UCC--UAA---------GAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUUA--AAG-AGCAAGUGGC-GUGCAUGAAA
AACY020994419.1/441-536   AUAGGUUUCUUGCU-U---AUC--CUAA--------GAGCAAGUGGUGCGGAUGG-GUAAC------------UC-CCGCC--CUG-UUUCUUGCUU--CAG---GAUA--AAG-AGCAAGUGGC-GUGCAUGAAA
AACY021173470.1/304-207   UGAGGUUUCUUACUUU---ACC--UAA---------GAGUAAGUGGUGCGGAUGGAGGUAA------------CUCCCGCC--CUG-UUUCUUACUU--CAG---GUAA--AAG-AGUAAGUGGC-GUGCAUGUAA
AACY022099058.1/560-461   AAGAGUUUCUCUGU-UCUCUAAAAUAAA--------AACAGAGUGGUG-GAG------UCAUUAUGACCCU------CUUA--GAG-UUUCCAGUUU--CUC---UA----AAA-AACUGGUGGC-GAGCCUGCUC
AACY023437546.1/946-849   UUUGGUUUCUUGCUUC---C----UCAAA-------GAGCAAGUGGUGCGGAUGGAGGUUA------------CUCCCGCC--UGG-UUUCCAAUUU--CCA---GUCA--AAA-AAUUGGUGGC-GAGCCUGAGU
AACY022874153.1/551-454   CAUGGUUUCCUGCUUC---C-U--UAAA--------GAGCAGGUGGUGCGGAUGGAG-UUUA--C---------UCCCGCC--UGG-UUUCUUGUUU--CCA---GUUA--AAG-AACAAGUGGC-GAGCCUAGGG
AACY020166190.1/1316-1219 AUGAGUUUCUUGCU-U---CUC--UCAA--------GAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--CAG-UUUCCUGCCU--CUG---GUCA--AAG-GGCAGGUGGC-GAGCCUGAGU
AACY023363708.1/876-974   GAUGGUUUCUUGCU-U---AUC--CUAA--------GAGCAAGUGGUGCGGAUGG-GGUUC-AUAC-------UC-CCGCC--CUG-UUUCUUGCUU--CA----GAUA--AAG-AGCAAGUGGC-GUGCAUGAAA
AACY020485999.1/3304-3207 CAACUUUUCCUAGUUU---CG---UAA---------AACUAGGUGGUGCGGAUGG-GAUA----AC-------UC-CCGCC--GAG-UUUCUUGUUUU-CUC---GUACUCAA--AACAAGUGGC-GAGCCUGAGU
AACY023558097.1/628-529   AUAAGUUUCUUGCU-U---CUU--UCAA--------GAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUUA--AAG-AGCAAGUGGC-GUGCAUGUAA
AACY020498360.1/1176-1081 UUUGGUUUCUUGAU-U---C-C--UAA---------AAUCAAGUGGUGCGGAUGGAGAUA----AC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AACAAGUGGC-GUGCAUGGAG
AACY023447645.1/875-779   AUGAGUU-CUUGCU-U---CUC--UCAA--------GAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUCA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY022190565.1/62-161    CGGAGUUUCUUGCU-U---CUC--UCAA--------GAGCAAGUGGUGCGGAUGG-GGUU-UAUAC-------UC-CCGCC--CAG-UUUCUUGCUU--CUG---GUUA--AAG-AGCAAGUGGC-GUGCAUGUAA
AACY020486822.1/926-830   GUAGGUUUCCAAUU-U---C-C--UAAAA-------GAAUUGGUGGUGCGGAUGGGGAAUU---UU-------UCUCCGCC--U-G-UUUCCUAGUU--C-A---GUCA--AA--ACUAGGUGGC-GAGCCUAGCA
AACY023580067.1/846-943   UUGAGUUUCUUGCU-U---CUC--CUAA--------AAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG-----UA--AAG-AGCAAGUGGC-GUGCAUGAAG
AACY023935885.1/561-491   -------------------------------------------UGGUGCGGAUGG-GAUUA---UC-------UC-CCGCA--GAGAUUUAGUUAUUA-CUC---UUCA--AAA-AUAACUUGGC-GUGCAUGAAA
AACY021909184.1/632-534   UCGGGUUUCCAGUUUU---UCC--AUAA--------GAACUGGUGGUGCGGAUGG-GAAAC---UC-------UC-CCGCC--UGG-UUUCUUAUUU--CCA---GUCA--AAA-AAUAAGUGGU-GGAUCCAAAU
AACY020238087.1/519-614   GAUGGUUUCUUGCUUU---A-C--CAAA--------GAGCAAGUGGUGCGGAUGG-GUUAC------------UC-CCGCC--CUG-UUUCUUGCUU--CAG---GUAA--AAG-AGCAAGUGGC-GAGCCUGCAA
AACY021992908.1/267-170   AAGUCCUCGUCGGAUG---GACAAUAAAUA------UGCCGACUGGUGCGGAUGG-GGUUA------------CC-CCGCC---UG-UUUCUUAUUU--CA----GUCA--AA--AAUAAGUGGC-GAGCAUACAA
AACY020339347.1/240-335   UUCGGUUUCCUUGU-U---C-C--UAA---------AAUAAGGUGGUGCGGAUGG-GAUUA---UC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AAUAAGUGGC-GUGCAUGUAA
AACY020832060.1/441-538   UUGAGUUUACUGCC-U---CUC--UAAA--------GGGCAGUUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GCCA--AAG-AAUUGGUGGC-GAGCCUGAAA
AACY020337922.1/1019-1117 UUGAGUUUCUUGCU-U---CUC--CUAA--------AAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUA---AAG-AGCAAGUGGC-GUGCAUGAAA
AACY022941420.1/383-284   UAGAGUUUCCUGCU-U---CUC--UAAA--------AAGCAGGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUCA--AAG-AGCAAGUGGC-GUGCAUGUAA
AACY020473179.1/1523-1620 AGAUCCCCGUAGGA-U---AAGGGUUA---------AGCCUACUGGUGCGGAUGG-GAUA----AC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUAA--AAG-AAUUGGUGGC-GAGCCUGCAA
AACY020182006.1/560-463   AUGAGUUUACUGCC-U---CUC--UCAA--------GGGCAGUUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUCA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY023931023.1/219-314   UCUGGUUUCUUGUU-U---C-C--UAA---------AAACAAGUGGUGCGGAUGGAGGAAA------------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUUA--AAG-AGCAAGUGGC-GUGCAUGAAA
AACY020171136.1/1252-1156 GUAGGUUUCCAAUU-U---C-C--UAAAA-------GAAUUGGUGGUGCGGAUGG-GAUA----AC-------UC-CCGCC--UGG-UUUCUUGCCU--CCA---GUCA--AAG-GGCAAGUGGC-GAGCCGAGCA
DQ149023.2/163184-163278  GACAGUUUCUUACUUU---A----GAAA--------AAGUAAGUGGUGCGGAUGG-GGUUA------------CC-CCGCC--UGG-UUUCUACAUU--CCA---GUA---AAG-AUGUAGUGGUGGAGUCAACGA
AJ630128.1/122806-122905  CCGAGUCUUGG-AAUG---ACU--UAAAU-------CUUACCCUGGUGCGGAUGG-GAUCU--CUC-------UC-CCGCC--UGG-UUUCUUGCUU--CCA---GUCA--AAA-AGCAAGUGGU-GGUGCCAAAU
AACY022600388.1/475-570   AUGAGUUUACGGCA-U---CUC--UCAA--------AUGCCGUUGGUGCGGGUGG---GUU-ACUA----------CCGUC--CAG-UUUCUUGCUU--CUG---GUCA--AAG-AGCAAGUGGC-GUGCAUGGCA
AACY020544385.1/218-121   GAUGGUUUCUUGCUUU---A-C--CCAA--------GAGCAAGUGGUGCGGAUGGAGGUAA------------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUAA--AAG-AGCAAGUGGC-GUGCAUGAAA
AACY022620773.1/199-100   AGUUAUUCGU------CACGGAUGGACGUUAACAGC-----ACUGGUGCGGGUGAAGAUA-------------UCGCUGCC--UGG-UUUCUUGUUU--CCA---GUUA--AAG-AACAAGUGGC-GUGCAUGUGC
AACY023442510.1/1000-1097 AUGAGUUUACUGCC-U---CUC--UCAA--------GGGCAGUUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUUA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY020933926.1/713-811   UAAGGUUUAUUGCU-U---C-CUUUAAA--------GAGCAAUUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUUA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY020455774.1/1003-1097 CUAAGUUUCCUAGU-U---C----UUAA--------AACUAGGUGGUG-GAG------UCC---UAGGACCCU------CU-AAGGAAUUAGUUAUUA-CCUU--AUAA--AA--AUAACUUGGC-GUGCAUGGAA
AACY023903445.1/226-128   AUAGUCUUGGGAUGAC---U----UAAAAA------GCA-CCCUGGUCGGGAUGGGUUCUU---AC-------GACCCCUC--GGG-UUUCUUGCUU--UUC---CAU---AAG-AGCAAGUGGU-GGAGCUGAGU
AACY022132775.1/191-93    UCGGGUUUCUUGCUUU---UCC--UUAA--------GAGUAAGUGGUGCGGAUGG-GUUU----AC-------UC-CCGCC--UGG-UUUACAUGUU--CCA---GUCA--AAA-AUAUGUUGGUGGAGUCAAUUA
AACY021012095.1/286-191   AUAGGUUUCUUGCU-U---AUC--CUAA--------AAGUAAGUGGUGCGGAUGG-GUAAC------------UC-CCGCC--CUG-UUUCUUGCUU--CAG---GAUA--AAG-AGCAAGUGGC-GUGCAUGUAA
AACY020181470.1/1426-1330 GUAGGUUUCCAAUU-U---C-C--UAAAA-------GAAUUGGUGGUGCGGAUGG-GAUA----AC-------UC-CCGCC--CAG-UUUCUUGCCU--CUG---GUCA--AAG-GGCAAGUGGC-GAGCCUGGCA
AACY023429295.1/699-796   AUGAGUUUCUUGCU-U---CUC--UCAA--------GAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUUA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY020077076.1/391-486   UUUAGUUUCCUUGU-U---C----UUAA--------AAUAAGGUGGUGCGGAUGG-GAUUA---UC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AACAAGUGGC-GUGCAUGUAA
AACY021336111.1/354-453   UUUGGUUUCUUGCU-U---CUC--CCAA--------GAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUAA--AAG-AGCAAGUGGC-GUGCAUGUAA
AACY020166155.1/731-634   UAGAGUUUACGGCA-U---CUC--UCAA--------AUGCCGUUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUAA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY020238002.1/2256-2159 UGAGGUUUCUUACUUU---ACC--UAA---------GAGUAAGUGGUGCGGAUGGAGGUAA------------CUCCCGCC--CUG-UUUCUUACUU--CAG---GUAA--AAG-AGUAAGUGGC-GUGCAUGUAA
AACY023865031.1/116-206   CUGAGUUUCUUGCU-U---UUCUAUAA---------GAGCAAGUGGUGCGCU------ACAUCCG--------------CG--UAG-UUUCCUAGUU--CUA---CACA--AAA-ACUAGGUGGC-GAGCAUAUUA
AACY020027476.1/1789-1887 AAUUAUUCGU------CACGGAUGGACGUUAACAGC-----ACUGGUGCGGGUGAAGAUA-------------UCGCCGCC--UGG-UUUCCAAUUU--CCA---GUAA---AG-AAUUGGUGGC-GCGGCAUGUA
AACY020177781.1/2128-2032 GUAGGUUUCCAAUU-U---C-C--UAAAA-------GAAUUGGUGGUGCGGAUGGGGAAUU---UU-------UCUCCGCC--U-G-UUUCCUAGUU--C-A---GUCA--AA--ACUAGGUGGC-GAGCCUAGCA
AACY020314185.1/3337-3436 UCGGGUUUCUUGCU-U---CUCC-UUAA--------AAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCUUUCUU--CCA---GUCA--AAG-AGAAAGUGGUGGUGCCAAAAC
AACY020696823.1/335-432   AUUGUUUUCUUGCU-U---UUC--UCAA--------AAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUCA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY020798727.1/433-532   AAUGGUUUCUUGCUUU---ACC--UAA---------GAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUAA--AAG-AGCAAGUGGC-GUGCAUGAAA
AACY020070251.1/563-659   ACUUUUUUCUUGCUUU---A-C--UUAA--------AAGCAAGUGGUGCGGAUGG-GGUA----AC-------UC-CCGCC--CUG-UUUCUUGCUU--CAG---GUAA--AAG-AGUAAGUGGC-GAGCCUGCAA
AACY020551206.1/2476-2379 AUGAGUUUCUUGCU-U---CUC--UCAA--------GAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUUA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY020306749.1/1699-1597 UGGAGUUUCCAAUU-U---CUC--UAAA--------GAAUUGGUGGUGCGGAUGG-GGUUUUCAAC-------UC-CCGCC--GAG-UUUCCAAUUUU-CUC---GUAAUCAA--AAUUGGUGGC-GAGCCUAAGG
AACY020001553.1/1082-1177 UUAAGUUUCUUUGUUU---AGA--UAA---------AACAAAGUGGUGCGGAUGG-G-UUA--CU---------C-CCGCU--CAG-UUUCUUGCUU--CUG---AUUA--AAA-AGCAAGUGGC-GUGCAUGACA
AACY022080678.1/157-60    UAAGGUUUCUUGCUUU---UCC--UAA---------GAGCAAGUGGUGCGGAUGG---AUUUAACUC---------CUGCC--CUG-UUUCUUGCUU--CAG---GAUA--AAG-AGCAAGUGGC-GAGCCUGCAA
AACY020318368.1/175-274   CUGUGUCUUGG-AAUG---A-CAUUAAA--------CUUACCCUGGUGCGGAUGG-GAUAU--CUC-------UC-CCGCC--UGG-UUUCUUGUUU--CCA---GUCA--AAG-AACAAGUGGU-GGAUCCAAUU
AACY020948399.1/595-676   UUCAGAUGGU------GUCUU--------------------ACUGGUUCGUA------CCAAGGGAC------------AUAAUGG-UUUCUUGUUU--CCA---ACCA--AAG-AACAAGUGGC-GAGCCUGAAU
AACY022119961.1/132-232   UAAAGUUUCCUGCU-U---CUA--UCAA--------AAGCAGGUGGUGCGGAUGG-GGUUUUAUAC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AACAAGUGGC-GUGCAUGGUA
AACY023515813.1/1399-1302 AAAAGUUUCUUGCU-U---CUU--CCAA--------GAGCAAGUGGUGCGGAUGGAGGAAA------------CUCCCGCU--CAG-UUUCUUGCUU--CUG---AUCA--AAG-AGCAAGUGGC-GUGCAUGUAA
AACY022759608.1/715-811   AUGAGUUUACGGCA-U---CUC--UCAA--------AUGACGUUGGUGCGGAUGG-GGUU----AC-------UC-CCGCC--CAG-UUUCUUGCCU--CUG---GUCA--AAG-GGCAAGUGGC-GAGCCUGAGU
AACY021224282.1/688-786   UAAGGUUUCUUGCUUU---ACC--UAA---------GAGCAAGUGGUGCGGAUGG-GUUAC---GA-------CC-CCGCC--CUG-UUUCUUGCUU--CAG---GUAA--AAGGAGCAAGUGGC-GAGCCUGUAG
AACY020070251.1/216-310   CAAAGACUCGG-UAAG---UCG--UAAAA-------CUAGCCCUGGUCGGGAUGGUCUUU-------------AGACCCCU--GCG-UUUCUUAGUU--CGU---------AAA-ACUAAGUGGUGGAGUCAAUUU
AACY022109548.1/492-587   UUCGGUUUCCUUGU-U---C-C--UAA---------AAUAAGGUGGUGCGGAUGG-GAUUA---UC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AACAAGUGGC-GUGCAUGUAA
AACY023444729.1/383-288   UAAGGUUUCUUGCUUC---C----UUAAA-------GAGCAAGUGGUGCGGAUGG-GGUUA------------CC-CCGCC--UGG-UUUCCAAUUU--CCA---GUUA--AAG-AAUUGGUGGC-GAGCCUGAAU
AACY020216288.1/1049-954  UGAGGUUUCCUUGU-U---C-C--UAA---------AAUAAGGUGGUGCGGAUGG-GAUUA---UC-------UC-CCGCC--AGG-UUUCUUGUUU--CCU---GUAA--AAG-AACAAGUGGC-GUGCAUGUAA
AACY020166678.1/1869-1966 AUGAGUUUACUGCC-U---CUC--UCAA--------GGGCAGUUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUUA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY022761328.1/548-643   CCAGGUUUCUUGCU-U---C-C--UAA---------AAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUCA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY023523876.1/945-1044  GAUGGUUUCUUGCUUU---ACC--UAA---------GAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUUA--AAG-AGCAAGUGGC-GUGCAUGAAA
AACY021492079.1/262-367   UGGUGCCCGCAAGAUAAGGCACAAUAAAAA------UUCUUGCUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUCA--AAG-AAUUGGUGGC-GUGCAUGAAA
AACY023346890.1/1037-937  UUUGGUUUCUUGCU-U---UUCCAUCAAA-------AAGCAAGUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUCA--AAG-AAUUGGUGGC-GAGCCUGAAU
AACY022938970.1/517-612   UUCGGUUUCCUUGU-U---C-C--UAA---------AAUAAGGUGGUGCGGAUGG-GAUUA---UC-------UC-CCGCC--AGG-UUUCUUAUUU--CCU---GUAA--AAG-AAUAAGUGGC-GUGCAUGUAA
AACY023431705.1/989-1088  UGUGUCUUGA--AAUG---A-CAUUAAA--------CUUACUCUGGUGCGGAUGG-GAUAU--CUC-------UC-CCGCC--UGG-UUUCUUGCUU--CCA---GUUA--AAA-AGCAAGUGGUGGUGCCAAAUC
AACY020498360.1/1278-1183 UUGAAUCUCGGAAA-G---AUU--UAAAA-------AUUGCCCUGGUCGGGAUGG-GUUAU---UG-------AC-CCCUC--GGG-UUUCCUGUUU--CCU---------AAA-AACAGGUGGUGGAGUCACUUA
AACY020168213.1/709-807   UCUGGUUUCUUGCU-UUC-C-CA-UAAAA-------AAGCAAGUGGUGCGGAUGG-GGCA----A--------CC-CCGCC--CAG-UUUCUUGCUU--CUG---GUCA--AAG-AGCAAGUGGC-GAGCCUGCAU
AACY024051567.1/417-514   UCGGGUUUCUUGUU-U---UUCCAUAA---------GAACAAGUGGUGCGGAUGG-GAUA----UA-------UC-CCGCC--UGG-UUUCUUAUUU--CCA---GUCA--AAA-AAUAAGUGGU-GGAUCCAAAU
AACY020334999.1/666-568   UCGGGUUUCCAAUU-U---UUCCAUAA---------GAAUUGGUGGUGCGGAUGG-GAUAC---UC-------UC-CCGCC--UGG-UUUCUUAUUU--CCA---GUCA--AAG-AAUAAGUGGU-GGAUCCAAAU
AACY020822675.1/265-363   UCUGGUUUCUUGCU-U---CUCCAUAAAA-------AAGCAAGUGGUGCGGAUGG-GGUA----A--------CC-CCGCC--UGG-UUUCUUGCCU--CCA---GUCA--AAG-GGCAAGUGGC-GAGCCUGAGU
AACY020938674.1/506-608   UUAGGUUUCUUGCCAUU--C-CU-UUAAA-------AGGCAAGUGGUGCGGAUGG-AGGUU---AC-------UC-CCGCC--GAG-UUUCCAAUUUU-CUC---GUAAUCAA--AAUUGGUGGC-GAGCCUGAGU
AACY020341961.1/1685-1780 UUUGGUUUCUUGCU-U---C-C--UAA---------AAGCAAGUGGUGCGGAUGG-GAUUA---UC-------UC-CCGCC--AGG-UUUCUUAUUU--CCU---GUAA--AAG-AAUAAGUGGC-GUGCAUGUAA
AACY021982229.1/530-627   AUGAGUUUACUGCC-U---CUC--UCAA--------GGGCAGUUGGUGCGGAUGG-GACUC---UC-------UC-CCGCC--UGG-UUUCCAAUUU--CCA---GUUA--AAG-AAUUGGUGGC-GAGCCUGAGU
AACY020315589.1/451-353   UCGGGUUUCUUGUUUC---UCC--UCAA--------GAACAAGUGGUGCGGAUGGAGAAU----AC-------UC-CCGCC--UGG-UUUACAUGUU--CCA---GUCA--AAA-AUAUGUUGGU-GGUAAAUCCC
AACY020223597.1/172-75    AGUGGUUUCUUGCUUU---ACC--UAA---------GAGCAAGUGGUGCGGAUGGAGGUAA------------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUAA--AAG-AGCAAGUGGC-GUGCAUGAAA
AACY020933311.1/213-311   UUGAGUUUCUUGCU-U---CUC--CCAA--------AAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GUA---AAG-AGCAAGUGGC-GUGCAUGAAA
AACY023538876.1/509-608   AUAGGUUUCUUGCUUU---ACC--UAA---------AAGCAAGUGGUGCGGAUGGAGGUAA---CA-------CUCCCGCC--CUG-UUUCUUGCUU--CAG---GAUA--AAG-AGCAAGUGGC-GUGCAUGUAA
AACY021194674.1/423-518   UGGAGUUUCCAGUU-U---CUC--UCAA--------AAACUGGUGGUGCGGAUGG-GGCA----A--------CC-CCGCC--CAG-UUUCUUGCUU--CUG---GAUA--AAG-AGCAAGUGGC-GAGCCUGAAA
#=GC SS_cons              ::::::::<<<<<<.<...___..____........>>>>>>>,,,,,,,,,<<<.<<___...__.......>>.>>>-A..AAA.---<<<<<<_..aaa...a___..___.>>>>>>::::.::::::::::
#=GC RF                   uauagUUUcuugcu.u...cuc..UaAA........aagcaagUGGUGCGGAuGG.Gguua...uc.......cC.CCgCC..ugG.UUUccugcUU..Cca...GUaA..AAG.AgcaggUGGC.GaGccUgaaa
//
# STOCKHOLM 1.0

#=GF AC   RF01762
#=GF ID   whalefall-1
#=GF DE   Whalefall-1 RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   37.00
#=GF TC   37.60
#=GF NC   35.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   Whalefall-1_RNA_motif
#=GF SQ   14


AAFZ01000800.1/742-687   GUAUCUCCCCUCGG-GGGGAGACAGAAUUCGCGCUUGCGGGAAUUCAGAGGGAGGAC
AAFZ01025436.1/615-560   GUGUCCCUCCUUGG-GGAGGGACAGAGACCAAACAUGUUUUGUCUCAGGGUGAGGAC
AAFZ01000554.1/1801-1856 AUAUCUCCCCUCGG-GGGGAGACAGAUUUCACGCUUGCGAGGAAUCAGAGGGAGGAC
AAFZ01028207.1/114-169   GUGUCCCUCCUAGG-GGAGGGACAGAGUUCUUGCUUGCAAGAGCUCAGGGUGAGGGC
AAFZ01002938.1/1165-1221 GUAUCUCCGCUCGGGGGGGAGACCGAUUUCACGCCUGCGGGAAAUCAGAGGGAGGAC
AAFZ01002938.1/1115-1060 GUGUCCCUCCUUGG-GGAGGGACAGAGAUAAAACUUGUUUUGUCUCAGGGUAAGGAC
AAFZ01000800.1/776-831   GUGUCCCUCCUAGG-GGAGGGACAGAGUUCUUGCUUGCAAGAGCUCAGGGUGAGGAC
AAFZ01028207.1/80-25     GUAUCUCCCCUCGG-GGGGAGACAGAAUUCGCGCUUGCGGGAAUUCAGAGAGAGGAC
AAFY01026329.1/670-723   UCACCUCUCCUUUA-GGAGAGGUCGAAACUACUAAU-AGUAGUUUC-GGGUGAGGAU
AAFZ01000554.1/1750-1695 AUAUCCCUCCAUGG-GGAGGGACAGCGACAAAACUUGUUUUGUCUCUGGGUGAGGAC
AAFZ01026864.1/634-689   GUAUCUCCCCUCGG-GGGGAGACAGAAUUCACGCUUGCGGGAAUUCAGAGGGAGGAC
AAFZ01025436.1/666-721   GUAUCUCCCCUCGG-GGGGAGACAGAUUUCUCGCUUGCGGGAAAUCAGAGGGAGGAC
AAFZ01026413.1/98-153    GUAUCUCCCCUCGG-GGGGAGACAGAAUUCACGCCUGCGGGAAUUCAGAGGGAGGAU
AAFZ01027168.1/332-278   GUGUCCCUCCUUGG-GGAGGGACAGAGACA-AGCGUGUUUUGUCUCAGGGUGAGGAC
#=GC SS_cons             :::<<<<<<<____.>>>>>>>--<<<<<<<<<____>>>>>>>>>:::::::::::
#=GC RF                  GUAUCuCuCCUuGG.GGaGaGACAGAguucacgCuUGcgugaacUCAGgGuGAGGAC
//
# STOCKHOLM 1.0

#=GF AC   RF01763
#=GF ID   ykkC-III
#=GF DE   Guanidine-III riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   37.00
#=GF TC   37.40
#=GF NC   34.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF RN   [2]
#=GF RM   28001372
#=GF RT   Biochemical Validation of a Third Guanidine Riboswitch Class in Bacteria.
#=GF RA   Sherlock ME, Breaker RR
#=GF RL   Biochemistry. 2017;56:359-363.
#=GF CC   Although the structure of ykkC-III RNAs does not resemble ykkC/yxkD RNAs,
#=GF CC   both have a structure complexity that led to the proposal that they
#=GF CC   represent riboswitches. The ykkC-III motif has a rigidly conserved ACGA
#=GF CC   sequence within it that resembles a less rigidly conserved ACGA or ACGG
#=GF CC   sequence found in mini-ykkC RNAs, but it is unknown whether this
#=GF CC   observation relates to a biological relationship. Biochemical validation
#=GF CC   has been presented to show that this motif is a third class of guanidine
#=GF CC   riboswitches.[2]
#=GF WK   YkkC-yxkD_leader
#=GF SQ   39


AP006618.1/133448-133513     GACGAGCCCG----GUGCG--------CGGGC--UCCCGGACGAGGGGU---GCCGUACCCGGAGU--GCGAC--AAGACGG-CCCGA-
CP000910.1/2096309-2096249   AAAGGGC-------CAAAG-----------GC--GCCCGGACGAGGUGC---GCCGUACCCGGCCA--GCGAC--AAGACGG-CGUAAG
CP000511.1/851388-851320     ACAGGCGUCG----CGUGUUC------CGGCG--CCCCGGACGAGGUGC---GUCGUACCCGGUCA--GCGAC--AAGACGG-CGCGAU
AM849034.1/2863085-2863022   GAUGGGCGC-----CCAUCC--------GCGC--UCCCGGACGA-GGGA---UCAGUACCCGGAAC--GCGAC--AAGACUG-GCCAG-
ABJH01000172.1/10128-10201   CGCGCCCCCGCU--UUGCUAC----GGUGGGG-ACACCCGACGAGACGC---GCCGUACCGGGCUU--UCGCA--AAGACGA-CGCACC
CP000113.1/4374426-4374485   CGUGAGG-------GUGU------------CU-GGCCCGGACGAGGCGC---GCCGUACCCGGUCA---GGAC--AAGACGA-CGCGAC
AM711867.1/3063871-3063808   GUCGGGCGC-----CCUCCC--------GCGC--UCCCGGACGA-GGGA---UCAGUACCCGGAAC--GCGAC--AAGACUG-GCCAG-
AM746676.1/8188359-8188291   GCGGCGCUC-----CUUCAGACA-----GAGC-GUCCCGGACGAGACGC---GCCGUACCCGGUCA---GGAU--AAGACGA-CGCAGC
AP011115.1/5208127-5208067   AAAUCGUCG-----ACA-----------CGAC--AUCCGGACGA-GCGC---ACCGUACCCGGCCA--GCGAC--AAGACGG-UGCCC-
CP000580.1/1319367-1319304   GCCAUGUCA-----CCAGU---------UGAC---ACCGGACGAGCGGC---ACCGUACCCGGCCA--GCGAC--AAGACGG-CGCUUU
CR628336.1/661276-661213     GAUAUGCUAU----AAA----------AUAAU--CUCCGGACGAGACGC---GCCGUACCCGGUUA---AGAC--AAGACGA-CGCCUU
CP000656.1/85042-85109       GCAGGCGCCG----UCGAUC-------CGGCG--CCCCGGACGAGGUGU---GCCGUACCCGGUCA--GCGAC--AAGACGG-CGCGUU
CP000454.1/4240999-4241061   AGGCUUUCC-----CUUCC---------GGAG-CCUCCGGACGA-CGGU---UCAGUACCCGGCAC--GCGAC--AAGACUG--GCCA-
CP000359.1/2285879-2285947   CGGU-CGGCC----UUAUA--------GGCUGCGCCCCGGACGA-GAGCACCGCCGUACCCGGUCA---CGAC--AAGACGG-CGCGGA
BX842652.1/324410-324345     UCAGUUUC------UGCGACU--------GAGGUGCCCGGACGAUGUGC---GACGUACCCGGUCA---GGAC--AAGACGA-CGCUUU
ABJF01000294.1/7123-7044     GUAUGCCCUUUUGCUACG-----GUGGAGGGGAACCCCCGACGAGACGC---GCCGUACCGGGUAGCUGGCUGAAAAGACGA-CGCACC
CP001341.1/3865849-3865912   CCAA-GGCUC----CGCACCC------GAGCC---UCCGGACGA-CGGU---UCAGUACCCGGCAC--GCGAC--AAGACUG-GCCA--
AAMN01000002.1/564690-564754 UCAGAGCCUG----GGAC---------CAGGC--UUCCGGACGAGGGGC---GCCGUACCCGGCAC--GCGAC--AAGACGG-CCCGC-
AE017354.1/593290-593227     GAUAUGCUAU----AAA----------AUAAU--CUCCGGACGAGACGC---GCCGUACCCGGUUA---AGAC--AAGACGA-CGCCUU
CR628337.1/644770-644707     GAUAUGCUAU----AAA----------AUAAU--CUCCGGACGAGACGC---GCCGUACCCGGUUA---AGAC--AAGACGA-CGCCUU
CP000325.1/3207260-3207196   ACAGAGCCUU----GAUC---------AAGGC--UCCCGGACGAUGGGU---GCCGUACCCGGUGU--GCGAC--AAGACGG-CCCGG-
AL939114.1/119358-119291     CCUUUGCUAC----CUUGG--------GAAGC--ACCCCGACGAGACGC---GCCGUACCGGGCUG--AAGGCA-AAGACGA-CGCACC
AE016958.1/3831493-3831556   GUGCCGUCAG----CAA----------CUGAC---ACCGGACGAGGGGC---CCCGUACCCGGCCA--GCGAC--AAGACGG-CGCCGU
CP000750.2/209444-209507     AGCGAACCC-----GGCGCA--------GGGU--UCCCGGACGA-GGGU---GCCGUACCCGGUGU--GCGAC--AAGACGG-CCUGC-
CP000675.2/685132-685069     GAUAUGCUAU----AAA----------AUAAU--CUCCGGACGAGACGC---GCCGUACCCGGUUA---AGAC--AAGACGA-CGCCUU
CP000854.1/3478073-3478137   ACAGAGCCUU----GAUC---------AAGGC--UUCCGGACGAUGGGU---GCCGUACCCGGUGU--GCGAC--AAGACGG-CCCGG-
ABIN01000081.1/32257-32319   GAGACGUCAG----CAC----------CUGAC---ACCGGACGAGGGGC---CCCGUACCCGGCCA--GCGAC--AAGACGG--GCGCC
CP000518.1/1318365-1318302   GCGAUGUCA-----CCAGU---------UGAC---ACCGGACGAGCGGC---ACCGUACCCGGCCA--GCGAC--AAGACGG-CGCUCA
CP000088.1/1465653-1465596   CCCGAGC-------CUCA------------GC---CCCGGACGAGGUGC---GCCGUACCCGGUCA---GGAC--AAGACGG-CGCGGC
AANZ01000001.1/452592-452651 UGCUUGGCA-----AUC-----------UGCC----CCGGACGAGACGC---GCCGUACCCGGUUA---UGUA--AAGACGA-CGCCCU
CP000480.1/1755118-1755055   GCGACGCCA-----GCACA---------UGGC---ACCGGACGAGGGGCG--CCCGUACCCGGCCA--GCGAC--AAGACGG--GCCUC
AAOB01000006.1/32110-32049   GGGUAGCUG-----CAACGA--------CAGC---UCCCGACGA-CGGA---UCAGUACCGGGUAC--GCGAC--AAGACUG-GCCA--
CP000479.1/4438905-4438968   GUGCCGUCA-----ACAAC---------UGAC---ACCGGACGAGGGGC---CCCGUACCCGGCCA--GCGAC--AAGACGG-CGCCGU
CP000656.1/5615876-5615812   GCGG-CGUCC----AUUUCC-------GGAUG-CCGGCGGACGA-GGGA---GCAGUACCCGCACA----GAC--AAGACUGACUCGC-
CP000113.1/446679-446736     AGAUUGCA------GCCC-----------UGC----CCGGACGAGAUGC---GCCGUACCCGGUUA----CGU--AAGACGA-CGCCCU
CP000474.1/3894383-3894446   UGAAGGUUCC----CCUCU--------GGAAC--CUCCGGACGA-CGGU---UCAGUACCCGGCAC--GCGAC--AAGACUG--GCCA-
CP001131.1/4934528-4934594   UGGC-CGCGC----GACCCC-------GCGCG-ACCCCGGACGAGGCGC---GUCGUACCCGGUGA---CGAC--AAGACGA-CGCGAG
ABJI02000500.1/27579-27638   UGCUACGU------UGGA-----------ACG--ACCCCGACGAGACGC---GCCGUACCGGGUAG----GAA--AAGACGA-CGCACC
ACVP01000007.1/106973-107037 UUCGC-CGCG----GCUUG--------CGCGA-GCCCCGGACGA-GGGA---GCCGUACCCGGCAA-CGCGAC--AAGACGG--CCAG-
#=GC SS_cons                 :::::<<<<<...._____........>>>>>..-------------<<...<<<<<_________.._____..___>>>>.>>>:::
#=GC RF                      gcagugcccc....uuacu........ggggc..ccCCGGACGAGggGc...GcCGUACCCGGuca..GcGAC..AAGACGg.CgCacc
//
# STOCKHOLM 1.0

#=GF AC   RF01764
#=GF ID   yjdF
#=GF DE   yjdF RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF SE   Published; PMID:20230605;
#=GF SS   Published; PMID:20230605;
#=GF GA   45.00
#=GF TC   45.20
#=GF NC   44.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20230605
#=GF RT   Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT   archaea and their metagenomes.
#=GF RA   Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL   Genome Biol. 2010;11:R31.
#=GF WK   YjdF_RNA_motif
#=GF SQ   62


CP000903.1/4024493-4024394   UGAAAG-AGAUAC-AAAAACACA----------------------------GUUCUGGUCGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCAG------------UAUUU--CUAAUUUUUUU
CP000114.1/99777-99875       UCGUUA-UAGCAU-AAAAACACG----------------------------UU-GCAGUUGGU-AGUCU-GCAA--GCGUUC-------------AGU----------------------GAACGUCAGUAACCU-------------------------U-CCCUCC---AGGUCGUCCAU------------UGCAA--UUUAAUAUUUA
AAPZ02000001.1/582696-582796 ACCUUA-GAAAGU-AAAAACACA----------------------------GU-UCGGUUGGU-AGUCC-GGAC--AUCAGU-------------UCAA---------------------GCUGAUCAGUAUCCU-------------------------U-CCUCUCC--GGGAUGUCCCU------------CUUUC-AUAAUUUAUUU-
AM180355.1/2040488-2040585   AUCUAU-AAAGAU-AAAAACACA----------------------------GU-CUGGUUGGU-AGUCC-AGAC--GCAGC--------------AAUA----------------------GCUGUCAGUAACCU-------------------------G-CCUCCUU---GGUUGUCCGU------------UCUUU--AGAAAGUAAUU
CP000413.1/273421-273525     CCUAAG-GAAAGU-AAAAACACG----------------------------AU-UCGGUUGGU-AGUCC-GAAU--GUAUAA-------------UUAUUAA-CU---------------UUAUAUCAGUAACCU-------------------------U-CCUCCU---AGGAUGUCCAU------------CUUUC--CUAAUAAAUUU
CP001283.1/3985527-3985427   UGAAAG-AAAUAC-AAAAACACA----------------------------GUACUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCCUCC-GGGAUGUCCCG------------UAUUU--CUAAUUUUUUA
AE017194.1/1016995-1017101   ACUUUA-GAGUGA-AAAAACACA----------------------------GU-UCGGUUGGU-AGUCC-GGAC--GCAAUAAUU----------AUUU------------------AAUUAUUGUCAGUAACCU-------------------------UCCCCCCU---GGGAUGUCCAU------------CACUC-AUGUAAUAAAC-
CP001176.1/4159074-4158975   UGAAAG-AAAUAC-AAAAACACA----------------------------GUUCUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUCUUUUA
CP001598.1/3993206-3993107   UGAAAG-AAAUAC-AAAAACACA----------------------------GUACUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUUUUUUA
ABDQ01000001.1/474183-474288 UUCUAU-AGAGAU-AAAAACACA----------------------------GUUUCGGUUGGU-AGUCC-GAAC--CUAUC--------------UAAUUUAAC-----------------GUUAGCAGUAACCU-------------------------GCCCUCCUG--GGGUUGUCCCU------------UCUCU--AUGUUUUAGAU
AE016877.1/4116917-4116818   UGAAAG-AAAUAC-AAAAACACA----------------------------GUUCUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUCUUUUA
AE015929.1/268742-268639     AUAAAG-AAAUGU-AAAAACACA----------------------------AU-UGGGUUGGU-AGUCC-CAAU--GCAAAU-------------UACUUAU------------------AUUUGUCAGUAACCU-------------------------U-CCUCCUC--AGGUCGUCCAU------------CAUUU--CAAUUUUAAAU
CP000485.1/3979564-3979464   UGGAAG-AAAUAC-AAAAACACA----------------------------GUACUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCCUCC-GGGAUGUCCCG------------UAUUU--CUAAUUUUUUA
AF270263.1/1085-1188         AUAAAG-AAAUGU-AAAAACACA----------------------------AU-UGGGUUGGU-AGUCC-CAAU--GCAAAU-------------UACUUAU------------------AUUUGUCAGUAACCU-------------------------U-CCUCCUC--AGGUCGUCCAU------------CAUUU--CAAUUUUAAAU
ABDT01000058.2/47084-46985   AUAAAA-GGAGAU-AAAAACACU----------------------------AU-UCUGUUGGU-AGUCA-GAAU--CUAUUA-------------UUU----------------------UAAUAGCAGUAACCU-------------------------G-CCCUCCU--GGGUUGUCCGU------------UCUCU--GGAAUUUUUUA
CP000726.1/2061998-2061898   UAGCUU-UGAGAU-AAAAACACG----------------------------AU-UCGGUUGGU-AGUCC-GAAU--GGGGU--------------AAUUA---------------------GCCCUCAGUAACCU-------------------------G-CCCUCCUG-GGGUUGUCCAU------------UCUCU--AAAUUUAGCUG
ACLT01000088.1/50310-50211   UGAAAG-AAAUAC-AAAAACACA----------------------------GCUCUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUCUUUUA
AAYW02000008.1/106021-105897 AAAAGU-AAAGAU-AAAAACGCAACGUAUGCAGU-----GAUGCAUACCAGAG-CCGGUAGGU-AGCCC-GGCC--GUCCUG-------------CAUAU--------------------UAGGGUAAGUAACCU-------------------------G-CCCCUCC--GGGUUGUCCAU------------UCUUU--GCUCAUUUCAA
AP008230.1/2980037-2980137   AACAUG-GAACAU-AAAAACACG----------------------------GU-CCGGUUGGU-AGUCC-GGAU--GCGCCG-------------AAUUGAC------------------CGGUGUC-GUAUCCU-------------------------UCCCCCCUC--GGGAUGUCCAU------------UGUUC--AUUAUUUU---
ABAX03000012.1/28997-29098   CAGCGC-AAAGAU-AAAAACACA----------------------------GUCCCGGCCGGU-AGUCC-GGGC--GCAG---------------AGAUAAAAG------------------CUGUCAGUAACCU-------------------------G-CCUCCUC---GGUUGUCCAU------------UCUUU--GCUGCCAAAAG
AL009126.3/1275756-1275858   GGUAAA-GAAUGA-AAAAACACG----------------------------AU-UCGGUUGGU-AGUCC-GGAU--GCAU---------------GAUUGAGA-------------------AUGUCAGUAACCU-------------------------U-CCCCUCCUCGGGAUGUCCAU------------CAUUC--UUUAAUAUCUU
CP000387.1/2058556-2058454   AGCUAC-UAAGAU-AAAAACACA----------------------------GUUCUGGUUGGU-AGUCC-AGAC--GCAAAAAA-----------CCA--------------------UUUUUUGUCAGUAACCU-------------------------U-CCUCCUU---GGUUGUCCAU------------UCUUA--GGGAUUUUUA-
CP000413.1/275566-275671     UCUAUG-GAAAGU-AAAAACACA----------------------------AU-UCGGUUGGU-AGUCC-GAAU--AUAUAA-------------UCAUAUAGCU---------------UUAUAUCAGUAACCU-------------------------U-CCUCCU---AGGAUGUCCAU------------CUUUC--CUAAUAUUUUU
CP000764.1/2923703-2923605   CUGUAG-AAAUAC-AAAAACACA----------------------------GU-UCGGUUGGU-AGUCC-GGAC--GCAUA--------------CGAG----------------------UAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCAG------------UAUUU--CUGAAUCUUUU
CP001215.1/3994592-3994493   UGAAAG-AAAUAC-AAAAACACA----------------------------GUACUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUUUUUUA
AE017194.1/3941275-3941176   UGAAAG-AAAUAC-AAAAACACA----------------------------GUUCUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUUUUUUU
AP006716.1/192943-193045     AUAGAG-AAAUGU-AAAAACACA----------------------------AU-UGGGUUGGU-AGUCC-CAAU--GCAAAUG------------UAAU--------------------CAUUUGUCAGUAACCU-------------------------U-CCUCCUC--AGGUCGUCCCU------------CAUUU--CAAGUUAUAUA
CP000560.1/2746219-2746117   UAAUGA-GAAUGA-AAAAACACA----------------------------AU-UCGGUUGGU-AGUCC-GGAU--GCAU---------------GAUUUAAA-------------------AUGUCAGUAACCU-------------------------U-CCCCUCCUCGGGAUGUCCAU------------CAUUC--UUCAGUAAAUU
AAVO02000014.1/31411-31532   AAUGAC-AAAGAU-AAAAACGCAAA--GCAUUUU-------AUUAUGCGAGAG-CUGGUAGGU-AGCCC-AGCC--GUCCUAU------------GUUU--------------------AUAGGGUAAGUAACCU-------------------------G-CCCCUCC--GGGUUGUCCGU------------UCUUU--GUUUGGAAAUA
CP000721.1/1839650-1839548   UAUUUA-AGAGAU-AAAAACACU----------------------------GUUUCUGUUGGU-AGUCA-GAAC--CUAUAU-------------UAUA---------------------AUAUAGCAGUAACCU-------------------------GCCCUCCUG--GGGUUGUCCAU------------UCUCU-GUGAAUUUAUA-
CP000024.1/228896-229023     CCCAAC-UAAGAU-AAAAACACA----------------------------GUUCUGGUUGGUAAGUCC-AGACACGUAGG--------------CGAG----------------------CCUAUCAGUAACCUAAGGAUAUGAAUAGAAAUGAAGAGU---------------AGUCCAUCAAGGCUACUCUUUUUC--GUCAAAAGAAC
CP000001.1/4030705-4030606   UGAAAG-AAAUAC-AAAAACACA----------------------------GUUCUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUUUUUUU
AJ938182.1/408566-408666     AUAUAG-AAGUGU-AAAAACACA----------------------------AU-UGGGUUGGU-AGUCC-CAAU--GCAGUU-------------UUAA---------------------AACUGUCAGUAACCU-------------------------U-CCUCCUC--GGGUCGUCCGU------------CAUUU--CUAAUAAAACU
AE017198.1/275419-275520     GCUAAG-GAAAGU-AAAAACACA----------------------------AU-UCGGUUGGU-AGUCC-GAAU--GUAUGA-------------UUUAU--------------------UCAUAUCAGUAACCU-------------------------U-CCCUCCU--AGGAUGUCCCU------------CUUUC--CUCUUAUUUUU
AE015927.1/625938-626042     UUUAGU-AGAGAU-AAAAACACA----------------------------GU-UCGGUUGGU-AGUCC-GAAC--CUAUUUGA-----------UUU--------------------UUAAAUAGCAGUAACCU-------------------------GCCCUCCUG--GGGUUGUCCAU------------UCUCU--AUGAUUAAAUU
ABHG02000017.1/362821-362918 AUCUAU-AAAGAU-AAAAACACA----------------------------GU-CUGGUUGGU-AGUCC-AGAC--GCAGC--------------AAUA----------------------GCUGUCAGUAACCU-------------------------G-CCUCCUU---GGUUGUCCGU------------UCUUU--AGAAAGUAAUU
AARF01000365.1/613-724       GAAGUG-GAGUGU-AAAAACACA----------------------------GU-CUGGUUGGU-AGUCCUAGAC--ACACGUC------------GUCAUGACCAAA------------GACGUGUCAGUAACCU-------------------------U-CCCCCUC--GGGAUGUCCCU------------CACUA--CGGGAACUUCA
ABED02000029.1/585317-585449 UAAAAG-CAGGAU-AAAAACGCAACGC--AUUUCUUCCUGAGAGAUGCUAGAG-CUGGUAGGU-AGCCC-AGCC--GUCUGCACC----------GCAC------------------GGUGUAGGUAAGUAACCU-------------------------UCCCCUCC---GGGUUGUCCAU------------UCCUG--UAAGGAUUUAU
AL766843.1/100087-100185     UCGUUA-UAGCAU-AAAAACACG----------------------------UU-GCAGUUGGU-AGUCU-GCAA--GCGUUC-------------AGU----------------------GAACGUCAGUAACCU-------------------------U-CCCUCC---AGGUCGUCCAU------------UGCAA--UUUAAUAUUUA
AE017355.1/3979781-3979681   UGAAAG-AAAUAC-AAAAACACA----------------------------GUACUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCCUCC-GGGAUGUCCCG------------UAUUU--CUAAUUUUUUA
AE009948.1/100059-100157     UCGUUA-UAGCAU-AAAAACACG----------------------------UU-GCAGUUGGU-AGUCU-GCAA--GCGUUC-------------AGU----------------------GAACGUCAGUAACCU-------------------------U-CCCUCC---AGGUCGUCCAU------------UGCAA--UUUAAUAUUUA
ABGC03000029.1/55866-55990   AAACGC-AAAGAU-AAAAACGCAACGUACAUCUUU------GAUGUGCCAGAG-CCGGUAGGU-AGCCC-GGCC--GUCCUAU------------AUAA--------------------AUAGGGUAAGUAACCU-------------------------G-CCCCUCC--GGGUUGUCCAU------------UCUUU--GUUCAAUCAAU
CP001336.1/4011715-4011819   UAAAAA-UAACAU-AAAAACACG----------------------------GU-CCGGUUGGU-AGUCC-GGAU--GCGUUG-------------AAUUGAC------------------CGGUGUC-GUAUCCU-------------------------U-CCCCCUC--GGGAUGUUCGU------------UGUUAGCUUUAGCAUAUA
ABBV01000209.1/1887-1792     AUAAAU-AAAUAU-AAAAACACA----------------------------GUUCUGGUUGGU-AGUCC-AGAC--GCA----------------GCAA------------------------UGUAAGUAACCU-------------------------G-CCUCCUU--AGGUUGUCCAU------------UCUUU--AUAAAAAAAUU
ACNG01000092.1/71520-71421   UGAAAG-AAAUAC-AAAAACACA----------------------------GUUCUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUUUUUUU
AE017334.2/3993306-3993207   UGAAAG-AAAUAC-AAAAACACA----------------------------GUACUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUUUUUUA
CP000728.1/2191605-2191505   UAGCUU-CGAGAU-AAAAACACG----------------------------AU-UCGGUUGGU-AGUCC-GAAU--GGGGU--------------AAUUA---------------------GCCCUCAGUAACCU-------------------------G-CCCUCCUG-GGGUUGUCCAU------------UCUCU--AAAUUUAGCUG
AE016879.1/3993179-3993080   UGAAAG-AAAUAC-AAAAACACA----------------------------GUACUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUUUUUUA
CP000416.1/2190739-2190641   -AGUGA-CAGAAUAAAAAACACG----------------------------GU-CUGGUUGGU-AGUCC-AGGC--GCGGCU-------------GAA----------------------AGCCGUCAGUAACCU-------------------------G-CCUCCUU---GGUUGUCCCUA-----------UUUUG--UUAGUCAUUU-
AM412317.1/2133357-2133257   UAGCUU-UGAGAU-AAAAACACG----------------------------AU-UCGGUUGGU-AGUCC-GAAU--GGGGU--------------AAUUA---------------------GCCCUCAGUAACCU-------------------------G-CCCUCCUG-GGGUUGUCCAU------------UCUCU--AAAUUUAGCUG
CP001186.1/4127317-4127218   UGAAAG-AAAUAC-AAAAACACA----------------------------GCUCUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUUUUUUA
BA000033.2/425335-425435     AUAUAG-AAGUGU-AAAAACACA----------------------------AU-UGGGUUGGU-AGUCC-CAAU--GCAGUU-------------UUAA---------------------AACUGUCAGUAACCU-------------------------U-CCUCCUC--GGGUCGUCCGU------------CAUUU--CUAAUAAAACU
ACMZ01000099.1/116495-116396 UGAAAG-AAAUAC-AAAAACACA----------------------------GCUCUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUUUUUUA
AAEK01000054.1/27482-27581   UGAAUG-AAAUAC-AAAAACACA----------------------------GUUCUGGUUGGU-AGUCC-AGAC--GCAUG--------------AUUU----------------------CAUGUCAGUAACCU-------------------------U-CCCCUCC--GGGAUGUCCCG------------UAUUU--CUAAUUUUUUU
AE001437.1/1718166-1718277   UUAUAA-GAAGAU-AAAAACACA----------------------------GU-UUGGUUGGU-AGUCC-AAAC--GCAUUUAUAUU--------CAUAU---------------AAAAUAAAUGUCAGUAACCU-------------------------G-CCCUCGC--GGGUUGUCCAC------------UCUUC--UUAAAAACUUA
ABCC02000044.1/34328-34178   AAAAGC-AAAGAU-AAAAACACAACGCAGGAUAA-------AAACCUGCAGAG-CUGGUAGGU-AGUCC-AGCC--GCAUUCCUAUAGUCCUGCUUUAACU------GGCGGGGAGACAGGGAUGUCAGUAACCC-------------------------UCCCUCCUU--GGGUCGUCCAU------------UCUUU--GUUCAUCACAU
AAYW02000014.1/30067-30191   CAAAAC-AAAGAU-AAAAACGCAACGUGCAUCUUU------AAUGUGCCAGAG-CCGGUAGGU-AGCCC-GGCC--GUCCUAU------------AUAA--------------------AUAGGGUAAGUAACCU-------------------------G-CCCCUCC--GGGUUGUCCAU------------UCUUU--GUUCAAUAAAU
CP000673.1/3572617-3572509   UAAAUU-AGAGAU-AAAAACACA----------------------------GUUUUGGUUGGU-AGUCC-AAAC--CUGUCUAUA----------UUCU------------------UAUAGAUGGAAGUAACCU-------------------------UCCCUCCUG--GGGUCGUCCCU------------UCUCU--AUGUCAAAUUU
CP001083.1/2188308-2188208   UAGCUU-UGAGAU-AAAAACACG----------------------------AU-UCGGUUGGU-AGUCC-GAAU--GGGGU--------------AAUUA---------------------GCCCUCAGUAACCU-------------------------G-CCCUCCUG-AGGUUGUCCAU------------UCUCU--AAAUUUAGCUG
CP000423.1/2847352-2847256   CAUUGC-GCUAUC-AAAAACACA----------------------------GU-CUGGUUGGU-AGUCC-AGAC--GCGGC--------------UUAG----------------------GCUGUCAGUAUCCU-------------------------U-CCUCCUU---GGAUGUCCAG------------AUUGC--GUGAAAA-UCU
AGMY01000008.1/65276-65178   -GAUUUAUGAUAU-AAAAACACG----------------------------UU-GCAGUUGGU-AGUCU-GCAA--GCAUCA-------------UGA----------------------UGAUGUCAGUAACCU-------------------------U-CCCUCC---AGGUCGUCCUU------------UAUCA--AAUUUUCUUUU
AL935263.2/1767846-1767748   AUUAGC-GAAAUU-AAAAACACG----------------------------GU-CUGGUCGGU-AGUCC-AGAC--GCAGC--------------AACG----------------------GCUGUCAGUAACCU-------------------------G-CCUUCCUU--GGUUGUCCGA------------AUUUC--GUUAGUGAAAU
#=GC SS_cons                 :::(((.(((((,.,,,,,,,,,............................<<.<<<<_____.___>>.>>>>..<<<<<<.............____.....................>>>>>>,,,,,,,,,.........................<.<<<____..>>>>,,,,,,,............)))))..)))::::::::
#=GC RF                      uaacac.gaagaU.AAAAACACA............................gu.ccGGUuGGU.AGUCC.ggac..gcaggc.............uuau.....................gccuguCAGUAACCU.........................u.CCcccuu..gGGauGUCCaU............ucuuc..gugaauauuau
//
# STOCKHOLM 1.0

#=GF AC   RF01765
#=GF ID   srg1
#=GF DE   srg1
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Gardner PP
#=GF SS   Predicted; Gardner PP
#=GF GA   70.00
#=GF TC   144.00
#=GF NC   36.40
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0045892; negative regulation of transcription, DNA-templated;
#=GF RN   [1]
#=GF RM   15175754
#=GF RT   Intergenic transcription is required to repress the Saccharomyces
#=GF RT   cerevisiae SER3 gene.
#=GF RA   Martens JA, Laprade L, Winston F
#=GF RL   Nature. 2004;429:571-574.
#=GF WK   SRG1_RNA
#=GF SQ   2


AAEG01000006.1/258554-259104 UAAUGCCUUUGUUUGGCCAAGCUAUGUGCAAAUAUCACAAAUUAAAAA-UUUGGUUAAGCAGUUAGGCUGGACCUAAUAUUUUAGAAAAACCUAAUUUUUUUUGUGGACCCAUUUUCGAUAUUUACUCACAAAUGGAAU-UCAAGGGGAACAACUUCGGUCU--CAGCACUUUAAUUAUUCUUCUCGUUCCCACCUAAUUUCGCAAUUUAUUGUCCUUGACUUCUACCACGAGAAA-AAAAUUAAGAAAAUGCAACGCUGCCCGUGCAGGGUUUUCUGAGCGGGAUGAAAAAAUCAGACAAAUAUCCAAGUUAUGAGUAAUUACUUUGUUGGAAGGAGGGAGCAGAGCAUAAGGAAAUUCUUAAAACUGUUAUGUAUAUAAAGGAAGAACCAUUUCUAGUUAUUUCACUUUUU-GAUACUUGUCAACUAUCUUAGUAAAAAUACAGAACUCUAUAAAGAACCACAGAAAAAUCGACAGCAAUGACAAGCAUUGACAUUAACAACUUACAAAAUACCUUUCAACAAGCUAUGAAUAUGAGCGGCUCCCCAGGCGCUGU
AABY01000111.1/26714-26159   CAAUGCCUUUGUUUGACCAUGUUGUGUGCUAAUAUGACAAAUUAAAAAUUUUAGUUAAGCAUUUGGGCUGGCCUUAAUAUUUAACAAAAAGCUAAUUUUUUUUGUGGGCCCACUUUCGAUAGUUAGUCACUAGCGGAAGCUCAGGAAGAGCAGCUUUGGUCUCUCAGCACUUUAAUCCUGCUUCUCGUUCCCACUUAAUUUCGCAGUUUAUUGUCCUUGACUUCUACCACGAGAAAAAAAAUUAGGAAAAUACAACACUGCCCGUGCAGAGUUUUCUGAGCGGAAUGAAAAAAUUAAAUUAAUGUCCAAGUUAUGAGUAAUUACUUCGUUGUAGGGAGGGAGCAGAGCCAAAGGAAAUUUUUAAAAUUGUUAAAUAUAUAAAGGAAGAACCAUUCCUGAUUACUUUACUUUUUCGAUUCUUGUCAGUUAUCUUAGUA-AAAUACAAAACUCUAUAAAGAACCACAGGAAAAUCAGCAGCAAUGACAAGCAUUGACAUUAACAACUUACAAAAUACCUUUCAACAAGCUAUGAAUAUGAGCGGCUCUGCAGGCGCUGU
#=GC SS_cons                 {{{{{{,,,<<<<<<<<<<<<---<<<<_______>>>>---------->>>>>>>>>>>>{{{{-{{{{,,,<<<<____>>>>,,,,,,,,,,,{{{{{{{{{{{,[[[-[[[[[[[[[-[[[[[[[-[[-[[[[,,,,,,,<<<<_____>>>>,((((,,,,<<<-<<<<<<<-<<-<<<<<<<--------------<<<<____>>>>-------------->>>>>>>-->>>>>>>>>---->>>,,,,,,,<<<<<-<<<<____>>>>->>>>>,,,,,,,,,,,)))),,,,,]]]]--]]-]]]]]]]------]]]]]]]]]--]]],,,[[[[,,<<<<<____>>>>>,,,((((,,,<<<<--<<<<<<<<<<<________>>>->>>>->>>>---->>>>,,,,,,<<<<___>>>>,.,,,,)))),,]]]],,,,,,,,}}}}}}}}}}},,,,}}}}--}}}},,}}}}}},,,,,,,,,,,,,,,,,,,,,,,,<<<<________>>>>,,,,<<<<-<<____>>->>>>::
#=GC RF                      caauGCCUUuGuuugaCcaaguUauGugCaAAUAUcaCaAAUUAAAAAuuuugGuuaagCaguuaGGCuGGaCcuaaUAUUuuagAAAAAgCUAAUuuuuuuuGuGGaCCCAcuucCgauguuuacuCaCaaauGGaAucUCAagaaGAaCAaCuucGgucucuCAGcaCuuuaauuauuCuuCuCGuUCCCACuUAAUUUCgCaaUUUAuuGuCCUUGACUUCUACCaCGaGaaAAaaaauuaagAAAAugCAACaCUGcCCGuGCaGaGUUUuCuGAgCGGgAUGAAAAAAUuagacaAAUauCCaAGuuAuGaguaaUUACUUcguuGgaagGAGGGAGCaGaGCauaaggAAAUucuuaAAAcuGuUAaguauAUaaaGgaagaacCAUUuCUaguuAcuucACuuuUUcGauacUUGUCAacuaUCUuaguA.AAAUaCagAACuCuAUAAAGAACCaCagaaaaaUCaaCaGCAAugacAAGCauugACAUUAACAACUUACAAAAUACCUuuCaACAAGCUAuGaaUAUGaGCGGCuCugCaGGCGCuGU
//
# STOCKHOLM 1.0

#=GF AC   RF01766
#=GF ID   cspA
#=GF DE   cspA thermoregulator
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20129052
#=GF SS   Published; PMID:20129052
#=GF GA   78.00
#=GF TC   78.00
#=GF NC   77.90
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   20129052
#=GF RT   The cspA mRNA is a thermosensor that modulates translation of the
#=GF RT   cold-shock protein CspA.
#=GF RA   Giuliodori AM, Di Pietro F, Marzi S, Masquida B, Wagner R, Romby P,
#=GF RA   Gualerzi CO, Pon CL
#=GF RL   Mol Cell. 2010;37:21-33.
#=GF WK   CspA_mRNA_5'_UTR
#=GF SQ   15


CP000946.1/174765-174338     AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUG-U------AG-UAAGGCAAGU--C---CC--U-UCAA-GAG-UUAU-C-GUU-GAUA-CCCCUCGUA-GUGCACAUUCCUU-U--AA--CG-CUUC-A-AAAU----CUGUA--------AAG-C---ACG--C--CA---UA--U-C-GCC----GA-AA--GGCACACU------UA-AUUA---UUAA-A-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAG-GCUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGAUGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUGUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGC-CUGUA---AUCU---C-UGCU--UAA--A--AGCAC--A---GA--A--UCUAA----GAUCCCUGCCAUUU-GGCGGGGAUUUUUUU
CP000822.1/4602942-4603373   AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUU-U------AG-UAAGGCAGUC--C---CC--U-UCAA-GAG-UUAUCC-GUU-GAUA-CCCCUCGUA-GUGCGCAUUUCCU-U--AA--CG-CUUA-AAAAAU----CUGUA--------AAG-C---ACG--C--CA---UA--U-C-GCC----GA-AA--GGCACACU------UA-UUUU---UUAAAA-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGAUAAAG-GCUUCGGCUUCAUCACUCCUGACGAUGGCUCCAAAGACGUGUUCGUACACUUCUCUGCUAUCCAGAACGACGGUUACAAAUCCCUGGAUGAAGGUCAGAAAGUUUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGC-CUGUA---AUCU---U-AGCU-UUAU--A--AGCUC--A---GA--A--UUGAA----GAUCCCUGCCAAUC-GGCGGGGAUUUUUUU
L23115.1/459-834             AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUG-U------AG-UAAGGCGAGU--C---CC--U--CAA-GAG-UUAU-C-GUU-GAUA-CCCCUCGUA-GUGCACAUUCCUU-U--AA--CGUCUUC-A-AAAU----CUGUA--------AAGUC---AUGCUC--CA---UA--U-C-GCC----GA-AA--GGCACACU------UA-AUUA---UUAA-A-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAG-GCUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGAUGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUGUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCAGCUAACGUAACCUCC-CUGUA---A-------------------------------------------------------------------------------
ABEH02000004.1/260631-260204 AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUU-U------AG-UAAGGCAAGU--C---CC--U-UCAA-GAG-UUAU-CCAUUAGAUA-CCCCUCGUA-GUGCGCAUUUCCU-U--AA--CG-CUUA-AAAAAU----CUGUA--------AAG-C---ACG--C--CA---UA--A-C-GCC----GA-AA--GGCACACU------UA-UUUU---UUAAAA-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGAUAAAG-GCUUCGGCUUUAUUACUCCUGAUGACGGUUCUAAAGACGUGUUCGUACACUUCUCCGCUAUUCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUUUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGC-CUGUA---AGCU---U-------AAA--A--AGCUC--A---GA--A--UUUUG----AAUCCCUGCCUGAU-GGCGGGGAUUUUUUU
AF017276.1/479-855           AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUU-U------AG-UAAUGCAAGU--C---CG--U-CCAAUGAG-UUAU-CCAUUAGAUA-CCCCUCGUA-GUGCGCAUUUCCU-U--AA--CG-CUUC-A-AAAU----CUGUA--------AAG-C---ACG--C--CA---UA--A-CGGCC----GA-AA--GGCACACU------UA-AUUA---UUAA-A-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGAUAAAG-GCUUCGGCUUUAUUACUCCUGAUGACGGUUCUAAAGACGUGUUCGUACACUUCUCCGCUAUUCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUUUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGC-CUGUA---A-------------------------------------------------------------------------------
CP000647.1/4296745-4297166   GCAGGUUUG-A-UGUACAGACC-A-C--AGAG-CAGUC-G------AA-U-AGAGCAGU--C----C--U-UCUA-AGG-UUAUCC-AAA-GAUA-CCCC-CGUA-GUGAACUUUCCCU-U--UA--UC-GCUU-U-AAAU----CUGUA--------GUC-C---AGA--C--CC---CU--A-C-GCC----GC-AA--GGCUCACU------UA-UUUU--UUUAA-A-GGUAAUU--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAG-GCUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGACGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGCUACAAAUCCCUGGACGAAGGUCAGAAAGUAUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGCAACGUAACUUCU-CUGUA---AGUU---CAAGC-----------CGCUA--A---GA--A--UCGAG----AAUCCCUGCCUGAU-GGCGGGGAUUUUUUU
CP000653.1/190938-191361     GUCGGUUUG-U--UCACAGACC----U-AAAG-CAGUU-U------AG-UUAAGC-AGU--C---C----A-GAU-GAG-UUAU-C-UUA-GAUA-CCCUUCGUA-GUGACCCUUCCUC-U--AU--CG-CUUA-A-AAAU----CUGUA--------ACA-C---AUU--C--CAUCAUC--G-C-GCC----GG-AA--GGCAAAAC------AA-AUAU---UUAA-AAGGUAAAA--U-CUAUGUCUGGUAAAAUGACUGGUCUGGUAAAAUGGUUCAACGCUGAUAAAG-GUUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGAUGUAUUCGUACACUUCUCUGCUAUCCAGAACGAAGGCUACAAAUCUUUGGACGAAGGCCAGAAAGUUUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCAGCAGCUGGUAACGUUGUAAGC-CUGUA---AGCUU-CC-AACU--CAG--C--AGCAA--A---GA--A--UUUAA----AAACCCGCC--UCU--GGCGGGUUUUUUUC
ABXW01000053.1/281917-281471 AUCGGUUUG-AAAGUACAGACC-U-AUUUAUGAAAGCA-A------GU-UUUGAAAAGUUCC---CC--A-UCAA-GUGUUAUC-C-AUU-GAUAUCCACUCGUA-GUGAAUUCCUCCU-A--AU--UAGUUCC-AUAAGU----AUAAA--------GAAGUAUCAAA--C--CU---AU--A-U-GCC----GU-GU--GGCAACAA------UU-AAAA---UUUA-A-AGGAAUU--CAAUAUGUCUAAUACAAUGACUGGUUUAGUAAAAUGGUUUAACGAAUCUAAAG-GCUUUGGCUUUAUUUCUCCUGCUGAUGGCAGCAAAGAUGUGUUCGUACACUUCUCUGCAAUUCAAAGCGACAGCUUCAAAACGCUGAACGAAGGACAAAAAGUUAGCUUCUCAGUAGAGAAUGGUGCAAAAGGUCCAGCGGCUGUAAACGUC-GUAGC-UCUUUAAGAUAC---C-CGCU--UAA--UACAGCGC--U---UA--AAAUUUCA----AACCCCUGCCAAUU-GGCGGGGGUUUUUCG
ABJD02000101.1/494629-495045 UACUGAGU-----UUGUGUUCU-A-AA-GAAGAAAGUU-A------UC-CCAGAUAG--------CC--U-U------U-GAC--C-GU--GACG-CU--UCAUC-UUGGUUUUUUCCU-GAUUA--AA-UAGU-U-GACU----CUGGC--------CCA-U-----------------A--UAU-GCC----GAAAA--GGCAAGUUUUUUUGAU-GUUA---UAUA-G-GAAAAGU--CAA-AUGUCCGACAAAAUGAAAGGUCAAGUUAAGUGGUUCAACGAGUCUAAAG-GCUUCGGUUUCAUCACUCCUGCUGAUGGUAGCAAAGACGUUUUCGUUCACUUCUCUGCCAUUCAGGGCGCUGGUUUCAAAACUCUGGCAGAAGGCCAGCAAGUUGAAUUCACCAUUGAAAAUGGUGCGAAAGGCCCAGCAGCUGCUAACGUAA------CUGCA---AUCU---A-AGCU--UAA--U--UGCUU--AACUGA--UUUUCUAA----AGCCCGUCAUUUUUAAUGACGGGCUUUUUC
AAOS02000014.1/93711-93269   CUCGGCCUG-U-GGUACAGACCUA-UU-UAUG-CACGA-CAUCUUGAG-UAAAGUGGUU--CAUA-U--U-UAAA-GCG-UUAU-C-GUU-GAUAGCUCUUCACU-GACGAAUUUCCUU-C--AU--AG-UGCC-U-CCAU----AAGUAACGACUGAUAA-C---CGG--C--UA---UAACA-C-GCC----CA-UGGCGGCAAAAU------UU-UUUA---AUAA-A-GGAAAUA--CACA-UGUCUAACAUGAUGAAAGGUCAAGUAAAGUGGUUCAACGA-GUCUAAAGGCUUCGGUUUCAUCACUCCAGCUGAUGGCAGCAAAGACGUGUUCGUUCACUUCUCUGCUAUCCAAGAUCAAGGCUUCAAGACCCUGGCUGAAGGCCAGAAUGUACAGUUCUCUAUCGAGAACGGUGCUAAAGGUCCGUCUGCAGCAAACGUA-ACUG--CAAUC---UAAU---U-GGCC--UUU-----GGCUG--A---UU--A--UA-AA----AAAACCCGCUAA---GGCGGGUUUUUUACU
M30139.1/461-888             AACGGUUUG-A-CGUACAGACC-A-UU-AAAG-CAGUG-U------AG-UAAGGCAAGU--C---CC--U-UCAA-GAG-UUAU-C-GUU-GAUA-CCCCUCGUA-GUGCACAUUCCUU-U--AA--CG-CUUC-A-AAAU----CUGUA--------AAG-C---ACG--C--CA---UA--U-C-GCC----GA-AA--GGCACACU------UA-AUUA---UUAA-A-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAG-GCUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGAUGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUGUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGUAACGUAACCAGC-CUGUA---AUCU---C-UGCU--UAA--A--AGCAC--A---GA--A--UCUAA----GAUCCCUGCCAUUU-GGCGGGGAUUUUUUU
ACCI02000028.1/45583-45145   ACUGGUUUGGA-AGUACAGGCC-UAUU-UAUGUUAGUC-A------GUUUUAAGAUGUU--C--ACC--A-UUAA-GCG-UUAU-C-UCA-GAUA-CCACU-UCA-UUGCGAAUUCCUUCU--AAUUAA-UUCC-C-AUAAGUACCACAA--------GAA-C---AAA--CCGCA---AC--A-U-GCC----UU-AU--GGCAAUUU------UA-AAAA--AUUAA-A-GGAAAUU--CUAUG--UCUAAUACAAUGACUGGUACAGUAAAAUGGUUUAACGAUGAUAAAG-GUUUUGGUUUUAUCACUCCUGCAGACGGCAGCAAAGAUGUAUUUGUUCACUUUUCUGCAAUUCAAAGUGAUAACUUCAAAUCAUUAGCAGAAGGCCAACAAGUUUCAUUCACCAUUGAAAAUGGUGCUAAAGGCCCAGCAGCAGCUAACGUUAUC--G-C--UA---AAUA---A-CGAU--AAACGA--AUCGC--U---AAGCA--UUCAA----AAACCUCGCUAAAU--GCGAGGUUUUUUCG
AALD02000025.1/10362-9916    CCCGGUUGA-C-AGUAACAUUU-A-UG-CAAG-CAGUUUU------AG-UAAAGCAGUU--C---CCCGU-AUUA-GCG-UUAU-CAGACAGAUA-CCUCUUCUCCGC-GAAAUUCCUU-C--UA--AG-UGCCCC-AUAA----GUUGU--------GCC-C---AAG--C--CU---AU--U-C-GCUCGCCUA-UGGCGGCAAUCA------AAAAUAA---UUGA-A-GGAAGUAUC-UCUAUGUCUAAUAAAAUGACUGGUUUAGUAAAAUGGUUUAACGCUGACAAAG-GUUUUGGUUUCAUCUCUCCUGCUGACGGCAGCAAAGACGUGUUCGUUCACUUCUCUGCCAUCCAGAGCAAUGAUUUCAAAACUUUAGAAGAAGGCCAGAAUGUUGAGUUCUCUAUCGAGAAUGGCGCUAAAGGCCCGGCAGCGGCGAAUGU-UGUUGCUCUGUA---AGAGUGAA-UA--ACUGA--ACC--UAAUAC---CC--A--ACUCA----UUGGAGUUACAGCU-GUAACUUCAAGGACG
ABWL02000023.1/204545-204970 AACGGUUUG-A-CGUACAGACC-A-UU-ACAG-CAGUU-U------AG-UAAGGCAAGU--C---CC--U-UCAA-GAG-UUAU-C-GUU-GAUA-CCCCUCGUA-GUGAGCAUUUCCU-U--UA-CUG-UUAA-A-AAAU----CUGUA--------GAG-C---ACG--C--CA---UA--U-C-GCC----GA-AA--GGCACACU------UA-UUUU--UUAAA-A-GGUAAUA--CACUAUGUCCGGUAAAAUGACUGGUAUCGUAAAAUGGUUCAACGCUGACAAAG-GUUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGACGUGUUCGUACACUUCUCUGCUAUCCAGAACGAUGGUUACAAAUCUCUGGACGAAGGUCAGAAAGUUUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCGGCAGCUGGCAACGUAACCAGC-CUGUA------------AGCU--UAA-CA--AGCUC--A---AA--A--UUCUG----AAUCCCUGCCAAAC-GGCGGGGAUUUUUUU
ABWM02000027.1/244578-245001 GUCGGUUUG-U-UACACAGACC----U-AAAG-CAGUU-U------AG-UUAAGC-AGU--C---C------AGA-UUG-UUAUCC-AUA-GAUA-CCCUUCGUA-GUGACCCUUCCUU-C--AU--CG-CUUA-A-AAAU----CUGUA--------ACG-C---AA---C--CA---UC--G-C-GCC----GG-AA--GGCACAAC------AA-AUUUUUAAU-A-A-GGUAAUU---UCUAUGUCUGGUAAAAUGACUGGUCUGGUAAAAUGGUUCAACGCUGAUAAAG-GUUUCGGCUUCAUCACUCCUGACGAUGGCUCUAAAGACGUGUUCGUACACUUCUCUGCUAUCCAGAACGAAGGCUACAAAUCUCUGGACGAAGGUCAGAAAGUGUCCUUCACCAUCGAAAGCGGCGCUAAAGGCCCAGCAGCUGGUAACGUUGUAAGC-CUGUA---AGCU---U-C-----CAA--C--UCAGC--A---GC--A--AAGAAUUCUAAAACCCGCCUUCU-GGCGGGUUUUUUCGU
#=GC SS_cons                 :::<<<<<<._.____>>>>>>.,.,,.,,[[.-[[[[.-......--.---[[--[[[..[...[[..[.[---.--[.[[[-.[.[[[.[[-[.[[,,,((((.(((------((((.(..((..,<.<<<_._.____...._____........>>>.>...,,,..,..,,...,,..,.,.<<<....__.__..>>>,,,,,......,,.,,,,...)))).).))-----..))))))),<<<<<______>>>>>,,,,,,,,,,,]]]]]]]]]-]]]]-]]].]----]]]]]]--]]]]-]],,((((((,,,,,,,<<_____>>,,<<<<<<-<<<<<<-<<<<<<--<<<________>>>>>>>>>---->>->>>>>>>>>>,,,,,,)))))),,,,<<<-<<<___>>>>>><<<<<<<<<______>>>>>-.>>>>,...,<<<...-.<<<<..___.._..>>>>-..>...>>..,..,,,<<....<<<<<<<<<<____.>>>>>>>>>>>>:::
#=GC RF                      auCgGucug.a.agUAcagaCc.A.uu.aAaG.cAGug.u......ag.UaAggcaagu..C...Cc..u.uuaA.Gag.uuaU.C.guu.GAUA.CCccUCgua.guGaacaUUcCuU.u..aa..ag.cucc.a.AaAU....cUguA........gag.c...Aag..C..Ca...ua..a.c.GCC....ga.aa..GGCAaaau......ua.aUua...uuaA.a.GguAAUa..CacuauGUCcaguAaAAUGacugGUauaGUAAAAUGGUUCaacGaugacAaag.GcUUcGgcuucAUcaCUCCuGacgAugGCagcAAAGAcGUgUUCGUacACuUCuCUGCcAucCAggaCGauGGuUuCAAauCccUGgacGAAgGuCAGaAaGUguacUUCaCcaUcgAAAacGGcGCcAAAgGCCCggcaGCugcuAACGUaagcaGc.CuguA...Aucu...u.cGcu..uaa..a..agCgc..a...ga..A..Uuuaa....aacccccgccaauU.ggcggggguuuuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF01767
#=GF ID   SMK_box_riboswitch
#=GF DE   SMK box translational riboswitch
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Gardner PP
#=GF SS   Published; PMID:18806797; Gardner PP
#=GF GA   45.00
#=GF TC   48.30
#=GF NC   38.30
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0006446; regulation of translational initiation;
#=GF DR   GO; 0004478; methionine adenosyltransferase activity;
#=GF RN   [1]
#=GF RM   17360376
#=GF RT   S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits
#=GF RT   to the SMK box translational riboswitch RNA.
#=GF RA   Fuchs RT, Grundy FJ, Henkin TM
#=GF RL   Proc Natl Acad Sci U S A. 2007;104:4876-4880.
#=GF RN   [2]
#=GF RM   16491091
#=GF RT   The S(MK) box is a new SAM-binding RNA for translational regulation of SAM
#=GF RT   synthetase.
#=GF RA   Fuchs RT, Grundy FJ, Henkin TM
#=GF RL   Nat Struct Mol Biol. 2006;13:226-233.
#=GF RN   [3]
#=GF RM   18806797
#=GF RT   Crystal structures of the SAM-III/S(MK) riboswitch reveal the
#=GF RT   SAM-dependent translation inhibition mechanism.
#=GF RA   Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ke A
#=GF RL   Nat Struct Mol Biol. 2008;15:1076-1083.
#=GF RN   [4]
#=GF RM   18443629
#=GF RT   Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine.
#=GF RA   Wang JX, Breaker RR
#=GF RL   Biochem Cell Biol. 2008;86:157-168.
#=GF RN   [5]
#=GF RM   18374645
#=GF RT   Riboswitches that sense S-adenosylhomocysteine and activate genes involved
#=GF RT   in coenzyme recycling.
#=GF RA   Wang JX, Lee ER, Morales DR, Lim J, Breaker RR
#=GF RL   Mol Cell. 2008;29:691-702.
#=GF WK   SMK_box_riboswitch
#=GF SQ   25


ACHK01000062.1/4026-4119     U--UGUUAC---AA-----GUUCCCGAAAGGAUUUAGCAAGUAAUUGUCGUUACUUAC-UAAAGAUGCCUUGUAACC---GAAA----------CUA----------------------------UUUAGGGGGAAU--AACAUUAUG
ACBD01000055.1/1906-1985     GUUCGUUGC---AA-----GUUCCCGAAAGGAUCCGU-----------------AGGA-CGGAGAUGCCUUGUAACC---GAAU----------UUA----------------------------ACUAGGGGGAAU-CAUUAUAAUG
ACAJ01000030.1/519-601       GUCCGUUGC---AA-----GUUCCCGAAAGGAUUCGC----------------AGCUG-CGAAGAUGCCUUGUAACC---GAAU----------CGA--------------------------AAUUUAGGGGGAAU-ACAAAAAAUG
ACAO01000044.1/534-615       GUCCGUUGC---AA-----GUUCCCGAAAGGAUUCGC----------------AGCUG-CGAAGAUGCCUUGUAACC---GAAA-------CAUAUA-----------------------------UUAGGGGGAAU--ACAAAAAUG
AE017198.1/564018-564088     UUCGGUU-----AA-----GGUCCCGAAAGGAUUCGU---------------UUUUAA-CGAAGAUGCCUUGUAACC---GAAA------------------------------------------GAUGGGGGACU------CUAUG
CP000233.1/487061-487146     AAUAGUUAC---AAUC--CAUUCCCGAAAGGAUUCGU---------------UUUAAA-CGAAGAUGCCUUGUAACC---AAAU-----UACUUAUA---------------------------AUAAUGGGGGAAU---UAAAU---
ACLL01000026.1/19090-19198   CUUCGUUAU--GAAGC-AAAUUCCCGAUAGGAUUCAC--------------UUAAUUG-UGAAGAUGCCUUGUAACC---GCAA----------CUACAAAACUACUACUAGAGUUUCGACUAGAAUAUGGGGGAAU----UAA----
ACGV01000186.1/13246-13351   UCUCGUUAU--AAAGC-AAAUUCCCGAUAGGAUUCAC--------------UUUACUG-UGAAGAUGCCUUGUAACCACUAAAU-GUUUCAAUUGUAAC----------------------UUGCAUAUGGGGGAAUUAACACACAU-
CP000422.1/681467-681547     GUAAGUUAC---UAGU---GUUCCCGAUAGGAUUAGU---------------UAUCCAA--AAGAU-CCUUGUAACC---GAAA----------UUA--------------------------AAUUUAGGGGGAAU----UUACAUG
ACIZ01000041.1/43695-43782   UAGAGUUGC---AAUACA--UUCCCGAUGGGGUUCGUUA-----------GCGAUUAA-CGAACAUGCCUUGUAACC---GAAA----------AUC----------------------------AUGAGGGGGAA--ACAAACGAUG
FM177140.1/914403-914491     UAGAGUUGC---AAAACA--UUCCCGAUGGGGUUCGUCA----------AAGCUAUGA-CGAACAUGCCUUGUAACC---UAAA----------AUA----------------------------AUAAGGGGGAA--ACAAAACAUG
CP000413.1/483009-483080     UUCGGUU-----AA-----GGUCCCGAAAGGAUUCGC--------------UUUUUAA-CGAAGAUGCCUUGUAACC---GAAA------------------------------------------GAUGGGGGACU------CUAUG
CP000517.1/1692576-1692488   UAUCGGUUC---AA------GUCCUGAAAGGAUUCACU------------AUUAUUAG-UGAAGAUGCCUUGUAACC---GAAUA-GCUAAUGUCUA----------------------------UAUGGGGGGAC-----UAUUAUG
ACIL02000003.1/164571-164483 GUCAGUUACAACAAUAAA--UUCCCGAUGGGAUUCAUU-------------UUCUUAA-UGAAGUUGCCUUGUAACC---AAU-----------CUA--------------------------CAAAAUGGGGGAA---AUUACUAUG
CP000033.3/1626537-1626447   UAUCGGUUC---AA------GUCCUGAAAGGAUUCAUUA----------AAUAAUUAG-UGAAGAUGCCUUGUAACC---GAAU-AGCCGAUGUCUA----------------------------UAUAGGGGGAC-----UAAUAUG
ACGH01000133.1/29066-28984   GUAGGUUAU---GAG-----UUCCCGAUAGGAUUCACG-------------CCAGACG-UGAAGAAGCCUUGUAACC---UAAA--------AAAUA----------------------------UAUAGGGGGAA----AUAAAAUG
ACLN01000012.1/57665-57589   UACGGUU-----AA-----GGUCCCGAGAGGAUUCGA-----------------AAUU-CGAAGAUGCCUUGUAACC---GAUU--------UUUUA------------------------------AAGGGGGAC--UUCUAUUAUG
CR954253.1/1355763-1355676   AUUUGUUAC---AA------GUCCUGAUAGGAUUCACC-------------AAAUUGG-UGAAGAUGCCUUGUAACC---GUGUA--------GCUA-------------------------GUCUAUAGGGGGAC-ACAUAUAGAUG
ACKR01000001.1/1180-1268     UAUCGGUUC---AA------GUCCUGAGAGGAUUCACU------------AUGAUUAG-UGAAGAUGCCUUGUAACC---GAAU-AGCCAAUGUCUA----------------------------UAUAGGGGGAC-----UAAUAUG
ABHH01000037.1/13513-13426   GAGGUUUGC---AAUUCGGAUUCCCGAGAGGAUUCACU-------------UUUAAAG-UGGAGAAGCCUUGUAACC---GAAA--------AUUUA------------------------------AAGGGGGAA--CAAAGUAAUG
ACKZ01000012.1/36527-36446   AAAAGUUAA---AAAUGAUAUUCCCGAAAGGAUGCAC-----------------CAUG-UGUAGAUGCCUUGUAACC---GGAA----------UUG-----------------------------AAUGGGGGAA---AAAGAAAUG
AF401669.1/1455-1540         UAGAGUUAU---AAGAAG--UUCCCGAUAGGAUUCAC---------------ACACCG-UGAAGAGGCCUUGUAACC---GACA---------CAUA----------------------------UAUAGGGGGAA-ACAUAGAAAUG
ACGU01000017.1/23671-23581   UAUCGGUUC---AA------GUCCUGAUAGGAUUCAUUA----------CUUAGUUAA-UGAAGAUGCCUUGUAACC---GGAU-AGCCAAUGUCUA----------------------------UAUAGGGGGAC-----UAAUAUG
ADEX01000093.1/3153-3076     AUCGGUU-C---AA------GUCCUGAUAGGAUUCGU-----------------UAUA-CGAAGAUGCCUUGUAACC---GAA------------UAGC---------------------UUGUCUAUAGGGGGAC------AUUAUG
CP003032.1/1501869-1501780   AAGCGUUAC---AACU--CAUUCCCGAUAGGAUUCACG-------------CUUUUAG-UGAAGAUGCCUUGUAACC---ACAA----------AUAU------------------------AAUGAAUGGGGGAAU--UUUAUUAUG
#=GC SS_cons                 :::::::::...::::...((((((,,<<<<-<<<<<..............______>.>>>>---->>>>,,,,<<...____..........___............................____>>))))))..:::::::::
#=GC RF                      uuuaGUUac...AAgu...auUCCCGAaAGGAUuCac..............uuauuag.uGaAGAUGCCUuGUAACC...GaAa..........cUA............................uuaaGGGGGAau..aauAauAUG
//
# STOCKHOLM 1.0

#=GF AC   RF01768
#=GF ID   flavi_FSE
#=GF DE   ribosomal frameshift site
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:19196463
#=GF SS   Published; PMID:19196463
#=GF GA   70.00
#=GF TC   82.10
#=GF NC   40.40
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200969;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   19196463
#=GF RT   A conserved predicted pseudoknot in the NS2A-encoding sequence of West
#=GF RT   Nile and Japanese encephalitis flaviviruses suggests NS1' may derive from
#=GF RT   ribosomal frameshifting.
#=GF RA   Firth AE, Atkins JF
#=GF RL   Virol J. 2009;6:14.
#=GF WK   West_Nile_fever
#=GF SQ   7


EF429200.1/3558-3619 GGGCCUUCUGGUCGUGUUCUUGGCCACCCAGGAGGUCCUUCGCAAGAGGUGGACGGCCAAGA
AY453411.1/3564-3625 GGGCCUUCUGGUGAUGUUUCUGGCCACCCAGGAGGUCCUGAGGAAGAGGUGGACGGCCAGAU
FJ495189.1/3567-3628 GGGCCUUCUGGUGAUGUUUCUGGCCACCCAGGAGGUCCUUCGCAAGAGGUGGACGGCCAGAU
AY898809.1/3566-3627 GGGCCUCUUGGUAGUUUUCCUGGCCACCCAGGAGGUCUUGAGGAAGAGGUGGACGGCCAGAA
X03467.1/3565-3626   AGGCCUUCUGGUGAUGUUUCUGGCCACCCAGGAGGUCUUGAGGAAGAGGUGGACGGCCAGAC
DQ666451.1/3558-3619 GGGCCUUCUGGUCGUGUUCUUGGCCACCCAGGAGGUCCUUCGCAAGAGGUGGACAGCCAAGA
FJ151394.1/3558-3619 GGGCCUUCUGGUCGUGUUCUUGGCCACCCAGGAGGUCCUUCGCAAGAGGUGGACAGCCAAGA
#=GC SS_cons         <<<<<<<<<<<______AAAAAAA___>>>>>>>>>>>:::::::::::::::::aaaaaaa
#=GC RF              GGGCCUuCUGGUggUGUUccUGGCCACCCAGgAGGUCCUuaGcAAGAGGUGGACGGCCAgaa
//
# STOCKHOLM 1.0

#=GF AC   RF01769
#=GF ID   greA
#=GF DE   Enterobacteria greA leader
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20920266
#=GF SS   Published; PMID:20920266
#=GF GA   60.00
#=GF TC   61.40
#=GF NC   53.90
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   20920266
#=GF RT   Premature terminator analysis sheds light on a hidden world of bacterial
#=GF RT   transcriptional attenuation.
#=GF RA   Naville M, Gautheret D
#=GF RL   Genome Biol. 2010;11:R97.
#=GF WK   Enterobacteria_greA_leader
#=GF SQ   25


CP000653.1/3921956-3921833     GCCAUACUACGGUGCAACGCCCUGUAAAGUAAACGAUGACCCAUAGUGAACUUCGCGGUAAAAU-ACGUAUCAAAUUGAAAAAU-UGCU-GCUGACCUGGAACUUUGCUUCC-GGGUCAGUUU-UCUUU
CP000964.1/547166-547288       GUCAUACUACGGUGCAACGCCCAGUAAAGUAAACGAUGACCCAUAAUGAACUUCGGGGUAAAAU-ACCUAUCAA-AUGAAAAAU-UGCU-GCUGACCUGGGGAGUGUUUCCC-GGGUCGGUUU-CUUUU
AE014075.1/3762565-3762444     GUCAUACUACGGCGCAACGCCCUAUAAAGUAAACGAUGACCCUUCGGGAACUCCAGGGUAAAAU-GACUAUCAAAAUG-UGAAU-UGUA-GCUGACCUGGGACU-UGUACCC-GGGUCGGUAU-UUUUU
ABVX01000023.1/64195-64319     GUCAUACUACGGUGCAAUAAGGUCUAAAGUAAACGAUGACCCUCAUUGAACUCUGGGGUAAAAU-ACGUAUCAAAAUGCAAAAC-CGCU-ACUAGCCUGGAAAUUUUGUUCCGGGGCUGGUUG-CUUUU
ABAK02000001.1/2786947-2786825 GUCAUACUACGGCGCAACGCCCUAAAAAGUAAACGAUGACCCAUAGGGAACUCCAGGGUAAAAU-GGUUAUCAAAGAG-GAAAU-UGUA-GCUGACCUGGGACUGCGCGCCC-GGGUUGGUGU-UUUUU
BX571874.1/85651-85526         ACAAUACUAAGGCGCAAAGUGGGGAAAAGUAAACGAUGACCCAUCACCAAGUCUACGUUAGAAUGAUAUAUUAAUAUGUAAAAUAUGAU-UGUGAACUCUGGGUAGUCCUAU-GGUUUGCACU-AUUGU
FM211050.1/45033-44909         ACAAUACUAAGGUGCAAAGUGGGGAAAAGUAAACGAUGACCCAUCACCAAGUCUACGUUAGAAUGAUACAUUAAUAUGUAGAAA-UGAU-UGUGAACUUUGGGUAACUCUGU-AGUUUACAUG-AUUGU
CP000647.1/3952494-3952372     GUCAUACUACGGUGCAACGCCCAGUAAAGUAAACGAUGACCCAUAAUGAACUUCGGGGUAAAAU-ACCCAUCAAA-UGAAAAAU-UGCU-GCUGACCUGGGGAGUGUUUCCC-GGGUCGGUUUCUUUU-
CP000038.1/3508005-3507884     GUCAUACUACGGCGCAACGCCCUAUAAAGUAAACGAUGACCCUUCGGGAACUUCAGGGUAAAAU-GACUAUCAAAAUG-UGAAU-UGUA-GCUGACCUGGGACUU-GUACCU-GGGUCGGUAUUUUUU-
CP000036.1/3206058-3206179     GUCAUACUACGGCGCAACGCCCUAUAAAGUAAACGAUGACCCUUCGGGAACUUCAGGGUAAAAU-GACCAUCAAAAUG-UGAAU-UGUA-GCUGACCUGGGACUU-GUACCC-GGGUCGGUAUUUUUU-
CP000783.1/3511736-3511612     GUCAUACUAAGGCGCAUCGCCCUGCAAAGUAAACGAUGACCCUUCGGGAACUUCAGGGUAAAAU-ACGUAUCAAAUUGCAAAAU-CGUU-CCUGACCUGGGGCUUUGUCUCC-GGGUCAGUUUUCUUUU
CP001127.1/3367755-3367633     GUCAUACUACGGCGCAACGCCCUAAAAAGUAAACGAUGACCCAUAGGGAACUCCAGGGUAAAAU-GGUUAUCAAAGAG-GAAAU-UGUA-GCUGACCUGGGACUGCGCGCCC-GGGUUGGUGUUUUUU-
AM286415.1/493871-493990       --CAUACUACGGUGCAACGAGGGCGAAAGUAAACGAUGACCCUAAAGGAACUCUACGUUAAAAU-GCAUAUCAAAAUGCAAAAU-UGAUCCUGACUUGGGGUUU-UGGCUCC-GGGGUG--AU-UUUUU
CP000826.1/530219-530340       GUCAUACUACGGUGCAUUCAGGGAAAAAGUAAACGAUGACCCUCAAGGAACUCUAAGCUAAAAU-GCGUAUCAAAAUGCAAAAU-CGAUCC-UGACUUGGGCAA-CUGUUCC-GAGUCA-GGC-UUCUU
CP000034.1/3120337-3120217     GUCAUACUACGGCGCAACGCCCUAUAAAGUAAACGAUGACCCUUCGGGAACUUCAGGGUAAAAU-GACUAUCAAAAUG-UGAAU-UGUA-GCUGACCUGG-ACUU-GUACCC-GGGGCGGUAUUUUUU-
CU468135.1/394538-394659       GCCAUACUACGGUGCAUCGUGGUGGAAAGUAAACGAUGACCCCUAUGGAACUCUGGGGUAAAAU-ACGUAUCAAAUUGCGAAAU-UGAU-UCUGGCCUGGAGCU--UGCUCC-GGGUCAGGUU-UCUUU
AP008232.1/664508-664628       GUCACACUACGGUGCAA-ACAGGGAUAAGUAAACGAUGACCCACACCGAACUCUGCGGUAAAAU-ACGUAUCAAAAUGCAAAAC-UGAGGCUGGCCUGGGAAGC--GAUUCC-GGGGUC-GCU-UCCUU
BX950851.1/766215-766336       GUCAUACUACGGCGCAAUAAGGUCUAAAGUAAACGAUGACCCUCAUUGAACUCUGGGGUAAAAU-ACGUAUCAAAAUGCAAAAC-CGCUGCUAGCC-UGGAUAUUUUGUUCU-GGGGCUGGUU-GC--U
CP000668.1/4087530-4087411     GUCAUACUACGGUGCAACGAGGGAGAAAGUAAACGAUGACCCUAAAGGAACUCUACGUUAAAAU-GCAUAUCAAAAUGCAAAAU-UGAUCCUGACUUGGGGUUU-UUGGCCC-UAGGUU--UU-UUU--
ABVY01000071.1/7189-7310       GUCAUACUACGGCGCAACAAGGGCUAAAGUAAACGAUGACCCUCAUUGAACUCUGGGGUAAAAU-ACGUAUCAAAAUGCAAAAC-CGCUGCUAGCC-UGGAAAUUUUGUUCC-GGGGCUGGUU-GC--U
CP000822.1/4232313-4232191     GUCAUACUACGGCGCAAUGCCCUGGAAAGUAAACGAUGACCCAUAGGGAACUCCAGGGUAAAAU-ACGUAUCAAAUUG-AGAAU-UGUA-GCUGACCUGGGGCUUUGUACCC-GGGUCGGUAU-UUUUU
ABWM02000035.1/307238-307115   GUCAUACUACGGUGCAUGGCACUGCAAAGUAAACGAUGACCCAUAGUGAACUUCGCGGUAAAAU-GCGUAUCAAAUUGAAAAAU-UGCU-GCUGACCUGGGACUUUGUUCCC-GGGUCGGUUUUCUUU-
AALC02000010.1/59051-58928     GCCAUACUACGGUGCAACGAGGGCGAAAGUAAACGAUGACCCUAAAGGAACUCUACGUUAAAAU-GCAUAUCAAAAUGCAAAAU-UGAU-CCUGACUUGGGUUUUUUGCUCC-AGGAGUGAUU-AUUUU
AALD02000019.1/26388-26268     GCCAUACUACGGUGCAACGAGGGCGAAAGUAAACGAUGACCCUAAAGGAACUCUACGUUAAAAU-GCAUAUCAAAAUGCAAAAU-UGAU-CCUAACCUGGUUUUUUUGCUUC-AGG---GGUG-AUUGU
ABWL02000026.1/97946-98069     GUCAUACUACGGCGCAACGCCCCAAAAAGUAAACGAUGACCCAUCGGGAACUCCAGGGUAAAAU-GAUCAUCAA-AUAGAGAAU-UGUA-GCUGACCUGGGACCUUGAGCCCCGGGUCGGUAU-UUUUU
#=GC SS_cons                   <<<<<----<<--<<_____________>>--->>>>>>><<____>>,,,,,,,,<<<<____.___>>>>,,,,,,,,,,,,.,,,,.<<<<<<<<<<<________>>>.>>>>>>>>::.:::::
#=GC RF                        GuCAUACUACGGuGCAAcGcgguaaAAAGUAAACGAUGaCCcuuaagGAACUcuagGgUaAAAU.acauAuCAAAAUGcAAAAU.UGau.cccgacccgggaaUuuuuuccc.gggucggguU.uUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01770
#=GF ID   rimP
#=GF DE   Gammaprotebacteria rimP leader
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20920266
#=GF SS   Published; PMID:20920266
#=GF GA   47.00
#=GF TC   47.50
#=GF NC   46.50
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   20920266
#=GF RT   Premature terminator analysis sheds light on a hidden world of bacterial
#=GF RT   transcriptional attenuation.
#=GF RA   Naville M, Gautheret D
#=GF RL   Genome Biol. 2010;11:R97.
#=GF WK   Gammaproteobacteria_rimP_leader
#=GF SQ   46


AAJV02000002.1/284148-284048 GACCGCAGUUGCGGUUAUAGGGUUCAGUUA----UAUAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUCUGA------------------------------------CUAC-A-GAAUAACUGGGC-U-UUA-A-GCCCUUUUUUU
FM211050.1/37967-37868       AGCCACUG-GCAGCAAACAGGGUCCAGUUG----CAUAAAGCCCCG-AAU-UU---CGGGGUUUUUUGUUAUUUGA------------------------------------CAAC-A-GAACUACUGGGC-UAAUA-A-GCCCUUUUUUU
ABVX01000008.1/23131-23230   CGCUGGUUAGCGGU-AUUAGGGUCCAGUUG----CAUAAAGCCCCG-AUUUUU---CGGGGUUUUUUGUUAUUUGG------------------------------------CAAC-A--AACAACUGGGC-UAUUA-G-GCCCUUUUUUU
X00513.1/256-356             AGACCGCAGUUGCGUUAUAGGGUUCAGUUA----UAUAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUCUGA------------------------------------CUAC-A-GAAUAACUGGGC-UUUAG---GCCCUUUUUUU
ABVY01000044.1/9411-9509     AUCGGUAA--GCGGUAUUAGGGUCCAGUUG----CAUAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUUUGG------------------------------------CAAC-A--AACAACUGGGC-UAUUA-G-GCCCUUUUUUU
ACDJ01000021.1/57221-57121   AACCGCAGGUGCGGUUAUAGGGUUCAGUUA----UCUAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUCUGA------------------------------------CUAC-A-GAAUAACUGGGC-UUUAG---GCCCUUUUUUU
CP000964.1/558120-558220     GAUCGCCAUGGCGAUCUCAGGGUUCAGUUA----UCUAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUCUGA------------------------------------CUUC-A-GAAUAACUGGGC-UAUAC---GCCCUUUUUUU
AAKK02000040.1/26-152        GGCUAUUCUUAACGUAUCAGGGUCCAGCAG----CAUAAAACCCCG-ACU-AU---CGGGGUUUUUUGUUAUCUGAGCUUUUUGAAAUA---------GCUCAGAGACUGCUUGGU-U-UUUUGAUUGGGC-UCUGA---GCCCUUUUUUU
AM942759.1/3742590-3742688   UCUCGAUUGGCAAGUUACAGGGUCCAGUUG----CAUAAAGCCCCG-AAU-UU---CGGGGUUUUUUGUUAUCAGA------------------------------------GAAU-A--GAAUACUGGGC-UAUAA---GCCCUUUUUUU
CP000783.1/3504596-3504497   CGCGCAUC-GCGGUUUACAGGGUUCAGUUA----UUAAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUCUGG------------------------------------CUAA-A-GAAUAACUGGGC-UAUAU---GCCCUUUUUUU
ACFN01000055.1/4437-4563     GACUAUUCUUAACGUAUCAGGGUCCAGCAG----CAUAAAACCCCG-ACU-AU---CGGGGUUUUUUGUUAUCUGAGUUUUUUAAAUGA---------CUCAGGUCACUGCUUGGU-U-UUUUGAUUGGGC-UCUGA---GCCCUUUUUUU
ACCV01000105.1/33197-33065   AGAUAUCGUUUAACUAUCAGGGUCCAGCAA----CAAAAAACCCCG-ACUUUU---CGGGGUUUUUUGUUAUCUAAAUUUUCCCAAUGGGAA----AAUUUGGUGUUUUGCUUGGA-A-UUUAAAUUGGGC-UCUGA---GCCCUUUUUUU
ABGR01000008.1/16688-16815   GGCUAUUCUUAACGUAUCAGGGUCCAGCAG----CAUAAAACCCCG-ACU-UU---CGGGGUUUUUUGUUAUCUGAGUUUUUAUAAAUCA--------ACUCGGGUAUUGCUUGGU-U-UUUUGAUUGGGC-UCUGA---GCCCUUUUUUU
AAKI02000297.1/79-211        AGCGAUUCUCAAUUUAUCAGGGUCCAGCAA----UAAAAAACCCCG-ACUUAA--UCGGGGUUUUUUAUUAUCUAAAUUUCCUUUUUAGGG-----GGUUUAGGUAUUUGCUUGGU-A-UUUAAAUUGGGC-UCUAA---GCCCUUUUUUU
CR378664.1/317617-317725     AGCUUGCUGUGGUA-AUCAGGGUCCAGUAA----UAAAAAACCCCGUAUU------CGGGGUUUUUUAUUAUCUGAAAUAUG------------------------ACAAUUCAGA-U-AUU-CACUGGGC-UUUUG---GCCCUUUUUUU
BA000037.2/2751107-2750973   GGUUGUU--UAACGUAUCAGGGUCCAGCAA----CAAAAAACCCCG-ACUAAU---CGGGGUUUUUUGUUAUCUGUACUUCUCGCUGGUGCGAGUUUUGUACAGAUAGUGCUUGGU-U-UUUAUAUUGGGC-UCUGA---GCCCUUUUUUU
CP000789.1/3438539-3438411   GGCUAUUCUUAACGUAUCAGGGUCCAGCAG----CAUAAAACCCCG-ACU-UU---CGGGGUUUUUUGUUAUCUGAGUUUUUGUAAUUUA-------ACUCGGAUCACUGCUUGGU-U-UUUUGAUUGGGC-UCUGA---GCCCUUUUUUU
CU468135.1/401912-402011     CGCGAUUC-GCGGUUUACAGGGUCCAGUCA----CAAUAAGCCCCG-AUAUUU---CGGGGUUUUUUGUUAUCAGG------------------------------------AAGC-A-GCAUCACUGGGC-UAUAG---GCCCUUUUUUU
AP008232.1/671761-671861     AGCCGCCU-GCGGUUUACAGGGUCCAGUCA----CUUAACGCCCCG-AUUUUU--UCGGGGUUUUUUGUUAUUUCA------------------------------------CA-C-A-GUAAUACUGGGC-UAAUU-A-GCCCUUUUUUU
AAOU01000003.1/121117-121227 UAUAGAGCCUCGGUAAUCAGGGUCCAGUAA----UAAAAAACCCCGUAAU-----UCGGGGUUUUUUAUUAUCUGAAACAUG------------------------ACCAUU-CAG-G-UAUCUACUGGGC-U-UUA-U-GCCCUUUUUUU
AAUT01000040.1/34161-34029   AGAGCAUUCUCAUUUAUCAGGGUCCAGCAA----UAAAAAACCCCG-ACUUAA--UCGGGGUUUUUUAUUAUCUAAAUUUCCUUUUUAAGG-----GUUUUAGGUAUUUGCUUGGU-A-UUUAAAUUGGGC-UCUAA---GCCCUUUUUUU
ABJD02000102.1/137191-137292 AACCCGUU--GGCACUACAGGGUCCAGUUU----CAUAAAGCCCCG-AAAUUU---CGGGGUUUUUUGUUAUUUGA------------------------------------CAAUCG-AAUUAACUGGGC-UUUUAUA-GCCCUUUUUUU
AAZW01000011.1/118096-117964 GAUGGCACUUAGCAUAUAAGGGUCCAGCAA----CA-AAAACCCCG-GCUUAU--ACGGGGUUUUUUGUUAUCUAAGCAUUUGUAAAUGCGU----UUAGAUAAUGUUUGCUUGGA-A-UUUAAAUUGGGC-U-UUG-A-GCCCUUUUUUU
ABCH01000018.1/94192-94067   ACUUUUUCUUAGUG-AUCAGGGUCCAGCAA----CAAACAACCCCG-ACU-UU---CGGGGUUUUUUGUUAUUUGAGCUUUUUGAAACG---------CUCGAAUAAAUGCUUGGA-A-UUUAAAUUGGGC-UAUAU---GCCCUUUUUUU
CP000388.1/2026440-2026551   CAGUGAGAAUAGUGGACUAGGGUCCAGAAA----CAAAAAGCCCCG-CUUGUA---CGGGGCUUUUUGUUAUCCUUUUUAU-------------------------CCUGUUUUUA-A-UUUAUUCUGGGC-UUAUG---GCCCUUUUUUC
AAMR01000012.1/106719-106584 GAUGACACUUAACAUAUAAGGGUCCAGCAA----CA-AAAACCCCG-GCUUAU--ACGGGGUUUUUUGUUAUCUAAGCAUUUGUAAAUGCCUU-UAGAUGAUAAUGUUUGCUUGGA-A-UUUAAAUUGGGC-U-UUG-A-GCCCUUUUUUU
ABXW01000015.1/44860-44761   CGGUAAACCCAUGCACUAUGGGUCCAGUUA----CA-AAAGCCCCG-AAU-UU---CGGGGUUUUUUGUUAUUUGA------------------------------------CAAUCG-AAUUAACUGGGC-U-UUA-U-GCCCUUUUUUU
CP001139.1/508510-508619     GUCACGCAAGUGGCAUUCAGGGUCCAGCAG----UAUUAAACCCCGCAAU-UA---CGGGGUUUUUUGCUAUCUGAAACA---------------------------GACUGUUUU-U-UAAGAAUUGGGC-C-UUG-A-GCCCUUUUUUU
FM178379.1/657831-657944     GUCACGCAAGUGGCAUUCAGGGUCCAGCAG----UAUUAAACCCCGCAAUUAU---CGGGGUUUUUUGCUAUCUGAAACA---------------------------GACUGUUUU-U-UAAAAAUUGGGCCUUUUA-GUGCCCUUUUUUU
CP000644.1/1036084-1036197   CGCUGCGAGGCGACAAUCAGGGUAAAGCGC-------CAAGCCCCG-AUUUGACAUCGGGGCUUUUUGUUAUGUGCGAUUUA-----------------------CUCUGAAUCGA-U-AUCUAUCUGGGC-U-UUA-U-GCCCUUUUUUU
ABST01000015.1/29723-29827   UCAGAUAUAUAGUGGACUAGGGUCCAAAAAUUUGUAAAAAGCCCCU-GCUUGU--AAGGGGCUUUUUUCGUUUAUG------------------------------------CGGU-A-UC-AAAAUGGGC-U-UUA-U-GCCCUUUUUUC
ABCQ01000011.1/22596-22502   GUCACGCAAGUGACAUACAAGGUCUAGUAG----UAAGAAGCCCCG-CCUUAUAGUCGGGGCUUUUUAUUUUUUAA------------------------------------AUU----------ACGGGC-A-UUU---GCCCUUUUUUU
CU928145.2/3675518-3675419   ACCGCAGUUGCGGU-UAUAGGGUUCAGUUA----UAUAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUCUGA------------------------------------CUAC-A-GAAUAACUGGGC-U-UUA-G-GCCCUUUUUUU
BA000031.2/2582372-2582246   GACUAUUCUUAACGUAUCAGGGUCCAGCAG----CAUAAAACCCCG-ACU-A---UCGGGGUUUUUUGUUAUCUGAGUUUUUUAAAUGA---------CUCAGGUCACUGCUUGGU-U-UUUUGAUUGGGC-UCUGA---GCCCUUUUUUU
CP000034.1/3108834-3108735   AUCGCAGUUGCGGU-UAUAGGGUUCAGUUA----UAUAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUCUGA------------------------------------CUAC-A-GAAUAACUGGGC-U-UUA-G-GCCCUUUUUUU
CP000886.1/3418657-3418558   ACCGCCGUUGCGGU-UAUAGGGUUCAGUUA----UCUAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUCUGA------------------------------------CUAC-A-GAAUAACUGGGC-U-UUA-G-GCCCUUUUUUU
BX950851.1/777161-777259     GUUUGUAA-GCGGUAU-UAGGGUCCAGUUG----CAUAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUUUGG------------------------------------CAAC-A--AACAACUGGGC-UAUUA-G-GCCCUUUUUUU
CP000036.1/3216868-3216967   ACCGCAGUUGCGAU-UAUAGGGUUCAGUUA----UAUAAAGCCCCG-AUUUAU---CGGGGUUUUUUGUUAUCUGA------------------------------------CUAC-A-GAAUAACUGGGC-U-UUA-G-GCCCUUUUUUU
BX571874.1/78585-78486       AGCCACUG-GCAGCAAAUAGGGUCCAGUUG----CAUAAAGCCCCG-AAUUU----CGGGGUUUUUUGUUAUUUGA------------------------------------CAAC-A-GAACUACUGGGC-UAAUU-A-GCCCUUUUUUU
CP000308.1/64828-64729       AGCCGCUUUGCGGCAAACAGGGUCCAGUUG----CAUAAAGCCCCG-AAUUU----CGGGGUUUUUUGUUAUUUGA------------------------------------CAGC-A-GAAUCACUGGGC-UAUUA-A-GCCCUUUUUU-
CP000627.1/173987-174119     AGCGAUUCUCAAUUUAUCAGGGUCCAGCAA----UAAAAAACCCCG-ACUUAA--UCGGGGUUUUUUAUUAUCUAAAUUUCCUUUUUAAGG-----GUUUUAGGUAUUUGCUUGGU-A-UUUAAAUUGGGC-UCUAA---GCCCUUUUUUU
CP002469.1/669471-669605     GGUUGUU--UAACGUAUCAGGGUCCAGCAA----CAAAAAACCCCG-ACU-AA--UCGGGGUUUUUUGUUAUCUGUACUUCUCGCUGGUGCGAGUUUUGUACAGAUAGUGCUUGGU-U-UUUAUAUUGGGC-UCUGA---GCCCUUUUUUU
AALD02000019.1/19182-19082   AGCCGCUUUGCGGCAAACAGGGUCCAGUUG----CAUAAAGCCCCG-AAU-UU---CGGGGUUUUUUGUUAUUUGA------------------------------------CAGC-A-AAAUCACUGGGC-UAUUA-G-GCCCUUUUUUU
ABWM02000035.1/298394-298294 GGCCACAGUUGUGGCUAUAGGGUUCAGUUA----UCUAAAGCCCCG-AUUUUU---CGGGGUUUUUUGUUAUCUGA------------------------------------CUAC-A-GAAUAACUGGGC-U-UUA-C-GCCCUUUUUUU
ABXV02000023.1/176901-176803 UGGUAAACCCAUGCGUUAUGGGUCCAGUUA----CA-AAAGCCCCG-AUA--U---CGGGGUUUUUUGUUAUUUGA------------------------------------UAAU-CGAAUUAACUGGGC-UAUAU---GCCCUUUUUUU
ACCI02000081.1/112964-112862 GGUGAACCCGUGCACUACAGGGUCCAGUUG----CAUAAAGCCCCG-AAU-UU---CGGGGUUUUUUGUUAUUUGA------------------------------------CAAUCG-AAUUAACUGGGC-UUUUAUA-GCCCUUUUUUU
#=GC SS_cons                 ::::::::::::::::::::::::::::::....:::<<<<<<<<<.______...>>>>>>>>>---------------...........................---------.-.--------<<<<._____._.>>>>:::::::
#=GC RF                      agcuauuuuuaguuuaucAGGGUCCAGuaa....cAuAAAgCCCCG.AuUUaU...CGGGGcUUUUUGUUAUcUgAauuu...........................uugcuuugu.a.uuuuaAuUGGGC.UaUua.a.GCCCUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01771
#=GF ID   rnk_leader
#=GF DE   Enterobacteria rnk leader
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20920266
#=GF SS   Published; PMID:20920266
#=GF GA   50.00
#=GF TC   53.80
#=GF NC   47.30
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   20920266
#=GF RT   Premature terminator analysis sheds light on a hidden world of bacterial
#=GF RT   transcriptional attenuation.
#=GF RA   Naville M, Gautheret D
#=GF RL   Genome Biol. 2010;11:R97.
#=GF WK   Enterobacteria_rnk_leader
#=GF SQ   13


ABEH02000009.1/149631-149523 UUGAGGAUUUAC---CCGAAUGUGAACUAAAUCACUUCAAAGACGGGGGAAGUCUCAGUAUCAUCAUGAGAGUU-AAACCCUCGCCG-CCAGACGGUGAGGGUUUUCUUUUGGG
ABKX01000004.1/85567-85675   AUGAGGAAUUCC---CUGAAUGUGACGUAAAUCACUUCAAAGUGUGGGCAACAGUCAGUAUCAUCAUGUGAGUU-AAACCCUCGCCG-CCUGACGGUGAGGGUUUUCUUUUGGG
CP000822.1/2352673-2352781   UUGAGGAUUUCC---CCGAAUGUGAGCUAAAUCACUUCAAAGAAGGGGGAAGUCUCAGUAUUAUCAUGAAAGCU-AAACCCUCGCCG-CCUGACGGUGAGGGUUUUCUUUUGGG
CU928158.2/2546710-2546818   UAUGGGAUUUGC---CUUAAUGUGACCUGAAUCACUUCAAAGAGUGUUAAACUCUCAGUAUCAUCAUACGAGUU-AAACCCUCGCCG-CCUGACGGUGAGGGUUUUCUUUUGGG
L37900.1/1-104               -----GAAUUCC---CUGAAUGUGACGCAAAUCACUUCAAAGAGUGAGCAACAGUCAGUAUCAUCAUGUGAGUU-AAACCCUCGCCG-CCUGACGGUGAGGGUUUUCUUUUGGG
CP000653.1/1263900-1263791   UUCAUCUGCGCG---AUGAAUGUGACAUUCAUCACUUCAAACUUCGGUGUUCAGCCAGUAUCAUCAGGAGAGAUAAAACCCUCGCUG-CCAUACGGCGAGGGUUUUCUUUUGGA
CP000783.1/2664979-2665091   UUCUGCUUUAAGCCCCGUUUCGUGAGCUGGCUCACUUCAAACGGCGCGCAAGGCUGAGUAUCAUCCCCUGACGC-GGACCCUCAUCGUUUUGACGGUGAGGGUUUUUCUUUGGA
CP001144.1/717328-717220     UUGAGGAUUUAC---CCGAAUGUGAACUAAAUCACUUCAAAGACGGGGUAAGUCUCAGUAUCAUCAUGAGAGUU-AAACCCUCGCCG-CCAGACGGUGAGGGUUUUCUUUUGGG
U00096.2/643344-643236       UUGAGGAAUUCC---CUGAAUGUGACGCAAAUCACUUCAAAGAGUGAGCAACAGUCAGUAUCAUCAUGUGAGUU-AAACCCUCGCCG-CCUGACGGUGAGGGUUUUCUUUUGGG
CP000964.1/3964507-3964614   ---GGGCGUUGCACGCUGAAUGUGCGUUUCAUCACUUCAAACUACCGGCAACUCUCAGUAUGAUGGUAGGACCU-UAACCCUUGCC--CUUUUCGGCGAGGGUUUUCUUUUACG
AM075208.1/61626-61516       --CUGCUUUAAGCCCCGUUUCGUGAGCUGGCUCACUUCAAACGGCGCGCAAGGCUGAGUAUCAUCCCCUGACGC-GGACCCUCAUCGUUUUGACGGUGAGGGUUUUUCUUUGGA
ACDJ01000003.1/196674-196566 UUGAUGAUUUAC---CUGAAUGUGAACUAAAUCACUUCAAACAUGGGGUAAGUCUCAGUAUCAUCAUAAAAGCU-AAACCCUUGCCG-CCUGACGGUGAGGGUUUUCUUUUGGG
ABWM02000020.1/143967-143859 UUCAUAUGGCGU---AUGAAUGUGACCUUCAUCACUUCAAACUUGCCUCUUCAGCCAGUAUCAUCAGGAGAGUU-AAACCCUCGCUG-CCAGACGGCGAGGGUUUUCUUUUGGA
#=GC SS_cons                 ::::::::::::...::<<<-<<<<______>>>>>>>------------------------------------.<<<<<<<<<<<<._____>>>>>>>>>>>>:::::::::
#=GC RF                      UUcaggauUuac...CuGaaUGUGAacUaaAUCACuuCAAAcaguGgGcAAcucUcAGUAUCAUCaugaGAguU.aaACCCUCgCCG.CcuGACGGcGAGGGUuuUCUUUUGGg
//
# STOCKHOLM 1.0

#=GF AC   RF01772
#=GF ID   rnk_pseudo
#=GF DE   Pseudomonas rnk leader
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20920266
#=GF SS   Published; PMID:20920266
#=GF GA   55.00
#=GF TC   59.40
#=GF NC   47.40
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   20920266
#=GF RT   Premature terminator analysis sheds light on a hidden world of bacterial
#=GF RT   transcriptional attenuation.
#=GF RA   Naville M, Gautheret D
#=GF RL   Genome Biol. 2010;11:R97.
#=GF WK   Pseudomonas_rnk_leader
#=GF SQ   15


CT573326.1/5681142-5681037 UCCUGCGGGCUUGUGUAUUUGCCCCGCUGUGGUAGUGUCAGGUU-CUGCGUCAUU-GACGCCAGAAGC------AUUUCGCAAACCCCGCCCUU---GGGCGGGGUUUUGCUUUAUC
CP000926.1/5906275-5906173 CGCAGGG-GCUUGAGUAUUUACCCGGCUGUGGUAGUGUCGGGUU-CUGCGUCGGU-GACGCCAAAGC--------CUUCUCAAACCCCGCCCUU---GGGCGGGGUUUUGCUUUAUU
CP000949.1/260995-261099   CGCGCAG-GCUUGAGUAUUUGCCCGGCUGUGGUAGUGUCGGGUU-AUGCGUCGGU-GACGCCA-AAGC------ACUCAUCAAACCCCGCCCU--CUGGGCGGGGUUUUGCUUUAUC
AAKW01000062.1/99029-99133 AGUCGCUGGCGGGCCGUCUCUCCU-GAUAGGGGGGAUGUUGCUAAUUCCUGCGACUGUGUUAGUGUC----------CGGGAAAACCCCGCCUU-CGGGCGGGGUUUUUGCUUUUUU
CP000304.1/571551-571664   UGCAGCCCGCGAGUU-UACUGGCCUGCGGGCUGGGGUCUUGCUUAUUCGGGCUGCUGUGAUAGUGUCUCCGGCAGGUCAGCAAAACCCCGCCUU-CGGGCGGGGUUUUG-CUUUUUU
CP000058.1/5678052-5678156 CGCGUCGG-GUUGUGUAUUUACUGCGCUGUGUUAGUGU-CGGAA-CCUG-CUUCU-CCAGAUUGAGAG------GCCCGUAGAACCCCGCC-CACCCCGGCGGGGUUUUGUUUUAUU
AE016853.1/248590-248694   CGGGUCG-GGUUGUGUAUUUGUUGCGCUGUGUUAGUGUCAGACC-CUGC-UUCUC-CAGAUCGAGAA-------GCCCGUAAAACCCCGCC-UGCCCCGGCGGGGUUUUGUUUUAUU
ACOQ01000736.1/3904-3800   CGGCCCA-UCUUGUUUAUUUGGUGUGCUGUGGUAGUGUC--CGG-GUAC-GCCUC-AACUCAUCGAGG------UCCGUGAGAACCCCGCCGUUUACUGGCGGGGUUUUGCUUUUUU
CP000075.1/194091-193989   CCGCGUCGGGUUGUGUAUUUACUGCGCUGUGUUAGUGUCAGGCC-UUG--CCUCU-GCAGACAAGAG-------GCUCGUCAAACCCCGCCAAU---UGGUGGGGUUUUGUUUUAUU
CP000744.1/6214989-6214888 CGCAGGCGGGCCGUC---UCUCCU-GAUAGGGGGGAUGUUGCUA-AUU--CCUGC-GACUGUGUUAGU------GUCCGGGAAAACCCCGCCUU-CGGGCGGGGUUUUUGCUUUUUU
AE015451.1/5960068-5959966 CGCAGGG-GCUUGAGUAUUUGCCCGGCUGUGGUAGUGUCGGGUU-CUGCGUCGGU-GACGCCA-AAGC-------CUUCUCAAACCCCGCCCUU---GGGCGGGGUUUUGCUUUAUU
AE004091.2/5940584-5940481 -GUCGCUGGCGGGCCGUCUCUCCU-GAUAGGGGGGAUGUUGCUAAUUCCUGCGACUGUGUUAGUGUC----------CGGGAAAACCCCGCCUU-CGGGCGGGGUUUUUGCUUUUUU
AM181176.4/6501022-6500917 UGAGGCCGUCUUGUUUAUUUGUGACGCUGUGGUAGUGUCCGGGU-AC---GCCUC-AACUCAUCGAGG------CCCGUGAGAACCCCGCCUUUUCCUGGCGGGGUUUUGCUUUUUU
CP000094.2/6163495-6163390 GGAGCGUAGCUUGUAUAUUUUUUGAGCUGUGAUAGUGUCCGGAA-AC---GCCUC-AACCCAUCGAGG-----CCUGGUGAGAACCCCGUCUUU-UUUGGCGGGGUUUUGCUUUUUU
AEAP01000464.1/18716-18820 CGCGUCG-GGUUGUGUAUUUACUGCGCUGUGUUAGUGU--CGGA-CUCUGCUUCU-CCAGAUUGAGAG------GCCCGUAGAACCCCGCC-CACCCCGGCGGGGUUUUGUUUUAUU
#=GC SS_cons               :<<<<<------------<<<<<<_____>>>>>>---------.----->>>>>.------------......------<<<<<<<<<<<<__.__>>>>>>>>>>>>::::::::
#=GC RF                    cgccgcugGCUuGUgUAUUuaccccGCUGggguaGuGUcuGgua.uUccGgcggc.gacuuagugagg......gcucggaAAAcCCCgcCcUU.CggGgcGGGgUUUuGCUUUuUU
//
# STOCKHOLM 1.0

#=GF AC   RF01773
#=GF ID   rpsL_pseudo
#=GF PI   rpsL_psuedo;
#=GF DE   Pseudomonas rpsL leader
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20920266
#=GF SS   Published; PMID:20920266
#=GF GA   70.00
#=GF TC   77.90
#=GF NC   67.70
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   20920266
#=GF RT   Premature terminator analysis sheds light on a hidden world of bacterial
#=GF RT   transcriptional attenuation.
#=GF RA   Naville M, Gautheret D
#=GF RL   Genome Biol. 2010;11:R97.
#=GF WK   Pseudomonas_rpsL_leader
#=GF SQ   9


AM181176.4/6053534-6053399 GGUCGGGGCCUUGCCUUGACUGGGGGCAAGAUCCUCUUUAGACUCUUGUACCCCUAAAUUUGGCGGGAA-UU-CGUUCCUGCCAUU--UUGCUUUUCUUGCAAGACAAUAGCGUCGCAAGACAA-CAGUGGAGCUAGUAGA
CP000058.1/5232061-5231927 UGUCGGGGCUUUGUCUUGACUGGGGACGGGAUCCUCUUUAGACUCUUGUACCCCUAAAUUUGGCGGGGC-UU-GUGCCCUGUCAUU--U-GCUUUUCUUGUAAGACAAUAGCGUCGCAAGACAA-CAGUGGAGCUAGUAGA
ABZR01000046.1/10924-11058 GGCCGGGGCUUUGUCUUGACUGGGCACAGGAUCCUCUUUAGACUCUUGUACCCCUAAAUUUGGCGGGGC-GU-UUGUCUCGUCAAU--U-GCUUUUCUUGUAAGACAAUAGCGUCGCAAGACAA-CAGUGGAGCUAGUAGA
CP000926.1/563756-563893   GGUCGGGGCCUCGUCUUGACUGGGUGCAAGAUCCUCUUUAGACUUUUGUACCCUUAAAUUUGGUGAGGC-UC--CGUCUCGCCAAUUUUUGGCUUUCUUGCAAGACAAUAGAGUCGCAAGACAAUCAGUGGAGCUAGUAGA
CP000076.1/6367185-6367066 GGCCGGGGCCUUGCCUUGACUGGGGGCAAGAUCCUCUUUAGACUCUUGUACCCCUAAAUUUGGUGGAGC-UC-CUGCUCUGCCAUU--UUGUUUAU----------------GUCGAAAGACAA-CAGUGGAGCUAGUAGA
CP000680.1/4291589-4291464 UAGCGGGGCUUUGCCUUGACUGGGGGCGUGAGUCUCUUUAGACUCAUGCACCCCUAAAUUUGGCAGGGCGUU-UGGCUCUGCCAUC--UUUAUU-----------UGUGAGCGUCGAAAGACAA-CAGUGGAGCUAGUAGA
CP000304.1/888140-888260   AGCCGGGGCCU-GCCUUGACGGUGGGCGAGAAGCUCUUUAGACUCUCGUACCCCUAAAU-UGGCGGGGC-UUCGUGCCCUGCCAUU--UU--------------UCGUUUGUGUCGAAAGACAA-CAGUGGAGCUAGUAGA
AAKV01000070.1/2420-2299   AGCCGGGGCUUUGUCUUGACGGUGUACAAGAACCUCUUUACUAUUUUGUACCCCGAAAAUUGGCAGGGC-GC-AUGCUCUGUCAUU--UCGUUUGU--------------GUGUCGUAAGACAAUCAGUGGAGCUA-UAGA
CP001157.1/602240-602359   CUGCCGGGCCUUGCCUUGACUGGGUUUCGGAGUCUCUUUAGACUUACGGACCC-UAAAUUUGGCAGGGCGGA-CCGCUCUGCCAUU--UUGUUUAU----------------GUCGAAAGACAA-CAGUGGAGCUAGUAGA
#=GC SS_cons               :::<<<<<<___>>>>>>,,,<<<-<<<<<<--<<____>>-->>>>>>->>>,,,,,,,<<<<<<<<<.__.__>>>>>>>>>,,..,,,,,,,,........,<<-<<<<<<<____>>>--.------->>>>->>::
#=GC RF                    aguCggGgCuUUGcCuuGACuGgGugCgggaucCuCUUUaGAcucccGcACcCcUAAAUUuGGcgGggc.uu.uugccCcgCCauU..UUGuUUuU........acaauaGcGuCGaAAGaCAA.CAGUGGAgCuaGugGA
//
# STOCKHOLM 1.0

#=GF AC   RF01774
#=GF ID   rpsL_ricks
#=GF DE   Rickettsia rpsL leader
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20920266
#=GF SS   Published; PMID:20920266
#=GF GA   60.00
#=GF TC   64.30
#=GF NC   48.80
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 37 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   20920266
#=GF RT   Premature terminator analysis sheds light on a hidden world of bacterial
#=GF RT   transcriptional attenuation.
#=GF RA   Naville M, Gautheret D
#=GF RL   Genome Biol. 2010;11:R97.
#=GF WK   Rickettsia_rpsL_leader
#=GF SQ   7


AE006914.1/171220-171350 AACAUACUUGCUUUUAUGGAAAAAGUAAUUAUAAUUUAAAUUUAGUGUAAUU----------UACAAAUUCUU-AUAAUUUGUAUUUAGAAAUGAUUGAAAAU--AAAGGGUGGAAGUA-UUUUUCACCCUUUAAUUAUC-GUAUA
CP001612.1/172039-172169 AACAUACUUGCUUUUAUGGAAAAAGUAAUUAUAAUUUAAAUUUAGUGUAGUU----------UACAAAUUCUU-AUAAUUUGUAUUUAGAAAUGAUUGAAAAU--AAAGGGUGGAAGUA-UUUUUCACCCUUUAAUUAUC-GUAUA
CP000847.1/178030-178161 AACAUACUUGCUUUUAUGGAAAAAGUCAUUAUAAUCUGAAUCUAGUGUAUUU----------UACAAAUUCUU-AUAAUUUGUAUUUAGAAAUUAUUCAAAAU--AAAGGGUGGAAGUA-UUUUGCUCCCUUUAUUUAUCUGUAUA
CP000849.1/284262-284404 AACAUACUUGCUUUUAUGGAAAAAGUAAUUAUAAUUUAAAUUUAGUGUAAUUUAAUUUGACAGUGUAAAUAUA-UUAUUUACAUUUGUAAAAUCAUUUAAAAUUCAAAGGGCAAAAGUA-GUUUUUGCCCUUUAAUCAUC-GUAUG
CP000409.1/152235-152365 AACAUACUUGCUUUUAUAGAAAAAGUAAUUAUAAUUCAAGUUUAGUAUAAUU----------UACAAAUGCUU-AUAAUUUGUAUUUAGAAAUGAUUUAAAAC--UAAAGGGUGGAGUGUUUUUCACCCUUUAG-UUAUC-GUAUA
CP000683.1/175879-176010 AACAUACUUGCUUUUAUGGAAAAAGUAAUUAUAAUUUAAAUUUAGUGUAAUU----------UACAAGUUCUUAAUAAUUUGUAUUUAGAAAUGAUUGAAAAU--AAAGGGUGGAAGUA-UUUUCCACCCUUUAAUUAUC-GUAUA
CP000766.2/173657-173786 AACAUACUUGCUUUUAUGGAAAAAGUAAUUAUAAUUUAAAUUUAGUGUAAUU----------UACAAAUUAUA-AGAAUUUGUAUUUAGAAAUGAUUGAAAAU--AAAGGGUGGAAGUA--UUUUCACCCUUUAAUUAUC-GUAUA
#=GC SS_cons             :::<<<-<<<<<<<<_____>>>>>>>>->>>,,,,,,,,,,,,,,,,,,,,..........<<<<<<<<___.__>>>>>>>>-------------------..<<<<<<-<<<<<__._>>>>>->>>>>>:::::::.:::::
#=GC RF                  AACauaCuugCuuuuAUGGAaaaaGuaaUuauAAUUUAAAUUUAGUGUAaUU..........uacaaauucUu.aUaauuuguaUUuagAAAUgAUUuAAAAU..aaaGGGuggaagUA.uuuuccaCCCuuuAAUuAUC.GUAUA
//
# STOCKHOLM 1.0

#=GF AC   RF01775
#=GF ID   RsaOG
#=GF DE   RNA S.aureus Orsay G
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20200491;
#=GF SS   Published; PMID:20200491;
#=GF GA   50.00
#=GF TC   66.70
#=GF NC   43.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20200491
#=GF RT   RsaOG, a new staphylococcal family of highly transcribed non-coding RNA.
#=GF RA   Marchais A, Bohn C, Bouloc P, Gautheret D
#=GF RL   RNA Biol. 2010;7:116-119.
#=GF WK   RsaOG
#=GF SQ   7


AE015929.1/1922262-1922118   GUAAC--AGGGG-GAGCGAUUAG---ACAAAGGGGUAG-AGCUACAUAUUAG----AUAGCUG---UAUAA-------UCGUUCAA-------GUUAC--AUCAAAACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUU-GUCGGCUAGUUAUUGACUAGCCGAUUUUUUA
ACLP01000007.1/203464-203616 GUAAC--AGGGUAGAACGAUUUCA-AACAAAGGGGUAGGGGCUAUAUAACAG----AUAGCUC------AA-GGUGAGUCGUUCGG-------GUUAC--AUCGAAACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUUUGUCGGCUAGCAAAUGACUAGCCGAUUUUUUA
AP006716.1/765455-765606     GUAAC--AGGGGAGAACGAAUUCA-AACAAAGGGGUAGAAGCUAUAUAACAG----AUAGCUUGUUGUGAA-------UCGUUCAA-------GUUAC--AUCGAAACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUU-GUCGGCUAGCAGAUGACUAGCCGAUUUUUUU
AM295250.1/1811732-1811579   GUAACU-AGGAGAUAGCACUGAUGUAACAAAGGGGUAA-UGAUAAAUCAUAGUCGUGUGAUUUAUUAAAAA--------CGUGCAAAUCACUAGUUAAUA-----AACAUCUUCAAUA-UUAUUACUUACUUUCCUUUCUAU---GCCGACUAGU--AUCGCUAGUCGGUUUUUU-
ACFR01000001.1/324548-324692 GUAAC--AGGGG-GAGCGAUUAG---ACAAAGGGGUAG-AGCUAUAUAACAG----AUAGCUGU---GUAA-------UCGUUCGA-------GUUAC--AUCAAAACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUU-GUCGGCUAGCUCGUGACUAGCCGAUUUUUUC
AP008934.1/636073-636227     GUAACAAAGGGG-UAGCGAAUAGAUGGCAAAGGGGUAG--GCU--AUUACAU----AUAGUUU--UGUUAACAUCUAUUUGUUCGA-------GUUACUAAUCA-AACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUUAACCGGCUAGC--GACGCUAGUCGGUUUUAUU
BX571857.1/2358758-2358615   GUAAC--AGGGG-GAGCGAUUAA---ACAAAGGGGUAG-AGCUAUAUAACAG----AUAGCUU----UUAA-------UCGUUCAA-------GUUAC--AUCACAACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUU-GUCGGCUAGCACGUGACUAGCCGAUUUUUUU
#=GC SS_cons                 <<<<<..-----.<<<<<<<<<--.---AAAAAAA---.<<<<<<_______....>>>>>>-..--->>>.......>>>>>>--.......>>>>>..-------------------------------aaaaaaa------.<<<<<<<<<_______>>>>>>>>>::::::
#=GC RF                      guaaC..AGGgG.gagCgauuaua.aACAAAGGGGUAg.aGcuauAUaAcAG....auagCuu..Uauuaa.......ucGuucaA.......Guuac..AUCaaAACAUCUUCAAUAUUUAUUACUUACUUUCCUUUCUAUUU.gcCGgCuaGcaaaUgaCuaGcCGguUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF01776
#=GF ID   RatA
#=GF DE   RNA anti-toxin A
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Predicted; Clustal;
#=GF SS   Predicted; RNAalifold;
#=GF GA   49.00
#=GF TC   49.10
#=GF NC   48.90
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   20156992
#=GF RT   Abundance of type I toxin-antitoxin systems in bacteria: searches for new
#=GF RT   candidates and discovery of novel families.
#=GF RA   Fozo EM, Makarova KS, Shabalina SA, Yutin N, Koonin EV, Storz G
#=GF RL   Nucleic Acids Res. 2010;38:3743-3759.
#=GF WK   TxpA-RatA_toxin-antitoxin_system
#=GF SQ   16


DQ489738.1/8021-8110         ---UAAUGAAUACAGA-AAAAAGGAAGCCUUGCGCU-AACAAGACUUCCUAU-GUAGAGCCGUUUAAGACGGUGACA-AUACUAUG--AUUAUUAAAUA
ACLM01000095.1/11756-11846   ---UAAUGUAGACAGA-AAAAGGGAAGCCCCGCUAG-AACAGGACUUCCCAU-GUAGAGCCGUUAAAGACGGUGGCAGAUUUUAAC--GAUAUUUAAUA
AY662330.1/18650-18561       ---UAAUGUAGACAGA-AAAAGG-AAGUCCCGAGUG-AACGGGACUUCCCAU-GUAGAGCCGUUAAAGACGGUGGCAGAUUUUAAC--GAUAUUUAAUA
FM204883.1/249209-249122     ---UAAUGAGAACAGA---AAAAGGGCAGUUGCUCUAAACA-ACUACCCU-AUGCAGAACCGUUUAAGACGGUGGCAUAUCUUU---AAUUAUUAAAAA
ACGG01000042.1/1740-1652     ---UAAUGUAGACAGA-AAAAGGGAAGCCCCGCUGG-AACAGGACUUCCAAU-GUAGAGCCGUUUAAGACGGUGGCA-AACUUAAU--A-GAUUAGACU
CP000415.1/13878-13789       ---UAAUGAAUACAGA--AAAAGGAAGCCUUGCGCU-AACAAGACUUCCCAUUAUAGAGCCGUAUAAGACGGUGGCA-AACUUAAA--ACGAUUAAAUA
ACAW01000002.1/45619-45704   ---UAAUGGUAAUGAA---AAGAGAG-CUAUGCUGU-AACAUACCUCUCUGAUGUAGAGCCGUUUAAGACGGUGACCUUUUUGA-----UUAUUUAAAA
ACAU01000003.1/175567-175652 ---UAAUGAAAAUGAA---AAGAGAG-AUAUGCUUC-AACAUACCUCUCUGAUGUAGAGCCGUUUAAGACGGUGACUUUUUGAA-----UUAUUUAAAA
AB450918.1/9399-9314         ------UGUA-AUAGA--AAAGGGAAGCCUUGCGCU-AACAAGACUUCCCAUGCAAGCCGCUUCAAAGGCGGUGUCAGAAAUUUAA--UAAACGAUUU-
AE016830.1/3119060-3118974   ---UAAUGAUAAAGAA---AAGAGAG-AUAUGCUUCCAACAUAUCUCUCUGAUGUAGAGCCGUUUAAGACGGUGACCAAUUUUA-----UUAUUUAAAA
ACIX01000195.1/4673-4585     CUAUAAUAGCAUUGAA---AAGAGAG-AUAUGCUGU-AACAUACCUCUCUAGUGUAGAGCCGUUUAAGACGGUGACCGAUUUUG-----UUACAAAAAA
ACGL01000022.1/26464-26555   -UAUAACAGCAAUGAA---AAGAGAG-AUAUGCGAC-AACAUACCUCUCUGGUGUAGAGCCGUUUAAGACGGUAGCGAUUUUUAGUGAUUUAUAAAAA-
ACAZ01000089.1/41765-41845   ---UAAUGGAUACGAA---AAGAGGA-GU-UGCGCU-AACA-ACUCCCCUAA--CAGCACCGUUUAAGACGGUGACCAGCUUAA---UAUUAUUUU---
ADDU01000011.1/21451-21362   ---UAAUGUAGACAGA-AAAAGG-AAGCCCCGCUAG-AACAGGACUUCCCAU-GUAGAGCCGUUAAAGACGGUGGCAUAACUUAAU--ACGAUUAAAUA
ACGU01000057.1/13625-13535   ---UAAUUUAGACAAACAAAAAGGAAGCCUUGCAUU-AACAAGACUUCCCCA-GUAGAGCCGUUUAAGACGGUAGCAAUUAAUUA---GUGAUUAAAUA
CP002621.1/2562843-2562928   ---UAAUGAAAAUGAA---AAGAGAG-AUAUGCUUC-AACAUACCUCUCUGAUGCAGAGCCGUUUAAGACGGUGACCAUGUUAA-----UUAUUUAAAA
#=GC SS_cons                 ...:::::::::::::...:::::::::<<<<____.__>>>>---------------<<<<<<___>>>>>>:::::::::::::..:::::::::::
#=GC RF                      ...UAAUGuaaAcaaA...AAGaGAaGaccuGCuuu.AACaggaCUucCuauUGUAGAgCCGUuUAAgACGGuGgCaaauuUUaAu..auuAUUaAAuA
//
# STOCKHOLM 1.0

#=GF AC   RF01778
#=GF ID   Evf-2_5p
#=GF DE   Embryonic ventral forebrain-2 long ncRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published;
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   51.70
#=GF NC   38.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.41 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19620975
#=GF RT   Balanced gene regulation by an embryonic brain ncRNA is critical for adult
#=GF RT   hippocampal GABA circuitry.
#=GF RA   Bond AM, Vangompel MJ, Sametsky EA, Clark MF, Savage JC, Disterhoft JF,
#=GF RA   Kohtz JD
#=GF RL   Nat Neurosci. 2009;12:1020-1027.
#=GF WK   DLX6-AS1
#=GF SQ   13


ABBA01045755.1/62535-62676   AAUUUCACACCUGGAUGUGCUCACUCAACCAAGAAUAUAGAGAAAGAGCUUCUGCCCUGAGACUCAGA---AAAAUAUUCUCC--UGUGCUU----UGGUUCAGUAUAGAUUUCU--AAACCCUGAUCAUUGCUUAAGAGAUAUUCACUGAGG--
AANG01392993.1/322-181       AAUUUCACACCUGGAUGUGCUCACUCAACCAAGAAUAUAGAGAAAGAGCUUCUGCCCUGAGACUCAAA---CAAAUAUUCUCC--UCUGCUU----CUGUUCAGUAUAGAUUUCU--AGACCCUGAUCAUUGCUUAAGAGAUAUUCACUGGUG--
AAKN02016916.1/7363-7222     AAUUUCACACCUGGAUGUGCUCACUCAACCAAGAAUAUAGAGAAAGAGCUUCUGUCCUGAGACUCAGA---AAAAUAUUCUCC--UCUGCUU----CGGUGCAGAAUAGAUUUCU--AGACUCUGAUCAUUACUCAAGAAGUAUUCACUGGGG--
AAYZ01202484.1/3447-3306     AAUUUCACACCUGGAUGUGUUCACUCAACCAAGAAUAUAGAGAAAGCGCUUCUGCCCUGAGACUCAGA---AAAAUAUUCUCC--UCUGCUU----CGGUUCAGUAUAGAUUUCU--AGUCCCUGAGCAUUGCUAAAGACAUAUGCACUGGGG--
ABRQ01150972.1/3041-2901     AAUUUCACACCUGGAUGUGCUCACUCAACCAAGAAUAUAGAGAAAGAGCUUCUGCCCUGAGACUCAGA---AAAAUAUUCUC---UCUGCUU----CUGUUCAGUAUAGAUUUCU--AGACUCUGAACCUUGCUUAAGAGACACUCACUGAGG--
ABQF01008523.1/7559-7418     AAUUUCACACCUGGAUGUGCUCACUCAACCAAGAAUAUAGAGAAAGAGCUUCUGCCCUGAGACUCAGA---AAAAUAUUCUCC--ACUGCUU----CUGUUCAGUACAGAUUUCU--AGACCCCGAUCCUUGCUUAGCAGAUUUUCCGAGGGG--
AC122240.4/114868-114723     AAUUUCACACCUGGAUGUGCUCACUCAACCAAGAAUAUAGAGACAGAGCCUCUGCCCUGAGACUCAGA---GAAACGCUCUCC--UGUGCCUCCCUCCGCUCAGUAUAGAUUUCU--AGACCCUGAUCAUUGCUUAAGAGAUAUUCACCGGGG--
AAPN01242591.1/1056-927      AAUUUCACACCUGGAUGUACCCACUCGACCAAGAAUAGGGAGAAAA------------GAGAUUCAGA---GAACUCUCCCUC--UAUGCUU----CCGUUCAGAGUAGUUUGCU--AGACCCUGGUCAUUGCUUAAGCGAUACUCACGGGGU--
AC145963.5/118998-119096     AAUUUCACACCUGGAUGUGCUCACUCAACCACGAAUAUAGGGAAAGCGCUUCUGCCCUGAGCCGCAGA---AAAAUACCCCGC--ACCGCUC----GGGCUCGG-------------------------------------------C----GUA
AC004774.1/119959-119818     AAUUUCACACCUGGAUGUGCUCACUCAACCAAGAAUAUAGAGAAAGAGCUUCUGCCCUGAGACUCAGA---AAAAUAUUCUCC--UGUGCUU----UGGUUCAGUAUAGAUUUCU--AAACCCUGAUCAUUGCUUAAGAGAUAUUCACUGAGG--
AABR05111398.1/7995-7854     AAUUUCACACCUGGAUGUGCUCACUCAACCAAGAAUAUAGAGACAGAGCUUCUGCCCCGAGACUCAGA---AAAAUACUCUCC--UGUGCCU----CGGCUCAGUAUAGAUUUCU--AGACCCUGAUCAUUGCUUAAGAGAGAUUCUCUGGGG--
AAWZ02000486.1/101706-101857 AAUUUCACACCUGGAUGUGCUCAGUCAACCAAGAAUCUAGAGAAAGAGCUUCUGCCCUAAGACGCAGACAAAAAAUAUUCUCUCCUCUGCUUCUU-CUCUCCACUGUAGAUUUCUUUAGACCCUCAUCCCUGCUUAAGAGGUUGUGGCACGGG--
AAGW02035477.1/7607-7470     AAUUUCACACCUGGAUGUGCUCACUCAACCAAGAAUAUAGAGAAAGAGCUUCUGCCCUGAGACUCAGA---AAAAUAUUCUC-----UGCCU----CGGUUCAGUAUAGAUU-CU--AGACCCUGGUCAUUGCCCGAGAGAUAUUCACUGGGG--
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::...::::::::::::..:::::::....:::::::::::::::::::..::::::::::::::::::::::::::::::::::::..
#=GC RF                      AAUUUCACACCUGGAUGUGCUCACUCAACCAaGAAUaUAGAGAaAGaGCUUCUGCCCUGAGaCuCAGA...aAAaUauuCucC..ucUGCuU....cgGuuCAGuaUAGaUUuCU..AGACCCUGauCaUUGCUuAAGaGauauUcaCuGGGG..
//
# STOCKHOLM 1.0

#=GF AC   RF01779
#=GF ID   AS1726
#=GF DE   AS1726 sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19555452
#=GF SS   Published; PMID:19555452
#=GF GA   50.00
#=GF TC   98.90
#=GF NC   39.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19555452
#=GF RT   Identification of small RNAs in Mycobacterium tuberculosis.
#=GF RA   Arnvig KB, Young DB
#=GF RL   Mol Microbiol. 2009;73:397-408.
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   2


ABLN01000308.1/12170-12094 GUCGCCGGCGGCGGUGACUAGCCGCACCGCGACCAGGUUGUCGCAGCUCAGUCCGAAACGUC-GAGUCGUCCAACCCA
AAYK01000242.1/35984-36061 GUCGCCGGCGGCGGUGACUAGCCGCACCGCGACCAGGUUGUCGCAGCUCAGUCCGAAACGUCGGAGUCGUCCAACCCA
#=GC SS_cons               <<<<<--<<<<<________>>>>>--->>>>>--<<<<<--<<-<<<<-<<_____>>---->>>>->>->>>>>::
#=GC RF                    GuCGCCGGCGGCGGUGACUAGCCGCACCGCGaCCAGGuuGUCgCAgCuCAGuCCGAAaCGUCGGaGuCGuCCaaCCCA
//
# STOCKHOLM 1.0

#=GF AC   RF01780
#=GF ID   AS1890
#=GF DE   AS1890 sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19555452
#=GF SS   Published; PMID:19555452
#=GF GA   39.00
#=GF TC   39.80
#=GF NC   33.80
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19555452
#=GF RT   Identification of small RNAs in Mycobacterium tuberculosis.
#=GF RA   Arnvig KB, Young DB
#=GF RL   Mol Microbiol. 2009;73:397-408.
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   2


CP000717.1/2147764-2147872 CGCGCGGCUCUGCCAACGACUCCGGUGCGAAGUACCAGCUCGCCGUCGGAAGCAUCAAGAGUCCACACCGCGUCGCUCACGCCACGACUGUAUUCAGACGACCUGCCUG
ABLL01000114.1/51868-51976 CGCGCGGCUCUGCCAACGACUCCGGUGCGAAGUACCAGCUCGCCGUCGGAAGCAUCAAGAGUCCACACCGCGUCGCUCACGCCACGACUGUAUUCAGACGACCUGCCUG
#=GC SS_cons               :((,,<<<<<<---------<<<<<-<<<<-<<____>>>>>->->>>>>------->>>>>>,,,,,,<<<<_____>>>>,,<<-<<<____>>>->>,,,,)):::
#=GC RF                    CGCGCGgCuCuGCCAACGACuCCGgUGCGaAGcACCAgCuCGCCGcCGGaAGCAUCAaGaGcCCACACCGCGuCGCUCaCGCCACGACuGUAUUCaGACGACCUGCCUG
//
# STOCKHOLM 1.0

#=GF AC   RF01781
#=GF ID   ASdes
#=GF DE   ASdes TB sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19555452
#=GF SS   Published; PMID:19555452
#=GF GA   40.00
#=GF TC   40.10
#=GF NC   38.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19555452
#=GF RT   Identification of small RNAs in Mycobacterium tuberculosis.
#=GF RA   Arnvig KB, Young DB
#=GF RL   Mol Microbiol. 2009;73:397-408.
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   26


ABOW01000043.1/45149-45216 AACUCGACAGGGUC-GACCGAUCGGGUCACCACCAGGUAGUCGCGCAGCGCGAUGCCGUGCCGAUUCUC
ACBV01000076.1/17877-17810 AGCUCCACGGGGUC-GACCGAUCGGGUCACUACCAGAUAGUCGCGCAGCGCGAUGCCGUGCCGGUUCUC
CP000854.1/5910337-5910270 AGCUCGACCGGGUC-GACGGAGCGGGUCACCACCAGGUAGUCACGCAGCGCGAUGCCGUGUCGGUUCUC
CP000479.1/741834-741901   AGCUCGACCGGGUC-GACCGCGCGGGUGACCACCAGGUAGUCGCGCAGCGCGAUCCCGUGCCGGUUCUC
CU458896.1/756161-756228   AGUUCCACCGGGUC-CACCGAGCGGGUGACCACCAGGUAGUCGCGGAUGGCGAUGCCGUGCCGGUUUUC
CP000511.1/5450693-5450626 AGCUCGACGGGGUC-GACGUUGCGGGUGACGACGAGGUAGUCGCGCAGCGCGAUGCCGUGCCGGUUCUC
CP000518.1/4827580-4827513 AGCUGGACGGGGUC-GACCGCGCGGGUGACGACGAGGUAGUCGCGCAGCGCGAUGCCGUGCCGGUUCUC
CP000325.1/4056543-4056610 AGCUCUACGGGGUC-GACAGCACGUGUCACCACCAGAUAGUCACGCAGCGCGGUGCUGUGUCGGUUCUC
AL583924.1/251751-251684   AGCUCCACCGGAUC-GACCGCGCGGGUCACCACCAGAUAGUCGCGCAGCGCGAUUCCGUGCCGGUUUUC
CP000384.1/5231097-5231164 AGCUCCACCGGGUC-GACCGCGCGGGUGACGGUGAGGUAGUCGCGCAGCGCGAUGCCGUGCCGGUUCUC
AP008957.1/5245002-5244935 AGCUCGACGGGGUC-GACUGCGCGCGUGACGACGAGGUAGUCACGCAUCACGAUGCCGUGACGGUUCUC
CP000431.1/5141047-5141114 AGCUGGACGGGGUC-GACGGCGCGGGUCACAACGAGGUAAUCGCGCAUCACGAUGCCGUGACGGUUCUC
AP006618.1/628411-628478   AGCGCGACCGGAUC-CACACCGCGGGUGACCACCAGGUAGUCGCGCAUCACGAUGCCGUGCCGGUUCUC
CP000667.1/2082755-2082688 AGGGCCACCGGGUC-GACCGCCCGGGUCACCGUCAGGUAGUCACGGAUCGCGAUGCCGUGCCGCGCCUC
AE016958.1/2449739-2449806 AAUUCCACCGGGUC-CACCGAUCGAGUGACCACGAGGUAAUCGCGCAGCGCGGUGCUGUGCCUGGCCUC
CP000480.1/5844982-5844915 AGCUCCACCGGAUCGCACG-CACGCGUGACGACCAGGUAGUCGCGCAGCGCGAUGCCGUGGCGGUUCUC
CT573213.2/730970-731037   AGGGCGACCGGGUC-GACCCCCCGGGUGACCAUCAGGUAGUCGCGCAUCGCGAUCGCGUGGCGGCCCUC
ACEW01000495.1/5831-5898   AGCUUGUCCGGGUC-CACGGCGCGCGAGGCCAGCAGGUAGUCGCGCAUCACGAUGCCGUGGCGGCCCUC
AP011115.1/6481856-6481789 AGUGCGACGGGAUC-GACGGCACGCGUCACCAUCAGGUAGUUGCGGAGCACGAUGGAGUGCCGGUUCUC
ABLL01000079.1/4038-3971   UUGGCGACCGGGUC-GACUUCCCGGGUCACCACCAGGUAUUCGCGCAGUGCGAUGGCGUGCAGGUGCUC
CP001966.1/3647076-3647009 AGCUUGACCGGGUC-GACCGCGCGGGUCACCAGGAGGUAGUCGCGCAUGGCGAUGCCGUGCCGGUUCUC
CP001700.1/2466540-2466607 AGCGCCACCGGGUC-GACGGCGCGGGUGGUCAGCAGGUAGUCGCGGAUCGCGAUGCCGUGCCGGCCCUC
CP001736.1/7522303-7522236 AGCUCGACCGGGUC-GACGCCGCGGGUGACCACCAGGUAGUCGCGCAACGCGAUCCCGUGCCGGCCUUC
CP001737.1/1088633-1088700 AGCUUGACCGGGUC-GACCCCGCGGGUGACCACCAGGUAGUCGCGCAGCGCGAUGCCGUGCCGGCCCUC
CP001814.1/2028639-2028706 AGGGCGACCGGGUC-GACCGCGCGGGUGACCGUCAGGUAGUCGCGGAUGGCGGUGCCGUGCCGGCCCUC
CP001802.1/4211361-4211295 GGGCCGUCG-GAUC-CACCCCGCGGGUGACCACGAGGUAGUCGCGCAUGACGAUGCCGUGCCGGUUCUC
#=GC SS_cons               :::(((-((,<<<-.<<<<_____>>>>>>>,,,,<<<<-<<<<<___>>>>>>>>>,))-))):::::
#=GC RF                    AGcucgACcGGGUC.gACcgCgCGgGUcACCAccAGGuAGUCGCGCAgCGCGAUgCCGuGccggUuCUC
//
# STOCKHOLM 1.0

#=GF AC   RF01782
#=GF ID   ASpks
#=GF DE   ASpks TB sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19555452
#=GF SS   Published; PMID:19555452
#=GF GA   52.00
#=GF TC   52.00
#=GF NC   51.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19555452
#=GF RT   Identification of small RNAs in Mycobacterium tuberculosis.
#=GF RA   Arnvig KB, Young DB
#=GF RL   Mol Microbiol. 2009;73:397-408.
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   77


ACHO01000102.1/1739-1816   CUUCACCGACCCCAACCACAAAGGUUCUCCC-GGCUCCCCCCGAUCUUGCCCAUAAGUGGCCAACAACGCCUGAGCCUC
CP000325.1/2633019-2633093 CUUGAUCGAACCCACCCACAACGGCCGACCC-GGCUC---ACGAUCUUGCCCAUAAACUGCCAACAACGCCUGAGCCUC
AY373435.1/87516-87590     CUUUACCGACCCCAGCCACAACGGCCGGUC----CACCGGACGAUCCUGCCCAUACGUGGCCAGCAGCGCCUGAGCCUC
CP000854.1/2120934-2120861 UUUGAUCGAGCCCACCCACAGCGGCUGAUCC-GUCGG---GCGUCCCUGCCCAUAGGUGGCCAACAACGCCU-CGGCUU
AL583917.1/183315-183241   CUUAAUUGAGCCCACCCACAACGGCUGGUC----UGCCGGACGUCCCUGCCCAUACGUGGCCAGCAAUGCCUGCGCUUC
DQ116941.2/41188-41114     CUUGAUCGAGCCCAGCCACAGCGGCUGUUCA-GGCUC---CCGGUCCUGCCCGUAAGUGGCGAGCAGUGCCUGGGCCUC
DQ885223.1/16824-16750     CUUCACGGAGCCCAGCCACAGCGGCCGAUC----CGCAUCCCGGUCCUGACCAUAGGUGGCCAACAACGCCUGCGCCUC
ACHP01000061.1/2873-2947   CUUGAUUGAGCCCACCCACAGCGGCUGCUC----CGCUGGACGUCCCUGCCCGUAGGUGGACAGCAAUGCCUGCGCUUC
CP000850.1/1439122-1439048 CUUGAUCGAGCCCAGCCACAGCGGCCGGUCC-GGCUC---GCGGCCCUGACCGUAGGUUGCCAACAGCGCCUGUGCCUC
AB241068.1/31162-31088     CUUGAUCGAGCCCAGCCUCAGCGGCCGAUC----CUCGGGACGAUCCUGACCGUAGGUGGCAAGCAGCGCCUGAGCCUC
DQ983361.1/13526-13452     CUUCAACGACCCCAGCCACAACGGCCGGUC---GC-CCGGACGGUCCUGGCCAUACGUGGCCAGCAACGCCUGCGCCUC
AY947889.1/31966-31892     CUUCAACGACCCCAGCCACAGCGGCUGACC----CUCCGGCCGCUCCUGCCCGUAGGUGGCCAGGAGCGCCUGGGCCUC
ABIN01000326.1/1855-1781   UUUGAUCGACCCCAGCCACAGCGGCCGGUC----CGCGGGCCGGUCCUGCCCGUAGGUGGCCAGAAGCGCUUGCGCCUC
ACEV01000078.1/34422-34496 CUUGAUCGACCCGAGCCACAGCGGCUGGUC----CCCGGAACGGUCCUGACCGUAGGUGGCCAGCAAUGCCUGCGCCUC
ACEX01000725.1/1517-1443   CUUGAUGGAGCCGAGCCACAGCGGCUGAUC----CUCCGGCCGCUCCUGACCGUACGUGGCCAGCAGCGCCUGCGCCUC
DQ249341.1/19326-19252     CUUCAAUGACCCCAGCCACAGCGGCUGAUC----CUCCGGCCGCUCCUGACCGUAGGUGGCCAGGAGUGCCUGGGCCUC
AB193609.1/28918-28992     CUUCACCGCACCCAGCCACAACGGCCGCUC----CGCAGAAUGCGCCUGACCAUAGGUGGCCAGCAGCGCCUGUGCCUC
EF990140.1/20397-20471     CUUCAACGAGCCCAGCCACAACGGCCGCUC----CGCGGGCCGAUCCUGGCCGUAGGUCGCCAGCAACGCCUGCGCCUC
DQ351275.1/34835-34761     CUUCAGGGACCCCAACCACAACGGCCGAUC----CGCAUCCCGGUCCUGACCGUAGGUGGCCAGCAGCGCCUGCGCCUC
AJ575648.1/7360-7286       CUUCAGCGAGCCGAGCCACAGCGGCUGGUC----CGCCGGACGGCCCUGGCCGUAGGUGGCCAGCAGCGCCUGCGCCUC
AB070940.1/62113-62039     CUUCACGGAGCCGAGCCACAGCGGCCGGUCG--GC--CGGACGGUCCUGCCCAUAGGUGGCCAGCAGCGCCUGGGCCUC
EU443633.1/90996-90922     CUUGACCGAGCCCAGCCACAGCGGCUGGCC----CGUGGGCCGGUCCUGCCCGUACGUGGCCAGGAGCGCCUGCGCCUC
AY330485.1/49895-49821     CUUCACCGAACCCAGCCACAGCGGGUGGCC----GGCAGGACGGUUCUGCCCGUAGGUGGCCAGCAACGCGUGCGCCUC
AM420293.1/4575606-4575680 CUUGAUCGAGCCCAGCCACAGCGGUCGGCCG--GC--GGGGCGGUCCUGCCCGUAGGUGGCCAGCAACGCCUGGGCCUC
DQ272520.1/44029-43955     CUUCAACGAGCCGAGCCACAGCGGCCGUUC----CGCGGGCCGCCCCUGCCCGUACGUGGCCAGCAGCGCCUGCGCCUC
AB088224.2/78764-78838     CUUCACCGACCCCAGCCACAACGGCCGACCC-GGAUC---ACGCCCCUGCCCAUACGUCGCCAGCAGCGCCUGCGCCUC
AJ278573.1/57317-57243     CUUCACCGACCCCAGCCACAACGGCCGUUC----CACAGGCCGCUGUUGGCCGUACGUGGCCAGCAGCGCCUGCGCCUC
BA000030.3/3537854-3537780 CUUGACCGAGCCCAGCCACAGCGGCUGCUCG--GCGC--UCCGCUCCCGGCCGUAGGUGGCCAGCAGCGCCUGUGCCUC
AF040570.3/33112-33038     CUUGACCGAGCCCAGCCACAGCGGUUGCUGC-GGGUC---GCGGCCCUGGCCGUAGGUGGCCAGCAGCGCCUGGACCUC
DQ149987.1/24965-24891     CUUCAACGAGCCCAGCCAGAGCGGCCGGUC----CACCGGGCGGCCCUGGCCGUAGGUGGCCAGCAGUGCCUGUGCCUC
FJ872523.1/67713-67787     CUUGAUCGACCCCAGCCACAGCGGUCGGUC----CUCGGGGCGGCCCUGGCCGUAGGUGGCCAGCAGCGCCUGCGCCUC
AM992894.1/57327-57253     CUUGACGGAGCCCAGCCACAGCGGCCGGUC----CGCGGGACGGUCCUGCCCGUACGUGGCGAGCAGCGCCUGCGCCUC
AM778535.1/35090-35016     CUUCAGCGAACCCAGCCAGAGCGGCCGUUGG-GCCGG---ACGGUCCUGUCCAUAGGUGGCCAGCAGGGCCUCCGCCUC
ACEW01000646.1/24872-24798 CUUCAGGGAGCCCAGCCACAGCGGGCGGUC----CGCCGGGCGUUCCUGCCCGUACGUGGCCAGCAGUGCCUGCGCCUC
AJ300302.1/38594-38668     CUUCACCGAACCGAGCCAGAGCGGCCGGCC----CUCCUCACGCUCCUGCCCGUACGUGGCCAGGAGCGCCUGCGCCUC
CP000667.1/3498019-3497946 CUUGACUGAUCCGAGCCAUACCGGUUGCUCC-GGCGC---CCGCCCCUGCCCGUAGGUGGCCAGAAUCGCCU-CGGCUU
DQ176871.1/41145-41071     CUUCAACGAGCCCAGCCACAGCGGCCGUUC----GGCAGGACGCUCCUGCCCGUAGGUGGCCUGGAGCGCCUGCACCUC
FJ872525.1/68398-68472     CUUGAUGGAGCCCAGCCAGAGCGGCCGGUU----CCCGGGGCGGUCCUGCCCGUAGGUGGCGAGCAGCGCCUGGGCCUC
EU301739.1/21169-21243     CUUCACCGAGCCGAGCCACAGCGGCCGGUC----CGCGGGCCGGUCCCGCCCGUAGGUGGCCAGCAGCGCGUGCGCCUC
ABJF01000253.1/13421-13347 UUUGAUCGAGCCGAGCAGCAGCGGCCGGUC----CGCCGACCGGUCCUGGCCGUAGGUGGCCAGCAGCGCCUGCGCCUC
AB435553.1/54914-54840     CUUCAGCGAACCCAGCCACAACGGCCGGUC----CGCCGACCGGGCCUGUCCGUAGGUGGCGAUCAACGCCUGCGCCUC
ACEZ01000034.1/7648-7722   CUUCAACGACCCCAGCCACAACGGCUGUUC----GUCGGUGUGGUCCUGACCGUAAGUGUUCAGCAGCGCCUGCGCCUC
AB363939.1/62008-62082     CUUCACCGAGCCCAGCCACAACGGCUGUUC----CCCGGAACGCUCCUGGCCAUAUGUGUCGAGCAGGGCCUGGGCUUC
ABYA01000007.1/18827-18759 CUUCAGCGAACCCAGCCACAGCGGCCG-------CUC---GCGGUCCUGGCCGUAGGUGGCCAGCAGCGCCUGCGCCUC
FM173265.1/60520-60446     CUUCACCGAGCCCAGCCACAGCGGCCGGCC----GUCCGCCCGUUCCUGCCCGUAGGUGGCCAGGAGUGCCUGCGCUUC
AP011115.1/4466351-4466422 CUUGACGGAGCCGAGCCACAGCGGCCGGCC----CUC---CCGGCCCUGCCCGUACGCGGCCAGCAGCGCCUGCGCCUC
AP009493.1/7331862-7331788 CUUCACCGACCCCAACCACAACGGACGACC----CUCCGGCCGGUCCUGGCCGUACGUCGCCAGCAAUGCCUGAGCCUC
AY442225.1/12405-12331     CUUCACCGACCCCAGCCACAGCGGCCGUCC----CUCCGGCCGCUCCUGGCCGUAGGUGGCCAUCAGGGCCUGGGCCUC
EU827593.1/24706-24638     CUUGAGCGAGCCCAGCCACAGCGGCUG-------CUC---GCGGUCCUGCCCGUAGGUGGCGAGCAGCGCCUGCGCCUC
AB089954.2/42131-42057     CUUCACCGAGCCGAGCCAGAGCGGUCGUCC----CUCCGGUCGCCCCUGCCCGUAGGUGGCCAGCAGCGCCUCGGCCUC
ACES01000072.1/521-453     CUUGAGCGAGCCGAGCCAGAGCGGCCGGUC----C------CGGUCCUGGCCGUAGGUGGCCAGGAGCGCCUGGGCCUC
AY310323.2/100244-100318   CUUGAUGGAGCCGAGCAGCAGCGGCCGGUC----CUCGGGCCGGUCCUGCCCGUACGUCGCCAGCAGCGCCUGGGCCUC
AF440781.1/18383-18309     CUUCACCGACCCGAGCCACAACGGCCGCUC----CGCCGAACGCCCUUGGCCGUACGUGGCGAGCAGGGCCUGCGCCUC
DQ897668.1/47801-47727     CUUGAUCGAGCCGAGCCAGAGCGGCCGCUC----CGCUGUGUGCGCCUUGCCGUAGGUCGCCAGCAGCGCCUGCGCCUC
DQ450945.1/278-204         CUUGACGGAGCCGAGCCAGAGGGGUUCGUC----GCCCGGCCGGUCCUGGCCGUACGUGGCCAGCAGCGCCUGCGCCUC
DQ272522.1/12501-12430     CUUGACCGAGCCGAGCCAGAGGGGUUCGCC----CGC---CCGUUCCUGGCCGUAGGUGGCCAGCAGGGCCUGUGCCUC
CT573213.2/2804363-2804289 CUUCAGCGACCCCAGCCACAGCGGGUCGGC----CGCGUCCCGGUCCUGCCCGUAGGUCGCCAGGAUCGCCUGCGCCUC
ABYC01000016.1/10010-10084 CUUGACCGAGCCGAGCAGCAGCGGCCGGUC----CUCCGGGCGGUCCUGGCCGUAGGUGGCGAGGAGCGCCUGGGCCUC
DQ884175.1/58497-58429     CUUCACCGACCCCAGCCACAACGGCU---C----CUC---GCGAUCCUGGCCAUAGGUGGCGAGCAAGGCCUGUGCCUC
CP000820.1/4103109-4103183 CUUCAGGCUCCCCAGCCACAGCGGCUCGCC----GGCCGGCCGGCCCUGCCCGUAGGUGGCCAGCAGCGCCUGCGCCUC
AF357202.1/6136-6062       CUUCACCGAGCCGAGCAGCAGCGGCUUGUC----CUCGUCGCGCUGCUGACCGUAGGUGGCGAGCAGCGCCUGCGCCUC
AJ871581.1/19441-19515     UUUGAGCGAUCCCAGCCACAGGGGCUGGCCG--GC--GUCGCGGUCCCGGCCGUAGGUGGCCAGCAACGCCUCGGCCUC
DQ174320.1/1017-943        CUUCACCGAGCCGAGCAGCAGCGGCCGCUC----CGGGUCGCGGUCCUGGCCGUACGCGGCCAGCAGCGCCUGCGCCUC
AL939127.1/37816-37890     CUUCAGCGAGCCCAGGUACAGCGGCCGGCC----CUCCGCCCGGUCCUGGCCGUACGUCGCCAGCAGUGCCUGGGCCUC
ABYX01000217.1/5176-5102   CUUCACGGAGCCGAGCCACAGCGGCUGCUC----CGCCGGGCGGUCCGCGCCGUACGUCGCGAGCAGGGCCUGCGCCUC
AY118081.2/48373-48302     CUUCAGCGAACCAAGCCACAAAGGCCGCCC----CGCGUCGCG---CUGCCCAUACGUCGCCAACAACGCCUGCGCUUC
AY509120.1/55569-55498     CUUCAACGAACCAAGCCGCAACGGCCGACC----CGCAUCCCG---CUGCCCAUACGUCGCCAACAACGCCUGCGCCUC
ACEY01000056.1/27545-27471 CUUGAGUGAGCCGAGGUACAGGGGCCGGCC----CUCCGCCCGGUCCUGGCCGUACGUCGCCAGCAGUGCCUGGGCCUC
AY354515.1/26777-26703     CUUCAGCGAGCCCAGCCAGAGCGGCUUGGCGGGA-UC---CCGGUCCCGGCCAUAGGUCGCCAGCAGUGCCUGGGCCUC
AF079138.1/34082-34008     CUUCAGCGUCCCCAGCCGCAGCGGCUGCCC----CGGGGCGCGCCCCUGCCCGUACGUGGCGAGCAGCGCCUGCGCCUC
ABYB01000295.1/8504-8430   CUUGACGGAGCCGAGCCAGAGCGGCUGUCC----GGCGUCGCGUGCCGCCCCGUAGGUGGCGAGGAGGGCCUGUGCCUC
U78289.1/37388-37314       CUUCAGCGAGCCGAGCCACAGCGGGUGGUC---GCCG-GAACGGUUCCGUCCGGAGGCGGCGAGCAGCGCCCCGGCCUC
AF453501.1/66079-66147     CUUGACCGAGCCCAGCAGCACCGGUU---C----GGC---CCGGUCCUGCCCGUAGGUGGCCAGGAUCGCCUGCGCCUC
CP001630.1/3075151-3075083 CUUGAUCGAGCCCAGCCACAGCGGCU----------CGGUGCGGUCCUGACCGUAGGUGGCCAGCAGCGCCUGCGCCUC
CP001778.1/4412204-4412278 CUUCAGCGAGCCCAGCCACACCGGGUCCUG----UUCGUCACGUCCCUGGCCAUAGGUGGCCAGCAGGGCACGGGCUUC
AM238664.2/537680-537754   CUUCAAGGACCCCAGCCACAGGGGUCGUUC----CGCGUCCCGCUCCUGCCCGUAGGUGGCCAACAGCGCCUGCGCCUC
AY899214.1/12042-11968     CUUGAUGGAACCCAGCCACAGCGGACGGCC----CGCGGGCCGGUCCUGCCCGUACGUCGCCAGCAGCGCCUGCGCCUC
#=GC SS_cons               :::::::::::::<<<<_____>>>>----....<<<----<<---<<<-<<<____>>>->>>--->>--->>>::::
#=GC RF                    CUUcAuCGAgCCcagCCACAgCGGcuGguC....cgCgggaCGgUCCUgcCCgUAgGuGGCcAGCAGCGCCUGcgCCUC
//
# STOCKHOLM 1.0

#=GF AC   RF01783
#=GF ID   b55
#=GF DE   Mycobacterium B11
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19555452
#=GF SS   Published; PMID:19555452
#=GF GA   70.00
#=GF TC   85.30
#=GF NC   44.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19555452
#=GF RT   Identification of small RNAs in Mycobacterium tuberculosis.
#=GF RA   Arnvig KB, Young DB
#=GF RL   Mol Microbiol. 2009;73:397-408.
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   2


CP000717.1/707415-707475   CGGGACUCCUGAGAAGGAUCCUGUAGGCCGCAGCCCCACCCACGGGUGGGGCUGACGUGCG
ABOW01000034.1/21447-21507 CGGGACUCCUGAGAAGGAUCCUGUAGGCCGCAGCCCCACCCACGGGUGGGGCUGACGUGCG
#=GC SS_cons               :<<<<-<<<<____>>>>>>>>----<<<<<<<<<<<<<<____>>>>>>>>>>->>->>:
#=GC RF                    CgGGACUCCUGAGAAGGAUCCuGUAGGCCGCAGCCCCACCCACGGGUGGGGCUGACGUGCG
//
# STOCKHOLM 1.0

#=GF AC   RF01784
#=GF ID   bablM
#=GF DE   bablM sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19531245
#=GF SS   Published; PMID:19531245
#=GF GA   38.00
#=GF TC   38.50
#=GF NC   37.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19531245
#=GF RT   Identification of candidate structured RNAs in the marine organism
#=GF RT   'Candidatus Pelagibacter ubique'.
#=GF RA   Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ,
#=GF RA   Breaker RR
#=GF RL   BMC Genomics. 2009;10:268.
#=GF WK   Pelagibacter_ubique
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   12


AACY022623031.1/87-18        GAAUCCAUUUAAUUCAAUCACAGGUUGACCGUGGAAUCCGUUUGGAGUCUAAUUGUUUUAUACAAAAUGG
AAPV01000001.1/773255-773186 GAAUCUAGUUAUUUCAAUCUCAGGUUGACGCAAGAAUCCGUAUGGAGUCUAAUUGUUUUAUACAAAAUGG
ABVS01000001.1/442698-442630 GAAUCCAAAUAAUUCAAUCUCAGGUUGACCCAAGAAUCCAUUUGGAGUCUAAUUAUUUUAUACA-AAUGA
AACY020041855.1/608-677      GAAUCUGAUUAAUUCAAUCUGAAGUUGACCGUAGAAUCCAUUUGGAGUCUAAUUGUUUUAUAUAAAAUGG
AACY020678804.1/140-71       GAAUCCAUUUAAUUCAAUCACAGGUUGACCGUGAAAUCCGUUUGGAGUCUAAUUGUUUUAUAGAAAAUGG
CP000084.1/120150-120219     GAAUCCAUUUAAUUCAAUCACAGGUUGACCGUGGAAUCCGUUUGGAGUCUAAUUGUUUUAUAGAAAAUGG
AACY022598114.1/714-783      GAAUCCAUUUAAUUCAAUCACAGGUUGACCGUAAAAUCUGUUUGGAGUCUAAUUGUUUUAUACAAAAUGG
AACY020004049.1/744-813      GAAUCUGUUUAAUGCAAUCUGGAGUUGACCGUGGAAUCCAUUUGGAGUCUAAUUGUUUUAUAUAAAAUGG
AACY021947363.1/564-495      UAAUCCAAUUAAUUCAAUCUGAAGUUGACCGUGGAAUCCAUUUGGAGUCUAAUUGUUUUAUACAAAAUGG
AACY022595230.1/346-415      GAAUCUAUUUAAUUCAAUCACAGGUUGACCGUAGAAUCUGUUUGGAGUCUAAUUGUUUUAUACAAAAUGG
AACY020043180.1/1483-1414    GAAUCCAUUUAAUUCAAUCACAGGUUGACCGUGGAAUCCGUUUGGAGUCUAAUUGUUUUAUAGAAAAUGG
AACY021346272.1/249-318      GAAUCCAUUUAAUUCAAUCACAGGUUGACCGUGGAAUCCGUUUGGAGUCUAAUUGUUUUAUAUAAAAUGG
#=GC SS_cons                 :::::::::::::<<<<<_____>>>>>----<<<-<<<____>>>->>>::::::::::::::::::::
#=GC RF                      GAAUCcAuUUAAUUCAAuCacAGgUUGACCGUaGAAUCCgUUUGGAGUCuAAUUGUUUUAUAcAAAAUGG
//
# STOCKHOLM 1.0

#=GF AC   RF01785
#=GF ID   blv_FSE
#=GF DE   ribosomal frameshift site
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:15629717
#=GF SS   Published; PMID:15629717
#=GF GA   34.00
#=GF TC   34.40
#=GF NC   33.50
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200528;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   15629717
#=GF RT   An extended signal involved in eukaryotic -1 frameshifting operates
#=GF RT   through modification of the E site tRNA.
#=GF RA   Bekaert M, Rousset JP
#=GF RL   Mol Cell. 2005;17:61-68.
#=GF WK   Bovine_leukemia_virus
#=GF SQ   2


M10987.1/1604-1630 GGGGGGACUUAGCGCCCCCCAAACCGU
D00647.1/1812-1838 GGGGGGACCUAGCGCCCCCCAAAUCAU
#=GC SS_cons       <<<<<<_____AAA>>>>>>::::aaa
#=GC RF            GGGGGGACuUAGCGCCCCCCAAAuCaU
//
# STOCKHOLM 1.0

#=GF AC   RF01786
#=GF ID   c-di-GMP-II
#=GF DE   Cyclic di-GMP-II riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Predicted; Weinberg Z;
#=GF SS   Predicted; Weinberg Z;
#=GF GA   35.00
#=GF TC   35.10
#=GF NC   34.80
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0035438; cyclic-di-GMP binding;
#=GF RN   [1]
#=GF RM   20705859
#=GF RT   An allosteric self-splicing ribozyme triggered by a bacterial second
#=GF RT   messenger.
#=GF RA   Lee ER, Baker JL, Weinberg Z, Sudarsan N, Breaker RR
#=GF RL   Science. 2010;329:845-848.
#=GF WK   Cyclic_di-GMP-II_riboswitch
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   54


BAAW01001404.1/567-484         AAUAAAUCUGGAAGU-AAUGAUAAAU--UCU-CUUU-AUUUGGGC-ACUUU---------------------G-AGGAUUU-UGAACUAGUAGUGCAACCCGCCAACAAUUAA
AAWL01000006.1/67971-67888     ACUGCAA-UGGGUGU-GAUGAAGUCC--GGA-CAGUAAUGUGGGC-ACUUA---------------------G-UCCGGAC-CGAGCAAGUAGUGCAACCGACCAGAUGCAAA
AP009049.1/1160074-1160160     CAAAUUGAGGGGAAC-GAUGAGGUAC--ACA-CUUUAAUUUGGGC-AUCCU--------------------UG-UGUGUAUUGGAGUUAGUGAUGCAACCGACCCUGUAUUCA
AM180355.1/3826693-3826610     AAUAUUU-UAGAAAC-UGAGAAGUAU--AUC-UUAUUA-UUGGGC-AUCUG--------------------GA-GAUAUAU-GGAGUUAGUGGUGCAACCGGCUAUGAAUAUA
BA000004.3/387918-388001       AAUCAAUAGGGAAGC-AACGAAGCAU--AGC-CUUU-AUAUGGAC-ACUUG---------------------G-GUUAUGU-GGAGCUACUAGUGUAACCGGCCCUCCUUUAA
AE015927.1/474745-474827       AUUUUAAGAGGAAAU-UUUGAACUAU--AUA-CUU--AUUUGGGC-ACUUU---------------------G-UAUAUAG-GGAGUUAGUAGUGCAACCGACCUUGAUUAAU
BA000016.3/197260-197343       AAAUGUUAUAGAAAC-GUUGAUGUAU--AUU-CUGU-AUUUGGGC-AUCUG---------------------G-AAUAUGC-UGAGUUAGUGAUGCAACCGACUAUAUUUAUA
AE000513.1/1919839-1919755     CUGUCGAAGAGACGC-GAUGAAUCCC--GCC-CUGUAAUUCGGGC-ACCUC---------------------G-GACGGGA-GGAGCAAGUGGUGCGACCGGCUUUUCGUUGG
CP000724.1/3560727-3560645     AAAAAUG-UAGAGCA-AAUGAACUGC--AGG-UAU--ACAUGGAC-GCCUU--------------------AA-ACUGCAG-GGAUGUAGUGGCGUAACCGACUAACAAUAUU
ACOM01000005.1/2090470-2090387 CAUGUAGUUGGAAAC-GAAGAAUAGU--UCU-CUCA-AUCUGGGC-ACCUU---------------------G-GGAACUA-GGAGUUAGUGGUGCAACCCGCCAGCAAAUUA
CP000246.1/171340-171423       AAAUGUUAUAGAAAC-GUUGAUGUAU--AUU-CUGU-AUUUGGGC-AUCUG---------------------G-AAUAUGC-UGAGUUAGUGAUGCAACCGACUAUAUUUAUA
AM180355.1/3306767-3306682     AAAUAUUAUAGAGAU-GUUGAAGUAU--AUU-CUAUUA-UUGGGC-ACCUUA-------------------UG-GAUAUAC-UGAGUCAGUGGUGCAACCGGCUAUGAAUAUA
CP000721.1/1272636-1272718     UGUAUAUAAGGAAAC-UGUGAUUCGA--AUA-UUU--ACUUGGGC-ACUUU---------------------A-UAUUCGA-UGAGUUAAUAGUGCAACCGACCUUUUUAUUA
CP000721.1/2550212-2550295     AUUACAAUUGGAAGC-UAUGAAGAAU--UCU-UUCU-AAGUGGGC-ACUUU---------------------A-AGAGUUU-GGAGCUAGUUGUGCAACCGACCAAUUAAGAU
AACY020292692.1/343-428        GAGGCGUCCGGAGGC-GAUGACCCGCUGAUC-CCC--AUUUGGGC-AUCAA--------------------GG-GACGCGG-CGAGCCAGUGAUGCAACCGGCCGGACGGCUA
AE001437.1/648479-648561       UAUUUGUUUGGAAAC-AAUGAUGAAU--UUC-UUUA-AAUUGGGC-ACUUG---------------------A-GAAAUUU-UGAGUUAGUAGUGCAACCGACCAA-CGAUUA
AJ965256.1/1260708-1260792     AAAUUAAGGGGAAGC-GUUGAGCCGC--UAC-CCAU-AUGUGGUUCACUCG---------------------G-AUAGCGG-GGAGCUAAUAGUGAAACCGGCCCUUUAGGGG
AAFX01078109.1/475-391         UCACCCUUCAGAGGC-UUAGAUGCCU--ACC-CCGCAACUUGGGC-GCUUG---------------------G-GGUACGC-GGAGCCAGUAGCGCAACCGGCCGAGGGCUUC
CP000359.1/298588-298670       UUCUUGUUCCGGGGC-GAAGAGGCGU--GUG-GUGU-AUCCGGGC-ACCUG---------------------C-CACACGC-GGAGCCAGUGGUGCGACCGACG-AACCGUGA
AE001437.1/3752962-3752879     UUAAGCGUUGGAGAC-UGUGAAGAAU--UUC-UUGU-AUUUGGGC-ACCUU---------------------A-GAAAUUU-GGAGUUAGUGGUGCAACCUGCCAACAAUAAU
CP000721.1/2207052-2207135     ACAAAGAUUGGGAAC-UAUGAAGAAU--UCU-CUGU-AUUUGGGC-AUCUU---------------------G-AGAAUUU-AGAGUUAAUGAUGCAACCCACCAAUCAAAAC
AE000513.1/692045-692129       AAGUGGUUUUGAAGC-AGGGAAGCAU--CUG-ACGC-AUUCGGGC-GCCUU--------------------GU-CAGAUGU-GGAGCGAGUGGCGCGACCGGCAAAGCUGUGG
ABDX01000006.1/72290-72207     AAAUGUUAUAGAAAC-GUUGAUGUAU--AUU-CUGU-AUUUGGGC-AUCUG---------------------G-AAUAUGC-UGAGUUAGUGAUGCAACCGACUAUAUUUAUA
AACY020292692.1/175-258        UCGCGAUUCGAGGGC-GAUGACGCUC--GUU-CUGCAACAUGGGC-GCUUG---------------------G-AACGAGC-CGAGCCAGUAGCGCAACCGAUCGG-UCGACG
AACY023761929.1/1009-1091      AUAAUUUGGUG-GGC-GUUGAUGUGC--CCU-UUGU-AUCUGGUC-GCUUG---------------------A-GGGGUAC-GGAGCCAAUAGCGAAACCGCCGCCGUCAUAG
CP000312.1/175590-175673       AUAUGUUAUAGAAAC-GUUGAUGUAU--AUU-CUGU-AUUUGGGC-AUCUG---------------------G-AAUAUGC-UGAGUUAGUGAUGCAACCGACUAUAUUUAUA
AP009389.1/2908378-2908465     GAGAUAGUGUGAAGC-AGUGAUCUUG--CAG-CUA--AUAUGGUC-ACUUUUU----------------ACGG-CUGCAAG-UGAGCUAAUAGUGAAACCGGCACACUGAUGC
CP000923.1/1535517-1535600     AUUUUAUAAAGAGUA-GAUGAAGUGA--GGC-UAU--AUGUGGGC-ACUUU--------------------AU-GCCUCAC-GGAUACAGUGGUGCAACCGGCUUUAUGUCGG
ABFD02000011.1/154500-154415   AAAUAUUAUAGAGAU-GUUGAAGUAU--AUU-CUAUUA-UUGGGC-ACCUUA-------------------UG-GAUAUAC-UGAGUCAGUGGUGCAACCGGCUAUGAAUAUA
AAOX01000007.1/31274-31356     AAGAAUAUAGAACAC-UGUGAUGAGC--GGU-UUUU-AUUU--GC-ACUUU--------------------AA-ACCGCUU-GGAGUGACUAGUGCAGCCGGCCAAUGAUCUA
AM180355.1/3801149-3801064     CCUAUUUAUAGAAAC-UGUGAAGUAU--AUC-UUAA-ACCUGGGC-ACUUAA-------------------AA-GAUAUAU-GGAGUUAGUAGUGCAACCUGCUAUAAAUAUA
CP001098.1/2206138-2206055     UAUUGAAUGGGAAGC-UAUGAACUCU--UCU-UUGU-ACGUGGUC-ACUUG---------------------A-AGGAGAG-GGAGCUAGUAGUGAAACCGCCCCGACCGGGG
CP000382.1/1875256-1875172     UUUUUAAAAGGAGACAUUUGAACUAU--AUA-CUUU-AUUUGGGC-ACUUU---------------------G-UAUAUAG-GGAGUCAUUAGUGCAACCGACCUUAUUUUAU
ABHE02000039.1/57574-57489     UAAUAAAAUAGAAAC-GUUGAUUUAU--GUU-CUGUAAUGUGGGC-ACCUU--------------------AG-AGCAUAU-UGAGUUAGUGGUGCAACCGGCUAUGAAAUUG
ABHD02000026.1/148456-148371   AAAUAUUAUAGAGAU-GUUGAAGUAU--AUU-CUAUUA-UUGGGC-ACCUUA-------------------UG-GAUAUAC-UGAGUCAGUGGUGCAACCGGCUAUGAAUAUA
AM180355.1/4105882-4105797     UAAUAAAAUAGAAAC-GUUGAUUUAU--GUU-CUGUAAUGUGGGC-ACCUU--------------------GG-AGCAUAU-UGAGUUAGUGGUGCAACCGGCUAUGAAAUUG
AAFX01024083.1/557-455         CACCACUGUGGACGC-UUUGAUCCGG--UGU-CUUG-AUUUGGUC-GCUUAACGUCUGGAACUUUUGACGAGG-GCGCCGG-GGAGCGAGUAGCGAAACCGGCCAC--UGGUA
ABDU01000054.2/14999-15082     AAAUGUUAUAGAAAC-GUUGAUGUAU--AUU-CUGU-AUUUGGGC-AUCUG---------------------G-AAUAUGC-UGAGUUAGUGAUGCAACCGACUAUAUUUAUA
CP000721.1/3552610-3552527     AGAACAAUUGGAAGC-GAUGAAAAAU--UCU-CUAU-AUCUGGGC-ACUUU---------------------G-AGAAUUU-GGAGCUAGUUGUGCAACCGACCAAUUAAAAC
ABHG02000025.1/45887-45804     AAUAUUU-UAGAAAC-UGAGAAGUAU--AUC-UUAUUA-UUGGGC-AUCUG--------------------GA-GAUAUAU-GGAGUUAGUGGUGCAACCGGCUAUGAAUAUA
AAFX01082705.1/413-329         AUCGAUUUCGGAUGC-CUUGAUCCGA--CCG-CUGA-AUGUGGGC-ACUUA--------------------GG-CGGCCGG-GGAGCAGGUAGUGCAACCGACCGUUCCGCAC
CP000721.1/4868650-4868568     UGUCAU-AAGGAAAC-UUUGAUCCAU--AUA-UUUU-AAUUGGGC-ACUUU---------------------A-UAUAUGG-UGAGUUAGUAGUGCAACCGACCUUUAUAUUU
CP000721.1/4369760-4369677     AUAGUAAUUGAGAGC-UAUGAAGAAU--UCU-UUUU-AUGUGGAU-AUUUU---------------------A-AGAAUUU-CGAGCUAUCUGUGCAGUCGACCAAUUUAAAC
CP001078.1/3290558-3290475     UAUAAAGUUGGAGAU-UAUGAAUAGU--UCU-CUUU-AUUUGGGC-ACCUU---------------------G-AGAACUA-GGAAUCAGUGGUGCACCCGGCCAACAAAUUA
CP001116.1/102374-102291       AUAACGGCACGAAGC-AAUGAAAUGU--UCG-AUGU-AACCGGGC-ACCUA---------------------U-CGAACAU-GGAGCUAGUGGUGCGACCGACGUUUCAUACG
ABSO01005747.1/296-213         GUCAAUAUCGGACGC-GCGGAUGCCU--CGC-CUG--AAAUGGGC-ACUUA--------------------GG-GUGAGGC-GGAGCGAGUAGUGCAACCGACCGACCCCAGU
ABVK02000002.1/96520-96604     AGGCACCUCGGAGGC-GACGAAGCCU--GUC-CUGCAAUCUGGGC-GCCUG---------------------G-GACAGGU-GGAGCCAGUGGCGCAACCGGCCGAGGGCGGG
CP001276.1/419946-420032       CGACACCCCGGAGGC-GAAGAAGCGC--UGC-CUGAGCGUUGGGC-GCCAGU-------------------GG-GCAGCGU-GGAGCCAGUGGCGCACCCGGCCGGGAUAUCC
CP002042.1/3024809-3024724     GGGGGGUUCGGAGGC-GACGAACUGU--GUCACCCA-AUAUGGGC-ACCAA---------------------GGGGCACAG-GGAGCUAGUGGUGCAACCGGCCGAACACCGC
CP001791.1/1643284-1643367     ACGACAAUUGGAUGC-UGAGAAGAAA--UGGGUACU-AUCUGGGC-ACUUA---------------------A-CCAUUUU-GGAGCUGCUAGUGCAACCGGCCGG-AGACAU
CP001720.1/3973350-3973434     GAGUUUCUUGGGAAC-UAUGACAUCA--ACU-CUUU-AUCUGGGC-AUCUU--------------------AG-AGUUGAU-UGAGUUAGUGAUGCAACCGACCUUGAAGAAA
CP001743.1/2770688-2770773     ACCAAGUUCGGAGGU-GAUGAUCCGUGAUUC-CCA--AUCUGGGC-ACCAA--------------------GG-GAAACGG-GGAGCCAGUGGUGCAACCGGCCGAACCCAAA
CP001824.1/1154935-1155018     GUGAGCG-CGGAGGC-GAUGACGCGC--GGG-CUGUAAUUUGGGC-ACCUC---------------------G-CCCGCGC-CGAGCCUGGGGUGCAACCGGCCGGCUAAGAC
CP001825.1/388010-388096       AAUUAGCGUAGAGGC-GACGAAGUCC--GCU-UACCUAUAUGGGC-ACCAUG-------------------GG-AGCGGAU-GGAGCCACUGGUGCAACCGGCUACUGAGAAG
#=GC SS_cons                   <<<<<<<<<<<-<<<.------<<<<..<<<.<___.____AAAA.AAA__...................._>.>>>>>>>.--->>>---aaaaa--aa-->>>>>>>>>>>
#=GC RF                        cacccauuuGGAgGC.uaUGAaccgu..gcc.cUuu.AUuUGGGC.ACuUu....................gg.ggcacgg.GGAGCcAGUaGUGCAACCGgCCaaaugggug
//
# STOCKHOLM 1.0

#=GF AC   RF01787
#=GF ID   drz-agam-1
#=GF DE   drz-agam-1 ribozyme
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF AU   Burge S; 0000-0002-2506-927X
#=GF SE   Published; PMID:19965505
#=GF SS   Published; PMID:19965505
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   36.90
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   19965505
#=GF RT   Widespread occurrence of self-cleaving ribozymes.
#=GF RA   Webb CH, Riccitelli NJ, Ruminski DJ, Luptak A
#=GF RL   Science. 2009;326:953.
#=GF WK   Ribozyme
#=GF SQ   7


ABKQ02020491.1/358-277       GGCUGACAAAAUCCUUUCCCAACCUCCACGUGGUGUCGGCUGGAU-AAUG-CAUUAGA-A--------AUGU-UGCAUUUACCAACUGGGAAGG
AAAB01008963.1/187589-187670 GGCUGACAAAAUCCUAUCUCUACCUCCUCGUGGUGUCAGCCGGAA-UGU-GCAGUAUC-AG--------U-ACUGCAUAUACCAACAGAGAGGG
ABKQ02024829.1/1362-1282     GGCUGACAAAACCCUGUCCCAACCUCCACGUGGUGUCGGCUGGAU-AAUG-CUGCAUU-A---------UGU-UGCAUUUACCAACUGGGAAGG
AAAB01008948.1/518160-518081 -GCUGGUAAAAUCCUUUCCCAACCUCCACGCGGUACCGGCUGGA-AUAUG-CU-CAUAG-U--------U-GAUGCAUAUACUGACAGGGAAGG
AAAB01008963.1/177333-177414 GGCUGACAAAAUCCUAUCUCUACCUCCUCGUGGUGUCAGCCGGAA-UGUG-CAGUAUC-AG--------U-ACUGCAUAUACCAACAGAGAGGG
AAGE02020265.1/668-747       UGCCCAGCAACUCCUAUCCCUACCUCCUCGCGGUACUGGCCGGGG-UACG-AGGAA-C--U--------U-UGGUCGUAUGCUGACAGGGAAGG
AAGE02004888.1/192770-192860 UGCCCAGCAACUCCUUUCCCUACCUCCUCGCGGUACUGGCCGGGG-UACG-AGUAACCCAGUGAGAACUU-UGUUCGUAUACUGAUAGGGAAGG
#=GC SS_cons                 ::::::::::::(((((((((<<<_______>>>,,,,,,,,,,<.<<<<.<<<<<__.__........_.>>>>>>>>>>,,,,)))))))))
#=GC RF                      gGCUgAcaAAaUCCuuUCCccACCUCCuCGuGGUaucGGCcGGAu.uaug.ccgcauc.Ag........U.ugugcauuuaCuaAgaGGGaaGG
//
# STOCKHOLM 1.0

#=GF AC   RF01788
#=GF ID   drz-agam-2-2
#=GF DE   drz-agam-2-2 ribozyme
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19965505
#=GF SS   Published; PMID:19965505
#=GF GA   38.00
#=GF TC   38.30
#=GF NC   37.70
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   19965505
#=GF RT   Widespread occurrence of self-cleaving ribozymes.
#=GF RA   Webb CH, Riccitelli NJ, Ruminski DJ, Luptak A
#=GF RL   Science. 2009;326:953.
#=GF WK   Ribozyme
#=GF SQ   5


AAAB01008846.1/3701932-3701742 AUCAGCCUUCGUUCUGUAAACGGGGUUGGAUCCGAC--------------UCUCAUAGGCUCUCCAA-C-CCAACUCCUACU-CAAUACGUCCUCGUCGUACAGAACGGUAACAUGUU-UU-CCGAACAUCCGCGCUUGGGUAUACGAGUAUACACCUUACCCAACCCUCGCCAACGGGGAGGAUGGAA-AACAUGGCUAAAUUGAGAGGG
ABKP02019106.1/17123-17317     UUUAGUUUUAGCUCUGUA-AUGGGAUGGGAUCCGAAGCCCCAUUGAGGGAUAAUACAGGCUCUCCCA-U-CCAACUCCUAUUCCAACACGUCCUCGUCGUACAGAGUGGUAACAUGUGUCA-CCACAUAUCCAAGCUUGGGU------ACACGGGCUUGACCCAACCCC------UUGGGCGGAUGGUGGCACAUGGCGAACCAGGAGGGG
ABKQ02003975.1/826-637         AGCAA--UACCUCGCUGAUACGGGGGUGGAUCCGAAGCCUCU-AGAAGGUUAACAUAAGCUCUCCAC-CUCCUACUCCUACU-UAAUAUGUCCCCGUCGUACAGAACGGUAACAUGUC-UC-UCAAUUAUCCAAGCUUGGGU------AUACGGGGAA-ACCCAUCCCC------UUGGGCGGAUGGGU-UGCAUGGCUAAAUUGAGAGGG
AB212871.1/896-707             ACCAUCUCUCAUAUUGUAUAU-AGUAUGGAUCCGAAGCCUCU-UGAAGAUUAACAUAGACUCUCCA-C--CUCACUUCAAUU-CAAUACGUUCCCGGCGUAUAGAAUGGUAACAUGUC-UCUCCAAAUAUCUGAGCUUGGGU------AAACGUGAAA-ACCCAAUCCC------UUGGGAAGAUGGGU-GAUAUGGCUAAAUUGAGUGGA
AY291392.1/684-497             CCCAGUUCCGGGGCCGUUCACUGG-----AUCCGAAGCCUCU-AGAAGGAUAAUAUAGGCACUCCAU-ACCCUACUCCGACU-CAAUACGUCCCCGUCGUACAGAAUGGUAACAUAUC-UCUCCAAAUAUCUGAGCUUGGGU------AUACGGGGAA-ACCCAACCCC------UUGGGAAGAUUGGG-UAUAUGGCUAAAUUGAGCGGA
#=GC SS_cons                   ::::::::::BBBBBBB:::::<<<<<<<<-<<_________.______________>>--->>>>>.>.>>,,,CCCC,CC.CCCCAAA,<<____aaabbbbbbb>>--(((((((.((.((----((((,,,,<<<<<<......__________.>>>>>>,<<<......__>>>,)))))))).)))))))::::cccccccccc
#=GC RF                        aucAguuuucguucuGUAuAcgGGguuGGAUCCGAAGCCuCu.uGAaGgaUAAcAUAGGCUCUCCaa.c.CCaACUcCuAcU.CAAUACGUCCuCGUCGUAcAGAAuGGUAaCAUguc.cc.CcAAAUAUCcgAGCuUGGGU......AuAcGgGaaa.ACCCAacCCc......UugGGagGAUgGgg.gacAUGgCuAAAUUGAGaGGg
//
# STOCKHOLM 1.0

#=GF AC   RF01789
#=GF ID   EBER1
#=GF DE   Epstein-Barr virus EBER1
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:17381320
#=GF SS   Published; PMID:17381320
#=GF GA   50.00
#=GF TC   51.50
#=GF NC   35.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17381320
#=GF RT   The challenge of viral snRNPs.
#=GF RA   Conrad NK, Fok V, Cazalla D, Borah S, Steitz JA
#=GF RL   Cold Spring Harb Symp Quant Biol. 2006;71:377-384.
#=GF WK   Epsteinâ€“Barr_virus-encoded_small_RNAs
#=GF SQ   3


EF187849.1/115-280   AGGACCUACGCUGCCCUAGAGGUUUUGCUAGGGAGGAGACGUGUGUGGCUGUAGCCACCCGUCCCGGGUACAAGUCCCGGGUGGUGAGGACGGUGUCUGUGG-----UU----GUCUUCC------------------------CAGACUCUGCUUUCUGCCGUCUUCGGUCAAGUACCAGCUGGUGGUCCGCAUGUUU
AF200364.1/1235-1424 AAGACCUACGCUGCCCUAGCGGUUCUGCUAGGGAGGAGAUUGGUGCGGCUUAUGCCGCCCGUCCCGGGUACAAGUCCCGGGAGGUGACGGUAGCGUCUGUAU-----UU----GCCCUGUAUCAGGUGUAUAGCUGCUCUCUCGCAGUCGCUGCUAUCAGCCGUCUCCGGUCCGAUGCCAGCUGGUGGUCUGCUCUUUU
AY037858.1/6652-6823 GGGACCUACGCUGCCCUAGCGGUUAUGCUGGGGAGGAGAUGAGUGUGACUUAAAUCACCCGUCCCGGGUACAAGUCCCGGGUGGUGAAGACGGGGUCUGGUGCUGCU--AAAAGUUUGGA------------------------CAGUCCCCGGUUUCUGCUCUCUUCGGUUCA-AACCAGCUGGUGGUCCGCCUGUUU
#=GC SS_cons         :[[[[[-[[[[[,<<-<<<________>>>>>,,(((((((-(,<<<<<____>>>>><<<-<<<<<<_______>>>>>>>>>,,<<<-<<<-<-<<<-<<.....__...._____>>........................>>>->->>>>>>,,,,))))))))<<_______>>]]]--]]]]]]]::::::::
#=GC RF              agGaCCUaCGCuGCCCuaGcGGUUuUGCuaGGGAGgaGacgaGUGcGgcUuaagcCgCCCgUCCCGGGUACAAGUCCCGGGcGGUGaagacgGuGUCuGugg.....UU....Gucuucc........................CaGuCuCcgcuuUCuGCcguCucCGGUccaauaCCaGCUGGuGGuCcGCuugUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01790
#=GF ID   htlv_FSE
#=GF DE   ribosomal frameshift site
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:8416368
#=GF SS   Published; PMID:8416368
#=GF GA   45.00
#=GF TC   48.40
#=GF NC   38.20
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200206;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   8416368
#=GF RT   Characterization of ribosomal frameshifting for expression of pol gene
#=GF RT   products of human T-cell leukemia virus type I.
#=GF RA   Nam SH, Copeland TD, Hatanaka M, Oroszlan S
#=GF RL   J Virol. 1993;67:196-203.
#=GF WK   Human_T-lymphotropic_virus
#=GF SQ   8


AF033817.1/2252-2294 GCCUCCAGGCCUUGCAACACUUGGUCCGGAAGGCCCUGGAGGC
AF074966.1/2601-2643 GCCUCCAGGCCUUGCAACACUUGGUCCGGACGGCCCUGGAGGC
M10060.1/2600-2642   GCCUCCAGGCCUUAAAUGACCUGGUCUCCAAGGCCCUGGAGGC
AF412314.1/2604-2646 GCCUCCAGGCCUUAAAUGACCUGGUCUCCAAGGCCCUGGAGGC
EF076684.1/112-154   GCCUCCAGGCCUUGCAACACUUGGUCCGGAAGGCCCUGGAGGC
DQ462191.1/2494-2536 GCCUCCAGGCCCUGACUGACCUGGUUUCCAGGGCCCUGGAGGC
EF488483.1/2519-2561 GCCUCCAGGCCCUAAUAGACCUGGUCUCCAAGGCACUGGAGGC
L02534.1/2610-2652   GCCUCCAGGCCCUGCAACACCUGGUCCGGAAGGCCUUGGAGGC
#=GC SS_cons         <<<<<<<<<<<<<-<____________>->>>>->>>>>>>>>
#=GC RF              GCCUCCAGGCCuUGcAagACCUGGUCuggAaGGCCCUGGAGGC
//
# STOCKHOLM 1.0

#=GF AC   RF01791
#=GF ID   F6
#=GF DE   F6 TB sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19555452
#=GF SS   Published; PMID:19555452
#=GF GA   46.00
#=GF TC   47.30
#=GF NC   45.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19555452
#=GF RT   Identification of small RNAs in Mycobacterium tuberculosis.
#=GF RA   Arnvig KB, Young DB
#=GF RL   Mol Microbiol. 2009;73:397-408.
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   16


AAYK01000249.1/14008-14065   CGGAUAGCCCCGUGUUGUUGUCUGACCC-CCGACCCCGACGGCAAUGCGGGGCAAUCCC
CP000854.1/597647-597704     UGGAAAGCCCCGUGUUGUGGUCUGACCC-CCGACCCCGACCGCAACGCGGGGCAAUCCG
ACBV01000006.1/72121-72178   CGGAUAGCCCCGCGUUGUGGUCUGACCC-CCGACCCCGGCCGCAGCGCGGGGCAAUCCG
ACFI01000224.1/33352-33295   CGGAUAGCCCCGUGUUGUGGUCUGACCCCCCGACCCCGACGGCAAUACGGGGC-AUCCC
CP000480.1/417737-417794     CGAGUAGCUCCGUGUUGCCGUCUGACCC-CCCGACCCGACGGCAACACGGGGCCAUUUA
CP000656.1/424191-424135     CGAAUAGCUCCGUGUUGCCGUCUGACCC-CCGACC-CGACGGCAACACGGGGCUCUUGU
ACNO01000104.1/457638-457694 AUGACAGCCCCGUGUUGCUGCCUGACCC-CCGACC-UGGCAGCAGCGCGGGGCUCUCGU
CP000511.1/285368-285425     GGGAUAGCUCCGUGUUGCCGUCUGACCC-CCCGACCCGACGGCAACACGGGGCUCUCAU
CP000518.1/275971-276028     CUGAUAGCUCCGUGUUGCCGUCUGACCC-CCCGACCCGACGGCAACACGGGGCCACUUU
AP011115.1/5730260-5730316   CUGUCAGCCCCGUGUUGCUGCCUGACCC-CCGACC-UGGCAGCAGCGCGGGGCUCUUGC
AM420293.1/8115015-8115071   CGGAUGACCCCGCGAUGCUGUCGGACCC-CCGACC-UGGCAGCACCGCGGGGCCUUCCA
CU458896.1/4517597-4517540   UGAGUAGCCUCGCGCCACCGUCCGACCC-CCCGACCCGACGGCGGCGCGGGGCUGCCUA
ACEV01000089.1/36188-36243   ACUACGACCCCGUGAUGCUGGCGGACCC-CCGACC-UGGCAGCAUCACGGGGU-UUCCA
CP001630.1/8103669-8103613   CCAGUAGCCCCGAAGUGCUGUCGGACCC-CCGACC-UGGCAGCACCUCGGGGCUCUUCC
CP001683.1/4223190-4223245   CGGAUGACCCCGUGAUGCUGGCGGACCC-CCGACC-UGGCAGCAUCACGGGGU-UUCCA
CP001737.1/5932731-5932675   AGGGCGACCCCGGACAGCUGCCGGACCC-CCGACC-UGGCAGCUGUGCGGGGUCACUUC
#=GC SS_cons                 :<<<<-<<<<<<<<<<<<<<<<______.________>>>>>>>>>>>>>>>>->>>>:
#=GC RF                      cggauAGCCCCGuGuUGCcGuCuGACCC.CCGACCCcGaCgGCAaCaCGGGGCuaucca
//
# STOCKHOLM 1.0

#=GF AC   RF01792
#=GF ID   eiav_FSE
#=GF DE   ribosomal frameshift site
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:3003905
#=GF SS   Published; PMID:3003905
#=GF GA   40.00
#=GF TC   42.30
#=GF NC   36.10
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200197;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   3003905
#=GF RT   Equine infectious anemia virus gag and pol genes: relatedness to visna and
#=GF RT   AIDS virus.
#=GF RA   Stephens RM, Casey JW, Rice NR
#=GF RL   Science. 1986;231:589-594.
#=GF RN   [2]
#=GF RM   3035786
#=GF RT   Nucleotide sequence analysis of equine infectious anemia virus proviral
#=GF RT   DNA.
#=GF RA   Kawakami T, Sherman L, Dahlberg J, Gazit A, Yaniv A, Tronick SR, Aaronson
#=GF RA   SA
#=GF RL   Virology. 1987;158:300-312.
#=GF RN   [3]
#=GF RM   12970412
#=GF RT   Characterization of RNA elements that regulate gag-pol ribosomal
#=GF RT   frameshifting in equine infectious anemia virus.
#=GF RA   Chen C, Montelaro RC
#=GF RL   J Virol. 2003;77:10280-10287.
#=GF RN   [4]
#=GF RM   1575083
#=GF RT   Translational suppression in retroviral gene expression.
#=GF RA   Hatfield DL, Levin JG, Rein A, Oroszlan S
#=GF RL   Adv Virus Res. 1992;41:193-239.
#=GF WK   Equine_infectious_anemia
#=GF SQ   5


AF033820.1/1797-1831 GGGGCUCAAGGGAGGCCCCAGAAACAAACUUUCCC
EU375544.1/1273-1307 GGGGCUCAGGGGAGGCCCCAAAAGCAAACCUUCCC
AF327877.1/1733-1767 GGGGCUCAGGGGAGGCCCCAAAAACAAACUUUCCC
M87574.1/258-292     GGGGCUCAAGGGAGGCCCCAGAAGCAAACUUUCCC
EF418583.1/1273-1307 GGGGUUCAGGGGAGGCCCCAGAAACAAACUUUCCC
#=GC SS_cons         <<<<<_________>>>>>::::::::::::::::
#=GC RF              GGGGCUCAGGGGAGGCCCCAGAAACAAACUUUCCC
//
# STOCKHOLM 1.0

#=GF AC   RF01793
#=GF ID   ffh
#=GF DE   ffh sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF AU   Meyer MM; 0000-0001-7014-9271
#=GF SE   Published; PMID:19531245
#=GF SS   Published; PMID:19531245
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19531245
#=GF RT   Identification of candidate structured RNAs in the marine organism
#=GF RT   'Candidatus Pelagibacter ubique'.
#=GF RA   Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ,
#=GF RA   Breaker RR
#=GF RL   BMC Genomics. 2009;10:268.
#=GF WK   Pelagibacter_ubique
#=GF **   seedtax: Bacteria; unclassified sequences
#=GF SQ   89


ABEF01041528.1/252-304         -AAA-CAAA---GGUAUCG-ACACUAGU-CAGCGAGGGUUCGCCCACUAGUGC-GAUU-UUU
ABID01000001.1/620465-620516   UGACGUCG-----GGAUCG-CCCCCAGU-CAGCGCGU-UGCGCCCACUGGGGC-AUUU-GUG
CP000830.1/337335-337284       CUGUGCAG-----GGAUCG-CCACCCGU-CAGCGCGU-UGCGCCCACGGGUGC-CUUU-CCG
CP000264.1/722337-722286       CGUCCGCA-----GGAUCG-CCCCCCGU-CAGCGAGU-UUCGCCCACGGGGGC-AAAU-CUC
ABXE01000005.1/474503-474554   UUGCAUGA-----GGAUCG-CCACCAGU-CAGCGCGU-CGCGCCCACUGGUGC-GUUU-CUC
AATR01000007.1/128120-128172   CGGUCUCA-----GGAUCG-ACAUCAGU-CAGCGAGU-UUCGCCCACUGGUGUUAAUU-GCG
CP000577.1/2858994-2858943     CACGACCG-----GGAUCG-CCACCCAU-CAGCGCGA-UGCGCCCAUGGGUGC-CGUU-GUG
ABVS01000001.1/307524-307576   AAACAAAG-----AGAUCG-ACACUAGU-CAGCGAGGCUUCGCCCACUAGUGC-GAUU-ACU
ABSK01000020.1/158486-158537   CCACGCAA-----GGAUCG-CCCCCAGU-CAGCGCGU-UGCGCCCACUGGGGU-UAAA-CUG
AAMO01000005.1/155351-155300   CGUUGCGG-----GGAUCG-CCACCAGU-CAGCGCGU-CGCGCCCACUGGUGC-AAUC-GUC
AAOT01000022.1/32279-32331     GCCCGUCG-----GGAUCG-CCCCCCGU-CAGCGAGCGUUCGCCCACGGGGGC-GUUU-GCC
CP000084.1/260256-260205       AAACAAAG-----AGAUCA-ACACUAGU-CAGCGAUA-UUCGCCCACUAGUGC-GAAA-CUG
ABSH01000046.1/28800-28749     UAGACUGA-----GGAUCG-CCCCCCGU-CAGCGCGU-UGCGCCCACGGGGGC-UCUA-CUG
ABCL01000001.1/633361-633412   CUGUGUCG-----GGAUCG-CCCCCCGU-CAGCGCGU-UGCGCCCACGGGGGC-GUUU-AUC
ACOA01000003.1/1141569-1141620 AUGUUCAG-----GGAUCG-CCCCCCAC-CAGCGAGU-UUCGCCCGUGGGGGC-AUUU-GUG
CP000661.1/172455-172506       CUUGUCCG-----GGAUCG-CCACCCAU-CAGCGCGA-UGCGCCCAUGGGUGC-CGUU-GUU
AATQ01000012.1/82408-82357     UUUGCCCG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-CAUU-CUG
CP000490.1/1013005-1013056     CUUGCCGG-----GGAUCG-CCCCCCGU-CAGCGCGU-UGCGCCCACGGGGGC-GUUA-CUG
AAMS01000004.1/308726-308675   CAUUCAGG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-GUUC-CUG
AAMT01000001.1/87588-87537     UUAUGCCG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-GCUA-CUG
ABCR01000008.1/127115-127064   UUUGGCCG-----GGAUCG-CCCCCCGU-CAGCGCGU-UGCGCCCACGGGGGA-GAUU-GGC
AAYA01000021.1/1331-1382       AUGGCCCG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-AUUU-CCG
ABXS01000046.1/690533-690482   GCAGCCAA-----AGAUCG-ACCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AUUU-GUG
AALY01000001.1/1810888-1810837 CCUGCCCG-----GGAUCG-CCCCCCAC-CAGCGCGU-UGCGCCCGUGGGGGC-AAUU-GUG
ACNW01000095.1/91055-91106     UAUGCCCG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-UGUU-UCG
ACCW01000020.1/70965-70914     UCGUUCAG-----GGAUCG-CCCCCCAC-CAGCGAGU-UUCGCCCGUGGGGGC-AAUG-CCA
CP000362.1/1269963-1269912     UGCAACCG-----GGAUCG-CCCUCCGU-CAGCGCGU-UGCGCCCACGGGGGC-AAAA-CCA
AAXZ01000001.1/683078-683027   GAUGCUUG-----GGAUCG-CCCUCCAC-CAGCGUGU-UACGCCCGUGGGGGC-GUUU-GUG
AAYB01000002.1/428943-428892   AUAUCAGG-----GGAUCG-CCCUCCGU-CAGCGCGU-CGCGCCCACGGGGGC-GCUA-CUG
AALV01000001.1/423960-424011   GCGGCCAG-----AGAUCG-CCCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AUUU-GCG
AANB01000002.1/544189-544138   CUUGUCGG-----GGAUCG-CCCUCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AAUU-GCG
CP000377.1/2739930-2739981     UUUGCCAG-----GGAUCG-CCCUCCAC-CAGCGCGU-UGCGCCCGUGGGGGC-AAAC-CUU
ABIE01000022.1/29479-29428     AUUGCCGG-----GGAUCG-CCCUCCAC-CAGCGUGU-UACGCCCGUGGGGGU-GAUU-GCG
ABXL01000036.1/20582-20633     GAUCCCAG-----AGGUCA-ACACCCGA-CAGCGCGA-UGCGCCCUCGGGUGA-UUUU-UUG
CP000628.1/3527839-3527890     GAUCCCGG-----AGGUCA-ACACCCGA-CAGCGCGU-UGCGCCCUCGGGUGC-UUUU-UGG
ABOG01005133.1/88-35           GAAUUCCA-----GGAUCG-CCCCCCGUCCAGCGAGGUUUCGCUCACGGGGGU-AUUG-GUG
ABIA02000001.1/8978-8927       GAUCCCGG-----AGGUCA-CCACCCGA-CAGCGCGA-UGCGCCCUCGGGUGU-UGUU-UGG
AP009384.1/4516671-4516722     GGGUCCGG-----AGGUCA-CCGCCCGA-CAGCGCGU-UGCGCCCUCGGGCGC-GUUU-CUC
AL591688.1/3522329-3522379     GAGCCCGG-----AGGUCA-ACACCCGA-CAGCGCGU-UGCGCCCUCGGGUG--GUUU-UUG
CP000633.1/3538560-3538610     GUUCCCGG-----AGGUCA-ACACCCGA-CAGCGCGA-UGCGCCCUCGGGUG--AUUU-UUG
CP000494.1/368234-368183       GAGGCCGG-----AGGUCA-ACGCCCGA-CAGCGCUA-UGCGCCCUCGGGCGC-AAAU-GUG
CP000250.1/397403-397351       GAGACCGG-----AGGUCA-ACGCCCGA-CAGCGCGA-UGCGCCCUCGGGCGC-CAUAAGUG
CP000781.1/1675762-1675712     GGGUCCGG-----AGGUCA-CCGCCCGA-CAGCGCGU-UGCGCCCUCGGGCGC-GAU--CUG
AAFX01130413.1/507-455         GCGCCCAA-----GGGUGC-ACGCCGGU-CAGCGAGGUUUCGCCCACCGGCGU-CUUU-GUC
CP001096.1/263306-263254       GAGGCCGG-----AGGUCA-ACGUCCGA-CAGCGCGA-UGCGCCCUCGGGCGC-AAUAAGUG
CP000758.1/1121355-1121406     GAUCCCGG-----AGGUCC-ACAUCCGA-CAGCGCGA-UGCGCCCUCGGGUGC-UGUA-UCG
CP000283.1/583300-583249       GAGGCCGG-----AGGUCA-ACGCCCGA-CAGCGCGA-UGCGCCCUCGGGCGC-GAAC-GUG
ACCU01000015.1/1002967-1002917 UUCCCGGA-----GGUUC--ACAUCCGA-CAGCGCGA-UGCGCCCUCGGGUGU-CAAA-CUG
CP001488.1/1778730-1778679     GAUCCCGG-----AGGUCC-ACACCCGA-CAGCGCGA-UGCGCCCUCGGGUGC-CGUG-ACC
AACY023196554.1/144-92         CAUGUUCA-----GGAUCG-CCCCCCGU-CAGCGAGGUUUCGCCCACGGGGUC-AAUU-UUG
AACY023876466.1/1379-1328      -----UAGCAGUUGGAUCG-CCCCCCGU-CAGCGAGU-UUCGCCCACGGGGGU-AAUU-ACG
AACY020558092.1/912-963        UAAC----AG-UUGGAUCG-CCCCCCGU-CAGCGAGU-UUCGCCCACGGGGGUAAGU--GGG
AACY020314903.1/269-217        GGUCCAUA-----AGAUCG-CCGUUCGU-CAACGAGGCUUCGUACACGAACGC-AAUA-CUU
AACY020277128.1/1252-1200      UUCAAAAG-----GAAUCG-CCAUCCGU-CAACGAGGGUUCGUCCACGGAUGC-UUUU-GUU
AACY023061866.1/133-185        UUCACAAU-----GAAUCG-CCAUCCGU-CAACGAGGGUUCGUCCACGGAUGU-UUUU-GUU
EU016673.1/15743-15714         ---------------------CACUAGU-CAGCGAGGGUUCGCCCACUAGUG----------
AACY023081810.1/148-96         UUCACAAU-----GAAUCG-CCAUCCGU-CAACGAGGGUUCGUCCACGGGUGC-UUUU-GUU
AACY020537384.1/5298-5349      GAUCGCGG-----GGAUC-ACCACCGGU-CGGCGAGU-UUCGCCCACCGGUG--CAUUUUGC
AACY021910620.1/877-825        UUCACAGU-----GAAUCG-CCAUCCGU-CAACGAGGGUUCGUCCACGGAUGC-UUUU-GUU
AACY022176703.1/377-428        CCCUCUUU-----GGAUCU-ACAUCCGU-CAGCGUUG-UACGCCCGCGGGUGC-CAUU-ACG
AAFX01131867.1/488-457         ------------------A-CCGCCCGA-CAGCGCAA-UGCGCCCUCGGGCGU---------
AACY023681284.1/528-562        -----------------CG-ACACUAGU-CAGCGAGGCUUCGCCCACUAGUGC-G-------
AACY020533898.1/2363-2414      UUGGGCAG-----GGAUCG-CCCCCCGU-CAGCGCGU-UGCGCCCACGGGGGC-GUCU-GUG
AACY020307803.1/379-431        AAGUGCCG-----GGAUCGCCCCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-GCUU-GUG
AACY021683092.1/259-208        UUGCCCAA-----GGAUCG-CCACCCGU-CAGCGCGU-UGCGCCCACGGGUGC-GUUU-UUG
AACY020400269.1/2767-2715      -GAA-CAAA---GAGAUCG-ACACUAGU-CAGCGAGGGUUCGCCCACUAGUGC-GAUUACU-
AACY020080831.1/570-622        GGUCCAAA-----AGAUCG-CCGUUCGU-CAACGAGGCUUCGUACACGAACGC-GAUA-CUU
AAYC01000003.1/36039-36090     CCUGUCAG-----GGAUCG-CCCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AAUU-CUG
CP000031.1/3449415-3449466     UUGUCCGG-----GGAUCG-CCCUCCAC-CAGCGUGU-UACGCCCGUGGAGGC-GAUU-GUG
ABXM01000014.1/117294-117243   CGUGCCAG-----GGAUCG-CCCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AAUU-GCG
ABXF01000044.1/222593-222644   CGUGCCAG-----GGAUCG-CCCCCCAC-CAGCGUGU-UACGCCCGUGGGGGC-AAAC-UCG
ACNZ01000021.1/2003-2054       UGGGUCGG-----GGAUCG-CCCUCCAC-CAGCGCGU-UGCGCCCGUGGGGGC-AAAC-CUU
CP000390.1/3614033-3613982     GAUCCCGG-----AGGUCA-ACACCCGG-CAGCGCAA-UGCGCCCCCGGGUGC-UUUU-CGG
AAUW01000013.1/152797-152746   GAUCCCGG-----AGGUUA-CCAUCCGA-CAGCGCGU-UGCGCCCUCGGGUGU-CAAA-CUG
CP001029.1/673842-673894       GAGGCCGG-----AGGUCA-ACGUCCGA-CAGCGCGUCUGCGCCCUCGGGCGC-CCUU-GUC
CP000524.1/76871-76922         GAUCCCAG-----AGGUCA-ACACCCGA-CGACGCGU-UGCGUUCUCGGGUGU-UAUU-UUG
CP000463.1/366625-366676       GAGACCGG-----AGGUUA-ACGCCCGA-CAGCGCUG-UGCGCCCUCGGGCGC-AAAA-UUG
BA000012.4/3476818-3476869     GAUCCUGG-----AGGCCA-ACACCCGG-CAGCGCAA-UGCGCCCCCGGGUGC-UUUU-UGG
ABPX01008569.1/496-547         AGGAGACA-----GAAUGA-CCAUCCGC-CAGCGCGU-UGCGCCCGCGGGUGC-UGCU-UUG
CP000115.1/3019357-3019408     GGGGCCGG-----AGGUCA-ACGCCCGA-CAGCGCUG-UGCGCCCUCGGGCGC-AAAC-GUG
CP000738.1/3241936-3241986     GAGCCAGG-----AGGUCA-ACAUCCGA-CAGCGCGU-GGCGCCCUCGGGUG--GUUU-UUG
CP001196.1/260758-260809       GACGCCGG-----AGGCCA-ACGCCCGA-CAGCGCUG-UGCGCCCUCGGGCGU-AAAC-GUG
CP001001.1/3845723-3845671     GAGGCCGG-----AGGUCA-ACGCCCGA-CAGCGCGUCCGCGCCCUCGGGCGC-GAUG-GGC
AM260525.1/2496302-2496251     GAUCUCAG-----AGGUCA-ACAUUCGA-CGGCGCGA-UGCGUUCUCGGGUGC-UAUU-UUG
BX897700.1/1505050-1504999     GAUCUCAG-----AGGUCA-ACAUCCGA-CGGCGCGA-UGCGUUCUCGGAUGC-CACU-UUA
AATP01000001.1/786255-786204   CCGCCCGG-----AGGUCA-CCAUCCGC-CAGCGAGU-UUCGCCCGCGGAUGG-CGUU-UUG
BX897699.1/1849078-1849027     GAUCUCAG-----AGGUCA-ACAUCCGA-CGGCGCGG-UGCGUUCUCGGAUGC-UGCU-UUG
CP001349.1/2975644-2975695     GAGGCUGG-----AGGCCA-ACGCCCGA-CAGCGCGA-UGCGCCCUCGGGCGC-GUCC-GGC
CP001016.1/3804515-3804563     AAACCCCG-----G---CC-ACGCCCGG-CAGCGCGU-UGCGCCCCCGGGCGC-GUUU-UGC
#=GC SS_cons                   ::::::::.....::::::.:<<<<<<<.--<<<<__._>>>>-->>>>>>>:.::::.:::
#=GC RF                        gaucCCaG.....GGAUCG.CCaCCCGu.CAGCGcGu.UgCGCCCaCGGGuGC.aaUU.gUG
//
# STOCKHOLM 1.0

#=GF AC   RF01794
#=GF ID   sok
#=GF DE   sok antitoxin (CssrC)
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:17462020
#=GF SS   Published; PMID:17462020
#=GF GA   39.00
#=GF TC   39.00
#=GF NC   38.80
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   17462020
#=GF RT   An antisense RNA controls synthesis of an SOS-induced toxin evolved from
#=GF RT   an antitoxin.
#=GF RA   Kawano M, Aravind L, Storz G
#=GF RL   Mol Microbiol. 2007;64:738-754.
#=GF RN   [2]
#=GF RM   3049248
#=GF RT   Nucleotide sequence and transcriptional analysis of a third function (Flm)
#=GF RT   involved in F-plasmid maintenance.
#=GF RA   Loh SM, Cram DS, Skurray RA
#=GF RL   Gene. 1988;66:259-268.blast
#=GF RN   [3]
#=GF RM   21483688
#=GF RT   An integrated approach for finding overlooked genes in Shigella.
#=GF RA   Peng J, Yang J, Jin Q
#=GF RL   PLoS One. 2011;6:e18509.
#=GF CC   Also identified in Shigella as CssrC [3]. 
#=GF WK   Hok/sok_system
#=GF SQ   91


AP009241.1/56560-56717       GGGCGCUUGAGGCUGUAUGCCG-AAAG------CGUUUU--------------------------------------------------------------------------GUGGACGGUAUACAGCAGAAAGCCCCAGG-------------------CGAUUUUUU----------------UAUCAAUCAA-CCAGGGGC--UCUACUGU-AAUGC-CUAGACAA-CAUU-AUAGU--A--G--CCCG-AUAAC-CGCCGUAA-GGCAAUG----GAGGGGCUAUG----AUG
ABHS01000025.1/47614-47458   GGGCGCUUGAGGCUGUAUGCCG-AAAG------CGUUUU--------------------------------------------------------------------------GUGGACGGCAUGUAGCAGAAAGCCCCAGG-------------------CGAUUUUUU----------------UAUCAAUCAA-CCCAGGGC---CCACUGU-AAUGC-CUAGACAA-CAUU-AUAGU--A--G--CCCG-AUGAC-GGCCGAAA-GGCAAUG----GAGGGGCUGCG----AUG
CU928147.1/73141-73298       GGGCGCUUGAGGCUGUAUGCUG-AAAG------CGUUUU--------------------------------------------------------------------------GUGGACGGCAUGCAGCAGAAAGCCCCAGG-------------------CGAUUUUUU----------------UAUCAAUCAA-CCCAGGGC--UCUACUGU-AAUGC-AUGAACAA-CAUU-AUAGU--A--G--CCCG-AUAAC-CGCCGAAA-GGCAAUG----GAGGGGCUGCG----AUG
CP000946.1/3985248-3985400   GGGUGCUUGAGGCUAUCUGUCU-CAGG------CAUUAG--------------------------------------------------------------------------CUGAACGGCAGAUAGAGAAAAGCCCCGAG-------------------UGAUAUUU------------------UACUAUCAA-CCCGAGGC---CC-CCUA-UAUG--CUGAACA--CAUG-UAGA--GU--G--CCUC-UUACU-GACCGUAA-GGUCAAG---GAGAAGAGAGCA----AUG
ACDM01000082.1/323-171       GGGUGCUUGAGGCUGUCUGUCU-CAGG------CAUUAG--------------------------------------------------------------------------CUGAACGGCAGAUAGAGAAAAGCCCCGAG-------------------UGAUAUUU------------------UACCAUCAA-CCCGAGGC---CUCCUAU--AUG--CUGAACA--CAU--GUAGA-GU--G--CCUC-UUACU-GACCGUAA-GGUCAAG---GAGAAGAGAGCA----AUG
CU928158.2/3642079-3641927   GGGUGCUUGAGACUGUUUGUCU-CAGG------UAUUCA--------------------------------------------------------------------------CCGAAAGGCAGACAGAGAAAAGCCCCACC-------------------UGACU---------------------AUAAAUCAA-AGUGAGGC---UG--CCUCUAUGC-UUCAACAA-CAUA-AGG-U-UA--G--CCUC-UUACU-CGUUGGAA-AUCAACA---CAGGAGGCUGGG---AAUG
CP000826.1/4004855-4005007   GGGCGCUUGAAGCUUUCUGCUU-CAGG------CCCUGG--------------------------------------------------------------------------GUGGGAAGCAGAAAGAAGAAAGCCCCAAA------------------CUGACU---------------------CUUAAUCAG-AAUGAGGC--UUCACCAU-ACUGC-AUCAACAC-CAGC-AUGGU--A--G--CCUC-UUAAC-CGCAGAAA-UGCAACG----GA-GGGCUGAC----AUG
BX571867.1/279818-279969     GGGUGCUUGAGACUUUCUGUCU-UAAG------CAUUAU--------------------------------------------------------------------------GUUUCAGGCAGAAAGAGAAAAGCCCCAUC-------------------CGACU---------------------AUAAAUCGA-AAUGAGGC---U-ACCCC-UAUGC-CUAG-CAA-CGUA-AGGCU--A--G--CCUC-UUACC-UGAUAAAA-AGCAAGGA--GAGAAGGCUAUG----AAG
CP000247.1/3834978-3834827   GGGUGCUUGAGACUGUUUGUCU-CAGG------UAUUCA--------------------------------------------------------------------------CCGAAAGGCAGACAGAGAAAAGCCCCACC-------------------UGACU---------------------AUAAAUCAA-AGUGAGGC---CC--CUC-UAUGC-AUAGACAC-CAUA-AGGUU--A--G--CCUC-UUACU-CGUUGGAA-AUCAACA---CAGGGGGCUGGG---AAUG
AAJU02000004.1/243000-242849 GGGUGCCUGAGACUUUCUGUUUUCAGG------C--UAA--------------------------------------------------------------------------CCGGGAAUCAGAAAGACGAAGGCCCCGAC-------------------CGAUAU--------------------UUCUAUCAA--CCGAGGC---CAACGAA-UGAAC-CAAG-CAA-UUCA-AAUGU-UA--G--CCUC-UUACC-CGCCAUCC-GGCAAGG---AGAAAGGCUAUG----AAG
EU370469.1/625-785           GGGCGCUUGAGGCUGUAUGCCG-AAAG------CGUUUU--------------------------------------------------------------------------GUGGACGGUAUACAGCAGAAAGCCCCUGG-------------------AGAUUUUUU----------------UAUCAAUCAA-CCAAGGGC--UCUACUGU-AAUGC-CUCAACAA-CAUU-AUAGU--A--G--CCUG-AUAAU-UUAGAUAUG-UGUACAU-CCUACCGGAAAAG----AUA
AAJX02000070.1/2508-2357     GGGUGUCUGAGCCUUUCUGGUU-CAGG------CAAGAC--------------------------------------------------------------------------GCAGGUACCAGAAAUGCGAAGACCCCACU-------------------UGUUAAUC------------------CAUUAACU--CGUGAGGC--CUGCAUGA-AGUAC-CUUAACAC-UACU-GAUUG-UA--G--CCUC-UUCCU-UGCAGAGA-GGUCAA--------AGUUUAUG----ACG
CP000654.1/103940-104112     UGGCGCUUGAGGCUUUUUGCCU-CAUG------AUGUUCGGGUGGUUU--------------------------------------------------------GUUAUCGUGUUGUGAGGCAAAAAGCAGAAAGCCCCGA--------------------AGUUAAUUC----------------UCAUUAACCA---CGAGGC---UUGAUCUGUAUGC-CUAGACAA-CAUC-AGAUU--A--G--CCGC-UUACC-UGCCGAAA-GGCAAGGA-GAAGAAGGCC-------AUG
ABKX01000002.1/444399-444256 GGGUGCUUGAGACUGUUUGUCU-CAGG------UAUC-A--------------------------------------------------------------------------CCGAAAGGCAGACAGAGAAAAGCCCCACC-------------------UGACU---------------------AUAAAUCAA-AGUGAGGC-----UACCC-UAUGC-CUGAACAC-CAUA-AGGUU--A--G--CCUC-UUACU-CGUUGGAA-AUCAACA----C--AGUGU-------AUG
AAJT02000001.1/165748-165899 GGGUGCCUGAGACUUUCUGUUUUCAGG------C--UAA--------------------------------------------------------------------------CCGGGAAUCAGAAAGACGAAGGCCCCGAC-------------------CGAUAU--------------------UUCUAUCAA--CCGAGGC--CAACGAA--UGAAC-CUAG-CAA-UUCA-GAUCU-UA--G--CCUC-UUACC-CGCCAUCC-GGCAAGG---AGAAAGGCUAUG----AAG
CP000783.1/4129279-4129449   CGGCGCUUGAGGCUUUUUGCCU-CCGG------CAAUCAGCAAAGUU---------------------------------------------------------ACCGCUAUGGCGGAUGGCAGAAAGAAGAAAGCCCCGAA-------------------GGUCAAUUU----------------UCAUUAACCA--ACGAGGC---U-GUCUC-CAUA--CUGAACA--UAUG-CAGAU-UA--G--CCUC-UUACC-CGUCGCAA-GACAAGG----AAAAGAAGCUG----AUG
CP000964.1/192830-192980     GGGUGCUUGAGACUGUGUGUCU-CAGG------UAUUCA--------------------------------------------------------------------------GCGGGAGAUAGACAGAGAAAAGCCCCACC-------------------UGAUAG----------------------UAAUCAA-AGUGAGGC-----UCCCC-UAUGC-AUGAACAC-CAUA-AGAGU--A--G--CCUC-UUACU-UGUUGAAA-AUCAACA---CUGGAGGCGAGG---AAUG
CP000970.1/1758710-1758861   GGGUGCCUGAGACUUUCUGUUUUCAGG------C--UAA--------------------------------------------------------------------------CCGGGAAUCAGAAAGACGAAGGCCCCGAC-------------------CAAUAU--------------------UUCUAUCAA--CCGAGGC--CAA-CGAA-UGAAC-CUAG-CAA-UUCAGAUCA--UA--G--CCUC-UUACC-CGCCAUCC-GGCAAGG---AGAAAGGCUAUG----AAG
AP000342.1/47193-47369       CGGCGCUUGAGGCUUUCUGCCU-CAUG-----ACGUGAAGGUGGUUU---------------------------------------------------------GUUACCGUGUUGUGUGGCAGAAAGAAGAUAGCCCCGUAG----------------UAAGUUAAUUU----------------UCAUUAACCACCACGAGGC-----AUCCC-UAUGU-CUAGUCCA-CAUC-AGGAU--A--G--CCUC-UUACC-GCGCUUUG-CGCAAGGA-GAAGAAGGCC-------AUG
CP001065.1/48786-48957       CGGCGCUUGAGGCUUUUUGCCU-CAUG-----ACGUGAAGGUGGUUU---------------------------------------------------------GUUACCGUGUUGUGUGGCAGAAAGCAGAAAGCCCCGU--------------------AGUUAAUUU----------------UCAUUAACC--CACGAGGC--C-CACUGU--AUGU-CUAACCAA-CA---CCAGUAUG--G--CCUC-UUACC-GUGCAAAU-UGCAAGG----AGGAGUAAACC----AUG
AP001918.1/62807-62978       CGGCGCUUGAGGCUUUCUGCCU-CAUG-----ACGUGAAGGUGGUUU---------------------------------------------------------GUUGCCGUGUUGUGUGGCAGAAGGACAAAAGCCCCGUA-------------------GUUAAUUUU----------------UCAUUAACC--CACGAGGC-----CCCUG-CAUGC-UUAGACAA-CAUC-AGGAU--A--G--CCUC-UUACU-GCGCUUUG-CGCAAGGA-GAAGAAGGCC-------AUG
ABHQ01000054.1/2301-2152     GGGUGCUUGAGGCUAUCUGCCU-CGGG------CAUGAA-------------------------------------------------------------------------CACCAACGGCAGAUAGAUAAAAGCCCCACC-------------------CGACU---------------------AUAAAUCGA-AGUGAGGC-----CCCUA-UAUG--CUCGUCA--CAUA-UAGAU--U--G--CCUC-UUACG-GACCGAAA-GGUCAAG----GAGAAGCAGGC---UAUG
CP001122.1/55073-54901       CGGCGCUUGAGGCUUUCUGCCU-CAUG-----ACGUGAAGGUGGUUU---------------------------------------------------------GUUACCGUGUUGUGUGGCAGAAGGCAGAAAGCCCCGUA-------------------GUUAAUUUU----------------UCAUUAACC--CACGAGGC--C-CCCUGU--AUGU-CUGAUCAA-CA---ACAGU--AUGG--CCUC-UUACC-GUGCUUAA-UGCAAGG----AGGAGUAAACC----AUG
ABAN01000078.1/2541-2393     GGGUGCUUGAGGCUGUCUGCCU-UAAG------CGCUUG--------------------------------------------------------------------------CUGACAGGUAGAUAGAUAAAAGCCCCACC-------------------CGACU---------------------AUAAAUCGA-AGUGAGGC-----CCCUA-UAUG--CUCGUCA--CAUA-UAGAU--U--G--CCUC-UUACG-GACCGAAA-GGUCAAG----GAGAAGCAGGC---UAUG
AAMK02000020.1/20388-20545   GGGUGCUUGAGGCUGUCUGGCGUUAAG------CAUUCG--------------------------------------------------------------------------CGAGGUUCCAGAUGGACAAAAGCCCCAGG-------------------CGAUAU--------------------UUCUAUCAA-CCUGAGGC---UUACGUU-CGAAC-CCAAACAA-UUCG-AAUGU-UA--G--UCUC-UUCUU-UGCAGGGA-GGCAAGA---CAUGCUGACAAAA--UAUG
ACID01000034.1/135104-134960 GGGUGCUUGAGGCUGUCUGGCGUUAAG------CAUUCG--------------------------------------------------------------------------CGAGGUUCCAGAUGGACAAAAGCCCCAGG-------------------CGAUAU--------------------UUCUAUCAA-CCUGAGGC---UUACGUU-CGAAC-CCAAACAA-UUCG-AAUGU-UA--G--UCUC-UUCUU-UGCAGGGA-GGC---------------AAGA---CAUG
FM180568.1/3114053-3113904   GGGUGCUUGAGGCUGUCUGGCGUUAAG------CAUUCG--------------------------------------------------------------------------CGAGGUUCCAGAUGGACAAAAGCCCCAGG-------------------CGAUAU--------------------UUCUAUCAA-CCUGAGGC---CUACGUU-CGAAC-CUAAGCAA-UUCG-GAUGU-UA--G--UCUC-UUCUU-UGCAAGGA-GGCAAG----------ACAUUG---UAUG
CP000648.1/132472-132638     UGGCGCUUGAGGCUUUUUGCCU-CAUG-----ACGUGAAGGUGGUUU---------------------------------------------------------GUUACCGUGUUGUGUGGCAGAAAGCAGAAAGCCCCGU--------------------AGUUAAUUU----------------UCAUUAACC--CACGAGGC--C-CACUGA--AUGU-CUAGUCAA-CA---CCAGUAUG--G--CCUC-UUACC-GUGCAAUU-UGCAAGG----AGGUG---U------AUG
CP000795.1/24168-24339       CGGCGCUUGAGGCUUUCUGCCU-CAUG-----ACGUGAAGGUGGUUU---------------------------------------------------------GUUACAGUGUUGUGUGGCAGAAGGACAAAAGCCCCGUA-------------------GUUAAUUUU----------------UCAUUAACC--CACGAGGC---CUCUGC---AUGU-CUAGUCCA-CGUC-AGUAU--G--G--CCUC-UUACC-GUGCAAAU-UGCAAGG----AGGAGUAAACC----AUG
CP000646.1/142098-142240     GGGUGCUUGAGGCUGUCUGUCU-CAAG------CGCA-A--------------------------------------------------------------------------GCAAGAGCCAGAUAGACGAAAGCCCCGAA-------------------GGUCAAUUU----------------UCAUUAACCA--ACGAGGC---CCAACAU-AAUGU-UCGCAAAA-C-UG-AUGUU--A--G--CCUC-UC--U-CGACGC--------------AGGAGGCAAGU----AUG
CP001063.1/1314748-1314923   GGGUGCUUGAGGCUAUCUGUCU-CAGG------CAUGAAC------------------------------------------------------------------------ACUGAAAGGCAGAUAGAGAAAAGCCCCAGU-------------------UAACAUUUCGCGUCCUGCAAGACGCUUAACAUUAA-UCUGAGGC---CCAAUCU-AUGU--CUCA-CAA-AUGU-AGGUU--A--G--CCUC-UUACG-UGCCGAAA-GGCAAGGG-GAAGCAGGCUAUG----AAG
AAJW02000017.1/47594-47768   GGGUGCUUGAGGCUGUCUGCCU-CGGG------CAUGCA-------------------------------------------------------------------------GCCGUAAGGCAGACAGAGAAAAGCCCCAGU-------------------UAACAUUACGCGUCUUGCAGGACGCUUAACAUUAA-UCUGAGGC---CAAAUCU--AUGA-CUUACAAA-CUU--AGGUU--A--G--CCUC-UUACG-UGCCGAAA-GGCAAGGA-GAAGUAGGCUAUG----AAG
AAMJ02000091.1/1687-1857     CGGCGCUUGAGGCUUUCUGCCU-CAUG-----ACGUGAAGGUGGUUU---------------------------------------------------------GUUAUCCUGUUGUGUGGCAGAAGGACAAAAGCCCCGU--------------------AGUUAAUUU----------------UCAUUAACC--CACGAGGC---CUCUG---CAUGU-CUAGUCCA-CGUC-AGUAU--G--C--CCUC-UUACC-GUGCAAAU-UGCAAGG----AGGAGUAAACC----AUG
AM286415.1/3445379-3445187   GGGUGCUUGAAGCUGUCUGCUU-UGGG------CAUUGUUUGAAUCAGUGCUGUAAGUG---------------------------------UCUUGGUAAAAACAGUUGUUGUCAUAAAGCAGAUAGGAAAAAGCCCCGUA------------------------CUGA----------------CGUUAAUCAA-UACGAGGC---UC--CCU-AAUGC-CUGG-CAA-CAUU-ACGCU--A--G--CUUC-UUACC-UGCUGAAA-GGCAAAAC--AUGGAGGCCAAA---UAUG
AM933172.1/1475526-1475701   GGGUGCUUGAGGCUAUCUGCCU-CAGG------CAUGAAC------------------------------------------------------------------------ACCAAAAGGCAGAUAGAGAAAAGCCCCAGUUAACAUUACGCGUCCGGCAAGA---CGC----------------UUAACAUUAA-UCUGAGGC---CAAUUU--CAUGC-UUUG-CA--CAUG-UAGGU-UA--G--CCUC-UUACG-UGCCGAAA-GGCAAGGA-GAAGCAGGCUAUG----AAG
CP001164.1/2148806-2148632   GGGUGCUUGAGGCUGUCUGCCU-CGGG------CAUGCC-------------------------------------------------------------------------ACCGUAAGGCAGACAGAGAAAAGCCCCAGU-------------------UAACAUUACGCGUCCUGCAAGACGCCUAACAUUAA-UCUGAGGC---CAAUUU--CAUG--CUAGACA--CAUG-UAGGU-UA--G--CCUC-UUACG-CGCCGAAA-GGCAAGGA-GAAGCAGGCUAUG----AAG
ABHO01000077.1/209-39        GGGUGCUUGAGGCUGUCUGCCU-CGGG------CAUGCC-------------------------------------------------------------------------ACCGUAAGGCAGACAGAGAAAAGCCCCAGU-------------------UAACAUUACGCGUCCUGCAAGACGCCUAACAUUAA-UCUGAGGC---CAAUUU--CAUG--CUAGACA--CAUG-UAGGU-UA--G--CCUC-UUACG-CGCCGAAA-GGCAAG-----GAGAAGCAGCU----AUG
CP000266.1/1412870-1413044   GGGUGCUUGAGGCUGUCUGCCU-CGGG------CAUGCC-------------------------------------------------------------------------ACUGUAAGGCAGACAGAGAAAAGCCCCAGUUAACAUUAC-GCGUCCUGC--------AAGA----------CGCUUAACAUUAA-UCUGAGGC---CCAAUCU-AUGU--CUCA-CAA-AUGU-AGGUU--A--G--CCUC-UUACG-UGCCGAAA-GGCAAGGA-GAAGCAGGCUAUG----AAG
ABHK02000002.1/69092-69263   GGGUGCUUGAGGCUGUCUGCCU-CGGG------CAUGCC-------------------------------------------------------------------------ACCGUAAGGCAGACAGAGAAAAGCCCCAGUUAACAUUAC-GCGUCCUGC--------AAGA----------CGCUUAACAUUAA-UCUGAGGC---CCAAUCU--AUGC-UUCACAAA-CGU--AGGUU--A--G--CCUC-UUACG-CGCCGAAA-GGCAAGG----AGAAGCAGGUU----AUG
CU928163.2/1875359-1875185   GGGUGCUUGAGGCUAUCUGCCU-CGGG------CAUGAA-------------------------------------------------------------------------CACCAAAGGCAGAUAGAGAAAAGCCCCAGUUAACAUUAC-GCGUCCUGC--------AAGA----------CGCUUAACAUUAA-UCUGAGGC---CAAUUU--CAUG--CUAGACA--CAUG-UAGGU-UA--G--CCUC-UUACG-AGCCGAAA-GGCAAGGA-GAAGCAGGCUAUG----AAG
CU928162.2/1707615-1707441   GGGUGCUUGAGGCUAUCUGCCU-CGGG------CAUGAA-------------------------------------------------------------------------CACCAACGGCAGAUAGAGAAAAGCCCCAGU-------------------UAACAUUAUGCGUCUUGCAGGACGCUUAACAUUAA-UCUGAGGC---CAAUUU--CAUG--CUAGUCA--CAUG-UAGGU-UA--G--CCUC-UUACA-CGCCGAAA-GGCAAGGA-GAAGCAGGCUAUG----AAG
AM942760.1/22898-22749       GGGUGCUUGAUCCUGUCCGGUU-CAAG------CAUUUA--------------------------------------------------------------------------GUGAGAGCCAGAUAGAAGAAAGCCCCGAUA-----------------AGGUUAUUUA----------------UUACCAUAA---UCGAGGC---UGCAAUUCUCUAC-UUAG-CAC-UAGA-AAUUG--U--G--CCUC-CUAAU-AA--GUUA-GGAG-------UCAAGGAAA------AUG
ACGN01000130.1/20772-20597   GGGUGCUUGAGGCUAUCUGUCU-CAGG------CAUGAAC------------------------------------------------------------------------ACCAAAAGGCAGAUAGAGAAAAGCCCCAGUUAACAUUACGCGUCCGGCAAGA---CGC----------------UUAACAUUAA-UCUGAGGC---CAUAUCU-AUGCU-CUACACAC-G--U-AGGUU--A--G--CCUC-UUACG-UGCCGAAA-GGCAAGGA-GAAGCAGGCUAUG----AAG
AAJV02000067.1/8393-8567     GGGCGCUUGAGGCUGUCUGCCU-CGGG------CAUGCC-------------------------------------------------------------------------ACCGUAAGGCAGACAGAGAAAAGCCCCAGUUAACAUUACGCGUCCGGCAAGA---CGC----------------UUAACAUUAA-UCUGAGGC---CAUAUCU-AUGCU-CUACACAC-G--U-AGGUU--A--G--CCUC-UUACG-UGCCGAAA-GGCAAGGA-GAAGCAGGCUAUG----AAG
AE014075.1/1338132-1338303   GGGUGCUUGAGGCUAUCUGUCU-CAGG------CAUGAAC------------------------------------------------------------------------ACCAAAAGGCAGAUAGAGAAAAGCCCCAGUUAACAUUAC-GCGUCCUGC--------AAGA----------CGCUUAACAUUAA-UCUGAGGC--CAUAUCU---AUGC----GACA--CAUA-GAGAU-UA--G--CCUC-UUACG-GACCGAAA-GGUCAAG----GAGAAGCAGGC---UAUG
CU928145.2/1790013-1789839   GGGUGCUUGAGGCUAUCUGCCU-CAGG------CAUGAA-------------------------------------------------------------------------CACCAAAGGCAGAUAGAGAAAAGCCCCAGUUAACAUUACGCGUCCUGCAAG---ACGU----------------UUAACAUUAA-UCUGAGGC---UCAAUCU-AUGA---ACGGCAAAUC-U-AGGUU--A--G--CCUC-UUGCG-UGCCGAAA-GGCAAGGA-GAAGCAGGCUAUG----AAG
ABEI01000019.1/53404-53231   GGGUGCUUGAGGCUGUUUGCCU-GGAG------CAUU-C--------------------------------------------------------------------------GUGAAAGGCAGACAGAGAAAAGCCCCAGU-------------------UAACAUUCGGCGUCUUGCAGGACGCUUAACAUUAA-ACUGAGGC---CACAUCU-AUGCU-CUACACAC-G--U-AGAUU--A--G--CCUC-UUACG-GACCGAAA-GGUCAAGGAGAAGUAGGCUAUG----AAG
AAOU01000061.1/12615-12444   GGGUGCUCUUGGCUGUCUGUCA-GGAG------CAUAACAACUGUCA---------------------------------------------------------CUGGAUGUCGUGACUGGCAGAUAGACGAAAGCCCCGAA-------------------AGUUAAUU------------------UCUUAACCA--ACGAGGC---AAUCUGA-UGAAA-CUCGACAC-UUCU-GAUGU-UA--G--CCUC-UAUUU-AAUUGAGA-GGCAAGA----CGUAUGCUGCG----AAG
ABEW01000010.1/112387-112557 GGGUGCUUGAGGCUGUUUGCCU-GGAG------CAUU-C--------------------------------------------------------------------------GUGAAAGGCAGACAGAGAAAAGCCCCAGU-------------------UAACAUUCGGCGUCUUGCAGGACGCUUAACAUUAA-ACUGAGGC---CACAUCU-AUGCU-CUACACAC-G--U-AGAUU--A--G--CCUC-UUACG-GACCGAAA-GGUCAAG----GAGAAGCAGGC---UAUG
AF250878.1/91161-91322       CGGUGCUGGAGGCUUU-UGCCC-CAGC------CAGCAGAUUCA---------------------------------------------------------------CUGUUUGACUGUGGUAAAAAGCAGAAAGCCCCG---------------------AGUAAUUUU----------------UUCAAAUUAA-CCCGAGGC-----CCCUG-UAUG--CUAGUCA--CAUU-CAGAG-UA--G--CCUC-UUACC-CGCUUAAA-UGCAAGGA-GAAGAAGGCC-------AUG
DQ472416.1/369-196           GGGUGCUUGAGGCUGUUUGCCU-GGAG------CAUU-C--------------------------------------------------------------------------GUGAAAGGCAGACAGAGAAAAGCCCCAGU-------------------UAACAUUCGGCGUCUUGCAGGACGCUUAACAUUAA-ACUGAGGC---CA-AUCC-AAUGC-UUGAACAA-CUGA-AGAU--UA--G--CCUC-UUAAC-CGUAAGAA-AUCAACUU-ACAGGAGGCUGUA----AUG
CP001254.1/10217-10072       GGGUGCUCUUGGCUGUUUGGCA-AGAG------CAUAGAU-----------------------------------------------------------------------UUGCAAAGGCCAGAUAGACGAAAGCCCCGU--------------------AGUUAAUC------------------CAUUAACCA--ACGAGGC--AAUCUAA--UGUAC-AUAG-CAA-UACA-GAUAG-UA--G--CCUC-UUUAC-UUUU----------------AAGGGGCAAGU---UAUG
CP000036.1/1691393-1691204   GGGUGCUUGAGGCUAUCUGCUU-CAGG------CUAUCUGCUUCAGG----------------------------------------------------------CAUGAACACCAAAAGGCAGAUAGAGAAAAGCCCCAGUUAACAUUACGCGUCCGGCAAGA---CGC----------------UUAACAUUAA-UCUGAGGC---CAAUUU--CAUGC-UUUG-CA--CAUG-UAGGU-UA--G--CCUC-UUACA-UGCCGAAA-GGCAAGGA-GAAGCAGGCUAUG----AAG
CU928164.2/1565220-1565391   GGGUGCUUGAGGCUAUCUGCCU-CGGG------CAUGGA-------------------------------------------------------------------------CACCAACGGCAGAUAGAGAAAAGCCCCAGUUAACAUUAC-GCGUCCUGC--------AAGA----------CGCUUAACAUUAA-UCUGAGGC---CAAUUU--CAUG--CUAGACA--CAUG-UAGGU-UA--G--CCUC-UUACG-UGCCGAAA-GGCACGGA-GAAGCAGGCU-------AUU
ACDL01000057.1/15730-15879   GGGUGCCUGAAGCUUUCCGGUUUCAGG------UUAACU--------------------------------------------------------------------------CUGAGGUCUGGAAAGAUGAA-GCCCCAGG-------------------AGAUAUUUC----------------UAUCAAUCC----UGGGGC---UGCCACUCCGAGC-CUCAACAA-CUCG-GAUGG-UA--G--UCCC-UUCUU-CGCAUGGA-GGCAAUA----UAAA------C----AUG
CP000243.1/593144-593294     GGGUGCCUGAAGCUUUCCGGUUUCAGG------UUUACU--------------------------------------------------------------------------CUGAGGUCUGGAAAGAUGAAGCCCCAGGA-------------------CGAUAUU--------------------UCUAUCAACCCUGGGGC--UACCUACC-CAAAC-CUGAACAA-UUUG-GAUGG-UA--G--UCCC-UUCUU-CGCAUGGA-GGCAAUA----UAAA------C----AUG
CP000802.1/643770-643919     GGGUGCCUGAAGCUUUCCGGUUUCAGG------UUUACU--------------------------------------------------------------------------CUGAGGUCUGGAAAGAUGAA-GCCCCAGG-------------------AGAUAUU--------------------UCUAUCAACCCUGGGGC---UGCCACUCCAAAC-CCGAACAA-UUUG-GAUGG-UA--G--UCCC-UUCUU-CGCAUGGA-GGCAAUA----UAAA------C----AUG
CP000893.1/48333-48495       GGGUGCUCUUGGCUUUUUAGCA-AGAG------CAUGGAAAUGCU--------------------------------------------------------------GUUAUGUAACUUGCUAGAAAGUUGAAAGCCCCGAA-------------------UGAACU--------------------AUAAAUUCA-AACGAGGC-----CUACAAUGUAC-CUAAGCAA-UACA-AAUAG-UA--G--CCUC-UUUAC-UUUUAGGA-GGCAA------GAUAUGCCGAA----AAG
ABXW01000018.1/18803-18653   GGGUGCUUGAUCUUGCUCAGUU-CAAG------CAUUUA-------------------------------------------------------------------------UUUUUGGUCUGGGAAAGAAAAAGCCCCGUU-------------------AGUGAU--------------------AUUCACCAA---CGAGGC---UGCACUC-CCAA--CCAGACAA-UCGG-GAGUG--U--G--CCUC-UUAAU-AAAAGAGA-GGUCAAG----GAGAAAUGACA----AAG
AAWP01000034.1/13780-13614   GGGUGCUCUUGGCUUGCUGCCA-UGAG------CAUUUCUCUAAGU------------------------------------------------------------AGUAUUUGCAAGUGGUAGAAAGUACAAAGCCCCGAA-------------------UGAACU--------------------AUAAAUUCA-AACGAGGC---C-GUGUA-UGUAU-CUGA-CAG-UACA-AAUAC-UA--G--CCUC-UUUGC-CACAAGGA-GGCAACG---AAAAAUGCCAAA----AAG
ACLE01000080.1/97507-97370   GGGUGCUUGGAUCGUUUUGGUU-CAAG------CAUUGC--------------------------------------------------------------------------GCUAGAGCCAAAAAGACAAAAGCCCCGAA-------------------UUUUAUUUU----------------CAUAAA---A-UCCGAGGC-----AGUCU-CAAAG-CUCAACAA-CUUG-AUUCU-----G--CCUC-CUUUA-UU-----------AAA----AGGAGUCA-------AUC
DQ517526.1/191770-191612     UGGUGCUGGAGGCUUUUG-CCC-CAGC------CAGCGGUAACA---------------------------------------------------------------CUGUUUGACUGUGG-UAAAAGCAGAAAGCCCCGA---------------------GUAAUUU------------------UUCAAUUAA-CCCGAGGC---CC---CU-GUAUG-CUAGUCAC-ACAC-AGCGU--A--G--CCUC-UUGCC-UGCUUAAA-UGCAAGGA-GAAGAAGGCC-------AUG
ABVP01000024.1/175578-175727 GGGUGCUUGGAUCAAUCUGGUU-CAAG------CAUUUG--------------------------------------------------------------------------CUAAAUGCCAGAAAGAGAAAAGCCCCGGA-------------------AAAUAUAU------------------UUAUAUUA--ACCGAGGC-----GGACU-CAAAC-CUGA-GAA-CUUG-AUUCU-----G--CCUC-CUUAU-AGAGGAGC-UGUCAAG----AAAAUGAACAA----AUA
ABEJ01000002.1/220588-220439 GGGUGCUUGAGACUGUUUGUCU-CAGG------UAUUUA--------------------------------------------------------------------------CCAAAAGGCAGACAGAGAAAAGCCCCACC-------------------UGACUAUA------------------AAUCAAAAG-UGCAUUGC---ACCCAUU-AUUG--AUCU-CUU-CAAU-AACGA--A--G--CUA--UCCCC-UACAGUAU-UUCA-------GAACGUCCAAC---CAUG
ABEH02000004.1/254317-254466 GGGUGCUUGAGACUGUUUGUCU-CAGG------UAUUCA--------------------------------------------------------------------------CCAAAAGGCAGAGAGAGAAAAGCCCCACC-------------------UGACUAUA---------------------AAUCAAAAGUGCACUGCGACCAUUA-UUGAU-CUCU-----UCAA-UAACG--A--A--GUGA-UCUCC-UGCAGUAU-UUCA-------GAAUGUCCAAC---CAUG
CP000880.1/3918156-3918305   GGGUGCUUGAGACUGUUUGUCU-CAGG------UAUUCA--------------------------------------------------------------------------CCAAAAGGCAGAGAGAGAAAAGCUCCACC-------------------UGACUAUA------------------AAUCAAAAG-UGCACAGC---ACCCAUU-AUUG--AUCU-CUU-CAAU-AACGA--A--G---UGA-UCUCC-UGCAGUAU-UUCA-------GAACGUCCAAC---CAUG
CP000034.1/2636309-2636522   GGG--------UUUUUCUGCUC------------AUUAUUAGCUCCUUCUGAUGCCAUUCUAUUUCAGGAAGGAGUGUCCGUUAAACUCAGGCUACCUCAGUUUGUUAUCCUGUCGUGUGGCAGAAGGACAAA-AGCCCCGU-------------------AGUUAAUUU----------------UCAUUAACC--CACGAGGC---CUCUGC---AUGU-CUAGUCCA-CGUU-AGUAU--G--G--CCUC-UUACC-GUGCAAAU-UGCAAGG----AGGAGUAAACC----AUG
ABHR01000099.1/158-1         GGGUGCUUGAGGCUGUCUGCCU-CGGG------CAUGCC-------------------------------------------------------------------------ACCGUAAGGCAGACAGAGAAAAGCCCCAGU-------------------UAACAUUACGCGUCCUGCAAGACGCCUAACAUUAA-UCUGAGGC---CAAUUU--CAUG--CUAGACA--CAUG-UAGGU-UA--G--CCUC-UUACG-CGCCGAAA-GGCA----------------------AGG
BA000007.2/3607574-3607423   GGGUGCUUGAGGCUGUCUGGCGUUAAG------CAUUCG--------------------------------------------------------------------------CGAGGUUCCAGAUGGACAAAAGCCCCAGG-------------------CGAUAU--------------------UUCUAUCAA-CCUGAGGC---UCGCGUU-CGAAC-GUAG-CAA-UUCG-GAUGU-UA--G--UCUC-UUCUU-UGCAGGGA-GGCAA------GACAUGCUAAC----AAA
ABJT01000010.1/166914-166741 GGGUGCUUGAGGCUAUCUGCCU-CGGG------CAUGAA-------------------------------------------------------------------------CACCAACGGCAGAUAGAGAAAAGCCCCAGU-------------------UAACAUUACGCGUCCUGCAAGACGCUUAACAUUAA-UCUGAG-C---UCAAUC--CAUG--CUGA--AA-CAUGUAAGUU--A--GCCUCUC-UUACU-GUGCGAAA-GGCAGGAG--AAGCAGGCUAUG----AAG
FM178382.1/14748-14914       GGGUGCUUUUGGCUAUCAACCG-AAAG------CAUAACGUAA-----------------------------------------------------------------GUUUUGUAGACGGUAGAUAACUAAAAACCCCGAA-------------------AGUAAAUUU---------------UCAUUCACUA---ACGAGGC--UUUAGAUA-UGUAC-UUCAACAA-UACG-GAUCU-UA--G--UCUC-UAUUU-UAAUAAGA-GGCAAGU----AAAAUGCUAAA----AAA
AM293859.1/39766-39602       GGGUGCUUUUGGUGUUCGACCA-AAAG------CAGUUCGAAA-----------------------------------------------------------------GAUUUGCUGGCGGUAGAAAAUCAAAAACCCCGAA-------------------UGAACU--------------------GUAAAUUCA-AACGAGGU--UUUAGAGA-UGUAC-CUAGACAA-UACA-AAUCU-UA--G--CCUC-UAUCU-CGAUUUAU-UUCAAUG---CAAAAUUGAAGG----AGG
CR378676.1/54713-54555       GGGUGCUCUUGGAUAUCUGUCA-GGAG------CAUAACAACA-----------------------------------------------------------------GUUUUGUGAAUUUCAGAUAGAUGAAAGCCCCGUU-------------------A---AUUU------------------UUCAAUCAA---CGAGGC---CAACAGA-UGUAU-CUAGACAA-UUCUGAUUGU-UA--G--CCUC-UCUUA-CCAAAGAG-GGCAAG------CUAUGCCGAA----AAG
CP000022.1/5383-5548         GGGUGCUUUUGGUUAUCAAUCG-AAAG------CAUGACACAA-----------------------------------------------------------------GUUUUGCAGACGGUAGAUAAACAAAAACCCCGAA-------------------AGUAAAUUU----------------UCAUUAACUA--ACGAGGU--UUAAGUGA-UGUAC-CCA-ACAA-UGCA-AAUCU-UA--G--CCUC-UAUUU-UGAUAAGA-GGCAAGU----AAAAUGCUGAA----AAA
AE014073.1/1446627-1446475   GGGUGCCUGAGACUUUCUGUUUUCAGG------C--UAA--------------------------------------------------------------------------CCGGGAAUCAGAAAGACGAAGGCCCCGAC-------------------CGAUAU--------------------UUCUAUCAA--CUGUACU--GCACCCAU-UUUG--UUGGACGA-UGAA-AUGGA--A-UA--GCCC-CUAAU-AUGUCAAA-GCCAAAA---UACCCUUUUGAA----AAG
AP001918.1/2780-2928         GGGUGUCUGAGCCUUUCUGGUU-CAGG------CAAGAC--------------------------------------------------------------------------GCAGGUACCAGAAAUGCGAAGACCCCACU-------------------UGUUAAUC------------------CAUUAACU--CGUGAGGU--CUGCAUGA-AGUAC-CUUAACAC-UACU-GAUUG-UA--G--CCUC-UUCCUU----GCA-------------GAGAGGUCAAAGUUUAUG
AY686591.1/50436-50280       GGGCGCUUGAGGCUGUAUGCCG-AAAG------CGUUUU--------------------------------------------------------------------------GUGGACGGCAUGUAGCAGAAAGCCCCAGG-------------------CGAUUUUUU----------------UAUCAAUCAA-CCCAGGGC---CCACUGU-AAUGC-CUCAACAA-CAUU-AUAGU--A--G--CCCG-AUGAC-GGCCGAAA-GGCAAUG----GAGGGGCUGCG----AUG
X17311.1/246-398             GGGUGCUUGAGGCUGUCUGUCU-CAGG------CAUUAG--------------------------------------------------------------------------CUGAACGGCAGAUAGAGAAAAGCCCCGAG-------------------UGAUAUUU------------------UACCAUCAA-CCCGAGGC---CUCCUAU--AUG--CUGAACA--CAU--GUAGA-GU--G--CCUC-UUACU-GACCGUAA-GGUCAAGG-AGAAGAGAGCA------AUG
CP000036.1/3567623-3567472   GGGUGCUUGAGACUGUUUGUCU-CAGG------UAUUCA--------------------------------------------------------------------------CCGAAAGGCAGACAGAGAAAAGCCCCACC-------------------UGACU---------------------AUAAAUCAA-AGUGAGGC--UA--CCCU--AUGC-CUGAACAC-CAUA-AGG-U-UA--G--CCUC-UUACUCGUUGGAAAUCAACAC-----AGGGGGCUGGG---AAUG
AF550679.1/124252-124427     -GGCGCUUGAGGCUUUCUGCCU-CAUG-----ACGUGAAGGUGGUUU---------------------------------------------------------GUUGCCGUGUUGUGUGGCAGAAAGAAGAUAGCCCCGUAG----------------UAAGUUAAUUU----------------UCAUUAACCACCACGAGGC-----AUCCC-UAUGU-CUAGUCCA-CAUC-AGGAU--A--G--CCUC-UU-AC-CGCGCUUUGCGCAAGGA-GAAGAAGGCC-------AUG
D00364.1/184-341             GGGCGCUUGAGGCUGUAUGCCG-AAAG------CGUUUU--------------------------------------------------------------------------GUGGACGGUAUACAGCAGAAAGCCCCUGG-------------------AGAUUUUUU----------------UAUCAAUCAA-CCAAGGGC--UCUACUGU-AAUGC-CUAGACAA-CAUU-AUAGU--A--G--CCCG-AUAAC-CGCCGUAA-GGCAAUG----GAGGGGCUAUG----AUG
AY849933.1/863-715           GGGUGCCUGAGACUUUCUGUUUUCAGGC----UAACC------------------------------------------------------------------------------GGGAAUCAGAAAGACGAAGGCCCCGAC-------------------CGAUAU--------------------UUCUAUCAA--CCGAGGC--CAACGAA--UGAAC-CUAG-CAA-UUCA-GAUCU-UA--G--CCUC-UUACC-CGCCAUCC-GGC-AAGG-AGAA-AGGCU-------AUG
ABWM02000022.1/23364-23513   GGGUGCUUAAGACUUUCUGUCU-UGAG------CAUU-G--------------------------------------------------------------------------UUGAGGGACAGAAAGUGGAAAGCCCCG---------------------GGAAAU--------------------UUGCAUUUA-CCCGAGGC--UACCCCCU-CAACU-ACCCACAA-GUUG-AGGGU--A--G--CCUC-UUAUU-CUUUUUUU-GACAAGGA-GUAAAAGGC--------AUG
ABWL02000002.1/519511-519654 GGGUGCUUGAAGCUAUCUGCUU-CAGG------UACU------------------------------------------------------------------------------UUGCGGCAGAUAGAGAAAAGCCCCACU-------------------CGACU---------------------CUAAAUCGA--AUGAGGC-----CCCUA-UAUGC-CAG-ACA--CAUA-CAGGC-UA--G--CCUC-UUACC-CGCCGAAA-GGCAAGG----AG-AUGUUAGC---CAUG
AALF02000002.1/2188-2381     GGGUGCUUGAAGCUGUCUGCUU-UGGG------CAUUGUUUGAAUCAGUGCUGUAAGUGC--------------------------------CUUGGUAAAAAACAGUUGUUGUCAUAAAGCAGAUAGGAAAAAGCCCCGUA-------------------CUGAA---------------------GUUAAUCAA-UACGAGGC-----UCCCU-AAUGC-CUAG-CAA-CAUU-ACGGU--A--G--CUUC-UUACC-UGCUGAAA-GGCAAGAC--AUGGAGGCCAAA---UAUG
CP001063.1/928871-928696     GGGUGCUUGAGGCUAUCUGUCU-CAGG------CAUGAAC------------------------------------------------------------------------ACCAAAAGGCAGAUAGAGAAAAGCCCCAGUUAACAUUAC-GCGUCCUGC--------AAGA----------CGCUUAACAUUAA-UCUGAGGC---UCAAUC--CAU-G-CUGAACAC--AUGUAGGUU--A--G--CCUC-UUACG-UGCCGAAA-GGCAAGGA-GAAGCAGGCUAUG----AAG
AE016796.2/715565-715707     GGGCGCUUAGACAUACCCAUGUCGAAG------CGUUAG--------------------------------------------------------------------------CCAAAACAUGGAUAUGAAAAAGCCCCGAA-------------------UGAACU--------------------AUAAAUUCA-AACGAGGC---CU-UUAC-CAUGU-AUAAGCAA-CUUG-AUAAU--A--G--CCUC-UUACU-UC-----------AU-----AGGAGGCAAGU---UAUG
AALD02000001.1/197570-197416 GGGUGCUUGAAGCUGUCUGCUU-UAAGUGCUUGCA----UC----------------------------------------------------------------------AGGCUGAGAGUAGGCAGAGAAAAGCCCCGUA-------------------UCA-----A----------------UGUUAAUCAA-UACGAGGC---CCUCUGU-AAUG--CACGACAA-CAUU-ACGGU--A--G--CCUU-UUACC-CGCCGAAA-GGCAA-------GGAGGCUGAA---GAUG
ABXV02000074.1/20935-21088   GAUUGCUUUCCCCUAUCUGGUU-CAAG------CAUUUA--------------------------------------------------------------------------GUGAGAGCCAGAAAGAAGAAAGCCCCGAUA-----------------UAGUAGU--U----------------GUACUAUUA---UCGAGGC---UGCAAUU-CUUAA-CUUAUCAU-UUUG-AAUUG--C--G--CCUCCUUAUU-UAUAAGGA-GUCAAGG----AAAAUGAC--C----AAG
ACCI02000067.1/141766-141911 GGGUGCUUGGAUCAUUUUGGUU-CAAG------CAUU-A--------------------------------------------------------------------------GUGAGAGCCAAAAAGACGAAAGCCCCGAA-------------------UU-UAGAUG----------------UUAAUCUUAA-UCCGAGGC-----AGUCU-CAAACACACAACAA-UUUG-AUUCU-----G--UCUC-CUUUU-AGAAAAGG-AGUC-------AAGAGGA--------AUG
AALC02000011.1/85567-85374   GGGUGCUUGAAGCUGUCUGCUU-UGGG------CAUUGUUCGAAUCAGAUAGAGAGUUGC--------------------------------UUUGAAAUAGAGCAGAUGUUGCCAUAAAGCAGAUAGGAAAAAGCCCCGUA------------------------CUGA----------------CGUUAAUCAA-CACGAGGC-----UCCCU-AAUG--CACGACAA-CAUU-ACGGU--A--G--CCUU-UUACC-CGCCGAAA-GGCAAGGC--AAGGAGGCUGAA---UAUG
#=GC SS_cons                 :<<-<<<----<<<<<<<<<<_.____......______........................................................................._______>>>>>>>>>>---->>>>>----...................---------................----------.----<<<<...--<<<<-.<<<<_.________.>>>>.->>>>..-..>..>>>:.:::::.::::::::.:::::::....:::::::::::....:::
#=GC RF                      GGGUGCUUGAGucuuUCUGccU.cAgG......CAUuaa.........................................................................gucgaaaggCAGAaagaaAAAAGCCCCagu...................aGauAuUuu................UuauuAUcAA.uacGAGGC...cuacccu.cauGc.CUagaCAA.Caug.Agggu..A..G..CCUC.UUACc.ugccgAAA.gGCAAgG....AggAGGcuAaa....AUG
//
# STOCKHOLM 1.0

#=GF AC   RF01795
#=GF ID   FourU
#=GF DE   FourU thermometer RNA element
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:17630972
#=GF SS   Published; PMID:17630972; Bateman A
#=GF GA   60.00
#=GF TC   61.90
#=GF NC   35.40
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   17630972
#=GF RT   FourU: a novel type of RNA thermometer in Salmonella.
#=GF RA   Waldminghaus T, Heidrich N, Brantl S, Narberhaus F
#=GF RL   Mol Microbiol. 2007;65:413-424.
#=GF CC   FourU is a small thermoregulator element found upstream of the agsA gene
#=GF CC   in Salmonella species. The four Us occlude the Shine-Dalgarno (SD)
#=GF CC   sequence by base pairing. It has been suggested that this element is
#=GF CC   related to that found in Yersina pestis LcrF. Two further potential FourU
#=GF CC   regulators were found in S. aureus groES and B. melitensis dnaJ [1].
#=GF WK   FourU_thermometer
#=GF SQ   3


CP000647.1/1773227-1773291 GGACAAGCAAUGCUUGCCUUUAUGUUGAGCUUUUGAAUGAAUAUUCAGGAGGUUAAUUAUGGCAC
CP001144.1/2031534-2031470 GGACAAGCAAUGCUUGCCUUGAUGUUGAACUUUUGAAUAGUGAUUCAGGAGGUUAAUGAUGGCAC
CP001127.1/1302123-1302187 GGACAAGCAAUGCUUGCCUUAAUGUUGAACUUUUGAAUAGUGAUUCAGGAGGUUAAUGAUGGCAC
#=GC SS_cons               <<-<<<<<___>>>>>>>-----<<<<<-<<<<<<<<<____>>>>>>>>>->>>>>::::::::
#=GC RF                    GGACAAGCAAUGCUUGCCUUaAUgUUgAaCUuuUGAAUagugAUUCAggAGGUuAAugAUGGCAC
//
# STOCKHOLM 1.0

#=GF AC   RF01796
#=GF ID   frnS
#=GF DE   Fumarate/nitrate reductase regulator sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20070527
#=GF SS   Published; PMID:20070527
#=GF GA   60.00
#=GF TC   65.80
#=GF NC   56.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20070527
#=GF RT   Reprogramming of anaerobic metabolism by the FnrS small RNA.
#=GF RA   Durand S, Storz G
#=GF RL   Mol Microbiol. 2010;75:1215-1231.
#=GF RN   [2]
#=GF RM   20075074
#=GF RT   Translational regulation of gene expression by an anaerobically induced
#=GF RT   small non-coding RNA in Escherichia coli.
#=GF RA   Boysen A, Moller-Jensen J, Kallipolitis B, Valentin-Hansen P, Overgaard M
#=GF RL   J Biol Chem. 2010;285:10690-10702.
#=GF WK   FnrS_RNA
#=GF SQ   16


ABHL02000002.1/1575228-1575345 GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGCGCUCCAUA-UUGUCUUACUUCCUU---UUUUGAAUUACUGCAU--AGCA--CAAUUGAUUCGUACGACG-CCGACUUUGA---U-----GAGUCGGCUUUU
CP000653.1/2328462-2328346     GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGCGCUCCAUA-UUGUCUUACUUCCUU---UUUUGAAUUACUGCAU--AGCA--CAAUUGAUUCGUACAAUG-CCGACUA-AA---U-----UAGUCGGCUUUU
AE014613.1/1620721-1620604     GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGCGUUCUAUA-UUGUCUUGCUUCCUU---UUUUGAAUUACUGCAU--AGCA--CAAUUGAUUCGUACGACG-CCGGCUUAGA---U-----UAGUCGGCUUUU
BX950851.1/2262447-2262562     GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGCGCUCCAUA-UUGUCUUACUUCCUU---UUUUGAAUUACUGCAU--AGCA--CAAUUGAUUCACACCACG-CCGACAGU-----U-----UUGUCGGCUUUU
CU468135.1/1871882-1871996     GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGUGCUCCAAU-UUGUCCUUCUUCCUU---UUUUGAAUUGAUGCAU--AGCA--AAUUUGAUUCCUACGACA-CCGGCUUU-----------UAGCCGGUUUUU
AM286415.1/2309472-2309353     GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGCGCUCCAUAUUUGUAAUACUUUUAU---UUUUGAAUUACUGCAU--AGCA--CA--UAAUUGUUACGAUG-CCGAUGUUGUCUCA-----ACAUCGGCAUUU
CP000826.1/2871962-2871844     GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGUGCUCCAUAAUUGUCUUACUUUCUUAUAUUUAGAAUUACUGCAU--AGCA--C-AUUGAUUCAUACGAUG-CCGGU-UUAA---U------CACCGGCAUUU
ACNQ01000010.1/32764-32647     GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGCGCUCCAUAUUUGUUAUACUUUUAU---U-UUGAAUUACUGCAU--AGCA----UUUAAUUGUUACGGUG-CCGAUGUUGA---AA---AACAUCGGCAUUU
CP000901.1/2507910-2508030     GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGCGCUCCAUAUUUGUUAUACUUUU-A---UUUUGAAUUACUGCAU--AGCAUUUAAUUGUUACUGUCAACGACGGAUGAAAA---G-----UGAUCCACUUAU
ABJD02000101.1/846016-846135   GCAGGUGAAUGCAACGUUGAGCGAUGAACGU-UGUGCUCCAUAAUUGUAGUUUUUCUCA---UAUUGAGUUCUUGUAC--AGAA--UAAUUGACCACUGUAAUG-CCGAUGUAUA---U----UGCAUCGGCUUUU
AAUB01000020.1/15-132          GCCGGUGAUUGCACGGUCAAGCGAU-GGCGGUUGCGCUCCCUAUUUGUUAUACUUUUAU---U-UUGAAUUACUGCAU--AGCA----UUUAAUUGUUACGGUG-CCGAUGUUGA---AA---AACAUCGGCAUUU
ABVP01000026.1/412582-412461   GCAGGUGAAUACAACGUUGAGCGAUGAACGU-UGUGCUCCAUAAUUGUAGUUUUUCUCA---UAUUGAGUUCUU-AAUACAGAA--UAAUUGACCAUUAUUACA-CCGAUGUUUA---UU---AACAUCGGUUUUU
FM180568.1/1575675-1575792     GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGCGCUCCAUA-UUGUCUUACUUCCUU---UUUUGAAUUACUGCAU--AGCA--CAAUUGAUUCGUACGACG-CCGACUUUGA---U-----GAGUCGGCUUUU
BX571867.1/230895-230773       GCAGGUGAAAACAACGUUAAGCGAUGAACGU-UGUUCUCCGUAAUUGUAGUUUUUCUCA---CAUA-AGUCUUUAUAC--AGAA--UAAUUGCCCAUUCUUGUG-CCGAUAUUAU---UUUAUAAUAUCGGCUUUU
AE017220.1/1763236-1763119     GCAGGUGAAUGCAACGUCAAGCGAUGGGCGU-UGUGCUCCAUA-UUGUCUUACUUCCUU---UUUUGAAUUACUGCAU--AGCA--CAAUUGAUUCGUACGACG-CCGGCUUAGA---U-----UAGUCGGCUUUU
ABXV02000011.1/370001-369882   GCAGGUGAAUGCAACGUUGAGCGAUGAACGU-UGUGCUCCAUAAUUGUAGUUUUUCUCA---UAUUGAGUUCUUAUAC--AGAA--UAAUUGACCACUGUAAUG-CCGAUGUCUU---U----UACAUCGGCUUUU
#=GC SS_cons                   <<<<--<<<<<<<<<<<<________>>>>>.>>>>>>>----->>>>,,,,,,,,,,,...,,,,<<<<<<-<<<<_..>>>>..---->>>>>>,,,,,,,<.<<<<<<<___..._.....>>>>>>>>::::
#=GC RF                        gCagGUGAgugCAaCGucAAGCGAUGggCGu.UGcgcUCCAUAauuGuauUacUUcuuu...UuUUgagucacUgcaU..agcA..uAAUugacucuUacgAuG.CCGacguuaa...u.....acguCGGCuUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01797
#=GF ID   fstAT
#=GF DE   Fst antitoxin sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Predicted; Mafft;
#=GF SS   Predicted; RNAalifold;
#=GF GA   72.00
#=GF TC   72.20
#=GF NC   71.90
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.77 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   20156992
#=GF RT   Abundance of type I toxin-antitoxin systems in bacteria: searches for new
#=GF RT   candidates and discovery of novel families.
#=GF RA   Fozo EM, Makarova KS, Shabalina SA, Yutin N, Koonin EV, Storz G
#=GF RL   Nucleic Acids Res. 2010;38:3743-3759.
#=GF CC   It is located on the opposite strand of SprA1 sRNA (PMID: 22198463).
#=GF WK   Par_stability_determinant
#=GF SQ   22


AE015929.1/2256502-2256404 GCGAGUAGUGAGGGGAUUUUUGUUGGUG-U-GGCUAUAU--GUCACCUAU--UAAUUAUUUGUUGCGUUU---AUUAAGCCAAUGAGUAAAAAACGCAAUGGCACAGC
AP008934.1/2506940-2507035 UGCGGUAGUGAGGGGAUUUUU--UGAUG-C-GUCUUAAC--GUCGCCU------UCUAUUUAUUGCGUUUACUACUAAGCCAAUAAGUAAAAUACGCAACUGCACAGC
DQ008307.1/40-135          UGCGGUAGUGAGGGGAUUUUU--UGAUG-C-GACUUAAC--GUCGCCU------UCUAUUUAUUGCGUUUACUACUAAGCCAGUAAGUAAAAUACGCAACUGCACAGC
ACHE01000086.1/1746-1838   UGCAGUAGUGAGGGGAUUUUU-UAGGUG-U-GGCUAUA---GUCGCCU------AUUUAUUGUUGCGAUU---ACGUAGCCAAUGCGUAAAUAACGCAACAAUACAAC
ACJB01000054.1/75997-75903 UGUGGUAGUGAGGGGAUUUU---UGAUG-C-GGCUUAAC--GUCGCCU------UCUAUUUAUUACGUUUACUACUAAGCCAGUAAGUAAAAUACGCAACUGCACAGC
AP006716.1/2623440-2623538 CGCAAUAGUGAGGGGAUUUUU--AGGUG-C-UGGCUAAU--AUCGCCUAUUUUUUCUUAUUGUUACGUGU---ACGUAGCCAAUACGUAAAUAACGCAACAAUACAAC
ACFR01000012.1/63973-63880 CGCAAUAGUGAGGGGAUUUUUGUUGGUG-U-GGCUAUAU--GUCACCU------AUU-UUUAUUGCGUUU---ACUUAGCCAAUGAGUAAAAAACGCAAUGGCACAGC
ABSA01000004.1/2717-2811   UGCGGUAGUGAGGGGAUUUUUAUUGGUG-C-GGCUAUAU--GUCACCU------AUUUUGUAUUGCGUCU---ACUUAGCCAAUAAGAAAAAAACGCAAUGGCACAGC
ACJC01000084.1/1214-1308   UGUGGUAGUGAGGGGAUUUU---UGAUG-C-GGCUUAAC--GUCGCCU------UCUAUUUAUUGCGUUUACUAUUAAGCCAGUAAGUAAAGUACGCAACUGCACAGC
CABA01000077.1/143-235     UGCCGUAGUGAGGGGAUUUUU-UAGGUG-U-GACUAUA---GUCGCCU------AUUUAUCGUUGCGAUU---GCGUAGCCAAUGCGUAAAUAACGCAACAAUACAAC
CP000737.1/18464-18372     GGCAAUAGUGAGGGGAUUUUU-UAGGUG-U-GGCUAUG---GUCGCCU------AUUUAUUAUUGCGAUU---ACGUAGCCAAUGCGUAAAUAACGCAAUAAUACAAC
AJ938182.1/1418444-1418344 UGCAGUAGUGUGGGGAUUUUU-UCGAUGCU-GGCUUAUAAAGUCACCUAU--UAAUUAUUUGUUGCGUUU---ACUAAGCCAAUAAGUAUAAUACGCAACAGCACAGC
ACLP01000034.1/9958-9861   GGAAGUAGUGAGGGGAUUUUU--AGGUG-U-GACUAUA---GUCGCCUAUUUUUUCUUAUCGUUGCGAUU---GCGUAGCCAAUGCGCAAAUAAUGCGACGAUACAAC
DQ008306.1/31-129          UCCGAUAGUGAGGGGAUUUUU-UAGGUG-U-GGCUAUA---GUCGCCUAUUUUUUCUUAUCGUUUCGAUU---GCGUAGCCAAUGCGCAAAUAAUGCGACGAUACAGC
AM180066.1/444-354         UGCGGUAGCGAGGGAAUUUUU-UUGGUG-U-UACUA-----GUCGCCU------AUUUAUCAUUGCGUUU---GCGUAGUCAUUUCGCAGAUAAAGCAACGACGCAAC
DQ390456.1/47560-47471     GGCCGUAGUAAGGGGAUUUUU--UGGUG-U-GACUA-----GUCGCCU------AUUCGUCAUUACGCUU---GCGUAGCCAAUGCGCAAAUAUCGCAACGAGACAAC
CP000703.1/2592789-2592885 UGCCAUAGUGAGGGGAUUUAUUUAGGUGUU-GGUUAUUU--GUCACCU-----UUUUUAUUGUUGCGCGU---UCGUAACCAAUGUGCAAAAAACGCAACAAGACAGC
CP000029.1/586820-586729   UGCAAUAGUGUGGGGAUUUUU--AUGUG-U-GUCUAUG---GUUGCCU------AUUUAUUAUUGCAAUU---ACAUAUCCAAUGAGUAAAUAAUGCAAUAAUACAAC
EU366902.1/26166-26075     GGAAAUAGUGAGGGGAUUUUU--UGGUG-C-AGCU--AU--GUCGCCU-----UAUUAUUUGUUACGAUU---GUUUAGCCAAAACGUGAAAAUCGCAACAAUGCAUC
AP009351.1/2659412-2659323 CGCAAUAGUGAGGGGAUUUUUUUCGGUG-U-AGCU--AG--GUCGCCU------AUUUAUCAUCGUGUUU---GCGUAGCCAAUGCGUA---AACACAGUACCACUAA
GQ900478.1/17160-17260     UGCAGUAGUGUGGGGAUUUUU-UCGAUG-CUGGCUUAUAAAGUCGCCUAU--UAAUUAUUUGUUGCGUUU---ACUAAGCCAAUAAGUAUAAUACGCAACAGCACAGC
AB125341.3/7709-7616       GCAAAUAGUGAGGGGAUUUUUGUAGGUG-U-GGCUAUU---GUCGCCU------AUUUUUCCUUGCGAUU---ACGCAGCCAAUGCGUAAAUAACGCAAUAAUACAAC
#=GC SS_cons               :::::::(((,,,,,,,,,,,.,,,,,<.<.<<<_____..>>>>>,,......,,,,,,,<<<<<<<--...<<<_________>>>----->>>>>>>,,))):::
#=GC RF                    uGcagUAGugAGGGGAUUUUU.UuGGUG.c.ggcUauau..gucgCCU......aUUuuUugUuGCGuUU...gCguAGCCAAUacGcAAAaAaCGCaAcaacaCAaC
//
# STOCKHOLM 1.0

#=GF AC   RF01798
#=GF ID   g2
#=GF DE   G2
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19555452
#=GF SS   Published; PMID:19555452
#=GF GA   70.00
#=GF TC   102.40
#=GF NC   42.20
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19555452
#=GF RT   Identification of small RNAs in Mycobacterium tuberculosis.
#=GF RA   Arnvig KB, Young DB
#=GF RL   Mol Microbiol. 2009;73:397-408.
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   2


ABLM01000102.1/76080-76146 CUUCAGCGGGGGGCUUAUCGAUGCAUCCCCACCCCAUCCCUCGAGAUAAGAUCCCCCGCUGGCCCUC
ABQH01000203.1/2703-2637   CUUCAGCGGGGGGCUUAUCGAUGCAUCCCCACCCCAUCCCUCGAGAUAAGAUCCCCCGCUGGCCCUC
#=GC SS_cons               ::<<<<<<<<<<<<<<<<<<<<<___________>>>>------>>>>>>->>>>>>>>>>>:::::
#=GC RF                    CUuCaGCGGGGGgCUUaUCGaUGCAUCCCCACCCCAuCCCUCGAGAuAAGAuCCCCCGCuGgCCCUC
//
# STOCKHOLM 1.0

#=GF AC   RF01800
#=GF ID   gadd7
#=GF DE   growth arrested DNA-damage inducible gene 7
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:2658040
#=GF SS   Predicted;
#=GF GA   70.00
#=GF TC   181.30
#=GF NC   41.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   2658040
#=GF RT   Early clinical experience with a simple method for autotransfusion in
#=GF RT   cardiac surgery.
#=GF RA   Szecsi J, Batonyi E, Liptay P, Orosi P, Medgyessy I, Peterffy A
#=GF RL   Scand J Thorac Cardiovasc Surg. 1989;23:51-56.
#=GF WK   gadd7
#=GF SQ   2


U26834.1/1-753 G--GAAGCUGAGGUUUUUCCUAUGUCUGAACAAUGACGCCAUCGUUUUCUGGGUCUUCGAAGCAGUUGCAAAGAAAUGCCCAGAUGGAGGACAGAGGGCCAAACCACCCCAGUGAAUUCAUAACAGGAGAUAACUUGCUUAAGACCUGACUGUUUUUAAAAGCGAAUGCCAGUGAGUGAAAUGCCAGCUCCCUGUACAGUUACUAGAGCUCCUGGGAAUGCAUGGCCAGUGACACAAGUGAGAAUUGGAUGUUAUGACCGUCCAGAAAAGACAAGAUGAGAAAGUGCAGUAUUGACUGUCUUCAAACGCACCUGUCCUUGCUCAAGUGCUGGGAUUGUGUGCCAACGGCUAUGAUAGAUAUGAAUAGAGCACGAGAUAAUGUGCUUACAGAAAGUUGGUUGAAUUGAAUGCAAUUAAUGUUUGGAGGCACUUAGUCUUCUAGUGUUUGAAUGUGGAUGGAAUUAAAGCUGGGUUUGUAGUGAGCCAUUAGGAUUAUGGCAAAUGUCUAGUGUACAGAAUUCAGUGUAGGCCGGGAGUUGAGACUGGUGUGUGUUUAGUGGAUUAUCUGAUCAGCACAUGUGUGACAGUGUUGAUCACAAGUCAUUGCCAGCUCUGUUCAUUUUCUUCCCUGGUCUAACUCAAUAAUUGCCAUCAUGAAAAUUCUGGGUGACUUUUUGUGACUAAAGUCCCAUUGUAAGCCACAUUCUUUGUCCAGCAGUGCUCACUGACUGCUGAAAUAAAUGUUCAUUUGCAAC
L40430.1/1-754 CGGGAAGCUGAGGUUUUUCCUAUGUCUGAACAAUGACGCCAUCGUUUUCUGGGUCUUCGAAGCAGUUGCAAAGAAAUGCCCAGAUGGAGGACAGAGGGCCAAACCACCCCAGUGAAUUCAUAACAGGAGAUAACUUGCUUAAGACCUGACUGUUUUUAAAAGCGAAUGCCAGUGAGUGAAAUGCCAGCUCCCUGUACAGUUACUAGAGCUCCUGGGAAUGCAUGGCCAGUGACACAAGUGAGAAUUGGAUGUUAUGACCGUCCAGAAAAGACAAGAUGAGAAAGUGCAGUAUUGACUGUCUUCAAACGCACCUGUCCUUGCUCAAGUGCUGGGAUUGUGUGCCAACGGCUAUGAUAGAUAUGAAUAGAGCACGAGAUAAUGUGCUUACAGAAAGUUGGUUGAAUUGAAUGCAAUUAAUGUUUGGAGGCACUUAGUCUUCUAGUGUUUGAAUGUGGAUGGAAUUAAAGCUGGGUUUGUAGUGAGCCAUUAGGAUUAUGGCAAAUGUCUAGUGUACAGAAUUCAGUGUAGGCCGGGAGUUGAGACUGGUGUGUGUUUAGUGGAUUAUCUGAUCAGCACAUGUGUGACAGUGUUGAUCACAAGUCAUUGCCAGCUCUGUUCAUUUUCUUCCCUGGUCUAACUCAAUAAUUGCCAUCAUGAAAAUUCUGGGUGAC-UUUUGUGACUAAAGUCCCAUUGUAAGCCACAUUCUUUGUCCAGCAGUGCUCACUGACUGCUGAAAUAAAUGUUCAUUUGCAAC
#=GC SS_cons   :{{{{,<<<<<<<-----<<<<-<---<<<<-<<<____>>>->>>>->>>>>->>>>-->>>,{{--{{{{{---{{{{{{{{,,,,{{{{{{{{{{{,{{{{{{{-{{{{{,,,<<<<<-<<-<<-------<<<<<<<<<<<______>>>>>--->>>>>>--->>->>-->>>>>,,,,{{{{{{{{,,,,,,<<--<<<<_____>>>>---->>,,{{{{----{{{{,,{{{---{{{{{{{{{{,,,,[[[[[[[-[--[[[[[--[-[[[[,,((((--((((-(-((((((((,,,<<<<--<<<<<-<<______>>->>>>>->>>><<<___>>>,,)))-))))))-))))--)))),,,,,,,,<<<<<<-<<<<--<<<<<<<<_________>>>>>>>>->>>>->>>>>>,,,,]]]]-]--]]]]]---]-]]]]]]],,,,,,,<<<<______>>>>,,<<<<<_______>>>>>,}}}}}}}}}}-}}},<____>,}}}}-}}}}}}}}}}}},,}}}}}-}}}-}}}},,,,<<<<---<<<<<<<<<<-<<_____>>>>>>>>>>>>-->>>>,,,}}}--}}}}}}}},<<<<<-----<<<<______________>>>>---->>>>>,}}}}}}}}--.}}}}}--}},,,,,}}}}-<<<<<<<--<<<<<--<<---<<<<<<<________>>>>>>>->>-->>>>>--->>>>>>>:
#=GC RF        gggGaAGCuGagGUUUUUCCcaUGUcUgaaCAauGAcGcCaucGuucUCugGGUCcuCGAaGCAGuUGCaaagAAAcgCCCaGaUGGAGgaCaGaGGGCcaaaCCaCcCCaGuGAAuuCacAaCAGGAGAUAAcucGCuuaagaCcUGAcUGucuuUAAaaGCgaAUGCCAGuGAguGaaAUGcCagCuCCCUGUAcAGcUACcaGAGcUcCugGGAAUgCAUGGCCAGUGaCaCAAGugAGAacugGacguuAUGACCguCCaGaAAagaCaAGaUgaGaAAGuGCAGuauuGacuguCuuCaAAcgCaCcUguCCcUGCUcAAGUGCUgGGacUGuGcGCCAAcGGCUAuGaUaGacauGaauaGAGCaCGAGAUAAUGuGCcuACagaAAguugguuGAAUUGAAUGCaaccaacGucuGGagGCaCUUAGuCuccuAGuGucuGAAuGuGGacGGAAUUAAAgCugGGUUUGcaGcGAGCCauUAGGAUUauGGCAaacguCcaguGcaCAGAAUUCAGuGuAGGCCGGGaGcuGAGaCuGGUGuGUGuuuAGUGGacuAUcuGauCagCaCAuGUGUGACaGuGcuGauCacAaguCAUUGCCAGCuCuGucCAuuuuCUUcccuGGccUAAcUcAAUAAUUgCCaUcAUGaaaaUuCuGGGcgAc.cuuuGUGaCUAAAGuCccAuuGcaagccaCauucUuuGUcCaGCaGuGcUcAcUGaCuGCuGAaaUAaauGuUcAcuugCaac
//
# STOCKHOLM 1.0

#=GF AC   RF01802
#=GF ID   HSUR
#=GF PI   HSUR1
#=GF DE   Herpesvirus saimiri U RNA1/RNA2
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published; PMID:17381320
#=GF SS   Published; PMID:17381320
#=GF GA   50.00
#=GF TC   53.40
#=GF NC   43.80
#=GF TP   Gene; snRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000274; snRNA;
#=GF RN   [1]
#=GF RM   17381320
#=GF RT   The challenge of viral snRNPs.
#=GF RA   Conrad NK, Fok V, Cazalla D, Borah S, Steitz JA
#=GF RL   Cold Spring Harb Symp Quant Biol. 2006;71:377-384.
#=GF RN   [2]
#=GF RM   15916956
#=GF RT   Small nuclear RNAs encoded by Herpesvirus saimiri upregulate the
#=GF RT   expression of genes linked to T cell activation in virally transformed T
#=GF RT   cells.
#=GF RA   Cook HL, Lytle JR, Mischo HE, Li MJ, Rossi JJ, Silva DP, Desrosiers RC,
#=GF RA   Steitz JA
#=GF RL   Curr Biol. 2005;15:974-979.
#=GF WK   HSUR
#=GF SQ   4


M28071.1/1837-1695 ACACUACAUAUUUAUUUA--UUUAUUUCUUAGUAAUGUUUACUGGAACUUAAAUCUGU-GAUAACCUAAACUAAAAGUCUCA-AACAACCCGUUACUUGCU--GACCAAUUUUUGUAGGUACUGGGUGUAAAUA--U--GAUGACCGGUACCA
M21438.1/2-144     ACACUACAUAUUUAUUUA--UUUAUUUCUUAGUAAUGUUUACUGGAACUUAAAUCUGU-GAUAACCUAAACUAAAAGUCUCAAA-CAACCCGUUACUUGCU--GACCAAUUUUUGUAGGUACUGGGUGUAAAUA--U--GAUGACCGGUACCA
M28071.1/2665-2551 ACACUACAUAUUUAUUG---UUUAUUUAUAC------CUGAU--------AAUGCUGC-UUUAAUCACA-CACG---------AGGUAUC------GCUUC--UACUAAUUUUUGAAAGCGCUGGGUGUACAUA--UUUAAAAACCAGCGCUG
M55264.1/3425-3311 ACACUACAUAUUUAUUGUAUUUUAUUUAUUAAUGC--------------------UGCUUUAAACCUCA-CACA--------CA-------AGGAUUUGCUUCUACUAAUUUUUGAAAGCACUGGGUGUAUAUAGCU--AAAAACCAGUGCUA
#=GC SS_cons       ::::::::::::::::::..::::::::::<<<<<..-<<--........------<_.__________.>---.........--->>--.->>>>>----..--------------<<<<<<<<_________.._.._____>>>>>>>>:
#=GC RF            ACACUACAUAUUUAUUua..UUUAUUUaUuaguac..uuuAc........AAauCUGu.uuuAAcCuaA.CaaA.........AacaacC.gguacuUgcU..uACuAAUUUUUGaAgGcaCuGGGUGUAaAUA..U..aAaaACCaGugCcA
//
# STOCKHOLM 1.0

#=GF AC   RF01803
#=GF ID   GABA3
#=GF DE   Editing element of GABA-3 exon 9
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Gardner PP
#=GF SS   Published; PMID:17369310
#=GF GA   57.00
#=GF TC   58.40
#=GF NC   55.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   17369310
#=GF RT   Editing modifies the GABA(A) receptor subunit alpha3.
#=GF RA   Ohlson J, Pedersen JS, Haussler D, Ohman M
#=GF RL   RNA. 2007;13:698-703.
#=GF WK   GABRA3
#=GF SQ   52


S62908.1/1076-1129           AAAGUGGCAUAUGCGACGGCCAUGGACUGGUUCAUAGCCGUCUGUUAUGCCUUU
AANN01751877.1/2324-2271     AAGGUGGCGUAUGCGACGGCCAUGGAUUGGUUCAUAGCCGUCUGUUAUGCCUUU
X12362.1/1050-1103           AAAGUGGCAUAUGCGACGGCCAUGGAUUGGUUCAUGGCCGUGUGUUAUGCCUUU
AANH01000564.1/319153-319100 AAGGUGGCAUAUGCCACUGCCAUGGACUGGUUCAUGGCAGUGUGCUACGCCUUU
AAVX01049780.1/465-518       AAAGUGGCAUACGCCACUGCCAUGGAUUGGUUCAUUGCUGUGUGUUAUGCCUUC
DQ086494.1/320-373           AAGGUGGCCUAUGCCACGGCCAUGGACUGGUUCAUCGCCGUGUGCUACGCCUUC
AALT01589287.1/1066-1013     AAGGUGGCAUAUGCCACCGCUAUGGACUGGUUCAUCGCUGUGUGCUAUGCCUUC
AAFR03012717.1/28787-28734   AAAGUGGCCUAUGCCACAGCCAUGGAUUGGUUUAUUGCAGUGUGUUAUGCCUUU
AF411006.1/734-787           AAAGUAGCCUAUGCCACUGCCAUGGACUGGUUUAUAGCAGUGUGUUAUGCAUUU
BAAE01211982.1/3859-3806     AAAGUGGCCUACGCCACCGCCAUGGACUGGUUCAUUGCUGUGUGCUACGCUUUU
BX664715.25/63784-63731      AAAGUGGCGUAUGCUACCGCCAUGGACUGGUUCAUAGCUGUCUGCUAUGCCUUC
AANG01134232.1/591-644       AAAGUGGCUUAUGCGACAGCCAUGGACUGGUUCAUAGCUGUGUGCUAUGCUUUC
AAPN01143914.1/1278-1331     AAAGUGGCCUAUGCCACUGCCAUGGACUGGUUCAUUGCCGUCUGCUACGCCUUU
AAPY01578670.1/1538-1485     AAAGUGGCUUACGCAACCGCCAUGGACUGGUUCAUUGCUGUCUGUUACGCCUUU
CAAA01087468.1/18653-18706   AAAGUGGCCUAUGCCACAGCCAUGGACUGGUUCAUUGCUGUCUGCUAUGCAUUU
CAAE01015042.1/49047-49100   AAAGUGGCCUACGCCACAGCUAUGGACUGGUUCAUCGCUGUCUGCUAUGCCUUC
BC079777.1/996-1049          AAAGUGGCCUAUGCAACAGCCAUGGACUGGUUCAUUGCAGUCUGCUAUGCUUUU
AAQQ01555063.1/6155-6102     AAAGUGGCUUAUGCUACUGCCAUGGACUGGUUUAUUGCUGUUUGUUAUGCUUUU
AAYZ01114260.1/2259-2206     AAAGUGGCUUAUGCAACUGCCAUGGACUGGUUCAUUGCUGUCUGUUAUGCAUUU
ABDC01566860.1/715-768       AAGGUGGCUUAUGCAACAGCUAUGGAUUGGUUUAUUGCAGUGUGCUAUGCCUUU
S55933.1/1025-1078           AAAGUGUCCUAUGCGACUGCCAUGGAUUGGUUCAUAGCUGUCUGUUUUGCUUUU
AANU01122202.1/22130-22078   AAAGUGUCAUAUGCCACUGCCAUGGAUUGGUUCAUAGCUGUUUGCUUUG-CUUU
AY574250.1/913-966           AAGGUGGCUUAUGCAACGGCCAUGGACUGGUUUAUUGCAGUGUGCUAUGCCUUC
AAIY01397026.1/3714-3767     AAGGUGGCCUACGCCACAGCCAUGGAUUGGUUUAUCGCUGUGUGCUAUGCCUUC
X94342.1/883-936             AAGGUCUCCUAUGCCACCGCCAUGGACUGGUUCAUCGCCGUCUGCUUCGCAUUU
ABPL01005892.1/125-178       AAAGUGGCCUAUGCCACCGCCAUGGACUGGUUCAUGGCUGUGUGCUAUGCCUUU
ABVD01219697.1/1691-1638     AAAGUGGCUUACGCAACUGCCAUGGACUGGUUCAUAGCCGUGUGCUAUGCCUUU
BT072045.1/8-61              AAGGUGGCCUAUGCCACAGCCAUGGACUGGUUCAUUGCAGUCUGCUAUGCCUUU
ABRO01098209.1/8417-8364     AAGGUGGCCUACGCCACGGCCAUGGACUGGUUCAUCGCCGUGUGCUAUGCUUUU
AAWR02000829.1/58348-58401   AAAGUGGCUUAUGCGACAGCCAUGGACUGGUUCAUAGCCGUGUGCUACGCUUUU
AAKN02056084.1/33891-33944   AAAGUGGCGUACGCGACGGCCAUGGACUGGUUCAUAGCCGUCUGUUAUGCCUUC
ABRQ01310440.1/782-729       AAAGUGGCUUAUGCCACAGCAAUGGAUUGGUUUAUUGCAGUGUGCUAUGCCUUU
AAGV020371009.1/1739-1686    AAGGUGGCAUAUGCUACAGCCAUGGAUUGGUUUAUUGCAGUGUGCUAUGCCUUU
ABRP01300236.1/282-229       AAAGUGGCCUACGCCACGGCCAUGGACUGGUUCAUCGCCGUCUGCUACGCCUUC
ABRT010131250.1/5485-5432    AAAGUGGCAUAUGCAACUGCCAUGGACUGGUUUAUUGCUGUUUGUUAUGCAUUU
ABQO010663047.1/1990-1937    AAAGUGUCCUAUGCUACUGCCAUGGAUUGGUUCAUAGCUGUGUGCUUUGCCUUU
ABRR01322078.1/1211-1158     AAAGUGGCGUACGCGACGGCCAUGGACUGGUUCAUCGCGGUGUGCUACGCCUUC
EU124509.1/412-465           AAAGUGUCAUACGCUACUGCCAUGGACUGGUUCAUUGCCGUAUGCUUUGCCUUU
ABGA01372764.1/1905-1852     AAAGUGGCUUAUGCAACUGCUAUGGACUGGUUUAUUGCCGUUUGUUAUGCAUUU
ABPK01030344.1/336-389       AAAGUCUCCUAUGCCACAGCCAUGGAUUGGUUCAUUGCUGUUUGCUUUGCCUUU
ABRN01434353.1/10428-10375   AAAGUGUCUUAUGCGACCGCCAUGGAUUGGUUUAUAGCUGUUUGCUUUGCUUUU
AK290453.1/1132-1185         AAAGUGGCCUACGCCACCGCCAUGGACUGGUUCAUAGCUGUGUGCUAUGCCUUC
AAGU03083042.1/65636-65689   AAAGUGGCUUAUGCCACGGCCAUGGACUGGUUCAUAGCUGUGUGCUACGCCUUU
AAGW02050317.1/23800-23747   AAAGUGGCUUACGCCACUGCCAUGGACUGGUUCAUUGCUGUGUGCUAUGCUUUU
AAPE02017168.1/133730-133783 AAAGUGGCUUAUGCUACUGCCAUGGACUGGUUUAUUGCUGUUUGCUAUGCAUUU
AAGU03005368.1/31044-31097   AAAGUGUCGUAUGCAACUGCCAUGGAUUGGUUCAUAGCUGUUUGCUUUGCUUUU
AAEX03003042.1/539261-539208 AAGGUGGCUUAUGCCACUGCUAUGGAUUGGUUCAUUGCAGUGUGCUAUGCCUUU
X54244.1/1109-1162           AAGGUGGCCUACGCCACUGCCAUGGAUUGGUUUAUAGCGGUGUGCUAUGCCUUU
BC035055.1/1046-1099         AAAGUGUCCUAUGCUACCGCCAUGGACUGGUUCAUAGCUGUCUGCUUUGCUUUU
AAWZ02026476.1/2453-2506     AAAGUGGCCUAUGCAACUGCCAUGGACUGGUUCAUGGCCGUCUGUUAUGCCUUU
CAAB02000558.1/34536-34483   AAGGUGGCCUACGCCACCGCCAUGGACUGGUUCAUGGCGGUGUGCUACGCCUUU
AAQR03160834.1/5873-5820     AAAGUCGCCUAUGCCACCGCCAUGGACUGGUUCAUAGCCGUGUGCUACGCCUUU
#=GC SS_cons                 <<<--<<<-<<-<<<<<<<<-<<<<<____>>>>>->>>>>>->>>>->>>>>>
#=GC RF                      AAAGUgGCuUAUGCcACcGCCAUGGACUGGUUCAUuGCgGUgUGCUAUGCcUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01804
#=GF ID   Lambda_thermo
#=GF DE   Lambda phage CIII thermoregulator element
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:2532257
#=GF SS   Published; PMID:2532257; Bateman A
#=GF GA   50.00
#=GF TC   70.10
#=GF NC   45.20
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   2532257
#=GF RT   Alternative mRNA structures of the cIII gene of bacteriophage lambda
#=GF RT   determine the rate of its translation initiation.
#=GF RA   Altuvia S, Kornitzer D, Teff D, Oppenheim AB
#=GF RL   J Mol Biol. 1989;210:265-280.
#=GF RN   [2]
#=GF RM   16438677
#=GF RT   RNA thermometers.
#=GF RA   Narberhaus F, Waldminghaus T, Chowdhury S
#=GF RL   FEMS Microbiol Rev. 2006;30:3-16.
#=GF CC   There is an evidence supporting presence of a riboswitch upstream of the
#=GF CC   thermometer.[2] 
#=GF WK   Lambda_phage
#=GF SQ   5


M13767.1/3-60              UAAGGAGCACACCAUGCAAUAUGCCAUUGCAGGGUGGCCUGUUGCUGGCUGCCCUUCC-
CP000243.1/1246604-1246546 UAAGGAGCACACCAUGCAAUAUGCCAUUGCAGGGUGGCCUGUUGCUGGCUGCCCUUCCG
AY736146.1/34404-34346     UAAGGAGCACGCCAUGCAAUAUCAUUUUGCCGGGUGGCCCAUUGCUGGCUGCCCUUCUG
CP000026.1/2520723-2520781 UAAGGAGCACGCCAUGCAAUAUAGUUUUGCCGGGUGGCCCAUUGCUGGCUGCCCUUCUG
CP001144.1/624595-624537   UAAGGAGCACGCCAUGCAAUAUCGUCUUGCCGGGUGGCCCAUUGCUGGCUGCCCUUCUG
#=GC SS_cons               :::<<-<<<--<<<-<<<<<<-<<<<<<____>>>>>>->>>>>>>>>->>>>>:::::
#=GC RF                    UAAGGAGCACgCCAUGCAAuaUgccaUUGCcGGGuggcCuaUUGCUGGCUGCCCUUCuG
//
# STOCKHOLM 1.0

#=GF AC   RF01807
#=GF ID   GIR1
#=GF DE   GIR1 branching ribozyme
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Predicted; Infernal;
#=GF SS   Published; PMID:16141078
#=GF GA   100.00
#=GF TC   115.90
#=GF NC   66.20
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000588; autocatalytically_spliced_intron;
#=GF DR   GO; 0008380; RNA splicing;
#=GF RN   [1]
#=GF RM   16141078
#=GF RT   An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme.
#=GF RA   Nielsen H, Westhof E, Johansen S
#=GF RL   Science. 2005;309:1584-1587.
#=GF RN   [2]
#=GF RM   12458083
#=GF RT   DiGIR1 and NaGIR1: naturally occurring group I-like ribozymes with unique
#=GF RT   core organization and evolved biological role.
#=GF RA   Johansen S, Einvik C, Nielsen H
#=GF RL   Biochimie. 2002;84:905-912.
#=GF RN   [3]
#=GF RM   19667762
#=GF RT   Group I introns: Moving in new directions.
#=GF RA   Nielsen H, Johansen SD
#=GF RL   RNA Biol. 2009;6:375-383.
#=GF WK   GIR1_branching_ribozyme
#=GF SQ   12


AJ938153.1/1498-1693 UUUUGGUUGGGUUGGGAAGUAUCAUGGCUAAUCA-CCAUG-AUGCAAUCGGGUUGAACACUUAAUUGGGUUAAAACGG-----UGGGGG------ACG-A---UCC-CGUAA----CAU------------------CCGUCCU-A------------------------ACGGCGACAGACUGCACGGCCCUGCC-UCUUAGGUGUGU-UCAAUGAACAGUCGUUCC------GAAA---GGAAGCAUCCGGUAUCCCAAGACAAUCAAAU
AM497929.1/1-198     CUGUUAUUUAUGAC---CGU--------UGUUGU---------GCGAUGGGGUUCAUACCUUUAUC-UGCCAAAACGGGACCUCUGUUG------AGGUA---UAA-CCAAU----AUU------------------CCGUACUAAGGAUUUC--G-------GUCCGGAACGUCUAGAGACUACACGGCAGACCAAUUUUGUGGUGGUAUGAAUGGAUAGUCCCUAG------UUACCAUCUAGGCAUCCCAUAC------AAAAUGGUUA
AM497930.1/1-209     CUGUUAUU--------GAGGGCGUU-------CU---AGU-GUGCAAUGGGGUUCAUACCUUUAUU-UGCCAAAACGGGACCUCUGUUGAGGUAUAAA-AUUCUAA-CGAAU----UGA-------------AUAUUCCGUACU-AAGGAUUU--A-------AUCCGGAACGUCUAGAGACUACACGGCA-AACC-AAUUUGGUGGUA-UGAAUGGAUAGUCCCUAG-----UGAACCAUCUAGGCAUCCCAUAC------AAAAUGGUUA
AM497931.1/1-200     CUGUUAUUG-------AAGGACGU----UCUAGA-------GUGCGAUGGGGUUCAUACCUUUAUC-UGCCAAAACGG-----GACCUC------UGU-U---GAG-GUAUA----UAU----------UGAAUAUUCCGUACU-AAGGAUUU--A-------AUCCGGAACGUCUAGAGACUACACGGCAG-ACCAUUGUUGGUGGUA-UGAAUGGAUAGUCCCUAG-----UGAACCAUCUAGGCAUCCCAUAC------AAAAUGGUUA
AM497932.1/1-207     CUGUUAUU--------GAGGACGUU-------CU---AGU-GUGCAAUGGGGUUCAUACCUUUAUU-UGCCAAAACGG-----GACCUC------UGU-U---GAG-GUAUA--AUUCU----AACGAAUUAAUAUUCCGUACC-AAGGAUUU--A-------AUCCGGAGCGUCUAGAGACUACACGGCA-AACC-AAUUUGGUGGUA-UGAAUGGAUAGUCCCUAGU----UGAACCAUCUAGGCAUCCCAUAC------AAAAUGGUUA
AM167886.1/221-427   CUGUUAUUA-------AAGGACGUU-------UU---AGU-GUGCGAUGGGGUUCAUACCUUUAUU-UGCCAAAACGG-----GACCUC------UUU-U---GAG-GUAUA-GAUUCU---AACGAAUUGAAUAUUCCGUACU-AAGGAUUU--A-------AUCCGGAACGUCUAGAGACUACACGGCA-AACC-AUU--GGUGGUG-UGAAUGGAUAGUCCCUAG-----UGAACCAUCUAGGCAUCCCAUAC------AAAAUGGUUA
U80250.1/227-423     CUGUUAUU----------GAACGGC-----CGUU---GUU-GUGCGAUGGGGUUCAUACCUUAAUC-UGCCAAAACGG-----GACCUC------UGU-U---GAG-GUAUA---ACCA-------------AUAUUCCGUACUAAGGAUUUC--G-------AUCCAGAACGUCUAGAGACUACACGGUAG-ACCAAUUUUGGUGGUA-UGAAUGGAUAGUCCCUAG------UAACCAUCUAGGCAUCCCAUAC------AAAAUGGUUA
DQ768723.1/878-1093  CUGUUAUUG-------GAGGAUAUU-------GA---AGUCAUGCGAUGGGGUUUAUACUUUUAUU-UGCCAAAACGG-----GACCUC------UGU-U---GAG-GUAUA--GAUCUCGCAAGAGGUUGAAUAUUCCGUACU-AAGGAUCUCUG-------AUCCGGAAAGUCUAGAGACUACACGGCAAAGCC-AUAGUGGCUAGUAUAAAUGGAUAGUCCCUAG-----UUAACCAUCUAGGCAUCCCAUAC------AAAAUGGUUU
AM167878.1/227-437   CUGUUAAUUGU-----GGGUGUAUU--------U---AGU-GUGCAAUGGGGUUCAUACCUUAAUU-UGCCAAAACGG-----GACCUC------UGU-U---GAG-GUAUAAAAUUCU-GAAAAGAAUUGAAUAUUCCGUACU-AAGG--UA--C-------AUCCGGAACGUCUAGAGACUACACGGCA-AACCAAUUUUGGUGGUA-UGAAUGGAUAGUCCCUAG------UAACCAUCUAGGCAUCCCAUAC------AAAAUGGUAA
Y10190.1/227-437     CUGUUAAUU-------GUGGGUGUA---UUUAGU-------GUCGAAUGGGGUUCAUACCUUAAUU-UGCCAAAACGG-----GACCUC------UGU-U---GAG-GUAUAAAAUUCU-GAAAAGAAUUGAAUAUUCCGUACU-AAGG--UA--C-------AUCCGGAACGUCUAGAGACUACACGGCA-AACCAAUUUUGGUGGUA-UGAAUGGAUAGUCCCUAG------UAACCAUCUAGGCAUCCCAUAC------AAAAUGGUAA
DQ388519.1/880-1088  CAGCUGUUUUGAUAC-AUGCUCGACUU-UCUUUUUCUCUU-GUGCAAUGGGGUUUAUGAGUUAAUU-AGCCAAAACGG-----GACCUU------AAA-A---AGGUGUAAG----UAA------------------CCGUACUAAGUUCGUA--A-------GAACGGAAUGUCUAGAGACUACACGGCUG-AGCGAUUUAGCUCUCA-UAAAUGGAUAGUCCUCAG-----UAUACCAUCUGAGCAUCCCAUAC------AAAAUGGUUA
AJ001399.1/226-444   CUGUUAUUG-------GAAUUUGAU--------A---GUU-GUGCGAUGGGGUUCAUACCUUAA-C-UGCCAAAACGG-----GACCCC------UUU-U---GGG-GUAUA--AAUCU-UGUAAAAGGAUUAUAUUCCGUACU-AAGGAUAU--UUGAUAAUAUCCGGAAUGUCUAGAGACUACACGGCA-AGCC-AAUU-GGUGGUA-UGAAUGGAUAGUCCCUAGUUUUUUUUACCAUCUAGGUAUCCCAUAC------AAAAUGGUAA
#=GC SS_cons         :[[[[[[[[.......,,<<<<<<<.....____...>>>.>>>>,((((((,,AAAAAA,,,,,,.BBBB,,,<<<<.....<<<<<<......___._...>>>.>----....>>-.............----->>>><<_.________.._......._________>>,,,<-<<<<<---bbbb--<<<._____>>>aaaa.aa------>>>>>><<<<.....________>>>>,,,)))))),,......,]]]]]]]]:
#=GC RF              CuguuauUu.......aaGcacgau.....uuuu...auc.gugCaAuGGGgUUcAUaccUUaAUu.uGCCAAAACGG.....ggccuc......ugu.u...gag.guAua....ccu.............AUAUUCCGUaCU.AaGgauuu..a.......AUcCGGAAcGuCUAGAGACUaCACGGCagAgCC.auUUuGGcggua.UgAAUGGAuAGUCCcuaG.....UuaAcCAUCuagGCAuCCCaUAC......AaAaugguaA
//
# STOCKHOLM 1.0

#=GF AC   RF01808
#=GF ID   MicX
#=GF PI   A10
#=GF DE   MicX Vibrio cholerae sRNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Gardner PP
#=GF SS   Predicted; CMfinder
#=GF GA   75.00
#=GF TC   96.60
#=GF NC   71.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17590231
#=GF RT   RNase E-dependent processing stabilizes MicX, a Vibrio cholerae sRNA.
#=GF RA   Davis BM, Waldor MK
#=GF RL   Mol Microbiol. 2007;65:373-385.
#=GF WK   MicX_sRNA
#=GF SQ   10


CP000626.1/331571-331760     AUAAUAAC--GAUAAGGGCGA-CGUAA--AGUCGCCCAUUUUGUCUCUUCU--UAACAU--UAAUUGGUUUGGCCGCCGAC-AAGUUA-AGAAGCUUCAAUUCUGGCGUUACGCAUAGCUGGCUGUUAGCUCUAUUCCUUACUAG-UUCACGACUAACAGUUU-UUGUAACCA-AAACCUGAGCUUAG-CUCGGGUUUUUUUAUG
ABCH01000001.1/19775-19585   AUAAUAAC--GAUAAGGGUGAUCGCAA--GGUCACCCGUUUUUUUGUCUUGUUUGACACU-CAAUUGGUUUGGCCGCCGAC-AAGUCAGAUAAGA----UCACUGGUGUUACGUAUAGCUGGCUGUUACCAGGAUUCCUUACUAU-C--ACGAAUAACAGUUUCUUGUAACCGAU-GCCUGAGCUUAGUCUCGGGCGUUUUCUUU
AAND01000001.1/379408-379215 AUAAGAAAGACAAAAGAGCGACCGU-U-AGGUCGCUC--UAUAUUGGCAUUUUUAUUACAUCAUUUGGUUUGGCCGCCGAU-CAGUAAUAAAAAU---AACCCUCAGGUUACGCAUAGCUGGCUACUAAUCAGGUUCCUUACGCUAUUAAUGAUUAGUGGUUU-UUGUAACUC-UAACCCAGGUACUUACUUGGGUUUUUUUAU-
AAZW01000001.1/161990-161797 AUAAGAAAGA-AAAAGAGCGACCUUCG-UGGUCGCUC--UAUAUUGGCAUUUUUAUUACAUCAUUUGGUUUGGCCGCCGAU-CAGUAAUAAAAAU---AACCCUCAGGUUACGCAUAGCUGGCUACUAAUCAGGUUCCUUACGCUAUUAAUGAUUAGUGGUUU-UUGUAACUC-UAACCCAGGUACUUACUUGGGUUUUUUUAU-
AAMR01000001.1/281169-280976 AUAAGAAAGA-CAAAGAGCGACCUUAU-AGGUCGCUC--UGUAUUGGCAUUUUUAUUACAUCAUUUGGUUUGGCCGCCGAU-CAGUAAUAAAAAU---AACCCUCAGGUUACGCAUAGCUGGCUACUAAUCAGGUUCCUUACGCUAUUAAUGAUUAGUGGUUU-UUGUAACUC-UAACCCAGGUAUUUACUUGGGUUUUUUUAU-
AAWP01000001.1/1050-855      AGAAUAACUAGAAAAGGGCGACCAUAU--GGUCGCCCUUAUAUUUAGCAUCGAUAUUACA-AUUUUGGUUUGGCCGCCGAU-CAGUAAUAUCAGG--CUAUAUUGGCGUUACGCAUAGCUGGCUGUUAGCUUAGUUCCUUACGCU-UUAAUCACUAACAGUUUCUUGUAACCA-UAACCUGAGUCUAGACUCAGGUUUUUUUAU-
AAKK02000017.1/55451-55647   AGAAUAACUAGAAAAGGGCGACCACAU--GGUCGCCCUUAUACGUAGCACGGAUAUUACA-AUUUUGGUUUGGCCGCCGAU-CAGUAAUAUCUUGGCUUUUAUUGGCGUUACGCAUAGCUGGCUGUUAGCUUAGUUCCUUACGAU-UCAAUCACUAACAGUUU-UUGUAACCA-UAACCUGAGUUUAGACUCAGGUUUUUUUAU-
ACCV01000131.1/51068-50879   AUAAGAAC--GAUAAGGGCGACCGCGA--GGUCGCCCAUUUUGUAUCUCGA--CUUAACA-AUUUUGGUUUGGCCGCCGAU-CAGUUAAGAAGAGUGCAAUUCUGGCGUUACGCAUAGCUGGCUGUUAGUGAGAUUCCUUACUGU-UU-ACUUCUAACAGUUU-UUGUAACCA-AAACCCGG--UUUGUCCCGGGUUUUUUUAU-
BA000038.2/471144-471335     AGGAUAAG--AAUAAGAGCGACCGUAUCAGGUCGCUCGUUUUAUUACUUUU--UAUUACC-CAUUUGGUUUGGCCGCCGAUCUAGUAAUAGAAAG---UAUCAUGGCGUUACGCAUAGCUGGCUGUUAGCUUUGUUCCUUACGAU-U--AUCACUAACAGUGU-UUGUAACCAAUUGCCUGAGUUUGUCCUCAGGCUUUUUUGU-
AAWQ01000001.1/189388-189583 AGAAUAACUAGAAAAGGGCGACCAUAU--GGUCGCCCUUAUAUUUAGCAUCGAUAUUACA-CUUUUGGUUUGGCCGCCGAU-CAGUAAUAUCCUGC-UUCUAUUGGCGUUACGCAUAGCUGGCUGUUAGCUUAGUUCCUUACGAU-UCAAUCACUAACAGUUU-UUGUAACCA-UAACCUGAGUCUUGACUCAGGUUUUUUUAU-
#=GC SS_cons                 :::::::::::::::<<<<<<<<____..>>>>>>>>,,,,,,,<<<---<<<<<<<<<-.---<<<<<______>>>>>-.-->>>>>>>>>->...>>,,,,,,,<<<<<<-------<<<<<<<<<________________._______>>>>>>>>>-.->>>>>>,,.,<<<<<<<<<____>>>>>>>>>:::::::.
#=GC RF                      AuAAuAAcuAgAaAAGgGCGACCguau..GGUCGCcCuUuuuaUuaccauugcuauuACa.cauUuGGuUUGGCCgCCgAU.cAGUaauagcaag...uauacUggcGUUACgCAUAGCUggCuGuUAgcuuggUUCCUUACgaU.UuAAugAcUAaCaGuuU.UuGUAACca.uaaCCcGaGuuUugaCuCgGGuuUUUUUaU.
//
# STOCKHOLM 1.0

#=GF AC   RF01809
#=GF ID   symR
#=GF DE   SymR antitoxin
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:17462020
#=GF SS   Published; PMID:17462020
#=GF GA   61.00
#=GF TC   62.20
#=GF NC   60.40
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   17462020
#=GF RT   An antisense RNA controls synthesis of an SOS-induced toxin evolved from
#=GF RT   an antitoxin.
#=GF RA   Kawano M, Aravind L, Storz G
#=GF RL   Mol Microbiol. 2007;64:738-754.
#=GF WK   SymE-SymR_toxin-antitoxin_system
#=GF SQ   20


CU928163.2/5124400-5124476   AGUCAUAACUGCUAUUC-UCCAGGAAUAGUGAUUGUGAUUAGCGAUGCGGGUGUGUUGGCGCACAUCCGCACCGCGCU
ABHU01000001.1/389853-389929 AGUCAUAACUGCUAUUC-CCUAUAAAUAGUGAUUGUGAUUAGCGGUGCGGGUGUGUUGGCGCACAUCCGCACCGCGCU
CU928158.2/3159788-3159712   AGUCAUAACUGCUAUUC-UCCUGAAAUAGUGAUUGUGAUGAGCGGUGCGGGUGUGUUGGCGCACAUCCGCACCGCGCU
J03150.1/2069-1993           AGUCAUAACUGCUAUUC-UCCGAUAACAGCGAUUGUGAUUAGCGGUGCGGGUGUGUUGGCGCACAUCCGCACCGCGCU
AAJW02000024.1/23047-22971   AGUCAUGAUUACUAUUC-UCCAUAAAUAGUGAUUGUGAUGAGCGGUGCGGGUGUGUUGGCGCACAUCCGCACCGCGCU
BAAW01000314.1/3854-3930     AGUCAUAAUUGCUAUUC-CGUAUAAAUAGUGAUUGUGAUGAGCGAUGCGGAUGUGUUGGCGCAUAUCCGCAUCGCGCU
CAAS01000756.1/1650-1574     AGUCAUGAUGGCUAUUC-UCCUGGAAUAGUGAUUGUGAUGAGCGAUAUGGCCGUGUUCCCGCACGGCCAUAUCGCGCU
ABKX01000006.1/282336-282260 AGUCAUGAUUGCUAUUC-UCGGUAAAUAGUGGUUGUGACGAGCGGUGCGGGUGUGUUGGCGCACAUCCGCACCGCGCU
FM180568.1/4906003-4906079   AGUCAUGAUUACUAUUC-UCGUGAAAUAGGGAUUGUGAUGAGCGGUGCGGGUGUGUUGGCGCACAUUCGCACCGCGCU
CP000857.1/4764132-4764208   AGUCAUGGUCUCUAUUC-CUUUUCAAUAGGGAUUGUGAUUAGCGGUGCGGGCGUGUUGGCGCACGCUCGCACCGCGCU
ACBF01000003.1/198787-198863 AGUCAUGAUGGCUAUUC-UCCUAAAAUAGUGAUUGUGAUUAGCGAGGCGCUCGUGUUGCAGCACGGGCGUCUUGCGUU
CP001113.1/4749379-4749455   AGUCAUGAUGGCUAUUU-CCAUUGAAUAGUGAUUGUGAUUAGCGAGGCGCUCGUGUUGCAGCACGGGCGUCUUGCGUU
ABAM02000001.1/421238-421313 AGUCAUGAUGGCUAUUC--CCUAAAAUAGUGAUUGUGAUGAGCGAUAUGGCCGUGUUCCCGCACGGCCAUAUCGCGCU
Y11005.1/4191-4114           AGUCAUGAUGGCUAUUCCUCUAGAAAUAGUGAUUGUGAUUAGCGAGGCGCUCGUGUUGCAGCACGGGCGUCUUGCGAA
X17591.1/2190-2114           AGUCAUGAUUGCUAUUC-CUUCGAAAUAGGGAUUGUGAUUAGCGAGGCGCUCGUGUUGCAGCACGGGCGUCUUGCGAU
CP000886.1/4782918-4782994   AGUCAUGAUGGCUAUUC-CUUCGAAAUAGUGAUUGUGAUGAGCGAUAUGGCCGUGUUCCACCACGGCCAUAUCGCGCU
ABFF01000010.1/33389-33313   AGUCAUGAUGGCUAUUC-CUUGAAAAUAGUGAUUGUGAUGAGUGAGAUGGCCGUGUUCCCGCACGGCCAUAUCGCGCU
ABFG01000006.1/234107-234031 AGUCAUGGUCUCUAUUC-CUUUUCAAUAGGGAUUGUGAUUAGCGAGGCGCUCGUGUUGCAGCACGGGCGUCUUGCGAA
ABWL02000016.1/286479-286556 AGUCAUGGUCUCUAUUCCUAUUCCAAUAGUGAUUGUGAUUAGCGAGGCGCUCGUGUUGCAGCACGGGCGUCUUGCGAA
CP001383.1/4578086-4578162   AGUCAUGAUUACUAUUC-UCUAUAAAUAGUGAUUGUGAUUAGCGGUGCGAGUGUGUUGGCGCACAUCCGCACCGUGCU
#=GC SS_cons                 <<<<<<<<--<<<<<<<._____>>>>>>>-->>>>>>>>-<<<-<<<<<<<<<<<____>>>>>>>>>>>->>>:::
#=GC RF                      agUCAugaUugCUAUUc.ucuuugAAUAGcGAuugUGAuuAGCGaugCGgccGUGuUGgcgCACggcCGcauCGCGcU
//
# STOCKHOLM 1.0

#=GF AC   RF01810
#=GF ID   pntA
#=GF DE   pntA sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19531245
#=GF SS   Published; PMID:19531245
#=GF GA   54.00
#=GF TC   54.00
#=GF NC   53.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19531245
#=GF RT   Identification of candidate structured RNAs in the marine organism
#=GF RT   'Candidatus Pelagibacter ubique'.
#=GF RA   Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ,
#=GF RA   Breaker RR
#=GF RL   BMC Genomics. 2009;10:268.
#=GF WK   Pelagibacter_ubique
#=GF SQ   10


AACY020043448.1/763-824      UUUUAUGGAUAAUGAAAACCAUAAAAAUACCUGGAACAAUUUUACAAAAUUUGUGUUGUGGG
AAPV01000001.1/326636-326575 UUUUAUGGACAAUCAAGACCAUAAGAAUACCUGGAAUAAUUUCACAAAGUUUGUGUUGUGGG
AACY023236858.1/1041-1102    UUUUAUGGAUAAUAAAAACCAUAAAGAUGCUUGGAUUAAUUUCACUAAAUUUGUGUUGUGGG
AACY023782316.1/994-1055     UUUUAUGGAUAAUGAAAACCAUAAAAAUACCUGGAACAAUUUUACUAAAUUUGUGUUGUGGG
AACY022713819.1/171-110      UUUUAUGGAUAAUGAAAACCAUAAAAAAACCUGGAACAAUUUUACAAAAUUUGUGUUGUGGG
AACY023941244.1/682-743      UUUUAUGGAUAAUGAAAACCAUAAAAAUACCUGGAAUAAUUUUAUAAAAUUUGUGUUGUGGG
AACY020724196.1/672-733      UUUUAUGGAUAAUGAAAACCAUAAAAAUACCUGGAAUAAUUUUACAAAAUUUGUUUUAUGGG
AACY020917115.1/270-209      UUUUAUGGAUAAUGAAAACCAUAAAAAUACCUGGAAUAAUUUUACAAAAUUUGUUUUGUGGG
AACY020036207.1/1115-1054    UUUUAUGGAUAAUGAAAACCAUAAAAAUACCUGGAAUAAUUUUACAAAAUUUGUGUUAUGGG
AACY023876655.1/876-815      UUUUAUGGAUAAUGAAAACCAUAAAAAUACCUGGAAUAAUUUUACAAAAUUUGUGUUGUGGG
#=GC SS_cons                 <<<<<<<<__________>>>>>>>>---<<<<<<<<<<___________>>>>->>->>>>
#=GC RF                      UUUUAUGGAUAAUgAAAACCAUAAAAAUACCUGGAAuAAUUUUACAAAAUUUgUGUUGUGGG
//
# STOCKHOLM 1.0

#=GF AC   RF01811
#=GF ID   PtaRNA1
#=GF DE   Plasmid transferred anti-sense RNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20220307
#=GF SS   Published; PMID:20220307
#=GF GA   47.00
#=GF TC   48.20
#=GF NC   46.80
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   20220307
#=GF RT   A novel family of plasmid-transferred anti-sense ncRNAs.
#=GF RA   Findeiss S, Schmidtke C, Stadler PF, Bonas U
#=GF RL   RNA Biol. 2010;7:120-124.
#=GF WK   PtaRNA1
#=GF SQ   16


ABBK01000836.1/13023-13093 UUGCCAUACUUCACCUCUCAAGCAGGUGUUG--UUGUGGAAGUGCCGGCCGGUUGCC----GCCGGCCGGUGCGCUU
ABBL01001689.1/12636-12564 UUGCCAUGCUUCACCUCUCUAGCAGGUGUUGAUACGUGGAAGUGCCGGCCGGUUGCC----GCCGGCCGGUGCGCUU
CP000539.1/2701179-2701249 UUGCCAUGAUUCACCUCUCUAACAGGUGGGU---UGUGGAAGUGUCGGCCGGCCC--C-ACGCCGGCCGACGCGCUU
CR555306.1/49879-49951     UUGCCAUGAUUCACCUCUCCAUCAGGUGUUG---AGUGGACGUGCCGGCUGGCCCGCA-AUGCCGGCCGGCACGCUU
BX571965.1/3877448-3877518 UUGCCAUACUUCACCUCUCAAGCAGGUGUUG--UUGUGGAAGUGCCGGCCGGUUGCC----GCCGGCCGGUGCGCUU
AM778842.1/16676-16746     UUGCCAUGAUUCACCUCUGUGGUAGGUGGGU---UGUGGAAGUGUCGGCCGGCCC--C-ACGCCGGCCGGCGCGCUU
ACKA01000056.1/33168-33240 UUGCCAUGCUUCACCUCUCUAGCAGGUGUUGAUACGUGGAAGUGCCGGCCGGUUGCC----GCCGGCCGGUGCGCUU
CP000514.1/1919475-1919548 CUGUCAUGUGUCACCUCUCUGUCAGGUGGUA---UGUGGAAAUGCGGGCCGGUGCACCAUCACCGGCCCGUGUGCUU
AM747720.1/196863-196793   UUGCCAUACUUCACCUCUCAAGCAGGUGUUG--UUGUGGAAGUGCCGGCCGGUUGCC----GCCGGCCGGUGCGCUU
CP000542.1/3727911-3727841 UUGCCAUGAUUCACCUCUGUGGUAGGUGGGU---UGUGGAAGUGUCGGCCGGCCC--C-ACGCCGGCCGGCGCGCUU
CP000450.1/679737-679808   UUGUCAUAAUUCACCUCUCCAGUAGGUGUUG---AUUGAAAGUGCCGGGCUGGUUGU--GGCCAGCCCGGUGCGCCU
CP000450.1/2385523-2385452 UUGUCAUAAUUCACCUCUCCAGUAGGUGUUG---AUUGAAAGUGCCGGGCUGGUUGU--GGCCAGCCCGGUGCGCCU
AM039952.1/2484380-2484309 UUGCCAUGAUUCACCUCUCCAUCAGGUGGGU--UAGUGGAAGUGUCGGCCGGCCC--U-ACGCCGGCCGACGCGCCU
CP000438.1/1316061-1315990 UUGCCAUGAUUCACCUCUCCAUCAGGUGGGU--UAAUGGAAGUGUCGGCCGGCCC--C-ACGCCGGCCGACGCGCCU
AE014073.1/2606276-2606347 UUGUCAUAAUUCACCUCUCCAGUAGGUGUUG---AUUGAAAGUGCCGGGCUGGUUGU--GGCCAGCCCGGUGCGCCU
CP000521.1/792290-792219   UUGUCAUAAUUCACCUCUCCAGUAGGUGUUG---AUUGAAAGUGCCGGGCUGGUUGU--GGCCAGCCCGGUGCGCCU
#=GC SS_cons               :::<<<--<--<<<<<_______>>>>>-->...-->>>--<<<<<<<<<<<<____..__>>>>>>>>>>>>::::
#=GC RF                    UUGcCAUgcUUCACCUCUCuAgcAGGUGuug...ugUGgAAGugcCGGcCgGcucgc..acgCcGgCCGgcgCGCuU
//
# STOCKHOLM 1.0

#=GF AC   RF01812
#=GF ID   Pxr
#=GF DE   Pxr regulatory sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20489016
#=GF SS   Published; PMID:20489016
#=GF GA   100.00
#=GF TC   129.20
#=GF NC   60.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF RN   [1]
#=GF RM   20489016
#=GF RT   Adaptive evolution of an sRNA that controls Myxococcus development.
#=GF RA   Yu YT, Yuan X, Velicer GJ
#=GF RL   Science. 2010;328:993.
#=GF RN   [2]
#=GF RM   27621281
#=GF RT   Spontaneous Reversions of an Evolutionary Trait Loss Reveal Regulators of
#=GF RT   a Small RNA That Controls Multicellular Development in Myxobacteria.
#=GF RA   Yu YN, Kleiner M, Velicer GJ
#=GF RL   J Bacteriol. 2016;198:3142-3151.
#=GF RN   [3]
#=GF RM   29133885
#=GF RT   A conserved stem of the Myxococcus xanthus sRNA Pxr controls sRNA
#=GF RT   accumulation and multicellular development.
#=GF RA   Yu YN, Cooper E, Velicer GJ
#=GF RL   Sci Rep. 2017;7:15411.
#=GF CC   Downregulates genes responsible for the formation of fruiting bodies in
#=GF CC   Myxococcus xanthus, inhibiting the transition from growth to development
#=GF CC   in the presence of abundant nutrients.[1] Two-component system operon
#=GF CC   (histidine kinase gene and a Ïƒ54 response regulator) is associated with
#=GF CC   production and processing of Pxr sRNA.[2] Folds into 3 steam loops. SL1
#=GF CC   and SL 2 are highly conserved across mycobacteria and SL1 is necessary for
#=GF CC   the regulatory function. However, a conserved eight-base-pair segment of
#=GF CC   the variable SL3 is necessary for PxR accumulation and multicellular
#=GF CC   development.[3]
#=GF WK   Pxr_sRNA
#=GF SQ   2


CP000113.1/1258215-1258322 AAGCGAGGCUGAAGGCGGUUCCCCCCCACCCCUUCAGCACUUCCGGUGAGUCACCUUGAGAAGA-CCCGCGGCCCGGCACCUCUUUGGGGUGUCGGGCCGCCUUCUUUU
AAMD01000048.1/41147-41039 AAGCGAGGCUGAAGGUGGUUCCCCCCCACCCCUUCAGCACUUCCGGUGAGUCACCUUUAGAAGAACCCGCGGCCCGGUACCCUCUUGGGGUAUCGGGCCGCCUUCUUUU
#=GC SS_cons               ::::<<<<<<<<<<<-<<<________>>>>>>>>>>>->>>,,<<<<___>>>>---<<<<<-----<<<<<<<<<<<<<<_____>>>>>>>>>>>>>>>>>>>:::
#=GC RF                    AAGcgaGGcuGaaGGuGGuUcccccccaCCCCuuCagCACucccGGuGAGUCaCCUUuaGaaGAAcccGcGGcccGgcacccuuUUGgggugcCgggCCgCCuuCuUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01813
#=GF ID   rdlD
#=GF DE   rdlD antitoxin
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Predicted; Gardner PP;
#=GF SS   Predicted; Gardner PP;
#=GF GA   50.00
#=GF TC   51.20
#=GF NC   48.50
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   URL; http://srnamap.mbc.nctu.edu.tw/gene_query.php?acc=sRNAG0029;
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   12123448
#=GF RT   Molecular characterization of long direct repeat (LDR) sequences
#=GF RT   expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide
#=GF RT   and a cis-encoded small antisense RNA in Escherichia coli.
#=GF RA   Kawano M, Oshima T, Kasai H, Mori H
#=GF RL   Mol Microbiol. 2002;45:333-349.
#=GF WK   LdrD-RdlD_toxin-antitoxin_system
#=GF SQ   52


U00096.2/1268547-1268611       UUCUGGUU-CAAGAUUAGCCCCCGUUCUGUUGUCAGGU-UG-UACCU-CUCAACGUGCGGGGGUUUUCU
CP001164.1/4545387-4545450     GUCUAGGUUCAAGAUUAGCCCCCGUGGUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUU--
AP009048.1/1270901-1270965     UUCUGGUU-CAAGAUUAGCCCCCGUUCUGUUGUCAGGU-UG-UACCU-CUCAACGUGCGGGGGUUUUCU
CP001164.1/1636702-1636766     UGAUGGUU-CAAGAUUAGCCCCCGUUCUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
CP000948.1/1308788-1308852     UUCUGGUU-CAAGAUUAGCCCCCGUUCUGUUGUCAGGU-UG-UACCU-CUCAACGUGCGGGGGUUUUCU
CU928160.2/3765623-3765686     GUCUAGGUUCAAGAUUAGCCCCCGUUAUGUUGUCAGGU-AC-AUACC-UGCAACGUGCGGGGGUUUU--
CP000948.1/1309857-1309922     GUCUGGUUUCAAGAUUAGCCCCCGUUUUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
CP000036.1/1833334-1833269     UUCUGGUUUCAAGAUUAGCCCCCGUUCUAUUGUCAGGU-UA-AACCU-CUCAACGUGCGGGGGUUUUCU
BA000007.2/4442282-4442345     GUCUAGGUUCAAGAUUAGCCCCCGUGGUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUU--
U00096.2/1269616-1269681       GUCUGGUUUCAAGAUUAGCCCCCGUUUUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
CP000802.1/3728641-3728704     GUCUAGAGUCAAGAUUAGCCCCCGUGGUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUU--
CU928163.2/4161481-4161544     GUUUGGGUUCAAGAUUAGCCCCCGUGAUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUU--
AP009048.1/1271970-1272035     GUCUGGUUUCAAGAUUAGCCCCCGUUUUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
AE005174.2/4509509-4509572     GUCUAGGUUCAAGAUUAGCCCCCGUGGUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUU--
CP000948.1/1309322-1309387     GUCUGGUUUCAAGAUUAGCCCCCGUUCUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
CP000034.1/1171413-1171478     GUCUGGUUUCAAGAUUAGCCCCCGUUUUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
CP000800.1/1360632-1360696     UGAUGGUU-CAAGAUUAGCCCCCGUUCUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
AE014073.1/1265919-1265984     GUCUGGUUUCAAGAUUAGCCCCCGUUUUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
AP009048.1/1271435-1271500     GUCUGGUUUCAAGAUUAGCCCCCGUUCUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
CP000036.1/1832799-1832734     GUCUGGUUUCAAGAUUAGCCCCCGUUUUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
CP000036.1/3545747-3545810     GUUUGGGUUCAAGAUUAGCCCCCGUGAUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUU--
U00096.2/3698159-3698222       GUCUAGAGUCAAGAUUAGCCCCCGUGGUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUU--
AP009048.1/3940279-3940216     GUCUAGAGUCAAGAUUAGCCCCCGUGGUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUU--
CU928162.2/4136462-4136525     GUCUAGGUUCAAGAUUAGCCCCCGUGAUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUU--
AP009240.1/1337157-1337221     UUCUGGUU-CAAGAUUAGCCCCCGUUCUGUUGUCAGGU-UA-AACCU-CUCAACGUGCGGGGGUUUUCU
CP000946.1/2655216-2655151     GUCUGGUUUCAAGAUUAGCCCCCGUUUUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
CP000970.1/1947771-1947707     UUCUGGUU-CAAGAUUAGCCCCCGUUCUGUUGUCAGGU-UG-UACCU-CUCAACGUGCGGGGGUUUUCU
CU928145.2/1365693-1365758     GUCUGGUUUCAAGAUUAGCCCCCGUUUUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
U00096.2/1269081-1269146       GUCUGGUUUCAAGAUUAGCCCCCGUUCUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
CU928161.2/3914771-3914836     GUCUAGAUGCAAGAAUGGCCCCCGUGAUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUUCU
CP000800.1/4011999-4012064     GUUCAGGUUCAAGAAUGGCCCCCGUGAUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUUCU
CU928158.2/3612102-3612167     GUGUAGGUUCAAGAAUGGCCCCCGUGAUGUUGUCAGGU-GC-AUACC-UGCAAUAUGCGGGGGUUUUCU
AAMJ02000001.1/310597-310662   GUUUGGAUGCAAGAAUGGCUCCCGUGGUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUUCU
ABKX01000002.1/256421-256356   GUUUGGGUUCAAGAUUAGCCCCCGUGAUGUUGUCAGGU-GA-AUACC-UACAACGUGCGUUGGUUUUCU
AACY021297865.1/214-148        GUUGAGGAUCAAGGUUAGCCCCCGUUUUGUUGCCAGGU-UU-AUACCGAACAACGUGCGGGGGUUUUCU
BAAW01000824.1/1035-1100       GUCUGGAGUCAAG-UUAGCCCCCGUUUUGUUGCCAGGU-UU-AUACCGAACAACGUGCGGGGGUUUUCU
CU928158.2/3611620-3611684     GUUUGGGUUCAAGAUUAGCCCCC-UCAUAUUGUCAGGU-GC-AUACC-UGCAACAUGCGGGGGUUUUCU
BAAW01007045.1/159-224         GUCUAGAUGCGAGGUUAGCCCCCGAUACGUUGCCAGGU-UU-AUACC-AACAACGUGCGGGGGUUUUCU
ABHM02000002.1/768378-768437   GUCUGGUUUCAAGAUUAGCCC------UGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
ACDJ01000026.1/205972-206037   GUUCAGGUUCAAG-UCAGCCCCCGUUUUGUUGCCAGGU-UU-AUACCGAACAACGUGCGGGGGUUUUCU
ABAN01000001.1/255710-255645   GUUUGGGUUCAAG-UUAGCCCCCGUCAGGUUGCCAGGU-UU-AUACCAGUCAACGUGCGGGGGUUUUCU
AE014613.1/2521594-2521658     GUCUGGGGUCAAG-UUAGCCCCCGUAAUGUUG-CCGGUGAA-UACCG-AACAAUGUGCGGGGGUUUUCU
ABEW01000004.1/282038-281972   GUUGAGGAUCAAGUUUAGCCUCCGUCAGGUUGCCAGGU-UU-AUACCAGUCAACGUGCGGAGGUUUUCU
Z26657.1/1498-1562             GUCUGGAGUCAAG-UUAGCCCCCGUAAUGUUGUCCGGU-GAAUACCG-AACAAUGUGCGG-GGUUUUCU
BAAW01001321.1/910-844         GUUCAGGUUUGAGAGUAGCCCCCGAUACGUUGCCAGGU-UG-AUACCAAACAACGUGCGGGGGUUUUCU
AAJV02000001.1/68674-68609     GUUCGGGUUCAAGAUUAGCCCCCGUUAUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUUCU
CU928164.2/4212861-4212926     GUUAAGGUUCAAGAUUAGCCCCCGUGAUGUUGUCAGGU-GC-AUACC-UGCAACGUGCGGGGGUUUUCU
ACGN01000005.1/33137-33202     GUUUGGGUUCAAGAUUAGCCCCCGUGAUGUUGUCAGGU-GC-AUACC-UGCAAUAUGCGGGGGUUUUCU
ACBF01000002.1/223649-223584   GUUGAGGUUCAAG-UUAGCCCCCGUCAGGUUGCCAGGU-UU-AUACCAGUCAACGUGCGGGGGUUUUCU
ABAK02000001.1/4632451-4632387 GUCUAGGAUCAAG-UUAGCCCCCGUAAUGUUGCC-GGU-GA-AUACCGAACAAUGUGCGGGGGUUUUCU
FM200053.1/2401289-2401353     GUCUAGGGUCAAG-UUAGCCCCCGUAAUGUUGCC-GGU-GA-AUACCGAGCAAUGUGCGGGGGUUUUCU
CP001509.3/1258539-1258604     GUCUGGUUUCAAGAUUAGCCCCCGUUUUGUUGUCAGGU-UU-UACCU-CUCAACGUGCGGGGGUUUUCU
#=GC SS_cons                   ::::::::::::::::<<<<<<<<<--<<<<<--<<<_.__.__>>>.-->>>>>->>>>>>>>>::::
#=GC RF                        GUcUgGgUUCAAGAUUAGCCCCCGuuauGUUGUCaGgU.uu.aucCu.uuCAACgUgCGGGGGUUUUCU
//
# STOCKHOLM 1.0

#=GF AC   RF01814
#=GF ID   rhtB
#=GF DE   rhtB sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19531245
#=GF SS   Published; PMID:19531245
#=GF GA   55.00
#=GF TC   57.00
#=GF NC   52.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19531245
#=GF RT   Identification of candidate structured RNAs in the marine organism
#=GF RT   'Candidatus Pelagibacter ubique'.
#=GF RA   Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ,
#=GF RA   Breaker RR
#=GF RL   BMC Genomics. 2009;10:268.
#=GF WK   Pelagibacter_ubique
#=GF SQ   14


AACY023290537.1/381-299        UUAUGCUAAAAUUUAUAAGAUAGUCCUUCUUAGCCAUCUUUAGCUCCCGGUUUU--U-A-AGGACUAUC-CAACUCAUUAAAAUGCUU
AAPV01000001.1/904764-904848   UGAUAUUAUCAUUCCUAAGAUAGUCCUAUUUAGCCAUCUUUAGCUCCCGGUUUUAUU-U-AGGACUAUC-CAAACAACAAAAUGCUUC
CP000084.1/1297698-1297616     AUGGUAUCUUCAAACUUAGAUAGUCCAUCUUAGCCAUCUUUAGCUCCCGGUUUU--U-U-UGGACUAUC-CAAACAACAAAAUGCUUC
ABVS01000001.1/1317618-1317536 GAGUGAUAUUAUGUAUUUGAUAGUCCUUCUUAGCCAUCUUUAGCUCCCGGUUUU--U-A-AGGACUAUC-CACGCAUACUUAAAAUGU
AACY023574107.1/79-139         ---------------------AGUCCUUCUUAGCCAUCUUUAGCUCCCGGUUUU--U-A-AGGACUAUCUAUACUCAAAAUGCUUC--
AACY020471298.1/1159-1077      UGUGAUAAAUUUUCCAUAGAUAGUCCUUCUUAGCCAUCUUUAGCUCCCGGUUUU--U-A-AGGGCUAUC-CAUCCAAUCAAAAUGCUU
AACY023559914.1/352-423        -----------GCUAUCUGAUAGUCCUUCUUAGCCAUCUUUAGCUCCCGGUUUU--U-A-AGGACUAUCUGCACUUGAAAUGUUCCC-
AACY023219241.1/614-530        UGAUAAUAUUAUAUUUAAGAUAGUCCUAUUUAGCCAUCUUUAGCUCCCGGUUUU-AUUU-AGGACUAUC-CAAACCUUUAAAAUGCUU
AACY023302908.1/1224-1306      UGUGAUAAAUUUUCCUUAGAUAGUCCUUCUUAGCCAUCUUUAGCUCCCGGUUUU--U-A-AGGGCUAUC-CAUCUAAUCAAAAUGCUU
AACY020453971.1/1551-1635      UGAUAUUAUCAUUUCUAAGAUAGUCCUAUUUAGCCAUCUUUAGCUCCCGGUUUU-AUUU-AGGACUAUC-CAAACAACAAAAUGCUUC
AACY022011012.1/756-674        AUGAUAUUAUACUACUUAGAUAGUCCUAUCUAGCCAUUUUUAGCUCCCGGUUUU--U-U-AGGACUAUC-CAGUUCUCAUGAAAAAAA
AACY020028678.1/1521-1605      UGAUAAUAUCAUUUUUAAGAUAGUCCUAUUUAGCCAUCUUUAGCUCCCGGUUUU-AU-UUAGGACUAUC-CAAACGACAAAAUGCUUC
AACY021297163.1/833-749        UGAUAAUAUCAUAUUUAAGAUAGUCCUAUUUAGCCAUCUUUAGCUCCCGGUUUU-AUUU-AGGACUAUC-CAAAUCUUUAAAAUGCUU
AACY023519131.1/1102-1171      -------------UAUUUGAUAGUCCUUCUUAGCCAUCUUUAGCUCCCGGUUUU--U-A-AGGACUAUCUGCACUUGAAAUGUUCCC-
#=GC SS_cons                   ::::::::::::::::::<<<<<<<<<----<<<<_____________>>>>--..-.-.>>>>>>>>>.::::::::::::::::::
#=GC RF                        ugauaaUAuuauuucUuAGAUAGUCCUucUUAGCCAUCUUUAGCUCCCGGUUUU..U.u.AGGACUAUC.cAaauaauaAaAauccuu
//
# STOCKHOLM 1.0

#=GF AC   RF01815
#=GF ID   rpsB
#=GF DE   rpsB sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19531245
#=GF SS   Published; PMID:19531245
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19531245
#=GF RT   Identification of candidate structured RNAs in the marine organism
#=GF RT   'Candidatus Pelagibacter ubique'.
#=GF RA   Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ,
#=GF RA   Breaker RR
#=GF RL   BMC Genomics. 2009;10:268.
#=GF WK   Pelagibacter_ubique
#=GF SQ   4


AACY023816545.1/62-195    CACACAUGGG--UGC-G----G-----------------CA-----------G-----CAAUC-C-UG------CCAUCCGGU-GUUGU-U---UUUUGGCAGUCGCGCUGCGCUAACGCAACCGCUCCUGCUACA-----GCAGA-----------------AAACAGCUCUCA--CCCAUGGAGGUUUAACCGGUAAA------AGGAGAUUGGC--
AACY022185521.1/386-528   CACACAUAAACCGGCACAUGGUUCUGGGUGUUGGGGGUCUGCUUUAAGACUUCUGAUCGAAU---------------CGUGGUUUCUAU-U---U-------------------------UUCUUUU-------------------ACAAAAAG------UUUAAGUAGAACGGGGGUUUAUGGAGGCCUAACCCAUACAA-----AGGAAA--UUAAA
AACY023834473.1/1343-1500 CACACACGGG--GGC-G----G-----------------CA-----------G---CUUUC---C-UG------CCAUCCGGU-GUCUU-UAUGUACCUGUCAUGCCGCAUUUAUUGCGGCAUCUUUAGCCAGACCCCGCAACCAGUGCGGGGUGACAAUAUGAAAAGACUCUCC--UCCGUGGCGGAUUAACCGGUAAAAGGA-UUGUAG--------
AACY023788472.1/590-729   CACACGCGGG-CAAU-G----CGGC-----------CUUCG----------GG--G--AGACAUCCCGACAGUCGC-UCCGGU-GUCUGAAAUCUCAGGUUUUCCGCCAAGUUAUGGCGUUUUUCUGAGAC----------------------------------CAGAUGACAGG-CCCGCGGUGGACCAACCGGAGAAGAUCUUAU-----------
#=GC SS_cons              (((-((((((.(,,,.<....<---...........---<<..........-<.._______..>.>>......>>.,,,,,,.<<<<<.<..._____________________________________...............________......____>>>>>>,,,,,).))))))))):::::::::::::::.....::::::..:::..
#=GC RF                   CaCACacGGg.CgGC.G....gucu...........gUcCg..........uG..aucaaAU..C.cG......cC.UcCGGU.gccuu.U...UuuuggUuaucgCgcAgUuAUuGCGuuuuuuUUAguc...............acaaaaag......uUuAAaaggcuCuagG.cCCguGGuGGacUAACCGGUAAAA.....AGgAgA..uua..
//
# STOCKHOLM 1.0

#=GF AC   RF01816
#=GF ID   RsaA
#=GF DE   RNA Staph. aureus A
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19786493
#=GF SS   Published; PMID:19786493
#=GF GA   50.00
#=GF TC   81.90
#=GF NC   46.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0042710; biofilm formation;
#=GF RN   [1]
#=GF RM   19786493
#=GF RT   A search for small noncoding RNAs in Staphylococcus aureus reveals a
#=GF RT   conserved sequence motif for regulation.
#=GF RA   Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C,
#=GF RA   Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
#=GF RL   Nucleic Acids Res. 2009;37:7239-7257.
#=GF RN   [2]
#=GF RM   24651379
#=GF RT   A non-coding RNA promotes bacterial persistence and decreases virulence by
#=GF RT   regulating a regulator in Staphylococcus aureus.
#=GF RA   Romilly C, Lays C, Tomasini A, Caldelari I, Benito Y, Hammann P, Geissmann
#=GF RA   T, Boisset S, Romby P, Vandenesch F
#=GF RL   PLoS Pathog. 2014;10:e1003979.
#=GF RN   [3]
#=GF RM   28379505
#=GF RT   The RNA targetome of Staphylococcus aureus non-coding RNA RsaA: impact on
#=GF RT   cell surface properties and defense mechanisms.
#=GF RA   Tomasini A, Moreau K, Chicher J, Geissmann T, Vandenesch F, Romby P, Marzi
#=GF RA   S, Caldelari I
#=GF RL   Nucleic Acids Res. 2017;45:6746-6760.
#=GF CC   Represses the translation of the transcriptional regulator MgrA by binding
#=GF CC   to its mRNA, enhances biofilm formation and decreases bacterial
#=GF CC   virulence.[2] Other mRNAs, including SsaA-like enzymes involved in
#=GF CC   peptidoglycan metabolism and the secreted anti-inflammatory FLIPr protein
#=GF CC   were validated as direct targets of RsaA.[3]
#=GF WK   Rsa_RNA
#=GF SQ   7


AASB02000218.1/20944-21082   AGUUAACCAUUACAAAAAU-U--GUAUAG-AGUAGCGACUGUAUAAUUUCUAUUGAGGUUAACGUUUAUAUGUAGUGAUAGUAGUU-AAAGUUCUCCCAA---GG-AAGACUACU-------CGGGUACA-CUUUGCUA----UGAGCAAAGUGUACUUU
ACJB01000048.1/6761-6895     AGUUAACGAUUACAAAGGA-U--AUAUUGG-GUAGCGACUGUAUAUUCUCUA---AAGUUAACU-UAAUACGUAGU---AGUGGUU-AAAGUUCUCCCAA---GG-A-UACUACU-------AGGAAGCA-CACUUCGAGUUCUCCGGAGUGUGUUUCUU
ACFR01000002.1/333063-332930 AGUUAACGAUUACAAAGAA-U--AUAUUGG-GUAGCGACUGUAUAUUCUC---UGAAGUUAACU-UAAUACGUAGU---AGUGAUU-AAAGUUCUCCCAA---GG-A-UACUACUA----GGAAGGCACA-CUUCGAGU----UCUCCGAAGUGUGCUUU
AE015929.1/355648-355784     AGUUAACGAUGACAGUGAA-U--AUAUUGA-GUAGCGACGGUAUAUUCUA---UGAGGUUAACU-AUAUACGUAGU---AGUGAUUUAAAGUUCUCCCAA---GG-A-UACUACAA---CAUAAGAGCCUAGUACAUCU----UAAUUGUACAGGCUCUU
AP008934.1/2193098-2192965   AGUUAACUGUUACAG-ACA-U--GUAUUGA-GUAGCGACAAUAUA----C---AACAGUUAAUA-UUAAAUUAAGU---AGUGAUUAAAAGUUCUCCCAA---AC-A-CACUACAUUCAACAAAGGCACA-CUUAUUUA----UGUGAUGAGCGUGCCUU
AP006716.1/2405577-2405444   AGUUAGCAAUUUA--UGAAUA--AUAUUGA-GUAGCGACAAUAUUUUCAU---AGUUGUUAAUG-UU---CAGAGU---AGUAAUU--AAGUUCUCCCAAAACAU-A-UACUACACU--AUAAUAGCCUG-AGGCAUAG----UAAGUGCCUCAGGUUAU
ACLP01000011.1/14896-15018   AGUUAAUAAAU----CAAA-AUUGUGCUGG-GUAGCGACAGCACUUUUGCGA-UU-UGUUAAUG-UU---CAGAGU---AGUAAUG--AAGUUCUCCCAA---ACCA-UACUACU------UGAAGUACA-CUUUUU---------UAAAAGUGUACUUU
#=GC SS_cons                 :<<<<<<<-------<<<<.<..<<<<<<_._______>>>>>>>>>>>-...--->>>>>>>,.,,,,,,,,,,,...<<<<<<<.-----<<<_____...>>.>.>>>>>>>,....,,,<<<<<<<.<<<<<<__....___>>>>>>>>>>>>>:
#=GC RF                      AgUUAaCcAUUAcAacgaa.u..gUacuGa.GUAGCGACaguAcauucgc...ugagGuUAAcu.UuAuAcguAGU...aGUagUc.AAAGUUcuCCCAA...ag.A.gAcuACua....uaaaggcaCg.cuccgcua....UaagcggagcGugccuU
//
# STOCKHOLM 1.0

#=GF AC   RF01817
#=GF ID   RsaB
#=GF DE   RNA Staph. aureus A
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19786493
#=GF SS   Published; PMID:19786493
#=GF GA   55.00
#=GF TC   58.50
#=GF NC   38.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19786493
#=GF RT   A search for small noncoding RNAs in Staphylococcus aureus reveals a
#=GF RT   conserved sequence motif for regulation.
#=GF RA   Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C,
#=GF RA   Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
#=GF RL   Nucleic Acids Res. 2009;37:7239-7257.
#=GF WK   Rsa_RNA
#=GF SQ   2


CP000255.1/1846919-1846975 UAUUAUUAGUGUUAAUUGUAGCGCAUCCCAAUUAAAUAUUGCAACCUAUUUUAUU---AU
BA000018.3/1778009-1778068 AAUUAUUAGUGUUAAUUGUAGCGCAUCCCAAUUAAAUAUUGCAACCUAUUUUAUUAAAAU
#=GC SS_cons               ::::::::<<<<<<____>>>>>>,,,,<<<<_____>>>>------<<<<<___>>>>>
#=GC RF                    aAUUAUUAGuGuUAAUUGUAgCgCAUCCCAAUUAAAUAUUGCAACCUAUuuuAUUaaaAU
//
# STOCKHOLM 1.0

#=GF AC   RF01818
#=GF ID   RsaC
#=GF DE   RNA Staph. aureus C
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19786493
#=GF SS   Published; PMID:19786493
#=GF GA   100.00
#=GF TC   215.30
#=GF NC   31.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19786493
#=GF RT   A search for small noncoding RNAs in Staphylococcus aureus reveals a
#=GF RT   conserved sequence motif for regulation.
#=GF RA   Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C,
#=GF RA   Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
#=GF RL   Nucleic Acids Res. 2009;37:7239-7257.
#=GF WK   Rsa_RNA
#=GF SQ   3


CP000046.1/712455-712016   CAUCUCUUUUAACCACAGAGAUGCGUUAGAAGUUCUUCUAAUACAAUUUAUACAACGCCAUUCCCUACACACUCUUAUAAAAGAGAUUCACGCGCGUCAAUAAAUUGUAUUACAUACUAACUAAAAAGCUUUUCUUAAUCGUACUAACGAAGUUAGAGGUUCUUAUGUGAUUGGACAACUGUUCUCCCUACUAGACUUUUAGCAUAGCUGGUUAAAAGUACUAUUACAGAUUGUUCAAUUGUAUGCCCCUUUCCUUUGAACGGAAUAUUAAAAGCUAUGUGCAGUAACUUUUAAUAGGCAUACCACUUUUGCAUCAAGCUAUAAAUAAUCGCAUACUUUGAUAUUUAAUCUGGCCUAUCAAAGUAAACAUCUAUGGUUUCCUC-CCCCCAUAGAUCCUUAAGCCACACUCAUCCGAUGUCAUAUGAGUGUGGCUAUUUUUU
BA000033.2/675434-674994   CAUCUCUUUUAACCACAGAGAUGCGUUAGAAGUUCUUCUAAUACAAUUUAUACAACGCCAUUCCCUACACACUCUUAUAAAAGAGAUUCACGCGCGUCAAUAAAUUGUAUUACAUACUAACUAAAAAGCUUUUCUUAAUCGUACUAACGAAGUUAGAGGUUCUUAUGUGAUUGGACAACUGUUCUCCCUACUAGACUUUUAGCAUAGCUGGUUAAAAGUACUAUUACAGAUUGUUCAAUUGUAUGCCCCUUUCCUUUGAACGGAAUAUUAAAAGCUAUGUGCAGUAACUUUUAAUAGGCAUACCACUUUUGCAUCAAGCUAUAAAUAAUCGCAUACUUUGAUAUUUAAUCUGGCCUAUCAAAGUAAACAUCUAUGGUUUCCUCCCCCCCAUAGAUCCUUAAGCCACACUCAUCCGAUGUCAUAUGAGUGUGGCUAUUUUUU
CP002110.1/2670773-2671212 CAUCUCUUUUAACCACAGAGAUGCGUUAGAAGUUCUUCUAAUACAAUUUAUACAACGCCAUUCCCUACACACUCUUAUAAAAGAGAUUCACGCGCGUCAAUAAAUUGUAUUACAUACUAACUAAAAAGCUUUUCUUAAUCGUACUAACGAAGUUAGAGGUUCUUAUGCGAUUGGACAACUGUUCUCCCUACUAGACUUUUAGCAUAGCUGGUUAAAAGUACUAUUACAGAUUGUUCAAUUGUAUGCCCCUUUCCUUUGAACGGAAUAUUAAAAGCUAUGUGCAGUAACUUUUAAUAGGCAUACCACUUUUGCAUCAAGCUAUAAAUAAUCGCAUACUUUGAUAUUUAAUCUGGCCUAUCAAAGUAAACAUCUAUGGUUUCCUC-CCCCCAUAGAUCCUUAAGCCACACUCAUCCGAUGUCAUAUGAGUGUGGCUAUUUUUU
#=GC SS_cons               <<<<<<<_________>>>>>>>,<<<<<---------<<<<<<<<<<<<<---<<<<-------------<<<<<___>>->>>-------->>>>-->>>>>>>>>>>>>---->>>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,,,,,,,,,<<<<-<<<<<<<<---------<<<<<<<<<<-<_______>->>>>>>>->>>-->>>>->>>>->>>>,(((((((,,,<<<<_______>>>><<<<<<<<<-<<_______>>->>>>>>>>>))))))),,,,,,<<<__________________>>><<<<<<<<<<____________>>>>>>>>>>,,,<<<<<<<<_______.___>>>>>>>>,,,,,<<<<<<<<<<<<__________>>>>>>>>>>>>:::::::
#=GC RF                    CauCuCuUUUAACCACaGaGauGCGuuaGAAGUUCUUCuaauaCaauuuauACAaCGCCAUUCCCUACACACuCuuAUAaaAGaGAUUCACGCGCGuCAauaaauuGuauuaCAUACuaaCUAAAAAGCUUUUCUUAAUCGUACuaaCGAAGuuaGAGGUUCUUAUGuGauuGGaCaaCuGuUCUCCCUACuaGaCuuuuaGCAUAGCUGGUuaaaaGuACuaUUaCaGAuuGuUCaauUGuauGCCCCUuuCCUUUGAACGGaauauuaaaaGCuaUGUGCAGuaACuuuuaauaGGCauaCCACUUUuGCAUCAAGCUAUAAAUAAUCGCauaCuuuGauaUUUAAUCUGGCCuauCaaaGuaAACauCuauGGUUUCCUC.CCCCCauaGauCCUUAaGCCaCaCuCauCCGAUGUCAUauGaGuGuGGCuAUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01819
#=GF ID   RsaD
#=GF DE   RNA Staph. aureus D
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19786493
#=GF SS   Published; PMID:19786493
#=GF GA   50.00
#=GF TC   90.40
#=GF NC   46.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19786493
#=GF RT   A search for small noncoding RNAs in Staphylococcus aureus reveals a
#=GF RT   conserved sequence motif for regulation.
#=GF RA   Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C,
#=GF RA   Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
#=GF RL   Nucleic Acids Res. 2009;37:7239-7257.
#=GF WK   Rsa_RNA
#=GF SQ   8


CP000736.1/736444-736268   GUCUGCUAUAAUGU-UUUU-AACUUCUU----C------AAUA--------GAGAAGUUAUCUCCUUUGUGUUGUUUAUAAU----AACAAAACAAAUUUU--GCUCGAA-GUACUAUGACUGUACCUAGUCCUUACUGUC-AUAUGUACAAUAAUAUUCAUUUCCCAUAAAAG-CCAAGUGUAUU------------A------------C----CAUGUG-CACUUGGUUUUU
ACJB01000051.1/27775-27588 GUCUGCUAUAAUGA-UUUU-AACUUCUU----G------AA-A--------GAGAAGUUAUCUCCUUUGUGUUGUUUAUAGU----AACAAAACAAAUUUU--GCUCGAA-GUACUGUGACAGUACCUAGUCCUUACCGUU-ACAAGUACAUUAAUAUUCAUUUCCCAUAAAAG-CCAAGUAUAAG------------AAGUGUCUCCUCAC----UUUCUA-UACUUGGUUUUU
ACHE01000025.1/48344-48158 GUCUGCUAUAAUAA-UUUU-AACUUCUU----G------AA-A--------GAGAAGUUAUCUCCUUUGUGUUGUUUAUAGU----AACAAAACAAAUUUU--GCUCGAA-GUACUGUGACAGUACCUAGUCCUUACCGUU-ACAAGUACAUUAAUAUUCAUUUCCCAUAAAAG-CCAAGUAUAAA------------AAGUG----UCUC-CUCACUUUUA-UGCUUGGUUUUU
AP006716.1/2282592-2282780 AUUUGCUAUAAUGU-GUAU-AACUUCUU----A------AUAA--------GAGAAGUUAUCUCCUUUGUGUUGUUUAUAGU----AACAAAACAAAUUUU--GCUCGAA-GUACUGUGACAGUACCUAGUCCUUACCGUU-ACAAGUACAUUAAUAUUCAUUUCCCAUAAAAA-CCAAGUAUAUAGAGUGUCUCCUCA------------C----CCUACA-UACUUGGUUUUU
ACLP01000017.1/18463-18274 GUUUGCUAUACUAU-GUAU-AACUUCUU----A------AUUA-------CAAGAAGUUAUCUCCUUUGUGUUGUUUAUAGU----AACAAAACAAAUUUU--GCUCGAA-GUACUGUGACAGUACCUAGUCCUUACCGUU-ACAAGUACAUUAAUAUUCAUUUCCCAUAAAAA-CCAAGUAUAUA------------AAGUGUCUCCUCAC----UUUGCA-UGCUUGGUUUUU
CP000253.1/639887-639711   GUCUGCUAUAAUGU-UUUU-AACUUCUU----C------AAUA--------GAGAAGUUAUCUCCUUUGUGUUGUUUAUAAU----AACAAAACAAAUUUU--GCUCGAA-GUACUAUGACUGUACCUAGUCCUUACUGUC-AUAUGUACAAUAAUAUUCAUUUCCCAUAAAAG-CCAAGUGUAUU------------A------------C----CAUGUG-CACUUGGUUUUU
AP008934.1/2141452-2141653 GUUUGCUAUAAUAAAAUCU-AUCUUCUU----A------UUGAUAGCCAAUAAGAAGCCAUCUCCUUUGUGUUGUUUAUAGUAACAAACAAAACAAUUUUU--GCUCGA--GUAUAUUUUUAGUACCUAGUCCUUACUAAU-UAU-GUACAAUUA-AUUCAUUUCCCGUAAAAA-CCAAGUAAUGAU---------GAAUGUGUCUCCUCAC----UUCAAU-UACUUGGUUUUU
AM295250.1/303015-302816   GUUUGCUAUAAUAA-AUUUCAACUUCCUUAGU-CAAUAGAUUA--------AGGAGGUUAUCUCCUUUGUGUUGUUUACAAU----AAACAAACAAAAUUUUCGCUCGAAUGCAC-GU-CCAGUACCUAGUCCUUACUGUUUAC--GUGUA-UCAAAUUCAUUUCCCGUAAAAGACCAAGUAAUGA------------UUGUGUCUCCCCAC----AUUCAUAUACUUGGUCUUU
#=GC SS_cons               ::::::::::::::.:::<.<<<<<<<<...._......____........>>>>>>>>>,,,,,<<<<<-<<<<<______....>>>>>->>>>>,,,,..,,,,,,,.<<<<<<<<<<-<<<_________>>>->>>.>>>->>>>------------------------.<<<<<<<<<<_............______________....___>>>.>>>>>>>:::::
#=GC RF                    GUuUGCUAUAAUaa.uUuu.aaCuuCuu....a......AuuA........aaGaaGuuaUCUCCuuuGuGuuguuUAUAgU....aacaaAaCaaauUUU..GCUCGAA.GuacugugacAGuaCCUAGUCCUuaCuguc.acaaguaCAuUaAuAUUCAUUUCCCaUAAAAg.CCaaGuaugga............AuGUGUCUCcucaC....uuUcca.uaCuuGGUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01820
#=GF ID   RsaE
#=GF PI   ncr22; ncr629
#=GF DE   RNA Staph. aureus E (RoxS)
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19786493
#=GF SS   Published; PMID:19786493
#=GF GA   66.00
#=GF TC   67.20
#=GF NC   61.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006446; regulation of translational initiation;
#=GF DR   GO; 0055114; oxidation-reduction process;
#=GF RN   [1]
#=GF RM   19786493
#=GF RT   A search for small noncoding RNAs in Staphylococcus aureus reveals a
#=GF RT   conserved sequence motif for regulation.
#=GF RA   Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C,
#=GF RA   Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
#=GF RL   Nucleic Acids Res. 2009;37:7239-7257.
#=GF RN   [2]
#=GF RM   25643072
#=GF RT   A nitric oxide regulated small RNA controls expression of genes involved
#=GF RT   in redox homeostasis in Bacillus subtilis.
#=GF RA   Durand S, Braun F, Lioliou E, Romilly C, Helfer AC, Kuhn L, Quittot N,
#=GF RA   Nicolas P, Romby P, Condon C
#=GF RL   PLoS Genet. 2015;11:e1004957.
#=GF CC   It was shown to be regulated by the presence of nitric oxide (NO). In
#=GF CC   Bacillus subtilis it controls expression of genes with functions related
#=GF CC   to oxidative stress and oxidation-reduction reactions and it was renamed
#=GF CC   RoxS (for related to oxidative stress).[2]
#=GF WK   Rsa_RNA
#=GF SQ   15


ABQL01000005.1/214304-214418 GUGAAAUUGAUCACA-AA-CAAAC---A-----UU--AC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGUC--GUUAA-----GACAUA--UGAAACCGCGCU---U-----AUCCCGGCGCGGUUUCUUU
ABFU01000021.1/68350-68459   GUGAAGUUGAUCACA-AA-CAAAC---A------UAUAC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUU--C--GUAAA-----G-GAAA--ACCCCUUGUAAC-----------CUAGUUACAAGGGGUUU
CP000922.1/2095013-2094892   GUGAAGUGAAUCACA-AU-CAAAC---AAACUUAU--AC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGUC--UUUAU-----GACAAAGAAAAAGGACUCGG---C-----AUCCCCCGAGUCCUUUUUC
ABCF01000041.1/14193-14301   AAGAAGUUGAUCACA--A-CAAAC---A------UAUAC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUU-----UGUAU--------AAG--AAAACCCGUUGU---C-----UUCGGACAACGGGUUUUCU
AP009484.1/660819-660915     AUGAAAUUGAUCACA-UACCAAAC---A------U--AC--CCCUUUGUUUGA--GUGAAAGAUUUCUCCCAUCCCCUUUGU--------------------U---UAAUACCGUG-----U-----AUACAGACACGGUAUUUUU
AP008934.1/1857525-1857428   AUGAAAUUAAUCACAUAA-CAAAC---A------U--AC--CCCUUUGUUUGAA-GUGAAAAAUUUCUCCCAUCCCCUUUGU--------------------U---UAGCGCCGUGU----A-----AUCAG-ACACGGCGUUUUU
AM295250.1/605317-605414     AUGAAAUUAAUCACAUAA-CAAAC---A------U--AC--CCCUUUGUUUGAA-GUGAAAAAUUUCUCCCAUCCCCUUUGU--------------------U---UAGCGCCGUGUC---U-------GAAUACACGGCGUUUUU
CP000255.1/991517-991614     AUGAAAUUAAUCACAUAA-CAAAC---A------U--AC--CCCUUUGUUUGAA-GUGAAAAAUUUCUCCCAUCCCCUUUGU--------------------U---UAGCGUCGUG-----U-----AUUCAGACACGACGUUUUU
CP000817.1/1311650-1311762   GUGAAAUAAAUCACAAAA-CAAAC---A------U--ACACCCCUUUGUUUGAACGUGAAC-AUUUCUCCCAUCCCCUUUGU--------GAA---------AA--AGAAGCGUCUCUAUC-GGUCGAGGAUAGAGGCGUUUCUUU
ACNH01000027.1/21597-21717   GUGAACGAAUUCACA-UA-CAAAC---A------UAUAC--CCCUUUGUUUGAACGUGAAAAU-UUCUCCCAUCCCCUUUAAUAUUUUUAUAAGC-CGUAAAGA--AGAAGACCUGGU---G-----UUUACACCAGGUCUUCUUC
ACLW01000041.1/9530-9650     GUGAACGAAUUCACA-UA-CAAAC---A------UAUAC--CCCUUUGUUUGAACGUGAAAAU-UUCUCCCAUCCCCUUUAAUAUUUUUAUAAGCCGUAAAGAA--GAAGACCUGGUG---U-----UUU-ACACCAGGUCUUUUU
CP000002.3/1262536-1262653   GUGAAAUUGAUCACA-AA-CAAAC---A------UUUAC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGU--CGUUAAGA-CA--UAAU--AGAAACCGCGCU---U-----AUCCCGGCGCGGUUUCUUA
ABRX01000001.1/691882-691767 GUGAAAUUAAUCACA-UA-CAAAC---A------U-UAC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGUC--GUUAA-----GACAUA-GUGAAACCGCGCU---U-----AUCCCGGCGCGGUUUCUUC
CP001638.1/846669-846782     GUGAACGAAGUCACA-AA---AACCUUA------U--AC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGUUGUC--UUGGC-----AACAAG--GAAAAGCCCGGC---------AUUCAGCCGGGCUUUUCCU
CP002472.1/906962-907066     GUGAAGUUGAUCACA-AG-CAAAC---A------U--AC--CCCUUUGUUUGACCGUGAAAAAUUUCUCCCAUCCCCUUUGU--UC--GUGUU-----G---AA--AGAGGCCUUGCA---A-----A----CGCAAGGCCUCUUU
#=GC SS_cons                 ::<<<<<<--<<<<-.--.<<<<<...<......_..__.._____>>>>>>--->>>>-->>>>>>,,,,,,,,,,,,,,,<.-<.._____.....>.->,,..,<<<<<<<<<<<..._....._____>>>>>>>>>>>:::
#=GC RF                      gUGAAauuaaUCACA.aA.CAAAC...A......U..AC..CCCUUUGUUUGAaCGUGAAAaauUUCUCCCAUCCCCUUUGUu.Uc..uuuAa.....g.aaaa..agaggccgcgcc...u.....aUuaaggcgcggccucUUu
//
# STOCKHOLM 1.0

#=GF AC   RF01821
#=GF ID   RsaH
#=GF DE   RNA Staph. aureus H
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19786493
#=GF SS   Published; PMID:19786493
#=GF GA   50.00
#=GF TC   65.70
#=GF NC   39.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19786493
#=GF RT   A search for small noncoding RNAs in Staphylococcus aureus reveals a
#=GF RT   conserved sequence motif for regulation.
#=GF RA   Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C,
#=GF RA   Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
#=GF RL   Nucleic Acids Res. 2009;37:7239-7257.
#=GF WK   Rsa_RNA
#=GF SQ   5


AASB02000221.1/5610-5733   GUACCUUCGAUAACGAA-U-A-AA---CAUC---UCUUAAA-AGUAU-GUGUAAA------ACGCUGCAUGAUACAAACGAAGGUAAAAAUUUGACUCCCUUUAGUAGUGGACCCGUACGUUAAUCGUGCGGGUCGUUUUU
ACJB01000052.1/52570-52693 GUACCUUCGAUAAUUAAUU-A-AA---CAUC---UCUUAAUUAGUAU-GAGU-AU------ACCCCAUAAUAUACUAACGAAGGUAAA-UUUUGACUCCCUUUAGUAGUGGAUCCAUGCGAGCAACGUAUGGAUCCUUUUU
AM295250.1/435451-435575   GUACCUUCGAAAAUUAA-UUA-AACAUCUCU---UAAUUAA-AAACA-GUAU---------ACCCCAUAAUAUACGUGCGAAGGUGAAAUUUUGACUCCCUUUAGUAUUGGGCCUAUGCGAGAAGCGUAUAGGUCCAUUAU
AP008934.1/1987118-1986996 AUACCUUCGAUAUUAAU-U-A-AU---CAUC---UCUUAAU-UAUUUCGAGU-AU------ACCCCAUAAUAUACUAACGAAGGUGAAAUUUUGACUCCCUUUAGUAGUGG-CCUGUACGCAUUGCGUAUAGGCCUAUAUU
AP006716.1/2148633-2148502 GUACCUUCGCUAUAGUA-G-AUUU---CAAUAUCUCUGACU-AAAUU-GAGUAUACCCCAUAGACUACACAAAAUAAACGAAGGU-CAAUUUUGACUCCCUUUAGUAGAA-GCCCAUGCGAGAAUCGUGUGGGCUCUUUGU
#=GC SS_cons               :((((((((,,,,,,,,.,.,.,<...<<<<...<______.>>->>.>><<.__......_____>>,,,,,,,,,,)))))))),,,,,,,,,,,,<<<<____>>->><<<<<<<<<_____>>>>>>>>>:::::::
#=GC RF                    GuACCUUCGaUAauuaA.u.A.au...Cauc...ucUuAau.aguau.Gagu.aa......AccCuacAauAuAcaAACGAAGGUaaAAUUUUGACUCCCuUUAGUAguGGgCCcaugCGagaAuCGuaugGGcccuUUuU
//
# STOCKHOLM 1.0

#=GF AC   RF01822
#=GF ID   RsaJ
#=GF DE   RNA Staph. aureus A
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19786493
#=GF SS   Published; PMID:19786493
#=GF GA   100.00
#=GF TC   287.10
#=GF NC   89.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19786493
#=GF RT   A search for small noncoding RNAs in Staphylococcus aureus reveals a
#=GF RT   conserved sequence motif for regulation.
#=GF RA   Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C,
#=GF RA   Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
#=GF RL   Nucleic Acids Res. 2009;37:7239-7257.
#=GF WK   Rsa_RNA
#=GF SQ   3


CP000736.1/2588121-2588407 AUAACUAUAAUUUUUGGCAAAAUUUUGACCUUGCUAUUGAAAUGACUAAGGCUUCUUACGAAAUUUGGGCAGAUAUAAACAGCGAUUCGUUAAAAUAUGUCAGUUAAAAUUAAUAAUUGCAUUAUUUCUUAACAAAAAGACAUCCUAGCUUUACCAUGUUGUGAAACAAUCCAUUAAUUGUAAUAUUACGUUGAGCGCCUUGUUCAUCAAUGCUAUAAUUAGUUACAUAAUAAAUUGAACAUCUAAAUAUACCAAAUCCCCUCACUAUUGCCCUAGUGAGGGGAUUU
AJ938182.1/2439575-2439861 AUAACUAUAAAUUUUGGCAAAAUUUUGACCUUGCUAUUGAAAUGACUAAGGCUUCUUACGGAAUUCGGGCAGAUAUAAACAGCGAUUCGAUAAAAUAUGUCAGUUGAAAUUAAUAAUUGCAUUAUUUCUUAAUAAAAAGACAUCCUAGCUUUACCAUGUUGUGAAACAAUCCAUUAAUUGUAAUAUUACGUUGAGCGCCUUGUUCAUCAAUGCUAUAAUUAGUUACAUAAUAAAUUGAACAUCUAAAUACACCAAAUCCCCUCACUAUUGCAGUAGUGAGGGGAUUU
BA000033.2/2500286-2500572 AUAACUAUAAAUUUUGGCAAAAUUUUGACCUUGCUAUUGAAAUGACUAAGACUUCUUAAGGAAUUCGGGCAGAUAUAAACAGCGAUUCGAUAAAAUAUGUCAGUUAAAAUUAAUAAUUGCAUUAUUUCUUAACAAAAAGACAUCCUAGCUUUACCAUCUUGUGAAACAAUCCAUUAAUUGUAAUAUUACGUUGAGCGCCUUGUUCAUCAAUGCUAUAAUUAGUUACAUAAUAAAUUGAACAUCUAAAUACACCAAAUCCCCUCACUAUUGCCCUAGUGAGGGGAUUU
#=GC SS_cons               :{{{{{{,,,,,,,,<<<<<____>>>->>,,[[-[[[[[--[[[-[[[[[[,,,,,,,(((((----(((<<<<<<---<<<<___>>>>---->>>>>>,<<<<____>>>>,,,)))---))))),,,,,,,,,,,,,,,,,,,<<<<----<<<<-<<<--<<<<<______>>>>>-->>>->>>>->>>>]]]]]]-]]]]]]]]]],,,,,,}}}}}}----------------------------<<<<<<<<<<<<<<______>>>>>>>>>>>>>>
#=GC RF                    AuaaCuaUAAaUUUUGGCaaAAUUuuGACCUUGCUauuGaAAuGaCcaaGgCUUCUUAcGgaauUcGGGCaGacauaAACagCGAUUCGcuAAAAuauguCAguuaAAAUuaacAAUuGCAUUauucCUUAAcAAAAAGACAUCCUAGCucUACCacguUgugAAaCaauCCAUUAauuGuAAcacUacguUgaGCGcCuugUuCauCaauGCUAUAAUuaGuuaCAUAAUAAAUUGAACAUCUAAAUAcACCaaauCCCCuCaCuaUUGCccuaGuGaGGGGauuu
//
# STOCKHOLM 1.0

#=GF AC   RF01823
#=GF ID   rspL
#=GF DE   rpsL sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19531245
#=GF SS   Published; PMID:19531245
#=GF GA   37.00
#=GF TC   37.50
#=GF NC   36.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19531245
#=GF RT   Identification of candidate structured RNAs in the marine organism
#=GF RT   'Candidatus Pelagibacter ubique'.
#=GF RA   Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ,
#=GF RA   Breaker RR
#=GF RL   BMC Genomics. 2009;10:268.
#=GF WK   Pelagibacter_ubique
#=GF SQ   6


AACY022375643.1/586-670      UUGGCGAUAAUUUUUGGUUGGAAUGUAGUG-C-----AUUA--GCACUAAACGCUGCCACAA-AUAACAUGUCAGUUAUU-U-CA-UC-AAAAAUAAA
AACY020349958.1/529-446      UUGGCGAUAAUUUUUGGUUGGAAUGUAGUG-C-----AUUA--GCACUAAACGCUGCCACAA-AUAACAUGUCAGUUAUU-U-CA-UC-AAAAAUAA-
AACY020879984.1/571-654      UUGGCGAUA-UUUUUGGUUGGAAUGUAGUGAU-----AUU---ACACUAAACGCUGCCACAA-AUAACCUGUCAGUUAUU-U-CA-UC-AAAAAUAUA
ABNY01009418.1/8-97          UUGGCGAUGUUUUUGGUUUGGAAUGUAGUG-UUA-GCUUUA-GACACUAAACGCUGCCAUAA-AUAACCUGUCAGUUAUU-U-CU-CU-CAAAAACAA
ABVS01000001.1/844565-844656 UUGGCGAUA-UUUUUGGUUGGAAUGUAGUA-CCUGCUAAUA--GUACUAAACGCUGCCACAAAAUAACCUGUCAGUUAUUUU-CA-CCUAAAAAUAAA
CP000084.1/1074301-1074209   UUGACGCUG-UUUUUGGUUGGAAUGUAGUA-CCU-ACUUUACGGAACUAAACGCUGCCACAAAAUAACCUGUCAGUUAUU-UUCACUC-AAAAAUAUA
#=GC SS_cons                 :::::::::.:((((((--((((((<<<<<.<__.______..>>>>>>,,,<<<<______._________>>>>)))).).)-.)).)))):::::
#=GC RF                      UUGGCGAUa.UuuuuGgUUGgaauguaGug.ccu.acauUA..gcaCuaAACgCuGCCAcAA.AUAACcUGUCaGuuauu.u.CA.cC.aaaaAuAaA
//
# STOCKHOLM 1.0

#=GF AC   RF01824
#=GF ID   RUF20
#=GF DE   RNA of unknown function 20
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Predicted;
#=GF SS   Predicted; WAR
#=GF GA   60.00
#=GF TC   134.70
#=GF NC   27.70
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   URL; http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=RUF20;
#=GF RN   [1]
#=GF RM   19119416
#=GF RT   Non-coding RNA prediction and verification in Saccharomyces cerevisiae.
#=GF RA   Kavanaugh LA, Dietrich FS
#=GF RL   PLoS Genet. 2009;5:e1000321.
#=GF WK   RNA_of_unknown_function
#=GF SQ   6


ABSV01000776.1/6989-6547   ACGUGGGUUUUUUUU-CGAAUUGAGUGAUUAUGCAACCAUACAGGAACCUUACAUAAGCGCAAGUAGUUGAAUAGUGGAUUCAAGAAGCAAAACUUUACUACCGGUAAA-AACAUUAGAACGAAAUAAAAGUGCUGAAUCUUAAAAGUAAAAUAUAUACUU-GGAUAAGAAUUCCCAGGGAAA-CUGGGUACCUCGUUUUCCUGUUGCACUAUUUUUUUAGAUUCUUUCUUGAUUUUUUACCAAUCGCCU-GAUGAAAAUACCUUCCAGAGCAGAGAACAACAGUAGAAG-UAUGCUGAAAAAG-UUAGUAUGAGAAGUUUGAAUUGUUUAGAUAAUAUAAAA-GUGACAUCUAAUAUGACUAAUAUAAAAAUAGUAAG-UAUGGUAAUCAAAAAAAGAUAC-AAACAAUGUAUAUAUAUAAAGGAAAAA-UAACCUGCGAAUAUUGAGAAAAA
AABY01000015.1/30646-31070 ACGUGGGUUUUUUUU--GAAUUGGAUGAUUAUGCAACCAUACAGGAACCUUACAUAAGCGCAAGUAGUUGAAUAGUAGAUCUAACCAGUAAAACUUUACUACCAGUGGG-AUUAAUGGAACGAAUUAGACGUACUCGAUCUUGCAAGUAAAAUCUACGCACAGGAUAAGAAGUCCCAGGGGAAGCUAGGUACUUC--UUUCCCGCUGCAAUAUUUUUCUAAAUUCUGUCUUGAUUUUCUUCAAAUUGCUU-GAGGAAAAUAACUUCUA-----------------AGCAG-UAUGCUGAGAAGGGUUGGCAUGGGAUGUUUGAAUUGUUUAGAUAAUAUAAAA-GAGACAUCUAAUAUGACUAAUA-AAAAAUAGUAAG-UAUGGUAUACAAAAAAAAAUAC-AAAGAACGUGUAUAUAUAAAGGAAAAA-UAACCUGCGAAUAUUGAGAAAAG
ABPD01000774.1/893-1336    ACGUGGGUUUUUUUUUCGAAUUGAGUGAUUAUGCAACCAUACAGGAACCUUACAUAAGCGCAAGUAGUUGAAUAGUGGAUUCAAGAAGCAAAACUUUACUACCGGUAAA-AACAUUAGAACGAAAUAAAAGUGCUGAAUCUUAAAAGUAAAAUAUAUACUU-GGAUAAGAAUUCCCAGGGAAA-CUGGGAACCUCGUUUUCCUGUUGCACUAUUUUUUUAGAUUCUUUCUUGAUUUUUUACCAAUCGCCU-GAUGAAAAUACCUUCCAGAGCAGAGAACAACAGUAGAAG-UAUGCUGAAAAAG-UUAGUAUGAGAAGUUUGAAUUGUUUAGAUAAUAUAAAA-GUGACAUCUAAUAUGACUAAUAUAAAAAUAGUAAG-UAUGGUAAUCAAAAAAAGAUAC-AAACAAUGUAUAUAUAUAAAGGAAAAA-UAACCUGCGAAUAUUGAGAAAAA
D50617.1/131497-131055     ACGUGGGUUUUUUUUUCGAAUUGAGUGAUUAUGCAACCAUACAGGAACCUUACAUAAGCGCAAGUAGUUGAAUAGUGGAUUCAAGAAGCAAAACUUUACUACCGGUAAA-AACAUUAGAACGAAAUAAAAGUGCUGAAUCUUAAAAGUAAAAUAUAUACUU-GGAUAAGAAUUCCCAGGGAAA-CUGGGAACCUCGUUUUCCUGUUGCACUAUUUUUU-AGAUUCUUUCUUGAUUUUUUACCAAUCGCCU-GAUGAAAAUACCUUCCAGAGCAGAGAACAACAGUAGAAG-UAUGCUGAAAAAG-UUAGUGUGAGAAGUUUGAAUUGUUUAGAUAAUAUAAAA-GUGACAUCUAAUAUGACUAAUAUAAAAAUAGUAAG-UAUGGUAAUCAAAAAAAGAUAC-AAACAAUGUAUAUAUAUAAAGGAAAAA-UAACCUGCGAAUAUUGAGAAAAA
AACG02000045.1/48871-49185 ACGUGGGCUCUCU----GAAUUACAAGAUUAUGCAACCACACAGGAACCUUACAUAAGCGUAAGCCGUUAAUUGCUGGAUUCAGGAAAUAAAACUCUACUAAUAGCGGGGAAUAACAGAGGUUUGAAGGUGCACUUGAUCUUAUCAGUAAUAUAUAUAUAU---AUAUAUAUAUAUAGAUGUGUGUAUGUACAC---AUUUUUAACGCAAGGAGG--CAAGAGAAGCCAUUGAUAGCGUUCUC-CUGUUC-GGCUAUUCUGUUUUUAU--------------------UCUUUUUCUAAACAC--UUGCAACCAUCUGAAUGA------UAGCUACUGAAGGAGGAGCCCAUCCCUG-------------------------------------------------------------------------------------------------
AACH01000433.1/4759-4338   ACGUGGGUUUUUU-----AAUUGCAUGAUUAUGCAACCAUACGGGAACCUUACAUAAGCGCAGGUCGUAAAACAAUGAAUUCAAGAACCAAAACGGUGCUACUGAUUGA-AAUGAUUGAACAAACUGGGUAUGCU-AAUCUUGCAAGUAAAAUAUGCACUAAGAAUGAGAAGCUUCAGAGAAUUCCGGUUUUUUCA-AUUCCAUCUAUCUUAACUUUCAAUUAAAUUACUUGAAGAAAGAAUAUCUGUUUAGGAGAAAACGACGCUGA-------------------AAG-UCUGUUAAAAGA--UGAGUCUGACAUGUGUGA--UAUUUAGAUAAUAUAAAAAGAGAGAUCUGAUAUGAAUAAUAUAGAAAUAGUAAAAUAUGGUAUACAGAAAAAAAAACCAAAUAUUAUGUAUAUAUAAAGAAAAAAAUAACCUGCGAAUAUUGAGAAGUA
#=GC SS_cons               :{{{{{{{{-{{{{,..,,,,,,,,,,,,,,,,,,[[[[[[,,,,,,,,,,,,,,,,<<____>>,,,,,,<<_____>>,,,,,,<<_______>>,,,,,,((-(((.---(-(((-(-(((---------(,,<-<<<<<--<<<_________>>>-.--->>>>>-->,,<<<<<<<----<<____>>--.>>>>>>>,,)---------------)))-)-))-)-)--)))-)),,,,,,,<.---<<________>>->.................,,,,,.,<<<<<<<_____.>>>>>>>,,,,,,,,,,,,,,,,,<<<<<_________._____>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,.]]]]]],,,,,,,,,,,,<<<<.<_____>>>>>,,,,,,,,,,,,}}}}.-}}}}}}}}::::::::::::::
#=GC RF                    ACGugGGUUUUUUuU..GAAUUGaaUGAUUAUGCAACCAUACAGGAACCUUACAUAAgCGcAAGcaGUUgAauAgUGGauUCAAGAAgcAAAACUcUACUAcuggUgag.AAuaauaGAgcgaaaUAgauGUgCUuaAuCuuaaAaGuAAAAUAUAuaCuu.GgAuaaGaAuuuccaGggaaaucUggGuACcuCg.uuucCuguUGCAauAuuuUUcuAgAuucucuCuUgAuuucucaccAauuGuuu.GaugaAAAUaacUucaa.................AGAAg.UaugcugAAAAaG.UcagcaugAgAuGUuUGAAUUgUUuaGauAAUAUAAAA.GaGAcauCuaAUAUGAcUAAUAUAAAAAUAGUAAg.UAUGGUAauCAAAAAAAaAuAC.aAAuAauGUaUAUAUAUAAAGgAaAAA.UAACCugCGAAUAUUGAGAAAaA
//
# STOCKHOLM 1.0

#=GF AC   RF01825
#=GF ID   RUF21
#=GF DE   RNA of unknown function 21
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Predicted;
#=GF SS   Predicted; WAR
#=GF GA   60.00
#=GF TC   139.10
#=GF NC   50.20
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   URL; http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=RUF21;
#=GF RN   [1]
#=GF RM   19119416
#=GF RT   Non-coding RNA prediction and verification in Saccharomyces cerevisiae.
#=GF RA   Kavanaugh LA, Dietrich FS
#=GF RL   PLoS Genet. 2009;5:e1000321.
#=GF WK   RNA_of_unknown_function
#=GF SQ   5


AABY01000015.1/103580-104263 GUUUUCCAUUUUCUACAAAUUAAAAAAAGAAAAAAAACCGAAAUAGUGAAAAA-UUCGGGGUUGGCCUUGGCUA-AACUG-ACCCACCCACAAUUUAUCCAAAAAAUUUAUCCACCUAACCCCAGAUCACUGCAAACGAA--------------------------------AUGUAUAUCACUAUUCACGC-GU-GGUUCCAAUUAUGGCGGCUAGAUGACGAAGGCUUGAUCAGCUA----CUGCUGUAAAAUAAUGAAACUAAAAGCGCCGUA--UUGUUGAUAAUC-UACCCAUGGCAUGUACAGGG-AACAGUGUGCU-UGUGAGAGGGACAAUCCAAAGCAGUAGGUUUUUGUUUAUGAUUGGUUUAUAACAGAAUUUUGGGGAAAAAGG-GGGACACCAUAAGUGCAUGUUUCA------AAACUAUUAAUAUGUUGUAGCCUUCUUUCUUCAAACAUUGCACUCUGUUGUUGCUUUUCCUUAAG-AAAUCUUUUCUCCAAAUAACACC-----UUGAUUCUUUU--UUAUCGG------UCUCCUUAUAUAUAU-AUAUAUAU--------------ACCAAUACUCGGGGUG------UCUUUUUUAGCCGCCGAUGUGAGGAUC-GAAAAUCAUUAUCUCGAAAGGGUAAAGGUUGUUAAGAUAGUAUAUACAUAUACAUAUACAUAUAUAUAUAUACAUAUAUAUAUAUAUUGAAUUACAUACUUCAAUAAGGAAUGGUAUAAGAUUUUUCGUACGGUAAUA
AACH01000252.1/3233-3922     AUUUUCCAUCUUCAAAAA-----GAAAAAAAAUAGAACCAUAUGGAUGAAAAAGUUCGGGGUUAGCCUUGGCUAUAGGUGGACCAAAAC-CGAUUAACC--AUACAUUUGGCCAC-CAACCCCGGAUCACUGCAAACGAAAAAGUAUGGGGAUGCUCCCC----GGCAUUGAAUAUGUAUCACUAUUAACGUCACCAGAUUGAAAUGUACCGGCUAGAUGAAGACUAUUUGAUCAGCUAGUUACUUCUAUCGAAUAAAGUGGCCAAAACCAACUCA--UUAUAGGUCAUGAUAU----AGUAAGCAGGAAG---UAUUGGAAUAUGUGGAGAGAAAACUGUGAAAACUGCUUUUUCUGUUUAUAGUUGGUUUAUAGAGGAAGUAUUAGGAAACUGG-GGCACAACAAUAAUACGUGUUCCA------CAACUUUCAGCGCGGGUGUGUCUUCUUUUCCUGCUUGAGAUAGCGCUAUGUCACUGUUCCUCAUUUGAAGAUUUGUUUUGAUCAAAAAUAU-GUUCAACUCUUUU--UCACCGGC---UUUCUCUUUUUAUAUUUAAUACAUAUU----------UGUUCCAAUACUCGGUGCG-------UCUUCUUAGCCGCCGAAGUGAGAUUU-CAGAAUCAUCAACGUGAAAGGGUAAAAACAGUUAGGAUAGUAUAU----------------------------AUGUAUAUAUAAAUUUAAUUACAUACUUCAAUAAGGAAUGGUAU-AGAUUUUUCGUGGA-UAAUA
AACI02000272.1/9810-9122     UUCCUCCAAAUGAAAAAAAAAAAAUAAAAAAAAUAAACGGAA-GAGUGAAAAAGUUCGGGGUUAGCAAAGACUG-AAGUGGAUCCAUACAUA----AACUAGAUUUUUUGGCCACCCAACCCCGGAUCGCUGGACACGAAAUAGUUUG-------UGAGCACUCCGGGUAGCACAUAUAUCACUCUUCACGAUAU-UAAUCGGAUCUUGGCGGCUAAAUGAUGAAGAUCCCACCACUCAU---CGUUUGUUAAAUGGGAAUAGUAGAGGCAGCGCAUCUUGUUUAUAAUACUAUAUGGAACAUGGAAAAAG-UGAAUCUUAUC-UGGGGGGUGGAGCGACCGGAAGAAGACAUACGUUUUUGUGCCUAGUUCAUGAUGCAUUGUUGAAGGAAGGGC-CGGACUUUUUGAAUGUAAGCAUCAAACCCUCACCCUGACAAAAAAUGUGGCUUUCUUUCUCUUGAAGAGGUCCUGUCUUUUUCCCUUUUUUGGCUUGUAGUUUUG--CUGUAUGAUGUUGCGGUUCAGUUUCCUUACUUAUUUGC---CGUCCGUAUUUAUAUAUAA-------------------AUUCUGCU-CUCCGGGCG------GUCCUUUUAGCCGCCGAAGUGAGCAUU-GAAAAUCAAGAGCUUGAAAGGGUAAAGGUAGUUAAGAUAGUAUA--------------------------------UAUAUAUAAAUUGAAUUAUAUAUUUCAAUAAGGAAUGGUAUGAAAUUUUUCGUGGAUUAGUU
AAEG01000069.1/38244-37551   GUUUUCCAUUUUCUUGAAAUU--AAAAAGAAAAAAAACCGAAAUAAUGAAAAA-UUCGGGGUUAGCCUUUGCCA-AAGUGUACCCACCCACAAUUUACCCAGAAUUUUUAUUCAUGCAACCCCAGAUCACUGAAUACGAA--------------------------------AUGUAUAUCAUUUUUCACGC-GG-GGUUCCAACUAUGGCGGCUAGAUGAUGAAGGAAUAAUAAGCAAC---CUACUGCUAAAUAAAAGGACU-GAAGCAGCGUA--UUGUUGAUAAUCAGACCUAUGCUUGGUACAAAAUUGUAAUGGAAU-UAUGGAAAUAACAAUAUAAAACA-CAGUUUUUUGUUCAUGAUUAGUUCUCAACAAAAUUCUGGGGAAACAGGUGGAAUACCAUAAGCACCGCUUCCA------CAAUCAUCAACAUGUUGUAAUCUUCUUUCUUUGGAAGCAGCAGUCCUUUAUUACUUUUCUUUUAGUAAAUCCCUGAUCUGCGUAAUAUUG----CAAGUUCUUUU--UUAUCGG------CCUCCUUAUAUAUAU-AUAUCUAUA----------UUCACUAAUACUCGGGGUGUUUUUUUUUUUUUUAGCCGCUGAAGUGAGGAUCAAAAAAUCAAUAGCUCGGAAGGUUAAAGGUUGUUAAGAUAGUAUAUACAUAUAUAUGUAC----AUAUACAUAUACAUAUAUACAUUUUGAAUUACAUACUUCAGUAGGGAAUGGUAUAAAUUUUUUCGUACGGUAAUA
AAFW02000176.1/28550-27849   GUUUUCCAUUUUCUUGAAAUU--AAAAAGAAAAAAAACCGAAAUAAUGAAAAA-UUCGGGGUUAGCCUUUGCCA-AAGUGUACCCACCCACAAUUUACCCAGAAUUUUUAUUCAUGCAACCCCAGAUCACUGAAUACGAA--------------------------------AUGUAUAUCAUUUUUCACGC-GG-GGUUCCAACUAUGGCGGCUAGAUGAUGAAGGAAUAACAAGCAAC---GUACUGCUAAAUAAAAGGACU-GAAGCAGCGUA--UUGUUGAUAAUCAGACCUAUGCUUGGUACAAAAUUGUAAUGGAAU-UAUGGAAAUCACAAUAUAAAACA-CAGUUUUUUGUUCAUGAUUAGUUCUCAACAAAAUUCUGGGGAAACAGGUGGAAUACCAUAAGCACCGCUUCCA------CAAUCAUCAACAUGUUGUAAUCUUCUUUCUUUGGAAGCAGCAGUCCUUUAUUACUUUUCUUUUAGUAAAUCCCUGAUCUGCGUAAUAUUG----CAAGUUCUUUU--UUAUCGGCCUCCU------UAUAUAUAU-AUAUAUAUAUAUAUCUAUAUUCACUAAUACUCGGGGUGUU-UUUUUUUUUUUAGCCGCUGAAGUGAGGAUC-AAAAAUCAAUAGCUCGGAAGGUUAAAGGUUGUUAAGAUAGUAUAUACAUAUAUAUGUAC----AUAUACAUAUACAUAUAUACAUUUUGAAUUACAUACUUCAGUAGGGAAUGGUAUAAAUUUUUUCGUACGGUAAUA
#=GC SS_cons                 :::::::::::::::::::::..::::::::::::::::::::::{{{{{{{{.,,,(((((<<<<____>>>>.,,<<<________>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,))))),,,,,,,,,,,,,,,,,................................,,,{{{{{{{,,,,,,,,,,.,,.,,,,,,,,,,,[[[[[[[[[[[,,,,,,,,,,,,,,,,,,,,,,...,,,,,,,,,,,,,,,,,,,,,,,,<<<<<____..>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,,.,,((((,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<______________>>>>>>>,,,,,<<<<<<<___.________________________......______________________________________________________>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,....,,,,,,,,,,,..,,,,,,,,...,,,,,,,,,,,,,,,,,.,,,,,,,,,..........,,,,,,,,,,)))),,,,,......,,,,,]]]]]]]]]]],,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<------<<<<<<<_____________...._____________>>>>>>>------>>>>>>,,,,,,,,,,,,,,,,}}}}}}},,,}}}}}}}}:::::::::
#=GC RF                      gUUUUCCAUuUUcuaaAAAuu..AAAAAaAAAAAAAACcGAAauAaUGAAAAA.UUCGGGGUuaGCcUUgGCua.AAgUGgACCcAcaCAcAAUUuAcCcAgAAuuUUUaucCAccCAACCCCaGAUCACUGaAaACGAA................................AUauaUAUCAcUaUUcACGc.au.gGuUCcAAuUaUgGCGGCUAgaUGAuGAAGauuUaAucAgCuAu...CUuCUGuuAAAUAAaaagAcUAgAagCagCGuA..uuGuuGAUAAUcauAucUauaauauGuAcAAAg.uGuAuUGgAaU.UguGggaagaAcAaUauaAAAcAagAguUuucuguuuAUGaUUaGUUcauaacagaaUUuUGagGaAagaGg.gGaAcAcCAUaAauaCaugUUcCA......CAAccaUcAAcAuGuUGUaguCUUCUUUCUuUggAaGaaGuAgUccuUUaUUaCcuUuCcuuaauUaAAucuuUGaUCUGaaUAAuAuUg....uaAgUUCUUUU..UUAUCGGC...cuUCUcuuUaUAUAUAU.AUAuAUAUa..........UuuaCuAAUAcuCgGGGuG......uUuUUuuUAGCCGCcGAAGUGAGgAUu.aAAAAUCAauAgCUuGAAAGGgUAAAGguaGUUAAGAUAgUAUAUaCAUAUAuAUgUAC....AUAUAcAUAuAuAuAUAUAcAuaUUGAAUuacAUACUUCAAUAAGGAAUGGUAuaAaaUUUUUCGuacagUAAUA
//
# STOCKHOLM 1.0

#=GF AC   RF01826
#=GF ID   SAM_V
#=GF DE   SAM-V riboswitch
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19531245
#=GF SS   Published; PMID:19531245
#=GF GA   41.00
#=GF TC   41.00
#=GF NC   40.70
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0046500; S-adenosylmethionine metabolic process;
#=GF RN   [1]
#=GF RM   19776155
#=GF RT   A variant riboswitch aptamer class for S-adenosylmethionine common in
#=GF RT   marine bacteria.
#=GF RA   Poiata E, Meyer MM, Ames TD, Breaker RR
#=GF RL   RNA. 2009;15:2046-2056.
#=GF RN   [2]
#=GF RM   19531245
#=GF RT   Identification of candidate structured RNAs in the marine organism
#=GF RT   'Candidatus Pelagibacter ubique'.
#=GF RA   Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ,
#=GF RA   Breaker RR
#=GF RL   BMC Genomics. 2009;10:268.
#=GF WK   SAM-V_riboswitch
#=GF SQ   6


AACY023226915.1/901-837      AAUUAAGCCGGGC--AGUUGAACCAUAUUGUGCGCCCUGCAUU-UGCUUAAGCACUAAA-AAGGAGAAA
ABOH01000803.1/30-94         AUUAAAGCCGGGU--AUUUGAACCGUAUUGUGCACCCUGCAUU-UGCUAAAGCACUAAA-AAGGAGAAA
CP000084.1/732850-732787     AAUUGGUAAAGGU--AGUUGAACUGUAUUGUGCACCUUGCAUAGAGCUAAAGCACUAAA-AA--AGUAA
ABVS01000001.1/912548-912482 AUAAUCGGUAGGC--AUUUGAACUGUAUUGUGCGCCUAACAUAAAGUUAAAGCACUAAAAAAGGAGUAA
AAPV01000002.1/208413-208345 AUUAUCGGUAGGCGCAUUUGAACUGUAUUGUACGCCUUGCAUAAAGCAAAAGUACUAAAAAAGGAGUAU
CP000084.1/1127423-1127359   AAUUAAGCCGGGC--AGUUGAACCAUAUUGUGCGCCCUGCAUU-UGCUUAAGCACUAAA-AAGGAGAAA
#=GC SS_cons                 :::::::::<<<<..__________________>>>>::::::::::::::::::::::.:::::::::
#=GC RF                      AuUaaaGgugGGc..AuUUGAACuGUAUUGUGCgCCcUGCAUaaaGCUAAAGCACUAAA.AAGGAGuAA
//
# STOCKHOLM 1.0

#=GF AC   RF01827
#=GF ID   SAR11_0636
#=GF DE   SAR11_0636 sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19531245
#=GF SS   Published; PMID:19531245
#=GF GA   67.00
#=GF TC   68.10
#=GF NC   66.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19531245
#=GF RT   Identification of candidate structured RNAs in the marine organism
#=GF RT   'Candidatus Pelagibacter ubique'.
#=GF RA   Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ,
#=GF RA   Breaker RR
#=GF RL   BMC Genomics. 2009;10:268.
#=GF WK   Pelagibacter_ubique
#=GF SQ   13


AACY020109561.1/586-675      GGUUGUAUUUUGAGUCCGUAAUUGAAUCAAAAGUGAAUCAAAACGUGAACAU-CAAAACCACAUUUUGUAUGCUUGUGGAUAACUUCAACC
EF107105.1/11251-11340       GGUUGUAUUUUGAGUCCGUAAUUGAAUCAAAACUGAAUCAAAACGUGAACAU-CGAAACUAUAUUUUGUAUGCUUGUGGAUAACUUUAACC
EF107103.1/360-271           AGUUGUAUUUUGAGUCUGUAACUGAAUCAAAAGUGAAUCAAAACGUGAACAU-CCAAACUACAUUUUGUGUGCUUGUGGAUAACUUCAACC
AAPV01000001.1/267511-267422 GGUUGUAUUUUGAGUCUGUAACUGAAUCAAAGGUGAAUCAAAACGUGAACAU-UGAAACUACAUUUUGUGCUCUUGUGGAUAACUUCAACC
ABVS01000001.1/545059-545148 GGUUGUAUUUUGAGUCUGUAACUGAAUCAAAAGUGAAUCAAAAGGUGAACAU-UGGAACUACAUUUUGUGUACUUGUGGAUAACUUUAACC
DQ088853.1/1297-1208         GGUUGUAUUUUGAGUCUGAAACUGAAUCAAAAGUGAAUCAAAACGUGAACAU-CCAAACUACAUAUUGGGGACUUGUGGAUAACGUUAACC
DQ088852.1/941-1030          GGUUGUAUUUUGAGUCUGAAAUUGAAUCAAAAGUGAAUCAAAACGUGAACAU-UGAAACUACAUUUUGAUACGUUGUGGAUAACUUUUACA
AACY024103422.1/358-269      GGUUGUAUUUUGAGUCCGUAAUUGAAUCAAAAGUGAAUCAAAACGUGAACAUCCAAA-CUACAUUUUGUAUGCUUGUGGAUAACUUCAACC
AACY023666470.1/1117-1028    GUUUGUAUUUUGAGUCCGUAAUUGAAUCAAAAGUGAAUCAAAACGUGAACAUCCAGA-CUACAUUUUGUAUGCUUGUGGAUAACUUCAACC
AACY022748921.1/521-436      U--UGUAUUUUGAGUCCGUAAUUGAAUCAAAAGUGAAUCAAAACGUGAACAU-CAAAACUACAUUUUGUAUGCUUGUGGAUAACUUCA--A
AACY020521394.1/1-86         U--UGUAUUUUGAGUCCGUAAUUGAAUCAAAAGUGAAUCAAAACAUGAACAU-CAAAACUACAUUUUGUAUGCUUGUGGAUAACUUCA--A
AACY020955001.1/242-159      ---UGUAUUUUGAGUCCGUAAUUGAAUCAAAAGUGAAUCAAAACGUGAACAU-CAAAACUACAUUUUGUAUGCUUGUGGAUAAGUUCA---
AACY021181531.1/341-252      GGUUGUAUUUUGAGUCUGUAACUGAAUCAAAAGUGAAUCAAAACGUGAACAU-CAAAACCACAUUUUGUAUGCUUGUGGAUAACUUCAACC
#=GC SS_cons                 (((((,,,<<<<<-<<------<<<-<<<____>>>->>>------>>--->.>>>>,<<<<<___________>>>>>,,,,,,,)))))
#=GC RF                      gguuGUAUuuuGaGuCuGuAAuuGaAuCaAAAGuGaAuCaAAAcGUGaACAu.CaaaACcaCaUUUUGuaugcUuGugGAUAAcUUCaacc
//
# STOCKHOLM 1.0

#=GF AC   RF01828
#=GF ID   SprD
#=GF DE   Small pathogenicity island RNA D
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20532214
#=GF SS   Published; PMID:20532214
#=GF GA   100.00
#=GF TC   160.00
#=GF NC   42.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20532214
#=GF RT   A Staphylococcus aureus small RNA is required for bacterial virulence and
#=GF RT   regulates the expression of an immune-evasion molecule.
#=GF RA   Chabelskaya S, Gaillot O, Felden B
#=GF RL   PLoS Pathog. 2010;6:e1000927.
#=GF RN   [2]
#=GF RM   16183745
#=GF RT   Small RNA genes expressed from Staphylococcus aureus genomic and
#=GF RT   pathogenicity islands with specific expression among pathogenic strains.
#=GF RA   Pichon C, Felden B
#=GF RL   Proc Natl Acad Sci U S A. 2005;102:14249-14254.
#=GF WK   SprD
#=GF SQ   2


ACHD01000263.1/80388-80529 GGGCGUUUUCAAGGAGCGCCUUUCAUUUUUUAUGUAUUGCUCCUUUUCGGGCUAGUUUAUUAAAUUUAUUUUUGCGCUUUCCAAAUCAAUGUAUAUGUGUUAUAUUGUUUAUGGGAAGUAGGUAAGCAUUUCGGUGCUUACC
BA000018.3/2007178-2007037 GGGCGUUUUCAAGGAGCGCCUUUCAUUUUUUAUGUAUUGCUCCUUUUCGGGCUAGUUUAUUAAAUUUAUUUUUGCGCUUUCCAAAUCAAUGUAUAUGUGUUAUAUUGUUUAUGGGAAGUAGGUAAGCAUUUCGGUGCUUACC
#=GC SS_cons               <<<<<<<<_____>>>>>>>>,,,,,,<<<-<<<-<<<<<<<______>>>>->>>->>>->>>,,,,,,,,,,,<<<<<<<<<<-<<<<<<<_______>>>>>>>->>->>>>>>>>,<<<<<<<<<____>>>>>>>>>
#=GC RF                    gGGCGcucUCAAGgagCGCCcUUCAUUuuuUaugUacuGCcCCUUUUCGgGCUaguUcauUaaaUUUAUUUUUGCgCuucCCaaaUCaauguaUAUGUGUuacauuGUuuAuGGgaaGcAGGuaaGCacUUCGguGCuuaCC
//
# STOCKHOLM 1.0

#=GF AC   RF01829
#=GF ID   sR6
#=GF DE   sR6 snoRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:10775111
#=GF SS   Predicted; Mfold; Moore B
#=GF GA   60.00
#=GF TC   89.20
#=GF NC   35.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF RN   [1]
#=GF RM   10775111
#=GF RT   Homologs of small nucleolar RNAs in Archaea.
#=GF RA   Omer AD, Lowe TM, Russell AG, Ebhardt H, Eddy SR, Dennis PP
#=GF RL   Science. 2000;288:517-522.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


CP000077.1/368187-368239 GGAUGAUGACCAAAUAGACUGAAAGAUGAAGAAAUGCACCUCAACUGACUAAA
AF195100.1/1-53          GGAUGAUGACCAAAUAGACUGAAAGAUGAAGAAAUGCACCUCAACUGACUAAA
#=GC SS_cons             <<_______>>------------<<-<<<-<________>>>>->>:::::::
#=GC RF                  GGAUGAUGACCAAAUAGACUGAAAGAUGAAGAAAUGCACCUCAACUGACUAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01830
#=GF ID   StyR-44
#=GF DE   Salmonella enterica Typhi npcRNA 44
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:20460466
#=GF SS   Predicted; CMfinder
#=GF GA   54.00
#=GF TC   54.00
#=GF NC   53.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.57 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20460466
#=GF RT   Experimental identification and characterization of 97 novel npcRNA
#=GF RT   candidates in Salmonella enterica serovar Typhi.
#=GF RA   Chinni SV, Raabe CA, Zakaria R, Randau G, Hoe CH, Zemann A, Brosius J,
#=GF RA   Tang TH, Rozhdestvensky TS
#=GF RL   Nucleic Acids Res. 2010;38:5893-5908.
#=GF WK   Bacterial_small_RNA
#=GF SQ   34


AE014613.1/2690822-2690714   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAACG------AAAGUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAUGAUGAAUCG----AAAGAAACAUCUUCGG-
AY116932.1/331-439           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UC--GAA--ACAC---UGAACAACG------AAAGUUGUUC-----GUGAGUCUCUC-A---AA-CUUUCGCAACAC-GAUGAUGAGUCG-----AAAGGGACAUCUUCGG
AF100900.1/239-352           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAACG------AAAAUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAUGAUGAAUCGUAAGAAAAGAAACAUCUUCGG
ABHU01000059.1/3214-3111     -----AAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---UGAACAACG------AGAGUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAUGAUGAAUCG-----AAAGAAACAUCUUCGG
CP000857.1/4171432-4171538   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAACG------AAAGUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAGAAUGUUUU-------ACGAAACAUCUUCGG
ABKX01000004.1/394099-393989 CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---UGAAUAGUCG----AAAGAUUAUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAUGAUGAAUCG-----AAAGAAACAUCUUCGG
CP001113.1/4386681-4386779   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAACG------AAAGUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAAG---------------UGAAACAUCUUCGG
CP000468.1/4355748-4355847   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---UGAACAACG------AAAGUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACUCUGAAG---------------UGAAACAUCUUCGG
CP000880.1/3459447-3459349   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAACA------UAAGUUGUUC-----GUGGGUCUCUC-A---AA-UUUUUGCAACGU-GAAG---------------UGAAACAUCUUCGG
AB236014.1/275-381           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACAC---AGAACAAUG------CGAAUUGUUC----CGUGGGUCUCUC-A---AA-UUUUCGCAA-UU-GAUGGUGUUUU-------ACGAAACAUCUUCGG
FJ410388.1/548-654           CUUU-AAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAGCU------CA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAAGUC-GGUGAUGAAUCG-----AAAGAAACAUCUUCGG
AF259999.1/375-477           CACUUAAAAUCUG-AUCA-GCUGAAAU--U----GA--ACAC---UGAC--ACG------AACUUUGUUC-----GUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAUGAUGAAUCG-----AAAGAAACAUCUUCGG
EU623145.1/240-345           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAGUG------AA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCGACAC-GAUGAUGUUUC-------ACGAAACAUCUUCGG
CP000822.1/185538-185640     CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACAC-GU-------AA-AGUGUGU-----AUGAGUCUCUC-A---AA-UUUUCGCAACAC-GAAG-UGUUUC-------ACGAAACAUCUUCGG
BAAW01000727.1/1098-993      CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAUGU------UA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCGACAC-GAUGAUGUUUU-------ACGAAACAUCUUCGG
EU623354.1/239-345           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACAUCUUU------AAUGGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCGACAC-GAUGGUGUUUU-------ACGAAACAUCUUCGG
CP000964.1/5488123-5488018   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACUGUU------UA-AGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCGACAC-GAUGGUGUUUU-------ACGAAACAUCUUCGG
AJ010486.1/1772-1875         CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACAC--UU------AA-GGUGUGU-----UCGAGUCUCUC-A---AA-UUAUCGCAAUGC-GGCGAUGUUUU-------ACGAAACAUCUUCGG
EU721606.1/377-485           CUUAAAAAAUCUGGAUCCUCCUGAAUA--UU--GAA--ACAC---UAAACAAAA------AAAGUAGUUC-----AUAAGGCACUC-A---CA-UUUGCGCAAUGC-GAAGAUUUAUCC-----UAUGAAAAAUCUGCUG
AY116919.1/393-498           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAGUC------AA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCGACAC-GUGGGUGUUUU-------ACGAAACAUCUUCGG
EU623213.1/394-491           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAGUU------AA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAACCA-GAAG---------------UGAAACAUCUUCGG
DQ399552.1/94-191            CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAUGU------UA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAAUCA-GAAG---------------UGAAACAUCUUCGG
CP000647.1/3202639-3202542   CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACUGUU------UA-AGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAAUCA-GAAG---------------UGAAACAUCUUCGG
EU623091.1/238-331           CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACACAGUU------AA-UGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAAUCU-GAAG-------------------ACAUCUUCGG
AF047424.1/240-332           CUUUAAAAAUCUGGAACAAGCUGAAAA--UU--GAA--ACAA---UAAACGCGU------AA--GCGUUU-----AUGAGUCUCUCUA---AA-UUAUCACA-CCU-GAAG-------------------ACAUCUUCGG
AY706746.1/462-568           CUUUAACAAUCUGGAACAAGCUGAAAA--UUCGAAA--ACAA--UCGAAUUGCUUUUAACAA-GUGAUUC-----GAGAGUCUCUC-A---AA-UGCUUGCAGCAC-GAAG---------------UGAAACACCUUCGG
AY591328.1/395-501           CUUUAACAAUCUGGAACAAGCUGAAAU--UC-GAAA--ACAC--UCGGAUUGCUUUUAAUAAAGUGAUCC-----GAGAGUCUCUC-A---AA-UGCUUACAGCAC-GAAG---------------UGAAACACCUUCGG
AY587142.1/1755-1856         CUUUAACAAUCUGGAACAAGCUGAAAA--UU--GAA--AC-A---CACAUUAUUG----AAAAAUAGUGU-----GGGGAACUCUC-A---AA-ACUCC--AAGUU-GAAGUGUUAUGC-----AAAUAG------GCAG
AF373202.1/1777-1883         CUUUAACAAUCCGGAACAAGCUGAAUAAUU--UGAA--ACGACGGCAUAUGAAUG----UGAAUUCAUGUGUUGUUCGAGUCUCUC-A--A-AAUACUCGCAUCCC-GAGA--------------------CACUUUCGG
AF548140.1/2032-2148         CUUUAACAAUCCGGAACAAGCUGAAAA--UU-UGAA--ACAC----AUGCUGAAGU-GCAAACUCAGUAU-----GCGAGUCUCUC-AAACGA-AGUAAGCAAACC-UGAGAUAACGCG-----CAAGCGUUAUCACUGU
EU285525.1/2391-2498         CUUUAACAAUCUGGAACAAGCUGAAAA--UUCGAAAAUACUC----GGAUUGCUUUUAAUAAAGUGAUCC-----GAGAGUCUCUC-A---AA-UGCUUACAGCAC-GAAG---------------UGAAACACCUUCGG
FJ517952.1/425-528           CUUUAACAAUCUGGAACAAGCUGAAAA-AUU-GAAA--ACAA--AUCAAUAUAUCA-CCGAGGUAUAUUG-----GUGAGUCUCUC-A---AA-AUCUCA-AAUCU-GAAAAGU-----------------ACUCUUCAG
FJ518551.1/451-563           CUUUAACAAUCUGGAACAAGCUGAAAA-AUU-GAAA--ACAA--AUCAAUAUAUCA-CCGAGGUAUAUUG-----AUGAGUCUCUC-A---AA-AUCUC--AAACU-UUGAAUGUGUU-------UUUCGACAUCGAAGU
ABWM02000001.1/211-104       CUUUAAAAAUCUGGAUCAAGCUGAAAA--UU--GAA--ACGA---CACAUCUAU------AA-GGUGUGU-----UCGAGUCUCUC-A---AA-UUUUCGCAAGUC-GAUGAUGAAUCG-----AAAGAAACAUCUUCGG
#=GC SS_cons                 :::::::::::::::::::<<-<<<<<..<<..---..-<<<...-<<<<<<<_......___>>>>>>>.....>>>--------.-...>>.>>>>>>>----<.<<-<<<<____.......______>>>>->>>:
#=GC RF                      CUUUAAaAAUCUGGAuCAAGCUGaaaa..Uu..GAA..ACgc...ugcAcagcu......AAagcugUgc.....gcGAGUCUCUC.A...aA.uuuuCGCAAcac.gaaGauguaUc.......AuGAAAcauCUucgG
//
# STOCKHOLM 1.0

#=GF AC   RF01831
#=GF ID   THF
#=GF DE   THF riboswitch
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Ames T
#=GF SE   Published; PMID:20659680
#=GF SS   Published; PMID:20659680
#=GF GA   36.00
#=GF TC   36.70
#=GF NC   35.30
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.60 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0046653; tetrahydrofolate metabolic process;
#=GF RN   [1]
#=GF RM   20659680
#=GF RT   A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate.
#=GF RA   Ames TD, Rodionov DA, Weinberg Z, Breaker RR
#=GF RL   Chem Biol. 2010;17:681-685.
#=GF WK   Tetrahydrofolate_riboswitch
#=GF SQ   97


BABA01009937.1/46-141          ---UC-AGAGUAGAAAACGAUGCGUUA-----------------AGUG-UCCAGCAGAC-GGGGAGUUGCUGCCGGAACGAA-A-AGC---------------------------AAA--------------------------GCUUGCGGUAUCGUUU-UCGCAUCCCGCUG-A---
BABB01000157.1/63-158          ---GC-AGAGUAGACACAUGUGCGUUA-----------------AGUG-CCGGAUGAAC-AGGGAGUUGUCACCCGGACGAA-A-AG----------------------------AAAA------------------------U-CUUGCGGUACAUGAG-UCGCAUCCCGCUG-C---
BABF01004573.1/52-147          ---GC-AGAGUAGGUUUGUGUGCGUUA-----------------AGUG-CUGGUUGAAC-AGGGAGUUGUCAGCCGGACGAA-A-AG----------------------------AUUU------------------------U-CUUGCGGUACACGAA-UCGCAUCCCGCUG-C---
BABE01004909.1/284-381         -A-GC-AGAGUAGGUCAGGAAGCGUUA-----------------AGUA-CCAUCUGAAC-GGGGAGUUGUCAGACGGGCGAA-A-AG----------------------------UUUA------------------------U-CUUGCGGUUUCCUGG-UCGCAUCCCGCUG-U-U-
BAAU01016335.1/416-525         ---GC-AGAGUAGGUAUAUGUGCGUUA-----------------AGUG-CCGGAUGAAC-AGGGAGUAGUCAACCAGACGAA-A-GGGG------------------------CAAGAUAUGA---------------AACUGUUCCUGCGGUACAUGAG-CCGCAUCCCGCUG-C---
BAAV01010818.1/618-715         -A-GC-AGAGUAAGUGCCUACGCGUUA-----------------AGUG-CCGGA-GUAC-GGGGAGUUGACAUCUGGACGAA-A-GCC---------------------------UUCG-------------------------GGCUGCGGUGUAAGCA-UUGCAUCCCGCUG-C-U-
BABG01026644.1/586-688         ---GC-AGAGUAGGAAUACAGGCGUUA-----------------AGUG-CUGGUUGAAC-AGGGAGUUGUCAGCCGGACGAA-G-AGAC------------------------CCUCCGG----------------------GGUUUCGCGGUCAGUAUU-CCGCAUCCCGCUG-C---
BAAX01022545.1/141-43          CAA-C-AGAGUAAGACCCUGCGCGUUA-----------------AGUG-CCGCAUCAAC-GGGGAGUUGUGCUGCGGACGAA-G-GU----------------------------AUUA--------------------------GCCGCGGUGCAGGGU-CUGCAUCCCGCUG--CUG
BABG01004557.1/3-100           CAA-C-AGAGUAAGGCCAUGUGCGUUA-----------------AGUG-CCGCAUCAAC-GGGGAGUUGUGCUGUGGACGAA-G-G-----------------------------UGUA------------------------C--CCGCGGUGCAUGGU-CUGCAUCCCGCUG--CUG
BAAX01002679.1/2103-2006       CAA-C-AGAGUAAGGCUAUGCGCGUCA-----------------AGUG-CCGCAUCAAC-GGGGAGUUGUGCUGCGGACGAA-G-GG----------------------------AGA---------------------------CCCGCGGUGCAUGGC-CUGCAUCCCGCUG--CUG
BAAU01000940.1/627-724         CAA-C-AGAGUAAGGCUAUGCGCAUCA-----------------AGUG-CCGCAUCAAC-GGGGAGUUGUGCUGCGGACGAA-G-GG----------------------------AGA---------------------------CCCGCGGUGCAUGGC-CUGCAUCCCGCUG--CUG
BABE01017430.1/618-522         -U-GC-AAAAUAGGAUUUUAUGCGUCA-----------------AGUG-UUCGGUGAAU-GGGGAGUUGUCACUGAAACGAA-A-AG----------------------------UGCG------------------------U-CUUACGGUAUAUUAU-CCGCACCCG-UUG-C-A-
BABE01001528.1/194-88          UA-GC-GAAGUAGGAUUUUAUGCGUCA-----------------AGUG-UUCACAGGCU-GGGGAGUCGCC-GUGAAACGAA-A-AGCA------------------------GAAAGCGU--------------------GCUGCUUACGAUAUAAUUU-CCGCACCCG-UUG-C-UA
BABD01033677.1/236-329         ----C-AGAGUAGG-AACAGCGCGUCA-----------------AGUG--CGUCGGGAU-GGGAAGUUGUCCGGCG-ACGAA-G-GGG--------------------------CUGCG-----------------------CGCCCCGCGGUGCUGUUG-CCGCUUCCG-CUG-----
BAAZ01000245.1/2377-2470       ----G-GGAGUAGG-AACUGUGCGUUA-----------------AGUA-CCGGUCGGAU-GGGAGGUUGCC-GCCGGGCGAA-G-GAG--------------------------CUUCG------------------------GCUCCGCGAUACGGUUA-CCGCAACCG-CCU-----
BAAZ01020636.1/794-894         -U-UU-AGAGUAGGAAAUAAAUAGUAA-----------------A--GACUUAAUAAACGGGGAAGUUGUUAUUAGG--GCNAA-UAA--------------------------AUAUU------------------------UUUAUGCCUUAUUAUUU-UCGCAUUCCGCUA-AGA-
BABA01028836.1/106-1           ----C-AGAGUAGGGUAG-AUGCGUGUACAUUA----GUCUACA-GUG-UCUGAGG-ACGGGGACGUGA-CCUCGGAACGAA-U-GGC---------------------------GAAA-------------------------GCCUACGAUAUUUUAC-CCGUCGUCCGCUG-C---
AAPZ02000001.1/1062273-1062367 ----U-GGGGUAGGAAUCUCAGAGUUA------------------UUGUCUAACGGAAC-GGAAUGU-GAACGUUAGAAGGA-G-GCU--------------------------AAUGA-----------------------CUAGCUGC-UUUGUUAUU-CCGCAUUCA-CCA-----
AACY023280528.1/886-799        ----C-AGAGUA-GAUAGGAAGCAUUA-----------------AGUG--UUAAGAAAU-GGGUUGUUGUUCUUAA-ACGA--A-GC----------------------------AUAU------------------------C-GCUAUGAUUUUCUGU-C-GCAACCG-CUG-----
CP001098.1/71606-71705         -G-GC-AGAGUAGGUGGCUAUGCGUAAA---------------UAGUG-CUUAAGG-AU-GGGACGUUG-CCUUAAGACGAAAU-GCC---------------------------UAUC------------------------AGGCUGCGGUAUAGCCA-CCGCGUCCG-CUG-U-C-
ABAW02000025.1/72799-72896     -A-GC-AGAGUAGGAUAGGAAGCGUUA-----------------AGUA-UCUUCUGAAC-GGGGAGUUGUCAGAAGGGCGAA-A-AGA---------------------------UUU--------------------------UCUUGCGAUUUCUUAU-CCGCAUCCCGCUG-U-U-
AE015927.1/1800312-1800211     -G-UU-AGAGUAGGUGAUUGCGCGUGA-----------------AGUG-CUAGUUGGAU-AGGAUGUUGCC-ACUAGACGAA-A-AAAU------------------------CUUUU-G----------------------GAUUUUGCGAUGCAUAUA-CCGCUUCCG-CUA-A-C-
ABEE02000015.1/221133-221224   -G-GC-AGAGUA-GGAAACUUGCAUUA-----------------AGUG-UUACAAG-AU-GGGAUGUUGC-UUGUAAACGAA-G-AG----------------------------AUUU--------------------------CUCGUGGUUAGUUUU-C-GCAUCCA-CUG-U-U-
CP000422.1/1424554-1424642     ----U-GGAGUAGGAAUCGAUGCGUUA-----------------AGUG-CCAACAAGAC-GGAGAGUUGCUUGUUGGACGAA-U-G-----------------------------CUUG------------------------U--CAGCGAUAUCGAUU-CCGCAU--C-UCG-----
CR936503.1/348925-349019       ----C-GGAGUAGGGAUUAAAGCGUUA-----------------AGUG-CUGGUGGAAC-GGAAUGU-GAACACCAGACGAA-G-AGC--------------------------AGUAA------------------------UGCUCGCGGUUUUAGUC-CCGCAUUCG-CCG-----
CP000414.1/123971-124060       -------GGGUAGAUUGAUGCGCGUUA-----------------AGUG-CAGCGGAGAC-GGAAUGU-GAGCCGCUGACGAAAC-AA----------------------------ACAUU----------------------CA-UUGCUAGCAUUUU-U-UCGUGUUAG-C-------
ABDQ01000031.1/13491-13593     -G-GC-AGAGUAGGUAUUUGUGCGUUA-----------------AGUG-UCAGUGGAAC-GGGAAGUUGUCCAUUGAACGAA-A-AAUG-------------------------AAUUU-----------------------UCAUUUGCGGUGCAUAUA-UCGCAUUCCGCUG-C-C-
AAQK01002842.1/285-380         ---AC-AGAGUAAAAAUAUGUGCGUUA-----------------AGUG-CCUUUAACAC-GGGGAGUUGGUUAAGGAACGAA-A-AG----------------------------UUAU------------------------U-CUUGCGGUACAUAUU-UUGCAUCCCGCUG-U---
CP000724.1/4463946-4464038     -G-GC-AGAGUA-GGUGUUAUGCGUUA-----------------AGUG--UUAGGGGAU-GGGAAGUUGCUCCUAA-ACGAA-G-AA----------------------------CUCA------------------------U-UUCGCGAUAUAACAC-C-GCGUCCA-CUG-U-C-
BABG01026548.1/656-558         -G-AC-AGAGUAGGUUAACGUGCGUAA-----------------AGUG-CCUGAGGGAC-GGGGAGUUGUCCUCAGGACGAA-C-ACU---------------------------GAAA-------------------------GGUGGCGGUACGUUUU-CCGCAUCUCGCUG-U-U-
CP000939.1/904743-904843       -A-AC-AGAGUAGGUAAUUACACGUUA-----------------A--GGUUUAGAGGAC-GGGAAGUUGUCUCUAAA-AGAA-A-AAUC------------------------UUUAA-A----------------------AGAUUUGCGAUGU-GUUA-CCGCAUUCCGCUG-U-U-
AAQL01011279.1/614-718         -A-GC-GAAGUAGGAUUUUAUGCGUCA-----------------AGUG-UUCACAGGCU-GGGGAGUCGCC-GUGAAACGAA-A-AGCA------------------------GAAAGCGU--------------------GCUGCUUACGAUAUGAUUU-CCGCACCCG-UUG-C-U-
ABCC02000039.1/266095-266205   ---GC-AGAGUAGGUAUAUGUGCGUUA-----------------AGUG-CCGGCUGGAC-AGGGAGUUGUCAGCUGGACGAA-A----GAGGA-----------------UUCCCAAA-GGGAA--------------ACUGUC---UGCGGUACAUAUG-CCGCAUCCCGCUG-C---
AAYG02000031.1/153078-152980   -A-GC-AGAGUAGAAGUAUGUGCGUUA-----------------AGUG-CCGGUUGGAC-GGGGAGUUGCCAGCAGGACGAA-A-AGU---------------------------GAAU-------------------------GCUUGCGGUACAUAUU-UCGCAUCCCGCUG-C-U-
AAQK01008307.1/175-79          -AA-C-AGAGUAAGACCCUGCGCGUUA-----------------AGUG-CCGCAUCAAC-GGGGAGUUGUGCUGCGGACGAA-G-GU----------------------------AUUG--------------------------ACCGCGGUGCAGGGU-CUGCAUCCCGCUG--CU-
CP000382.1/1647712-1647607     -G-GC-AGAGUAGGUAUUUGUGCGUUA-----------------AGUG-UCAUUGGAAC-GGGAAGUUGUCCAUUGAACGAA-A-AAUG------------------------AAUUUAU---------------------UUCAUUUGCGGUGCAUAUA-UCGCAUUCCGCUG-C-C-
AAQK01002704.1/947-835         -U-GC-AAAAUAGGUUUCCAUGCGUCA-----------------AGUG-UUUUGUGGAU-GGGGAGUUGCCACAGAAACGAA-A-AG-UCGG-------------------UUCGCGUGCGGA----------------CCGGA-CUUACGAUAUGGUUA-CCGCACCCG-UUG-C-A-
CP000853.1/2619446-2619544     ----C-AGAGUA-GAUAUUGCGCGUUA-----------------AGUG-UUGAAGG-AU-GGGAAGUUG-CCUUCAAACGAA-A-AAUAG----------------------UACCAU-GU--------------------ACUAUUUGCGGUGCAAUAU-C-GCAUCCG-CUG-----
CP000407.1/125748-125890       ---AC-AGAGUA-GAUGGUUUGCGUCA-----------------AGUG-UAUGUGG-AU-GGGGUGUUG-CCACAUAACGAA-G-CUGAUCUUUGCUUGCAUCUGAUGUCUCCUAGAG-UAGGAACAUUGGUCCUGGCUGAGAGUAGCGCGGUAAACCAU-U-GCAUCCG-CUG-U---
CP000423.1/2247840-2247748     ---UA-GGAGUAGGAACCUGCGCGUUA-----------------AGUG-CUGCCGGAAC-GGAAUGU-GAACGGCAGACGAA-G-AC----------------------------AAGU--------------------------GUCGCGGUGCAGGUG-CCGCAUU-CGCCU-G---
CP000724.1/4839802-4839709     -G-AC-AGAGUA-AAUAAUAUGCGUAA-----------------AGUG--UCAAAGGAU-GGAACGUUGUAUUUGA-ACGAA-G-AGC---------------------------AAAU-------------------------GCUUGCGACAUAUUAU-U-GCGUUCG-CUG-U-U-
CP000673.1/3903929-3904044     -A-GC-AGAGUAGAACGUUGUGCGUAAAUCAUU----GAUUUGCAGUG-CCUUCUGAAC-GGGGAGUUGUCAGAGGGACGAA-A-AGCC-------------------------UUUUA-----------------------GGGCUUACGGUACAAGGU-UCGCAUCCCGCUG-C-U-
AAVO02000004.1/164832-164736   -U-GC-AAAAUAGGAUCAUAUGCGUCA-----------------AGUG-UUCAGCGAAU-GGGGAGUUGUCGCCGAAACGAA-A-AG----------------------------UCCG------------------------U-CUUACGGUAUAUGAU-CCGCACCCG-UUG-C-A-
AE001437.1/2534636-2534729     -A-GC-AGAGUA-GAUAUUGUGCGUCA-----------------AGUG-UUAGAGG-AU-GGGAAGUUG-UCUCUAAACGAA-A-AG----------------------------CUUA-----------------------GU-CUUGCGGUUCAAUAU-C-GCUUCCG-CUG-U-U-
AP007281.1/1983266-1983360     ----U-GGGGUAGGAAUCUCAGAGUUA------------------UUGUCUAACGGAAC-GGAAUGU-GAACGUUAGGAGGA-G-GCU---------------------------UAUAA----------------------CUAGCUGC-UUUGUUAUU-CCGCAUUCA-CCA-----
AAQK01005422.1/60-187          -G-GC-AGAGUAAGCUUCCGUGCGUGA-----------------AGUG-CCGAGUGGAC-AGGGAGUUGUCACUCGGACGAA-G-AGACAGGAAG-------------GCGAUGAGUCUGUCAUCG----------CCAUCCCGUCUCGCGGUACGGAAG-CUGCAUCCCGCUG--CU-
ACHL01000137.1/17495-17397     -UA-C-AGAGUAGAAAAUAAAGCGUUA-----------------AGUG-CUAAGAGGAU-GGGAUGUUGCCUCUUGGACGAA-G-GAC---------------------------GUAA------------------------UGUUCGCGGUUUUAUUU-UCGCAUUCG-CUG--CA-
AP009049.1/1524197-1524313     -A-GC-AGAGUA-AAUAUUAUGCGUAA-----------------AGUG-UUAGAGA-AU-GGGAGGUUG-UCUCUAAACGAA-A-AGCUUAAAU---------------ACUUGUUAU-AUAAG-------------AUUUAAAGCUUACGAUAUAAUAU-U-GCUUCCG-CUG-U-U-
CP000233.1/1666649-1666554     ------GGGGUAGGAAUCCUUGCGUAA-----------------CGGA-CUAAUGGAAC-GGAAUGU-GAACAUUAGUAGAUUA-AGU--------------------------CCGAUA----------------------UGACUUAGCGUUUGGUUU-CCGCAUUCA-CC------
AAQK01006702.1/2245-2148       ---GC-AGGAUA-GUUGCUUCGGACUC-----------------AGUG-CUCCGGGGAC-GGGGAGUUGUCCCGGGGACGAA-A-AGC--------------------------CAGAU------------------------GGCUUACGGUGCGGCAU-CCGCAUCCCGCUG-C---
CP000416.1/852209-852116       ----C-GGAGUAGGAAAUAAAGCGUCA-----------------AGUG-CCGGUGGAAC-GCAAUGU-GAACACCGGACGAA-G-GGC---------------------------AAUU------------------------GGCCCGCGAUUUUAUUU-CCGCAUUGG-CCG-----
CP001348.1/1695232-1695339     -G-GC-AGAGUAGAUUUUUGUGCGUUA-----------------AGUG-CCGGAAGGAC-GGGAAGUUGCCUUUCGGACGAA-A-AACAA-----------------------UAAUUUUU--------------------AUUGUUUGCGGUACAAAUA-UCGCAUUCCGCUG-C-C-
CP000727.1/864723-864823       -A-AC-AGAGUAGGUAAUCACACGUUA-----------------A--GGUUUAGAGGAC-GGGAAGUUGUCUCUAAA-AGAA-A-AGUC------------------------UUUAA-A----------------------AGAUUUGCGAUGUG-UUA-CCGCAUUCCGCUG-U-U-
AAXG02000014.1/43071-43187     -G-GC-AGAGUAGGAGCGCGUGUGCAGUACCUCGCAAGGGGUCCAGUG-CCGGCGGGAC-GGGGAGUUGUCCGCCGGACGAA-A-AGC--------------------------CACA-------------------------GGCUUGCAGUACGCCCU-CCGCAUCCCGCUG-C-C-
ABGD02000012.1/179260-179163   -G-GC-AGAGUAGGAACCGGCGCGUUA-----------------AGUG-CCGCCUGAAC-GGGGAGUUGUCAGGCGGACGAA-A-AGA---------------------------GUU--------------------------UCUUGCGGUGCCGGUU-UCGCAUCCCGCUG-C-U-
ABFY02000012.1/69214-69315     -A-GC-AGAGUAGGAAAACGUGCGUUA-----------------AGUG-CCAGCCGGAC-GGGGAGUUGCCGGCGGGACGAA-A-AGUA------------------------AGGAUU-------------------------ACUUGCGGUACGUUUU-UCGCAUCCCGCUG-C-U-
ABWO01000186.1/26189-26089     -A-GC-AGAGUAAGAGUAUGUGCGUUA-----------------AGUG-CCAGUUGGAC-GGGGAGUUGCCAGUCGGACGAA-A-AGC--------------------------AAAAU------------------------UGCUUGCGGUACAUACU-CUGCAUCCCGCUG-C-U-
ABYI02000015.1/33605-33505     -A-GC-AGAGUAGAGAUGUGUGCGUUA-----------------AGUG-CCAGCCGGAC-GGGGAGUUGCCGGCAGGACGAA-A-AGCC-------------------------UGGAA-------------------------GCUUGCGGUACAUAUC-UCGCAUCCCGCUG-C-U-
ABVQ01000035.1/347941-347845   -A-GC-AGAGUAGAAUUUUGUGCGUUA-----------------AGUG-CUGAGUGAAC-AGGGAGUUGUCAUUCGGACGAA-A-AG----------------------------AUUU--------------------------CUUGCGGUACAGAAU-UCGCAUCCCGCUG-C-U-
CP001078.1/2874589-2874491     -G-AC-AGAGUAGAUAUUUGCGCGUUA-----------------AGUG-UUAAGAGGAC-GGGAAGUUGCCUUUUAAACGAA-A-AAC---------------------------UUUU-------------------------GUUUGCGGUGUAAAUA-UUGCAUUCCGCUG-U-U-
ACCJ01000114.1/2562-2664       -U-GC-AGAGUAGGUUUAUGCGCGUUA-----------------AGUG-CCGGCUGAAC-AGGGAGUUGUCAGCUGGACGAA-A-AGGG-------------------------AAUCA-----------------------UCCCUUGCGGUGCGUAGG-CCGCAUCCCGCUG-C-A-
ACEC01000113.1/20426-20527     -A-GC-AAAGUAGACAUUUGCGCGUUA-----------------AGUG-UCCGAUGAAC-GGGGAGUUGUCAUCGGAACGAA-G-GGAA------------------------GUUUCU-------------------------UCCUGCGGUGCAAAUG-UUGCAUCCCGUUG-C-U-
ACOK01000004.1/41711-41613     -U-GA-AGAGUAAAAAUGCGUUCGUUA-----------------AGUG-UUGACUGAAC-GGGGAGUUGUCAGUCAAACGAA-A-AGC---------------------------UUCG-------------------------GCUUGCGGUUCGUAUU-UUGCAUCCCGCUU-C-A-
ABQR01000045.1/213424-213528   -A-GC-AGAGUAGGCAUAUGUGCGUUA-----------------AGUG-CCGGCUGAAC-AGGGAGUUGUCAGCUGGACGAA-A-GGAACC---------------------UUCGGUU-------------------------UCCUGCGGUACAUAAG-CCGCAUCCCGCUG-C-A-
ACIN02000021.1/2207-2306       -A-GC-AGAGUAGAAAAUCUAGCGUAA-----------------AGUG-CCAGCCGGAC-GGGGAGUUGCCGGCAGGACGAA-G-AGU--------------------------UAAAU-------------------------GCUCGCGGUGAGGUUU-UCGCAUCCCGCUG-U-U-
ACAO01000008.1/73651-73753     -A-UC-AGAGUAGGAAAUAAAGCGUUA-----------------AGUG-CUGAAAGGAU-GGGAUGUUGCCUUUCGGACGAA-G-AACG------------------------AUCAUU------------------------CGUUCGCGGUUUUAUUU-UCGCAUUCG-CUGCA-U-
ACIP02000001.1/94372-94274     -U-GC-AGAGUAGAAACCACGGCGUUA-----------------AGUG-CCUCCUGAAC-AGGGAGUUGUCAGUGGGACGAA-G-AGG---------------------------GGAU-------------------------CCUCGCGGUCAUGGUU-UCGCAUCCCGCUG-C-U-
ACAJ01000006.1/70988-71087     -A-UC-AGAGUAGGAAAUAAAGCGUUA-----------------AGUG-UCGAAAGGAU-GGGAUGUUGCCUUUUGGACGAA-G-AAC--------------------------GAUUC-------------------------GUUCGCGGUUUUAUUU-UCGCAUUCG-CUGCA-U-
ACCF01000156.1/25104-25200     -A-AC-AGAGUAGGUUCCUGCGCGUUA-----------------AGUG-CUUUCUGAAC-GGGGAGUUGUCAGAAGGACGAA-A-AG----------------------------GUUU--------------------------CUUGCGGUGCAGGUU-CCGCAUCCCGCUG-A-C-
ACJM01000014.1/36600-36692     -U-GC-AGAGUA-GGUGGCAUGCGUUA-----------------AGUG-CUAAGGG-AU-GGGAAGUUG-CCCUUAGACGAA-A-GGU---------------------------UUA--------------------------UCCUGCGAUAUGUCAC-C-GCAUCCA-CUG-C-C-
ABIL02000006.1/201569-201478   -C-GC-AGAGUA-GAUAAGAUGCGUUA-----------------AGUG-UUAAAGG-AU-GGGAAGUUG-CCUUUAAACGAA-A-AC----------------------------GAAA--------------------------GUUGCGGUAUCUUAU-U-GCGUCCG-CUG-U-G-
ACBZ01000165.1/18004-18100     -U-GC-AAAAUAGGAUUUCAUGCGUCA-----------------AGUG-UUCAGUGGAU-GGGGAGUUGCCGCCGAAACGAA-A-AG----------------------------UACG------------------------U-CUUACGAUAUGAGGU-CCGCACCCG-UUG-C-G-
ACKX01000080.1/10519-10620     -U-GC-AGAGUAGAGAAUAAAGUGGUU-----------------AGUG-CCCGACACAC-AGGGAGUUGGUGUCGAGACGAA-G-AGCC-------------------------GAAUC------------------------GGUUCCCAGUUUUAUUU-UCGCAUCCCGCUG-C-C-
ACKZ01000029.1/132325-132227   -A-UC-AGAGUAGACUUUAUUGCGUUA-----------------AGUG-CCCGGAGGAU-GGAAUGUUGCCACUGGGACGAA-A-AUG---------------------------GAAA-------------------------CAUUGCGAUAAUUUAG-UCGCAUUCG-CUGCA-U-
ACIL02000003.1/15754-15855     -A-CC-AGAGUAAGAAAAGAAGCGUUA-----------------AGUG-AUAGCGAGAU-GGAAUGUUGCUC-CUAUACGAA-A-AAAUG----------------------CUGGACA-------------------------UUUUGCGGUUUCUUUU-CUGCAUUCG-CUG-C-A-
ABHH01000004.1/97682-97579     -A-UC-AGAGUAGGAAAUAAAGCGUUA-----------------AGUG-UCGCUGGGAU-GGGAUGUUGCCC-GCGAACGAA-A-GAUU-------------------------GUUUAG---------------------GCAAUUUGCGGUUUUGUUU-CUGCAUUCG-CUGCA-U-
CP001034.1/2651359-2651454     -G-GU-AGAGUA-GGUGUCUCGCGUUA-----------------AGUG-CCAAGGG-AU-GGGACGUUG-CCCUUGGACGAA-A-GCU--------------------------AUUAA------------------------GAGCUGCGUUGGGACAU-C-GCGUUCG-CUA-U-C-
AM946015.1/1244497-1244587     -G-AC-AGAGUA-GAUGGUUUGCGUUA-----------------AGUG--UAUGUGAAU-GGGAUGUCGUCACAUA-ACGAA-G-C-----------------------------UUAU------------------------U--GCGCGGUAAAUCAU-C-GCAUCCG-CUG-U-U-
ABJK02000016.1/18473-18563     -C-AC-AGAGUA-GAUGAUUCGCGUCA-----------------AGUG--UGUGUGAAU-GGGAUGUCGUCACACA-ACGAA-G-CA-----------------------------AUU--------------------------UGCGCGGUGAAUCGU-U-GCAUCCG-CUG-U-U-
ACGC01000009.1/96239-96150     -A-UC-AGAGUA-GAUAAAGAGCAUUA-----------------AGUG--UUAGGAAAU-GGGUUGUUGUUCCUAA-ACGAA-G-C-----------------------------GAAU---------------------------GCGUGAUUCUUUAU-C-GCAACCG-CUG-C-C-
AP008971.1/956558-956470       -A-AC-AGAGUAGG-GUUGAUGCGUUU-----------------AGUG--UAAUGGGAU-AGGGAGUUGCCCAUUA-ACGAA-A-------------------------------UCAU----------------------------UGCGAUAUCAAUG-CCGCUUCCG-CUG-A-U-
DQ489736.1/97227-97326         -------GGGUAGAUAGUUGUGCGUUA-----------------AGUG-UGAAGGAAAC-GGAAUGU-GGGCCUUCAACGAA-A-UGUUUUCG-----------------AUAUUGAAA-------------------------ACGUGCGAUGCAACUG-UCACAUUCACC-------
ACLL01000013.1/10304-10210     -G-UU-GGGGUAGGAACUCCAGAGUUA------------------UUGUCCAGCGGAAC-GGAAUGU-GAACGCUGGAAGGA-G-GCC---------------------------GCAG-------------------------GGCUGC-UUUGGUUUU-CCGCAUUCA-CCA---C-
ACGV01000122.1/3906-3812       -U-GUUGGGGUAGGAAUUACCGAGUUA------------------UUGUCCAGCGGAAC-GGAAUGU-GAACGCUGGAAGGA-A-GU----------------------------AUUA--------------------------GCUGC-UUGAUAAUU-UCGCAUUCA-CCA-C-A-
ACGH01000132.1/62035-62149     -U-AU-GGGGUAGGAAACAAUGCGUUA-----------------AGUG-UUGAAGGGAC-GGAAUGU-GACCUUCAAACGAA-A-ACCAAUCGGCU----------UCGACUUGCUGAU------------------------UGGUUGCGGUGUUGUUU-UCGCAUUCG-CCA-U-U-
ABYO01000283.1/48498-48413     -A-UC-AGAGUA-GAUAAAGAGCGAUU-----------------AGUG-CU-GGAAAAU-GGGUUGUUGUUUCC-AGACGAA-A----------------------------------C------------------------U---UCCGAUUCUUUAU-C-GCAACCG-CUG-A-C-
ACIQ02000013.1/140241-140142   -C-GC-AGAGUAGAGAUCCGAGCGGUA-----------------AGUG-UCCUCGA-AC-GGGGAGUUG-ACGAGGAACGAA-G-CUG---------------------------AGAGC----------------------CUCAGCGCGGUUCGGAUC-CCGCAUCCCGCUG-C-G-
ABWK02000009.1/209906-209808   -A-GC-AGAGUAGGUGUUUAUGCGUUA-----------------AGUG-CCGGGUAUAC-GGGGAGUUGAUAGCCGGACGAA-A-GCC---------------------------AUCA-------------------------GGCUGCGGUGUAAGCA-UUGCAUCCCGCUG-C-U-
ACTV01000001.1/67473-67374     -U-GC-AGAGUAGAUUUGUAUGCGUAA-----------------AGUG-CCCUCUGGAU-AGAGAGUUGCUGGAAGGACGAA-A-AGG---------------------------UAAA-------------------------UCUUACGGUGUACAAACUCGCAUCUCGCUG-C-A-
AP012027.1/393698-393787       -A-GC-AAAGUA-AAUGACACGCGUUA-----------------AGUG-CAUACAG-AU-GGGAAGUUG-CUGUAUGACGAA-G-C-----------------------------GAAA---------------------------GCGCGGUGUGUUAU-U-GCGUCCG-UUG-C-G-
ACGS02000005.1/10939-11039     -A-CA-GGGGUAGGAAGUCCUGCGUCA-----------------CGGG-CUGACGGAAC-GGAAUGU-GAACGUCAGCAGAA-A-GGUCC----------------------UGUCAUU------------------------GGCCUGC-GUGGUUCUU-CCGCAUUCA-CC--A-U-
ACBY02000010.1/41255-41369     -U-GC-AGAGUAGGGAUCCGCGCGUGGGGCAGUG---GCCCCGAAGUG-CCUGACCGAC-GGGGAGUUGUGG-CAGGACGAA-GUGAC--------------------------CGGAA------------------------GGUCCGCGGUGCGCAUC-CCGCAUCCCGCUG-C-U-
FP929037.1/1870907-1871006     -C-GC-AGAGUAGGGGAGCAGGCGUUA-----------------AGUG-CCGGAUGGAC-AGGGAGUUGCCGUCCGGACGAA-G-AAG--------------------------GAAAC-------------------------CUUCGCGGUCUGUUCC-CCGCAUCCCGCUG-C-A-
ABYJ02000297.1/736-845         -A-GC-AGAGUAGAACUCUGUGCGUUA-----------------AGUG-CCAUGUGAAC-AGGGAGUUGUCACACGGACGAA-A-AACAAAAG----------------CGCUGCUUUU-------------------------GUUUGCGGUACAGAAU-UCGCAUCCCGCUG-C-U-
ACHM02000003.1/346335-346246   -U-AC-AGAGUAGG-GUUGAUGCGUUU-----------------AGUG--UAAUGGGAU-AGGGAGUUGCCCAUUA-ACGAA-A-------------------------------UUAU----------------------------UGCGAUAUCAAUG-CCGCUUCCG-CUGAU-A-
AP010655.1/1460325-1460413     ---AC-AGAGUA-GAUGAUUCGCGUUA-----------------AGUG-UGUGUGA-AU-GGGAUGUCG-UCACACAACGAA-G-C-----------------------------CAUA------------------------A--GCGCGGUGAAUCAU-U-GCAUCCG-CUG-U---
ACCL02000010.1/116901-116811   -A-GU-AGAGUA-GGUCUUAUACGUAA-----------------AGUG-UCAUCGGA-U-GGGGAGACUUCCGGUGAACGAA-G-G-----------------------------GUUA---------------------------CCGCGUUAUAUGAC-C-GCUUCCG-CUA-C-U-
#=GC SS_cons                   .(.((.((----(((((((((((,,,,.................,<<-.<<<<<<<<__._AAAAAA__>>>>>>>>>>,,,.<.<<<.........................._____........................_>>>>,,,))))))))).))aaaaaa-.))).).).
#=GC RF                        .g.gc.aGAGUAGggugccgugcGUuA.................AGUG.ccggcgggAc.GGGgaGUUGcccgccggACGAA.g.ggc..........................aaaau........................ugcccGCGguacggcac.cCGCAUcCg.Cug.c.c.
//
# STOCKHOLM 1.0

#=GF AC   RF01832
#=GF ID   ROSE_2
#=GF DE   Repression of heat shock gene expression (ROSE) element
#=GF AU   Bateman A; 0000-0002-6982-4660
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:11726689
#=GF SS   Published; PMID:16438677; Bateman A
#=GF GA   65.00
#=GF TC   69.10
#=GF NC   63.90
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   11726689
#=GF RT   A mRNA-based thermosensor controls expression of rhizobial heat shock
#=GF RT   genes.
#=GF RA   Nocker A, Hausherr T, Balsiger S, Krstulovic NP, Hennecke H, Narberhaus F
#=GF RL   Nucleic Acids Res 2001;29:4800-4807.
#=GF RN   [2]
#=GF RM   15466035
#=GF RT   Replicon-specific regulation of small heat shock genes in Agrobacterium
#=GF RT   tumefaciens.
#=GF RA   Balsiger S, Ragaz C, Baron C, Narberhaus F
#=GF RL   J Bacteriol 2004;186:6824-6829.
#=GF RN   [3]
#=GF RM   16438677
#=GF RT   RNA thermometers.
#=GF RA   Narberhaus F, Waldminghaus T, Chowdhury S
#=GF RL   FEMS Microbiol Rev. 2006;30:3-16.
#=GF CC   This family represents a 5' UTR cis-regulatory element found in heat shock
#=GF CC   mRNAs and is known as the ROSE (repression of heat shock gene expression)
#=GF CC   element. The ROSE element is a negative regulator of heat shock gene
#=GF CC   expression. The secondary structure is thought to be regulated by
#=GF CC   temperature. This regulation blocks access to the ribosome binding site
#=GF CC   under normal conditions. During heat shock however, the structure changes
#=GF CC   freeing the ribosome binding site and allowing expression to occur [1,2].
#=GF CC   This family includes predicted members of the family from
#=GF CC   gamma-proteobacteria.
#=GF WK   Repression_of_heat_shock_gene_expression_(ROSE)_element
#=GF SQ   14


AE014073.1/3889302-3889230   UCUGGCUA-CC-UGACCUGUCCAUUGUGGAAGGUC-UUACAUUCUCGCUGAUU-UCAGGAGCUAUUGAUUAUGCGUA
CP000247.1/4051984-4051912   UCUGGCUA-CC-UGACCUGUCCAUUGUGGAAGGUC-UUAGAUUCUCGCUGAUU-UCAGGAGCUAUUGAUUAUGCGUA
ABAO01000013.1/76283-76210   UCUGGCAAUCC-UGGCCUGUCCAUGAUGGAAGGUC-UGACAUUCUCGCUGAUU-UCAGGAGUUUAUGAUUAUGCGUA
CP000026.1/3798554-3798481   UCUGGUAAUCC-UGGCCUGUCCAUGAUGGAAGGUC-UGACAUUCUCGCUGAUU-UCAGGAGUUUAUGAUUAUGCGUA
AE017220.1/3951363-3951290   UCUGGCAA-UCUUGGCCUGUCCAUGAUGGAAGGUC-UGACAUUCUCGCUGAUU-UCAGGAGUUUAUGAUUAUGCGUA
CP000647.1/4480191-4480116   CCGGGUUA-CCGCGGCCUGUCCACGAUGGAAGGUCAUUUGAUUCUCGCUGAUUUUCAGGAGCUAUUUACUAUGCGUA
AAMJ02000001.1/206930-206858 UCUGGCUA-CC-UGACCUGUCCAUUGUGGAAGGUU-UUACAUUCUCGCUGAUU-UCAGGAGUUAUUGAUUAUGCGUA
CP000036.1/3699544-3699616   UCUGGCUA-CC-UGACCUGUCCAUUGUGGAAGGUA-UUACAUUCUCGCUGAUU-UCAGGAGCUAUUGAUUAUGCGUA
ACDJ01000026.1/381061-380989 CCUGGCUA-CC-UGACCUGUCCAUGAUGGAAGGUC-AAUUAUUCUCGCUGAUU-UCAGGAGCUAUUGAUUAUGCGUA
CP000880.1/3768228-3768301   CCUGGCAA-UCCUGACCUGUCCAUGAUGGAAGGUC-GGACAUUCUCGCUGAUU-UCAGGAGCUAAUGAUUAUGCGUA
CP000653.1/14627-14699       GUUGGCUC-AG-UGGUCUGUCCAUCGUGGAAGGCC-AAAAUGACUUGCUGAUU-UCAGGAGCUUUGAUUUAUGCGUA
BAAW01000185.1/6674-6747     CCGGGUAA-UAACGACCUGUCCAUGAUGGAAGGUC-AUAAAUUCUCGCUGAUU-UCAGGAGCUUUUUAUUAUGCGUA
ABWL02000023.1/393416-393344 CCUGGCUA-CC-UGACCUGUCCAUGAUGGAAGGUC-UCACAUUCUCGCUGAUU-UCAGGAGCUAUUGAUUAUGCGUA
ABWM02000027.1/68830-68902   CGGGGGCA-CAGAAGCCUGUCCAUGGUGGAAGGCU-ACAU-CUCUCGCUGAUU-UCAGGAGUUUUAAUUUAUGCGUA
#=GC SS_cons                 ::::::::.::.:<<<<<-<<<_____>>>>>>>>.---<<--<<<-<<<___._>>>>>>---->>::::::::::
#=GC RF                      ucuGGcuA.cc.UGgCCUGUCCAUgaUGGAAGGcC.uuAcaUUCUCGCUGAUU.UCAGGAGcUaUugAUUAUGCGUA
//
# STOCKHOLM 1.0

#=GF AC   RF01833
#=GF ID   astro_FSE
#=GF DE   ribosomal frameshift site
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:8248142
#=GF SS   Published; PMID:8248142
#=GF GA   70.00
#=GF TC   76.30
#=GF NC   44.60
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200202;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   8248142
#=GF RT   RNA sequence of astrovirus: distinctive genomic organization and a
#=GF RT   putative retrovirus-like ribosomal frameshifting signal that directs the
#=GF RT   viral replicase synthesis.
#=GF RA   Jiang B, Monroe SS, Koonin EV, Stine SE, Glass RI
#=GF RL   Proc Natl Acad Sci U S A. 1993;90:10539-10543.
#=GF WK   Astrovirus
#=GF SQ   4


FJ755404.1/2807-2861 GGGCCCCAGAAGACCAAGGGGCCCAAACCUACCACUCAUUAGAUGCAUGGAAAUC
L23513.1/2807-2861   GGGCCCCAGAAGACCAAGGGGCCCAAAAUUACCACUCAUUAGAUGCGUGGAAAUU
AF141381.1/2828-2882 GGGCCCCAGAAGACCAGGGGGCCCAAAACUACCACUCACUAGAUGCAUGGCAGCU
L23508.1/159-213     GGGCCCCAGAAGACCAAGGGGCCCAAAAUUAUCACUCAUUAGAUGCAUGGAAAUC
#=GC SS_cons         <<<<<<<_AA___AAA_>>>>>>>:::::::::::::::::::::::aaa:::aa
#=GC RF              GGGCCCCAGAAGACCAAGGGGCCCAAAAuUACCACUCAUUAGAUGCAUGGAAAUu
//
# STOCKHOLM 1.0

#=GF AC   RF01834
#=GF ID   fiv_FSE
#=GF DE   ribosomal frameshift site
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:1310175
#=GF SS   Published; PMID:1310175
#=GF GA   53.00
#=GF TC   55.80
#=GF NC   38.70
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200015;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   1310175
#=GF RT   Identification and analysis of the gag-pol ribosomal frameshift site of
#=GF RT   feline immunodeficiency virus.
#=GF RA   Morikawa S, Bishop DH
#=GF RL   Virology. 1992;186:389-397.
#=GF WK   Feline_immunodeficiency_virus
#=GF SQ   5


M25381.1/1893-1927   GGGGCGAGCUGCAGCCCCAGUGAAUCAAAUGCAGC
AF361320.1/1266-1300 GGGGCUAGCUGCAGCCCCAGUGAACCAAGUGCAGC
X57002.1/1898-1932   GGGGCGAGCUGCAGCCCCAGUGAAUCAAGUGCAGC
AJ304979.1/25-59     GGGGCGAGCUGCAGCCCCAGUAAACCAAGUGCAGC
AY600517.1/1898-1932 GGGGCGAGCUGCAGCCCCGGUAAAUCAAGUGCAGC
#=GC SS_cons         <<<<<__AAAAAA>>>>>:::::::::::aaaaaa
#=GC RF              GGGGCGAGCUGCAGCCCCAGUGAAUCAAGUGCAGC
//
# STOCKHOLM 1.0

#=GF AC   RF01835
#=GF ID   HIV_FS2
#=GF DE   ribosomal frameshift site
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:1575083
#=GF SS   Published; PMID:1575083
#=GF GA   44.00
#=GF TC   47.20
#=GF NC   43.70
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200205;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   1575083
#=GF RT   Translational suppression in retroviral gene expression.
#=GF RA   Hatfield DL, Levin JG, Rein A, Oroszlan S
#=GF RL   Adv Virus Res. 1992;41:193-239.
#=GF RN   [2]
#=GF RM   3031510
#=GF RT   Genome organization and transactivation of the human immunodeficiency
#=GF RT   virus type 2.
#=GF RA   Guyader M, Emerman M, Sonigo P, Clavel F, Montagnier L, Alizon M
#=GF RL   Nature. 1987;326:662-669.
#=GF WK   HIV
#=GF SQ   19


U83413.1/240-284     CUUGGCCCAUGGGGAAAGAAGCCCCGCAAUUUCCCCAUGGCCCAG
AY932812.1/1249-1293 CUUGGUCCCUGGGGAAAGAAGCCUCGCAACUUCCCCAUGACCCAA
AY932816.1/1292-1336 UUUGGCCCAUGGGGAAAGAAGCCUCGCAACUUCCCCAUGACCCAA
U22047.1/2373-2417   AUUGGCCCAUGGGGAAAGAAGCCUCGCAACUUCCCCGUGACCCGA
DQ973524.1/11-55     AUGAGCCCCCGGGGAAAGAAGCCCCGCAAUUUCCCCGUGGCUCAA
AY509260.1/1850-1894 AUGGGCCCCCGGGGAAAGAAGCCCCGCAACUUCCCCGUGGCCCAA
D00835.1/2604-2648   AUUGGCCCCUGGGGAAAGAAGCCCCGCAAUUUCCCCGUGGCCCAA
L07625.1/2383-2427   UUAGGACCCUGGGGAAAGAAGCCUCGCAACUUCCCCAUGACCCAA
M15390.1/1848-1892   CUGGGCCCUUGGGGAAAGAAGCCCCGCAACUUCCCCGUGGCCCAA
AB100245.1/1524-1568 UUUGGCCCCUGGGGAAAGAAGCCUCGCAACUUCCCUGUAGCCCAA
AY611491.1/1473-1516 UUG-GCCCAUGGGGAAAGAAGCCCCGCAAUUUCCCCAUGGCUCAA
DQ307022.1/2150-2194 AUAAGCCCCCGGGGAAAGAAGCCUCGCAACUUCCCCGUGGCCCAA
AY932806.1/1253-1297 UUUGGACCUUGGGGAAAGAAGCCUCGCAACUUCCCCAUGGCCCAG
J04498.1/1847-1890   UUGGA-CCAUGGGGAAAGAAGCCCCGCAACUUCCCCGUGGUCCCA
M31113.1/1850-1894   UUGGGCCCAUGGGGAAAGAAGCCCCGCAAUUUCCCUGUGGCCCAA
X52223.1/1849-1893   AUGGGCCCACGGGGAAAGCAGCCCCGCAACUUCCCCGCGGCCCAA
M83293.1/2020-2064   UUUGGCCCAUGGGGAAAGAAGCCCCACAACUUCCCCAUGGCCCAA
M30895.1/1849-1893   AUGGGUCCAUGGGGAAAGAAGCCCCGCAACUUCCCCGUGGCCCAA
M30502.1/2405-2449   UUGGGCCCACGGGGAAAGAAGCCUCGCAACUUCCCCGUGACCCAA
#=GC SS_cons         :<<<<--<<<<<<<<<-<--<<___>>-->>>>>>>>>>->>>>:
#=GC RF              uUgGGCCCacGGGGAAAGAAGCCcCGCAACUUCCCCguGGCCcAA
//
# STOCKHOLM 1.0

#=GF AC   RF01836
#=GF ID   weev_FSE
#=GF DE   ribosomal frameshift site
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:19895695
#=GF SS   Published; PMID:19895695
#=GF GA   40.00
#=GF TC   40.60
#=GF NC   39.20
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200969;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   19895695
#=GF RT   Bioinformatic evidence for a stem-loop structure 5'-adjacent to the
#=GF RT   IGR-IRES and for an overlapping gene in the bee paralysis dicistroviruses.
#=GF RA   Firth AE, Wang QS, Jan E, Atkins JF
#=GF RL   Virol J. 2009;6:193.
#=GF WK   Western_equine_encephalitis_virus
#=GF SQ   6


EU708192.1/1780-1806 GGCGUCUGCCUGGGGAAGGCAGACGCC
M24200.1/1600-1626   GGCGCCUACCUGGCGAAGGUNGACGCC
AF339479.1/3017-3043 GGCGUCUACCUCUCGAAGGCAGACGCC
AF103728.1/9960-9986 GGCGUCUACCUGGGGAAGGUAGACGCC
DQ393792.1/2365-2391 GGCGUCUGCCUGGGGAAGGUGGACGCC
U90536.1/2446-2472   GGCGCCUACCUUGCGAAGGUAGACGCC
#=GC SS_cons         <<<<<<<<<<<_____>>>>>>>>>>>
#=GC RF              GGCGUCuaCCUGGgGAAGGuaGACGCC
//
# STOCKHOLM 1.0

#=GF AC   RF01837
#=GF ID   toga_FSE
#=GF DE   togavirus ribosomal frameshift element
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:18822126
#=GF SS   Published; PMID:18822126
#=GF GA   40.00
#=GF TC   50.00
#=GF NC   37.40
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r201068;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   18822126
#=GF RT   Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma.
#=GF RA   Firth AE, Chung BY, Fleeton MN, Atkins JF
#=GF RL   Virol J. 2008;5:108.
#=GF WK   Alphavirus
#=GF SQ   3


AJ238578.1/2651-2679   GAGGGUGGUCGGCUCUGCUGGUCAUCCUU
AJ316244.1/10393-10421 GAGGGUGGUCAGCCCUGCUGGUCAUCCUU
DQ149204.1/10267-10295 GAGGGUGGUCAGCUCUGCUGGUCAUCCUU
#=GC SS_cons           <<<<<<<--<<<<___>>>>-->>>>>>>
#=GC RF                GAGGGUGGUCaGCUCUGCuGGUCAUCCUU
//
# STOCKHOLM 1.0

#=GF AC   RF01838
#=GF ID   sobemo_FSE
#=GF DE   sobemovirus ribosomal frameshift elemental
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:10848968
#=GF SS   Published; PMID:10848968
#=GF GA   55.00
#=GF TC   57.40
#=GF NC   35.00
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200196;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   10848968
#=GF RT   Regulation of -1 ribosomal frameshifting directed by cocksfoot mottle
#=GF RT   sobemovirus genome.
#=GF RA   Lucchesi J, Makelainen K, Merits A, Tamm T, Makinen K
#=GF RL   Eur J Biochem. 2000;267:3523-3529.
#=GF WK   Cocksfoot_mottle_virus
#=GF SQ   5


Z48630.1/1623-1701   GCAAUCCGGCCUUUAAACUACCAGCGGGCGGGCU---CCCUACGGGGCAGUCCGCCCUUGGCCAACUUAUCGAGUACGCGGG
AM883097.1/442-523   GACCACGUUCCUUUAAACUGCCAGGGGGCGGGCUCGAGCCUUCGGGCGAGUCCGCCCUUGGACGGCUUAUCCAACUCGGAGA
DQ680848.1/1623-1701 GCAAUCCGGCCUUUAAACUACCAGCGGGCGGGCU---CCCUACGGGGCAGUCCGCCCUUGGCCAACUUAUCGAGUACGCGGG
AM990928.1/2051-2129 GAAGGUGAGCCUUUAAACUACCAGCGGGCGGACC---UCCUACGGGAGAGUCCGCCCUUGGAAGGCUUAUUCAGCUUGGGAA
AF055888.1/1715-1793 GUUGCGGAGCCUUUAAACUACCAGCGGGCGGCAG---GGUCAAGGCCCUUGCCGCCCUUUCUCAACUUGCAGGCUACGACUU
#=GC SS_cons         :::::::::::::::::::::::::<<<<<<<<<...<<<____>>>->>>>>>>>>:::::::::::::::::::::::::
#=GC RF              GaaaucgaGCCUUUAAACUACCAGCGGGCGGgcu...gcCUAcGGgccaguCCGCCCUUGGaCaaCUUAUcgAguaCGggga
//
# STOCKHOLM 1.0

#=GF AC   RF01839
#=GF ID   eeev_FSE
#=GF DE   eastern equine encephalitis ribosomal frameshift element
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:18822126
#=GF SS   Published; PMID:18822126
#=GF GA   80.00
#=GF TC   87.50
#=GF NC   54.40
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r201065;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   18822126
#=GF RT   Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma.
#=GF RA   Firth AE, Chung BY, Fleeton MN, Atkins JF
#=GF RL   Virol J. 2008;5:108.
#=GF WK   Eastern_equine_encephalitis_virus
#=GF SQ   6


AF159551.1/2412-2484 GCUGUGGGCCGGCUUUUUUACUUGUCUGCGGCGCCUUGGGCGCCGCAGCGUACGAACACACAGCAGUGAUGCC
AF159555.1/2412-2484 GCUGUGGGCCGGCUUUUUUACUUGUCUGCGGCGCCUUGGGCGCCGCACCGUACAAACACACAGCAUUGAUGCG
DQ241303.1/9897-9969 GCUGCGGUCCGGCUUUUUUACUUGUCUGCGGCGCCUUGGGCGCCGCAGCAUACGAACACGCAGCAGUGAUGCC
EF151503.1/9916-9988 GCUGCGGUCCGGCUUUUUUACUUGUCUGCGGCGCCUUGGGCGCCGCAGCAUACGAGCACACGGCUGUGAUGUC
X05816.1/2526-2595   GCUGUGGGCCGGCUUUUUUACUUGUCUGCGGC-GCUUGG--GCCGCAGCGUACGAACACACAGCAGUGAUGCC
U01558.1/2412-2484   GCUGUGGGCCGGCUUUUUUACUUGUCUGCGGCGCCUUGGGCGCCGCAGCGUACGAACACACAGCAGUGAUGCC
#=GC SS_cons         :::::::::::::::::::::::::<<<<<<<<<<___>>>>>>>>>>:::::::::::::::::::::::::
#=GC RF              GCUGuGGgCCGGCUUUUUUACUUGUCUGCGGCGCCUUGGGCGCCGCAGCgUACGAACACACAGCAGUGAUGCc
//
# STOCKHOLM 1.0

#=GF AC   RF01840
#=GF ID   ovine_lenti_FSE
#=GF DE   ribosomal frameshift element
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:15629717
#=GF SS   Published; PMID:15629717
#=GF GA   45.00
#=GF TC   51.10
#=GF NC   38.50
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200523;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   15629717
#=GF RT   An extended signal involved in eukaryotic -1 frameshifting operates
#=GF RT   through modification of the E site tRNA.
#=GF RA   Bekaert M, Rousset JP
#=GF RL   Mol Cell. 2005;17:61-68.
#=GF WK   Visna_virus
#=GF SQ   14


AY454176.1/676-729   AGGGGGCCACGUGUGGUGCCGUCCGCGCCCCCUAUGUUGUAACAGAAGCACCAC
AY454226.1/682-735   AGGGGGCCACGUGUGGUGCCGUCCGCGCCCCCUAUGCUUUAACAGAAGCACCAC
AY454223.1/682-735   AGGGGGAUACGUGUGGUGCCGUCCGCUCCCCCUAUGGAAUAACUUCAGCACCAC
AY454232.1/679-732   AGGGGGCCACGUGUGGUGCCGUCCGCGCCCCCUAUGCUGUAAGCGAAGCACCAC
AY454171.1/676-729   AGGGGGAUACGUGUGGUGCCGUCCGCUCCCCCUAUGGAAUAACUGACGCACCAC
AY454168.1/667-720   CGGGGGAUACGUGUGGUGCCGUCCGCUCCCCCUAUGGCAUAACAAAUGCACCAC
AY454166.1/682-735   CGGGGGACACGUGUGGUGCCGUCCGCUCCCCCCAGGGAAUAACUGAUGCACCAC
AY454184.1/682-735   CGGGGGAUACGUGUGGUGCCGUCCGCUCCCCCUAUGGAAUAACAGAAGCACCAC
AF479638.1/1797-1850 AGGGGGCCACGUGUGGUGCCGUCCGCACCCCCUAUGUUGUAACAGAAGCACCAC
EU293537.2/1860-1913 AGGGGGCCACGUGUGGUGCCGUCCGCACCCCCUAUGCAGUAACGGAUGCACCAC
AF322109.1/1834-1887 AGGGGGCUACGUGUGGUGCCGUCCGCACCCCCUAUGGAGUAACGCAAGCACCAC
AY454217.1/678-731   CGGGGGCUACGUGUGGUGCCGUCCGCGCCCCCUAUGGAGUAACAGAAGCACCAC
AY454169.1/682-735   CGGGGGCCACGUGUGGUGCCGUCCGCGCCCCCUAUGGAAUAACAACAGCACCAC
AY454179.1/679-732   AGGGGGCCACGUGUGGUGCCGUCCGCUCCCCCUAUGGAAUAACAUCAGCACCAC
#=GC SS_cons         <<<<<<<_____AAAAAAA_______>>>>>>>-<<<____>>>:::aaaaaaa
#=GC RF              aGGGGGccACGUGUGGUGCCGUCCGCgCCCCCuAuGgaaUAaCagAaGCACCAC
//
# STOCKHOLM 1.0

#=GF AC   RF01841
#=GF ID   veev_FSE
#=GF DE   venezuelan equine encephalitis virus ribosomal frameshift element
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:18822126
#=GF SS   Published; PMID:18822126
#=GF GA   55.00
#=GF TC   78.00
#=GF NC   52.50
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r201057;
#=GF DR   GO; 0075523; viral translational frameshifting;
#=GF RN   [1]
#=GF RM   18822126
#=GF RT   Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma.
#=GF RA   Firth AE, Chung BY, Fleeton MN, Atkins JF
#=GF RL   Virol J. 2008;5:108.
#=GF WK   Venezuelan_equine_encephalitis_virus
#=GF SQ   10


AY986475.1/9911-9981   CUGUGUAGUGCCUUUUUUAGUCGUGGCCGGCGCCGCAGGCGCCGGCGCCUACGAGCACGCGACCACGAUGC
U55360.2/9928-9998     CUGUGUAGUGCCUUUUUUAGUCGUGGCCGGCGCCGCAGGCGCCGGCGCCUACGAGCACGCGACCACGAUGC
AF448537.1/9960-10030  UUGCGUCGUGCCUUUUUUAGUCGUGGCCGGCGCCGUAGGCGCCGGCGCUUACGAGCACGCGACCACGAUGC
AF075257.1/10009-10079 CUGUAUGGUGCCUUUUUUAGUGCUGGCCGGCGCCGCAGGCGCCGGCGCCUUCGAACACGCGACCACGAUGC
M14937.1/2426-2493     CUGUGUCGUGCCUUUUUUAGUCAUGGCCGGCGCCGCA-GCGCCGGC--CUACGAGCACGCGACCACGAUGC
AF075255.1/9810-9880   UUGCGUGGUGCCUUUUUUAGUGCUAGCAGGCGCCGCAAGCGUCGGCGCCUACGAACACGCGACCACGAUGC
AF075259.1/9827-9897   UUGCUUUGUGCCUUUUUUAGUCCUAGCCGGCGCCGCCGGCGCCGGCGCUUACGAGCACGCAACAACGAUGC
AF075254.1/9972-10042  UUGCGUAGUUCCUUUUUUAGUCCUAGCAGGCGCCGCAAGCGUCGGCGCCUACGAGCACGCAACCACGAUGC
AF075258.1/9925-9995   UUGCGUGGUGCCUUUUUUAGUGCUAGCCGGCGCCGUAGGCGCCGGCGCAUUCGAGCACGCGACCACGAUGC
AF075256.1/9896-9966   CUGUGUGCUGCCUUUUUUAGUGCUGGCCGGCGCCGUAGGCGCCGGCGCAUACGAGCACGCGACUACGAUGC
#=GC SS_cons           :::::::::::::::::::::::::<<<<<<<<<___>>>>>>>>>:::::::::::::::::::::::::
#=GC RF                uUGuGUaGUGCCUUUUUUAGUccUgGCCGGCGCCGcAGGCGCCGGCGCcUACGAGCACGCGACcACGAUGC
//
# STOCKHOLM 1.0

#=GF AC   RF01842
#=GF ID   mycoplasma_FSE
#=GF DE   mycoplasma ribosomal frameshift element
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:7476162
#=GF SS   Published; PMID:7476162
#=GF GA   88.00
#=GF TC   88.50
#=GF NC   46.80
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r200011;
#=GF DR   GO; 0006452; translational frameshifting;
#=GF RN   [1]
#=GF RM   7476162
#=GF RT   Characterization of IS1221 from Mycoplasma hyorhinis: expression of its
#=GF RT   putative transposase in Escherichia coli incorporates a ribosomal
#=GF RT   frameshift mechanism.
#=GF RA   Zheng J, McIntosh MA
#=GF RL   Mol Microbiol. 1995;16:669-685.
#=GF WK   Mycoplasma
#=GF SQ   3


U01217.1/534-620 AAAUGAAGUUCUAAA-AAAGUGAAAAGCCUUGGUAGAGAUCUUUGACUCAAGUCAACCAAGGCAAGAGAAAAUAAAAAAAAUUUAUAA
L33926.1/533-620 AAAUGAAGUACUAAAAAAAGUGAGAAGCCUUGGUAGAGAUCUUUGACUCAAAUCAACCAAGGCAAGAAAAAAUAAAAAAAAUUUAUAA
X17372.1/577-663 AAUCGAAGCACUAAA-AAAGUGAAAAGCCUUGGUAGAGAUCUUUGACUCAAAUCAACCAAGGCAAGAAAAAAUAAAAAAAAUUUAUAA
#=GC SS_cons     :::::::::::::::.::::::::::<<<<<<<<<<<_______________>>>>>>>>>>>:::::::::::::::::::::::::
#=GC RF          AAauGAAGuaCUAAA.AAAGUGAaAAGCCuuGGuaGaGAUCUUUGACUCAAauCaaCCaaGGCAAGAaAAAAUAAAAAAAAUUUAUAA
//
# STOCKHOLM 1.0

#=GF AC   RF01843
#=GF ID   neisseria_FSE
#=GF DE   neiserria ribosomal frameshift element
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Published; PMID:11943474
#=GF SS   Published; PMID:11943474
#=GF GA   50.00
#=GF TC   57.60
#=GF NC   34.20
#=GF TP   Cis-reg; frameshift_element;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001427; cis_regulatory_frameshift_element;
#=GF DR   URL; http://recode.ucc.ie/recode/r201055;
#=GF DR   GO; 0006452; translational frameshifting;
#=GF RN   [1]
#=GF RM   11943474
#=GF RT   Recoding: translational bifurcations in gene expression.
#=GF RA   Baranov PV, Gesteland RF, Atkins JF
#=GF RL   Gene. 2002;286:187-201.
#=GF WK   Neisseria_gonorrhoeae
#=GF SQ   4


ABZQ01000083.1/5704-5743   GCCCUGAAGCGGAUGCCGCCCAAACGCCCGUUCAGACGGC
ABZF01000077.1/5667-5706   GCCCUGAAGCGGAUGCCGCCCAAACGCCCGUUCAGACGGC
CP000381.1/1368994-1369033 ACCCUGAAGCGGAAACCACCCAAACGCCCGUUCAGACGGC
CP002420.1/845080-845041   GCCCUGAAGCGGAAACCGCCCAAACACCCGUUCAGACGGC
#=GC SS_cons               <<<<<<<<<<<--<<_____>>-->>>--->>>>>-->>>
#=GC RF                    GCCCUGAAGCGGAuGCCGCCCaAACGCCCGUUCAGACGGC
//
# STOCKHOLM 1.0

#=GF AC   RF01844
#=GF ID   SmY
#=GF DE   SmY spliceosomal RNA
#=GF AU   Jones T
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF AU   Marz M; 0000-0003-4783-8823
#=GF SE   Published; PMID:19106623
#=GF SS   Published; PMID:19106623
#=GF GA   39.00
#=GF TC   39.80
#=GF NC   37.80
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17283210
#=GF RT   A novel family of C. elegans snRNPs contains proteins associated with
#=GF RT   trans-splicing.
#=GF RA   MacMorris M, Kumar M, Lasda E, Larsen A, Kraemer B, Blumenthal T.
#=GF RL   RNA 2007;13:511-520.
#=GF RN   [2]
#=GF RM   8752084
#=GF RT   Direct analysis of nematode cis- and trans-spliceosomes: a functional role
#=GF RT   for U5 snRNA in spliced leader addition trans-splicing and the
#=GF RT   identification of novel Sm snRNPs.
#=GF RA   Maroney PA, Yu YT, Jankowska M, Nilsen TW
#=GF RL   RNA 1996;2:735-745.
#=GF RN   [3]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF RN   [4]
#=GF RM   16344563
#=GF RT   Organization of the Caenorhabditis elegans small non-coding transcriptome:
#=GF RT   genomic features, biogenesis, and expression.
#=GF RA   Deng W, Zhu X, Skogerbo G, Zhao Y, Fu Z, Wang Y, He H, Cai L, Sun H, Liu
#=GF RA   C, Li B, Bai B, Wang J, Jia D, Sun S, He H, Cui Y, Wang Y, Bu D, Chen R
#=GF RL   Genome Res. 2006;16:20.
#=GF RN   [5]
#=GF RM   19106623
#=GF RT   A survey of nematode SmY RNAs.
#=GF RA   Jones TA, Otto W, Marz M, Eddy SR, Stadler PF
#=GF RL   RNA Biol. 2009;6:5-8.
#=GF WK   SmY_RNA
#=GF SQ   61


ABLA01022309.1/286-367       GUGUACACCCUUUUGUGCGGAGGGCCUUUUGCUGAAGACCCUUUUUUGACAAUUUUUGGC--AGGCCC--AA-----CGGAAUU--GGGCCUU
ABLA01020015.1/643-564       AAGCGUGUUAACUGAAUGUGA-GGCCUUGUUCUGAAGACC-CUUUU-CACAAUUUUUGGC--AGGCUU-AAC-----CGAA-GUU-AGGCCUU
AAQA01004525.1/621-545       CGUGUCUAAGCUUUGA--CCAGGGCCUUG--UCCAAGACCCGGCGA--ACAAUUUUUGGC--UGCCUU-CCC-----AGGA-GGG-AGGGCAA
AAGD02000734.1/1216-1299     CAUCGAACUACAAUACCUUUAAGGCCUUU--CCUAAGACCUCGACU--AGAAUUUUUGGAAAACCCUG-UCUA---UUCUUUAGG-CAGGGUG
AY948626.1/1-77              GUUAAACCAUAACUA-ACUCAGGGCCUUG--UUAAAGACCCGAAGU--ACAAUUUUUGAAG--CCCUG-UCU-----CUCG-AGG-CAGGG-G
ABKE01005116.1/1436-1359     UGUUGUAUCAAAAAUGAUUCAGGGCCUCG--AACGAGACCCGUAG---CCAAUUUUUGGA--AGCCUC-UCC-----GCCA-GGA-GGGGUUA
AAGD02000138.1/22681-22759   UGGUGCACCUCGU-AUUCUAUGGGCCUUC-UUUCAAGACCCUGAAA--UAAAUU-UUGGAG-ACCCGU-CAU-----UCCG-AUG-GCGGGUG
AAGD02000039.1/125318-125238 GUUAAAUCUAUAACACU-UCAGGGCCUUA--AUAAAGACCCGUCGU--ACAAUUUUUGGAC-GCCCU-UUCC----UUCACAGGAC-UGGGUG
ABKE01004475.1/9889-9811     GUAUUGAACAAAAUAAGUUCAGGGCCUCA--ACCGAGACCCGGUG---UCGAUUUUUGGUG-AGCUCU-UCA-----AUGC-UGA-AGAGCUU
AAGD02003931.1/16353-16435   CCAGAGAAAUUGAAAGU-GCAGGGCCUUU--CUCAAGACCCCAAGU--ACAAUUUUUGCA--ACCCUG-CCAGA-AUUUAGUUGG-UAGGGUA
ABKE01005169.1/4197-4275     CGUUUGUAAACCAAUCUAUCAGGGCCUCU--ACCGAGACCCAGAGU--CCAGUUUUUGGG--AACCUC-CCA-----CGCU-UGG-GGGGUUA
AY948619.1/1-82              -GCUAUUUAUAAACGCUCUCAGGGCCUUG--CAAAAGACCCAGUGA--ACAAUUUUUGGAGAACCCUGUCCU-----UUCG-AGGUCAGGGUA
AAGD02003917.1/38429-38510   UGUGAUGUUAUAUUGCUUUCAAGGCCUUC--CUUAAGACCUGAAGA--ACAAUUUUUGGAA-ACCCU-CUCC----UUCAUUGGGC-AGGGUG
ABKE01001494.1/7214-7136     AUCUGAGUCUUCGCACUUUCAGGGCCUCA--CUUGAGACCCAGUGA--CCAGUUUUUGGA--AACCUU-CCA-----UGCU-UGG-AAGGUUA
AY948618.1/1-77              CGAUUUCUUAUAAUACU-UCAGGGCCUUA--CUAAAGACCCAGUGU--ACAAUUUUUGCAG--CCCUG-UCU-----UCUG-AGG-CAGGG-G
AAGD02003021.1/21044-20964   UUUAGUAAUAGUAGUCUUUCAGGGCCUUC--CUUAAGACCCGAAGA-AUUAAUUUUUGGAG-ACCCUUU-UC-----UUUG-GA-UUAGGGUG
CAAC02000462.1/976913-976833 UCAUUAAAUACUUGAGU-ACAGGGCCUUU--CACAAGACCCGAUGU--ACAAUUUUUGGAG-ACCCUG-UCCU---CUCUC-GGG-CAGGGUU
CAAC02000563.1/974923-975001 UAAAAUCCUUCAUA----GCUGGGCCUUC--CUUAAGACCCUAAGC--ACAAUUUUUGGG--CGCCUG-UCGUG-CAACAG-CGG-CGGGUGA
CAAC02000462.1/705691-705775 CAGUAUCUAGUAUUUCA-UCGAGGCCUUC--UUGAAGACCUUAAGU--AUAAUUUUUGGAA-ACCCUG-UUCUAAUAUUUUAGGA-CAGGGUA
AAGD02003490.1/1866-1944     UCUAGUAUAGUUCUUCUUGCUGGGCCUUC--UUUAAGACCCUAAGA--UAAAUU-UUGGAC-GC-CUG-UCU----CUAAGGAGG-CAG-GUG
CAAC02000462.1/704986-705070 GUAUCUAUCAUUUUAUUUUUGAGGCCUUC--UACAAGACCUUAAGA--ACAACUUUUGGAG-ACCCUG-UCCUAAUAUUUG-GGG-CAGAGUA
CAAC02000563.1/936173-936250 UGUUCUAUUAAAA-UCAUUCAGGGCCUUA--CUUAAGACCCGGUGU--ACAAUUUUUGGA--GCCCUG-UCG-----CUUG-CGG-CAGGGUA
CAAC02000462.1/702204-702287 CAGCAUCUAGCAUUUCA-UCGAGGCCUUC--AAUAAGACCUUCAGA--ACAAUUUUUGGAG-ACCCUGUCCUAA-UUUUUG-AGG-CAGGGAA
AM286192.1/1-75              -----UUCGCUAAACCU-CCAAGGCCUUU--CAUAAGACCUAGUGA--ACAAUUUUUGGGG-ACCCUA-UCU----UUUUA-AGG-UAGGGUU
CAAC02000563.1/970744-970823 UUUGCUAGUCUAUCUCUUGCCGGGCCUUC--CUCAAGACCCUAAGC--ACAAUUUUUGGGC-ACCC-G-UCGC---AGCAA-CGG-C-GGGUG
CAAC02000462.1/677031-677114 CGGUAUCUAGCAUUUCA-UCGAGGUCUUC--UUUAAGACCUUUAGA--ACAAUUUUUGGAA-ACCCUG-UCUCAUUAAUUG-GGG-CAGGGUA
ABKE01004848.1/8512-8590     UCGUAUUAAAUCAAUCUCUCAGGGCCUCG--AUAGAGACCCAGAAU--CCAGUUUUUGGA--GGUCUU-CCA-----CACU-UGG-GAGGUUA
U52372.1/141-211             ----AGCAACCACGAAGUUCAGGGCCUU---AUGAAGACCCGAAGG--ACAAUUUUUGGAG--GCCC--CUC-----CGAG-GAG--GUGC-G
AY948625.1/1-79              GUUAAUUCAU--UAACUUCCAAGGCCUUA--CACAAGACCUAGUGG--ACAAUUUUUGGAG-ACCCUA--UCU---AGCCGUGA--UAGGGUG
ABKE01001809.1/14253-14175   AGGUGCAAUACAAG-CUCUCAGGGCCUUU--ACCAAGACCCAGAGU--CCAGUUUUUGGAG-AACCCU--CC----GGCUAAGG--GGGGUUG
AAGD02003917.1/20955-20874   AUUCUUAUUAUUUCUUAUUCAGGGCCUUC--CUUAAGACUCAAAGU--ACAAUUUUUUGAG-AUCCUG-UCC----UUCAGUGGG-CAGAGUG
AAGD02000138.1/4186-4109     UUUCUAACCAGAAAGACAGCAGGGCCUUA--CUAAAGACCCGUACU--ACAAUUUUUGCAG--CCCUG-UUC-----UUCG-GAG-CAGGG-G
AAGD02003917.1/31970-31893   AUGUAUGUUAUUUCUUCCUCAAGGCCUUC--CUUAAGACCUGUAGU--ACAAUUUUUGGAG-ACCCUG---UC---CUUUA-G---UAGGGUG
AAGD02001043.1/36538-36616   UAAAUUGUAACAACAC--ACAAGGCCUUG--UUUAAGACCUGCUGU--AAAAUUUUUGGAGA-CCCUG-UCC----UUCAUUGGG-CAGGG-A
AAGD02000138.1/4670-4592     UCGUUUAAUAUAACUUAUUCCGGGCCUUG--UAAAAGACCCCAAGA--ACAAUUUUUGCA--GCCCUGU-UC-----UUUG-GA-UCAGGGUA
ABLG01001501.1/18637-18562   AACGUUACCGUUUUUA-UCGCGGGCCUUAAGUUGAAGACCCAGCGU-UACAUUUUUUGGA--GUCCCG---C-----GGGA-G---CGGGAU-
AY948621.1/1-78              --AUAUAAUAUAUCACUGUCAGGGCCUUA--CAAAAGACCCAGUGA--ACAAUUUUUGCAAA-CCCUG-UCU----UCUUGAAGG-CGGGG--
Z99281.1/227472-227552       -AAUAUAAUAAAACACUGUCAGGGCCUUA--CAAAAGACCCACUGA--UCAAUUUUUGAAA-ACCUUG-UUC----UCUUGAGGG-CACGGUA
AAGD02003917.1/24628-24709   GUGUAUUUUAUAUUGCCAUCAAGGCCUUA--CUUAAGACCUGAAGU--ACAAUUUUUGGAG-ACCCUG-UCC----UUUAUUGGG-CAGGGUG
CABB01001438.1/774-851       AAACGUUACCUUUUAUAUCGCGGGCCUUGAGAUGAAGACCCAGCGUUUACAUUUUUUGGAG-UCUC----AC-----GGGA-GU----GAGAU
AY948610.1/10-90             ACUUAAAUAACAAAAAACCCAAAGCCUAA--CUCAGGACUUGGUA---ACAAUUUUUGGAG-ACCCUA-ACU----UUUAUUAGU-UAGGGUG
ABEG02000330.1/63208-63287   AAUUCUAAUGAAUCACUCUCAGGGCCUUG--AAUAAGACCCAGUGA--ACAAUUUUUGGAG-ACCCUAA-UC-----UGAG-GA-AUAGGGUG
ABLE03031906.1/4817-4736     GUUGUGAAAUAAUCAAAUACAGAGCCUUU--AAGAAGACUCAAAGU--ACAAUUUUUGCAA-ACCCUAUCU-----UUUCCA-AGUCAGGGUA
ABEG02006677.1/6392-6472     UAUUCUAAUGAAUACCUCUCAGGGCCUUU--UAUAAGACCCAGUGA--ACAAUUUUUGCAG-ACCCUCUUCC-----UUU--GGUUGAGGGUG
ABEG02007269.1/45295-45217   GGUUAUAAAGAUUUUUAUACCGGGCCUUA--CAGAAGACCCCAAGU--ACAAUUUUUGCA--GCCCUUU-CC-----UUCG-GG-UCAGGGUA
ABEG02004204.1/7028-7107     GUGUAAUUUUAAUUACUCUUAAGGCCUUG--AAUAAGACCCAGUGA--ACAAUUUUUGGAG-ACCCUA-UUC-----UCAG-GAA-UAGGGUG
ABEG02000330.1/84043-83964   AGUGUAAUUGAAUGACUCUCAGGGCCUUG--AACAAGACCCAGUGA--ACAAUUUUUGGAG-ACCCUA-UUU-----UUCG-GAG-UAGGGUG
ABEG02000320.1/43721-43800   CAACUAACAACACACCUCUCAGGGCCUUG--AUCAAGACCCGGUGA--ACAAUUUUUGGAG-ACCCUA-UUC-----UUCG-GAG-UAGGGUG
ABEG02002988.1/1297-1213     AGCUUCUAUCAACAUUAUUCAGGGCCUUA--CCCAAGACCCGGUGU--ACAAUUUUUGGAA-ACCCUG-UCCGG-UUUUAUAGGG-CAGGGUU
ABLE03034152.1/2957-3037     UUCUUACACCUAGUGUGAACCGGGCCUUG--UUGAAGACCCUAAGC--ACAAUUUUUGCA--GCCCUGU-CC----UUCUUUGG-UCAGGGUA
ABLE03024394.1/701-620       GUUGUGAAAUAAUCAAAUUCAGAGCCUUU--AAGAAGACUCAAAGU--ACAAUUUUUGCAA-ACCCUAGCUU-----UUCC-AAGUCAGGGUA
ABLE03019653.1/787-707       GUUGUGAAAUAAUCAAUUGCAGAGCCUUG--AAAAAGACUCCAAGU--ACAAUUUUUGCGA-ACCCUG-UUC----AAUUU-GGA-UAGGGUU
ABLE03002930.1/381-461       AAUUAUAUCCCAUUG-UUACAGGGCCUUU--AAGAAGACCCACAGU--ACAAUUUUUGAAA-ACCCUGCUCU-----UUCU-AGAUCAGGGUG
ABEG02000321.1/1748-1827     AAAUGAUCUAAAUAUCUCUCAGGGCCUUG--AAUAAGACCCAGUGA--ACAAUUUUUGGAG-ACCCUA-UUC-----CUAG-GAA-UAGGGUG
ABEG02000330.1/83363-83442   ACAAAUGAUCUAAAUAUCUCAGGGCCUUG--CAUAAGACCUAGUGA--ACAAUUUUUGGAG-ACCCUA-UUC-----UCAG-GAA-UAGGGUG
ABEG02001922.1/4022-3943     CAAAUGAAAAAAAACCUCUCAGGGCCUUG--AAUAAGACCCAGUGA--ACUAUUUUUGGAG-ACCCUA-UUC-----GAAA-GGA-UAGGAUG
ABEG02007269.1/44791-44716   UGAUUUCUUAAAAA--UCACCGGGCCUUA--CUAAAGACCCCAAGU--ACAAUUUUUGCAA--CCCUGU-CC-----UUCG-GG-UCAGGG-A
FO081731.1/174636-174555     CAGCACGAUUUAACACUCUCAGGGCCUUA--CAAAAGACCCAGUGA--ACAAUUUUUGCAA-ACCCUGUCCU-----UUCA-AGGUCAGGGUA
ABEG02002029.1/20936-21015   CUAUUGAAUAACUCACUUUCAGGGCCUUG--CAUAAGACCCAGUGA--ACAAUUUUUGGAG-ACCCUUC-UC-----UUCG-GA-UUAGGGUG
ABEG02002681.1/22113-22189   AUUCUUAUGAAU-AUACUGCAGGGCCUUC--AUCAAGACCCAGUGA--ACAAUUUUUGGG--ACCCUA-UUC-----UUU--GAA-UAGGGUA
ABLE03031906.1/5018-5099     GUCAAAUAAUAAUAAAUUGCAGAGCCUUU--AAGAAGACUCAAAGC--ACAAUUUUUGCGA-ACCCUGAUC-----UUGCUA-GGUCGGGGUA
#=GC SS_cons                 :::::::::::::::::::::<<<-<<<_..___>>>->>>-----..-------------.<<<<<<.<<<.....____.>>>.>>>>>>:
#=GC RF                      auuuauaauauauuacuuuCAGGGCCUUa..cuuAAGACCCagaGu..ACAAUUUUUGGAG.acCCug.ccc.....uuag.ggg.caGGgua
//
# STOCKHOLM 1.0

#=GF AC   RF01845
#=GF ID   enod40
#=GF DE   Early nodulin 40
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:17452360
#=GF SS   Published; PMID:17452360
#=GF GA   45.00
#=GF TC   50.00
#=GF NC   44.40
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0009877; nodulation;
#=GF RN   [1]
#=GF RM   17452360
#=GF RT   Identification of conserved secondary structures and expansion segments in
#=GF RT   enod40 RNAs reveals new enod40 homologues in plants.
#=GF RA   Gultyaev AP, Roussis A
#=GF RL   Nucleic Acids Res. 2007;35:3144-3152.
#=GF WK   ENOD40
#=GF SQ   35


AF352373.1/2144-2429         AUGAAGCUCUUU---UGGCAAAAAUCC------AUCAAUGGUUCUUGAUUCAUGAAGAAGCAUGGAUUAA-CAGUGUGAGAGGG---------------------------------------UCCUCACCCCUC-ACACUCCACCACU-----UCCAACAGUUUGUUUUGGUUUUAGCUAUUGGCUUCUGUAAUCACCAAGGGAUAGCAUACAUAGUAUUAAUCUCUAUGACUAA-------------------------------------CAGAAGCAUAUAAGCAUUCUCCAU-UGGAGCAAA--GGCUUUCUUUGGCUACAGCU----AGGGCAAGCCGGCAAGUCAUCACA-AAAAGGC-AUG----GACUCCAUU-A--GGGGUCCU
AF352375.1/51-328            AUGGAACUCUCU---UGGCAAAAAUCC------AUCCAUGGUUCUUGAAUAAGCACGCAUCAUU----AA-CAGUGUGAGAGGG---------------------------------------UCCUCAUCCCUC-ACACUCCACCACU-----UCCAACAGUUUGUUUAGGC-UUAGCUAUUGGCUUCUCUAAUCACCAAGGGAUAUGCAUACAAAAAACAUUCUCUAUGACUAA-------------------------------------CAGAAGCAUAUAAGCAUUCUCCAU-UGGAGCAAA--GGCUUUCUUUGGCUACAGCC----UAGGCAAGCCGGCAAG---UCACA-AAAAGGC-UUG----GACUCCAUU-A--GGGGUCCU
AJ271787.1/322-595           AUGAAGCUCUGC---UGGCAGAUUUCC------AUCCAUGGUUCUUAA-AUAAGCAUGAAGAGA-----A-GUGUGAAAGUGUG---------------------------------------CUGUCACCUCUC-ACACUCCUCCACU-----UCCAACAGUUUGUUUGGGCUUUAGCUUUUGGCUUCUGUGAUCACCAUGGAGGUAUGCUCAAACAUUCUCUCUGAGUAGCAGA--------------------------------------AGAAGCAGAUGAGCAUUCUCCAAAAGGAGCAGA--GACUU----UGGCUACAGCC-----UGGCAAGCCGGCAAG---UCACA-AAAAGGCAAUG----GACUCCAUUAG--GGGUUCGA
X69154.1/47-319              AUGGAGCUUUGU---UGGCUCACAACC------AUCCAUGGUUCUUGA-AGAAGCUUGGAGAGA-----A-AGGGGUGUGAGAGGAGAG--------------------------------GGUGCUCACUCCUC-ACACUCCCUCACU-----UAAAACAGUUUGUUUUGGC--UUAGCUUUGGCUUCUCUGAUCAACAAGGGAUGUGUUCUAACAUUCUUUCUUGAGUGGCG-----------------------------------------GAAGCAGAUACACAUUCUCCGA-CGGAGGAGA--GGC-U----UGGCUACAGCC-----UGGCAAACCGGCAAG---UCACAAAAAAGGCAAUG----GACUCCAUU----GGGGUCUC
D13503.1/19-286              AUGGAGCUUUGU---UGGCAAACAUCC------AUCCAUGGUUCUUGA-AGAAGCAUGGAGAUA----AAGGGGUGUGAGAGGG---------------------------------------UCCUCACCACUC-ACACUCCUCCACU-----UAAAACAGUUUGUUUUGGC--UUAGCUUUGGCUUCUCUAAUCAACAAGGGAUGUGUUCUAACAUUCUCUCUUGAGUGGCA-----------------------------------------GAAGCAGAUAUGCAUUCUCCAA-AGGAGGAGA--GGCUU----UGGCUACAGCC-----UGGCAAACCGGCAAG---UCACG-AAAAGGCAAUG----GACUCCAUU----GGGGUCUC
AF061818.1/11-229            AUGGAG-----------------------------------------AAAAAGGA--------G----------UGUGAGAGGG---------------------------------------UCCUUACCCUUC-ACACUCCUCCACU-----UUCAACAGUUUGCUUGUGC--UUAGCUUUGGCUUCUCUAAUCAACAAGGGAUGUGUUUAAACAUUCUGUGAGUGGCAGA--------------------------------------------AGCAGAUAUGCAUUCUCCAA-AGGAGGAGA--GGCUA----UGGCUACAGUC-----AGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GACUCCAUU----GGGGUCU-
X86441.1/44-307              AUGAAGUUUUGU---UGGCAAGCAUCC------AUCCAUGGUUCUUAAGAAGCAUGGAGAGAAA-----G-GAGUGUGAGAGGG---------------------------------------UCCUUACCCCUC-ACACUCCCCCUCU-----UUCGACAGUUUGCUUGCGC--UUAGCUUUGGCUUCUCUAAUCAACAAGGGAUGUGCUUAAACAUUCUGUGAGUGGCAAA--------------------------------------------AGCAGAUAUGCAUUCUCCAA-AGGAUAAGA--GGCUU----UGGCUACACUC-----AGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GACUCCAUC----GGGGUCUC
Y12714.1/54-325              AUGAAGCUCUGU---UGGCAAAAAUCC------AUCCAUGGUUCUUAA-AGAAACAUGGGAAGA--------AGUGUGAGAGGG---------------------------------------UCCUUAACUCCUCACACUCUCCCACU-----UCCAACAGUUUGCUUGUGC-UUAGCUAUUGGCUUCUCUAAUCACCAAGGGAUAUGCUGAAACAUUCUCAUUCUCUCUGAGUAG------------------------------------CAGAAGCAGAUAAGCAUUCUCUAA-AGGAGGAGA--GGCUU----UGGCUACAGCU-----UGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GACUCCAUU-A--GGGGUUCU
AF426838.1/99-390            AUGAAGCUUCUUUGUUGGCAAAAAUCA------AUUCAUGGUUCUUAAAACAAACAUGGAGAGA--------AGUGUUAGAGGGUUGUAUUAA-------------------------ACAAAACCCUUUACACU---CUCCCUCCAUUUU--CAAAAACAGUUUGCUUUGUGCUUUAGCUAUUGGCUUCUCAUAUCACAAAGAGAUUAUAUGUUUUUUUCUGAGUAGCAGAAG-----------------------------------------CAAAUAAUUAAGCAUUUUUCUCCGAAGGAUCAGAAGUUUU--UUGGUUAUAGCA-----UGGCAAACCGGCAAG---UCACA-AAAAGGCAACG----GAUUCCUUUUU--GGGAUCUU
AF426839.1/97-390            AUGAAGCUUCUUUGUUGGCAAAAAUCA------AUUCAUGGUUCUUAAAACAAACAUGGAGAGA--------AGUGUAAGAGGGUUGUAUUAA-------------------------ACAAAACCCUUUACACU---CUCCCUCCAUUUU--CAAAAACAGUUUGCUUUGUGCUUUAGCUAUUGGCUCCUCAUAUCACAAAGAGAUUAUAUGUUUUUU--UUUCUGAGUAGCAGA-------------------------------------AGCAAAUAAUUAAGCAUUUUUCUCCAAAGGAUCAGAAGUUUU--UUGGUUAUAGCA-----UGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GAUUCCUUUUU--GGGAUCUU
X80264.1/96-381              AUGAAGCUUCUUUGUUGGGAAAAAUCA------AUCCAUGGUUCUUAAAACAAACAUGGAGAGA--------AGUGUGAGAGGG-UAUUAAA--------------------------CAAAAACCCUACACACU---CUCCCUCCAUUUU--CCUAAACAGUUUGCUUUGUGCUUUAGCUUUUGGCUUCUCAUAUCACAAAGGGAUUAUGCUUUUUUCUGAGUAGCAGAAGC-------------------------------------------AAAUAAUUAAGUAUUUUUCUCCAAAGGAUCAGAAGCUU----UUGUUAUAGCA-----UGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GAUUCCUUUUU--GGAGUCUU
X80263.1/45-330              AUGAAGCUUCUUUGUUGGCAAAAAUCA------AUCCAUGGUUCUUAAAACAAACAUGGAGAGA--------AGUGUGAGAGGG-UAUUAAA--------------------------CAAAAACCCUACACACU---CUCCCUCCAUUUU--CCUAAACAGUUUGCUUUGUGCUUUAGCUUUUGGCUUCUCAUAUCACAAAGGGAUUAUGCUUUUUUCUGAGUAGCAGAAGC-------------------------------------------AAAUAAUUAAGUAUUUUUCUCCAAAGGAUCAGAAGCUU----UUGUUAUAGCA-----UGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GAUUCCUUUUU--GGAGUCUU
CT025841.2/1930-2215         AUGAAGCUUCUUUGUUGGCAAAAAUCA------AUCCAUGGUUCUUAAAACAAACAUGGAGAGA--------AGUGUGAGAGGG-UAUUAAA--------------------------CAAAAACCCUACACACU---CUCCCUCCAUUUU--CCUAAACAGUUUGCUUUGUGCUUUAGCUUUUGGCUUCUCAUAUCACAAAGGGAUUAUGCUUUUUUCUGAGUAGCAGAAGC-------------------------------------------AAAUAAUUAAGCAUUUUUCUCCAAAGGAUCAGAAGCUU----UUGUUAUAGCA-----UGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GAUUCCUUUUU--GGAGUCUU
L32806.1/65-350              AUGAAGCUUCUUUGUUGGCAAAAAUCA------AUCCAUGGUUCUUAAAACAAACAUGGAGAGA--------AGUGUGAGAGGG-UAUUAAA--------------------------CAAAAACCCUACACACU---CUCCCUCCAUUUU--CCAAAACAGUUUGCUUUGUGCUUUAGCUUUUGGCUUCUCAUAUCACAAAGGGAUUAUGCUUUUUUCUGAGUAGCAGAAGC-------------------------------------------AAAUAAUUAAGCAUUUUUCUCCAAAGGAUCAGAAGCUU----UUGUUAUAGCA-----UGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GAUUCCUUUUU--GGAGUCUU
L32805.1/170-455             AUGAAGCUUCUUUGUUGGCAAAAAUCA------AUCCAUGGUUCUUAAAACAAACAUGGAGAGA--------AGUGUGAGAGGG-UAUUAAA--------------------------CAAAAGCCCUACACACU---CUCCCUCCAUUUU--CCUAAACAGUUUGCUUUGUGCUUUAGCUUUUGGCUUCUCGUAUCACAAAGGGAUUAUGCUUUUUUCUGAGUAGCAGAAGC-------------------------------------------AAAUAAUUAAGCAUUUUUCUCCAAAGGAUCAGAAGCUU----UUGUUAUAGCA-----UGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GAUUCCUUUUU--GGAGUCUU
X83683.1/60-376              AUGAAGCUUCUUUGUUGGCAAAAAUCA------AUCCAUGGUUCUUAAAAUCAAACAUGGAGAG-----A--AGUGUGAGAGGGUUAAUUAGUUGGUACUAAUUAUGAUUAGUACUAAUUACAUCAUCCUUUACA-CUCUCCCUCCAUUUUUACAAAAACAGUUUGCUUUGUGCUUUAGCUAUUGGCUUCUCAUAUCAUAAAGGGAUGUGCUUUUUUCUGAGUAUCAGAAGCA--------------------------------------------AAUAAUUAAGCAUUUUUCUCUAUUGGAUCAGAAGCUU----UGGUUAUAGUA-----UGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GAUUCCUUUUU--GGAGUCUU
X81064.1/62-368              AUGAAGUUUCUUUGUUGGCAAAAAUCA------AUCCAUGGUUCUUAAAAACAAAUAUGGAGUG-----A--AGUGUGAGAGGGCUAAUUAGUUGCUAAUU---------ACUACUAAUUACAUCAUCCUUUACA-CUCUCCCUCCAUUUUUACAAAAACAGUUUGCUUUGUGCUUUAGCUAUUGGCUUCUCAUAUCAAAAAGGGAUGUGCUUUUUUCUGAGUAGCAGAAGCA--------------------------------------------AAUAAUUAAGCAUUUUUCUU-CAAAGAUCAGAAGCUU----UGGUUAUUGUA-----UGGCAAACCGGCAAG---UCACA-AAAAGGCAAUG----GAUUCCUUUUU--GGAGUCUU
AARH01003665.1/167911-168144 AUGGAAGUCUCU---UGUCGAGAAUAUUCAUUCAUCCAAGGGCCUUUAAAAGCGA-------------------GGGCCGAGGG----------------------------------------GUUCCUCACAC---CCUCCUCCAGA----AUUUAACAGUUUGCUUGUGC--UUAGUCAUUGUCU----------------------------------AUGCUGGCUAC--------------------------------------------AACAUGAAGCUUUUGCUCUGAAAGCCAGCAAAGUCUU----UGGCCAAUGCAUA-UCUGGCAAACCGGCAAG---UCACAGAAACGGCACGGUCACGACUCUUUUCU--GGUUUUU-
AARH01004278.1/36417-36661   AUGGAAAUCUCU---UGUCAAGAAUACUCAUCCAUCCAAGGCCCUUGAGGAGCGAGGGGGGGUU--------UUGGAGCGAGGG------------------------------------------AUCCCUCAC---CCUCCUCCAAA----AUUCAACAGUUUGCCUGUGC-UUAGCCAUUGUCGACUAUGCUAACUACAUAAUGAAGCUUUU--------------------------------------------------------------GCUCUAAAAGC----------UAGCUGGCAGAGUCUU----CGGUUAAUGCAUG-CCUGGCAAACCGGCAAG---UCACA-GAACGGCAACG----GGCUC-GGUCA--CGAGUCUU
AASG02004929.1/11970-11715   AUGCUAGUCUUU---UGUCAACAAGCC------AUCCAUGGCUCUUGAAAAGCAUAGGGGGCUU----------GGAGUGAGGGAUUA-----------------------------------AGUCCCUUUGAU-CUCUCACUCCAAAAU--UUCGAACAGUUUGCCUGUGCUUAUAGCCAUUGGCUAUGCUAAUCAUCGAAGCUGCCCUGAUAAA------------------------------------------------------------GAGAAGCAUCGUUUGAAGAC-AAAGCAUAG--UGUUU----UGGUUAAUGCCU--GCAGGUAGACCGGCAAG---UCACA-GAACGGCACCA----GACUCGGUU-A--UGAGUCU-
AM156924.1/147-327           AUGUGU---------UGGGAUGAAGAG------UUUCAUGGUUCUUGAAAAUCAU--------GG---CA-CUUGGAGUGAG------------------------------------------CUGCAUUUGUG---UUCACUCCACA----CUCA----ACUCGUCUGCUC---CGCGAAUUUGCA-----------------------------------------------------------------------------------------GAAG---AGGGCUUAACCUUU--------------------UGGCUAAUUCA-----GGGCAAACCGGCAAG---UCACA-CAACGGCAAUG----GACUCUGCU-----GAGUCUU
AY388519.1/3282-3584         AUGCAG---------UGGGAUGAAGCA------AUCCACGGGUCUUAG-AAAAGAUAGGCAAGU--------UGGAGUGGAGGAG--------------------------------------UUUUAAACUGCA---GGGCAGUUAUGUU--GCUCGAAUUUGUUCAAAAAUAUCGACAAAUACAUGUUGGAUUCUCCAAAUUCAACGUGAUUAUAACAACAUCUCUGGAGAGUCCGAGCAAACAUAAUUCCUCCCUAUACAAUUUCAAGUUUGCUCAUACUUAGCC----------AAAUUAUGUGUGGAUAU--AUGGCAAAAGGA-----UGGCAAACCGGCAAG---UCACA-AAACGGCAAUUG-UGGACUCCGUUUU--GGAGUCUU
X98716.1/69-332              AUGCAG---------UGGGAUGAAGCA------AUCCAUGGGUCUUAGGAAAAGAGAGGCAAUU-----A-GUUGGAGUGAAUUA---AG-------------------------------GACUUUUAAAUGCC---CUUCCUCCAAAUA-CAAUUUCAAGUUUGUUCAUACUUUGCCAAUUUCUCUGCUAGAAUUCCAGAAAAUGCAGCAAAAAAGGAAAGUGUUUAUGGAU------------------------------------------UGAUAAUCACAC----------UAAUAGCAAA-GGAUG---UUGGCAAAAGCA-----UGGCGAACCGGCAAG---UCACG-AAACGGCAAUG----GACUCCGUUUU--GGAGUCUU
AK220907.1/64-219            AUGAAACCGGCA----------------------------------GAAAAAAUGCAGACAAAG-----C-CAUUUAAGGAAGA-GAC-----------------------------------AGAGGAACCUCA---GUUUGGAAAAUCU--CCCCAACAGUUUGUUUA-GC-UUGG--CC----AU-----------------------------------------------------------------------------------------GAGAAGCAAGG------------------------------------AGG-------AGACAAAACGGCAAG---UCAUA-UAUCGGCAUCA----GGCUC---------GAGUUUU
AC009398.6/45612-45448       AUGAAACCGGCA----------------------------------GAAAAAAUGCAGACAAAG-----C-CAUUUAAGGAAGA-GAC-----------------------------------AGAGGAACCUCA---GUUUGGAAAAUCU--CCCCAACAGUUUGUUUA-GC-UUGG--CC----AU-----------------------------------------------------------------------------------------GAGAAGCAAGG------------------------------------AGG-------AGACAAAACGGCAAG---UCAUA-UAUCGGCAUCA----GGCUCGUGUUUUUCGAGUUCU
CT833477.1/79-315            AUGGUGGGUGCA---UGGCAGGAGCAU------CUUCAUGGUUCUUGAGAUCGGGAGCAGCAUA-----A--GCAGUAUGAGGAUGGAGAA----------------------------GAAUGGCUGUGCUGUU--CCUUCUCCUCCU----UCUCAAGAACUCUUCAGUUUGUCCAUGCCUUCAU------------------------------------------------------------------------------------------GGCAUAAUUCCCUGGAUUCC-AGAAUCUCU--GGG------UGGCUUAGGGAGGUAUGAACAAACCGGCAAG---UCAUA-AAUCGGCAAUAG-UGAGCUCCGAC-U--GGAGCUUA
AAAA02006932.1/4657-4897     AUGGUGGGUGCA---UGGCAGGAGCAU------CUUCAUGGUUCUUGAGAUCGGGAGCAGCAUA-----A--GCAGUAUGAGGAUGGAGAA----------------------------GAAUGGCUGUGCUGUU--CCUUCUCCUCCUCC-UUCUCAAAAACUCUUCAGUUUGUCCAUGCCUUUCAU-----------------------------------------------------------------------------------------GGCAUAAUUCCCUGGAUUCC-AGAAUCUCU--GGG------UGGCUUAGGGAGGUAUGAACAAACCGGCAAG---UCAUA-AAUCGGCAAUAG-UGAGCUCCGAC-U--GGAGCUUA
CU405621.1/59-299            AUGGUGGGUGCA---UGGCAGGAGCAU------CUUCAUGGUUCUUGAGAUCGGGAGCAGCAUA-----A--GCAGUAUGAGGAUGGAGAA----------------------------GAAUGGCUGUGCUGUU--CCUUCUCCUCCUCC-UUCACAAGAACUCUUCAGUUUGUCCAUGCCUUUCAU-----------------------------------------------------------------------------------------GGCAUAAUUCCCUGGAUUCC-AGAAUCUCU--GGG------UGGCUUAGGGAGGUAUGAACAAACCGGCAAG---UCAUA-AAUCGGCAAUAG-UGAGCUCCGAC-U--GGAGCUUA
AF542513.1/13-217            AUGGAAGGCGCA---UGGCUCGAGCAU------CUUCAUGGCUCUUGAGAGCGGA--------A--------GCAGGACCAGCG---------------------------------------GGAUGAACCGCA-AAGCUGAGCUCCUG---GGCAGGGAGCGCUUCAGCUUUGUGGUGCCUCUCCU-----------------------------------------------------------------------------------------GACCUCUCAGG----------CGGUCGGCUGAGGU------------ACGCGC--GAGCACGAAUCGGCAAG---UCACA-AAACGGCAAUGG-UGAACUCCGGC-A--GGAGUCUA
AF538351.1/3775-3969         AUGGAAGAUGCA---UGGCUUGAGCAU------CUACAUAGUUCUUGAGAGCAGA-------------------AGCAUGAUGA---------------------------------------GGAUGAACCACA-AAGCUGAGCUCCUG---CUUAAGAAGCGCUUCAGUCUUAUGGUUCCUAUCCU-----------------------------------------------------------------------------------------GAGCUCCCAGG----------UGGUUGUCUGAGGU------------ACGC--------ACGAACCGGCAAG---UCACA-AAACGGCAAUGG-UGAACUCCAGC-A--GGAGUCU-
AB024055.1/2687-2885         AUGGAAGAUGAA---UGGCUUGAACAU------GCACAUGGUUCUUGAGAGAGCA--------G-----A-AGCAGGAGGAGGA---------------------------------------UGGAGAGCAAUG---GCUGAGGUCCAG---CUCAAGAAGCUCUUCGACUCCAUGGUGCAUUUCCU-----------------------------------------------------------------------------------------GGCCUCCUAGG----------UGGUUGGCUGAGGU------------AUGC--------ACAAACCGGCAAG---UCACA-AAACGGCAUUGG-UGAGCUCCAGC-A--GGAGUACA
CR855213.1/27806-28003       AUGGAAGAUGAA---UGGCUUGAACAU------GCACAUGGUUCUUGAGAGCAGC--------A--------GGAGGAGGAGGA---------------------------------------UGAAGAGCAAUG---GCUAAGCUCCAG---UUCAAGAAGCUCUUCAACUCCAUGGUGCCUUUCC------------------------------------------------------------------------------------------GGCCUCCUAGG----------UGGUCGGCUGAGGU------------ACGCA-------CCAAACCGGCAAG---UCACA-AAACGGCAAUGGUGAAACUCCAGC-A--GGAGUCCA
AJ487686.1/61-299            AUGAAGCCUUUUA-CUGAUGAUAGAAU------GUUCAUGGGUUCUACAAAGCAUGGGACCAG-----------GGGAAGAGGU---------------------------------------UCGACACCCCCA--CACUGCUCUAGA-----UUCUUAACUCUGCUGAUGCUUUUAGCCAUUGCGUCCACUAACUGGAGCGGCACGCGGUAAA--------------------------------------------------------------GCACUCCGGGA----------UAGUAGAGCAGUGCUU---UUGGCUGAAGCG-----CGGCAAAUCGGCAAG---UCACA-GAACGGCAAUG----GACUCGGCUCA--CGAGUCC-
EU947336.1/69-261            AUGGAAGAUGCA---UGGCUUGAGCAU------CUGCAUGGUUCUUGAGAGUUAA--------A--------GCUGCACGACGAUGGA----------------------------------UAGUGGAAACAGA---GCUUCUCAAGA-----AGC----AUUCGUUUUCGU---GGUGCCUUUCCU-----------------------------------------------------------------------------------------GACCUCCUUGG----------UGGUCAGCUGAGGU------------GCGC--------ACAAACCGGCAAG---UCACA-AUACGGCAAUGG-CGGAUUCCAUU-A--GGAGUCCU
BT130927.1/58-298            AUGGUGGGUGCA---UGGCAGGAGCAU------CUUCAUGGUUCUUGAGAUCGGGAGCAGCAUA-----A--GCAGUAUGAGGAUGGAGAA----------------------------GAAUGGCUGUGCUGUU--CCUUCUCCUCCUCC-UUCUCAAGAACUCUUCAGUUUGUCCAUGCCUUUCAU-----------------------------------------------------------------------------------------GGCAUAAUUCCCUGGAUUCC-AGAAUCUCU--GGG------UGGCUUAGGGAGGUAUGAACAAACCGGCAAG---UCAUA-AAUCGGCAAUAG-UGAGCUCCGAC-U--GGAUCUUA
#=GC SS_cons                 ::::::::::::...::::::::::::......:::::::::::::::::::::::::::::::........::<<<_______.......................................____________..._____>>>,,,,,..,,,,,,,,<<<<<<-------------<<<__________________________________________________............................................____________________.________________....______>>>--.....-->>>>>>-------...-----.-----------....<<<<<______.._>>>>>::
#=GC RF                      AUGaAGcUUuuU...UGGCAagAAuCa......AUCCAUGGUUCUUaAAAaaagaaaGGgaAga........aGgGagaGAGGG.......................................uccUcAaCuaca...cuUCcuCcAcuuU..cuucAAcAgUUUGcUUauucuUUuAgccuuugccUuUucAuucaaCAAAGGaauuauuuuuauauuaaaaUcucuguaga............................................aAuAuuuAaGCAUUuUuCuc.aaaagaucaGAGGcUU....UGGCUAaagCA.....uGgCAAAcCGGCAAG...UCACA.AAACGGCAAUG....GACUCCgUUUU..GGAGUCUU
//
# STOCKHOLM 1.0

#=GF AC   RF01846
#=GF ID   Fungi_U3
#=GF DE   Fungal small nucleolar RNA U3
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Marz M; 0000-0003-4783-8823
#=GF SE   Published; PMID:19875933
#=GF SS   Published; PMID:19875933
#=GF GA   95.00
#=GF TC   96.10
#=GF NC   91.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.23 -Z 549862.597050 CM SEQDB
#=GF CL   CL00100
#=GF DR   SO; 0001179; U3_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300259;
#=GF DR   snoopy; Homo_sapiens300287;
#=GF RN   [1]
#=GF RM   9016512
#=GF RT   The uRNA database.
#=GF RA   Zwieb C
#=GF RL   Nucleic Acids Res 1997;25:102-103.
#=GF RN   [2]
#=GF RM   10567566
#=GF RT   Nuclear retention elements of U3 small nucleolar RNA.
#=GF RA   Speckmann W, Narayanan A, Terns R, Terns MP
#=GF RL   Mol Cell Biol 1999;19:8412-8421.
#=GF RN   [3]
#=GF RM   19875933
#=GF RT   Comparative analysis of eukaryotic U3 snoRNA.
#=GF RA   Marz M, Stadler PF
#=GF RL   RNA Biol. 2010;6:503-507.
#=GF CC   Small nucleolar RNAs (snoRNAs) are involved in the processing and
#=GF CC   modification of rRNA in the nucleolus. There are two main classes of
#=GF CC   snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member
#=GF CC   of the box C/D class. Indeed, the box C/D element is a subset of the six
#=GF CC   short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C,
#=GF CC   C', and D. The U3 snoRNA secondary structure is characterised by a small
#=GF CC   5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C,
#=GF CC   C', and D), the two domains being linked by a single-stranded hinge. Boxes
#=GF CC   B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs,
#=GF CC   and boxes C' and D form the C'/D motif. The latter is functionally similar
#=GF CC   to the C/D motifs found in other snoRNAs. The 5' domain and the hinge
#=GF CC   region act as a pre-rRNA-binding domain. The 3' domain has conserved
#=GF CC   protein-binding sites. Both the box B/C and box C'/D motifs are sufficient
#=GF CC   for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary
#=GF CC   for nucleolar localisation, stability and hyper-methylation of U3 snoRNA.
#=GF CC   Both box B/C and C'/D motifs are involved in specific protein interactions
#=GF CC   and are necessary for the rRNA processing functions of U3 snoRNA.
#=GF WK   Small_nucleolar_RNA_U3
#=GF SQ   66



X05499.1/123-455               -UAAC-ACAUU--CUA----CAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUCCCA--UAACC-UUUGUACCC--CAGAGUGAGAAACCG--------AAAUUGA------AUCUAAAUU------------------------AGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCU-----AUAAUUUUGAAUAAAAAUUUUCU---------U------------UGCCGUUGCA--------------UUUGUAGUUUUU-U-C----------------------------------CUUUG------------------------------------------GAAGUAAUU-ACA-AU-------AUUUUAUGGCG-----------------------CGAUGAUCUUGACCCAU--------CCUAUGU--ACUUCUUU---UUUG---AAGG----G--AUAGGGC------------------------------------------------UCUA-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
M18578.1/157-489               -UAAC-ACAUU--CUA----CAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUCCCA--UAACC-UUUGUACCC--CAGAGUGAGAAACCG--------AA-----AUGA--AUCUAAAUU------------------------AGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUA----UAAUUUUGAAUAAAAAUUUUGCU---------U------------UGCCGUUGCA--------------UUUGUAGUUUUU-U-C----------------------------------CUUUG------------------------------------------GAAGUAAUU-ACA-AU-------AUUUUAUGGCG-----------------------CGAUGAUCUUGACCCAU--------CCUAUGU--ACUUCUUU---UUUG---AAGG----G--AUAGGGC------------------------------------------------UCUA-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
M26648.1/338-671               -UAAC-ACAUU--CUA----CAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUCCCA--UAACC-UUUGUACCC--CAGAGUGAGAAACCG--------AAAUUGA------AUCUAAAUU------------------------AGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUA----UAAUUUUGAAUAAAAAUUUUGCU---------U------------UGGCGUUGCA--------------UUUGUAGUUUUU-U-C----------------------------------CUUUG------------------------------------------GAAGUAAUU-ACA-AU-------AUUUUAUGGCG-----------------------CGAUGAUCUUGACCCAU--------CCUAUGU--ACUUCUUU---UUUG---AAGG----G--AUAGGGC------------------------------------------------UCUA-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
AJ507112.1/1-294               -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGGUC-AC-GU-CCC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUCGAUGAGUGAGA--UA-CC-CUUACACCC-UCAAAGUGAGACUAUA--------UUU--AG---C--UU-------------------------------------GACUGUGAUCCUUAGCGGUCUG-------------------GUCAUCUACCUAUUUU---------U------------UGCCUUUUAG-------------UUAUAAGACUU-G-G-A-----------------------------------UUUA------------------------------------------UCCUGUGUC-U---U---------UUAAAAGGAG-----------------------CGAUGAUCUUGACCCCU--------UUCUUCA--U--ACUUC---UUCG---GAGG----UUUUAGAU-----------------------------------------------------U-GGGGUGGGUGUAAGUGGC--AGUCUGACAAGU
X05498.1/323-655               -UAAC-ACAUU--CAA----CAGUAGGA-UCAUUUCUAUAUUAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGCCCCA--UAACC-UUUGUACCC--CAGAGUGAGGAAAUG-------A-AAUCGA------AUUUAAAUU------------------------AGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCU-----AUAAUUUUGAAUAAAAUUUUGCU---------U------------UGCCGUUGCA--------------AUUGUGAUAACU-U-C----------------------------------CUUUG------------------------------------------GAAUUUGUU-GCG-AU-------AUUUAAUGGCG-----------------------CGAUGAUCUUGACCCAU--------CCUAUGU-----GCUUCCAUUUUG---GAAG----G--AUAGGGA------------------------------------------------UUCA-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
HQ329066.1/118-440             -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCCAUAGGUC-GC-GU-CCC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUGAGA--UUACC-CUUAUACCC-UCAAAGUGAGAUAAUA--------AC-----AUGA--AAUUUUUUGCUUGACCG-------UGAUUCUUUGCAAUCUGG-----------CCAUC-------------------------UACUUAUAAUGUU---------U------------UGCCUUUAAC--------------UUUUUUUUGAUG-C--UAAC-------------------------CUANU------CAUA-------------------------------GGUGA-UGCAUUUAA-UAU-U---------UAUAAAGGAG-----------------------CGAUGAUCUUUACCCUU--------UUCAU----UGUGCCUU---CUAG---GAGG----AUUUUGAA-----------------------------------------------------U-UGGGUGGGUAUAAGUGGC--UGUCUGACANGU
Z78433.1/167-580               -UAAC-ACAUU--CUA----UAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AUGAGCCACUGAAUC---CAACUUGGUUGAUGAGCCGCA--UAACC-UUUGUACCC--UAGAGUGAGAAACAU--------AC-----UUCC--GAAGUUGACGCCUCUCCCGC-AAGGGAGAUAUAGUUUGGUUCCGUAAUCCUAAGCGGUUCGGUCAUCUGUACUGUCUCUUCAAAACCCCUUGCGUU---------U------------UGCUGUUUGC--------------GUAUGCCCGUUA-U-ACA------------------------------AGUUUACU----------------------------------------UGGAAAUGGG-CUG-U---------UAAAAUGGCG-----------------------CGAUGAUCUUUACCCAU--------CAUGUAU-ACUUCU------CUCAGUGGAAG-----GAACAUGUGUUUUAUGGCCUAGGAGUUGAGUGUCUUGGACAUGAAUUCUCUGUUCAGGGUC-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
X91005.1/72-372                -UGUG-CCU------A----UAGUAGGA-UCAUUUCUAUAGUUU-AC-GU-CCC-----UCU--UUGUCUCUU-CUA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGGUAUA--UA-CC-UUUGUGCCC--UAGAGUGAGAUUAAAC-----UU--U---C------AUUUAGCUUGUCUAU-----------AAUCCUUUGCGGUUUA-----------GUCAUCU----------------------AUUCUUUGAAGUUU---------U------------UGCCUUUUUU--------------GUUUAUUCCUGA-U-U----------------------------------AUUAUCCUUG-------------------------------UGAUAUUGUCAUGGA-UGU-CU-------UAUAAAAGGAG-----------------------CGAUGAUCUCGACCCUA--------UCUAUG-----CACUUU---UUCG---AAAG-----GGAUAGA-----------------------------------------------------UGUGGGUGGGUGCAAAU-----------------
EU526092.1/80-340              ---------AC--CAA----CAGGAGAA-UCAUUUCUAUAGUAU-UU-GU-CCUC---UUUU--GUGUUCCCU--AA--AGGAGCCACAGAUCC---CACCCGGGUUGAUGAACU--A--UAUCC-UCGUUUCCC--AACAGUGAGGUCCCU--------UU-----UA---------------------------------------------------------------------------------------------UUUUACU---------C------------UCGCUCUGCCUGAA------AAGGUGGCGAUCUUGC---------------------------------------UUCAC----------------------------------------U--GCAUGAU-UGU-A---------UAGAGAGUGG-----------------------CGAUGAUCUGUACCCCGAU----UUCCCAA----GGUCUGCC---UUCG---GGCG----C--UUGGG-----------------------------------------------------C-GGGGUGGGUUUCGAUGGA--AGUCUGACCGG-
EU526096.1/108-373             ---------AC--CAA----CAGGAGAA-UCAUUUCUAUAGUAU-UU-GU-CCUC---UUUU--GUGUUCCCU--AA--AGGAGCCACAGAUCC---CACCCGGGAUGAUGAACU--A--UAUCC-UCGUUUCCC--AACAGUGAGGUCCUU--------UU-----U-------------------------------------------------------------------------------------------------AUUU---------U------------UUACUCUCGUCUUGCCUGCAAAGGU---GGCGAUCU-G-C----------------------------------UUUAUA----------------------------------------AGUAGAU----UGU-A---------UAGAGAGUGG-----------------------CGAUGAUCUGUACCCCGAUUUUUUU--CUCAA--GGUCUGCC---UUCG---GGCG----CUU--GGG-----------------------------------------------------C-GGGGUGGGUUUCGAUGGA--AGUCUGACCGG-
X56189.1/89-342                -AUCG-ACGAU--ACU----CCAUAGGA-UCAUUUCUAUAGUAU-AC-GU-CCG-----GCU--UGGGUUUCC-UAA--CCUAGCCACAGAACU---CAACACGGAUGAUGAUAGAAG----GCA-CCGUUGCCC-GCAGAGUGAGAAUUUU--------UA-----CUU---------------------------------------------------C---------------------------------------------U----------U------------UGAGGAUGUG-------------CUGAUCGAUUUGG---C----------------------------------UUUUU------------------------------------------G-CUUAAUU-GUU-G--------UGCUAUCUUU-AU------------------UUGCGAUGAUCUCUUACAUG--------AUAUG-U-------UCC---UUUU---GG--------UCGUGU-----------------------------------------------------C-AUGUAGGGCAGCUGGUGU--UUUCUGACGUGU
X13850.1/316-569               -CGUA-UCGAU--ACU----CCAUAGGA-UCAUUUCUAUAGUAU-AC-GU-CCU-----UCU--UGGGUUUCC-UAA--CCUAGCCACAGAAGU---GAACACGGAUGAUGAUAGGAG--GCACC-GUUG--CCU--CAGAGUGAGGACUUU--------UA-----AUU---------------------------------------------------CU----------------------------------------UUGAAG---------G------------CAUGCUUUUC--------------GAUU------AG-G-U----------------------------------UUUUU------------------------------------------ACCUAAUU-------GUUUUGCUGUCAGAGUAUG-----------------------CGAUGAUCUCUUACAUG--------AUAUGUU--U-----CC---UUUU---GG--------UCGUAU-----------------------------------------------------U-AUGUAGGG--CAGCUGGUGUUUUCUGACGUGU
EU526093.1/1-192               ----------------------------------------------------------------------------------------------------CCGGGUUGAUGAACU--A--UAUCC-UCGUUUCCC--AACAGUGAGGUCCCU--------UU-----UA---------------------------------------------------------------------------------------------UUUUACU---------C------------UCGCUCUGCCUGAA------AAGGUGGCGAUCUUGC---------------------------------------UUCAC----------------------------------------U--GCAUGAU-UGU-A---------UAGAGAGUGG-----------------------CGAUGAUCUGUACCCCGAU----UUCCCAA----GGUCUGCC---UUCG---GGCG----C--UUGGG-----------------------------------------------------C-GGGGUGGGUUUCGAUGGA--AGUCUGACCGG-
EU526095.1/1-182               -----------------------------------------------------------------------------------------------------GCGGUUGAUGAUCA--A--UAUCC-UCGGCGCCC--AACAGUGAGGUCCUU-------------------------------------------------------------------------A------------------------------------UUUACUC----------------------UCGCUCUGCCUGC-------AAAG----GUGGC-------GG-----------------------------UCGCUUCAC----------------------------------------G--GCGAUUG---U-A---------UAGAGAGUGG-----------------------CGAUGAUCUGUACCCCGAU----UUCCAGAG----GUCUGCC---UUCG---GGCG------CUUUGG-----------------------------------------------------C-GGGGUGGGUGUCGAUGGA--AGUCUGACGC--
ACIW01002196.1/621-842         -AGCG-CAGUA--CUU----CA-UAGAA-UCAUUUCUAAUAGUA-UG-CA-UCCUU-CUCUG--A-GUUACU--CUA---AGUAGCCACAGAAUCUCCAUCCUGGUUGAUGACUAUCA----GCC-UCGAUGUCC--CGGAGUGAGGCCUUA--------UUUACGACU---------------------------------------------------GC------------------------------------------------------------------------------------------------------------------------------------------------UUCG----------------------------------------------------------------------------GCGGU-------------CGUGGCGAUGAUCUUCAGCUAA--------CCGG-----CUGUGUAC---UUCG---GU-CA--CA---CCGG-----------------------------------------------------A-AGGCAGGACGUUGAUGGC--AAUCUGACAGGC
AACG02000145.1/3310-3640       ---UA-ACACA--UUCA--ACAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAG-CCCA--UAACC-UUUGUACCC--UAGAGUGAGA--------------------AAUUGAAAUUAAUCUAA-------------------AUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCU-----AUAAUUUUUAACAAAUUUUGCUU----------------------UGCCGUUGCA--------------UUUGUAAUUUCU-U-C----------------------------------CUUUG------------------------------------------GAAGCUUUU-ACG-AU-------CUUUAAUGGCG-----------------------CGAUGAUCUUGACCCAU-------------CCUAUGUACUUC---CUUUUUGGAAGGGAUAGGGCUUC-----------------------------------------------------A-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
AAGI01000148.1/11337-11117     -GCUG-CAGUA--CUU----C-AUAGAA-UCAUUUCUAU-AGUU-AGUCG-UCCUC-UUCUG--A-GCUUCU--CAA---AAAAGCCACAGAUUCUCCAACCUGGUUGAUGAGUUUCA----GCC-CCGAUGUCC--CGGAGUGAGGCCUUA---------UUACGAUU---------------------------------------------------GC------------------------------------------------------------------------------------------------------------------------------------------------UUCG----------------------------------------------------------------------------GCAAA-------------CGUGGCGAUGAUCUUCAGCCAA--------CUGG-----UCUCGUAC---UUCG---GU-CG--AG---CUGG-----------------------------------------------------A-CGGCAGGACGUUGGUGGC--AAUCUGACAGGC
AAHF01000006.1/1528382-1528680 ----U-ACUAC--AGU----UC--AAAGAAUCACUUUAGAGUAG-AC-GU-CCCAC-CUCUG--A-GCUCUU-CUA----AAGAGCCACAGAAUCUCCACCCUUGCUGAUGACUGCUA--UGUCC-UCGAUGCCC--UAAAGUGAAGCCGUU--------CUUACUCC-----------------------------------------------------C-----------------------------------------------GAUU-CGACC------------UUGCUUCG-U-------------UCCGACGCUCUGA---ACGAC--------------------------UUGUUGCAAAACAA--------------------------------GCUUGU-UCGGGCU-GUU-G--------GAUGUUGCUCUGGUCCAG---------GGAGUGGUGAUGAUCUUGACCUUG--------UCCUGAC--GUCUAGAC---UUCG---GUCG-----GUC-GGA-----------------------------------------------------C-UUGGUGGGUGUCGA-GGA--GGUCUGAAAGGU
AACM02000135.1/152192-152462   -GUCG-ACAAU--ACU----UCAGAGAA-UCAUUUCUAUAGUAU-UC-GA-CCUU---CUCU---UGGUUCC-CUAA--AAGAGCCACAGAUCC---CACCCUGGUUGAUGAGUG-UA--UAUCC-UCGACACCC--UAGAGUGAAUACC-UU-----GGUCCUCUCGCCC----------------------------------------------UAUCCGCAA-------------------------------------GGAUGG---------------------------------------------------------C-G-GUGG---------------------------CUGUCUCGUGCA-----------------------------------GCUGCUGU------------------------------AUAGAGAGUU---UGUUUCCUCUUGAUGAUCUCGACCCCA--------GCUGUG----GUCUGCC---UUCG---GGCG------CGUGGC-----------------------------------------------------U-GGGGUGGGUGUUGAUGGA--CGUCUGACAGGC
AABZ01000565.1/2656-2323       -UAAC-ACAUU--CUA----CAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGCCCCA--UAACC-UUUGUACCC--CAGAGUGAGG--------------------AACUAAAAUUAAAUCUAA------------------AUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUA---UAAUUUUGAAUCAAAAUUUUGCUU----------------------UGCCGUUGCA--------------UUUGUAAUUUCU-U-C-----------------------------------UUCG------------------------------------------GAAGUUAUU-ACG-AU-------AUAAAAUGGCG-----------------------CGAUGAUCUUGACCCAU-------------CCUAUGUACUUC--C-UUUUUGGAAGGGAUAGGGCUUC-----------------------------------------------------A-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
AAFO01000024.1/12981-13296     -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGGUC-AC-GU-CCC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUGAGA--UUACC-CUUGUACCC-UCAAAGUGAGAAAU-----------------AACAUGAAAUUUU---------------------------UGCUUGACUGUGAUUCUUUGCAAUCUGGU---------------CAUCUACUUAUA-AUGUU---------U------------UGCCUUUGACUU---------GAUGCUAGCCUUUCU-U-U-----------------------------------UUUG------------------------------------------AAGGUAAUG-C-A-GCU-----AUUAUAAAGGAG-----------------------CGAUGAUCUUUAUCCUU--------UUCA----UUGUGCCUU---CUAG---GAGG---AU-UUUGAA-----------------------------------------------------U-UGGGUGGGUACAAGUGGC--UGUCUGACAAGU
AAKD03000017.1/74657-74959     --ACU-GCCAC--AGU----UC--AAAGAAUCACUUUAGAGUAG-AC-GU-CCCAC-CUCUG--A-GCUCUU-CUA----AAGAGCCACAGAAUCUCCACCCUUGCUGAUGACUGCUA--UGUCC-UCGAUGCCC--UAAAGUGAAGCCGUU--------CUUACUCC-----------------------------------------------------C-----------------------------------------------GCCU-CGACC------------C------CGCGGC--------GCUCCGACGCUCACA---ACGAU-------------------------UCUGUCGCAAGACGG-------------------------------AGUCUGU-UUGGGCU-GUU-GGUU---GCUGCG-----AUGGUCCAG---------GGAGUGGUGAUGAUCUUGACCUUG--------UCCUGAC--GUCUUGAC---UUCG---GUCG-----GUC-GGA-----------------------------------------------------U-UUGGUGGGCGUCGA-GGA--GGUCUGAAAGGU
AAIM02000163.1/33709-33431     -GUCG-ACAAU--ACU----UCAGAGAA-UCAUUUCUAUAGUAU-UC-GA-CCUU---CUCU---UGGUUCC-CUAA--AAGAGCCACAGAUCC---CACCCUGGUUGAUGAAUG-AA--UAUCC-UCGAUGCCC--UAGAGUGAAUACCCCUUUUCUGGUCCUCUCGAUC----------------------------------------------UGUCCGCAA-------------------------------------GGAUGG---------------------------------------------------------C-G-GUGGU-------------------------CUGCUCUUUUGAGU---------------------------------GGCUGCUGU------------------------------AUAGAGAGA-----UGUUACUCUUGAUGAUCUCGGCCCUU--------GGGACG----GUCUGCC---UUCG---GGCG------CGUUCU-----------------------------------------------------U-GGGGCGGGCAUUGAUGGA--CGUCUGACAGGC
Z78438.1/1-404                 -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGCCGAA--GAACC-UUUGUACCC--AAGAGUGAG---------------------AAAAAAGAAUGUAUUA---------------------UUAGCUUGGUCCACAACCCUUAGCGGUUUGGCCAU----------CUACUCCCACAUUUUUGCUU----------------------UGCCUUUUGCAU---------AUGGUUUGUGUAUGG-A--UAGAGAACUUAGCUUGGUGGUUUAGAAGUAGGAAUUUCGAUUCUAUGCUUUUUGAACUUACCGGCUUUUUUCUUGUUUUAACUCC-UGCA-UGA-ACCG--CCUUUUAAUUGGCG-----------------------CGAUGAUCUUUGCCCAG--------UUUGUGGACUU--CUUC---GUGA---GGGG---ACAAACGUA-----------------------------------------------------U-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
AAFT01000078.1/54796-55089     -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGGUC-AC-GU-CCC-----ACU--UUGACUCUU-CUA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGCGAGA--UACCC-UU-AUGCCC-UCAAAGUGAGA--------------------AUAGAUUUAGC--------------------------------UUGUCCACGAUCCUUUGCGGUCUGGUC-------------AUCUAUAAUUUGU---------------U------------UGCCUUUUAU-------------UU--AGCGC-AGA-G-C----------------------------------UUUGU------------------------------------------GCUCUUGCG-UU--U---------UCAAAAGGAG-----------------------CGAUGAUCUUGACCACU--------UUCUAAA-U---GCUCU---CUCG---GGAG----UCUUAGUU-----------------------------------------------------A-GUGGUGGGCAUAAGUGGC--UGUCUGACAAGU
X56982.1/37-291                -AUCG-ACGAU--ACU----CCAUAGGA-UCAUUUCUAUAGUAU-AC-GU-C--------CG--GCUUGGGUUUCCU--AACCU-AGCCACAGAACUCAACACGGAUGAUGAUAGGAG--GCACC-GUUG--CCC-UCAGAGUGAGGACUUUUAA-UUCUUUGA-AGGCA-------------------------------------------------UGC-----------------------------------------------U------UUU------------CGAUUAGGU------------------------------------------------------------------UUUU-----------------------------------------U-------------------------ACCUAAUUGUUUUGCUGU-----CUUUCUAUGCGAUGAUCUCU-UACAU--------GAUAUGUUUCC---------UUUU-------G--GU-CGUAUU-----------------------------------------------------A-UGUA-GGG--CAGCUGGUGUUUUCUGACGUGU
M26649.1/1-333                 -GUCG-ACGUA--CUU----CA-UAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUCCCA--UAACC-UUUGUACCC--CAGAGUGAGA--------------------AACCGAAAUUGAAUCUAA------------------AUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUA---UAAUUUUGAAUAAAAAUUUUGCUU----------------------UGGCGUUGCA--------------UUUGUAGUUUUU-U-C----------------------------------CUUU------------------------------------------GGAAGUAAUU-ACA-AU-------AUUUUAUGGCG-----------------------CGAUGAUCUUGACCCAU-------------CCUAUGUACUUC---UUUUU-UGAAGGGAUAGGGCUCU-----------------------------------------------------A-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
AAIH02000008.1/92390-92109     -CUUG-CCUAC--AGU----UC--AAAGAAUCACUUUAGAGUAG-AC-GU-CCCAC-CUCUG--A-ACUCUU-CUA----AAGAGCUACAGAAUCUCCACCCUUGCUGAUGACUUCUA--UGUCC-UCAAUGCCC--UAAAGUGAAGCCGUG--------UUUACUUC-----------------------------------------------------C-----------------------------------------------GUCU-CGACG------------G--------U--------------UGGUAUCUGCGA---ACGA---------------------------CUCGCUUCGGUGA---------------------------------GCUUGU-UCG-AG--UGC-C---------UC-------UCGUCCAG---------GGAGUGGUGAUGAUCUUUACCUUG--------UCUCGAU--GUCUUGAU---UUCG---GUCG-----GUC-GGA-----------------------------------------------------C-UUGGUGGGUGUUGA-GGA--GGUCUGAAAGGU
AAVQ01000002.1/348681-348368   -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGGUC-AC-GU-CCC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUGAGA--UA-CC-CUUAUACCC-UCAAAGUGAG---------------------AUACUAGUUUAG------------------------------CUUGUCCGUGAUUCUUUGCAAUCCG-------------------GUCAUCUACGUUUUGU---------U------------UGCCUUUUAG--------------UAUAAUCGCC------UGCGGUA--------------------UUUUGGAUUCGUUCCAAUAGC-----------------------UGCUAAUGAU--------------U----------UAAAAGGAG-----------------------CGAUGAUCUUUACCCUU--------UGUGA--CAUG--CCUU---CUAG---GAGGA--CU--UUGCA-----------------------------------------------------U-UGGGUGGGUAUAAGUGGC--UGUCUGACAAGU
AAID01000422.1/14605-14873     -AUCG-ACAAU--ACU----UCAAAGAA-UCAUUUCUUUAGUAA-AC-GU-CCUU--CUUCU--GU-GUUCU-CUAC--AAGAGCCACAGACUC---CAACUGGGACGAUGAGCC-----GAUCC-UCGAUGCCC--UAGAGUGAAACCG-UU-----UUUGCUUUCGUUUC---------------------------------------------UCUCCGCAA-------------------------------------GGAGGG--------------------------------------------------------AC-G-AGUUGA-----------------------GUCCUGGCAA-CAGUGA------------------------------CUUGAUUUGU------------------------------AUAGA------------AAGUGGUGAUGAUCUCGACCCUC--------UUUUGG------UUCUC---UUAG---GAGU------CUGGAU-----------------------------------------------------U-GGGGUGGGUGUUGAUGGA--CGUCUGACCAGU
FM992690.1/915250-915563       -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGGUC-AC-GU-CCC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUGAGA--UUACC-CUUGUACCC-UCAAAGUGAGAAAU-----------------AACAUGGAAUUUU---------------------------UGCUUGACUGUGAUUCUUUGCAAUCUGGU---------------CAUCUACUUAUA-AUGUU---------U------------UGCCUUUGACUU---------GAUUCU----UUCCU-U-U----------------------------------UUUUU-----------------------------------------UGAGGUUAUG-C-A-UCU-----AUUAUAAAGGAG-----------------------CGAUGAUCUUUACCCUU--------UUCA----UUGUGCCUU---CUAG---GAGG---AU-UUUGAA-----------------------------------------------------U-UGGGUGGGUACAAGUGGC--UGUCUGACAAGU
Y00887.1/157-490               -UAAC-ACAUU--CUA----CAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUCCCA--UAACC-UUUGUACCC--CAGAGUGAGA--------------------AACCGAAAUUGAAUCUAA------------------AUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUA---UAAUUUUGAAUAAAAAUUUUGCUU----------------------UGCCGUUGCA--------------UUUGUAGUUUUU-U-C----------------------------------CUUUG------------------------------------------GAAGUAAUU-ACA-AU-------AUUUUAUGGCG-----------------------CGAUGAUCUUGACCCAU-------------CCUAUGUACUUC---UUUUU-UGAAGGGAUAGGGCUCU-----------------------------------------------------A-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
CU633898.1/197623-197353       -GUCG-ACAAU--ACU----UCAGAGAA-UCAUUUCUAUAGUAG-UC-GU-CCUC---UUUU--GU-GUUCC-CUAA--AGGAGCCACAGAUCC---CACCCGGGUUGAUGAACG--A--UAUCC-UCGGCGCCC--AACAGUGAGGAGCCUUU---UUUUACUCUCGACC----------------------------------------------UGCCUGCAA-------------------------------------AGGUGG---------------------------------------------------------C-G-GUCGC--------------------------UGGCCUUUGUGCU----------------------------------GCGGCUGU------------------------------AUAGA------------GAGUGGCGAUGAUCUGUACCCCG-------AUUUCUCGAGGUCUUGCC---UUCG---GGCG---CUU---GAA-----------------------------------------------------C-GGGGUGGGUGUCGAUGGA--AGUCUGACCGGC
AAKE03000008.1/313515-313815   --UCU-GCCAC--AGU----UC--AAAGAAUCACUUUAGAGUAG-AC-GU-CCCAC-CUCUG--A-GCUCUU-CUA----AAGAGCCACAGAAUCUCCACCCUUGCUGAUGACUGCUA--UGUCC-UCGAUACCC--UAAAGUGAAGCCGUU--------CUUACUCC-----------------------------------------------------C-----------------------------------------------GACU-CGACC------------UUGCUUCG-U-------------UCCGACGCUCUGA---ACGAC--------------------------UUGUUGCAAAACGA--------------------------------GCUUGU-UCGGGCU-GUU-G--------GAGGUUGCUCUGGUCCAG---------GGAGUGGUGAUGAUCUUGACCUUG--------UCCUGAC--GUCUAGAC---UUCG---GUCG-----GUC-GGA-----------------------------------------------------C-UUGGUGGGUAUCGA-GGA--GGUCUGAAAGGU
CR382137.2/1282518-1282222     -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGGUC-AC-GU-CCC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUGAGA--UACCC-UU-AUACCC-UCAAAGUGAGA--------------------ACUAUAUUUAG-------------------------------CUUGUCUGUAAUCCUUAGCGAUUCGGUC-------------AUCUAUUAUUUGU---------------U------------UGCCUUUUAUC-----------UUG--AAGAUUUGG-A-A-----------------------------------UUUA------------------------------------------UUCCUCAUC-UU--U---------ACAAAAGGAG-----------------------CGAUGAUCUUUACCCUU--------UUUUA----UAUACUUC---UUCG---GAUG----UUUUAAAC-----------------------------------------------------U-AGGGUGGGUGUAAGUGGC--UGUCUGACAAGU
AAGT01000619.1/74722-75016     -AUCG-ACAAU--ACU----UCAAAGAA-UCAUUUCUUUAGUAA-AC-GU-CCUU--CUUCU--GU-GUUCU-CUAC--AAGAGCCACAGACUC---CAACUGGGAAGAUGAGUC-----GUUCC-UCAAUGUCC--UAGAGUGAA-GCC-UU------UUGCUUUCGUUUUAUUUCU-------------------------------CUUUUUCUUUCUCUCUU------------------------------------UUGGGGGAAGGGGGAGA------------GAGGAGUA--------------------------AU-G-UUGUU-------------------------UUUUGGUAA-CAAG---------------------------------AAAUGAUGU------------------------------AUAGA------------AAGUGGUGAUGAUCUCGACCCCU--------UUUUGA------UUGGC---UUCG---GUCG------UUGGAU-----------------------------------------------------U-GGGGUGGGCGUUGAUGGA--UGUCUGACCAGU
AM270263.1/106525-106819       -UUUG-CCUAC--AGU----UC--AAAGAAUCACUUUAGAGUAG-AC-GU-CCCAC-CUCUG--A-GCUCUU-CUA----AAGAGCCACAGAAUCUCCACCCUUGCUGAUGACUGCUA--UGUCC-UCGAUGCCC--UAAAGUGAAGCCGUU---------UUACUUC-----------------------------------------------------C-----------------------------------------------GACU-CGACC------------UUG------CA-----------UUUGCACGCUCUGU-U-ACAAU--------------------------CUGUUUUCGGAUAG--------------------------------ACUUGU-UUCGGGU-GUC-G--------GUG----UGAUGGUCCAG---------GGAGUGGUGAUGAUCUUUACCUUG--------UCAUGAU--GUCUUGAC---UUCG---GUCG-----GUC-GGA-----------------------------------------------------C-UUGGUGGGUGUCGA-GGA--GGUCUGAAAGGU
CR382132.1/3135255-3135515     -AGUG-AC-GU--AUU----CCAUAGGA-UCAUUUCUAUAGGAC-AU-GU-CUC----U--C--AUGACUUCUUAAA--AGAAGCCACUUAUUC---AAACUUGGUUGAUGAGAUAGA----ACC-UGCAAACCC--CAGAGUGAGAACACAUU----UGUU-----UGAUUG-------------------------------------------UUUGUCCUUGUG--------------------------------ACUCAGUCAUCUU-AUUA---------------------------------------UUCCC--GGC-G-C-----------------------------------GCAA------------------------------------------GCGUUCAAG-GAG--------------------------------------------CGAUGAUCUUGUCCCUU--------UGUU-----UGAGCCUC---UCUG---GAGG-----AGUGACU-----------------------------------------------------U-CGGGUGGGUUUGUAUGGC--AGUCUGACAAGU
AACD01000007.1/392675-392393   UGCCU-UCUAC--AGU----UC--AAAGAAUCACUUUAGAGUAG-AC-GU-CCCU--CAUUG--A-GCUCAU-CUA----AUGAGCCACACCCC--CAACCCUUGCUGAUGACUUCUA--UGUCC-UCGAUGCCC--UAAAGUGAAGCCGUG--------UUUACUCC-----------------------------------------------------C-----------------------------------------------GCCU-CGACC---------------------UU------------GUCUUCUCCGGU----ACAA---------------------------ACUGCUUUGGCGG---------------------------------GCUUGU--UCC-GA-GUU-GGC-----GCCU--------GGUCUAG---------GGAGUGGUGAUGAUCUUGACCUUG--------UCGUGGC--GUCUUGAC---UUCG---GUCG-----GCC-UGA-----------------------------------------------------C-UUGGUGGGUGUCGA-GGA--GGUCUGAAAGGC
AP007157.1/1106755-1106474     -CUUG-CCUAC--AGU----UC--AAAGAAUCACUUUAGAGUAG-AC-GU-CCCAC-CUCUG--A-ACUCUU-CUA----AAGAGCUACAGAAUCUCCACCCUUGCUGAUGACUUCUA--UGUCC-UCAAUGCCC--UAAAGUGAAGCCGUG--------UUUACUUC-----------------------------------------------------C-----------------------------------------------GCCU-CGACG------------G--------U--------------UGGUAUCUGCGA---ACGA---------------------------CUCGCUUCGGUGA---------------------------------GCUUGU-UCG-AG--UGC-C---------UC-------UCGUCCAG---------GGAGUGGUGAUGAUCUUUACCUUG--------UCUCGAU--GUCUUGAU---UUCG---GUCG-----GUC-GGA-----------------------------------------------------C-UUGGUGGGUGUUGA-GGA--GGUCUGAAAGGU
ABHY02000006.1/221131-220868   -AUCG-ACGAU--ACU----CCAUAGGA-UCAUUUCUAUAGUAU-AC-GU-C--------CG--GCUUGGGUUUCCU--AACCU-AGCCACAGAACUCAACACGGAUGAUGAUCGGUA--GCGCC-AUUG--CCC-GAAGAGUGAGAUAUUACUU-UCUUACUGAAUGGA------------------------------------------------UGCU-----------------------------------------------UU-----GUA------------GCUGGAUCC------------------------------------------------------------------UUUU-----------------------------------------U-------------------------GGAUCAAGUUGCAUAAUGGCAUCUGUUCAAGGCGAUGAUCUCU-UGCAU--------GAAUUGUUUCC---------UUUU--U----G--GU-CGAUUC-----------------------------------------------------A-UGUA-GGG--UAGUUGGCGUUUUCUGACGUGU
AAPO01000024.1/184329-184622   -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGUAG-AC-GU-CCC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUUAUGAUUACCC-UU-ACACCC-UCAGAGUGAGA--------------------AACACAAUUUUUU---------------------------UGCUUGACUAUGGUUCUCGAUAAUCUA--------------------GUCAUCUAGUUUGUU---------U------------UGCCUUGUUAG-----------CCAAUUAC--------------------------------------------UUUAC-----------------------------------------U--------G-UAA-U---------UGCGAAGGAG-----------------------CAAUGAUCUUGACCUUU--------UUUACUUUAUG--CCUU---UUUG---GAGG---AAAUUGUUU-----------------------------------------------------A-AAGGUGGGUGUAAGUGGC--UGUCUGACAAGU
CR380956.2/371024-371465       -UAAC-ACAUU--CUA----UAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGCCACA--GAACC-UUUGUACCC--CAGAGUGAGAAACAAAC----CCAA-----UGGAGGUGACAUCUCUUCCGAAAG------GAAGAUGCAGUUUGGUUCCGUAAUCCUAAGCGGUUCGGUCAUCUG----UACUGUCCCUUCGCCCAACCCUUACG---UUU-------------UGCUGUUUGCG-----------UAUAGAAUUGGUUU-G-AUGCCC-----------------------ACAGGACUUCGGUCUUG------------------------------CGGGUGGACGACCUC-UUC-GACC--CCUUCAAAAUGGCG-----------------------CGAUGAUCUUUACCCAU-------------CUUGUGUACUUCU-CUUCGU-GGAAGGGACAAGUUUUUAUGGCCUAGGAGUUGAUAUCUUU------CGGGACAUCUUCUCUGUUUGGGUCU-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
AARE01001423.1/987-1250        -GACG-ACU-U--ACU----UCUAAGAA-UCAUUUCUAUAGUAU-AC-GU-CUCCUUCUGAU--UUUUUCGC-UUUA---GCGACAGAAUCCC----CACUCUUGCGGAUGACCU-UA--UGUCC-AGUAUGCCC--UAAAGUGAAACCGU----------GUGUUCC-----------------------------------------------------C-----------------------------------------------GCCU-CGACU------------U----------------------------------C-G-AUCAGA-----------------------UCUGGAUUCU-GUCCGG------------------------------GUUCUGUCGCU-----------------------------GUCCAG----------GGAAUGGUGAUGAUCUUGACCUUG--------CGCUAGC--GUCUUGAC---UUCG---GUCG-----GCUGCGU-------------------------------------------------------CUGGUGGGUGUACU-GGA--GGUCUGAAAGAG
CABE01000015.1/623590-623290   -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGUAG-AC-GU-CCC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGAUGAUGAGGUCU----UGUCA--CCAGUCCAU-AAAGUGAGAACC-----------------AAUUUUGCU-----------------------------------UGACUAUGGUUUCUUAUAGCCUAG------------------UCAUCAAUUUGUUUUU---------U------------UGCCUCGUUAAU----------CAUUGCAAUUCUGU-U-U---------------------------------CUUCG------------------------------------------GGAACUUUU--UGC-A--------AUGUAGAGGAG-----------------------CGAUGAUCUUGAUCCUA--------UUUC---UUUAUACCCU----UUC---GGGGG--GAAUCGAUU-----------------------------------------------------U-GGGGUGGACUGU--UGGC--UGACUGACAAGU
AATM01000124.1/21634-21887     -AUCG-ACGAU--ACU----CCAUAGGA-UCAUUUCUAUAGUAU-AC-GU-C--------CG--GCUUGGGUUUCCU--AACCU-AGCCACAGAACUCAACACGGAUGAUGAUUGGAA--GCACC-GUUG--CCC-GAAGAGUGAGGCAAUUCUU--UCUUCGGGAGGG---------------------------------------------------AU--------------------------------------------------------A------------ACAGGAUCU------------------------------------------------------------------UUUUU----------------------------------------C-------------------------AGGUUCUGUUCUCCC----------UCUUCAGCGAUGAUCUCU-UACAC--------CUCUGGUUUCUC-GUCC---CCU----GGACG--GU-CCCGUC-----------------------------------------------------G-UGUA-GGG--CAGCUGGUGUAUUCUGACGUGU
AAFM01000009.1/176808-176515   -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGGUC-AC-GU-CCC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUGAGA--UA-CC-CUUACACCC-UCAAAGUGAG---------------------ACUAUAUUUAG-------------------------------CUUGACUGUGAUCCUUAGCGGUCUG-------------------GUCAUCUACCUAUUUU---------U------------UGCCUUUUAG-------------UUAUAAGACUU-G-G-A----------------------------------UUUA-------------------------------------------UCCUGUGUC-UU--U----------UAAAAGGAG-----------------------CGAUGAUCUUGACCCCU--------UUCUU--CAUA--CUUC---UUCG---GAGGU--UU--UAGAU-----------------------------------------------------U-GGGGUGGGUGUAAGUGGC--UGUCUGACAAGU
AAFU01000765.1/105651-105383   -GUCG-ACAAU--ACU----UCAGAGAA-UCAUUUCUAUAGUAU-UC-GU-CCUC---UUUU--GU-GUUCC-CUAA--AGGAGCCACAGAUCC---CACCCGGGUUGAUGAACG--A--UAUCC-UCGGCACCC--UACAGUGAGAUCC-UUU---UUUUACUCUCGUUC----------------------------------------------UGCCUGCAA-------------------------------------AGGCGG---------------------------------------------------------C-G-GUUG----------------------------UUGCUUCGUGCU----------------------------------GCGACUGU------------------------------AUAGA------------GAGUGGCGAUGAUCUGUACCCCGG------CUUUCUUGAGGACUUGCC---UUCG---GGCG---CUC---AGG-----------------------------------------------------C-GGGGUGGGUAUCGAUGGA--AGUCUGACCGGC
AAJN01000140.1/146399-146113   ------------------------AAAGAAUCACUUUAGAGUAG-AC-GU-CUCU--CAUUG--A-GCUUUU-CUA----AAAAGCCACAGAAUCUCCACCCUUGCUGAUGACUGCUA--UGUCC-UCGAUGCCC--UAAAGUGAAGCCGUG--------UUUACUUC-----------------------------------------------------C-----------------------------------------------GCCG-CGACC------------GCGU---CCGUUU--------CCGC--AUCUUG------AUACGC------------------------CUUGUCUUCGGACGA--------------------------------GCGUGU---GUCGG-GUG-UCUG--GGGCGGG---CAUCGGUCAAG---------GGAGUGGUGAUGAUCUUGACCUUG--------UCUUGAC--GUCG-GAC---UUCG---GUCG-----GUC-GGA-----------------------------------------------------C-UUGGUGGGUGUCGA-GGA--GGUCUGAAAGGU
AJ507113.1/1-287               -GUCG-AC-GU--ACU----UCAUAGGA-UCAUUUCUAUAGGAC-AC-GU-C-------CCU--UUGACUCUUUUAAAAAAGAGCCACUGUUUC---CAACUUGGUUGAUGAGGUAGA--UA-CC-CUUGUGCCC--AAGAGUGAGAAGUU----------------UACUAGUUUGUCCGGAU--------------------CCUUAGCGGUCUGGUCAU----CU--------------------------------AUCACUUUU---------U------------UGCCUUUAG----------------UUUGUGGGAGU-U-A-----------------------------------CUUG------------------------------------------UAACUCUCC-U---------------UAAAGGAG-----------------------CGAUGAUCUUGACCCUU--------UG--UUG--UGUACUCU---UUAG---GGAG-----GGACUCU-----------------------------------------------------U-AGGGUGGGUGCAAGAGGC--AGUCUGACAAGU
AJ507111.2/71-377              -AUAG-ACUAACACCUUCCAAAGUAGGA-UCAUUUCUAUAGUUU-AC-GU-CCC-----UCU--UUGACUCUU-CUA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGCCGUA--UA-CC-UUUGUGCCC--UAGAGUGAGAAAUA----------------CAAUUUAGCUUGUCUAUAAC-------------CCUUAGCGGUUUAGUCAUCUAU----U---------------------------------UUAAUUUUG---------C------------CUUUUGUUAC--------------AAAGGAACUCGU-C-C-----------------------------------UUAU------------------------------------------GGACUUGAUGCCU------------UUAUAAAGGA---------------------GCGAUGAUCUUGACCCUG--------UUUA-----UGAACUUU---UUCG---GAAG----G-GAUAAA----------------------------------------------------UA-UGGGUGGGUGCAAAUGGC--AGUCUGACAAGU
EU526091.1/80-338              -ACCGCACUUU--ACA----GG--AGAA-UCAUUUCUAUAGUAU-UU-GUCCUC----UUUU--GUGUUCCC--UAA--AGGAGCCACAGAUCC---CACCGCGGUUGAUGAUCA--A--UAUCC-UCGGCGCCC--AACAGUGAGGUCCUUA-----UUUAC--UCUCGCUC------------------------------------------UGCCUGC-----------------------------------------AAAGGU---------G-------------GCG----------------------------GUCG-C-------------------------------------UUCAC----------------------------------------G-GCGAU------------------------UGU-AUAGA------------GAGUGGCGAUGAUCUGUACCCCGAU----UU-CCAGA---GGUCUGCC---UUCG---GGCG----C-UUUGG------------------------------------------------------C-GGGGUGGGUGUCGAUGGA--AGUCUGACGCG-
AJ507109.2/108-392             -UGCA-AC-------------AGUAGGA-UCAUUUCUAUAGUUU-AC-GU-CCC-----UCU--UUGACUCUU-CUA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGAUAUA--UA-CC-UUUGUGCCC--UAGAGUGAGGUUUUUG------U-U-----UA---GCUUGUCCA-------------------------CAACUCUUUGC---------AGUUUGG----------------------UCAUCUACAAAUU----------U------------UGCCUUUUCU-------------UCA--UAAUUUGA-A-C-----------------------------------UUCG------------------------------------------GUUCAUGUU-A---U---------UUCAAAGGAG-----------------------CGAUGAUCUCGACCCAG----------UUUAU--G-UACUUC---UUCG---GAAG---GGAUAGACC-----------------------------------------------------U-UGGGUGGGCGCAAAUGGC--AGUCUGACAAGU
AACQ01000009.1/90506-90829     -GUCG-ACGUA--CUU----C-AUAGGA-UCAUUUCUAUAGGUC-AC-GU-CCC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUGAGA--UUACC-CUUAUACCC-UCAAAGUGAGAUAAUAAC----AU-G-----A----AAUUUUUUGCUUGACCGU-------GAUUCUUUGCAAUCUGGCCA---------UCUA----------------------------CUUAUAAUGUU---------U------------UGCCUUUAAC--------------UUUUUUUUUGAU-G-CUAACC------------------------UAGUC------AUAG--------------------------------GUGAUGCAUUUAAU-AU--U---------UCUAAAGGAG-----------------------CGAUGAUCUUUACCCUU--------UUCA----UUGUGCCUU---CUAG---GAGG----AUUUUGAA-----------------------------------------------------U-UGGGUGGGUAUAAGCGGC--UGUCUGACAAGU
AACI02000279.1/5254-4922       -UAAC-ACCUU--UUA----CAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGUCCCA--UAACC-UUUGUACCC--CAGAGUGAGAAACUG-------A-A-----AUU--AAAUCUAAAUUAGCU--------------UGGUCCGCAAUCCUUA---------GCGGUUCGGCCAUCUA----UAAUUUUGAAUAAAAAUUUUGCU---------U------------UGCCGUUGCA--------------UUUGUGACUUCU-U-C----------------------------------CUUUG------------------------------------------GAAGUUGUC-ACU-A---------CUAAAUGGCG-----------------------CGAUGAUCUUGACCCAU--------CCUAU--GUACUUCCUU---UUUG---GAAG---GG--AUAGGGC------------------------------------------------UUUA-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
ABPO01000470.1/2611-2943       -UAAC-ACAUU--CAA----CAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGCCCCA--UAACC-UUUGUACCC--UAGAGUGAGAAAUUG--------AA-----AUUA-AUCGAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUA---------UAAUUUU---------------------UUAACAAAUUUUGCU---------U------------UGCCGUUGCA--------------UUUGUAAUCUCU-U-C----------------------------------CUCUG------------------------------------------GAAGCUUUU-ACG-AU-------CUUUAAUGGCG-----------------------CGAUGAUCUUGACCCAU--------CCUAU--GUACUUCCUU---UUUG---GAAG---GG--AUAGGGC------------------------------------------------UUCA-UGGGUGGGUACAAAUGGC--AGUCUGACAAGU
AABY01000172.1/20003-19670     -AACG--CAUU--CAA----CAGUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGCCCCA--UAACC-UUUGUACCC--UAGAGUGAGGAAAUG-------A-A-----AUU--AAAUCUAAAUUAGCU--------------UGGUCCGCAAUCCUUA---------GCGGUUCGGCCAUCUA----UAAUUUUGAAUAAAAAUUUUGCU---------U------------UGCCGUUGCA--------------UUUGUAAUUUUU-U-C----------------------------------CUUUG------------------------------------------GAAGUUAUU-ACG-AU-------AUUUAAUGGCG-----------------------CGAUGAUCUUGACCCAU--------CCUAUGU--ACUUCCUU---UUUG---GAAG-----GGAUAGGAC------------------------------------------------UUCA-UGGGUGGGUACAAACGGC--AGUCUGACAAGU
ABJE01001085.1/27369-27101     -UAAU-CCCUU--CCU----CAGGAGAA-UCAUUUCUAUAGUAU-UC-GA-CCUA---CUCU--G-GGUUCU-CCAA--AAGAGCCACAGAUCC---CACCCUGGUUGAUGAUUG--A--UAUCC-UCGACACCC--UAGAGUGAAUGGCUCU-----GGUUGC-CCUCGCA---------------------------------------------CUGCCUGCA-------------------------------------AAGGUG---------G--------------CGGCUCUU--------------G----------C-C------------------------------------CUUCUC----------------------------------------G-GGU----------------------GAGCUG--UAUAAGA---------GGGCGUUUUAUGAUCUCGUCCCUG--------CUUCGCG--GUCUUGCC---CUUG---GGCG-----CGC-GGG-----------------------------------------------------C-GGGGUGGGUGUUGACGGA--CGUCUGACAGGC
AABX02000070.1/138290-138029   -ACCA-ACA-------------GGAGAA-UCAUUUCUAUAGUAU-UU-GU-CCUC---UUUU--GUGUUCCCU--AA--AGGAGCCACAGAUCC---CACCCGGGUUGAUGAACU--A--UAUCC-UCGUUUCCC--AACAGUGAGGUCCCUUUU--AUUUUAC-UCUCGCU---------------------------------------------CUGCC-UGA-------------------------------------AAAGGU---------G--------------GCGAUCU--------------------------U-G-C-----------------------------------UUCAC----------------------------------------UGCAU----------------------GAUUGU--AUAGA------------GAGUGGCGAUGAUCUGUACCCCGAU----UU--CCCAA--GGUCUGCC---UUCG---GGCG----CUUGGG-------------------------------------------------------C-GGGGUGGGUUUCGAUGGA--AGUCUGACCGGC
AATT01000185.1/15906-16168     -GUCG-AC-CA--ACU----CUUCAGGA-UCAUAUGUAGAGUUCGUU-GU-ACU-----AUA--CUAGCUUUUUCAA--AAGAGCUACACUUAA---CAACAUGGAUGAUGAGACGAA----GGA-CAACCACUC--AAGGG-GAA---GUG---------------------------------------------------------------------CAGGA------------------------------------CAUUUUG---------U------------GACAAUUGGG--------------GU-----UUUUU-U-C----------------------------------AUUUGA----------------------------------------AGAAGAU------------------GCUAAUUGUUCGAUUUG---------UCUUGGUUGAAGAC--UACUCCUGA-----UUGCUGGAC--U---UGCC---CUUG--UGGCA-----GUCUGGC-----------------------------------------------------C-AGGAAGGGUGGAUGGCCC--UGUCUGACAUGU
AATT01000185.1/2392-2654       -GUCG-AC-CA--ACU----CUUCAGGA-UCAUAUGUAGAGUUCGUU-GU-ACU-----AUA--CUAGCUUUUUCAA--AAGAGCUACACUUAA---CAACAUGGAUGAUGAGACGAA----GGA-CAACCACUC--AAGGG-GAA---GUG--------CA-----GG---------------------------------------------------AC-----------------------------------------AUUUUG---------UGACAAUUGGGGUUUUUUUCAUU--------------UGAAGAAGAUGC-U-A----------------------------------GUUGU------------------------------------------UCGAUUUGU-CUU-G---------GUUGAAGAC---------------------------------UACUCCUGA-----UUGCUGGAC--U---UGCC---CUUG--UGGCA-----GUCUGGC-----------------------------------------------------C-AGGAAGGGUGGAUGGCCC--UGUCUGACAUGU
AFQF01003453.1/39631-39357     -GUCG-ACAAU--ACU----UCAGAGAA-UCAUUUCUAUAGUAU-UC-GA-CCUU---CUCU---UGGUUCC-CUAA--AAGAGCCACAGAUCC---CACCCUGGUUGAUGAAUG-AA--UAUCC-UCGAUGCCC--UAGAGUGAAUACCCCUUU--UGGUCCUCUCGAUC----------------------------------------------UGUCCGCAA-------------------------------------GGAUGG---------------------------------------------------------C-G-GUGGU--------------------------UGCUCUUU-GAGU---------------------------------GGCCGCUGU------------------------------AUAGAGAGA-----UGUUACUCUUGAUGAUCUCGGCCCCC--------AGAGCG----GUCUGCC---CUCG---GGCG------CGCUUU-----------------------------------------------------U-GGGGCGGGCAUUGAUGGA--CGUCUGACAGGC
ABDG02000022.1/919092-919362   -AACA-ACUUC--AA-----CAGGAGAA-UCAUUUCUAUAGUAU-UU-GU-CUCU---UGCU--UUGGUUCC--CAA--AAGAGCCAUCGAAUC---CACCCUGGUUGAUGAUUG-CA--UAUCC-UCGAUACCC--AAGAGUGAAUUUUCUG------GUC----C-----------------------------------------------------U---------------------------------------------------------C------------UCGCUCUGUCCG---------CAAGGAUGGCGGCAGUAGC----------------------------------CUCGU------------------------------------------G-CUUCUGC-UGU-A---------UAGAGAGCUGUUUU--------------CUUCUUGAUGAUCUCGACCCUA--------UCCGUG---GUCAUGCC---UUCG---GGCG------CACUGG-----------------------------------------------------U-AGGGUGGGUGUCGAUGGA--CGUCUGACAGGC
AE016816.3/565015-565319       -ACCG-ACG-U--ACU----UCAUAGGA-UCAUUUCUAUAGGAA-UC-GU-CAC-----UCU--UUGACUCUU-CAA--AAGAGCCACUGAAUC---CAACUUGGUUGAUGAGCAUCA--GAGCC-UCUGCACCC--CAGAGUGAG---------------------AACAAAGAUUGUUU-------------------------UAGCUUGGCCAUAAUCCUUAGCGGUUUGGC----------------CAUCUGCAACCUUUGCU---------A------------UGCCUUUGCAA-----------UCAGU--CGCAACC-G-G------------------------------------CUU-----------------------------------------GCCGGCGGCG-CAG-C----------UAAAAGGCG-----------------------CGAUGAUCUUGGCCCGC-------------UCUGUGCACUUC---UUCG--UGAAG----GGACAGUU-----------------------------------------------------G-CGGGUGGGAGCAGAUGGC--AGUCUGACAAGU
AAIL02000034.1/934416-934691   -AACA-ACCUU--UUG----CAGGAGAA-UCAUUUCUAUAGUAU-UC-GU-CUC-----UCGCUUUGGUUCC--CAA--AAGAGCCAUCGAAUC---CACCCUGGUUGAUGAUUG-UA--CAUCC-UCGAUACCC--AAGAGUGAAUACUUU--------UU----U-G--------------------------------------------------GUCC----------------------------------------------U-------CU------------CGCUCUGUCCGC---------AAGGACGGCGGCGGU-U-G----------------------------------CUCUUU----------------------------------------GUGGCUUCCG-CUG-U-----------AUAGAGAGUUGUU-------------UCUCUUGAUGAUCUCGACCCUG--------CCGGU---UCUUUUGUC---UUCG---GGCA----U--GCUGG-----------------------------------------------------U-AGGGUGGGUGUCGAUGGA--CGUCUGACAGGC
ABDF02000091.1/852020-852294   -ACAA-ACCGC--CCU---ACAGGAGAA-UCAUUUCUAUAGUAU-UC-GU-CUCU---UGCU--UUGGUUCC--CAA--AAGAGCCAUCGAAUC---CACCCUGGUUGAUGAUUG-UA--UAUCC-UCGAUGCCC--AAGAGUGAAUUUUUA--------UG-----GUCCUCUC--------------------------------------GCCC-------UGUCCGCA-----------------------AGGAUGGC-----------------------------------GGC-------------A-GUUGCCUUUGU-G-C----------------------------------UUCUGC----------------------------------------UGUAUAGAG-----AGU------UGUUU-------UUU----------------CUCUUGAUGAUCUCGACCCUG--------CCGGUG----GUCUGCC---UUCG---GGCG------CGCUGG-----------------------------------------------------U-AGGGUGGGUGUCGAUGGA--CGUCUGACAGGC
#=GC SS_cons                   .:::<.<<<<<..<<<....--<<<<<<.____>>>>>>>>>>>.>-.>>.>,,.....<<<..-<<<<<<<<.___..>>>>>>>>->>>---...---((((--------------..--(((.(((((((((..,,<<<----------........--.....----..............................................------..-....................................-------.........-............<-<<<<<<--..............--<<<<<<--<<.<.<..................................______........................................_>>>>-->>>.>>>.-.........-->>>>>>->.......................------->>>,<<<<<<........<<<<<<<..----<<<<...____...>>>>....->>>>>>>.....................................................>.>>>>>)))))))))-)))..-------)))):
#=GC RF                        .gucg.ACauu..ccu....caauAGgA.UCAUUuCUauaggaa.uC.GU.ccC.....ucu..uUGgcucuU.CAA..AagagcCACagaAuC...CAACuuGGUUGAUGAgucauA..UAgCC.ucuguaCCC..uAgAGUGAGaacuUu........uu.....auua..............................................uaauCc..A....................................uuuuuuU.........u............cgccuuuuuc..............uuuggcccuUcc.u.c..................................uUUuua........................................ggagguuggg.cca.a.........uuaaaaggcg.......................CGAUGAUCUcuaCCCau........cccggcc..uuuucgcC...UUcG...Ggcg....uggccggg.....................................................a.uGGGuGGGuacagaUGGc..aGUCUGACaaGU
//
# STOCKHOLM 1.0

#=GF AC   RF01847
#=GF ID   Plant_U3
#=GF DE   Plant small nucleolar RNA U3
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19875933; Gardner PP
#=GF SS   Published; PMID:19875933; Gardner PP
#=GF GA   80.00
#=GF TC   80.30
#=GF NC   79.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.66 -Z 549862.597050 CM SEQDB
#=GF CL   CL00100
#=GF DR   SO; 0001179; U3_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300259;
#=GF DR   snoopy; Homo_sapiens300287;
#=GF RN   [1]
#=GF RM   9016512
#=GF RT   The uRNA database.
#=GF RA   Zwieb C
#=GF RL   Nucleic Acids Res 1997;25:102-103.
#=GF RN   [2]
#=GF RM   10567566
#=GF RT   Nuclear retention elements of U3 small nucleolar RNA.
#=GF RA   Speckmann W, Narayanan A, Terns R, Terns MP
#=GF RL   Mol Cell Biol 1999;19:8412-8421.
#=GF RN   [3]
#=GF RM   19875933
#=GF RT   Comparative analysis of eukaryotic U3 snoRNA.
#=GF RA   Marz M, Stadler PF
#=GF RL   RNA Biol. 2010;6:503-507.
#=GF CC   Small nucleolar RNAs (snoRNAs) are involved in the processing and
#=GF CC   modification of rRNA in the nucleolus. There are two main classes of
#=GF CC   snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member
#=GF CC   of the box C/D class. Indeed, the box C/D element is a subset of the six
#=GF CC   short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C,
#=GF CC   C', and D. The U3 snoRNA secondary structure is characterised by a small
#=GF CC   5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C,
#=GF CC   C', and D), the two domains being linked by a single-stranded hinge. Boxes
#=GF CC   B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs,
#=GF CC   and boxes C' and D form the C'/D motif. The latter is functionally similar
#=GF CC   to the C/D motifs found in other snoRNAs. The 5' domain and the hinge
#=GF CC   region act as a pre-rRNA-binding domain. The 3' domain has conserved
#=GF CC   protein-binding sites. Both the box B/C and box C'/D motifs are sufficient
#=GF CC   for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary
#=GF CC   for nucleolar localisation, stability and hyper-methylation of U3 snoRNA.
#=GF CC   Both box B/C and C'/D motifs are involved in specific protein interactions
#=GF CC   and are necessary for the rRNA processing functions of U3 snoRNA.
#=GF WK   Small_nucleolar_RNA_U3
#=GF SQ   24



X52629.1/325-543             ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACCUCUGUUUCCUUG-AUUUC-UCAAGA-GACAG-GCCCUUAACCCUGGUUGAUGAACC-AUG-ACCGUGCGGCUAGAGCGUGAUUG-------ACGGCUAC-GAU--CGUC----CUCG--GACGCAUCCAG--UGCUGU-------AGAGGAUCGUU-ACUCG-GCUCG--GU-UUCU--------ACCUUGCCGG---GGUGGUCGCACGGC----GGUCUGACAGGUC
X52630.1/529-746             ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACCUCUGUUUCCUUG-AUUUC-UCAAGA-GACAG-GCCUUAAACCCUGGUUGAUGAACC-AUG-ACCGUGCGGCUAGAGCGUGAUUG-------ACGGCUAC-GAU--CGUC----CUUG--GAUGCAUCCGG--UGCUGU-------AGAGGAUCGUU-A-CUC-GGCUC--GG-UUCUA-------CCUUGUCGGG----GUGGUCGCACGGC----GGUCUGACAGGUU
AB265221.1/2418-2307         ACAACCUUACUUGAACAGGAUCUGUUCUAUUGGCUCG--U---ACCACUAUAUCCUUG-AGUUC-UAAGGA-GACAG-GAAACCAAGUCUGGUGGAUGAAUC-AUG-GCCAUUAGGCCAGCCC--------------------------------------------------------------------------------------------------------------------------------------------------------
AB007644.1/28030-28248       ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACCUCUGUUUCCUUG-AUUUC-UCAAGA-GACAGGCCCUU-AACCCUGGUUGAUGAACC-AUG-ACCGUGCGGCUAGAGCGUGAUUG------A-CGGCUACG-AU--CGUC----CUCG--GACGCAUCCGG--UGCUG-------UAGAGGAUCGUUAC-UCG-GCUCG--GU--UUCU-------ACCUUGCCGG---GGUGGUCGCACGGC----GGUCUGACAGGUC
AARH01001777.1/338669-338456 ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGAUCG--U---ACCUCUGUAUCCUUA-AUCAC-UAAGGA-GACAG-GAACCUAAGCCUGGUUGAGGAAUU-GUG-ACCGCUUGAUCAUAGCGUGAGUA---------AUGGCU-UGA-UUGUC----CUCG-UGAUCAUCAUGG--CUGU---------AGAGGAUCGUU---UCC-UAGCC--A--UUUAC------C-UGGCUGGGA----AUGGUCUUGCGGU----UGUCUGACAGGGU
AP004474.1/40162-40381       ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACAACUGUAUCCUUG-AGUUC-UAAGGA-GACAGGAACCA-AAGUCUGGUUGAUGAACA-CUG-ACCGUGUGAUCAGAGCGUGAUUA-----AUAGUC-GUCCGAU-UGACC----UUCG--GGUUCAUCAGA--UCGACGG-----UGGAGGAUCGU----UCU-CAGCG--GG-UAUCA-------CCGGCUGGGG-----UGGUCACACGGU----UGUCUGACAGGCU
ABEU01014426.1/8756-8528     ACGACUAUACUUGAACAGGAUCUGUUCUAUAGU-GCG--U---ACAUCUGAUCUGUGUUCUCC-AACACAG-A-CAA-GACCUUCAACCCGGACGAUGAUUC-AGG-GCUCUCCGGCCUGAGCGCGAUUGCCGCGGCUGGUGCCAGUGG-CCCCC----UUGC--GGGGGCCGGA---GC--CAGCCUGCCAGAUGAACGUC---CCG-CCUCC-----UCAUUC----CU--GGGGGCGG--UGAUGGACGGAGAGC----GUUCUGACGGGC-
ABXC01000575.1/44008-43791   ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGAUCG--U---ACCGCUGCAUCCUUG-ACUAA-UAAGGA-GGCAA-GCACUUAAGCCUGGUUGAUGAGUC-AUG-ACCUGUGGGCCAGAGCGUGAUUA-------ACGGCCA-GGAU-UAAGC----UUGA-UGCUGGGUCUGG--UGCUGU-------AGAGGAUCGUU-C-CUG-GUUGG--GU-CCU---------GCCUAGCUGG---GGUGGCCCAUGGGU----UGUCUGACAGGC-
AASG02024127.1/1647-1860     ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACCUCUGUAUCCUUU-AUCAC-AAAGGA-GACAGGAACUC-AAGUCUGGUGGAUGAAUC-AUG-ACCGUGUGAUCAGAGCGUGAUUA--------ACGGCUG-GAG-GAUCU----UUCU--GGGUUCUCAGG--GCUGU--------AGAGGAUCGUA---CCU-AGGCU--GC-CUA---------GCUGACUGGG----AUGAUCGCAUGGU----UGUCUGACAGACU
X14411.1/488-704             ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACCAUUGUAUCCUUG-AAUUC-UAAGGA-GACAG-GAAUCCAAGUCUGGUUGAUGAAGC-AUG-GCCAUGUGACCAGAGCGUGAUUA-------ACAGCUAUCCAU-GGUUU----CUC---GAGCUGUGGUU--ACAGU--------AGAUGAUCGUU-C-UUA--GACCCUUA-AUCU--------CAGGCC-UAA---GAUGGUCUCAUGGC----UGUCUGACAGAC-
X63065.1/858-1075            ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACCGCUGCAUCCUUU-ACCAA-UAAGGA-GGCAAGCACUU-CAGUCUGGUUGAUGCAUC-UG--ACCUCUGGGCCAGAGCGUGAUUA------ACGGCCA-GGAUU--CCCU----UAUG--GGGGCAAUCCA--CGGCUG------UAGAGGAUCGUU---CCU-GC-CU--UGCUCAU-------GCUUGUGCAGG----GUGGCCCAGAGGU----UGUCUGACAGACU
AL606444.3/140424-140208     ACGACCUUACUUGAACGGGAUCUGUUCUAUAGGCUCG--U---ACCGUUGCAUCCUUG-ACUAA-UAAGGA-GGCAA-GCACUUAAGCUUGGUUGAUGACGC-AUG-ACCUGUGGGCCAGAGCGUGAUUA-------ACGGCC-----G-GAUCACUGGCUGAUUUGAUCC--CAC--GGCUGU-------AGAGGAUCGUU-U-CUU-GCCGG--GC-CUC---------GCCUGGCCAG---GAUGGCUCUCAGGU----UCUCUGACAGGC-
AC144759.11/63139-62925      ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGAUUG--U---ACUACUGUGUCCUUG-AUUUC-UAAGGA-GAUAGGAACAU-AUGUCUGGUAGAUGAGUU-GUG-ACCGUGUGAUCAGAGCGUGAUUA--------ACGGCC-AGGA-UGAUG----UGUG--CAUCAUCUUCA--GCUGU--------AGAUGAUCGUU---CUU-GGCCU--AG-UUCAA-------CUAA-CCGGG----AUGGUCACAUGGU----UGUCUGACAGAUU
AJ001179.1/171-392           AUGACCGUACUUGAACAGGAUCUGUUCUAUAGG-UCA--U---ACACCUG-UCUGUGUUCUUC-AACUCAG-A-CAA-GUUCCUCAACCCAGACGAAGACAU-GCAGCCCCGG-CGCCUGAGCGCUACGUA----UGACCAC-UGUGGCCGUGCC----GCU---GGCACGG-ACG--CGUGGU------U-CUGGAUGAAC-G-UCC-CGCCG-----AGACCAUUCCAC--CGGCAGGG----AUGGUGCUCGGGG---CAUUCAGAUGGGU-
AC189322.2/92619-92834       ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACCUCUGUAUCCUUG-AUUUC-UAAGGA-GACAG-GCCCCUAAACCUGGUUGAUGAAUC-AUA-GCCGUGCGAUCUGAGUGUGAUUA-------ACGGUUA--CGA-UUCUC----CUCG--GAGUCUC-U-G--CACUGU-------AGAGGAUCGCU-A-UCC-GGUUA--GG-UUUGA-------CCUCUCCGGG----GUGGUCGCACGGU----UGUCUGACAGGCC
ABIM01001008.1/15000-15216   ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGUUCG--U---ACCUCUGUUUCCUGG-AGUUC-GAAGGA-GACAG-GAUCUCAAGUCUGGCGGAUGAAUC-GUG-ACCGUGUGAUCAGAGCGUGAUUA-------AUGGCAGAAGCG-GUU------CUCG----AACCGUUGA--UGCUGU-------AGAGGAUCGUU-C-UCA-GU-UG--GGUUUGAU-------CCUG-ACUGG--GGGUGGUCACCCGGU----UAUCUGACAGACC
AAAA02023191.1/14338-14116   ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACCGUUGCAUCCUUU-ACCAA-UAAGGA-GGCAA-GCACUCAAGUCUGGUUGAUGCGAC-AUG-ACCUCUGGGCCAGAGCGUGAUUA-------ACGGCCAGGAUG-ACUCC----CGAUGCGGGCUCAUCCGACGGCUGU-------AGAGGAUCGUU---CCU-GC-CU--GGUUCACU-------CCAGUGCAGG----GUGGCCCAGAGGU----UGUCUGACAGACA
AL606650.5/82385-82608       ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACCGUUGCAUCCUUG-ACUAA-UAAGGA-GGCAA-GCACUCAAGCUUGGUUGAUGACGC-AUG-ACCUGUGGGCCAGAGCGUGAUUG-------ACGGCCCGGAUC-AUUUC----CGUG-UGAAUUGAUCCCGCGGCUGU-------AGAGGAUCGUU-C-CUU-GCCGG--GC-UUUC--------GCUUGGUCAG--GGUUGGCCCAUAGGU----UGUCUGACAGGCA
Z29641.1/759-982             ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGAUCG--U---ACUGUUGCAUCUUUG-AUUAA-UAAGAA-GGCAA-GUACUUAAACCUGGUUGAUGAGAAUUUG-ACCUGUGGGCCAGAGCGUGAUUU------AACGGC-CAGGAC-UUUGC----CUUGGUGCAUUGUCUGG--AGCUGC-------AGAUGAUCGUU-C-UUG-GCCAG--GC-UUAAU-------GUCUGGCUAG---GGUGGCCUACAGGC----UGUUUGACAGGUU
Z11883.1/3211-3429           ACGACCUUACUUGAACAAGAUCUGUUCUAUAGGCUCG--U---ACCACUGUAUCGUUG-ACUUC-UAAGGA-GAUAG-GAAACCAAGUCUGGUGGAUGAAUC-GUG-GUCAUGAAACUCGAGUGUGAUG--------AUUGUUCUUCAG-GGCCU----UUCG--GGGUCAUUGUG--UGCAGU-------AGAUGAUUGUU-C-UCA-GC-CU--GG-UUUGC-------CCGUCCCUGA---GAUGGUCUCAUGGC----AGUCUGACAGACU
AC225244.1/2684-2865         ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACUGCCAGCAGGGUU-GGACU-UAUC---GCCGG-G------GGCCCGGUUACCGUCAC-CUG-GCGGUAACCGCGCAAAACCACGA--------------------UAAAU----UUGC--A-------------------------AUUUGAAAUUU---------GAA--UU-CAA-A-------AAUUCGGCAA---ACCGCGGUUACCGCGCGAUGUGUGACGGGCC
ACCP01000231.1/27198-26976   UCGACUGUACUUGAACAGGAUUCAUACU-UCAGUUGGUAA---ACCCUCGUCAGUAUU-CUCC--AAUACUUGACAA-GCUCCUCAUGUCAGACGAAGACUG-AAG-CUCACCUAGUCUGAGCCGGAAAU------CUGCGAUUCUCCU-AUGAC----GCCU-AGUCA--GGGAU--UUCGCU-------UGAUGAUGGCC-CC---CCGUCG--ACAUUCCA------AGUCGGGG---CUGGACGGCUAGGUGAC----GUUCUGAUGGCUA
CP001331.1/215080-214858     UCGACUGUACUUGAACAGGAUUCAUUUCUACAG-UAG--AUACACCCUAAUCAGUAUU-CUCCA-AAUACU-GACAA-GCUUCUCAUGUCGGAAGAAGAGUA-AUG-ACUCCCUAGUCUGAGCCGGAAGU------CUGCAUCGCUCCCAAGGUU----GAAA--GACCAGGGAC---UGUGCU-------UGAUGAUGGCC---CCC-UAACA-----UCAUUC-----C--AGUUGGGGC-GGACGGCUAGGGAGC----GUUCGGACGGCUG
FN594951.1/2080023-2080236   ACGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCG--U---ACCUCUGUAUCCUUG-AGUUC-UAAGGA-GACAG-GAACCUCAGUCUGGUGGAUGAACA-AUG-ACCGUGCGAUCAGAGCGUGAUUAA----CU---GCUUAACCU-G-CUU----UGUU--GGGUCAGG-GC--UGU----------AGAGGAUCGUU-C-UCA-GCCGA--GC-UUUG--------GCUCGACUGG---GAUGGUCGCACGGU----UGUCUGACAGAC-
#=GC SS_cons                 <<<-<<<-----<<<<<<___>>>>>>--->>>->->..>...,,,,<<<<-<<<<<<._____.>>>>>>.->>>>.--------(((((-----------.---.((((((((((((,<<<<------.......<<<<<<<<<<<<.<<<<<....____..>>>>>>>>>>>..>>>>>>.......------->>>>.,.<<<.<<<<<..<<._____.......>>>>>>>>>>...,,))))))))))))....-------))))):
#=GC RF                      aCGACCuUACUUGAACAGGAUCUGUUCUAUaGGcUCG..u...ACcucuGuauccuuu.auuuc.aaagga.GaCag.GaucuUaAgcCcGGuuGAuGAauc.aUG.gCcgugcggcCaGagcguGAuua.......accgcccccccc.gcgcc....uuug..ggcgcgggggg..ggcggu.......AGAuGAUcguu.c.ccc.gcccg..gg.uuauu.......cccgggcggg...GauGgccgcacgGc....ugUCUGACgGgcu
//
# STOCKHOLM 1.0

#=GF AC   RF01848
#=GF ID   ACEA_U3
#=GF DE   ACEA small nucleolar RNA U3
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19875933
#=GF SS   Published; PMID:19875933
#=GF GA   55.00
#=GF TC   55.00
#=GF NC   54.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00100
#=GF DR   SO; 0001179; U3_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300259;
#=GF DR   snoopy; Homo_sapiens300287;
#=GF RN   [1]
#=GF RM   9016512
#=GF RT   The uRNA database.
#=GF RA   Zwieb C
#=GF RL   Nucleic Acids Res 1997;25:102-103.
#=GF RN   [2]
#=GF RM   10567566
#=GF RT   Nuclear retention elements of U3 small nucleolar RNA.
#=GF RA   Speckmann W, Narayanan A, Terns R, Terns MP
#=GF RL   Mol Cell Biol 1999;19:8412-8421.
#=GF RN   [3]
#=GF RM   19875933
#=GF RT   Comparative analysis of eukaryotic U3 snoRNA.
#=GF RA   Marz M, Stadler PF
#=GF RL   RNA Biol. 2010;6:503-507.
#=GF CC   Small nucleolar RNAs (snoRNAs) are involved in the processing and
#=GF CC   modification of rRNA in the nucleolus. There are two main classes of
#=GF CC   snoRNAs: the box C/D class, and the box H/ACA class. U3 snoRNA is a member
#=GF CC   of the box C/D class. Indeed, the box C/D element is a subset of the six
#=GF CC   short sequence elements found in all U3 snoRNAs, namely boxes A, A', B, C,
#=GF CC   C', and D. The U3 snoRNA secondary structure is characterised by a small
#=GF CC   5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C,
#=GF CC   C', and D), the two domains being linked by a single-stranded hinge. Boxes
#=GF CC   B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs,
#=GF CC   and boxes C' and D form the C'/D motif. The latter is functionally similar
#=GF CC   to the C/D motifs found in other snoRNAs. The 5' domain and the hinge
#=GF CC   region act as a pre-rRNA-binding domain. The 3' domain has conserved
#=GF CC   protein-binding sites. Both the box B/C and box C'/D motifs are sufficient
#=GF CC   for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary
#=GF CC   for nucleolar localisation, stability and hyper-methylation of U3 snoRNA.
#=GF CC   Both box B/C and C'/D motifs are involved in specific protein interactions
#=GF CC   and are necessary for the rRNA processing functions of U3 snoRNA.
#=GF WK   Small_nucleolar_RNA_U3
#=GF SQ   28


AAEL01000384.1/2844-2571       U-C-GAC--UGUACUCGA--AC--GGGA--UCAUUUCU-AU-AGUG-AAUC-CGAU----CGUAUUGG-GCUACAGCUC---UUGACAACACCUC------UGUCCGUGACGAUGAGUUAUC-CAUCC-CGCCGG-GAACGGGAAGCGUAGCC-UGUUUCUACUCUGCUCUUAUCUGGUUCCUCUUAUCUCCUUU---GGAAUUUAAGUUGGUCCAGGUAAUGCGCUUAUGUAUGCUUGCAC-GGCA--UUGAUGACCCAGC-GGAGUUUC-------------------------------UUGGG-------------UUG-GAACUC-CGAGCGGUGUGGAUGA-UUCUGAACGGCC
AAEE01000003.1/883306-883038   U-C-GAC--UGUACUCGA--AC--GGGA--UCAUUUCU-AU-AGUG-AAUC-CGAU----CGUAUUGG-GCUACAGCUC---UUGACAACACCUC------UGUCCGUGACGAUGAGUUAUC-CAUCC-CGCCGG-AAACGGGAAGCGUAGCC-UGUUUCUACUCUGCUCUUAUCUGGUUCCUCUUAUCUCCUUU---GGAGUUUAAGUUGGUCCAGAUAAUGCGCUUAUGUAUGCUUGCAC-GGCA--UUGAUGACCCAGC-GGAGUUUC-------------------------------UUGGG-------------UUG-GAACUC-CGAGCGGUGUGGAUGA-UUCUGAA-----
AAZY02000001.1/850089-849864   U-C-GAC--UGUACUCGA--AC--AGGA--UCAUUUCU-AU-AGUG-AAUC-CGAA----UGUACUGA-GCUACAGAAC---UUGACAACACCUC------UAUCCGUGAAGAUGAGUUAUC-CAUCC-CACCAU--AAUGGGAAGUGUAGCA--CAUCCCUA---------------------GGUCCUCAUCUU--UGAGUC---------------------------UCAGGGAUGCG--GUU--UUGAUGACCUGGU-GGACCUCUUU---------------------------UCUUAG-G-----------GGGA--GGGUC-CUAAUGGUGUGGAUGA-UUCUGAACGG--
ABPA01000112.1/172751-172525   U-C-GAC--UGUACUCGA--AC--AGGA--UCACUUCU-AU-AGUA-GAUC-CGCU----UGUUCACC-UGCACAGCGA---CAGACAACACCUU------AAGUCGUGACGAUGAGUUGUA-CAUCC-AGCCAU--CCCUUGAAGGGAGGCU-CCCUGUGC-----------------------GAUUGGUUUCAU-ACCAAC---------------------------UUCCUCAGGGC-AGCU--UUGAUGAUACCGG-GGCAGCUGG-----------------------------CGAAA--------------GCC-AGUUGCUCCAAUGGCGAGGAUGA-UUCUGAACGACA
AAXT01000002.1/1019139-1019340 U-C-GAC--UGUGCUCGU--AC--AGGA--UCACUUCU-AU-AGUG-A--AUCUGUU-UACCGGUGCC-AUCAGCGACA---GUUGCUGUCAA--------CAGCCGUGAUGAUGAGUUGUA-CGUUC--UGCCG--UUCACGGAAUUAAGUU--AUCAA---------------------------AUUUUUUAAUUU--------------------------------------GCUUG--ACG--UCGAUGAAGUA-----UGUUAA------------------------------CCUAUAU------------GGU--GACA----GCGGUAUUGAACGA-AUCUGAACGGCA
AAGK01000001.1/1919070-1918894 U-C-GAC--UGUGCUCGU--AC--AGGA--UCACUUCU-AU-AGUU-GAUU-CUACU--ACAGAGAUU-ACCAGCGACA---GGUUACGUCAA--------CGCCCGUGAUGAUGAGUUAGU-CGCUC--UGCCG---GUCCGGAAAUGU------------------------------------------UCACAA---------------------------------------CG----------UCGAUGACAC-G--AAAAAG---------------------------------UCU--------------------CUUUU-UCACGGCAUCGAGCCA-UUCUGAGCGGAC
L20948.1/2128-1985             A-A-GAC--CGUACUCUG-AAC--AGAA--UCG-UUUU-AUGAGUACAACCUCUU-----AAUUGAAA----AGAAACCGAG---UUUCAA------------AUCCUGAUGAAGAC-GGUUGCUUUCUCC-GCC----CGGAGA-------------------------------------------------GCGU----------------------------------------------------------UUCG----------A-------------------------------UUGAA-------------C-------------GGCAGGAGAGAGU-UCCAGAAGGAUU
AAHK01001296.1/4547-4689       A-A-GAC--CGUACUCU-------GAACAGAAUCGUUUUAUGAGUACAACCUCUU-------AAUUG-----AAAAAUA---ACCGAGUUUC---------AAAUCCUGAUGAUGAC-GGUUGCUGGCUCC-GCC----CGGA-------------------------------------------------GAGCGU----------------------------------------------------------UUCG------------------------------------------AUGAA-------------C-------------GGCAGGAGCUGGU-UCCAGAAGGAUC
AF277396.1/1-143               A-A-GAC--CGUACUCU-------GAACAGAAUCGUUUUAUGAGUACAACCUCUU-------AAUUG-----AAAAAAA---ACCGAGUUUC---------AAAUCCUGAUGAUGAC-GGUUGCUUUCUCC-GCC----CGGA-------------------------------------------------GAGCGU----------------------------------------------------------UUCG------------------------------------------AUGAA-------------C-------------GGCAGGAGAGAGC-UCCAGAAGGAUC
L32919.1/391-533               A-A-GAC--CGUACUCU-------GAACAGAAUCGUUUUAUGAGUAUAACCUCUU-----------AA-UGGAAAAGAA---ACCGAGUUUC---------AAAUCCUGAUGAAGAC-GGUUGCUUUCUUC-GCC----CGGA-------------------------------------------------GAGCGC----------------------------------------------------------UUCG------------------------------------------AUGAA-------------C-------------GGCAGAAGAAAGU-UCCAGAAGGAUU
AC159431.1/40447-40589         A-A-GAC--CGUACUCU-------GAACAGAAUCGUUUUAUGAGUACAACCUCUU-----------AA-AUGAGAAAUA---ACCAACAACC---------AAAUCCUGAUGAUGAA-GGUUGCUGGCUCC-GCC----CGGA-------------------------------------------------GAGCUG----------------------------------------------------------UUCG------------------------------------------AUGAA-------------C-------------GGCAGGAGCCGGU-UCCAGAAGGAUC
ABFJ01000157.1/25362-25134     A-U-GAC--CACACUCUA---C--AGGA--UCUUUUGUAU--AGU-UG--GUCUCC-----CGUCAUC-GUA---CUCC---UACGUUGACAAACCC--UAAACGCACGAUGAAGAUAGAGAGGUCCA-UCACCU--GAGCGUGAGGCAGGAUCAUCGUC----------------------------CUACUCCUUUGUGG------------------------------GCAGGCGCUG-AUUC-CUCGAUGACCGU-----GCGCUACCGUA--------------------UGGCUCUUCGUGAGC------AACGGU-AGCAC-----UGGUGGUUGGAUCAUUCCGAAUGCG-
X63787.1/1352-1607             A-A-GAC--UGUACUUAU--AC--AGGA--UCU-UUCUUAU-AGUA-AUUA-CUUACUGUAAGUU-UC-UUC---AUUU---GAAGACAACAACU-----CAAUCUAGGAUGAUUAAAAGGA-CACUCUCAUCCG-UAAAUGGGAUACAGAAA--CCAUUAGUAUUUUAUU-----CUCUUCGGAGAAUAGGUAUUUU----------------------------------------UGCG-UUUC--ACGAUGAUCAUC--CAUCGCUGUGUUUGACCGA---------UCGUCUAUACGAAAAGU-----------CACC-AGCGGU-UGGAGGGUGUGAGUGC-UUCUGACUAGAU
AAGF03001549.1/107810-107555   A-A-GAC--UGUACUUAU--AC--AGGA--UCU-UUCUUAU-AGUA-AUUA-CUUACUGUAAGUU-UC-UUC---AUUU---GAAGACAACAACU-----CAAACUAGGAUGAUUAAAAGGA-CACUCUCAUCCG-UAAAUGGGAUACAGAAA-CCAUUAGUAU-------------------UUUACUCUCUUCG--GAGAGUA-------------------------GGUAUUUUUGCG-UUUC--ACGAUGAUCAUC--CACCGCUGUGUUUGA----------------CCGAUCGUCUAU-ACGAG---AAGUCACC-AGUGGU-UGGAGGGUGUGAGUGC-UUCUGACUAGUU
CAAL01000666.1/2246-2006       A-A-GAC--UGUACUCGU--AC--AGGA--UCA-UGUCUAU-AGUA-GUUA-CUUAC--ACUUUGCUU--CA--GCAAA---UGUAGGCAACCAAC----CAAGCUAGAAUGAUUCAGCAUG-CACUCUGAUCUA-UAAUUAGGAAUAUGAAU-CCAUU-----------------------------CUAUUUC---AUG----------------------------------GAAUGCG-AUUC--GCGAUGCCCAUCCAUAUUUGUUGUGCCCU-----------------AAUAUUCUUUAUGGAUAUUGGAGCCUUC-AAAUAU-GUGAAGAUUUGAGUGU-GUCUGACUAGCU
AAXJ01000064.1/51579-51769     U-C-GAC--UGUACUCGA--AC--AGGA--UCACUUAU-GU-AGUG-AAUU-CCU------UUCGUUC-ACAAGAGUAC---UCUUGACAAAACCC----UAAACCGUGAUGAGGAGUUGUA-UACCC-CACCCU--AAUGGAGGUGUAGUCA-GUAC------------------------------A--GUCAUGU-----------------------------------------ACU-CGAC-UUCGAUGAUCCA-----UCCC---------------------------------GUAU-------------------GGGA---GUGGGGUGUGGGUAU-UGCUGAGCGGUU
AAQM02000080.1/173151-172925   U-C-GAC--UGUACUCGA--AC--AGGA--UCACUUCU-AU-AGUA-GAUC-CGCU----UGUUCACC-UGCACAGCGA---CAGACAACACCUU------AAGUCGUGACGAUGAGUUGUA-CAUCC-AGCCAU--CCCUUGAAGGGAGGCU-CCCUGUGCGAU----------------UGGUUUC----------AUACCAA------------------------CUUCCUCAGGGCA--GCU--UUGAUGAUACCGG-GGCAGCUGG-----------------------------C-GAAA-------------GCC-AGUUGCUCCAAUGGCGAGGAUGA-UUCUGAACGACA
AF047723.1/3939-3797           A-A-GAC--CGUACUCUG-AAC--AGAA--UCGUUUUU-UG-AGUACAACCUCUUA----AA-----UG---AGAAAUA---ACC---AACAACC------AAAUCCUGAUGAUGAA-GGUUGCUGGCUCC-GCC----CGGAGA-------------------------------------------------GC-----------------------------------------UG-----------------UUCG------------------------------------------AUGAA-------------C-------------GGCAGGAGCCGGU-UCCAGAAGGAUC
AM910996.2/2755426-2755663     U-C-GAC-GAAUACUUAG--UC--AAGA--UCAUUGCU-AU-AGUAUUUG--UGAU----GUUUUAUU-GUUAUAAAUA---AACAG---AUUAU------CAAAAGUGAUGAUGAAAAGGC-GCGGC----UCUAUAAAUGAAAAUAU-UUC--GAUUUCCUU-------------------CAAGU-----UCUU-UAGAAAU------------------------UGUUGGGAAUCCG-AAA-CAUAGAUGAUCAA-----UUUUGGCCUCCAGGGA----------UUCUUCCCUCG-----U-----------UGGCUGAAAAA-UCAGGAGUUUGUCGCC-AGCUGAACUUUA
AAKM01000010.1/511642-511878   U-C-GAC-GAAUACUUAG--UC--AAGA--UCAUUGCU-AU-AGUAUUUG--UGAU----GUUUUAUU-GUUAUAAAUA---AACAG---AUUAU------CAAAAGUGAUGAUGAAAAGGC-GCGGC----UCU--AUAUAUGAAAAAAUUU-CGAUUCCCUUCG--------------AGUUCUUU----------AGAAUUU-------------------------GUUGGGAAUCCG-AAAC-AUAGAUGAUCAA-----UUUUGGCCUCCAGGGA-----------UUCUUCCCUCGU---U-----------GGCC-GAAAAA-UCAGGAGCUUGUCGCC-AGCUGAACUU-A
ABGU01007180.1/78-319          U---GACG-AAUACUUAG--UC--AAGA--UCAUUGCU-AU-AGUAUU--UGUGAU----GUUUUAUU-GUUAUAAACA---AACAG---AUUUU------CAAAAGUGAUGAUGAA---CA-GACGC-UGCUCU--AAAUUGAAUUGUUUUC--GAAUUUUUC------------------AACUUC----------UUAGGAAA----------------------UUGUAAAACUUCCGAAAA-AUUACAUGAUAUU-----AUUUUGUUGGCAAAUUGAAUUUUUAUUUUUUUUGCCAAUAA----------------U--AAAUA--AAUGAGCUUGCGUC--CGCUGAACUUAC
ABGY01002343.1/3113-3355       U---GACG-AAUACUUAG--UC--AAGA--UCAUUGCU-AU-AGUAUU--UGUGAU----GUUUUAUU-GUUAUAAACA---AACAG---AUUUU------CAAAAGUGAUGAUGAA---CA-GACGC-UGCUCU--AAAUUGAAUUGUUUUC--GAAUUUUUC------------------AACUUC----------UUAGGAAA----------------------UUGUAAAACUUCCGAAAA-AUUACAUGAUAUU-----AUUUUGUUGGCAAAUUGAAUUUUUAUUUUUUUUGCCAAUAA----------------U--AAAUA-AUAUGAGCUUGCGUC--CGCUGAACUUAC
AAYL01000061.1/287048-286822   U-C-GAC--UGUACUCGA--AC--AGGA--UCACUUCU-AU-AGUA-GAUC-CGCU----UGUUCACC-UGCACAGCGA---CAGACAACACCUU------AAGUCGUGACGAUGAGUUGUA-CAUCC-AGCCAU--CCCUUGAAGGGAGGCU-CCCUGUGCGAUUGG----------UUUCAUA----------------CCAA-------------------------CUUCCUCAGGGC-AGCU--UUGAUGAUACCGG-GGCAGCUGG-----------------------------CGAAAG--------------CC-AGUUGCUCCAAUGGCGAGGAUGA-UUCUGAACGACA
ACBR01002269.1/175-425         UGCCGAC----UACUUAGUC--CAAGGA--UCAUUGCU-AU-AGUA-UUU--GUGAU--GUUUUAAUU-GUUAUAAACA--AAACAG---AUUUU------CAAAAGUGAUGAUGAA---CA-GACGC-UGCUCU--AAAUUGAAUUGUUUUC--GAAAUUUUU-------------------CC---A-CCUUCUU-AAGGAAAAU---------------------UGUAAAACUUUCCG-AAAAAUUACAUGAUAUU-----AUUUUGUUGGCAAAUUGAA----UUUUUAUUUUUUU------UGC--------CAAUCAUAAAUA--AAUGAGCUCGCGUC--CGCUGAACUUAC
ABGS01008675.1/273-514         U---GACG-AAUACUUAG--UC--AAGA--UCAUUGCU-AU-AGUAUU--UGUGAU----GUUUUAUU-GUUAUAAACA---AACAG---AUUUU------CAAAAGUGAUGAUGAA---CA-GACGC-UGCUCU--AAAUUGAAUUGUUUUC--GAAUUUUUC-------------------AA------CUUCUU-AGGAAAU------------------------UGUAAAACUUCCG-AAAAAUUACAUGAUAUU-----AUUUUGUUGGCAAAUUGAAUUUUUAUUUUUUUUGCCAAUAA----------------U--AAAUA--AAUGAGCUUGCGUC--CGCUGAACUUAC
FR798998.1/216638-216496       A-A-GAC--CGUACUCU-------GAACAGAAUCGUUUUAUGAGUACAACCUCUU-----------AA-UUGAAAAGAA---ACCGAGUUUC---------ACAUCCUGAUGAUGAC-GGUUGCUUUCUCC-GCC----CGGA-------------------------------------------------GAGCGU----------------------------------------------------------UUCG------------------------------------------AUGAA-------------C-------------GGCAGGAGAGAGU-UCCAGAAGGAUC
V00190.1/62-271                A-U-GAC--CAAACUCU----U--AGGA--UCAUUUCUAG--AGUAUC--GUCUAU-----UAAAAUU-AUU---CAUC---AAUAAUUUUUCCUCUUUCACAGCUAGGAUGAUGAUACACACUCACUAUACGA---AAGCGUGAAACCGUUA--UUAUCAAAU------------------GAUUCAUUUAUUUGUU-----------------------------------------AUU--AAC-AUUGAUGACCGU-----CUAAUU------------------------------CAGGGA-------------UGA-AUUGG------UUGUAUGGUGGGAUUCGUACUGGCU
FR796455.1/229233-229091       A-A-GAC--CGUACUCU-------GAACAGAAUCGUUUUAUGAGUACAACCUCUU-----------AC-UUGAAAAGAA---ACCGAGUUUC---------AAAUCCUGAUGAUGAC-GGUUGCUUUCUCC-GCC----CGGA-------------------------------------------------GAGCGU----------------------------------------------------------UUCG------------------------------------------AUGAA-------------C-------------GGCAGGAGAGAGU-UCCAGAAGGAUC
#=GC SS_cons                   <.<.<-<..<-<<<<---..--..<<<<..____>>>>.--.>>>>.>-->.>>>,....,,<<<<<<.<<<_______...>>>>>>>>>----......--(((((--------------.(((((.((((((..,,<<<<------<<<-..<________...................__..__._______.____.............................._______>--.->>>..------->>>>.....<<<<-<_.............................______.............__>.->>>>,.,,,))))))-)))))-.------))))):
#=GC RF                        u.c.GAc..uGuACUCga..AC..AggA..UCAUUucU.AU.AGUa.aAUc.Cgau....cuuuuuuu.guuAuAaauA...aacaaaaaaccuU......aAaccguGAUGAUGAauuGua.caccC.cgcccc..AAcggggAauguggcu..gauUuuuuU...................au..uc.ucUuuuU.auag..............................aaaguuuccG.agcc..UuGAUGAcccg.....cuucUgu.............................caUaaa.............uuc.agaaga.ugAggggcgUGgguga.UuCUGAacgguc
//
# STOCKHOLM 1.0

#=GF AC   RF01849
#=GF ID   alpha_tmRNA
#=GF PI   10Sa_RNA; SsrA; tmRNA
#=GF DE   Alphaproteobacteria transfer-messenger RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19617710
#=GF SS   Published; PMID:19617710
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.80
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 16.48 -Z 549862.597050 CM SEQDB
#=GF CL   CL00001
#=GF DR   SO; 0000584; tmRNA;
#=GF DR   URL; http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=S14.001;
#=GF DR   GO; 0006401; RNA catabolic process;
#=GF RN   [1]
#=GF RM   8972778
#=GF RT   Phylogenetic analysis of tmRNA secondary structure.
#=GF RA   Williams KP, Bartel DP
#=GF RL   RNA 1996;2:1306-1310.
#=GF RN   [2]
#=GF RM   8990402
#=GF RT   Probing the structure of the Escherichia coli 10Sa RNA (tmRNA).
#=GF RA   Felden B, Himeno H, Muto A, McCutcheon JP, Atkins JF, Gesteland RF
#=GF RL   RNA 1997;3:89-103.
#=GF RN   [3]
#=GF RM   11752287
#=GF RT   The tmRNA Website: invasion by an intron.
#=GF RA   Williams KP
#=GF RL   Nucleic Acids Res 2002;30:179-182.
#=GF RN   [4]
#=GF RM   12140330
#=GF RT   BRUCE: a program for the detection of transfer-messenger RNA genes in
#=GF RT   nucleotide sequences.
#=GF RA   Laslett D, Canback B, Andersson S
#=GF RL   Nucleic Acids Res 2002;30:3449-3453.
#=GF RN   [5]
#=GF RM   12520048
#=GF RT   tmRDB (tmRNA database).
#=GF RA   Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J
#=GF RL   Nucleic Acids Res. 2003;31:446-447.
#=GF RN   [6]
#=GF RM   19617710
#=GF RT   Variations on the tmRNA gene.
#=GF RA   Mao C, Bhardwaj K, Sharkady SM, Fish RI, Driscoll T, Wower J, Zwieb C,
#=GF RA   Sobral BW, Williams KP
#=GF RL   RNA Biol. 2010;6:355-361.
#=GF CC   Bacterial tmRNA, also known as 10Sa RNA or SsrA, is named for its dual
#=GF CC   tRNA and mRNA-like properties. Its role is to liberate the mRNA from a
#=GF CC   stalled ribosome. To accomplish this part of the tmRNA is used as a
#=GF CC   reading frame that ends in a translation stop signal. The broken mRNA is
#=GF CC   replaced in the ribosome by the tmRNA and translation of the tmRNA leads
#=GF CC   to addition of a proteolysis tag to the incomplete protein enabling
#=GF CC   recognition by a protease. Recently a number of permuted tmRNA genes have
#=GF CC   been found encoded in two parts. tmRNAs have been identified in eubacteria
#=GF CC   and some chloroplasts but are absent from archaeal and eukaryote nuclear
#=GF CC   genomes.
#=GF WK   Transfer-messenger_RNA
#=GF SQ   111


CP000301.1/3618224-3618577   GGGCUUCCGC-UACCGAAAAUCGCCCCUAUAUU-UGCAGUGCCAG-----UGCG----CUGGCUAUGACAAUAAA-CCGC-CGUCGCAAUAAACCAUUCGGACCCGGG-GGCAGUA-CCCGGCGCCUCCACCAAAGUCCG------------------------------CGAAAUCCGCGGGC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGGCGGGGGCG-AAACAGGAUCGACGA-GGGC-GUAAAGGGCG-AGCU--UUUGUCCGGAAUGGU-UCC--GCCGUG----------------------------------AUCGG-GCCAUGC---AAUAGUUGCCAACGACAACUAUGCUCCG---------------------------GUUGCUCAGGCAGCGUAA--CGCUGCUUGAAA-GACC-ACA-UGAAAGUCCUGGCGGG-UUAAGCGCCGCCAGGCGGGGUUC-----GGAGGC-GCCUGGCAACAGAA--GCCUCC--ACU
AM040264.1/1369640-1370006   CCCCUUCCAAUCGGUAAAAACCACGCCUAUAUA-CGUCCUGUCGGC----GCAA---GCCGACUAUGGUGAUAAA-CGGA-CGGUGUAAUAAACCCAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCACAGCACAGCUUG------------------------------CCGAUCAGGCUGUGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUGGCGGGGGCG-AAACAGGAUCGACAA-GGGU-GUAAAGAUCG-CUCU--UUUACUCGGCAUGAU-ACC--ACCGUU----------------------------------AUCGG-GUCAACA--GAGUAGUUGCAAAUGACAACAAUGCUCAG------------------------GGUUAUGCUCUCGCUGCCUAA-UGGCGGUGCGGGA-AACCCACUCUA-AAGUCCUUAGGG--UUAGCC-CCUUAAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CU234118.1/5766292-5766657   GCUCUGUGCAUCGGCCCGCGGGCGGCCUAUAUA-GGGGACGCCGG-----CUUG----CCGGCUAUGGAAAUAAA-UCGC-CGUCGAAAUAAACCAUUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAGCCCGU------------------------------CCCGUCGAGUGGCUGAGACGGGU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGGCGGGGGCG-AAAUAGGAUCGACGA-GGGC-GUAAAGGGCG-AGCU--UUUUCCCGGUAUUGU-UCC--GCCGUU----------------------------------AUCGG-GCUACUG--CAAUAGUUGCCAACGACAACUUUGCUCCG---------------------------GUUGCUCAGGCUGCGUAA--CGCAGUUUGAAA-GACC-ACCUUA-AAGUCCUAACGGG-UUAAGCUCCGUUAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP000031.1/2032649-2032301   GCCAUUGCGCUUG-CCCGCAGAGCGACUAUAUU-CAACCUGUUCC-----CUCG----GGAACUAUGGACAUAAA-CGC--GCUCGUAAUAAGCGGUUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAGACACCC--------------------------------UCGUUGGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUCAUGGGGCCG-AAACAGGAUCGACGGA-CGU-CUAAAGGGGUU-AGC-UUUGUCUCGGCGGGGU-ACC--ACCGUU----------------------------------AUCGGU-CCGCAA-AGCAUAAUUGCCAACGACAAUCGUGCUCCG---------------------------GUUGCUCUGGCUGCGUAA---GCAGUCCGAAA-CACCGAAACUU-AAGCCCUUGCGC--CUAGCA-GCGUAAGGCGGGGUUC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--AUU
AAFX01005130.1/1457-1103     AAACUUGUCCUUGAGCCCUCAAAUCCCUAUCUUGGUCCCUGCCGGG----GCAA---CUCGGCUAUGUCGGUAGACUGUC-GCGUGGAAUAAACACUUCGGACCCGGGGGGCAGUACCCCGGCGCCUCCACCACCAGCCG------------------------------CAGGCCGAAGAUUUUCGGCGGUU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUGACGGGGGCG-AAAUAGGAUCGACGA-GUGCAAUAAAGACGC--GGU-UGCCGAUCGGUAUGGAUGCC--ACCGU-----------------------------------GACGGC-UCAAUC--ACACAAGUGCCAACGAUAACGAGGCG------------------------------CUCGCUAUUGCUGCGUAA-CUGACGGCCUGACGGUCUGACGUUACAAAGCUAAAG-------------------CGCGGUU------GGACCCCACCGGGCAACAGAA-GGGGAUUC-C--
CP000301.1/3157375-3157020   UGUGUGGUGACCGCGGACGAUCUGGGCUACAAU-GGUCAGGUC-------GCAA------GACGAUGGCGCUGAAACUCA-ACGCGGACU--GCGGG-CAGACCCGGG-GGCAGUA-CCCGGCGCCUCCACCCGAGCAGCUGACAAUGCGAGAUCUCGU-------UUUUACGAGUUCUCAUUCCGUGCGACGGACUUUGUCGAGCUGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCGGCGGGGGCG-AAACAGGAUCGAUGG-CCGC-GAAGAAGUGU--UGAAUUGUUCCCGGCAUGAU-ACC--GCCGUU----------------------------------AUCGG-GUCAAAA---CCUAAAUGCAAACGAUAACGUUCGCAUG---------------------AACGAAGUGCGCCUCGCGGCGUAA--------------------------------CCGUU-------------------CGGGGUA--------GGUCCACCUAGCAACAGAA-CGGCC----AUG
CP000524.1/955018-955372     CCCCUUCCCCAAAAACUAUUCUUCCUCUAUACU-UAGAAAGCUGG-----UUUU----CUAGCUAUGGUAAUAAA-UGGA-CAAUGAAAUAAGCUCAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAGUAUA-------------------------------AUUGAAGGAAUUAUAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGGCGGGGGCG-AAAUAGGAUCGACAA-GAGU-GUAAAGAUUG-CUCU--UUUACUCGGCAUUGU-ACC--ACCGUU----------------------------------AUCGG-ACUAAAU--GAGUAGUUGCAAAUGACAACUAUGCGGAA---------------------------GCACGUCUCGCCGCUUAA---GCGGUGCGAAU-GUUUCAA--ACUAAGUCUUAAUCU--GUCGCA-AGGUUAAGCGGGGUUC-----GAAGGC-ACCUGGCAACAGAA--GCCUUC--ACU
AANB01000015.1/22110-21760   CCACUUCAAAUUCGCCCUACAAUCCCUUAUGUU-ACAGAUGUUCC-----UUCG----GGAACUAUGGACAUAAA-UGC--GCUCGUAAUAAACGGAUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAAACAUGCU-------------------------------UCAUUUGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAUCAUGGGGUCG-AAACAGGAUCGACGGA-CGU-CUAAAGGGGUU-AGC-UUUGUCUCGGCUGUCU-GCC--ACCGUU----------------------------------AUCGGC-GAAAAC-UGUACAAUUGCAAAUGACAAUCGUGCUCCG---------------------------GUAGCCCUGGCUGCGUAA---GCAGUUCGGAA-AACCGAAACUU-AAGUCCUUUCGC--CUAGCA-GCGACUGGCGGGGUUC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--ACU
AM236080.1/3407250-3407612   GCCCUUCCCUUGGGCUGAGGAAACCACUAUAUC-AGCGUUGCCGGCU---UUCG--GGUCGGCUAUGGCGAUAAA-UGAG-CGGUGUAAUAAACCUAUUGGACCCGGGGG-CGGUA-CCCGGCGCCUCCACCAAAAACCGG------------------------------CGGUCUUAAAGGCCGGCU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGAUGGGGGCGAAA-CAGGAUCGACAA-GGGU-GUAAAGAUCG-UCUU--UUUGCUCGGCAUUGU-ACC--GCCGUU----------------------------------AUCGG-GCUAAAA--UUGUAGUUGCAAACGACAACUAUGCGGAA---------------------------GCUCGUCUCGCUGCUUAA-UCGCGGUGUGACA-CUUCAAUC---AAAGUCCUAGUGG--UUCGCA-CCUCUAGGCGGGGUCC-----GAAGGC-ACCUGGCAACAGAA--GCCUUC--ACC
BX572604.1/108883-109251     GCCCUUUCGUCGGCGGACAUUGCCCCCUAUAUU-GGGAGCGUCGGG----GCAA---CCCGACUAUGGAAAUAAA-UGGC-CGCCGCAAUAAACCAUUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCCAAGCCCGUUCUUC--------------------------------UCGUUUCGAAAAGGCGGGU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGGCGGGGGCG-AAAUAGGAUCGACGA-GGGC-GUAAAGGGCU-CGCU--UUUUCCCGGUAUUGU-UCC--GCCGUU----------------------------------AUCGG-GCUACUG--CAAUAGUUGCCAACGACAACUAUGCUCCG---------------------------GUUGCUCAGGCUGCGUAA--CGCAGUUUGAAA-GACC-ACUUUA-AAGCCCUAACGGG-UUAAGCUCCGUUAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
ABCR01000005.1/360737-360391 CCCUUUGCAAAGC-CGCUCCACACGCCUAUAUU-CACCGUGUCCC-----CUCG----GGGACUAUGGGCAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAUAAACCC--------------------------------UCGUUGGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAACAAGGGGCCG-AAACAGGAUCGACGAA-CGU-GUAAAGGUGU--GGC-UUUGUCCCGGUGAGAU-ACC--ACCGUU----------------------------------AUCGGU-UCAUAA-AGCAUAAUUGCCAACGACAAUCGUGCUCCG---------------------------GUCGCCGUUGCCGCGUAA---GCGGUAACUUG--ACCGAAAUCU-AAGCCCAGGCCU--CUAGCA-AGGUCUGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACU
AAAP01002233.1/734-389       ----------------------------------CGCUUUGCCGGUC---GCAA--GGCCGGCUAUGGCGAUAAA-CGUU-CUUCGCAAUAAACCUAUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAGAACCCAGGACCG--------------------------------AUGGCCGCAGAGUGUCGGCGGUGUUGGGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCGGCGGGGGCG-AAAUAGGAUCGACGA-GGGC-GUAAAGGGGG--AGC-UUUCGCUCGGCAUGGU-UCC--GCCGUU----------------------------------AUCGG-GCCUUUG--CAAUAGUUGCCAACGACAACUUUGCUCCG---------------------------GUGGCUGUCGCCGCGUAA---GCGGUGCCAAA-AACCGACCU--AAAGUCCUA-GCGG-GUAGCACCGCAUAGGCGGGGUUC-----GGAGGU-ACCUGGCAACAGAA--ACCUCC--ACU
CP000319.1/3009373-3009747   UACCUUUCUUCCUGAGCCCUCGCAGACUAUAUU-CAGAGCGCCGG-----UUCG----CCGGCUAUGGAAAUAAA-CGGC-CGUCGUAAUAAACCAUUCGGACCCGGG-GGCAGUA-CCCGGCGCCUCCACCAGAUCCCGACCCGAACCCA------------------------------UGAUACGCAUAAAUUUGGCGGGU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCGGCGGGGGCG-AAACAGGAUCGACGA-GGGC-GUAAAGGGCU-CGCU--UUUUCUCGGUAUGGU-UCC--GCCGUU----------------------------------AUCGG-GCUAUGC---AAUAGUUGCAAACGACAACUAUGCUCCG---------------------------GUUGCUCAGGCUGCGUAA--CGCAGUUUGAAA-GACC-AUUCUG-AAGUCCUGACGGG-UUAAGCUCCGUCAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP000133.1/2914438-2914800   GCCCUUUCCUUGGACGGAGGAAAUCACUAUAUC-AACCCUGCCGGCU---UUCG--GGCCGGCUAUGGCAAUAAA-UGAG-CGGUGUAAUAAACCUAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAAACCGG------------------------------CGGCAUCGAAGGACGGCU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGAUGGGGGCG-AAAUAGGAUCGACAA-GGGU-GUAAAGAUCG-ACUU--UUUGCUCGGCAUUGU-ACC--GCCGUU----------------------------------AUCGG-GCUAAAA--UUGUAGUUGCAAACGACAACUAUGCGGAA---------------------------GCUCGUCUCGCUGCUUAA-UCGCGGUGUGACA-CUUCAAUC---AAAGUCCUAGUGG--UUCGCA-CCUCUAGGCGGGGUCC-----GAAGGC-ACCUGGCAACAGAA--GCCUUC--ACC
M73824.1/24-382              GCCCUUUUCUUGGGCGUCGGAAAGACCUAUAUG-ACGAGUGCCGUC----UUCG---GGCGGCUAUGGCAAUAAA-CGGG-CGAUGCAAUAAACCCAUUGAACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAAACCGG------------------------------CCUGUGCAGACCGGCU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGAUGGGGGCG-AAAUAGGAUCGACAA-GGGC-GUAAAGAUCG-ACUU--UUUGCUCGGCAUUGU-ACC--ACCGUU----------------------------------AUCGG-GCUAAAC--UUAUAGUUGCAAACGACAACUAUGCUGAA---------------------------GCACGUCUCGCUGCCUAA-CGGCGGUGCGACA-CUUCAAAU---CAAGUCCUUCCGG--GUAGCA-CCGUAAGGCGGGGUCC-----GAAGGC-ACCUGGCAACAGAA--GCCUUC--ACC
AAAP01003788.1/2380-2059     G-GCUGGCGCUUCGUUGCGGCCCGCUUUAUAGUGGCGGUUGCCGG-----GCAA----CCGGCUAUGACGCUAAA-CGCC-ACACGGAAUAGACGUUACGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAUUUC------------------------------CCGGCCCACGACGCGGGCCGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCUUGGGGGCG-AAAUAGGAUCGACGU-GCGCAGUAAAGGUCU--GGU-UUGCGUUCGGCAUGAU-ACC--ACCGUU----------------------------------AUCGG-GUCAAUC-CUAACAAGUGCCAACGACAACGUUGAACUU------------------------------GCCGCUGCGGCUUAG-----------------------------UCCGUAAG-------------------CGCGGUCC-----GGGGGGAACCGGGCAACAGAACUCCCCCC--ACU
ABCL01000004.1/58204-58555   CCCUUUGCAAGCC-GCCUCAGAGCGCCUAUGUA-UGGGGUGUUCGC----GCAA---GCGGACUAUGGACAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAAACAUCCU-------------------------------UCAUUUGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUCAUGGGGUCG-AAAUAGGAUCGACGAA-CGU-CUAAAGGGGUUAUGC-UUUGUCCCGGUGAGGU-ACC--ACCGUU----------------------------------AUCGGU-CCGAAA-CGUACAGUUGCAAAUGACAACCGUGCUCCG---------------------------GUGGCCGUUGCUGCGUAA---GCAGUAACCAA--ACCGAAACUU-AAGCCCUUGCGC--UUAGCC-GCGUAAGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACU
CR767821.1/595057-594727     UUUAUUGACUUAUAAGCAGUAUAGUAAUAAAAU-ACAGCUGUGC------UUUU-----GCACUAUGGCAAUAAA-UGC-AUCUUAGAAUAAAUGUAUUGGACCCGAG-GGCAGUG-CUCGGCAUCUCCACUGUUG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUAUGGGGAUG-AAACAGGCUCGACA-UGCAUAGUAAAGGGGA-UAGC-UUUUGCUCGGUGAGAA-AACA-GCCGUU-------------------------------UCAAGUGA--UCAAAA-CUUAUAAGUGCAAACGAUAAUUUCGUUUCUGCUAAUGAUAAUAAUAGCACU---GCUAACUUAGUAGCUGCUUAG---------UUUUAAAAUU----------------AG-------------------CACGGUUUUUU--GGGGUUUUCCGGGUAACAGAA-AAACCCC--UCA
AALY01000002.1/96576-96227   CCCUUUGCUUUGC-CCGCGCCCGCGCCUAUAUUCCUCCCUGUCCC-----CUUG----GGGACUAUGGACAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGUCUCCACCAACCAUCCU-------------------------------UCAUUUGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUCAUGGGGACG-AAAUAGGAUCGACGAA-CGU-CUAAAGGGGUU-AGC-UUUGUCUCGGCGGGGU-GCC--ACCGU-----------------------------------AUCGGC-CCGAAC-AGUACAAUUGCAAAUGACAAUCGUGCUCCG---------------------------GUCGCAAUGGCUGCGUAA---GCAGUCGGAGU-AACCGAAACUU-AAGCCCUUGCCU--CUAGCC-AGGUAAGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACU
AATP01000005.1/142376-142006 CCUCUUUUCACGUCCGGCGAUCCCUCUUAUAUUUGCAGAUGCCGGA---CCAAC---UCCGGCUAUGGCGAUAAA-CGUU-CGAUGCAAUAAACCUUUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAUGUCUCAUGAAGUCCG------------------------------CUUUUCGGAUCCGAUGGGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAUGGCGGGGGCG-AAAUAGGAUCGACGA-GGGC-GUAAAGAUCG-GAUU--UUUGCUCGGAAUGGU-UCC--GCCGUU----------------------------------AUCGG-GCCGUAU--CAAUAGUUGCAAACGACAACUAUGCGGAA---------------------------GCACGUCUCGCCGCGUAA---GCGGUGCGAUA-GCUUCGA--AUUAAGCCCUGGGGG--UUCGCA-CUUCUAGGCGGGGCUC-----GGAGGC-GCCUGGCAACAGAA--GCCUCC--ACU
AALZ01000003.1/153302-153648 CCCCUUGCAAAGC-AAAUCACGCCCCUUAUAUC-UGGGGUGUCC------UUCG-----GGACUAUAGGUAUAAA-CGC--GCAUGUAAUAAGCGGUUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAACCAUCCG-------------------------------UCAUUUGCG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUCAUGGGGUCG-AAAUAGGAUCGACGAA-CGU-CUAAAGAUGU--UGC-UUUAUCUCGGCUGACU-GCC--ACCGUU----------------------------------AUCGGC-GUAAAA-UGUACAAUUGCAAAUGACAAUCGUGCUCCA---------------------------AUGGCGAUGGCCGCGUAA---GCGACCGGAAC-UAUUGAAACUU-AAGUCCUUACGU--UUAGCG-ACCUAAGGCGGGGUUC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--ACU
AAFZ01020819.1/368-10        GNCCUUUAAACAUCGNCCACGAUGCCCUAUAUU-CCUCGUGUCAG-----CUUG----CUGACUAUGGCGAUAAA-CGCG--CUCGUAAUAACCAGACCGGACCCGGG-GGCAGUA-CCCGGCGGCUCCACCAUUACCU-----------------------UCCGCUUGUAUUGGCAAGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAUAUGGGGCCG-AAACAGGAUCGACGGA-UGG-GUAAAGGAGAC-UGC-UUUUGCCCGGG-UGA--GG---CCCGAU----------------------------------ACAGGC-UCAUUC--UUAAAGUUGCCAAUGACAACUUUGCUGAA------------------------GAAGUCCGUCUCGCUGCCUAG---UCAGCGCGUCU-AACUUCGACAUGAACUCCUGGGUG--UUCGCA-CGCUCAGGCGGGGUCC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP000236.1/751387-751720     UAUAUUGACUUAUAUAAAAUAUAGUAUUAUAAUAACAGUUGUGCU-----UUU-----AGCACUAUGGCAAUAAA-GGC-AUCUUAAAAUAGAUGUAUUGGACCCGAG-GGCAGUG-CUCGGCAUCUCCACUUCAGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCAUGGGGAUG-AAACAGGAUCGACA-UGCAUAGUAAAGGGGA-UAGU-UUUUGCUCGGUGAGAA-AACA-GCCGUU--------------------------------UAAAUGC--UCAAAA-UUUAUAAGUGCAAACGAUAAUUUCGUUUUUGCUAAUGAUAAUAAUAGCAGU---GCUAACUUAGUAGCUGCUUAG---------UUUUAUUAUU----------------AG-------------------CGCGGUUUUUUUAAGGGUUUUCCGGGCAACAGAA-AAACCCUU-U--
CP000283.1/3723645-3724002   GCCCUUUCGCCCCAAGCCAUUGCCCCCUAUAUU-GGAAGCGUCGGG----GCAA---CCCGACUAUGGAAAUAAA-UGGC-CGUCGUAAUAAACCAUUCGGACCCGGG-GGCAGUA-CCCGGCGCCUCCACCAAAGCCCG--------------------------------------UGAUUCCGCGGGU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGGCGGGGGCG-AAAUAGGAUCGACGA-GGGC-GUAAAGGGCU-UGCU--UUUUCUCGGUAUUGU-UCC--GCCGUU----------------------------------AUCGG-GCUAAUG--CAAUAGUUGCCAACGACAACUAUGCUCCG---------------------------GUUGCUCAGGCUGCGUAA--CGCGGUUUGAAA-GACCAAGUCUA-AAGUCCUAACGGG-UUAAGCUCCGUUAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
AAFZ01006233.1/268-620       CCCCUUGAAACCCUGCCCCCGUGGCCCUAUAUC-AGAAAUGUCUCG----CUUG---CGGGACUAUGGUGAUAAA-CGC--GCAUGUAAUAAACGGAUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAAAACACCUG------------------------------UCUUUGCAGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGUAUGGGGUCG-AAAUAGGAUCGACGGA-CGU-CUAAAGAUGUU-UGC-UUUUGCUCGGUGAGUU-ACC--ACCGUU----------------------------------AUCGGU-ACAUUU-AAGCUAGUUGCAAAUGACAACAGAGCUCCA---------------------------GUUGCCCUGGCUGCGUAA---GCAGUCCGGAA-UACUGAAAACUU-AGUCCUAGGCU---UUGC--AGCCUAGGCGGGGUCC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACU
AATQ01000080.1/722-371       CCCUUUGAAUCCG-CCCGCAACCUGCCUAUAUU-CAGAUCGUUCC-----CUCG----GGAACUAUGGGCAUAAA-CGC--GCAUGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAAAUCACCCU------------------------------UCGUUGGGGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGCAUGGGGCCG-AAACAGGAUCGACGAA-CGU-GUAAAGAUGU--AGC-UUUGUCCCGGUGAGAU-ACC--ACCGUU----------------------------------AUCGGU-UCACAU-UGCAUAAUUGCCAACGACAAUCGUGCUCCG---------------------------GUCGCUCUGGCUGCGUAA---GCAGUCCGAAA-GAUCGAAAUCU-AAGUCCUUUCGC--CUAGCA-GCGUAAGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACU
CP000449.1/2220782-2221139   CCCCUUCAAUGCACACCCGCGAUCCCCUAUAUU-GAGGGGGUCGG-----CUUG----CCGACUAUGGCGAUAAA-CGCG--CUCGUAAUAACCGGACCGGACCCGGG-GGCAGUA-CCCGGCGGCUCCACCAUAACUGUUCU-------------------------------GCGUUGGCGGAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUGCUUGGGGCCG-AAACAGGAUCGACGGA-CGG-GUAAAGGGGAU-GGC-UUUCGCCGGGG-UGA--GG---CCCCUU----------------------------------ACAGGC-UCAUUU--UCAGAGUUGCCAACGACAACUUUGCUGAA------------------------GAGGUCGCUCUCGCUGCGUAG---UCAGCGCGGGU-AAUCUCGCACUAAACUCCUAUUCC-CUUUAGCCGGAAUAGGCGGGGCCC-----GGAGGC-GCCUGGCAACAGAA--GCCUCC--ACU
AAPJ01000003.1/58640-58270   GGGCUUUUCAUGGCGGAAUCCCCUGCCUAUAUU-GCGCGUGCCGGC---UUCGU---GCCGGCUAUGGCGAUAAA-CGGC-CGAUGAAAUAAACCUUUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCUGAACCCAUCCCCUCG--------------------------------CGGCGAUCCCGCGGCGAUGGGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCAGGCGGGGGCG-AAAUAGGAUCGACGA-GGGU-GUAAAGAUCG-GACU--UUUGCUCGGCAUGGU-UCC--GCCGUU----------------------------------AUCGG-GCCUAUU---UGUAGUUGCAAACGACAACUAUGCGGAA---------------------------GCACGUCUCGCAGCGUAA---GCUGCGCGAUC-GCUUCAA--UUUAAGCCCUGGAGG--UUCGCA-CUUCUAGGCGGGGUCC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP000107.1/489336-489001     UGUAUUGACUUAUA-GAAAUAUAGUAUUAUAAUUACUACCGUGUU-----UUA-----AGCACUAUGGCAAUAAA-GGC-AUCUUAAAAUAGAUGUAUUGGACCCGAG-GGCAGUG-CUCGGCAUCUCCACUUAUUA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUAUGGGGGUG-AAACAGGAUCGACA-UGCAUAGUAAAGGGGA-UAGU-UUUUGCCCGGUGAGAA-AGCA-GCCGUU--------------------------------UAAAUGC--UCAAAA-UUUAUAAGUGCAAACGAUAAUUUCGUUUUUGCAAAUGACAAUAAUAGCAGUGUUGCUGGCUUAGUGGCUGCUUAG---------UUUUGUCAUU----------------AG-------------------CGCGGUUUUUUAGAGGGUUUCCCGGGCAACAGAA-AAAUCCUCU---
AP007255.1/1448584-1448905   AGGCUGGCGCUUCCGAUCGGGCCGCUUUAUAGU-GGGGAUGCCGG-----GCGA----CCGGCUAUGACGCUAAA-CGCC-ACACGGAAUAGACGUUACGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAUUUC------------------------------CCGGCCCAGGACGCGGGCCGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACAUCGGGGGCG-AAACAGGAUCGACGU-GCGCAGUAAAGGUCU--GGU-UUGCGUUCGGCAUGAU-ACC--ACCGUU----------------------------------AUCGG-GUCAAUC-CUAACAAGUGCCAACGACAACGUUGAACUU------------------------------GCCGCUGCGGCUUAA-----------------------------CCCGUAAG-------------------CGCGGUCC-----GGGGGGAACCGGGCAACAGAACUCCCCCC--ACU
CP000248.1/935031-935397     CCCCUUUUCAU-UUGGCGCGCGCUCCCUAUAUGGGGUCGUGCCGGU----UCAG---GCCGGCUAUGGUGAUAAACUGCG-GCGUGCAAUAGGCACAGCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAUCACCAC------------------------------CGGCUGCAAAAGGUCGGGCCUUGUUGUCGCAAGGGU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUUGAUGGGGCCG-AACUAGGAUCGACGU-GUGU-UGAAAAGCGU--UGU-UUUCACCCGGGCUGAG--UAA-CCCGUU----------------------------------CAAGG-CUCAAAA-CUCACAAGUGCCAACGACAACGAAGCA------------------------------CUUGCUCUCGCGGCGUAAUUCUAGGGGCUAACGCCCUGAAGUUACUAAGUUAGAG-------------------CACGGUUC-----GGACCGAACCGGGUAACAGAA-UCGGAAAC-C--
CP000115.1/2573162-2573520   ACCCUUUUUUCCUUGCGCCGUGCGGACUAUAUU-GAAGUCGCCGG-----UUCG----CCGGCUAUGGAAAUAAA-UGGC-CGCCGCAAUAAACCAUUCGGACCCGGG-GGCAGUA-CCCGGCGCCUCCACCAGAGCCCGAACGUGGC--------------------------------UGAUUCGGGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUGGCGGGGGCG-AAACAGGAUCGACGA-GGGC-GUAAAGGGCU-CGCU--UUUUCCCGGUAUGGU-UCC--GCCGUU----------------------------------AUCGG-GCUAUGC---AAUAGUUGCAAACGACAACUAUGCUCCG---------------------------GUUGCUCAGGCUGCGUAA--CGCAGUUUGAAA-GACC-ACUCUG-AAGCCCUGACGGG-UUAAGCUCCGUCAGGCGGGGUCC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
AAMY01000004.1/164286-163929 ACCCUUUUUUCCUCACGUUUUGCAGACUAUAUU-GAAAGCGCCGG-----UUCG----CCGGCUAUGGAAAUAAA-UGGC-CGCCGCAAUAAACCAUUCGGACCCGGG-GGCAGUA-CCCGGCGCCUCCACCAGAGCCCGA------------------------------CUCGGCAGAUUUGGGU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUGGCGGGGGCG-AAACAGGAUCGACGA-GGGC-GUAAAGGGCU-CGCU--UUUUCCCGGUAUGGU-UCC--GCCGUU----------------------------------AUCGG-GCUAUGC---AAUAGUUGCAAACGACAACUAUGCUCCG---------------------------GUUGCUCAGGCUGCGUAA--CGCAGUUUGAAA-GACC-ACUCUG-AAGUCCUGAUGGG-UUAAGCUCCGUCAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
AE005673.1/2312487-2312851   ACCCUUCCAUUGGCUGGGCGAAGUCCCUAUAUU-GGAUCUGUCCGGC---UUCG--GCCGAACUAUGGGGAUAAA-CGCG--CACGUAAUAAGCGGACUGGACCCGGG-UGCGAUU-CCCGGCGGCUCCACCAAAUCUC-----------------------UCCCGCGUUAUCACGGGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUGCAUGGGGCCG--AUCAGCAUCGACAGA-CGU-GUAAAGGUGUC-UGC-UUUCUCUCGGCUUGG--CCC--ACCGUU-----------------------------------UCGGG-CCUUUA---UCUAAAUGCGAACGAUAACUUCGCUGAA------------------------GAGUUCGCCGUCGCUGCGUAA--UGCGGUGCAGGUGAAUUCGCCUCUUAAGUCCUAGGGG--UUCAGA-UCCCUAGGCGGGGCCC-----GGAGGGAGCCUGCCAACAGAA-UCCCUCC--ACC
DQ344920.1/1-293             -----------------------------------GGGGUGUCAGGAG--UUCG-CUUCUGACUAUGGCAAUAAA-CGGA-AUAUGGAAUAGGCGUAGUGGACCCGGG-GGCGGUA-CCCGGCGUCUCCACCAAAUAUCCAG------------------------------CCUUGCAAGGGUUUGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACAACUGGGGACG-AAACAGGCUCGACAC-GCGCAGUAAAGAUAU--UCU-UUUUGCCCGGUAUUGU-ACC--ACCGUU----------------------------------AUCGG-GCUAUUU--UUACAAGUGCCAAUGAUAACUCUGAGGUG---------------------------CUCGCUGUUGCUGCAUAA-----------------------------GCGAUAAG-------------------CGCGGUUC----GGGAGGGCACCGGGCAACAGAA-GCCCUCCC-A--
AAMO01000004.1/358180-358531 ACCGUUGAAAUCCGCCGCCCCCGGUCCUAUAUC-UGGGCUGUCCG-----GCAA----CGGACUAUGGACAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAAAUCACCCG------------------------------UCGUUGGAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGAUCUGGGGCCG-AAACAGGAUCGACGGA-CGU-CUAAAGGGGUU-UGC-UUUGUCCCGGUGAGUU-ACC--ACCGUU----------------------------------AUCGGU-ACGCUA-AGCAUAAUUGCCAACGACAAUCGUGCUCCG---------------------------GUCGCUCUGGCUGCGUAA---GCAGUCCGAAA-GACCGAUCUUU-AAGUCCUAGGCU--CUAGCA-AGUCUGGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--AUU
AAXZ01000005.1/27392-27743   CACCUUGAAACUUUGCCGCAGGUCCCCUAUUUU-AAAUCUGUCC------UUCG-----GGACUAUGGCGAUAAA-CGC--GCUCGCAAUACACGGAUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAACAAACCCU------------------------------UCAUUUGGGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGCAUGGGGUCG-AAAUAGGAUCGACGGA-CGU-CUAAAGGGGUU-AGC-UUUUGCUCGGUGAGAU-ACC--ACCGAU----------------------------------AUCGGU-UCAAUA-UAGCUAGUUGCAAAUGACAACAAAGCACCG---------------------------AUGGCUCUGGCUGCGUAA---GCAGUUCGAAA-UAUCGAAAACUUAAGCCCUACCGC--UUUGCG-GCCGUAGGCGGGGUUU-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--GCU
AM494475.1/749773-750142     GUUAUUGUAAAUAAAAAAUCAUAAUGUUAUAAU-UAAUAAGCU-------AAUA------AGCUAUGGCAAUAAG-UUUU-AUUAAGAAUAGAGGUAGUGGACCCGGG-GGCAGUA-CUCGGCACCUCCACCAAGCUAUG--------------AAGUAGUUGUG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUUACGGGGGUG-ACAAAGUUUCGACAC-ACCUAAUAAAAUAAU--AAA-UUUUGCCCGAUAUGAU-UCC--GUCGU--UUUAAGCAGUAUUUAUAAAAAUUGUUUAAA-----UGGG-UCAAAA--AAAGAAAUGCAAAUGAUAACAUAAAGCAUUCUACAGACGGUAAUUUCCAA---UUGAGUGCAUUAGCAGCUUAA---------------------GGAAAUUGGCGUACUG-------------------AGCGGUAG----UAGGGCUUACCGGGCAACAGAA-AAGCCCUA-AU-
AACY023257757.1/506-804      GUUAUUGAAUCUAUUGUAA-UUCCUUUUAUAUU-AAUAAUGUUGG-----UUUU----CCAACUACGACGAUAAA-CGAA-UUUCGUAAUAACCAUUGCGGACGUGGG-GGCAGUA-CCCACCACCUCCACCAU-UACA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUUAUGGGGGUG-AACUAGAUUCGACG-GAUG-ACUAAAGGCUA--UUC-UUUCGUUCGGGAUUGU-UCC--ACCGU-----------------------------------GACGGG-CUAAUU---UAUAAUUGCUAACGAAAGUUACGCA---------------------------------CUUGCU---GCCUAA---------UUAACUUU------GUUAAUUAAGUAGA-------------------CGGGGUCC-----GGGGC--ACCUGGCAACAGAA--CGCCCC--UUA
AAUW01000011.1/35774-36143   CCUCUUUCAAUUCAAGACCGAAGACCUUAUAUC-AGGGCUGCUGG-----UUCG----CCAGCUAUGGCAAUAAAUGGU--CAGUGAAAUAAACCUAUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCCAAGCCCA-------------------UGGGGCU-AAGCUUCAGAAACUCCAUGGGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGGCGGGGGCG-AAAUAGGAUCGACGAG-GGC-GUAAAGACUG--UGC-UUUUGCUCGGCAUUGU-ACC--ACCGUU----------------------------------AUCGG-GCUUUCU--UAAUAGUUGCAAAUGACAACUAUGCUAUG------------------------GACAACGCUGUCGCAGCGUAA---CGCUGCGCCGG--UAGUCCACU--AAGUCCUUUGAG--GUAGCA-CUCACGGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
AAMS01000009.1/24813-24464   CCUCUUGCAUUGUGACGGAUGAAAGCCUACCUC-UGAAGUGUCC------UUCG-----GGACUAUGGACAUAAA-CGC--GCUCGUAAUACGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGUCUCCACCAAACACUGC-------------------------------UCAUUUGGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCCAUGGGGACG-AAACAGGAUCGACGAA-CGU-CUAAAGGGGUU-UGC-UUUGGCUCGGUGAGUU-ACC--ACCGUU----------------------------------AUCGGU-ACAAAA-AAGCUAGUUGCAAAUGACAACAAAGCACCA---------------------------AUGGCGAUGGCUGCGUAA---GCAGUCGGAAC-UAUUGAAACCUUAAGCCCUAUGGU--UUUGCG-ACCAUAGGCGGGGUCC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--ACC
CP000774.1/2650350-2649991   AGACUUCAAA-UAAGGAAUUUUGCCCCUAUAUUGAUGGGUGCCGGACGG-AUUUCCGACCGGCUAUGGCGAUAAA-CGGA-UUGUGUAAUAAACCAUUCGGACCCGGG-GGCAGUA-CCCGGCGCCUCCACCAAUUUUC------------------------------CCUGUCGCGGCAGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACCUUGGGGGCG-AACCAGGAUCGACGA-GGGU-GUAAAGACAG-UCUU--UUUGCCCGGCAUGGU-UCC--GCCGUC----------------------------------AUCGG-GCCGUUU---UAUAGUUGCCAACGACAACUAUGCUGAG---------------------------GCGCGUCUCGCUGCUUAA--UGCAGUGCGACA-ACCUCGA--UUUAAGUCCUUACCU--UUAGCC-GGGUAAGGCGGGGUUC-----GGGGGC-ACCUGGCAACAGAA--GCCCCC--ACU
AAFX01020036.1/454-805       GCUCUUUUUUCCGGGCGCGUUCUCCCCUAUAUU-GAGAACGCCGGC----GCAA---GCCGGAUAUGGCGAUAAA-CGGC-CGUCGUAAUAAACCUUUCGGACCCGGG-GGCAGUA-CCCGGCGGCUCCACCCAAGCCC------------------------------GGCGCGGACGGGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGGCGGGGCCG-AAACAGGAUCGACGA-GGGC-GUAAAAGGCG-CGCU--UUUGCCCGUUAUGGU-UCC--GUCGUU----------------------------------AUCGG-ACCAAAU---CAUAGUUGCCAACGACAACUAUGCUCCG---------------------------GUUGCUCAGGCCGCGUAG----CGGCUUGAAA-GACCGAUU---NCAGUCCUAGCGGG-UUAAGCUCCGAUAGGCGGGGUCC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
AALV01000002.1/267819-268165 CCCCUUGCAAAGC-AAAUCACGCCCCUUAUAUC-UGGGGUGUCC------UUCG-----GGACUAUGGGUAUAAA-CGC--GCAUGUAAUAAGCGGUUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAAACAUCCG-------------------------------UCAUUUGCG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUCAUGGGGUCG-AAAUAGGAUCGACGAA-CGU-CUAAAGAUGU--UGC-UUUAUCUCGGCUGACU-GCC--ACCGUU----------------------------------AUCGGC-GUAAAA-UGUACAAUUGCAAAUGACAAUCGUGCUCCA---------------------------AUGGCGAUGGCCGCGUAA---GCGACCGGAAC-UAUUGAAACUU-AAGUCCUUACGU--UUAGCG-ACCUAAGGCGGGGUUC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--ACU
CP000699.1/3791524-3791866   GGCCUUCAAAUCCGCUGCGCACCCUCCUAUAUC-GGGGGUGCCGGG----UUCG---CCCGGCUAUGGCGAUAAAUGAUG-UCGUGGAAUAGAUGCAGCGGACCCGGG-GGCAGUA-CCCGGCGGCUCCACCACAAAUCCCGG------------------------------AUUUCCGGGGCU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGUGACGGGGCCG-AACCAGGAUCGACGU-GUAU-UCAAAGACGA--UGU-UUUUGCCCGGCCUGAA--UGC-GCCGUU---------------------------------AAACCG-UUCGAAC--CUACAAGUGCCAACGAUAACGAGGCG------------------------------CUCGCGAUUGCCGCGUAA--CUGAGUCCUAACGGAC-GACGUUACAAGGCUUAAG-------------------CGCGGUUC-----GGUCCGCACCGGGCAACAGAA-GCGGAAUC-C--
CP000661.1/734144-733796     CCACUUGCGUUUUUGCACCGGCGCGGCCAUAUU-AUCUUCGUCCC-----GUAA----GGGACUAUGGAUGUAGA-CGG--GCUUGUGA-AGCUGGAUCGGACGGGGG-UGCGAUU-CCCCCCACCUCCACCAUUUUACCC-------------------------------UUGGAAACAAGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUUGCGGGGGUG-AUAUAGGGUCGACGGA-CGG-UGGAGUGAGUA-CCU--GCAUCUCGGUUGGAC-GC---GCCGUU----------------------------------AUCUGC-UCA-AU-CGCAUAGUUGCCAACGACAACCGUGCUCCG---------------------------GUGGCUCUGGCUGCGUAA---GCAGCUCGAAC--AUCGAAACUU-AAGUCCUUGCGC--UUAGCC-GCGUAAGGCGGGGUUC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--ACU
CP000250.1/2312257-2311889   GCCCUUCCGCCCCAAGCCAUUGCCCCCUAUAUU-GGGAAGGUCGGG----GCAA---CCCGACUAUGGAAAUAAA-UGGC-CGUCGUAAUAAACCAUUCGGACCCGGG-GGCAGUA-CCCGGCGCCUCCACCCAAGCCCGC------------------------------CUGUUUCGAGUUGGAAGCGCGGGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGGCGGGGGCG-AAACAGGAUCGACGA-GGGC-GUAAAGGGCU-UGCU--UUUUCCCGGUAUUGU-UCC--GCCGUU----------------------------------AUCGG-GCUAUGC---AAUAGUUGCCAACGACAACUAUGCUCCG---------------------------GUUGCUCAGGCUGCGUAA--CGCAGUUUGAAA-GACCAAGUCUG-AAGUCCUGACGGG-UUAAGCUCCGUUUGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP000230.1/2560658-2560992   GGGCUUUGCAUCGGCGACGAUCCCCCCUAUAUU-GGGGGUGCCGG----CUUGU----CCGGCUAUGACGCUAAA-CCCU-UUAUGGAAUAAGCGUUGUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAUUCGCCCAA------------------------------GUCUCCGGCCUCAGCGCCGGAGACCGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUUCCUGGGGGCG-AAAUAGGAUCGACAC-GCGUGGUAAAGAUAA--AGG-UUGUGUUCGGCAUGGUAUCC--ACCGUU----------------------------------AUCGG-GCCAACU-CUGACAAGUGCCAACGACAACGUUGAACUU------------------------------GCCGCUGCGGCCUAA--------------------------ACACCCGUAAG-------------------CGCGGUUC----GGGGGGGCACCGGGCAACAGAA-GCCCCCCC-A--
AAOT01000013.1/6290-5940     GGGCUUGAGCGGCGCGGGGCGCGCGCCUAUAUU-CCGGGUGUCUC-----GCAG----GAGACUAUGGACAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAUACACCU--------------------------------UCGUUGGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAACAUGGGGCCG-AAACAGGAUCGACGAA-CGU-CUAAAGGGGUU-AGC-UUUGUCUCGGUGAGGU-ACC--ACCGUG----------------------------------AUCGGU-CCGUAA-AGCAUAAUUGCCAACGACAAUCGUGCUCCG---------------------------GUCGCCGUUGCUGCUUAA---GCAGUAACGAA-GAUCGAAAUCUUAAGCCCUUGCGC--CUAGCA-GCGUAAGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACU
AAMV01000001.1/228171-228523 CCCUUUGCAAGCG-GGAUCAGAGCGCCUAUGUA-UAGGGUGUUCGC----GCAA---GCGGACUAUGGACAUAAA-CGC--GCUCGUAAUACGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAAACAUCCU-------------------------------UCAUUUUGGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUCAUGGGGUCG-AAACAGGAUCGACGAA-CGU-CUAAAGGGGUUAUGC-UUUGUCUCGGUGAGGU-ACC--ACCGUU----------------------------------AUCGGU-CCGAAA-CGUACAGUUGCAAAUGACAACCGUGCUCCG---------------------------GUGGCCGUUGCUGCGUAA---GCAGUAACCAA--ACCGAAACUU-AAGCCCUUGCGC--UUAGCC-GCGUAAGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACU
BX897700.1/1020822-1021174   CCCCUUUUCCAAAGACUGUUCUUCAUCUAUAUU-UAGAGAGCUGG-----CUUA----CCAGCUAUGGUAAUAAA-UGGA-CAAUGAAAUAAACUCAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAAUAUAA------------------------------CAAAAAUUAUAU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGGUGGGGGCG-AAAUAGGAUCGACAA-GGGU-GUAAAGAUUG-CUCU--UUUACUCGGCAUAGU-ACC--ACCGUC----------------------------------AUCGG-ACUAAAU--GAGUAGUUGCAAAUGACAACUAUGCGGAA---------------------------GCACGUCUCGCUGCUUAA--UGUAGUGUGAAU-GUUUCAA--ACUAAGCCUUAAAUC--GUCGCA-GAUUUAAGCGGGGUUC-----GAAGGC-ACCUGGCAACAGAA--GCCUUC--ACU
BX897699.1/1215921-1216276   CCCCUUUUCCAAAAGCUGUUCUUCAUCUAUACU-UAAAGAGCUGG-----CUUG----CCAGCUAUGGUAAUAAA-UGGA-CAAUGAAAUAAGCUUAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAAUAUAAUUUG-------------------------------UUUUUUUAUAU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUAGUGGGGGCG-AAACAGGAUCGACAA-AAGU-GUAAAGAUUG-CUCU--UUUACUCGGUAUAGU-ACC--ACCGUU----------------------------------AUCGG-ACUAAAU--GAGUAGUUGCAAAUGACAACUAUGCGGAA---------------------------GCACGUCUCGCUGCCUGA--GGUGGUGUGAAU-GCUUCAA--ACUAAGUCUUAAACC--GUCGCA-GGUUUAAGCGGGGUUC-----GAAGGC-ACCUGGCAACAGAA--GCCUUC--ACU
CP000577.1/824978-824624     CCGCUUGCGGAGGCCGCCCCUCCCGCCUAUAUU-CCGCCUGUCCGGG---GCAA--CCCGGACUAUGGACAUAAA-CGC--GCUCGUCAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAACAGUCCC-------------------------------UCGUUGGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCGGAGGGGGCCG-AAACAGGAUCGACGAA-CGU-CUAAAGGGGUU-GGC-UUUGUCCCGGUGAGGU-ACC--ACCGUU----------------------------------AUCGGU-CCGAAA-AGUACAGUUGCCAACGACAACCGUGCUCCG---------------------------GUGGCUCUGGCUGCGUAA---GCAGUUCGAGU-UAUCGAAACUU-AAGCCCUUGCGC--UUAGCC-GCGUAAGGCGGGGUUC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--ACU
AE017321.1/841744-841409     UAUCUUGACAUUUAUUAAAUAUUACUAUACAAU-AACUAUGUGUAU----UUU----AUACACUAUGGCAAUAAA-AUUA-CCUUGUAAUAGGUGUAUUGGACCCGAG-GGCAGUA-CUCGGCGCCUCCACCAUGUUUUU-AAU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUACAUGGGGGCG-AAUAAGAAUCGACA-UGCAUAGUAAAGAUGG--UAA-CUUUGCUCGGUUAGAU-ACC--ACCGCU----------------------------------AAGAGU-UCAUAG---UUUAAACGCAAACGAUAAUUUUGCUGCUGAAGGUGAU---------------GUUGCGGUAGCU---GCUUAA-------UUUAAGCACUAUA-ACUUCAUUACUAUAAG-------------------CACGGCUU-----AGGGAACGCCGGGUAACAGAA-GUUCCCC--CCA
CP000738.1/2073040-2073401   GCCCUUUUCUUAGGCCCCGGAAAGACCUAUAUG-ACGUGUGCCGUC----UUCG---GGCGGCUAUGGCAAUAAA-CGGG-CGAUGCAAUAAACCCAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAAACCGG------------------------------UCGGAAUUCGAGACCGGCU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGAUGGGGGCG-AAAUAGGAUCGACAA-GGGC-GUAAAGAUCG-ACUU--UUUGCUCGGCAUUGU-ACC--ACCGUU----------------------------------AUCGG-GCUAAAC--UUAUAGUUGCAAACGACAACUAUGCUGAA---------------------------GCACGUCUCGCUGCCUAA-CGGCGGUGCGACA-CUUCAAAU---CAAGUCCUUCCGG--GUAGCA-CCGUAAGGCGGGGUCC-----GAAGGC-ACCUGGCAACAGAA--GCCUUC--ACC
AACY020211829.1/1070-776     UCUCUUUAAAAAGUCUCAAUAUCCAACUAUAUU-CAGAUUGCUGGG---GAUAU---CCCAGCUAUAGGGAUAAA-CGGC-UUGCGUAAUACCCAUUACGGACCCGGG-GGCGGUA-CCCGGCACCUCCACCAUAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUAGGGGGUG-AUAUAGGAUCGACG-AAUGC-UUAAAGGUAA-GUUU--UUCUCUCGGUAUUGU-ACC--ACCGUU----------------------------------AUCGG-GCUAUUU---UAUAAAUGCUAACGAUGAAUUAGCG------------------------------------CUCGCUGCUUAA------------------------UCUAAUU------------------AGGUAAGCGCGGUUC----GGGAGAC-ACCGGGCAACAGAA--GUCUCCC-ACU
CP000362.1/2178326-2177978   CCCCUUGAGGUUCGGGCGCGAUUGGCCUAUAUU-CAUAGCGUCC------UUCG-----GGACUAUGAACAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAAACAUCCU-------------------------------UCAUUUGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAUCAUGGGGUCG-AAACAGGAUCGACGAA-CGU-CUAAAGGGGUU-UGC-UUUGUUUCGGCUGUCU-GCC--ACCGUU----------------------------------AUCGGC-GAAACU-UGUACAAUUGCAAAUGACAAUCGUGCUCCA---------------------------GUUGCGAUGGCCGCGUAA---GCGGUUUCAGC-GACUGAAACUU-AACUCCUUGGGU--UUAGCG-ACCUAAGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACU
CP000356.1/1017818-1018174   GCCCUUUCCAAGCGCCGGCGGGUUUCCUAUAUG-GGGGGUGUCGGC----UUCG---GCCGACUAUGAGGAUAAAUGGUG-UCGUGGAAUAGACACAGCGGACCCGGG-GGCAGUA-CCCGGCGGCUCCACCACAAACCCGCGU------------------------------UUCUUCGAAGGACGCGCGGGUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUGACGGGGCCG-AACCAGGAUCGACGU-GUGU-UCAAAGACGA--UGC-UUUCUUCCGGGCUGAG--UAA-CCCGUU----------------------------------AAAGG-CUCAAAA-CCAAUAAGUGCUAACGAUAACGAAGCA------------------------------CUCGCUCUUGCUGCCUGACCGAUAAGCCUCACGGCCUAAGGUUAGACAAAUAGAA-------------------CGCGGUUC-----GGACCGAACCGGGCAACAGAA-UCGGAAAC-C--
CP000264.1/2391964-2392320   GACCUUGAAUCCAACGCCCGCCCCUCGUAUAUC-UAGCGUGUUCC-----UUCG----GGAGCUAUGGACAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAACACACCCU------------------------------UCAUUUGGGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGCUUGGGGUCG-AAAUAGGAUCGACGAA-CGU-CUAAAGGGGUU-AGC-UUUGUCCCGGUGAGUU-ACC--ACCGUU----------------------------------AUCGGU-ACACAU-CGUACAGUUGCAAAUGACAACCGUGCUCCG------------------------GCAAUGGCUCUCGCAGCGUAA---GCUGUCCUGAG-UCGCCGACUUU-AAGCCCUAGCGC--CUAGCC-GCGUUAGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACU
AAYC01000002.1/78925-78573   GCCCUUGCAAAUCCUUCCGUCUCAUCCUAUUUC-AAGGAUGUUCC-----CUCG----GGAACUAUGGACAUAAA-UGC--GCUCGUAAUAAACGGAUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAACCAUGCU-------------------------------UCAUUUGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAUCAAGGGGUCG-AAAUAGGAUCGACGGA-CGU-CUAAAGGGGUU-AGC-UUUGUCUCGGCUGUCU-GCC--ACCGUU----------------------------------AUCGGC-GAAAAC-UGUACAAUUGCAAAUGACAAUCGUGCUCCG------------------------GCAAUGGCUCUGGCUGCGUAA---GCAGUUCGGGU-CGCCGAAACU--AAGUCCUCUCGC--CUAGCC-GCGUGAGGCGGGGUUC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--ACU
ABEF01049701.1/982-1274      UAAAUUGAAUCUUUAAAAU-AAAGUUUUAUAUU-AUUGAUGUUGG-----UUUU----CCAACUACGACGAUAAA-CGAA-UUUCGUAAUAAACAUUGCGGACGUGGG-GGCAGUA-CCCACCACCUCCACCAUUGACA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUUAUGGGGGUG-AACCAGAAUCGACG-AGUG-UCUAAAGGCUA--UUC-UUUCGUUCGGGAUUGU-UCC--GUCGUU----------------------------------AUCGGG-CUAAAU---UAUAAUUGCAAAUGAUAAAUUUGCU---------------------------------CUCGCU---GCUUAA---------UUAAU--------------UUAAGAAAG-------------------CGCGGUCU-----GGGGC--ACCGGGCAACAGAA--CGCCCC--UAG
AE017196.1/117378-117039     UAUCUUGACAUUUAUUUAAUGUUGCUAUAUAAU-AGCUAUGUACAU----UUU----GUGUACUAUAGCAAUAAA-AUUA-CCUUGUAAUAGGUGUAUUGGACCCGAG-GGCAGUA-CUCGGCGUCUCCACCAUGUUUUUUAAU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUAUGUGGGGACG-AAUAAGGAUCGACA-UGCAUAGUAAAGAUGG--UAG-CUUUGCUCGGUUAGAC-ACC--ACCGCU----------------------------------AAGAGU-UCAUAA---UUUAAAUGCAAACGAUAAUUUUGCUGCUGAAGACAAUGUC------------GACGCAAUAGCU---GCUUAA-------UUUAAGCACUAUA-ACUUCAUUGCUAUAAG-------------------CACGGUUC-----AGGGAACGCCGGGUAACAGAA-GUUCCCC--AAA
AAPV01000001.1/883753-883453 UUUAUUGAAUCUCUCUCAA-AUGCUUUUAUAGU-AAUAGUGUUGG-----CUUG----CCAACUACGACGAUAAA-CGAA-UUUCGUAAUAACCAUUACGGACGUGGG-GGCAGUA-CCCACCACCUCCACCAUUUACA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUUACGGGGGUG-AAAUAGGAUCGACG-GGUG-ACUAAAGGCUA--UUC-UUUCGUUCGGGAUUGU-UCC--ACCGU-----------------------------------AACGGG-CUAAAC---UUUAAAUGCUGACGAAAGUUACGCA---------------------------------CUUGCU---GCAUAA---------UUAACUUAG-----GUUAAUUAUAGAAG-------------------CACGGUCU-----GGGGC--ACCGGGUAACAGAA--CGCCCC--UAC
M73823.1/763-1130            CCCCUGUCUUUCUAAACCUUUGCCCCCUAUAUU-GGGGGUGCCGG-----UUCG----CCGGCUAUGGAAAUAAA-CGGU-CGUCGUAAUAAACCAUUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAGCCCA------------------------------CCAGCGGGCUAGCCCUAGAAGCGGGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGGCGGGGGCG-AAAUAGGAUCGACGA-GGGC-GUAAAGGGCG-UGCU--UUUUCCCGGUAUUGU-UCC--GCCGUU----------------------------------AUCGG-GCUACUG--CAAUAGUUGCCAACGACAACUUUGCUCCG---------------------------GUUGCUCAGGCUGCGUAA--CGCAGUUUGAAA-GACC-AUCUUA-AAGUCCUAACGGG-UUAAGCUCCGUUAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP000758.1/1882155-1881788   CCUCUUCCAAUCAUGAUCAACCGCGCCUAUAUA-CGGCGUGUCGGC----GCAA---GCUGACUAUGGUGAUAAA-UGGA-CGGUGUAAUAAACCCAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAGAAUACAAAUCAG-----------------------------CCUAUCGGUUUGUAU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUGGCGGGGGCG-AAACAGGAUCGACAA-GGGU-GUAAAGAUCG-CUCU--UUUACUCGGCAUGAU-ACC--ACCGUU----------------------------------AUCGG-GUCAAUU--GAGUAGUUGCAAAUGACAACAAAGCUCAG------------------------GGUUAUGCUCUCGCUGCCUAA-UGGCGGUGCGGGA-AACCCACUCUA-AAGUCCUUAGGG--UUAGCC-CCUUAAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
AJ235273.1/40992-40464       UACCUUUACAUUUUAAUUAAAUUCAGGCAUAAUAUUUGGUGCUA------AUA------UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAUACUCGAUGAACUUCAAAAAUUUGCUGCGUCGUCUUAUUAAGUGCUGUGGUAUUUAUGUGUUCAGUAACUGCUGUUGCUCUUUGUAUUGUUGACUCAUUGUUCUUUUUGUAGUUGAUUUUCGUAUAUUCUGUAUGAUUUUAAUACAGCUUAAAUAUAUGAGUAUCAUAAACAAUUGAUAAAAUGAAAGAGUAAUAUUGAAAAAAGAUAAGUAGUAUU------------------------------------------------------------------UUUUUUGGGGGCG-AAAUAGGAUCGACGU-GCCUAAUAAAAAAGU--UGC-UUUUACUCGGUAUGAU-UCC--ACCG----GU-GGU------UUUU----GCC-AU-------AUGGA-UCAAAA-CAAAGAAACGCAAACGAUAAUCGUUAU---GUAGGUGUU---------------CCAGCUUUAGCUGCAGCUUAA--------------------------------GCCUA-------------------CGCGGCUG-----GGGAUUUGCCGGGCAACAGAA-AAAUCCC--AU-
CP000084.1/10219-10519       UUUAUUGAAUCUCUCUCAA-AUGCUUUUAUAGU-AAUAGUGUUGG-----CUUG----CCAACUACGACGAUAAA-CGAA-UUUCGUAAUAACCAUUACGGACGUGGG-GGCAGUA-CCCACCACCUCCACCAUUUACA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUUACGGGGGUG-AAAUAGGAUCGACG-GGUG-ACUAAAGGCUA--UUC-UUUCGUUCGGGAUUGU-UCC--ACCGU-----------------------------------AACGGG-CUAAAC---UUUAAAUGCUGACGAAAGUUACGCA---------------------------------CUUGCU---GCAUAA---------UUAACUUAG-----GUUAAUUUUAGAAG-------------------CACGGUCU-----GGGGC--ACCGGGUAACAGAA--CGCCCC--UAC
CP000377.1/1546153-1546528   CCCUUUAACUCCC-CUCCAAACCACCCUAUAUU-UGGAGUGUUCC-----UUCG----GGAACUAUGGACAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAAAUCACUUCCGGCUUUCUCCU------------------UCGUUUGGGGAGUUUAUUCGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCGGGGGGCCG-AAAUAGGAUCGACGGA-CGU-CUAAAGGGGUU-AGC-UUUGUCUCGGCUGUCU-GCC--ACCGUU----------------------------------ACCGGC-GAAAAC-AGUACAAUUGCAAACGACAAUCGUGCUCCG---------------------------GUUGCUCUGGCUGCGUAA---GCAGUUCGAGUCGAACCGACUUU-AAGUCCUAGCGC--CUAGCC-GCGUUAGGCGGGGUUC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--ACU
AAFX01039956.1/551-202       AUUCUUGAGGUUGGGAGAUGAAAUCCCUAUAUC-CGAACUGCCGGG----GCAA---CCCGGCUAUGUCGGUAGAAUGUC-GGGUGGAAUAAGCAUUUCGGACCCGGGGGGCAGUACCCCGGCGCCUCCACCACCAGCAGCAACGG------------------------------AUGUGCCGAGCUGUU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCUGAUGGGGGCG-AAAUAGGAUCGACGA-GUGCAGUAAAGGCCU--GGU-UGCCGAUCGGUAUGAG-ACC--ACCGU-----------------------------------GACGG-CUCAUCA---CACAAGUGCCAACGAUAACGAGGCG------------------------------CUCGCUCUUGCUGCGUAA-CUGAGGUCCUAACGGAUUGAAGUUACAAGGCUAAAG-------------------CGCGGUU------GGACCCCACCGGGCAACAGAA-GGGGAUUC-C--
AAFZ01019330.1/635-282       GCCCUUGCGGAAGGCACCUGAUUACACCAUAUU-AGCCGUGCCGG-----CUUG----CCGGCUACGGUGCUAAA-CGCC-AAGCGGAAUAAGCACAGCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCACAAGCU------------------------------GCGUUUGAGAUUUUUAACGGAAUUUCGGCGCGCGCCACGCGGUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUGAUGGGGGCG-AAAUAGGAUCGACGC-GUGUAAUAAAGGCUU--GGU-UUGUGCUCGGCAUGGU-ACC--GCCGAU----------------------------------AUCGG-GCCAUUU--UGAUAAGUGCCAAUGAUAACACAGAAGCA---------------------------CUUGCUGUCGCGGCCUAA---------------------CACGCCAUAACGACAA-------------------CGGGGUUC-----GGGCGGCACCUGGCAACAGAA-GCCGCCC--ACU
ABCG01000005.1/83617-83273   ACACUUCACA-UUAAGCGAUUGGUCGCUAUAUG-GGAGCUGCCGGU----UUCG---ACCGGCUAUGGCGAUAAACUGCG-CUGUGCAAUAGGUACAACGGACCCGGG-GGCAGUA-CCCGGCGGCUCCACCAUAACCCGCG------------------------------GAUAUCACGUGGUU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGACGGGGCCG-AACUAGGAUCGACGU-GUGC-UGAAAGACAG--UGU-UUUCGUCCGGGCUGAG--UAA-CCCGUAA---------------------------------AACUG-UUCACAA-CACACAAGUGCCAACGAUAACGAAGCA------------------------------CUCGCUCUCGCAGCGUAAUCUGACGGGCUAACGCCCUGAUCUUACAAAGCUAAAG-------------------CGCGGUU------GGACCC-ACCGGGCAACAGAA-GCGGAUUC-C--
CP000781.1/1621594-1621958   CCCCUUUCAUCGCCGGCGGGCGACGCCUAUAUU-CGUUCUGCCGAC----GCAA---GUCGGAUACGGCGAUAAA-UGGG-UGUCGGAAUAAGCCUUUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAGCCCAACUUC------------------------------CCCUUCAGGGAGGCGGGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCGGCGGGGGCG-AAAUAGGAUCGACGA-GGGU-GUAAAGGGCA--UAC-UUUCGCUCGGCAUGGU-UCC--GCCGUC----------------------------------AUCGG-GCCGAAC--UGAUAGUUGCGAAUGACAACUAUGCUCCG---------------------------GUUGCUCAGGCCGCGUGA---GCGGUUUGACG--AUCGAAAUC-AAAGUCCUA-CCGG-GUAGCACUGGCUAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP000708.1/1361096-1361462   CCCCUUCCAAUCGGUAAAAACCACGCCUAUAUA-CGUCCUGUCGGC----GCAA---GCCGACUAUGGUGAUAAA-CGGA-CGGUGUAAUAAACCCAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCACAGCACAGCUUG------------------------------CCGAUCAGGCUGUGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUGGCGGGGGCG-AAACAGGAUCGACAA-GGGU-GUAAAGAUCG-CUCU--UUUACUCGGCAUGAU-ACC--ACCGUU----------------------------------AUCGG-GUCAACA--GAGUAGUUGCAAAUGACAACAAUGCUCAG------------------------GGUUAUGCUCUCGCUGCCUAA-UGGCGGUGCGGGA-AACCCACUCUA-AAGUCCUUAGGG--UUAGCC-CCUUUAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
AAYA01000018.1/3752-3404     CCCUUUGCAAGCG-GCCCGACGGCGCCUAUAUC-AGAGAUGUUCC-----UCAG----GGAACUAUGGGCAUAAA-CGC--GCAUGUAAUAAACGGAUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAAACAUCCC-------------------------------UUCGUUGGGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAAAUGGGGCCG-AAACAGGAUCGACGAA-CGC-GUAAAGAUGU--AGC-UUUGUCCCGGUGAGAU-ACC--ACCGUU----------------------------------AUCGGU-UCACAA-AGUACAAUUGCCAACGACAAUCGUGCUCCG---------------------------GUUGCAGUUGCUGCGUAA---GCAGUGACGAG--ACCGAAAUCU-AAGUCCUUGCGC--CUAGCA-GCGUAAGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACU
BA000012.4/1222284-1222644   GGCCUUUCAUUUCCACGCAACGCCCCCUAUAUU-CGUUUUGUCGG----CUUGA----CCGACUAUGGCGAUAAA-UGGG-CGAUGAAAUAAGCCGUUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAAGCCG------------------------------CUGUUGACGACAGAGCGGUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGCUGGGGGCG-AAAUAGGAUCGACGA-AGGU-GUAAAGAUCG-UACU--UUUGCCCGGCAUUGU-ACC--ACCGUC----------------------------------AUCGG-GCUAAAC--UUAUAGUUGCCAACGACAACUAUGCGGAA---------------------------GCACGUCUCGCUGCUUAA--UGCAGUGCGAUA-GCUUCAA--AUCAAGCCCUAGGGG--UUCGCA-CUUCUAGGCGGGGUUC-----GGAGGU-ACCUGGCAACAGAA--ACCUCC--ACU
AAMT01000004.1/95263-94914   CCCCUUCUCAAACCCCAAGGUCCGGCCUAUAUC-UGUCCUGUCCC-----UUUG----GGGACUAUGGGCAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAAACACCCG-------------------------------UCGUUGGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGACAUGGGGCCG-AAACAGGAUCGACGAA-CGU-GUAAAGGUGU--UGC-UUUGUCCCGGUGAGAU-ACC--ACCGUU----------------------------------AUCGGU-UCACAA-UGCAUAAUUGCCAACGACAAUCGUGCUCCG---------------------------AUCGCUCUGGCUGCCUAA---GCAGUCCGAAA-GAUCGAAAUUU-AAGCCCUUGCGC--CUAGCA-GCGUAAGGCGGGGUUC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--ACU
CP000490.1/1718173-1718526   UCCCUUGCGUGCCGAAACGGCGGCGCCUAUAUU-CGUGGGGUUCGGG---UUCG--CCCGGACUAUGGACAUAAA-CGC--GCAGGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAGAAUCCC--------------------------------UCGUUGGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCACAUGGGGCCG-AAACAGGAUCGACGAA-CGU-CUAAAGCUGUU-UGC-UUUGUCUCGGUGAGCU-ACC--ACCGUC----------------------------------AUCGGU-GCAAAA-UGUACAGUUGCCAACGACAACCGUGCUCCG---------------------------GUGGCUCUGGCUGCGUAA---GCAGCUCGGGU-AACCGAAACUU-AAGCCCUUCCGC--CUAGCA-GCGUAAGGCGGGGCCC-----GCAGGA-GCCUGGCAACAGAA--UCCUGC--ACC
CP000087.1/411033-411553     AACCUUUACAAAUUAAUCAAAUUAAGCGAUAAUAGUAAGUGCUA------AUA------UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAUAAUGU--------------GCUAUGUCAUUCCUGAAUGGAACAAAAGCCGUCUUCGGUGUCAUCCCGUGGCUUGCUAACUAGAUCCAGCAUAAAGCGAGAUAUAUCGAGCUUUUAAUUUUAAAAAGUUACUUUGUUUGUAAUUUUUACUGGAUCCCGUGGACAAGCCACGGGAUGACAAGCUCUAUAAGGCAAUGACAUAACAAUAAAAAUAGUGCAA----------------------------------------------------------------UGACAGGGGGGCG-AAAUAGGAUCGACGU-GCCUAAUAAAAAAAU--UGC-UUUUACUCGGGAUGAU-UCC--GCCG----CA-GGC------UUUU----GCC-UU-------ACGGG-UCAAAA-CAAAGAAACGCAAACGAUAACUAUCGUUCCGCAGGUACU---------------CCAGCUUUAGCUGUAGCAUAA--------------------------------ACCUG-------------------CACGGCUU----GGGGGUUUGCCGGGUAACAGAA-AAACCCUC-A--
CP000030.1/459834-459503     GUGCUUGACUUCCGCGCCCAUUGGUAAUACAAU-CUGCCCGUG-------GUUU------CACUAUGGCAAUAAA-GGCC-UCUUGGAAUAGGCGUUUUGGACCCGAG-GGCAGUG-CUCGGCAUCUCCACUGUUGCU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUGUAUGGGGAUG-AAACAGGAUAGACA-GACGCAAUAAAGAGGA-CGGC-GUUUGCUCGGUGGGAAUUCCA-GCCGUA--------------------------------UAAGUGGG-UCAUUU--UUAUAAGUGCAAACGAUGAUUUCGUUGCCGCUAAUGAUAACAUGGAAACA---GCUUUCGUAGCUGCUGCCUAG--------UUUUUGUCUUU----------------AG-------------------CGCGGUUUU---GGGGGCUUACCGGGCAACAGAA-AAGCCCCC-G--
AATR01000001.1/174322-174669 CGACUUUAAAAAAAAAAAAUUACACGUUAUAAG-AUAAAUGUCUC-----UUUA----GGGACUAUGGUAAUAAA-CGC--GCAUGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGACUCCACCAUAAUCCA--------------------------------UCAUUUGUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAGUUUGGGGUCG-AAAUAGGAUCGACGGA-CGU-CUAAAGAUGUU-AGC-UUUUGCCCGGUGCGGU-GUC--GCUGUU----------------------------------AUCGAC-CCAUUU-AAGCUAGUUGCAAAUGACAACAAAGCACCG---------------------------AUGGCUUUGGCUGCGUAA---GCGGUCCGAAA-UAUUGGAACCUUAAGUCUUAGGCC----UGC--GGUCUAAGCGGGGUCC-----GGAGGU-ACCUGGCAACAGAA--ACCUCC--ACU
AAMW01000003.1/16014-15672   CCCCUUUUCUUUUGCCCGCGCGACGCCUAUAUC-AAUGGUGUUCGC----UUCG---GCGGACUAUGGCGAUAAAUUGCU-GCGUGCAAUAGGCACAACGGACCCGGG-GGCAGUA-CCCGGCGGCUCCACCAUAAACCCCGG------------------------------UUUUACGGGAUU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUGACGGGGCCG-AACUAGGAUCGACGU-GGGC-UGAAAAGCGU--AGU-UUUUGCUCGGGCUGAG--UAA-CCCGUA----------------------------------AUAGG-CUCAUUC--UCAUAAGUGCCAACGAUAACGAAGCA------------------------------CUCGCAGUUGCAGCGUAAUUUUAAGGCCUAACGGUCUGAAUUUACAAAGCUAAAG-------------------CGCGGUU------GGACCC-ACCGGGCAACAGAA-GCGGAUUC-C--
CP000390.1/1871839-1872208   CCCCUUUCAUCGGCCGGAUCUCAUGCCUAUAUU-GGGUCUGUCGGU----UUCG---GCCGACUAUGGCGAUAAA-CGGA-CGAUGCAAUAAGCCAUUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAGAAACCGCCGG------------------------------CCCAUGCGAUGCGAAGGGCGGCU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUGAUGGGGGCG-AAAUAGGAUCGACGA-GGGU-GUAAAGAUCG-GACU--UUCGCUCGGCAUGGU-ACC--ACCGUU----------------------------------AUCGG-ACCGAAC-CUUAUAGUUGCCAACGACAACUAUGCGGAA---------------------------GCACGUCUCGCUGCUUAA--UGCAGCGCGAUA-GCUUCAA--UUCAAGUCUCAGGCC--GUCGCA-GGCCUGAGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP000009.1/1559423-1559099   UCCCUUGCGACGGGACACGCGCACUCCUAUGUUCAGCAGUGCAAGGGG--UUCG-UCCCCGGCUAUGGCGAUAAA-CGGU-AAGUGAAAUAAGUGUUGUGGACCCGGG-GGCAGUG-CCCGGCGUCUCCACCAAGAACAACCCC------------------------------UCGCAAAAGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUCUGUGGGGACG-AAACAGGCUCGACAC-GCAUGGUAAAGACUU--AUC-UUUUGCCCGGCAUUGU-ACC--ACCGUC----------------------------------AUCGG-GCUAAAC--UUACAAGUGCCAACGAUAACUCAGAGGUG---------------------------CUCGCUGUCGCUGCAUAA-----------------------------GCGAUAAG-------------------CGCGGUUC----GGGAGGGCACCGGGCAACAGAA-GCCCUCCC-A--
CP000053.1/198997-199588     GACCUUUACAUUUUAAUCAAAUUAAGGCAUAAUAUUUGGUGCUA------AUA------UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAAACUUUCUAAAUAACUUGCUUCUAAAGGUAAUUUGUACGUCGAACCGGUACUCGAAUCCUCACGUACCAAGUGUACGCUGCGGUUCGAGGUGAAGUGUCUCCUUUUAUUAGCGGCGUCAUUUAGAAAAGUUUAAAUAUAUAAUAUAAUAAAGAGUAGACAAUACGAAGAUCAACUUCAAAAAGAGCAAGGAGUUCACAAGGCGAGGAGCGAAGCGUAUACUUAAUACGUGAACACCGCAGCUCUUGUAGAACGACGUAGCCAAUUUUUGAAGUUCAUCGAGUAUUUUAUGGGGGCG-AAAUAGGAUCGACGU-ACCUAAUAAAAAGAU--UGC-UUUUACUCGGGAUGAU-UCC--GCCG----AU-GGC------UUU-----GCC-AU-------AUGGG-UCAAAA-CAAAGAAACGCAAACGAUAAUAAUCGUUAUGUAGGU------------------GCAGCUUUA---GCAGCUUAA--------------------------------UCCUA-------------------CGCGGCUG-----GGGGUUUGCCGGGCAACAGAA-AAACCCC--ACA
CP000394.1/2038929-2038616   CCUCUACCAAAGCAGGCAGUUAUACCUUAUAUA-GAAGUCGUCAG-----UUCG----CUGACUAUGGUGAUAAA-CGGC-GAGUGGAAUAAGCGUAGUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAUAUAACUCCG------------------------------UUCUGCGGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUUCAUGGGGGCG-AAACAGGCUCGACGC-GCGCGGUAAAGACUC--GUU-UUUUGCCCGGCAUGGU-UCC--GCCGUU----------------------------------AUCGG-GCCAUAU---UACAGGUGCCAAUGAUAAUCAUGAGGCG---------------------------CUCGCUGUCGCUGCAUAA-----------------------------GCGAUAAG-------------------CGCGGUUC-----GGGGGGCACCGGGCAACAGAA-GCCCCCC--ACU
CP000463.1/2367908-2367544   CCCCUUCCCU-GCGGCGUCACGAUGCUUAUAUUCGAUCCUGCCGG-----UUCG----CCGGCUAUGACAAUAAA-CGGU-CGUCGCAAUAAACCAUUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCCAAGCCCG------------------------------CUCGCCAGCUUUCAGCGCGGGU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGGCGGGGGCG-AAAUAGGAUCGACGA-GGGC-GUAAAGGGCG-AACU--UUUGUUCGGUAUGGU-UCC--GCCGAU----------------------------------AUCGG-GCCAAUG--CAAUAGUUGCCAACGACAACUUUGCUCCG---------------------------GUUGCUCAGGCAGCGUAA--CGCUGUUUGAAA-GACCAAGUCUA-AAGUCCUAACGGG-UUAAGCUCCGUUAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
AABW01000001.1/899123-899631 GACCUUUACAUUUUAAUCAAAUUAAGGCAUAAUAUUUGGUGCUA------AUA------UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAAACUUU--------------CUAAAUAACUUGCUCCUAAAGGUAAUUUGUACGUCGAUCCGGUAUUCGAAUCCUCACGUUACUUGCGUGUACCCUGCAGUUCUGCGUUCCGUGUUGCCUUCAAAUUUCUCUUUAUUAGCUACGUCAUUUAGAAAAGUUUAAAUAUGUAAUAACUCUUAAAGAGUAGACAAUACGAAGUUCAUCGAGUA---------------------------------------------------------------------------UUUUUGGGGGGCG-AAAUAGGAUCGACGU-GCCUAAUAAAAAGAU--UGC-UUUUACUCGGGAUGAU-UCC--GCCG----AU-GGC------UUGU----GCC-AU-------AUGGG-UCAAAA-CAAAGAAACGCAAACGAUAAUAAUCGUUCUGUAGGUCAU---------------UUAGCUUUA---GCAGCUUAA--------------------------------UCCUA-------------------CGCGGCUG----GAGGGUGUGCCGGGCAACAGAA-CAACCCUC-ACU
CP000158.1/3121357-3121004   GGGCUUACCAUCGCGCGCGGUAUCCCCUAUAUU-GGCGAUGUC-------UUCG------GACUAUGGCGAUAAA-CGCG--CGUGUAAUAAGCGGCUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAAAAGCAGA-------------------------------UCAGCAAUGGUCUGUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUGACGGGGCCG-AAAUAGUGUCGACGGA-CGU-GUAAAGACGA--GGC-UUUCGCUCGCU-UGA--GCU---GCGUU----------------------------------AGAAGC-UCAAAAGCAAAUAGUUGCAAAUGACAACUUUGCUGAG------------------------GGCGAAUUGCUCGCCGCGUAA---GCGGUGACGGU-UUUUCCGA-CCUAAGUCCUGGGGC--UUCAGA-CCCCUAGGCGGGGCCC-----GGGGGC-GCCUGGCAACAGAA--GCCCCC--ACC
CP000235.1/821889-821561     UUGCUUGACUUUCUCCAUGUGCUGGCGUACAAU-CCUUUCGUGA------UCUU-----UCACUAUGGCAAUAAA-AGUUA-CUUGGAAUAGACGUUUUGGACCCGAG-GGCAGUG-CUCGGCAUCUCCAC-GUGU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUGCGGGGAUG-AGACAGGUUAGACA-GGCGUAGUAAAGAAGC-UGGC-UGUUGCUCGGUGGGAAUUCCA-GCCGUA--------------------------------UAAUUGGG-UCAUAU--UUAUAAGUGCAAACGAUGAUUUCGUUGCCGCUAAUGACAACGUGGAAACA---GCUUUCGUAGCUGCAGCCUAG----------UGUGCCUUU----------------AG-------------------CGCGGUCUC---GGAGGCUUACCGGGCAACAGAA-AAGCCUCC-AUU
AE017197.1/910842-910294     UACCUUUACAUUUUAAUCAAAUUCAGUAAUAAUAUUUGGUGCUA------AUA------UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAUAUUCGAUGAACUCCAAAAAUUUGCUGCGUCAUUUUAUUAAGUGCUGUGGUCUUUAUGUGUUAAGUAACUGCUCACGCUUUUUGUAGUUGAUCUAUAUAUGUAUGAUUUUCGGUUUAAAUUGAAUUUAAUUUUGAGAAAUGCGCGAAGUUUACAAAUGAAUAUAUGAGCUAUGAGCAUCACGAACAAUUGAUAAAAUGAAAGAGUAAUAUUAAAUAAAGUAAAGAUAAGUAGAA-------------------------------------------------UUUUUUGGGGGCG-AAAUAGGAUCGACGU-GCCUAAUAAAAAAAU--UGC-UUUUACUCGGUAUGAU-CCC--ACCG----AU-GGC------UUUU----GCC-AU-------AUGGG-UCAAAA-CAAAGAAACGCAAACGAUAAUAAGCGUUAUGUAGGUGUU---------------GCCGCUUUAGCUGCAGCUUAA--------------------------------UCCUA-------------------CGCGGCUU-----GGGAUUUGCCGGGCAACAGAA-AAAUCCC--AU-
AAYB01000003.1/353054-352706 CCCCUUGCGUGCCGCAUCAUCCUUGCCUAUUUA-AGGGAUGUCC------UUCG-----GGACUAUGGACAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGUCUCCACCAAACACCCU-------------------------------UCAUUUGGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCUAUGGGGACG-AAAUAGGAUCGACGAA-CGU-CUAAAGGGGUA-AGC-UUUGUCUCGGUGAGUU-ACC--ACCGUU----------------------------------AUCGGU-ACAAAU-UGUAUAGUUGCAAAUGACAACAAUGCACCG---------------------------AUGGCAGUCGCAGCGUAA---GCUGUGCCUAA-UAUCGAACCUU-AACUCCUUAGGU--UUUGCG-ACCUAGGGCGGGGUUC-----GCAGGU-ACCUGGCAACAGAA--ACCUGC--ACU
CR925678.1/574919-574586     UUUAUUGACUUAUAAGCAGUAUAGUAAUAAAAU-ACAGCUGUGC------UUUU-----GCACUAUGGCAAUAAA-UGC-AUCUUAGAAUAAAUGUAUUGGACCCGAG-GGCAGUG-CUCGGCAUCUCCACUGUUGUU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUAUGGGGAUG-AAACAGGCUCGACA-UGCAUAGUAAAGGGGA-UAGC-UUUUGCUCGGUGAGAA-AACA-GCCGUU-------------------------------UCAAGUGA--UCAAAA-CUUAUAAGUGCAAACGAUAAUUUCGUUUCCGCUAAUGAUAAUAAUAGCACU---GCUAACUUAGUAGCUGCUUAG---------UUUUAUAAUU----------------AG-------------------CACGGUUUUUU--GGGGUUUUCCGGGUAACAGAA-AAACCCC--UCC
CP000494.1/6332038-6332405   GGUCUGUGCAUCCACCGCCGAGCGGCCUAUAUA-GGGGGUGCCGG-----CUUG----CCGGCUAUGGAAAUAAA-UCGC-CGUCGAAAUAAACCAUUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAGUCCG------------------------------CCUUGGAGACAUCUCGGAUGUCGGGC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGGCGGGGGCG-AAAUAGGAUCGACGA-GGGC-GUAAAGGGCG-AGCU--UUUUCCCGGUAUUGU-UCC--GCCGUU----------------------------------AUCGG-GCUACUG--CAAUAGUUGCCAACGACAACUUUGCUCCG---------------------------GUUGCUCAGGCUGCGUAA--CGCAGUUUGAAA-GACC-ACCUUA-AAGUCCUAACGGG-UUAAGCUCCGUUAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP000697.1/45716-46058       GAUCUUUCACAGCCGGUGUCCUUCACCUAUAUA-GAGCGCGUCGG-----GCAA----CCGACUAUGGCGAUAAA-CGAU-GCGUGGAAUAAGCGUAGUGGACCCGGG-GGCAGUA-CCCGGCGCCUCCACCAGUUUCCCCG------------------------------CCGGUCCGGUUCGCAUUGCGCAAAUCGAACCGCCGGCGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUCAUGGGGGCG-AAACAGGCUCGACAC-GCGUGGUAAAGACCC--AUC-UUUCGCUCGGCAUGGU-UCC--GCCGUC----------------------------------AUCGG-GCCGUAU---GACAAGUGCCAACGAUAACUUCGAGGCG---------------------------CUCGCUGUCGCUGCAUAA-----------------------------GCGAUAAG-------------------CGCGGCAC-----GGGGGGCGCCGGGCAACAGAA-GCCCCCC--ACC
CP000237.1/377443-377759     GCAGUUGAAGUUAUUGCGUUUGUUUGAUACGAUAAGCGGCGCGC-----UGUUUU----GCGCUAUGACAAUAAAUGGUU-UUUCGUAAUAGGUAUCUUGGACCCGAA-GGCGGAG-UUCGGCACCUCCACCGUUU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCGGGGGUG-AUUUAGUUUCGACA-GGUA--UUAAAGGCUA--AAC-UUUUGUUCGGU-UGA--GUGAUCCCGUG----------------------------------AUUCACAACACUU-UUUAUAAGUGCAAACGACAAUUUUGAAGCUGGUUCUGCUGAA------------UAUGCAGUAGCU---GCCUAG-------UUUAUAGGUAGUAC--------------AG-------------------CGCGGUUU-----GGGGCG-GCCGGUCAACAGAA-CUGCCCC--AGU
CP000157.1/1820824-1820479   UCACUUCACA-UUAAGGCGUUUUCGCUUAUAUG-GGACCUGUCCGU----UUCG---GCGGGCUAUGGUGAUAAACUGCG-GUGUGUAAUAGACGCAACGGACCCGGG-GGCAGUA-CCCGGCGGCUCCACCAAAAAGCGCAUA------------------------------UUUACAGGCGCUU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCUGAUGGGGCCG-AACCAGGAUCGACGU-GUGU-UGAAAGGCAU--UGU-UUUCACCCGGGCUGAG--UAU-CCCGCAA---------------------------------AACUG-UUCAAAA-CACACAAGUGCCAACGAUAACGAAGCA------------------------------CUCGCUCUCGCAGCGUAACAUGACGGCCUAACGGCCUAACGUUACAAAGCUAAAG-------------------CGCGGUU------GGACCC-ACCGGGCAACAGAA-GCGGAUUC-C--
CP000830.1/2457766-2458115   GCCUUUGCAUCCGGCGCACCCAAUGCCUAUAUC-UGAUCUGUCC------UUCG-----GGACUAUGGACAUAAA-CGC--GCUCGUAAUAAGCGGAUCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCAACAGCCCUG------------------------------UCGUUUGCAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAGAGGGGGCCG-AAACAGGAUCGACGAA-CGU-CUAAAGGGGUU-AGC-UUUGUCUCGGCUGGGU-GCC--ACCGUU----------------------------------AUCGGC-CUAAAU-UGUACAGUUGCAAACGACAACCGUGCUCCG---------------------------GUGGCCGUUGCUGCGUAA---GCAGUAACAAC--ACCGAAACUU-AAGUCCUUGCGC--CUAGCA-GCGUAAGGCGGGGUUC-----GCAGGC-ACCUGGCAACAGAA--GCCUGC--ACA
CP000927.1/3636841-3637206   GCCCUUCCAUCGGCGGGUCCCACCCCCUAUAUU-GAUCCUGUUCGGG---UUCG--CCCGGACUAUGGGGAUAAA-CGCG--CACGUAAUAAGCGGACUGGACCCGGG-UGCGAUU-CCCGGCGGCUCCACCAA-UCUC-----------------------UCCCGAGUUAUCACGGGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUGCAUGGGGCCG--AUCAGCAUCGACAGA-CGU-GUAAAGGUGUUAUGC-UUUCUCUCGGCGUGG--CUC--ACCGU-----------------------------------AUCGGG-CCGCUA--AACUAACUGCGAACGAUAACUUCGCUGAA------------------------GAGUUCGCUAUCGCCGCGUAA--UGCGGUGCUAGUGAAUUCGCGCCUUAAGUCCUAGGGG--UUCAGA-UCCUUAGGCGGGGCCC-----GGAGGGAGCCUGCCAACAGAA-UCCCUCC--ACU
CP000943.1/1217233-1217596   GGGCUUCAAAACCGGCGCGCCUGCCUCUAUAUU-CGGUAGGCCGGCC---GCGA--GGUCGGCUAUGGCGAUAAA-CGUU-CUUCGCAAUAAACCUAUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCCAAGCCCAGCCCGU--------------------------------------------UCCGGCG--GGCUGGGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCGGCGGGGGCG-AAAUAGGAUCGACGA-GGGC-GUAAAGGUUG--GAC-UUUCGCUCGGCAUGGU-UCC--GCCGUU----------------------------------AUCGG-GCCAAUG--CAAUAGUUGCCAACGACAACUAUGCUCCG---------------------------GUGGCGGUCGCCGCGUAA---GCGGUGCCCAA-GACCAAAC---AAAGUCCUA-GCGG-UUAGCAUCGCAUAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP001612.1/1041556-1041048   GACCUUUACAUUUUAAUCAAAUUAAGGCAUAAUAUGUGGUGCUA------AUA------UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAAACUUU--------------CUAAAUAACUUGCUCCUAAAGGUAAUUUGUACGUCGAUCCGGUAUUCGAAUCCUCACGUUACUUACGUGCACCCUGCGGUUCUACGUUCCGUGUUGCCUUCAAAUUUCUCUUUAUUAGCUACGUCAUUUAGAAAAGUUUAAAUAUGUAAUAACUCUUAAAGAGUAGACAAUACGAAGUUCAUCGAGUA---------------------------------------------------------------------------UUUUUGGGGGGCG-AAAUAGGAUCGACGU-GCCUAAUAAAAAGAU--UGC-UUUUACUCGGGAUGAU-UCC--GCCG----AU-GGC------UUGU----GCC-AU-------AUGGG-UCAAAA-CAAAGAAACGCAAACGAUAAUAAUCGUUCUGUAGGUCAU---------------UUAGCUUUA---GCAGCUUAA--------------------------------UCCUA-------------------CGCGGCUG----GAGGGUGUGCCGGGCAACAGAA-CAACCCUC-ACU
AE007869.2/2007192-2007562   CCCCUUUUCUAAGGCCGGCGAAACGCCUAUAUG-AGCCUUGCCGGG----GCAA---CCCGGCUAUGGCGAUAAA-CGGU-CGGUGUAAUAAACCUAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAAACCGG------------------------------CGGGAUCUCAAGAUGAGGCCGGCU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGAUGGGGGCG-AAAUAGGAUCGACAA-GGGC-GUAAAGAUCG-AACU--UUUGCUCGGCAUGAU-ACC--GCCGUU----------------------------------AUCGG-GUCACAA--GUGUAGUUGCAAAUGACAACAACGCUAAG------------------------GAAUACGCUCUCGCUGCCUAA-UGGCGGUGCGGGA-AUUCCGCU-CU-AAGUCCUUACGG--UUAGCC-CCGUAAGGCGGGGUUC-----GGAGGU-ACCUGGCAACAGAA--ACCUCC--ACC
AE006914.1/1031328-1030820   GACCUUUACAUUUUAAUCAAAUUAAGGCAUAAUAUUUGGUGCUA------AUA------UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAAACUUU--------------CUAAAUAACUUGCUCCUAAAGGUAAUUUGUACGUCGAUCCGGUAUUCGAAUCCUCACGUUACUUGCGUGUACCCUGCGGUUCUGCGUUCCGUGUUGCCUUCAAAUUUCUCUUUAUUAGCUACGUCAUUUAGAAAAGUUUAAAUAUGUAAUAACUCUUAAAGAGUAGACAAUACGAAGUUCAUCGAGUA---------------------------------------------------------------------------UUUUUGGGGGGCG-AAAUAGGAUCGACGU-GCCUAAUAAAAAGAU--UGC-UUUUACUCGGGAUGAU-UCC--GCCG----AU-GGC------UUGU----GCC-AU-------AUGGG-UCAAAA-CAAAGAAACGCAAACGAUAAUAAUCGUUCUGUAGGUCAU---------------UUAGCUUUA---GCAGCUUAA--------------------------------UCCUA-------------------CGCGGCUG----GAGGGUGUGCCGGGCAACAGAA-CAACCCUC-ACU
CP000849.1/1136359-1135839   AACCUUUACAAAUUAAUCAAAUUAAGCGAUAAUAGUAAGUGCUA------AUA------UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAUAAUGU--------------GCUAUGUCAUUCCUGAAUGGAACAAAAGCCGUCUUCGGUGUCAUCCCGUGGCUUGUUAACUAGAUCCAGCAUAAAGCGAGAUAUAUCGAGCUUUUAAUUUUAAAAAGUUACUUUGUUUGUAAUUUUUACUGGAUCCCGUGGACAAGCCACGGGAUGACAAGCUCUAUAAGGCAAUGACAUAACAAUAAAAAUAGUGCAA----------------------------------------------------------------UGACAGGGGGGCG-AAAUAGGAUCGACGU-GCCUAAUAAAAAAAU--UGC-UUUUACUCGGGAUGAU-UCC--GCCG----CA-GGC------UUUU----GCC-UU-------ACGGG-UCAAAA-CAAAGAAACGCAAACGAUAACUAUCGUUCCGCAGGUACU---------------CCAGCUUUAGCUGUAGCAUAA--------------------------------ACCUG-------------------CACGGCUU----GGGGGUUUGCCGGGUAACAGAA-AAACCCUC-A--
AL591688.1/2291104-2291462   GCCCUUUUCUUGGGCGUCGGAAAGACCUAUAUG-ACGAGUGCCGUC----UUCG---GGCGGCUAUGGCAAUAAA-CGGG-CGAUGCAAUAAACCCAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAAACCGG------------------------------CCUGUGCAGACCGGCU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGAUGGGGGCG-AAAUAGGAUCGACAA-GGGC-GUAAAGAUCG-ACUU--UUUGCUCGGCAUUGU-ACC--ACCGUU----------------------------------AUCGG-GCUAAAC--UUAUAGUUGCAAACGACAACUAUGCUGAA---------------------------GCACGUCUCGCUGCCUAA-CGGCGGUGCGACA-CUUCAAAU---CAAGUCCUUCCGG--GUAGCA-CCGUAAGGCGGGGUCC-----GAAGGC-ACCUGGCAACAGAA--GCCUUC--ACC
CP000683.1/1122306-1121801   GACCUUUACAUUUUAAUCAAAUUAAGGCAUAAUAUUUGGUGCUA------AUUA-----UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAAACUUU--------------CUAAAUAACUUGCUCCUAAAGGUAAUUUGUACGUCGAUCCGGUACUCGAAUCCUCACGUUACUUGCGUGUACGCUGCGGUUCUGCGUUCCGUGUCGCCUUCAAAUGCCUCUUUAUUAGCUACGUCAUUUAGAAAAUAAAUAUAUAAUAACUCUUAAAGAAUAGACAAUACGAAGUUCAUCGAGUA------------------------------------------------------------------------------UUUUUGGGGGGCG-AAAUAGGAUCGACGU-GCCUAAUAAAAAGAU--UGC-UUUUACUCGGGAUGAU-UCC--GCCG----AU-GGC------UUUU----GCC-AU-------AUGGG-UCAAAA-CAAAGAAACGCAAACGAUAAUAAUCGUUCUGUAGGUCGU---------------UUAGCUUUA---GCAGCUUAA-------------------------------CCCCUA-------------------CGCGGCUG----GAGGGUGUGCCGGGCAACAGAA-AAACCCUC-G--
AE008917.1/633789-633423     CCCCUUCCAAUCGGUAAAAACCACGCCUAUAUA-CGUCCUGUCGGC----GCAA---GCCGACUAUGGUGAUAAA-CGGA-CGGUGUAAUAAACCCAUUGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCAAAGCACAGCUUG------------------------------CCGAUCAGGCUGUGU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUGGCGGGGGCG-AAACAGGAUCGACAA-GGGU-GUAAAGAUCG-CUCU--UUUACUCGGCAUGAU-ACC--ACCGUU----------------------------------AUCGG-GUCAACA--GAGUAGUUGCAAAUGACAACAAUGCUCAG------------------------GGUUAUGCUCUCGCUGCCUAA-UGGCGGUGCGGGA-AACCCACUCUA-AAGUCCUUAGGG--UUAGCC-CCUUAAGGCGGGGUUC-----GGAGGC-ACCUGGCAACAGAA--GCCUCC--ACU
CP000847.1/1045451-1046020   GACCUUUACAUUUUAAUCAAAUUAAGGCAUAAUGUUUAGUGCUA------AUA------UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAUACUCGAUGAACUUCACAAAUUGGCUACUUCGUCCUAU-AAGUACUGCGGUGCUCACGUAUUAAGUAUACGCUCCACUCCU-UGUCUUAUGGACCCAUUGCUCUUUUUGAAGUUGAUCUUCGUAUACCAGUCGAUGUCAAUACUGCUUGUACUUUAAAAAGUGAAUUUUAUUU-UGAGAAGUGAGCACCAGCAGCCUAUACUUAAUAGGUGAGGAUGCAAAUCCUUGAUAAGAUGAAAUUCAAUUUUUAAAGUACAAGCAGUA--------------------UUUUAUGGGGGCG-AAAUAGGAUCGACGU-GCCUAAUAAAAAGAU--UGC-UUUUACUCGGGAUGAU-UCC--GCCG----AU-GGC------UUUU----GCC-AU-------AUGGG-UCAAAA-CAAAGAAACGCAAACGAUAAUAAUCGUUCUGUAGAU------------------UUAGCUCUA---GCAGCUUAA--------------------------------UCCUA-------------------CGCGGCUG-----GGGGUUUGCCGGGCAACAGAA-AAACCCC--ACA
CP000908.1/2977312-2977689   GCUCUUCAAAACCGCCGUCGGCCUCUCUAUAUU-CGCUUUGCCGGUC---GCAA--GGCCGGCUAUGGCGAUAAA-CGUU-CUUCGAAAUAAACCUAUCGGACCCGGG-GGCGGUA-CCCGGCGCCUCCACCCGAACCCAGGACCGAUGG--------------------------------CCGCACGGCCUCAGC-GUGUUGGGU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCCGGCGGGGGCG-AAAUAGGAUCGACGA-GGGC-GUAAAGGGUG--AAC-UUUCGCUCGGCAUGGU-UCC--GCCGUU----------------------------------AUCGG-GCCUUUG--CAAUAGUUGCCAACGACAACUUUGCUCCG---------------------------GUGGCUGUCGCCGCGUAA---GCGGUGCCAAA-AACCGACCU--AAAGUCCUA-GCGG-GUAGCACCGCAUAGGCGGGGUUC-----GGAGGU-ACCUGGCAACAGAA--ACCUCC--ACU
AE008692.2/540534-540186     GCUAUUGCCUUUAUGGCUGUCCGACCUUAGCUA-GAGAGCGUCAC-----UUCG----GUGACUACGAUGGUAGACUGUU-AAGUGAAAUAGACUCGACGGACCCGGAGGGCAGUACUCCGGCGCCUCCACCAACAGCCG------------------------------CGGAUAGCAAGCCACUGUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUUGAUGGGGGCG-AAACAGGAUCGACGU-GUGUAGUAAAGACUU--GAU-UGCCAUCCGGCGUGAU--UGA-GCCGUU---------------------------------AAACCG-AUCAUUU--UUAUAAGUGCCAACGAUAACGAGGUA------------------------------CUCGCUGUUGCUGCGUAA-UGGAAACCUUCACGGGUAGACAUUACUAAGUAAGAG-------------------CGCGGUU------GGGCUGCACCGGGCAACAGAA-GCAGAUUC-C--
CP000766.2/1038340-1037832   GACCUUUACAUUUUAAUCAAAUUAAGGCAUAAUAUUUGGUGCUA------AUA------UAGCUAUAGUAAUAAA-CGUA-AUUUAGAAUAGAGGUUGCGGACUCGGG-GGCAGUA-CCCGACGCCUCCACCAAAACUUU--------------CUAAAUAACUUGCUCCUAAAGGUAAUUUGUACGUCGAUCCGGUAUUCGAAUCCUCACGUUAAUUGCGUGUACCCUGCGGUUCUUUGUUCCGUGUCGCCUUCAAAUUUCUCUUUAUUCGCUAGGUCAUUUAGAAAAGUUUAAAUAUGUAAUAACUCUUAAAGAGUAGACAAUACGAAGUUCAUCGAGUA---------------------------------------------------------------------------UUUUUUGGGGGCG-AAAUAGGAUCGACGU-GCCUAAUAAAAAGAU--UGC-UUUUACUCGGGAUGAU-UCC--GCCG----AU-GGC------UUGU----GCC-AU-------AUGGG-UCAAAA-CAAAGAAACGCAAACGAUAAUAAUCGUUCUGUAGGUCGU---------------UUAGCUUUA---GCAGCUUAA--------------------------------UCCUA-------------------CGCGGCUG----GAGGGUGUGCCGGGCAACAGAA-AAACCCUC-ACU
CP002156.1/1625575-1625943   GGACUUCAAAUCUUUACCCACAGCCCCUAUGUU-ACCUGUGAUGC-----UUCG----GUAUCUAUAGCGAUAAAUGGCG--UUCAGAAUAAGCGGCCCGGACCCGGG-GGCGGUA-CCCGGCGGCUCCACCACAUGACUUCUC----------------------------UCCCUCGGGGGGGGGGAGCCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCGGCGGGGCCG-AAAUAGGAUCGACGGA-CGU-GUAAAGGUUC--GGC-UUUCGCUCGGA-UGG--CC---UCCGUU----------------------------------AUUGGG-CCAUGA-UGAAUAGUUGCCAAUGACAACUCUUCGGAA------------------------GGUUUCGCUCUCGCUGCGUAA--CGCGGUGCAAGC-AAACCACUAUUAAAGCCCUAGGCC-CUUUCCC-GGUCUAGGCGGGGUCC-----CGGGGA-ACCUGGCAACAGAA--UCCCCG--ACU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::.::::::<<<<<.....____....>>>>>---(((((----.-(((.((((--------(((-(((,,,<<<<<._______.>>>>><<<<<<<____________...............................__________________...................................................................................................................................................................................................................................______>>>>>>>.,,,,,,,,,,,,))).)))--------))))..))).--)))))AAAA:BBB:.BBB..aaaa::..................................:::bbb.bbb:::.::::::::::::::::::::::::::::::........................:::::::::::::::::::::.........:::::.::::..:.....::::::::::...................::CCCC::.....DDDDDDDcccc::::::::::.ddddddd..:::
#=GC RF                      gacCUUuacauuuuaaucaaauuaagcUAUAaU.uuuggUGccgg.....uUag....ccggCUAUgGcgAUAAA.cgca.ccuuggAAUAgAcgcuuCGGACcCGGG.GGCAGUA.CCCGgCGcCUCCACCAaaacucua...............................uaaguaauguguuuuuua...................................................................................................................................................................................................................................uuuuauGGGGgCG.AAAuAGGAUCGACGa.gcgUAaUAAAgaagg..ugc.UUUcgCcCGGuAUGaU.uCC..gCCGUU..................................AucGGg.uCAAAa.caaAuAAaUGCAAACGAuAAcuaugcuucu........................guaguuguagUuGCaGCuUAA.........uuaaa.aauu..a.....AAgucuuaug...................CGcGGUUc.....GGgGuuUaCCgGGCAACAGAA.aaaCcCC..Acu
//
# STOCKHOLM 1.0

#=GF AC   RF01850
#=GF ID   beta_tmRNA
#=GF PI   10Sa_RNA; SsrA; tmRNA
#=GF DE   Betaproteobacteria transfer-messenger RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19617710
#=GF SS   Published; PMID:19617710
#=GF GA   84.00
#=GF TC   84.90
#=GF NC   83.10
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00001
#=GF DR   SO; 0000584; tmRNA;
#=GF DR   URL; http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=S14.001;
#=GF DR   GO; 0006401; RNA catabolic process;
#=GF RN   [1]
#=GF RM   8972778
#=GF RT   Phylogenetic analysis of tmRNA secondary structure.
#=GF RA   Williams KP, Bartel DP
#=GF RL   RNA 1996;2:1306-1310.
#=GF RN   [2]
#=GF RM   8990402
#=GF RT   Probing the structure of the Escherichia coli 10Sa RNA (tmRNA).
#=GF RA   Felden B, Himeno H, Muto A, McCutcheon JP, Atkins JF, Gesteland RF
#=GF RL   RNA 1997;3:89-103.
#=GF RN   [3]
#=GF RM   11752287
#=GF RT   The tmRNA Website: invasion by an intron.
#=GF RA   Williams KP
#=GF RL   Nucleic Acids Res 2002;30:179-182.
#=GF RN   [4]
#=GF RM   12140330
#=GF RT   BRUCE: a program for the detection of transfer-messenger RNA genes in
#=GF RT   nucleotide sequences.
#=GF RA   Laslett D, Canback B, Andersson S
#=GF RL   Nucleic Acids Res 2002;30:3449-3453.
#=GF RN   [5]
#=GF RM   12520048
#=GF RT   tmRDB (tmRNA database).
#=GF RA   Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J
#=GF RL   Nucleic Acids Res. 2003;31:446-447.
#=GF RN   [6]
#=GF RM   19617710
#=GF RT   Variations on the tmRNA gene.
#=GF RA   Mao C, Bhardwaj K, Sharkady SM, Fish RI, Driscoll T, Wower J, Zwieb C,
#=GF RA   Sobral BW, Williams KP
#=GF RL   RNA Biol. 2010;6:355-361.
#=GF CC   Bacterial tmRNA, also known as 10Sa RNA or SsrA, is named for its dual
#=GF CC   tRNA and mRNA-like properties. Its role is to liberate the mRNA from a
#=GF CC   stalled ribosome. To accomplish this part of the tmRNA is used as a
#=GF CC   reading frame that ends in a translation stop signal. The broken mRNA is
#=GF CC   replaced in the ribosome by the tmRNA and translation of the tmRNA leads
#=GF CC   to addition of a proteolysis tag to the incomplete protein enabling
#=GF CC   recognition by a protease. Recently a number of permuted tmRNA genes have
#=GF CC   been found encoded in two parts. tmRNAs have been identified in eubacteria
#=GF CC   and some chloroplasts but are absent from archaeal and eukaryote nuclear
#=GF CC   genomes.
#=GF WK   Transfer-messenger_RNA
#=GF SQ   7


CP000089.1/4390256-4389925 GGCGAAACCGGCUCUUGAAAAACCACCCCCCCGCCCCCAUAAUUGAAAGC-------------------------AUGGUUGUAAUUCCGGCAAUCUGGAGGCGUUCUGGACAGGGGUUCGAUUCCCCUCACCUCCACC-CAAGGGCAUUCCGCUGAGUGUU---UUUGG-AUGGGGGUGUACUGGUCUCGACAGGGCGGACAAAGGUGCGCAGGCAACUCGUCAGGCGAUCGACGUUAAUGAAGCAAAUCCAUAAUUGCCAAUGAUGAGCAAUUCGCUAUUGCCGCCUAAAAACGGU--UAGCCGGGGCUGCUAGA-GCCUUGUUACCAAAGA-UAGC---CGGCGGGGACUUCGGUCCCCGUCG--UCA
CR555306.1/77117-77443     AAACUCCCGUAGACUUGAAUCGAAGGGGCACUGCCCUUAUAGUGCAAAGC-------------------------AUGGUUGUAAUUCCGGCAACCCGGAGACGUUCUGGACGCGGGUUCGAUUCCCGCCACCUCCACA--GUGGGCAUUC--UCAAGAGUG---UUCAGUGUGGGGGUGCACCGGUUUCGACAGGGCGGGCAAUGGUGAGCAGGCAACCCGAGAGGCGACGGACGUAAUCCGCGCAAAUCCACAAACGCCAACGAUGAGCGUUUCGCUGUAGCCGCUUAA----GGCAACAGCCGGGGCCGCCUGA-GCCCUGUUACCAAAGA-CGGC---UGGCGGGGGCUUCGGCCCCCGCU---UCA
AY911532.1/1-232           -------------------------------------------------------------------------------------------------GGAGGCGUUCUGGACGCGGGUUCGAUUCCCGCCACCUCCACC-UAAGAG--UUU--CGGAGAGUU---CUUAG-GUGGGGGUGUACUGGCUUCGACAGGGCGGGCAAAGGUGCGCAGGCAACUCGUCAGGCGAUCGACGUUAAUGAAGCAAAUCUCCAAACGCCAACGAUGAGCGUUUCGCAAUCGCCGCUUAA----GGCUUUUGCCGAGGCUGCUUGA-GCCUUGUUACCAAAGAAAAGC---CGGU-------------------------
AY911531.1/1-237           -------------------------------------------------------------------------------------------------GGAGGCGUUCUGGACAGGGGUUCGAUUCCCCUCACCUCCACC-CAAGGGCAUUCGGCUGAGUGUG---UUUGG-UUGGGGGUGUACUGGCUUCGACAGGGCGGGCAAAGGUGCGCAGGCAACCCGAGAGGUGACGGACGUAAUCCGCACAAAUCCAUAAUUGCCAAUGAUGAGCAAUUCGCUAUCGCCGCCUAAAAACGGC--UAGCUGGGGCCGCUGAA-GCCUUAUUACCCAAGA-CAGC---CGGC-------------------------
CP000090.1/1256851-1257210 CCACGCAAACUGCCUUGACGCUGCC-GGCAGGACGCGUAGAAUCUGGACCGUCGGGGGCUGCAAGGUUCCCGAUAAUGGUUGU-GAACCUUCUUCUUGAAGGCCUUCUGGACGGCGGUUCGAUUCCGCCCAGGUCCACCAGAAGCACAUUGCACGGGCAGUGCGCUUCUG-AUGGGCCUGACCUGGUUUCGACAGGGGGAGAUAGGGUCGUGAGGCAACUCGUCAGAGAA--GACGUUAAAACUAAAUCGAAGUAAAUGCUAACGACGAAAAGUUUGCAUUGGCCGCCUAACAGCCGC-----CUUGGGUUGUAACUGACCUCGAAACAGAAAAGUUACUGACAAGGGCUCCUUCGGGGGCCCUUG-UUCA
CP000092.1/566047-566406   GCACGCAAACUGCCUUGACGCUGAC-GGCAGCGGGCGUAGAAUCUAGAGCGUUGGGGGCCGCAAGGUUCCCGAUAAUGGUUGU-GAACCUUCUUCUUGAAGGCCUUCUGGACGGCGGUUCGAUUCCGCCCAGGUCCACCAGAAGCACAUUGCACGGGCAGUGCGCUUCUG-AUGGGCCUGACCUGGUUUCGACAGGGGGAGAUAGGGUCGUGAGGCAACUCGUCAGAGAA--GACGUUAAAACUAAAUCGAAGUAAAUGCUAACGACGAAAAGUUCGCAUUGGCCGCCUAACAGCCGC-----CUUGGGUUGUAACUGACCUCGAAACAGAAAAGUUACUGACAAGGGCUCCUUCGGGGGCCCUUG-UUCA
CP001281.2/1313664-1313991 CCUCGCACAGGCAUUGAAUGCAGCC-GCCGACCUGCGUAAGAUCGCGGAC-------------------------AUGGUUGUAAUCCCGGCAAUCUGGAGGCGUUCUGGACAGGGGUUCGAUUCCCCUCACCUCCACC-CAAGUGCAUUC--GGGAGUGUG---CUUGG-GUGGGGGUGUACCGGUUUCGACAGGGCGGGCAAAGGUGAGCAGGCAACCCGAGAGGCGACGGACGUAAUCCGCGCAAAUCCAUAAACGCCAACGAUGAGCGUUUCGCACUGGCCGCUUAA----GGCCUAUGCCGAGGCUGCUUGA-GCCUUGUUACCAAAGAAAAGC---CGGUGGGGACUUC--GGUCCCCAUCGUCA
#=GC SS_cons               :::::::::::::::::::::::::.::::::::::::::::::::::::.........................::(((((-.---((-((-((((-----(((((((,,,<<<<<_______>>>>><<<<<<<___.______________________..._____.__>>>>>>>,,,,,,,,,,,,)))))))-----))))--))-)))))))<<<<________>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,,,,AAAA,<<<<<<.aaaa___________>>>>>>...,,<<<<<<<<<____>>>>>>>>>..:::
#=GC RF                    acacgcAaauugaCUUGAagcugac.ggCagcgcgCgUAuAAUcuagAgC.........................AUgGUUGU.auuCCggcaaccuGgAGGCgUUCUGGACGggGGUUCGAUUCCccCCAccUCCACC.cAAGggCAUUccacgGAgaGUg...UUuuG.aUGGGggUGuaCUGGUUUCGACAGGGcGgGcaAaggugagcAGGCAACcCGucAGgcgAcggaCGUuAauaauacAaauccaUAAAuGCcAAcGAuGAgcauUUCGCaaUgGCCGCcUAAaAaCgGC..uaGCugGGGcUGcugcu.gCCUuGuuACcaAAgagcagC...CgccgggggccUCGGggcccccgg..UCA
//
# STOCKHOLM 1.0

#=GF AC   RF01851
#=GF ID   cyano_tmRNA
#=GF PI   10Sa_RNA; SsrA; tmRNA
#=GF DE   Cyanobacteria transfer-messenger RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19617710
#=GF SS   Published; PMID:19617710
#=GF GA   70.00
#=GF TC   70.00
#=GF NC   67.50
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00001
#=GF DR   SO; 0000584; tmRNA;
#=GF DR   GO; 0006401; RNA catabolic process;
#=GF RN   [1]
#=GF RM   8972778
#=GF RT   Phylogenetic analysis of tmRNA secondary structure.
#=GF RA   Williams KP, Bartel DP
#=GF RL   RNA 1996;2:1306-1310.
#=GF RN   [2]
#=GF RM   8990402
#=GF RT   Probing the structure of the Escherichia coli 10Sa RNA (tmRNA).
#=GF RA   Felden B, Himeno H, Muto A, McCutcheon JP, Atkins JF, Gesteland RF
#=GF RL   RNA 1997;3:89-103.
#=GF RN   [3]
#=GF RM   11752287
#=GF RT   The tmRNA Website: invasion by an intron.
#=GF RA   Williams KP
#=GF RL   Nucleic Acids Res 2002;30:179-182.
#=GF RN   [4]
#=GF RM   12140330
#=GF RT   BRUCE: a program for the detection of transfer-messenger RNA genes in
#=GF RT   nucleotide sequences.
#=GF RA   Laslett D, Canback B, Andersson S
#=GF RL   Nucleic Acids Res 2002;30:3449-3453.
#=GF RN   [5]
#=GF RM   12520048
#=GF RT   tmRDB (tmRNA database).
#=GF RA   Zwieb C, Gorodkin J, Knudsen B, Burks J, Wower J
#=GF RL   Nucleic Acids Res. 2003;31:446-447.
#=GF RN   [6]
#=GF RM   19617710
#=GF RT   Variations on the tmRNA gene.
#=GF RA   Mao C, Bhardwaj K, Sharkady SM, Fish RI, Driscoll T, Wower J, Zwieb C,
#=GF RA   Sobral BW, Williams KP
#=GF RL   RNA Biol. 2010;6:355-361.
#=GF CC   Bacterial tmRNA, also known as 10Sa RNA or SsrA, is named for its dual
#=GF CC   tRNA and mRNA-like properties. Its role is to liberate the mRNA from a
#=GF CC   stalled ribosome. To accomplish this part of the tmRNA is used as a
#=GF CC   reading frame that ends in a translation stop signal. The broken mRNA is
#=GF CC   replaced in the ribosome by the tmRNA and translation of the tmRNA leads
#=GF CC   to addition of a proteolysis tag to the incomplete protein enabling
#=GF CC   recognition by a protease. Recently a number of permuted tmRNA genes have
#=GF CC   been found encoded in two parts. tmRNAs have been identified in eubacteria
#=GF CC   and some chloroplasts but are absent from archaeal and eukaryote nuclear
#=GF CC   genomes.
#=GF WK   Transfer-messenger_RNA
#=GF SQ   27


CP000111.1/58363-58090       CUGUCAGAAUAUAAAUGUCCAA-------------------UUGGACUAGGUGAUCUCAACCGAUGUUUCGGACAGCGGUUCGAUUCCGCUCAACUCCACU---------------------------------UUUUGGGGUUGUAAUGGUUUCGACGGGGCAUAAGGAAGGUGACUGAAGCCGGCUCGGUUAGAGCAAA-AACACAAACGCUAACAAAAUCGUUAGUUUCUCCCGUCAAAC-AGCACUA--GUUGCCGCUUGAUCC---UUAAGGAGAUGGGGUGAUAUCAGCCUUAUC--AACC-AAAUGAUACGC-GGAGUCUGGAAGGACUC
AF251551.1/107-422           GUGGCAGGAUGAACAGGCUCGUC------UUC-------GGACGAACUAGGUGGUCCACACCAGUGUCUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCCCCGACCCACCGCCCCGCAGGCGGUGCGUCAUCCCGGGGCUGCAAUGGUUUCGACGGGGCAUGAGGAGGGUGACUGAAGCCUGCUCGGUCAGAGCGAA-CCCGUAACAGCGAACAACAUCGUUCGUUUCUCCCGUCAAGC-CGCCCCC--GUGGCUGCCUGACACUCUUAACGGAGACGGGGUGAGGUCAGCCUUGUC--ACCC-AAAUGACCCAU-GGGGCCUGGAAGGGCCC
CP000435.1/2143849-2143563   AUGCCAGAAUGACAAAGUCCGUU------CUU-------GAACGGACUAGGUGGUCCACACCGGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCUCC-----------------------------CUUCGGGGCUGCAAUGGUUUCGACGGGGCAUAAGGAGGGUGACUGAAGCCUGCUCGGUAAGAGCAAAUCCCGUAACUGCGAACAACAUCGUACGUUUCUCCCGUCAAGC-AGCCCCU--GUUGCUGCCUGACCCUAUUAAGGGAGAUGGGGUGAAGUCAGCCUUAUC--ACCC-AAGUGACUCGU-GGGGGUG-GAAUGCCCC
CP000110.1/2063624-2063339   CUGUCAGAAUGACAGGGUCCGGC------UUC--------GUCGGACUAGGUGAUCCACACCAGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCCCC----------------------------UCACGGGGCUGCAAUGGUUUCGACGGGGCAUGAGGAGGGUGACUGAAGCCUGCUCGGUGAGAGCAAA-CCCGUAACUGCGAACAACAUCGUUCGUUUCUCCCGUCAAGC-AGCCCCU--GUUGCUGCCUGACCCUU-UAAGGGAGAUGGGGUGAGGUCAGCCUUAUC--ACCC-AAAUGACUCAU-GGGGGCUGGAAGGCCCC
AY082655.1/1-251             --------------------------------------------------------------AGUGUCUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCCCCGACCCACCGCCCCGCCGGCGGUGCGUCAUCCCGGGGCUGCAAUGGUUUCGACGGGGCAUGAGGAGGGUGACUGAAGCCUGCUCGGUCAGAGCGAA-CCCGUAACAGCGAACAACAUCGUUCGUUUCUCCCGUCAAGC-CGCCCCU--GUGGCUGCCUGACACUCUUAACGGAGACGGGGUGAGGUCAGCCUUGUC--ACCC-AAAUGACCCAU-G----------------
AAOK01000001.1/151207-151493 CUGUCAGAAUGGCAAGGUCCGGU------UUC-------GACCGGACUAGGUGAUCCACACCAGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCCCCU---------------------------UCCCGGGGCUGCAAUGGUUUCGACGGGGCAUGAGGAGGGUGACUGAAGCCUGCUCGGUGAGAGCAAA-CACGUAACUGCGAACAACAUCGUUCGUUUCUCCCGUCAAGC-AGCCCCU--GUUGCUGCCUGACCCU--UAGGGGAGAUGGGGUGAAGUCAGCCUUAUC--ACCC-AAUUGACUCAC-GGGGGCUGGAAGGCCCC
CP000554.1/345306-345599     CUGUCAGAAUGGAAUUGUCCACC------UUU-------UGGCGGACUAGGUGAUCCACACCAGUGUCUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCUCUUUCA--------------------GGUUUCUUGGGGCUGCAAUGGUUUCGACGGGGUAUGAGGAGGGUGACUGAAGCCUGCUCGGUAUGAGCAAC-UACGUAACUGCGAACAACAUCGUUCGUUUCUCCCGUCAGCC-UGCCCUC--GUGGCUGCCUGACCCU--UAGGGGAGAUGGGGUGAGGUCAGCCUUAUC--ACCC-AAAUGACUCAU-GGGGGCUGGAAGGCCCC
CP000576.1/66662-66389       CUGUCAGAAUAUAAAUGUCCAA-------------------UUGGACUAGGUGAUCUCAACCGAUGUUUCGGACAGCGGUUCGAUUCCGCUCAACUCCACU---------------------------------AUUUGGGGUUGUAAUGGUUUCGACGGGGCAUAAGGAAGGUGACUGAAGCCGGCUCGGUUAGAGCAAA-AACACAAAUGCUAACAAAAUCGUUAGUUUCUCCCGUCAAAC-AGCACCA--GUUGCUGCUUGAUCC---UAAAGGAGAUGGGGUUAUAUCAGCCUUAUC--AACC-AAAUGAUACGA-GGAGUCUGGAAGGACUC
CP000095.2/94949-94671       CUGUCAGAAUAUGUAUGUCUAUU------UUC-------UAAUGGACUAGGUGAUUCACACCAGUAUCUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAU----------------------------------AAAUGGGGCUGCAAUGGUUUCGACGGGGUAUCAGGAGAGUGACUGAAGCCUGCUCGGUCAGAGCAAA-ACCAUAACUGCUAACAACAUCGUUAGUUUCUCCCGUCAAAC-AGCCCCU--GUUGCUGCUUGAUCUUU-UA--GGAGAUGGGGUCAGGUCAUCCUUAUU--ACCC-AAUUGAUCCAU-GGAGCCUGGAAGGGCUC
CP000552.1/66237-65963       CUGCCAGAAUAUAAAUGUCCAA-------------------UUGGACUAGGUGAUCUCAACCGAUGUUUCGGACAGCGGUUCGAUUCCGCUCAACUCCAUU-----U---------------------------UUUUGGGGUUGUAAUGGUUUCGACGGGGCGUAAGGAAGAUGACUGAAGCCUGCUCGGUUAGAGCAAA-AACACAAACGCUAACAAAAUCGUUAGUUUCUCCCGUCAAAC-AGCACCA--GUUGCUGCUUGAUUU---CAAAGGAGAUGGGGUGAUAUCAGCCUUAUC--AACC-AAAUGAUCCAA-GGAGCCUGGAAGGGCUC
BA000045.2/2366624-2366330   AAGCUGCCGUUGGUUUGUCUUUCCCCAACGUACGUGAAAAGGGAGACUAGGGUGCGUGAUCGGCUGUUCUGGACAGGGGUUCGAUUCCCCUCAUCUCCAC-----CA---------------------------ACUCGGGGAUGUACUGGCUUCGACAGGGCAAUUAGAGCGUAACUGAAGCCUGCUCGGUUAGAGCAAA-AAACCAAGUGCUACUAACAACGUAGUUCCCUUCGCUCGCGCCCGCGCUACUGUCGCGGCCUGAGU------AAGG-CGGGGUUG--GUAGAUAACCUUGUAAACCAAAACUACCCAAAAGGCCCCUUCGGGGGCC
CP000097.1/444511-444799     CUGUCAGAAUGACAGGGUCCGGU------UU---------ACCGGACUAGGUGAUUCACACCAGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCUCCC--------------------------CUCUUGGGGCUGCAAUGGUUUCGACGGGACAUAAGGAGGGUGACUGAAGCCUGCUCGGUUAGAGCAAAUCUCGUAACUGCGAACAACAUCGUACGUUUCUCCCGUCAAGC-AGCCCCU--GUUGCUGCCUGACCCUUUUAAGGGAGAUGGGGUGAAGUCAGCCUUAUC--ACCC-AAAUGACUGCU-UGGGGGUGGAAGCCCCC
AY082654.1/1-251             --------------------------------------------------------------AGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCCCCGACCCACCGCCCCGCCGGCGGUGCGUCAUCCCGGGGCUGCAAUGGUUUCGACGGGGCAUGAGGAGGGUGACUGAAGCCUGCUCGGUAAGAGCGAA-CCCGUAACAGCGAACAACAUCGUUCGUUUCUCCCGUCAAGC-CGCCCCC--GUGGCUGCCUGACACUCUUAACGGAGACGGGGUGAGGUCAGCCUUGUC--ACCC-AAAUGACCCAU-G----------------
AANP01000006.1/143839-144126 CUGUCACAAUGACAAGGUCCGAU------CUU-------GAUCGGACUAGGUGAUCCACACCAGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCCCCU---------------------------UCCCGGGGCUGCAAUGGUUUCGACGGGGCAUGAGGAGGGUGACUGAAGCCUGCUCGGUGAGAGCAAA-CCCGUAACUGCGAACAACAUCGUUCGUUUCUCCCGUCAGAC-CGCCCCU--GUGGCUGCCUGACCCAA-UAAGGGAGAUGGGGUGAGGUCAGCCUUAUC--ACCC-AAAUGACUCGC-GGGGGCUGGAAGGCCCC
AE017126.1/75610-75328       CUGUCAGAAUAUAUAUGUCCAUU------UUG--------AAUGGACUAGGUGAUUCACACCAUUAUCUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAU----CUA---------------------------UUCUGGGGCUGCAAUGGCUUCGACGGGGUUCUAGGAGUUUGACUGAAACCUGCUCGGUUAGAGCAAA-ACCAUAACUGCUAACAAAAUCGUUAGUUUCUCCCGUCAAAC-AGCACCU--GUUGCUGCUUGACCUUA-UAAAGGAGAUGGGGUUAGAUCAGCCUUAUC--AACC-AAAUGAUCCAU-UGGGCUUGGAAGAGCCC
CP000551.1/67862-67589       CUGUCAGAAUAUAAAUGUCCAA-------------------UUGGACUAGGUGAUCUCAACCGAUGUUUCGGACAGCGGUUCGAUUCCGCUCAACUCCACU---------------------------------AUUUGGGGUUGUAAUGGUUUCGACGGGGCAUAAGGAAGGUGACUGAAGCCGGCUCGGUUAGAGCAAA-AACACAAAUGCUAACAAAAUCGUUAGUUUCUCCCGUCAAAC-AGCACCA--GUUGCUGCUUGAUCC---AAAAGGAGAUGGGGUUAUAUCAGCCUUAUC--AACC-AAAUGAUACGA-GGAGUCUGGAAGGACUC
CT978603.1/322496-322207     CUGCCACAAUGAAGGAGUCCGGU------CCU--------UCCGGACUAGGUGACUCAAACCAGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUUCUCCCC-------------------------AUCGCGGGGCUGCAAUGGUUUCGACGGGGCAACAGGAGGGUGACUGAAACCUGCUCGGUAAGAGCAAA-CCCGUAACUGCGAACAACAUCGUUCGUUUCUCCCGUCAAGC-AGCCCCU--GUUGCUGCCUGACCCAAGUAAGGGAGAUGGGGUGAGGUCAGCCUUAUC--ACCC-AAUUGACCCAC-UGGGGCUGGAAGGCCCC
CT971583.1/1943082-1942797   CUGUCACAAUGGCAGUGUCCGGA------UCU--------UCCGGACUAGGUGAUCCACACCAGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCCCCU---------------------------CUCCGGGGCUGCAAUGGUUUCGACGGGGCAUGAGGAGGGUGACUGAAGCCUGCUCGGUGAGAGCAAA-CCCGUAACUGCGAACAACAUCGUUCGUUUCUCCCGUCAAGC-AGCCCCU--GUUGCUGCCUGACCCU--UAGGGGAGAUGGGGUGAAGUCAGCCUUAUC--ACCC-AAAUGACUCAU-GGGGGCUGGAAGGCCCC
AATZ01000001.1/849412-849122 CUGUCAGAAUGACAGGGUCCGGU------UU---------GCCGGACUAGGUGAUUCACACCAGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCAUCCCC------------------------CCUCUUGGGGCUGCAAUGGUUUCGACGGGACAUAAGGAGGGUGACUGAAGCCUGCUCGGUUAGAGCAAAUCUCGUAACUGCGAACAACAUCGUACGUUUCUCCCGUCAAGC-AGCCCCU--GUUGCUGCCUGACCCUUUUAAGGGAGAUGGGGUGAGGUCAGCCUUAUC--ACCC-AAAUGACUCGU-UGGGGCUGGAAGGCCCC
BX569689.1/342027-342314     CUGUCACAAUGACAGGGUCCGGU------UC---------ACCGGACUAGGUGAUCCACACCAGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCACCCUU------------------------CCACAAGGGGCUGCAAUGGUUUCGACGGGGCAUGAGGAGGGUGACUGAAGCCUGCUCGGUGAGAGCAAA-CCCGUAACUGCGAACAACAUCGUUCGUUUCUCCCGUCACGC-AGCCCCU--GUUGCUGCCUGACCCU--UAGGGGAGAUGGGGUGAAGUCAGCCUUAUC--ACCC-AAAUGACUCAU-GGGGGCUGGAAGGCCCC
CP000553.1/112771-112493     CUGUCAGAAUAUAUAGGUCUAUU------UUC-------UAAUGGACUAGGUGAUUCACACCAGUAUCUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAU----------------------------------AAAUGGGGCUGCAAUGGUUUCGACGGGGUAUCAGGAGAGUGACUGAAGCCUGCUCGGUCAGAGCAAA-ACCAUAACUGCUAACAACAUCGUUAGUUUCUCCCGUCAAAC-AGCCCCU--GUUGCUGCUUGAUCUUU-UA--GGAGAUGGGGUCAGGUCAUCCUUAUU--ACCC-AAUUGAUCCAC-GAGGCCUGCAAGGGCCU
AAUA01000001.1/737908-737622 CUGUCAGAAUGGCAAGGUCCGGU------UUC-------GGCCGGACUAGGUGAUCCACACCGGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCCCCU---------------------------UCCUGGGGCUGCAAUGGUUUCGACGGGGCAUAAGGAGGGUGACUGAAGCCUGCUCGGUAAGAGCAAA-CCCGUAACAGCGAACAACAUCGUUCGUUUCUCCCGUCAAGC-AGCCCCU--GUUGCUGCCUGACCCU--UAGGGGAGAUGGGGUGAGGUCAGCCUUAUC--ACCC-AAAUGACUCAU-GGGGCCUGGAAGGGCCC
AANO01000002.1/287125-286821 CUGUCACAAUGACAAGGUCCGUC------CUC-------GGGCGGACUAGGUGGCUCACACCGGUGCUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCACCCCGCUGCGG----------CGGCGGUGUCCGCGGGGCUGCAAUGGUUUCGACGGGGUAUGAGGAGGGUGACUGAAGCCUGCUCGGUAAGAGCAAA-CCCGUAACAGCGAACAACAUCGUUCGUUUCUCCCGUCAGAC-CGCCCCU--GUGGCUGCCUGACUCCU-AUAGGGAGAUGGGGU-AGGUCAGCCUUAUC--ACCC-AAAUGACCCAUGGGGGGCUGGAAGGCCCC
CP000878.1/65239-64946       CUGCAAAAAUAGAAAUGUCCAUU------CUC-------CAAUGGACUAGGUGAUCCACACCAGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUAACAAAUCA----------------------AUCUUAAGGGGCUGCAAUGGUUUCGACGUGACAACAGGAGGGUGACUGAAGCCUGCUCGGCAUGAGCAAA-CACAUAAACGCUAACAAAAUCGUUAGUUUCUCCCGUCAGAC-AGCACCU--GUUGCUGCCUGACCCUAUUAAGGGAGAUGGGGUUAGAUCAGCCUUAUC--ACUC-AAAUGAUCUAU-GGGACCUGGAAAGGUCC
BX548175.1/1677929-1677634   CUGUCAGAAUGGAAGUGUCCCCC------UUU-------UGGCGGACUAGGUGAUCCACACCAGUGUCUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUUCCUCUUUUA--------------------GGUGUCUUGGGGCUGCAAUGGUUUCGACGGGGUAUGAGGAGGGUGACUGAAGCCUGCUCGGUAAGAGCAAA-UCCGUAACUGCGAACAACAUCGUUCGUUUCUCCCGUCAGCC-UGCCCUC--GUGGCUGCCUGACCCUAAUAAGGGAGAUGGGGUGAGGUCAGCCUUAUC--ACCC-AAAUGACCCAU-GGGGGCUGCGAGGCCCC
BX548174.1/56618-56342       CUGCCAGAAUAUAAAUGUCCAA-------------------UUGGACUAGGUGAUCUCAACCGAUGUUUCGGACAGCGGUUCGAUUCCGCUCAACUCCAUUUUC------------------------------AUUUGGGGUUGUAAUGGUUUCGACGGGGCGUAAGGAAGAUGACUGAAGCCUGCUCGGUUAGAGCAAA-AACACAAACGCUAACAAAAUCGUUAGUUUCUCCCGUCAAAC-AGCACCA--GUUGCUGCUUGAUCU---CAAAGGAGAUGGGGUGAUAUCAGCCUUAUC--AACC-AAAUGAUCCAA-GGAGCCUGGAAGGGCUC
ABSE01000018.1/180569-180851 CUGCCACAAUGACGGAGUCCGGU------UUC-------GGCCGGACUAGGUGGCUCACACCAGUGUUUCGGACAGCGGUUCGAUUCCGCUCAGCUCCAUU---------------------------------UCACGGGGCUGCAAUGGUUUCGACGGGGCAUGAGGAGGGUGACUGAAGCCUGCUCGGUCAGAGCAAA-CCCGUAACAGCGAACAACAUCGUUCGUUUCUCCCGUCAAGC-UGCCCCC--GUGGCCGCCUGACAUCUCUAAGGGAGAUGGGGUGAGGUCAGCCUUAUC--ACCC-AAAUGACCGCU-UGGGGGUGGAAGCCCCC
#=GC SS_cons                 ::::::::::::::::<<<<<<<......___......._>>>>>>>,,(((-((((---((-((((((((,,,<<<<<_______>>>>><<<<<<<_________...........................____>>>>>>>,,,,,,,,,,,,))))))))--))-))))-))),,,,,,<<<<<_____>>>>>,,.,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<.<<<<___..__>>>>->>>>>>,,,,.,,,,<<-<<<<<<<<_______>>>>>>>>..-->>.,,,,,,,,,,,.,<<<<<<____>>>>>>
#=GC RF                      cUGucAgaAUaaaaauGuCcggc......uUu.......agccgGaCUAgGuGacccacACcacuGuccCGGACAGcGGUUCGAUUCCgCUCAgCuCCAUUccuccu...........................ucuuGGgGcUGcAAUGGUUUCGACGgggCagaAgGAggguGaCuGAAGCCuGCUCGGUuAGAGCaAA.aacguAAcuGCuAACAAcAUCGUuaGUUUCUCCcgcccagc.cGCcCcu..GUgGCgGccugagccuu.UAAaGGAgauggGGcgAggUcAgCCuuauc..AcCC.AAAUGAccCAu.gGGgcccggAAgggcCC
//
# STOCKHOLM 1.0

#=GF AC   RF01852
#=GF ID   tRNA-Sec
#=GF DE   Selenocysteine transfer RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Gardner PP
#=GF SS   Published; PMID:10682860
#=GF GA   47.00
#=GF TC   47.00
#=GF NC   46.90
#=GF TP   Gene; tRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.39 -Z 549862.597050 CM SEQDB
#=GF CL   CL00001
#=GF DR   SO; 0005857; selenocysteinyl_tRNA;
#=GF DR   GO; 0030533; triplet codon-amino acid adaptor activity;
#=GF DR   URL; http://gtrnadb.ucsc.edu/;
#=GF DR   URL; http://trnadb.bioinf.uni-leipzig.de/;
#=GF RN   [1]
#=GF RM   10682860
#=GF RT   Eukaryotic selenocysteine tRNA has the 9/4 secondary structure.
#=GF RA   Mizutani T, Goto C
#=GF RL   FEBS Lett. 2000;466:359-362.
#=GF RN   [2]
#=GF RM   9023104
#=GF RT   tRNAscan-SE: a program for improved detection of transfer RNA genes in
#=GF RT   genomic sequence.
#=GF RA   Lowe TM, Eddy SR
#=GF RL   Nucleic Acids Res 1997;25:955-964.
#=GF WK   Transfer_RNA
#=GF SQ   109


CP000112.1/1531804-1531715 GGAAGCGUA---UC--GU-CA-C-CGGU-GUGGCGCCCGGUCUUCAAAACCG-G--U--GGACG-GCUGAGA-----GGUCGUCG--GUAGGUUCGACUCCUA---UACGCUUCC----
X75790.1/378-471           GGAAGCGUA---UC--GU-CA-C-CGGU-GUGGCGCCCGGUCUUCAAAACCG-G--U--GGAAG-GUCGAGA-----GGUCUUCG--GUAGGUUCGACUCCUA---UACGCUUCCGCCA
AM180252.1/236707-236618   GGAAGCGUA---UU--GC-CA-C-CGGU-GUGGUACUUGGUCUUCAAAACCA-G--U--GUCAG-GCUGAGA-----GGUCUGAG--GUAGGUUCGACUCCUA---UACGCUUCC----
CP000527.1/2088048-2088137 GGAAGCGUU---UU--CU-AU-C-CGGU-GAUAGGCCCGGUCUUCAAAACCG-G--U--GGUAG-GUCGAGA-----GGUCUACG--GUAGGUUCGACUCCUA---UACGCUUCC----
AE017285.1/1369596-1369507 GGAAGCGUU---UU--CU-AU-C-CGGU-GAUAGGCCCGGUCUUCAAAACCG-G--U--GGUAG-GUCGAGA-----GGUCUACG--GUAGGUUCGACUCCUA---UACGCUUCC----
CP000473.1/4117336-4117425 GGAAGCGUA---UU--UC-AU-C-CGGU-GGUGGGCGUGGUCUUCAAAACCA-C--U--GAGCG-GCCGCAA-----AGCCGCUG--AUCGGUUCGACUCCGA---UACGCUUCC----
CP000859.1/2690342-2690435 GGAAGUGCG---CA--GC-GUUC-UGGU-GAUGCUCCCGGACUUCAAAUCCG-G--U--GUGGG-GCGCUAAC--ACCGUCCCGG--GUGGGUUCGAUUCCCA---UGCACUUCC----
CP000252.1/931834-931927   GGAAGUGCCA--AG--GU-CA-C-UGGU-GGGCCUCCCGGACUUCAAAUCCG-G--U--GUGGG-GCGCUAAA--ACCGUCCCAG--GUGGGUUCGAUUCCCA---UGCACUUCC----
CP000478.1/1085869-1085963 GGAAGCGCCA--AG--CU-CA-C-UGGU-GGGGCUCCCGGACUUCAAAUCCG-G--U--GCGGG-GUAGUGAAG-GCUGUCCCGG--GUGGGUUCGAUUCCCA---UGCGCUUCC----
CP001390.1/1963878-1963785 GGAAGCACGA--CC--GU-CG-C-UGGU-GGGCGGCCCGGUCUUCAAAACCG-G--U--GAGGG-GGAUGAGA--AAUCUCCCUG--GUGGGUUCGAUUCCCA---UGUGCUUCC----
CP000142.2/981495-981588   GGAAGCGCG---UC--GG-UCGC-UGGU-GGGCCGCCCGGUCUUCAAAACCG-G--U--GUGGG-GGGUGAGA--AACUUCCCAG--GUGGGUUCGAUUCCCA---UGCGCUUCC----
AE017180.1/909828-909735   GGAGGUACG---UC--GG-UCGC-UGGU-GGGCCGCCCGGUCUUCAAAACCG-G--U--GUGGG-GGUUGAGA--AAACUCCCAG--GUGGGUUCGAUUCCCA---UGUACCUCC----
CP000698.1/4043694-4043787 GGAAGCACG---UC--GG-UCGC-UGGU-GGGCCGCCCGGUCUUCAAAACCG-G-UG--GGGGG-GAUGAGAA---AUCUCCCCG--GUGGGUUCGAUUCCCA---UGUGCUUCC----
AE017143.1/1662251-1662341 GGAAGUGAG---UC--GU-CU-C-CGGU-GAGACGGCAGGAUUUCAAAUCCU-G--U--UAAGG-ACGCCAG-----CGUGCUUGG-GUGGGUUCGACUCCCA---UUCACUUCC----
AE004439.1/1994469-1994558 GGAGGAGCG---UC--GU-UU-C-CGGU-GAAGCGGCAGGACUUCAAAUCCU-G--U--UGAGG-UUGCCAG-----CAAUCUCGG-GUGGGUUCGACUCCCA---UUCUCCUC-----
AE016827.1/2264473-2264383 GGAAGGUCG---UC--GU-GU-C-CGGU-GAUGCGGCAGGACUUCAAAUCCU-G--U--UAGGG-CUGCCAG-----CAGUCCUGG-GUGGGUUCGACUCCCA---UGACCUUCC----
CP000851.1/552724-552634   GGAAGAACG---UC--GU-UU-C-CGGU-GAAACGUCUGGAUUUCAAAUCCA-G--G--UGGGG-CUGCCAG-----CAGUCCCGG-GUAGGUUCAACUCCUA---UGUUCUUCC----
AE014299.1/117643-117553   GGAAGAACG---UC--GU-CU-C-CGGU-GAGGCGUCCGGAUUUCAAAUCCG-G--G--UAGGG-CUGCCAG-----CAGUCCUGG-GUAGGUUCGACUCCUA---UGUUCUUCC----
CP000653.1/86005-85915     GGAAGAUCG---UC--AU-CU-C-CGGU-GAGGUGGCUGGAUUUCAAAUCCA-G--U--UGGGG-ACGCCAG-----CGUUCCCGG-GCAGGUUCGACUCCUG---UGAUCUUCC----
X17419.1/71-161            GGAAGAUCG---UC--GU-CU-C-CGGU-GAGGCGGCUGGACUUCAAAUCCA-G--U--UGGGG-CCGCCAG-----CGGUCCCGG-GCAGGUUCGACUCCUG---UGAUCUUCC----
X13994.1/39-129            GGAAGAUCG---UC--GU-CU-C-CGGU-GAGGCGGCUGGACUUCAAAUCCA-G--U--UGGGG-CCGCCAG-----CGGUCCCGG-GCAGGUUCGACUCCUG---UGAUCUUCC----
Y00299.1/1-91              GGAAGAUCG---UC--GU-CU-C-CGGU-GAGGCGGCUGGACUUCAAAUCCA-G--U--UGGGG-CCGCCAG-----CGGUCCCGG-GCAGGUUCGACUCCUG---UGAUCUUCC----
X15993.1/1-91              GGAAGAUCG---UC--GU-CU-C-CGGU-GAGGCGGCUGGACUUCAAAUCCA-G--U--UGGGG-CCGCCAG-----CGGUCCCGG-GCAGGUUCGACUCCUG---UGAUCUUCC----
CP000783.1/4104750-4104660 GGAAGAUCG---UC--GU-CU-C-CGGU-GAGGCGGCUGGACUUCAAAUCCA-G--U--UGGGG-CCGCCAG-----CGGUCCCGG-GCAGGUUCGACUCCUG---UGAUCUUCC----
AM286415.1/4504272-4504182 GGAAGAUCA---UC--GU-CC-C-CGGU-GGGGCGGCUGGACUUCAAAUCCA-G-AU--GGGGC--CGCCAG-----CG-GCCCUUGGCAGGUUCGACUCCUG---UGAUCUUCC----
AE009952.1/4494849-4494759 GGAAGAUCA---UC--GU-CC-C-CGGU-GGGGCGGCUGGACUUCAAAUCCA-G--A--UGGGG-CCGCCAG-----CGGUCCCUG-GCAGGUUCGACUCCUG---UGAUCUUCC----
BX571859.1/132063-132153   GGAAGAUCA---UC--GU-CC-C-CGGU-GGGGCGGCUGGACUUCAAAUCCA-G--A--UGGGG-CCGCCAG-----CGGUCUCUG-GCAGGUUCGACUCCUG---UGAUCUUCC----
S68104.1/22-108            GAUCG-------UC--GU-CU-C-CGGU-GAGGCGGCUGGACUUCAAAUCCA-G--U--UGGGG-CCGCCAG-----CGGUCCCGG-GCAGGUUCGACUCCUG-------UGAUCGCCA
CP001026.1/883433-883524   GGAAGGCAU---UC--GU-AU-C-CGGU-GGUACGGCUGGACUUCAAAUCCA-G--U--UGGGG-GUGUCAG----ACACUCCCGG-GUCGGUUCGACUCCGG---CUGCCUUCC----
CP000441.1/181325-181416   GGAAGGCAU---UC--GU-AU-C-CGGU-GGUACGGCUGGACUUCAAAUCCA-G--U--UGGGG-GUGUCAG----ACACUCCCGG-GUCGGUUCGACUCCGG---CUGCCUUCC----
CP000089.1/1945019-1944928 GGAAGAG--A--UC--GUUCC-C-CGGU-GGGACGGCCGGUCUUCAAAACCG-G--C--AGGGC-CUGUCAA----ACAGGCUUGG-GUAGGUUCGACUCCUG---CUCUCUUCC----
CP000744.1/5687422-5687332 GGAAGGC-AA--UC--AC-GC-C-CGGU-GGCGUGGCCGGACUUCAAAUCCG-G--U--GGGGGACGGCAG------CCGUUCCUGGGUGGGUUCGACUCCCAC--U-GCCUUC-----
CT573326.1/585849-585940   GGAAGGCA-A--UC--GC-GC-C-CGGU-GGCGCGGCCGGGCUUCAAACCCG-G--U--UGGGG-ACGGCAG----CCGUUCCCGG-GCAGGUUCGACUCCCG---CUGCCUUCC----
CP000712.1/599150-599241   GGAAGGCA-A--UC--GC-GC-C-CGGU-GGCGCGGCCGGGCUUCAAACCCG-G--U--UGGGG-ACGGCAG----CCGUUCCCGG-GCAGGUUCGACUCCCG---CUGCCUUCC----
CP000438.1/5658498-5658407 GGAAGGCA-A--UC--AC-GC-C-CGGU-GGCGUGGCCGGACUUCAAAUCCG-G--U--GGGGG-ACGGCAG----CCGUUCCUGG-GUGGGUUCGACUCCCA---CUGCCUUCC----
AE004091.2/5387858-5387767 GGAAGGCA-A--UC--AC-GC-C-CGGU-GGCGUGGCCGGACUUCAAAUCCG-G--U--GGGGG-ACGGCAG----CCGUUCCUGG-GUGGGUUCGACUCCCA---CUGCCUUCC----
AP009384.1/1285115-1285024 GGAGGAGAA---GC--GU-CC-C-UGGU-GGGGCGUCCGGACUUCAAAUCCG-G-GA--GGGGC-CGCGAG------CCGGUCCUUGGUGGGUUCGACUCCCA---CUCUCUUCC----
CP000781.1/736404-736313   GGAAGAGAA---GC--GU-CC-C-UGGU-GGGGCGUCCGGACUUCAAAUCCG-G-GA--GGGGC-CGCGAG------CCGGUCCUUGGUGGGUUCGACUCCCA---CUCUCUUCC----
CP000489.1/2841628-2841537 GGAAGAGAA---GC--GU-CC-C-CGGU-GGGGCGGCCGGACUUCAAAUCCG-G--U--UGGGG-CAGUGAG----CCUGUCCCGG-GUGGGUUCGACUCCCA---CUCUCUUCC----
CP000759.1/151860-151951   GGAAGGG-AU--GC--AU-GC-C-CGGU-GGCAUGUCCGGACUUCAAAUCCG-G--G--AGGGG-CCGAUAG----ACGGUCUUUG-GUGGGUUCGACUCCCA---UUCUCUUCC----
AE006469.1/15716-15807     GGAAGAGAA---UC--AU-GC-C-CGGU-GGCAUGUCCGGACUUCAAAUCCG-G--G--UGGGG-CAGCGAG----GCUGCCUUGG-GUGGGUUCGACUCCCA---UUCUCUUCC----
CP000462.1/2791529-2791616 GGAA-GCUGA--UG--GG-GU-C-UGGU-GGCCUCCUCGGUCUUCAAAACCG-A--U--GAGAG-CCGAGA------AGGCUUUG--GCAGGUUCGAUUCCUG---CCUC-UUCC----
CR378679.1/301124-301037   GGAAG-UGGA--UG--GG-GU-C-UGGU-GGCCCUCCCGGUCUUCAAAACCG-A--C--GUGAG-CUGAAU------AGGCUUUG--GCAGGUUCGAUUCCUG---CUC-CUUCC----
AE017226.1/1090480-1090567 GGAAG-CAGA--UG--GG-GU-C-UGGU-GGCUCCCGCGGUCUUCAAAACCG-U--A--GGUUG-CAUAAU------UCGCAAUG--GCAGGUUCGAUUCCUG---CCU-CUUCC----
AF486635.1/7426-7518       G-GAAGAUUA---G--CGUAU-C-UGGU-GAUCGCCACUGACUUCAAAUCAG-A--UGAA-AGG-AUAGUUGA--CUAUUCUU-UG-GGGAGUUCGAUUCUCU---CAUCUUCU-----
CP000644.1/1890799-1890712 G-GAAGUUGA--UG--GG-GU-C-UGGU-GGCCUCCUCGGUCUUCAAAACCG-A-UG--UGAGC-CGAGA--------AGGCUUUG-GCAGGUUCGAUUCCUG---CCUCUUC-C----
CP000361.1/1529552-1529458 GGGAGGUUAG--UG--UA-C--C-UGGU-GGGCACCACAGGCUUCAACCCUGAU--U--GACGG-UUUUGAUGA-CAACGCCGUG--GGAGGUUCGAUUCCUU---CACCUUCUC----
CP000776.1/280492-280400   GAGAGU---A--AG--UC-GUGC-CGGU-GGCGAUCGCGGACUUCAAAUCCG-A--U--GAAAG-GGCGGUUGA-CCGUUCUUUG--GGGGGUUCGAUUCCCUC-----ACUCUCUC--
ABGA01167771.1/2921-2836   GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUG----AAGG
AL031595.4/5352-5437       GCUCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGU---------GACAGA---GUGGUUCAAUUCCAC---CUUUGUAGG----
DQ239475.1/307-392         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGC----
DQ093101.1/322-407         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGC----
DQ093098.1/316-401         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGC----
DQ239477.1/307-392         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGC----
DQ239476.1/307-392         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGC----
AY609110.1/307-396         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGAAG
AY609112.1/313-402         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGACG
X56108.1/461-550           GCCCGGAUGA--CC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGAGG
DQ093102.1/249-338         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGAGU
DQ093097.1/316-405         GCCCGAAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGACU
AY609123.1/309-398         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGACU
DQ093099.1/316-405         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGACA
AY609094.1/307-396         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGN---GUGGUUCAAUUCCAC---CUUUCGGGCGACA
DQ093100.1/258-347         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGGUA
DQ239472.1/307-396         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGGCA
AY609101.1/307-396         GCCCGRAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGGCA
AY609098.1/307-396         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGGCR
AY609120.1/306-395         GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGGCG
L22019.1/155-240           GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-UUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGC----
L34835.1/153-242           GCCCGGAUGA--UC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-UUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGGGA
AF133045.1/240-329         GCCCGGAUGA--UC--UC-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-UUAGC---------GACAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGGGA
M34507.1/553-638           GCCCGG--AUGACC--CU-CA-G-UGGU-CUGGGGUGCAGGCUUCAAACCUG-U--A--GCUGU-CUAGC---------GACAGA---GUGGUUCAAUUCCAC-CUU--UCGGGC----
AF135236.1/327-412         GCCCGGAUGA--AC--CU-CG-G-UGGU-CCGGGGUGCAGGCUUCAAACCUG-U--A--GCUGC-CUAGC---------GGCAGA---GUGGUUCAAUUCCAC---CUUUCGGGC----
AF135237.1/607-696         GCCCGGAUGA--AC--CU-CG-G-UGGU-CCGGGGUGCAGGCUUCAAACCUG-U--A--GCUGC-CUAGC---------GGCAGA---GUGGUUCAAUUCCAC---CUUUCGGGCGACU
M34509.1/93-182            GCCCCACUGA--AC--UU-CG-G-UGGU-CCGGGGUGCGGACUUCAAAUCCG-U--A--GUCGA-UUUGC---------GUCGAA---GUGGUUCGAUUCCAC---CUGGGGGGCGAAU
AY572241.1/1-90            GCCCGGAUGA--CC--UC-CU-C-UGGU-GAGGGGUGCAGGCUUCAAACCUG-U--A--GUGGU-CGCAA---------GGCCAA---GCUGUUCAAUUCAGC---CUUCUGGGCGCCA
DQ508143.1/1-88            GCCGCGAUGA--GC--UC-AG-C-UGGU-GCUGGGUGCGGGCUUCAAACCCG-U--A--GGUGA-GUUGC--------UCUCACA---GCCGUUCGAUUCGGC---CUUCGUGGCG---
DQ508819.1/1-88            GCCACGAUGA--GC--UC-AG-C-UGGU-GCUGGGUGCGGGCUUCAAACCCG-U--A--GGCGA-GUUGG--------ACUCGCA---GCCGUUCGAUUCGGC---CUUUGUGGUG---
AY268554.1/1-90            GCCGCUGUGA--CC--UU-GG-C-GGGU-GCUGAGUGCGGUCUUCAAAACCG-U--A--GAGGC-CGGGA---------GGCCUA---GUGGUUCAUUUCCAC---CUCGGCGGCGCCA
AE009439.1/188240-188326   GCCGCCGC-----CACCG-GG-G-UGGU-CCCCGGGCCGGACUUCAGAUCCG-G--C--GCGCC-CCGAGU-------GGGGCGC---GGGGUUCAAUUCCCC----GCGGCGGCC---
L77117.1/111768-111852     --CGCGGGGU--AC--CG-GG-CUUGGUAGCCCGGGGCGGACUUCAGAUCCG-U--C--GAGGG-CGAGA---------GCCCUC---GGGGUUCGAUUCCCC---CCCUGCGC-----
AL845295.21/63402-63482    GUAGUCGUG----G--CC-GA-G-UGGU-UAAGGCGAUGGACUUCAAAUCCA-U--U--G--GG-GUCUC---------CCCGCG---CAGGUUUGAAUCCUG---C-CGACUAC----
AM420293.1/3920342-3920251 GGAGGCGUAA--GG--GC-UC-C-UGGU-GGACCCCGCGGUCUUCAAAACCG-A--C--GUGGC-CGGGCAU----CUCGGUCAG--GCGGGUUCGAUUCCCG---UCCGCCUCC----
CP000384.1/5501874-5501964 GGAGGCGUA---UC--CG-GU-C-UGGU-GACCGGCGCGAUCUUCAAAAUCG-U-CG--AACGG-CAGGAU------CUGUCGUUG-GCGGGUUCGAUUCCCG---UCCGCCUCC----
CP000479.1/413640-413550   GGAGGCGUG---UC--CG-GU-C-UGGU-GACCGGCGCGGUCUUCAAAACCG-U--G--GAACG-GCAGACG----CUGCCGCUG--GCGGGUUCGAUUCCCG---UCCGCCUCC----
AE016958.1/391186-391096   GGAGGCGUG---UC--CG-GU-C-UGGU-GACCGGCGCGGUCUUCAAAACCG-U--G--GAACG-GCAGACG----CUGCCGCUG--GCGGGUUCGAUUCCCG---UCCGCCUCC----
CP000141.1/1070391-1070299 GGGAGUG-AC--UG--GG-UC-C-UGGU-GGGCCCCGCGGGCUUCAAACCCG-U-UG--U-UGG-GCGGUAAA--ACCGUCCA-UG-GUAGGUUCGAUUCCUA---UUCACUCCC----
AP008230.1/3504173-3504081 GGGAAUG-GA--UG--GA-UC-C-CGGU-GGGUUCCGCGGACUUCAAAUCCG-U--U--GUCGG-GUGGGUGA--UCCGGCCGAG--GUAGGUUCGACUCCUA---CACAUUCCC----
AP008230.1/634648-634740   GGGGACG-AA--UG--GA-UU-C-CGGU-GGAUCCUGCGGACUUCAAAUCCG-U--U--AUCGG-GUGGGUGA--UCCGGCCGAG--GUAGGUUCGACUCCUA---CACGUUCCC----
CP000724.1/2399957-2400049 GGGGGUA-GA--UG--GG-UU-C-UGGU-GUGCCCUCUGGUCUUCAAAACCA-G--C--GCGAG-GGGUUAGU--AGCCUCUUGG--GUGGGUUCGAUUCCCA---CGUACUCCC----
CP000853.1/1831799-1831707 GGGAGUA-GA--UG--GG-UG-C-UGGU-GUGCCCUAUGGUCUUCAAAACCA-U--U--GUGAG-GGGUUAGU--AGCUUCUUAG--GUGGGUUCGAUUCCCA---CGUACUCCC----
AP008971.1/1261179-1261271 GGGAAUU-GA--UG--GG-UG-C-UGGU-GUGCCCUGCGGUCUUCAAAACCG-U--C--UCAGG-UAGUUAGG--AGCUGCCCGG--GUAGGUUCGAUUCCUA---CCAUUUCCC----
CP000930.2/1058233-1058140 GGGGGUG-AA--UG--AG-GA-C-UGGU-GUCCUCCCUGGGCUUCAAACCCA-CGUG--GCGCG-CGGCCAAC--CCGGGCGCGG---UAGGUUCGAUUCCUA---CCCACUCCC----
Z26950.1/333-432           GGGGGUG-GA--UC--GG-GC-C-UGGU-GGCUUGCCUGGACUUCAAAUCCA-GUUG--GCGCG-CGGGCUAACCCCGGGCGCGG---UGGGUUCGAUUCCCA---CACACUCCCGCCA
AP009389.1/993932-993839   GGGAGUG-GA--UG--GU-GC-C-UGGU-GGUGCUCCUGGUCUUCAAAACCA-GUCG--UCGGG-CAGCGCU----CCUGUCCGUG-GUGGGUUCGAUUCCCA---CACACUCCC----
AP006840.1/2784369-2784275 GGGAGUA-GA--UC--GG-GU-CCUGGU-GGCCCGCACGGUCUUCAAAACCG-C-UU--GAGCC-GUAGUGAU--CCUGCGGCUG--GUGGGUUCGAUUCCCA---CAUACUCCC----
CP000939.1/3225886-3225796 -GGAGUA-GA--UA--GG-UG-C-UGGU-GUGCCUGCCGGUCUUCAAAACCG-AGUU--GUC----GUGCUAAGACCAC---GAUGGGUGGGUUCGAUUCCCA---CAUAUUCC-----
CP000727.1/3037863-3037773 -GGAGUA-GA--UA--GG-UG-C-UGGU-GUGCCUGCCGGUCUUCAAAACCG-AGUU--GUC----GUGCUAAGACCAC---GAUGGGUGGGUUCGAUUCCCA---CAUAUUCC-----
CP000728.1/3208409-3208319 -GGAGUA-GA--UA--GG-UG-C-UGGU-GUGCCUGCCGGUCUUCAAAACCG-AGUU--GUC----GUGCUAAGACCAC---GAUGGGUGGGUUCGAUUCCCA---CAUAUUCC-----
CP000386.1/2002699-2002611 -GGAAUGCG----U--GG-GC-C-UGGU-GGCCCGGCCGGUCUUCAAAACCG-G--U--UUGCG-GCCGCGGA--GCGGCCGUGG---GUGGUUCGAUUCCCC---CGCAUUCC-----
CP001364.1/3018605-3018697 GAGAGCGCA---UG--UG-GC-C-CGGU-GGCUGUCGCGGUCUUCAAAACCG-UUGG--GCGGA-GUGACGAA---CUACGCCGG---UGGGUUCGACUCCCA---CGCGCUCUC----
CP001001.1/1556357-1556269 GGAGGCG-AA--CG--GG-GU-C-UGGU-GGCCCUCCUGGUCUUCAAAACCA-G--C--GGUAC-GCCAAC------AGCGUACG--GUGGGUUCGAUUCCCA---UCCGCUUCC----
CP000943.1/3239300-3239388 GGAGGCG-AU--CG--GG-GU-C-UGGU-GGCCCUCCUGGUCUUCAAAACCA-G--C--GGCAC-GCGAAC------AGCGUGCG--GUGGGUUCGAUUCCCA---UCCGCCUCC----
CP000158.1/2615764-2615674 GGAGGUG-AC--UG--GA-GU-C-UGGU-GGCUUCCCUGGUCUUCAAAACUA-U--G--GACAC-GCCGGCA----AGGCGUGUG--GUGGGUUCGAUUCCCA---UCCACCUCC----
CR522870.1/363837-363930   GGAAGUGGA---CG--GA-GCAC-UGGU-GGCUCCCCCGGAUUUCAAAUCCG-G--U--GUAAC-GGGUUAAU--AGCUCGUUAG--GUGGGUUCGAUUCCCA---UGCACUUCC----
CP000769.1/2231090-2230996 GGCAGAGCGU--CC--UA-GG-C-UGGU-GCCGGGCCCGGUCUUCAAAACCG-G--U--GGAUG-GUGCUGAGA-GGCGCUGUUG--GGGGGUUCGAUUCCCC---UGCUCUGCC----
CP000251.1/2130853-2130947 GGCAGAGCGU--CC--UA-GG-C-UGGU-GCCGGGCCCGGUCUUCAAAACCG-G--U--GGAUG-GUGCUGAGA-GGCGCUGUCG--GAGGGUUCGAUUCCCU---UGCUCUGCC----
CP000113.1/5535546-5535640 GGUAGGGCUU--CC--GG-AC-C-UGGU-GGCCGGCCCGGUCUUCAAAACCG-G--U--GAGGG-GCGCCGAGA-GGCGUCCCUG--GCGAGUUCGAUUCUCG---UGCCCUACC----
AE000657.1/727371-727465   GGGAGAGGUU--GG--CC-GG-C-UGGU-GCCGCCCCGGGACUUCAAAUCCC-G--U--GGGAG-GUCCCGCAA-GGGAGCUCCG--GAGGGUUCGAUUCCCU---CCCUCUCCC----
#=GC SS_cons               (((((((((,..,<..<<.<<.<.____.>>>>>><<<<<<_______>>>>.>..>..,<<<<.<______.....__>>>>>,..,<<<<_______>>>>...)))))))))....
#=GC RF                    Gggggggcga..uc..gg.cc.c.UGGU.gggccguccGGgCUUCAAAcCCg.g..a..Ggggg.cuagcaa.....cggccccg..GggGGUUCGAUUCCcc...cgccccccC....
//
# STOCKHOLM 1.0

#=GF AC   RF01853
#=GF ID   mtDNA_ssA
#=GF DE   Mitochondrial DNA control region secondary structure A
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Gardner PP;
#=GF SS   Published; PMID:18845547
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   18845547
#=GF RT   Evidence for variable selective pressures at a large secondary structure
#=GF RT   of the human mitochondrial DNA control region.
#=GF RA   Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC,
#=GF RA   Amorim A
#=GF RL   Mol Biol Evol. 2008;25:2759-2770.
#=GF WK   MtDNA_control_region
#=GF SQ   53


AY966398.1/1-104           --CUU-UCAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCC-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUGUACG
AY595133.1/1-106           UUCUU-UCAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGUU-AUGUAUUUCGUACAUUA-CUGCUAGCCACCAUGAAUAUUGUACA
AY005559.1/5-110           UUCUU-UCAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-NUUACCCAUCAACA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUGCACG
DQ145833.1/1-106           UUCUU-UCAUGGGGAAGC-AG--A---UUUGGGUGCC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCU-AUGUAUCUCGUACAUUA-CUGCCAGCCACCAUGAAUAUCGUACG
AY957299.1/18-123          GUUCU-UUAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUGUACG
AY210520.1/2-107           UUCUU-KSRUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUGUACG
AY398125.1/1-106           UUCUU-UCAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCU-AUGUACUUCGUACAUUA-UUGCCAGUCACCAUGAAUAUUGUACG
AF392313.1/24-129          UUCUU-UCAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGNCAGCCACCAUGAUUAUUGUNCG
AF011222.1/2-107           UUCUU-UCAUGGGGGAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAGCA-AC--CGCU-AUGUAUCUCGUACAUUA-CUGUUAGUUACCAUGAAUAUUGUACA
D38113.1/15442-15546       UUCUU-UCAUGGGGAAGC-AA--A---UUUAGGUACC-ACC--UAAGUA---CUGG-CUCAUUCAUUA-CA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUCGUACA
AM392418.1/441-546         UUCUU-UCAUGGGGAGGC-AA--A---UUUGGGUACC-ACC--CAAGUA---UUGG-CUAACCCAUCAAUA-AU--UAUC-AUGUAUGUCGUGCAUUC-CUGCCAGACACCAUGAAUAAUGCACA
U84319.1/1-105             UUCUU-UCAUGGGGAAGC-AA--A---UUUAAGUACC-ACC--UAAGUA---UUGG-CUUAUUCAUUA-CA-AC--CACU-AUGUAUUUCGUACAUUA-CUGCUAGCCACCAUGAAUAUUGUACA
AJ812285.1/1-106           UUCUU-UCAUGGGGAGAC-AA--A---UUUGGGUGCC-ACC--CAAGUA---UUAG-CUAACCCACCAACA-AU--UGUC-AUGUAUAUCGUGCAUUA-CUGCUAGCCACCAUGAAUAAUAUACA
AF240457.1/17-122          UUCUU-UCAUGGGGAGAC-AA--A---UUUGGGUACC-ACC--CAAGUA---UUAG-CUAACCCACCAAUA-AU--UGUU-AUGUAUGUCGUGCAUUA-CUGCCAGUCACCAUGAAUAAUAUACA
AF089820.1/1-106           UUCUU-UCAUGGGGAGAC-GA--A---UUUGGGUGCC-ACC--CAAGUA---UUAG-UUAACCCACCAAUA-AU--UGUC-AUGUAUGUCGUGCAUUA-CUGCCAGCCACCAUGAAUAAUGUACA
AJ586555.1/1-105           UUCUU-UCAUGGGGAAGC-AA--A---UUUAAGUGCC-ACC--CAAGUA---UUGG-CUCAUUCACUA-UA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUAUAUA
DQ367568.1/10-114          UUCUU-UCAUGGGGAGGC-AA--G---UUUAAGUACC-ACC--UAAGUA---UUAG-CCUAUUCAUUA-CA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUCGUACA
AY126678.1/1-101           ----U-UCAUGGGGAAGC-AA--A---UUUAAGUACC-ACC--UAAGUA---UUAG-CUUAUUCAUUA-CA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUGUACA
AY079509.1/1-106           UUCUU-UCAUGGGGAGAC-AA--A---UUUGGGUACC-ACC--CAAGUA---UUAG-CUAACCCAUCAAUA-AU--UAUC-AUGUAUAUCGUGCAUCA-CUGCCAGACACCAUGAAUAAUGUACG
AADA01019444.1/1181-1288   UAUUU-UCAUGAGGAGGC-AA--U---UUUGGGUACU-ACC--CAAGUA---UCGA-CCCACCCCCCUACG-ACAAUUCC-AUGUAUAUCGUGCAUUA-CUGCUAGCCACCAUGAAUAUUACAUA
D38115.1/15473-15575       UUCUU-UCAUGGGGGAUC-AG--A---UUUGGGUACC-ACC--CCAGUA--------CCGACCCAUUUCCA-GC--GGCCUAUGUAUUUCGUACAUUC-CUGCCAGCCAACAUGAAUAUCACCCA
X97707.1/15484-15586       UUCUU-UCAUGGGGGACC-AG--A---UUUGGGUGCC-ACC--CCAGUA--------CUGACCCAUUUCUA-AC--GGCCUAUGUAUUUCGUACAUUC-CUGCUAGCCAACAUGAAUAUCACCCA
D38114.1/15447-15549       UUCUU-UCAUGGGGAGAC-AA--A---UUUGGGUACU-ACC----AGUA---UUAG-CUAACCCA-UCAUA-AU--UAUC-AUGUAUGUCGUGCAUUA-CUGCCAGACACCAUGAAUAAUGUACA
AF338873.1/498-602         UAUUC-UCAUGUGGAAGC-UG--U---UUUGAGUACA-ACC--CCAGUA---UUAA-CCUGUUCUUCCACA-AC--C-CU-AUGUACUUCGUACAUUA-CUGCUAGCCCCCAUGAAUAUCGUACA
EF363489.1/1-105           UAUUC-UCAUGUGGAGGC-UG--U---UUUGAGUACA-ACC--CCAGUA---UUAA-CCCGUUCUCUCACA-AC--U-CU-AUGUACUUCGUACAUUA-CUGCCAGUCCCCAUGAAUAUUGUACA
AANU01037963.1/1241-1138   GUAUU-CUAUG-GGGUGCAAG--C---UUUAAGUGCA-ACU--UAAGUA---CUAA-UUUAUUUAUCAG---AC--CCUU-AUGUAAUUUGUGCAUUA-CUGCUAGCCAACAUGAAUGUUAUAUA
AF311725.1/1-104           UAUUC-UCGUGUGGAAGU-AA--U---UUUGGGUACA-ACC--CCAGUA---UCGA-UCUAUCCC-CUAUA-AU--UUU--AUGUACUUCGUACAUUA-CUGCUAGCCCCCAUGGAUAUUGUACA
AY661547.1/79-183          GUAUU-CUAUG-GGGUGCAAG--C---UUUAAAUGCA-ACU--UAAGUA---CUAA-UUUAUU--UUAGCACAC--CCUU-AUGUAAAUCGUGCAUUA-CUGCUAGCCAACAUGAAUAUUAUAUA
AF338877.1/498-602         UAUUC-UCAUGUGGAAGC-GG--U---UUUGAGUACGGACC--CAG-UA---CCAA-CCCACCC-UCCCCC-AA--CUCU-AUGUACUUCGUACAUUA-CUGCCAGCCCCCAUGAAUAUUGUACA
AF311722.1/1-104           UAUUC-UCAUGUGGAAGC-UG--U---UUUGAGUACA-ACC--CUAGUACAACCCA-UUUUCCCAUG-----AC--CUU--AUGUACUUCGUACAUUA-CUGCUAGUCCCCAUGAAUAUUGUACA
AANU01130438.1/6303-6200   GUAUU-CUAUG-GGGUGC-AA--A--CUUUAAAUGCA-ACU--UAAGUA---CUAA-UUAUUUUAUCAG---AC--CCUU-AUGUAAAUCAUGCAUUA-CUGCUAGCCAACAUGAAUAUUACAUA
AANU01020701.1/941-838     GUCUU-UUAUG-GUAUGCAAG--C---UUUAAAUGCA-ACU--UAAGUA---UUAA-ACAUUUCAAUAA---AC--UUUU-AUGUAAAUCGUGCAUUA-CUGUUAGCCAACAUGAAUACUAUAUA
AANU01062068.1/156-257     ---UU-CUUUGGGGUGAA-AG--C---UUUAAAUGUA-ACU--UAAGUA---CUAA-UUUAUU--UUAACACAC--UCCU-AUGUAAUUCGUGCAUUA-CUGCUAGCCAACAUGAAUAUUAUAUA
AC187501.2/31050-30946     GUAUU-CUAUG-GGGUGCAAG--C---UUUAAAUGCA-ACU--UAAGUA---CUAA-UUUAUU--UUGUCAGAC--CCCC-AUGUAAAUGGUGCAUUA-CUGCUAGCCAACAUGAAUGUUAUAUA
DQ661674.1/395-291         GUAUU-CUAAGGGG--GC-AC--AACCACAAAGUACA-AUU--UAAGU----AUAA-CCUAAUC-UUAUAU-GC--CCCU-AUGUAAUUCGUGCAUUA-CUGCUAGUCACCAUGGAUAUUAUAUA
EU004480.1/1275-1379       GUAUU-CUAAGGGG--GC-AU--AACCAUAAAGUACA-AUU--UAAGUA---CGAU-CUAAUUUUAU--AU-GC--CCCU-AUGUAAUUCGUGCAUUA-CUGCUAGUCACCAUGGAUAUUAUAUA
AY397669.1/89-193          GUAUU-CUAAGGGG--GC-AU--AACCACAAAAUACA-AUU--UUAGUA---UAAU-CUAAUUUUAU--AU-GC--CCUU-AUGUAAUUCGUGCAUUA-CUGCUAGUCACCAUGGAUAUUAUAUA
AY682605.1/56-160          GUAUU-UUAUGUUGUACA-AG--C--CCCACAGUACA-ACC--UUAGCA---CUAG-CUAACUU-UUA-AU-GC--CACU-AUGUAAUUCGUGCAUUA-CUGCUAGCCAACAUGAAUAAUAUAUA
DQ355301.1/15466-15572     GCAUU-CUAUAGGGGUAC-AA--UC-CUUAAAGAUCA-ACU--UAAGUA---CUAA-UCCAAUU-UUAUGU-AC--CCCU-AUGUAAUUCGUGCAUUA-CUGCUUGUCACCAUGAAUAUUAUAUA
DQ373494.1/306-403         AUGUU-GUAUGA----GC-UU--C---AUAAGACA---GUC--CUAGUA---UUAA-CCUGCUCA-UAA-U-AC--UACU-AUGUAAUUCGUGCAUUA-CUGCUAGCCAACAUGUAUAAUAUAUA
AF376805.1/1-104           --AUU-UGAUGUUGGUGU-GA--AC-CUUACAAUACA-AUC--UUAGUA---CUAA-CUUGUUUCU-A-AU-GC--UACU-AUGUAAUUCGUGCAUUA-CUGCUAGCCAACAUGAAUAAUAUAUA
U88994.1/95-195            UUUAU-UGAUGGACUAGC-AA-------UGAAGU----ACU--UUGGAA---GUAU-GCAUAACAUUUCAA-AC--UUUU-AUGUAAUUUGUGCAUUA-AUGCUUAACCCCAUGAAUAAUAUAUA
U88999.1/94-198            CUCUA-UUAUUGGUGGAC-UAGCA---AUAAAGU----ACU--UUGCAA---GUAC-AUGCAACACUUCAA-AC--UUCU-AUGUAAUUAGUGCAUUA-UUGUUCAACCCCAUGAAUAAUAUAUA
AY048783.1/237-333         CUGUU-UUGUG-GACAUU-AA-CA---UGU-----CC-------GCGUA-----GGCAUAAUGUACC-AAG-AC-AUAUU-AUGUAUAUCGUACAUUAAUUGAUAGUCCCCAUGAAUAUUAAGUA
U89000.1/97-197            UUUAU-UGAUGGACUAGCGAU-GA---AGUACUUUAC-AAGCAUACGUA---G------CGUUUA---CAA-AC--UCCU-AUGUAAUUUGUGCAUUA-AUGCUUGC-CACAUGAAUAAUAUAUA
U88992.1/96-196            UUUAU-UGAUGGACUAGC-AA-------UGAAGU----ACU--UUGUAA---GUAU-GCAUAAUAUUUCAA-AC--UUUU-AUGUAAUUUGUGCAUUA-AUGCUUGGCCCCAUGAAUAAUAUAUA
DQ241236.1/84-184          CUUAU-UGAUGGACGAAC-AU-------CAAAGU----ACU--UUAUAA---GUAC-ACACAACAUCUCAA-UU--GGUU-AUGUAAUUAGUGCAUUA-UUGUUAAACCCCAUGAAUAAUGCACA
DQ241248.1/84-184          CUUAU-UGAUGGCUCAAC-AUUAA---AGUACUUUAC-AAG--UACAUA-----------UAAUAUUUAAA-UU--GGUU-AUGUAAUUAGUGCAUUA-AUGCUUAACCCCAUGAAUAAUGUACA
DQ241250.1/84-184          CUUAU-UGGUGGUUCAAC-AU-------UAAAGU----ACU--UUACAA---GUAC-AUAUAUUAUUUAAA-UU--GGUU-AUGUAAUUAGUGCAUUA-AUGUUUAACCCCAUGAAUAAUGUACA
U89008.1/99-199            AUUAU-UGGUGGACUAAC-GA-------UAAAGU----ACU--UUGCAG---GUAC-AUGCAACACCCCAA-AC--UUCU-AUGUAAUUAGUGCAUUA-UUGUUUAGCCCCACGAAUAAUACAUA
AY196756.1/84-184          UUUAU-UGAUGGACUAGC-AA-------UGAAGU----ACU--UUGCAA---GUAU-GCAUAACAUUUCAA-AU--UUUU-AUGUAAUUUGUGCAUUA-AUGUUUUGCCCCAUGAAUAAUACAUA
AACZ03060926.1/95317-95212 UUCUU-UCAUGGGGAAGC-AA--A---UUUGGGUACC-ACC--CAAGUA---UUGG-CUAACCCACCAACA-AC--CGCC-AUGUAUAUCGUGCAUUA-CUGCCAGCCACCAUGAAUAUUAUAUA
AACZ03034773.1/2787-2681   --UGUAUUCUGGUAAAGC-ACCCA---UUUGGGUAUA-ACC--CAAGUA---UUGACCUGCCCCAUUAAUA-AU--UUUC--UGUAUAUUGUGCAUUA-CUGCUAGCCAACAUGAAUAUUAUAUA
#=GC SS_cons               ::::(.((((((((--((.((..,...,<<<<<<___.>>>..>>><<-...<<<<.________>>>>--.>>..,,,,.<<<<<_____>>>>>,,.))))---))-))))))):::::::::
#=GC RF                    uUuUu.ucAUGgggaagC.Ag..a...UuuggGUaCa.ACc..caaguA...uuga.cUaauucAucaaaa.ac..uucU.AUGuAaUUcGUgCAUUA.cUGcUAGccacCAUgaaUAuUAUAuA
//
# STOCKHOLM 1.0

#=GF AC   RF01854
#=GF ID   Bacteria_large_SRP
#=GF PI   SRP_bact_l; SRP_bact
#=GF DE   Bacterial large signal recognition particle RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19838050
#=GF SS   Published; PMID:19838050
#=GF GA   60.00
#=GF TC   60.00
#=GF NC   59.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 549862.597050 CM SEQDB
#=GF CL   CL00003
#=GF DR   URL; http://rnp.uthscsa.edu/rnp/SRPDB/SRPDB.html;
#=GF DR   SO; 0000590; SRP_RNA;
#=GF DR   GO; 0006617; SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition;
#=GF DR   GO; 0048501; signal recognition particle, plasma membrane targeting;
#=GF RN   [1]
#=GF RM   12520023
#=GF RT   SRPDB: Signal Recognition Particle Database.
#=GF RA   Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T
#=GF RL   Nucleic Acids Res 2003;31:363-364.
#=GF RN   [2]
#=GF RM   12140321
#=GF RT   Prediction of signal recognition particle RNA genes.
#=GF RA   Regalia M, Rosenblad MA, Samuelsson T
#=GF RL   Nucleic Acids Res 2002;30:3368-3377.
#=GF RN   [3]
#=GF RM   19838050
#=GF RT   Kinship in the SRP RNA family.
#=GF RA   Rosenblad MA, Larsen N, Samuelsson T, Zwieb C
#=GF RL   RNA Biol. 2009;6:508-516.
#=GF CC   The signal recognition particle (SRP) is a universally conserved
#=GF CC   ribonucleoprotein involved in the co-translational targeting of proteins
#=GF CC   to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA
#=GF CC   (RFAM:RF00017) and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal
#=GF CC   SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54
#=GF CC   proteins. In most bacteria, the SRP consists of a 4.5S RNA and the Ffh
#=GF CC   protein (a homologue of the eukaryotic SRP54 protein). Some Gram-positive
#=GF CC   bacteria (e.g. Bacillus subtilis) have a longer eukaryote-like SRP RNA
#=GF CC   that includes an Alu domain [2]. The Alu domain of the longer SRP RNAs is
#=GF CC   not included in this model and therefore the reported bounds of some
#=GF CC   members are incorrect. The Signal Recognition Particle Database (SRPDB)
#=GF CC   [1] provides compilations of SRP components, with phylogenetic data and
#=GF CC   structural illustrations.
#=GF WK   Signal_recognition_particle_RNA
#=GF SQ   92


CP000764.1/25247-25511       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCU-UCUC-GAGGUUAU-GUUACU-GUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUACG---CAACGAGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUUCUCUCG-UGUG---CCGUAGG--AGUGC-CUGAACUG-----AGCU-AACU-GCUUGA--GUAACGCUUAUG-G-UAC--GUAAUCGACAGA-AGGUGCACGG
AE015929.1/2386853-2386584   CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-ACUUA---AUUCCUUUGUU-GAGGGCGU-AUUUUU-GUGAAG-UCUGCC-CGAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-GUCG-ACUUCG--GUAACGUUUAU--GAUAU--GCGUUCGAUACAAAGGUGCAUGG
CP000730.1/508055-508324     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
CP000485.1/25122-25386       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-----AGCGAGGCCGAAUCCCUUCUCG--AGGUUAU-GUUGCU-GUAAGG-CCUGCCUUAAGUA--AGUGGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCUAACUG--CUUAA--GUAACGCUUAU--GGUAC--GUAAUCGACAGA-AGGUGCACGG
CP000029.1/101125-101225     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUUAG----------------------------------------------------------------
X06802.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
D26185.1/90020-90284         CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
CP000728.1/33073-33316       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-GUUGA---AUUCUUCGCCU--AGGCUUU--AACU-UGUGGGG-UCUG--GCCUGUAAAAGUGGU---GUU-GA-UAAUUGGGU---CCCACG---CAACGAAAA--UUC-AUGAACUCCGUCAGAUCCGGAAGGAAGCAGCGGUAAGUGAACACUUUCG-UGUG---CCGUGGA--UAAAC-CUGAUUUG-----AGCUAACU-GUACAGGUAACG---CUCAU--AAGUUA------------------------
AE001437.1/136141-136243     -------------------------------------------------------------------------------------------------------------------------------------GAAUUGGGU---CCCACG---CAACGGAAA--UUC-AUGAACUCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGUGAAAUCUUCCG-UGUG---CCGUGGA--UAAAU-CUGAUUUG-----AGU----------------------------------------------------------
CP000736.1/536869-536969     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
BX571857.1/485579-485679     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
BA000017.4/525852-525952     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
D11420.1/5-270               CCGUGCUAAGCAGGCGAGGUAGCGGUGCCCCAUA--CCCGCAAUCCGCUCU-AGGAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-GUAAGG-UCUGCC-UUAAGUAAGU-GGC---GUU-GA-CGUCUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCUG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGAGCACGG
D12926.1/388-490             -------------------------------------------------------------------------------------------------------------------------------------GGAGCGGGU---CCUGUG---CAACGCG---AACCCAUGAACCUGGUCAGGUCCGGAAGGAAGCAGCCAUAAGUGGAUCAUCGCG-UGUG---CCGCAGG--GUAGC-CUGCUCUG-----AGC----------------------------------------------------------
AE016879.1/25115-25379       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCU-UCUC-GAGGUUAU-GUUGCU-GUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUAA--GUAACGCUUAUG-G-UAC--GUAAUCGACAGA-AGGUGCACGG
U15684.1/154-183             ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCAUGUCAGGUCCGGAAGGAAGCAGCAU-----------------------------------------------------------------------------------------------------------------
AL596173.1/263987-263721     UCGUGCUAGAC-GGGGAGGUAGCGGCGCCCUGUAA-CCCGCAAUCCGCUCU-AGCGGG-GUUGA---AUUCCU-CAUUUGAGGCAUC-GUAAUU-GUUUGGUCU-GCC-CUUGACAAGU-GGU---GUU-GA-AGGUUGGGU---CUUGCG---CAAUGGGAA--CCU-GUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAUCAGUGCUUCUCA-UGUG---CCGCGAG--GUUGC-CUGGCCCG-----AGCU-AACU-AUCAAG--GUAACGCAGGU--GAUUG--CAUGUCGAGGUG-AGGUGCGCGA
AF269831.1/1333-1433         --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUUAG----------------------------------------------------------------
BA000018.3/501420-501689     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
CP000716.1/1385812-1385778   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAACCGGGUCAGGUCCGGAAGGAAGCAGCCCUAAG-------------------------------------------------------------------------------------------------------------
CP000726.1/37731-37974       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-GUUGA---AUUCUUCGCCU--AGACUUU--AACU-UGUGGGG-UCUG--GCCUGUAAAAGUGGU---GUU-GA-UAAUUGGGU---CCCACG---CAACGAAAA--UUC-AUGAACUCCGUCAGAUCCGGAAGGAAGCAGCGGUAAGUGAACACUUUCG-UGUG---CCGUGGA--UAAAC-CUGAUUUG-----AGCUAACU-GUACAGGUAACG---CUCAU--AAGUUA------------------------
CP000448.1/35764-35828       CCGUGCUAGAU-GGGGAGGUAGCGGUGCCCUGUA-ACCUGCAACCCGCUAU-AGCAGG-GUCGA---AUUCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
AF269814.1/2629-2729         --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUUAG----------------------------------------------------------------
X52144.1/697-961             CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
CP001186.1/24962-25226       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCC-UCUC-GAGGUUAU-GUUGCU-GUAAGG-UCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUGA--GUAACGCUUAUG-G-UAC--GUAAUCGACGGA-GGGUGCACGG
CP000227.1/25236-25338       -------------------------------------------------------------------------------------------------------------------------------------CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGC----------------------------------------------------------
CP001175.1/2823285-2823387   -------------------------------------------------------------------------------------------------------------------------------------AGGUUGGGU---CUUGCG---CAAUGGGA--ACCU-GUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGCAGUGCUUCUCA-UGUG---CCGCGAG--GUCGC-CUGGCCCG-----AGC----------------------------------------------------------
AE017225.1/25229-25331       -------------------------------------------------------------------------------------------------------------------------------------CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGC----------------------------------------------------------
CP000246.1/54302-54566       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-AUCGA---AGUCCUCAUA--GAGGCUCU--AACUU-GUGGAG-UCUG--CCCUAUGUAAGUGGU---GUU-GA-GAGUUGGGC---CCCACG---CAAUGGAAA--CCU-GUGAACCUCGUCAGGUCCGGAAGGAAGCAGCGAUAAGCAGUCAUUUUCA-UGUG---CCGUGGA--UACGU-CUGGCUUG-----AGCUAACU-GCAUAGGUAACG---UUCAU--AAGUU--AUUGUCG-AAGUGAGGUGCACGG
CP000002.3/30682-30947       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUAC-UC-GCAAUCCGCUCG-AGCGAG-GCCGA---AUCCCUUUCUC-GAGGUUCG--UUUACUUUAAGG-UCUGCC-UUAAGCAAGU-GGU---GUU-GA-CGCUUGGGU---CCUGCG---CAAUGGGA--AUCC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGGAACCUUCCA-UGUG---CCGCAGG--GUUGC-CUGGGCUG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
ACHE01000060.1/4624-4355     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-ACUUA---AUUCCUUUGUU-GAGGACGU-AUUUUU-GUGAAG-UCUGCC-CGAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-GUCG-ACUUCG--GUAACGUUUAU--GAUAU--GCGUUCGAUACAAAGGUGCAUGG
D11419.1/5-270               CCGUGCUAAGCGGGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGCGAG-GCUGA---AUUCCU-UUCU-GAGGCUGG-UAUCCU-GUAGGG-UCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUCCGGGU---CCUGCG---CAAUGGGA--AUCC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGGACACCCCCA-UGUG---CCGCAGG--GUUAC-CUGGACUG-----AGCU-AACU-ACUUAA--GUAACGCUUAU--GGGUG--CCAGUCGACAGA-AGGUGCACGG
CP000560.1/27594-27646       ----------------------------------------------------------------------------------------------------------------------------------------------------------------GA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCU---------------------------------------------------------------------------------------------------
AM180355.1/20131-20368       --GUACUAGAU-GGGGAGGUAGCGGUGCCCUGUA-ACCUGCAAUCCGCUAU-AGCAGG-AUUGA---AUUCCAUCUAA--AGGCUUA-UUUUCU-GUAGG--GCCG--CCCUAAAUAAGUGGU---GUU-GA-UGCUUAGGU---CCUGCG---CAAUGAAAG--CUC-AUGAACCCCGUCAGAUCCGGAAGGAAGCAGCGGUAAGUGAUCACUUUUG-UGUG---CCGUGGG--GGUGC-CUAAGUUG-----AGCUAACU-GUUUUGGUAACG---CCUAUGG------------------------------
AF368293.1/5-274             CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
D11417.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-UCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
CP001215.1/24988-25252       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCU-UCUC-GAGGUUAU-GUUGCU-GUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGG---ACCCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUAA--GUAA-CGCUUAU-GGUAC--GUAAUCGACAGA-AGGUGCACGG
CP000255.1/508278-508378     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
AP006627.1/47077-47179       -------------------------------------------------------------------------------------------------------------------------------------CGUUUGGGU---UCUGCG---CAACGGA---AACCCAUGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGUGGACCCUUCCG-UGUG---CCGCAGA--GGUGC-CUGGAUCG-----AGC----------------------------------------------------------
CP001185.1/1535075-1535038   -------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGAACCGGGUCAGGUCCGGAAGGAAGCAGCCCUAAGC------------------------------------------------------------------------------------------------------------
D13041.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AE017194.1/25229-25331       -------------------------------------------------------------------------------------------------------------------------------------CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGC----------------------------------------------------------
X12642.1/292-556             CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
ACFR01000004.1/173539-173639 --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUUAG----------------------------------------------------------------
D11412.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGC-AG-GCCGA---AUCCCC-UCUC-GAGGUUAU-GUUGCU-GUAAGG-UCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUGC--GUAACGCUUAUG-GCUAC--GCAAUCGACAGA-AGGUGCACGG
D11416.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AE015927.1/24077-23975       -------------------------------------------------------------------------------------------------------------------------------------GAAUUGGGU---CCCACG---CAACGGAAA--CUC-AUGAAACCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGUGAUAAUUUUCG-UGUG---CCGUGGA--UAAAC-CUGGUUUG-----AGU----------------------------------------------------------
AE017333.1/30486-30751       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUAC-UC-GCAAUCCGCUCG-AGCGAG-GCCGA---AUCCCUUUCUC-GAGGUUCG--UUUACUUUAAGG-UCUGCC-UUAAGCAAGU-GGU---GUU-GA-CGCUUGGGU---CCUGCG---CAAUGGGA--AUCC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGGAACCUUCCA-UGUG---CCGCAGG--GUUGC-CUGGGCUG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AM412317.1/37716-37959       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-GUUGA---AUUCUUCGCCU--AGACUUU--AACU-UGUGGGG-UCUG--GCCUGUAAAAGUGGU---GUU-GA-UAAUUGGGU---CCCACG---CAACGAAAA--UUC-AUGAACUCCGUCAGAUCCGGAAGGAAGCAGCGGUAAGUGAACACUUUCG-UGUG---CCGUGGA--UAAAC-CUGAUUUG-----AGCUAACU-GUACAGGUAACG---CUCAU--AAGUUA------------------------
D11415.1/5-268               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGC-AG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UCAAGG-UCUGCC-UUAAAUAAGU-GGU---GUU-GA-CGUCUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GUUUAA--GUAACGCUUGG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AL591984.1/65413-65311       -------------------------------------------------------------------------------------------------------------------------------------AGGUUGGGU---CUUGCG---CAAUGGGA--ACCU-GUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGCAGUGCUUCUCA-UGUG---CCGCGAG--GUCGC-CUGGCCCG-----AGC----------------------------------------------------------
CP000382.1/2507879-2507649   -CGUGCUAGAC-GGGAAGUUAGCGGUGUCCUGU--ACCUGCAAUCCGCUAU-AGCAGG-GUUGA---AUUCCUCGUUG--AGGCUUU-AAAAUG-GGAGG--UCUG--GCUUAUAUAAGUGGC---GUU-GA-GAAUUGGGC---CCUACG---CAAUAGGAA--CUC-AUGAACCCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGUGAGAACUCCUA-UGUG---CCGUAGG--UAAAC-CUGGUUUG-----AGUUAACU-AUAUAAGUAACG----------------------------------------
CP000727.1/37731-37974       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-GUUGA---AUUCUUCGCCU--AGACUUU--AACU-UGUGGGG-UCUG--GCCUGUAAAAGUGGU---GUU-GA-UAAUUGGGU---CCCACG---CAACGAAAA--UUC-AUGAACUCCGUCAGAUCCGGAAGGAAGCAGCGGUAAGUGAACACUUUCG-UGUG---CCGUGGA--UAAAC-CUGAUUUG-----AGCUAACU-GUACAGGUAACG---CUCAU--AAGUUA------------------------
BA000043.1/27043-27145       -------------------------------------------------------------------------------------------------------------------------------------CGUCUGGGU---CCCGCG---CAAUGGG---AUUCCGUGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGCGGAUGCUCCCA-UGUG---CCGCGGG--GACGC-CUGGGCUG-----AGC----------------------------------------------------------
BA000004.3/46485-46751       CCGUGCUAGGU-GGGGAGGUAGCGGUGCCCUGUCA-CUCGCAAUCCGCUAU-AGCGAG-GCUGA---AUCCCU-UCUA-GAGGUUUU--GUCACCGUAGGG-UCUGCC-CUAAGUAAGU-GGU---GUU-GA-CGCUUGGGU---UCUACG---CAACGAAA--ACCC-ACGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGUGGCCCCUUUCG-UGUG---CCGUAGA--GUCGC-CUGGGCCG-----AGCU-AACU-GCUCAG--GUAACGCCUAGG-GUGGC--AUGAUCGAAGGA-AGGUGCACGG
CP000702.1/1631640-1631756   --------------------------------------------------------------------------------------------------------------------------------GGGGGCGAUGAAGA-CCGGGUCCCACGCAACGGA-ACCCU-GUGAACCUGGUCAGGCCCGGGAGGGAGCAGCCAUAAGCAGGUGUUUCCGUGUG---CCGUGGGGG-AG-CC-CGGUUGGAGCCUU-------------------------------------------------------------
CP000253.1/444208-444308     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
CP000046.1/524416-524685     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
CP000001.1/25120-25384       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCU-UCUC-GAGGUUAU-GUUGCU-GUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUAA--GUAACGCUUAUG-G-UAC--GUAAUCGACAGA-AGGUGCACGG
CP001283.1/25232-25334       -------------------------------------------------------------------------------------------------------------------------------------CGUUUGGGU---CCUGCG---CAACGGG---ACCCCGUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGC----------------------------------------------------------
AE017262.2/2736493-2736285   --------------------------------------------------------------GA---AUUCCU-CAUUUGAGGCAUC-GUAAUU-GUUUGGUCU-GCC-CUUGACAAGU-GGU---GUU-GA-AGGUUGGGU---CUUGCG---CAAUGGGA--ACCU-GUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGCAGUGCUUCUCA-UGUG---CCGCGAG--GUCGC-CUGGCCCG-----AGCU-AACU-AUCAGG--GUAACGCAGAU--GAUUGC--AUGUCGAUGUG-AGGUGCGCGA
D11421.1/5-270               CCGUGCUAAGCGGGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
CP001598.1/25015-25279       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGCGAG-GCCGA---AUCCCU-UCUC-GAGGUUAU-GUUGCU-GUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA--CCCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGGUCUUCUCG-UGUG---CCGCAGG--AGUGC-CUGAACCG-----AGCU-AACU-GCUUAA--GUAACGCUUAUG-G-UAC--GUAAUCGACAGA-AGGUGCACGG
D14472.1/475-743             CCGUGCUAGAC-GGGGAGGUUGCGGUGCCCUGUAA-CCUGCAAUCCGCAAUAGCCAGG-GUGUG-A-AUUCCU-AUCC-UAGGUUUU--CUUAU-GUGAGG--CUGCCGUUGAUGGCGGCGGU---GUU-GA-GGAGCGGGU---CCUGUG---CAACGCGA--ACCC-AUGAACCUGGUCAGGUCCGGAAGGAAGCAGCCAUAAGUGGAUCAUCGCG-UGUG---CCGCAGG--GUAGC-CUGCUCUG-----AGCU-GCUA-CCAUAA--GUAACGCUCGG--AUAAG-GAUUAUCGAAGAU-AGGUGCACGG
CP000703.1/536798-536898     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
AP009324.1/527299-527399     --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
D11422.1/5-266               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUAU-AGCAGG--CUGA---AUCCCU-UCUA-GAGGUUUU--GUCACCGUAGGC-UCUGCC-CUAAGUAAGU-GGU---GUU-GA-CG-UUGGGU---UCUACG---CAACGAAA--ACCC-ACGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGUGGCCCCUUUCG-UGUG---CCGUAGA--GUCGC--UGGGCCG-----AGCU-AACU-GCUCAG--GUAACGCUAGG--GUGGC--AUGAUCGACAGA-AGGUGCACGG
CP000141.1/2376482-2376447   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAACCGUGUCAGGUCCGGAAGGAAGCAGCACUAAG-------------------------------------------------------------------------------------------------------------
D49784.1/286-550             CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-AUCGA---AGUCCUCAUA--GAGGCUCU--AACUU-GUGGAG-UCUG--CCCUAUGUAAGUGGU---GUU-GA-GAGUUGGGC---CCCACG---CAAUGGAAA--CCU-GUGAACCUCGUCAGGUCCGGAAGGAAGCAGCGAUAAGCAGUCAUUUUCA-UGUG---CCGUGGA--UACGU-CUGGCUUG-----AGCUAACU-GCAUAGGUAACG---UUCAU--AAGUU--AUUGUCG-AAGUGAGGUGCACGG
AL009126.3/26420-26684       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AP006716.1/2548377-2548277   --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAAUCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCCUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUUAG----------------------------------------------------------------
D11413.1/5-264               CCGUGCUAAGCGGGGGAGGUAGCGGUGCCCUAUA--CUCGCAAUCCGCUCU-AGC-AG-GCCGA---AUCCCC-UCUC-GAGGUUAU-GUUGCU-GUAAGG-UCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAACGGGA---CCC-GUGAACCUUGUCAGGUCCGGAAGGAAGCAGCAAUAAGCGGU-CUUCUCG-UGUG---CCG-AG---AGUGC-CUGAACCG-----AGCU-AACU-GCUUGA--GUAACG-UUAU--GGUAC--GUAAUCGACAGA-AGGUGCACGG
D11414.1/5-268               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGC-AG-GCCGA---AUUCCU-UCUU-GAGGUUAG-CUCAUC-UUAGGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUACG---CAAUGGGA--AUCU-GUGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGCAGAACCUCUCA-UGUG---CCAUGGG--GUCGC-CUGAACCG-----AGCU-AACU-GCUUAA--GUAACGCCUGG--GGUGG--CUAAUCGACAGA-AGGUGCACGG
X14796.1/291-555             CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--GUUGC-CUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
CP000557.1/25310-25574       CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGCGAG-GCUGA---AUCCCU-UCUC-GAGGUUAG-UCUGUU-GUGAGG-UCUGUC-UCAAGCAAGU-GGU---GUU-GA-CGUCUGGGU---CCCGCG---CAAUGGG---AUUCCGUGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGCGGAUGCUCCCA-UGUG---CCGCGGG--GGUGC-CUGGGCUG-----AGCUA-ACU-ACUUGA--GCAACGCUCGG--GGCAGC--UAAUCGACAGA-AGGUGCACGG
CP000232.1/28709-28775       CCGUGCUAGAU-GGGGAGGUAGCGGUGCCCUGUA-ACCCGCAAACCGCUAU-AGCGGG-GUUGA---AGUCCCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
BA000016.3/54529-54793       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-AUCGA---AGUCCUCAUA--GAGGCUCU--AACUU-GUGGAG-UCUG--CCCUAUGUAAGUGGU---GUU-GA-GAGUUGGGC---CCCACG---CAAUGGAAA--CCU-GUGAACCUCGUCAGGUCCGGAAGGAAGCAGCGAUAAGCAGUCAUUUUCA-UGUG---CCGUGGA--UACGU-CUGGCUUG-----AGCUAACU-GCAUAGGUAACG---UUCAU--AAGUU--AUUGUCG-AAGUGAGGUGCACGG
CP000721.1/5829625-5829394   ---UGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAU-AGCAGG-AUUGA---AUUCCUCGCUU--AGGUAUU--AGCGAUUUAUAG-UCUG--ACUUUUGUAAGUGGU---GUU-GA-UGACUGGGU---CCCACG---CAAUGGAAG--CCC-AUGAACCUCGUCAGAUCUGGAAGGAAGCAGCGAUAAGUGGUUCCUUCCA-UGUG---CCGUGGA--UCAAU-CUGGUCUG-----AGCUAACU-GCAUUAGUAACG---U------------------------------------
AE008691.1/46248-46514       CCGUACUAGAU-GGGGAGGUAGCGGUGCCCUGUAG-CCUGCAACCCGCUAU-AGCAGG-GUCGA---AUUCCCAGGCU-GAGGCCUGA-UUUCU-GUAAGG-CCUG--GCGCAAGUAAGUGGCGUU-GA-UACUUGA-GU--CCUGCG------CAACGGAGA--UUU-GCGAACCCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGCAAACACCUCCG-UGUGCCGCAGG--GGU-GCUUGAGUGG--------AGCUAACU-GCUUGCGUAACG---CUUAU--GGGGA--CAGGUCG-AAGCUGGGUGUACGG
X15523.1/2-266               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUCU-AGCGAG-GCUGA---AUCCCU-UCUC-GAGGUUAG-UCUGUU-GUGAGG-CCUGUC-UCAAGUAAGU-GGU---GUU-GA-CGUCUGGGU---CCCGCG---CAAUGGGA--UUCC-GUGAACCCUGUCAGGUCCGGAAGGAAGCAGCAGUUAGCGGAUGCUCCCA-UGUG---CCGCGGG--GGCGC-CUGGGCUG-----AGCC-AACU-GCUUGA--GCAACGCUCGG--GGCAG--CUAAUCGACAGA-AGGUGCACGG
BA000028.3/30821-31086       ACGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CUCGCAAUCCGCUAU-AGCGGG-GCCGA---AUUCCC-ACUC-GAGGUGGG-ACGACU-UUAUGG-UCUGAC-UUAAGGGAUU-GGU---GUU-GA-CGCCCGGGU---CCUGCG---CAACAGGA--ACCC-ACGAAUCCUGUCAGGUCCGGAAGGAAGCAGCAGUAAGUGGUUAUUCUUG-UGUG---CCGCAGG--GAAGC-CUAGGCCG-----AGCC-AUGA-ACUUAU--GUAGCGCAUAG--GGUCG-UUUCAUCGACAGU-GGGUGCACGU
CP000724.1/39593-39767       --GUGCUAGAC-GGGGAGGUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAU-AGCAGG-GUUGA---AUUCCU-CAUG-GAGGCUUG-UUGCUU-GUAGGG--CUGGC-CUAGAUAAGU-GGU---GAU-GA-GAAUUGGGU---CCUACG---CAAUGAA---AACUCAUGAACUCCGUCAGAUCCGGAAGGAAGCAGCGGUAAG-------------------------------------------------------------------------------------------------------------
CP000813.1/551215-551244     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCAUGUCAGGUCCGGAAGGAAGCAGCAU-----------------------------------------------------------------------------------------------------------------
D11418.1/5-269               CCGUGCUAAGC-GGGGAGGUAGCGGUGCCCUGUA--CCUGCAAUCCGCUCU-AGCAGG-GCCGA---AUCCCU-UCUC-GAGGUUCG-UUUACU-UUAAGG-CCUGCC-UUAAGUAAGU-GGU---GUU-GA-CGUUUGGGU---CCUGCG---CAAUGGGA--AUUC-AUGAACCAUGUCAGGUCCGGAAGGAAGCAGCAUUAAGUGAAACCUCUCA-UGUG---CCGCAGG--UUGCC-UUGGGCCG-----AGCU-AACU-GCUUAA--GUAACGCUUAG--GGUAG--CGAAUCGACAGA-AGGUGCACGG
AE000512.1/1124728-1124612   --------------------------------------------------------------------------------------------------------------------------------GGGGGCGAUGAAGA-CCGGGUCCCACGCAACGGA-ACCCU-GUGAACCUGGUCAGGCCCGGGAGGGAGCAGCCAUAAGCAGGUGUUUCCGUGUG---CCGUGGGGG-AG-CC-CGGUUGGAGCCUU-------------------------------------------------------------
AC025951.19/16428-16528      --------------------------------------------------------------------------------------------------------------------------------------AUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AG-----------------------------------------------------------
AJ938182.1/468421-468690     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
CP000568.1/2549377-2549203   --GUGCUAGAC-GGGGAGGUAGCGGUGCCCUGUU-ACCUGCAAUCCGCUAU-AGCAGG-GUCGA---AUUCCUAUAAU--AGGCAUG-CUUCUG-UAAGG--UCUG--CCCUUUGCAAGUGGC---GAU-GA-AAAUUGGGU---CCUACG---CAACGGAAG--CCU-AUGAACCCCGUCAGGUUCGGAAGAAAGCAGCGGUAAG-------------------------------------------------------------------------------------------------------------
AP008934.1/2359274-2359174   --------------------------------------------------------------------------------------------------------------------------------------AUCUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAAUCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCGUA-UGUG---CCGUAGG--GUUGC-CGAGAUUUAG----------------------------------------------------------------
AP009351.1/497755-498024     CCGUGCUAGGU-GGGGAGGUAGCGGUUCCCUGUA--CUCGAAAUCCGCUUUAUGCGAG-GCUUA---AUUCCUUUGUU-GAGGCCGU-AUUUUU-GCGAAG-UCUGCC-CAAAGCACGU-AGU---GUUUGAAGAUUUCGGU---CCUAUG---CAAUAUGA--ACCC-AUGAACCAUGUCAGGUCCUGACGGAAGCAGCAUUAAGUGGAUCAUCAUA-UGUG---CCGUAGG--GUAGC-CGAGAUUU-----AGCU-AACG-ACUUUG--GUUACGUUCGU--GAAUU--ACGUUCGAUGCUUAGGUGCACGG
CP000312.1/54097-54361       CCGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUAA-CCUGCAAUCCGCUAC-AGCAGG-AUCGA---AGUCCUCAUA--GAGGCUCU--AACUU-GUGGAG-UCUG--CCCUAUGUAAGUGGU---GUU-GA-GAGUUGGGC---CCCACG---CAAUGGAAA--CCU-GUGAACCUCGUCAGGUCCGGAAGGAAGCAGCGAUAAGCAGUCAUUUUCA-UGUG---CCGUGGA--UACGU-CUGGCUUG-----AGCUAACU-GCAUAGGUAACG---UUCAU--AAGUU--AUUGUCG-AAGUGAGGUGCACGG
AP009049.1/3810996-3810763   -CGUGCUAGAU-GGGGAGUUAGCGGUGCCCUGUA-ACCUGCAAUCCGCUAU-AGCAGG-GUUGA---AUUCCUGGCUU--AGACUUU-AAAAUG-UGAGG--CCUG--CCCCAUAAAAGUGGC---GUU-GA-GAGCUUGGU---CCCACG---CAACAAGAA--CUC-AUGAACCCCGUCAGGUCCGGAAGGAAGCAGCGGUAAGUGAAUAUUUUUG-UGUG---CCGUGGA--UAAAC-CUGGUUUG-----AGUUAACU-AUAUGGGUAACG---CU-----------------------------------
#=GC SS_cons                 [[[[[[[((((.<<<<<<<<___>>>>>>>>,,,..<<<<<<_________.>>>>>>.)))),...,,,<<<.<<<<..<<<<<<-..<<<<<.<<<<<-.--<<...<<<<<<--<<.<<<...---.--.<<<<<<<<<...<<<<<<...<<-<<<<<..<<<<.<<<---<<<<<----<<<____>>>---->>>>>->>>>>>>-->>>>>.>>--...->>>>>>..--->>.>>>>>>>-.....->>>.->>..>>>>>>..->>...>>>>>..>>>>>...>>>>>>.>>>>.>>>]]]]]]]
#=GC RF                      cCGuGCcgggc.gGGGggcuAGCggucCCCuGUA..CccGCgAUCCGCUau.cGCggG.gcccA...AUuCCu.cccc..cGgcccu..ccccc.gugggG.uCug...ccgagcaAgg.gGc...Guu.GA.cgcccgGGc...ccugcG...caAcggga..accc.gugAACcccGuCAGGuCCGGAAGGaAGCAgCgguAagcgggucuucccg.ugUG...CCgcagg..guugC.Ccgggcgg.....AgCc.Acc..gcucgg..gca...cccac..ggggg...ggguCg.gggg.aGGgGCaCGg
//
# STOCKHOLM 1.0

#=GF AC   RF01855
#=GF ID   Plant_SRP
#=GF PI   SRP_euk_arch
#=GF DE   Plant signal recognition particle RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19838050
#=GF SS   Published; PMID:19838050
#=GF GA   105.00
#=GF TC   105.10
#=GF NC   104.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00003
#=GF DR   URL; http://rnp.uthscsa.edu/rnp/SRPDB/SRPDB.html;
#=GF DR   SO; 0000590; SRP_RNA;
#=GF DR   GO; 0006617; SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition;
#=GF DR   GO; 0005786; signal recognition particle, endoplasmic reticulum targeting;
#=GF RN   [1]
#=GF RM   11839493
#=GF RT   Towards the structure of the mammalian signal recognition particle.
#=GF RA   Wild K, Weichenrieder O, Strub K, Sinning I, Cusack S
#=GF RL   Curr Opin Struct Biol 2002;12:72-81.
#=GF RN   [2]
#=GF RM   10678824
#=GF RT   Crystal structure of the ribonucleoprotein core of the signal recognition
#=GF RT   particle.
#=GF RA   Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA
#=GF RL   Science 2000;287:1232-1239.
#=GF RN   [3]
#=GF RM   11243816
#=GF RT   Structural and energetic analysis of RNA recognition by a universally
#=GF RT   conserved protein from the signal recognition particle.
#=GF RA   Batey RT, Sagar MB, Doudna JA
#=GF RL   J Mol Biol 2001;307:229-246.
#=GF RN   [4]
#=GF RM   12520023
#=GF RT   SRPDB: Signal Recognition Particle Database.
#=GF RA   Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T
#=GF RL   Nucleic Acids Res 2003;31:363-364.
#=GF RN   [5]
#=GF RM   12140321
#=GF RT   Prediction of signal recognition particle RNA genes.
#=GF RA   Regalia M, Rosenblad MA, Samuelsson T
#=GF RL   Nucleic Acids Res 2002;30:3368-3377.
#=GF RN   [6]
#=GF RM   19838050
#=GF RT   Kinship in the SRP RNA family.
#=GF RA   Rosenblad MA, Larsen N, Samuelsson T, Zwieb C
#=GF RL   RNA Biol. 2009;6:508-516.
#=GF WK   Signal_recognition_particle_RNA
#=GF SQ   63


AC146941.8/20211-20507     ----GAGUUGAUUAACACCAACUUGUGACCCAUG-UGGGAGCAC-CAAGGUGAUG-G--AACA-UGG----CUGGUUU--GCUUAGCGGGUU-GGG-CU-GUAG-G-GUACAC------------UAUGCUGGCCU-GCCCACUCCAAGUUG-AGAGU-UGGGCCA-UGG-GAUUUG-GGCGAAGGCU-CAGAUCU-CC-UGGUCA----CU-AG-AA-UGGAGGGAUCCGCAUGAGGCUGGUUUUACAGAGCAGUGAACACU-UCCU-UCUCU-UGACAGUGGAGGGAUC-ACAGGCUGCAG-UAU-U-CUUGGC-UUAUA--UGGCC-UGGUGA-G-CCUAG-CACAC-UGAACCAUCA------
ABCN01005680.1/1602-1315   GCC-GGCUGGAGUAACGACCAGUUGUCACCCGAG-UGGGGGC----CAAGCGGAU-G--GAGG-AAC----AUACGGC----------CCUUCGGUCGU-GAUC-G-CUCCCGU----------C---GAUAGCGU-GUCCUCUGUGAGUUC-ACAGU---CGGCA--AGGUCAUCGCCCUGACGGGU-GAUUGAC-CU-GGUUG-----AU-GA-UU-AGUCCCGCACCGCGUGAGGCAGGAA--ACUGAGCAGCGAAAAGG-GGCA-GCUGC-GGACGGCACAAGGAUC-GCAUGCUUGAGGGAGUG-GCAUGG-CCACCC-GAGGG-GUCC----UC-UGU--GGG-ACCAACUACCGUUU---
AP006364.1/60840-60536     GCC-GAGUUGGGUUACUCCAGCUUGUGACCCAAG-UGGGGGCAC-CAGGUUGAUG-G--AACAUGGU----UCUGGCU---UUCGUUAGGCU-GGG-CU-GUUA-G-AUGCAA------------UAUUCUGGCCU-GCCCACUCCAAGUUG-AGAGU-UGGACCG-UGG-GGCUUG-GGCGAAGGCC-CUUGUCU-CU-CGGCCC----CU-AA-AC-UGGAGGGCAAAGCGUGAGGCUGGUUUCACAGAGCAGCGAAUACC-UCUG-GCUCC-UGACAGUGGAGGGAUA-ACAGGCUGAUG-CAC-U-CUCAGC-CCAUU--GUGCC-UAGUGG-G-CCUGG-CCUCU-UGAACCAUCAUCUUU-
Z29111.1/1-302             GUU-GAGCUUAGUAACGUGGGCUUGUAACCCAAG-UGGGGAUGU-UAAUGUGGUG-G--AAUG-UUG----GGCUGUA---CCAGAU-GGUU-GGGCUU-GG---U-GGGCUA------------AUUUCUGACUU-GCCCUAUCCAAGCUU-AGAGU-UGGAUCA--UGUGGCCCA-AUUGAAGAAA-UGGACUA-CU-UGAUUC----GU-AA-AG-UGGGGCGGAAUGCGUGAGGCUGGUUUCACAGAGCAACGAUAAG--UUUC-GCUCU-AAGCGGUGGAAGGAUA-ACGAGUCGGUGUUCU---CUGAGU-CCAGU-AACGCC-UGAUGG--GUUGCU-CCAA-UUAAACCACCAUUUUU-
X65984.1/1-307             GCC-GGUCUUAGCAACGUGGGCCUGUAACCCAAG-UGGGGGCAU-GUGGGAAAUG-G--GACU-UUG----GGUCAAC---CUAGUG-GAUC-GGGUCC-AGUG-U-UAGCUG------------CUUACUGGUCU-GCCCAUUCCAAGCCG-GGAGU-UGGGCUG--AGUGACCUG-GGCGAAGGGC-UGGGUUG-CG-CACGUC----CU-AG-AG-UGGAGGGCAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACC-UCCC-GCUCU-CGGCAGUGGAAGGAUA-ACGGGCCGGUG-CUA-C-CUGGGU-CCACC-AUGCUU-CACUAG-GCUGACUCUUAA-UAGGACCAUUUCUUUU-
X13913.1/1-298             NCC-GAGCU-AGUUGCGAGAGCUUGUAACCCGAG-UGGGGGCAUUAAAGUGAUGU-G--AACNCUGU---UGUA-GCG----CUGCG-GGCCUGGUCUG-GG---U-GUGCUA-------------CUGCUGGCCC-GCCCGUUCCAAGUUGCGUAGU--GGACCGCCUGGGGCUUA-UGCGAAAGC--UGGGUCU-CA-CGGUC-----CAUAA-UG-UGGCAGGCACAGCGUGAGGCUGGCUUCACAGAGCAGCGACAACU-GCCC-GCUUC-CAACGGUGGAAGGAUA-AUGGGCCGCUG-CAC-U-CCUAGGACCAAU-UGGGCCUCGCAG----CCUAC-UCCA-GCAGACCACC-------
Z29101.1/1-303             GUC-GAGCUUAGUAACGUGGGCUUGUAACCCAAG-UGGGGAUGU-UAAGGUGGUG-G--AAUA-UUG----GGCUGUC---CCAGAU-GGCU-GGGCUU-GG---U-GGGCUA------------AUUUCUGGCCU-GCCCUAUCCAAGUAC-AGAGU-UGGAUCA--UGUGGUCCA-AUUGAAAGAA-UGGGCUA-CU-AGAUUC----CU-AA-AG-UGGGGUGGAC-CCGUGAGGCUGGUUUCACAGAGCAACGAAAAAC-UUCC-GCUUU-GUGCAGUGGAAGGAUA-ACGGACCGGUGCCUU---CCAAGU-UCCAUUAAUGCC-UGAUGG--GCUGUU-CUAG-UUAAACUACCACAUUU-
AC136507.19/21662-21924    ----GAGUUGAAUAACACCAACUUGUAACCCAUG-UGGGAGCAU-CAAGGUGAUG-G--AACAUGGC----UGUGU-----CUUAACAGGUU-GGG-CU-GUAG-G-GUACAU------------UAUGCUGGCCU-GCCCACUCCAAGUUG-AGAGU-UGGGCCA-UGG-GAUUUG-GGCGAAGGCU-CAGAUCU-CC-UGGUCA----CU-AG-AA-CGGAGGGAUCCGCAUGAGGCUGGUUUCACAGAGCAGUGAUCACU-UCCU-UCUCU-UGACAGUGGAGGGAUU-ACAGGCUGCUG-UAU-U-CUCAGC-CCAUA---------------------------------------------
AP010413.1/68444-68724     -------------------AGCUUGUAACCCAAG-UGGGGGCAC-CAAGGUGAUG-G--AACAUGGC----UCUGGU----GUCGUUGGGCU-GGG-CU-GUUA-G-CUGCAA------------UAAG-UGGCCU-GCCCACUCCAAGUUG-AGAGU-UGGGCCA-UGG-GGCUUU-AGCGAAGGCU-CUAGCUU-CC-UGGUUC----CU-AA-AC-UGGAGGGCACGGCGUGAGGCUGGUUUCACAGAGCAGCGAUAACC-UCCG-GCUCC-UGACAGUGGAGGGAUA-ACGGGCCGCUG-CAC-U-CUCAGC-CCACU--ACGCC-CGGUGA-G-CCUGG-CCUCU-UGAACCAUCAU-----
EU957112.1/2-304           -CC-GAGCUCAGUAGCGAGAGCUUGUAACCUAAG-CGGGGGCAU-UAAGGUGGUG-U-GGAUGUUUC---CUGACGG-----AUUCUGGGCCUGGGCCU-G-UA-U-GUGCCA-----------C-UGGCCGGCCU-GCCCGUUCCAAGUUG-GUUGU--GGCUGG-UGG-GGCUCG-GGCGAAGGCC-UGGGCCU-CU-UUAGA-----CCUGA-AG-CGGCAGGCAUGGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACU-GCCC-GCUUC-CAACGGUGGGAGGAUA-ACAGGCCGCUG-CAU-U-GCAAGC-CCAACUCGG-UC-CAGAG---CC-UCA-UUAA-ACAGACCACCAUCUUU-
Z29112.1/1-303             GUC-GAGCUUAGUAAUGUGGGCUUGUAACCCAAA-UGGGGGCAU-UAAUGUGGUG-G--AAUG-UUG----GGCUGUA---CCAGAU-GGUU-GGGCUU-GGU----GGGCUA------------AUUUCUGACUU-GCCCUAUCCAAGCUU-AGAGU-UGGAUCA--UGUGGCCCA-AUUGAAGAAA-UGGACUA-CU-UGAUUC----GU-AA-AG-UGGGGCGGAAUGCGUGAGGCUGGUUUCACAGAGCAACGAUAAGU-UUCC-GCUCU-AAGCGGUGGAAGGAUA-ACGAGUCGGUG-UUC--UCUGAGU-CCAGU-AAUGCC-UGAUGG--GCUGCU-CUAA-UUAAACCACCACUUUU-
AARH01003811.1/60212-60278 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACAACC-UCCC-GCUCC-UGGCAGUGGAAGGAUA-AC-------------------------------------------------------------------------
Z46745.1/134-436           GUC-GAGCUUAGUAACGUGGGCUUGUAAUCCAAG-UGGAGACAU-CAAAGUGGUU-G--AAUA-UUG----GGCUUUA---CCAGAA-GGUU-GGGCUU-GG---U-GGGCUU------------AGUUCUGGCCU-GCCCUGUCCAAGCAC-AGAGU-UGGAUCA--CGAGGCCCA-AAUGAAAAUA-UGGGCUU-CU-UGAUUC----CU-AA-AG-UGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACAGC-UCCC-GCUCU-GUGCAGUGGAAGGAUA-AUGGGUCGGUGUCUUA--UCAAGU-UCAGU-AACGCC-UAAUGG--GUUGCU-CCAA--UAAACAACCACCUUU-
AL161495.2/164946-164641   GUC-GAGCUAAGUAACAAUAGCUUGUAACCCAUG-UGGGGACAU-UAAGAUGGUG-G--GACACUGG----UUCGG-----UUCCUCGGAUC-GGUUCU-GAUG-U-GGGCAU------------GUUUCUGAGCU-GCCCAGUCCAAGCUG-UGAGU--AAUUAG-UGUUGAGUUG-AGCGAAGGCU-UGGCUCA-UG-CAGGUU----CU-AG-AGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACU-UCCC-GCUUA-CAGCAGUGGACGGAUC-ACGGUUUAGCG-UCG-C-UCAGAA-CCACU-AUGGCC-UGCUGG-U-CCGAU-CUCAUAUGAACCACCAUUUU--
X13914.1/1-303             NCC-GAGCU-AGUUGCGGGAGCUUGUCACCCAUG-UGGGGGCAU-UGAGGCGGUG-U-GGAUGCUUG----GUGCGGU----UUGUU-GGCCUGGGCUU-GUGA-U-GUAACC-------------UUGCUGGCCU-GCCCGUUCCAAGUUG-GUAGU--GGGCUG--GGUGGCUGG-GGCGAAAGCU-UCGCCUU-CU-CAGGC-----CU-UA-AG-UGGCAGGCACCACGUUAGGCUGGUUUCACAGAGCAGCGACAACU-GCC-CGCUUC-CAACGGUGGAAGGAUA-ACAGGCCGCUG-CAG-C-AUGGGC-CCGCUCUGGGCC-UCCUA---CCCCGCCAU-A-GCAGACCACCAUCUUU-
X72228.1/320-625           GUC-GAGCUAAGUAACAAUAGCUUGUAACCCAUG-UGGGGACAU-UAAGAUGGUG-G--GACACUG-----GUUCGGU----UCCUCGGAUC-GGUUCU-GAUG-U-GGGCAU------------GUUUCUGAGCU-GCCCAGUCCAAGCUG-UGAGU--AAUUAGUGUUGAGU-UG-AGCGAAGGCU-UGGCUCA-UG-CAGGU-----UCUAG-AGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACU-UCCC-GCUUA-CAGCAGUGGACGGAUC-ACGGUUUAGCG-UCG-C-UCAGAA-CCACU-AUGGCC-UGCUGG--UCCGAU-CUCAUAUGAACCACCAUUUU--
X69901.1/3886-4191         GUC-GAGCUAAGUAACAAUAGCUUGUAACCCAUG-UGGGGACAU-UAAGAUGGUG-G--GACACUGG----UUCGG-----UUCCUCGGAUC-GGUUCU-GAUG-U-GGGCAU------------GUUUCUGAGCU-GCCCAGUCCAAGCUG-UGAGU--AAUUAG-UGUUGAGUUG-AGCGAAGGCU-UGGCUCA-UG-CAGGUU----CU-AG-AGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACU-UCCC-GCUUA-CAGCAGUGGACGGAUC-ACGGUUUAGCG-UCG-C-UCAGAA-CCACU-AUGGCC-UGCUGG-U-CCGAU-CUCAUAUGAACCACCAUUUU--
Z46744.1/234-533           ----GAGCUUAGUAACGUGGGCUUGUAAUCCAAG-UGGAGACAU-CAAAGUGGUU-G--AAUA-UUG----GGCUUUA---CCAGAA-GGUU-GGGCUU-GG---U-GGGCUU------------AGUUCUGGCCU-GCCCUGUCCAAGCAC-AGAGU-AGGAUCA--CGAGGCCCA-AAUGAAAAUA-UGGGCUU-CU-UGAUUC----CU-AA-AG-CGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACAGC-UCCC-GCUCU-GUGCAGUGGAAGGAUA-AUGGGUCGGUGUCUUA--UCAAGU-UCAGU-AACGCC-UAAUGG--GUUGCU-CCAA-UAAA-CAACCACCUUU-
AP003333.4/45380-45697     GCC-GAGCUCAGUAGCGAGAGCCUGUAACCCAAG-CGGGGGCACUAAAGGUGGCU-GCGGAUGU-UU---GGUGUGG----AUUCUGAUCCUGGGCCCC-AUGU-U-GUUGUA-----------AUCUUGCUGGCUUGCCCGUUCCAAGUUGCGUAGU--GGGCCG-GAGGGGCUUU-GGCGAAGGCC-UUUG-CU-UUGCUUCUCCGGCCCUAA-AG-UGGCAGGCACAGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACU-GCCC-GCUUC-CAUCGGUGGAAGGAUA-ACAGGCUGCUG-CAC-C-UUGGGC-CCGCUUCUGGCCC-AGAGU---CCCUC-UACA-ACAGACCACCAUCUUU-
Z29109.1/1-240             --------------------------------------------------------------G-UUG----GGUUGAC---CCAGAU-GGUU-GGGUUC-GG---U-AGGCUU-----------AUAGUCUGGCCU-GCCCUCUCCAAGCAU-GGAGU-UGGAUCA--CGUGGCUUA-GUCGAAAGACCUGGGUUG-CU-UGAUUC----CU-AA-AG-UGGGGUGGACUGCGUGAGGCUGGUUUCACAGAGCAACGAACAGC-UUCC-GCUCU-GUGCAGUGGAAGGAUA-ACGGGUCAGUG-CUCA--GCGAGU-CCAGUUAACGCCCUGAUGG--GCUGCU-CCAA-CUAAA------------
AC079888.10/27802-27492    GCC-GAGCCAGGUAGCGUUGGCUUGUCACCCGAG-CGGGGGCAA-UAAGGUGGUG-UUGGAUGCCUGG-UCGUUUGCG-----CUUGGGGUCU-GCGCC-UGUG-G-UUUGCA-----------C-UAUGCGGCCC-GCCCGUUCCAAGUUGCGUAGCG-UGUGUG--GGGCGCCUG-GGCGAAGGCU-CGAGCGU-CCCUGCAC-----CU-AG-AG-UGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACC-GCCC-GCUUC-CAACGGUGGAAGGAUA-ACGGGCCGCUG-CAG-C-CCUGGC-CCGCUUCCGGCC--CAAGU--GCCUUC-CAUG-GCAGACCACCACCUUU-
CT485797.2/99364-99662     ----GAGUUGAUUUACACCAACUUGUAACCCAUG-UGGGAGCAA-CAAGGUGAUG-G--AACAUGAU----UGUGU-----CUUAACAGGUU-GGG-CU-GUAG-G-GUACAU------------UAUGCUGGCCU-GCCCACUCCAAGUUG-AGAGU-UGGGCCA-UGG-GAUUUG-GGCGAAGGCU-CAGAUCU-CC-UGGUCA----CU-AG-AA-CGGAGGGAUCCGCAUGAGGCUGGUUUCACAGAGCAGUGAACACU-UCCU-UCUCU-UGACAGUGGAGGGAUC-ACAGGCUGCAG-UAU-U-CUCAGC-CCAUA--UGGCC-UGGUGA-G-CCUAG-CC-AU-UGAACCAUCAUUUUU-
AL161496.2/127430-127734   GUC-GAGCGAAGUAACAUGAGCUUGUAACCCAUG-UGGGGACAU-UAAGAUGGUG-G--AACACUGG----UUCGG-----GUCCACGGGCC-GGUUCU-GUUG-C-UGGCAU------------GUUUCUGGGCU-GCCCAGUCCAAGCUG-UGAGU--AAGACG-UGU-GUGUCA-AGCGAAGGCU-UGGCUCA-AA-CGGCUG----CU-AA-AGUUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUUACU-UCCC-GCUUA-CAGCAGUGGACGGAUC-ACAGUUUGGCG-UCG-C-UCAGAA-CCACU-AUGGCC-UGCUGG-U-CCGAU-CUCAUCUGAACCACCAUUUU--
X65983.1/1-306             GAC-GGGCUUAGCAACGUGGGCCUGUAACCCAAG-UGGGGGCAU-GUGGGAAAUG-G--GACU-UUG----GGUCAAC---CUAGUG-GAUC-GGGUCC-AGUG-U-UAGCUG------------CUUACUGGUCU-GCCCAUUCCAAGCCG-GGAGU-UGGGCUG--AGUGACCUG-GGCGAAGGCU--GGGUUG-CG-CAGCUC----CU-AG-AG-UGGAGGGCAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACC-UCCC-GCUCU-CGGCAGUGGAAGGAUA-ACGGGCCGGUG-CUA-C-CUGGAU-CCACC-AUGCUU-CACUGG-GCUGACUCUUAA-UAGGACCAUUUCUUUU-
AJ236706.1/161-459         ---------UAGCAACGUGGGCCUGUAACCCAAG-UGGGGGCAU-GUGGGAAUUG-G--GACU-UUG----GGUCAAC---CCAGUG-GAUC-GGGUCC-AGUG-C-UAGCUG------------CUUACUGGUCU-GCCCAUUCCAAGCCG-GGAGU-UGGGCUG--AGUGACCUG-GGCGAAGGCC-UGGGUUG-CG-CAGCUC----CU-AG-AG-UGGAGGGCAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACC-UCCC-GCUCU-CGGCAGUGGAAGGAUA-ACGGGCCGGUG-CUA-C-CUGGAU-CCACC-AUGCUU-CACUGG-GCUGACUCUUAA-UAGGACCAUUUCUUUU-
Z29110.1/1-274             ------------------------------CAAG-UGGGGAUGU-UAAGGUGGUG-G--AAUA-UUG----GGCUGUC---CCAGAU-GGCU-GGGCUU-GG---U-GGGCUA------------AUUUCUGGCCU-GCCCUGUCCAAGCAC-AGAGU-UGGAUCA--CGAGGCCCA-AAUGAAAAUA-UGGGCUU-CU-UGAUUC----CU-AA-AG-UGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACAGC-UCCC-GCUCU-GUGCAGUGGAAGGAUA-AUGGGUCGGUGUCUUA--UCAAGU-UCAGU-AACGCC-UAAUGG--GUUGCU-CCAA--UAAACAACCACCUUU-
X13958.1/1-302             GGC-GAGCUUAGUAACGUGGGCUUGUAAUCCAAG-UGGAGACAU-CAAAGUGGUU-G--AAUA-UUG----GGCUUUA---CCAGAA-GGUU-GGGCUU-GGU----GGGCUU------------AGUUCUGGCCU-GCCCUGUCCAAGCAC-AGAGU-UGGAUCA--CGAGGCCCA-AAUGAAAAUA-UGGGCUU-CU-UGAUUC----CU-AA-AG-UGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAA-CGC-UCCC-GCUCU-GUGCAGUGGAAGGAUA-AUGGGUCGGUG-UCU-UAUCAAGU-UCAGU-AACGCC-UAAUGG--GUUGCU-CCAA--UAAACAACCACCUUU-
AC005662.3/47366-47062     GUC-GAACUCAGUAACGCGGGCUUGUGAUCCAAG-UGGAGACAA-UAAGGGGAUG-G--GACG-UUG----GGUCGAU--CUCAUUG-GGCC-GGGUUC-GGGU-U-GGGCUA------------UAUUCUGGCCC-GCCCAUUCCAAGUUG-GGAGU-UGAGGCA--UGGGCUUCG-AGCGAAGGCU-CGGGUCU-CA-UGUCUU----CU-AG-AG-UGGGGGAGACCGCGUGAGGCUGGUUUCACAGAGCAGCGUCCACC-UCCC-GCUCU-UGACGGUGGAAGGAUU-ACGGGCCAUUG-CCU---UCCGAG-CCCACUAUGACC-CAAUAA-G-CCGCU-CCGA-UUGGACCAUCACUUU--
X65990.1/1-301             -----GGCCUAGCAACGUGGGCCUGUAACCCAAG-UGGGGGCAU-GUGGGAGAUG-G--GACU-UUG----GGUCAGC---CCAUUG-GAUC-GGGUCC-AGUG-U-UAGCUG------------CUUGCUGGUCU-GCCCAUUCCAAGCCG-AGAGU-UGGGCUG--UGUGAUCUG-GGCGAAGGCU-GGGGUCG-CA-CAGCUC----CU-AA-AG-AGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACCACC-UCCC-GCUCU-CGGCAGUGGAAGGAUA-ACGGGUCGGUG-CUA-C-UUGGGC-CA-CC-AUGG-U-CACUGC-AUGCACUCUUAAUCAGA-CCAUCUCUUUU-
Z29103.1/1-304             GCC-GAGCUUUGUAACGUGGGCUUGUAACCCGAG-UGGGGGCAA-CAAUGUGGUG-G--AAUG-UUG----GGUCCAU---CUUGAUGGAU--GGGCUU-GA---A-GGGCUA-----------AUGUUCUGGCCU-GCCCUGUCCAAGCAC-AGAGU-UGGGUCA--AGUGGUCUA-UACGAAAGUA-UAG-CCA-CU-UGGCCU----UU-AG-AG-UGGGAUGGACUGCGUGAGGCUGGUUUCACAGAGCAACGACUAGU-CCCC-GCUCU-GUGCAGUGGAAGGAUC-ACGGGCUAGUGCUCU---UUGAGU-CCUAACAAAAACCUGAUAG--GUUGCC--UAA-UUAAACCAUCACUUUU-
AP009658.1/43412-43714     GCC-GAGCUUG--CACGAUAGCUUGUAACCCGAA-UGGGGGCAC-CAAGAUGGUG-G--AACAUGGC----UAUGAC----UUCACUGGGUU-GGU-CU-GGUG-G-UUGCAC------------CUUGUUGGCCU-GCCCGCUCCAAGUCG-AGAGG-UGGGCCA-UGU-GUCUUU-AGUGAAAGCU-AAGGUCU-UG-UGGUUC----CU-AG-AC-AGGAGGGCAAAGCGUGAGGCUGGUGUCACAGAGCAGCGAACACU-UCUG-GCUCC-UGACAGUGGAGGGAUA-ACAGGCUGCUG-CAC-C-UUCAGC-CCACA-AAUGCC-UAGUGA-A-CCCAG-CUACC-UGAACUAUCAUUUUC-
AC136507.19/79013-79284    ---------------------------ACCCAUG-UGGGAGCAA-CAAAGGGAUG-G--AACA-UGG----CUGUGU----CUUAACAGGUU-GGG-CU-GUAG-G-GUACAC------------UAAGCUGGCUU-GCCCACUCCAAGUUG-AGAGU-UGGGCCA-UGG-GAUUUG-GGCGAAGGCU-CAGGUCU-CC-UGGUCC----CU-AG-AA-CGGAGGGAACCGCAUGAGGCUGGUUUCACAGAGCAGUGAACACU-UCCU-UCUCU-CGACAGUGGAGGGAUU-ACAGGCUGCUG-CAU-U-CUCGGU-CCAUA--UAGCC-UGGUGA-G-CCUAG-CCCAU-UGAACCAUCA------
AC005275.1/105500-105803   GUC-GAGCUAAGUAACAUGAGCUUGUAACCCAUG-UGGGGACAU-UUAGAUGGUG-G--AACACUG-----GUUCGGG---UCCACG-GGCC-GGUUCU-GUUG-U-UGGCAU------------GUUUCUGGGCU-GCCCAGUCCAAGCUG-UGAGU--AAGACG--UGUGUGUCA-AGCGAAGGCU-UGGCUCA-AA-CGGCUU----CU-AA-AGUUGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACU-UCCC-GCUUA-CAGCAGUGGACGGAUC-ACAGUUUAGCG-UCG-C-UCAGAA-CCACU-AUGGCC-UGCUGG--UCCGAU-CUCAUAUGAACCACCAUUU---
X55111.1/801-1106          GUC-GAGCUAAGUAACAAUAGCUUGUAACCCAUG-UGGGGACAU-UAAGAUGGUG-G--GACACUG-----GUUCGGU---UCCUCG-GAUC-GGUUCU-GAUG-U-GGGCAU------------GUUUCUGAGCU-GCCCAGUCCAAGCUG-UGAGU--AAUUAG-UGUUGAGUUG-AGCGAAGGCU-UGGCUCA-UG-CAGGUU----CU-AG-AGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACU-UCCC-GCUUA-CAGCAGUGGACGGAUC-ACGGUUUAGCG-UCG-C-UCAGAA-CCACU-AUGGCC-UGCUGG--UCCGAU-CUCAUAUGAACCACCAUUUU--
X14661.1/23-309            -----------------------UGUAACCCGA-GCGGGGGCAU-UAAGGUGGUG-C-GGAUUCUUU---GCGAUGG----CUUUCUGGGCCCGGGCUC-GCU-AU-GUGCCU-----------U-UGGCCGGCCU-GCCCGUCCCAAGUUG-GUAGU--GGCUGG-CGGAGGCUUU-AGCGGAAGCU-UUGGUCU-CU-CCAGA-----CCUGA-AG-UGGCAGGAAUGGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUCGCCC-GCUUC-CAACGGUGGGAGGAUA-ACGGGCCGCUG-CAC-U-UCGAGC-CCAACUCAGGCC-CAGAG---CC-UCA-CUAA-GCAGACCACCAUCUUU-
X65985.1/1-303             ----GGCCUUAGCAACGUGGGCCUGUAACCCAAG-UGGGGGCAU-GUGGGAAAUG-G--AACA-UUG----GGUCAGC---CCAGUG-GAUC-GGGUCC-AGUG-U-UAGCUG------------CUUACUGGUCU-GCCCAUUCCAAGCCG-GGAGU-UGGGCUG--AGUGACCUG-GGCGAAGGCC-UGGGUUG-CG-CAGCUC----CU-AG-AG-UGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACC-UCCC-GCUCC-CGGCAGUGGAAGGAUA-ACGGGCCGGUG-CUA-C-UUGGUC-CA-CC-AUGU-U-CACUGGUCCUGACUCUUAA-UCGGACCAUUUCCUUU-
AF069442.1/64156-64461     GUC-GAGCUAAGUAACAAUAGCUUGUAACCCAUG-UGGGGACAU-UAAGAUGGUG-G--GACACUGG----UUCGG-----UUCCUCGGAUC-GGUUCU-GAUG-U-GGGCAU------------GUUUCUGAGCU-GCCCAGUCCAAGCUG-UGAGU--AAUUAG-UGUUGAGUUG-AGCGAAGGCU-UGGCUCA-UG-CAGGUU----CU-AG-AGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACU-UCCC-GCUUA-CAGCAGUGGACGGAUC-ACGGUUUAGCG-UCG-C-UCAGAA-CCACU-AUGGCC-UGCUGG-U-CCGAU-CUCAUAUGAACCACCAUUUU--
X65986.1/2-304             -----GUCUUAGCAACUUGGUCCUGUAACCCAAG-UGGGGGCAU-GUGGGAAAUG-G--AACU-UUG----GGUCAAC---CCAGUG-GUNC-GGGNCC-AGUG-C-UAGCUG------------CUUACCCGGCU-GCCCAUUCCAAGCCG-GGAGG-UGGGCUG--AGGGACCUG-GGCGAAGGCU-NNNGGNNGCG-CA-CUC----CU-AG-AC-UGGAGGGCAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACC-UCCC-GCUCU-CGGCAGUGGAAGGAUA-ACGGGCCGGUG-CGC-C-UUGAGC-CAACA-CUGUUC-AACUGG-GCUGACUCUUAA-UAGGACCAUUUCUUUU-
Z29261.1/1-303             GCC-GAGCUUAGUAACGUGGGCUUGUAACCCAAG-UGGGGAUGU-UAAGGUGGUG-G--AAUA-UUG----GGCUGUC---CCAGAU-GGCU-GGGCUU-GG---U-GGGCUA------------AUUUCUGGCCU-GCCCUAUCCAAGCAC-AGAGU-UGGAUCA--UGUGGUCCA-AUUGAAAGAA-UGGGCUA-CU-AGAUUC----CU-AA-AG-UGGGGUGGACCGCGUGAGGCUGGUUUCACAGAGCAACGAAAAAC-UUCC-GCUUU-GUGCAGUGGAAGGAUA-ACGGACCGGUGCCUU---CCAAGU-UCCAUUAAUGCC-UGAUGG--GCUGCU-CCAA-UUAAACCACCACUUU--
Z29105.1/1-303             GUU-GAGCUUAGUAACGUGGGCUUGUAAUCCAAG-UGGAGACAU-CAAAGUGGUU-G--AAUA-UUG----GGCUGUA---CCAGAU-GGUU-GGGCUU-GG---U-GGGCUA------------AUUUCUGACUU-GCCCUAUCCAAGCUU-AGAGU-UGGAUCA--UGUGGCCCA-AUUGAAGAAA-UGGACUA-CU-UGAUUC----GU-AA-AG-UGGGGCGGAAUGCGUGAGGCUGGUUUCACAGAGCAGUGAACAGC-UCCC-GCUCU-GUGCAGUGGAAGGAUA-AUGGGUCGGUGUCUUA--UCAAGU-UCAGU-AACGCC-UAAUGG--GUUGCU-CCAA-UAAACAACCACCUUU--
Z29106.1/1-302             GCC-GAGCUUAGUAAUGUGGGCUUGUAACCCAAA-UGGGGGCAU-UAAUGUGGUG-G--AAUG-UUG----GGCUGUA---CCAGAU-GGUU-GGGCUU-GG---U-GGGCUA------------AUUUCUGACUU-GCCCUAUCCAAGCUU-AGAGU-UGGAUCA--UGUGGCCCA-AUUGAAGAAA-UGGACUA-CU-UGAUUC----GU-AA-AG-UGGGGCGGAAUGCGUGAGGCUGGUUUCACAGAGCAACGAUAAG--UUUC-GCUCU-AAGCGGUGGAAGGAUA-ACGAGUCGGUGUUCU---CUGAGU-CCAGU-AACGCC-UGAUGG--GUUGCU-CCAA-UUAAACCACCAUUUUU-
X72229.1/323-627           GUC-GAGCUAAGUAACAUGAGCUUGUAACCCAUG-UGGGGACAU-UUAGAUGGUG-G--AACACUGG----UUCGG-----GUCCACGGGCC-GGUUCU-GUUG-U-UGGCAU------------GUUUCUGGGCU-GCCCAGUCCAAGCUG-UGAGU--AAGACG-UGU-GUGUCA-AGCGAAGGCU-UGGCUCA-AA-CGGCUU----CU-AA-AGUUGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACU-UCCC-GCUUA-CAGCAGUGGACGGAUC-ACAGUUUAGCG-UCG-C-UCAGAA-CCACU-AUGGCC-UGCUGG-U-CCGAU-CUCAUAUGAACCACCAUUUU--
AC146941.8/78907-78613     ----GAGUUGAUUAACACCAACUUGUGACCCAUG-UGGGAGCAA-CAAAGGGAUG-G--AACA-UGG----CUGUGU----CUUAACAGGUU-GGG-CU-GUAG-G-GUACAC------------UAAGCUGGCUU-GCCCACUCCAAGUUG-AGAGU-UGGGCCA-UGG-GAUUUG-GGCGAAGGCU-CAGGUCU-CC-UGGUCC----CU-AG-AA-CGGAGGGAACCGCAUGAGGCUGGUUUCACAGAGCAGUGAACACU-UCCU-UCUCU-CGACAGUGGAGGGAUU-ACAGGCUGCUG-CAU-U-CUCGGU-CCAUA--UAGCC-UGGUGA-G-CCUAG-CCCAU-UGAACCAUCA------
Z29107.1/3-303             ---CGAGCUUAGUAACGUGGGCUUGUAAUCCAAG-UGGAGACAU-CAAAGUGGUU-G--AAUA-UUG----GGCUUUA---CCAGAA-GGUU-GGGCUU-GG---U-GGGCUU------------AGUUCUGGCCU-GCCCUGUCCAAGCAC-AGAGU-UGGAUCA--CGAGGCCCA-AAUGAAAAUA-UGGGCUU-CU-UGAUUC----CU-AA-AG-UGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACAGC-UCCC-GCUCU-GUGCAGUGGAAGGAUA-AUGGGUCGGUGUCUUA--UCAAGU-UCAGU-AACGCC-UAAUGG--GUUGCU-CCAA-UAAA-CAACCACCUUU-
X65991.1/1-303             -----GGCCUAGCAACGUGGGCCUGUAACCCAAG-UGGGGGCAU-GUGGGAAAUG-G--GACU-UUA----GUUCGGC---CCAUUG-GAUC-GGAUCC-AGUG-U-UAGCUG------------CUUGCUGGGCU-GCCCAUUCCAAGCCG-AGAGU-UGAGCUG--UGUGAGCCG-GACGAAGGUC-UGGCUUG-GU-CAGCUC----CU-AA-AG-CGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACAACC-UCCC-GCUCU-CGGCAGUGGAAGGAUA-ACGGGCCGGUG-CUG-C-UUGGAC-CCACC-AUGGUU-CACUGA-GCUGACUCUUAA-UAGGACCAUUUCUUUU-
AJ236703.1/157-424         ----------AGCAACGUGGGCCUGUAACCCAAG-UGGGGGCAU-GAGGGAAAUG-A--GACU-UUG----GGCCGAC---CCGAGA-GAUC-GGAUUC-AGUG-U-CGGCUG------------AUUACUGGUUC-GCCCGUUCCAAGCAA-AGAGC-UGGGCUG--GGUGAGUUG-GACGAAGGUC-UGGCUUA-CU-CAGCUC----CU-AA-AG-CGGUGGGUAACGCGUGAGGCUGGCUUCACAGAGCAGCGACUACC-UCCC-GUUCU-UGGCAGUGGAAGGACA-ACGAGCCGGUG-CUG-C-CUGGGC-UCACC-AUGGUU-CACU---------------------------------
Z29260.1/92-303            ---------------------------------------------------------------------------------------------------------------UA------------G-UUCUGGCCU-GCCCUGUCCAAGCAC-AGAGU-AGGAUCA--CGAGGCCCA-AAUGAAAAUA-UGGGCUU-CU-UGAUUC----CU-AA-AG-CGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACAGC-UCCC-GCUCU-GUGCAGUGGAAGGAUA-AUGGGUCGGUG-UCUU-AUCAAGU-UCAGU-AACGCC-UAAUGG--GUUGCU-CCAA--UAAACAACCACCUUU-
Z29104.1/1-304             GCC-GAGCUUAGUAAUGUGGGCUUGUAACCCAAA-UGGGGGCAU-UAAUGUGGUG-G--AAUG-UUG----GGCUGUA---CCAGAU-GGUU-GGGCUU-GG---U-GGGCUA------------AUUUCUGGCCU-GCCCUAUCCAAGCAC-AGAGU-UGGAUCA--UGUGGUCCA-AUUGAAAGAA-UGGGCUA-CU-AGAUUC----CU-AA-AG-UGGGGUGGACCGCGUGAGGCUGGUUUCACAGAGCAACGAAAAAC-UUCC-GCUUU-GUGCAGUGGAAGGAUA-ACGGACCGGUGCCUU---CCAAGU-UCCAUUAAUGCC-UGAUGG--GCUGCU-CCAA-UUAAACCACCACUUUU-
Z29099.1/1-304             GCC-GAGCUCAGUAGCGUGGGCUUGUAACUCAAG-UGAGGGCAU-CAGUGUGGUG-G--AAUG-UUG----AACAUGC---CCAGAA-GGUA-GGGCUU-GUG----UGACAA------------UUCUCUGGCCU-GCCCUGUCCAAGCAA-AGAGU-UGGGUCU--UGUGGGCCA-AGCGAAGGCU-UGGGCUG-CU-GGGCUC----CU-AA-AG-UGGGGUGGACUGCGUGAGGCUGGUUUCACAGAGCAACGAAUAGC-UCCC-GCUCU-GUGCAGUGGAAGGAUA-ACGAGCCAGUG-UCA--UAUAAGU-UCAACGAAUGUC-UGAUGG--GCUGUU-CUAG-UUAAACUACCACAUUU-
AJ236705.1/163-430         ----------AGCAACGUGGGCCUGUAACCCAAG-UGGGGGCAU-GAGGGAAAUG-A--GACU-UUG----GGCCAGC---CCAGAG-AGUC-GGAUUC-AGUG-U-CGGCUG------------AUUACUGGUUC-GCCCGUUCCAAGCAA-AGAGC-UGGGCUG--GGUGAGUUG-GACGAAGGUC-UGGCUUA-CU-CAGCUC----CU-AA-AG-CGGUGGGUAACGCGUGAGGCUGGCUUCACAGAGCAGCGACUACC-UCCC-GUUCU-UGGCAGUGGAAGGACA-ACGAGCCGGUG-CUG-C-CUGGGC-UCACC-AUGGUU-CACU---------------------------------
X71484.1/3-290             GCC-GGCUGGAGUCACGUCCAGUUGUCACCCAUG-UGGGGGC----CAAGCGGAU-G--AAGG-AAC----AUAUGGC----------UCUCCGGUCGU-GAAC-G-CUUCCGU----------C---GAUAGCGU-GUCCUCUUCGAGUCC-ACAGU---CGGCA--AGGUCGCUGCCCUGAUGGGU-GGCUGAC-CU-GGUUG-----AU-GA-UU-AGUCCCGCACCGCGUGAGGCAGGAA--ACUGAGCAGCGAAAAGG-GACA-GCUGC-GGACGGCGAAAGGAUC-GCAUGCUUGAGGAGGUG-CCACGA-CCACCC-GGGGG-GUCC----UC-UGU--GGG-ACCAACUACCGUUU---
ABXC01006351.1/33720-33416 ---------CUGUAGCGGGAGCUUGUGACCCGAG-CGGGGGCAACAAGGUGGUGU-G--GAUG-CUG----UGCGACG---GUUUC---UCU-GGGCCU-G----G-GCCUGUGGUGUGCCUUUGCUUGCUGGCCU-GCCCGUCCC-AAGUU-GGUAG-UGGUUGG--CGGGGCUCU-UGCGAAGGCU-UGGGCCU-CU-CCGAAC----CU-AA-AG-CGGCAGGAAUGGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACU-GCCC-GCUUCCAACGG-UGGGAGGAUA-ACAGGCCGC-UGCACC--AUUAGC-CCAACUUAGGGCCCAGAGC--CUCACU-AUAG--CAG-ACCACCAUCUUU
AP003253.3/106424-106741   GCC-GAGCUCAGUAGCGAGAGCCUGUAACCCAAG-CGGGGGCACUAAAGGUGGCU-GCGGAUGUUUGGUGUGGAUUCU---GAUCCUGGGCCC-CAUGU-UGU----UGUAAU-----------C-UUGCUGGCUU-GCCCGUUCCAAGUUGCGUAGU--GGGCCG-GAGGGGCUUU-GGCGAAGGCC-UUUGCUU-UGCUUCUCCGGCCCU-AA-AG-UGGCAGGCACAGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACU-GCCC-GCUUC-CAUCGGUGGAAGGAUA-ACAGGCUGCUG-CAC-C-UUGGGC-CCGCUUCUGGCC-CAGAGU-C-CCUCUA-CAA--CAGACCACCAUCUUU-
AB295118.1/595-292         GCU-GAGCUGAGUAACGUUAGCUUGUAACCUAAG-UGGGGGCAA-UAAAGUGAUG-G--GACAU-GG----CUCGGGC--UAUGCUC-GGUC-GGGCUG-UU-A-G-AUGCAU------------AAUUCUGGCCU-GCCCGCUCCAAGUUA-AGAGC-UGAGUCA--UGGGAUUUG-GGCGAAGGCU-CAGGUCU-CU-UGGCUC----CU-AA-AC-UGGAGGGCACAGCGUGAGGCUGGUUUAACAGAGCAGCGAGCACC-UCCG-GCUCC-UGACAGUGGAGGGAUA-ACAGGCUGCAG-CAC-U-UUCAGC-CCACC-AUGACC-GGGUGU--ACCAAG-CUC--CUGAACCAUCAUUUUU-
FJ404770.1/43347-43044     GCU-GAGCUCAGUAACGUGGGCUUGUAACCCAAG-UGGGGGCAU-UAAGGUUACU-G--AACG-UUG----GGCCGUU---CCAAUU-GGCU-GGACUC-AA---G-GUGCUA------------UUUACUGGCCC-GCCCGUUCCAAGCGG-GGAGU-UGGCCCA--CGGAAUCCA-GGCGAAGGCU-UGGGCUU-CG-AGGGCC----UU-AG-AG-AGGAGGGCACCGCGUCAGGCUGGAUUUACAGAGCAGCGAUAACU-UCCC-ACUCU-CUGCAGUUGAAGGAUA-ACGGGCCGGUG-CUCC--UUGGGU-CCAAC-AAAGCC-AGUUGA-AUCGGUC-UUAA-UUGGACAGUAACCUUU-
AASG02000222.1/20689-20386 GCC-GGGCUUGGCAACGCGAGCCUGUAACCUGAG-UAGGGGCAU-UAAGGUGGUG-G--GACG-UUA----CUCUGGC---CCAGUA-GGCU-GGAUUC-GGCG---UGACUA------------UGAUCUGGCUC-GCCCGUUCCAAGCUA-AGAGU-UGAUCCA--UGUGGCUUG-GGCGAAGGCC-CGGGCUC-CA-UGGGUC----CU-AG-AG-CGGAGGGCACAGCGUUAGGCUGGUUUCACAGAGCAGCGAUAACC-UCCC-UCUCU-UGGCAGUGGAAGGAUA-ACGGACCGGUG-UUA-C-CCGGAG-CCAUA-GAAGCC-UAAUGG--ACCGUG-UGAA-CUGGACCAUCAUUUUU-
AC190028.8/62420-62724     GCC-GAGCUGAGUCACGUUAGCUUGUGACCCAAG-UGGGGGCAC-UAAGGUGGUG-G--AACA-GCU---CAUUGGCU---UUGCUG-GGUU-GGACUG-UG---G-CUGCAA------------UAAGUUGGCCU-GCCCACUCCAAGUUG-AGAAU-UGAAUCA--UGGGACUUAAAGCGAAGGCA-UAGGUCU-CC-UGGUUC----UU-AG-AG-UGGAGGGCACUGCGUGAGGCUGGUUUCACAGAACAGCGAACACC-UCCC-AUUCC-CAACAGUGGAGGGAUA-ACAGGUUGCUG-CAAC--CACAGU-CCACC-AUGGCC-UGGUGA--GCCUAG-AUGC-UUGGACCAUCACUUUU-
AM457057.2/4282-3977       GCC-GAGUUCAGUCGCGGGAACUUGUAACCCAAG-UGGGGGCAU-UAAGGUGGGC-G--GAUG-UUG----GUUCGGU---UGAGCA-GGUA-GGGCCU-GAUG---GGGUUA------------AAUGCUGGCCU-GCCCGUUCCAAGUUG-GGAGA-UGAGUCU--CGACAUCCG-GGCGAAGGCC-UGGGUGG-CG-UGGCUC----CU-AG-AGUUGGAGGAAACCGCGUGAGGCUGGUUUCACAGAGCAGCGUCCACC-UCCC-GCUCC-CGUCGGUGGAAGGAUA-ACUGGCCGGUG-CUC-C-ACAGGU-CCAAC-AACGCC-UCCUGA-GCCGCUC-ACAA-UCUGACAUCCACCUUU-
AAAA02010927.1/7990-7685   GCC-GAGCUCAGCAGCGCGAGCUUGUAACCCGAG-CGGGGGCAU-UAAGGUGGUG-U-GGACG-UUG---CCGUAUGG---CUGCGG-GCCU-GGGUUG-GCA----GUGCCA-------------UAGAUGGCCC-GCCCGUUCCAAGUUGCGUAGU-UGGGCCG-GCGGGGCUUG-AGCGAAAGCU-CUGGCCU-CA-CGUUUC---CCU-AG-AG-UGGCAGGCAUUGCGUGAGGCUGGCUUCACAGAGCAGCGAAUACU-GUCC-GCUUC-CAACGGUGGAAGGAUA-ACGGGCCGCCG-CAC-U-GCUGGC-CCGCU-UGGGUC-UCGCAG--CCUACU-CCAA--CGGACCACCACUUUU-
ABIM01017697.1/2595-2290   GCC-GGGCCUGGCAACGCGGGCUUGUCACCCAAG-UGGGGGCAU-UAAGAUGGUU-G--GAGG-UUG----GAUAGGU---CCAGAA-GGUU-GGGCUUCGAAG-G-GAUUAA------------AAAUCUGACCC-GCCCGUUCCAAGAGG-AGAGU-UGAGUUG--CGUGCCCUCCAGCGUAGGCU-UGGGGCU-CG-CCUCUC----UU-AG-AG-CGGAGGGGACCGCGUGAGGCUGGAA--ACAGAGCAACGAAAACC-UCCC-GCUCU-CUUCAGUGGAAGGAUU-ACGGGCCGGUG-CUC-A-UCAGGU-CCAUU-AACGCC-UGAUGG--ACCCUCCACAA-UUCAACAACCAUCUUU-
AC189438.2/31077-30776     GUC-GAGCUCAGUAACAAGAGUUUGUGACCCAUG-UGGGGACAA-CAAGAUGGUG-G--AACA-CUG----UCCCGGC---CCACC--GGUC-GGUUCU-GU---C-UGGCAU-------------CUUCUGGACC-GCCCAGUCCAAACCG-AGAGU--GAUCCG--UUUGUGUUA-GGCGAAGGCU-UGACUCA-GG-CGUUUC----CUAAAGAG-GGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUCACC-UCCC-UCUCU-CGGCAGUGGACGGAUA-ACGGAUGAAAG-CCAC--UCAGAU-CCACA--UGGCC-UGGUGG--CUCGUACCCAG-CUGAACCACCAUCUUU-
ABRL01000488.1/5816-6128   GCC-GAGCUCAGUAGUGAGAGCUUGUAACCCAUG-UGGGGGCAU-C-AGGUGGUG-U-GGAUG-GUU---G-GUGCUG---AAUUUG-GGCUUGGGUUC-AUGU-UGUUGUUAA----------CUAUGCUGGCUU-GCCCGUUCCAAGUUGAGUAGU-GGGUGGG--AGGGGCUUC-GGCGAAAGCCUUGGGUCU-CU-CCGGCC----CU-GA-AGUUGGCAGGCACGGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACU-GCUC-GCUUC-CAACUGUGGAAGGAUAAACAGGCCGCUG-CAC-C-AUGGGC-CCGCUUCUGGCC-CAGAGU--UCCAC--UAUU-ACAGACCACCAUCUUU-
U85037.1/1-298             GCC-GCGAA----------UUCGCGGCG-CCGAG-CGGGGGCAA-UAAGGUGGUGCG--GAUG-CCU----GGUCGUUUGCUCUUU--GGCCUGGGCCU-GUGG-U-UCGCUC-------------UAUGCGGCCC-GCCCGUUCCAAGUUGCGUAGC--GUGUAU-GGGGCGCCCU-GGCGAAAGCU-AGAGCGU-CC-CUGCAC----CU-AG-AG-UGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACC-GCCC-GCUUC-CAACGGUGGAAGGAUU-ACGGGCCGCUG-CAG-C-CCUGGC-CCGCUUCCGGCC--CAUGU--GCCUUC-CAUG-GCAGACCCCCAUCUUU-
#=GC SS_cons               <<<.<<<<<<<<....>>>>>>>>....<<<<...>>>>>>>...<<<<<<<<<<.<...<<<.<<<....<<<<<<....<<<<<<.<<<<.<<<<<<.<<.<...<<<.<<................<<<<<<<.<<<<.<<<<<<<<<<.<<<<<..<<<<<<..<<<<<<<<<.<<<....>>>.>>>>>>>.>>.>>>>>>....<<....>>.<<<<<<<...<<<<<....<<<......>>>....>>>>>.>>>.>>>>.>>>>>.>>>>>.>>>>>>>....>>>>>>>>>>>.>>>.>.>>>>>>.>>......>>>>.>>>>>>..>>>>>>..>>>..>>>.>>>>>>>>>>>.
#=GC RF                    GcC.gaGCucagUAACcugaGCuuGUAACCCaAG.uGGGGgCAu.aaagguGgug.G..auca.uug....ggugggu...ccagua.Ggcc.GGgCcu.ggug.u.gugcca............uuuuccgGCCc.GcCCauuCCAagccg.ggAGc.Ugggcca..aGgggccca.aGCGAAGGCu.ugggccc.Cu.uggccc....Cu.AA.aG.gGGagggaAaggCGuGAGGCuGGuUUCACaGAGCAgCGacaacc.uCCc.gCUcc.cggcaGUGGaaGGAUA.aCgGGCcggug.cac.c.ccagGc.CCAau.aaggcC.uacugg..cccacc.ccaa.augaACcacCaccuuu.
//
# STOCKHOLM 1.0

#=GF AC   RF01856
#=GF ID   Protozoa_SRP
#=GF PI   SRP_euk_arch; 7SL
#=GF DE   Protozoan signal recognition particle RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19838050
#=GF SS   Published; PMID:19838050
#=GF GA   65.00
#=GF TC   65.00
#=GF NC   64.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.96 -Z 549862.597050 CM SEQDB
#=GF CL   CL00003
#=GF DR   URL; http://rnp.uthscsa.edu/rnp/SRPDB/SRPDB.html;
#=GF DR   SO; 0000590; SRP_RNA;
#=GF DR   GO; 0006617; SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition;
#=GF DR   GO; 0005786; signal recognition particle, endoplasmic reticulum targeting;
#=GF RN   [1]
#=GF RM   11839493
#=GF RT   Towards the structure of the mammalian signal recognition particle.
#=GF RA   Wild K, Weichenrieder O, Strub K, Sinning I, Cusack S
#=GF RL   Curr Opin Struct Biol 2002;12:72-81.
#=GF RN   [2]
#=GF RM   10678824
#=GF RT   Crystal structure of the ribonucleoprotein core of the signal recognition
#=GF RT   particle.
#=GF RA   Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA
#=GF RL   Science 2000;287:1232-1239.
#=GF RN   [3]
#=GF RM   11243816
#=GF RT   Structural and energetic analysis of RNA recognition by a universally
#=GF RT   conserved protein from the signal recognition particle.
#=GF RA   Batey RT, Sagar MB, Doudna JA
#=GF RL   J Mol Biol 2001;307:229-246.
#=GF RN   [4]
#=GF RM   12520023
#=GF RT   SRPDB: Signal Recognition Particle Database.
#=GF RA   Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T
#=GF RL   Nucleic Acids Res 2003;31:363-364.
#=GF RN   [5]
#=GF RM   12140321
#=GF RT   Prediction of signal recognition particle RNA genes.
#=GF RA   Regalia M, Rosenblad MA, Samuelsson T
#=GF RL   Nucleic Acids Res 2002;30:3368-3377.
#=GF RN   [6]
#=GF RM   19838050
#=GF RT   Kinship in the SRP RNA family.
#=GF RA   Rosenblad MA, Larsen N, Samuelsson T, Zwieb C
#=GF RL   RNA Biol. 2009;6:508-516.
#=GF WK   Signal_recognition_particle_RNA
#=GF SQ   18


FJ525416.1/205-262             ------------------------------------------------------------------------------------------------------------UGGA-----CCAGCGAGG-------GUGAUUUGCUGCGUU------GACGUGGUGCUC-UGCUUGGCUGUGUGU-CGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
FJ525408.1/181-319             --------------------------------------------------------------------------------UCCUAGGUGG-AGCGGGG----GUGUCGUGGA-----CCAGCGAGG-------GUGGCGCGCUGCGUU------GACGCGGUGCUC-UGCUUGGCUGUGUGU-CGGUGUG----GCCUGCCCCCCUGUAGAGG-GGUGUCGUAGGC-UACCCG-UUGAA-GCGAGGGAAACC---------------------------------------------------------------------------------------------------------------------------------------------------
AATU01000494.1/2267-2357       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGA-AAGGUAUAC-CGCCCCAGGCUGGUAAACAGAGCAGGGAAAAGCCCUCGCUCUUG-GUAG-UGGGA-GGAUCUCGUAUCA---------------GAAUUCUGA----UGUG-----------------------------------------------
AATU01000494.1/6247-5993       -------------GGC-----GCCAACUUGUCA-CGGGCAUG-----------CU----------UCUGUCCGGGUA--GUUAGGUGUGA-GGGUUGUGGCAUGCGUUAUUGUG----ACGCUGUCC-----CCAGGAUGU------------GGAUGAUGCGUCCAUCCCAAACCAGGAGUUGAC-AU-----UGAGGUAUAGUCGUAAGAC-AGUACAUCG-AG-GUCA--CUAAGGA-AAGGUAUAC-CGCCCCAGGCUGGUAAACAGAGCAGGGAAAAGCCCUCGCUCUUG-GUAG-UGGGA-GGAUCUCGUAUCA---------------GAAUUCUGA----UGUGUC---------------------------------------------
AF006750.1/731-1010            -GCCGGAGC----CU--------UGCUCUGUAA-CCUU-------------------------------CGGGGGCU---UUCACCAGCUGAACAGGG---AGCUGUCUGGA-----CCAGCAUAGGG-----UGCUUG-C-GGCGUU------GACGUGGUGCUC-UGCUUGGCUGUGUGU-CGGAGGCCUCCGGGUGCCCCCUUGCAGAAGGGGCGCGCCC-CCUCCG----UUAAA-GUAGAGGAAC-UGGGUCAGGCCGGCA-ACGGAGCAGCCCA-CCU-CGCGCACGUCUGCCG-UUGCA-GAACCACACCGCG--------GA-GCCUG-UCAUCA----CCUGCGC--------CCCAGGCGA----UCCUGUG-AAGCUUU---------
CAAI01007232.1/3195-2917       ----------------GGGGUAUGCAGCUGUAACCGUAAGGGGAA-AGCAAAGUAAUUUGCGCAGCCUUUAAGGGAU-------GU-UACUCAUGCC------ACGAGAA----------AUUC--------AAUAUAUAAGA-----------GCUC--UCGUCUAUUGCAAGAUAUAAGUUACU-GA-----GCAUGUUAUGUUGGAAAG--AUAACAUGC-UGUAGUA--AUAAUG-AAUUGCGGAA-CGCCUUAGGCUGGAA-ACAGAGCAGGGUU-AGCAAUCGCUUGUA-UACGGUGCAA-AGUUUGCGAU-GAGC----------GAUUAGUAUAUC----UCGAA-----------UCUCGU----CAAGCAUG--GUAAGC---------
FJ525415.1/205-262             ------------------------------------------------------------------------------------------------------------UGGA-----CCAGCGAGG-------GUGAUUUGCUGCGUU------GACGUGGUGCUC-UGCUUGGCUGUGUGU-CGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
FJ525420.1/185-318             -----------------------------------------------------------------------------------CAGGCUC-AGCGGGG----AGGACGUGGA-----CCAGCGAGG-------GUGAUUUGCUGCGUU------GACGUGGUGCUC-UGCUUGGCUGUGUGU-CGGUGUG----GCCCGCCCCCCUGCAGAGG-G-UGGCGCGGGU-CCGCCG-UUGAA-GCGAGGGAACC----------------------------------------------------------------------------------------------------------------------------------------------------
ABGV01001023.1/2243-2016       ---------------------------CUGUUA-CAUUCUUGGGACUGCAUU-UC-GAUGCA--AAAGGAAUGGGAU-------GC-UAU-AAUAUUU-----CUGAGAA----------UUUUC-------AAUAUCUUAAAA----------AUUC--CCGCCUAUCACAAGACGUCAGUUACU-GA-----ACAUAUUCUUCUGGAGAG--AGAAUAUGU-UGAAGUA--AUGAUG-AAUCAUGAAC-CGCCUCAGGCUGGAA-ACAGAGCAGGGUU-AGUGAUCGCUGACG-UACGGUGUGA-AGAUUACGGUUGA-------------------------------------------------------------------------------
FJ525405.1/185-314             -----------------------------------------------------------------------------------CAGGCUC-AGCGGGG----AGGACGUGGA-----CCAGCGAGG-------GUGAUUUGCUGCGUU------GACGUGGUGCUC-UGCUUGGCUGUGUGU-CGGUGUG----GCCCGCCCCCCUGCAGAGG-G-UGGCGCGGGU-CCGCCG-UUGAA-GCGAGGG--------------------------------------------------------------------------------------------------------------------------------------------------------
AAEE01000004.1/317188-316924   ----------------------CCCAGCUGUAA-CCAA-------------------------------GUGGAGUC--GUUAAAGGUUU-AGGAUGGG-----AUACUG----UGUCACUAC----------AUCCCGGAAGUAACA-UUGCACGAUGGCUGCCCAUUACAAGGCUGCAGU-CUCUAG-----AGUUGCCUUGGUGGAGACC-GAGGUGACU-UGUGAG---AUAGUG-AAACCCGUAC-CGCCGGAGGCUGGAA-ACAGAGCACGGAAAAGGGUUCGCUGUAG-UACGGUGUAA-GGAUAACAGUAGUUGUGUAAC------UUCCUGGCAUC---UCAGUGAU------UCGCGAGA----UUC----------------------
FJ525406.1/185-314             -----------------------------------------------------------------------------------CAGGCUC-AGCGGGG----AGGACGUGGA-----CCAGCGAGG-------GUGAUUUGCUGCGUU------GACGUGGUGCUC-UGCUUGGCUGUGUGU-CGGUGUG----GCCCGCCCCCCUGCAGAGG-G-UGGCGCGGGU-CCGCCG-UUGAA-GCGAGGG--------------------------------------------------------------------------------------------------------------------------------------------------------
FJ525409.1/182-318             --------------------------------------------------------------------------------UCCUAGGUGG-AGCGGGG----GUGUCGUGGA-----CCAGCGAGG-------GUGGCGCGCUGCGUU------GACGCGGUGCUC-UGCUUGGCUGUGUGU-CGGUGUG----GCCUGCCCCCCUGUAGAGG-GGUGUCGUAGGC-UACCCG-UUGAA-GCGAGGGAAA-----------------------------------------------------------------------------------------------------------------------------------------------------
AF095839.1/1746-2062           -CCUGGAGGGUGUCA-----CGCCCCUCUGUCA-CCUGAG----------------------------UUGGGAGGCACUGUGUGCCUGG-GACUGCCCCACACACCCUAGG--CCUCCCUUGGCCUGSUUGCACCAUGGUGCCAUGCA-----GAGACUGCGCCCACUGAAAGACAGCUGC-CCUCACU----GGCACCGCC-UGGCAACAUUGGCGGUGUC-UUGGAGGC-UAUGAUGCGGAGGGGAC-UGGGCAAGGCUGGCA-ACAGAGCAGCCAAAACCUCCCACAGCUG-UCAGU-UCAG-GGAACACGCAGUU--------GAGUGGUGCUGCAG----CAGGUU-GGG-----CUGAGGGUG--CAAGGUAGG--ACUGGGCAUACC----
AAYL01000136.1/137917-137852   GGUGAGCGUAA--CG-------UCUCGCUGUCA-CCUGA-----------------------------GUGGGGGUCG-UCCGUUGGUGG-CAGG-------AGAAUCGCG-----CUU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
ABPA01000048.1/6564-6851       GGUGAGCGUAA--CG-------UCUCGCUGUCA-CCUGA-----------------------------GUGGGGGUCG-UCCGUUGGUGG-CAGG-------AGAAUCGCG-----CUUCCCUGC------CUGGCACCGGG--UACAA---GUGACAAUCUGCCCCUUGCAAGGCCGCAGU-CUCCGG-----UGGGAUGGGGACGGAGGUC-CCCAUCUCU-CGGGUG---AUGAUG-AGACGCGCAA-CGCCUCAGGCUGGAA-ACAGAGCAGGGAAAAGUGUCCGCUGUGGCGCAG-AGCAG-GGAUCACAGAGUGUCAC----------CCCGGCUGAA------CAGGGCA-----GGUGGAGG--------AGCU--CCUCACACCGCGUUU
AAGK01000005.1/1261640-1261910 -CCUGGCU-----UA---------UUGCUGUAA-CUC---------------------------------UUGAGGC---ACGAGUGUGAACAUGA-----GGGUUUGUAUU--------GGGU---------CGGCGGUGCUCGGCG--------GCGCCUGUCU-GCUAAAAUUCUGAGU--CGGUU-----GCGCGCUUUUGUGUAAGCU-UUAGAUCGC-GACUGC----UACGG-CUAGGCGGAC-CGCUCCAGGCUGGCA-ACAGAGCAGGGAAUAGCUGACGCUCAGA-CUGA-CUAGCAAGACUGCAGAUGU---------AGCUUGAACCCGC-UUC---GACUUGAACUACAUUGUACCCAC-CAGGACAUGC-UCG------------
FJ525418.1/182-320             --------------------------------------------------------------------------------UCCUAGGUGG-AGCGGGG----GUGUCGUGGA-----CCAGCGAGG-------GUGGCGCGCUGCGUU------GACGCGGUGCUC-UGCUUGGCUGUGUGU-CGGUGUG----GCCUGCCCCCCUGUAGAGG-GGUGUCGUAGGC-UACCCG-UUGAA-GCGAGGGAAACC---------------------------------------------------------------------------------------------------------------------------------------------------
#=GC SS_cons                   ......................:::::::::::.<<<<...............................>>>>----...----------.-------....-((((((---.....---(((((........-((((((((------......--((((((((((-(((((((((((((((.<<<<<<.....<<<<<<<<<<<<____>>>.>>>>>>>>>.>>>>>>,..,<___>.<<<<<<<---.<<<<<----<<<___._>>>---->>>>>.>>>>>>>))))))).)))-.))))).))---))))))))..............)))))))).......)))))..........)))))).............................
#=GC RF                        ......................ucucgCUGUaA.Ccug...............................cagGGGuc...uuguguGUgu.aAugggg....acccccuaGa.....Ccagcucc........agcucggcgugaguu......GAcccuccGcCcAuugcaggaccucaGU.ccccgg.....gggugCuccgcuGuAgagc.ggaGcaccc.ccgggga..auaaag.gggcgcgaAC.cgCcccAGGCUGGaA.ACAGAGCAggGaa.agcgcccGCugagg.uccG.ugcaa.gGAUcaCggaggg..............cgccgagc.......ggagc..........aggggg.............................
//
# STOCKHOLM 1.0

#=GF AC   RF01857
#=GF ID   Archaea_SRP
#=GF PI   SRP_euk_arch
#=GF DE   Archaeal signal recognition particle RNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:19838050
#=GF SS   Published; PMID:19838050
#=GF GA   89.00
#=GF TC   89.00
#=GF NC   88.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00003
#=GF DR   URL; http://rnp.uthscsa.edu/rnp/SRPDB/SRPDB.html;
#=GF DR   SO; 0000590; SRP_RNA;
#=GF DR   GO; 0006617; SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition;
#=GF DR   GO; 0048501; signal recognition particle, plasma membrane targeting;
#=GF RN   [1]
#=GF RM   11839493
#=GF RT   Towards the structure of the mammalian signal recognition particle.
#=GF RA   Wild K, Weichenrieder O, Strub K, Sinning I, Cusack S
#=GF RL   Curr Opin Struct Biol 2002;12:72-81.
#=GF RN   [2]
#=GF RM   10678824
#=GF RT   Crystal structure of the ribonucleoprotein core of the signal recognition
#=GF RT   particle.
#=GF RA   Batey RT, Rambo RP, Lucast L, Rha B, Doudna JA
#=GF RL   Science 2000;287:1232-1239.
#=GF RN   [3]
#=GF RM   11243816
#=GF RT   Structural and energetic analysis of RNA recognition by a universally
#=GF RT   conserved protein from the signal recognition particle.
#=GF RA   Batey RT, Sagar MB, Doudna JA
#=GF RL   J Mol Biol 2001;307:229-246.
#=GF RN   [4]
#=GF RM   12520023
#=GF RT   SRPDB: Signal Recognition Particle Database.
#=GF RA   Rosenblad MA, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T
#=GF RL   Nucleic Acids Res 2003;31:363-364.
#=GF RN   [5]
#=GF RM   12140321
#=GF RT   Prediction of signal recognition particle RNA genes.
#=GF RA   Regalia M, Rosenblad MA, Samuelsson T
#=GF RL   Nucleic Acids Res 2002;30:3368-3377.
#=GF RN   [6]
#=GF RM   19838050
#=GF RT   Kinship in the SRP RNA family.
#=GF RA   Rosenblad MA, Larsen N, Samuelsson T, Zwieb C
#=GF RL   RNA Biol. 2009;6:508-516.
#=GF WK   Signal_recognition_particle_RNA
#=GF SQ   53


AE009439.1/935907-935595     ------GGGCU----AGGCCGGCGGGCUGGCG-GUCCG-CU--------GUAACCCGAAAU---CCGCCUCAUGCGGGGGCCG---AAGCCGAGGGG--GCGGCC-CGGUCCCCCGGAGUACCGGCCCCCCGGA-CCCGACCGAUGACCCUCCGGCCCCCCG-GGGGC-CCGGGGUGGCGGGGC-CGCCGCCGGAGGGCGGCGCGCCACCGCCUUU--GCCGGGGCACCGGGUCAGGCCCGAGAGGGAGCAGCCCACCCCGGACCCGCGGCCGCUCGGGGGUCGCCGGAGG--CAGGUCGGCCGGGGGAG-UACCG-G-GCUCCGGG-GGCCG-GGUCCA-CCCCUCGGCGCGCCC-------
M21085.1/1-303               ------CGGGU---AGGGCCGGGGGC-UCGCC-CUCCC-CC--------GAGCCCCGAAAU---GGGCGUAAUGCGGGGGCCA---GUAACCCGCAC-GUCGGCCGUAGU--GGUCCAG-GGCAG--ACCCGGC-CG-ACCCAU--GACCCCCGU-CCCGCG-GGGCC-GG-CG-GCGCGGAGCC-CCCUCCGGAGGGAGGGAGGCUACCGCCCUUA-CCGGGGGAACCAGGCCAGGCCCGGAAGGGAGCAACCUAACCCCGGACGCCCGGCGUUCGCGGGGCCACGGGGU--GAGGCAACGGCCGGGCC-CCCUG-CC-CUGGGC--CCCUACGGCUGGCGUGCGGG---GGCCG-------
BX950229.1/1461662-1461973   -----GUGGCU----AGGCUGGGAAGUUAGGC-GUUUC-CU--------GUAACUCGAAAU---CGCCUUU--GCGAGAGCCG---AAAACUUGAGG--GCGGUUUUAAA-UU-CUGUCGCCCAU-U--CUCAA-GUUUUGUGUAGACAUUUCGU-CCUUUG-GGGUA-AGAUGGAGGAGG-AACCUUUUUUGUAAGAAAAAGACAAACCUCCCUUA-UCUUUCGAACCCCGUCAGGCCCGGAAGGGAGCAGCGGUAGAAAGAACUUCA-ACGCUCAGAGGGUUGCGGAAUC-GAGCAGAACUUGAGGUA-CAAUG-GGUUUCAGGA-UUUUU-CACCCA-CCUCAAGGA-AGCCACUUU---
Y08257.1/50499-50810         GGGG-UCAGGG---AGGGUGGGGGAUCUCGCC-AAUCC-CU--------AUUACCCGCA-----AGGCGUAAUGCGGGCACCA---GUAACUCCUAC-CCUAUGG-UGU--CUCCUAUCUGUAG---GUCCCAG-UGGAGCG-AU-GAAGCCUGC-CCAGCG-GGGCU-UGGCGGUCAUGGGCUUUCUCUCCGGAGGGAGAGAAAGUACCAUGAUAG-CUGGGGGAAU-CGGCGAGGCCCGGAAGGGAGCAGCCGUGCC-UGGACGCC-AGCGUUCGCUGGUCAACAGCCA--GA-GUGAAACUGGGGUA-AACCU-AUAGAUAGG---UAGG-CCAUGGGGUAGGGG---GUCUGGCCCCAU
AE010299.1/4874795-4875109   -UGA-UGAGCU----AGUCCGGGUAGCCCGGC-GUUAC-CU--------GUAACCCGAAAU---CGCCGAUAUGCGGGGGACG---AAGCCAAUGGA--AGAUGC-GUCA---AAGGGAUUCCAG--CCUGUGA-UCUCAACUGAGAAACCCCGU-CCUGCU-UGGAU-G-AUGCAGGUAUGUGGACUUGCUGGAAAACAGGUCCUC-AUACCCUAA-CUGCGGAAACCGGUCGAGGCCCGGAAGGGAGCAGACUCACUGUGGGCAACCGUCGCUUGCGGGGUCGCGGGGUG-GAGAAGAGAUUCCAGUC-UACUG-AAAUCUCCC---AGAU-ACAACG-ACCUGCGGUGUGCUCAUCA---
AJ248283.1/57201-56912       -------------------------------C-GUCCC-CU--------GUAACCGGAAAC---CGCCGAUAUGCCGGGGCCG---AAGCCCGAGGG--GCGGUU-CCCG---AAGCCGCCUCCGGAAGCCAGG-GCCGAACGAUGAGUCCUCGU-CCCGCG-GGGUG-C-CCGGUGGGGG-AGGCACGGCUGAAGGGCCGUGCUAA-CCCCCUUUA-GGCCCCAAACCCCGCAAGGCCCGGAAGGGAGCAGCGGUAGGGGCCACGGAGCACGCUCGCGGGGGUGCGGGGAU-GAGGUAGGCCCUGGUGA--AAGG-AGGCGGUGG---AGGG-UUCCCA-CCCUCGGGCGUGCCCGCCG---
AABC05000008.1/184483-184786 -UAC-UGGACU----AGACCGGGGAGCUAGGC-ACUCC-CU--------GUGACCCG-------UGCCGAAAUGCGGGGGCGA---CUGUCUGGUGA--GGGCAACCAGG--C--CUUUGGCAGU-CUUCAUGA-AAUCGUA---GAGUCUCUGU-CCUUUU-GGAUC-G-GGGGUUUGCAUAUGCAACUUCAAAGGAUGAUGCAUA-UACAAUCUG-UCGGGAAAACCCCGCCAGGCCCGGAAGGGAACACCGGUAUUCCGAACCAUCGAUGCUGAGAGGGU-GCGGGGAG-GAGAGGAAGUGGAGGA---CGCU-ACCAAAACA--CCUGG---UCU--GAACCAGAUGUGUCCAGUA---
AE008384.1/1111798-1111484   -UGA-UGAGCU----AGUCCGGGUAGCCCGGC-GUUAC-CU--------GUAACCCGAAAU---CGCCGAUACGCGGGGGACG---AAGCCAAAGGA--AGAUGU-GCCA---GAGAGAUUCCAG--CCUGAAG-UCUCAACUGAGAAGCCCCGU-CCUGCU-UGGAU-G-GUGCAGGUAUGCGGGCCUGCUGGAAAACAGGUUCUC-AUACCCUAA-CCGUGGAAACCGGUCGAGGCCCGGAAGGGAGCAGACUCACUGUGGGCAACCGUCGCUUGCGGGGUCGCGGGGUG-GAGAAGAGAUCUCAGCC-UACUG-GAGCUUCCG---AGGC-GCAGCG-ACCUGAGGCGUGCUCAUCA---
AE004437.1/460192-459888     ------GGACU----AGGCCGGGCGGUUUGGC-UCCGC-CC--------GACACCCGUGAGA-CAGUCAUC-AGCGGGGGCCG---AACACCGGGC---GCGUCC-GACC---GCCGCGGUCGG--GCCCCGGA-AGCCAACGUGGAAGCCUCGU-CCGUCG-GGGAC-GG-CGGU-CCGCGGCGUGCGCCCGCAGGGGCGUUCCGUCGUGGUUCG--ACGGUGGCAACCCGCCAGGCACGGAAGUGAGCAGCGGACCACCGAACGCCCGUCGCUCGACGGGUCGCGGGGUG-GAGAAGGCGACCGGGAC-UACCC-GGCCGGGAA---CGCC-GGGCUA--CCCCGAC--UGUCCAC-----
AE000782.1/798067-798376     --GG-UGGGCU----AGGCCGGGGGGUUCGGC-GUCCC-CU--------GUAACCCGAAAC---CGCCGAUACGCGGGGGCCG---AAGCCGAGGG---GAGGCC-UGUC--A-AGCGGGCGGCA-GCGGUUCC-AGGCACCGCAGAGUCCUCGU-CCCGGA-GGGCC-GG-CGGUUAUGGCCGGGCUGCCCGGAGGGGCUGUCCG--CCAUAUUAG-CCGGGGGGAACGGCCCAGGCCCGGAAGGGAGCAGGCUAACCCCGGACGACCGGCGCUUCCGGGGGUGCGGGGAG-GAGGUGCCUGGGGCUUC--AAGC-CGCCCGUAA---GGCA-GGUCGA--CCCGAGGCGUGCCCACC----
AP006878.1/259360-259673     -CGG-CGGGCU----AGGCCGGGGGGUUCGGC-GUCCC-CU--------GUAACCGGAAAC---CGUCGAUAUGCCGGGGCCG---AAGCCCGGGGG--GCGGUU-CCCA---AAACCGCGCCCGGAAGCCGGG-GCACAACGGUGAUCCCUCGU-CCCGGG-GGGCC-G-GCGGUGGGCG-AGGUCCGGCUGGAGGGCCGGGCUAA-CGCCCUUUG-CCCGCCGAACCCCGCCAGGCCCGGAAGGGAGCAGCGGUAGGCGGGACGUGCGGCGCUCCCGGGGUAGCGGGGGU-GAGC-GAGCCCCGGUGG--AAGG-GCGCGGCGG---AGGG-UUCCCA-CCCCCGGGCGCGCCCGCCG---
X17240.1/3-316               -CGG-CGGGCU----AGGCCGGGGGGUUCGGC-GUCCC-CU--------GUAACCGGAAAC---CGUCGAUACGCCGGGGCCG---AAGCCCGGGGG--GCGGUU-CCCG---AAGCCGUUCCCGGAAGCCGGG-GCACAACGGUGAUCCCUCGU-CCCACG-GGGCC-G-GCGGUGGGCG-GGGUCCGGCUGGAGGGCCGGGCUAA-CGCCCUUUG-CCCGCCGAACCCCGUCAGGCCCGGAAGGGAGCAGCGGUAGGCGGGACGUUCGGCGCUCGUGGGGUAGCGGGGGU-GAGC-GAGCCCCGGUGG--AAGG-GGACGGUGG---AGGG-UCCCCA-CCCCCGGGCGCGCCCGCCG---
BA000001.2/48876-48562       -CGG-CGGGCU----AGGCCGGGGGGUUCGGC-GUCCC-CU--------GUAACCGGAAAC---CGCCGAUAUGCCGGGGCCG---AAGCCCGAGGG--GCGGUU-CCCG---AAGCCGCCUCUGGAAGCCAGG-GCCGAACGAUGAGUCCUCGU-CCCGCG-GGGUG-C-CCGGUGGGGG-AGGCACGGCUGAAGGGCCGUGCUAA-CCCCCUUUG-GGCCCCAAACCCCGCAAGGCCCGGAAGGGAGCAGCGGUAGGGGCCACGGAGCACGCUCGCGGGGGUGCGGGGAU-GAGGUAGGCCCUGGUGA--AAGG-AGGCGGUGG---AGGG-UUCCCA-CCCUCGGGCGUGCCCGCCG---
CP000077.1/72170-72476       -UGG-UCAGGU---AGGGUGGAGGGUCUCGCC-AGCCC-UU--------AUA-CCCACA-----UGGCGCAACGUGGGCACCA---GUAACUCCUAU-GCUAUAA-UAC---CUGCUCUUCGAG---AUCCCAG-UCUAACU-AU-GAUCAUCGC-CCGACG-GGGCG-AGAUAGUCGUGGGUUCCCUUUCUGGAGGGAGAGGGAAUUCCACGUUGA-CCGGGGGAAC-CGGCCAGGCCCGGAAGGGAGCAACCGUGCC-CGGCUAUC-CGCGUUCGUCGGUCUCCGAU-AG-GAGG-AAGACUGGGGGUAAAUCU-CGGGGAGUA---AGGG-UUAUGGCAUAGGGG---AGCUGACCA---
AF395888.1/190-495           ------GGACU----AGGUCGGGCAGUUAGGC-CCUGC-UC--------UUCACCCGCGAAAUAGGUCUUU-AGCGGGGACCG----AACACGGGC---GCGUCC-GGUC-AGACCGGCGCGGG---CCCCGGA-AGCCAACGUAGAAACCUCGU-CCUUCG-GGGAC-A-GCGGUUCCGCGUACCCCUUCCGCAGGGAAGGGUUCGCGCGGUUUA--UCGGUGGUACCCCGCCAGGCGCGGAAGCGAGCAGCGGACCAUCGGACGUGCGUCGCUCGAGGGAUCGCGGGGUG-GAGGAGGCAACCGGGAU-UCCCC-A-CGUCGGA--ACGCC-GGGCAA--CCUCGC---UGUCCAC-----
X17238.1/1-314               -UGA-UGAGCU----AGUCCGGGUAGCCCGGC-GUUAC-CU--------GUAACCCGAAAU---CGCCGAUAUGCGGGGGACG---AAGCCAAUGGA--AGAUGC-GUCA---AAGGGAUUCCAG--CCUGUGA-UCUCAACUGAGAAACCCCGU-CCUGCU-UGGAU-G-AUGCAGGUAUGUGGACUUGCUGGAAAACAGGUCCUC-AUACCCUAA-CUGCGGAAACCGGUCGAGGCCCGGAAGGGAGCAGACUCACUGUGGGCAACCGUCGCUUGCGGGGUCGCGGGGUG-GAGAAGAGAUUCCAGUC-UACUG-AAAUCUCCC---AGAU-ACAACG-ACCUGCGGUGUGCUCAUC----
CP000745.1/730274-730491     ------UGGCU----AGGCUGGGAAGUUAGGC-GUUUC-CU--------GUAACUCGAAAU---CGCCUUU--GCGAGAGCCG---AAAACUUGAGG--GCGGUUUUAAA-UU-CUGUCAUUCAU-U--CUCAA-GUUUUGUGUAGACAUUUCGU-CCUUUG-GGGUA-AGAUGGAGGAGG-AACCUUUUUUGGAAGAAAAAGACAAACCUCCCUUA-UCUUUCGAACCCCGUCAGGCCCGGAAGGGAGCAGCGGUAGA--------------------------------------------------------------------------------------------------------
CP000300.1/1590253-1589939   -UGG-CGGGCU----AGUCUGGGUAGGCCGGC-GUUAC-CU--------AUAACCCGAAAU---CGUCGAUAUGCGGGAGACG---AAGCCAAAAGA--AGUUGU-UUUG---AUCAUAUCUAAA--CCUGUGA-UCUCAACUGAGAAGCCCCGU-CCUGCU-UGGAU-GA-UGUUGGUAGAAGAACUAAUUGGAGAAUUGGUUUUC-CUAUCUUUA-CAGUGGGAACCAGUCGAGGCCCGGAAGGGAGCAGACCUACCAUUGACAUUUGUCGCUUGUAGGGCUGCGGGGUG-GAGGAGAGGUUGCAGAU-CAUUU-GGAUUUGUG--ACAA--GCGGCA-ACUCGCGGUAUGCCCGCCA---
CP000099.1/801978-801664     -UGA-UGAGCU----AGUCCGGGUAGCCCGGC-GUUAC-CU--------GUAACCCGAGAU---CGCCGAUACGCGGGGGACG---AAGCCAAGGGA--AGAUGC-GUCG---AAGGGACUCCAG--CCUGGAA-UCUCAACGGAGAAGCCCCGU-CCUGCU-UGGAU-GG-UGCAGGUAUGCGGGUUUGCUGGAGAGCAGGUCUUC-AUACCAUAA-CUGCGGAAACCGGUCGAGGCCCGGAAGGGAGCAGACUUACUGUGGGCAACUAUCGCUUGCGGGGCUGCGGGGUG-GAGAAGAGGUCCCAGUC-UCCUG-GUAUCUCC---AAGAU-UCAACG-ACCCGAGGCGUGCUCAUCG---
L77117.1/552541-552856       -UGC-AUGGCU----AGGCCGGGGGGUUGGGC-GUCCC-CU--------GUAACCCGAAAU---CGCCCUUAUGCGGGGGCCG---AAAACUUGGGG--GCGGCAUGUCC-UC-CAGUCCUUCCU-U-CCCAGA-CUCCUCGAU-GAGGUCUCGU-CCCGUG-GGGCU-CGGCGGUGGGGG-AGCAUCUCCUGUAGGGGAGAUGUAA-CCCCCUUUA-CCUGCCGAACCCCGCCAGGCCCGGAAGGGAGCAACGGUAGGCAGGACGUCG-GCGCUCACGGGGGUGCGGGACG-GAGAAGGAAUCUGGGGG-CGAGG-GAGGACUG-G-AGGACAUGCCCA-CCCCAAGGA-AGCCAUGCA---
AE009950.1/9572-9886         -CGG-CGGGCU----AGGCCGGGGGGUUCGGC-GUCCC-CU--------GUAACCGGAAAC---CGCCGAUAUGCCGGGGCCG---AAGCCCGGGGG--GCGGUU-CCCA---AAGCCGCUCCCAGAAGCCGAG-GUCGAACGAUGAGUCCUCGU-CCCGCG-GGGUG-C-CCGGUGGGGG-AGGCACGGCUGAAGGGCCGUGCUAA-CCCCCUUUG-GGCCCCGAACCCCGCAAGGCCCGGAAGGGAGCAGCGGUAGGGGCCACGGAGCACGCUCGCGGGGGUGCGGGGAU-GAGAUAGGCCUCGGUGG--AUGG-GAGCGGUGG---AGGG-UUCCCA-CCCUCGGGCGUGCCCGCCG---
AE017261.1/1492109-1491805   --GC-UGGACU----UGGCCGGGAAGCCAGGC-ACUUC-CU--------GUUACCCGA------AGCCUAAAUGCGGGGGCGA---CAGCCGGUUGA--GGGCAACCAGG--C-CUCCAUAGGGU-CCCUGUGG-AAGCAAU---GAAUCUCUGU-CCUCCUUGGUCC-U-GGG-UUUAUGCGUGCAUUUCCAAAGGGAGAUGCAUG-CAUAAUCUG-UCCGGUGAAC-CCGCCAGGCCCGGAAGGGAGCAACGGUGGCUGGAACCAAGGAUGCUAGGAGGGU-GCGGGGAC-GAGUGGAAGCAGGGGGC--AGCC-CUAUGGGCG--CCUGG---UCC--GAUUCCGGCGUGUCCAGCA---
M22560.1/122-427             ------UGGCU----AGGCUGGGAGGUUAGGC-GUCUC-CU--------GUAACUUGAAAU---CGCCUUU--GCGAGAGCCG---AAAACUUGGGG--GCGGCA-UAAG-UUCCCAAAUUUCAU-U--CUUAA-UUAGUAUGUCGACGUUUCGU-CCUUUG-GGGUA-AGAUGGUAAGAG-ACUCUCUUUCUUAAGAAAGAGUCAAACUCUUUUCG-UAUUUCGAAACCCGCCAGGCCCGGAAGGGAGCAACGGUAGAAUUUACUUCG-ACGCUCAAGGGGUAGCGGGGCU-GAGUACUAAUUAAGGCA-AAAUG-AGAUUUGG-U-GCUUU-UGUCCA-CCCCAAGGA-AGCCA-------
M32222.1/946-1255            ------AGGCU----AGGCCGGGGGGUUAGGG-GUCCC-CU--------GUAAGCGCAAAU---CCCCUAUAUGGCGCGGCCG---AAGCCCAGGAG--GCGGCA-AGACCGCCAGACAUCGGC-CUGAGGGUU---AAACAAU-GAAGCCUCGU-CCCACA-GGGCC-A-CCGGUGGCGA-GGGUCCAGCUGGAGGGCUGGACCUAAUCGCCUUUG-CUGCGGGAAC-GGGUCAGGCCCGGAAGGGAGCAGCCCUACCGCAGACGGAUGGUGCUUGUGGGUCAACGGGGUG-GA-GUCUAUAACCCUCAGAUCAC-CGGUGUCUGGUGGUCU-UGUCCA-CUCCUGGGCGUGCCU-------
CP000493.1/1383623-1383896   ------CGGGU---AGGGCCGGGGGGCUCGCCCUCCCC-CC--------ACG-CCCGAAAC---GGGCGCAAUGCGGGGGCCA---GUAACCCGGCUUGGGGCUG-UAGG--CCCCCGCGGCAG----ACCCAG-CCGACCAAU--GACCCCCGU-CCCGCGG-GGCC-GG-CGGCGGCGGAG-CCCCCUCCGGAGGGAGGGCGGCUACCGCCCUUGCCGGGGGAACC-AGGCCAGGCCCGGAAGGGAGCAACCUAACCCCGGACGCCCGGCGUUCGCGGGGGCGCGGGGUGAGG-CAACGGCUGGGCC---CGCU-GCC-------------------------------------------
AL445063.1/194108-194411     -UGC-CAGACU----UGGCCGGGGGGUUAGGC-GUCCC-CU--------GUA-CCCGA------AGUCUAGAUGCGGGGGCGA---CAGCCCGGUGA--GACCAC-CUGG---GUUUCUGCCAGG-CCCUGCGG-AAUCAAU---GAUCUCCUGU-CCCUCU-GGAUC-G-GAGGCCCAUGGACACGAUCUCAAAGGAGAACGCGCC-CAUGGCUUG-CCAGGGGAAC-GCGCCAGGCCCGGAAGGGAGCAACGACACCCUGGACUCUCGAUGCUGGAGGGGU-GCGGGGGU-GAGAGGAAACAGGGGGU--ACCU-GACAGGACG--CCCA----GACC-GAACCGGGUGUGUCUGGCU---
BA000011.4/1475624-1475328   -UGC-CAGACU----UGGCCGGGGGGUUAGGC-GUCCC-CU--------GUA-CCCGA------AGUCUAGAUGCGGGGGCGA---CAGCCCGGUGA--GACCAC-CUGG---GUUUCUGUCAGG-CCCCGUGG-AAUCAUU---GAUCCUCUGU-CCCUCU-GGAUC-G-GAGGCCUGCAUGUACAUCCUCAAAGGAGGGUGUAUG-UGCAGCCUA-CCAGGGGAAC-GCGCCAGGCCCGGAAGGGAGCAACGACACCCUGGACUCUCGAUGCUGGAGGGGU-GCGGGGGU-GAGAGGAAGCGGGGGGU--ACCU-GGCAGGACG--CCCA----GACC-GAACCGGGUGUG----------
AE000666.1/1717964-1718273   -----UGGGCU----AGACCGGAGGGUUAGGG-GUCCU-CU--------GUAAGCGCAAAU---CCCCUAUAUGGCGCGGUUG---AAGUUCGGGGG--ACGGCU-GAUU--GACUGUCCAUCGG--CCCUGAU-GGUCGGUGUCGAAGCCUCGU-CCCGCA-GGAUC-AG-UGGUGAUGG-GGCCCUGACUGGAGGGUCAGGGUAAACCAUCUUAG-UCAUGGGAAC-GGGUCAGGCCUGGAAAGGAGCAGCCCUACCAUGGACAGCUGAUGCUUGCGGAUUAACGGGGUG-GAGCCGGUCAUCAGGAU-CACCG-GCGGAUGGA--AGAUC-UGUCAA-CCCCUGAACGUGCCCA------
X17237.1/1-310               --GG-UGGGCU----AGGCCGGGGGGUUCGGC-GUCCC-CU--------GUAACCCGAAAC---CGCCGAUACGCGGGGGCCG---AAGCCGAGGG---GAGGCC-UGUC--A-AGCGGGCGGCA-GCGGUUCC-AGGCACCGCAGAGUCCUCGU-CCCGGA-GGGCC-GG-CGGUUAUGGCCGGGCUGCCCGGAGGGGCUGUCCG--CCAUAUUAG-CCGGGGGGAACGGCCCAGGCCCGGAAGGGAGCAGGCUAACCCCGGACGACCGGCGCUUCCGGGGGUGCGGGGAG-GAGGUGCCUGGGGCUUC--AAGC-CGCCCGUAA---GGCA-GGUCGA--CCCGAGGCGUGCCCACC----
X01698.1/169-472             ------GGACU----AGGCCGGGCGGUUUGGC-UCCGC-CC--------GACACCCGUGAGA-CAGUCAUC-AGCGGGGGCCG---AACACCGGGC---GCGUCC-GACC---GCCGCGGUCGG---CCCCGGA-AGCCAACGUGGAAGCCUCGU-CCGUCG-GGGAC-GG-CGGU-CCGCGGCGUGCGCCCGCAGGGGCGUUCCGUCGUGGUUCG--ACGGUGGCAACCCGCCAGGCACGGAAGUGAGCAGCGGACCACCGAACGCCCGUCGCUCGACGGGUCGCGGGGUG-GAGAAGGCGACCGGGAC-UACCC-GGCCGGGAA---CGCC-GGGCUA--CCCCGAC--UGUCCAC-----
X15364.1/827-1136            -----UGGGCU----AGACCGGAGGGUUAGGG-GUCCU-CU--------GUAAGCGCAAAU---CCCCUAUACGGCGCGGUCG---AAGUUCAGGGG--ACGGCU-GAUC--GACUGUUUAUCGG--CCCUGCU-GAUUGGUGUCGAAGCCUCGU-CCCGCA-GGAUC-AG-UGGUGAUGG-GGCCCUGACUGGAGGGUCAGGGUAAACCAUCUUAG-UCAUGGGAAC-GGGUCAGGCCUGGAAAGGAGCAGCCCUACCAUGGACAGCUGAUGCUUGCGGAUUAACGGGGUG-GAGCCAGUCAGCGGGAU-CACCG-GUAAAUGGA--AGGUC-UGUCAA-CCCCUGAACGUGCCCA------
AY596297.1/1196460-1196149   --GA-UGGACU----AGGUCGGGGGGCUAGGC-CCCCC-UC--------CUUGCCCGCACUG-UGGUCUUG-AGCGGGGACCG---AACACCGGGG---GCGUCC-GGUC--UGACGGACGUGG--ACCCCGUG-AGCUAACGUGGAAGCCUCGU-CCCACG-GGGAC-G-GCGGUCCGCGUGGUCGCACCUGCAGGGGUGCGCCCA-CGUGGUUAA-ACGAUGGCACUCCGCCAGGCACGGAAGUGAGCAGCGGACCAUCGAACACCCGUCGCUCGUGGGGUCGCGGGGUG-GAGGAGGCAAACGGGAU-UACCC-G-CGUCCGA--ACGCC-GGGCCA--UCCUGGC--UGUCCGUUC---
BA000023.2/2064430-2064125   -GGG-UCGGGU---AGGGUGGGGAGUCUCGCC-AGCUC-CU--------GUAACCCCG------UGGCGUA-AUGGGGCACCA---GUAACCCUUAU-GCCAUGA-UAC---CUACCUCUCUAG---AUCCCAG-CUGAACGAU--GAGCACCGC-CCGGUG-GGGCG-AGACGGACGCGAAUCUCCUCUCUGGAGGGAGAGGGGAUAUCGCGUCAA-CCGGAGGAAU-CGGCCAGGUCCGGAAGGGAGCAACCGUGU-CCGGCCGUC-CGCGUUCACCGGUCACCGGUGU--GA-GAAAGGCUGGGGGUAAAUCU-AGAGAGGAA---AGGA-UCAUGGCAUAAGGG---GGCCGACCC---
X17239.1/2-308               -UGG-UCAGGU---AGGGUGGAGGGUCUCGCC-AGCCC-UU--------AUA-CCCACA-----UGGCGCAACGUGGGCACCA---GUAACUCCUAU-GCUAUAA-UAC---CUGCUCUUCGAG---AUCCCAG-UCUAACUAU--GAUCAUCGC-CCGACG-GGGCG-AGAUAGUCGUGGGUUCCCUUUCUGGAGGGAGAGGGAAUUCCACGUUGA-CCGGGGGAAC-CGGCCAGGCCCGGAAGGGAGCAACCGUGC-CCGGCUAUC-CGCGUUCGUCGGUCUCCGAUAG--GA-GGAAGACUGGGGGUAAAUCU-CGGGGAGUA---AGGG-UUAUGGCAUAGGGG---AGCUGACCA---
CP000609.1/65016-64799       ------UGGCU----AGGCUGGGAAGUUAGGC-GUUUC-CU--------GUAACUCGAAAU---CGCCUUU--GCGAGAGCCG---AAAACUUGAGG--GCGGUUUUAAA-UU-CUGUCAUUCAU-U--CUCAA-GUUUUGUGUAGACAUUUCGU-CCUUUG-GGGUA-AGAUGGCAGAGG-AACCUUUUUUGGAAGAAAAAGACAAACCUCUUUUA-UCUUUCGAACCCCGUCAGGCCCGGAAGGGAGCAGCGGUAGA--------------------------------------------------------------------------------------------------------
CP000743.1/1346658-1346343   -AAU-AUGGCU----AGGCUGGGGGGUUAGGC-GUCCC-UU--------GUAAUCUGAAAC---CGCCUUUAUGCAGAAGCCG---AAAACUUGGGA--GAGGUAUGUAU---AUUUACCAUUCA--UUCCUGA-GCUUUGUGGUGAUAUUUCGU-CCUAUG-GGGUAUAGGUGGUAAGGG-AGCUCCAUCUGUAGGGAUGGAGAAAACUCUUUUUA-UUUGCCGAACCCCGCCAGGUCCGGAAGGGAGCAACGGUAGGCGGAACUCCG-ACGCCCAUAGGGUAGCGGAAUU-GAACAGAACUUAGGGGC-AAUGG-AUGGUAAAU---UGCA-UAUCCA-UCCCAAGGA-AGCCACUUU---
ABSD01000021.1/38175-37865   -UGC-CAGGCU----AGGCCGGGGGGUUAGGC-GUCCC-CU--------GUAACCCGAAAG---CGUCUAUACGCGGGGGCGA---CAGCCGAGGG----CGGUG-UAAC--CAGGCCCGUUUCA--GACCAUG-CAGCCCUGUUGAAGCUCUGU-CCUCCG-GGGUC-G-CGGGAGCGCUGUGG-GCUUUCGGAGGGAAGCUCCAC-AGCGCUUUG-CCACGGGAACCCCGCCAGGCCCGGAAGGGAGCAGCGGUACCGUGGACCGUUGGCGCUCGGAGGGUAGCGGGGCG-GAGGGGCUGUAUGGGCC-CCUGG-AAUGGGUUC---UGGG-CAUCC---ACCUCGGCGUGCCUGGCA---
CP000855.1/1150343-1150030   -CGG-CGGGCU----AGGCCGGGGGGUUCGGC-GUCCC-CU--------GUAACCGGAAAC---CGCCGAUAUGCCGGGGCCG---AAGCCCGGGGG--GCGGUU-CCCA---AAGCCGCCUGCGGAAGUCGGG-GCACAACGAUGAUCCCUCGU-CCCACG-GGGCC-G-ACGGUGGGCG-GGGUCUGGCUGGAGGGCCGGACUAA-CGCCCUUUG-CCCGCCGAACCCCGCCAGGCCCGGAAGGGAGCAGCGGUAGGCGGGACGUUCGGCGCUCGUGGGGUAGCGGGGGU-GAGC-GAGCCCCGAUGG--AAGC-GGACGGUGG---AGGG-UUCCCA-CCCCCGGGCGCGCCCGCCG---
CP000477.1/1549337-1549652   -UGG-CGGGUU----AGUCCGGGUGGUUCGGC-GUCAC-CU--------GUAACCCGAAAU---CGCCGAUAUGCGGGGGACA---AAGCUGGUGGG--CGACUU-UAUG--CGCCGUGUAUUCA--GCCCAUC-UGCGUACAAUGAUUCUCCGU-UCUGUA-GGGAC-GG-CAUCGGUCAGGGAGUCAGCCGGAGGGCGGGCUCGC-UGGCCCUAA-CUGCAGGCACCGGUUCAGGCCCGGAAGGGAGCAGACCCACUGCGGGUAACCGUCGCUUACAGGAUCGCGGGGAG-GAGAAAGCAGAUGGAUC-AACUG-GUACGCGGU---GCUU-CUGGCA-ACCUCCAGCGCACCCGCCA---
AM114193.2/620849-620534     -UGG-CGAGCU----AGUCCGGGUGAUUCGGC-GUCAC-CU--------GUAAUCCGAAAU---CGUCGGCAUGCGGAGGACG---AAGCCCGUGGA--AGGCGU-UUUC-UGACGCAUGA-AGG--CCUUGCUUUCUCUACGUUGAAGAUCCGU-CCUGCU-GGGUU-AG-CGGUGGUAAAUCGCCGUGCUGGAGAGCACGUCGAC--UGCCUUGA-UUGCGGGGACCGGCACAGGCCCGGAAGGGAGCAUGCUAACCGUGGACAACUGACGCUUGCAGGGGCACGGGUUG-GAGGAAAGGGGCAAGAC-AACCUA-UCAUGUGC---GGUA-ACGACG-ACCUAAGGCGCGCUCGCUA---
CP001403.1/1958409-1958722   -AUG-GGGCCAGGGAGGGUGGGGGAUCUCGCC-AAUCC-CU--------GUGACCCGCA-----AGGCGUAAUGCGGGCACCA---GUAACUCCUAC--CCCAUGGUGUC--UCCUAUCUGUAG---GUCCCAG-UGGAGCUAU--GAAGGCUGC-CCAGCG-GGGCU-UGGCGGUCAUGGGCUUCCUCUCCGGAGGGAGGGGAAGUACCACGAUAG-CUGGGGGAAU-CGGCGAGGCCCGGAAGGGAGCAGCCGUGCC-CGGACGCC-AGCGUUCGCUGGUCAACAGCC---AGAGUGAAACUGGGGCA-AGCCU-AUAGAUAGG--UAGGC-CAUGGA-GUAGGGGGUCUGGCCCCAU---
CP000968.1/1864-2174         -CGG-UGGGGU---AGGACCGGGGGGGUAGCC-GUCCC-CU--------C-AACCGGA------AGGCUAA-UGCCGGGGUCAGUAACUCCCGGGGG--CGAGUUGAU-G--GUAGGGGGUCCC--UAUCUCCU-CCUAGCCGAUGAACCUCGGU-CCCGGU-GGACC-G-GCGGUGGUGAUA-ACCCAUCCGGAGGGAUGGG-GAA-UCACCUUUA-CCACC-GAACCGGGUCAGGCCCGGAAGGGAGCAGCCCUAAGGUGGACGUUCGGUGCUGCCGGGUA-ACUGGGGG-AAGGGUAUGGGGAGAAC--A-GG-GAAACUCGAUCC-AUC-AACUCC-ACCUCGGGGGAGCCCACCG---
AM180088.1/725061-725372     -GUG-UGGACU----AGGUUGGGCAGUUAGGC-CCUGCUCU--------UCAACCCACCAUU-UCGGUCUUGAGUGGGAACCA---AAU--CCGGGU--GCGUUC-GGUC--AGACCGGUGCAGG--CCCCGGA-AGCCAACUAAGAAACCUCGU-CCUUCG-GGGAC-G-GCGGUCCGUU-GACGCUGACCGCAGGGUCAGUCCGA-GACGGUUCG-UCGCCGGUAUCCCGUCAGGCGCGGAAGCGAGCAGCGAACUGGUGAACGUUCGUCGCUCGAAGGGCCGCGGGGUG-GAGGAGGCAACUGGGAC-UCCCU-GUAUCGGAA---CGCC-GAGCAA-CCCUGU----UGUCCGCUA---
CP001365.1/875764-875453     -AAG-UGGACU----AGGUCGGGCGGUUAGGC-CCCGC-UC--------GUCACCCGUGAGG-UAGUCUUU-AGCGGGGACCG----AACAGCGGGC--GCGUCC-GGUC--UGACCGGCGCGGG--CCCCGAG-AGCCAACGUGGAAGCCUCGU-CCGCCG-GGGAC-AG-CGGUCCGCGACG-CCCGCUCGCAGGAGCGGUCCGU-CGCGGUUCG-UCGGCGACACUGGGUCAGGCGCGGAAGCGAGCAGCCCACCGCCGGACGCCCGUCGCUCGUCGGGUCGCGGGGUG-GAGAAGGCAACCGGGAU-ACCCC-ACGUCGGAA---CGCC-GGGCCA-CCCCGCU---UGUCCGCCA---
AADL01001717.1/1012-1317     -AGC-CGGACU----AGGUUGGGAAGCCAGGC-UCUUC-CU--------GUUACCCGA------AGCCUAUACGCGGGAACGA---CAGUCCAGAGA--GGCCAA-CCUG---GCCUCUGUUAAG----CCUUG-AGGAAUCAAUGAGAUUUCGG-CCCAGC-GGAUC-G-GAGGAUUACAGAAAGCAAUUCAAAGGAAAUGUUUUC-CGUAACUUA-UUCACCAACC-CCGCCAGGUCCGGAAGGGAGCAACGGUAGGUGGAACUUUUGGUGCUGCUGGAU-ACCGGGGUC-GAGUGAACUCGGGGGUA-AACUU-AGCAGGACG--UCAG----GCCC-AAUCUGGGCGCGUCCGGUA---
CP000562.1/2424731-2425040   -ACG-GGGACU----AGCCUGGGUGGCUCGGC-GUCAC-CU--------GUUACCCGAAAC---CGCCGUCA-GCGGGGGGCG---AAGUCUGAGGA--AGGCCG-CAGC---GGCCUGCAGGAU-CCUCUGCG-UCCCGACGGAGAAGCCUCGU-CCCAUG-AGGUC-G-GCGGAAAGGGAUCAAUGCCCCGGAGGGGGCGGCGA--CC-U-UUUG-CCGCGGGUACCGGUUCAGGCCCGGAAGGGAGCAGACUUACCGUGGACGUUCGGCGCCCAUGGGGUUGCGGGGUG-GAGGAGGGAUGCAGCGGUGAAU----GCUUGUG---CGCA-CGGUCG-ACCAAGGACGUGUCCCCAA---
CP000816.1/174380-174069     -AAC-CGGGGU---AGGGCCGGAGGGCUCGCC-CCCCU-CCCCCCGUAAGGGGCCCGAAUU---GGGCGAAAGGCGGGGGCCA---GUAACUCCCCG--AGGCUC-CCCG--CGGUCCCGUGGGG--GGCGUCG-UCCGCGCAAU-GGCCCUCGC-CCCGCG-GGGCC-C-GCGGUGGCGG-AGCCUCCGCCGAAGGGCGGAGGUCAACCGCCUUAA-CCGGGGGAACCAGGUCAGGCCCGGAAGGGAGCAGCCUAACCCCGGCCGCGGCGCGUUCGCGGGAGAACGGGGG--GAGCGCGGGCGGCGCUG-ACCCC-CGCGGGGGC----------GCCG-CGGGG-----GCUCCGGUC---
CP000742.1/842166-842480     -AUU-AUGGCU----AGGCUGGGAAGUUAGGC-GUCUC-CU--------GUAACUCGAAAU---CGCCUUU--GCGAGAGCUG---AAAACUUGGGG--GCGGCU-UAAA--AUCGUACCUUCCA--UUCCCAA-GUCCUGUAUUGACAUCUCGU-CCUUUG-GGGUA-CGAUGGAGAAGG-AGUCUUUUCUGGAAGGAAAAGCUAAACCUUCCUAA-UCUUUCGAACCCCGUCAGGCCCGGAAGGGAGCAGCGGUAGGAAGAACUUCA-ACGCUCAGAGGGUUGCGGGAUA-GAGCAGGAUUUGGGGUUAAGUGG-UUGUUACGA--UUUUU-UGCCCA-CCCCAACGA-UGCCUUUUU---
CP001690.1/2109770-2110081   -UGA-UGGACU----AGGUCGGGCAGCUAGGC-CCUGC-CC--------UUUACCCGCAACU-UCGGCCUUUAGCGGGGACCG---AAC--CCGGGU--GCGUCC-GGUC--AGACCGGUACGGG--CCCCGGG-AGCCAACGCAGAAGCCUCGU-CCGUCG-GGGAC-A-GCGGUCCGUG-GAAGUCGUCCGCAGGGUCGGCUGAACCGCGGUUCG-UCGGUGACACUCCGCCAGGCGCGGAAGCGAGCAGCGGAUCACCGGACGUAUGUCGCUCGAGGGAUUGCGGGGUG-GAGGAGGCAACCGGGAU-UCCCC-GCACCGGAA---CGCC-GGGCAA-CCCCGU----CGUCCACCA---
CP000678.1/753569-753254     -UAU-AUGGCU----AGACUGGAGGGUUAGGG-GUCCU-CU--------GUAAGCACACAC---CCCCUUU--GGUGCAGUUG---AAGUUCAAAAG--GCGGCU-UUUU--AAGGAAUUAUGAG-CCUAAGAA-AAACGACAUAGAAACUUCGU-CCUACA-GGAUU-GA-UGGUGAUGG-GACUUUUACUGGAGGGUAAAAGUUAAUUAUCUUAA-AUAUGGGAAU-GUGUCAGGCCCGGAAGGGAGCAGCUCUACCAUUAACAGUUGAUGCUUGUAGAACCACGGGGUG-GAGUUGGGUUUUUUAGAUAACUU-GUAGUUUUG--AGAUU-AGUCCA-CUUUUGAACAUGCCAUUUU---
CP002372.1/1321052-1321364   -CGG-CGGACU----AGGCUGGGGGGUUCGGC-GUCCC-CU--------GUAACCCGAAAC---CGUCGAUAUGCGGGGGCCG---AAGCCCGAGGG--GCGGUU-CCUG---AAUCCAGCGGCG-GAAGCCGG-GGUAAACGAUGAGCCCUCGU-CCCACG-GGGCC-G-GCGGUGGGCG-GGGCGGAGCUGAAGGGCUCCGCUAA-CGCCCUUUG-CCCGCCGAACCCCGCAAGGCCCGGAAGGGAGCAGCGGUAGGCGGGACGUUCGGCGCUCGUGGGGUAGCGGGGGC-GAGGGAGUCCCGGUGG---AAGC-CGCUGGAGG---AGGG-UUCCCA-CCCUCGGGCGCGUCCGCCG---
CP001687.1/91679-91367       -AAC-UGGACU----AGGCCGGGCGGUUAGGC-CCCGC-UC--------UCACCCCGCGCU--AUGGUCUUCAGCGGGGGCCG----AAACCCGGGG--GCGUCC-GUGC--AGACGGGCGCGGG--CCCCGUU-AGCCAACGUCGAAGCCUCGU-CCUGCG-GGGGU-AG-CGGUCGGCACUGAAUCGCCUGCAGGGGCGUGCCGG-UGUCGUUAA-CCGGGGGCAAUCCGCCAGGCGCGGAAGCGAGCAGCGGACCCCUGGACACCUGCCGCUCGCAGGGUCGCGGGGUG-GAGGAGGCACGCGGGAU-UCCCC-ACGCUCGAA---CGCC-GGGCCA-UCCCGGG---CGUCCACUC---
CP001688.1/1905269-1904958   -AGAGUGGACU----AGGUCGAGGGGUUAGGC-CCCCC-UC--------CUCGCCCGCACU--ACGGUCUUGAGCGGGGACCA---AAC--UCGGGG--GCGUCC-GGUC--UGCCGGACGCAGG--CCCCGUG-AGCUAACGUCGAAGCCUCGU-CCAACG-GGGAC-AG-CGGUCCACACGGCUGCGCCUGCAGGGGCGUUCGCC-UGUGGUUAG-ACGAGGGCACUCCGCCAGGCACGGAAGUGAGCAGCGGACCCUCGUACACCUGUCGCUCGUCGGAUCGCGGGGUG-GAGGAGGCAAACGGGAC-UACCU-GCGCCCGAA---CGCC-GGGCAA-UCUCGC----UGUCCAUCU---
#=GC SS_cons                 .[[[.[[[[[[....(((((<<<<<<<_____.>>>>>.>>........,,,,<<<<<<<_..._______>>>>>>>)))))...,((((((((((..((((((.(((-..-((((((((((((..(((((((.(((((((((---((((((((.((((((.(((((.(((((<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>->>>>>>>,,.<<<<<<<---<<<<<----<<<____>>>---->>>>>>>>>>>>,))))))))))-))))))---)))))))).))))))))))))))))-.--))).)))))))))...)))-.)))))).))))))))))]]]]]]]]]...
#=GC RF                      .cgg.cgGGcu....cGGCcgGGgGgcUaGGC.gcCcC.Cu........GUaACCcGaacu...cGcCguugugCgGGgGCCg...acgccccgggg..ccgccc.cccg..ucccccccccggg..ccccgcg.ucccuccccuGAccccccGu.CCcgcg.GGGcc.gGgcGgcggcgggcccccccuCcGgAGgGagggggggcAccgccguua.ccggggcAACccgGcCAGGCCCGGAAGGGAGCAgCcgggccccggACgcCcggCGCUcgcgGGguagCgggggg.ggggagggacgcggggu.aAccc.ggggggggg...gggu.gggcgg.ccccggggcgagCCcgccg...
//
# STOCKHOLM 1.0

#=GF AC   RF01858
#=GF ID   RsaF
#=GF DE   RNA Staph. aureus F
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:19786493
#=GF SS   Published; PMID:19786493
#=GF GA   60.00
#=GF TC   65.20
#=GF NC   49.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19786493
#=GF RT   A search for small noncoding RNAs in Staphylococcus aureus reveals a
#=GF RT   conserved sequence motif for regulation.
#=GF RA   Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C,
#=GF RA   Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
#=GF RL   Nucleic Acids Res. 2009;37:7239-7257.
#=GF WK   Rsa_RNA
#=GF SQ   4


CABA01000085.1/50894-51012 UUGUUUAGCGUCGUGUAUUCAGACACGACGUUUUUUUAUGUUCUUUUUUAAUAAGAGAGAAGUGAAGUUGUAUAAAAAUGUAUUAAAUAUGCACUUUUUAUACAUUAACGAUUAAUAUA
ACHD01000003.1/67076-66958 UUGUUUAGCGUCGUGUAUUCAGACACGACGUUUUUUUAUGUUCUUUUUUAAUAAGAGGGAAGUGGAGUUGUAUAAAAAUGUAUUAAAUAUGCACUUUUUAUACAUUAACGAUUCAUAUA
CP000255.1/991580-991698   UUGUUUAGCGUCGUGUAUUCAGACACGACGUUUUUUUAUGUUCUUUUUUAAUAAGAGGGAAGUGAAGUUGUAUAAAAAUGUAUUAAAUAUGCACUUUUUAUACAUUAACGAUUCAUAUA
BX571857.1/959384-959502   UUGUUUAGCGUCGUGUAUUCAGACACGACGUUUUUUUAUGUUCUUUUUUAAUAAGAGGGAAGUGAAGUUGUAUAAAAAUGUAUUAAAUAUGCACUUUUUAUACAUUAACGAUUAAUAUA
#=GC SS_cons               ::::::<<<<<<<<<<______>>>>>>>>>>,,<<<<<-<<<<<<<<<___>>>>>>>>>>>>>>--<<<<<<<-<<<<<<<_____>>>>>>>->>->>>>>:::::::::::::::
#=GC RF                    UUGUUUagCGuCGuGuAUUCAGaCaCGaCGcuUUuucacGuuCccucuuAAUaagaggGaagugaaGUuGuauaaAaguGcauUAAAUaugCacuUuuUauaCaUUAACGAUUaAUAUA
//
# STOCKHOLM 1.0

#=GF AC   RF01859
#=GF ID   Phe_leader
#=GF DE   Phenylalanine leader peptide
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   55.00
#=GF TC   55.00
#=GF NC   54.90
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.86 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000836; mRNA_region;
#=GF DR   GO; 0006520; cellular amino acid metabolic process;
#=GF RN   [1]
#=GF RM   360214
#=GF RT   Nucleotide sequence of the leader region of the phenylalanine operon of
#=GF RT   Escherichia coli.
#=GF RA   Zurawski G, Brown K, Killingly D, Yanofsky C
#=GF RL   Proc Natl Acad Sci U S A. 1978;75:4271-4275.
#=GF RN   [2]
#=GF RM   21177642
#=GF RT   Two groups of phenylalanine biosynthetic operon leader peptides genes: a
#=GF RT   high level of apparently incidental frameshifting in decoding Escherichia
#=GF RT   coli pheL.
#=GF RA   Gurvich OL, Näsvall SJ, Baranov PV, Björk GR, Atkins JF
#=GF RL   Nucleic Acids Res. 2010;39:1-14.
#=GF WK   Attenuator_(genetics)
#=GF SQ   71


ABVX01000063.1/6342-6467       CAUGACGAAUAAACUGUUC---UUCUUCG-UA-UU-CUUUUUCACC---------UU--CCC--CUGAUU---UGG-GA--GGC-G-A-UU-CGUC-GU-------------AAGAGCAAGAAUACGAAGACGAAC--A--A--AAAAGCCUCCUG---ACCAGGAGGCUUUUUUU-AU
ABVY01000102.1/6316-6441       CAUGACAAAUAAACUGUUC---UUCUUCG-UA-UU-CUUUUUCACC---------UU--CCC--CUGAUU---UGG-GA--GGC-G-A-UU-CGUC-GU-------------AAGAGCAAGAAUACGAAGACGAAC--A--A--AAAAGCCUCCUA---ACCAGGAGGCUUUUUUU-AU
CU928158.2/475392-475267       AAUGAAACAAACACCGUUC---CUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAAC----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAAACAGAAUGCGAAGACGAAC--A--A--UAAGGCCUCCCA--AAUCGGGGGGCCUUUUUU-AU
BX950851.1/3766208-3766333     CAUGAUAAAUAAACCGUUU---UUCUUCG-UA-UU-CUUUUUCACC---------UU--CCC--CUGAUU---UGG-GA--GGC-G-A-UU-CGUC-GU-------------AAGAGCAAGAAUACGAAGACGAAC--A--A--AAAAGCCUCCUG---ACAAGGAGGCUUUUUUU-AU
AAKB02000001.1/3261022-3260897 CAUGAAACACACACCGUUU---UUCUUCG-CA-UU-CUUUUUUAUC---------UU--CCC--CUGAAA----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAAACAGAAUGCGAAGACGAAC--A--A--UAAGGCCUCCCA--AAUCGGGGGGCCUUUUUU-AU
CP000036.1/2641439-2641564     CAUGAAACACACACCGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAAU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAAACAGAAUGCGAAGACGAAC--A--A--UAAGGCCUCCCA--AACCGGGGGGCCUUUUUU-AU
CP000034.1/2566676-2566550     CAUGAAACACACACCGUUU---UUCUUCG-CA-UU-CUUUUUUACC--------AUU--CCC--CUGAAU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAAACAGAAUGCGAAGACGAAC--A--A--UAAGGCCUCCCA--AAUCGGGGGGCCUUUUUU-AU
ABHW01000042.1/27505-27630     CAUGAAACACACACCGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAAU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAAACAGAAUGCGAAGAAGAAC--A--A--UAAGGCCUCCCA--AAUCGGGGGGCCUUUUUU-AU
AACY021111109.1/462-586        CGUGAAACGACUAGCGUUC---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAAC----GG-GA--GGC-G-A-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--CAAGGCCUCCCA--AA-CGGGAGGCCUUUUUU-AU
CP000964.1/1216577-1216453     CAUGAAACGUGUCCCGUUC---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGACC----GG-GA--GGC-A-A-UU-CGUC-GU-------------AUAAGAAAGAAUGCGAAGACGAAC--A--A--UAAGGCCUCCCA--C-CCGGGAGGCCUUUUUU-AU
AM933172.1/2760279-2760404     UAUGAAGCUAACCCGGUUU---UUCUUCG-CA-UU-CUUUUUUAUC---------UU--CCC--CUGACU----GG-GA--GGC-G-U-UU-CGUC-AU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--GAAGGCCUCCCC--CACCGGGAGGCCUUUUUU-AU
CP001113.1/2810634-2810759     UAUGAAGCUAACCCGGUUU---UUCUUCG-CA-UU-CUUUUUUAUC---------UU--CCC--CUGACC----GG-GA--GGC-G-U-UU-CGUC-AU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--GAAGGCCUCCCC--CACCGGGAGGCCUUUUUU-AU
ABKX01000001.1/775502-775379   CAUGAAACAUACUCCGUUC---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAAC-----G-GA--GGC-A-U-UU-CGUC-GU-------------GUGAAACAGAAUGCGAAAACGAAC--A--A--UAAGGCCUCCCA--AA-CCGGAGGCCUUUUUU-AU
CP000653.1/3354244-3354369     CAUGAAAUAUACCCCGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAUU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--CAAGGCCUCCCA--AACCGGGAGGCCUUUUUU-AU
BAAW01013391.1/206-81          CAUGAAACUUGUCCCGUUC---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAAU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--UAAGGCCUCCCA--CAACGGGGGGCCUUUUUU-AU
CP000822.1/3653020-3653144     CAUGAAACUUAUCCCGUUC---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAAU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAAAAAGAAUGCGAAGACGAAC--A--A--UAAGGCCUCCCA--CA-CGGGAGGCCUUUUUU-AU
CAAQ01002953.1/267-141         UAUGAAGCUCACCCGGUUU---UUCUUCG-CA-UUUCUUUUUUAUC---------UU--CCC--CUGACC----GG-GA--GGC-G-U-UU-CGUC-AU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--GAAGGCCUCCCC--CACCGGGAGGCCUUUUUU-AU
CP000826.1/976810-976684       CAUGCUCCGUAAACCGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAUU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--G--CAAAGCCUCCUG-AAAUCAGGGGGCUUUUUUU-AU
CP000880.1/252138-252014       UAUGCAACUAGCUCAGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAUC----GG-GA--GGC-G-U-UU-CGUC-AU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--GAAGGCCUCCCA--CACCGGGGGGC-UUUUUU-AU
AM286415.1/981117-980993       AAUGAUUAAUAAAGUGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAUU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--CAAAGCCUCCCA---AGCGGGAGGCUUUUUUU-AU
CP000783.1/622003-621879       CAUGAAGCAACACGCGUUU---UUCUUCG-CU-UU-CUUUUUUACC---------UU--CCC--CUGAAC----GG-GA--GGC-G-U-GU-CGUC-GU-------------AC-AGAAAGCAAGCGAAGACGAAC--U--A--ACAGGCCUCCCA--CUCCGGGGGGCCUUUUUU-AU
AP008232.1/980916-980791       CAUGACAACACCGUCGUUU---UUCUUCG-CU-UU-CUUUUUUAAC---------UU--CCG--UUGCUAA-GAGG-CC--CGC-G---CU-CGUC-GU-------------GUGAGAAAUAAAGCGAAGACGAAC--C--G--CAAAGCCUCCUG--AAACAGGGGGCUUUUUUU---
BX936398.1/1012105-1011981     GAUUCUCAAUAAAGUGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUAAUU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--GAAAGCCUCCCA---AGCGGGAGGCUUUUUUU-AU
CU468135.1/2953379-2953512     GAUGAAACCCGUAUCGUUU---UUCUUCG-CA-UU-CUUUUUUACCUUCUUUACCUU--CCC--CUGAUC---AGG-GA--GGC-G-A-UU-CGUC-GU-------------GUAAGAAGUCAUGCGAAGACGAAC--A--A--UAAAGCCUCCCC----CCGGGAGGCUUUUUUU-UU
CP000901.1/3696226-3696353     GAUUCUCAAUAAAGUGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUAAUU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAA--U--A--AAUAUCCUCCGGCAUAGCCGGAGGUUUUUCAU-AU
X60420.1/299-423               AAUGAAACCUGAUCUGUUU---UUCUUCG-CU-UU-CUUUUUUACC---------UU--CCC--CUGAAC----GG-GA--GGC-C-A-UU-CGUC-GU-------------GUGAAAAUGAAAGCGAAGACGAAC--A--C--CGAAGCCUCCCA---ACCGGGAGGCUUUUUUU-UG
CP000789.1/1011988-1011867     CAUUCAACAAA-CCUGUUU---CUUUUUG-AC-UU-CUUUUUC--C---------UU--CCA--UAG--U----UG-GA--GGG-G-C-UA-ACUC-GUU-----------UGUGAAAGAAAAGUCAAAAACAAAC--A-----GAAAGCCUCCCA--CAUCGGGGGGCUUUUUUU-AU
AAPH01000053.1/27723-27600     GAUGACAAUACGCCUGUUU---UUCUUUA-GC-UU-CUUUUUUAUG---------UC--ACC--CUAGU-----GG--A--GGC-G-A-UU-CGUU-AC-------------GCAAAAAAUAAGCUAAAGACGAAU--A--G--ACAGCCUCCUCU--GACCAAGGAGGCUUUUUU-GU
AAZW01000034.1/43904-43783     GCAAACUCAAUCUUUGUUU---AUUUUUG-AC-UU-CUUUUUU--C---------UU--CCG--UAAA-U----CG-GA--GGC-U-A----AGUC-GUU-----------UUAGAAAAACAAGUCAAAAACGAAC--A--A--GAAGCCUCCCAC---ACUAGGGAGGCUUUUUU-AU
AAPS01000032.1/7970-8090       CAUUUAACCU-CACUGUUU---AUUUUUG-AC-UU-CUUUUU--CC---------UC--CCA--UAGUUG---GAG-GG---GC-GAA-CU-CGU--UU-------------GUGAAAGAAAAGUCAAAAACAAAC--A--G--A-AAGCCUCCCA--AAUCGGGAGGCUU-UUUU-AU
ACFN01000146.1/39072-39193     CACUUAACCU-CACUGUUU---AUUUUUG-AC-UU-CUUUUUC--C---------UU--CCA--UAG--U----UG-GA--GGG-G-C-UA-ACUC-GUU-----------UGUGAAAGAAAAGUCAAAAACAAAC--A-----GAAAGCCUCCCC--ACUCGGGAGGCUUUUUUU-AU
AAKK02000051.1/23374-23254     CAUUUAACCU-CACUGUUU---AUUUUUG-AC-UU-CUUUUUC--C---------UC--CC---AUAGUCG-GA-G-GG---GC-GAA-CU-CGU--UU-------------GUGAAAGAAAAGUCAAAAACAAAC--A--G--A-AAGCCUCCCA--AAUCGGGAGGCUU-UUUU-AU
AAUB01000228.1/183-57          GAUUCUCAAUAAAGUGUUU---UUCUUCCCCA-UA-GUGUAGAAC----------UU--CCC--CUAAUU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAU--A--A---AUAUCCUCCGGCAUAGCCGGAGGUUUUUCAU-AU
ACCV01000159.1/28887-28768     GCAAACAAACAACCUGUUC---UUUUUUG-AC-UU-CUUUUUU------------CU--CCA--CUAAAU---UUG-GA--GGCAG-C-CU-CGUU-UG--------------CGGAAGAUAAGUCAAAAACGAAC--A--G--GAAGCCUCCCAC------UGGGAGGCUUUUUU-AU
ABJD02000101.1/756439-756563   AAUUAUAUGCAAAUCGUCG---CUUUUCG-UU-UC-UUCUUUUACU---------UUAG--CACCUGAGUU-UC----G--GGG-G-C-UU-GCGC-GC-------------GUAAGAAAAGAAACGAAAAGUUAC--G--C--UAAAGCCUCCGU-----CAGGAGGCUUUUUUG-UU
CP000472.1/3971464-3971582     CAAAAUCCUAACUGC---G---UUUUUUA-CU-UU-CUUUUUUAUG---------CC--CCC--CACCCUC--GGA-GG--CGG-A-A-UU--UCG-GU-------------GUAAAAACGAAAGUGAAAAU------U--C--CAAAGCCUCCCA--CA-CGGGAGGCUUUUUUA-AU
CP000891.1/1537498-1537382     AAUGAUAACAGCAGCUU------UUUUUA-CU-UU-CUUUUUUACA---------CC--CCC--ACUCUA----GGAGG--CGG-A-U-UU-ACU--GU-------------GUAAAAACGAAAGUAAAAA-------U--C--CAAAGCCUCCCA---ACUGGGAGGCUUUUUUG-UC
CP001252.1/3669220-3669337     AAUGAUAACAGCAGCUU------UUUUUA-CU-UU-CUUUUUUACA---------CC--CCC--CACUCUA--GGA-GG--CGG-A-U-UU-ACU--GU-------------GUAAAAACGAAAGUAAAAA-------U--C--CAAAGCCUCCCA---ACUGGGAGGCUUUUUUG-UC
CP000606.1/1236423-1236304     AAUGAACACCCAAGC---U---UUUUUUA-CU-UU-CUUUUUUAUU---------CC--ACC--CUUCUA----GG-GAGGCGG-A-A-UU--UCG-GU-------------GUAAAAACGAAAGUAAAAAU------U--C--CAAGGCCUCCCA--UUAUGGGGGGCUUUUUUA-UU
ABCH01000026.1/57679-57560     GUACCCGAUUAAUCUGUUC---UUUUUUG-AC-UU-CUUUUUU------------CU--CCA--CUAGGC---UUG-GA--GGC-U-UCUU-CGUU-UU--------------CGAAAGAAAAGUCAAAAACGAAC--G--G--AAAGCCUCCCAA------UGGGAGGUUUUUUU-AU
ABVP01000026.1/500726-500603   AAUGUUAA--AUAUCGCUU---UUUUCCG-UU-UC-UUUUUUUACUUU-----AGCG--C----CUAAUUCAAG---GG-GGC------UU-UUGC-GC-------------GUAAGAAAAGAAACGAAAAGUAGC--G--C--CUGAGCCUCCAA--UA--UGGAGGCUUUUUUG-UU
CP000961.1/1603510-1603389     GAAACAACUUAACGUUCAC---UUUUUUA-CU-UU-CUUUUUUAUU---------CC--CCC--CAUACA----GG-GA--GGC-G-G-AA-UUUCGGU-------------GUAAAAACGAAAGUGAAAAU------U--C--CAAAGCCUCCCA--C-UAGGGGGGCUUUUUUG-UG
ACNS01000001.1/177701-177579   UAUGAUGCAUA--CAGUUA---UUUUUCG-CU-UC-UUUUUUUACU---------UU--AGCGCCUGAUU--------A--CAG-G-A-GG-CUUGCGC-------------GUAAGAAUAGAAACGAAAAAUAGC--G--C--CGAAGCCUCCCA---UCGUGGAGGCUUUUUUG-UU
AAOH01000006.1/263743-263622   CAAAAUCACCGUAUUUACU---UUUUUAG-CU-UU-UUUAU-GGAC---------CA--CCU--AAAUUU----GG-GA--GGC-G-A-UUCCGUC-AC-------------GGC-AUAAAAAAGUCAAAACG--A--A--U--UCAAGCCUCCCA---ACCGGGAGGCUUUUUUU-UU
CP000507.1/1088263-1088138     CAUGAAAUUUACCGUGAAUGCAGUUUUUA-CU-UU-CUUUUUUAUUC------ACUU--CCC--CUGAG-----GA-GG--CGG-A-U-UU-UCU--GU-------------GUAAAAACGAAAGUGAAAAU--UC---------AAAGCCUCCCA-CCACCGGGAGGCUUUUUUG-UU
AAWF01000042.1/6438-6560       GACACCUCAUUUCCUGUAC---UUUUUUG-AC-UU-CUUUUU---U---------CU--CCA--AUAAUGU--UUG-GA--GGC-UCG-CU-CGUU-GU--------------UCAAAGACAAGUCAAAAACGAAC--A-----GAAAGCCUCCUC---UCAAGGGGGCUUUUUUU-AU
ACLE01000020.1/34798-34920     AAUGUUAA--AUAUCGCUU---UUUUCCG-CU-UC-UUUUUUUACU---------UU--AGCGCCUAAUU-----U-UG--GGG-G-C-UU-UUGC-GC-------------GUAAGAAAAGAAACGAAAAGUAGC--G--C--CGGAGCCUCCAU----UUUGGAGGCUUUUUUG-UU
BX571867.1/333276-333152       AACAUUAUGUCUUUAGCUU---UUUUUCG-CA-UC-UUUUUUUACUUU----AGCAC-------CUGAAUUCAG----G--GGG-C-U-UU-GCGC----------------GUAAGAAAAGAAACGAAAAGUAGC--G--C--CUGAGCCUCCGU----UGUGGAGGCUUUUUUG-UU
CP000644.1/3503246-3503368     ACCUAUGCACGCACCAUUC---UUCUUUG-CU-UU-CUCGUUUAUC---------CG--GCC--CACAUGA--GGG-AA--GGC-CCU-GU-CGUC-GC-------------GUGAAC-AGCAACCAAAGACGAAU--C------GAGCCUCCCCU-----AGUGGAGGCUUUUUU-UU
CP000931.1/1348238-1348118     AAUAAAAUCCAUACUGC-U---UUUUUUA-CU-UU-CUUUUUUAUG---------CC--CCC--CACCCUC--GGA-GG--CGG-A-A-UU--UCG-GU-------------GUAAAAACGAAAGUAAAAAU------U--C--CAAAGCCUCCCA--CA-UGGGAGGCUUUUUUA-UA
CP000851.1/1284656-1284538     CAAAAUCCAUACUGU---A---UUUUUUA-CU-UU-CUUUUUUAUG---------UC--CCC--CACCCUC--GGA-GG--CGG-A-A-CU--UUG-GU-------------GUAAAAACGAAAGUAAAAAU------U--C--CAAAGCCUCCCA--CA-UGGGAGGCUUUUUUA-UA
AE014299.1/1425124-1425006     GAAAACAAAUACCCUAGCG---UUUUUUA-CU-UU-CUUUUUUACA---------CC--CCC--ACUCUA----GGAGG--CGG-A-U-UU-ACU--GU-------------GUAAAAACGAAAGUAAAAAUC-----------CAAAGCCUCCCA----CUGGGAGGCUUUUUCG-UC
CP000821.1/1390785-1390664     GACAUUAUAUAACGUUCAC---UUUUUUA-CU-UU-CUUUUUUAUU---------CC--ACC--CAUCUC----GG-GA--GGC-G-G-AG-UUUCGGU-------------GUAAAAACGAAAGUGAAAAU------U--C--CAAAGCCUCCCA---CUAGGGAGGCUUUUUUG-UA
CP000447.1/3502166-3502287     GAACAAAAAAAUAUUCAGC---CUUUUUA-UU-UU-CUUUUUUAUU---------CA--GCC--CACCCC---UGG-AG--GCG-G-A-UU-UUCU-GU-------------GUAAAAACGAAAAUGAAAAU------U--C--UAAAGCCUCCCA---ACUGGGAGGCUUUUUUG-UC
CU928163.2/2033912-2033788     CAAGCAAUGAAUGCUGCUA---UUUUCCG-CU-UC-UUUUUUUACUUU-----AGCU--CCU--GACUCC----AG-GA-GGC------UA---GC-GC-------------GUGAGAAGAGAAACGGAAAACAGC--G--CCUGAAAGCCUCCCA-----GUGGAGGCUUUUUUU-GU
ABXW01000077.1/6386-6505       CAUGAAACUAA----AUGC---UGUUUUC-UU-UU-UCUUCUUUAG---------CC--ACU--CACAUU---AAG--G--GGC-U-U-UU--GUC-GU-------------UCGAGAAAAAAAAGAAGACAAUAU--U--U--UAAAGCCUCCUA---CCUAGGGGGCUUUUUUA-UU
ACDJ01000007.1/23401-23525     CAAGCAUGA-AUGCUGCUA---UUUUCCG-CU-UC-UUCUUUUACUUU-----AGCA--CCU--GAACUC----AG-GA--GG----C-UU---GC-GC-------------GUGAAAGAAGAAACGGAAAACAGC--G--CCUAAAAGCCUCCCU----GGUGGAGGCUUUUUUU-AU
AE014075.1/1955244-1955120     CAAGCAAUGAAUGCUGCUA---UUUUCCG-CU-UC-UUUUUUUACUUU-----AGCA--C----CUGACUCCAG---GA--GGC-----UA--GC--GC-------------GUGAGAAGAGAAACGGAAAACAGC--G--CCUGAAAGCCUCCCA-----GUGGAGGCUUUUUUU-GU
ABAN01000011.1/149818-149695   CAAGCAUGA-ACGCUGCUA---UUUUCCG-UU-UC-UUUUUUUACU---------UU--AGCACCUGAUUC--C----A--GGA-G-G-CU--AGC-GC-------------GUGAAAAACGAAACGAAAAACAGCGCA--A--AAAAGCCUCCUG-----AUGGAGGCUUUUUUU-GU
CP000647.1/2386625-2386501     CAAGCAUGA-AUGCUGCUA---UUUUCCG-CU-UC-UUUUUUUACUUU-----AGCA--CCU--GAACUC----AG-GG-GGC------UU---GC-GC-------------GUGAAAGAAGAAACGGAAAACAGC--GCCA--GAAAGCCUCCCC----UGUGGAGGCUUUUUUC-GU
CP000462.1/1191016-1190882     ACUCAUGCACGCACCAUUC---UUUUUUG-CU-UU-CUCGUUUAUC---------CG--GCC--CUCAUGA--GGG-AA--GGC-C-C-GU-CGUC-ACGUGAAGCACUCGCGUAAAC-AGAAAGCAAAGACGAAU--C------GAGCCUCCCCU-----AGCGGAGGUUUUUUU-UU
CP002457.1/1319390-1319277     AAUGACAGCAA-CUU--------UUUUUA-CU-UU-CUUUUUUACA---------CC--CCC--ACUCUA----GGAGG--CGG-A-U-UU-ACU--GU-------------GUAAAAACGAAAGUAAAAA-------U--C--CAAAGCCUCCCA---AAUGGGAGGCUUUUUUG-UC
AALE02000041.1/17282-17158     AAUGAUCAAUAAAGUGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAUU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--UAAAGCCUCCCA--GA-CGGGAGGCUUUUUUU-AU
ACCD01000044.1/6255-6379       GAUGAUCAAUAAAGUGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAUU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--UAAAGCCUCCCA---AGCGGGAGGCUUUUUUU-AU
BA000037.2/709275-709154       GCAAAUCCACUCUCUGUUU---AGUUUUG-AC-UU-CUUUUU---U---------CU--UCG--AUA--G----CG-GA--GGG-G-C-UA-ACUC-GUU-----------UGUGAAAGAAAAGUCAAAAACAAAC--A-----GAAAGCCUCCCA--CAUCGGGGGGCUUUUUUA-UU
ABWL02000021.1/490662-490537   CAUGAAACUUGUCCCGUUC---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAAU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--UAAGGCCUCCCA--CACCGGGGGGCCUUUUUU-AU
ABXV02000042.1/6448-6567       AAUGAAUUUAA----AUUU---UGUUUUC-UU-UU-UCUUCUUUAG---------CC--ACU--CUUAUU---AAG--G--GGC-U-U-UU--GUC-GU-------------UCGAGAAAAAAAAGAAGACAAAAU--U--U--UAAAGCCCCCUC---UUUUGGGGGCUUUUUUU-AU
AALF02000003.1/44877-44755     UAUGAUACAUG--CAGUUA---CUUUUCG-CU-UC-UUUUUUUACU---------UU--AGCGCCUGAUUU--C----A--GGA-G-G-CU--UGC-GC-------------GUAAGAAUAGAAACGAAAAAUAGC--G--C--CUAAGCCUCCCA---UCGUGGAGGCUUUUUUG-UU
ABWM02000032.1/6775-6899       UAUGAAACAUACGCCGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAUU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--CAAGGCCUCCCU---ACCGGGAGGCCUUUUUU-AU
AALC02000063.1/6237-6361       GAUGAUCAAUAAAGUGUUU---UUCUUCG-CA-UU-CUUUUUUACC---------UU--CCC--CUGAUU----GG-GA--GGC-G-U-UU-CGUC-GU-------------GUGAUAAAGAAUGCGAAGACGAAC--A--A--UAAAGCCUCCCC---AGCGGGAGGUUUUUUUUUA-
ACCI02000099.1/122515-122398   UAUGAAUCUUA----AUUU---UGUUUUC-UUUUU-CUUCUUUAGC---------AA--CUC--CUAAUU----GG-G---GGC-U-U-UU--GUC-GU-------------UCGAGAAAGAAAAGAAGACAAAAU--U--A--GAAAGCCCCCUC-----UAGGGGGCUUUUUUU-AU
#=GC SS_cons                   :::::::::::::::((((...-((((((.((.((.((((-((((,.........,<..<<<..______....>>.>>..<<<.<._.__.>>>>.,,.............))))-))))))))))))))-))))..-..-..-<<<<<<<<<<_...___>>>>>>>>>>::::.::
#=GC RF                        aAUgAaacauauacuGuUc...UUuUUcG.cu.Uu.cuuuUUuacu.........uu..cCc..CUgAuu....gG.ga..Ggc.g.u.UU.cguC.GU.............guaAaaaagaAagCgAAaAcgAaC..a..a..uAAagCCuCCca...AccgGGaGGcuUUUUUu.uU
//
# STOCKHOLM 1.0

#=GF AC   RF01860
#=GF ID   Afu_455
#=GF DE   A. fumigatus snoRNA Afu_455
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   48.00
#=GF TC   48.50
#=GF NC   44.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6


AM921935.1/1-92              UUGAGUGAUGACU-CUACGACACGCU-AAGGCAUUCCUCAAACUUAA-U-CACCAUGUGGAAUCUGUC-UAAAAUUAAGUUUCAGCCUUGUCUGACU
AABX02000029.1/278047-278134 CUCCUUGAUGAUC-AACGUACAAAAU-AGGGAAUUCCUCAAGCUUAA-UACAUCAUGUGGAAUACUUU-A-----CUAGUUUCAGCCUUGUCUGAUU
ABIS01003448.1/3219-3312     GAUUAUGAUGACUAUUACGACAUGCA-AAGGCAUUCCUCAAACUUAA-U-CACCAUGUGGAAUCUGUCAUGUUAUCAAGUUUCAGCCUUGUCUGAUC
ABKI01000091.1/15116-15209   UUCUAUGAUGACC-CUACGACAUGCGAAAGGCAUUCCUCAAACUUAAGU-UAUCAUGUGGAAACUGUC-AAUUUACAAGUUUCAGCCUUGUCUGAUU
ACBU01000926.1/293813-293905 UUAUAUGAUGACC-CUACGACAUGCA-AAGGCAUUCCUCAAACUUAAGU-UAUCAUGUGGAAACUGUC-AAUUUACAAGUUUCAGCCUUGUCUGAUU
AAIL02000020.1/32785-32875   CUGUAUGAUGAAC-AUUUGACAC-CU-CAGGGAUUCCUCAUGCUUAA-UAUACGAUGUGGAUACCGUG-UUUUAU-AAGUUUCAGCCUUGUCUGACC
#=GC SS_cons                 .................................................................................................
#=GC RF                      UUGAGUGAUGACU.CUACGACACGCU.AAGGCAUUCCUCAAACUUAA.U.CACCAUGUGGAAUCUGUC.UAAAAUUAAGUUUCAGCCUUGUCUGACU
//
# STOCKHOLM 1.0

#=GF AC   RF01861
#=GF ID   TB9Cs1H1
#=GF DE   Trypanosomatid snoRNA TB9Cs1H1
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   55.00
#=GF TC   59.10
#=GF NC   43.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   4


AAHK01019181.1/18-80         AGCACAGAAGAUGAAGCCGGCUGUGGCUG---AACAGUGCUGCGUCGGUGCCGACACUGUGCGAGA
AAGZ01000003.1/384014-383952 AGCACAGAAAAUGAAGCUAGUUAUGGCGU---ACCGCUGCUGCUCUAGUGCCGACACUGUGCGAGA
FR799613.1/642090-642154     AGCGCAGCCUAGGAAACCAGUGCAUGCAAGCC-CUUGUGCUGCCCUGGUGCCGAAACUGCGCAAGA
FR798998.1/755783-755718     CGCGCAGUCUAGGAAACCAGUGCAUGCGUGAGACUUGUGCUGCGCUGGUGCCGAAGCUGCGCAAGA
#=GC SS_cons                 :<<<<<<--------<<<<<_________...____________>>>>>------->>>>>>::::
#=GC RF                      AGCgCAGaauAuGAAaCCaGUucuuGCgu...AcuuGUGCUGCgCuGGuGCCGAaACUGcGCaAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01862
#=GF ID   TB10Cs4H2
#=GF DE   Trypanosomatid snoRNA TB10Cs4H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   55.10
#=GF NC   35.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.49 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   4


AAHK01000100.1/7901-7970       ACGCCUUUGUCUAACACCCCGCACCGCGAGCACUAUUUCCCGGCGGGGUGAUUUCAGAGGGCGGAGAUUC
AAHA01000001.1/3203800-3203735 CCGUCUCUGUCUAACGCCUCACA-UGU---GCAGAAAUCGUUGUGGGGCGAUUUCAGGAGGCGGAGAUAU
FR798992.1/176034-175968       ACGUCUCUGUCUAACGGGGUGCGGUGC---UGCUCUGUCGGCGCACCUCGAUUUCAGGAGACGGAGAUGA
FR796414.1/181883-181817       ACGUCUCUGUCUAACGGGGUGCGACGC---UGCUCUGUCGGCGCACCUCGAUUUCAGGAGAUGGAGAUGA
#=GC SS_cons                   :<<<<<<<------<<<<<<<<<____...___________>>>>>>>>>------>>>>>>>:::::::
#=GC RF                        ACGcCuCUGUCUAACGccccGCgauGC...uacUaUgUCgucGCggggCGAUUUCAGGaGgCGGAGAUga
//
# STOCKHOLM 1.0

#=GF AC   RF01863
#=GF ID   TB10Cs2H2
#=GF DE   Trypanosomatid snoRNA TB10Cs2H2
#=GF AU   Doniger T; 0000-0001-6708-8404
#=GF AU   Michaeli S
#=GF AU   Unger R
#=GF AU   Osuch I
#=GF SE   Predicted; WAR;
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   66.70
#=GF NC   48.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   15840815
#=GF RT   A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in
#=GF RT   Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA
#=GF RT   modification.
#=GF RA   Liang XH, Uliel S, Hury A, Barth S, Doniger T, Unger R, Michaeli S
#=GF RL   RNA. 2005;11:619-645.
#=GF WK   Trypanosome_H/ACA_box_snoRNAs
#=GF SQ   3


AAHA01000001.1/2715113-2715179 CUCAGGGAGUUCUGUACGCCGCUGAGUGGUAUUGCUCGCUUAGUGGAGCGAUUUACUCCCCAGAUUU
AAHA01000001.1/2715588-2715654 CUCAGGGAGUUCUGUACGCCGCUGAGUGGUAUUGCUCGCUUAGUGGAGCGAUUUACUCCCCAGAUUU
AAHA01000001.1/2716063-2716129 CUCAGGGAGUUCUGUACGCCGCUGAGUGGUAUUGCUCGCUUAGUGGAGCGAUUUACUCCCCAGAUUU
#=GC SS_cons                   ::::<<<<<<--------<<<<<<<<<<________>>>>>>>>>>-------->>>>>>:::::::
#=GC RF                        CUCAGGGaGuUCUGUACGCCgCugaGuGGUAUUGCUCgCuuaGuGGAGCGAUUUaCuCCCCAGAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF01864
#=GF ID   plasmodium_snoR21
#=GF DE   small nucleolar RNA snoR21
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   90.00
#=GF TC   135.80
#=GF NC   46.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17901154
#=GF RT   Structural RNAs of known and unknown function identified in malaria
#=GF RT   parasites by comparative genomics and RNA analysis.
#=GF RA   Chakrabarti K, Pearson M, Grate L, Sterne-Weiler T, Deans J, Donohue JP,
#=GF RA   Ares M Jr
#=GF RL   RNA. 2007;13:1923-1939.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


AAKM01000009.1/910633-910779 UUUUUAAUGAUGAUACGAUGACGAGUAUGAAAAAGUAAA--GAGGAUUUAUUACCGUUUUUAAGUACAUGUUUUAU-GUACUUACUAAUUCGUAAUGAAU--CGAUUUCUUUAUUUUUA-AAGAAUGAUUAUUUGAGGCAUUUGGCUGAAAAA
AANS01001223.1/1059-1203     AUUUUUAUGAUGAAAAGAUGACGAGUAUGAAAAAAUUAA--GAAUAUUUGUUAUUAUUCUUAAAUAUAUGUUUUAU-AUAUUUAUUAAUGUAUAAUUAAU--AA---UCUUAAUUUUUAUCAUCAUGAUUAUUUGAGGCAUUUGACUGAAAAA
AABL01000250.1/6452-6597     UUUUUAAUGAUGAAACGAUGACGAGUAUGAAAAAGUGAA--AAUUGUUUAUUAUUAUUUUUAAAUACAUGUUUUAU-GUAGUUAUUAAUAUUUAAUAAAUGUAU---UUUUCAUUUUUAUU-GCAUGAUUAUUUGAGGCAUUUGGCUGAAAAA
AASM01000478.1/7-153         AUUUUUAUGAUGAA-AGAUGACGAGUAUGAUCGGAUAAAAGGAAUAUUUGUUAUUAUUCUUAAAUAUAUGUUUUACCCUAUUUAUUAAUGUAUAAUUAAU--AA---UCUUAAUUUUUAUCAUCAUGAUUAUUUGAGGCAUUUGACUGAAAAA
#=GC SS_cons                 :<<<<::::::::::::::::::::::::::::::::::..:::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::..::...:::::::::::::::::::::::::::::::::::::::::>>>>:
#=GC RF                      AUUUUUAUGAUGAAAAGAUGACGAGUAUGAAAAAAUUAA..GAAUAUUUGUUAUUAUUCUUAAAUAUAUGUUUUAU.AUAUUUAUUAAUGUAUAAUUAAU..AA...UCUUAAUUUUUAUCAUCAUGAUUAUUUGAGGCAUUUGACUGAAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01865
#=GF ID   Vg1_ribozyme
#=GF DE   Manganese dependent ribozyme in Vg1 mRNA
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Published; PMID:18753150
#=GF GA   90.00
#=GF TC   108.40
#=GF NC   39.30
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF DR   GO; 0010042; response to manganese ion;
#=GF RN   [1]
#=GF RM   18753150
#=GF RT   A manganese-dependent ribozyme in the 3'-untranslated region of Xenopus
#=GF RT   Vg1 mRNA.
#=GF RA   Kolev NG, Hartland EI, Huber PW
#=GF RL   Nucleic Acids Res. 2008;36:5530-5539.
#=GF WK   Vg1_ribozyme
#=GF SQ   4


BC090232.1/1587-1727 GAUGUUGUUAAUAAUAAUAUCUUAGAAGAACAUGGUAUAUAACCUGAUGACUUUU-CUAUUUCACUAAAAUUAGAUGAGGUGCUUGCACUAUUCACUGCACAGAGGCGUAAUCCUCCAAUAUGAAAAUAAAAAAAUAUAUAA
AF041844.1/1541-1679 AAUAAUAAUAAUAAUAAUAUCUUGGAAAAACAGGGUAUAUAAACCAUUGACUCUUAUUAUUUCACUAAAAUUAGAUUAGGUACUUGCACAAUUCACUGCACAGAG---UAAUCCUCCAAUAUGAAAAGAACAUUAAAAAAUA
CR855548.2/1536-1653 AAUGAUGAUGAUAAUGUAAUGU--GGU----------GAUU------------GCUCUGUUUCACUAAAAUGGGGUAGGGUACUGGCACUAUUCACUGCAAAGAGGUAUACUCCUCAUAAAUGGAUAAAAUUGUCCUUAUGA
BC161554.1/1544-1661 AAUGAUGAUGAUAAUGUAAUGU--GGU----------GAUU------------GCUCUGUUUCACUAAAAUGGGGUAGGGUACUGGCACUAUACACUGCAAAGAGGUAUACUCCUCAUAAAUGGAUAAAAUUGUCCUUAUGA
#=GC SS_cons         <<<<<<<<<___>>>>>>>>>:<<<<<<<-<<<<<<_____>>>-->>>-->>>>->>><<<<<,,,,,,,<<<-<<<<<<<____>>>>-->>>>>>,,,,<<<<______>>>>,,,,,>>>>>::::::::::::::::
#=GC RF              gauauuauuAAUaauaauaucUuagaagaACauGguAUAUAacCuaauGAcucuuAcuauuuCacUAAAAUuaGAugagGugcUUGcaCcAUucaCugcAcAGaGgcgUAAUcCuCcAAUAuGaaaAuAAaAaaAaAaAaaA
//
# STOCKHOLM 1.0

#=GF AC   RF01866
#=GF ID   ceN33
#=GF DE   C. elegans snoRNA ceN33
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted; Osuch I
#=GF GA   75.00
#=GF TC   89.30
#=GF NC   41.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.72 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   17903271
#=GF RT   Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap
#=GF RT   structures in Caenorhabditis elegans.
#=GF RA   Jia D, Cai L, He H, Skogerbo G, Li T, Aftab MN, Chen R
#=GF RL   BMC Mol Biol. 2007;8:86.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5


AY948672.1/1-119             CAAGCCUCC-UGGCGCUGCUAUUAGCCG-GGAUUCAUAGGC-UGGCGAUGAUUGAGAUUGUUCCCACACGCAAUUUCUCCUGAUC---CACAUGAAGGCUAAACUUCCUUGGACGUCUGAGCCGC
CAAC02000589.1/214835-214717 CAAGCCUCC-CGACGCUGCUAUAAGUCG-GGGCGCAUAGGCGAGGCGAUGAUUGAGAG-AUUCCCACACGCAAUUUCUACUGAUC---CGCAUGAAGGUUAAACUUCCUUGGACGUCUGAGCCGC
AAGD02001053.1/233627-233746 CAAGCCUCCUUGACGCUGCUAAUAGUCUUGGAUUCAUAGGC-UGGCGAUGAUUGAGAU-AUUCCCACACGCAAUUUCUGCUGAUC---CACAUGAAGGUUAAACUUCCUUGGACGUCUGAGCCAC
ABLE03023995.1/5294-5411     CAAGCCUC--UGGCGCUGC-AUUUGCCA-GAAAC--AAGGC-GGGCGAUGAUUGAUAGAUUUACCACACGCAAUUUCGCCUGAUCGUCGAAAUGAAGGUUAAACUUCCUUGGACGUCUGAGCCAC
DQ789427.1/1-73              -------------------------------------------GGCGAUGAUUGAGAG-AUUCCCACACGCAAUUUCUACUGAUC---CGCAUGAAGGUUAAACUUCCUUGGACGUCUGA-----
#=GC SS_cons                 :::::::::.<<<<______________.____________.________________.__________________________...________________________________>>>>:
#=GC RF                      CAAGCCUCC.cGgCGCUGCUAuuaGuCa.GgAuuCAuAGGC.uGGCGAUGAUUGAgAg.aUUcCCACACGCAAUUUCuaCUGAUC...cacAUGAAGGUUAAACUUCCUUGGACGUCUGAGcCgC
//
# STOCKHOLM 1.0

#=GF AC   RF01867
#=GF ID   CC2171
#=GF DE   caulobacter sRNA CC2171
#=GF AU   Osuch I
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold;
#=GF GA   60.00
#=GF TC   61.30
#=GF NC   54.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18373523
#=GF RT   Small non-coding RNAs in Caulobacter crescentus.
#=GF RA   Landt SG, Abeliuk E, McGrath PT, Lesley JA, McAdams HH, Shapiro L
#=GF RL   Mol Microbiol. 2008;68:600-614.
#=GF WK   Caulobacter_crescentus
#=GF SQ   13


ABRU01000031.1/61545-61745 --A--GUCGAAAGGAGGUGAUCCAGUGUCUCAUUGUCAUCAAUCGCGU-GCGGUGGC--------------------------C-GCGACCCUGGUCCUCGG----------------------------------AGAGGUCCGGGCCUGA-----------C--------------------------------CU------UUUGGUUGGCGCU--AACGCCCG------UCGGGCUGUUUUGGCGCUGUUCAGGCUGAGUGUUGUGGUCCGGCCGUUCG--CGGUCAGACAAUGAA-GGGCCGUCGCG-GCGA------------------CGCGGCGGCCC
CP001340.1/2404317-2404494 CAACAACUGAAAGGAGGUGGUCCAGUGUCUCAUUGUCUCCAACCGCGGUCGCAAGUC--------------------------G-UGACCUGGAGCCCGAAGAG--------------------------------CGAGGUCUCCGCCU-AAGGCGUU-GAG-----------------------------------C-GC-CAAGGGUUUCGAGU--CACUGGCUGCGAGA--------------------------------------------------GCGGCUACGACGAUGGA-GGGCCGCCCCGAGCGA-----------------UCGGGGCGGCCC
CP001029.1/672910-673080   CAACGAACGAAAGGAGGUGAUCCAGUGUCUCAUUGUCAUCAGCCGUCGCC-GACGAC--------------------------CAAGGCCUGGACCGUUACCUC--------------------------------CGGCGUGUGCGCCU-AACGCAUU----CGCG---------------------------GGAUU-AC-GACAGGUUUCGUCG--GAC-----------UGA-------------------------------------------CCGG-----UUCGACAAUGGAAGGGCCGCCCCCA---------------------UCGGGGCGGCCC
CP000927.1/3423147-3423321 CAACAACUGAAAGGAGGU-GACCAGUGUCUCAUUGUCUCCAACCGAGGUCGCAAGUC--------------------------G-UGACCUGGAGCCCGAAGAU--------------------------------CGAGGUCUCCAACUGACGGCGUU-GAA-----------------------------------C-GC-CUAAGGUUUGAAGU--CAC--GCCGCGAC---------------------------------------------------GCGGCUACGGCGAUGGA-GGGUCGUCCCGAGCAA-----------------UCGGGGCGGCCC
CP001298.1/654289-654458   CAACGAACGAAAGGAGGUGAUCCAGUGUCUCAUUGUCAUCAGCCGUCGCCG------ACGACCAAGACCUGGACUGUUGCCUC--CGGCG--------------UGUGCGCCUAACGCACCCGCGGGAUCUCAGCA-----------------------------------------------------------------------GGUUUCGUCG--GAC-----------UGA-------------------------------------------CCGG-----UUCGACAAUGGA-AGGGCCGCUCCU---------------------CGGGGCGGCCCU
CP001016.1/1823235-1823408 AACACAUCGAAAGGAGGUGAUCCAGUGUCUCAUUGUCUUACAUCGCGGGCC-----C----------------------------GGACCUGGCA---------U-----------------------------CA------UGCCUUCUUGGGGGCUU-UCG-----------------------------------G-CCUCUAAGCCGCCUUAUUCCGGGAUCGCGGAC---------------------------------------------------CGCGAUCCGACAAUGGA-AGGACCGUCUC-----CCGAGCAGUUUUGCGAA-GGGGCGGUCCU
CP000908.1/709036-709205   CAACGAACGAAAGGAGGUGAUCCAGUGUCUCAUUGUCAUCAGCCGUCGCCG------ACGACCAAGACUUGGACUGUUGCCUC--CGGCG--------------UGUGCGCCUAACGCACCCGCGGGAUCUCAGCA-----------------------------------------------------------------------GGUUUCGUCG--GA------------CUGA------------------------------------------CCGG-----UUCGACAAUGGA-AGGGCCGCCCCU---------------------CGGGGCGGCCCU
AE005673.1/2378341-2378518 CAACAACUGAAAGGAGGUGGUCCAGUGUCUCAUUGUCUCCAACCGCGGUCGCAAGUC--------------------------G-UGACCUGGAGCCCGAAGAG--------------------------------CGAGGUCUCCGCCU-AAGGCGUU-GAG-----------------------------------C-GC-CAAGGGUUUCGAGU--CACUGGCUGCGAGA--------------------------------------------------GCGGCUACGACGAUGGA-GGGCCGCCCCGAGCGA-----------------UCGGGGCGGCCC
AAAP01001663.1/83-252      CAACGAACGAAAGGAGGUGAUCCAGUGUCUCAUUGUCAUCAGCCGUCGCCG------ACGACCAAGACCUGGACCGUUGCCUC--CGGCG--------------UGUGCGCCUGACGCAUUCGCGGGAUUACGGCA-----------------------------------------------------------------------GGUUUCG-------------------UCGGGC-------------------------------------CGACCGG-----UUCGACAAUGGA-AGGGCCGCCCCA---------------------UGGGGCGGCCCU
CP001349.1/2884631-2884796 CAACAACGGAAAGGAGGUGAUCCAGUGUCUCAUUGUCAUCAGCCGCGGUCG------UCGGC----------------GGACU--UGGCCUGGAUCG------U-----------------------------------CGCCUCCGGCCUUUGCGCCU-GA------------------------------------G-CG-CCGA---UUGA-GG--AA--GCCGCCGGAC--------------------------------------------------CGCGGUCCGGCAAUGGA-AGGGCCGCUCCGGAAA-----------------CGGAGCGGCCCU
CP001280.1/754889-755037   AACGUAUCGGAAGGAGGUGAUCCAGUGUCUCAUUGUCAUUUGCUGCGGGCC-----C----------------------------GGACCUG------------GAC--------------------------UCG---------C-GCCAGUGAGGUUUUCG-----------------------------------C-CU-CCUAGGCGUCAGGU-------UCGCGGAAA--------------------------------------------------CGCGGUCCGACAAUGGAAGGGUCGUCCG--GGAA--------------------GGGCGGCCC
CP000747.1/1464672-1464502 CAACAGCUGAAAGGAGGUGAUCCAGUGUCUCAUAGUUCCACCCGUAGUUCGGUGACC--------------------------G-UGACCUGGGCCUCCGCGUU--------------------------------UGAGGUCCGCGCCU-AAGUCAUU-GCU-----------------------------------UCGG-CAA-CAGGUUCG-G--AAC---CCGCACU---------------------------------------------------GCGG-ACCGACUAUGGA-AGGGCCGCCCCGACGA------------------GGGGCGGCCCU
CP000943.1/2675436-2675272 CAACAACCGAAAGGAGGUGGUCCAGUGUCUCAUUGUCAUCAGCCGC---------------------------------------------------------------------------------------------------------------------AGGCAUCGGUGGCCCUGACCUGGAUCGUCGCCUCC---------GGCUUCGC------------------AGCCUGAGCGCACGACA---------------CGGGUCGCCGGGCUGCGG-----UUCGGCAAUGGAAGGGUCGCUCCGGGAGA-----------------CCGGGGCGGCCC
#=GC SS_cons               ::::::::::::<<<_____>>>,,,,,,((((((((,,,,,,,,,<<<<<....._............................>>>>>,,,,,...............................................,,,,,,,,.,....................................................,,,,,,,,,,,,,..,,,...<<......___...........................................____..>>.,,,))))))))-.<<<<<<<<<<<_____................._>>>>>>>>>>>
#=GC RF                    cAAcaAucGAAAGGAGGUGAUCCAGUGUCuCAUuGuCaUcAgCCGcggccg.....C............................cggccUggaa...............................................cuccgcCU.a....................................................uaaGGuUUcguau..aAc...Cg......uga...........................................ucgG..cG.UuCGaCaAUGgA.gGGcCggCcCgaGagA.................ucGgGccGgCCc
//
# STOCKHOLM 1.0

#=GF AC   RF01871
#=GF ID   MALAT1
#=GF DE   Metastasis associated lung adenocarcinoma transcript 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; RNAz; Eberhardt R
#=GF GA   70.00
#=GF TC   72.40
#=GF NC   68.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 38.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 2000147; positive regulation of cell motility;
#=GF RN   [1]
#=GF RM   17270048
#=GF RT   A screen for nuclear transcripts identifies two linked noncoding RNAs
#=GF RT   associated with SC35 splicing domains.
#=GF RA   Hutchinson JN, Ensminger AW, Clemson CM, Lynch CR, Lawrence JB, Chess A
#=GF RL   BMC Genomics. 2007;8:39.
#=GF RN   [2]
#=GF RM   20937273
#=GF RT   MALAT-1 enhances cell motility of lung adenocarcinoma cells by influencing
#=GF RT   the expression of motility-related genes.
#=GF RA   Tano K, Mizuno R, Okada T, Rakwal R, Shibato J, Masuo Y, Ijiri K, Akimitsu
#=GF RA   N
#=GF RL   FEBS Lett. 2010;584:4575-4580.
#=GF CC   MALAT 1 (metastasis associated lung adenocarcinoma transcript 1) is also
#=GF CC   known as NEAT2 (noncoding nuclear-enriched abundant transcript 2). It is a
#=GF CC   large, infrequently spliced RNA, which is highly conserved amongst
#=GF CC   mammals. It is highly expressed in the nucleus [1]. It is associated with
#=GF CC   metastasis, and positively regulates cell motility via the transcriptional
#=GF CC   and/or post-transcriptional regulation of motility-related genes [2].
#=GF WK   MALAT1
#=GF SQ   17


ABRP01112167.1/2069-1975   AAAUG-AAUU-GAUGAGCA------------AUACAAUGAAGAUCAA-AUGUCCAUCUCAA-AAUACUGCUUU-UACAAAAGCAGAAUAU--AAG--UGAAAUG-AAAUGAAAAUGA
AAGV020417860.1/1991-1901  ---UG-AAUU-GAUGAAACAC---------UUAAAAAUGAAGAUCAA-AUGUCCAUCUCA--AAUACUGCUUU-UACAAAAGCAGAAUAU--AAA--AGAA----AAAUGAAAAUGA
ABGA01013318.1/1214-1126   UAA------U-GAUGAGAA------------AUACAAUGAAGAGCCA-AUGUCCAUCUCAA-AAUACUGCUUU-UACAAAAGCAGAAUAA--AAG--CGAAAUG-AAAUGAAAAUG-
ABRT010445981.1/4276-4184  UAAUG-AAUU-GAUGAGAA------------AUGCAAUGAAGAUCAG-AUGUCCAUCUCAA---AACUGCUUU-UACAAAAGCAGAAUUU--UAA--AAAGAUG-AAAUGAAAAUGA
AAFC03015964.1/24262-24162 UAAUG-AAUU-GAUGAAAAAUAAAAAUAACGAUACAAUGAAGAUCAAAAUGUCAAUCUC---AAUACUGCUUU-UACAAAAGCAGAAUUA--AAA----AAGCG-AAAUGAAAA---
AAFR03057539.1/2772-2674   UUAUG-AACGCUAUUUU-A-----------UUUGCAAUGAAGAGAGA-AAUUUCACCUCGA-AAUGCUGCUUU-UACAAAAGCAGAAUGAUUAAA--AGAGAGAAAAAGGAAAAUGC
AAPN01356548.1/1259-1360   UAACAAAAUU-UAUGAGAAAAUACCU--A-UUUCCAAUGAAGAGAAA-GUAUCCAUCUCCA-AAUGCUGCUUU-UACAAAGGCAGAGAAA--AAG--CGCA----CACUGAAAAUCU
ABDC01174332.1/5507-5597   UAAUG-AAUU-GAUGAGAA------------AUACAGUGAAGAUCAA-AUGUCCGUCACAA-AAUACUGCUUU-UAGAAAAGCAGAAUUU--AAA---GAA----AAAUGAAAAUCA
AAWR02037822.1/3627-3723   UAACG-AAUU-GAUGAGAA------------AUACAAUGAAGAUCAA-AUGUCCAUCUCCA-AUUACUGCUUU-UACAAAAGCAGAAUAAAAAAG--CGAAAUG-AAAUGAAAAUGA
FJ209305.1/3870-3963       UAAUG-AAUU-GAUGAGAA------------AUACAAUGAAGAGGCA-AUGUCCAUCUCAA-AAUACUGCUUU-UACAAAAGCAGAAUAA--AAG--CGAAAAG-AAAUGAAAAUG-
AAKN02038533.1/90323-90414 UAAGG-AAUU-GAUGAGGA--------------ACAACGAAGAGCAA-AUGUCCACCACAA-A-CCCUGCUUUUUACAAAAGCAAAAUAA---AG--UGAAAUG-AAACAAAAAUGA
AANU01213847.1/4092-3999   UAAUG-AAUU-GAUGAGAA------------AUACAAUGAAGAGCCA-AUGUCCAUCUCAA-AAUACUGCUUU-UACAAAAGCAGAAUAA--AAG--CGAAAUG-AAAUGAAAAUC-
AAEX03011638.1/22240-22150 UAAUG-AAUU-GAUGAGAAA-----------UAACAACGAAGAUCAA-AUAACCAUCUCAA-AAUACUGCUUU-UACAAAAGCAGAAUAA--AAC---AAA-----AUGAAAAAUGG
AACZ03082520.1/19366-19459 UAAUG-AAUU-GAUGAGAA------------AUACAAUGAAGAGCCA-AUGUCCAUCUCAA-AAUACUGCUUU-UACAAAAGCAGAAUAA--AAG--CGAAAUG-AAAUGAAAAUG-
CABD02064759.1/1698-1791   UAAUG-AAUU-GAUGAGAA------------AUACAAUGAAGAGCCA-AUGUCCAUCUCAA-AAUACUGCUUU-UACAAAAGCAGAAUAA--AAG--CGAAAUG-AAAUGAAAAUG-
AAGW02079994.1/5712-5616   UAAGG-AAUU-GAUGAGAA-------------UUGAAUGAAGAUCAA-AUAUUCAUCUCAAAAAUGCUGCUUU-UACAAAAGCAGAAUAA--AAAAGCGAAAUG-AAAUGCAAAUGA
AAQR03147648.1/19088-19179 UAAUG-AAUU-GAUGAGAG------------AUACAGUGAAGAUGAA-AUGUCCGUCACAA-AAUACUGCUUU-UACAAAAGCAGAAUAA--AAG----AAAAG-AAAUGAAAAAC-
#=GC SS_cons               :::::.::::.::::::::............::::::::::::::::.:::::::::::::.:::::::::::.::::::::::::::::..:::..:::::::.::::::::::::
#=GC RF                    UAAuG.AAUU.GAUGAGAA............aUaCAAUGAAGAucaA.AUgUCCAUCUCaA.AAUaCUGCUUU.UACAAAAGCAGAAUaA..AAg..cGAAAuG.AAauGAAAAUGa
//
# STOCKHOLM 1.0

#=GF AC   RF01872
#=GF ID   MEG3_2
#=GF DE   Maternally expressed 3 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; RNAz; Eberhardt R
#=GF GA   60.00
#=GF TC   63.70
#=GF NC   53.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.82 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001641; lincRNA gene;
#=GF DR   GO; 0030308; negative regulation of cell growth;
#=GF RN   [1]
#=GF RM   20032057
#=GF RT   Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform
#=GF RT   structure, expression, and functions.
#=GF RA   Zhang X, Rice K, Wang Y, Chen W, Zhong Y, Nakayama Y, Zhou Y, Klibanski A
#=GF RL   Endocrinology. 2010;151:939-947.
#=GF RN   [2]
#=GF RM   14602737
#=GF RT   A pituitary-derived MEG3 isoform functions as a growth suppressor in tumor
#=GF RT   cells.
#=GF RA   Zhang X, Zhou Y, Mehta KR, Danila DC, Scolavino S, Johnson SR, Klibanski A
#=GF RL   J Clin Endocrinol Metab. 2003;88:5119-5126.
#=GF RN   [3]
#=GF RM   17569660
#=GF RT   Activation of p53 by MEG3 non-coding RNA.
#=GF RA   Zhou Y, Zhong Y, Wang Y, Zhang X, Batista DL, Gejman R, Ansell PJ, Zhao J,
#=GF RA   Weng C, Klibanski A
#=GF RL   J Biol Chem. 2007;282:24731-24742.
#=GF CC   MEG3 (maternally expressed 3) is a maternally expressed, imprinted
#=GF CC   noncoding RNA gene. At least 12 different isoforms of MEG3 are generated
#=GF CC   by alternative splicing [1]. Expression of MEG3 is lost in cancer cells
#=GF CC   [1,2]. It acts as a growth suppressor in tumour cells, and activates p53
#=GF CC   [2,3].
#=GF WK   MEG3
#=GF SQ   16



AJ320506.1/97369-97470       AUGUCCUGAGCAAAAGGGUCCCUUUGGGAACCUCUCAGGAGGGGGACCCGGGUCAGGGGC--GACCAGCAUCUUGCUGGCAACUCCGUGGGU-GGGGUGGGGUGG
ABRN01400937.1/2248-2352     AUGUUCUGAAUGGAAGAGUCCCUGUGGGAACUUCUCAGGAGGGGGACCUGGGCCAAGGGCUUGACCAGCAUCUCACUGGCGAUUCCAAGGCCCAGGGUGGGCUUC
ABRP01223345.1/860-963       AUGUCCUGAAUGGAAAGAUCCCUUUGGGAACUUCUCAGGAGGGGGACCUGGGCCAAGGGCUCCACCAGCAUCUCACUGGCAAUUCCAAGGCCC-AGGUGGGCUUC
ABGA01039453.1/21-119        ------UGAAUGGAAGGAUCCCUUUGGGAAAUUCUCAGGAAGGGGACCUGGGCCAAGGGCUUGACCAGCAUCCUGCUGGCAACUCCAAGGCCCUGGGUGGGCUUC
AAFC03006116.1/720-824       AUGGUCUGAAAGGAAGGGUCCCUUUGGGAACUUCUCAGGAGGGAGACCUGGGCCAAGGGCUCGGCCAGCAUCUCCCUGGCAAUUCCAAGGCCCAGGGUGGGCUUC
ABDC01449453.1/1159-1263     ACGUCCUGAAUUGAAGGAUCCUUUUGGAAUUUUCUCAGGAGGGGGACCUGGGCCAAGGGCUUGACCCGCUUCUCCCUGGCAGUUCCAAGCCCCUGGGUGGGUGUC
AAWR02020057.1/75398-75502   AUGUCCUGAACGGAAAGAUCCCUUUGGGAACUCCUCAGGAGGGGGACCUAGGCCAGAGGCUCCUCUAGCAUCUCACUGGCGAUUCCAAGGCCCAGGGUGGGCUUG
AY314975.1/512-616           AUGUCCUGAAUGGAAGGAUCCCUUUGGGAAAUUCUCAGGAGGGGGACCUGGGCCAAGGGCUUGGCCAGCAUCCUGCUGGCAACUCCAAGGCCCUGGGUGGGCUUC
ABRR01415346.1/750-853       AUGUCCUGAAUGGAAGGGUCCCUUUGGGAACUUCUCAGGAGGGGGACCUGGGCCAAGGGCUCAACCAGCAUCUCACUGGCAAUUCCAAGGCCC-GGGUGGGCUUC
AANG01539762.1/1248-1144     ACGUCCUGAACGGAAGGAUCCCUUCGGGAACUUCUCAGGAGGGGGACCUGGGCCAGGGGCUCGACCAGCAUCUCACUGGCAAUUCCAAGGCCCAUGGUGGGCUUC
AB171764.1/522-626           AUGUCUUGAAUGGAAGGAUCCCUUUGGGAACUUCUCAGGAGGGGGACCUGGGCCAAGGGCUUGACCAGCAUCCUGCUGGCAACUCCAAGGCCCUGGGUGGGCUUC
AAQR03046504.1/40290-40394   AUGUCCAAAAUGGAAGGAUCUGUUUGAGAACUUCUCAGGAGGGGGACCUGGGCCAAGGGCUUGACAAACAUCUCACUGGCAAUUCCAAGGCCCUGGGUGGGCUUC
GQ183502.1/528-632           AUGUCCUGAAUGGAAGGAUCCCUUUGGGAAAUUCUCAGGAGGGGGACCUGGGCCAAGGGCUUGGCCAGCAUCCUGCUGGCAACUCCAAGGCCCUGGGUGGGCUUC
AAEX03006004.1/374612-374716 AUGGCCUGAACGGAAGGAUCCCUUUGGGAACUUCUCAGGAGGGGGACCUGGGCCAAGGGCUUGACCAGCAUCUCACUGGCAAUUCCAAGGCUCAGGGUGGGCUUC
AAPE02055141.1/4394-4497     AUGUCCUGAAUAGAAGGAUCCCUUUGGGAACUUCUCAGGAGGGGGACCUGGGCCAAGGGCUCCGCCAGCAUCUCACUGGCAAUUCCAAAG-CCGUGGUGGGCUUC
EF517525.1/274-378           ACGUCCUGAAYGGAAGGGUCCCUUUGGGAACGUCUCGGGAGGCCGACCUGGGCCAAGGGCACAACCAGCAUCUCACUGGCAAUUCCAAGGCCCUGGGUGGGCUUC
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      AuGUCCUGAAuGGAAGGaUCCcUUUGGGAAcuUCUCAGGAGGGGGACCUGGGCCAaGGGCUugaCCAGCAUCUcaCUGGCAAuUCCAAGGCCCuGGGUGGGcUUC
//
# STOCKHOLM 1.0

#=GF AC   RF01873
#=GF ID   PISRT1
#=GF DE   Polled intersex syndrome regulated transcript 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   70.00
#=GF TC   70.60
#=GF NC   67.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   11726932
#=GF RT   A 11.7-kb deletion triggers intersexuality and polledness in goats.
#=GF RA   Pailhoux E, Vigier B, Chaffaux S, Servel N, Taourit S, Furet JP, Fellous
#=GF RA   M, Grosclaude F, Cribiu EP, Cotinot C, Vaiman D
#=GF RL   Nat Genet. 2001;29:453-458.
#=GF RN   [2]
#=GF RM   15965789
#=GF RT   Characterization of Pisrt1/Foxl2 in Ellobius lutescens and exclusion as
#=GF RT   sex-determining genes.
#=GF RA   Baumstark A, Hameister H, Hakhverdyan M, Bakloushinskaya I, Just W
#=GF RL   Mamm Genome. 2005;16:281-289.
#=GF RN   [3]
#=GF RM   14687082
#=GF RT   Exclusion of PISRT1 as a candidate locus for canine Sry-negative XX sex
#=GF RT   reversal.
#=GF RA   Kothapalli KS, Kirkness E, Natale LJ, Meyers-Wallen VN
#=GF RL   Anim Genet. 2003;34:467-469.
#=GF RN   [4]
#=GF RM   16137905
#=GF RT   Pisrt1, a gene implicated in XX sex reversal, is expressed in gonads of
#=GF RT   both sexes during mouse development.
#=GF RA   Loffler KA, Combes AN, Wilhelm D, Beverdam A, Bowles J, Koopman P
#=GF RL   Mol Genet Metab. 2005;86:286-292.
#=GF CC   PISRT1 (polled intersex syndrome regulated transcript 1) is a noncoding
#=GF CC   RNA. It has been implicated in the polled intersex (PIS) mutation in goats
#=GF CC   [1]. It has been shown not to be involved in sex determination in the
#=GF CC   rodent Ellobius lutescens [2] and in dogs [3], and is unlikely to be
#=GF CC   involved in sex-specific gonad differentiation in mice [4].
#=GF WK   PISRT1
#=GF SQ   18


AC119740.6/80294-80400       UUUAUUUUAUUCUUCAACAUU-AAGGUAACUGCAAACAUAUUGUUGAAGGAAAAUAAAAGGUACUU-----CUCAGG---CUUUCGUCUGCAAUAACUUAAAGAAAAGGACCCAGA
AAWR02009104.1/65509-65615   UUUAUUUUAUUCUUCGACAUU-AAGGUAACUGCAAACAUAUUGUCGAAAGAAAAGAAAAGGUACUU-----UUCAGG---CUUUAGUCUGCAAUAACUUACCGAAAAGGACCCAGA
ABRR01299912.1/550-656       UUUAUUUUCUUCUUCAACAUG-AAGGUAACUGCAAACAUAUUGUUGAAAGAAAAUAAAAGGUACUU-----UUCAGG---CUUUCGUCUGCAAUAACUUAAAGAAAAAGACCCAGG
ABRO01254954.1/1706-1812     UUGAUUUUAUUCUUCAACAUU-AAGAUAACUGCAAGCAUAUUGUUGAAGGAAAAUAAAAGGUAUGU-----CUCAGG---UUUUAGUCUGCAAUAACUUAAAGAAAAGGACCCAGG
AAPY01177949.1/1368-1474     UUUAUUUUAUUCUUCACCAGU-AAGGUAACUGCAAACAUAUUGUUGAAAGAAAAUAAAAGGUACUU-----CUCGGG---GUUUAGUCUGCAAUAACUUAAAGAAAAGGACCCAGA
AAKN02013167.1/63073-63179   UUUAUUUUAUUCCUCAACAUU-GAGGUAACUGCAAACAUAUUGUUAAAAGAAAAUAAAAGGUACUU-----CUCAGG---CUGUAGUCUGCAAUAACUUAAAGAAACGGACCCAGA
ABRP01054422.1/149-43        UUUAUUUUAUUCUUCAACAUU-ACGGUAACUGCAAACAUAUUGUUGAAAGAAAAUAAAAGGUGCUUU----UUCAGG---CUUUAGUCUGCAAUAACUUA-AGAAAAGGACCCAGA
AAFC03054403.1/1207-1313     UUUAUUUUAUUCUACAACAUG-AAGGUAACUGCAAACAUAUUGUUCAAAGAAAAUAAAAGGUACUU-----UUCAGG---CUUUAGUCUGCAAUAACUUAAAGGAAAGGACCCAGA
AAQQ01169652.1/6073-6183     UUUAUUUUAUUCUUCGACAUUUAAGGUAACUGCAAACAUAUUGUUGAAAGAAAAUAAAAGGUACUU-----CUCAGGCUUUUUUAGUCUGCAGUAACUUAAAGAAAAGAACCCAGA
AAYZ01323450.1/12784-12889   UUUAUUUUAUUCUUCAACAUU-AAGGUAACUGCAAAUGUAUUGUUGAAAGAAAAUAAA-GAUAGUU-----CUCGGG---CUUUAGUCUGCAAUAACUUAAAGAAAAGGACCUAGA
AANN01200282.1/1135-1029     UUCAUUUUAUUCUUUAGCUUU-AAGGUAACUACAAACACAUUGUUCAGGGAAGAGAAAAGGUACAU-----UUCAGC---CUUCAGUCUGCAAUAACUUAGAGAAAAGGACCCAGA
AAHY01080867.1/20646-20540   UUUAUUUUGUUCCUCAAUAUU-AAGGUAACUGCAAACAUAUUGCUGAAAGAAAAUAAAAGGUAUGU-----CUCCCG---CUUUAGUCUGCAAUAACUUAAAGAAACAGACUCAGG
AAIY01446543.1/5822-5933     UUUAUUUUCUUCUUCAACAUU-AAGGUAACUGCAAACAUAUUGUUGAAAUAAAAGUUACAUUUCCCCCCCCUUCAGA---CUUUAGUCUGCAAUAACUUAAAGAAAAGGACCCAGA
AAPE02006179.1/20670-20776   UUUAUUUUAUUCUUCAACAUU-AAGGUAACUGCAAACAUAUUGUUGAGAGAAAUGAAGAGGUACUU-----UUGGGG---CUUUAGUCUGCAAUAACUUAAAGAAAAGGACCCAGA
AABR05156428.1/3532-3426     UUUAUUUUGUUCCUCAACAUU-AAGGUAACUGCAAACAUAUUGUCGAAAGAAAAUAAAAGGUACGU-----CUCCAG---CUUCGGUCUGCAAUAACUUAAAGAAGCAGACUCGGG
AAGW02015277.1/12422-12317   UCUAUUUCGUUUUUCAACAUU-AAGGUAACUGCAAACAUAUUGUUGAAAGCAAAUAAA-GGUACUU-----CUCUGA---CUUUAGUCUGCAAUAACUUAAAGAAAAGGACCUAGG
AAEX03013630.1/134031-134130 UAUAUUUUAUUCUUCAACAUU-AAGGUAACUGCAAACAUAUUGGUGAAAGAAAAUAAAAGGUACUU-----UUCA----------GUCUGCAAUAACUUAAAGAAAAAGACCCAGA
AAQR03062493.1/36869-36975   UUUAUUUUAUUCUUCAACAUU-AAGGUAACUGCAAACAUAUUGUUAAAAGAAAAUAAAAGGUACUU-----CCCAGG---CUUUAGUCUGCAAUAACUUAAAGAAAAGGACCCACA
#=GC SS_cons                 :::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::.....::::::...::::::::::::::::::::::::::::::::::::
#=GC RF                      UUUAUUUUaUUCUUCAaCAUU.AAGGUAACUGCAAACAUAUUGUUGAAAGAAAAuAAAAGGUaCuU.....cUCaGG...cUUUaGUCUGCAAUAACUUAaAGAAAaGGACCCAGa
//
# STOCKHOLM 1.0

#=GF AC   RF01874
#=GF ID   MIAT_exon1
#=GF PI   RNCR2; Gomafu
#=GF DE   Myocardial infarction associated transcript exon 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   110.00
#=GF TC   117.80
#=GF NC   61.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 45.83 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0005634; nucleus;
#=GF DR   GO; 0001708; cell fate specification;
#=GF RN   [1]
#=GF RM   17066261
#=GF RT   Identification of a novel non-coding RNA, MIAT, that confers risk of
#=GF RT   myocardial infarction.
#=GF RA   Ishii N, Ozaki K, Sato H, Mizuno H, Saito S, Takahashi A, Miyamoto Y,
#=GF RA   Ikegawa S, Kamatani N, Hori M, Saito S, Nakamura Y, Tanaka T
#=GF RL   J Hum Genet. 2006;51:1087-1099.
#=GF RN   [2]
#=GF RM   17623775
#=GF RT   The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a
#=GF RT   subset of neurons.
#=GF RA   Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S
#=GF RL   J Cell Sci. 2007;120:2498-2506.
#=GF RN   [3]
#=GF RM   20459797
#=GF RT   The long noncoding RNA RNCR2 directs mouse retinal cell specification.
#=GF RA   Rapicavoli NA, Poth EM, Blackshaw S
#=GF RL   BMC Dev Biol. 2010;10:49.
#=GF CC   MIAT (myocardial infarction associated transcript), also known as RNCR2
#=GF CC   (retinal non-coding RNA 2) or Gomafu, is a noncoding RNA. Single
#=GF CC   nucleotide polymorphisms (SNPs) in MIAT are associated with a risk of
#=GF CC   myocardial infarction [1]. It is expressed in neurons, and located in the
#=GF CC   nucleus [2]. It plays a role in the regulation of retinal cell fate
#=GF CC   specification [3].
#=GF WK   MIAT_(gene)
#=GF SQ   10


AB266844.1/2-136           AGGGAGGGAGGCUGCGGACGAGUGCGGGGAGGAGUUUGAGAUGGGAGGC-GCUUGCAGGGGCUCCCCCAGUUCUGCGCUGUGAGCCGGGG-CACAAAGAG--CCCUCUGCAC-UAGCGCCGCAGGACC---GCGGACCCGAGG
AAFC03084114.1/31671-31805 CGGGAGGGAGGCUGCGGACGAGGGCGGGGAGGAGUUUGCGAUGGGAGGC-GCCUGCAGGGGCUCCCCCAGUUCUGCGCUGUGAGCCGGGG-CACAAAGAG--CUCUCUGCAC-UGGCGCCGCAAGACC---GCGGACCCGAGG
CT737259.5/102734-102600   AGGGAGGGAGGCUGCGGACGAGUGCGGGGAGGAGUUUGCGAUGGGAGGC-GCUUGCAGGGGCUCCCCCAGUUCUGCACUGUGAGCCCGGG-CACAAAGAG--CCCUCUGCAC-UGGCGCCGCAGGACC---GAGGACCAGGAC
ABRQ01066697.1/476-609     AGGGAGGGAGGCUGCGGACGAGUGCGGGGAGGAGUUUGCGAUGGGAGGC-GCUUGCAGGGGCUCCCCCAAUUCUGCGCCUUGAGCCGGG--CACAAAGAG--CCCUCUGCAC-UCUUGCCGCAGGACC---GCGGACCCCAGG
AAPY01200724.1/1719-1855   AGGGAGGGAGGCUGCGGACGAGAGCGGGGAGGAGUUUGCAAUGGGAGGU-GCUUGCAGGGGCUCCCC-AGUUCUGCGCUGUGAGCCGGGG-CACAAAGAGAGCCCUCUGCACCUCGUGCCGCAGGACC---GCGGACCCGAGG
AAWR02038447.1/30227-30093 AGGGAGGGAGGCUGCGGACGAGCGCGGGGAGGAGUUUGCGAUGGGAGGC-GCUCGCAAGGGCUCCCCCAGUUCUGCGCUGAUAGCCCGGG-CACAAAGAG--CCCUCUGCAC-UCGCGCCGCAGGACC---GCCGACCCGAGG
ABDC01360925.1/511-648     GGGGAGGGAGGCUGCGGACGAGCGCGGGGAGGAGUUUGCGAGGGGAGGCAGCUUGCAGGGGCUCCCCCAGUUCUGCGCUGCGAGCCCGGGGCACAAAGAG--CCCUCUGCAC-UCGCGCCGCAGGGCC--CGCGGAACCGAGG
AAKN02007326.1/79137-79003 AGGGAGGGAGGCUGCGGACGAGUGCGGGGAGGAGUUUGCGAGGGGAGGC-GCUUGCAAGGGCUCCCCCACUUCUGCGCUGUGAGCAGGGG-CACAAAGAG--CCCUCUGCAC-UCCAACCUUCGCACC---GUGAACCCGAGG
AAGW02064803.1/25152-25286 CGGGAGGGAGGCUGCGGACGAGUGCGGGGAGGAGUCUGCGCUGGGAGGC-GCUUGCAGGGGCUCCCCCAGUUCUGCGCCGAGAGCCGCGG-CACAAAGAG--CUCUCUGCGC--CCACCAGAGGUAAG--CGGCCGCCCGCGU
AB300594.1/194-328         AGGGAGGGAGGCUGCGGACCAGAGCGGGGAGGAGUUUGCGAGGGGAGGC-GCUUGGGAGGACUCCCCCAGUUCU--GUUAAGAGCUG-GG-CACAAAGAG--CCCUUUGCAC-UCCAGCCGCAGGAGCGAGGAGGAGCCGAGC
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::.:::::::::..::::::::::.:::::::::::::::...::::::::::::
#=GC RF                    aGGGAGGGAGGCUGCGGACGAGuGCGGGGAGGAGUUUGCGauGGGAGGC.GCUUGcagGGGCUCCCCCAgUUCUGCGCuguGAGCcgGGG.CACAAAGAG..CcCUCUGCaC.UcgcgCcGcaGgAcc...GcggacCCGaGg
//
# STOCKHOLM 1.0

#=GF AC   RF01875
#=GF ID   MIAT_exon5_1
#=GF PI   RNCR2; Gomafu; MIAT
#=GF DE   Myocardial infarction associated transcript exon 5 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF AU   Burge S; 0000-0002-2506-927X
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   100.00
#=GF TC   131.20
#=GF NC   67.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005634; nucleus;
#=GF DR   GO; 0001708; cell fate specification;
#=GF RN   [1]
#=GF RM   17066261
#=GF RT   Identification of a novel non-coding RNA, MIAT, that confers risk of
#=GF RT   myocardial infarction.
#=GF RA   Ishii N, Ozaki K, Sato H, Mizuno H, Saito S, Takahashi A, Miyamoto Y,
#=GF RA   Ikegawa S, Kamatani N, Hori M, Saito S, Nakamura Y, Tanaka T
#=GF RL   J Hum Genet. 2006;51:1087-1099.
#=GF RN   [2]
#=GF RM   17623775
#=GF RT   The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a
#=GF RT   subset of neurons.
#=GF RA   Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S
#=GF RL   J Cell Sci. 2007;120:2498-2506.
#=GF RN   [3]
#=GF RM   20459797
#=GF RT   The long noncoding RNA RNCR2 directs mouse retinal cell specification.
#=GF RA   Rapicavoli NA, Poth EM, Blackshaw S
#=GF RL   BMC Dev Biol. 2010;10:49.
#=GF CC   MIAT (myocardial infarction associated transcript), also known as RNCR2
#=GF CC   (retinal non-coding RNA 2) or Gomafu, is a noncoding RNA. Single
#=GF CC   nucleotide polymorphisms (SNPs) in MIAT are associated with a risk of
#=GF CC   myocardial infarction [1]. It is expressed in neurons, and located in the
#=GF CC   nucleus [2]. It plays a role in the regulation of retinal cell fate
#=GF CC   specification [3].
#=GF WK   MIAT_(gene)
#=GF SQ   9


AAIY01390116.1/3685-3833   GCAUGGUGUGGUGAAGCUACUAACC----CAGGGCUCGGCCGGGACUGUUGUGGCGUGUGAC-----AAGGUGCCUGGCCUUCUGCCAACCGACUAACCCACUAACCAGGCCCGAGCAUGCCCUACUAACCC-----CUCCCCGCAGGCAGACCCUACUAACG
AAKN02007326.1/69815-69666 GCAUGGUGUGAUUAACCUACUAACC----CAGGGCUCGGCCAGGAC-GCUGUGGCGCGUGCCGUGCCGAGGUGCCUGGCCUUUUGCCAACCGACUAACCCACUAACCAGGCCCGAGCAUGCCCUACUAACC--------CUGCGCAGCCAGACCCUACUAACU
AALT01065999.1/224-368     GCAUGGUGGAAUUAACCUACUAACC----CAGGGCUCGGCCGGGAC-GCUGUGGUGUGUGAC-----GAGGUGCCUGGCCUUCUGCCAACUGACUAACCCACUAACCAGGCCCGAGCAUGCCCUACUAACC--------CCGCGCAGCCAGACCUUACUAACC
AAYZ01682535.1/731-873     GCAUGGUCUGAUUAACCUACUAACCCA---AGGGCUCGGCCGGGA------UGCUGUGUGAC-----AAGGUGC-UGGUCUUCUGUCAACCGACUAACCCACUAACCAGGUCCGAGCAUGCCCUACUAACCC-----CUUCCCGCAGCCAGACCCAACUAACC
AB266844.1/13882-14030     GCAUGGUGUGAUUAACCUACUAACC----CAGGGCUCAGCCGGGAC-GCUGUGGCGUGUGAC-----GAGGUGCCUGGCCUUCUGCCAACCAACUAACCCACUAACCAGGCCCGAGCAUGCCCUACUAACCAC----CCCCCCGCAGCCAGAUCCUACUAACU
AB300594.1/4464-4613       GCAUGGUGUGAUUAACCUACUAACCAACCCAGGGCUCGGCCAGGAC-GCUGUGGCACGCGAC-----GAGAUGCCUGGCCUUCUGUCAACCGACUAAUCCACUAACCUGGCCCGAGCAUGUCCUACUAACC-------CCGCAGCAGCCAAACCCUACUAACU
ABRQ01066702.1/4312-4456   GCAUGGUGUGAUUAACCUACUAACC----CAGGGCUCGGCCAGGACCGCUGUGGCGUGUGAC-----ACGAUGUCUGGCCUUCUGCCAGCUAACUAACCCACUAACCAGGCCCGAGCAUGCCCUACUAACC---------CCUGCAGCCAGACCCUACUAACU
AAEX03014771.1/11650-11794 GCAUGGUGUGAUUAACCUACUAACC----CAGGGCUCGGCCGGGAC-GCUGUGGCGUGUGAC-----GAGGUGCCUGGCCUUCUGCCAACCAACUAACCCACUAACCAGGCCCGAGCAUGCCCUACUAACC--------CCCUGCAGCCAGACCCUACUAACC
AAQR03069495.1/36963-37115 GCAUGGUGUGAUUAACCUACUAACC----CAGGGCUCGGCCGGGAC-GCUGUGGAGUGUGAC-----GAGGUGCCUGGCCUUCUGCCAGCCAACUAACCCACUAACCAGGCCCCAGCAUGCCCUACUAACCCCCUGCCACCCCGCAGCCAAACCCUACUAACU
#=GC SS_cons               :::::::::::::::::::::::::....:::::::::::::::::.:::::::::::::::.....::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.......:::::::::::::::::::::::::
#=GC RF                    GCAUGGUGuGaUuAAcCUACUAACC....cAGGGCUCGGCCgGGAC.GcUGUGGcGuGuGaC.....gaGGUGCCUGGCCUUcUGcCAaCcgACUAAcCCACUAACCaGGCCCGAGCAUGcCCUACUAACC.......uccccGCAGcCAGACCCuACUAACu
//
# STOCKHOLM 1.0

#=GF AC   RF01876
#=GF ID   MIAT_exon5_2
#=GF PI   RNCR2; Gomafu
#=GF DE   Myocardial infarction associated transcript exon 5 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   75.00
#=GF TC   81.20
#=GF NC   48.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.44 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005634; nucleus;
#=GF DR   GO; 0001708; cell fate specification;
#=GF RN   [1]
#=GF RM   17066261
#=GF RT   Identification of a novel non-coding RNA, MIAT, that confers risk of
#=GF RT   myocardial infarction.
#=GF RA   Ishii N, Ozaki K, Sato H, Mizuno H, Saito S, Takahashi A, Miyamoto Y,
#=GF RA   Ikegawa S, Kamatani N, Hori M, Saito S, Nakamura Y, Tanaka T
#=GF RL   J Hum Genet. 2006;51:1087-1099.
#=GF RN   [2]
#=GF RM   17623775
#=GF RT   The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a
#=GF RT   subset of neurons.
#=GF RA   Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S
#=GF RL   J Cell Sci. 2007;120:2498-2506.
#=GF RN   [3]
#=GF RM   20459797
#=GF RT   The long noncoding RNA RNCR2 directs mouse retinal cell specification.
#=GF RA   Rapicavoli NA, Poth EM, Blackshaw S
#=GF RL   BMC Dev Biol. 2010;10:49.
#=GF CC   MIAT (myocardial infarction associated transcript), also known as RNCR2
#=GF CC   (retinal non-coding RNA 2) or Gomafu, is a noncoding RNA. Single
#=GF CC   nucleotide polymorphisms (SNPs) in MIAT are associated with a risk of
#=GF CC   myocardial infarction [1]. It is expressed in neurons, and located in the
#=GF CC   nucleus [2]. It plays a role in the regulation of retinal cell fate
#=GF CC   specification [3].
#=GF WK   MIAT_(gene)
#=GF SQ   10


AAGV020563742.1/271-349    UGGUGCUGUGCUCUGA-CCUACUAACUUGGCC-UUACUAACCCCAUUU-----UCUUACUAACCCCAGCCCUGCCGAGCUCUGGGC
AAHX01073119.1/8055-8135   UGGUGCUGUGCUCUGA-CCUACUAACCUGGCC-CUACUAACUGG-UUU-CUCUUCUUACUAACCC-AGCCCUGCCGAGCUCUGGGC
AAIY01390116.1/4426-4507   UGGUGCACUGCUCUGA-CCUACUAACCCAGCCUCUACUAACCCUGGUU---UUUCUUACUAACCCCGGCCCUGCCGAGCUCUGGGU
AAKN02007326.1/69107-69027 UGGUGCUGUGCUG--A-UUUACUAACCCGGCC-CUACUAACCUGGUUU-CUCUUCUUACUAACCCCAGCCCUGCCGAGCUCUGGGU
AALT01065999.1/975-1052    UGGUGCUGUGCUC-----UUACUAACCCAGACCCUACUAACCCUGGUU---UCUCUUACUAACCCCAGCCCUGCCGAGCUCUGGGC
AANN01774047.1/2391-2313   UGGCGCUGUGCUCUGAACCUACUAACCCGGCC-CUACUAACCCGG-----UCUUCUUACUAACCC-AGCCCUGCCGAGCUCUGGGU
CAAA01027373.1/4860-4787   UGAUGCUGUGCU--------ACUAACCCGGCC-CUACUAAC-UGGUUU-CUCUUCUUACUAACCC-AGCCCUGCCGAGCUCUGGGC
Z99774.1/38335-38419       UGGUGCUGUGCUCUGA-CUUACUAACCCAGCCCCUACUAACCCUGUUUUCUCUUCUUACUAACCCCAGCCCUGCCGAGCUCUGGGC
AAGW02064803.1/37006-37085 UGGCGCUGCGCUCUGA-CAUACUAACCCAGCCCCUACUAACCCUGUUU-----UCUUACUAACCCCAGCCCUGCCGAGCUCUGGGC
AACN011068952.1/172-256    UGGUGCUGUGCUCUCA-CUUACUAACCCCGCCCCUACUAACCUCGUUUUCUCUUCCCACUAACCCCAGCCCUGCCGAGCUCUGGGC
#=GC SS_cons               ::::::::::::::::.:::::::::::::::::::::::::::::::..::::::::::::::::::::::::::::::::::::
#=GC RF                    UGGUGCUGUGCUCUGA.CuUACUAACCCgGCCcCUACUAACCcuGuUU..UcUUCUUACUAACCCCAGCCCUGCCGAGCUCUGGGc
//
# STOCKHOLM 1.0

#=GF AC   RF01877
#=GF ID   MIAT_exon5_3
#=GF PI   RNCR2; Gomafu
#=GF DE   Myocardial infarction associated transcript exon 5 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   90.00
#=GF TC   93.30
#=GF NC   62.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 16.26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005634; nucleus;
#=GF DR   GO; 0001708; cell fate specification;
#=GF RN   [1]
#=GF RM   17066261
#=GF RT   Identification of a novel non-coding RNA, MIAT, that confers risk of
#=GF RT   myocardial infarction.
#=GF RA   Ishii N, Ozaki K, Sato H, Mizuno H, Saito S, Takahashi A, Miyamoto Y,
#=GF RA   Ikegawa S, Kamatani N, Hori M, Saito S, Nakamura Y, Tanaka T
#=GF RL   J Hum Genet. 2006;51:1087-1099.
#=GF RN   [2]
#=GF RM   17623775
#=GF RT   The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a
#=GF RT   subset of neurons.
#=GF RA   Sone M, Hayashi T, Tarui H, Agata K, Takeichi M, Nakagawa S
#=GF RL   J Cell Sci. 2007;120:2498-2506.
#=GF RN   [3]
#=GF RM   20459797
#=GF RT   The long noncoding RNA RNCR2 directs mouse retinal cell specification.
#=GF RA   Rapicavoli NA, Poth EM, Blackshaw S
#=GF RL   BMC Dev Biol. 2010;10:49.
#=GF CC   MIAT (myocardial infarction associated transcript), also known as RNCR2
#=GF CC   (retinal non-coding RNA 2) or Gomafu, is a noncoding RNA. Single
#=GF CC   nucleotide polymorphisms (SNPs) in MIAT are associated with a risk of
#=GF CC   myocardial infarction [1]. It is expressed in neurons, and located in the
#=GF CC   nucleus [2]. It plays a role in the regulation of retinal cell fate
#=GF CC   specification [3].
#=GF WK   MIAT_(gene)
#=GF SQ   16


AAFC03084113.1/23536-23154 CAGAGCCCGCCAGCCGCUAAGCC----AGGGCCACACCUGGGGGUGAUUUUAUGCCUCACCUCCAGUAGGCACCUUGGUCUCUUUG-GGCU----AAUCUCUGGCUCCUCUGCACUAACUCUUGCUC-UCACCCAGCUAAUCCCUGCCUCGCCCUGGCUGCCCCAG-GGGCUGA--CCAUUAACAGCCAGCCCUGCC-CAUCUUGGGGGGCUCCAGGCUCCUG-GCCUGG-CUC---UGACCUGCUCUUAAUUAACCUCUCCUUCACCU-GACUAACUC-CUGCCUCCCCGAUCUGUUCCUUUCAGCAGAAACUAACGGCUUGUGGAUUUCUUUCUGACUAACAACAGGUC--UAACACUCC-UC-GUCA-CUAUUACUAUUAACAGCUUGGAU---GUCGGCAUGGCUGGG
AAIY01364537.1/257-601     CAGAGCCCGCCAGCCGCUAAGCC----AGGGCCACACCUGGGGGUGAGU--GUACCUCACCUCCAGUAGGCACCUUGGUCUCUUUG-AGCU----AAUCUUUGGCUCUCUUGCACUAACUCUUGCUC-UCCCUCGGCUAAUCC----------CUGGCUGCCCCCG-GGGCUGC--CCACUAACAGUCAGCC------UGCUCAGGCGGGCUCCAGGCUCUUG-GCCUGG-CUC---UGA-UGGCUCCUA----------------------CUAACGG-CUGCCUUCCCGGUCUGUUCCUUUCAGCAGAAACUAACGGCUUGUCUCUUUCUUUCUGACUAACAACAGGUC--UAUCACUUCCUC-AUUAACGAUUCCUAUUAACAGCUUG-AG---GUCUGCAUGGCUGGG
AAKN02007326.1/68067-67692 CAGAGCCCGCCAGCCGCUGAGCC----GGGGCCACACCUGGGGGUGACUUCAUGCCUCACCUCCAGUAGGCUCCU-GGCCUCUCUA-GGCU----GAUCUCUGGCUCCCGCGCACUAACUCUUGCUC-UCGCCCAGCUACUCCCCGCCUCGCCCUGGCUGCCC--A-GGGCUGC--CCACUAACAGCCAAUCUCGCC-CAC-U--GGGGGCUCUGGACUCCCU-GCCUGG-CUC---GGGCCGGCUCUUAAUUAACUUCCCUUCCCCCU-GACUAACUC-CUGCCUUCC-GGUCUGUUCCUUUCAGCGGAAACUAAUGGCUUGUGGACUUCUUUCUGACUAACAGCAGGUG--UAACAGUCC-UG-GUUA-CCACGACUAUUAACAGCUUGGUG---GGCAGCAUGGCUGGG
AAWR02038447.1/16435-16049 CAGAGCCCGCCAGCCGCUGAGCC----GGGGCCACACCUGGGGGUGAUGUGCUGCCUCACCUCCAGUAGGCACCUUGGUCUCU--G-AGCUACUCGCUCCCUGGCGCCCUCGCACUAACUCUUGCUC-UCCCCCAGCUAACCCCUGCCUCGCCCUGGCUGCCCCGG-GGGCUG---CCCCUAACAGCCGACCCCGCC-CGCCU--GGGAGUCCCAGGCUCCCG-GCCUGACUCCCUCCGAGCGGCUCGUAAUUAACCUGUCCUUCACCUCCACUAACGC-CUGCCCUCCUGGUCUGUUCCUUCCAGCAGAAACUAAUGGCUUGUGGAUUUCUUUCUGACUAACAACAGGUC--UAACACUCC-UC-GUCA-CUAUUACUAUUAACAGCUUGGAU---GUCGGCAUGGCUGGG
AB266844.1/15734-16110     CAGAGCCCGCCAGCCGCUAAGCC----GGGGCCACACCUGGGGGUGAUUUCAUGCCUCACCUCCAGUAGGCACCUUGGUUUCUUUG-GGCU----AAUCUCUGGCUCCCUUGCGCUAACUCUUGCUC-UCACCCAGCUAAUCCCUGCCUCACCCUGACUGCCCCAG-GGGCUGA--CCACUAACAACCAACCUGGCCCUGUCU--GGGGGUUCCAGGCUCCUG-GCCUGG-CCC---UGACCGGUUCUUAAUUAACCUUUCCUUCACCUUGACUAACUC-CUGCCUUCCUGGUCUGUUCCUUUCAGCAGAAACUAAUGGUUUGUGGAUUUUUUUCUGACUAACAACAGGUC--UAACAUUCC-UC-GUUA-CU------GUUAACAGCUUGGAU---GUCGGCAUGGCUGGG
AB300594.1/6064-6424       CAGAGCCCGCCAGCUGCUAAGCC----AGGGCCACACCUGGGGGUGAUUUCAUGCCUCACCUCCAGUAGGCUCAU-GGCCUCUCUG-GGCU----AACCUCUGGCUCUUUUGCACUAACUCUAGCUC-UCCCCCAGCUAAUCCCUGCCUUUCCCUGGCUGCCCCA-GGGGCUGA--CCACUAGCAGCCAGCCCCGCC-CACCC-GCGGGGCUCCAGGCUCCU----------UU---AAACC-----------AACCACCCUUUCCUCUGGACUAAUGUU-UGCCUUUCUGGUCUGUUCCUUCCGGCAGAAAUGAAUGGCU-GUGGAUUUCUCUCUGACUAA---CAGGUC--UCAUACUCC-UC--UCC-CUGUUACCACUAACGGCUUGGAUGAUGGCGGCGUGGCUGGC
ABDC01310358.1/2225-2593   CAGAGCCCGCCAGCCGCUAAGCC----AGGGCCACACCUGGGAGUGAUUUCGUGUCUCACCUCCAGUAGGCACCUGGGUCUCUUUG-GGCU----AAUCUCUGGCUCCCUCGCACUAACUCUUGCUC-UCACCCAGCUAAUCCC-------CCCUGACUGCCCCAG-AGGCUGG--CCACUAACAACCAACCCAGCC-UGUCU--GGGGGCUCCAGGCUCCUG-GCCUGG-CUU---UGACCAGCUCUUAAUUAACGUCUCCUUCAUCUUGACUAACUC-CUGCCUUCCUGGUCUGUUCCUUUCAGCAGAGACUAAUGGCUUGUGGAUUUCUUUCUGACUAACAACAGGUC--UAACACUCC-UC-GUUA-CU------AUUAACAGCUUGGAU---GUCAGCAUGGCUGGG
ABRN01366351.1/16024-16406 CAGAGCCCGCCAGCUGCUAAGCC----AGGGCCACACCUGGGGGUGAUUUUAUGCCUCACCUCCAGUGGGCACCUUGGUCUCUUUG-GGCU----AAUCUCUGGCUCCUUUGCACUAACUCUUGCUC-UCACCCAGCUAAUCCCUGUCUCGCCCUGGCUGCCCCAGAGGGCUGA--CCACUAACAGCCAACCCUACC-CAUCU--GGGGGCUCCAGCCUCCUG-GCCUGG-CUC---UGACCUGCUCUGAAUUAACCCCUCCUUCACCU-GACUAACUC-CUACCCUCCUGAUCUGUUCCUUUCAGCGGAAACUAACGGCUUGUGGAUUUCUUUCUGACUAACAACAGGUC--UAACCCGCC-UCAGUCA-CUAUUACUAUUAACAGCUUGGAU---GUCGGCAUGGCUGGG
ABRO01450990.1/211-585     CAGAGCCCGCCAGCUGCUCAGCC----GGGGCCACACCUGGGGGUGACUCCAUGCCUCACCCCCAGUAGGCACCUUGGCCUCUUUG-GGCU----CCU-UGUGGCUCUCUUGCACUAACUCUUGCU------------AAUCCCUGCCUCGCCCUGGCUGUCCUGA-GAGCUGACCCCACUAACAGCCAACCCUGCC-CACCU--GCGGGCUCCAGGCUCCCAAGCCUGG-CUU---UGACCGGCUCGGAAUUAACCUCUCUUCCCUCUUGACUAACUA-AUGGCUUCCUGGUCUGUUCCCUUCAGCAGAAACUAAUGGCUUGUGGAUUUCUUUCUGACUAACCUCAGAUCUCUAGCACUGC-UC-GGUA-CCAUGACAAUUAACAGCUUGGAU---GUCCGCAUGGCUGGG
ABRP01133688.1/15976-16353 CAGAGCCCGCCAGCCGCUAAGCC----AGGGCCACACCUGGGGGUGAUUUUAUGCCUCACCUCCAGUAGGCACCUUGGUCUCUUUG-GGCU----AAUUUCUGGCUCCCUUGCACUAACUCUUGCUG-UCACCCAGCUAAUCUCUGCCUUGCCCUGGCUGCCCCUGAGGGCUGA--CCACUAACAGCCAACCCUGCC-CAUCU-GCGGGGCUCCAGGCUCUUG-GCCUGG-CUC---UGACAGCCUCUUAAUUAACCUCUCCUUUACCUCGACUAACUU-CUGCCCUCCUGGUCUGUUCCUUUCAGCAGAAACUAACGGCUUGUGGAUUUCCUUCUGACUAACAACAGGUC--UAACACUUU-UC-GUUA-CU------AUUAACAGCUUGGAU---GUCGGCAUGGCUGGG
ABRQ01066702.1/6237-6601   CAGAGCCCGCCAGCCGCUGAGCC----AGUGCCACACCUGGGGGUGAUUUAAUGCCUCACCUUCAGUAGGCACCUUGG----------GCU----AAUCUCUGGCUCCCUUGCACUAACUCUUGCUC-UCACUCAGCUAAUCCAUGCCUUCCCCUGGCUUCCCCUG-GGGCUGA--UCGCUAACAGCCAACUUCACC-CACCU--GGGGGCUCCAGGUUCCUG-ACCUGG-CUC---UGACUAGCUCUAAAU-AACUUCUCCUUUACCUGGACUAACUC-CUGCCCUCUGGGUCUGUUCCUUUCAGCAGAAACUAACGGCUUGUGGAUUUCUUUCUGACUAACAACAGGUC--UAACACUCC-UC-AUUA-CU------AUUAACAGCUUG-AU---GUCUGCAUGGCUGGG
CT737259.5/88637-88262     CAGAGCCCGCCAGCUGCUAAGCC----AGGGCCACACCUGGGGGUGAUUUUAUGCCUCACCUCCAGUAGGCACCUCGGUUUCUUUG-GGCU----AAUCUUUGGCUCCUUUGCACUAACUCUUGCUC-UCACCCAGCUAAUCCCUGCCUCGCCCUGGCUGCCCCUGGGGGCUGA--CCUCUAACAGCCAGCCCUGCC-CAGGU--GGGGGCUCCAGGCUCCCG-GCCUGG-CUC---UGAUCUGCUCUUAAUUAACCUCUCCUUCACCC-GACUAACUC-CUGCCCUACUGAUCUGUUCCUUUCAGCAGAAACUAACGGCUUGUGGAUUUCUUUCUGACUAACAACAGGUC--UAACACUCC-UG--------GUUACUAUUAACAGCUUGGAU---GUCGGCAUGGCUGGG
AAGU03075289.1/6370-6001   CAGAGCCCGCCAGCUGCUGAGCC----AGGGCCACACCUGGAGGUGAUUUUAUGCCUCACCUCCAGUAGGCACCUUGG----------GCU----AAUCUCUGGCUCCCUUGCACUAACUCUUGCUC-UCACCCAGCUAAUCCGUGCCUCACCCUGGCUUCCCCUG-GGGCUGA--CUGCUAACAGGCAACCCUGCC-CACCU--GGGGGCUCCAGGCUG-UG-GCCUGG-CUC---UGACUGGCUCUUAAU-AACUUCUUGUUUACCUAGACUAACUC-CUGCCCUCCUGAUCUGUUCCUUUCAGCAGAAACUAACGGCUUGUGGAUUUCUUUCUGACUAACAACAGGUC--UAACACUUC-UC-AUUA-CUAUUACUAUUAACAGCUUG-AU---GUCUGCAUGGCUGGG
AAEX03014771.1/13247-13577 CAGAGCCCGCCAGUCGCUGAGCCAGCCGGGGCCACACCUGGGGGUGACGUCACGCCUCACCUCCAGGAGGCCCCCGGGUCUGUGUGUGGGC----UCCCUGCGGCUCCUCUGCACUAACU--UGCUC-UCCCGC---------------------GGCUGCCUCGG-GGGCUG---CCC--------------------GCCU--GGG-GCCCCAGGCUCCAG-GC-----UCC---CGCCCGGCUCCGUGCAG-------CUUCGCCUCGACUAACCC-CUGCCCUCCCGGUCUGUUCCUCGCAGCGGACACUAACGGCUUGUGGAUUUCUCCCUGACUAACAGCAGGUC--UAACGCUCC-UC-GUUA-CCGCCCCU-UUAGCAGCUUGGAU---GCCGGCAUGGCUGGG
AABR05033787.1/16536-16915 CAGAGCCCGCCAGCUGCUAAGCC----AGGGCCACACCUGGGGGUGAUUUCAUGCCUCACCUCCAGUAGGCUCAU-GGCCUCUCCG-GGCU----AACCUCUGGCUCCUUUGCACUAACUCUAGCUCCUCCCCCAGCUAAUCCCUGCCUCUCCCUGGCUGCCCCAAGGGGCUGA--CCCCUAGCAGCCAGCCCCGCC-CAUCCAGGGGGGCUCCAGGCUCCUG-GCCUGG-CUU---UGGCCGGCUUCUU-UGAACCACCCUUUCCUCUGAACUAAUGUUGUGCCUUUCUGGUCUGUUCCUUCCGGCAGAAAUGAAUGGCU-GUGGAUUUCUCUCUGACUAA---CAGGUC--UCACACCCC-UC--UCC-CUGUUACCACUAACGGCUUGGAU---GGCGGCGUGGCUGGU
AAQR03069495.1/38867-39213 CAGAGCCCGCCAGCUGCUAAGCC----GGGGCCACACCUGGGGGUGAUUUUAGGUCUCACCUCCAGUAGGCACCUUGGUCUCUUUG-GGCU----AAUCUCUGGCUCCCUCGCACUAACUCUUGCUC-UUACCCAGCUAAUCCU-------ACCUGACUGCCCCAG-AGGCUGC--CC--------------------UGUCC--GGGGGCUCCAGGCUCCUG-GCCUGG-CUC---UGACUGGCUCUUAAUUAACCUCUCCUUCAUCUUGACUAACUC-CUGCCUUUCCGGUCUGUUCCUUUCAGCAGAAACUAAUGGCUUGUGGAUUUCUUUCUGACUAACAACAGGCC--UAACACUC-----AUUA-CU------AUUAACAGCUUGGAU---GUCAGCAUGGCUGGU
#=GC SS_cons               :::::::::::::::::::::::....:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::....::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::.:::::::..:::::::::::::::::::::.:::::..::::::::::::::::::.::::::.:::...::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..:::::::::.::.::::.:::::::::::::::::::::::...:::::::::::::::
#=GC RF                    CAGAGCCCGCCAGCcGCUaAGCC....gGGGCCACACCUGGGGGUGAuuUcauGCCUCACCUCCAGUAGGCaCcUuGGuCUcUuUG.GGCU....aauCUcUGGCUCccuuGCACUAACUCUuGCUC.UCaCcCAGCUAaUCCcuGCCUcgCCCUGGCUGCCCCaG.GGGCUGa..CCaCUAaCAGcCAaCCcuGCC.cgccu..GGGGGCuCCAGGCUCCuG.GCCUGG.cuc...uGaccgGCUCuuaaUuAACcucuCcUucacCUuGACUAACuc.cUGCCuUcCuGGUCUGUUCCUUuCaGCaGAaACuAAuGGCUUGUGGAUUUCUuUCUGACUAACaaCAGGUC..UaaCacucC.Uc.gUua.CuguuaCuAUUAACaGCUUGGAu...GuCgGCaUGGCUGGg
//
# STOCKHOLM 1.0

#=GF AC   RF01879
#=GF ID   TUSC7
#=GF PI   LOC285194;
#=GF DE   Non-coding RNA LOC285194
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; RNAz; Eberhardt R
#=GF GA   65.00
#=GF TC   92.30
#=GF NC   52.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20048075
#=GF RT   Recurrent focal copy-number changes and loss of heterozygosity implicate
#=GF RT   two noncoding RNAs and one tumor suppressor gene at chromosome 3q13.31 in
#=GF RT   osteosarcoma.
#=GF RA   Pasic I, Shlien A, Durbin AD, Stavropoulos DJ, Baskin B, Ray PN, Novokmet
#=GF RA   A, Malkin D
#=GF RL   Cancer Res. 2010;70:160-171.
#=GF CC   LOC285194 is a non-coding RNA which is often deleted in osteosarcoma.
#=GF CC   Deletion of this gene is associated with poor survival of osteosarcoma
#=GF CC   patients. It may act as a growth suppressor in osteoblasts [1].
#=GF WK   Long_non-coding_RNA
#=GF SQ   25


AANN01289908.1/1868-2032   ACACACUAAGAAAUACA-AAGAGGGA----------AGUAUGACUGCUAUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAGUCACAUUGCUUCAAAGUUAACAAAAACAAAGAGAGCAGAGGCAGCUUCA-CUGGG-AACAACACCCGUCCAUCAA-UGAGGAUGAGCUA--AU
ABRN01424432.1/1142-1304   ACAAGCCAGGAGACAGA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAGUCCCUCUGCUUCAAAGU-AAUCAAAACAAAGAAAGCUGAGCCACCUUCA-CUGGG-AACAACUCCUGUCCAUCAAACAAGAAUGAACUC----
ABRO01083507.1/1438-1598   ACAAGCUAAGAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCCUUUGCUUCAAAGU-AACCAAAACAAAGAAAGCUGAGCCAGCUUU-----GG-AACAACACCUGUCUAUCAGACAAGAAUGAGCUA--AU
ABRP01082835.1/2605-2769   ACAAGCCAAGAGACACA-AAGGGAAA----------AGUGUGACUGUUCUGAAAGCAA-AACAAACGAAUAUCUCCAGAGGGGAUUAGUCCUCCUGCUUAGAAGU-AACCAAAGCAAAGAAAGCUAAGCCUGCUUUAACUGGG-AAGAGCACCUGCCCAACAGACAAGUAUGAGCUA--AU
ABGA01117378.1/24862-25026 ACAAUCUAAGAGACACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCUUCUGCUUCAAAGU-GACUAAAACAAAGAAAGCUGAGCCAGCUUCA-CUGGA-AACACCACCUGUCCAUCAGACAAAGAUGAGCUA--AU
AC124193.2/14028-14190     ACAAGCUAAGAGAUACA-AAGG-AAA----------AGUAAGGCUGCUAUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCCUCUGCUUCAAAGG-AUC-UGUGCAAUGGAAGUGUUGCCAGCUUCU-CUAGU-AACAGCACCUGUCCAUCAGACAAGGAUGAGCUA--AU
ABRT010112553.1/1935-2099  ACAAGCUAAGAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCUUCUGCUUCAAAGU-AACCAAAACAAAGAAAGCUGAGCCAGCUUCC-CUGGG-AACAACACCUGUCCGUCAGACAAGGAUGAGCUA--AU
AAFR03033448.1/16789-16962 AGGAGCAAACAGAUACU-CAGAGAAAAGGGGGGAAAGCAGAGGAUGCUUCAAAAGCAA-AACAAACAAACAAAACCAGAGGGAAUAAGUCCCUCUGCUUCAAAGA-AACUCAAACCAAGAAAACUAAGCUGGUUUCC-CUAGG-AAAAACAGCUGCCCAUCAACCAAGAAUGAGUUU--AU
AAFC03071026.1/1523-1685   ACAAGCCAAGAGAUACA-AAGAGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAGUCCCUCUGCUUCAAAGU-AACCAAAACAAAGCGAGCUGAGCCAGCUUCA-CUGGG-AACGACUCCUAUCCAUCAAACCAGAAUGAGCUC----
AAYZ01116308.1/2672-2832   ACAAACUAAGAGAUACA-AAGG-GAA----------AGUGUGACUGUUCUGACAGCAAAAACAAGCAAUAUUCUCCAGAGGGGAU--AUCCCUCUGCUUCAAGUA-AGC-GGAAGCAAGCAAGGCCAGCCAGCUUCA-CUGGG-AACAACACCUGUCCAUCAGACAAGGCUGAGUUA--AU
ABVD01409869.1/1999-2162   ACAAGCCUAGAGAUAUG-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAGAAACAAGCAAGUAUCUCCAAAGGGGAUUAGUCCCUGUGCUUCAAAGU-AACUAAAACAAAGAAAGCUGAGCCAGCUUCA-AGGGG-AACAGCACCU-UCCAUCAGACAAGGAUGAGCUA--AU
AAQQ01255229.1/715-879     CCAAGCUAAGAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCUAGAGGGGAUUAAUCCCUCUGCUUCAAAGU-AACCAAAACAAAGAAAGCUGAGCCAGCUUUG-CUGGG-UACCACACCUGUCCUGCAGACAAAGAUGAGCUA--AU
AAPY01263281.1/212-377     ACAAGCUAAAAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAACUAUCUCCAGAGGGGAUUAAUCCCUCUGCUUCAAAGU-AACCAAAACAAAGAAAGCUGAGCCAGCUUCA-CGGGGAAACAACACCUGUCCAUCAGACAAGGAUGAGCUC--AU
ABDC01172505.1/1998-2162   ACAAGCUAAGAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCUUCUGCUUCAAAGU-AACCAAAACAAAGAAAGCUGAGCCAGCUUCA-CUGAG-AACAACACCUGUCCAUCAGACAAGGAUGAGCAA--AU
AAWR02011954.1/14871-14707 ACAAGCCAAGAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCUUAUAUCUCCAGAGGGGAUUAGUCCCUCUGCUUCAAAGU-AACCAAAACAAAGAGAGAUGAGCCAGCUUCA-CUGGG-AACAACACCUGUCUGUCAGACGAGGAUGGGCUGGC--
AADA01232009.1/16411-16575 ACAAUCUAAGAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCUUCUGCUUCAAAGU-AACUAAAACAAAGAAAGCUGAGCCAGCUUCA-CUGGA-AACAACACCUGUCCAUCAGACAAGGAUGAGCUA--AU
AACN010675924.1/113-277    ACAAGCCAAGAGAUACA-AAGGGAAA----------AGUGUGAUUGCUUUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAGUCCCUCUGCUUCAAAGU-AACCAAAAUAAAGAGAGCUGAGCCAGCUUCA-CUGGG-AACAGCACCUGUCCAUCAGGCAAGGCUGAGCUA--AU
ABRR01676511.1/133-294     ACAAGACAAUAGAUACA-AAAGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAACUAUCUCCAGAGGGGAUUAGUCCCUCUGCUUCAAAGU-AACCAAAACAAAGACAGCCGAGCCAGCUUCC-CUG-G-AACAACACCUGCCCAUCAAACAAGUAUGAGAUC----
AAKN02035545.1/92342-92506 CCAAGCUAAGAGAUACA-AAGGGAAA----------AGUGUGACUGUUCUGACAGCAGAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCCUCUGCUUCAAAGU-AACCAAAACAAAGAAAGCUGAGCUAGUUUCA-CAGGA-AACAACACCUGUCCAUCAGACAGGGGUGAGCUA--AU
AANU01278878.1/39399-39235 ACAAGCUAAGAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCUUCUGCUUCAAAGU-AACUAAAACAAAGAAAGCUGAGCCAGCUUCA-CUGGA-AACAACACCUGUCCAUCAGACAAGGAUGAGCUA--AU
AC108713.2/77074-76910     ACAAUCUAAGAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCUUCUGCUUCAAAGU-AACUAAAACAAAGAAAGCUGAGCCAGCUUCA-CUGGA-AACAACACCUGUCCAUCAGACAAGGAUGAGCUA--AU
AAGU03049348.1/1336-1172   ACAAGCCAAGAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAGUUACUCUGCUUCAAAGU-AACGAAAACAAAGAAAGCUGAGCCAGCUUCA-CCGGC-AACACCACCUGUCCCUCAGACAGGGAUGAGCCA--AU
CABD02251226.1/30269-30433 ACAAUCUAAGAGAUACA-AAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCUUCUGCUUCAAAGU-AACCAAAACAAAGAAAGCUGAGCCAGCUUCA-CUGGA-AACAACACCUGUCCAUCAGACAAGGAUGAGCUA--AU
AAPE02022450.1/28502-28667 ACAAGCCAAGAGACAAAAAAGGGAAA----------AGUGUGACUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAGUCUCCCUGCUUCAAAGU-AACCAAAACAAAGAGAGCUGAGCCUGCUUCC-CAGGG-AAUAACACCUGUCCAUCAGACAAGGAUGAGCUA--AU
AABR05027448.1/19480-19643 ACAAGCUAAGAGAUACA-AAGGGAAA----------AGUAAGGCUGCUCUGACAGCAAAAACAAGCAAAUAUCUCCAGAGGGGAUUAAUCCCUCUGCUUCAAAGU-ACCC-AAGCAAGGGAAGUGGUGCCAGCUUCU-CUAGU-AACAACACCUGUCCAUCAGACAAGGAUGAGCUA--AU
#=GC SS_cons               :::::::::<<<<<-------------------------------<<_______>>-------------->>>>><<<<<<<<_____>>>>>>>>::::::::::::::::::::::::<<<<<<___>>>>>>:::::::::::::::::::<<<_____>>>::::::::::::::::
#=GC RF                    AcAAgCuAAgagauACA.AAGGGAAA..........AGUGUGAcUGCUcUGAcAGCAAAAACAAGCAAAUaucucCAgaGGGgAUUAauCCCucUGCUUCAAAGu.AACuaAAACAAAGAaAGCugAGCcaGCUuCa.CUGGg.AAcAACAcCUGucCAUCAgaCAAGgAUGAGcUa..AU
//
# STOCKHOLM 1.0

#=GF AC   RF01880
#=GF ID   Xist_exon1
#=GF DE   X-chromosome inactivation gene exon 1
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Gardner PP
#=GF SS   Predicted; RNAz; Gardner PP
#=GF GA   50.00
#=GF TC   56.10
#=GF NC   39.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.72 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0009048; dosage compensation by inactivation of X chromosome;
#=GF RN   [1]
#=GF RM   16778056
#=GF RT   The Xist RNA gene evolved in eutherians by pseudogenization of a
#=GF RT   protein-coding gene.
#=GF RA   Duret L, Chureau C, Samain S, Weissenbach J, Avner P
#=GF RL   Science. 2006;312:1653-1655.
#=GF RN   [2]
#=GF RM   1985261
#=GF RT   A gene from the region of the human X inactivation centre is expressed
#=GF RT   exclusively from the inactive X chromosome.
#=GF RA   Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R,
#=GF RA   Willard HF
#=GF RL   Nature. 1991;349:38-44.
#=GF RN   [3]
#=GF RM   16273071
#=GF RT   Mapping of conserved RNA secondary structures predicts thousands of
#=GF RT   functional noncoding RNAs in the human genome.
#=GF RA   Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF
#=GF RL   Nat Biotechnol. 2005;23:1383-1390.
#=GF CC   Xist is an RNA gene on the X chromosome of the placental mammals that acts
#=GF CC   as major effector of the X inactivation process. The Xist RNA, a large (17
#=GF CC   kb in humans) [1] transcript, is expressed on the inactive chromosome and
#=GF CC   not on the active one. It is processed similarly to mRNAs, through
#=GF CC   splicing and polyadenylation, however, it remains untranslated. It has
#=GF CC   been suggested that this RNA gene evolved at least partly from a protein
#=GF CC   coding gene that became a pseudogene [2]. The inactive X is coated with
#=GF CC   this transcript, which is essential for the inactivation. X lacking Xist
#=GF CC   will not be inactivated, while duplication of the Xist gene on another
#=GF CC   chromosome causes inactivation of that chromosome. This Xist exon was
#=GF CC   identified in a screen for conserved and structured elements in the human
#=GF CC   genome [3].
#=GF WK   XIST
#=GF SQ   24


AANN01200569.1/3260-3186   AAAUA-AAAAUCC-ACCCCUGCAUUAAGCACUUGAUGAUC--G------UUGAAGAAAGAAAGGACUUCACUUCU-GCUACCUGAU---
ABRN01023547.1/660-744     AAAUC-AAAAUCCGACCCCAGCAUUAGCCAUGGGGUAGGU--GUUCCUCUUGAGGAAGGCAGGGAUUCCUCUUCU-GCCACCUGUCGGC
L10731.1/167-81            AAAUC-AAAAUCCGACCCCAGCAUUAGCCAAGGGGUAGGUGUGCUCCUCUUGAGGAAGGCAGGAAUUCCUCUUCU-GCCACCUGUUGGC
ABRO01484274.1/70-153      AAAUC-UCAAUCCAAUCCCAGGCUUGGCCAUAGGGUACAU--GUUCCUGUAGGGGACAGUAGAGGUUCCUUUUCU-GC-ACCUCUUAGC
ABRP01195257.1/300-383     AAAUC-AAAGUCCAACCCCAGCAUUAGCCACGGGGUAAGU--GUUCCUCUUGAGGAAGGCAGGGAUUCCUCUUCU-GC-ACCUGAUGGC
ABGA01241177.1/901-985     AAAUC-AAAAUCCGACCCCAGCAUUAGCCAAGGGGUAGGU--GUUCCUCUUGAGGAAGGCAGGAAUUCCUCUUCU-GCCACCUGUUGGC
AALT01125325.1/576-659     -AGCAAUAAAUCCGACCCCAGCAGUAGCUAAGGGGUAGGU--UGUUCUC-UGAGGAAGGUAGGGAUUUCUCCGGU-ACUACCUAAUGGA
L04961.1/2266-2197         AAAUC-AAAAUGCAACCCCAGCAAUAGUCAUGGGGUAGAU--UUU-----GGAAGAAGGUAGG-AUUCUACCUCU----------UCAC
ABRT010581360.1/279-363    AAAUC-AAAGUCCAACCCCAGCAUUAGCCACGGGGUAGGU--GUUCCUCUUGAGGAAGACAGGAAUUCCUCUUCU-GCCACCAGUUGGC
AJ421481.1/118268-118184   AAAUC-AAAAUCCGACCCCAGUAUUAGCCACGGGGUAGGU--GUUCCUCUUGAGGAAGGCAGGGAUUCCUCUUCU-GCCAACAGUUGGC
AAHX01111727.1/42624-42555 AAAUC-AAAAUCCAACCCCAGCAAUAGUAAUGGGGUGGAU--UCU-----AGAAGAAGGGAGG-AUUCUACCUC----------CUGGC
AAPY01379542.1/424-506     AAACC-AAAAUCCGACCCCAGCAUUAGCCACGGGGUAGGU--UCUCCUCUCGAAGAAGGCAGG-AUUCCUCUUCU-GCCACCUGU-GGA
ABDC01412462.1/213-297     CAAUC-AAAAUCCGACCCCAGCAUUAGCCACGGGGUAGGU--GUUCCUCUGGAGGAAGGCAGGAAUUAUUCUUCU-CCCACCUGUUGGG
ABRQ01553772.1/1320-1396   --AUC-AAAAUCCGAACCCUGCAUUAGCCACCAGGUAGGU--GAUCGAU------CCGGUAGGGAUCCUCCUUCU-GCCACAUGGUGAC
ACBE01497821.1/848-932     AAAUC-AAAAUCCGACCCCAGCAGUAGCCACGGGGUAGGU--GUUCCUCUUGAGGAAGGCAGGGAUUCCUCUUCU-GCCACCUGCUGGC
AAKN02029935.1/44004-43920 AAAUC-AUAAUCCAACUCUAGCAUUAGCCAUGGGUUUAGC--AUUCCUCUUGAGGAAAGCAGGGGUUCCUCUUUU-GCCCCCCAUUGGC
L10733.1/165-81            AAAUC-AAAAUCCGACCCCAGCAUUAGCCAAGGGGUAGGU--GUUCCUCUUGAGGAAGGCAGGAAUUCCUCUUCU-GCCACCUGUUGGC
AAPE02004049.1/6296-6212   AAAUC-AAAAUCGAACCCCAGCAUUAGCCACAGGGUAGGU--GUUCCUCUUGAAGAAGGGAGGGAUUCCUCUUCU-GCCACCUGUUGGC
AAEX03026517.1/35626-35710 UAAUC-AAAAUCCGACCCCAGCAUUAGCCAUGGGGUAGGU--GUUCCUCUUGAGGAAGGUAGAGACUCCUCUUCU-GCCACCUGUUGGC
U50910.1/3031-2963         AAAUC-AAAAUCCGACCCCAGCAUUAGCCACGGGGUAGAU--GUUCCUCCUGAGAAAGGCAGG-AUUUCCCUU----------------
U50911.1/5943-5859         AAAUC-AAAAUCCGACCCCAGCAUUAGCCACGGGGUAGGU--GUUCCUCUUGAGGAAGACAGGGAUUCCUCUUCU-GCCACCUGUUGGC
AJ310130.1/14082-13998     AAAUG-AAAUUUCAACCCCAGCAUUAGCCAAGGGGUAGAC--GAGCCUGUGGAAGGAGGCAGG-AUUCCACCUCUGGCCAAGGCUUUAU
AJ310127.1/14981-14897     AAAUC-AAAUUUCAACCCCAGCAUUAGCCAUGGGGUAGAC--GAGCCUGUGGAAGGAGGCAGG-AUUCCACCUCUGGCCAGGGCUUUAC
AJ310129.1/10758-10674     AAAUG-AAAUUUCAACCCCAGCAUUAGCCAUGGGGUAGAC--GAGCCUGUGGAAGGAGGCAGG-AUUCCACCUCUGGCCAGGGCUUUAC
#=GC SS_cons               :::::.::::::::::::::::::::::::::::::::::..:::::::::::::::::::::::::::::::::.:::::::::::::
#=GC RF                    AAAUC.AAAAUCCgACCCCAGCAUUAGCCAuGGGGUAGGU..GuUCCUcUuGAGGAAGGcAGGGAUUCCuCUUCU.GCCACCuguUGGC
//
# STOCKHOLM 1.0

#=GF AC   RF01881
#=GF ID   Xist_exon4
#=GF DE   X-chromosome inactivation gene exon 4
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Gardner PP
#=GF SS   Predicted; RNAz; Gardner PP
#=GF GA   100.00
#=GF TC   107.60
#=GF NC   47.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.43 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0009048; dosage compensation by inactivation of X chromosome;
#=GF RN   [1]
#=GF RM   16778056
#=GF RT   The Xist RNA gene evolved in eutherians by pseudogenization of a
#=GF RT   protein-coding gene.
#=GF RA   Duret L, Chureau C, Samain S, Weissenbach J, Avner P
#=GF RL   Science. 2006;312:1653-1655.
#=GF RN   [2]
#=GF RM   1985261
#=GF RT   A gene from the region of the human X inactivation centre is expressed
#=GF RT   exclusively from the inactive X chromosome.
#=GF RA   Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R,
#=GF RA   Willard HF
#=GF RL   Nature. 1991;349:38-44.
#=GF RN   [3]
#=GF RM   16273071
#=GF RT   Mapping of conserved RNA secondary structures predicts thousands of
#=GF RT   functional noncoding RNAs in the human genome.
#=GF RA   Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF
#=GF RL   Nat Biotechnol. 2005;23:1383-1390.
#=GF CC   Xist is an RNA gene on the X chromosome of the placental mammals that acts
#=GF CC   as major effector of the X inactivation process. The Xist RNA, a large (17
#=GF CC   kb in humans) [1] transcript, is expressed on the inactive chromosome and
#=GF CC   not on the active one. It is processed similarly to mRNAs, through
#=GF CC   splicing and polyadenylation, however, it remains untranslated. It has
#=GF CC   been suggested that this RNA gene evolved at least partly from a protein
#=GF CC   coding gene that became a pseudogene [2]. The inactive X is coated with
#=GF CC   this transcript, which is essential for the inactivation. X lacking Xist
#=GF CC   will not be inactivated, while duplication of the Xist gene on another
#=GF CC   chromosome causes inactivation of that chromosome. This Xist exon was
#=GF CC   identified in a screen for conserved and structured elements in the human
#=GF CC   genome [3].
#=GF WK   XIST
#=GF SQ   25


ABBA01059641.1/2139-2264   UCCUCAGAAGAAUAGGCUUGUUGUUUUACAGUGUUAGUGAUCCAUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAAGCUCACUACCACUGGGCAACAACCCUA
AADA01036557.1/415-290     UCCUCAGAAGAAUAGGCUUGUUGCUUUACAGUGUUAGUGAUCCAUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAAGCUCACUACCACUGGGCAACAACCCUA
AANU01175104.1/59559-59683 UCCUCAGAAGAAUAGGCUUGUUGCUUUACAGUGUUAGUGAUCCAUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAA-GCUCACUACCACUGGGCAACAACCCUA
AAPY01750750.1/6544-6419   UCCUCAGAAGAAUAGGCUUGUUGCUUUACAGUGUUAGCGACCCAUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAAGCUCACUACCACUGGGCAACAACCCUA
ABDC01374823.1/303-178     UCCUCCAAAGAAUAGGCUUGUUGCUUUACAGUGUUAGUGACCCAUUCCCUUUGACGAUCUC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAAGCUCACUACCACUGGGCAACAACCCUA
AJ421481.1/139381-139506   ACCUCAAAAGAAUAGGCCUGUUGCUUUACAGUGUUAGUGACCCAUUCCCUUUGACGAUUCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAGAUUCACUACCACUGAGCAACAACUCUA
AAQQ01705614.1/1075-950    UCCUCAGAAGAACAGGCUUGUUGCUUUGCAGUGUUAGUGACCUUUUCCCUUUGACGAUCCC-CAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAAGCUCACUGCCACUGGGCAACAACCCUG
AAYZ01592848.1/861-736     UCCUUGGAAGAAUGGGCUUGUUGCUUUACAGUGCUAGUGAUCCAUUCCCUUUGACGAUCCU-UAGGUGGAGCUGGGGCAUGAGGAUCCUCCCGGGGAAAAGCUCAUUAUCACUGGGCAACAACCCUA
AJ310127.1/24710-24835     UCCCCAGAAGUAUGGACUUGUUGCCUUGCGGUGCUGGCGACCUAUUCCCUUUGACGACCCC-UAGGUGGAGAUGGGGCAUGAGGGUCCUCCAGGGGAAUAGCUCACCAGCACUGGGCAACAGUCCUA
AJ310129.1/20817-20942     UCCCCAGAAGUAUGGACUUGUUGCCUUGCGGUGCUGGCGACCUAUUCCCUUUGACGACCCC-UAGGUGGAGAUGGGGCAUGAGGGUCCUCCAGGGGAAUAGCUCACCAGCACUGGGCAACAGUCCUA
AJ310130.1/23673-23798     UCCCCAGAAGUAUGGACUUGUUGCCUUGCGGUGCUGGCGACCUAUUCCCUUUGACGACCCC-UAGGUGGAGAUGGGGCAUGAGGGUCCUCCAGGGGAAUAGCUCACCAGCACUGGGCAACAGUCCUA
U41394.1/4138-4263         CCCCCAGAAUUGUGGGCUUGCUGCUUUGCAGUGCUGGCGACCUAUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAUAGCUCACCACCACUGGGCAACAGGCCUA
AAIY01330989.1/2005-2128   UCCUUAAAAUAAUAGGCUUGUUGUCUUG--GUGGUAGUGACCCAUUCCCUUUGACGAUCCU-UUGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAAGCUCACUAACACUGGGCAACAACUCUA
AANN01820944.1/1549-1423   UUUCCCUCAGAAUAGGCUUGUUGCUUUACAGUACUGGUGAUCCAUUCUCUUUGAUGAUCCCCUAGGUGGAGAUGGGGCAUGAGGAUCCUCCAAGGGAAAGACUCAUCAUCACUGGGCAACAGCCUUA
DQ845733.1/12259-12384     CCCUCAAAAGAAUAGGCCUGUUGCUUUACAGUGGUAGUGACCUGUUCCCUUUGACGGCCCC-GAGGUGGAGAUGGGGCUUGAGGACCCUCCAGGGGAAAAGCUCACUACCACUGGGCAACAAUCCUA
AALT01447951.1/2352-2227   UCUUCCUCUAAAUAGGCUUGCUGCUUUACAGUGUUGGUGACACUUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAGUCUCACUACCACUGGGCAACAACCCUA
AAWR02034174.1/31933-31808 UCCUCAGAAGAAUAGGCUUGUUGCUUUAUGGUGUUAGUGACCCAUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAGGCUCACUACCACUGGGCAACAAGCCUA
AAKN02029936.1/11291-11415 UCUUUGGGAGAAUAGACUUGUUGCUUUGCCGUGCUAGUGACCUAUUCCCUUUGAUGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAAGCUCACUAUCACUAGGCAA-AACCCUA
M97168.1/11570-11695       UCCUCAGAAGAAUAGGCUUGUUGUUUUACAGUGUUAGUGAUCCAUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAAGCUCACUACCACUGGGCAACAACCCUA
AAGV020764122.1/1131-1006  UCCUCCAAACAAUAGGCUUGUUGCCUUACAGUGUUAGUGACCCAUUCCCUUUGAUGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAAGCUCAUUACCACUGGGCAACAACCCUA
AAEX03026517.1/14255-14130 UCCUCAGAAGAAUAGGCUUGUUGCUCUACAGUGUUAGUGACCCGUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAAAGCUCACUACCACUAGGCAACAACCCUA
AABR05180219.1/36601-36476 UCCCCCAGAGUCUGGGCUUGGUGCUUUGCAGUGCUGGCGACCUAUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAUAGCUCACCGCCACUGGGCAACAGGCCUA
AAPE02004052.1/5630-5755   UCCUUAGAAGAAUAGGCUUGUUGCUUUGCAGUGUUAGUGACCUAUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAUAGCUCACUACCACUGGGCAACAACCCUA
AAGU03047922.1/15623-15748 UCCAUAAAAUAAUAGGCUUGUUGUCUUACAGUGUUAGUGACCCAUUCCCUUUGAAGAUCCU-UAGGUGGAGAUGGGGCAUGAGGAUCUUCCAGGGGAAAUGCUCACUAACUCUGGUCAACAACUCUA
GQ201417.1/7759-7884       CCCCCUUAUGCAAGGGCUUGCUGCUUUGCAGUGCUGGUGACCUAUUCCCUUUGACGAUCCC-UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAUAGCUCACCACCACUGGGCAACAGCCCUA
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    uCCucagaAgaAUaGGCUUGuUGCuUUaCaGUGuUaGuGAcCcaUUCCCUUUGAcGAUCCC.UAGGUGGAGAUGGGGCAUGAGGAUCCUCCAGGGGAAaaGCUCACuAcCACUGGGCAACAacCCUA
//
# STOCKHOLM 1.0

#=GF AC   RF01882
#=GF ID   TUG1_1
#=GF DE   Taurine upregulated gene 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   84.20
#=GF NC   68.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.27 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0042478; regulation of eye photoreceptor cell development;
#=GF RN   [1]
#=GF RM   15797018
#=GF RT   The noncoding RNA taurine upregulated gene 1 is required for
#=GF RT   differentiation of the murine retina.
#=GF RA   Young TL, Matsuda T, Cepko CL
#=GF RL   Curr Biol. 2005;15:501-512.
#=GF CC   TUG1 (taurine upregulated gene 1) is a long non-coding RNA expressed in
#=GF CC   retina and brain. It was first identified in a screen for genes
#=GF CC   upregulated by in developing retinal cells in response to taurine. It is
#=GF CC   required for the normal development of photoreceptors in the retina [1].
#=GF WK   TUG1
#=GF SQ   21


AAPY01201424.1/594-738       UUCUUUGUUAAUUGUCAGCUGCUCUU-ACC--------AAAUUCCAAGCC-AUUAUCCAGCAAACACUAU---AAAAA-----UGUUUGAACAGUUGAAUUUCAAACAUUUU---CAUUUUGUGGAGUGGUGCUUACCAAGUGGUACAGCUCU--AAGCAAGUGA-ACA
AAKN02007240.1/7009-6865     UUGUUUCUUUGUUGUCAGCUGCUUUU-AUC--------AAAUUUCAGACC-AUUGUCCAGCAAACACUAU---AAAAA-----UGUUUGAAUAAUUGAAUUUCAAACAUUUU---CAUUUUGUGGAGUGGUGCUUACCAAGUGGUACAGCUCU--AAGCACGUGG-AUA
AAQQ01619694.1/1600-1742     UUCUUUGUUAAUUGUCAGCUGCUUUU-AUC--------AAAUUCCAGUCU-GUUAUCCAGCAAACACUA-----AAAA-----UGUUUGAACAGUUGGAUUUCAAACAUUUU---AACUUUGUGGAGUGGUGCUUACCAAGUGGUACAGCUCU--AAGCAAGUGA-ACA
ABVD01362184.1/618-761       UUCUUUGUUACUUGUCAGCUGCUUUU-AUC--------AAAUUCCAGGCC-AUUAUCCAGCAAACACUGU---AGAAA-----UGUUUGAACAGUUGGAUUUCAGGCAUUUU---UGUUUUGUGGAGUGGUGCUUACCA-GUGGUGCAGCUCU--AAGCAAGAGA-ACA
AAFC03000995.1/48176-48319   UUCUUUGUUAAUUGUCAGCUGCUUUUUAUC--------AGAUUCCAGGCC-AUUGUCCAGCAAACACUAU---AGAAA-----UGUUUGAACACUUGGAUUUCAAACAUUUU---CGUUUUGUGGAGUGGUGCUUACC--GUGGUACAGCUCU--AAGUAAGCAA-AUG
AAGV020322347.1/4564-4707    UUCUUUGUUACUUAUCAGCUGCUUUU-AUC--------AAAUUCUAGGCC-AUUAUCCAGCAAACACUAU---AGAAA-----UGUUUGAACGGUUGGAUUUCAAACAUUUU---CAUUUUGUGGAGUGGUGCUUACCA-GUGGUACAGAUCU--AAACAAGUGA-ACA
ABRP01135829.1/7839-7982     UUCUUUGUUAAUUGUCAGCUGCUGUU-AUC--------AAAUUCCAGGCC-AUUAUCCAGCAAACACUAU---AGAAA-----UAUUUGAACAGUUGGAUUUCAAACAUUUU---CGUUUUGUGGAGUGAUGGUUACCG-GUGGUACAGUUCU--AAGCAAGUGA-ACA
AALT01389871.1/315-459       UUCUUUGUUAAUUGUCAGCUGCUUAU-AUC--------AAAUUCCAGGGCCAUUAUCCAGUAAACACUAU---AGAAA-----UGUUUGAACUGUCGGAUUUCAAACAUUUU---UGUCUUGUGGAGUGGUGCUUAUCA-GUGGUAAAGCUCU--AAGCAAGUGA-AUA
AAYZ01038147.1/2526-2673     UUCUGUGUUAAUUGUCAGCUGCUUUU-AUC--------AAAUUCCAGGCC-AUUAUCCAGUAAACACUAUUACAAAAA-----UCUUUGAACAGUUGGAUUUCAAACAUUUU---CACUUUGUGGAGUGGUGCUUAGCAAGUGGUACAGCUCU--AACCAAGUGA-ACA
ABRO01110160.1/2923-3073     UUCUUUGUUACUUGUCAGCUGCUCUU-UUUUUUAAUCAAAAGUCCAGGUC-AUUUUCCAGCAAACACUA-----AAAA-----UGUUUGAACAGUUGGAUUUCAAACAUUUU---CAUUUUGUGGAGUGGUGCUUACCAAGUGGUACAGCUCU--AAGCAAGUGA-ACG
ACBE01381112.1/367-508       UUCUUUGUUA-UUGUCAGCUGCUUUA--UC--------AAAUUCCAGGCCCAUUAUCCAGCAAACACUAU---AGAAA-----UGUUUGA-CAGUUGUAUUUCAAACAUUUU---CUCUUUGUGGAGUGGUGCUUACCA-GUGGUACAGCUCU--AAGCAAGUGA-ACA
ABRT010072612.1/6901-7041    UUCUUUGUUAAUUGUCAGCUGUUUUU-AU---------AAAUUCCAGG-C-UGUAUCCAGCAAACACUAU---AAAAA-----UGUUUGAGCAGUUGGAUUUCAAACAUAUU---CAUUUUGUGGAGUG---CUUACCAAGUGGUACAACUCU--AAGCAAGUGACACA
ABRN01152533.1/11356-11213   UUCUUUGUUCAUUGUCAGCUGCUUUU-AUC--------AAAUUCCAGGCC-AUUAUCCAGCAAACACUAG---AGAAA-------UUUGAACACCUGGAUUUCAAACAUUUUUUUCAGUUUGUGGAGUGGUGCU-ACCA-GUGGUACCGUUCU--AAGCAAGCAG-GCA
AAIY01381730.1/2592-2452     UUCCUUGUUAAUUGUUAGCUGCUUCG-AUC--------AAAUUCCAGACC-AUUAUC----AAACACUAU---AGAAA-----UGUUUGAGCAAUUUAAUUUCAAACAUUUU--UCAUAUUGUGGAGUGGUGCUUACCA-GUAGUACAGCUCU--AAGCAAAUGA-ACA
DQ517434.1/212-358           UUGUUUGUUUAUUGUCAGCUGCUUUU-AUC--------AAAUUCCAGGCC-AUUAUCCAGCAAACACUAU---UAAAA-----UGUUUGAACAGUUGGGUUUCAAACAUUUU---UGUUUUGUGGAGUGGUGCUUAUUAAGUGGUACAGCUCUCUAAGCAAGUGA-ACA
AC004542.1/125663-125807     UUCUUUGUUAGUUGUCAGCUGCUUUU-AUC--------AAAUUUCAGGCC-AUUAUCCAACAAACACUAU---AAAAA-----UGUUUGAACAAUUGGAUUUCAAACAUUUU---CGUUUUGUGGAGUGGUGCUCACCAAGUGGUACAGCCCU--AAGCAAGUGA-ACA
AAGW02067666.1/31961-32112   UUCUUUGUUAAUUGUCAGCUGCUUUUUAUC--------AAAUUCCAGGCC-AUUAUCCAGUAAACACUAA---AAAAAAAAAAUGUUUGAACAGUUGCGUUUCAAACAUUUU---CACUUUGUGGAGUGGUGCUUACCAAGUGGUACAGCUCU-UAAGCAAGUGA-ACA
AAEX03014798.1/255890-256033 UUCUUUGUUAAUUGUCAGCUGCUUUU-AUC--------AAAUUCCAGGCC-AUUGUCCAGCAAACACUAU---AGAAA-----UGUUUGAACAGUUGGAUUUCAAACAUUUU---CAUUUUGUGGGGUGGUGCUUACCA-GUGGUACAGCUCU--AAGCAAGUGA-ACA
AAGU03075131.1/60923-60784   UUCUUUGUUAAUUGUUAGCUGCUUUU-AUC--------CAAUUCCAGACC-AUUAUC----AAACACUAU---AGAAA-----UGUUUGAACAGUUGGAUUUCAAACAUUUU---CGUAUUGUGAAGUGGUGCUUACCA-UUGGUACAGCUCU--AAGUAAAUGA-ACA
AAQR03184908.1/24291-24433   UUCUUUGUUAGUUGUCAGCUGCUUUU-AUU--------AAAUUCCAGGCC-AUUAUCCAGCAAGCACUA-----AAAA-----UGUUUGAACAGUUGCAUUUCAGACAUUUU---CAUUUUGUGGAGUGGUGCUUACAAAGUGGUACAACUCU--AAGCAAGUGA-ACA
AAHX01080812.1/99949-100095  UUGUUUGUUUGUUGUCAGCUGCUUUU-AUC--------AAAUUCCAGGCC-AUUAUCCAGCAAACACUAU---UAAAA-----UGUUUGAACAGUUGGGUUUCAAACAUUUU---CGUUUUGUGGAGUGGUGCUUAUCAAGUGGUACAGCUCUCUAAGCAAGUGA-ACA
#=GC SS_cons                 ::::::::::::::::::::::::::.:::........::::::::::::.:::::::::::::::::::...:::::.....:::::::::::::::::::::::::::::...::::::::::::::::::::::::::::::::::::::..::::::::::.:::
#=GC RF                      UUcUUUGUUaaUUGUCAGCUGCUuUU.aUC........AAAUUCCAGGcC.aUUaUCCAGcAAACACUAu...agAAA.....UGUUUGAACagUUGgaUUUCAAACAUUUU...cauuUUGUGGAGUGGUGCUUAcCAAGUGGUACAGcUCU..AAGCAAGuGA.ACa
//
# STOCKHOLM 1.0

#=GF AC   RF01883
#=GF ID   TUG1_2
#=GF DE   Taurine upregulated gene 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   90.00
#=GF TC   91.00
#=GF NC   81.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.61 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0042478; regulation of eye photoreceptor cell development;
#=GF RN   [1]
#=GF RM   15797018
#=GF RT   The noncoding RNA taurine upregulated gene 1 is required for
#=GF RT   differentiation of the murine retina.
#=GF RA   Young TL, Matsuda T, Cepko CL
#=GF RL   Curr Biol. 2005;15:501-512.
#=GF CC   TUG1 (taurine upregulated gene 1) is a long non-coding RNA expressed in
#=GF CC   retina and brain. It was first identified in a screen for genes
#=GF CC   upregulated by in developing retinal cells in response to taurine. It is
#=GF CC   required for the normal development of photoreceptors in the retina [1].
#=GF WK   TUG1
#=GF SQ   17


AADB02020457.1/3795192-3795278 ---AAAAAG--UGUUGGUCUUUUUGCUCUUUUGUAAUUAAAUCCGGAUGUACCUCAAAAGA--CUU-AA-GACUGUGGUGAU-----AAGAUGCUUUCCUC
ABRN01372171.1/6841-6929       ---AAGAUG--UGUUGGUCUUUUAGCUCUUUUGUAAUUAAAUCUGGAUGUACCUCAAAAGAAUCUU-AA-GACUGUGGUGAU-----AAGAUGCUUUCCUC
AAFC03000995.1/48466-48554     ---CAAAUG--UGUUGGUCUUUUAGCUCUUUUGUAAUUAAAUCUGGAUGUACCUCAAAAGAAUCUU-GA-GACUGUGGUGAU-----ACUAUGCUUUCCUC
ABRP01135829.1/8139-8226       ---AAAAUG--UGUUGGUCUUUUAGGUCUUUUGUAAUUAAAUCUGGAUGUACCUCAAAAGAACAUU-AA-GACUGUGGUGAU-----A-GGUGCUUUCUGC
AAHX01112096.1/12704-12791     ---AAACUG--UGUUGGUCUU--AGCUCUUUUGUAAUUAAAUCUGGAUGUACCUCAAAAGACUCUA-UAAGACUGUGGUGUU-----AAAAGGCUUUCCUC
AAQQ01619694.1/1898-1985       ---AAACUG--UGUUGGUCUUU-AGCUCUUUUGUAAUUAAGUCUGGAUGUACCUCAAAAGAAUCUU-UA-GACUGUGGUGAU-----AAGAGGCUUUCCUC
AAHY01090246.1/37479-37390     -AAAAACUC--UGUUGGUCUU--AGCUCUUUUGUAAUUAAAUCUGGAUGUACCUCAAAAGACUCUU-UAAGACUGUGGUGUU-----AAAAGGCUUUCCUC
AACN010058815.1/1283-1192      ---AAAACG--UGUUGGUCUUUUAGCUCUUUUGUUAUUA--UCUGGAUGUACCUCAAAAGAAUCUU-AA-GACUGUGGUGAUCUUAUAAGAUGCUUUCCUC
AAYZ01038147.1/2826-2914       ---AAAAUG--UGUUGGUCUUUUAGUUGUUUUGUAAUUUAAUCUGGAUGUACCUCAAAAGAACCUU-AA-AAGUGUGGUGAU-----AAGGUGCUUUCCUC
AAWR02038334.1/140369-140284   ---AAAAUG--UGUUGUUCUUUUAGUUCUUUUGUAAU----UCUGGAGGUACCUCAAAAGAAUCUU-AAAGACUGUGGUGAU-----AAGAUGCUUUCCUC
AAKN02007240.1/6723-6638       AGAAAGAUG--U---GUUCUUU-AGCUCUUUUGUAAUUAAAUCUGGAUGUACCUCAA--GACUCUU-AA-GACUGUGGUGAU-----AAGAGGCUUUUCUC
AAPY01652640.1/776-864         ---AAAAUG--UGUUGGUAUUUUAGCUGUUUUGUAAUUAAGUCUGGUUGUACCUCAAAAGAAUCUU-AA-GACUGUGGUGAU-----AAGAUGUUUUCCUU
ACBE01078004.1/8740-8831       -GAGAAGUGAUGGUUGGUCUUUUAGCUCUUUUGUAAUGAAAUCCGGACGCACCUUAAACAAACCUU-AA-GACUGUGGUGU------AAGAUGCUUUCCUC
AC004542.1/125954-126040       ---AAAAAG--UGUUGGUCUUUUUGCUCUUUUGUAAUUAAAUCCGGAUGUACCUCAAAAGA--CUU-AA-GACUGUGGUGAU-----AAGAUGCUUUCCUC
DQ517434.1/508-595             ---AAACUC--UGUUGGUCUU--AGCUCUUUUGUAAUUAAAUCUGGAUGUACCUCAAAAGACUCUUUAA-GACUGUGGUGUU-----AAAAGGCUUUCCUC
DQ517435.1/107-194             ---AAACUC--UGUUGGUCUU--AGCUCUUUUGUAAUUAAAUCUGGAUGUACCUCAAAAGACUCUUUAA-GACUGUGGUGUU-----AAAAGGCUUUCCUC
AAGW02067666.1/32254-32342     ---AAAAUG--UGUUGGUCUUUUUGCUCUUUUGUAAUUAAAUCUGGACGUACCUCAGAAGAAUCUU-GG-AAGUGUGGUGAU-----AAGGUGCUUUCCUC
#=GC SS_cons                   ...::::::..:::::::::::::::::::::::::::::::::::::::::::::::::::::::.::.::::::::::::.....::::::::::::::
#=GC RF                        ...aAAaUG..UGUUGGUCUUUUAGCUCUUUUGUAAUUAAAUCUGGAuGUACCUCAAAAGAaUCUU.aA.GACUGUGGUGaU.....AAGAuGCUUUCCUC
//
# STOCKHOLM 1.0

#=GF AC   RF01884
#=GF ID   LINC00901
#=GF PI   BC040587; 
#=GF DE   Non-coding RNA BC040587
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; RNAz; Eberhardt R
#=GF GA   55.00
#=GF TC   55.10
#=GF NC   54.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.91 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20048075
#=GF RT   Recurrent focal copy-number changes and loss of heterozygosity implicate
#=GF RT   two noncoding RNAs and one tumor suppressor gene at chromosome 3q13.31 in
#=GF RT   osteosarcoma.
#=GF RA   Pasic I, Shlien A, Durbin AD, Stavropoulos DJ, Baskin B, Ray PN, Novokmet
#=GF RA   A, Malkin D
#=GF RL   Cancer Res. 2010;70:160-171.
#=GF CC   BC040587 is a long non-coding RNA which is often deleted in osteosarcoma.
#=GF CC   Deletion of this gene is associated with poor survival of osteosarcoma
#=GF CC   patients [1].
#=GF WK   Long_non-coding_RNA
#=GF SQ   30


AANN01182270.1/2379-2530     GU-UUGAUUUUUCCUUU-UAACUGCAAUGAGGUCACACUUAGGCAUUUGUGACAUAGCAGC---------AGGUUGCCAUG-GAGAUGAUAGCUUCAUCAGCAACUCUGCUUUGCAAUGACUUCACAGCAAGGUUACUAAGAAGCAGAUGGGCUGUGAAGGAGA
ABRN01177379.1/14063-14212   CU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCAC-CUCCUGGGUUUGUGACAUAGCAGU----------GGUUGCCACC-GAGAUGAUAGCUUUAUCAGCAACUCUGCUUUGCAAUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUAUGAAGGAGA
ABRO01203502.1/2539-2690     GC-UUGAUUUUUCCUCU-UCACUGUGGUGAGGUCAGAUUCCUGCAUUUGUGACAUAGCAGC---------AAGUUGCCAUG-GAGAUGAUAGCUUUAUCAGUAGCUGUUCUUUCCCAUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
AC069504.7/6628-6779         GU-UUGAUUUCUCCUUU-UAGCUGCAGUGAGGUCACACUCCUGCAUUUGUGACAUAGCAGC---------AGGUUGUCAUG-GAGAUGAUAGCUUUAUCAGCAACUCUGCUGUGCAAUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
ABRP01153709.1/3987-4138     GU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCACACUCCUGUGUUUGUGACAUAGCAGU---------GGGUUGCCAUG-GAGAUGACAGCUUUAUCAGCAACUCUGCUGAGCAAUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
ABGA01218642.1/40691-40540   GU-UUGAUUUCUCCUUU-UAGCUGCAGUGAGGUCACACUCCUGCAUUUGUGACAUAGCAGC---------GGGUUGUCAUG-GAGAUGAUAGCUUUAUCAGCAACUCUGCUGUGCAAUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
AAGV020105443.1/1072-1223    GU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCACACUCCUGUGCUUGUGACAUAGCAGC---------GGGUUGCCAAG-GAGAUGAUAGCUUUAUCAGCAACUCCUCUUUGCAGUGACUUCACAGCAAGGUUACAAAGAAGCAGAUGGGCUGUGAAGGAGA
AALT01637021.1/900-749       GU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCACACUCCUGUGUUUGUGACAUAGCAGU---------GGGUUGCCAUG-GAGAUGAUAGCUUUAUCAGCAACUCCACUUUGCAAUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
AC098735.4/33847-33996       -U-CUUAUUUCUCCU-U-UAACUACACUGAGGUCACACCCCUAUGUUUGUGACAUAGCAGC---------AGGUUGCCAUG-GAGAUGAUGGCUUUAUCAGCCACACUACCUUGCCAUGACCUCACAACAAGGUUACCAAGAAGCAGAUGGGCUGUGAAACAGA
ABRT010169842.1/656-807      GU-UUGUUUUCUCCUUU-UAACUGCAAUGAGGUCACACUCCUGCAUUUGUGACAUAGCAGC---------AGGUUGCCAUG-GAAAUGAUAGCUUUAUCAGCAACUCUGCUUUGCAAUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
AAFR03033451.1/125985-126135 AA-UUUA--UCCCCUUCUUCCCUGCAGUGAGGUCACAAUCCUGUGUUUGUGACAUAGCAGU---------CAGUUGCCAUG-GAGAUGAUUGCUUUAUCACCAACUCCUCUUUGCAAUGACUUCACAGCAAGGUUAUGGAGAAGCAGAUGGGCUGUGAAGGAGA
AAYZ01061849.1/1143-1294     AU-UUGAUUUCUCCUUA-UAACUGCAGUGAGGUCACACUCCUGCAUUUGUGACAUAGCAGU---------AGGUUGCCAUG-GAGAUGAUAGCUUUAUCAGCAACUCUGUUUUGCAAUGACUUCACAGCAAGGUUACCAAGGAGCAGAUGGGCUGUGAAAGAGA
AAFC03028366.1/6999-7149     GU-UUGAUUUCUCCCUU-UAACUGUAGUGAGGUCACACUCCUAGGUUUGUGACAUAGCAGC---------A-GUUGCCAUG-GAGAUGAUAGCUUUAUCAGCAACUCCACUUUGCAAUGACUUGACAGAAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
AAPN01021282.1/1020-893      ---------------------CCGCGGUGAGGUCACGGCUCUGUGGCGGUGACAUCGCCAC---------CGGUUGCCACG-GAGAUGAAGGCUGAACCCCCCGAUCAGCGGCGUGACGACCGCCCUGCAAGGUUGCAGGGAAGCAGAUGGGCUGGGAG-----
AAHX01069476.1/43624-43474   -U-CUUAUUUCUCCUUU-AAACUCCACUGAGGUCACACUCCUAUGUUUGUGACAUAGCAGC---------AGGUUGCCAUG-GAGAUGACGGCUUUAUCAGCAACCGUGUCUUGCCAUGACCUCACAACAAGGUUAGCAAGAAGCAGAUGGGCUGUGAAACAGA
AAQQ01255276.1/3103-3250     -CUGGGAUUUCUCCUUU-UAACUGCAGUGAGGUCACACUACUGUGUCUGUGACAUAGCUGC---------AGGUGGCGAUGGGAGAUGACAGCUUUAUCAGCA-CUCUGCUUUGCAAUGACUUCACAGCAGGGUA---CAGGAGCAGAUG-GCUGGGAAGGAGA
ABVD01114368.1/1358-1509     GU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCACACUCCUGUGCUUGUGACAUAGCAGC---------GGGUUGCCAUG-GAGAUGACAGCUUUAUCAGCAGCUCUUGUUUGCAGUGACUUCACAGCAAGGUUACAAAGAAGCAGAUGGGCUGUGAAGGAGA
AAIY01388070.1/1540-1380     GU-UUGAUUUCUCCCUU-UAACCACCAUGAGGUCACACUCCUGUGUUUGUGACAUCGCAGCAUAGCAGCGGGGUUACCAUG-GAGAUGACAGCUUUAUCAGCAACUCCACUUUGCAAUGACUUCACAGCCAGGUUACCAAGAAGCAGAUGUGCUGUGAAGAACA
AAPY01263309.1/5195-5346     GU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCACAUUCCUGUGUUUCUGACAUAGCAGC---------AGGUUGCCAUG-GAGAUGGUAGCUUUAUCAGCAACUCUGCUUUGCAAUGACUUCACAGCAAGGUUACCACGAAGCAGAUGGGCUGUGAAGGAGA
ABDC01140724.1/2927-3077     GU-CUGAUUUCUUAUUU-AAACUGCAGUGAGGUCACACUCCUGGGUUUGUGACAUAGCAGC---------AGGUUGCUAUG-GAGAUGAUAGUUUUAUCAGCAACUCU-CUUUGCAAUGACUUCACAGCAAGGUUACAAUGAAGCAGAUGGGCUGUGAAGAAGA
AAWR02011952.1/44966-44815   GU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCACACUCCUGUGUUUGUGACAUAGCAGC---------GGGUUGCCAUG-GAGAUGAUAGCUUUAUCAGCAACUCCUCUUUGCAGUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
AANG01271987.1/1976-2127     GU-UUGAUUUCUCCUUU-UAACUUCAGUGAGGUCACACUCCUGUGUUUGUGACAUAGCAGC---------GGGUUGCCAUG-GAGAUGAUAGCUUUAUCAGCAACUCUGCUUUGCAAUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
AAKN02035552.1/14199-14350   GU-UUGAUUUCUCCUUU-UAACUUCAGUGAGGUAACACUCCUGCAUUUGUGACAUAGCAGC---------AGGUUGCCAUG-GUGAUGAUAGCUUUAUCAGCAAUUCUGUCUUGCAAUGAUUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
AANU01278870.1/1050-900      GU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCACACUCCUGCAUUUGUGACAUAGCAGC---------GGGUUGUCAUG-GAGAUGAUAGGUUUAUCAGCAACUCUGCUUUGCAGUGACUUCACAGCAAGGUUACCAAG-AGCAGAUGGGCUGUGAAGGAGA
AACZ03024603.1/19094-18943   GU-UUGAUUUCUCCUUU-UAGCUGCAGUGAGGUCACACUCCUGCAUUUGUGACAUAGCAGC---------GGGUUGUCAUG-GAGAUGAUAGCUUUAUCAGCAACUCUGCUGUGCAAUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
AAPE02022451.1/1280-1431     GU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCACACUCCUGUGUUUGUGACAUAGCAGU---------GGGUUGCCAUG-GAGAUGAUAGCUUUAUCAGCAACUCUGCUUUGCAGUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
AAGU03049345.1/13315-13164   GU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCACACUCCUGUGUUUGUGACAUAGCAGC---------GGGUUGCCAUG-GAGAUGAUAGCUUUAUCAGCAACUCCACUUUGCAAUGACUUCACAGCAAGGUUACCAGGAAGCAGAUGGGCUGUGAAGGAGA
AAGW02015609.1/71215-71064   GU-UUGAUUUCUCCUUU-UAACUGCAGUGAGGUCACACUCUUGCAUUUGUGACAUAGCAGC---------GGGUUGCCAUG-GAGAUGAUAGCUUUAUCAGCAACUCUGCUUCGCAAUGACUUCACAGCAAGGUUACCAAGGAGCAGAUGGGCUGUGAAGGAGA
AACN010008840.1/2325-2174    GU-UUGAUUUCUCCUUU-UAACUUCAGUGAGGUCACACUCCUGUGUUUGUGACAUAGCAGC---------AGGUUGCCAUG-GAGAUGAUAGCUUUAUCAGCAACUCUGCUUUGCAAUGACUUCACAGCAAGGUUACCAGGAAGCAGAUGGGCUGUGAAGGAGA
AAQR03138685.1/17028-17179   AU-CUAAUUUCUCCUUU-AUACUGCAGUGAGGUCACAUUCCUGGGUUUGUGACAUAGCAGC---------AGGUUGCCAUG-GAGACAAUAGUUUUAUGAGUAACUCUGCUUUGCAAUGACUUCACAGCAAGGUUACCAAGAAGCAGAUGGGCUGUGAAGGAGA
#=GC SS_cons                 ::.::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::.........:::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      gu.uUGAUUUCUCCUUU.UaaCugCagUGAGGUCACAcUcCUGuGuUUGUGACAUaGCaGC.........gGGUUGCCAuG.GAGAUGAuaGCUUuAUCaGCaacUCugCuuuGCaAUGACuUCaCaGCaAGGUUACcaaGAAGCAGAUGGGCUGuGAAGgAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01885
#=GF ID   HSR-omega_1
#=GF PI   HSR-omega_1; ; DLX6-AS1_2
#=GF DE   Heat shock gene hsromega conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   80.00
#=GF TC   92.20
#=GF NC   33.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.27 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001641; lincRNA gene;
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0016607; nuclear speck;
#=GF DR   GO; 0042981; regulation of apoptotic process;
#=GF RN   [1]
#=GF RM   10984439
#=GF RT   Omega speckles - a novel class of nuclear speckles containing hnRNPs
#=GF RT   associated with noncoding hsr-omega RNA in Drosophila.
#=GF RA   Prasanth KV, Rajendra TK, Lal AK, Lakhotia SC
#=GF RL   J Cell Sci. 2000;113:3485-3497.
#=GF RN   [2]
#=GF RM   19737742
#=GF RT   The developmentally active and stress-inducible noncoding hsromega gene is
#=GF RT   a novel regulator of apoptosis in Drosophila.
#=GF RA   Mallik M, Lakhotia SC
#=GF RL   Genetics. 2009;183:831-852.
#=GF RN   [3]
#=GF RM   20065067
#=GF RT   Improved activities of CREB binding protein, heterogeneous nuclear
#=GF RT   ribonucleoproteins and proteasome following downregulation of noncoding
#=GF RT   hsromega transcripts help suppress poly(Q) pathogenesis in fly models.
#=GF RA   Mallik M, Lakhotia SC
#=GF RL   Genetics. 2010;184:927-945.
#=GF CC   The heat shock gene hsromega is a long non-coding RNA which produces a
#=GF CC   number of transcripts. These transcripts include a nuclear transcript,
#=GF CC   hsromega-n, which is detected as small speckles in the interchromatin
#=GF CC   space and co-localises with heterogeneous nuclear RNA-binding proteins
#=GF CC   (hnRNPs) [1]. Hsromega-n interacts directly and indirectly with a number
#=GF CC   of regulatory proteins including hnRNPs, cAMP response element binding
#=GF CC   binding protein (CBP), proteasome, and Drosophila inhibitor of apoptosis
#=GF CC   protein 1 (DIAP1). Through these interactions, it has roles in the
#=GF CC   regulation of apoptosis [2] and the suppression of poly(Q) toxicity [3].
#=GF WK   Hsromega
#=GF SQ   13


AAFS01000208.1/10013-9936      ACAACUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUACGCAAACGCGUAG
AANI01014362.1/14677-14602     ACACGUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUACGCGA--UCGAUA
AAPP01019520.1/1057-1134       ACCACUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAUGUUGAUACGCGAACGCGUAC
AAPT01020159.1/556430-556506   ACAAGUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUGAAAAGUUGAUACGCGA-AUCGAUC
AAPU01011178.1/205842-205767   ACACGUUAACCAAGCAUUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUACGCGA--UCGAAC
AAQB01009437.1/2975909-2975986 ACACGUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUACGCGUGAUCGAUC
AASS01005805.1/431-507         ACCACUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUAU-CGAUAUCGAUC
M14558.1/1200-1274             -CACUUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUACGCGA--UCGAAC
U18307.1/1713-1789             ACCACUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUAU-CGAUAUCGAUC
X05347.1/1362-1436             ACACUUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUU-GGCGUUGAAAGUUGAUACGCGA--UCGAAC
X04188.1/1639-1715             ACCACUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUAU-CGAUAUCGAUC
M14557.1/1176-1252             ACCACUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUAU-CGAUAUCGAUC
X16337.1/1526-1603             ACAACUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUACGCAAACGCGUAG
#=GC SS_cons                   ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                        ACaacUUAACCAAGCAAUAUGUAUUUCUUUCUCUAAACUUUAUAGUUGGGCGUUGAAAGUUGAUAcGCGAuauCGauc
//
# STOCKHOLM 1.0

#=GF AC   RF01886
#=GF ID   HSR-omega_2
#=GF DE   Heat shock gene hsromega conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   55.00
#=GF TC   56.90
#=GF NC   32.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.15 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001641; lincRNA gene;
#=GF DR   GO; 0016607; nuclear speck;
#=GF DR   GO; 0042981; regulation of apoptotic process;
#=GF RN   [1]
#=GF RM   10984439
#=GF RT   Omega speckles - a novel class of nuclear speckles containing hnRNPs
#=GF RT   associated with noncoding hsr-omega RNA in Drosophila.
#=GF RA   Prasanth KV, Rajendra TK, Lal AK, Lakhotia SC
#=GF RL   J Cell Sci. 2000;113:3485-3497.
#=GF RN   [2]
#=GF RM   19737742
#=GF RT   The developmentally active and stress-inducible noncoding hsromega gene is
#=GF RT   a novel regulator of apoptosis in Drosophila.
#=GF RA   Mallik M, Lakhotia SC
#=GF RL   Genetics. 2009;183:831-852.
#=GF RN   [3]
#=GF RM   20065067
#=GF RT   Improved activities of CREB binding protein, heterogeneous nuclear
#=GF RT   ribonucleoproteins and proteasome following downregulation of noncoding
#=GF RT   hsromega transcripts help suppress poly(Q) pathogenesis in fly models.
#=GF RA   Mallik M, Lakhotia SC
#=GF RL   Genetics. 2010;184:927-945.
#=GF CC   The heat shock gene hsromega is a long non-coding RNA which produces a
#=GF CC   number of transcripts. These transcripts include a nuclear transcript,
#=GF CC   hsromega-n, which is detected as small speckles in the interchromatin
#=GF CC   space and co-localises with heterogeneous nuclear RNA-binding proteins
#=GF CC   (hnRNPs) [1]. Hsromega-n interacts directly and indirectly with a number
#=GF CC   of regulatory proteins including hnRNPs, cAMP response element binding
#=GF CC   binding protein (CBP), proteasome, and Drosophila inhibitor of apoptosis
#=GF CC   protein 1 (DIAP1). Through these interactions, it has roles in the
#=GF CC   regulation of apoptosis [2] and the suppression of poly(Q) toxicity [3].
#=GF WK   Hsromega
#=GF SQ   10


AAFS01000208.1/9763-9677 GUCGUUUCUAUCAGAUU--GAUUGUGCGGAUUGUGU---UA--UAGGAACUCCGGUGUAUCGACUUCUCUGCUCUACUAAGGGUGAACCCUACA
AAPP01019520.1/1315-1403 CUCGAAUAAGUGGGAUU--GAUUUUGCGGAUUGUGU---UAUAUAGGAACACUGCUGUAUCGACUUCUCUGCUCCACUAAGGGUGAACCGUAAU
AASW01005169.1/371-285   CUCGAUUCUGUCAGAUU--GAUUGUGCGGAUUGUGU---UA--UAGGAACACUGGUGUAUCGACUUCUCUGCUCCACUAUGGGUGAAGGAUACC
U18307.1/1956-2042       CUCGAUUCUGUCAGAUU--GAUUGUGCGGAUUGUGU---UA--UAGGAACACUGGUGUAUCGACUUCUCUGCUCCACUAUGGGUGAAGGAUACC
X16337.1/1777-1863       GUCGUUUCUAUCAGAUU--GAUUGUGCGGAUUGUGU---UA--UAGGAACUCCGGUGUAUCGACUUCUCUGCUCUACUAAGGGUGAACCCUACA
X05347.1/1578-1665       GUCGUUUUUAUCAGAUUGUGAUUGCGUGGAUUGAAUAUA--UAUAGGA----ACCUGUAUCGACUUCUCUGCUCUACUAAGACUUGUUCAAAAG
M13240.1/582-668         CUCGAUUCUGUCAGAUU--GAUUGUGCGGAUUGUGU---UA--UAGGAACACUGGUGUAUCGACUUCUCUGCUCCACUAUGGGUGAAGGAUACC
X04188.1/1882-1968       CUCGAUUCUGUCAGAUU--GAUUGUGCGGAUUGUGU---UA--UAGGAACACUGGUGUAUCGACUUCUCUGCUCCACUAUGGGUGAAGGAUACC
M14558.1/1417-1504       GUCGUUUUUAUCAGAUUGUGAUUGCGUGGAUUGAAUAUA--UAUAGGA----ACCUGUAUCGACUUCUCUGCUCUACUAAGACUUGUUCAAAAG
M14557.1/1419-1505       CUCGAUUCUGUCAGAUU--GAUUGUGCGGAUUGUGU---UA--UAGGAACACUGGUGUAUCGACUUCUCUGCUCCACUAUGGGUGAAGGAUACC
#=GC SS_cons             :::::::::::::::::..:::::::::::::::::...::..:::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  cUCGaUUcUgUCAGAUU..GAUUGUGCGGAUUGuGU...ua..UAGGAACaCuGgUGUAUCGACUUCUCUGCUCcACUAaGGGUGaagcauAcc
//
# STOCKHOLM 1.0

#=GF AC   RF01887
#=GF ID   DLX6-AS1_1
#=GF PI   Evf1_1;
#=GF DE   Embryonic ventral forebrain RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   75.50
#=GF NC   45.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 40.06 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0045893; positive regulation of transcription, DNA-templated;
#=GF DR   GO; 0030900; forebrain development;
#=GF RN   [1]
#=GF RM   15183307
#=GF RT   Developmental regulation of EVF-1, a novel non-coding RNA transcribed
#=GF RT   upstream of the mouse Dlx6 gene.
#=GF RA   Kohtz JD, Fishell G
#=GF RL   Gene Expr Patterns. 2004;4:407-412.
#=GF RN   [2]
#=GF RM   16705037
#=GF RT   The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved
#=GF RT   region and functions as a Dlx-2 transcriptional coactivator.
#=GF RA   Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD
#=GF RL   Genes Dev. 2006;20:1470-1484.
#=GF CC   Evf-1 (Embryonic ventral forebrain-1) is a developmentally-regulated long
#=GF CC   non-coding RNA. In rats, it is expressed in neurons in the subventricular
#=GF CC   zone of the developing forebrain. Its expression is linked to that of the
#=GF CC   Shh (sonic hedgehog) and Dlx families of genes, which are important in
#=GF CC   ventral forebrain and craniofacial development [1]. An alternatively
#=GF CC   spliced form of Evf-1, Evf-2, forms a stable complex with the Dlx-2
#=GF CC   protein. This complex activates transcription of Dlx-5 and Dlx-6 [2].
#=GF WK   DLX6-AS1
#=GF SQ   15


AANN01792448.1/1306-1126     ACUUCUCUUGAGGAUUCAGUAGAGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGUGAGACAGGCAUUCACUGACAAGAAGGAACAUUUAAAUUUUGCCAAAUAAGUUCAUUAGUAUUCAGAAAGCUUUGCAACACUCAUAUUUAAUAAACCUUUCCAUUACAGUGUAAGAAAU-
AACC02000013.1/910577-910398 AUUUCUCCUGAGGGUACAAUAGAGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGAGAGACAGACAUUCACUGACAAGAAG-AACAUUUAAAUUUUGGCAAAUAAGUUCAUUAGUAUUCAGAAAGCUUUGCACCCCUCAUAUUUAAUAAACCUUUCCAUUACAGAGUAAGAAAU-
AAWR02013862.1/6077-6256     AUUUCUCUUGAGGGUACAAUAUUGUCUAAUUUUCUUCAUUAUUCAAUGUGGAUUCUGUUAAGUGAGACAGGCAUUCACUGACAAGAAGGAACAUUUAAAUUUUGGCAAAUAAGUUCAUUAGUAUUCAGAAAGCUUAGCACCCCUUAUAUU-AAUAAACCUUUCCAUUACAGAGUAAGAAAC-
ABRT010013038.1/895-1074     AUUUCUCUGGAGGGCACAAUAGAAUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGUGAGACAGGCAUUCACUGACAAGAAG-AACAUUUAAAUUUUGGCAAAUAAGUUCAUUAGUAUUCCAAAAGCUUUGCACCCCUCAUAUUUAACAAACCUUUCCAUUACAGAGUAAAAAAU-
ABVD01412771.1/1590-1768     UUUGUUUUUGAGGGUAUAGUAGAGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGUGAGGCAGGCAUUCACUGACAAGAAG-AACAUUUAAAUUUCGGCAAAUGAGUUCAUUAGUAUUCACAAAGCUUUGCACCCCUCAUGUUCAAUAAACCUCUCUAUUACAGAGAAAGAAA--
ABRR01115815.1/1629-1807     AUAUCCUUUGAGGGUACGAUGUGGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUAUUAAGUAAGACAGGCAUUCACU---AAGGACGAAUACUUAAAUUUUGGCAAGUAAGUUCAUUUGUAUUCAGAAAGCUUUGCACUCCUCAUAUUUAAUAAACCUUUCCAUUACAGAGUAAAGAAAU
AAIY01400228.1/2213-2392     AUUUCUCUGGAGGGUACGAUAUAGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGUGAGACGGGCAUUCACUGACAAGAAG-CGCAUUUCAAUUUUGGCAAAUAAUUUCAUUAGUAUUCACAAAGUUUGGUAUCCCUUAUAUUUAAUAAACCUUUCCAUUGCAGAGUAAAAAAU-
ABRP01070477.1/22517-22697   AUUUCUCUUGAGGGUAUGAUAUAGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGUGAGACAGGCAUUCACUGACAAGAAAGAACAUUUAAAUUUUGGCAAAUAAGUUCAUUAGUAUUCAGAAAGCUUUGCUCCCCUCAUAGUUAAUAAACCUUUCCAUUACAAAAUAAGAAAU-
AAQQ01558328.1/1265-1444     AUUUCUCUUGAGAGUACGAUAAAGUCUAAUUUUCCCCAUUAUUCAAUUUGGAUCCUGUUAAGCGAGACAGGCAUUCACUGACAAGAAG-AACAUUUCAAUUUUGGCAAAUAAGUUCAUUAGUAUUCAGAAAGCUUUGCACCCCUCAUAUUUAAUAAACCUUUCCAUUACAGAGUAAGAAAC-
AAKN02016914.1/5934-6110     AUUUCUCUUGAGGGUACGACAGAGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGUGAGACAGGCAUUCACCAACAAGAA----CAUUUAAACUUUGGCUAAUAAGUUCAUUAGUAUUAAGAAAGCUUUGCACCCCUCAUAUUUAAUAAACCUUUCCAUUACAGAGUAAGAAAU-
AC122240.4/64177-64356       AUUUCUCUUGAGGGUACGAUAGAGUCUAAUUUUCUUCAUUAUUCAAUUUGGUGCCUGUUAAGUGAGACAGGCAUUCACUGACAAGAAG-AACAUUUAAAUUUUGGCAAAUAAGUUCAUUAGUAUUCAGAAAGCUUUGCAACCCUCAUAUUUAAUAAACCUUUCCAUUACAGAGUAAGAAAU-
AAPE02008847.1/118460-118639 AUUUCUCUGGAGGGUAUGAUAUAGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGUGAGACAGGCAUUCA-UGACAAGAAAGAACAUUUAAAUUUUGGCUAAUAAGUUCAUUAGUAUUCAGAAAGCUUUGUGCCCCCCAUAUUUAAUAAAUCUUUCCAUUACAGAGUAAGAAAU-
AACN010010072.1/3139-2959    ACGUCCCUUGAGAGCAGAAUAUAGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGUGAGACAGGCACUCACUGAUAAGAAGGAACAUUUAAGUUUUGGCAAAUAAGUUCAUUAGUAUUCAGAAAGCUUUUCACCCCUCAUAUUUAAUAAACCUUUCCAUUACAAAGUAAGAAAU-
AAGU03015811.1/27774-27618   AUUUCUCUUGAGGGUACGAUACAGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGUGAGACAGGCAUUCACUGACAAGAAG-AACAUUUCAAUUUUGGCAAAUAAGUUCAUUAGUAUUCACAAAGCUUUGCAUCCCUCAUAUUUAAUAAAC------------------------
AAGW02035474.1/81890-82069   AUUUCUCUUGAGGGUACGAUCAAGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGUGAGACAGGCAUUCACUGACAAGAAG-AGCAUUUAAAUUUCGGCAAAUAAGUUCAUUAGCAUUCAGAAAGCUUUGCACCCCUCAUAUUUAAUAAACCUUUCCAUUACAGAACAAGAAAU-
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.
#=GC RF                      auuUCucUuGAGGGuAcgaUauaGUCUAAUUUUCUUCAUUAUUCAAUUUGGAUCCUGUUAAGuGAGACAGGCAUUCACUGACAAGAAg.aaCAUUUaAAUUUuGGCaAAUAAGUUCAUUaGUAUUCAgAAAGCUUuGCacCCCUCAUAUUUAAUAAACCUUUCCAUUACAGaGuAAGAAAu.
//
# STOCKHOLM 1.0

#=GF AC   RF01888
#=GF ID   DLX6-AS1_2
#=GF PI   Evf1_2;
#=GF DE   Embryonic ventral forebrain RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   150.00
#=GF TC   152.60
#=GF NC   148.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 44.87 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0045893; positive regulation of transcription, DNA-templated;
#=GF DR   GO; 0030900; forebrain development;
#=GF RN   [1]
#=GF RM   15183307
#=GF RT   Developmental regulation of EVF-1, a novel non-coding RNA transcribed
#=GF RT   upstream of the mouse Dlx6 gene.
#=GF RA   Kohtz JD, Fishell G
#=GF RL   Gene Expr Patterns. 2004;4:407-412.
#=GF RN   [2]
#=GF RM   16705037
#=GF RT   The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved
#=GF RT   region and functions as a Dlx-2 transcriptional coactivator.
#=GF RA   Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD
#=GF RL   Genes Dev. 2006;20:1470-1484.
#=GF CC   Evf-1 (Embryonic ventral forebrain-1) is a developmentally-regulated long
#=GF CC   non-coding RNA. In rats, it is expressed in neurons in the subventricular
#=GF CC   zone of the developing forebrain. Its expression is linked to that of the
#=GF CC   Shh (sonic hedgehog) and Dlx families of genes, which are important in
#=GF CC   ventral forebrain and craniofacial development [1]. An alternatively
#=GF CC   spliced form of Evf-1, Evf-2, forms a stable complex with the Dlx-2
#=GF CC   protein. This complex activates transcription of Dlx-5 and Dlx-6 [2].
#=GF WK   DLX6-AS1
#=GF SQ   19


AAHY01051190.1/2155-2361     AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAGAGUACAUUCAACCCUAAUAAGGAGAUGUCUCAGUUUAUCAGUUUU-CUGUCAAUCAUUAAAACAAGAAAAAUGAAACUUGCAAUUAUAUACAAGGAGACAUAAC-UCCUAAUUCCUUCUUCCUACCUGAAGCAGAAGAAUUUUAAUUGCUU--GGAAAAAUAUGAUUUUUCUUUU
AAQQ01558328.1/1452-1658     AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAGAGUACAUUCAACCCUAAUUCAGAGAUGUCUCAGUUUAUCAGUUUU-CUGUCAGUCACUAAAACAAGAAAAAUGAAACAUGCAAUUAUAUACAAGGAGACAGAAC-UCCUAAUUCUUUCAUCCCAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAGAUUUUUGUUUU
AAGV020161035.1/4535-4741    AAUAGUCAAACAAAUUAGCGAUGAGGCCACCAGGAGAGUAUAUUCAACCCCAAUUCAGAGAUGUCUCGGUUUAUCAGUUUU-CUGUCAAUCAUUAAAACAAGAAAAAUGAAACAUGCAAUUAUAUAUAAGGAGACAGAAC-UCUGAAGUCUUUCAUCCUUGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAAAAGAUUUUUGUUUU
ABBA01045758.1/12184-12390   AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAGAGUACAUUCAACCUGGAUUCAAAGAUGUCUCAGUUUAUUAGUUUU-CUGUCAAUCAUUAAAACAAGAAAGAUGAAACAUGCAAUUAGAUACAAGGAGACAGAAC-UCCUAAUUCUUUCAUCCUAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAGAUUUUCGUUUU
ABDC01134893.1/2108-2314     AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAGAGUACAUUCCACCCUGAUUCAGACAUAUCUCAGUUUAUCAGUUUU-CUGUCAAUCAUUAAAAUAAGAAAGAUGAAACAUGCAAUUACAUACAAGGAGACAGAAU-UCCUAAUUCUUUCAUCCUAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAGAUUUUUGUUUU
ABRT010013038.1/1082-1288    AAUAGUCUAACAAAUUAGCAACAGGGCCACCAAGAGAGUACAGUCAACCCUGAUUCAGAGAUGUCUCUGUUUAUCAGUUUU-CUGCCAAUCAUUAAAACAAAAAAGGUGAAACAUGCAAUUAUAGACAAGGAGACAGAAC-UCCUAGUUCUUCCAUCCUAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGGAAAAUAAGACUUGUGUUUU
AAHX01028381.1/35995-35789   AAUAGUCAAACAAAUUAGUAAUGGGGCCACCAAGAGAGUACAUUCAACCCUCAUAAGAAGAUGUCUCGGUUUAUCAGUUUU-CUGUCAAUCAUUAAAGCAAGAAAGAUGAAACUUGCAAUUAUAUACAAUGAAACACAAC-UCCUAAUUCUUCUAUCCUACCUGAAGCAGAAGAGUCUUAAUUGCUU--GGAAAAAAAAUAUUUUUCUUUC
ABVD01005901.1/2148-2354     AAUAGUCAAACAAAUUAGUGAUGGGGCCACCAGGAGAGUACCUUCAACCGUGAUUCAGAGAUGUCUCAGUUUAUCAGUUUU-CUGUCAAUCAUUAAAACAAGAAAGAUAAAACAUGAAAUUAUAUACAAGGAGACAGAAC-UCCAAAUUCUUUCAUCCUUGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAGAUUUUUGUUUU
AACN010010072.1/2951-2746    AAUAGUCAAACAAAUUAGCAAUGGAGCCACCAAGAGAGUACAUUUACCUCUGAUUCAGAGAUGUCUGAGUUUAUCAGUUUU-CUGCCAAUCAUUAAA-CAACAAAGAUGAAACAUGCAAUUAUAUACAAGGAGACAGAAC-UCCUAAUUCUUUCAUUCUAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAGACUUUUAUUUU
ACBE01072604.1/90-294        AAUAGUCAAACAAAUUAGCAAUGGAGCCACCAAGAGAGUACAUUCAAC-CUGAUUCAAAGAUGUCUCAAUUUAUCAGUUUU-CUGUCAAUCAUUAAA-CAACAAAAAUGAAACAUGCAAUUAUACACAAGGAGAAAUAAC-UCCUAAUUCUUUCAUUCUAGCUGAAGCAGAAGAGUUUUAAUUGCUU--GGAAAAAUAAGAUUUUUAUUUU
AAWR02013862.1/6264-6465     AAUAGUCAAA-----UAGCAAUGGGGCUACCAAGAGAGUACAUUCAACCCUGGUUCAGUGAUGUCUCAGGUUAUCAGUUUU-CUGUCAAUCAUUAAAACAAGAAAGAUGAAACAUGCAAUUAUAUACAAGGAGAAAGAAC-UCCUAAUUCUUUCAUCUUAGCUGAAGAAGAAGAGUUUUAACUGCUU--GGAAAAAUAAGAUUUUUGUUUU
ABRN01434825.1/4865-5066     ACUAGUCAAACAGAUUAGCAAUGGGACCACCAAGAGAGUACAUUCAACCCCAAUUCAGAGAUGUCUCAGUUUAUCUGUUUU-CUGUCAAUCAUUAA-----GAAAGAUGAAAUAUACAAUUAUGUGCAAGGAGACAGAAC-UCCUAAUUCUUUCAUCCUAGCUGAAGCAAAAGAAUUUUAAUUGCUU--AAAAAAAUUAGAUUUUUGUUUC
AAIY01400228.1/2400-2606     AAUAGUCAAACAAAUUAAUGAUGGGGCCACCUCAAGAGUAGAUUCA-CCCCAAUUCAGAGAUGUCUCAGUUGAUCAGUUUU-CUGUCAAUCAGGAGAACAGGAAAAAUGAAAUAUGCAAUUAUAGUUGGGGAGGCAGUACCUCUUCAUUCUUUCAUCCCAGCUGAAGCAGAAGAGUCUUAAUUGCUU--GGAAAAAUAAGAUUUUUGUUUC
AAFC03001286.1/40876-41081   AAUAGUCAAACAAAUUAGCAAUGGGGCCACUAAGA--GCACAUUCAACCCUGAUUCAGAGAUGUUUCAGUUUAUCUGUUCU-CUGUCAAUCAUUAAA-CAAGAAAGAUGAAAUAUACAGUUAUGUACAAGGAGACAGAAC-UCCUAAUUCUUUCAUCCUAGUUGAAGCAAAAGAAUUAUAAUUGCUUGAAAAAAAAUAAGACUUUUGUUUC
ABRR01115815.1/1815-2012     AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAAAGUACAUUCAACACUGAUUCAGAGAUAUCUCAGCUUAUCUGUUUU-CUAUCAGUUAUGGAA-CAAGAAAGAUGAAAUAUGCAAUUAUAUACAAGGAAACAUAAC-UCCUAAUUCUUUCAUUCUAGAUGAAACAAGAG--------UUGCUU--AAAAAAAUAAGACCUUUGUUUU
AC122240.4/64364-64570       AAUAGUCAAACAAAUUAGCAAUGGGGCCACCAAGAGAGUACAUUCAACCCUAAUAAGGAGAUGUCUCAGUUUAUCAGUUUU-CUGUCAAUCAUUAAAACAAGAAAAAUGAAACUUGCAAUUAUAUACAAGGAGACAUAAC-UCCUAAUUCCUUCUUCCUACCUGAAGCAGAAGAAUUUUAAUUGCUU--GGAAAAAUAUGAUUUUUCUUUU
AAPE02008847.1/118645-118851 AAUAGUCAAACAAAUUAGCAGUGGGGGCACCAAGAGAGCACAUCCAUCCCUGAUUCAGAGAUGUCUUCGUUUAUCAGUUUU-CUGUCAAUCAGUAAAACAAGAAAGAUGAAACAUGCAAUUAUAUACAAGGAGACAGGAC-UCCUAAUUCUUUCACCCGAGCUGAAGCAGAAGAGUUUUAAUUGCUU--UGAAAAAUGAGAUUUUUGUUUU
AAQR03012796.1/7005-7205     AACAGUCAAACAAAUUAGCAAUGAGGCCACCAAGAGAGUACAUUCAACCCUGAUUCAGAGAUAUCUCAGUUUAUCAGUUUUUCUGUCAAUCAUUAAAAUAAGAAAGAUGAAACAUCCAAUUAUACACAAGGAGACAGAAU-UC-------UUUCAUCAUAGCCAAGACAGAAGAAUUUUAAUUGCUU--GGAAAAGUAAGACUUUUGUUUU
AAGW02035474.1/82077-82283   AAUAGUCAAACAAAUUAGCAAGGAGGCCACCAAGAGAGUAUAUUCAACCCUGAUUCAGAGAUGUCUUGGUUUAUCAGUUUU-CUGUCAAUCAUCAAAACAAGAAAAAUGAAACAUGCAAUUACAUACAAGGAGUCAGAAC-UCAUAAUUCUUUCAUCUCAGCUGAAGCAGAAGCAUUUUAAUUGCCU--GGAAAAAUGUGAUUUUUGUUUU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::..::::::::::::::::::::::
#=GC RF                      AAUAGUCAAACAAAUUAGcaAuGGGGCCACCAaGAGAGUAcAUUCAaCcCugAUucaGAGAUGUCUcaGuUUAUCaGUUUU.CUGUCAAUCAuuAAAaCAAGAAAgAUGAAAcaUGCAAUUAuAuaCAAGGAGaCAgaAC.UCcuaAUUCUUUCAUCcuaGcUGAAGCAGAAGAgUuUUAAUUGCUU..gGAAAAAUaaGAuUUUUgUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF01889
#=GF ID   lincRNA-p21_1
#=GF DE   LincRNA-p21 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   75.00
#=GF TC   79.60
#=GF NC   33.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.61 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0042981; regulation of apoptotic process;
#=GF RN   [1]
#=GF RM   20673990
#=GF RT   A large intergenic noncoding RNA induced by p53 mediates global gene
#=GF RT   repression in the p53 response.
#=GF RA   Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D,
#=GF RA   Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks
#=GF RA   T, Rinn JL
#=GF RL   Cell. 2010;142:409-419.
#=GF CC   LincRNA-p21 is an large intergenic non-coding RNA. Transcription of
#=GF CC   lincRNA-p21 is induced by p53. It interacts with heterogeneous nuclear
#=GF CC   riboprotein K (hnRNP-K) and has an important role in the p53-dependent
#=GF CC   apoptotic responses to DNA damage [1].
#=GF WK   Long_non-coding_RNA
#=GF SQ   2


AC167363.3/78060-78233   AACUUAAGCAAACCUGCAGACUGGUAAGCAAACACACACACUUCAGUUGACCCGGGCAAGGUUCUAGUAGGAAGUACUAUGUGAUUUUUUUUUUUUUUUCACACUCAGAACAUAAGUGUCAAUGCUCUCGCUAUGAAGAGGAGUCACAGGAUUGGCUGGGGUGGUGAAAGCGAA
AAHX01099811.1/1225-1058 CGCUUAAACAAACCUGCAGACUGGUAAGCAAACACACGUACUUCAGCUGACCCGGGCAAGGUUCUAGUAGGAAGUAUUGUGUGAUUAUUUUUUU---UUCACACUCAGAACGUAAGUGCCAAGGCUCUCACUAUGAAGAGGAGUCACAGGAUUGGCUGGGGUGACUGGGGU---
#=GC SS_cons             ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  agCUUAAgCAAACCUGCAGACUGGUAAGCAAACACACguACUUCAGuUGACCCGGGCAAGGUUCUAGUAGGAAGUAuUgUGUGAUUuUUUUUUUuuuUUCACACUCAGAACgUAAGUGuCAAgGCUCUCgCUAUGAAGAGGAGUCACAGGAUUGGCUGGGGUGguggggGuGaa
//
# STOCKHOLM 1.0

#=GF AC   RF01890
#=GF ID   lincRNA-p21_2
#=GF DE   LincRNA-p21 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   70.00
#=GF TC   73.90
#=GF NC   65.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.30 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0042981; regulation of apoptotic process;
#=GF RN   [1]
#=GF RM   20673990
#=GF RT   A large intergenic noncoding RNA induced by p53 mediates global gene
#=GF RT   repression in the p53 response.
#=GF RA   Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D,
#=GF RA   Khalil AM, Zuk O, Amit I, Rabani M, Attardi LD, Regev A, Lander ES, Jacks
#=GF RA   T, Rinn JL
#=GF RL   Cell. 2010;142:409-419.
#=GF CC   LincRNA-p21 is an large intergenic non-coding RNA. Transcription of
#=GF CC   lincRNA-p21 is induced by p53. It interacts with heterogeneous nuclear
#=GF CC   riboprotein K (hnRNP-K) and has an important role in the p53-dependent
#=GF CC   apoptotic responses to DNA damage [1].
#=GF WK   Long_non-coding_RNA
#=GF SQ   2


AC167363.3/76459-76510     GUGGAGCUGUGGUUAGUUCCUUUGUGUGGCUUAACUGUUGGCCCAGUUUUCC
AABR05094644.1/38118-38169 GUGAAGCUGUGGUUCGUUCCUUUGUGUGGCUUAACUGUUGGCCCAGUUUUCC
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GUGgAGCUGUGGUUaGUUCCUUUGUGUGGCUUAACUGUUGGCCCAGUUUUCC
//
# STOCKHOLM 1.0

#=GF AC   RF01891
#=GF ID   TUG1_3
#=GF DE   Taurine upregulated gene 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   90.00
#=GF TC   90.40
#=GF NC   65.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.91 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0042478; regulation of eye photoreceptor cell development;
#=GF RN   [1]
#=GF RM   15797018
#=GF RT   The noncoding RNA taurine upregulated gene 1 is required for
#=GF RT   differentiation of the murine retina.
#=GF RA   Young TL, Matsuda T, Cepko CL
#=GF RL   Curr Biol. 2005;15:501-512.
#=GF CC   TUG1 (taurine upregulated gene 1) is a long non-coding RNA expressed in
#=GF CC   retina and brain. It was first identified in a screen for genes
#=GF CC   upregulated by in developing retinal cells in response to taurine. It is
#=GF CC   required for the normal development of photoreceptors in the retina [1].
#=GF WK   TUG1
#=GF SQ   24


AADD01174110.1/3063-3299     CUGUGC--CUCCU--GAUUGCUGAGUGUUCA----CCUGGACCUUCUGACUACCUUCC-CUGUGCUAUU--CCAUCAGCCUACAGAC-CUGGUACCUGGAUUUUUGCCCGAGAU-GAUUC---CUAC-CACCUUACUACUGACGAAGACACCCAUUCCAGUGG-ACCACUGUGACCCAGGAGGC--AUUCAGCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUGUCUUGUUCUACCCAGAUUCAGCACAGCCCUUUA
AAWR02038334.1/138536-138302 CUGUGC--CUCCU--GAUUGCUGAGUGUUCA----CCUGGAUCUUCUGACCACCUUCC-UUGUGCUCUU--CCGUCAGCCUACAGAU-GUGGUACCUGGAUUUUUGCCCAUGGU-GAUUG---CUAC-CACCUUACUACUGAAGAAGACAUCAUU-CCAGUGG-AC-ACUGUGACCCAAGAGGC--AUUCAGCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUGUCCUGUUCUACCCAGAUUCAGCACAGCCCUUUA
ABRT010072613.1/1017-1254    CUGUGC--CUCCU--GAUUGCUGAGUCUUCA----CCUGGACCUUCUGACUACCUUCC-UUGUGCUAUAUUCCAUCAGCCUACAGAU-CUGGUACCUGGAUUUUUACCCAUGGU-GAUUC---CUGC-CACCUUACUACUGAAGAAGACACCAUU-CCAGUGG-ACCACUGUGACCUAAGAGGC--AUUCAGCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUGUCCUGUUCUACCCAGAUUCAGCACAGCUCUAUA
ABRN01372171.1/8717-8951     CUGUGC--CUCCU--GGUUGCCGAGUGUUCA----CCUGGACCGUCUGACCACCUU----UGUGCUAUU--CCAUCAGCCUACAGAU-CUGGUACCUGGAUUUUUGCCCAUGGU-GAU--U--CUAC-CACCUUACUACUGAAGAAGACAUCAUU-CCAGUGG-ACCACUGUGACCCAGGAGGC--AUCCAGCAAAUCAUCAUGAUGUGGCCUUCACCUC-ACUCCUGUCCUGUUCUACCGAGAUUCAACACAGCCCUUUG
AANG01587864.1/631-865       CUGUGC--CUCCU--GAUGGCUGAGUGUUCA----CCUGGACCUUCUGACCACCUUCC-UUGUACUGUU--CCAUCAGCCUAUAGAU-CUGGUACCUGGAUUUUUGCCCAUGGU-GAUUC---CU-U-CACCUUACUGCUGAAGAAGACACCAUU-CCAGUGG-ACCAUGGUGAUCCAAGAGGC--AUUCAACCA-UC---AUGAUGUGGCCUUCAUCUCCACUCCUGUCCUGUUCUACCCAGAUUCAGCACAGCCCUUUA
AAQQ01619695.1/422-656       CUGUGC--CUCCU--GAUUGCUGAGUGUUCA----CCUGGACCUUCUGACCACCUUCC-UUCUGCUAGA--CCAUCAGCCUACAGAC-CUGGUACCUGGAUUUUUGCUCAUGGU-GAUUC---CUGC-CACUUUACUACUGAAGAAGGCAUCAUU-CCAGUGG-AC-ACUGUGACCCAAGAGGC--AUUCAUCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUUUCCUGUUGUACCCAGAGUCAGCACAGCCCUUUA
AAFC03000995.1/50051-50289   CUGUGC--CUCCU--GGUUGCCGAGUGUUCA----UCUGGAUCUUCUGAUCACCUU----UGUGCUAUU--CCAUCAGCCUACAGAU-CUGGUACCUGGAUUUUUGCCCAUGGU-GAUGGAUUCUGC-CACCUCAGUGCUGAAGAAGACAUCAUU-CCAGUGG-ACCACUGUGAUCUAGGAGGCGUAUCCAGCGAAUC---AUGAUGUGGCCUUCACCUCCACUCCUGUCCUGUUCUACCCAGAUUCAACACAGCCUUUUG
AALT01486602.1/1525-1295     CUGUGC--CUCCU--GAUUGCUGAGUGUUCA----CCUGGAUCAUCUGACUACCUUCC-UUGUGCUGUU--CCAUCAGCCUACAGUU-CUGGUACCUGGACUUUUGCCCGUGGU-GACUA---CUAC-CACCUUACUACUGAAGAAGACAUCUUU-CCAGUGG-ACCACUGUGAACCAAGAGGC--AUUCAGCCA-UC---GUGAUGUGGCCUUCAUCUCCACUCC-----UGUCCUACCCAGAUUGAGCACAGCCCUUUA
ABVD01060064.1/402-636       CUAUGA--CUCCU--GAUUGCUAAGUGUUCA----CCUGGACCUUCUGACCACCUUCC-UUCUGCUAUU--CCAUCACU--ACAGAU-CUGGUACCUGGAUUUUUGCCCAUGUUUGAGUC---CUAC-UACCUUACUACUGAAGAAGACACCAUU-CCUGUGG-ACCACUGUGACCCAAGAGGC--AUUCAGCCA-UG---AUGAUGUGGCCUUCACCUCCACUCUUUUCCUGUUCUACCCAGAUUCAACACAACCCCUUA
AAPY01652640.1/3064-3302     UUGUGCUCUUCCU--GAUGAUUGAGUGUUCA----CCUGGAUUUUCUGACCACCUUCCCUUGUGCUAUU--CUGUCAGCCUACAGAUUCUGGUACCUGGAUUUUUACCCUUGGU-GAUUU---CUAC-CACCUUACUACUGAAGAAGACACCAUU-CCAGUGG-ACCACUGUGACCUAAGAAGC--AUUCAGCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUGUCCU-UUCUACCCAGAUUCAGCACAGUCUUUUA
DQ517435.1/583-818           CCGUGC--CUCCU--GAUUGCUGAAUGUUCA----CCUGGACCUGCCAAUGACCUUCC-UUCUGCUACU--CCAUCAGCCUACAGAC-CUGGUACUUGGAUUUUUGUCCAUGGU-GAUUC---CUUC-CACCUUACUACUGAAGAAGACACCAUU-CCAGUGG-ACCACUGUGACCCAAGAAGC--AUUCAGCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUGUCCUACUCUGCCCAGAUUCAGCACAGCCCUUUA
ABRO01110160.1/5413-5647     CUGUAC--CUCCU--GAUUGCUGAAUGUGCA----CUUGGACCUUCUGAUGACCUGCC-UUCUGCUAUU--CCAUCAGCCUGUAGAC-CUGGUGUCUGGAUUUUUGCCCAGGAU-GAUUC---CUAC-CACCUUACUACUGAAGAAGACACCAUU-CCAGUGG-ACCACUGUGACCCAAAAGGC--AUUCAGCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUGUCCU-UACUACCCAGAUUCAGCACAGCCCUUUA
ABRP01135829.1/9720-9955     CUGUGC--CUCCU--GAUUGCUGAGUGUUCA----CCUGGACCUUCCAACUACCUUCC-UUGUGCUGUC--CCAUCAGCCUACAGAU-CUGGUACCUGGAUUUUUGCCCAUGGU-GAUUC---CUAU-CACUUAACUACUGAAGAAGACACCAUU-CCAGUGG-ACCACUGUGACUCAAGAGGC--AUUCAGCCA-UC---AUAUCUUGGCCUUCACCUCUAUUCUUGUCCUUUUCUACACAGAAUGAGCACCACCCUUUA
AAKN02007240.1/5089-4859     CUGUGC--UUCCU--GAUUGCUGAGUGUUCA----CCUGGACCUUCUGACCACCUU-----CUGCUGGC--CCAUCAUCCUACACGU-CUGGUACUUGGAUUUUUGCCCAUGGU-GAUUU---GUAU-CAACCUACUACUGAAGAAGACAUCAUU-CCAGUGG-ACCACUGUGA-UCAAGAGAC--UUUCAGCCA-UG---ACAGUGUGACCUUGACCUGUACUCCAGUUGUGGUCUGCCCAGAUUCAGCACAGCCCUUGG
AAYZ01038147.1/4648-4884     AUGUGC--CUCCUCUGAUUGCUGAGUGUUCA----CGUGGACCUUCUGAUCACCUUCC-UUGUGCUGUU--CCAUUGGCCUACAAAU-CUGGUAC-UGGAUUUUUACCCAUGGU-GAUUU---CUAC-CACCUUACUACUGAUGAAGACACCAUU-CCAGCGG-ACCACUGUGAUCCAAGAGGC--AUUCAGCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUGUCUUGUUCUACACAGAUUCAGCACAGCCUUUUA
AAIY01381730.1/839-604       CUGUGC--CACCUGUGAUUGCU--GUGCUCA----CCUGAACCUUCUGACCACCUUCU-UGGUACUGGU--CCAUCAGUCUCCAGAA-CUGGUACCUGGGUUUUUGCCCAUGGU-GAUUCUC-CUAC-CACCUUACUACUGAAGAAGGCAUGAUU-CGAAUGGGACCAUUGUGACCCAAGACGC--AUUCAGCUA-UC---AC---GUGGCCUUUACUUCCACUCCUGUCCAGCUCUGCCCAGAUUCAACACAACUCUUUA
BC037986.1/729-965           CUGUGC--CUCCU--GAUUGCUGAGUGUUCA----CCUGGACCUUCUGACUACCUUCC-CUGUGCUAUU--CCAUCAGCCUACAGAC-CUGGUACCUGGAUUUUUGCCCGAGAU-GAUUC---CUAC-CACCUUACUACUGACGAAGACACCCAUUCCAGUGG-ACCACUGUGACCCAGGAGGC--AUUCAGCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUGUCUUGUUCUACCCAGAUUCAGCACAGCCCUUUA
DQ517434.1/984-1219          CCGUGC--CUCCU--GAUUGCUGAAUGUUCA----CCUGGACCUGCCAAUGACCUUCC-UUCUGCUACU--CCAUCAGCCUACAGAC-CUGGUACUUGGAUUUUUGUCCAUGGU-GAUUC---CUUC-CACCUUACUACUGAAGAAGACACCAUU-CCAGUGG-ACCACUGUGACCCAAGAAGC--AUUCAGCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUGUCCUACUCUGCCCAGAUUCAGCACAGCCCUUUA
AAGU03075131.1/59038-58802   CUGUGC--CUCCU--GAUGGCU--GUGUUCA----CCUGGACCUUCUGACCACCUUCC-UUGUACUGUU--CCAUCAGUCUGCAGAA-CUGGUACCUGGAUUUUUGCCGAUGGU-GAUUCUC-CUCCUCACCUUACUACUGAAGAAGGCACUAUU-CCAGUGG-ACCACUGUGACCCAAGAGGC--AUUCAGCCA-UG---AUGAUGUGGCCUUUACCUCCACUCCUGUCUUCUUCUACCCAGAUUCAUCACAGCCUGUUA
AAGW02067666.1/34121-34356   CUGUGC--CUCCU--GAUUGCUGAGUGUUCA----CGUGGACCUUCUGAUCACCUUCC-UCGUGCUGUU--CCAUCGGCCCACAGAU-CUGGUACCUGGAUUCUUGCCCAUAGU-GAUUU---CUAC-CACCUUACUACUGAUGAAGACACCAUU-CCAGUGG-ACCACUGUGAUCCAGGAGGC--GUGCAGCCA-UC---GUGAUGUGGCCUUUACCUCCACUCCUGUCCUGUUCUACCCAGAUUCAGCACAGCCUUUUA
AAPE02050782.1/21719-21495   --UUAU-----CU----UACCUGUUUUGUC-----CCUGGACUUUCUGACCAUCUUCC-UUGUGUU-----CACUCAGCCUACAGAU-UUGGUACCUGGAUUUCUGUCCAUGGU-GAUUU---CUGU-CACCUUACUACUGAAGAAGAUACCAUU-CCAGUGG-ACCACUGUGACCCAAGGGAC--AUUCAACCA-UC---AUGAUGUGGUCUUCACCUCCAUUCCUGUCCUCCUCUACCCAGAUUGAGCACCAUCCUUUA
AAQR03184908.1/26196-26421   CUGUGC--CUCCU--GAUUGCUGAGUGUUCA----CCUGGACCUUCUGACUACCUU-----GUACUAUU--CCAUCAGGAUACAGAU-CUGAUAUCUGGAUUUUUGCCCAUGGU-GAUUC---CAAC-CACCUUACUACUGAUGAAGACACCAUU-CCAGUGA-ACCACUGUGACCCAAGAGAC--AUUUAGCCA-UU---AUGAUGUGGCCUUUACCUCCACUGCUGUCCUGUUCUACC------CAGCACAGCCCUUUA
BC089106.1/426-662           --GUGC--CUCCU--GAUUGCUGAAUGUUCAUUCACCUGGACCGUCCAAUGACCUUCC-UUCUGCUACU--CCAUCAGCCUACAGAC-CUGGUACUUGGAUUUUUGUCCAUGGU-GAUUC---CUAC-CACCUUACUACUGAAGAAGACACCAUU-CCAGUGG-ACCACUGUGACCCAAGAAGC--AUUCAGCCA-UC---AUGAUGUGGCCUUUACCUCCACUCCUGUC-UACUCUGCCCAGAUUCAGCACAGCCCUUUA
AAEX03014798.1/257823-258052 CUGUGC--CUCCU--GAUUGCUGAGUAUUCA----UCUGGACCUUCUGACCACCUUCC-UUGUACUAUU--CCAUCAGCCUACAGAU-CUGGUACCUGGAUUUUUGCCCUUGGU-GAUUC---CU-U-CACCUUACUGCUGAAGAAGACACCAUU-CCAGUGG-ACCACUGUGAUCCAGGAGGC--AUUCAACCA-UC---AUGAUGUGGCCUUCACCUCCACUCC-----UGUUCCACUCAGAUUCAGAACAGCCCUUUA
#=GC SS_cons                 ::::::..:::::..::::::::::::::::....:::::::::::::::::::::::.::::::::::..::::::::::::::::.::::::::::::::::::::::::::.:::::...::::.:::::::::::::::::::::::::::.:::::::.::::::::::::::::::::..:::::::::.::...::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      CUGUGC..CUCCU..GAUuGCUGAGUGuUCA....CcUGGAcCuUCUGAccACCUUCC.UugUGCUguu..CCaUCAGcCUaCAGau.CUGGUACcUGGAUUUUUGCCCaUGGU.GAUUc...CUac.CACCUUACUACUGAaGAAGaCAcCaUU.CCAGUGG.ACCACUGUGAcCCAaGAgGC..aUuCAGCcA.Uc...AUGaUGUGGCCUUuACCUCCACUCCUGUCcUguUCUaCCCAGAUUcAgCACaGCCcUUUa
//
# STOCKHOLM 1.0

#=GF AC   RF01892
#=GF ID   TUG1_4
#=GF DE   Taurine upregulated gene 1 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   100.00
#=GF TC   118.40
#=GF NC   76.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.75 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0042478; regulation of eye photoreceptor cell development;
#=GF RN   [1]
#=GF RM   15797018
#=GF RT   The noncoding RNA taurine upregulated gene 1 is required for
#=GF RT   differentiation of the murine retina.
#=GF RA   Young TL, Matsuda T, Cepko CL
#=GF RL   Curr Biol. 2005;15:501-512.
#=GF CC   TUG1 (taurine upregulated gene 1) is a long non-coding RNA expressed in
#=GF CC   retina and brain. It was first identified in a screen for genes
#=GF CC   upregulated by in developing retinal cells in response to taurine. It is
#=GF CC   required for the normal development of photoreceptors in the retina [1].
#=GF WK   TUG1
#=GF SQ   25


AADD01174110.1/3623-3803     UGGGAUCAAAUCAAAGGCACAGUGAACUCCUCAUAGCAUCUUCUUUGGAAUUACUCAGGAACCAGAACU---UUUUACACAAAU-GUAAGAAAUUCUACCAAGGAGUCCCCUU-ACCUAACAGCAUCUCACAAGGCUGCA-CCAGAUUCCAGAAAAGGC--UUCUCUUGAUAC-AUCA---AGGUAGAACCUC
AAWR02038334.1/137977-137800 UGGGAUUAAAACG--GGCACAAUGAACUCCUCAUAGCAUCUUCUUUGGGAUUACUCAGGAACCAGAACU---UUUCACACAAAU-GUAAGAAAUUCUACCAAGGAAUCCCUUU-GCCUAACAGCAUCUCACACAGCUCCAAUCAGAUGCCAGAAAAGGC--CUC--UUGAUAC-AUCC---AGGUAGAACCUA
ABRT010072613.1/1567-1744    UGGGAUCAAAUCAAAGGCACAGUGAACUCCUCAUAUCAUCUUCUUUGGGAUCACUCAGGAACCAGAAC-----CUCACACGAAU-GUAAGAAAUUCUACCAAGGAGUCCCUUU-ACCUAACAGCGUCUCACAAGACUCCAGUCAGAUUCCAGAAAAGAC--UUC--UUAAUAC-AUCA---AGGUAGAACCUC
ABRN01372171.1/9261-9437     UGGGAUUAAAACAAAGGCACAGUGAA---CUCACAGCAUCUUCUUUGGGAUUACUCAGGAACCAGAACU---UUUCACACAAAU-GUAAGAAAUUCUACCAAGGAAUCCCUUU-ACCUAACAGCAUCUCACAAAGCUCCAAUCAGAUUCCAGAAAAGGC--CUC--UUGAUAC-AUCC---AGGUAGAACCUA
AANG01587864.1/1193-1364     UGGAAUUAAAACAAAGGCACAGUGAA---CUCA--GCAUCU---UUGGGAUUACUCAGGAACCAGAACU---UUUCACACAAAU-GUAAGAAAUUCUACCAAGGAAUCCCUUU-AUCUAACAGCAUCUCACAAAGCUCCAAUCAGAUUCCAGAAAAGGC--CUC--UUGAUAC-AUCC---AGGUAGAACCUA
AAQQ01619695.1/992-1169      UGGGAUCAAAA-GAAGGCACAGUGAAUUCCUUAUAGCAUCUUCUUUGGGAUUACUCAGGAACCAGAACU---CUUCACA-AAAC-AUAAGAAAUUCUACUAAGGAAUCCCUUU-ACCUAAUGGCAUCUCACAAGACUACAGUCAGACUCAAGAGAAGGC--CUC--UUGAUAC-AUCA---AGAUAGCACCUA
AAFC03000995.1/50601-50777   UGGGAUCAAAACAAAGGCACAGUGAA---CUCACAGCAUCUUCUUUGGGAUUACUCAGGAACCAGAACU---UUUCACACAAAU-GUAAGAAAUUCUACCAAGGAAUCCCUUU-ACCUAACAGCAUCUCAUAAAGCUCCAAUCAGAUUCCAGAAAAGGC--CUC--UUGAUAC-AUCC---AGGUAGAACCUA
AALT01486602.1/978-800       UGGGAUUGAGACAAUGACACAGUGAACUCCUCAUAGCAUCUUCUUUGGGAUUACUCAGGAACCAGAACU---UUUCACACAAAU--UAAGAAAUUCUACCAAGGAAUCCCUUA-AUCUAACAGCAUCUCACAAAGCUCCAAUCAGAUUCCCGAAAAGGC--UUC--UUGACAA-AUCC---AGGUAGAACCUG
ABVD01060064.1/935-1114      UGGGAGCAAAACAAAGACAUAGUGAACUCUUCAUAGCAUCUUCUUUGGGAUUACUCAGGAACCAGAACU---UUUCAAACAAAU-GUGAGAAAUUCUACCAAGGAAUUCCUUU-ACCUAACAGCAUCUCACAAAGCUCCAGUCAGAUUCCAGAAAAGGC--UUC--UUGAUAC-AUCA---AGGUAGAAACUG
AAPY01652640.1/3609-3789     UGGGAUCAAAACAAAGGCACAGUGAAUUCCUCAUAGCAUCUUCUUUGGGAUUACUCAGGAACCAGAACU---UGUCACACAAAU-GUAAGAAAUUCUGCCAAGGAAUUCUGUU-ACUUAAGAGCAUCUCACAAGGCUCCAAUCAGAUCCCAGAAAAGGC--UUC--UUGAUACCAUCA---AGGUAGAACCUA
DQ517435.1/1152-1328         UGGGAUCAAAACCAAGGCAUUUUGAAUUCCUCAUAGUAUCAUCUUCGGG-UUACUCAGGAACCAAAACU---UUUCACACCAAU-UUAAGAAAUUCUACUGAGGAAUCCCUUU-ACCUAAC--CAUCUCACAAGGCUUCAACCAGAUUCCUGAAAAGGC--CUC--UUGAUAU-AUCA---AGAUAGAACCUA
ABRO01110160.1/5960-6129     UGGGAUCAAAACAAAGACACAGUGAACUCCUAGC---AUCAUCUUUGGGAUUACUCAGGAACCAGAACG---UUUCAUACAAAU-AUAAGAAAUUCUACCAAGGAAUCCCUUA-ACCUAACAGCAUUUCACAAGGCUCCAGUCAGA-------AAAGGC--UAC--UUGAUAC-AUCA---AGAUAGACCCUA
ABRP01135829.1/10240-10416   -CGGAUUAAAACAAAGGCACAGCAAAGUCCUCGUAGCAUCUU--UAGGGAUUACGCGAGGACCAGAACU---UUUAACACAAAU-GUAAGAAAUUUUACCAAGGAAUCCCUUU-ACUUAACAGCAUCUCAUAAAGCUCCAAUCAGGUUCCAGAAAAGGC--CUC--UUAAGAC-AUCC---AGGUAGAACCUA
AAKN02007240.1/4553-4374     UGGGAUCAAAACCAAGGCACAGUGAAUUCUUCAUAGCAUCUUCUUUGGGAUUACUCAGGAACCAGAACU---UUUCACAUAAAU-GUAAGCAGUUCUGCCAAGGAAUCCCUUU-AUCUAACAGGAUCUCACAAGGCUCCAGUCAGAUUCCAGAAAAGGC--CUC--UUUAUAC-AUCG---AGAUAAAACCUA
AAYZ01038147.1/5212-5394     UGGGAUCAAAACAAAGGCACAGUGAA--CUUGAC---ACCCUCUUCAGGAUUACUCAGGAACCAGAACUGAUUUUCACACAAAUUAUAAGAAAUUCUACCAAGGAAUCCCUUUUGCCAGACAGCAUUUCACAAGCCUCCAAUCAGAUUCCAGAAAAGAC--CUC--UUGAUAC-AUCAUCAAGGUGAAACCUA
AAIY01381730.1/297-122       UGGGAUCAAAACAAAGAUACAG--AACUUUUCAUAGCAUCUUCUAUGGGAUUACUCAGGAACCAGAGUU---U-UCACACAAAU-GUAAGAAAUUCUACCAAGGAAUCCCUUU-AUGUAACAACAUCUCACAGAGCUCCAAUCAGAUCC-AGAAAAGAC--CUC--UUGAUCU-AUCA---AGGUAGAAUCUA
AK000749.1/1033-1213         UGGGAUCAAAUCAAAGGCACAGUGAACUCCUCAUAGCAUCUUCUUUGGAAUUACUCAGGAACCAGAACU---UUUUACACAAAU-GUAAGAAAUUCUACCAAGGAGUCCCCUU-ACCUAACAGCAUCUCACAAGGCUGCA-CCAGAUUCCAGAAAAGGC--UUCUCUUGAUAC-AUCA---AGGUAGAACCUC
DQ517434.1/1553-1729         UGGGAUCAAAACCAAGGCAUUUUGAAUUCCUCAUAGUAUCAUCUUCGGG-UUACUCAGGAACCAAAACU---UUUCACACCAAU-UUAAGAAAUUCUACUGAGGAAUCCCUUU-ACCUAAC--CAUCUCACAAGGCUUCAACCAGAUUCCUGAAAAGGC--CUC--UUGAUAU-AUCA---AGAUAGAACCUA
BC037986.1/1289-1469         UGGGAUCAAAUCAAAGGCACAGUGAACUCCUCAUAGCAUCUUCUUUGGAAUUACUCAGGAACCAGAACU---UUUUACACAAAU-GUAAGAAAUUCUACCAAGGAGUCCCCUU-ACCUAACAGCAUCUCACAAGGCUGCA-CCAGAUUCCAGAAAAGGCUUCUC--UUGAUAC-AUCA---AGCAUUUUGUGA
AAGU03075131.1/58493-58316   UGGGAUCAAAACAAAGACGCAGUGAACUUUUC-UCGCAUCUUAUAUGGGAUUACUCAGGAAUCAGAACUUAACCACA--CAAAU-AUAAGAGAUUCUACCAAGG-AACCCUUUUACAUAACAGCAUCUCACAAAGCUCCAAUCAGAUCC-AGAAGGG-C--CUC--UUGAUAC-AUCA---AGGUAGAACCUA
AAGW02067666.1/34696-34875   UGGGAUCAAAACAGAGGCACAGUGAACUCCUCAUAGCAUCUUCUUUGGGAUUACUCAGGAACCAGAACU---UUUCACACAAAU-AUAAGAAAUUCUGCCAAGGAAUCCCUUU-ACCAAACAGCAUCUCACAAGGCUCCAAUCAGAUUCCAGAAAAGGC--CUC--UUGAUAC-AUCA---AGGUAGAACAUA
AABR05180830.1/7854-8030     UGGGAUUGAAACCAAGGCAUACUGAAUUCCUCAUAGUAUCAUCUGUGGG-UUACUCAGGAACCAAAACU---UUUAACACCAAU-UUAAGAAAUUCUACUGAGGAAUCCCUUU-AUCUAAC--CAUCUCACAAGGCUUCAACCAGAUUCCUGAAAAGAC--CUC--UUGAUAU-AUCA---AGAUAGAACUUA
AAPE02050782.1/21178-21006   UGGGAUUAAAACAAAGGCCUAGUGAAGUCCUCAUAGCAUCU---UUGGGAUUAUUCAGGAACCAGAACU---UUUCACACAAAU-GUAAGGAAUUUUACAAAGGAAUCC-UUU-ACC---CAGCAUCUCACAAAGCUUCAAUCAGAUUCCAGAAAAGGC--CAC--UUGAGAC-AUCC---AGGUAGAACCUA
AAQR03184908.1/26737-26916   UGGGAUCAAAACAAAGGCACAGUGAACUCCUCAUUGCAUCUUCUUUGGGAUUACUCAGGAACCAGAACU---UUUCACACAAAU-GUAAGAAAUUCUACCAAGGAAUCCCUUU-ACCUAACAGCAUCUCAAAAGUCUCCAAUCAGAUGCCAGGAAAGGC--CUC--UUGAUAC-AUCA---AGGUAGAACCUU
AACN010693513.1/724-897      UGGGAUUAAAACAAAGGCACAGUGAA---CUCACAGCAUCU---UUGGGAUUACUCAGGAACCAGAACU---UUUCACACAAAU-GUAAGAAAUUCUACCAAGGAAUCCCUUU-ACCUAACAGCAUCUCACAAAGCUCCAAUCAGAUUCCAGAAAAGAC--CUC--UUGAUAU-AUCC---AGGUAGAACCUA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::...::::::::::::.::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::..:::..:::::::.::::...::::::::::::
#=GC RF                      UGGGAUcAAAaCaAAGGCacAGUGAAcUCcUcAuaGCAUCuUCUuuGGGAUUACUCAGGAACCAGAACU...UuUcACACaAAU.gUAAGaAAUUCUACcAAGGAaUCCCuUU.AccUAACAGCAUCUCACAaggCUcCAauCAGAUuCCaGAAAAGGC..cUC..UUGAuAc.AUCa...AGgUaGaacCUa
//
# STOCKHOLM 1.0

#=GF AC   RF01894
#=GF ID   PCA3_2
#=GF DE   Prostate cancer antigen RNA 3 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   100.00
#=GF TC   111.10
#=GF NC   63.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.44 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10606244
#=GF RT   DD3: a new prostate-specific gene, highly overexpressed in prostate
#=GF RT   cancer.
#=GF RA   Bussemakers MJ, van Bokhoven A, Verhaegh GW, Smit FP, Karthaus HF,
#=GF RA   Schalken JA, Debruyne FM, Ru N, Isaacs WB
#=GF RL   Cancer Res. 1999;59:5975-5979.
#=GF WK   PCA3
#=GF SQ   20


AL390239.16/366-774          UCUCUUUGACCCAUUAUUUCAGACUUAAAAA-CAAGCAUGUUUUCAAAUGGCACUAUGAGCUGCCAAUGAUGUAUCACCACCAUAUCUCAUUAUUCUCCAGUAAAUGUGAUAAUAAUGUCAUCUGUUAACAUAAAAAAA-G-UUUGACUUCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCAGCUACACACUGCUUGACAUAUAUUGUUAGAAGCACCUC--GCAUUUGUGGGUUCUCUUAAGCAAAAUACUUGCAUUAGG-UCUCAGCUGGGGCUGUGCAUCAGG-CGGUUUGAGA-AAUAUUCAAUUCUCAGCAGAAGCCAGAAUUUGAAUUCCCUCAUCUUUU-AGGAAUCAUUUACCAGGUUUGGAGA-------GGAUUCAGACAGC-UCAGGUG
ACBE01399883.1/2260-2668     UCUCUCUGACCCGUUAUUGCAGAUUUAAAAA-CAACCAUGUUUUCAAAUGGCACUACGAGCUGCCAAUGAUGUAUCACCAUCAUAUCUCAUUAUUCUCCACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAA-G-UUUGACUUCACAGAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCGGCUACACACUGCUUGACAUAUAUUGUUAGAAGCACCUC--GCAUUUGCGAGUUCUCUUAAGCAAAAUACUUGCAUUAGG-UCUCAGCUGGGGCUGUGCACCAGG-CAGUUGGGGA-AACAUUCAAUUCUCAGUGGAAGCCAGAAUUUGAAUUCUCUCAUCUUUU-AGGAAUCAUUUACUAGGUUUGGAGA-------GUAUCCAGGCAGC-UCAGGUG
ABRR01126459.1/2549-2140     UCUCUUUGACCCAUUAUUGCAGACUUAAAAA-CAAGCAUGUUUUCAAAUGGUGCCAUGAGCUGCCAAUGAUGUAUCACCAUCGUAUCUCAUUAUUCUCCACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAA-G-UUUGACUUCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCGGCUACACACUGCUUGACACAUACUGUUGGAAGCACCUC--GCAUUUGCAAGUUCUCUUAAGCAAAAUACUUGCAUUAGG-UCUCAGCUGGGGCUGUGCAUCAGG-CAGUUUGGAGGAAUAUUCAAUUCUCAGCGGAAGCCAGAAUUUGAAUCCUCUCAUCUUUU-AGAAAUCAUUUACUAGGUCUGAAGA-------GGAUUCAGGCAGC-UCAGGUG
ABRT010205933.1/1962-1555    CCUUUUUGACCCAGUAUUGCAGACUUAAAAA-CAAGCAUGUUUUCAAAUGGCGCUAUGAGCUGCCAAUGAUGUAUCACCAUCAUAUCUCAUUAUUCUUUGCUAAAUGUGAUAAUAAUGUGAUCCGCUAACAUAAAAAAA-G-UUUGACUUCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCAGCGACACACUGCUUGACACAUAUUGCGAGAAGCACCUC--GCAUUUGCGGGUUCUCUUAAGCAAAAUACUUGCAUUAGG-UCCCAGCUGGG-CUGUGCAUCAGG-CAGUUUGGGA-AAUAUUCAAUUCUCAGCGGAAGCCAGAAUUUGAAUUCUCUCAUCUUUU-AGGAAUCAUUUACCAGGUUUGAAGA-------GGCUUAAGGCAUC-UCAGGUG
ABVD01093143.1/1434-1024     UCUCUCUGACCCAUUAUUGCAGACUUAAAAA-CUAGCAUGUUUUCAAAUGGUGCUAUGAGCUGCCAGUGACGUAUCACCACCAUAUCUCAUUAUUCUCCACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAAAG-UUUGACUCCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUGACUCCUACCAUCGGCUACACACUGCUUGACACAUAUUGUUAGAAGCACCUC--GCAUUUGCGAGUUCUCUUAAGCAAAAUACUUGCAUUAGGGUCUCAGCUGGGGCCGUGCAUCAGG-CAGUAUGGGG-AAUAUUCACUUCUCAGCAGAAGCCAGAAUUUGAAUUCUCCCAUCUUUU-AGGAAUCAUUUACCAGGUUUGGAGA-------GGAUUCAGGCAGC-UCAGGUG
AAPY01551684.1/7379-6971     UCUCUUUGACCCAUUAUUGCAGACUUAAAAA-CAAGCAUGUUUUCAAAUGGCGCUCUGAGCCUCCAAUGAUGUAUCACCGCCAUAUCUCAUUAUUCUCCACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAA-G-UUUGGCUUCACAAAAGCAGCUGGAAACGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCGGCUACACACUGCUUGACACAUAUUGUUAGAAGCACCUC--ACAUUUGCGGGUUCUCUUAAGCAAAAUACUUGCAUUAGA-UCUCAGCUGGGGCUGUGCAUCCGG-CGGUUUGGGA-AAUAUUCCGUUCUCAGCGGAAGCCGGAUUUUGAAUUUUCUCAUCUUUU-UGGAAUCAUUUACCAGGUUCAGAGA-------GGAUCCAGGCAGC-UCAGGUG
ABRQ01181306.1/5499-5091     UCUCUUUGACCCAUUAUUGCAGACUUAAAAA-CAAGCAUGUUUUCAAAUGGUGCUACGAGCUGCCAAUGAUGUAUCACCACCAUAUCUCAUUAUUCUCCCCUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAAAG-UUUGACUCCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCAGCUCCACACUGCUUGACACAUAUUGUUAGAAGCACCUC--GCAUUUGCGAGUUCUCUUAAGCAAAAUACUUGCAUUAGG-UCUCAGCUGGGGCUUUGCAUCAGG-CAGUUUGGGG-AAUAUUCGGUUCUCAGUGGCAGCCAGAAUUUGAAUUCUCUCAUCUUUU-AAGAAUCAUUUACCAGGUUUGGAGA-------GGAUUCAGGCA-C-UCAGGUA
ABRN01403962.1/1152-743      ACUCUUGGACCCAUUAUUGCAGACUUAAAAA-CAAGCAUGUUUUCAAAUGGCGCUACGAGCUGCCAAUGAUGUAUCACCACCGUAUCUCAUUAUUCUCCACUAAAUGUGUUAGUAAUGUGAUCUGUUAACAUAAAAAAA-G-UUUGACUUCACAAAAGCAGCUGGAAACGGACAACCAUAAUAUGCAUAAAUCUAACUCCUACCAUCGGCUACACACUGCUUGACACAUAUUGUUAGAAGCACCUC--GCAUCUGCAAGUUCUCUUAAGCAAAAUACUUGCAUUAGG-UCUCAGCUGGGGCUGUGCACCAGG-CAGUUCGGAGGAAUAUUCAAUUCUCAGCGGAAGCCAGAAUUUGAAUCCUCUCAUCUUUU-AGGAAUCAUUUACUAAGUUUGGAAA-------GAACUCAGGCAGC-ACAGGUG
AANN01773566.1/2971-3381     UCUCUUUGACCCAUUAUUGCAGACUUAAAAAACAAGCAUGUUUUCAAAUGGUGUUAUGAGCUGUCAAUGAUGUAUCACCAUCAUAUCUCAUUAUUCUUGACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAAAG-UUUGACUUCACAAAAGCAGCUGGAAAUGGACAAUCACAAUAUGCAUAAAUCUAACUUCUACCAUCGGCUACACACUGCUUGACACACAUUGUUAGAAGCACCUC--GCAUUUGCAAGUUCUCUUAAGCAAAAUACUUGCAUUAGG-UCUCAGCUGGGGCUGUGCAUCAGG-CAGUUUGGGG-ACUAUUCAGUUCUCAGUGGAAGCCAGAAUUUGAAUUCUUUCAUGUUUU-AAGAAUCAUUUACCAGGUCUGGAGU-------AGAUUCAGACAAC-UCAGGUG
AAFR03054099.1/3001-3408     UCUCUUUGACCCAUUAUUACAGACUUAAAAA-CAAGCAUGUUUUCAAAUGGCGCUAUGAGCUGCCAAUGAUGUAUCACUGCCAGAUCUCAUUAUUCUUCUCUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAAAG-UUUGGCUCCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCAGCUACACACUGCUUGACACAUAUUGUUAGAAGCACCUC--GCAUUUACGAGUUCUCUUAAGCAAAAUACUUGCAUUAGG-ACUCAGCUGGGGCUGUACAUCAGG-CAGUUUGGGG-AAUAUUCAAUUCUCAGUGGAAGCCAGAAUUUAUAUUCUCUCAUCUCUU-AGGAAACAUUUGCCAGGUUCUGAGA-------AAACACACGCAGU---AGGUG
AAYZ01083938.1/4806-5219     UCUCUUUGCCCCAUUAUUGGAGAUCUAAAAA-CAAGCAUGUUUUCAAAUGGCGCUCUGAGCUGCCAAUGAUGUAUCACCACCAUAUCUCAUUAUUCUCCACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUUAAAAA--G-UUUAACUUCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCGGCUACACACUGCUUGACACAUAUUGUAAGAAGCACCUC--GCAUUUGCGGCUCCUCUUAAGCAAAAUACUUGCAUUACG-UCUCAGCUGGGGCUAUGCAUCAGG-CAGCUUGGGG-AAUAUUCAGUUCUCAGCAGAAGCC-GAAUUUGAAUUCUUUCAUCUUGG-AGGACUCAUUUACCAGGUUUGGGGGUCGGGGGGGGUGUAGGCAAC-UCAGGUG
ABRP01067478.1/19985-19575   UCUCUUUGACCCAUUAUUGCACACUUAAAAAACAAGCAUGUUUUCAAAUGGCGCUAUGAGCUGCCAAUGAUGUAUCACCAUCAUAUCUCAUUAUUCUCCACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAAAG-UUUGACUUCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCGGCUACACACUGCUUGACACAUAUUGUUAGAAGCACCUCUCACAUUUGCGAGUUCUCUUA--CAAAAUACUUGCAUUAGG-UCUCAGCUGGGGCUGUGCAUCAGG-CAAUUUGGGGGAAUAUUCAAUUCUCAGCAGAAGCCAGAAUUUGAAUUCUCUCAUCUUUU-AAGAAUCAUUUAUCAGGUCCAGAGA-------GGAUGU-GGCAGC-UCAGGUG
AAIY01356133.1/5404-4998     UCUCUCUGACCCAUUAUUGCAGACUUAAAAA-CAAGCAUGUUUUCAAAUGGUGCUAUGAGUUGCCAAUGAUGUAUCACCACCGUAUCUCAUUAUUCUCUACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAA--G-UUUGACUCCACAAAAGCAGCUGGAAAUGGACAACCGCAAUAUGCAUAAAUCUAACUCCUACCAUCGGAUGCACACUGCUUGACACAUAUUGUCAGGAGCACCUC--GCAUCUGCGAGUUCUCUUAAGCAAAAUGCUCGCAUUAGU-UCUCAGCUGGGGCUGUGCAUCAGG-CAGGCUGGGG--AUAUUCAGUUCUCAGCAGAAGCCGGAAUUGGAAUGCGCUCAUCUUUG-AGGAGGCUUUUACCAGGUGUGGGGA-------GGACACAGGUGCU-UCCUCAG
AC126674.3/100224-100630     UCCCUUUGACCCAUUAUUGCAGACUUAAAAA-CAAGCAUGCGUUCAAAUGGUACUGUGAGCUGCCGAUGAUGUAUCGCUCCCAUAUCUCAUUAUUCUCUGCUAAAUGUGAUAAUAAUGCGAUCUGUUAACAUAAAAA---G-UUUGGCUCCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUGGCUCCUACCAUCGGCCACACUCUGCUUGACACAUAUUGUUAGAAGCACCUC--UCAUUGGUGGGCUCUCGUAAGCAAAAUACUUGCAUUAGG-GCUCAGCUGGGGCUCAGCAUCAGG-CAGUUUGGAA-AAUAUUCAGUUCUCAGCAGAAGCCAGAACUUGAAUCCUCACGUCUUUU-AGGACUCGUUUGCCAGGUCUGGAGA-------GGACUGUGUCAGC-UCAGGAG
AAKN02026226.1/133404-133810 UGCACAGCAAAGACUACUGCAGGCUUCAAAA-CAAGCAUGUUUUCAAAUGGUGCUAUGAGUUACCAAUGAUGUAUCACCACCAUAUCUCAUUAUUCUUCACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAA--G-UUUGACUUCACAAAAGCAGCUGGAAAUGGACAACCAGCAUAUGCAUAAAUCUAACUCCUACCAUCGGCUACACACUGCUUGACACAUAUUGUUAGAAGCACCUC--ACAUUUGCGGCUUCUCUUCAGCAAAAUACUUGCAUUAGA-UCUCAGCUGGGGCCGUGCAUCAGG-CAGUUUGGGA-AAUAUUACCCUCUCACGAGAGGCCAGAAUUUCAAUUCCAUCGUCUUGU-AGGAGUCAUUUACUGGGUCCAGCAA-------GGAUUCAGGCAGC--CAGGUG
ABRO01173124.1/1448-1054     UCUCUCUGACCCAUUAUUACAGACUUCCAAA-CAAGCACG---------------AUGAGCUGCCAAUGAUGUAUCACCACCCUAUCUCAUUAUUCUCCACUAAAUGUGAUAAUAAUGCGAUCUGUUCACAUAAAAAAAAGUUUUGACCUCACAAAAGCAGCUGGAAAUGGACAGCCACCAUACGCAUAAAUCUAACUCAUACCAUUGGCCGCACACUGCUUCACACACAAUGUUAGAAGAACCUC--CCCUCCGUGGGUUCUCGGAAGCAAAAGGGUUGUAUUAGG-UCUCAGCUGGGGCUGCGCACCAGG-CACUG-GGGG-AAUAUUCAGUGCUCAGCAGAAGGCUGAAUUUGCAUGUCCUCGUCUUUU-GGAAAUCAUUUACCAGGUUUAGAGA-------GGAUUCAGGCAGC-UCAGGUG
AAGU03017338.1/57723-57315   UCUCUCUGACCCAUUAUUGCAGACUUAAAAA-CAAGCAUGUUUUCAAAUGGCGCUAUGAGCUGCCAAUGAUGUAUCACCACCAUAUCUCAUUAUUCUCCACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAA-G-UUUGACUCCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCGGCUACACACUGCUUGACACAUAUUGUUAGAAGCACCUC--GCAUUUGCGAGUUCUCUUAAGCAAAAUACUUGCAUUAGG-UCUCAGCUGGGGCUGUGCAUCAGG-CAGUUUGGGG-AAUAUGCAAUUCUCAGCGGAAGCCAGAAUUUGAAUUCUCUCAUCUUU-UAGGAAUCAUUUACCAGGUCUGGAGA-------GGAUUCGAGCAGC-UCAGGUG
AAQR03015068.1/89633-90039   UCUCUCUGACCCAUUAUUACAGACUUAAAAA-CAAGCAUGUUUUCAAAUGGUGCUAUGAGCUGCCAAUGAUGUAUCACCACCAUAUCUCAUUAUUCUCUACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAA-G-UUUGACUUCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCAUCAGCUACACACUGCUUGACACAUAUUGUUAGGAGCACCUC--GCAUUUGCGGGUUCUCUUAAGCAAAAUACUUGCAUUAGG-UCUCAGCUGGGGCUGUGCAUCAGG-CGGUUUGGGA---UAUUCAGUUCUCAGUGGAAGCCAGAAUUUGAAUUCUCUCAUCUUUU-AGGAAUCAUUUAGCAGGUUUAGAGA-------GCAUGCAGGCAGC-UCAGGUG
AAHX01009757.1/32694-33097   UCCCUUUGACCCAUUAUUGCAGACUUAAAAA-CAAGCAUGCUUUCAAAUGGUACUAUGAGUUGCCAAUGAUGUAUCACCCCCUUAUCUCAUUAUUCUCUGCUAAAUGUGAUAAUAAUGCGAUCUGUUAACAUAAAAA---G-UUUGGCUCCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUGGCUCCUACCAUCGGCUGCACUCUGCUUGACACAUAUUGUUAGAAGCACCUC--UUCUUGGUGAGCUCUCGUAAGCAAAAUACUUGCAUUAGG-ACUCAGCUGGGG-UGAGCAUCGGGGCAGUUUGGAA-AAUAUUCAGUUCUCAGCAGAAGCCAGAACGUGAAGCCUCAUGUCUUUU-AGGAAUCAUUUACCAGAUCUGGAGA-------GGAGUGUGGCAGCAUCC----
AAGW02048440.1/78710-78304   UCUCUUUGACCCAUUAUUGCAGACUUAAAAA-CAAGCAUGUUUUCAAAUAGCGCUCUGAGCUGC-AAUGAUGUAUCACCACCAUAUCUCAUUAUUCUCCACUAAAUGUGAUAAUAAUGUGAUCUGUUAACAUAAAAAAAAG-UUUGACUUCACAAAAGCAGCUGGAAAUGGACAACCACAAUAUGCAUAAAUCUAACUCCUACCCUCGGCUGCACACUGCUUGACACAUAUUGUAAGAAGCACCUC--GCAUUUGCAGGCUCUCUUAAGCAAAAUACUUGCAUUAGG-UCUCAGCUGGGGCUGUGCAUCAGG-CAGUUUGGGA-AAUAUUCAAUUCUCAGCAGAAGCCAGAAUUGGAAUUCUCUCAUUU--G-AGGACUCAGUUACCAGGUUUGGGGA-------GGAUUCAGGCGGC-UCAGGUG
#=GC SS_cons                 :::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..:::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::.::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::.......:::::::::::::.:::::::
#=GC RF                      UCucUuuGACCCAuUAUUGCAGACUUaaAAA.CAAGCAUGuUUUCAAAUGGuGCUaUGAGcUGCCAAUGAUGUAUCACCacCaUAUCUCAUUAUUCUccaCUAAAUGUGAUAAUAAUGuGAUCUGUUaACAUAAAAAAA.G.UUUGaCUuCACAAAAGCAGCUGGAAAUGGACAACCAcaAUAUGCAUAAAUCUaACUCCUACCAUCGGCuaCACaCUGCUUGACACAUAuUGUuAGAAGCACCUC..gCaUuuGcGgGuUCUCuUAAGCAAAAUaCUUGCAUUAGG.uCUCAGCUGGGGCUguGCAuCaGG.CaGuuuGGGg.AAUAUUCagUUCUCAGcgGAAGCCaGAAUUUGaAUuCucuCaUCUUuu.aGGAauCaUUUACcAGGUuugGaGa.......GgauucaGGCAgC.UCaGGuG
//
# STOCKHOLM 1.0

#=GF AC   RF01895
#=GF ID   mir-193
#=GF DE   microRNA mir-193
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   62.10
#=GF NC   59.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.61 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000082;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [2]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [3]
#=GF RM   18511220
#=GF RT   Identification of novel chicken microRNAs and analysis of their genomic
#=GF RT   organization
#=GF RA   Shao P, Zhou H, Xiao ZD, He JH, Huang MB, Chen YQ, Qu LH
#=GF RL   Gene. 2008;418:34-40.
#=GF RN   [4]
#=GF RM   18469162
#=GF RT   A microRNA catalog of the developing chicken embryo identified by a deep
#=GF RT   sequencing approach
#=GF RA   Glazov EA, Cottee PA, Barris WC, Moore RJ, Dalrymple BP, Tizard ML
#=GF RL   Genome Res. 2008;18:957-964.
#=GF RN   [5]
#=GF RM   20180025
#=GF RT   Cloning and characterization of microRNAs from porcine skeletal muscle and
#=GF RT   adipose tissue
#=GF RA   Cho IS, Kim J, Seo HY, Lim DH, Hong JS, Park YH, Park DC, Hong KC, Whang
#=GF RA   KY, Lee YS
#=GF RL   Mol Biol Rep. 2010;1:1.
#=GF RN   [6]
#=GF RM   19917043
#=GF RT   MicroRNA identity and abundance in porcine skeletal muscles determined by
#=GF RT   deep sequencing
#=GF RA   Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C,
#=GF RA   Thomsen B
#=GF RL   Anim Genet. 2010;41:159-168.
#=GF RN   [7]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [8]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [9]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [10]
#=GF RM   18945293
#=GF RT   Annotation of 390 bovine miRNA genes by sequence similarity with other
#=GF RT   species
#=GF RA   Strozzi F, Mazza R, Malinverni R, Williams JL
#=GF RL   Anim Genet. 2009;40:125.
#=GF RN   [11]
#=GF RM   18392026
#=GF RT   Discovering microRNAs from deep sequencing data using miRDeep
#=GF RA   Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S,
#=GF RA   Rajewsky N
#=GF RL   Nat Biotechnol. 2008;26:407-415.
#=GF RN   [12]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [13]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [14]
#=GF RM   12919684
#=GF RT   Embryonic stem cell-specific MicroRNAs
#=GF RA   Houbaviy HB, Murray MF, Sharp PA
#=GF RL   Dev Cell. 2003;5:351-358.
#=GF RN   [15]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [16]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [17]
#=GF RM   20360741
#=GF RT   The genome of a songbird
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF RN   [18]
#=GF RM   12554859
#=GF RT   New microRNAs from mouse and human
#=GF RA   Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T
#=GF RL   RNA. 2003;9:175-179.
#=GF RN   [19]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [20]
#=GF RM   17965199
#=GF RT   In vitro and in silico annotation of conserved and nonconserved microRNAs
#=GF RT   in the genome of the marsupial Monodelphis domestica
#=GF RA   Devor EJ, Samollow PB
#=GF RL   J Hered. 2008;99:66-72.
#=GF RN   [21]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [22]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction method
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [23]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF RN   [24]
#=GF RM   18849523
#=GF RT   In-depth characterization of the microRNA transcriptome in a leukemia
#=GF RT   progression model
#=GF RA   Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M,
#=GF RA   Yung E, Piper J, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst
#=GF RA   M, Hansen CL, Marra MA, Humphries RK
#=GF RL   Genome Res. 2008;18:1787-1797.
#=GF RN   [25]
#=GF RM   16766679
#=GF RT   Identification and characterization of two novel classes of small RNAs in
#=GF RT   the mouse germline: retrotransposon-derived siRNAs in oocytes and germline
#=GF RT   small RNAs in testes
#=GF RA   Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N,
#=GF RA   Imai H
#=GF RL   Genes Dev. 2006;20:1732-1743.
#=GF RN   [26]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   Mir-193_microRNA_precursor_family
#=GF SQ   17



AAMC01046550.1/7846-7948           CGUGACUAGUGUGGUUUCGGAGUCGGGAUUUUGGGGGCGAGAUGAGC-UAAUGAUUUAUCCAACUGGCCCGCAAAGUCCCGCUUCUGGAAGUCA---CUUUGUUCUG
ABQF01032828.1/14160-14058         UUGGAAGGCUGUGGUUCCAGAGUCGGGGUUUUGGGGGCGAGAUGAGC-UUAUGUUUUAUCCAACUGGCCCACAAAGUCCCGCUUUUGGUGGUCA---CUUUGUUCUG
AC040173.5/123187-123086           UUUGGAGGCUGUGGUCUCAGAAUCGGGGUUUUGAGGGCGAGAUGAGU-UUAUGUUUUAUCCAACUGGCCCUCAAAGUCCCGCUUUUGG-GGUCA---UUCUGGACAG
AANU01212177.1/6700-6599           UUUGGAGGCUGUGGUCUCAGAAUCGGGGUUUUGAGGGCGAGAUGAGU-UUAUGUUUUAUCCAACUGGCCCUCAAAGUCCCGCUUUUGG-GGUCA---UUCUGGACAG
AC192135.4/139009-138908           UUUGGAGGCUGUGGUCUCAGAAUCGGGGUUUUGAGGGCGAGAUGAGU-UUAUGUUUUAUCCAACUGGCCCUCAAAGUCCCGCUUUUGG-GGUCA---UUCUGGACAG
AC012626.10/35226-35125            UUUGGAGGCUGUGGUCUCAGAAUCGGGGUUUUGAGGGCGAGAUGAGU-UUAUGUUUUAUCCAACUGGCCCUCAAAGUCCCGCUUUUGG-GGUCA---UUCUGGACAG
AAYZ01061201.1/1569-1673           UUCGGAGGCCGUGGGCCCAGAAUCGGGGUUUUGAGGGCGAGAUGAGU-UUAUGUUUUAUCCAACUGGCCCACAAAGUCCCGCUUUUGG-GGUCAUUCGGAACAGCGA
AC154564.3/156534-156433           UCUGGAGGCGGUGGGCCCAGAAUCGGGGUUUUGAGGGCGAGAUGAGU-UUGUGUUUUAUCCAACUGGCCCACAAAGUCCCGCUUUUGG-GGUCA---UCCUAACAGC
AAWR02036433.1/21914-21813         UUUCGAGUCUGUGGUCCCAGAAUCGGGGUUUUGAGGGCGAGAUGAGU-UUAUGUUUUAUCCAACUGGCCCACAAAGUCCCGCUUUUGG-GGUCA---UUCCAAACAG
CU138533.13/78727-78830            AGAAAGCAUUGUGAUUUCAGUGACGGGACUUUGGGGGCGAGAUGAGUAUUGAUCUCUAUCCAACUGGCCCGCAAAGUCCCGCUUCUGGGACUCA---CCCUCACAGC
AANG01161763.1/213-315             GGAGACGCGCGGGAGCUGAGGGCUGGGUCUUUGCGGGCGAGAUGAGG-GUGUCGG---UUCAACUGGCCUACAAAGUCCCAGUCCUCGGCCCCCAGGACCGGCAGCU
AANU01121342.1/16348-16248         CGAGACGGAUGGGAGCUGAGGGCUGGGUCUUUGCGGGCGAGAUGAGG-GUGUCGG---AUCAACUGGCCUACAAAGUCCCAGUCCUCGGCCCCC--GUGACCAGCGU
AC003101.2/150032-150131           CUCCGAGGAUGGGAGCUGAGGGCUGGGUCUUUGCGGGCGAGAUGAGG-GUGUCGG---AUCAACUGGCCUACAAAGUCCCAGUUCUCGGCCCCC---GGGACCAGCG
AL731726.11/12313-12415            CAAGACGGACGGGAGCUGAGAGCUGGGUCUUUGCGGGCAAGAUGAGA-GUGUCAG---UUCAACUGGCCUACAAAGUCCCAGUCCUCGGUCCCCAGGACCGGCAUUU
AAFR03044744.1/21764-21662         GUGGGAGGAUGGGAGUUGAGGAUUGGGUCUUUGUGGGCGAGAUGAGG-GUGUCAG---UUCAACUGGCCUACAAAGUCCCAGUUCUCGGUUCCCAGGACCUGCGCCC
ADDD01126760.1/6488-6386           UCAGAAGGCUGUGGUUCCAGAGUCGGGGUUUUGGGGGCGAGAUGAGC-UUAUGUUUUAUCCAACUGGCCCACAAAGUCCCGCUUUUGGUGGUCA---CUUUGUUCUG
AAEX03004507.1/73030-72929         UUUGGAGGCUGUGGUCCCAGAAUCGGGGUUUUGAGGGCGAGAUGAGU-UUAUGUUUGAUCCAACUGGCCCACAAAGUCCCGCUUUUGG-GGUCA---UUCUAAACAU
#=GC SS_cons                       ::::::::::::::::<<<<<<-<<<<-<<<<<-<<<<-<<-<<___.____________>>->>->>>>->>>>>->>>>->>>>>>::::::...::::::::::
#=GC RF                            uuugaaGgauGuGgucccAggaucGGGgcUUUGaGGGCGAGAUGAGu.uUaUguuUUAUcCAACUGGCCCaCAAAgUCCCgcuccUggggguCa...uucugaacau
//
# STOCKHOLM 1.0

#=GF AC   RF01896
#=GF ID   mir-142
#=GF DE   microRNA mir-142
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   73.00
#=GF TC   81.40
#=GF NC   65.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000084;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [2]
#=GF RM   14573789
#=GF RT   Reduced accumulation of specific microRNAs in colorectal neoplasia
#=GF RA   Michael MZ, O' Connor SM, van Holst Pellekaan NG, Young GP, James RJ
#=GF RL   Mol Cancer Res. 2003;1:882-891.
#=GF RN   [3]
#=GF RM   19917043
#=GF RT   MicroRNA identity and abundance in porcine skeletal muscles determined by
#=GF RT   deep sequencing
#=GF RA   Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C,
#=GF RA   Thomsen B
#=GF RL   Anim Genet. 2010;41:159-168.
#=GF RN   [4]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [5]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [6]
#=GF RM   15325244
#=GF RT   Altered expression profiles of microRNAs during TPA-induced
#=GF RT   differentiation of HL-60 cells
#=GF RA   Kasashima K, Nakamura Y, Kozu T
#=GF RL   Biochem Biophys Res Commun. 2004;322:403-410.
#=GF RN   [7]
#=GF RM   18392026
#=GF RT   Discovering microRNAs from deep sequencing data using miRDeep
#=GF RA   Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S,
#=GF RA   Rajewsky N
#=GF RL   Nat Biotechnol. 2008;26:407-415.
#=GF RN   [8]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [9]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [10]
#=GF RM   17306260
#=GF RT   Identification and characterization of microRNAs from the bovine adipose
#=GF RT   tissue and mammary gland
#=GF RA   Gu Z, Eleswarapu S, Jiang H
#=GF RL   FEBS Lett. 2007;581:981-988.
#=GF RN   [11]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [12]
#=GF RM   15345052
#=GF RT   Microarray analysis of microRNA expression in the developing mammalian
#=GF RT   brain
#=GF RA   Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P,
#=GF RA   Constantine-Paton M, Horvitz HR
#=GF RL   Genome Biol. 2004;5:R68.
#=GF RN   [13]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [14]
#=GF RM   12919684
#=GF RT   Embryonic stem cell-specific MicroRNAs
#=GF RA   Houbaviy HB, Murray MF, Sharp PA
#=GF RL   Dev Cell. 2003;5:351-358.
#=GF RN   [15]
#=GF RM   16750530
#=GF RT   Identification of microRNAs from different tissues of chicken embryo and
#=GF RT   adult chicken
#=GF RA   Xu H, Wang X, Du Z, Li N
#=GF RL   FEBS Lett. 2006;580:3610-3616.
#=GF RN   [16]
#=GF RM   20360741
#=GF RT   The genome of a songbird
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF RN   [17]
#=GF RM   12007417
#=GF RT   Identification of tissue-specific microRNAs from mouse
#=GF RA   Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T
#=GF RL   Curr Biol. 2002;12:735-739.
#=GF RN   [18]
#=GF RM   18256158
#=GF RT   MicroRNA profile of Marek's disease virus-transformed T-cell line MSB-1:
#=GF RT   predominance of virus-encoded microRNAs
#=GF RA   Yao Y, Zhao Y, Xu H, Smith LP, Lawrie CH, Watson M, Nair V
#=GF RL   J Virol. 2008;82:4007-4015.
#=GF RN   [19]
#=GF RM   18032731
#=GF RT   Xenopus microRNA genes are predominantly located within introns and are
#=GF RT   differentially expressed in adult frog tissues via post-transcriptional
#=GF RT   regulation
#=GF RA   Tang GQ, Maxwell ES
#=GF RL   Genome Res. 2008;18:104-112.
#=GF RN   [20]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [21]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF RN   [22]
#=GF RM   17965199
#=GF RT   In vitro and in silico annotation of conserved and nonconserved microRNAs
#=GF RT   in the genome of the marsupial Monodelphis domestica
#=GF RA   Devor EJ, Samollow PB
#=GF RL   J Hered. 2008;99:66-72.
#=GF RN   [23]
#=GF RM   15919954
#=GF RT   MicroRNA expression in zebrafish embryonic development
#=GF RA   Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de
#=GF RA   Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH
#=GF RL   Science. 2005;309:310-311.
#=GF RN   [24]
#=GF RM   15592404
#=GF RT   Sequence and comparative analysis of the chicken genome provide unique
#=GF RT   perspectives on vertebrate evolution
#=GF RA   International Chicken Genome Sequencing Consortium
#=GF RL   Nature. 2004;432:695-716.
#=GF RN   [25]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [26]
#=GF RM   16766679
#=GF RT   Identification and characterization of two novel classes of small RNAs in
#=GF RT   the mouse germline: retrotransposon-derived siRNAs in oocytes and germline
#=GF RT   small RNAs in testes
#=GF RA   Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N,
#=GF RA   Imai H
#=GF RL   Genes Dev. 2006;20:1732-1743.
#=GF RN   [27]
#=GF RM   15937218
#=GF RT   The developmental miRNA profiles of zebrafish as determined by small RNA
#=GF RT   cloning
#=GF RA   Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John
#=GF RA   B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T
#=GF RL   Genes Dev. 2005;19:1288-1293.
#=GF WK   MicroRNA
#=GF SQ   13


AAFR03045441.1/27253-27358 AGACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCAAUGUAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUGGGCUUCGGAG
AL604022.21/36673-36778    GGACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCACUGGAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGCACUGUGGGCUUCGGAG
CU393486.7/169334-169439   GGACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCACUGGAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGCACUGUGGGCUUCGGAG
AAQQ01354427.1/3593-3488   GAACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCACUGGAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUGGGCUUCGGAG
AANU01173044.1/25471-25366 GGACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCACUGGAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUGGGCUUCGGAG
AC023992.8/2092-1987       GGACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCACUGGAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUGGGCUUCGGAG
ACBE01421816.1/6085-6190   GGACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCACUGGAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUGGGCUUCGGAG
AAWR02012934.1/8078-7973   GGACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCACUGGAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUGGGCUUCGGAG
ABRP01047127.1/2527-2422   GGACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCACUGGAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUGGGCUUCGGAG
AC197930.3/5013-5118       GGACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCACUGGAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUGGGCUUCGGAG
AC004687.2/82254-82359     GGACAGACAGACAGUGCAGUCACCCAUAAAGUAGAAAGCACUACUAA-CAGCACUGGAGGGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUGGGCUUCGGAG
CAAK05054211.1/4292-4186   AAAAGGACGUACAGUGCAGUCAUCCAUAAAGUAGAAAGCACUACUAAACCCCUCGCCACAGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUUGGCUGCUGGG
CAAB02002247.1/1156-1050   GUGUGCUUGUACAGUGCAGUCAUCCAUAAAGUAGAAAGCACUACUAAACUCUUUGCCACAGUGUAGUGUUUCCUACUUUAUGGAUGAGUGUACUGUUGUCUUCAGGG
#=GC SS_cons               ::::::::::<<<<<<<<-<<<-<<<<<<<<<<<-<<<<<<<<<___.______________>>>>>>>>>->>>>>>>>>>>->>>->>>>>>>>:::::::::::
#=GC RF                    ggAcagAcagaCaGugCaGuCacCCauaaaGuaGAaagCaCuaCUAA.CagcacuggAggGUGuaGuGuuuCCuaCuuuauGGAuGaGuGcaCuGugGgCUuCgGaG
//
# STOCKHOLM 1.0

#=GF AC   RF01897
#=GF ID   mir-188
#=GF DE   microRNA mir-188
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   72.90
#=GF NC   68.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000113;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17616659
#=GF RT   Patterns of known and novel small RNAs in human cervical cancer
#=GF RA   Lui WO, Pourmand N, Patterson BK, Fire A
#=GF RL   Cancer Res. 2007;67:6031-6043.
#=GF RN   [2]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [3]
#=GF RM   16973894
#=GF RT   Mouse microRNA profiles determined with a new and sensitive cloning method
#=GF RA   Takada S, Berezikov E, Yamashita Y, Lagos-Quintana M, Kloosterman WP,
#=GF RA   Enomoto M, Hatanaka H, Fujiwara S, Watanabe H, Soda M, Choi YL, Plasterk
#=GF RA   RH, Cuppen E, Mano H
#=GF RL   Nucleic Acids Res. 2006;34:e115.
#=GF RN   [4]
#=GF RM   19917043
#=GF RT   MicroRNA identity and abundance in porcine skeletal muscles determined by
#=GF RT   deep sequencing
#=GF RA   Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C,
#=GF RA   Thomsen B
#=GF RL   Anim Genet. 2010;41:159-168.
#=GF RN   [5]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [6]
#=GF RM   18945293
#=GF RT   Annotation of 390 bovine miRNA genes by sequence similarity with other
#=GF RT   species
#=GF RA   Strozzi F, Mazza R, Malinverni R, Williams JL
#=GF RL   Anim Genet. 2009;40:125.
#=GF RN   [7]
#=GF RM   18392026
#=GF RT   Discovering microRNAs from deep sequencing data using miRDeep
#=GF RA   Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S,
#=GF RA   Rajewsky N
#=GF RL   Nat Biotechnol. 2008;26:407-415.
#=GF RN   [8]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [9]
#=GF RM   15652478
#=GF RT   Phylogenetic shadowing and computational identification of human microRNA
#=GF RT   genes
#=GF RA   Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E
#=GF RL   Cell. 2005;120:21-24.
#=GF RN   [10]
#=GF RM   17306260
#=GF RT   Identification and characterization of microRNAs from the bovine adipose
#=GF RT   tissue and mammary gland
#=GF RA   Gu Z, Eleswarapu S, Jiang H
#=GF RL   FEBS Lett. 2007;581:981-988.
#=GF RN   [11]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [12]
#=GF RM   19170227
#=GF RT   Identification and expression profiling of microRNAs during bovine oocyte
#=GF RT   maturation using heterologous approach
#=GF RA   Tesfaye D, Worku D, Rings F, Phatsara C, Tholen E, Schellander K, Hoelker
#=GF RA   M
#=GF RL   Mol Reprod Dev. 2009;76:665-677.
#=GF RN   [13]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [14]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [15]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF RN   [16]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [17]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [18]
#=GF RM   18215311
#=GF RT   miRNAminer: a tool for homologous microRNA gene search
#=GF RA   Artzi S, Kiezun A, Shomron N
#=GF RL   BMC Bioinformatics. 2008;9:39.
#=GF WK   Mir-188_microRNA_precursor_family
#=GF SQ   14


AY865946.1/456-562           GAGCCCUUCCCUGCUCCCUCUCUCACAUCCCUUGCAUGGUGGAGGGUGAGCUUUAUGAAAACCCCUCCCACAUGCAGGGUUUGCAGGAUGGUGAGCCUCAGCUUUCC
AY865949.1/463-569           GAGCCCUUCCCUGCUCCCUCUCUCACAUCCCUUGCAUGGUGGAGGGUGAGCUUUAUGAAAACCCCUCCCACAUGCAGGGUUUGCAGGAUGGUGAGCCUCAGCUUUCC
AAFC03003598.1/102742-102636 GAACCUUUCCCUGCUCCCUCUCUCACAUCCCUUGCAUGGUGGAGGGUGAGCUUUCUGAAAACCCCUCCCACAUGCAGGGUUUGCAGGAUGGUGAGCCUCGGCUUUUC
AAHX01109195.1/15201-15307   GAACCCUUCCCUGCUCCCUCUCUCACAUCCCUUGCAUGGUGGAGGGCGAGCUCUCUGAAAACUCCUCCCACAUGCAGGGUUUGCAGGAUGGUGAGCUUCAGCUUUCC
AY865948.1/447-553           AAGCCCUUCCCUGCUCCCUCUCUCACAUCCCUUGCAUGGUGGAGGGUGAGCUUUCUGAAAACCCCUCCCACAUGCAGGGUUUGCAGGAUGGCGAGCCUCAGCUUUCC
AC207100.2/80625-80731       AAGCCCUUCCCUGCUCCCUCUCUCACAUCCCUUGCAUGGUGGAGGGUGAACUUUCUGAAAACCCCUCCCACAUGCAGGGUUUGCAGGAUGGCGAGCCUCAGCUUUCC
AAFC03070558.1/67548-67443   GAAGAAUGAACUGCUCCUUCUCCCGUACCCAUUGCAUAUCGGAGC-UGUGAAUUCUCAAAGCACCUCCUAUGUGCAUGGAUUACAGGAGGGGGGAGCCCUGUCAUCA
AAWR02023860.1/6393-6498     ACCUUCUGAUUUGCUUUCUCUCUUACAUGCCUUGAGUGUAGGACCGUUGGCAUCUUAAUUAC-CCUCCCACACCCAAGGCUUGCAGGAGGGCAAGCCUUUUCCUUCC
AACN010221336.1/1105-1210    ACCUUCUGACUUGCUUUCUCUCUUACAUGCCUUGAGUGUAGGACCGUUGGUAUCUUAAUUAC-CCUCCCACACCCAAGGCUUGCAGGAGGGCAAGCCACCUCCUUCC
AY865950.1/143-248           ACCUCCCGACUUGCUUUCUCUCCUCCAUGCCUUGAGUGUAGGACCGUUGGCAUCUUAAUUAC-CCUCCCACACCCAAGGCUUGCAGAAGAGCGAGCCUUCUCUUCCC
AY865948.1/97-202            ACCUCCCGACUUGCUUUCUCUCCUCCAUGCCUUGAGUGUAGGACCGUUGGCAUCUUAAUUAC-CCUCCCACACCCAAGGCUUGCAGAAGAGCGAGCCUUCUCUUCCC
AY865949.1/110-215           ACCUCCCGACUUGCUUUCUCUCCUCCAUGCCUUGAGUGUAGGACCGUUGGCAUCUUAAUUAC-CCUCCCACACCCAAGGCUUGCAGAAGAGCAAGCCUUCUCUUCCC
AAHX01109195.1/14801-14906   GCCUACAGAUUUGCUUUUUCUCUUCCAUGCCUUGAGUGUAGGACUGUUGACAUCUUAAUUAC-CCUCCCACACCCAAGGCUUGCAGGAGAGCAAGCCUUCUCUUCUC
AAPE02033846.1/35993-36098   GAAGAAUGAACUGCUCCUUCUCCCAUACCCAUUGCAUAUCGGAGU-UGUGAAUUCUCAAAGCACCUCCUGUGUGCAUGGAUUACAGGAGGGCGAGCCUUGUCAUCAU
#=GC SS_cons                 ::::::::::::<<<<<<--<<---<<--<<<<<-<<<--<<<______________________>>>-->>>->>>>>-->>-->>-->>->>>>:::::::::::
#=GC RF                      gaauccUgaccUGCUcccUCuCucaCAUcCCuUGcguGuuGGAgcGUgaGcaUuuUaAaaACaCCUCCCACacgCAaGGuUUGCAGgAgggcgAGCCUcauCuUucc
//
# STOCKHOLM 1.0

#=GF AC   RF01898
#=GF ID   mir-363
#=GF DE   microRNA mir-363
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   100.00
#=GF TC   102.20
#=GF NC   99.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00110
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000138;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   20360741
#=GF RT   The genome of a songbird
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF RN   [4]
#=GF RM   19917043
#=GF RT   MicroRNA identity and abundance in porcine skeletal muscles determined by
#=GF RT   deep sequencing
#=GF RA   Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, Bendixen C,
#=GF RA   Thomsen B
#=GF RL   Anim Genet. 2010;41:159-168.
#=GF RN   [5]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [6]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [7]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [8]
#=GF RM   17105755
#=GF RT   Discovery and profiling of bovine microRNAs from immune-related and
#=GF RT   embryonic tissues
#=GF RA   Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC,
#=GF RA   Capuco AV, Smith TP
#=GF RL   Physiol Genomics. 2007;29:35-43.
#=GF RN   [9]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [10]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [11]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction method
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [12]
#=GF RM   18215311
#=GF RT   miRNAminer: a tool for homologous microRNA gene search
#=GF RA   Artzi S, Kiezun A, Shomron N
#=GF RL   BMC Bioinformatics. 2008;9:39.
#=GF RN   [13]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [14]
#=GF RM   18392026
#=GF RT   Discovering microRNAs from deep sequencing data using miRDeep
#=GF RA   Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S,
#=GF RA   Rajewsky N
#=GF RL   Nat Biotechnol. 2008;26:407-415.
#=GF RN   [15]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   Mir-363_microRNA_precursor_family
#=GF SQ   7


AY866361.1/1332-1419         UGUUUUGCUGUUGUCGGGUGGAUCACGAUGCAAUUUUGAUGAGUAUCAUAGGAGAAAAAUUGCACGGUAUCCAUCUGUAAACCGCAGG
FP015951.3/28491-28404       UGUUUUGCUGUUGUCGGGUGGAUCACGAUGCAAUUUUGAUUAGUAUCAUAGGAGAAAAAUUGCACGGUAUCCAUCUGUAAACCGCAGG
ABGA01101316.1/638-551       UGUUUUGCUGUUGUCGGGUGGAUCACGAUGCAAUUUUGAUUAGUAUCAUAGGAGAAAAAUUGCACGGUAUCCAUCUGUAAACCGCAGG
AAFC03125572.1/1660-1747     UGUUUUGCUGUUGUCGGGUGGAUCACGAUGCAAUUUUGAUUAGUAUAAUAGGAGAAAAAUUGCACGGUAUCCAUCUGCGAACCGCAGG
ACBE01507560.1/2570-2657     UGUUUUGCUGUUGUCGGGUGGAUCACGAUGCAAUUUUGAUUAGUAUAAUAGGAGAAAAAUUGCACGGUAUCCAUCUGUAAACCGCAGG
BX571778.7/42192-42105       UGUUUUGCUGUUAUCAGGUGGAACACGAUGCAAUUUUGGUUGGUGUAAUAGGAGGAAAAUUGCACGGUAUCCAUCUGUAAACCGCAGG
AAEX03026925.1/968624-968537 UGUUUUGCUGUUGUCGGGUGGAUCACGAUGCAAUUUUGAUGAGUAUAAUAGGAGAAAAAUUGCACGGUAUCCAUCUGUAAACCGCAGG
#=GC SS_cons                 :::::::::<<<--<<<<<<<<<--<<-<<<<<<<<<--<<<______>>>---->>>>>>>>>>>-->>>>>>>>>-->>>::::::
#=GC RF                      UGUUUUGCUGuugUCgGguGGauCACGAuGCaauuuuGAuuaGUAUaAuagGAGAaaaauuGCaCGGUauCCauCcGUAaaCCGCAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01899
#=GF ID   mir-2241
#=GF DE   microRNA mir-2241
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   72.80
#=GF NC   58.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000821;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode species
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   10


ABKE01012904.1/313-215     UUGCUACUCGCAACGUCCCUUAUCUUCUGAAAUCCAGGUUUCGAUCACUAAUUGGU-GUGAUCACCGGGAUUCUCAGUGGAUUAGGGCAUCGAGUCAGCU
ABKE01012904.1/440-342     UUGCUACUCGCAACGUCCCUUAUCUUCUGAAAUCCAGGUUUCGAUCACUAAUUGGU-GUGAUCACCGGGAUUCUCAGUGGAUUAGGGCAUCGAGUCGGCU
ABKE01012904.1/186-88      UUACUACUCGCAACGUCCCUUAUCUUCUGAAAUCUCUGUUUCGAUCACUAAUUGGA-GUGAUCCCAGGGAUUCUCAGUAGAUUAGGGCAUCGAGUCGGCU
ABKE01000303.1/40120-40216 GCUCUAUUCGAUACGCCUCUGAUCUUCA-GGAUCCCUGUCUGAACACAGAAAUUGA-GUGUUCGCAAGGUUUCC-UCAAGAUCAGGGCUUCGAGUCAGCU
ABKE01000303.1/40396-40492 GCUCUUUUCGAUACGCCUCUGAUCUUCA-GGAUCCCUGUCUGAACACAGAAAUUGA-GUGUUCGCAAGGUUUCC-UCAAGAUCAGGGCUUCGAGUCAGCU
ABKE01007499.1/3103-3007   GCUCUAUUCGAUACGCCUCUGAUCUUCA-GGAUCCCUGUCUGAACACAGAAAUUGA-GUGUUCGCAAGGUUUCC-UCAAGAUCAGGGCUUCGAGUCAGCU
ABKE01007499.1/2558-2462   GCUCUAUUCGAUACGCCUCUGAUCUUCA-GGAUCCCUGUCUGAACACCGAAAUUGA-GUGUUCGCAAGGAUUCC-UCAAGAUCAGGGCCUCGAAUCAACU
ABKE01000303.1/40258-40354 GCUCUAUUCGAUAUUGCCUUGAUCUUCA-GGAUCCCUGUCUGAACACAGAAAUUGA-GUGUUCGCAAGGAUUCC-UCAAGAUCAGGGCUUCGAGUCAGCU
ABKE01003450.1/5005-5103   CCGCUACUCGACACGUCCCAAAUCCUCAUGAAUCCCGGUUUUGAUCACUAGUUGCA-GUGAUCACCGGGAUUCUAUGAAGAUCUGGGCUUCGAGAAGGCU
ABKE01002372.1/17266-17360 UUGCUAUUCGCCAUGCCCCC-AUCCUCAAAAAUUCCGA---GAACCACGAAUUGAAUGUGGUCUC-GGGCUUCUUUGAGGAUAAGGGCUUCGGGUCAGCU
#=GC SS_cons               :::::<<<<<----<<<<---<<<<--<<<<<-<<-<<<----<<___________.>>---->>>->>->>->>>-->>>>-->>>>-->>>>>:::::
#=GC RF                    uuuCUacuCGauAcGcCcCugAUCuUCaggaAUCCcgGuuUgaAcaacgAAuUggA.gUGuUCaCcgGGaUuCccugaaGAUcAgGgCuUCGaguCaGCU
//
# STOCKHOLM 1.0

#=GF AC   RF01900
#=GF ID   mir-2024
#=GF DE   microRNA mir-2024
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   72.50
#=GF NC   55.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000697;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18830242
#=GF RT   Early origins and evolution of microRNAs and Piwi-interacting RNAs in
#=GF RT   animals
#=GF RA   Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan
#=GF RA   BM, Rokhsar DS, Bartel DP
#=GF RL   Nature. 2008;455:1193-1197.
#=GF WK   MicroRNA
#=GF SQ   7


ABAV01022222.1/21091-20999 CCAAUAAGUGCUACUGCUUCAAAAUAUCGGUGUUGGGUAAAAGGUCACCUUUUAACACAGUACCGAUAUUGUGAAGCACGUUUGCAAAUUAAA
ABAV01022225.1/903-811     CCAAUAAGUGCUACUGCUUCAAAAUAUCGGUGUUGGGUAAAAGGUCACCUUUUAACACAGUACCGAUAUUGUGAAGCACGUUUGCAAAUUAAA
ABAV01014371.1/264-173     CCAAUAAGUGCUACUGCUUCAAAAUAUCGGUGUUGGGUAAAAGGUCACAUUUUCA-ACAGUACCGAUAUUGUGAAGCACGUUUGCAAAUUAAA
ABAV01034789.1/1206-1297   CCAAUAAGUGCUACUGCUUCAAAAUAUCGGUGUUGGGUAAAAGGUCACAUUUU-ACACAGUACCGAUAUUGUGAAGCACGUUUGCAAAUUAAA
ABAV01014372.1/994-903     CCAACAAGUGCUACUGCUUCAAAAUAUCGGUGUUGGGUAAAAGGUCACAUUUU-ACACAGUACCGAUAUUGUGAAGCACGUUUGCUUAGGAAC
ABAV01014373.1/3308-3217   CCAACAAGUGCUACUGCUUCAAAAUAUCGGUGUUGGGUAAAAGGUCACAUUUU-ACACAGUACCGAUAUUGUGAAGCACGUUUGCUUAGGAAC
ABAV01014373.1/3554-3463   ACAUCAGGUAGACUUGCUUCAGAAUAUUGGUGCUGGGCAAAAGGUCACAUUUU-GCACAACACCAAUAUUCUGAGGCACUUCUGCUGAAGGAA
#=GC SS_cons               :::::::::<<-<<<<<<<<<-<<<<<<<<<<<<<-<<-<<<<______>>>>.>>->>>>>>>>>>>>>->>>>>>>->>-->>::::::::
#=GC RF                    cCAauAAGUGcuacuGCuuCaAaauaucGGugcuGGGuAaaagGUCACauuuu.aCACagcaCCgauauuguGaaGCaCguuUgCaaAuuAAa
//
# STOCKHOLM 1.0

#=GF AC   RF01901
#=GF ID   mir-284
#=GF DE   microRNA mir-284
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   96.00
#=GF TC   102.00
#=GF NC   62.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000228;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17994087
#=GF RT   Evolution of genes and genomes on the Drosophila phylogeny
#=GF RA   Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC,
#=GF RA   Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM,
#=GF RA   Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW,
#=GF RA   Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D,
#=GF RA   Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak
#=GF RA   SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK,
#=GF RA   Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S,
#=GF RA   Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A,
#=GF RA   Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher
#=GF RA   AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD,
#=GF RA   Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC,
#=GF RA   Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey
#=GF RA   J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S,
#=GF RA   Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter
#=GF RA   GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz
#=GF RA   MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J,
#=GF RA   Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P,
#=GF RA   Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S,
#=GF RA   Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L,
#=GF RA   Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky
#=GF RA   E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L,
#=GF RA   McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P,
#=GF RA   Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S,
#=GF RA   Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M,
#=GF RA   Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli
#=GF RA   D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D,
#=GF RA   Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie
#=GF RA   MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S,
#=GF RA   Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz
#=GF RA   MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M,
#=GF RA   Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W,
#=GF RA   Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W,
#=GF RA   Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E,
#=GF RA   Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang
#=GF RA   J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A,
#=GF RA   Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K,
#=GF RA   Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A,
#=GF RA   Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A,
#=GF RA   An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A,
#=GF RA   Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C,
#=GF RA   Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y,
#=GF RA   Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De
#=GF RA   Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M,
#=GF RA   Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D,
#=GF RA   Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR,
#=GF RA   Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez
#=GF RA   N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L,
#=GF RA   Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P,
#=GF RA   Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X,
#=GF RA   Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P,
#=GF RA   Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T,
#=GF RA   Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V,
#=GF RA   Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N,
#=GF RA   Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E,
#=GF RA   Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F,
#=GF RA   Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N,
#=GF RA   Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N,
#=GF RA   Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y,
#=GF RA   Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk
#=GF RA   T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q,
#=GF RA   Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W,
#=GF RA   Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I
#=GF RL   Nature. 2007;450:203-218.
#=GF RN   [2]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [3]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [4]
#=GF RM   12844358
#=GF RT   Computational identification of Drosophila microRNA genes
#=GF RA   Lai EC, Tomancak P, Williams RW, Rubin GM
#=GF RL   Genome Biol. 2003;4:R42.
#=GF WK   MicroRNA
#=GF SQ   10


AAPU01011034.1/21117-21020   GUUGCAGUUCCUGGAAUAAAGUUGACUGUGUCGCCUGUAAGGGGA-AGGCUUUUGCAUUGCUUACAAAGUCAGCAACUUGAUUCCAGCAACUGCGGCCC
AASR01017048.1/711-808       GUUGCAGUUCCUGGAAUUAAGUUGACUGUGUAGCCUGUGAGG-GCAAGGCUUGAAUACUGCUCCUGAAGUCAGCAACUUGAUUCCAGCAAUUGCGGCCC
AAKO01000258.1/87086-87183   GUUGCAGUUCCUGGAAUUAAGUUGACUGUGUAGCCUGUGAGG-GCAAGGCUUGAAUACUGCUCCUGAAGUCAGCAACUUGAUUCCAGCAAUUGCGGCCC
AAPQ01006464.1/198522-198619 GUUGCAGUUCCUGGAAUUAAGUUGACUGUGUAGCCUGUGAGG-GCAAGGCUUGAGUACUGCUUCUGAAGUCAGCAACUUGAUUCCAGCAAUUGCGGCCC
AAPP01015631.1/94293-94196   GUUGCAGUUCCUGGAAUUAAGUUGACUGUGUAGCCUGUGAGG-GCAAGGCUUGAGAACUGCUUCAGAAGUCAGCAACUUGAUUCCAGCAAUUGCGGCCC
AANI01014593.1/63537-63634   GUUGCAGUUCCUGGAAUUAAGUUGACUGUGUAGCCUGUAAAGGGA-AGGCUUGUGCACUGCUUACAAAGUCAGCAACUUGAUUCCAGCAAUUGCGGCCC
AAPT01019305.1/181359-181456 GUUGCAGUUCCUGGAAUUAAGUUGACUGUGUAGCCUGUAAGAGGA-AGGCUUGUGCACUGCUUACAAAGUCAGCAACUUGAUUCCAGCAAUUGCGGCUC
AE014297.2/8377336-8377239   GUUGCAGUUCCUGGAAUUAAGUUGACUGUGUAGCCUGUGAGG-GCAAGGCUUGAAUAAUGCUCCUGAAGUCAGCAACUUGAUUCCAGCAAUUGCGGCCC
AAEU02000033.1/42587-42490   GUUGCAGUUCCUGGAAUUAAGUUGACUGUGUAGCCUGUGAGG-GCAAGGCUUGAGUACUGCUUCUGAAGUCAGCAACUUGAUUCCAGCAAUUGCGGCCC
AAQB01009392.1/110679-110581 GUUGCAGUUCCUGGAAUUAAGUUGACUGUGUAGCCUGUUAGGGGAAAGGCUUGAGCAUUGCAUACUAAGUCAGCAACUUGAUUCCAGCAAUUGCGGCCC
#=GC SS_cons                 (((((((((-((((((((((((((-(((,,,<<<<<______.___>>>>>,,,,,<<<________>>>)))))))))))))))))-)))))))))::
#=GC RF                      GccGCaguuCCuGGaaucaaGuuGACuGUGUaGCCuGUaAGG.GaAaGGCuUgaguacuGCuuauaAaguCaGCaaCuugauuCCaGCaacuGCggCcC
//
# STOCKHOLM 1.0

#=GF AC   RF01902
#=GF ID   MIR439
#=GF DE   microRNA MIR439
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   65.00
#=GF TC   65.30
#=GF NC   63.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000092;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   15805478
#=GF RT   Cloning and characterization of microRNAs from rice
#=GF RA   Sunkar R, Girke T, Jain PK, Zhu JK
#=GF RL   Plant Cell. 2005;17:1397-1411.
#=GF WK   MicroRNA
#=GF SQ   5


AC151407.1/78181-78276   ACCUACCCUGUCGAACUCACGUAGUUCGACAUGUACCUGUCGAACUGUGGUUGUUCGAUAGGUAUCCCUGUCGAACCGCGGUUGUUCGAUAGGGUG
AP000391.2/80939-80844   ACCUACCCUGUCGAACUCACGCAGUUCGACAUGUACCUGUCGAACUGUGGUUGUUCGAUAGGUAUCCCUGUCGAACCGCGGUUGUUCGACAGGGUG
AC092173.3/95355-95450   ACCUAUCCUGUCAAACUGACGCAGUUCAACAUGUUCCUGUCGAAUUGUGGUUGUUCGAUAGGUACCCCUGUCGAACCGCGGUUGUUCGACAGGGUG
AP005504.3/136385-136480 ACCUAUCCUGUCGAACUGACGCAGUUCGACAUGUACCUGUCGAACUGUGGUUGUUCGAUAGGUAUCCCUGUCGAACCGCGGUUGUUCGACAGGGUG
AP004621.3/49336-49241   ACCUACCCUGUCGAACUGACGCAGUUCGACAUGUACCUGUCGAACUGUGGUUGUUCGAUAGGUAUCCCUGUCGAACCGCGGUUGUUCGACAGGGUG
#=GC SS_cons             :::<<<<<<<<<<<<<---<<<-<<<<<<<<-<<<<<<<<<<<<<_______>>>>>>>>>>>>>--->>>>>>>>->>>--->>>>>>>>>>>>>
#=GC RF                  AcccacccugucgaacUgAcGcAGuucgacaUguaccugucGaacUGUGGUUguuCgacagguaccccugucgaaCcgCgGUUguucgacagggug
//
# STOCKHOLM 1.0

#=GF AC   RF01903
#=GF ID   mir-500
#=GF DE   microRNA mir-500
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   62.00
#=GF TC   63.10
#=GF NC   60.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000139;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [2]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [3]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [4]
#=GF RM   16566924
#=GF RT   Identification of new central nervous system specific mouse microRNAs
#=GF RA   Wheeler G, Ntounia-Fousara S, Granda B, Rathjen T, Dalmay T
#=GF RL   FEBS Lett. 2006;580:2195-2200.
#=GF RN   [5]
#=GF RM   18945293
#=GF RT   Annotation of 390 bovine miRNA genes by sequence similarity with other
#=GF RT   species
#=GF RA   Strozzi F, Mazza R, Malinverni R, Williams JL
#=GF RL   Anim Genet. 2009;40:125.
#=GF RN   [6]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [7]
#=GF RM   18392026
#=GF RT   Discovering microRNAs from deep sequencing data using miRDeep
#=GF RA   Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S,
#=GF RA   Rajewsky N
#=GF RL   Nat Biotechnol. 2008;26:407-415.
#=GF RN   [8]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF RN   [9]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [10]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [11]
#=GF RM   19784364
#=GF RT   Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic
#=GF RT   stem cells and neural precursors
#=GF RA   Goff LA, Davila J, Swerdel MR, Moore JC, Cohen RI, Wu H, Sun YE, Hart RP
#=GF RL   PLoS One. 2009;4:e7192.
#=GF RN   [12]
#=GF RM   20433717
#=GF RT   Deciphering the porcine intestinal microRNA transcriptome
#=GF RA   Sharbati S, Friedlander MR, Sharbati J, Hoeke L, Chen W, Keller A, Stahler
#=GF RA   PF, Rajewsky N, Einspanier R
#=GF RL   BMC Genomics. 2010;11:275.
#=GF RN   [13]
#=GF RM   19267191
#=GF RT   Identification and characteristics of cattle microRNAs by homology
#=GF RT   searching and small RNA cloning
#=GF RA   Long JE, Chen HX
#=GF RL   Biochem Genet. 2009;47:329-343.
#=GF RN   [14]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [15]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [16]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF RN   [17]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF RN   [18]
#=GF RM   18215311
#=GF RT   miRNAminer: a tool for homologous microRNA gene search
#=GF RA   Artzi S, Kiezun A, Shomron N
#=GF RL   BMC Bioinformatics. 2008;9:39.
#=GF RN   [19]
#=GF RM   16274478
#=GF RT   Identification of clustered microRNAs using an ab initio prediction method
#=GF RA   Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T,
#=GF RA   van Nimwegen E, Zavolan M
#=GF RL   BMC Bioinformatics. 2005;6:267.
#=GF RN   [20]
#=GF RM   20668074
#=GF RT   Identification and analysis of expression of novel microRNAs of murine
#=GF RT   gammaherpesvirus 68
#=GF RA   Zhu JY, Strehle M, Frohn A, Kremmer E, Hofig KP, Meister G, Adler H
#=GF RL   J Virol. 2010;1:1.
#=GF RN   [21]
#=GF RM   20459774
#=GF RT   Ultra-high throughput sequencing-based small RNA discovery and discrete
#=GF RT   statistical biomarker analysis in a collection of cervical tumours and
#=GF RT   matched controls
#=GF RA   Witten D, Tibshirani R, Gu SG, Fire A, Lui WO
#=GF RL   BMC Biol. 2010;8:58.
#=GF WK   Mir-500_microRNA_precursor_family
#=GF SQ   26


ABRN01086721.1/3805-3894   UUCUGGCUCCCCCUCUCUAAUCCUUGCUACCUGGGUGAG-AGUGCUUUCUGAAUGCAAUGCACCUGGGCAAGGAUUCUGAGAGAGGGAGCA
AAFC03070558.1/69695-69606 UCCUGGCUCCCCCUCUCUAAUCCUUGCUACCUGGGUGAG-AGUGCUUUCUGAAUGCAAUGCACCUGGGCAAGGAUUCUGAGAGAGGGAGCA
AC231645.2/58039-58128     UCCUGGUUCCCCCUCUCUAAUCCUUGCUACCUGGGUGAG-AGUGCUUUCUGAAUGCAGUGCACCCAGGCAAGGAUUCUGCAAGGGGGAGUG
AF222686.1/113650-113739   UCCUGGUUCCCCCUCUCUAAUCCUUGCUACCUGGGUGAG-AGUGCUUUCUGAAUGCAGUGCACCCAGGCAAGGAUUCUGCAAGGGGGAGUG
AAFC03003598.1/91612-91523 GUUGUGGCUCCCCUCUCUAAUUCUUGCUCCCCAGGUGAG-AGUGCUUUGUGAAUGCAAUCCACCUGGGCAAGGAUUCUGAAUGUGAGAGCU
AAWR02023860.1/11219-11308 GCUCUGCUCCCCCUCUCUAAUCCUUGCUACCUGGGUGAG-AGUGUUGUCUGAAUGCAAUGCACCUGGGCAAGGAUUCCGAGAGCGAGAGCU
AANU01113553.1/3072-2983   GCUCUGCUCCCCCUCUCUAAUCCUUGCUACCUGGGUGAG-AGUGCUAUCUGAAUGCAAUGCACCUGGGCAAGGAUUCUGAGAGCGAGAGCU
AAWR02023860.1/13036-13125 UUCUGGCUCCCCCUCUCUAAUCCUUGCUACCUGGGUGAG-AGUGCUUUCUGAAUGCAAUGCACCUGGGCAAGGAUUCCGAGAGGGAGAGUG
AAWR02023860.1/12501-12589 AUUCUGCUCUCCCUCUCUCAUCCUUCGUCCCUGGGUGAG-AGUGCUUUCCGAAUGCAAUGCACCUGGGCAAGGAUUCCAGAGGGCGAGG-C
AF198097.2/14653-14742     GCUCUGCUCUUCCUCUCUAAUCCUUUGUCCCUGGGUGAG-AGUGCUUUCUGAAUGCAAUGCACCCGGGCAAGGAUUCUGAGAGGGUGAGCC
AC231645.2/57092-57181     GCUCUGCUCUUCCUCUCUAAUCCUUUGUCCCUGGGUGAG-AGUGCUUUCUGAAUGCAAUGCACCCGGGCAAGGAUUCUGAGAGGGUGAGCC
AC231645.2/61969-62058     GCCCUGCUCCCCCUCUCUAAUCCUUGCUAUCUGGGUGCU-AGUGCUGGCUCAAUGCAAUGCACCUGGGCAAGGAUUCAGAGAGGGGGAGCU
AC207100.2/91733-91822     GCCCUGCUCCCCCUCUCUAAUCCUUGCUAUCUGGGUGCU-AGUGCUGGCUCAAUGCAAUGCACCUGGGCAAGGAUUCAGAGAGGGGGAGCU
AAFC03070558.1/65597-65508 UGCCCUGCCCACCCCUCUAAUCCUUGCUCUCUGGGUGCU-AGUGCUGUCUCCAUGCAAUGCACCUGGGCAAGGAUUCAGAGAGGGUGGGCU
AL663104.17/11455-11365    CCUCUGCUCCCCCUCUCUAAUCCUUGCUAUCUGGGUGCUUAGUGCUAUCUCAAUGCAAUGCACCUGGGCAAGGGUUCAGAGAAGGUGAGCU
AL663104.17/15743-15654    UGCUUGCUCCCCCUCUCGAAUCCUUGGAACCUAGGUGUG-AAUGCUGCUUCAGUGCAACACACCUGUUCAAGGAUUCAAAGAGGCUGAGCC
AAHY01206841.1/10272-10361 UGCUUGCUCCCCCUCUCGAAUCCUUGGAACCUAGGUGUG-AAUGCUGCUUCAGUGCAACACACCUGUUCAAGGAUUCAAAGAGGCUGAGCC
ABRN01086721.1/2503-2592   UGUCUGCUCCCCCUCUCGAAUCCUUGGAACCUAGGUGUG-AGUGCUGCUCUAGUGCAACACACCUAUUCAAGGAUUCAAAGAGGCUGAGCC
AAFC03003598.1/91130-91041 UGUCUGCUCCCCCUCUCGAAUCCUUGGAACCUAGGUGUG-AGUGCUGUUCUAGUGCAACACACCUAUUCAAGGAUUCAAAGAGGCUGAGCC
AC207100.2/86095-86184     UGUCUGCUCCCCCUCUUGAAUCCUUGGAACCUAGGUGUG-AGUGCUAUUUCAGUGCAACACACCUAUUCAAGGAUUCAAAGAGGCUGAGCC
AC231645.2/56325-56414     UGUCUGCUCCCCCUCUUGAAUCCUUGGAACCUAGGUGUG-AGUGCUAUUUCAGUGCAACACACCUAUUCAAGGAUUCAAAGAGGCUGAGCC
AF222686.1/111936-112025   UGUCUGCUCCCCCUCUUGAAUCCUUGGAACCUAGGUGUG-AGUGCUAUUUCAGUGCAACACACCUAUUCAAGGAUUCAAAGAGGCUGAGCC
ABGA01112817.1/1234-1323   UGUCUGCUCCCCCUCUCGAAUCCUUGGAACCUAGGUGUG-AGUGCUAUUUCAGUGCAACACACCUAUUCAAGGAUUCAAAGAGGCUGAGCC
AAWR02023860.1/11754-11843 UGUCUGCUCCCCCUCUCGAAUCCUUGGAACCUAGGUGUG-AGUGCCAUUUCAGUGCAACACACCUAUUCAAGGAUUCAAAGAGGCUGAGCC
AAEX03026348.1/14125-14214 UAUCUGCUCCCCCUCUCGAAUCCUUGGAACCUAGGUGUG-AGUGCUAUUUCGGUGCAACACACCUAUUCAAGGAUUCAAAGAGGCUGAGCC
AABR05175918.1/22621-22710 GCUCUGCUCGUCCUCUCUAAUCCUUUGUCCCUGGGUGAA-AAUGCUAUUUGUAUGCAAUGCACCCGGGCAAGGAUUUGGGGAAGGUAAGCC
#=GC SS_cons               ::::::<<<----<<<<-<<<<<<<-<<---<<<<<<--.--<<<_________>>>--->>>>>>>>->>>>>>>---->>>>-->>>::
#=GC RF                    uuucuGCuCccCCcCucuAAUCCUUgcuaCCcgGGUGag.AGUGCUaUuUgAaUGCAAugCACCcgggCAAGGAUUCagAgaGgguGaGCu
//
# STOCKHOLM 1.0

#=GF AC   RF01904
#=GF ID   HOTAIR_1
#=GF DE   HOTAIR conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   44.00
#=GF TC   48.30
#=GF NC   43.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.14 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   20393566
#=GF RT   Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer
#=GF RT   metastasis.
#=GF RA   Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T,
#=GF RA   Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver
#=GF RA   MJ, Sukumar S, Chang HY
#=GF RL   Nature. 2010;464:1071-1076.
#=GF WK   HOTAIR
#=GF SQ   9


AAIY01412966.1/1772-1808   UAUUUUACUGUCCAAAGGAGUCAAUUAAUUAGCGCCU
AALT01140141.1/1488-1452   UAUUUUACUGUCCAAAGGAACCAAUUAAUUAGUGCCU
ABRQ01001830.1/1444-1408   UAUUUUACUGUCCAAAGGAAUCAAUUAAUUAACACCU
ABVD01271340.1/4487-4451   UAUUUUACCUUCCAAAGGAAUCAAUUAAUUAACGCCU
AC160979.2/198368-198403   UAUUUUACAGUCCA-AGGAAUCAAUUAAUUAGUGCCU
ACBE01235903.1/1845-1881   UAUUUUACUGUCCAGAGGAAUCAAUUAAUUAGUGCCU
DQ926657.1/1046-1010       UAUUUUACAGUCCAAAGGAAUCAAUUAAUUAGCGCCU
AACN010527833.1/198-162    UAUUUUACUGUCCAAAGGAAUCAAUUAAUUAGAGCCU
AAQR03076666.1/20712-20748 UAUUUUACAAUCCAAAGGAAUCAAUUAAUUAGAGCCU
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::
#=GC RF                    UAUUUUACuGUCCAAAGGAAUCAAUUAAUUAGcGCCU
//
# STOCKHOLM 1.0

#=GF AC   RF01905
#=GF ID   HOTAIR_2
#=GF DE   HOTAIR conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   66.80
#=GF NC   56.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.10 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   20393566
#=GF RT   Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer
#=GF RT   metastasis.
#=GF RA   Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T,
#=GF RA   Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver
#=GF RA   MJ, Sukumar S, Chang HY
#=GF RL   Nature. 2010;464:1071-1076.
#=GF WK   HOTAIR
#=GF SQ   11


DQ926657.1/965-897         GAGAUAGAGGUGCUUGGCCAGCUCUCUGGUCUUGUUA---ACAAGCCUCAUCAUAAAGAUGGAGAUGAUAAG
ABDC01092784.1/2249-2317   GAGAUAGAUGUGCAUGGCCAGCUAGCUGGUCUUGUUA---ACAAGCCUCAUCAUAAAGAUGGAGAUGAUAAG
ABRQ01001830.1/1360-1292   GAGAUAGAUGUGCAAGGCCAGUUCACUGGUCUUGUUA---ACAAGCCUCAUCGUAAAAAUGGAGAUGAUAAG
ABGA01242765.1/13298-13227 GAGAUAGAGGUGUGUGGCCAGCUCUCUGGUCUUGUUAAUAACAAGCCUCGUCAUAAAGAUGGAGAUGAUAAG
AANN01406764.1/2815-2747   GAGAUAGAUGUGCGUGGCCAGCCCGCUGGACUUGUUA---ACAAGCUUCAUCAUAAAGAUGAAGAUGAUAAG
AAQQ01620880.1/3048-2980   GAGAUAGAUGUGAGUGGCCAGCUCGCUGGUCUUGUUA---ACAAGCCUCACCAUAAAGAUGGAGAUGAUAAG
CAAA01172819.1/25533-25465 GAGAUAGAUGUGCGUGGUCAGAUCGCUGGUCAUGUUA---ACAAGCCUCGUCAUAAAGAUGGGGAUGAUAAG
AAIY01412966.1/1867-1934   GAGAUAGAUAUGUGUGGCCAG-UCUCUGGUGCUGUUA---ACAAGCCUCAUCAUAAAGAUGGAGAUGAUAAG
AACN010527833.1/118-53     GAGAUAGAUGAGCGCGGCUGGC---CCGGCCUUGUUA---ACAAGCGUCCUCAUAAAGAUGCAGCUGAUAAG
AAQR03076666.1/20792-20860 GAGAUAGAUGUGCGUGGCCAGCUCGCUGGUCUUGUUA---ACAAGCCUCGUCAUAAAGAUGGAAAUGAUAAG
AAPE02030940.1/7322-7390   GAGAUAGAUGUGCUGGGCCAGCUUGCUGGUCUUGUUA---ACAAGCCUCGUCAUAAAGAUGAAGAUGAUAAG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::...::::::::::::::::::::::::::::::::
#=GC RF                    GAGAUAGAUGUGcguGGCCAGCUCgCUGGUCUUGUUA...ACAAGCCUCaUCAUAAAGAUGGAGAUGAUAAG
//
# STOCKHOLM 1.0

#=GF AC   RF01906
#=GF ID   HOTAIR_3
#=GF DE   HOTAIR conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   80.00
#=GF TC   92.00
#=GF NC   68.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.68 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   20393566
#=GF RT   Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer
#=GF RT   metastasis.
#=GF RA   Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T,
#=GF RA   Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver
#=GF RA   MJ, Sukumar S, Chang HY
#=GF RL   Nature. 2010;464:1071-1076.
#=GF WK   HOTAIR
#=GF SQ   17


AACN011070975.1/185-88       UUAUAAGGAAGGCGUCG-GUCCUCCAUUUCAGCCUUUCUUUCUGCCAGGACGU-GGCCGUAGCAUUUCUAGUCUCGUAAACACUGGACUCUUUGGGGCCU
AAFC03010049.1/159-62        UUAUAAGGAAGGCGUCG-GUCCUCCAUUUCAGCCUUUCUUUCUGCCAGGACGU-GGCCGUGGCAUUUCUGGUCUUGUAAACACUGGAGUUUUAGGGGCCU
AAHY01125231.1/162411-162314 UUAUAAGGAAGGCGUCG-GUCCUCCAUUUCAGCCUUUCUCUCUGGAAGGACUU-AGCGCUGGCAUUUCUGGUCUUGUAAACACAGGACUUUUUUUUUUUU
AAIY01410415.1/2041-2138     UUAUAAGGAAAGCGUCG-GUCCUCCAUUUCAGCCUUUCUCUCCGCCAAGACGU-GGCCGUAGCAUUGCUGGUCUUGUAAACAUCGAUCUCUUUGGGGCCU
AAKN02014967.1/8229-8133     UUAUAAGGAAGGCGACA-GUCCUCUGUUUCAGCCUUUCUCUCCAGAAGGACU-U-GCAGUGGUAUUUCUGGUCUUGUAAACACUGGACUGUAUGGGACUU
AAPY01653817.1/363-266       UUAUAAGGAAGGCGUCG-GUCCUCCAUUUCAGCCUUUCUCUCUGCCAGGACGU-GGCCGUGGCAUUUCUGCUCUUGUAAACACCAGGCUCUUUGGGGCCU
AAQQ01620880.1/606-508       UUAUAAGGAAGGCGUCG-GUCCUCCAUUUCAGCCUUUCUCUCCAGAAGGACGCUGGCAGUGGCAUUUCUCAUCUUGUAAACACUGGAUUCUAUGGGACAU
AAWR02031290.1/184811-184909 UUAUAAGGAAGACGUCGGGUCCUCCAUUUCAGCCUUUCUUUCUGCCAGGACGC-GGCCGUGGCAUUUCUGGUCUUGUAAACACUGGACUCUUCGGGGCCU
ABRN01244786.1/827-730       UUAUAAGGAAGGCGUCA-GUCCUCCAUUUCAGCCUUUCUUUCUGCCAGGACGU-GGCCGUGGCAUUUCUGGUCUUGUAAACACUGGACUCUUUGGGGCCU
ABRO01112174.1/1737-1639     UUAUAAGGAAGGCGUCGGGUCCUCCAUUUCAGCCUUUUUCUCUAGAAGGAAGC-AGCAGUGGCAUUUCUGGUCUUGUAAACACUGGACUCGGUGAGACUU
ABRP01034310.1/2254-2157     UUAUAAGGAAGGCGUCGGGUCCUCCAUUUCAGUCUUUCUUUCUGCCAGGACGU-GGCCGUGGCAUUUCUGGUCU-GUAAACACUGAACUCUUUGGGGUCU
ABRQ01001829.1/8553-8456     UUAUAAGGAAAGCGUGG-GUCCUCCAUUUCAGCCUUUCUCUCUGCCAGGAUGU-GGCUGUGGCAUUUCUAGUCUUGUAAACACUGGUCUCUUUGGGAUCU
ABVD01271340.1/2114-2017     UUAUAAGGAAGGCGUCG-GUCCUCCAUUUCAGCCUUUCUCUGUGCCAGGACGU-GGCCAUGGCAUUUCUGGGCUUGUAAACACCGGACUCUUUGGGGUCU
AC116663.1/72317-72412       UUAUAAGGAAGGCGUCG-GUCCUCCAUUUCAGCCUUUCUCUCAGGAAGGACUU-AGCGCUGGCAUUUCUGGUCUUGUAAAUACAGGACUUUUUUUUUU--
DQ926657.1/411-315           UUAUAAGGAAGGCGCCG-GUCCUCCAUUUCAGCCUUU-UCUCUGCCAGGACGC-GGCCGUGGCAUUUCUGGUCUUGUAAACAUCAGACUCUUUGGGGCCU
AAQR03076666.1/23108-23204   UUAUAAGGAAGGCGUCG-GUCCUCCAUUUCAGCCUU-CUCUCUGCCAGGACGU-GGUCGUGGCAUUUCUGGUCUUGUAAACACCGGACUCUUUGGGGCCU
AAGU03007240.1/26328-26425   UUAUAAGGAAAGCGUCG-GUCCUCCAUUUCAGCCUUUCUCUCUGCCAGGACGU-GGCCGUAGCAUUUCUGGACUUGUAAACACCGGUCUCUUUGGGGCCU
#=GC SS_cons                 :::::::::::::::::.:::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UUAUAAGGAAGGCGUCG.GUCCUCCAUUUCAGCCUUUCUcUCuGccAGGACGU.GGCcGUGGCAUUUCUGGUCUUGUAAACACuGGaCUcUuUGGGgccU
//
# STOCKHOLM 1.0

#=GF AC   RF01909
#=GF ID   CDKN2B-AS
#=GF PI   ANRIL
#=GF DE   CDKN2B antisense RNA 1 intronic convserved region
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; RNAz; Eberhardt R
#=GF GA   75.00
#=GF TC   83.40
#=GF NC   37.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.86 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   20386740
#=GF RT   Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate
#=GF RT   with ANRIL Expression.
#=GF RA   Cunnington MS, Santibanez Koref M, Mayosi BM, Burn J, Keavney B
#=GF RL   PLoS Genet. 2010;6:e1000899.
#=GF RN   [2]
#=GF RM   20541999
#=GF RT   Molecular interplay of the noncoding RNA ANRIL and methylated histone H3
#=GF RT   lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a.
#=GF RA   Yap KL, Li S, Munoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, Gil J, Walsh
#=GF RA   MJ, Zhou MM
#=GF RL   Mol Cell. 2010;38:662-674.
#=GF RN   [3]
#=GF RM   21151178
#=GF RT   Long non-coding RNA ANRIL is required for the PRC2 recruitment to and
#=GF RT   silencing of p15(INK4B) tumor suppressor gene.
#=GF RA   Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, Xiong Y
#=GF RL   Oncogene 2010;0:0-0.
#=GF CC   CDKN2B-AS, also known as ANRIL (antisense non-coding RNA in the INK4
#=GF CC   locus) is a long non-coding RNA consisting of 19 exons, spanning 126.3kb
#=GF CC   in the genome, and spliced product is a 3834bp RNA. It is located within
#=GF CC   the p15/CDKN2B-p16/CDKN2A-p14/ARF gene cluster, in the antisense
#=GF CC   direction. Single nucleotide polymorphisms (SNPs) which alter the
#=GF CC   expression of CDKN2B-AS are associated with many diseases, including
#=GF CC   coronary artery disease, diabetes and many cancers [1]. It binds to
#=GF CC   chromobox 7 (CBX7) within the polycomb repressive complex 1 and to SUZ12,
#=GF CC   a component of polycomb repression complex 2 and through these
#=GF CC   interactions is involved in transciptional repression [2,3].
#=GF WK   CDKN2BAS
#=GF SQ   25


ABRN01430132.1/22538-22687   UCCUCAGACCUUGCUUCCCUCCUCCUUUCUCACUGUAGA-GAAACAGGAAGUGUUGUUUAUUAAUA-AGCCUGACCAGGGUCACACCCAAGGUAGUAACCGA--GUUUU-ACUUCUCCUGGUCUUGGGGAGAGGCUCAAGGAUCAGGGACAAGCU
ABRP01140997.1/60-207        UCCUCAGA-CUUGCUUCCCUCCUCCUUUCUCACUGUAGA-AAAACAGGAAGAGAUGUUUAUUAAUA-AGACUGACUGGGGUCAUGCCUAAAACGAUAUCAGA--UUUUU-AUCUCUCUUGGGUUUAGGAA-UGGUUCUAGGAUCAAGGACUAUAC
AAGV021004046.1/584-733      UCCUCAGACCUUGCUUCCCUCCUCUUUUCUCACUGUGGA-GAAACAGGAAGCGAUGUUUAUUAACA-AGAUUGACUGGGGUCACACCCAAGGCAAUAUCAGA--UUAUU-ACCUCUCCUGUGCCUGGUAAGAGGUUCAAGGAUCGAGGACAAGCU
ABGA01074202.1/20086-19937   UCCUCGGACCUUGCUGCCCUCCUCCUUUGUCACUGUGGA-GAAACAGGAAGGAAUGUUUAUUAGCA-AGACUGACUGGGGUCACACCCAAGGCAAUAUCAGG--UUUUU-ACCUCUCCCAGGCCUGGGAAGAGGUUCAAGGAUCAAGGACAAGCU
AALT01488511.1/3140-3005     UCAUUGUGCCUUGCUUCCCUCCCCU----GCACUAUAGA-GAA-GAGGAAGGAAACUUU---AAUA-AGACAAAAUCUGUUCACACCCAAGGCAAUAUCAGA--UCUUU-AUACCUCGUAGGCUU------AAGUUCCAAGGUCAAGAACGAGUU
AL844161.18/39484-39632      UCCUCGGACCUUGCUUCCCUCCUCCUCUGUCGUUGUGGA-GAAACAGGAAGGAAUGUUUAUUAACA-AGGCUGGCUGGGGCCACACCCAAAGCAAUAUCAGA--GUUUU-ACCUCUCCUGGGCCUGGGAAGAGGUCCAAAGAUCAAGGGC-AGCU
ABRT010153172.1/1197-1347    UGCUUGGACCUUGCUGCCCUCCUUCUUUGUCACUAUGGA-GACACAGGAAGGCAUGUUUAUUAGCAAAGACUGACUGGGGUCACACCCAAAACAAUAUCAGA--UUUUC-ACCUCUCCUGGACCUGGGAAGAGGUCCAAGGAUUGAGGACUAGCU
AAFC03086670.1/5381-5232     UCUUCAGAACUUGUUCCGCUUCUCCUUGCUCACUGGAGA-GAAACAGGAAGUGUUGUUUAUUAAUA-AGCCUGACCAGGGUCACACCCAAGGCAAUAUCAGG--GCUUU-ACCUCUCCUGGGCUUGGGGAGAGGUUCAAAGAUCAAGGAUAUGCU
ABVD01288334.1/5284-5433     UCCCUGGACCUUGCUUCCCUCCUCCCUUCUCACUAUGGA-GAAACAGGAAGGGAUGUUUAUUAACA-AAGCUGACUGAGGUCACGCCCAAGGCAAUAUCAGG--UUAUA-ACCUCUCAUGGGCCUGGCAAGAAGUUCAAGGAUCGAGGGCAAGCU
AAQQ01036574.1/349-499       -CCUCCAACCUUGUUUCCCUCCUCCUUUGUCACUGUGGA-GAAACAGGAAGGAAUGUUUAUUAAAAAAGGCUGACUAGGGUCACACCCAUAGUAAUAUCAGA--UUUUUAACCUCCCCUGGCCUUGAGAAGAGGUUCAAAGAUCAGGGCCCAGCU
AAIY01523762.1/1681-1550     UCCUUGGGCCUUGCUUCCCUCCUCCUUUCUUGCUGCGGA-GAAACAGAAG-------------------GCUGAUGUGAGUCA--CUCAAAGCAGUAUCCAAACCCUUU-GCAUCUCCUGGGUCUAGAAAGGAAUCCAAGGAGCAAGGAUAAGCU
ABDC01122139.1/636-785       UCCUAGGACCUUGCCUCUCUCCUCCUCUGUCACUGUGGA-GAAACAGGAAGUAAUAUUUAUUAACA-GCUCUGACUGGGGGCACGCCCAAAGCAAUAUCAGA--UUUUC-ACCUCUCCUGGGCCUGGGAAGAGGUUCAAGGAUCAAGGACAAGCU
AAWR02015924.1/45272-45421   UCCUCGGACCUUGCUUCCCUCCUCCUUUCUCACUGUAGA-GAAACAGGAAGGGAUGUUUAUUAAUA-AGACUGACUGGGGUCACACCCAAGGCAAUAUCAGA--UAUUU-ACCUCUCCUGGGCUUGGGAAGAGGUUCAAGGAUCAACAACAAGUU
AADA01262132.1/3267-3118     UCCUCGGACCUUGCUGCCCUCCUCCUUUGUCACUGUGGA-GAAACAGGAAGGAAUGUUUAUUAGCA-AGACUGACUGGGGUCACACCCAAGGCAAUAUCAGG--UUUUU-ACCUCUCCCAGGCCUGGGAAGAGGUUCAAGGAUCAAGGACAAGCU
AACN010953971.1/399-548      UCCUCAGACCUUGCUUCCCUCCUCUUUUCUCACUGUAGG-GAAACAGGAAGUCAUGUUUAUUCAUA-AGAUGGACUGGGAUCACACCCAAGGCAAUAUCAAA--CCUUU-ACCUUUUCUGGGCUUGGGAGGAUGUGCAAGGAUCAAGGACAAGCU
ABRQ01242774.1/3143-3270     UCCUGUUGCCUUGGUUAACUCCUUUCUUCUCACUGUGGA-GAAACAGGAAGU------------------UUGAUGGGGGU--UUCCCAAGGCAGUAUGUGA--GCUCU-ACUUCUUCUGGUCCUAG---GAAGUACAGAUGUCAAGGAUAAACU
AANG01430098.1/293-442       UCCUCAGACCUUGCUUCCCUCCUCUCUUCUCACUGUAGG-GAAACAGGAAGUCAUGUUGAUUAAUA-AGACUGCCUGGGAUCACACCCAAGGCAAUGUCGAA--UCUUU-ACCUCUUCUGGGCUUGGGAAGAGGUGCAAAGAUCAAGGGCAAGCU
ABRR01116628.1/488-621       UCCUCAGAGC----------------GUCUCACUGUAGA-GCAACAGGAAGUGUUGUUUAUUAAUA-AGCCUGACUGAGGUCACACCCAAGGCAACAUCAGA--GCUUC-ACCUCUCUUGGGCUUGGGGAGAGGUUCAAGGAUCAAGGACAAGCU
AAKN02003584.1/23783-23931   -CCUCUGCCCCUGCUUCCCUCCUCUUUUGUCGCCAUGAAGCAAACAGGAAGGAAUGUUUAUUAGCA-GGGCUGACUGGGGUCACACCCAACGCAGUAUCAGA--UUUUU-ACCUCUGCUGGGCUUGGGAAGAGGUUCAAGGAUCAAGGCC-AGCU
CT027658.2/93561-93710       UCCUGGGACCUUGCUGCCCUCCUCCUUUGUCACUGUGGA-GAAACAGGAAGGAAUGUUUAUUAGCC-AGACUGACUGGGGUCACACCCAAGGCAAUAUCAGG--UUUUU-ACCUCUCAUGGGCCUGGGAAGAGGUUCAAGGAUCAAGGACAAGGU
AAPE02035629.1/89741-89889   CCCUUGCACCUUGCUUCCGUCCUCCUUUCUCACUGUAGA-GAAACAGGAAGGGAU-UUUAUUAAUA-AGAAUGACUGGGGUCACACUUAAAACAACAUCAGA--UUUUG-AUCUCUUCUGGGCUUGGAAAAUGGUUCAAGGAUCAAGGAGCAGCU
AABR05126888.1/7653-7801     UCCUCGGACCUUGCUUCCCUCCUCCUCUGUCAUUGUGGA-GAAACAGGAAGGAAUGUUUAUUAACA-AGGCUGGCUGGGGUCACACCCAAAGCAAUAUCAGA--GUUUU-ACCUCUCCUGGGCCUGGGAAGAGGUCCAAAGAUCAAGGGC-AGCU
AAGW02033082.1/8439-8588     UCCUCCGACCUUGCUUCCCUCCUCUUCUGUCACUGUGGA-GAAACAGGAAGGAAUGUUUAUUAACA-AGGCUGGUUGGGGUCACAUCCAAGGCAAUAUCAGC--UUUUU-ACCUCUUCUGGGCCUGGGAAGUGGUCCAAGGAUCAAGGACAAGCU
AAQR03014001.1/23581-23433   UCCU-GGACCUUGCCUCCCUCCUCCUCUGUCACGGUGGA-GAAACAGGAAGUAAUGUUUAUUAACA-ACACCGAUUGGGGUCACACCCAAGGCCAUAUCAGA--UUUUC-ACAUCUUCUGGGCCUUGGAAGAGGUUCAAGGAUCAAGGACAAGCU
AAGU03018860.1/104890-104760 UCCUCAGGCCUUGCUUCCCUCCUCCUUUCUCACUGUGGA-GAAACAGGAAGG------------------CUGACGAGGG--ACGCCUAAGGCAGUAUCAGA--UCUCU-ACCUCUCCUGGGCCUGGGAAGAAGUGCAAGGAUCAAGGAUAAGCU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::..:::::.:::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UCCUcggaCCUUGcUuCcCUCCUCcUuUcUCACUGUgGA.GAAACAGGAAGggaUGUUUAUUAauA.AGaCuGacugGGGUCACaCCCAAgGCAaUAUCaGa..uuUUu.ACcUCUccUGGGCuUGGGAAGagGUuCaAGGAUCAAGGacaAGcU
//
# STOCKHOLM 1.0

#=GF AC   RF01910
#=GF ID   mir-506
#=GF DE   microRNA mir-506
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   78.00
#=GF TC   84.80
#=GF NC   62.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000130;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [4]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [5]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [6]
#=GF RM   15965474
#=GF RT   Identification of hundreds of conserved and nonconserved human microRNAs
#=GF RA   Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A,
#=GF RA   Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z
#=GF RL   Nat Genet. 2005;37:766-770.
#=GF RN   [7]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [8]
#=GF RM   18215311
#=GF RT   miRNAminer: a tool for homologous microRNA gene search
#=GF RA   Artzi S, Kiezun A, Shomron N
#=GF RL   BMC Bioinformatics. 2008;9:39.
#=GF RN   [9]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [10]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   Mir-506_microRNA_precursor_family
#=GF SQ   8


AC069023.5/118895-118809   CAAUAGACACCCAUCGUGUCUUUUGCUCUGCAGUCAGUAAAUAUUUUUUUGUGAAUGUGUAGCAAAAGACAGAAUGGUGGUCCAUUG
EF444997.1/38685-38771     CAAUAGACACCCAUCGUGUCUUUUGCUCUGCAGUCAGUAAAUAUUUUUUUGUGAAUGUGUAGCAAAAGACAGAAUGGUGGUCCAUUG
AC193096.1/9822-9908       CAAUAGACACCCAUCGUGUCUUUUGCUCUGCAGUCAGUAAAUAUUUUUUUGUGAAUGUGUAGCAAAAGACAGAAUGGUGGUCCAUUG
AL928580.4/7361-7447       CAAUAGACACCCAUCGUGUCUUUUGCUCUGCAGUCAGUAAAUAUUUUUUUGUGAAUGUGUAGCAAAAGACAGAAUGGUGGUCCAUUG
AANU01171359.1/25447-25533 CAAUAGACACCCACCUUGUCUUUUGCUCUGCAGUCAGUAAAUAUUUUUUUGUGAAUGUGUAGCAAAAGACAGAAUGGGGGUCCAUUG
AL845290.7/23172-23258     AAAUAGAUACCCACCAUGCCUUUUGCUCUGCACUCAGUAAAUAAUAAUUUGUGAAUGUGUAGCAAAAGACAGGAUGGGGAUCCAUUA
AABR05067213.1/58778-58864 AAAUAGAUACCCACCAUGCCUUUUGCUCUGCACUCAGUACAUAAUCAUUUGUGAAUGUGUAGCAAAAGACAGGAUGGGGAUCCAUUA
AACZ03075990.1/12398-12484 CAAUAGACACCCAUCGUGUCUUUUGCUCUGCAGUCAGUAAAUAUUUUGUUGUGAAUGUGUAGCAAAAGACAGAAUGGUGGUCCAUUG
#=GC SS_cons               <<<<-<<<--<<<<<-<<<<<<<<<<<--<<<-<<<-<<<<______>>>>>>>->>>-->>>>>>>>>>>>>->>>-->>>->>>>
#=GC RF                    caauAGacACCCacCguGuCuuuuGCuCUgCaguCaGuaaaUAuUuuuuuguGaAuGuGUaGCaaaaGaCaGgAuGGuGguCCauug
//
# STOCKHOLM 1.0

#=GF AC   RF01911
#=GF ID   MIR2118
#=GF DE   microRNA MIR2118
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   85.00
#=GF TC   87.00
#=GF NC   84.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000745;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19103661
#=GF RT   Characterization and expression profiles of miRNAs in rice seeds
#=GF RA   Xue LJ, Zhang JJ, Xue HW
#=GF RL   Nucleic Acids Res. 2009;37:916-930.
#=GF RN   [2]
#=GF RM   19584097
#=GF RT   Clusters and superclusters of phased small RNAs in the developing
#=GF RT   inflorescence of rice
#=GF RA   Johnson C, Kasprzewska A, Tennessen K, Fernandes J, Nan GL, Walbot V,
#=GF RA   Sundaresan V, Vance V, Bowman LH
#=GF RL   Genome Res. 2009;19:1429-1440.
#=GF RN   [3]
#=GF RM   18687877
#=GF RT   A diverse set of microRNAs and microRNA-like small RNAs in developing rice
#=GF RT   grains
#=GF RA   Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C
#=GF RL   Genome Res. 2008;18:1456-1465.
#=GF WK   MicroRNA
#=GF SQ   7


AK107452.1/44-233          CUUGGGAAGAGGAAGAAAGAGAGGCUCCAAGAGUAGUAGGACUGGGAACAUAUGAGAAAGCAUGAGCUCUAUCCAUCUAUCCAUCCCCUCCCAUUCGCUAGAAUGUUGCAGGUGGAGAUUUCGCUCUUAUGUUUUCUCGAUGCCUCCCAUUCCUAUCGUUCUUGGAACUUCCUUCCUCUUCCUUUUUUUU
ABXC01004286.1/22374-22204 GUGAGCUGGGAAGAGGAAGAGAGGGCCUAAGAGCAGUGGGAAUGGGAACAUGGAGGAAAGCCUAUCCUGU----------UUGUUUCCUCCU-----CCAGAAA--CAGAGGUGGAAGCUUGG-UCCGGUGUUU-CCCAAUGCCUCCCAUUCCUAUUGUUCUUAAGUGCUCCAUCCUUUUCCUUUUGGCU
AL606706.3/90986-90819     GCAGGGAAGAGGAAGAAAGAGAGACUCUAAGAGUGAUGGGAAUAGGAACAUGGAGGAAAGCCUAAAGCUAAA--------UUUUCUGCUC--------CAGUAU--UGGAGCUAGAGAUUUG----CUCAGUUUUCCCGAUGCCUCCUAUUCCUACCAAUCUUAGGUACUCCUUCCUCUUCCUUUUAGCU
EU963940.1/42-191          GUGAGCCAGGAAAAGGAUGAAAGAUUCUAAGAGCACUAGGAAUAGGAACAUGAAGGAAAGCAU------------------UAU----------------------UGUGCAUGGAGAUUUAGGCCUGAUGUUUUCCUGAUGCCUCCUAUUCCUAAGGCUCUUAGGUUCUCCUUCCCUUUCCUUAUGGCU
AP003219.3/56146-55997     GGCAGGGGCAAAGGAAGCAUGAGCUUGUGGGAGUUGUAGGAAUGGAUGCGUAGAGAAAGAAAUGAAAUCU----------------------------------------GAACCAGAUUUGUGAUUUGAUUCUUUCCUAUGACGUCCAUUCCAAUGAUUUCCAGUCGCUCCUUCCUUGACCCAAACUGC
AC135459.3/86834-87003     GCAGGGAAGAGGAAGAAAGAGAGCCUCUAAGAGCGAUGGGAAUAGGAACAUGGAGGAAAGCCUGAAGCUAAA--------UUUUCUACUC--------CAGUAU--CGGAGUUAGAAAUUUG--CUCUGCGUUUUCCCGAUGCCUCCUAUUCCUACCGAUCUUAGGUACUCCUUCCUCUUCCUUUAAGCU
CR855188.1/55094-54926     AUCAGGAAGAGGAAGAAA-AGAGGGUCUGAGAGCGGUGGGCAUGGGAACAUGGAGGAAAGCCCAAACUCU----------UCUUCGCCUC--------UAGAAC--UAGGGGCUGAGAUUUGGUUUCCUUGUUUUCCUGAUGCCUCCCAUGCCUAUUGUUCUCAGAUGCUCCUUCCUCUUCCUUUUGGUU
#=GC SS_cons               ::::::::<<<<<-<<<---<<<--<<<<<<<<<<-<<<<<<<<<<<-<<<-<-<<<<<<<_________..........__________........______..________________________>>>>>>>>->>>-->>>>>>>>>>>->>>>>>>>>>-->>>->>>->>>>>:::::::::
#=GC RF                    guuaGgaAGaagaAGaaaGAGAGguccugaGAgcggUaGGaAUGGGaACaUggAGGAAagcaUgAacUcU..........uuuUcucCUC........uAGaAu..uggAGaugGAGAUUUggguuuuauguuUUCCcgAuGCCuCCCAUuCCuAucguUCucaggugCUCCuuCCucuuCCUUuuaguU
//
# STOCKHOLM 1.0

#=GF AC   RF01912
#=GF ID   mir-2807
#=GF DE   microRNA mir-2807
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   95.00
#=GF TC   95.00
#=GF NC   94.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000826;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF RN   [2]
#=GF RM   20229201
#=GF RT   Novel microRNAs in silkworm (Bombyx mori)
#=GF RA   Cai Y, Yu X, Zhou Q, Yu C, Hu H, Liu J, Lin H, Yang J, Zhang B, Cui P, Hu
#=GF RA   S, Yu J
#=GF RL   Funct Integr Genomics. 2010;10:405-415.
#=GF WK   MicroRNA
#=GF SQ   7


BABH01003652.1/5395-5511 UCUCCAUAGCGUAAAAGUUAAGUCAAAUUUGUAUGGAGUUGGAACGUUUGCCUAUGUUUGCCGCUAGGGGCACUGUUCCAGCUGCAUACAAAUUUCAGGUAACUCUUACGUUAUCGA
BABH01037118.1/2260-2144 UCUCGAUAGCGUAAAAGUUAAGUCAAAUUUGUAUGAAGUUGGAACGCUUGCCUAUGUUUGCCGCUAGGGGCACUGUUCCAGCUGCAUACAAAUUUCAGGUAACUUUUACGGUUUCGA
AADK01031287.1/1688-1804 UCUCGACAGCGUAAAAGUUAAGUCAAAUUUGUAUGGAGUUGGAAUGUUUGCCUAUGUUUGCCCCGGGGGUCAUUGUUCCAGCUGCAUACAAAUUUCAGGUAACCUUUACGCUAUCGA
BAAB01052019.1/1046-930  UUUCGAUAGCGUAAAAGUUAAGUCAAAUUUGUAGGGAGUUGGAACGUUUGCCUAUGUUAGCCGCUAGGGGCGCUGUUCCAGCUGCAUACAAAUUUCAGGUAAUUUUUACGCUAUCGA
AADK01004249.1/5460-5576 UCUCGAUAGCAUAAAAGCUAACUCAAAUUUGUAGGGAGUUGGAACGUUUGCCUAUGUUUGUCGCUAGGGGCACUGUUCCAGCUGCAUACAAAUUUCAGGUAACUUUUACGCUGUCGA
BAAB01123010.1/2740-2856 UCUCGAUAGUAUAAAAGUUAACUCAAAUUUGUAUGGAGUUGAAACAGUUGCCUACGUUUGCCGCUAGGAACGCUGUUCCAACUGCAUACAAAUUUGAGUUAACUUUUACGCUGUCGA
BABH01026841.1/3762-3878 AACGUUCUCGAUAGCGUAAAACUAAAAUUUGUAUGGAGUUGGAACGUUUGCUUAUGUUUGCCACUAGGGGCGCUGUUCCAGCUGCAUACAAAUUUCAGUUAACUUUUACGCUAUGGA
#=GC SS_cons             ::::::::::::<<<<<<<<----<<<<<<<<<<<-<<<<<<<<<<--<<<<<--<<_____>>--->>>>>->>>>>>>>>>->>>>>>>>>>>---->>>>>>>>::::::::::
#=GC RF                  ucUcgAuAgcaUaaaaguuaAgUcaaauuuGuauGGaGuuGGaacguUuGccuAUGcUUGcCgCuAGgggCacuguuCCagCuGCauaCaaauuucAGguaacuuuuACGcUaUcGA
//
# STOCKHOLM 1.0

#=GF AC   RF01913
#=GF ID   mir-2778
#=GF DE   microRNA mir-2778
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   95.00
#=GF TC   98.50
#=GF NC   83.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000827;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF RN   [2]
#=GF RM   20229201
#=GF RT   Novel microRNAs in silkworm (Bombyx mori)
#=GF RA   Cai Y, Yu X, Zhou Q, Yu C, Hu H, Liu J, Lin H, Yang J, Zhang B, Cui P, Hu
#=GF RA   S, Yu J
#=GF RL   Funct Integr Genomics. 2010;10:405-415.
#=GF WK   MicroRNA
#=GF SQ   7


BABH01054017.1/649-747     UCACGGAGAAACUCACGGCAAAAGUUUUUUUGCAUAUCCUGCACAGUUUCAGUUCUCGCAGAGUACGCAAAAAA-CAAUUUUGACGUGAGUGCUCUACAG
AADK01008457.1/7807-7708   UCAUGGAGAAACUCACGGCAAAAGUUUUUUUGCAUAUCCUGCACAGUUUCAGUUCUCGCAGAGUACGCAAAAAAUCAAUUUUGACGUGAGUGCUCUACAG
BABH01054017.1/45-144      UCACGGAGACACUCACGGCAAAAGUUUUUUUGCAUAUCCUGCACAGUUUCAGUUCUCGCAGAGUACGCAAAAAAACAAUUUUGACGUGAGUGCUCUACAG
AADK01008457.1/11128-11029 UCACGGAGAAACUCACGGCAAAAGUUUUUUUGUAUAUCCUGCACAGUUUCAGUUCUCGCAGAGUACGCAAAAAAACAAUUUUGACGUGAGUGCUCUACAG
AADK01008457.1/7354-7255   UCAUGGAGAAACUCACGGCAAAAGUUUUUUUGCAUAUCCUGCACAGUUUCAGUUCUCGCAGAGUAGGCAAAAAAACAAUUUUGACGUGAGUGCUCUACAG
AADK01008457.1/7656-7557   UCACGGAGAAACUCACGGCAAAAGUUAUUUUGCAUAUCCUGCACAGUUUCAGUUCUCGCAGAGUACGCAAAAAAACAAUUUUGACGUGAGUGCUCUACAG
AADK01008457.1/6600-6501   UCACGGAGAAACUCACGGCAAAAGUUUUUUUGCAUAUCCUGCACAGUUUCAGUUCUCGCAGAGUACGCAAAAAAACAAUUGAGUAUUUACCUUUUGAUGU
#=GC SS_cons               :::::::::::<<<<<<-<<<<<<<<<<<<<<<-<<--<<<<--<<________>>->>>>-->>->>>>>>>>>>-->>>>>->>>>>>::::::::::
#=GC RF                    UCAcGGAGAAACucacgGCaaaaGuuuuuuuGcAuaUCCuGCACaGUUUCAGUUCuCGCaGAGuacgCaaaaaaaCAAuuuuGacgugaGugcUcuAcAg
//
# STOCKHOLM 1.0

#=GF AC   RF01914
#=GF ID   mir-932
#=GF DE   microRNA mir-932
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   55.00
#=GF TC   55.40
#=GF NC   53.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000588;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010;42:6-9.
#=GF RN   [2]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF RN   [3]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF RN   [4]
#=GF RM   18714353
#=GF RT   The silkworm (Bombyx mori) microRNAs and their expressions in multiple
#=GF RT   developmental stages
#=GF RA   Yu X, Zhou Q, Li SC, Luo Q, Cai Y, Lin WC, Chen H, Yang Y, Hu S, Yu J
#=GF RL   PLoS One. 2008;3:e2997.
#=GF RN   [5]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [6]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [7]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF RN   [8]
#=GF RM   18651924
#=GF RT   In silico prediction and characterization of microRNAs from red flour
#=GF RT   beetle (Tribolium castaneum)
#=GF RA   Singh J, Nagaraju J
#=GF RL   Insect Mol Biol. 2008;17:427-436.
#=GF WK   MicroRNA
#=GF SQ   5


BAAB01137739.1/1246-1337   GAGGGUGUUGAGGCUUCAAUUCCGUAGUGCAUUGCAGUGCAUGCUGCCACCU---GCAAGCAGUGCGGGAGUGAGGCUGAGGCAUGCCUUAACUA-
AAWU01016737.1/86715-86620 GAUCUUGUAAUGGCUUCAAUUCCGUAGUGCAUUGCAGUGUAUUUUUUCACCUACUGCAAGCAAUGUGGAAGUGAAGCUGAUUGCAAUGGAAAGCGC
AAJJ01002053.1/7802-7709   CGGAGUGC-GUGUCUUCAAUUCCGUAGUGCAUUGCAGUGUUUGUAGCAGCAGUCUGCAAGCAGUGCGGAAGUGAGGAUUCGUCUCUGCUAUCCUU-
AC004277.1/28838-28743     UUGGUUUUGAAGUUUUCAAUUCCGUAGUGCAUUGCAGUGUGUUUCAUUAUUUACUGCAAGCGCUGCGGAUUUGGCAACUUUGACGACCUUCAUCAU
AAGH01003759.1/5919-5824   UUGGUUUUGAAGUUUUCAAUUCCGUAGUGCAUUGCAGUGUGUUUAAUUAUUUACUGCAAGCGCUGCGGAUUUGGCAACUUUGACGACCUUCAUCAU
#=GC SS_cons               ::<<<<<<<<<<<<<<<<-<<<<<<<-<<<-<<<<<<<<____________>>>>>>>>>>>->>>>>>>->>>>>>>>>>>>->>>>::::::::
#=GC RF                    uaggucgcggcggccuCAAuuCCGuAGuGCAUUGCaGugUaUuUuauuAcuuaCuGCAAGCaaUgCGGaagUGaggccgccgccgaccuuaAuuau
//
# STOCKHOLM 1.0

#=GF AC   RF01915
#=GF ID   mir-2238
#=GF DE   microRNA mir-2238
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   81.80
#=GF NC   59.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000822;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode species
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   4


ABKE01003698.1/3164-3283   UCCUUUUUUCUGGUACCUAGUCUUUUCUCUU-UCCCGUUCACUCUUCUCGUCAGUCGAUGAUCGAAUAUAGAAUGACAGAACAGUGCGCGAGAAGGAAGACUAGCUUCCGUGUGAUAGUGU
ABKE01009364.1/1-103       ------------GGAACUAGUCUGCCGA--CUUCCCGUCUACUCCUUUCGUCA-UUGAU--ACGAAU-UCGAAUGACAAUCGAGUGGGUGAGAAGGAAGACUUGCUUCCUUGGUUGGUCAU
ABKE01002728.1/14129-14010 AAUUUUAUUCUGGUAUCUAGUCGAUCCUCUU-UCCCAUUCACUCUUCUCGUCAGUCGAUGAUUGAAUAUCGAAUGACAGAUCAGUGCGCGAGAAGGAAGACUAGCUUCCGUGAUGGUGUUU
ABKE01000098.1/36649-36530 GAUCUUUUUCUGGUAACUAGUCGAUCCUCUU-UCCCGUUCACUCUUCUCGUCAGUCGAUGAUUGAAUAUCGAAUGACAGAUCAGUGCGCGAGAAGGAAGACUAGCUUCCGUGAUAGUGUUC
#=GC SS_cons               :::::::::::<<---<<<<<<--<<-<<<<.-------<<<<--<<<-<<<<-<<<<<<______>>>>>>->>>>>>>-->>>>--->>>>->>-->>>>>>--->>::::::::::::
#=GC RF                    aauuUUuUUCUGGuAaCuaGuCuacccuCuc.UCCCgUucaCuCuucuCGuCaGucgaugAuuGAAuaucgaAuGaCagaucaGugcGcgaGaAggAAGaCuaGCUUCCgUGauaguguuU
//
# STOCKHOLM 1.0

#=GF AC   RF01916
#=GF ID   mir-988
#=GF DE   microRNA mir-988
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   65.00
#=GF TC   68.50
#=GF NC   43.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000724;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [2]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010;42:6-9.
#=GF RN   [3]
#=GF RM   18463636
#=GF RT   Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells
#=GF RA   Kawamura Y, Saito K, Kin T, Ono Y, Asai K, Sunohara T, Okada TN, Siomi MC,
#=GF RA   Siomi H
#=GF RL   Nature. 2008;453:793-797.
#=GF RN   [4]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [5]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF RN   [6]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF WK   MicroRNA
#=GF SQ   4


AAWU01031362.1/14278-14363       -----------GACCCGCUGCGGGUGUGUGCUUUGUGACAACGAGAUUCAGC--UUUGAAAUCAUCCCCUUGUUGCAAACCUCACGCUUGCGGUGGGGG-----
AAGE02017684.1/78061-77987       ----------------GCUGCGGGUGUGUGCUUUGUGACAAUGAGAUUCGGU---UCGAUAUCAUCCCCUUGUUGCAAACCUCACGCUUGCGGU----------
AE013599.4/8046473-8046377       CGGCG--GUACCGGGCAUUUUGGGUGUGUGAUUUGUAGCAAAGUGAUAUGUA--UUUG--AUCAUCCCCUUGUUGCAAACCUCACGCCAAAGAUGA-UCUGCGA
AAAB01008807.1/10005270-10005171 --GUGGAGCAUUGGACAUUGCCGGUGUGUGUUUUGUGACAAUGAGAUUUAAUAGUUUAAGUUCAUCCCCUUGUUGCAAACCUCACGCUGGCGGUGUUUCCGA--
#=GC SS_cons                     ..:::..::::<<<<<<<<<<-<<<<<<-<-<<<<<<<<<<-<-<<<_____.._________>>>->->>>>>>>>>>->->>>>>>->>>>>>-.>>>>:..
#=GC RF                          ..GuG..GuAucgggCacugcggGuGuGUGuuuuGugaCaauGaGauuuaau..UUUgAaaUCauCCCCuuGucgCaaaCCUCaCgCcugcgguGa.cccga..
//
# STOCKHOLM 1.0

#=GF AC   RF01917
#=GF ID   MIR2587
#=GF DE   microRNA MIR2587
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   68.00
#=GF TC   68.50
#=GF NC   65.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000835;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19767456
#=GF RT   Genome-wide Medicago truncatula small RNA analysis revealed novel
#=GF RT   microRNAs and isoforms differentially regulated in roots and nodules
#=GF RA   Lelandais-Briere C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C,
#=GF RA   Gouzy J, Crespi M
#=GF RL   Plant Cell. 2009;21:2780-2796.
#=GF WK   MicroRNA
#=GF SQ   4


CR954186.2/74768-74865  ---AGGUGUCAUGGUCAUUGUUGACCGUUCAUAUGAACCCUGCAAUAAC-----AUUGCAACUUGUGUGGGGUUCAUAUAACGGUCAACUGAGACCUUUGACAUCA----
AC126778.9/57788-57892  CGGUGGUGUCAUGGUCAUUGUUGACCGUUCAUAUGAACCCUGCAAUAGC-----AUUGCAGCUUGUGUGGGGUUCAUAUAACGGUCAACAGAGACCAUUGACAUCAAAGA
AC148719.51/27834-27725 CGAUGGUGUCAUGGUCAUUGUUGACCGUUCAUAGGAACCCUGCAAUUGCAAUGCAUUGUAGCUUGUGUGGGGUUCAUAUAACGGUCAACAGAGACCCUUGACAUAAAAAA
AC174327.15/38435-38539 CGGUGGUGUCAUGGUCAUUGUUGACCGUUCAUAUGAACCCUGCAAUAGC-----AUUGCAGCUUGUGUGGGGUUCAUAUAACGGUCAACAGAGACUCUUGACAUCAAAGA
#=GC SS_cons            :::::<<<<<<-<<<<-<<<<<<<<<<<<-<<<<<<<<<<--<<---<_....._______>--->>-->>>>>>>>>>>>>>>>>>>>>>->>>>-->>>>>>::::::
#=GC RF                 cGguGguGuCaUGGuCAcuGuuGaCCGuuCauauGaaCCCUGCaAUagC.....AUUGcAgcUUGuGUGGGGuuCauauaaCGGuCaaCagAGaCCuUuGaCaccAAAgA
//
# STOCKHOLM 1.0

#=GF AC   RF01918
#=GF ID   mir-1249
#=GF DE   microRNA mir-1249
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   115.20
#=GF NC   53.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000667;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [2]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [3]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [4]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [5]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [6]
#=GF RM   17989215
#=GF RT   RNA sequence analysis defines Dicer's role in mouse embryonic stem cells
#=GF RA   Calabrese JM, Seila AC, Yeo GW, Sharp PA
#=GF RL   Proc Natl Acad Sci U S A. 2007;104:18097-18102.
#=GF RN   [7]
#=GF RM   18945293
#=GF RT   Annotation of 390 bovine miRNA genes by sequence similarity with other
#=GF RT   species
#=GF RA   Strozzi F, Mazza R, Malinverni R, Williams JL
#=GF RL   Anim Genet. 2009;40:125.
#=GF RN   [8]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   4


ABGA01165301.1/6990-7095   CUCAGAUUAUUGUUGGCAUGGGGAGGAGGGAGGAGAUGGGCCAAGUUCCCUCUGGCUGGAACGCCCUUCCCCCCCUUCUUCACCUGGCGAACUCCUACUCGUCCUU
AL008718.23/22697-22592    CUCAGAUUAUUGUUGGCAUGGGGAGGAGGGAGGAGAUGGGCCAAGUUCCCUCUGGCUGGAACGCCCUUCCCCCCCUUCUUCACCUGGCGAACUCCUACUCGUCCUU
AANU01293572.1/34858-34753 CUCAGAUUCUUGUUGGCAUGGGGAGGAGGGAGGAGAUGGGCCAAGUUCCCUCUGGCUGGAACGCCCUUCCCCCCCUUCUUCACCUGGCGAACUCCUACUCGUCCUU
AAFC03104372.1/35525-35420 CUCAGAUUCUUGUUUGCAUGGGGAGGAGGGAGGAGAUGGGCCACGUUCCCUCUGCCUGGAACGCCCUUCCCCCCCUUCUUCACCUAGCGAACUCCUACUCGUCCUU
#=GC SS_cons               :::::::::::<<<-<<--<<<<<<<<<<<-<<-<<-<<<<---<<<<<________>>>>>>>>>->>->>>>>>>>>>>->>-->>->>>::::::::::::::
#=GC RF                    CUCAGAUUaUUGuugGCAUGGGgaGgaGGGAGGAGaUGGGCCAaGuuCCCUCUGgCUGGaaCGCCCUuCCCCCCCucCucCACCUgGCGaaCUCCUACUCGUCCUU
//
# STOCKHOLM 1.0

#=GF AC   RF01919
#=GF ID   mir-1419
#=GF DE   microRNA mir-1419
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   48.20
#=GF NC   37.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000570;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF WK   MicroRNA
#=GF SQ   5


AAPN01388726.1/410-301   UCCUGGGCAGAGUGAUGGUGUCACGCACAGUGCCGGGAGGUGGCAUCAGGUGCUAACUCGUUUCCUGAUAUCAUCACCCAGCAUCGCGCAUGUCCAUCAAGCACCUUGGG
AAPN01082172.1/4253-4144 UCCGGGGCAGGGUGAUGGUGUCACAUGCAUUACUGAGAGAUGUCAUCACACGCUACCUCAUUCUGUGAUGUCAUCACUCAGUACCGCACAUGUCCACCGAGAGCCGCGGG
AAPN01135969.1/4053-4158 UCCAGGGCAGAUUGAUGGUGUCACACACAAUGCUGGGAGACGUCAUCACGUGCUACCU---CCGGUGAUGUCAGCACCCAGCACCAUG-AUGUCCACCGAGAACAACGGG
AAPN01135970.1/4702-4809 UCCUGGGCACAGUGAUGG--UCAUGCACAGUUCUGGGAGAUGUUAUCACGUGCUAUCUCAUUCGGUGAUAUCGUCACCCAGCACCGCACAUGUCCAUCAAGAGCCGCGGA
AAPN01135971.1/4068-4177 UCCUGGGCACAGUGAUGGUGUCAUGCACAGUGCUGGGAGAUGUUAUCACGUGCUAUCUCAUUCAGUGAUAUUGUCAUCCAGCACAGCACAUGUCCAUCAAGAGCCACGGG
#=GC SS_cons             ::::(((((,,,,,,,,<<<<___>>>>,<<<<<<<<-<<<<-<<<<<<_______________>>>>>>->>>>->>>>>>>>,,,,,,))))):::::::::::::::
#=GC RF                  UCCuGGgCagAgUGAUGGuGuCAcaCaCAgugCuGGGAGauGucauCacgUGCUAuCUCaUUcuguGaugUCauCACCCaGcaccgcaCAuGuCCAuCaAGagCcacGGG
//
# STOCKHOLM 1.0

#=GF AC   RF01920
#=GF ID   mir-764
#=GF DE   microRNA mir-764
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   92.10
#=GF NC   51.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000707;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [2]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [3]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [4]
#=GF RM   18215311
#=GF RT   miRNAminer: a tool for homologous microRNA gene search
#=GF RA   Artzi S, Kiezun A, Shomron N
#=GF RL   BMC Bioinformatics. 2008;9:39.
#=GF RN   [5]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF WK   Mir-764_microRNA_precursor_family
#=GF SQ   6


AACN010276644.1/993-884      UAUUUUCAAUCUAAAAUCUAGGAGGCAGGUGCUCACUUGUCCUCCUCCGUGCUUGGAAAAUACAGGGAGGAGGCCAUAGUGGCAACUGUCACCAUGAUUGAUUUCGUUGG
BX005219.12/49495-49602      UCAACACAAUCU-GAAUCUUGGAGGCAGGUGCUCACAUGUCCUCCUCCAUGCUUA-UAAAUACAUGGAGGAGGCCAUAGUGGCAACUGUCACCAUGAUUGAUUUCGUUGG
AANU01095684.1/3694-3803     UAUUUUCAAUCUAAAAUCUAGGAGGCAGGUGCUCACUUGUCCUCCUCCAUGGUUGGAAAAUACAGGGGGGAGGCCAUAGUGGCAACUGUCACCAUGAUUAAUUUCGUUGG
AADA01065421.1/1907-2016     UAUUUUCAAUCUGAAAUCUAGGAGGCAGGUGCUCACUUGUCCUCCUCCAUGCUUGGAAAAUACAGGGAGGAGGCCAUAGUGGCAACUGUUACCAUGAUUAAUUUCGUUGG
AAWR02039288.1/134902-135011 UAUUUUCGAUCUAAAAUCUAGGAGGCAGGUGCUCACUUGUCCUCCUCCAUGCUUGGGAAAUACAGGGAGGAGGCCAUAGUGGCAACUGUCACCAUGAUUGAUUUCCUUGG
AABR05183474.1/6980-7087     UCAACACAAUCA-AAAUCUCGGAGGCAGGUGCUCACAUGUCCUCCUCCAUGCCUA-CACAUACAUGGAGGAGGCCAUAGUGGCAACUGUCACCAUGAUUGAUUUCGUUGG
#=GC SS_cons                 ::::::::::::::<<<<--<<-<<<<<-<<<-<<<<<<-<<<<<<<<-<<___________>>->>>>>>>>->>->>>>>>>->>>>>->>-->>>>:::::::::::
#=GC RF                      UauuuuCAAUCuaAaauCUaGGAGgCaGGuGCUCaCuuGUCCuCCuCCAuGcuUgGaAaAUACagGGaGGaGGCCaUaGuGGCaACuGuCACCAUGauugAUUUCgUUGG
//
# STOCKHOLM 1.0

#=GF AC   RF01921
#=GF ID   mir-1296
#=GF DE   microRNA mir-1296
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   90.00
#=GF TC   112.80
#=GF NC   67.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000649;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [3]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF RN   [4]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [5]
#=GF RM   20433717
#=GF RT   Deciphering the porcine intestinal microRNA transcriptome
#=GF RA   Sharbati S, Friedlander MR, Sharbati J, Hoeke L, Chen W, Keller A, Stahler
#=GF RA   PF, Rajewsky N, Einspanier R
#=GF RL   BMC Genomics. 2010;11:275.
#=GF RN   [6]
#=GF RM   18945293
#=GF RT   Annotation of 390 bovine miRNA genes by sequence similarity with other
#=GF RT   species
#=GF RA   Strozzi F, Mazza R, Malinverni R, Williams JL
#=GF RL   Anim Genet. 2009;40:125.
#=GF RN   [7]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [8]
#=GF RM   19508715
#=GF RT   Identification and analysis of miRNAs in human breast cancer and teratoma
#=GF RT   samples using deep sequencing
#=GF RA   Nygaard S, Jacobsen A, Lindow M, Eriksen J, Balslev E, Flyger H, Tolstrup
#=GF RA   N, Moller S, Krogh A, Litman T
#=GF RL   BMC Med Genomics. 2009;2:35.
#=GF WK   MicroRNA
#=GF SQ   6


AAWR02008041.1/39709-39598   UCAACGAAUCACCUACCUAACUGGGUUAGGGCCCUGGCUCCAUCUCCUUUAGGAAAACCUUCUUUGGGGAGUGGGGCUUCGACCCUAACCCAGCUGGGCUGUAACACUGCUG
AAQQ01285376.1/1141-1030     UCAACGAAUUACCUACCUAACUGGGUUAGGGCCCUGGCUCCAUCUCCUUUAGGAAAACCUUCUGUGGGGAGUGGGGCUUUGACCCUAACCCAGCUGGGCUGUAAUACUACUG
AADB02013109.1/161463-161352 UCAACGAAUCACCUACCUAACUGGGUUAGGGCCCUGGCUCCAUCUCCUUUAGGAAAACCUUCUGUGGGGAGUGGGGCUUCGACCCUAACCCAGGUGGGCUGUAACACUGCUG
AC022022.10/21212-21101      UCAACGAAUCACCUACCUAACUGGGUUAGGGCCCUGGCUCCAUCUCCUUUAGGAAAACCUUCUGUGGGGAGUGGGGCUUCGACCCUAACCCAGGUGGGCUGUAACACUGCUG
AAFC03009900.1/4503-4614     UCAACGAGUUGCCUACCUAACUGGGUUAGGGCCCUGGCUCCAUCUCCUUUAGGAAAACCUUCUGUGGGGAGUGGGGCUUUGACCCUAACCUAGCUGGGCUGUAACACUGCUG
AADC01091081.1/15063-14952   UCAACGAAUCACCUACCUAACUGGGUUAGGGCCCUGGCUCCAUCUCCUUUAGGAAAACCUUCUGUGGGGAGUGGGGCUUCGACCCUAACCCAGGUGGGCUGUAACACUGCUG
#=GC SS_cons                 :::::::::::::::<<<<-<<<<<<<<<<<-<--<<<<<<<<--<<<-<<<<<_____>>>>>->>>-->>>>>>>>-->->>>>>>>>>>>->>>>::::::::::::::
#=GC RF                      UCAACGAAUcACCUACCcaACuGGGuuaGGGCCCUgGCcCCacCUCCcUcaGgaAAACCucCugUgGGGAguGGgGCcUcGACCCuaaCCCaGgugGGCUGUAAcACUgCUG
//
# STOCKHOLM 1.0

#=GF AC   RF01922
#=GF ID   mir-654
#=GF DE   microRNA mir-654
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   45.60
#=GF NC   42.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000409;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   18186931
#=GF RT   Identification of novel homologous microRNA genes in the rhesus macaque
#=GF RT   genome
#=GF RA   Yue J, Sheng Y, Orwig KE
#=GF RL   BMC Genomics. 2008;9:8.
#=GF RN   [4]
#=GF RM   18945293
#=GF RT   Annotation of 390 bovine miRNA genes by sequence similarity with other
#=GF RT   species
#=GF RA   Strozzi F, Mazza R, Malinverni R, Williams JL
#=GF RL   Anim Genet. 2009;40:125.
#=GF RN   [5]
#=GF RM   18215311
#=GF RT   miRNAminer: a tool for homologous microRNA gene search
#=GF RA   Artzi S, Kiezun A, Shomron N
#=GF RL   BMC Bioinformatics. 2008;9:39.
#=GF RN   [6]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [7]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF RN   [8]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   MicroRNA
#=GF SQ   6


AADD01141098.1/1457-1560   CUGAGCCCUCCAGGGUAAGUGGAAAGAUGGUGGGCCGCAGAACAUGUGCUGAGUUCGUGCCAUAUGUCUGCUGACCAU-----CACCUUUAGAAGCCCCCUUUCGCUGA
AC121784.2/118742-118845   CAGUGCCCUCCUCGGUAAGUGGGAAGAUGGUAAGCUGCAGAACAUGUGUGUUUCUCAUGUCAUAUGUCUGCUGACCAU-----CACCUUUGGGUCUCUGCCUGUGGAGC
AAFC03087120.1/1102-999    AGCCCCCAACCUGGGUUAGUGGAAAGGUGGUGGGCUGCAGAACAUGUGCUUCCUUCGUGUCAUAUGUCUGCUGACCAU-----CACCUUUAGAAGCCCCCCUCUCGCUG
AADC01118575.1/83093-83196 CUGAGCCCUCCAGGGUAAGUGGAAAGAUGGUGGGCCGCAGAACAUGUGCUGAGUUCGUGCCAUAUGUCUGCUGACCAU-----CACCUUUAGAAGCCCCCUUUCGCUGA
AL132709.5/81392-81289     CUGAGCCCUCCAGGGUAAGUGGAAAGAUGGUGGGCCGCAGAACAUGUGCUGAGUUCGUGCCAUAUGUCUGCUGACCAU-----CACCUUUAGAAGCCCCCUUUCGCUGA
AL132709.5/81773-81665     CCCCCCACUCCAGGGUAAGUGGAAAGUCGGUGGACCUCAGAACAUGUGCUGAAUUCGUGCCAUAUGUCUGCGGACCACCCACCCGCCUUGAGGAGACCCCUCUCGCAAG
#=GC SS_cons               ::::::::::::<<<<------<<<<-<<<<<<---<<<<<-<<<<<<<_________>->>>>>>>>>>>--->>>>.....>>->>>>---->>>>:::::::::::
#=GC RF                    cugagCccUCCagGgcAAGUGGaAAGauGgUGGGCcgCAGAACAUgUGcugaaUUCGUgcCAuAUGUCUGcuGACCAc.....CaCCUUuAGaAgcCccCuUucgcuga
//
# STOCKHOLM 1.0

#=GF AC   RF01923
#=GF ID   mir-711
#=GF DE   microRNA mir-711
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   51.50
#=GF NC   39.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000748;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [2]
#=GF RM   16582102
#=GF RT   The expression profile of microRNAs in mouse embryos
#=GF RA   Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K,
#=GF RA   Mirochnitchenko O, Inouye M, Kato I
#=GF RL   Nucleic Acids Res. 2006;34:1765-1771.
#=GF RN   [3]
#=GF RM   18215311
#=GF RT   miRNAminer: a tool for homologous microRNA gene search
#=GF RA   Artzi S, Kiezun A, Shomron N
#=GF RL   BMC Bioinformatics. 2008;9:39.
#=GF WK   Mir-711_microRNA_precursor_family
#=GF SQ   5


AC190272.8/53341-53246     ACCAUGAUGAACUGACUUUGAGUCUCUCCUCAGGGUGCUGCAGGCAAAGCUGGGGACCCAGGGAGAGACGUAAGUGAGGGGAGAUGCUGGGACAGA
L23982.1/20007-20102       ACCAUGAUGAACUGACUUUGAGUCUCUCCUCAGGGUGCUGCAGGCAAAGCUGGGGACCCAGGGAGAGACGUAAGUGAGGGGAGAUGCUGGGACAGA
AAWR02008514.1/16619-16714 CUGCAGACUCCCUGACUUUAAGUCUCUUUUCAGGGUGCCACAGGCAAAGCUGGGGACCCAGGGAGAGACGUAAGUAAGGGGAGAUGUUAGGGUGGA
AC005903.5/60778-60683     ACCAUGAUGAACUGACUUUGAGUCUCUCCUCAGGGUGCUGCAGGCAAAGCUGGGGACCCAGGGAGAGACGUAAGUGAGGGGAGAUGCUGGGACAGA
AABR05157096.1/34747-34842 AUCCCCUGUGCCUAACUUUGAAUCUCUUCGUAGGGUGCUUCAGGGAAAGCUGGGGACCCUGGGAGAGAUGUAAGUCAAGGGGGAUGCCAAGGUGGA
#=GC SS_cons               :::::::::::<<-<<<<---<<<<<<<<-<-<<<<-<<-<<<______>>>>>->>>>->>>>>>>>>-->>>>->>::::::::::::::::::
#=GC RF                    aucaugauuaacugaCuuUgAGuCuCuccucAGGGuGCcgCaGGcAAAGCuGgGGaCCCagggaGaGaCGUaaGugagGGGAGAUGcuagGauaGA
//
# STOCKHOLM 1.0

#=GF AC   RF01924
#=GF ID   mir-2774
#=GF DE   microRNA mir-2774
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   75.00
#=GF TC   75.00
#=GF NC   74.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000829;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF WK   MicroRNA
#=GF SQ   4


BAAB01032014.1/1661-1587 AAAAAAACAUUCGGACCAUCGGUCUACCGAGCAAUAUCACCCGCUCGGUGGAAGAUCGUCCCUCCGUCGUUAAGU
AADK01028607.1/1610-1537 ACAACAACAUUCGGACCGUCGGUCUAUAGAGCAAUAUCACCCGCUCGGUGGAAGACCUUCCCUUCGUCGU-UAUC
AADK01002177.1/7257-7183 ACAACAACAUUCGGACCGUCGGUCUACCGAGCAAUAUUACCUGCUCGGUGGAAGAUCGUCCCUUUGUCGUAUAUC
BAAB01011354.1/544-470   ACAACAACACCCGGACCGUCGGUCUACCGAGCAAUAUCACCCGCUCGGUAGAAGAUCUUCCCUUUGUCGUAUAUA
#=GC SS_cons             ::::::::::::<<<<-<<<--<<<<<<<<<<__________>>>>>>>>>>->>>->>>>::::::::::::::
#=GC RF                  AcAAcAACAUUCGGAcCgUCGGUCuAccGAGCAAUAUcACCcGCUCggUgGAAGAcCgUCCCUUuGUCGUauAuu
//
# STOCKHOLM 1.0

#=GF AC   RF01925
#=GF ID   MIR1428
#=GF DE   microRNA MIR1428
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   85.00
#=GF TC   89.80
#=GF NC   71.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000575;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18312648
#=GF RT   Identification of novel and candidate miRNAs in rice by high throughput
#=GF RT   sequencing
#=GF RA   Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK
#=GF RL   BMC Plant Biol. 2008;8:25.
#=GF RN   [2]
#=GF RM   19103661
#=GF RT   Characterization and expression profiles of miRNAs in rice seeds
#=GF RA   Xue LJ, Zhang JJ, Xue HW
#=GF RL   Nucleic Acids Res. 2009;37:916-930.
#=GF RN   [3]
#=GF RM   18353984
#=GF RT   Genome-wide analysis for discovery of rice microRNAs reveals natural
#=GF RT   antisense microRNAs (nat-miRNAs)
#=GF RA   Lu C, Jeong DH, Kulkarni K, Pillay M, Nobuta K, German R, Thatcher SR,
#=GF RA   Maher C, Zhang L, Ware D, Liu B, Cao X, Meyers BC, Green PJ
#=GF RL   Proc Natl Acad Sci U S A. 2008;105:4951-4956.
#=GF RN   [4]
#=GF RM   18687877
#=GF RT   A diverse set of microRNAs and microRNA-like small RNAs in developing rice
#=GF RT   grains
#=GF RA   Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C
#=GF RL   Genome Res. 2008;18:1456-1465.
#=GF WK   MicroRNA
#=GF SQ   5


AP003793.1/15957-16080   GGUUAGUGCGUUUUGCAAAUUCGCAGGCCCUAUCUUGUGGUAUGAACUGAGUACGCGAUGAUUUAUCCUGCGUAUUGGGGGCUUACCAUAAGAUAAAGCCGUGAAUUUGCAAAACGUUCAAACC
EU563913.1/488-611       GGUUAGUGUACUUUGCGAAUUCACAGGCCCUAUAUUGUGGUAUGAACUGAGUACGCGAUGAUUUAUGGUGCAUAUUGGGGGCUUACCAUAAGAUAAUGCCAUGAAUUCGCAAAGUGUUCAAACC
AP004317.1/76457-76580   GGUUAGUGCGCUUUGCGAAUUCACGGGUCUUAUCUUGUGGUAUGAACUGAGUACGUAAUGAUUUAUGGUGCAUAUUGGGGGCUUACCAUAAGAUAAUGCCAUGAAUUCGCAAAGCGUUCAAACC
AC097447.4/55138-55261   AGUUAGUGCGCUUUGCGAAUUCACAGGCCCUAUCUUGUGGUAUGAACUGAGUACGCGAUGAUUUAUGGCGCAUAUUGGGGGCUUACCAAAAGAUAAUGCUGUGAAUUUGCAAAGCGCUCAAACC
AP005259.3/117578-117455 GGUUAGUGUGCUUUGCGAAUUCACAGGCCCUAUCUUGUGGUAUGAACUAAGUACGCGAUGAUUUCUGGUACGUAUUGGGGGCUUACCAUAAGAUAAUGCCGUGAAUUCGUAAAGCGUUCAAACC
#=GC SS_cons             ::::::::<<<<<<<<<<<<<<---<<<--<<<<<<<<<<<<-<--<<-<<<<-<<<___________>>>->>>>->>-->->>>>>>>>>>>>-->>>-->>>>>>>>>>>>>>::::::::
#=GC RF                  gGUUAGUGcGcuuuGCgaauuCaCAGGcCcuaucuuguGGuaUGAACugaguaCGcgAUGAUUUaUggcgCauauuGgGGGCUuaCCacaagauaAugCCgUGaauucGCaaagCguUCAAACC
//
# STOCKHOLM 1.0

#=GF AC   RF01926
#=GF ID   mir-981
#=GF DE   microRNA mir-981
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.70
#=GF NC   44.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000710;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20444247
#=GF RT   Bioinformatic prediction, deep sequencing of microRNAs and expression
#=GF RT   analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon
#=GF RT   pisum
#=GF RA   Legeai F, Rizk G, Walsh T, Edwards O, Gordon K, Lavenier D, Leterme N,
#=GF RA   Mereau A, Nicolas J, Tagu D, Jaubert-Possamai S
#=GF RL   BMC Genomics. 2010;11:281.
#=GF RN   [2]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [3]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [4]
#=GF RM   18500992
#=GF RT   Cloning, characterization, and expression of microRNAs from the Asian
#=GF RT   malaria mosquito, Anopheles stephensi
#=GF RA   Mead EA, Tu Z
#=GF RL   BMC Genomics. 2008;9:244.
#=GF RN   [5]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010;42:6-9.
#=GF RN   [6]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF RN   [7]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF WK   MicroRNA
#=GF SQ   3


AAGE02007302.1/184866-184756     AAUAUUCAAAAAACCUUGCCUGGAUCGGGUUUCGC-GGCGAACGGGCUUC-C-----ACCAUGAUGAAUAGC-AGUUCGUUGUCGACGAAACCUGCACAUUGCAAGGCAUAUGACAUCG
AAAB01008846.1/10080559-10080442 CGUGGGGCAGCAGCCUUAUCUGGAUCGGGUUUCGCUGGCUAACGUGUUGUGCGAGCGAGCAAAAAAAACUUC-AAUUCGUUGUCGACGAAACCUGCACGGAGUAAGGCACGGAGCACCA
AAIZ01004132.1/2301-2191         UGAUGCGAAAAAUCCACAUUGAAAUCGGGUUUCGUUA-ACAGCGGGCUGUUA---U---GAAUAAAUCAACAA-GUUCGUUGUCGACGAAACCUGCAUGCUGUGUGGAGAAACAACAAA
#=GC SS_cons                     ::::::::::::<<<<<<<------<<<<<<<<<<---<<<<<<<<<_____..._._______________._>>>>>>>>>-->>>>>>>>>>------>>>>>>>:::::::::::
#=GC RF                          uguagugaAaaAgCCuugccuggAUCGGGUUUCGuUgGacAaCGgGcUgUuc...u.AgcAaaAaAaauauc.AgUuCGuUguCGaCGAAACCUGCAcguugcaaGGcauaaaacaucA
//
# STOCKHOLM 1.0

#=GF AC   RF01927
#=GF ID   MIR1222
#=GF DE   microRNA MIR1222
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   90.00
#=GF TC   101.10
#=GF NC   64.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000410;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17601824
#=GF RT   Common functions for diverse small RNAs of land plants
#=GF RA   Axtell MJ, Snyder JA, Bartel DP
#=GF RL   Plant Cell. 2007;19:1750-1769.
#=GF RN   [2]
#=GF RM   16824179
#=GF RT   Novel micro-RNAs and intermediates of micro-RNA biogenesis from moss
#=GF RA   Talmor-Neiman M, Stav R, Frank W, Voss B, Arazi T
#=GF RL   Plant J. 2006;47:25-37.
#=GF WK   MicroRNA
#=GF SQ   5


ABEU01007920.1/13167-13034 GACUGUGCGUC-GAUGCAA-CUGCUCUAAUCAUUUUCGUACCAGUGUAUUCCUUCAAACCUCUUCUCU-U-GACUGUAGU---GGUGGCCUGAAGGAGUUCAUUGGUACACAAAUCUUGAGAGCAUGGA----GGAAAAUAGAGU
ABEU01009865.1/26140-26268 AGUUGAAUGUGUG--C--GGUUGU-GGGGAUAUUGACGUGCUGGUGAGCUCCUUCAAGCUCGAGUGUG-C---GUCUUGC-CACGGC-CUUGAAGGAGUUCAGUGGUACAUCAAUGUCCAUGGCAUACU---C--AAGGCGGGAC
ABEU01005809.1/86770-86904 AGCUGAUGUUGUUA-U--UAUUGUUACGGGCAUUCGUGUGCUGGUGAACUCCUUCAUGCACAAGUGCGGC---UCUUCGCGCACCAG-CUUUAAGGGGUUCACUGGUAUAUGAAUGCACAUGGCAUGAU---CUGAUCACGGGAG
ABEU01006038.1/22275-22138 CGGCGAGCGUG-AAAA-AACUUGCUACAAUCAUUUUCGUACCAGUGCGUUCCUCCAAACCACCACGCU-CACGUUGAUGCGAAGUUGGUCUGAAGGAGUUCAUUGGUACACAAAUCAUAAGAGCAUGGA----GGACCGGAGAAU
ABEU01010965.1/39082-39214 ACACGACAUAGCUG-----GUUGUUGUGGGCAUUCUUGUGCUAGUAAACUCCUUCAUGCAGAAGUGCG-C---UUCUA--GCACCUG-CUUGAAGGAGUUCAUUGGUAUAUAAAUGCCCACAACAUGAUGACCGAUUAACGUGAG
#=GC SS_cons               ::::::::::::::.:..:::<<<<<-<<<<<<<<--<<<<<<<<<<<<<<<<<<<--<-<<-<<<<_._..._____>>>>->>->.-->>>>>>>>>>>>>>>>>>>-->>>>>>>>->>>>>::::...:::::::::::::
#=GC RF                    aguuGAgugUGuuA.u..agUUGcugugggcAUUcucGUaCcagUGaacuCCUuCAagCaccagcgcg.C...uUuUugcgcAgguG.CuUGaAGGaguuCAcugGuACAugAAUgcccAcagCAUGau...CGGAuaacgGgAu
//
# STOCKHOLM 1.0

#=GF AC   RF01928
#=GF ID   Mico1
#=GF DE   Maternal intergenic circadian oscillating RNA 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   60.00
#=GF TC   82.10
#=GF NC   49.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.32 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   19029831
#=GF RT   Novel imprinted transcripts from the Dlk1-Gtl2 intergenic region, Mico1
#=GF RT   and Mico1os, show circadian oscillations.
#=GF RA   Labialle S, Croteau S, Belanger V, McMurray EN, Ruan X, Moussette S,
#=GF RA   Jonnaert M, Schmidt JV, Cermakian N, Naumova AK
#=GF RL   Epigenetics. 2008;3:322-329.
#=GF CC   Maternal intergenic circadian oscillating 1 (Mico1) and Mico1 opposite
#=GF CC   strand (Mico1os) are lon non-coding RNAs. Their expression shows circadian
#=GF CC   oscillations [1].
#=GF WK   Long_non-coding_RNA
#=GF SQ   3


EF648170.1/1551-1755       GGAAGGCAGAGGGUUUUGCUUGGAUCUCUUGGCUGACCACGUGGCCAUACGUUCAACACUCCAGGAUGCCUGUUCCUGGAGCCAGACAGAAAAUGAGUUAGGGCUGCAAACAGGAUCUGAGUGGCCCCCUGCUCUGGAGAGGCCCCUCCAUGUAAACAGAACGAGUUUCUGGGAAACGUACAGAAGGCCAGGCUGUCGGGAAAGG
AAHX01046576.1/10295-10495 GGAAGGCAGAGGGUUUUGCUUGGAUCUCUGGGCUGGCCACGUGGCCAUACGUUCAACAGUCCACGCUGCCUGUUCCUGGAG----ACAGAGAGUAAGUUAGGGCUGCAAACAGGAUCUGAGUGGCCCCCUGCUCUGGAGAGGCCCCUCCAUGUAAACAGAACAAGUUUCUGGGAAACAUACAGAAGGCCAGACUGUCGGGAAAGG
ABDC01285622.1/9496-9699   GGCAGCCAGACAGUUUUGCUUGGAUCUCUGGGGCGGCCACGUGGCCAUGCGUUCCGUGCUCGGAGAGGACUGUGCCCAGAGCCAGCCAGAAAGUGACUUACAGCUGAAAACAGGAUUUGAAUGACUUC-UGCUCUGGGGAGGCCCCUCAGGAUAAACAGUGAGCAUUUCUGGGAAAUGUACACAAGGCCAGACUGUCGGGAAAGG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GGaAGgCAGAggGUUUUGCUUGGAUCUCUgGGcuGgCCACGUGGCCAUaCGUUCaacacUCcagGauGcCUGUuCCugGAGCCAGaCAGAaAgUgAgUUAggGCUGcAAACAGGAUcUGAgUGgCccCCUGCUCUGGaGAGGCCCCUCcaugUAAACAGaacgagUUUCUGGGAAAcgUACAgAAGGCCAGaCUGUCGGGAAAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01929
#=GF ID   bxd_1
#=GF DE   Bithoraxoid conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   75.00
#=GF TC   90.80
#=GF NC   40.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.74 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF RN   [1]
#=GF RM   17174895
#=GF RT   Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in
#=GF RT   cis by transcriptional interference.
#=GF RA   Petruk S, Sedkov Y, Riley KM, Hodgson J, Schweisguth F, Hirose S, Jaynes
#=GF RA   JB, Brock HW, Mazo A
#=GF RL   Cell. 2006;127:1209-1221.
#=GF RN   [2]
#=GF RM   17568198
#=GF RT   A model for initiation of mosaic HOX gene expression patterns by
#=GF RT   non-coding RNAs in early embryos.
#=GF RA   Petruk S, Sedkov Y, Brock HW, Mazo A
#=GF RL   RNA Biol. 2007;4:1-6.
#=GF CC   Bithoraxoid (bxd) is a long non-coding RNA found in Drosophila. It
#=GF CC   silences the expression of the Ultrabithorax (Ubx) gene by transcriptional
#=GF CC   interference [1,2].
#=GF WK   Bxd_(gene)
#=GF SQ   6


M27998.1/427-343             CAACCACCGCAUGCAAAUGG------UCGGCCAAUUGUUUGAUGAAUUGCGGCCAAAAGUCAAGGGUUCAUUGCC-AGGAUUAGUAGGUAGU
AASW01022759.1/1812-1728     CAACAGCCGCAUGCAAAUG------CUCGACCAAUUGUUUGAUGAAUUGCGGCCAGAAGUCAAGGGUUCAUUGCC-AGGAUUAGUAGGUAGU
AAEU02000022.1/249384-249295 CAACAGCCGCAUGCAAAUGGAAAUGCUCGGCCAAUUGUU-GAUGAAUUGCGGCCAGAAGUCAAGGGUUCAUUGCC-AGGAUUAGUAGGUAGU
AAPP01019539.1/298608-298524 CAACAGCCGCAUGCAAAUG------CUCUGCCAAUUGUGUGAUGAAUUGUGGCCAGAAGUCAAGGGUUCAUUGUC-AGGAUUAGAAGGUAAG
AAFS01000023.1/26211-26295   CGACAGCCACAUGCAAAUG------CCCUGCCAAUUGUUUGAUGAAUUGCGGCCAGAAGUCAAGGGUUCAUUGGC-AGGAUUAGUAGGUAAA
AAQB01009402.1/672075-671992 ---AAACUUCCUGCAGAAAC-----UGCUGCCAAUUGUUUGAUGAAUUGCGGUAAGAAGUCAAGGGUUCAUUGGCUGGGAUUAGUAGGUAAG
#=GC SS_cons                 ::::::::::::::::::::.....::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::
#=GC RF                      CaACAGCCgCaUGCAaAUGg.....cuCuGCCAAUUGUUUGAUGAAUUGCGGCCAGAAGUCAAGGGUUCAUUGcC.aGGAUUAGUAGGUAgu
//
# STOCKHOLM 1.0

#=GF AC   RF01930
#=GF ID   bxd_2
#=GF DE   Bithoraxoid conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   80.00
#=GF TC   91.00
#=GF NC   62.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.30 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF RN   [1]
#=GF RM   17174895
#=GF RT   Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in
#=GF RT   cis by transcriptional interference.
#=GF RA   Petruk S, Sedkov Y, Riley KM, Hodgson J, Schweisguth F, Hirose S, Jaynes
#=GF RA   JB, Brock HW, Mazo A
#=GF RL   Cell. 2006;127:1209-1221.
#=GF RN   [2]
#=GF RM   17568198
#=GF RT   A model for initiation of mosaic HOX gene expression patterns by
#=GF RT   non-coding RNAs in early embryos.
#=GF RA   Petruk S, Sedkov Y, Brock HW, Mazo A
#=GF RL   RNA Biol. 2007;4:1-6.
#=GF CC   Bithoraxoid (bxd) is a long non-coding RNA found in Drosophila. It
#=GF CC   silences the expression of the Ultrabithorax (Ubx) gene by transcriptional
#=GF CC   interference [1,2].
#=GF WK   Bxd_(gene)
#=GF SQ   5


AADE01000036.1/167774-167684 GGCAUCAGUUUUCAAGAUGGAGGUCACCGUCGCUGUCGCCCCGGUUUUUCUUUCAA--CUGACGCUUCAAUUGAAACAUGUGUGGGGUGUCUG
AAEU02000022.1/247419-247329 GGCGUCGGUUUUCAAGAUGGAGGAC-CUUUAGCAGUCGUCCCGUUUUACUUCCAAAA-CGGACGCUUCACUGGCAACAUGUGUGGGGUGCCUG
AAPP01019539.1/297056-296971 AGCAUCAGUUUUCAAGAUGGUGG-------AACUGUCGCCCCGGUUUUCCUCCAAAAUCGGACGCCUCGGUGGCAACAUGUGUGGGGCGUCUG
AAPQ01006451.1/675877-675788 GGCGUCGGUUUUCAAGAUGGAGGAC-CUUCAACAGUCGUCCCGCUUUUCCUCCAAAA-GGGACGCUUCACUGGCAACACGUGUGGGGUGUC-G
M27997.1/352-262             GGCGUCUGUUUUCAAGAUGGAGGCC-CUUUAACAGUCGUCCCGUUUUUCCUCCAAAA-CGGACGCUUCACUGACAACAUGUGUGGGGUGUCUG
#=GC SS_cons                 :::::::::::::::::::::::::.:::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::
#=GC RF                      GGCgUCgGUUUUCAAGAUGGaGGaC.CuuuagCaGUCGuCCCGgUUUUCCUCCaAAA.CGGACGCUUCacUGGcAACAUGUGUGGGGUGUCUG
//
# STOCKHOLM 1.0

#=GF AC   RF01931
#=GF ID   bxd_3
#=GF DE   Bithoraxoid conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   70.00
#=GF TC   102.10
#=GF NC   37.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.43 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF RN   [1]
#=GF RM   17174895
#=GF RT   Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in
#=GF RT   cis by transcriptional interference.
#=GF RA   Petruk S, Sedkov Y, Riley KM, Hodgson J, Schweisguth F, Hirose S, Jaynes
#=GF RA   JB, Brock HW, Mazo A
#=GF RL   Cell. 2006;127:1209-1221.
#=GF RN   [2]
#=GF RM   17568198
#=GF RT   A model for initiation of mosaic HOX gene expression patterns by
#=GF RT   non-coding RNAs in early embryos.
#=GF RA   Petruk S, Sedkov Y, Brock HW, Mazo A
#=GF RL   RNA Biol. 2007;4:1-6.
#=GF CC   Bithoraxoid (bxd) is a long non-coding RNA found in Drosophila. It
#=GF CC   silences the expression of the Ultrabithorax (Ubx) gene by transcriptional
#=GF CC   interference [1,2].
#=GF WK   Bxd_(gene)
#=GF SQ   4


AC095017.1/68822-68686       GGGUAAUAAA-AAUUGAAAAUUAUUUAACCGACAACUCGACAUGGUCUGCUUUGGAAAUCUCUAGUGUUUA-CGUUGCGAAAACAAUUGAAAUCAUAACAAUAAAAUCAAAUUCGAAAUUUGCGAGCGGUGGGUGGAUA
AAPP01019539.1/295825-295690 UUGCAAUAAA-AAGGAAAAAUUAUUUAACCAACAACUCGACAUGGUCUGCUCUGGAAAUCUCCAGUGUUUA-CGUUGCGAAAACAAUUGAAAUCAUAACAAUAAAAUCAAAUUUGAAAUUUGUGAGAGGUAAG-AGGUA
AAPU01011051.1/190926-190793 AUGUAGUAGACAAGGCGACAUGCCCUCGUCGAGAA-UGGCUCAGCUCUAUGCUGGAAAUCUCCAGUGUUUA-CAUUGCGAAAACAAUUGAAAUCAUAACAAUAAAAUCAAAUUCGAAAUUUGUGA---GUACGCGAACG
M27995.1/534-398             GGGUAAUAAA-AAUUGAAAAUUAUUUAACCGACAACUCGACAUGGUCUGCUUUGGAAAUCUCUAGUGUUUAACGUUGCGAAAACAAUUGAAAUCAUAACAAUAAAAU-AAAUUCGAAAUUUGCGAGCGGUGGGUGGAUA
#=GC SS_cons                 ::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      guGuAaUAaA.AAgggaAaAUuauuUaacCGAcAACUcGacauGgUCUgcucUGGAAAUCUCcAGUGUUUA.CgUUGCGAAAACAAUUGAAAUCAUAACAAUAAAAUCAAAUUcGAAAUUUGuGAGcGGUggGuGgaua
//
# STOCKHOLM 1.0

#=GF AC   RF01932
#=GF ID   bxd_4
#=GF DE   Bithoraxoid conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   40.00
#=GF TC   72.60
#=GF NC   36.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.90 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF RN   [1]
#=GF RM   17174895
#=GF RT   Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in
#=GF RT   cis by transcriptional interference.
#=GF RA   Petruk S, Sedkov Y, Riley KM, Hodgson J, Schweisguth F, Hirose S, Jaynes
#=GF RA   JB, Brock HW, Mazo A
#=GF RL   Cell. 2006;127:1209-1221.
#=GF RN   [2]
#=GF RM   17568198
#=GF RT   A model for initiation of mosaic HOX gene expression patterns by
#=GF RT   non-coding RNAs in early embryos.
#=GF RA   Petruk S, Sedkov Y, Brock HW, Mazo A
#=GF RL   RNA Biol. 2007;4:1-6.
#=GF CC   Bithoraxoid (bxd) is a long non-coding RNA found in Drosophila. It
#=GF CC   silences the expression of the Ultrabithorax (Ubx) gene by transcriptional
#=GF CC   interference [1,2].
#=GF WK   Bxd_(gene)
#=GF SQ   5


AC095017.1/68615-68509       GAGC-GGCGAUGUGAGAAAAUUUCCAGCACAAGCCCAAAUAAGCAAAGGUAAAUGGCAAAUGGGUGAAAUGCUCAAGAAAAUGAAGCCAACGAGG---AGCAGCGCCAAAA
AAPP01019539.1/295634-295532 GACC-UGGGAUGUGAGAAAAUUUGCAGCACAAGCCCAGAAA----CAGCCAAAAGGUAAAUGGGUGAAGUGCUCAAGAAAAUCAAGCCAACGAGC---AGCAAAGCCAAAA
AANI01017135.1/194974-194868 GAGCUGGCUAUGUGAGAAAAUGUUUUGCACAAGUCGAAAACCA-AAAGUAUAAAGGUAAAUGGGUGAAAUGCUAAAGAAAAUCAACUCAACGAGC---AACAACAGAGAGG
AAIZ01000582.1/33812-33914   GAGC-UGCGAUGUGAGAAAAUGGUCUGAACAAGCCGAAAUA-------UAUAAAGGUAAAUGGGCGAAAUGCUCAAGAAAAUCAGCUCGAAGAGCUCGAAAAUCCGAGAAA
M27995.1/327-222             GAGC-GGCGAUGUGAGAAA-UUUCCAGCACAAGCCCAAAUAAGCAAAGGUAAAUGGCAAAUGGGUGAAAUGCUCAAGAAAAUGAAGCCAACAAGG---AGCAGCGCCAAAA
#=GC SS_cons                 ::::.::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::...:::::::::::::
#=GC RF                      GAGC.gGcGAUGUGAGAAAAUuuuCaGcACAAGCCcAaAuaag.AaAGuuaAAaGGuAAAUGGGUGAAaUGCUcAAGAAAAUcAagcCaAcGAGc...AgcAgcgccgAaa
//
# STOCKHOLM 1.0

#=GF AC   RF01933
#=GF ID   bxd_5
#=GF DE   Bithoraxoid conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   67.40
#=GF NC   34.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.06 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF RN   [1]
#=GF RM   17174895
#=GF RT   Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in
#=GF RT   cis by transcriptional interference.
#=GF RA   Petruk S, Sedkov Y, Riley KM, Hodgson J, Schweisguth F, Hirose S, Jaynes
#=GF RA   JB, Brock HW, Mazo A
#=GF RL   Cell. 2006;127:1209-1221.
#=GF RN   [2]
#=GF RM   17568198
#=GF RT   A model for initiation of mosaic HOX gene expression patterns by
#=GF RT   non-coding RNAs in early embryos.
#=GF RA   Petruk S, Sedkov Y, Brock HW, Mazo A
#=GF RL   RNA Biol. 2007;4:1-6.
#=GF CC   Bithoraxoid (bxd) is a long non-coding RNA found in Drosophila. It
#=GF CC   silences the expression of the Ultrabithorax (Ubx) gene by transcriptional
#=GF CC   interference [1,2].
#=GF WK   Bxd_(gene)
#=GF SQ   5


AAPP01019539.1/295414-295358 AACCCAACCAACCAGU-UCAGCAACGCGAACUCCGAACUUAAUCGAAACAUCAAAGGA
AAPU01011051.1/190382-190325 GACUCAACCAACCAGUUUCGACAACGCGAACUCCGAACUUAAUCGAAACAUCAAAGGA
AAST01029201.1/717-661       GACCUAACCAACCAGU-UCGGCAACGCGAACUCCGAACUUAAUCGAAACAUCAAAGGA
AC095017.1/68409-68353       GACCUAACCAACCAGU-UCGGCAACGCGAACUCCGAACUUAAUCGAAACAUCAAAGGA
M27995.1/122-66              GACCUAACCAACCAGU-UCGGCAACGCGAACUCCGAACUUAAUCGAAACAUCAAAGGA
#=GC SS_cons                 ::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::
#=GC RF                      GACCuAACCAACCAGU.UCGGCAACGCGAACUCCGAACUUAAUCGAAACAUCAAAGGA
//
# STOCKHOLM 1.0

#=GF AC   RF01934
#=GF ID   bxd_6
#=GF DE   Bithoraxoid conserved region 6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   75.50
#=GF NC   35.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.40 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF RN   [1]
#=GF RM   17174895
#=GF RT   Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in
#=GF RT   cis by transcriptional interference.
#=GF RA   Petruk S, Sedkov Y, Riley KM, Hodgson J, Schweisguth F, Hirose S, Jaynes
#=GF RA   JB, Brock HW, Mazo A
#=GF RL   Cell. 2006;127:1209-1221.
#=GF RN   [2]
#=GF RM   17568198
#=GF RT   A model for initiation of mosaic HOX gene expression patterns by
#=GF RT   non-coding RNAs in early embryos.
#=GF RA   Petruk S, Sedkov Y, Brock HW, Mazo A
#=GF RL   RNA Biol. 2007;4:1-6.
#=GF CC   Bithoraxoid (bxd) is a long non-coding RNA found in Drosophila. It
#=GF CC   silences the expression of the Ultrabithorax (Ubx) gene by transcriptional
#=GF CC   interference [1,2].
#=GF WK   Bxd_(gene)
#=GF SQ   6


M27993.1/293-198             CCCGCAGGCAACCUCAUCAUCAAGCCGUUUUCAUUUAAUUUUCAUGCACAUUUAAUGGCGUCUGUUAUUGGCUUUUAACGAGAUUUUCACUCCACC
AAPP01019539.1/289815-289723 CCCGCAGGCUGCCUCAUC---AAGCCGUUUUCAUUUAAUUUUCAUGCACAUUUAAUGGCGUCUGUUAUUGGCUUUUAACGAGAUUUCCACUCCAUG
AADE01000036.1/159988-159896 CCCGCAGGCCGCAUCAUC---AAGCCAUUUUCAUUUAAUUUUCAUGCACAUUUAAUGGCGUCUGUUAUUGACUUUUAACGAGAUUUCCACUUCAUC
AAPT01019384.1/10402-10310   CCCACAGCCCGCCUCAUC---AAGCGGUUCUCAUUUCAUUUUCAUGCGCAUUUAAUGGCGUCUGUUAUUGACUUUUAACGAGAUUUCCACUUCAGC
AAQB01009402.1/657486-657395 CCUCCUCUUCCGCUCAUC---AAGCCGUUUUCAUUUCAUUUUCAUGCACAUU-AAUGGCGUCUGUUAUUGACUUUUAACGAGAUUUCCACUUCAGC
AAPU01011051.1/183059-182967 UCGACAGUCCGCCUCGUC---AAGCGGUUCUCAUUUCAUUUUCGUGCGCAUUUAAUGGCGUCUGUUAUUGGCUUUUAACGAGAUUUCCACUCGACU
#=GC SS_cons                 ::::::::::::::::::...:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      CCcgCaGgCcgCCUCAUC...AAGCcGUUuUCAUUUcAUUUUCAUGCaCAUUUAAUGGCGUCUGUUAUUGgCUUUUAACGAGAUUUCCACUuCAuc
//
# STOCKHOLM 1.0

#=GF AC   RF01935
#=GF ID   bxd_7
#=GF DE   Bithoraxoid conserved region 7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   60.00
#=GF TC   87.90
#=GF NC   43.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.42 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF RN   [1]
#=GF RM   17174895
#=GF RT   Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in
#=GF RT   cis by transcriptional interference.
#=GF RA   Petruk S, Sedkov Y, Riley KM, Hodgson J, Schweisguth F, Hirose S, Jaynes
#=GF RA   JB, Brock HW, Mazo A
#=GF RL   Cell. 2006;127:1209-1221.
#=GF RN   [2]
#=GF RM   17568198
#=GF RT   A model for initiation of mosaic HOX gene expression patterns by
#=GF RT   non-coding RNAs in early embryos.
#=GF RA   Petruk S, Sedkov Y, Brock HW, Mazo A
#=GF RL   RNA Biol. 2007;4:1-6.
#=GF CC   Bithoraxoid (bxd) is a long non-coding RNA found in Drosophila. It
#=GF CC   silences the expression of the Ultrabithorax (Ubx) gene by transcriptional
#=GF CC   interference [1,2].
#=GF WK   Bxd_(gene)
#=GF SQ   3


L32205.1/40138-40073         UGUAUUUUUAGGUAUC-CGUAUAAUUGACUUUUUGACUUUGAACUGC---ACUGUCGCAGGUCGUUGACU
AAPP01019539.1/289696-289631 UGUAUUUUUAGGUAUC-CGUAUAAUUGACUUUUUGACUUUGGAUCGC---UUUGUGGCAGGUCGUUGACU
M27993.1/191-122             UGUAUUUUUAGGUAUCGCGUAUAAUUGACUUUUUGACUUUGAACUGCCGACUGGUCGCAGGUCGUUGACU
#=GC SS_cons                 ::::::::::::::::.::::::::::::::::::::::::::::::...::::::::::::::::::::
#=GC RF                      UGUAUUUUUAGGUAUC.CGUAUAAUUGACUUUUUGACUUUGaAcuGC...uuuGUcGCAGGUCGUUGACU
//
# STOCKHOLM 1.0

#=GF AC   RF01936
#=GF ID   mir-63
#=GF DE   microRNA mir-63
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   55.00
#=GF TC   82.00
#=GF NC   52.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000823;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19755563
#=GF RT   Repertoire and evolution of miRNA genes in four divergent nematode species
#=GF RA   de Wit E, Linsen SE, Cuppen E, Berezikov E
#=GF RL   Genome Res. 2009;19:2064-2074.
#=GF WK   MicroRNA
#=GF SQ   5


ABKE01004162.1/545-660 GGUACCCGAACCAUAAUCCAUGUGGGGUUCCAUUCGCAUGAGUUUCAUGGACUCGAUUCAUAGAUCUAUGACACUCAAUGCGAGAUGGGACCUCGGUGGACCAUUGGUACGGUACC
ABKE01004162.1/694-809 GGUACCCGAACCAUAAUCCAUGUGGGGUUCCAUUCGCAUGAGUUUCAUGGACUCGAUUCAUAGAUCUAUGACACUCAAUGCGAGAUGGGACCUCGGUGGACCAAUGGUUCGGUACC
ABKE01004162.1/396-511 GGUACCCGAACCAUAAUCCAUGCGGGGUUCCAUUCGCAUGAGUUUCAUGGACUCGAUUCAUAGAUCUAUGACACUCAAUGCGAGAUGGGACCUCGGUGGACCAAUGGUUCGGUACC
ABKE01004162.1/843-954 CCCACCAGAGCCUU---CCACCUGGGGUUCCAUUCGUAUGAGUUUCAUGGACUUUCCCUACAGCUCUAUGACACUGAGUGCGGAGUGGAACCCCUAUGGAU-AAUAGUUCUUUGAU
ABKE01004162.1/247-362 UCUACCCGAAUCAUAGUCCAUGUGGGGUUCCAUUCGCAUGAGUUUCAUGGACUCGAUUCAUAGAUCUAUGACACUCAAUGCGAGAUGGGACCUCGGUGGGCCAAUGGUUCAGUACC
#=GC SS_cons           <<<<<-<<<<<<<<--<<<<<-<<<<<<<<<<<<<<<<<<<<<-<<<<<<<-<<________>>>>>>>>>->>>>->>>>>>>->>>>>>>>>>>>>>>--->>>>>>>>>>>>>
#=GC RF                ggcacCcGaaccauAauCCacgcGgGGucCCacuCGcaugaGuUuCaugGaCucgauucAuAgauCcauGaCaCucAaugCGagauGGgaCCcCgguGGaccAaugguuCggugcc
//
# STOCKHOLM 1.0

#=GF AC   RF01937
#=GF ID   mir-2780
#=GF DE   microRNA mir-2780
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   93.79
#=GF TC   93.80
#=GF NC   93.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000828;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF WK   MicroRNA
#=GF SQ   4


AADK01022399.1/933-1020 CCACGGUGAAAAGGGUGUUAAAUGAAGACUUAUG--GCUUCGGGCAUGUCGAAGAAAAACAGGACAUCGUUUGAAUGCUCGUCUAAUGGA
BABH01015754.1/123-35   CCACGGUGAAAAGGGUGUUAAAUGAAGACUUAAG-AGCUUCGGGCAUAUCGGAGAAAAACAGGACAUCGUUUGAAUGCUCGUCUAAUGGA
AADK01030925.1/245-158  CCACGGUGAAAAGGGCGUUAAAUGAAGACUUA-GG-GCUUCGGGCAUAUCCAAGAAAAACAGGACAUCGUUUGAAUGCUCGUCUAAUGGA
BABH01059425.1/160-74   CCACGGUGAAAA-GGUGUUAAAUGAAGACUUA-GG-GCUUCGAGCAUAUCGAAGAAAAACAGGACAUCGUUUGAAUGCUCGUCUAAUGGA
#=GC SS_cons            <<<----<<---<<<<<<<<<<<<<-<-<<<---..-<<<<<<_____>>>>>>------>>>->->>>>>>>->>>>>>->>--->>>:
#=GC RF                 CCaCGGUGaAAAGgGcguuaaauGaAGACuuAaG..GCuucGgGCAUacCgaaGAAAAACagGACAuCguuugAaugCuCGuCUAAuGGA
//
# STOCKHOLM 1.0

#=GF AC   RF01938
#=GF ID   mir-1251
#=GF DE   microRNA mir-1251
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   86.20
#=GF NC   37.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000621;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [2]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [3]
#=GF RM   18945293
#=GF RT   Annotation of 390 bovine miRNA genes by sequence similarity with other
#=GF RT   species
#=GF RA   Strozzi F, Mazza R, Malinverni R, Williams JL
#=GF RL   Anim Genet. 2009;40:125.
#=GF RN   [4]
#=GF RM   18402656
#=GF RT   Hidden layers of human small RNAs
#=GF RA   Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub
#=GF RA   CO, Kai C, Kawai J, Yasuda J, Carninci P, Hayashizaki Y
#=GF RL   BMC Genomics. 2008;9:157.
#=GF RN   [5]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [6]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   4


ABRN01423257.1/3678-3761 GUCAGCUAUGUGGACUCUAGCUGCCAAAGGCGCUUCUCCUUCUGAACCGAGCGCUUUGCUCAGCCAGUGUAGACAUGGCCUGAU
AC007351.40/28866-28783  GUCAGCUAUGUGGACUCUAGCUGCCAAAGGCGCUUCUCCUUCUGAACAGAGCGCUUUGCUCAGCCAGUGUAGACAUGGCCUGAU
AC124573.4/34671-34588   GUCAGCUAUGUGGACUCUAGCUGCCAAAGGCGCUUCUCCUUCUGAACAGAGCGCUUUGCUCAGCCAGUGUAGACAUGGCCUGAU
AC125204.4/161105-161022 GUCAGCUAUGUGGACUCUAGCUGCCAAAGGCGCUUCUCCUUCUGAACAGAGCGCUUUGCUCAGCCAGUGUAGACAUGGCCUGAU
#=GC SS_cons             :::::::::<<<-<<-<<-<<<<---<<<<<<<<<-<<_____>>--->>>>>>>>>--->>>>->>->>--->>>::::::::
#=GC RF                  GUCAGCUAUguGGaCUCuAGCuGCCAaagGCGCuuCuCCUUCUGaACagaGCGCuuuGCUCaGCCaGUGuAGACauGGCCUGAU
//
# STOCKHOLM 1.0

#=GF AC   RF01939
#=GF ID   mir-761
#=GF DE   microRNA mir-761
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   65.00
#=GF TC   73.30
#=GF NC   53.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000709;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [2]
#=GF RM   18215311
#=GF RT   miRNAminer: a tool for homologous microRNA gene search
#=GF RA   Artzi S, Kiezun A, Shomron N
#=GF RL   BMC Bioinformatics. 2008;9:39.
#=GF RN   [3]
#=GF RM   16954537
#=GF RT   Many novel mammalian microRNA candidates identified by extensive cloning
#=GF RT   and RAKE analysis
#=GF RA   Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J,
#=GF RA   Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld AJ, Mano
#=GF RA   H, Plasterk R, Cuppen E
#=GF RL   Genome Res. 2006;16:1289-1298.
#=GF WK   MicroRNA
#=GF SQ   4


AL589663.19/6037-5971      CAAGCGGAGGAGCAGCAGGGUGAAACUGACACAGUUCUGGUGAGUUUCACUUUGCUGCUCCUCCUGA
ABRN01368725.1/9348-9414   CAAGAGGAGGAGCAGCAGGGUGAAACUGACACAGUUCUGGUGAGUUUCACUUUGCUGCUCCUCCUGA
AAFR03050922.1/43866-43932 CAAGAGGAGGAGCAGCAGGGUGAAACUGAGACAGUUCUGGUGAGUUUCACUUUGCUGCUCCUCCUGA
AAIY01702440.1/290-224     CAAGAGGAGGAGCAGCAGGGUGAAACUGACACAGUUCUGGUGAGUUUCACUUUGCUGCUCCUCCUGA
#=GC SS_cons               :::::<<<<<<<<<<<<<<<<<<<<<<-<<-<<____>>>>->>>>>>>>>>>>>>>>>>>>>>:::
#=GC RF                    CAAGaGGaGGaGCaGCaggGuGaaaCuGacACaGUUCuGguGaGuuuCaCuuuGCuGCuCCuCCUGA
//
# STOCKHOLM 1.0

#=GF AC   RF01940
#=GF ID   hvt-mir-H
#=GF DE   microRNA hvt-mir-H9
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   55.00
#=GF TC   57.20
#=GF NC   42.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000783;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19403687
#=GF RT   Novel microRNAs (miRNAs) encoded by herpesvirus of Turkeys: evidence of
#=GF RT   miRNA evolution by duplication
#=GF RA   Yao Y, Zhao Y, Smith LP, Watson M, Nair V
#=GF RL   J Virol. 2009;83:6969-6973.
#=GF RN   [2]
#=GF RM   19328516
#=GF RT   MicroRNAs of Gallid and Meleagrid herpesviruses show generally conserved
#=GF RT   genomic locations and are virus-specific
#=GF RA   Waidner LA, Morgan RW, Anderson AS, Bernberg EL, Kamboj S, Garcia M,
#=GF RA   Riblet SM, Ouyang M, Isaacs GK, Markis M, Meyers BC, Green PJ, Burnside J
#=GF RL   Virology. 2009;388:128-136.
#=GF WK   MicroRNA
#=GF SQ   4


AF291866.1/121538-121628 UAGGCUUGGGCACGGUCCUUCUCGCGGAUAGCGUAGAUGUCUCUAUUCGUUAACAGCUACAUUGUCCGCAGGGAUCUAGCCACAUGGCAAU
AF291866.1/121390-121479 GACAGUUGGGGCAUA-CUUUCUCAUGGACCCCCGAGUUGUGUCUAUUCGUUAACAGCUAGGCCGUCCAUGAGGUCGUAGGCACCCAGUAAU
AF282130.1/115651-115740 GACAGUUUGGGCAUA-CUUUCUUAUGGACCGCCGAGGUGUGUCUAUUCGUUAACAGCUAGGCCGUCCAUGAGGUCGUAGGCACCCAGUAAU
AF291866.1/121857-121945 CCAGGCUUGGGCGU--AUUUUCUCCGGUGAGCGUAGCUGCCUGUAGUCGUUAGCAGCUACGUUGUCCGCGGGAUUCUAGCCACCUGGCAAU
#=GC SS_cons             :::::::::::::::.:::<<<<<<<<<<<<<<<<<-<<<____________>>>->>>>>>>>>>>>>>>>>::::::::::::::::::
#=GC RF                  uAaggUUuGGgcaua.cUUucccgcGGacagCguAGaUGucUcUAuUCGUUAaCAGCUacGcuguCCgcgggguucUAGcCACcugGuAAU
//
# STOCKHOLM 1.0

#=GF AC   RF01941
#=GF ID   MIR1223
#=GF DE   microRNA MIR1223
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   79.20
#=GF NC   56.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000383;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17601824
#=GF RT   Common functions for diverse small RNAs of land plants
#=GF RA   Axtell MJ, Snyder JA, Bartel DP
#=GF RL   Plant Cell. 2007;19:1750-1769.
#=GF RN   [2]
#=GF RM   16824179
#=GF RT   Novel micro-RNAs and intermediates of micro-RNA biogenesis from moss
#=GF RA   Talmor-Neiman M, Stav R, Frank W, Voss B, Arazi T
#=GF RL   Plant J. 2006;47:25-37.
#=GF WK   MicroRNA
#=GF SQ   8


ABEU01014840.1/83780-83655   ---------------AGACUAGAGGGUCAGCAAGGGUGUGUGACUCUAUAAUCCAAG--CUGUGCUAGUAGAUCGCUUAAGAUCGAAGUGCACACCAAGCAUUCGAUUGUAGAGUCAUACACCUCCACUGACACUUCUAGUCU--------------
ABEU01004661.1/58892-59017   --UGACCAUGACAA-GCAAUGGAGCUUCGACAAGGGUGUUUGACUCUACUACCCGUG--------AACCCCAUCAGAU-------GGAGAUAUG---------UGGUUGUAGAGUCAUGCACCUCUGCCGAGGCUCCUGCUUUUUACUCCUUU----
ABEU01000497.1/158443-158573 AGUGAGUGGGUCAGCAGCAUGGAGGUUCGACAAGGGUGCUUGGCCCUACUACCCGUG--------AACCCACCCAA---------GGAGAGACG---------UGGUUGUAGAGUCACGCACCUCUGCCGAGCCUCCUGCUCGUUGUGCUUCUUCUU
ABEU01004661.1/59156-59279   --CAAGCCUCGUUC-AGCAGGGUGCUUCAGCAAGGGUGCUUGAUUCUACUACCCGUC--------GACCCAUUAGA---------GGAGCGACG---------CGGUUGUAGAGUCACGCACCUCUGUUGAGCACCCUGCUCGGAGUAAAGAU----
ABEU01000497.1/159210-159342 GCGGCGAUGGAUACUAGACUCGAGGUCGAACAAGGGUGUGUGACCCUACAAUCCGAA--ACGCGAGACUUAAU-GCUU----------CGCCUG---------CGAUUGUAGAGUCAUACACCUCUGCUAG-CCUUCCGGUCU-UCCGCUCUAAGCU
ABEU01008976.1/81410-81263   ---CCCUUCAACACAAGGCUGAAGGGUCAGCAAGGGUGUGUGACUCUACUAUCUGAA--CUGUGCGAUUUGAUUGCCUCGUAAUGAGGCGUACAUAAAGCUUUUGAUUGUAGAGUCAUGCACCUCUACUGG-GCCUUCAGUCUAAUUUUUCUGC---
ABEU01014840.1/83440-83300   GGUUCACUCUAUUCAAGGUUGGAUUGUCAGCAAAGGUGUGCGACUCUAUAAUCCAAAGCUUGUGGGAGGAAUUCACCU----------CGCCUGUGA-----CCGAUUGUAGAGUCAUACACCUCUACUGA-CCUUCCAGUCUCUUUGCUCACAGCU
ABEU01008976.1/82012-81890   GCAAUGAAAUGGAACAGCAUGGAGCUUCAGCAAGGGUGCUUGACUUUAUAACCCG----------GCUUAAAUUAA---------------UCG---------UGGUUGUAGAGUCAUGCACCUCUGCUGGCUCUCCUGCUUGGACAUUAUACUUGU
#=GC SS_cons                 ..::::::::::::::::::<<<<--<<<----<<<<<<-<<<<<<<<<-<<<____..___________________......._________........._>>>->>>>>>>>>->>>>>>---->>>-->>>>:::::::::::::::::...
#=GC RF                      ..uaaguuuuauAcaAGaaUggagguuCaGCAAGGGUGcgUGACuCUAcaAcCCGaa..cUGUGcgAcuaaaUcacuU.......aGacguacG.........uGgUUgUAGaGUCAUgCACCUCUgCuGagccuccuggUCuuuuuucuuuuu...
//
# STOCKHOLM 1.0

#=GF AC   RF01942
#=GF ID   mir-1937
#=GF DE   microRNA mir-1937
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000704;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18849523
#=GF RT   In-depth characterization of the microRNA transcriptome in a leukemia
#=GF RT   progression model
#=GF RA   Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, Heuser M,
#=GF RA   Yung E, Piper J, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst
#=GF RA   M, Hansen CL, Marra MA, Humphries RK
#=GF RL   Genome Res. 2008;18:1787-1797.
#=GF RN   [2]
#=GF RM   20215419
#=GF RT   MicroRNA transcriptome in the newborn mouse ovaries determined by massive
#=GF RT   parallel sequencing
#=GF RA   Ahn HW, Morin RD, Zhao H, Harris RA, Coarfa C, Chen ZJ, Milosavljevic A,
#=GF RA   Marra MA, Rajkovic A
#=GF RL   Mol Hum Reprod. 2010;16:463-471.
#=GF WK   MicroRNA
#=GF SQ   171


AC132342.3/142353-142478     UGGGGUCUCUGAGA-AU-U-G-GGG----U---AGGC-------------CAUAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--C-AU-GUA-AGAU--CCCC------G-AA-------GCU------U-AG-U-C-U--C-----UGCUCAAGUCCCG-GGAUG-AGCUGGCUAGCACCCCAAUGACUCAAGAGAAA
CT030242.6/134502-134619     -----UUCUUGGGG-UU-C-U-GGG----U----GCUC-------------CCAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GUA-GGAC--CCCC------C-CA-------AUAU-G--GC-GA-C-U-C--C-----CACUCUAAUCCAG-GGAUA-GGGUGC--ACC-CACGA-ACACGCAAGAAUC-
AC116463.9/53797-53917       -----GUCUCGGUC-UC-U-U-GGG----U----GGUC-----------GCGUCAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAU--CCCC-----------------AAAG-G--GA-GA-U-C-C--U-----CACUCAAGCCUCG-GGAUG-UGGCGCGGACC-CAAGAGAGACGCGGAGACCG
AC005743.5/112916-112798     -----GUCUAGGGU-CU-C-U-GGG----U----GGUC-----------GCACUGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAC--AGCCGCGGACC-CAAGA-AGACACUGAGACCG
AAHY01194834.1/482-602       -----GUCUAGGAC-CU-CU-GGGG----U----GGUC-----------GCGCUGAU-----C-CCG-GG-AC-G--AGU-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAC--AGCCGCGGACC-CAAGA-AGACACUGAGACCG
AC127415.3/61247-61364       -----CUUCAGGGU-UC-C-U-GGG----U----GUCA------------CGCAGAC-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAACUCCCG---AUU-CGGCGUGCACC-CAAGAAUCACGAAUAGAACA
AAHX01083112.1/28935-28815   -----CAUUCGAGU-CU-C-C-GGG----G----GUCAC----------GCUCCUAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A----AU-GAA-AGAC--CCCC------A-AA-------UUUGGG--GA-GA-C-U-U--U-----CGCUCCAGUCAUG-GGUUG-GGGU----ACC-CCCAGGAAACACGAGAAGCC
AC166358.5/82417-82534       -----UUCAUGGGG-UU-C-U-GGG----C----GCU-------------CCCAAAU-----C-CC-G-G-AA-G--AGC-C-C-CC--A--A-AU-GUA-AGAC--CCCC------C-G--------AUAU-G--GG-GA-C-U-G--C-----CAUUGUAGUCCAG-GGAUA-GGGCAC--ACC-CACGA-ACACGAAAGAAUCC
CAAA01060265.1/1635-1751     -----CUUUGGGGU-UC-C-U-GGG----U----GUCA------------CGCAAAU-----C-UC-A-G-UG-G--AAC-U-U-CC--A--A-AU-GAA-AGAC--CCUA-----------------GUGG-G--GA-GA-C-C-C--C-----CACUCAAGUCCUG-AGAUG-GCGCACGCACC-CAA---AGAAUCAUGAGAGA
AAHY01024841.1/8802-8684     -----UUCUCGGGU-UU-C-U-GGG----U----GCC-------------CCCAAAU-----C-CC-G-G-AA-G--AGC-C-C-CC--A--AGAU-GUA-AAAC--CCCC-----------------CUUC-A--GG-GG-A-C-C--C-----CACUCUAAUCUCA-GGAGA-GAGAGCACACC-CAA-AGAAACACGAGAAUCC
AC111084.12/32595-32477      -----UUUCGGGGU-UC-C-U-GGG----U----GUCA------------CGCAGAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-GU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAAUUCCCC--GAUU-CGGCAUGCACC-CAAGAAUCACGAACAGACGA
CAAA01114016.1/7729-7846     -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------CGCAGAU-----C-UC-G-G-UG-G--AAC-C-U-CC--A--A-AU-GAA-AGAA--CUCA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAGCUCCCG---AUU-CGGCGUGCACC-CAAGAAUCGCGAAUAGAACA
CAAA01090871.1/528-409       -----GUCUAGGGU-CU-C-U-GGG----U----GGUC-----------GCGCUGAU-----C-CC-A-G-ACCG--AGC-C-C-CC--A--A-AU-AAA-AGAC--CCCC-----------------UCAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAC--AGCCGCGGACC-CAAGA-AGACACCAAGACCA
AAHY01163937.1/688-808       -----GUCUCGGUC-UC-U-U-GGG----U----GGUU-----------GCAUCAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAU--CCCC-----------------AAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAUG-UGGCGCGGACC-CAAGAGAGACUGAAAUGGCG
AAHY01003221.1/26787-26669   -----GUCUAGGAC-CC-C-U-GGG----U----GGUC-----------GCGCAAAU-----C-CC-A-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CACC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGUCUCG-GGAAC-A-UCGCGCACC-CAGU-GGGACACUGAGACUG
AAHY01141809.1/36942-37059   -----UUUCGGGGU-UC-C-U-GGG----U----GUCA------------CACAGAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AUAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAAUUCUC---GAUU-CGGCGCGCACC-CAGGAAUCACGAACAGACGA
AC125326.4/24916-24801       -----GUCUAGGAC-CU-C-U-GGG----U----UGUC-----------GCGCUGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAC--AGCCGCGGAAC-CA----AGACACUGAGACCG
AAHY01061290.1/14988-15108   -----GUCUCGGUC-UC-U-U-GGG----U----GGUC-----------GCGUCGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GUA-AGAC--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAUG-UGGCGCGGACC-CAAGAGAGACGAGGAGACUG
BX544874.5/11626-11743       -----UUUCGGGGU-UC-C-U-GGG----U----GUCA------------UGCAGAU-----C-UC-G-C-UG-G--GGC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-U-C--C-----CACUCAAUUCCCG---AUU-CGACGUGUACC-CAAGAAUCACGAACAGAACA
AC139673.9/254227-254109     -----AUUUCGAGU-CC-U-U-GGG----G----ACCC------------CUCAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GUA-GGAC--CCCC------A----------AGAA-G--GA-GC-C-C-C--C-----CACUCAAGUCUUG-GGACU-CGGGGU--UAC-CCAAAGAAACAUGAGAGACC
AAHY01057606.1/14377-14267   -----AUCUAGGAC-CC-C-U-GGG----U----GGUC-----------ACGCAGAU-----C-CC-G-G-AU-G--AGC-C-C-CC--A--C-CU-GAA-AAAC--CCCC-----------------GAAG-G--GA-G------------------UCAAGUCUCG-GGAAU-A-GUGCGCACC-UAGCA-AGACACUGAGACCG
CAAA01139322.1/31228-31110   -----UUCUCAGGU-UU-C-U-GGG----U----GUC-------------CCCAAAU-----C-CC-G-G-GU-G--AGCAC-C-CA--A--G-AU-GUA-AGGC--CCCC-----------------UUAC-G--GG-GA-C-U-C--C-----CACUCUAGUCUCA-GGAGA-GAGAGAGCACC-CAA-AGAAACACAAGAAUCC
AC116580.4/69268-69376       -----GUCUAGGAC-CU-C-U-GGG----U----GGUC-----------GCGCUGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--G---------------------UCAAGCCUCA-GGAC--AGCCGCGGACC-CAAGA-AGACACUGAGACCG
AAHY01060131.1/27181-27298   -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------CGCAGAU-----C-UC-G-G-UG-G--AAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAACUCCUG---AUU-CGGCAUGCACC-CAAGAACCACGAACAGAACA
AAHY01067049.1/19265-19148   -----UUUCGGGGU-UC-C-U-GGG----U----GUCA------------CACAGAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCCA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAAUUCCCG---AUU-UGGCGUGCACC-CAAGAAUCACGCUCCGGGUC
AAHY01111907.1/30494-30377   -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------CGCAGAU-----C-UC-A-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAACCCCCG---AUU-CGGCGUGCACC-CAAGAAUCACAAACAGAACA
AAHY01166748.1/3680-3798     -----GUCUAGGGU-CU-C-U-GGG----U----GGUC-----------GCGCAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-UU-GAA-AGAC--CCCC------G-AA-------GGA------A-GA-C-C-C--U-----CACUCAAGCCUCG-GGAC--AGCCGCAGACC-CAAGA-AGACACUGAGACCG
AC165416.12/54705-54588      -----UGUUAUGAC-UC-C-U-GGG----U----GGUC------------AUCAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--C-AU-GUU-GGAC--CCCC------C-C--------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGUCUCA-GG-----GAUCACGAGC-CCAGAAAGCCACAACAGUCA
AAHY01060355.1/348-230       -----GUCUCGGUC-UC-U-U-GGG----U----GGUC-----------GCGUCAAU-----C-CC-G-G-AC-G--AGC-C-C-AC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GA-A-G-C--U-----CACUCAAGCCUCG-GGAUG-UGGUGU--ACA-CAAAAAGCUAUUUAAUAAAG
CAAA01151772.1/7740-7857     -----UUUCAGGGU-UC-C-U-AGG----U----GUCA------------UGCAAAU-----C-UC-G-U-UG-G--GGC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAAUUCCCG---AUU-UGGCGUGCACC-CAAGAAUCACGAACAGACAA
AAHY01210554.1/8351-8465     -----CUUUGGGGC-UC-C-U-GGG----G----GUCA------------CGCAAAU-----C-CU-G-A-AC-A--AGC-C-C-UC--A--C-AU-GAA-AGAC--CCCC-----------------AUGG-G--GA-GA-C-C-C--U-----CACUCAAGUCUCU-GUAUG-GUGCGC--ACC-CAA---GGAAACAGGAAAGA
CAAA01186857.1/12974-13091   -----CUUUGGGGU-UC-C-U-GGG----U----GUCA------------CGCAGAU-----C-UC-G-G-UG-G--AAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAGCUCCU---GAUU-CGGCGUGCACC-CAAGAAUCACGAAUAGAACA
AC140365.4/66008-66126       -----GUCUAGGAC-CU-C-U-GGG----U----GGUC-----------GCGCUGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAU--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAC--AGCCGUGGACC-CAAGA-AGACACUGAGACCA
CAAA01015466.1/1994-1878     -----UCUCAG-GU-UU-C-U-GGG----U----GCC-------------CCCAAAU-----C-CC-G-G-AC-A--AGC-ACC-CA--A--G-AU-GUA-AGGC--CCCC-----------------UUUC-A--GA-GACC-C-C--C-----CACUCUAGUCUCG-GGAGA-GAGACCACACC-CA---AAGAAACAUGAGAAU
CAAA01115897.1/3019-2905     -----CUUUGGGGU-UC-C-U-GGG----U----GUCA------------UGCAGAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAC--CUCC-----------------GUGG-G--GA-UA-A-C-C--C-----CACUCAAGUCAUG-AGAUA-GCGUGC--ACC-CAA---AGAAUCAAGAUAGA
AAHX01102209.1/31592-31710   -----UCUUCGGGG-UC-U-G-GGG----U----GGUC-----------ACAAAGAU-----C-CC-G-G-AU-G--AGC-C-C-CC--A--A-AU-UUA-AGAU--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----UACUCAAGUCUUG-GGA---AGUUGCAGAAC-CCAGACACACGAGAGACCAG
AAHY01145123.1/805-923       -----UCUACGGUC-U--C-U-GGG----U----GGUC-----------ACGCUGAU-----C-CC-G-G-AC-C-GAGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAC--AGCCGCGGACC-CAAGA-AGACACUGAGACCG
AC102365.32/109247-109365    -----UUCUCGUGU-UU-C-U-GGG----U----GCU-------------CCCAAAU-----C-CC-G-G-AU-G--AGC-C-C-CC--A--AGAU-GUA-AGAC--CCCC-----------------UUUC-G--GG-AA-C-C-C--G-----CACUCCAGUCUCA-GGAGA-GAGAGCGCACC-CAA-AGAAACACGAGAAUCC
AAHY01009611.1/16122-16003   -----UUCUCGGGU-UU-C-U-GGG----U----GUC-------------CCCAAAU-----C-CU-G-G-AC-G--AGC-C-C-CC--A--AGAU-GUG-AUAC--CCCC------U-UU-------UCA-----GG-AG-C-C-C--C-----CACUCUAGUCUUG-GGAGA-GAGAGCACAC--CUAAAGAAACACAAGAAUCC
CAAA01024954.1/64045-63927   -----UUUCGGAGU-UC-C-U-GGG----U----GUCA------------CGCAGAU-----C-UC-G-G-UG-G--AAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CUCUCAAUUCUUG---AUU-UGGUGUGCACCCAAAGAAUCACGAAAAGAACG
AAHX01093414.1/4263-4386     -----CAUUUGAGU-CU-C-C-GGG----U---GGGUCA---------CGCUCCCAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC------A-AA-------CUUGGG--GA-GA-C-U-C--U-----CGCUCCAGUCACA-GGUUG-AGGU----ACC-CCCAAGAAACGCGAGUAGCU
AAHY01032146.1/2920-2803     -----UUUCCGGAU-UC-C-U-GGG----U----GUCA------------CGCAGAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAG--CCUA-----------------GUGA-G--GA-AA-C-C-U--C-----CACUCAAUUCUCG-A--UU-UGGAGUGCACC-CAAGAAUCAAGAACAGAACG
CAAA01119468.1/3239-3121     -----UUCUUGGGU-UG-C-C-GGG----U----GCC-------------CCCAAAU-----C-UU-G-G-AC-A--AGC-C-C-CC--A--AGAU-GUA-AGGC--CCCC-----------------UUUC-A--GG-UA-C-C-C--C-----CAUUCUAGUCUGG-GGAGA-GAGAGCUCACC-CAA-AGAAACACGAGAAUCC
AC131776.5/137585-137702     -----CUUCUGGGU-UC-C-U-GGG----U----GUCA------------CACAGAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAGCUCCCG-AUUCA-GCUUGC--ACC-CAAGAAUCACGAAUAGAACA
AAHY01231071.1/593-713       -----GUCUAGGGU-CU-C-U-GGG----U----GGUC-----------GCGCUGAU-----C-CC-G-G-ACCG--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------AAAG-G--GA-GA-C-C-C--U-----CACUCAAGUCUCG-GGGAC-AGCCGCGGACC-CAAGA-AGACACUGAGACCG
AAHY01469398.1/618-498       -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------CACAGAU-----C-CC-A-G-UG-G--GGC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAACUCCCACCAAUU-CGGCGUGCACC-CAAGAAUCACGAACAGACGA
AC131720.2/148401-148520     -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------CACAAAU-----C-UC-G-U-UG-G--GAU-C-U-CC--A--A-AU-GAA-AGAC--CAU------------------AGUG-G--GA-GA-C-C-C--C-----CACUCAAGUCCUG-AGAUG-GUGUGUGCACCCAAGGAAUCACGGGAGACUGG
AC117254.3/118580-118463     -----AUUUUGAGU-CC-U-U-GGG----G----ACCC------------CUCAAAU-----C-CU-G-G-AC-G--AGC-C-C-CC--A--A-AU-GUA-GGAC--CCCA-----------------AGAA-G--GA-GC-C-C-C--C-----CACUCAAGUCUCA-GAAUG-UGGGGU--UAC-CAAAAGAAACACGAGAGACC
AC107676.10/65385-65500      -----CGUUAUGAC-UC-C-U-GGG----U----GGUC------------GUCAAAU-----C-CC-A-G-AU-G--AGC-C-U-CG--A--U-AU-GUA-GGAC--CCCC-----------------GAAG-G--GA-GA-C-C-A--U-----CACUGAAGUCUCA-GG-----GAUCGCGAGC-UCAGAAAGCCACAACAGUCA
AAHY01003035.1/12657-12541   -----UGUUAUGAC-UU-C-U-GGG----U----GGUC------------GUGGAAU-----C-UC-A-G-AU-G--AGC-C-C-CC--A--C-AU-GAA-GGAA--CUCC------C----------GAAG-G--GA-GA-C-C-C--U-----CACUCCAGUCUCA-GGAAU-CGC----GAGC-CCAGAUAGUCACAACAGUCA
AAHY01655117.1/342-461       -----GUCUAGGAC-CU-C-U-GGG----U----GGUC-----------GCGCUGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------AAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGACA-GCCACGGGACC-CAAGA-AGACACUGAGACCG
AAHX01271855.1/282-398       -----UCUUCGGAC-UC-U-G-GGG----U----GGUC-----------GCGAAGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAU--CCCC------G-AA----------G-A--GA-GA-C-C-C--U-----UUCUAAAGUCGCA-GGAAA-UCGCGG--ACC-CCAG--ACACAGAGAGACCA
AC147514.12/159277-159159    -----UUCUUGGGU-UU-C-A-GGG----U----GCC-------------CCCAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--AGAU-GUA-AGAC--CCCC-----------------UUUC-G--GG-GA-C-C-C--C-----CACUCUAGUCUCA-GGAGA-GAGCACACACU-CA-AAGAAACUUGAGAAUCC
AC079644.9/146038-145918     -----GUCUCGGUC-UC-U-U-GGG----U----GGUC-----------GCGCCUAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAUA-UGGCGCGGACC-CAAAUGAGACACAGAGACCG
AAHY01341790.1/461-346       -----UUCUUGGGG-UU-C-G-GGG----U----GCCC------------CCAAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--CGAU-GUA-GGAC--CCCA------A-AU-------UUA------G-GG-A-C-C--C-----CGCUCUAAUCCAG-GAACA-GGGAAC--ACC-CACGA---ACACAAGAAUCC
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AAHY01046142.1/2419-2539     -----GUUUAGGAC-CC-C-U-GGG----U----GGUA-----------GCGCAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--C-AU-GAA-AGAC--CCCC------C-AC-------GAAG-G--GA-GA-C-C-C--U-----CACUCAAAUCUUG-GGA---AGGCGCACACC-CAGU-GAGACGCUGAGACCG
AC122767.16/82484-82601      -----UUUUGGGGU-UC-C-U-GGG----U----GUCA------------CACAGAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------AUGG-G--GA-AA-C-C-C--C-----CACUCAACUCCCG---AUU-UGGCGUGCACC-CAAGAAUCACAAACAAACAG
AAHY01149173.1/413-288       -----UUCAUGGGG-UU-C-U-GGG----C----GCU-------------CCCAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GUA-AGAU--CCCC------C-CACCCCCCGAUAU-G--GG-GA-C-U-G--C-----CAUUGUAGUCCAG-GGAUA-GGGCGC--ACC-CACGA-ACACGCAAGAAUCC
AC116385.5/38962-39079       -----UUUUGGGGU-UC-C-U-GGG----U----GUCA------------CACAGAU-----C-UC-G-C-UG-G--GGC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAACUCCCG---AUU-UGGCGUGUACC-CAAGAAUCACGAACAGACGA
CAAA01197673.1/527-410       -----UUCGGGGGU-UC-C-U-GGG----U----AUCA------------CGCAGAU-----C-UC-G-G-UG-G--AAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAGCUCCC---GAUU-CGGUGUGCACC-CAAGAAUCAUGAAUAGAACA
AC134471.3/31150-31269       -----UUCUCGGGU-UU-C-U-GGG----U----GCC-------------UCCAAAU-----C-CC-G-G-AU-A--AGC-C-C-AC--A--AGGU-GUA-AGAC--CCCC------U----------UUCG-G--GG-AC-C-C-C--C-----CACUCUAGUCUUC-GGAGA-GAGAGAACAUG-CA-AAGAAACACAAGAAUCC
AAHX01118863.1/631-746       -----GUCUAGGAC-CC-C-U-GGG----U----GGUC-----------GCGCAGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GC-C-C-C--C-----CACUCAAGUCUCG-GGA-A-AGACGCGCACC-CAGUA-GGACGCAG---ACA
AC132423.4/124117-123996     -----AUUUCAAGU-UC-U-U-GGG----G----ACCC------------CUCAAAU-----C-CC-G-G-AC-G--AGC-C-C-GC--A--A-AU-GUA-AGAUGCCCCC------C-CA-------AGAA-G--G--AG-C-C-C--C-----CACUCAAGUCUCA-GGAUG-CAGCGUC-ACC-CAAAA-AAACAUGAGAGACC
CAAA01201832.1/551-674       -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------CGCAAAU-----C-CC-G-G-AU-G--AGC-C-C-CC--A--C-AU-GAA-AGAA--CCCC------C----------AUAG-G--GA-GA-C-C-C--CCCCCGCACUCAAGUCUUG-GGAUG-G--CGCACACC-CAAGGACAACACGAAAGACC
AC183955.2/142724-142606     -----UCUUCGGAG-UC-C-U-GGG----U----GGUC-----------ACGCUGAU-----C-CC-A-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAU--UCC------------------AAGU-G---G-AG-C-C-C--C-----UUCUCAGAUCUCA-GGACAAUAGCGGACACC-CAAGA-AUUCACAAUAGACC
AC124175.2/39190-39071       -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------UGCAAAU-----C-UU-G-G-UG-G--AAC-C-U-CC--A--A-AU-GAA-AGAC--CUCA-----------------GUGG-G--GA-GA-C-CCC--C-----CACUCAAGUCCCA-AGACA-GUGCGCACACC-CAAGG-AAUCACGAGAGACU
AAHY01069871.1/10805-10924   -----UUCUCGGGU-UU-C-U-GGG----A----GCU-------------CCCAAAU-----C-CA-G-G-AC-G--AGC-C-C-CCCAA--A-AU-GUA-AGAC--CCCU-----------------UUUU-G--GU-GG-CCC-C--C-----CAUUAUAGUCUCG-GGAGU-AAGAGAGCACC---CUAAGAACAUGAGAAUCC
AAHY01676060.1/199-317       -----UUCUCAGGU-UU-C-U-GGG----U----GCC-------------CCUAAAU-----G-CC-G-G-AC-A--AGC-C-C-AC--A--AGGU-GUA-AGAC--CCCC-----------------UUUC-A--GG-GA-C-C-C--C-----CACUCUAGUCUCG-GGAGA-GAGAGAACAUG-CA-AAGAAACACAAGAAUCC
AC121795.3/97551-97434       -----UUUCGGGGU-UC-C-U-GGG----U----GUCA------------CGCAGAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-U--C-----CACUCAAUUCUCG---AUU-UGGCGCGCACC-CAGGAAUCACGAACAGAGGA
AAHY01725139.1/423-543       -----GUCUAGGAC-CU-C-U-GGG----U----GGUC-----------GCGCUGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC------C-GA--------AGG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAC--AGCCGCGGACC-CAAGA-AGACACUGAGACCG
AL592224.17/98704-98583      -----GUCUAGGAC-CU-C-U-GGG----U----GGUCG----------CGCUGAUU-----C-CC-G-G-CC-AACGCA-C-C-AA--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAGGCCUCG-GGAC--AGCCGCGUACC-CAAGA-AGACACUGAGACCA
AAHX01033915.1/10671-10788   -----UCUUUGGGG-UC-U-G-GGG----U----GGUC------------GAGAAAU-----C-CC-G-G-AC-G--AAC-C-C-CC--A--A-AU-GAA-ACAU--CCUG-----------------GAAA-G--GA-UA-C-A-C--C-----CACUCAAGUCUCC-GGAA---GUCGCAGAAC-CCAGACACAUGAGAGACCAA
AAXN01037173.1/205-323       -----CAUUCGAGU-CU-C-C-GGG----G----GUCAC----------GCUCCUAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A----AU-GAA-AGAC--CCCC------A-AA-------CUUGGG--GA-GA-C-U-C--U-----CGCUCCAGUCACG-GGUUG-GGGU----ACC-CCCA--GGAAACAUGAGUAG
AC113014.9/72984-73102       -----GUCUAGGAC-CC-C-U-GGG----U----GGUU-----------GCGCAGAU-----C-CU-G-G-AC-G--AGC-C-C-CC--A--A-CU-GAA-AGAC--CCCC-----------------AAAG-G--CA-GA-C-A-C--U-----CACUCCAGUCUCG-GGAAU-AG-CGCGCACC-CAGCA-AGACACUUAGACUG
AL845533.9/24098-23980       -----UUUCGGGGU-UU-C-U-GGG----U----GUCA------------CGCAAAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-ACCC-C-C--C-----CACUCAAUUCCCA---AUU-CAGUGAGCACC-CAAGAAUCACGAACAGAACA
AC154562.2/155881-155760     -----UUCUCGGGU-UU-C-U-GGC----C----ACU-------------CCCAAAC-----C-CC-A-G-AC-G--AGC-C-C-CCCAA--A-AU-GUA-AGAC--CCCC------C-CU--------UUC-A--GG-GA-C-C-C--C-----CACUCUAGUCUCA-GGAGU-GAGAGAGCACC-CAA-AGAAACACAAGAAUCC
AAHX01069859.1/126189-126088 -----GUCUAGGAC-CC-C-U-GGG----U----GGUC-----------GCGCAGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-UG-AAA-AGAC--CCCC-----------------GAAG-G---G-AG-C-C-C--C-----CACUCAAGUCUCG-GGA--------------------AAGACGCUACUGCUG
AC166710.7/40167-40291       -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------CGCAAAU-----C-CC-G-G-AU-G--AGC-C-C-CC--A--C-AU-GAA-AGAA--CCCC------C----------AUAG-G--GA-GA-C-C-C--CCCCCGCACUCAAGUCUUG-GGAUG-G--CGCACACCCAAGGAAACACGAAAGACCAU
AL672233.18/6867-6984        -----CUUUGGGGU-UC-C-U-GGG----U----GUCA------------CGCAGAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAGCUCCCG---AUU-CAGCAUGUACC-CAAGAAUCACGAAUAGAACA
AAHY01135874.1/2074-2190     -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------CGUAGAU-----C-UC-G-G-UG-G--AAC-C-U-CC--A--A-AU-AAA-AGAA--CCUA------------------GUA-G--GG-AA-A-C-C--C-----CACUCAGCUCCCG---AUU-CGGCGUGCACC-CAAGAAUCACGAAUAGAACA
CAAA01205506.1/15525-15407   -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------CGCAGAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CUCA------G----------UGGG-G--GA-AA-C-C-C--C-----CACUCUGCUCCC---GAUU-CGGCGUGCACC-CAAGAAUCACGAAUAGAACA
AAHY01201128.1/1670-1552     -----UUCUUGGGU-UU-C-U-GGG----U----GCC-------------CCCAAAU-----C-CA-G-G-AA-G--AGC-C-C-CC--A--A-AUUGAA-AGAC--CC----------AA-------UUUU-G--GG-GA-C-C-C--C-----CACUCUAAUCUCA-GGAGA-GAGAGCGCACC-CAA-AGAAACAUGAGAAUCC
CAAA01131629.1/239-359       -----UGUUAUGAC-UC-C-U-GGG----U----GGUC-----------AUCUAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--C-AU-GUU-GGAC--CCCC------C-C--------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGUCUCA-GGGCA-UCACGC--AGC-CCAGAAAGCCACAACAGUCA
CAAA01082003.1/38576-38462   -----CUUCGGGGU-UC-C-U-GGG----U----GUCA------------CGCAAAU-----C-CC-G-A-AC-G--AGC-C-C-CC--A--C-AU-GAA-AGAC--CCCU-----------------GUGG-G--GA-GA-C-C-C--C-----CACUCAAGACUCG-GGAUG-G--CGCUCACU-CAA---GGAAACAUGAAAAA
AAHY01148252.1/1107-990      -----CUUUGGGGU-UC-C-U-GGG----U----GCCA------------CACAGAU-----C-UC-A-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAGCUCCCG---AUU-CGGCGUGCACC-CAAGAAUCACGAAUAGAACA
AAHY01128924.1/715-831       -----GUCUAGGGU-CU-C-U-GGG----U----GGUC-----------GCGCUGAU-----C-CC-G-G-AC-G--AGA-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAC--AGCCGC--GAC-CAAGA-AGACACCGAGACCA
AAHY01252441.1/611-732       -----GUCUAGGAC-CU-C-U-GGG----U----GGUC-----------GUGCUGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC------C----------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGGAC-AGCCGCGGAUCCCAAGA-AGACACUGAGACCG
AAHY01742378.1/556-675       -----GUCUAGGAC-CC-C-U-GGG----U----GGUC-----------ACGCAAAU-----C-UC-G-G-UC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC------C----------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGUCUCG-GGA-A-CGUCGCGCACC-CAGUG-GGACACUGAGACCG
CAAA01013731.1/7499-7620     -----GUCUAGGGU-CU-C-U-GGG----U----GGUCG----------CGCUGAAU-----C-CC-G-G-ACCG--AGC-C-C-CC--A--A-AU-GAAAAGAC--CCCC-----------------AAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUAG-GGACA-A-CCGCGGACC-CAAGA-AGACACUGAGACCG
CAAA01022709.1/16832-16715   -----UUCGGGGGU-UC-C-U-GGG----U----GUCA-----------CGCAGAAU-----C-UC-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAAUUCCCG----UU-UGGUGUGCACC-CAAGAAUCACGAACAGACCA
AAHY01116113.1/6953-7075     -----UUCUCGGGU-UU-C-U-GGC----C----GCU-------------CCCAAAC-----C-CC-A-G-AC-G--AGC-C-C-CC--AAAA-AU-GUA-AGAC--CCCC------C-CC-------UUUC-G--GG-GA-C-C-C--C-----CAUUCUAGUCUCA-GGAGU-GAGAGAGCACC-CAA-AGAAACACAAAAAUCC
AAHY01097998.1/1606-1730     -----UUCUUGGGG-UU-C-U-UGG----C----GCU-------------CCCAAAU-----C-CC-A-G-AC-G--AGC-C-C-CC--A--G-AU-GUA-GGAA--CCCCCCCCCCC-CG-------AUAU-G--GG-GA-C-C-U--C-----CACUCUAAUCCAG-GGAUA-GUGUGC--ACC-CACGA-ACACGCAAGAAUCC
AAHY01034088.1/11089-11205   -----UUUCGGGGU-UC-C-U-GGG----U----GUCA------------CACAGAU-----C-UU-G-G-UG-G--GAC-C-U-CC--A--A-AU-GAA-AGAA--CCUA-----------------GUGG-G--GA-AA-C-C-C--C-----CACUCAAUUCACG----UU-CGGCGCGCACC-CAAGAAUCACGAACAGACGA
AAHY01082961.1/5613-5731     -----GUCUAGGAC-CU-C-U-GGG----U----GGUC-----------GCGCUGUU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCCUCG-GGAC--AGCAGCUGACC-CAAGA-AGACACUGAGACCG
AAHY01039250.1/11706-11582   -----AUCUAGGAC-CC-C-U-GGG----U----GGUC-----------GCGCAAAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCCC---CCC-CU-------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGUCUCG-GGAUU-AGCAC-ACACC-CAGCA-AGACACUGAGACCA
AAHX01454084.1/181-299       -----CCUUUGGGU-CU-C-C-GGG----G----GCUA-----------CACCAGAU-----C-CU-G-G-AC-G--AGC-C-C-CC--A--G-AU-GAA-AGAA--CCCC------A-AA-------UAGG-G--GA-GU-C-U-C--U-----CACUCCAGUCUCG-GGAUG-GCGUGC---CC-CAGGA--AACACGAGUAGCC
AAHY01279545.1/747-631       -----U---AGGGU-CU-C-U-GGG----U----GGUC-----------GCGCUGAU-----C-CU-G-G-ACCG--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----CACUCAAGCUUCG-GGAC--AGCCGCGGACC-CAAGA-AGACACUGAGACCG
AAHX01027785.1/37708-37593   -----CUUCCGGGU-UC-U-U-GGG----G----GUCG------------UACAGAU-----C-CC-G-A-AC-G--AGA-C-C-CC--A-CA-AU-GUA-GGAC--CCCU-----------------GUCG-G--GA-G--A-C-C--C-----CACUCCAGUCUCG-GGAUU-GUAC----UAC-GCCAAGAAACGCAAGAGACA
AABR05148239.1/3960-3835     -----AAGUUGGUC-UU-C-G-GAG----AUGAAGGCAG----------UCACUGAU-----C-CC-U-G-AC-G--AGC-C-U-CC--A--A-AU-GAA-AGAC--CCCC------A-GA-------GCAG-G--GA-GA-C-C-C--U-----CACUCAAGUCUCA-GGAUG-ACAAG---ACC-CCCCAAUAACUCACAAGAGA
AABR05007169.1/7189-7307     ------UCUUCGGAGUC-U-G-GGG----U----GGUC-----------ACGCAGAU-----C-CC-G-G-AU-G--AGC-C-G-CC--A-UU-AU-GAA-AGAU--CCCA------C----------GCAG-A--GA-GA-C-C-C--U-----UACUCAAGUCUUG-GGAAA-UCGCGG--ACC-CCAG--ACACAGAGAGACCA
AABR05129581.1/10374-10492   -----GCUCAGGGC--C-U-G-GGG----C---------------------AGUGAU-----CUCU-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCCU------GGUA-------GCAG-G--GA-GA-C-C-C--U-----CACUCAAGUCUCG-GGAUG-AUGCGACGCCC-UAAGUAACUCACAUGAGACC
AABR05077256.1/37449-37332   -----GUCUAGGAC-CC-C-U-GGG----U----GGUC-----------GCGCAGAU-----C-CC-G-G-AC-G--AGC-C-C-CC--A--A-AU-GAA-AGAC--CCC------------------GAAG-G--GA-GC-C-C-C--C-----CACUCAAGUCUCG-GGA-A-AGACGCGCACC-CAGUA-GGACACAGACACCG
AAHX01070763.1/12132-12015   -----CGUUUGGGG-UC-C-U-GGG----U----AGUC-----------ACACAGAU-----C-CC-G-G-AC-U--AGC-C-CCCC--A--A-AU-GAA-AGAG--CCCC-----------------AAAG-G--GA-GG-C-C-C--C-----CCCUCAAGUCUUG-AG-UC-AGCUGCACAC----CGAAAGACACACAGAUGA
AABR05150414.1/3430-3545     -----UCUUUGGGG-UC-U-G-GGG----U----GGUC-----------GAGAAGAU-----C-CC-G-G-AU-G--AGC-C-C--C--A--A-AU-GAA-AGAU--CCCC-----------------GAAG-G--GA-GA-C-C-C--U-----UACUCAAGUCUCG-GGAAA-UCACGG--ACC-CCAG--ACACAGAGAGACCA
AAHX01073404.1/2456-2341     -----CUUCAGGGU-CU-G---GGG----U----GGUU-----------GUGAAGAU-----C-CC-A-C-AC-A--AGC-C-C-CC--A--A-AU-GAA-GGAU--CCUG-----------------GAAG-G--GA-GA-C-C-C--U-----UACUCAAGUCUCG-GGAAA-UC--GC--AGU-CCCAAGACACAGAGAGACCA
AABR05132596.1/16416-16297   -----UCUUCGGAG-UU-G-U-GGG----U----GGUU------------GGUAGAU-----C-CC-G-G-AC-G--AGU-C-C-CC--A--A-AU-GAA-AGAC--CACC------G-GG-------GUGG-G--GAAGA-C-C-C--C-----CACUCAAAUCUCG-AGAUG-ACG--C--AAC-CACCAAGAACUCACGAGAAA
AABR05178446.1/7833-7949     -----UCUUCGGGG-UU-C-U-UGG----G----GGUC-----------AUACAGAU-----C-CA-A-G-AC-G--AGC-C-C-CC--A-CA-AU-GUA-GGAC--CGCU-----------------CUCA-G---G-AG-A-C-C--C-----CACUCCAGUCCCG-GGAUU-----GUACUCC-CCAAAGAAACGCAAGAGACC
AAHX01441859.1/1958-2072     -----UCUUCGGGG-UC-U-G-GGG----U----GGUC-----------ACGAAGAU-----C-CU-G-G-CC-G--AGC-C-C-CC--A--A-AU-GAA-AGAU--CCCU------G-AA----------G-A--GA-GA-C-C-C--U-----UACUCAAGUCCCG-GGAAA-UCCUGG--ACC-CC----AGACACAGGGAGAC
#=GC SS_cons                 .....:::::<<<<.<<.<.<.<<<...._....____............_______.....>.>>.>.>.--.>..>>>.>.>.::..:..:.::.:::.::::..::::.................::::.:..::.::.:.:.:..:.....:::::::::::::.:::::.:::::::::::.::::::::::::::::::::
#=GC RF                      .....uUuUaGGgc.uc.c.u.GGG....u....Ggua............CgCaaAU.....C.CC.g.g.AC.g..agc.C.C.CC..A..A.AU.GAA.AGAc..CCCC.................guaG.G..GA.GA.C.C.C..c.....CACUCAAGUCUCG.GGAua.agGcGcgcACC.CAAGAaAaACacaaaaAcCa
//
# STOCKHOLM 1.0

#=GF AC   RF01943
#=GF ID   mir-999
#=GF DE   microRNA mir-999
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   51.10
#=GF NC   44.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.19 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000852;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [2]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010;42:6-9.
#=GF RN   [3]
#=GF RM   19961592
#=GF RT   Direct sequencing and expression analysis of a large number of miRNAs in
#=GF RT   Aedes aegypti and a multi-species survey of novel mosquito miRNAs
#=GF RA   Li S, Mead EA, Liang S, Tu Z
#=GF RL   BMC Genomics. 2009;10:581.
#=GF RN   [4]
#=GF RM   20167119
#=GF RT   Identification of microRNAs expressed in two mosquito vectors, Aedes
#=GF RT   albopictus and Culex quinquefasciatus
#=GF RA   Skalsky RL, Vanlandingham DL, Scholle F, Higgs S, Cullen BR
#=GF RL   BMC Genomics. 2010;11:119.
#=GF RN   [5]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF WK   MicroRNA
#=GF SQ   4


AAWU01001445.1/28151-28270   UAGCAGGAAAACACGCCGGUCACCCGCAGGGACGCGGUCUGGCAGGAAAUAAUUUGGCAUUAGAUUCAAAUGUUAACUGUAAGACUGUGUCUUUGAGG--GCGAUCCUCACCAUCCACGUUC
AAST01016047.1/649-529       GGAGAAGAAAGGAUGCCGCUCAAUUACCCCGACAUAGUCGUACGGUGAAUG-UUGUGUAUUGGAGACCAAUGUUAACUGUAAGACUGUGUCUCGGUGGUUGCCAGCCCAGCCACACAGCCCA
AC008195.6/52633-52513       GGAGAAGAAAGGAUGCCGCUCAAUUACCCCGACAUAGUCAUACGGUGAAUG-UUGUGUAUUGGAGACCAAUGUUAACUGUAAGACUGUGUCUCGGUGGUUGCCAGCCCAGCCACACAGCCCA
AAGE02006027.1/163141-163260 CUCACCAGAUUACCGGAAGACGCUUGCAGGGACGCGGUCGUGCAGGAAAUUAUUUGGCAUUAGAUUCAAAUGUUAACUGUAAGACUGUGUCUUUGCGG--GUGAUCAUUGGCAGCGGUUAUC
#=GC SS_cons                 ::::::::::::::::::::<--<<<<<<<<<<<<<<<<-<<<<<--------<<<<<<<<<<___>>>>>>>>>>>>>>>->>>>>>>>>>>>>>>>..>:::::::::::::::::::::
#=GC RF                      ugaaaagAAagaauGccgguCAauugCcggGACacaGUCguaCaGuaAAUgAUUuggcAUUgGAuuCcAAUguuaACuGuaAGACuguGUCucgGcgg..GcgAuCcuaGcCAuacAuuuua
//
# STOCKHOLM 1.0

#=GF AC   RF01944
#=GF ID   mir-2518
#=GF DE   microRNA mir-2518
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   64.20
#=GF NC   43.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000858;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010;42:6-9.
#=GF WK   MicroRNA
#=GF SQ   4


AADE01004179.1/712-816   CGGCCAACGGGCAGCCACACACACACACACGACCGGAUCGAACCCGUUGCGAAUCGAACUUGGUUUGAGUUCGAGCAGCGGGUCGAUCCGAGCCAUAGCCCAGCC
AADE01002220.1/6104-6208 CGGCCAACGGGCAGCCACACACACACACACGACCGGAUCGAACCCGUUGCGAAUCGAACUUGGUUUGAGUUCGAGCAGCGGGUCGAUCCGAGCCAUAGCCCAGCC
AAFS01004834.1/3830-3741 --------GGGCAGCCACAC----ACACACGACCGGAUCGAACCCGUUGUGAAUCGAACUUGGUUCGAGUUCGAGCAGCGGGUCGAUCCGAGCCAUAGCCCA---
AADE01002220.1/2022-2113 --------GGGCAGCCACACAC--ACACACGACCGUUUCGACCCCGUUGCGAAUCGAACUUGGUUUGAGUUCGAGCAGCGGGUCGAUCCGAGCCAUAGCCCA---
#=GC SS_cons             ::::::::((((,,,,,,,,,,,,,<____>,,<<<<<<<<-<<<<<<<<---<<<<<<<<_____>>>>>>>>>>>>>>>>>>>>>>>>,,,,,,,))))::::
#=GC RF                  cggccAAcGGGCAGCCACACAcAcACACACGACCGgauCGaaCCCGcuGcGAAuCGaaCucGGUUugaGuuCGagCagCGGGuCGaucCGAGCCAUAGCCCAgcc
//
# STOCKHOLM 1.0

#=GF AC   RF01945
#=GF ID   mir-1388
#=GF DE   microRNA mir-1388
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.80
#=GF NC   46.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000805;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19397817
#=GF RT   Parallel DNA pyrosequencing unveils new zebrafish microRNAs
#=GF RA   Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL,
#=GF RA   Moura GR, Santos MA
#=GF RL   BMC Genomics. 2009;10:195.
#=GF RN   [2]
#=GF RM   18463306
#=GF RT   Conservation of small RNA pathways in platypus
#=GF RA   Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z,
#=GF RA   Kellis M, Grutzner F, Stark A, Hannon GJ
#=GF RL   Genome Res. 2008;18:995-1004.
#=GF RN   [3]
#=GF RM   19758457
#=GF RT   Characterization of bovine miRNAs by sequencing and bioinformatics
#=GF RT   analysis
#=GF RA   Jin W, Grant JR, Stothard P, Moore SS, Guan LL
#=GF RL   BMC Mol Biol. 2009;10:90.
#=GF RN   [4]
#=GF RM   20360741
#=GF RT   The genome of a songbird
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF WK   MicroRNA
#=GF SQ   4


CR391935.9/148582-148684   UGAUGGAUGAGCAGUGCUUUCCAGGACUGUCCAACCUGAGAAUGCUUGAGUUUU--GGUCAAUCUCAGGUUCGUCAGCCCAUGAAAAACUGUCUCGCUCAAAGCC
AAPN01132708.1/7352-7452   UGUUCAGUGGGGGGCGUGU-CUAGGACUGUCUAACCUGAGAAUGGUGAUGUGUGAGGGUCAAUCUCAGGUUCGUCAGCCCAUGAAA---CGCCUUCUCCAGAUCC
ABQF01028257.1/27499-27599 GCCCCAGUGAGGGGCACC-UCGAGGACUGUCUAACCUGAGAAUGGUGAAACAUCAAGGUCAAUCUCAGGUUCGUCAGCCCAUGAGA---UGCCUUCUCCAGAGCG
AAFC03042420.1/16151-16252 CCGCC--UGGGCGGUGCCU-UCAGGACUGUCCAACCUGAGAAUGGUGAGCAUCCAGGGACAAUCUCAGGUUUGUCAGCCCGCAAGGUGCCGUCCCCUCCCCAGCA
#=GC SS_cons               ::::::::<<<<<<<<-<<.<--<<-<<<-<-<<<<<<<<<-<<_______________>>->>>>>>>>>->->>>->>-->->>--->>>>>>>>::::::::
#=GC RF                    uguucagUgggcGgcgccu.cuAGGACuGUCuaaCCuGaGaAuGgUgAaauuuuAgGGuCaAuCuCaGGuucGUCaGCCCAugAagaaccgcCgccccCaaAgCa
//
# STOCKHOLM 1.0

#=GF AC   RF01946
#=GF ID   KCNQ1OT1_1
#=GF DE   KCNQ1 overlapping transcript 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   70.00
#=GF TC   74.10
#=GF NC   45.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 14.71 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18299392
#=GF RT   Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by
#=GF RT   targeting to the perinucleolar region.
#=GF RA   Mohammad F, Pandey RR, Nagano T, Chakalova L, Mondal T, Fraser P, Kanduri
#=GF RA   C
#=GF RL   Mol Cell Biol. 2008;28:3713-3728.
#=GF WK   KCNQ1OT1
#=GF SQ   8


AC021424.6/175786-175323   CUGGCC-UGGCUGGGAGGUGGCCUGGGAAGGGACCUGUGUUUC-UCAAGCCCGCGCCCUCGGGGCCU--GGGGGUGGGGCCCCAGCAGAUGUCUGGAUUUGGUAGCCAGGGCCUGGAGCCGGAUGCUGAGAAUGAGGCCUGCAACUCAUUUCCCCAUUAAACAUUCUGAGAACAUCUGCACCGGUUUCCAAGGCUUCUCCCUCACUAAUUGCUUUGAUUAUUGUGUGAAGUUAAGAACUGGCACAUUUCCGCGAUGUUGUGAUGAAGGUGAAAAGAUCGCUCUUAAUUAGAUUAAAAACAUUUUUUUCUUCCUGUGUAAUUUUGUCUUGAAAA-UCAAGGCCACUUUUUU---------GUUUUCUCCAUCCAAAGACCUCCAGAAACUUUCCUCCCCACCUCUCCAGAGGUUUCUGGGGAAUGUCCUGUGAGCUCAACUCUUGGAGAAGAUAGUGCUUAACCCAGAUUCCAUUGUAU
AAGV020622655.1/1134-1587  CUGGCC-UGGCCGGGAGGUGGCCUGGGAAGGGACCUGUGUUCC-UCCAGCCUGCGCCCCGGGGGCCU--GGGGGUGGGGCCCCAGCAGAUGUCUGG-UUUGGUAGCCAGGGCCUGGAGCCGGAUGCUGAGAACGAGGCCUGCAGCUCAUUUCCCCAUUAAACAUUCUGAGAACAUCUGCA-------CCAG----UUUCCCUCGCUAAUUGCUUUGAUUAUUGUGUGAAGUUAAGAACUGGCACACAUCCUCGAUGUUGCGAUGAAGGUGAAAAGAUCACUCUUAAUUAGAUUAAAAACAUUUUUUUCUCCCUCUGUAAUUUCGCCUUGAAAA-UCAAGGCCAUUUUUUUU-------UGUUUGCUUCAUCCAAAGACCUCCAAAAACUUUCCUCUCUAUCUCUUCAGAGGUUUCUUGGGAAUGUCCUGUGAGCUCAGCUCUUGGAGAAGAUAGUGCUUACCCCAGAUUCCAGCGGCC
AACN011056274.1/547-141    -----------------------------------------------------------CGGGGCCU--GGGGGUGGGGCCCCAGCAGAUGUCUGGAUUUGGUAGCCAGGGCCUGGAGCCGGAUGCUGAGAACGAGGCCUGCAACUCAUUUCCCCAUUAAACAUUCUGAGAACAUCUGCACCGGUUUCCAAGGCUUCUCCCUCACUAAUUGCUCUGAUUAUUGUGUGAAGUGAAGCACUGGCACGUUUCCGCGAUGUUGUGAUGAAGGUGAAAAGAUCGCUCUUAAUUAGAUUAAAAACAUUUUUUUCUUCCUCUGUAAUUUUGCCUUGAAAA-UCAAGGACACUUUUUU---------GUUUUCUUCAUCCAAAGACCUCCAGAAACUCUCCUCCCCACCUCUCCAGAGGUUUCUUGGGAAUGUCCUGUGAGCUCAACUCUUGGAGAAGACAGUGCUGAGCCCAGAUUCCAUUGUAU
ABRO01118002.1/1953-2422   CUGGCC-UGGCUGU-UGGCAGCCUGGGAAGGGACCUGUGUUUC-UCAAGCCCGCACCCUCGGGGCGU--GGGGG-GGAGGCCCAACAGAUGUGUGGAUUUGGUAGCCAGGGCCUGGAUCCGGAUGCUGAGAAUGAGGC-UGCAACUCAUUUCCCCAUUAAACAUUCUGAGAACAUCUGCACGGGUGUCCAAGGCCUCUCCCUCACGACUUGCUUUGAUUAUUGUGUGAAGUUCAGAACUGGCACACUGCCGCCAUGUUGGGAUGAAGGUGAAAAGAUCGCUCUUAAUUAAAUUAAAGACAUUUUUUUCUUCCUGUGUAAUUUUGCCUUGAAAAAUCAAGGCCACUUUUUUUUUCUUGUUGUUUUCUUCAUCCAAAGACCUCCAGACACUUUCCUCCCCACCUCUCCAGAGGUU-CUGGGGAAUGUCCUGUGAGCUCAGCUCUUGGAGAAGAUAGUGCUUAACCCAGAUUCCAUUGUAU
AAYZ01343456.1/3368-3827   GUGGCCAUGGAGGGCCUGCGGGUUGGGGUCUGACUUAUCUGGGAGGCAGCCUGCACCCUCGGGGCCCCAGGGGGUGGGGCCCCAGCAGAUGUCUGGGAUUGGUAGCCAGGGCCUGGAGCCGGAUGCCGAGAAGGAGGCCUGCAACUCAUUUCCCCAUUAGACGUUCUGAGAACACGUGCACCAGCUUCCAAGCUUUCUCCCUCCCGAACCGCCCUGAUUAGUGUGUGAAG-----AACUGGCACAUCUCCACGAGGUUGUAAGGAAGGUGAAAAGAUCGCUCUUAAUUAGAUUAAAAACAUUGUUUUCUUCCUGUGUCAUUUUGCCCUGAAAA-UCAAGGCCAAUUUUUU---------CCUUUCUUCAUCCAAAAGCCUUCAGAAAGCUCCCUCUGCACCUCUCUGGAGGGUCAUAUUACAUUUUCCUGGGAACCUGCCCUGAACAUGUGCAGUGGGAGAUCUGG---CCAGUGACU
AAGU03089033.1/59051-59503 CUGGCC-GGGCUGGAAGGUGGCCUGGGAAGGGACCUGUGUUC--UCAAGCUUGCACCCUCGGGGCCU--GGGGGUGGGGCUG-AGCAGAUGUCUGGAUUUGGUAGCCAGGGCCUGGAGCCGGAUGCGGAGAGCCAGGCCUGCAAUUCAUUUCCCCAUUAAACAUUCUGAGAACAUCUGCAGCU-CUUCCAAGGCUUCUCCCGCGCUAAUUGCUCUGAUUAGUGUGUGAAGUUAGGACCUGGCACAG---CGCGGUGCUGUGAUGAAGGUGAAAAGAUCACCCUUA----GAUUAAAAACAUUUUUUUCUCCCUCUGUAAUUUCGCCUUGAGAA-UCAAGGCCGUUUUCU---------UGAUCUCUUCAUCCAAAGACCUCCAGAAACUU-CCUCCCCACCUCUCUAGAGGUUUCUGGGGCGUGUCCGGUGAGCUCAGCUCCUGGAGAAGACAGUGCUUAGCCCAGAUUCCAUCCUGU
AABR05014402.1/1338-1796   CUGGCC-UUGCUGG-AGGCAGCCUGGGAAGAGACCUGAGUUUC-UCAAGCACACGCCUUCCAGGCCU--GGGGGUGGGGCCCCAGCAGAUGUCUGGAUUUGGUAGCCAGGGCCUGGAGCCGGAUGCUGAGAAUGAGGCCUGCAACUCAUUUCCCCAUUAAACAUUCUGAGAACAUCUGCACCAGUUUCCAAGGCUUCUCCUU----AAUUGCUUUGAUUAUUGUGUGAAGUUAAGAACUGGCACAUUUCCGUGAUGUUGUGAUGAAGGUGAAAAGAUCGCUCUUAAUUAGAUUAAAAACAUUUUUUUCUUCCUGUGUAAUUUCUCCUUGAAAA-UCAAGGCCACUUUUUU---------GUUUUCUUCAUUCAAAGACCUCCAGAAACUUUCCUCCCCACCUCUCCAGAGGUUUCUGGGGAAUGUCCUGUGAGCUCAACUUUUGGAGAAGAUAAUGCUUAACCCAGAUUCCAUUGUAU
AAGW02076532.1/15879-16312 CCAGA--GAGCUGGGGUCUGGCCUGGCUGGGAGGC------------AGCGUGCGCCCCCGGGGCCC--GGGGGUGGGGCCCCAGCAGAUGUCUGGG---------------CUGCAGCCGGAUGCUGAGGAGGAGGCCUGCGGCUCAUU--CGCACUCAGCGUCCUGAGAACAUCUGUGGCGGCGUCCGAGGCUUCGCCCUCGCUGAUCGCUGUGAUUCUCGUGUGAAGGCCAGAACUGGCUCAUUUCCGCGGUGCUGUGAUGAAGGUGAAAAGAUGCCUCUUAAUUAGAUUAAA-ACAUUUUUUUCUUCCUGUGUAAUUUGGCCUUGAGAA-UCAAGGCCACUUUUUU---------GUUUUCUUCAUCCCAAGGCCUCCAGGAACUUCCCUCCCCACCUCUCCAGAGGUUUCUGGGGAAUGCCGUGUGAGCUCAGCUCCUGGAGGAGAGCGUGCUUAACCCAGAUUCCAUUGUGU
#=GC SS_cons               ::::::.::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::..::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::.........:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    cuGGcC.ugGcuGGgagGugGccUGGGaaggGaccUgugUuuc.ucaAGCcuGCgCCCuCGGGGCcu..GGGGGUGGGGcCcCAGCAGAUGUcUGGauUUGGUAGCCAGGGCCUGGAGCCGGAUGCuGAGaAuGAGGCCUGCaaCUCAUUUCCcCAUUaaaCaUUCUGAGAACAucUGCaccgGuuUCCaAGgcuUCuCCCuCgCuaauuGCuuUGAUUauUGUGUGAAGuuaaGaaCUGGCaCAuuuCCgCGauGuUGuGAuGAAGGUGAAAAGAUcgCUCUUAAUUAGAUUAAAaACAUUuUUUUCUuCCUgUGUaAUUUuGCCuUGAaAA.UCAAGGCCAcUUUUUU.........GuUUUCUUCAUCCaAAGaCCUcCAGaaAcuUuCCUCccCACCUCUCcaGAGGuUucUgGGGaAUGUccuGuGaGcuCagCuCuuGGaGaaGauaGUGcuuaacCcaGAUUCCAuuGuaU
//
# STOCKHOLM 1.0

#=GF AC   RF01947
#=GF ID   KCNQ1OT1_2
#=GF DE   KCNQ1 overlapping transcript 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   60.00
#=GF TC   76.10
#=GF NC   46.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.99 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18299392
#=GF RT   Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by
#=GF RT   targeting to the perinucleolar region.
#=GF RA   Mohammad F, Pandey RR, Nagano T, Chakalova L, Mondal T, Fraser P, Kanduri
#=GF RA   C
#=GF RL   Mol Cell Biol. 2008;28:3713-3728.
#=GF WK   KCNQ1OT1
#=GF SQ   18


AC124055.6/24797-24602       GGGGAGGGAGGUGUGGAAGCUGGUUUGCCG-GGGCCACCCAGUGUGGGCUCAGGAAGGGAAGGAAUGUGACCAAG-----GCUGGGUGUGGCUGGGGAGAGC--ACAGCCAGUUGUGGG-UUUUUCUUGGGGCCCAGAUAGAUGUGAGCAGAGCUGGAGGC-CCCUCUCUC--CCAGC----CCCCGGCACACACACUAGGACCUUUCUUCA
AAWR02038047.1/26711-26906   GGGGAGGGAGGUGUGGAAGCUGGUUUGCUG-GGGCCACCCAGUGUGGGCUCAGGAAGGGAAGGAAUGUGACUGAG-----GCCGGGUGUGGCUGAGGAGAGC--GCAGCCAGUUGUGGG-UUUUUCUUGGGGCCCAGAUAGACGUGAGCAGAGAUGGAGGC-CCCUCUCUC--UCAGC----CCCCACCACACACACUAGGACCUUUCUUCA
ABRT010535670.1/253-443      GAGGAGGGAGGUGUGGAAGCUG-----CCG-GGGCCACCCAGUGUGGGCUCAGGAAGGGAAGGAAUGUGACUGAG-----GCUGGGUGUGGCUGGGGAGAGC--ACAGCCAGUUGUGGG-UUUUUCUUGGGGCCCAGAUAGAUGUGAGCAGAGCGGGAGGC-CCCUCUCCC--CCAAC----CCCCAGCACACACACUAGGGCCUUUCUUCA
AAKN02038604.1/125070-124874 GGGAAGGGAGGUGUGCAAGCUGCUUUGCGG--GGCCACCCAGUGUGGGCUCAGGAAGAGAAGGAAUGCGACUGAG-----GCUGGGUGUGGCUGGGGAGAGC--ACAGCCAGUUGUGGG-UUUGUCUUGGGGCCUAGAGAGACGUGAACGGAGAUGGAGGC-CUCUCUCUCUCCCAGC----CCCCAGCACACACACUAGGACCUUUCUUCC
AANG01058623.1/644-839       GGGGAGGGAGGUGUACAAGUUGGGUUG-UG-GGGCCACCCAGUGUGGGCUCAGGAAGGGAAGGAAUGUGACCGAG-----GCCGGGUGUGGCUGAGGAGAGC--ACAGCCAGUUGUGGG-UUUUUCUUGGGGCCCAGAUAGACGUGAGCAAAGAUGGAGGGGCCCUCUCUC--GCAGC----CCCCGCCACACACACUAGGACCUUUCUUCG
ABRN01281482.1/648-843       CGGGAGGAAGCUGUGGAGGCUGGUUUGCUG-GGGCCACCCAGUGCGGGCUCAGGAAGGGAAGGAAUGUGACCGAG-----GCCGGGUGUGGCUCAGCAGAGU--GCAGCCAGUUGUGGG-UUUUUCUUGGGGCCGAGAUAGACGUGAGCAGAGAUGGAGGC-CCCUCUCUC--UCAGU----CCCCACCACACACACUAGGACCUUUCUUCA
ABDC01330647.1/477-672       GGGGGCAGAGGUGUGGAGGCUGGUUUGCUG-GGGCCACCCAGUGUGGGCUCAGGAAGGGAAGGAAUGCAACUGAG-----GCUGGGUGUGGCAGGGGAGGGC--ACAGCCAGCUAUGGG-UUUUUCUUGGGGCCCACAGAGAUGUGAGCAGAGCCGGAGGC-CCCUCUCCC--CCAGC----CCCCAGCACGCACACUAGGACCUUUCUUUG
AAFC03060667.1/30651-30844   GGGGAGGAAGGUGUGGGAGCUGGUUUGCCG-GGGCCACCCAGUGUGGGCUCAGGAAGGGAAGGAAUGUGACCGAG-----GCCGGGUGUGGCUGAGGAGAGU--GCAGCCAGUUGUGGG-UUUUUCCUGGGGCCGAGAUGGACGUGAGCAGAGAUGGAGGC-CCCUCUCUC--U--GC----CCCCACCACACACACUAGGACCUUUCUUCA
AAPY01120034.1/5696-5896     AGGAAGGGAAGUGUGGAAACUGGUUUGUCAAGGGCCACCCAGUGUGGGCUCAGGAAGAGAAGGAAUGUGACUGAG-----GCUGGGUGUGGCAGAGGAGAGC--ACAGCCAGUUGUGGG-UUUUUCUUGGGGCCCAGAUAGAUGGGAACAGAGGUGGAGGC-CCCUCUCUC--CCAGCACCCCCCCAGCACACACACUAGGACCUUUCUUCA
ABRP01273152.1/3423-3619     GGGGAGGGCGGUGUGGAAGCGGGCUUGCUG-GGGCCACCCAGUGCGGGCUCGGGAAGGGAAGGAAUGUGGCUGA------GGCGGGUGUGGCUGAGGGGGGGGCGCAACCGCCUGUGGG-UUCUUCUUGGGGCCCAGAGAGAUGUGAGCCGAGAUGGAGGCCCCU-CUCCC--UCGGC----CCCCGGCACGCACACUCGGACCUUUCUUCA
ABRO01118004.1/8649-8840     GUGAGGUAGGAGGUGAGAGCUGGUGAGCCG-GGGCCGCCCAGGGUGGGCUCAGGAAGGGAAGGAAUGUGGCUGAG-----GCUGGGUGUGGCUGGGGAAAAC--UCAGCUAGUUGUGGG-UUUUUCUUGGGGCCCAGAGACACAUGAGCAGAGGUGGAGGC-CCCUCUCCC--C-AGC----CCCCA--GCAUAGACUAGGACCUUCCCCA-
ABRQ01502827.1/901-1084      --AGGAAGAGG-GGGGACACUGCUGUGCUG-GG-CCACC-GGUGUGGGUGCAGGC-GGGAAGGAAUGUGCCUAG--------CGGGUGUGGCGAGGA---GU--GUAGCCAGCUGUGGG-UUUUUCUUGGGGCCCAGAGAGACAUGGGCAGAGAUGGCCGC-CCCGCUCCC--CCGGC----CCCCACCACACACACUGAGACCUUUCUUUA
AANN01105104.1/899-721       GGGGAGAGAUGUGUGGAGGCUGCUCUGCUG-GGGCCACCCAGCGUGGG--CGGGAAGGGCAGGAAUGCGGCUGAAACUGAGGCGGGCGCGGCUGUGGGGACA--GCAGCCAGCGGUGGG-UUUUCCGCGGGGCCCAGA------------------GAGGCCCCU--UCGC--UCGGC----CC-CUGCACGCACACUGGGACCUUUCUUCA
AAPE02057644.1/2072-2261     GGGGAGGGCGGCGUGGAGCUGG--CUGCUG-GG-CCACCCAGUGCGGGCGCAGGAAGGGAAGGAAUGUGGCUGA------GGCGGGUGUGGCUGAGCAGGGC-CC-AGGGAGCUGUGGGGUUUUUCUUGGGGCCCAGAGAACCCCGAGCAGAGAUGGAGGCCCCUUCUCCC--UCUGC----C--CGGCAC--ACACUGGGACCUUUCUUCG
AAGW02076532.1/31996-32186   GGGGAGGGAGGUGUGCAGGCUUGGUUGCUG-GGGCCACCCAGAU--GGCUCAGGAAGGGAAGGAAUGAGCGUGAG-----G-UGGGUGUGGCUGCGGAGAGC--ACAGCCAGUGGUGGG-UUU-UCUUGGGGCCCAGAGAGACGUGAGCAGAGAUGGAGGC-CCCUCUCGC--CCAGC-----CCCCGCACACACACUAGGACCUUUCUUCA
AAEX03011557.1/80641-80835   GGGGAGGGAGGUGUAGAAGCGGGGUUG-UG-UGGCCACCCAGUGUGGGCUCAGGAAAGGAAGGAAUGUGACUGAG-----GCCGGGUGUGGCUGAGGAGAGC--ACAGCCAGUUGUGGG-UUUUUCUUGGGGCCCAGAUAGACGUGAGCCGAGAUGGAGGC-CCCUCUCUC--UGGGC----CCCCACCACACACACUAGGACCUUUCUUCA
AAQR03144846.1/321-129       GGGGAGAGAGGUGUUUAAGCUAGUUUGCUG-AGGCCACCCAGUGUGGGCUCAGGAAGGGAAGGAAUGUGACUGAG-----GCUGGGUGUGGCUGGGGA--GC--ACAGCCAGUUAUGGG-UUUUUCUUGGGGCUCUGAUAGAUGUGAGCAGAGCUGGAGGC-CCCUCUCUC--CCAGC----CCCAA-CACACACACUAGGACCUUUCUUCA
AABR05014403.1/14942-15135   GGGAAGGGAGGAGUGGGAGCUGGUUUGUGG--GGCCACCCAGGGUGGGCUCAGGAAGGGAAGGAAUGUGACUGAG-----GCUGGGUGGGGCUAGGGAGAGC--ACAGCCAGUUGUUGG-UUUUUCUUGGGGCCCAGAAAGAUUUGAACGGACACGGAAGC-CCCUCUCUC--CCAGC----CCC-AGCGCACACACUAGCAUCUUUCUUCG
#=GC SS_cons                 ::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::.....::::::::::::::::::::::..:::::::::::::::.:::::::::::::::::::::::::::::::::::::::::.:::::::::..:::::....::::::::::::::::::::::::::::::
#=GC RF                      GGGGaGgGaGGuGUGgaagCuGguuUGCuG.GGGCCACCCAGuGuGGGCuCaGGAAGGGaAGGAAUGuGaCuGAG.....GcuGGGUGuGGCuGgGgaGaGc..gCAGCcAGuuGUGGG.UUUUUCuUGGGGCCcAGAgAGacguGAGCaGAGauGGAGGC.CCcUCUCuC..cCaGC....CCCCagCaCaCACACUaGGACCUUUCUUca
//
# STOCKHOLM 1.0

#=GF AC   RF01948
#=GF ID   KCNQ1OT1_3
#=GF DE   KCNQ1 overlapping transcript 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   60.00
#=GF TC   70.20
#=GF NC   38.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.78 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18299392
#=GF RT   Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by
#=GF RT   targeting to the perinucleolar region.
#=GF RA   Mohammad F, Pandey RR, Nagano T, Chakalova L, Mondal T, Fraser P, Kanduri
#=GF RA   C
#=GF RL   Mol Cell Biol. 2008;28:3713-3728.
#=GF WK   KCNQ1OT1
#=GF SQ   9


AC021424.6/153260-153145     AAACAUGCCUUUGAAUUGGAAA-GCCAGAACUUUUU--GCAAAAUAAUUUGAAAAGUUUGUUGAACCUUAAA-CCUUUCCUGAUGACUCCUUCCUUCUGAACUUAA-CUCGUUAAA-GUUGC
AAKN02038604.1/124558-124443 AAACAUGCCCGGGAAUUAGAAA-GCCAGAACUUUUU--GCGAAAUAAUUCGAAAAGUUUGUUGAACCUUAAA-CCUUUCCUGAUGACUCCUUCCUUCUGAACUUCA-CUCAUUAAA-GUUGC
AAWR02038047.1/27233-27348   AAGCAUGCCUUUGAAUUUGAAA-GCCAGAACUUUUU--GCAAAAUAAUUCAAAAAGUUUGUUGAACCUUAAA-CCUUUCCUGAUGAUUCCUUCCUUCUGAAGUUAA-CUCGUUAAA-GUUGC
AF313069.1/487-605           AAACAUGCCUUUGAAUUGGAAA-GCCAGAACUUUUUUUGCAAAAUAAUUCAAAAAGUUUGUUGAACCUUAAA-CCUUUCCUGAUGACUCUUUCCUUCUGAACUUCA-CUCGUUAAAAGUUGC
ABDC01330647.1/1037-1154     AAACACGCCUUUGAAUGGGAAA-GCCAGAACUUUUU--GCAAACUAAUUCGAAAAGUUUGCUGAACCUUAAAACCUUUCCUGAUGACUCCUUCCUUCUGAACUUAAACUUGUUAAA-GUUGC
ACBE01354043.1/875-989       AAACA-GCCUUUGAAUUUGAAA-GCCAGGACUUUUU--GCAAAAUAAUUCAAAAAGUUUGUUGAACCUUAAC-CCUUCCCUGAUGAGUCCUUCCUUCUGAAGUUAA-CUCGUUAAA-GCUGC
AAQQ01580780.1/1283-1395     GCAAGCGCCUGGCGAUUGGAAA--GCAGAGCAUUCU--GCAAAAUGAUUCAAAAAGUUUGUUGAAC-UUAAA-CCUCUCCUGACGACUCCUUGCUUCUGAACUGCA--CUGUUAAA-GUCGC
AAGW02076532.1/32479-32595   AAACACGCCUCUGAAUUGGAAAAGCCAGAACUUUGU--GCAAAAUAAUUCGAAAAGUUUGUUGAACCUUAAA-CCUUUCCUGAUGACUCCUUCCUUCUGAACUUAA-CUCGUUCAA-GUCGC
AABR05014403.1/15454-15571   GAACAUGCCUUUGAAUUGGAAA-GCCAGAACUUUUUU-GCAAAAUAAUUCAAAAAGUUUGUUGAACCUUAAA-CCUUUCCUGAUGACUCCUUCCUUCUGAACUUCA-CUCGUUAAAAGUUGC
#=GC SS_cons                 ::::::::::::::::::::::.:::::::::::::..::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::.:::::::::.:::::
#=GC RF                      aaACauGCCUuuGaAUUgGAAA.GcCAGAaCUUUuU..GCAAAaUaAUUCgAAAAGUUUGUUGAACCUUAAa.CCUUUCCUGAUGAcUCCUUcCUUCUGAAcUuaA.CUcGUUaAA.GUuGC
//
# STOCKHOLM 1.0

#=GF AC   RF01950
#=GF ID   KCNQ1OT1_5
#=GF DE   KCNQ1 overlapping transcript 1 conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   120.00
#=GF TC   165.10
#=GF NC   37.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.65 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18299392
#=GF RT   Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by
#=GF RT   targeting to the perinucleolar region.
#=GF RA   Mohammad F, Pandey RR, Nagano T, Chakalova L, Mondal T, Fraser P, Kanduri
#=GF RA   C
#=GF RL   Mol Cell Biol. 2008;28:3713-3728.
#=GF WK   KCNQ1OT1
#=GF SQ   15


AJ006345.1/252890-253115   ACAUGCUCUGAUUCGCAAUUUUAAAA-AAUCCCU-CUAGCUGGAGCAUAAAUCCUGAAACAGACCCACUUUUCUCCU---CAGCAUGUUAGGAAACACAUUAAAAUACACCCAUAAUCAAGCAACUCAAUCCUU-AAAUUUUUCUCCUACUGAGUAUCUGGAAAACAGGUGCAGAAAUGGAUCAUUUGAGACACCAUAGAAAUCUGGUUAAUCCUGCCUGCCUGCUUUCCUU
AAFC03060667.1/59366-59591 ACAUGCUCUGAUUCACAAUUUAAAAA-GAUCCCU-CUAGCUGGAGCAUAAAUCCUGAAACAGGCCCACUUUUCUCUU---CAACAUGUUUGGAAACACAUUAAAAUAGAAUUCUAAUCAAGCAACUCAAUCCUU-AAAUUUUUCUCCUAGUGAGUAUCUGGAAAACAGGUGCAGAAAUGGAUCAUUUGAGACACCAUAGAAAUCUGGUUAAUCCUGCCUGCCUGCUUUCCUU
ABDC01326871.1/698-923     AUAUGCUCUGGUUCGCAAUUUAAAAA-GAUCACU-CUAGCUGGGGCAUAUAUCCUGAAACAGACCCACUUUUCUCUU---CAGCACAUUUGGAAACACAUUAAAAUAUAACCAUGAUCGAGCAACUCAAUCCUU-AAAUUUUUCUCCUAGUGAGUAUCUGGAAAACAGGUGCAGAAAUGGAUCAUUUGAGACACCAUAGAAAUCUGGUUAAUCCUGCCUGCCUGCUUUUCUU
ABRR01406579.1/3985-4210   ACAUGCUUUGAUUCGCAAUUUAAAAA-GAUCCCU-CUAGCUGGAGCAUAAAUCCUGAAACAGACCCACUUUUCUCUU---UAGCAUGUUUGGAAACACAUUAAAAUAGGGCCGUAAUCAAGCAACCCAAUCCUU-AAAUUUUUCUCCUAGCGAGUAUCUGGAAAACAGGUGCAGAAAUGGAUCAUUUGAGACACCAUAGAAAUCGGGUUAAUCCUGCCUGCCUGCUUUCCUU
ABRN01281485.1/4332-4558   ACAUGCUCUGAUUCACAAUUUAAAAAAGAUCCCU-CUAGCUGGAGCAUAAAUCCUGAAACAGGCCCACUUUUCUCUU---CAGCAUGUUUGGAAAUACAUUAAAAUAGAGCUGUAAUCAAGCAACCCAAUCCUU-AGAUUCUUCUCCUAGUGAGUAUCUGGAAAACAGGUGCAGAAACGGAUCAUUUGAGACACCGUAGAAAUCUGGUUAAUCCUGCCUGCCUGCUUUCCUU
AAQQ01580785.1/4458-4682   ACAUGCUCUGAUUCGCAAUUUUAAAA-GAUCCUU-CUAGCUGGAGCAUGAAUCCUGAAACAGAUCCACUUUUCUCUU---CAGCAUGUUUGGAAACACAUUAAAAUAGAACCAUGAUCA-GCAACCCAAUCCUU-AAAUUGUUCUCCUAGUGAGUAUCUGGAAAACAGGUGCAGAAAUGGAUCACUUGAGACACCAUAGAAAUCUGGCUAAUCCAGCCAGCCUGCUUUCCUU
EU746661.1/2111-1886       ACAUGCUCUGAUUCGAAAUUUUAAAA-GAUCCUU-CUAGCUG-AGCAUAAAUCCUGAAACAGAUCCACUUUUUUUCU--UCAGUAUGUUUGGUAAUAUAUUAAAAUAGAACCAGAAUCAAGCAAUCCAAUCCUU-AAAUUUUUCUCCUAGUGAGUAUCUGGAAAACAGGUGCAGAAAUGGAUCAUUUGAGACACCAUAGAAAUCUGGUUAAUCCUGCCUGCCUGCUUUCCUU
ABRO01118009.1/1114-1338   ACAUGCUCUGAUUCGCAAUUUUAAAA-G-CCCCU-CUAGUUGGAGCAUAAAUCCUGAAACAGAUCCACUUUUCUCUU---CAGCAUGUUUGGAAACACAUUAAAAUAGAACCAUAAUCAAGCAACCCAAUCCUU-AAAUUUUUCUCCUAGUGAAUAUCUGGAAAACAGGUGGAGAAAUGGAUCAUUUGAGACACCAUAGCAAUCUGCUUAAUCCUGCCGGCCUGCUUCCCUU
AAWR02038047.1/50992-51214 ACAUGCUCUGAUUCGGAAUUUUAAAA-GAUCCGU-CUAACUGGAGCAUAAAUCCUGAAUCGGGCCCACUUUGCUCUU---UAGCAUGUUUGGAA--ACAUUAAAAUAGAACCGUAAUCAAGCAACCCAAUCCUU-AAAUUUUUCUCCUAGUGAGUAUCUGGAAAACAGGUGCAGAAAUGGAUCAUUUGAGACACCAUAGAAAUCCGGUUAAUCC-GCCUGCCUGCUUUCCUU
CAAA01139533.1/33040-32817 ACAUGCUCUGAUUCGAAAUUUUAAAA-GAUCCUU-CUAGCUGGAGCACAAAUCCCAAAACAGAUCCACUUUUUUUCU--UCAGUGUGUUUGGUAACACAUUAAAAUAGAACUAUAAUCAAGCAAUCCAAUCCUUUAAAUUUUUCUCCUAGU----AUCUGGAAAACAGGUGCAGAAAUGGAUCAUUUAAGACACCAUAGAAAUCUGGUUAAUCCUGCCUGCCUGCUUUCCUU
ACBE01354040.1/6332-6558   ACAUGCUCUGACUCCCGAUUUAAAAA-GAUCCCUCUUAGCUGGAGCGUAAAUCCCGAAACAGGCCCACUUUUCUCUU---CAGCAUGCUUGGAAACACAUUAAAAUAGAACCGUAAUCAAGCAACCCAAUCCUU-CAGUUUUUGUCCCAGCGAGUAUCUGGAACACAGGUGCAGAGAUGGAGCAUUCGAGACACCAUAGAAAUCUGGUUAAUCCUGCCUGCCGGCUCUCCUU
AABR05014405.1/3215-3442   UUGGACUCU-AUUCGCAAUUGUAAAA-GAUCCUU-CUAACUGGGGCAUACAUCCCGAAACACCCUCUUUUUUUCCCCCGUCAGCGUGUCUGGUAACACAUUAAAAUAGAAUCGUAAUCAAGCAAUC-AGUCCUUUAUAUUUUCCUCCUAGUGAGUAUCUGGAAAACAGGUGCAGAAAUGGAUCAUUUGAGACACCGUAGAAAUCUGGUUAAUCCUGCCUGCCUGCUUUCCUU
AAGW02076532.1/51240-51462 ACAUGCUCUGAUUCGCAGUUUAAAAA-GCUCCCU-UUAGCUGGAGCAUAAAUCCCAAAACAGAGCCACUUU-CUCCU---CAGCAUGUUUGGAA--ACAUUAAAAUAGACCCACAAUCAAGCAACCCGAUCCUU-ACAUUUUUCUCCUCGUGAGUCUCUGGGAAACAGGUGCAGACAUGGCUCAUUUGAGACACCAUAGAAAUCUGGUUAAUCCUGCCUGCCCGCUCUCCCU
AAQR03144845.1/2360-2136   AUAUGCUCUGAUUCACAAUUUAAAAA-GAUCCCU-CUAGCUAGAGCAUAAAUCCUGAAACAGAACCACUUUU-UCUU---CAGCUUGUUUGGAAACACAUUAAAAUAGAACCAUAAUCAGGCAACUCAAUCCUU-AAAUUUUUCUCCUAGUGAGUAUCUGGAAAACAGGUGCAGAAAUGGAUCAUUUGAGACACCAUAGAAAUCUGGUUAAUCCCGCCUGCCUGCUUUUCUU
AAGU03089034.1/6934-7155   ACACGCUCUGACUCUCAUCUUAAAAA-GAUCCCU-CCAGCUACAGCAUAAGUCCUAAAACAGGCC-ACUGUUCUCUU---CGGCGUGUUUGGAA--ACAUUAAAAUAGAGCUGUAAUCAAGCAAGCCGAUCCUU-AAAUUCUUCUCCUAGCGAGUAUCUGGGAAACAGGUGCAGAAACGGAUCAUCUGAGACACCAUAGAAAUCCGUUUAAUCC-GCCUGCCUGCCUUCCUU
#=GC SS_cons               ::::::::::::::::::::::::::.:::::::.::::::::::::::::::::::::::::::::::::::::::...::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    acAuGCUCUGAuUCgcAaUUUuAAAA.GaUCCcU.cUAGCUGGaGCAUAaAUCCuGAAACAGacCCaCUUUUcUCuU...CAGCaUGUUUGGaAAcACAUUAAAAUAGAaccguaAUCAAGCAAccCaAUCCUU.aaAUUuUUCUCCUaGuGAGUaUCUGGaAaACAGGUGCAGAaAUGGaUCAUUUGAGACACCaUAGAAAUCuGgUUAAUCCuGCCuGCCuGCUuUCCUU
//
# STOCKHOLM 1.0

#=GF AC   RF01951
#=GF ID   SOX2OT_exon1
#=GF DE   SOX2 overlapping transcript exon 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; RNAz; Eberhardt R
#=GF SS   Predicted; RNAz;
#=GF GA   65.00
#=GF TC   68.20
#=GF NC   54.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.49 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0007275; multicellular organism development;
#=GF RN   [1]
#=GF RM   12612584
#=GF RT   Mutations in SOX2 cause anophthalmia.
#=GF RA   Fantes J, Ragge NK, Lynch SA, McGill NI, Collin JR, Howard-Peebles PN,
#=GF RA   Hayward C, Vivian AJ, Williamson K, van Heyningen V, FitzPatrick DR
#=GF RL   Nat Genet. 2003;33:461-463.
#=GF RN   [2]
#=GF RM   19767420
#=GF RT   Complex architecture and regulated expression of the Sox2ot locus during
#=GF RT   vertebrate development.
#=GF RA   Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC,
#=GF RA   Mattick JS
#=GF RL   RNA. 2009;15:2013-2027.
#=GF CC   SOX2 overlapping transcript (SOX2OT) is a long non-coding RNA, containing
#=GF CC   at least 5 exons. The SOX2 gene, an important regulator of neurogenesis,
#=GF CC   lies within one of the introns of SOX2OT [1]. SOX2OT and SOX2DOT (an
#=GF CC   isoform of SOXOT transcribed from a distal highly conserved element) are
#=GF CC   expressed in zones of neurogenesis within the brain. It is associated with
#=GF CC   central nervous system structures in zebrafish and chicken embryonic
#=GF CC   brains, and is dynamically regulated during embryogenesis [2]. SOX2OT may
#=GF CC   play a role in vertebrate development [2].
#=GF WK   SOX2OT
#=GF SQ   29


AANN01366326.1/1470-1700     ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAAAACUCCCCGUGCAC----UAGGGCUGACUGUAGCUGGGGGAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUACAGUCAGCUGGUCCCUCUCCUCAGGUGUAGACCACCU-----AUUAUCAUUUUACCU-GUUUUGAUUCUCUGAUGA-GCAAAGUCCCAAGACUUAUCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
ABRN01126490.1/7524-7752     ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGGAAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUAUAGUCAGCUGGC-CCUCUUCUCAGGUGUAGAUCACCA-----AUUAUCAUUUCACCU-GUUUUGAUUCUCUGAUGA-GGAAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
AC125613.2/39238-39007       ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAAAACUCCCCUUGCAC----CAGGGCUGACUGUAGCUGGGGGAAGACAUUUUACUCAUUUGCUCUUUCCUUUCAUACAGUCAGCUGGUCCCUCUUCUCAGGUGUAGAUCACCU-----AUUAUAAUUUUACCUAAUUUUGAUACUCUGAUAA-GGAAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCACUUA----CAAGACAGCUCU
ABRO01225737.1/1212-1442     ACAGCUUUGGACAAAAGUCUACACA-GCCAGU-----GCAUCU-GAA-ACUCCCC-UUUGC----ACAGGCUGACUGUAGCUGGGAGAAGACAUUUUACUCAUUUGCUCUCUCCCUUCAUGUGGUCAGCUGGCCCCUCUUCUCAGGUGUAGAUCACCU-----AUUAUAAUUUCACCUAAUUUUGAUCCUCUGAUGG-GGAAA-UCCCCGAACUAAUCAACUGAGAUAGGCCUUACUUC----CAAGGCAGCCCU
ABRP01114048.1/897-1125      ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGGGAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUGCAGUCAGCUGGC-CCUCUUCUCAGGUGUAGAUCACCU-----AUUAUCACUUCACCU-GUUUUGAUUCUCUGAUGA-GGAAAGUCCCAGGACUUACCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
ABGA01081645.1/4683-4453     ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----CAGGGCUGACUGUAGCUGGGGGAAGACAUUUUACUCAUUUGCUCUUUCCUUUCAUACAGUCAGCUGGUCCCUCUUCUCAGGUGUAGAUCACCU-----AUUAUAAUUUUACCUAAUUUUGAUACUCUGAUAA-GGAAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCACUUA----CAAGACAGCUCU
AAGV020241585.1/5541-5772    ACAGCUUUGGACAAAAGUGUA--GA-GCCAGUGCAGUGCAUUU-GAA-ACUCCCCUAGCAC----AAGGGCUGACUGUAGCUGGGGGAAGACAUUUUACUCAUUUGCUCUCUUCUUUCAUACAGUCAGCUGGUCCAUCUUCUCAGGUGUAGAUCACCU-----AUUAUAAUUUCACCU-GUUUUGAUACUCUGAU----GAAAGUCCCAGGACUUGUCAGCUGGGAUAGGCCUCAUUUA----CACGACAGCUCU
AALT01445771.1/2327-2101     ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCCUGCAC----AGGAGCUGACUGUAGCUGGG-GAAGACAGUUUACUCAUUUGCUCUCUCUUUU--CAUAGUCAGCUGGUCCCUCUCCUCAGGUGUACAUCACCU-----AUUAUCAUUUCACCU-GUUUUGGUUCUCUGAUGA-GGAAAGUCCUAGGACUUGUCGGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
AC137708.16/84396-84183      ACAGCUUUGAACAAAAGUCCA--CA-GCCAGU-----GUGUUC-CAA-G-UCCC--UGCUC----A-GGGCUGACUGUGGCAGGGG----ACACUCUCC-UGCUGGCUCUCUCUGUCCACAC--UUAGCUGGCUCCUGUCCUCAGGUGCACGGCCACA---------CCCUCGCACCCAACCUUGAUCCUCUGAUGG-GGAAGGUCCCAGGACUUGUCUGCUGGGACAGGCCUCACCCC----CAAG--AGCUCU
AAFR03036277.1/29988-29757   ACAGCUUUGGACAAAAGUCUA--GA-GUCUCU-----GCAUUG-GUA-ACUCUCCGUGCACGCACAAGGGCUGACUGGGGCUGUGGGAAGACAUUUUCCUUAUUUGCCUUCUCCUUUCUUCCAGUCAUCUUGUCCCUCUUCUCAGGUGUUGUUCACCU-----AUUAUCAUUUCACCU-GUACUGGUCCUCUGUGGG-GGAAAGUCCUGGGACUUGUCAGCUGGUCUAGGCCUCAU--A----AAAGACAGCUCU
AAFC03058731.1/39912-40140   ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGGAAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUACAGUUAGCUGGC-CCUCUUCUCAGGUGUAGAUCACGU-----AUUAUCAUUUCACCU-GUUUUGAUUCUCUGAUGA-GGCAAGUCCCAGGACUUAUCAGCAGGGAUAGGCCUCAUUGC----CAAGACAGCUCU
AAPN01099322.1/2430-2657     ACAGCUUUGGACAAAAGUCUG--UA-GCCAGU-----GCAUUC-GUA-ACUCCCCUUACAC----AAGGGCUGACUGAGGCUGUGGGAAGACAUUUUACUCAUUUGCUUUCUUUUUUCUUAGAGUCAUCUUGU-CCUUUUCUCAGGUGUUUAUCACCU-----AUUAUCCUUUCACCU-GUAUUGGUACUCUGGUGGGAGAAAGUCCCAGGAAUUGUCCGCCGGUAUAGGCCUCAUUA------AAUGCAGCACU
AAHX01016250.1/33739-33953   ACAGCUUUGAACAAAAGUCCA--CA-GCCAGU-----GUGUUC-CAA-G-UCCC--UGCAC----A-GGGCUGGCUGUGGCAGGGG----ACACUCUCC-UGCUGGCUCUCUCUGACCACACA-UUAGCUGGCUCCCAUCCUCAGGUGCACGGCCACA---------CCCUUGCACCCAACCUUGAUCCUCUGAUGG-GGAAGGUCCCAGGACUUGCCAGCUGGGACAGGCCUCACCCC----CAAG--CGCUCU
AAIY01585989.1/8148-7939     -------------AAAGUCUG--CA-GCCCGA-----GCAUUU-GAA-ACUCCCC-UUCAC----AAGGGCUGACUGUAGCUGGGGGAAGACGGUCUACUCAUCUGCUCUCUCCU----UUCAGCCAGCGGGC-UGUCUUCCCAGGUGUAGAUCACCU-----AUUCUAACUUCACCU-GUUUUGAUACCCUGAUGA-GGAAAGUCCCAGGACUUGUCAGCUGGGAUAGGCCCCAU-GA----CAGGGCCGCUCG
AAPY01688537.1/200-425       ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGACUGACUGUAGCUGUGGGAAGACAUUUUCCUCAUUUGCUCUCUCCUUGCA-GCAGUCAGCUGGUCCCUCUUCUCAGGUGUAAAUCACCU-----AUUAUAAUUUCCCCCAGUUUUGAUACUCUGAUGA-GGAGCGUCCCAGGACUUCUCAGCUGGGGUAGGCCUCA--------CAGGACAGCUGU
AAWR02011604.1/18990-19219   ACAGCUUUGCACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUGGCCGGGGGAAGACAGUUUACUCAGUUGCUCUCUCCUUUCAUACAGUCAGCUGGUCCCUCUUCUCAGGUGUAGAUCACCU-----AUUACCACUUCACCU-GUUUUGAUUCUCUGAUGA-GGAAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCAUUCA----CAAGACACCUCU
AADA01128044.1/22312-22542   ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----CAGGGCUGACUGUAGCUGGGGGAAGACAUUUUACUCAUUUGCUCUUUCCUUUCAUACAGUCAGCUGGUCCCUCUUCUCAGGUGUAGAUCACCU-----AUUCUAAUUUUACCUAAUUUUGAUACUCUGAUAA-GGAAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCACUUA----CAAGACAGCUCU
ABRQ01540146.1/2411-2186     ACCUUUCUGGACA-AAGUCUA--CA-GUCAGU-----GCCUGU-GAA-ACUCCCCU-UUAC----AACAGCUGACUACAGCUGGGUAAAGACGUUUUUCUCCUUUGCUCUCUCUUCUCAUACAGUCAGCUGGUCAGUUUCCUCAGAUGUACAUCACCU-----GUUAUAAUUUCACCC-GUGUUGCUACUCUGUUGG-GGAAAGCCCCAGGGCUUAUCAACUGGUACAGGCCUCAUUC-----CUAGACAUCUC-
AANG01283917.1/126-354       ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGGGAAGACAGUUCACUCAUUUGCGCUCUCCUUUCAUACAGUCAGCUGGC-CCUCUUCUCAGGUGUAGAUCACCU-----AUUAUCAGUUCACCU-GUUUUGAUUCUCUGAUGA-GGAAAAUCCCGGGACUUAUCAGCCGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
ABRR01048073.1/2456-2683     AUAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----CAGGGCUGACUGUAGCUG-GGGAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUACAGUCAGCUGGC-CCUCUCCUCAGGUGUAGAUCAUCU-----AUUAUCAUUUCACCU-GUUUUGAUUCUCUGACGA-GGAAGGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
AAKN02040493.1/80620-80846   AGAGCUUUGGACAA--GUCUA--CAGACCAGU-----GCAUUU-GAA-AUUCUCUCCGCAC----CAGGGCUGAGUGUAGCU--GGGAGGACAUUUUACUCAUCUGGGCUCUCCCUUCCCACAGUCAGCUGGUCCCUCUGCUCAGGUGUAGAUCACCU-----AUUAGAAUUUCACCAAAUUUUGAUAGUCUGCUGA-GGAAAGUCCCAGGAUUUAGCAGCUGGGAUAGGCCUCACUCA-----AAGACAGCUCU
ABQF01023293.1/142705-142930 ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUC-GUA-ACUCCCCAUGCAC----AAGAGCUGACUGUGGCUCUGGGAAGACAUUUUACUCAUUUGAUUUCUUUUUUCUUGUAGUCUUCUUGU-CCAGUUCUCAGGUGUUUACCACCU-----AUCAGAAUUUCACCU-GUAUGGGUCCUGUGCUUG-AGAAAGUCCCAGGACCUGUCAGCUG-CAUAGGCCUCAU--A----AAAGACAGCUCU
AANU01300153.1/26633-26403   ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-AUUCCCCUUGCAC----CAGGACUGACUGUAGCUGGGGGAAGACAUUUUACUCAUUUGCUCUUUCCUUUCAUACGGUCAGCUGGUCGCUCUUCUCAGGUGUACAUCACCU-----AUUAUAAUUUUAUCUAAUUUUGAUACUGUGAUAA-GGAAAGUCCCAGGACUUAUCAGCUGGGACAGGCCUCUCUUA----CAAGACAGCUCU
AAWZ02017091.1/182975-183205 ACAGCUUUGGACAAAAGUCUA--UA-GCCAGA-----GCAUUCAGUA-AUUCCCCAUGCAC----AAGAGCUGACUGUGUCUCUGGGAAGACAUUUUACUGGUCUGCUUUCUUAUUUCCU--AGUUUUCUAGU-UCUUCUCUCAGGUGUUUGAUACUU-----AUUUGUCUCUCACCU-GCCUG-GGGCACUGCUUG-AGAAUAUUCUGCACCAUGUCAGCUGAUGUAGGUCUCAUAAAGAGUAAAGACAGCUCU
AAPE02008683.1/49518-49286   ACAGCUUUGGACAAAAGUCUA--UA-GCCCGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGG-GAAGACAGUUUACUCAUUUGCUCUCUCCUUUCAUGCAGUCAGCUGGC-CCUCUUCUCAGGUGUAGAUCACCUAACCCAUUAUCAUUUCACCU-GUUUUGAUUCUCUGAUGA-GGAAAGUCCCAGGACUUAUCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
AAGW02014129.1/117891-117663 AGAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUCU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGAGAAGACAUUUUACUCAUUUGCUCUCUCCUUUCAUACGGUCAGCUGGUCCCUCUUCUCAGGUGUAGAUCC-UU-----AGCCUAAUUUCACUA-AUUUUGAUACUCUGAUGA-GGAAAGUCCCAGGACUUAUCAGCUGGGACAGGCCCCACUUU----CGAGACAGCUCU
AAEX03017260.1/647400-647628 ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUU-GAA-ACUCCCCUUGCAC----AAGGGCUGACUGUAGCUGGGGGAAGACAGUUGACUCAUUUGCUCUCUCCUUUCACACAGUCAGCUGGC-CCUCUUCUCAGGUGUAGAUCACCU-----AUUAUCAUUUCACCU-GUUUUGAUUCUCUGAUGA-GGAAAAUCCCAGGACUUAUCAGCUGGGAUAGGCCUCAUUUA----CAAGACAGCUCU
AADN03005748.1/46889-46664   ACAGCUUUGGACAAAAGUCUA--UA-GCCAGU-----GCAUUC-GUA-ACUCCCCAUGCAC----AAGAGCUGACUGUGGCUCUGGGAAGGCAUUUUACUCAUUUGCUUUCUUUUUUCUUAUAGUCUUCUUGU-CCAGUUCUCAGGUGUUUACCACCU-----AUUUGAAUUUCACCU-GGGUGGGUACUGUGUUUG-AGAAAGUCCCAGGACUUGACAGCCG-UAUAGGCCUCAU--A----GAAGGCAGCUCU
AAQR03159363.1/19-244        ACAGCUUUGGACAAAAGUCUA--CA-GCCAGU-----GCAUUU-GAA-AGUCCCCCUGCAC----CGGGGCUGACUGUAGCUGGGGAAAGACAUUUCACUCAUUCGCUCUUCCCUUUCAUGCA-CCAGCUGGUCCCUCUCCUCAGGUGUAGACCACCU-----AUUAUAAUUUCACCCAAUUUUGAUACUCUGAUGA-GGAAAGUCCCAGGACUUCCCAGCUGGGAUAGGCCUCA--------CAAGACAGCUGU
#=GC SS_cons                 :::::::::::::::::::::..::.::::::.....::::::.:::.:::::::::::::....:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.....:::::::::::::::.::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::....::::::::::::
#=GC RF                      ACAGCUUUGGACAAAAGUCUA..uA.GCCaGU.....GCaUUu.GaA.AcUCCCCuUGCAC....aaGGGCUGACUGuaGCUGgGGGAAGACAuUUUaCUcaUUUGCUcUCUccuUUCaUacAGUCagCUgGucccUcUuCUCAGGUGUagauCaCCU.....AUUauaaUUUCACCu.guuUUGaUaCUCUGaUgg.GGAAaGUCCCaGGaCUUguCaGCUGGgauAGGCCUCAuuua....cAaGaCAGCUCU
//
# STOCKHOLM 1.0

#=GF AC   RF01952
#=GF ID   SOX2OT_exon2
#=GF DE   SOX2 overlapping transcript exon 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   45.00
#=GF TC   57.70
#=GF NC   38.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.10 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0007275; multicellular organism development;
#=GF RN   [1]
#=GF RM   12612584
#=GF RT   Mutations in SOX2 cause anophthalmia.
#=GF RA   Fantes J, Ragge NK, Lynch SA, McGill NI, Collin JR, Howard-Peebles PN,
#=GF RA   Hayward C, Vivian AJ, Williamson K, van Heyningen V, FitzPatrick DR
#=GF RL   Nat Genet. 2003;33:461-463.
#=GF RN   [2]
#=GF RM   19767420
#=GF RT   Complex architecture and regulated expression of the Sox2ot locus during
#=GF RT   vertebrate development.
#=GF RA   Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC,
#=GF RA   Mattick JS
#=GF RL   RNA. 2009;15:2013-2027.
#=GF CC   SOX2 overlapping transcript (SOX2OT) is a long non-coding RNA, containing
#=GF CC   at least 5 exons. The SOX2 gene, an important regulator of neurogenesis,
#=GF CC   lies within one of the introns of SOX2OT [1]. SOX2OT and SOX2DOT (an
#=GF CC   isoform of SOXOT transcribed from a distal highly conserved element) are
#=GF CC   expressed in zones of neurogenesis within the brain. It is associated with
#=GF CC   central nervous system structures in zebrafish and chicken embryonic
#=GF CC   brains, and is dynamically regulated during embryogenesis [2]. SOX2OT may
#=GF CC   play a role in vertebrate development [2].
#=GF WK   SOX2OT
#=GF SQ   14


BC041898.2/209-277         AAAGCCUGACAGGUUUCUUCGGAAAAGUGGCCAUCCAUGGAAUGAAUGAAAUGUUCUCUUUCUAUUCCA
AALT01445771.1/1960-1892   AAAGCCUGACAGGUUUCUCUGGAAAAGUGGCCAUCCAUGGAAUGAAUGAAAUGUUCCCUUUCUCUUCCA
AAKN02040493.1/81032-81100 AAAACCUGACAGGUUUCUUCGGGAAAGUGGCCAUCCAUGGAAUGAGUGAAAUGUUCUCUUUCUGUUCCA
AAPY01688537.1/555-623     AAAGCCUGACAGGUUUCUCCGGAAACGUGACCAUCCACGGAAUGAAUGAAAUGUUCUCUUUCUAUUCCA
ABRO01225737.1/1582-1650   CAAGCCUGACAGGUUUCUCCAGGAAAGUGGCCAUCCAUGGAAUGAAUGAAAUGUUCUCUUUCUAUUCCA
AAFC03058731.1/40275-40343 AAAGCCUGACAGGUUUCUCCGGGAAAGUGACCAUCCAUGGAAUGAAUGAAAUGUUCCCUUUCUAUUCCU
AANN01366326.1/1881-1949   AAAGCAUGACAGUUUUCUCCGGAAAAGUGGUCAUCCAUGGAAUGAAUGAAAUGUUCCCUUUCUGUUCCA
AAGV020241585.1/5906-5973  AAACCCUGACAGCUUUCUCUGGAAAAGUGGCCAUC-AUGGAAUGAAUGAAAUGUUCCCUUUCUAUUCCA
AAHX01016250.1/34120-34186 CAAACCUGACAGAUUUCUCCAGAAAAGUGGCCAUCCAUGGAAUGAGUGAAAU--ACUCUUUCUAUUCCA
ABRP01114048.1/1258-1324   AAAACCAGACAGUUUUCUCCGGAAAAGUGGCCAUCCAUGGAAUGAAUGAAAUGUUCCCUU-CUA-UCCA
AC137708.16/84020-83954    CAAACCUGACAGAUUUCUCCAGAACAGUGGCCAUCCAUGGGAUGAGUGAAAG--CCUCUUUCUAUUCCA
ABRQ01540146.1/2165-2098   CAAGCUUGACAGGUAUCUCCAUAAAAGUGGCCAUCCA-GGAAUGAAUGAAGUGUUCCCUUUCUGUUCCA
ABQO010031765.1/709-777    AUAGUGUGACAGGUUUCAGCGAAAAGGGGGUCCUCCUCGGAAUGAAUGAAAGGUCCUUUUCCCAUUCCA
AAPE02008683.1/49152-49084 AAAACCUGACAGGUUUCUCUGGAAAAGGGGCCUUCCGUGGAAUGAAUGAAAUGUUCCCUUUCUAUUCCA
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    aAAgCcUGACAGgUUUCUcCGGAAAaGUGGCCAUCCaUGGAAUGAAUGAAAUGUUCuCUUUCUaUUCCA
//
# STOCKHOLM 1.0

#=GF AC   RF01953
#=GF ID   SOX2OT_exon3
#=GF DE   SOX2 overlapping transcript exon 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   70.00
#=GF TC   83.00
#=GF NC   59.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.82 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0007275; multicellular organism development;
#=GF RN   [1]
#=GF RM   12612584
#=GF RT   Mutations in SOX2 cause anophthalmia.
#=GF RA   Fantes J, Ragge NK, Lynch SA, McGill NI, Collin JR, Howard-Peebles PN,
#=GF RA   Hayward C, Vivian AJ, Williamson K, van Heyningen V, FitzPatrick DR
#=GF RL   Nat Genet. 2003;33:461-463.
#=GF RN   [2]
#=GF RM   19767420
#=GF RT   Complex architecture and regulated expression of the Sox2ot locus during
#=GF RT   vertebrate development.
#=GF RA   Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC,
#=GF RA   Mattick JS
#=GF RL   RNA. 2009;15:2013-2027.
#=GF CC   SOX2 overlapping transcript (SOX2OT) is a long non-coding RNA, containing
#=GF CC   at least 5 exons. The SOX2 gene, an important regulator of neurogenesis,
#=GF CC   lies within one of the introns of SOX2OT [1]. SOX2OT and SOX2DOT (an
#=GF CC   isoform of SOXOT transcribed from a distal highly conserved element) are
#=GF CC   expressed in zones of neurogenesis within the brain. It is associated with
#=GF CC   central nervous system structures in zebrafish and chicken embryonic
#=GF CC   brains, and is dynamically regulated during embryogenesis [2]. SOX2OT may
#=GF CC   play a role in vertebrate development [2].
#=GF WK   SOX2OT
#=GF SQ   11


BC016393.1/9-284           UGGCAAAGCUAG-GCUAGGUCUUGGAGGCUGGUGUAAGGCGAUGU-GGGUGAAGGCAGGAGGCUGAUGG----AAAGACUGGGGGGAAGAAAAGCCGAAAUGGAUUCA--CGGUGCCUUGGAUGAAGGACGAG----AGGGG-AACUGCAAGCU-CCUUCAACUGGUUCUGUCCGGUGAGAAGUGAUCA-AGCUU--GGGCUGACAAGAGGCUCAGGGAGCCCUCACGUUCUUUCGCUUUUUUACCUGCCAAUCAAACUGCUACAAGACAACACCCUGAUCUGGCAUGGACAU
AAGV020163728.1/399-671    UGGCAAAGCUAG-GCUAGGUCUUGGAGGCUGGUGUAAGGCGAUGC-GGGUGAAGGCA-GAGGCUGUUGG----AGAGACUGGGGAGAAGAAAAACCGAAAUGGAUUCA--CGGUGCCUUGGAUGGAGGACGAG----AGGGG-AAUUGCAGGCU-CCUUCAACUCGUUCUGUCCGGUGAGAAGUGAUCA-AGCUU--GGGCUGACAAGAGGCUCAGGGAGCC--CACGUUCUUUCCCUUUUUUACCUGCCAAUCAAACUGCUACAAGACAACACCCUGAUCUGGCGUGGACAU
AAYZ01043855.1/3336-3608   UGGCAAAGCUAG-GCUAGGUCUUGGAGGCUGGUGUGAGG--AUGC-GGGUGAAGGCAGGAAGCUGAUGG----AGAGACUGGGGGGAAGAAAAGCCGAAAUGGAUUCA--CGGUGCCUUGGAUGGAGGAGGAG----AGGGG-AACUGCAAGCU-CCUUCAACUCAUUCUGUCCGGUGAGAAGUGAUCA-AGCUU--GGGCUGACAAGAGACUCAGGGAGCCUUCCCGUGCUUU-GCUUUUUUACCUGCCAAUCAAACUACUGCAAGACAACACCCUGAUCUGGCAUGGACAU
ABRO01132409.1/2494-2771   GUGCAAAGCUAG-GCUAGGUC-UGGAGGCUGGUGUAAGGCGAUGC-GGGUGAAGGCAGGAGGCUGAUGGAGAGAGAGACUGGGGGGAAGAAAAGCCGAAAUGGAUUCA--CGGUGCUUGGGAUAGAGGACGAG---AAGGGG-AACUGCUAGCU-CCUUCAACUCGUUCUGUCCGGUGAGAAGUGAUCA-AGCCU---GGCUGACAAGAGGCUCAGGGAGCCCUCACGUACUUU-GCUUUUUUACCUGCCAAUCAAACUGCUACAAGACAACACCCUGAUCUGGCAUGGACAU
AAKN02040495.1/8460-8723   UGGCAAAGCUAG-GCUAGGUCUUGGAGGCUGCUGCAAGGCGACGC-GGGUGAAGGCAGGCGGCCGA-------------UGGGGAGAGGAAAAGCCGAAAUGGAUUCG--CGGUGACUUGGAUGGAGGCUGA------GGGG-AACUGCGCGCU-CCUCCAACUCGUUCUGUCCGGUGAGAAGUGAUCG-AGCUU--GGGCUGACAAGCGGCUCAGGAAGCCCUCACGUUCUGA-GCUUUUUUACCUGCCAAUCAAACUGCUACAAGACAACACCCUGAUCUGGCACGGACAU
AC137708.16/6368-6097      AGGCAAAGCUAG-ACUAGGUCUUGGAGGCUGGUGUAAGGUGGUGC-GCGG-AAGGCAGGACGCUGAUGG----GAGAGACUGGUCGAAGAAAAGCCUAAAUGGAUUCU--CCGUGCUUUGGAUGGAGAAAGAG----GGGGG-AAGUGCGAGCU-CCUUCAACUCGUUCUGUCCGGUGAGGAGUGAUCC-AGCUU--GGGCUGACGAGAGGCUC-CGGAGCCUUCACGUUCAGU-GC-UUUUUACCUGCCAAUCAAACUGCUACAAGACAACACCCUGAUCUGGCAUGGUCGC
AAPN01061097.1/3331-3597   CGGCAAAGCUAG-GCUAGGAUUUGGAAGGUGGUGUGAGGCGAAGC-GGCUGGAGGCAGGAGGCUAGCGG--------AUUGGGGGGAAGAAAAGCCGAAAUGGAUUCC--CGGGUUCAUGGAUGGAA---GAG----AAGGG-AGUUUCGAAUU-CCUGCAGCUCGGUCUGUCCGGAGAGAAGUGAUCA-AGCCC--CGGCUGUCGAGAGGCUCAGGGAGCCUUUACGUUUUUUCGC--UUUUACCUGCCAAUCAAACUGCUACAAGACAACACCCUGAUCUGGCAUGGACAU
ABRQ01082586.1/2945-3215   AGGCAAAGCUAG-GCUAGGUCUUUGA-GCUGGAAUGAGGCGCUGCUGGGUGAAGCACGGAUCCUGAUGA----AUAGACUGGGGAAAAAAAAAGCCGAAAUGGAUUCU--CGCUGUCU--GGCUGGAGACGAG----AGGCG-AACUGCAGGCU-CCUGCGACUCGUUCUGUCCGA-GGACAGUGAUCA-GGC-U--GGGCUGACGGAAGGCUCAGGGAACC-UCACGUUCUUUCGCGUUUUUACCUGCCAAUCAAACCGCCACGAGACAACACCCUGGUCUGGCUUGGACAC
AAPE02008680.1/2410-2136   UGGCAAAGCUAG-GCUAGGUCUUGGAGGCUGGUGUGAGGCGAAGC-GGGCGAAGGCAGGAGGCUGAUGG----AGAGACUGGGGGGAAGAAAAGCCGAAAUGGAUUCA--CCGUGCCUUGGAUGGAGGAUGAG----AAAGG-AACUGCAGGCU-CCUUCAACU-GCUCUGUCCGGUGAGAAGUGAUCU-AGCUU--GGGCUGACAGGAGGCUGAGGGAGCCCUCACGUUCUUUCGCUUUUUUACCUGCCAAUCAAACUGCUACAAGACAACACCCUGAUCUGCCAUGGACAU
AAHX01016256.1/20172-20444 AGGCAAAGCUAG-GCUAGGUCUUGGAGGCUGGUGGAAGGCGGUGC-GGGU-AAGGCAGGACGCUGAUGG----GAGAGACUGGUCGAAGAAAAGCCGAAAUGGAUUCU--CCGUGCCUUGGAUGGAGGAAGAG----GGGGG-AAGUGCGAGCU-CCUUCAACUCGUUCUGUCCGGUGAGGAGUGAUCC-AGCUU--GGGCUGACAAGAGGCUC-CGGAGCCUUCAUGUUCAGU-GCUUUUUUACCUGCCAAUCAAACUGCUACAAGACAACACCCUGCUCUGGCAUGGACGU
AB092842.1/7177-7438       GUUAAAAGCUAGGGCUAGGACUUGGAG-------------GAC-----GUGUAGGCA---AACGGAAGG----AGA--GCCGGGGGAAGAAAAGCCGAAAUGGAUUCAUUCUCCGUCCUGGCUGGAGGAGGAGAGGAGCGGGGACGUGCGGGCUGCCUGCAGCUGCCUCUGUCCGGUGAGAAGUGCUCCCAGCCCCGCGGCUGACUCG-GGCUCGGGAGUCCGCGCGGACUUU-CGC--UCGAAGCUGCCAAUCAAACCGCUAACCGCCACCACCCUGCGCUGGCACCGACAU
#=GC SS_cons               ::::::::::::.::::::::::::::::::::::::::::::::.:::::::::::::::::::::::....:::::::::::::::::::::::::::::::::::..:::::::::::::::::::::::....:::::.:::::::::::.::::::::::::::::::::::::::::::::::.:::::..::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    ugGcAAAGCUAG.GCUAGGuCUUGGAGGcUGGuGugAGGcGauGC.GGGuGaAGGCaGGaggCuGauGG....agagacugGGGgGAAGAAAAGCCGAAAUGGAUUCa..CgguGccuUGGaUgGAGGauGAG....agGGG.AacUGCggGCU.CCUuCAaCUcguUCUGUCCGGuGAGaAGUGaUCa.AGCuu..gGGCUGaCaaGaGGCUCaGGGagCCuucacGuucuuuCGCuUUuuuAcCUGCCAAUCAAACuGCUAcaaGaCAaCACCCUGauCUGGCauGGACau
//
# STOCKHOLM 1.0

#=GF AC   RF01954
#=GF ID   SOX2OT_exon4
#=GF DE   SOX2 overlapping transcript exon 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   40.40
#=GF NC   31.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0007275; multicellular organism development;
#=GF RN   [1]
#=GF RM   12612584
#=GF RT   Mutations in SOX2 cause anophthalmia.
#=GF RA   Fantes J, Ragge NK, Lynch SA, McGill NI, Collin JR, Howard-Peebles PN,
#=GF RA   Hayward C, Vivian AJ, Williamson K, van Heyningen V, FitzPatrick DR
#=GF RL   Nat Genet. 2003;33:461-463.
#=GF RN   [2]
#=GF RM   19767420
#=GF RT   Complex architecture and regulated expression of the Sox2ot locus during
#=GF RT   vertebrate development.
#=GF RA   Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC,
#=GF RA   Mattick JS
#=GF RL   RNA. 2009;15:2013-2027.
#=GF CC   SOX2 overlapping transcript (SOX2OT) is a long non-coding RNA, containing
#=GF CC   at least 5 exons. The SOX2 gene, an important regulator of neurogenesis,
#=GF CC   lies within one of the introns of SOX2OT [1]. SOX2OT and SOX2DOT (an
#=GF CC   isoform of SOXOT transcribed from a distal highly conserved element) are
#=GF CC   expressed in zones of neurogenesis within the brain. It is associated with
#=GF CC   central nervous system structures in zebrafish and chicken embryonic
#=GF CC   brains, and is dynamically regulated during embryogenesis [2]. SOX2OT may
#=GF CC   play a role in vertebrate development [2].
#=GF WK   SOX2OT
#=GF SQ   10


AC117415.7/93637-93529     CGCGGGUCCAAG-CCUGUAGCCCCAAAUCGG-AUAAUCUCUGCAGCU-GAUAACAAGC--AAAAG--AGAAGC-CAGGCAACAGCC-AUAUUAAAGAAGAAAA-CAAUCAACUCUGAGG
AALT01268037.1/157-49      CGCGGGUCCUAG-CCUGUAGCCCCCAAUCGG-AUAAUCUCUGCAGCU-GAUAACAAGC--AGAAG--CGAAGC-CAGGCAACAGCC-AUAUUAGAAAAGAAUA-CUGUCAACUCUGAGG
AAYZ01043859.1/320-428     CGCGGGUUCAAG-CCUAUAGCCCCCAAUCGG-AUAAUCUGUGCAGCU-GAUAACAAGC--CAAAG--AGAAGC-CAGGCAAGAACC-AUAUUAAAGAAGAAAA-CAAUCAACUCUGAGG
AAPN01427697.1/6192-6084   CGCGGGUGCAAG-CGUGUAGCCCAAAUUCGG-AUAAUCUUUCCAGCU-GAUAACAAGC--GAAAG--AGAAGC-CAGGCGUCAGCC-AAAUUAAAGAAGAAAA-CUGCCAACUCUGAGG
AAIY01797440.1/794-680     CGCGGGUCCAAGGCCUGUAGCCCCAAAUCGGGAUAAUCUCUGCAGCUUGAUAACGAGC--AAAAG-GAGAAGC-CAGGCAACAGCCCAUAUUAAAGAAGAAAAGCAAUCGACUCUGAGG
AAFC03045141.1/26492-26601 CGUGGGUCCAAG-CCUGUAGCCCCAAAUCGG-AUAAUCUCUGCAGCU-GAUAACAAGC--AAAAG--AGAAGC-CAGGCAACAGCC-AUAUUCAGCCCCAGAGAUCUAACCUUCUCGGG
ABRQ01082590.1/2614-2722   CGCGGGUCCAAG-CCUGUAGCCCCAAGUCGG-AUAAUCUCUGCAGCU-GGUAACAAG----GCAGCCAGAAGC-CAGGCGGCAGCC-CUAGUCGAGAAGGAAG-CCACCAGCGCCGAGG
AABR05085448.1/5273-5381   CGCGGGUCCAAG-CCUGUAGUCCCAAAUCGG-AUAAUCUCUGCAGCU-GGUUACACGC--AAAAG--AGAAGC-CAGGCAACAGAC-AUAUUACAGAAGAAAG-CUCUCGACUCCGAGG
AAPE02008677.1/2320-2214   CGCGGGUCCAAG-CCUGUAGCCCCAGAUCGG-AUGAGCUAUGCAGCU-GAUAACAAGC--AAAAGAGAGAAGC-CAGGCAACAGAC-AUAAUAAAGAAGAAAA-----CAACUCUGAGG
AB092842.1/19369-19469     CGCG------G----UGUAGCCCCAAUUCGG-ACAAUCUCUGCAGCC-GGUCGCAAGCCCCAAAG--AGAAGCGCUGGCGCCCGCC-AGAUAGGAGGA--GAG-CUCCGCCGUCGGUGC
#=GC SS_cons               ::::::::::::.::::::::::::::::::.:::::::::::::::.::::::::::..:::::..::::::.::::::::::::.::::::::::::::::.:::::::::::::::
#=GC RF                    CGCGGGUcCAAG.CCUGUAGCCCCaAaUCGG.AUAAUCUcUGCAGCU.GaUaACAAGC..aAAAG..AGAAGC.CAGGCaaCAGCC.AuAuUaaAGaAGAaAg.CuaucaacUCuGaGG
//
# STOCKHOLM 1.0

#=GF AC   RF01955
#=GF ID   NEAT1_1
#=GF DE   Nuclear enriched abundant transcript 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   39.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.34 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0042382; paraspeckles;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   19217333
#=GF RT   An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential
#=GF RT   for the structure of paraspeckles.
#=GF RA   Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A,
#=GF RA   Lawrence JB
#=GF RL   Mol Cell. 2009;33:717-726.
#=GF WK   NEAT1
#=GF SQ   17


EF177379.1/476-595         CCAGCAGCCCC--UUUUUUUCCAGACCAAG-GGCUGUGAACCCGCCUGGGGAUGAGGCC-UGGUCUUGUGGA-ACUGAACUUAGCUCGACGGGGCU-----GACCGCUCUGGC--CCAGGGUGGUAUGUAAU
ABRP01112173.1/1638-1517   CCAGCAGUCCCC-UUUUUUUCCAGACAAAG-GGUUGUGAACCCUCCUGGGGAUGAGGCC-UGGUCUUGUGGAAACUCAACUUAGCUUCGCGGGGCU-----GACGGCUCUGGC--CCAGGGUGGUAUGUAAU
ABRN01286765.1/1669-1548   CCAGCAGCCCCC-UUUUUUUCCAGACAGAG-GGUUGUGAACCCGCCUGGGGAUGAGGCC-UGGUGUUGUGGAAACUGAACUUAGCUUCGCGGGGCU-----GACAGUUCUGGC--CCAGGGCGGUAUGUAAU
AAQQ01114696.1/500-378     CCAGCAGCCCCCGUUUUUUUCCAGACAAAG-GGUUGUGAACCUGCCUGGGGAUGAGGCC-UGGUCUUAAGGAAACUGGACUUGGCUUCGCGGGCCU-----GACAGCUCUGGG--CCAGGGUGGUAUGUAAA
ACBE01352828.1/240-357     UCAGCAGCCCCC-UUUUUUUUCAGA----G-GGUUGUGAACCCGCGUGGGGAUGAGGCC-UGGUCUUGUGGAUACUGAACUUAGCUUCGCGGGCCU-----GACAGCUCUGGC--CCAGGGUGGUAUGUAAU
AAWR02004968.1/30426-30305 CCAGCAGCCCCC-UUUAUUUCCAGACAAAA-GGUUGUCAACAAACCUGGAAAUGAGUCC-UGGUCUUGUGGAAACUGAACUCAGCUUCGUGGGGCU-----GACCGCUCUGGC--CCAGGGUGGUAUAUGAC
EF397601.2/432-553         CCAGCCGCCCCC-UUUUUUUCCAGACAAAG-GGGUGUGAGCCCGCCUGGGGAUGAGGCC-UGGUGUGGUGGAAACUGACCUUAGCUUCGCGGGGCU-----GACAGCUCCGGC--CCAGGGCGGUAUGUAAU
AAFC03096522.1/7233-7353   CCAGCAGCCCC--UUUUUUUCCAGACAAAG-GGUUGUGAGCCUGCCUGGGGAUGAGGCC-UCAUGUGGUGGAAGCUGCCCUUAGCUUCGCGGAGCU-----GACAGCUCUGGC--CCAGGGCGGUAUGUAAG
ABDC01174326.1/623-745     CUAGCAGCCCCC-UUUUUUUACAGACAGAG-GGUUGUGAACCAGCCUGGGAAUGAGGCCCUGGUCUUGUGGAAACUGAACUUAGCUCUGCUGGGGU-----GACAGCUCUGGC--CCAGGCUGGUAUGUAAC
CAAA01052165.1/20002-19881 CCAGCAGACCCC-UUUUUUUCCAGAUAAGG-GGUUGUGAACCCACCUGGGGAUGAGGCC-UGGUCUUAUGGAAGGUGGACUUAGCUUCGCUGGGCG-----GACAGCUCUGGC--CCAGGGUGGUAUGUAAU
AAKN02038533.1/33689-33811 CCAGCAGCCCUC-UUUUUUUCCAGACAAAAAGGGUGCCAGCCCAUCUGGGGCUGAGGCC-UGGUCUUGUGGAAACUGGAUUUAGCUUCGCAGGGCA-----GACAGCUCUGGC--CCAGGGUGGUAGGUAAU
AAYZ01096775.1/8704-8824   CUGGCAGCCCUG-UUUUUUUCCAGACAGAG-GGUUGUGAGCGCACCUGGGGAGGAGGCC-UGGUCUUGUGGAAGCUGAACUUAGCUGCGCCAGGCU-----GACAGCUCUG-C--CUGAGGUGGUAUGGAGU
AAHX01009292.1/53182-53308 CCAGCAAAUCGC-UUUUUUUCCAGAUAAGG-GGUUGUGAACCCACCUGGGGAUGAGGCC-UGGUCUUAUGGAAAGUGGACUUAGCUUCGCUGGGCUAGGCCGACAGCUGUGGC--CCAGGGUGGUAUGUAAU
AALT01408676.1/475-364     CCAGCAGCCCCCCUUUUUUUGCAGACCGAG-GGUCGUGAGCUCGCCUGGCGACGCGGCC-UGG--------GAAC--AGCUUGGUCUCGCGGG-CU-----GAGUGCUCUGGC--CCCGGGUGGUAUGUAAG
ABRQ01170408.1/6056-6168   CCAGCAGCCC------------AGACAAAG-CAUUGUGAACCUACCUGGGGAUUAGGCC-UAGUCUUGUGGAAACUGAACUUAGCUUCGUGGGGCU-----GACAGCUCUGGCGACCAGGCCAGGAGAGGCC
AAEX03011638.1/87241-87129 ----CCCCCCCC-UUUUUUUUCAGA----G-GGUUGCGAACCCGCGAGGGGAUGAGGCC-UGGUCUUGUGGAAACUGAACUUAGCUUCGCGGGCC------GACAGCUCUGGC--CUAGGGUAGUGUGUAAU
EF177378.1/442-563         CCAGCAGACCCC-UUUUUUUCCAGAUAAGG-GGUUGUGAACCCACCUGGGGAUGAGGCC-UGGUCUUAUGGAAGGUGGACUUAGCUUCGCUGGGCG-----GACAGCUCUGGC--CCAGGGUGGUAUGUAAU
#=GC SS_cons               ::::::::::::.:::::::::::::::::.::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::.....::::::::::::..:::::::::::::::::
#=GC RF                    CCAGCAGcCCcC.UUUUUUUcCAGACaaaG.GGuUGUGAaCccgCCUGGGGAUGAGGCC.UGGUCUUGUGGAAaCUGaaCUUAGCUuCGCgGGGCu.....GACaGCUCUGGC..CCaGGGUGGUAUGUAau
//
# STOCKHOLM 1.0

#=GF AC   RF01956
#=GF ID   NEAT1_2
#=GF DE   Nuclear enriched abundant transcript 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   60.00
#=GF TC   74.70
#=GF NC   50.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.89 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0042382; paraspeckles;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   19217333
#=GF RT   An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential
#=GF RT   for the structure of paraspeckles.
#=GF RA   Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A,
#=GF RA   Lawrence JB
#=GF RL   Mol Cell. 2009;33:717-726.
#=GF WK   NEAT1
#=GF SQ   13


EF177379.1/841-945         CCUUUUGGACUUUU-----CUCUAGGUU-UGGCGCUAAACUCUUCUUGUGAGCUCACUCCACCCCUUCUUCCUCCCU-UUAAC----------UUAUCCAUUCACUUAAAACAUUACCU---GGU
ABDC01174326.1/965-1074    CCCUUUGGACUUUU-----CUCUAGGUU-UGGUGCUAAACUCUUC-UGUGAGCUCACUCUACCCCU-----CUCCCU-UUAACUCUCUCAAGGGUAU-CAUUCACUUAAAACGUUGCCUCU-GGU
ABRT010652660.1/303-401    CCCUUUGGACU-----------UAGGGU-UGGUGCUAACCUCUUC-UGUGAGCUCACUUUGCCCCUCCU-CCUCCCU-UUAACUUUC---------UCCAUUCACUUAAAUCCUUGCC-CU-GGU
ABRP01112173.1/1324-1212   CCCUUUGGACUUUUC----CUCUAGGUU-CGGUGCUAACCUCUCC-UGUGAGCGCACUCUACC---CCU-CCUCCCU-UUAACUCUCUCGAGGUUGUCCGUUCUCUUAAAAUAUUGCUUCU-GGU
ABRR01570143.1/1273-1160   CCCUUUGGACUUUUC----CUCUAGGUUCCCGUGCUAACCUCUUC-UGUGAGCUCACUCUGCC---CCU-CCUCCCU-UUAAUUCUCUCGAGGUUAUCCAUUCGCUUAAAACAUUGCUUCU-GGU
AANG01068077.1/703-818     CCCUUUGGACUUUUC----CUCUAGGUU-CCGUGCUAACUUCUUC-UGUGAGCUCACUCUGCCCUUCCU-CCUCCCU-UUAACUCUCUCGAGGUUGUCCAUUCGUUUAAAACAUUGCUUCU-GGU
AAQQ01114696.1/217-105     CCCUCUGGAUUU-------CCCUAAGUU-CGAUGCUAAACUCUUC-UGUGAGCUCACUCUACCCCUCCU-CCUCCCU-CUAACUCUCUUGAGGUUAUCCCUUCACUUAAAACCUUGCCUCU-GGU
AAWR02037820.1/1067-1182   CCCUUUGGACUUUCC----CUCUGGGUU-CGGUGCUAACCUCUUC-UGUGAGCUUGCUCUGCCCCUCCU-CCUCCCU-UUAACUCUGUCAAGGUUAUCACUUCACUUAAAACCUUGCUUCU-GGU
ABRN01286765.1/1350-1234   CCCUUUGGACUUUUC----CUCUAGGUU-CCAUGCUUACCUCUUC-UGUGACCUCACUCUACCCUUCCU-CCUCCCUCUUAACUCUCUCGAGGUUACCCCUUCACUUAAAACGUUGCUUCU-GGU
AAPY01121104.1/986-870     CCCUUUGGACUUUUCCUCUCUCUAGGUU-CCGUGCUAACCUCUCC-UGCGAGCUCACUCUAC---UCCU-CCUCCCU-UUAGCUUUCUCGAGGUUAUUCCUUCACUUAACAUGUUGCCUCU-GGU
AAHX01009292.1/53457-53566 CUCUCUGGACUUUGC------CUAGGUU-CCGUGCU-UCCUCUUC-UGUGGUCUCACUCUUCCC-UACU-CUUCCCC-CUCACUCU---GAGGUUAAGGGUUCACUUAAAACCUUGCCUCUGGGU
AACN010689528.1/698-811    CCAUUUGGACUUUUC---UCUCUAGCUU-CGGUGCUAA---CUUC-UGUGAGCUCACUCUGCCCCUCCU-CCUCCCU-UUAGCUUUCUCAAGGUUAUCCAUUCACUUAAAGCAUUGCUUCU-GGU
EF177378.1/732-841         CUCUCUGGACUUUGC------CUAGGUU-CCGUGCU-UCCUCUUC-UGUGGUCUCACUCUUCCC-UACU-CUUGCCC-CUCACUCU---GAGGUUAAGGGGUCACUUAAAACCUUGCCCCUGGGU
#=GC SS_cons               :::::::::::::::....:::::::::.::::::::::::::::.:::::::::::::::::::::::.:::::::.:::::::::::::::::::::::::::::::::::::::::::.:::
#=GC RF                    CCCUuUGGACUUUuC....CUCUAGGUU.CgGUGCUAacCUCUUC.UGUGAgCUCACUCUgCCCcUcCU.CCUCCCU.uUaACUcUCUCGAGGUUAuccaUUCaCUUAAAaCaUUGCcUCU.GGU
//
# STOCKHOLM 1.0

#=GF AC   RF01957
#=GF ID   NEAT1_3
#=GF DE   Nuclear enriched abundant transcript 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   55.00
#=GF TC   57.80
#=GF NC   36.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.61 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0042382; paraspeckles;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   19217333
#=GF RT   An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential
#=GF RT   for the structure of paraspeckles.
#=GF RA   Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A,
#=GF RA   Lawrence JB
#=GF RL   Mol Cell. 2009;33:717-726.
#=GF WK   NEAT1
#=GF SQ   18


EF177379.1/1163-1321         UAGUGUUCCUCAUGGCGAGCAGAUGGAACCGGGAGACAUGGAGUCCCU-GGCCAGU-------GUGAGUCCUAGCAUUGCAGGAGGGGAGACCCUGGAGGAG-----AGAGCCCGCCUCAAUUGAUGCCUGCAGAU---UGAAUUUCCAGAGGCUUAGGAGGAGGA--AG-UUCUCCA
ABRR01570143.1/937-779       UAGUGUUCAUCAUGGCGAUCAGAUGGCACCGGGAGAAAUGGAACCCCU-GGCCAGU-------GUGAGUCGUAGCAGAGCAGGAGGGGAGACCCUGGAGGAG-----AGAGCCCGCCUAAAUUGAUGUCUGCAGAU---UGAAUUUCCAGAGGCUUAGGAGGAGGA--AG-UUCUCCA
EF397601.2/1088-1245         UAGUGUUCAUCAUGGCGAGCUGAUGGCACCAGGAGGA-UGGAGCCCCU-GGCCAGU-------GUGAGUCCUAGCAGUGCAGGAGGGGAGACCCUGGAGGAG-----AGAGCCCGCCUAAAUUGAUGUCUGCAGAU---UGAAUUUCCAGAGGCUUAGGAGGAGGA--AG-UUCUCCA
AAWR02037820.1/1398-1556     UAGUGUUCAUCAUGGCGACCAGAUGGCACCAGGAGAAAUGGAGCCCCU-GGCCAGU-------GUGAGUCAUAGCAGUGCAGGAGGGGAGACCCUGGAGGAG-----AGAGCCCGCCUAAACGGAUGCCUGCAGAU---UGAAUUUCCAGAGGCUUAGGAGGAGGA--AA-UUUUCCA
ABRP01112173.1/991-840       UAGUGUUCAUCAUGGCGAUCAGAUGGCACCAGGAGAAAUGGAGCCCCU-GGCCA---------AUGAGUCCUAGCAGUGCAGGAGGGGAGACCCUGGAGGAG-----AG--CCCGCCUAAUUUGAUGCCUGCAGAU---UGAAUUUCCAGAGUCUUAGGAG---GA--AG-UUCUCCA
ABRT010652660.1/610-768      UAGUGUUCCUCAUGGCGAGCAGAUGGCACCAGGAGAAACGGAGCCCCU-GGCCAGU-------GUGAGUCAUACCAGUGCAGGAGGGGAGUCCCUGGAGAAG---CCAG--CCCACCUAAACUGAUGCCUGCAGAU---UGAAAUUACAGAGGUUUAGGAGAAGGA--AG-CUCUCCA
ACBE01352828.1/939-1098      UAGUGUUCAUCGUGGUGAUCAGAUGGCACCAGGAGAAAUGGAGCCCAU-GGCCAGU-------GUGAGUCGUAGCAGUGCAGGAGGGGAGACCCUGAAGGAG-----AGAGCCCGCCUAAGUUGAUGUCUGCAGAU---UGAAUUUCCAGAGGCUUAGGAGGUGGA--AGUUUCUCCA
AAFC03127117.1/36870-36712   UAGUGUUCAUCAUGGCGAUCUGAUGGCACCAGGAGAAAUGGAGCCCCU-GGCCAGU-------GUGAGUCGUAGCGGUGCAGGAGGGGAGACCCUGGAGGAA-----AGAGCCCGCCUAAAUUGCUGUCUGCAGAG---UGAAUUUCCAGAGGCUUAGGAGGAGGA--AG-UUCUCCA
AAPY01121104.1/650-494       UAGUGUUCAUCAUGGCGAGCAGAUGGCACCAAGAGAACUGGAGCCCCU-GGCCAGU-------AUGAGUCGUAGCAGUGCAGGAGGGGAGACCCUGGAGGAG-----AG--CCCGCCUAAAUUGAUGUCUGCAGAUGAUUGAAUUUCCAGAGGCUUAGGAG---GA--AG-UUCUCCA
ABRQ01073711.1/291-134       UAGUGUUCAUCGUG-CGAUCAGAUGGCACCAGGAGGAGUGGCGCCCCU-GGCCAGU-------GGGAGACGUAGCAGUGCAGGAGGGGAGACCCUGGAGGAG-----AGAGCCCACCUAAAUUGAUGCCUGCUGAU---UGAAUUUCCAG--GCUUAGGAUGAGGAGGAG-UUCUCCA
ABDC01174326.1/1302-1457     UAGUGUUCAUCAUGGCGAGCAGAUGGCACCAGGAGAAAUGGAGCCCCU-GGCCAGU-------GUGAGUCGUAGCAGUGCAGGAGGGGAGACCCUGGAGGAGAGCAGAGAGCCCGCCUAA--------CUGCAGAU---UGAAUUUCCAGAGGCUUAGGAGGAGGA--AG-UUCUCCG
ABRN01073279.1/412-252       UAGUGUUCAUCAUGGCAAGCCGGUGGCACCAGGAGAAAUGGAGCCCCU-GGCCAGU-------GUGAGUCGUAGCCGUGCAGGAGGGGAGACCCUGGAGGAGGAG--AGAGCCCGCCUAAAUUGAUGUCUACAGAU---UGAAUUUCCAGAGGCUUAGGAGGAGGA---G-UUCUCCA
AAGV020174835.1/2555-2389    UAGCCUUCGUCAUGGCGACCAGAUGGCACCAGGAGACAUGGAGCCCCCUGGCCAGUGUCCCGUGUGAGUCGUAGCAGUGCAGCAGGGGAGACCCUGAAGGAG-----AGAGCCCGCCUAAGUUGAUGCCUGCAGAU---UGAAUUUCCAGAGGCUUAGGAGGAGGA--AG-CUCUCCA
ABVD01917905.1/127-287       CCGCAUUCGUCAUGGCGAUCAGAUGGCACCAGGAGAAAUAGAGCCCCU-GGCCAGUGUC----CUGAGUCGUAGCAGUGCAGGAGGGGAG-CCCUGAAGGAG-----AGAGCCUGCCUAAAUCGAUGCCUGCAGAU---UCAGUUUGCAGAGGCUUAGGAGGAGGA--AG-CUCUCCA
BC025215.1/400-551           UAGUGUUCACCAUGGCAAGCAGAUGGCACCAGGAGAUAUGGAGCCCC--UGCCAGU-------GUGAGUCGUAGCAGUGCAGGAGGGCUCACCCUGGAGGAG-----ACAG-CGGCCUCGGUUGACGCCUACACAG---UGAAUU-CCAGAGGCUUAGGAAGCG-----C-GUC-CCU
AAHX01009292.1/53776-53927   UAGCGUUCACCAAGGCAAGCAGAUGGCGCCAGGAGACAUGGAGCCCCCCUGCCAGU-------GUGAGUCGUAGCAGUACAGGAGGGCACACCCUGGAGGAG---ACAG---CUGCCUAAGUUGAUGUCUGCACAG---UGAAUU-CCAGAGGCUUAGGAA--------G-CUCUGCG
AAPE02007326.1/20394-20237   CAGUGUUCAUCAUGGCAAUCAGAUGGCACCAGGACAAAUGGAGCUC-U-GGCCAGU-------GUGGGGCCUAGCAGUGCAGGAGGGGAGAUCCUGAAGGAG-----AAAGCCUGCCUAAACUGAAGCCGGCCAAC---UGAAUUUCCAGAGUCUUAGGAGAAGAA--AA-UUCUCCA
AAEX03016094.1/174667-174515 UAGUUUUCAU---UGUGAUCA---GAUACCAGGAAGAACGGAGCCCCU-GACCAGU-------GUGAGUCAUAGCAGUGCAGGAGAAGAGACACUCCAGGAG-----AGAGCCCACCUAAGUUUAUGUCUGCAGAC---UGAAUUUCCAGAGGCUUAGGAUAUGGA--AG-UUCUUCA
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::.:::::::.......:::::::::::::::::::::::::::::::::::::::.....:::::::::::::::::::::::::::::...:::::::::::::::::::::::::::..::.:::::::
#=GC RF                      UAGugUUCaUCaUGGCGAuCaGAUGGcACCAGGAGaaaUGGAGCCCCu.GGCCAGU.......GUGAGuCgUAGCaGUGCAGGAGGGGAGACCCUGgAGGAG.....AGAGCCcGCCUaAauuGAuGcCUGCagAu...UGAAUUUcCAGAGGCUUAGGAggaGGA..AG.uUCUcCa
//
# STOCKHOLM 1.0

#=GF AC   RF01959
#=GF ID   SSU_rRNA_archaea
#=GF DE   Archaeal small subunit ribosomal RNA
#=GF AU   Gutell RR
#=GF AU   Nawrocki E; 0000-0002-2497-3427
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Published; PMID:11869452
#=GF SS   Published; PMID:11869452
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.25 -Z 549862.597050 CM SEQDB
#=GF CL   CL00111
#=GF DR   URL; http://www.rna.ccbb.utexas.edu/;
#=GF DR   URL; http://oberon.fvms.ugent.be:8080/rRNA/ssu/index.html;
#=GF DR   URL; http://rdp.cme.msu.edu/html/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   11283358
#=GF RT   Crystal structure of the ribosome at 5.5 A resolution.
#=GF RA   Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH,
#=GF RA   Noller HF
#=GF RL   Science 2001;292:883-896.
#=GF RN   [2]
#=GF RM   11869452
#=GF RT   The comparative RNA web (CRW) site: an online database of comparative
#=GF RT   sequence and structure information for ribosomal, intron, and other RNAs.
#=GF RA   Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng
#=GF RA   B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR
#=GF RL   BMC Bioinformatics. 2002;3:2.
#=GF WK   Ribosomal_RNA
#=GF SQ   86



CP002839.1/427707-426237             AUUCCGGUUGAUCCUGCCGGAGGUCAUUGCUAGUGGAGUCCGAUUUAGCCAUGCUAGUU-GCACG--------AGU---UU--------AG----ACU--------CGU--AGCAGAUAGCUCAG-UAACACGUGGCCAAACUACCCUCUGGAUCGGGAUAACCU--C-G-GGAAACUGAGGC-UAAUCCUGAAUAGCGUUCUCAC-CCUGGAGU---GGGGAGAACGUGAAAUGC-------------UCCG------------------GCGCCAGAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCAGUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGUAUCUGAGACAAGAUACCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCCAGUGCGAUAAGGGGACUCC-AU-CUGCGAGGGC---AU-A-UC---GUCCUCGCUUUUCUGUACCGU--AAGGUGGUACAGG-AAU-AAGGGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCCCGAGUGAUGACCGCUAUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCAGGCAA-GUCCAUCGGGAAAUCCGCGCGCCCAACGC-GCGGGCGUCCGGUGGAACCUGC-UU--GGCUUGGG-ACCGGAAGACCUG-AGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGGUGGCGAAAGCGCCUCAGGAAGACGGAUCCGACGGUGAGGGACGAAAGCUCGGGUCACGAACCGGAUUAGAUACCCGGGUAGUCCGAGCUGUAAACGAUGUCUGCUAGGUGUGGCACAGGC-UA-C-GAGCCUGUGCUGUGCCGUAGGGAAGCCGUGAAGCAGACCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCAUCGACAGC-AGGAGUGACGAUCAGGUUGAUGACCU-UAUC-AGA----CCUGCUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACUC-CUAAUUGCCAGC-AACACC--CUCGUGGUG-GUU--G-GGUACAUUAGGAGGACUGCCAGUGC-CAAACUGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGUGCUGGGCG-ACACGCGGGCUACAAUGGCCGAGACAGUGGG-A-UGC-AACGCCGAAA-GGC--GACGCUAAUCUCCGAAA--CUCGGUCGUAGUUCGG-AUUGCGGAUUGAAACUCAUCCGCAUGAAGCUGGAUUCGGUAGUAAUCGCGCCUCAGAAGGGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCCUGG-----------------UCA-----------CCAGGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCA
AE004437.1/1875505-1876977           AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUU-GUGCG--------GGU---UU--------AG----ACC--------CGC--AGCGGAAAGCUCAG-UAACACGUGGCCAAGCUACCCUGUGGACGGGAAUACUCU--C-G-GGAAACUGAGGC-UAAUCCCCGAUAACGCUUUGCU-CCUGGAAG---GGGCAAAGCCGGAAACGC-------------UCCG------------------GCGCCACAGGAUGCGGCUGCGGUCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCCAUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGUACGAAAGUGCGAUAAGGGGACUCC-GA-GUGUGAAGGC---AU-A-GA---GCCUUCACUUUUGUACACCGU--AAGGUGGUGCACG-AAU-AAGGACUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGUCCGAGUGAUGGCCGAUCUUAUUGGGCCUAAAGCGUCCGUAGCUGGCUGAACAA-GUCCGUUGGGAAAUCUGUCCGCUUAACGG-GCAGGCGUCCAGCGGAAACUGU-UC--AGCUUGGG-ACCGGAAGACCUG-AGGGGUACGUCUGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCGCCGGUGGCGAAAGCGCCUCAGGAGAACGGAUCCGACAGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGUCCGCUAGGUGUGGCGCAGGC-UA-C-GAGCCUGCGCUGUGCCGUAGGGAAGCCGAGAAGCGGACCGCCUGGGAAGUACGUCUGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCCCCGACAGU-AGUAAUGACGGUCAGGUUGAUGACCU-UACC-CGA---GGCUACUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACUC-CUAAUUGCCAGC-AGUACC-CUUUG-GGUA-GCU--G-GGUACAUUAGGUGGACUGCCGCUGC-CAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGGGCUGGGCA-ACACGCGGGCUACAAUGGUCGAGACAAUGGG-A-AGC-CACUCCGAGA-GGA--GGCGCUAAUCUCCUAAA--CUCGAUCGUAGUUCGG-AUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGCAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAUCACCCGAGUGGGGUUCGGAUGAGGCCGGC----------------AUGC-----------GCUGGUC-AAAUCUGGGCUCCGCAA----GGGGGAUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
AB073365.1/1-1472                    AUUCCGGUUGAUCCUGCCGGAGGUCAUUGCUAUUGGAGUUCGAUUUAGCCAUGCUAGUC-GCACG--------AGU---UC--------AU----ACU--------CGU--GGCAGAUAGCUCAG-UAACACGUGGCCAAACUACCCUAUGGAGAACGAUAACCU--C-G-GGAAACUGAGGC-UAAUAGUUCAUACGGCUCUCUC-CCUGGAAA--UGGGUUGAGCCCGAAACGC-------------UACG------------------GCGCCAUAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCAAUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUUUACACUGCACGACAGUGCGAUAAGGGAACUCC-AA-GUGCGAGGGC---AU-A-GA---GCCCUCGCUUUUCUGAACCCU--AGGGUGGUUCAGG-AAC-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCAGCUCGAGUGAUGACCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCGAGAGG-GUCCGUCGGGAAAUCUGCUCGCUCAACGA-GCAGGCGUCCGGCGGAAACCAA-UC--GGCUUGGG-ACCGGAAGACCUG-AGGGGUACGUCUGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGGUGGCGAAAGCGCCUCAGGAAGACGGAUCCGACAGUGAGGGACGAAAGCUGGGGUCACGAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCUCACUAGGUGUGGCACUGGC-UA-C-GAGCCAGUGCUGUGCCGUAGGGAAGCCGUGAAGUGAGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCUCCGACAGUAUGCAGUGACAGUCAGUGUGAUGAGCU-UACU-UGA----GCUACUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACUC-UUAAUUGCCAGC-AUAGGC-CUUUG-GCCU-GAU--G-GGUACAUUAGGAGGACUGCCAGUGC-UAAACUGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGAGCUGGGCU-ACACGCGGGCUACAAUGGUCGAGACAGUGGG-A-UGC-AACCCCGAGA-GGG--GGCGCUAAUCUCCGAAA--CUCGAUCGUAGUUCGG-AUUGCGGGCUGAAACUCGCCCGCAUGAAGCUGGAUUCGGUAGUAAUCGCCUCUCAGAAGGAGGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCCCAG-----------------AG------------AUGGGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
AJ585956.2/1-1497                    -UUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUC-AAGGGGG---CGUCCC---UU--------CU----GGGACG---CCACC--GGCGGACGGCUCAG-CAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCC--C-G-GGAAACUGGGGC-UAAUCCCCCAUAGGCCUGGGGU-ACUGGAAG---GUCCCCAGGCCGAAAGGGA------------GCCGUAA-----------GGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUA-GGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGG-GAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCC-CA-GUGCCGUGCC----U-C-U----GGCACGGCUUUUCCGGAGUGU--AAAAAGCUCCGGG-AAU-AAGGGCUGGGCAAGG-CCGGUGGCAGC-CGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAA-GUCCCUGGCGAAAUCCCACGGCUCAACCG-UGGGGCUCGCUGGGGAUACUGC-GG--GCCUUGGGCACCGGGAGAGGCC-GGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGC-UU-C-GAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGA-GCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCU-CACCGGGGGCGACGGC--AGGAUGAAGGCCAGGCUGAAGGUCU-UGCC-GGA----CGCGCCGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGC--GCCC-CCAGUUGCCAGU-CCCUCC-CGCUCGGGAG--GG--A-GGCACUCUGGGGGGACUGCCGGCGA-UAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAG-UAUGCCCCGAAACCCCCGGGCU-ACACGCGCGCUACAAUGGGCGGGACAAUGGG-A-CCC-GACCCCGAAA-GGG--GAAGGGAAUCCCCUAAA--CCCGCCCUCAGUUCGG-AUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-ACUCCACCCGAGCGGGGCCCAGGUGAGGCCCGAUCUC-----------CUUCGG------GAGGUCGGGUC-GAGCCUGGGCUCCGUGA----GGGGGGAGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUACGGCU-CGAUCACCUCCU
AY243109.1/1-1476                    AUUCCGGUUGAUCCUGCCGGAGGCUAUUGCUAUCGGGGUCCGAUUCAGCCAUGCUAGUU-GUACG--------GGU---UU--------AG----GCC--------CGU--AGCAAAUAGCUCCG-UAACACGUGGUCAAACUACCCUCUGGACCGGGAUAUCCU--C-G-GGAAACUGAGGU-CGAUCCCAGAUACUGCUUUCAU-GUUGGAAC---ACAGAAAGUCGGAAACGG-------------UCCG------------------CCGCCGGAGGACGUGACUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAA-GAACCCGGAGACGGUAUCUGAGACAAGAUACCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCCAGUGCGAUAAGGGGACCCC-GA-GUGCGAGGGC---AU-A-CA---GUCCUCGCUUUUCGUGACCGU--AAGAAGGUCUCAG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGCCCGCCGCGGUAAAACCGGCAGCUCGAGUGAUAGCCACUNUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCGAACAG-GUCCGUCGGGAAAUCCACCCGCUCAACGG-GUGGACGUCCGGCGGAAACCAG-UC--GGCUUGGG-GCCGGGAGACCAG-AGAGGUACGUCCGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCGCCGGUAGCGAAAGCGUCUCUGGAGAACGGACCCGACGGUGAGGGACGAAAGCUUGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCAAGCUGUAAACGAUGCUCGCUAGGUGUGGCGUUGGC-UA-C-GAGCCAGCGCUGUGCUGUAGGGAAGCCGAGAAGCGAGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCGGCACCGACAGUGUGCAGUGACAGUCAGUCUGAUGGGCU-UACU-UGA----GCCACUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--GUCC-CUAAUUGCCAGC-AGCAGC--CUUGUGCUG-GCU--G-GGUACAUUAGGGAGACUGCCGUCGC-AAAGACGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGUGCCGGGCG-ACACGCGGGCUACAAUGGCCGAGACAGUGGG-A-CGC-UACCCCGAGA-GGG--GGCGCUAAUCUCCUAAC--CUCGGUCGUAGUUCGG-AUUGCGGGUUGAAACCCACCCGCAUGAAGCUGGAUUCGGUAGUAAUCGCAUUUCAGAAGAGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAUCACCCGAGUGAGGUCCGGAUGAGGCCGGCG----------------CAA----------CGCCGGUC-GAAUCUGGGCUUCGCAA----GGGGGAUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCUUGGAUCACCUCCU
EU155925.1/1-1465                    --UCUGUUUGAUCCCGGCGGAGGCCACUGCUAUCGGAGUUCGAUUAAGCCAUGCGAGUC-GAGAG-------GU-----GC---------A----AGAC-------CUC--GGCAUACUGCUCAG-UAACACGUGGACAACCUACCCUAUGGAGGGGGAUAACCC--C-G-GGAAACUGGGGA-UAAUACCCCAUAGACUAUGAAU-GCUGGAAU---GCUUUGUANUUGAAA-GG-------------UCCG------------------CCGCCAUAGGAUGGGUCUGCGGCCGAUUA-GGUUGUUGUUGGGGUAACGGCCCAACAAGCCUGUAAUCGGUACGGGUUGUGGGAGCAA-GAGCCCGGAGAUGGAUUCUGAGACACGAAUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUUUACAAUGCGGGAAACCGUGAUAAGGGAACUCC-GA-GUGCCCGU------A-A-AA-----UCGGGCUGUCCAUCUGUUU--AAAUAACAGGUGA-AGA-AAGGGCCGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCGGCUCGAGUGGUGGCCACUAUUACUGGGCUUAAAGCGUUCGUAGCUGGUCUGUUAA-GUCUCUGGGGAAAUCUACUGGCUUAACCA-AUAGGCGUUUCAGGGAUACUGG-CA--GACUAGGG-ACCGGGAGAGGUG-AGGGGUACUCCAGGGGUAGGAGUGAAAUCCUGUAAUCCUUGGGGGACCACCUGUGGCGAAGGCGCCUCACCAGAACGGCUCCGACAGUGAGGGACGAAAGCUGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGCGCGUUAGGUGUAUCGGUGAC-CA-C-GAGUCACCGAGGUGCCGAAGAGAAAUCGUGAAACGUGCCGCCUGGGAAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACAGGUGGA-GCCUGCGGUUUAAUCGGACUCAACGCCGGAAAUCU-CACCGGAUAAGACAGC--UGGAUGAUAGUCGGGCUGAAGACUC-UACU-UGA----CUAGCUGAGAGGAGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACUGUGAAGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCAC--GCCA-ACAGUUGCCAGC-UCGUCC--UCCG-GGAU-GGU--G-GGGACACUGUUGGGACCGCCUCUGC-UAAAGAGGAGGAAGGAAUGGGCAACGGUAGGUCAG-CAUGCCCCGAAUUAUCCGGGCU-ACACGCGGGCUACAAUGGGUGGGACAAUGGG-U-AUC-GACACCGAAA-GGU--GAAGGCAAUCUCCUAAA--CCCAUCCUUAGUUCGG-AUUGUGGGCUGCAACUCGCCCACAUGAGGCUGGAAUCUGUACUAAUCGUGUCUCAACAUGGCACGGUGAAUAUGUCCCUGCUCCUUGCACACACCGCCCGUC-AAACCACCCGAGUGAGGUCUUGAUGAGGCCGUCGU--------------UUAU---------GCGGCGGUC-GAAUCUAGGUUUUGCAA----GGGGGGUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
CP001404.1/1448626-1450122           AAUCCGGUUGAUCCUGCCGGACCCGACCGCUAUCGGGGUGGGGCUAAGCCAUGGGAGUC-GUACG-------CUCC---CGGG----CAAG----GGAG-------CGU--GGCGGACGGCUGAG-UAACACGUGGCUAACCUACCCUGAGGAGGGAGAUAACCC--C-G-GGAAACUGGGGA-UAAUCUCCCAUAGGCGAGGAGU-CCUGGAAC---GGUUCCUCGCUGAAAGGCUCAUGG--GCUAU----UCCCCG-----CUCAUGAGCGCCUCAGGAUGGGGCUGCGGCCCAUCA-GGUAGUUGGGGGGGUAAGGGCCCCUCAAGCCUAUAACGGGUAGGGGCCGUGAGAGCGG-GAGCCCCCAGUUGGGCACUGAGACAAGGGCCCAGGCCCUACG-GGGCGCACCAGGCGCGAAACGUCCCCAAUGCGCGGAAGCGUGAGGGCGCCACCCC-GA-GUGCUCCCGU--------A-----AGGGAGCUUUUCCCCGCUCU--ACAAAGGCGGGGG-AAU-AAGCGGGGGGCAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCCCCGCGAGUGGUCGGGACUCUUACUGGGCCUAAAGCGCCCGUAGCCGGCCCGGCAA-GUCACUCCUUAAAGACCCCGGCUCAACCG-GGGGAA-UGGGGGUGAUACUGU-CG--GGCUAGGG-GGCGGGAGAGGCC-AGCGGUACUCCCGGAGUAGGGGCGAAAUCCUCAGAUCUCGGGAGGACCACCAGUGGCGAAAGCGGCUGGCUAGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGCAGCAAAAGGGAUUAGAUACCCCUGUAGUCCCGGCUGUAAACAAUGCAGGCUAGGUGUCACAUGGGC-UU-A-GAGCCCAUGUGGUGCCGCAGGGAAGCCGUUAAGCCUGCCGCCUGGGGAGUACGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGA-ACCUGCGGCUCAAUUGGAGUCAACGCCUGGAAUCU-UACCAGGGGAGACCGC--AGGAUGACGGCCAGUCUAACGACCU-UGCC-UGA----CUCGCGGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGUUGUGAAAUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCU--ACCA-CUAGUUGGUAUC-CUGGUC--UCCG-GGCC--GG--G-ACCACACUAGUGGGACUGCCGGCG--UAAGCCGGAGGAGGGAGGGGGCCACGGCAGGUCAG-CAUGCCCCGAAACCCCUGGGCC-GCACGCGGGUUACAAUGGCAGGGACAGCGGGAU-UCC-GACCCCGAAA-GGG--GAAGGUAAUCCCUUAAA--CCCUGCCGCAGUUGGG-AUCGAGGGCUGAAACUCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCAGAUCAACAAUCUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUCCACCCGAGUAGGAGAGGGGUGAGGCCCCUUGC------------CUUUG-------GGUGGGGGGUC-GAGCUUCUCUCCUGCAA----GGGGGGAGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCAU
CP000852.1/130828-129150             AAACCGGUUGAUCCUGCCGGACCCGACCGCUAUCGGGGUGGGGCUUAGCCAUGCGAGUC-AAGCG-------CCCC---AGGGA-CCCGCU----GGGG-------UGC--GGCGCACGGCUCAG-UAACACGUGGCCAACCUACCCUCGGGAGGGGGAUAACCC--C-G-GGAAACUGGGGC-UAAUCCCCCAUAGGGGAAGGGU-GCUGGAAG---GCCCCCUCCCCGAAAAGAGCC-------ACG----UCCGGUACCCGGCGCGGCUCGCCCGAGGAUGGGGCUACGGCCCAUCAUGGUAGCUGGCGGGGUAACGGCCCGCCAGGCCGAAGACGGGUGGGGGCCGUGAGAGCGG-GAGCCCCGAGAUGGGCACUGAGACAAGGGCCCAGGCCCUAUG-GGGUGCAGCAGGCUCGAAUACUCCGCAAUGCGGUAACCCGCGACGGGGCCACCCC-GA-GUGCCGCCC----GA-U-GA----GGGCGGCUUUUCCCCCGUGU--AAGUAGCUGGGGG-AAU-AAGCGGGGGGCAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCUCCGCGAGUGGUCGGGGUGUUUACUGGGCCUAAAGCGCCCGUAGCCGGCCCGGUAA-GUCACCCCUGAAAUCCAUGGGCUCAACCC-AUGGGC-CGGGGGUGAUACUGC-CG--GGCUUGGG-GGUGGGAGAGGCC-GAGGGUACUCCCGGGGUAGGGGCGAAAUCCGAUAAUCCCGGGAGGACCACCAGUGGCGGAAGCGCUCGGCUGGAACACGCCCGACGGUGAGGGGCGAAAGCUGGGGGAGCAAAGGGGAUUAGAUACCCCUGUAGUCCCAGCUGUAAACGAUGCGGGCUAGCUGUUGGGUGGGC-UU-A-GUGCCCGCCCAGUGGCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAACCUGGCACUGGGCCACAAGCCCAGGCCGGGGCGGAAGGCUGAAAGGCGGCGGGCCGUGCCGGAGUUCCCCGACGGGAACUAGAUAUCCAACAAAGUACAGUAAACUCAGAACCCUCCUUUUUUAGCACUCACAUCCUCAACUUUACCCUGGCACUUUACCCCGGCACGGCCGCCGCCCAGCAUACUUAAAGGAAUUGGCGGGGGGGCACCACAAGGGGUGAA-GCUUGCGGCUUAAUUGGAGUCAACGCCGGAAACCU-CACCCGGGGCGACAGC--AGGAUGAAGGCCAGGCUAACGACCU-UGCC-GGA----CGAGCUGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGUGUCCAGUUAAGUCUGGCAACGAGCGCGACCCCC--GCUC-CCUGUUGCUACC-CUACCC--UUCG-GGGU-GGG--G-GGCACACAGGGAGGACUGCCGGCG--UAAGCCGGAGGAAGGAGGGGGCCACGGCAGGUCAG-UAUGCCCCGAAACCCCGGGGCU-GCACGCGAGCUGCAAUGGCGGGGACAGCGGG-U-UCC-GACCCCGAAA-GGG--GGAGGCAAUCCCGUAAA--CCCCGCCCCAGUAGGA-AUCGAGGGCUGUAACUCGCCCUCGUGAACGUGGAAUCCCUAGUAACCGCGUGUCACCAACGCGCGGUGAAUACGUCCCUGCCCCUUGCACACACCGCCCGUC-GCGCCACCCGAGGGGAUCCUUAACGAGGCCCCCUGG-------------GUAA--------CUGGGGGGUC-GAGUUGGGGGUCCCCAA----GGGGGGCGAAGUCGUAACAA------G--GUGGCCGUAGGGG----------AACCUGCGGCC-GGAUCACCUCCU
EU887286.2/1-1472                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUU-GCGCG--------AGU---UC--------AG----ACU--------CGC--AGCAGAUAGCUCAG-UAACACGUGGUCAAGCUACCCUGCAGACACGGACAACCU--C-G-GGAAACUGAGGC-UAAUCCGCGAUACCGAUCCCAC-GCUGGAAU---GCCGGGAUCUACAAACGC-------------UCCG------------------GCGCUGCAGGAUGCGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCGCGCAAGUGCGAUAAGGGGACUCC-GA-GUGCGAGGGC---AU-A-UA---GUCCUCGCUUUUGAGAACCGU--AAGGUGGUUCUCG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCAAGUGAUGGCCAAUCUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCGUGAAA-GUUCGUCGGGAAAUCCAUCCGCUCAACGG-AUGGGCGUCCGGCGAAAACUUC-AC--GGCUUGGG-ACCGGAAGGCUCG-AGGGGUACGUCCGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCGCCGAUGGCGAAAGCACCUCGAGAAGACGGAUCCGACAGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCCGUAAACGAUGUUCACUAGGUGUGGCACAGGC-UA-C-GAGCCUGUGCUGUGCCGUAGGGAAGCCGAGAAGUGAACCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCUCCGACUAC-AGUAAUGACGGCCAGGUUGAUGACCU-UGCCACGA----GCUGUAGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCAC--GCAC-CUAAUUGCCAGC-AGCAGU--UCCG-ACUG-GCU--G-GGUACAUUAGGUGGACUGCCAGUGC-CAAACUGGAGGAAGGAAUGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGAGCUGGGCU-ACACGCGGGCUACAAUGGCCGAAACAAUGGG-U-UGC-UAUCUCGAAA-GAG--AACGCUAAUCUCCGAAA--UUCGGUCGUAGUUCGG-AUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCAUUUCAGAAGAGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCUAUC----------------GCAA-----------GAUAGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
EU155900.1/1-1469                    --UCUGUUUGAUCCUGCCGGAGGUUACUGCUAUCGAGGUUCGACUAAGCCAUGCGAGUC-GAAUG---------UA---GC--------AA----UA---------CAU--GGCGUACUGCUCAG-UAACACGUGGACAACCUACCCUUAGGUCGGGGAUAAACC--C-G-GGAAACUGGGUA-UAAUACCCGAUAGUCCUCGACU-GCUGGAAU---GCAUCGAGUGCUAAA-GC-------------UCCG------------------GCGCCUAAGGAUGGGUCUGCGGCCUAUCA-GGUAGUAGUGGGUGUAGCGUACCUACUAGCCUACGACGGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGAUGGAUUCUGAGACACGAAUCCAGGCCCUACG-GGGUGCAGCAGGCGCGAAAACUUUACAAUGCUGGAAACAGCGAUAAGGGGACCUC-GA-GUGCCAGGUU------A-CA---AAUCUGGCUGUCGUGAUGCCU--AAAAAGCAUUGCA-UAGCAAGGGCCGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCGGCUCGAGUGGUAACCGUUAUUAUUGGGUCUAAAGGGUCUGUAGCCGGCCGGAUAA-GUCUCUUGGGAAAUCUGGCAGCUUAACUG-UCAGGCUUUCAGGGGAUACUGU-CU--GGCUCGAG-GCCGGGAGAGGUG-AGAGGUACUUCAGGGGUAGGGGUGAAAUCUUGUAAUCCUUGAAGGACCACCAGUGGCGAAGGCGUCUCACCAGAACGGACCUGACGGCAAGGGACGAAAGCUAGGGGCACGAACCGGAUUAGAUACCCGGGUAGUCCUAGCCGUAAACGAUACUCGCUAGGUGUCGGCCACGG-UG-C-GACCGUUGUCGGUGCCGUAGGGAAGCCGUGAAGCGAGCCACCUGGGAAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGGGUGGA-GCUUGCGGUUUAAUUGGAUUCAACGCCGGAAAUCU-UACCGGGACCGACAGC--AAUAUGAAGGCCAGGCUGAAGACUU-UGCC-GGA----UUAGCUGAGAGGUGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACUGUGAAGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCAC--GCCC-ACAGUUGCCAGC-GUACUC--UCCG-GAGU-GAC--G-GGUACACUGUGGGGACCGCCGCUGC-UAAAGCGGAGGAAGGAAUGGGCAACGGUAGGUCAG-UAUGCCCCGAAUAUCCCGGGCU-ACACGCGAGCUACAAUGGUUGGUACGAUGGG-U-AUC-UACCCCGAAA-GGG--GAUGGAAAUCUCCUAAA--GCCAAUCUUAGUCCGG-AUUGAGGGCUGCAACUCGCCCUCAUGAAGCUGGAAUCCGUAGUAAUCGCGUUUCAACAGAACGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAACCACCCGAGUAGGGUCUGAAUGAGAGCGCUUCC-------------UUC---------GGAGGCGUUC-GAAUUUGGGCUUUGCAA----GGGGGGUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
CP002656.1/419124-417628             AUUCCGGUUGAUCCUGCCGGACCCGAUCGCUAUAGGGGUAGGGUUAAGCCAUGGGAGUC-GUACG-------CUCU---CGG-----GAAG----AGGG-------CGU--GGCGGACGGCUGAG-UAACACGUGGCUAACCUAACCUUGGGUCUCGGAUAACCC--C-G-GGAAACUGGGGC-UAAUCCGGGGCAGAUAAGGAGA-UCUGGAAC---GACUCCUUAUCUAAAGGCC------------UCUCGGCUGAUCCCGUCGAGAGGUGCCCAAGGAUGGGGCUGCGGCCCAUCA-GGCUGUUGGGGGAGUAAAGGUCCCCCAAACCUAUAACGGGUAGGGGCCGUGGGAGCGG-GAGCCCCCAGUUGGGCACUGAGACAAGGGCCCAGGCCCUACG-GGGCGCACCAGGCGCGGAACGUCCCCAAUGCGGGAAACCGUGAGGGCGUUACCCC-UA-GUGCCCUC------G-C-AA-----GAGGGCUUUUCUCCACUCC--AGAAAGGUGGAGG-AAU-AAGCGGGGGGCAAGA-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCCCCGCGAGUGAUCGGGACGUUUAUUGGGCUUAAAGCGCCCGUAGCCGGCCUACAAA-GUCACCGUUUAAAGACCCGAGCCCAACUC-GGGGAA-UGGCGGUGAUACUUG-UA--GGCUAGGG-GGCGGGAGAGGUC-GGAGGUACUCCCGGAGUAGGGGCGAAAUCCUCAGAUCCCGGGAGGACCACCAGUGGCGAAAGCGUCCGGCUAGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGUAGCAAAUAGGAUUAGAUACCCUAGUAGUCCCGGCUGUAAACGAUGCAGGCUAGGUGUCACGUAGGC-UU-U-GGGCCUACGUGGUGCCGCAGGAAAACUGGUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGA-ACCUGCGGCUCAAUUGGAGUCAACGCCUGGAAUCU-CACCGGGGGAGACCGC--AGGAUGACGGCCAGGCUAACGACCU-UGCC-AGA----CUCGCGGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGUUGUGAAAUGUCCGGUUAAGUCCGGCAACGAGCGAGACCCCC--ACUU-CUAGUUGGUAAU-CGUCUC--UCUG-GAGG--CG--A-UCCACACUAGAAGGACUGCCGGUGU-UAAACCGGAGGAAGGAGGGGGCCACGGCAGGUCAG-CAUGCCCCGAAACUUCCGGGCC-GCACGCGGGUUACAAUGGCAGGGACAGCGGG-A-UCC-GACCCCGAAA-GGG--GAAGGCAAUCCCACAAA--CCCUGCCUCAGUUGGG-AUCGAGGGCUGAAACUCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCGGGUCAACAACCCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUCCACCCGAGUGGAGGUGAAGUGAGGCCCCUUGCC-----------CUUAGG------GGUGGGGGGUC-GAGCUUCUCCUCCGCGA----GGGGGGAGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCAC
JF802157.1/4-1486                    CUUUCGGUUUGUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUC-GCACG--------AGU---UU--------AG----ACU--------CGU--AGCAUAUAGCUCAG-UAACACGUGGCCCAACUACCCUACAGACCGCGAUAACCU--C-G-GGAAACUGAGGC-CAAUAGCGGAUAUCACUCUCAU-GCUGGAGU---GCAGAGAGUGAGAAACGU-------------UCCG------------------GCGCUGUAGGAUGUGGCUGCGGCCGAUUA-GGUAGAUGGUGGGGUAACGGCCCACCAUGCCGAUAAUCGGUACAGGUUGUGAGAGCAA-GAGCCUGGAGACGGUAUCUGAGACAAGAUACCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAGGGGGACUCC-GA-GUGUGAGGGC---AU-A-UA---GCCCUCGCUUUUCUGUACCGU--AAGGUGGUUCAGG-AAC-AAGGACUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGUCCAAGUGAUGGCCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCUUGCUGUGUAA-GUCCAUUGGGAAAUCGACCAGCUCAACUG-GUCGGCGUCCGGUGGAAACUACCACCAGGCUUGGG-GCCGAGAGACUCAAACGGGUACGUCCGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCACCAAUGGGGAAACCACGUUGAGAGACCGGACCCGACAGUGAGGGACGAAAGCCAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACAAUGCUCGCUAGGUAUGUCACGCGC-CA-U-GAGCACGUGAUGUGCCGUAGGGAAGACGAUAAGCGAGCCGCCUGGGAAGUACGUCUGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGAAAUCU-CACCGGUCCCGACAGU-AGUAAUGACGGUCAGGUUGACGACUU-UACC-CGA---CGCUACUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACUU-CUAGUUGCCAGC-AAUACC--CUUGAGGUA-GUU--G-GGUACACUAGGAGGACUGCCGCUGC-UAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGGACCGGGCA-ACACGCGGGCUACAAUGGCUCUGACAGUGGG-A-UGC-AACGCCGAGA-GGC--GACGCUAAUCUCC-AAA--CGGAGUCGUAGUUCGG-AUUGCGGGCUGAAACCCGCCCGCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGAAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGGGGUCCGGAUGAGGCCGUC----------------AUGC-----------GACGGUC-GAAUCUGGGCUCUGCAA----GGGGGCUUAAGUCGGAACCCU----UG--U-AGCCUUAGAGGUCCCCCCGCCAUUCU----UC-CGGUUUCUUCUU
AB108676.1/1-1473                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUC-GCGCG--------GGU---UU--------AG----ACC--------CGC--GGCAGAUAGCUCAG-UAACACGUGGCCAAACUACCCUAUGGACGGAGAUAACCU--C-G-GGAAACUGAGGC-UAAUAUCCGAUACAGCUCGCAC-GCUGGAGU---GCAGCGAGCUGGAAACGU-------------UCCG------------------GCGCCAUAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAAUGGCCCACCGUGCCGAUAAUCGGUACAGGUUGUGAGAGCAA-GAGCCUGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAGGGGGACUCC-GA-GUGCGAGGGC---AU-A-CA---GUCCUCGCUUUUCUGCACCGU--AAGGUGGUACAGG-AAC-AAGUGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCACGAGUGAUGGCCGAUUUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCGAGCAA-GUCUGUUGGGAAAUCCACGCGCUCAACGC-GUGGGCGUCCAGCGGAAACUGU-UC--GGCUUGGG-GCCAGAGGACUCG-AGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGGUGGCGAAAGCGCCUCGAGAAGAUGGACCCGACGGUGAGGGACGAAAGCUUGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCAAGCUGUAAACGAUGCUCGCUAGGUGUGCCGCAGGC-UA-C-GAGCCUGCGCUGUGCCGUAGGGAAGCCGAGAAGCGAGCCGCCUGGGAAGUACGUCUGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCACCGACAAC-GGUAAUGAUGGCCAGGUUGAUGACCU-UACC-CGA---CGCCGUUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--AUCC-UUAAUUGCCAGC-AGCAUC--CUUGUGAUG-GCU--G-GGUACAUUAGGGAGACCGCCACGGC-UAACGUGGAGGAAGGAACGGGCAACGGUAGGUCAG-CAUGCCCCGAAUGUGCUGGGCA-ACACGCGGGCUACAAUGGCCGGGACAGUGGG-A-AGC-UAAUCCGAGA-GGA--UACGCUAAUCCCCUAAA--CCCGGUCGUAGUUCGG-AUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGAAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAUCACCCGAGUGGGGUCCGGAUGAGGCCAUC----------------AUGC-----------GAUGGUC-GAAUCUGGGCUCCGCAA----GGGGGAUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
AB671511.1/1-1473                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUU-GCACG--------GGU---UU--------AG----ACC--------CGU--AGCAGAAAGCUCAG-UAACACGUGGCCAAACUGCCCUAUGGACAAGAACAACCU--C-G-GGAAACUGAGGC-UAAUUCUUGAUAUAGCUCUCAU-GCUGGAGU---GCAGAGAGCUAGAAACGU-------------UCCG------------------GCGCCAUAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGAGGUAACGGCCCACCGUGCCGAUAAUCGGUACAGGUUGUGAGAGCAA-GAGCCUGGAGACGGUAUCUGAGACAAGAUACCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCCAGUGCGAUAGGGGGACUCCCGAAGUGCGAGGGC---AU-A-UA---GCCCUCGCUUUUCCACACCCU--AAGGCGGUGUGGG-AAU-AAGAACUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGUUCGAGUGAUGGCCGAUAUUAUUGGGCCUAAAGCGUUCGUAGCUGGCCAGUCAA-GUUCGUCGGGAAACCUACCCGCUUAACGG-GUAGCCGUCCGGCGAAAACUGA-UU--GGCUUGGG-ACCGGGAGACUUG-AGGGGUACGUCCGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCACCGAUGGCGAAAGCACCUCAAGAGCACGGAUCCGACAGUGAGGAACGAAAGCUGGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCUCGUUAGGUAUGGCACAGGC-UA-C-GAGCCUGUGCUAUGCCGUAGGGAAGCCGU-AAGCGAGCCGCCUGGGAAGUACGUCUGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCACCGACAAUGUGCAGUGAAGGCCAGUUUGAUGAGCU-UGCU-GGA----GCCAUUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCAUCCUGUUAAGUCAGGCAACGAGCGAGAUCCGC--GCCC-UUAGUUGCCAGC-AGCAUC--UUGC-GAUG-GCU--G-GGUACACUAGGGGGACUGCCGCUGC-UAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAG-CAUGCCCCGAAUGUGCUGGGCA-ACACGCGGGCUACAAUGGCCAAGACAACGGG-U-CGC-UACCCCGAGA-GGG--GACGCUAAUCCCAUAAA--CUUGGUCGUAGUUCGG-AUUGAGGGCUGCAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAUAAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUAGGGUCCGGAUGAGGCCAUC----------------AUGC-----------GAUGGUC-AAAUCUGGGCUUUGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGAGG----------AAUCUGCGGCU-GGAUCACCUCCU
EF468473.1/1-1470                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUUGGGAUCCGAUUUAGCCAUGCUAGUC-GUACG--------AGU---UC--------AC----ACU--------CGU--GGCGAAUAGCUCAG-UAACACGUGGCCAAACUACCCUUCGGAGCGCAAUACCCU--C-G-GGAAACUGAGGC-UAAUAGCGCAUACCAUACCACC-ACUGGAAU---GAGUGGUAUGCCAAACGC-------------UCCG------------------GCGCCGAAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCAAUAAUCGGUAUGGGUCAUGAGAGUGA-GAACCCAGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAGGGGGAUCCC-AA-GUGCACAGGC---AU-A-GC---GCCUGUGCUUUUCGACACCCU--AAGGCGGUGUCAG-AAU-AAGGGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCCCAAGUGAUGGCCGAUCUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCACGCAA-GUCCAUCGGGAAAUCCACCUGCCCAACAG-GUGGGCGCCCGGUAGAAACUGC-GU--GGCUUGGG-ACCGGAAGGCGCG-ACGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCGCCGAUGGCGAAAGCACGUCGCGAGAACGGAUCCGACAGUGAGGGACGAAAGCCAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACAAUGUCUGCUAGGUGUGGCUCCCAC-UA-C-GAGUGGGUGCUGUGCCGUAGGGAAGCCGCUAAGCAGACCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCAUCGACUGU-AGUAAUGACGAUCAGGUUGAUGACCU-UAUC-CGA----GCUUCAGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--AUCC-UUACUUGCCAGC-AGUAUC--GCGA-GAUA-GCU--G-GGGACAGUAGGGAGACCGCCGUGGC-UAACACGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGUGCUGGGCA-ACACGCGGGCUACAAUGGUCGAGACAAAGGG-U-UCC-AACUCCGAAA-GGA--GACGGUAAUCUCAGAAA--CUCGAUCGUAGUUCGG-AUUGUGGGCUGCAACUCGCCCACAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCACAAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCGCGC-----------------CAC-----------GCGCGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
GU208827.2/1-1472                    AUUCCGGUUGAUCCUGCCGGAGGUCAUUGCUAUCGGGGUCCGAUUUAGCCAUGCUAGUC-GCGCG-------GGUU--------------A----GACC-------CGC--GGCGUAUAGCUCAG-UAACACGUGGCCAAACUACCCUACAGACGAGAACAACCU--C-G-GGAAACUGAGGC-UAACACUCGAUACGCGUUGACC-GUUUGAAC---ACGUCGACGCUCAAACGC-------------UCCG------------------GCGCUGUAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCCAGUGCGAUAAGGGGACCCC-GA-GUGAAAGGGC---AU-A-UC---GCCCUUUCUUUUCUGAACCGU--AGGGAGGUUCAGG-AAC-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCGAGUGAUGACCGAUUUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCGCGCAA-GUCCGUCGGGAAAUCCACCCGCUUAACGG-GUGGGCGUCCGGCGGAAACUGU-GC--GGCUUGGG-ACAGGAAGGCUCG-AGGGGUACGUUCGGGGUAGGAGUGAAAUCCCGUAAUCCUGAACGGACCACCGAUGGCGAAAGCACCUCGAGAGGACUGAUCCGACAGUGAGGGACGAAAGCUGGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGUUCGCUAGGUGUGACACUCAC-UA-C-GAGUGAGUGUUGUGCCGCAGGGAAGCCGCUAAGCGAACCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGUAACCU-UACCAGCCCCGACUAC-GGUGAUGACGGUCAGGUUGAUGACCU-CGCCACGA---CGCCGUAGAGAGGUGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACUC-UUAAUUGCCAGC-AUGUCC--CUUGAGGAU-GAU--G-GGUACAUUAGGAGGACUGCCGCCGC-CAAGGCGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGGGCUGGGCA-ACACGCGGGCUACAAUGGCCGAGACAAUGGG-U-UCC-AACCCCGAGA-GGG--AGCGGUAAUCUCAGAAA--CUCGGUCGUAGUUCGG-AUUGUGGACUGCAACUCGUCCACAUGAAGCUGGAUUCGGUAGUAAUCGCAUUCCAGGAGAGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGGGGUCCGGAUGAGGCCUGC-----------------CUA-----------GCAGGUC-GAAUCUGGGCUCCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
CP001994.1/695600-697074             AUUCUGGUUGAUCCUGCCAGAGGUUACUGCUAUCGGUGUUCGACUAAGCCAUGCUAGUU-AAAUG-------UUCU---U---------CG----UGAA-------CAU--AGCGGACUGCUCAG-UAACACGUGGACAAUCUGCCCUUGGGUUCAGCAUAACCC--C-G-GGAAACUGGGGA-UAAUUCUGAAUAGAUCACACAU-GCUGGAAU---GCUUUGUGAUUUAAA-GA-------------UCCG------------------UCGCCCAAGGAUGGGUCUGCGGCCUAUCA-GGUUGUAGUGGGUCUAGAGUACCUACUAGCCAACGACGGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGAUGGAUUCUGAGACAUUAAUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCGGGAAACCGCGAUAAGGGGACACC-GA-GUGCCAGCAU------A-CA---AUGCUGGCUGUCCACAUGUGU--AAAUAGCAUGUGA-UAGCAAGGGCCGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCGGCCCGAGUGGUAAUCACUAUUAUUGGGUCUAAAGGGUCCGUAGCCGGUUUAAUCA-GUCUUCCGGGAAAUCUGACAGCUCAACUG-UUAGGCUUCCGGGGGAUACUGU-UA--GACUUGGG-ACCGGGAGAGGUA-AGAGGUACUACAGGGGUAGGAGUGAAAUCUUGUAAUCCCUGUGGGACCACCAGUGGCGAAGGCGUCUUACCAGAACGGGUCCGACGGUGAGGGACGAAAGCUGGGGGCACGAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGCUCGCUAGGUGUCUGGAAUGG-UG-C-GACCGUUUCAGGUGCCGCAGGGAAGCCGUGAAGCGAGCCACCUGGGAAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACGGGUGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAACU-CACCGGGGGCGACAGC--AAUAUGUAGGUCAAGCUAAAGACUU-UACC-UGA----AUCGCUGAGAGGAGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACUGUGAAGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCGU--GCCC-ACUGUUGCCAGC-AUAUCC--UUCG-GGAU-GAU--G-GGUACUCUGUGGGGACCGCCGAUGC-UAAAUCGGAGGAAGGUGCGGGCUACGGUAGGUCAG-UAUGCCCCGAAUCUCCCGGGCU-ACACGCGGGCUACAAUGGUUGGGACAAUGGG-C-UCC-UACACUGAAA-AGU--GACGGUAAUCUCAUAAA--CCCAGCCGUAGUUCGA-AUUGAGGGCUGAAACCCGCCCUCAUGAAGCUGGAAUCCGUAGUAAUCGCGUUUCAAUAUAGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAACCACCCGAGUGAGGUAUGGGUGAGGGCGCGGAC-------------UUAG--------UGCUGCGUUC-GAACCUAAAUUUCGCAA----GGGGGGUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
HM159612.1/1-1470                    AUUCCGGUUGAUCCUGCCGGAGGACAUUGCUAUUGGGAUUCGAUUUAGCCAUGCUAGUC-GAACG--------AGU---UC--------AC----ACU--------CGU--GGCACAUAGCUCAG-UAACACGUGGCCAAGCUACCCUUCAGUCGGCAAUACCCU--C-G-GGAAACUGAGGC-UAAUAGCCGAUACGAAACAGAC-GCUGGAAU---GCACUGUAUUCCAAA-GA---------------CA------------------CCGCUGAAGGAUGCGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCAGUAAUCGGUACGGGUGAUGAGAGUCA-GAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGAAAGUGCGAUAGGGGAAUCCC-GA-GUGCGAGGGC---AUAU-UA---GCCCUCGCUUUUGUUGACUCU--AAGGCGGUCAACG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCAAGUGAUGUCCCAUAUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCGACCAA-GUCUAUCGGGAAAUCCACCUGCCCAACAG-GUGGGCGUCCGGUAGAAACUGG-CC--GGCUUGGA-ACCGGAAGGCUCA-GAGAGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCCGGACGGACUACCGAUGGCGAAAGCACUCUGAGAAGACGGCUUCGACAGUGAGGGACGAAAGCUCGGGUCUCAAACCGGAUUAGAUACCCGGGUAGUCCGAGCCGUAAACAAUGCUCGUUAGGUGUGGCACCCAC-UA-C-GAGUGGGUGCUGUGCCGCAGGGAAGCCGCUAAACGAGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCCCCGACAUC-AGUAAUGACAGUCAUGUUGACGACAUCCACU-CGA----GCUGAUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCAUCCUGUUAAGUCAGGCAACGAGCGAGAUCCAC--GUUC-CUAAUUGCCAGC-ACCAUC--GCAC-GAUG-GGU--G-GGUACAUUAGGAAGACUGCCAGUGC-UAAACUGGAGGAAGGAAUGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGGGCUGGGCA-ACACGCGGGCUACAAUGGUCAGGACAACGGG-U-UCC-AACGCUGAGA-AGC--GACGGCAAUCUCGCAAA--CCUGGUCGUAGUUCGG-AUUGCGGGCUGAAACUCGCCCGCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGCAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAAGCCCUG----------------UCAC-----------CAGGGUU-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
FJ868734.1/1-1467                    -UUCCGGUUGAUCCUGCCGGAGGUCAUUGCUAUUGGGGUCCGAUUUAGCCAUGCCAGUU-GCACG--------AGU---UC--------AU----ACU--------CGU--GGCGAAAAGCUCAG-UAACACGUGGCCAAACUACCCUACAGAGAACGAUAACCU--C-G-GGAAACUGAGGC-UAAUAGUUCAUACGGGAGUCAU-GCUGGAAU---GCCGACUCCCCGAAACGC-------------UCAG------------------GCGCUGUAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCAAGUGCGAUAAGGGGACCCC-AA-GUGCGAGGGC---AU-A-UA---GUCCUCGCUUUUCUCGACUGU--AAGGCGGUCGAGG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCAAGUGAUGACCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCACGAAG-GUUCAUCGGGAAAUCCGCCAGCUCAACUG-GCGGGCGUCCGGUGAAAACCAC-GU--GGCUUGGG-ACCGGAAGGCUCG-AGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGAUGGCGAAAGCACCUCGAGAAGACGGAUCCGACGGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCUCGCUAGGUGUGACACAGGC-UA-C-GAGCCUGUGUUGUGCCGUAGGGAAGCCGAGAAGCGAGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCUCCGACUAC-AGUGAUGACGAUCAGGUUGAUGACCU-UAUCACGA---CGCUGUAGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACUU-CUAAUUGCCAGC-AGCAGU--UCG--ACUG-GCU--G-GGUACAUUAGAAGGACUGCCGCUGC-UA-AGCGGAAGAAGG-ACGGGCAACGGUAGGUCAGUUAUGCCCCGAAUGA-CUGGGCUUAC-CGCGGGCUAUAUGGUCCGAGAGAAUGGG-U-UGC-UUUCUC-AAA-AAG--AACGCUAUUUCCCUAACUCCCUGAUCGUAGUC--G-GAUGAGGGCUA-AACCUGCCCCCCUAGAACUGGAUCCGGUAGUUAUCCCAUUUCAAUAGAGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCCACC----------------ACAC-----------GGUGGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
AB078022.1/266-1952                  ACUCCGGUUGAUCCUGCCGGACCCGACCGCUAUCGGGGUAGGGCUAAGCCAUGGGAGUC-GAACGC-----CCCGC---CG--------CU----GCGGG-----GCGU--GGCGGACGGCUGAG-UAACACGUGGCUAACCUACCCUCGGGACGGGGAUAACCCCUC-G-GGAAACUGGGGC-UAAUCCCCGAUAGGCGGGGGGUGCCUGGAAG---GGUCCUCCGCCGAAAGGGGCCGCG-GGGGGU----UAUCGC-----CCGCGGUCCGCCCGAGGAUGGGGCUGCGGCCCAUCACGGUAGUUGGCGGGGUAAUGGCCCGCCAAGCCUACGACGGGUAGGGGCCGUGAGAGCGG-GAGCCCCCAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACG-GGGCGCACCAGGCGCGAAAACUCCGCAAUGCGGGCAACCGUGACGGGGCUACCCC-GA-GUGCCCCCCU---------U---GGGGGGGCUUUUCCCCGCUGU--AAGUAGGCGGGGG-AAU-AAGCGGGGGGCAAGA-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCCCCGCGAGCGGUCGGGGUGCUUACUGGGCCUAAAGCGCCCGUAGCCGGCUCGACAA-GUCCCCGCCUAAAGCCCCGGGCUCAACCC-GGGGAG-UGGCGGGGAUACUGU-CG--GGCUAGGG-GGCGGGAGAGGCC-GAGGGUACUCCCGGGGUAGGGGCGAAAUCCAUUAAUCCCGGGAGGACCACCAGUGGCGAAGGCGCUCGGCUGGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCGGCUGUAAACGAUGCGGGCUAGGUGUUGGGCGGGC-GUGC-GAGCCCGCCCAGUGCCGCAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAAGGUCCGCGGGAGGGUUCCUGACGUGGUUAAG------------------------------------------------------------------------------UAGAAUUGUUACCCUCCCCGGGCCCAGCAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGA-GCCUGCGGCUUAAUUGGAGUCAACGCCGGGAACCUCCACCGGGGGCGACAGC--AGGAUGACGGCCAGGCUGAAGGCCU-UGCC-CGA----CGCGCUGAGGGGAGGUGCAUGGCCGUCGCCAGACCAGCUGUAGGCGCCCGCACGGUACGCUGAAUAUAGUGUAAAUUAGAAGUACCUUAGGAGAAGACCUUAAGAUCUCUUCACUUUAAUAAACGCGCCGUGCGGGCGCCUGUGCUGGGGCGAACUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCC--GCCC-CUAGUUGCCAUC-CCCGGG--GCGA-CCCG--GG--G-GGCACACUAGGGGGACUGCCGCCGC-UAAGGCGGAGGAAGGAGGGGGCAACGGCAGGUCAG-CAUGCCCCUAAACCCCCGGGCU-GCACGCGGGCUACAAUGGCGGGGACAGCGGG-U-GCC-GACCCCGAAA-GGG--GGAGGCAAUCCCUCAAA--CCCCGCCUCAGUUGGG-AUCGAGGGCUGCAACUCGCCCUCGUGAACGUGGAAUCCCUAGUAACCGCGCGUCAUCAUCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACUGCCCGUC-GCUCCACCCGAGGGGGGAGGGGGUGAGGCCCUCUCC-------------GCCG--------GGAGGGGGUC-GAACCCCCUCCCCCCGA----GGGGGGAGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCC
AE000782.1/1790478-1788987           AUUCUGGUUGAUCCUGCCAGAGGCCGCUGCUAUCCGGCUGGGACUAAGCCAUGCGAGUC-AAGGGGCUUGUAUCCC---UU--------CG----GGGAUGCAAGCACC--GGCGGACGGCUCAG-UAACACGUGGACAACCUGCCCUCGGGUGGGGGAUAACCC--C-G-GGAAACUGGGGC-UAAUCCCCCAUAGGGGAUGGGU-ACUGGAAU---GUCCCAUCUCCGAAA-GCG------------CUUA------------------GCGCCCGAGGAUGGGUCUGCGGCGGAUUA-GGUUGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCCGUACGGGCCAUGAGAGUGG-GAGCCCGGAGAUGGACCCUGAGACACGGGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGUCAGCCG-GA-GUGCUCGCGC---A----UC---GCGCGGGCUGUCGGGGUGCCU--AAAAAGCACCCCA-CAGCAAGGGCCGGGCAAGG-CCGGUGGCAGC-CGCCGCGGUAAUACCGGCGGCCCGAGUGGCGGCCACUUUUAUUGGGCCUAAAGCGUCCGUAGCCGGGCUGGUAA-GUCCUCCGGGAAAUCUGGCGGCUUAACCG-UCAGACUGCCGGAGGAUACUGC-CA--GCCUAGGG-ACCGGGAGAGGCC-GGGGGUAUUCCCGGAGUAGGGGUGAAAUCCUGUAAUCCCGGGAGGACCACCUGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGACGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACGAUGCGGACUAGGUGUCACCGAAGC-UA-C-GAGCUUCGGUGGUGCCGGAGGGAAGCCGUUAAGUCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACGGGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGGAAGCU-UACCGGGGGAGACAGC--GGGAUGAAGGUCGGGCUGAAGACCU-UACC-AGA----CUAGCUGAGAGGUGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACUGUGAAGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--GCCC-CCAGUUGCCAGC-GGUUCC-CUUCGGGGAA-GCC--G-GGCACACUGGGGGGACUGCCGGCGC-UAAGCCGGAGGAAGGUGCGGGCAACGGCAGGUCCG-UAUGCCCCGAAUCCCCCGGGCU-ACACGCGGGCUACAAUGGCCGGGACAAUGGG-U-ACC-GACCCCGAAA-GGG--GUAGGUAAUCCCCUAAA--CCCGGUCUAACCUGGG-AUCGAGGGCUGCAACUCGCCCUCGUGAACCUGGAAUCCGUAGUAAUCGCGCCUCAAAAUGGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAGCCACCCGAGUGGGCCAGGGGCGAGGGGGUGGCC-------------CUA---------GGCCACCUUC-GAGCCCAGGGUCCGCGA----GGGGGGCUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
CP001787.1/622143-623617             AUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUCGGGGUCCGACUAAGCCAUGCGAGUC-AAGGG------GCUCC---UU--------CG----GGAG------CACC--GGCGCACGGCUCAG-UAACACGUGGCUAACCUACCCUCGGGAGGGGGAUAACCU--C-G-GGAAACUGAGGC-UAAUCCCCCAUAGGGGAGGAGG-UCUGGAAC---GAUCCCUCCCCGAAA-GC-------------UCCG------------------GCGCCCGAGGAUGGGGCUGCGGCGGAUUA-GGUAGUUGGUGGGGUAACGGCCCACCAAGCCGACGAUCCGUACGGGCCCUGAGAGGGG-GAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUCCGCAAUGCACGAAAGUGCGACGGGGGGACCCC-GA-GUGCCAUCCC----A-A--C---GGGAUGGCUUUUCCGGAGUGU--AAACAGCUCCGGG-AAU-AAGGGCUGGGCAAGU-CCGGUGCCAGC-AGCCGCGGUAAUACCGGCGGCCCAAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCCAGUAA-GUCUCUGCUUAAAUCCUGCGGCUCAACCG-CAGGGC-UGGCAGAGAUACUGC-UG--GGCUUGGG-ACCGGGAGAGGCC-GGGGGUACCCCAGGGGUAGCGGUGAAAUGCGUUGAUCCCUGGGGGACCACCUGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGACGAAGGCCAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACUCUGCGGACUAGGUGUCGCGUCGGC-UU-C-GGGCCGACGCGGUGCCGAAGGGAAGCCGUUAAGUCCGCCGCCUGGGGAGUACGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACGGGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGGCAUCU-CACCAGGGGCGACGGC--AGGAUGAAGGCCAGGUUGACGACCU-UGCC-AGA----CGCGCCGAGAGGUGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGUAACGAGCGAGACCCGU--GCCC-CAUGUUGCAACC-UCCUCC--UCCG-GGAG--GA--G-GGCACUCAUGGGGGACCGCCGGCGC-UAAGCCGGAGGAAGGUGCGGGCAACGACAGGUCCG-CAUGCCCCGAAUCCCCUGGGCU-ACACGCGGGCUACAAUGGCCGGGACAAUGGG-A-AGC-GACCCCGAAA-GGG--GGAGCGAAUCCCCUAAA--CCCGGUCGUAGUCCGG-AUCGAGGGCUGUAACUCGCCCUCGUGAAGCCGGAAUCCGUAGUAAUCGCGCCUCACCAUGGCGCGGUGAAUGCGUCCCUGCUCCUUGCACACACCGCCCGUC-ACGCCACCCGAGUUGAGCCCAAGUGAGGCCCUGUCC-------------GCAA--------GGGCAGGGUC-GAACUUGGGUUCAGCAA----GGGGGGCGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCU
AADL01001500.1/4238-2769             ACUCCGGUUGAUCCUGCCGGCGGCCACCGCUAUCAAGUUCCGACUAAGCCAUGCGAGUC-AAGGU--------AUC---GU--------AA----GAU--------GCC--GGCAAACUGCUCAG-UAACACGUGGAUAAUCUAACCUUGAGUAAGGGAUAACCU--C-G-GGAAACUGAGGA-UAAUACCUUAUAAUUGCUUAAA-ACUGGAAU---GUUUAAGCAAUAAAA-GU-------------UCAG------------------ACGCUCAAGGAUGAGUCUGCGACCUAUCA-GGUAGUAGGUGGUGUAAUGGACCACCUAGCCUCAGACGGGUACGGGCCCUGGGAGGGG-UAGCCCGGAGAUGGACUCUGAGACAUAAGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAACACUGUGCAAUGCGCGAAAGCGCGACACGGGGAGCUU-GA-GUGUCUUGGC------A-UA---GCCAAGACUUUUCUCAUUCCU--AAAAAGCAUGAGG-AAU-AAGUGCUGGGUAAGA-CGGGUGCCAGC-CGCCGCGGUAACACCCGCAGCACAAGUGGUGGUCACUUUUAUUGAGCCUAAAGCGUUCGUAGCCGGUUUUGUAA-AUCUUUAGAUAAAGCCUGAAGCUUAACUC-CAGAAA-GUCUGAAGAGACUGC-AA--GACUUGAG-AUCGGGUGAGGUU-AAACGUACUUUCAGGGUAGGGGUAAAAUCCUGUAAUCCCGGAAGGACGACCAGUGGCGAAAGCGUUUAACUAGAACGAAUCUGACGGUAAGGAACGAAGGCUAGGGUAGCAAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACAUUGCCCAUUUGAUGUUGCUUUUCC-GU-U-GAGGGAAGGCAGUGUCGGAGCGAAGGUGUUAAAUGGGCCGCUUGGGAAGUAUGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCGCAACGGGAGGA-AUGUGCGGUUUAAUUGGAUUCAACGCCGGAAAACU-CACCGGGAACGACCUG--UGCAUGAGAGUCAACCUGACGAGUU-UACU-CGA----UAGCAGGAGAGGUGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUAGGGCGUUCACUUAAGUGUGAUAACGAGCGAGACCCAC--AUCU-UUAAUUGCAAAU-GUAUAU--GAGA-AUAU--GC--A-UGCACUUUAGAGAAACCGCCAGCGC-UAAGUUGGAGGAAGGAGUGGUCGACGGCAGGUCAG-UACGCCCCGAAUUUCCCGGGCU-ACACGCGCAUUACAAAGAACGGGACAAUACG-U-UGC-AACCUCGAAA-GGG--GAAGCUAAUCG-CGAAA--CCCGUCCAUAGUUAGG-AUUGAGGGCUGUAACUCGCCCUCAUGAAUCUGGAUUCCGUAGUAAUCGCGGGUCAACAACCCGCGGUGAACAUGCCCCUGCUCCUUGCACACACCGCCCGUC-AAACCAUCCGAGUUGGUGUUGGAUGAGGUUUAAUUC-------------GAGA--------GGGUUAAAUC-AAAUCUGAUGUCGGUGA----GGAGGGUUAAGUCGUAACAA------G--GUAUCCGUAGGGG----------AACCUGCGGAU-GGAUCACCUCCA
AJ890141.1/1-1475                    -UUCUGGUUGAUCCUGCCAGAGGUUACUGCUAUCGGAGUUCGAUUAAGCCAUGCGAGUC-UAAAG------GUUUC---UU--------CG----GAAA------CCUU--GGCGGACUGCUCAG-UAACACGUGGAUAACCUACCCUUGGGACUGGAAUAACCC--C-G-GGAAACUGGGGA-UAAUACCGGAUAGAUCAGGGAU-GCUGGAAU---GCACCUUGAUCCAAA-GC-------------UCCG------------------GCGCCCAAGGAUGGGUCUGCGGCCUAUCA-GGUAGUAGUGGGUGUAACGUACCUACUAGCCAACGACGGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGAUGGAUUCUGAGACACGAAUCCAGGCCCUACG-GGGUGCAGCAGGCGCGAAACCUUUACAAUGUGCGAAAGCAUGAUAAGGGAACUCC-GA-GUGCCAGUAU------C-UA---AUACUGGCUGUCCUUGUGCCU--AAAACGCACAAGA-UAGCAAGGGCCGGGUAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCGGCCCGAGUGGUAGCCGCUAUUAUUGGGUCUAAAGGGUCCGUAGCCGGUUCGAUAA-GUCCUCUGGGAAAUCUGGUUGCUUAACAA-UCAGACUGCCAAGGGAUACUGU-CG--AACUUGAG-ACCGGGAGAGGUA-AGAGGUACUUCAGGGGUAGGAGUGAAAUCUUGUAAUCCCUGGGGGACCAUCUGUGGCGAAGGCGUCUUACCAGAACGGGUCUGACGGUGAGGGACGAAAGCUGGGGGCGCAAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGCUCGCUAUGUGUCAGGUACGG-UG-U-GACCGUAUCUGGUGCCGUAGGGAAGCCGUGAAGCGAGCCACCUGGGAAGUACGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACGGGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGAAAUCU-UACCGGGGGAGACAGC--AGAAUGAAGGUCAGGCUGAAGACCU-UACC-AGA----UCCGCUGAGAGGAAGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACUGUGAAGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCGU--GCCC-ACAGUUGCCAGC-AUGCCC--UUCG-GGGC-GAU--G-GGUACUUUGUGGGGACCGCCGCUGC-UAAAGCGGAGGAAGGAGCGGGUUACGGUAGGUCAG-UAUGCUCCGAAACUCCCGGGCU-ACACGCGGGCUACAAUGGUUGGGACAAUGGG-A-AUC-AACACCGAAA-GGU--GAAGGCAAUCUCCUAAA--CCCAAUCGAAGUCCGG-AUUGAGGGCUGCAACUCGCCCUCAUGAAGCUGGAAUCCGUAGUAAUCGCGUUUCAACACAGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAACCAUCUGAGUGAGGUUUGGAUGAGGGUCUUCC--------------UUAU---------GGGGGAUUC-GAAUCUGGGCUUCGCAA----GGAGGGUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
AEMB01000004.1/2051-578              AUUCUGUUUGAUCCUGGCAGAUGCUACUGCUAUUGGGAUUCGAUUAAGCCAUGCAAGUC-GAACG--------AGU---UU--------AG----ACU--------CGU--GGCGUACGGCUCAG-UAACACGUGGAUAACCUACCCUUAGGACUGGGAUAACCC--U-G-GGAAACUGGGGA-UAAUACUGGAUAGGCGAUUAUU-CCUGUAAU---GGUUUUUUGUUUAAAUGU-------------UUUU------------------UCGCCUAAGGAUGGGUCUGCGGCCGAUUA-GGUAGUUGGUUAGGUAAUGGCUUACCAAGCCUUUGAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGAUGGAACCUGAGACAAGGUUCCAGGCCCUACG-GGGUGCAGCAGGCGCGAAACCUCCGCAAUGUGAGAAAUCGCGACGGGGGGAUCCC-AA-GUGCCAUUCU---UA-A-C----GGGAUGGCUUUUCAUUAGUGU--AAAGAGCUUUUGG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCAGCUCUAGUGGUAGCAGUUUUUAUUGGGCCUAAAGCGUCCGUAGCCGGUUUAAUAA-GUCUCUGGUGAAAUCCUGCAGCUUAACUG-UGGGAAUUGCUGGAGAUACUAU-UA--GACUUGAG-AUCGGGAGAGGUU-AGAGGUACUCCCAGGGUAGAGGUGAAAUUCUGUAAUCCUGGGAGGACCGCCUGUUGCGAAGGCGUCUGACUGGAACGAUUCUGACGGUGAGGGACGAAAGCUAGGGGCGCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCGGACUUGGUGUUGGGGUGGC-UU-U-GAGCUGUCCCAGUGCCGAAGGGAAGCUGUUAAGUCCGCCGCCUGGGAAGUACGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGCGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGACAUCU-CACCAGAGGCGACAGC--UGUAUGAUAGCCAGGUUGAUGACUU-UGCU-UGA----CUAGCUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCAC--GCCC-UUAGUUACCAGC-GGAUCC--UUUU-GGAU-GCC--G-GGCACACUAAGGGGACCGCCUAUGA-UAAAUAGGAGGAAGGAGUGGACGACGGUAGGUCCG-UAUGCCCCGAAUCCUCUGGGCA-ACACGCGGGCUACAAUGGCUGAGACAAUGGG-U-UCC-GACGCCGAAA-GGC--GGAGGUAAUCCUCUAAA--CUUAGUCGUAGUUCGG-AUUGAGGACUGUAACUCGUUCUCAUGAAGCUGGAAUGCGUAGUAAUCGCGUGUCACAAUCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-ACGCCACCCAAAAAGGGAUUGGAUGAGGAUGUAAUG-------------UUU---------GGUUAUAUUC-GAAUCUAGUUUUUUUAA----GGAGGGCGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCU
EU686642.2/21786-23257               AAUCCGGUUGAUCCUGCCGGACCUGACUGCUAUCGGAUUGAUACUAAGCCAUGCGAGUC-U-U---------UGUA---GU--------AA----UAC---------AA--GGCAGACGGCUCAG-UAACACGUAGUCAACCUACCCUAUGGACAAGAAUAAUCU--C-G-GGAAACUGGGCA-UAAUUCUUGAUAGAUCAUAAUG-CCUGGAAU---GGUUUAUGGUUAAAAUGA-------------UUCG------------------UCGCCAUAGGAUGGGACUGCGGCCUAUCA-GCUUGUUGGUGAGGUAAUGGCCCACCAAGGCGAUUACAGGUACGGGCUCUGAGAGGAG-AAGCCCGGAGAUGGGUACUGAGACACGGACCCAGGCCCUAUG-GGGCGCAGCAGGCGAGAAAACUUUGCAAUGUGCGAAAGCACGACAAGGUUAAUCC-GA-GUGAUUUCUG----C-U-A----AAGAAAUCUUUUGCCAGUCAU--AAAACCACUGGUG-AAU-AAGGGGUGGGCAAGUUCUGGUGUCAGC-CGCCGCGGUAAAACCAGCACCUCAAGUGGUCAGGAUGAUUAUUGGGCCUAAAGCAUCCGUAGCCGGCUUUGUAA-GUUUUCGGUUAAAUCCAUGUGCUCAACGC-AUGGGC-UGCCGAAAAUACUGC-AU--GGCUAGGG-AGUGGGAGAGGUA-GACGGUACUCAGUAGGAAGGGGUAAAAUCCUUUGAUCUAUUGAUGACCACCUGUGGCGAAGGCGGUCUACCAGAACACGUUCGACGGUGAGGGAUGAAAGCUGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCAGACUCGAUGAUGCAUUGGC-AU-AAUAGCCAGUGCAGUGUCGCAGGGAAGCCGUUAAGUCUGCCGCCUGGGAAGUACGUACGCAA-------------------------------------GUAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAA-GCCUGCGGUUCAAUUGGAGUCAACGCCAGAAAUCU-UACCCGGAGAGACAGC--AGAAUGAAGGUCAAGCUGAAGACUU-UACC-AGA----CAAGCUGAGAGGUGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGAUGUCCUGUUAAGUCAGGUAACGAGCGAGAUCCCU--GCCA-CUAGUUGCUAUC-AUUAUU-CUCAGGAAUA--GU--GGGGCGAAUUAGUGGGACUGCCGUUGU-UAAAACGGAGGAAGGAAGGGGCUACGGCAGGUCAG-UAUGCCCCGAAACUCUGGGGCC-ACACGCGGGCUGCAAUGGUAGUGACAAUGAG-U-UCC-AAACUCGAAA-GAG--AGUGGCAAUCUCU-AAA--CGCUACCACAGUUAUG-ACUGAGGGCUGUAACUCGCCCUCACGAAUAUGGAAUCCCUAGUAACCGCGUGUCAUUACCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GUUUCAUCGAAGUUUGCUUUUAGCGAGGUGAUGUUU-------------AAU---------UGGCAUUAUC-GAACUUGAGGUAAGCGA----CGAGGGAAAAGUCGUAACAA------G--GUGUCCGUAGGGG----------AACCUGCGGAC-GGAUCACCUCCU
AGIW01000001.1/27172-28667           ACUCCGGUUGAUCCUGCCGGUCCCGACCGCUAUCGGGGUGGGGCUAAGCCAUGGGAGUC-GUACGC-----CCCGC---CG--------CU----GCGGG-----GCGU--GGCGGACGGCUGAG-UAACACGUGGCUAACCUACCCUCGGGAGGGGGAUAACAC--C-G-GGAAACUGGUGC-UAAUCCCCCAUAGAGGAGGGGG-CCUGGAAG---GGUCCCUCCUCGAAAAGGUGUGGC--AGGGG----UUAACGC----UGCCACACCGCCCGAGGAUGGGGCUACGGCCCAUUA-GGUAGUUGGCGGGGUAACGGCCCGCCAAGCCGAUAAUGGGUAGGGGCCGUGAGAGCGG-GAGCCCCCAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACG-GGGCGCACCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGUGACGGGGCCACCCC-GA-GUGCCCCC------U-U-AC-----GGGGGCUUUUCCCCGCUGU--AGGAAGGCGGGGG-AAU-AAGCGGGGGGCAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCCCCGCGAGUGGUCGGGACGAUUAUUGGGCCUAAAGCGCCCGUAGCCGGCUCGGCAA-GUCUCCUCCUAAAUCCUCGGGCUCAACCC-GAGGAU-UGGAGGAGAUACUGC-CG--AGCUAGGG-GGUGGGAGAGGCC-GAGGGUACUCCCGGGGUAGGGGCGAAAUCCUAUAAUCCCGGGAGGACCACCAGUGGCGAAGGCGCUCGGCUGGAACACGCCCGACGGUGAGGGGCGAAAGCCGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCGGCUGUAAACGAUGCGGGCUAGGUGUUGGGUGGGC-CU-A-GAGCCCACCCAGUGCCGCAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUCAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGA-GCCUGCGGUUCAAUUGGAGUCAACGCCGGGAAUCU-CACCGGGGGAGACAGC--AGGAUGACGGCCAGGUUAAAGGCCU-UGCC-UGA----CGCGCUGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCUGUGAAGUGUCCGGUUAAGUCCGGAAACGAGUGAGACCCCC--ACCC-CUAGUUGCGACC-CGGGGC--UACG-GCUC--CG--G-GGCACACUAGGGGGACUGCCGCCGUUUAAGGCGGAGGAAGGAGGGGGCCACGGCAGGUCAG-CAUGCCCCGAAUCCCCCGGGCU-ACACGCGGGCUACAAUGGCGGGGACAAUGGG-A-UCC-GACCCCGAAA-GGG--GGAGGCAAUCCCUCAAA--CCCCGCCGUAGUUGGG-AUCGAGGGCUGCAACUCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCGUGUCAACAUCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUCCACCCGAGGGGAGGGGGAGUGAGGCCUGGCCC-------------UCU---------GGGUCGGGUC-GAACUCCCCCUCCCUGA----GGGGGGAGAAGUCGUAACAA------G--GUAGCCGUACCGG----------AAGGUGCGGCU-GGAUCACCUCCU
EU686634.1/4190-5654                 AAUCCGGUUGAUCCUGCCGGAGGCGACCGCUAUUGGAGUUCGAUUAAGCCAUGCGAGUC-UAGAG---------GC---UU--------AG----GC---------CUC--GGCGUACCGCUCAG-UAACACGUGGAUAACCUGCCCUGUUCAGGGGGAUAACCU--C-G-CGAAAGUGAGAA-UAAUACCCCAUAGUUCACCAUG-CCUGGAAC---GGUUGGUGGAUGAAA-GC-------------UCAG------------------GCGGAACAGGAUGGGUCUGCGGCGUAUCA-GGUAGUAGGGGGUGUAAUGGACCUCCUAGCCCUCGACGCGUACGGGUUGUGGGAGCAA-UCGCCCGGAGAUGGAUUCUGAGACACGAAUCCAGACCCUACG-GGGUGCAGCAGGCGCGAAAACUUGACAAUGCGAGAAAUCGUGAUCAGGGAACUCC-AA-UUGUCCCCGU----U-U-U----ACGGGGUUCUGAAUUGACUCU--AAACAGGUCGAGU-AAU--AGGGGCGGGAAAUA-UCGGUGCCAGC-CGCCGCGGUAAUACCGAAGCCCCAAGUGGUCGUCGUUCUUAUUGGGCCUAAAACGUCCGUAGCCGGUUUGGUAC-AUUCGUGGGUAAAUCAGACAGCUUAACUG-UCUGAA-UUCUGCGAGCACGGC-CA--AACUUGAG-ACCGGGAGAGGUG-UAGGGUACCUGCGGGGUAGGGGUAAAAUCCUGUCAUCCCGUAGGGACCACCAGUUGCGAAGGCUCUACACUAGAACGGAUCUGACGGUCAGGGACGAAGCCUAGGGGCACGAACCGGAUUAGAUACCCGGGUAGUCCUAGGUGUAAACGCUGUGGACUUUGUGUCGGGAAACC-UU-A-GAGGAUUCUCGGUGCCGGAGUGAAGAUGUUAAGUCCACUGCCUGGGGAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUGCAACGAGAGGA-GCGUGCGGUUUAAUUGGAUUCAACGCCGGAAAACU-CACCAAAGCCGACUGU--UAUAUGAAGACCAGCGUAACGAGCU-UGUC-GGA----UUUUCAGAGAGGUAGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACCGUAAGGCGUUCUGUUAAGUCAGAUAACGAACGAGACCCCC--AUCG-UCAUUUGCUAAC-CCUUUC--UCCG-GAAA--GG--G-CGCACUAUGGCGAGACCGCUGGCGU-GAAGUCAGAGGAAGGCGGGGGCAACGGUAGGUCAG-UAUGCUCCGAAUGCUUUGGGCU-ACACGCGCGCUACAAAGGACGGGACAAUGGG-C-AGC-UACUCCGAGA-GGA--GAUGCUA-UCCCG-AAA--CCCGUUCGUAGUUCGG-AUCGUGGGCUGUAACUCGCCCUCGUGAAGCUGGAUUUCGUAGUAAUCGCGUCUCAAAAUGGCGCGGUGAAUAUGCCCCUGCUCCUUGCACACACCGCCCGUC-AAACCAUCUUAGUUUGGGGUGGGUGAGGCUACCUUU-------------UAU---------UGGGGUAUUC-GAGCCUGCCUUAGACAA----GGAGGGUUAAGUCGUAACAA------G--GUACCUGUAGGGG----------AACCUGCAGGU-GGAUCACCUCCU
AB627357.1/1-1472                    AUUCCGGUUGAUCCUGCCGGAGGUCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUC-GCACG--------GGU---UC--------AG----ACC--------CGU--GGCGAAUAGCUCCG-UAACACGUGGCCAAUCUACCCUACGGACCGGUAUAACCU--C-G-GGAAACUGAGGC-UAAUCCCGGUUACGGCUCUCAU-GCUGGAAC---GCCGAGAGCUGGAAACGU-------------UCCG------------------ACGCCGUAGGAUGAGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAA-GAACCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAGGGGGACUCC-GA-GUGCGGAGGC---AU-A-GU---GCCUUCGCUUUUGUGCACCCU--AAGGCGGUGCACG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCGAGUGAUGACCGAUCUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCGGGCAA-GUCCGUCGGGAAAUCUACCAGCUCAACUG-GUAGGCGUCCGGCGGAAACUGC-UC--GGCUUGGG-ACAGGGAGACUCG-AAGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGAUGGCGAAAGCACUUCGAGAGAACUGAUCCGACGGUCAGGGACGAAAGCUGGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGUUCGCUAGGUGCGACGCAGAC-UA-C-GAGUCUGUGUUGUGCCGUAGGGAAGCCGAGAAGCGAACCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCCCCGACUGU-AGGAAUGAAUCCCAGUGUGAUGAGCU-UGGA-AGA----CCUACAGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--GUCC-CUAAUUGCCAGC-AAGACC--CUUGAGGUC-GUU--G-GGUACAUUAGGGAGACUGCCGCCGC-CAAGGCGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGGGCUGGGCU-ACACGCGGGCUACAAUGGUCAGGACAAUGGG-U-UCC-UACCCCGAGA-GGG--GACGGUAAUCUCAGAAA--CCUGGUCGUAGUUCGG-AUUGUGGGCUGAAACUCGCCCACAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCACAAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCCUGG----------------GUUG-----------CCAGGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCA
HQ215547.1/1-1474                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUC-GCACG--------GGC---UC--------AG----ACC--------CGU--GGCAGAUAGCUCAG-UAACACGUGGCCAAACUACCCUACAGAUCGUGAUAACCU--C-G-GGAAACUGAGGC-UAAUAACGAAUACAGCUCACAG-AUUUGAAU---AUCGUGAGCUGGAAACGC-------------UACG------------------GCGCUGUAGGAUGUGGCUGCGGCCGAUUA-GGCAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACAGGUGGUGAGAGCCA-GAGCCUGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAAGGGGACUCC-GA-GUGCGAGGGC---AU-A-UA---GUCCUCGCUUUUGUCGACCGU--AAGGUGGUCGACG-AAU-AAGGACUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGUCCGAGUGAUGGUCGACAUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCGAGCAA-GUCUGUCGGGAAAUCCAGUAGCUCAACUA-CUGGACGUCCGGUGGAAACUGU-UC--GGCUUGGG-ACCGGAAGAUCCA-AGGGGUACGUCCGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCACCGAUGGCGAAAGCACCUUGGAAGCACGGAUCCGACAGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCCGUUAACGAUGCCCGCUAGGUUUGGCGCAGGC-UA-C-GAGCCUGCGCUGUGCCGAAGUGAAGACGU-AAGCGGGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCACCGACAAC-AGUGAUGACGGUCAGCUUAACGAGCU-UACC-CGCG-ACGCUGUUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCGU--AUCC-GUAAUUGCCAGC-AAUACC--CUUGUGGUA-GUU--G-GGUACUUUACGGAGACUGCCACGGC-UAACGUGGAGGAAGGAGCGGGCAACGGUAGGUCAG-CAUGCCCCGAAUGUGCUGGGCA-ACACGCGGGCUACAAUGGCCGGGACAACGGG-U-CGC-GACGCCGAGA-GGC--GGAGCUAAUCCCUUAAA--CCCGGUCGUAGUUCGG-AUUGUGGGCUGAAACUCGCCCACAUGAAGCUGGGUUCGGUAGUAAUCGCGUGUCAGAAGCGCGCGGUGAAUCCGUCCCUGCCCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCCUGG----------------AUUC-----------CCAGGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
JF421970.1/1-1471                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUGGGGAUCCGAUUUAGCCAUGCUAGUC-GCACG--------AGU---UU--------AG----ACU--------CGU--GGCAGAUAGCUCAG-UAACACGUGGCCAAACUACCCUCUGGACGGGAAUAUCCU--C-G-GGAAACUGAGGC-CAAUACCUGAUAUCACUUCACU-CCUGGAAU---GGAUGGAGAGUCAAACGC-------------UCCG------------------GCGCCAGAGGCUGUGGUUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCAGUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGUAUCUGAGACAAGAUACCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAAGGGGAUCCC-CA-GUGCGAGGGC---AU-A-CA---GUCCUCGCUUUUCACCACCGU--ACGAUGGUGGUGG-AAC-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCGAGUGAUGGCCGUUCUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCACGCAA-GUUCGUCGGGAAAUCCACGCGCUCAACGC-GUGGGCGUCCGGCGAAACCUGC-GU--GGCUUGGG-ACCAGACGACCCA-GAGGGUACGGCCGGGGUAGGAGUGAAAUCCUGUAAUCCCGGCCGGACCACCGGUGGCGAAAGCGCUCUGGGAGGAUGGAUCCGACGGUGAGGGACGAAAGCCAAGGUCACGAACCGGAUUAGAUACCCGGGUAGUCUUGGCCGUAAACGAUGUCCGUUAGGUGCGGCGUAGGC-UA-C-GAGCCUGCGCUGUGCCGCAGUGAAGACGCUAAACGGACCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUUAACGCCGGACAUCU-CACCAGCAUCGACAAUGUGCAGUGACAGUCAGUGUGAUGAGCU-UACU-AGA----GCCAUUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--AUCC-UUAAUUGCCAGC-ACUGGC--GCGA-GCCA-GGU--G-GGUACAUUAGGGAGACUGCCGUGGC-CAACACGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGUGCUGGGCG-ACACGCGGGCUACAAUGGCCGAGACAGUGGG-A-CGC-AACCCCGAGA-GGG--GACGCUAAUCUCCGAAA--CUCGGUCGUAGUUCGG-AUUGAGGGCUGAAGCUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCCACUCAGAAGGUGGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGGGGUCCGGAUGAGGCUCGG-----------------UUC-----------CCGAGUC-GAAUCUGGGCUCCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
CP002590.1/1332074-1330569           AAACCGGUUGAUCCUGCCGGACCUGACCGCUAUCGGGGUGGGGCUAAGCCAUGCGAGUC-GCGCG------CCCGG---GG--------CG----CCGG------GCGC--GGCGCACGGCUCAG-UAACACGUGCCCAACCUACCCUCGGGAGGGGGACAACCC--C-G-GGAAACUGGGGC-UGAUCCCCCAUAGGGGAAGGGC-GCUGGAAG---GCCCCUUCCCCCAAAGGGA------------UCUCGGGCGAUC-UCCCGGGAUCCGCCCGAGGAUGGGGGCACGGCCCAUCA-GGUUGUUGGCGGGGUAACGGCCCGCCAAGCCGAAGACGGGUAGGGGCGGUGAGAGCCGUGAGCCCCGAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACG-GGGUGCAGCAGGCGCGAAUACUCCGCAAUGCGGGCAACCGCGACGGGGCCACCCC-GA-GUGCCGGGC----GA-A-GA----GCCCGGCUUUUGCCCGGUGU--AAGGAGCCGGGCG-AAU-AAGCGGGGGGUAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCCCCGCGAGUGGUCAGGGUGAUUACUGGGCUUAAAGCGCCCGUAGCCGGCCCGGCAA-GUCGCUCCUGAAAUCCCCGGGCUCAACCC-GGGGGC-CGGGGGCGAUACUGC-CG--GGCUAGGG-GGCGGGAGAGGCC-GCCGGUACUCCGGGGGUAGGGGCGAAAUCCUAUAAUCCCCGGAGGACCACCAGUGGCGAAAGCGGGCGGCCAGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGGAGCAAAGGGGAUUAGAUACCCCUGUAGUCCCGGCUGUAAACGAUGCGGGCUGGCUGUCGGCCGGGC-UU-A-GGGCCCGGCCGGUGGCGUAGGGAAACCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGGGCACCACAAGGGGUGAA-GCUUGCGGCUUAAUUGGAGUCAACGCCGGAAACCU-UACCCGGGGCGACAGC--AGGAUGAAGGCCAGGCUAACGACCU-UGCC-GGA----CGAGCUGAGAGGAGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGUGUCCGGUUAAGUCCGGCAACGAGCGAGACCCCC--ACCC-CUAGUUGCUUCC-CCGCUC--UUCG-GGAC-GGG--G-GGCACACUAGGGGGACUGCCGGCG--UAAGCCGGAGGAAGGAGGGGGCCACGGCAGGUCAG-UAUGCCCCGAAACCCCGGGGCU-GCACGCGAGCUGCAAUGGCGGGGACAGCGGG-A-UCC-GACCCCGAAA-GGG--GGAGGCAAUCCCGUAAA--CCCCGCCCCAGUAGGGAAUCGAGGGCUGCAACUCGCCCUCGUGAACGUGGAAUCCCUAGUAACCGCGUGUCACCAACGCGCGGUGAAUACGUCCCUGCCCCUUGCACACACCGCCCGUC-GCACCACCCGAGGGAGUUCUCUGCGAGGCCCCUUGCCUGG----GGCAA----CC---CGGGUGGGGGGAC-GAGCAGAGAACUCCCGA----GGGGGGUGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCU
EU887285.2/1-1472                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUUGGAGUUCGAUUUAGCCAUGCUAGUU-GCACG--------AGU---UU--------AG----ACU--------CGU--AGCGGAAAGCUCAG-UAACACGUGGUCAAACUACCCUAUAGACCAGCAUAACCU--C-G-GGAAACUGAGGC-UAAUACUGGAUAACGCCCUCAC-GUUUGAAC---ACAGAGGGCCGGAAACGC-------------UCCG------------------GCGCUAUAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGAUGGAUUCUGAGACAAGAAUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUUUACACUGCACGACAGUGCGAUAAGGGAACUCC-AA-GUGCGAGGGC---AU-A-UA---GUCCUCGCUUUUGUGUAUCGU--AAGGUGGUACACG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCAAGUGAUGGCCAAUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCGAACAG-GUCCGUCGGGAAAUCUGCUCGCUCAACGA-GCAGGCGUCCGACGGAAACCAG-UU--GGCUUGGG-GCCGGAAGACCCA-AGGGGUACGUCUGGGGUAGGAGUGAAAUCCUGUAAUCCUAGACGGACCACCGAUCGCGAAAGCACCUUGGGAGGACGGACCCGACGGUGAGGGACGAAAGCUAGGGUCACGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCUCGCUAGGUGUGGCACAGGC-UA-C-GAGCCUGUGCUGUGCCGUAGGGAAGCCGAGAAGCGAGCCGCCUGGGAAGUACGUCUGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCACCGACAAU-AGCUGUGACGGUCAGUUUGAUGAGCU-UACU-AGA----GCUUUUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCAUCCUGUUAAGUCAGGCAACGAGCGAGAUCCGC--GUCC-GUAAUUGCCAGC-AGCACC--CUUGUGGUG-GCU--G-GGUACAUUACGGAGACUGCCGCUGC-UAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAG-CAUGCCCCGAAUGUGCUGGGCU-ACACGCGGGCUACAAUGGCCAAGACAAUGGG-U-UCC-AACCCCGAGA-GGG--GACGGUAAUCUCCGAAA--CUUGGUCGUAGUUCGG-AUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGCUUCAGCAGAGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCCAUC----------------AGGC-----------GAUGGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
D26489.1/301-1793                    AUUCCGGUUGAUCCUGCCGGACCAGAUCGCUAUGGGGAUAGGGCUAAGCCAUGGGAGUC-GUACG-------CUCU---CGG-----UAAG----AGGG-------CGU--GGCGGACGGCUGAG-UAACACGUGGUCAACCUAACCUCGGGACUUGGAUACCUC--C-G-GGAAACUGGAGC-UAAUCCAAGAUAGGCAAAGGAA-UCUGGAAC---GAUCCUUUGCUUAAAGGCC------------UCUAGGCUAAUACUGUCUAGAGGUGCCCGAGGAUGGGACUGCGGCCCAUCA-GGCUGUUGGUGGGGUAAUGGCCCACCAAACCGAUAACGGGUAGGGGCCGUGGGAGCGG-GAGCCCCCAGUUGGGCACUGAGACAAUGGCCCAGGC--UACG-GGGCGCACCAGGCGCGAAACGUCCCCAAUGCGGGAAACCGUGAGGGCGCUAUCCC-CA-GUGCCUCC------G-A-UA-----GGAGGCUUUUCCCCACUUU--AGAACGGUGGGGG-AAU-AAGCGGGGGGCAAGG-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCCCCGCGAGUGAUCUGGACGUUUAUUGGGCUUGAAGCGCCCGUAGCCGGCCCAUAAA-GUCACUGUUUAAAGACCCGGGCUCAACCC-GGGAAA-GGGCAGUGAUACUUA-UG--GGCUAGGG-GGCGGGAAAGGUC-GGAGGUACUCCCGGAGUAGGGGCGAAAUCCGUAGAUCCCGGGAGGACCACCAGUGGCGAAAGCGUCCGGCUAGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGCAGCAAAAGGGAUUAGAUACCCCUGUAGUCCCGGCUGUAAACGAUGCAGGCUAGGUGUCGCGUGGGU-CU-A-GAGCCCGCGCGGUGCCGCAGGGAAACCGGUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGA-AC-UGCGGCUCAAUUGGAGUCAACGCCUGGAAUCU-UACCGGAGGAGACCGC--AGUGUGACGGUCAGGCUAAUGACCU-UACC-UGA----CUCGCGGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGUUGUGAAAUGUCCGGUUAAGUCCGGCAACGAGCGAGACCCCC--ACCU-CUAAUUGGCAUU-CUCUCC--CCCG-GGAG--GG--A-CCCACAUUAGAGGGACUGCCGUCGU-UAAGACGGAGGAAGGAGGGGGCCACGGCAGGUCAG-CAUGCCCCGAAACUUCUGGGCC-GCACGCGGGUUACAAUGGCAGGGACAACGGG-AGUCC-AACCUCGAAA-GGG--GGAGGUAAUCCCUUAAA--CCCUGCCUCAGUUGGG-AUCGAGGGCUGAAAUUCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCACGUCAACAACGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUCCACCCGAGU-GAGAAGAAGUGAGGUUUCUUGC------------CUUCGG------GGUGGGGAAUC-GAACUUCUUCUCCGCGA----GGGGGGAGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCAC
D87971.1/1-1465                      AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGUGUCCGAUUUAGCCAUGCGAGUU-GUACG--------------UU--------UA---C-----------CGU--AGCAAACUGCUCAG-UAACACGUGGCCAAACUGCCCUAUGGACCGGAAUAACCU--C-G-GGAAACUGAGGC-UAAUUCCGGAUACCACAUUCAU-CCUGGAAU--UGGAGAAUGUGCGAAAUGC-------------UCCG------------------GCGCCAUAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUCAUGAGAGUGA-GAGCCCGGAGACGGACUCUGAGACACGAGUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAGGGGGACACC-GA-GUCCGAGGGC---AU-A-GA---GCCCUCGCUUUUCUGAACCGU--AAGGAGGUUCAGG-AAC-AAGGGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCAGCCCAAGUGAUGGCCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCGUGCAA-GUUCGUCGGGAAAUCCACUCGCUUAACGA-GUGGGCGUCCGGCGAAAACUGC-UC--GGCUUGGG-ACCGGAAGAUCCA-AGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGAUGGCGAAAGCACCUUGGAAGGACGGAUCCGACAGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCCGUAAACGAUGCUCGCUAGGUGUGGCGCAGGC-UA-C-GAGCCUGCGUUGUGCCGUAGG-AAGCCGUGAAGCGAGCCGCCUGGGAAGUACGUCUGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCUCCGACAGC-AGUAAUGACGGUCAGGUUGAUGACCU-UACC-CGA---CGCUGCUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACCU-CUAGUUGCCAGC-AGCAUC--UUGC-GAUG-GCU--G-GGUACACUAGGGGGACUGCCGUCGC-UAAGACGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGAGCUGGGCU-ACACGCGGGCUACAAUGGCCAAGACAGUGGG-A-UGC-GACACCGAGA-GGU--GAAGCUAAUCUCCUAAA--CUUGGUCGUAGUUCGG-AUUGCGGACUGAAACCCGUCCGCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGAAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGGGGUCCGGAUGAGGCCUGG-----------------CUA-----------CCAGGUC-GAAUCUGGGU-CCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
CP000505.1/367745-366245             ACUCCGGUUGAUCCUGCCGGACCCGACCGCUAUCGGGGUGGGGCUAACCCAUGGAAGUC-UAGGA-------GCCG--GGGCU----AC--G-GCCGGC-------UCC--GGCGGACGGCUCAG-UAGCACGUGGCUAACCUACCCUCGGGAGGGGGAUAACCC--C-G-GGAAACUGGGGA-UAAACCCCCAUAGGCGCGGACA-CCUGGAAU---GGGUCCGCGCUGAAAGGGCCACGG--UACCA----UGCUUA------CCGUGGCCGCCCGAGGAUGGGGCUGCGCCCUAUCA-GGUAGUUGGCGGGGUAACGGCCCGCCAAGCCGAUAACGGGUGGGGGCCGUGAGAGCGG-GAGCCCCGAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACG-GGGUGCACCAGGGGCGAAACUUCCGCAAUGCGGGAAACCGUGACGGAGUCACCCC-GA-GUGCCACCC----GA-A-GA----GGGUGGCUUUUGCCCGGUCU--AAAAAGCCGGGCG-AAU-AAGCGGGGGGCAAGC-UUGGUGUCAGC-CGCCGCGGUAAUACCAACCCCGCGAGUGGUCGGGACGUUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCCGGUAA-GUCCCUCCUUAAAGCCCACGGCUCAACCG-UGGGA--GCGGAGGGAUACUGC-CG--GGCUAGGG-GGCGGGAGAGGCC-GGGGGUACUCCUGGGGUAGGGGCGAAAUCCUAUAAUCCCAGGAGGACCACCAGUGGCGAAGGCGCCCGGCUAGCACGCGCCCGACGGUGAGGGACGAAAGCUGGGGGAGCAAAGGGGAUUAGAUACCCCCGUAGUCCCAGCUGUAAACGAUGCGGGCUAGGUGUUGGACGGGC-UU-C-GAGCCCGUCCAGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAA-GCUUGCGGUUUAAUUGGAGUCAACGCCGGAAACCU-UACCGGGGGCGACAGC--AGGAUGAAGGCCAGGCUGACGACCU-UGCC-AGA----CGAGCUGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------GGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGGAACGAGCGAGACCCCC--GCCC-CUAGUUGCUACC-CAGCCC--UUCG-GGGC--UG--G-GGCACUCUAGGGGGACUGCCGGCGA-UAAGCCGGAGGAAGGUGGGGGCUACGGCAGGUCAG-UAUGCCCCGAAACCCCCGGGCU-ACACGCGAGCUGCAAUGGCGGGGACAGCGGG-U-UCC-GACCCCGAAA-GGG--GGAGGUAAUCCCUUAAA--CCCCGCCUCAGUAGGA-AUCGAGGGCUGCAACUCGCCCUCGUGAACGUGGAAUCCCUAGUAACCGCGUGUCACCAACGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUCCACCCGAGGGAGGCCUAGGUGAGGCCUCCUGCC-----------GACGA-------GGUGGGAGGUC-GAACCUGGGCCUCCCAA----GGGGGGAGAAGUCGUAACAA------G--GUGGCCGUAGGGG----------AACCUGCGGCC-GGAUCACCUCCU
AP011532.1/106584-108054             UUUCUGGUUGAUCCUGCCAGAGGUCACUGCUAUCGGUGUCCGAUUAAGCCAUGCGAGUC-GUGAG--------GGG---UU--------AU----GCC--------CUC--GGCGGACUGCUCAG-UAACACGUGGAUAACCUGCCCAAGGGUCUGGGAUAACCC--C-G-GGAAACUGGGGA-UAAUACCGGAUGGAUCACUAGU-GCUGGAAU---GCUUGGUGGUCGAAAGGC----------------A------------------ACGCCUUUGGAUGGGUCUGCGGCGGAUUA-GGUUGACGCCGGUGUAACGUACCGGCGUGCCUGUAAUCCGUACGGGUUGUGGGAGCAA-GAGCCCGGAGAUGGAUUCUGAGACACGAAUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUCUACAAUGCAGGCAACUGCGAUAGGGGGACAUC-GA-GUGGCAUCCA----C-C-U----UGGGUGCCUGUCCAACCGUCU--AAAAAACGGUUGU-UAGCAAGGGCCGGGUAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCGGCUCGAGUGGUGGCCGAUAUUAUUGAGUCUAAAGGGUCCGUAGCCGGCUUUGCAA-GUCCCCUGGGAAAUCCAGCGGCUUAACCG-UUGGGCUUUCAUGGGAUACUAC-AU--UGCUUGGG-ACUGGGAGAGGUA-GGAGGUACUCGGGGGGUAGGGGUGAAAUCCUGUAAUCCUCCGGGGACCACCGGUGGCGAAGGCGUCCUACCAGAACAGGUCCGACGGUGAGGGACGAAAGCUAGGGGCACGAACCGGAUUAGAUACCCGGGUAGUCCUAGCCGUAAACGAUGCCCGCUAGGUGUCACGACGGU-CG-U-GAAUCGUCGUGGUGCCGUAGGGAAGCCGCGAAGCGGGCCACUUGGGAAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGGGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGGAAGCU-UACCGGGAUCGACAGU--UGUAUGAAGGCCAGGCUGAAGACCU-UGCC-GGA----CUAGCUGAGAGGAGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCAU--UUCC-ACUGUUGCUAAC-GACUCC--GCGA-GGAG-GGC--G-AGUACACUGUGGAGACCGCUGGCGC-UAAGUCAGAGGAAGGAUUGGUCGACGGUAGGUCAG-UAUGCCCCGAAUAUCCCGGGCU-ACACGCGGGCUACAAUGGAUAGGACAAUGGG-U-AAC-UACACCGAAA-GGU--GGCGUCAAUCUCUUAAA--CCUAUCCUUAGUUCGG-AUUGAGGGCUGGAACUCGCCCUCAUGAAGAUGGAAUCCGUAGUAAUCGCAUUUCAAAACAGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAACCACCCGAGCGGGGCGUGAAUGAGGAUCCUUUU-------------CAU---------UGAAGGACUC-GAAUUCAUGUUCUGUAA----GGGGGGUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
EU686616.2/36651-38121               AAUCCGGUUGAUCCUGCCGGAGGCUACCGCUAUUGGAGUUCGAUUAAGCCAUGCGAGUC-GAGAG-------UCUU--------------A----GGGA-------CUC--GGCGCACCGCUCAG-UAACACGUGGGUAACCUGCCCUAUGCUGGGGGAUAACCU--C-G-GGAAACUGAGAA-UAAUACCCCAUAGUUCACCACG-CCUGGAAC---GGUGGGUGGAUCAAA-GC-------------UCCG------------------GCGGCAUAGGAUGGGCCUGCGACGUAUCA-GGUUGUAGGGGGUGUAACGUACCCUCUAGCCAUCAACGCGUACGGGUGUUGGGAGACA-UAGCCCGGAGAUGGAUUCUGAGACACGAAUCCAGACCCUACG-GGGUGCAGCAGGCGCGAAAACUUGGCAAUGCGAGCAAUCGUGACCAGGGAACUCC-AA-GUGGCUGGGG---UA-A-U----ACCCAGUUUUUUCUUGACUCU--UCAAAGGUCUUGG-AAU-AAGGGGUGGGUAAGG-ACGGUGCCAGC-CGCCGCGGUAAUACCGGCGCCUCAAGUGGUAGUCGCUUUUAUUGGGCCUAAAACGUCCGUAGCCGGUCUGGUGC-AUUCGUGGGUAAAUCAACCCGCUCAACGG-GUUGAA-UUCUGCGAGCACGGC-CA--GACUUGGG-ACCGGGAGAGGUG-UGGGGUACUCUCAGGGUAGGGGUAAAAUCCUGUCAUCCUGAGAGGACCACCUGUUGCGAAGGCGCCACACUAGAACGGAUCCGACGGUCAGGGACGAAACCUAGGGGCACGAACCGGAUUAGAUACCCGGGUAGUCCUAGGUGUAAACGCUGUGGACUUGAUGUUGGGGGCGC-UC-C-GAGCGCUCUCAGUGUCGAAGCGAAGGUGAUAAGUCCACUGCCUGGGGAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUGCAACCUGAGGA-UUGUGCGGUUUAAUUGGAUUCAACGCCGGAAAACU-CACCAUAGCCGACGGA--CAAAUGAAGGCCAGCGUAACGAGCU-UGCU-GGA----UUGUUCGAGAGGUAUUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACCGCAAGGCGUUCUGUUAAGUCAGAUAACGAACGAGACCCUC--AUCC-CUAUUUGCCAAC-CAGAUC--CCCG-GAUC--UG--A-CGCACUAUAGGGAGACCGCUGGCGC-UAAGUCAGAGGAAGGCGAGGGCAACGGUAGGUCAG-UAUGAUCCGAAUGCUAUGGGCU-ACACGCGCAAUACAAAGGACGGGACAAUGGG-C-UGC-AACUCCGAGA-GGAACGACGCUA-UCCC-GAAA--CCCGUUCGUAGUUCGG-AUUGAGGGCUGUAACUCGCCCUCAUGAAGCUGGAUUAGGUAGUAAUCGCGUCUCAAUAGGGCGCGGUGAAUAUGCCCCUGCUCCUUGCACACACCGCCCGUC-AAACCAUCUUAGUUGGGGGUGGGUGAGGCUACCUUA-------------ACCA--------UGGGGUAUUC-GAGCCUGCCUUUGACAA----GGAGGGUUAAGUCGUAACAA------G--GUAUCUGUAGGGG----------AACCUGCAGAU-GGAUCACCUCCU
CP000867.1/859135-860601             AUUCCGGUUGAUCCCGCCGGAGGCCACUGCUAUUGGGAUUCGACUAAGCCAUGCGAGUC-U-AU---------GGU---UU--------CG----GCC---------AU--GGCGGACGGCUCAU-UAACACGUGGUUAACAUACCCUCAGGUGGGGGAUAACCU--U-G-GGAAACUGAGGA-UAAUACCCCAUAGAAAAAGCAG-UCUGGAAU---GAUUCUUUUUCGAAA-GC-------------ACAU------------------GCGCCUGAGGAUUGGACUGCGCUCGAUUA-GGUAGUUGGUGGGGUAAUGGCCCACCAAGCCUACGAUCGGUACGGGCCUUGAGAGAGG-GAGCCCGGAGAUGGGGACUGAGACACGGCCCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUCCGCAAUGCACGAAAGUGCGACGGGGGGAUCCC-AA-GUGCUCAUGC------A-CA---GCAUGGGCUUUUAUCAAGUGU--AAACAGCUUGAGG-AAU-AAGGGCUGGGCAAGU-UCGGUGCCAGC-AGCCGCGGUAACACCGACGGCCCGAGUGGUGGCCACUCUUAUUGGGCCUAAAGCGUCCGUAGCCGGUCCAGUAA-GUCCCUGUUUAAAUCCUGCGGCUUAACCG-CAGGAC-UGGCAGGGAUACUGC-UG--GACUUGGG-ACCGGGAGAGGAC-AAGGGUACUUCAGGGGUAGCGGUGAAAUGUGUUGAUCCUUGAAGGACCACCUAUGGCGAAGGCACUUGUCUGGAACGGGUCCGACGGUGAGGGACGAAAGCCAGGGGCGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACUCUGCGAACUAGGUGUUAGGUGGGC-CC-C-GUGCCCAUCUAGUGCCGAAGGGAAGCCGUUAAGUUCGCCGCCUGGGGAGUACGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGGGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGGCAUCU-CACCAGGAGCGACAGC--AUGAUGACGGCCAGGUUGACGACCU-UGCC-UGA----AGCGCUGAGAGGUGGUGCAUGGCCAUCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGCGAGGCGUCCUGUUAAGUCAGGUAACGAGCGAGACCCGU--GCCC-UAUGUUGCUACU-UUUUCC--UCCG-GGAG--AA--A-GGCACUCAUAGGGGACCGCUGGCGC-UAAGUCAGAGGAAGGAGCGGGCAACGAUAGGUCCG-CAUGCCCCGAAUCUCCUGGGCU-ACACGCGGGCUACAAUGGCUAGGACAAUGGG-C-CGC-AACCCUGAAA-AGG--GACGCAAAUCUCCUAAA--CCUAGUCGUAGUUCGG-AUCGUGGGCUGUAACUCGCCCACGUGAAGCUGGAAUCCGUAGUAAUCGCAGUUCAUAAUACUGCGGUGAAUGUGUCCCUGCUCCUUGCACACACCGCCCGUC-ACACCACCCGAGUUGGGUUGAAGUGAGGCCUUGGCC-------------UUU---------GGCUAGGGUC-GAACUUGGGCUCAGCGA----GGGGGGUGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCU
AB201309.1/18052-19543               ACUCCGGUUGAUCCUGCCGGACCUCACUGCUAUCGGGGGGAGACUAAGCCAUGCAAGUC-U-AGG-------CCCA---UAGCC--ACCUG----UGGG-------CCU--GGCGUACGGCUCAG-UAACACGUGGCCAACCUACCCUGAGGAGGCGGAUAACAC--C-G-GGAAACUGGUGCAUAAACCGCCAUAGGUGAGAGGA-UCUGGAAC---GACCUCUCGCCGAAAGAUGU---------AC---ACGGGGAUG-CCUGUGUACAUGCCUCAGGAUGGGGCUGCGGCCCAUCA-GGUAGUUGGUGGGGUAACGGCCCACCAAGCCUAUAACGGGUACGGGCCCUGAGAGGGG-GAGCCCGGAGAUGGACUCUGAGACAAGAGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGCUCACGCGUGACGGGGUCACCCC-GA-GUGCCACC-----CU-C-GU-----GGUGGCUUUUGCGCAGUGU--AAAAAGCUGCGCG-AAU-AAGCGGGGGGCAAGA-CGGGUGUCAGC-CGCCGCGGUAAUACCCGCUCCGCGAGUGGUGAGGACUAUUACUGGGCUUAAAGCGUCCGUAGCCGGCUCGGCGU-GCUCCGCGUUAAAUCCAGCAGCCUAACUG-CUGGGC-CGCGCGGAUGACUGC-CG--GGCUUGGG-GGUGGGAGAGGGC-AGCGGUAUUCCCGGGGUAGGGGUAAAAUCCACUGAUCCCGGGAGGACCACCAGUGGCGAAGGCGGCUGCCCAGAACACGCCCGACGGUGAGGGACGAAAGCUGGGGGAGCGAUCGGGAUUAGAUACCCCGGUAGUCCCAGCCGUAAACGAUGCGGGCUUGGCGUCGGAGCGGC-UA-C-GAGCCGUUCCGGUGCAGAAGGGAAACCAUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGA-CGUUGCGGCUUAAUUGGAGUCAACGCCGGAAACCU-UACCGGGGGCGACAGC--AGGAUGAUGGCCAGGUUAAAGGCCU-UGCC-GGA----CGAGCUGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGUGCGUGCCGUGAGGUGUCCUGUUAAUUCAGGCAACGGACGAGACCCGC--GCCU-CCAGUUGCGACC-GG-GCC--GAAA-GGCG--CC--G-AGCACUCUGGAGGGACUGCCCCGG--AAACGGGGAGGAAGGAGCGGGCUACGGCAGGUCAG-UAUGCCCCGAAUCCCCCGGGCC-GCACGCGACGUUCAAUGGUGGGGACAGUGGG-C-UGC-GACCCCGAAA-GGG--GAAGCCAAUCCCU-AAA--CCCCACCUCAGUAGGG-AUCGAGGGUUGCAACUCGCCCUCGUGAACGCGGAAUCCCUAGUAACCGCCCGUUACCACCGGGCGGUGAAUACGUCCCCGCUCCUUGCACACACUGCCCGUC-GCUGCACCCGAGCUGGAACUGGGCGAGGGCCCGUCU-------------CGU---------UGGCGGGUUC-GAGCCCGGUUCUGGUGA----GGGGGCAGAAGUCGUAACAA------G--GUGGCCGCACGGG----------AACGUGUGGCC-GGAUCACCUCCU
CP000077.1/1108628-1107135           AUUCCGGUUGAUCCUGCCGGACCCGACCGCUAUCGGGGUAGGGAUAAGCCAUGGGAGUC-UUACA-------CUCC---CGGG----UAAG----GGAG-------UGU--GGCGGACGGCUGAG-UAACACGUGGCUAACCUACCCUCGGGACGGGGAUAACCC--C-G-GGAAACUGGGGA-UAAUCCCCGAUAGGGAAGGAGU-CCUGGAAU---GGUUCCUUCCCUAAAGGGCUAUA----GGCU----AUUUCCC---GUUUGUAGCCGCCCGAGGAUGGGGCUACGGCCCAUCA-GGCUGUCGGUGGGGUAAAGGCCCACCGAACCUAUAACGGGUAGGGGCCGUGGAAGCGG-GAGCCUCCAGUUGGGCACUGAGACAAGGGCCCAGGCCCUACG-GGGCGCACCAGGCGCGAAACGUCCCCAAUGCGCGAAAGCGUGAGGGCGCUACCCC-GA-GUGCCUCC------G-C-AA-----GGAGGCUUUUCCCCGCUCU--AAAAAGGCGGGGG-AAU-AAGCGGGGGGCAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCUCCGCGAGUGGUCGGGGUGAUUACUGGGCCUAAAGCGCCUGUAGCCGGCCCACCAA-GUCGCCCCUUAAAGUCCCCGGCUCAACCG-GGGAAC-UGGGGGCGAUACUGG-UG--GGCUAGGG-GGCGGGAGAGGCG-GGGGGUACUCCCGGAGUAGGGGCGAAAUCCUUAGAUACCGGGAGGACCACCAGUGGCGGAAGCGCCCCGCUAGAACGCGCCCGACGGUGAGAGGCGAAAGCCGGGGCAGCAAACGGGAUUAGAUACCCCGGUAGUCCCGGCUGUAAACGAUGCGGGCUAGGUGUCGAGUAGGC-UU-A-GAGCCUACUCGGUGCCGCAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGA-ACCUGCGGCUCAAUUGGAGUCAACGCCUGGAAUCU-UACCGGGGGAGACCGC--AGUAUGACGGCCAGGCUAACGACCU-UGCC-UGA----CUCGCGGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGUUGUGAAAUGUCCGGUUAAGUCCGGCAACGAGCGAGACCCCC--ACCC-CUAGUUGGUAUU-CUGGAC--UCCG-GUCC--AG--A-ACCACACUAGGGGGACUGCCGGCG--UAAGCCGGAGGAAGGAGGGGGCCACGGCAGGUCAG-CAUGCCCCGAAACUCCCGGGCC-GCACGCGGGUUACAAUGGCAGGGACAACGGG-A-UGC-UACCUCGAAA-GGG--GGAGCCAAUCCU-UAAA--CCCUGCCGCAGUUGGG-AUCGAGGGCUGAAACCCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCGGGUCAACAACCCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUCCACCCGAGCGAGAAAGGGGUGAGGUCCCUUGC------------GAUAA--------GUGGGGGAUC-GAACUCCUUUCCCGCGA----GGGGGGAGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCAU
CP001941.1/1422346-1423823           ACUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUCGGGCUCCGACUAAGCCAUGCGAGUU-UAGGG------GCUCC---UU--------CG----GGGG------CACC--GGCGGACGGCUCAG-UAACACGUGGACAACCUACCCUCGGGUGGGGGAUAACCU--C-G-GGAAACUGAGGC-UAAUACCCCAUAGGGGAAAGGU-ACUGGAAG---GUCCUUUCCCUGAAA-GC-------------UCCG------------------GCGCCCGAGGAUGGGUCUGCGGCCUAUCA-GGUAGUUGGUGGUGUAAAGGACCACCAAGCCUGCGACGGGUACGGGCCCUGAGAGGGG-UAGCCCGGAGAUGGACUCUGAGACACGAGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUCGCAAUGCGCGAAAGCGCGACGAGGGGAGCCC-GA-GUGCCCUUCC---UU-U-U----GGGAGGGCUUUUCCGGAGUCU--AAAAAGCUCCGGG-AAU-AAGGGCUGGGCAAGA-CGGGUGCCAGC-CGCCGCGGUAAUACCCGCAGCUCGAGUGGUGGCCACUAUUAUUGAGCCUAAAGCGUCCGUAGCCGGACCCGCAA-AUCCCUGGGUAAAUCCUGGUGCUCAACAU-CAGGAA-UUCCGGGGAGACUGC-GG--GUCUUGGG-ACCGGGAGAGGCC-GGAGGUACUCCCGGGGUAGGGGUAAAAUCCUGUAAUCCCGGGGGGACCACCUGUGGCGAAAGCGUCCGGCUUGAACGGCUCCGACGGUGAGGGACGAAGGCCAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACGCUGCCCGCUUGGUGUUGUCGGUCU-CU-C-GGGGGCCGGCAGUGCCGGAGCGAAGGUGUUAAGCGGGCCGCUUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGAGAGCACUGCAACGGGAGGA-GCGUGCGGUUUAAUUGGAUUCAACGCCGGAAAACU-CACCGGGGGCGACCGG--CACAUGUGGGCCAGGCUGACGACCU-UGCC-CGAAUAAGAGCCGGAGAGGUGGUGCAUGGCCAUCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUAGGGCGUUCACUUAAGUGUGAUAACGAGCGAGACCCCC--GUCC-CCAGUUGCCACC-UGUCCC--UCCG-GGGG--CA--G-AGCACACUGGGGAGACCGCCAGCGC-UAAGCUGGAGGAAGGUGGGGUCAACGGUAGGUCAG-UACGCCCCGAAUCCCCCGGGCU-ACACGCGCGCUACAAAGGGCGGGACAAUGGG-U-UGC-GACCCCGAAA-GGG--GGAGCUAAUCCU-GAAA--CCCGUCCGUAGUUCAG-AUCGAGGGCUGUAACUCGCCCUCGUGAAGCUGGAUUCCGUAGUAAUCGCGGGUCAACAUCCCGCGGUGAAUGCGCCCCUGCUCUUUGCACACACCGCCCGUC-AAACCAUCCGAGUUGGCUCUAGGUGAGGCCCUGUUC-------------UAU---------GGGCAGGGUC-GAACCUGGGGUCAGCGA----GGAGGGUUAAGUCGUAACAA------G--GUAUCCGUAGGGG----------AACCUGCGGAU-GGAUCACCUCCU
AL445067.1/179220-177749             ACUCCGGUCGAUCCUGCCGGCGGUCACUGCUAUCAGGUUCCGACUAAGCCAUGCAAGUC-AUGGG--------GCC---GU--------AA----GGC--------ACC--GGCGAACAGCUCAG-UAACACGUGGAUAAUUUACCCUCAGGCGGGGCAUAACCU--C-G-GGAAACUGAGGC-UAAUUCCCCAUAGUCAUUACAA-ACUGGAAU--GGUUGUAAUGAUGAAA-GC-------------UUCU------------------GCACCUGAGGAUAAGUCUGCGGCCUAUCA-GGUAGUAGGUGGUGUAAAGGACCACCUAGCCUAAGACGGGUACGGGCCCUGAAAGGGG-GAGCCCGGAGAUGGACUCUGAGACAACAGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUGUGCAAUGCGCGAAAGCGCGACACGGGGAGCCU-GA-GUGCCUUGAC---UU-U-UU---GUCAAGGCUUUUCUGAUGCCU--AAAAAGCAUCAGG-AAU-AAGGGCUGGGCAAGA-CGGGUGCCAGC-CGCCGCGGUAACACCCGCAGCUCGAGUGGUGAUCACUUUUAUUGAGUCUAAAGCGUUCGUAACCGGUCUUAUAA-AUCUUCAGAUAAAUUCUUCCGCUUAACGG-AAGAAC-UUCUGAAGAGACUGU-AA--GACUUGGG-ACCGGGUGAGGUU-GAAUGUACUUUCAGGGUAGGGGUAAAAUCCUGUAAUCCUGAAAGGACGACCGGUGGCGAAAGCGUUCAACUAGAACGGAUCCGACGGUGAGGGACGAAGGCUAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGCUGCCCACUUGGUGUUGCUUCUCC-GU-U-GAGGGGGGGCAGUGCCGUAGCGAAGGUGUUAAGUGGGUCACUUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCGCAACGGGAGGA-GCGUGCGGUUUAAUUGGAUUCAACGCCGGAAAACU-CACCGGGAGCGACCUU--CGGAUGAGGGUCAACCUGACGAAUU-UACC-CGA----UAGAAGGAGAGGUGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUAGGGCGUUCACUUAAGUGUGAUAACGAGCAAGACCCCC--AUCU-CUAAUUGCCAGA-CUGUCU--UUGC-GGGC--AG--A-GGCACUUUAGAGGGACCGCCAGCGC-UAAGCUGGAGGAAGGAGGGGUCGACGGCAGGUCAG-UACGCCCCGAAUCUCCCGGGCU-ACACGCGCGCUACAAAGGACGGGACAAUGAG-U-UGC-AACCUCGAAA-GGG--GAAGCUAACCUCG-AAA--CCCGUUCGUAGUCAGG-ACUGAGGGCUGUAACUCGCCCUCACGAAUGUGGAUUCCGUAGUAAUCGUAGGUCAACAGCCUACGGUGAAUAUGCCCCUGCUCCUUGCACACACCGCCCGUC-AAACCAUCCGAGCUGGUGUUGGAUGAGGGUCCGUCC-------------UCU---------GGAUGGAUUC-GAAUCUGAUGUCAGUGA----GGAGGGUUAAGUCGUAACAA------G--GUAUCCGUAGGGG----------AACCUGCGGAU-GGAUCACCUCCA
DQ156348.1/18595-20063               AAUCCGGUUGAUCCUGCCGGAGGCGACCGCUAUUGGAAUUCGAUUAAGCCAUGCGAGUC-GAGAG-------UCUU--------------A----GGGA-------CUC--GGCGUACCGCUCAG-UAACACGUGGGUAACCUGCCCUGUGCUGGGGAAUAACCU--C-G-GGAAACUGAGAA-UAAUGCCCCAUAGUUCACUACG-CCUGGAAC---GGUGGGUGGAUCAAA-GC-------------UCCG------------------GCGGCACAGGAUGGGCCUGCGGCGUAUCA-GGUUGUAGGGGGUGUAACGUACCCUCUAGCCUUCAACGCGUACGGGUUGUGGGAGCAA-UCGCCCGGAGAUGGAUUCUGAGACACGAAUCCAGACCCUACG-GGGUGCAGCAGGCGCGAAAACUUCACACUGCAGGAAACUGUGAUGAGGGAAUUCC-AA-GUGGCUAGAC------A-AA---GUCUAGUCUUUUUGUAACUUU--UAAUCGGUUACAG-AAU-AAGGGGUGGGAAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCACCUCAAGUGGUCGUCGCUUUUAUUGGGCCUAAAACGUCCGUCGCCUGUUUGGUAC-AUUCGUGGGUAAAUCAACCAGCUUAACUG-GUUGAA-UUCUGCGAGGACGGC-CA--GACUAGGG-ACCGGGAGAGGUA-UGGGGUACUCUCAGGGUAGGGGUAAAAUCCUGUCAUCCUGAGGGGACCACCUGUUGCGAAGGCGCCAUACUAGAACGGAUCCGACGGUCAGGGACGAAGCCUAGGGGCACGAACCGGAUUAGAUACCCGGGUAGUCCUAGGUGUAAACGCUGUGGACUUGGUGUUGGGGAUUC-UA-C-GAGUAUCCCCAGUGCCGGAGUGAAGAUGUUAAGUCCACUGCCUGGGGAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACAGCAACGAGAGGA-GCGUGCGGUUUAAUUGGAUUCAACGCCGGAAAACU-CACCAGUGCCGACGGA--CAUAUGAAGAUCAGCGUGAUGAGCU-UAUU-GGA----UUGUUCGAGAGGUAGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACCGUAAGGCGUUCUGUUAAGUCAGAUAACGAACGAGACCCCU--AUCGUCUAUUUGCUAAA-CGGAUC--UCCG-GAUU--CG--U-CGCACUAUAGCGAGACCGCUGGCGU-GAAGUCAGAGGAAGGUGGGGGCAACGACAGGUCAG-UAUGCUCCGAAUGCACUGGGCU-ACACGCGCGCUACAAAGGCCAGGACAAUGGG-UCUGC-CACGCCGAGA-GGC--GGCGCUA-UCCC-GAAA--CCUGGUCGUAGUUCGG-AUCGAGGGCUGUAAUUCGCCCUCGUGAAGCUGGAUUUCGUAGUAAUCGCGUCUCAAAAUGGCGCGGUGAAUAUGCCCCUGCUCCUUGCACACACCGCCCGUC-AAACCAUCUUAGUUGGGGGUGGGUGAGGCUACCUUU-------------UUU---------UGGGGUAUUC-GAGCCUGCCUUCGACAA----GGAGGGUUAAGUCGUAACAA------G--GUAUCUGUAGGGG----------AACCUGCAGAU-GGAUCACCUCCU
AF028689.1/1-1477                    CUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUUGGGUUUCGAUUAAGCCAUGCAAGUU-GAACG-------AUCC---CU-------UGC----GGGU-------CGU--GGCAUACGGCUCAG-UAACACGUGGAUAACCUAACCUUAGGACUGGGAUAACCC--C-G-GGAAACUGGGGA-UAAUACCGGAUAUGUAGGGUUG-CCUGGAAU---GGUACCCUAUUGAAAUGU-------------UCCG------------------ACGCCUAAGGAUGGAUCUGCGGCAGAUUA-GGUAGUUGGCGGGGUAAAUGCCCACCAAGCCAGUAAUCUGUACGGGUUGUGAGAGCAA-GAGCCCGGAGAUGGAACCUGAGACAAGGUUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUCCGCAAUGCACGAAAGUGCGACGGGGGAAACCC-AA-GUGCCACUCU---UA-A-C----GGGGUGGCUUUUCUUAAGUGU--AAAAAGCUUUUGG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCAGCUCAAGUGGUGGCCAUUUUUAUUGGGCCUAAAGCGUUCGUAGCCGGCUUGAUAA-GUCUCUGGUGAAAUCCCACAGCUUAACUG-UGGGAAUUGCUGGAGAUACUAU-UA--GGCUUGAG-GCCGGGAGAGGCU-GGAGGUACUCCCAGGGUAGGGGUGAAAUCCUAUAAUCCUGGGAGGACCACCUGUGGCGAAGGCGUCCAGCUGGAACGGACCUGACGGUGAGUAACGAAAGCCAGGGGCGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACGAUGUGGACUUGGUGUUGGGAUGGC-UC-C-GAGCUGCCCCAGUGCCGAAGGGAAGCUGUUAAGUCCACCGCCUGGGAAGUACGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGCGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGACAUCU-CACCAGGGGCGACAGC--AGAAUGAUAGCCAGGUUGAUGACCU-UGCU-UGA----CAAGCUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCAC--GCCC-UUAGUUACCAGC-GGAUCC--UUCG-GGAU-GCC--G-GGCACACUAAGGGGACCGCCAGUGA-UAAACUGGAGGAAGGAGUGGACGACGGUAGGUCCG-UAUGCCCCGAAUCCCCUGGGCU-ACACGCGGGCUACAAUGGCUAGGACAAUGGG-U-UCC-GACACUGAAA-AGU--GAAGGUAAUCUCCUAAA--CAUAGCCUUAGUUCGG-AUUGAGGGCUGUAACUCGCCCUCAUGAAGCUGGAAUNCGUAGUAAUCGCGUGUCAUAACCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-ACGCCACCCAAAAAGGGUUUGGAUGAGGCCCUAGUC-------------UUA---------GGUUAGGGUC-GAAUCUGGGUUCUUUGA----GGAGGGCGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCU
HM159597.2/1-1470                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGGGUCCGAUUUAGCCAUGCUAGUU-GUACG--------AGC---UU--------AC----ACU--------CGU--AGCAAAUAGCUCCG-UAACACGUGGCCAAACCACCCUACAGAGAACAAUAACCU--C-G-GGAAACUGAGGC-UAAUAGUUCAUACCCGUCUUAC-GCUGGAAU---GCCAAGACGCGCAAACGU-------------UCCG------------------ACGCUGUAGGACGUGGCUGCGGCCGAUUA-GGUUGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAA-GAACCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCAAGUGCGAUAAGGGGACCCC-GA-GUGCGAGGGC---AU-A-CA---GUCCUCGCUUUUCAGCACCGU--AGGGAGGUGCUGG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCGAGUGAUGGCCGAUCUUAUUGGGCCUAAAGCGUUCGUAGCCGGCCACGCAA-GUUCAUCGGGAAAUCCGCCAGCCUAACUG-GCGGGCGUCCGGUGAAAACUGC-GU--GGCUUGGG-ACCGGAAGACCCG-AAGGGUACGUCUUGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCGCCGAUGGCGAAAGCACUUCGGGAAGACGGAUCCGACGGUGAGGAACGAAAGCCAGGGUCUUGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACGAUGUCUGCUAGGUGCGACCCCCAC-UA-C-GAGUGGGUGUUGUGCCGUAGGGAAGCCGCUAAGCAGACCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCAUCGACAGC-AACAAUGACGAUCAGGUUGAUGACCU-UAUC-AGA----GCUGCUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACUC-CUAAUUGCCAGC-ACCGGG--UUCG-CCCG-GGU--G-GGUACAUUAGGAGGACUGCCGUGGC-UAACACGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGUGCUGGGCU-ACACGCGGGCUACAAUGGCCAAGACAAUGGG-U-UCC-AACCGCGAAA-GCG--GACGGUAAUCUCCUAAA--CUUGGUCGUAGUUCGG-AUUGAGGGCUGAAACCCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGCAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGGGGUCCGGAUGAGGCCGAG-----------------UUC-----------CUCGGUC-GAAUCUGGGCUCCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
AJ133792.1/2-1467                    UUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUCGGGGUUUGACUAAGCCAUGCGAGUC-GAGAG-------GUUU---C---------------GGAC-------CUC--GGCGUACUGCUCAG-UAACACGUGGACAAUCUGCCCUGGAGUGGAGGAUAAUCC--C-G-GGAAACUGGGGG-UAAUACUCCAUAGUUCGUAGAG-GCUGGAAU---GCCUAUCGAAUGAAA-GA-------------UCCG------------------UCGCUCCAGGAUGAGUCUGCGGCCGAUUA-GGUAGUUGUUGGGGUAAAGGCCCAACAAGCCUGUCAUCGGUACGGGUUGUGGGAGCAA-GAGCCCGGAGAUGGAUUCUGAGACACGAAUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUUUACCAUGCGGGCAACCGUGAUAAGGAAACCCC-GA-GUGCCAGC------A-C-AG-----GCUGGCUGUCCAUCAGUGU--AAAUAACUGGUGA-AGA-AAGGGCCGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCGGCUCGAGUGGUGGCCGCUAUUACUGGGCUUAAAGGGUCCGUAGCUUGAUAAUUGG-GUCCCUUGAGAAAUCCGCCAGCUUAACUG-GCGGGCGUUCAGGGGAAACUGG-UU--UUCUAGGG-ACCGGGAGAGGUG-AGAGGUACUGCCGGGGUAGGAGUGAAAUCCUGUAAUCCCGGUGGGACCACCUAUGGCGAAGGCAUCUCACCAGAACGGGUCCGACAGUGAGGGACGAAAGCUGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCGCGUUAGGUGUGUCAGUGAC-CA-C-GUGUCACUGAGGUGCCGAAGGGAAACCGUGAAACGCGCCGCCUGGGGAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGGGUGGA-GCCUGCGGUUUAAUCGGACUCAACGCCGGAAAUCU-CACCGGAUAAGACAGC--UGAAUGAUAGUCGGGAUGAAGACUC-UACU-UGA----CUAGCUGAGAGGAGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACUGUGAAGCAUCCUGUUUAGUCAGGCAACGAGCGAGACCCAC--GCGA-CCAGUUGCCAGC-UUGACC--UUCG-GGUU-GAU--G-GGGACACUGCUCGGACCGCCUCUGC-UAAAGGGGAGGAAGGAAUGGGCAACGGUAGGUCAG-CAUGCCCCGAAUUAUCCGGGCU-ACACGCGGGCUACAAUGGAUAGGACAAUGGG-U-UUC-GACACCGAGA-GGU--GAGGAUAAUCUCCUAAA--CCUAUCCGAAGUUCGG-AUUGCGGGUUGUAACUCACCCGCAUGAAGCUGGAAUCCGUAGUAAUCGCGUUUCAACAUAGCGCGGUGAAUAUGUCCCUGCUCCUUGCACACSCCGCCCGUC-AASCCACCCGAGUGAGGUCUUGAUGAGGUUGUGUCG-------------U-----------UGACAUGAUC-GAAUCUGGGUUUUGCAA----GGGGGGUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
ACXM01000006.1/275750-274277         ACUCCGGUUGAUCCUGCCGGCGGUCACUGCUAUCGAGUUCCGACUAAGCCAUGCGAGUC-ACAGG---------CC---GU--------AA----GGU--------ACU--GGCAGACGGCUCAG-UAACACGCGGAUAAUCCACCCUUAGGUGGGGCAUAUCCU--U-G-GGAAACUGAGGU-UAAUUCCCCAUAGAUCCCGAAA-ACUGGAAU---GUUACGGGUUCUGAAAGU-------------UACG------------------ACGCCUAAGGACGAGUCUGCGGCCUAUCA-GGUUGUAGGUGGGGUAAAGGCCCACAUAGCCUAUGACGGGUACGGGCCCUGAGAGGGG-UAGCCCGGAGAUGGGUUCUGAGACACGAACCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUCGCAAUGCGCGCAAGCGCGACGAGGGGAACUC-GA-GUGCCAUUGUC-A-U-U-UUU-GAUGAUGGCUUUUCUUGAUCCU--AAAAAGAUCAGGG-AAU-AAAAGCUGGGUAAGA-CGGGUGCCAGC-CGCCGCGGUAAUACCCGCAGCUCAAGUGGUGGCCACUAUUAUUGAGCCUAAAGCGUCCGUAGCCGGUCUUGUAA-AUCUCUGGGUAAAUCCUGCCGCUUAACGG-UGGGAA-UGCUGGAGAGACUGC-AA--GACUGGGG-AUCGGGUGAAGCG-AGAGGUACUCCUGGGGUAGGGGUAAAAUCCUGUAAUCCUGGGGGGACGACCGGUGGCGAAAGCGUCUCGCUAGAACGACUCCGACGGUGAGGGACGAAGGCUAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGCUGCACACUUGGUGUUGCCCCUUC-UU-C-GGGAAAGGGCAGUGCCGGAGCGAAGGUGUUAAGUGUGCCGCUUGGGGAGUAUGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGAGAGCACCGCAACGGGAGGA-GCGUGCGGUUUAAUUGGAUUCAACGCCGGAAAACU-CACUAGGGAAGACCAU--GGUAUGAGGGUCAACUUGAAGAAUU-UACU-CGA---UUACAUGGAGAAGUGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUAAAGCGUUCACUUAAGUGUGAUAACGAGCGAGACCCCC--AUCC-ACUUUUGCCAGU-ACUGUC--GCGA-GACA--GC--A-CGCACUAUGUGGAGACUGCCAGUGU-UAAACUGGAGGAAGGAGAGGUCAACGGCAGGUCAG-UAUGCCCCGAAUUCCCUGGGCU-ACACGCGCGCUACAAAGGACGGAACAAUGGG-C-UGC-AAUUCCGAAA-GGA--AGAGCCAAUCCCG-AAA--UCCGUUCGUAGUUCAG-ACUGAGGACUGUAAUUCGUCCUCACGAAGCUGGAUUCCGUAGUAAUCGCGAUUCAACAAAUCGCGGUGAAUAUGCCCCUGCUCUUUGCACACACCGCCUGUC-AAGCCAUCCGAGUUGGUUCUGGAUGAGGGAACAUUU--------------UUU---------GAUGUUUUC-GAAUCCAAGAUUGAUGA----GGAGGGCUAAGUCAUAACAA------G--GUAUCCGUAGGGG----------AACCUGCGGAU-GGAUCACCUCCU
CP000968.1/1326563-1328058           AGACCGGUUGAUCCUGCCGGAGGGAACCCCUAUCGGGCUCGCACUAAGCCAUGCGAGUCUGCUGG-------GGGC---CC--------CU----GCCC-------CUGGCGGCGCACGGCUCCG-UAAUACACGGUCAACCUGUCCUGGGGACCGGGAUAACCU--C-G-GGAAACUGAGGU-UAAUACCGGAUAGGGGUGGAUU-CCUGGAAU---GGGUCCACCCCUAAAGUAGGCGGGGGGACGG----CCCC----------GCUGAGGCCCCAGGGUGGGACCGUGGCCUAUCA-GGUAGUAGGUGGGGUAACGGCCCACCUAGCCUAAGACGGGUACGGGCUCUGAGAGGAG-GAGCCCGGAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACG-GGGCGCAGCAGGCGGGAAACUUCCCCAAUGCGCGCAAGCGUGAGGGAGUGAGCCC-GA-GUGCCGCCC----GC-U-GA----GGGCGGCUGUUCCCCUGUGU--AAAAAGCAGGGGGUAGG-AAGGGGAGGGUAAGG-CUGGUGCCAGC-CGCCGCGGUAAAACCAGCUCCCCGAGGGGUUCCCACGCAUACUGGGCCUAAAGCGUCCGUAGCCGGCCCCGUAA-GUCCUCGGUUAAAUCCGCCUGAA-GACAG-GCGGAC-CGCCGAGGAUACUGC-GG--GGCUAGGG-AGCGGGAGGGGCC-GAGGGUAUUCCGGGGGGAGCGGUAAAAUGCGUAGAUCCCCGGAGGACCACCAGUGGCGAAGGCGCUCGGCUGGAACGCGUCCGACGGUGAGGGACGAAAGCUGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGCCGGCUAGGUGCCGGCUGAGG-UU-UCGGCCUCAGCCGGUGUCGAAGCGAAGGCAUUAAGCCGGCCGCCUGAGGAGUACAGCCGCAA-------------------------------------GGCCGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGACGGGGGGGCACCACAAGGGGUGAAUGCCUGCGGCUCAAUUGGACUCAACGCCGGGAAUCU-UACCGGGGGCGACAGC--AGGAUGAAGGUCAGGCUGAAGACCU-UACC-UGA----CGCGCUGAGGGGUGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCC--GCCC-UCAGUUGCCAGC-GGGGCC--UUAC-GGCUGGCC--G-GGCAAACUGGGGGGACUGCCGGCGA-AGAGCCGGAGGAAGGAGGGGGCUACGGCAGGUCAG-UAUGCCCCUAAUCCCCCGGGCC-GCACGCGGGCUGCAAUGGGCGGGACAGCGGG-A-UGC-GACCCCGAGA-GGG--GGAGCAAAUCCCUGAAA--CCCGCCCGUGGUUGGG-AUCGAGGGUUGCAACUCGCCCUCGUGAACCCGGAAUCCCUAGUAACCGCGGUUCUCCAUACCGCGGUGAAUACGUCCCUGCCCCUUGUACACACCGCCCGUC-AACCCACCCGAGUGGACUUGGGGCGAGGCCCAGCUC-------------AA-U---------GGCUGGGUC-GAGCUUUGGGUCCGCGA----GGGGGGGUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCC
JF509453.1/1-1510                    AUACCGGUUGAUCCUGCCGGACCCGACCACUAUCGGGGUGGGGCUAAGCCAUGGAAGUC-GAACGC-----UCCGC---AA--------GC----GCGGG-----GCGU--GGCAGACGGCUGAG-UAACACGUGGCCAACCUACCCUCGGGACGGGGAUAGUCU--C-G-GGAAACUGGGGC-UAAUCCCCGAUAGGCGGAGAUG-CCUGGAAG---GGUUCUCCGCCUAAAGGGCUAGG---CCGCU----GUGAAG------GCCUAGCCGCCCGAGGAUGGGGCUGCGGCCCAUCAUGGUAGUUGGCGGGGUAACGGCCCGCCAAGCCGAUAACGGGUAGGGGCCGUGAGAGCGG-GAGCCCCCAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACG-GGGUGCACCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGUGACGGGGCCACCCC-GA-GUGCCCC------GA-A-GA------GGGGCUUUUCCCCGCUGU--AAGAAGGCGGGGG-AAU-AAGCGGGGGGCAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCCCCGCGAGUGGUCGGGACGUUUACUGGGCCUAAAGCGCCCGUAGCCGGCCCGGCAA-GUCCCCACUGAAAUCCCUGGGCUCAACCC-GGGGGC-GGGUGGGGAUACUGC-CG--GGCUAGGG-GGCGGGAGAGGCC-GAGGGUACUCCCGGGGUAGGGGCGAAAUCCGAUAAUCCCGGGAGGACCACCAGUGGCGAAGGCGCUCGGCUGGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCGGCUGUAAACGAUGCGGGCUAGGUGUUGGGCGGGC-UU-U-GAGCCCGCCCAGUGCCGCAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGA-GCCUGCGGCUUAAUUGGAGUCAACGCCGGGAAUCU-UACCGGGGGCGACAGC--AGGAUGACGGCCAGGCUAACGACCU-UGCC-CGA----CACGCUGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGCGUCCGGUUAAGUCCGGCAACGAGCGAGAUCCCC--ACCC-CCAGUUGCUAUC-CCGGUC--UCCG-GACC--GG--G-AGCACACUGGGGAGACUGCCGCCGA-UAAGGCGGAGGAAGGAGGGGGCCACGGCAGGUCAG-CAUGCCCCGAAUCCCCCGGGCU-GCACGCGGGCUACAAUGGCGGGGACAGCGGG-U-GCC-GACCCCGAAA-GGG--GGAGGUAAUCCCUGAAA--CCCCGCUGUGGUUGGG-AUCGAGGGCUGAAAUUCGCCCUCGUGAACGUGGAAUCCCUAGUAACCGCGCGUCAACAUCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUCCACCCGAGCGGAGGAGGGGUGAGGUGCACUCCGUUGCCGGGUAAC----CCGGUGGCGGGGUGUAUC-GAACCCGUCCUCCGCAA----GGGGGGAGAAGUCGUAACAA------G--GUAGCCGUACCGG----------AAGGUGCGGCU-GGAUCACCUCCU
EU686635.1/915-2414                  ACUCCGGUUGAUCCUGCCGGACCCGACUGCUAUCGGAUUAGGACUAAGCCAUGCGAGUU-GAACG-------CUCU---UUGACUAUGUUA----AGAG-------CGU--GGCAAACUGCUCAG-UAACACGUUGCCAACCUACCCUAAAGAUAUGAAUAACCC--C-G-GGAAACUGGGAU-UAAUGCGUUAUAAGUCAGGAAU-CCUGGAAU---GGAUCUUGACUAAAA-GAAUUG------AAG----AGCAUGU---UCAUCGGUUCGCUCUAGGAUGGGGCCGCGUCCGAUCA-GGUUGUUGGUGGGGUAAAGGCCCACCAAGCCUAUAACCGGUACGGGCUUUGAGAGAAG-UAGCCCGGAGAUGGACCCUGAGACACAGGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUUCGCAAUGCGCGCAAGCGUGACGAGGCUAAUCC-GA-GUGUUACCU----GC-U-GA----AGGUAACUUUUGUUAAGUUU--AAUUCGCUUAAAG-AAA-AAAGGGAGGGCAAGC-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCUCCCUGAGUGGUCGGGGUGUUUAUUGGGCCUAAAGCAUCCGUAGCUUGUUUUAUGA-GUCUUUCGUUAAAUCUGACGGCUUAACCG-UUAGGC-UGCGUAAGAUACCGU-AA--AACUAGGA-GGCGGGAGAGGCU-GAUGGUACUCCAAGGGUAGGGGUAAAAUCCACUGAUCCAUGGAAGACCACCAAUGGCGAAGGCGGUCAGCCAGAACGCGCUCGACGGUGAGGGAUGAAAGCUGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCGAGCUAGGUGAUGGAGUGAU-UA-U-GUAUUACUUCAGUGCCACAGGGAAGCCGUUAAGCUCGCCGCCUGGGGAGUACGAUCGCAA-------------------------------------GAUUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAA-GCCUGCGGUUCAAUUGGAGUCAACGCCGGGAAUCU-UACCAGGAGCGACAGC--AGGAUGAAAGUCAAGUUGGAGACUU-UACU-AGA----CAAGCUGAGAGGUGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCC--ACCG-UUAAUUGCUUUC-AGCGAC-CGUAGGGUUG--CU--GGAGAUAUUUAGCGGGACUGCUACCGC-UAAGGUGGAGGAAGGAGGGGGCCACGGCAGGUCAG-UAUGCCCCGAAACUCCUGGGCU-ACACGCGGGCUGCAAUGGUAGGUACAAUGAG-U-UUC-GACCUCGAAA-GGG--GAAGGUAAUC-CCGAAA--ACCUACCCCAGUUGUG-ACUGAGGGCUGAAACUCGCCCUCACGAAUCUGGAAUCCCUAGUAAUCGCGUGUCAACAUCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUUCACCCGAGUUGGGUUUGGGCGAGGUAACGCCU-------------AAU---------UGACGUUGUC-GAACCUGAGCUCAACAA----GGGGGGAGAAGUCGUAACAA------G--GUGGCCGUAGGGG----------AACCUGCGGCC-GGAUCACCUCCU
AE017261.1/472186-470716             ACUCCGGUUGAUCCUGCCGGCGGCCACUGCUAUCAAGUUCCGACUAAGCCAUGCGAGUC-AAGGG--------GCC---GU--------AA----GGC--------ACC--GGCGUACCGCUCAG-UAACACGCGGAUAAUCUACCCUCGGGAAGGGCAUAACCU--C-G-GGAAACUGAGGC-UAAUUCCCUAUAGCCAUUCAGA-ACUGGAAU---GUUUGGAUGGUGAAG-GC-------------UCCG------------------GCGCCCGGGGAUGAGUCUGCGGCCUAUCA-GGUAGUAGGUGGUGUAACGGACCACCUAGCCUAAGACGGGUACGGGCCCUGGGAGGGG-UAGCCCGGAGAUGGACUCUGAGACACUAGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUGUGCAAUGCGCGCAAGCGCGACACGGGGAGCUU-GA-GUGUCUUGGC---AA-A-A----GCCAAGACUUUUCUUAUGCCU--AAAAAGCAUAAGG-AAU-AAGGGCUGGGUAAGA-CGGGUGCCAGC-CGCCGCGGUAACACCCGCAGCUCAAGUGGUGGUCACUUUUACUGAGCCUAAAGCGUUCGUAGCCGGCUUUGUAA-AUCUCCAGGUAAAUUCUAGCGCUUAACGU-UAGAUC-UCCUGGAGAGACUGC-AA--AGCUUGGG-ACCGGGUGGGGUU-GAACGUACUUUCAGGGUAGGGGUAAAAUCCUGUAAUCCUGGAAGGACGACCGGUAGCGAAGGCGUUCAACUAGAACGGAUCCGACGGUGAGGAACGAAGGCUAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACUCUGCCCACUUGGUGUUGCCUUUCC-GU-U-GAGGGGAGGCAGUGCCGGAGCGAAGGUGUUAAGUGGGCCGCUUGGGGAGUAUGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCGCAACGGGAGGA-AUGUGCGGUUUAAUUGGAUUCAACGCCGGAAAACU-CACCGGGAGCGACCUG--UGGAUGAGAGUCAACCUGACGAGUU-UACU-CGA----UAGCAGGAGAGGUGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUAGGGCGUUCACUUAAGUGUGAUAACGAGCGAGACCCCC--AUCU-CCAAUUGCAAUU-ACCUAC--GCGG-GUAG--GU--A-AGCACUUUGGAGAGACCGCCAGCGC-UAAGCUGGAGGAAGGAGGGGUCGACGGCAGGUCAG-UACGCCCCGAAUCUCCCGGGCU-ACACGCGCAUUACAAAGGGCAGGACAAUGCG-U-UGC-AACCUCGAAA-GGG--GAAGCUAAUCGCC-AAA--CCUGUCCGUAGUUAGG-AUUGAGGGCUGUAACUCGCCCUCAUGAAUCUGGAUUCCGUAGUAAUCGCGGGUCAACAACCCGCGGUGAAUAUGCCCCUGCUCCUUGCACACACCGCCUGUC-AAACCAUCCGAGCUGGUGUUGGAUGAGGGUUAGCUC-------------GAGA--------GGGUUAGCUC-AAAUCUGAUGUCAGUGA----GGAGGGUUAAGUCAUAACAA------G--GUAUCUGUAGGGG----------AACCUGCAGAU-GGAUCACCUCCU
CP001742.1/177775-176279             ACUCCGGUUGAUCCUGCCGGACCCGACUGCUAUCGGGGUGAGGCUAAGCCAUGGGAGUC-GCGCG-------CCCA---GCC------GCCG--CUGGG-------CGC--GGCGCACGGCUGAG-UAACACGUAGCUAACCUACCCUCGGGACGGGGAUAACCC--C-G-GGAAACUGGGGC-UAAUCCCCGAUAGGCGAGGGGG-CCUGGAAU---GGUCCCUCGCCGAAAGGGACCCU----GGGG----GGUUAUCG--CCUGGGGUCCGCCCGAGGAUGGGGCUGCGGCCCAUCAUGGUAGUUGGCGGGGUAAUGGCCCGCCAAGCCGACGACGGGUAGGGGCCGUGGGAGCGG-GAGCCCCCAGAUGGGCCCUGAGACAAGGGCCCAGGCCCUACG-GGGCGCACCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGUGACGGGGUCACCCC-GA-GUGCUCCCGU--------A-----AGGGAGCUUUUCCCCGCUGC--AAGGAGGCGGGGG-AAU-AAGCGGGGGGCAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCCCCGCGAGUGGUCGGGACGUCUACUGGGCCUAAAGCGCCCGUAGCCGGCCCCGUAA-GUCCCUCCUGAAAGCCCUGGGCUCAACCC-AGGGAG-UGGGGGGGAUACUGC-GG--GGCUAGGG-GGCGGGAAAGGCC-GGGGGUACCCCAGGGGUAGGGGCGAAAUCCGAUAAUCCCUGGGGGACCACCAGUGGCGAAAGCGCCCGGCUGGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCGGCUGUAAACGAUGCGGGCUAGGUGUCGGGCGGGCGUU-A-GAGCCCGCCCGGUGCCGCAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUUAAGGAAUUGGCGGGGGGGCAC-ACAAGGGGUGGA-GCCUGCGGCUCAAUUGGAGUCAACGCCGGGAACCU-CACCGGGGGCGACAGC--AGGAUGACGGCCAGGCUAACGACCU-UGCC-CGA----CGCGCUGAGGGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCUGUGAAGUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCC--GCCC-CUAGUUGCGACC-CGGCGG--GAGA-CCGC--UG--G-GGCACACUAGGGGGACUGCCGCCGC-UAAGGCGGAGGAAGGAGGGGGCCACGGCAGGUCAG-CAUGCCCCUAAACCCCCGGGCU-GCACGCGGGCUACAAUGGCGGGGACAGCGGG-A-UCC-GACCCCGAAA-GGG--GGAGGCAAUCCCUCAAA--CCCCGCCGUAGUCGGG-AUUGGGGGCUGUAACUCGCCCCCAUGAACCUGGAAUCCCUAGUAACCGCGCGUCAACAUCGCGCGGUGAAUACGUCCCUGCCCCUUGUACACACUGCCCGUC-GCUCCACCUGAGAGAAGGAGGGGUGAGGCUUCCUCC-------------UUCG--------GGAGGGAGUC-GAACCCCUCCUUCUCGA----GGGGGGAGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCUC
GU797786.1/1-1468                    --UCCGGUUGAUCCUGCCGGACCCGACUGCUAUCAGAGUGGGACUAAGCCAUGCGAGUC-A-ACG---------CC---GC--------AA----GG---------CGU--GGCAUACGGCUCAG-UAACACGUAGUCAACAUGCCCAGGGGACGUGGAUAACCU--C-G-GGAAACUGAGGA-UAAACCGCGAUAGGCCAAGGUU-UCUGGAAU---GGACCAUGGCUGAAAUCU-------------A-UA------------------UGGCCCCUGGAUUGGACUGCGGCCGAUCA-GGCUGUUGGUGAGGUAAUGGCCCACCAAACCUGUAACCGGUACGGGCUUUGAGAGAAG-GAGCCCGGAGAUGGGCACUGAGACAAGGGCCCAGGCCCUAUG-GGGCGCAGCAGGCGCGAAACCUCUGCAAUAGGCGAAAGCCUGACAGGGUUACUCU-GA-GUGAUGCCC----GC-U-AA----GGGCAUCUUUUGGCACCUCU--AAAAAUGGUGCAG-AAU-AAGGGGUGGGCAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCACCCCGAGUGGUCGGGACGAUUAUUGGGCCUAAAGCAUCCGUAGCUUGUUCUGCAA-GUCCUCCGUUAAAUCCACCUGCUCAACAG-AUGGGC-UGCGGAGGAUACUAC-AG--GGCUAGGA-GGCGGGAGAGGCA-AGCGGUACUCAGUGGGUAGGGGUAAAAUCCUCUGAUCCACCGAAGACCACCAGUGGCGAAGGCGGCUUGCCAGAACGCGCUCGACGGUGAGGGAUGAAAGCUGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCAGACUCGGUGAUGGGUUGGC-UU-C-GCGCCAACCCAGUGCCGCAGGGAAGCCGUUAAGUCUGCCGCCUGGGGAGUACGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAA-GCCUGCGGUUCAAUUGGAGUCAACGCCGGGAAUCU-UACCGGGGGCGACAGC--AGAGUGAAGGUCAAGCUGAAGACUU-UACC-AGA----CAAGCUGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGUAACGAGCAAGAUCCCU--GCCU-CUAGUUGCUACC-UCUGUU-CUCAGGAACG--GA--GGGGCUAAUUAGAGGGACCGCCGCCGC-UGAGGCGGAGGAAGGAGGGGGCUACGGCAGGUCAG-UAUGCCCCGAAACCCUCGGGCC-ACACGCGGGCUGCAAUGGUAAGGACAGCGGG-C-UCC-GAUCCCGAAA-GGG--GGAGGCAAUCCCUCAAA--CCUUACCUCAGUUAUG-AUUGAGGGCUGAAACUCGCCCUCAUGAAUAUGGAAUCCCUAGUAACCGCGUGUCACCAUCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUUCACCGAAGCUGGUUCUUGGCGAGGUGGCGCCU-------------AAU---------UGGCGCUAUC-GAACCUGGGGUCAGCAA----CGGGGGAGAAGUCGUAACAA------G--GUAGUCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCU
AGNT01000024.1/9062-7586             AUUCUGGUUGAUCCUGCCAGAGACUACCGCUAUCGGAGUCCGAUUGAGCCAUGCUAGUC-CACCG-------GCCU---U---------------UGGC-------CGG--GGCGGAUAGCUGAG-UAACACGUGGCCAACCUGCCCUAUGGACGAGGAUAACCU--C-G-GGAAACUGAGGC-UAACCCUCGAUAGUAGAGAGUU-ACUGGAAA--UGUUCUCUCUGCGAAAUGU-------------UCCG------------------ACGCCAUAGGAUGGGGCCGCGGCUGAUUA-GGUCGUUGGUGAGGUAACGGCUCACCAAGCCGAUAAUCAGUAGCAGCCGUGAGAGCGG-GAGCUGUCAGUCGGCUUCUGAGACAAGAAGCCGGGCCCUACG-GGGUGCAGCAGGCACGAAACCUUCACAAUGCACGCAAGUGCGAUGGGGGGACUCC-GA-GUGUGGUCUUCCC-A-C-A-AGGAAGGCCACUUUUCUGCACUGU--AAGGAGGUGCCGG-AAC-AAGGGGUGGGCAAUA-CUGCUGCCAGC-CGCCGCGGUAAUAGCAGAACCCCGAGUGGUAGUCGUUAUUAUUGGGCUUAAAGUGUUCGUAGCCGGCCGUGUAA-GUCCGCUGUGAAAUCCAGGCGCUUAACGU-CUGGGCGUGCAGCGGAUACUGC-AC-UGGCUUGGG-ACCGGACGGUGUC-GAGGCUAUUCCAAGAGUAGGGGUGAAAUCCUAAAAUUCCUGGAGGAGCGCCUGUGGCGGAAGCGCUCGACAAGUACGGAUCCGACGGUGAGGAACGAAAGCCAGGGGAGCAAAGCGGAUUAGAUACCCGCGUAGUCCUGGCCGUUAACAUUGCCUGUUUGAUGUCAGCCAACC-UU-C-GGGGUUGGCUGGUGCCGAAGUGAAAACGUUAAACAGGCCGCCUGGGUAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGACGGGGGAGCACCACAACCGGUGGA-GGCUGCGGUUUAAUUAGAUCAAACGCAGCGCACCC-UACCAGAGCCGACAGC--AGAAUGACGGUCAGCUUGAAGAGCU-UACC-UGA----CGCGCUGAGAGGAGCUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCUGUGAAGUGUCCGGUUAAGUCCGGUAACGAGCGAGACCCGC--AUCC-AAUGUUGCCACG-GAGCCG--CUUGUCGGU--UU--C-GGCACUCGUUGGAGACCGCUGGCGA-UAAGUCAGAGGAAGGAGCGGGCCACGGUAGGUCAG-UAUGGCCCGAAUGCUCUGGGAU-ACACGCGGCCUACAAUGGCCGGGACAAAGAG-A-CGC-GACCCCGAAA-GGG--GAAGCUAACCUCCUAAA--CCCGGUCUUAGUACGG-AUCGAGGCCUGCAACUCGGCCUCGUGAAGGCGAAAUCGGUAGUAGUCGCUGAUCAUCAUUCAGCGGCGAAUAAGUCCCUGCUCCUUGUACACACUGCCUGUC-AAGUCACCCGAGUCAGGUUCAGACGAGUCCCUCC---------------AUUU----------GGAGGCGC-AAGUCUGAGCUUGGCAA----GGGGGGCUAAGUCAUAACAA------G--GUAGCCGUUGGGG----------AACCAGCGGCU-GGAUCACCUCCA
EU563854.1/20-1509                   UUUCCGGUUGAUCCUGCCGGACCCGACUGCUAUGGGGGUAGGGCUAAGCCAUGGGAGUC-GAACG-------CUCU---CGG-----UAAG----AGGG-------CGU--GGCAGACGGCUGAG-UAACACGUGGCUAACUUACCCUCGGGACCUGGAUAACUC--C-G-GGAAACUGGAGC-UAAUCCAGGAUAGACAAAGAGU-UCUGGAAC---GAUUCUUUGUCGAAAGGCCCU-------UAG----GCUGUAUCCCGUCUAAGGGUGCCCGAGGAUAGGGCUGCGGCCCAUCA-GGCUGAUGGCGAGGUAACGGCUCGCCAAACCGAUAACGGGUAGGGGCCGUGAGAGCGG-GAGCCCCCAGUUGGGCACUGAGACAAGGGCCCAGGUCCUACG-GGGCGCACCAGGCGCGAAACGUCUCCAAUGCGGGAAACCGUGAGAGCGCUACCCC-CA-GUGCCCUC------G-A-AA-----GAGGGCUUUUCCCUACUGC--AGACAGGUAGGGG-AAU-AAGCGGGGGGCAAGG-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCCCCGCGAGUAGUCGGGACGCUUACUGGGCUUAAAGCGCCCGUAGCCGGCCCUAAAA-GUCACUGCUUAAAGCCCCGGGCUCAACCC-GGGAAA-GGGCAGUGAUACUAU-AG--GGCUAGGG-GGCGGGAGAGGCC-GGAGGUACUCCCAGAGUAGGGGCGAAAUCCACAGAUCCUGGGAGGACCACCAGUGGCGAAAGCGUCCGGCCAGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGUAGCAAAAGGGAUUAGAUACCCCUGUAGUCCCGGCUGUAGACGAUGCACGCUAGGUGUCGCGUAGGC-UU-C-GGGCCUGCGCGGUGCCGCAGGGAGACUGGUAAGCCUGCCGCCUGGGGAGUAUGCCUGCAA-------------------------------------GGGCGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGA-ACCUGCGGCUCAAUUGGAGUCAACGCCUGGAAUCU-CACCGGGAGAGACCAC--AGGAUGACGGCCAGGCUAACGACCU-UGCC-AGA----CUCGUGGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGUUGUGAAAUGUCCGGUUAAGUCCGGCAACGAGCGAGACCCCC--ACCA-UUAGUUGGUAUC-UCGGUC--UCCG-GAUC--GA--G-ACCACACUAGUGGGACUGCCACCGU-UAAGGUGGAGGAAGGAGGGGGCCACGGCAGGUCAG-CAUGCCCCGAAACUCCCGGGCC-GCACGCGGGUUACAAUGGCAGGGACAGCGGG-A-UCCCUACCCCGAGA-GGG--GGCGGCAAUCCCUCAAA--CCCUGCCUCAGUUGGG-AUCGAGGGCUGAAACUCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCACGUCAACAUCGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUCCACCCGAGUGAGGAAGAAGUGAGGCUUCUUGCC-----------CUUCGG------GGUGGGGAGUAGGAGCUUCUUCCUCGCGA----GGGGGGAGAAGUCGUAACAA------G--GUAUCCG-----U----------AA---GCUG---GAAUCGCCCCGU
FJ889134.1/1-1473                    AUUCCGGUUGAUCCUGCCGGAGGUCAUUGCUAUUGGGGUCCGAUUUAGCCAUGCUAGUU-GCGCG---------AC---UU--------AG----AU---------CGC--AGCGGAAAGCUCAG-UAACACGUGGCCAAACUACCCUGCAGAGGAGCAUAAUCU--C-G-GGAAACUGAGGC-UAAUACUCCAUACCGCACUCAC-GUUGGAAC--GACCGAGUGCACUAAACGC-------------UCCG------------------GCGCUGCAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGCUAAGGGGACCCC-AA-GUGCGAGGGC---AU-A-CA---GUCCUCGCUUUUGUGUACCGU--AAGGUGGUACACG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCAAGUGAUGACCGAUUUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCGCGUAG-GUUCGUCGGGAAAUCCAUCCGCUCAACGG-AUGGGCGUCCGGCGAAAACCAC-GU--GGCUUGGG-ACCGGAAGGCUCG-AGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCGCCGAUGGCGAAAGCACCUCGAGAAGACGGAUCCGACAGUGAGGGACGAAAGCUGGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACAAUGCCUGUUAGGUGUGGCACCGAC-UA-C-GAGUCGGUGCUGUGCCGUAGGGAAGCCGAUAAACAGGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCAUCGACUGU-AGCAAUGAUCAUCAGGUUGAUGACCUCUAUGUUGA----GUUACGGAGAGGGGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGUGAGACCCGC--ACUC-UUAAUUGCCAGC-AUCGCG--UUCG-CGCG-GAU--G-GGUACAUUAGGAGGACUGCCGCUGC-UAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGUGCUGGGCU-ACACGCGGGCUACAAUGGCCGAGACAAUGGG-U-UCC-UACCUCGAAA-GAG--GAUGGUAAUCUCAGAAA--CUCGGUCGUAGUUCGG-AUUGAGGGUUGAAACUCACCCUCAUGAAGCUGGAUUCGGUAGUGAUCGCGUCUCAGAAGGGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCAUUCG----------------CAA----------CGAAUGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
JF802164.1/13-1465                   AACUCGGUGAUUCCUGCCGGAGGCCAUUGCUAUCAGGGUCCGAUUUAGCCAUGCUAGUC-GCACG--------AGU---UC--------AC----ACU--------CGU--GGCAUAUAGCUCCG-UAACACGUGGCCAAACUACCCUUCGGAGACGCAUAACCU--C-G-GGAAACUGAGGC-UAAUUCGUCACACGGCUUUCAA-CCUGGAAU---GAUGAAAGCCUCAAACGC-------------UCCG------------------GCGCCGAAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAA-GAACCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAAGGGGACCCU-GA-GUGCACAGGC---AU-A-GU---GCCUGUGCUUUUCUCGACCGU--AGGGAGGUCGAGG-AAC-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCGAGUGAUGGCCGAUCUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCAGGCAA-GUCCGUCGGGAAAUCCACGUGCUCAACAU-GUGGGCGACCGGCGGAAACUGC-CC--GGCUUGGG-ACCGGAAGGCGCG-ACGGGUACGUCCAGGGUAGGAGUGAAAUCCCGUAAUCCUGAACGGACCGCCGAUGGGGAAACCACGUCGCGAAAACGGAUCCGACAGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCCGUAAACGAUGCCUGUUAGGUGUGGCCCCCGC-UA-C-GAGCGGGUGCUGUGCCGUAGGGAAGCCGCUAAACAGGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCAUCGACUGU-GGUAAUGACGGUCAGGUUGAUGACCU-CGCCACGA----GCCACAGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--AUCC-GUACUUGCCAGC-AGCACU--CAUC-GUGG--CU--G-GGGACAGUACGGAGACCGCCGUGGC-UAACACGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGUGCUGGGCA-ACACGCGGGCUACAAUGGUCAGGACAAUGGG-U-UCC-AACUCCGAAA-GGA--GACGGUAAUCUCACAAA--CCUGAUCGUAGUUCGG-AUUGUGGGCUGCAACUCGCCCACAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGCAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCUCCC----------------GAGA-----------CGGAAUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAACUCGUAACCA------G--GUAG----------------------------CC-UUAUCUCCUCCG
EU686628.2/16670-18140               ACUUCGGUUGAUCCUGCCGAAGGCUACUGCUAUUGGAGUUCGAUUAAGCCAUGCGAGUC-UAAGG-------GAUC---UU--------CG----GAUC-------CCU--GGCGUAAUGCUCAG-UAACACGUGGAUAAUCUACCCUCAGGUGGGGCAUAAACC--C-G-GGAAACUGGGGC-CAAUUCCCCAUAGAUACAGAUG-GCUGGAAU---GCUUCUGUAUUCAAA-GC-------------UCCG------------------GCGCCUGAGGAUGAGUCUGCGGCCUAUCA-GGUUGUAGUCAGGGUCAUGACCUGACUAGCCAGCGACGGGUAUGGGGUGUGAGAGCAC-UUGCCCAGAGAUGGUUUCUGAGACACGAAACCAGGCCUUCCGGGGGCGCAGCAGGCGCGAAAACUUCGCAAUGCGGGAAACCGUGACGAGGGAACUCC-AA-GUGUCUAUGC------A-UU---GCAUAGACUGUUUUUUAGCCU--AAAUAGCUAUUAG-AGU-AAGGGGUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCACCCCGAGUGGUAGCCACUAUUAUUGGGCCUAAAGCGUUCGUAGCCGGUUUGGUAA-AUUCUUGGGUAAAUCGUACCGCUUAACGG-UGCGGA-UUCCGGGGACACUAC-CA--GACUUGAG-ACCGGGGGAGAUC-AGAGGUACUUGCGGGGGAGCGGUGAAAUGUUGUAAUCCCGCAGGGACCACCAGUGGCGAAGGCGUCUGAUCAGAACGGCUCUGACGGUGAGGAACGAAACCCUGGGGCGCAAACGGGAUUAGAUACCCCGGUAGUCCAGGGCGUAAACGCUGCUGACUUGGUGUUGGGGAUCC-UA-C-GAGGAUGUCCAGUGCUGGCGCGAAGGUAUUAAGUCAGCCGCCUGGGGAGUACGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUGCAACGUGUGGA-GCGUGCGGUUUAAUUGGAUUCAACGCCGGAAAACU-CACCGGGGGCGACGGU--UACAUGAAGGCCAAGCUGAUGACUU-UGCC-UGA----UUUUCCGAGAGGUGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACCGUAAGGCGUUCUGUUAAGUCAGAUAACGAACGAGACCUCC--GUCA-CCAUUUGCUAUU-CUUCUC--UCCG-GAGG--GG--G-AGCACUAUGGUGGUACCGCCACUGU-UAAAGUGGAGGAAGGAGGGGGCAACGGUAGGUCAG-UAUGCCCCGAAUCUCCCGGGCU-ACACGCGCGCUACAAAGGGCAGGACAAUGGG-C-UUC-GACACCGAAA-GGU--GGAGGCAAUCCCG-AAA--CCUGCUCGUAAUUCGG-AUUGAGGGCUGCAAUUCGCCCUCAUGAAGCUGGAAUACGUAGUAAUCGCGGGUCAACAUCCCGCGGUGAAUAUGCCCCUGCUCCUUGCACACACCGCCCGUC-AAACCACCUUAGUUGGGUCUGGACGAGGGUUUGUC--------------UUCU---------GACACGCUC-GAAUCUGGGUUCAGCGA----GGAGGGUUAAGUCGUAACAA------G--GUAUCCGUAGGGG----------AACCUGCGGAU-GGAUCACCUCCU
FP565147.1/57324-55843               ACACUGGUUGAUCCUGCCAGAGGCUACUGCCAUCAGAGUUCGAUUAAGCCAUGUUAGUC-GAGGGUG--CUUCUUC---UU--------CG----GAAGAAG-UAACCC--GGCGGACGGCUCAG-UAACACGUGGAUAACUUGCCCUUGGGUCCGGGAUAACCC--CUG-AGAAAUUGGGGA-CAAUACCGGAUAGGGCAUCGAUAGCUGGAAU---GCGCGAUGUCCAAAA-GC-------------UGAG------------------GCGCCCAAGGAUAGGUCUGCGGCCGAUUA-GGUUGUUGUUGAUGUAAUGGAUCAACAAGCCUGCAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGAUGGGUUCUGAGAAAAGAACCCAGGUCCUACG-GGACGCAUCAGGCGCGAAAACUUUACAAUGUGCGAAAGCACGAUAAGGGAACUCU-GA-GUGCCUCC------U-A-U------GGAGGCUGUUCAGGUGUCU--AAAAAGCACUUGA-AGU-AAGGGCUGGGUAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCAGCCCAAGUGGUAGCCACGAUUAUUGGGUCUAAAGCGUCCGUAGCCGGCCAGGUAA-GUUCUUUGGGAAAUUUAACCGCUCAACGG-UUAAGCUUUCAGGGAAUACUGC-UU--GGCUUGGG-ACCGGGAGAGGUC-AGAGGUACUUCAAGGGUAGGGGUGAAAUCCGUUAAUCCUUGAGGGACCACCAGUAGCGAAGGCGUCUGACCAGACCGGGUCCGACGGUGAGGGACGAAGGCUAGGGUCGCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCGGGCCAGGUGUUGGCAUUAC-UG-C-GAGUGAUGUCAGUGCCGAAGGGAAGCCGUUAAGCCCGCCAUCUGGGGAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGGGUGGA-GCCUGCGGUUCAAUUGGAUUCAACGCCGGAAAACU-CACCGGAGGCGACAGC--AAGAUGAAAGUCAGGCUGAAGACCU-UACU-GGA----UUAGCUGAGAGGUGGCGCAUGGCCGUCGAC--------------------------------------------------------------------------------------------------------------------------AGUUCGUGUCGUGAAACAUCCUGUUAAGUCAGGCAACGGGCGAGACCCGC--GCUC-ACAGUUGCCAGC-AUCUCC--GUAA-GGAG-GAU--G-GGAACUCUGUGAGGACUGCCGCCGC-UAAGGUGGAGGAAGAAGCGGGCCACGGUAGGUCAG-UAUGCCCCGAAUCCUCCGGGCU-ACACGCGUGCUACAAUGGAUAGUACAAUGAG-U-AUC-GACCCCGAAA-GGG--GAAGGUAAACCCCUAAA--ACUAUCCUUAGUUGGG-AUCGAGGGCUGCAACUCGCCCUCGUGAACCUGGAAUCCGUAGUAAUCGCAUCUCAAAAUGGUGCGGUGAAUAUGUCCCUGCUCCUUGCACACACCGCCCGUC-AAGCCAGCCGAGUGGGAUUUAGGUGAGGUCAUGUUU--------------UUU---------GGCAUGUUC-GAACCUAAGUCUCGUAA----GGGGGGCUAAGUCGUAACAA------G--GUAGCCGUAGAGG----------AAUCUGCGGCU-GGAUCACCUCCU
AB201308.1/19565-21032               ACUCCGGUUGAUCCUGCCGGACCCGACUGCUAUCGGAUUGGGACUAAGCCAUGCGAGUC-A---A-------CUCC---GC--------AA----GGGG-------U----GGCGCACGGCUCAG-UAACACGUAGUCAACCUACCCUGGGGACGGGGAUAACCU--C-G-GGAAACUGAGGC-UAAACCCCGAUAGGCCAUGGCU-CCUGGAAU---GGGCUAUGGCUGAAAUCU-------------A-UA------------------UGGCCCCAGGAUGGGACUGCGGCCGAUCA-GGUUGUUGGUGGGGUAAUGGCCCACCAAGCCUAUAACCGGUGCGGGCUCUGAGAGGAG-GAGCCCGGAGAUGGGCACUGAGACAAGGGCCCAGGUCCUAUG-GGGCGCAGCAGGCGCGAAACCUCCGCAAUGGGCGAAAGCCCGACGGGGUCAGUCC-GA-GUGGUUCCC----GC-U-GA----GGGAACCUUUUGCCAGCUGU--AAACAGGCUGGCG-AAU-AAGGGGUGGGCAAGU-UUGGUGUCAGC-CGCCGCGGUAAUACCAGCACCCCGAGUGGUCGGGACGAUUAUUGGGCCUAAAGCAUCCGUAGCCGGCCCAGUAA-GUCCUCCGUUAAAUCCAACGGCUCAACCG-UUGGGC-UGCGGGGGAUACUGC-UG--GGCUAGGG-GACGGGAGAGGCG-AGGGGUAUUCCCGGGGUAGGGGUAAAAUCCACUGAUCCCGGGAGGACCACCAGUGGCGAAGGCGCCUCGCUAGAACGUGCCCGACGGUGAGGGAUGAAAGCUGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGUAGGCUCGGUGUUGGGCUGCC-UC-A-GUGGCAGCCCAGUGCCGCAGGGAAGCCGUUAAGCCUACCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAA-GCCUGCGGUUUAAUUGGAGUCAACGCCGGGAACCU-UACCAGGGGUGACAGC--AGGAUGAAGGUCAAGCCAAAGACUU-UACC-AGA----CAAGCUGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGUAACGAGCGAGACCCUC--GCAU-CCAGUUGCUACC-AUCACU-CUUUGGAGCG--GU--GGGGCUAACUGGAUGGACUGCCGCCGA-UAAGGCGGAGGAAGGAGGGGGCUACGGCAGGUCAG-UAUGCCCCGAAACCCCUGGGCC-ACACGCGGGCUGCAAUGGUAGGGACAAUGGG-U-UCC-GACCCCGAAA-GGG--GGAGGCAAUCCCC-AAA--CCCUACCCCAGUUAUG-AUUGAGGGCUGCAACCCGCCCUCAUGAAUCUGGAAUCCCUAGUAAUCGCGUGUCACCAUCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUUCACCCGAGGUGGGCUUGCGUGAGAUGGUGCC--------------UCUU---------GGUAUCAUC-GAACGCAAGCUUGCUGA----GGGGGGAGAAGUCGUAACAA------G--GUGGCCGUAGGGG----------AACCUGCGGCC-GGAUCACCUCCU
CP002117.1/740158-741625             AUUCUGGUUGAUCCUGCCAGAGGUCACUGCUAUCGGGGUUCGAUUAAGCCAUGCGAGUC-GAGAG--------GGU---UU--------AG----ACC--------CUC--GGCGGACUGCUCAG-UAACACGUGGAUAACCUGCCCUAAGGUGGAGGAUAACCC--C-G-GGAAACUGGGGA-UAAUACUCCAUAGGCUAGGGAU-ACUGGAAU---GUUUCCUAGCCAAAA-GU-------------UCCG------------------GCGCCUUAGGAUGGAUCUGCGGCCGAUUA-GGUAGUUGUUGGGGUAACGGCCCAACAAGCCUGUAAUCGGUACGGGUUGUGGGAGCAA-GAGCCCGGAGAUGGAAUCUGAGACACGAUUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUUUACAAUGCAGGAAACUGUGAUAAGGGAACCCC-GA-GUGCUCGU------A-C-AC-----GCGAGCUGUCCAGGUGUGC--AAAAAGCAUCUGA-AGA-AAGGGCCGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCGGCUCGAGUGGUGACCACUAUUAUUGGGCUUAAAGCGUUCGUAGCUGGACUCUUAA-GUCUCUUGGGAAAUCCGCCGGCUCAACCG-GCGGGCGUCCAAGAGAUACUGA-GU--GUCUAGGA-ACCGGAAGAGGUA-AGAGGUACUUCGGGGGUAGGAGUGAAAUCCUGUAAUCCUCGAGGGACCACCGAUGGCGAAGGCAUCUUACCAGGACGGCUUCGACAGUGAGGAACGAAAGCUGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGCGCGUUAGGUGUACUGGUGAC-CA-C-GAGUCACCUGGGUGCCGAAGGGAAACCGUGAAACGUGCCGCCUGGGAAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGGGUGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGGAAGCU-CACCGGAUAGGACAGC--GGAAUGAUAACCGGGCUGAAGACUC-UGUU-UGA----CCAGCUGAGAGGAGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACUGUGAAGCAUCCUGUUUAGUCAGGCAACGAGCGAGACCCAC--GCCA-ACAGUUGCCAGC-AUGUUC--UCCG-GAAU-GAU--G-GGGACACUGUUGGGACCGCCUCUGC-UAAAGGGGAGGAAGGAAUGGGCAACGGUAGGUCAG-CAUGCCCCGAAUUAUCCGGGCU-ACACGCGGGCUACAAUGGUCGGGACAAUGAG-C-AAC-GACACUGAGA-AGU--GUAGUCAAUCUCCUAAA--CCCGUCCCAAGUUCGG-AUUGUGGGCUGUAACUCGCCCACAUGAAGCUGGAAUCCGUAGUAAUCGCGUUUCAAAAUAGCGCGGUGAAUGCGUCCCUGCUCCUUGCACACACCGCCCGUC-AAACCACCCGAGUGAGGUUUGGAUGAGGCUGUGGU--------------UUUU---------GCCGCAGUC-GAAUCUAGGUUUUGCAA----GGGGGGUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
HM159600.2/1-1471                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGGGUCCGAUUUAGCCAUGCUAGUC-GCACG--------AGU---UC--------AU----ACU--------CGU--GGCAUAUAGCUCAG-UAACACGUGGCCAAACUACCCUGUGGACCAGCAUAACCU--C-G-GGAAACUGAGGC-UAAUUCUGGAUAUCGCCCACAU-CCUGGAGU---GGAGUGGGCGUGAAACGU-------------UCCG------------------GCGCCACAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCCAUAAUCGGUACGGGUGAUGAGAGUCA-GAGCCCGGAGACGGUAUCUGAGACAAGAUACCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCGAGUGCGAUAGGGGGACCCC-GA-GUGCGAGGGC---AU-A-CA---GUCCUCGCUUUUCACCACUGU--AAGGUGGUGGUGG-AAU-AAGUGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCACGAGUGAUGGCCGAUCUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCAGACAG-GUCCAUCGGGAAAUCUGCACGCCCAACGU-GCAGGCGUCCGGUGGAAACCAG-UU--GGCUUGGG-GCCGGAAGAUCCA-GGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCCGGACGGACCACCGGUGGCGAAAGCGCCCUGGAAGGACGGACCCGACGGUGAGGGACGAAAGCUAAGGUCACGAACCGGAUUAGAUACCCGGGUAGUCUUAGCUGUAAACGAUGUCCGCUAGGUGUGGCGCAGGC-UA-C-GAGCCUGCGCUGUGCCGCAGUGAAGACGCUAAGCGGACCGCCUGGGAAGUACGUCUGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCGGCACCGACAGC-AGUAAUGACAGUCAGGCUGAUGCCUU-UACU-CGA---CGCUGCUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGAUCCGU--AUUC-UUAAUUGCCAGC-AACGCC--GUGA-GGCG-GUU--G-GGUACAUUAGGAAGACUGCCGCCGC-CAAGGCGGAGGAAGGAGCGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGUGCCGGGCG-ACACGCGGGCUACAAUGGCCGAGACAGUGGG-A-UGC-AACCCCGAGA-GGG--GGCGCUAAUCUCCUAAA--CUCGGCCGUAGUUCGG-AUUGCGGGCUGAAACCCGCCCGCAUGAAGCUGGAUUCGGUAGUAAUCGCCGUUCAGAAGACGGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAUCACCCGAGUGGGAUCCGGAUGAGGCCCGG-----------------UUC-----------CCGGGUC-GAAUCUGGGUUCCGCAA----GGGGGAUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
HE574571.1/17306-18807               AAUCCGGUUGAUCCUGCCGGACCCGACCGGUAUCGGGGUGGGGCUAAGCCAUGCAAGUC-GUACGU-----CCCCC---AGCC---ACG--U-GGGGG-------GCGU--GGCGCACGGCUCAG-UAGUACGCAGCUAACCUACCCUAAGGAGGGGGAUAAUCC--C-G-GGAAACUGGGGC-UAAUCCCCCAUAGACCUAGGGU-ACUGGAAG---GUCCCUAGGUCGAAAGGGACUG-----GCCG----GCAUGCC----GGCCAGUCCGCCUUAGGAUGGGGCUGCGUCCGAUCA-GGUAGUUGGUGGGGUAAAGGCCCACCAAGCCUAUGACCGGUGCGGGCUCUGAGAGGAG-GAGCCCGGAGAUGGACCCUGAGACAAGGGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUCGCAAUGCCCGAAAGGGUGACGAGGCUACCCC-GA-GUGCCGUCC----GC-U-GA----GGACGGCUUUUGCCGGGUCU--AAAAAGCCCGGCG-AAU-AAGGGGAGGGCAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCUCCCCGACUGGUCGGGACGAUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCCUGUGU-GUGGUCCGUUAAAUCCAGCGGCUCAACCG-CUGGGC-UGCGGAUCAUACUAC-AG--GGCUAGGG-GGCGGGAGAGGCC-GGGGGUACUCCGCGGGUAGGGGUAAAAUCCGCUGAUCCGCGGAAGACCAACAGUGGCGAAGGCGCCCGGCCAGAACGCGCCCGACGGUGAGGGACGAAAGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACGAUGCUCGCUAGGUCUUGGCGAAGC-UU-A-GGGCUUCGCCAGGGCCGCAGGGAAGCCGUUAAGCGAGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAA-GCCUGCGGUUUAAUUGGAGUCAACGCCCGGAACCU-UACCAGGGGUGACGGC--AGGAUGAAGGUCAGGCUAAAGACCU-UACC-UGA----CAAGCCGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCUGUGAAGUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCUC--GCUG-CCAGUUGCUUCC-CCACUC-CGAAAGGGGU-GGG--G-AGGAAACUGGCAGGACCGCCGCCGA-UAAGGCGGAGGAAGGAGGGGGCUACGGCAGGUCAG-UAUGCCCCGAAACCCCUGGGCC-ACACGCGGGCUGCAAUGGUGGGGACAAUGGG-A-UCC-GAACCCGAAA-GGG--GGAGGUAAUCCCG-AAA--CCCCACCGUAGUUGGG-AUCGAGGGCUGCAACCCGCCCUCGUGAACCUGGAAUCCCUAGUAAUCGCGGGUCACCAUCCCGCGGUGAAUACGUCCCCGCUCCUUGCACACACCGCCCGUC-GCUCCACCCGAGUGGGCCCCCGGCGAGGUGACAUCC-------------UGCG--------UGGUGUCAUC-GAACCGGGGGUCCGCGA----GGGGGGAGAAGUCGUAACAA------G--GUGGCCGUACCGG----------AAGGUGCGGCC-GGAUCACCUCCG
AJ318041.1/1-1500                    ACUCCCGUUGAUCCUGCGGGAGGCCACCGCUAUCUCCGUCCGGCUAACCCAUGGAAGGC-GAGGG-------UCCC---CGGG----UAAG----GGGG-------CCC--GCCGCACGGCUGAG-UAACACGUCGGUAACCUACCCUCGGGACGGGGAUAACCC--C-G-GGAAACUGGGGC-UAAUCCCCGAUAGGGGAUGGGU-GCUGGAAG---GCCCCAUCCCCGAGAGGGGCUA-----GCGG----UACUUCCC--CCGCUAGCCCGCCCGAGGAUGGGCCGGCGGCCCAUCA-GGUAGUUGGCGGGGUAAUGGCCCGCCAAGCCGAAGACGGGUAGGGGCCGUGAGAGCGG-GAGCCCCCAGAUCGGCACUGAGACAAGGGCCGAGGCCCUACG-GGGCGCACCAGGGGCGAAACCUCCGCAAUGCGGGAAACCGUGACGGGGGGACGGA-GA-GUGCCGGAGGGCGUU-A-U-G-CUCUCCGGCUUUUGGGGAGUGU--AAGUAGCUCCCCG-AAU-AAGCGGUGGGCAAGA-GGGGUGGCAGC-CGCCGCGGGAACACCCCCACCGCGAGCGGUGGCCGUGAUUAUUGGGCCUAAAGGGGCCGUAGCCGGGCCGGUGU-GGCUCCGGUGAAAUCCUCGGGCUCAACCC-GAGGGCGCGCCGGAGCUACUAC-CG--GCCUAGGG-ACCGGGAGGGGCC-GACCGUACUCCCGGGGGAGCGGUGAAAUGCUGUAAUCCCGGGAGGACGACCCGUGGCGAAAGCGGUCGGCCAGAACGGGUCCGACGGUGAGGGCCGAAGGCCGGGGGCUAGAACGGGAUUAGAGACCCCGGUAUUCCCGGCUGUCAACGCUGCGGGCUACCUGCUGGGCGGGC-UA-C-GAGCCCGCCCAGUGGGGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUAGGCGGGGGAGCAC-ACAAGAGGUGGG-GUGCGCGGUUUAAUUGGAUUCGACGCCGGGAACCU-CACCGGGGCUGACAGC--ACAAUGAUGGUCGGCCUGAAGGGCC-UACC-GGA----GGCGCUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCCUGUGCCGUGAGGUGCCCUGUUAAGUCAGGAAACAGGCGAGACCCGC--GCCC-GCAGUUGCGACG-GCC-----GAAA----G--GC--C-GGCACACUGCGGGGACUGCCGGGG--AAACCCGGAGGAAGGUGCGGGCGACGGCAGGUAUG-CAUGCCCCGAAUGCCCCGGGCU-ACACGCGCGCAUCAAUGGGCGGGACAGGGGG-C-CGC-GACCCCGAAA-GGG--GGAGCAAAUCCCC-AAA--CCCGCUCUCAGUCCAG-AUCGAGGGCUGCAACUCGCCCUCGUGACGGCGGAAUCUCUAGUAGUCGGACGUCACCAGCGUCCGGCGAAUACGUCCCUGCUCCUUGCACUCACCGCCCGUC-AAGCCACCCGAGCUGGGGCCUAGCGAGGCCGUGGGGG-----------GUUCGC------CCCCCACGGUC-GAGCUAGGCCCCGGCGA----GGGGGGCUAAGUCGACACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCU
GU951431.1/1-1465                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUUCGAUUUAGC-AUGCUAGUU-GUACG-------U-------C--------UA-------A-------CGU--AGCGAAAAGCUCCG-UAACACGUGGCCAAACUACCCUGUGGAGGGCCAUAACCU--C-G-GGAAACUGAGGC-UAAUAGCCCAUACGACGCCCAC-GCUGGAAU---GCCGGGCGGCCGAAAUGC-------------UCCG------------------GCGCCACAGGAUGUGGCUGCGGCUGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCAGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCCAGUGCGAUAAGGGGACCCC-GA-GUGCGAGGGC---AU-ACUA---GCCCUCGCUUUUCACAACCGU--AGGGAGGUUGUGG-AAC-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCGAGUGAUGACCGCUGUUAUUGGGCCUAAAGCGUCCGUAGCUGGCCACGCAA-GUCCGUCGGGAAAUCCACUAGCUCAACUA-GUGGGCGUCCGGCGGAAACUGC-GU--GGCUUGGG-ACCGGAAGGCUCG-AGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCGCCGAUGGCGAAAGCACCUCGAGAGAACGGAUCCGACAGUGAGGGACGAAAGCUGGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCCGUAAACGAUGCCAGUUAGGUGUGGCAGAGGC-UA-C-GAGCCUCUGCUGUGCCGUAGGGAAGCCGAGAAACUGGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCUCCGACUAC-AGUGAUGACGACCAGGUUGAUGACCU-UGUCACGA---CGCUGUAGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACUC-UUAAUUGCCAGC-AUCAGG--UUUC-CUGG--AU--G-GGUACAUUAAGAGGACUGCCGCUGC-UAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGAGCUGGGCU-ACACGCGGGCUACAAUGGUCAGGACAAUGGG-U-UCC-AACCUCGAAA-GAG--GACGGUAAUCUCCGAAA--CCUGGUCGUAGUUCGG-AUUGUGGGCUGAAACUCGCCCACAUGAAGCUGGAUUCGGUAGUAAUCGCGUUUCAGCAGAGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGGGGUCCGGAUGAGGCCUGG-----------------CUC-----------CCAGGUC-GAAUCUGGGCUCCGCAA----GGGGGCUUAAGUCG-AACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
ADCE01000012.1/46258-47753           AUUCCAGUUGAUCCUGCUGGAGGUCACUGCUAUUGGGAUUCGAAUGAGACAUGCAAGUU-C-AUC-------UAUU---AGG-----UAAU----AGUA-------GAU--UGCGUACGGCUGAGGCAACACAUAGAUAACGUAACGUUAUGAGGAGGAUAUCCU--C-G-GGAAACUGAGGU-UAAUACUCCAUAGCAAUAAUU--UUUGAAAU---AAUUUUAUUGUGAAAGGUUAU--------UU----CUAAUACC--GAAAUAAUACGCAUAACGAUCGGUCUAUGCCUGAUUA-GACUGUUGGUGAGGUAACGGCUCACCAAAUCUUAGAUCAGUAGGGGCCAUGGAAGUGG-UUUCCCCCAGAAGGGUACUGAGACAAGGACCCUAGCACUACG-GUGUGCAGCAGUCCCGAAAACUCCACAAUGCGCGAAAGCGUGAUGAGGGAAUCCC-AA-GUGUUCUUUC--CGU-U-UC--GGAAGGAACUUUUGCCACGUUUUGAAAUGGCGUGGCG-AAU-AAGGGCUGGGCAAG--CGGGUGCCAGC-AGCCGCGGUAAUACCUGCGGCCCGAGUUGUGACCAUUAUUAUUGAGUCUAAAGCGUUCGUAGCUGGUUUGGAUA-GUUGGUGCUUAAAUCUUUUCGUUUAACGG-AAAGGCACGGUAUAAAUACUUC-UA--GACUAGAG-GCCGGGAGGGGAG-AUGGGAACUUUUCGGGUAGGAGUAAAAUCCUUUAAUCCGAAAAAGACCACCAAUAGCGAAGGCACAUCUCCAGAACGGACCUGACGGUGAGGGACGAAGGCUAGGAGAACAAACCGGAUUAGAUACCCGGGUAGCCCUAGCAGUAAACGCUGCUUACUAUACGUUGCAUUUCC-U--U-GAGGAAAUGCAGUGUGACAGCGAAGGCGUUAAGUAAGCCACUUGGGGAGUAUAAUCGCAA-------------------------------------GGUCGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACAAAAACGGGUGAA-AUUUGCGGUUUAAUUGGAUUCAACUCCGGGAAUCU-UACCAGAAGCGACAGC--AAUAUGAAGGUCAGUCUGAAGAACU-UACC-AAA----UGCGCUGAAAGGUGUUGCAUGGCCAUCAUC--------------------------------------------------------------------------------------------------------------------------AGUUAGUAUCUUGAGACGUCCCGUUAAGUCGGGUAACUAACAAGACCCUC--UUCU-AUAUUUGCUAAC-AUGCAA--UCCG-UUGCGAAU--G-AGCAAAAUAUAGAGACUGCUUUCG--AAAGAAAGAGGAAGGUGAGGGCGACGGUAGGUCAG-UACGACCCUAAUCCUCUGGGCU-ACACGCGAAUUGCAAUGGUAAAGGCAAUAGG-A-UGC-CACUCCGAAA-GGA--GGAGCUAAUCCCCGAAU--CUUUACCCUAGUUCGA-AUCGAGGUCUGUAACUCGGCCUCGUGAAGGCGGAAUCCGUAGUAACCGCGUUUCAACAAAGCGCGGUGAAUACUUUCCUGCUCAUUGCACACACUGCCCGUC-AAACCAAACAAGUUGGAUUUAGAUGAGAUUGUCGUU---------------A---------UGCGAUAACC-GAAUCUAGGUUCAGUGA----GUAGGGUUAAGUCGCCACAA------G--GUAGCCGUAUGGG----------AACAUGCGGCU-GGAUCACCUCCU
HE582783.1/1-1484                    UUUCCGGUUGAUCCUGCCGGAAGAUACUGCUAUUGGGAUUCGAUUAAGCCAUGCAAGUU-GAAUG--------AAU---UU--------AU----AUU--------CAU--GGCGUACGGCUCAG-UAACACGUGGAUAACUUACCCUUAGGACUGGAAUAACUC--U-G-GGAAACUGGAGA-UAAUACCGGAUAUUAAGCUAUG-CCUGGAAU---GGUUUGCUUAUGAAAAGUU-----------C-UUCUA-------------AGUUCGCCUAAGGAUAGAUCUGCGGCUGAUUA-GGUCGUUGGUGGGGUAAAGGCCCACCAAGCCGAUGAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGAUGGAACCUGAGACAAGGUUCCAGACCCUACG-GGGUGCAGCAGGCGCGAAACCUCCACAAUGUACGAAAGUGCGAUGGGGGGAUCCC-AA-GUGCUAUUCU---AU-A-A----AGAAUAGCUUUUAAUUAGUGU--AAAAAGCUUUUAG-AAU-AAGAGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCUCAAGUGGUAUCUGUUUUUAUUGGGCCUAAAGCGUUCGUAGCCGGUUUAAUAA-GUCUUUGGUGAAAGCUUGUAGCUUAACUA-UAAGAAUUGCUGGAGAUACUAU-UA--GACUUGAA-GUCGGGAGAGGUU-AGAGGUACUACCGGGGUAGGGGUGAAAUCCUAUAAUCCUGGGAGGACCACCUGUGGCGAAGGCGUCUAACUAGAACGAUCUUGACGGUGAGUAACGAAAGCCAGGGGCGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACGAUGUGGACUUGGUGUUGGAAUGGC-UU-C-GAGUUGUUCCAGUGCCGAAGGGAAGCUGUUAAGUCCACCGCCUGGGAAGUACGGUCGCAA-------------------------------------GACUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGCGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGACAYCU-CACCAGGAGCGACAGC--AGAAUGAUAAUCAGGUUGAUGACCU-UAUU-UGA----CUAGCUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCAC--GCCC-UUAGUUACCAGC-AURAUC--UCCG-GAUCGUAU--G-GGCACACUAAGGGGACCGCCAGUGA-UAAACUGGAGGAAGGAGUGGACGACGGUAGGUCCG-UAUGCCCCGAAUCUCCUGGGCU-ACACGCGGGCUACAAUGGCUAUGGCAAUGGG-U-UUC-UACACUGAAA-AGU--GCUGGUAAUCUCCUAAA--CAUAGUCUUAGUUCGG-AUUGAGGGCUGUAACUCGCCCUCAUGAAGCURGAAUGCGUAGUAAUCGCAUGUCACAACCGYGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-ACACCACCCAAAAAGGGUUUGGAUGAGGCAGUAGUU------------GUCAA-------AUGCUAUUGUC-GAAUCUAGGUUUUUUGA----GGAGGGUGAAGUCGUAACAA------G--GUAGCCGUAKGGG----------AACCUGCGGCU-GGAUCACCUCCU
AE009439.1/518289-516776             ACUCCGGUUGAUCCUGCCGGAGGCCACCGCUAUCGGGGUCCGACUAAGCCAUGCAAGUC-GAGGG-------CCGCCCG--GC---AAU--GGGGGCGG-------CCC--GGCGGACGGCUCAG-UAACACGUGGGUAACCUACCCUCGGGACGGGGAUAACCC--C-GGCGAAAGUGGGGC-UAAUCCCCGAUAGGCGGGGCGG-CCUGGAAC---GGUCCUCCGCCGAAAGGGCCCGG----GCCC----AUGCCG-----CCCGGGUCCGCCCGAGGAUGGGCCUGCGGCCGAUUA-GGUAGUUGGCGGGGUAACGGCCCGCCAAGCCGAUAAUCGGUACGGGCGGUGAGAGCCG-GAGCCCGGAGACGGGGACUGAGACAAGGCCCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGCAACCGCGACGGGGGGACCCC-GA-GUGCCGUCGGG-G-C-A-AAGCCCCGGCGGCUGUACCGGGGUGU--AAAAAGCCCCGGGUAGA-AAGCGGCGGGCAAGA-CCGCUGCCAGC-CGCCGCGGUAAUAGCGGCGCCGCAAGUGGUGGCCGCUUUUAUUGGGCCUAAAGGGGCCGUAGCCGGUCCCGUGG-GUCCCCGCCGAAAGCCCGCGGCUUAACCG-CGGGAGUCGGCGGGGAAACUGC-GG--GACUUGGG-ACCGGGAGAGGCC-GGAGGUACCCCCGGGGUAGGGGUGAAAUCCUGUCAUCCCGGGGGGACCGCCAGUGGCGAAGGCGUCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAAGCCGGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCCGGCUGUAAACGAUGCGGACUAGGUGUUGGGGCGGC-CA-C-GAGCCGCCCCAGUGCCGUAGGGAAGCCGUUAAGUCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACCGGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGAAACCU-UACCGGGGGCGACAGC--AGGAUGAAGGCCAGGUUGACGACCU-UGCC-GGA----CGAGCUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGUAACGAGCGAGACCCCC--GCCC-GCAGUUGCCAGC-GGGCCC-CGUAAGGGGC-GCC--G-GGCACUCUGCGGGGAUCGCCGCCGU-UAAGGCGGAUGAAAGUGGGGGCGACGGCAGGUCCG-UAUGCCCCGAAACCCCCGGGCU-ACACGCGGGCUACAAUGGCGGGGACAAUGGG-A-UCC-GACCCCGAAA-GGG--GGAGGAAAUCCCCUAAA--CCCCGUCGUAGUUCGG-AUUGCGGGCUGCAACUCGCCCGCAUGAAGGUGGAAUCGGUAGUAACCGUGCCUCAGAAUGGCACGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-ACGCCACCCGAGCCCCCCGGGGGCAAGCCCCCGGUC------------CGCAA-------GGGCUGGGGGC-GAGCCCCCGGGGGGUGA----GGGGGGCGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCA
FJ868733.1/1-1464                    -UUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUU-GCACG--------AGU---UU--------AG----ACU--------CGU--AGCAUAUAGCUCAG-UAACACGUGGCCAAACUACCCUACAGACCGCGAUAACCU--C-G-GGAAACUGAGGC-CAAUAGCGGAUAUAACUCUCAU-GCUGGAGU---GCCGAGAGUUAGAAACGU-------------UCCG------------------GCGCUGUAGGAUGUGGCUGCGGCCGAUUA-GGUAGAUGGUGGGGUAACGGCCCACCAUGCCGAUAAUCGGUACAGGUUGUGAGAGCAA-GAGCCUGGAGACGGUAUCUGAGACAAGAUACCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAGGGGGACUCC-GA-GUGUGAGGGC---AU-A-UA---GCCCUCGCUUUUCUGCACCGU--AAGGUGGUGCAAG-AAU-AAGGACUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGUCCAAGUGAUGGCCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCUUGCUGUGUAA-GUCCAUUGGGAAAUCGACCAGCUCAACUG-GUCGACGUCCGGUGGAAACUAC-AC--AGCUUGGG-GCCGAGAGACUCA-ACGGGUACGUCCGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCACCAAUGGGGAAACCACGUUGAGAGACCGGACCCGACAGUGAGGGACGAAAGCCAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACAAUGCUCGCUAGGUAUGUCACGCGC-CA-U-GAGCACGUGAUGUGCCGUAGUGAAGACGAUAAGCGAGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCGGUCCCGACAGU-AGUAAUGACAGUCAGGUUGACGACUU-UACU-CGA---CGCUACUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCAACCACUU-CUAGUUGCCAGC-AAACCC-CUGCG-GUGG--UU--G-GG-UCACUAGGAGGACUGC-AUUGC-UA-AAUGGAGGAAGGA-UGGGCAACGGUAGGUCAG-UAUGCU-CGAAUGGACCGGGCA-AC-CGCGGGCUACAAUGGCUAUGAAAGUGGG-A-C-C-CACGCCGAGA-GGC--GAA-CUUAUCUCC--AA--CGUAUUCGUAUUC-GG-AUUGCGG-CUGAACCCC---CCCGUAAAACUGGAUCGGAUUAUACCGGUU--GCAAAAC---GCCGGGAAAAC-UUCCUGCUUUU-G---ACACCGC-CGUAAAAACCCAGUGGG-----GUCCGGAGAGCCUUUACGGAGGGC---UCAAU----CU---GGCUCGAGGGGGU-UAUUCGUACAAGGACGGAGGAAUCGGGUGGAGUCGUAACAA------G--GUAGCCGUAGAGG----------AAUCUGCGGCU-GGAUCACCUCCU
JN120803.1/1-1473                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUC-GCACG--------GGC---UU--------AG----ACC--------CGU--GGCAUAUAGCUCAG-UAACACGUGGCCAAACUACCCUAUAGACCAUGAUAACCU--C-G-GGAAACUGAGGC-UAAUCGUGGAUAUCGCAUUCAC-GCUUGAAC--UGCCGAAUGCGAGAAACGU-------------UCCG------------------GCGCUAUAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCAGUAAUCGGUACGGGUGGUGACAGCCA-GAACCCGGAGACGGUAUCUGAGACAAGAUACCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAGGGGGACUCC-GA-GUGCGAGGGC---AU-A-UA---GCCCUCGCUUUUUUCGACCCU--AAGGUGGUCGACG-AAU-AAGGACUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGUCCGAGUGAUGGCCGCUGUUAUUGGGCCUAAAGCGUCCGUAGCUUGUCGUGAAA-GUCUAUCGGGAAAUCGACGCGCUCAACGC-GUCGGCUUCCGGUGGAAACUGC-AC--GGCUUGGG-GCCGGAAGACUCA-GCGGGUACGUCUGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCACCAAUGGCGAAAGCACGCUGAGAAGCCGGACCCGACAGUGAGGGACGAAAGCCAGGGUCCCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACGAUGCUCGUUAGGUCUGCCGUGCAC-UA-C-GAGUGCACGGUGAGCCGAAGUGAAGACGAUAAACGAGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGUCCCGACAGU-AAUAACGACGGUCAGCUUGACGAGCU-UACC-CGA----GUUACUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCAUCCUGUUAAGUCAGGUAACGAGCGAGACCCGC--AUCU-GUAGUUGCCAGC-GAUACC--CUUGUGGUA-GUC--G-GGUACACUACAGAGACCGCCGACGC-UAAGUCGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGGACCGGGCA-ACACGCGGGCUACAAUGGUCGAGACAAUGGG-U-UGC-GAUACCGAGA-GGU--AGAGCUAAUCUCCCAAA--CUCGAUCGUAGUUCGG-AUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGAAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCCAUC----------------AUGC-----------GAUGGUC-AAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGAGG----------AAUCUGCGGCU-GGAUCACCUCCU
HE574568.1/7093-8592                 AUUCCGGUUGAUCCUGCCGGACCCGACUGCUAUCGGGGUGAGACUAAGCCAUGCGAGUC-GUGCG-------CCCU---CGGGU--AUGCG----AGGG-------CGC--GGCGCACGGCUCAG-UAACACGUAGCUAACCUACCCUGAGGAGGGGGAUACCCC--C-G-GGAAACUGGGGU-UAAUCCCCCAUAGGUCUGGAUA-CCUGGAAU---GGGUUCAGGCCAAAAUGGA------------UCUGCGCGCAUCCUGCACAGGUCCGCCUCAGGAUGGGGCUGCGGCCCAUCA-GGUAGUUGGCGGGGUAAAGGCCCACCAAGCCGAUAACGGGUGCGGGCUCUGGAAGGAG-GAGCCCGGAGAUGGGCACUGAGACAAGGGCCCAGGUCCUACG-GGGCGCAGCAGGCGCGAAACCUCCACAAUGCGGGAAACCGCGAUGGGGUUACCCC-GA-GUGUCGCCC----GC-U-GA----GGGCGACUUUUCUGGGGUCU--AAAAAGCCCCAGG-AAU-AAGGGGAGGGCAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCUCCCCGAGUGGUCGGGACGUUUAUUGGGCCUAAAGCGCCCGUAGCCGGCCCGGUGU-GUCUCCCGUCAAAUCCGCCGGCUCAACCG-GCGGAC-CGCGGGGGAUACUAU-CG--GGCUAGGG-GGCGGGAGAGGUC-GGGGGUACUCCCGGGGUAGGGGUAAAAUCCUCUGAUCCCGGGAAGACCACCGGUGGCGAAGGCGUCCGGCCAGAACGCGCCCGACGGUGAGGGGCGAAAGCUGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCGGGCUAGGUGCUGGAGGGGC-UA-C-GGGCCCCUCCAGUGCCGCAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGGGCAC-ACAAGGGGUGAA-GCCUGCGGUUCAAUUGGAGUCAACGCCCGGAACCU-UACCAGGGGUGACAGC--AGAAUGACGGUCAGGUUAAAGACCU-UACC-UGA----CGCGCUGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------GGCUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGAAACGAGCGAGAUCCCC--ACCA-CCAGUUGCCAUU-CCGUCCCCUCUAGGGAU--GG--AAGGCGAACUGGUGGGACUGCCGCCGA-CAAGGCGGAGGAAGGAGGGGGCUACGGCAGGUCAG-UAUGCCCCGAAACCCCUGGGCU-ACACGCGGGCUGCAAUGGUGGGGACAAUGGG-A-GCC-GAACCCGAAA-GGG--GGAGGUAAUCCUC-AAA--CCCCACCCCAGUUAUG-AUUGAGGGUUGCAACUCACCCUCAUGAAUCUGGAAUCCCUAGUAACCGCGCGUCACCAUCGCGCGGUGAAUACGUCCCUGCCUCUUGCACACACCGCCCGUC-GCUCCAUCCGAGUUCGUCUCCAGUGAGGUGGCGUCU-------------CGU---------UGGCGCCAUC-GAACUGGAGGCGGGCAA----GGAGGGAGAAGUCGUAACAA------G--GUGGCCGUACCGG----------AAGGUGCGGCC-GGAUCACCUCCU
AEIY01000173.1/3517-2038             AUUCUGGUUGAUCCUGCCAGAGACUACCGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUC-CACCG-------AGUC---UU---------U----GACU-------UGG--GGCAUAUAGCUGAG-UAACACGUGGCUAACCUGCCCUGUGGAUGGGUAUAACCU--C-G-CUAACGUGAGGC-UAAUACCCAAUAUCAGAUGAG--GAUGGAAGUAAUCUUCAUCUGUGAAACGU-------------UCUG------------------ACGCCACAGGAUGGGGCCGCGGCUGAUUA-GGUUGUUGGUGAGGUAACGGCUCACCAAGCCGAUAAUCAGUAGCAGGGGUGAGAGCCC-GAGCUGUCAGUCGGCAUCUGAGACAAGAUGCCGGACCCUACG-GGGUGCAGCAGGCACGAAACCUUCACAAUGCACGCAAGUGCGAUGGGGGGACUCC-GA-GUGCAGUCUUC-CAA-A-A-CGGAAGGCCGCUUUUCUGCACUUU--AAGCAGGUGCCGA-AAC-AAGGGGUGGGCAAGA-CGGCUGCCAGC-CGCCGCGGUAAUAGCCGCACCCCGAGUGGUAGUCAUUGUUAUUGGGCUUAAAGUGUUCGUAGCCGGACACACAA-GUCUGCUGUGAAAUCCAUGCGCUUAACGU-AUGGACAUGCAGCGGAUACUGC-GU--GUCUAGGA-ACCGGACGGCGUC-GAGGCUAUUCCCGGGGUAGGGGUGAAAUCCUAAAAUCCUGGGAGGAGCACCUGUGGCGAAAGCGCUCGACGAGUACGGAUUCGACGGUGAGGAACGAAAGCCAGUGGAGCAAAACGGAUUAGAUACCCGUGUAGUACUGGCUGUAAACAUUGUGCGUUUGAUGUCGGACAACC-UC-C-GAGGUUGUCCGGUGCCGAAGUGAAAACGUUAAACGCACCGCCUGGGGAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGACGGGGGAGCACCACAACCGGUGGA-GGCUGCGGUUUAAUUAGAUCAAACGCAGAGCACUC-UACCAGAGCCGACAGC--AGAAUGAAGGUCAGCUUGAAGAGCU-UACC-UGA----CGCGCUGAGAGGAGCUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGUGUCCGGUUAAGUCCGGUAACGAGCGAGACCCGC--AUCA-CAUGUUGCCAUG-GAUCCC--UUCG-GGGA--UU--C-GGCACUCGUGUGAGACCGCUGGCGA-UAAGCCAGAGGAAGGUGCGGGCCACGGUAGGUCAG-UAUGGCCCGAAUGCUCUGGGAU-ACACGCGGCCUACAAUGGCCGGGACAAAGAG-A-UGC-AACUCCGAGAUGGA--GAAGCUAAUCUCCUAAA--CCCGGUCGUAGUACGG-AUCGAGCCCUGCAACCCGGGCUCGUGAAGGCGAAAUCGGUAGUAGUCGCUGAUCAUCAUUCAGCGGCGAAUAAGUCCCUGCUCCUUGUACACACUGCCUGUC-AAGUCACCCGAGUCAGGUUCAGACGAGGAUCGCUCU--------------U----------UGAGUGAGAC-AAGUCUGAGCUUGGCAA----GGGGGGCUAAGUCAUAACAA------G--GUAGCCGCUGGGG----------AACCAACGGCU-GGAUCACCUCCA
CP000559.1/403630-405096             AUUCUGGUUGAUCCUGCCAGAGGCCAUUGCUAUCAGGGUUUGACUAAGCCAUGCGAGUC-GAGAG-------GUGU--------------A----AGAC-------CUC--GGCAUACUGCUCAG-UAACACGUGGUUAACCUGCCCUAAGGUGGAGAAUACUCC--C-G-GGAAACUGGGGC-UAAUGCUCCAUAGUGGAUAUGU-CCUGGAAU---GGUAUAUCCUCGAAA-GA-------------UCCG------------------UCGCCUUAGGAUGGGACUGCGUCCGAUUA-GGUUGUUGGCGGGGUAACGGCCCACCAAGCCUUUUAUCGGUACGGGUUGUGGGAGCAA-GAUCCCGGAGAUGGAUUCUGAGACAUGAAUCCAGGCCCUACG-GGGCGCAGCAGGCGCGCAAACUUUACAAUGCGAGCAAUCGUGAUAAGGAAACCCU-GA-GUGCCUGU------C-G-AU-----GCAGGCUGUUCAUAUAUCU--AAAUCAUAUGUGA-AGA-AAGGGCAGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCUGCUCGAGUGAUGGCCACUAUUACUGGGUUUAAAGCGUCCGUAGCUUGACUGUUAG-GUCUCUUGGGAAAUCUUCGCGCUCAACGU-GAAGGCGUCUAAGAGAUACCGG-CA--GUCUUGGA-ACUGGGAGAGGUA-AACCGUACUUCGGGGGUAGGAGUGAAAUCUUGUAAUCCUCGAGGGACGACCUAUGGCGAAGGCAGUUUACCAGAACAGCUUCGACAGUGAGGGACGAAAGCUGGGGGAGCAAACGGGAUUAGAUACCCCGGUAGUCCCAGCCGUAAACAAUGUGCGUUAGGUGUGUCGGUAAC-CA-C-GUGUUACUGAUGCGCCGAAGAGAAAUCGUGAAACGCACCACCUGGGAAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACAGGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGACAUCU-CACCGGAUAAGACAGC--UGAAUGAUUGUCAAUCUGAAGGUUU-UACA-UGA----CUAGCUGAGAGGAGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACUGUGAAGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCAC--GCCG-ACAAUUGCCAGC-AGCAUC--UCCG-GAUG-GCU--G-GGGACAUUGUCGGGACCGCCUCUGC-UAAAGGGGAGGAAGGAAUGGGCAACGGUAGGUCAG-CAUGCCCCGAAUUAUCCGGGCU-ACACGCGGGCUACAAUGGACGGGACAAUGGG-U-AAC-AACACCGAAA-GGU--GCAGUCAAUCUCCGAAC--CCCGCCCUUAGUUAGG-AUUGCGGGUUGCAACUCACCCGCAUGAAUCUGGAAUCUGUAGUAAUCGCGUUUCACUAUAGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAACCAUCCUAGUGGGGUUUGGAUGAGUCCCUGGUC-------------UU-U---------GCCGGGGUC-GAAUCUAGGUUCCGUGA----GGAGGGUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
EU686620.1/7971-9471                 AAUCCGGUUGAUCCUGCCGGACCCGACUGCUAUCGGAUAGAGAUUAAGCCAUGCUAGUU-GAACA-------UUUC---UUAAC-UAUG--U-GAGAAG-------UGU--AGCGUACUGCUCAG-UAACACGUGGUCAACCUGCCCUAGAGACGUGUAUAACCC--C-G-GGAAACUGGGAC-UAAUACGCGAUAAGUCAUAUUU-UCUGGAAU---GGUUUAUGAUAUAAAGGAUU---------UU---UCAAACAUG-UUUGAUUUAUUGCUUUAGGAUGGGACUGCGGCCGAUCA-GGUUGUUGGUGGGGUAAUGGCCCACCAAGCCUAUUACCGGUGCGGGCUUUGAGAGAAG-GAGCCUGGAGAUGGACACUGAGAAAAGGGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUUCGCAAUGUGCGAAAGCACGACGAGGUUAAUCC-GA-GUGCAACAU----GC-U-GA----AUGUAGCUUUUGAUAAGUGU--AAGUAGUUUAUUG-AAU-AAGGGGAGGGAAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCUCCCCGAGUGGUCGGGACGAUUAUUGGGCCUAAAGCAUCCGUAGCCUGUUCUGUAG-GUCUUAUGUUAAAACCAAUUGCUUAACAA-UUGGAC-UGCAUGAGAUACCAC-AA--AACUAGGA-GGCGGGAGAGGUG-GACGGUACUCCACGGGUAGUGGUAAAAUGCUCUGAUCCGUGGAAGACCACCAGUGGCGAAGGCGGUCCACCAGAACGCGCUCGACGGUGAGGGAUGAAAGCUGGGGUAGCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCAAGCUAGGUGAUGGAUUAGC-CA-C-GUGUUAAUCCAGUGCCGCAGGGAAGCCGUUAAGCUUGCCGCCUGGGGAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAA-GCCUGCGGUUCAAUUGGAGUCAACGCCGGGAACCU-UACCAGGAGAGACAGC--AGGGUGAAGGUCAAGCUGAAGACUU-UACC-AGA----CAAGCUGAGAGGAGGCGCAUGGCCGUCGAC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCUU--GCCA-UUAAUUGCUUCCAUCGAUC--GCAA-GGUU--GGCGG-AGCUAGUUAAUGGGACUGCCGUCGC-UAAGACGGAGGAAGGAAGGGGCCACGGCAGGUCAG-UAUGCCCCGAAACUCUUGGGCC-ACACGCGGGCUGCAAUGGUAGGCACAAUAGG-U-ACC-GAAUUCGAAA-GAA--UGAGGCAAUCCC-AAAA--UCCUACCCCAGUUGUG-AUUGAGGGCUGCAACUCGCCCUCAUGAAUCUGGAAUCCCUAGUAACCGCGUGUCAACAUCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GCUUCACCCGAGUUGGGUUUGGGGGAGGUAGUAUCU-------------UAU---------UGGUAUUAUC-GAACCUAGGUUCGACAA----GGGGGGAGAAGUCGUAACAA------G--GUGGCCGUAGGGG----------AACCUGCGGCC-GGAUCACCUCCU
EU155918.1/1-1467                    --UCCGUUUGAUCCUGGCAGAGGCUACUGCUAUCGGGGUCCGACUAAGCCAUGCGAGUU-GAGAG-------GGGU----A--------A------GCC-------CUC--GGCGAAUUGCUCAG-UAACACGCGGACAACCUGCCCUUGGGUCCGGGAUAACCC--C-G-GGAAACUGGGAC-UAAUACCGGAUAGAUCAAGGAU-ACUGGAAU---GUUCCCCGGUCUAAA-AC-------------UCCG------------------GUGCCCAAGGAUGGGUCUGCGGCCUAUCA-GGUAGUAGUGGGUGUAACGUACCUACUAGCCUACGACGGGUAAGGGUUGUGAGAGCAA-GAGCCCUGAGAUGGAUUCUGAGACAUGAAUCCAGGCCCUACG-GGGUGCAGCAGGCGCGAAAACUUUACACUGCGGGAAACCGCGAUAAGGGGACCCC-GA-GUGCCAGCAC------C-UA---GUGCUGGCUGUCCCGCUGUCU--AAACAACAGUGGU-UAGCAAGGGCCGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCGGCCCGAGUGGUAGCCGUUAUUAUUGGGUUUAAAGGGUCCGUAGCCGGCCUGUUAA-GUCUCUUGGGAAAUCUGGCGACUUAAUCG-UCAGGCGUCCAAGAGAUACUGA-CA--GGCUUGGG-ACCGGGAGAGGUG-GGAGGUACUCCAGGGGUAGGGGUGAAAUCUCGUAAUCCUUGGGGGACCACCGAUGGCGAAGGCAUCCCACCAGAACGGGUCCGACGGUGAGGGACGAAAGCUGGGGGCACGAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCUCGCUAGGUGUCAGGUGCGG-UG-C-GACCGCAUCUGGUGCCGCAGUGAAAACUUGAAGCGAGUCACCUGGGAAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACGGGUGGA-GCCUGCGGUUCAAUUGGAUUCAACGCCGGAAAGCU-UACCGGGUCAGACAGC--AAUAUGAAGGUCAAGCUAAAGACUU-UACC-GAA----UUCGCUGAGAGGAGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUAUCGUGAGACAUCCUGUUAAGUCAGGCAACGAGCAAGACCCGU--GCCU-ACAGUUGCCAGC-AUACCC--UCCG-GGGU-GAU--G-GGCACACUGUGGGGACCGCCGCUGC-UAAAGCGGAGGAAGGAGCGGGCUACGGUAGGUCAG-UAUGCCCCGAAUCAUCCGGGCU-ACACGCGGGCUACAAUGGUUGGGACAAUGGG-C-ACC-UACACCGAGA-GGU--GAUGGUAAUCUCCUAAA--CCCAGCCUUAGUUCGG-AUUGAGGGCUGCAACUCGCCCUCAUGAAGCCGGAAUCCGUAGUAAUCGCGUAUCAACAUCACGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAACCAUGCGAGUGAGGUCUGAAUGAGGGCUUGCU---------------UU----------AACAAGUUC-GAAUUUAGGCUUCGCGA----GUGGGGUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
ACXL01000009.1/96377-97845           AUUCCGGUUGAUCCUGCCGGCGGCCACUGCUAUCAGGUUUCGGCUAAGCCAUGCGAGUC-UAGGG--------AUC---GC--------AA----GAU--------ACC--GGCAUACUGCUCAG-UAACACGCGGAUAAUCUGCCCCCAGGUGAAGAAUACCCU--C-G-GGAAACUGAGGC-UAAUACUUCAUAAUCACUAUAU-GCUGGAAU---GCUUUGGUGAUGAAA-GA--------------AUU------------------UCGCCUGAGGAUGAGUCUGCGGCCUAUCA-GGUCGUAUGUGGUGUAAUGGACCACAUAGCCUAAGACGGGUACGGGCCUUGAAAGAGG-GAGCCCGGAGAUGGACUCUGAGACAUUAGUCCAGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUGUGCAAUGCGCGAAAGCGCGACACGGGAAGCCU-GA-GUGCCUUAAC------A-CA---GUUAAGGCUUUUCUCAAGCCU--AAAAAGCUUGAGG-AAU-AAGAGCUGGGUAAGA-CGGGUGCCAGC-CGCCGCGGUAACACCCGCAGCUCGAGUGGUGGUCACUUUUAUUGAGCCUAAAGCGUUUGUAGCCGGAUCCGUAA-AUCUCCAGGAAAAUUCCUUCGCUCAACGA-AGGACC-UUCUGGAGAGACUGC-GG--AUCUAGGG-ACCGGGUGAGGUU-GAAUGUACUUCUGGGGUAGGGGUAAAAUCCUGUAAUCCUGGAAGGACGACCGGUGGCGAAGGCGUUCAACUAGAACGGAUCCGACGGUGAGGAACGAGGGCUAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACACUGCCCACUUGAUGUUGCAUCUCC-GU-G-UAGGGGGUGCAGUGUCGUAGCGAAGGUGUUAAGUGGGCCGCUUGGGGAGUAUGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGGGAGGA-GCGUGCGGUUUAAUUGGAUUCAACGCCGGAAAGCU-CACCAGGAGCGACCUU--UGAAUGAGAGUCAACUUGACGAGCU-UACU-CGA----UAGAAGGAGAGGUGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUAGGGCGUUCACUUAAGUGUGAUAACGAGCGAGACCCCC--AUCU-UUAAUUGCCAUC-AUGUUC--GAGA-GAAU--GU--G-GGCACUUUAAGGGGACCGCCAGCGC-AGAGCUGGAGGAAGGAGGGGUCGACGGCAGGUCAG-UACGCCCCGAAUCUCCUGGGCA-ACACGCGCGCUACAAAGGACAGGACAAUGGG-C-UGC-GACCUCGAAA-GGG--GAAGCUAAUCUCG-AAA--CCUGUUCGUAGUUAGG-AUUGAGGGCUGUAACUCGCCCUCAUGAAUCUGGAUUCCGUAGUAAUCGCGGGUCAACAUCCCGCGGUGAAUAUGUCCCUGCUCCUUGCACACACCGCCCGUC-AAACCAUCCGAGCUGGUGUUGGAUGAGGCUUUGCUC-------------AUAU--------GGGCAGAUUC-GAAUCUGGUGUCAGUGA----GGAGGGUUAAGUCGUAACAA------G--GUAUCCGUAGGGG----------AACCUGCGGAU-GGAUCACCUCCA
CR937012.1/17145-18616               AUUCUGGUUGAUCCUGCCAGAGGCUACUGCUAUCGGGGUUCGAUUAAGCCAUGCGAGUU-AAAUG-------UUCU---U---------CG----UGAA-------CAU--AGCGAACUGCUCAG-UAACACGUGGAUAACCUACCCUUAGGACCGGAAUAACCC--C-G-GGAAACUGGGGA-UAAUACCGGAUAAGCCAUAGAC-GCUGGAAU---GCCCUAUGGUUCAAA-GC-------------UCCG------------------GCGCCUAAGGAUGGAUCUGCGGUCUAUCA-GGUUGUAGUGGGUGUAACGUACCUACUAGCCGACGACGGAUACGGGUUGUGAGAGCAA-GAGCCCGGAGAUGGAUUCUGAGACACGAAUCCAGGCCCUACG-GGGUGCAGCAGGCGCGAACACUUUACAAUGCGGGAAACCGCGAUAAGGGAACCCC-GA-GUGCCAGCAU----C---AA---AUGUUGGCUGUCCAGAUGAUU--AAAAAUCAUUUGU-UAGCAAGGGCCGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCGGCCCGAGUGGUAGCCGUUUUUAUUGGGUCUAAAGGGUCCGUAGCCGGCCUGAUAA-GUCCUUUGGGAAAUCUGGCAGCUUAACUG-UCAGGCUUCUAAGGGAUACUGU-CA--GGCUUGGG-ACCGGAAGAGGUA-AGGGGUACUCCAGGGGUAGGAGUGAAAUCUUGUAAUCCCUGGGGGACCAUCUGUGGCGAAGGCGCCUUACCAGAACGGGUCCGACGGUGAGGGACGAAAGCUAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCUCGCUAGGUGUCAGACACGG-UG-C-GACCGUGUUUGGUGCCGCAGGGAAGCCGUUAAGCGAGCCACCUGGGAAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACGGGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGAAAACU-CACCGGGUGCGACAGC--AAUAUGUAGGUCAGGCUGAAGGUCU-UACC-UGA----AUCGCUGAGAGGAGGUGCAUGGCCGUCGUC--------------------------------------------------------------------------------------------------------------------------AGUUCGUACUGUGAAGCAUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--GCCC-ACAGUUGCCAGC-AUGUUC--UCCG-GAAC-GAU--G-GGUACACUGUGGGGACCGCCGCUGC-UAAAGCGGAGGAAGGAACGGGCUACGGUAGGUCAG-UAUGCCCCGAAUCUCCCGGGCU-ACACGCGGGCUACAAUGGUUGGGACAAUGGG-C-ACC-UACCCUGAAA-AGG--GACGGUAAUCUCCUAAA--CCCAACCGUAGUUCGG-AUUGAGGGCUGUAACUCGCCCUCAUGAAGCUGGAAUCCGUAGUAAUCGCGUUUCAACAUAGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAACCAUGCGAGUGAGGUCUGGGUGAGGGCAUGUUU---------------A---------UGACAUGUUC-GAACCUGGGCUUCGCAA----GUGGGGUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
DQ078753.1/38568-37097               ACUCCAGUUGAUGGUGCUGGAGGACGCUGCUAUCGGGGUUCGCCUAAGCCAUGCAAGUC-A-GGG-------CAGC---U---------AG----UCUG-------CCC--GGCGAACGGCUCAG-UAACACGUGGGCAACCUACCCUGGAGUGGGGGAUAACCU--C-G-GGAAACUGAGAG-UAAUACCCCAUAGGGGAGAGGU-ACUGGAAG---GUCCUCUCCCUGAAA-GCC------------UUCG-----------------GGCGCUCCAGGAUGGGCCUGCGGCGGAUUA-GGUAGUUGGUGGGGUAACGGCCCACCAAGCCUAAGAUCCGUACCGGCUGUGGGAGCAG-GAGCCGGGAGAAGGGGACUGAGACAAGGCCCCUAGCCCUACG-GGGUGCAGCAGGCGCGAAACCUCUGCAAUGCCCGAAAGGGUGACAGGGGGACCCC-GA-GUGGUAGC------U-U-U------GCUACCUUUUCUGGAGUGC--AAAAAGCUCCAGG-AAU-AAGGGCUGGGCAAGA-CCCGUGCCAGC-CGCCGCGGUAAUACGGGCAGCCCGAGUGGCGUCCACGCAUACUGGGCCUAAAGCGUCCGUAGCCGGUCUAGGGGAGCUCCUGGUGAAAUCGGCAGGCUUAACCU-GUCGGCUGGCCAGGAGAACCAC-UA--GACUAGGG-ACCGGGAGAGGCC-GGAGGUAUUCCUGGGGUACCGGUAAAAUGGUAUAAUCCUAGGAGGACCUACGGUGGCGAAGGCGUCCGGCUAGAACGGGUCCGACGGUGAGGGACGAAGGCCAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAUGAUGCGGGCUUGGUGUUGCGUAACC-CA-C-GAGGUUGCGCAGUGCCGGAGGGAAGCCGUUAAGUCCGCCGCCUGGGGAGUACGCCCGCAA-------------------------------------GGGUUAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAACCAAUUGGCGGGGGAGUACUACAAGGGGUGGA-GGCUGCGGUUCAAUCGGACGCAACGCCGAGAAUGU-UACCGGGGGCGACAGC--AGGAUGAAGGUCCGUCUGAAGGGCG-UACC-AGA----CACGCUGAGAGGUGGUGCAUGGCCACCAUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGUGAGGUGUCCACUUAAGUGUGGCAACGAGCGAGACCCGU--GCCU-CUAGUUGCGACC-UAGAUU-CUCCGGGAUC--UA--G-GGCACUCUAGAGGGACUGCCGGCGA-UAAGUCGGAGGAAGGAGCGGGCGAUGGUAGGUCUG-UAUGCCCCGAAUCUCCCGGGCU-ACACGCGGCCUACAAUGGUCGGGACAACGGG-A-CGC-GACCCCGAAA-GGG--GAAGCUAAUCCCUUAAA--CCCGGCCCCAGUUCGG-AUUGAGGGUUGAAACUCACCCUCAUGAAGCUGGAAUCCCUAGUAAUCGCGGGUCACCAUCCCGCGGUGAAUACGUCCCUACUCCUUGUACACACCGCCCGUC-AAGCCACCCGAGUGGGGUCUAGAUGAGGCGAGGUCC-------------UAU---------GGGCCUUGAC-GAAUCUGGGCUCUGUGA----GGGGGGCUAAGUCGUAACAA------G--GUAUCCGUAGGGG----------AACCUACGGAU-AGAUCACCUCCU
GQ282618.1/1-1471                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUC-GCACG--------GGU---UC--------AG----ACC--------CGU--GGCAGAUAGCUCAG-UAACACGUGGCCAAACUACCCUAUGGAUCGAGACAACCU--C-G-GGAAACUGAGGC-UAAUCUCGAAUACGGUUUCCAC-UCUGGAGU---GAGGGAAACUAGAAACGC-------------CCCG------------------GCGCCAUAGGAUGUGGCUGCGGCCGAUUA-GGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUUUACACUGCACGACAGUGCGAUAAGGGGACUCC-GA-GUGCGAGGGC---AU-A-UA---GUCCUCGCUUUUGUACACCGU--AGGGAGGUGUACG-AAU-AAGGGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCCCGAGUGAUGGCCGCUAUUAUUGGGCCUAAAGCGUCCGUAGCCAGCCAGACAG-GUCCGUCGGGAAAUCCAGUCGCUCAACGA-CUGGGCGUCCGGCGGAAACCAG-CU--GGCUUGGG-GCCGGAAGAUCCG-AGGGAUACGUCCGGGGUAGGAGUGAAAUCCAGUAAUCCUGGACGGACCACCGGUGGCGAAAGCGCCUCGGAAAGACGGACCCGACGGUGAGGGACGAAAGCUAGGGUCACGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCUCGCUAAGUAUGGCACACAC-UA-C-GAGUGUGUGCUGUGCUGUAGUGAAGACGAGAAGCGAGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCAGCUCCGACAGU-AGGAGUGACGGUCAGUGUGAUGAGCU-UACC-AGA----CCUACUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACUC-CUAAUUGCCAGC-AAUACC--CUCGUGGUA-GUU--G-GGUACAUUAGGAGGACCGCCACGGC-UAACGUGGAGGAAGGAACGGGCAACGGUAGGUCAG-CAUGCCCCGAAUGAGCUGGGCU-ACACGCGGGCUACAAUGGCCAGGACAACGGG-U-UCC-AACCGCGAAA-GCG--GACGGUAAUCUCUGAAA--CCUGGUCGUAGUUCGG-AUUGAGGGCUGAAAUUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGCUUCAGAAGAGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCCGCC-----------------UAC-----------GGCGGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
EU559699.1/4667-6161                 ACUCCGGUUGAUCCUGCCGGACCCCACUGCUAUCGGGAUAGGACUAAGACAUGCUAGUC-AAGCG-------CUCU---CCAGC--CAA--A-GGAGAG-------UGC--GGCGCACAGCUCAG-UAACACGUGGCUAACCUGCCCUUGGGAUAGGGACAACCC--C-G-GGAAACUGGGGC-UAAUCCCCAAUAGGUGAAGUGC-UCUGGAAU---GAGCCUUCGCCCGAAAGGAUGC------UUG----CGCUAUGC-UCGCAAGCUUCGCCCGAGGAUGGGGCCGCGACCGAUCA-GGUUGUUGGUGAGGUAAUGGCUCACCAAGCCUUUAACCGGUGCGGGCCGUGGGAGCGG-GAGCCCGGAGAUGGGCACUGAGACAAGGGCCCAGGCCCUACG-GGGCGCAGCAGUCGCGCAAACUUUGCAAUACACGAAAGUGUGACAGGGCUAUCCC-GA-GUGCCGUCC----GC-U-GA----GGAUGGCUUUUACCCAGUCU--AGAACGCUGGGGG-AAU-AAGGAGAGGGCAAGU-CUGGUGUCAGC-CGCCGCGGUAAUACCAGCUCUCCGAGUGGUGUGGAUGUUUAUUGGGCCUAAAGCAUCCGUAGCUGGCCAGGUUA-GUCCCCUGUUAAACCCACCGAAUUAAUCG-UUGGAU-UGCGGGGGAUACUGC-CA--GGCUAGGG-GACGAGAGAGGCA-GACGGUAUUUUCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGAAGACCACCAGUGGCGAAGGCUGUCUGCUAGAACGCGCCCGACGGUGAGGGAUGAAAGCUGGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCCAGCUGUAAACGAUGCAGGCUAGGUGUUUGGGCGGC-CA-C-GUGCCGCUCUAGUGCCGCAGGGAAGCUGUUAAGCCUGCCGCCUGGGGAGUACGGUCGCAA-------------------------------------GAUUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGAA-GCUUGCGGUUUAAUUGGAGUCAACGCCGGAAAUCU-CACCGGGAGCGACAGC--AGUUUGAAGGCCAGAUUAAAGGUCU-UGCC-AGA----CGAGCUGAGAGGAGGUGCAUGGCCGUCGCC--------------------------------------------------------------------------------------------------------------------------AGUUCGUGCCGUGAGGUGUCCUGUUAAGUCAGGCAACGAUCGAGACCCGC--GUCC-UCUGUUGCCACU-GGUU-----UUG---AG--CC--A-GGCACACUGAGGAGACCGCCGCUGA-UAAAGCGGAGGAAGGAGCGGGCCACGGCAGGUCAG-UAUGCCCCGAAUCUCCCGGGCC-ACACGCGAGCUGCAAUGGCAGGUACAAUGGG-U-UCC-GACCUCGAAA-GGG--GGAGGCAAUCUCG-AAA--GCCUGCCGUAGUUGGG-AUUGAGGGUUGAAACUCACCCUCAUGAACAUGGAAUCCCUAGUAAUCGCGUGUCACUAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-GUUCCACCCGAGCGACUCUUGGGUGAGGCGUGGUCU-------------UUAU--------UGGCUGCGUC-GAAUCUUAGUUUUGUAA----GGGGGGAAAAGUCGUAACAA------G--GUGGCCGUAGGGG----------AACCUGCGGCC-GGAUCACCUCCU
EF533954.1/1-1468                    --UCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUUGGGAUUCGAUUUAGCCAUGCUAGUC-GCACG--------AGU---UC--------AG----ACU--------CGU--GGCGAAUAGCUCAG-UAACACGUGGCCAAACUACCCUUCGGAGCUCCAUACCCU--C-G-GGAAACUGAGGC-UAAUAGAGCAUACCACAAUCCA-GCUGGAAU---GAGGAUUGUGCCAAACGC-------------CCCG------------------GCGCCAUAGGAUGUGGCUGCGGCCGAUUA-GGUAGAUGGUGGGGUAACGGCCCACCAUGCCAAUAAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGUAUCUGAGACAAGAUACCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACCUUUACACUGCACGACAGUGCGAUAAGGGGACUCC-GA-GUGCGAGGGC---AU-A-UA---GUCCUCGCUUUUCUGUACCGU--AGGGAGGUACAGG-AAC-AAGUGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCACGAGUGAUGGCCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCGUGCAA-GUCCGUUGGGAAAUCGACGCGCUCAACGC-GUCGGCGUCCAGCGGAAACUGU-UC--GGCUUGGG-GCCGGAAGACCUG-GGGGGUACGUCCGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCACCAAUGGCGAAAGCACCUCAGGAGGACGGACCCGACGGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCUCGCUAGGUGUGCCACAGGC-UA-C-GAGCCUGUGCUGCGCCCUAGGGAAGCCGAGAAGCGAGCCGCCUGGGAAGUACGUCUGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCGGUCCCGACAGU-AGUAACGACAGUCAGUUUGACGAACU-UACU-CGA----GCUACUGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--ACUU-CUAGUUGCCAGC-AAUACC--CUCGAGGUA-GUU--G-GGUACACUAGGAGGACUGCCGCUGC-UAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGGACCGGGCA-ACACGCGGGCUACAAUGGCUACGACAGUGGG-A-UGC-UACGCCGAGA-GGC--GACGCUAAUCUCU-AAA--CGUAGUCGUAGUUCGG-AUUGCGGGCUGAAACUCGCCCACAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCACAAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGAGGUCCGGAUGAGGCGCGU-----------------UCC-----------ACGCGUC-GAAUCUGGGCUUCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
HQ530525.1/1-1478                    AUUCCGGUUGAUUCUGCCGGAGGCUACUGCUCUGGGAGUCGGAUUAAGCCAUGCUAGCG-GAGGG-------CAGU---U---------CG----GCUG-------CCC--CGUGAAUAGCUCAG-UAACACGUGGUCAACCUACCCUUGGGAUCGGGAUAACCC--C-G-GGAAACUGGGGA-UAAUCCCGAAUAAGUGGGGGU--UCUGGAAA---GGUCCCUCGCUGAAAUGC-------------UCAG------------------GCGCCCAAGGAUGUGACUGCGGCCUAUUA-GGUAGUUGGCGAGGUAAUGGCUCACCAAGCCGAAGAUGGGUACGGGCCCUGAGAGGGG-GAGCCCGGAGAUGGAGACUGAGACAAGGCUCCAGGCCCUACG-GGGCGCAGCAGGUGCGAAAAUUCCGCAAUGCGUGCAAGCGCGACGGAGUGACUCC-CA-GUGCCGAUGGUCUAA-C---G-ACCGUCGGCUUU-UCGGAGCGU--AAAAAGCUUCGGGUAAU-AAGGGCCGGGUAAGA-CUGGUGCCAGC-CGCCGCGGUAACACCAGCGGCUCGAGUGGUAGCCGAUUUUAUUGGGCCUAAAGCGUCCGUAGCCGGACUGGCAA-GUCCCUUGUGAAAUCGGGCGGCUUAACCG-CUCGGCGUGCAGGGGAAACUGU-CA--GUCUUGGG-GUCGGCAGGCGCC-GAGGGUACUCCAGGGGUAGCGGUGAAAUGCUAUAAUCCCUGGGGGACCGCCAGUGGCGAAAGCGCUCGGCGGGGCCGAACCCGACGGUGAGGGACGAAAGCCAGAGGAGCGAACCGGAUUAGAUACCCGGGUAGUUCCGGCCGCAAAGAAUGUGGGCUAGGUGCUUGGUGUUC-CU-C-GAGAACACUAGGUGCCGAAGGGAAGCCGUUAAGCCCACCGCCUGGGAAUUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGAAAUUGGCGGGGGAGCACCACAAGGGGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGACAUCU-CACCGGGGGCGACGGC--AGAGUGAAGGCCAAGUCGACGACUU-UGCC-GGA----CUCGCCGAGAGGUGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUAUCGUGAGACGUCCUGUUAAGUCAGGCAACGAGCGAGACCCUU--CCCU-CUAGUUGCCAGC-GGAUUC-CACUG-GAAU-GCC--G-GGCACUCUAGAGGCACCGCUGCCGA-UAAGGCAGAGGAAGGAGAGGGCGACGGUAGGUCCG-UAUGCCCCGAAUCCCCCGGGCA-ACACGCGGGCUACAAUGCGUAGGACAGAGGG-C-UGC-GACCCCGAGA-GGG--GGAGCUAAUCCCU-AAA--CCUACGCCUAGUUCGG-AUCGAGGGCUGCAACCCGCCCUCGUGAAGCUGGAAUCCCUAGUAACUGUGUGUCACUAUCGCACGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAGCCAUCCGAGUGGGAUCUGGAUGAGGUCUGCUCG-------------AUU---------UGAGCAGGUC-AAAUCCGGGUUUCGCAA----GGAGGGCUAAGUCGUAACAA------G--GUAGCUGUAGGGG----------AAUCUGCGGCU-CGAUCACCUCCU
AEIX01000219.1/3680-2194             AUUCCGGUUGAUCCUGCCGGAGACUACCGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUC-CACCG-------AACC---UU---------U----GGUU-------CGG--GGCGGAAAGCUGAG-UAACACGUGGCCAACCUACCCUGUGGACAGGAAUAACCU--C-G-GGAAACUGAGGA-UAAUGCCUGAUAGCAGAACCAU-GCUGGAAA--CGCAGGUUCUGUGAAAUGA-------------CACG------------------UCGCCACAGGAUGGGGCCGCGGCUGAUUA-GGUUGUCGGUGAGGUAACGGCUCACCGAGCCCGUAAUCAGUAGCAGCCGUGGGAGCGG-UAGCUGCCAGUCGUGUUCUGAGACAAGAACACGGGCCCUACG-GGGCGCAGCAGGCACGAAACCUUUACAAUGCACGCGAGUGCGAUAGGGGGACUCC-GA-GUGCGUUCUUCCC-A-C-A-AGGAAGGACGCUUUUCUGCACUGU--AAGGAGGUGCAGG-AAC-AAGGGGUGGGCAAGA-CUGCUGCCAGC-CGCCGCGGUAAUAGCAGCACCCCGAGUGGUAGUCGUUAUUAUUGGGCUUAAAGUGUACGUAGCCGGACCUGUAA-GUCUGUUGUGAAAUCCACGCGCUUAACGCAGUGGAAGCGCAACGGAUACUAC-AG--GUCUAGGG-ACCGGAGGACGCC-GAGGCUAUUCCAUGGGUAGGAGUGAAAUCCUAAGAUCCAUGGAGGAGCACCAGUGGCGAAAGCGCUCGGCGACUACGGAUCCGACGGUGAGGUACGAAAGCCAGGGGAGCAAAACGGAUUAGAUACCCGUGUAGUCCUGGCCGUCAACAUUGUCCGCUCGACAUGGCCCAACC-UU-U-GUGGUUUGGCUGUGUCCAAGUGAAAACGUUAAGCGGACCGCCUGGGUAGUACGGUCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGACGGGGGAGCACCACAACCGGUGGG-GGCUGCGGUUUAAUUAGAUCAAACGCAGCGCACCC-UACCAGAGCCGACAGC--AGAAUGACGGUCAGCUUGAAGAGCU-UACC-CGA----CGCGCUGAGAGGAGCUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUGCCGCGAGGUGUCCGGUUAAGUCCGGUAACGAGCGAGACCCGU--ACCC-UAUGUUGCCACG-GAGACA--CUAGCUGUC--UU--C-GGCACUCGUGGGGGACCGCUGGCGA-UAAGCCAGAGGAAGGAGCGGGCCACGGUAGGUCAG-UAUGGCCCGAAUGCUCUGGGAU-ACACGCGGCCCACAAUGGCCGGUACAAACAG-A-AGC-CACCCCGAGA-GGG--GAAGCUAAUCUGCCAAA--ACCGGUCCCAGUCCGG-AUCGAGGCCUGCAACUCGGCCUCGUGAAGUCGAAAUCGGUAGUAGUCGCUGGUCAUCAUCUAGCGGCGAAUAAGUCCCUGCUCCUUGUACACACCGCCUGUC-AAGUCACCCAAGUCAGGUUCAGACGAGCCUCCCACC---------------U---------AGUGGGAAGC-AAGUCUGAGCUUGGCAA----GGGGGGCUAAGUCAUAGCAAACAGUU-GUGACCCCGAACCGG----------AAGGUUUGAGG-AAAAAUCUGGCU
M32222.1/1572-3051                   ACUCCGUUUGAUCCUGGCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCAAGUC-GAACG-------GGCC---UU--------G-----UGCC-------CGU--GGCGAACGGCUCAG-UAACACGUGGACAACCUACCCUGGGGUCCGGGAUAACCC--C-G-GGAAACUGGGGC-UAAUCCCGGAUAGGCGAGGUCU-CCUGGAAU---GGGGCCUCGCCGAAAGGUC------------UUUUG----------------ACCGCCCCAGGAUGGGUCUGCGGCCGAUUA-GGUAGUUGGUAGGGUAACGGCCUACCAAGCCUACGAUCGGUACGGGUUGUGAGAGCAA-GAGCCCGGAGACGGGGCCUGAGACAAGGCCCCGGGCCCUACG-GGGCGCAGCAGGCGCGAAAACUCCGCAAUGCGCGAAAGCGCGACGGGGGGACCCC-CA-GUGCCACUCC---GU-A-A----GGAGUGGCUUUUCCGGAGUGU--AAAAAGCUCCGGG-AAU-AAGGGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAACACCGGCAGCCCGAGUGGUGGCCGCGUUUAUUGGGCCUAAAGCGUCCGUAGCCGGUCCGGUAA-GUCUCCGGUGAAAGCCCGCAGCUCAACUG-CGGGAGUAGCCGGAGAUACUGC-CG--GACUUGGG-GCCGGGAGAGGCC-GGAGGUACCCCCGGGGUAGGGGUGAAAUCCUGUAAUCCCGGGGGGACCACCUGUGGCGAAGGCGUCCGGCUGGAACGGGCCCGACGGUGAGGGACGAAAGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCCGUAAACGAUGCGGACUUGGUGUUGGGGCAAC-CU-C-GAGUUGCCCCAGUGCCGAAGGGAAGCCGUUAAGUCCGCCGCCUGGGGAGUACGGCCGCAA-------------------------------------GGCUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACCACAACGCGUGGA-GCCUGCGGUUUAAUUGGAUUCAACGCCGGACACCU-CACCGGGGGCGACGGC--AGGAUGAUGGCCAGGUUGAUGACCU-UGCC-UGA----CGAGCCGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGC--GCCC-CUAGUUGCCAGC-GGGUCC-CGUAAGGGAC-GCC--G-GGCACACUAGGGGGACCGCCAGCGA-UAAGCUGGAGGAAGGUGCGGGCGACGGUAGGUCCG-UAUGCCCCGAAACCCCCGGGCU-ACACGCGGGCUACAAUGGCCGGGACAAUGGG-U-ACC-GACCCCGAAA-GGG--GGAGGUAAUCCCAUAAA--CCCGGCCGUAGUUCGG-AUCGAGGGCUGCAACUCGCCCUCGUGAAGCUGGAAUGCGUAGUAAUCGCGGGUCACUAUCCCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-ACGCCACCCAAACGGGGUUCGGAUGAGGCCAUGGCC-------------UCU---------GGCCAUGGUC-GAAUCCGGGCCCCGUGA----GGAGGGCGAAGUCGUAACAA------G--GUAGCCGUAGGGG----------AACCUGCGGCU-GGAUCACCUCCU
JF449412.1/5-1475                    AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUCUCGGGGUCCGCCUUAGCCAUGCUAGUC-GUACG--------GGC---UC--------GG----ACC--------CGU--GGCGAACAGCUCAG-UAACACGUGGCCAAACUACCCUCGAGACCGGGAUAACCU--C-G-GAAAACUGAGGC-UAAUCCCGGAUAGCGGUCCCAG-GCUGGAAU---GCGGGGAUCGCGAAAGGC-------------UCCG------------------GCGCUCGAGGACGUGGCUGCGGCCGAUUA-GGUAGACGGUGAGGUAACGGCUCACCGUGCCGAUAAUCGGUACGGGGCAUGAGAGUGC-GAGCGCGGAGACGGUGUCUGAGACAAGACACCGGGCCCUACG-GGGCGCAGCAGGCGCGAAACGUUUACACUGCGCGAGAGCGCGAUAACGGGACCCC-GA-GCGCGAGGGC---AU-A-UC---GCCCUCGCUUUUCCGGACCGU--AAUGUGGUCCGGG-AAC-AAGGGCUGGGCAAGA-CCGGUGCCAGC-CGCCGCGGUAAUACCGGCAGCCCGAGUGAUGGCCGCGAUUACUGGGCCUAAAGCGUCCGUAGCCGGCCGGGCAA-GUCCGUCGGGAAAUCCGCGCGCCCAACGC-GCGGGCGUCCGGCGGAAACUGC-UC--GGCUAGGG-ACCGGGAGACCUG-CGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCCGGACGGACCGCCGAUGGCGAAAGCACCGCAGGAGACCGGAUCCGACGGUGAGGGACGAAAGCCGGGGUCACGAACCGGAUUAGAUACCCGGGUAGUCCCGGCCGUAAACGAUGCCCGCUAGGUGUGGCGCGGGG-UA-C-GACCCCGCGCUAUGCCGCAGCGAAGGCGCUAAGCGGGCCGCCUGGGAAGUACGUCCGCAA-------------------------------------GGAUGAAA--------------------------------------------------------------------------------------------------------------------------------------------CUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGA-GCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCU-CACCGGCCCCGACUGC-AGUGGUGACGGCCAGGCUGAUGCCCU-UGCU-CGA----GCUGCAGAGAGGAGGUGCAUGGCCGCCGUC--------------------------------------------------------------------------------------------------------------------------AGCUCGUACCGUGAGGCAUCCUGUUAAGUCAGGUAACGAUCGAGACCCGU--GCAC-CUAGUUGCCAGC-GGUGUC-CACCG-GACA-GCC--G-GGUACACUAGGUGGACCGCCGGUGC-CAAACCGGAGGAAGGCGCGGGCAACGGUAGGUCAG-UAUGCCCCGAAUGGGCCGGGCG-ACACGCGGGCUACAAUGGCCGGGACAAUGGG-U-UCC-AACACCGAGA-GGU--GACGGUAAUCCCCGAAA--CCCGGUCGUAGUUCGG-AUUGCGGGCUGGAACUCGCCCGCAUGAAGCUGGAUUCGGUAGUAAUCGCGCCUCAGAAAGGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUC-AAAGCACCCGAGUGGGGUCCGAAUGAGGCCUGG-----------------UCA-----------CCAGGUC-GAAUCUGGGCUCCGCAA----GGGGGCUUAAGUCGUAACAA------G--GUAGGCGUAGGGG----------AAUCUGCGGCU-GGAUCACCUCCU
#=GC SS_cons                         :::<<<<<_______>>>>>,{{{{{{{{{{,{{{{{{{{{{-----{{{-{{{,,<<<.--<<<.......<<<<...__........__....>>>>.......>>>..>>>,,,,,,[[[,,.,,,,((((((((--((---(((((((,<<<<----<<<<..<.<.<____>>>>>>>.----->>>>,,,,<<<<<<<<-.<<______...>>>>>>>>>>,,,,,,<<.............____..................>>,)))))))--))))))))))<<<--<-.<<<--<<<<<<<<_______>>>>>>>>>>>----->>>>,,<<<<<<<<____>>>>.--->>>>]]],<<<<<<__________>>>>>>,<<<<____.>>>>,,,}}}}}}-},,,,,<-<<<---<<<<<____>>>>>->>>>,}}}}}}}.}}.,,<<<<<<<<...__._.__...>>>>>>>>,,,<<<<<<<<__.._____>>>>>>>-.-->.,,<<<<<<-------.<<<<-----<<.____>>------->>>>>>>>>>,}}}}}}}}}},,,,,,,,,,{{{-----{,[[[[-[-[[[,<<<<<<<-<.<<<<<<<<<<----<<<<<<<_____>>>.>>>>--->>>>>>>>>-->>>>.>>..>>>,,,((.(((((((--((((.(((<<--<<<<<<<<---<<<______>>>------>>>>>>>>-->>,,,,<--<<____>>>)))))))-))))))-))),,,]]]]--]]]],,,,<<<<<<---<<---<<<<_________>>>>--->>>>>>>>,,,,,,,,,,((((((,,<<<<<<<<<<<<<<.__._.__>>>>>>>>>>>>>>,,,<<____>>,,,,,))))))}}}},<<<------<<<<____.....................................>>>>----............................................................................................................................................>>>,,,,,,,,{{{{{-{{{{{{{--{{,,{{{{{{{{.{{{{{{{{{,,,,<<<<________>>>>,,,,,,.,,{{{{{{{,,,<<<<..<<------<<<<<<<_______>>>.>>>>.---....>>->>>>,,,[[-[[[[--[[[[[[[[[,,..........................................................................................................................,((((((<<<____>>>,,<<<<______>>>>,,)))))),,,,,((((..,<<<.<<<<---<<--<.<<<<<<..____.>>>>..>>..>.>>---->>>>>>>,,<<<<<<<<__.___>>>>>>>>,,,,,)))),,,,]]]]-]]]---.]]]]]]]],,,,}}}}}}},,,.}}-}}}}}}}}}},,,<<<<<<<-----<<<.-.-<<.--<<<<____.>>>..>-->>---->>>-----..>>>>>>>,,,,,,<--.-<<<<<<<<________>>>>>>>>--->,,,,,}}}}},,,,,<<<<<<<<_______>>>>>>>>,,,,,,}}---}}}}}}}}}}-}},,<-<<-<<-<.-<<<<<<<<--<<<<<<<<<<<<<<<<<<<<<<<<<.............____........>>>>>>>>>>.>>>>>>>>>>>>>>>--....>>>>>>>>-->->>-->>--......>..,<<<<<<<<<<__..........__>>>>>>>>>.>:::::::::::
#=GC RF                              AuUCcGguUGAUCCUgcCgGAggccaccgCuAucGGgguccGauUaAGCCAuGcuAGuc.gagcg.......ccgc...uu........au....gcgg.......cgc..ggCguAcaGCucAG.UAACgCGcgGccAAccUAcCCucggGacggggAUAccCc..C.g.GGAAACuGgGgg.UAAUacccgAUAggggggggcu.gCUGGAAu...GcgcccccccugAAAuGc.............uccg..................gCGCccgaGGAUggggCcgCGcCcgAUcA.GGcaGucGGcgGgGUAAcGGcCcgCCgagCCuauaAgcgGUAcGGGccguGAGAgcgg.gAGCCCggaGAcGGgcuCUGAGACAaGagcCCgGGCCCUACG.GGGCGCAgCaGGCgCGAAAacUccgCAaugCgcGaaAgcGcgAcgggGggaccCC.ga.GUGccgccgc...au.a.ua...gcggcggCUuUcccccggcgU..AAaaagccggggG.AAg.AAGgGgcGGGcAAGa.CcGGUGuCAGC.CGCCGCGGUAAuACCgGCgcCcCgaGcgguggccauuaUUAuUGGGCcUAAAGcGucCGcAgCcGGcccggcAa.GucccccgggAAAuCcgcggGCUcAACcc.gcgGacgcccgggggauACugc.cg..ggCUuGGG.gccGgccGAggcc.ggggGUAcucccgGGGUAGggGugAAAccCuaUaAUCCcgggagGACcACCacUGGCGAAaGCgcccggccaggcCggacCCGACgGugAGGgaCGAAAGCcgGGGgagCgAAccGGAUUAGAUACCCggGUAGcCCcgGCuGUAAACgaUGcggGcUaggugccgggcgggc.uu.c.GagcccgcccggcgccGuAGgGAAGcCGuuAAgCccgCCGCCUggGgAGUACggcCGCAA.....................................GgcuGAAA............................................................................................................................................CuuAAAGGAAUuGGCgGgGGaGCaCcaCAAcggguGca.GccuGCGGuUUAAccgGAuUCAACGCcggaaAuCU.cACCgGgggcGACaGc..cgaAUGAagGccaGguUgAaGAcCu.ggCc.uGA....cgagCuGAGAGGaGGugCAuggCCgcCGuC..........................................................................................................................AGcuCGugCcGUGAgGcGUCCuGUUAAGUCaGGcAaCGagCGAGACCCcc..accc.ccagUUGCcAuc.gcggcc..uuug.ggcc..gc..g.gGcAcacugggggGACcgCcggcGc.uAAgccgGagGAAGGAggGGGCaACGgcAGGuCAG.caugCCCCGAAucccCcGGGCu.aCACGCgggCugCAAUGgccgggACAauGgG.u.ucC.gAcccCGAaA.Ggg..gaaGguAAUCcCuuAAA..cccggcCuuAGUugGG.AccGaGGgCUGuAACUCGcCCuCggGAAccuGGAauccgUAGUAacCGCgcgUCAacAucgcGCGguGAAUAcGuCCCuGCuCCuuGCACaCACcGcCCGUC.acgcCacccgAGcggggcccgggcgcGgccccgccc.............uuua........gggcggggcC.gagcccgggccccgCaA....ggggGgcgAAGUCGUAgCAA......G..GcggCCGcaggGG..........AAccugCGGcc.gGAUCACCUCcu
//
# STOCKHOLM 1.0

#=GF AC   RF01960
#=GF ID   SSU_rRNA_eukarya
#=GF DE   Eukaryotic small subunit ribosomal RNA
#=GF AU   Gutell RR
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Nawrocki E; 0000-0002-2497-3427
#=GF SE   Published; PMID:11869452
#=GF SS   Published; PMID:11869452
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17.38 -Z 549862.597050 --mxsize
#=GF SM   128--noali CM SEQDB
#=GF CL   CL00111
#=GF DR   URL; http://www.rna.ccbb.utexas.edu/;
#=GF DR   URL; http://oberon.fvms.ugent.be:8080/rRNA/ssu/index.html;
#=GF DR   URL; http://rdp.cme.msu.edu/html/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   11283358
#=GF RT   Crystal structure of the ribosome at 5.5 A resolution.
#=GF RA   Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH,
#=GF RA   Noller HF
#=GF RL   Science 2001;292:883-896.
#=GF RN   [2]
#=GF RM   11869452
#=GF RT   The comparative RNA web (CRW) site: an online database of comparative
#=GF RT   sequence and structure information for ribosomal, intron, and other RNAs.
#=GF RA   Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng
#=GF RA   B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR
#=GF RL   BMC Bioinformatics. 2002;3:2.
#=GF WK   Ribosomal_RNA
#=GF SQ   91



DQ248314.1/1-1801                  UACCUGGUUGAUUCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAAGUCUAAGU------------------------------AUAAGCAA--UCU---------------AUACGGU-GAA-ACUGCGAAUGGCUCAUUA-AAUCAGUUAUCG-UU-UAUUUGAUAG-----------------------------------------------------------------------UACCUUACUACAUGGA-UAACCGU-GGUAAUUCUAGAGCUAAUACAUGCUAAAA----ACCUCGACU------------------------------------------------------------------UC-GGAA--G-GGGUGUAUUUAUUAGAUAAAAA--ACCAAU------------------------------------------------------------------------------GCCCUUCG----GGGCUC------------CUUGGUGAUUCA--UGAUAACUUAAC---------GAAUCGC---AUGGCCUUGC-----------------------GCCG---GCGA-UGGUUCA-UUCA-AAUUUCUGCCCUAUCA-ACU-U--UCGAUGG-UA-GG--AUAGU-GG------CC-UACCAU-GGUUUCAACGGGUAACGGGGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUCCCGACA-----CG-GGGA----GGUAGUGACAAUAAAU--------------------ACUG-AUA-CAG-G-GCUC--------------UUUUGG-GU--CU-UGUA-AU--UG---GAAUG-AGUA--------C-AAU-UUAA-A----UCCCU--U-A-ACGAGGAACAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUUGAACCUUGGGCCUG---GCUGGCCGGUCCGCCUAACCGCGUGUACUGGUCCGGCCGGGCCUUUCCUUCUGGGGAGCCGCAUGCCCUUCACUGGGUGU----------------------------------------------------------------------------------------------------------------------------------------------GUCGGGGAACCAGGACUUUUACUUU-GAAAAAAUUAGAGUGUUCAAAGCAGGCC----------------------------------------------UAUGC--UCGAAUACAU-UAGCAUGGAAUAAUAGAAU-AGGACGUGUGGUU-------------------------------------------------------------------------------------------------------CUAUUUUGUUGGUUUCUAGGACCG----CCGUAAUGA-UUAAUAGGGA--UA--GUC--GGGGGCAUCAGUAUUC-AA-U-UGUCAGA----GG------UGAAAUUC-UUGGAUUUAUU-GAA--GA-CUAACUA--CUGC-GAAAGCA---UUUGCCA-AGGAUGU---UUUCAU-U-AAUCAGU-GAACGAAAGUUAGG-GGAUCGAAGACGAUCAGAUAC-CGUC-GUAGU-CU-UA-ACCAUA-AACUAUGCCG-ACUAGG--GAUCGGGCG-A-UGUU---AUUAUUUU--------------------------------------------------------------GACUCGCU-CGG-CA------CCU------------------UACGAGAAAUCA--AAGUCUUUGGGU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGA-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGAAA-CUCA-CCAGGUCCA-G------ACACAU-UAAGGAUUGA-CA-GA---------UUGAGAGCUCUU-UCU-UGAUU-AUGUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGC--UUAAUU-GCGA-UAACGA-ACGAGACCUUAAC-CUGCUAAA-U-AGCCCGGUCCGCUU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGGCGGGCCGCUGGCU-UCUUAGAG-GGA-C-UAUCG-GC----------------------------------------------------------UCAA--GCCGAUGGAAGUUUGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGCGCU-ACACUGACAGAGCCAACGAGUAC-----------------------------------------------------------------------AUCACC-UUGGC--CGGAA--GGU-C-UG------GG-UAAU-CUU-GUUAAA---------------------------------------CUCUGUC--GUGCUG-GGGAUAGAGCAUUGC-------------AAUUAUUG-CUCU-UCAACGAGGAAUUCCUAGUAA-GCGC-A-AGUCA-UCAGCUU-GC-GCUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAA-UGGCUCAGUGAG--GCCUU-CG-GACUGG-----CA-CAGGG---ACGUU---------------------GGCAACGACGA-C--CCAG----U---G-CCGGAAAGUUCGUC-AAACU-UGGUC-AUUUAGAGGAAGNNNAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
AY947720.1/1-1819                  UCUCCGAUUGAUUCUGU---CGGCGAUU-AUAUGCUUAUCUCAAAGGCUAAGC-CAUGCAUGUCAAAGU------------------------------UCAUACUG-CCUU---------------AAAUGGU-GAA-ACCGCGAACGGCUCAUUA-CAACAGCUAUUA-UA-UACUUGAUCU-----------------------------------------------------------------------UGAUUUCCUACGUGGA-UAACUGU-GGUAAUUCUAGAGCUAAUACAUGCACCAA---AGCUCCGAUU---------------------------------------------------------------UUAUU-GA----C-GAGCGCAUCUAUUAGAUUAAA---ACCAAU-----------------------------------------------------------------------------CGAGCUUUAAACGGCUCGUU----------AAUUGGUGACUCU--GAAUAGCUUAGC---------UGAUCGC---AUGGUCUAGU-----------------------ACCG---GCGA-CAUAUCU-AUCA-AGUAUCUGCCUUAUCA-ACU-U--UCGAUGG-UA-GU--UUAUG-UG------CC-UACCAU-GGUUGUAACGGGUAACGGAGAAU--AAGG------------------------GUUCGAC-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACUUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-ACUCUCAGCA-----AG-AGGA----GGUAGUGACGAAAAAU--------------------AACG-AGA-CCG-U-UCUC---------------AUUGA-GG--CC-GGUU-AU--CG---GAAUG-GGUA--------C-AAU-UUAA-A----CCUGU--U-A-ACGAGGACCUAUGAGAGGGCAA-GCC-UGGUGCCAGCAGCCGC-GGUAACUCC--AGCUCUC-AAA-GU-GUAUAUCGU-UAUUGCUG-CGGUUAAA---A--------AGCUC-GUAGUUGGAAUCCAGCUUGA---CGACAUGGUCCAUUUAUUGGAUGUGAACUAUGAUCGUAGGCUAAUCUAUGUUGGUUUUCCUUGCGUUACCUUGAUCGGUC--------------------------------------------------------------------------------------------------------------------------------------------GCGUAAGGUGGCUAGCGAGUUUACCUU-GAAAAAAUUAGAGUGCUUAAUGCGGGCUUA--------------------------------------------AAAGC--CUGAAUAUUC-GUGCAUGGAAUAAUAGAAU-AGGAUCU-CGGUU-------------------------------------------------------------------------------------------------------CUAUUUUGUUGGUUUUCUGAUCUG----AGAUAAUGG-UUAAGAGGGA--CA--GAC--GGGGGCAUUCGUACCG-CU-G-CGUGAGA----GG------UGAAAUUC-UUGGACCGUAG-CGA--GA-CGUCCCA--CUGC-GAAAGCA---UUUGCCA-AGAAUGU---CUUCAU-U-AAUCA-A-GAACGAAAGUCAGA-GGUUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UG-ACCGUA-AACGAUACCA-ACUAGC--GUUCCGUCA-G-UGGU---AAUUAC----------------------------------------------------------------GCCUUGAC-GGG-CA------GCU------------------UACCGGAAACGA--AAGUUUUUCGGU--------UCCGGGGG-AA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGA-AAUUGACGG-AAGGGCA-C-CACCA-GGG-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUCA-CCUGGCCCG-G------ACACCG-UGAGGAUUGA-CA-GA---------UUGAGAGCUCUU-UCU-UGAUU-CGGUGGU-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUUAUU-CCGA-UAACGA-GCGAGACUCUAGC-CUACUAAA-U-AGUCGGCAAAUAAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCGUGAAAUGUUUGUGCGACU-UCUUAGAG-GGA-C-AAGCG-GU---------------------------------------------------------GUUCA--GCCGCAUGAA--GUUGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CCAGGGCUGCACGCGCGCU-ACACUGGAGGAAUCAACGUGCUA------------------------------------------------------------------------UGUCC-AUUGU--CGAAA--GGC-A-UU------GG-UAAC-CCG-UUGAAA---------------------------------------AUCCUCC--GUGCUC-GGGAUAGGGAAUUGC-------------AAUUAUUU-CCCU-UGAACGAGGAAUCCCUAGUAA-GUGU-G-AGUCA-UCAGCUC-AC-GCUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUGCCCGGGAC--UGAG-CCGUUUCGAGAA--AAGCG-GA-GACUGC-----UG-UAUUG---AAGCCGA-----------------AUAUUUGCGGUGG-A--AAUA----CUCUG-GUGGAAAUCGCCUU-AAUCG-CAGUG-GCUUGAACCGGGCAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
GQ223284.1/15-1777                 AACCUGGUUGAUCCUGC---CAGUAGUC-AUACGCUUAUCUCAAAGAUUAAGC-CAUGCACGUCUAAGU------------------------------AUA-GCAU----U---------------AUACAGU-GAA-ACUGCGAAUGGCUCAUUA-UAUCAGUUAUAG-UU-UAUUUGAUGU-----------------------------------------------------------------------UAAACACUUACUUGGA-UAUCUGU-AGUARUUCUAGAGUCAAUACAUGCUAAAA----AGCCACUAG------------------------------------------------------------------UA-AUAG--U-GGUUGCAUUUAUGACUUUGUAA--UCCAAU-----------------------------------------------------------------------------UC------A-----------------------UUGGUGAUACU--ACAUAACUUCGC---------UAAUUGA------UCAUUUU-----------------------GA-----UCAA-UAUAUCA-UUCA-AGUUUCUGCCCUAUCA-GCU-U----GAUGG-UA-GU--GUAUU-GG------CC-UACCAU-GGCGUUAACGGGUAACGGAGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAGACGGCUACCACAUCCAUGGAAGGCAGCAGGCGCGUAAAUUACC--C-AAUCCUGACU-----UA-GGGA----GGUAGUGAAAAUAAAU--------------------ACCG-AUA-UGG-U-GGGU---------------UUAUC-CU--AC-UAUA-AU--UG---GAAUG-AGAU--------A-ACU-GUAA-A----UAUGU--U-G-UUGAUAUUCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGUUG-CAGUUAAA---G--------CGUUC-GUAGUUGAUAUUGUUGUAUA---CAAUGCUCCUUCGGGUAGCGUUGUAUUCAUUUGUGGGAAUUUGUUUUCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGUUCCCCUAUUACUGU-GAGCAAAUUAGAGUGUUCAAAGCAGACG-----------------------------------------------AUGU--UUGAAUACAU-UAGCAUGGAAUAAUAAUGU-UGUCGUA-UGAC------------------------------------------------------------------------------------------------------------AUCCAUUGGAUUGUGUUAUA----UGAUGUGGA-UUAAUAGAAA--CA--GUU--GUGGGUAUUCAUAUUU-CA-U-AGUGAGA----GG------UAAAAUUC-UUGGAUCUAUG-GAA--GA-UGAACUA--CUGC-GAAAGCA---UUUACCA-AGGAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUAGG-GGAUCGAAGAGGAUCAGAUAC-CCUC-GUAGU-CU-UA-ACUAUA-AACUAUGCCA-CUUAUG--UGUUGUCUA-A--CUC---AUCUUUUU--------------------------------------------------------------GAGUUUGG-CAU-UG------CAU------------------UAUGAGAAAUCA--AAAGCUUUGGGU--------UCCGGGGG-GA-G--UAUGG-UCGCAAGU-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-UACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGAAA-CUUA-CCAGGUCAG-G------ACAUGG-GAAGGAUUGA-CA-GA---------UUGAGAGUUCUU-UCU-UGAUU-CCUUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUAAUU-CCGU-UAACGA-ACGAGACCUUUGU-GUGGGAGU-U-AGUAAUUAUGUCGC--------UUGGUAU--------------------------------------------------------------------------------------------------------------------------------------------------------------AUAUGUAUUUAUAUACUUGACAUAUAUUACUUUACACCUC-AGA-C-AAUGG-AA---------------------------------------------------------GAUUA--UUCCAUGGAAGUUAAAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CCUGGGCCGCACGCGUGCU-ACACUGAUGAGUAGAAUGGGUUAAUACUGC-------------------------------------------------------AUUUAUUGCUUUCCC-UUGAC--CGAGA--GGU-C-UG------GG-UAAU-CCU--UUAAU---------------------------------------ACUCAUC--GUGCUG-GGGAUUGAUUCUUGU-------------AAUUAUUA-AUCA-UGAACGAGGAAUUCCUAGUAA-ACGC-A-AGUCA-UCAUCUU-GC-AUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCACCUACCGAU--UGGA-UAUUGUGACGAA--CCUUG-CA-GAGUGA-----GU-UCUA-----UUCA----------------------GCAA-UGGA-----UAGU----A---U-UUACGAAGUCAUGU-AAAUC-GUAAU-AUCUAGAGGAAGGUGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
ABGT01000365.1/676-2833            AACCUGGUUGAUCUUGC---CAGUAGUC-AUAUGCUUGUCUCACAGAUUAAGC-CAUGCAAGUGAAAGU------------------------------ACAUAUGUAAAUA---------------AUAUAUU-GAA-ACUGCGAACGGCUCAUUA-AAACAGUUAUAA-UC-UACUUGAUGU-------------------------------------------------------------------------UUUUAAUAUAAGGA-UAACUAC-GGAAAAUCUGUAGCUAAUACUUGUGAAA-----AUACCUUUUGAUAUAUACAUAU------------------------------------AUAUAUAUAUGUAUGUAUCAUUAA--G-GUAUGUAUUUGUUAGAUAUAAG--AAUAAA-------------------------------------------------------------------------------AUAAAUA----U-------------------AAUUGAAUUA--UAACAAAGAAGA---------AACACAU-------AAAAUA-----------------------U------GUGU-AUUAUCA-AUCG-AGUAUCUGACCUAUCA-GCU-U--UUGAUGU-UA-GG--GUAUU-GA------CC-UAACAU-GGCUAUGACGGGUAACGGGGAAU--UAGA------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACC--C-AAUUCUAAAA-----AA-GAGA----GGUAGUGACAAGAAAU--------------------AACA-AUA-CAA-U-AUCG-------------AAAAAUG-AU--UU-UGUA-AU--UG---GAAUG-AUAG--------G-AAU-UUAC-A----AGGUU--C-C-UAGAGAAACAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-AUAUAUUAA-AAUUGUUG-CAGUUAAA---A--------CGUUC-GUAGUUGAAUAUUAAAGAAU---CCGAUGUUUCAUUUAAACUGGUUUGGGAAAACCAAAUAUAUUAUAUAUUUUGCUUUGUUCAAAAUAAGGUUUUCUAAUAAAUUAUGUUUUUAUCAGAUAUGACAGAAUC-----------------------------------------------------------------------------------UUUUUUAAAAUCUCUUCAAUAUGCUUUUAUUGCUUUUGAGAGGUUUUGUUACUUU-GAGUAAAAUUAAGUGUUCAUAACAGACGGGUAGUCAUGA-------------------------UUGAGUUCAUUGUGU--UUGAAUACUA-CAGCAUGGAAUAACAAAUA-UGAAUAA-GCUAAUUAUUUUUU------------------------------------------------------------------------------------UUUUUCAUAAUUUUUUUUGAUAUUCUUAUUAGCU----UAGUUACGA-UUAAUAGGAG--UA--GCUUUGGGGGCAUUCGUAUUC-AG-A-UGUCAGA----GG------UGAAAUUC-UAAGAUUUUCU-GGA--GA-CGGACUA--CUGC-GAAAGCA---UUUGCCU-AAUCUAU---UUCCAU-U-AAUCA-A-GAACGAAAGUUAAG-GGAGUGAAGACGAUCAGAUAC-CGUC-GUAAU-CU-UA-ACCAUA-AACUAUACCG-ACUAGG--UGUUGGAUG-A-AUAU---AAAAAAUAUAUAAAUAUGUAGCAUUUCUUAGG--------------GAAUGUUGAUUUUAUAUUAGAAUUGCUUCCUU-CAG-UA------CCU------------------UAUGAGAAAUCA--AAGUCUUUGGGU--------UCUGGGGC-GA-G--UAUUC-GCGCAAGC-GAGAAA--G-UU-AAAAG-AAUUGACGG-AAGGGCA-C-CACCA-GGC-GUGGAG-CUUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUCA-CUAGUUUAA-G------ACAAGA-GUAGGAUUGA-CA-GA---------UUAAUAGCUCUU-UCU-UGAUU-UCUUGGA-UGGUGAUGCAUGGCCGUU-UUUAGU-UCG-UGAA-UAUGA-UUUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGAUCUUAAC-CUGCUAAU-U-AGCGGUAAGUACACUAUAUUUUUAUUUGAAAUUGAAUAUAGGUAAUUAUACAUGUUUAUUCAGUGUUCAAAUUAGGAUAUUUUUUUAUUA-----------------------------------AAAUAUUCUUUUCCCUGUUUUACUAAUAAUUUGUUUUUUUUUACUCUAUUUCUCUCUUCUUUUAAGAAUGUACUUGCUUGAUUAAAUAAAGCU-UCUUAGAG-GAA-C-AGUGU-GU---------------------------------------------------------AUCUA--ACACAAGGAAGUUUAAGGCAAC-AACAGGU-C-UGUGAUGUCCU-UAGAUAA-ACUAGGCUGCACGCGUGCU-ACAAUGAUAUAUAUAACAAGUUGUUAAAAAUGUACUUAU--------------------------------------AAAUAAGUGUGUACAAUUUUUCC-UGUAC--UGAAA--AGU-A-UA------GG-UAAU-CUUUAUCAGU---------------------------------------AUAUAUC--GUAAUU-GGGAUAGAUUAUUGC-------------AAUUAUUA-AUCU-UGAACGAGGAAUGCCUAGUAA-GCAU-G-AUUCA-UUAGAUU-GU-GCUGACUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGAA-AGAUAUGAUGAA--UUGUU-UG-GAUAUGAA-UUAA-AAUAAU--GAAAU----------------------UUUAUAUUUC-U--GAUU----U---UUUCUAGAAGAACUGU-AAAUC-CUAUC-UUUUAAAGGAAGGAGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
AF439347.1/2-2048                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUCACCUCAAGGAUUAAGC-CAUGCAUGUCGAAGU------------------------------AUAAACUA--GUA----------------UACGGU-GAA-ACUGCGAACGGCUCAUUA-AAUCAGUUGCAA-UC-GAAGUGGCGA---------------------------------------------------------------------UAUCAGGUCUUGAUCGGA-UAACACU-GGCAAAUCUAGUGCUAAUACGUCC---------GGCUGGUAGAGGCG-----------------------------------------------------AGCAAUCGCGUCUGC--C-GGCCGCACUUACUAGCUGCUGC-UGCCAACGGGCUGGAGG---------------------------------------------------------CGCCCUCGUGACGCCCCC-----GGCUCC-----------CCCCGACGAGCCA--UAGUAAGGA-GU---------UGACCGC----CCCC----------------------------GCGG---GCGG-CGUGCCA-UUCG-AGCUUCUGCACUAUCA-UCU-C--AGGUUGG-UA-GA--GUAGU-GG------UC-UACCAA-GGAGUUUACGGUUAACGGAGGAU--UAGG------------------------GUUCGAC-U-CCGGA--GAAUGAGCCUGAGAGACGGCUCAUACAUCCAAGGAUGGCAGCAGGCGCGAAAAUUACC--C-AAUGUACAAA-----GU-ACGA----GGUAGUGACAAGGAAU--------------------AUCG-GGG-CCU-G-UGGGC-----------AUUUUGCC-CA--UGCGGCC-GC--UG---ACAUG-GACC--------G-GCU-CCAA-A----GGUGC--C-G-GUGA-AUACGAGUCGAGGGAAAGGUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCGA-CCA-GC-GUAUAUUAA-AGUUGUUG-CAGUUAAA---A--------CGUUC-GUAGUUUGACUUGCGGGGUG--CGAGAACAGUGGUUUAUGGUUUUGGGGGUCAGCGCGGGGGGAUUGGCUUCGGUCAGUACCCUUGCGUCCCCGGAUCCAGCGCGGGGGGGUGUGCAGCGCUUGAAUAAAGUGCUGCGCGCUUUUACGCG----------------------------------------------UUCCGUCCUAACGGGCGGGGCCCUUCGUCAGCACUCUGUUUGCGCGUGCCUUCACCGGUGCGCGCGAUUACCAU-GAGGAAAUAGGUACGUUCAAAGUAGGGUGGCGGUCACUGCUAGCGCUGUA---AUAGGCGCGCAGACCCGCCCGUCCCG--UUGAACAGGC-CAGCAUGGGAUAAUGUGCU-ACGACUC-GGCGUCA--------------------------------------------------------------------------------------------------GUAGUACGUUGGCUUGCAGCGGAUGCA----GAGUAAUGG-UUGAUAGGAG--UGAGUGC--GUGGGCAUCAGGACCA-GA-C-GGGGACA----GG------UGAAAUAG-GAUGAUCCGUC-UGA--GA-CUAUCGG--GAGC-GAAAGCG---UUUGCCA-AGUACAC---UUUCAU-U-AAUCA-A-GAUCGAAAGCCAGG-GGAUAGAAGGCGAUUAGACAC-CACC-GUAUU-CC-UG-GCCAUA-AACCAUACCA-ACUAAG--AAUUGGGAG-U-GCAU---UCCAUUUUUUAU-----------------------------------------------------UUUUGGUUCCUCU-CAG-CG------CUC------------------AUAGAGAAAUCGUUAAGUUUUCGGGU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-GAAGG-CAUUGACGG-AGAGAUA-C-CACAA-GAC-GUGGAG-UCUG-CGGC-UCAAUUUGACUCAACACGUA-AAC-CUUA-CCAGGCCCA-G------ACGUGC-GUGGGAUUGA-CA-GA---------UUGAUAGUUCUU-UCA-UGAUU-GCAUGGU-UGGUGGUGCAUGGCCGUU-CUUAGC-CCG-UAAC--GUAA-GUCGUCUGC--UUUAUU-GCGA-UAACGA-GCGAGACCUCUGU-UG-UCAAA-U-ACGCUGCACGUGCUCUGUGUUCCGCGUGCCGGCCUCU----------------------------------------------------------------------------------------------------------------------------------------------UUUUUUGGCUGGCUUGCGCGGCGGCACCUGUGCGGGCGU-UCUUGGCG-AGA-C-UGUUG-GCGA-----------------------------------------------------UUUCAAA--GCCAAAGGAAGGUAGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGC-CCUGGGCCGCACGCGUACU-ACACUGCCUGAUUCAGGAGGAUUU--------------------------------------------------------------------UUUUCAGC-UGGCC--UGAAG--GGG-U-CG------GC-UACU-C---GUGAAU---------------------------------------AUCAGGC--GUGGCU-GGGAUUGGGGCUUGG-------------AACUAUGC-CCCA-UGAACAAGGAAUGUCUAGUAG-GCGC-G-CUUCA-CAAAGAC-GC-GCCGAUUCU---GUC-CCUGUCCCUUGUACACACCGCCCG-UCGCUUGAUCCGAU--UGGU-UAUUUUGGCGAG--UUCUU-CG-GACGCAC---UGU-CCUCCA--UUGCCGCGC-------------UGCGAGGCGCUGUGA-G--GUGG----G---C-UGCGGAAGUUGUGC-GAGCC-UAAAG-AAUUAGAGGAACAAGAAGUCGUAACAAG-GUAU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
AAPQ01003438.1/3513-5394           GAUCUCGC----CCUGCUCUGAGUAGUU-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------ACACACGA--AUU----------------AAAAGU-GAA-ACCGCAAAAGGCUCAUUA-UAUCAGUUAUGG-UU-CCUUAGAUCG-----------------------------------------------------------------------UUAACAGUUACUUGGA-UAAUUGU-GGUAAUUCUAGAGCUUAUACAUGCAAUUAA--AACAUAAACC----------------------------------------------------------------UUAU-GGGA--C-AUGUGCUUUUAUUAGGCUAAA---ACCAAG-----------------------------------------------------------------------------UGAUCGCAA----GAUCGUUA--------UAUUGGUUGAACUC--UAGAUAAAAUGC---------AGAUCGU---AUGGUCUUGU-----------------------ACCG---ACGA-CAGAUCA-UUCA-AAUGUCUGCCCUAUCA-UCU-U--UUGAUGG-UA-GU--AUCUA-GG------AC-UACCAU-GGUUGCAACGGGUAACGGGCAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGCCAGCAGGCUCGGGGA----------------GAU-------------------AGUGACGAAAAAU--------------------AACA-AUA-CAG-G-ACUCA------------UAGCCGA-GG-CCC-UGUA-AU--UG---GAAUG-AGUA--------C-ACU-UUAA-A----UCCUU--U-A-ACAAGGACCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGUUG-CGGUUAAA---A--------CGUUU-GUAGUUGAACUUGUGUUUCA--UGCGGGUAGUACAACUUACAAUUGUGGUAAGCGUAUUACCGGUGGAGUUCUUAUGUGUGAUUAAAUACUUGUAUUUUUUCAUAUGUUCCUCCUAUUUAAAACCU-----------------------------------------------------------------------------------------------GCAUUAGUGCUCUUAAACUAGUGUUAUUGUGGGCCGGUACUAUUACUUU-GAACAAAUAAGAGUGCUUAAAGCAGGCUUC-------------------------------------------AAAUGC--CUGAUUAUUAUGUGCUUGGGAUAAUGAAAU-AAGACCU-CUGUU-------------------------------------------------------------------------------------------------------CUGCUUUCAUUGGAUUUCAGAUCAA--GAGGUAAUGA-UUAAUGGAAG--CA-AUUU--GGGGGAAUUAGUAUUA-CG-A-CGCUAGA----GC------UGAAAUUC-UUGGACCGUCG-UAA--GA-CUACCUU--AAGC-GAAAGCA---UUUGCCA-AAGAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUAGA-GGUUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UU-UA-ACCAUA-AAAGAUGCCA-GCUAGC--AAUUGGGUG-U-AGCU---ACUUUAAUCG----------------------------------------------------------AUCAUUCAUU-CAG-UC------GCU-----------------UCCCGGGAAACCA--AAGCUUUUGGGC--------UCCGGGGG-AA-G--AAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGUA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAACA-UUUA-CCAGGUACG-A------ACAUAA-GUGUGUAAGA-CA-GA---------UUGAUAGCUCUU-UCU-CGAAU-CUAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA--GUGA-UUUCUCUGG--UUAAUU-CCGA-UAACGA-ACGAGGCUCAAAU-AUAUUAAA-U-AGAUAUCUUCAGGAUUAUGGUGCUGAAACUUAUAUAGCCUUCAUUCAUGGUGGCAGUAAAAUGUUUA----------------------------------------------------------------------------------UUGUGUUUGAAUGUGUUUAUGUAAGAGGAGCCGUACCUGUUGGUAUGUCUCAUUAUAAUGACACUACCU-UCUUAAAU-GGA-C-AAAUU-GC---------------------------------------------------------GUCUA--GCAAUAAUGAG-AUUGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAU-----------GCACGCGCGCU-ACAAU------AAUAUU--------------------------------------------------------------------------------UCC-UAGAC--CGAGA--GGU-C-CG------GG-UAAA-CCG-CUGAAC---------------------------------------CGCUUUC--AUGCUU-GGGAUUGUGAACUGA-------------AACU-GUU-CACA-UGAAC------CUGCAU---------------------U----------GAUUAC---GUC-CCUGCCCC-UGUACACACCGCCCG-UCGCUACUACGGAU--UGAA-UUAUUUAGUGAG--GUCU--CU-GACGCC-----UU-GCGUG------------------------------UUACG------G--UUGU----U---U-CGCAAAAGUUGACC-GAACU-UGAUU-AUUUAGAGGAAGUAAAAGUCGUACCAAG-GUUU-CCGUAGG---UGAACCUACGGAAG-GAUCAUUA
JF930872.1/1-1872                  UAACUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUAAAUUC---UU---------------GUACGAU-GAA-ACUGCAGACGGCUCAUUA-CAACAGUGAUAA-AC-UAAUAGACUUU--------------------------------------------------------------------CGGGUUUUACCUUUUGGA-UAACCGC-AGUAAAUC-GGGGCUAAUACAUACAAGCG---AUGGGUGACU---------------------------------------------------------------GGCAACAGAA--G-CUCAGCGAUUAUUAGCAUUCU---ACCAAU-------------------------------------------------------------------------------GCCUUCG----GGUUUU--------------GGGUGAUACC--GAAUAAUAUUGC---------AGAUCGA----GGAUUU--------------------------AUCU---UCGA-CAAGUCU-ACUG-UGUCACUGCCCUAUCA-ACU-U--UCGAUGG-UA-CG--GUAUU-GG------CC-UACCAU-GGUUGUAACGGGUAACGGGGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAAUGGCUACCACUUCUACGGAAGGCAGCAGGCGCGCAAAUUACU--C-AAUCCCAAUA-----CG-GGGA----AGUAGUGACAAUAAAU--------------------AUCA-AUA-CCU-A-UCCA--------------AUUUUG-GA---G-GGCA-AU--UG---AAAUG-AACA--------C-AAA-UUAA-A----ACUCU--U-A-AUUA-ACACAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-AUAUACUAA-AGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUUGAAGUUUAAGGUUU---ACUGGGUUUAUGUCAGUUAUCACUUCGUGGUCAACUCGACACCAGUAUCUCUUUCUUAAUAGUUCAGCUUGUAUUAUCUU------------------------------------------------------------------------------------------------------------------------------------------UGAUAGUGCUUGUUUGGACAUUUCACUGU-GAGAAAAUUGUGGUGUUUAAAGCAGGCG---------------------------------------------UCUCGC--CUGAUCUUUUGCAGCAUGGUAUGAUGAAAC-AUGACAU-UUUA-----------------------------------------------------------------------------------------------------------CGCUAUUGGUUUGCGUUUAAA----GUGUAAUGA-UUAAUAGGGA--UG--GAU--GGGGGUGUUCAUAUUG-GU-G-GGCGAGA----GG------UGAAAUUC-GUUGACCCUAU-CAA--GA-UGAACUU--CUGC-GAAAGCA---UUCACCA-AAUACUU---CCCCAU-U-AAUCA-A-GAACGAAAGUUUGG-GGAUCGAAGACGAUCAGAUAC-CGUC-GUAGU-CC-AA-ACUAUA-AACUAUGUCG-ACCAGG--GAUCGGUUA-A-AAUU---UUUUCAA---------------------------------------------------------------AAUUUAAU-CGG-CA------CCU------------------UGUGAGAAAUCA-UGAGUGUUUAGAU--------UCCGGGGG-GA-G--UAUGG-UCGCAAGU-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA---CACAAUGGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACUCGGGAAAA-CUUA-CCAAGCUAA-G------AUAUAG-UAAGGAUUGA-CA-GA---------CUAAAAGAUCUU-UCA-UGAUU-CUAUAAG-UGGUGGUGCAUGGUCGUU-CUUAGU-UGG-UGGA--GCGA-UUUGUCUGG--UCAAUU-CCGA-UAACGG-ACGAGACCUCGAC-CUGCUAAC-U-AGUAGUAUUUAUUAGUCGAUAUAGACGAUAGCUUUUCUGGGGUUUGGAAUGAUUU---------------------------------------------------------------------------------------------------------CGGUCAUCUCCUGCUUCAAGGAGUGUGUAGUCUGACUCGAUAGGUACGAAUUAAAACU-UCUUAGAG-GGA-C-UACCU-GC---------------------------------------------------------CUCAA--GCAGGCGGAAGUCCGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUAC-CUUGGGCCGCACGCGCGCU-ACAAUGUAGGAAACAAAAAGGCU---------------------------------------------------------------------------CC-UGGUC--CGGAA--GGA-U-UG------GG-UAAU-CAU-UUGAAU---------------------------------------UUCCUAC--GUAACU-GGGCUUGAUCUUUGU-------------AAUUAUUG-AUCA-UAAACGAGGAAUUCCUUGUAA-GCGU-A-AGUCA-UUACCUU-AU-GCUGAAUAU---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--CGAA-UGAUACGGUAAA--GUUAA-CG-GAUCGU-----UU--UAUC----UGUG----------------------GCAA-CACU--G--AUAU----A---A-AUUAAAAGUUAUUU-AAAUC-UCAUU-GUUUAGAGGAAGGAGAAGUCGUAACAAG-GUAU-CCGUAGG---UGAACCUGCGGAUG-GAUCAUUU
EF527144.1/2-1600                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGACUAAGC-CAUGCACGUCUAAGU------------------------------ACAAACUA--AAU----------------GAUGGU-GAA-ACUGCAAAUGGCUCAUUA-CAACGGUUAUGA-UG-UACCCGGGAG-----------------------------------------------------------------------------UUCCGAUGGA-UAUUUCC-AGUAACACUAGAACUAAUACAUGUCCCU-----------------------------------------------------------------------------------------------GCGUUUAUUAGUUUCAC---ACAGUC-----------------------------------------------------------------------------CG------------------------------UCGCUGAGUCA--UGGUAAACA-GU---------UGAUCGA------------C------------------------------UCGA-CGUCCCG-GAAC-AGUUUCCGCCCCAUCA-GCU-U---CGAUGG-UU-GG--GUAUU-GG------CC-UACCAU-UGCAACAACGGGUAACGAGGAAU--UAGG------------------------GUUUGAU-U-UCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCUACGGAUGGCAGCAGGCGCGCAAAUUACC--C-AAUGCAGACA-----CU-GUGA----GGUAGUGACGAGAAAU--------------------AAUA-AAG-CGG-G-AC----------------UUCU---GU--UU-CGCU-AU--UA---UAAUG-AGUA--------A-CAA-CCAA-A----GGUCG--U-U-ACGAUUAGCAACUGAUGGGAAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUACC--AGCGUCA-GUA-GC-AUAUAUUAA-AAUUGUUG-CAGUUAA----A--------CGUCC-GUAGUCUGUACGUCGUCCCA---AACUCACUGCAGUCUUGCGUCUUCUUCACUGAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCGCAAGUAUCUGCAGUCACUCCCUU-GAUCAAAUUAGGUUGUUCAAGGUAGACA----------------------------------------------GAGG---CUUCAUAUUU-UCACAUGGAAUUGGGUGAG-GGAACUU-AAGAG-------------------------------------------------------------------------------------------------------UUUAAGUUUCUCGUCUU--------------------------AGGAU--CA--UCC--GGGGUCAUUCGUACUC-GU-C-CGCGAGA----GG------UGGAAUUC-UUGGACCGGGC-GAA--GA-CGACCAG--CAGC-GAAAGCA---UCUGUCA-GGGAUGU---UUUCUG-C-GACAA-A-GGACGAAGGCCAGG-GUAUCGAAGACGAUUAGAUAC-CGUC-GUAGU-CC-UG-ACUGUA-AACUAUGCCA-ACUUGG--GUCUUGCUG-G--------GCUAAUGC-----------------------------------------------------------------UUUGU-GAG-AC------CCA------------------C-ACAGAAAUGA--AAGUGUAUGGGU--------UCUGGGGG-UA-G--UAUGG-ACACAAGU-CUGAAA--C-UU-GAAGG-AAUUGACGG-AAGAGCA-C-CAUAA-GAC-GUGGAG-CUUG-CGGC-UUAAUUUGACUCAACGCGGGAAAA-CUUA-CCAGGUCAA-G------ACAUGG-GCGUGAUUGA-CA-GG---------CUAAU-GACUUU-UCU-CGAUU-CCAUGGA-UGGUGGUGCAUGGUCGCA-CUUAGU-UGG-UGCA--GUGA-UUUGUCAGG--UUUAUU-CCGG-UAACGA-ACGAGACCUCGGC-CUUGUAAA-U-AGCUU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCU-GCUUACAG-GGA-C-AUUGG-CG---------------------------------------------------------G-CUA--CGCCAAGGAAGUUCGAGGCAAU-UGCAGAU-C-UGGAAUGCCCU-UAGAUGU-CCUGGGUCGCACGCGUGCU-ACAAUGACGCCACGAGCGAGG----------------------------------------------------------------------------UUG-CGUGA--CGAAA--GUU-A-CG------CA-UAAU-C---AGCAGU---------------------------------------CGGCGUC--UUAA---GGGACAGUCUCUUGA-------------CACUGUGG-GACU-CUAACUAGGAAUGUCUCGUAA-GCAC-A-AGUCA-ACAUCUU-GU-GUUGAUUAC---GUC-CCUGCUCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--CGAG-UGUUUAGAUGAA--UUUGA-UG-GAC----------------------------------------------AUGA---------------------------GGAAGUCAAAU-AAAUC-UGAGC-ACUUAGAGGAAGGAGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAU-GAUCCUUC
AADA01325358.1/2166-292            AACUUGGUUGAUCCUAC---CAGUACC--AUAUGCUUGUCUCAAAGAUUAAGC-UAUACAUGUCUAAGU------------------------------AUGCAGGG--CCG---------------GUACAGU-GAA-AAUGCGAAUGGCUCAUUA-AAUCAGUUACGG-UU-CUUUUGGUCGCU------------------------------------------------------------------CUCUCCUCUCCUACUCGCA-AAACUGU-GGUAAUUAUAGAGUUAAUACAUGCCGAAG---GGCGCUGAUCCCC---------------------------------------------------------UUCGCGGGGAAGA--U-GCGUGCAUUUAUCAGAUCAAA---ACCAACCCGGUCAGCCCCUUUUCA-----------------------------------------GCCCCGGCCUUGGGGGGUCAGGUACC-----ACCGUC------------UUUGGUGACUCU--AGAUAGCCUCGGG-------CUAAUCGC---ACGCCCCCCG----------------------UGGCA---GGGA-CAACCCA-UUGG-AACGUCUGCCCUAUCA-ACU-U--UCGAUGG-UA-GU--CGCUG-UG------CC-UACCAU-GGUGACCACGGGUGAAGGGGAAU--CAGG------------------------GUUGGAU-U-CUGGA--GAGGGAGCCUGAGAAAUGGCUACCACAUUCAAGGAAGGCAGCAGGCAUGCAAAUUACC--C-ACUCCCGACC-----CG-AGGA----GGUAGUGACCAAAAAU--------------------AACA-AUA-CAG-G-ACUC--------------UUUCGA-GG-UCC-UGUA-AU--UG---GAAUG-AGUC--------C-ACU-UUAA-A----UCCUU--U-A-ACGAGGAUCCAUUGGAGGGCAA-GUC-UAGUGCCAGCAGCAGC-GGUAAUUCC--AGCUCCA-AUA-GC-AUAUAUUAA-AGUUGCUG-CAGUUAAA---AUCUGCAGCAACUU--UAGUUGCUGGAUCUUGGGAG-AGGGCAGGCGGUCCGCCGGGAGGCGAGCCACAGCCCGUCCCCGCCCCUUGCCUCUUGGCGCCCCCUUGAUGCUCUUAGCUG------------------------------------------------------------------------------------------------------------------------------------------AGUGUCCCGGGGCCUGAAGCGUUUACUUU-GAAAAAAUUAGAGGGUUCAAAGCAGGUCCA-------------------------------------------AGCCGC--CUGGAUACCU-CAGCUAAGAAUAAUGGAAU-AGGACCG-CGGUU-------------------------------------------------------------------------------------------------------CUAUUUUCUGGGUUUUCAGAACUG----AGGCCAUGA-UUAAGAGGGA--CG--GGC--GGGGGCAUUCGUAUUG-CG-C-CGCUAGA----GG------UGAAAUUC-UUGGACCGGCG-CAG--UU-CGGACCA--GAGU-GAAAGCA---UUUGCCA-AGAAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUCGGA-GGUUCGAAGACGAUCAGAUAC-CGUC-GUAGU-UC-CG-ACCAUA-AACGAUGCCG-ACUGGA--GAUGUGGCG-G-CGUU---AUUCCCAU--------------------------------------------------------------GACCCGCU-GGG-CA------GCU------------------UCCAAGAAACCA--AAGUCUUUGGGUUUUUAGGUUCCGGGGG-G--G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGGUGG-AAGGG-A-C-AACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACAUGGGAAAA-AUCA-CCCGG-CCG-G------ACACGG-ACAGGAUUGA-CA-GA---------UUGAUAGCUCUU-UCU-CUGUU-CCAUGGG-UGGUGGUGCAUGGCC-----UUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUAAUU-CCGA-UAACCA-AGGAGACUCUGGC-AUGCUAAC-U-AGUUACACGACCCC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAGCGGUCGGCGUCCCCCAACU-UCUUAGAG-GGA-C-AAGUG-GC---------------------------------------------------------GUUCA--GCCACCGGAA--ACUGAGCAAU-AAUAGGU-C-UGUGAUGCCCU-UAGAUGU-CCAGGGCUGCACGUGCGCU-ACACUGACUGGCUCAGU--GUUU----------------------------------------------------------------------GCCUACC-CUACG--UGGCA--GAG-G-CG------GG-UAAC-CUG-CUGAAC---------------------------------------CCCAUUC--GUGAUG-GGGAUGGGGGAUUGC-------------AAUUAUUC-CCCA-UGAAGGAGGAAUUUCCAGUAA-GUGC-G-GGUCA-UAAGCUU-AC--CUGA---A---GUC-CCUGCCCUGUGUACACACUGCCCG-UCACUACUACUGAU--AGGA-UGAUUUAGUGAG--GCCCU-CG-GAUCGG-----CC-CCGCC----GGGUCA------------------GCCCACUGCCCU-G--GCAG----AG-CG-CUGAGAAGACAGGC-GAACU-UGACU-AUCUAGAGGAAGUAAAAGUCAUAACAAA-GUUU-CCGUAGG---UGAACCUGCGGAGA-GAUCAUUA
AM168092.1/1-1880                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAGGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUAAGUCC---UU---------------GUACGAC-UAG-ACUGCAGACGGCUCAUUA-CAACAGUUGUUG-UC-UACAGGACAUC-------------------------------------------------------------------CGCGCUUUUGCGUUUUGGA-UAACCGC-AGUAAAUC-GGGGCUAAUACAUAUAAACG---AAGGAAUGACU-------------------------------------------------------------GGUAACGGAAG--U-UUCUGCGAUGGAUUUAGCUAUU--CAACCG-------------------------------------------------------------------------------GCCUUGU----GUUU----------------GUUGGAACC---GAUCCAUAUUGC---------UAAUCGG--CUAUUAGUUUA----------------------CUAAUAGCCUGA-UGAGUUC-UAUG-AACAACUGCCCUAUCA-ACU-U----GAUGG-UA-AG--GUAUU-GG------CU-UACCAU-GGUUGUAACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGACGCCUGAGAAACGGCGUCCACAUCUACGGGUGGCAGCAGGCGCGUAAAUUACC--C-AAUCUCAAUA----GAG-AGGA----GGUGGCGACAAUAAAU--------------------CCUG-AUG-CCUAU-AGGC--------------UCACGC-CU--AG-GGCA-AU--UA---GAAUA-AGUA--------C-AAA-AUAA-A----UCCAU--U-A-ACCA-AUGUAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUACUAA-UGUUGUUG-CAGUUAAA---A--------CGCUC-GUAGCUUAAAAACACGGAUC---AUUUUUUAGCUAAAUCGAUUGCCACCUGGAAACAGGUGAGGUGAUUUAUUUGGCAUGGCACGUGCUGGUUGGGUUUGUUG-------------------------------------------------------------------------------------------------------------------------------------------GUUCGCUCUAGCAAGCUUAGUCAACUGU-GCAUAAACCUUGAUGCUCAAGGUAAAGACCG-----------------------------------------UAGGUCU--GUGAUACUAA-GUGCAUGGUAUUGUAGAAC-AUGGUAA-CAGG---------------------------------------------------------------------------------------------------------UGGCUUUGUUGGUUGGGUCACUA----GUGCAAUGA-UUAAUAGGGA--GG--AGC--GGGGGCCUUCAUAUUG-AU-G-GGCGAGA----GG------UGAAAUUC-GUUGACCCUAU-CAA--GA-UGUCCUA--CAGC-GAAAGCA---UUGGCCA-AGUGCCU---CUCCAU-U-AGUCA-A-GAACGAUAGUUUGG-GGAUCAAAGACGAUCAGAUAC-CGUC-GUAGU-CC-AA-ACCAUA-AACGAUGUCG-ACCAGU--GAUUAGGCA-C-GUCAC-CUUUCUAGA--------------------------------------------------------------GAACUGCC-UAG-GA------ACU-----------------UAGUGGGAAACCAUUGAGUUUUUGGAC--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA---CACCAUGGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUUA-CCAAGCUCU-G------AUAUGA-UAAGGAUUGA-CA-GA---------CUAAAAGAUCUU-UCA-UGAUC-GCAUAAG-UGGUGGUGCAUGGUCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCAGG--UCAAUU-CCGG-UAACGG-ACGAGACCUCGAC-CUGCUAAC-U-AGUGACAAUUAGAUUGUCGUAUGGGCGAAGUUAGUUCGGCAGCUACUUAAUGGGCA--------------------------------------------------------------------------------------------------------ACUGUUAGGUAGUUGACGUAUUGAUUGUAGCCUGGCAAUGUAGUUGUUAUAUUUUCCU-UCUUAGAG-GGA-C-UUCCA-GC---------------------------------------------------------UUUAA--GUUGGAGGAAGUCCGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUAU-CUUGGGCCGCACGCGUGCU-ACAAUGUAGGCGCUAAUAGGCAU----------------------------------------------------------------------UUUACCC-UUUAC--CUAGA--GGU-A-GA------GG-UAAC-C---UACAAU---------------------------------------CCCCUAC--GUGAUG-GGGAUUGACCACUGU-------------AACU-GUG-GUCA-UCAACGAGGAAUUCCUUGUAG-GCGU-G-CGUCA-CUAUCGC-AC-GCCGAAUCU---GUC-CCUGCCCUCUGUACACACCGCCCG-UCGCUCCUACCGAU--CGAA-CGUCCAGGUAAA--GUCGA-CG-GACUGU-----CU-UC---------------------------------GAAA------------GU----U---G-AUAGAAAGUCCAUU-GAACC-UCGUC-GUUUAGAGGAAGGAGAAGUCGUAACAAG-GUAU-CGGUAGG---UGAACCUGCAGAAG-GAUCAA--
AF249202.1/4-2039                  UACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUGAGU------------------------------UCGCCCCC----A---------------GCAAGGG-UAA-ACCGCGAAUGGCUCAGUA-CUACGGUCCUGG-UU-CCUUAGGCGAGACGGCCCCA-------------------------------------------------CCCCGCGAGGGGAAAGGGCAGAUUCGGA-UAACUGU-GGCAAAUCCAGAGCUAAUACGUGCGUUCG---AGCCCCUUUCCUGUCGUCCCCU--------------------------------------CCUUUCGGGGGGUGGCGGCGGGA--G-GGGCGCUUUUAUUAGCAGCUAG--ACCGGCGUCGCCCCUGC-------------------------------------------------------CCUUCACGGGGUAGGGCUUC----CUCCGU------------UCAGGCGAACUC--UGGAUAACGAGC---------AGACCGC--UACGUCCUCAU----------------------GGACG---GCGG-CGCGCCU-UUCA-AGCGUCCGCCCUAUCA-AAU-G--UCGACGG-UC-GG--UUACA-CG------CC-GACCGU-GUUGGCCACGGGUGACGGGGAAU--CGGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCACGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAACUUACC--C-ACUCCCGGCA-----CG-GGGA----GGUAGUGACGAGAAAU--------------------AACG-AGC-GGG-C-CCUU---------------AGUGG-GG--AU-ACGU-UU--CG---GGAUG-AGCG--------C-AGU-CCAA-A----UACCU-GA-U-GCGACGACCAAUCGGAG-GCAA-GCC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCG-AUA-GC-GUAUACUAA-AGCUGUUG-CAGUUAAA---A--------AGCUC-GUAGUUGGUCCUCGGGGCGG---GAGUCGGCGGACCCGGACCACCCAAGCCCCGCCGCCACGGGGCCGGUGUUCAUCCGGCGUCGGUCUUUCGUCCCUGAGCGCCGGUCACUCCCGUCGUCGGGUCGCCU---------------------------------------------------------------------------------------CCCCCUACCCUGGAGGAGCGCGGGUCGCGGCGGGCGGCCGGCCUCGUCACCUU-GAAAAAAUUGGAGUGUUCAAGGCGGGCA----------------------------------------------UUUGC--UCGGACAGCG-UCGCAUGGCAUGGCCGUUA-CGGACCG-CCGU--------------------------------------------------------------------------------------------------------CCCCUCGGCCGGUCUAAGGGACGG----AGGUAUUGG-UUCACAGAGG--CG--GAC--GGGGGCAUUCGUACGG-AG-G-CGGGAGA----GG------UGAAAUUC-GUUGAUCGCCG-ACG--GA-CGAACGA--GAGC-GAAAGCA---UUUGUCA-AGAACGU---UUUCGU-U-AAUCA-A-GAACGAAAGUCUGA-GGCUCGAAGACGAUCAGAUAC-CGUC-GUAGU-UC-AG-ACCGUA-AACGAUGCCG-ACCGGC--GAGCAGCGG-A-GGUC---UAAACUGUGG---------------------------------------------------------UAGGAACCCGCGCGC-GC------CCC------------------CGAGGGAAGCCA--GAGUCUUUGGGU--------UCCGGGGG-GA-G--UAUGG-UCGCAAGG-CUGA-A--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGGG-UCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUCA-CCCGGUCCG-G------ACAC-G-CGAGGAUUGA-CA-GA---------CC-AGAGAUCUU-UCU-UGAUU-CGGUGGG-UGGUGGUGCAUGGCCGUU-CCUAGU-CGGGUGGA--GCGA-UCUGUCUGG--UUAAUU-CCGGAUAACGG-GCGAGACUCUGCC-CUGCUAAU-U-AGCGCGGCGGCGACUGGCGAAAUAACCCAUGGUUAGUCCGCCCGCGUCGAGCCGGCCGUGUCGUCGUUG------------------------------------------------------------------------------GUGGGGCCUCGUGUCACUCCUUCGCGCGCGGUCGGUCCGGCGUGCGCGCGCCGCCACGCCAGAAACAGGCU-UCUUAGAG-GGA-C-GGGCG-GU---------------------------------------------------------AAACA--GCCGCACGAA--GGUGAGCGAU-AACAGGU-C-UGUGAUGCCCU-UAGACGU-CCGGGGCCGCACGCGUGCU-ACAAUGGGGGAGGCAGCGCGAUA---------------------------------------------------------------------UUACGUCC-CUGCC--CUAAC-GGCG-U-CG------GG-AAAG-CGC--ACAGU---------------------------------------CUCCCCC--CCGACC-GGAAUCGGGGCUCGC-------------AACUGUGC-CCCG-UGAACGAGGAAUUCCCAGUAG-GCGC-G-GGUCA-UAACCCU-GC-GCCGACUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACCAUCGGU---GGA-CGGCCUAGCGAG--GACUUUCG-GACCGG-----AA-CG--G----GGCG----------------------GCUCACGCGU-C----CU----C---U-CCGGGAAGAGGCCC-CAACU-CGGUC-GCCCGGAGAUAGUAAAAGUCGUAACAAG-GUUU-CCGUAG----UGAACCUGCGGAAG-GAUCAUUA
AY730405.1/2-1661                  UACUUGGUUGAUCCUGC---CAA-GGAA-GCACACUAUGGUCAUAGAUUAAGC-CAUGCAAGUGUAAGU------------------------------UCAGGUA--------------------------AC-UAA-ACUGCGAAUAGCUCAUUA-ACACACUCAUAA-UC-UACUUGGAACCAAU--------------------------------------------------------------UUUUUAAAAAUUUUAAAUGGA-UAGCAGG-AGUAAUUCUCGUGCUAAUACAUGAAAUU-----------------------------------------------------------------------------------------------UUAAUAAUCUUAAAUUAA-----------------------------------------------------------------------------------------------------------------------------AUC--AGAUUAUUUUUA---------AUACCUU---------UUAA------------------------------UAGG-UAAUCCA-AUCG-AAUGAGUGACCUAUCAGGCC-A----GUACU-UA-GG--GUCUU-UA------CC-UAAGUA-AGCUAUCACGGGUAACGGGCGGU--UACC------------------------GUCGUAC-UGCCGGA--GAAGGCGCCUGAGAGAUAGCGACUAUAUCCACGGGUAGCAGCAGGCGCGAAACUUACC--C-ACUCGAGACU-----AU-CGGA----GGUGGUAAUGACCAGU--------------------UAUA-A----UU-A-AGGA--------------AUUUUC-CU--UA-------U--UA---UAUAG-GAAU--------A-UAC-UUUU-C----CAGUA--U-A-UUGU-AACCUAGCAGAGGGCCA-GUC-UGGUGCCAGCAGCUGC-GGUAAUUCC--AGCUCUG-CAA-GU-UUGCUCCCA-UAUUGUUG-UAGUUAAA---A--------CGCUC-GUAGUCUGAAUUAUUUUAAU---UUAAAUUUUUUAAAUUAAAAUUUAGUUUUUAUUUU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUAAAAACGUUCACUGUGGAACAAAUCAGAACGCUUAAAGUAAUUU---------------------------------------------UCUUUA--UUGAAUGAUU-UAGCGCAGUAUGAAAUUUU-UACCUUU-UAAA----------------------------------------------------------------------------------------------------------------UUUUAAUUAAUUUAAC----AAGUAAU-A-UCAAAGAGAA--UA--AUC--GGGGAUAGAUCUAUUU-CA-U-GGCGAAC----AG------CGAAAUGU-UUUGACCCAUG-AGA--GA-GAAACGA--AGGC-GAAAGCA---UCUAUCA-AGUGUAU---UUCUAU-C-GAUCA-A-GGGCGAGAGUAGGA-GUAUCCAACCGGAUCAGAGAC-CCGG-GUAGU-UC-CU-ACCUUA-AACUAUGCCG-ACAAGG--UUUUGUUUU-U----------UUUAAU-----------------------------------------------------------------AAAAG-CAG-UA------CCA------------------UAGGAGAAAUCA--UAGUUCAUGGGC--------UCUGGGGG-AA-C--UACGA-CCGCAAGG-CUGAAA--C-UU-GAAGG-AAUUGACGG-AAGGGCA---CACCA-GGG-GUGGAG-CUUG-UGGC-UUAAUUUGAAUCAACACGGGAAAA-CUUA-CCAGGACCA-G------AUAUUUUUAAUGACUGAUCA-GG---------CU-AUAGGUCUU-UCA-GGAUA-UGAUUUU-UGGUGGUGCAUGGCCGUU-GGUGGU-GCG-UGGG--UUGA-CCUGUCUAGCGUUGAUU-CAGA-UAACGA-GCGAGAUUAUCAC-CAAUUAAA-U-AUAUAAAUAUUUUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUAAAAUAAUUUAUUU-UCUAAUUG-GGA-C-UCCCU-GC---------------------------------------------------------GUCUA-AGCAGGAGGAAGAUGGUAGCAAU-AACAGGU-C-CGUGAUGUCCUUUAGAUGC-UCUGGGCUGCACGCGCGCU-ACAAUGUUAUAAUCAAAGAGGUUUGCUAAAUC----------------------------------------------------GAUAGAUUAUCUUUUU-UUUUA--AAGAU--UUC-A-UA------GC-UACU-CUG--UUAAU---------------------------------------AUAUAAC--GUAGUU-GGGAUUGAUAAUUGU-------------AAU-CAUU-AUCA-UGAACCAGGAAUCCCUUGUAA-AUGC-G-UGUCA-ACAACGC-GC-GUUGAAUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGAA-UGACUCGGUGAA--AUCAU-UG-GAUCAU-----UU-U----------------------------------UUUUU-----------------A---A-AUGAAAAGGUGAUU-AAAUC-ACGUU-AUUUAGAGGAAGGAGAAGUCGUAACAAG-GUAA-CGGUAGG---UGAACCUGCCGUUG-GAUCAA--
AF011457.1/15-2036                 AACCUGGUUGAUCCUGC---CAGUACU--AUAUGCUUGUCUCAAAGCCUAAGC-CAUGCAAAUCUAAGA------------------------------UCAAUCAU--AUGCGGUUUCGGCCGUGUAUAAUGA-UAG-UCUGUGGAAGGCUCAUUA-UAACAGUUAUAC-UC---CUAGCCAC----------------------------------------------------------------------UGGAAAGUUUACAAGGA-UACCACC-GUUAACUGCAGCGAUAAUACUUGUUCCC-----UUCGGGGUGGU----------------------------------------------------------AAUAGUAUUUGUG--C-UGAAGCCUAGCUAUUGUAACCU--AGUUUUUCGGGUGUGGCAACAUAUUCGGG------------------------------GAAUUAGGAAUCGACCGCUAGCAGGUGCCUUCG----GGCGCG-----------GGAAAGUGAAUUAACAAGGUUUUCAUA---------AGGCCUU---UCAGGUUUGCUU-------------------UUUCUA---GUGG-CCAGGCA-GAGG-AGUUUCUUACCUAUCA-GCU-C----GUUGU-UU-GU--UUAAA-GG------AC-AAACCA-GGCUUUGACGGGUA-CGGGGAAU--CAGU------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAAUCGCUACCACAUCUAAGGACGGCAGCAGGCGCGCAAAUUACC--C-AAUCUCAAUA-----CG-AGGA----GGUAGUGACAAGCUAUAGUGAC--------UCCACACUAU-UUA-GUG-G-GGAGG-----------UAUUGUCU-UU--UG-ACGA-UU--UU---CCAUG-AUUU--------G-GGU-GUAG-A----UAACC--C-U-UAGAGUAGCCAUUGGAGGAAAA-GUC-UGGUGCCAGCA-CCGC-GGUAAUUCC--AGCUCCA-AGA-GC-GUAUAUUAA-UACUGCUG-UAGUUAAA---A--------CGCCC-GUAGUAUACCUAAGAGUGUG---CGUGUAGUAAUUAGUUUUGUCAGAGGACGGUCGGCGAGUGUUUAUCACACUUGCUUGCCUUACUUUUGGCAAACUUCAGUCGGGCUGGAUCUUUGGUCCUCGUCUGACAGU-------------------------------------------------------------------------------UGCUGCGCGUGUACUUGUCCACGGUUCAUCCGUGAGGCCCAUUUGGGUUGCAACUGU-AAAUAAAUCGUUGUGCUUAAAGCGGGCUAUGA---------------------------------------UACUCUGC--CAGAGCGAUU-UAGCAUGGGACUGCAGAGU-AGCUGUA-UUUGAGUGAAGG----------------------------------------------------------------------------------------UUGUACUUCGGUAUGGCUGGAUCUUGGUACAG----CGCUUGUAA-U----GGAGCUCAG--GGU--GAGGCCCCGGGUACCA-UG-A-GGCUAGA----GG------UGAAAUUC-UGAGACCCUCA-UGU--GA-CCAACUA--AGGC-GAAAGCUGUCGUGGGCC-ACCACAA---GCUCGU-C-UAUCA-G-GGACGAAAGUUGGG-GGAUCGAAGACGAUUAGAUAC-CGUC-GUAGU-CC-CA-ACUAUA-AACGAUACCA-ACCGAG-UAUUUGGGAA-G-ACAC--UAUCCCAGC--------------------------------------------------------------GAUCUUCU-CAG-AA------CUC------------------A-AGGGAAACCU-UAAGUCUUUGGGU--------UCUGGGGG-GA-G--UAUAG-UCGCAAGA-CCGAAA--C-UU-AAAGG-AAUUGACGG-AAAGGCA-C-CACCA-GGA-GUGGAG-UCUG-CGGC-UUAAUUCGACUCAACACGGGGAAA-CUCA-CCAGGUCAG-G------ACACAA-GUUUGAUUGA-CA-GG---------UUAAUAGCCCUU-UCU-UGAUU-GUGUGGU-GGGUAGUGCAUGGCCGUU-UCCAGU-UCG-UGGA--GUGA-UCUGUCUUG--UUAAUU-CAGA-UAACGA-ACGAGACCUAAGC-CU-UUAAC-U-AGCCGUAGGCCUUUUCCUUCGGGGAAGGGUUAGUUUGUCGGA------------------------------------------------------------------------------------------------------------------------------------ACUGGCUUCGGCCUUUUCCAAAACCUACGAGACUUUUGUCAGCU-UCUUAAAG-GGA-C-UUCAU-UCG------------------------------------------------------UAAACUA--GGAUGAGGAAGAUUUAGGCCAU-AACAGGU-C-UGUGAUGCUCU-UAGAUGU-CCUGGGCUGCACGCGUACU-ACAAUAACGGUAYCAGCGAGCGCUAUG-------------------------------------------------------------GUUUUUAACCCC-UUAUC--CUAAU-AGGA-U-UG------GG-AAAA-CUU-UUCAAA---------------------------------------CACCGUU--AUGACA-GGGAUCGAGGAUUGG-------------AAC--AUC-CUCG-UGAACGAGGAAUUCCUAGUAA-GCGU-G-GUUCA-UCAUACC-AC-AUUGAUUAC---GUC-CCUGCCUUUUGUACACACCGCCCG-UCGCUCCUACCGAU--GGGA-CGAAGAGAUGAA--CCUGG-CG-GACCAA-----AC-C----------------------------------GCAA-------------G----G---U-AAGGGAAACCAGUU-AAAUC-UCUUC-GUCUGUAGGAAGGAAAAGUCGUAACAAG-GUCU-UCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
DQ158858.1/1336-3258               UAGCUGGUGGAUCCUGC---CAGUAGUU-AUAUGCUCGUCUUCAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------GUAAACCA--CUG--------------------GU-GA--ACUGCGAAUGGCUCAUUA-UACCAGUUAUAA-UC-UAUUUGGUGG------------------------------------------------------------------------UAUGGACUACUCGGA-UACCCGU-AGUAACUCUGUGGCUAAUACGUGCGAAUU----UCCCCAACUCAUCC----------------------------------------------------GUCAAGGAGAUUAGGA--G-GGGCGUAUUUAUUAGUUAUAAA--CGCUAGCCUCGACACUCA----------------------------------------------------GCCUUAAGUUAUAGCCUGAGUG----UAGAGA-----------UCGUGUUGAAUCA--UAAUAACUG-UC---------GAAUCGU---AUGGCCGUUUAGCUACUAGUAUAGCUGAACAACGCUA---ACGA-UGCUCCA-AUCA-AAUUUCUGCCCCAUCA-UCU-UGCACGUUGG-UA-GG--GUAGU-GG------CC-UACCAA-AGAAAUGACGGGUAACGGGGAAU--UGGC------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAGACGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAACUUACC--C-AAUCCUGACG-----CA-GGGA----GGUAGUGACGAAACAU--------------------ACCC-UAG-UAU-A-GAUC---------------CGUGA-UC--U--UGUA-UA--GG---GAAUG-CAUC--------C-AAU-CUAA-A----CCGUU--G-G-GUGAUGACCGAUUGGAGGGCAA-GAC-UGGUGCCAGCAGCCGC-GGUAAUACC--AGCUCCA-AUA-GC-AUAUAUUAG-UGUUGUUG-CGGUUAAA---A--------CGUCC-GUAGUCGAAUUAAAGGCUCG---UAACGCGUCUGACGCUAGGAGUUACUGGGGUGACCAUCCCCAAGGGGUAGCUUGUGUAGCCCUGCGGAGAUAUCGCCCCA--------------------------------------------------------------------------------------------------------------------------------------------------------------UGUUACCUU-GACGAAAUUGUGGUGUUCAUAGCAAGUACG------------------------------------------GAGUACU--CUAGGCACAA-UAGCAUGGAAUAACAACGC-AAGGACU-CCGACC-----------------------------------------------------------------------------------------------------CGGAUUGCGCUAGCGCUCGGGAUCG----GAGGAAGGA-UUAAUAGGAG--CA--GUC--GGGGGCGGUCGUAUUC-CA-U-UGCUAGA----GG------UGAAAUUC-GGUGACCAAUG-GAG--GA-CGAACAA--CAGC-GAAAGCA---UCCGUCC-AGUAUGU---UUUCAU-U-GAUCAGU-GGACGAAAGCUAGG-GGAGCGAACACGAUUAGGCAC-CGUGUGUAGU-CC-UA-GCCGUA-AACGAUACCG-ACUAGG--GGUUGGUGG-A-CGUU--CUUCUCGAU--------------------------------------------------------------AGCUCCAU-CAG-CA------CCU------------------UAUGAGAAAUCA-CAAGCUUUCGGGU--------UCCGGGGG-GA-G--UACGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGGCGG-AAGGGCA-C-CACAA-GGC-GUGGAG-CUUG-CGGC-UUAAUUUGACUCAACGCAGGAAAA-CUUA-CCAGGUCCG-U------ACAUAG-GGAGGAUUGA-CA-GA---------UUGAUAGCUCUU-UCU-UGAUU-CUAUGGG-AGGUGGUGCAUGGCCGUU-UCUAGU-UCG-UGAG--UUGA-CUUGUCAGG--UUAAUU-CCGG-UAACGA-GCGAGACCUCAAC-UC-CUAGC-G-AGCUCAGUACGUUGAAUAUCCGGUGUAGACUUGGGUACAACCAAGAUCCACGAAGG-------------------------------------------------------------------------------------------------------GAGUAGCUUGGUGAAGGCAAUCCGGGUAUGGGCCAGGACCGAGCAUUACGAAAUGAGCA-UCCUAGGA-GGA-C-GCUUG-GU---------------------------------------------------------GGGAA--ACCAAGGGAGGCAUGAGGCGAU-AGCAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCUGCACGCGCGCU-ACAAUGGUGCGAGCAAUGAGAUG------------------------------------------------------------------------AGGGC-UGAAC--CGAGA--GGU-U-UG------GC-GCGC-CUC--GUAAA---------------------------------------CCGCACC--CUGCCA-GGGAUAGAUCAUUGC-------------AAUUGUUG-AUCU-UGAACGAGGAAUGCCUAGUAA-GCAC-G-AGUCA-UCAGCUC-GU-GCUGAAUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUGCCAAU---GGA-UCGGCUGGAGAG--AGCGA-GA-GAU-----------CGACC----AGGG----------------------UAACACCCUC-G-CGUUG----U--------AGACCUCCCUC-GAUCC-GUCAGUAUCUAAAGGAAGGAGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAG-GAUCAUCG
L29264.1/16-2087                   UAUCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUUUCAAGGACUUAGC-CAUGCAUGCCUCAGA------------------------------AUCACUGC--AUU-----------------UGCAG-GAA-UCUGCGCAUGGCUCAUUA-CAUCAGACGUAA-UC-UGCCGCAAGAAUUU-------------------------------------------------------------AGCGGUUUACCGUUCUAUUGGA-UAACUUGUGCGAAACGCCAAGCUAAUACAUGAACCAA----CCGGGUGCUCU-----------------------------------------------------------CCUUUUGCGGGA--C-GCA-GCGAAUGAAUGACAGUAA--AACCAA-----------------------------------------------------------------------------UGCCUUCAC----GGGCAGUAACA-CCUAGCCGUGUUGACUCA--AUUCAUUCCGUGC------GAAAGCCGA---------UUUC------------------------------CCGG-UUUUU-U-GACG-AACAACUGCCCUAUCA-GCU-U--GUGAUGG-CC-GU--GUAGU-GG------AC-UGCCAU-GGCGUUGACGGGAG-CGGGGGAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAAUAGCUACCACUUCUACGGAGGGCAGCAGGCGCGUAAAUUGCC--C-AAUGUCAAAAAAAAACG-AUGA----GGCAGCGAAAAGAAAU--------------------AGGU-UUC-AUA-G-UCCC--------------UUUCGG-GA--UU-GUGA-UU--UC----AAUG-GGGG--------A-UAU-UUAA-ACCCAUCCAA--U-A-UCGAGUAACAAUUGGAGGACAA-GUC-UGGUGCCAGCACCCGC-GGUAAUUCC--AGCUCCA-AAA-GC-GUAUAUUAA-UGCUGUUG-CUGUUAAA---G--------GGUUC-GUAGUUGAACUGAGGGCCGUUGAGUGCGCUGUCCGGUCCACCCCGUUCGGGUGUGUGGCCUCAGCCUUGCGGUCCGUGAACACUCAGAAACAAGAAACACGGGAGUGGUACCUUUCCUGAU--------------------------------------------------------------------------------------------------------UCACGCAUGUCAUGCAUGCCAGGGGGCGUCCGUGAUUUUUACUGU-GACUAAAGAAGUGUGACCAAAGCAGUCA---------------------------------------------UUCGAC--UUGAAUUAGA-AAGCAUGGGAUAACAAAGG-AGCAGCC-AUUGGGCUACCGUUUCGGCUUUUGUUGGUUUUAGAGGUCCUUUG-------------------------GAGAUUGUGGGGCUGCGCGACCGGCGUCAACCUCGCGGUUGGCGCUUUCGGCUUGCCGACUCG---CGGCCUAGGA-AUGAAGGAGA-GUA--GUC--GGGGGAGAACGUACCC-GA-G-CGUCAGA----GG------UGAAAUUC-UUGGACCGCAC-GGA--GA-CGAACUA--CAGC-GAAGGCA---UUCUUCA-AGGAUAC---UUUCCU-C-AAUCA-A-GAACCAAAGUGUGG-GGAUCAAAGAUGAUUAGAGAC-CAUU-GUAGU-CC-AC-ACUGCA-AACGAUGACA-CCCAUG--AAUUGGGGA-C-UUUC---UGCGGGGGGCUUGCCGGGACGGUCGCUACUAAAUCUACGUGCACUUUCCAUCUGCUUCGGGCAACAAGGGAAUGCCCU-CAG-CA------CAUCUGUU-------CUACUUCACGCGAAAGCUUUGAGGUUACAGUC--------UCAGGGGG-GA-G--UACGU-UCGCAAGA-GUGAAA--C-UU-AAAGA-AAUUGACGG-AAUGGCA-C-CACAA-GAC-GUGGAG-CGUG-CGGU-UUAAUUUGACUCAACACGGGGAAC-UUUA-CCAGAUCCG-G------ACAAGA-UGAGGAUUGA-CA-GA---------UUGAGUGUUCUU-UCU-CGAUU-UCUUGAA-UGGUGGUGCAUGGCCGCU-UUUGGU-CGG-UGGA--GUGA-UUUGUUUGG--UUGAUU-CCGU-CAACGG-ACGAGAUCCAAGC-UG-CCCAG-U-AGAAUCCAGAAUUGUCCAUAGGAUAGCUUACUCGCUGG--------------------------------------------------------------------------------------------------------------------------------------------UGGCUUCUUGCCAACGCGGACCGACAUUCGGUCGGAUUCU-UCUCUGCG-GGA-U-UCCCU-GU---------------------------------------------------------UUUGC--ACAGGGUGAAAUUUUGGGCAAC-AGCAGGU-C-UGUGAUGCUCC-UCAAUGU-UCUGGGCGACACGCGCACU-ACAAUGUCAGUGAGAACAAGAAAAACGAU----------------------------------------------------------AUUUCGUCGGACC-UACAUGAUCAAA--AGU-G-UG------GG-GAAU-CCA-CGGAAUC-------------------------------------ACAUAGAC--CCACUU-GGGACCGAGGAUUGC-------------AAUUAUUG-GUCGCGCAACGAGGAAUGUCUCGUAG-GCGC-A-GCUCA-UCAAACU-GU-GCCGAUUAC---GUC-CCUGCCAUUUGUACACACCGCCCG-UCGUUGUUUCCGAU---GAU-GGUGGAAUACAG--GUGAU-CG-GACGAA-----GC-GGACC----------------------------------C------U--GUCU----G---C--UCGAAAGUUCACC-GAUAU-UUCUU-CAAUAGAGGAAGCAAAAGUCGUAACAAG-GUAG-CUGUAGG---UGAACCUGCGGAAG-GAUCAGGA
AFSQ01000300.1/3123-4891           UACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-AAUGCAUGUGUAAGU------------------------------AUGAAAAA-AUUU---------------AGAUUGU-GAA-ACUGCGAAUGG-UCAUUA-AAUCAAUCAUAG-UU-UUUUUUUCAU----------------------------------------------------------------------GGUACCUACUACUCGAA-UAAUCGU-AGUAAUUCUAAAGCUAAUACAUGCAACAA----ACCCCGAGA---------------------------------------------------------------UCUGG---AA--A-GGGCACAUUUAUUAGAUAACAG--GUCAAC-----------------------------------------------------------------------------CUGGGCUCU----GCCAUUG----------UUUAGAAGAUUCA--UGAUAACUUGAC---------GGAUCGA---AAAGCCU--------------------------GCCG---GUGA-CGCAUCA-UUCA-AAUUUAUGCCCUAUCA-ACU-U--UUGAUGG-UA-GG--AUAGA-GG------CC-UACCAU-GGUGGUGACGGGUGACGGAGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUCCUGACA-----CG-GGGA----GGUAGUGACAAUAAAU--------------------AACA-AUA-CCG-G-GCUC---------------AUUGA-GU--CU-GGUA-AU--UG---GAAUG-AGUA--------C-AAU-CUAA-A----CCCCU--U-A-ACGAGUACCCAUUGGAGGGCAA-GUC-UGGUGCCA---GCA-----CAAACCCCGAGAUCUGGAAA-GG-GCACAUUUA-UUAGAUAA-CAGGUCAACCUG--------GGCUCUGCCAUUG--UUUAGAAGAUU---CAUGAUAACUUGACGGAUCGAAAAGCCUGCCGGUGACGCAUCAUUCAAAUUUAUGCCCUAUCAACUUUUGAUGGUAGGAU---------------------------------------------------------------------------------------------------------------------------------------------AGAGGCCUACCAUGGUGGUGAUGGGU-GAUGGAGAAUUAGGGUUCAAUUCCGAAGAGGGA-------------------------------------GCCUGAGAA--ACGGCUACCA-CAUCCAAGGAAGGCAGCAG-GGGCGCA-AAUU----------------------------------------------------------------------------------------------------------ACCCAAUCUUGACACGGGGAGG----CAGUGACAA-UAAAUAACAA--UA---CC--GGGGUCAUUGAGA-----A-U-GGUAAUU----GG------CGAAUUUA-UUAUAUUUUUG-AAA--GA-CGAACAA--CUGC-AAAAGAA---UUUGCCA-AGGAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUGGG-GGCUCGAAGACGAUCAGAUAG-CAUC-CUAGA-CU-CA-AUCAUA-AACGAUGCCA-ACCAAG--UAUCAGCGG-A-UGUU---GCUUUUUG--------------------------------------------------------------GACACUGU-CGG-CA------CCU------------------UAUGAGAAAUUU-AAAAUCUUUGGGU--------UCUCGGAG-GA-U--UAUGA-UCACAAAG-UUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-UGA-GUAGAC-CAUG-CGGC-UUAUAUUGACU-----CA--AAAA-CUUA-CCAGGUACG-G------ACAUAG-UAAUGAUUGA-CA-GA---------CUGAGAGAUCUU-UCU-UGAUU-CUAUUGC-UGGUGAUGUAUGGCCGUU-CUUCAU-UGG-UGGA--GCGA-UUUGUUUGG--UUAAUU-CCAU-UAACGA-ACGAGACCUUAGC-CUACUAAC-A-AGCAAUGCGGAGGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUCUUCCGUGGCCAGCU-UCUUAAAG-GGG-U-UAUAG-CC---------------------------------------------------------UUUUA--GACCAAGAAAU-AUAAGGCAAU-AACAGGU-A-UGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGUGGGCU-ACACUAAUUUAUUCAACAAGUCU-----------------------------------------------------------------------AUAGCC-UUGGC--CGAAA-AAGU-C-CG------GG-UAAU-CUU--UGAAA---------------------------------------UUUCAUC--GUGAUG-UGGAUAGAUCAUUGC-------------AAUUGUUG-GUCU-UCAAUGAGGAAUUCCUAGUAA-GCAC-G-AGUCA-UCGGCUC-GU-GUUGACUAC---GUC-CUUGCCCUUUGUACACACUACCCG-UCGCUCCUACCGAU--UGAA-UGGUCCAGUGAA--GUGUU-UG-GAUCAU-----GG-C---------------------------------------------------G----A---C-AUCGGCGGUUCACC-AAACC-UUAUC-CUUUAGAGGAAAGAGAAGCCGUAACAAG-GUUU-CCAUAGA---UGAACCUGCAGAAA---UCAUUA
AF488396.1/2-1799                  AACCUGGUUGAUCCUGC---CAGUGGU--AUAUGCUUGUCUCAAAGACUAAGC-CAUGCAAGUGCCAGU------------------------------AUGAGUGA-CUCU---------------ACAUAAC-GAA-ACUGCGAAUGGCUCGGUA-AAACAGCUAUAA-UU-UAAUCGGGGG-------------------------------------------------------------------------UAAUACUACUUGGA-UAACCGU-AGUAAUUCUAGAGCUAAUACAUGCUACAU----AAAGUGGAC----------------------------------------------------------------UUUG-GUUC--A-CGGUACAAGGUAUUAGAUACA---AACAAC-----------------------------------------------------------------------------AG---UUUU-----------------------CUGUUGAUU----CAUACUUUUUGU--------CUGAUCGCGUGCAUUCGUGCC-----------------------GAGA---UCGA-CGCCCCG-UUUA-AAUUUCUGACCUAUCA-ACU-A---UGAUGG-UA-AG--GUAGG-GU------CU-UACCAU-GGUUGUGACGGGUAACGGACCGU--GGGU------------------------GCGGGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAACUUACC--C-AAUGCGGACA-----CC-GCGA----GGUAGUGACAAGAAAU--------------------AGCA-AUA-GAG-G-GCCU--------------GAUGGG-CU--UU-UCUA-AU--UG---GAAUG-AGAA--------C-AAU-GUAA-A----CGGCU--U-A-UCGAGGAGCCAGCAGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCUG-UAA-GC-GUAUACCAA-AGUUGUUG-CAGUUAAA---A--------CGCUC-GUAGUCGAACCUUGGUGGGA---UGGCGUGGUGCAUUCGUAAGAUUGUUUGCUGCGCCUUGCACCUUUGUGGAUUGGCGGCAGCCUGGUUCUUUAUUGAGUUG----------------------------------------------------------------------------------------------------------------------------------------------GGCUGUUGCUGCCACCGUUUACUGU-GAAUAAAUUAAAGUGUUCAAAGCAAGCG---------------------------------------------UUUGCC--CUGAAUACAU-UAGCAUGGAAUAAUAGAAA-AGGACCU-GUGUUU-----------------------------------------------------------------------------------------------------UCUUUUCUGUUGGUUUGUGAAAAUC----GGGUAAUGA-UUAAGAGGGA--CG--GUC--GGGGGUAUUUGUAUUC-CG-G-CGUUAGA----GG------UGAAAUUC-UUAGAUCGCCG-GAA--GA-CAAACAG--CUGC-GAAAGCG---UCUACCA-AGGACGU---UUUCAU-U-GAUCA-A-GAACGAAAGUAAGG-GGAUCGAAGACGAUCAGAUAC-CGUC-GUAGU-CC-UU-ACUAUA-AACGAUGAGG-ACUGGG--GAUCGGGCG-U-GGCC---GCUUAA----------------------------------------------------------------GGUACGCU-CGG-CA------CCC------------------UCCGCGAAAGCA--AAGUGUUUGCUU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-U-CACCG-GGU-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUUA-CUAGGUCAG-G------ACAUCG-UAAGGAUUGA-CA-GA---------UUGAGAGCUCUU-UCU-UGAUU-CGAUGGU-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UCUGUCUGG--UUAAUU-CCGU-UAACGA-GCGAGACCUGGGC-GUGCUAGC-U-AGGCGCCACUACUA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUUUGGUAGUGUUUGUGGUUCCU-ACCUAGAC-GGA-C-UGCAG-GC---------------------------------------------------------UUCUA--GCCUGCGGAAGCUCCAGGCAAU-AACAGGU-C-UGAGAUGCCCU-UAGAUGU-CCUGGGCCGCACGCGUGCU-ACACUGAAUGGUUCAACGGGUGA---------------------------------------------------------------------------GG-UGAUG--CGAGA--GCA-U-UA------CC-GAAU-CUC---UAAA---------------------------------------UCCAUUC--GUGAUG-GGAAUAAUGGUCUGC-------------AAUUUUUC-CAUU-UGAACGAGGAAUACCUUGUAA-GCGU-G-GGUCA-UCAUCCC-GC-GCUGAAUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGAG-UGGUCCGGUGAG--GCCUU-GU-GAGAUC-----UG-AGAGUC-ACUGGUA-------------------UCUUUUUACCAG-U--CUUU----C---G-GUUCAACCUUGGUC-AAACC-UUAUC-ACUUAGAGGAAGGAGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAGG-AUACAAGC
X76638.1/1-2082                    AACCUGGUUGAUCCUGC---CAGUAAUC-AUAUGCUUGUCUCUAAGCUUAAGC-CAUGCAUGUCUAAGU------------------------------UCAAACGU--------------------UUAAUGU-GAG-ACUGCGAAAGGCUCAGUA-AAUCAGCUAUAA-UC-UAUUUGAUUG------------------------------------------------------------------------UUAACUCCCAGUGGA-UAACCGU-GGGAAAUCUAGAGCUAAUACAUGCAACUA----AACUGUACCCU-----------------------------------------------------------GUCAAAGGGGUG--C-AGUAGCAUUUAUUGGAAAUACC--AACUUUGGG-----------------------------------------------------------------------CGAGUGGGUUUA----CCUGCUCGU-----CUAGAUAGGUGAAUCU--GGAUAACUG-GC---------UGAUCGU---AUGGCCUUGU-----------------------GCUG---ACGA-CGUUUCA-AUUG-AAUUUCUGCCCUAUCA-ACU-U----GUUGG-UA-AG--GUAGU-GG------CU-UACCAA-GGUUGUAACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAAUGGCUACCACAUCCAAGGGAGGCAGCAGGCGCGCAAAUUACC--C-AAUCCACAAU-----GU-GGGA----GGUGGUGACGAGAAAU--------------------AUUA-GGU-CGU-U-UUCC-------------CUCAGGG-AA--UG-CGAU-AC--UG---AAAUG-AGCA--------C-AAU-UUAG-A----ACAUU--U-G-UCGAGUAACAACUGAAGGGCAA-GUC-UGGUGCCAGCAGCCGC--GUAAUUCC--AGCUUCA-GUA-GU-GUAUAUUAA-UGCUGCUG-CGGUUAAA---A--------CGCUC-GUAGUUGAAUGACGAAGCAC---GGGACGAUACUUUAACGUAUGCUACAUCAAACCGUGUUGCAGUAUUGCGAANNAGACCACGUCUGUCUAGCGAUGGUGCAGCAUGGCGUGGCGUAUGUUAAUUAACAGUCGUUCCGGGC--------------------------------------------------------------UACUAGAUUGUGAGAAUGGUGAAUGGUCUUCACUGACUGCUCAUCGUGUCUCGCAGAGUGUGCCUU-GAAUAAACCAGAGUGCUCAAAGCAGGCA---------------------------------------------UGUUGC--UUGAAUGUUAAUAGCAUGGAACGAACAAAU-GUGAUUU-CGUGUACUGACAAGUAAUGCACAAUGAUUUACAUUGUUG-----------------------------------UGCACUAACUGGCAGUACAUAGCACCAACCACCAAGGCGGAUGUUGGUUUCCGUUUUG----GGGUGAUGA-UUAAAAGGGG--CG--GUU--GGGGGCAUUGGUAUUU-GG-C-CGCGAGA----GG------UGAAAUUC-UUGGACCGGCC-AAG--GA-CUAACAA--AUGC-GAAGGCA---UCUGCCA-AGACCGU---UCCCGU-U-GAUCA-A-GAGCGAUAGUGAGA-GGUUCGAAGACGAUCAGAUAC-CGUC-CUAGU-UC-UC-ACUGUA-AACUAUGCCA-ACCCGG--GAUCAGUUU-U--GAG---CUAAGUAUAA---------------------------------------------------------ACGCUCGUGGU-UGG-UC------CCC------------------U--GGGAAACCU-UAAGUUUUUAGGU--------UCCGGGGG-GA-G--UAUGG-UUGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUCA-CCCGGUCCG-G------ACAUCG-AUAGGAUCGA-CA-GA---------CUGAUAGAUCUU-UCG-UGAUA-CGGUGUA-UGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGAA--GUGA-UUUGUCAGG--UUUAUU-CCGG-UAACGA-ACGAGACCAUAUU-CU-CCAUU-UACGGAGUCGAUGCAGCAUCAGCCUGUCAGGGGCAACUCUGCCAGGCGAAGUGCGACGAUUAAAUUGGUGAUUC-----------------------------------------------------------------------CCCGGUACCUGUAUCGAGGGAUUGCUUUUUUUCCAUUGACUAAGCAUUGUGUAGCCUUAAAAACUGCAUAGUGCG-CUAUGGAG-AGA-C-AACCG-GGUA----------------------------------------------------UAUCCAAA--GCCGGAGGAC--GUAUGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCGGGGCCGCACGCGCGCU-ACAAUGGUAACAACAGAAAGA----------------------------------------------------------------------------GUC-UGGUU--CGAAA--GAA-U-CA------GG-UAAU-C---AUAAAU---------------------------------------UGUUACC--GUAAUG-GGGACUGUGCUUUGU-------------AAUUAUCG-CACA-CGAAAGAGGAAUUCCUAGUAA-GUGC-U-CGGAA-UCAACGA-GU-GCUGAUUGC---GUC-CC-GCCCUUUGUACACACCGCCCG-UCGCUACUACCGAG--UGAA-UGGUGUCAUGAU--GCCUU-GU-GACCGG----ACG-UCGUA----GACGG-------------------UGCAAGCCGUCG-A--ACGA----U---G-CUGGAAUCAAUGUA-AAAUG-GCGCA-AUUUCGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
AF093247.1/6-1995                  AACCUGGUUGAUCCUGC---CAGUAGU--GUAUGCUUUUCCUAAAGAUUAAGC-CAUGCAUGCCUAAGACU-------------------------AUGAGGAAGCA--AUU----------------CUCUCU-GAA-UCUGCGAACGGCUCCGCA-AACCAGUUGUAA-AC-CAUAGCAGCGUUCCGCCCGGC-----------------------------------------------UUCAGCAAUGGGGCCGGGCAUUAUAUGGA-UAACCGU-GGUAAUUCUGAGGCUAAUACAUGACA-------CACUAACCC-----------------------------------------------------------------GUC-GGGC--U-GGGGGCAACCUCGGCUUGGUG---GGGGACGUGCGAUAAACACCGGCUA--------------------------------------CAAUUAAAAAUACCGCGAAAAGGACGCAC----GUUCAG------------ACCGCCAUCCAA--ACGGGGGAGGGG--------GCUUCGGC---UUCGG--AAC-----------------------CCGG---GCGG-CCCCUGC-AACG-GGCUUCUGACCUAUCA-ACU-A----GACGG-CA-GC--GUAAG-GG------ACAUGCUAU-GGUAACAACGGGUA-CAGAGGAU--UAGG------------------------GUUCGAU-C-CUGGA--GAGUGGGCCUGAGAGAUUGCUCAUACUUCUAAGGAAGGCAGCAGGCGCGCAACGUUCC--C-CUUGGGCAAA-----GC-UCGA----GGGCGUUAUGGGAAAU--------------------AUGA-AUG-CUU-G-CCUU-----------------UAC-GG--UG-GGCA-AU--UC---AAAUG-GGUU--------U-GUC-GUAA-A----CAGGC--U-C-UCGAGUAACAAUUAGAGGACAA-GUC-UGGUGCCAGCACCCGC-GGUAAUUCC--AGCUCUA-AUA-GC-AUACGUUAA-AGUUGUUG-CGGUUAAA---A--------CGCUC-GUAGUCGGCUUCAGACCAUCA-GAAGCCUGGCUCGGGGUCUCGGGUCUGUGCCUCGCAAGGGGUGCGCCUUGGUCUUGGGCCGGGUGGGCGGCGGUCAAUCGUGCCCAGUGGCGUGUCGCGGCUUGCCGUGGCUUACAGGGCCUU--------------------------------------------------------CGGGAUCAAAACCCGGCUUCCGCAAGGGGGUCGGGUCCCGUCGGUCUGGCUCUGGGUACCAAUUACCAU-GAUUAAACCGGAGUGAUCAAAGCAAACCGCU-----------------------------------------GCGGUUA--CUGCACGGAU-UAGCAUGGCAUAAGGAUGC-GUCGGGU-UGGUC-------------------------------------------------------------------------------------------------------UCGUAGCGGGCCUCCUCGGCAAUU----CCGCGAA--------AGGGG--UG--UUC--GGGGGCAGCCGAAUUG-CC-G-GGCUAGU----GG------UGAAAUAC-GUUGACCCUGG-CAA--GU-CGACCGA--AAGC-GAAAGCA---GCUGUCA-AGGGCAC---ACCCGU-U-GAUCA-A-GAGCGAAAGUUAAG-GGUUCGAAGACGAUCAGAUAC-CGUC-GUAGU-CU-UA-ACUAUA-AAUGAUACUG-GCCAGG--GAUAGGGCA-A-UGUC---CAUCUC----------------------------------------------------------------GACUCCCC-CCG-GA------CUU------------------U-UGGGAAACCA--AAGCCUAUGAGU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA---CACAA-AGA-GUGGAA-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUCA-CCGGGUCCA-G------AUACAU-GGAUGAAAGA-CA-AG---------CUGAUAGACUUU-UCU-CAAUU-AUGUAAG-UGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA--GUGG-UUUGUCUGG--UCUAUU-CCGA-UAACGA-GCGAGACCCCAAC-GGUCUAAA-U-AGGGGCCGCAGCCCGGCUCGGCUCGCCUUCACGG----------------------------------------------------------------------------------------------------------------------------------------------------GUGGGCCUUGCUAGCAGCGCGCUUCGAAGGCAAGCU-UCUUAGAC-GGA-U-CGGGG-CC---------------------------------------------------------GAUAA--GGUCUCUGAA--AUGGGUUAAU-AACAGGU-C-AGUCAUGCCCU-UAGAUGU-UCCGGGCCGCACGCGCGUU-ACAAUGGGGGGCAAAACGAGUGUCCGU-------------------------------------------------------------CAGGGCUUUUCC-GCCGC--CUACC--GGU-G-GU------GG-UAAC-C---CGUAGG---------------------------------------GCCCCCC--UUGACU-GGGCUAGUCUCUUGC-------------AAUUAUUG-GUCU-UCAACGAGGAAUUUUUAGUAG-GCGC-G-GGUCA-UUAACCC-GU-GCCGAAUGC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUGCUACCGAU--UGGG-UUUCGCGGUUAC--GUAUU-CG-GAGAUU-----CU-UUCAA---CUGCUGC-----------------CGCAAGGCGGCGG-G--CGAC----U---G-GGUCUAAGUCUAAA-UUACC-GCACG-GCCUAGAGGAAGCAGAAGUCGUAACAAG-GUAA-UCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
ACVC01000016.1/1500-51             CAUCCGGUCGAUCCUGC---CGGAGCG--CGACGCUCUCCCCAAGGACGAAGC-CAUGCAUGCC--CGC------------------------------UCACCC---------------------------GG-GAC-GCGGCGGACGGCUCAGGA-CGACGGUUGCAC-CC-CCCGCGGCGG------------------------------------------------------------------------UCCCUGCUAGCCGGA-CACCGCU-GGCAAC-CCGGCGCCAAGACGUGCGC-------------------------------------------------------------------------------------------------GCAA----------------GGGCGG-----------------------------------------------------------------------------GCGCCCGCG----GGCGAG------------CAGCGUGACGCA--------GCGA------------------------------------------------------------------CGGCCCG-CCCG-GGCUUCCGGGGCAUCA-CCC-G----GUCGG-CG-CG--GUCGC-GG------CG-CGCCGA-GGGCCCGACGCCUGGCGGAGAAU--CAGG------------------------GUUCGAC-U-CCGGA--GAGCGGGCCUGCGAGACGGCCCGCACAUCCAAGGACGGCAGCAGGCGCGGAACUUGCC--C-AAUGCGCGGC-----GC-GCGA----GGCAGCGACGGGGA------------------------GC-G-----------------------------------------------C--GC---GAGCG-AGGC--------G-GGC-CCAC-A----GCCCC--C-G-CCGCGGA----GCCGAGGGCAAGGUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCGG-CGA-GC-GUCGCGCGG-CGCUGCUG-CAGUUAAA---A--------CGCCC-GUAGUUGGCCCCCCGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCCAC-GAGGAAACGGGAGCGCUCCAGGCAGGCCCG-------------------------------------------UUGGAC---------CCG-CCGCGUGGGACCGCGCAGC-GGGCGAG-GCGC-----------------------------------------------------------------------------------------------------------------------------GCC----GCGGCAGCC-CCGAGGAGAG--CG--GGC--GGGGGCACCGGUACCG-GC-C-GGGGACG----GG------UGAAACAG-GAUGAUCCCGC-CGA--GA-CCGCCGG--CCGC-GCAGGCG---CCUGCCA-AGACCGC---CUCUGU-C-AAUCA-A-GGGCGAAGGCCGGG-GGCUAGAAGGCGAUCAGACAC-CACC-GUAUU-CC-CG-GCCGUA-AACGGUGCCG-CCCCGC--GGCCGGCGC-G-----------CGCGU-----------------------------------------------------------------CCCGC-CGG-CC------GC-------------------CCAGGGAAACCG-GGAGGCUCCGGGC--------UCUGGGGG-GA-G--UAUGG-CCGCAAGG-CUGAAA--C-UU-GAAGG-CAUUGACGG-AGGGGUA-C-CACCA-GAC-GUGGAG-UCUG-CGGC-UCAAUCUGACUCAACGCGCG-CAC-CUCA-CCAGGCCCG-G------ACGCGC-GGAGGACCGA-CA-GC---------CGGGC-GCGCUU-UCG-CGAUC-GCGCGGG-CGGUGGUGCAUGGCCGCU-CCCAGC-CCG-UGGC--GCGA-GCCGUCUGC--UCCAUU-GCGA-CAACGA-GCGAGACCCCGGC-CG-CGGGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCCGCG-GGA-C-GGCCC-GC---------------------------------------------------------G-CGA--GCGGGAGGACG-GCGGGGCGAU-AGCAGGU-C-UGUGAUGCCCU-CAGACGC-CCUGGGCCGCACGCGCGCU-ACACUGGCGGGGCCAGCCGGC----------------------------------------------------------------------------------GCC--CGCGA--GGA-C-----------------GCG-CGGAGC---------------------------------------CCCCGCC--GUGGCC-GGGACCGCGGGCUGG-------------AAC--GCC-CCCG-CGCACCAGGAAUGUCUUGUAG-GCGC-C-CGCCC-CCACCGC-GC-GCCGGACGC---GUC-CCUGCCCCUUGUACACACCGCCCG-UCGCUCCUACCGAC--UGGG-CGCGGCGGCGAG--CGUCC-CG-GAC--------------------------------------------------C--------------------------GGAAGGGCCGC-GAGCC-CCCGC-GCCUGGAGGAAGGAGAAGUCGUAACAAG-GUAU-CCGUAGG---UGAACCUGCGGAUG-GAUCCCUC
CABX01000103.1/7705-5898           AACCCUCUAGAA---GG---AAGCAAG--GAAGGCUCGUCUCAAAGAUUAAGC-CAUGCAUGUGUAAGU------------------------------CUAAAUAG--UUU----------------UAGUGU-GAA-ACUGCGAAUGGCUCAUUA-UAUCAGUUAUAG-UU-UAUUUGGAAU-------------------------------------------------------------------------AGUUUCUAUAUGGA-UAACCGU-AGUAAUUCUAGGGCUAAUACAUGUGUU------UUCUUUGAUG-------------------------------------------------------------GGCAACCAUUA--A-AGAAGUACUUAUUAGACAUAAA--AC-----------------------------------------------------------------------------------CAAUUUA----AUGUUG------------UU--GUGAGUAA--UAAUAAUUGUUGA------CUUUAUCGC---AUGCU-UGUU-----------------------AGUA---GCGA-UGUUCCU-UUCA-AGUUUCUGCCCUAUCA-GCU-U--UCGAUGG-UA-GU--GUAUU-GG------AC-UACCAU-GGCAGUAACGGGUAACGAAGAAU--UUGG------------------------GUUCGAU-U-UCGGA--GAGGGAGCCUGAGAGAUGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACC--C-AAUCCUGACA-----CA-GGGA----GGUAGUGACAAUAAAU--------------------CUCA-AUA-CGA-A-GCC----------------UUU-G-GU--UU-UGUA-AU--UG---AAUUG-AGAA--------C-AAU-GUAC-A----AUCGU--U-A-UCGAUAAACAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-CGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUUGAAGUUUAGA-----------UAAUUUAUUGAAAGUGUUUGUAUUCGUACAUUCUACUUUUAUGUAAGUUAUCGACAUCCAGGUGGGUGCCAUGGUUCCGCAA---------------------------------------------------------------------------------------------------------------------------------GGAACUGUGGUACUAGACUGGUCAUUUACUGU-GAGAAAAUUAGAGUGUUUAAAGCAGACUUUU-----------------------------------------AUUCAGU--UUGAAUAGAU-UAGCAUGGAAUAAUAAGAU-UGGCUUU-CAUAG-------------------------------------------------------------------------------------------------------UCGAUUUUUUGGUUUGU--UUAUG----AAAGCAAGA-UUAAUAGGGA--CA--GUU--GGGGGUAUUCAUAUUC-AA-U-AGCUAGA----GG------UGAAAUUC-UAUGAUUUAUG-GAA--GA-UGAACUA--GUGC-GAAAGCA---UUUACCA-AGGAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGCUAGG-GGAUCAAAGAGGAUUAGAUAC-CCUC-GUAGU-CU-UA-GCUAUA-AACGAUACCG-ACUAGG--AGUUAGUAG-A-UGAU---CCAAUG----------------------------------------------------------------GUGUCUAU-UAG-UA------CCU------------------UAUGAGAAAUCA--AAGUCUUUGGGU--------UCCGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGAAA-CUUA-CCAGGUCCA-G------ACAUAG-GAAGGAUUGA-CA-GA---------UUGAUAGCUCUU-UCU-UGAUU-CUAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUUAUU-CCGA-UAACGA-ACGAGACUUCCGC-CUAUUAGU-U-GGAUGAAAUGGGAU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUAGUAAUGCCCCAUUGUAAUUUUUCAUCA-ACUUAGAG-GGA-C-ACUGU-GC--------------------------------------------------------GUUUGA--GUACGGGGAAGCUGGAAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCUGCACGCGCGCG-ACACUGAACUAUUCAACGAGU----------------------------------------------------------------------------AUC-UGAGU--CGAUA--GAC-U-UG------GG-AAAU-CUU-UUGAAA---------------------------------------AUAGUUC--GUGAUG-GGGAUUGAUGCUUGU-------------AAUUUUUC-AUCA-UGAACGAGGAAUUCCUAGUAA-AUGC-A-AGUCA-UCAACUU-GC-GUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCACCUACCGAU--UGGA-UGAUCCGGUGAA--CACUU-UG-GAUUUU-----UA-AUUAU---UUAUCG-------------------GCUUGCUGGUAG-A--UAGU----U---G-AAGAGAAGUCGUGU-AAAUC-UUAUC-AUCUAGAGGAAGGUGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
DQ093794.1/1-1758                  -ACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCGCAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUAAACAG--AUU-----------------ACAGU-GAA-ACUGCGAAUGGCUCAUUA-AAACAGUUAUUG-UU-UGCUUGGAGU-------------------------------------------------------------------------AUUUUUCCACCGGA-UAUCCGU-GGAAAUCCUACAGCUAAUACGUAGCCAAU-----------CC---------------------------------------------------------------UUUAG-GGGA--------UGUAGCAUAUUAGUUUGA--ACAAUC-----------------------------------------------------------------------------GGCACAUUU----UUGAUGUGU------GAAUUAUGAGAAAUU--UUAUGCACG-------------AAUCGU-------AUAUCA-----------------------U------ACGA-CAGUCCA-UCAA-AGUUUCUGACCUAUCA-GGU-U--CCGACGG-UU-GG--GUAUU-GG------CC-AACCGU-GCCUAUAACGGGUAACGGGGGAU--UAGG------------------------GUUUGAU-U-UCGGA--GAGGGAGCAUGAGAGAUGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACC--U-AUCCCUGACU-----CA-GGGA----GGUAGUAAACAGAAAU--------------------AAUG-GCA-CAU-G-UU-----------------UUA---AA--CA-UGUG-AU--CG---GAACG-AAUG--------G-UUU-CUAA-A----UAAAA--C-C-AUGA-AAGCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUACC--AGCUCCA-AUA-GC-GUAUAUUAU-UGAUGUUG-CAGUUAAA---A--------AGUUC-GUAGUUUGACUUUGCCUGUU---UAUUAGAUUCUAAAUAUUAUGUUUGGAAUCAAUUUAAGCAGAGAUUUGCAGAACAACACAACAUGCAUUGCGUGUUUGUG----------------------------------------------------------------------------------------------------------------------------------------------------GAGUUUAGCAUAUUACUUU-GAGUUAAUCGGCGUGUUCCACGCAGGCU---------------------------------------------UUUGUC--UUGAACGAUU-UACCAUAGAAUAACAAAUU-UAUGAUU-UUGU-----------------------------------------------------------------------------------------------------------GUCUUUGUUUGUUCGGACACA----UUAUCUAUA-CGAAUAAGAA--CG--GUU--GAGGGCAUUCGUAUUC-AA-C-UGCCAGA----GG------UGAAAUUC-UUUGAUUAGUU-GAG--GA-CGAACAA--UUGC-GAAAGCA---UCUGCCA-GGGACGU---UUCUGU-U-GAUCA-A-GAACGAAAGUUAGG-GGAUCGAAGAUGAUUAGAUAC-CGUU-GUAGU-CC-UA-ACCAUA-AACUUUACUA-UCCAAG--AGUUGGAUU-A--GUU---AUUUUA----------------------------------------------------------------UACUCUUC-CAG-UA------CUU------------------UUUGAGAAAUCA-UAAGUCUUUGAGU--------UCUGGGGG-GA-G--UAUAG-UUGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CUUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUUA-CCAGGACAA-G------ACAUAA-GAAGGAUUGA-CA-GA---------UUGAUCGCUCUU-UCU-UGAUU-UUAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA--GUAA-UUUGUCUGG--UCAAUU-CCGU-UAACGA-ACGAGACCUCAAC-UAACUAAU-U-GGUGAUGUUUAUGUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUAAAUAUAAAUAUCCG-UGUUAGAA-GGA-C-CAUGU-GU---------------------------------------------------------GUUUA--ACACAAGGAAGCGUGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUAU-CCUGGGCAGCACGCGUGCU-ACAGUGAUAUAUAUAAUGUGUUA---------------------------------------------------------------------------CA-CCACC--UGAGA--GGG-C-GG------UG-CAAU-CAU---AAAU---------------------------------------GUAUAUC--AAUACA-GGGAUUGCUUGUUGG-------------AAU-GUCA-AGCA-UGAACGAGGAAUUCCUAGUAA-GCGU-G-UAUCA-UUAGUUC-GC-GUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCGUCUAUUGAU--UAGG-UAGCAUCAUGAG--UGAGG-CA-GAGGAG-----AA-AUAUU---UUUAG---------------------AUUCGUCUAAU-U--UUAU----U---U-UACUGAAGCCCCGC-GAAUG-GUGCU-ACCCAGAAACAGACAAAGUCGUAACAUG-GUUU-CUGUAGG---UGAACCUGCAGAAG-GAUCAA--
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L81935.1/1-2018                    --CCUGGUUGAUCCUGC---CAGUAGCG-AUAUGCUCGUCUUAAAGAUUAAGC-CAUGCAAGUCUCAGU------------------------------ACAGACUG---UA---------------AUAAAGU-GAA-GCCNCGAAUGGCUCAGUA-AAACGGUUGUGA-UC-GGUGAGACGG-----------------------------------------------------------------------AGAGAUCCUAAUUGGA-UAACUGU-GGCAAUUCUAGAGCUAAUACAUGCCUG------UUCGCGACCCG-----------------------------------------------------------CUUCGGCGGUAA--G-CGCAGCAUUUGUGCAGCCACC---ACCGGC-----------------------------------------------------------------------------GUUCCCUGC----GGGGUUCGUCU--CGGAGUCCGAUGAAUCG--GAACANACA-GU---------CGAUCGC---ACGGUCAAGU-----------------------ACCG---GCGA-CGCGUCU-CGAU-GGUGACCGACUUAUCA-ACU-G--UAGACGG-CU-GG--GUAUU-GN------CC-CNCCGU-GGUUACCACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAAGGAGCCUGAGAGACGGCUACUACAUCCAAGGAAGGCAGCAGGCGCGCAACUUACC--C-AAUCCCUGAA-----CG-GGGA----GGUAGUGACGAAAAAU--------------------AACG-AUG-CGA-G-ACUCG------------AUACCGAUGU--CU-UGUG-AU--CG---UAAUG-AGUG--------C-GCC-GUAA-A----CAGGU--G-U-GCAAUGAUCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-AUAUACUGA-AACUGUUG-CGGUUAGA---A--------AGCUC-GUAGUUGGAUGUUCAUUCUCG-AGCUCACGGUGUCAGCUAGCCUGACUUACCGUGGUGACGGUCGGUCGCGUUGCACCCGGUGCUCCGGUGCUGUACUCGCGGUCCGUCCACUCCGGGACAUUAUUUGUCCCGUCGC------------------------------------------------------------------------UUCACCCUUCCGUCUCUCUUCACUGAGUUUCGGCUUGGGCUGGCGGCAGUGAAAUUACCUU-GAAAAAAUUAGAGUGCUCAAAUCAGGCU---------------------------------------------CAUUGU--CUGAAUACGG-AUGCUUGGAAUAAUGGAAG-AGGACCA-CGAGU-------------------------------------------------------------------------------------------------------CCUAGUUCCUGUUGGUCGGACCUC---GUGGUAAUGA-UUAAUAGGGG--CC--GAC--GGGGGCAUUCGUACUG-UG-G-GGCGAGA----GG------UGAAAUUC-UGAGACCCCCG-CAA--GA-CGAACAA--GAGC-GAAAGCA---UUUGCCA-AGGAUGU---UUUCAU-U-GAUCA-A-GAACGAAAGUCAGA-GGUUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UG-ACCAUA-AACUAUGCCA-ACUGGC--GAUUGGCCG-G-CGACG-CUUUUGUGA--------------------------------------------------------------AGCCUGGU-CAG-AC------UCC------------------CUCGGGAAACCA--AAGUUUUUGGGC--------UCCUGGGG-AA-G--UACGG-UUCCAAAA-CUGAAA--C-UU-AAAGG-AAUUGACGG-A-GGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGUAAA-CUCA-CCAGGCCCG-G------ACGCUG-GGAGGAUUGA-CA-GA---------CUGAU-GAUCUU-UCU-UGAUU-CAGUGAU-UGGUGGUGCAUGNCCGUU-CGUAGU-UGG-UGGA--GUGA-UCUGUCAGG--UUAAUU-CUGA-UAACGA-ACGAGACAUUUGU-CUAUUAAA-U-AGAGUCCGCGGGACCGAACUAGGGGAUGCUUGAGUUUGAAGCGUGCCAAGCGUAGGUUGUCUCUCAGUGUCGGGUC----------------------------------------------------------------CGUCCCACAGCUGUAGAGCACCUCGCCUCUGGUCACUGUCUGAAGCCAGGCGUUUCUGAAAAAGUCCCCGGCACCUCU-UCUUAAAG-GUA-C-AGGCG-ACGU-----------------------------------------------------GAUGAAA--GUCGCAGGAAGGGAGAUGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CCUGGGCUGCACGCGCGCU-ACAAUGGCCGUGUCAGCGAGUUU--------------------------------------------------------------------------UUC-CUGCC--CGAGA--GGG-U-UG------GG-UAAU-CUC-CUGAAA---------------------------------------CGCGGUC--GUAGUC-GGGACCGGGGAUUGC-------------AAUUAUUC-CCCG-UGAACUGGGAAUUCCCAGUAG-UCGC-G-AGUCA-CCAGCUC-GC-GGCGAUCGA---GUC-CCUGCCCCUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAG-CGGUUGAUCGAG--GUCCU-CG-GACCGC-----GU-CCCUU----GCAAGG-----------------CUUGCUCCUUGCC-U--GUGG----UA-CC-GCGGGAGGUUGACC-GAGGU-UAGUC-GUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUU-
DQ378017.1/3-2157                  UAUCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------CCAAGCUGUGUUU---------------ACACGGC-GAG-ACCGCGGACGGCUCAUUAAAAUCAGUCGUUG-UC-CAAAUGGGCC----------------------------------------------------------------------AGUCCUUACUACUUGGA-UAACUGU-GGUAAUUCCAGAGCUAAUACAUGCAACUGUUAACCCCGAAGGCGGGAG---------------------------------------------------CUUGCCUCUUGCUCGA--C-GGGUGCUUUUAUUAGACCAA----ACCGCUGGGAG------------------------------------------------------------------AGACUCACGUCUCUC----GACUCGC---------UGUGUGGUGACUCU--GGAUAACCAAUUUU-----GACAAGCGC---ACGUACCCCUCG------------------UGGGACG---GCGC-UGCCACU-UUCG-AGUGUCUGCCUUAUCA-GCU-G--UCAACCG-UU-CG--UUACA-CG------CG-ACCGAU-GGCUUUGACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGCAGCCUGAGAGACGGCUACCACGUCCAAGGACGGCAGCAGGCACGCAAAUUACC--C-AAUCCCAGCAC--CUGG-GGGA----GGUAGUGACGAAACCU--------------------AACG-AUG-CGG-GCGCCC-------------UUUACGG-GC--CC-CGCA-AU--CG---GAAUG-AGCA--------C-UUU-CUAA-A----CAACC--U-G-UUGAGAACCUACUGAAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUUCA-GUA-GC-AUCUAUUAA-AGUUGCUG-CGGUUAAA---A--------GGCUC-GCAGUUGAAUGUCAGUGCCG---GUUGUUGGUAGGUGGACGUUGGGAUGUCAGUUAAAGGCGCAAGCCAACUGGUCGCUCCCGUCCGUUAAAAGCCUCCGCGACCGUGUACACAGUGGCGCCAAG------------------------------------------------------------------------------------------------CGGAGGGGAUGCGUUCGCGUGUUCUUCUCUCUGGUGCCAAUGUCACCCU-GAGUAAAUCAGAGUGCUUAAAGCAGUCGUAUUGGGCGCAAGCCUUUGAACACAGUCGCUCCUUCGCGGGUGACACGGAC--AGACUUGGUU-UUGCAUGGCAUGUCAGAAC-ACGACGU-CGGGCGCUGGCUC---------------------------------------------------------------------------------------AGAGUUCUUCUCAGUGGUAUAAGCCAGCCUCG----ACGUACUGA-UUAAAAGGGC--UU--GUC--GAGGGCAUUGGUAUUG-CG-G-AGCGAGA----GG------UGAAAUUC-UAUGACCUCCG-CAA--GA-CCGCCCG--AAGC-GAAAGCG---UCUGCCA-AGGAUG----UUUCAU-U-AAUCA-U-GAACGAAAGUUAGA-GGAUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UA-ACCUUA-AACGAUGCCA-ACCAUC--AAUCCGCGC-G-CAGC---ACCCUCUUUG---------------------------------------------------------CGGGCUCG-GC-GGG-CA------GCUCUC------------UAUCACGGGAAACCA--GGGUCUCUGGGU--------UCCGGGGG-GA-G--UCUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAAGGCA-C-CACCA-GGC-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGCAAU-CUCA-CCAGGCCAG-C------ACUCUA-GCAUGAUUGA-CA-GA---------UUGAGAGCUCUU-UCU-CGAUU-CAGUGGA-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UCUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACUCUCCC-CUGCUAAC-U-AGUCGGUUGGAUCUUGAUCUGCGAGUGUGUGCCCUGUGAGGUGCUUGGUUGUUGCUGCGUGCGUGUUUGUGUCCCCAGCAAUG-------------------------------------------------GGUGAUCCUGCGCGUGCGUUGGUGGCUUCCAUUGCUUCGCUGGUAACGCAUACUCCAAGUCCGCCGCUUGUCUUAGAGAAUAUUCU-UCUUAGAG-GGA-U-CCACG-GC--------------------------------------------------------UCUGAA--GCCGUCAGAGACUGAGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGC-UCUGGGCCGCACGCGCGCU-ACAAUGCCGGGCACAGCAGGUGU----------------------------------------------------------------------UUCUUCC-UGCUC--CGAGA--GGA-G-CG------GG-CAAC-CCU-CUGAAAGCCCCAUACUUGACUUGCGUCGCCUUCACGGGCGCGCAGGAGCGGC--GUGCUU-GGGCCUGGGGCUUGC-------------AAUUAUUC-CCCA-CAAACGAGGAAUGCCUAGUAG-CGGU-G-GGUCACUGAGCCC-GC-CGUGACUGA---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGGG-UGUACCAGUGAG--AGCCU-UG-GACUGG-----CG-GCCGU----UGCUUUC---------------CUUCAUGGUAGCAA-A--CGGA----CU-CG-ACUGAAAGAGGUCC-GAACU-GGUGC-ACUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAA-CUGCGGAAG-GAUCAUUA
AF368508.1/1-1900                  -UUCUGGUUGAUUCUGC---CAGUAGUC-AUAUGCUCGUCUUUAAGAUUAAGC-CAUGCAAGUCUAAGA------------------------------UCAGGAAG--GUU---------------UACCUUC-GAA-UCUGCGGAUGGCUCAUUA-AACCAGUGUUAA-UC-UAUCAGAUUA----------------------------------------------------------------------------ACAUAGACGGA-UACCCCA-GGCAAAUCUUGGACUAAUACGCGCAACAUAACAGCUCUGACU---------------------------------------------------------------UUCAU-GGAA--G-GAGUGUGCUUACAAGUCCAAAACCAUCGCU-----------------------------------------------------------------------------UGAAACUUG----UUUCUUGC-------UUUGAAAUUGAAGAA--AUGUAACUUCAC---------UGAUCGU-----AGCACGUC-----------------------ACU----ACGA-CAUGUCU-GACA-AGACACUGACCCAUCA-ACU-U----GAUAU-UU-GG--CUAUA-GC------CC-AGAUAU-GGUUACAACGGGUAACGGGGAAU--GAAG------------------------GUUCGAU-U-CCGGA--GAGGCAGCCUGAGAAACGGCUACCGGUCCUAAGGGAGACAGCAGGCGCGAAAAUUACC--C-AAUGCUGACC-----UA-GUGA----GGUAGUGACGAUAAAU--------------------AACA-AUC-CGA-G-UAUU---------------UUUAA-UA--UU-UGGA-AU--UG---GAAUG-AGAA--------A-ACA-UUAA-A----UCACU--U-A-ACGA-AAUCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUUA-AAUUGCUG-CAGUUAAA---A--------CGCCC-GUAGUCAAACUUCUUGGGGC---AAGGUGGCAGAGUCAGUUCAACUGUCUAUAUGGCAAACUUCCACUCUUAUUAAACCCCCCAUACAGCAGUUAAGUCUUUUAGCUCCGGGAUGAUAAACACCGUCAACAACUCG--------------------------------------------------------------------------GCAGUACCAUCUAACUAGCACCUCUCUAUUCAGUAGGUGUGGCUAUUAGACGUUUACCUU-GAUUUAAUCAAAGCGUUCAAAGCAGGCAAU-------------------------------------------AACAGC--CCGAAUGUAU-AAGCAUGGAAUAAUAAAAG-AUGACCU-UUGG--------------------------------------------------------------------------------------------------------UCCUUUUGUUGGUUUUAAGACCAU----CGGUAAUGA-UGAAAGGAGU--AG--GUU--CGGGGCAUUAGUAUUU-AC-U-CGCUAGA----GG------UGAAAUUC-UUGGAUUGAGU-AAA--GA-CUAUCUA--CAGC-GAAAGCA---UUUGCCA-GGGACCU---ACUUGU-C-GAUCA-A-GGACGAAAGUUGGG-GGAUCGAAGAUGAUUAGAUAC-CGUC-GUAGU-CC-CA-ACAGUA-AAUGUUGCCA-ACUCUG--AGUCGGUGA-A--------CUUACAUA-----------------------------------------------------------------AUCAU-CAU-CU------CC-------------------CCCGAGAAAUCG-CAAGUUUUUGGGU--------UCCGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACAA-GGA-GUGGAG-CUUG-CGGC-UUAAUUUGACUCAACACGGGACAA-CUUA-CCUAGUCCA-G------ACAUAG-UGAGGAUUGA-CA-GA---------UUAAAGGAUCUU-UCU-UGAUU-CUAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA--CUGA-UCUGUCUAG--UUAAUU-CUGA-UAACGA-GCGAGACCCUCGU-CUAUUAAU-U-AGGGUUGCGUACCUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGGUAUGAUUCAUCCU-UCUUAGAG-AGA-C-ACUUG-AUGG----------------------------------------------------UUUUUAUA--AUCAAUGGAAGUUGAAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CUAGGGCAGCACGCGUGCU-ACACUGAUAGUUACAACGAGUAUUUGGCA---------------------------------------------------------UUUAUGUCAUAGCC-UGUAC--CGUAA--GGU-C-UG------GG-GAAA-CCC--UUAAU---------------------------------------UGCUAUC--GUGCUG-GGGAUAGUCUAUUGC-------------AAUUCUUG-GACU-UGAACGAGGAAUUCCUAGUAA-UCGU-A-UAUCA-UCAGUAU-AC-GUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAA-UGGGUUAAUGAG--GAUUU-CG-GAAUGA-----CG-AAGCU----ACAACUUCCAUG-----GGGUCUGUCUUAAUUGGGU-A--CCUG----U---C-AAAAGAAGUUAUCC-GAAUU-UGCAC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
AJ250699.1/221-2005                AUUGUGGUCGAUCCCGC---CACCCCU--CUGAACUAGCGUUCGAGACUAAGC-CAUGCAAGUGUAAGC------------------------------UCAAGACC-UCUC---------------GUAGGUC-GAA-GCCGCAGACGGCUCCGUA-CAAGGCAGUUAA-UC-UACGGUCCAG------------------------------------------------------------------------CGAAAAAUCUACGGA-UAUCUCU-GGUAAG-CUAGAGCCAAUACGUGUUACCA----AUUCUCCGUGAGU-------------------------------------------------------CCUUCGGGGCGAGC--G-GGGUGCAGUUAUCGGAACGAGG-----UAG-----------------------------------------------------------------------------CGUGCUUCG----GCGCGCA----------AUCAGAGGACUCU--AGAUAACCUUGC---------CGACCGU-----GUAUAUUA-----------------------UCC----ACGG-CGUGGAC-CACG-AGACUGCCACCUAUCA-ACU-U--UUGACGG-UA-GG--GUAUU-GG------CC-UACCGU-GGUUGCAACGGGUA-CGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGUAGGCCUGAGAAACGGCCGCCAUUGCCACGGCACACAGCAGGCGCGCAAAUUUGU--C-AAUAUUCGAA----AGA-AUGA----ACGAGUGAGAACGUAU--------------------GGUC-GGG-UGG-G-ACGA---------------AUUUC-GU-UAC-CGCC-AC--GU---CGAUG-AGAC--------U-AGU-CCAA-A----AAGCU--A-G-UCGA-AUGCCACUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCG-GUA-GU-UCACGGGAU-UAUUGCUG-AGACUAAA---A--------CGUCC-GUAGUCGCAACUAGCACCAC---CCCGGUGCCAGGUAUAUCUCGUAAUGAGAUUGCCUGGCUCGGGGCGGCACGGCCCUGGUGACGUUAGCGCGUCACUUGCG-----------------------------------------------------------------------------------------------------------------------------------------------------------GCCCGCAUCCUU-GACCUAAACCAAACGAUCAAAGUGAGCU-----------------------------------------------CGUG--CUCGAUGGUU-UUGCAUGGAAUCGUGGAAC-GGGGCCG-GCGU--------------------------------------------------------------------------------------------------------------UCUGUACUUCGAGAGCGC----UGGCGACGA-UCAACGGGAG--CG--AUC--AGGGGUGAGGGAACUG-AA-G-GGCGAGG----GG------UAAAAUCU-GAUGAGCCUUU-CAA--GA-CCACCGA--AAGC-GAAAGCA---UUCACCA-GGAGCGU---UUCCGU-C-GAUAA-A-GGACUGAAGCCACC-GUAGUGAACUGGAUUAGAUAC-CCAG-GUAUC-GG-UGUGCCCCA-AACUAUGCCA-ACCGGC--CGGAUGCUC-G-AUUU---ACUUUCG---------------------------------------------------------------UGGCGAGU-AUU-CG------GUC------------------C-GAGGAAGCUG--GAGCGAUUUGGC--------UUCUGGGA-GA-U--UACGG-CUGCAAAG-UUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CAUCA-GGC-CUGGAU-UAUG-UGGC-UCAAUUGGAUUCGACGCCCAGUAC-CCAA-CCAGGACCG-G------AGCACC-CGACGAAGCA-CU-GC---------UCGAA-UAGCCU-UGC-CGAUG-AGUGUGC-GGGUGGUGCAUGGUCGCC-G-UAGU-UCG-UGAG--GUGA-CUUGUCUGG--UUAAUU-CCGA-CAACGA-ACGCAACCGCCCC-GU-UCGAC-U-AUCGAGCCCUGCGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAUUUGCGUUCGGCCCUUAGGAA-ACUCGAAC-UGA-CAAACUC-GUGGAGCG--------------------------------------------GGUCUACCGCAA--CCGAGAGGAAG-CUACGGCGAU-GGCAGGU-C-UGUGAUGCCCC-UAGAAGC-CCUGGGUUGCACACGUCAU-ACAAUGCCCGUCCGAACGCGCUU-------------------------------------------------------------------------ACGC-CGUGC--CGAGA--GGU-A-CA------GCUUAAU-CGU-CGUAAA---------------------------------------AGCGGGC--CCAGUU-GGGAUCGAGGAUUGC-------------AAUUGUUC-CUCG-UGAACGCGGAAUGCCUCGUAG-GGGC-G-GGUCA-UCAACUC-GC-CCCGAAUAA---GUC-CCUGUCCUUUGUACACACCGCCCG-UCAUUACAGCCAAU--GCAU-CGUCAGCGUCAA--GAGGC-UG-GACAGA-----CU-GCACU---------------------------------UC------G--GUGC----G---G-CCCGAAAAGCCCCU-GAACG-UCGAU-GAGACUAGGGUGUACAAGUCGUAACACG-GUCC-CCGUAGG---UGAACCUGCGGGGG--AUCACCC
U20858.1/1-1791                    AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUAGCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUAAACAC-GUUU---------------GUACUGU-GAA-ACUGCAGAUGGCUCAUUA-CAACAGUUACAG-UU-UAUUUGACAA------------------------------------------------------------------------UUGAGCAUUACCGGA-UACCCGU-AGUAACUCUAGGGCUAAUACGUGACAAAA---CCUCUCUC-----------------------------------------------------------------------------G-AGGCGUGCAUAUUAGCUUAAAA---------------------------------------------------------------------------------------CCAAUUC----UGGUUG------------------CAACCA--UAAUAUUCUGUC---------GGAUCGC--GUUGAC--CUC-----------------------GUCA---GCGA-CAUGUCA-UUCA-AGUUUCUGACCUAUCA-GCU-C--GUGACGG-UA-GA--CUAUU-GG------CC-UACCGU-GGCUUUGACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGCAGCCUGAGAAACGGCUACCACAUCCACGGAAGGCAGCAGGUGCGCAAAUUACC--C-AAUCCUGACA-----CA-GGGA----AGUAGUGACAAGCAAU--------------------AACG-AUGAUCA-G-CU-----------------UAC---AG--UU-GAAA-UU--CG---GAAUG-AGAA--------C-AAU-GUAA-A----AGCCU--U-A-UCGACCACCAAGUGGAGGGCAA-GCC-UGGUGCCAGCAGCCGC--GUAAUACC--AGCUCCA-CUA-GC-GUAUACUAA-AGUUGCUG-CUGUUAAA---A--------CGCUC-GUAGUUGGAUAUCAGUCCGG---GAGGGGCACGGGCUCCGCCGCGCGUAUGCCGCUCAGUCUCGAUCCCUGGCUCCCGCCCGGCCCCCCUGACUUAAUUCAGAGCUGCCCAUCUGCUC---------------------------------------------------------------------------------------------------------------GGUCAAACGGGUCGGGCGGGCGUGUUCUGAUCUAUUACUUU-GAGAAAAUUAAAGUGCUCAAAGCAGGCA----------------------------------------------GGCGC--CUGAAUGCAU-UAGCAUGGAAUAAUAAAAC-ACGACUU-UGGCA------------------------------------------------------------------------------------------------------GUUAGUUUUGUUGGUUUUUGGGCCG----GAGUAAUGA-UUGAUAGAAA--CA--AUU--GGGGGUGCUAGUAUCG-CC-A-GGCCAGA----GG------UAAAAUCC-UUUGAUUCUGG-UGA--GA-CUACCUU--AUGC-GAAAGCA---UUCACCA-AGCGUGU---UUUCUU-U-AAUCA-A-GAACUAGAGCCGGG-GGAUCGAAGACGAUCAGAUAC-CGUC-GUAGU-CC-CA-GCCAUA-AACGAUGUCG-ACUAAG--CAUUGGGCA-A----------UCAGAC-----------------------------------------------------------------UUCCU-CAG-CG------CUU------------------UGUGAGAAAUCA--AAGUUUUCGGAC--------UCAGGGGG--A-G--UAUGC-UCGCAAGA-GUGAAA--U-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GUU-GUGGAC-UGGG-CGGC-UCAAUUUGACUCAACACGGGAAAA-CUUA-CCAGGUCCA-G------ACAUAG-UCAGGAUUGA-CA-GA---------UUGAA-GUUCUU-UCA-UGAUU-CUAUGAA-UAGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACCUCAGC-CGUCUAAC-U-AGCUGUCGCUAGCG-------------AU--------------------------------------------------------------------------------------------------------------------------------------------------------------GUACUGCUAGCGCUUGUUCGCAAGAUCAGCU-UCUUAGAG-GGA-C-AAUCU-GU---------------------------------------------------------GCUCA--GCAGAUGGAAGCUUGAGGCUAU-AACAGGU-C-AGUGAUGCCCU-UAGAAGG-UCUGGGCUGCACGCGCGCU-ACAAUGACCCAGUCAGCGGGCCG-------------------------------------------------------------------------ACCC-GAGCC--UGAGA--AGG-C-GA------GG-UAAU-CCC---CAAA---------------------------------------CUGGGUC--CAAGUU-GGGAUAGAUGAUUGC-------------AAUUAUUC-AUCU-UGAACAAGGAAUAUCUAGUAA-ACGC-A-AGUCA-UCAACUU-GC-AUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGAA-UAAUCAGAUGAA--CUGAG-UG-GAU-------------GGG----CGUA---------------------GUCCUUUACGC-C--CC---------------CAAAGCUCCGU-GAAUC-UUAUU-AUUUAGAGGAAGGAAAAGUCGUAACAAG-GUUA-CCGUAGG---UGAACCUGCAGAAG-GAUCAA--
DQ826570.1/1-1868                  --CCUGGUUGAUCCUGC---CAGUAGUG-AUAUGCUUGUCUUAAAGAUUAAGC-CAUGCAUGUAUCAGU------------------------------ACAAGCCU---UA---------------CUAAGGU-GAA-ACCGCGAAUGGCUCAUUA-AAUCAGUUAUUA-UU-UAC-UGGCCG----------------------------------------------------------------------AGACUGUGAUACAUGGA-UAACUGU-GGUAAUUCUAGAGCUAAUACAUGCAACCG---AGCCUCAGCCCGGC-------------------------------------------------------CUCUCGGGGCCGGC--G-GGGCGCUUUUAUUGGCUGAAA---ACCGAUG---------------------------------------------------------------------------ACUGCCUUCU----GGCAGUCG-------UUAUCUGUUGAAUCA--CAAUAACAUUGUG-------UGGAUCGU---ACGGUCUCGC-----------------------ACCG---ACGA-CGCGCCU-UUCA-AAUGUCUGCCCUAUCA-GCU-C--UCGACGG-UU-AG--CUAGU-GG------CU-GACCGU-GGCCGUGACGGGUAACGGGGAAU--CUGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAGACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAACUUACC--C-ACUCCCAGUU-----CA-GGGA----GGUAGUGACAAUAAAU--------------------ACCU-UAC-AGA-G-GUACCG---------UUUACCGGU-AU--CU-CUCA-AA--CG---GAAUG-AGUA--------C-AAC-GUGA-A----UCCUU--U-A-ACGAGGAUCAACUGGAGGGCAA-GCC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-GUA-GC-GUAUAUUAA-AGCUGUUG-CGGUUAAA---A--------AGCUC-GUAGUUGGAUAUCAGUGCGU---GUCCACGUCCGGUAUGCCCGCGGUUGGCGUUCGCGCGCCGCCGUGGGCUUCCAAAUAUCGGCUGGCCGCAUUCAAUGGUGCCGGAUCCGUUGACGGG-----------------------------------------------------------------------------------------------------------CCGUUCUUACGAGGGGCCUGUCGGCGACCGGCGACGUUACCUU-GAACAAAUUAGAGUGCUCAAAGCAGGCUCU-------------------------------------------CAAUGC--CUGCAUAUAU-AUUCAUGGAAUUGGAGAAU-ACGUCCC-UGGCU-------------------------------------------------------------------------------------------------------CGAUUUGGUUGGUUUUGCGAGUCGA--AGGGAAAUGA-UUAACAGGGA--CU--GAC--GGAGGCAUUCGUAUUG-CG-G-CGCGAGG----GG------UGAAAUCC-UGUGACCGUCG-CAC--GA-CGAACUA--CUGC-GAAAGCA---UUUGCCG-AGAAUGU---UUUCAU-U-AGUCA-A-GAACGAAAGUUAGA-GGUUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UA-ACCGUA-AACGAUGUCG-ACCAGC--AAUCCGCAA-C-AGUC---ACUCUAUG--------------------------------------------------------------GACUGUGC-GGG-CA------GCUU---------------CCCCGGGGAAACCA--GAGUUUUCAGAC--------UCCGGGGG-GA-G--UAUAG-GUGCAAAA-CAGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CUUG-CGGC-UUAAUUUGACUCAACACGGGACAA-CUCA-CCAGGCCCG-G------ACACUG-UAAGGAUUGA-CA-GA---------CUGAGAGCUCUC-UCU-UGAUU-CAGUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--UUGA-UUUGUCUGG--UUUAUU-CCGA-UAACGA-ACGAGACUCUGGC-CUAUUAAACU-UGACGCCUGUCGUG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUUACUGUACGACGGCGCGCU-UCUUAGAG-GGA-U-CAUCG-GC--------------------------------------------------------GUCCCA--GCCGAAGGAA--AGAGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCUGCCCGCGUGUU-ACACUGAAGUGGUCAGCGCGCCGU-------------------------------------------------------------------UCAACGUCC-CUCUC--CGUGA--GGA-G-CG------GG-CAAA-CGU-UUGAAC---------------------------------------CCUUUUC--GUGAUG-GGAAUUGGGGGUUGC-------------AAUUGUCC-CCCA-UGAACGAGGAAUUCCAAGUAA-GCGC-A-GGUCA-CUAGCCU-GC-GUUGAUUAA---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU---GGA-UGAUUUGGUGAG--GUCGC-CUAGACUGG-----CU-GC-------UGGC----------------------UUCG-GCCGU------GC----G---G-UCGGAAAGACGCCC-AAACU-UGGUC-GUCUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
DQ683562.1/6-1692                  UACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAGGAUUAAGC-CAUGCAUGUUCCAGU------------------------------AUGAGUUU---UG---------------AUAUAAC-GAA-ACUGCGAAGGGCUCAUUA-AAUCGGUUAUUA-AA-CAAUCGACGA---------------------------------------------------------------------------UUCACAUAUGGU-UAUCCGU-GACAAUUCUACGGUUAAUACAUGCUUUGC-----------CA---------------------------------------------------------------CUUUG-UGGU--------GCCUUUAUUUCGACUAUG--GCUGAC-------------------------------------------------------------------------------AGCUUCG----GCUGAU--------------CGUCGUGAAG--AAAUUAUCUGUG--------CUUAUCGU-------UCUUCU----------------------GA------AAGA-AGCGUCG-AAGU-UAUUUCCGCCCUAUCA-GCU-U--UCGUCGG-UA-AC--GUAGU-GG------UU-UACCGU-GGCAGUGACGGGUAACGGGGAAU--UAGG------------------------GUUUGAC-U-CCGGA--GAGGGAGCCUGAGAAAUGGCUACCACAUCUAAGGAUGGCAGCAGGCGCGCGAAUUACC--C-AAUCCUAUAC-----UA-GGGA----GGUAGCGACAAGAAAU--------------------AACA-ACA-UAG-G-UAU----------------UUU-G-UA--UU-UAUG-AU--UG---GAAUG-GAGG--------G-ACC-GUAG-C----GUAUC--C-C-CUGA-AAGCCAUUGGAGGGCAA-GAC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-ACA-GC-GUAUAUUAA-UGUUGCUG-CAGUUAAA---A--------CGCUC-GUAGUUGUUGUCCAACUGUA---CGUCGAACUUCUUAUGAAGUACGUCUCCACAGUUUAGCGGAACUCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAUUCCGCCAAAACCUU-GAGGAAAGAUUAGUGUUCCAAGCAGUUC-----------------------------------------------CACU--UUGUCCUCCC-CAGCAUGGUAUUUCACCUA-UUCGAAG-AAGA------------------------------------------------------------------------------------------------------------------UCAUUGCCAAAUCU----UCAUCAUAC-AAAAUAGAAA--CU--CAA--GGGGGUAUACGUAUUU-UA-A-UGUCAGA----GG------UGAAAUUC-CUGGAUUAUUA-AAA--GA-CGAACAA--UUGC-GAAAGCA---UUCGCCA-AGCGAUU---UUUCUU-U-GAUCA-A-GAACGAAAGUUAGG-GGAUUGAAGACGAUCAGAUAC-CGUC-GUAAU-CC-UG-ACUGUA-AACUAUGCCA-ACUUGU--CGCAGGUAG-A-UCUU---UCGUC-----------------------------------------------------------------GAAUCUAU-CGU-CG------GCU------------------UUUGAGAAAUCA--AAGUCUUUGGGU--------UCUGGGGG-GA-G--UAUGA-UCGCAAGC-UUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CUUG-CGGC-UUAAUUUGACUCAACACGGGAAAU-CUCA-CCAGCCCCA-C------ACAUAA-GGAGGAUUGA-CA-GU---------UUGAUAGUUCUU-UCU-UGAUU-CUAUGGA-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UCUGUCUGG--CUAAUU-CCGU-UAACGA-ACGAGAUCUUAAC-CUACUAAC-U-AGAAAGUUCAACAUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCU-UCUUAGAG-GGA-CACUUAA-UC---------------------------------------------------------GUUUA--GAUUAGGGAAGUUUGAGGUAAU-AACAGGU-C-UGUGAUGCCCC-UAGACGU-UCUGGGCUGCACGCGCGCU-ACAAUAGUACGCACAGCGAGUAU-------------------------------------------------------------------------UACC-AAGCU--CGAAA--GGG-C-AA------GG-UAAA-CUA--AGAAA---------------------------------------AGGUACU--GUAAUU-GUUAUAGAUCCUUGU-------------AAUUAUUG-AUCU-UCAACGAGGAAUUCCUAGUAA-GUAU-G-UGUCA-UCAUCAC-GC-ACUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGGA-UGAGGCGAUGAA--ACUCU-CG-GACGAG-----GC-UU---------------------------------UAUUA-----------AG----A---U-UUUGAAAGAGAUUU-GAAUC-GGUUC-AUUUAGAGGAAGGAGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAGG
AY781428.1/1-2002                  --CCUGGUUGAUCCUGC---CAGUAGU--AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGCCUGAGU------------------------------ACAAGCCU--UAA---------------UUAAGGC-GAA-ACCGUGAAAGGCUCAUUA-AAUCAGUCAUAA-UU-CUUUGGGCCCAGAAC------------------------------------------------------------CAUAUUCUAAUGGUUAUUUGGA-UAACUGU-GGUAAUUCUAGAGCUAAUACAUGCCUCGA----GUUCCGAUUCGCGUAC-------------------------------------------------CACUUGUGGAACCGAAG--A-GGACGCAAUUAUUAGAUUUAA---ACUGUC-----------------------------------------------------------------------------CUCUCGAAG----GACAGU------------UUUGAUGAAUCU--GGAUAAUACUAGUUACCAAGCCGAGCGC--UUAGGUCUCCG----------------------UACCG---GCGC-CAUACCA-UUCA-AGAGUCUGCCCUAUCA-GGC-U--UCGAUUG-UA-GG--UUAAA-UG------CC-UACAAU-GGCUUUGACGGGUAACGGGGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCACGCAACUUCCC--C-ACUUGCGGAA-----CG-CAGA----GGGAGUGACAAAAUCU--------------------AACG-AUG-UGA-G-UCUC--------------UUCCGA-GG-CCU-CACA-AU--CG---GAAUG-ACUC--------CUACC-UUAA-A----UAAGU--G-G-AGGAGGAUCUAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-AUAUGUUAA-UUUUGCUG-CGGUUAAA---A--------AGCUC-GUAGUUGGACCUCAUUUUAA---AACUCAGAAAAAAUUAUUAUUUUUUUUUAUAUUGAGUUGAGGUUAAAAUAUGUCACCAUUACGUCACUAAAUUCGUUUUACGGUACUUUGU----------------------------------------------------------------------------------------------------------------------ACGGUAAUCGAUAGUGACGUGGGUGGCAGGAUCACUUU-GAAAAAAUUAGAGUGCUUAGAGCAAGCUAUGCAC-----------------------------------UUUACGAUGC--CUGUAUGGUC-GUGCAUGGAAUGAUGGAAU-ACGAUCU-CGGCC-------------------------------------------------------------------------------------------------------CCGUUACGGCGGGGUAU------G----AGAUAAUGA-UUAAAGGAAA--CA--GAC--GGGGGCGUUCGUAUUG-CG-A-CGCGAGC----GG------UGAAAUGC-GUUGACCGUCG-CAG--GA-CGACCUA--CUGC-GAAAGCA---UUCGCCA-AGAAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUAGA-GGAUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UA-ACCGUA-AACUAUGCAA-ACCGGU--CAUACGUCG-G-AGUU---AUUCCCAC--------------------------------------------------------------GACUCGAC-GUG-CU------ACC------------------CACGGGAAACCA--GAGUAA---UGC--------UCCGGGGG-AA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAC-CUUA-CCAGGCCCG-G------ACACCG-AAAGGAUUGA-CA-GA---------UUAAAAGCUCUU-UCU-CGAUA-CGGUGGG-UAGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GCGA-UCUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACUCUAGU-CUACUAAC-U-AGUCGUCAAACUUCAACCCGAGGCUUCAUUACGGCUUUGUGAAGCUGCUUUCUGUUGUUGCCGAUGCGCGGUGCUUGGUCUCGU-----------------------------------------------ACCUUGUGCUGUUGCGUCGUGAGUGGCGCNGNUUGUGGUUAGCAUUGUCGUUAUAGCCAAUAUGUCGGGUACUUUGACGCAUAAUCU-UCUUAGAG-AGA-U-AAGCG-AC---------------------------------------------------------GUCUA--GUCGUCUGAG--AAAGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CCUGGGCUGCACGCGCGCU-ACAAUGGAUGGUGUAGUGUGU----------------------------------------------------------------------------UUC-UGCUC--CGACA--GGA-G-UG------GG-AAAU-CAU-AUCAAA---------------------------------------CCCAUUC--UCGCUC-GGGAUUGGGGCUUGC-------------AAAUAUUU-CCCA-UGAACGAGGAAUUCCCAGUAA-GCAC-G-GCUCAUUCAAGCC-GU-GCUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAA-UGAUUCAGUGAG--GACGU-UG-GACUGU-----CG-CUCUU---UGAUU----------------------CUCGUAAUCU-AUUAGAG----A--AG-ACGGGAAGAUGCCC-AAACU-UGAUC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
EU542594.1/1-1899                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCGAAGAUUAAGC-CAUGCAAGUCUAAGU------------------------------UCAAACGG--AAUUU-----------UGAUACGUG-GAA-ACUGCGAAUGGCUCAUUA-AAUCAGUCUUAA-UU-UGGUCGGAGGAAGCUC----------------------------------------------------------UCUGUUUUGGAGAGGUAUACGGA-UAACCGU-ACAAAAGGUAGAGCUAAUACGUGCCGAGA---AAGCGGGGUCCGUG-------------------------------------------------------AAUUAUCACGGUCG--C-UGCGGGUUUUAUUAGAAUUACA-AGACGACGGC-----------------------------------------------------------------------UUUGUACCUUUG----GGUGCGGG-------GUUUGAGUUGAAUCA--UGGUAACAAGAA--------UGGAUUGC---GGGUUGUGCUUG------------------CACGGCU---GCGA-UGUACCG-AUGG-AAAGUCUGCCCUAUCA-CCU-G--UCGACGG-UA-GG--AUAGA-GG------CC-UACCGU-GGGGAUAACGGGUAACGGGGGAU--UAGA------------------------GUUUUAU-A-CCGGA--GAGGGCGCCUGAGAGAUGGCGACCACUUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUGGCGACA-----UG-CCGA----GGUAGUGAAGAACAAU--------------------AACG-AUG-GGC-G-GGUC--------------UUAGAA-CU--UG-CCCA-AU--UG---GAAUG-AGUU--------U-AAA-UUAC-A----ACCCU--A-U-UCGAGGAGCAACUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-GUA-GU-GUAUAUCAA-AGUUGUUG-CGGUUAAA---A--------AGCUC-GUAGUUGGAUUUCCCGGGAA--UUUUGGGUGUGGGAUGUGGUCAUUUGAACUGCGGCCAUGCCUUUACCGGUGGUUGUGCUCUCCUUCUGGGGG---------------------------------------------------------------------------------------------------------------------------------------------------------------GGUAGGACGUGUACUUU-GAACAAAUUAGAGUGCUCAAGACAGGCGAUUUU-------------------------------------AUAAUUGCU--GUGAAUAGAU-UAGCAUGGAAUAACGGGUAUAAACUCU-CUUCU-------------------------------------------------------------------------------------------------------CGGGAUUGUUGUUUUGACGAGGAG----GGGGAAUGA-UGGAUAGGGA--CA--GGU--GUGGGCAUUGAGAUUG-UU-A-CGUCAGA----GG------UGAAAUUC-UUAGAUCGUAG-CAG--GA-UUAGCAG--ACGC-GAAAGCA---UUUGUCA-AGGAUGU---UUUCAU-U-GAUCA-A-GAACGAAAGUUGGG-GGAUCGAAGACGAUUAGAUAC-CGUC-GUAGU-CU-CA-ACCAUA-AACGAUGCCA-GCUAGG--GAUUGGAGG-G-GGCA---CGAGACUUUCU--------------------------------------------------------CACUACUUUUU-CAG-CA------CCU-----------------UUACGAGAAAUCC-AAAGCGUUUGGGU--------UCCGGGGG-AA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-UAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUUA-CCAGGCCCA-G------ACAUAA-AAAGGAUUGA-CA-GA---------UUGAAAGCUCUU-UCU-UGAUC-UUAUGGA-UGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA--GUGA-UUUGUCUGC--UUGAUU-GCGA-UAACGG-ACGAGACCUUGUG-UG-GAUGU-U-GCUGGGCCCAAGAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUGUGCUUGGGACCCGGG-ACCUUCUG-CGA-C-UGCUG-UAUG-----------------------------------------------------UGUUUUA--ACCAGAGGAAGUUCUAGGCUAA-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGCGCU-ACAAUGGGAGGGAUAGCGAGCUUGUUGCCGGGGCGUUUUUCGUA----------------------------CUUUUGUUGCGGGGAGUGGCCUGGUGCC-UGGUC--CGAGA--GGG-C-UG------GG-GAAA-CUG--GCAAG---------------------------------------ACCUUCU--GUGACU-GGGAUUGGUCUUUGU-------------AAUUGUGG-GCCA-UGAACGAGGAAUUCCUUGUAA-ACGC-A-CGUCA-UCAACGU-GC-AUUGAAUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUUCUACCGAU--UGGA-UGAAUAGGUGAG--UGUUU-UG-GAGGUC-----UG-GCUGU---UGUUG---------------------GGCAACUGAUC-G--GGGU----U---G-GGCUGAGGAUGUGC-AAAUC-UGUUU-AUCUAGAGGAAGAAGAAGUCGUAACAAGAGUAU-CUGAAG----UGAACCUGCAGAAG-GAUCAAAA
EF513182.1/2-1881                  AACCUGGUUGGUCCUGC---CAGAAUC--AUAUGCUUGUCCCGAAGCUUAAGC-CAUGCAUGUCUCCGA------------------------------ACAAUAGU-AGCU---------------UGAUCUA-GAA-UCUGCGAACGGCUCCGUA-UAUCUGUUACAA-AC-CCCCACCGCC------------------------------------------------------------------------GACCGACCAUCGGCA-UAACCAC-GGUAAUUCUGUGGCUAAUACGUGUACUAC----GGGCGCUGCCUGC-------------------------------------------------------CCGCAAGGGCGGGC--G-GCCCCGGUCUUGCCGGACGACC--AACGGC-------------------------------------------------------------------------------GGUGCAA----ACCGCU------------CGCGCGAGCGCU--GGCAAGGGUACC---------UGACCGG------GCAAACA----------------------AGU-----CCGG-CGCGUGU-GAUG-CGCACCAGACCUAUCA-ACU-A----GAUAC-CC-AG--GCAUU-GC------CU-GGACAU-GGUGACUACGGGUA-CAGAGAAU--UAGG------------------------GUUCGAU-U-CUGGA--GAGGUAGCCUGAGAGAUCGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAACGUUCC--C-AAUGGGGAUA-----CC-CUGA----GGACGUGAAGGGAUAU--------------------ACCA-AUG-CCC-G-GCCU---------------UUAAA-GC--CG-GGCA-AU--UG---GAAUG-GGGA--------A-CAU-CUAA-A----CCCCA--C-A-CCGAGUAACAAUUGGAGGACAA-GUC-UGGUGCCAGCACCCGC-GGUAAUUCC--AGCUCCG-AUA-GC-AUCUUAUUA-AGUUGUUG-CAGUUAAA---A--------CGCUC-GUAGUCCAAACCAGUGCGCC--CGCUAGGUUCCUAGUACUGCCUGACCAUGCGCUCCCUCCUAACCGGAGUGGGGUGCGGGCUGGCGGGGACGGUUCUGGGCGGCCACUAUUGAGCCGGGGGAACCG---------------------------------------------------------------------------------------------GGCGGGUGGGGCUUCAGUGCUCCGCCUGCCUGCCCCUGGCACAUUACUUU-GAACAAACGUGAGCGCUCCAAGCAGGCCAU-------------------------------------------AUCGGCCCUUAAAACCCG-CAGCAAAGAAUAACCCAAC-AGGUACU-CACC-----------------------------------------------------------------------------------------------------------UGUUCGUUGGUACAGGUAUCG----GGUAAAUGA-UCUAUAGGGG--CG--AUC--GGGGUGGGCCACAUGC-CA-G-GGGUAGG----GG------UGAAAUCC-GUUGAUCCUUG-GCA--GG-UGAACUA--GAGC-GAAAGCA---GCCCACA-AGUACGC---AUCCUU-U-GAUCA-A-GAACGAAAGUCUGG-GGAUCGAAGAUGAUCAGAUAC-CAUC-GUAGU-CC-AG-ACCCUA-AAUGAUGCCG-GCCAUG--GAUGGGCUC-U-CGUC---CAUCCC----------------------------------------------------------------GACCCAGC-CCG-CA------CUU------------------UAUAGGAAACUA-UAAGCGUUUGGGC--------UCCGGGGG-GA-G--UAUGG-UCGCAAGA-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGAGCA---CACAA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGAAA-CUCA-CUAGGGCAA-G------AGAAUG-GUAGGAUAGA-CA-GC---------CGAUCAGGGCUU-UCA-UGAUU-CGUUCAG-UGGUGGUGCAUGGUCGUU-CUUAGU-UCG-UGGA--UUGA-UUUGUCUGG--UCUAUU-CCGC-UAACGA-GCGAGAACCCACC-CU-----C-U-CGUGGUUAGGAUCCUUGAGCAUGCCGCUACCCUAAUGGCCC-------------------------------------------------------------------------------------------------------------------------------------GCAAGGGACUCCUGGGGUUCUGGCUGAAAAAGCUCCUGGACUCG-AUCCGGAG-GGA-C-CGGCU-UC---------------------------------------------------------GAUAA--GGAGCUGGCA--GCGGGUCAAU-AACAGGU-C-AGUGAUGCCCU-UAGAUGC-UCUAGGCCGCACGCGCGCU-ACAAUGGGGCAAGUACCGGGU----------------------------------------------------------------------------CCC-UGUGC--CUUAA--GGCCA-CG------GG-GAAU-CCG--GGAAA---------------------------------------GUGCCCC--UUAUCC-GGGAUAACGCCGUGU-------------AACU-CGG-CGUU-UGAACAAGGAAUUUCUAGUAG-UCAU-G-GGUCA-CCAGCCC-GU-GACGAUUCU---GUC-CCUGCUCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGGG-CUGCGAGGUGAG--UUGCU-UG-GAGCUA-----AA-CCGGG---G--------------------------GCAAC------C--CCGG-----------CGCGAAGAGAGGC-GAACC-CUGCG-GCCUAGAGGAAGGAGAAGUCGUAACAAG-GUAU-CCGUAUG---UGAACCUCCGAAAG-GAUCACCU
AY781417.1/1-1807                  --CCUGGUUGAUCCUGC---CAGUAGUU-AUAUGCUCGUCUCAAAGCCUAAGC-CAUGCAUGUCUAAGU------------------------------UCAGACAA----U---------------AAAUAGU-GAA-ACCGCAAAAGGCUCAUUA-AAUCAGUUUUUG-UU-UAUUUGUUAA------------------------------------------------------------------------UGAUUGAUAAUUGGA-UAUCUGU-GGCAAUUCUAGAGCUAAUACAUGCAAAUA---UACUCUGACC----------------------------------------------------------------GAAA-GGAAUAU-GAGUGCUUUUAUUAGUACCAA---ACCAAU------------------------------------------------------------------------------GUGGUUGG----CCACUUG----------GAAUGGUGACUCU--GGAUAAUAUUGC---------CUAGUGA--AAGUGCCUAUA-----------------------GUGCU-GGCAC-AUAAUCU-UUCA-AGUGUCUGCCUUAUCA-GCU-G----CAUUG-UU-GG--GUACC-UG------CC-UACAAU-GGCUGUAACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAUGGCAGCAGGCGCGCAAAUUACC--C-AAUCCCAGCA-----CG-GGGA----GGUAGUGACGAAAAAU--------------------AACG-GUG-CAA-GGAUCU--------------AUCAAG-GC--CU-UGUA-AU--UG---GAAUG-AAUA--------G-AGU-UUAA-A----AAAUU-GU-A-CUGAGUACCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUG-GC-AUAUAUUAA-AGUUGUUG-UGGUUAAA---A--------AGCUC-GUAGUUGGAAUCUUGCCUGA---GGAGUUAGUGGAAGCCGAAUGGUUUUCUUCUAUAGAGUUCAGGCUUUUGCCUUGAGAACAAAUAGUGCUCUUGACUGGGU-----------------------------------------------------------------------------------------------------------------------------------------GUUUUUUGAAUUGUCAAGCACUAUUACCUU-GACUAAAUUCGAGUGCUUAAAGCAGGCG----------------------------------------------UUUGC--CUGAAGAGAU-GUUCAUGGGAUGAUGGAAC-AUGAUCU-CUGUU-------------------------------------------------------------------------------------------------------CUGUUUGUUGGUUUGAGAUAAAAG----AGAUAAUGA-UAAAUGGAAG--CA--AGC--GGGGGCAUUUGUACUG-CU-A-CGCUAGA----GG------UGAAAUUC-UUGGACCGUAG-CAU--GA-CAAACUA--AAGC-GAAAGCA---UCUGCCA-AGGAUGU---UUCCGU-U-AAUCA-A-GAACGAAAGUUAGA-GGAUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UA-ACUGUA-AACUAUGCUG-ACCAGC--UAUCUGCCG-G-CGUU---AUUCCCAU--------------------------------------------------------------GACUCGGC-AGG-CC------GCU------------------UCCGGGAAACCA--GAGUUUCUGAGU--------UCCAGGGG-AA-G--UAUGG-UUGCAAAU-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACAA-GGA-GUGGAG-CCUG-UGGC-UUAAUUUGACUCAACACGGGAAAC-UUUA-CCAGGCCCA-G------ACAGUA-GAAUGAUUGA-CA-GA---------UUGAAAGCUCUU-UCU-CAAUU-UAUUGGU-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUUAUU-CCGA-UAACGA-ACGAGACUCUGGC-CUACUAAA-U-AGGGAGCAGGUUGUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGCGCCUGCGGUGUCU-UCUUAGAG-GGA-U-AAGCU-GC---------------------------------------------------------UACCA--GCAGCAAGAG--AUUGAGCGAU-AACAGGU-C-UGGUAUGCCCU-UAGAUGC-UCUGGGCCGCACGCGCGCU-ACAAUGGUAGCGUCAGCGUGCUG--------------------------------------------------------------------------AGC-AUCUC--UGAGA--GGA-G-GU------GU-CAAU-CAU--UGAAA---------------------------------------UGGUACC--GUGGUU-GGGAUUGGGGCUUGC-------------AAUUGUUU-CCCA-UGAACUAGGAAUUCCUAGUAG-GCGC-A-GGUCC-UUAGCCU-GC-AUCGAUUAA---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAG-UGCACCAGUGAG--GGCUU-UG-GACUGG-----CAUCCUUG---GUGGG----------------------UUCUCCCCGC-C--UUGGC--UU---G-AUGGGAAGAUGUCC-GAGCU-GGUGU-ACUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
EU004604.1/15-1853                 AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUCGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUAAAUAU--UUC-----------------AAAUU-AAA-ACUGCGAACGGCUCAUUA-AAUCAGUUUAAC-UC-UAAACAGCAA-------------------------------------------------------------------------UUCAUUAUUUCGGA-UAACUGU-AGUAAUUCUAGAGCUAAUACGUAUGCAAA----ACAUC--UG---------------------------------------------------------------------CAAA--G-GUGUUUGCCGAGGGAUUAUAGG--CUAAGA-----------------------------------------------------------------------------UA------------------------------AUAUGAUUAUA--CCCUCGAUG-CG---------AAACCUU-------CCAUUG-----------------------G------AAGG-UAUGUUG-UUUG-AUAUUCUGCCCUAUCA-ACU-U--UUGACGG-UA-GU--GUCGU-GG------AC-UACCAU-GGUGAUGACGGGUAACGGGGAAU--AAGG------------------------GUUCGAU-U-CCGGA--GAGGGGGCCUGAGAAAUGGCCACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUCUCAAUU-----CG-AGGA----GGUAGUGACAAGAAAU--------------------AGCA-AUGCCUU-G-GCUC-------------UUAAUGG-GU--CU-GGCA-AU--UG---CAAUG-AGCA--------U-AUA-UUAA-A----ACUCU--U-A-ACGAGGAACAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AUUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUCUAUGAUGAAACUUU---UCGAUCUGUUUAGAGUGCUUUCUUCAUGGAAGUAUCUUUUAAGCUACGAAUUGUUUUAUAGAGUCUCCUAACGAUGGCUAUUAAGU---------------------------------------------------------------------------------------------------------------------------------UAGUGUCGCUUUAAAUGGAUGACUUCUACCUU-GAGUAAAAUAGAGUGUUUAAAGCAUACAGU--------------------------------------------UUUGU--AUGAAUAUAU-UAGCAUGGGAUAGUAAUAA-UGAUGAG-AAUU--------------------------------------------------------------------------------------------------------------------UGUCAAUCUAAU----CAUUAGUGG-UUAAUAGGAG--CA--GUC--GGGGGCGUUCAUAUUC-AG-U-GGUCAGA----GG------UGAAAUUC-UUGGAUUCACU-GAG--GA-UGAACAG--AUGC-GAAAGCG---UUCGCCA-AGGAUGU---UUUCAU-U-GAUCA-A-GAACGAAAGUUAGG-GGAUCGAAGAUGAUCAGAUAC-CGUC-GUAGU-CC-UA-ACCGUA-AACUAUGCCG-ACCGAG--AAUCGGAGG-A-UGUU---AAAUGAAU--------------------------------------------------------------GACUCCCC-CGG-AA------CUC------------------AUAGAGAAAUCU-UGAGUCUUUGGGU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA---CACCA-GAA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAU-CUCA-CCAGGUCCG-G------ACAUUA-GAAUGAAUGA-CA-AG---------UUAAA-GCCUUU-UCA-UGAUU-UGAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--UUGA-UUUGUCUGC--UUAAUU-GCGA-UAACGA-ACGAGACCCCCUU-UUACUAAA-U-AGAAAAUACAUAACAUAAAUGUYGAAAGCGGGGACCACGAAAGUAG----------------------------------------------------------------------------------------------------------------------------UUUACUACCUAGUGCAACCGUCGGAAACUGUGGAUAAUGUAUUGAGCU-UCUUAGAA-AGR-A-UAAAG-CUAAA---------------------------------------------------ACUUAAAA--AUAUAUAUUACUCGGGG-CAAU-AACAGGU-C-AGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGCGCU-ACAAUGACAAAA-----UGGAAA----------------------------------------------------------------------AGGUUAC-UAGAU--UUAAC-GGUU-U-CG------GU-UAAU-CCA--GUAAU---------------------------------------CUUUCCC--AUAACC-GGGAUUGGUGGUUGC-------------AAUUAUCC-GCCA-UGAACGAGGAAUUUCUAGUAG-GUAU-G-GUUCA-CUAAACC-AU-GCCGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUUCUACCGAU--UGAA-UGGUUCGGUGAA--AUCCU-CG-GACUAG-----AA-UUCAU---AUUAG---------------------GGCAACCUGAU-U--UGUA----U---U-UUAGGAUGAGGAGU-AAAUU-GAAAC-AUUUAGAGGAAGAAGAAGUCGUAACAAG-GUCU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
AF439350.1/2-1783                  AACCUGGUUGAUCCUGC---CAGUAUU--AUACGCUCACGUCAAGGACUAAGC-CAUGCAUGUGUAAGA------------------------------ACGGGCUU---------------------UACGCC-CAA-UCUGUGGAAGGCUCAUUA-CACGAGUCAGAA-AC-UCGUUGACUG---------------------------------------------------------------------------GUUGCAUUUGGA-UAACCCU-ACCAACUGUCGUGAUAAUACAUAGGCAAG-----------CC----------------------------------------------------------------UUCG-GGCG--------ACCUGGUGUUCACUAUG---UGAGGU-----------------------------------------------------------------------------GG-----GA-----------------------CAUCAGCAGGG--GGCAACCCCUGCA-------GGAACCGG-------CUUCGC----------------------GG------CUGG-UCUGUUA-AAUG-UCUCACUUCCCUAUCA-GCU-U----GUAGG-UU-GG--GUAUG-UU------CC-AAUCCA-UGCAGCAACGGGUA-CGGGGAAU--CAGU------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGACGGCAGCAGGCGCGCAAAUUACC--C-AAUCAUAACAA--AUGA-UGGA----GGUAGCGACCACAAAU--------------------AGCA-GCC-UCC-C-AGUUUUC-------UGGGGGGGAG-CC--AU-UAGG-CU--AG---CAAUG-GAAC--------C-AUG-GUAA-A----CGUGU--G-G-AAGAGAAACUAUUAGAGGACAA-GUCUUGGUGCCAGCACCCGC-GGUAAUUCC--AGCUCUA-AGA-GC-UUACACCUA-CAUUGUUG-CAGUUAAA---A--------CGCUC-GUAGUCUAUGAGAAGACCAC--GACUGAGGUACUGGGCUGCCUUCGGGGGCUAUGCCUUCCACUGUCCUCUCGAGGCUCAGUGGAACACCCAGGACUCAAGUC------------------------------------------------------------------------------------------------------------------------------------------------------GCUGGCUUAAUAAUCGU-GAACAAAUCAGUGCGAUCGAUGCGGGCCGUGC--------------------------------------AUAAGUUGC--UUGAAUG-CC-CAGCAUGAAAUUAUCCCUA-GACCUAG-UUGU-----------------------------------------------------------------------------------------------------------------------------CUG----AUGUGACGA------GAGAC--UG--GUU--GAAGCUCCUGGUAUUG-CG-U-GCGCAGA----GG------UGAAAUUC-CGAAAUUCGCG-CAA--GA-CGACCUG--AAGC-GAAGGCU--GAUGAGCU-CCCACGU---CUCUGU-C-GAUCA-G-GAACGAAAGUCAGG-GGAUCGAAGAUGAUUAGAUAC-CGUC-GUAGU-CC-UG-ACCGUA-AACCAUACCA-CCAGUU--GGUUGGUUC-G-AAAC---ACAAAGA---------------------------------------------------------------GAUCACCC-CAG-AA------AAC------------------A-AGGGAAACCG-AAAGGUCUCGGGU--------UCUGGGGG-GA-G--UAUAG-UCGCAAGG-CCGAAA--C-UU-AAAGG-AAUUGACGG-AAAGGCA-C-CACCA-GGG-GUGGAG-UCUG-CGGC-UUAAUUCGACUCAACACGGGAAAA-CUCA-CCAAGUCCA-G------AUAGCG-UUAUGAUUGA-CA-GG---------UUAAUAGUCCUU-UCU-UGAUU-CUCUAAU-AGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA--GUGA-UCUGUCUAG--UUAAUU-CUGU-UAACGA-ACGAGACCUUUGC-CG-UUGAU-U-G------AACUACUGCUAACCGGCUCUGC--------------------------------------------------------------------------------------------------------------------------------------------------------------UGGUACAGUAGUCGGCCUACGGGCCAA---C-CCACAACG-GGA-C-GAUACAGCG------------------------------------------------------UACCCCA--GCGUAAGGAAGUUAAAGGCAAU-AACAGGU-C-UGUGAUGCUCU-AAUAUGU-CUUGGGCCGCACGCGUACU-ACAAUGGUGACUUUAGUGAGCAAGCACCGACGCGGCCC---------------------------------------UGUCUAGACAGGUCUGCAUCUCC-ACUAC--UCAGA-ACGU-A-UA------GG-UAAU-CUU--UCAAA---------------------------------------CGUCAUC--AUGACU-GGGAUAGUAGGCUGU-------------AAA--GUC-UACU-CCAACGAGGAAUCCCCCGUAA-GCGC-G-AGUCA-UCAUCCC-GC-AUUGACUAC---GUC-CCUGCCUUUUGUACACACCGCCCG-UCGCUCCUACCG-U--UGGA-CUUGAAGGUGAG--CUCGG-UA-GAGCC------------------AGAC----------------------CUCUGGUCA-----------------A-CGGCGAAACCGAAC-AAAUC-UUCGU-GUCUGUAGGAAGGAGAAGUCGUAACAAG-GUUU-UCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
AY190083.1/15090-13125             UAUCUGGUUGAUCCUGC---CAGUAUU--AUAUGCUGAUAUUAAAGGCUAAGC-CAUGCAUGUCUAAGU------------------------------ACAAAGUC--CUA---------------GAAGGAU-GAA-ACCGUGAACGGCUCAUUA-CAACAGUCAUAG-UA-GAGUUAAUUU------------------------------------------------------------------------UAAAGAAAA---GGA-UAUUCCA-GUGAAUUAUUGAGUUAAUACCACUGAAAA----GCUUACG-----------------------------------------------------------------------------A-GAGUAGAAUCUUGUGAGGUUGA--AAAGUUGCGCG------------------------------------------------------------------UGUAAUUUUUCAUAA----GGAUAU------------UUUUUUGAGUAA--AAAGUACCAGCC--------ACAAUAGA---UGAACCUGGUUA-------------------AGUUUU---ACUA-GUAAUUA-ACAU-ACUUUCUGAUCUAUCA-AUU-U----GUUGG-UA-GU--AUAGA-GG------AC-UACCAA-GAUUAUUACGGAUGACGAGGAAU--UAGG------------------------GUUUGAC-A-UCGGA--GAGGGAGCUUUCAAGAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUGGGAGAC-----CC-UUGA----GGUAGUGACGAUAUAU--------------------AAC---UC-AAG-U-AAGA-------------GAUAAUC-UU--GU-UUGA-A----G---GGAUG-AAGA--------C-GGU-AUAA-A----GUACC--G-U-ACGA-AAUCGAUUAGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCUA-AAA-GU-GUAUAUUAA-AGUUGUUG-UGGUUAAA---A--------CGCUC-GUAGUUGAUAAUGACUGUUU---AAUUGUGUCACAAAAAAUCCAACAAGUCUAAGACUAUUGGAUGUCGGCAUAGUUUUUACAUAGGGCUUUAAAAUGUGUUG-----------------------------------------------------------------------------------------------------------------------------------------------ACCAACAUGUUUUGGGAUUUCUUU-GAGAAAAACAAAGUGCUUGAAGCGGAUU---------------------------------------------UUAGUG--AUGAAUGAUU-GAGCAUGGUACAAGUCUGA-AGGGGAU-AGAA------------------------------------------------------------------------------------------------------------------------AUAUUGCU----GGAGGAUGA-UUAGAAGGAU--UC--GAC--GGGGUAAUAAAGAAAA-UU-G-UGGGAGA----GG------UGAAAAUU-CAUGAUCACAA-UAA--GA-UUGUCUA--GAGC-GAAAGCA---UUUUACC-AGCACGG---AUUCAU-U-AAUCA-A-GAACGACAGUUAGG-GGAUCGAAGACGAUUAGAUAC-CGUC-GUAGU-CC-UG-ACUAUA-AACGAUAUGA-ACUGAA--GAUUAUACC-U-GUAC---AGAAAGGGAACCUCUUUUUUAUUUCGG------------------------UAAGAAAUGUUUCCGAAUUGUUAGGUA-UAA-CA------AUCAAGGCCUCUGUGGGAUUCAAGGAGAAAUCCUUGAGUCUCUACAU--------UUCAGGGG-GA-G--UAUGG-UUGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA---CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUUA-CCAAGACCG-A------ACAUUA-GAGGGAUUGA-CA-GA---------UUUAGGGUUCUU-UCA-AGAUU-UAAAGAG-GAGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA--CUGG-UUUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACUGAAAC-CUAUUAAU-U-AGUAUAUCUUUGAC---------AGGGGA--------------------------------------------------------------------------------------------------------------------------------------------------------------UAUCAUGCGAAAGCAUAUUAGGAAUUAAAUU-UCUUAGAG-GGA-CAACUUU-UAGAUAGUCCUCCCAGCGGUAUAUGAGUA---CUAACCGUACUUUUUAUUUCUGGAGGGAUUAA--UGAAAGGGAAGCGUUCAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGACAU-CUUGGGCCGCACGCGCGCU-ACAAUGGAAGAAGAAAAGAGUUUAGUCAAGGAAUUAUUUCAUUUGGUUCUGCCAAGUGGAGUGAUUUCUAAAAAAUGGACACAAGAAUUUUUGACUAGCC-GAUAU--UUAAA--AAC-G-GA------GG-AAAA-CUC--AAAAC---------------------------------------UUUGGAC--AUGUUCUGGGAUAGAUGAUUGU-------------AAUUAUUU-GUCU-UUAACCAGGAAUUCCUUGUAA-UACC-A-UGUCA-UUAGCAU-GG-GAUGAAUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGAA-CAAAGAGGUGAA--AUUUU-AA-GACGAU-----GA-A----------------------------------UAAUU------------U----U---C-AUUGGAAUGGAUUU-AAACC-UCCUU-AUUUAGAGGAAGGAGAAGUCGUAACAAG-GUUU-UCGUAGG---UGAACCUGCGUAAG-GAUCAUUC
AF011455.1/7-2126                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAGGAUUAAGC-CAUGCAUGUGUAAGAUCGGCAUAGUUUUGGGAAGUAGGUUCGCCUACAACCCU--UAU---------------UCAUUGU-UAA-UCUGUGAAAGGCUCAUUA-AACAAGUUAUGA-AU-UUAGCCACCUGGU---------------------------------------------------------------ACAACCCUUCGGGGAUGGGAA-UAACACU-GUCAACUGCAGCGAUAAUGCCUACGAUUA---CUGUUGAAUU---------------------------------------------------------------------AAGU--A-GACAGUAGACACUAGAGUAUGG--GUGAGUCCGCUCUAUUGUUAGCUGGGAUGAUCUUUCGACUCGU--UGGAAGGUCUGAACAGUUGUCGACCAUUAGAUUUUCGUUUGCUUGCA----AGCGAAU----------GCAGCGUGAAUGACUUAGCGUCCUAAU--------AAGACCUA---CGGCUUUCUUGU-------------------UGACUA---GUGG-CCAGGAA-GAUA-UGUUUCUAAUCUAUCA-GCU-C---AGUAGU-UU-CG--GUAAA-GG------CG-AAACGA-GGCUAUAACGGAUA-CGGGGGAU--UGGU------------------------GUCCAAC-U-CCGGA--GAGAGAGCCUGAGAAACGGCUAUCACAUCUAAGGACGGCAGCAGGCGCGUAAAUUACC--C-AAUCCUAAUU-----CA-GGGA----GGUAGUGACAAGACAUAGCGA---------CUUUACACCA-AUCGGUG-G-AAAG--------------GUACCA-CA--UU-GUGG-UU--UG---AAAUG-GAUG--------G-AGA-UUAA-A----CCUCU--C-C-AUGAGUAGCAAUUAGAGGACAA-GUC-UGGUGCCAGCACCCGC-GGUAAUUCC--AGCUCUA-AAA-GU-GUAUAUUAA-UACUGUUG-UAGUUAAA---A--------CGCCC-GUAGUAAACCAAAGGGUUAU--AGUUAUUGAUCUGACCAGUACUGUUCGUAACGUCAGCCACGUAUUGURGGUGAUAGGACGAAUAAGGACAGGUCCUCGGUCUCUAACGGAAGCCAAAGGGUUCGCCCAAGUAGCAUCCGCCAUGG-----------------------------------------------------GAUAGGUCAAUGAUUAUGGCUCGCUCCCUGCCAGUCCGCAAGGUCUGGUAGGGCCAUUUGGCACAACCGU-AAACAAAUCAGAGUGCUCCAAGCAGGCAAUGUUAGGG-----------------------------GUAACCCAUUUGC--UUGAAUGAUU-UAGCAUGGAAUUGUCACGA-AGCCGAU-CGGAAACUUCGA-----------------------------------------------------------------------------------------GGGUUUACCUGAGAAGUGGAAGAUCCGGCGC----UCGCAAUGA------GACAC--UG--GUA--GAGGAUCCAAGUACUA-UG-G-CGCGAGA----GG------UGAAAUUC-AGUGACCGCCA-UAU--GA-CUAUCUA--AUGC-GAAAGCAGUUGUGAUCC-AGAACGU---GUCUGU-C-AAUCA-G-GGACGAAAGUUAAG-GGAUCGAAGAUGAUUAGAUAC-CGUC-GUAGU-CU-UA-ACCGUA-AACGAUACCA-ACACGA--GAUUGGUAG-U-GAGA---CUUUUA----------------------------------------------------------------GAUCCUAU-CAG-AA------UC-------------------CAAGGGAAACCGUUAAGUUUUUGGGU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAAGGCA-C-CACCA-GGA-GUGGAG-UAUG-CGGC-UUAAUUCGACUCAACGCGGGGAAA-CUCA-CCAAGUUAG-G------AUGUGA-AUAUGAUUGA-CA-GA---------UUAAG-GUUCUU-UCU-UGAUU-UUACAGA-AGGUGGUGCAUGGUCGUU-CUUAGU-UCG-UGGA--GUGA-UUCGUCUUG--UUAAUU-CAGU-UAACGA-GCGAGACCUUAAC-UUGCUAAU-U-AAGGUACAGGGACUUCUUCGGUUGUCCGUCGUUUCGUUGGGGAAGU---------------------------------------------------------------------------------------------------------------------------GUAUACUUUCUCAGGAAAUCUGUACUGUCGCUGGUUUACCAGUGAUGCU-UCUUAGAG-GUA-C-AGCAC-UC---------------------------------------------------------GUCCA--GAGUGAGGAAGUUUAAGGCAAU-AACAGAU-C-UGUGAUGCCCU-UAGAUAU-CUUGGGCUGCACGCGUACU-ACAAUAUUAAUAGCAACAAGUAACGUAGAGUCA-------------------------------------------------UUCUUCGGAAUGCAACCC-UGGUC--CGAAA--GGA-U-UG------GG-AAAU-CUU-AUCAAA---------------------------------------GAUUAAU--GUGACA-GGGAUCGAGGUUUGU-------------AA---AUC-CUCG-UGAACGAGGAAUUCCUAGUAA-GCAU-G-AUUCA-UCAUGUC-GU-AUUGGCUUC---GUC-CCUGCCUUUUGUACACACCGCCCG-UCGCUCGUACCGAC--UGAA-UAGAGGUAUGAA--UUUGA-UG-GACCAG-----CG-UGGC-------------------------------GCUAA---------GCCA----U---G-CGAGAAAAUCAACU-GAAUU-UCUCU-AUUUGUAGGAACGAGAAGUCGUAACAAG-GUCU-UUGUAGG---UGAACCUGCAGAAG-GAUCAAGC
Z17224.1/1-1545                    UACCUGGUUGAACCUGC---CAGAAGG--GCAAGCUAAGAUUAAGGAUUAAGC-CAUGCAUGCC-AGGU------------------------------AUAAGCUA--AUA---------------CACAGGU-GAA-ACUGCGAACGGCUCAUUA-AAUCAGUUGAAA-UG-UCUCGUGCUU-------------------------------------------------------------------------UAUUCGUAGUCGGC-UAAUACG-GGCAACUCUCUUACUAAU-CGUGCUU-------------------------------------------------------------------------------------------------CGUUACAUCGGUAGUGAG--AGCGAU-----------------------------------------------------------------------------CU------C-----------------------GGGUUGAUUUA--UGUUGUAAA-AA---------UGACUGU-------------------------------------------UAGG-CAGGCAC-GAUC-AGCUUCUGACGCAUCA-UUA-A----GUAGG-AG-AA--GUAAA-GG------UU-AUCCUA-UGAGUUCACGCGUACCGGAGAAU--UAGG------------------------GUUCGAC-U-CCGGA--GAAUGAGCAUGAGAGACGGCUCAUAGUUCUAAGGGAGGCAGCAGGCGCGGAAAUUGCC--C-AAUGUACAAA----CGU-ACGA----GGCAGUGACGAAAAAU--------------------CUUG-AGC-CGG-C-UU-----------------------AG--GC-CGGU-AU--UA---AGCUG-AGCG--------A-GGC-GCAC-A----CACCC--U-C-GCGA-ACGCAAUUAGUGGGAGA-GCA-UGGUGCCAGCAGCCGC-GGUAAUUCC--AUCACUG-AUA-GC-UUUCUCUUA-CGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGCCGUUGUUAGCCCCGC---G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUCACUUU-GAGAAAAUCGGAGUGUUCAUUACAGGGA----------------------------------------------AACCG--CUGCACAGUA-CAGCAAAGAAUGACAUUGC-UCCCCGG-CGAC------------------------------------------------------------------------------------------------------------------------------GG----GGGGUACGG-AGUAUAUGGC--GG--CGC--GGGACUGAUAGUAUUU-GG-U-GGGGACA----GG------UGAAAUAG-GAUGAUCCACC-AAG--GA-CUUUCAA--CAGC-GAAGGCA---GUCGGUA-AGCGCCG---UCCAGU-U-GGUCA-A-GAGCGAAAGUGUGA-GGAUAGACGAUGAUUAGAAAC-CGUU-UUAUU-UC-AC-GCCUUA-AACGAUACCAUCUCAGA--AGCGGGCUC-A---------------------------------------------------------------------------------GAAGU-CCG-CA------UCU------------------CAAGGGAAACCG--CAAGUUUCGGGU--------UCUGGGGG-AA-G--UAUGA-UUGCAAGA-UUGAAA--C-UU-GAAGG-UAUUGACGG-AAAGAUA-C-CACAA-GAC-GUGGAG-UCUG-CGGC-UCAAUUUGACUCAACACGCA-AAU-CUUA-CCAGACCCA-G------AUGCUU-UACGGAGCAA-CA-GA---------UUAAGAGUUCUU-UUG-CGAUU-GGGCAGU-UGGUGGUGCAUGGCCGCU-CCUAGU-UCG-UGGU--GUAA-ACUGUCUGC--CUUAUU-GCGU-UAACGA-GCGAGACAACCAC-CC-CCAGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUGGGG-GGA-G-CGCCU-GC---------------------------------------------------------GUUGA--GCAGGACGAACGUGGUUGCUCU-AGCAGGU-C-UGUGAUGCCCU-UAGACAC-UCUGGGCCGCACGCGUACU-ACAAUGUCGGCUGCACAGCGU----------------------------------------------------------------------------CGC-CC-GC--CUGAA--GGC-C-CG------GC-CAUU-CGU-GUGAAC---------------------------------------CGCCGAC--GUGGUA-GGGAUCGGAGAUUGG-------------AAUUUUUC-U-CG-UGAACGAGGAAUGUCUUGUAG-GUCU-G-CGUUA-UUAGCGC-GGGGCUGACUAU---GUC-CCUGUCUUUUGUACACACCGCCCG-UCGCUCCUACCGAC-UUGGA-UGUUUUGGUGAG--UUGUC-CA-GAGUGC-----GC-GUCG---------------------------------------------CGGC----A---U-GCACGAAGUUCUGC-GAACC-CCAAU-GUCUGGAGGAAGGAGAAGUCAUAACAAG-GCUG-CUGUAGG---GGAACCUGCAGCCG-GAUCAUUA
AF255685.1/1-2152                  UACCUGGUUGAUCCUGC---CAGUAGCC-AUAUGCUCGUUUUAAAGGUUAAGC-CAUGCAAGUCUCAGU------------------------------ACAGGUCG--CUU----------------ACGGCC-GAA-ACCGCGGAUGGCUCAUUA-UAUCAGUUUUAA-UC-CGUAUGAUUU---------------------------------------------------------------------------AUCACAAUUGGA-UACCUGU-GGCAAUUCUAGAGCUAAUACAUUAUUAUAA--UAAAUUUACACUCUAUCCU---------------------------------------------UUCUGGUUCAGAGUCUGUA--A-AA--GCAAUCAUCACCACCAUA-AACCGAUCAU-----------------------------------------------------------------------AAAAAGGAAUUC----UCCUUUGG-------UGCUAUGGUGAUUCA--GGAUGAGCGUUG--------CAGAGCGC--AAAGGUCAUUG----------------------AACCG---CCGC-UAUAUUA-UGCG-AGUUUCUGCCCUAUCA-ACU-U----UACUG-UA-AG--GUAUU-GG------CC-UACAGU-GGUGUUCACGGGUAACGGGGAAU--CUGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAUAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGGAAAUUAAC--CUAAUACUAGCU-----CU-GUGA----GUUAGUGACGAAAAAU--------------------AUUG-AUG-UGU-G-UCUCC------------UAAUGGA-GC--CU-CACG-AU--CG---AAAUG-AGUU--------U-AUC-UUAA-A----UCCUU--ACU-GCAAGGAGCUAUCGGAGGGCAA-GCC-UGGUGCCAGCAGC-GC-GGUAAUUCC--AGCUCCU-UUA-GC-GUAAUUUAA-UAUUGCUG-CGGUUAAA---G--------UGCUC-GUCGUUGGAUUUCUUUAAAC---GGUGCUGGGCACCCGUGCCUUGAUUUCGAGCUUUAUCCUAUAAAGUCUUUACAUUUGUAAUUUUCCCUUCCCUCUUCGAGGAUGGGUUAUACUAGUUUUGAAUAACGGAAAGCUCGCACCUUGAAUGGGUGUCUAGCCAGAAUAUUUAAGUAUCUAGCAGUAGCGUAAAGCUAUCUAUGCUAGAAACGAGGUUGGUACACUAAAUGCUCUUUGUUGUGUGUUUAGUGGUGCCGACACUUUUCACUUU-AAUAAAAUUGGAGUGUUCAUAGCAGGUGUUAAUAU---------------------------------UUUCGAGUCGC--CUGACUAAAG-ACGUCUGGAAUGAAGGAAU-AAGACCU-CUGUUCGGAU--------------------------------------------------------------------------------------------AUUUCUGAUCGAUUUUUUUGUUCGAAGCUG----AGGUAAUGA-UUAACAGGGA--CU--GCC--GGGGGCAUUAGUAUUG-CA-G-CGCGAGA----GG------UGAAAUUC-UAUGACCGUUG-CAA--GA-CUACCUA--CUGC-GAAAGCA---UUUGCCA-AGAAUGU---UCUUAU-U-AAUCA-U-GAACUAAAGUUAGA-GGAUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UA-ACCCUA-AACAAUGCUA-ACCAGC--AAUCCGCUC-G-UGUC---ACUGGG----------------------------------------------------------------GACUGAGC-GGG-AU------CC-------------------CCCGGGAAACCA--GAGUCUUUGAGU--------UCCGGGGG-GA-G--UAUGG-UUGCAAAA-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GAA-GUG--G-CCUG-CGGC-UUAAUUUGACUCAACACGGGGAAA-CUCA-CCAGGUCCG-G------ACCCCG-GAAGGAUUGA-CA-GA---------UUAAA-GUUCUU-UCU-CGAUU-CGGAGGA-AGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUGAUU-CCGA-UAACGA-ACGAGAUUCUUUC-CUCCUAAU-U-UGUCGUCGGAUCGAAACCUGAAACGGGAACAGAUUCCUCCUUUUUAGUGCGCGGUAAUGUUCGCAAUUCGAUGAAAAUUAAGAAUUUUCGUGCA---------------------------GUCUCUGCUCUAUUAUAUUUUUCAUCGAUUCGAGCUUGUCGUUCCUAUUAUUGGAAAACCCGUCAAAGGUUGUCCGUCGAAAUAAAAUAUUUCUUCA-UCUUAGCG-GUA-U-CGGCG-GU---------------------------------------------------------GUCCA--GCCGCACUAA--AAAGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCUGCACGCGCGCG-ACAAUGAAGGGAGCAGCGUGUUG--------------------------------------------------------------------------UCC-CAUUC--CGAAA--GGA-A-AU------GG-CAAU-CAU-UUGAAA---------------------------------------CCCCUUC--UCGAUU-GGGAUUGGGGAUUGU-------------AAGUUUUU-CUCA-UAAACGAGGAAUUCCUUGUAC-GCGU-A-GGUCGUUCAGCUU-UC-GCUGAAUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUUCCGAU--UGAAGUGGCUGAGUGAG--GUUAU-UG-GACUGU-----CG-UUAAA----CGCA----------------------AAUUUUGCUA-A--AAAA----AU-GG-ACAGGAAGAUGCCCCGAACU-UGGUC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAG----UGAACCUGCGGAAG-GAUCAUUA
DQ013351.1/1-2093                  UACCUGGUUGAUCCUGC---CAGUGAUC-AUAUGCUUGUCUCAAAGCUUAAGC-CAUGCAAGUCUAAGU------------------------------UCAGGCUU--GUUCCUUU----CGGGGAGCGAGCC-GAA-ACUGCGAACGGCUCAUUA-G-UCAGAUAAGG-UU-CCUUGGCGAAA-------------------------------------------------------------------AGCGGGUCGGUUUAAUGGA-UAACUGU-GGUAAUUCUAGAGCUAAUACAUGCAACGC----ACCGUGGUCCCCCUCUUUUUCUCCA-------------------------------AGCUAAAGGUUUUUGAAGAAGGGGAA--A-CG--GCAUUUAUUCUCUGGACU--AGAUCGCCCUAGCCUGCGAAGCUA-----------------------------------------CCGUCAAAAGUAGCGACGGGGCGAAG-----CGACAA------------GUGUUGAAAUCC--GAAUAACUGUGC---------CGAUCGC---GGGGUCUUUCCGG-----------------GCCCCCG---ACGA-CUUUGCC-AUGA-AGUGUCUGUCCCAUCA-AUU-G--GCGAUGG-UC-GG--CGACC-UG------CC-UACCAC-GGUGUUGACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGCGAAACGGCUACCACCUCCAAGGAGGGCAGCAGGCGCGCAACUUACC--C-AAUCCCGACA-----CG-GGGA----GGUAGUGACGAAAAAU--------------------AACG-UGG-CGG-G-GCCCU------------UUCGUGG-UC--GC-CGCG-GG--CG---GAAUG-AGCG--------C-AAU-UUAA-A----AGAGU--G-U-GCGAGGAGCUAUUGGAGGGCAA-GCC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-CUAUAUCGG-AGUUGCUG-CGGUUAAA---A--------AGCUC-GUCGUUGGAUCUCGGAGGCG---GCACGGUCGGGCGCGAUACGCUGCGGGUCCGACCGGCGAUUUCUCGGCCGUCCCUAACCGGCGCGCGGGGCGAGGUGGACCUCGCGGUCCUGCCUCGUU-------------------------------------------------------------------------------------------------------UUUCUCCUUCGCGGGAGAGAACCCGCCGCAUUUUUUGUCUACCUU-GAAAAAAUUAGAGUGCUAAAGGCAGGCUAAAA---------------------------------------CCCCGAGC--CUGAAUAUUUCGUGCAUGGAAUAAGCGGGG-AUGCUCU-UUUUCCGGAGGGUGGUCCGGC-----------------------------------------------------------------------CGACUUGGCGACGUCGCUUUCGCUGUCGGCUUUGCCGGAG----AGCUAGGAU-UCGAGAGGAA--CG--GUG--GGGGGCGAGCGUACCG-GG-C-GGGGAGA----GG------UGAAAUUU-UGUGAUCCGCU-CGG--GA-CGACUCG--AAGC-GAAAGCG---CUGGCCC-CGGACGU---CUUCCU-U-AAUCC-A-GAACGAAGGUGGGU-GGAGCAAAGACGAUCAGAUAC-CGUC-GUAGU-AC-CG-ACGGUA-AACGCUGCCG-ACCG-G--GCCGCGGAC-G-AGGC---UCGAGAACAGCGG---------------------------------------------------UUAUGGACCCGUCC-GUG-GC------GGC------------------UUCGGGCAACCUGAGAGUUUACGGGU--------UCCGGGGG-UA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-GAAGG-AAUUGACGG-AAGGGCA-C-CACAA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGCAA-CUUA-CCCGGUCCG-G------ACAUCG-UCAGGAUUGA-CA-GACG-----CUCGUGCAGUUCUU-UCU-CGAUU-CGAUGGG-UGGUGGUGCAUGGCCGUU-CGUGGC-UGG-UGAA--GUGA-AAAGUCUGG--UUUAUU-CCGC-UAACGG-GCGAGGC-CUCGC-CC-UUAAC-U-AGUCGGCUCGUGGUUCUCGAAUCUUAGUCUCCCCUCGGGG----------------------------------------------------------------------------------------------------------------------------------------AGCAGGGAGAACAUCGGGCGAGUCGAAGCGGUCGUCGCUACU-UCUUAGGG-GGA-U-CCCGA-GCA------------------------------------------------------AGCUUAA--GCUAGGUGAG--AGAGAUCAAU-AACAGGU-C-AGUGAUGCCCU-UAGAUGU-CCGGGGCCGCACGCGCGCU-ACACUGAAGACGAAAGCGCGAGUGCCUACGGUCUUGGUUUGGUCAGGCCGGG-----------AACCCGCCCCGAGAGGGGAGGUUGGGGCCGUUCCUUCGGGGGC--GGUCU--CGC-C-UACAACGGGU-UAAC-CGU-GCCAAU---------------------------------------CGUCUUC--GUGCUG-GGGAUCGGGGCUUGU-------------AACUCAGC-CCCG-UGAACGAGGAAUUCCGAGUAG-GCGU-C-CGUCA-UCAGCUG-GC-GCCGAUUAA---GUC-CCUGCCUUUUGUACACACCGCCCG-UCGCUACCUCCGAU--AGAA-UGGCUAAGCGAG--GCCGU-UG-GACUGG-----GC-CCGUC------------------------------UUCG-------G--ACGG----G---A-CCGGAAAGGCGUUC-GAGCU-UAAUC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
EF999899.1/1-2149                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUCGUUCAAGGAUUAAGC-CAUGCAUGUCUCAGC------------------------------GCAAAUGG--AAC----------------AACAGU-UGG-UCUGUGAAUGGCUCCUUA-CAUCAGCAGUCA-UC-UAUGUGAUAGAGUGUGCU------------------------------------------------------UGGCCAAGCUGCAUGGCCCAAUGGA-CAUCCAC-AAUAACCUUGUGGCUAAUACACGAAAGCAG--AUGUCUGCCACAUCAUGUGGGUU------------------------------------CAGCAGUGCUGUUCCCACAGUGGU--G-GACUGCAAACAGCUCCUGAAAG--ACCAGC-----------------------------------------------------------------------------ACCCUAACA----GGGUAGCAU------UGACUGGGUGAAUCA--GGCUGUUCCAAA---------GGGACAUUGCACUGGCAGCUCACAAGC--------CUGGUUUACCAGG-CAUGC-UUGAUCA-CAUG-AACUUCUGACCUAUCA-GCU-U---UGACUG-UG-GU--GCAGU-GG------AC-CACAGU-GGCCUUGACGGGUAACGGAGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACUACCAAGGUGGGCAGCAGGCGCGCAAAUUGCC--C-AAUACAAAGCCA-AAUU-GUGA----GGCAGCAACGAACUGC--------------------AGCA-AUC-AUG-C-CCAC--------------UUAUGU-GG--GU-UUGA-CU--UG---GAAUG-GAUG--------C-UAU-CCAA-A----CACAG--C-C-AUGAGUAACAAGUGGAGGGCAA-GUC-UGGUGCCAGCAGCUGC-GGUAAUUCC--AGCUCCA-UUG-GC-GUAUACUAA-CAUUGCUG-CUGUUAAA---A--------CACUC-GUAGUCUGCCACAGGGAUCC---AGGUCUGGCAGAUGGCUGGCUUGUGGUGCUUCGGCACUGCAGGCUUGGGUAAAACCUCUGUCAGUAUGUCCUGGUCCCAACCUUGGAUGCUGAGAUGCUCCUGCAUGAAGCCCUCUUAAGUGAGGGUCAAAGCUAUCUUGCAG--------------UCAAUGCUUGUUGGGCAAUCCAAGGCAUGACCCUGUGUCAGCCUAUCUCUACAUGGGCCCAUAACCGGAGUUCAGCAUCAGAGCAACCCU-GGUAAACUCAGUGUGCUUCAAGCAACCGUU--------------------------------------------CUGGC--UUGUAUGCCA-UC-CAGUGAAUUGCAGAGC-AACGAUC-AGCCUUGGCUAAGAGUUGUGCUGGCCUUGGUGACAAAUCUGAGCAAUG-----------------UGGGGCUUCCCCCUAGCUGUGGCCUGGCCUCGGUCAUGGUCCACUGCCCAGGUGGGGAGUCACCAAA----CGGACAUGA-U----GGAAG--AG--UUC--AGAGUGGAAGAUACUG-CA-A--GCCAGA----GU------GAAAAUUC-UUAGACCGCUG-CAA--GA-UCAACUG--CAGC-GAAGGCG---UUCUGCA-AGAGCUC---GUUCGU-C-GAUCA-A-GAAUGAGAGUG-GG-GGAACAAAGAUGAUCAGACAC-CGUC-GUAGU-CCACU-ACAGUA-AACCAUGCCA-GCCAGG--CUUUGGUGA-G--GCA---AGAUCCUC--------------------------------------------------------------UACUUCAU-CAG-UG------CCAUGCCC--------CCUACAACGAGAAAUCC-ACAGCCUGUGGGU--------UCAGGGGG-GA-G--UACUG-UCGCAAGG-CAGAAA--C-UU-AAAGG-AAUUGACGG-AAUGGCA-C-CACAA-GGC-GUGGAA-UAUG-CGGC-UUAAUUUGACUCAACACGGGGAAU-GUUA-CCAGGUCAG-G------ACACUG-UCAGGAUGGA-CA-GA---------UUGAGAGCUCUU-UCU-UGAUU-CAGUGGA-UGGUGGUGCAUGGCCGCU-CCUGAU-CGG-UGGA--GUGA-UUUGUCUGG--UUGAUU-CCGA-UAACGG-GUGAGAUAUCUGC-CU-UCCAA-U-AGCCCCAGUCACGCAUUGUAGGGAUGCCAUCAGGUGAAA-----------------------------------------------------------------------------------------------------------------------------------------CCUCGGUUGAUCCUCUGGUGCCUGAGUGUUCUGGGUUCAGCU-UCUCUGAG-GUG-C-UGUGU-CAG------------------------------------------------------CCACCAA--UGGCACGCAUGCUAGAGCCAAC-AGCAGGU-C-UGUGAUGCUCC-CAGAUGU-CCUGGGCCGCACGCGCAUU-ACAUUGACACAGUGAAGGUGCUAAGCUU-----------------------------------------------------------CCUUGUGAAGCCC-AUCUC--AGAAG--UGA-G-UU------GG-AAAC-CAU-GCAAAU---------------------------------------CUGUGGU--GUACUG-GGGAUAGAUGAUUGC-------------AACUGUCU-GCCU-UGAACGAGGAAUGCCUAGUAU-GCUU-G-UGUCA-UCAGCAC-AA-ACAGAUUGU---GUC-CCUGCCAUUUGUACACACCGCCCG-UCGUUGCUACCGAU---GAG-AGCAAGGCAGAG--UCAUC-AG-GAGACA-----AC-UACCC------------------------------CUUG-------G--GGCA----G---U-CAUUGAAAUUGGGC-AAUGC-CCUGC-UCUUAGAGGAAGCAAAAGUCGUAACAAG-GUUG-UUGUAGG---UGAACUGCCAAAAG-GAUCAA--
CACX01001817.1/31283-29564         UAUCUGAUUGAUCCUGU---CUGAAUUG-AUGUGCUUAUUUUAAAGAUUAAGC-CAUGCAUGUGUAAGU------------------------------ACA-AUGU--UUU----------------AAACAU-GAA-ACCGCGGAAAGCUCAUUA-UAACAGCUAUAG-AC-UACACGGUAA-------------------------------------------------------------------------AUAUUUUAGUUGGA-UAACUGA-GGUAAUUCUUGAGCUAAUACACGCUUUUUA--UACCACAU--------------------------------------------------------------------UA-------G-UGGUGCGUUUAUUUGAUUAAAC--CAUUUU-----------------------------------------------------------------------------UU------------------------------CGGUUGACUCA--AAAUAUCCUCGC---------UGAUUUU-------GUUACU------------------------------AAAA-CAUACCG-UAUG-UGUAUCUGGUUUAUCA-ACU-U--UCGAUGG-UA-GG--GUAUU-GG------CC-UACCAU-GGUUGUGACGGAUAACGGAGAAU--UAGG------------------------GUUCGAC-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGAAAAUUACC--C-AAUUUUAGUU-----AA-AAGA----GGUAGUGACGAAAAAU--------------------GACA-ACC-AAA-U-AUUA--------------UUUUUA-GU--AU-UUGG-AU--UG---AAAAU-CUUC--------A-AGU-UUAA-A----UAACU--U-G-UUGGUAA---AGGAAAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUACC--AGCUUUC-CAA-GU-GCAUAAAAU-GAUUGUUG-UGGUUAAA---A--------AGCUC-GUAGUUGGAUUAUAAAGAUU---GUGUAAUGAGCAUCUUGGAUGUUAUUUUCAUUACCAUCUUAUUUUUUUAUUAUAUUAGAAAUAAUAUAAUA---------------------------------------------------------------------------------------------------------------------------------------------------------------------ACUGUUACUUU-GAAUAAAUCAGAGGGUUCAAACCAGGCAUU-------------------------------------------AUAUGC--UUGUAUGGUC-UAGCAUGGAAUAACACUAU-AGAAAAA-GUUA---------------------------------------------------------------------------------------------------------------GUGUGGUUUCACUAUCU----UUUUCAUGA-UUAAUAGGAA--CA--AAC--GGGGGCAUUCGUAUCG-CU-A-CGUUAGA----GG------UGAAAUUC-UUGGACCGUAG-CGA--GA-CGUCCUA--CUGC-GAAAGCA---UUUGCCA-AGAAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUAGA-GGUUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UA-ACCGUA-AACUAUGCCU-ACUAGG--UGUAUGAAU-U--AUU---AGUUAU----------------------------------------------------------------AAUAAUUU-AUG-CA------CCU------------------UCUCGGAAACGA--AAGUCUUUCGGU--------UCCGGGGG-AA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUCA-CCCGGGCCG-G------ACACUA-UAAGGAUUGA-CA-GA---------UUGAUAGCUCUU-UCA-UGAUU-UAGUGGU-UGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA-UAUGA-UUUGUCUGG--UUGAUU-CCGA-UAACGA-GCGAGACUUUUAU-GU-UAUAU-U-AAAUUAUAUUAUUU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUAAUAAUAUUAAUU-UUAAUAAC-AGA-U-UAAUA-GU---------------------------------------------------------GUUUA--ACUAUUUGAG--AGAGAGCGAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CCGGGGCUGCACGCGCGCU-ACAAUGUAGUGAUCAUUAUGU----------------------------------------------------------------------------UCC-UGUUU--AGAGA--UAA-A-UG------GG-UAAA-CAU--UGAAA---------------------------------------ACAUUAC--GUAACU-GGGAGUGAAACUUGC-------------AAUUAUGU-UUCA-UGAACGAGGAAUUCCAAGUAA-ACGU-A-AGUCA-UUAGCUU-AC-AUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUGCCCGGAAC--UGAG-CAAUAUCGAGAG--GCAGG-AA-GAGAUA-----UA-AA-------UAAU----------------------UUUAUAUUU-------UU----U---A-UGUUAAAUCCUUCC-AAUCG-CUGUU-GUUUGAACCGGGCAAAAGUCGUAACAAG-GUUU-UCGUAGG---UGAACCUGCGAAAG-GAUCAUUU
AF304465.1/7-2089                  AACCUGGUUGAUCCUGC---CAGUHAUG-AUACGCUCGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUACAAAG----U---------------CUACUUU-GAA-ACUGCGAACGGCUCAUUA-G-CCAGUUAUAG-UU-UAUUUGAUGUAAUGAAUAGGAGUAUUUCGUGGUUGAAGUGGGUGUGGUUGAUACCAUAUCUACUGAACAAUGAUGUACUAAAAAGAGUCUACAGGGA-UAACCGU-AGUAAUUCUAGAGCUAAUACCAGGAGGUG----AUGUGUUGAUUGUGGUUGUUGUUGGUUGUGUUUAUGAUAAUAAUAAAGACAAGCAAACAACACGAACAAACAAUAAGAACCA--U-AUCCGCAUUUAUUAGAAAAUAA--AUC---------------------------------------------------------------------------------AUUCAAUA----AAAAGA------------AA-GAUGAAUCA--UAAUAAAAAAGU---------AAAUCGUU-GAUUUAGUAAA----------------------AUAAAA-GACGA-UGAAUCA-UUCA-AGUAUCUGAUCUAUCA-GCU-U---CGAUGG-UA-GG--GUAUU-GG------CC-UACGAU-GGCGUUGACGGGUAACGGAUCUU--UAGG------------------------GAGAGAA-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACC--C-AAUCCUAAAU-----CG-GGGA----GGUAGUGACAAGAAAU--------------------AGUG-AUG-AUG-U-GUUAU-----------AGAUAAAA-AU--AUGAUAA-AU--CGAAACAAUG-AGUG--------U-AAU-AUAU-A----UCCGU--U-A-ACGAGGAUCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUUGGUGUGAUGUGGUUG-GUGGCUUGGAGGUUAGUAUAUGAUAAUGUAAUGUUAUUGUAUAUUCUCUUAGUUAUUACUACUAAUGAGGAAGUAUAUGUG---------------------------------------------------------------------------------------------------------------------------------------------UAAACAAUACUUUCUUAAUUUACUGU-GAAAAAAUCAAAGCGUUCAAAGCAGGCUAAAAG------------------------------------GCAAUGAAAA--AAGAAUGUUA-UAGCAUGGAAUAAUGUUGU-UUGUGUU-UGUUAUGUUUUA----------------------------------------------------------------------------------------UGGUAAAUAUAAGUGAAUGAACCAUAAAAUAU----UGAUUAAAU-AGAAUAGGAA--CA--GUC--GGGGAUAUUCGUACUU-AU-A-AGUCAGA----GG------UGAAAUUC-UUGGAUUUUCU-AAA--GA-CGAACAA--CUGC-GAAAGCA---UUUAUCA-AGGAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUUGG-GGAUCGAAGAUGAUUAGAUAC-CAUC-GUAGU-CU-AA-ACCAUA-AACAAUGCCG-AUUCGA--GGGAGGUGU-G-UGGU---AGGUUGUGGUGAUGGGGUGUAGUAAUACAU------------------UUCUUCAUUACAACCAAUAAUAACAUUCAU-CUC-CA------UCG------------------UAUGCGAAAGCA--AAAUGUUUGGGU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CAUAA-GGC-GUGGAG-CCUG-CGGC-UCAAUUUGACUCAACUCGGGGAAA-CUUA-GCAGGGCAG-G------ACAAAA-AAAGGAUUGA-CA-GA---------UUGAAAGCUCUU-UCA-AGAUU-GUUUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGAUAAUGA-UUUGUCAGG--UUAAUU-CCGA-UAACGA-ACGAGACCUCAAG-GA-UGAGU-U-GGAUUGUAUUAAUA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAAAUGUUAAAUAUAAAUUC-UCCCCCUC-CGA-C-AUUUU-GCGAUAAAAA----------------------------------------AAUAAAAAAAAAUA--GCGGAAGGAAGUUUGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CCUGCGCCGCACGCGCGCU-ACAAUGGUUGGGUGAGUGAGUGUUGUUAUGUGGUGUUGUGU---------------------------------UUGGUAAUUCGAAGCACACCAUAUCC-UCGGU--CUAUU--GAC-C-UU------GG-UAAU-CUU--AUAAC---------------------------------------CCCAAUC--GUGAUA-GGGCUAGAUUCUUGU-------------AAUUAUUA-AUCU-UCAACGAGGAAUGCCUAGUAA-ACGC-A-AGUCA-UCAUCUU-GC-AUUGAAUAC---AUC-CCUGCCCUUUGUACACACCGCCCG-UCGCAUCUACCGAU---GAA-UUUUGCGGUGAA--GUCUU-GG-GAGUGG-----UG-UUAAU---UGUAUGUGUAA----------AAAGCGUUAAAUUAAU-A--UAAU----A---A-ACACGAACUUGAAU-AAACC-UUAAC-AUUUAGAGGAAGAUGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
AF249194.1/4-1999                  UACCUGGUUGAUCCUGC---CAGUAGUCUAUAUGCUUGUCUCAAAGGUUAAGC-CAUGCACGCCUAAGU------------------------------UCGUCCCC--UUA---------------GUACGGU-CAA-ACCGCGAAUGGCUCAUUA-GAUCAGUCCCGG-UU-CCUUUGGCACGCGA--------------------------------------------------------------CCGCCCCAGGUCACAUACGGA-UAACUGU-GGCAAAUCCAGAGCUAAUACGUGUAUUGUACUCGCCUGGUCUCGUCACG------------------------------------------------UUUCACGACGGACGGGAC--C-GGGCGCACUUAUUCGAACGAGG-CCGGUGUCCACGGCG-------------------------------------------------------------UGUUUGCGCACGUCUGG----ACUGUAA---------CGUAAUUGAGCUCU--AGGUAAUUGUCA---------CGACCGC--GACGUCCCUUGU---------------------GGACG---GCGG-CUAGCUG-AACA-AACGUCUGACCUAUCA-AAU-G--UCGACGG-UAAGG--GCACA-CG------CC-AACCGU-GUUAACGACGGGUGACGGGGAAU--CAGG------------------------GUUCUAU-U-CCGGA--GAGGGAGCACGAGAAACGGCUACCAAUUCUAAGGAGGGCAGCAGGCGCGCAACUUACC--C-AAUACCAGCU-----CG-GUGA----GGUAGUAACGAGAUAU--------------------AAUG-AUG-CGG-G-GCUC-------------GAGUCGG-GC--CG-CGCG-GU--CG---GAAUG-AGCC--------C-AGU-GUAA-A----AUCCU--G-AGGCGACGUUCCAUCGGAGGGCAA-GCC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCG-AUA-GC-GUAUACUAA-UCCUGCUG-CAGUUAAA---A--------AGCUC-GUAGUUGGAUCUCGGCGGUG---CGUGUUUCCCGUCUACGGUGUCGUGUUACAAGCCCGCGCUCGUCGCGGGUCACUUCGUCCGUAGCGGCGCCCACCGCCACCUCUGGUCUGCUCUCUCCCG-----------------------------------------------------------------------------------------------------GGCUCGGCCUUCACUGGUCGGGACCGGGUGGCAGACAGUUCACUUU-GAAAAAAUUAGAGUGUUCAAAGCGGGCGCC-------------------------------------------AGUCGC--UCGAAUAAUG-GUGCAUGGAAUGAUGGAUA-GGACCCC-CGUCU-------------------------------------------------------------------------------------------------------UAUUUCUGCCGGUCUCAGGGACGG----AGGUAAUGA-UUGGAAGAGG--CA--GCC--GGGGGCAUGCGUAUUG-CG-G-CGGGAGA----AG------UGAAAUUU-GAUGAUCGUCG-CAA--GA-CGUCCGA--GAGC-GAAAGCA---CUUGUCA-AGAGUGU---CUUUUU-UAGAUCA-A-GAACGAAAGUCGGA-GGCUCGAAGACGAUCAGAUAC-CGUC-GUAGU-UC-CG-ACCAUA-AACGUUGCCA-ACCGGC--GAUCUGCGU-U-GGUCU-CGAUUUUGG--------------------------------------------------------------GACCAGGC-GGG-AC------ACC------------------CCGGGGAAACCA--GAGUUUUGAGGU--------UCCGGGGG-GA-G--UAUGG-UUGCAAAA-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGGG-UCUGCCGGC-UUAAUUUGACUCAACACGGGAAAA-CUCA-CCCGGUCCG-G------ACACCG-CAAGGAUUGA-CA-GA---------CUGAG-GCUCAU-UCUACGAUU-CGGUGGG-UGAUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GCGA-UCUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACUCUACC-CUGCUUGU-U-AGCGUGUCUUCGUACGGCUAACUCUGCGUCCGUGGCAGGUUACGGGUGGCCUCACUCCCCCUCUCCUC-------------------------------------------------------------------------------ACGGUGGGGGCGAGCUGUCGGUCGUCAGUCCGCUCGGCGCGAAUUCACCCGAAUUCAUAACCCAAAUGGCU-UCUUAGAGAGGA-C-GGGCG-GU---------------------------------------------------------GGCCA--GCCGCACGAG--AAAGAGUGAU-AACAGGU-C-UGUGAUGCCCU-UAGACGU-CCGGGGCCGCACGCGUGCU-ACACUGGGGGGACCAGCGCGAUC-----------------------------------------------------------------------UCGUCC-UGACC--CGACC--GGUCU-CG------GG-AAAG-CUG-CUGAGU---------------------------------------UUCCCCC--GUGCUC-GGGACCGGGGCUUGU------------CCAUUGUGC-CCCG-CGAACGAGGAAUUCCCCGUAG-GCAC-G-GGUCA-UAACCCC-GU-GCCGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACCAUCGGU---GAA-CGGUCUAGCGAG--GGCCU-CG-GACUGG-----CA-A----------------------------------UUCGC-----------------U---G-CCGGGAAGACGCCC-GAACU-AGUUC-GCUUGGAGAUAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAA-CUGCGGAAG-GAUCAUUA
AFJA01011649.1/3084-1181           UCCCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------ACAUACCG--AAU----------------UAAGGU-GAA-ACCGCGAAUGGCUCAUUA-AAUCAGUUUUGG-UU-UCUUAGAUCG---------------------------------------------------------------------UACAACAAUUUACUUGGA-UAACUGU-GGUAAUUCUAGAGCUAAUACAUGCAAACCA-GAAUUCCACCC---------------------------------------------------------------AGAGAUGGGA--G-GAAUGCUUUUAUUAGAUCAAA---ACCAAUCGAUGUGGUGGACG-------------------------------------------------GUUCGUCCGUCUUCCCAUCGUCA----GCU----------------AUGAUGAUUCU--GAAUAACUUUGUG-------CUGAUCGU---ACGGUUUUCUA--------------------GCACCG---ACGA-CGGAUCU-UUCA-AAUGACUGCCUUAUCA-ACU-G--UCGAUGG-UA-GG--UUCUA-CG------CC-UACUAU-GGUUGUAACGGGUAACGGGAAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGUAGGCGCGCAAAUUACC--C-ACUCCCGGCA-----CG-GGGA----GGUAGUGACGAAAAAU--------------------AACG-AUA-CGG-G-ACUC--------------GUCCGA-GG-CCC-CGUA-AU--CG---GAAUA-AGU--------------------A----AC---------UCCAGCUCCAA-----------------------------------------------------UA-GC-GUAUAUUAA-AGUUGUUG-CGGUUAAA---A--------GGCUC-GUAGUUGAAUCUAUGUGUCG--CUGUGUCGGUUCACCGCUUGCGGUGUUUAACUGGCAUAAUGCGAUACGUCCUACCAUUGGGUUUAGCUUCUCUUCGGAGUUGCGGCCCAAGUUAAGCAUCCC--------------------------------------------------------------------------------------------------AUCGUGGUGCUCUUCGCUGAGUGUCGAGGUAGCUGGUAUGAUUACUUU-GAACAAAUUAAAAUGCUUAAAGCAGGCUAC------------------------------------------CUUCGCC--UUUGUAUUCU-GUACAUGGAAUAAUGGAAU-AGGACCU-CGAUUCUAUUUUGUUGUUUUUUGGAGCCCCGAGA---------------------------------------------UAAUGGUUAUGUGGGAGUGUAUUGUAUUUUAUGUUUGAUUAGUUGUAGAAUUU----UUGUAUAGU-UUGACAAUCG--UU---------GUGAAAUUGUA-UA-UA-U-GGCUGCA----AG------UGUAAAUG-A-CGAUUUAUG-AAAGGAA-CAAGUGG--UUGC-CA--GCG---UUUUGAA-UAAGUGU---UGUUGU-U-AAUUC-A-GUUUAGAA---------ACGGAAGUUGAAC-GGUCC-UGAC-GUGCG------------A-AACACUGCGA-AAUACG--AAUUAUAAG-A-UUCU---ACAUUUUA--------------------------------------------------------------CGAUUUUA-CGA-CGUUCACAAGU------------------UCAAUACUUAUU--GUGUUUUUGUGU--------UCUUAUUGUGA-GUUUAUUG-UUGC--UG-UGUUCU--C-UU-AAA------UAAAAG-GAUAGUU-C-UAAAA---A-UUCUAUUCCCA-CAGU-UAAUAGGGACGGAUGGUGACAAAC-UUCA-CCAGGCCCG-G------ACACCG-GAAGGAUCGA-AA-GA---------UUGAUAGCUCUU-UCU-UGAUU-CGUUGGG-UGGUGGUGCAUGGAAGUU-CUUAAU-UGG-UGCA--GCGA-UUUGUCUGG--UUAAUU-CCGA-UAGCCA-ACGAGACUCUGGC-CUGUUAAA-G-AGACGUAAAUUAUGGUAUCUUGAAGGCCCCCGGCUUC----------------------------------------------------------------------------------------------------------------------------------------------GGCCGGUGUGGUUUUAACUACCAACGGACAAUCAAAUCU-UCUUAGAG-GGA-C-AAGCA-GC---------------------------------------------------------UUUUU--GACGCUUGGAG-AUUGAGCAAU-AACAGAU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGUGCU-ACACUGAAGAAAUCAACGUGUUU--------------------------------------------------------------------------UCC-CUGGC--CGAAA--GGU-C-CG------AG-CAACACAC--UGAAC---------------------------------------CGCCUUC--GUGCUA-CGAAUUGGGGCUUGA-------------AAUUGUUC-GUCA-UGAACGAGGAAUUCCCAGUAA-ACGU-G-AGUCA-AAAGCUC-GC-GUUAAUUAC---UUC-CCAGCCAUUUGUACAUACCGCCCG-UCGCUACUGCCGAU--UGAA-UGAUUUAGUGAG--GUCUU-CG-GACUGG-----UG-CGCGG----CAAUG-------------------UCUCGGCAUUGC-C--UAUG----U--UA-CCGGAAAAAUAUCC-AAACU-UGAUU-AUUUAGAGGAAGUAAAAGUUGUAACAAU-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
AF255687.1/1-2116                  UACCUGGUUGAUCCUGC---CAGUAGC--GUAUGCUUGUCUCAAAGCUUAAGC-CAUGCAUGUCUAAGU------------------------------AGAAGCCC---UA---------------GCAAGGC-GAA-ACCGCGGAAGGCUCAUUA-AAUCAGUCUGAA-UC-UAA-AGGCAUUUGUUAGAA----------------------------------------------------UCGAUUUUGUCGCAUUUUUACUUGGA-UAACUGU-GGUAAUUCUAUAGCUAAUACAUGGACACC----GUGGUACCACUGUUUCA-----------------------------------------------CCUACGGCUGAAACAGAG--A-CC--GCUAUUGUUGCAUGGAAC-GCACUGG-----------------------------------------------------------------------------GAUUCUCAG----GAAUUUCAA-----UAAAAACGAUGAAUCA--CAACAAAUUAGC---------CGAGCGU---AUGGUCUCGA-----------------------ACCG---ACGC-UGUACCU-UUCG-AGCGACUGCCUUAUCA-GCU-U--UCGAUUG-UA-GG--GUAUU-GU------CC-UACAAU-GGCGAUAACGGGUAACGGGGAAU--CAGG------------------------GUUCGAUUC-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCACGCAAAUUACC--C-ACUCUCAGCA-----CG-GGGA----GGUAGUGACAAAAAAU--------------------AACG-AUG-CGU-G-UCUC-------------UUUCUGA-GG-CCU-CGCA-AU--CG---GAAUG-GAUU--------U-AUACUUAA-A----UCACU--G-A-AUGAGGAGCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAACUCC--AGCUUCA-GUA-GC-GUACGUUAA-CGUUGCUG-CGGUUAAA---A--------AGCUC-GUAGUUGGACCUUAAGUGCG---GACGGUCGAUUCACCCAUCGGAAUGCUAGCGGUCAAAGGAGUCAAAUCCGGAGGCCAAUAGCCUCGUUGGCUGAUAUCAACGGCCGAUUAUUCCGUCACUUGAUGAAGAUUUGUCG--------------------------------------------------------------------GUUUAUAUGUGUGUUGGGCACUCUCUCGGGUGUUCUAGCUCACGUGGCUGACAAUGUCACUUU-GCAAAAAUGAGAACGAUUAAGGUAGGCUGA--------------------------------------------AUGCC--AUGAAUAUUC-AUGCAUAGUACGAGAGAAU-AGGACUU-UGUCU-------------------------------------------------------------------------------------------------------CUGUUUGGU--GCACAGAAUGAUG----AAGUAAUGA-UUAAGAGAGA--CA--GAC--GGGGACGUUCGUACUG-CG-G-CGUUAGA----GG------UGAAAUUC-UUGGAUCGCUG-CAA--GA-CGAACAA--UCGC-GAAGGCA---UUCGUCC-AGAACGC---UUUUCU-U-AAUCA-A-GAACGAAAGUUAGA-GGAUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UA-ACCGUA-AACGAUGCUG-ACCGGC--UAUUAGUCG-G-UGUU--AUACCCAAA--------------------------------------------------------------CACACGAU-UAG-CA------ACC------------------CCCGGGAAACCA--GAGUCUUUGUGU--------UCCGGGGG-GAUG--UAUGG-UUGCAAGG-CUGAAA--C-UUAAAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGA---CUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUUA-CCAGGACAG-G------ACAUCG-GAAGGACUGA-CA-GA---------UUUUAAGCUCUU-UCU-CGAUU-CGAUGGG-UAGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGAUUUUGCC-CUGCUAAU-U-AGUCUGCUGAUUAUAUCGGGUCGUCUGUUCCUUCGGGUUCAGCGGCUUGGAACCUCAUGGCUUGGGUAUGCUUCGAUUGGGGGUGUAGGUGGUGCUUUGGGAAGACGGUGUGUUUGCGUCGGUUCUUCUGAGCUGUGCAGCACGCUGUUGGAUUAUUGCCUGUAAGCUUACGCUCUCGGUUGGUAUUCCUUGCCGAUUGUGGUGUCAGUAUUGUGUCU-UCUUAGAG-GGA-A-CGGCA-UC---------------------------------------------------------GUAUA--GUUGCACGAG--AUUGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CUUGGGCUGCACGCGCGCU-ACAAUGGAGAGAUCAACGCGCUU-----------------------------------------------------------------------UCUACC-UGCUC--CGAGA--GGA-G-UU------GG-GAAC-CCG-CUGAAA---------------------------------------UCUCUCC--UCAAUU-GGGAUUGCGGUUUGA-------------AAUUGUUC-CUCA-UGAACGAGGAAUUCCUGGUAA-GCGU-G-AAUCAAUCAGUUC-AC-GAUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAA-UGAUUCAGUGAG--GCUAU-UG-GACUGG-----CA-CCCCA----GAAUAGAA--------------AUUUAUUUCUUUCC-G--GGGG----U--UG-ACGGGAAGAUGUCC-AAACU-GGAUC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
GQ358729.1/1-1779                  -ACCUGGUUGAUCCUGC---CAGUGGUC-AUAUGCUCGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------UCAUAUCA--UUU---------------AAAUGAU-GAA-ACUGCGAAGCGCUCAGUA-AAUCAGUUAUCG-UC-UGUUCGAUCG-------------------------------------------------------------------------AUACAUGCCAUGGA-UAACUGU-GGCAAACCUAGAGCUAAUACAUGCAAAA-----UUCUUUGUU------------------------------------------------------------------UC-GGCA--A-AGAAGCAUUUAUCCAGCUAAA---CCAAUC-----------------------------------------------------------------------------GGGCCUUAA----AACCCA------------GUAGGUGAAUCU--AGAUAACUGUGC---------CGAUCGU-----UGCUUUAU-----------------------GCG----GCGA-UAUUUCG-AUUG-AGUUUCUGCCCUAUCA-ACU-U----GUUGG-UA-UG--GUAUU-GG------CC-UACCAA-GGUUUUGACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUCCAGACA-----UU-GGGA----GGUAGUGACGAGAAAU--------------------ACCG-GAC-UGG-A-UC----------------UUAC---GA--UC-CAGU-AC--UG---GAAUG-AACG--------A-UAU-GUAA-U----CAUUU--C-G-AUGAGGAUCUACUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-GUA-GU-GUAUAUCAA-CAUUGUUG-CGGUUAAA---A--------CGCUC-GUAGUUGGAUAACGAGGGUA---AAAUAAUUAUAUGAGCAAAUGCUCAUUGAUUAUUUUGCUCUUUUUAUUACAAGGGUCAAUACUUUGCUUAAUUGAAUUGU----------------------------------------------------------------------------------------------------------------------------------------------AUUGAAUACUUGUAUAGCGUGCCUU-GAAUAAAGCACAGUGCUCAAAGCAAGCG---------------------------------------------UAACGC--UAGAAUGUUA-UAGCAUGGAACGAAUAGAU-UGACCUG-AAUCAGUUUGUUG---------------------------------------------------------------------------------------GUAAAAAGUUACGCAAGUAACUAACCUGAAAC----GGGUCCUGA-UUAAAAGGGG--CA--UUU--GAGGAUGUUAGUACUU-GG-U-GGCGAGA----GG------UGAAAUUC-UUAGACCCACC-AAA--GA-CUCACUA--UUGC-GAAGGCA---UUCAUCA-AGAAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUGGA-GAAUCGAAGACGAUCAGAUAC-CGUC-CUAGU-UC-CAUACAGUA-AACUAUGCCA-GCUUGA--GAUUAGCUC-G----G---UAAACGAG--------------------------------------------------------------C--CAAGU-UGG-UC------UC-------------------UCCGUGAAAAC---AAGCUUUCGGGU--------UCCGGGGG-GA-G--UACGG-UCGCAAGU-CUGAAA--C-UU-AAAGA-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGCAA-CUCA-CCAGGUCCG-G------ACAUUG-AAAGGAUUGA-CA-GA---------CUGAUAGAUCUU-UCA-UGAUA-CAGUGAU-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UCUGUCAGG--UCUAUU-CCGG-UAACGA-GCGAGACCACGAU-CU-CUAUU-U-UCUUUCAGUAGCAU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUGUCGUUCUACUGAGA---AUAGAG-AGA-C-AACUA-GU----------------------------------------------------------UCAA--GCUAGGGGAA--GCGUGGCAAU-AACAGGU-C-UGUGAUGCCCU-UCGAUGU-UCUGGGCUGCACGCGCGCU-ACAAUGGCAGCGACAAAAAGCAU-------------------------------------------------------------------------CACC-UGCUC--UGAGA--AGA-G-UG------GG-AAAU-CUU-UAAAAU---------------------------------------CGCUGUC--GUGAUU-GGGAUUGAGCCUUGU-------------AAUAAUUG-CUCA-UGAAAUAGGAAUUCCUCGUAA-GCGU-G-AGUCA-CCAACUC-AU-GUUGAAUAC---GUC-UCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAA-UGUCUCUUCGAG--AAAGC-GG-GAUUGA-----UU-UUUAC------------------------------GCAA-------G--UAAG----A---G-UCGAGAGCUCUUUC-UAGAA-GAUGC-UUUGAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CUGUAGG---UGAACCUGCAGAAG-GAUCAUUA
AAWT01052623.1/137-1983            UAUCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUAUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------ACACGAUU---UU---------------AUAUAUC-GAA-ACCGCGGAUGGCUCAUUA-UAACAGCUAUGA-UU-UGAGAGAUAU----------------------------------------------------------------------UAUCAUUUGCCACAAGA-UAACUGU-GGUAAUUCUAGAGCUAAUAUUUUAUAGAA---UGCCGUGACU------------------------------------------------------------------CA-CGAA--G-CGGCGGAUUUAUUAGAUCAAA---ACUAAC-----------------------------------------------------------------------------CUGUCCUA-----GACAGUU----------AUUUGAUGACUCU--GGAUAACUUUAC---------UGAUCGU---ACGACCUCUG----------------------UGUUG---ACGA-CGAAUCUCUUGA-AAUGGCUGACCUAUCA-ACU-U--UCGAUGG-UA-AG--AUCAA-AG------CU-UACCAU-GGUUGUAACGGGUAACGGGGAAU--CAGU------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCCACGGAAGGCAGCAGGCGCGAAAAUUACC--C-AAUGCCGGUU-----CG-GCGA----GGUAGUGACAAUAAAU--------------------AACA-AUA-UGG-A-CCC----------------UAGUG-GU--UU-CAUA-AU--UG---CAAUG-AGAU--------U-AUU-UUAA-A----UACUU--U-U-UCAAGUAUCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AAA-GC-GUAUAUUAA-AGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUUGAAAUUGAGG--------UAGAUGUAAUUUGAAAUCUUAUGAUUGAUUAUUACUAUACCUUUUCUUCGUGUAUAUUAGUGAGGGACUUAAUUGUUUU---------------------------------------------------------------------------------------------------------------------------------------------UUACUAGUAACCGAAAUGUUUACUUU-GAAAAAAUUAGAGUGCUUAAAGCAGGCU----------------------------------------------UACGC--UUGUAUAUUG-UUGCAUGGAAUAAUAAAAU-AGGACUU-UGGUU-------------------------------------------------------------------------------------------------------UUAUUUUGUUUGGUUUUCUUAACU---AAAGUAAUGA-UUAAAAGAGA-CUG--CCG--GGGGGCAUAUGUAUGC-UGGG-UGCUAGA----GGG----UGGAAAUUCUUUAGACCAUCA-GCA--GAACAAACUA--CUGC-GAAAGCA---UUUGCCC-AAGAAAUGUUUUUCAU-A-AAUCAAA-GAACGAAAGUCAGAGGGAUCGAAGACGAUCAGAUACCCGUCCCUAGUUUC-UG-ACCAUAAAACUAUGCCC-ACCUGACAGUUUAGUAA-A-AGAU---GAAAUUAUUU---------------------------------------------------------UCUUUCUUUAC-UAG-AA-----GUCA------------------CCCGGGAAACCA-AAAUUCUUUGGGU--------UCCGGGGGGAA-G--UAUGGGUUGCAAAAGCUGGAAACU-UU-AAAGG-AAUGGACGGGAAGGGCA-C-CACAAGGGA-GUGAGC-CCUGCGGGCUUUAAUUGGACUCAACACCGGGAAAUCUCACCCCGGUCCGGG------ACACUGUGAGGGAUUGA-CA-GA---------UUGAUAGCUCUUUUCU-UGAUUUCGGUGGGGUGGUGGUGCAUGGCCGUUUCUUAGUUUGG-UGGG-AGCGAUUUUGUCAGG-GUUAAUUACCGA-UAACGAAACGAGACUAUGACAUUACUAAA-U-AGUGAAUUUAUAUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAUUGUAAAUUCUCACUUUCUUAGAA-GAAAU-AAAUA-GC---------------------------------------------------------GUUUA--GCUAUAUGAA--AUAGAGCAAU-AACAGGUGG-UGAGAUGCCCU-UAGAAGU-CCGGGUCCGCACCCGCGCU-ACAAUGGCAGUACUAACAAGUUU--------------------------------------------------------------------------UCC-UAACU--AGAAA--UAG-U-CG------GG-UAAU-CUC-UUGAAA---------------------------------------CACUGUC--GUAUCA-GGGAUUGUGAAUUGA-------------AAUUAUUU-CACA-UGAACGAGGAAUUCCUAGUAA-GCGC-A-AGUCA-CUAGCUU-GC-GCUCCUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAA-UGGUUUAGUGAG--AUUGU-UG-GAUUCU-----GA-UCUAA---GAAAU---------------------GGCAACAUUUC-U--AUGA----A---U-GGGAAAAGACACUC-AAACA-AGAUU-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCGUUU
AAKO01009387.1/1109-2568           AUUCUGGUUGAUCCUGC---CAGUAGUU-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------ACACACGA--AUU----------------AAAAGU-GAA-ACCGCAAAAGGCUCAUUA-UAUCAGUUAUGG-UU-CCUUAGAUCG-----------------------------------------------------------------------UUAACAGUUACUUGGA-UAACUGU-GGUAAUUCUAGAGCUAAUACAUGCAAUUAA--AACAUGAACC----------------------------------------------------------------UUAU-GGGA--C-AUGUGCUUUUAUUAGGCUAAA---ACCAAG-----------------------------------------------------------------------------CGAUCGCAA----GAUCGUUA--------UAUUGGUUGAACUC--UAGAUAACAUGC---------AGAUCGU---AUGGUCUUGU-----------------------ACCG---ACGA-CAGAUCU-UUCA-AAUGUCUGCCCUAUCA-ACU-U--UUGAUGG-UA-GU--AUCUA-GG------AC-UACCAU-GGUUGCAACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACC--C-ACUCCCAGCU-----CG-GGGA----GGUAGUGACGAAAAAU--------------------AACA-AUA-CAG-G-ACUCA------------UAUCCGA-GG-CCC-UGUA-AU--UG---GAAUG-AGUA--------C-ACU-UUAA-A----UCCUU--U-A-ACAAGGACCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGUUGCGGGUUAAA---C--------CGUUC-GUAGUUGAACUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGCUUCAUACGGGUA------------------------------------------------------------GUA-CAACUUACAAUUGUGGGUU-AGUACUA-UACC------------------------------------------------------------------------------------------------------------------------UUUAUGUA----UAUAAGCGA-AUUACCGGUG-------------GAGUUCUUAUAU-------------GU----GA------UUAAAUAC-UUGUAU-UUUU-UCA--UA-UGUUCCUCCUAUU-UAAAACC---UGCACUA-G---------UGCUCU-U-AAACG-A-GUGUUAUUGUGG----------------GCCGGUAC------------UA-UU-ACUUUG-AACAA-AUU-----AGA--GU------------------------------------------------------------------------------------------------------------GCU------------------UAAAGCAGGCUU--CA-------AAU--------GCCUG-----A-A--UAUUC-UGUGAAUG-GGGUAA----------------UGAAAU-AAG---A-C-CUC--------UG------UU-CUGC-UUUC----------------AUUG-GUUU-UCAGAUCAA-G------A---GG-UAAUGAUU-------------------AAUAGA----------AACA------GU-UUG-------GGCGCAUU-ACUA---UUA-CGAC--GCGA-GACGUG------AAAUU----C-U--------UGGACCGUACC-UG-UUGGG-U-UGUCCCAUUAUAAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACACUAGCU-UCUUAAAU-GGA-C-AAAUU-GC---------------------------------------------------------GUCUA--GCAAUAAUGAGAUUGAG-CAAU-AACAGAG-G-UGUGC----------AUGU-CCUGGGCUGCACGAACGCU-ACAAUGAAAGUAUCAACGUGUAU-------------------------------------------------------------------------UUCC-UAGAC--CGAGA--AGU-C-CG------GG-UAAG-CCG-CUGAAC---------------------------------------CACUUUC--AUGCUU-GGGAUUGUGAACUGA-------------AACU-GUU-CACA-UGAACUCGGAAUUCCCAGUAU-GUGU-G-AGUCA-UUAACUC-GC-AUUGAUUACGACGUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUUCCGAU--UGAA-UUAUUUAGUGAG--GUCAC-UG-GACGUG-----AUCACUGU---GACGC----------------------CUUGCGUGUU-A--CGGUU-GUU---U-CGCAAAAGUUGACC-GAACU-UGAUU-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---GGAACCUGCGGAAG-GAUCAUUA
AF279610.1/1-2137                  UACCUGGUUGAUCCUGC---CAGUUAUC-AUAUGCUUGUUUCAAAGAUUAAGC-CAUGCAUGUACAAGU------------------------------ACAAACUU--GAA---------------UAAAGUU-GAA-ACCGCAGACGGCUCAUUA-AAUCAGUCAUAA-AU-AAUGAAAUAUC-------------------------------------------------------------------GAAAAAACAGUUACUUGGA-UAACUGU-GGAAAAUCCAGAGCUAAUACAUGCACUUA---AGCUCGGACAAUCGUU--------------------------------------------------GUAACAAACGAUACAGA--A-GAGCGCAAUUAUUAGGUUUCA---AUA----------------------------------------------------------------------------------AAAGUUA----UUUUAU------------UG-GAUGACUCC--GGAUAAUCCUAG--------UCGAGCGCA-UAUGAUCUUAG----------------------UAUCA---GCGC-CAUAUUU-CAUA-AGAGACUGCCUUAUCA-GCU-U--UCGAUUG-UA-AU--UUAAA-UG------AU-UACAAU-GGCAAUAACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAAAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCACGUAAAUUACC--C-ACUCUCAGUU-----CG-AGGA----GGUAGUGACGAAAAAUACCGG---------UGACUUACUC-UAA-UAA-G-GGUU--------------UUGUCA-CCUAAU-UAUA-AA--AG---GAAUG-AGUU--------U-AUU-CUAA-A----AAUAU--A-U-UCAAUUACCUAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUACC--AGCUCCA-AUA-GC-GUAUAUAAAAAGUUGUUG-CAGUUAAA--AA--------AGCUC-CUAAUUGGAAUUUAUAAAAA---GCUGAUACAUAAUCAAAUUAGACGAUGUAUCAUAUGUGAACUAUAUUAAUGCGAUUGAGUAAUUAGUAUGUCUUAGUGCAAACUUUGAUUGAAAGUUAUUCUUAUUCGUAUGAUAUAAAGUAAUGUAUGGGUGAA-------------------------------GUCUUAAAAGAUUUAAUCGGUGUACAUAAUUUAAACGGAUAUCAACUCCAGAAGUUGAUAGUUUCGUUCAUUUUUCACUUU-GAAAAAAUUAGAGUGUUCAAAGCCGAGCUA------------------------------------------AAAUUGC--UCGAAUGUUA-UAUCAUUGUAUGAAAUAAC-AUGAUCU-CGUUUAGACU---------------------------------------------------------------------------------------------UUUUUGUCUUCUUUUAUUGAUCUAAAAUG----AGAUAAUGA-UUAAAAGGAA--CA--GCC--GGUGGCAUUGGUAUUA-CG-G-CGCUAGA----GG------UGAAAUUC-UUAGACCGUCG-UAA--GA-CUACCUA--CUGC-GAAAGCA---UUUGCCA-AGAAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUAGA-GGAUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UA-ACCAUA-AACUAUGCCA-ACUAGC--GAUCCGUCG-G-UGUC---AUAUCCAC--------------------------------------------------------------GACUCGAC-GGG-AA------GCC------------------CCUGGGAAACCU--AAGUUUUUGGGU--------UCUGGGGG-AA-G--UAUGG-UUGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGAA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUUA-CCAGGUCAG-G------ACAUUU-AAAGGACUGA-CA-GA---------UUGAUAGCUCUU-UCU-CAAUA-AAUUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGG-UCUGUCUGG--UUGAUU-CCGA-UAACGA-ACGAGAUUCUAUC-CUACUAAU-U-AGUAGGCGGAUCGUUUAAAACUUUAUUAUACUCUGUAGACUGAUAUUCUGAAAGUCAGUGUGACGUGUGUGCGUUAAUUUAUUGCUUAGCUUCG---------------------------GCUAUGGUGAUUUUUUGAUGUAUGUCGUUCAUUGAUGGAUCGUUAUAAACAUGUUGAGAGAGAUAUAUUUAAAGAAAAUACGUCCGUCUUAUAGUCU-UCUUAGAG-GUA-U-AAAUG-GCG------------------------------------------------------AACCCUA--GCCAAACGAG--AAAGAGCAAU-AACAGGU-C-UGUGAUGCGCU-UAGAUGU-CCUGGGCAGCACGCGCGCU-ACAAUGUAGUGAACAACGUGCAAUUAUUU---------------------------------------------------------UCCUAAAAUAAGCC-AUUUC--CGAAA--GGA-U-AU------GG-GAAC-CAU-AGUAAC---------------------------------------ACCCUAC--AUGGUU-GGGAUUGGUUAUUGU-------------AAUUUUUA-GCCA-UGAACCAGGAAUUCCUAGUAA-ACGU-G-GAUCAUUUAGUUC-GC-GUUGAUUAA---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAA-UGGUUAAGUAAG--GUCAU-UG-GACUAU-----CA-CUUUA---AUGAU----------------------UUCGUAUUAU-A--AAAG----U--UG-AUAGGAAGAUGUCC-GAAUU-GGAUC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-UCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
EU696948.1/1-2138                  CGACUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGACUAAGC-CAUGCACAUGUAAGAUCGGC--------------------AUAGGCUUUACUG--CUUCGGCA----GUUUGCUCAUUGU-UAA-UCUGUGGACAGCUCAUUA-UAACAGUUAUAC-AC-UUAGCCACUGGUACGU----------------------------------------------------------UUGGCGCAAGCCAAUUACAAGGA-UAACUUU-GUCAAAUGCAGCGAUAAUACUUGAGUGAC----GAGUCGGUG------------------------------------------------------------------CA-AGCC--G-ACUGGCAUUAGCGUCUAUGUCU-CACGAUUGUGAGGAAACCGCGCUACUGUAACUCUUGGUUUACUGGCGGGCUUGCUCGUCAGUGGCCGGAGCGUCGACCAUUAGGAGUGCGCAA----GCACACA---------AAGUUUGUCAGACA--GUGUUUUAAUAA--------GGCUCUGU---AUGGUAGCUUU---------------------UACUA---GUGG-CCAGGAA-GAGG-UGUUUCUUAUCUAUCA-GCU-G--AAGUUGU-UU-CA--GUAAG-GG------UA-AAACAC-GGCGAUUACGGAUA-CGGGGGAU--CAGU------------------------GUCUGAU-U-CCGGA--GAGGGAGCCUGAGAAAUGGCUACUACAUCUAAGGACGGCAGCAGGCGCGAAAAUUACC--C-AAUCUCAAUU-----CG-AGGA----GGUAGUGACAAGAAAUAACAA---------CUUUACACCA-UUU-GGU-G-GAAA-------------GGUACUA-UC--UA-AUAG-UU--UG---GAAUG-GUUU--------U-AGA-UUAA-A----AUUCU--A-U-UAGAGUAACGACUAGAGGAAAA-GUC-UGGUGCCAGCACCCGC-GGUAAUUCC--AGCUCUA-GUA-GC-GUAUAUUAA-UACUGUUG-UAGUUAAA---A--------CGCUC-GUAGUUGACCUAAGGACCAU---AGGUUUGAAUUCGGACUUACCCGUCUUAUGUAGCUCCGUGUUAUAACGGGGUUGCGGGGCGCGUGGUUGGUACCACGGCAUCCUGCCCCAUGGAUUUCAUCCUUGGGUGUUCAGGUGUG--------------------------------------------------------------GGUUCUACCUGUGGUACGAUCCUUGCCAAUGGUUCGCCAUUGGUAAAGGCCUUAUGGUACAACUGU-AAACAAAUCAGAGUGCUCAAAGCAGGCAUUGUUAAUGGGGA---------------------UUUAUCCUCAGUUUUGC--UUGAAUGAUU-UAGCAUGGGAUUGUCUUGG-AGCCGUG-AAUAGUGCCUAU-----------------------------------------------------------------------------------------UCGUUCUCGGGUAGGUUGCUGUUCACUGGCG---CUUGUAAUGU-GAAGCAGGGA-----------GAGGGCUCAAGUACUA-UG-G-UGCUAGA----GG------UGAAAUUU-AGAUACCAGCA-UAU--GA-CUUUCUG--AUGC-GAAAGCUGUUAUUGUCC-AAUACAC---UUCUUU-C-GAUCA-G-GGACGAAAGUUAGG-GGAUCGAAGAUGAUUAGAUAC-CGUC-GUAGU-CC-UA-ACUAUA-AACGAUACCA-ACAAGA--GAUUGGUAGUG-AAAC--CAUUUAAUA--------------------------------------------------------------GAUCCUCU-CAG-AA------UC-------------------CAAGGGAAACCU-AAAGUCUUUGGGU--------UCUGGGGG-GA-G--UAUAG-UCGCAAGG-CCGAAA--C-UU-AAAGG-AAUUGACGG-AAAGGCA-C-CACCA-GGA-GUGGAG-UUUG-CGGC-UUAAUUCGACUCAACGCGGGAAAA-CUCA-CCAGGUCAG-G------ACAGAG-GUAUGAUUGA-CA-GG---------UUGAAAGUCUUU-UCU-UGAUU-CUCUGGA-UGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA--GUGA-UUUGUCUUG--UUAAUU-CAGU-UAACGA-ACGAGACCUUAAC-CUACUAAC-U-AGGCUAUAGGCCAGCUUUCGGGCUGGUUAGUUUCUUUCGGGGUGGUUCGUAUG-------------------------------------------------------------------------------------------------------------AGCCAUCUCUUUGAAACCUAUAAUAUGGGUCUUCACUUUCGGGUGGAGUCCUUGCU-UCUUAGAG-GGA-C-AAUCU-UCGU----------------------------------------------------UUAUAUUA--GAGUAAGGAAGUUUAAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CCUGGGCAGCACGCGUACU-ACACUGUUAAUACUAACAAGUCAGUACAAUGUGAA----------------------------------------------UCUUCGGUGUUCACUGGCC-UUCUC--CUUAA-AGGA-G-UG------GG-AAAU-CUU-UUCAAA---------------------------------------CAUUAAC--GUGACA-GGGAUAGCUGUUUGG-------------AAU--UCC-AUCU-UGAACGAGGAAUUCCUAGUAA-UCGC-G-AUUCA-UUAUAUC-GC-AUUGAUUAC---GUC-CCUGCCUUUUGUACACACCGCCCG-UCGCUCCUACCGAU--GGAA-CAAAAAGGUGAA--UUUGA-CG-GACUUG-----AC-C----------------------------------UCGGC-----------------C---U-UGGGGAAAUUAACU-GAACC-UUUUU-GUUUGUAGGAAGGAGAAGUCGUAACAAG-GUCU-UCGUAGG---UGAACCUGCGGAGG-GAUCAGGA
AF011461.1/15-1863                 AACCUGGUUGAUCCUGC---CAGUAGC--AUAUGCUCAUCUCGAAGAUUAAGC-CAUGCAUGUCUAAGA------------------------------GCAAUCUG--UUCUCGCA-----AGAGAAAACCGU-GGA-UCUGCGAAUAGCUCCUUA-CAAGAGUCAUAA-AC-AAGCUAACAA-------------------------------------------------------------------------UGCUUCUACAAGGA-UAGCGUU-GUCAAAUGCAACGAUAAUACUUGCAAUAA-----------GC----------------------------------------------------------------GAUG-GCGC--------AAAUCUCAGGAUUUGAU---CGCCAU-------------------------------------------------------------------------------------A------------------------AGUGUAGCCC--UUUGGGUUACGC---------AGACUAA-------CGUUAC-----------------------G------UUAG-CUUGAUA-GAAG-UGUUUCUUCCCUAUUA-GCU-G---UGAUGG-UA-GG--GUAAA-GG------CC-UACCAU-GGCUAUUAUGGGUC-CGGGGAAU--CAGU------------------------GUUCGAU-U-CCGGA--GAGGCAGCCUUAGAAACAGCUACCAUGUCCAAGGAUAGCAGCAGGCGCGAAAAUUACU--C-AAUUCUAAUC----AGA-GAGA----AGUAGUGAAAAGACAU--------------------AACG-AUU-UCC-U-ACAUCUGU-----GGGAAAGUACU-CU--UU-UGAG-UU--UG---AAAUG-GUCG--------C-ACU-GUAA-A----UAGGU--G-C-GAGAGUAUCAAGUGGAGGACAA-GUC-AGGUGCCAGCACCCGC-GGUAAUUCC--UGCUCCA-CAA-GC-AUAUACUAA-UGUUGCUG-UAGUUAAA---A--------CGUUC-GUAGUCCAUGUAAGUGCCAA---UCUGUGCGAAUCGGGUAGUCCAACUUUAGUCUUAAGGGGAAACUUUUAGGACUAGAGGACUGGAGGAAACUCCAGUCAGGGCUGCUCCUUGCCGGUUAAAUGC-----------------------------------------------------------------------------------------------GUCUUCGGACGCAUCGGGGUUUGUACAGAGAGGUGCGAUCCACAACUGU-GAGUAAAUCAGCGUGUUCAAAGCAGGCUUUGGGAGGAUU-------------------------UAUCCUCCCUUGUGC--UUGUAUGCUA-AAGCAUGGAAUUGUAACAU-ACUGACG-UCAAG-------------------------------------------------------------------------------------------------------UCACAAUCGUGG----------------------------AAAAGGAAACAG--ACG--GAGGGCACAAGUAUUC-CG-GUGACCAGG----GG------UGAAAUCC---GUACUCCCG-GAA--GA-CUACCAG--AUGC-GAAAGCGG-UUUUGCCC-ACGGCGU---UUCCGU-U-GAUCA-A-GAACGAGAGUCAAG-GGAUCGAAGAUGAUUAGAUAC-CGUC-GUAGU-CU-UG-ACCGUA-AACUAUACUG-CCAAGA--GUUUGGGGA-U-AUGAC-ACCAUUAUU--------------------------------------------------------------GAUCUCCU-CAG-AA------UC-------------------UAAGGGAAACCG-AAAGUUUUCGAGU--------UCUGGGGG-AA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAAGGCA-C-CACCA-GGA-GUGGAG-UCUG-CGGC-UUAAUUCGACUCAACACGGGGAAA-CUCA-CGAAGGCAA-G------AUGUGG-AUAGGAUUGA-CA-AG---------UUAAA-GACUUU-UCU-UGAUU-CUACAAG-UGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGG--UUAA-CUUGUCUGG--UUAAUU-CCGA-UAACGA-GCAAGACCUCGGC-UG-CUAAU-U-AGGUGGGUAGUUUU----GAUCUUCGGGU--------------------------------------------------------------------------------------------------------------------------------------------------------------CGAAAUUACUCUAGCGUUUCGGCGCGUUACU-UCUUAGCA-GGA-C-AACCU-GC---------------------------------------------------------GUUAA--GCAGGGGGAAGCUCGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGC-CUUCGGCAGCACGCGUACU-ACAAUGUUAAAAUAAGCAAGUUAAUGAGUC--------------------------------------------------------CAUCAGGAUUCGGC-UGCUC--AUAGC--UGA-G-UG------GC-UAAA-CUU-GUAAAA---------------------------------------UUUUAAC--AUGACA-GGGAUUGGUCAUUGG-------------AAG--UGG-ACCA-UGAACGAGGAAUUCCUCGUAA-UCGC-A-AGUCA-UCAUCUU-GC-AAUGAUUAC---GUC-CCUGCCUUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGGA-GAAAGAAGUGAA--AUGGA-AG-GAUU-------------------GGCC----------------------UCCG-GGUCU-A------------------AAGAAUUCCCUU-GAACU-UCUUU-CUCUGUAGGAAGGAGAAGUCGUAACAAG-GUCU-UCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
AF011464.1/15-2088                 AACCUGGUUGAUCCUGC---CAGUACU--AUAUACUUGUCUCAAAGAUUAAGC-CAUGCAAUUGUCAGA------------------------------AAAUCAUG--UUCAGUCGC--AAGAUUGAAAAUUGUGAA-UCUGAGACUCGCUCCUUA-AACAAAUCCUAG-UG-CAUCCUUUAGUUUGAAUAU----------------------------------------------------GUUGUAUAACAUGUUUAUUAAAUGGA-UACCUGA-CCUAACUGGUCAGUUAAUACAUGAUAAC-----UUUAGUAGU---------------------------------------------------------------CAUCU-AUUU--U-UAAAUUGAAUUUUGGUGACUA---AUAUUGGAAACUUUUUCGGAAGUGGA-------------------------------------AGAUACGCAGACCUACAGAACAGGGUUUA----CCU----------------GAUAUGAGUCU--UUUGAUUCUUUG---------GAAUCAA---GAAAU--UUA-----------------------ACUG---AAGG-CCUUAAG-GAAC-AAGGAUUUAAGGAUUA-GUU-A----GUUGG-UA-CG--GUAGU-GU------CC-UAUCAA-GACUAUAAUCCUUA-CGAGAAAU--UAUC------------------------GUUUGAU-U-UCGGA--GAGAGAGCCUUAAAAACCGCUAUCACGUCUAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUAUCAAUU-----CG-AUGA----GGUAGUGACAAGACGU--------------------AAUG-ACC-UCC-C-ACUUUUAU-----GAGGGUUAUCC-GC--AA-GGAU-AU--UA---CAAUG-GUCU--------G-AAA-UUAA-A----AUUCU--C-A-GAGAGAAACGACUAGAGGAAAA-GUC-UGGUGCCAGCACCCGC-GGUAAUUCC--AGCUCUA-GUA-GU-AUAUAUUAA-UGUUGUUG-UAUUUAAA---A--------CGUUC-GUAGUUUACUUAAGUUAUUU---UUUAUUAUUGUCGGUUUAUUAACUCUACUUUUAUUUUAUGUGAAUAAAGUAAAGGGUUCACCUUCGGGUCGAUUUAAGGGAAGAUAACUCUUUAUUGGUGAGAAACAAUGUAGAGCUAUU------------------------------------------------------------UAUCAAAGCAUAAAUAGUAUCUUAUUGUGGAUCAUGGCAAUAAUUGAAAAGUAACGUUUAGAAGUGA-GAAAAAAUCUAUAUGCUUCAUGUAAGCUAAACCGUUCUAAUCUU--------------CGGAAAAGAACAAUUUUUUGC--UUGAAAGUUA-UAGCUUGCUAUCCUUUAAA-AUUGUAU-GGAAGUU--------------------------------------------------------------------------------------------------AUUAUCCUUAGAGGUAAUAAAAGAAAU----ACAGUGUUU-AUAAUGGAAC-UCA--UGU--CAAGUUAACAGUAUUA-CU-A-AGAUAGA----GG------UGAAAUUC-AAUAACCCUAG-UAA--GA-CUACCUA--AUGC-UAACGCA---GUUAACA-AGACUGG---CUUCAU-C-AAUCA-G-GAACUAAAGUUAGA-GGAUCGAAGAUGAUUAGAUAC-CGUU-GUAGU-UC-UA-ACCGUA-AACUAUUUCG-ACAGAA--AAUUGGUAU-U-AAAU--AUUUUUAAA--------------------------------------------------------------GAUAAUAU-CAG-AG------UUC------------------A-AGGGAAACCU-UAAGUUUUUGGAA--------UAUAGGGG-GA-A--UACGA-ACGCAAGU-UUGAAA--C-UU-AAAAG-AAUUGACGG-AAAAGCA-C-CACCA-GGU-GUGGAU-UCUG-CGGC-UUAAUUCGACUCAACGCGGGGAAA-CUUG-CCAAGUUAG-G------AUACAA-GUAGGAUUGA-CA-GA---------GUAAA-GCUCUU-UCU-UGAUU-UUGUAGU-UGGUGGUGCAUGGCCAUU-CUUAGU-UCG-UGGA--GUGA-UUUGUCUUG--UUAAUU-CAGA-UAACGA-GCGAGACCUAAGC-CA-AUAUU-U-UUUAUGCUUUUUAUUUUCUUGUAAAAUAGAAUGACAAAA-----------------------------------------------------------------------------------------------------------------------------------------ACUUCUAUUCAAAAACUAGAAAUAGUCGAAUACGAAGGUUAG---UUAUUG-GGA-U-ACCUU-AUUUUUUA--------------------------------------------UUACCGUUCAAA--GGAAGGUGAAACGUUAGGCAAU-AAUAGGU-C-UGUGAUGCCCU-UAGAUAU-CUUGGAAUGCACGCGGGAU-ACAAUAAUUAAGAUAAUAAGUUUAUUUUAAUUUACAUUGUGU--------------------------------UUUUUGCAUUAAUUGUAAGUAAAACC-UGUUU--CGAAA--GGA-A-UG------GG-AAAU-CUC--CAAAU---------------------------------------CUUAAUU--UUGACA-AGGAUUGUCUCUUGU-------------AAC--AGA-GACA-UGAAAGAGGAAUACCUAGUAG-GCGU-G-AGUCA-ACACCUC-GC-ACCGAUUAA---GUC-CCUGCUUUUUGUACACACCGCCCG-UCGCAUCAAGGAAC-ACGAU-UGAAGUCAUGAA--GCUUA-CG-GAUAGA-----UU-AC---------------------------------AUUA------------GU----G---A-UUUAAAAGUAAACU-GAAUG-GUUUU-UAUCUUACCAUGAUGAAGUCGUAACAAG-GUUU-UCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
AF448162.1/1-1957                  --ACUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGACUCGAAGAUUAAGC-CAUGCACGUGUAAGU------------------------------ACAUGCCU---AG---------------ACACGGU-AAG-ACCGCGAAUGGCUCAUUA-AAUCAGUCGUAG-UU-CCUUGGACAG----------------------------------------------------------------------AAUGAAAGUUACUUGGA-UAACUGU-GGCAAUUCUAGAGCUAAUACAUGCGUCUCA--AGCUCUGACCUCUGCCUG-----------------------------------------------CGCAAGUAGGUAGCGGGA--C-GAGCGCACUUAUUAGACCAAG---ACCAACCGG-----------------------------------------------------------------------GCCGAAAGGUCC----CGUACAA---------UGUCUGGUGACUCU--GGAUAACCAUAG--------CUGACCGC---ACGGCCUUCG----------------------AGCCG---GCGG-CGUAUCC-UUUA-AGUGUCUGCCCUAUCA-ACU-G--UCGAUGG-UA-AG--UGAUC-UG------CU-UACCAU-GGUGUUGACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCAUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-ACUCCUGGCA-----CA-GGGA----GGUAGUGAAGAGCAAU--------------------AACG-GCC-GGG-G-ACUCC-----------AUUGCGGA-GG--CC-UCGGGAU--CG---GAAUG-AGCG--------A-GAC-UCAA-A----CACUC--U-C-GCGAGUAUCUAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUACCAA-AGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGCUGAAUCACGGGUCCG---GUGCGGCCGCGGGAGCCCCUUUGCUGCGGUCGGGUCGGUGUCUGGUCUUCGGGCCGGCCCGGCUCGGUCGUUGGUGAGGGGGUCUUCUCGAUUCGGCCGUUCUUCAACCAGUUAGCGAC---------------------------------------------------------------CUGAACGUCGGACGCCUCCCGGUGCCCUUAAUUGCGGUGUCUCGAGGUCCCGGCCAGUUUACUUU-GAAAAAACAAGAGUGCUCAAAGCAGGUCUCGAA------------------------------------AGAAACUAGC--CUGAAUUCUU-UAGCAUGGAAUAAUGGAAU-AGGACCU-CGGUU-------------------------------------------------------------------------------------------------------CUGUUCUGUUGGUCUUUUUCCGAACUGGAGGUAAUGA-UUAAGAGGGA--CU--GCC--GGGGGCAUUCGUAUUG-CG-G-GGCGAGA----GG------UGAAAUUC-UUGGACCCUCG-CAA--GA-CGAACAA--CAGC-GAAAGCA---UUUGCCA-AGAAUGU---UUUCAU-U-AGUCA-A-GAACGAAAGUCAGA-GGUUCGAAGACGAUCAGAUAC-CGUC-CUAGU-UC-UG-ACCAUA-AACGAUGCCA-ACUAGC--AGUUCGAGG-G-CGUU---UGUUACG---------------------------------------------------------------GACCUCUC-GAG-CG------GCC------------------UCCGGGAAACCA--AAGUGCUUGGGU--------UCCGGGGG-UA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGAAA-CUUA-CCCGGUCCG-G------ACACUG-AAAGGAUUGA-CA-GA---------UUGAGAGCUCUU-UCU-CGAUU-CGGUGAG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACUCUAGC-CUGCUAGU-U-AGUGCGUCGACACU-----------CCAA--------------------------------------------------------------------------------------------------------------------------------------------------------------ACGUUCUAGUGCGAGUCGGCGCGUGUCAACU-UCUUAGAG-GGA-A-AAGUG-GC---------------------------------------------------------GCCUA--GUCACACGAG--AUUGAGCAAU-AACAGCU-C-UGUGAUGCCCU-UAGAUGU-CCGGGGCCGCACGCGCGCU-ACACUGAAGGAGGCAACGGGUGU----------------------------------------------------------------------CCUGUUC-UGGCC--GGAGA--CGC-C-CG------GG-CAAU-CCG-UUCAAC---------------------------------------CUCUUUC--GUAGUA-GGGAUUGGGCUUUGC-------------AAUUCUCG-CCCA-UGAACCAGGAAUUCCUAGUAA-GCGC-A-GGUCA-UCAGCUU-GC-GUUGAUUGC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU---GAG-UGAUGCAGUGAG--ACCUU-UG-GACUUG-----CC-CAAAC---GACCGGGGUGGC--------GGCAACGUCCCUCGGAU-C--UGUG----C---G-CAAGGAAGAACGUC-AAACU-GUAUU-CCUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
AY851265.1/1-1912                  UACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGACUAAGC-CAUGCAAGUGCAAGC------------------------------GCACACCG---CU---------------GAACGGU-GAA-GCCGCGAAUGGCUCAUUA-CAGCAGUCAUUG-UU-CGCAAGAA--------------------------------------------------------------------------CUGAUGUCACUUGGA-UAACUGU-GGAAAUUCUAGAGCUAAUACUGCCUCGAA----GCUCGGUCG--------------------------------------------------------------CGCGCAACGCU--CGGAGCGCAUUUAUUAGAACAAA---ACCAAUCGGAC-------------------------------------------------------------------GCAGGCUAUCUAUU----GGUCUGGGUCCGCGAAAGGUUGGUGAAUCG--GAAUAACUAUGC---------UGAUCGC---ACGGUCCAGC-----------------------ACCG---GCGA-CGA-ACU-UUGA-AAUGACUUGCUCAUCA-ACU-U--UCGAUGG-UA-CG--CUACG-UG------CU-UACCAU-GGUGACAACGGUUAACGGAGAAU--CAGG------------------------GUUCGAC-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCACGCAAAUUACC--C-ACUCCCAGAU-----CG-GGGA----GGUAGUGACGAAAAAU--------------------AACG-GAA-CGU-A-UCUC---------------CAUGA-GA--CG-CGUU-AC--CG---GAACG-ACUG--------A-GCC-GUAC-A----CAAGC--U-C-GGCUAAAUCUAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGCUG-CGGUUAAA---C--------CGCUC-GUAGUUGGAUUGCGGAUGUC---GACGACGGUCGUCCUAAGCAGGAGUCGUUCCGUCGCUCGUCACCUGUUCGAUCAAGAUUGCCCUGGAUGCUCUUCAGUGA------------------------------------------------------------------------------------------------------------------------------------------GUGUCCUUGGCGACUUGAAAGUUUACUUU-GAGAAAAUGGAAGCGCUCAAGGCAAGCCGU--------------------------------------------GAUGC--UUGAACCGUG-GUGCAUGGAAUAAUAGAAAGAUGGCCU-CAGUG-------------------------------------------------------------------------------------------------------CUAUUUUGUUGGUUUGCGGCUAUG----AGGCAAUGA-UUAAAAGAGA--CA--GAC--GGGGACAUUCGUAUUG-CU-G-CGUUAGA----GG------UGAAAUUC-UUGGAUCGCAG-CAA--GA-CGACCAA--UUGC-GAAAGCA---UUUGUCA-AGAAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUAGA-GGUUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UG-UG-ACCGUA-AACGAUGCCA-ACCAGC--GAUUCGGCG-A-CGUU---CUUUUUAU--------------------------------------------------------------GACUCGCU-GAG-CA------GCU------------------UCCGGGAAACCA--AAGUGUUUCGGU--------UCCGGGGG-AA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CAUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUCA-CCCGUUCCG-A------ACACUG-UGAGGAUUGA-CA-GA---------UCAAGAGCUCUU-UCU-UGAUU-CAGUGGG-UAGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GCGA-UUUGUCUGG--CUAAUU-CCGA-UAACGA-ACGAGACUCUGGC-CUACUAAC-U-AGCGGCGGUAUUCACGUCUCUCGCGACGCCGUGCCUACGUGUCGGCUGAG--------------------------------------------------------------------------------------------------------------------CACAGUCGCCGUUCGCGCGAGCUCCGCGGACACCUGCAGUCCGGCGACCGCU-UCUUAGAG-GGA-C-CAGCG-ACAC----------------------------------------------------UUUCGCAA--GCCGCACGAG--AAAGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-ACGGGGCUGCACGCGUGCU-ACACUGACGGCGUCAGCGUGCGU----------------------------------------------------------------------UCAAGCC-CGGCC--UGGCA--AGG-C-CG------GG-AAAU-CGG-CUGAAA---------------------------------------CGUUCUC--GUGACU-GGGACAGGGAAUUGC-------------AAUUAUUU-CCCU-CGAACGAGGAAUUCCCAGUAA-GCGC-G-AGUCA-UCAGCUU-GC-GUUGACUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGGA-UGAUUUAGUGAG--GCCUU-UG-GACCGA-----UG-CCGCCGGUGUUCGGC-----------------CCGGUGGUUGAAC-C--ACGG----C---G-UCGGGAAGCUGGCC-GAACC-AAACC-AUCUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
AY781414.1/1-2045                  --CCUGGUUGAUCCUGC---CAGUCACC-AUACGCUUGGUUCACAGAUUAAGC-CAUGCAUGUGUCAGUG----------------------------CCCUGCUGC--CUU----------------UCCGUG-GAGUACCGCGAACGGCUCCUUA-AUACGGUCGCAG-CC-CAAAGGACUGUGUC-------------------------------------------------------------CUGGCUUUCGAGCCCGGUUGGA-UAACUUU-GGCAAUUCUAGAGCUAAUACAUGUGCAAA----AUGUCCGGGGG----------------------------------------------------------AGUAACGUCCCCC--G-GCAACCAC---UGUGCCUAAGG--AACCACC---------------------------------------------------------------------------GGUGCUUUCU----AGCCCAAAA-----UGACCCGGUCGAAGCC--ACA---CAAUGG--------UAGAGCGC--UUAGGCCUCGC-----------------------GCCG---GCGC-CCGCACC-UACG-AAUGUCUGUCUUAUCAGGCU-U----GAUGC-UA-GU--CCACA-CC------UC-UAGCAU-GGCUUCGACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAAUGGCUACCACCUCUAUGGAGGGCAGCAGGCGCGCAACUUACC--C-ACUCUCGGCC-----CG-AGGA----GGUAGUUACGAGGCAU--------------------CCCG-GAG-UGG-G-UGGC---------------UUGGC-CA--UU-CGCA-UC--CG---GGCUA-AGUA--------U-GGG-CCAG-U----GAUCU------GUGAGGCAAGAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUG-GC-GUAUGUGAA-AGUUGCUG-CGGUUAAA---A--------CGCUC-GUAGUUGGGCGNCCUCUCGG---GAACGCAUUUCCUGUACAACGGGACCUUUCGUGGGGAGACGAGUGUCUCGCGCGGUAUUGGAGGUCGACUUUCUGGCAACAGGGGUCCCUUCAGUACACCCGCGUUUCUACUCUUCCCUUCGUCUCGGUCCCGGGGA--------------------------GGUGUGCCCCGAAGAAGACAACCGACCCGAACGGGUAGGCGAGCCUUCGGGCUUACCUAUCACCGCAAAGGUCGCACUCGCCUU-GCACAAAUUUGAGUGAUCAAAGCAGGCGGGUGAAA---------------------------------ACUACACGCUU--GUAGAUCGUU-CCAAAUGGCACGAAUGAAA-AGGACAG-UCGCA-------------------------------------------------------------------------------------------------------CCGCUUGGGCUGGUUCCCGGCAUGC-GGUUGUAAUGA-UUAACAGGGG--AU--GAC--GGGGGCACACGUAUUG-UC-A-GGCUAGG----GG------UGAAAUCC-AAUGACCCCGA-CAA--GA-CGACCUA--AAGC-GAAAGCA---UGUGCCC-AGGAUUC---UUCCAU-U-AAUCA-A-GAACGAAAGUUAGA-GGAUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UA-ACUGUA-AACUAUGUCG-ACCGGC--AAUGCGUCG-A-UGUC---UCUG------------------------------------------------------------------GACACGAC-GUG-CG------GCU------------------CCCGGGAAACCA--GAGUCUUCGGAC--------UCCGGGGG-GA-G--UACGG-UCGCAAGU-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CUUG-CGGC-UUAAUUUGACUCAACACGGGAAAU-CUUA-CCAGGCCAA-A------ACGCUC-AACUGACCGA-CA-GG---------CUAAU-GACCUU-UCC-CAAUG-CUGUAGA-CAGUGGUGCAUGUCCGUU-CCUAGA-UGG-UGGA--GUGA-UCUGUCUGG--UUGAUU-CCGA-UAACGA-ACGAGACUCCGAC-CUAUCANA-U-AGAUCAUAUCAGAAUGGAGGCUAAUACCCAUGCUGGCGCAUCGCGAGCGUGGAUGGAGCGGU--------------------------------------------------------------------------------------------UUCGGCGUUAAGCCGGACUGCCUCUAUAAGCGCGAACGUGCGUCUAGCAGGGUGCCUUCGAUCU-UCUUGGAG-GGA-G-AAGCG-GA---------------------------------------------------------UCGAA--ACCGUGAGAA--AUGGGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUNC-CCUGGGCGGCACGCGUGCG-ACAGUGGUGAGGUCGACGUGCUA--------------------------------------------------------------------------CUC-UACCC--CGAAA--GGG-G-CG------GG-CAAU-CAC-CCAUUC---------------------------------------UCACGAC--UAGGUU-GGGAUUGGAGCCUGA-------------AAUUAUUU-UCCA-UGAACCAGGAAUUCCCAGUAU-GUGU-U-GGUCA-UCAACCC-GC-UCCGAUUGA---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU---GGA-CGUCCUGGUCAG--GAUCA-UG-GACUGG-----AC-CGAAU----NCCGCGCGU------------GAAUGCUCGCCUGGC-G--GACG----G---A-UCGGAAAGAGAGCC-GAACU-UGGGC-GUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUU-
ADTU01016567.1/23020-21180         UCCCUGGUUAAUUCUGC---CAGUAGUC-AUAUACUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUCAGU------------------------------GCAUGCCG--AAU----------------UAAAAU-GAA-ACCGC-------UCAUUU-AAUCAGUUAUGG-UU-CAUUAGGUUG---------------------------------------------------------------------UACCCACAUUUACUUAGA-UAACUGU-AGUAAUUCUAGAGCUAAUACAUGCAAAAUA-GAGUCCCGACC---------------------------------------------------------------AAUGAUGGAA--G-AGACGCUUUUAUUAGAUCAAA---AUCAAUCGAUGGCGAA--------------------------------------------------------CGGUUAUCCAUCCAUCCACC----GUUUAU------------UUUGGUAACU----GAAUAACUG--------------AUCGC---ACGAUUUUAG----------------------CACCA---GCGA-UGCAUCU-UUCA-GAUAUUUGCUUUAUCA-ACU-G--UCGAUGG-UA-AG--UUCU---G------CU-UAUCAU-UGUU---ACGGGUAACGAGGAAU--CAGG------------------------AUUUGAU-U-CCGGAGAGAGAAAAUCUGAAAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUAGU--C-ACUUCCGGCA-----CG-GGGA----GGUAGUGACGAAAAAU--------------------AACA-AUA-CGG-A-ACUC--------------AUCCGA-GG-ACC-CGUA-AU--CG---GAAUG-AGUG--------U-ACU-UUAA-A----UCCUU--U-A-ACGAGGAUCCAUUGGAGGACAA-GUC-UGGUGCUAGCAGCCAC-GGUAAUUCC--AA-------UU-GC-AUAUAUUAA-AGUUAUUG-CGGUUAAA---A--------AGCUC-GUAGUUGAAUCUGUAUCGCA--CACUGUCAGUUCACCCCUUGUGUUUAACUGGUGAUGUGGGACGUCCUACUGGUGAGCUUAGCCUCGCGAGGGGACGGCCCAACUAAUAUCCCAUUGC------------------------------------------------------------------------------------------------------------AGUGCUCUUUACUGAAUGUCGAAUCGGGAGAUACGUUUACUUU-GAACAAAUUAGAGU----AACGCAGGUUAU-------------------------------------------UCUGA----------AUA-CUGCAUGGAA--------U-AGGACCU-CAGUU-------------------------------------------------------------------------------------------------------CUAUUUUAUUGGUUUUUGGAACUCU--GAAGUAAUGAAUUAAUAGAGA--UA--GAU--GGAAGCAUUCGUAUUG-CG-A-UGUUAGA----GGAAAACGUGAAAUUC-UUGGAUCAUCG-CAA--GA-CAGA------AGC-GAAAGCA---UUUGCCA-AAAAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUAGA-GGUUCGAAGGCGAUCAGAUAC-CGUC-CUAAU-UC-UA-AUCAUA-AAUGACG--U-GCUAGC--GAUCCGCCG-A-AGUU---CCUUCGAU--------------------------------------------------------------GACUUGGC-GGG-CA------GCU------------------UCCUGUGAACCA--AAGCUUUUGGAU--------UCUGGGGA-AA-G--UAUGG-U-----UG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGG-----CACCA-GGA-GUGGAG--------GC-UUAAUUUGACUCAAUACGGGAAAC-CUCA-CCAGGCCAA-GGAUCUAAGACCG-GAAGGAUUGA-CA-GA---------UU----GCUCUU-UCU-UGAUU-UGGUGGA-UGGUGGUGC--GUUC-----UUUGU-UGG-UGGA--GCGA-UUUGUCUGA--UUAAUU-CCAA-UAACGA-ACGAGAUCUUAGC-CUGCUAAAGU-AGGCGACCUUAUGGUAUGGCGAAGACCUCCGGCUUC------------------------------------------------------------------------------------------------------------------------------------------------GGUCGGUGGGUUUUUACUACCAACAUACAAACAAAUCU-UCUUAGAG-GGA-C-AGGCA-GC---------------------------------------------------------UUCUA--GCCGCACGAGA-UUGAG-CAAU-A--AGGU-C-UGUGAUGCCUU-UAGAUGU-UCUGGAGUGUACGCAUGCU-ACACUGAAGGAAUCAGCGUGUGC--------------------------------------------------------------------------------CCU--AGCCA--AAA-G-AC--------------CCG-GAUAAC---------------------------------------CUCCUUC--GUGCUA-GGGAUUGAGACUUGU------------UAAUUAUUC-CCCA-UAAACGAGGAAUUCCCAGUAA-GCGC-G-AAUCA-UAAGCUC-GC-AUUAAUUAC---GUC-CCUUCCCUUUGUACACACCGCCUG-UCGCUACUAUCGAU--UAAA-UGAUUUAGUGAG--GUUUU-CG-GAUUGG-----UGCGCGGC---AAUGC----------------------GUUG-GCAUU-G--CCGAU-AUU---G-CCGAGAAGAUGAUC-AAACU-UGAUU-AUUUAGAGGAAAUAAAAAUCGUAACAAG-GUUU-CUAUAAG---UGAACCUGCGGAAG-AAUCAUUA
AAQR03176856.1/2658-4433           UACCUGGUUGAUCCUGC---CAGUAGC--AUAUCUUUGUCUCAAAGAUUAAGC-CAUGCAUGUUUAAGU------------------------------ACAUGCAG--CUU---------------GUACAGA-GAA-ACUGUGAAUGACUCAUUA-AAUCAGUUAUGG-UU-CCUUUGGUCA------------------------------------------------------------------------CUCUUGCAGUUUGGA-UAA--GU-GACAAUUCUAUAGCUCAGACAUGCUGAUG---GGUGCAAACUCC-----------------------------------------------------------UUUGUGGGGGGA--U-GUGUGCAUUUCUUAGAUCAAAA--CCAACCUGGUGAG--------------------------------------------------------------CUCCUCUGCAGCCCUGG----GACUGG------------GGAUGGGUGCUU--AGAUAACCUCAGG-------CUGAUUGC---AUGCCCCACCU---------------------UGGCA---GUGA-UGUCCCA-UUUC-AACAUCUGCCCUAUCA-ACU-U--UUAAGGC---------UAGU-UG-------------CU-GG--ACCACGGGUGAUGGGGAAUCACAGCUCAAUUAUGGAGAGGGAGCCUGAAGUUCAAU-U-AUGGA--GAGGGAGCCUGAAAAAUGGGUACCACAUCCAAGGCAGGCAACAGGCACACAAAUCACC--C-ACUCCCAUCU-----UG-GGGA----GGUUGUGGUGAAAAGU--------------------AACA-AUA-CAG-GAACCC--------------UUUGAG-GC--UC-UAUA-AU--UG---GAAU--ACUC--------C-AAU-UUAA-A----UCUUU--U-A-ACGAGGAUCCAUUGGAAGGCAA-GUC-UGG----AAUAGUCGU-GGUAAUUCC--AGCUCCA-AAA-GU-GUAUAUUAA-AGUUGCUG-CAGUUAAA---A--------AGAUC-CUAGUUGGAGCUUGAGAGUG---GGUGGGGAAGUCUGCUGAGAGGUGAGCUACUGCCUGCCCCUGCCCCUUGCCUGUUGGUGUCCUCUUGAUGCUCUUAGCUG--------------------------------------------------------------------------------------------------------------------------------------------AGUGUCCCACAGAGUCUGAAAUAAUUU-GAAAAAAUUAC--UGCUCAAAGCUGGCAUG-------------------------------------------AGCUGC--CUGGAUACCG-UAGCUAGGAAUAGUGCAAU-AAGGCUG-UGGUU-------------------------------------------------------------------------------------------------------CUGCUUUGUUGGUUUUUGGUACUG----AGGCCAUGA-UGAAGACGGA--GG--GCU--GGAGGUGUUCCUAUUA-CA-U-GACUAGA----GG------UAAAAUUC-UUCAACCAGUG-CAA--GA-CGAC--U--AUAG-CAAACCA---UUUCCCA-AGAAUGU---UUUCGU-U-AAACA-G-GAAUGAAAGCCAAA-UGAUUCAAGGUGAUCAGAUAC-CAUU-GUAGU-GC-UC-ACCAUA-AAUGAUGGUU-ACUGGC--CAUGUGGAG-G-CAUU---AUUCCCAU--------------------------------------------------------------GACCUACU-GGG-CA------GCU------------------UCUGGGAAACAA--AAGUCUUUGGGU--------UCCAGAGA-GA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGAUGG-AAGGGCA-C-CACUA-GGAAGUAGAG-ACUG-UGGC-UUAAUUUGACUCAACACAUGAAAC-CUCA-CAUGACCUG-G------ACAUGA-ACAGGAUUGA-UA-GA---------UUGAUAGCUCUU-U-----AUU-CUGUGGG-UGCUGGUGCAUGGCCAUU-UUUAGU-UGG-UAGA--GCGA-UUU----------------------------C-----UCUGGC-AUGCUAAC-U-AGUUAUGUGAUCCC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGCAGUAGGCAUCUCCCAACU-UCUUAGAG-GGA-A-AAAUG-GU---------------------------------------------------------GUUGG--GCCACUGAAGAUUGAGAG---U-AACUGGC-CUUGUGAUGCCCU-UAGAUGC-CUGGGGCUGCAUACGUGCU-ACGCUGACUGGCUCAGU--GUUU---------------------------------------------------------------------GCCUACCC-UAUGC--UGGCA--GGU-G-UG------GG-UAAC-CUG-UUGAAU---------------------------------------GUCAUUC--AUGAUG-GGG-AUGGAGAUUGC-------------AAUUAUUC-CCCA-UGCACGAGGAAUUCCCAGUAA-GUGG-------A-AUAA----UC-UUGCCUUAA---UUC-CCUGCCCUUUGUACACACUGCCCA-UUGGUACUACCAAU--UGGA-UGAUUUACUAAG--GCCCU-CG-GAUCAG-----UC-CU---------------------------------AGUGG-----------UG----C---A-CUGAGAAGAUGGUU-GAACU-UGA-----CAAGCGCAAGUAAAAGUCUUA---AG-GUUU-CAGUAGG---UGAACGUGCAGAAA-GACCAUUA
X97158.1/1-1861                    -ACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------UCAAACUU--AAU---------------UGACAGU-GAA-ACCGCGAAUAGCUCAUUA-AACCAGCUAUAA-UU-UAUUGGAUCU------------------------------------------------------------------------UGCACUAUAGUUGGA-UAACUGU-GGCAAAUCUAGAGCUAACACAUGCAAUAG---AGCUUUUUGGAUUUCC---------------------------------------------------GUUAAAAGAAGUCAGA--G-AAGGGCAAUUGUUAGUAAAAUA--ACCAAU-----------------------------------------------------------------------------CAGAGGAUA----UUUAUAGACUC--UGGUUAUUGGUGACUCU--GGACAAUUUUGC---------CGAUCGU---AAGGCCUAGA-----------------------GCCG---ACGA-UAGAUCC-UUCA-AGUGUCUGCCCUAUCA-ACU-U--UCGAUGG-UA-GG--GUAUC-GG------CC-UACCAU-GGUUGUAACGGGUAACGGAGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUUAGAAACAGCUCCUACUUCCAAGGAGGGCAGCAGGCGCGCAAACUACC--C-AAUCCCGGUU-----CG-GGGA----GGUGGUGACGAAAAAU--------------------GUCGGACG-AGU-C-AACC---------------UUUGG-UU--UG-CUCG-AU--CG---AGAUGGAGAU--------U-GAA-AUAA-A----AACUC--U-A-ACGA-AAGCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGUUG-CAGUUAAA---A--------CGCUC-GUAGUUGGAAUUAGGAUUGC---UAAUUUUUUGUCAUCAUGUGACGAAUCAUUAUGAAUCCCUAUGUUAGUUGUUUUCAGUUCUCUUUAUUGAGUGCUGUGAA----------------------------------------------------------------------------------------------------------------------------------------------------UGACUACAAAUUUUACUUU-GAAAAAAUUAGAGUGCUCAAAGCAGGCCGU-------------------------------------------AAGUGU--CUGGAUGUUG-UUGCAUGGGAUAAUGGAAU-AGGACCU-CUGU--------------------------------------------------------------------------------------------------------UCUAUCUGUUGGUUGAUGAACUUG----AGGUAAUGA-UUAAGAGGGA--CA--GUC--GGGGGCAUUCAUACUG-CA-G-CGUUAGA----GG------UGGAAUUC-UUGGAUCGCUG-UAU--GA-UGAACAA--CUGC-GAAAGCA---UUUGCCA-AGAAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUCAGA-GGCGCGAAGACGAUCAGAUAC-CGUC-GUAGU-UC-UG-ACCGUA-AACCAUGUCG-ACUAAC--GAUUCGCUC-A-GUUC---CAACUAAUAA---------------------------------------------------------UCGGUCUGAGU-GAG-GA------GUU------------------UACGGGAAACCA--AAGUUUUUGGAU--------UCCGGGGG-AA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCCG-CGGC-UCAAUUUGACUCAACACGGGAAAA-CUUA-CCCGGACUG-G------ACACUG-GAAUGAUAGA-CA-GA---------UUGAUGGCUCUU-UCU-UGAUU-CAGUGAU-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GCGA-UUUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACUCUAGC-CUGCUAAA-U-AGGAUAAUGACUGC---------UUUCAG--------------------------------------------------------------------------------------------------------------------------------------------------------------UUUAAAUUGAAAAUCAGUGGUCAUGUAUUCU-UCUUAGAG-GGA-C-UGGUG-UUCGGCU-----------------------------------------------UAAUAAUGUA--GACACACGAA--AUAGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CCGGGGCUGCACGCGCGCU-ACACUGAAGGAAUCAUUGGGUGU---------------------------------------------------------------------AUUUGUCC-UAACC--CGAGA--GGG-U-AU------GG-AAAU-CCG--UGAAA---------------------------------------CUCCUUC--GUGAUA-GGGAUUGUGCGAUGU-------------AAUUG-CG-CACA-UGAACGAGGAAUUCCUUGUAA-GCGC-G-AGUCA-UUAGCUC-GU-GUUGAAUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCACUACUACUGAU--UGAA-UGGUUUAGUGAG--GUCAU-UG-GAUU-------GA-UCUCC----UUGUGUUG-------------AUUAAUUGAUACGAU-G--GAGA----U---U-UGAGUAAGAUGAUC-GAACU-UGGCC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
EF526886.1/2-1806                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGCUUCAAGGAUUAAGC-CAUGCAAGUGUC-GA------------------------------GUAAAUAA---CU---------------GCACAGU-UGA-UCUGCGUACAGCUCAUU----ACAGUCGUAA-UC-UACCUGCAUGAA-----------------------------------------------------------------UGACUCUGUCAUCGAGUGGA-UAACUUC-AGUAACUUCGAAACUAAUACAUGGACGAGA--AAUCGAGUAGCCGUUCAGCACAA------------------------------------GGAGUAACAUCCGAGUGUGGCUCC--A-CGAUGCUUUUGGUCGUAAUAGA--AACUGG-----------------------------------------------------------------------------UCAAUCAG-----AUUGAAU---------CUAUUGUGGCAUCA--GACCAUUCUGUA---------CAAGGAA--ACCGUUGCUUG----------------------CAACA---UUCC-GUGUGCG-GUUG-AGCGACUGACCUAUCA-GCU-U----GUUUG-CA-AU--GUAUU-GG------AC-UGCAGA-GGCUUUGACGGGUAACGGAGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGUGAAACGGCUGCCAUGUCUAAGGACAGCAGCAGGCGCGCAAAUUGCC--C-AAUACUAGCA----UGA-GCGA----GGCAGCGACGAGAAGU--------------------AUUU-ACC-UUG-U-GCUA-------------CAUUGUA-UC--AC-GAGG-AC--AG---AAAUU-GGUG--------A-UAU-CCAA-A----ACCAU--C-C-CUGAGGAUCGACUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUACUAA-UGCUGUUG-CUGUUAAA---A--------AGCUC-GUAGUUCGAUAAGGAUUGAU---UCUGGUUCAGAUUCAGUGCUUCGCAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUUGCUGCAAUGGAGAAUUGGACCU-GAGAAUAUC---GUGCCAUAGUCAGUUCCU-------------------------------------------ACGGG----------UUC-UGCUGUGGUACUAAGCUCU-AGUUUAC-CGGU--------------------------------------------------------------------------------------------------------------------------------------------A-UUAACAGGGA--UG--AAC--GGAGCAGUGUGUACUG-GC-U-CGCGAGA----GG------UGAAAUUC-UUAGACCGUGC-CAG---A-CAAACGU--AAGC-GAAGGCA---UUCUGCA-AGUAUAU---CUUCAG-U-AAUCA-A-GAACGAGAGUGCAG-GGAUCGAAGAUGAUCAGCUAC-CGUC-GUAGU-CU-GCUACCGUA-AACGAUGCGA-ACUUGG--GAUCAGCCG-U-CGCC---AAUCUUUUUC---------------------------------------------------------GAUUACCAGGC-UGG-AA------CCUACUUAC-----UUCUCCUAGCGCGAAAGCUUUAAGUUUAUGCGU--------UCAGGGGA-GA-G--UACAG-UUGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAUGACA-C-CACAA-GGC-GUGGAU-GCUG-CGGC-UUAAUUUGACUCAACACGGGGAAU-CUCA-CCAGGUCAG-G------ACGCAU-GUUGGAUUGA-CA-GA---------UUGAAAGCUCUU-UCU-UGAUU-AUGUGUA-UGGUGGUGCAUGGCCGCU-CCUGGU-UGG-UGGA--GUGA-UUUGUCUGG--UUGAUU-CCGU-UAACGA-ACGAGAUCUUGGC-CC-UUCAA-U-GACAGUUUGAUCGUAUCUGUAAUCCAGUCGACGC---------------------------------------------------------------------------------------------------------------------------------------------------GCUUGCGUGCUCGCACUGGACGAGAUCUUGUCUUGUA-CC-CAAGG-GGA-C-GAUGC-GU---------------------------------------------------------GUUGACAAUGCAUGGAAGUGCGAGCCAAU-AGCAGGU-C-UGUGAUGCUCC-UAGAUGU-CCUGGGCUGCACGCGGCAU-ACAAUGGUGAAGAAAACGAGUUUGGUU-------------------------------------------------------------UGUUUGAGCUCC-UUGUG--CGAAA--UCA-U-UG------GG-GAAU-CUG-UGGACA---------------------------------------CUUCAUC--GUAUUG-GGGAUCGUUGCUUGC-------------AAUUAUUU-GCCU-UGAACCAGGAAUGCCUUGUAG-ACAC-A-ACU-A-GCAAAUU-GU-AUCGAAUAC---GUC-CCUGCCGUUUGUACACACCGCCCG-UCGUUGCAAUCGAU--CGGU-UCAAUGCUAGAG--GUCUUCCA-GAGGUG-----AG-UU-------CGAU----------------------CCUGUAUUG-------UC----U---U-UGCCAAAGUUGAUC-AAUAG-CAUUG-AACUAGAGAAUGCAAAAGUCGUAACAAG-GUUG-CUGUAGG---UGAACCUGCAGAAG-GAUCAA--
AY781421.1/1-1932                  --CCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUCGUCUCAAAGACUAAGC-CAUGCAUGUCUGAGU------------------------------UCCGAGUG--AUU---------------UGAGAAUCGAA-ACCGCACAAGGCUCAGUA-AAACAGUCAUUA-UC-UGCUGUUGUA-----------------------------------------------------------------------CCUGUGCCCAAAUGGA-CAACUGU-GGCAAUUCUAGAGCUAAUACAUGCGCUGC----AUCCGCUUC---------------------------------------------------------------CGUUGAGGUG--C-GGGUGCCCUUAUUUUGCCAAAG--CCAAUA-----------------------------------------------------------------------------UAGGCCUCG----GCCUGUA---------GUCGUGUUGAAUCU--GGAUAAGUGUAG---------GGAGCAAAAUUUGGUUGUGA----------------------GACCA---AUGC-AUUGAAU-UUGA-AGUGUCUGCCUUAUCA-GCU-U----GACUU-UA-GG--UUAAG-CU------CC-UAAAGU-GGCUGUAACAGGUGACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAAUGGCUACCACGUCUAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-ACUUCCAGCA-----GG-GAGA----GGUAGUGACGAAAAAU--------------------AACG-AUG-CGG-GUGCUC--------------AUCCGA-GG-CCU-CGCA-AU--CG---GAAUG-AGUG--------U-UGC-UUAA-A----GGAUG--A-C-AUGAGUACCUAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGCUG-UGGUUAAA---A--------CGCUC-GUAGUUGAAGUCCUGCUCCA---GCCCUCUGGCACUGUAACUGCAAAGUGCUUUGCUGGUUGGGGUUUUACUGGGGCGGCCUGUUGCCAUGCUGCGAGAUGCCCUUAAC---------------------------------------------------------------------------------------------------------------------------------UGGGUGUCGCGCUGUUGGUUAGUGUUUACUUU-GAAAAAAUUAGAGUGCUCAAAGCAGGCGUA-------------------------------------------UUGUGU--CUGUAUGGUG-GUGCAUGGAAUAAUAGAAA-AGGUCUU-UGGCUC-----------------------------------------------------------------------------------------------------CUGUUUGGAUUGGUUUUAAGAGCAUC--GAAGAAAUGA-UUAACGGAGG--CA--GGC--GGGGGCAUUCGUACUG-CG-G-CGCUAGA----GG------UGAAAUUC-UUGGACCGUCG-CAU--GA-CGAACAA--CUGC-GAAAGCA---UUUGCCA-AGAAUGU---UUUCGU-U-GAUCA-A-GGACGAAAGCCUGG-GGCUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-CC-AG-UCCGUA-AACUAUGCCG-ACCAGC--GAUCUGCCG-G-AGUC---GUACCCAU--------------------------------------------------------------GACCUGGC-AGG-AA------GCU------------------UGUGGGAAACCA--AAGUUUUUGGGU--------UCCAGGGG-AA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGAAA-CUGA-CCAGGCCCG-A------ACACUG-AAAGGACUGA-CA-GA---------UUGAGAUCUCUC-UCU-CGAUA-CAGUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--ACGA-UUUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACUCUAAC-UUGCUAAC-A-AGUUGGUGGGUUGUUCUCAUGAUGUGUUGCUGGCGUGCUGGUUGUGGUGGAGCU------------------------------------------------------------------------------------------------------------CGUCUCUGCUGUGGCGGGUACUGUCGGCAAGAAACUUGGGUCCCACCUUAUGCGCU-UCUUAGAA-GGA-U-UAGUG-GU--------------------------------------------------------UGCUUA--ACCACAAGAAAGAGAGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCUGCACGCGCGCU-ACAAUGAAGUAGACAAGAGGAUG-------------------------------------------------------------------------AUCC-UUCAC--UGAAG--AGU-GCUG------GG-UAAU-CCU-AUAAAA---------------------------------------CUACUUC--GUGCUU-GGGCUUGGAAGUUGA-------------AAGUUUCC-UCCA-UGAACAAGGAAUUCCAAGUAA-GUGC-C-AGUCA-UCAACUG-GU-GCUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGGA-UGGUGAGGUGAG--GUCGU-UG-GAUCAG-----CC-CCUUU----GUGAUCUCUUUUUCCAUCUUCGGGUGGAGAGUCACC-U--CGGG----CC-AG-CUGAGAAGAUGUCC-AAGCU-UUGCA-AUCUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUU-
AF083018.1/6-1645                  UACCUGAUUGAUUCUGU---CAGUGGUG-AUAAGCUUAUGUCCAAGAUUAAGC-CAUGCAAGUAAAAGU------------------------------GCCAGCUA--CUCGGUUU-----UCGGACCUUAGU-UGA-ACUGCGGAUUACUCAUUG-CA-AUGUUUUGA-AA-AAA-GCUGAA------------------------------------------------------------------------AAGACGUGUAAGGGA-UAUAUAC-GGCAAAUCUGGGUCUAAUACAGGAUUACG-----------------------------------------------------------------------------UACA-------------CCUAGCUAUGGAUAAAGA----------------------------------------------------------------------------------------------------------------------AAUCGAAGAG--AAUGGCCGU-----------------------CCACUUAUU-----------------------GCGG---AU---UGACAGC----C-GGAACCAACACCAUUU-UCU-G----GUUGG-UG-GU--GUAUU-GG------UG-CA--AA-UAGGACAAUGGUUG-CGGAUGAU--AGUU------------------------GUCGGGC-G-UCGGA--GAAUACGCUUGAGAAACGGCGAAUACUUCUAAGGAAGGCAGCAGGCUCGCAAAUUACCCAU-ACUUCUAAUU-----UU-GAGCGGGUGGUAGUGACAACAAAU--------------------ACCG-AAA-CUU-U-CCUC--------------AUACGA-GG-----AGCU-AU--UG---GAAUG-AUUU--------U-CUU-UUAA-A----CCGAG--A-U-CGCAGGAUCUAUGAGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAACUCC--AGCUCUU-AAA-GU-UUAUACCAU-AUCUGCUA-UGGUUGGA---A--------UGCAU--UACUUUGGAUUCUAUUUGC---CGGUGCAGCUUCGGUUGCGCAUGCCGGCG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAUACUCC-GAGUCUCACGGAGUGUUCAAAACAAGAC---------------------------------------------AUUUGC--UUGAACGAUCAUUGCAUGGGAUAUUGGAAA-AGGACUA-UGAGC-------------------------------------------------------------------------------------------------------UCUUAAUCUUGGUUUCG----GCC----UAGUAAUGG-AUAGCAGGGU--CU--GCC--GGGGGCGUACGUAUCG-UC-C-CGCGAGG----GG------UGAAAUCC-GUAGACCGUGA-CGA--GA-CGACCAA--GAGC-GCAAGCA---UACGCCA-AGAAAAG---ACCCGC-U-AACCU-CUGGGCGAGAGCCUGA-CGAUUAAAGACGAUUAGAUAC-CGUC-GUAGU-UU-UA-UCUGUG-AACGAUGGGA-ACUGAC--UG-AAGUUU-U-AUGC---GAAGUACU--------------------------------------------------------------ACAAGAGU-UGUUUG------AAU------------------UCCUGGAAACGU-CGAGUAU---CCC--------UCCAGGGG-UA-G--UAUUG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGCGCA-C-CACCA-GGA-GUGGAG-CCUG-UGGC-UUAAUUUGACUCAACACGGAGAAA-CUUA-CCCAGCCAU-C------ACGUUU-AGUGGAUGGA-CCUGC---------GAAAGUGAGCGU-UCU-UGAUU-UUACGAA-UAGUGGUGCAUGGUCGAU-UUUAGU-UCG-UGGG--UUGA-UCUCUCAGC--UUAAUU-GCGU-UAACGA-ACAAGAUACAGAA-ACCCCAAA-A-GGUUA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUCC-AAGUGGGU-UCA-A-CGGUU-AC---------------------------------------------------------UUCCA-AAUUUCUAUGAAAGUUGUGCUAU-AUCAGGU-C-UGU-ACGCUCU-ACGAUGG-CUGGGGCCGCACGCGUGCU-ACACUUAGGUCCACAGCGAGUUCU--------------------------------------------------------------------UAAUCAGA-GCGGG--UAAACCCACU-C-UG------AC-GAAC-CAA-UGCAAU---------------------------------------GGACCUUCGUGGAUU-GGGAUUGUAAUUUGCACGUUUGCCGGCUAAUUCGAU-AUCG-UGAACAAGGAAUUCCUAGUAA-GCGU-UCAGUCA-UCAUCUU-AC-ACUGAAUGC---GUC-CCUGCGCUUUGUACACACCGCCCG-UCGCUACCGGGGACUCUGAG-CUGCGGCGAGAA--GAA-------------------------------------------------------UUUUU---------------------------------UUCU-GAUCGUCCGCG-GCUUGAACCCGGUAAAAGUCGUAACAAG-GUAC-CGGUAGG---UGAACCUGCAGCUG-GAUCAUCG
GQ398061.1/4159-5972               UUUCCGAUUGAUCUUGU---CGGUGGC--UUUCCUUUGUCUUGAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUGAACUG--GUU----------------UAAGGU-GAA-ACUGCGUACGGCUCAUUA-CAUCAGCUAUAACUU-UCUUUGAUCA------------------------------------------------------------------------UAAAUUCUAAAUGGAAUAACCGA-GGAAAAGCCUGGGCUAAUACAUGCGACA-----AUUCCGGUA----------------------------------------------------------------GUAA-UAUC--G-GAAUGCUUUUAUUAGAUCAAA---ACCUUC-----------------------------------------------------------------------------UAGUUCUUU----AACCGGAACU----GUUUGUUGGUGACUCU--AAAUAACUUUGUG-------UUGAUCGU---AUGACCUUUG----------------------UGUCG---ACGA-CAUAUCU-UUCA-AGUGUCUGACUUAUCA-ACU-U--UAGACGG-UA-CA--UUAUA-UG------UC-UACCGU-GGUUGUAACGAGUA-CAGAGAAU--CAGG------------------------GUUUGGU-U-CUGGA--GAGGCCGCCUGAGAAACGGCGACCACUUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-ACUCUCAAAA-----CG-AGGA----GGUAGUGAAGAGAAAU--------------------AACG-AUG-UUA-G-UCUU---------------AUUUA-GG--CU-GACA-AU--CG---GAAUG-GGAA--------C-ACU-GUAA-A----CAGGU--U-A-UCGAUUAACAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-AG-GAAAACUAA-AGUUGCUG-UGUUUAAA---A--------AGCUC-GUAGUUGAAUUUCGGGUAUU---UGUUGCUAGCUGGUCUAACUGGCCAUGUUGGUUAACAGAUCCUCAUUUGCUGGACGGCUGGCGAUGAUCUUUAUCGAUUG---------------------------------------------------------------------------------------------------------------------------------------------UCGUCAGUUGCCAGAACGUUUACUUU-GAGAAAAUUAGAGUGCUAAAAGCAGGCU----------------------------------------------UUCGC--CUAUAUA-UA-UUGCAUGGAAUAAUGAAAU-AAGAUCU-CGAUU-------------------------------------------------------------------------------------------------------UUAUUUCGUUGGUUUUAGAAAUUG----AGAUAAUGA-UUAAUAGGAU--CA--GAG--GGGGGCGUACGUACUG-UG-G-UGUGAGA----GG------UGAAAUUC-UUGGAUCGCCA-CAG--GA-CGAACAG--CAGC-GAAGGCG---UUCGCCA-AGAAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUUGA-GGUUCGAAGACGAUUAGAUAC-CGUC-CUAGU-UC-AA-ACCAUA-AACGUUGCCA-ACUGUC--UUUUAGAUG-C-GGUU---AUUUAUAU--------------------------------------------------------------GACUCAUC-UGG-CG------GAU------------------CUCGAGAAAUCU--AAGUUUUUAGGU--------UCCGGGGG-AA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAAG-AAUUGACGG-AAGGACA---CACAA-GAA-GUGGAG-CCUG-UGGC-CUAAUUUGACUCAACACGGGAAAC-CUUA-CUCGGCCAG-G------ACACUU-UUAGGAUUGA-CA-GA---------UUGAGAGCUCUU-UCU-UGAUU-AGGUGGG-UGGUGGUGCAUGGUCGUU-CGUAGU-UCG-UGGA--GCGA-UUUGUCUGA--UUAAUU-UCGA-UAACGA-ACGAGACUCCGGC-UUACUAAA-U-AGUCUAAAGUUCGA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGGACUUUUCAAGACU-UCUUAGCA-GGA-U-AAGUG-GCAC-----------------------------------------------------UUUUUAA--GCCACACGAA--AUGGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CCGAGGCUGCACGCGCGCU-ACACUGGAGAGUUCAGAAUGUUU------------------------------------------------------------------------CUUCC-UACUU--CGACA--GAA-G-UG------GG-UAAC-CAU--GAAAU---------------------------------------UCUCUUC--GUGACU-GGGAUCGGAGCUUGC-------------AAUUAUUC-UCCG-UCAACGAGGAAUUCCUAGUAA-GCACUA-UUUCA-UCAGAAU-GU-GCUGAUUAU---GUC-CCUGUCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAA-UGUUUUAGUGAG--AUCUU-CG-GCUUGG-----UUUUCCGA---GCGGC---------------------UCUCGGGUCGU-U--CGGUU-UUU---A-UCGAAAAGAUGCUC-AAACU-GGAUC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUAU-UCGUAGG---UGAACCUGCGUAUG-GAUCAUUA
X13160.1/1-1964                    UACCUGGUUGAUCCUGC---CAGUAGU--GUAUGCUUCUCCUAAAGACUAAGC-CAUGCAUGUCUCCGA------------------------------AUAGAAGAGCAAG---------------UCUCUCU-GAA-UCUGCGAACGGCUCCGCA-UACCAGUUGUAA-AC-CAUAGCAAGCAAGCCGCGUUGUU--------------------------------------------GCCGCAAGGCGACGGCGCGGUUCACAGGGA-UAACCCU-GGUAAUUCUGAGGCUAAUACAAGAACGUA----CCACCCGCUUCGACC--------------------------------------------------CGUAAGGGGAGGGCGGG--G-GUUGUGUGACCCAGGUCGCAAA--UAUUAACUGGGAGUGGCCAC-------------------------------------------------ACGAUCUGACCACCAUACCAAAC----GGUUAUCC-------GCUUCGAAAGCUUCG--GUGAGUAACGGC---------GGAUUUC----------UGG------------------------------GUGG-CUCUCGC-UGUG-UGCUUCUGACCUAUCA-ACU-A----GAUGG-CA-GC--GUAAC-GG------ACAUGCCAU-GGUAACAACGGGUA-CAGAGGAU--AAGG------------------------GUUCGAU-C-CUGGA--GAGUGGGCCUGAGAGAUUGCUCACACUUCUAAGGAAGGCAGCAGGCGCGCAACGUUCC--C-AUUGGGCAAA-----GC-UCGA----GGGCGUUAGGGGACAU--------------------AUGA-AUG-CCU-G-CC----------------UUAU---GG--UG-GGCA-AU--UC---AAAUG-GGAC--------U-GUU-UUAA-A----CAUCC--U-A-UCGAGUAACAAUUAGAGGACAA-GUC-UGGUGCCAGCACCCGC-GGUAAUUCC--AGCUCUA-AUA-GC-AUACGUUAA-AGUUGUUG-CGGUUAAA---A--------CGCUC-GUAGUCGGCUCCAGACCUUC---AGAGCCUUGAUUCGGGACACUGGGUCAGCUGCUCUUCUCCAAGAGCGCGCCAACUACUGAUGAUAGGGGACGUCGGUCAAUCGUGCCCUGGGCUGUCUCCCCCCCGGGGGAGUCA-----------------------------------------------------------------------CAGGGUCGUUCAGCGGUCUUCGCGAUCGCGGUUCGGCUCGGCUCGGGGUACCAAUCACCAU-GAUUAAACCGUAGUGACCAAAGCACGUCUU--------------------------------------------UAGAC--GGGCACGGCA-CAGCAUGGGACGAAACGCA-CCGGGCU-CGCCU-------------------------------------------------------------------------------------------------------UUUUUUUGCGGGGGCGUGACUCGG----UAAAAGCGA-A----AGGGA--UG--UUC--GAGGGUGACCGAAUUG-CU-G-GGCGAGU----GG------UGAAAUAC-GUUGACCCUAG-CAA--GU-CGACCAA--AGGC-GUAAGCA---GUCAUCA-AGGGCAU---UCCCGU-U-GAUCA-A-GAGCGAAAGUUAAG-GGUUCGAAGACGAUCAGAUAC-CGUC-GUAGU-CU-UA-ACUAUA-AAUGAUGCAG-ACCAGG--GAUAGGACA-G-UGUC---CAUCUC----------------------------------------------------------------GAC-UCUU-CCG-GA------CCU------------------U-GGAGAAAUCA-CGAGUCUAUGGGU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA---CACAA-AGA-GUGGAA-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUCA-CCAGGUCCG-G------AUACAC-GUAUGAAAGU-CA-AG---------CUGAAAGACUUU-ACU-CAAUG-AUGUAAG-UGGUGGUGCAUGGUCGUU-CUUAGU-UCG-UGGA--UUGA-UUUGUCUGG--UUUAUU-CCGA-UAACGA-GCGAGACCCCGGC-GUUCCUAA-U-AGGGGUGGCAGCCA---GACCGGUCGCAA--------------------------------------------------------------------------------------------------------------------------------------------------------------GACAGGUUAGCUCGCCACCUGAAGUUAUGCU-UCUUAGAC-GUA-U-CAGAG-CC---------------------------------------------------------GAUAA--GGUUCUUGAA--AUGGGUUAAU-AACAGGU-C-AGUCAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGCGUU-ACAAUGGCAUGUAAAACGAGUGCUUGA-------------------------------------------------------------ACAAGGCGUCCC-ACGGC--CGAAA--GGU-C-GU------GG-UAAC-C---CUUAGU---------------------------------------CCCUGCU--UUGACU-GGGACAGAUCUUUGC-------------AAUUAUUG-GUCU-CAAACGAGGAAUUUUUAGUAA-UCGC-A-GGUCA-UUAACCU-GC-GUUGAAUGC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUGCUACCGAU--UGGG-UUUUACAGUUAC--GCGUU-CG-GAGGAC-----GA-UGUUU---UCGGGUC-----------------UUAACGGGCUCCG-G--GGCG----U---C-GGCCAAAGUUCUAA-CUACU-GUACG-GCCUAGAGGAAGCAGAAGUCGUAACAAG-GUAA-UCGUAGG---UGAACCUGCGUUUG-GAUCAUUA
AF439351.1/2-1948                  AACCUGGUUGAUCCUGC---CAGUAUUG-AUAUGCUUAUUUCGAAGAUUAAGC-CAUGUAAAUGUAAGU------------------------------GCA-UCAU---UU---------------CCUUUGA-UAA-ACUGUGCAAGGCUCAAUA-AACGAUUUAUAA-AC-ACCACGUCUU----------------------------------------------------------------------GCUUAAUCCUAUAAGGA-UAACGCA-GUCAAAAGCAUCGAUAAUACUUGCUCUCUU-AAUCAUCAAAA----------------------------------------------------------------UUGU-AUAU--G-AUGAGAAU----------AAUA--AACACC-------------------------------------------------------------------------------UAAUGAA----UUA-----------------GGUUUAUUUU--CUAAAUUUAUUU---------AGAAUUA----ACAC----------------------------GUGG---UAGU-UUAGUCG-AU-G-AUUUUAUCAUCUAUCA-GUU-U----UAUAA-GU-GU--UUAAU-UU------AC-ACUCAU-GACAACCACAGAUA-CGGAUAAU--CAGU------------------------GUUUGAU-U-CCGGA--GAAAGAGCCUUAAAAAUGGCUACUAGUACCAAGGUUUGCAACAGGCGCGAAAAUUAUC--C-AAUGCGAAUAUA-UUUC-GCGA----GAUAGUGAAAAGAAAUAAGCAUCCUAUACUAUUUCAGUUU-AGG-AGU-A-CCGG--------------UUAGUU-GA--UA-AUCAGUU--UA---CAAUG-GUAA--------C-AAA-UUAG-A----UAUUU--G-U-UAGAGAAACAAUUAGAGGUCAA-GUC-AGGUGCCAGCAUCCGC-GGUAAUACC--UGCUCUA-AUA-GU-CUAUAAUAA-AAUUGUUG-UGGUUAAA---A--------CGCUC-GUAGUCAAUUCAAGGGAGUA---AGUUCUAAAGUCAAUUAGGUUUAUCUAGACCAAAAACUAUUUUAAUAGUUCAAGGUUUAGUCCUUUCAGGAGUCGUUAUUGAUAGUAACUUUAAUUUUAGCAUUAUCUUUUUUAAACCUUUUUAUU-------------------------------------------------UAACCAAAAUAAUUAGGCUUUAUUAGAGUACAUAUGCGGCUUUAGUCUUAAAUCCCGACCAAACAAUCCUGU-GACUAAAUUAACGCGAUUAAAGCAGGAUUUGUUAA---------------------------------UGACAGAUUCU--UUGAAUCUGU-UAUUUUGUGAUGUAACAUACAUCAGCA-UAGCA-------------------------------------------------------------------------------------------------------UCUAUUUUCAAGAUAGUUUUCUAU----UUUGAAUAG-AUAAUAGGAC-CAG--AUU--CAAGUUCUCAGUACUU-GC-U-AAUCAGG----GG------UGAAAUCC-GUAUAGUUAGC-AAA--GA-CUACCAA--AGGC-GAAAGCA---GAGAACC-AGAACUG---GUCUAU-U-GAUCA-G-GAGCUAGAGUUAAG-GGAACAAAGAUGAUUAGAUAC-CGUC-GUAGU-CU-UA-ACUAUA-AACUAUACUA-AUUAGA--GCUUGUACA-A-AGCC--GUGUUAUUA--------------------------------------------------------------GAUUUAUA-CAU-GA------AC-------------------CCCGAGAAAUCU-CAAAUUUUUGAGU--------UCCAGGGG-AA-G--UAUAU-UCGCAAGA-AUGAAA--C-UU-AAAGG-AAUUGACGG-AAAUUCA-C-CACCA-GGA-GUGGAG-UUUG-CGGC-UUAAUUCGACUCAACGCGUGAAAA-CUUA-CCAAAUCCA-A------AUUAUG-UAAAGAUUGA-CA-GG---------UUAAU-GACUUU-UCU-UGAUU-CAUAAAA-GAGUGGUGCAUGGUCGUU-CUCAGU-UCG-UGGA--UUAA-UCUGUCUAC--UUAAUU-GUGU-UAACGA-GCGAGACCUUAAU-UAACUAAU-U-AGUAUCAUGUAAUUUUAACUUGUUUGAAAUCA--------------------------------------------------------------------------------------------------------------------------------------------------------AAAUCGAAAAUAACCAUUAAUAAUGGUUUUUUCU-UCUUAGUA-AAA-C-UUAGC-UCGAU--------------------------------------------------UUAACAACA--GAGUCAGGAA--GUAAGGCUAU-AACAGAU-C-UGUUAUGCCCU-CAGAUGU-UUUGGGCAGCACGCGUACU-ACAUUGAUAGUUUCAGUAAGUUUAAGCGUUAAG--------------------------------------------------AGUCAUUUUAACACUCC-GGGUU--UUAAA--UAA-U-GA------GG-UAAA-CUA--CAAUC---------------------------------------ACUUAAC--AAAUCA-GGAAUUAAGGAUUGU-------------AAA--UUC-CUUA-UGAACAAGGAAUUCCUAGUAA-UAGU-A-AAUCA-UCAUUUU-CC-AAUGAUUAC---GUC-CCUGAAUUUUGUACACACCGCCCG-UCGCUCCUACCAAU--UGAA-UAAAAAGAUAAA--AUUGA-UG-GAAAAU-----G-------------------------------------UUAAA---------------------G-AUUUAAAAUUAAUU-AAAUC-UUUGU-AUUUGUAGGAAGGAGAAGUCGUAACAAG-GUUU-UCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
AF249200.1/4-2005                  UACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGACUAAGC-CAUGCAUGUCUGAGU------------------------------UCGCCCCA-UACC---------------GCACGGG-CAG-ACCGCGGAAGGCUCAGUA-AACCAGUCCGAG-UU-CCUUAGGUGACGGG--------------------------------------------------------------CCCCUGACCGGGCCCGACGGA-UAACUGU-GGCAAAUCCAGAGCUAAUACGUGGUGUGACAGAGCCCCGACCCGCGACGGCUCGCGCGCACCCCU-----------------UAACCGGGGUGUGCCGCGGCGUCCGAGCGGGGA--A-GGGCGCCUUUAUUAGUACCGAG--ACCGGCUCGACCCCGUCGCUCU--------------------------------------------CUUAACCGGGAUGCCGGCGGGGGCGA----CCCACG-----------GCCUGGUGAACUC--UGGGUGACGGCC---------CGAACGC--UACGUCCUCCG----------------------GGACG---GCGG-CGCUCCU-UACA-AGCGUCUGCCCUAUCA-GAU-G--UCGACGG-U--GG--CCAUG-GG------CC-AACCGU-GUCGCCGACGGGUAACGGGGAAU--CGGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCACGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-ACUCCCGGUC-----CG-GGGA----GGUAGUGACGAGAAGU--------------------AACG-GUGGCGG-G-ACCC-------------GAGUCGG-GC--CC-CGCG-GU--CG---GAAUG-AGCG--------C-AGU-CCAACA----ACCCUGAC-G-GCGACGACCAAUCGGAGGGCAA-GCC-UGGUGCCAGCAACCGC-GGUAAUUCC--AGCUCCG-AUA-GC-GUAUACUAA-AGCUGCUG-CAGUUAAA---A--------AGCUC-GUAGUUGGAUCUCGGGGGGG--GCGCCGCGAAAGGAGGUGGGCUCACCAUUCCCCGCGGCGACCCCUCUACAAGUCGCCGGCUCCCCCGCGGCCGUCCUUGAC----------------------------------------------------------------------------------------------------------------------------------------UGGGCGUCCCGGGCGGCCGGCUCCUCACUUU-GAAAAAAUUAGAGUGUUCAAGGCGGGCCCA--------------------------------------------CGCGC--CCGGAUACCG-UCGCACGGAAUGAUGGAAG-AGGACAG-CCGUCCC--------------------------------------------------------------------------------------------------ACACAUCACGGCCGGUCUCAGGGACGG----AGGUAAUGA-UUGACAGGGA--UG--AUC--GGGGGCAUCCGUACCG-CG-G-CGGGAGA----AG------UGAAACUU-GAUGAUCGUCG-CGA--GA-CGGCCGA--GAGC-GAAAGCA---CUUGCCA-AGAGCGU---UUUCCU-U-AAUCA-A-GAACGAAAGUCGGA-GGUUCAAAGACGAUUAGAUAC-CGUU-GUAGU-UU-CG-ACCCUA-AAUGUUGCCG-ACCGGC--GAUCCGCGG-A-GGUC---CCGCCUGG--------------------------------------------------------------GACCGCGC-GGG-CG------GCC------------------CUCGGGAAACCA--GAGUCACUGGGU--------UCCGGGGG-GA-G--UAUGG-UCGCAAGU-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGGG-UCUG-CGGC-UCAAUUUGACUCAACACGGGGAAA-CUUA-CCCGGUCCG-G------ACACCG-CCAGGAUUGA-CA-GA---------CCGAG-GCUCUU-UCU-UGAUU-CGGUGGG-UGGUGGUGCAUGGCCGUU-CCUAGU-CGG-UGGA--GCGA-UCUGUCUGG--UUAAUU-CCGA-UAACGG-ACGAGACUCCGGC-CUGCCAGU-U-AGCGUCGGGGCGUCAUCGAGGCGGUCGCGGCGUCCGUCAACGCCUCCCGUGCGUGCGAGCGCCGUUC----------------------------------------------------------------------------------ACGCGCGCGUCUCCGCGCCGGGUCGGUAGGGCCCGCGCCGCCCCGGUCGCCCCCCGACCGAUCAGACUU-UCUUAGAG-GGA-C-CGGCG-GU---------------------------------------------------------GGCCA--GCCGCCACGAG-AAGGAGCGAUAAACAGGU-C-UGUGAUGCCCU-UAGACGUUCCGGGGCCGCACGCGUGCUAACACUGGGGGAGCCAACGCGGCU----------------------------------------------------------------------GACCGCC-UGGCC--CGAAG-GGUG-U-CG------GG-AAAG-CGU--UGAGU---------------------------------------CUCCCCC--UGGACU-GGGCCCGGGGCUUGG------------CCACUGUGC-CCCG-CCAACGAGGAAUUCCCCGUAG-GCGC-G-GGUCA-UAACCCC-GC-GCCGACUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACCAUCGGU---GGA-CGGCCUAGCGAG--GACCU-CG-GCAU----------------------C----------------------CUCGCGCC----------------------GGGAAGACGCCC-GAACUCCGGUC-GCUCGGAGAUAGUAGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAA-CUGCGGAAG-GAUCAUUA
AY179971.1/1748-9                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUAAAAGAUUAAGC-CAUGCAAGUCUAAGU------------------------------GUAAAUGU--UUU-----------------AUAUU-GAA-ACUGCAGAAAGCUCAUUA-UAUCAGUUAGAG-UU-UAUUUGAUUG-----------------------------------------------------------------------UCGCGAUUACAAUGGA-UAACCGU-AGUAAUUCUAGAGCUAAUACAUGUCGCAA---AUUUCUAU--------------------------------------------------------------------UA-------A-GAAAGAAGAUAUUAGAAAGAA---GCUAAC-----------------------------------------------------------------------------AU----AUU-----------------------GUAUUGAUUCA--UAGUAUUGUCUC---------UAAUCGC-------ACAUAU-----------------------U------GCGA-UAGGUCA-UUCA-AUUUUCUGCCCUAUCA-GCU-G---GGAUGU-UA-GU--GUCUU-GA------AC-UAACAU-GGCAUACACGGGUAACGGAGGAU--CAGG------------------------GUCCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUAC-ACUUCUAAGGAAGGCAGCAGGCGCGUAAAUUACC--C-AAUCCCGAUA-----CG-GGGA----GGUAGUGACAAGGAAU--------------------AACA-AUA-CCG-G-ACUU--------------UUACAA-GC--CU-GGUA-AU--UG---GAAUG-AGAA--------C-AAU-GCAA-A----AACCU--U-A-CCUAGGAUCUAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAACACC--AGCUCCA-AAA-GC-AUAUAUUAA-CGUUGUUG-CAGUUAAA---A--------GGCUC-GUAGUCAAAUUUGUGUUCUC---GAGCAUAUGUGACGCAUCUUGUAUGCAAAACAGUGCUUUAGUUCAUCAUAUUUGUAAACAUCUCUUCUCUUGAUUGAGUU--------------------------------------------------------------------------------------------------------------------------------------------UGAUUUGGUUACAAGUACAUUUACUGU-GAGGAAAUCAGAGUGUUCAAAGCAAGCAAU--------------------------------------------UUUGU--UUGGAUGCUA-CAGCAUGGAAUAAUAAUAU-ACGGUUG-UUAC--------------------------------------------------------------------------------------------------------------UAUUUUGGCUUUUGUAUC----AAGUAAUGA-UUGAAAGAGG--UA--GUC--AGGGGUGCUAGUACUU-AG-C-GGUCAGC----GG------UGAAAUGC-AGAAAUCCGUU-AAU--GA-CUAUCAA--UCGC-GAAAGCA---UUCAUCA-GUGAUAU---UUUCUU-U-GAUCA-A-GAACGAAAGUUGAG-GGAUCGAAAACGAUCAGAUAC-CGUU-GUAGU-CU-CA-ACCGUA-AACGAUGCCA-ACUAGA--GAUUGGUGG-A-GAUU---GAAAU-----------------------------------------------------------------AACUCCUU-CAG-CA------UCU------------------UUCGAGAAAUUA--CAGUUUUUGGGU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CCGAAA--C-UU-AAAGN-AAUNGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CUUG-UGGC-UUAAUUUGACUCAACACGGGAAAU-CGUA-CCAGGUCCG-G------ACAUAG-UAAGGAUUGA-CA-GA---------UUGAA-GAUCUU-UCU-UGAUU-CUAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GCGA-UUUGUCUGG--UUAAUU-CCGU-UAACGA-ACGAGACCUCUUC-UUACUAAU-U-AGAUUACAAACAUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGUACAUUU-UCUUAGAG-GAA-C-UAUCG-AU---------------------------------------------------------UUAUC--GUCGGAGGAAGUGAGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGUGCU-ACACUGAUGA-------AAGCAA----------------------------------------------------------------------UCAUUUA-CAAAG--UUAAA-UACU-U-UU------UU-UAAU-CUG-CAAAAU-----------------------------------------UCAUC--GUGUUU-GGGCUUGGUGUUUGA-------------AAUUUACU-GUCA-CCAACGAGGAAUUCCUAGUAA-AUAU-G-AGUCA-UGAACUU-GU-AUUGAAUAU---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGAA-UGGUCCGGCGAG--CACUC-UG-GAGUUA-----G-----------UGCG----------------------UUUAUCGCAU----------------A-UAGCAAAGUUGUGC-AAACC-UUAUC-AUUUAGAGGAAGGAGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAAG
AF497743.1/1-2002                  UACCUGGUUGAUCCUGC---CAGUAGUU-AUAUGCUUGUCUAAAAGCUUAAGC-CAUGCAUGUCUAUGU------------------------------UCAGCUCC--UUU---------------GAGGGGU-GAA-ACCGCGAAUGGCUCAUUA-UAUAAGUUGUGG-CA-UAUUGGUCAG-----------------------------------------------------------------------AGCGUUUUUACUUGGA-UAACUGU-GGGAAUUCUAGAGCUAAUACAUGCAUUCA---GGCUUUGACUCCU---------------------------------------------------------GGCAACGGGAGGA--G-GAGCGCUUUUAUUAGAUCGAA---GCCAACCUGGGUGUACGCUU------------------------------------------------GUCGUGCAUUCCGGUCUGCAGGCU----UGUUUUGC-------GGGCUUGAUGACUCU--GGAAAACUACAGG-------CCAAUUGA---AUCUCGUUCU-----------------------GAGG---UCUA-UGUGACC-AUAU-GGCAACUUAUCGAUCA-GCU-U----GAUUG-AU-GU--GUAUU-GG------AC-AACAAU-GGCUGUUACCGAUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-ACUCCUGGUU-----CA-GGGA----GGUAGUGACGAGAAAU--------------------ACCG-G-G-AAG-G-GACA--------------UUGUUG-UC--CC-CGCU-CC--CG---GAAUG-AGAC--------G-AUU-UUAA-A----CCUCU--U-U-ACGAGGACCCAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAACUCC--AGCUCCA-AUA-GC-GUAUAUUAA-UAUUGCUG-CGGUUAAA---A--------AGCUC-GUAGUUGGAUUUGAGCUCCG---GCCGGUGUCAGCAGGGUCGUGGUACGGUCUCUGUCUGUGCCGGUGCCGGGCUUCUGGUUGUCGGGUGGCCGGCCGGGACGGCGGCUGUUGGCUCUUGGGGUGACC------------------------------------------------------------------------------------------CUUGGGCUGUGGCUGCUGGCCUGGUGGCAAGGCGCUCGGUUGAGUUUACUUU-GAGAAAAGGAGAGUGCUUAAGGCAGGCUUGU-----------------------------------------UAUGUCU--GUGGAUCUCG-GUGCAUGGAAUAAUGGAAC-AGGGCCU-CGCGC-------------------------------------------------------------------------------------------------------CUGUGUUUGUUAGUUUCGGGGUGCCCCGAGGCAAUGA-UUAAGAGGGA--CG-GUUC--GGGGGCAUUCGUACUG-UA-G-GGGGAGA----GG------UGAAAUUC-UUGGAUCCCUG-CAA--UA-CGAACAA--CUGC-GAAACGA---UUUGCCA-AGGACGU---CCUUAU-U-AAUCA-A-GAACGAAAGUUAGA-GGUUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UC-UG-ACUGUA-AACGAUGCCA-ACUGAC--AAUCGGCCC-CUGGUC---GCGAGUAA--------------------------------------------------------------GACGGGGU-UGG-CA------GCC------------------UCCGGGAAACCA--AAGUUUUUGGGU--------UCCGGGGG-GA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACAA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAC-CUCA-CCAGGCCCG-G------ACACUG-GUAGGAUUGA-CA-GAUCUUUCCCCAUGAA-GCUCUU-UCU-CGAUU-CAGUGGG-UGGUGGUGCAUGGCCGUU-CGUGGU-UGG-UGGA--GCGA-UCUGUCUGG--UUCAUU-CCGA-UAACGA-ACGAGAUUCUGUC-CUGCUAAC-U-AGGUGAUUACUCUG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGCUCGUUGCAGCGUUUAUCAGUGCU-UCUUAGAG-GGA-C-GGGCG-GCGC-----------------------------------------------------UUGAUAA--GCCGCACGAAG-UCAGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UCGAUGC-CCUGGGCCGCACGCGCGCU-ACACUGAAAGAGACAACGCGCUCCCUUCCCUCGUGGAGGG------------------------------------CUAGGCCGUUUGUCGGUGCGUUCC-CGGUU--CGAAA--GGA-U-CG------GG-CAAU-CGC--UGAAUCUCUUGUGG---------------------UAUGUAUGUGCCUUUC--GUGGUU-GGAAUUGUGGCUUGA-------------AAUUGUGC-CUCA-UGAACCAGGAAUUCCCAGUAA-GCGC-G-AGUCA-GUAGCUU-GU-GUUGAUAAC---GUCCCCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--CGAG-UGAUGUAGUGAG--GCUUU-UG-GACCGU-----UC-AGGAAC--GAGGCUGCGGUGCUC-GCUCGCGGGCGCUGUGGCCUG-U--AUUU----C---C-CCGGGAAGAUGGCC-GAACU-GGAUC-GCUCAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
GU230754.1/1-1921                  CGACUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGA------------------------------UCGCUCGG--AACCCGCA-----AGGGUUUAUCGG-UAA-UCUGCGAAAGGCUCAUUA-UAACAGUUACAA-AC-UUAGCCACUA-----------------------------------------------------------------------GUUUAUCUUACAAGGA-UAACACA-GCCAACUGCAGCGAUAAUACUUGCUCAAAA--GCCAGUGAAU------------------------------------------------------------------UG-AAUA--G-CUGGUGAGCAAUAGCAUUAAAG--------------------------------------------------------------------------------------GAACGUAU----GCUAUU------------UA-------CCU--CGAAAGAGGUGU---------UGACCGC-------AGCAAU------------------------------GUGG-CCUAGAG-GAAG-UAUUUCUUCCUUAUCA-GUU-A----GUUGU-UU-CA--GUAAG-GG------UG-AAACAA-GACACUUACGGGUA-CGGGGAAU--CAGU------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAAUGGCUACUACAUCUAAGGAGGGCAGCAGGCGCGAAAAUUACC--C-AAUCCUAACAA--UUUU-GGGA----GGUAGUGACAAGAAAU--------------------AACG-ACC-UCA-C-ACGCAGACUC-UGUCGGUGGGAGG-GU-ACU-UCGG-UU--UG---CAAUG-GUCC--------U-AGU-UUAA-A----UCUCU--A-G-GAGAGUAUCGAUUGGAGGACAA-GUC-UGGUGCCAGCACCCGC-GGUAAUUCC--AGCUCCA-AAA-GC-AUAUACUAA-AAUUGCUG-UAGUUAAA---A--------CGCUC-GUAGUUUAUACGUAGGAGAU--UAUUGAGAUCACUUGGUGUGGCGAACAUUUUCGUACCAUUACACUCAUUUUAUGGGUCUUGGUAUCGAAAGUGACCUUACGGUUUAUUCGUCACAUCCUUAGGCGACGA-------------------------------------------------------------------------------------GUGGCUAAUACCCAUGAGUCACAAGUGUGAUCAGUAACUCUGCCCAGGAACCGU-GAACAAAUUAAUGUGUUUAAGGCAAGCUCGUGUAU--------------------------------UCAAUACAUAGC--UUGAAUAAUU-UAGCAUGGAACCACUAUAC-CCUCCUU-UUGG------------------------------------------------------------------------------------------------------------------------------------AGGGACCUG-GUAAUAAAAGCUCG--GCG--GAGGACUCUGGUAUUG-CG-C-ACUUAGA----GG------UGAAAUUC-CGAUAUUUCCG-CAA--GA-CGAACGG--AUGC-GUAGGCUGUCAUUGCCC-AUCACAC---CUUUAU-U-GAUCA-G-GAACGAGAGUCAGG-GGAUCGAAGAUGAUUAGAUAC-CGUC-GUAGU-CC-UG-ACUGUA-AACUAUACUA-ACAAGA--GUUUGUGUA-G-ACACU-ACUCUGUAU--------------------------------------------------------------GAUCUUCG-CAG-AA------UC-------------------CAAGGGAAACCU-CAAGUUUUUGGGU--------UCUGGGGG-GA-G--UAUAG-UCGCAAGG-CCGAAA--C-UU-AAAGG-AAUUGACGG-AAAGGCA-C-CACCA-GGA-GUGGAG-UUUG-CGGC-UUAAUUCGACUCAACGCGGGGAAA-CUCA-CCAGGUUAG-G------ACAGAG-GAGAGAUUGA-CA-GG---------UUGAGAGUCCUU-UCU-UGAUU-CUUUGAU-UGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA--GUGA-UCUGUCUAC--UUAAUU-GUGU-UAACGA-ACGAGACCUUAAC-CUGCUAAU-U-AGCGCAUGGGUCGGUAAAACGAUCAUUUCACCCUUU-----------------------------------------------------------------------------------------------------------------------------------------------GGGUGCUUGCUAUCUCAUAAUUCCUGAAUUAUGAGUGCU-UCUUAGAG-GGA-C-AAUAC-GCGUUGAAAU-----------------------------------------UUUUUUCAUACCA--GCGUGGGGAAGUUUAAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUAU-CCUGGGCGGCACGCGUACU-ACAAUGUUAUUAUCAACGAGCAACAUCCAAGCCCC---------------------------------------------UUCGCGGGAUCACUUGAGCC-UAUAC--UUUAAGUAGU-A-UG------GG-GAAU-CUU--UGAAA---------------------------------------UGGUAAC--CUGACU-GGGAUAGCUGUUUGG-------------AAU--UAC-AUCU-UGAACGAGGAAUUCCUAGUAA-GCGC-A-AGUCA-UCAUCUU-GC-AUUGACUAC---GUC-CCUGCCUUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGGA-UAGACAGGUGAA--CUUGA-UG-GACCUC-----UA-U---------------------------------------------------U----U---U-GAGGGAAAUUUAUU-AAACC-UUUCU-GUCUGUAGGAAGGAGAAGUCGUAACAAG-GUCU-CCGUAGG---UGAACCUGCGGAGG-GAUCGGGA
JF412715.1/1-1728                  -ACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUUUCAAAGAUUAAGC-CAUGCAGGUGUAAGU------------------------------AUAGAUCA--AUU----------------UACGAU-GAA-ACUGCGAACAGCUCAUUA-GAAUACUUAUAA-AU-AACACGGUGA------------------------------------------------------------------------CUAUCAUUAUAUGGA-UAUCCAU-GGUAAUUCUGGAGUUAAUACAUGCCGAU-----AAUUUUGUU---------------------------------------------------------------------UACA--A-AAUUGCAGCCAUGAUUGAAUC---GCCGAC-----------------------------------------------------------------------------UUGGGUUCU----GCCCAA-------------UUGGAGGAUCC--GCGUGGACUUGU---------GAAUCGC--------UUUUU------------------------------GCGA-UAGACCG-UUUU-AAUUUGUGACCUAUCA-GCU-U---CGUCGG-UA-AG--GUAUU-GG------CU-UACCGA-GGCGAUUACGGGUAACGGAGAAU--UGGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGGUGGCAGCAGGCGCGCAAAUUACU--C-AAUCCCGACA-----CG-GGGA----GGUAGUGACAAAAAAU--------------------AACA-GCA-CGA-U-GC----------------UUUU---GC--UU-CGUG-AC--UG---UAAUG-AGCA--------A-AAU-UUAC-A----AAAGU--A-U-GUGAGUAUCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AAUUGUUG-CAGUUAAA---G--------CGUUC-GUAGUUUAUGUUACACAGUA---AAGCAGGUUAGAGACUCAGGUUUUGAGUUCUCGUCUGUUUUUCCUGUCGUGUAGUUUACUGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACUAUUACUUU-GAGUAAAUGAAUUUGCUCCAAGCAAGCU----------------------------------------------UUAGC--UUGUACCGCU-CAGCAUGGAAUAAUAUAAU-AUAACUC-CCUAU-------------------------------------------------------------------------------------------------------CGGCACGUCGGCGAGUCGAAUGGG----ACGUGAUGA-UUGAUAAGGA--CA--GUC--GGGGGCAUUUGUAUUU-GC-U-GGAGAGA----GG------UGAAAUUC-UAAGACCCGGC-AAA--GA-CAAACUG--AGGC-GAAAGCU---UUUGCCC-AGGAUGU---GCCUGU-U-AAUCA-A-GGACGAAAGUUGGG-GGAUCGAAGACGAUUAGAUAC-CGUC-GUAGU-CU-CA-ACCGUA-AACAAUGCCG-ACAUAA--UUUCGGCGA-A--GUA---AGUUUAUA--------------------------------------------------------------GUCUUCUU-CGG-AG------UUA------------------CCAGAGAAAUCA--AAGUCUUUGGGC--------CCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUCGACUCAACGCGGGAAAU-CUCA-CCAGGCCCG-A------ACAUAA-UUAUGAUUGA-CG-GA---------UGAAAAGAUCUU-UCU-CGAUU-CUAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-CGG-UGAG--GUGA-CUUGUCUGG--UUAAUU-CCGA-UAACGG-ACGAGAUCUCGAC-UUAUUAAA-U-AGACACUUUGAUUU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUAUCGAAGCGUCU-UCUUAAUG-GGA-C-AUUGG-AU---------------------------------------------------------GUUCA--UUCCAAGGAAGUUCGAGCCUAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGG-CCUGGGCUGCACGUGCGCU-ACAUUGACUAAAGCAGAAAGUUC---------------------------------------------------------------------------CC-UUGGU--CGAUA--GAU-C-CG------GG-AAAU-CUU--UGAAA---------------------------------------UUUCGUC--GUACUU-GGAAUCGGUGAUUGC-------------AAUUAUUC-ACCG-UGAACGAGGAAUUCCUUGUAA-GUGC-A-AUUCA-CUACAUU-GU-GCUGACUGC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUUCAACCGAU--UGGA-UGAUUCGGCAAA--UUUCG-UG-GACAUU-----AG-CAGC-------------------------------UUUAU---------GCUG----C---C-GAUGGAAGCAAUGU-GAGCC-ACAUU-AUCUAGAGGAUGAAGAAGUCGUAACACG-GUAU-CCGUAGG---UGAACCUGCGGAUG-GAUCAUUA
AF255686.1/1-2160                  UACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUUUUAAAGGUUAAGC-CAUGCAUGUCUUAGU------------------------------ACAGGCGU--CCU---------------GACAGCC-GAA-ACCGCGGAUGGCUCAAUA-UACCAGUAGCAA-UC-CGC-AAGAUU------------------------------------------------------------------------UUUAUCCCUAGUGGA-UACCCGU-GGCAAACCUAGAGCUAAUACGCUUUCA-------------AG---------------------------------------------------------------AUUCG-CUAC--------GAUCCCACUAUUUUUAAA--GCCUUAUGGUAUAGUGAUCUAG---------------------------------------------CGAACAGCAAUUAUUAGAAGCCUCA----GCUUUAG---------CUGCGGGUGAGUCU--GAGUAUCGAUGC---------UACGCGC--UAUGGUCCAUAA--------------------GUACCA---GCGC-UAAUCUU-UGCG-AGCUUCUGACCUAUCA-GCC-A----GAUGG-UA-AG--GUAAG-UG------CC-UACUAU-GGCUACGACGGGUAACGGGGAAU--CUGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAUAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGGAAUUUAAC--CUAGUACUAGCU-----CU-GUGA----GUUAGUAACGAAAAAU--------------------CUUG-AUG-UGG-G-GUUUCC----------UAAACCGA-GC--CU-CACA-AU--CG---AAAUG-AGUU--------U-AUC-AUAA-AA-ACCCUAU--U-U-GCGAUAAACUAUCGGAGGGCAA-GCC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-UUA-GC-AUAAUCCAA-UGUUGCUG-CGGUUAAA---G--------UGUUC-GUAGUUGGCUUUGAACGAGA---GUUUCCACCCGCUUCUUUAAAUAUAUAUUUAACCCGCGCUUUUUUUUUAAGUUCGGUUGUUGUCGUUCUUUAUUAAAAUAAAAAAAUGCGCGGAAAAUAUUGAAAAAAAUUACGCGGUGCGGAAACGAAAACCGGCGUACUUA--------------GUUCCUCGUCGAGCUUGGUACCCGGUAAAAAUGCUCGGUACUCGGUAUCCUCUUCAUUGAGUGUACCUUGGAACCGGCACUAUUCACUUU-AAUAAAAUUGGAGUGUUUAUAACAGGUCUGAGGAAG------------------------------ACAAUUCACGCGC--UUUACUAAAA-ACGUCUAGCACGAUGAAAU-AAGACUC-GGGUUCUAAA---------------------------------------------------------------------------------------------AAUUUUGGCUUUUAAUAUUUGGAACUCCG----AAGUAAUGA-UUAACGAGAA--CU--GCC--GGGGAUAUUAGUAUUG-CA-G-CGCGAGA----GG------UGAAAUUC-UGUGACCGUUG-CAA--GA-CUGCCUA--CAGC-GAAAGCA---UUUAUCA-AGAAUGU---UUUUAU-U-AAUCA-C-GAUCCAAAGUUAGA-GGAUCGAAGGCGAUCAGAUAC-CGCC-CUAGU-UU-UA-ACCAUA-AACUAUGCUA-ACUAGC--AAUCCGCUU-U-UGUUA-CCGUUUGCA--------------------------------------------------------------GAGCAAAC-GGG-AU------CC-------------------CCCGGGAAACCA--AAGUUUCUCAGU--------CCCGGGGG-GA-G--UAUAG-UUGCAAAG-CUGAAA--CCUU-AAAGGCAAUUGACGG-AAGGGCANC-CACCA-GGA-GUGGAG-CCUG-CGGC-UCAAUUUGACUCAACACGGGAAAA-CUCA-CCAGGUCCG-G------ACCCCG-UAAGGAUUGA-CA-GG---------UUGAAGGAUCUU-UCU-CGAUU-UGGUGCA-AGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUGAUU-CCGA-UAACGA-ACGAGAUUCUUGC-CUCCUUAU-U-UGUGGUCAGAUCGAGUCCUAAGGCGCGGUAUAAAAUAUUUUUGCGCGACUCUUUUUUUUAUACGGUUCGUUCUUUUAAAGUUUUAUAGUUNCCUAAAUU-----------------AUAUUAAAAAAGCUAUAAUCUUUCGAGACGACCGUUUAACUUGUCGCAAAAAAAAAUACAAAGACCAAGCCUGAGGCCGUCUGACGAAAUACACCAUAUUCA-A-UUGGCG-GUA-U-UGGCG-GU---------------------------------------------------------GUCCA--GCCGUAAUAA--AAAGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU--CUGGGCUGCACGCGCGCC-ACAUUGAUGCGUGCAGCAUGCUU--------------------------------------------------------------------------UCC-CGUUC--AGAAU--UGA-A-GC------GG-CAAU-CAU-UUCAAA---------------------------------------CCGCUUC--GCGGUU-GGGAUUGCGGAUUGU-------------AAGUUUUC-CCCG-UAAACGAGGAAUGCCUUGUAC-GCGC-G-GGUCGUAAAGCUC-GA-GCUGAAUAC---GUC-CCUGCCCUUUGUACACACCGCCCGCUCGCUACUUCCGAU--UGAG-UGGCUAAGUGAG--GUAAU-UG-AACCGU-----UU-UUUUA----AAAAGUU----------------UUUAUAUCUUGUA-A--CAGA----A---A-ACGGAAAGAUUCCC-CAGCC-UAGUC-ACUUAGAGGAAGUAA-AGUCGUAACAAG-GUUU-UCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
X89484.1/1-1828                    UACCUGGUGGAUCCUGC---CAGUUGUC-AUAUGCUCGUCUCAAAGCCUAAGC-CAUGCAUGUCUCAGU------------------------------ACAUACUU---UA---------------CCAAAGU-GAA-ACCGCGAAUGGCUCAUUA-CAUCAGUUAUGG-UU-CCUUAGAUCG----------------------------------------------------------------------UACGCAUCCUACUUGGA-UACCUGU-GGCAAUUCCAGAGCUAAUACAUGCUACAGG-UGUCUCCGGCCG-------------------------------------------------------------GGCAACCGGAC--G-GGGUGCCGUUACCAUUCAAAAG--ACCAAAC--------------------------------------------------------------------------GGUCCGCUUCU----GCGGCCGAC------UCAUUUGGUGACUCU--AAGUAACCUCUAG------GCAGAUCGC---ACGGC-AAGC-----------------------ACCG---GCGAGCGCAUCU-AUCA-AAUGUCUGCCUCAUCACACU-G--UGGAUGG-UG-GG--UUAUU-GG------CC-CACCCU-GGUGAUUACGGGUAACGGGGAAU--CAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCUAUGGAAGGCAGCAGGCACGCAAAUUACC--C-ACUCCCGGCA-----CG-GGGA----GGUAGUGACGAAAAAU--------------------AACG-AUG-CGG-G-ACUC--------------AUCCGA-GG-CCC-CGUA-AU--CG---GAAUG-GAUC--------C-ACC-CUAA-A----CAGUU--G-G-GUGA--ACCUAUCGGAGUGCAA-GUC-UGGUGCCAGCAGACGCCGGUAAGUCC--AGCUCCG-AUAGGC-GUAUACUAA-AGUUGCUG-CGGUUAAA---A--------AGCUC-GUAGUUGGAUCUGGGUCUCG---GGCGGUCGGUUCGCCGUCAGCGUGUCAACUGGCCGUACCGGACGUCUUCUCGGUUUCCCCGGUCUGCUCUUCACCGAGUG-------------------------------------------------------------------------------------------------------------------------------------------GACCGGGGGAUUCCGGGACGUUUACUUU-GAACAAAUUAAAGUGCUCAAAGCAGGCU---------------------------------------------AUUCGC--CUGGAUGCUGGUUGCAUGGAAUAAUGGAAC-AGGACCU-CGGU--------------------------------------------------------------------------------------------------------UCUCUCUGUUGGUUUUCGAACCAG----AGGUAAUGA-UUAAAAGGGA--UU--GAC--GGGGGCUUGAGUAUUG-CG-A-GGGGAGA----GG------UGAAAUUC-UAGGAUCCUCG-CAA--GA-CUACCUA--CAGC-GAAAGCA---UUUGCCA-AGAAUGU---CUUCAU-U-AAUCA-A-GAACGAAAGUUAGA-GGUUCGAAGGCGAUUAGAUAC-CGCC-CUAGU-UC-UA-ACCAUA-AACGAUGCCA-UCCAGC--GAUGCGCAA-G--GUU---CAAGAA----------------------------------------------------------------CACCGUGC-GCG-CA------GC-------------------CCCGG-AAACCU--GAGAUUUCGGGU--------UCCGGGGG-GA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACAA-GGC-GUGGGA-CGUG-CGGC-UCAACUUGACUCAACACGGC-AAA-CUUA-CCAGGCCCG-G------ACACCG-CAAGGAUUGA-CA-GA---------UUGAGAGCUCUC-UCG-UGAUU-CGUUGGA-UGGUGGUGCAUGGCCGAU-UUUAGU-UGG-UGGA--GCGA-UUUGUCUGC--UUGAUU-GCGA-UAACGA-ACGAGACUCCU-C-CUAUUAAC-U-AGGCGUCGGGGUAU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GUGUUCCCCCGGCGCAUCAAACCUCU-UCUUAGAG-GGA-C-CGGUU-GU---------------------------------------------------------CGCAA--GCAGCAAGAG--UGGGAGCUAA-AUCAGGU-C-AGUGAUGCCCU-UCGAUGC-CCUGGGCCGCACGCGCGUC-ACACUGAAGGAGACAACGCGUCU--------------------------------------------------------------------------UCC-CCUGC--CGAGA--GGU-A-CG------GG-UAAC-CGC--UGAAC---------------------------------------CUCCUUC--GUGAUA-GGGACCGGGGAUUGC-------------AAUUAUUC-CCCG-CGAACGAGGAAUGCCCAGUAA-GCGC-G-AGUCA-UCAGCUC-GC-GUUGAUCGA---GUC-CCUGCCCUUUGUGCACACCGCCCG-UCGAUGCAUCCGAU--CGAG-UGAUACGGUGAG--GCCUU-UG-GACCGG-----CGCCUGCG----GGGG----------------------UUCCACCUUC-C--GCAGGAACC---G-UCGGGAAGACGGCC-GAACC-UGGUC-ACUUAGAGGAAGCAAAAGUCGUAACAAG-GUUU-GGGUAGG---UGAACCUGCAGAAG-GAUCAUUA
FJ917205.1/5-1982                  ACUCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUAAAAGAUUAAGC-CAUGCACGUGUAAGU------------------------------ACAGACUA--AUUA-------------UAAAUAGA-GAA-ACCGCGAACGGCUCAUUA-AAUCAGUCGAAG-UU-CACUGGACGU---------------------------------------------------------------------UGGCCUCAGGUACUUGGA-UAACUGU-GGUAAUUCUAGAGCUAAUACAUGCAAUCA---AGCUGCUCUCCUCACGCGGGC-----------------------------------------UGGUCCCAUUUUGUGAGGGGU--G-GAGCGCACUUAUUAGAUCAAA---ACCAAUUUCGCCU--------------------------------------------------------------GUACAGCUGAGCUGUCU----GGCAAUG---------UUUUUGAUGACUCU--GGAUAAAUA-GC---------UGAUCGU---AUGGCCAUACGA-------------------GAGCCG---AUGA-UACGUCC-AUCA-AGCGUCUGACCUAUCA-AAU-G--UCGAUGG-UA-AG--CGCUU-UG------CA-UACCAU-GUUCACAACGGGUGACGGGGAAU--CAGG------------------------GUUUGAU-U-CCGGA--GAGGGAGCAUGAGAAACGGCUGCCACAUCCAAGGAAGGCAGCAGGCGCGUAACUUACC--C-ACUCCUAGAU-----CG-GGGA----GGUAGUGACAAGAAAU--------------------AACA-AUA-CGU-G-AAUGCUG-------AAGCUAUUCG-GC--CU-CGUA-AU--UG---GAAUG-AUUAGACACAUUG-AAU-GUAA-A----AACUA--U-A-AUUAGAAUCUAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AAA-GC-GUAUAUGUG-AAUUGUUG-CGGUUAAA---A--------CGCUC-AUAGUCGGAUCUCAGGUAUC---CUUUUUGAGUUGUGCAGCGUGCAAUAACAACGCCGCUGGUAAUGUUUGCGCAUGUUGUACACCUUUAGCGAUCCUAUUAAAGUCGUUUGGCAGUCUCCCUU---------------------------------------------------------------------------------------------------GGUACUAUUUAGUUAGUGCCUUGGGCAUCCCGACGUUCGGUUACCGU-GAACAAAUUGAAGUGUUCAAAGCAGGCUAG-------------------------------------------CAACGC--UUGUACAAUC-GCGCAUGGAAUAACAGAAG-AGGACCU-CGGGUGA---------------------------------------------------------------------------------------------------AAUUUUGUUGGUUUUGAGCAGCCGCG----AGGUAAUGA-UUAAUCAGUC--CA--GAC--GAGGACAUGCGUAUUU-CG-U-GGGUAAA----GG------UGAAAUUU-AGAGAUCCACU-GAG--GA-CGAACUG--AAGC-GAAGGCG---CUUGGCA-CGAACGG---UUCUAU-U-GAUCA-A-GAACGAUGGUCAAG-CUAGUCAAGACGAUCAGAUAC-CGUC-GUAGU--U-CG-ACAGUA-AACAAUGCCA-ACUGGC--CAUUCGGGU-U-AGUU---AGCAUUUGUGUUAGCAUG------------------------------------------UUUUAUCUUUAACCUAUC-GAG-CG------GUC------------------UUCGGGAAACCA--AAGUUUUUGGGU--------UCCGGGGA-UA-G--UAUGG-UUGCAAAA-CUGAAA--U-UU-AAAGG-AAUUGACGG-AAGAGCA---CACCA-GGA-GUGGAG-CCUG-UGGC-UUAAUUUGACUCAACACGGGGAAC-CUCA-CCCGGUCCG-G------ACACUG-GAAGGAUUGA-CA-GA---------CUGAGAGCUCUU-UCU-UGAUU-CAGUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GCGA-UCUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACUCUAGC-CUAUUAAA-U-AGCUCGCUGUUUUUGAUCAACUUAUCACACUU-------------------------------------------------------------------------------------------------------------------------------------------------------CGUGUGUGACGCACAAUGACAGUUUGCAUGAUGCU-UCUUAGAG-GGA-U-AUGUG-GC---------------------------------------------------------GUUUA--GCCUCGCGAA--AUUGAGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-CCGGGGCUGCACAUGCGCU-ACACUGAUAGAAUCAGCGUGAAUA-------------------------------------------------------------------UCAAUGCCC-UCCUC--CGUAA--GGA-G-UG------GG-AAAU-CAA-AUGAAA---------------------------------------CUCUUAC--UUGCCU-GGAAUUGGGGCUUGC-------------AAUUUUUC-CCCA-UGAACAUGGAAUUUCGAGUAA-UCGC-G-UGUCA-UGAGCUC-GC-GUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUAUCGAU--UGAA-CGUUUAAGUGAG--GGCCU-CA-GAUUGG-----CC-GGAAG----CCUGAU------------------UUCAAAUUAGGUAU--UGCC----G---G-AGGAAAAGACGCUC-GAACU-CGAGC-GCUUAGAGAAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAGGGAUCAUUA
AF011463.1/5-1908                  UAUCUGGUUGAUCCUGC---CAGUAUU--AUAUGCUUAUUUCGAAGAUUAAGC-CAUGCAAAUGUGAGA------------------------------UCGGAUCG--GUCGUGCA----AACGACUGACUUU-CAA-UCUGUGUACAGCUCCAUA-UAAGAUUUAUAA-CCGCCGCUGGUUG------------------------------------------------------------------------UGUCAUUUAGAAGGA-UAACGCA-ACCAAAUGUAGCGAUAAUACUUGAGAAAU----------------------------------------------------------------------------------------------AAACGAUAAAGCUCAAAG--------------------------------------------------------------------------------------------------------------------------GAAUCAGCUUUAUCCGCUCA---------GGGUUUC---CUGGGUGUUA-----------------------ACCG---AUGG-UCGAUCA-GGCG-GGUUUAUUACUGAUCA-GUU-A----GACAA-CU-GU--UUCAA-UA------AC-AGUUGU-GACAGUCACCAGUA-CGGGGAAU--UAGU------------------------GUUCGAU-U-CCGGA--GAAGGAGCCUGAGAAACAGCUACUAGUGCCAAGGCAUGCAGCAGGCGCGAAACUUACC--C-AAUGCGAACAU--AUUC-GCGA----GGUAGUGAAAAGAAAUAAGCA---------UCUUUCCUUU-AUU-GGG-A-AAGAG------------UACCGGU-UU--UA-CUGG-UU--UA---CAAUG-GCAA--------C-GCA-UUAG-A----CUUGU--G-U-UGGAGUAACAAUUGGAGGGAAA-GUC-AGGUGCCAGCAGCCGC-GGUAAUACC--UGCUCCA-AUA-GU-GUAUGAUAA-CAUUGCUG-CAGUUAAA---A--------CGUUC-GUAGUCGCCCUAAGGGGUUU---UAGAUUGAAGUCGGUUGAUUUAAUCCUAUUAGUGCUGUUAUUCUAAUAACUCACUAGAAGGUCGAUUUUCGGAGUCCUUUGGGACUUAUUAGAUCUUCCAUAGCGUGCCUUGGGUUUUGUUC---------------------------------------------------------UUAACUUAGGUUUUGAUCAUGCCUAUAGUGUCACGUGAUUUCGAUUUAUUGCCCCGAUUUUAACCUGU-GAGCAAAUUAGUGCGAUCAAAGGAUGAU----------------------------------------------UAGUG--GUGGCUUACU-CUUCACGGAGUGGCUAUUU-GUGAUGC-AACAUACUUUAG-----------------------------------------------------------------------------------------CACAGAACCAGUUGUUCCGGUUGUUCUGCAA----CCGGUAUAG-ACAAUAGAAC-CAG--GAA--CAGGCUUUCGGUAUUU-AC-U-GAUGAGG----GG------UGAAAUCC-GUAUAGUCCGU-AAG--GA-CCCACGG--AGGC-GAAAGCG---GAAAGCU-AGUACUG---AUUCAUAU-GAUGA-G-GAACGAGAGCCAGG-GGAGCAAAGAUGAUUAGAUAC-CGUC-GUAGU-CC-UG-GCUGUA-AACUAUACAA-AUUAGA--GAUUGUAUG-A-AACC---AUAUAACA--------------------------------------------------------------GAUUCUUA-CAG-GA------UCC------------------CCCGAGAAAUCC-UAAAUUUUUGUGU--------UCUUGGGG-GA-G--UAUAU-UCGCAAGA-ACGAAA--C-UU-AAAGG-AAUUGACGG-AAAUUCA-C-CACCA-GGA-GUGGAU-UCUG-CGGC-UUAAUUCGACUCAACGCGUGGAAA-CUUA-CCAGAACCA-G------ACUAUG-GAAAGAUUGA-CA-AG---------CUAAU-GACUUU-UCU-UGAUU-CGUAGAA-UAGUGGUGCAUGGUCGUU-CUCAGU-UCG-UGGA--UUGG-UCUGUCUAC--UUAAUU-GUGA-UAACGA-GCGAGACCUCCGU-UA-UUAAU-U-AGCAACUCUGUAUU-------CCUAUUGC--------------------------------------------------------------------------------------------------------------------------------------------------------------UGGAAUCGGUAUUUGGGUUUUUAACCCAUCU-UCUUAAUA-AGA-C-UCUAC-UCGAUU------------------------------------------------CAAUAAAACA--GAGUAGGGAAGUUGGAGGCCAU-AACAGAU-C-UGUUAUGCCCU-UAUAUAU-UCUGGGCGGCACGCGUAAU-ACAAUGUUUUUGCCAACGAGUUAGGUU-------------------------------------------------------------AAUCGCCGUACC-AAGUU--UGAUA--AGA-C-AA------GG-AAAG-CUU-UUGCAAUC-----------------------------------CUUUAUUUC--AAGGCU-GGGAUUGAAGAUUGU-------------AAG--UUC-UUCA-UGAACCAGGAAUUCCUAGUAA-UCGC-A-AAUCA-ACAUUUU-GC-AAUGAUUAC---GUC-CCUGAGUUUUGUACACACCGCCCG-UCGCUCCUACCAAU--UGAA-UCGGAAGAUGAA--AUUGC-UG-GAUUUU-----CG-UA---------------------------------UUCUA-----------UG----C---G-GAGAGAAAGCACUU-AAAUC-UUUCU-AUUUGUAGGAAGGAGAAGUCGUAACAAG-GUAU-UCGUAGG---UGAACCUGCGGAAG-GAUCAA--
AF011459.1/15-1985                 AACCUGGUUGAUCCUGC---CAGUAUU--AUAUGCUCAAGUCAAGGGCUAAGC-CAUGCACGUCUAAGA------------------------------ACGUAGGC---UU---------------CAGCCAU-CAA-UCUGUGGAAGGCUCAUUA-CACGAGUUAGAA-AC-UCUCUUACCG----------------------------------------------------------------------CGCCAUUCUCAUUGGGA-UAACACU-GCUAAAUGUAGUGAUAAUACCUAAAGUAC----GCAUG--CU---------------------------------------------------------------GCAUC-AGG---C-AUGCACCUGAUGUCCACUGCA---GCGCAGACAC---------------------------------------------------------------------CAUGCGGCGUGAA----UGCAGGACAU----CACCCAGAGAAGCACU--GUCUUCUCAUAG---------GAACCGU------UGAUCAU-----------------------CA-----GCGG-UCGACUA-GUAG-UCUUACUUCUCUAUCA-GCU-U----GGCGG-UU-AG--GUAAG-GA------CA-AAUCGU-GGCAACAACGGAUA-CGGGGAAU--CAGU------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGACAAACGGCUACCACAUCCAAGGACGGCAGCAGGCGCGAAAAUUACC--C-AAUCAUAACAC--CUCA-UGGA----GGUAGCGACAACUAAU--------------------AGCG-ACCUUCU-G-GAUUCUUCUAGAAGGGUACCACCA-UC--CG-GUGG-UU--UG---CAAUG-AGUU--------C-AUC-GUAA-A----UAACU--G-A-GCGAGUAACAAUUGGAGGACAA-GUU-CGGUGCCAGCACCCGC-GGUAAUUCC--GACUCCA-AGA-GU-GUACACCUA-CAUUGCUG-CAGUUAAA---A--------CGCUC-GUAGUCUAUACAAAGACCAA---UCACCAUAGGGCACGUGGCCAGCAGCGCGCAUUUGCCUGCUGAUUUCUGUUUGUGGUGGCGGCCCGUGCGAUCUCAUUCACGCGGUGUGUCUGCGCCA--------------------------------------------------------------------------------------------------------CUGACAGAACGUCGUGCCACUAUGUGWUUAGGCUUUUUCGAUCGU-GAACAAAACAGUGCGAUCAAAGCAGGCACUGU--------------------------------------AAUAUCAGC--UCGAAUGUAC-UAGCAUGAAACCGAAUAAA-UAAGCUG-UUGC-------------------------------------------------------------------------------------------------------------------CCAUAUGCAUCAG----UUGCAUCCA-AUAAUAGGAGGCUG--AUG--UAGGGUACUGGUAUUG-CU-G-GCGCAGA----GG------UGAAAUUC-CGACAUUCUAG-CAA--GA-CCGUCAG--AAGC-GAAAGCUG-ACACAUCU-CUUGCGC---CUCCAU-U-GAUCA-G-GAACGAAAGUUAGG-GGAUCGAAGAUGAUUAGAUAC-CGUC-GUAGU-CC-UA-ACCGUA-AACUAUACCA-CCAGGC--GGUUGGUGG-A-ACAC---AACAGA----------------------------------------------------------------GAUUCUCU-CAG-AU------GCC------------------C-AGGGAAACCA-AAAGGUUUUGGGU--------UCUGGGGG-GA-G--UAUAG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAAGGCA-C-CACCA-GGG-GUGGAG-UCUG-CGGC-UUAAUUCGACUCAACACGGGAAAA-CUCA-CCAAGUCCA-G------AUAGUG-UAAUGAUUGA-CA-GG---------UUAAUAGCCCUU-UCU-UGAUU-CUCUAAU-AGGUGGUGCAUGGCCGUU-CUUAGU-UCG-UGGA--GUGA-UCUGUCUAG--UUAAUU-CUGU-UAACGA-ACGAGACCUUUAC-CA-UUG-A-U-UGAGAAGUUGAUAGCUUGCUUCGGUGAGCACAACUUGUA-----------------------------------------------------------------------------------------------------------------------------------------UAGGUAAUGCGCGGCAUCCUCUGCCACAUACCGCUUCACACG-CUACAAUG-GGA-C-GAUACUGCG-------------------------------------------------------AAUAAA--GCGUAAGGAAGGUAGAGGCAAU-AACAGGU-C-UGUGAUGCUCU-AAUAUGU-CUUGGGCUGCACGCGUACU-ACAAUGGUGUUACCAACAGGUAAGCACUGGUUGUGGCGGCCGGAUCGAC-----------------AUUUACUUGUCGCCGCCGGCCCGGCACAUCCUCC-AACAU--UAYUA-AGAU-G-AA------GG-UAAU-CCC--AAAAG---------------------------------------UGGCAUC--CUGUCU-GGAAUAGAAGACUGU-------------AAC--GUC-AACU-UGAACAAGGAAUCCCCCGUAA-GCGU-G-AGUCA-ACAUCUC-GC-AUUGACUAC---GUC-CCUGCCUUUUGUACACACCGCCCG-UCGCUCCUACCG-U--UGGA-GUUGAAGGUGAG--UCUGG-CG-GAUGGCGCCCAGA-UGAGC---CUACCG--------------------UAUCACGGAAA-G--CUCA----G---CAUCCAGAAACCAGAC-AAAUC-UUUUU-CUCUGUAGGAAGGAGAAGUCGUAACAAG-GUUU-UCGUAGG---UGAACCUGCAGAAG-GAUCAAGC
Z22518.1/1-1837                    UACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCGUUGUCUCGUUGCCUGC-UGUCUAAGU------------------------------ACAAGCCG--AUU----------------CAAGGC-GAA-ACCGCGAAUGGCUCAUUA-AAUCAGCUAUGA-UU-CAUUGGAUCUG--------------------------------------------------------------------UACCCACAUUUACUUGGA-UAACUGU-GGUAAUUCUAGAGCUAAUACAUGCCCAGA---GUCUCUGACC-----------------------------------------------------------------GCA-AGGA--A-GAGCGCUUUUAUUAGUUCAAAA--CCGGUC-----------------------------------------------------------------------------GGGCCUUCG----GGUCCGUCAC---CCUGGUGUGUUGAAUCU--GAAUAACUUUUC--------UCACGCAC------GGUCUCC-----------------------GCGA---GGGC-CGCCUCU-UUCA-AGUGU-UGCCUUAUCA-GCU-U--UCGAUUGUAA-GG--UUACUACG------CC-UUCAAU-GGCUAUUACGGUUA-CGGGUAAU--CAGG------------------------GUUUUAU-U-CCGUU--UUCCCCCCCUUGGGAACGGGUACCACAUCUAAGGAAGGCCGGAGGGACGGCAAUUACC--C-AA-CCCGGCA-----CG-GGGA----GGUAGUGACCGAAAAU--------------------AACG-AUG-CGA-G-ACUC--------------AUCCGA-GC--CU-CGCA-AU--CG---GAAUG-AGUA--------C-ACU-UUAA-A----UGGUU--U-A-ACGAGGAUCCAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGUUG-CGGUUAAA---A--------AGCUC-GUAGUUGGAUUUCAGUUCUG---GACUGACGGUUACCGCCCGGUGAUCACUGUCACGCUCCGAACACUUUGACCAUCCGCUGGCCCACGGGGUGCCCUUUUCC-----------------------------------------------------------------------------------------------------------------------------------------CAAUUUCCCCUGGCCCGGAGAGUUUACUUU-GAAAAAAUUAGAGUUCUCAAAGCAGGCUACA----------------------------------------CUGACGGC--CUGAAUGCCU-AUGCAUGGAAUAAUGGAAU-AGGACCU-CGGUU-------------------------------------------------------------------------------------------------------CUAUUUUGUCGGUUUUCUGAACCC---GAGGUAAUGA-CUAAU-GGAA--CA--GGC--GGGGUCAUUC-UAUU---G-A-CGCUAGA----GG------U-AAAUUC-UUGGACCGUCG-CAA--GA-CGAACUA--CU-C-GAAAUCA---UUUGCCA-AGGAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUAGA-GGUUCGAAG-CGAUCAGAUAC-CGCC-CUAGU-UC-UA-ACCAUA-AACGAUUCUG-ACCA----CAUCCGCCG-G-AGUU---AUUCCCAU--------------------------------------------------------------GAC-CGGC-GGG-GA------GCU------------------UCCGGGAAACCA--AAGUCUUUGGGU--------UCCGGGGG-AA-G--UAUGG-UUGCAAAG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGG----CUG-CGGC-UUAAUUUGACUCAACACGGGGAAC-CUCA-CCAGGCCCA-G------ACACCG-GAAGGAUUGA-CA-GA---------UUGAGAGCUCUU-UCU-UGAUU-CGGUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--ACGA-UUUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACCCUAGC-CUACUAAC-U-AGUCGACGGAUCUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGCAAUUGGUGUCCAGUCGCAGCUUCU-UCUUACAG-GGA-A-ACGGG-CA---------------------------------------------------------AUUCU--AGCCGCACGAG-AUUGAGCAAU-AACAGGC-U-UGUGAUGCCCU-UAGAUGU-UCUGGGC-GCACGCGCGCU-ACACUGAAGGGAUCAACGUGUCC---------------------------------------------------------------------------UC-CCCUC--CGAGA--GGA-G-CG------GG-UAA--CCC-GUGAAA---------------------------------------UCCUUUC--AUGAUA-GGGAUUGGGGUUUGC-------------AAUUGUUCUCCCA-UGAACGAGGAAUUCCCAGUAAGGCGC-A-AGUCA-UGGGAUU-GC-GUUGAUUAC---G---CCUGCCCUUCGUACACAC-GCCCGGUCGCUACUACCGAU--UGAA-UGAUUUAGUGAG--GCUUC-GG-AUUGGC-----GC-UCUUGG--AUGCCUGGCCCGCCU-UCCGGUGGGCUUUUUAGGCGC-C--UCGA----G--CU-GACUAAAGAUGUCC-AAACU-UGAUC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUA
HM004353.1/6-2056                  UACCUGGUUGAUCCUGC---CAGCAGUC-AUACGCUUGCUUCAAGGAUUAAGC-CAUGCAAGUGCU-GA------------------------------GUAAAUGG--UUA-----------------ACAGU-UGA-UCUGCGAACGGCUCAUUA-UACCAGUCGUAA-UC-UGCCCGGAUAAG-----------------------------------------------------------------UGGCUCAGCCAUCGAGUGGA-UACCUCC-ACCAACCGUGAAGCUAAUACAUGGACGACA--GAUUGGUACUCCGUCCAAGCAGCA-----------------------------------AGGGGAAACCUGAGUUGUGGAGUA--U-CGAUGCUACUGGUCGGGAACAG-AAACUAA-----------------------------------------------------------------------------CCCGUUUCA----UCGCGGAG--------UCUUCGUGGAAACA--GACCACUGAGCG---------CAAGGAU-----UCCUUCGA-----------------------GGA----AACC-GUGUCUG-GUUG-AACGACUGACCUAUCA-GCU-U----GACUG-UA-GU--GUAGU-GG------AC-UACAGU-GGCCUUUACGGGUAACAGAGGAU--CAGG------------------------GUUCGAC-U-CUGGA--GAGGGAGCCUGAGAAACGGCUACCAUGUCUAAGGACAGCAGCAGGCGCGCAAAUUGCC--C-AAUGCUAACA-----CGCGCGA----GGCAGCGACGAGAAGU--------------------AUUU-ACU-GCG-UUUACAC------------UUUGUUG-UG--AC-GUAG-AU--AG---AAAUG-GAUG--------G-CAU-CCAA-A----ACCAC--C-A-CUGAGGAUCGAUCGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCG-AGA-GC-GUAUACUGA-UGCUGUUG-CCGUUAAA---A--------CGCUC-GUAGUUCGAUUAGAAGAAGC---UUUGGUUUGUGAGUCAGUGUGUAUCGUCCGCGGUCACAUUCGAUGCAAGCUGUGUGGGUUUCUUCUGCUUUGGUGACUCGUGGUUGAAGUCUCAUUA----------------------------------------------------------------------------------------------------------ACUUGAGAUGGAGAUUGCUACGCGGGUACCAUUGUCGAUACCGA-AAACAAAACAGCGUGUUCAAAGCAGUCU----------------------------------------------AGCGA--CCGAAUGAUU-CAGUUUGGGAUAUCAGAGG-AUGGAGC-GUUCAAGCUAUCUUUGUUGGUUUCUCAGUUUGGAUCGCGGAAUUGAUUGAACGCUUGUCCUGCGUGUCCUAUCUACUUGAGGUGGGUUCAGGCUUUCCAACAUGGUGUUAGGCUCGUAUGGAAACGUUCAGU----CCUUCUGAA-UUAACAGAGG--CG--ACG--GGGACUGUAUCUAUUG-GA-A-GGCGAGG----GG------UGAAAUCC-UUAGACCCUUC-CAA--GA-GAAACGA--CAGC-GAAGGCA---UUCAGUA-AUGGCGC---CUUCAU-U-AAUCA-A-GAACGAGAGUGCAG-GGAUCGAAGAUGAUCAGAUAC-CGUC-GUAGU-CU-GCUACUGUA-AACGAUGCGA-ACUCGG--GACCGGAUU-G-GGUAUUCAUUCACAU--------------------------------------------------------------GACAUUUC-CGG-GA------CCUCACUUC------CUCUCCUUCGGGAAACCAUUAAGUGUCUGCGU--------UCGGGGGG-AA-G--UGCGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AUUUGACGG-GACGACA-C-CACAA-GGC-GUGGAU-GCUG-CGGC-UUAAUUUGACUCAACGCGGGGAAC-CUUA-CCAGGUCAG-G------ACGCGC-GGCGGAUUGA-CA-GA---------UUAAAAGCUCUU-UCU-UGAUU-GCGUGUA-UGGUGGUGCAUGGCCGCU-CCUAGU-UCG-UAGG--GUGA-CCCGUCUGG--UUAACU-CCGA-UAACGA-ACGAGAUCCCGAC-CU-CUCAU-U-GUCUGCAGGAUCGCUUUGUAGGUUCGACCUUGAC---------------------------------------------------------------------------------------------------------------------------------------------------UCUCGAGUCCUUGGGAAGGCUGAGAUGGCUGUAGAAA-AGUCAGAG-GGA-C-GGCGC-AU---------------------------------------------------------GUCGACAAUGCGCGGAAGGGCGGGCCAAU-AGCAGGU-C-UGUGAUGCUCC-UAGAUGU-CCUGGGCUGCACGCGGCAU-ACAAUGAUCGUGGUAACAAGCUUGGUU-------------------------------------------------------------UGUUUGAGCUCC-UUACA--AGACA--UUG-U-UG------GG-GAAC-CUU-UUCAAU---------------------------------------CACGAUC--GUAGUU-GGGAUAGAUGCUUGC-------------AACUAUUU-GCCU-UGAACCAGGAAUGCCUUGUAG-GCGC-A-CUUCA-GCAAGGU-GC-ACCGAAUAC---GUC-CCUGCCGUUUGUACACACCGCCCG-UCGCUGCAACCGAU--UGGU-UGACUAAUAGAA--CGGUUCUG-GAGAGG-----CA-CCGUAU-CAAUCC----------------------UUCUGGAAUG-U--UCGG----A---G-UAUCGAAAUUCUGU-GAUAU-CUGUC-AACUAGAGGAUGCAGAAGUCGUAACAAG-GUUG-CUGUAGG---UGAACCUGCAGAAG-GAUCAA--
AM168070.1/1-1873                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUAAAGGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUAGUCCU---------------------CACGGACGAA-ACUGCAGACGGCUCAUUA-CAACGGUCGCUG-GU-CACAGGACACGCG----------------------------------------------------------------GCGGGGCAACUCGCUGUGGA-UAACCGC-AUUAAAUC-GGGGCUAAUACAUACAAAAC----CGAGUGGAC---------------------------------------------------------------GACUG-GGCA--A-CUGGAAGUUCGCGCGAUGGAUU--AACCCU-----------------------------------------------------------------------------UCGACUGAC----CUCUUGG----------UUUGGUUGGAACC--GAUUCAUGUUGU---------UAGUCGG-----CGC-UUCG-----------------------GCG----CCGA-UUUGUUC-UAGA-CGCGACUGCCCUAUCA-GCU-U----GACGG-CA-AG--GUCUU-GG------CU-UGCCGU-GGCUGUAACGGGUAACGGAGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGACGCCUGAGAAACGGCGUCCACACCUACGGGUGGCAGCAGGCACGUAAAUUUCC--C-AAUGUCAAUA-----CG-AUGA----GGGAGCGACAAUAAAU--------------------ACUUUUAG-UCC-U-GGUC--------------GCAAGA-UC--AG-GACU-CAACAA---GAUUA-AGCA--------C-AAA-GUAA-A----UAAAU--U-A-GCCAGUAU-UAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-ACA-GU-AUAUACUAA-AGUUGUUG-CAGUUAAA---A--------CGUUC-GUAGCUUAAAUACAGGUCUG---UGUAAUUGCUUGUCACGUCGUUCGCGGCGUGACAAGCGCAGGCGCGGUAGAUUGUCAUGUCUAGUCGGCAA--------------------------------------------------------------------------------------------------------------------------------------------------------CGGCUAGGCGCGGCGUUCAACUGU-GCAUAAAUCUUGAUGCUCAAGGUGAGUCCAG-----------------------------------------GCGUGGA--CGGGAAAACA-GUGCAUGGUAUUGUAGAAG-AAGACGU-GGCAA-------------------------------------------------------------------------------------------------------CGUCUAGGUUGGUUGGU--UGUCC----AGGUAAUGA-UUAAUAGGGA--GG--AGC--GGGGGCUGUCGUAUUG-AC-G-GGCGAGA----GG------UGAAAUUC-GUUGACCCUGU-CAA--GA-CGCACAA--CGGC-GGAAGCA---GCAGCCA-AGUGCCU---CUCCAU-U-AGUCA-A-GAACGAUAGUCUAG-GGAUCAAAGACGAUCAGAUAC-CGUC-GUAGU-CU-AG-ACCAUA-AACUAUGUCG-GCUAAC--ACUUGGCGA-C--GUG---CUCUCCGA--------------------------------------------------------------GGCGUCUC-CAG-GA------GUU------------------UGUGGGAAACCA-UAAGCUUUUGGAC--------UCUGGGGG-GA-G--UAUGG-CCGCAAGA-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA---CACCAUGGC-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAC-CUUA-CCAAGCUCA-G------AUAUGU-AUAGGAUUGA-CA-GA---------CUAAUAGAUUUU-UCA-UGAUC-GCAUAAG-UAGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCAGG--UCAAUU-CCGG-UAACGG-ACGAGACCUCCAU-UUGCUAAC-U-AGUCGCGGCGACGGGUUCGACUGGCGAGGGUCGGACGGCGCGGCUGCCUGGUCGAAAGGC------------------------------------------------------------------------------------------------UGGGUAAGUGCGUCGUACGGUUAGUAGCCUGGGCUCGUCUUCGCGGAAUAAAUAAAGUAACU-UCUUAGAA-AUA-C-UUCCG-AC---------------------------------------------------------ACCAA--GCCGGAGGAAGUUGGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUAU-CUUGGGCCGCACGCGUGCU-ACAAUGUAGACGCGAAUAAGCUCU-------------------------------------------------------------------AAAAAUGCG-CGGCG--CGAAA--GCG-U-CG------CG-GAAA-C---AGCAAU---------------------------------------CGUCUAC--GUAACA-GGGACUGACGGUUGC-------------AAU-AACG-AUCA-CGAACGAGGAAUGCCUUGUAG-GCGC-G-AGUCA-UCAUCUC-GC-GCCGAAUCU---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--CGGA-CGGCGAGGUGAA--GACGA-CG-GACUGU-----AU-CCUUC-----------------------------------------A--CGGG----A---C-GCGGAAAGUCGUUU-AAACC-UUGUU-GUCUAGAGGAAGGAGAAGUCGUAACAAG-GUAU-CGGUAGG---UGAACCUGCAGAAG-GAUCAA--
AF484694.1/1-1472                  CACCAGGUUGAUUCUGC---CUGACGU--AUGCGCUUGUCUUGAAGAUUUAGC-CAUGCAAGCUAGCG---------------------------------AAGCCU---------------------UAUGGU-GGA-GCGGCGGACAGCUCAGUA-AUACAGUUAUUA-UU-UACUCGUAGU----------------------------------------------------------------------------AUGUAUACGGA-UAACCAU-GGUAAG-CUAUGGCUAAUACGUGAACAG-----------------------------------------------------------------------------------------------GUUAUUGC------------AUA------------------------------------------------------------------------------------------------------------------GAUGAAACA----GCGAUAACUG---------AGAGAGC-------------------------------------------AAUC-GACUACG-ACUA-AGUUUCUGGCCUAUCA-GCU-A----GAUGG-UA-AG--GUAAU-GG------CU-UACCAU-GGCUAUAACGGGUAACGGGAAAU--CAGU------------------------GUUUGAU-U-CCGGA--GAGGGAGCCUGAGAAAUAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACC--C-AAUUCCUUAG----CGG-GAGA----GGUAGUGAAGAGACAU--------------------GAAG-U----------------------------UCU----------------A--CU---UAGAG-ACUG--------U-ACG-GUAA-A----AUAGU--A-C-AGGA---UCUACUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-GUA-GC-GCAUAUAAU-AGUUGCUG-CAGUUAAA---A--------CGUCC-GUAGUUGAUCACAAGGUAUU---CUUCUGCAUAGUAUUUGUGGAGUGUAUCU-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAUACUGU-GAGAAAAAUAUGGUUCUCAAAGCGGAUU-------------------------------------------------AC--GUGAGUAAUU-UAGCAUGGGACAUGGUGAA-U------------------------------------------------------------------------------------------------------------------------------------------------------------AUAGGAA--CA--GAU--GAUGGCAAUAGUAUUC-AG-C-AGUUAGA----GG------UGAAAAUC-GUUGACCUGCU-GAG--GA-CUCUCUG--AAGC-GAAAGCG---AUUGUCA-AGUAUGU---CUCCGU-U-AAUAA-A-GGACUUAAGCUGGA-GUAUCGAAGAUGAUUAGAUAC-CGUC-GUAGU-UC-CA-GCUGUA-AACUAUGCCG-ACUAGG--UGAGGCC----------------GUCA--------------------------------------------------------------------GG-CUG-CG------CCU------------------UAGGAGAAAUCA--AAGUUUUUGGGC--------UCUGGGGA-UA-G--UAUGG-AUGCAAAU-CUGAAA--C-UU-AAAGA-AAUUGACGG-AAGGACA-C-CACAA-GGA-GUGGAU-UGUG-CGGC-UUAAUUUGACUCAACGCGGGGCAA-CUUA-CCAGGGCCG-A------AUGCAU-AGGAGAUCGG-CU-GU---------CUGAGAGGGUAC-CCG-AGAUU-AUGCAGG-AGGUGGUGCAUGGCCGUU-UUCAAC-ACG-UGGG--GUGG-CCUGUCUGG--UUAAUU-CCGU-AAACGC-GUGAGGCCUGGGA-AG-CAAUU-C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUGCU-UGA-C-GGAUA-GC---------------------------------------------------------GGCAA--GCUAUAGGAA--GACAGGCUAU-AACAGGU-C-AGUGAUGCCCC-UAGAUGU-UCUGGGCUGCACGCGCAAU-ACAAUGGUAUAGU----GAGACU----------------------------------------------------------------------------A-UGUAC--UGAAA--AGU-A-UG--------------CUU---UAAG---------------------------------------CUAUAUC--GAAUCU-GGGAUAAGCUCUUGU-------------AAA--UGA-GUUU-UGAACGAGGAAUUCCUAGUAA-UCGC-A-GGUCA-UAAUGCU-GC-GAUGAAUGC---GUC-CCUGUUCUUUGUACACACCGCCCG-UCACUAUCUUAGAU---GGA-UGUAUCGGUGAA--AUGGC-UG-GAC----------------------------------------------GAAA---------------------------GAAAGGCAGUU-GAACC-UAUAC-AAUUAGAUAAGAUAUAAGUCGUAACAAG-GCUG-CUAUAGG---UGAACCUGUGGCAG-GAUCAUUA
EF526713.1/1-1709                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUAUAAGU------------------------------AUAAAUUU--GUU----------------UAUGGU-GAA-ACUGCGAAUGGCUCAUUA-CAACGGUUAUAG-UU-UACUUGAGAU---------------------------------------------------------------------------AUAACUACUGGA-UACCCGU-AGUAACUCUAGAGCUAAUACAUUUAUCGG----GACAUCA-----------------------------------------------------------------------------G-UCUCGUGUUUAUUAGAUUUCA---CCGAAC-------------------------------------------------------------------------------AGAUUU-----UCUGU---------------UGGGGAGUCA--UGAUAAAUUAAC---------GAAUCGU----------GUA------------------------------UCGA-UGCUUCA-AACA-AGUUUCCGUCCCAUCA-GCC-A---UGAUGG-UU-GC--GUAUU-GG------AC-UACCAU-GGCAGUUACGGGUAACGAGGAAU--UGGG------------------------GUUCGAU-U-UCGGA--GAGGGAGUCUGAGAAACGGCUACCACAUCUACGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUGUAAAUA----UGU-AUGA----GGUAGUGACAAGAAAU--------------------AUCA-AAG-UAA-C-C-----------------UUCG----G--GC-UACU-AU--UG---AAAUG-GGUA--------A-AAU-UUAA-A----CAAUU--U-U-ACGAGGAGCAACUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGCAACACC--AGCUCCA-GUA-GC-GUAUAUUAA-AGUUGUUG-CAGUUGAA---A--------CGCUC-GUAGUCUGAUUCAAUCCGCA---AGGAAAUAAUCGCUCGCCUCGAAAUACAGUGCAGUCAUCCGUCUGGGAAUAUCCUCCCCCCCCUACCACCG------------------------------------------------------------------------------------------------------------------------------------------------------GGUGGGGGUUCCGGGGUUUUUCCCCU-GAAAAAUUUAG--GGUUUCAGGCAGGCA------------------------------------------------AAC--CUUAAAACUC-CGCCAUGGAAGAAGAGGAA-AAAACUU-AGCU--------------------------------------------------------------------------------------------------------------GUUUGGGGGCUUGAAAAG----AAAAAAUUU-UUUAG-GGAC--CA--GUC--GAAGGCCAUUUUACUUUAA-U-CGAAAAG----AG------UGGAAUUU-UUGGGCCGGUUUAAU--GCCAAACCAA--AAGCGGAAGGCU--UCUGCCCA-AGGAUGU---UUUCUU-U-GAUCA-A-GAACGAAGGUCAAG-GUAUCGAAGACGAUCAGAUAC-CGUC-GUAGU-CC-UG-ACUGUA-AACUAUGCCG-ACUGGG--GUUCAAUGA-U-AAGA---AAUAAGAU-----------------------------------------------------------------AUCGU-UGGGGA------UCC------------------AGAGAGAAAUCA--AAGUUUUUGGGU--------UCUGGGGGAAA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-GAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGC-GUGGAG-CUUG-CGGC-UUAAUUUGACUCAACGCGGGGAAA-CUUA-CCAGGUCAA-A------ACAUGC-GAAGGAUUGA-CA-GG---------CUGAUAGUCCUU-UCU-CGAUU-GCAUGGC-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--CUGA-UUUGUCUGG--UUAAUU-CCGG-UAACGA-ACGAGACCUUGGC-CUGCUAAC-U-AGAUAGUGUACUUC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGUGCACUAAGCU-UCUUAGAG-GGA-C-AAUGG-UG---------------------------------------------------------G-UUA--CAUCACUGAAGCUCAAGGUAAU-AACAGGU-C-UGUUAUGCCCU-UAGAUGU-CCUGGGCCGCACGCGUGCU-ACACUGACACACUCAGCAAGC----------------------------------------------------------------------------CAC-UUGGU--CGGCA--GAU-C-AA------GU-AAAU-C---AUCAAA---------------------------------------GUGUGUC--UUGUUA-GGGACAGUUCCUUGU-------------AAUUGUGG-AGCU-CUAACAAGGAAUGCCUAGUAA-GUGC-A-AGUCA-ACAUCUU-GU-GCUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAUUUCGAG-UGAUUAGGUGAGCCUUCCU-CG-AACC---------------------------------------------GCAA--------------------------GGAAAGAGAAAC-AAAUC-UAACU-ACUUAGAGGAAGGAGAAGUCGUAACAAG-GUUU-CUGUAGG---UGAACCUGCAGAAG-GAUCAA--
DQ520952.1/1-1748                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUAAGCUU---UU---------------AUACGGC-GAA-ACUGCGAAUGGCUCAUUA-AAACAGUUAUAG-UU-UACUUGAUUU------------------------------------------------------------------------UCAAACCCCCAUGGA-UAACCGU-GGUAAUUCUAGAGCUAAUACAUGCGAAAA----AACAAAUCU----------------------------------------------------------------UGCG-GGCU--C-UGUUGUAUUUAUUAGAUAACUA--ACCAAU-----------------------------------------------------------------------------GA-----GC-----------------------UUGGUGAUUCA--UAA---ACUAUC---------UUCUC-----------UCAU------------------------------CCGA-CAUAUCA-UUCA-CCUAAAUGACCUAUCA-GCUCU--UUGCAGG-AA-ACCUUUUUA-GGGGUUUGGC-CUUCCGUGGCUAUGACGGGUAACGGGGAAU--UAGG------------------------GUUCGAA-A-GUUGA--GAGGGUUCCAAAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUCCCG--G-UAUCCUUUCC-----AA-GGGG----AAAUGUGACUUAAAAU--------------------AACU--UA-CCA-G-GGCU---------------UAACA-CU--CU-UGUA-AU--UG---GAAUG-AGUG--------A-AGU-AUAA-A----CCCCU--U-U-ACGAGUAUCAAUUGGAGGGCAA-GUC-UUUACAGAGCAGUUCA-GGUAAU-GG--AGAUCCC-UUG-GAGGUAUAAAGA-AGUUGUGG-AUAUUAAA---A--------AGCUC-GUAGUUGGAUUUCUGUUGUA---UAAUCUAUAAUAUUACUAAGGUAUAUAUUAUAUUAAUAUCCUCCCCUAGGUUAUAGGACUAAAUAAUUCCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------AAACUUUACUUU-GAGAAAAUUAGAGUGCUUAAAGCAGGCA---------------------------------------------ACUGCC--UUGAAUACUC-CAGCAUGGAAUAAUAAGUA-AGGACUU-UUGU---------------------------------------------------------------------------------------------------------CUUUCUUAUUGGUUCUAGGACAA----AAGUAAUGG-UUAAUAGGGA--CA--GUU--GGGGGCAUU----UUG-GA-C-CAGCAGGCUAUGG------UGAUAUCC-UUAGCCUAUUU-AAA--GU-UUUUCUA--CCCC-GAAAGCA---UUUGCCA-AGGAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUAGG-GGAUCGAAGACGAUCAGACCU-GGUC-GUAGG-GC-AG-AGCAUA-AUCUAUGCAA-UAGAGA--GAAAGGAGG-U-UGUA---ACU-------------------------------------------------------------------UACUCCUU-CAG-CA------CCU------------------UAUGAGAAAUCA--AAGUCUUUGGGU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUUUAA--C-UU-AAAUU-AAUUGACG--AAGGGCA-CGCACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGAUUCACACCGUUAAAA-CUCA-CCCCGCCCA-G------ACUUAG-GAAGGAAUGA-CA-GA---------UUGAUAGCUCAA-CCU-UGAUU-UUAUGGG-UGGAAGUGCAUGGUAUAU-CUUAGA-AGG-UGGA--GUGA-AUUGUCUGG--UUAAUU-CCGU-UAACGA-ACGUUUCAUUAAC-UCACUAAA-U-AAAUAAUAGAAAAAU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUUUUUCACUAGGAUCU-GGCUAGAG-GUA-C-UGUGC-GU---------------------------------------------------------GUGUA--ACGCGAUUAAGUUUGAUUCAAU-AACUUCU-C-UGUGAUGGACU-UAGAUGA-CCUGGGCUCUACGCGCGUU-CCACUGAUUUCGCCAACGAGAGU------------------------------------------------------------------------ACGUC-AGGCU--UCGAA-UUAG-U-GG------GU-AAUU-CAU-AUGAUU---------------------------------------AUGCAUC--GUUAUG-GGGAUAUUACAUUGU-------------AAUUAUUG-AUCU-UUAACGAGGAAUUCCUAGUAA-GCGC-A-AGUCA-UCAGCUU-GC-GCUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGAG-UGAUUCGGUGAA--UAAUU-CG-GACCAU-----GC-UACG-----AGUA----------------------GCAAAUA-------CAUA----G---C-AAGGAAAGUUUCGU-AAAUU-AUAUC-ACUAGACCGAAGCCCUUGUCGUUUCAAG-GUUU-UCGUAGG---UGAACCUGCAGAA--CCUAAAUA
DQ812526.1/5960-7454               UAUCUGGUUGACCCUGC---CAGGAUA--GCAUACUUCUCUUAAAGAUUAAGC-CAUGCAUGCCUAUGUGUAGA--------------------CAGUUAUAUUCAU-UAUU---------------GUGGAGC-GAAGACGGCGAACAGCUCAUU--UAUCAGUGGU-U-AG-UACAUGCAAU--------------------------------------------------------------------------GUAUUUCGUUGGA-UAGUAAC-GGAAAAUCUGUUAGUAAUACAUGAACUA-----------------------------------------------------------------------------------------------UGUUUAGU-------------------------------------------------------------------------------------------------------------------------------------AUUCU----ACUAAAGAUA---------AUAGUAA-------------------------------------------GUAC-GUUUGCA-UAUC-UGCCACUGCAGCAUCA-UCU-U--ACGUUGG-UG-GG--GUAUU-UG------CC-UACCAA-GGAUUCGACGCUUA-CGGGGAAU--UAGG------------------------GUUUGAC-U-CCGGA--GAAUGAGCAUGAGAAACAGCUCAUACAUCUAAGGAAGGCAGCAGGCGCGGAAAUUGCC--C-AAUGUAUUCG-----UU-ACGA----GGCAGUGACAAGAAAU--------------------GAAG-GGU-AC----------------------UUUU----------GUAC-AC--CA---UCUAG-GGCC--------U-GUU-AUAU-C----UAAGC--U-A-ACCGGU---UAUUCGUGGGAAA-GCU-CGGUGCCAGCAGCCGC-GGUAAUUCC--GACACGG-AGA-GU-AUUCUAUUG-UGUUGCUG-CAGUUAAA---A--------AGUUC-GUAGUUUAUUUUCUUU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUCACUAU-AAGUAAAUCUAAGUGUUUAUAACUACUUAA-------------------------------------------CUGUUU---------UUA-UAGUAUGAAAUUAUAAUGC-G---------------------------------------------------------------------------------------------------------------------------------------------------------------GUAU--UU--GGC--GUAGUUUGGGGUACUC-GA-U-AGGGACA----GG------UGAAAUAG-GAUGAUCUAUC-GAA--GA-CCAACGG--UAGC-GGAGGCU---CCCAACGCAGUCUAA---GUAUCA-C-GAUCA-A-GAACUAAAGUCAGG-GGAUAGACGACGAUUAGAAAC-CGUU-UUAUU-CC-UG-ACCCUA-AACGAUGUCG-CCUAGC--UGAUGGGGU-U--------------UU-----------------------------------------------------------------UACUU-CAU-UU------GC-------------------CAAGAGAAAUCG-UAAGGUUUCAGAC--------UCUGGGGG-AA-G--UAUGA-UCGCAAGG-UUGAAA--C-UU-GAAGG-GAUUGACGG-AGAGGUA-C-CACCA-GAC-GUGGAG-UCUG-CGGC-UCAAUUUGACUCAACACGCA-AAU-CUUA-CUAGGCCCA-G------AAGCUU-UGAGGAUUGA-CA-GA----------UGAGUGAUCUU-UCA-UGAUU-AAGUUGU-UGGUGGUGCAUGGCCGUU-CUUAGU-CCG-UGAU--UUAA-AUUGUCUGC--UUUAUU-GCGA-UAACGA-ACGAGACCUCUAU-CAGAUUAA-U------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAUCUG-AGA-C-UGCUA-GU---------------------------------------------------------GAUGA--ACUAGAGGAAGGCAGAGGCAAA-AACAGGU-C-UGUGAUGCCCU-UAGAAGC-CCUAGGCCGCACGCGUACU-ACAAUGGCAGGUUCAUCGUGU----------------------------------------------------------------------------UGC-UUCCC--UGAAA--AUG-G-UG------GC-AGUU-CAU---UAAA---------------------------------------ACUUGUC--GUGGUU-AGGCUUGAAGGUUGA-------------AAUUAUCC-UUCA-UAAAUGAGGAAUGUCUAGUAA-GUGU-A-GGUUA-UGAAUCU-AC-GCUGAUUAC---GUC-CCUACCCCUUGUACACACCGCCCG-UCGCUCCUACUGAU-UGGGA-AGAUCUGGUGAG--UUAUU-CG-GACCUA-----CA-UUUCG--------------------------------UAU------C--GUUA----U---G-UAGCAAC-AAUUGC-GAGCC-CGCUC-UUCUAGAGGAAGGAGAAGUCGUAACAAG-GCUG-CUGUAGG---GGAACCUGCAGCAG-GAUCAUUA
ACSY01002401.1/4267-2174           UAACUGGUCGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUGAAUAG--UAUUC----------UUGAUACUGU-GAA-ACUGCGAAUGGCUCAUUA-AAUCAGUUAUAG-UU-UAUUUGAUAGUUUGCAACUCG-----------------------------------------------UUUUUCGGAGCGGUGUUGUGCUAGACGGA-UAGCCGU-GGUAAUUCUAGAGCUAAUACGUGCGACAA----GGCCCGAGAGAGAGGUGUGU----------------------------------------GUAUGCACAUUUUUCCUUUCGA--G-GGCUGCAUUUGUUAGGUAUAAA--GCCAGC-----------------------------------------------------------------------------AGG----------AACAUG------------ACUGGUGAAUCA--GAAUAACUUUGC---------UGACCGU----CACACUUUUG--------------------UGUGUG---AUGG-UGUCUCA-UUCG-AAUUUCUGCCCUAUCA-ACU-U--UCGAUGG-UA-AG--GUAUU-GG------CU-UACCAU-GGUGACAACGGGUGACGGGGAAC-AUUUG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAGACGGCUACCACUUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUCCUGACA-----CA-GGGA----GGUAGUGACAAUAAAU--------------------ACCA-AUG-CAC-G-GUGUU------------UUUAUGC-AC--UG-UGCA-AU--UG---GAAUG-AGAA--------C-AAU-GUAA-A----GACCU--U-A-UCAAGGAACAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AAA-GC-GUAUACUAA-AGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUUGGAUUUCAUGCGGG---GUUCAGCGGUGUGUGGUGGGGGAGAGACACUGUUUCGCCCUUGCCCCGCACUGUUUGCACUCUGCAGUUUUAAUAUUCCCUGGUGGCGCCUUUGGCGCGUGCCCUUG--------------------------------------------------------------------------------------AUUGGGUGUGUGUCAAGUCACGUAGUGGUGGGGCGCUGUUGGGGGCUUUACUUU-GAAAAAAUUAGAGUGUUCAAAGCAGGCAGUCAU-------------------------------------UUGAUUUGC--UUGAAUAGAU-UAGCAUGGAACAACGGAAG-AGGACUU-UUGGGCCUGUACUGUUGGCGUGUGGUGCGGGGUGU-------------------------------------------GUGGAGUGAGAAACCGCAAGGUUCUCUUGUUCCUCCCUCACCACAUCGGGUCUG----AAGUAAUGA-UUAAUAGGGA--CG--GUU--GGGGGCACUGGUAUUU-CG-U-UGUCAGA----GG------UGAAAUUC-UUGGAUUUACG-AAA--GA-CCGCCGA--CUGC-GAAAGCA---UUUGCCA-AGGACGC---UUUCAU-U-GAUCA-A-GAACGAAAGUUAGG-GGAUCGAAGACGAUUAGAUAC-CGUC-GUAGU-CU-UA-ACCAUA-AACGAUGCCG-GCCAGG--GCUCGGUGGGC-AGCA---CAAACUUUUAUCA---------------------------------------------------AGUGGUGGCGCCAU-CGG-GA------CCU------------------UUAGGGAAACCA--AAGCGUUUGGGU--------UCCGGGGG-GA-G--UAUGA-UCGCAAGA-UUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGAAA-CUCA-CCAGGUCCA-G------ACAUGG-GAAGGAUUGA-CA-GA---------UUGACAGCUCUU-UCU-UGAUU-CCAAGGG-AGGUGGUGCAUGGCCGUC-C--AGC-UUU-UGUU--GUGA-AAUCUCUGU--UUGAUU-ACGG-UAAACG-GCGAGACCUUGAC-UUGCUGAU-U-GGUGUGCGCCUGCGUUAGCAGGCGUUGGA--------------------------------------------------------------------------------------------------------------------------------------------------------------GAUUACGCGCAAGCGUGUCUCUCAUCACACC-ACUCAGAG-GGA-C-ACUCG-GCGUUGCU---------------------------------------------AUUGAGCGUAA--GCCGAAGGAAGUUUGAGGCGAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCUGCACGCGCGCU-ACACUGACGGGGGCAGCGAGUAUGCUUUGGGUGUUUGUGGUGGGGAAA-------------------GUCUUGUGCUUUUCUACGACAGACAUCUAUUCC-UGCGC--UGGAA--GGC-G-UG------GG-GACU-CUU-GUGAAA---------------------------------------ACCCGUC--GUGCUG-GGGAUAGAUGCUUGC-------------AAUUAUUC-AUCU-UGAACGAGGAAUUCCUAGUAA-GCGC-A-AUUCA-ACAGAUU-GC-GUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAA-UGGUUUAGUGAG--GCCUC-GG-GAUUGG-----CG-CGUGG---GCGCUGGCAA------------CAGCUGCCCAUGUGU-U--UCUU----U---G-CUGAGAACCUGGUC-AAACU-UGAUC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUUC
CP000881.1/7352-5480               UACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUUAAGGAUUAAGC-CAUGCAUGUCUCAGU------------------------------AUAAACGA-UUUU---------------AUACGGU-GAA-ACUGCGAAUGGCUCAUUA-CAACAGUUAUAG-UU-UAUUUGAUCG-----------------------------------------------------------------------UGCGGUACUACGUGGA-UAACCGU-AGGAAUUCUAGAGCUAAUACAUGCCCCAU----CGCUUUCGAAGUUUUUUAAUUUUUUUUCUUU-------------------UUUAAAAGGAAAAAAAAAAAGAAAAAAUUAGA--A-AGUGGGAUUUAUUAGAUCAAA---AACCAA-----------------------------------------------------------------------------UCGCUUUAG----AGCGUG-----------GCGGGAUGAAUCA--UAAUAACUUUCC---------GAAUCGC---AAGGCUAUAAAU------------------UGAGCCG---GCGA-UAUAUCA-UUCA-AAUUUCUGCCCUAUCA-ACU-U--UCGAUGG-UA-GG--GUAGU-GG------CC-UACCAU-GGUGUUGACGGGUGACGGAGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUCCUGACU-----AA-GGGA----GGUAGCGACAAGAAAU--------------------AACG-AUA-AAA-G-GCCU--------------UUUCAG-GU--CU-GUUU-AU--UG---GAAUG-AGGA--------U-AAU-UUAC-A----CCCCU--U-C-UCGAGUAUCCAUUGGAGGGCAA-GCC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GU-GUAUAUUAA-AGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUCGAAUGUAGAGUCUC--AAACGCUGAGAUGUCUUUUUUUAUUAGGAGACAAUUUUUUUUGGCGUUUUAGAUUCUUUUUUACCGAUUACUAUUUGUUUUUAAUUA---------------------------------------------------------------------------------------------------------------------------------AACAAAUUUGGUAUAUCGGUAAUUUUUACUGU-GAAUAAAUUAGAGUGUUCAUGGCAGGCC---------------------------------------------AAGGGC--UUAAAUAUCU-CAGCAUGGAAUAAUAGAAU-AGGACUUCUGGUU-------------------------------------------------------------------------------------------------------CUAUUUUGUUGGUUUUUGGAGCCG----AAGUAAUGA-UUAAUAGGAA--UA--GUU--GGGGGCACUCGUACUC-CG-U-UGUCAGA----GG------UGAAAUUC-UUGGAUUUACG-GAA--GA-CGAACAA--CUGC-GAAAGCA---UCUGCCA-AGGAUGU---UUUCAU-U-GAUCA-A-GAACGAAAGUUAGG-GGAUCGAAGACGAUUAGAUAC-CGUC-GUAGU-CU-UA-ACCAUA-AACUAUGCCG-ACUGGG--GAUUGGUAG-A-UGUA---UCAAUUAC--------------------------------------------------------------GACUCUAU-CAG-CA------CCC------------------UAUGAGAAAUCA--AAGUCUCUGGGU--------UCUGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGC-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUUA-CCAGGUCCG-G------ACAUAG-GAAGGAUUGA-CA-GA---------UUGAGAGCUCUU-UCU-UGAUU-CUAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUAAUU-CCGU-UAACGA-ACGAGACCUUAAC-UUGCUAAU-U-AGUUACCUGGGCGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAACGUCCAAGGAAAAAAAUU-UCUUAGCA-GGA-C-GAUCC-GU---------------------------------------------------------GAUUA--GCGGAUGGAGGUGUGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGCGCU-ACAAUGAUGCAAUCAACGAGUGC-----------------------------------------------------------------------UGUACC-UUAAC--CGAAA--GGU-U-UG------GG-AAAA-CUU--GCAAA---------------------------------------UUGCAUC--GUGUUA-GGGAUAGAUGAUUGC-------------AAUUAUUC-AUCU-UGAACGAGGAAUGCCUUGUAA-GCGU-G-AGUCA-UCAACUC-GC-GCUGAAUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGGA-UGGUCCGGUGAA--AUGUU-CG-GAUUUA-----AA-CAUUU----UCGC----------------------GGGU-GCGAAUU--UAUG----U---U-UUAAAAAGUUCAUU-AAGCC-UUACC-AUCUAGAGGAAGGAGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAUAA
AJ278035.1/3-1807                  UAUCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUAAGCGA--CUU---------------GUACUGU-GAA-ACUGCGAAUGGCUCAUUA-AAUCAGUUAUGG-UU-UCUUUGAUGG-----------------------------------------------------------------------UACCUUGCUACUUGGA-UACCCGU-AGUAAUUCUAGAGCUAAUACAUGCAGGAA----UGCCCGACU------------------------------------------------------------------UC-GGAA--G-GGCUGUAUUUAUUAGAUAAGAA--ACCUUC-----------------------------------------------------------------------------UCGGGUUCG----CCCGGUU----------GUGUGCUGAGUCA--UAAUAACUGCUC---------GAAUCGC---ACGGCUCUAC-----------------------GCCG---GCGA-UGGUUCA-UUCA-AAUUUCUGCCCUAUCA-GCU-U--UCGAUGG-UA-GG--AUAGA-GG------CC-UACCAU-GGCGUUAACGGGUAACGGAGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAGAUGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUGCC--CGAAUCCUGACA-----CA-GGGA----GGUAGUGACAAGAAAU--------------------AACA-AUA-CAG-G-GCUA--------------CUUCUA-GU--CU-UGUA-AU--UG---GAAUG-AGUA--------C-AAC-UUAC-A----UCUCU--U-C-ACGAGGAUCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AAA-GC-GUAUAUUAA-AGUUGUUG-CAGUUAAA---A--------CGCUC-GUAGUCGGGUUUCGGGUCGG---GCCGAGCGGUCUGCCGAUGGGUAUGCACUGUUUGGCGCGGCCUUCUUUCCGGAGACCGCGGCUACUCUUAACUGAGCGGG-----------------------------------------------------------------------------------------------------------------------------------------------CGUGGGAGACGGAUCGUUUACUUU-GAAAAAAUCAGAGUGUUUCAAGCAGGCAGC-------------------------------------------UCGCUC--UUGCAUGGUA-CAGCAUGGGAUGAUUGAAU-AGGACUC-CGGUG-------------------------------------------------------------------------------------------------------CUAUUUUGUGGGUUUCGAACACCA---GGAGUAAUGA-UUAACAGGGA--CA--GUC--AGGGGCACUCGUAUUC-CG-U-CGAGAGA----GG------UGAAAUUC-UCAGACCAAUG-GAA--GA-CGAACCA--CUGC-GAAAGCA---UUUGCCA-GGGAUGU---UUUCAC-U-GAUCA-A-GAACGAAAGUUAGG-GGAUCGAAGACGAUCAGAUAC-CGUC-GUAGU-CU-UA-ACCAUA-AACCAUGCCG-ACUAGG--GAUUGGAGG-G-UGUU---CGUUUC----------------------------------------------------------------GACCUCUU-CAG-CA------CCU------------------UACGGGAAACUA--AAGUCUUUGGGU--------UCCGGGGG-GA-G--UAUGG-UCACAAGG-CUGAAA--C-UU-AAAGG-AAUUAACGA-AAGGGUC-C-CCCAA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGAAA-CUUA-CCAGGUCCA-G------ACAUUG-UUAGGAUUGA-CA-GA---------UUGAGAGCUCUU-UCU-UGAUU-CGAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUAAUU-CCGA-UAACGA-ACGAGACCGUAGC-CUGCUAAA-U-AGUCCCGCGAACUU-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUGUUGGCGGCCGACU-UCUUAGAG-GGA-C-AACUU-GU---------------------------------------------------------GACCA--ACAAGUGGAAGUUUGCGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGCGCU-ACACUGAAGCACUCAACGAGUCC--------------------------------------------------------------------------ACC-UCGAC--CGACA--GGU-C-UG------GG-AAAC-CUU-UUGAAA---------------------------------------UUGCUUC--GUGAUG-GGGAUAGAUUAUUGC-------------AACUAUUA-AUCU-UCAACGAGGAAUUCCUAGUAA-GCGC-A-UGUCA-UCAGCGU-GC-GUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUCCUACCGAU--UGAA-UGAUCCGGUGAG--GCCCC-CG-GACUGG-----GG-CGACG---CAUUCG-------------------GUUCGCCGGACG-C--GACG----C---U-CCGGGAAGCUGUCC-AAACC-UUAUU-AUUUAGAGGAAGGAGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAAG-GAUCAAGC
AF070445.1/1-1802                  AACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUAAACAA-UUCU---------------AUACUGU-GAA-ACUGCCAAUGGCUCAUUA-AAUCAGUUAUAG-UU-UAUUUGAUAA----------------------------------------------------------------------UACCUACACUACUUGGA-UAACCGU-GGUAAUUCUAGAGCUAAUACAUGCACAAA----AGCCCGACU-----------------------------------------------------------------UCU-GGAA--G-GGCUGUAUUUAUUAGAUACAAA--ACCAAU-----------------------------------------------------------------------------GCGGGGCAA----CCCGGUU----------CUUUGGUGAUUCA--UAAUAACUUCGC---------GAAUCGC---AUGGCCUUGU-----------------------GCCG---GCGA-UGAUUCA-UUCA-AAUUUCUGCCCUAUCA-ACU-U--UCGAUGG-UA-AG--GUAUU-GG------CU-UACCAU-GGUUACAACGGGUAACGGAGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACUUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUCCUGACA-----CA-GGGA----GGUGGUGACAAAAAAU--------------------AACA-AUG-CAG-G-ACUU--------------UUCGAA-GC--CU-UGCA-AU--UG---GAAUG-AGAA--------C-AAU-CUAA-A----CCCCU--U-A-UCGAGUAUCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUUGGAUUUUGGA--UU---GCGUCUAACGGUCGGCCGUGAGGUUCGUACUGUUGGGUGCUUUCUUCUUCUCGAAGACCACGUGUGCCCUUAACUGAGUG---------------------------------------------------------------------------------------------------------------------------------------------UGCGUGGGGUUCGGGACUUUUACUGU-GAG-AAAUUAGAGUGUUCAAAGCAGGCA----------------------------------------------UUUGC--UUGAAUAUUG-CAGCAUGGAAUAAUGGAAU-AGGAUCA-CGAUC-------------------------------------------------------------------------------------------------------UUAUUUUGUUGGUUUCUAGGAUCG----AGAUAAUGA-UUAAUAGGGA--UA--GUG----GGGCAUUAAUAUUU-AA-U-UGUCAGA----GG------UGAAAUUC-UUGGAUUUAUG-AAA--GA-UUAACUU--CUGC-GAAAGCA---UUUGCCA-AGGAUGU---UUUCGU-U-AAUCA-A-GAACAAAAGUUAGG-GGAUCGAAGACGAUCAGAUAC-CGUC-GUAGU-CU-UA-ACCAUA-AACUAUGCCG-ACUAGG--GAUUGGCGG-G-CGAU---UAUUAUAU--------------------------------------------------------------GUCCCCGU-CAG-CA------CCU------------------UAUGAGAAAUCA--AAGUUUUUGGGU--------UCCGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUCA-CCAGGUCCG-G------ACAUAG-UAAGGAUUGA-CA-GA---------UUGAGAGCUCUU-UCU-UGAUU-CUAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUAAUU-CCGU-UAACGA-ACGAGACCUUAAC-CUACUAAA-U-AGUUACGUCAUUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGAAUGACGGCGAACU-UCUUAGAG-GGA-C-UAUCG-GA---------------------------------------------------------UUCAA--AACGAUGGAAGUUUGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGCGCU-ACACUGACGAAGUCAGCGAGUAU------------------------------------------------------------------------CUCCC-UUCAC--CGGAA--GGU-G-UG------GG-UAAU-CUU-GUGAAA---------------------------------------CUUCGUC--GUGAUG-GGGAUAGAUCAUUGC-------------AAUUAUUG-AUCU-UCAACGAGGAAUUCCUAGUAA-GCGC-G-AGUCA-UCAGCUCGGC-GUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCUACUACCGAU--UGAA-UGGUUUAGUGAG--GUUUC-GG-GACUUG----GCG-CUCAU---GAGGU---------------------GGCAACACCAC-A--UCUG----U---G-CUGGGAACUUGAAC-AAACU-UGAUC-AUUUAGAGGAAGUAAAAGUCGUAACAAG-GUUUCCCGUAGGUGGUGAACCUGCAG----GAUCAA--
EF050072.1/12-1709                 AACCUGGUUGCUCCUGC---CAGUAGUC-AUACGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------ACAAGCCC---UU---------------GUACGGU-GAA-ACUGCGAAUGGCUCAAUA-AAUCGGUUUUAA-GA-CACUUGAUAG-------------------------------------------------------------------------UCUCUCUACUUGGA-UAACCGU-AGCAAUUCUAGAGCUAAUACAUGCUAU-------------CC----------------------------------------------------------------UUCG-GGU---------GAGCUUAUUAGAUCCAAC---------------------------------------------------------------------------------------CACAACC----GUGGU-------------------GAGUCA--UAGUAAUCAAUC---------UGAUUGG-------CGCAAG------------------------------CCGA-CGGUUCA-AUCU-CGAUUCCGCCCUAUCA-GCU-U--UCGACGG-UA-GG--GUAUU-GG------CC-UACCGU-GGCGUUAACGGGUAACGGAGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACC--C-AAUCCUAAAG-----CA-GGGA----GGUAGUGACAAUAAAU--------------------ACUG-ACG-CCG-G-AUUC---------------AAUGA-AU--CU-GGUA-A----A---GAAUG-AGAA--------C-AGU-CUAA-A----ACCCU--U-A-UCGAGGACCCAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUUGAAUUUCGGGUUUC---CGGCGCUCCCGCUUCAUUGCGGGGACACGGGGACCCUCCUCGCCUU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGGCGUCAUUUACUGU-GGAAAAAUUAGAGUGUUCAAAGCAGGCA----------------------------------------------AUCGC--UUGAAUACAU-UAGCAUGGAAUAAUAAGAU-AGGAUUA-CGUC-----------------------------------------------------------------------------------------------------------UAUUUUGUUGGUUGCGGACGA----UAAUAAUGA-UUAAUAGGGA--UA--GUU--GGGGGUGUCCGUAUUG-AG-C-UGUCAGA----GG------UGAAAUUC-UUGGAUUUGCU-CAA--GA-CGAACUA--CUGC-GAAAGCA---UUCACCA-AGGAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUCAGG-GGAUCGAAGAGGAUUAGAUAC-CCUC-GUAGU-CU-UG-ACCAUA-AACUAUGCCG-ACUCGG--GAUUGGCAG-A-CGUU---GUAUC-----------------------------------------------------------------GACUCUGU-CAG-CA------CCG------------------UAUGAUAAAUCA--AAGUCUUUGGGU--------UCCGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AAGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGGAAA-CUUA-CCAGGUCCA-G------ACAUAG-UUAGGAUUGA-CA-GA---------UUGAGAGCUCUU-UCA-UGAUU-CUAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUAAUU-CCGU-UAACGA-ACGAGACCUCCGC-CUGCUAAA-U-AGACGGGUCCUGUU---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCAGGGUCCCGUCU-UCUUAGAG-GGA-C-UAUCG-GC--------------------------------------------------------GUUAUA--GUCGAUGGAAGUUGGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGUGCU-ACACUGACCGGCGCAACAAGUUU----------------------------------------------------------------------AUUUCCU-UGGCU--CGACA--GGC-C-UG------GG-UAAU-CUU--CGAAC---------------------------------------GCUGGUC--GUGAUG-GGGAUAGAUCCUUGC-------------AAUUUUUG-AUCU-UCAACGAGGAAUUCCUAGUAA-AUGC-A-AGUCA-UCAUCUU-GC-GUUGAUUAC---GUC-CCUGCCCUUUGUACACACCGCCCG-UCGCACCUACCGAU--UGAA-UGGUCCGGUGAA--ACCUC-CG-GAUUGC------C-UGGCC------------------------------CCUGC------G--GCCA----G---C-GCGAGAAGUUGGUU-AAACC-UUACC-AUUUAGAGGAAGGUGAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCAGAAG-GAUCAAAG
AJ564772.1/7-1816                  UACCUGGUUGAUCCUGC---CAGUAGUC-AUAUGCUUGUCUCAAAGAUUAAGC-CAUGCAUGUCUAAGU------------------------------AUACACCU---UU---------------ACACGGU-GAG-ACUGCGAAUGGCUCAUUA-AAUCAGUUAUAG-UU-UAUUUGAUAG------------------------------------------------------------------------UGCCUACUACUUGGA-UAACCGU-AGUAAUUCUAGAGCUAAUACAUGCAACAA----GUCCCGACU-----------------------------------------------------------------UCU-GGAA--G-GGAUGUAUUUAUUAGAUAUACA-AACCAACCG------------------------------------------------------------------------UGGGGGGAAACC----UUCAUGU---------CCUUUGGUGAGUCA--UAAUAACUUCGC---------GAAUCGC---AUGCC-UUCG-----------------------GGCG---GCGA-UGAUUCA-UUCA-AAUUUCUGCCCUAUCA-GCU-U--UUGAUGG-UA-GU--GUAUU-GG------AC-UACCAU-GGCGUUUACGGGUAACGGAGAAU--UAGG------------------------GUUCGAU-U-CCGGA--GAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACC--C-AAUCCUGACA-----CA-GGGA----GGUAGUGACAAUAAAU--------------------AACA-AUA-CUG-G-ACUU--------------UUUCAA-GU--CU-AGUA-AU--UG---GAAUG-AGAA--------C-AAU-CUAA-A----UACCU--U-A-UCGAGUAUCAAUUGGAGGGCAA-GUC-UGGUGCCAGCAGCCGC-GGUAAUUCC--AGCUCCA-AUA-GC-GUAUAUUAA-AGUUGUUG-CAGUUAAA---A--------AGCUC-GUAGUUGGAUCUCAGGGUGA---GCUCAGUUGGUCAGCCUAAUUGGUCAGAACUGGCUGACUCUCCCUUGUUUCUGAAUCCCGGUCGGAGUUAAUUCUUCGUU-----------------------------------------------------------------------------------------------------------------------------------------------CGUGGACUUCAGAUCGUUUACCUU-GAAAAAAUUAGAGUGUUCAAAGCGGGCG----------------------------------------------UUUGC--UUGAAUACAU-UAGCAUGGAAUAAUGGAAU-AGGACCC-UGGUU-------------------------------------------------------------------------------------------------------CUAUUUUGUUGGUUUUGAGGACCA----GAGUAAUGA-UUAAUAGGGA--UA--GUU--GGGGGCAUUCAUAUUU-AA-U-UGUCAGA----GG------UGAAAUUC-UUGGAUUUAUG-AAA--GA-UGAACUU--CUGC-GAAAGCA---UUUGCCA-AGGAUGU---UUUCAU-U-AAUCA-A-GAACGAAAGUUAGG-GGAUCGAAGAUGAUCAGAUAC-CGUC-GUAGU-CU-UA-ACCAUA-AGCUAUGCCG-ACUAGG--GAUUGGGAG-C-GGUU---UGUUCAUU--------------------------------------------------------------GACCCUCU-CAG-CA------CCU------------------UACGAGAAAUCA--AAGUUUUUGGGU--------UCCGGGGG-GA-G--UAUGG-UCGCAAGG-CUGAAA--C-UU-AAAGG-AAUUGACGG-AGGGGCA-C-CACCA-GGA-GUGGAG-CCUG-CGGC-UUAAUUUGACUCAACACGGGAAAA-CUUA-CCAGGUCCA-G------ACAUAG-GAAGGAUUGA-CA-GA---------UUGAAAGCUCUU-UCU-UGAUU-CUAUGGG-UGGUGGUGCAUGGCCGUU-CUUAGU-UGG-UGGA--GUGA-UUUGUCUGG--UUAAUU-CCGU-UAACGA-ACGAGACCUUAAC-CUGCUAAA-U-AGUUACGACGAUAC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UCUGUAUCGGCGGACAACU-UCUUAGAG-GGA-C-UACUG-GG--------------------------------------------------------GUUACA--CCCGGUGGAAGUUUGAGGCAAU-AACAGGU-C-UGUGAUGCCCU-UAGAUGU-UCUGGGCCGCACGCGCGCU-ACACUGACUGGAUCAACGAGUGG-----------------------------------------------------------------------UCCACC-UUGGC--UGAAG--AGU-C-UG------GG-UAAU-CUU-GUAAAA---------------------------------------UCCAGUC--GUGAUG-GGGAUAGAUUAUUGC-------------AAUUAUUA-AUCU-UCAACGAGGAAUUCCUAGUAA-GGGU-G-GUUCA-ACAGACC-GC-CCUGAUUAC---GUC-CCUGCCCCUUGUACACACCGCCCG-UCGCUACUACCGAU--UGGA-UGGUCCGGUGAG--AACUC-UG-GAUUGC-----GG-UUGAUG--UGCCG----------------------GUCUCCGGUG-C--AUGA----C---U-GCGAGAAGUUGAUC-GAACC-UUAUC-AUCUAGAGGAAGUAAAAGUCGUAACAAG-GUUU-CCGUAGG---UGAACCUGCGGAGG--AUCAAAG
#=GC SS_cons                       :::<<<<<_______>>...>>>,{{{-.{{{{{{{,{{{{{{{{{-----{{.{-{{{,,<<---<<<..............................----<<__..___..............._____>>.---.>>>>>,,,,,,[[[,,,,.,,((((--((--.((.----((((,,......................................................................,,,,,,,,,,,<<<<--.--<<<<<.<<_____>>>>>>>----->>>>,,,,,,....<<<<<--<<...............................................................______>>--..>.>>>>,,,,<<<<<<--------..<<<<--.............................................................................--<<<____....>>>---............-->>>>------..>>>>>>,,,,,,.........,,,<<<<...-<<<<_____.......................>>>>...>>>>.,,,)))).---).)))--))))<<<--<-.<<<.-..---<<<<.<<.<<.._____.__......>>.>>>>>>.>>>----->>>>,,,<<<<<<<<..____........................>>>>---.>.>>>]]..],<<<<<<__________>>>>>>,<<<<____>>>>,,,}}}}}}-},,,,,<-<<<..-.--<<<<<___.....>>.>>>-....>>>>,}}-}}}}}},,....................,,<<.<<<.<<<.<.<<<<..............____>>.>>..>>.>>>>.->..>>...,,,,,.,<<<........-.<<<.____._....__>>>..>.-.>>,,,,,,,,,<<<<<<-----.--<.<<<-----<<____>>.------->>..>>>>>>>.>,}.}}.}}}}}}},,.,,,,,,,,.[[[-----...[........,((((.---(((--------------...--------------------------------------------------------------------------------------.................................................................................................................................--------------------------------.------------------------------...........................................------..----------.-------------------.-------.-----.......................................................................................................------------------------....---------.------((((..((..(((..--(((((((<<--<<<.<<.<.<<---<<....<_......_____>>>.------>>>>>.>>>..--.>>,,,,<..--<<.____>>>...))))))).-)))))-...))))--.-.)))--.-.)))),,,,<<<<<<.---<<---<<<<_________.>>>>.--->>.>>.>>.>>,,,,.,,,,,,((((.((,<<<..--<<<<<<<.<.-<<<...________..............................................................>>>>>>>>.>>>.--......>>>..................,,,<<____>>,..,,)))----)))........]]]],<<<.--.-..---<<.<<____>>.>>----..>.>>.,,,,,.,,,{{{{{-.{{{{{{{.-.-{{,,.{{{.{{{{{{.{{{{.{{{{.,,,,<<<<________>>>>,,,,.,,,,.{{{{{{{,,.,......,<<<<<.--------<<.<<.<<.........________>>>>.>>-.-----.>>>>>,,.,[[-[[[[--[[[[[[[[.[,,,((.(((.(<<<..____.>>>,,<<<<..______.>>>>.,,)))).)),,,,,((((,<.<<-<<<<-.-.<<<<_________________________..............................................................................................................................................................___________________________>>>>.-->>>>>>.>,,.<.<<<<<.<<........................................................._____..>>>>>>>>,,,,,)))),,,,].]]]-]]].-.--]-]]]]]]].,,,,,}}.}}}}},,,}}-}}}}}}}}.}},,,<<<<<<<-----<<<---......................................................................-----<<.--<<<..<____..>>>.>.--......>>.----.>>>.------.......................................>>>>>>>..,,,,,,.<---<<<<<<<<___............._____>>>.>>>>.>--->,,,,,}}}}},,,,,<.<<<<.<.<<___.____>>>.>>.>>>,,,,,,...}}-.--}}}}}}}}}}-}},,<-<<-<<.-<-<<<<<<<<--<..-<<<.<<<<<<<<<--<..<<<<<.<<.<<<<<<.....<<.<<<<<....<<<<......................_____>>>>-.>..>>>>....>...>.>>>>>>>>>>>>>>.-->>>.>>>>>.>>>>>-->>>>>>>>-->->>-->>-->.,<<<.<<<<<<<...____>>>>>>>>>>.::::::::
#=GC RF                            uACCUGGUUGAUCCUGC...CAGUaguc.aUAcgCUUcucUccaAGAUUAAGC.CAUGCAUGUcUAaGu..............................acAaacuu..aUu...............auAcggu.GAA.aCuGCGaAuGGCUCAUUA.aAucAGUuauaa.uc.uauuugauau......................................................................uuuaaauuuuAcauGGA.UAcCucu.gguAAuUccagaGgUAAUACaugcaaaaa....cccccaacc...............................................................auuaguggga..g.ggggGcauuuauuagauaaaaa..accaau.............................................................................uagccuuua....ggcuuu............uuugguGAaUca..uaauaacuuugc.........ugAucgc...acggccuuuu.......................gccg...gcga.uguauca.uucg.aauuUCUgacCuAUCA.gcu.u..UcGaugg.ua.gg..gUAuu.gG......cc.uaccau.ggcuaUaACgGgUAACGGggaAU..cAGG........................GUucGAU.u.CCGGA..GAGGcaGCCUGAGAAACGGCugCCACuuCuAAGGaaGGCAGCAGGCGCGcAAAUUaCC..C.AAUcccgaca.....cg.ggGA....GGuAGUgAggAgagAU....................Aacg.aug.cgg.g.ccuc..............uUauga.gg..cc.cgca.Au..cg...gAAUG.Agua........u.acu.uUAA.A....uaagu..u.a.acGAGgAuCaAuuGGAGGGCAA.GUC.UGGUGCCAGCAGCCGC.GGUAAUUCC..AGCUCCa.aUA.Gc.gUAuacuAA.aGUUGUUG.cgGUUAAA...A........aGcuC.GUAgUuGaauuuaaguuuuu...uuuuuuguuuuauuuuauuuuuuuuuuuauuguuuuuuuauuuuuuuuuuuuuuuuauuaucuuuuuuuuuuuuuauguauauuuu.................................................................................................................................guuuuuuuuuuaguaucuguaauuuUuACUuU.GAaaAAAUuAgAGUGuUcAAAGCAGGcuau...........................................auuugc..uUGaAUauuu.uaGCAUGGaAUaAuagaau.Aggacuu.ugguu.......................................................................................................uuuuuuuguugguuuuuagaauug....agguaAUGA.UUAAuAGgga..cg..ccc..GGgGgcgcccGUAuug.cg.c.cGcuAGa....gG......UGAAAuuC.uuuGAuCggcg.caa..GA.CgAaCuc..aaGC.GAAAGCg...ggcgcCc.AgggcgU...uccCaU.U.aAuCA.A.GagCGAAAGuuaGg.GGAucGAAGacGAUcAGAUAC.CguC.GUAgu.cC.ua.aCcaUA.AACgAUgcca.aCuggc..gauuggccg.a.aguc...auuuuuau..............................................................gacucggc.cag.ca......gcc..................uacGgGAAAcCa..AAGuuUUUGggc........UCcgGGGG.GA.G..UAUgG.ucGCAAgg.CuGAAA..C.UU.AAAGG.AAUUGACGG.AAGGGCA.C.CACcA.GGa.GUGGAG.ccUG.CGGC.UUAAuuuGACUCAACACgggaAAA.CUuA.CCaGgcCcG.G......Acaccg.gaAGGAUUGA.cA.Ga.........UUgAuAGcuCUu.UCU.uGAUU.cggugGg.UgGUGGUGCAUGGcCGuU.cUUAGu.ucG.UGga..GUGA.ucUGUcuGG..UUAAUU.CCgg.UAACga.aCGAGACcccaac.cuacuaau.U.aGcuuauugauuuuuuuuuaauuuuuuua..............................................................................................................................................................uauuuuuuaaauuuauauuauaauuuaagCu.UCuuagag.gGA.c.ccccg.gc.........................................................guuuA..gccgggggAAGuuugggGCAAg.AaCAGgU.C.UGUGAUGCCCu.UAGAUGg.cCuGGGCuGCACGCGggCU.ACAaUGacggacucAacgaGuuu......................................................................uuuuucC.uuguc..cGAaA..gga.c.ug......Gg.uAAu.Cuc.uugAAa.......................................guccguC..gUGaUu.GGGAuuGaggauUGu.............AAUUauuc.cuCa.ugAACGAGGAAUuCCUAGUAa.gcgc.g.agUCA.UcAgcuc.gc.gcuGAuUAC...GUC.CCUGCCCUUUGUACACACCGCCCG.UCGcUcCuaCCGAu..Uggg.ugauccgguGAg..guccu.cc.Gaccgu.....cc.ccccc....cgcc......................uuaauggcgu.g..gggg....g...g.acgggAggaggacc.aAacc.ggauc.accuaGAGGaaGgAgAAGUCGUAACAAG.GUuu.ccGUAGG...UGAACCUGCggaaG.GAUCAuua
//
# STOCKHOLM 1.0

#=GF AC   RF01962
#=GF ID   RMST_1
#=GF PI   NCRMS
#=GF DE   Rhabdomyosarcoma 2 associated transcript conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   46.80
#=GF NC   35.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.76 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20062813
#=GF RT   Rmst is a novel marker for the mouse ventral mesencephalic floor plate and
#=GF RT   the anterior dorsal midline cells.
#=GF RA   Uhde CW, Vives J, Jaeger I, Li M
#=GF RL   PLoS One. 2010;5:e8641.
#=GF WK   RMST_(gene)
#=GF SQ   14


AK056164.1/56-115          CGCUGAAUAUCUUCAGGAAAA-U-GGGUUCCAUGAGAAGUGACAUCCUCCUCGAAUCAAAAG
ABDC01169378.1/653-712     UGCUGAGUAACUCCAGGAAAA-U-GGGUUCCAUAAGAAGUGACAUCCUCCUCGAAUUGAAAG
ABRP01000327.1/11814-11874 CACUGAGUAUCUUCAGGAAAACU-GGGUUCCAUAAGAAGUGACAUCCUCCUCGAAUUGAAAG
AAGV020089238.1/809-869    CGCUGAGUAUCUUCAGGAAAAAU-GGGUUCCAUAAGAAGUGGCAUCUUCCUCGAAUUGAAAG
AAFC03057064.1/5067-5007   CACUGAGUAUCUCCAGGAAAAAU-GGGUUCCAUAAGAAGUGGCAUCCUCCUGGAAUUGAAAG
AAHX01048283.1/361-302     CACGGACUAUCCUCAGGAAAA-U-GAGAUCCAGGAGAAGUGACGCCCUCCUCGAACUGAAAG
AANN01550621.1/9727-9666   CACUGGGUCUCUUCUGGAAAAAAUGAGUUCCAUCAGAAGUGACAUCCUCCUCGAAUUGAAAG
AAPY01087484.1/2268-2327   CACUGAGUAUCUUCAG-AAAAAU-GGGUUCCUUAAGAUGUGACAACCUCUUCGAAUGGAAAG
AAWR02024754.1/13067-13127 CACUGAGUAUCUUCAGGAAAAAC-GGUUUCCGUCAGAAGUGGCAUCCUCCUCAAAAUGAAAG
ABVD01649746.1/413-473     CAUUGAGUAUCUUCAGGAAAAAU-GGGUUCCAUAAGAAGUGGCUUCCUCCUUGAAAGGUAAA
AACN010416103.1/1061-1121  AACUGAGUAUCUUCGGGAGAUAU-GGGCUCCAAAAGAAGUGGCAUCCUCCUCGAAUGGAAAG
AAGU03008644.1/26564-26625 CGCUGAGUAUCUUCAGAAAAAAAAGGGUUCCAUAAGAAGUGGCAUCCUCCUCGAGUUGAAAG
AAQR03016746.1/20978-20918 CGCUGAGUAUCUCCAGGAAAAAU-GGGUUCCACGAGAAGUGACAUCCUCCUCGAACUGAAAG
AAPE02006931.1/97314-97254 CACAGAGCAUCUUCAAGAAAAAU-GGGUUUCCUGAGAAGAGGCAUCCUCCUCGAACUGAAAG
#=GC SS_cons               :::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::
#=GC RF                    CACUGAGUAUCUUCAGGAAAAAU.GGGUUCCaUaAGAAGUGgCAUCCUCCUCGAAuuGAAAG
//
# STOCKHOLM 1.0

#=GF AC   RF01963
#=GF ID   RMST_2
#=GF PI   NCRMS
#=GF DE   Rhabdomyosarcoma 2 associated transcript conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   45.00
#=GF TC   47.70
#=GF NC   43.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.94 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20062813
#=GF RT   Rmst is a novel marker for the mouse ventral mesencephalic floor plate and
#=GF RT   the anterior dorsal midline cells.
#=GF RA   Uhde CW, Vives J, Jaeger I, Li M
#=GF RL   PLoS One. 2010;5:e8641.
#=GF WK   RMST_(gene)
#=GF SQ   16


AC007351.40/28304-28169    UUCUCAGGAUGAUGGAGU-GAGUGAUGGAAUAGGUUGCCAACU-GUAGUUACUCCACUCAGCA---CAGAAUGG-CUGCGGGGAA-A-UAUAAUCAGACAUGCCCAAAGAAGUCUGCUUAGGGUGAAACAAAUACCUUUGAGGU
ABRR01116066.1/686-820     UUCUCAGACUGAUGGAGU-GAGUGACGGAGUAGGUUGCCAACU-GUAGUUGCUCCACUCAGCA---CAGAAUGG-CUGCGGGGAA---UAUAUUCAGACAUUCCCAGAGAAGUCUGCCCAGGGUGAAACAAAUACCUUUGAGGU
ABVD01062018.1/1120-1254   UUCUCAGACUGAUGGAGU-GAGUGAUGGAGUGGGUUGCCAACU-GUAAUUGUUCCACUCAGCG---CAGAAUGG-CUGUGGACAA-UAU--AUUCAGGCAUCCCUAAAGAAGUCUGCCCAGGGUGAAACAAAUACAUUUGAGGU
ABDC01155932.1/15103-15237 UUCUCAAGCUGAUGGAGU-GAGUGAUGGAGUGGGUUGCCAACG-GUAGUUACUCCACUCAGCG---CAGAAUGG-CUGCAGGGAA-UAU--AUUCAGACAUCCCCAAAGAAGUCUGCCCAGGGUGAAACAAAUACCUUUCAGGU
ABRP01000330.1/2991-3125   UUCUCAGGCUGAUGGAGU-GAGUGACGGCAUGGGUUGCCAACU-AUAGUUAUUCCGCUCAGUA---CAGAAUGC-CUGUGGGGAG---UAGAAUCAGGCAUGCCCAAAACAGUCUUCCCAGGGCAAAACAAAUACCUUUGAGGU
AAWR02024754.1/38845-38977 UUCUCAUGCUGAUGGAGU-GAGUGAC--AGUGGGGUGCGAACU-GUAGUUACUCGACUCAGCU---CAGAAUGG-CUGCGGGGAA-CGU--AUUCAGACAUACCCAAGGAAGUCUGCCCAGGGUGAAACAAACACCGUUGAGGU
AAPY01590416.1/2399-2533   GUCUCAGGCUGAUGGAGU-GAGUGAUGGAGUGGGUUGCCAACU-GUCAUUACUCCACUUGGUG---CAGAAUAA-CUGUCAGAAA-UCU--AUUCACAUAUGCCCAAAGAAGUCUGCCCAGGGUGAAACAAAUGCCUUUGAGGU
ABRN01423257.1/4219-4353   UUCUCAGGCUGAUGGAGU-GAGUGAUGGAGUGGGUUGCCAACC-GUAGUUACUCCACUCAGUG---CAGAAUGG-CUGCAGGGAA-UAU--AUUGAGAUACGCCCAAAAAACUGUGCCCAGAGUGAAACAAGUACCUUUGAGGU
ABRQ01017953.1/1179-1313   UUCUCGGGCUUCUGGAGU-GAGUGAUGGUGUGGGUUGCCGGCU-GUAGUUACUCCACUCAGCG---CAGAGUGG-CUGCGGGGAA-UGU--AUUCAGACAUCCCCCAAGACGUCUGCCCUGGGUGAGACAGAUGCCUCUGAGGU
AAFC03041894.1/39005-38865 UUUGCAGCCUCAUGGAGC-GAGUGACGGAGUGGGUUGCCAACUUGUAGUGACUCCACUCAGCAACGCAGAAUGG-CUGCGGGAAA-UGUGUAUUCAGAUAAGCCCAAAGAAGUCUGCCCAGGGUGAAACAAGUACCUUUGAAGU
AALT01661591.1/8761-8627   UUCUCAGAUCGGUGAGAGUGAAUGACG-AGUGAGUUGUCAAUG-GUAGUUACUUCGCUCAGCG---CAGAAUGA-CUGCAGGGAA-UAU--AUUCUGACAUACCCAAAGAAGUCUGCCCAGGGUGAAACAAUUACCUUUGGGGU
AAPE02006931.1/72166-72033 UUCUCAGGCUGAUGGAGU--GGUGACGGAGUGGAUUGACAACU-GUAGUUUCUCCACUCAGUG---CAGAAUGG-CUGCAGGGAA---CAAAUGCAGACAUGUCCAGAGAAGUCUGCCCAGGGUGAAACAAAUAUCUUUGAGGU
AAQR03016745.1/21876-21742 UUCUCAAGCUCAAGGAGU-GAGUGAUGGAGUCAGUUGCCAGCU-GUAGUUACGCUGCUCCAUG---CAGAAUGG-CUGCAGGGAA-UAU--AUUCAGACAUGCCCCAAGAAGUCUGCUCAGGGUGACACAAAUACCUUUGAGGU
AAGW02034243.1/72428-72293 UUCUCGGGCUGAUGCUGUUAAGUGAUGGAGUGGGUUGCCAACU-GUAGUUGCUGCACUCAGCG---CCUAAUGG-CUCUGGGGAA---CAUACUCAGACAUGCCCAGAGAAGUCUGCCUGGGGUGAAACAAGUACCCUUGAGGU
AAGU03008644.1/55026-55160 UUCUCAGGCUUAUGGAGA-GAGUGAUGGUGUAGGUUGCCAACC-GUAGUUACUCCAUAGAGCG---CAGAGUGG-CUGCGGGGAA-UAU--ACUCAGGCAUCUCCCAAGAAGUCUGCCCAGGGUGAAACAAAUACCUUUGAGGU
AF429305.1/57-193          UUCUCAGGAUGAUGGAGU-GAGUGAUGGAAUAGGUUGCCAACG-GUAGUUACUCCACUCAGCA---CAGAAUGGUCUGCGGGGAAAUAU--AAUCAGACAUGCCCAAAGAAGUCUGCUUAGGGUGAAACAAAUACCUUUGAGGU
#=GC SS_cons               ::::::::::::::::::.::::::::::::::::::::::::.:::::::::::::::::::...::::::::.::::::::::.:::..:::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UUCUCAGgcUgaUGGaGu.GAGUGAuGGaGUgGGUUGCCAACu.GUAGUUaCUcCaCUCaGcg...CAGAAUGG.CUGcgGGGAA.uaU..AuUCAGaCAUgCCCaaAGAAGUCUGCCCaGGGUGAaACAAaUACCUUUGAGGU
//
# STOCKHOLM 1.0

#=GF AC   RF01964
#=GF ID   RMST_3
#=GF PI   NCRMS
#=GF DE   Rhabdomyosarcoma 2 associated transcript conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   55.00
#=GF TC   59.20
#=GF NC   53.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20062813
#=GF RT   Rmst is a novel marker for the mouse ventral mesencephalic floor plate and
#=GF RT   the anterior dorsal midline cells.
#=GF RA   Uhde CW, Vives J, Jaeger I, Li M
#=GF RL   PLoS One. 2010;5:e8641.
#=GF WK   RMST_(gene)
#=GF SQ   16


AF429305.1/204-312         AAGGAAGGA-GAGACUGUUUCUACAGGUGUCAUACAAAAAUCAAUACUGAGCCAAGGAUUAUUGGAUCCCAUAGAACCACGGAGACUUGGUAGUGAAAUUCUUCCAAAGG
ACBE01245135.1/1255-1363   AAGGAAGGA-GAGGCUGUUUCUACAGGUGUCAUAGAAAAAUCAAUAUUGAGCCACGGAUUAUUGGAUCCCAUAGAACCAUGGAGACUUGGCAGUGAAAUUCUUCCAAAGG
AANU01209576.1/2613-2721   AAGGAAGGA-GAGACUGUUUCUACAGGUGUCAUAGAAAAAUCAAUACUGAGCCAAGGAUUAUUGGAUCCCAUAGAACCAUGGAGGCGUGGCAGUGAAAUUCUCCCAAAGG
ABRT010541375.1/4111-4219  AAGGAAGGA-GAGGCUGUUUCUACAGGUGUCAUAGGAAAGUCAAUACUGAGCCACGGAUUAUUGGAUCCUACAGAACCAUGGAGACUUGGCAGCGAAAUUCUUCCAAAGG
AAFC03093132.1/58863-58971 AAGGAAGGA-GAGGCUGUUUCUACAGGUGUCAGAGAAAAAUCGAUACUGAGCCAUGGAUUAUUGAAUCCCGUAGAACCAUGGAGGCUUGGCAGUGAAAUUCUUCCAAAGG
ABDC01155932.1/15824-15932 AAGGAAGGA-GAGGCUGUUUCUACAGGUGUCUUCAAAAAAUCGAUACUGAGCCACGGAUUAUUGGAUCCCACAGAAGCAUGGAGACUUGGCAGUGAAAUUCUUCCAAAGG
AAYZ01074743.1/3353-3461   AAGGAAGGA-GAGACUGUUUCUACAGGUGUCAUAGAAAAAUCAAUGCCAAGCCAUGGAUUAUUGGAUGCUGCAGAACCACAGAGAUGUGGCGGUGAAAUUCUUCCAAAGG
AALT01661591.1/7713-7605   AAGGAAGGA-GAGGCUGUUUCUACAGGUGUCAUUGAAAAAUCAAUACUGAGCCACAGAUUAUUGGAUCCCAUAGAACCAUGGAGGCUUGGCAGUGAAAUUCUUCUAGAGG
ABRO01032941.1/1508-1616   AAGGAAGGA-GAAGCUGUUUCUACAGGUGUCAUACAAAAAUCAAUACCGAGCUACGGAUUAUUGGAUCUCGUAGAACCAUGGAGGCUUGGCAGUGAAAUACUUCCAAAGG
AC125204.4/159690-159582   AAGGAAGGA-GAGGCUGUUUCUACAGGUGCCACAGAAAAAUCGAUGCUGAGCCUCGGAUUAUUGGAUCCCAUAGAACCGUGGAGACUUGGCAGUGAAAUUCUUCCAAAGG
ABRN01423257.1/4946-5054   AAGGAAGGA-GAGGCCAUUUCUACAGGUGUCAUAGAAGAAUCGAUAUUGAGCCAUGGAUUAUUGGAUCCCAUAGAGCCACAGAGACUUGGCAGUGAAAUUCUUCCAAAGG
AANN01292645.1/1222-1114   AAGGAGGGA-GAGGAUGUUUCUACAGGUGUCACAGAAAAAUCAAUCCCGAGCAACGGAUUAUUGGAUCUCAUAGAACCAUGGAGACUUGGCAGUGAAAUUCUUCCAGAGG
AAHX01048282.1/26038-26147 AAAGAAAGGCGAGGCUGUUUCUACAGGUGCCACAGAAAAAUCGAUGCCGAGUCACGGAUUAUUGGAUCCCACAGAACCAUGGAGACUUGGCGGUGAAAUUCUUCUAAAGG
ABRP01000330.1/3711-3813   AAGGAA-GA-GAGGCUGUUUCUACAGGUGUCAUAGAAAA--UCAUACUGAG-CACGGCUUAUUGCCUCCCAUAGAACCAUG--GACUUGGCAGUGAAAUUCUUCCAAAGG
AAQR03016745.1/21161-21053 AAGGAAGGA-GAGGCAGUUUCUACAGGUGUCUUAGAAAAAUCAAUACUAAGCCACGGAUUAUUGGAUGCCACAGAACCAUGGAGACUUGGCAGUGAAAUUCUUCCAAAGG
AAPE02006931.1/71433-71325 AAGGAAGGA-GAGGCUGUUUCUACAGGUGUCAUAGAAAAAUCAAUGCUGAGCCACGGAUUAUUGGGUCCCAUAGAACCAUGGACACAUGGCAGUGAAAUUCUUCCCAAGG
#=GC SS_cons               :::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    AAGGAAGGA.GAGGCUGUUUCUACAGGUGUCAuaGAAAAAUCaAUaCuGAGCCAcGGAUUAUUGGaUCCCauAGAACCAUGGAGaCuUGGCAGUGAAAUUCUUCCAAAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01965
#=GF ID   RMST_4
#=GF PI   NCRMS
#=GF DE   Rhabdomyosarcoma 2 associated transcript conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; Pfold:
#=GF GA   40.00
#=GF TC   44.40
#=GF NC   38.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.37 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20062813
#=GF RT   Rmst is a novel marker for the mouse ventral mesencephalic floor plate and
#=GF RT   the anterior dorsal midline cells.
#=GF RA   Uhde CW, Vives J, Jaeger I, Li M
#=GF RL   PLoS One. 2010;5:e8641.
#=GF WK   RMST_(gene)
#=GF SQ   17


AC007351.40/26869-26763    GGUGUUCCUAGGUUUGGAAAUAUAAAU-CCCAUGGGAA-GUCAGCUG-AAGACCAUUUUAUG----CAUCACUCAUCCUGUUA-GAGCCCUGUGCUGUUCUGUCUCUCUAUAAGG
ABDC01155933.1/347-454     GGUGUUCCUAGGUUUGGAAAUAUAAAU-CCCGUGGGAA-GUCAGCUG-AAGAACAUUUUAUG----CAUCGCUCAUCCUAUUAUGAGCCCUGUGCUAUUCCAUCUCUCUACAAGG
ABRR01116067.1/2127-2234   GGUGUUCCUAGGUUUGGGAGUAUAAAU-CCCAGGGGAA-GUGAGCUG-AAGAACAUUUUAUG----CAUCACUCAUCCUAUUAUGAGCCCUGUGCUGCUCCAUCUCUCUACAAGG
AAWR02024754.1/40260-40367 GGUGUUCCUAGGUUUGGAAGUGUAAAU-CCCAGGAGAA-GUGAGCUG-AAGAACAUUUUAUG----CAUCACUCAUCCUAUUAUGAGCCCUGUGCUGUUCUCUCUCUCUACAAGG
AAFC03041894.1/37589-37484 GGUGUUCCUAGGUUUGGAAACAUAAAU-CCCAGGGGAA-GUGAGCUG-AAGAACAUUUUAUG----CAUCACUCAUCCUAUUAUGAGCCCUAUGCUGCUCCAUCUCU--ACAAGG
ABRP01000330.1/4407-4514   GGUGUUCUUAGGUUUGGAAAUAUAAAU-CCCAGGAGGA-GUAAGCUG-AAGAACAUUUUAUG----CAUCACUCAUUCUAUUAUGAGCCCUCUGCUGUUCCAUCUCUCUACAAGG
ABVD01062018.1/2510-2617   GGUAUCCCUAGGUUUGGAAGUAUAAAU-CCCAUGGGAA-GUCAGCUG-AAGAACAUUUUAUG----CUUCACUUAUCCUAUUAUGAUCCCUGUACUGUUCCUUCUCUCUACAAGG
ABRN01423257.1/5650-5757   GGUGUUCCUAGGUUUGGAAGCAUAAAU-CCCAGGGGAA-GUGAGCUG-AAGAACAUCUCAUG----CAUCACUCGUCCUAUCGUGAGCCCUGUGCUGCUCCAUCUCUGUACAAGG
AAPY01590416.1/3846-3955   GGUGUUCCUAGGUUUGGAAGUAUAAAU-CCCGUGGGAAGGUCAGCUGAAAAAACAUUUUAUG----CAUCGCUCAUCCUAUUAUGAGCCCUGCGCUGUUUCAGUUCUUUUCAAGG
AAYZ01074743.1/4046-4152   UGUGUUCCUAGG-UCGGAAGCAUCAAU-CCCAGGGGAA-GCCAACUG-CAGAACAUUUUAUG----CAUCGCUCAUCCUGUUAUGAGCCUGGUGCUGUUCCAUCUCUCUACAAGG
AAGV020089246.1/406-513    AGUGUUCCUAGGUUUGGAAGUAUAAAU-CCCAUGGGAA-GUCAACUG-AAGAAUAUUUUAUG----CUUCACGUAUCCUAUUAUGAACUUUGUACUGUCCCAUCUUUCCACAAGG
AANN01381698.1/1014-1120   GGUGUUCCUCGAUUUGGAAGCAUAAAU-CACUGGGGAA-GUGAGCUG-GAAAACGUUUUAUG----CAUUGUCCAUCCUAUUACAAGCCUGGUGCUGAUCCAUUUCUC-ACAAGG
AAHY01087653.1/17690-17583 GGUGUUCCUGGUUUGGGAAGUAUAAAU-CCCGUGGGAA-GUCAACUG-GAGGACAUUUUACG----CGUCACUCAUCCUAUUAUGAGCCUGCUGCUCCUCCGUCUCUUGACAAGG
AAPE02006931.1/70721-70616 GGUGUUCCUAGGUCUGGAAGGAUAAAU-CCCAGGGGAA-GUGAGCUG-CAGAACAUUUUAUG----CAUCACUCAUUCUAUUAUGAGCCCUCUGCUGCUCCAUCUCU--ACAAGG
AAGU03008644.1/56481-56587 GGCAUUCCUAGGUUUGGAAGGAUAAAU-CCCAUGGGAA-GUCAGCUG-AAGAACAUUUUAUG----CAUCGCUCAUCCUGUUAUGA-UCCCGUGUUGCACCAUCUCUCUACAAGG
AAHX01048282.1/26759-26870 GGUGUUCCUGGUUUGGGAAGUAUAAAU-CCCGCGGGAA-GUCAACUG-GAGAACAUUUUACGCGUCCGUCACUCAUCCUAUUAUGAGCCUGCUGCUCUUCCUUCUCUGGACAAGG
AAQR03016745.1/20260-20152 GGUGUUCCUAGGUUUGGAAACAUAAAUCCCCCCGGGAA-GGCAGUUG-AAGAACAUUUUCUA----CAUCACUCAUCCUAUUAUGAGGCCUCUGCUGUUCCGUCUCUCGCCAAGG
#=GC SS_cons               :::::::::::::::::::::::::::.::::::::::.::::::::.::::::::::::::....:::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GGUGUUCCUaGGUUuGGAAGuAUAAAU.CCCauGGGAA.GUcAGCUG.aAGAACAUUUUAUG....CaUCaCUCAUCCUAUUAUGAGCCcugUGCUGuUCCaUCUCUcuaCAAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01966
#=GF ID   RMST_5
#=GF PI   NCRMS
#=GF DE   Rhabdomyosarcoma 2 associated transcript conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   58.00
#=GF TC   67.20
#=GF NC   34.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.46 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20062813
#=GF RT   Rmst is a novel marker for the mouse ventral mesencephalic floor plate and
#=GF RT   the anterior dorsal midline cells.
#=GF RA   Uhde CW, Vives J, Jaeger I, Li M
#=GF RL   PLoS One. 2010;5:e8641.
#=GF WK   RMST_(gene)
#=GF SQ   21


AC007351.40/24834-24709      UGGCAGUUAAAGAACAGAAACA--GCAAUAAGACUGCGUGGCUA-CAUUUUCCCAGUGCCACCAACUGGGAUUUAAGCUGACU-AACAUUUUGAAAGCCCAGCCCAUUUCAUUCACAGCAGG-AUGGCAGG
ABRR01116067.1/4013-4141     UGGCAGUUAAAGAACAGAAACAGAGAAAUAAGACUGCAUGGCUA-CAUUUUCCCAGUGCCACCAACUGGGAGUUAAGCUGACU-AACAUUUUGAAAGCCCAGCCCAUUUCGUUCACAGCAGGCAUGGCAGG
AAFC03041894.1/35718-35590   UGGCCGUUAAAGAACAGAAACAGAGCAGUAAGACUGCGUGGCUA-CAUUUUCCCAGUGCCACCAACUGAGAGUUAAGCUGACU-AACGUGUUGAAAGCCCAGCCCAUUUCGUUCACAGCAGGCAUGGCAGG
AAPY01590416.1/5711-5838     UGGCCGUUAAAGAACAGAAACAGAGCAAUAAGCCUCCGCGGCCA-CACUUUCCCAGUGCCGCCAGCUGGGAGUUAAGCUGACU-AACAUUUUGAAAGCCCAGCCCAUUUCGUUCUCAGCAGG-AUGGCAGG
ABRN01423257.1/7760-7888     UGGCAGUUAAAGAACAGAAACAGAGCAAUAAGACUGCAUGGCUA-CAUUUUCCCAGUGCCACCAACUGGGAAUUAAGCUGACU-AACAUUUUGAAAGCUCAGCCCACUUUGUUCCCAGCAGGCAUGACAGG
ACBE01245136.1/1423-1549     UGGCAGUUAAAGAACCGAAACA--GCAAUAAGACUGCGCAGGCA-CAUUUUCCCAGUGCCACCAACUGGGCGUUAAGCUGACU-AACGUUUUGAAAGCCCAGCCCAUUUCGUUCACAGCAGGCAAGGCAGG
AAKN02013867.1/67002-66877   UGGCAGUUAAAGGACAGAAACA--GCAAUAAGACUGUCUGGCUC-CAUUUUCCCAGUGCCGCCAGCUGGGAGUUAAGCUGACU-GACGUUGUGAAAGCCUGGCCCAUUUCGUUCACAGCAGG-AAGGUAGG
AAGV020089246.1/2258-2386    UGGCAGUUAAAGAACAGAGACGGAGCACUAAGACUGCAUGGCUA-CAUUUUCCCAGUGCCACCAACUGGGAGUUAAGCUGACU-AACAUUUUCAAAGCCCAACCCAUUUCCUUCACAGCAGGCAUGGUAGG
AAIY01702199.1/777-905       UGGCAGUGAGAGAACCGAAACAGAGCAAUAAGACUGCACGGCUA-CAUGUUCCCAGUGCCACCAACUGGGAGGUAAGCUGACU-AACAUUUUGAAAGCCCAGCCCAUUUCGUUCACAGCAGGCAUGGCAGG
ABVD01062018.1/4385-4513     UGGCAAUUAAAGAACAGAAACAGAGCAAUAAGACUGCACGGCUA-CAUUUUCCCAGUGCCACCAACUGGGAGUUAAGCUGACU-AACAUUUUGAAAGCCCAGCCCGUUUACUUCACAGCAGGCAUGGUAGG
AAWR02024754.1/42116-42244   UUGCAGUUAAAGAACAGAAACAGAGCAGUAAAACUGCAUGGCCA-CAUUUUCCCAGGGCCACCAACUGGGAGUUAAGCUGACU-AACAUUUUGAAAGCCCGGCCCAUUUCAUUCACAGCAGGUGCGGCAGG
AAYZ01074744.1/314-441       UGGCAGUUAAAGAACAGAAACAGAGCAAUGAGACUGCCUGGCUA-CAUGUUCCCAGUACCACCUACUGAGAGUUAAGCAGACA-AACAUUUUCAGAGCCCAGCCCAUUUUGUUCCCAGCAGG-AUGGCAGG
AAQQ01564790.1/206-331       UGGCAGUUAAAGGACAGCAGCA--GCAGUCCGACCGCCUGGCUC-CAUUUUCCCAGUGCCACCGACUGGGAGUUAAGCUGACU-AACGUUUUGAAAGCCCGGCCCAUUUCGUUCUCAGUGGG-ACAGCAGG
ABRO01032941.1/4765-4891     UGGCAGUUAAAGGACAA-AACA--GCAAUAAGGCUGCCUGCCUUACAUUUUUCCAGUGCCACCAACUGGGCAUUAAGCUGGCUUAACAUUUUGAAAGCCCAGCCCAUUUGGUUCACAGCAGG-AUGGCAGG
ABRQ01017954.1/1251-1374     UGGCAGUUAAAGAACAAAAACAGAGCAAUAAGCCUGCAUGGCUA-AAUUUUCCCAGUGCCACUAACUGGGAGUUCAGCUGACU-AAGACUGUGCAAGCCUAGCCCAUUUCGCUCACAGCAG-----GCAUG
AANN01292644.1/1215-1087     UGAUGGUUUCAGAACAGAAACAGAGCAGUGAGACUGUGUGACUG-CUUUUCCCCAGUGCCACCAGCUGGGAGUUAAGCUGACU-AACAUUUUGAAGGCCCAGCCUGUUUCACUCACAGCAGGCCUGGCAGG
AAQR03016745.1/18430-18303   UGGCAGUUAAAGAACAGAAACAGAGCAGUAAGAGUGAGCCGCUA-CAUUCUCCCAGUACCACCAACUGGGAGUUAAGCUGACU-AACACUUUGAAAGCCCAGCCCAUUCCGUUCGCAGCAGG-AUGGCAGG
AAEX03009962.1/105269-105397 UGGUAGUUAAAGAACAGAAACAGAGCAGUAAGACUGCAUGGCUA-CAUUUUUCCAGUGCCACCAACUGGGAGUUAAGCUGGCU-AACAUUUUGAAAGCCCAGCCCAUUUCGUUCACAGCAGGAAAGGCAGG
AAGW02034243.1/68820-68693   UGGCAGUUAAAGAACAGAAACAGAGCAAUGAGACUGCCUGGCUA-CAUUUUCCCAGUGCCACCAACUGGGAGUUAAGCAGACA-AACAUUUUGAAAGCCCAGCCCAUUUUGUUCCCAGUAGG-AUGGCAGG
AABR05143105.1/77609-77484   UGGCAGCUAAAGGACAGGAGCA--GCAAUAAGGCUGCCUGGCUA-CAUUUUCAUAGUGCCACCAACUGCGAGUUAAGCUGACA-AACAUUUUGAGAGCUCGGCCCAUUUCAUUCACAGCAGG-AUGGCAGG
AF429305.1/612-737           UGGCAGUUAAAGAACAGAAACA--GCAAUAAGACUGCGUGGCUA-CAUUUUCCCAGUGCCACCAACUGGGAUUUAAGCUGACU-AACAUUUUGAAAGCCCAGCCCAUUUCAUUCACAGCAGG-AUGGCAGU
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::.::::::::
#=GC RF                      UGGCaGUUAaAGaACAGaAACAGAGCAaUaAGaCUGcguGGCUa.CAUUUUCCCAGUGCCACCaaCUGGGAGUUAAGCUGACU.AACaUUUUGAAAGCCCaGCCCAUUUcgUUCaCAGCAGG.auGGCAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01967
#=GF ID   RMST_6
#=GF PI   NCRMS
#=GF DE   Rhabdomyosarcoma 2 associated transcript conserved region 6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   90.00
#=GF TC   90.70
#=GF NC   67.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20062813
#=GF RT   Rmst is a novel marker for the mouse ventral mesencephalic floor plate and
#=GF RT   the anterior dorsal midline cells.
#=GF RA   Uhde CW, Vives J, Jaeger I, Li M
#=GF RL   PLoS One. 2010;5:e8641.
#=GF WK   RMST_(gene)
#=GF SQ   18


AF429305.1/738-940           GGGUGACUGAUCGUACCCGCCAGCUGGCUAAUGUCAUAAUUAACAAA-GUUGCUACUACAUCUGCAAAGUUUAAUCGAAAAAUUUGCCAGUGAUAUGAUGGCCUUGUCACAGAGAUCACAAGGGACACGGAGUU--------GACUUUUGCUCAAGGUGGAACGACAGAGCUGUGUAGGCAAGAUGAGAAAUUGCGAACUUGUUCGGCCAAA
AAWR02024754.1/75205-75407   GGUUGACUGAUUGUACCCGCCAGCUGGCUAAUAUCAUAAUUAACAAA-GUUGCUACUACGUCUGCAAAGUUUAAUCGAAAAAUUUGCCAGUGAUAUGAUGGCAUUGUCACAAAGAUCACAAGGGACACCGAGUC--------GACUUUUGCUCAAGGUGGAACGGCAAAGCUAUGUAGGCAAGACGAGAAAUCGCGAACUUGUUCAGCCAAA
AAPY01590406.1/7839-8041     GGGUGACUGAUCGUACCCGCCAGCUGGCUAAUAUCAUAAUUAACAAA-GUUGCUACUGCGUCUGCAAAGUUUAAUCGAAAAAUUUGCCAGUGAUACGAUGGCAUUGUCACGGAGAUCAUAGGGGACACGGAGUC--------GACUUUUGCUCAAGGUGGAAUGGCAAAGCUGUGUAGGCAAAAUGAAAAAUUGCAAACUUGUUCAGCCAAA
ABDC01155944.1/4987-5190     GGGUGACUGAUCGUCCCCGCCAGCUGGCUAAUAUCAUAAUUAACAAAAGUUGCUACUACGUCUGCAAAGUUUAAUGGAAAAAUUUGCCAGUGAUACGAUGGCAUUGUCACAGAGAUCACAAGGGACACGGAGCC--------GACUUUUGCUGAAGGUGGAACGGCAGAGCUGUGUAGACAAGAUGAGAAAUUGUGAACUUGCUCAGCCAAA
ABRN01423263.1/473-675       GGUUGACUGAUUGUACCUGCCAGCUGGCUAAUAUCAUAAUUAACAAA-GUUGCUACUGCGUCUGCAAAGUUAAAUCGAAAAAUUUGCCAGUGAUAUGAUGUCAUUGUCACAAAGAUCACAAGGGACUCGGAGUC--------GACUUUUGCUCAAGGUGGAACGGCGAAGCUGUGUAGGCAAAAUGAGAAAUCUCAAACUUGUUCAGCAAAG
AAFC03093132.1/97757-97958   GGUUGACUGAUUGUACCUGCCAGCUGGCUAAUAUCAUAAUUAACAAA-GUUGCUACUACGUCUGCAAAGUUUAAUCGAAAAAUUUGCCAGUGAUAUGAUGGCAUUGUCACAAAGAUCACAAGGGACUUGGAGUC--------GACUUUCGCUCAAGGUGGAACGGCAGAGCUGUGGAGGCAAA-UGAGAAAUCUUGAACUUGUUCAGCCAAA
ABRP01000335.1/4033-4235     GGUUGACUGAUUGUACCCGCCAGCUGGCUAAUAUCAUAAUUAACAAA-GUUGCUACUACGUUUGUAAAGUUUAAUCGAAAAAUUUGCCAAUGAUAUGAUGGCAUUGUCACAGAGAUCACAAGGGACACGUUGUC--------GACUUUUGCUCAAGGUGGACCGGCAAAGCAGUAUAGGCAAGAUGAGAAAUUCUAAACUUGUUCAGCCAAA
AAGV020089253.1/1983-2186    GGGUGAUUGAUCGUACCCGCCAGCCGGCUAAUAUCAUAAUUAACAAA-GUUACUA-UACGUCUACAAAGUUUAAUCGAAAAAUUUGCCGGUGAUAUGAUGGUAUUGUCAUAAAGAUCACAAGGGACACAGAGUGUC------AACUUCUGCUCAAGGUGGAGCGGCAGAGCUGUGUAGGCAAGAUGAGAAACGGCCAACUUGUUCAGCCAAA
AAHX01048282.1/57958-58160   GGGUGACUGAUUGUCCCUGCCAGCUGGCUAAUAUCAUAAUUAGCAAA-GUUGCUACCACAUCUGCAAAGUUUAAUCGAAAAAUUUACCAGUGGUAUGAUGGCAUUGUCACCAUGAUCCCAAGGGAAUCGGAGUC--------GACUUCUGCUUCAGGAGGAACGGCAAGGCUGUAUAGCUGAGAUGAGAAAUUGUAAACUUGCUCAGCCAAA
AALT01535338.1/2869-2667     CGUUGACUGAUUGUACUCACCAGCUGGCUAAUAUCAUAAUUAACAAA-GUUGCUACUAUGUCUGCAAAGUUUAAUCGAAUAAUUUGCCAGUGAUAUGAUGACAUUGUCACAAAGAUCACAAGGGACACAGAGUU--------GACUUUUGCUCAAGGUGGAACGGCAAAGCUCUAUAGACAAGAUGAGAAACCGUGAACUUACUCAGCCAAA
ABRT010087602.1/9228-9428    GGGUGAGUGAUCGUACCUGCCAGCUGGCUUAUGUCAUAAUUAACAAA-GUUGCUACUAUGUCUGCAAAGUUUAAUUGAAAAAUUUGCCAGUGAUAUGACGACACUGUCACAG--AUCACAAGGGACACAGGGCC--------GAUUUUAGCUGCUAGUGGAACGGGGAAGCUGUGUUUGCAAGAUGGGAAAUUGAGGACCUGUUCAGCCAAA
ABRQ01017964.1/458-660       GGGUGACUGAUCACACCCGCCAGCUGGCUAAUGCCAUAAUUAACAAA-GUUGCUACUACGUCUGCAAAGUUUAAUAAAAAAAUUUGCCAACAAUAUGAUGGCACUGUCAGAGAGAUCACAGGGGACCUGGAGUC--------GACUUGCUCUCAAGGUGGAGUGACAAAGCUGCCUUCUCAAGAUGAAAAAUUGUGAGUUUGUUCAGCCAAA
CAAA01062036.1/13375-13577   GGGUGACUGAUUGUCCCUGCCAGCUGGCUAAUAUCAUAAUUAGCAAA-GUUGCUACCACAUCUGCAAAGUUUAAUCGAAAAAUUUACCAGUGGUAUGAUGGCAUUGUCACCGCGAUCCUGAGGGAAUCAGAGUC--------GACUUCUGCUUCAACUGGAAUGGCAAGGCUGUAGAGCUGAGAUGAGAAACUGUAAACUUGCUCAGCCAAA
AAQQ01081930.1/5082-5292     GGGUGACUGAUGGCACACUCCAGCUGGUUAAUAUCAUAAUUAACAAA-GUUGUUUCUACAUUGGUAAAGUUUAACUGGAAAAUUUACCAGUGAUAUGAUGGCAUUGUCAUGAAGAUUACAAGGGACACAGGGACAAGGAGUCGACUUUUGCUCAAGGCUGAACGGCAAAGCGGUGUAAGCAAGAUGAGAAACUGCAAACUUGGAAGGCAAAG
AAGU03008645.1/32805-33007   GGGUGACUGAUCGCACCCACCAGCUGGCUAACACCAUAAUUAACAAA-GUUGCUACUACAUCUGCAAAGUUUAAUCCAAAAAUUUGCCAGCAAUAUGAUGGCAUUGUCACUGAGAUCACAAUGGACACGGAGUC--------GACUUUUGCUCAAGGUGGAACGGCAAAGCCGUGUUGGCAAGAUGAAGAAUCGCAAAAUUGUUCAGCCAAA
AAQR03016744.1/107003-106801 GGGUAACUGAUCAGACCCGCCAGCUGGCUAAUAUCAUAAUUAACAAA-GUUGCCACUGCGUCUGCAAAGUUUAAUCGAAAAAUUUGCCAGGGAUAUGAUGGCAUUGUCACAGAGAUCACAAGGGACACGGAGCC--------GACUUCUGCUGAAGGUGGAGCGGCAGAGCUGUGCUGGCAAGAUGAGGAAUUACGAAGUUGUUCAGCCAAA
AAGW02034243.1/30938-30736   UGGUGACUGAUCAUACCCGCCAGCUGGCUAAUAUCAUAAUUAACGAA-GUUGGUGCGACGUCUGCAAAGUUUAAUCGGAACAUUUACCAGCGAUGUGAUGGCAUCGUUACGAAGAUCACAAGGGACCUGGCCGU--------GACUUUUGCCCAAGGAGGAAUGGCAAAGCUGUGCAGGCGAAAUGAGAAAUUGCAAACUUGUUCAGCCAAA
AAPE02006931.1/42296-42094   GGUUGACUGAUUGUACCCGCCAGCUGGCUAAUAUCAUAAUUAACAAA-GUUGCUACUACGUUGGCAAAGUUUAAUCGGAAAAUUUGCCAGUGAUAUGAUGGCAUUGUCACAAAGAUCACAAGGGACACGGAGCC--------CACUUCUGCUCAAGGUGGAACGGCAAAGCUGUGUAUGCAAGCGGAGAAAUCGCAAACUUGUUCAGCCAAA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::........::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      GGgUGAcUGAUuGuaCccgCCAGCUGGCUAAUaUCAUAAUUAACAAA.GUUGcUaCuaCgUcuGCAAAGUUUAAUcGaAAAAUUUGCCAGuGAUAUGAUGGCAUUGUCAcagaGAUCaCAAGGGACacgGaGuc........GACUUuuGCUcaAGGuGGAacGGCAaAGCuGUguaggCaAGAUGAGAAAuugcgAAcUUGuUCaGCcAAa
//
# STOCKHOLM 1.0

#=GF AC   RF01968
#=GF ID   RMST_7
#=GF PI   NCRMS
#=GF DE   Rhabdomyosarcoma 2 associated transcript conserved region 7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   100.00
#=GF TC   126.50
#=GF NC   61.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 44.55 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20062813
#=GF RT   Rmst is a novel marker for the mouse ventral mesencephalic floor plate and
#=GF RT   the anterior dorsal midline cells.
#=GF RA   Uhde CW, Vives J, Jaeger I, Li M
#=GF RL   PLoS One. 2010;5:e8641.
#=GF WK   RMST_(gene)
#=GF SQ   22


AC018659.35/164554-164287    UGUGUAGAAAUGAACUCUUGUCAGAGUUUCA-AAGGAAUUAACGUUUUUU-------GGUAA-----AAUGUGCUAAUGUAAAGAGUGAGAAGAUUAGUGAUACAUAAUGA-AAGCAAUGCAUUCUUUCACAUGGAAAUGGGAAUAUAAUAAAUGUCCUGCAGGUGAUUGGGGCUGUAGCAAUUUUAUUGAAGAUUAAAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCCUUCUGAAAUUAAAA-GCCAGAGCUGAAUUAUUCUGCUCAAUUUAAAUGCAAA
ABRP01000335.1/6030-6298     UGUGUAGAAAUGAACUCUUGUCAGAGUUUCA-AAGGAAUUAAUAUUUUUUU------GGUAA-----AAUGUGCUAAUGUAAAGAGUUAGAAGAUUAGUGGUGCAUAAUGA-GAGCAAUGCAUUCUUUCGCAUGGAAAUGGGAAUGUAAUAAAUGUCCCGCAAGUGAUUGGGGCUGUAGCAAUUUUAUUGAAGAUUAAAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCCUUCUGAAAUUAAAA-GCCGGAGCUGAAUUAUUCUGGCCAAUUUAAAUGCAAA
ABRN01423263.1/2463-2729     UGUGUAGAAAUGAACUUUUGUCAGAGUUUCA-AAGGAAUUAAUAUUUUU--------GGUAA-----AAUGUGCUAAUGUAAAGAGUUAGAAGAUUAGUGAUGCAUAAUGA-AGGCAAUGCAUUCUUUCACAUGGAAAUAGGGAUAUAAUAAAUGUCCUGCAGGUGAUUGGGGCUGUAGCAAUUUUAUUCAAGAUUAAAGUUUGAUUGACCUUUGUUGGGGUGAUUAACCCUUCUGAAAUUAAAA-GCCAGAACUGAAUUAUUCUGACCAAUUUAAAUGCAAA
AAWR02024754.1/77182-77448   UGUGUAGAAAUGAACUCUUGUCAGAGUUUCA-AAGGAAUUAAUAUUUUU--------GGUAA-----AAUGUGCUAAUGUAAAGAGUUAGAAGAUUAGUAAUGCAUAAUGA-AAGGCAUGCAUUCUUUCACGUGGAAAUAGAAAUAUAAUAAAUGUCCUGUAGGUGAUUGGGGCUGUAGCAAUUUGAUUGAAGAUUAAAGUUUGAUUGACCUUUGUUAAGGUGAUUAACCCUUUUGAAAUUAAAA-GCUGGAGCUGAAUUAUUCUGCCCAAUUUAAAUGCAAA
AAGV020089254.1/1080-1349    UGUGUAGCAAUGAACUCUUGUCAGAGUUUCA-AAGGAAUUAAUAUUUUUUUU-----AGCAA-----AAUGUGCUAAUGUAAAGAGUCAGAAGAUUAGUGAUGCAUAAUGA-AAGUAAUGCAUUCUUUCGCAUGGAAAUAGGAAUAUAAUAAAUGUCCUGCAGGUGAUUGGGGCUGUAGCAAUUUUAUUGAAGAUUAAAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCCUUCUGAAAUUAAAA-ACCAGAGCUGAAUUGCUCUGUCUAAUUUAAAUGCAAA
AALT01535338.1/927-658       UGUGUACAAAUGAACUCUUGUCAGAGUUUCA-AAGGCACUAAUAUUUUUUUU-----GGUUA-----AAUGUGCUAAUGUAAAGAGUUAGAAGAUUAGUGAGGCAUAAUGA-AAGCAAUGCAUUCGUUCGCAUGGAAAUAGGAAUAUAAUAAAUGUCCUGCAGGUGAUUGGGGCUGUAGCAAUUUUAUCGAAGAUUAAAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCCUUCUGAAAUUAAAA-GCCAGGACUGAAUUAUUCUAGCCAAUUUAAAUGCAAA
AANN01186171.1/1699-1438     UGUGUAGAAAUGAACUCGUGUCAGAGUUUCAAAAGGAAUUAAUAUUUUU--------GGUAA-----AAUGUGCUAAUGCAGAG----AGAAGAUUAGUGGUGGGUAAUGA-AAGCAGUGCAUUCUUUCGUAUGGAAAUAGAACUAGAGUAAAUGUCCUGCAGGUGAUUG-GGCUGUAGCAAUUUUGCUGAAGAUUAAAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCCUUCUAGAAUUAAAA-GCCAGGGCUGAAUUAUUCUG-CCAAUUUAAAUGCAAA
ABRO01032943.1/17242-17508   UGUAUAGAAAUGAACUCUUAUCAGAAUUUCA-AAGGAAUUAAUAUUUCU--------GGUAA-----AAUGGGCUAAUAUAAAGAGUUGGAAGAUUAGUGAUGCAUAAUGA-AUAAAAUGCAUUCUUUCACAUGGAAAUAAGAGUAUAAUAAAUGUCCUGCAGGUGAUUGGGGCUGUUGCAAUUUUAUUGAAGAUUAAAGUUUGAUUGACCUUUAUUGGGGCAAUUAACCUUUCUGAAAUUAAAA-GCCAGAUCUGAAUUAGUCUGUCCCAUUUAAAUGCAAA
AAIY01559142.1/2171-2437     UGUGUAGAAAUGAACUCUCGUCCGACUCUCA-AAGGAAUU-AUAUUUUG--------GGCAA-----AAUGUGCCAAUGUAAAGAGUUAGAAGAUUAGCGUUUCAUAAUGA-AAGCAAUGUAUUCUUUGACAUGGAAAUAGAAAUAUAAUAAAUGUCCUGCAGGUGAGAGGGGCUGUACCAAUUUUAUUGAAGAUUAAAGUUUGAUUGACCUUUGUGAGGGUGAUUAACCCCUGUGAAAUUAAAAAGCCAGAGCUGAAUGAUUCUGUCCAAUUAAAAUGCAAA
AAQQ01081930.1/7103-7374     UGUGUGGAAAUGAACUCUUGUUAGAGUUUCA-AAGGAAUUAAUAUAUUUUUUUUU--GGUAA-----AAUGUGCUAAUGUAAAGAGUUAGAAGAUUAGUGAUGUUUAAUGA-AUAGAAUGCAUUCUUUCUCAUGGAAAUGGGAAUAUAAUAAGUGUCCUGUAGGUGAUUG-GGUUGUAGCAAUUUUAUUGAAGAUUAAAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCUCUCAGAAAUUAAAA-GCCAGAUUGGAAUUAGUCUGUCCAAUUUAAAUGCAAA
ABQO010539469.1/575-296      UGUGUAGAAAUGAACUCUUGUCAGAGUUUCA-AUAGAAUUAAUAUUUUUAGUAAUAUGUUAAUGGUGAAUGUGCUAAUGUAAAGAGUUAGAAGAUUAGUGAUGCAUAAUGA-AAGUAAUGCAUUCUUUUGCAUGAAAAUAGGAAUAUAAUAAAUGUCCUUCAGGUGAUUGAAGCUGCAGUAAUUUUAUUGAAGAUUAAAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCCUUCUGAAAUUAAAA-GCCCAGGCUAAAUUAUUCUGUCCAAUUUAAAUGCAAA
AAFR03039564.1/17605-17326   UGUGUAGAAAUGAACUCUUGUCAGAGUUUCA-AUGGAAUUAAUAUUUUUAGUAAAAUGUUAAUAGUGAAUGUGCUAAUGUAAAGAGUUAGAAGAUUAGUGAUGCAUAAUGA-AAGUAAUGCAUUCUUUUGCAUGAAAAUAGGAAUAUAAUAAAUGUCCUUCAGGUGAUUGAAGCUGCAGUAAUUUUAUUGCAGAUUAAAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCCUUCUGAAAUUAAAA-GCCCGGAUGAAAUUAUUCUGUUCAAUUUAAAUGCAAA
ABRQ01017964.1/2466-2722     UGUGUAGAAAUGAACUCCUGUCAGAGUUUCA-AACAAAUUAAUAUUUUU--------GGUAA-----AAUGUGCUGAUGUAAGGAGCUGGAAGAUUAGUGGUGCGAGGUGACAAGUAGUACAUUCCUUUGCAUGGAAAUAGCAA-----------UCCUGCAGGUGACUGAGGCUGUAGCAGUUUUAUUGAAGAUUCAAGUUUGAUUGACCUCUGUUAGGGUAAUUAACCUUUCUGAAAUUAAAA-ACCAGAGCUGAAUUAUUCUGUCCAAUUUAAAUGCAAA
AAKN02013867.1/35226-34962   AGUGUAGAAAUCAACUCUUGUCAGAAUUUCA-AGAGAAUUAAUAUUUU---------GGAA------AAUGUGCUAAGGUAAAGAGUUAGAAGAUUAGUGAAGCGCAAUGA-AUGAAAUGCAUUCUUUUAUGUGAAAAUACAAAAAGAAUAAAUGUCCUGCAGGUGAAUGGGGCUGUAGCAAUCUUAUUUAGGAUGAAAGUCUGAUUGGCCCUUAUUAGGAUGAUUAACCUUUCUGAAAUUAAGA-GCCACCCCUGAAUUAGUCUGUCCAAUUUAAAUGCAAA
AAPN01014432.1/10882-10604   UGUGUAGAAAUGAACUCUCAUCAUAGUUUCA-AUGAAAUUCAUAAUUUUAGUAAAAUGUUAAUGGUUAAUGUGCUAAUUUAAAGAGUGAAAAGAUUAGUGAUGUGUGACUA-AAGUAAUGCAUUCUAUUGCAUGGAAAUAGGAAUAUAAUAAAUGUCCUGCAGGUGAUUG-AGCUACUGCAAUUUUAUUGAAGAUUAAAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCCUUCUGAAAUUAAAA-GCCAGUGCUAAAUUGUUCUGUCCAAUUUAAAUGCAAA
ABRT010087602.1/11169-11433  UGUGUAGAAACGAACUCUUGUCAGAGUUGCA-AAGGAAUUAACGUUUUUUU------GGCAA-----AAUGUGCUAAUAUAAAGAGUUAGAAGAUUAGUAAUGCCGAGUGA-AAGCCACACGCUCUUGCGCACGGAAACAGGCACGUGCUCCGUGUCCUGCGGGCGACUG-GGCUGCAGCAAUUUUAUUGAAGAUUGAAGUUUGAUUGACCCACGUUGAGGUGGCUAACCCUUCUGAA-UUAAAA-ACCAGAGC-GGAUUAUUCUGCUCAAUUUA-AUGCAAC
AC125204.4/125809-125547     UAUAUAGAAAUGCACGUUUUUCAGACUUCCAAAAGAAUUUAAUAUUUUCA-------GUUUA-----AUU-UGGUAAGGUAAAG----AGACAAUUAGUGACACGUA-GGA-AUAAAAUGUGUUCUUUCACAUGGAAAUGGGAAUAUAAUAAAUGUCCUGCAGGUGAUUGGACCCAUCACAAUUUUACUGAAGAUUAAAGUUUGACUGACCUUUGUUAGGGUGAUUAACCUUUCUGAAAUUAAAA-ACUCCACCUGAAUUAGUCUGUCUAAUUUAAAUGCAAA
AAYZ01074752.1/1292-1551     UGUGUAGAAAUUAACUCU-GUUAGAGUUUCAGAAAAAUUU----UGUUU-------UG-UAC-----AGUGUGAUAAUGUAAGGGGUUG---CAUUAGUGAAGCCUAAUGA-AGAAAAUGCAUUCUUUCACGUAGUAAUAGGAAUCUAAUAAGUCUCUUGCGUGUGAUGGGAGCUCUAGCAAUUUUAUUGAGAAUUAAAGCUUGAUUGACCUUCGUUAAGGUGAUUAACCCUUCUAAAAUUAAAA-GCCAGAUGUGAAUUAUGCUGUCCAAUUUAAAUGCAAA
AADN03001533.1/213102-212839 UGUGUAGAAAUGAGCUCUUGUAAUAGUUUCA-GAGGAAUUAAUAAUUUUAGUAAAAUGUUAAUGGCAGAUGUGCUAAUAUAAAGAGUUAGAAGAUUAGCGAUG-----------------CAUUCUUUUGCAUGGAAAUAAGAAUAUAAUAAAUGUCCUGCAGGUGACUGAAGCUGCUGCAAUUUUAUUGGAGAUUAAAGUUUGAUUGACCUUUGCUGAGGUGAUUAACCCUCCUGAAAUUAAAA-GCCGGUGCUAAAUUAUUCUGUCCAAUUUAAAUGCAAA
AABR05143105.1/46204-45940   UAUGCAGAAAUGAACUUUUCCCAGAGUUCCAAAAGAAUUUAAUAUUUUUA-------GUUGA-----AUUCAGUAAACAGAAAG----AGACAUUUGGUGACACAUAAGGA-AUAAAAUGUGUUCUUUCCCAUGGAAAUGGGAAUAUAAUAAAUGUCCUGCAGGUGAUUGGGCCCAUCGCAAUUUUUGUGAAGAUUAAAGUUUGACUGACCUUUGUUAGGGUGAUUAACCUUUCUGAAAUUAAAA-ACUCCAUCUGAAUUAGUCUGUCUAAUUUAAAUGCAAA
AAGU03008645.1/34800-35066   GGUGUAGAAAUGAACUCUUGUCAGAGUUUCC-AAGGAAUUAAUAUUUUC--------GGUAA-----AAUGUGCUAAUGUAAAGAGUUAGAAGAUUAGUGGUGGGUAAUGA-AAGUAAUGCAUUCUUUUGCAUGGAAAUAGAAAUAUAAUAAAUGUCCUGCAGGUGAUGGGGGCUGUAGCAAUUUUAUUGAAGAUUCAAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCUUUCUGAAAUUAAAA-GCCAGAGCUGAAUUAUUCUGUCCAAUUUAAAUGCAAA
AAGW02034243.1/29055-28790   UGUGUAGAAAUGAACUCU-GUCAGAGUUUCAAA-GGAAUUAAUAUUUUU--------GGUACA----A-UGUGCUAAUGUAAGGAGUUAGAAGAUUAGUGAUUCAUAAUGAAGAAAA-UGCAUUCUUUCACGUGGUAAUAGGAAUUUAAUAAAUGUCCUGCAGGUGAUGGGGGCUGUAGCAAUUUUAUUGAGAAUUACAGUUUGAUUGACCUUUGUUAGGGUGAUUAACCCUUCUGAAAUUAAAA-GCCAUAGCUGAAUUAUGCUGUCUCAUUUAAAUGCAAA
#=GC SS_cons                 :::::::::::::::::::::::::::::::.::::::::::::::::::.......:::::.....::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::
#=GC RF                      UGUGUAGAAAUGAACUCUUgUcAGAGUUuCA.AaGGAaUUAAUAUUUUuu.......Gguaa.....AaUGUGcUAAugUAAaGAGUuaGAaGAUUAGUGaugcauAauGA.AaguaAUGCaUUCUUUcgCaUGGAAAUaGgaAuaUAaUAAaUGUCCUGCAGGUGAuuGGGGCUGuaGCAAUUUUauUGaaGAUUaAAGUUUGAUUGACCUUUGUUaGGGUGAUUAACCcUUCUGAAAUUAAAA.GCCagagcUGAAUUAuUCUGuCCAAUUUAAAUGCAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01969
#=GF ID   RMST_8
#=GF PI   NCRMS
#=GF DE   Rhabdomyosarcoma 2 associated transcript conserved region 8
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   95.60
#=GF NC   61.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20062813
#=GF RT   Rmst is a novel marker for the mouse ventral mesencephalic floor plate and
#=GF RT   the anterior dorsal midline cells.
#=GF RA   Uhde CW, Vives J, Jaeger I, Li M
#=GF RL   PLoS One. 2010;5:e8641.
#=GF WK   RMST_(gene)
#=GF SQ   22


AC018659.35/136688-136547    CGGGAAGGAGGCCAGUGCUACCAGGG-UUAUCUCACAACCUCAGAUGCUGGAUAAGUCGACGGAGGCAGAAUCGCUUUGGGAUGACAUUCAGAAAGC-CUGGAGUGAUUACUUGCAAGAGAAAA-GCCUACCUAUUC-UUUCCAAG
AAPY01087498.1/694-835       GGGGAAAGAGGCCAGUGCUACAAGGG-UUAUCUCACAACCUCAGAUGCUGGAUAAGUCCAAGGAGGCAGAAUCGCUUUUGGAUGACAUUCAGAAAGG-CCGGAGUGAUUAUUUGGAAGAGAAAA-GCCUGCCUAUUCUUU-CCAAG
AALT01152168.1/290-148       AGGGAAGGAGGCCAGUGCGACCAGGG-UUAUCUCAAAGCCUCAGAUGCUGGAUAAGUCGGGGGAGGCAGAAUCGCUUUGGGAUGACAUUCAGAAAGG-CUGGAGUGAUUAUUUGGAAGAGAAAA-GCCUCCCUAUUCAUUUCCAAG
AC235682.1/15558-15700       GGGGAAGGAGGCCAGUGCUAGGAGGG-UUAUCUCACUGCCUCAGAUGCUGGAUAAGUCGAAGGAAGCAGAAUCGCUUUUGGAUGACAUUCAGAAAGG-CCGGAGUGAUUAUUUGGGAGAGAAAA-GCUUGCCUAUUCUUUUCCAAG
AAFC03093132.1/128947-129089 AGAGAAGGAGGCCAGUGCUACCAGGG-UUAUCUCGCAGCCUCAGAUGUUGGAUAAGUCGAAGGAGGCAGGAUCGCUUCAGGAUGACAUUCAGAAAGG-CCGGAGUGAUUAUUGGGAAGAGAAAA-GCCUACCUAUUCUUUUCUAAG
AAWR02024755.1/18978-19120   GGGGAAGGAGGCCAGUGCGACGAGGG-UUAUCUCAGAGCCUCAGAUGCUGGAUAAGUCGAAGGAGGCAGACUCGCUUUUGGAGGACAUUCAGAAAGG-CCAGAGUGAUUAUUUGGAAGAGAAAA-GCCUGCCUAUUCUUUUCCAAG
ABRR01116081.1/11499-11640   CAGAAAAGAGGCCGGUGCUAC-AGGG-UUAUCUCGCAGCCUCAGAUGCUGGAUAAGUUGGGGGAGACAGAAUCGCUUUUGGGUGACAUUCAGAACGG-CUGGAGUGAUUAUUUGGAAGAGAUAA-GCCUACCUAUUCUUUUCCAAG
AAIY01406812.1/4067-3929     AGGGAUGGAGGCCAGUGCUCUGAGGG-UUAUCUCCCAGCCUCAGAUGCUGGAUAAGUCGAAGGAGGCAGAAUCGCUUUUGGAUGACAUUCAG----G-UCGGAGUGAUUAUUUGGAAGAGAAAAAGCCUGCCUGUUCUUU-CUAAG
AAYZ01074763.1/2813-2954     AGCGAAGGAGGCUAGUGCUACCAGGG-UUAUCGCACAACCUCAGAUACUGGACAAGUUGAAGGAUGCACAAUCGCUUCUGGAUGACGUUCAGAAAGG-CCGGAAUGAUGAUUUGGAUGAGA-AAAGCCUGCCUAUUCUUU-CCAGG
AAKN02013867.1/9241-9100     GGGGAAGGAGGCCAAUGGUACAGGGG-UUAUCUCCCAACCUCAGAUGCCGGAUAAGUCAGGGGGUGCAGAACCGCUUCUGGAUGACAUUCAGAAACG-CUGGAGUGAUUAUUUGGAAGAGA-AAAGCCUACCUAUUCUUC-CCAAG
AAQQ01081945.1/6434-6574     AGGGAAGGAGGCCAAUGCUACAAGGG-UUAUCUCACAACCUCAGAUGCUGGGUAAGUCGAAGGAGACAGAAUCGCUUCUGGAUGACAUUCAGA-AGG-CCGGAGCGAUUAUUUGGGAGAGA-AAAGCCUGCCCUAUUCUU-UCGAG
AAPN01014431.1/30087-29950   AGUGAAGGAGGCCAGUGCCAUGAGGG-UUAUCUCACAGCUCCAGAUGCUGGAUAAGUUGAAGGAGGCAGAAUCGUUUUUGGAUGACAUUCAGAAAGGCCU-GAGUGAUUAUUUGGAGAAGAAAA-GACUA-----UUCUUUCCAAG
ABRO01249224.1/550-691       GGGGAAGAAGACCAAUGUUACAGGG--UUAUCUCACGACUUCAGAUGCUGGAUAAGUCCAAGGAGACAGAAUCGCUUCUGCAUGACAUUCAGAAAAG-CUAGACUGAUUAUUUGGAAGAGAGAAAGCCCGCCUAUUCUUU-CCAAG
AANN01526683.1/4319-4176     AGGGAAGGAGGCCAGUGCUACCAAGU-UUAUCUCCAAGCCUCAGAUGCCGGAUAAGUCCAAGGAAGGAGAAUGGCUGGGGGAUGACAUUCAGAAAGG-CCCCAGUGGUUAUUUGCAAGAGAAAAAGCCUGCCUAUUCUUUCCCAAG
ABQF01015694.1/2706-2844     AGUGAAGGAGACCAAUGCCACAAGGG-UUAUCUCGCAGCCCCAGAUGCUGGAUAAGUUGAAGGAGGCAGAAUCGCUUUUGGAUGACAUUCAGGAAGGCCUUGAAUUAUUAUCUGGUGAAGAAAA-GACUA-----UUCUUUUCAAG
AC125204.4/99534-99395       AGGGAAGGAGGCCAAUGCUACA-GGG-UUAUCUCCUAACCUCAGAUGUUGGAUAAGUCCAUGGAAACAGCAGCGCUUCUGGAUGGC-UUCAGAAAGG-CUGGAGUGAUUGUUUGGACGAGA-AAAACCCGCCUAUUCAUU-CAAAG
AAQR03016744.1/78152-78010   GGGGAAGGAGGCCAGUGCUGCCAGGGGUUAUCUCCCGACCUCAGAUGCUGGAGGAGUCCAAGGAGGCAGAGUUGCUGCGGGAUGACAUUCAGAAAGG-CUGGAGUGAUUAUUUGGGAGAGAAAA-GCCUGCCUAUUCUUG-CCAAG
AACN010449748.1/528-666      CGGGAAGGAGGCC-GCGCU-CGAGGG-UUAUCUCGCCGCCUCAGAUGCCGGG-AAGCCCAAGGA-GCCCAGGCGCUUCUGGACGACGUUCAGCAAGG-CCGCGGGGAUUCCUGCGCGGAGAGGA-GCCUGCCUGUUCUGUUCCAAG
AADN03001533.1/193544-193406 AGUGAAGGAGACCAAUGCCAUGAGGG-UUAUCUCGCAGCCCCAGAUGCUGGAUAAGUUGGAAGAGGCAGAAUCGCUUUUGGAUGACAUUCAGGAAGGCCUUGAAUGAUUAUUUGGGGAAGAAAA-GACUA-----UUCUUUCCAAG
AAWZ02012452.1/253186-253063 CGUAAAGGAGGCCAGUGCCACCAGGG-UUAUCUCCUAGCUCCAGAUGCUGGAUAAGUU----GAA-----UCGCUUUU-GGAUGACAUUCAGG-----UCUGAGUGAUGAUUUGGAGAAGAAAA-GACCA-----UUCUUCCCGAG
AABR05143105.1/20803-20665   AGGGAAGGAGGCCAAUGCUACAAGGG-UUAUCUCUCAACCUCAGAUGUUGGAUAAGUCA--GGGAACAGCGUCGUUUCUGGAUGGC-UUCAGACAGG-CCGGACUGACUGUUUGGAAGAGA-AAAACCUGCUUAUUCUUU-CAAAG
AAGU03008645.1/61779-61920   AGGGAAGGAGGCCAGUGCUAUGAGGG-UUAUCUCACAGCCUCAGAUGCUGGAUAAGUCGAGGGAGGCAGAAUCGCUUUUGGAUGACAUUCAGAAAGG-CCAGAGUGAUUAUUUGGAAGAGAAAA-GCCUGCCUAUUCUUU-CCAAG
#=GC SS_cons                 ::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::.:::::::::::::::::::::
#=GC RF                      aGgGAAGGAGGCCAgUGCuacgAGGG.UUAUCUCacagCCUCAGAUGCUGGAUAAGUcgaaGGAgGCAGaaucGCUUuuGGAUGACaUUCAGaAAGG.CcgGAgUGAUUaUUUGGaaGAGAaAA.GcCUgCCUaUUcuUUuCcAAG
//
# STOCKHOLM 1.0

#=GF AC   RF01970
#=GF ID   RMST_9
#=GF PI   NCRMS
#=GF DE   Rhabdomyosarcoma 2 associated transcript conserved region 9
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   65.00
#=GF TC   69.20
#=GF NC   63.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.38 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20062813
#=GF RT   Rmst is a novel marker for the mouse ventral mesencephalic floor plate and
#=GF RT   the anterior dorsal midline cells.
#=GF RA   Uhde CW, Vives J, Jaeger I, Li M
#=GF RL   PLoS One. 2010;5:e8641.
#=GF WK   RMST_(gene)
#=GF SQ   28


AC018659.35/136389-136197    CUGCCUU-AGACAAAGAAUGCACUCG-GAGCCCCAACACACCUAAAGCCA---UGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACACGGAGUCAGCAGAAAAUGAGAAAGUAGAGCUCGUGCUGU---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
AAGV020089263.1/424-616      CUGCCUU-AGACAAAGGAUACACCCG-GAGCCCCACCACACCUAAAGCCA---CGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUAGAGCUCGUGCUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
AAWR02024755.1/19270-19462   CUGCCUU-AGACAAAGGAUGCACUGG-GAGCCCCACCACACCUCAAGCCA---UGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUAGAGCUCACGCUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
AC235682.1/15852-16043       GUGCCUU-AGACAAAGGACGCAC-GG-GAGCCCCACCACACCUAGAGCCA---CGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUAGAGCUCGUGCUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAAG
AAIY01406812.1/3781-3588     CUGACUU-AAACAAAGGAGGCACUUGGGGCCCCCACCACACCUAAAGCCA---CGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACACGGAGUCAGCAGAAAAUGAGAAAGGAGAGCUCGUGCUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
ABRQ01017969.1/3629-3820     CUGCGUU-AGACAAAGGAUGCACU-G-GAGCCCCACCACACCUAAAGGCA---CGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUCGAGCUCGUGCUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGACUU-CAUGAGG
AAFC03093132.1/129241-129433 CUGCCUU-AGACAAAGGAGGCACUCG-GAGCCCCACCACACCUCAAACCA---CGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGGAAGGAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUGGAGUUCGUGCUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGUUU-CAUGAGG
AC125204.4/99243-99051       CUGCCUU-AGACAAAGGAAGUGCUUG-GAGCCCCACCACACCUAAAACCA---UGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGACAGCAGAAAAUGAGAAAGUAGAGAUCGUGCUGC---GAAUAAUUCCAGCGA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
ABRP01000338.1/6046-6238     CUGCCUU-AGACAAAGGAUGCACUCA-GAACCUCACCACACCUAAAGCCA---UGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUAGAGCUCGUGCUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--AGAAUGGCUC-CAUGAGG
AAYZ01074763.1/3120-3311     CUGCCUU-ACACAAUGGAUACACUUG-GCGCCCCACCACACCUAAAGCCA---CACUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUGGAGCUCGUGCUGC---GAAUAAUCCU-GCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
AAKN02013867.1/8936-8744     CUGCCCU-AGACAAAGGAUGCACUUG-GAUCCCCACCACACCUAUAACCA---CGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGACAGCAGAAAAUGAGAAAGUAGAGCUCGUGCUGC---GAAUAAUUCCAGUGA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
ABRN01423266.1/3006-3198     CUGCCUU-AGACAAAGGAUGCACUCG-GAGCCCCGCCACACCUUAAGCCA---CGCUCUGAAGGAUCUGCCCAGCUCACUUUUAAUCACGAGCAAGGAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUAAAGCUCGUGGUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CACGAGG
ABRO01249224.1/910-1103      CUGCCUU-AAACAAAGGAUGGACUGCCAAGCCCCACCACAUCUCAAACCA---UGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCACGAGAAAGAAA-UUACCCACAUGGAGACAGCAGAAAAUGAGAAAGUAGAGCUCGUGCUGC---GAAUAAUUCCGGCGA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
ABRR01116081.1/11788-11980   CUGCCCG-AGACAAAGGAUGCGCUCA-GAGCCCCACCACACCUGGAGCCA---CGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCGGGAGAACGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUAGAGCUCGUGCUGC---GAAUCAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CGUGAGG
AAHX01048282.1/85626-85818   UUGCCUU-AGACAAAGGAUGCUCUUG-GAGUCCCACCACACCUAAAACCA---CGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGACAGCAGAAAAUGAGAAAGGAGAGAUCGUGCUGC---GAAUAAUUCCAGCGA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
AAQQ01081945.1/6731-6920     CUGCU-U-AGACAAAGGCUGUCCUUG-GAGCCCCAACACACCCCAAGC-A---CGCUUUGAAGGAUCU-CCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGACAGCAGAAAAUGAGAAAGUUGAGCUCGUGCUGC---GAAUAAUUCCAGCGA-GUGCCAAGGGGCUAGUUGA--GGAAUGACUU-CAUGAGG
AAPN01014431.1/29797-29605   CCUUUCUGAGACAAAGAAUCCACUCU-GAGCCCAACCACACCUAA-GAAA---UGCUUUGAAGGAAUUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAAAAAGUAGAGCUCGUGCUGU---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GAAAUGGCUU-CAUGAGG
AANN01526683.1/4045-3852     CCACCUU-AGACAAAGGCUGCUCUCA-GGGCCUCACCGCACCUAGGAGCA---GGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCACGGGAAAAAAAAUUAUCCACAUGGAGUCAGCAGAAAAUGAGAAAGUAGAACUCACGCUGC---GAGUAAUUCUAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
ABQF01015694.1/2975-3163     CCUUUUUGAGACAAAGGAUCCACUCC-ACCUCC-----UACCUAAGGAAA---UGCUUUGAAGGAAUUGACAAGCUCACUUUUAAUCACAAGAGAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAAAAAGUAGAGCUCGUGCUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GAAAUGGCUU-CAUGAGG
ABRT010183405.1/2872-3059    CUGCUC--AGACAAGGGGUGCUCUUG-GAGCCC--CCACACCUCUAGCCG---UGCUUUGAAGGCUCUGCCAAGCCCACUUUUAAUCCUGAGAAAGAAA-UCACCCACACGGAGUCCGCAGAAAAUGAGAAAGUGGAGCUCGUGCUGC---GAAUCGUUCCAGCCA-GGGCCCCGGGGCUAGUGGA--GGAACGGC---CGUGGGG
AAFR03039563.1/286089-285893 GUAUCCUGAGACAAAGAAUUCGCUCCGGAGCCCCACCACACCUAAAAAAAAAAUGCUUUGAAGGGAUUGCCAAGCUCACUUUUAAUCAUGGGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAAAAAGUAGGCCUCGUGCUG----AGAUAAUUCCAGCGA-GUGCCAAGGGGCUAGUUGA--GAUAUGGCUU-CAUGAGG
ABQO010625947.1/912-1107     AUCUCGUGAGACAAAGGAUUCGCUCCUGAGCCCCGCCACACCUAAAAAAAA-AUGCUUUGAAGGGUUUUCCAAGCUGACUUUUAAUCAUGGGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAAAAAGUGGGCCUCGUGCUG----AGAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GAUAUGGCUU-CAUGAGG
AAPY01087498.1/991-1187      CUGCCUU-AGACAAAGGAUGUACUUG-GAAGCCCACCACACCUAAAGCUA---CGCUUUGAAGGAUCUGCCAAGCUCACUUUUA-UCAUGAGAAAGAAA-UUACCCACAUG-AGUCAGCAGAAA-UGAGAAAGUAGAGCUCGUGCUGAGAAAAAUAUCUUCCGCAGCGCACAGCAGCCCAAGUUGAAGGAGAUGCCUUCCACGAAG
AAQR03016744.1/77847-77655   CUUCCCU-AGACAAAGGAUGCACUCG-GAGCCCCACCACACCUAAAGCCA---CACUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAGGUAGAGCUCGUGCUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
AADN03001533.1/193238-193046 -CUUUCUGAGACAAAGGAUCCACUCC-ACAUCCAGCCACACCUAAAGAAA---UGCUUUGAAGGAAUUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAAAAAGUAGAGCUCGUGCUGU---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GCAAUGGCUU-CAUGAGG
AAPE02006931.1/14355-14162   -UUACU--AGACAAAGGAUGCGCCCG-AAACCCCACCACACCUAAAGCCA---CGCUUUGGAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUAGAGCUCGUGGUGCUCCGAGUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGG
AAGU03008645.1/62071-62263   CUGCCUU-AGACAAAGGAUGCGCUCC-GAGCCCCACCACACCUAAAGCCG---CGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACAUGGAGUCAGCAGAAAAUGAGAAAGUAGAGCUCGUGCUGC---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CACGAGG
AF429306.1/721-913           CUGCCUU-AGACAAAGAAUGCACUCG-GAGCCCCAACACACCUAAAGCCA---UGCUUUGAAGGAUCUGCCAAGCUCACUUUUAAUCAUGAGAAAGAAA-UUACCCACACGGAGUCAGCAGAAAAUGAGAAAGUAGAGCUCGUGCUGU---GAAUAAUUCCAGCAA-GUGCCAAGGGGCUAGUUGA--GGAAUGGCUU-CAUGAGA
#=GC SS_cons                 :::::::.::::::::::::::::::.:::::::::::::::::::::::...::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::...:::::::::::::::.:::::::::::::::::::..::::::::::.:::::::
#=GC RF                      cugccuU.AGACAAaGGaugcaCUcg.GagcCCCaCCACACCUaaAgccA...uGCUUUGAAGGaucUGCCAAGCUCACUUUUAAUCauGaGaAAGAAA.UUACCCACAuGGAGuCAGCAGAAAAUGAGAAAGUaGAGCUCGUGCUGc...GAAUaaUUCCaGCaA.GuGCCaaGGGGCUAGUUGA..GgaAUGGCUU.CAuGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF01971
#=GF ID   RMST_10
#=GF PI   NCRMS
#=GF DE   Rhabdomyosarcoma 2 associated transcript conserved region 10
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   55.00
#=GF TC   57.80
#=GF NC   35.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.13 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20062813
#=GF RT   Rmst is a novel marker for the mouse ventral mesencephalic floor plate and
#=GF RT   the anterior dorsal midline cells.
#=GF RA   Uhde CW, Vives J, Jaeger I, Li M
#=GF RL   PLoS One. 2010;5:e8641.
#=GF WK   RMST_(gene)
#=GF SQ   21


AF429306.1/937-1090          UAGCC--CACCAGUCGGGUAGGCAGCAUUC-AAUCCUUCUAUG-CCUUCUUUCGCCACCUGUUGAGGUCUUUCUUCUGAAACAAA-GAAGAAAUAGACAAAUCAGACUUGCCCUCUUGGAAAUGUGGUCCAGAUUUCUCUACUCCCAAGCUCCAAAAAA
AAPY01087500.1/804-957       UAGCC--CACCAGUCUGGUAGGCAGCAUUC-AACCCUUCUAUG-CCUUCUCUUGCCAACUGUUGAGGUCUUUCUUUUGAAAUAAA-GAAGAAAUAGACAAAUCAGACUUACCCUCUUGGAAAUGUGGUCCAGAUUUCUCUACUCCCAAGUUCCAAAAAA
ABDC01155953.1/418-571       UAGCC--CACCAGUCUGGCAGGCAAUGUUC-AAUCCUUCCAUG-CCUUCUCUCGCCAACUGUUGAGGUCUUUCUUUUGAAACAAA-GAAGAAAUAGACAAAUCAGACUUGCCCUCUUGGAAAUAUGGUCCAGAUUUCUCUACUCCCAAGCUCCAAAAAA
ABRT010183406.1/698-851      UAGCC--CACCUGUCUGUUAGGCAGCUCUC-GAUCCUUCUGUG-CCUUCUCUCACCAACCGUUGAGGUCUUUCUUCUGAAACAAA-GAAGAACUAGACAAAUCAGACUUGCCCUCUUGGAAAUGUGGUCCAGAUUUCUCUACUCCCAAGCUCCAAGCCA
AAKN02013867.1/5688-5535     UAGCC--CAGGAUUUGGGUAGGCAGCAUUC-AAUCCUUCUCUG-CCUUUUUCCGUCAACCGUUGAGGUCUUUCUUCUGAAACAGA-GAAGAAAUACACAAAUCAGACUUGUCCUCUUGGAAAUGUGGUCUAGAUUUCUCUACUCCCAAGCUCCAAAAAC
AAIY01406812.1/611-459       CAGCU--CACCAGUCUGGUAGGAACCAUUC-AGUCCUCCUAUG-CCUUCUUUCUCCAACUG-UGUGGUCUUUCUUCUGAAACAAA-GAAGAAAUAGCCAAAUCAGAAUUGCCCUCUUGGAAUUGUGGUCCAGAUUUCUCUACUCCCAAGCUUCACAAAU
ABRQ01017970.1/1694-1847     CAACC--UACCAGUCUGGUAGGCAGCAUUC-ACUCCUCCUCUG-CCUUCUUUCUCCAACUGGUAUGGUCUUUCUUCUGAAACAAA-GAAGAAAUAGACAAAUCAGAAUUAUCCUCUUGGAAUUGUGGUCCAGAUUGUUUUACUCCCAAGCUCCAAAAAG
AAWR02024755.1/22761-22912   UAGCC--CACCCGUCUGGCAGGCAGCAUUUCAAUCCUCCUAUG-CCUUCUUUCUC---CUCUUGUGGUCUUUCUUCUGAAACAAG-GAAGAAACAGUCAAAUUAGAUUUGCCCUCUUGGAAAUGUGGUCCAGAUUGCUCUACUCCCAAGCUCCAGAAAA
ABRR01116082.1/1475-1625     UAGCC--UGCUGAUCUGGGAGGGAGCAUUU-AGUCCUCCUAUG-CCUCCUUUCUC---CAGCUGUGGUCUUUUUUCUGAAACAAA-GAAGAAAUAGUCAAAUCAGACUUGCCCUCUUGGAAAUGUGGUCCAGAUUGCUCUACUCCCAAGCUCCAGAAAA
AAGV020089264.1/1245-1398    CAGCC--CACCAGUCUGGUAGGUAGCCUUC-AAUCCUCCUAUG-CCUCAUUUCUCUAACUAUUAGAGUCUUUCUUCUGAAACAAA-GAAGAAAUAGACAGAUCAGGAUUGCUCUUUUGGAAUUGGGGUCCAGAUUGCUCUACUCCCAAGCUCCAGAAAA
ABRN01423267.1/1381-1531     UAACC--CGCCAAUCUGGGAGGCAGCAUUU-GGUCCUCCUAUG-CCUCCUUUCUC---GUGAUGUGGUCUUUCUUCUGAAACAAA-GAAGAAAUAGUCAAAUCAGAUUUGCCUUCUUGGAAAUGUGGUCCAGAUUGCUCUACUCCCAAGCUCCAAAAAA
AALT01152167.1/3161-3013     UAGCC--CGCCAGUCUAGUAGGCAGCAUUC-GCGCCUCCUGUG-CCUUCUUUCUC---CU--UGUGGUCUUUCUUCUGAAACAAA-GAAGAAAGAGUCAGAUCAGACCUGCCCUCUUGGAAAUGUGGUCCAGAUUGCUCUACUCCCAAGCUCCAAACAG
ACBE01245156.1/1346-1496     UAGCC--CACCAGUCUGGUAGGCAGCGAUC-AGUCCUCCCAUG-GCUUCUUUCUC---CUGUGGCAGUCUUUAUUCUGACACAAA-GAAGGAAUCGUCAAGUCAGACUUGACCUCUUGGAAAUGUGGUCCAGAUUGCUCUACUCCCAAGCUCCAAAAAG
AACN010889736.1/452-302      UAGCC--UGCCAGCCUGGUAGGUAGUGGUC-GGUCCUCCUAUG-GCUUCUUUCUC---CUGUGGUGUUCUCUAUUCUGAAACAAA-GAAGAAAUAGUCAAAUCAGACGUGCCCUCUUGGAAAUGUGGUCCAGAUUGCUCUACUCCCAAGCUCCAAAAAA
ABRP01000339.1/2438-2591     AAACUAUUAAUAGCCUGGUAGGCAGCAUUC-AGUCCUCCUAUG-UCUUCUUUCUC---CUGUUGUGGUUUUUCUUCUGAAACAAAAGAAGAAAUUGUCAAAUCAGACUUGCCCUCUUGGAAGUGUGGUCCAGAUUGCUCUACUCCCAAGCUCCAGCAAA
AAFC03093132.1/132549-132698 UAGCC--UGCCCAUCCUG-AGGCUGCAUUU-AGUUUUCCUAAG-CCUCCUUCCUC---CUCUUGUGGCCUCUCUUCUGAAACAAA-GAAGAAACAGUCCAAUCAGACUUGCCCUCUUGGAAAUGUGGUCCAGAUUGCUCUACUCCCAAGCUCCUAAAAA
AAPE02006931.1/10934-10784   UAGCC--CACCAGACUGGGAGGCAGCAUUC-AGUUCUCCUAUG-CCUUCUUUCUC---CUGGUGUGGUCUUUCUUCUGAAACAAA-GAAGACAUUGUCAAAUCAGACUUGCCCUCUUGGAAAUGUGGUCCAGAUUGCUCUACUCCCAAGCUCCAAAAAA
AAQR03016744.1/74463-74310   UAGCC--CACCAGUCUGGCAGGCAAUAUUC-AAUUCUUCCAUG-CCUACUCUCACCAACCAUUAAGGUCUUUCUUUUGAAACAAA-GAAGAAAUUGACCAAUCAGACUUGCCCUGUUGGAAAUGUGGUCCAGAUUUCUCUACUCCCAAGCUCCAAAAAA
AAHX01048282.1/89057-89210   UAGCC--CACUCACUUGU-AGGCAGCAUUC-CAACCUUCUGUGACUUUUUCUCGACAACUUUUGAGGUCUUUCUUCUGAAACAAA-GAAGAAAUAGACAAACCAGAUUUGUCCUCUUGGAAAUGUGGUCCAGAUUUCUCUACUCCCAAUCUCCAAAAUA
AAGU03008645.1/65779-65932   CUGUC--CACCAGUCUGGUAGGCAGCAUUC-AGUCCUCCUAUG-CCUUCUUUCUCCAACUGGUGUUGUCUUUCUUGUGAAACAAA-GAAGAAGUAGACAAAUCAGAAUUGCCCUCUUGGAAUUGUGGUCCAGAUUGUUCUACUCCCAAGCUCCAAAAAG
AAGW02034242.1/7763-7614     UAGCC--CACCAGUCUGGUAGGCAGCACUU-AAUCCUUCUAUG-CCUUCUUCCGCCAACUGUUGAGGUCUUUCUUCUGAA----ACGAAGAAAUAGACAA-UCAGACUUGUCCUCUUGGAAAUGUGGUCCAGAUUUCUCUACUCCCAAGCUCCAAAAAA
#=GC SS_cons                 :::::..:::::::::::::::::::::::.::::::::::::.:::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      uAGCC..caccaguCuGGuAGGcAGCauUc.aguCCUcCUaUG.cCUucUuUCuCcAaCuguUGuGGUCUUUcUUcUGAAACAAA.GAAGAAauaGuCaAAUCAGAcUUGcCCUCUUGGAAaUGUGGUCCAGAUUgCUCUACUCCCAAGCUCCAaaAaa
//
# STOCKHOLM 1.0

#=GF AC   RF01972
#=GF ID   H19_1
#=GF DE   H19 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   53.30
#=GF NC   39.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 37.53 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   1363808
#=GF RT   Monoallelic expression of the human H19 gene.
#=GF RA   Zhang Y, Tycko B
#=GF RL   Nat Genet. 1992;1:40-44.
#=GF WK   H19_(gene)
#=GF SQ   35


BC053636.1/935-865         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
AAPY01607917.1/1901-1971   GAGGCACCGAUCACUGCUCCGUCGCUGCCC-AC-GAGGCCCUCCUUGGCCAUGGGCUCUGGAGGCCAGUGCCC
AF214115.1/1092-1022       GAGGCACCGAUCACUGCUCCGUCGCCGCCC-GC-AAGGCCCUCCUUGGCCACGGACUCUGGAGGCCAGUGCCU
AAKN02038607.1/34760-34690 GAGGCACCGAUCACUGCUCCGUCGUCACCU-GC-GAGGCCCACCUUGGCCACAGGCUCUGGAGGCCAGUGCCU
AF190058.1/714-646         GAGGCACCGAUCCCGG-UCCGCCGCCGCCC-GC-GAGGCCCACCUUGGCCACGG-CUCUGGAGGCCAGUGCCU
ACBE01354129.1/1652-1723   GAGGCACCGAUCCCUGCUCCGUCGUCGCCC-GCAGAGGCCCACCUUGGCCACGGGCUCCGGAGGCCAGUGCCC
M97348.1/880-810           GAGGCGCCGAUCACUGCUCCGUCGCCGCCC-GC-AAGGCCCGCCUUGGCCGCGGGCUCUGGAGGCCAGCGCCC
ABRP01221690.1/1794-1865   GAGGCACCGAUCCCUGCUCCGUCACCGCCC-GCGCUGGCCCGCCUUGGCCACGGGCUCCGGAGGCCAGUGCCC
AAYZ01478517.1/931-1000    AGGGCGCCGAUCU-CGCUCCAUCGCAGCCCAUC--AGGCCCACCUUGGCCACGGGCUCAGGAAGCCAGCGCCC
AF190056.1/755-685         GAGGCACCGAUCCCUGCUCCGUCGUCGCCC-GCGGAG-CCCACCUCGGCCACGGGCUCUGGAGGCCAGCGCCC
AJ566210.1/5618-5549       AAGGCACCGAUCC-CGCUCCGUCAUCGCCC-GCAGAGGCCCGCCUUGGCCACGGGCUC-GAAGUCCAGUGCCC
AAWR02038016.1/7406-7476   GAGGCACCGAUCACUGCUCCAUCGCCGCCC-GCACAGGCCCGCCUUGGCCGCGGGCUCCGGAGUCCAG-GCCC
ABRN01220595.1/5512-5580   --CGGACCGAUCCAUGCUCCGUCACCGCCC-GCAGAGGCCCGCCUUGGCCAUGGGCUC-GGAGGCCAGUGACC
AC004556.1/51722-51792     GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
AY091484.1/1481-1411       AAGGCACCGAUCC-CGCUCCGUCAUCGCCCAGCAGAGGCCCGCCUUGGCCACGGGCUC-GAAGUCCAGUGCCC
BC025150.1/163-93          GAGACACCGAUCACUGCUCCGUCGCCGCCC-GC-AAGGCCCUCCUUGGCCACGGACUCUGGAGGCCAGUGCCU
BC098439.1/696-626         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
BC006831.1/566-496         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
BC007513.2/606-536         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
BC009853.1/63-1            GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCCCU-----C--GUGCC-
X07201.1/1693-1625         GAGUCACCGAUCACUGCUCCGUCGCCGCCC-GC-AAG-CC-UCCUUGGCCACGGACUCUGGAGGCCAGUGCCU
BC069247.1/724-654         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
AF190057.1/799-729         GAGGCACCGAUCCCUGCUCCGUCGACGCCC-GCAGAGGCCCGCCUUGGCC-CGGGCUCUGGAGGCCAGUGCCU
BC110657.1/935-865         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
BC063626.1/678-608         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
AY849926.1/1117-1048       GAGGCACCGAUCC-CGCUCCGUCAUCGCCC-GCAGAGGCCCGCCUUGGCCACGAGCUC-GAAGUCCAAUGCCC
BC015952.2/818-748         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
BC053637.1/620-550         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
AF125183.1/11402-11332     GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
M32053.1/2135-2065         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
X58196.1/853-783           GAGACACCGAUCACUGCUCCGUCGCCGCCC-GC-AAGGCCCUCCUUGGCCACGGACUCUGGAGGCCAGUGCCU
BC013067.1/178-108         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
AF049091.1/6811-6741       GAGACACCGAUCACUGCUCCGUCGCCGCCC-GC-AAGGCCCUCCUUGGCCACGGACUCUGGAGGCCAGUGCCU
BC063564.1/698-628         GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
AF087017.1/9628-9558       GAGGCACCGAUCCCGGCUCCGUCGCCGCCC-GC-GAGGCCCGCCUUGGCCACGGGCUCUGGAGGCCAGUGCCU
#=GC SS_cons               ::::::::::::::::::::::::::::::.::.:::::::::::::::::::::::::::::::::::::::
#=GC RF                    GAGGCACCGAUCcCuGCUCCGUCGCCGCCC.GC.GAGGCCCgCCUUGGCCACGGGCUCUGGAGGCCAGUGCCu
//
# STOCKHOLM 1.0

#=GF AC   RF01973
#=GF ID   H19_2
#=GF DE   H19 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   51.00
#=GF NC   34.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   1363808
#=GF RT   Monoallelic expression of the human H19 gene.
#=GF RA   Zhang Y, Tycko B
#=GF RL   Nat Genet. 1992;1:40-44.
#=GF WK   H19_(gene)
#=GF SQ   23


AC004556.1/52666-52734     CAGCUCCCC-UCGUCCAACCAGCUGCCACGUCCUGUAA-CCAAAAGUGACCGGGAUGAAUGCCUGGCUCCC
ABRO01334164.1/451-520     CAGCUCCCCCUUGUCCAACCAGCCGCCACGUCCUGUAA-CCAAAAGUGACCGGGAUGAAUGCCUGGCUCCC
AAYZ01478517.1/1819-1888   CAGCUCCCCCUCGUCCGACCAGCUGCCACGUCCUGUAA-CCAAAAGUGACCGGGAUGAAUGUCUGGCACCC
ABRQ01472806.1/821-890     UAACACCCCUUUGUCCAACCAGCUGCCACGUCCUGUAA-CCAAAAGUGACCGGGAUGAGUGUCUGGCUCCC
BC099104.1/232-163         CAGCUCCCCUGUAUCCGACCAGCCGCCACGUCCUGUAA-CCAAAAGUGACCGGGAUGAAUGUCUGGCUCCC
AAKN02038607.1/33773-33704 CAGCUCCCCCUUGUCCGACCAGCCACCACGUCCUGUAA-CCAAAAAUGACCGGGAUGAAUGUCUGGCUCCU
AAPY01119966.1/755-824     CUGCUCCCUCGUGUCUGACCAGCCGCCACGUCCUGUAA-CCAAAAGUGACCGGGAUGAAUGUCUGGCUCCC
ABRP01221691.1/361-428     CAG-UCCCCCUUGUCC-ACCAGCCGCCACGUCCUGAAA-CCAAAAUUGACCGGGAUGAAUGUCUGGCUCCC
AAWR02038016.1/8387-8456   CAGCUCCCCCUCGUCC-ACCAGCCGCCACGUCCUGAAAACCAAAAUUGACCGGGAUGAAUGUCUGGCUCCC
ABRN01220595.1/6478-6544   CAGCUCCCC--CGUCC-ACCAGCUGCCACGACCUGAAA-CCAAAAUUGACCGGGAUGAAUGCCUGGCUCCC
AY044827.1/34802-34735     CAACUCCCC-CUGACC-ACCAGCCGCCACGACCUGAAA-CCAAAAUUGACCGGGAUGAAUGCCUGGCUCCC
AY091484.1/578-512         AAGCCCCCC--UGUCC-ACCAGCCGCCACGACCUGAAA-CCAAAAUUGACCGGGAUGAAUGCCUGGCUCCC
AF214115.1/69-3            CAGC--CCCUGUAUCCGACCAGCCGCCACGUCC-GUAA-CCAAAAGUGACCGGGAUGAAUGUCUGGUCCCC
AY849926.1/148-83          AAG-ACCCC--UGUCC-ACCAGUCGCCACGAUCUGAAA-CCAAAAUUGACCGGGAUGAAUGCCUGGCUCCC
AANN01084361.1/801-736     CUCCUCCCC--UGUC--ACCAGCCGCCACGUCCUGAAA-CCAGAAAAAACCGGGAUGAAUGCCUGGCUGAC
EU502716.1/6440-6375       AAG-ACCCC--UGUCC-ACCAGUCGCCACGAUCUGAAA-CCAAAAUUGACCGGGAUGAAUGCCUGGCUCCC
AF125183.1/10458-10390     CAGCUCCCC-UCGUCCAACCAGCUGCCACGUCCUGUAA-CCAAAAGUGACCGGGAUGAAUGCCUGGCUCCC
M32053.1/1191-1123         CAGCUCCCC-UCGUCCAACCAGCUGCCACGUCCUGUAA-CCAAAAGUGACCGGGAUGAAUGCCUGGCUCCC
AF049091.1/5815-5746       CAGCUCCCCUUUAUCCGACCAGCCGCCACGUCCUGUAA-CCAAAAGUAACCGGGAUGAAUGUCUGGCUCCC
AF087017.1/8686-8618       CAGCUCCCC-UCGUCCAACCAGCUGCCACGUCCUGUAA-CCAAAAGUGACCGGGAUGAAUGCCUGGCUCCC
X07201.1/706-637           CAGCUCCCCUUUAUCCGACCAGCCGCCACGUCCUGUAA-CCAAAAGUAACCGGGAUGAAUGUCUGGCUCCC
AC187029.8/154545-154477   CGGCUCCCC-UUGUCC-ACCAGCCGCCACGUCCUGAAACCAAAAACUGACCGGGAUGAAUGCCUGGCUCCC
AAQR03144870.1/3968-3900   CAGCUCCCC-UGGUCCGACCAGCCGCCACGUCCUGUAA-CCAAAAGUGACCGGGAUGAAUGUCUGGCUUCC
#=GC SS_cons               :::::::::.::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::
#=GC RF                    CaGCUCCCC.uuGUCCgACCAGCCGCCACGUCCUGuAA.CCAAAAgUGACCGGGAUGAAUGcCUGGCUCCC
//
# STOCKHOLM 1.0

#=GF AC   RF01974
#=GF ID   H19_3
#=GF DE   H19 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   46.00
#=GF TC   47.40
#=GF NC   44.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.46 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   1363808
#=GF RT   Monoallelic expression of the human H19 gene.
#=GF RA   Zhang Y, Tycko B
#=GF RL   Nat Genet. 1992;1:40-44.
#=GF WK   H19_(gene)
#=GF SQ   5


AF087017.1/8457-8342   AUGUCCAAGGUGCUCCUUGGCUCCCACAAGCUCUCCUCCAGCACCCCAUCUUCCCCUGGUUGCCCCUCGGUUCCCCACUUCCCCAGUUUCCCCCGUUACCCCCCACCCAUCCCACC
AC004556.1/52895-53010 AUGUCCAAGGUGCUCCUUGGCUCCCACAAGCUCUCCUCCAGCACCCCAUCUUCCCCUGGUUGCCCCUCGGUUCCCCACUUCCCCAGUUUCCCCCGUUACCCCCCACCCAUCCCACC
AF125183.1/10229-10114 AUGUCCAAGGUGCUCCUUGGCUCCCACAAGCUCUCCUCCAGCACCCCAUCUUCCCCUGGUUGCCCCUCGGUUCCCCACUUCCCCAGUUUCCCCCGUUACCCCCCACCCAUCCCACC
M32053.1/962-847       AUGUCCAAGGUGCUCCUUGGCUCCCACAAGCUCUCCUCCAGCACCCCAUCUUCCCCUGGUUGCCCCUCGGUUCCCCACUUCCCCAGUUUCCCCCGUUACCCCCCACCCAUCCCACC
AP000446.5/40407-40521 AUGUCUAAGGCACUCCUUGGCUCCCACAAGCUCUCUUCUAGUGCCUCAUCUUCCUCUGGUUGCCUCUCGACUCCCCACUUCCCCAGUUUCCCUCAUUACCCCC-ACACCUUCCACC
#=GC SS_cons           ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                AUGUCcAAGGuGCUCCUUGGCUCCCACAAGCUCUCcUCcAGcaCCcCAUCUUCCcCUGGUUGCCcCUCGGuUCCCCACUUCCCCAGUUUCCCcCGUUACCCCCCACcCaUcCCACC
//
# STOCKHOLM 1.0

#=GF AC   RF01975
#=GF ID   HOTAIRM1_1
#=GF DE   HOX antisense intergenic RNA myeloid 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   70.00
#=GF TC   75.00
#=GF NC   50.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 40.23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   19144990
#=GF RT   A myelopoiesis-associated regulatory intergenic noncoding RNA transcript
#=GF RT   within the human HOXA cluster.
#=GF RA   Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR,
#=GF RA   Kapranov P, Weissman SM, Newburger PE
#=GF RL   Blood. 2009;113:2526-2534.
#=GF WK   HOTAIRM1
#=GF SQ   14


AC004079.1/78519-78643     CACCGUUUUAGUGGCAUUUAAAUCCCCGGCGCUCCGC-CGUCUAGGUGACGCGCAGUCGCCCCCCCAGGCAGCCUAGGCGGCGGCA---GCUGCUGCGGCGACUGCAAAGGCCGAUUUGGAGUGCUGGA
AANG01383093.1/6089-6214   CACCGUUUCAGUGGCAUUUAAAUCCCCGGCGCUCCUCCAGUCUAGGUGACGCGCAGUCGCCCCCCCAGGCGGCCCAGGCGGCGGCA---GCUGCUGCGGCGGCUGCAAGGGCAGAUUCGGAGCGCUGGG
ABRO01036369.1/72-199      CACUGUUUCAGUGGCAUUUAAAUCCCCGGCGCUCCUC-AGUCUGGGUGACGUGCCGUCGCCCCCCCAGGCAGCCCAGGCGGCGGCAGCUGCAGCUGCGGCGGCUGCAAAGGCAGAUUCAGAGCGCUGGA
AAKN02039089.1/5983-6107   CACCGUUUCAGUGGCAUUUAAAUCCCUGGCGCUCCUC-CGCCUAGGUGACGCGCAGUCGCCCCCCCAGGCAGCCCAGGCAGCGGCA---GCAGCUGCGGCGCCUGCCACGGCAGAUUCGGAGCGCUGGG
AAWR02014100.1/90879-91003 CACCGUUUCAGUGGCAUUUAAAUCCCGGGCGCUCCUC-AGUCUAGGUGACGCGCAGUCGCCCCCCCAGGCAGCCCAGGCGGCGGCA---GCAGCUGCGGUGGCUGCAAGGGCAGAUUCAGAGCGCUGGG
AAGV020346967.1/2189-2313  CACCGUUUCAGUGGCAUUUAAAUCCCCGGCGCUCCUC-CGUCUGGGUGACGCGCAGUCGCCCCCCCAGGCAGCCCAGGCGGCCGCA---GCAGCGGCGGUGGCAGCAACCGCCCAUUCGGAGCACUGGG
ABRP01099855.1/207-331     CACCGUUUCAGUGGCAUUUAAAUCCCCGGCGCUCCUC-AGUCUAGGUGACGCGCAGUCGCCCCCCCAGGCAGCCCAGGCGACGGCG---GCAGCUGCGACGGCUGCAAGGACAGAUUCGCAGCGCUGGG
ABRT010305835.1/90-212     CACCAUUUCAGUGGCAUUUAAAUCCCCGGCGCUUCUC-CGUCUAGGUGACGCGCAGUCGCCCCCCCAGGCAACCCAAGAGGCGGCA---GCAGCUGCGGCGGCUGCCACGGCAGAUUCG--GUGCUGGG
AAQQ01071855.1/104-228     CACCGUUUCAGUGGCAUUUAAAUCCCCGGCGCUCCUC-UGUCUAGGUGACGCGCAGCAGCCCCCCCAGGCAGCCCAGGCGACGGCA---GCAGCUGCAGCGGCUGCAACGACAGAUUCCGAGCGCUGGG
AAFC03094354.1/97532-97659 CACCGUUUCAGUGGCAUUUAAAUCCCCGGCGCUCCUC-AGUCUAGGUGACGCGCAGUCGCCCCCCCAGGCAGCCUGGGCGGCGGCAGCAGCAGCUGCGGCGGCCGCAGGGGCAGAAGCGGAGCGCUAAG
AAYZ01055278.1/10927-11050 CACCGUUUCAGUGGCAUUUAAGU-CCCGGCGCUCCUC-GGUCUAGGUGACGCGCAGUCGCCCCCCCAGGCGGCCCAGGAGGCGGCA---GAAGCUGCGGUGGCUGCCAACGCAGCUUCACAGCUCUGGG
AANU01289429.1/101-4       CACCGUUUCAGUGGCAUUUAAAUCCCCGGCGCUCCGC-CGUCUAGGUGACGCGCAGUCGCCCCCCCAGGCAGCCCAGGCGGCGGCA---GCUGCUGCGGCGA---------------------------
AC116662.1/86579-86455     CACCGUUUCAGUGGCAUUUAAAUCCCCGGCGCUCCUC-AGUGUAGGUGACGCGCGCUCGCCCCCCCAGGCAGCCCGGGCCGCGGCG---GUAGCUACGGCCGCUGCCGGAGCUGACUUGGAGCAUUGGG
AAGW02035950.1/13970-13846 CACCGUUUCAGUGGCAUUUAAGUCCCCGGCGCUCCUC-CGUCUAGGUGACGCGCAGUCGCCCCCCCAGGCAGCUCAGGAGGCGGCA---GAAGCUGCGGCGGCUGCAACUGCAGCUUCACAGCCCUGGG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::...::::::::::::::::::::::::::::::::::::::::
#=GC RF                    CACCGUUUCAGUGGCAUUUAAAUCCCCGGCGCUCCUC.aGUCUaGGUGACGCGCaGUCGCCCCCCCAGGCAGCCCaGGcGGCGGCa...GcaGCUGCGGcGGCuGCaaggGCaGauUcggAGCgCUGGG
//
# STOCKHOLM 1.0

#=GF AC   RF01976
#=GF ID   HOTAIRM1_2
#=GF DE   HOX antisense intergenic RNA myeloid 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   37.00
#=GF TC   44.80
#=GF NC   34.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   19144990
#=GF RT   A myelopoiesis-associated regulatory intergenic noncoding RNA transcript
#=GF RT   within the human HOXA cluster.
#=GF RA   Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR,
#=GF RA   Kapranov P, Weissman SM, Newburger PE
#=GF RL   Blood. 2009;113:2526-2534.
#=GF WK   HOTAIRM1
#=GF SQ   7


AC004079.1/81295-81509     GCAUCCGCGGCUCAGCCAAGCUGUUGUUUUAAAAGAGCAAUAAAAAUGAAUUAUGACU-AAACGCCUUCUAACUUAAUGCUUUCGGACGGGGAUCCCCGG------CAAAUAACGUAAGAGGAUUUUU---AUUUGUGCAUGUGUUCCUGCAAUUGAUCU----CUUUGAUGACAUUCUCAUUCAUAGAAAGCGUUUGAUUUAUGAGCG-UAGGACGAAUCGCAUCCAGG
ABRO01036369.1/2807-3020   GCAUUCGCUGCUCAGCCAAGCUGUUGUUUUUAAAGAGCAAUAAAAAUGAAUUAUGACU-AAAUGCCUUCUAACUUAAUGCCUUCGGACGGGGAUCCCCAG------CAAAUA-CGUAAGAGGAUUUUU---AUUUGUGCAUGUGUUCCUGCAAUUGAUCU----CUUUGAUGACAUUCUCAUUCAUAGAAAGCAGUUGAUUUAUGAGCU-UAGGACGAAUCGUAUCCAGG
AAPN01063686.1/769-988     GCAUCCGCAGCUCAGCCAAGCUGUUAUUUUAAAAGAGCAAUAAAAAUGAAUUAUGACU-AAACGCCUCCUAACUUAAUGCUUUCGGACGGGGUUCCCCAGCCCAGGCAAAUA-CGUAAGAGGAUUUUU---AUUUGUGCAUGUGUUCCUGCAAUUGAUCU----CUUUGAUGACAUUCUCAUUCAUAGAAAGAGUUUGAUUUAUGAGUG-UAGGAAGAAUCGCAUCUAGC
AC163712.3/121395-121614   GCGGCCGCAGCUCAGCCAAGCUGUUGUUUUAAAGGAGCAAUAAAAAUGAAUUAUGACU-AAACGCCUUCUCACUUAAUGGUUUUAGACGGGGAUCCCCAGCCCCGGCAAAUA-CGUAAGAGGAUUUUU---AUUUGUGCAUGUGUUCCUGCAAUUGAUCU----CUUUGAUGACAUUCUCAUUCAUAGAAAGCGUUUGAUUUAUGACUU-UAGGAAGAAUUGCGUUCAGC
AAFR03047697.1/31523-31302 GCAUCGGCAGCUUAUCCAAGCUGUUGUUUUAAAAGAGCAAUAAAAAUGACUUAUAGCUUAAACGCCUCCUAACUUAAUGCUUUCCGACGGGGAUCCCCAGCUCGGGCAAAUA-CGUAAGAGGACUUGU---AUUUGUGCAUGUGUUCCUGCGAUUGAUCU----CUUUGAUGACAUUCUCAUUCAUAGAAAGAGUUUGAUUUAUGAGCACUAGGAAGAAUCUUAUCCAGC
AC145789.3/24347-24573     CCAGCCGCUGGAAAGCCAAGCUGUUGUUUUAAUAGAGCAAUAAAAAUGAAUUAUAGUUUAAACGCCUUCGAGCUUAGAGCUUCUGGAUGGA-AUCCCCAGUCCAGACUAAUA-CGUAAGAGGUUUUUUUUUAUUUGUGUGUGAGCUCCUGCAAUUGAUCUUCCCCCUCGAUGACAUCCUCGUUCAUAGAACGUAUUUGAUUUAUGAGAU-UAGGAAGAAUUGCAUCCAGC
AAWZ02022933.1/14144-13925 GCACCUGAAGCCUAGCCAAGCUGUUGUUUUAACAGCGCAAUAAAAAUGAAUUAUGACU-AACCGCCUCCUCGCUUAAUGGUUUUAGACGGGGAUCCCCAGGCCGAGCAAAUA-CGUAAGGAGAUUUUU---AUUUGUGCAUGUGUUCCUGCCAUUGAUUU----CUUCGAUGACAUUCUCAUUCACAGAAAGCGGGUGAUUUAUGGGUU-UAGGAAGAAUUGCAUCCAAC
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::...:::::::::::::::::::::::::::::....:::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::
#=GC RF                    gCauCcGcaGcucAGCCAAGCUGUUGUUUUaAaaGaGCAAUAAAAAUGAaUUAUgacU.AAaCGCCUuCuaaCUUAauGcuUuugGAcGGGGaUCCCCaGccCgggCaAAUA.CGUAAGaGGauUUuU...AUUUGUGcaUGuGuUCCUGCaAUUGAUcU....CuUuGAUGACAUuCUCaUUCAuAGAAaGcguuUGAUUUAUGaGuu.UAGGAaGAAUuGcaUCCAGc
//
# STOCKHOLM 1.0

#=GF AC   RF01977
#=GF ID   HOTAIRM1_3
#=GF DE   HOX antisense intergenic RNA myeloid 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   37.00
#=GF TC   43.90
#=GF NC   32.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.76 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   19144990
#=GF RT   A myelopoiesis-associated regulatory intergenic noncoding RNA transcript
#=GF RT   within the human HOXA cluster.
#=GF RA   Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR,
#=GF RA   Kapranov P, Weissman SM, Newburger PE
#=GF RL   Blood. 2009;113:2526-2534.
#=GF WK   HOTAIRM1
#=GF SQ   11


AC004079.1/82173-82231     GGUCUGUUUUGCCUGAACCCAUCAACAGCUGGGAGAUUAAUCAACCACACUGAAAAUGU
ABRT010305838.1/514-572    GGUCUGCUUUGCCUGAGUCCAUCAACAGCUGGGAGAUUAAUCAACCACACUGAAAAUGA
CAAA01010317.1/3510-3452   GGUCUGUUUUUCCUGAACCCAUCCACAGCUGGGAGAUUAAUCAACCACACUGAAAAUGG
ABRR01276308.1/2083-2140   GGUCUG-UUUGCCUGGACCCAUCAACAGCUGGGAGACUAAUCAACCACACUGAAAAUGU
AAPY01076957.1/2330-2388   GGUCUGUUUUGCCUGAACCCAUCAACAGCUGGGAUAUUGAUCAACCACAUGGAAAAUGC
ABVD01851011.1/311-368     GGUCUG-UUUGCCUGGACUCAUCCACACCUGGGAGACUAAUCAACCACACUGAAAAUGU
ABRO01036369.1/3649-3703   GGUCUGUUUUGCCUGAACCUAU---CAGCUGGGAGAUUAAUCGACCACACUG-AAAUAU
AAIY01403574.1/1325-1380   GGUCUG-UUUGCCUGGACCCAUCAACAGCUGAGAGACUAAUCAACC--ACUGAAACUGU
ABRQ01114923.1/3708-3765   GGUCUC-UUUGCCUGGACCCAUCGACAGCUGGGAGACUAAUCAACCUCUCUGAAAAUGC
AALT01437814.1/1047-990    GGUCUG-UUUGCCUGGACCCAUCAGCAGCUGGGAGACUAAUGGACCACGGUGGAAAUGU
AAGW02035950.1/10461-10403 GGUCUGUGUUGCCUGAACCCAUCAACAGCUGGGAGAUUAAUCAGCCACGCUGAAAAUGU
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GGUCUGUUUUGCCUGgACCCAUCaACAGCUGGGAGAuUAAUCAACCACaCUGAAAAUGu
//
# STOCKHOLM 1.0

#=GF AC   RF01978
#=GF ID   HOTAIRM1_4
#=GF DE   HOX antisense intergenic RNA myeloid 1 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   45.30
#=GF NC   35.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.87 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   19144990
#=GF RT   A myelopoiesis-associated regulatory intergenic noncoding RNA transcript
#=GF RT   within the human HOXA cluster.
#=GF RA   Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR,
#=GF RA   Kapranov P, Weissman SM, Newburger PE
#=GF RL   Blood. 2009;113:2526-2534.
#=GF WK   HOTAIRM1
#=GF SQ   10


AC004079.1/82251-82352     GGGGUUGAAAUGUGGGUGUUUGAAACAAAAGUGUAUA-AACAAAUGAAUUGUUGAUAACUUAGUUAUUGACCUGGAGACUGGUAGCUUAUUAAAGAAACUCCG
ACBE01077414.1/9750-9851   GGGGUUGGAAUGUAGAUGUUUGAAACAAAUGUGUAUA-AAUAAAUGAAUUGUUGAUAACUUAGUUAUUGACCUGGAGACUGGUAGCUUGUUAAAGAAACUCCA
AAIY01403574.1/1403-1504   GGGGUUGGAAUGUAGAUGUCUGAAACAAACGUGUAUA-AAUAAAUGGAUUGCUGAUAACUUAGCUAUUGACCUGGAGACUAGUAGUUUGUUAAAGAAACCCCA
AAKN02039089.1/9540-9640   GGGGUC-GAAUGUAGAUGUUUCAGACAAACGUGUAUA-AAUAAAUGAAUUGUUGGUAACUUAGUUAUUGACCUGGAGACUGAUAGCUUGUUCAAGAAACUCCA
AAPY01076957.1/2419-2520   GGGAUCAGAAUGUAGAUGUUUAAAACAAAUGUGUAUA-AAUAAAUGAAUUGUUGGUAACUUAGUUAUUGACCUGAAGACUGUUAGCUUGUUAAAGAAACUCCA
ABRO01036369.1/3733-3834   GGGGUUAAAAUGUAGAUGUUUGAAACAAAUGUGUAUA-AAUAAAGGAAUUGUUGAUAACUUAGUUAAAAACAUGGAGACUAGCAGCUAGUUAAAGAAACUCCA
AAGV020346969.1/819-920    AGGGGUGGAACAUAGAUGUUUGAAACAAACGUGUAAA-AAUAAAUGAAAUGUUGAUAACUUAGUUAAUGACCUAGAGACUGGUAGCUUGUUCAGGAACCUCCA
ABRQ01114923.1/3795-3894   GGGGCUGGAAUGUAGAUGUUUGAAAGAAACGUGUAAA---UAAAUGAAUUGUGGAUAACUUAGUUAUUGGCCUGGAGACUAGUAGCUUGUUAAAGAAACUCCA
AAQQ01071857.1/581-671     GGGGUUGGAAUGUAGAUGUUUGGGACCAAUGUGUAUA-AAUAAAUGAAUUGUUGAUAAC----UUAUUGACCUGG-------UAGCUUGUUAAAGAAACCCAG
AAGW02035950.1/10379-10279 GG--CUGGAAUGCAGAUGUUUGAAACAAAUGUGUAUUCAAUAAAUGAAUUGUUGAUAACUUAGUUAUUGGGCUGGAGACUGGUCGCUGGUCAGAGAAACGCCA
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GGGGuUGGAAUGUAGAUGUUUGAAACAAAuGUGUAuA.AAUAAAUGAAUUGUUGaUAACUUAGUUAuUGaCCUGGAGACUGGUAGCUuGUUaAAGAAACuCCa
//
# STOCKHOLM 1.0

#=GF AC   RF01979
#=GF ID   HOTAIRM1_5
#=GF DE   HOX antisense intergenic RNA myeloid 1 conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   67.10
#=GF NC   52.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.29 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   19144990
#=GF RT   A myelopoiesis-associated regulatory intergenic noncoding RNA transcript
#=GF RT   within the human HOXA cluster.
#=GF RA   Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR,
#=GF RA   Kapranov P, Weissman SM, Newburger PE
#=GF RL   Blood. 2009;113:2526-2534.
#=GF WK   HOTAIRM1
#=GF SQ   10


AC004079.1/82362-82506       UUCCUGGAGUUGGG-GGUUUCUGUAGGCACUUU-AUUUCUCCACUUUCAAGAGC---UUGGGCUUGGCCCAAAUCUUAGACUGUCCAAUUCUGCCUCUAUUACCAAUUUAAAUCUAUGGCUUGAACCUGUGCACU-GAAAAUCAAAUCCUU
ABRT010305838.1/698-842      AUCCUGGAGUUGAG-GGUUUCUGUAGGCACUUU-AUUUCUCCAUUUUCAAAUGC---UUGGGCUUGGCCCAAAUCUUAGGCUGCCCAAUCCUGUUUUUAUUACCAAUUUAAAUCUAUGGCUUGAACCUGUACACU-GAAAACCAAAUCCAU
AAFC03094354.1/101361-101503 UUCCUGGAGUUGGA-GGUUUCUGUAGGCACUUU-AUUUCUCCACUUUCAAAAGC---UUGGGCUUGGCCCAACUC--AGGCUGCCCAAUCCUGUUUCUAUUGCCAAUUUAAAUCUAUGGCUUGAACCUCUACGUU-GAAAACCUAAUCCAU
ABRR01276309.1/113-258       UUCCUGGAGUUGGG-GGUUUCUGUAGGCACUUU-GUUUCUCCACUUUCAAAAGC---UUGGGCUUGGCCCAGCUCUGAGGCUGCCCAAUCAUGUUUCUAUUACCAAUUUAAAUCUAUGGCUUGAACCUCUACAUUGAAAAACCAAAUCCAU
AANG01383093.1/9893-10040    UUCCUGGAGUUGGGCGGUUUCUGAAGGCACUUUUAUUUCUCCACUUUCAAAAGC---UUGGGCUUGGCCCAACUGUGAGGCUGCCCAAUCCUGUUUCUAUUACCAAUUUAAAUCUAUGGCUUGAACCUCUACACUGAAAAACCAAAUCCAU
AAWR02014100.1/94686-94829   AUCCUGGAGUUGG--GGUUUCUGUAGGCACUUU-AUUUCUCCACUUUCAAAAGC---UUGGGCUUGACCCAACUCUGAGGCUGCCCCAUCCUGUUUCUAUUACCAAUUUAAAUCUAUGGCUUCAACCUCUACACU-AAAAACCAAAUCCAU
AAQQ01071857.1/681-823       UUCCUAGAGCUGG--GGUUUCAGUAGGCACUUU-AUUUCUCCACCUUCAAAAGC---UUGAGCUUG-CCCAACUCUUAGGCUGCCCAAUCCUGUUUCUAUUACUAAUUUAAAUUUAUGGCUUGAGCCACUACACU-GAAAGCCAAAUCCAU
AAGV020346969.1/923-1067     UUCCU-GAGUGGGG-GAUUUCUGUAGGCACUUU-AUUUCUCCAGUUUCAAAAGC---UUCGGCUUGGCCCGAAUUAGGGGCUGUCCGAUCCUGUUUCUAUUACCCAUUCAAAUCUAUGGCUUGAACCUCUGCACUGAAAAAUCAAGUCUAU
AAQR03057532.1/15102-15250   UUCCUGGAGUUGAG-GGUUUCUGUAGGCACUUUUAUUUCUUUAUUUUCAAGAGGAGGUUGGGCCUGGCUCAAAUCUUAGGCUGCCCAAUCUUGUUUCUAUUACCAAUUUUAAUCUAUGGCUUGAUCCUGUACACU-GAAAACCAAAUUCAU
AC186206.6/149801-149946     UUCCUGGAGUUGGG-GGUUUCUGUAGGCACUUU-AUUUCGCCACUUUCAAAAGC---UUGGGCUUGGCUCAGCUCUGGGGCUGCCCAAUUCUGUUUCUAUCACCAAUUUAAAUCUAUGGCUUGAACCUCUACACUGAAAAACCAAAUCCAU
#=GC SS_cons                 ::::::::::::::.::::::::::::::::::.::::::::::::::::::::...::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::
#=GC RF                      uUCCUGGAGUuGGG.GGUUUCUGUAGGCACUUU.AUUUCUCCAcUUUCAAaaGc...UUGGGCUUGGCcCAacUcugaGGCUGcCCaAUccUGUUUCUAUUACCaAUUUaAAUCUAUGGCUUGAaCCUcUaCAcU.gAAAAcCaAAUCCaU
//
# STOCKHOLM 1.0

#=GF AC   RF01981
#=GF ID   PCGEM1
#=GF DE   Prostate-specific transcript 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   75.00
#=GF TC   80.80
#=GF NC   35.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.34 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0042981; regulation of apoptotic process;
#=GF RN   [1]
#=GF RM   11050243
#=GF RT   PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer.
#=GF RA   Srikantan V, Zou Z, Petrovics G, Xu L, Augustus M, Davis L, Livezey JR,
#=GF RA   Connell T, Sesterhenn IA, Yoshino K, Buzard GS, Mostofi FK, McLeod DG,
#=GF RA   Moul JW, Srivastava S
#=GF RL   Proc Natl Acad Sci U S A. 2000;97:12216-12221.
#=GF WK   PCGEM1
#=GF SQ   26


ABRT010120442.1/19901-20032 AAAACAAAGGUGCCUUUGCCAAUAUUA-UGUUUCUUUUUGACAAGUUCUGUGAUUUCUGAGGGGAA-UCCACUAUAAAUGGGAUCAGGUCAUUCAUUUAUGUUGUGUGCAAAUAUAAUUUAAAGAUACAACCUC
AAWR02006906.1/78254-78385  AAAACAAAGGUGCCUUUGCCAAUAUUC-UGUUUCAAUUUGACAAGCCCUGAGAUUUCUGAGGGGAA-UUCUCUGUAAAUGGGAUCAGGUCAUUUAUUUAUGUUGUGUGCAAAUAUAAUUUAAAGAUACAACCUC
AAQQ01274680.1/800-931      AAAAUAAAGGUGCCUUUGCCAAUAUUG-UGUUUCCCUUUGACAAGUCCUGAGAUUUCUGAGGGGAA-UCCACUAUAAAUGGGAUCAGGUCAUUCUUUUAUGUUGUGUGAAAAUAUAAUUUAAAGAUACAACCUC
ACBE01286838.1/2102-1970    AAAACAAAGGUGCCUUUGCCAAUAUUUAUGUUUCGCGUUGACAAGCCCUGAGAUUUCUGAGGGGAA-UCCACUAUAAAUGGGAUCAGGUCAUUUGUCUAUGUUGUGUGCAAAUAUAAUUUAAAGAAACAACCUC
ABRO01239012.1/9679-9809    AAAACAAAGGUGCCUUUGCCAGUAUUC-UAUUCCCUUU-GACAAGCCUUGAGAUUUCUGAGGGGAA-UCCAUUAUAAAUGGGAUCAGGUCAUUCAUUUAUGUUGUGUGCAAAUAGAAUUUAAAGAUACAACCUA
ABRP01216160.1/6221-6347    AUAACAAAGGUGCCUUUGCCAAUAUUA-UGUUUCGCUUUGACAAGCCCUGAGAUUUCUGAGGGGAA-UCCAUUAUAAAUGGGAUCAGGUCAUUCACUUAUGUUGUGUGUAAAUAUAA-----AGAUACAACCUU
ABRR01171585.1/643-773      AAAACAAAGGUGCCUUUGCCAAUAUUA-UGUUUUGCUUUGACAAGCUCUGAGAUUUCUGAGGGGAA-UUCAGUGUAAAUGGGAUCAAGUCAUUCAUUUAUGUUGUGUACAAAUAUAAUCUAAAGAUACA-CCUC
AAGV020175204.1/760-891     AAAACAAAGGUGCCUUUGCCAAUAUUA-UGUUUCUCUUUGACAAGCACUCAGAAUUCUGAGGGGAA-UCCACUAUAAAUGGGAUCAGGUUAUUCAUUUAUGUUGUGUUCAAAUAUAAUUUUAUGAUACAUCCUC
ABRN01176965.1/1796-1927    AAAACAACGGUACCUUUGCCAAUAUUG-UGUUUUACUUUGACAAGCUCUGAGAUUUCUGAGGGAAA-UCCUUUAUAAAUGGGAUCAGGUCAUUCAUUUAUGUUGUGUAGAAAUAUAAUCUAAAGAUACAACCUC
AAFC03092123.1/55149-55279  AAAACAAAGGUGCCUUUGCCAAUAUUA-UGUUUUACUUUGACAAGCUCUGAGAUUUCUGAGGGGAA-UCCAUUAUAACUGAGAUCAGGUCAGUCAUUUAUGU-GUAUACAAAUAUAAUCUAAAGAUACAACGUU
AALT01212979.1/1961-2091    UAAACAAAGGUGCCCUUGCCAAUAUUA-UGUUUUAUAUUGACAAGCUCCUAGAUUUCUGAGGGGAA-UCCACUGUAAAUGGGAUCAGGUCAUUCAUUUAUGCUGUGUGCAAAUAUAAUUUUAAGAUACA-CCUC
AAYZ01342299.1/411-542      AAAACAAAGGUGCCUUUGCCAAUAUUA-CAUUUCUCUUUGACAAGGCUUGAGAUUUCUAAGGGGAA-UCCACUAUAAAUGGGAUCAGGGAGUUUAUUUAUAUUGUGUGCAAUUAUGUCUUAAAGAUUCAACCUU
AAPY01282042.1/2537-2656    GAAACAAAGGUGCCUUUGCCAAUCUU-------------GACAAGCCUUGAGAUUUCUGAGGGGAA-UCCACUAUAAAUGGGAUCAGGUCACUUAUUUAUGUUGUGUGCAAAUACAAUUUAAAGACACAGCCUC
ABVD01122195.1/2918-3050    AAAACAAAGGUGCCUUUGCCAAUAUUU-UGUUUCGCUUUGACAAGCUCUCAGAAUUCUGAGGGGAAAUCCACUAUAAAUGGGAUCAGGUUAUACGUUUAUGUUGUGUUCAAAUAUAGUUUUAAGAUACACACUC
AAIY01050252.1/6920-6789    GAAACAAAGGUGCCUUUGCCAAUGUUA-CAUCUUGCUUUGACAAGGCAUGUGCUUUCUGAGGGGAA-UCCACUACAAAUGGGAUCAGGUCAUUCAUUUAUGCUGUGUUCAUAUAUAAUUUUAAGAUACAGCCUC
CAAA01000231.1/1940-1809    AAAACAAAGGUGCUUUUGCCAAUAUUU-UGUUUCCUUUUGACAAGCCUUGAAGUUUCUGAGGGGAG-UCCACUGCAAAUGGAAUCAAGUCUUUCAAUUAUGCUGAGUGCAAAUACAAUUUAAAGAUACAACUCC
AANN01270179.1/1185-1057    CAACUAAAGGCACCUUUGCCCAUAUCA-UGUGGGACUUUGACAAGCUCGGAGGUUUCUGAGGGUAA-UCCACUCUGAAUGGGAUCAGGUCAGUCAUUUACUUUGUAUGCACAGACUAU-UAAAAAUAC--UCUA
AF223389.1/634-764          AAAACAAAGGUGCCUUUGCCAAUGUUA-UGUUUCUUUUUGACAAGCCCUGAGAUUUCUGAGGGGAA-UUCAC-AUAAAUGGGAUCAGGUCAUUCAUUUACGUUGUGUGCAAAUAUGAUUUAAAGAUACAACCUU
AAPE02003033.1/17476-17607  AACACAAAGGUGCCUUUGCCAAUAUUA-CAUUUCGCUUUGACAAGUCCUGAGAUUCCUGAGGGGAA-UCCAGGAUAAAGGGGAUCAGGUCGGUCAUUUAUGUUGUGUGUCAACAUCACUUAAAGAUACAGCCUC
AACN010169586.1/708-839     GAAACAAAGGUGCCUUUGCCAAUAUUA-UGUUUUGUGUUGACAAGCCCUGAGAUUUCUGAGGGGAA-UCCGCUAUAAAUGGGAUCAGGUCAUUCAUUUACGCUGUGUGCAAACAUAAUUUAAAGAUUCAACCUC
AAGW02003420.1/79078-78947  AAAACAAAGGUGACUUUGCCAAUAUUA-UGUUUCUCUUUGACAAGGCCCAAGAUUUCUAAAGGGAA-UCCACAGUAAAUGGGAUCAGGUCAUUCAUUUAUGUUGCGUGCAAAUAUAAUUUAAAAAUACAACCUU
AAGU03009855.1/14854-14724  AAAACAAAGGUGUCUUUGCCAAUAUUA-UGUUUUGCUUUGACAAGGCAUGAGAUGUCUGAGGG-AA-UCCACUAUGAAUGGGAUCAGGCCAUUCAUUUAUGUUGUGCACAAAUAUAAUUUUAAGAUACGACCUC
AAQR03124810.1/29169-29300  GAAACAAAGGUGCCUUUGCCAAUAUUA-UGUUGCUUUUUGACAAGCCCUGAGAUUUCUGAGGGGAA-UCCACUAUAAAUGGGAUCAGGUCAUUCAUUUAUGUUGUGCGCAAAUAUAAUUUAAUGAUACAACCUC
AC013401.10/133122-133252   AAAACAAAGGUGCCUUUGCCAAUGUUA-UGUUUCUUUUUGACAAGCCCUGAGAUUUCUGAGGGGAA-UUCAC-AUAAAUGGGAUCAGGUCAUUCAUUUACGUUGUGUGCAAAUAUGAUUUAAAGAUACAACCUU
ADDF011069823.1/1173-1043   AAAACAAAGGUGCCUUUGCCAAUGUUA-UGUUUCUUUUUGACAAGCCCUGAGAUUUCUGAGGGGAA-UUCAC-AUAAAUGGGAUCAGGUCAUUCAUUUACGUUGUGUGCAAAUAUGAUUUAAAGAUACAACCUU
AEKP01052459.1/43744-43614  AAAACAAAGGUGCCUUUGCCAAUGUUA-UGUUUCUUUUUGACAAGCCCUGAGAUUUCUGAGGGGAA-UUCAC-AUAAAUGGGAUCAGGUCAUUCAUUUACGUUGUGUGCAAAUAUGAUUUAAAGAUACAACCUU
#=GC SS_cons                :::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                     aAAACAAAGGUGCCUUUGCCAAUaUUa.UGUUucucUUUGACAAGcccuGAGaUUUCUGAGGGGAA.UCCAcUaUAAAUGGGAUCAGGUCauUCaUUUAUGUUGUGUgcAaAuAuaAUUUaAAGAUACAaCCUc
//
# STOCKHOLM 1.0

#=GF AC   RF01982
#=GF ID   PYLIS_1
#=GF DE   Pyrrolysine insertion sequence 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   70.00
#=GF TC   78.30
#=GF NC   59.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001268; recoding_stimulatory_region;
#=GF DR   GO; 0030631; pyrrolysine incorporation;
#=GF RN   [1]
#=GF RM   16164991
#=GF RT   Evidence for the existence in mRNAs of a hairpin element responsible for
#=GF RT   ribosome dependent pyrrolysine insertion into proteins.
#=GF RA   Theobald-Dietrich A, Giege R, Rudinger-Thirion J
#=GF RL   Biochimie. 2005;87:813-817.
#=GF RN   [2]
#=GF RM   23557142
#=GF RT   Effects of using coding potential, sequence conservation and mRNA
#=GF RT   structure conservation for predicting pyrroly-sine containing genes.
#=GF RA   Theil Have C, Zambach S, Christiansen H
#=GF RL   BMC Bioinformatics. 2013;14:118.
#=GF WK   PYLIS_downstream_sequence
#=GF SQ   20


AE008384.1/1718065-1717966 UAGGGACCAGAGACUUCCCUGUCAGCUCAGGGAAAUAUAUCCUCUGACUGCAUGGGAGGCCAGAUCUCAUCAGACAGCCACGAAGUGUCACAGCUCAACG
CP002101.1/1642005-1641906 UAGGGUCCUGAGACUUCACUGACUGCCCAGGGUAACAUCGCUGCCGAUGCACCUGGUGGCAUGAACUCAAAUGAUAGUCAUGAAGUCUCUCAGCUAAACG
CP000099.1/1021649-1021748 UAGGGCCCAGAGACCUCCCUGUCCGCUCAGGGAAAUAUUUCCGCUGACUGCGCCGGCGGAAUGACCUGCACGGACAGCCACGAGGUCUCGCAACUAAACG
CP002105.1/1812377-1812278 UAGGGCUGCGAAACAGCAUUGAGUCCUGCCGGAUGUAUUGCUGCAGACCAUGACGGCGGGAUGAAAGAAUCUGAUAGCCAUGAGGUAUCCCAGUUAAAUG
CP003108.1/1695878-1695977 UAGGGGAAUGAAACAUCAUUAAGUGCCGCAGGGGUUAUAUCUGCUGACUUUGAAGGCGGCAUGAGGCCAUCUGAUUCACAUGAGGUUUCUCAGCUGAAUG
CP002101.1/1638776-1638677 UAGGGUCCUGAGACUUCACUGACUGCCCAGGGUAACAUCGCUGCCGAUGCACCUGGUGGCAUGAACUCAAAUGAUAGUCAUGAAGUCUCUCAGCUAAACG
CP002069.1/1024499-1024400 UAGGGACCCGAGACCUCACUGUCUGCUCCAGGUAACAUCUCUGCUGAUGCUGUCGGCGGACUUAACCCUGCAGACAGCCAUGAGGUCUCACAGCUUAAUG
CP001720.1/26566-26665     UAGGGGAAUGAAACUUCACUUUCACCUGCCGGAGUUAUCGCUGCAGAUUUUCCCGGUGGGAUGAGGCCUUCUGACAGCCAUGAGGUAUCACAGUUAAAUG
AE010299.1/3708277-3708376 UAGGGCCCAGAGACCUCCCUGUCCGCUCAGGGAAACAUCUCAGCCGACUGCGCAGGCGGGAUGCAGAGCACUGACAGCCACGAGGUCUCGCAACUUAACG
CP000099.1/1024459-1024558 UAGGGCCCAGAGACCUCCCUGUCCGCUCAGGGAAAUAUUUCCGCUGACUGCGCCGGCGGAAUGACCUGCACGGACAGCCACGAGGUCUCGCAACUAAACG
CP000300.1/884467-884368   UAGGGACCAGAGACUUCCCUGUCAUCUCAGGGUAACAUCGCUUCCGACUGUGUCGGUGGCCAGAUGACAAGUGACAGCCACGAAGUAUCACAGCUCAACG
AE010299.1/171967-171868   UAGGGCCCGGAGACUUCCCUGUCUGCUCAGGGAAAUAUAUCCUCUGACUGCGUUGGCGGCCAGAUCUCUUCGGAUAGCCACGAAGUCUCCCAGCUCAACG
CP002069.1/1343002-1342903 UAGGGACCCGAGACCUCACUGUCUGCUCCAGGUAACAUCUCUGCUGAUGCUGUCGGCGGACUUAACCCUGCAGACAGCCAUGAGGUCUCACAGCUUAAUG
CP000300.1/891986-891887   UAGGGACCUGAGACUUCCCUGUCCGCUCAGGGAAACAUCGCUUCCGACUGUGUCGGUGGUCAGGUAACAAGUGACAGCCACGAAGUAUCACAGCUCAACG
CP002101.1/678530-678629   UAGGGUCCUGAGACUUCACUGACUGCCCAGGGUAACAUCGCUGCCGAUGCACCUGGUGGCAUGAACUCAAAUGAUAGUCAUGAAGUCUCUCAGCUAAACG
CP000099.1/4669928-4669829 UAGGGCCCAGAGACCUCACUGUCCGCCCAGGGAAACAUUUCCGCUGACUGUGCCGGCGGAAUGACCUGUACGGACAGUCACGAGGUCUCGCAACUCUGUG
AE008384.1/4063990-4064089 UAGGGACCAGAGACUUCCCUGUCAGCUCAGGGAAAUAUAUCCUCUGACUGCAUGGGAGGCCAGAUCUCAUCAGACAGCCACGAAGUGUCACAGCUCAACG
CP001994.1/1169281-1169182 UAGGGCCCUGAGACUUCCCUGUCUGCACAGGGUAACAUCGGUGCAGACUGUGUCGGUGGUAUGAACUCCAACGACAGCCACGAAGUCUCCCAGCUGAACG
CP001994.1/1152873-1152774 UAGGGCCCUGAGACUUCCCUGUCUGCACAGGGUAACAUCGGUGCAGACUGUGUCGGUGGUAUGAACUCCAACGACAGCCACGAAGUCUCCCAGCUGAACG
AF230870.1/2087-2186       UAGGGCCCAGAGACUUCCCUGUCCGCUCAGGGAAAUAUUUCCGCUGACUGCGCCGGCGGAAUGACCUGCACGGACAGCCACGAGGUCUCGCAACUCUGUG
#=GC SS_cons               :::::::::<<<<<<<<----------------------<<<<<<<_______>>>>>>>--------------------->>>>>>>>:::::::::::
#=GC RF                    UAGGGaccuGAgACcUCaCUGuCuGCucagGGaAAuAUcuCcgCcgAcugugucgGcgGaaUGAacucaacuGAcAGcCAuGAgGUcUCaCAGCUaAAcG
//
# STOCKHOLM 1.0

#=GF AC   RF01983
#=GF ID   Pinc
#=GF DE   Pregnancy induced noncoding RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   76.50
#=GF NC   50.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.82 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   16574773
#=GF RT   A noncoding RNA is a potential marker of cell fate during mammary gland
#=GF RT   development.
#=GF RA   Ginger MR, Shore AN, Contreras A, Rijnkels M, Miller J, Gonzalez-Rimbau
#=GF RA   MF, Rosen JM
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:5781-5786.
#=GF WK   Pinc
#=GF SQ   16


AC132854.8/147957-147804     CUUUUCCCAGCAGGAAAGAGACCAGCUAAAG-UAGCAUGCAAUGUCCUUCCUGUUCCCAUGCAGCUGGCCGAGGCUUCUCUUCCCUCUGCU-CAAAUCCGAUUUGUA-UUUCU-UCCUUGUUAAUACCCCCAGAGUGCUCCAUGUUUCUUC-CAGCCGG
ABGA01326131.1/27770-27617   CUUUCCUGAGUAGGAAAGAGAUCAGGUCAAG-UAGCAUACAAUAUCCUUCUUAUUCCCAUGCAGAUGUCUGAGGCUUCUUUCCCCUUUGGU-CCAAUCUGAUUUGUA-UGUCU-UCUUGGUUAAUACCCCCAGAGUGCUCUAGGCUGCUUU-CUGCCUA
ABDC01005436.1/27213-27366   CUUUCCUGAGCAGGAAAGAGACCAGGUCAAG-UAGCAUAUAAUAUCCUUCUUAUUCCCACGCAGAUGUCUGAGGCUUCCUUCUCCUUUGGU-CAAAUCUGAUUUGUA-UUUUU-UCUUGGUUAAUGCCCCCAGAGUGCACUAGGCUGCUUU-CUGCCUA
ABRO01042765.1/1201-1354     CUUUGCUGAGCAGGAAAGAAACCAGGUAAAG-UAACAUAUCAUAGCCUUCUUAUUCCCAGGCAGAUGUCUGAGGCUUCUCUUUCCUUUGGU-CAAAUCUGAUUUGUA-UUUCU-UCUUGGCUAAUACCUCUAGAGUGCUCCAGGCUGCUUU-CUGCCUG
AANU01248012.1/27533-27381   CUACUCAGGGUAGGAAAGAGAUCAGGUCAAG-UAGCAUAUAAUAUCCUUCUUAUUCUCAUGCAGAUGUCUGAGGCUUCUUUCCCCUUUCGU-CCAAUCUGAUUUGUA-UGUCU-UCUUGGUUAAUACCCCCAGAGUGCUCUAGGCUGCUUU-CUGCCU-
ABRP01082648.1/1252-1405     UUUUCCUGAGCCGGAAAGAGGCCAGGUAAAG-UAGUAUAUGAUAUCCUUUUUAUUCCCAUGCAGAUGUCCAUGGCUUCUUUUUCCUUUGGU-CAAAUCUGAUUUGUA-UUUCU-UCUUGGUUAAUACCCCCAGAGUGCUCCAGGCUGCUUU-CUGCCUG
AADA01044868.1/12436-12280   CUUUCCUGAGUAGGAAAGAGAUCAGGUCAAG-UAGCAUACAGUAUCCUUCUUAUUCCCCUGCAGAUGUCUGAGGCUUCUUUCCCCUUUGGUUCCAAUCUGAUUUGUACUGUCUAUCUGGGUUAAUACCCCCAGAGUGCUCUAGGCUGCUUU-CUGCCUC
AAWR02039923.1/130371-130523 CUUUCCUGAGCUGGAAUGAGGCCAGGUAGAG-UGGUAUGUGAUAUCCUUCUUAUUCCCAUGCAGAUGUCUGUGGCUUCUCUUUCCUUUGGU-CAAAUCUGAUUUGUC-UUUCU-UCUUGGUUAAUACCCCCAGGGUGCUCCAGGCUUCUU--CUGCCUG
AAQQ01278409.1/2750-2896     CUUUCCUGAGCAGGAAAGAGACCAGAUAAAG-GAGCAUAUUA-GACCUUCUUAUUCCCAUGCAGAUGUCUGAGGCUUCU------UUUGGU-CAAAUCUGAUCUGUA-UUUCU-UCUUGGUUAAUACCCCCAGAGUGCUGCAGGCUGCUUU-CUGCCUG
AAPY01286331.1/2135-2283     CUUUUCUGAGCAGGAAAGAGACUAGGUAAAG-UAGCAUGUAAUAUC---CUUAUUCCCACACAGAUGUCUGAAGCUUCUUUCUCCUUUGGU-CAAACCUGAUUUGUA-UUUCU-UCUUG-UUAAUGCCCCCAGAGUACUG-AGGCUGCUUU-CUGCCUG
ABRN01417855.1/8752-8905     CUUUCCUGAGCCAGAAAGAGGACAGCUAAAA-GAGUAUAUGAUAUCCUUUUUAUUCCCAUGCAGAUGUCUGAGGCUUCUUUUUCCUUUGGU-CAAAUCUGAUUUUUA-UUUCU-UCUUAGUUAAUACCCCCAGAGCACUGCAGCCUUCUUU-CUGCCUG
AAFC03029933.1/2355-2201     CUUUCCUGAGCCGGAAAGAGACUGGGUAAAAAGACUCUAUGAUAUCCUUUUAAUUCCCAUGCAGAUGUCGGAGGCUUCUUUUUCCUUUGGU-CAAAUCUGAUUUGUA-UUUCU-CCUCGGCUAAUACCCCCAGAGCACUCCAGCCUGCUUU-CUGCCUG
ABRQ01097924.1/4464-4617     UGUUCUUGAGCAGGAAAGGGACCAGGUAGAA-UAGCAUACAGUAUCUCUCUUAUUCCCACGCAGAUGUCUGAG-CUUCUUUUUCCUUUGGU-CAAAUCUAAUUUGUA-UUUCC-UCCUGGUUAAUACCACCAGAGUGAUUCAGGCUGCUUUUCUGCCUG
AAQR03031438.1/21712-21559   CUUUCCUGAGCAGGAAAGAGACCACGUCAAG-UUGCAUAUAGUAUCUUUCUUAUUCCCAUGCUGAUGUCUGAGGCUUCCUUUUUCUUUGGU-CAAAUCUGAUUUGUA-UUUUU-CCUUGGUUAAUACCUCCAGAGUGCACUAGGCUGCUUU-CUGCCUA
AAGW02042674.1/22106-22257   -CUUCCGGAGCAGGACAGAAACCAGGUAAAU-UAGCAUGUAAUAUCCUUCCCGUUCCUGUGCAGAUGUCUGAGGCUUCUUUCUCCUUUAGU-CAAAUCUGAUUUCUA-UUUCU-UCUUGGUUAAUACCCCCAGAGUGCUCCUGGCUGCUUG--UGCCCA
AAGU03009321.1/49997-49843   CUUUCCUGAGCAGGAAAGAGACCAGGUGAAG-UAGCAUAUAAUAUCUCUCUUAUUCCCAUGCAGAUGUCUGAGGCUUCUUUUUCCUUUGGU-CAAAUCUGAUUUGUA-UUUCU-UCCUGGUUAAUACCAUCAGAAUGUUCCAGGCUGCUUUUCUGCCUG
#=GC SS_cons                 :::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::.:::::.:::::::::::::::::::::::::::::::::::::.:::::::
#=GC RF                      CuUUcCuGAGCaGGAAAGAGacCAGgUaAAg.uaGcAUauaaUAUCcUUcUuaUUCCCauGCAGAUGUCuGaGGCUUCUuUuuCCUUUGGU.CaAAUCUGAUUUGUA.UuUCU.UCuuGGUUAAUACCcCCAGAGUGCUccAGGCUgCUUu.CUGCCug
//
# STOCKHOLM 1.0

#=GF AC   RF01984
#=GF ID   ZEB2_AS1_1
#=GF DE   ZEB2 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   107.90
#=GF NC   66.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.79 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   18347095
#=GF RT   A natural antisense transcript regulates Zeb2/Sip1 gene expression during
#=GF RT   Snail1-induced epithelial-mesenchymal transition.
#=GF RA   Beltran M, Puig I, Pena C, Garcia JM, Alvarez AB, Pena R, Bonilla F, de
#=GF RA   Herreros AG
#=GF RL   Genes Dev. 2008;22:756-769.
#=GF WK   ZEB2-AS1
#=GF SQ   11


AC009951.10/111477-111604 CUAUAAAAGAUGUAACAGAUGCAAACUGUAACACAAGGGCCAUUAACCCUUUCUCUGCCG---GGCACACUCAGU-----------CCCC-ACGCCCCACACCUAUUGUCUCCUG---UG--CUAGA----AGCUUUGCAGAAAACCUGGAA
AAPY01129433.1/450-577    CUAUAAAAGAUGUAACAGAUGCAAACUGUAACACCAGGGCCAUUAACCCUUUCUCCGCCG---AGCACGCUCAAU-----------CCCC-ACGCCCCGCACCUAUUGUCUCCUG---GG--CUAGA----AGCUUUGCGGAAAACCUGGAA
AAYZ01070491.1/538-666    CUAUAAAAGAUGUAACAGAUGCAAACUGUAACACAAGGGCCAUUAACCCUCUCUCUGCCG---AGCACGCUCAGU-----------CCCCCACGCCCCGUACCUAUUGUCUCCCG---UG--CGAGA----AGCCUUGCGGAAAACCUGGAA
AAGV020005346.1/1320-1446 CUAUAAAAGAUGUAACAGAUGCAAACUGUAACACAAGGGCAAUUAACCCUUUCUCUGCCU---CGCA-GCUCAGU------------CCUCACGCUCCGCACCUAUUGUUUUCUG---UG--CUGGA----AGCUUUGCGGAAAACCUGGAA
AALT01117094.1/310-448    CUAUAAAAGAUGUAACAGAUGCAAACUGUAACACAAGGGCCAUUAACCCUUUCUCUGCCG---ACCACACUCAGUUCCCCCCACCCCCCC-ACGCCCGGCACCUAUUGUCUCCUG---UG--CUGGA----AGCUUUGCGGAAAACCUGGAA
ABRO01040214.1/3002-3131  CUAUAAAAGAUGUAACAGAUGCAAACUGUAACACAAGGGCCAUUAACCCUUUCUCUGCCUCC-AGUACACUCAGU-----------CCCU-ACGCCCCGCACCUAUUGUCUCCCA---UG--CUCGA----AGCGUUGCGGAAAACCUGGAA
AAIY01392335.1/1922-1795  CUAUAAAAGAUGUAACAGAUGCAAACUGUAACACAAGGGCCAUUAACCCUUUCUCUGCCU---AGCACACUCCAU-----------CCCC-ACGCCCCACACCUAUUGUCUCCCU---UG--CGAGC----AGCUUUUGGGAAAACCUGGAA
AJ536044.1/8089-7959      CUAUAAAAGAUGUAACAGAUGCAAACUGUAACACAAGGGCCAUUAACCCUUUCUCUGCCGCCCAGCACGCCCAGU-----------CCCU-ACACCCUGCACCUAUUGUCUCCGG---UG--CCACA----AGCUUUGCGGAAAACCUGGAA
AAKN02006305.1/2021-1887  CUAUAAAAGAUGUAACAGAUGCAAACUGUAACACAAGGGCCAUUAACCCUUUCCCUGCCGCCAAGCACACUGGGU-----------CCCC-ACGCCCCGCACCUAUUGUCUCCUG---UG--UUAGAUAGAAGCUUUGCGGAAAACCUGGAA
AAFR03008502.1/385-513    CUAUAAAAGAUGUAACAGAUGCAAACUGUAAAACAAGGGCAAUUAACCCUUUCUCUGCCG----GCAAACUCUGU------------CCU-AGCCCCAGCACCUAUUGUCUACUGCUAUA--CUAGA----AGCUUUGCAGAAAACCUGGAA
ABQF01009547.1/1942-1813  CUAUAAAAGAUGUAACAGAUGCAAACUGUAAAACAAGGGCAAUUAACCCUUGCUCUCCUG---AGCAGGAUGCCC------------CCUCGCCUUCC-CAUCUAUUGUCUUCUC--CUGCACUGGG----AGUUUUGCAUAAAACCUAAAA
#=GC SS_cons              ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::...::::::::::::...........::::.::::::::::::::::::::::::...::..:::::....:::::::::::::::::::::
#=GC RF                   CUAUAAAAGAUGUAACAGAUGCAAACUGUAAcACAAGGGCcAUUAACCCUUUCUCUGCCg...aGCAcgCUcagU...........CCCc.ACgCcCcGCACCUAUUGUCUcCug...UG..CuaGa....AGCuUUGCGGAAAACCUGGAA
//
# STOCKHOLM 1.0

#=GF AC   RF01985
#=GF ID   ZEB2_AS1_2
#=GF DE   ZEB2 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   70.00
#=GF TC   72.10
#=GF NC   49.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.58 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   18347095
#=GF RT   A natural antisense transcript regulates Zeb2/Sip1 gene expression during
#=GF RT   Snail1-induced epithelial-mesenchymal transition.
#=GF RA   Beltran M, Puig I, Pena C, Garcia JM, Alvarez AB, Pena R, Bonilla F, de
#=GF RA   Herreros AG
#=GF RL   Genes Dev. 2008;22:756-769.
#=GF WK   ZEB2-AS1
#=GF SQ   11


AC009951.10/112644-112704 CUCAAUAAAACUUUUCCUGGGCUGGAUAGCAAAGGACACCUUUGGUUACCUGAAUGAACAG
ABRT010013693.1/1888-1948 CUCAAUAAAACUUUUCCUAGGCUGGGUAGCAAAGGGCACCUUUGGUUACCUGAAUGGACAG
AAYZ01070492.1/377-437    CCCAAUAAAACUUUUCCUAGGCUGGGUAGCAAAAGACACCUUUGGUUACCUGAGUGAACAG
ABDC01106861.1/794-854    CUCGAUAAAACUUUUCCUAGGCUGGGUAGCAAGAGGCACCUUUAGUUACCUGAAUGGACAG
AAPY01129433.1/1607-1667  CCCAAUAAAACUUUUCCUAGACUGGGAAGCAAAAGUCACCUUUGGUUACCUGAGUGGACAG
AALT01095907.1/181-241    CUCAAUAAAACUUUUCUUAGGUUGGGGAGCAAAAGACACCUUUAGUUACCUGAAUGCACAG
ABRN01387273.1/957-1013   CUCGAUAAAACUUUUCCCAGGCUGGGUAGUAAAAGGCACCUUUGGUUACCUGAAUGG----
ABRR01244211.1/1702-1761  CUUAAUAAAACUUUUCCUAGGCUGAGUAGCAAAAGGCACCUUUGGUUACCUG-AUGGACAG
AAIY01392335.1/732-672    CUCAAUCAAACUUUUCCCAAGCUGGGUAGCGAAAGGCACCUUUGGUUACCUGGAUGGACAG
AAGV020005347.1/44-104    CUCAAUAAAACUUUUGCUAACCUAGGUAGCAAAAGGCACCUUUGGUUACCUGAGUGGGCAG
AAGW02004835.1/1025-965   CCCAAAAAAACUUUUCCUAGGCAGGGUAGCAAAAGGCACCUUUGGUUACCUGAAUGGACAG
#=GC SS_cons              :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                   CUCAAUAAAACUUUUCCUAGGCUGGGUAGCAAAAGgCACCUUUGGUUACCUGAAUGGACAG
//
# STOCKHOLM 1.0

#=GF AC   RF01986
#=GF ID   ZEB2_AS1_3
#=GF DE   ZEB2 antisense RNA 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   55.00
#=GF TC   59.60
#=GF NC   42.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.03 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   18347095
#=GF RT   A natural antisense transcript regulates Zeb2/Sip1 gene expression during
#=GF RT   Snail1-induced epithelial-mesenchymal transition.
#=GF RA   Beltran M, Puig I, Pena C, Garcia JM, Alvarez AB, Pena R, Bonilla F, de
#=GF RA   Herreros AG
#=GF RL   Genes Dev. 2008;22:756-769.
#=GF WK   ZEB2-AS1
#=GF SQ   11


AC009951.10/113485-113585    UUCUCCCCCCCUCCACCCCCCCCUCCCCGCCCGUCAAGC----CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUACAGAG------UACAGGGCGGAAAACGG-UGCACAC
AAWR02006337.1/2121-2221     UCCACGCCCCCCCAACCCCCCCCAACCCCCCCGUCAAGC----CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUACAGAG------UACUGGGCGGAAAACGG-UGCACAC
ABRR01244212.1/625-722       CCCUCCCUUCUCCACGCCCCCCCCCCC---CCGUCAAGC----CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUACAGAG------UACAGGGCGGAAAACGG-UGCACAC
ABRQ01002007.1/2303-2397     UCCACGCCCCCCCC-CCCCCCCC-----CCCCGUCAAGC----CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUACUGAG------UACAGGGCGGAAAACGG-UGCACAC
AAGV020005347.1/884-984      UCCACGCCCUCCCCCCCACCCCCCACCCCCCCGUCAAGC----CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUACAGAG------UACAGGGCGGAAAACGG-UGCACAC
AAFC03025663.1/10795-10695   GCCCCCCCUCCCCCCCCUCCUCACACCCCCCCGUCAAGC----CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUACAGAG------UACAGGGCGGAAAACGG-UGCACAC
AAHX01021510.1/1095-1190     UCCACGCCCCCCCAACCCCCCCC-----CCCCGUCAAGU----CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUGCAGAG------UACUGGGCGGAAAACGG-UGCACAC
BC031611.1/531-630           UCCACGCCCCCCCCCCCCCCCCC-----CCCCGUCAAGCAAGCCUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUGCAGAG------UACUGGGCGGAAAACGG-UGCACAC
ABRT010013693.1/2697-2801    CCCUCCCUUCUCCACGCCCCCCCCCCCU--CCGCCAAGC----CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUACAGAGACAGAGUACAGGGCGGAAAACGG-UGCACAC
AAYZ01070492.1/1221-1317     CCCUCCCUUCUCCACGCCUCCCCCCCC----CCCCCAGC----CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUACAGAG------UACAGGGCGGAAAACGG-UGCACAC
AAGU03011001.1/227530-227431 CCCUCCCUUCUCCACGCCCCCCCCCCC-ACCCGUCAAGC----CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUACUGAG------UACAGGGCGGAAAACG-GUGCACAC
#=GC SS_cons                 :::::::::::::::::::::::::::.:::::::::::....::::::::::::::::::::::::::::::::::::::......:::::::::::::::::.:::::::
#=GC RF                      uCCuCcCcuCcCCaccCcCCCCCccCC.cCCCGuCAAGC....CUUUGGCAUCAUUAUCCUCAUCACUAAAUCCUaCaGAG......UACaGGGCGGAAAACGG.UGCACAC
//
# STOCKHOLM 1.0

#=GF AC   RF01987
#=GF ID   ZEB2_AS1_4
#=GF DE   ZEB2 antisense RNA 1 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   52.00
#=GF NC   42.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 40.07 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   18347095
#=GF RT   A natural antisense transcript regulates Zeb2/Sip1 gene expression during
#=GF RT   Snail1-induced epithelial-mesenchymal transition.
#=GF RA   Beltran M, Puig I, Pena C, Garcia JM, Alvarez AB, Pena R, Bonilla F, de
#=GF RA   Herreros AG
#=GF RL   Genes Dev. 2008;22:756-769.
#=GF WK   ZEB2-AS1
#=GF SQ   13


AC009951.10/114069-114146 GAUAUUAAACGGCAUGGGGUCUAAGUUUUGGAGUAUA------UAUUUUUU-GAUAUUACAAUUAAAGUAAGAUUAAAAAGAAAA
AAWR02006337.1/2713-2790  GAUAUUAAACGGCAUGGGGUCUAAGUUUUGGAGUAUA------UAUUUUUU-GAUGUUGCAAUUAAAGUAAAAUUAAAAAAGAAA
ABRT010013693.1/3336-3413 GGUAUUAAACGGUAUGGGGUCUAAGUUUUGGAGUAUA------UAUUUUUU-GAUAUUGCAAUUAAAGUAAAAUUAAAAAGAAAA
ABRP01000729.1/406-483    GAUAUUAAACGGCAUGGGGUCUAAGUUUGAGAGUAUA------UAUUUUUU-GAUAUUGCAAUUAAAGUAAAAUUAAAAAGAAAG
ABRO01040216.1/512-587    AAUAUUAAACGGCAUGGGGUCUAAGUUUUGGAAUAUA--------UUUUUU-GAUAUUGCAAUUAAAGUAAAAUUAAAAAGAAAA
AAYZ01070492.1/1770-1849  GAUAUUAAACGACAUGGGGUCUAAGUUUUGGAGUACAGU----UUUUUUUU-GAUAUUGCAAUUAAAGUAAAAUUAAAAAGAAAA
AAGV020005347.1/1495-1569 GAUAUUAAACGGCAUGGGGUCUAAGUUUUGGAGUAU---------UUUUUU-GAUAUUGCAAUUAAAAUAAAAUUAAAAAGAAAA
AAIY01400155.1/505-427    GAGAUAAAACGGCAUGGGGUCUAAGUUUUGGGGCAUA-----UAUUUUUUU-GAUAUUGCAAUUAAAGUAAAAUUAAAAAGAAAA
ABVD01900951.1/431-514    GAUAUUAAACGGCAUGGGGUCUAAGUUUUGGAGUUUUUUUUUUUUUUUUUU-GAUAUUGCAAUUAAAGUACAAUUAAAAAGAAAA
ABQO010814774.1/1183-1261 GAUAUUAAACUGCAUGAGGUCUAAGUUUUUCAAGGUU-----UUUUUUUUU-GAUAUUGCAAUUAAAAUAAAAUUAAAAAAAAAA
AABR05100543.1/9635-9712  GACAUUAAACUGUGUGGGGUCUAAGUUUUGAAGUGCA------UAUUUUUU-GAUAUUGCAAUUAAAGUAAAAUUAAAAAGAAAA
ACIV010208397.1/173-96    GAUAUUAAACGGCAUGGGGUCUAAGUUUUGGAGUAUA------UAUUUUU-UGAUAUUGCAAUUAAAGUAAAAUUAAAAAGAAAA
AAHY01015713.1/3107-3031  GACACUAAACUGUGUGGGGUCUAAGUUUUGAAGUGCA------UAUUUUU--GAUAUUGCAAUUAAACUAAAAUUAAAAAGAAAA
#=GC SS_cons              :::::::::::::::::::::::::::::::::::::......::::::::.:::::::::::::::::::::::::::::::::
#=GC RF                   GAuAUUAAACGGCAUGGGGUCUAAGUUUUGGAGUaUa......UaUUUUUU.GAUAUUGCAAUUAAAGUAAAAUUAAAAAGAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF01988
#=GF ID   SECIS_2
#=GF DE   Selenocysteine insertion sequence 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   70.00
#=GF TC   73.60
#=GF NC   64.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001274; SECIS_element;
#=GF DR   GO; 0001514; selenocysteine incorporation;
#=GF RN   [1]
#=GF RM   8634916
#=GF RT   Solution structure of mRNA hairpins promoting selenocysteine incorporation
#=GF RT   in Escherichia coli and their base-specific interaction with special
#=GF RT   elongation factor SELB.
#=GF RA   Huttenhofer A, Westhof E, Bock A
#=GF RL   RNA. 1996;2:354-366.
#=GF WK   SECIS_element
#=GF SQ   4


U00096.2/4296977-4296923   GUGUCUGACACGGCCCAUCGGUUGCAGGUCUGCACCAAUCGGUCGGUAAUGGCGC
CU928158.2/4397661-4397715 GCGUCUGACACGGCCCAUCGGUUGCAGGUCUGCACCAGUCGGUCGGUAACGGCGC
ABXW01000042.1/36779-36725 GUGUCUGACACGGCCCUUCGGUUGCAGGUCUGCAGCGUUCGGUCGGUAAUGGCGC
BAAW01013798.1/777-831     GCGUCUGACACGGGCCAUCGGUUGCCGGUCUGCGCCCAUCGGUCGGUGACGGCGC
#=GC SS_cons               <<<<<--<<-<<<<<-<<-<<<-<<<____>>>>>>->>->>>>>>>--->>>>>
#=GC RF                    GcGUCUGACACGGCCCauCGGuUGCaGGUCuGCaCCaauCGGUCGGUAAuGGCgC
//
# STOCKHOLM 1.0

#=GF AC   RF01989
#=GF ID   SECIS_3
#=GF DE   Selenocysteine insertion sequence 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   63.00
#=GF TC   63.20
#=GF NC   62.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.41 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001274; SECIS_element;
#=GF DR   GO; 0001514; selenocysteine incorporation;
#=GF RN   [1]
#=GF RM   8634916
#=GF RT   Solution structure of mRNA hairpins promoting selenocysteine incorporation
#=GF RT   in Escherichia coli and their base-specific interaction with special
#=GF RT   elongation factor SELB.
#=GF RA   Huttenhofer A, Westhof E, Bock A
#=GF RL   RNA. 1996;2:354-366.
#=GF WK   SECIS_element
#=GF SQ   24


U00096.2/4083263-4083205     GUCUGACACGGACCAACGGUAGCAAGUCUUGCUCCAACAUUUGGUCGCGGUGCGAUGAC
ACIS01000002.1/49906-49848   GUCUGACACGGACCGACGGUGGCAAGUCUUGCCCCAACAUUCGGUCGCGGUGCCAUGAC
CP001196.1/2730327-2730269   GUCUGACACGGACCGACGGUGGCCAGUCUGGCCCCAACAUUCGGUCGCGGUGCAAUGAC
AAOJ01000002.1/997131-997189 AUUUGACACGGCCCAACGGUAGCAAGUCUUGCUCCAACAUUUGGCCGCGGUGCGAUGAC
CP000687.1/999439-999497     ACCUGACACGGACCAACGGUAGCAAGUCUUGCUCCAACAUUUGGUCGCGGUGCCAUGAC
CP001280.1/3656664-3656722   GUCUGACACGGACCAACGGUGGCCAGUCUGGCUCCAACAUUUGGUCGCGGCGCAAUGAC
ACFT01000041.1/14706-14764   ACCUGACACGGACCUACGGUAGCAAGUCUUGCUCCAAGUUUCGGUCGCGGUGCGAUGAC
CP000304.1/2349128-2349070   GUCUGACACGGACCGACGGUGGCAGGUCUUGCCCCUUCAUUCGGUCGCGGUGCCAUGAC
CP000759.1/142279-142337     GUCUGACACGGCCCGACGGUGGCGAGUCUCGCCCCAACAUUUGGCCGCGGAGCAAUGAC
CP000089.1/1955933-1955875   GUUUGACACGGUCCGACGGUGGCCAGUCUGGCUCCGACAUUUGGCCGUGGCGCAAUGAC
AE014299.1/109279-109337     AACUGACACUCCCCAACGGUAGCAAGUCUUGCUCCAACAUUUGGGCGUGGUGCCAUGAC
AACY020487847.1/1254-1196    GUCUGACACGGCCCGACGGUGGCAGGUCUUGCCCCGACGCUAGGCCGUGGUGCGAUGAC
CP000869.1/1698931-1698873   GUCUGACAUGGCCCGACGGUGGCAGGUCUUGCCCCGACAUUUGGCCGUGGAGCGAUGAC
AE006469.1/1962-2020         GUCUGACACGGCCCUACGGUGUCCAGUUUGGGCCCAACAUUUGGCCGUGGAGCGAUGAC
CP000891.1/125447-125505     AACUGACACUCUCCAACGGUAGCAAGUCUUGCUCCGACAUUUGGACGUGGUGCCAUGAC
CP000473.1/1037857-1037799   GUUUGACACGGCCCCACGGUCUCCAGUUUGGGGCCCACGUUCGGUCGCGGUGCGAUGAC
AY240957.1/17572-17630       GUCUGACACGGCCCGACGGUGGCAAGUCUUGCCCCGACGUACGGCCGUGGUGCCAUGAC
CT573326.1/577333-577391     GUCUGACACGGCCCGACGGUGGCAAGUCUUGCCCCGACGUAUGGCCGUGGCGCGAUGAC
AP009384.1/1294599-1294541   GUCUGACACGGCCCCACGGUGUCCAGUUUGGGCCCAACUUUUGGCCGUGGCGCGAUGAC
FM209186.1/5733622-5733564   GUCUGACACGGCCCGACGGUGGCAAGUCUUGCCCCGACGUUUGGCCGUGGAGCCAUGAC
CP001154.1/771413-771355     GUCUGACACGGCCCGACGGUGGCAAGUCUUGCCCCUUCGUUUGGCCGUGGCGCCAUGAC
CP001131.1/4289299-4289357   GUUUGACACGGUCCAACGGUGGCCGGUCUGGCCCCCACGUUCGGCCGUGGCGCGAUGAC
ABSQ01032958.1/205-147       GUUUGACACGGCCCCACGGUGGCCGGUCUGGCCCCGACGUUUGGCCGUGGCGCGAUGAC
CP001726.1/1986484-1986426   GUUUGACACAGCCCCACGGUUGCCGGUCUGGCAGCAACAUUCGGUCGCGGUUCGAUGAC
#=GC SS_cons                 ::::::<<<<<<<-<<-<<-<<<<<___>>>>>>>----->>>>>>>>>::::::::::
#=GC RF                      GUCUGACaCGgcCCaACGGUgGCcAGUCUgGCcCCaACaUUuGgcCGuGGuGCgAUGAC
//
# STOCKHOLM 1.0

#=GF AC   RF01990
#=GF ID   SECIS_4
#=GF DE   Selenocysteine insertion sequence 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   38.00
#=GF TC   38.20
#=GF NC   37.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001274; SECIS_element;
#=GF DR   GO; 0001514; selenocysteine incorporation;
#=GF RN   [1]
#=GF RM   11271425
#=GF RT   Molecular analysis of the grd operon coding for genes of the glycine
#=GF RT   reductase and of the thioredoxin system from Clostridium sticklandii.
#=GF RA   Graentzdoerffer A, Pich A, Andreesen JR
#=GF RL   Arch Microbiol. 2001;175:8-18.
#=GF WK   SECIS_element
#=GF SQ   24


AJ276209.1/5787-5824         GGUACUUGUACUCGUUGCGGCGCAACGAUGGUUAAAGA
AAML04000014.1/49774-49737   GGUACUUGUACUCGUUGCGGUGCAACGAUGGUAAAAGA
Y17872.1/4866-4903           GGCACUUGUACUCGUUGCGGAGCAACGAUGGUAAAAGA
ABCC02000029.1/62426-62389   GGUACCUGUACUCGUUGCGGUGCAACGAUGGUUAAGGG
CU928158.2/3083924-3083887   GGCACUUGCACUCGUUGCGGCGCAACGAUGGUCAAAGA
ABHD02000024.1/23679-23716   GGUACUUGUACUCGUUGUGGAGCAACGAUGGUAAAAGA
ABFY02000016.1/123601-123564 GGCACUUGUACUCGUUGCUGUGCAACGAUGGCUAAAGA
AAEW02000010.1/118947-118910 GGUACCUGUACUCGUUGCGGUGCAACGAUGGUCAAAGA
AE017226.1/2151739-2151702   GGCACAUGUACUCGUUGCGGUGCAACGAUGGUUAAAGA
AAPH01000001.1/716438-716475 GGCACUUGCACACGUUGCGGCGCAACGAUGGUUAAAGA
ABWP01000016.1/3397-3434     GGUACUUGUACUCGUUGCGGUGCAACAAUGGUUAAAGG
AP008971.1/485428-485391     GGUACUUGUACACGUUGCGGUGCAACGAUGGUAAAAGC
ABQR01000006.1/19013-18976   GGGACCUGUACUCGUUGCGGUGCAACGAUGGUUAAAGG
BAAZ01014709.1/593-630       GGUACCUGCACUCGNUGCGGCGCAACGAUGGUCAAAGA
AAXA02000002.1/19340-19303   GGUACCUGUACACGUUGCGGUGCAACGAUGGUAAAAGA
ABEE02000016.1/485010-485047 GGUACUUGUACACGUUGCGGAGCAACGAUAGUAAAAGA
ABYI02000036.1/76891-76854   GGCACCUGCACACGUUGCGGCGCAACGAUGGUAAAAGA
CP000724.1/3686484-3686447   GGCACCUGUACACGUUGCGGUGCAACGAUGGUGAAAGA
ACIN02000019.1/22183-22146   GGCACCUGUACACGUUGCGCUGCAACGAUGGUUAAAGA
ACIQ02000013.1/247684-247721 GGAACCUGUACUCGUUGCGGUGCAACGAUGGUUAAAGA
ACJX02000007.1/157353-157316 GGAACCUGUACUCGUUGCGGUGCAACGAUGGUAAAGGA
CP001684.1/2813600-2813563   GGCACUUGUACUCGUUGCGGUGCAACGAUGGUUAAAGU
CP001959.1/3095254-3095291   GGAACUUGUACUCGUUGCGGUGCAACGAUGGUUAAAGC
CP001818.1/1195028-1194991   GGUACCUGCACUCGUUGCGGCGCAACGAUGGUGAAGGA
#=GC SS_cons                 ::::<<------<<<<<<___>>>>>>-->>:::::::
#=GC RF                      GGuACcUGUACUCGUUGCGGUGCAACGAUgGUuAAAGA
//
# STOCKHOLM 1.0

#=GF AC   RF01991
#=GF ID   SECIS_5
#=GF DE   Selenocysteine insertion sequence 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   61.50
#=GF NC   35.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001274; SECIS_element;
#=GF DR   GO; 0001514; selenocysteine incorporation;
#=GF RN   [1]
#=GF RM   15659354
#=GF RT   A selenocysteine tRNA and SECIS element in Plasmodium falciparum.
#=GF RA   Mourier T, Pain A, Barrell B, Griffiths-Jones S
#=GF RL   RNA. 2005;11:119-122.
#=GF WK   SECIS_element
#=GF SQ   3


AAKM01000001.1/1082307-1082372 ACUGAACGAAUGAAGAAUUAUUCCAAAAUCCCGAGCUGA----GGAAGGAAUAGCUCUGACAUGUUCACA
AL844507.2/710533-710464       AGUGAACGAAUGAAGAAUUGUUCCUAAAUCCUGAAUAAAUAUAGGAAGGAACAAAUUGGACAUGUUCAUU
AM910996.2/1038758-1038823     AGUGAACGAAUGAAGAAUUAUUCCGAAAUCCUGAGCAGA----GGAAGGAAUAGCUCUGACAUGUCCACA
#=GC SS_cons                   :<<<<<<<-----<<<-<<<<<<<----<<<________....>>>->>>>>>>->>>---->>>>>>>:
#=GC RF                        AgUGaACgAAUGAaGAAuUgUUCCuAAAUCCUGAgcagA....GGAAGGAAcAacUCuGACAuGUuCAca
//
# STOCKHOLM 1.0

#=GF AC   RF01992
#=GF ID   VIS1
#=GF PI   HIS-1
#=GF DE   Viral integration site 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   100.00
#=GF TC   122.40
#=GF NC   64.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.59 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   9031624
#=GF RT   Evolutionary conservation of putative functional domains in the human
#=GF RT   homolog of the murine His-1 gene.
#=GF RA   Li J, Rhodes JC, Askew DS
#=GF RL   Gene. 1997;184:169-176.
#=GF WK   VIS1
#=GF SQ   27


U10269.1/831-1031            -UGGCAAGGCUGACAUAGC--UUUUACUGAUC-UGUCUGUUU-AGUGAGUGGACAGGA-UGCCAGUCUGGCAGUUUGCAUUGGCAAUAAAUCACUACUAGACAUUUUAUUUAAAAU-CUGGCACUGGCUU-UGGAGAGGUGAGGGAUUGUCAAUUUGUUUUUAUUUUG-AGGCCAGGCACAA-UCAUAACACAAACAGGCCACCUGGAAAC
AAHX01021520.1/88041-87840   -UGGCAGGGCCAACGUAGC--UUUUACUGAUU-UGCCUGUUU-AGCAAGUGGACAGGA-UGCCAGUCUGGCAGUUUGUGUUGACGAUAAAUCACAACUAGACAUUUUAUUUAAAAU-CUGGCACUGGCUU-GGGAGAGGUGAGGGAUUGUCGAUUUGUUUUUAUUUUGGAGGCCAGGCACAA-UCAUAACACAAACAGGCCACCUGGAAAC
ABDC01349465.1/5059-5260     -UGGCAAGGUUGACAUAGC--UUUUACUGAUU-UGUCUGCUU-AGUAGGUAAGCGGGGCUGCCAGUCUGGCAGUUUGCAUUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAA-UUGGCACUGGCUU-GGGGGAGGUAAGGGAUUGUCAAUUUGUUUUUAUUUUG-AGGCCAGGCACAA-UCAUAACAUACACAGGCCACCUGGAAAC
ABRO01323638.1/1086-1287     -UGGCAAGGUUGACCUAGC--UUUCACUGAUU-UGUCUGCUU-AGUAGGUAAAUGGGGCUGCCAGUCUGGCAGUUUGCAUUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAA-UUGGCACUGGCUU-GGGGGAGGGGAGGGACUGUCAAUUUGUUUUUAUUUUG-AGGCCAAGCACAG-UCAUAACAUACACAGGCCACCUGGAAAC
ABRQ01083001.1/213-413       -GGGCAAAGUUGACAUAGU--UUUUACUGAUU-UGUCUGCUUAGU-AGGUAAUGGGA-CUGCAAGUCUGGCAGUUUGCGUUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAU-UUGGCUCUGGCUUGGGGGA-GGUAAGGAAUUGUCAAUUUGCUUUUAUUUUG-AGGCCAGGCACAA-UCAUAACACACAUGGGCCACCUGGAAAC
ABVD01000942.1/1332-1533     -GGGCAAGUUUGACCUAGC--UGUUACUGAUU-UGUCUGCUU-AGUAGGUAAAUGGGGUAGCCAAUCUGGUAGUUUGCAUUGGUAAUAAAUCACCACUAGACAUUUUAUUUAAAAA-UUGGCACUGGCUU-GGGGGAGGUAAGAGAUUAUCAAUUUGUUUUUAUUUUG-AGGCCAGGCACAA-UCAUAACACACACAGGCCACCUGGAAAC
AAWR02006338.1/126668-126867 -GGGCAAGGUUGACAUAGU--UUUUACUGAUU-GGUCUGCUU-AGUAGGUAAAUGGGGCUGCCAGUCUGGCAGUUUGCACUGGCCAUAAAUCACCACUAGACAUUUUAUUUAAAAA-UUGGCACUGGCUU-GGGGGAGGUAAGGGAUCGUCAAUUUGCUUUUCUUUUG-AGGCCAGGCACAA-UCAUAACACAC--AGGCCGCCUGGAAAC
ABRR01127926.1/4715-4916     -GGGCAACGUUGACAUCGC--UUUUACUGAAU-UGUCUGCUUAGG-AGGUGAAUGGGGCUGCCAGUCUGGCAGUUUCCACUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAG-UUGGCUCUGGCUUGAGGGA-GGUAAGGGAUUGUCAAUUUGCUUUUAUUUUG-AGGCCAGGCACAA-UCAUAACACACACAGGCCACCUGGAAAC
AAFC03109165.1/81244-81044   -AGGCAAGGUUGACAUUGG--UUUUACUAAUU-UGUCUGCUU-AGUAGGUAAAUGGGGUUGCCAGUCUGGCAGUUUGCACUGGCAAUAAAUCACCACUAGACAUUUUAUUUUAAAA-UUGGCACUGGCUU-GAGGGAGGUAAAGGAUUGUCAAUUUGCUUUUAUUUGA--GGCCAGGCACAA-UCAUAACAAACAUAGGCCACCUGGAAAC
ABRN01387294.1/22195-22395   -GGGCAAGGUUGACAUAGA--UUUUACUGAUU-UGUCUGCUU-AGUAGGUAAAUGGGGUUGCCAGUCUGGCAGUUUGCAGUGACAAUAAAUCACCGCUAGACAUUUUAUUUAAAAA-UUGACACUGGCUU-GCGGGAUGUAAGGGAUUGUCAAUUUGCUUUUAUUUGA--GGCCAGGCACAA-UCAUAACACACACAGGCCACCUGGAAAC
AAGV020005392.1/620-821      -GGGCAAGGUUGACAUAGU--UUUUUCUGUUU-UUUCUGUUU-AGUAGGUAAAUGGGGCUGCUAGUCUGGUAGCUUGCAUUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAA-UUGGCUGUGGCUU-GGGGGAGGUAAGGAAUUGUCAAUUUGCUGUUAUUUUG-AGGCCAGGCACAA-UCAUAAUGCACACAGGCCACCUGGAAAC
AAKN02006300.1/15682-15492   ---------------UGGCAAUGCUACUGGUU-UGUCUGCCUACUUAGGUGAAUGGGGCUGCCAGUCUGGCAGUUUGCAUUGGCAAUAAAUCACCAGUAGACAUUUUAUUUAAAAA-UUGGCACUGAUUUGGGGGA-GGUAGGGGAUUGUCAAUUUGUUUUUAUUUUG-AGGCCAGGCAUAG-UCAUAACACACACAGGCCACCUGGAAAC
AAQQ01584859.1/1510-1710     -UGGCAAG-UUAACAUAGC--UUUGACUGAUU-UGUCUGUUU-AGUAGGUAAAUGGGGCUGCCAGUCUGGCAGUUUGCAUUGGCAAUAUAUCACCACUAGACAUUUUAUCUAAAAA-UUGGCCAUAGUUU-GGGUGAGGUAAGGGUUUGUCAAUUUGUUUUUAUUUUG-AAGCCAGGCAUAA-UCAUAAUGCUCACAAGCCACUUGGAAAC
AAYZ01070532.1/7886-8085     -UGGCAAAAUGGAUCUAGC--UUUCCCUGAUU-UGUCUGCUU-UGUAGGUACACGGGGCUGCCAGUCUGACAGUUUGCGUUGGCAAUAAAUCACCAUCAGAUAUUUUAUUUCAAAA-UUGGCACUGACUU-GGUGAAGGUAAGGGAUUGUCAAUUCAUUUUUAUUUUG-AGGCCAGGC--GA-UGAUAACACACAAAAGUCACCUGGAAAC
AALT01491474.1/6681-6880     ------AGGUUGUUUCAGCAAACAAACUGAUU-UGUUUGCUUAGU-AGGUAACUGGG-CUGCCAGUCUGGCUCUCUGCAUUGGCAAUAAAUCACCACUAGAUGCUUUAUUUUAAAAAUUGGCACUGGCUUGAGGGGUGGUGAGGGAUUGUCAAUUUGCUCUUAUUUUG-AGGCCAGGUACAA-UUAUCAUGCACACAUGCCACCUGGAAAC
AAIY01439786.1/1398-1200     UGGGCAAAAAAAACAUAGCU-UUUUACUGCUU-UGUCCACUUAGG-AGGUAACAGGA-CUGCCAACCUGGCAGUGUGCAAUGACAACAAAUCACCACGAGACGUUUCAUUUAAAAA-UUGGCACUGCUUUUGGGGA-GGUAAGGGAUUGUCAAUUUGCAUUUAUUUUA-AGGCCAGGCACAA-UCAUAA----CACUCCCCACCUGGGCAC
AAFR03008508.1/39298-39497   ----UUAGGUUGAUGUGGC--UUUUCCUGAUGAUGCCUGCUU-GGUAGGUAAAUUAGGCUGCCAAUCUGGCAGUUUUCAUUGUCAAUAAAUCUAUUCUAGACACUUUAUUUAAAAG-UUGGCACUGGUGU-AGAGGAGGUAAGGGACUGUAAAUUUUCUUUUAUUUAG-AGGCCAGGAAUAA-UCAUAACAAACAUAGACCACCUGGAAGC
U09772.1/881-1081            -UGGCAAGGCUGACAUAGC--UUUUACUGAUC-UGUCUGUUU-AGUGAGUGGACAGGA-UGCCAGUCUGGCAGUUUGCAUUGGCAAUAAAUCACUACUAGACAUUUUAUUUAAAAU-CUGGCACUGGCUU-UGGAGAGGUGAGGGAUUGUCAAUUUGUUUUUAUUUUG-AGGCCAGGCACAA-UCAUAACACAAACAGGCCACCUGGAAAC
AF307319.1/293-433           -------------------------------U-UGUCUGCUU-A-UGAAUGGACAGGA-UGCCAGUCUGGCAGUUUGCAUUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAU-UUGGCACUGGCUU-GGAAGAG-UGANGGAUUGUCAAUUUGUUUUUAUUUUG-AAGCCAGGCAC-------------------------------
U56440.1/5840-6042           -UGGCAAGGUUGACAUAGC--UUUUACUGAUU-UGUCUGUUUUAGUAGGUAAAUGGGGCUGCCAGUCUGGCAGUUUGCAUUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAA-UUGGCACUGGCUU-GGCGGAGGUAAGGGAUUGUCAAUUUGUUUUUAUUUUG-AGGCCAGGCACAA-UCAUAACAUACACAGGCCACCUGGAAAC
U56439.1/4333-4533           -UGGCAAGGCUGACAUAGC--UUUUACUGAUC-UGUCUGUUU-AGUGAGUGGACAGGA-UGCCAGUCUGGCAGUUUGCAUUGGCAAUAAAUCACUACUAGACAUUUUAUUUAAAAU-CUGGCACUGGCUU-UGGAGAGGUGAGGGAUUGUCAAUUUGUUUUUAUUUUG-AGGCCAGGCACAA-UCAUAACACAAACAGGCCACCUGGAAAC
AF307310.1/379-495           ------------------------------------------------------------GCCAGUCUGGCAGUUUGCACUGGCAAUAAAUCACCACUAGACAUUUUAUUUUAAAA-UUGGCACUGGCUUGAGGGA-GGUAAAGGAUUGUCAAUUUGCUUUUAUUUUG-AGGCCAGGCAC-------------------------------
AAPE02013820.1/33832-33630   -GGGCAAGGUUGACCUAGC--UUUUACUGAUU-UGUCUGUUU-AGUAGGUAAAUGGGGCUGCCAGUCUGGCAGUUUGCACUGGCAAUAAAUCACCACGAGACAUUUUAUUUAAAAA-UUGGCACUGGCUUUGGGGGAGGUGAGGGAUUGUCAAUUUGCUUUUAUUUUG-UGGCCAGGCACAA-UCAUAACACACACAGGCCACCUGGAAAC
AAGW02004834.1/58037-57836   -UGGCAAGGUUCACCUAGC--UUUCACUGAUU-UGUCUGGUU-AGUAGGUAAAUGGGGCUGCCAGUCUGGCAAUUUGCAUUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAA-UUGGCACCGGCUU-GGAGGAGGUAAGGGAUUGUCAACUCGCUUUUGUUUUG-AGGCCAGACACAG-UCAUAACACACAAAAGCCACCUGGAAAC
AAGU03011001.1/29250-29050   -GGGCAAGGUUGACAUAGC--UUUUACUGAUU-UGUCUGCUUAGU-AGGUAACGGGA-CUGCCAGUCUGGCAGUUUGUGUUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAA-UUGGCACUGGCCUGGGGGA-GGUAAGGAAUUGUCAAUUUGCUUUUAUUUUG-AGGCCAGGCCCAA-UCAUAACACACACAGGCCACCUGGAAAC
AACN010165493.1/494-294      -GGGCAAGGUUGACAUAGC--UUUUACUGAUU-UGUCUGCUU-AGUAGGUAAAUGGGGCUGCCAGUCUGGCAGUUUGCACUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAA-UUGGCACUGGCUC-GGGGGAGGU-AGGGGUUGUCAAUUUGCUUUUAUGUUG-AGGCCAGGCACAA-UCAUAACACACACAAGCCACCUGGAAAC
AAQR03097656.1/86881-87080   -UGGCAAGGUGGACAC-GC--UUCUGCUGAUU-UGUCUGCUU-AGUAGGUAAGUGGG-CUGCCAGGCUGGCAGUUUGCAUUGGCAAUAAAUCACCACUAGACAUUUUAUUUAAAAA-UUGGCACUGACCA-GGGGGAGGUAAGGGAUUGUCAAUUUGUUUUUAUUUUG-AGGCCAGGCACA-AUCAUAACAUACACAGGCCACCUGGAAAC
#=GC SS_cons                 .::::::::::::::::::..:::::::::::.:::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::.:::::::::::::::::::::::::::::::::::::.:::::::::::::.::::::::::::::::::::::::::::
#=GC RF                      .gGGCaAGGuugAcaUaGc..UuuuaCUGaUu.UGUCUGcUU.aGUAGGUaaaugGGGCUGCCAGUCUGGCAGUuUGCauUGGCAAUAAAUCACcaCuAGACAUUUUAUUUaAAAa.UUGGCaCUGGcuU.gGgGGaGGUaAGGGAUUGUCAAUUUGcUUUUAUUUuG.AGGCCAGGCACAA.UCAUAAcacACAcagGCCACCUGGAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF01996
#=GF ID   mir-995
#=GF DE   microRNA mir-995
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   78.30
#=GF NC   55.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000895;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [2]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010;42:6-9.
#=GF RN   [3]
#=GF RM   18463636
#=GF RT   Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells
#=GF RA   Kawamura Y, Saito K, Kin T, Ono Y, Asai K, Sunohara T, Okada TN, Siomi MC,
#=GF RA   Siomi H
#=GF RL   Nature. 2008;453:793-797.
#=GF RN   [4]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF WK   MicroRNA
#=GF SQ   9


AAIZ01006001.1/48785-48869     --GCUGCACAACGCAGCCCGGAUUCUGUGUGUGCUGCG----CUGUGUUC--UUAAAAGC---------CGUAGCACCACAUGAUUCGGCUGCGUGGU-C-A-GC----
AE014297.2/16561645-16561734   CACCUGCACCCCGCAGCCCGAAUUAUGUGGGAGCUGCG----CCGU--UU--CCGUAAUC---------CGUAGCACCACAUGAUUCGGCUUCGUGGUAC-A-GGAUAU
AASS01029797.1/1529-1618       CACCUGUACCCCGCAGCCCGAAUUAUGUGGGAGCUGCG----CCGU--UU--CCAAAGUC---------CGUAGCACCACAUGAUUCGGCUUCGUGGUGC-A-GGACAU
DQ378292.1/2068-1979           CAGCUGCACAACGAAGCCCGGAUACUGUGUGUGUUGCG----CUGU---U--UAGAGGUA---------CGUAGCACCACAUGAUUCGGCUUCGUGGUGC-ACGCAACU
AAPT01018750.1/3883-3988       AUGCUGUACAGUGAAGCCCGGAUUCUGUGUGUGCUGCGUUUGCUGAUUUG--CCAUACACAUAAAUAUACGUAGCACCACAUGAUUCGGCUUCGUGGUGCUA-GCAACU
AAPP01019564.1/136354-136265   CGCCUGUCCUACGCAGCCCGGAUUCUGUGGGAGCUGCG----CCGU--UC--UUUCUAUC---------CGUAGCACCACAUGAUUCGGCUUCGUGGUGC-A-GGGCAU
AAPQ01006441.1/1304016-1303927 CACCUGCACCCCGCAGCCCGAAUUAUGUGGGAGCUGCG----CUGU--UU--UCAGGAUC---------CGUAGCACCACAUGAUUCGGCUUCGUGGUGC-A-GGACAU
AAPU01011147.1/810709-810796   UAGCUGAACUACGAAGCCCGGGUUUUGUGUGUGCCGCG----CUGUUU------UGAGUA---------CGUAGCACCACAUGAUUCGGCUUGGUAGUAC-A-GGCUCA
AAQB01008976.1/639591-639498   AGGCUUCACCAAGCAGCCCGGAUUCUGCGAGUGCUGCG----CUACAACAAGAACUAAGA---------CGUAGCACCACAUGAUUCGGCUUCAUGGUGA-A-GUACAU
#=GC SS_cons                   ::<<<<-<<<-<<-<<<<-<<<<<<<<<<<--<<<<<<....________..________.........>>>>>>->>>>>>>>>>>>>>>->>->>>->.>.>>::::
#=GC RF                        aagCUGuaCcacGaAGCCCGgaUuaUGuGgGuGCugCG....CUGuuuUu..uuauaauc.........CGuaGCAcCaCAugAuuCGGCUUCgUgGugC.A.GcauaU
//
# STOCKHOLM 1.0

#=GF AC   RF01997
#=GF ID   mir-969
#=GF DE   microRNA mir-969
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   89.90
#=GF NC   54.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000879;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [2]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010;42:6-9.
#=GF RN   [3]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF WK   MicroRNA
#=GF SQ   8


AE014298.4/18018390-18018483 -AGUCUCUGUCCUACGUCCGAGUUCCACUAAGCAAGUUUUGAGAUCGUUUUAAAAACAAAAACUUGACACGUUGAGCUCGUUCGUGGG--AUGG-----ACU----------
AADE01001273.1/4151-4044     AGGAGCCUGUUCUACGUGCGAGUUCCACCAUGCAAGUUUUGAGCGUAUA-UGAAUCCAAAAACUUGACACGUUGAGCUCGUGCGUGGU--GCAGCCAA-AUCAUCGCAGCGC
AAQB01008838.1/4488-4586     A---UCCUGUCCUACGCAUGAGUUCCACUAAGCAAGUUUUGGGCAUAUUUCAAAAACAAAAACUUGACACGUUGAGCUCGUCUGUGUG--ACAG--------AACGAACAAC
AANI01015309.1/11735-11628   GCUU--CUGCCCUACGCACGAGUUCCACUAAUCAAGUUUUGAGCGGAUUCGAAAGUCGAAAACUUGACACGUUGAGCUCGUCCGUGGG--GCGGCAUUCAAGCCAGAAGAGC
AAPT01021333.1/25650-25757   GGGUGUCUGCCACACUUACGAGUUCCACUAUUCAAGUUUUGAGCGUAUU-UGAAAUCAAAAACUUGACACGUUGAGCUCGUGUGUGCGUUGCGG--AA-AUCAACUUACUCA
AAPU01009701.1/40639-40741   AUUUGGCUGUCCUACGAGCGAGUUCCACUAAUCAAGUUUUGAGUG--UUCGAAAAUCAAAAACUUGACACGUUGAGCUCGUCUGUGUG--GCAC-----AAGUUCAACAAAA
AAPP01019211.1/37252-37149   AUAUU-CUGUUUUACGUGCGAGUUCCACUAAGCAAGUUUUGAGAAUUUUUUAAAAACAAAAACUUGACACGUUGAGCUCGUCCGUGGG--GCAG-----AUAAUGUCAGCAG
AAPQ01006011.1/221977-222081 AAAUCUCUGUCCUACGUCCGAGUUCCACUAAGCAAGUUUUGAGAUCGUUUUAAAAACAAAAACUUGACACGUUGAGCUCGUUCGUGGG--AUGG-----AUUACUGCCGAAA
#=GC SS_cons                 :<<<--<<<<<<<<<<--<<<<<<<-<<----<<<<<<<<__________________>>>>>>>>---->>->>>>>>>-->>>>>>..>>>>.....>>>::::::::::
#=GC RF                      agguuuCuGcccuaCguaCGaGuUCCaCUAagCaaGUUUUGAGcguaUUuuAAAauCAAAAACuuGACACGuUGAgCuCGUucGuggg..gCaG.....accaucgaagaaa
//
# STOCKHOLM 1.0

#=GF AC   RF01998
#=GF ID   group-II-D1D4-1
#=GF DE   Group II catalytic intron D1-D4-1
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Weinberg Z
#=GF SS   Predicted; Weinberg Z
#=GF GA   35.00
#=GF TC   35.00
#=GF NC   34.90
#=GF TP   Intron;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00102
#=GF DR   SO; 0000603; group_II_intron;
#=GF DR   GO; 0000373; Group II intron splicing;
#=GF RN   [1]
#=GF RM   11377794
#=GF RT   The ins and outs of group II introns.
#=GF RA   Bonen L, Vogel J
#=GF RL   Trends Genet 2001;17:322-331.
#=GF RN   [2]
#=GF RM   11726522
#=GF RT   Control of branch-site choice by a group II intron.
#=GF RA   Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM
#=GF RL   EMBO J 2001;20:6866-6876.
#=GF RN   [3]
#=GF RM   12870716
#=GF RT   Group II introns: structure and catalytic versatility of large natural
#=GF RT   ribozymes.
#=GF RA   Lehmann K, Schmidt U
#=GF RL   Crit Rev Biochem Mol Biol 2003;38:249-303.
#=GF CC   Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi,
#=GF CC   plants and protists, and also in mRNA in bacteria. They are large
#=GF CC   self-splicing ribozymes and have 6 structural domains (usually designated
#=GF CC   dI to dVI. This model and alignment represents only domains V and VI. A
#=GF CC   subset of group II introns also encode essential splicing proteins in
#=GF CC   intronic ORFs. The length of these introns can therefore be up to 3kb.
#=GF CC   Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing
#=GF CC   with two transesterification steps. The 2' hydroxyl of a bulged adenosine
#=GF CC   in domain VI attacks the 5' splice site, followed by nucleophilic attack
#=GF CC   on the 3' splice site by the 3' OH of the upstream exon. Protein machinery
#=GF CC   is required for splicing in vivo, and long range intron-intron and
#=GF CC   intron-exon interactions are important for splice site positioning. Group
#=GF CC   II introns are further sub-classified into groups IIA and IIB which differ
#=GF CC   in splice site consensus, distance of bulged A from 3' splice site, some
#=GF CC   tertiary interactions, and intronic ORF phylogeny [1].
#=GF WK   Group_II_intron
#=GF SQ   237


BABE01001822.1/1052-982      UAA-C-CACUGU---ACAA----A-G--CAGUG-C------UGAAC-------GCACAGAAGUCAGCAGAGGUCAUAGUA-G-CC---------------------------------------------------GAAA-----------------------GGUGA--AGGAC
BAAX01000004.1/3665-3747     ACA-U-CAUGGU----UGA------A--AUAAG-A------UUUAU-------CAUGAGGAGUCAGCCGAGGCCAUAGUA-C-CU------------------U-AU-GG------------------------GCUAUA--G------ACC-AUG-------AGGAA--AGGGC
BAAZ01020238.1/406-496       UAA-C-CCAUGCU--GCAA-----GG--CAUGG-C------UGAAC-------CCACAGAAGUCAGUCUGGACCAUAGUA-C-CAGA-------------GAAG-UC-G---------------------------GUGAAA-------GUC-GACA-----GAGGGA--AGGGU
ABEF01005287.1/516-598       CGC-C-CAACCGA--GUGC-----CCAAGGUGC-G------CGGGA-------AGGCGGCAGUCAGGCGAGGCCAUAGUA-G-CU------------------G-CU-U---------------------------GCGCAC-----------AGC-------GGCGA--AGGGC
ABEF01029002.1/82-164        CGC-C-CAACCGA--GUGC-----CC--GAGGU-G----UGCGGGA-------AGGCGGCAGUCAGCCGAGGCCAUAGUA-G-CU------------------G-CU-U---------------------------GCGCAC-----------AGC-------GGCGA--AGGGC
BABD01009491.1/393-484       UGG-U-UUCAUCA--GCCA-----UA--GUAAC-A-----ACGAAU-------CAUAGGAAGUCAGCAGAUGUCAUAGUA-G-CGAAG------------AAGU-CC-G----------------------------GGAAA--------CC-GGAU----GGAGCAA--AGGAC
ABEF01054409.1/4022-4103     CUA-C-CUACCUC--GUGA-----GG--GGUGG-G----GAUGGGG-------CGCCAGAACUCAGCCGAGGCCAUAGUA-G-AU------------------G-CG-U----------------------------CACC----------G-CGU-------ACUGA--AGGGC
BAAZ01006171.1/1076-998      UAA-C-CGCUAUU--GUGA-----GA--UAGCG-U------UGAGC-------GUACAGAAGUCAGCAGAGGUCAUAGUA-G-CU------------------G----U---------------------------GUUUUU--------UU---C-------AGUGA--AGGAC
ABDH01035596.1/432-537       CAA-C-CCAUGCA--GUGA-----UG--UAUGG-C------UGAGC-------GUCCAGAAGUCAGCAGAGGCCAUAGUA-C-CGCUAAG-------GGGAUG------UCCCGUUU-----------AGAGGGAG------UAC--GAACG----G----AGCGGGA--AGGGC
ABDH01035596.1/1124-1231     CAA-C-CCAUACA--GUGA-----UG--UGUGG-C------UGAAC-------GUCCAGAAGUCAGCAGAGGCCAUAGUA-C-CGUGAAGU-----GGGAUGUC-UC-UGAAAU-----------------AUGGG------AGUACGAACG-GAG-------CGGGA--AGGGU
ABDH01036608.1/1187-1080     CAA-C-UCAUACA--GCGA-----UG--UAUGG-C------UGAAC-------GUCCAGAAGUCAGCAGAGGCCAUAGUA-C-CG------------------C-UA-AGGGGGAUGUCUC---UGAAAUACGGGA------GUA-CGAGCG-GAG-------CGGGA--AGGGC
ABDH01040768.1/976-1082      CAA-C-CCAUACA--GUGA-----UG--UAUGG-C------UGAAC-------GUCCAGAAGUCAGCAGAGGCCAUAGUA-C-CG------------------C-UA-AGGGGAAUGUCCC---GUGUAGAGGGAG------UAC--GAACG-GAG-------CGGGA--AGGGC
ABDH01033985.1/118-225       CAA-C-CCAUACA--GCGA-----UG--UAUGG-C------UGAAC-------AUCCAGAAGUCAGCAGAGGCCAUAGUA-C-CGCGAAGUGGAAGGGCCACC--UC-GAGAG------------------GGCAU------AC---GAACG-GA-------GCGGGA--AGGGC
ABDH01034986.1/727-617       CAA-C-CCAUACA--GCGA-----UG--UAUGA-C------UGAAC-------GUCCAGAAGUCAGCAGAGGCCAUAGUA-C-CGCGAAGGG----GAUAAUUC-UC-UGGAAAAC-------------GGACGGG------AAC--GAACG-GAG-------CGGGA--AGGGC
ABDH01025731.1/1242-1132     CAA-C-CCAUACA--GCGA-----UG--UAUGA-C------UGAAC-------GUCCAGAAGUCAGCAGAGGCCAUAGUA-C-CGCGAAGGGG--AUAAUUCU---C-UGGAAAAC-------------GGAUGGG------AAC--GAACA-G--A-----GCGGGA--AGGGC
BABG01000586.1/1039-970      -AA-C-CAUUGC---AUAA----A-G--CAAUG-C------UGAAC-------GCACAGAAGUCAGCAAAGGCCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGUGA--AGGAC
BAAV01030017.1/733-804       UAA-C-CAUUAUU--AUGA-----GG--UACUG-C------UGAAC-------GUACAGAAGUCAGCCGAGGUCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGCGA--AGGAC
BAAV01030018.1/656-585       UAA-C-CAUUAUU--AUGA-----GG--UAAUG-C------UGAAC-------GUACAGAAGUCAGCCGAGGUCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGCGA--AGGAC
BABD01028650.1/334-398       CUG---C-AUAAA--GCAA-----U-------G-------CUGAAC-------GCACAGAAGUCAGCAGAGGUCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGUGA--AGGAC
ABDH01009837.1/262-156       CAA-C-CCAUACA--GCGA-----UG--UAUGG-C------UGAAC-------GUCCAGAAGUCAGCAGAGGCCGUAGUA-C-CAUGAAGG------GGAAUGU-CC-CAUGUC----------------GAGGGAGAACAA--------AC-GGA------GCGGGA--AGGGC
ABDH01040428.1/83-190        CAA-C-CCAUACA--GUGA-----UG--UAUGG-C------UGAAA-------GUUCAGAAGUCAGCAGAGGCCGUAGUA-C-CGCGAGGGG---GAAUGUCU---C-UGAAAU-----------------ACGGG------AGUACGAACA-G--A-----GCGGGA--AGGGC
ABDH01037979.1/1142-1032     CAA-C-CCAUACA--GUGA-----UG--UAUGG-C------UGAAC-------GUUCAGAAGUCAGCAGAGGCCAUAGUA-C-CGCGAAGGG----GAUAACU---C-UCUGGAAGA-----------CGGAUGGG------AAC--GAACG-G--A-----GCGGGA--AGGGC
ABDH01002435.1/683-612       CAA-C-CCAUACA--GAGA-----UG--UAUGA-U------UGAGC-------GUCCAGAAGUCAGCAGAGGCCGUAGUA-C-C----------------------------------------------------GUGAAG----------------------GGGA--AUGUC
BABF01006785.1/257-176       CAA-C-GAUCAUG--GCGA-----CA--UGAUG-G------UGAAU-------CAUGAGAAGUCAGCCGAGGUCAUAGUA-G-UA------------------A-CG-----------------------------AUACUG--------AC-CGU-------UACGA--AGGAC
BABF01003176.1/1461-1542     CAA-C-GAUCAUG--GCGA-----CA--UGAUG-G------UGAAU-------CAUGAGAAGUCAGCCGAGGUCAUAGUA-G-UA------------------A-CG-----------------------------ACACUG--------AC-CGU-------UACGA--AGGAC
BAAW01003584.1/1480-1565     CAA-U-CUAUAUA--GUGA-----UA--UAUAG-C------UGAAC-------UAUCAGAAGUCAGCAGAAGUCAUAGUA-ACUC------------------C-GC-UA-------------------------A--UCGCG------AUA-GCG-------GAUGA--AGGAC
BAAW01000650.1/734-819       CAA-C-CUAUACA--GUGA-----UG--UAUAA-C------UGAAC-------UAUCAGAAGUCAGCAGAGGUCAUAGUA-ACUC------------------C-GC-UA-------------------------A--UCGCG------AUA-GCG-------GAUGA--AGGAC
BAAW01000769.1/1577-1492     CAA-C-AUAUACA--GUGA-----UG--UAUAA-C------UGAAC-------UAUCAGAAGUCAGCAGAGGUCAUAGUAAG-UC------------------C-GC-UA-------------------------A--UCGCG------AUA-GCG-------GAUGA--AUGAC
AP006840.1/2935999-2935914   UAA-C-CUGCGUC--GGGA-----GA--CGCAG-C------UGAAC-------CGGCAGAAGUCAGCAAAGGCCAUAGUA-C-CGG---------------CAG-G------------------------------GGGACG--------CC--CCG----ACCGGGA--AGGGC
AAQL01011911.1/2065-2134     -AA-C-CAUUGC---AUAA----A-G--CAAUG-C------UGAAC-------GUACAGAAGUCAGCAGAGGUCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGUGA--AGGAC
CP001336.1/1949734-1949817   UAC-C-CCAUGCA--GUGA-----UG--UAUGG-C------UGAAC-------AGUUGGAAGUCAGCA-AAGUCAU-GUA-C-CA------------------A-GA-UG------------------------GU--CAUGA------ACA-UCU-------UGGGA--AGGAC
CP000478.1/3922718-3922798   CUA-C-CGCUGUC--GAGA-----GG--CGGCG-G----GAAGGGU-------CGACAGAAGUCAGCAGAGGGCAUAGUA-G-GU------------------C-CU-U---------------------------CGA------------C-CGG-------ACUGA--AGGCC
CP001389.1/3003093-3003015   CUA-C-CGGCGUC--GAAA-----GG--CGUCG-G----GAUGGGG-------CGGCAGGAGUCAGCAGAGGCCGUAGUA-G-CC------------------G----G---------------------------ACCAA----------G---C-------GGUGA--AGGGC
AAPR01000002.1/105368-105438 ACC------------ACGAG---U---------------UGGUAUA-------AUAGAGAAGUCAGCCGAAGUCAUAGUA-G-UU------------------A-AU-G---------------------------AGCUGA--------AC-AUU-------AAUGA--AGGAC
CP000790.1/1758834-1758748   CUA-A-UGCAGCA--GUGA-----UG--UUGUG-U----GACGGGC-------AAUAAGAAGUCAGCAGAGGGCAUAGUA-C-CU------------------U-GA-GA-------------------------CAGUAC--------AAC-UUA-------AGGGA--AGGCC
CP000471.1/3862386-3862304   CUA-C-UGAUAUC--GUAA-----GG--UAUUG-G----GAUGGGG-------UGGCAGAAGUCAGCAGAAGCCAUAGUC-G-UU------------------A-CC-G---------------------------UAACU----------G-GGU-------AACGA--AGGGC
AAXY01000055.1/3436-3531     CGC-C-GAUAGGG--GUAA-----CC--CCGCC-G-----GUGAUU-------GAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------ACGC-CC-AU-------------------------CGUAAUG-------GUU-GGGAC---AGGGUGA--AGGCC
AATN01000186.1/7552-7634     CGC-G-ACGGCGA--GCAA-----UC--GUCAG-C-----GUGACU-------GAUCAGGAGUCAGCAGAGGCCAUAGUA-G-CGA----------------CA----C----------------------------CGAAA--------GG---UA-----ACGCGA--AGGGC
AACY022500726.1/299-215      CUA-C-UGACAUC--GAGA-----GA--UGUUG-G----GAUGGGA-------UAUCAGAAGUCAGCCGAGGCCGUAGUA-G-UG------------------A-UA-U---------------------------UAAACC--------GA-UAG-------CAUGA--AGGGC
CP000764.1/2269167-2269084   UAA-C-CUUACUU--AUGA-----AA--GUAAG-C------UGAAC-------AAUCAGAAGUUAGCAGAGGUCAUAGUA-C-CU------------------A-UC-UC-------------------------G-GCGCA--------AA-GAU-------AGGGA--AGGAC
ACDK01000011.1/30878-30962   CAU-A-ACCUAUA--GUGA-----UA--UAUAA-C------UGAAU-------UAUCAGACGUCAGCAGAUGUCAUAGUA-U-UU------------------C-GC-U---------------------------AAACGCG------UUA-GCG-------AAGGA--AAGAC
AB126575.1/258-342           UAA-C-CUUGCAU--AAGA-----GU--GCAAG-C------UGAAC-------GGUCAGAAGUCAGCAGAAGCCAUAGUA-C-CC-----------------GC-UU-G---------------------------GUCUAG--------AC-AAG------AGGGGA--AGGGC
AE001437.1/3712523-3712439   -AA-C-CUACAUA--GUGA-----UA--UGUAG-C------UGAAC-------UAUCAGAAGUCAGCAGAAGUCAUAGUA-C-CA------------------G-UU-CAG-----------------------UC---AUGA------AUG-AAC-------UGGGA--AGGAC
AAFX01034639.1/779-860       CUA-C-CGUCGCU--GAGA-----GG--CGAAG-G----GAUGAAG-------UUGCAGAAGUCAGCCGCGGGCAUAGUA-G-GU------------------U-CA-G---------------------------UCGA-----------C-CGA-------ACUGA--AGGCC
ACGV01000137.1/3911-3989     CAG-G-CGGUGCA--GUGA-----UG--UAGCG-U------UGAGU------AAGCCAGAAGUCAGCCGAGGUCAUAGUA-G-UC------------------U-GA-----------------------------GUAA-------------UCA-------GAUGA--AGGAC
BA000028.3/1473500-1473568   UAA-C-CCAUUCA--GCAA-----UG--GAUGG-C------UGAAC-------GGUCAGAAGUCAGCAGAAGUCAUAGUA-C-----------------------CC-C---------------------------UAC------------A-GG----------------GGAC
AAOX01000004.1/97946-97871   -AA-C-CUGCUUA--GUGA-----UA--AGCAG-C------UGAAC-------UAAGAGAAGUCAGCAGAAGCCAUAGUA-U-CA------------------A-CG-A--------------------------U---------------U-UGU-------UGAGA--AGGGC
BA000043.1/1495753-1495837   CAA-C-CGUUGGA--GCGA-----UC--CAACG-C------UGAAC-------GGACAGAAGUCAGCAGAGGUCAUAGUA-C-CC-----------------GU-CU-A---------------------------GCUUAG--------AU-AGA------AGGGGA--AGGAC
AE005672.3/2100079-2100000   CGUA-----------GUAA----C---------------AACGAAU-------CAUGAGAAGUCAGCCGAGCCCAUAGUA-G-UGAG-------------GAAA-CU-UC-------------------------CGUAAUG--------GA-AGUG-----GAGCGA--AGGGG
ABCC02000078.1/402-331       UAA-C-CAUUAUC--GAAA-----GA--UAGUG-C------UGAAC-------GUACAGAAGUCAGCCGAGGCCGUAGUA-G-UC---------------------------------------------------GGGA-----------------------GAUGA--AGGAC
AAQF01000163.1/3651-3730     CGU-C-CUGCAUG--GCAA-----CA--UGCAG-G-----AUGAUC-------AGGCAGGAGUCAGCCGAGGCCAUAGUA-G-UU------------------C-CG-G---------------------------GCAA-------------CGG-------AACGA--AGGGC
AATD01000250.1/438-352       CG----GCAGUCU--GCAA-----GG--AUAGU--AA-CAACGAAU-------GCCGAGGAGUCAGCAGAGGCCGAAGUA-G-CC------------------G-AC-C---------------------------GUGGGA--------CG-GUCA-----AGGCGA--AGGGC
CP000879.1/1359912-1359835   CAA-C-CCAUGCA--GCAA-----UG--UAUGG-C------UGAAU-------CUUGAGAAGUCAGCAGAGGUCAUAGUA-C-UC------------------A-UU-----------------------------GAAA-------------GAU-------GGGGA--AGGAC
BAAX01001491.1/349-259       UUG-C-CUUUAC---GAAA------G--UCAUG-GA---GUAAAGCUU---GCUGUGAGAAGUCAGCAGAUGCCAUAGUA-G-UG------------------G-AG-UUC----------------------UCG---AUA-------ACG-CUC-------CAUGA--AGGGC
AARF01000332.1/1445-1530     UAA-A-UUUGCUU--GUGA-----AA--GCAGA-C------UGAGC-------GUACAGAAGUCAGCAGACGCCAUAGUA-C-GC------------------A-AG-AA------------------------GUUGCAA--------CGC-CUU-------GCGGA--AGGGC
AL954747.1/2285516-2285600   CGC-G-UCCACUG--GCAA-----CG--GUGGG-C-----GUGACG-------GUGCAGAAGUCAGCAGAAGCCAUAGUA-G-GC------------------A-GC-C--------------------------AGGUGUC--------GG-GCU-------GCCGA--AGGGC
AAFZ01004663.1/99-168        CGAU------CUG--GUAA-----CA--G------------UGGUU-------GAAGAGGAAUCAGCCGAUGGCAUAGUA-G-GG------------------U-AU-C---------------------------GACC-------------AUA-------CCUGA--AGGCC
CP000874.1/280045-280123     CUA-C-CGGCGUC--GAAA-----GG--CGCCG-G----GAUGGGG-------CGGCAGGAGUCAGCAGAGGCCGUAGUA-G-CC------------------G----G---------------------------ACCAA----------G---C-------GGUGA--AGGGC
CP000924.1/2109166-2109074   UAA-C-CUAUAUC--GUGA-----GA--UAUAG-C------UGAAC-------AUUCAGAAGUCAGCUCAAGUCAUAGUA-C-UGUUUG---------AACCUA-CC-G---------------------------AAAGGA--------UA-GGU------AAGGGA--AGGAC
CR377166.1/4792-4866         CAG-G-CUCAAUA--GUAA-----UG--UUGAG-U------UGUCC------AUGACAGAAGUCAGCCGAGGCCAUAGUA-G-CC------------------A--------------------------------GUAA---------------U-------GGUGA--GGGGC
AAFY01003311.1/1109-1035     UA--C-CGACGUU--GCGA-----AA--CGUCG-G----GAUGAUC-------AUGCAGAAGUCAGCAGAGGCCAUAGUA-G-GU------------------G-CG----------------------------------------------CCU-------ACCGA--AGGGC
ACIO01000505.1/463-534       UAA-C-CACUAUC--GUGA-----GA--UAGUG-C------UGAAC-------GUACAGAAGUCAGCCGAGGUCGUAGUA-G-UC---------------------------------------------------GAGA-----------------------GAUGA--AGGAC
CP000879.1/1633076-1632999   CAA-C-CCAUACA--GCAA-----UG--UAUGG-C------UGAAU-------CUUGAGAAGUCAGCAGAGGUCAUAGUA-C-UC------------------A-UU-----------------------------GAGA-------------GAU-------GAGGA--AGGAC
AACY020536917.1/593-683      CGC-G-CGGCGGA--GUGA-----UC--CGCAG-C-----GUGAUC-------GGGCAGAAGUCAGCAGAGGCCAUAGUA-G-UGC----------------G---G-GCGC--------------------CGGG-AC---CG----GCGC-C--G-----GCGCGA--AGGGC
ABIC01000057.1/19363-19458   CGC-A-UGACGGG--GUAA-----CU--CGGUA-U-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------AUGC-CC-AU-------------------------CGUAAUG-------GUU-GGGAC---AGGGUGA--AGGCC
ABSR01024312.1/708-803       CGC-G-CCACGCA--GUAA-----UG--CGUGG-C-----GUGACC-------GGAUAGAAGUCAGCAGAGGCCGUAGGA-G-CUGG-------------CGGC-CC-UC------------------------AAGUGAAG--------AA-GGGCG---AAGGCAA--AGGGC
CP000423.1/82009-82081       AAA-G-CCUGUCA--GUGA-----UG--GCUGG-U------UGAAC------GAUAUAGGAAUUAGCCGAGGCCAUAGUA-G-UG---------------------------------------------------GUAA-----------------------CACGA--AGGGC
ABPR01011794.1/366-271       CGC-U-UUCUGUG--GUAA-----CA--CAGCG-A-----GUGAUC-------AAACAGAAGUCAGCCGAGGCCAUAGUA-G-CCCAA-----------CGCCA-GG-A---------------------------GUAAUG---------C-CCUGGA-CAUGGUGA--AGGGC
ABIC01000047.1/11708-11613   CGC-A-UGACGGG--GCAA-----CU--CGGCA-U-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------AUGC-CC-AU-------------------------CGUAAUG-------GUU-GGGAC---AGGGUGA--AGGCC
AACY020305625.1/403-315      CUA-U-ACUGGUA--GUGA-----UA--CUAGU-A----GAAGGGC-------UGUAAGGAGUCAGCAGACGGCAUAGUA-C-CA------------------C-AG-UCA-----------------------AGUAUAC--------AGA-UUG-------CGGGA--AGGCC
AB255435.1/20089-20173       CUC-C-CGGCGCC--GUAA-----GG--CGCCA-G----GAUGGGG-------CGGCAGAAGUCAGCCGACGCUGUAGUA-G-UG------------------C-UG-C---------------------------AAAACC--------GG-CAG-------CAUGA--AGGGC
AAFZ01028470.1/152-247       CGC-U-GGCAGAG--GUAA-----CU--UUGCC-A-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCCAACGGU----CAGCGUAA-UG-G---------------------------CUGAUA-----------CAU-------GGUGA--AGGCC
AAFZ01027222.1/417-512       CGC-U-GACGGGG--GCAA-----CC--CUGGC-A-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------ACGC-CC-AG-------------------------CGUAAUG-------GCU-GGGAC---AGGGUGA--AGGCC
ACGB01000015.1/8121-8050     AAA-C----------AAGA---------------U------UUAUC-------GUGAGGAAGUCAGCAGAGGCCAUCGUA-C-UG------------------G-AC-GG------------------------GU--UAUAG------ACC-GUC-------CAGGA--AGGGC
CP000879.1/1345398-1345321   CAA-C-CCAUGCA--GCAA-----UG--UAUGG-C------UGAAU-------CUUGAGAAGUCAGCAGAAGUCAUAGUA-C-UC------------------A-UU-G----------------------------GAA-------------GAU-------GAGGA--AGGAC
ACIH01000269.1/282-363       AA--U-CACGGU----UGA------A--ACAAG-A------UUUAU-------CAUGAGAAGUCAGCAGACGCCAUAGUA-C-CG------------------C-GA-AC------------------------AGUCGAC--------GGU-UCG-------AGGGA--AGGGC
AACY024109992.1/338-417      CUA-C-CGAAGUC--GAGA-----GG--CUUCG-G----GACGGGA-------GCGCAGAAGUCAGCAGAGGCCGUAGUA-G-CG------------------A-UC-G---------------------------AUG--------------GAU-------CGUGA--AGGGC
ACIN02000013.1/597849-597776 CAUA-----------GUAA----C---------------AAUGAAU-------GGCAAGAAGUCAGCAGAAGUCAUAGUA-C-CA------------------U-UA-CGG-----------------------UU-GCAAA--------CA-UAA-------UGGGA--AGGAC
CR377818.1/73098-73003       CGC-U-UUACGAG--GUAA-----CU--CGUUA-A-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------ACGC-CC-AU-------------------------CGUAAUG-------GUU-GGGAC---ACGGUGA--AGGCC
AATN01000130.1/14672-14750   CUG-G-GCGUUGG--GUAA-----CU--GGCGC-U----GAACACC-------GUGGAGAAGUCAGCAAAGGGCAUAGUA-G-GC------------------G----A----------------------------CGCC---------AC---C-------GCCGA--AGGCC
CP000494.1/6817882-6817802   CUGAG-GUCGUC---GUAA------G--GCGGC-C------GGAUCG----CGGCGCAGAAGUCAGCAGAGGGCGUAGUA-G-GC------------------G-GU-A---------------------------GCGU-------------GCC-------GCUAA--AGGCC
CR931678.1/881-960           CGUA-----------GUAA----C---------------AACGAAU-------CAUGAGAAGUCAGCCGAACCCAUAGUA-G-UGAG-------------GAAA-CU-UC-------------------------UGUAGUG--------GA-AGUG-----GAGCGA--AGGGG
CP000922.1/2424635-2424558   UAA-U-UUAC-----AUAA----------GUAG-C------UGAAU-------CAUCAGAAGUCAGCAGAGGUCAUAGUA-C-GA------------------A-UC-G---------------------------GUCUAG-------AAC-GAU-------UCGGA--AGGAC
CP000471.1/1386529-1386609   CUA-C-CGGCAUC--GAGA-----GG--UGCUG-G----GAUGGGU-------GUGCAGAAGUCAGCCGAGGGCAUAGUA-G-GG------------------G-UA-U---------------------------CGA------------C-CAC-------CCUGA--AGGCC
ACCJ01000631.1/1581-1510     UAA-C-CAUUAUC--GUGA-----GA--UAAUG-C------UGAAC-------GUACAGAAGUCAGCCGAGGUCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGCAA--AGGAC
AE015451.1/1820139-1820223   UAC-C-GCGCGUC--GAAA-----GG--CGACG-G----GAUGAGC-------GUGCAGAAGUCAGCCGAAGCCGUAGUAAG-UG------------------G-CG-----------------------------GUUAAC--------CG-CGC-------CACCA--AGGGC
CP000970.1/1127993-1127909   CUA-C-CGGUGCC--GUGA-----GG--CGCCG-G----GAUGGGG-------CGGCAGAAGUCAGCCGACGCCGUAGUA-G-UG------------------C-UG-C---------------------------AAAACC--------GG-CAG-------CAUGA--AGGGC
CP001157.1/2030512-2030589   CGU-C---GAGAG--GCGA-----C---------GG---GAUGAAC-------GGGCAGAAGUCAGCCGAAGCCGUAGUAAG-UG------------------A-CG-A---------------------------CCA-AC--------CA-CGU-------CACCA--AGGGC
ABIY02000064.1/52338-52415   UA--U-CUGGUU-----GA------A--ACAAG-A------UUUGU-------CGUGAGAAGUCAGCCGAAGCCAUAGUA-C-CU------------------G-UU-A---------------------------CUCACC--------AU-AAU-------GGGGA--AGGGC
BABG01000061.1/2090-2020     UAA-C-CAUUGC---AUAA----A-G--CAAUG-C------UGAAC-------GCAUAGAAGUCAGCAGAGGUCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGUGA--AGGAC
ACGV01000119.1/48880-48958   CAA-G-CGGUGCA--GUGA-----UG--UAGCG-U------UGAGU------AAGUCAGAAGUCAGCUGAGGUCAUAGUA-G-UC------------------U-GG-C----------------------------UA------------U-CUG-------GACGA--AGGAC
AE015928.1/3258231-3258143   UUG-U-CUUUAC---GAAA----U-G--UAUGG-A----GUAACG-CU--UGCCGUGAGAAGUCAGCAGAGGUCAUAGUA-G-UG------------------G-GA-C--------------------------UGUCGAU--------AU-UCC-------CAUGA--AGGAC
ACOQ01000035.1/3555-3639     UAC-C-GAUUGUC--GAGA-----GG--CGACG-G----GAUGGGC-------GUGCAGAAGUCAGCCGAGGCCGUAGUAAG-UG------------------G-CG-----------------------------GUCAAC--------CA-CGC-------CAUCA--AGGGC
CP000698.1/4539989-4539907   CUA-C-CGGCAUC--GAGA-----GG--UGCCG-G----GAUGGGU-------UGGCAGAAGUCAGCAGAGGCCAUACGA-G-UC------------------G-G--A---------------------------AUAACC--------GA--CC-------GACAA--AGGGC
AATO01000140.1/3089-3171     CGC-G-ACGGCGA--GCAA-----UC--GCCAG-C-----GUGACU-------GAUCAGGAGUCAGCAGAGGCCAUAGUA-G-CGA----------------CA----C----------------------------CGAAA--------GG---UA-----ACGCGA--AGGGC
AACY023033702.1/800-865      CGC-U-GUCACAG--GUAA-----CU--AUGGC-G-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G---------------------------------------------------------------------C-------------CAA--AUGCC
AE014299.1/2127107-2127202   CGC-A-UGACGGG--GCAA-----CU--CGGCA-U-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCCA-------------ACGC-CC-AU-------------------------CGUAAUG-------GAU-GGGAC---AUGGUGA--AGGCC
AAQL01001449.1/1780-1688     CGG-U-CUCAUUA--GCCG-----UA--GUAAC-A-----ACGAAC-------UGUGAGAAGUCAGCAGAGGUCGUAGUA-G-UGAAG-----------AAGUU-CC-U---------------------------GUAAU---------GG-GGAU----GGAGCGA--AGGAC
ABFU01000013.1/105600-105684 UAA-C-CUAUUUA--GCGA-----UG--AAUAG-C------UGAAC-------AGUCAGAAGUCAGCAGAAGUCGUAGUA-C-CA------------------A-UG-GU-------------------------A--UCUAG------AGC-CAU-------UGGRA--AGGAC
AE007317.1/1977673-1977594   CGUA-----------GUAA----C---------------AACGAAU-------CAUGAGAAGUCAGCCGAACCCAUAGUA-G-UGAG-------------GAAA-CU-UC-------------------------CGUAAUG--------GA-AGUG-----GAGCGA--AGGGG
AP006840.1/1256045-1256130   UAA-C-CCGGGCC--GAGA-----GG--CCCGG-C------UGAAC-------CGGCAGAAGUCAGCAAAGGCCAUAGUA-C-CGG---------------CAG-GG-G---------------------------GAC-----------GC-CCCG----AGCGGGA--AGGGU
BAAX01021590.1/679-772       UUU-U-UUUUUUU--ACGA-----AA--GAAGC-G-----GAGUACAGCUUACCGUGAGAAGUCAGCAGACGCCAUAGUA-G-UG------------------C-AA-UAG----------------------UCG---AUA-------ACG-UUG-------CCCGA--AGGGC
CP000879.1/461767-461690     CAA-C-CCAUGCA--GCAA-----UG--UAUGG-C------UGAAU-------CUUGAGAAGUCAGCAGAAGUCAUAGUA-C-UC------------------A-UU-G----------------------------GAA-------------GAU-------GAGGA--AGGAC
ACKR01000033.1/470-555       AGC-C-UGGU------CGA----------AAAA-G-----GUUAGU-------CGCAAGAAGUCAGCUGAGGUCAUAGUA-G-UGUUG------------AAAG-UC-U---------------------------UGUAAU--------GA-GACU----GGAGCGA--AGGAC
AAUQ01113241.1/415-494       CGU-C-CUUCAUG--GCAA-----CA--UGAAG-G-----AUGAUC-------GGGGAGGAGUCAGCAGAGGUCAUAGUA-G-UU------------------C-C------------------------------UCCAUG---------C--GG-------AAUGA--AGGAC
AACY023761684.1/335-430      CGC-U-UUGCGGG--GUAA-----CC--CGUCG-G-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------ACGC-CC-AU-------------------------CGUAAUG-------GAU-GGGAC---ACGGUGA--AGGCC
AP008230.1/5194786-5194706   AAA-C-CUGGUU-----GA------A--ACAAG-A------UUUAU-------CGUGAGGAGUCAGCAGAAGCCAUAGUA-C-UGA----------------G--GU-G---------------------------UUCUAG--------AC-AC-U-----GAAGGA--AGGGC
AACY023598940.1/773-690      CUA-U-CAUCAGA--GUGA-----UC--UGAUG-A----GAUGGAU-------UAUAAGAAGUCAGCCGAGGGCAUAGUA-G-GA------------------G-UA-A----------------------------UUUUC--------UG-CAC-------UCCGA--AGGCC
ACKS01000046.1/1850-1943     UAG-U-UGUUUUU--ACGA-----AA--GAAGC-GG---AGUAAAGCU--UGCCGUGAGAAGUCAGCAGACGCCAUAGUA-G-UG------------------G-AG-UAC-----------------------UC--GAU-A------GCG-CUC-------CAUGA--AGGGC
CP000705.1/1404855-1404777   CAA-G-CGGUGCA--GUGA-----UG--CAGUG-U------UGAGU------AAGCCAGAAGUCAGCCGAGGUCAUAGUA-G-UU------------------U-GA-A----------------------------UAA-------------UCA-------GAUGA--AGGAC
CR378679.1/156785-156880     CGC-U-UUACGAG--GUAA-----CU--CGUUA-A-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------AUGC-CC-AU-------------------------CGUAAUG-------GUU-GGGAC---ACGGUGA--AGGCC
CP000924.1/149160-149244     -AA-C-CCAUGCA--GUGA-----UG--UAUGG-C------UGAAC-------CUUGAGAAGUCAGCAGAGGUCAUAGUA-C-UU------------------A-UC-UA------------------------GA---CAUG-----AAUA-GAU-------AAGGA--AGGAC
ABPY01006227.1/344-263       CAG-U-GUGGGCA--GAGA-----UG--CUCAC-G----UAUGGGC-------CGGCAGAAGUCAGCCGAGGCCAUAGUA-G-UC------------------C-CG-U---------------------------UGCA-----------C-CGG-------GACGA--AGGGC
ACIN02000019.1/94928-94858   UAA-C-CAUUGC---CUAA----A-G--CAAUG-C------UGAAC-------GCACAGAAGUCAGCAGAGGUCAUAGUA-G-UC---------------------------------------------------GAGA-----------------------GACAA--AGGAC
ABSN01031768.1/741-660       CUA-C-CGUUAUC--GCGA-----GA--UAAGG-G----GAAGAGC-------GGGCAGAAGUCAGCCGAGGGCAUAGUA-G-CU------------------UG--------------------------------UAUGCA------GUA---G-------AGCGA--AGGCC
CP000879.1/1701939-1701862   CAA-C-CCAUGCA--GCAA-----UG--UAUGG-C------UGAAU-------CUUGAGAAGUUAGCAGAGGUCAUAAUA-C-UC------------------A-UU-G----------------------------GAA-------------GAU-------GAGGA--AGGAC
ACFY01000152.1/41930-41842   UAA-C-CAUUGC---AUAA----A-G--CAAUG-C------UGAAC-------GCAUAGAAGUCAGCAGAGGUCAUAGUA-G-CCA---------------AA---C-G---------------------------GAACAAG-----UUCC-G--UU--CGAGGUGA--AGGAA
BA000028.3/1840649-1840564   -AA-C-CCAUUCA--GCAA-----UG--GAUGG-C------UGAAC-------GGUCAGAAGUCAGCAGAAGUCAUAGUA-C-CCUG--------------CAU-AC-----------------------------UCGAGA--------AU-GUA------AGGGGA--AGGAC
BA000028.3/2645555-2645490   CAA-C-CAAGAUG--GUGA-----CA--UCUUA-G------UGAAU-------CACAAGAAGUCAGCAGAGGUCAUAGUA--------------------------------------------------------AUGC-----------U---------------A--ACGGC
CP000924.1/2099219-2099134   CAA-C-CCAUACA--GAGA-----UG--UAUGG-C------UGAAC-------UUUGAGAAGUCAGCAGAGGUCAUAGUA-C-UU------------------A-UC-UA------------------------GA-CAAU-A------AUA-GAU-------AAGGA--AGGAC
CP000698.1/1454809-1454891   CUA-C-CGACAUC--GAGA-----GG--UGUCG-G----GAUGGGA-------UGCCAGAAGUCAGCAGACGCCAUAUUA-G-UC------------------G-GC-C---------------------------UUACCA-----------GUU-------GAUGA--AGGGC
CR377818.1/74586-74491       CGC-U-GAUUGGA--GUAA-----UU--CAUUC-A-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------AUGC-CC-AU-------------------------CGUAAUG-------GUU-GGGAC---ACGGUGA--AGGCC
CP000514.1/3270192-3270302   UGA-A-GGGCGA---GUGA------U--CGCCC-G------UGAUCG----CGUUGCAGAAGUCAGCAGAGGGCAUAGUA-C-UG------------------C-GG-CCUACUCGGCGCGAUGUGAUAUUGCGAAGUGAAU--------AG-CGG-------CAGGA--AGGCC
CP000923.1/501706-501791     CAA-C-CCAUGCA--GUGA-----UG--UAUGG-C------UGAAC-------CUUGAGAAGUCAGCAGAGGUCAUAGUA-C-UU------------------A-UC-UAG-----------------------UC---AUGA------AUA-GAU-------AAGGA--AGGAC
CP000930.2/2574563-2574478   GAA-A-CCACGCC--GAAA-----GG--CGUGG-C------UGAAC-------CGGCAGGAGUCAGCAGAGGUCAUAGUA-G-GC------------------U-GG-C--------------------------C-CGACGU-----CCGG-CCA-------GAUGA--AGGAC
CU928162.2/3405399-3405482   UA--C-CGGCGCC--GUGA-----GG--CGCCG-G----GAUGGGG-------CGGCAGAAGUCAGCCGACGCCGUAGUA-G-UG------------------C-UG-C---------------------------AAAACC--------GG-CAG-------CAUGA--AGGGC
CP000539.1/2355543-2355459   UAC-C-GAGCGUC--GAGA-----GG--CGAUG-G----GAUGAGC-------GUGCAGAAGUCAGCCGAAGCCGUAGUAAG-UG------------------G-CG-A---------------------------AUAAC---------CG-CGC-------CACCA--AGGGC
BAAX01000072.1/1891-1802     UG----CCUUUAC--GAAA-----GU--CAUGG------AGUAAAGCU--UGCUGUGAGAAGUCAGCAGAUGCCAUAGUA-G-UG------------------G-AG-UUC----------------------UCG---AUA-------ACG-CUC-------CAUGA--AGGGC
EU116440.1/3350-3257         CGC-A-UGACGGG--GCAA-----CU--CGGCA-U-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCCAA------------CGC--CC-AU-------------------------CGUAAUG-------GAU-GG-G----AUAGCAU--ACCCC
CP000142.2/993674-993757     CUA-C-CGGCAUC--GCAA-----GG--UGUCG-G----GAUGGGU-------UGGCAGAAGUCAGCAGAGGCCAUAAUA-G-CC------------------G-GG-----------------------------CUAACC--------AC-UUU-------GGCGA--AGGGC
ACGC01000027.1/2-89          AGG-U-CUCACUA--GCGAAACAGUA--GUAAC-A-----ACGAAU-------AGUGAGAAGUCAGCAGAAGUCAUAGUA-C-UA------------------G-AA-A---------------------------GCAAA---------UU-UUC-------UAGGA--AGGAC
CP000563.1/2138079-2138174   CGC-A-UGACGGG--GUAA-----CU--CGGUA-U-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCCA-------------ACGC-CC-AU-------------------------CGUAAUG-------GUU-GGGAU---AUGGUGA--AGGCC
BABB01000070.1/5638-5707     -AA-C-CAUUGC---AUAA----A-G--CAAUG-C------UGAAC-------GCAUAGAAGUCAGCAGAGGUCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGUGA--AGGAC
AP008955.1/861214-861300     UAA-C-CGUCUCC--GUAA-----GG--AGUCG-C------UGAAC-------AUGCAGAAGUCAGCAGAAGCCAUAGUA-C-CCA---------------AA-----U---------------------------AAAGGA--------CGC---UUG-AACGGGGA--AGGGC
CP000924.1/181774-181859     CAA-C-CCAUACA--GUGA-----UG--UAUGG-U------UGAAC-------CUUGAGAAGUCAGCAGAGGUCAUAGUA-C-UU------------------A-UC-UA------------------------GA---CAUG-----AAUA-GAU-------AAGGA--AGGAC
CP000760.1/78344-78421       UA--C-CGCCGCU--GAGA-----AG--CGACG-G----AAUAGGG-------CGGCAGAAGUCAGCAGAUGCCGUAGUA-G-CC------------------G-U------------------------------ACC-----------GG--AC-------GGCGA--AGGGC
AAFY01007889.1/12-105        CG--G-CUCGAGA--GUAU-----UC--GCAUG-U------UGUGA-------GGACAGGAGUCAGCAGAAGCCAUAGUA-G-CCGAA-----------CGCCG-GG-A---------------------------GUAAUG---------U-CCCGGA-CAUGGUGA--AGGGC
AATO01000047.1/24779-24677   UA--C-CGACCCC--GAGA-----GG--UGUCG-G----GAUGCGC-------CUGCAGAAGUCAGCAGAAGGCAUAGUA-G-GUU----------------G---G-GGACGAAGCG--------GAGAGCCCGAGAAGA--------ACU-C--U-----GACCGA--AGGCC
AP007281.1/1523863-1523785   CAA-G-CGGUGCA--GUGA-----UG--UAGCG-U------UGAGU------AAGCCAGAAGUCAGCUGAGGUCAUAGUA-G-UC------------------U-GA-----------------------------GUAA-------------UCA-------GAUGA--AGGAC
AY204504.1/509-604           CGC-A-UGACGGG--GUAA-----CU--UGGCA-U-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCCA-------------ACGC-CC-AU-------------------------CGUAAUG-------GUU-GGGAU---AUGGUGA--AGGCC
AACY022525202.1/349-267      CUA-C-UAACAUC--GGAA-----GG--UGUUG-G----GAUGGGC-------CAUCAGAAGUCAGCCGAGGCCGUAGUA-G-UG------------------C-UG-A---------------------------AACCA----------A-CAG-------CAUGA--AGGGC
AP006840.1/1687643-1687728   UAA-C-CCGGGCC--GAGA-----GG--CCCGG-C------UGAAC-------CGGCAGAAGUCAGCAAAGGCCAUAGUA-C-CGG---------------CAG-G------------------------------GGGACG--------CC--CCG----ACCGGGA--AGGGC
AJ971342.1/2283-2188         CGC-U-GUUACAG--GUAA-----CU--GUGGC-G-----GUGAUA-------GAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------AUGC-CC-AG-------------------------CGUAAUG-------GCU-GGGAC---ACGGCCA--AGGCC
ACNC01000013.1/61231-61296   AGU-C-------G--AAAA-----U-------G-G------UUAGC-------CGCGAGAAGUCAGCCGAAGCCAUAGUA-G-UG------------------A-A------------------------------AUAA-----------A--UU-------CAUGA--AGGGC
CP000924.1/167953-168038     CAA-C-CCAUACA--GUGA-----UG--UAUGG-U------UGAAC-------CUUGAGAAGUCAGCAGAGGUCAUAGUA-C-UU------------------A-UC-UAG-----------------------UC---AUGA------AUA-GAU-------AAGGA--AGGGC
BABG01024022.1/650-574       CUA-C-CGAUGCC--GCAA-----GG--CAGAG-G----GAUGUUG-------ACAGGGAAGUCAGCCGAGGUCGUAGUA-G-AG------------------G--------------------------------CCGA-----------A---C-------CUCGA--AGGAC
BA000028.3/81954-82039       -AA-U-UCAUUCA--GCAA-----UG--GAUGG-C------UGAAC-------GGUCAGAAGUCAGCAGAAGUCAUAGUA-C-CCUG--------------CAU-AC-----------------------------UCGAGA--------AU-GUA------AGGGGA--AGGAC
ABCC02000034.1/164401-164493 CGG-U-CUCAUUA--GCCG-----UA--GUAAC-A-----ACGAAU-------UGUGAGAAGUCAGCAGAAGCCAUAGUA-G-UGAGG-----------AAGUU-CC-U---------------------------GUAAU---------GG-GGAC----GGAGCGA--AGGGC
AACY023761354.1/225-138      CUA-U-GGGAGCG--GCGA-----CG--CUACC-G----GAUGGGA-------UGUAAGAAGUCAGCAGAGGGCAUAGUA-G-UU------------------A-GC-UG------------------------CA---UGUA-----CGGC-ACU-------AACGA--AGGCC
AP007281.1/761097-761175     CAA-G-CGGUGCA--GUGA-----UG--UAGCG-U------UGAGU------AAGCCAGAAGUCAGCCGAGGUCAUAGUA-G-UC------------------U-GA-----------------------------GUAA-------------UCA-------GAUGA--AGGAC
AATO01000577.1/2421-2503     CGC-G-ACGGCGA--GCAA-----UC--GCCAG-C-----GUGACU-------GAUCAGGAAUCAGCAGAGGCCAUAGUA-G-CGA----------------CA----C----------------------------CGAAA--------GG---UA-----ACGCGA--AGGGC
CP000388.1/777551-777646     CGU-C-GACAAGG--GUAA-----CU--CUGUU-G-----GUUAUU-------AAGCAAAAGUCAGCAAAGGGCAUAGUA-G-CCAAACGCU----CAUCGUAA-UG-G---------------------------------UU----GGGA-CAU-------GAUGA--GGGCC
ACCJ01000054.1/1677-1606     UAA-C-CAUUAUC--GUGA-----GG--UAAUG-C------UGAAC-------GUACAGAAGUCAGCCGAGGUCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGCGA--AGGAC
CP000753.1/2606414-2606312   CGC-A-UGACGGG--GCAA-----CU--CGGCA-U-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCCAACGC------CCAUCG------CCC--------------------AUCG-CAAUG-------GAU----GGGACAUGGUGA--AGGCC
AE014075.1/4320421-4320505   CUA-C-CGGCGCC--GUGA-----GG--CGCCG-G----GAUGGGG-------CGGCAGAAGUCAGCCGACGCCGUAGUA-G-UG------------------C-UG-C---------------------------AAAACC--------GG-CAG-------CAUGA--AGGGC
CP000155.1/2179510-2179429   CUA-C-UCACCUC--GUGA-----GG--GGUGG-G----GAUGGAG-------CGCCAGAACUCAGCCGAGGUCAUAGUA-G-GU------------------G-CG-U----------------------------UACC----------G-CGU-------ACUGA--AGGAC
AP008230.1/5170715-5170636   AGC---CUGGUU-----GA------A--ACAAG-------AUUUAU-------CGUGAGGAGUCAGCAGAAGCCAUAGUA-C-GG-----------------AG-GU-G---------------------------UUCUAG--------AC-ACC------GAAGGA--AGGGC
BA000004.3/833755-833840     UAACC-UUGGUAU--GAGA-----GU--GCCAG-U------UGAAC-------GGUCAGAAGUCAGCAGAAGCCAUAGUA-A-CC-----------------GC-UU-G---------------------------AUCUAG--------AC-AAG------AGGGGG--AGGGC
CP000923.1/2037818-2037733   CAA-C-CCAUGCA--GUGA-----UG--UAUGG-C------UGAAC-------CUUGAGAAGUCAGCAGAGGUCAUAGUA-C-UU------------------A-UC-UA------------------------GA---CAUG-----AAUA-GAU-------AAGGA--AGGAC
ACDM01000096.1/25337-25261   UGA-G-CGUACC---GUAA------G--GUGCG-C------UGACCG----GCGGACAGGAGUCAGCAGAGGGCAUAGUA-G-GA------------------C----A---------------------------GGC-----------GC---G-------UCUGA--AGGCC
AACY020433947.1/66-9         CGC-U-GGCAGAG--GUAA-----CU--UUGCC-A-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAG-------------------------------------------------------------------------A--------------------GCC
AACY023383724.1/685-796      CUA-A-UAGAUCA--GAGA-----UG--ACCUA-U----GAUGCAC-------UUACAGAAGUCAGCCGACGUCAUAGUA-G-AU------------------G-AU-UUAAUCUUUCUGGAUUUUAAGGAGGGUC------CAC--AUCGA-AUC-------AUUGA--AGGAC
BAAY01001211.1/2655-2586     -AA-C-CAUUGC---AUAA----A-G--CAAUG-C------UGAAC-------GCACAGAAGUCAGCAGAGGUCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGUGA--AGGAC
AAOF01000026.1/28828-28906   CGC-G-UCUUGCG--GCAA-----CG--CAAGG-C-----GUGAUG-------GGGCAGAAGUCAGCAGAGGCCAUAGUA-G-CC------------------G-UG-G---------------------------GCA--------------CGC-------GGUGA--AGGGC
AAOF01000034.1/144-222       CGC-G-UCUUGCG--GCAA-----CG--CAAGG-C-----GUGAUG-------GGGCAGAAGUCAGCAGAGGCCAUAGUA-G-CC------------------G-UG-G---------------------------GCA--------------CGC-------GGAGA--AGGGC
AACY021722084.1/729-813      CUA-C-UGACAUC--GAGA-----GA--UGUUG-G----GAUGGGA-------UAUCAGAAGUCAGCCGAGGCCGUAGUA-G-UG------------------U-UA-U---------------------------UAAACC--------GA-UAG-------CACGA--AGGGC
AP006840.1/2401944-2401859   UAA-C-CUGCGUC--GGGA-----GA--CGCAG-C------UGAAC-------CGGCAGAAGUCAGCAAAGGCCAUAGUA-C-GGG---------------CAG-G------------------------------GGGACG--------CC--CCG----ACCGGGA--AGGGC
CP000142.2/1608710-1608793   CUA-C-CGGCAUC--GCAA-----GG--UGUCG-G----GAUGGGU-------UGGCAGAAGUCAGCAGAGGCCAUAAUA-G-CC------------------G-GG-----------------------------CUAACC--------AC-CUU-------GGCGA--AGGGC
ABSP01039541.1/229-310       CGC-C-UUGCAGG--GCAA-----CC--UGCCG-G-----GUGAUG-------AGGCAGAAGUCAGCAGACGCCAUAGUA-G-UC------------------U-CG-C---------------------------CGGUG----------G-CGU-------GACGA--AGGGC
CP000918.1/2124059-2123980   CGUA-----------GUAA----C---------------AACGAAU-------CAUGAGAAGUCAGCCGAGCCCAUAGUA-G-UGAG-------------GAAA-CU-UC-------------------------UGUAGUG--------GA-AGUG-----GAGCGA--AGGGG
AAFY01000006.1/6050-5969     UGA-C-AGCGAA---GCAA------U--UUGCU-G------UGAUCG----CAAUGCAGAAAUCAGCAGAGGGCAUAGUA-A-AU------------------G-AG-A---------------------------CUCUUG-----------CUC-------AUUGA--AGGCC
AAQL01004092.1/4400-4470     UAA-C-CAUUGC---AUAA----A-G--CAAUG-C------UGAAC-------GCAUAGAAGUCAGCAGAGGUCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGUGA--AGGAC
CP000930.2/162822-162752     AAAU-----------AAGA----------------------UUUGC-------CGUGAGGAGUCAGCAGAGGUCAUAGUA-C-UC------------------U-GU-GU------------------------AGUCGA--C------GAC-ACG-------GAGGA--AGGAC
ABSP01043891.1/522-442       CGC-G-GCGGAUC--GAGA-----GG--UCCGC-C-----GUGUGA-------GCCCAGAAGUCAGCCGAGGGCAUAGUA-G-CU------------------C-CG-A---------------------------GACC-----------A-UGG-------AGCGA--AGGCC
AP006840.1/990470-990555     UAA-C-CUGCGUC--GGGA-----GA--CGCAG-C------UGAAC-------CGGCAGAAGUCAGCAAAGGCCAUAGUA-C-CGG---------------CAG-GG-G---------------------------GAC-----------GC-CCCA----ACCGGGA--AGGGC
AACY023048287.1/460-365      CGC-U-GUUACAG--GUAA-----CU--GUGGC-G-----GUGAUA-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------AUGC-CC-AG-------------------------CGUAAUG-------GCU-GGGAC---ACGGUGA--AGGCC
CP000879.1/1124946-1124869   CAA-C-CCAUACA--GCAA-----UG--UAUGG-C------UGAAU-------CUUGAGAAGUCAGCAGAAGUCAUAGUA-C-UC------------------A-UU-----------------------------GAGA-------------GAU-------GAGGA--AGGAC
AATC01007263.1/440-354       CG----GCAGUCU--GCAA-----GG--AUAGU--AA-CAACGAAU-------GCCGAGGAGUCAGCAGAGGCCGAAGUA-G-CC------------------G-AC-C---------------------------GUGGGA--------CG-GUCA-----AGGCGA--AGGGC
AAOH01000001.1/357821-357916 CGC-U-UUACCGA--GUAA-----UC--GAUAA-A-----GUGAUU-------UAUCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------ACGC-CC-AU-------------------------CGUAAUG--------GA-GGGGA--CACGGUGA--AGGCG
AACY020363614.1/813-730      CAAAA-UUUUGUA--GUGA-----UA--CAUCA-U------UGGUU-------UGACAGAAGUCAGCAGACGCCAUAGUA-C-UU------------------U-UU-A---------------------------AUUUUU--------UU-AGG-------AAGGA--AGGGC
AACY023777253.1/1149-1240    UAC-C-UCAUACA--GCAA-----UG--UGUGU-G-----GGGAUU-------AGUGAGAAGUCAGCAGAGGUCAUAGUA-G-UG------------------A-GA-GAGA---------------------AAC------UAA--UACCA-UCU-------CCCGACUCGGAC
CP000924.1/1920618-1920533   CAA-C-CCAUGCA--GUGA-----UG--UAUGG-C------UGAAC-------CUUGAGAAGUCAGCAGAGGUCAUAGUA-C-UU------------------A-UC-UA------------------------GA---CAUG-----AAUA-GAU-------AAGGA--AGGAC
ACIH01000268.1/299-383       UAA-C-CCUGUUC--GUGA-----GA--GCAGG-C------UGAGC-------GUGCAGAAGUCAGCCGAUGUCAUAGUA-C-AC------------------A-GC-UUG-----------------------UC--GCG--------AGG-GCU-------GUGGA--AGGAC
AP008232.1/4061641-4061748   GCC-U-CGUGCCU--GAAA-----GG--GCAAC-AGUUAAAGCUGG-------AGUGAGAAAUCAGCAGAUGUCGUAGUA-G-CCGCAGUAGC--GGGGCCGA------UGA--------------------GUCCGUAAGU--------CA----A----ACGGCGA--AGGAC
ACIN02000005.1/141944-141874 UAA-C-CAUUGC---ACAA----A-G--CAAUG-C------UGAAC-------ACACAGAAGUCAGCAGAGGUCAUAGUA-G-UC---------------------------------------------------GAGA-----------------------GACAA--AGGAC
AAWL01000012.1/49486-49570   CAA-C-CCGGGUC--GAGA-----GG--CUCGG-C------UGAGC-------CGGCAGGAGUCAGCAGAGGGCAUAGUA-C-CUC----------------G--AA-G---------------------------GUCAUG-------AAC-UU-------CAGGGG--AGGCC
AB126574.1/258-342           UAA-C-CUUGCAU--AAGA-----GU--GCAAG-C------UGAAC-------GGUCAGAAGUCAGCAGAAGCCAUAGUA-C-CC-----------------G--CUUG---------------------------GUCUAC--------ACAAG-------AGGGGA--AGGGC
EU686596.1/37479-37384       CGC-U-UCCAGGG--GUAA-----CC--UUGGG-A-----GUGAUU-------AAGCAGAAGUCAGCAGAGGCCAUAGUA-G-UCAA-------------AUAC-CU-AC-------------------------CGUAAUG-------GAU-AGGAC---ACGGCGA--AGGGC
FJ817422.1/3245-3150         CGC-A-UGACGGG--GCAA-----CU--CGGCA-U-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCCAAC----------GCCU--AU-C---------------------------GUAAUGGA----UGGG-AU-A-----UGGUGA--AGGCC
AF323438.1/2287-2371         CUA-C-CGGCCCC--GAGA-----GG--UGACG-G----GAUGGGC-------GAACAGAAGUCAGCAGAGGCCGUAGUA-G-UU------------------G-CU-C---------------------------GAAACC--------GG-AGC-------GAUGA--AGGGC
AY065966.1/3999-3904         CGC-G-AACAGAG--GCAA-----CU--CUGUG-A-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------ACGC-CC-AU-------------------------CGUAAUG-------GUU-GGGAC---ACGGUGA--AGGCC
CP000148.1/3155527-3155444   CAG-G-GGAGCUG--AAAA----GCA--GCUUC-CU---CAUGUU--------CGGCAGAAGUCAGCAGAAGCCAUAGUA-G-UC------------------G-GC-C---------------------------UGACC----------A-GCC-------GAUGA--AGGGC
CP000685.1/4417848-4417768   UUU-U-UUUUACA--GAAC-----UA--UGGAU-A----ACAACU-G-----CCAUAAGAAGUCAGCAGAGGUCAUAGUA-G-GU------------------A-CU-A---------------------------CU-------------U-GGU-------ACUGA--AGGAC
CP000939.1/1490349-1490434   UAG-C-CUACAUA--UUGA-----UA--UGUAG-C------UGAAC-------UAUCAGAAGUCAGCAAAAGCCAUAGUA-C-UA------------------C-GU-G---------------------------AAUACGC-----GUUA-GUG-------UGGAA--AGGAC
CU633751.1/140225-140145     CUA-C-CGGCGUC--GAGA-----GG--UGUCG-G----GAUGGCG-------GUGCAGAAGUCAGCAGAGGCCAUAUUA-G-GC------------------G----A---------------------------GCCGUU--------GG---C-------GCUGA--AGGGC
ABCP01000005.1/147154-147076 UGA-A-CGCCGG---GCAA------C--CGGCG-U------UGACCG----GCAAACAGGAAUCAGCAGAGGGCAUGGUA-G-GU------------------U-CA-C---------------------------CC-------------G-UGA-------ACCGA--AGGCC
AM262984.2/24058-23974       UAC-C-GAGCGUC--GUGA-----GG--CGAAG-G----GAUGAAC-------GUGCAGAAGUCAGCCGAAGCCGUAGUAAG-UG------------------A-CG-A---------------------------AUGACC---------G-CGU-------CACCA--AGGGC
CP001034.1/2021984-2021902   GAA-C-CACGGU----UGA------A--AUAAG-A------UUUGU-------CAUGAGAAGUCAGCAGACUCCAUAGUA-C-UU------------------G-AU-GA------------------------GGUCGAC--------AUC-AUU-------AAGGA--AGGGA
CP000262.1/123103-123195     UGA-G-CGUUCUA--GACG-----UA--GUAAC-A-----ACGAAU-------GAUGAGAAGUCAGCCGAUGCCAUAGUA-G-CGAU-------------GAAA-CU-UC-------------------------UGUAAUG--------GA-AGUA-----GAGCGA--AGGGC
BA000040.2/9101321-9101242   UGA-G-ACCGUC---GCAA------G--ACGGC-C------UGACCG----CAGCGCAGAAGUCAGCCGAGGGCGUAGUA-G-GC------------------G-GC-A---------------------------GCGC-------------GCC-------GCUGA--AGGCC
AE016853.1/3762215-3762134   CGCCU-CAUGCCU--GAAA-----GG--GCGAC-GG---UGUGAGCC----GGAGCGAGAAGUCAGCAGCGGUCAUAGUA-G-CU------------------G-CG--------------------------------------------C-UGC-------AGCGA--AGGAC
AE015927.1/1265807-1265881   UAA-C-CUACAUA--GUGA-----UA--UGUGG-C------UGAAU-------UAUCAGAAGUCAGCAGAGGUCAUA----A-GU------------------U-UU-G---------------------------UAG------------A-UAU-------GCUGA--U-GAU
CP001390.1/1082819-1082897   CGC-G-GUAUCUG--GUAA-----CA--GCUGC-C-----GUGAUG-------GGGCAGGAGUCAGCAGAAGCCAUAGUA-G-GC------------------G-AU-A---------------------------GGAC-------------GUU-------GCCGC--AA-GC
ABME01114329.1/90-10         CGC-U-CU-----------------------GG-G------UGAUU-------GAGCAGAAGUCAGCAGAUGUCAUAGUA-G-CCAA-------------AUGC-UC-AU-------------------------CGUAACG-------GAU-GAGAC---AGGGUGA--AGGGC
AE017180.1/1028974-1029058   CGC-G-GCCUCUG--GUAA-----CA--GCUGC-C-----GUGAUG-------GGGCAGGAGUCAGCAGAAGCCAUAGUA-G-GC------------------G-CG-----------------------------GACGUU--------GC-CGCC-----AGCGAU--CCGGC
ABVL01000012.1/116535-116630 CUU-A-CCCGGG---GAGAU--CU-C--CUGUG-U-----GAGAGC------ACGGGAGAAGUCAGCAGAGGCCGUAGUA-G-UGAAG------------AGGC-CC-G---------------------------GCGAAA-------GUC-GGGA----AGAGCGA--AGGGC
CP000891.1/2709038-2708943   CGU-A-GGCUAG-AGGUGA----G-U--UGGCA-U-----GUGAUU-------AAGCAGAAGUCAGCAGACGGCAU-GUA-G-CCCA-------------ACGC-CC-AU-------------------------CGUAAUG-------GAU-GGGAC---ACGGUGA--AAGCC
ABLK01000025.1/39242-39167   CUA-C-UGGCGUC--GAGA-----GG--CGGCG-G----GAUGGUC-------GUGCAGAAGUCAGCAGAGGGCAUAGUA-G-GC------------------C--------------------------------GCG------------A---G-------GCUGA--AGGCC
ABBE01001046.1/300-375       CUA-C-UGGCGUC--GAGA-----GG--CGGCG-G----GAUGGCC-------AUGCAGAAGUCAGCAGAGGGCAUAGUA-G-GU------------------C--------------------------------GCG------------A---G-------GCCGA--AGGCC
CP000926.1/1828902-1828818   UAC-C-GAGCGUA--GAGA-----GG--CGACG-G----GAUGAGU-------GUGUAGAAGUCAGCCGAGGCCGUAGUAAG-UG------------------G-CG-A---------------------------UUAACC---------G-CGC-------CAUCA--AGGGC
L49337.2/9043-9126           CGC-CUUGCGCCU--GAAA-----GG--GCGACGGU---GUCGAGCC----GGAGCGAGAAGUCAGCAGAGGUCGUAGUA-G-CC------------------G-UA-U------------------------------------------C-CGC-------GGCGA--AGGAC
CP000318.1/155263-155181     CGUCU-CACGCCU--GAAA-----GG--GCGAC-G-----GCGAAAGC--CGGUGCGAGAAGUCAGCAGAGGCCGUAGUA-G-CU------------------G-G------------------------------GCA------------A--CC-------AGUCA--AGGGC
ABZR01000449.1/3277-3360     UAC-C-GAGCGUC--GAGA-----GG--CGACG-G----GAUGAGC-------GUGCAGGAGUCAGCUGAAGCCGUAGUAAG-UG------------------A-CG-A---------------------------AUAACC---------C-CGU-------C-CAA--GGGGC
ABLD01000063.1/514-409       CGCCU-CGUGCCU--GAAA-----GG--GCAAC-GG--CGUCGAGCC----GGAGCGAGAAGUCAGCAGAGGCCGUAGUA-G-UC------------------A-CA-GGACAGGUU----------GAUGAGGCC-GAA---------GCU-GGU-------GACGA--AGGGC
CP000958.1/298413-298518     CGCCU-UAUGCCU--GAAA-----GG--GCGAC-GG--CGUCGAGCC----GGAGCGAGAAGUCAGCAGAGGCCGUAGUA-G-UC------------------A-CA-GGACAGGUC-----------GAUGAGGC-UGAA--------GCU-GGU-------GACGA--AGGGC
CP000616.1/1222265-1222179   CGCCU-UGUGCCU--GAAA-----GG--GCGAC-GG--UGCUGAGCC----GGAGCGAGAAGUCAGCAGAGGCCGUAGUA-G-CC------------------G-CU-G---------------------------GUAU-------------GGG-------GGCAA--AGGGC
CP001794.1/3212939-3212863   CAA-C-CA-------GAAG------------UG-C------UGAAC-------GUACAGGAGUCAGCAGAGGCCAUAGUA-C-UG------------------G-AG-U---------------------------AAGAGA--------CGCCU-GA---AACAGGA--AGGGC
AALC02000129.1/296-371       UGA-G-UGCAUC---GUAA------G--GUGCG-C------UGACCG----GUGGACAGGAGUCAGCAGAGGGCAUAGUA-G-GA------------------C-GU--------------------------------------------G-ACG-------UCUGA--AGGCC
ACBX02000056.1/36407-36497   UUG-C-CUUUAC---GAAA------G--UCAUG-GA---GUAAAGCUU---GCUGUGAGAAGUCAGCAGAUGCCAUAGUA-G-UG------------------C-AA-UAG----------------------UCG---AUA-------ACG-UUG-------CACGA--AGGGC
GQ876745.1/312-402           UUU-U-UUUUAC---GAAA------G--AAGCG-G----AGUAAAGCU--UGCCGUGAGAAGUCAGCAGACGCCAUAGUA-G-UG------------------C-AA-UAG----------------------UCG---AUA-------ACG-UUG-------CACGA--AGGGC
CP003056.1/1154880-1154801   AAC---CUGGUU-----GA------A--ACAAG-------AUUUGC-------CGUGAGAAGUCAGCAGAAGCCAUAGUA-C-GG-----------------A--GA-UG-------------------------C--CUGGA------GCA-UC-------GAAGGA--AGGGC
CP001638.1/1803229-1803146   UAA-C-CUACUUA--GUGA-----UA--AGUAG-C------UGAAC-------CGUCAGAAGUCAGCAGAGGUCAUAGUA-U-UA------------------G-UU-G---------------------------GUCUAG-------AAC-AAC-------UGAGA--AGGAC
CP001734.1/1042239-1042312   CG--U-CGCGAGG-----------CU--UCGGG-A------CGGGC-------GGGCAGAAGUCAGCCGAGGGCAUAGUA-G-GU------------------C-CC-C---------------------------CGA------------C-CGG-------ACUGA--AGGCC
CP001638.1/537550-537635     CAA-C-CGUUGGA--GCGA-----UC--CAACG-C------UGAAC-------GGACAGAAGUCAGCAGAGGUCAUAGUA-C-UC-----------------G--UC-UA------------------------GCUUAAGA--------UA-GA-------AGGGGA--AGGAC
CP002637.1/2084759-2084830   CAA-C-CACAGCC--GAAA-----GG--CUGUG-C------UGAAU-------AUGCAGAAGUCAGCAGAGGCCAUAGUA-G-CC---------------------------------------------------GAGA-----------------------GGUGA--AGGGC
CP002457.1/4767921-4767838   CUA-C-UAACAUC--AUGA-----GG--UGUUG-G----GAUGGAC-------UACCAGAAGUCAGCCGAAGCCGUAGUA-G-UG------------------U-UG-----------------------------CUAACC--------AA-CAG-------CAUGA--AGGGC
ACDI02000016.1/13119-13200   CAA-G-UA-------GUAA------------CA-A------CGAAC-------CGUGAGAAGUCAGCAGAGGUCAUAGUA-G-CC------------------G-AC-AGGG--------------------UAAA---AA-AAU--CGGUA-GUC-------GGUGA--AGGAC
CP001791.1/422304-422378     CAA-G-GAAUUCA--GAGA-----UG--GAUUC-C------UGAAU-------CGUAAGAAGUCAGCCGAGGUCAUAGUA-A-UC------------------C-CA--------------------------------------------U-GGG-------GAUGA--AGGAC
CP001734.1/1006271-1006351   CUA-C-CGGCGUC--GCGA-----GU--CGUCG-G----GACGGGC-------GGGCAGAAGUCAGCUGAGGGCAUAGUA-G-GU------------------C-CC-C---------------------------CGA------------C-CGG-------ACUGA--AGGCC
AEDP01000005.1/5084-4999     CGAC---ACAGUA--GUAA-----CA--------A------CGAAC-------UAUGAGAAGUCAGCAGAAUCCAUAGUA-G-UUAGG-----------AAGU--U--UC-------------------------UGUAAUG--------GA--A-AU---GGAGCGA--AGGGA
CP003056.1/3201623-3201702   AAC---CUGGUU-----GA------A--ACAAG-------AUUUGC-------CGUGAGAAGUCAGCAGAAGCCAUAGUA-C-GG-----------------A--GA-UG-------------------------C--CUGGG------GCA-UC-------GAAGGA--AGGGC
CP001794.1/2099129-2099215   CAA-C-CAGAGUC--GAAA-----GG--CUCUG-C------UGAAC-------GUACAGGAGUCAGCAGAGGCCAUAGUA-C-UGGA-------------GUAA--------------------------------GGGACG--------CC---UGA---AACAGGA--AGGGC
CP001734.1/1611492-1611412   CUA-C-CGGCGUC--GCGA-----GG--CGUCG-G----GACGGGC-------GGGCAGAAGUCAGCCGAGGGCAUAGUA-G-GU------------------C-CC-C---------------------------CGA------------C-CGG-------ACUGA--AGGCC
CP002442.1/3218908-3218832   CAA-C-CA-------GAAG------------UG-C------UGAAC-------GUACAGGAGUCAGCAGAGGCCAUAGUA-C-UG------------------G-AG-U---------------------------AAGAGA--------CGCCU-GA---AACAGGA--AGGGC
AF453998.2/3077-2982         CGC-U-UUAUCGA--GUAA-----UC--GCUAG-A-----GUGAUU-------UAUCAGAAGUCAGCAGACGGCAUAGUA-G-CCAA-------------ACGC-CC-AU-------------------------CGUAAUG--------GA-GGGGA--CACGGUGA--AGGCC
ABYU02000017.1/89741-89815   CUU-G-UA-------GUAA------------UA-A------CGAAU-------GGCAAGAAGUCAGCAGAGGUCAUAGUAAA-CC------------------G-AU-G--------------------------G-UUGCA-------AAC-AUC-------GGCGA--AGGAC
AM489440.1/660-744           CUA-C-CGGCGUC--GUAA-----GG--UGCCG-G----GAUGGGG-------CGGCAGAAGUCAGCCGACGCCGUAGUA-G-UG------------------C-UG-C---------------------------AAAACU--------GG-CAG-------CAUGC--AGGGC
#=GC SS_cons                 <<-.<.<<<<<<<..____.....>>..>>>>>.>.....->>,,,.......,,,,,,,,<<<____>>><<<------.<.<<..................<.<<._...........................______........__.>>>.......>>>--..-->>>
#=GC RF                      caa.c.ccaccca..GugA.....ug..ggugg.g.....augAac.......agucAGAAgUCAGCAGAgGcCAUAGUA.g.cc..................g.cc.u...........................guaaua........ca.ggc.......ggcGA..AGGgC
//
# STOCKHOLM 1.0

#=GF AC   RF01999
#=GF ID   group-II-D1D4-2
#=GF DE   Group II catalytic intron D1-D4-2
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Weinberg Z
#=GF SS   Predicted; Weinberg Z
#=GF GA   36.00
#=GF TC   36.50
#=GF NC   35.30
#=GF TP   Intron;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00102
#=GF DR   SO; 0000603; group_II_intron;
#=GF DR   GO; 0000373; Group II intron splicing;
#=GF RN   [1]
#=GF RM   11377794
#=GF RT   The ins and outs of group II introns.
#=GF RA   Bonen L, Vogel J
#=GF RL   Trends Genet 2001;17:322-331.
#=GF RN   [2]
#=GF RM   11726522
#=GF RT   Control of branch-site choice by a group II intron.
#=GF RA   Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM
#=GF RL   EMBO J 2001;20:6866-6876.
#=GF RN   [3]
#=GF RM   12870716
#=GF RT   Group II introns: structure and catalytic versatility of large natural
#=GF RT   ribozymes.
#=GF RA   Lehmann K, Schmidt U
#=GF RL   Crit Rev Biochem Mol Biol 2003;38:249-303.
#=GF CC   Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi,
#=GF CC   plants and protists, and also in mRNA in bacteria. They are large
#=GF CC   self-splicing ribozymes and have 6 structural domains (usually designated
#=GF CC   dI to dVI. This model and alignment represents only domains V and VI. A
#=GF CC   subset of group II introns also encode essential splicing proteins in
#=GF CC   intronic ORFs. The length of these introns can therefore be up to 3kb.
#=GF CC   Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing
#=GF CC   with two transesterification steps. The 2' hydroxyl of a bulged adenosine
#=GF CC   in domain VI attacks the 5' splice site, followed by nucleophilic attack
#=GF CC   on the 3' splice site by the 3' OH of the upstream exon. Protein machinery
#=GF CC   is required for splicing in vivo, and long range intron-intron and
#=GF CC   intron-exon interactions are important for splice site positioning. Group
#=GF CC   II introns are further sub-classified into groups IIA and IIB which differ
#=GF CC   in splice site consensus, distance of bulged A from 3' splice site, some
#=GF CC   tertiary interactions, and intronic ORF phylogeny [1].
#=GF WK   Group_II_intron
#=GF SQ   144


BAAZ01023689.1/241-126         ---GGCGGAG------GGCCCGCCGGAACCG-CUAUA-CAGG-UGGAGGUUCCAAACC-ACC-CUAA--GGUGC-U-------GUAGU--CAAAA-GC-UA-UG-GUAUU-GAGCGU--UAG-GG--A-AAAGGC-AGAUAUA---------ACU-GU-CAGGUG-
AACY023809717.1/714-591        ---GGCGGAAC----CGACCCGCCGGAGUCU-GCCUG-CAGG-GGCCGGCUCCAAACC-ACCCCCGA--GCGGC-C-------UUGGC--UGAAG-AC-CG-UG-GUCGU-GAGCGU--CGGGGG--A-GAAGGC-GUAUCCACGUGG----UGC-GU-CAGGU--
CP000607.1/169645-169759       ---GAGGGUC------GACCCCUCGCCAUCG-GCUUG-CAGG-AGCAGGUGGCAAACC-ACC-GUAA--GCAGC-A-------UUGGU--CAAAA-GC-CC-UU-GUUGU-GAGCGU--UAC-GG--A-AAAGGU-ACC---A---GAA---GGU-AU-CAGG-U-
ACII01000059.1/2692-2577       ---GAUGGCA------GGCCCAUCGGAACCG-CUAUA-UAGG-UGGAGGUUUCAAAUC-ACU-CUGA--GGUGC-U-------GUAGU--CAAAA-GC-UA-UG-GUACU-GAGCGU--CAG-AG--A-AAAGGC-UGU---AC--AAA---ACA-GU-CAGG-U-
AAGA01008883.1/522-396         ---GGUGGAACCCGGCCCCCCACCGGUGUUUGUCCUA-CAGG-GGAGAGCAUCAAACC-ACC-AUAA--GGUGC-U-------UUGGU--AAAGA-GC-CA-AG-GUAUU-GAGCGU--UAU-GG--AAAAGGCU-GCG---UCAUGAG---CGU-GGUCAGG-U-
AACY020296161.1/627-508        ---GGUGGUA------GGCCCACCGAAGUCG-GCAGU-CGGA-UGCAGGCUUCAAACC-GGC-CCAA--GCUGCGC--------GCAU--AAAGA-GU-GC--GGGUAGU-GAGCGU--UGG-GU--GAAAAGGC-CGUACAAC--AAU---ACG-GU-CAGGU--
CP001046.1/380685-380803       ---GGGAGCA------GGCCUCCCGAAGUCG-GCUUU-CAGG-AGCAGGCUUCAAACC-GCC-CGGU--GCUGC-U-------GCGUC--CAAAA-GA-CG-UG-GUGGU-GAGCGA--CCGUGG--A-AAAGUC-ACC---CGGCUAG---GGU-GG-CAGG-U-
CP000820.1/7955550-7955431     ---GGGUUUUG----UGGCCACUCGAAGCCGCCCGAC-GGGU-CGGAGGCUUCAAGCC-ACC-CCGA--GCAGC-C-------UUAGC--UGACG-AC-UG-UG-GUGGU-GAGCGU--CG--GG--A-AAAGGC-GCG---CCGUGAG---CGC-GU-CAGG-C-
ABPY01009000.1/490-387         ---GAAGGAA-----AGGCCCUUCGGAAACG-GCUUG-CACG-AGCAGUUUCCAAACC-GCC-CUGA--GCUGC-U-------GCGGU--CAAAA-GC-CG-UG-GUGGU-GAGCGU--CA--GG--A-AACG---------GUA--------------CGGG-C-
AF348706.1/31586-31470         ---GGAGGUG------GGCCCUCCGGUCAGG-GUUUA-CAGG-AGCACAGACCAAACG-ACC-CGGU--GCUGC-U-------UCAUU--CUAAG-GAAUG-AG-GUGGU-GAGCGA-CUCG-GG--A-AAAGGC-AGAGAUCU--------ACU-GU-CA-C-G-
AL591985.1/1576432-1576314     ---GGGGGAC------GGCCCUCCGGGAUCG-GCUUU-CAGG-AGCGGGUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGU--AAAGA-GC-CG-UG-GUGGU-GAGCGU--CGG-AU--GAAACGUU-CGG---ACGAGAU---CCG-AG-CAGG-U-
AE015928.1/3256606-3256488     ---GAGGGUA------GGUCCCUCGCAAUCA-ACUUG-CAGG-AGUGGGUUGCAAACC-CGU-AUAU--GCUGC-U-------CUUUC--UCCAU-GGUCA-GG-GUAGU-GAACGA--UAU-AU--GAAAAGGC-AAUGUAUAA-------AUU-GU-CAGG-U-
AAPR01000002.1/106666-106784   ---GGAGGUA------GGUCCUCCGAUGAGGGUUUU--UAGG-AAAACUCAUCAAACC-ACUUCUAU--GACGC-A-------UCCAAGGCAACAA---AG-AU-GUGUG-AAGCGA--UAGAAG--A-AAAGGC-UAU---UUA--AA---AUA-GU-CAGG-U-
AAPR01000001.1/263264-263147   ---GAUGGUA------GAUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUUUAAACC-ACC-UAAA--GGUGC-U-------UUGAU--UAAUA-GU-CU-UG-GUAUU-GAGCGU--UUA-GG--A-GAAUCU-AGU---CCUAGAG---AUU-AG-CAGGU--
AAFX01011588.1/776-893         ---GGGGGAC------GG-CCCCCGGAGCCG-GCCUG-CAGG-GGUAGGCUUCAAACC-ACC-ACAA--GCUGC-A-------GGGGU--AAAGA-GC-CC-UU-GUGGU-GAGCGU--UGCUGG--A-AAAGGC-GGA---AGGUCAU---UCC-GU-CAGGU--
ABSN01010651.1/350-467         ---GAAGGAG------GGCCCUUCGAGAUCG-GCAAU-CAGG-UGUUGAUCUCAAGCC-ACC-GCAA--GCUGC-U-------GUCGU--UAAAA-GC-GA-UG-GUGGU-GAGCGU--UGC-GG--A-AACGGC-GGG---ACCAGAU---CCC-GU-CAGGC--
CU928163.2/269335-269452       ---GGUGGAA------GGCCCACCGGGAUCG-GCUGU-CGGA-AGCAGAUUCCAAACC-ACU-UCAU--GCUGC-U-------GUGGU--AAAGA-GC-CA-UG-GUAGU-GAGCGA--UGA-AG--U-AAAGCG-UGAGUGAA--AAC---UCA--G-CAGG-U-
AACY020307896.1/5-127          ---GGCGGAC-----CGACCCGCCGGAGUCU-GCCUG-CAGG-GGCCGGCUCCAAACC-ACCCCCGA--GCGGC-C-------UUGGC--UGAAG-AC-CG-UG-GUCGU-GAGCGU--CGGGGG--A-GAAGGC-GCAUCCAGGUGG----UGC-GU-CAGGU--
ABPY01007955.1/37-151          --GAAUUGGA---------CUAUCGGUAAAG-GCGAU-CAGG-CGAAUUUACCAAACC-GCC-UUGU--GGUGC-U--------GUGC--UUCAUGGC-AU--G-GUACU-GAGCGA--CAA-GGUUA-AAAGCA-GAA---CUUUCAG---UU---G-UA-G-GA
ABPU01007591.1/543-426         ---GAGGGCA------GGCCCCUCGAAGCCG-CCAUA-CAGG-UGGAGGCUUCAAACC-ACC-GUAA--GCUGCGC--------CGGU--AUAGA-GC-UG--GUGUGGU-GAGCGU--UAC-GG--A-AAAGGU-CUC---GCCAGAC---GGG-AU-CAGG-U-
ABSP01000946.1/1866-1749       ---GAGGGCG------GGCCCCUCGGCGUA--GCUUAUCAGGAGGC-GAUGCCAAACC-ACC-CUGA--GCUGC-A-------UCCGU--AAAGA-GC-GG-UU-GUGGU-GAGCGU--CAUGGG--A-AAAGGC-AGGAAUACU-------CCU-GU-CAGG-U-
AACY021016298.1/522-405        ---GAGGGUA-----UGGUCCCUCGAAGCCG-ACCGU-CAGG-GGUAGGUUUCAAACC-ACU-GCAA--GCUGCAA--------CGGU--AAAGA-GC-CG--UGGUGGU-GAGCGU--UGC-AG--A-AAAGGC-GGA----CGUUAG---UCC-GU-CAGGU--
AAPR01000009.1/143398-143270   ---GAUGGUA------AGUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUCUAAACC-CCC-UAAA--GGUGC-UGUUGUAAAGAGC--CCCGAAGCUUCGGGGGUGCU-GAGCGU--UUA-GG--A-GAAUCC-AAU---CCACGAG---GUU-GGCAAGG---
CP000272.1/357925-357806       ---GAUGGAA------AGCCCUUUGGAGUCG-GCGCG-CAAG-CGCUGACUCCAAACA-GCC-GUGA--GCUGC-C-------UCAGUCGGAAAC-GC-GG-CG-GUGGC-GAACGU--UAC-GAUUA-AAAGGC-GUG---AUU-AAA---CAC-GU-CA-U-G-
ABSQ01011590.1/228-110         ---GGGAGUGU---AUGGCCUCCCGAUGCCU-GCCUG-CAGG-GGCUGGCAUCAAACC-ACC-CCAU--GCUGC-U-------GCGGU--CAAAA-GU-CG-UG-GUGGU-UAGCGU--UGG-GG--A-AAAGGC-GG----ACUUGAU----CC-GU-CAGGU--
AJ488511.1/61923-61807         ---GGAGGUG------GGCCCUCCGGUCAGG-GUUUA-CAGG-AGCACUGACCAAACG-ACC-CGGU--GCUGC-U-------UCAUU--CUAAG-GAAUG-AG-GUGGU-GAGCGA-CUCG-GG--A-AAAGGC-AGAGAUCU--------ACU-GU-CA-C-G-
AAPR01000032.1/3411-3539       ---GAUGGUA------AGUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUCUAAACC-CCC-UAAA--GGUGU-UGUUGUAAAGAGC--UCCGAAGCCUCGGGGGUGCU-GAGCGU--UUA-GG--A-GAAUCC-AAU---CCACGAG---GUU-GGCAAGG---
ABSP01022156.1/401-520         ---GAGGGGA------GGCCCCUCGGAGCCG-ACUUG-CAGG-AGUUGGCUUCAAACC-ACC-UCAA--GCUGC-U-------GUGGU--CAAAA-GC-CA-UG-GUGGU-GAGCGU--UGU-GG--A-AAAGUC-ACGGCAUAA-GAC---UGU-GG-CAGGU--
CP000492.1/1680366-1680251     ---GAGGGUC------GGCCCCUCGCAAUCG-GCUUG-CAGG-AGCAGGUUGCAAACC-ACC-GUAA--GCGGC-U-------UGGGU--CAAAA-GC-CC-CG-GUCGU-GAGCGU--UAC-GG--A-AAAGGC-ACC-----GGGAA---GGU-GU-CAGG-U-
AAPR01000024.1/46198-46315     ---GAUGGUA------GAUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUUUAAACU-ACU-UAAA--GGUGC-U-------UUGAU--UAAUA-GU-CU-UG-GUAUU-GAGCGU--UUA-GG--A-GAAUCU-AGU---CCUAGAG---AUU-AG-CAGG-U-
CP000741.1/176119-176235       ---GGGGGAC------GGCCCUCCGGGAUCG-GCUUU-CAGG-AGCGGGUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGU--AAAGA-GC-CG-UG-GUGGU-GAGCGU--CGG-AU----GACGUU-CGG---ACGAGAU---CCG-AG-CAGGU--
AAPR01000036.1/9887-9770       ---GAUGGUA------AAUCCAUCAGAGUUG-UUGUA-UAGG-CAAUGGUUCUAAACC-CCC-CCAA--GGUGA-U-------UUGAU--UGAUA-GU-CU-UG-GUAUU-GAGCGU--UAA-GU--A-UAAUCC-AAU---CCACUAG---GUU-GG-CAAGU--
AAPR01000002.1/89791-89663     ---GAUGGUA------GGUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUCUAAACC-CCC-UAAA--GGUGC-UGUUGUAAAGAGC--CCCGAAGCCUCGGGGGUGCU-GAGCGU--UUA-GG--A-GAAUCC-AAU---CCACGAG---GUU-GGCAAGG---
AAMJ02000105.1/1106-1219       ---UAU----------GAGAGAUGAGGGGCG-GCGUC-CAGA-CGCCGCCUUCAAACC-GCC-UUGA--GCUGC-U-------GCCGU--UAAGA-GC-GG-UG-GUGGU-GAGCGU--CAA-GGUUA-AAAGGC-GCAGAACA--------UGU-GU-CAGG-U-
AY608901.1/230-348             ---GGAGGAU------GGCCCUCCGGGAUCG-GCUUU-CAGG-AGCGGGUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGU--AAAGA-GC-CG-UG-GUGGU-GAGCGC--CGG-AU--GAAAAGUU-CGG---ACGAGAU---CCG-AG-CAGG-U-
AACY020292880.1/337-460        ---GGCGGAAC----CGACCCGCCGGAGUCU-GCCUG-CAGG-GGCCGACUCCAAACC-ACCCCCGA--GCGGC-C-------UUGGC--UGAAG-AC-CG-UG-GUCGU-GAGCGU--CGGGGG--A-GAAGGC-GCAUCCAGGUGG----UGC-GU-CAGGU--
CP001046.1/528233-528350       ---GAGUGUG------CGCCUCCCGGAGUCG-AUUUG-UAGC-AGCAGGCUUCAAACC-GCC-CGGU--GCUAC-U-------GCGUU--AUAAG-GG-UA-UG-GUGGU-GAUCGC--CCGCGG--A-AAGGUC-ACC----CAUCAG---GGU-GG-CAAG-U-
BX571862.1/232878-232996       ---GAGGGCA------GGCCCCUCGAAGCCG-UUUUA-CAGG-AAAUGGCUUCAAACC-CCC-CACU--GCUGC-U-------GCGUU--UAAGA-GA-CG-UG-GUGGU-GAGCGA-GAUG-GG--A-AAAGGU-CGG---GCAUGAU---CCG-AU-CAGG-U-
AAOF01000003.1/257571-257448   ---GGAGGGAU----CGACCCUCCGGAGUCU-GCCUG-GAGG-GGCCGGCUUCAAACCGCCC-UCGU--GCGGC-A-------UUGGC--UGAAG-AC-CG-UU-GUCGU-GAGCGU--CGGGGG--A-GAAGGC-GGGUCCACGUGGA----CU-GU-CAGG-U-
AAPR01000018.1/57785-57913     ---GAUGGUA------GAUCCAUCAAAGUCG-UUGUA-UAGG-CGAUGGCUCUAAACC-CCC-UAAA--GGUGC-UGUUGUAAAGACC--CCCGAAGCCUCGGGGGUGCU-GAGCGU--UUA-GG--A-GAAUCU-AGU---CCUAGAG---AUU-AG-CAGG-U-
CP001108.1/80519-80405         ---GAGGGUC------GGCCCCUCGCUAUCG-GCUUG-CAGG-AGCAGGUGGCAAACC-ACC-GUAA--GCAGC-A-------UUGGU--CAAAA-GC-CC-UU-GUUGU-GCGCGU--UAC-GG--A-AAAGGC-CCC---A---AAA---GGU-AU-CAGG-U-
CP000758.1/647317-647435       ---GGGAGUG------GGCCUCCCGAAGCCG-ACCUG-CAGG-GGCCGACUUCAAACC-ACU-CCAU--GCUGC-U-------UCGUU--UCAAGAGA-CG-UG-GUGAU-GAGCGA--UGG-AG--A-AAUGGC-GGU---GCGCGAC---GCC-UA-UAGGU--
AAWS01000017.1/53865-53985     ---GGUGGUA------GACCCACCAAAGGCG-AUUUA-CAGG-AAUAGCCUUUAAACC-ACU-CUAC--GGUGC-U-------AUGAC--AGUAAUGU-UU-UG-GUAUU-GAACGG-CUAG-AG--A-AAAGGC-UCCGCUGG--UAC---GGA-GU-CAGGU--
AACY022081244.1/552-435        ---GAGAGAA------GGUCUCUCGACUAAG-AUGUA-CAGG-CAUAUUAGUCAAACC-GCC-UUAU--GGGGC-U-------UAGUC--UUCAC-GA-CU-UG-GUCUU-GAGCGA--UAG-GG--UCAAAGGC-ACUGCUAC--------CGU-UUGUAUG-G-
BA000007.2/2050761-2050877     ---GGUGGCA------GGCCCACCGGGAUCU-GCUGU-CGAA-AGUCGGUCCCAAACA-ACC-CC-G--GCUGC-U-------GUGGU--AAAGA-GC-CA-UG-GUAGU-GAGCGC--AGG-GG--G-AACGAU-CAG---ACGAGAU---CUG-AU-CC-UAU-
AACY020296230.1/1683-1564      ---GAGAGGA------GGUCUCUCGUGUCCG-GAUAA-CAGG-AUCUGGUCACAAACC-AGC-CCGU--CCUGC-G-------GCGGU--CAAGA-GC-CG-UU-GUGGG-GAGCGU--CGG-GUGUA-AAAGGC-GCGGCCC---GAC---CGC-GU-CAGG-U-
CP001076.1/126900-126782       ---GGAGGAU------GGCCCUCCGGGAUCG-GCUUU-CAGG-AGCGGGUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGU--AAAGA-GU-CG-UG-GUGGU-GAGCGC--CGG-AU--GAAAAGUU-CGG---ACGAGAU---CCG-AG-CAGGU--
ABSN01045240.1/98-214          ---GGGAGUG-----UGGCCUCCCGGAGCCG-GCCUG-CAGG-GGCAGGCUCCAAACC-ACC-CCAU--GCUGC-U-------GCGUC--CAAAA-GG-UG-CG-GUAGU-GAGCGA--UGG-GG--A-AAAGGC-GG----ACAUGAU----CC-GU-CAGG-U-
ACNL01000230.1/37135-37250     ---GACGGUG------GGCCCGUCGAAGUCG-CCAUA-CAGG-UGGAGAUUUCAAACC-ACC-UUAA--GGUGC-U-------GUAGU--CAAAA-GC-UA-UG-GUAUU-GAGCGU--UAA-GG--A-AAAGGC-AAU----CAAGA----AUU-GU-CAGG-U-
EF611303.1/15831-15947         ---GGAAGUA------GGCCUUCCGAAGUCG-GCUUG-CAGG-AGCGGACUUCAAACC-ACC-CGGU--GCUGC-U-------GCAUC--CAAAA-GG-UG-UG-GUGGU-GAGCGA--CCGAGG--A-AAAGUC-AUC---CCU-GAG---GAU-GG-CA-G-G-
AAKB02000001.1/4683607-4683707 ---GGUGGCA------GGCCCACCGGGAUCU-GCUGU-CGGA-AGUCGGUCCCAAACA-ACC-CCG---GCUGC-U-------GUGGU--AAAGA-GC-CA-UG-GUAG----------CAG-GG--A-AA--------GAUCAUCAGA-----------AGU-UC
AAGA01019987.1/408-289         ---GGUGGAAC----CGACCCACCAAUGUCG-UUUUA-UAGG-AGAAGGCGUUAAACC-ACC-UAAA--GGUGC-U-------GUUGU--AAAGA-GC-GA-UG-GUACU-GAGCGU--UUA-GG--A-AACGGC-UAG---UCAAGAA---CUG-GU-CAGG-U-
CP000471.1/785768-785884       ---GAGAGUG-----UGGCCUCUCGGAAUCG-GGUUG-CAGG-ACCGGGUUUCAAACA-GCG-UCGA--GCUGC-U-------UAGGU--AAAGA-GC-CU-UG-GUAGU-GAGCGU--CGG-CG--A-AAAGGC-GUU---GUG-GAA---AAC-GU-CA-U-G-
CU928162.2/337877-337993       ---GGAGGUG------GGCCCUCCGGUCAGG-GUUUG-CAGG-AACACUGACCAAACG-ACC-CGGU--GCUGC-U-------UCAUU--CUAAG-GAAUG-UA-GUGGU-GAGCGA-CUCG-GG--A-AAAGGC-AGAGAUCU--------ACU-GU-CA-C-G-
CP000820.1/8194388-8194276     ---GA-----------GGCCCUUCGGAGUCG-CCCUG-CGGG-GGGAGGCUCCAAACC-ACC-CAGC--GGUGC-C-------UUAGC--UGAAG-AC-UG-UG-GUGUU-GAACGG-UCUG-GG--A-AAAGUC-CGGGUGA----AC---CCG-GG-CAGG-U-
AAPR01000003.1/75791-75919     ---GAUGGUA------GGUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUCUAAACC-CCC-UAAA--GGUGU-UGUUGUAAAGAGC--UCCGAAGCCUCGGGGGUGCU-GAGCGU--UUA-GG--A-GAAUCC-AAU---CCACGAG---GUU-GGCAA-G-G-
CP000482.1/588498-588615       ---GAGGGCC------GGCCCCUCGGAGUCU-GCUUG-CAGG-AGCGGGCUUCAAACC-GCC-UCAA--GCUGC-A-------GGGGU--AAAGA-AC-CC-UU-GUGGU-GAGCGU--UGA-GG--A-AAAGGC-AAA---GUAUCAC---CCU-GU-CAGG-U-
CP000675.2/2800986-2800871     ---GGCGGCA------GCCCCGCCGAAGCAA-GCGAC-CAAG-AGCGGGCUUCAAACC-ACU-UCAU--GUGGCGC--------AUGU--AAAGA-GC-AU--GGGUCAU-GAGCGA--UGA-AG--A-AAAGUC-AGU---AA--GCA---ACU-GG-CAGG-U-
AACY023822632.1/808-931        ---GGCGGAAC----CGACCCGCCGGAGUCU-GCCUG-CAGG-GGCCGACUCCAAACC-ACCCCCGA--GCGGC-C-------UUGGC--UGAAG-AC-CG-UG-GUCGU-GAGCGU--CGGGGG--A-GAAGGC-GCAUCCAGGUGC----UGC-GU-CAGGU--
CP000252.1/744180-744291       ---UAU----------GACACAUAGAAGCCA-GCUUG-CAGA-AGCAGGCUGCAAACC-ACC-GUAA--GCGG--U-------GCUGG--UAAAGAUCCGGAUG--UCGU-AAGCGU--UAC-GG--AAAAC----UGC---AGUGAAA---GCA-UC-AG-G-U-
ACMX01000144.1/1584-1700       ---GG-GGAA------GGCCCAUCAAAAUCA-GUAUU-CAGG-UACAGGUUUCAAACC-ACC-UUUG--GGUGC-U-------GCAAU--CAAAA-GU-UG-UG-GUACU-GAGCGC--AAAUGG--A-AAAGGC-UAA---CAGAGA----UUA-GU-CAGG-U-
CP001108.1/2287479-2287365     ---GAGGGUC------GGCCCCUCGCCAUCG-GCUUG-CAGG-AGCAGGUGGCAAACC-ACC-GUAA--GCAGC-A-------UUGGU--CAAAA-GC-CU-UU-GUUGU-GAGCGU--UAC-GG--A-AAAGGU-ACC---A---GAA---GGU-AU-CAGG-U-
AE010299.1/5107575-5107458     ---GAGGGUG------GGCCCCUCGGAAUCG-CUAUA-CAGG-UAGAGAUUCCAAACC-ACC-AUAA--GCUGC-U-------GUGGU--CAAAA-GC-CA-UG-GUAGU-GAGCGU--UAU-GG--A-AAAGGC-GAG---ACUUGAC---CUC-GU-CAGG-U-
CP000491.1/19116-19233         ---GAGGGCA------GGCCCCUCGGGUUCG-GCGAU-CAGG-AGCCGAUCCCAAACC-ACC-ACAA--GCUGC-U-------GUCGU--AAAGA-GC-GA-UG-GUGGU-GAGCGU--UGU-GG--A-AACGGC-GGG---ACAUGAU---CCC-GU-CAGG-U-
AAPR01000015.1/110266-110149   ---GAUGGUA------GGUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUUUAAACC-ACC-UAAA--GGUGC-U-------UUGAU--UAAUA-GU-CU-UG-GUAUU-GAGCGU--UUA-GG--A-GAAUCU-AGU---CCUGGAG---AUU-AG-CAGG-U-
CP000800.1/1634986-1635102     ---GGUGGCA------GGCCCACCAGGAUCU-GCUGU-CGGA-AGUCGGUCCCAAACA-ACC-CC-G--GCUGC-U-------GUGGU--AAAGA-GC-CA-UG-GUAGU-GAGCGC--AGG-GG--G-AACGAU-CAG---ACGAGAU---CUG-AU-CC-UAU-
CP000542.1/4645377-4645265     ---GGG--CA------GGCAUCCCGAAGCCG-GCUUG-CAGA-AGCUCGCCUCACACC-CCC-CGGU--GCUGC-U-------GCGUU--CAAGA-GG-CG-CG-GUGGU-GAGCGA--CCG-GG--CGAAAGUC-A--UCCCUAG--------U-GU-CGCG-U-
AF386526.1/31835-31718         --A-GAGGUG------GGCCCUCCGGUCAGG-GUUUA-CAGG-AGCACAGACCAAACG-ACC-CGGU--GCUGC-U-------UCAUU--CUAAG-GAAUG-AG-GUGGU-GAGCGACUCCG-GG--A-AAAGGC-AGAGAUCU--------ACU-GU-CA-C-G-
ACMV01000283.1/2403-2519       ---GAGGAAA------GGC-CCUCGAAAUCG-GUAUU-CAGG-UACAGGUUUCAAACC-ACC-UUUG--GGUGC-U-------GCAAU--CAAAA-GU-UG-UG-GUACU-GAGCGC--AAAUGG--A-AAAGGC-UAA---CAGAGA----UUA-GU-CAGG-U-
AACR01000008.1/288-170         GAAGAUGGUC---------CCUUCGAAACCG-GCGGG-UAGAAGGCAGGGUUCAAACCAUUC-CAGCCUGCUGC-U-------AACGG--UAACA-AC-GU-CG-GUAGU-GAGCGG--CUG-GG--AAAAAAAC-AAG---AUG-------CUU-GU-CAGG-U-
ABLK01000149.1/1336-1239       ---GGGGGAC------GGCCCCGCGAAGUCG-GCUUG-CAGG-AGCAGGCUUCAAACC-GCC-ACAA--GCUGC-------------------------------GCGGG-UAGGGU--UGA-GU--CGCAAG------CAACGCCAGACGU-------CAUG-G-
AAPR01000024.1/36272-36399     ---GAUGGCA------GGUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUCUAAACC--CC-UAAA--GGUGC-UUUUGUAAAGAGC--CCAGAAGCUUCGGGGGUGCU-GAGCGU--UUA-GG--A-GAAUCC-AAU---CCACGAG---GUU-GGCAAGG---
AF261712.1/2402-2517           ---GGGAGAA------GGCCUCCCGGAGUCG-GCUUG-CAGG-AGCAGAUUCCAAACC-ACC-CGGU--GCUGC-U-------GCGUU--CAAAA-GG-CG-UG-GUGGU-GAGCGA--CCG-GG----GACGUC-AUCCGCA---GAG---GAU-GG-CG-G-G-
AY608903.1/214-334             ---GGGGGAC------GACCCUCCGGAAUCG-GCUUU-CAGG-AGCAGGUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGU--AAAGA-G--CG-UGUGUGGU-GAGCGCGUCGG-AU--GAAAAGUU-CGG---UCGAGAU---CCG-AG-CAGGU--
AF044503.1/9033-9153           ---GGUGGCA------GGCCCACCGGGAUCU-GCUGU-CGGA-AGUCGGUCCCAAAC--AAC-CCCG--GCUGC-U-------GUGGU--AAAGA-GC-CA-UG-GUAGU-GAGCGC-AGGG-GC--AGGGAAAG-AUCACGUAACGCU---GAU-UUUUUG----
ABSQ01001088.1/214-333         ---GAAGGUA------GGCCCUUCGGGUUCG-GCGAU-CAGGUCGCCGAUUCCAAGCC-ACC-GUGA--GCUGC-U-------GCGGU--CAAAA-GC-CG-UG-GUGGU-GAGCGU--CGC-GG--A-AACGUC-GGGACAAU--GAU---CCC-GG-CAGGC--
AAPR01000018.1/66732-66848     ---GAUGGUA------GACCCAUCAGAGUCA-UUGUA-CAGG-CGAUAGCUCUAAACC-AUC-UAAA--GUUGC-U-------UUGAU--UAAUA-GU-CU-UG-GUAUU-GAGCGU--UUA-GU--A-GAAUCU-AGU---CCUAGGG---AUU-AG-CA-GU--
DQ058415.1/100046-99943        ---GGAGGAU------GGCCCUCCGGGAUCG-GCUUU-CAGG-AGCGGGUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGU--AAAGA-GC-CG-UG-GUGGC------U--GGG-GCUUA-----------CUUUCCGCCG--C--------CGG-U-
CP001064.1/111457-111575       ---GAGGGAA------GGCCCCUCGGUGUCG-GCGUG-CAGG-CGCAGGCACCAAACC-ACC-CACU--GCUGC-U-------GCAUU--UAAGA-GA-UG-UG-GUGGU-GAGCGA-GAUG-GG--A-AAAGGU-CGG---ACGUGAG---CCG-AU-CAGG-U-
AATF01003618.1/267-147         ---GAGAGUA------GGUCUCUCGCAAUCG-CUUUG-CAGG-AAGAGGUUGCAAACC-GGU-GUAU--GCUGC-U-------UUCUCCCGAAAG-GGUUA-AG-GUAGU-GAACGA--UAC-AUUUA-AAAGGC-AGUGAUGA--------ACU-GU-CAGG-U-
CP000035.1/90894-90776         ---GAGGGAA------GGCCCCUCGGUGUCG-GCGUG-CAGG-CGCAGGCACCAAACC-ACC-CACU--GCUGC-U-------GCAUU--UAAGA-GA-UG-UG-GUGGU-GAGCGA-GAUG-GG--A-AAAGGU-CGA---ACGUGAG---CCG-AU-CAGG-U-
AACY022377776.1/466-349        ---GACGGAG------GGCCCGUCGGAGCCG-AUCAU-UAGG-GAUAGGCUUCAAACC-AGC-CCAA--GCGGC-U-------GUCAU--UAAGA-GU-GA-UG-GUCGU-GAGCGU--UGG-G---A-AAAGGC-AGGACAGC--GAU---CCU-GU-CAUG-G-
AACY020535361.1/306-183        ---GGCGGAAC----UGACCCGCCGGAGUCU-GCCUG-CAGG-GGCCGGCUCCAAACU-ACCCCCGA--GCGGC-C-------UUGGC--UGAAG-AC-CG-UG-GUCGU-GAGGGU--CGGGGG--A-UAGGGC-GCACCCAUGUGG----UGC-GU-CAGG-U-
CP000304.1/1829785-1829902     ---GGAAGUA------GGCCUUCCGAAGUCG-GCUUG-CAGG-AGCGGACUUCAAACC-ACC-CGGU--GCUGC-U-------GCGCC--CAAAA-GG-CG-UG-GUGGU-GAGCGA--CCGAGG--A-AAAGUC-ACC---CCU-GAG---GGU-GG-CAGG-U-
ABQZ01000206.1/524-406         ---GGAGGAU------GGCCCUCCGGGAUCG-GCUUU-CAGG-AGCGGGUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGU--AAAGA-GC-CG-UG-GUGGU-GAGCGC--CGG-AU--GAAAAGUC-CGG---ACGAGAU---CCG-AG-CAGGU--
AACY020304102.1/272-149        ---GGCGGAAC----CGACCCGCCGGAGUCU-GCCUG-CAGG-GGUCGGCUCCAAACC-ACCCCCGA--GCGGC-C-------UUGGC--UGAAG-AC-CG-UG-GUCGU-GAGCGU--CGGGGG--A-GAAGGC-GCAUCCAGGUGG----UGC-GU-CAGGU--
CP000740.1/481044-480926       ---GGAGGAU------GGCCCUCCGGGAUCG-GCUUU-CAGG-AGCGGGUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGU--AAAGA-GU-CG-UG-GUGGU-GAGCGU--CGG-AU--GAAAAGUU-CGG---ACGAGAU---CCG-AG-CAGG-U-
CP001108.1/672624-672507       ---GGAGGUG------GGCCCUCCGGAAUCG-CCGUA-CAGG-CGGAGAUUCCAAAUC-ACC-UGCU--GCUGC-U-------GCAUU--UAAGA-GG-UG-UG-GUGGU-GAGCGA--GCCAGG--A-AAAGGC-GGG---AUAAGAU---CCU-GU-CA-GA--
CP000724.1/658407-658524       ---GAAGGUC------GGUCCUUCGAAAUCG-GUAUG-CAGA-UACGGGUUUCAAACU-GCC-CAUA--GGUGC-U-------GUAGA--UUAAUGUC-UU-CG-GUAUU-GAGCGU-UAUG-GG--AAAAAGGC-UGUAUAA---------ACA-GU-CA-A-GU
CP000391.1/44667-44753         ---GGGGGUGG----GGCUCCCUCGGAGCC-----------------GGCUUCAAAGC-GCC-UCAA--GCU----------------GCU-----------------GU-GAGCGU--UGA-GG--A-AAAGGC-CGG---ACUUGAU---CCG-GU-CAGGU--
ABSP01044932.1/689-806         ---GAGGGGA------GGCCCCUCGGGGUCG-GCGUG-CAGG-CGCAGACUUCAAACC-GCG-GCAA--GCGGC-G-------UCGAU--CAAGA-GU-CG-UC-GUCGU-GAGCGU--UGC-CG--GAAAAGGC-GGAGGGU----AC---UCC-GU-CAGGU--
AACY021994855.1/670-552        ---GAGAGAA------GGUCUCUCGACUAAG-AUGUA-CAGG-CAUAUUAGUCAAACC-GCC-UUAU--GGGGC-U-------UAGUU--UUCAC-GA-CU-UG-GUCUU-GAGCGA--UAA-GG--UAAAAGGC-GGU---ACUACCA---UUU-GU-AAGG-U-
AACY023814675.1/141-264        ---GGCGGAAU----CGACCCGCCGGAGUCU-GCCUG-CAGG-GGCCGGCUCAAAACC-ACCCCCGA--GCGGC-C-------UUGGC--UGACGAG--CG-UG-GUCGU-GGGCGU--CGGAGG--A-GAAGGC-GCACCCAUGUGG----UGC-GU-CAGGU--
CP001087.1/3005378-3005495     ---GAGGGAG------GGCCCCUCGAAGCCG-CCAUG-CAGG-UGGAGGCUUCAAACC-ACC-GUAA--GCUGCGU--------CGGU--UAAGA-GC-CG--GGGUGGU-GAGCGU--UAC-GG--A-AAAGGC-AAG---ACCAGAU---UUU-GU-CAGG-U-
ABSO01010352.1/462-344         ---GAGGGAA------GGCCCCUCGGUGUCG-GCGUA-CAGG-CGCAGGCACCAAACC-ACC-CACU--GCUGC-U-------GCGUU--AAAGA-GA-CG-UG-GUGGU-GAGCGA-GAUG-GG--A-AAAGGU-CGG---GCUUGAU---CCG-AU-CAGG-U-
ACMW01000127.1/43857-43740     ---GAGGGAA------GGCCCCUCGAAAUCG-GUAUU-CAGG-UACAGGUUUCAAACC-ACC-UUUG--GGUGC-U-------GCAAU--CAAAA-GU-UG-UG-GUACU-GAGCGC--AAAUGG--A-AAAGGC-UAA---CAGAGA----UUA-GU-CAGG-U-
AL391753.1/87329-87216         ---UAU----------GAGAGAUGAGGGGCG-GCGUC-CAGA-CGCAGCCUUCAAACC-GCC-UUGA--GCUGC-U-------GCCGU--UAAGA-GC-GG-UG-GUGGU-GAGCGU--CAA-GGUUA-AAAGGC-GCAGAACA--------UGU-GU-CAGG-U-
AP008230.1/3741287-3741172     --U-GAGGAA------GGCCCUUUGGACUCG-GUAUU-CAGG-UACAGGGUUUAAACA-ACC-UUAA--GCUGC-U-------GUGUU--CAAAA-GG-CA-UG-GUAGUAGAGCGU--UAA-GG--A-AAAGGC-UGGGAUGA--------CUA-GU-UA-U-G-
AE010299.1/4030619-4030499     ---GAGGGUA------GACCCCUCGGACUCG-CUUUA-CAGG-AAGUUAUUCCAAACC-ACCCAUAA--GCUGC-U-------UUGGU--CAAAA-GC-CA-CG-GUAGU-GAGCAU--UAUGGG--A-AAAGGC-GAGGCUAU--GAC---UUC-GU-CAGGU--
CP000629.1/1749142-1749258     ---GAGGGUA------GGUCCCUCGAAGCCG-ACCGU-CAGG-GGUAGGUUUCAAACC-ACU-GCAA--GCUGCG--------ACGGU--AAAGA-GC-CG-U-GGUGGU-GAGCGU--UGC-AG--A-AAAGGC-GGA----UGUUAG---UCC-GU-CAGG-U-
BA000040.2/2212617-2212736     ---GGGAGUU-----UGGCCUCCCGGAGCCG-GCCUU-CAGG-GGCAGGCUUCAAACC-ACC-UCAU--GCUGC-C-------GCGUU--CAAAA-GG-CG-CG-GUGGU-GAGCGA--UGA-GG--AAAAAGGC-GGUGAAU---GAA---ACC-GU-CAGG-U-
ABSN01030198.1/477-596         ---GGGGGUG------GGCCCCCCGGAGCCG-GCUUG-CAGG-AGCAGGCUCCAAACC-ACC-UUAA--GCUGCGC--------UGGU--UAAGA-GC-CA--GGGUGGU-GAGCGU--UAA-GG--A-CAAGUC-AUGGCUAAU-GAC---CGU-GG-CAGG-U-
CP000934.1/3790671-3790555     ---GGUGGCA------GGCCCACCGCAUUCG-CUUUG-CAGU-AAGUGAGUGCAAACC-ACU-UCAA--GCGGC-A-------UUGAU--AAAGA-GU-CA-UU-GUCGU-GAGCGU--UGA-AG--A-AAAGUC-GGA---AUA-AAA---UUC-GG-CAGG-U-
CP000039.1/31507-31391         --A-UCACUG------GCGCUGACAGUCAGG-GUUUA-CAGG-AGCACUGACCAAACG-ACC-CGGU--GCUGC-U-------UCAUU--CUAAG-GAAUG-AG-GUGGU-GAGCGA-CUCG-GG--A-AAAGGC-AGAGAUCU--------ACU-GU-CA-C-G-
AAPR01000018.1/15562-15679     ---GAUGGUA------GAUCCAUCAAGGUCG-UUGUA-UAGG-CGAUGGCUUUAAACC-ACC-UAAA--GGUGC-U-------UUGAU--UAAUA-GU-CU-UG-GUAUU-GAGCGU--UUA-GG--A-GAAUCU-AGU---CCUAGAG---AUU-AG-CAGG-U-
AACY022919999.1/547-428        ---GGUGGUA------GACCCACCGAAGUCG-GCAGU-CGGA-UGCAGGCUUCAAACC-GGC-CCAA--GCUGCGC--------GCAU--AAAGA-GU-GC--GGGUAGU-GAGCGU--UGG-GU--GAAAAGGC-CGUACAAC--AAU---ACG-GU-CAGGU--
ABRD01000340.1/878-768         -----UGAAA------AAUUCA--GUGGCAG----GU-CAGCG----GGUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGC--AAAAGAGC-CG-UG-GUGGU-GCGCGU--CGG-AUGAA-AAAGUU-CGG---ACGAGAU---CCG-AG-CA-G-GU
AAYX01000002.1/228647-228529   ---GAGGGAG------GGCCCCUCGGGGCCG-GCGAU-CAGG-AGCCGGUCUCAAACC-GCC-ACAA--GCUGC-U-------GUCGU--AAAGA-GC-GA-UG-GUGGU-GAGCGU--UGU-GG--G-AACGGC-GGAACUUU--GAU---UCC-GU-CAGG-U-
ABPP01002110.1/335-217         ---GAGGGCA------GGCCCCUCGGAGCCG-CCGUA-CAGG-CGGAGGCUUCAAACC-ACC-CACU--GCUGC-U-------GCGUU--UAAGA-GA-CG-UG-GUGGU-GAGCGA-GUUG-GG--A-AAAGGC-CGGGCAC---GAC---CUG-GU-CAGG-U-
CP001110.1/1106159-1106274     ---GAGGGAA------GUCCCCUCGCAUUCG-GCUUG-CAGG-AGCAGGGUGCAAACC-ACC-GUAA--GCGGC-A-------UUAGU--CAAAA-GCC--CUU-GUCGU-GAGCGU--UAC-GG--A-AAAGGC-AUCGUAAA--------GAU-GU-CAGG-U-
CP001062.1/142488-142370       ---GAGGGAA------GGCCCCUCGGUGUCG-GCGUG-CAGG-CGCAGGCACCAAACC-AUC-CACU--GCUGC-U-------GCAUU--UAAGA-GA-UG-UG-GUGGU-GAGCAA-GAUG-GG--A-AAAGGU-CGG---ACGUGAG---CCG-AU-CAGG-U-
AF386526.1/146214-146096       ---GAGGGAA------GGCCCCUUGGUGUCG-GCGUG-CAGG-CGCAGGCACCAAACC-AUC-CACU--GCUGC-U-------GCAUU--UAAGA-GA-UG-UG-GUGGU-GAGCGA-GAUG-GG--A-AAAGGU-CGG---ACGUGAG---CCG-AU-CAGG-U-
CP000492.1/2568639-2568523     ---GAGGGUC------GGCCCCUCGCAAUCG-GCUUG-CAGG-AGCAGGUUGCAAACC-ACC-GUAA--GCGGC-U-------UGGGU--CAAAA-GC-CC-CG-GUCGU-GAGCGU--UAC-GG--A-AAAGGC-GCC---AUU-UAA---GGU-GU-CAGG-U-
AAPR01000001.1/289552-289435   ---GAUGGUA------GAUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUUUAAACC-ACC-UAAA--GGUGC-U-------UUGAU--UAAUA-GU-CU-UG-GUAUU-GAGCGU--UUA-GG--A-GAAUCU-AGU---CCUAGAG---AUU-AG-CAGG-U-
AAGA01020442.1/602-482         ---GGUGGAAC----CGACCCACCAGAAUCU-GCUUA-UAGG-AGCUGGUUCUAAACC-ACUUUUCU--GAUGC-A-------UCCAA--AGUAA-UU-UGUUU-GUGUG-AAGCGA--GGGAAG--A-AAAGGC-AG----ACUUGAU----CU-GU-CAGG-U-
CP000035.1/31147-31031         ---GGAGGUG------GGCCCUCCGGUCAGG-GUUUA-CAGG-AGCACUGAUCAAACG-ACC-CGGU--GCUGC-U-------UCAUU--CUAAG-GAAUG-AG-GUGGU-GAGCGA-CUCG-GG--A-AAAGGC-AGAGAUCU--------ACU-GU-CA-C-G-
AAPR01000025.1/41436-41308     ---GAUGGUA------GGUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUCUAAACC-CCC-UAAA--GGUGC-UGUUGUAAAGAGC--CCCGAAGCCUCGGGGGUGCU-GAGUGU--UUA-GG--A-GAAUCC-AAU---CCACGAG---GUU-GGCAAGG---
AACY023770432.1/1175-1293      ---GGUAGUA------GGUCUACCGAAGCCG-CUUUA-CAGG-AGGAGGCUUCAAACC-GCU-CUAC--GGUGC-U-------GUAUC--CUAAGGGA-UA-UG-GUGUU-GAACGG-UUAG-AG--A-AAAGGU-AUA----CACAAG---UAU-AU-CAGGU--
AAOF01000003.1/267524-267647   ---GGAGGGAU----CGACCCUCCGGAGUCU-GCCUG-CAGG-GGCCGGCUUCAAACCGCCC-UCGU--GCGGC-A-------UUGGC--UGAAG-AC-CG-UU-GUCGU-GAGCGU--CGGGGG--A-GAAGGC-GGGUUCACGUGG----CCC-GU-CAGG-U-
AACY020344070.1/3657-3773      ---AAGGGAC------GGCCCCC-GAUGCCG-GCUUG-CAGA-AGUGGGCUUCAA-CC-GCCAACAA--GCUGC-G-------UGGGC--AAAGA-GC-CU-UC-UUGUU-GAACGU--UGAUGG--A-AAAGUC-GGGGACA----AC---CCC-GG-CAGGU--
AAPR01000001.1/265869-265741   ---GAUGGUA------GGUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUCUAAACC-CCC-UAAA--GGUUC-UGUUGUAAAGAGC--CCCGAAGCCUCGGGGGUGCU-GAGCGU--UUA-GG--A-GAAUCC-AAU---CCACGAG---GUU-GGCAAGG---
AAPR01000001.1/258189-258072   ---GAUGGUA------GAUCCAUCAGAGUCG-UUGUA-UAGG-CGAUGGCUUUAAACC-ACC-UAAA--GGUGC-U-------UUGAU--UAAUA-GU-CU-UG-GUAUU-GAGCGU--UUA-GG--A-GAAUCU-AGU---CCUGGAG---AUU-AG-CAGG-U-
CP000946.1/2413416-2413301     ---GGUGGCA------GGCCCACCGGGAUCU-GCUGU-CGGA-AGUCGGUCCCAAA-C-AAC-CCCG--GCUGC-U-------GUGGU--AAAGA-GC-CA-UG-GUAGU-GAGUGC-AGGG-GG----AACGAU-CAG---ACGCGAU---CUG-AU-CCUG---
CR555306.1/2546503-2546625     ---GAGGGUA------GGUCCCUCGGAGUCG-GCUUU-CAGG-AGCGGGCUUCAAACC-ACC-CCAA--GCUGC-U-------GCGGU--CAAGA-GC-CGUCG-GUGGU-GAGCGU--UGG-GGUCAAAGCGUC-GGGGACG---UAC---CCC-GAGCAGG-U-
AAQF01000034.1/25023-24906     ---GAGGGCG------GGCCCCUCGGAUUCG-CCGGU-CAGG-CGGUGAUUCCAAACC-ACC-CUGA--GCUGC-U-------GGCGU--AAAGA-GC-GC-UG-GUGGU-GAGCGU--CAGAGG--A-AAAGGC-AAG---GUU-GAC---CUU-GU-CAGGU--
ABSN01061879.1/364-246         ---GAUAGUA------GGCCUAUCAGCAUCG-GCAUG-UAGC-UGCUGGUGCUAAACC-ACC-UGAA--GGUGC-U-------GUAUU--CAAAA-GA-UA-UG-GUACU-GAACGU--UCA-GG--U-AAAGAU-GUUGUAUA--AAC---AGC-AU-CAGG-U-
AP009240.1/1621164-1621280     ---GGUGGCA------GGCCCACCGGGAUCU-GCUGU-CGGA-AGUCGGUCCCAAACA-ACC-CC-G--GCUGC-U-------GUGGU--AAAGA-GC-CA-UG-GUAGU-GAGCGC--AGG-GG--G-AACGAU-CAG---ACGAGAU---CUG-AU-CC-UAU-
AAFX01045244.1/209-327         ---GGAGGUC------GGCCCUCCGGAGCCA-GCUUG-CAGG-AGCGGGCUUCAAACC-GCC-ACAA--GCUGC-G-------GCAGU--CAAAU-GC-UG-CC-GUGGU-GAGCGU--UGUUGG--A-AAAGGC-GGA---GUUAAAC---UCC-GU-CAGGU--
AE010299.1/4144166-4144046     ---GAGGGUA------GACCCCUCGGACUCG-CUUUA-CAGG-AAGUGAUUCCAAACC-ACCCAUAA--GCUGC-U-------UUGGU--CAAAA-GC-CA-CG-GUAGU-GAGCAU--UAUGGG--A-AAAGGC-GAGGCUAU--GAC---UUC-GU-CAGGU--
CP000035.1/166157-166039       ---GAGGGAA------GGCCCCUCGGUGUCG-GCGUG-CAGG-CGCAGGCACCAAACC-AUC-CACU--GCUGC-U-------GCAUU--UAAGA-GA-UG-UG-GUGGU-GAGCGA-GAUG-GG--A-AAAGGU-CGG---ACGUGAG---CCG-AU-CAGG-U-
AM999887.1/1044564-1044677     ---GAGGGAG------GGCCCCUCGGAGCCG-GUUUG-CAAG-AGCAGGCUUCAAACA-GCC-AUAA--GCUGC-U-------UUGGU--AAAGA-GC-UA-AG-GUAGU-GAGCGU--UAU-GG--A-AAAGGC-ACAAUUA---------UGU-GU-CA-U-G-
AY305378.1/240715-240832       ---CGGGGAC------GGCCCCUCGAAGUCG-GAUUG-CAGG-AGCGGGCUUCAAACC-GCC-ACAA--GCUGC-G-------UGGGU--GAAGA-GC-CC-CC-GUGGU-GAGCGU--UGUCGG--A-AAAGUC-GGGGGCA----AC---CUC-GG-CAGGU--
ABSP01050949.1/719-605         ---GGUGGAA------GGCCCACCGAAGUCU-GCUGU-CGGA-AGCUGGCUUCAAACC-ACC-UCAA--GCUGC-U-------UGUAU--UAAGA-GU-GC-AG-GUAGU-GAGCGU--UGA-GG--A-AACGUU-AAU---U---CAU---AUU-AG-CAGG-U-
AJ578434.1/2018-2139           ---GAGGGUA------GGCCCCUCGGGAUCG-GCUUU-CAGG-AGCGGGUCUCAAACC-AGC-CCAA--GCUGC-U-------GUGGU-AGAAGA-GC-CA-UG-GUGGU-GAGCGU--UGG-GU-CA-AAAGCCGCG---GACAUGAU--C-CGGGG-CAGG-U-
CT573071.1/463583-463472       ---GA----A------GUA---UCAGCAACG-CCAUA-CAGG-UGGGGUUGCCAAACC-GCU-CUAC--GCUGC-A-------AAAGC-UGCAAA-GC-UG-CU-GUAGU-GAACGG-AUAG-AG--A-AAAGGU-GGA---AGA-AAA---UCC-AU-CAGG-U-
ACDM01000050.1/114-9           ---GGUGGCA------GGCCCACCGGGAUCU-GCUGU-CGGA-AGUCGGUCCCAAA-C-AAC-CCCG--GCUGC-U-------GUGGU--AAAGA-GC-CA-UG-GUAGU-GAGCGC--AGG-GG--C-AGGG----------AAAGAU----------CACG-U-
AY075117.1/315-434             ---GAUUGAA---------CCACCAGCAGGG-ACUGU-CAAG-AGUAUCUGCUAAACC-GCC-UUAC--GGUGC-U-------UUUAU-UUAACA-AU-AG-AG-GUAUU-GAGCGG-CUAA-GG--A-AAAGGG-GCGAUGAAAGAAU---CGU-UU-CAGG-U-
AAXY01000005.1/171428-171548   ---GGAGGAA-----CCGAACGCCGGAGUCU-GCCUG-CUGG-GACUAGCUCCAAACC-ACC-CUGA--ACGGC-A-------UUGGC--UGAAG-AC-CG-UU-GCCGU-AAGCAU--CGG-GG--G-AAAGGC-UCAC-UCAGGUGG---UGU-GU-CAGG-C-
CP001720.1/4201681-4201564     ---GAGGGAA------GGCCCCUCGGAGCCG-CUAUG-CAGG-UAGAGGCUCCAAACC-ACC-GUAA--GCUGC-U-------GUGGU--CAAAA-GC-CA-UG-GUGGU-GAGCGU--UAC-GG--A-AAAGGC-GAA---GCAUGAC---UUU-GU-CAGG-U-
ABWL02000021.1/265952-266069   ---GGUGGCG------AGCCCGCCGGGAUCU-GCCGU-CGGA-GGCCGGUAUCAAACA-ACC-ACU---GCUGC-U-------GUGGU--AAAGA-AC-CA-UG-GUGGU-GAGUGC--AGG-GG--A-AACGCC-CGG---ACAAGAU---CUG-AGGCUAUA--
CP001720.1/747711-747825       ---GAGGGGA------GGCCCCUCGAACUCG-GUAUU-CAGG-UGCAGAGUUCAAACA-ACC-UUAA--GCUGC-U-------GUGUU--CAAAA-GG-CA-UG-GUGGU-GAGCGU--UAA-GG--A-AAAGGC-CGGAAUUA--------CCG-GU-CA-U-G-
CP001734.1/751467-751585       ---GGAGGUA------GGCCCUCCGGAGUCU-GCUGU-CGGA-AGCCGGCUUCAAACC-AAC-CCAA--GCUGCGC--------GUGU--UAAGA-GC-AC--GGGUGGU-GAGCGU--UGG-GU--GAGAAGGU-AGCGCUA---AAC---GUU-AU-CAGG-U-
AY608908.1/98-216              ---GGGGGAC------GGCCCCCCGGGAUCG-GCUUU-CAGG-AGCGGGUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGU--AAAGA-GC-CG-UG-GUGGU-GAGCGU--CGG-AU-GA-AAAGUU-CGG---ACGAGAU---CCG-AG-CAGG-U-
AY248839.1/69-187              ---GGAGGAC------GGCCCUCCGAGAUCG-GCUUU-CAGG-AGCAGAUCUCAAACC-AGU-CCGA--GCUGC-U-------GCGGU--AAAGA-GC-CG-UG-GUGGU-GAGCGU--CGG-AU-GA-AACGUU-CGG---ACGAGAU---CCG-AG-CAGG-U-
#=GC SS_cons                   ...<<<<<__......___>>>>><<<<<<-.<<<<_.___>.>>>->>>>>>---((.,<<.<<<<..<<-<<.<.......-<<<<.._____.>>.>>.->.>>->>.----->..>>>.>>..,.,,,<<<.<<<..._______...>>>.>>.>,,).).
#=GC RF                        ...GggGGua......GGcCCccCGgagccG.gcuca.CAGg.agcaggcucCAAAcC.acC.ccga..GcUGC.u.......ucggc..uaAaA.gc.cg.ug.GUggU.GAGCGu..cgg.Gg..A.AAAGcc.ggg...acaugAu...ccc.gg.CAGG.g.
//
# STOCKHOLM 1.0

#=GF AC   RF02000
#=GF ID   MIR1846
#=GF PI   C1674
#=GF DE   microRNA MIR1846
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   33.00
#=GF TC   33.00
#=GF NC   32.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000577;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19103661
#=GF RT   Characterization and expression profiles of miRNAs in rice seeds
#=GF RA   Xue LJ, Zhang JJ, Xue HW
#=GF RL   Nucleic Acids Res. 2009;37:916-930.
#=GF RN   [2]
#=GF RM   18687877
#=GF RT   A diverse set of microRNAs and microRNA-like small RNAs in developing rice
#=GF RT   grains
#=GF RA   Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, Helliwell C
#=GF RL   Genome Res. 2008;18:1456-1465.
#=GF WK   MicroRNA
#=GF SQ   21


AP005903.3/131196-131108   CCUCCCC-GCCGGAUCUCCCAGUGAGGAGGCUAGGGCCGCCGGGUCCGAUGAUCCCAUUCUCCUUGUCAGCGGAUCCGG-C-GCCCUAGAGA
AC083751.6/28677-28765     CUUUCCC-GCCGGAUCUCCCAAUGAGGAGGCUGGGGCCACCGGAUCCGAUGACCCCAUUCUCCUCGCCGGCGGAUCCAG-U-GCCCUAGAGA
AP004096.3/20776-20861     UUCCGCC-GCCGCAUCCGCCAACGAGGAGGCCGGGACCGCCGGAUCCGGUGACUUCGGCCUCUUCGCUGGCAGAUCUGG-C-CA---CUCUA
AC145127.1/508295-508383   AUGAGCC-GCCGGAUCUCCCAGUGAGGAGGCCGGGGCCGCUGGAUCCGGUGACCCCGUUCUCCUCGCCGGCGGAUCCGG-C-GCUCCAGAGA
AAAA02007834.1/24188-24100 CCUCCCC-GCCGGAUCUCCCAGUGAGGAGACUAGGGCCGCCGGAUCCGGUGAUCCCAUUCUCCUUGCCGGCGGAUCCAG-C-GCCCUAGAGA
AACV01011762.1/1701-1616   AUGAGCC-GCCGGAUCUCCAAGAAAGGAGGCCAGGGCCGCCGGAUUCGGUGACCCCAGUCUCCUCGCUGGCGGAUCUGG-C-GU---CCAGA
AC109929.2/56139-56053     ACGAGUC-GCCGGAUCUCCCCGUGAGGAGGCCGGGGCCGCCGGAUCCAGUGACCCCGUUCUCCUCGCCGGCGGAUCCGG-CAGC---CCAGA
AL831796.5/95253-95330     AUCACC--GCCGCAUCGGCCAACGGGGAGGCUGUGGCCUCCAGGUCUGGUGACC-CAGCCUCCCUGUUGGUGGAUCCGG-C----------U
AC087412.14/69387-69471    AUAAGCC-GCCGGAUCUCCUAGUGAGGAGGCCGGGACCGCCGGAUCCGGUGACCCCGGUCUCCUCGCCGGCGGAUCCG--U-GU---CAGAA
CU406257.1/183-269         UCCUGCC-GCCGCAUCCGCCAACAAGGAGGCCGGGACCGCCGGAUCCGGUGACUCCGGCCUCCUCGCCGGCAGAUCCGG-CCGU---UGUGA
AAAA02033363.1/27541-27626 AUGAGCC-GCCGGAUCUCCCAGUGAGGAGGCCGAGGCCGCUGAAUCCGGUGACCCCGGUCUCCUCGCCGGCGGAUCUAG-C-GC---AAAGA
AAAA02002495.1/10128-10040 CCUCCCC-GCCGGAUCUCCCAGUGAGGAGGCUAGGGCUGCCGGAUCCGGUGACCCCAUUCUCCUCGCCGGCGGAUCCGG-C-GCCCUAGAGA
CT837481.1/88-174          UCAUGCC-GUUGCAUUUGCUAGCGAGGAGGCCCGGGCCGCUGAAUCCGGCGACCCCGAUCUCUUCGCUAGCGGAUUUGGCC-GC---UCGGA
AAAA02031067.1/51056-50970 CUUUCCC-ACCGGAUCUCCCAAUGAGGAGGCUGGGGCCACCGGAUCCGAUGACCCCAUUCUCCUCGCCGGCGGAUCCAG-C-GC--CCUAGA
AP003416.4/111295-111380   CCGAGCA-GCCGGAUCUCCCAGUGAGUAGGCCCGGGCCGCCAGAUCCGGUGACCCCGGUCUCCUCGCCGGUGUAUCCGG-C-GC---CGCAG
AP003234.3/152723-152636   ACCAGCCAACCGGAUCCAUCGGCGGGGAGGCCGGGGUCGCCAGAUCCGGUGUCCCCGGCCUCCUCGCUGGACGAUUCGG-UGGC---GGCGA
AL713944.3/42642-42557     AUGAGCC-GUCGGAUCUCCUAGUAAGGAGGCCGGGGCCGUCAGAUCCGGUGACCCCGGUCUCCUCACCGGCGGAUCCGG-C-GC---CAAGA
BX000494.2/2831-2916       AUGAGCC-GCCGGAUCUCCCAGUGAGGAGGCCGGGGCCGCUGAAUCCGGUGACCCCGGUCUGCUCGCUGGCGGAUCCGG-C-GC---AAAGA
AK241448.1/194-280         ACUCGCC-GCCGCAUCCGCCAACGAGGAGGCCGGGACCACCGGAUCCGGUGACUCCGGCCUCCUCGCCGGCAGAUCCGG-C-CA--CUCUGA
AC091749.8/41104-41189     AUGAGCC-GCUGGAUUUCCCAGUUAGGAGGCCGGGGCCACCGGAUCCGGUGACCCCGGUCUCCUCGCCGGCGGAUCCGG-C-GC---CCAGA
AP005006.3/105040-104955   AUGAGCC-GCCGGAUCUCCCAGUGAGGAGGCCGGGGCCGCCGGAUCCGGUGACCCCGGUCUCCUCGCCGGUGGAUCCGG-C-GC---CCAGA
#=GC SS_cons               ::::::<.<<<<<<<<<-<<-<<<<<<<<<<<<<<<-<<<<<____>>>>>->>>>>>>>>>>>>>>->>->>>>>>>>.>.>:...:::::
#=GC RF                    auuagCC.GCcGgAUcccCcAgcgaGGAGgccgGGGCCgCcGGAUCCgGcGACCCcggcCUCCucgccgGcggAUcCgG.C.Gc...aaaGA
//
# STOCKHOLM 1.0

#=GF AC   RF02001
#=GF ID   group-II-D1D4-3
#=GF DE   Group II catalytic intron D1-D4-3
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Weinberg Z
#=GF SS   Predicted; Weinberg Z
#=GF GA   32.00
#=GF TC   32.00
#=GF NC   31.90
#=GF TP   Intron;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.96 -Z 549862.597050 CM SEQDB
#=GF CL   CL00102
#=GF DR   SO; 0000603; group_II_intron;
#=GF DR   GO; 0000373; Group II intron splicing;
#=GF RN   [1]
#=GF RM   11377794
#=GF RT   The ins and outs of group II introns.
#=GF RA   Bonen L, Vogel J
#=GF RL   Trends Genet 2001;17:322-331.
#=GF RN   [2]
#=GF RM   11726522
#=GF RT   Control of branch-site choice by a group II intron.
#=GF RA   Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM
#=GF RL   EMBO J 2001;20:6866-6876.
#=GF RN   [3]
#=GF RM   12870716
#=GF RT   Group II introns: structure and catalytic versatility of large natural
#=GF RT   ribozymes.
#=GF RA   Lehmann K, Schmidt U
#=GF RL   Crit Rev Biochem Mol Biol 2003;38:249-303.
#=GF CC   Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi,
#=GF CC   plants and protists, and also in mRNA in bacteria. They are large
#=GF CC   self-splicing ribozymes and have 6 structural domains (usually designated
#=GF CC   dI to dVI. This model and alignment represents only domains V and VI. A
#=GF CC   subset of group II introns also encode essential splicing proteins in
#=GF CC   intronic ORFs. The length of these introns can therefore be up to 3kb.
#=GF CC   Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing
#=GF CC   with two transesterification steps. The 2' hydroxyl of a bulged adenosine
#=GF CC   in domain VI attacks the 5' splice site, followed by nucleophilic attack
#=GF CC   on the 3' splice site by the 3' OH of the upstream exon. Protein machinery
#=GF CC   is required for splicing in vivo, and long range intron-intron and
#=GF CC   intron-exon interactions are important for splice site positioning. Group
#=GF CC   II introns are further sub-classified into groups IIA and IIB which differ
#=GF CC   in splice site consensus, distance of bulged A from 3' splice site, some
#=GF CC   tertiary interactions, and intronic ORF phylogeny [1].
#=GF WK   Group_II_intron
#=GF SQ   406


BABD01009491.1/198-368       UCCAUU---G-UGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGCCUG-A-------G-GC-AAACCAUU-G-G--UCCGA---------------------CGGACAG-AAA-U--CA--UG-UA-UAAGG---C-U-UA--CA--GU-UC---GGAUAAG-A-------------------------------C-UGCU--GA-------------------A----CAAGUU-GAAGUCC-----------------------AAUA----------GCUAACAGA-G----G--ACUG-G-U----A-----------------GU-AGACAUG-GCGGAUAGGU-GAU-GAGAAA-----G-A-U-A-----GCG---UA
ABEF01021683.1/396-565       ACUCCC---G-CGA-GGGG-G--C-GUC-UGGU-GGA-----------------------AGUCAU-A-------G-GU-GCGCAACC-G-U--GUCGA--------------------GCGAAAGC-GAA-G--CG--CC---GUAAGG---C-U-UC--GG--GG-AC---GGGUGAG-C-------------------------------C-GGCG--GC-------------------C----AGCGGC-GAAGCCC-----------------------AAUA----------UCUGUCGGG-A----GU-UCCC-G-G----G-----------------GU-AGUGGCG-ACGGGA---U-GGG-UGCGAA-----A-UCU-A-----GCG---GU
BAAY01013995.1/719-912       UUUAUC---G-UGA-GGUA-U--G-CAC-UGAA-GGA-----------------------AGCAGA-A-------CUGC-AAAAGUCU-G-U--ACCGA---------------------CGAACAG-AAA-G--UA--CA-UA-AGAGG---C-A-UA--AC--AA-UA-A-GGAUGAG-U-------------------------------A-UCCA--CA-------------------G----CAAUAC-GAAGUCCAAAACAGU-------GUUCUGAACAUGCU------AUUUAAUCAGA-U----UA-UUGU-U-C----U-----------------GU-AGAUGUA-CCGGCGA-AU--GA-CGGAAG-----G-A-A-AAAGCA------UU
BABD01035235.1/532-360       GUCUUG---G-UAA-CAAG-G--G-GUC-UGGA-GGA-----------------------AGCCGA-U-------A-GC-AAAACACU-G-G--CCUGA---------------------UGAACAA-GAA-G--CA--GA-UA-CUAGG---C-U-UA--UU--CG-AU---GGGUAAA-A-------------------------------G-GUCU--CA-------------------A----AUACUC-AAAGCCC-----------------------UAAU---------ACACGUACGG-A----GU-CGAA-U-A----A-----------------GU-AUAUCUG-ACAGGCAUA--AGU-GUGAAA-----G-CAG-C-----GCG---UC
ABEF01052776.1/2059-1888     GGAAGG---G-UGA-CCGA-C--C-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GCGUAAACCGU-G-A--GCCGA---------------------UGAACAA-GAA-U--CG--GA-UA-UGAGG---C-A-CU--GC--CAAGC-A-GGGCGAG-C-------------------------------G-GGCC--AA-------------------A----AGCCGC-GAAGCUC------------------------------------UUGUGGCCAA-G----GC---G--A-AGUGGU-----------------GU-AAAUCCG-GCGGUUG--U-GCG-GCGAAG-----G-AGU-G-----UGU---UC
BABA01006580.1/1045-1218     UCCUCG---G-UGA-CUUG-G--A-AUC-CGAA-GGA-----------------------AGCUGG-C-------G-GC-AAAAUCUC-G-A--CCUUA---------------------CGGACAG-GAA-C--UG--CA-UA-AAAGG---C-U-GU-ACA--UG-GA---GGACAAA-G-------------------------------C-UGCA--AA-------------------U----CAAGUU-UAAGUCC-----------------------UAUA----------ACUAUCCGA-A----UC-CAAGUA-U----G-----------------GU-AAAUGCA-GAGGACACAU-GAG-AUGAAA-----G-C-G-U-----ACU---UC
ABDH01040768.1/724-927       --CACU---G-CUA-AAU-------CUC-AACC-GGA-----------------------CGCC---A-------U-GC-ACAAUU---G-U--UCCGUACUUCAUGC--ACGUUUUAUG------------C--CG--UAGUA-UUCAG---C-A-AA-AGC--AA-GG-C-GGAUAAG-U-------------------------------U-U-CC--AU-------------------A---ACAAAAC-AAAAUCCAAAAAGGCCG---GACUGCCAUUGGCCUCCG-ACUUUACUGCCCGA-A----CC-UUGC-A-A----U-----------------GU-AAAUGCG-GCGGCCACAU-GGA-AUGAAG-----G-U-U-A-----CCG---AC
BABC01004326.1/82-257        CCUAUC---G-UGA-GGUAA-----AUC-UGAA-GGA-----------------------AGUCGG-C-------G-GC-AAACCUUU-G-AGUUCUGA---------------------GGAACAC-GAAGU--CA--CA----UGAGG---C-U-UA-AUU--UA-CU---GGGUAAG-C-------------------------------U-AGCC--UA-------------------A----CGAAGC-AGAGCCC-----------------------AAUA---------GCUCAUCCG-------AG---AACU-CUUUAU-----------------GU-AAAUGUGCGCAGAUAGAU-GAC-UGGAAA-----G-U-G-U-----ACG---UU
BABB01003816.1/2-167         --CAUC---G-UGA-GGUG------AAU-CGAA-GGG-----------------------AGCCCU-A-------G-GC-AAACCGUG-G-G--UCCGA---------------------CGAACAG-GAA-C--CG--CA----UCAGG---C-AUAU--GG--GA-GU---GGGUAAG-G-------------------------------U-GCCC--AA-------------------A----GAAACU-GAAGCCCC--------------------AA--------------GCUAUACGG-A----AC-UCUC-G-G----U-----------------GU-AAAUGCG-GCGGAUAGAU-GAC-GGGAAA-----G-A-U-U-----GUG---UU
BABF01010335.1/320-151       UUCAUC---G-CGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCUGG-A-------U-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GU----UAAGG---C-G-GC--GC--AG-CA---GGGUAAG-G-------------------------------U-GGCA--CU-------------------A----AUCACC-AAAGCCC-----------------------GAUA---------CUCACACGGA-A----CG-CUGU-G-A----C-----------------GU-AAAGCCG-ACAGGCAUA--AGC-AG--CG-----GAUCU-C-----UCA---AC
ABEF01054409.1/3816-3988     UCCACC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGC-A-------G-GC-AAAGCGCU-G-G--CCCGA---------------------CGAACAG-GAA-U--CG--CA-UA-CGAGG---C-G-GU--CA--CA-CC---GGGUGAG-A-------------------------------C-GGCC--AA-------------------U----AUCGUC-AAAGCCCAG------------------UACUUGC----------ACGGAC---------GG-UGUG-G-A----C-----------------GU-AAAUGCG-GCGGGUAUA--AGU-GUGACG-----G-U-C-A----CGCG---UC
ABEF01047012.1/325-153       UCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGA-A-------G-GC-AAAGCACU-G-G--CCUGA---------------------CGAACAG-AAA-C--CG--UA-UA-CGAGG---C-G-GC--CG--UC-GC---GGGUGAG-A-------------------------------A-GGCC--CA-------------------U----AUCUUC-AAAGCCC-----------------------GGUA---------CUUGCACGGA-A----GC-GGCG-G-A----C-----------------GU-AAAUGCG-GCGGGCAUA--AGU-GUGAAG-----G-U-CGC-----GCG---UC
BAAX01024110.1/737-566       UCCGUG---G-UGA-CGCG-G--A-AUC-UGAA-AGA-----------------------AGUCAG-C-------G-GC-AAAGAUCU-G-A--CCCGA---------------------CGCACAG-AAA-C--UU--GA-UA-UAAGG---C-U-AC--UU--AC-AG---GGAAAAG-G-------------------------------C-UGCA--AA-------------------A----AGAGUC-AAAGUCC-----------------------AAGA---------ACUACUCGGA-A----CA-GCAU-G-U----A-----------------GU-AAAUCAA-GUGGGUAUA--AGA-UGGAAA-----G-A-C-A-----AUA---UG
BAAU01003521.1/497-669       UCUAUC---G-UGA-GGUA-G--A-AUC-UGAA-GGA-----------------------AGUCAG-C-------G-GC-AAACAUCU-G-G--UCUGA---------------------CGGACAG-AAA-U--CC--GA-UA-UAAGG---C-C-UA-AGG--GU-GA---GGAUGAG-U-------------------------------C-UGCU--GA-------------------U----GAAGAC-AAAGUCC-----------------------GAUA----------ACUAUCCGA-A---AUC-ACCC-A-A----G-----------------GU-AAAUCGG-GCAGAUAUA--AGA-UGGAAA-----G-A-G-U-----AUG---UC
BAAX01001729.1/1065-894      UCCACC---G-CGA-GUUG-G--A-AUC-UGAA-AGA-----------------------AGCCGG-C-------G-GC-AAACAUCU-G-A--CCUAA---------------------CGGACAG-AAA-C--UU--CA-UA-CAAGG---C-A--U-AUG--AC-CG-U-GGGUAAG-G-------------------------------U-UGCA--AA-------------------A----AGAACC-AAAGCCC-----------------------UAUA---------GCUAUUCGGA-A----CG-GUCG-G------U-----------------GU-AAAUGAA-GUGGGUAUA--AGA-UGGAAA-----G-A-C-A-----AUG---CC
BAAX01021590.1/472-643       UUCAUC---G-UGA-GGUG-A--A-AUC-UGAA-AGA-----------------------AGCCGG-U-------G-GC-AAACAUCU-G-A--CCUAA---------------------CGUACAG-AAA-C--UU--CA-UA-CAAGG---C-AUAU--GA--CC-GU---GGGUAAG-G-------------------------------U-UGCA--AC-------------------A----CAGACC-AAAGCCC-----------------------CAUA----------GCUNUUCGG-A----AC-AGUC-G-G----U-----------------GU-ACAUGAA-GUGGGUAUA--AGA-UGGAAA-----G-A-C-A-----AUG---CC
BAAX01006391.1/326-155       UCCAUC---G-UGA-GUUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-C-------G-AC-AAAUAUCU-G-A--CCUAA---------------------CGGACAG-AAA-C--UU--CA-UA-UAAGG---C-AUGU--GA--CC-GU---GGAUAAG-A-------------------------------U-UGCC--UA-------------------A----CAAAUC-AAAGUCC-----------------------AAUA----------GCUAUUCGG-A----AC-GGUC-G-G----U-----------------GU-AAAUGAA-GUAGGCAUA--AGA-UGGAAA-----G-A-C-A-----AUG---CC
BAAX01026393.1/597-768       UCCACU---G-CGA-GGUG-G--A-AUC-UGAA-AGA-----------------------AGCUGG-C-------G-GC-AAACAUCU-G-A--CCUAA---------------------CGUACAG-AAA-C--UU--CA-UA-UAAGG---C-A-UU--UG--AC-CA-U-GGAUGAG-A-------------------------------U-UGCC--AG-------------------A----CAAAUC-AAAGUCC-----------------------CAUA---------GCUUUUCGGA-A----UG-GUUG-G------U-----------------GU-ACAUGAC-GUGGGUAUA--AGA-UGGCAA-----G-A-A-A-----UAG---CC
BAAY01007749.1/313-493       UCCAUC---G-AGA-GGCG-G--A-GUC-UGAA-GGA-----------------------AGCUGGAUGCCAGCGG-GC-AAACUCCC-G-A--ACCGA---------------------CGAACAG-AAA-U--CA--CA-UA-GUAGA---C-C-GU-AGA--GG-AA-C-GGACGAG-U-------------------------------G-UGCA--UA-------------------A----CAACAC-AAGAUCCA---------------------A-------------UGCUGCCCGA-A----UC-CCGU-G-C----G-----------------GU-AAAUGUG-GCGGUUAUGU-GGA-AGAAAAAA-AGG-C-G-G-----C-------
BAAW01000769.1/1804-1632     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAC-GGA-----------------------AGCCUA-A-------G-GC-AAAGCCUU-G-G--UCUGA---------------------GGUACAC-GAA-U--CA--CA-UU-UGAGG---C-U-CA-AAG--CU-AU---GGGUAAG-C-------------------------------U-UGCA--CG-------------------A----CAAAGU-AAAGCCC-----------------------UAUA----------ACUAUCAGA-A----AU-AGCU-A-G----A-----------------GU-AAUUGCG-GCAGAUAGAU-GAG-GUGAAA-----G-U-G-C-----AUG---UU
BAAW01000650.1/507-679       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCUA-A-------G-GC-AAAGCCUU-G-G--UCUGA---------------------GGUACAC-GAA-U--CA--CA-UU-UGAGG---C-U-CA-AAG--CU-AU---GGGUAAG-C-------------------------------U-UGCA--CG-------------------A----CAAAGU-AAAGCCC-----------------------UAUA----------ACUAUCCGA-A----AU-AGCU-A-G----A-----------------GU-AAAUGUG-GCAGAUAGAU-GAG-GUGAAA-----G-U-G-C-----GUG---UU
BAAZ01024986.1/598-401       UCCAUC---G-UGA-GGUG-G--A-AUU-UGAA-GAAAGCCGGAUUUUGGGAGUUGAAAGGUCUCC-CAA---UGG-GC-AAAACUUU-G-G--CCUGA---------------------CGAACAG-AAA-U--UG--CA-UA-UAAGG---C-C-GU--CA--GC-GA---GGGUAAG-U-------------------------------U-UGCA--UA-------------------A----CAAAAC-AAAGCCC-----------------------AGUA---------GCUACACGGA-A----UC-GCUU-U-C----G-----------------GU-AAAUGCG-GCAGGUA-A--AGA-GGGAAA-----G-A-A-U-----GUG---UG
BAAZ01000006.1/4724-4527     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GAAAGCCGGAUUUUGGGAGUUGAAAGGUCUCC-CAA---UGG-GC-AAAACUCU-G-G--CCUGA---------------------CGAACAG-AAA-U--CG--CA-UA-UAAGG---C-C-GU--CA--GC-GA---GGGUAAG-U-------------------------------U-UGCA--UA-------------------A----CAAAAC-AAAGCCC-----------------------AGUA---------GCUACACGGA-A----UC-GCUU-U-C----G-----------------GU-AAAUGCG-GCAGGUA-A--AGA-GGGAAA-----G-A-A-U-----GUG---UG
BAAZ01000126.1/5519-5716     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GAAAGCCGGAUUU--UGGGAGUUGAAAGGUCU-CCCA-AUGG-GC-AAAACUCU-G-G--CCUGG---------------------CGAACAG-AAA-U--CG--CA-UA-UAAGG---C-C-GU--CA--GC-GA---GGGUAAG-G-------------------------------U-UGCA--UA-------------------A----CAAAAC-AAAGCCC-----------------------AGUA---------GCUACACGGA-A----UC-GCUU-U-C----G-----------------GU-AAAUGCG-GCAGGUA-A--AGA-GGGAAA-----G-A-A-U-----GUG---UG
BABD01031468.1/250-53        UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GAAAGCCGGAUUUUGGGAGUUGAAAGGUCUCC-CAA---UGG-GC-AAAACUCU-G-G--CCUGA---------------------CGAACAG-AAA-U--CG--CA-UA-UAAGG---C-C-GU--CA--GC-GA---GGGUAAG-U-------------------------------U-UGCA--UA-------------------A----CAAAAC-AAAGCCC-----------------------AGCA---------GCUACACGGA-A----UC-GCUU-U-C----G-----------------GC-AAAUGCG-GCAGGUA-A--AGA-GGGAAA-----G-A-A-U-----GUG---CG
BABA01029713.1/479-677       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GAAAGCCGGAUUUUGGGAGUUGAAAGGUCUCC-CAA---UGG-GC-AAAACUCU-G-G--CCUGG---------------------CGAACAG-AAA-U--CG--CA-UA-UAAGG---C-C--G-UCA--GC-GA---GGGUAAG-G-------------------------------U-UGCA--UA-------------------A----CAGAAC-AAAGCCCA---------------------GUAGC----------UACACGGGA-A----UC-GCUUUC-C----G-----------------GU--AAUGCG-GCAGGUC-A--AGA-GGGAAA-----G-A-C-U-----GUG---UG
BAAV01015115.1/784-619       UCUAUC---G-CGA-GGUA-G--A-AUC-UGAA-GGA-----------------------AGCUGU-A-------A-GC-AAAUCUCU-G-G--UCCGA---------------------CGAACAG-AAA-U--CA--CA-UA-UAAGG---C-UAGG--CU--ACGAG---AGAUAAG-U-------------------------------U-GGCG--UG-------------------A----AGCAAC-GAAGUCUAAU-----------------AACUAUC----------ACCUUUGG-------CU-GU---U-C----------------------GU--UUCGUU-ACGGA----U-GGA-----AU-----G-G-A-U-----AUA---UU
BABD01001136.1/2158-2334     UUCACC---G-UGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGUCGU-U-------G-GC-AAAUCUCU-G-G--UCCGA---------------------CGGACAG-AAA-C--CG--CA-UA-CAAGG---C-UAGG--CU--AC-GA-G-AGAUAAG-U-------------------------------U-GGCA--UA-------------------A----AGCAAC-GAAGUCU-----------------------AAUA----------ACUACCACA-U----UU-GUGG-U-AGCAGA-----------------GU-AAAUGCG-GUGGAUGAAU-AAA-UU-AAA-----G-A-U-U-----GCA---GU
BAAY01003967.1/345-524       UCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCUGU-A-------A-GC-AAAUCUCC-G-G--UCCGA---------------------CGGACAG-AAA-U--CA--CA-UA-UAAGG---C-U-AG--GC--UACGA-G-AGAUAAG-U-------------------------------U-GGC---AA-------------------A---GAACAAC-GAAAUCUAAU-----------------AACUAUC----------ACUUUUGUA-G-------UAGC-A-G----A-----------------GU-AAAUGUG-GCGGAUAUAU-GGA-GAGAAAG---AG-C-G-A-----GCA---CC
BAAZ01007913.1/690-862       UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-C-------G-GC-AAACUUCC-G-G--UCUGA---------------------CGGACAG-AAA-U--CA--CA----UAAGG---C-A-UG--AU--AG-GA-U-GGGUAAA-G-------------------------------C-UGCG--UC-------------------G----AAAGCU-GAAGCCCG---------------------AAAGC----------UAAUCCGGA-A----UC-CCAU-G-G----U-----------------GU-GCAUGUG-GCAGAUAGAU-GGA-AGGAAA-----G-A-A-C-----CUG---UU
BABG01000233.1/1668-1498     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGGUGG-A-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UCAGG---C-U-AC-AGU--UA-A----GGAUAAG-A-------------------------------U-UGCA--AU-------------------U----CAAAUC-GAAGUCC-----------------------AAUA----------ACUACUCGG-G----AU-UAACUG-U----G-----------------GU-AAAUGUG-GCAGAUAGAU-GGA-GAGAAA-----G-A-A-A-----CGU---GU
BAAU01008431.1/39-209        GCCAUC---G-UGA-GGUG-G--A-AUU-CGAA-GGA-----------------------AGGUGG-A-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UCAGG---C-U-AC-AGU--UA-A----GGAUAAG-G-------------------------------U-UGCU--AU-------------------A----CAAACU-AGAGUCC-----------------------AAUA----------ACUACUCGG-A----AU-UAAUUG-U----G-----------------GU-AAAUGUG-GCAGAUGGAU-GGA-GAGAAA-----G-A-A-A-----CGU---GU
BABA01025377.1/375-545       UCCAUU---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGGUGG-A-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGUACAG-AAA-U--CA--CA----UCAGG---C-U-AC--AG--UU-GA---GGAUAAG-G-------------------------------C-UGCA--UA-------------------A----CAAACC-AAAGUCC-----------------------AAUA---------ACUACUCGGA-A----UC-AACU-G-U----A-----------------GU-AAAUGUG-GCAGAUAUAU-GGA-GAGAAA-----G-A-A-A-----CGU---GU
BABA01010263.1/538-368       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------GGCUGU-A-------A-GC-AAAUCUCU-G-G--UCUGA---------------------CAAACAG-AAA-U--CA--CA----UCAGG---U-U-GC--AG--UU-AA---GGAUAAG-G-------------------------------U-GGCU--AU-------------------A----CAAACU-AAAGUCC-----------------------AAUA---------ACUACUCGGA-A----UU-AGCU-G-U----A-----------------AU-AAAUGUG-GCAGAUAUAU-GGA-GAGAAA-----G-A-A-G-----UGU---GU
BAAX01034878.1/611-782       UCCAUC---G-UGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGGUCG-A-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UAAGG---C-U-AG--UC--AU-GG---GGAUAAG-G-------------------------------C-CGCC--UA-------------------A----CAGGUU-GAAGUCC-----------------------CAUA---------GCUACACGGA-A----CC-AUGA-A-U----A-----------------GU-ACAUGUG-GCAGACACAU-GGA-GAGAAA-----G-AGU-G-----CGU---UC
BAAV01001266.1/2173-2002     UCCAUC---G-UGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGGUCG-A-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UAAGG---C-U-AG--UC--AU-GG---GGAUAAG-G-------------------------------C-CGCC--AA-------------------A----CAGGUU-GAAGUCC-----------------------CAUA---------GCUACACGGA-A----CC-AUGA-A-U----A-----------------GU-AUAUGUG-GCAGACACAU-GGA-GAGAAA-----G-AGU-G-----CGU---UC
BAAV01028780.1/6-179         UCCCUC---G-UGA-GAUG-G--A-AUC-UCUA-UAG-----------------------AGGUCC-A-------G-GC-GUAUCUCU-G-G--UCUGA---------------------CGAACAA-AAC-U--CA-UCA----UAACG---U-U-AU--UC--AU-GG---GGAUUAG-G-------------------------------C-CGCC--GA-------------------A---CAUUGUU-GAACUCC-----------------------CUUA---------CCUACACUGA-A---CUC-AUGA-A-U----A-----------------UU-ACAUGUG-GCAAACACAU-GGA-GAGAAA-----G-A-G-U-----GCG---UU
BAAV01030018.1/889-695       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGAAGCUGGAUAUGGGGAACAUACUAACCCAU-G-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UCAGG---C-U-AU--GC--AU-GA---GGGUAAG-A-------------------------------C-UGCG--AU-------------------A----CAAGUU-GAAGCCC-----------------------UAUA---------ACUACACGGA-A----UC-AUGU-A-U----G-----------------GU-AAAUGUG-GCAGAUGGAU-GGA-GAGAAA-----G-A-AAC-----GUG---UG
BAAV01030017.1/500-694       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGAAGCUGGAUAUGGGGAACAUACUAACCCAU-G-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UCAGG---C-U-AU--GC--AU-GA---GGGUAAG-A-------------------------------C-UGCG--AU-------------------A----CAAGUU-GAAGCCC-----------------------AAUA---------ACUACACGGA-A----UC-AUGU-A-U----G-----------------GU-ACAUGUG-GCAGAUGGAU-GGA-GAGAAA-----G-A-AAC-----GUG---UG
BABG01006704.1/228-31        UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGAAGCUGGAUGUGAGGAAAAUACUAACUCAU-G-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGGACAG-AAAUU--CU--UA-UA-UGAGG---G-U-AU--GC--AU-GA---GGGUAAG-G-------------------------------U-UGCA--CG-------------------C----CCAAUC-GAACCAC-----------------------AAUA---------ACUACACGGA-A----UC-AUGC-A-U----G----------------A-U-AAAUGAG-GCAGAUGGAUGGGA-GAGAAA-----A-A-A-C-----GUG---UG
BAAY01028426.1/644-840       UCCAUC---G-UGA-GAUG-G--A-AUC-UGAA-GGAAGCUGGAUGUGAGGAAUAUACUAACUCAC-G-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CU--CA-UA-UGAGG---U-C-AU--GC--AU-GU---GGGUAAG-G-------------------------------C-AGCA--AG-------------------C----CAUGUU-GAAGCCC-----------------------GAUA---------ACUACCCGGA-A----UC-AUGC-G-N---UG-----------------AU--AAUGAG-GCCGAUGGAU-GGA-GAGGAA-----G-A-AAC-----GUG---UG
BABG01003417.1/1774-1970     UCCAUC---G-UGA-GAUG-G--A-AUC-UGAA-GGAAGCUGGAUGUGAGGAACAUACUAACUCAC-G-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGGACAG-AAA-U--CU--UA-UA-UGAGG---U-U-AU--GC--AU-GA---GGGUAAG-G-------------------------------U-UGCA--UA-------------------U----CAAAUC-GAAGCCC-----------------------AAUA---------ACUACACGGA-A----UC-AUGC-A-U----G-----------------AU-AAAUGAG-GCAGAUGGAU-GGA-GAGGAA-----G-A-AAC-----GUG---UG
BABG01019423.1/541-736       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGAAGCUGGAUGUGAGGAAUAUACCAACUCAC-G-------G-GC-CAAUCUUU-G-G--UCUGA---------------------CGAACAG-AAA-U--CU--CC-UA-UGAGG---U-C-GU--GC--CU-GU---GGGUUAG-A-------------------------------C-AGCG--AC-------------------C----CCUGUU-UUAGCCC-----------------------CAUU---------ACUACACGGA-A----UC-AUGC-G-U----G-----------------AU-UAAUGAG-GCGGCUUGGU-UGG-GAGGAA-----G-A-A-A-----CUG---UG
ABDH01016325.1/179-1         UCCGUU---G-CGA-GGCG-G--A-AUC-CGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGUUCC-G-G--GCCGA---------------------CGAACAG-GAA-C--CG--CA-UA-UAAGG---C-A-AA-AGC--AA-GG-C-GGACGAG-U-------------------------------U-UGCA--UA-------------------A----CAAAAC-GAAGUCCUAAAAGCCGG--ACUGUUAUAACGACCUCCG--GUUUGCUGCCCGA-A----CC-UUGC-A-A----U-----------------GU-AAAUGCG-GC------------------------G---G---------------
ABDH01034564.1/794-997       UCCACC---G-CGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGUUCC-G-G--GCCGA---------------------CGAACAG-AAA-C--CG--CA-UA-UAAGG---C-G-UU--GC--AA-GG-C-GGAUAAG-U-------------------------------U-U-CC--AA-------------------A---ACAAAAC-AAAGUCCCAAAAGACCGG-CCUGUUAUAAUGACCUCCG-GUCUUACUGCCCGA-A----CC-UUGC-G-A----U-----------------GU-AAAUGCG-GCGGCUAUAA-GGA-AUGAAG-----G-U-U-A-----CCG---AC
ABDH01006954.1/278-60        UCCGUC---G-CGA-GGUG-G--A-AUC-UGAA-GGACGAGAAC---------CCGUAGGGGUCUG-A-------G-GC-AAAGUUCC-G-G--GCCGA---------------------CAAACAG-AAA-C--CG--CA-UA-UAAGG---U-A-AA-AGC--AA-GG-C-GGACGAG-U-------------------------------U-U-CC--UA-------------------A---ACAAAAC-AAAGUCCAAAGGCCGGA--AAGGAAGAGAAUAGAUUUCGGCUGUACUGCCCGA-A----CC-UUGC-A-A----U-----------------GU-AAAUGCG-GCGGUUACAU-GGG-AUGAAG-----G-U-U-A-----UCG---GC
ABDH01036891.1/1195-1399     UCCGCC---G-CGA-GGCG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGUUCC-A-A--GCCGA---------------------CGAACAG-GAA-C--CG--CA-UA-UGAGG---C-A--U-GGC--AA-GG-C-GGACGAG-U-------------------------------U-UGCC--GA-------------------A----CAAAAC-GAAGUCCAAAAGGCCGGG-GAGUAAGAGAAUAAACCCCGACCGUACUGCCCGA-A----CC-UUGC-A-G----U-----------------GU-AGAUGCG-GCGGCCGCAU-GGA-AUGAAG-----G-U-U-A-----UCG---GA
ABDH01035596.1/178-382       UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGUUCC-G-G--GCCGA---------------------CGAACAG-AAA-C--CG--CA-UA-UAAGG---C-A--U-GGC--AA-GG-C-GGACGAG-U-------------------------------U-UGCC--UA-------------------A----CAAAAC-AAAGUCCAAAAGGCCGGA-GAACAAGAGAACAGAUUCCGGCUUUACUGCCCGA-A----CC-UUGC-A-G----U-----------------GU-AAAUGCG-GCGGCUAUAU-GGG-AUGAAG-----G-U-U-A-----CCG---GC
ABDH01035596.1/869-1073      UCCGUC---G-CGA-GGCG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGUUCC-G-G--GCUGG---------------------CGAACAG-AAA-U--CG--CA-UA-UAAGG---C-A-AU--GC--AA-GG-C-GGACGAG-U-------------------------------U-UGC---UA-------------------A---ACAAAAC-AAAGUCCAAAAGGCCGGA-GAGGAAGAGAACAGAUUCCGGUUUUACUGCCCGA-A----CC-UUGC-A-G----U-----------------GU-AAAUGCG-ACGGCUAUAU-GGG-AUGAAG-----G-U-U-A-----CUG---AC
ABDH01001467.1/594-798       UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAAUCCC-G-G--GCCGA---------------------CGAACAG-AAA-U--CG--CA-UA-UAAGG---C-A-UU--GC--AA-GG-C-GGACGAG-U-------------------------------U-UGC---UA-------------------G---GCAAAAC-GAAGUCCCAAAGGCCGGA-GAGGAAGAGAACAGACUCCGACCGUACUGCCCGA-A----CC-UUGC-A-G----U-----------------GU-AAAUGCG-GCGGCUGGAU-GGG-AUGAAG-----G-U-U-A-----UCG---GA
ABDH01003400.1/483-263       UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGACUGGAACC-------CGUAGGGUUCCCAG-A-------G-GC-AAAAUCCC-G-G--GCCGA---------------------CGAACAG-AAA-U--CG--CA-UA-UAAGG---C-A-UU--GC--AA-GG-C-GGACGAG-U-------------------------------U-UGCU--AA-------------------G----CAAAAC-GAAGUCCCAAAGGUCGAA-GAGGAAGAGAACAGACUUUGACCGUACUGCCCGA-A----CC-UUGC-A-G----U-----------------GU-AAAUGCG-GCGGCUGGAU-GGG-AUGAAG-----G-U-U-A-----UCG---GA
ABDH01025731.1/1497-1292     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGUCCC-G-G--GCCGA---------------------CGAACAG-AAA-C--CG--CA-UA-UAAGG---C-A-AU--GC--AA-GG-C-GGACGAG-U-------------------------------U-UGCA--UA-------------------A----CAAAAC-GAAGUCCAAAAAGGCCGGGGAGGAAGAAAACAGACUCCGGUUUUACUGCCCGA-A----CC-UUGC-A-G----U-----------------GU-AGAUGCG-GCGGCUAUAU-GGG-AUGAAG-----G-U-U-A-----UCA---GC
ABDH01030818.1/366-586       UCCAUC---G-CGA-GGAG-G--A-AUC-UGAA-GGACUGGAACC-------CGUAGGGUUCCCAG-A-------G-GC-AAAGUCCC-G-G--GCCGA---------------------CGAACAG-AAA-C--CG--CA-UA-UGAGG---C-A-AU--GC--AA-GG-C-GGACGAG-U-------------------------------U-UGCA--AC-------------------A----CAAAAC-GAAGUCCAAAAGGCCGGG-GAGGAAGAAAACAGACUCCGGUUUUACUGCCCGA-A----CC-UUGC-A-G----U-----------------GU-AGAUGCG-GCGGCUAUAU-GGG-AUGAAG-----G-U-U-A-----UCG---GA
ABDH01037979.1/1396-1192     UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGUCCC-G-G--GCCGA---------------------CGAACAG-AAA-C--CG--CA-UA-UAAGG---C-A-UU--GC--AA-GG-C-GGACGAG-U-------------------------------U-UGCC--GC-------------------C----CAAAAC-GAAGUCCAAAAGGCCGGG-GAGGAAGAGAACAGACCCCGACUGUACUGCCCGA-A----CC-UUGC-A-G----U-----------------GU-AGAUGCG-GCGGCUAGAU-GGG-AUGAAG-----G-U-U-A-----UCG---GC
ABDH01009837.1/515-311       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGUUCC-G-G--GCCGA---------------------CGAACAG-GAA-U--CG--CA-UA-UAAGG---C-A-AU--AC--AA-GG-C-GGACGAG-U-------------------------------U-UGCC--AA-------------------A----CAAAAC-GAAGUCCAAAAGACCGGG-AAGGAAGAGAAGAGAUUCUGGUUUUACUGCCCGA-A----CC-UUGU-A-A----U-----------------GU-AAAUGCG-GCGGCCACAU-GGG-AUGAAG-----G-U-U-A-----UUG---AC
ABDH01036608.1/1436-1237     UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGUCCC-G-G--GCCGA---------------------CGAACAG-AAA-U--CG--CA-UA-UAAGG---C-A-AU--GC--AA-GG-C-GGACGAG-U-------------------------------U-UGC---UA-------------------A---ACAAAAC-GAAGUCCUAAAGACCG----GAUUGUGAAUGACCUCCG--GUUUACUGCCCGA-A----CC-UUGC-A-G----U-----------------GU-AAAUGCG-GCGGCCACAU-GGG-AUGAAG-----G-U-U-A-----UUG---AC
BABF01003176.1/1231-1403     GCAAUC---G-UGA-GGUU-G--U-GGC-UGAA-GGA-----------------------AGUCGG-A-------C-GC-AAACUCCU-G-A--ACUGA---------------------CGAACAG-AAA-C--UA--GA-UA-CAAGG---C-U-GA--AU-UAG-GU-C-GGAUAAG-U-------------------------------C-UUCA--UC-------------------A----CAAGAC-AAAGUCCA---------------------A-------------UACUGCCCGA-A----AC-CUAU-A-C----A-----------------GU-AAAUCUA-GCAGUUACAU-AGG-AGGAAA-----G-U-U-U-----UCA---CU
BABF01006785.1/487-315       GCAAUC---G-UGA-GGUU-G--U-GGC-UGAA-GGA-----------------------AGUCGG-A-------C-GC-AAACUCCU-G-A--ACUGA---------------------CGAACAG-AAA-C--UA--GA-UA-CAAGG---C-U-GA--AU-UAG-GU-C-GGAUAAG-U-------------------------------C-UUCA--UC-------------------A----CAAGAC-AAAGUCCA---------------------A-------------UACUGCCCGA-A----AC-CUAU-A-C----A-----------------GU-AAAUCUA-GCAGUUACAU-GGG-AGGAAA-----G-U-U-U-----UCA---CU
BABG01020043.1/141-313       UUGUCA---G-UGA-UGGC-A--A-GGA-UGGA-GGA-----------------------AGUGGUGU-------A-GUGAUU-CUUUUG-A--GCGUA---------------------CGAACAG-AAA-C--UU--GA-UA-UAAGG---C-U--A-AAU--GG-U----GGAUGAG-A-------------------------------U-UGCA--UC-------------------A----CAAAUC-GAAGUCC-----------------------AAAA---------GGUAAACGUA-A----AA-CCAAGA-C----A-----------------GU-AAAUCAA-GACGUUG--UAAAA-G-AAAG-----A-G-G-A-----UUA---GU
BABF01001090.1/2371-2540     GUAUCA---G-UAA-UGAU-A--U-AGA-UGGA-GGA-----------------------AGUGGUGU-------A-GC-AAAGUUCUUG-A--GCCUA---------------------CGAACAG-AAA-C--UU--GA----UAAGG---C-G--A--UU--AG-GU---GGGGAAG-G-------------------------------C-UGCA--AA-------------------A----CAAGCC-GAAGCCC-----------------------AAAU---------GGUAAACGUA-A----AC-CGAA-G-U----U-----------------GU-AAAUCAA-GAGGUUG--U-GGA-AUGAAA-----G-A-U-U-----AGU---GU
CU928161.2/4643131-4642962   UUCAUC---G-CGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCUGG-A-------U-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GU----UAAGG---C-G-GC--GC--AG-CA---GGGUAAG-G-------------------------------U-GGCA--CU-------------------A----AUCACC-AAAGCCC-----------------------GAUA---------CUCACACGGA-A----CG-CUGU-G-A----C-----------------GU-AAAGCCG-ACAGGCAUA--AGC-AGGAAA-----G-U-C-G-----CGU---GA
AP008232.1/1927621-1927462   GCAAGG---G-UGA-CCGA-G--C-GUG-GGGA-GGA-----------------------AGUGUG-G-------A-GC-GAAACUGC-G-A--GCCAA---------------------UGAACAA-GAA-U--CG--GA-UA-GAAGG---C-G-CUGGUGAGGGCGAGAAACCGUGAAACUCUUGUGGU----------CAAGGCGAGGU------------------------------------------------------------------------------------------------------------G-G----C-----------------GU-AGUUCCG-GCGGUUG--U-GCA-GUGAAG-----G-AGU-G-----CGU---UC
BAAX01033178.1/267-96        UCCACU---G-CGA-GGUG-G--A-AUC-UGAA-AGA-----------------------AGCCGG-C-------G-GC-AAACAUCU-G-A--CCUAA---------------------CGUACAG-AAA-C--UU--CA-UA-UAAGG---C-A-UU-UGA--CC-AU---GGAUGAG-A-------------------------------U-UGCC--AG-------------------A----CAAAUC-AAAGUCC-----------------------UAUA----------GCUAUUCGG-A----AU-GGUU-G-G----U-----------------GU-AAAUGAA-GUGGGUAUA--AGA-UGGAAA-----G-A-A-U-----AAG---CC
CP000471.1/1072808-1072979   UUUACC---G-UGA-GGUA-A--A-AUC-UGAA-GGA-----------------------AACCGA-A-------A-GC-AAAGCGCU-G-A--UCCGA---------------------CGAACAG-GAA-U--CG--CA-UA-CGAGG---C-G-GU--CA--UG-CU---GGAUGAG-G-------------------------------A-GGGG--AC-------------------U----AUCUCU-AAAGUCC-----------------------GAAA---------CCUGUACGGA-G----AG-CAUG-G-A----C-----------------GU-AUAUGCG-GCGGAUAUA--AGC-GUGAAG-----G-U-G-C-----GUG---UG
BABG01015727.1/751-581       UCCAUU---G-UGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGCCUG-A-------G-GC-AAACCAUU-G-G--UCCGA---------------------CGGACAG-AAA-U--CA--UG-UA-UAAGG---C-U-UA--CA--GU-UC---GGAUAAG-A-------------------------------C-UGCU--GA-------------------A----CAAGUU-GAAGUCC-----------------------AAUA----------GCUAACAGA-G----G--ACUG-G-U----A-----------------GU-AGACAUG-GCGGAUAGGU-GAU-GAGAAA-----G-A-U-A-----GCG---UA
ABLK01000025.1/39449-39278   UCGCGG---G-CGA-CUGC-G--A-GUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGCGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GA-UA-AGAGG---C-G-AC--GC--AU-CG---GGGUAAG-G-------------------------------C-AGCC--AU-------------------A----AAGGUC-GAAGCCC-----------------------GAAA---------CUUGCACGGG-A----CG-AUGC-G-G----C-----------------GU-AUAUCCG-ACAGGCAUA--AGC-GUGAAG-----G-U-G-G-----GUG---CG
AL954747.1/2380049-2379881   AAGCCC---G-UGA-GGGA-U--U-GUC-UGGA-GGA-----------------------AGCCGG-A-------GUGCAAGAGGUGC-G-A--GGCGA---------------------CGGACAG-AAA-C--CG--CA-UA-GAAGG---C-C-GA--GG--CA-GG-CGAGGCGAG-C-------------------------------U-GGCA--CA-------------------U----GACAGC-GAAGCCCA---------------------A-------------------CGGU-AC--GCC-GGCC-A-C----G-----------------GU-AAAUGCG-GCGCUUG--U-GCA-CCGACA-----G-U-U-C-----GCG---UU
ABPU01011729.1/397-223       GCGCCC---G-UGA-GGGC-GAUC-AGC-UGAA-AGA-----------------------AGGCUG-U-------A-GCAAAAGGCAC-G-A--CCGUA---------------------GGAACAC-GAA-A--CG--GC--AGAGAGG---C-A-GG--GC--GC-G--GGCGAUGAG-C-------------------------------G-UGCU--AG-------------------G----UAACGC-AAAAUCCA---------------------A-------------CCGUCACCGA-AA--GAC-GCGU-C-A----A-----------------GU-AGAGCCG-UGCGGCA--C-GGG-CCGAAA-----G-U-U-C-----AUG---CA
AACY022491438.1/511-683      UCCAUC---G-UGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGCCGC-A-------G-GC-AAAGCACU-G-G--CCUGA---------------------CGAACAG-AAA-U--CG--CA-UA-UGAGG---C-G-GU--CA--CA-CC---GGGUAAG-G-------------------------------C-GUCA--AC-------------------U----AUCGUC-AAAGCCC-----------------------UGUA---------CUUGCACGGA-A----GG-UGUG-G-A----C-----------------GU-AAAUGCG-GCGGGCAUA--AGU-GUGAAG-----G-U-CAC-----GCG---UC
AAFX01034639.1/572-743       UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGC-A-------G-GC-AAAGCGCU-G-A--CUCGA---------------------CGAACAG-AAA-U--CG--CA-UA-UGAGG---C-A-UG--CA--GU-CU---GGAUGAG-A-------------------------------G-GGCA--AA-------------------U----GUCUUU-AAAGUCC-----------------------AAUA---------CCUGUACGGC-A----AG-AUUG-U-A----U-----------------GU-AAAUGCG-GCGAGUAUA--AGC-GUGAAA-----G-U-G-A-----GAG---CG
AACY023383724.1/466-636      UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCGCAAA-------U-CC-AAAUCGAC-C-A--GCCGA---------------------GGUACAC-AAA-C--GC--UG-UA-UAAGG---C-G-UC-UUU--CU-CC---GGGCGAG-G-------------------------------U-UGCC--UC-------------------A----UAAACC-AAAGCCC--------------------------A---------UCAUUACCAA-G----GG-AGUCUG-G----C-----------------GU-AAACAGC-GCGGUUG--G-GUC-GCCACA-----G-U-U-G-----UUU---GU
AAXY01000055.1/3119-3298     CGUCUC---C-GGA-ACGC-C--G-GCC-GGAA-GUA-----------------------AGCCGC-U-------A-GC-AAAGCUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G-UA--GG--CC-GG---AGGCGAG-U-------------------------------U-GGCA--CA-------------------AG-CCGACGGG-GCGGCCUCCC-----------------GCGAAGCCGC----GUGAUCUA----------AC-GGCC-A-C----C-----------------GU-AAAUGAU-GCAGUUG--C-GCA-GUGACA-----G-U-G-C-----AUG---UU
CP000923.1/2426623-2426451   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGUCGG-C-------A-GC-AGAAUUCC-G-G--GCUGA---------------------UGAACAA-AAA-C--CA--CA-UA-UGAGG---U-UGAC--UU--GG-AG-U-GGACGAA-U-------------------------------U-UGUA--CA-------------------U----CAAAAC-GAAAUCC------------------------AAC----------ACUGCUUGA-G----CU-CCGA-G-C----A-----------------UU-AAAAGUG-GCGGGUAUAU-GGG-AGGAAA-----G-U-U-A-----UCG---UU
AY911856.1/687-860           UCCACU---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGUCUA-A-------G-GC-AAAGUACU-G-C--ACCGA---------------------UGAACAA-GAA-G--UA--GC-UA-UAAGG---C-U-GG-AAC--UA-AC-U-GGAUAAG-A-------------------------------C-UGCA--UG-------------------A----CAAGUU-AAAGUCCA---------------------A-------------CACUACUCGA-A----GU-UACUUU-C----A-----------------GU-AAAGCUA-CCGGUGACAU-GGU-ACGAAA-----G-U-U-A-----AUA---UC
ABFU01000013.1/105385-105558 UCCAUG---G-UGA-CGUG-G--A-AUC-UGAA-GGA-----------------------AGCGAG-C-------G-GC-AAACCUCC-G-G--UCUGA---------------------GGAACAC-GAA-C--UU--CA-UA-UGAGG---C-UAAG--GU--AU-CG-UUGGAUGAG-U-------------------------------U-UGCU--AA-------------------A----CAAAAC-GAAGUCC------------------------------------UUUCUGUCGA-AG--GCG-AUAU-C-A----A-----------------GU-AAAUGGA-GCAGAUAGGU-GGA-GGGAAA-----G-A-U-U-----GCA---UU
BA000040.2/9101532-9101362   GUCAUC---G-UGA-GGUG-G--G-GUC-UGAA-GAA-----------------------AGCGUG-G-------A-GC-AAAGCCGC-G-G--CCCGA---------------------UGGACAA-ACA-C--CG--GA-UAACGAGG---C-C--U-ACC--CG-GC-C-GGACGAG-C-------------------------------G-AGCA--AU-------------------U----GAUCGC-GAAGUCCA---------------------A-------------GGUCAUCAAA-G----GU-CGGG-G-U----G-----------------GU-AAAUUCG-GCGGGCG--U-GCG-GUGAAG-----G-C-G-G-----UCG---GU
AACY023033702.1/513-677      UAAAUC---G-UGA-GAGA-U--A-GUC-UGGA-GGA-----------------------AGCCGC-U-------A-GC-AAAUCUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G--U--AG--GC-UG-A-AGGUGAG-U-------------------------------U-GGCA--CA-------------------A----GACAAC-AAAACCA-------------------------------------UGUGAUCUA-A----CG-GCC--A-C----C-----------------GU-AAAUGAU-GCAGCAG--U-GCA-GAGACA-----G-U-G-C-----AUG---UC
CP000478.1/3922512-3922683   UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGC-A-------G-GC-AAAGCGCU-G-G--CUCGA---------------------CGAAUAG-GAA-C--CG--CA-UA-UGAGG---C-G-GU---C--AU-GC-C-GGAUGAG-A-------------------------------G-GGCC--AA-------------------U----AUCUUC-AAAGUCC-----------------------GAUA----------CCUGUACGG-AA--GGC-GUG--G-G----C-----------------GU-AAAUGCG-GCGGGCAUA--AGC-GUGAAG-----G-U-G-G-----GUG---CG
AAQF01000163.1/3437-3601     GGAACC---G-CGA-GGGA-C--C-GUC-CGGA-GGA-----------------------AGCCGG-A-------GUGC-AAAGCUAU-G-A--GCCGA---------------------CGAACAG-AAA-U--GG--CA-UA-CAAGG---C-C-CA--GC--UU-CC---GGGCAAG-U-------------------------------C-AGCA--CA-------------------A----CAUGAC-GAAGCCC-------------------------------------CGGGUUCA-------GG-AGGU-A-G----G-----------------GU-AAAUGCC-GCGGUUG--U-GUA-GCGACA-----G-A-U-C-----ACG---UU
ABFU01000051.1/137020-137191 CUUAUC---G-UGA-GGUA-A--G-GGC-UGGA-GGA-----------------------AGCGUG-G-------A-AU-AAAAUCUU-G-G--CUUGA---------------------CGAACAG-AAA-C--CU--GA-UACUAAGG---C-U-CU--AC--AA-AG---GGAUAAG-G-------------------------------C-UCCA--UA-------------------A----CAAGUC-AAAGUCC-----------------------AAAA---------GAUGUGCGUA-A----CU-UUGU-A-G----G-----------------GU-AAAUCAG-GCAAGUA-A--AAG-AGGAAG-----G-A-U-A-----GUU---GU
CP001078.1/1933621-1933459   UCAAGC---A-UGA-GGUU-A--A-AUC-UGAA-GGA-----------------------AGACCA-A-------G-GC-AAA-CCUU-G-G--UCUGA---------------------GGUAUAC-GAA-U--CA--CA-UU-UGAGG---C-U-CA-AAC--CU-AU---GGGUAAA-C-------------------------------U-UGCU--AA-------------------A----CAAAGU-AAAGCCU-----------------------UACA----------ACUAUCAGA-A----AU-AGCU-A-G----A-----------------GU-AAAUGUG-ACAGGUU--U-GA-------------G-C-A-A-----ACU---UA
ABSP01048056.1/620-790       GCGGUC---G-UGA-GACCCG--U-CGC-UGAA-GGA-----------------------AGCGGG-G-------A-AC-GAACCGGC-G-G--GCCGA---------------------CGAACAG-AAA-C--CG--GA-UA-CGAGG---C-G-GU-GCC--GA-GC-A-GGGCGAG-C-------------------------------G-GGCG--UA-------------------U----GACCGN-GAAGCUC------------------------------------UCGUGACCAA-A----GA-UCGGUG-G----C-----------------GU-AGAUCCG-GCGGUCG--U-GCA-GGGAAG-----G-C-C-A-----GUG---UU
AAQL01011925.1/1446-1616     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGGUGG-A-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UCAGG---C-U-AU-AGU--UA-A----GGAUAAG-G-------------------------------U-UGCC--AA-------------------A----CAAACC-AAAGUCC-----------------------AAUA----------ACUACUCGG-A----AU-UAACUG-U----A-----------------GU-AAAUGUG-GCAGAUAUAU-GGA-GAGAAA-----G-U-G-A-----CGU---GU
AAOX01000004.1/98159-97985   UCCAUG---G-CGA-CGUG-G--A-AUC-UGAA-GGA-----------------------AGCCCU-A-------G-GC-AAAUCCUC-G-G--UCUGA---------------------GGUACAC-GAA-U--CA--CA-UU-UGAGG---U-G-GA-CUG--UU-UC-A-GGACGAG-U-------------------------------U-UGCA--AA-------------------A----CAAAAC-AAAGUCC-----------------------AAAA---------UAUCCCCGGA-U----GG-AACA-G-A----C-----------------AU-AAAUGUG-GCAGAUAUAU-GAG-GAGAAA-----G-U-G-G-----AUG---AA
AACY020363614.1/1041-871     UCCUUC---G-CGA-GGGG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-C-------G-GU-AAAUCUCU-G-G--CCUGA---------------------CGCACAG-AAA-U--CG--AA----UGAGG---C-C-GU-UGG--AU-GU---GGGUGAG-U-------------------------------C-UGCA--UA-------------------A----CAAGAC-AAAGCCCU--------------------AA--------------ACUAUCCGA-A----AC-AUUCCG-C----G-----------------GU-AGAUUCG-ACAGGUAUAU-GGA-GAGAAA-----G-U-U-C-----ACG---UU
AAPR01000002.1/105150-105345 CCAACC---A-UGA-GGUU-G--G-GAC-UGAA-GAUUAUUUGUG-------AUUGAUUAAUGAGC-AAAUACCGCUAC-AAAACUAG-G-U--ACUGA---------------------CGGACAG-AAA-C--CG--UA-CA-CGAGG---C-A-UU-UAU--GC-AC---GGGUAAG-C-------------------------------A-ACCA--AA-------------------U----CAUUGU-AAAGCCC-----------------------AAAG----------AAUGCCAAA-A----GU-GUAUUA-A----U-----------------GU-AGAUACG-GCAGGAA--U-CGA-GUGAAA-----G-A-A-G-----AUG---UA
CP000930.2/1676893-1677065   UCCGCC---G-CGA-GGCG-G--A-AUC-UGAA-GGA-----------------------AGCCAG-C-------G-GC-AAACCUCC-G-G--CCCGA---------------------GGACCAC-GAA-C--CC--CA-GG-UGAGG---C-U-AG--CG--GC-AG-UUGGAUGAG-C-------------------------------U-UGCC--GA-------------------A----CAAAGC-GAAGUCC------------------------------------UUGUCACCGA-AG--GCU-GCCG-A-G----A-----------------GU-AAAUGGG-GCGGGUAGAU-GGA-GGGAAA-----G-G-C-A-----ACG---UU
ABCP01000005.1/147368-147194 AUCAUU---G-UGA-GGUG-G--G-GUC-UGAA-GGA-----------------------AGCCCA-A-------U-CC-AAAGCUGC-G-G--GGCGA---------------------CGAACAG-GAA-C--CU--GA-UA-CGAGG---U-G-UG--GU--AC-AUCCGGGGCGAG-C-------------------------------G-GGCA--CG-------------------U----GACCGC-GAAGCCC-----------------------UCCA----------ACUGCGACC-GG--GGU-GUGC-U-U----U-----------------AU-AAAUCAG-GCGUCCA--C-GCA-GCGACA-----G-U-U-U-----UGU---GU
ABIY02000077.1/12313-12141   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-AGA-----------------------AGCUGG-C-------G-GC-AAACAUCU-G-G--UCUGA---------------------CGAACAG-AAA-C--UU--CA-UA-UAAGG---C-A-UA-AAA--AC-CG-U-GGGUAAG-G-------------------------------U-UGCU--AC-------------------C----CAAACC-AAAGCCC-----------------------UAUA---------GCUAUUCGGA-A----CG-GUU--A-A----U-----------------GU-AGAUGAA-GCAGACAUA--AGA-UUGAAA-----G-U-U-A-----AUA---CC
AACY022219196.1/516-686      AAACCC---G-CGAAGGG--A--U-GUC-UGGA-GGA-----------------------AGCCCA-A-------GCGC-AAAGGUGC-G-A--GCCGA---------------------CGGACAG-AAA-C--CG--CA-UA-GAAGG---C-U-CA--GU--CC-CU---GGGUGAG-U-------------------------------C-AGCA--CG-------------------A----GGUGAC-GAAACCCA---------------------UCAGG----------GCAAGACGC-U----CG-GCAC-G-U----C-----------------GU-UCUCGC---CUGCUG--C-GCA-CUCGAA-----C-C-C-A-----UGG---AG
AAGA01007726.1/109-273       UAAAUC---G-CGA-GAGA-U--A-GUC-UAGA-GGA-----------------------AGCCGC-U-------A-GC-AAAUCUGU-G-A--GCUGA---------------------UGAACAA-AAA-C--AU--CA-UA-UGAGG---C-G-UA--GG--CU-GG---AGACGAG-C-------------------------------U-AGCA--CA-------------------A----GAUAGC-GAAGUCA-------------------------------------UGUGAUCUA-A----C--GGCC-A-C----C-----------------GU-AAAUGAU-GCAGUUG--U-GCA-GAGAAA-----G-U-C-G-----AUG---CA
ACJM01000004.1/93719-93549   UCCACC---G-UGA-GGUG-G--A-GUG-UGAA-GGA-----------------------AGGCGG-C-------G-GC-AAAUCUCC-G-G--CCUGA---------------------CGAACAG-AAA-U--CG--UA----UCAGG---C-G-CA--AA--UU-GA---GGAUAAG-G-------------------------------C-UGCC--AA-------------------A----CGAGUC-GAAGUCC-----------------------AAUA---------GCUACACGGA-A----UC-AAUU-U-G----U-----------------GU-AAAUGCG-GCAGGUAGAU-GGA-GAGAAA-----G-A-C-U-----GCG---UU
ABIC01000047.1/11994-11830   UUAUCC---G-UGA-GGGU-U--G-GUC-UGAA-GGA-----------------------AGCCGC-U-------A-GC-AAAUUUGC-G-A--GCUGA---------------------UGAACAA-AAA-U--AU--CA-UA-UGAGG---C-G-UA--GG--CU-AG---AGGUGAG-U-------------------------------U-GGCA--CA-------------------A----GACGAC-GAAACCA-------------------------------------CGUGAUCUA-A----U--GGCC-A-C----C-----------------GU-AAAUGAU-GCAGCAG--U-GCA-AAGAAA-----G-U-U-C-----AUG---UU
CP000764.1/2269381-2269209   UCCGUG---G-UGA-CGCG-G--A-AUC-UGAA-GGA-----------------------AGUCGG-C-------G-GC-AAAUCUCC-G-G--UCUGA---------------------GGAACAC-GAA-C--UU--CA-UA-UGAGG---C-C-AG-GUA--UC-AU-U-GGAUGAG-A-------------------------------U-UGCU--AA-------------------A----CAAAUC-AAAGUCC-------------------------UU----------ACUGCCAAA-G----GU-GAUA-C-A----G----------------AGU-AAAUGAA-GCAGAUAGGU-GGA-GAGGAA-----G-A-A-U-----AUG---UG
ABQR01000114.1/85-255        GUAUCA---G-UAA-UGGU-A--U-AGA-UGAA-GGA-----------------------AGUGGUGU-------A-GC-AAAGUUCUUG-A--GCCUA---------------------CGUACAG-AAA-C--UU--GA----UAAGG---C-G--A--UG--AG-GU---GGGUAAG-G-------------------------------U-UGCU--AG-------------------A----CAAACC-AAAGCCC-----------------------CAAA---------GGUAAACGUAUA----AC-CGAA-G-U----U-----------------GU-AAAUCAA-GAGGUUG--UG-GA-ACGAAA-----G-A-U-G-----AGU---GU
ABCC02000057.1/83641-83473   CAUAUC---G-UGA-GAUG-U--G-GGC-GAGA-AGA-----------------------AGGGAU-A---------GC-GAAAUCGU-A-G--CCCUA---------------------CGGACAG-AAA-C--CU--GA-UAAUAAGG---C-G-UG--CA--UG-GC---GGGUAAG-U-------------------------------U-GGCU--UA-------------------A----AGCAAC-GAAGCCC-----------------------UAAA---------GGUAGCCGUA-A----CC-UAUG-U-G----C-----------------GU-AAAUUAG-GAGGGUA--G-ACG-AGGAAA-----G-A-A-C-------A---CG
CP000270.1/3159063-3158893   AUGAGG---G-CGA-CCGA-A--U-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GC-GAAACUGC-G-A--GCCGA---------------------UGAACAA-GAA-C--CG--GA-UA-GAAGG---C-G-UU-GCC--GA-CC-A-GGGCGAG-C-------------------------------G-CGCA--AA-------------------G----AAGCGU-AAAGCUC-------------------------------------UCGUGAUCA-A----GG---GG-A-GAUGGC-----------------GU-AGAUCCG-GCGGUUG--U-GCA-GUGAAG-----G-AGU-G-----CGU---UC
AAGA01002440.1/559-387       UCCAUG---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AACUGG-C-------G-GC-AAAGUCCU-G-G--CCUGA---------------------CGGACAG-AAA-C--UA--CA-UA-UAAGG---C-C-AA-AGU--UG-UC-C-GGAUAAG-G-------------------------------U-UGCA--CA-------------------C----CAAACC-AAAGUCCA---------------------A-------------UACUGCUCGG-A----GA-CAAC-A-U----G-----------------GU-AAAUGUA-GCAGGUAGAU-GGG-AUGAAA-----G-U-U-A-----UCG---UU
ABIC01000057.1/19077-19241   UUAUCC---G-UGA-GGAU-U--G-GUC-CGAA-GGA-----------------------AGCCGC-U-------A-GC-AAAUUUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G-UA--GG--CU-AG---AGGUGAG-U-------------------------------U-GGCA--CA-------------------A----GACGAC-GAAACCA-------------------------------------CGUGAUCUA-A----U--GGCC-A-C----C-----------------GU-AAAUGAU-GCAGCAG--U-GCA-AAGAAA-----G-U-U-C-----AUG---UU
ABQR01000115.1/78-247        GUAUCA---G-UAA-UGAU-A--U-AGA-UGGA-GGA-----------------------AGUGGUGU-------A-GC-AAAGUUCUUG-A--GCCUA---------------------CGAACAG-AAA-C--UU--GA----UAAGG---C-G--A--UU--AG-GU---GGGGAAG-G-------------------------------C-UGCA--AA-------------------C----CAAGCC-GAAGCCC-----------------------AAAU---------GGUAAACGUA-A----AC-CGAA-G-U----U-----------------GU-AAAUCAA-GAGGUUG--U-GGA-AUGAAA-----G-A-U-U-----AGU---GU
ACBW01000261.1/1-169         AUC------G-CGA-GUUG-G--A-AUC-UGAA-AGA-----------------------AGCUGG-C-------G-GC-AAACAUCU-G-G--UCUGA---------------------CGGACAG-AAA-C--UU--CA-UA-UAAGG---C-A-UA-AGA--CU-GU---GGGUAAG-G-------------------------------U-UGCA--AA-------------------G----CAAACC-AAAGCCC-----------------------UAUA----------GCUAUUCGG-A----AU-AGUC-A-A----U-----------------GU-AAAUGAA-GCAGACAUA--AGA-UUGAAA-----G-U-U-A-----AUA---CC
ABPW01005870.1/202-375       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCGUA-A-------G-AC-AAACCUCG-G-A--CUUGA---------------------CGAACAG-AAA-U--CG--GA-UA-GAAGG---C-C-CUGGGC--AG-CG---GGGUAAC-C-------------------------------C-AGCA--AU-------------------G----GAUGGG-GAGGCCC-----------------------AAUA---------GUCGUCCGGA-A----CG-CUGCGG-G----G-----------------GU-AGAUCCG-GCGAGCA--C-CGA-GGGAAA-----G-A-G-G-----GAU---GA
CP000879.1/461977-461804     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCCA-A-------G-GC-AAAGUCCC-G-G--UCCGA---------------------UGAAUAA-GAA-C--CA--GA-UA-CAAGG---C-U-AA--GU--GA-AG-U-GGACGAG-U-------------------------------U-UGCU--UU-------------------A----CAAAAC-GAAGUCC-----------------------AAUA---------GCUACCCAGA-A----CU-UCAC-G-G----A-----------------GU-AAAUCUG-GCGGAUAGAU-GGG-AUGAAA-----G-U-U-A-----UUG---CA
CP000270.1/3578056-3578226   AUGAGG---G-UGA-CCGA-G--U-GUG-GGAA-GGA-----------------------AGCGUGGA-------GCGC---AACUGC-G-A--GCCGA---------------------UGGACAA-GAA-C--CG--GA-UA-GAAGG---C-G-GU--GC--CG-AG-CAGGGCGAG-C-------------------------------G-GGCA--GA-------------------A----AACCGC-GAAGCUC-------------------------------------UCGUGAUCA-AG--GCG-AGGU-G-U----C-----------------GU-AAAUCCG-GCGGUUG--U-GCA-GUGAAG-----G-A-G-U----GCGU---UC
AY189967.1/1737-1907         ACUAUC---G-UGA-GGUA-G--C-GGG-GAGA-GGA-----------------------AGGGAU-A---------GC-GAAAUCGU-G-G--CUCUA---------------------CGAACAG-AAA-C--GU--GA-UAUGAAGG---C-G-UA--UA--UA-GC---GGAUGAG-G-------------------------------G-GGCU--AU-------------------A----AACUCU-AAAGUCCA---------------------A-AUA---------GGUAGUCGUA-A----CC-UAUA-U-A----C-----------------GU-AAAUCAC-GAGAGUA-A--ACG-AGGAAA-----GAUGU-C-----CG------
AP006840.1/2453345-2453176   UCCGUC---G-CGA-GGCG-G--A-AUC-UGAA-GGA-----------------------AGCCCG-A-------G-GC-AAAGCCAC-G-A--CCCGA---------------------GGAACAC-GAA-C--CC--CA-UA-GGAGG---C-U-GU--GC--CG-CU-C-GGGUGAG-C-------------------------------U-GGCC--GA-------------------A----CACAGC-AAAACCCG--------------------AA--------------GCUGCCAAA-G----GG-CGGU-G-C----G-----------------GU-AGAUGGG-GCGGGUG--C-GGG-GUGAAG-----G-U-C-A-----GCG---UC
AACY021991990.1/26-190       UAAAUC---G-UGA-GAGA-U--A-GUC-UGGA-GGA-----------------------AGCCGC-U-------A-GC-AAAUCUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G--U--AG--GC-UG-A-AGGUGAG-U-------------------------------U-GGCA--CA-------------------A----GACAAC-GAAACCA-------------------------------------UGUGAUCUA-A----CG-GCC--A-C----C-----------------GU-AAAUGAU-GCAGCAG--U-GCA-GAGACA-----G-U-C-C-----AUG---UU
ABWZ01000046.1/13590-13761   UCUAUC---G-UGA-GAUG-G--C-UUC-UGAA-AGA-----------------------AGUUGG-C-------A-GC-AAACAUUU-G-G--CUUGA---------------------CGGACAA-AAA-C--UU--CA-UA-CAAGG---U-A-UU--UA--AU-CG-U-GGACAAG-G-------------------------------U-UACC--AA-------------------A----CAGACC-AAAGCCU-----------------------CAUA---------GCUAUUCAGA-A----CG-GUU--G-G----U-----------------GC-AAAUAAA-AUAAGUAUA--AGA-UGAAAA-----G-A-C-A-----AGA---UC
CP001157.1/892105-892276     GUGAGG---G-CGA-CCGA-G--C-GUG-GGGA-GGA-----------------------AGCGCG-G-------A-GCGUAAAUCGU-G-A--GCCGA---------------------UGAACAA-GAA-C--CG--CA-UA-GAAGG---C-G-CU-GCC--GA-GC-A-GGGCAAG-C-------------------------------G-GGCC--AG-------------------U----AACCGC-GAAGCUC------------------------------------UUGUGACCAA-G----GC-GAGGUG-G----C-----------------GU-AGAUGCG-GCGGUUG--U-GCG-GUGAAG-----G-AGU-G-----CGU---UC
AACY022525202.1/553-384      CCUAUC---G-UGA-GGUA-G--G-AUC-UGAA-GGA-----------------------AGCUGA-A-------A-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GU----UUAGG---C-G-UU--GU--AG-CA---GGGUAAG-G-------------------------------U-GGCC--AU-------------------U----AUCACU-AAAGCCC-----------------------AAUA---------CUUGCAUGGA-A----UG-CUGC-A-A----C-----------------GU-AAAGCCG-ACAGGCAUA--AGC-AGGAAG-----G-U-C-G-----CGC---GA
AACY021497455.1/424-202      UUGGGC---G-UGA-GCCC-U--U-CAG-UGAA-GUA-----------------------AGCGGGAC-------U-AC-AAAAGUUA-G-U--ACUGA---------------------CGAACAG-GAA-U--CG--GA-UA-UGAGG---C-U-AU--GA--GG-UU---GGGUGAG-CAGGCACAGGGCGGAGCGUUAAGAAAUAGUCCGGUGGACUAUUUUAGUGACGAGCCAGGUUGCAGGGCGGGC-AAAGUCC------------------------------------CGUGCAAAGG-CG--GAA------G-U----A-----------------GU-AGAUCCG-GCAGGAA--U-UAA-CUGAGA-----G-C-U-A-----CUU---GU
AF380672.1/3935-4105         ACUAUC---G-UGA-GGUA-G--C-GGG-GAGA-GGA-----------------------AGGGAU-A-------G--C-GAAAUCAU-G-G--CUCUA---------------------UGAACAG-AAA-C--GU--GA-UAUGAAGG---C-G-UA--UA--UA-GC---GGAUGAG-G-------------------------------G-GGCU--AU-------------------A----AACUCU-AAAGUCCA---------------------A-AUA---------GGUAGUCGUA-A----CC-UAUA-U-A----C-----------------GU-AAAUCAC-GAGAGUA-A--ACG-AGGAAA-----G---A-U-----GUC---CG
AAFZ01001794.1/1205-1376     UCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCUG-U-------A-GC-AAAUUUGG-G-A--ACCGA---------------------CGAACAG-AAA-C--CG--GA-UA-CAAGG---C-C-CG--AC--AC-GU-G-GGACAAC-C-------------------------------G-UGCA--AU-------------------G----ACCCGG-GACGUCC-----------------------AAGA---------GGCCACCGUA-A----GC---GU-U-A----G----------------GGU-AAAUCCG-GCGGUU---U-UCA-AAGGAA-----G-AGGAA-----UAG---AC
CP000539.1/2355749-2355579   UCGCGG---G-UGA-CUGC-G--A-AUC-UGAA-GGA-----------------------AGCCCG-A-------G-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GA-UA--GAGG---C-G-GC--GC--AG-CG---GGGUAAG-A-------------------------------A-GGCC--AA-------------------A----AUCUUC-AAAGCCC-----------------------AAUA---------CUUGCACGGA-A----CG-CUGU-G-A----C-----------------GU-AGAUCCG-ACAGGCAUA--AGC-AGGAAG-----G-U-C-G-----CGC---GA
AACY023777253.1/905-1071     ---GUGAGGG-UGACCGAG-C--G-UGG-GGGA-GGC-----------------------AGGCUA-U-------C-UG-AAAACUGC-C-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-CGAGG---C-G--C--AC--AG-AGUG-GGGUGAG-U-------------------------------G-AGCA--CA-------------------A----CAUCAC-GAAAUCC--------------------------C---------GUCAUUCGG-------CU-CUGU-G------C-----------------GU-AAAUGAU-GCGGUUG--G-GCA-GUGGAG-----G-U-U-U-----CAG---GA
CP001157.1/1859143-1859314   GUGAGG---G-CGA-CCGA-G--C-GUG-GGGA-GGA-----------------------AGCGCG-G-------A-GCGUAAAUCGU-G-A--GCCGA---------------------UGAACAA-GAA-C--CG--CA-UA-GAAGG---C-G-CU--GC--CG-AG-CAGGGCAAG-C-------------------------------G-GGCC--AA-------------------U----AACCGC-GAAGCUC-------------------------------------UUGUGACCA-AG--GCG-AGGC-G-G----C-----------------GU-AGAUGCG-GCGGUUG--U-GCG-GUGAAG-----G-AGU-G-----CGU---UC
ABPW01004358.1/218-394       GUCGUC---G-UGA-GGCG-G--G-GUC-UGAA-GGA-----------------------AGCCCA-A-------U-GC-GAAAGCAC-G-G--GGCGA---------------------CGAACAG-AAA-C--CG--GA-UA-UGAGG---U-G-UG--AC--AG-GCUUGGGACCAC-C-------------------------------G-GGCA--CG-------------------U----GACUAGGGAAGUCC-----------------------UCCA---------UUCUCCCAUU-GG--GGC-CUGU-U-U----U-----------------AU-AAAUCCG-GCGUCUA--C-GUG-CGGAAG-----G-U-U-A-----CGU---GU
AP006840.1/3153132-3152963   UCCGUC---G-UGA-GGCG-G--A-AUC-UGAA-GGA-----------------------AGCCCG-A-------G-GC-AAAGCCAC-G-A--CCCGA---------------------GGAACAC-GAA-C--CC--CA-UA-GGAGG---C-U-GU--GC--CG-CU-C-GGGUGAG-C-------------------------------U-GGCC--GA-------------------A----CACAGC-AAAACCCG--------------------AA--------------GCUGCCAAA-G----GG-CGGU-G-C----G-----------------GU-AGAUGGG-GCGGGUG--C-GGG-GUGAAG-----G-U-C-A----GCGU---U-
ACIC01000122.1/4015-3848     GCCAUU---U-UUA-GUUA-G--A-AUC-UG-----------------------------CGGGGA-C-------A-GC-AAAUAUUU-G-G--CCCGG---------------------CGUACAG-GAA-U--UU--GA-UAUUAAGG---C-UUAC--GG--UA-GU---GGAUUAG-U-------------------------------U-UGCU--AC-------------------A----UACAAC-AAGGCUC-----------------------UAUA----------GCUAUCCAU-C----AC-UUCC-G-A----A-----------------GU-AAAUCAA-GUGGGUAUA--AGU-UGGAAA-----G-A-A-U-----AUG---UU
CP000879.1/1360122-1359949   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCCA-A-------G-GC-AAAGUCUC-G-G--UCCGA---------------------UGAACAA-GAA-C--CA--GA-UA-CAAGG---C-U-AA--GU--GA-AG-U-GGACGAG-U-------------------------------U-UGCA--UU-------------------A----CAAAAC-GAAGUCC-----------------------AACA---------GCUAUCCAGA-A----CU-UCAC-A-G----A-----------------GU-AAAUCUG-GCGGAUAGAU-GGG-AUGAAA-----G-U-U-A-----UUG---CA
ABSN01053836.1/410-236       GGUGCC---G-CGA-GGCA-C--UCAGCACGAA-AGC-----------------------AGUCCG-G-------A-GC-GAAGGCAC-G-A--CCGUA---------------------GGAACAC-GAA-C--AG--GC--AGCGAGG---C-C-GC--GA--UG-CG-GGCGAUGAG-C-------------------------------G-UGCG--AG-------------------A----GAACGC-GAAAUCC-----------------------CACU----------GUCACCGAA-AG--ACG-CAUC-G------G-----------------GU-AGAGCCU-GACGGCG--C-GGG-CCGAAA-----G-U-U-C-----AUG---CA
CP000924.1/2109396-2109224   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCGGC-A-------G-GC-AAAAUCUC-G-G--UCUGA---------------------UGAACAA-GAA-C--CA--GA-UA-GGAGG---C-U-GA-AUU--GG-GG-C-GGAUGAG-U-------------------------------U-UGCA--UU-------------------A----CAAAAC-GAAGUCCA---------------------A-------------CACUACCCGA-A----CC-CCAU-A-C----A-----------------GU-AAAUCUG-GCAGAUAUAU-GAG-AUGAAG-----G-U-U-A-----UCG---UU
AM260479.1/1921240-1921073   GAAAGG---G-UGA-CCGA-U--C-GUG-GGGA-GGA------------------------GCGCG-A---------GC-GAAGCUGC-G-A--GCCGA---------------------GGAACAC-GAA-C--CG--GA-UA-GAAGG---C-G-GU--GC--CGACC-A-GAACGAG-C-------------------------------G-GGCA--AA-------------------G----CUUCGC-GAAGUUC-------------------------UC----------GCGAUCAAG-G----GG-AGGC-G-G----C-----------------GU-AUAUCCG-GCGGUUG--U-GCA-GUGAAG-----G-A-G-U-----ACG---UU
ABSN01034868.1/429-258       UGAGGA---G-UGA-UCUU-C--G-CAG-UGAA-GGA-----------------------AGCAGG-A-------CUGU-AAAAUCCG-G-U--ACUGA---------------------CGAACAG-GAA-C--GG--CA-UA-AGAGG---C-U-AU--AU--AA-AG-U-GGAUAAG-C-------------------------------G-UGCA--CA-------------------G----CAACGU-AACGUCC-----------------------AAAU----------AGUAACAAA-A----UU-UUAU-A-U----A-----------------GU-AGAUGUC-GCAGUGA--U-UGG-AGGAAG-----G-A-A-A-----CGG---CU
ABSN01001583.1/123-292       UCGCUC---G-UGA-GGNC-G--G-CGC-UGAA-GGA-----------------------AGCGGG-G-------A-AC-GAACCCGC-G-A--GCCGA---------------------CGAACAG-GAA-C--CG--GA-UA-CGAGG---C-G-GC--CU--CG-AC-CAGGGCGAG-C-------------------------------G-GGCA--AC-------------------U----GACCGC-GAAGCUC------------------------------------UCGCGACCAA-GG--GG--CGAG-G-C----U-----------------GU-AAAUCCG-GCGGUUG--U-GCG-GGGACG-----G-C-C-A-----GAG---UC
ABSO01002283.1/1514-1344     CCCCGG---G-CGA-CUGG-G--G-GUC-UGAA-GGA-----------------------AGCCCG-A-------G-GC-AAAGCGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GA----UGAGG---C-A-UC--GU--AU-CG---GGGUGAG-G-------------------------------C-AGCC--AA-------------------A----ACAGCC-AAAGCCC-----------------------AAUA---------CUUGCACGGA-C----CG-AUGC-G-G----C-----------------GU-AUAUCCG-ACAGGCAUA--AGC-GUGAAG-----G-UGG-G-----UGC---GU
CP000448.1/1176911-1177081   UCCAUC---G-UGA-GGUG-G--A-AUC-CGAA-GGA-----------------------AGCCGG-A-------G-GC-AAACUUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UCAGG---C-A-UC--GU--AA-GC-U-GGGUAAG-G-------------------------------U-UGCG--CA-------------------A----CAAACU-GAAGCCC-----------------------GAAA----------CUAUCCGGA-A----GC-UUAC-G-G----U-----------------GU-AGAUGUG-GCAGAUAGAU-GGA-AGGAAA-----G-A-C-U-----GCG---UU
ACIH01000269.1/68-239        UCCACC---G-CGA-GGUG-G--A-AUC-CAAA-GGA-----------------------AGCUGG-A-------G-GC-AAACUUCC-G-G--CCCAA---------------------GGAACAC-GAA-C--AU--CA----UCAGG---C-A-UA--GG-AUA-CG---GGAUGAG-U-------------------------------C-UGCU--AA-------------------A----CAAGAC-GAAGUCC-----------------------AAUU---------AACUACACGG-A----CG-UACC-A-A----U-----------------GU-AAAUGAU-GUGGGUAUAU-GGA-AGGAAA-----G-U-G-A-----AUC---GU
ABPY01004568.1/138-307       UUCCGG---G-UGA-CCGG-A--A-GUC-UGAA-AGA-----------------------AGCGGG-A-------CUAC-AAGAGUCA-G-U--ACGGA---------------------CGAACAG-AAA-C--UA--CA-UA-AGAGG---C-A-UA--GC--UUUGU---GGGUGAG-U-------------------------------A-ACCA--CA-------------------U----CUUUGC-GAAGCCCGUAG--------------CCAAUAAAC-------------------------AUU--GC-U-A----U-----------------GU-AGAUGUA-GCCGCGA--U-AGA-CUCAAG-----G-A-U-A-----AAC---GA
CP000924.1/939012-939184     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCUUA-A-------G-GC-AAAAUCUC-G-G--UCUGA---------------------UGAACAA-GAA-C--CA--GA-UA-AGAGG---C-U-GA-AUU--GG-GA-U-GGAUGAG-U-------------------------------U-UGCG--UA-------------------A----CAAAAC-GAAGUCCA---------------------A---C----------ACUACCCGA-A----UC-CCAU-A-C----A-----------------GU-AAAUCUG-GCAGAUAUAU-GAG-AUGAAA-----G-U-U-A-----UCG---UU
BABG01005901.1/66-238        UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCUG-C-------G-GC-AAAUAUCU-G-G--UCUGA---------------------CGUACAG-AAA-C--UU--GA-UAUUAAGG---C-U-UA-AGG--AU-GU---GGAUAAG-U-------------------------------U-UGCU--AA-------------------A----CAAAAC-GAAGUCC-----------------------UAUA----------GUUGUCCGG-A----AC-AUCC-A-A----A-----------------GU-AAAUCAA-GCAGACAUA--AGA-UGGAAA-----G-A-A-U-----AUG---UC
AAXY01000001.1/57131-56967   CAACCC---G-CGA-GGCG-C--G-GUC-UGGA-GGA-----------------------AGCCGC-U-------G-GC-AAAGCUGC-G-A--GCUGA---------------------UGAAUAA-GAA-C--AU--CA-UA-UGAGG---C-G-UA-AGC--CG-GA----GGUGAG-U-------------------------------U-GGCA--CA-------------------A----GACGAC-GAAGCCG-------------------------------------CGUGAUCUG-A-------CGGCCA-C----C-----------------GU-AAAUGAU-GCAGUUG--U-GCG-GUGAAA-----G-U-U-C-----AUG---CU
AAUQ01111883.1/170-358       GUAUUG---G-UGA-CAAU-G--C-UUC-UGGA-GGAAGCCGCCG-------GAUAAAAUAUCCGGUA-------CCAC-GAAGGUGC-G-G--GGUGA---------------------CGAACAG-GAA-U--CG--GG-UA-UAAGG---C-G-CA--UG--CG-CU-G-GGACGAG-U-------------------------------C-UGCA--CA-------------------A----CAAGAU-AAAGUCC-----------------------UCUA----------UCCAUCAUA-G----GG-CGUA-U-C----C-----------------GU-AAACCCG-GCAUUCA--C-GCA-CUGAAA-----G-A-C-A-----UGU---GU
AACY021722084.1/512-682      UUCAUC---G-CGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCCGA-A-------G-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GU----UUAGG---C-G-UU--GU--UG-CA---GGGUGAG-G-------------------------------U-GGCG--AU-------------------U----AUCACU-AAAGCCC-----------------------AAUA---------CUUGCACGGA-A----UG-CAGC-A-A----C-----------------GU-AAAGCCG-ACAGGCAUA--AGC-AGGAAG-----G-U-CGC-----GCG---AC
AE015928.1/3258439-3258267   UCCCUC---G-CGA-GUUG-G--A-AUC-UGAA-AGA-----------------------AGCUGG-C-------G-GC-AAAUAUCU-G-G--UCUGA---------------------CGAACAG-AAA-C--UU--CA-UA-UAAGG---C-A--U-AUG--AC-CG-U-GGGUAAG-G-------------------------------U-UGCU--GA-------------------A----CAAACC-AAAGCCCU---------------------AUAGC----------UAUUCGGAA-A----CG-GUUG-G------U-----------------GU-AAAUGGA-GCAGACAUA--AGA-UAGAAA-----G-U-U-A-----AUA---CC
AE001437.1/3712752-3712578   UCCUUC---G-UGA-GGAG-G--A-AUC-UGAA-GGA-----------------------AGUACU-A-------G-GC-AAAUUCUC-G-G--UCUGA---------------------GGUAUAC-GAA-U--CA--CA-UA-CAAGG---C-U--U-AUC--UA-GGUA-GGACGAG-U-------------------------------U-UGCA--UA-------------------A----CAAAAC-AAAGUCCA---------------------A---C----------ACUAUCCGA-AU--UCC-UAGA-A------A-----------------GU-AAAUGUG-GCAGAUAUAU-GAG-AGGAAG-----G-U-U-G----UCGU---UC
ABVL01000012.1/116365-116534 GCGACC---G-UGA-GGUC-G--U-GGC-UGAA-AGA-----------------------AGUCGC-A-------G-GC-AAAACUCC-G-A--CCGCA---------------------GGAAGAC-AAA-C--UG--GC--AGAGAGG---C-C-GG--GC--GU-GG-G-CGACGAG-C-------------------------------G-UGCG--AG-------------------G----AACCGC-GAAGUCC-----------------------GAAG----------UCCAUCCAG-A----C--ACGU-C-A----G-----------------GU-AGAGCCA-GGCGGCG--C-GGA-GGGAGA-----G-U-U-C-----AGG---UU
CP000563.1/2137792-2137956   UUAUCC---G-CGA-GGAU-U--G-GUC-UGAA-GGA-----------------------AGCCGC-U-------A-GC-AAAUUUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G--U--AG--GC-UA-G-AGGUGAG-U-------------------------------U-GGCA--CA-------------------A----GACGAC-GAAACCA-------------------------------------CGUGAUCUA-A----UG-GCC--A-C----C-----------------GU-AAAUGAU-GCAGCAG--U-GCA-AAGAAA-----G-U-U-C-----AUG---UU
AAQL01001449.1/1974-1805     UUCACC---G-UGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCUGU-A-------G-GC-AAACCUCU-G-A--CYUGA---------------------CGGACAG-AAA-C--CA--CA-UA-UAAGG---C-U-GG--GA--AA-UA-C-GGAUAAG-A-------------------------------C-GGCA--AG-------------------A----AACAUC-GAAGUCCA---------------------AAAGU---------UGCUGGAAGU-A------------C-C----A-----------------GU-AAAUGUG-GCAGGUAUAU-GGA-GGGAAAG---AG-U-C-C-----GCA-----
BAAZ01020238.1/193-364       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGC-A-------G-GC-AAAGUUCU-G-A--GCCGA---------------------CGAACAG-AAA-U--CG--CA-UA-CAAGG---C-G-GG--GC--AG-AG-C-GGACGAG-A-------------------------------C-UGCA--AC-------------------A----CAAGUC-AAAGUCC-------------------------CA---------UACUACCCGG-A----CU-CUGC-C-A----C-----------------GU-AAAUGCG-GCGGCUACAU-GGA-AUGAAG-----G-C-U-A-----UUG---UA
AAVP02000002.1/15019-14842   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GAA-----------------------AGUUGU-A-------A-GC-AAAUCUCU-G-G--UCCGA---------------------CGGACAG-AAA-U--CA--CA-UA-UAAGG---C-U-AG--GC--UGUGA-G-AGAUAAG-U-------------------------------U-GGCC--AA-------------------A----AGCAAC-GAAGUCUAAU-----------------AACUAUC----------ACUUUUGUA-G-------CAGC-A-G----A-----------------GU-AGAUGUG-GCGGAUAUAU-GGA-GAGAAA-----G-A-G-C-----GUG---AA
CP000616.1/1222453-1222282   AUGAGG---G-CGA-CCGA-G--U-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GCGUAAAUCGC-G-A--GCCGA---------------------UGGACAA-GAA-C--UG--CA-UA-GAAGG---C-A-CU--GC--CG-AG-CAGGGCGAG-C-------------------------------G-GGCA--AG-------------------A----GACCGC-GAAGCUC-------------------------------------UCGUGAUCA-AG--ACG-AGGC-G-G----C-----------------GU-AAAUGCA-GCGGUUG--U-GCG-AUGAAG-----G-AGU-G-----CGU---UC
ACNC01000013.1/61022-61193   CUUACC---G-UGA-GGUA-A--G-GGC-UGGA-GGA-----------------------AGCGUG-G-------A-AU-AAAAUCUU-G-G--CUCGA---------------------CGAACAG-AAA-U--CU--GA-UACGAAGG---C-U-CU--AU--AA-AG---GGAUGAG-A-------------------------------C-UCCA--AG-------------------A----CAAGUU-AAAAUCC-----------------------AAAA---------GAUGUGCGUA-A----CU-UUGU-A-G----A-----------------GU-AAAUCAG-GCGAGUA-A--AAG-AGGAAA-----G-A-U-A-----GUG---GU
CP000919.1/2060174-2060011   GGAAAU---A-AGA-A----U--C-GUC-AGA--GGA-----------------------AGGGAU-A---------GC-GAAAUCGU-G-G--CUCUA---------------------CGAACAG-GAA-C--GU--GA-UAGUAAGG---C-G-UA--UA--UA-GC---GGAUAAG-G-------------------------------A-GGCU--UC-------------------A----AACUCU-AAAGUCCA---------------------AAAAG----------GUAGUCGUA-A----CC-UAUA-U-G----U-----------------GU-AAAUCAC-GAGAGUAAUU-G-------AA-----U-U-C-G-----GAC---UA
CP001034.1/1036205-1036372   UCACCG---G-UGA-CGGUGG--A-GUC-UGAA-GGA-----------------------AGCUGA-A-------G-GG-GGAAUUUG-G-A--ACAUA--------------------GUGAGAAC-AAA-C--CG--AG----GAUGG---C-C-UU--UU--AG-GU---GGGUAAC-C-------------------------------U-UGCA--AA-------------------U----UAUGGG-AAAGCCC-----------------------GAAA----------GCUGGAUA-------AC-CUAA-A-A----G-----------------GU-UAGGACG-GAUGCGU--U-CAA-AUUCAG-----G-C-A-A-----GCA---GA
CP000318.1/153618-153447     AUGAGG---G-UGA-CCGA-A--U-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GCGUAAAUCGU-G-A--GCCGA---------------------UGGACAA-AAA-U--CG--CA-UA-GAAGG---C-G-CU-GCC--AA-GC-A-GGGCGAG-C-------------------------------G-GGCA--UC-------------------G----AUCCGC-GAAGCUC------------------------------------UUGUGACCAA-G----GC-GAGGUG-G----C-----------------GU-AGAUGCG-GCGGUUG--U-ACG-AUGAAG-----G-AGU-G-----CGU---UC
AAOF01000026.1/28552-28716   GAUCCC---G-CGA-GGGA-U--G-GUC-UGAA-GGA-----------------------AGCCCG-A-------GUGC-AAACCUGC-G-A--GCUGA---------------------CGAACAG-AAA-U--UU--CA-UA-GAAGG---C-G-UA--GC--CG-CU---GGGCGAG-U-------------------------------C-AGCA--CA-------------------A----GAUGAC-GAAGCCCA---------------------ACAGU----------AC-------------GA-UGGU-A-G----C-----------------GU-AAAUGGG-GCCGUUG--U-GCA-GGGAAA-----G-U-U-G-----UCG---CU
CP000262.1/122926-123085     ACUAUC---G-UGA-G-UA-G--U-GGG-GAGA-GGA-----------------------AGGGAG-A---------GU-GAAAUCGU-G-G--CUCUA---------------------CAAACAG-AAA-C--GU--GA-UAUCAAGG---C-G-UA--UA--UA-GC---GGAUGAGUC----------------------------------------------------------------------U-AAAGUCCA---------------------AAAAA----------GUAGUAGUA-A----CC-UAUA-G-G----C-----------------GU-AAAU-AU-GAGAGUA-A--ACG-AGAAAA-----GAUGU-A-----CAC---CU
AP007281.1/1089886-1089712   UCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGUCUA-A-------G-GC-AAAGUACU-G-C--AUCGA---------------------UGAACAA-GAA-G--UA--GC-UA-UAAGG---C-U-GA-AAU--UA-AC-U-GGAUAAG-G-------------------------------C-UGCU--AG-------------------A----CAAGUU-GAAGUCCA---------------------A-------------UACUACUCGA-A----GU-UGGUCU-C----A-----------------GU-AAAGCUA-ACGAUGACAU-GGU-ACGAAA-----GCU-A-A-----UAU---UC
CP000930.2/401728-401900     UCCGCC---G-CGA-GGCG-G--A-AUC-UGAA-GGA-----------------------AGCCAG-C-------G-GC-AAACCUCC-G-G--CCCGA---------------------GGACCAC-GAA-C--CC--CA-GG-UGAGG---C-U-AG--CG--GC-AG-UUGGAUGAG-C-------------------------------U-UGCC--GA-------------------A----CAAAGC-GAAGUCC------------------------------------UUGUCACCGA-AG--GCU-GCCG-A-G----A-----------------GU-AAAUGGG-GCGGGUAGAU-GGA-GGGAAA-----G-G-C-A-----ACG---UU
AAQK01002312.1/431-602       AAAACA---G-CAA-UGU--U--U-AGG-GGGA-GGA-----------------------AGUGGAGU-------A-GC-AAAACCGUUG-A--GCCUA---------------------CGAACAG-AAA-C--UG--GA-UA-CGAGG---C-U--A-AAU--GG----C-GGGCGAG-A-------------------------------U-UGCA--GA-------------------G----CAAAUC-GAAGCCC-----------------------AAAA---------GGUAAACGUA-AC--G---CCAAGA-G----A-----------------GU-AAAUCCA-GAGGCUG--UG-CG-GUGAAA-----G-A-C-U-----UGU---GU
CP000958.1/2231412-2231241   AUGAGG---G-CGA-CCGA-A--U-GUG-GAGA-GGA-----------------------AGCGUG-G-------A-GCGUAAAUCGU-G-A--GCCGA---------------------UGGACAA-GAA-C--UG--CA-UA-GAAGG---C-G-CU--GC--CG-UG-CAGGGCGAG-C-------------------------------G-GGCA--AC-------------------G----CACCGC-GAAGCUC-------------------------------------UCGUGACCA-AG--GCG-AAGC-A-G----C-----------------GU-AAAUGCG-GCGGUUG--U-GCG-AUGAAG-----G-AGU-G-----CGC---UC
AACY020293300.1/1683-1512    UCGCGG---G-CAA-CUGC-G--A-AUC-UGGA-GGA-----------------------AGCCGA-A-------G-GC-AAAGCGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GA-UA-CGAGG---C-G-UU--GC--AG-CG---GGGUAAG-A-------------------------------C-GGCC--AA-------------------U----AUCGUC-AAAGCCC-----------------------GAAA---------CUUGCACGGA-A----CG-CUGU-G-A----C-----------------GU-AUAUCCG-ACGGGCAUA--AGC-GUGAAG-----G-U-G-G-----GUG---CG
ABSP01010711.1/442-610       GUCUCC---G-CAA-GGAG-A--CGGCG-CGAA-AGG------------------------GCGGG-A-------G-GC-CAACGCUC-G-A--CCGAA---------------------GGAACAC-AAA-U--GG--GC-AG-UGAGG---C-C-GG--AU--GU-CG-G-GGGCGAG-U-------------------------------G-UGCU--AG-------------------C----GAACAC-GAAGCCC-----------------------AAGA----------GCCACUGG-------CG-ACAU-U-C----G-----------------GU-AGCGCCC-AGAGGCG--C-GAG-CGGAUA-----GAA-C-A-----GAC---A-
CP000924.1/148935-149107     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCUUA-A-------G-GC-AAAAUCUC-G-G--UCUGA---------------------UGAAUAA-GAA-C--CA--GA-UA-AGAGG---C-U-GA-AUU--GG-GA-U-GGAUGAG-U-------------------------------U-UGCG--UA-------------------A----CAAAAC-GAAGUCCA---------------------A---C----------ACUACCCGA-A----UC-CCAU-A-C----A-----------------GU-AAAUCUG-GCAGAUAUAU-GAG-AUGAAA-----G-U-U-A-----UCG---UU
ABYT01000109.1/42248-42078   UUGGCA---G-UGA-UGUC-A--U-GGG-UGAA-GGA-----------------------AGUGGUGU-------A-GC-AAUUCUUUUG-A--GCGUA---------------------CGCACAG-AAA-C--UU--GA----UGAGG---C-U--A-AAU--GG-U----GGAUGAG-A-------------------------------U-UGCA--UU-------------------A----CAAAUC-GAAGUCC-----------------------AAAA---------GGUAAACGUA-A----AA-CCAAGA-C----A-----------------GU-AAAUCAA-GACGUUG--UGAAA-GAAAUA-----G---G-A-----CCC---AU
ABAW02000017.1/114601-114429 UUGACA---G-UGA-UGUC-A--A-GGG-UGGA-GGA-----------------------AGUGGUGU-------A-GCAAUUCUUUU-G-A--GCGUA---------------------CGAACAG-AAA-C--UU--GA-UA-UAAGG---C-U--A-AAU--GG-U----GGGUAAG-G-------------------------------U-UGCA--UU-------------------G----CAAACC-GAAGCCC-----------------------AAAC---------GAUAGACGUA-A----AA-CCAAGA-C----A-----------------GU-AAAUUAA-GACGUUG--U-GAA-AGAAAU-----A-G-G-A-----UUC---AU
AAFX01078006.1/394-564       GAAGCC---G-UGA-GGCC-A--G-ACC-GAAA-GAA-----------------------GGGUGU-A---------GC-AAAGACAC-G-A--CCGCA---------------------CGAACAG-AAA-C--AG--GC-GG-CGAGG---C-C-GG--GC--GC-GG-G-CGAUGAG-C-------------------------------G-GGCG--GG-------------------G----AACCGC-GAAAUCC------------------------AUC----------UGUCACCGA-AA--GAC-GCGC-A-A----G-----------------GU-AGAGCCU-GGCGGCA--C-GGG-UCGAAA-----G-U-A-C-----AUG---UU
ABRD01002738.1/3759-3927     GUGAGG---G-UGA-CCGA-G--C-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-UC-GAAACUGC-G-G--GCCGA---------------------UGGACAA-GAA-C--CG--GA-UA-UGAGG---C-G-GU--GC--CG-AC-CAGGGCGAG-C-------------------------------G-GGCA--AC-------------------G----AACCGC-GAAGCUC------------------------------------UUGUGACCAA-GA--GG--CGGU-G-G----C-----------------GU--AAUCCC-GCGGUCG--U-GCA-GGGAAA-----G-G-A-G-----UGC---GU
AATN01000908.1/2829-2659     CUGAGG---G-CGA-CCGA-U--G-GUG-GGAA-GGA-----------------------AGCGUG-G-------A-GC-GAAACUGC-G-A--GCCGA---------------------UGAACAA-GAA-C--CG--GA-UA-GAAGG---C-G-CU--GC--CGAGC-A-GGGCGAG-C-------------------------------G-GGCC--AG-------------------A----GACCGC-GAAGCUC------------------------------------UCGUGAUCAA-G----GC---G--A-AGUGGC-----------------GU-AGAUUCG-GCGGCUG--U-GCA-GGGAAG-----G-AGU-G-----CGU---UC
ACIN02000013.1/598066-597895 UCCAUU---G-UGA-GGUG-G--A-AUC-UGAA-GAA-----------------------AGUCGGAU-------G-GC-AAAUCUCC-A-G--UCUGA---------------------CAAAUAG-AAA-U--CA--CA----UCAGG---C-U-AU--GG--CU-AA---GGAUAAG-G-------------------------------U-UGCC--UG-------------------A----CAAACU-GAAGUCC-----------------------AAUA---------ACUACUCGGA-A----UU-AGCU-G-U----G-----------------GU-AAAUGUG-GUAGAUAGGU-GGA-GAGAAA-----G-A-A-A-----CGU---GU
ABCS01000007.1/29509-29339   CCAAGG---G-CGA-CUGA-G--G-GUC-UGAA-AGA-----------------------AGCGUG-A-------A-AC-GAACCAGC-G-G--GUCGA---------------------CGCACAG-AAA-C--CG--GA-UC-AGAGG---C-G-GG--GC--GC-CG-G-GGGCGAG-C-------------------------------G-UGCC--AG-------------------A----GAACGC-GAAGCUC--------------------------C---------UCGUGGCCGA-AC--ACG-GCGU-C-A----C-----------------GU-GCAUCCG-GCGAUCG--C-GCU-GGGAAG-----G-C-C-G-----GUG---UC
AATN01001104.1/233-407       GUCGUC---G-UGA-GGCG-A--G-GUG-CGGA-GGA-----------------------AGCCCA-A-------U-CC-AAAGGUGC-G-G--GGCGA---------------------UGAACAA-GAA-C--CG--GA-UA-UGAGG---C-G-UG-AUG--CA-UC-CGGGGCGAG-C-------------------------------G-GGCA--CG-------------------U----GACCGC-GAAGCCC-------------------------UC---------CAUCUGCGGU-UG--GGG-UGCAUU-U----U-----------------GU-AAAUCCG-GCGUCUA--U-GCA-GCGAAG-----G-U-A-A-----CGA---GU
AAYG02000023.1/36749-36621   UCUAUC---G-UAA-GGUA-G--A-AUC-UGAA-GGA-----------------------AGCUGU-A-------A-GC-AAACUCUU-G-G--UCCGA---------------------CGGACAG-AAA-U--CA--CA-UA-UGAGG---CUAGACAGAUGUACAAUCCAUCU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------GU-CUGUUUG-CCG--UG--C-AAA-AAAACA-----G-A-U-A-----ACA---AA
ABIK02000004.1/236759-236929 UUGAUA---G-UGA-UGUC-A--U-GGG-UGAA-GGA-----------------------AGUGGUGU-------A-GCGAUUCUUUC-G-A--GCGUA---------------------CGAACAG-AAA-C--UU--GA----UGAGG---C-U--A-AAU--GG-U----GGAUAAG-G-------------------------------U-UGCG--CA-------------------A----CAAACU-AAAGUCC-----------------------AAAA---------GGUAAACGUA-G----AA-CCAAGA-C----A-----------------GU-AAAUCAA-GACGUUG--U-GAA-AGAAAU-----A-G-G-A-----UUC---AU
AACY023823372.1/1351-1524    UCCGUC---G-CGA-GGCG-G--A-AUC-UGAA-GGA-----------------------AGCUGU-A-------G-GC-AAACUCCC-G-G--CCCGA---------------------CGAACAG-GAA-C--CG--CA-UA-CGAGG---C-A-GC--CA--CA-UC-U-GGGCGAG-A-------------------------------G-GGCC--AU-------------------G----AAACUC-GAAGCCC-----------------------AAUA---------GCUAUCUAGA-A----GA-UGUG-G-A----A-----------------GU-AGAUGCG-GCGGGUAGAU-GGG-AGGAAG-----G-U-C-G-----CGC---GC
AP006840.1/2402154-2401985   UCCGUC---G-CGA-GGCG-G--A-AUC-UGGA-GGA-----------------------AGCCGG-A-------G-GC-AAAGCCAC-G-A--CCCGA---------------------GGAACAC-GAA-C--CU--CA-UA-CGAGG---C-U-GU--GC--CG-CC-U-GGGUGAG-C-------------------------------U-GGC---GA-------------------A---CCACAGC-AAAACCCG--------------------AG--------------GCUGCCAAA-G----GG-CGGU-G-C----A-----------------GU-AGAUGGG-GCGGGUG--C-GGG-GUGAAG-----G-U-C-A-----GCG---UU
ACAA01000090.1/2806-2958     UCCAUC---G-UGA-GUUG-G--A-AU----------------------------------------C-------G-GC-AAACAUCU-G-G--UCUGA---------------------CGCACAG-AAA-C--UU--GA-UAUGAAGG---C-U-UA-AGG--AU-GU---GGAUGAG-U-------------------------------U-UGCA--UA-------------------A----CAAAAC-AAAGUCC------------------------AUA----------GUUAUCCGG-A----AC-AUCC-G-A----A-----------------GU-AAAUCAA-GCAGACAUA--AGA-UGGAAA-----G-A-A-U-------------
AACY020433947.1/353-189      CAACCU---G-CGA-GGGA-C--G-GUC-UAAA-GGA-----------------------AGCCUG-A-------C-GC-AAAACUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G-UA--GG--CU-GG---AGGCGAG-U-------------------------------U-GGCA--CA-------------------A----GACAAC-GAAGCCG-------------------------------------UGUGAUCUA-A----C--GGCC-A-C----C-----------------GU-AAAUGAU-GCAGUUG--C-GCA-GGGACA-----G-U-U-C-----AUG---CU
CP000924.1/2099443-2099271   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCUUA-A-------G-GC-AAAAUCUC-G-G--UCUGA---------------------UGAACAA-GAA-C--CA--GA-UA-AGAGG---C-U-GA-AUU--GG-GA-U-GGAUGAG-U-------------------------------U-UGCG--UA-------------------A----CAAAAC-GAAGUCCA---------------------A---C----------ACUACCCGA-A----UC-CCAU-A-C----A-----------------GU-AAAUCUG-GCAGAUAUAU-GAG-AUGAAA-----G-C-U-A-----UCG---UU
ABSQ01051720.1/490-662       UCCCGG---G-UGA-CCGG-G--A-AUC-UGAA-GGA-----------------------AGCCGU-A-------G-GC-AAACAUUU-G-U--UGUGA---------------------CGCACAG-AAA-C--CG--GA-UA-UAAGG---C-C-UG-UUC--UC-CU---GGGUAAC-U-------------------------------G-ACCA--CU-------------------G----AAUCAG-GAAGCCC-----------------------GAUA---------GUCAUUCGGA-A----AG-GAGGGG-G----G-----------------GU-AAAUCCG-GCGCAA---U-GAA-UGGAAA-----GAU-U-U-----ACU---AC
CP000270.1/1991158-1991329   GAGAGG---G-UGA-CCGA-U--C-GUG-GGAA-GGA-----------------------AGUGUG-G-------A-GU-GAAGCCGC-G-A--GCCGA---------------------UGAACAA-GAA-C--CG--GA-UA-GAAGG---C-G-GU--GC--C--GAUCAGGGCGAG-C-------------------------------A-GCCA--AA-------------------C----AACUGC-AAAGCUC------------------------------------UCGUGGUCAA-GG--GUC-AGGC-G-G----C-----------------GU-AAAUCCG-GCGGUUG--U-GCG-GUGAAG-----GAU-U-G-----CGU---UC
ABYO01000195.1/1020-852      UAGAUG---G-UGA-CAUC-U--A-GGA-GAGA-AGA-----------------------AGUAAU-A---------GC-GAAAUCGU-G-G--CUUGA---------------------CGAACAG-GAA-C--AG--AA-UA-CAAGG---C-G-UA--AC--AG-GU---GGGCAAG-C-------------------------------U-AGCA--GU-------------------A----GAUAGCAAAGACCC-----------------------AAAA---------GGUAACCGUA-A----AC-CUAA-A-G----C-----------------GU-AAAUUCU-GCAAGUA-A--ACG-AUGAAA-----G-U-A-U-------U---AG
ACOQ01000035.1/3350-3519     UCGCGG---G-CGA-CUGC-G--A-AUC-UGAA-GGA-----------------------AGCCCG-A-------G-AC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GA----UGAGG---C-G-GC--GC--AG-CG---GGGUGAG-G-------------------------------U-GGCC--AU-------------------A----AUCGCC-AAAGCCC-----------------------GAUA---------CUUGCACGGA-A----CG-CUGC-G-A----C-----------------GU-AGAUCCG-ACAGGCAUA--AGC-AGGAAG-----G-U-C-G-----CGC---GA
ABPT01001159.1/227-392       GUGCGG---G-UGA-CCGU-U--C-GUC-UGAA-GGA-----------------------AGCCCG-U-------UUGC-AAAUCCAC-G-A--GCCGA---------------------CGAACAG-GAA-U--CG--UA-UA-GGAGG---C-C-GA--GU--GC-CU---GGGUGAG-G-------------------------------U-GGCC--AA-------------------G----CGCACC-GAAACCC-------------------------------------ACCAAAGGA-G----G--GCUU-A-C----G-----------------GU-AAAUACG-GCGGUUG--C-GGG-GAGACA-----G-A-U-C-----GUG---UU
AATB01000058.1/86-256        UCUACC---G-UGA-GGAG----A-AUC-GAAA-GGA-----------------------AGCUAA-G-------G-AC-AAAAGUCU-G-G--CUCCA---------------------CGCACAG-AAA-C--UU--GA-UA-UAAGG---C-U-C-AAAG--UC-AG---GGGUAAG-G-------------------------------U-UGCU--AC-------------------A----CAAACC-AAAGCCC-----------------------GAUA----------GCUAUCCGG-A----CU-GACGA--G----A-----------------GU-AAAUCAA-GGGAGUAUA--AGA-CUGAAA-----G-A-U-U-----AUG---UU
BAAZ01000261.1/1578-1381     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GAAAGCCGGAUUU--UGGGAGUUGAAAGGUCU-CCCA-AUGG-GC-AAAACUCU-G-G--CCUGA---------------------CGAACAG-AAA-U--CG--CA-UA-UAAGG---C-C-GU--CA--GC-GA---GGGUAAG-U-------------------------------U-UGCA--UA-------------------A----CAAAAC-AAAGCCC-----------------------AGUA---------GCUACACGGA-A----UC-GCUU-U-C----G-----------------GU-AAAUGCG-GCAGGUA-A--AGA-GGGAAA-----G-A-A-U-----GUG---UG
CP000698.1/2512021-2512195   UCCGGG---G-CGA-CCCG-G--A-AUC-UGAA-GGA-----------------------AGCUGU-A-------G-GC-AAAGUCCU-G-G--CCCGA---------------------CGAACAG-GAA-U--CG--CA-UA-UGAGG---C-A-GC-CAC--AU-CU---GGGCGAG-A-------------------------------A-GGCA--AA-------------------C---AGA-UUC-AAAGCCC-----------------------GAUA---------ACCAUCCAGA-A----AG-AUGUGG-A----A-----------------GU-AGAUGCG-GCGGGUAUAU-GGG-AUGAAG-----G-U-C-A-----CGC---GC
CR378675.1/186458-186622     UUUUCA---G-UGA-GGGA-U--G-AUC-UAAA-GGA-----------------------AGUCGC-U-------A-GC-AAAACUGC-G-A--ACUGA---------------------UGAACAA-GAG-C--AU--CA-UA-UGAGG---C-G--U--AG--GU-CA-G-AGGCAAG-U-------------------------------U-GGCA--CA-------------------A----GACAAC-GAAGCCA-------------------------------------AGUGAUUUA-A----UG-AUC--A-C----C-----------------GU-AAAUGAU-GCCGUUG--U-GUA-GGGGCU-----G-A-G-G-----GUU---AG
ABPX01002982.1/188-360       GCCGCC---G-CAA-GGCG-G--G-GUC-UGAA-GGA-----------------------AGCUGG-A-------G-GC-AAAGCUGC-G-G--CCCGA---------------------CGAACAG-CAA-C--CG--CA-UA-CGAGG---C-G-GC--GU--CG-CG-U-GGGCGAG-A-------------------------------G-GGCC--AA-------------------G----AGACUC-GAAGCCC-----------------------GAUG----------UCAUCCGGA-A----CG-CGGC-G-G----C-----------------GU-AGAUGCG-GCGGGUAUGU-GCA-GCGAAG-----G-U-C-A-----CGC---GU
CP000879.1/1345608-1345435   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCCA-A-------G-GC-AAAGUCCC-G-G--UCCGA---------------------UGAACAA-GAA-C--CA--GA-UA-CAAGG---C-U-AA--GU--GG-AG-U-GGACAAG-U-------------------------------U-UGCA--UA-------------------A----CAAAAC-GAAGUCC-----------------------AACA---------GCUAUCCAGA-A----CU-UCAC-G-G----A-----------------GU-AAAUCUG-GCGGAUAGAU-GGG-AUGAAA-----G-U-U-A-----UUG---CA
CP000790.1/2079720-2079547   UUCACU---G-UGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCAAA-U-------G-GC-AAAACUUG-G-U--UGUGA---------------------CGAACAG-AAA-U--CU--GA-UA-GUAGG---U-C-AC--UA--CA-AC-UUGGGCAAC-C-------------------------------U-AGCC--AU-------------------A----GAUAGA-AUAGCCCA---------------------AUGCC----------UCGACGGGA-AG--UG--UGUA-G-U----G-----------------AU-AAAUCAG-GCACGG---C-CAA-GGGAAA-----G-A-G-C-----AAC---GU
CP000617.1/381912-382081     GUCGUC---G-UGA-GGCG-G--G-GUC-UGAA-GGA-----------------------AGCGUG-U-------A-GC-AAAGCCAC-G-A--CCUGA---------------------CGAACAG-AAA-C--CA--GA-UA-UGAGG---C-C--U-ACC--CG-GC-C-GGACGAG-C-------------------------------G-AGCA--AU-------------------G----GAUCGC-GAAGUCCG--------------------CA--------------ACCAUCAAG-G----GC-CGGG-G-U----G-----------------GU-AAAUCUG-GCAGGUG--U-GUG-GUGAAG-----G-C-G-G-----UUG---GG
BAAX01000824.1/4345-4516     UCCACU---G-CGA-GGUG-G--A-AUC-UGAA-AGA-----------------------AGCUGG-C-------G-GC-AAACAUCU-G-A--CCUAA---------------------CGUACAG-AAA-C--UU--CA-UA-UAAGG---C-AUUU--GA--CC-AU---GGAUGAG-A-------------------------------U-UGCA--AG-------------------A----CAAAUC-AAAGUCC-----------------------CAUA----------GCUAUUCGG-A----AU-GGUU-G-G----U-----------------GU-AAAUGAA-GUGGGUAUA--AGA-UGGAAA-----G-A-A-U-----AAG---CC
AARF01000332.1/1232-1404     UCGAUC---G-CGA-GGUC-G--A-AUC-UGAA-GGA-----------------------AGUCGG-C-------G-GC-AAAUCUCC-G-G--CCCGA---------------------GGAACAC-GAA-U--CU--CA-UA-GAAGG---C-UAAC--GU--UC-GU-U-GGAUGAG-G-------------------------------C-UGCU--UA-------------------A----CAAGUC-GAAGUCC-------------------------UU----------ACUGCCGAA-G----GC-GGAU-G-G---GA-----------------GU-AAAUGAG-ACGGGUAGGU-GGA-GAGGAA-----G-A-U-A-----GCG---UU
AAOH01000001.1/357512-357676 UAAAUC---G-CGA-GAGA-U--A-GUC-UGGA-GGA-----------------------AGCCGC-U-------A-GC-AAAUCUGC-G-A--GCUGA---------------------UGAACAA-AAA-C--AU--CA-UA-UGAGG---C-G-UA--GG--CU-GG---AGACGAG-C-------------------------------U-AGCA--CA-------------------A----GAUAGC-GAAGUCA-------------------------------------UGUGAUCUA-A----C--GGCC-A-C----C-----------------GU-AAAUGAU-GCAGUUG--U-GCA-GAGAAA-----G-U-C-A-----AUG---CA
AP008230.1/5170929-5170759   UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AACCGG-C-------G-GC-AAAGUUCC-G-G--CCCGA---------------------GGAACAC-GAA-C--AA--CA----UCAGG---C-G-CG-AAA--CG-UG---GGGUGAG-A-------------------------------C-UGC---GA-------------------A---ACAAGUC-AAAGCCC-----------------------AAAA----------GCUGCACGG-A----CA-UGUC-A-G----C-----------------GU-AAAUGUU-GCGGGUAUAU-GGA-AUGAAA-----G-U-G-A-----AUC---GU
ABIY02000122.1/116521-116350 UCCAUC---G-CGA-GUUG-G--A-AUC-UGAA-AGA-----------------------AGCUGG-C-------G-GC-AAACAUCU-G-G--UCUGA---------------------CGAACAG-AAA-C--UU--CA-UA-UAAGG---C-A-UA-UGA--CC-GU---GGGUAAG-G-------------------------------U-UGCG--AA-------------------A----CAAACU-AAAGCCC-----------------------UAUA----------GCUAUUCGG-G----AC-GGUU-A-G----U-----------------GU-AAAUGGA-GCAGACAUA--AGA-UUGAAA-----G-U-U-A-----AUA---CC
AP007281.1/113928-114101     UCCACU---G-UGA-GGUU-G--A-AUC-UGAA-GGA-----------------------AGUCUA-A-------G-GC-AAAGUACU-G-C--ACCGA---------------------UGAACAA-GAA-G--UA--GC-UA-UAAGG---C-U-GG-AAC--UA-AC-U-GGAUAAG-A-------------------------------C-UGCA--UG-------------------A----CAAGUU-AAAGUCCA---------------------A---C----------ACUACUCGA-A----GU-UACU-U-U---CA-----------------GU-AAAGCUA-CCGGUGACAU-GGU-ACGAAA-----G-U-U-A-----AUA---UC
ABCK01000003.1/156521-156690 UCACGG---G-UAA-CUGU-G--AGGUG-UGAA-GGA-----------------------AGCGAU-A-------G-G--AAGUAAGG-UGG--CCGGA--------------------GCGUAAGC-GAA-C--CU--GA----UACGG---C-A-CA--UU--AG-GA---GGGUGAG-U-------------------------------C-UGCA--AA-------------------A----CAUGAU-GAAGUCC-----------------------CAAU----------ACUUGAUCA-G----UC-CUAA-U-G----U-----------------GU-GCUUGAG-GUCGGUAAA--CCU-UACAGG-------G-A-G-----UCA---GU
AP006840.1/1937585-1937416   UCCGUC---G-UGA-GGCG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGCCAC-G-A--CCCGA---------------------GGAACAC-GAA-C--CC--CA-UA-GGAGG---C-U-GU--GC--CG-CU-C-GGGUGAG-C-------------------------------U-GGCC--GA-------------------A----CACAGC-AAAACCCG--------------------AA--------------GCUGCCAAA-G----GG-CGGU-G-C----G-----------------GU-AGAUGGG-GCGGGUG--C-GGG-GUGAAG-----G-U-C-A-----GCG---UU
CR522870.1/2858976-2858808   UUGUUG---G-UAA-CGGC-A--GGGUC-UAAA-GGA-----------------------AGCGAU-A-------G-G--AAGUGAGUGG-U--ACAUA--------------------GCGCAAGC-GAA-C--CU--GA----UUCGG---C-G-AU--GC--GG-GA---GGGUAAA-C-------------------------------G-UGCA--AA-------------------A----UAGCGU-AAAGCCC-----------------------AAUA---------CUUGGUCAG-------UC-CCGU-A-U----C-----------------GU-GUUUGAG-GAUGCGA--UUGCU-CACAGG-------G-A-G-----UUC---GC
AACY023834571.1/695-864      CAUCCC---G-UGA-GGGC-G--U-GUG-GGGU-GGA-----------------------AGCCCG-A-------G-GC-GAAUCGGA-G-U--CCCGA--------------------AUGAAAGU-GAA-U--CC--CC---GUAAGG---C-U-GG--UC--UG-UC-U-GGGCAAG-C-------------------------------G-UGCC--GU-------------------U----CAACGC-GACGCCC-----------------------GAUA---------UCCAACCGC-------GG-CAGG-A-C----A-----------------GU-AGUGGGG-GCGGCGG--C-GAC-GAGAAG-----U-C-A-U-----UCA---UC
CP000494.1/6818088-6817919   GUCAUC---G-CGA-GGUG-G--G-GUC-UGAA-GAC-----------------------AGCGUG-G-------A-GC-AAAGCCGC-G-G--CCCGA---------------------UGAACAA-ACA-G--CG--GA-UG-CGAGG---C-C--U-ACC--CG-UC-C-GGACGAG-C-------------------------------G-AGCU--GC-------------------C----AAUCGC-GAAGUCC------------------------ACG----------GUCAUCAAG-G----GG-CGGG-G-U----G-----------------GU-AAAUCCG-ACGGGUA--U-GCG-GUGAAG-----G-C-G-G-----UCG---GU
ABBE01001046.1/93-265        UCGCGG---G-CGA-CUGC-G--A-AUC-CGAA-GGA-----------------------AGCCCG-A-------G-GC-AAAGCGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GA-UA-CGAGG---C-G-AC--GC--GU-UG---GGGUAAG-G-------------------------------C-AGCC--AA-------------------A----AAGGCC-GAAGCCC-----------------------GAUA---------CUUGCACGGA-A----CG-ACGC-G-G----C-----------------GU-AGAUCCG-ACAGGCAUA--AGC-GUGAAG-----G-UGG-G-----UGU---GC
AACY020536917.1/279-445      GGUCCC---G-CGA-GGGG-C--G-GCC-UGGA-GGA-----------------------AGCCUG-A-------GCGC-AAAGGUGC-G-A--GCCGA---------------------CGGACAG-AAA-U--CG--CA-UA-GAAGG---C-C-UG--GU--CC-CC---GGGUGAG-U-------------------------------C-AGCA--CA-------------------A----GAUGAC-GAAACCC-----------------------UACA----------GGUGCA---------GG-GGAC-A-G----G-----------------GU-AAAUGCG-GCGGUUG--U-GCA-CCGAAA-----G-U-U-C-----AUG---UC
AAUQ01113241.1/201-365       GAUCUC---G-UGA-GGGG-U--U-GUC-UGAA-GGA-----------------------AGCCGG-A-------GUGC-AAAGCUAU-G-A--GCCGA---------------------CGAACAG-AAA-C--GG--UA-UA-CGAGG---C-C-CA--GU--UU-CC---GGGUAAG-U-------------------------------C-AGCA--CA-------------------A----CAUGAC-AAAGCCC-------------------------------------UGGGUUUA-------GG-AGAU-A-G----G-----------------GU-AAAUGCC-GCGGUUG--U-GUA-GCGAAA-----G-A-U-C-----ACG---UU
BA000028.3/2645785-2645613   GCUAUC---G-UGA-GGUA-G--U-GGC-UGAA-GGA-----------------------AGCCGG-A-------C-GC-AAACUCCU-G-A--ACUGA---------------------CGAACAG-AAA-U--UA--GA-UA-GAAGG---C-U-GG--AU-UAG-GU-C-GGAUAAG-U-------------------------------C-UGCA--UA-------------------U----CAAGAC-AAAGUCCA---------------------A-------------UACUGCCCGA-A----AC-CUAU-A-C----A-----------------GU-AAAUCUA-ACAGUUAUAC-GGG-AGGAAA-----G-U-U-U-----UCA---CU
ABSN01005101.1/400-232       GUUACC---G-UGA-GGUA-G--G-GUC-UGAA-GGU-----------------------AGCGCG-G-------A-GC-AAACCCAC-G-A--CCUGA---------------------CGAACAG-AAA-C--CA--GA-UA-UGAGG---C-C--U-AAC--GC-UG---GGACGAG-C-------------------------------G-GGCG--UA-------------------U----GACUGC-GAAGUCC------------------------AUA---------GCCAUCAAG-------CG-GCGGGA-C----G-----------------GU-AGAUCUG-GCGGGUG--C-GUG-GGGAAG-----G-C-G-G-----UCA---AA
AAFZ01027222.1/130-294       UUGACC---G-UGA-GGUC-U--G-GUC-UGGA-GGA-----------------------AGCCGG-A-------C-GC-AAAACUGC-G-A--GCUGA---------------------UGAACAA-AAA-C--AU--CA-UA-UGAGG---C-G--U--AG--GC-UG-A-AGGCGAG-A-------------------------------U-GGCA--CA-------------------A----GACAUC-GAAGCCG-------------------------------------CGUGAUCCA-A----CG-GCC--A-C----C-----------------GU-AAAUGAU-GCAGUUG--C-GCA-GGGACA-----G-U-U-C-----AUG---CU
AP008232.1/1047391-1047559   GCAAGG---G-UGA-CUGA-G--C-GUG-GGGA-GGA-----------------------AGUGUAGA-------G-A--GAAACUGC-G-A--GCCGA---------------------UGAACAA-GAA-U--CG--GA-UA-GAAGG---C-G-CU-GGC--GA-GC-A-GGGUGAG-U-------------------------------G-GGCU--AG-------------------A----AACCGU-GAAACUC------------------------------------UUGUGGUCAA-G----GC---G--A-GGUGGC-----------------GU-AGAUCCG-GUGGUUG--U-GCA-GUGAAG-------G-A-A-----UGC---GU
CP000874.1/279827-280000     GUCGUC---G-CGA-GGCG-G--G-GUC-UGAA-GGA----------------------AAGCUGU-A-------A-GC-AAAGUGCC-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--CA-UA-UAAGG---C-G-UC--CG--CA-UC-C-GGGCGAG-G-------------------------------G-AGCC--AA-------------------A----GUGCCC-GAAGCCC-----------------------GAUA----------UCACCCGGA-G----GG-UGCG-G-G----C-----------------GU-AGAUGCG-ACAGGUAUAU-GGC-ACGAAG-----G-U-C-A-----CGC---GC
ABSN01062041.1/670-498       UUUACC---G-UGA-GGCA-A--G-CAG-UGAA-GGA-----------------------AGCGAG-A-------CUAC-AAAACCCG-G-U--ACUGA---------------------CGAACAG-AAA-C--CG--AA-UA-UGAGG---C---AU--AU--AU-AC-UUGGGUGAG-C-------------------------------A-AGCA--CA-------------------C----CAUUGC-UAAGCCC-----------------------UAAG----------UUUACAAAA-AG--GGU-AUAU-A-U----------------------GU-AGAUUCG-GCAGGUA--U-UGG-AGGAAG-----G-A-A-A----AUGC---U-
ACDM01000096.1/25547-25377   GCCGUC---G-UGA-GGCG-G--G-AUC-UGAA-GGA-----------------------AGCGUG-G-------A-GC-AAAACCAU-G-A--CCUGA---------------------CGAACAG-AAA-U--CC--GA-UA-UGAGG---C-C-UA--CC--CG-GC-U-GGCGGAG-C-------------------------------A-AGCC--AU-------------------U----GAUUGC-AAAGGCC------------------------AUA----------ACCAUCAAG-A----GC-CGGG-G-G----G-----------------GU-AGAUUGG-GCAGGUG--U-GUG-GUGAAA-----G-CGG-C-----UGA---GC
ACGB01000023.1/2267-2439     GACAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGGGGC-A-------G-GC-AAAUUUCU-G-A--CCUGA---------------------CAAAGAG-AAU-C--CG--CA----UAAGG---C-CAAU--UU--GA-GA-U-GGAUAAG-G-------------------------------U-CGCC--AA-------------------A----CAGAUU-AAAGUCC-----------------------CAUA---------GCGAUUUGGA-A----UC-CCAA-A-G----G-----------------GU-AGAUGCG-GCAGGUGAAG-GGA-GAAAAA-----G-A-G-U-----GCG---UU
ABAW02000018.1/23263-23439   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGAUGG-A-------G-GC-AAAACUCC-G-G--UCUGA---------------------GGAAUAC-GAA-U--CA--CA----UCAGG---C-A-UA--UC--AU-GG---GGACAAG-U-------------------------------G-UGCA--AA-------------------A----CAACAC-AAAAUCCAAAAGAG--------UUGCGGAUAAGA-------------------------CU-AUGA-U-A----U-----------------GU-AAAUGUG-GCAGAUAUAU-GGA-GGGAAAG---AG-G-U-A-----UGA---UC
AAOH01000001.1/110462-110630 UAAAUC---G-UGA-GAGA-U--A-ACC-CGGA-AAA-----------------------AGCCGC-GAAAAUUCU-UU-AUAAU----A-A--AUAGA---------------------UGAACAA-AAA-C--AU--CA-UA-UUAGG---C-G-UA--GG--CU-GA---AGACGAG-C-------------------------------U-AGUA--CA-------------------A----GAUAGC-GAAGUCA-------------------------------------UGGGAUCUA-A----C--GGCC-A-C----C-----------------GA-AAAUGAU-GCAGUUG--U-GCA-AUGAAA-----G-U-U-A-----AUG---CU
AAXY01000055.1/4631-4810     CAACCC---G-CGA-GGCG-C--G-GUC-UGGA-GGA-----------------------AGCCGC-U-------A-GC-AAAGCUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G-UA--GG--CC-GG---AGGCGAG-U-------------------------------U-GGCA--CA-------------------AG-CCGACGGG-GCGGCCUCCCG---------------CGAAGCCA----------CGUGAUCUG-A----C--GGCC-A-C----C-----------------GU-AAAUGAU-GCAGUUG--U-GCA-GUGAAA-----G-U-U-C-----AUG---UU
AAXA02000015.1/229581-229412 UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GAA-----------------------AGCUGU-A-------A-GC-AAACUCUU-G-G--UCCGA---------------------CGGACAG-AAA-U--CA--CA-UA-UAAGG---A-U-UG--GA--AAUAC---GGAUAAG-U-------------------------------C-UGCA--AA-------------------A----GAAGAU-GAAGUCC-----------------------AAAA----------GUUGCUGGA-A----GUA-----C-G----A-----------------GU-AAAUGUG-GCGGAUAGAU-GAG-AGGAAA-----G-A-G-C-----GUG---CA
AANZ01000004.1/60175-60347   GUCGUC---G-UGA-GGCGUG--C-GUC-UGAA-GGA-----------------------AGCGUG-G-------A-GC-GAAUUCGC-G-G--CCUGA---------------------CGUACAG-GAA-U--CG--GA-UA-GUAGG---C-G-AU--GU--CG-AC-G-GGACGAG-C-------------------------------C-GCCA--AU-------------------G----CACGGC-GAAGUCC-----------------------UCUA----------UCCAUCGGA-A----AU-CGAC-G-U----C-----------------GU-AGAUCCG-GCGGGCG--U-GCG-AAGACA-----G-U-UGA-----UGA---AC
AP008232.1/2034676-2034845   GCAAGG---G-UGA-CUGA-G--C-GUG-GGGA-GGA-----------------------AGUGUG-G-------A-GC-GAAA-UGC-G-A--GCCGA---------------------UGAACAA-GAA-U--CG--GA-UA-GAAGG---C-G-CU--GG--CGAGC-A-GGGUGAG-C-------------------------------G-GGCG--AG-------------------A----AACCGU-GAAACUC------------------------------------UUGUGGUCAA-G----GCGAGGU-G-G----C-----------------GU-AGUUCCG-GCGGUUG--U-GCA-GUGAAG-----G-AGU-G-----CGU---UC
ABPY01006228.1/224-397       UCCGUC---G-CGA-GACG-G--A-AUC-UGAA-GGA-----------------------AGCGGA-A-------G-GC-AAACUCCC-G-G--CCCGA---------------------GGCACAC-GAA-C--CG--CA-UA-CGAGG---C-G-UC--UG--AU-CGGU-GGGCGAG-G-------------------------------G-GGCG--CA-------------------U----AGACCC-AAAGCCC-----------------------GAUG----------CCAUCCGGA-C----CG-GCCA-G-G----C-----------------GU-AUAUGCG-GCGGGUAUGU-GGG-AGGAAA-----G-U-C-G-----CGC---GU
AATO01004217.1/1025-851      GUCGUC---G-UGA-GGCG-A--G-GUG-CGGA-GGA-----------------------AGCCCA-A-------U-CC-AAAGCUGC-G-G--GGCGA---------------------UGAACAA-AAA-C--CG--GA-UA-UGAGG---C-G-UG-AUG--CA-UC-CGGGGCGAG-C-------------------------------G-GGCA--CG-------------------U----GACCGC-GAAGCCC-------------------------UC---------CAUCUGCGGU-UG--GGG-UGCAUU-U----U-----------------GU-AAAUCCG-GCGUCUA--U-GCA-GCGAAG-----G-U-A-A-----CGA---GU
CP000753.1/2606725-2606536   UUAUCC---G-CGA-GGAU-U--G-GUU-UGAA-GGA-----------------------AGCCGC-U-------A-GC-AAAUUUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G-UA--GG--CU-AG---AGGUGAG-U-------------------------------U-GGCA--GG-------------------GCCUCCCCCAC-GAAGU--AAGGGGAC-------AAGACGACGAAACC------ACGUGAUCUAA-U-------GGCC-A-C----C-----------------GU-AAAUGAU-GUAGCAG--U-GCA-AAGAAA-----G-U-U-C-----AUG---UU
AACY023761684.1/48-212       GAAGCC---G-CGA-GGCG-A--C-GUC-UGGA-GGA-----------------------AGCGGU-G-------A-GC-AAAACUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--GU--CA-UA-UCAGG---C-G-UA--GG--CC-GG---AGGCGAG-A-------------------------------U-GGCA--CA-------------------A----GACAUC-GAAGCCG-------------------------------------CGUGAUUCA-A----C--GGCC-A-C----C-----------------GU-AAAUGGC-GCAGUUG--U-GCA-GUGAAA-----G-U-U-C-----AUG---UC
CP000233.1/58787-58961       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGAAG-------------------CUCGAUGA-----------GC-AAACCACU-G-C--ACUGA---------------------UGAACAA-AAA-U--CG--AC-UG-UAAGG---C-C-AA--GG--GG-AG-A-GGAUAAG-G-------------------------------U-UGCU--GU-------------------A----CAAACU-GAAGUCCAA------------------UACUACU----------CGAAACAAA-C----C-------U-U----G-----------------GU-AAAGUCG-GCAGUGACAU-GGU-GGGAAA-----G-U-U-A-----UCG---UC
CP000970.1/1128197-1128028   UUCAUC---G-CGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------U-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GU----UAAGG---C-G-GC--GC--AG-CA---GGGUAAG-G-------------------------------U-GGCA--CA-------------------A----AUCACC-AAAGCCC-----------------------GAUA---------CUCACACGGA-A----CG-CUGU-G-A----C-----------------GU-AAAGCCG-ACAGGCAUA--AGC-AGGAAA-----G-U-C-G-----CGU---GA
AP008230.1/1955702-1955872   UCCAUC---G-UGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGCCAG-C-------G-GC-AAAGUUCC-G-G--CCUGA---------------------GGGACAC-AAA-C--AG--CA----UCAGG---C-G-CG-AAA--CG-UG---GGGUGAG-A-------------------------------C-UGCG--CG-------------------A----CAAGUC-GAAGCCC-----------------------AAAA----------GCUACACGG-A----CA-CGUC-A-G----C-----------------GU-AAAUGGU-GCGGGUAGAU-GGA-AUGAAA-----G-U-G-A-----AUC---AU
AP006840.1/1101239-1101408   UCUGUC---G-UGA-GGCG-G--A-AUC-UGAA-GGA-----------------------AGCCCG-A-------G-GC-AAAGCCAC-G-A--CCCGA---------------------GGAACAC-GAA-C--CC--CA-UA-GGAGG---C-U-GU--GC--CG-CU-C-GGGUGAG-C-------------------------------U-GGCC--GA-------------------A----CACAGC-AAAACCCG--------------------AA--------------GCUGCCAAA-G----GG-CGGU-G-C----G-----------------GU-AGAUGGG-GCGGGUG--C-GGG-GUGAAG-----G-U-C-A-----GCG---UC
ACCS01000007.1/74341-74512   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGCCCC-G-A--CCUGA---------------------GGACCAC-GAA-C--CC--AA-GG-UGAGG---C-U-GC--UG--CA-UU-C-GGGCGAG-U-------------------------------C-UGCU--AA-------------------A----CAAGAC-AAAGCCC-----------------------CAUA---------CAGCCAAGG-------GA-UGCA-G-C----A-----------------GU-AAAUUGG-GCAGGUACAU-GGG-GUGAAA-----G-C-G-A-----CCG---UU
AATN01000130.1/14456-14630   GUCGUC---G-CGA-GGCG-G--G-GUC-UGGA-GGA-----------------------AGCCCA-A-------U-CC-AAAGCUGC-G-G--GGCGA---------------------UGAACAA-GAA-C--CG--GA-UA-UCAGG---C-G-UG-AUG--CA-UC-CGGGGCGAG-C-------------------------------G-GGCA--CG-------------------U----GACCGC-AAAGCCC-------------------------GC---------CAUCUGCGGU-UG--GGG-UGCAUU-U----U-----------------GU-AAAUUCG-GCGUCUA--U-GCA-GCGAAG-----G-U-A-A-----CGU---GU
AP009389.1/2357763-2357595   GUCACC---GGUAAAGGUG-A--U-GUC-UGAA-GGA-----------------------AGCCGA-A-------G-GG-GGAACUUG-G-A--ACAUA--------------------GCGUAAGC-GAA-C--CG--GU----GUUGG---C-U-GC--UC--AG-GC---GGGUAAC-C-------------------------------U-UGCA--UA-------------------A----UAUGGG-AAAGCCC-----------------------GAAA----------GCUGGAUA-------AC-CUGA-G-A----A-----------------GU-UAGGACG-GAUGCGU--U-CAA-GUUCAG-----G-C-A-G-----GCA---GA
AAQL01007186.1/650-843       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GAAAGUCGGAUGUG-GGAACAGACUAACCACG-A---------GC-AAAUCUCU-G-G--UCUGA---------------------UGAACAG-AAA-U--CU--CA-UA-UAAGG---U-U-AU--GC--AU-GA---GGGUAAG-G-------------------------------C-UGCA--AG-------------------C----CAAGUU-AAAGCCC-----------------------AAUA---------ACUACAUGGA-A----UC-AUGC-G-U----G-----------------AU-AAAUGAG-GCAGAUGAAU-GGA-GAGGGA-----G-A-A-A-----CGU---GU
CP000232.1/476506-476674     CCCAUC---G-CGA-GGUG-G--A-AUC-CGAA-GGA-----------------------AGCUGG-A-------G-AC-AAGGCCAC-G-G--CCCGA---------------------UGAACAG-GAA-C--CC--CA-UA-CGAGG---C-U-GU--AC--CG-CC-C-GGAUGAG-C-------------------------------U-GGCA--CA-------------------A----CAAAGC-GAAAUCC-------------------------------------GGGCUACGA-AG--GGG-CGGU-A-G----A-----------------GU-AUAUGGG-GCGGGCG--C-GGG-GUAUAG-----G-U-U-A-----GCG---AU
AP008230.1/5195000-5194829   UCCACC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCAGUC-------G-GC-AAAGUUCU-G-A--CCCGA---------------------GGAACAC-GAA-C--AC--CA----UCAGG---C-G-CG-AAA--CG-UG---GGGUAAG-A-------------------------------C-UGCU--AA-------------------A----CAAGUU-AAAGCCC-----------------------AAAA----------GCUGCACGG-A----CA-CGUC-A-G----C-----------------GU-AAAUGUU-GCGGGUACAU-GGA-AUGAAA-----G-U-G-A----AUCG---U-
ABPR01009907.1/853-685       UUGCUG---G-UAA-CGGC-A--GGGUC-UGAA-GGA-----------------------AGCAAU-A-------U-G--AAGUGAGCGG-U--ACAUA--------------------GCACAAGC-GAA-C--CU--GA----UUCGG---C-A-UC--AU--AA-GG---GGGUAAG-C-------------------------------G-UGCA--AA-------------------A----UAGCGC-AAAGCCC-----------------------UAUA---------CCUGGUCAG-------CC-UUAU-G-G----U-----------------GU-GAUUGAG-GAUGGCA--UUGCU-CACAGG-------G-U-U-----CUC---GC
AACY023777304.1/705-876      GCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGC-A-------G-GC-AAAGCGCU-G-G--UUCGA---------------------CGAACAG-GAA-G--UG--CA-UA-UGAGG---C-G-GC--CA--UG-CU---GGGUGAG-G-------------------------------A-GGCA--AA-------------------U----AUCUUC-AAAGCCC-----------------------AAAU---------CUGACACGGA-A----AG-CAUG-G-U----C-----------------GU-AGAUGCG-ACGGAUAUA--AGC-GUGAAA-----G-U-G-A-----GUG---UG
ABIY02000077.1/74608-74437   UCCAUC---G-CGA-GUUG-G--A-AUC-UGAA-AGA-----------------------AGCUGG-C-------G-GC-AAACAUCU-G-G--UCUGA---------------------CGAACAG-AAA-C--CU--CA-UA-UAAGG---C-A-UA-UGA--CC-GU---GGGUAAG-G-------------------------------U-UGCG--AA-------------------A----CAAACU-AAAGCCC-----------------------UAUA----------GCUAUUCGG-G----AC-GGUU-A-G----U-----------------GU-AAAUGGA-GCAGACAUA--AGA-UUGAAA-----G-U-U-A-----AUA---CC
AACY020305625.1/610-442      CCCAUU---G-UGA-GGUG-G--G-AUC-UGAA-GGA-----------------------AGCUGA-U-------G-GC-AAAGUAUG-G-C--AGUGA---------------------CGCACAG-AAA-U--CA--GA----UUAGG-----U-AU--AU--AU-GA-CUGGGUAAC-C-------------------------------C-AGCC--AG-------------------A----GAUGGA-AUAACCC-----------------------GAAC----------UCGAACGGA-AG--UGC-AUAU-G-U----A------------------U-AGAUCUG-GCAUAG---C-CAU-ACGAAG-----G-A-G-C-----UAC---GU
ABIY02000064.1/52124-52297   UCCUUC---G-CGA-GGAG-G--A-ACC-UGAA-GGA-----------------------AGCUGG-C-------G-GC-AAACUCUC-G-G--CUCUA---------------------CGAACAG-AAA-C--UG--AU-UA-UAAGG---C-U-AC-AUU--UG-GA---GGACAAG-U-------------------------------U-UGCU--AA-------------------A---CAAAA-U-AAAGUCC-----------------------UAUA----------ACUAUCCGA-A----UC-CCUAUG-U----A-----------------GU-AGAAUCA-GAGGGUAUAU-GAG-AUGAAA-----G-C-G-U-----ACG---UU
AB126575.1/44-216            UCUGGG---G-UGA-CCCA-G--A-AUC-UGAA-GGA-----------------------AGUCGG-C-------G-GC-AAACCUCC-G-C--UCCUA---------------------GGAACAC-GAA-C--UU--CA-UA-UAAGG---C-U-AG--GU--AG-ACUU-GGGUGAG-A-------------------------------U-UGCC--UA-------------------A----CAAAUC-AAAGUCCA---------------------G--------------ACUGCCAAA-G---GGU-CUAC-C-G----A-----------------GU-AAAUGAA-GAGGAGACAU-GGA-GGGGAA-----G-A-A-U-----GUG---UA
ABPP01010957.1/286-117       GUCGUC---G-CGA-GGCG-G--G-GUC-CGCA-GGC-----------------------AGUGUG-C-------A-GC-GAACCCGC-G-A--CCCGA---------------------UGGACAA-GAA-C--CG--GA-GA-CGAGG---C-G-GU--AC--AG-GU-G-GGACGAG-C-------------------------------G-GGCG--GA------------------------UUCCGC-GAAGUCC------------------------------------AGGGCCACUA-AG--GGC-CUGU-G-C----C-----------------GU-AGAUCCG-GCGGGGG--U-GCG-GGGAAG-----G-CGG-U-----CGG---AC
AM902716.1/1113148-1113319   GCAAGG---G-CGA-CCGA-C--C-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GCGUAAACCGU-G-A--GCCGA---------------------UGAACAA-GAA-U--CG--GA-UA-CGAGG---C-A-CU--GC--CGAGC-A-GGGCGAG-C-------------------------------G-GGCA--AG-------------------A----AGCCGC-GAAGCUC------------------------------------UUGUGGCCAA-G----GUGAGGU-G-G----U-----------------GU-AUAUCCG-GCGGUUG--U-GCG-GUGAAG-----G-AGU-G-----UGU---UC
ABSP01029202.1/478-649       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGA-U-------G-GC-AAAACGCU-G-G--UCUGA---------------------CGAACAG-AAA-C--CG--CA-UA-CGAGG---C-G-GC--CA--UG-AC---GGACAAG-A-------------------------------G-GGCA--AU-------------------G----AGACUC-AAAGUCC-----------------------AGUU---------CUUGCACGGA-A----GU-CAUG-G-U----C-----------------GU-AGAUGCG-GCAGACAUA--AGC-GCGGAG-----G-U-C-A-----GUG---CG
AAFY01020218.1/733-903       CUUACC---G-CGA-GGUA-U--A-AUC-UGAA-GGA-----------------------AGCUAG-C-------G-GC-AAAAUUCC-G-A--UCUGA---------------------GGAACAA-GAA-U--AU--UA----UCAGG---C-G-CA-AUU--GU-UG---GGAUAAA-C-------------------------------U-UGCC--AA-------------------A----CAAAGC-AAAGUUU-----------------------AAAU----------ACUACACGG-A----CA-ACGA-A-G----U-----------------GU-AAAUGAU-ACGGGUACAG-GGA-AUGAAA-----G-C-U-A-----UUU---AC
AE014299.1/2126821-2126985   UUAUCC---G-CGA-GGAU-U--G-GUU-UAAA-GGA-----------------------AGCCGC-U-------A-GC-AAAUUUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G--U--AG--GC-UA-G-AGGUGAG-U-------------------------------U-GGCA--CA-------------------A----GACGAC-GAAACCA-------------------------------------GGUGAUCUA-A----UG-GCC--A-C----C-----------------GU-AAAUGAU-GCAGCAG--U-GCA-AAGAAA-----G-U-U-C-----AUG---UU
CP000891.1/2359830-2359642   UUAUCC---G-CGA-GGAU-U--G-CUC-UGAA-GGA-----------------------AGCCGC-U-------A-GC-AAAUUUAU-G-A--GCUGA---------------------UAAACAA-GAA-C--AU--CA-CA-UGAGG---C-G-UA--GA--CU-AG---AGGUGAG-U-------------------------------U-GGCA-GAGCUUCCCCACGCAGUAUGGGAACAAGACGAU-GAAACCA-------------------------------------CGUGAUCAA-A----U--AGCC-A-C----C-----------------AU-AAAUGAU-GCCGCAG--U-GCA-GAGAAA-----G-U-U-C-----AUG---UU
CP000879.1/1125156-1124983   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCCA-A-------G-GC-AAAGUCCC-G-G--UCCGA---------------------UGAACAA-GAA-C--CA--GA-UA-UAAGG---C-U-AA--GU--GA-AG-U-GGACGAG-U-------------------------------U-UGCC--AC-------------------U----CAAAAC-GAAGUCC-----------------------AACA---------GCUACCCUGA-A----CU-UCAC-G-G----A-----------------GU-AGAUCUG-GCGGAUAGAU-GGG-AUGAAA-----G-U-U-A-----UUG---CA
ABSR01024312.1/390-555       AAGGCC---G-CGA-GGAA-U--U-GUC-CGCA-GGA-----------------------AGCCCG-A-------GCGC-AAAGAUGC-G-A--GCCGA---------------------CGAACAG-AAA-C--UG--CA-UA-GAAGG---C-U-UA--GU--CC-UG---GGGCGAG-U-------------------------------U-GGCA--CU-------------------U----GACAAC-GAAGUCC-----------------------AAGG----------GUACA----------CG-GGAU-A-G----G-----------------GU-AAAUGCA-GCGGUUG--U-GCA-UCGACA-----G-A-U-C-----AUG---AA
ABSP01029686.1/658-829       GAAACC---G-UGA-GGU--C--A-GCC-UGAA-AGA-----------------------AGCGCG-U-------A-GC-AAAUGCAA-G-A--CCGUA---------------------GGAACAU-GAA-C--AA--GC--AGUGAGG---C---AG--GG--UG-UG-GGCGAUAAG-U-------------------------------G-UGCU--AG-------------------G----AAACAC-GAAAUCC-----------------------AACU----------GUUACCGAA-AG--ACG-CACC-A-A----------------------GU-AGAGCUU-GACGGCA--C-GGG-CAGAAA-----G-U-UUU-----AGC---AC
AAQL01008357.1/909-734       UCUAUC---G-UAA-GGUA-G--A-AUC-UGAA-GGA-----------------------AGCUGU-A-------A-GC-GAACUCUU-G-G--UCCGA---------------------CGGACAG-AAA-U--CA--CA-UA-UGAGG---C-U-AG--GU--UC-CG-CUUGGUAAG-U-------------------------------C-UGCC--AA-------------------A----UAAGAC-AAAGCCGUAA-----------------AGUUGCC---------GUUUGUAGGA-A----C-------C-G----A-----------------GU-AAAUGUG-GCGGAUAUAU-GAG-AGGAAAG---AG-C-G-U-----GCA-----
CP001034.1/611045-611216     CCCAUC---G-UGA-GGUG-G--G-AUC-UGAA-GGA-----------------------AGCUUA-A-------G-GC-AAAAUUCC-G-A--CCCAA---------------------GGCACAC-GAA-C--AU--CA----UCAGG---C-A-UA-AGG--UA-UG---GGAUGAG-U-------------------------------U-UGCA--AU-------------------A----CAAAAC-GAAGUCC-----------------------AAUC---------AACUACACGG-A----CA-UACC-A-G----U-----------------GU-AAAUGAU-GUGGGUACAU-GGA-AUGAAA-----G-U-U-A-----AUC---GU
ABZR01000449.1/3075-3241     UCGCGG---G-UGA-CUGC-G--A-AUC-UGAA-GGA-----------------------AGCCCG-A-------G-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAG-G--CG--GA----UGAGG---C-G-GC--AC--AG-CG---GGGUAAG-G-------------------------------C-GGCC--GC-------------------A----AUCGUC-AAAGCCC-----------------------AAUA---------CUUGCACGGA-A----CG-CUGU-G-A----A-----------------GU----UCUG-ACAGGCACA--AGC-AGGAAG-----G-U-C-G-----UGC---GA
ABSP01043891.1/735-571       GGGAUC---G-CGA-GGUC-U--C-GUG-GGAA-GGA-----------------------AGCCUC-A-------G-UC-AAAGCUGAUG-A--GCCGA---------------------CGAACAG-AAA-G--AU--CA-UA-UCAGG---C-U-GA--CG--GA-GC---GGACAAG-C-------------------------------U-GGCA--CC-------------------A----CACAGC-CAAGUCC-------------------------------------GGUGUUCA-------AC-UCCG-G-A----G-----------------GU-AAAUGAU-CCGGCUG--CG-CA-GCAAGA-----G-U-U-C-----ACG---UC
CP000155.1/2179715-2179544   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGU-A-------G-GC-AAAGCACU-G-G--CCUGA---------------------CGAACAG-GAA-U--CG--CA-UA-CGAGG---C-G-GC--CA--CA-CU---GGGUAAG-G-------------------------------C-GGC---AA-------------------A---UACCGUC-AAAGCCC-----------------------GUAC----------UUGCACGGA-A----GG-UGUG-G-A----C-----------------GU-AGAUGCG-GCGGGCAUA--AGU-GUGAAG-----G-U-C-A----CGCG---UC
CR522871.1/8127-7959         UUGCUG---G-UAA-CGGC-A--GGGUC-UGAA-GGA-----------------------AGCGAU-A-------G-G--AAGUGAGUGG-U--ACAUA--------------------GCGAAAGC-GAA-C--CU--GA----UUCGG---C-G-AU--GC--GG-GA---GGGUAAA-C-------------------------------G-UCCG--AA-------------------A----UAGCGU-GAAGCCC-----------------------AAUA---------CUUGGUCAA-------UC-CCGU-A-U----C-----------------GU-GCUUGAG-GAUGCGA--UUGCU-CACAGG-------G-A-G-----UUC---GC
AAFY01013036.1/490-660       UCUAUC---G-UGA-GGUA-G--U-GGC-UGAA-GGA-----------------------AGCGUG-U-------A-GC-GAAACUUU-G-A--ACCUA---------------------UGGACAA-GAA-C--UU--GA-UAAGAAGG---C-U-AU--GA--GG-U----GGACAAG-G-------------------------------U-AGCA--AU-------------------U----GAUACU-GAAAUCC-----------------------AAAG----------GUAAACGUA-A----AA-CC---G-AA-GUA-----------------GU-AAAUCAA-GAGGUAA--U-GAA-GUGAAA-----G-A-U-U-----AGA---AU
AP008955.1/811288-811460     UCUACC---G-UGA-GGUG-G--A-AUC-UGGA-GGA-----------------------AGCCGG-C-------G-GC-AAAGUCCC-G-A--CCUGA---------------------GGUACAC-GAA-U--CC--AA-UU-UGAGG---C-U-GU--UG--UA-UU-C-GGGCGAG-U-------------------------------C-UGCU--GA-------------------A----CAAGAC-GAAGCCC-----------------------UAUA---------CAGCCAAGG-------AA-UACA-G-C----A-----------------GUAAACUUGG-GCAGGUACAU-GGG-AUGAAA-----G-U-U-A-----UCG---CU
CP000921.1/536987-537157     ACUAUC---G-UGA-GGUA-G--C-AGG-GAGA-GGA-----------------------AGGGAU-A-------G--C-GAAAUCGU-G-G--CUCUA---------------------CGAACAG-GAA-C--GU--GA-UAGUAAGG---C-G-UA--UA--UA-GC---GGAUAAG-G-------------------------------G-GGCC--UC-------------------A----AACUCU-AAAGUCCA---------------------AAAAG----------GUAGUCGUA-A----CC-UAUA-U-G----C-----------------GU-AAAUCAC-GAGAGUA-A--ACG-AGGAAA-----G---A-U-----GUA---CG
ACIH01000268.1/85-257        UCUAUC---G-CGA-GGUA-G--A-AUC-UGAA-GGA-----------------------AGCCGG-C-------G-GC-AAAUCUCC-G-G--CCCGA---------------------GGAACAC-GAA-C--CU--CA-UA-UGAGG---C-U-GG--CA--UU-CG-UUGGAUGAG-G-------------------------------C-UGCA--UG-------------------A----CAAGUC-AAAGUCC------------------------------------UUACUGCCGA-AG--GCG-AAUG-A-G----A-----------------GU-AAAUGAG-GCGGGUAGAU-GGA-GAGGAA-----G-A-U-A-----ACG---CU
CP001472.1/3723475-3723644   ACCGUC---G-CGA-GGCG-G--G-GUU-UGAA-GGA-----------------------AGCGUG-G-------A-GC-AAAUGCGC-G-A--GUCGA---------------------UGGACAA-AAA-C--CG--GA-UA-CAAGG---C-G-U--GAG--CG-UA---GGGCGAG-C-------------------------------G-GGCA--AC-------------------U----UACCGC-GAAGCCC------------------------AUA---------UCCAUUAAG-------UA-CGCGG-AG----C-----------------GU-AGAUCCG-GCGACUG--U-GCG-CAGAAG-----G-CGA-U-----UGA---GC
ABGO01000001.1/116123-115947 CCCGUC---G-CGA-GGCG-G--A-AUC-UGAA-GGA-----------------------AGCCGA-A-------GCCC-CCAGUCGG-G-A--GCCGA---------------------CGAACAG-GAA-C--CG--GA-UA-UCAGG---C-C-GG--CG--UG-GC-G-GGGUCAG-C-------------------------------G-GGCA--AC-------------------G----GACCGC-GAAGCCC-----------------------AAUC----------UCACUCGGA-C----GCACACG-C-G----G-----------------GU-AAAUCCG-GCGGUCG--C-UCG-ACGAAGCA-ACG-C-A-A-----CUU---AC
CP000685.1/4418055-4417884   UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCAGU-A-------G-GC-AAACUCUU-G-G--CCUGA---------------------CGAACAG-AAA-C--UA--UA-UA-CAAGG---C-C-AG--AA--AU-GU-U-GGAUAAG-G-------------------------------U-UGCU--AU-------------------A----CAAACC-GAAGUCC-----------------------CAAA----------CUGUACGGG-A----AC-AUU--A-U----G-----------------GU-AAAUAUA-GCAGGCAGAU-GAG-AGGAAA-----G-U-U-A-----UCG---UU
AAFY01010105.1/774-610       UAAAUC---G-CGA-GAGA-U--A-GUC-UGAA-GGA-----------------------AGCCGC-U-------A-GC-AAAUCUGU-G-A--GCUGA---------------------UGACCAA-AAA-C--AU--CA-UA-UGAGG---C-G-UA--GG--CU-GG---AGACGAG-C-------------------------------U-AGCA--CA-------------------A----GAUAGC-GAAGUCA-------------------------------------UGUGAUCUA-A----C--GGCC-A-C----C-----------------GU-AAAUGAU-GCAGUUG--U-GCA-GAGAAA-----G-U-C-G-----AUG---CA
AATO01004044.1/998-824       GUCGUC---G-CGA-GGCG-G--G-GUC-UGGA-GGA-----------------------AGUCCA-A-------U-CC-AAAGCUGC-G-G--GGCGA---------------------UGAACAA-AAA-C--CG--GA-UA-UGAGG---C-G-UG-AUG--CA-UC-CGGGGCGAG-C-------------------------------G-GGCA--CG-------------------U----GACCGC-AAAGCCC-------------------------UC---------CAUCUGCGGU-UG--GGG-UGCAUU-U----U-----------------GU-AAAUUCG-GCGUCUA--U-GCA-GCGAAG-----G-U-A-A-----CGU---GU
ABVL01000047.1/3619-3450     GCGACC---G-CGA-GGUC-G--U-GGC-UGAA-AGA-----------------------AGUCGC-A-------G-GC-AAAACUCC-G-A--CCGCA---------------------GGAAGAC-AAA-C--UG--GC--AGAGAGG---C-C-GG--GC--GU-GG-G-CGACGAG-C-------------------------------G-UGCG--AG-------------------G----AACCGC-GAAGUCC-----------------------GAAG----------UCCAUCCAG-A----C--ACGU-C-A----G-----------------GU-AGAGCCA-GGCGGCG--C-GGA-GGGAGA-----G-U-U-C-----AGG---UU
CR378679.1/156499-156663     UUUUCC---G-CGA-GGAA-C--G-GUC-UGAA-GGA-----------------------AGCCGC-U-------A-GC-AAAACUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G--U--AG--GU-CA-G-AGGCGAG-U-------------------------------U-GGCA--CA-------------------A----GACGAC-GAAGCCA-------------------------------------AGUGAUUUA-A----UG-ACC--A-C----C-----------------GU-AAAUGAU-GCAGUUG--C-GCA-GUGAAA-----G-U-C-C-----AUG---UC
CP000936.1/1076401-1076564   GGAAAU---A-AGA-AUU-------GUC-AGAA-GAA-------------------------GGGA-U-------A-GA-GAAAUCGU-G-G--CUCUA---------------------CGAACAG-GAA-C--GU--GA-UAGUAAGG---C-G-UA--UA--UA-GC---GGAUAAG-G-------------------------------G-GGUC--UC-------------------A----AACUCU-AAAGUCCA---------------------AAAAG----------GUAGUCGUA-A----CC-UAUA-U-G----C-----------------GU-AAAUCAC-GAGAGUAAUU-G-------AA-----U-U-C-G-----UAC---UA
BAAV01019325.1/295-468       A-UACC---A-UAAAGGUA----G-GGG-UGAA-GGA-----------------------AGUGGUGU-------A-GC-AAUUCCUUUG-A--GCGUA---------------------CGAACAG-AAA-C--UU--GA-UA-CAAGG---C-U--A-AAU--GG-U----GGAUAAG-G-------------------------------U-UGCC--UU-------------------A----CAAACC-GAAGUCC-----------------------AAAA---------GGUAAACGUA-A----AA-CCAAGA-G----A-----------------GU-AAAUCAA-GACGUUG--UGAAG-GANACA-----GGA-U-U-----AGU---GA
AAOF01000010.1/2126-1951     UGACCG---G-AAA-CGGA-G--U-GUC-UGAA-GGA-----------------------AGCAUG-A-------G-GCAGAACCCGU-G-U--ACGUA--------------------GCGAACAGCGAA-C--CG--GC-UA-UAUGG---U-G-UU--GG--GG-AU-GAGGUCGAG-C-------------------------------C-GACG--UG-------------------A----CUAGGC-GAGGCCU-----------------------GAUA----------UCCGGAGAA-CU--GAA-CC---G-A----C-----------------AU-GAAGCCG-GACGGGA--U-ACG-GGGAGG----UG-G-U-G-----CGU---CU
AF339846.1/29490-29646       UCCUGA---G-CAA-UUGG-G--A-AUC-UGA-----------------------------------A-------G-GC-AAAAUGUG-G-A--UUUGA---------------------CGUACAG-GAA-G--UA--GA-UA-UUAGG---C-C-UA-AGC--CU-GG---GGGUAAG-C-------------------------------U-UGCA--UU-------------------G----GAAGAU-GACGCCC-----------------------AAAA---------UCCAUCCGUA-A----CC-GAGCAA-G----G-----------------GU-AAAUCUG-ACGAAU---C-CAC-AGGAAA-----G-A-A-G-------------
ACKS01000046.1/1624-1817     UUCAUC---G-UGA-GAUG-A--A-AUC-UGAA-GGA-----------------------AGCUGG-C-------G-GC-AAACAUCU-G-A--CCUAA---------------------CGAACAG-AAA-C--UU--CA-UA-UAAGG----CA-UA--UA--AC-CA-U-GGAUAAG-A-------------------------------U-UGCA--UA-------------------A----CAAAUC-AAAGUCC-----------------------UAUA---------GCUAUUCGGA-A----UG-GUUG-G-UGGAGUUUCCUUGAGCUUAGCGAAA-AAAUGAA-GUAGGUAUA--AGA-UGGAAA-----G-A-U-A-----AUG---UU
ABPW01002440.1/483-653       GUCGUC---G-CGA-GGCA-G--G-GUC-CGAA-GGC-----------------------AGUGUG-G-------A-GC-AAACCCGC-G-A--CCCGA---------------------UGGACAA-GAA-C--CG--GA-UA-CGAGG---C-G-GU--AC--AG-GU-G-GGACGAG-C-------------------------------G-GGCG--GA-------------------U----GACCGC-GAAGUCC------------------------AGG----------GCCAUCAAG-G----GC-CUGU-G-C----C-----------------GU-AGAUCCG-GCGGGGG--U-GCG-GGGAAG-----G-CGG-U-----CGG---AC
CP000418.1/20375-20206       UCUAUC---G-UGA-GGUA-G--A-AUC-UGAA-GGA-----------------------AGUCCU-A-------G-AC-GAAACAUC-G-A--AUCGA---------------------UGAACAA-GAA-G--UG--GC-UA-AAAGG---C-U-GG-AAA--CG-GU-G-GGAUGAG-A-------------------------------U-UACC--UA-------------------A----CAAAUC-GAAGUCC-------------------------CU---------GACCACUCGA-A----AC-CGUC-A-C----A-----------------GU-AAAGCCA-ACGGUU---U-GAU-GCGAAA-----G-C-U-A-----CUG---CU
AP006840.1/1687432-1687601   UCCGUC---G-CGA-GGCG-G--A-AUC-UGGA-GGA-----------------------AGCCGG-A-------G-GC-AAAGCCAC-G-A--CCCGA---------------------GGAACAC-GAA-C--CU--CA-UA-CGAGG---C-U-GU--GC--CG-CC-U-GGGUGAG-C-------------------------------U-GGC---GA-------------------A---CCACAGC-AAAACCCG--------------------AG--------------GCUGCCAAA-G----GG-CGGU-G-C----A-----------------GU-AGAUGGG-GCGGGUG--C-GGG-GCGAAG-----G-U-C-A-----GCG---UC
EF066650.1/144488-144317     GGCGCC---G-CGA-GGCC-G--U-GUG-GGGA-GGA-----------------------AGUCCG-A-------G-GC-GAACCGCA-G-C--ACCGA--------------------ACGAAAGU-GAA-C--CC--CC-GA-GCAGG---C-C-GG--AU--CG-AC-C-GGGUGAG-C-------------------------------G-UGCC--UA-------------------C----AAACGC-GACGCCC-----------------------AAAA----------UCCAACCGA-G----GU-CGAU-A-C----G-----------------GU-AGUGGGG-GCGGGAG--C-GGC-GGGACA-----U-C-C-A-----GUG---UU
ABLK01000531.1/2332-2161     UCCCGG---G-UGA-CUGG-G--A-GUC-UGAA-GGA-----------------------AGCCGGAU-------G-GC-AAAGCGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GA-UA-CGAGG---C-G-UG--GC--GA-CU---GGGUAAG-G-------------------------------U-GUCC--CA-------------------A----UUCACC-GAAGCCC-----------------------GAAA----------CUUGCACCG-A----CG-UUGC-U-A----C-----------------GU-AGAUCCG-ACAGGCAUG--AGC-GUGAAG-----G-U-G-G-----GUG---CG
CP000471.1/3862593-3862419   UCCAUC---G-UGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGCUGC-U-------G-GC-AAAGUUCC-G-G--CCCGA---------------------CGAACAG-GAA-U--CG--CA-UA-CGAGG---C-A--G--CC-AUA-UC-U-GGGCGAG-G-------------------------------G-AGCC--AU-------------------G----AUACCC-AAAGCCC-----------------------GAUC---------GUCAUCCAGA-A----GA-UAGG-G-A----A-----------------GU-AUAUGCG-GCGGGUAUAU-GGA-AUGAAG-----G-UCU-C-----GUG---UC
CP001157.1/4653345-4653174   GUGAGG---G-CGA-CCGA-G--C-GUG-GGGA-GGA-----------------------AGCGCG-G-------A-GCGUAAAUCGU-G-A--GCCGA---------------------UGAACAA-GAA-C--CG--CA-UA-GAAGG---C-G-CU--GC--CG-AG-CAGGGCAAG-C-------------------------------G-GGCC--AG-------------------U----AACCGC-GAAGCUC-------------------------------------UUGUGACCA-AG--GCG-AGGC-G-G----C-----------------GU-AGAUGCG-GCGGUUG--U-GCG-GUGAAG-----G-AGU-G-----CGU---UC
AAFY01007241.1/596-401       UAAUCC---G-UGA-GGAU-U--G-GUC-UGAA-GUA-----------------------AGCGAGAC-------U-AC-AAAGGUUG-G-U--ACUGACAUUCGGAAA-CGAUAGUUUUCGACCA----A-U--UG--AA-UA-AGAGG---C-U-UG--UA--AA-AU-C-GGAUAAG-U-------------------------------U-GCCA--CA-------------------U----CACAAC-AACGUCCAAAGC------------UCUGCAUAGA---------GAUUGU----------AU-UUUA-C-A----A-----------------GU-AGAUUCA-GCAGUGA--U-UAA-CCGAAG-----G-A-C-A-----AUU---AC
CP000753.1/2600782-2600594   UUAUCA---U-UGA-UGAU-U--G-GUU-UGAA-AGA-----------------------AGCCGC-U-------A-GC-AAAUUUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G-UA--GG--CU-AG---AGGUGAG-U-------------------------------U-GGCAGGGCCUUCCCCACUAAGUAAGGGGACAAGACGAC-GAAACCA-------------------------------------CGUGAUCUA-A----U--GGCC-A-C----C-----------------GU-AAAUGA--GCAACCA----GCC-UUCAACC--GCG-A-U-U-----UAU-----
CP000155.1/7212018-7211847   UUCACC---G-CGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AACCGA-A-------G-GC-AAACCACU-G-G--CCCGA---------------------CGAACAG-GAA-U--CG--CA-UA-GGAGG---C-G-GC--CA--UA-GC---GGGUGAG-G-------------------------------U-AGCC--CA-------------------U----ACUGCC-AAAGCCC-----------------------AAUA---------CUUACACGGA-A----GC-GAUG-G-A----C-----------------GU-AAAUGCG-GCGGGUAUA--AGU-GGGAAG-----G-U-C-A-----CGC---GC
ABAW02000024.1/28705-28860   UCUAUC---A-UGA-GGUG-G--A-AUC-UUAAAGGA-----------------------AGCCGG-U-------G-GC-AAAAUCUU-G-A--AUCUA---------------------UGGACAA-GAA-C--UG--GU-CA-AAAUG---C-A-CA-UAA--GG-UA---GGAUAAG-G-------------------------------U-UUCC--AA-------------------A----CAAAUC-AAAGUCU----------------------------------------------------UA------U-G----U-----------------GU-AAAAUCA-GAGGUUAUAU-GAG-AGGAAA-----G-U-U-A-----CUG---CA
ABLD01000001.1/438817-438988 GUGAGG---G-CGA-CCGA-G--C-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GC-GAAACCGC-G-A--GCCGA---------------------UGAACAA-GAA-C--CG--GA-UA-UGAGG---C-G-GU--GC--C--GAUCAGGGCGAG-C-------------------------------G-UGCA--AA-------------------G----AAGCGC-GAAGCUC------------------------------------UCGUGGUCAA-GG--AUC-AGGC-A-A----C-----------------GU-AAAUGCG-GCGGUUG--U-GCG-GUGAAG-----GAU-U-G-----CGU---UC
AAFX01107585.1/676-503       AUCGCC---G-GCA-GGCG-G--GGGUU-UGAU-AGA-----------------------AAGCACCA-------A-GCACAAUGCGC-G-A--GUCGA---------------------UGGACAA-AAA-C--CG--AA-UA-CAAGG---C-G-CG-AGC-----CC-C-GGACGAG-C-------------------------------G-GGCA--AG-------------------G----UACCGC-GAAGUCC------------------------AUA----------UCCAUCACG-C----GU---GCGA-A---GC-----------------GU-AGAUUCG-GCGACUG--U-GCG-CGGAAG-----G-CGGCU-----GAG---CU
AAQL01009711.1/579-409       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGGUGG-A-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UCAGG---C-U-AU--AG--UU-AA---GGAUAAG-G-------------------------------U-UGCC--AA-------------------A----CAAACC-AAAGUCC-----------------------AAUA---------ACUACUCGGA-A----UU-AACU-G-U----A-----------------GU-AAAUGUG-GCAGAUAUAU-GGA-GAGAAA-----G-U-G-A-----CGU---GU
CP000879.1/722601-722773     CCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCUGG-A-------G-GC-AAAAUCCC-G-G--CCUGA---------------------UGAACAA-GAA-C--UG--CA-UA-CAAGG---C-U-GA--AU-UGA-AG-U-GGAUGAG-U-------------------------------U-UACU--GA-------------------A----CAAAAC-GAAGUCC-------------------------GA---------CACUGCCCGA-A----UU-UCAU-A-C----A-----------------GU-AAAUGUG-GCGGGUAGCU-GAA-AUGAAA-----G-C-U-A-----UCG---UA
CP000922.1/2427915-2427742   UCCGUG---G-CGA-CACG-G--A-AUC-UGAA-GGA-----------------------AGCGAG-C-------G-GC-AAACUUCC-G-G--UCUGA---------------------GGAACAC-GAA-C--UU--CA-UA-UAAGG---C-U-AG--GU--AU-CA-UUGGAUGAG-U-------------------------------U-UGCU--AA-------------------A----CAAAAC-AAAGUCC------------------------------------UUUCUGCCGA-AG--GUG-AUAC-A-G----A-----------------GU-AAAUGAA-GCAGAUAGAU-GGA-AGGAAA-----GAU-U-G-----CAC---UC
AY437915.1/1844-2014         ACUAUC---G-UGA-GGUA-G--C-GGG-GAGA-GGA-----------------------AGGGAU-A-------G--C-GAAAUCGU-G-G--CUCUA---------------------CGAACAG-AAA-C--GU--GA-UAUGAAGG---C-G-UA--UA--UA-GC---GGAUGAG-G-------------------------------G-GGCU--AU-------------------A----AACUCU-AAAGUCCA---------------------A-AUA---------GGUAGUCGUA-A----CC-UAUA-U-A----C-----------------GU-AAAUCAC-GAGAGUA-A--ACG-AGGAAA-----G---A-U-----GUC---CG
AAFX01094026.1/625-796       GCGAGG---G-UGA-CCGA-G--C-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GCGUAAGCUGC-G-A--GCCGA---------------------UGAACAA-GAA-U--CG--GA-UA-GAAGG---C-G-CU--GC--CGAGC-A-GGGCGAG-C-------------------------------G-GGCC--AG-------------------A----AACCGC-GAAGCUC------------------------------------UCGUGAUCAA-G----GC---G--A-AGUGGC-----------------GU-AGAUCCG-GCGGUUG--U-GCA-GCGAAG-----G-AGU-G-----CGU---UC
ACFY01000039.1/47997-48190   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGAAGCCGGAUGUG-GGAACAGACUAAC------CA---CGG-GC-AAAUCUUU-G-G--UCUGA---------------------CGAAUAG-AAA-U--CU--CA-UA-UAAGG---U-U-AU--GC--AU-GA---GAGUAAG-G-------------------------------C-UGCC--AA-------------------C----CAAGUC-AAAGCUC-----------------------AAUA---------ACUAUACGGA-A----UC-AUGC-G-U----G-----------------AU-AAAUGAG-GCAGAUGGAU-GGA-GAGGAA-----G-A-A-A--------CGUGU
AE015451.1/4348934-4348764   UCGCGG---G-UGA-CCGC-G--A-AUC-UGAA-GGA-----------------------AGCCCG-A-------G-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GA-UA--GAGG---C-G-GC--AC--AG-CG---GGGUGAG-G-------------------------------U-GGCA--CA-------------------A----AUCGCC-AAAGCCC-----------------------AAUA---------CUUGCACGGA-A----CG-CUGU-G-A----C-----------------GU-AGAUCCG-ACAGGCAUA--AGC-AGGAAG-----G-U-C-G-----CGC---GA
CP000924.1/2284920-2284748   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCUUA-A-------G-GC-AAAAUCUC-G-G--UCUGA---------------------UGAACAA-GAA-C--CA--GA-UA-AGAGG---C-U-GA-AUU--GG-GA-U-GGAUGAG-U-------------------------------U-UGCG--UA-------------------A----CAAAAC-GAAGUCCA---------------------A---C----------ACUACCCGA-A----UC-CCAU-A-U----A-----------------GU-AAAUCUG-GCAGAUAUAU-GAG-AUGAAA-----G-U-U-A-----UCG---UU
ACGC01000013.1/180-10        UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCCU-A-------G-GC-AAACUCUU-G-G--UCCGA---------------------CGAACAG-AAA-U--CA--CA----UAAGG---C-A-GG--UA--CG-UA---GGAUAAG-G-------------------------------C-UGCC--AA-------------------A----CAAGUU-GAAGUCC-----------------------AAUA---------ACUACACGGA-A----UA-CGUA-A-A----U-----------------GU-AAAUGUG-GCAGAUAGAU-GAG-AGGAAA-----G-A-A-C-----AUG---CC
ABVL01000009.1/95198-95029   GCGACC---G-CGA-GGUC-G--U-GGC-UGAA-AGA-----------------------AGUCGC-A-------G-GC-AAAACUCC-G-A--CCGCA---------------------GGAAAAC-GAA-C--UG--GC--AGCGAGG---C-C-GG--GC--GU-GG-G-CGACGAG-C-------------------------------G-UGCG--AG-------------------C----AACCGC-GAAGUCC-----------------------GAAG----------UCCAUCCAG-A----C--ACGU-C-A----G-----------------GU-AGAGCCA-GGCGGCG--C-GGA-GGGAGA-----G-U-U-C-----AGG---UU
CP000473.1/4192588-4192759   ACCGCC---G-CGA-GGUG-G--G-GUC-UGAA-AGA-----------------------AGCGUA-U-------A-GC-AAAUGUGC-G-A--GUCGA---------------------UGGACAA-AAA-C--CU--GA-UA-CAAGG---C-G--U--UA--GC-GC-C-GGACGAG-C-------------------------------G-GGCA--AC-------------------U----UACCGC-GAAGUCC------------------------AUA----------UCCAUCAAG-G----GU-GCGA-A-G----C-----------------GU-AGAUUCG-GCGGCUG--U-GCA-CAGAAGA--CGG-C-U-G-----AAC---UU
ABSN01010931.1/247-78        GCGACC---G-UGA-GGGA-G--C-GUC-UGAA-GGA-----------------------AGCGGG-G-------A-AC-GAACCGAC-G-G--GCUGA---------------------CGAACAG-AAA-C--CG--GA-UA-UGAGG---C-G-GU-GCU--GA-UC-A-GGGCGAG-C-------------------------------G-GGCA--CA-------------------U----GACCGC-GAAGCUC------------------------------------UCGUGACCAA-A----GG-UCAGUG-G----C-----------------GU-AAAUCCG-GUAGUCG--U-GUC-GGGAAG-----G-C-C-A-----GUG---UU
CP000514.1/3269980-3270153   GUCAUC---G-CGA-GGUG-G--G-GUC-UGGA-GGA-----------------------AGCCCA-A-------C-GC-AAAUUGUC-G-G--GGCGA---------------------CGAACAG-GAA-C--UG--GA-UA-UGAGG---U-G-UG-ACG--UA-CU-CGGGGCGAG-C-------------------------------U-GGCA--CG-------------------U----GACAGC-GAAGCCC-------------------------UC----------CAUCCGCAA-CG--GGG-UGCGUU-U----U-----------------AU-AAAUCCA-GCGUCUA--C-GCC-AGGAAA-----G-U-C-U-----AGG---GU
CP001390.1/1082609-1082774   GUCUCC---G-CGA-GGAG-G--G-GUC-UGGA-GGA-----------------------AGCCGG-A-------GCGC-AAAGCUAU-G-A--GCCGA---------------------CGAACAG-AAA-C--AG--CA-UA-UAAGG---C-C-GU--CA--UC-C----GGGCAAG-U-------------------------------C-AGCA--CA-------------------A----CAUGAC-GAAGUCCCAUGG------------AUUCAGGAGA----------A----------------------A-U----G-----------------GU-AAAUGCU-GCGGUUG--U-GUA-GCGACA-----G-U-U-C-----ACG---UU
AP007281.1/1524100-1523927   UCCACU---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGUCUA-A-------G-GC-AAAGUACU-G-C--ACCGA---------------------UGAACAA-GAA-G--UA--GC-UA-UAAGG---C-U-GG-AAC--UA-AC-U-GGAUAAG-A-------------------------------C-UGCA--UG-------------------A----CAAGUU-GAAGUCCA---------------------A-------------UACUACUCGA-A----GU-UACU-U-U---CA-----------------GU-AAAGCUA-CCGGUGACAU-GGU-ACGAAA-----G-U-U-A-----AUA---UC
AACY020561240.1/23902-24066  UUAUCC---G-CGA-GGAU-U--G-GUU-UGAA-GGA-----------------------AGCCGC-U-------A-GC-AAAUUUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G--U--AG--GC-UA-G-AGGUGAG-U-------------------------------U-GGCA--CA-------------------A----GACGAC-GAAACCA-------------------------------------CGUGAUCUA-A----UG-GCC--A-C----C-----------------GU-AAAUGAU-GCAGCAG--U-GCA-AAGAAA-----G-U-U-C-----AUG---UU
BABB01000690.1/3756-3927     UCUAUC---G-UGA-GAUG-G--C-UUC-UGAA-AGA-----------------------AGUUGG-C-------A-GC-AAACAUUU-G-G--CUUGA---------------------CGGACAA-AAA-C--UU--CA-UA-CAAGG---U-A-UU--UA--AU-CG-U-GGACAAG-G-------------------------------U-UACC--AA-------------------A----CAGACC-AAAGCCU-----------------------CAUA---------GCUAUUCAGA-A----CG-GUU--G-G----U-----------------GC-AAAUAAA-AUAAGUAUA--AGA-UGAAAA-----G-A-C-A-----AGA---UC
AAWL01000012.1/49276-49445   CCAACC---G-UGA-GGUA-G--G-GUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAACCGC-G-G--CCUGA---------------------UGAACAA-GAA-C--CC--CA-UA-CGAGG---C-U-AG--AC--CG-UU-C-GGAUGAG-C-------------------------------U-GGCG--UA-------------------A----CACAGC-UAAAUCCC--------------------AG--------------GCUGCCAAA-G----GA-CGGU-A-G----A-----------------GU-AAAUGGG-GCAGGCG--U-GCG-GGGAAA-----A-U-C-A-----GCG---UU
AE015927.1/1265626-1265752   UCCACC---G-CGA-GGUG-G--A-AUC-UGAA-UGA-----------------------AGUCGA-A-------G-GC-AAAAUCUC-G-G--UCUGA---------------------GAAACAA-AACAAAGUUCAAUACUACCCAAGUCCCUAGGAGUAAAUAUAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGAUAUAU-GAG-AUGAAG-----G-U-U-G-----UUG---UU
ABSN01032104.1/568-737       UGAGCC---G-UGA-GGCC-G--U-GUG-GGGA-GGA-----------------------AGCCGGAU-------G-AC-GAAACGGA-G-U--CCUGA--------------------ACGAAAGU-GAA-G--CC--UC---GUAAGG---C-A-GG--UC--GG-GC---GGGUGAA-U-------------------------------G-UGCC--UC-------------------A----GAACAU-GACGCCC------------------------------------AGUUUUCCGA-GC--AGC-CCGA-C-A----C-----------------GU-AGUGAGG-ACCGGA---U-GAC-GCGAAA-----G-U-UCA-----UCG---NC
CP000926.1/1829108-1828938   UCGCGG---G-UGA-CUGC-G--A-AUC-UGAA-GGA-----------------------AGCCCG-A-------G-GC-AAAAUGCU-G-G--CCUGA---------------------CGUAAAG-GAA-G--CG--GA-UA--GAGG---C-G-GC--GC--AG-CG---GGGUGAG-A-------------------------------A-AGCA--AA-------------------U----AUCUUC-AAAGCCC-----------------------AAUA---------CUUGCACGGA-A----CG-CUGU-G-A----C-----------------GU-AGAUCCG-ACAGGCAUA--AGC-AGGAAG-----G-U-C-G-----CGC---GA
CP000388.1/777249-777413     UUGACU---G-CGA-GGUC-U--G-GUC-UGGA-GGA-----------------------AGCCGG-A-------C-GC-AAAGCUGC-G-A--ACUGA---------------------UGAACAA-GAA-C--UU--CA-UA-UAAGG---C-A-UA--GG--CU-AA---AGUUGAG-U-------------------------------U-GGCA--CA-------------------A----UGUGAC-GAAACCA-------------------------------------UGUGUUCUA-A----C--GGUC-A-C----C-----------------GC-AAAUGAU-GCA--UCAGU-GCA-GUGAAA-----G-U-U-C-----AUG---CU
CP000142.2/3351784-3351673   UCCACC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGC-A-------G-GC-AAACUUCC-G-G--CUCGA---------------------CGAACAG-GAA-U--CGCCGUGUACGGAACCGUACGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CG-GUG-GUG--U-GGG-AGGACG-----G-C-G-G-----GGG---UA
ACDK01000011.1/30650-30823   UCCAUA---G-UGA-AGUG-G--A-AUA-UUAA-GGA-----------------------AGUUGG-C-------G-GC-AAACCUUU-G-G--UCUUA---------------------GGUACAC-AAA-U--CA--CA-UU-UGAGG---U-U-UG-AUU--CU-UU---GGGUAAG-U-------------------------------U-UGAA--UA-------------------A----CAAAGC-GAAGCCC-----------------------AAUA----------ACUAUCAGA-A----AACAGAU-A-A----A-----------------GU-AUAUAUG-GCAGAUAGGU-GAA-GGGAAA-----G-U-A-C-----GCG---UU
AATN01000094.1/13798-13972   GUCGCC---G-CGA-GGCG-G--G-GUC-UGAA-GGA-----------------------AGCCCA-A-------U-CC-AAAGCUGC-A-G--GGCGA---------------------UGAACGA-AAG-C--CG--GA-UA-UCAGG---C-G-UG--AU--GU-ACUCGGGACGAG-C-------------------------------G-GGCA--CG-------------------U----GACCGC-GAAGUCC-----------------------UCCA----------UCUGCGGUU-GG--GGU-GCAU-U-U----U-----------------CU-AAAUCCG-GCGUCUA--U-GCA-GCGAAG-----G-U-A-A-----CGA---GU
FM211187.1/940809-940973     AAUAUC---G-UGA-GGUA-G--G-GGG-GAUA-GGA-----------------------AGGAAU-U-------A-GC-GAAAUCAA-G-G--UUCUA---------------------CAAACAG-AAU-C--GU--GA-CU-UGAAG---C-CAUA--UA--UA-GC---GGAUGAG-G---------------------------------------AA------------------------CU--CU-AAAAUCCA---------------------A-AUA----------GGUGUCGUA-A----CC-UAUA-U-A----C-----------------GU-AAAUUAC-GAGAGUAAAC-U---AGGAAA-----GAU-G-U-----ACG---GC
CP001581.1/2096175-2096008   UUUAUG---C-UUA-GAUG-A--A-AUA-UGAA-UGA-----------------------AAUCUA-U---------AC-AGAGUC-U-A-G--UCUGA---------------------GAGAUAG-GAA-U--UA--UA-UA--GAGU---C-U-UA--CU--AAUGA-U-GGAGAAG-U-------------------------------U-UGCU--AA-------------------G----CAAAAC-AAAGUCCA---------------------A-------------CACUAUCUAA-A----UCCUUAG-G-A----A------------------U-AAAUAUA-AGAGACAUAU-GAU-AUAAAG-----G-U-U-A-------U---AU
ABJK02000018.1/66514-66684   ACUAUC---G-UGA-GGUA-G--C-GGG-GAGA-GGA-----------------------AGGGAU-A-------G--C-GAAAUCGU-G-G--CACUA---------------------CGAACAG-AAA-C--GU--GA-UACGAAGG---C-A-UA--UA--UA-GC---GGACAAG-G-------------------------------U-GGCU--AA-------------------G----AACAUU-AAAGUCCA---------------------AAAAG----------GUAGUCGUA-A----CC-UAUA-U-G----C-----------------GU-AAAUCAC-GAGUGUAAAU-G---AGGAAA-----G---A-U-----GUA---CG
BA000004.3/833541-833713     UCUGGG---G-UGA-CCCA-G--A-AUC-UGAG-GGA-----------------------AGUCGG-C-------G-GC-AAACCUCC-G-C--UUCUA---------------------GGAACAC-GAA-C--UU--CA-UA-GGAGU---U-U-GG--GU--AU-AC-UUGGAAGAG-G-------------------------------U-UGCG--AA-------------------A----CAAAUC-AAAGUCC------------------------------------UUACUGCCGA-AG--GGU-AUAU-C-A----A-----------------GU-AAAUGAA-GAGAAGACAU-GGA-GGGGAA-----G-A-A-U-----GUG---UG
CP000252.1/1820020-1819857   GGAACC---A-UAG-GGCA-C--C-GUG-CGAA-GGA-----------------------CGCCGG-A-------GUGC-AAAGCUAU-A-A--GCUGA---------------------CGAACAG-AAA-C--AG--CA-UG-CAAGG---C-C-GA--GU--CU-CCUU----CAAA-U-------------------------------C-AGCA--CA-------------------A----CAUGAC-AAAGUCC-----------------------UGGA---------UUCU------------GG-AGAU-A-C----G-----------------UU-GAAUGCU-GCGGUUG--C-AGA-GUCACA-----G-U-U-C-----ACG---UU
ABVL01000008.1/262543-262374 GCGACC---G-CGA-GGUC-G--U-GGC-UGAA-AGA-----------------------AGUCGC-A-------G-GC-AAAACUCC-G-A--CCGCA---------------------GGAAGAC-AAA-C--UG--GC--AGAGAGG---C-C-GG--GC--GU-GG-G-CGACGAG-C-------------------------------G-UGCG--AG-------------------C----AACCGC-GAAGUCC-----------------------GAAG----------UCCAUCCAG-A----C--ACGU-C-A----G-----------------GU-AGAGCCA-GGCGGCG--C-GGA-GGGAGA-----G-U-U-C-----AGG---UU
ABPY01006227.1/578-408       GUCGCC---G-CGA-GGCG-U--C-GUG-GGAA-GGA-----------------------AGCGGC-A-------G-GC-AAAACGAU-G-A--CCUGA---------------------GGAACAC-GAA-C--CG--CA-UA-GGAGG---C-G-GA-CGU--UC-GG-C-GGACGAG-C-------------------------------G-GGCA--GA-------------------G----AGACGC-GAAGUCCG--------------------AA--------------GCGACCCGG-A----CC-GGACGG-A----C-----------------GU-AGAUGCG-GCGGGU---U-AUC-GGGAAG-----G-C-C-A-----CAC---GU
CP000423.1/81770-81945       UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GAA-----------------------AGCCAGAU-------GAGC-AAAAUACU-G-C--ACUGA---------------------UGAACAA-GAA-G--CG--GC-AA-CAAGG---C-CGAA-AGU--GA-C--U-GGAUGAG-G-------------------------------U-UGCC--AA-------------------G----CAAACUAAAAGUCC-----------------------AAUA----------CUAAUCGAA-U-------UCACAA-C----G-----------------GU-AAAGCUG-ACGGUGACAU-GGU-AUGAAA-----G-C-U-G-----AUA---GC
CP000789.1/2440476-2440303   UUCACU---G-UGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCAAA-U-------G-GC-AAAACUUG-G-U--UUUGA---------------------CGAACAG-AAA-U--CU--GA-UA-GUAGG---U-C-AC--UA--CA-AC-UUGGGCAAC-C-------------------------------U-AGCC--AU-------------------A----GAUAGA-AUAGCCCA---------------------AUGCC----------UCGACGGGA-AG--UG--UGUA-G-U----G-----------------AU-AAAUCAG-GCACGG---C-CAA-GGGAAA-----G-A-G-C-----AAC---GU
AATD01004050.1/265-96        UCCACC---G-CGA-GG-G-G--A-AUC-UGAA-GGA-----------------------AGGUGA-A-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-C--UA--CA----UCAGG---C-U-AU--GC--AC-AG---GGGUAAG-G-------------------------------C-CGCA--AA-------------------A----CAGGUC-AAAGCCC-----------------------AAUA---------ACUGUACGGA-A----CU-GUGC-A-U----A-----------------GU-AAAUGUG-GCAGAUAUGU-GGA-GAGAAA-----G-A-A-A-----CGU---GU
CR377818.1/73381-73220       UUUUCC---G-CGA-GGAA-C--G-GUC-UGAA-GGA-----------------------AGCCGC-U-------A-GC-AAAACUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--C-----UGAGG---C-G--U--AG--GU-CA-G-AGGCGAG-U-------------------------------U-GGCA--CA-------------------A----GACGAC-GAAGCCA-------------------------------------AGUGAUUUA-A----UG-ACC--A-C----C-----------------GU-AAACGAU-GCAGUUG--C-GCA-GUGAAA-----G-U-C-C-----AUG---UC
ACKR01000156.1/1851-1680     UUAGCG---G-UGA-CGCU-A--U-GGG-UGAA-GGA-----------------------AGUGGC-U-------A-GC-GAGUUUUCCG-A--GCCUA---------------------CGUACAG-AAA-C--CU--GG----UCAGG---C-C--A-AAU--GG-U----GGAUGAG-A-------------------------------C-UGCA--GC-------------------A----CAAGUU-AAAGUCC-----------------------AAAG---------GACAACCGUA-A----AA-CCAAGA-C----G-----------------GU-AAACCAG-GGGGCAG--UGGAA-AAUUAA----AG-A-U-G-----AAU---GU
ACGC01000016.1/181-11        UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCCU-A-------G-GC-AAACUCUU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UAAGG---C-A-GU--UA--CG-UA---GGAUAAG-C-------------------------------U-UGCC--AA-------------------A----CAAAGU-AAAGUCC-----------------------AAUA---------ACUACACGGA-A----UA-CGUA-A-A----U-----------------GU-AUAUGUG-GCAGAUAGAU-GAG-AGGAAA-----G-A-A-C-----AUG---CC
CP001132.1/626861-627040     GUCGUC---G-CGA-GGCG-G--G-GUC-UGGA-GGA-----------------------AGCCCA-A-------U-CC-GAGGCUGC-G-G--GGCGA---------------------UGAACAA-AAA-C--CG--GA-UA-UGAGG---C-G-UG-AUG--CA-UC-CGGGACGAG-C-------------------------------G-GGCA--CG-------------------U----GACCGC-GAAGCCCUCC-----------------AUCCAUC----------UGCGGUUGU-UG--GGA-UGCACU-U----U-----------------GU-AAAUCCG-G----CG----GCA-GCGCAGAAAGUG-A-C-G-----UGU-----
ABSP01039538.1/782-614       ACCGCC---G-CGA-GGCG-G--G-GUC-UGAA-GGA-----------------------AGCAUG-G-------A-UC-AAACGUGC-G-A--GUCGA---------------------UGGACAA-AUA-C--CG--GA-UA-UAAGG---C-G-CC-AGC-----GC-C-GGACGAA-G-------------------------------G-GGCA--AC-------------------U----UACCGC-GAAGUCC------------------------AUA----------UCCAUCAAG-G----GU---GC-G-AA--GC-----------------GU-AGAUCCG-GCGACUG--U-GCA-CGGAAG-----G-C-G-G-----CUG---AG
CP001157.1/2030300-2030469   UCGCGG---G-CGA-CCGC-G--A-AUC-CGAA-GGA-----------------------AGCCCG-A-------G-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GA----UGAGG---C-G-GU--AC--AG-CG---GGGUAAG-G-------------------------------U-AGCG--AA-------------------A----AUUGCC-AAAGCCC-----------------------AAUA---------CUUGCACGGA-A----CG-CUGU-G-A----C-----------------GU-AGAUCCG-ACAGGCAUA--AGC-AGGAAG-----G-U-C-G-----CGC---GA
CP001015.1/2015300-2015137   GGAAAU---A-AGA-A----U--C-GUC-AGA--GGA-----------------------AGAGAU-A---------GC-GAAAUCGU-G-G--CUCUA---------------------CGAACAG-GAA-C--GU--GA-UAGCAAGG---C-G-UA--UA--UA-GC---GGAUAAG-G-------------------------------A-GGCU--UC-------------------A----AACUCU-AAAGUCCA---------------------AAAAG----------GUAGUCGUA-A----CC-UAUA-U-G----U-----------------GU-AAAUCAC-GAGAGUAAUU-G-------AAUU-CGGAC-U-A-------------
CP000789.1/265550-265377     UUCACU---G-UGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCAAA-U-------G-GC-AAAACUUG-G-U--UGUGA---------------------CGAACAG-AAA-U--CU--GA-UA-GUAGG---U-C-AU--UA--CA-AC-UUGGGCAAC-C-------------------------------U-AGCC--AU-------------------A----GAUAGA-AUAGCCCA---------------------AUGCC----------UCGACGGGA-AG--UG--UGUA-G-U----G-----------------AU-AAAUCAG-GCACGG---C-CAA-GGGAAA-----G-A-G-C-----AAC---GU
AATN01000130.1/16835-17009   UUCGCC---G-CGA-GGCG-G--G-GUC-UGAA-GGA-----------------------AGCCCA-A-------U-CC-AAAGCUGC-G-G--GGCGA---------------------UGAACAA-AAA-C--CG--GA-UA-UCAGG---C-G-UG--AU--GU-ACUCGGGACGAG-C-------------------------------G-GGCA--CG-------------------U----GACCGC-GAAGUCC-----------------------UCCA----------UCUGCCGUU-GG--GGU-GCAU-U-U----U-----------------GU-AAAUCCG-GCGUCUA--U-GCC-GCGAAG-----G-U-A-A-----CGA---GU
AB255435.1/19885-20054       UUCAUC---G-CGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------U-GC-AAAAUGCU-G-G--CCUGA---------------------CGGACAG-GAA-G--CG--GU----UAAGG---C-G-GC--GC--AG-CA---GGGUAAG-G-------------------------------G-GGCA--CA-------------------A----AUCACC-AAAGCCC-----------------------GAUA---------CUCACACGAA-A----CG-CUGU-G-A----C-----------------GU-AAAGCCG-ACAGGCAUA--AGC-AGGAAA-----G-U-C-G-----CGU---GA
AAWL01000010.1/49364-49531   GCGCUG---G-UAA-CGGC-G--AGGUC-UGAA-GGA-----------------------AGCUGC-A-------G-GG-GGAACUCG-G-A--ACAUA--------------------GCGAAAGC-GAA-C--CG--AU----GUUGG---C-C-GC--UC--AG-GU---GGGUAAC-C-------------------------------U-UGCA--UG-------------------A----AGUGGG-AAAGCCC-----------------------GAAA----------GCUGAUUA-------AC-CUGA-G-A----G-----------------GU-UAGAACG-GAUGCGU--U-CAA-GUUAAG-----G-C-A-A-----GCA---AC
AAPZ02000002.1/583377-583550 UCCACU---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGUCUA-A-------G-GC-AAAGUACU-G-C--ACCGA---------------------UGAACAA-GAA-G--UA--GC-UA-UAAGG---C-U-GG-AAC--UA-AC-U-GGAUAAG-A-------------------------------C-UGCA--UG-------------------A----CAAGUU-AAAGUCCA---------------------A---C----------ACUACUCGA-A----GU-UACU-U-U---CA-----------------GU-AAAGCUA-UCGGUGACAU-GGU-ACGAAA-----G-U-U-A-----AUA---UC
AAFY01010928.1/586-750       UUAAUC---G-CAA-GGUU-U--G-GUC-UGGA-GGA-----------------------AGCCGC-U-------A-GC-AAAUUUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G--U--AG--GC-UA-G-AGGUGAG-U-------------------------------U-GGCA--CA-------------------U----GACGAC-GAAACCA-------------------------------------CGUGAUCUA-A----UG-GCC--A-C----C-----------------GU-AAAUGAU-GCAGCAG--U-GCA-AAGAAA-----G-U-U-C-----AUG---UU
AACY023823294.1/731-897      UUGGGC---G-UGA-GCCC-U--U-CAG-UGAA-GUA-----------------------AGCGGGAC-------U-AC-AAAAGUUA-G-U--GCUGA---------------------CGAACAG-GAA-U--CG--GA-UA-UGAGG---C-U-AU--GA--GG-UU---GGAUGAG-C-------------------------------A-GGCA--CA-------------------U----CACUGU-AAAGCCC-----------------------GAAA----------UUUAG----------AA-CC---G-AA-GUA-----------------GU-AGAUCCG-GCAGGAA--U-UAA-CUGAGA-----G-C-U-A-----CUU---GU
CP000918.1/1056162-1056325   GGAAAU---A-AGA-AUU-------GUC-AGAA-GAA-------------------------GGGA-U-------A-GC-GAAAUCGU-G-G--CUCUA---------------------CGAACAG-GAA-C--GU--GA-UAAUAAGG---C-G-UA--UA--UA-GC---GGAUAAG-A-------------------------------G-GGCC--UC-------------------A----AACUCU-AAAGUCCA---------------------AAAAG----------GUAGUCGUA-A----CC-UAUA-U-G----C-----------------GU-AAAUCAC-GAGAGUAAUU-G-------AA-----U-U-C-G-----UAC---UA
CP000249.1/2453947-2454114   GUCAUC---G-UGA-GGUG-G--G-GGC-GGGA-GGA-----------------------AGCCCG-A-------G-GCGAGACCCCU-G-C--ACCGA---------------------GGGACAC-GAA-C--CG--CG-UA-GGAGG---C-G-UU--UC--GG-UC---GGGUGAG-C-------------------------------C-AGCA--CG-------------------C----GAUGGU-GAAGCCC-----------------------GUCA----------CCGCCAAGA-A----GG-CCGG-G-G----C-----------------GU-AAACGCG-G--GCG---U-AGG-GGGACA-----G-C-G-G-----CUG---UU
CP000879.1/1633286-1633113   UCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCAA-A-------G-GC-AAAGUCCC-G-G--UUCGA---------------------UGAACAA-GAA-C--CA--GA-UA-CAAGG---C-U-AA--GU--GA-AG-U-GGACGAG-U-------------------------------U-UGCC--AC-------------------U----CAAAAC-GAAGUCC-----------------------AACA---------GCUACCCAGA-A----CU-UCAC-G-G----A-----------------GU-AGAUCUG-GCGAAUAGAU-GGG-AUGAAA-----G-U-U-A-----UUG---CA
CP001253.1/30088-30252       UUAUCC---G-CGA-GGAU-U--G-GUC-UGAA-GGA-----------------------AGCCGC-U-------A-GC-AAAUUUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G--U--AG--GC-UA-G-AGGUGAG-U-------------------------------U-GGCA--CA-------------------A----GACGAC-GAAACCA-------------------------------------UGUGAUCUA-A----UG-GCC--A-C----C-----------------GU-AAAUGAU-GCUGCUG--U-GCA-AAGAAA-----G-U-U-C-----AUG---UU
ACGV01000119.1/48643-48817   UCCACU---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGUCUA-A-------G-GC-AAAGUACU-G-C--ACCGA---------------------UGAACAA-GAA-G--UA--GC-UA-UAAGG---C-U-GA-GGG--UA-AC-U-GGAUAAG-G-------------------------------U-UGCU--UA-------------------A----CAAACU-GAAGUCCA---------------------A-------------UACUACUCGA-A----GU-UACUCU-C----A-----------------GU-AAAGCUG-ACGGUGACAU-GGU-ACGAAA-----G-U-UAA-----UAU---UC
ABYO01000244.1/64917-65085   UAGAUG---G-UGA-CAUC-U--A-GGA-GAGA-AGA-----------------------AGUAAU-A---------GC-GAAAUCGU-G-G--CUUGA---------------------CGAACAG-GAA-C--AG--AA-UA-CAAGG---C-G-UA--AC--AG-GU---GGGCAAG-C-------------------------------U-AGCA--GU-------------------A----GAUAGCAAAGACCC-----------------------AAAA---------GGUAACCGUA-A----GC-CCAA-G-G----U-----------------GU-AAAUUCU-GCAAGUA-A--ACG-AUGAAA-----G-U-A-U-------U---AG
AP006840.1/1255834-1256003   UCCGUC---G-CGA-GGCG-G--A-AUC-UGGA-GGA-----------------------AGCCGG-A-------G-GC-AAAGCCAC-G-A--CCCGA---------------------GGAACAC-GAA-C--CU--CA-UA-CGAGG---C-U-GU--GC--CG-CC-U-GGGUGAG-C-------------------------------U-GGC---GA-------------------A---CCACAGC-AAAACCCG--------------------AG--------------GCUGCCAAA-G----GG-CGGU-G-C----G-----------------GU-AGAUGGG-GCGGGUG--C-GGG-GCGAAG-----G-U-C-A-----GCG---UC
AP008232.1/144342-144501     GCAAGG---G-UGA-CCGA-G--C-GUG-GGGA-GGA-----------------------AGUGUAGA-------G-A--GAAACUGC-G-A--GCCGA---------------------UGAACAA-GAA-U--CG--GA-UA-GAAGG---C-G-CU-GGCGAGCAGGCUAGAAACCGUGAAACUCUU--------------GUGGUCAAG---------------------------------------------------------------------------------------------------------GCGA-GGUGGC-----------------GU-AGAUCCG-GCGGUUA--U-GCA-GUGAAG-------G-A-G-----UGC---GU
AACY020465365.1/1740-1570    AUGAGG---G-CGA-CCGA-G--U-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GC-GAAACUGC-G-A--GCCGA---------------------UGGACAA-GAA-C--CG--GA-UA-GAAGG---C-G-CU--GC--CG-AG-CAGGGCGAG-C-------------------------------G-GGCA--UG-------------------A----AUCCGC-GAAGC---------------------------UC----------UCGUGAUCA-AG--GCG-AAGC-G-G----C-----------------GU-AAAUCCG-GCGGUUG--U-GCA-GUGAAG-----GAG-U-G-----CGU---UC
AAFX01033861.1/539-372       GUCAUU---G-CAA-GGUG-G--C-CGC---GC-GAA-----------------------AGGGCGGA-------G-GC-AAACACUU-G-G--CCGCA---------------------GGAAUAC-GAA-C--GA--GC--AGUGAGG---C-A-GG--AA--GU-CG-C-GGGCGAG-C-------------------------------G-UGCG--AG-------------------U----AAACGC-AAAGCCCA---------------------A--------------AGCCAUCGA-A----CG-GCUU-U-C----U-----------------GU-AGAGCUC-GGCGGCG--U-GAG-UGGAAG-----G-A-C-C-----GGG---CG
AACY024108825.1/674-847      GGAACC---G-CGA-GGUU-C--UUAGCACGAA-AGA-----------------------AGGCCG-U-------A-GC-AAAGGCAC-G-A--CCGUA---------------------AGAACAU-GAA-A--CG--GC--AGCGAGG---C-A-UG--GC--GU-GG-G-CGAUGAGAAUGCGAG-------------------CAUCCG---------------------------------------C-GAAAUCC------------------------AAA----------AGUCACCGA-AA--GAC-ACGU-U-G----U-----------------GU-AGAGCCG-UGCGGCA--C-GGG-CCGAAA-----G-U-U-C-----GUA---CA
ABIY02000087.1/5400-5227     UCCUUC---G-CGA-GGAG-G--A-ACC-UGAA-GGA-----------------------AGCUGG-C-------G-GC-AAACUCUC-G-G--CUCUA---------------------CGAACAG-AAA-C--UG--AU-UA-UAAGG---C-U-AC-AUU--UG-GA---GGACAAG-U-------------------------------U-UGCU--AA-------------------A----CAAAAU-AAAGUCC-----------------------UAUA----------ACUAUCCGA-A----UC-CCUAUG-U----A-----------------GU-AGAAUCA-GAGGGUAUAU-GAG-AUGAAA-----G-C-G-U-----ACG---UU
CP000705.1/550671-550844     UCCACU---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGUCUA-A-------G-GC-AAAGUACU-G-C--ACCGA---------------------UGAACAA-GAA-G--UA--GC-UA-UAAGG---C-U-GG-AAC--UA-AC-U-GGAUAAG-A-------------------------------C-UGCA--UG-------------------A----CAAGUU-AAAGUCCA---------------------A---C----------ACUACUCGA-A----GU-UACU-U-U---CA-----------------GU-AAAGCUA-CCGGUGACAU-GGU-ACGAAA-----G-U-U-A-----AUA---UC
AATN01006855.1/275-449       GUCGCC---G-CGA-GGCG-G--G-GUC-UGAA-GGA-----------------------AGCCCA-A-------U-CC-AAAGCUGC-A-G--GGCGA---------------------UGAACGA-AAG-C--CG--GA-CA-UCAGG---C-G-UG--AU--GU-ACUCGGGACGAG-C-------------------------------G-GGCA--CG-------------------U----GACCGC-GAAGUCC-----------------------UCCA----------UCUGCGGUU-GG--GGU-GCAU-U-U----U-----------------GU-AAAUCCG-GCGUCUA--U-GCA-GCGAAG-----G-U-A-A-----CGA---GU
AE017180.1/1028761-1028929   GCCUCC---G-CGA-GGAG-G--G-GUC-UGAA-GGA-----------------------AGCCCG-A-------GCGC-AAAGCUAU-G-A--GCCGA---------------------CGAACAG-AAA-C--AG--CA-UA-CAAGG---C-C-GG--GG--UG-UC-C-GGGCAAG-U-------------------------------C-AGCA--CA-------------------A----CAUGAC-GAAGUCC--------------------------C----------ACGGAUUCA-G----GA-UGCC-A-A----G-----------------GU-AAAUGCU-GCGGUUG--U-GUA-GCCACA-----G-U-UCA-----CGU---U-
AAFY01000006.1/6263-6089     AUGAUC---G-UGA-GGUC-A--U-GGC-UGGA-GGA-----------------------AGCUCA-A-------G-GC-GAAAUCGC-G-G--GGCGA---------------------UGAACAA-GAA-C--CG--GA-UA-UGAGG---U-G-UG-AUC--UA-GGCG-GGGCCAG-C-------------------------------G-GGCA--CG-------------------U----GACUGU-UAAGCCC-----------------------UCCA---------UCUGCAACGG-G----CC-UAGGUU-U----U-----------------AU-AAAUCCG-GCGUCUA--C-GCG-AGGAAA-----G-U-U-A-----AGU---GU
CP000930.2/163047-162876     UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCUGG-C-------G-GC-AAACUUCU-G-G--UCUGA---------------------CGAACAG-GAA-C--UA--CA----UCAGG---C-AUAU--GU--AU-GC-U-GGGUGAG-A-------------------------------U-UGCA--UA-------------------A----CAAAUC-AAAGCCC-----------------------UAAA----------CUAUCCGGA-A----GC-AUAC-G-G----U-----------------GU-AAAUGUG-GCAGAUAUAU-GGA-AGGAAA-----G-A-U-U-----GCG---UU
ABSQ01021350.1/354-522       UCCUGG---G-CGA-CCAG-G--G-GUC-CGGU-AGA-----------------------AGUCAU-A-------G-GU-GCAACGCC-G-U--AUCGA--------------------ACGAGAGU-GAA-G--CG--CC---GUAAGG---C---AU--CU--GG-AC-C-GGGUGAG-U-------------------------------C-AGCC--CA-------------------C----GGUGAU-GAAGCCC-----------------------GAAA----------UCGGUUGGU-G----GU-CCAG-U-G----------------------GU-AGUGGCG-ACGAGA---U-GGC-GUUGAA-----G-UCU-G-----CUG---GU
AAWL01000003.1/15858-16027   CCUACC---G-CGA-GGUG-A--G-GUC-UGAA-GGA-----------------------GGCCGG-A-------G-GC-AAAACCGC-G-G--CCUGA---------------------UGAACAA-GAC-C--CC--CA-UA-CGAGG---C-U-GG--UC--CG-UU-C-GGAUGAG-C-------------------------------U-GGCG--CU-------------------A----CACAGC-AAAAUCC-------------------------UA---------GGCUGUCAAA-G----UA-CGGU-A-G----A-----------------GU-AAAUGGG-GCAGGCG--C-GGG-GCGAAG-----G-U-C-A-----GUG---UU
CP001157.1/2832118-2831948   GUAAGG---G-UGA-CCGA-G--C-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GC-GAAACUGC-G-A--GCCGA---------------------UGGACAA-GAA-C--CG--GA-UA-UGAGG---C-G-CU-GCC--GAGCA---GGGCGAG-U-------------------------------G-GGCG--AG-------------------A----AACCGC-GAAGCUC-------------------------UC----------GUGGCCAAG-G----UGA--GGUG-G----C-----------------GU-AAAUCCU-GCGGUUG--U-GCA-GUGAAG-----G-AGU-G-----CGU---UC
CP000879.1/1702149-1701976   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCCA-A-------G-AC-AAAGUCCC-G-G--UCCGA---------------------UGAACAA-GAA-C--CA--GA-UA-CAAGG---C-U-AA--GU--GG-AG-U-GGACGAG-U-------------------------------U-UGCC--UA-------------------A----CAAAAC-GAAGUCC-----------------------AACA---------GCUAUCCAGA-A----CU-UCAC-G-G----A-----------------GU-AGAUCUG-GCGGAUAUAU-GGG-AUGAAA-----G-U-U-A-----UUG---CA
ABCS01000001.1/27042-27212   CCGAGG---G-CGA-CUGA-G--G-GUC-UGAA-AGA-----------------------AGCGUG-A-------A-AC-GAACCAGC-G-G--GUCGA---------------------CGCACAG-AAA-C--CG--GA-UC-AGAGG---C-G-GG--GC--GC-CG-A-GGGCGAG-C-------------------------------G-UGCG--AG-------------------U----GAACGC-GAAGCUC-------------------------UU----------CGUGGCCGA-AC--ACG-GCGU-C-A----C-----------------GU-GCAUCCG-GCGAUCG--C-GCU-GGGAAG-----G-C-C-G-----GUG---UC
AACY020037398.1/1308-1478    AUGAGG---G-CGA-CCGA-G--U-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GC-GAAACUGC-G-A--GCCGA---------------------UGGACAA-GAA-C--CG--GA-UA-GAAGG---C-G-CU--GC--CGAGC-A-GGGCGAG-C-------------------------------G-GGCA--UG-------------------A----AUCCGC-GAAGCUC------------------------------------UCGUGAUCAA-G----GC---G--A-AGCGGC-----------------GU-AAAUCCG-GCGGUUG--U-GCA-GUGAAG-----G-AGU-G-----CGU---UC
CP000471.1/1069217-1069388   UUUACC---G-UGA-GGUA-A--A-AUC-UGAA-GGA-----------------------AACCGA-A-------G-GC-AAAGCGCU-G-A--UCCGA---------------------CGAACAG-GAA-U--CG--CA-UA-CGAGG---C-G-GU---C--AU-GC-U-GGAUGAG-G-------------------------------A-GGCG--AC-------------------U----AUCUCU-AAAGUCCG--------------------AA-ACC----------UGUACGGAG-A----GC-AUG--G-A----C-----------------GU-AUAUGCG-GCGGAUAUA--AGC-GUGAAG-----G-U-G-C-----GUG---UG
CR377166.1/4562-4731         UCUAUC---G-UGA-GGUA-G--A-AUC-UGAA-GGA-----------------------AGUCCU-A-------G-AC-GAAACAUC-G-A--AUCGA---------------------UGAACAA-GAA-G--UG--GC-UA-AAAGG---C-U-GG-AAA--CU-GU-G-GGAUGAG-A-------------------------------U-UACC--UA-------------------A----CAAAUC-GAAGUCC-------------------------CU---------GACCACUCGA-A----AC-CGUC-A-C----A-----------------GU-AAAGCCA-ACGGUU---U-GAU-GCGAAA-----G-C-U-A-----CUG---CU
AE016853.1/3762404-3762232   AGAAGG---G-CGA-CCGA-C--U-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GCGUAAACCGC-G-A--GCCGA---------------------GGUACAC-AAA-U--CG--CA-UU-CGAGG---C-G-GA-UCC--GGACA---GGGCGAG-C-------------------------------A-GCCA--AG-------------------U----GACUGC-AAAGCUC-------------------------UU----------GUGGCCUAA-G----UG-CCGGGU-A----C-----------------GU-AAAUGCG-GCGGUUG--U-GCG-GUGAAG-----GAU-G-G-----CGU---UC
AACY023598940.1/985-815      UUUACU---G-UGA-AGUA-G--A-AUC-UGAA-GGA-----------------------AGCUGA-A-------G-AC-GAAGUUAG-G-A--GGUAA---------------------CGAACAG-GAA-G--UA--GA-UA-CAAGG---C-U-UA--UA--UG-AA---GGGGAAG-U-------------------------------U-AGCA--UU-------------------G----AGUAAU-GAAACCC-----------------------AGUA---------AUUGAUCGUA-G----UU-UAUA-U-G----A-----------------GU-AAAUCUA-AUGCCUC--C-CUA-AUGAAA-----G-A-A-U-----UAU---GU
AAMK02000009.1/73106-72937   UUCAUC---G-CGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCUGG-A-------U-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GU----UAAGG---C-G-GC--GC--AG-CA---GGGUAAG-G-------------------------------U-GGCA--CA-------------------A----AUCACC-AAAGCCC-----------------------GAUA---------CUCACACGGA-A----CG-CUGU-G-A----C-----------------GU-AAAGCCG-ACAGGCAUA--AGC-AGGAAA-----G-U-C-G-----CGU---GA
CP000790.1/1553656-1553483   UUCACU---G-UGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCAAA-U-------G-GC-AAAACUUG-G-U--UGUGA---------------------CGAACAG-AAA-U--CU--GA-UA-GUAGG---U-C-AU--UA--CA-AC-UUGGGCAAC-C-------------------------------U-AGCC--AU-------------------A----GAUAGA-AUAGCCCA---------------------AUGCC----------UCGACGGGA-AG--UG--UGUA-G-U----G-----------------AU-AAAUCAG-GUACGG---C-CAA-GGGAAA-----G-A-G-C-----AAC---GU
ABXW01000014.1/145166-145335 UUCGUC---G-CAA-GGUA-A--A-AUC-UGAA-GAA-----------------------AGAUGA-A-------A-AC-AAAAUGCA-G-G--UCUGA---------------------CGAACAG-GAA-G--CG--AU----UUAGG---C-G-GU--GC--GG-CG---GGAUAAG-G-------------------------------U-GGCU--AU-------------------U----AUCGUC-AACGCCC-----------------------AAUA---------CUUAUACAGA-A----UG-CUGU-G-A----C-----------------GU-AGAGCCG-ACAGACAUA--GGC-AGGAAG-----G-U-C-G-----CAU---UU
ABHH01000009.1/56184-56012   UCCAUU---G-UGA-AGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------C-GC-AAACACUC-G-C--ACUGA---------------------CGAACAG-AAA-C--CU--CA-UA-UAAGG---C-U-GA-CUG--GA-GA-G-GGACGAG-C-------------------------------U-UGCU--AA-------------------A----CAAAGC-AAAGUCCA---------------------A-------------UACUGCACGA-A----UC-UUCU-A-C----A-----------------GU-AAAUGAG-GCAGUGACAU-GAG-UGGAAG-----G-U-U-A-----UCA---UU
AAGA01000948.1/2160-1980     UUAUCC---G-UGA-GGAU-A--G-GAC-UGCACGGA-----------------------AGCGAGCC-------U-AC-AAACUCUG-G-U--ACUGA---------------------CGAACAG-GAA-U--CU--GA-UA-CGAGG---C-U-AU--GC--GG-UA---GGGUAAG-C-------------------------------A-AACA--CA-------------------C----CAUUGU-AACGCCCAAG-----------------ACUCUAA----------GCAAUUGGA-GA--CUA-CC---A-AA-AUA-----------------GU-AGAUCAG-GCAGUAA--U-UAG-AGGAAA-----G-A-A-G-----AUG---UA
AAWL01000006.1/84276-84104   CCCAUU---G-CGA-GAUG-G--G-AUC-CUAA-GGA-----------------------AGUCGG-C-------G-GC-AAAUCUUC-G-U--UCUGA---------------------GGGAAAC-GAA-C--CG--CA-AA-UGAGG---C-U-AG--GG--GC-AG-UUGGUUGAG-C-------------------------------U-UGCG--UU-------------------A----CAAAGC-AAAGUCC------------------------------------UUGCUACCGA-AG--GUU-GCCC-A-G----A-----------------GU-AACUGCG-GCAGGUAGAU-GGA-GAGAAA-----G-A-C-A-----CUG---CU
AP007281.1/283930-284103     UCCACU---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGUCUA-A-------G-GC-AAAGUACU-G-C--ACCGA---------------------UGAACAA-GAA-G--UA--GC-UA-UAAGG---C-U-GG-AAC--UA-AC-U-GGAUAAG-A-------------------------------C-UGCA--CG-------------------A----CAAGUU-AAAGUCCA---------------------A---C----------ACUACUCGA-A----GU-UACU-U-U---CA-----------------GU-AAAGCUA-CCGGUGACAU-GGU-GCGAAA-----G-U-U-A-----AUA---UC
CP000494.1/4839511-4839342   GUCAUC---G-CGA-GGUG-G--G-GUC-UGAA-GAC-----------------------AGCGUG-G-------A-GC-AAAGCCGC-G-G--CCCGA---------------------UGAACAA-ACA-G--CG--GA-UG-CGAGG---C-C--U-ACC--CG-UC-C-GGACGAG-C-------------------------------G-AGCC--GC-------------------C----AAUCGC-GAAGUCC------------------------ACG----------GUCAUCAAG-G----GG-CGGG-G-U----G-----------------GU-AAAUCCG-ACGGGUA--U-GCG-GUGAAG-----G-C-G-G-----UCG---GU
ABBF01000617.1/20621-20450   AUGAGG---G-CGA-CCGA-A--U-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GCGUAAAUCGU-G-A--GCCGA---------------------UGAACAA-GAA-C--UG--CA-UA-GAAGG---C-G-CU--GC--CGAGC-A-GGGCGAA-C-------------------------------G-GGCC--CA-------------------U----AACCGC-GAAGCUC------------------------------------UCGUGACCAA-G----GC---G--A-AGCGGC-----------------GU-AGAUGCG-GCGGUUG--U-GCG-AUGAAG-----G-AGU-G-----CGU---UC
ABSP01023545.1/215-386       GCGAGG---G-CGA-CCGA-G--C-GUG-GGGA-GGA-----------------------AGCGUG-G-------A-GCGUAAACCGC-G-A--GCCGA---------------------UGGACAA-GAA-C--CG--GA-UA-CAAGG---C-G-CU--GC--CG-AG-CAGGGCGAG-C-------------------------------G-GGCA--UG-------------------A----UUCCGC-GAAGCUC------------------------------------UCGUGAUCAA-GG--CG--AAGC-G-G----C-----------------GU-AAAUCCG-GCGGUUG--U-GCG-GUGAAG-----G-AGU-G-----CGU---UC
AAFY01006107.1/640-466       AUGAUC---G-UGA-GGUC-A--U-GUC-UGGA-GGA-----------------------UGCUCA-A-------G-GC-GAAAUCGA-G-G--GGCGG---------------------UGAACUG-AAA-C--CG--GA-UU-GAGUG---U-G-UG-AUC--UA-GGUG-GGGCCAG-C-------------------------------G-GGCA--CG-------------------U----GACUGU-UAAGCCC-----------------------UCCA---------UUUGCAACGG-G----CU-UAGGUU-U----U-----------------AU-AAAUCCG-GCGUCUUCG---CG-AGGAAA-----G-U-U-A-----AGU---GU
AACY023018747.1/435-271      UAAAUC---G-UGA-GAGA-U--A-GUC-UGGA-GGA-----------------------AGCCGC-U-------A-GC-AAAUCUGC-G-A--GCUGA---------------------UGAACAA-GAA-C--AU--CA-UA-UGAGG---C-G--U--AG--GC-UG-A-AGGUGAG-U-------------------------------U-GGCA--CA-------------------A----GACAAC-GAAACCC-------------------------------------UGUGAUCUA-A----CG-GCC--A-C----C-----------------GU-AAAUGAU-GCAGCAG--U-GCA-GAGACA-----G-U-C-C-----AUG---UU
AACY022757771.1/211-38       GUUACC---G-UAA-GGUA-A--G-GUG-GGAA-GGA-----------------------AGCCGA-A-------G-GC-AAAACCUU-G-G--UCUGA---------------------GGAACAC-GAA-C--CA--CA-UA-GGAGG---C-GAAG-AAG--CU-GU---GGGCGAG-A-------------------------------G-GGCG--UU-------------------G----GUACUC-GAAACCC-----------------------AAAU---------ACCAUUCAG-------AC-AGCGAU-U----C-----------------GU-AGAUGUG-GCAGAUAUAU-GAG-GUGAAG-----G-U-C-A-----UGC---GU
ABIY02000100.1/41554-41726   UCCAUC---G-UGA-GGUG-G--A-AUC-UGAA-AGA-----------------------AGCUGG-C-------G-GC-AAACAUCU-G-G--UCUGA---------------------CGAACAG-AAA-C--UU--CA-UA-UAAGG---C-A-UA-AAA--AC-CG-U-GGGUAAG-G-------------------------------U-UGCU--AU-------------------C----CAAACC-AAAGCCC-----------------------UAUA---------GCUAUUCGGA-A----CG-GUU--A-A----U-----------------GU-AGAUGAA-GCAGACAUA--AGA-UUGAAA-----G-U-U-A-----AUA---CC
CP001634.1/1526530-1526692   UCACUG---G-UAA-CGGU-G--A-AUC-UGAA-GGA-----------------------AGCCUA-A-------G-GC-AAAAUCUG-G-A--ACUGA---------------------ACGAAAG-UGA-C--CA--GU----GUUGG---C-C-GG--UA--GA-GU---GGGUAAC-C-------------------------------U-UGCC--GU-------------------G----UAUGGG-GAAGCCC-----------------------GAGC----------UCCA-----------AC-UCUA-C-A----G-----------------GU-UUGGAUG-GCAGACGAAC-CCG-UAG-UA-----G-U-G-U-----UGA---AC
CP002442.1/369230-369059     UCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCUGG-A-------G-GC-AAACACUU-G-A--CCUGA---------------------GGUACAC-GAA-C--CC--AA-UG-GGAGG---C-C-GC--CA--CA-GU-C-GGACGAG-U-------------------------------C-UGCU--GG-------------------A----CAAGAC-GAAGUCC-----------------------UAA-----------GCCGCCAAG-G----GC-UGUG-G-A----G-----------------GU-AGAUUGG-GCAGGUGCAU-GAG-UGGAAA-----G-U-G-U-----CCA---UC
HE576794.1/786853-787024     UCCAUC---G-UGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGGUCG-A-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UAAGG---C-U-AG--UC--AU-GG---GGAUAAG-G-------------------------------C-CGCC--UA-------------------A----CAGGUU-GAAGUCC-----------------------CAUA---------GCUACACGGA-A----CC-AUGA-A-U----A-----------------GU-AGAUGUG-GCAGACACAU-GGA-GAGAAA-----G-AGU-G-----CGU---UC
CP003040.1/3442314-3442138   UUCACC---G-UGA-GGUA-A--A-AUC-UGAA-GGA-----------------------AGUCGU-U-------G-GC-AAAUCUCU-G-G--UCCGA---------------------CGGACAG-AAA-C--CG--CA-UA-CAAGG---C-U-AG--GC--UA-CGAG-AGAUAAG-U-------------------------------U-GGCA--UA-------------------A----AGCAAC-GAAGUCU-----------------------AAUA----------ACUACCACA-UUUGUGG-UAGC-A-G----A-----------------GU-AAAUGCG-GUGGAUGAAU-AAA-U-UAAA-----G-A-U-U-----GCA---GU
CP001791.1/2260887-2260719   UCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-C-------G-AC-AAACUCCU-G-U--ACCGA---------------------GGAACAC-GAA-C--CA--UA----UCAGG---C-A-CA-AAU--GG-GG-C-GGAUGAG-U-------------------------------C-UGCU--AU-------------------A----CAAGAU-AAAGUCC-----------------------AAU-----------ACUGCCCGA-A----CC-CCAC-A-G----U-----------------GU-AAAUAUG-GCGGCGA--U-AGG-ACGAAG-----G-A-G-A-----CAG---UG
CP001734.1/1006065-1006236   UCCACC---G-CGA-GGUG-G--G-AUC-UGAA-GGA-----------------------AGCCGC-A-------G-GC-AAAACGCU-G-G--CCUGA---------------------CGAACAG-GAA-U--CG--CA-UA-CGAGG---C-G-GC--CA--UG-CC---GGGUAAG-G-------------------------------A-GUCC--AU-------------------U----AUCUUC-AAAGCCC-----------------------UGUA---------CUUGUACGGA-A----AG-CUUG-G-A----C-----------------GU-AUAUGCG-GCGGGCAUA--AGC-GUGAAG-----G-U-G-G-----GUG---CG
CP001734.1/2612492-2612321   UCCACC---G-CGA-GGUG-G--G-AUC-UGAA-GGA-----------------------AGCCGC-A-------G-GC-AAAACGCU-G-G--CCUGA---------------------CGAACAG-GAA-U--CG--CA-UA-CGAGG---C-G-GC--CA--UG-CC---GGGUAAG-G-------------------------------A-GUCC--AU-------------------U----AUCUUC-AAAGCCC-----------------------UGUA---------CUUGUACGGA-A----AG-CAUG-G-A----C-----------------GU-AUAUGCG-GCGGGCAUA--AGC-GUGAAG-----G-U-G-G-----GUG---CG
CP003058.1/139321-139493     GACAUC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGGGGC-A-------G-GC-AAAUUUCU-G-A--CCUGA---------------------CAAAGAG-AAU-C--CG--CA----UAAGG---C-CAAU--UU--GA-GA-U-GGAUAAG-G-------------------------------U-CGCC--AA-------------------A----CAGAUU-AAAGUCC-----------------------CAUA---------GCGAUUUGGA-A----UC-CCAA-A-G----G-----------------GU-AGAUGCG-GCAGGUGAAG-GGA-GAAAAA-----G-A-G-U-----GCG---UU
CP001715.1/3649794-3649623   UCGCGG---G-UGA-CUGC-G--A-AUC-UGGA-GGA-----------------------AGCCGA-A-------G-GC-AAAGCGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GA-UA-CGAGG---C-G-GC--GU--AG-CG---GGGUGAG-G-------------------------------U-GUCC--GA-------------------G----AUCAUC-AAAGCCC-----------------------GAAA---------CUUGUACGGA-A----CG-CUGC-G-A----C-----------------GU-AGAUCCG-ACAGGCAUA--AGC-GUGAAG-----G-U-G-G-----GUG---CG
FP929043.1/1490640-1490483   UCUACC---G-UGA-GGUA-G--A-AUC-UGAA-GGA-----------------------AGCUGU-A-------A-GC-AAAUCUCU-G-G--UACGA---------------------CGAACAG-AAA-U--CA--CA-UA-UAAGG---C-U-AG-GCU--AC-GA-G-AGAUAAG-U-------------------------------U-GGCU--UA-------------------A----AGCAAG-AAGAACA-----------------------AAAA------------------------------AG-C-A----A-----------------GU-AAAUGUA-G---AAAAUC-AGGCAAUAAA-----G-C-U-U-----CUG---UC
CP001634.1/1109630-1109792   UCACUG---G-UAA-CGGU-G--A-AUC-UGAA-GGA-----------------------AGCCUA-A-------G-GC-AAAAUCUG-G-A--ACUGA--------------------ACGAAAGU-GAA-C--CA--GU----GUUGG---C-C-GG--UA--GA-GA---GGGUAAC-C-------------------------------U-UGCC--GA-------------------G----AAUGGG-UAAGCCC-----------------------GAGC----------UCCA-----------AC-UCUA-C-A----G-----------------GU-UUGGAUG-GCAGGAU--U-CGG-AUGAAA-----G-C-U-G-----UAU---GU
CP002637.1/2084547-2084719   UUCGUC---G-UGA-GGCG-A--A-AUC-UGAA-GGA-----------------------AGUCGG-C-------G-GC-AAACCUCU-G-G--CCUGA---------------------CGAACAG-GAA-C--CG--CA-UA-GGAGG---C-U-AU--CG--UU-GG---GGAUAAG-G-------------------------------C-CGCA--CU-------------------A----CAGGUC-GAAGUCC-----------------------CAUA---------GCUACACGGA-A----CC-AAUG-G-U----G-----------------GU-AGAUGCG-GCAGGUAGAU-GGA-GGGAAA-----G-A-A-A-----CGU---GU
CP001634.1/548743-548581     UCACUG---G-UAA-CGGU-G--A-AUC-UGAA-GGA-----------------------AGCCUA-A-------G-GC-AAAAUCCG-G-A--ACUGA--------------------ACGAAAGU-GAA-C--CA--GU----GUUGG---C-C-GG--UA--GA-GU---GGGUAAC-C-------------------------------U-UGCC--GU-------------------G----AAUGGG-UAAGCCC-----------------------GAGC----------UCCA-----------AC-UCUA-C-A----G-----------------GU-UGGGAUG-GCAGGAU--U-CGG-AUGAAA-----G-C-U-G-----UAU---GU
CP002472.1/2234220-2234049   UCCAUC---G-UGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGCUGG-A-------G-GC-AAAAUUCU-G-A--CCCGA---------------------GGAACAC-GAA-C--AU--CA----UUAGG---C-G-UA-CUC-UCA-CA---GGGUAAG-G-------------------------------C-UGCU--GA-------------------A----CAAGUC-AAAGCCC-----------------------AAAA----------GCUAUCCGG-A----UG-UGGA-A-A----C-----------------GU-AAAUGGU-GCGGGUACAU-GGA-AUGAAA-----G-U-G-A-----AUC---AC
CP001634.1/90026-90188       UCACUG---G-UAA-CGGU-G--A-AUC-UGAA-GGA-----------------------AGCCUA-A-------G-GC-AAAAUCCG-G-A--ACUGA--------------------ACGAAAGU-GAA-C--CA--GC----GUUGG---C-C-GG--UA--GA-GA---GAGUAAC-C-------------------------------U-UGCC--UU-------------------A----CAUGGG-GAAGCCC-----------------------GAGC----------UCCA-----------AC-UCUA-C-A----G-----------------GU-UGGGAUG-GCAGGAU--U-CGG-AUGAAA-----G-C-U-G-----UAU---GU
CP001791.1/422076-422243     UCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-C-------G-AC-AAACUCCU-G-U--ACCGA---------------------GGAACAC-GAA-C--CA--UA----UCAGG---C-A-CA-AAU--GG-GG-C-GGAUGAG-U-------------------------------C-UGCU--AU-------------------A----CAAGAU-AAAGUCC-----------------------AAU-----------ACUGCCCGA-A----CC-CCAC-A-G----U-----------------GU-AAAUAUG-GCGGCGA--U-AGG-ACGA-A-----G-U-A-G-----ACA---GU
CP002457.1/4768125-4767956   UUCACU---G-UGA-GGUG-A--A-AUC-UGAA-GGA-----------------------AGCUGA-A-------A-GC-AAAAUGCU-G-G--CCUGA---------------------CGAACAG-GAA-G--CG--GU----UUAGG---C-G-UU--GU--AG-CA---GGGUAAG-G-------------------------------U-GGCC--AA-------------------U----AUCGCC-AAAGCCC-----------------------AAUA---------CUUGCACGGA-A----UG-CUGC-A-A----C-----------------GU-AUAACCG-ACAGGCAUA--AGC-AGGAAG-----G-U-C-G-----CGC---GA
CP001634.1/1405449-1405611   UCACUG---G-UAA-CGGU-G--A-AUC-UGAA-GGA-----------------------AGCCUA-A-------G-GC-AAAAUCCG-G-A--ACUGA--------------------ACGAAAGU-GAA-C--CA--GU----GUUGG---C-C-GG--UA--GA-GU---GGGUAAC-C-------------------------------U-UGCC--GU-------------------G----AAUGGG-UAAGCCC-----------------------GAGC----------UCCA-----------AC-UCUA-C-A----G-----------------GU-UUGGAUG-GCAGGCU--U-CGG-AUGAAA-----G-C-U-G-----UAU---GU
CP001715.1/2040879-2041045   AAGGUC---G-UGA-GGAC-U--U-GUC-UGGA-GGA-----------------------AGCCGG-A-------G-CGCAAAAGUGC-G-A--GGCGA---------------------CGGACAG-AAA-C--UG--CA-UA-GAAGG---C-C-UG--GU--CU-GC---GGGCGAG-U-------------------------------U-GGCA--CC-------------------C----CAUGAC-GAAGCCC-----------------------AC------------CGGAUACG-------GC-GGAC-A-A----G-----------------GU-AAAUGCA-GCGCUUG--U-GCA-CGGAAA-----C-A-U-C-----GCG---UU
CP001634.1/219562-219400     UCACUG---G-UAA-CGGU-G--A-AUC-UGAA-GGA-----------------------AGCCUA-A-------G-GC-AAAAUCCG-G-A--ACUGA--------------------ACGAAAGU-GAA-C--CA--GU----GUUGG---C-C-GG--UA--GA-GA---GGGUAAC-C-------------------------------U-UGCC--UU-------------------A----CAUGGG-GAAGCCC-----------------------GAGC----------UCCA-----------AC-UCUA-C-A----G-----------------GU-UGGGAUG-GCAGGAU--U-CGG-AUGAAA-----G-C-U-G-----UAU---GU
CP001634.1/159638-159476     UCACUG---G-UAA-CGGU-G--A-AUC-UGAA-GGA-----------------------AGCCUA-A-------G-GC-AAAAUCCG-G-A--ACUGA--------------------ACGAAAGU-GAA-C--CA--GU----GUUGG---C-C-GG--UA--GA-GU---GGGUAAC-C-------------------------------U-UGCC--GA-------------------G----AAUGGG-UAAGCCC-----------------------GAGC----------UCCA-----------AC-UCUA-C-A----G-----------------GU-UUGGAUG-GCAGGAU--U-CGG-AUGAAA-----G-C-U-G-----UAU---GU
CP001634.1/1886296-1886458   UCACUG---G-UAA-CGGU-G--A-AUC-UGAA-GGA-----------------------AGCCUA-A-------G-GC-AAAAUCCG-G-A--ACUGA--------------------ACGAAAGU-GAA-C--CA--GU----GUUGG---C-C-GG--UA--GA-GU---GGGUAAC-C-------------------------------U-UGCC--GA-------------------G----AAUGGG-UAAGCCC-----------------------GAGC----------UCCA-----------AC-UCUA-C-A----G-----------------GU-UUGGAUG-GCAGGAU--U-CGG-AAGAAA-----G-C-U-G-----UAU---GU
CP001708.1/800104-800270     UAGAUG---G-CGA-CAUC-U--A-GGU-GAGA-AGA-----------------------ACGGAU-A---------GC-GAAAUCGU-G-G--CUUGA---------------------CAAACAG-GAA-C--AG--AA-UA-UAAGG---C-G-UA--AC--AG-GU---GGGCAAG-C-------------------------------U-AGCU--AU-------------------A----GAUAGC-AAAGACC-----------------------AAAAA--------GGUAACCGUA-A----AC-CCAA-A-G----C-----------------GU-AAAUUCU-GCAAGUAA---ACU-AU---------G-A-C-C-----AUU---UG
CP001638.1/1803443-1803271   UCUGUG---G-UGA-CGCG-G--A-AUC-UGAA-GGA-----------------------AGCGAG-C-------G-GC-AAACUUCC-G-G--UCUGA---------------------GGAACAC-GAA-C--UU--CA-UA-CAAGG---C-U-AG--GU--AU-CAUU-GGAUGAG-U-------------------------------U-UGCU--CA-------------------A----CAAAAC-AAAGUCC-----------------------U--U----------UCUGCCGAA-G---GUG-AUAC-A-G----A-----------------GU-AAAUGAA-GCAGAUAGAU-GGA-AGGAAA-----G-A-U-U-----ACA---UC
CP003056.1/3199685-3199514   UCCAUC---G-UGA-GAUG-G--A-AUC-UGAA-GGA-----------------------AGCUGG-A-------G-GC-AAAAUUCU-G-A--CCCGA---------------------GGAACAC-GAA-C--AU--CA----UUAGG---C-G-UA-CUC-UCA-CA---GGGUAAG-G-------------------------------C-UGCU--GA-------------------A----CAAGUC-AAAGCCC-----------------------AAAA----------GCUAUCCGG-A----UG-UGGA-A-A----C-----------------GU-AAAUGGU-GCGGGUACAU-GGA-AUGAAA-----G-C-A-A-----AUC---AC
CP003056.1/3201408-3201579   UCCAUC---G-UGA-GAUG-G--A-AUC-CGAA-GGA-----------------------AGCUGG-A-------G-GC-AAAAUUCU-G-A--CCCGA---------------------GGAACAC-GAA-C--AU--CA----UUAGG---C-G-UA-CUC-UCA-CA---GGGUGAG-G-------------------------------C-UGCC--AA-------------------A----CAAGUC-GAAGCCC-----------------------AAAA----------GCUAUCCGG-A----UG-UGGA-A-A----C-----------------GU-AAAUGGU-GCGGGUACAU-GGA-ACGAAA-----G-U-G-A-----AUC---AC
CP003058.1/1309865-1309693   GACACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGGUGC-A-------G-GC-AAAUCUCU-G-A--CCUGA---------------------CGAACAG-AAA-C--CG--CA----UAAGG---C-CAAU--UC--GG-GA-U-GGAUAAG-G-------------------------------G-AGUA--AA-------------------A----CAGACU-GAAGUCC-----------------------CAUA---------AUGACUCGGA-A----UC-CCCA-A-G----G-----------------GU-AGAUGCG-GCAGGUGGGU-GGA-GAGAAA-----G-A-G-U-----GUG---UU
CP001638.1/1431427-1431598   UCCGUG---G-CGA-CGUG-G--A-AUC-GGUA-GGA-----------------------AGCAGG-C-------G-GC-AAACUUCC-A-G--CCUGC---------------------GGAAUAC-GAA-C--UU--CA-UA-GGAGG---C-U-AG--GU--AU-UAUU-GGGGAAG-U-------------------------------U-UGCC-GCA-------------------A----CAAAAU-AAAGCUC-----------------------U--U----------UCUGCCGAA-G---GUA-AUGC-C-A----A-----------------GU-AAAUAAA-GCAGACG--U-AUA-CUGAAC-----G-G-U-A-----CGU---AC
CP001715.1/2026723-2026889   AAGGUC---G-UGA-GGAC-U--U-GUC-UGGA-GGA-----------------------AGCCGG-A-------G-CGCAAAAGUGC-G-A--GGCGA---------------------CGGACAG-AAA-C--UG--CA-UA-GAAGG---C-C-UG--GU--CU-GC---GGGCGAG-U-------------------------------U-GGCA--CC-------------------C----CAUGAC-GAAGCCC-----------------------AC------------CGGAUACG-------GC-GGAC-A-A----G-----------------GC-AAAUGCA-GCGCUUG--U-GCA-CGGAAA-----C-A-U-C-----GCG---UU
CP001727.1/305604-305760     UCCAUC---G-CGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAGCCCC-G-A--CCUGA---------------------GGACCAC-GAA-C--CC--AA-GG-UGAGG---C-C-GC--UG--CA-UU-C-GGGCGA--------------------------------------------------------------------CA------AAACCC-----------------------CAUA-----------CAGCCAAG-G----GA-UGCA-G-G----A-----------------GU-AAAUUGG-GCAGGUACAU-GGG-GCGAAA-----G-C-G-A-----CCG---UU
CP001791.1/994445-994613     UCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCCGG-C-------G-AC-AAACUCCU-G-U--ACCGA---------------------GGAACAC-GAA-U--CA--UA----UCAGG---C-A-CA--GU-CGG-GG-C-GGAUGAG-U-------------------------------C-UGCC--AG-------------------A----CAAGAU-AAAGUCC-----------------------GAU-----------ACUGCCCGA-A----CC-CCAC-U-G----U-----------------GU-AAAUAUG-GCGGCGA--U-AGG-AUGAAG-----G-A-G-A-----CAG---UG
CP001734.1/1042026-1042197   UCCACC---G-CGA-GGUG-G--G-AUC-UGAA-GGA-----------------------AGCCGC-A-------G-GC-AAAACGCU-G-G--CCUGA---------------------CGAACAG-GAA-U--CG--CA-UA-CGAGG---C-G-GC--CA--UG-CC---GGGUAAG-G-------------------------------A-GUCC--AU-------------------U----AUCUUC-AAAGCCC-----------------------UGUA---------CUUGUACGGA-A----AG-CAUG-G-A----C-----------------GU-AUAUGCG-GCGGGCAUA--AAC-GUGAAG-----G-U-G-G-----GUG---CG
CP001634.1/1414462-1414624   UCACUG---G-UAA-CGGU-G--A-AUC-UGAA-GGA-----------------------AGCCUA-A-------G-GC-AAAAUCCG-G-A--ACUGA--------------------ACGAAAGU-GAA-C--CA--GU----GUUGG---C-C-GG--UA--GA-GA---GGGUAAC-C-------------------------------U-UGCC--UU-------------------A----CAUGGG-GAAGCCC-----------------------AAGC----------UCCA-----------AC-UCUA-C-A----G-----------------GU-UGGGAUG-GCAGGAU--U-CGG-AUGAAA-----G-C-U-G-----UAU---GU
ACBX02000015.1/209132-208961 UCCACA---G-CGA-GGUG-G--A-AUC-UGAA-AGA-----------------------AGCUGG-C-------G-GC-AAACAUCU-G-A--CCUAA---------------------CGUACAG-AAA-C--UU--CA-UA-UAAGG---C-A-UU-UGA--CC-AU---GGAUGAG-A-------------------------------U-UGCA--AG-------------------A----CACAUC-AAAGUCC-----------------------CAUA----------GCUAUUCGG-A----AU-GGUU-G-G----U-----------------GU-AAAUGAA-GUGGGUAUA--AGA-UGGAAA-----G-A-A-U-----AAG---CC
HM368526.1/831-1002          UCCACC---G-UGA-GGUG-G--A-AUC-UGAA-GGA-----------------------AGCUGG-A-------G-GC-AAACACUU-G-A--CCUGA---------------------GGUACAC-GAA-C--CC--AA-UG-GGAGG---C-C-GC--CA--CA-GU-C-GGACGAG-U-------------------------------C-UGCU--GG-------------------A----CAAGAC-GAAGUCCU--------------------AA--------------GCCGCCAAG-G----GC-UGUG-G-A----G-----------------GU-AGAUUGG-GCAGGUGCAU-GAG-UGGAAA-----G-U-G-U-----CCA---UC
ACFX02000003.1/562543-562728 GUCAUC---G-CGA-GGUG-G--G-GUC-UGAA-GGA-----------------------AGCCGG-A-------G-GC-AAAACACU-G-G--CCUGUAAAAGUUGUACCCACAGGGCAUG------AUA-C--CC--GG----AUAGG---C-U-GU-GAA--GC-GU---GGAUGAG-G-------------------------------U-UACC--AA-------------------A----CAAACU-AAAGUCC-----------------------AAUA----------ACUGCACGG-A----AC-GCCA-G-C----A-----------------GU-AGACGGG-GCAGGUAUA--AGU-GGGAAA-----G-A-G-C-----GUG---UG
CP001993.1/182523-182357     ACUAUC---G-UGA-GGUA-G--C-AGG-GAGA-GGA-----------------------AGGGAU-A---------GC-GAAAUCGU-G-G--CUCUA---------------------CGAACAG-GAA-C--GU--GA-UAGUAAGG---C-G-UA--AA--UA-GC---GGAUAAG-G-------------------------------A-GGCU--UC-------------------A----AACUCU-AAAGUCCA---------------------AAAAG----------GUAGUCGUA-A----CC-UAUA-U-G----C-----------------GU-AAAUCAC-GAGAGUAAUU-G-------AAUU-CGGAC-U---------------
ACBX02000009.1/69307-69136   UCCAUC---G-UGA-GGUG-A--A-AUC-UGAA-AGA-----------------------AGCCGG-A-------G-GC-AAACAUCU-G-A--CCUAA---------------------CGAACAG-AAA-C--UU--CA-UA-CAAGG---C-AUAU--GA--CC-GU---GGGUAAG-G-------------------------------U-UGCU--AC-------------------U----CAAACC-AAAGCCC-----------------------UAUA----------GCUAUUCGG-A----AC-GGUC-G-G----U-----------------GU-AAAUGAA-GUGGGUAUA--AGA-UGGAAA-----G-A-C-A-----AUG---CU
ACBX02000056.1/36200-36371   UCCACU---G-CGA-GGUG-G--A-AUC-UGAA-AGA-----------------------AACUGG-C-------G-GC-AAACAUCU-G-A--CCUUA---------------------CGUACAG-AAA-C--UU--CA-UA-UAAGG---C-A-UU-UGA--CC-AU---GGAUGAG-A-------------------------------U-UGCU--AA-------------------A----CAAAUC-AAAGUCC-----------------------UAUA----------GCUAUUCGG-A----AU-GGUU-G-G----U-----------------GU-AAAUGAA-GUGGGUAUA--AGA-UGGAAA-----G-A-A-U-----AAG---CC
ACTV01000032.1/1588-1419     AUUAAC---G-UGA-GGGG-A----AUC-UGAA-GGA-----------------------AGGUGG-A-------G-GC-AAAUCUCU-G-G--UCUGA---------------------CGAACAG-AAA-U--CA--CA----UCAGG---C-U-AU--AG--UU-AA---GGAUAAG-G-------------------------------C-UGCC--UA-------------------A----CAAGCU-GAAGUCC-----------------------AAUA---------ACUACUCGGA-A----UU-AACU-G-U----A-----------------GU-AAAUGUG-GCAGAUAGAU-GGA-GAGAAA-----G-U-G-G-----CGU---GU
AE015928.1/3072876-3072704   UCCGUA---G-UGA-UUCG-G--C-AUC-UAAA-GGA-----------------------AGUCUU-A-------G-GC-AAAGCACU-G-A--CCUGA---------------------CGUACAG-AAA-C--UU--GA-UACUAAGG---C-AUAU--GA--GU-GU---GGGUAAG-U-------------------------------C-UGCC--AA-------------------A----CAAGAU-AAAGCCC-----------------------UAUA----------GCUAUAUGG-A----AC-ACUC-G-G----U-----------------GU-AAAUCAA-GCAGGUAUA--AGU-GUGAAA-----G-A-U-U-----AUA---UU
#=GC SS_cons                 <<<<<<..._.___.>>>>.>..>.---.----.---.......................-<<<<<.-.......-.<<.---<<<<<.<.<..<<<<-.....................-------.---.<..<<..<<.<-.----<...<.<.-<..<<..<<.<<...<<<<--<.<...............................<.<___..__..................._....__>>>>.--->>>>.......................----.........----------.-....>>.>>>>.>.-....>.................>>.-->>>>>.>>>>>>-..>.>>>.>>----.....>.>.-.-.....>>>...>>
#=GC RF                      uccacc...G.UGA.ggug.g..a.aUC.UGAA.GGA.......................Agccgc.a.......g.gC.AAAacucc.g.a..cCcGA.....................cGAACAg.aAA.c..cg..ca.UA.uaAGG...C.g.uu..gc..gc.gu...GGgcgAG.c...............................u.uGCa..aa...................a....cAaagC.aAAgcCC.......................aAuA.........uauugacgGA.A....ac.gcgc.a.u....c.................GU.AaAugcg.gCgGguA..u.gga.guGAAA.....G.u.u.a.....gug...gc
//
# STOCKHOLM 1.0

#=GF AC   RF02002
#=GF ID   mir-720
#=GF DE   microRNA mir-720
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   51.00
#=GF TC   51.10
#=GF NC   50.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000664;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18230126
#=GF RT   New miRNAs cloned from neuroblastoma
#=GF RA   Afanasyeva EA, Hotz-Wagenblatt A, Glatting KH, Westermann F
#=GF RL   BMC Genomics. 2008;9:52.
#=GF RN   [2]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   mir-720_microRNA_precursor_family
#=GF SQ   35


ABGA01067312.1/1557-1448   CCGGCUCUCACCCGGUGGUGUUAAU-AU--CUU--GCUGGGGCCUCCAG-AAUGUUUUGCCCA---GGG-GUGUUAGAGAAAACGCCACACUUUGAGAUGAAUU-AA-GAGUCCCUUAUUAG
AC117411.3/45749-45640     CCGGAUCUCACACGGUGGUGUUAAU-AU--CUC--GCUGGGGCCUCCAA-AAUGUUGUGCCCA---GGG-GUGUUAGAGAAAACACCACACUUUGAGAUGAAUU-AA-GAGUCCUUUAUUAG
AF064863.3/117542-117651   CUGGCUCUCGCCCAGUGGCGUUAAU-AU--CUU--GCUGGGGCCUCCAU-UAUGUUGUAUCCA---GGC-AAGUCAGAGAAAACGCCACACUUUGGGAUGAAUU-AA-GAGUCCUUUAUUAG
AC147686.2/145351-145244   CCAGCUCUCACCUGGUGGUGUUAAA-AU--CUC--ACUAGGGCUUCCA--AAUAUUGUACCCG---AGC-GAGUUAGAA-AAACGCCACACUUUGAGAUGAAUU-AA-GAGUCCUUUAUUAG
AC092329.3/58805-58913     AAGGCUCUCGCCCAGUGGCGUUAAU-AU--CUC--ACUGGGGCCUCCA--AAUCUUGUACCUG---AGU-AAGUUAGAGAAAACACCACACUUUGAGAAGAAUU-AA-GAGUCCGUUUAUUU
AADA01185238.1/8-116       CCGGCUCUCGCCCCGUGACGUUAAAAUU--CUC--GCUGGGGCCUCCA--AAUGUUGUACCCG---AGC-GAGUUAGAA-AAACGCCACACUCUGAGACGAAUU-AA-GAGUCCUUCAUUAG
ABGA01375608.1/6340-6450   GCGGCUCUUGCCCAGUGGGGUUAAU-AU--AUCUCGCUGGGGCCUCCAA-AUUGUUGUACCCA---AGC-GAGUUAGAA-AAAUGCCACACUUUGAGAUGAACU-AA-GUGUCCUUUAUUAG
ABGA01129425.1/2093-2200   CUGGCUCUUGCCUGGUGGCGUUAAU-UC---UC--GCUGGGGCCUCCAA-AUUGUUGUACUUG---AGC-GAGUUAGU-AAAAUGCCACAAUUUGAGACGAAUU-AA-GAGUCCUUUAUUAG
AADA01114695.1/7907-7799   CCAGCUCUCACCCAGUGGUGAAUAU-CU--CGC----UGGGGCCUCCAA-AUGUUGUAACCAA---GCG-AGUUAUGGAGAAACGCUACACUUUGAGAUUAAUU-GAGGAGUCCUUUAUUAG
ABGA01344024.1/2670-2561   CCGGCUCUUGCCCGGUGGUGGUAAU-AU--CUU--GCUGGGGCCUCCAU-UAUGUUGUAUCCA---GGC-AAGUUAGAGAAAACGCCACACUUUGAGAUGAAUU-AA-GAGUCCUUUAUUAG
ABGA01302017.1/6636-6528   CCGGCUCUCGCCCAGUGGCGUUAAAAUU--CUC--GCUGGGGCCUCCA--AAUGUUGUACCCG---AGC-GAGUUAGAUAA-ACGCCACACUUUGAGACAAAUU-AA-GAGUCCUUUAUUAG
ABGA01027034.1/20707-20814 CCGGCUCUCACCCAGUGGCGUUAAU-AU--CUC--GCUGGGGCCUCU-A-AAUGUUGUACCUG---AGC-GAGUUAGAA-AAACACCACACUUUGAGAUGAAUU-AA-GAGUCCUUUAUUAG
ABGA01106235.1/2438-2546   CCGGCUCUUGCCUGGUGGUGUUAAU-AU--CUC--ACUGGGGCCUCCA--AAUAUUGUACCUG---AGU-GAGUUAGAGAAAACAACACACUUUGAGAUGAAUU-AA-GAUUCUGUUUAUUU
ABGA01257724.1/20402-20295 CCAGCUCUAGCCCGGUGGCGUUAAA-AU--CUC--GCUGGGGCCUCCAA-CUGUUGUAGCCAA---GCG-A-GUUAGAA-AAACGCCACACUUUGAGACGAAUU-AA-GAGUCCUUUAUUAG
ABGA01295423.1/8067-7958   CUGGCUCUCACUUGGUGGUGUUAAU-AU--CUC--ACUGGCACCUCCAA-AAUGUUGUACCCA---GAU-GAGUUAGAGAAAAUGCCACACUUUGAGAUGAAUC-AA-GAGUCCUUUAUUAG
ABGA01294983.1/3821-3713   CCAGCUCUUGCCCGGUGGCAUUAAU-UU--CUC--ACUGGGGCCUCCAU-UAUGUUGUACCC----GGG-GUGUUAGAGAAAACACCGUACUUUGAGAUGAAUU-AA-GAGUCCUUUAUUAG
ABGA01180729.1/3274-3170   CCGGCUCUCGCCCGGUGGCGUU-----U--CUC--GCUGGGGCCUCCA--AAUGUUGUACCU----GAGCAAGUUAGAGAAAACGCCACAUUUUGAGACGAAUU-AA-GAGUCCAUUUAUUU
ABGA01359290.1/9723-9616   CCGGCUCUCGCCUGGUGGUGU-AAU-AU--CUC--GCUGGGGCCUGCAA-AUUGUUGUACCCA---AGC-GAGUU-AGGAAAACAUCACACUUUGAGAUGAAUU-AA-GAGUUCUUUAUUAG
AB019440.1/26121-26011     CCGGCUCUCGCCCAGUGGUGUUAAU-AU--CUC--GCUGCGGCCUCCAAAAAUGUUGUACCCA---GGC-GAGUUAGAGAAAACGCCACACUUUGAGACGAAUU-AA-GAGUCCUUUAUUAA
AC134698.10/151598-151704  CCGGCUCUUGCCCAGUGGCGAAUAU-CU--C----ACUGGGGCCUCCA--AAUGUUGUGACCAAGC--G-AGUUAUAGAGAAACGCCACACUUUGAGACAAAUU--A-GAGUCCUUUAUUAG
AC069528.10/33954-34060    CCGGCUCUUGCCCGGUGGCAUUAAU-AU--CUC--ACUGGGGCCCCCA--AAUGUUGUACUUG---AGU-GAGUUAGAGAAAACGCCACACUUUGAGAUGAAUU-GA-GAGACCAU--UUAG
AC007275.4/120766-120657   CCGGCUCUCACCCAGUGGAGUUAAU-UU--CUC--ACUGGGACCUCCAU-UAUGUUGUAUCCA---AGC-GAGUUAAAAAAUAUGCCACACUUUGAGACGAAUU-AA-GAGUCCUUUAUUAA
BS000634.2/34830-34722     CCAGCUCUCACCUGGUGGCAGAUAU-CU--CGC----UGGGGUCUCCAA-AUAUUGUAACCAA---GUG-AGUUAUAGAGAAACGCCACACUUUGAGACUAAUUAAA-GAGACCUUUAUUAG
CABD02255006.1/1471-1579   CCGGCUCUCGCCCGGUGGCAUUAAU-AU--CUC--GCUGGGGCCUCCA--AAUGUUGUACUUG---AGU-GAGUUAGAGAAAAUGCCACACUUUGGGAUGAAUU-GA-GAGUCCAUUUAUUU
AADA01310105.1/12098-11989 CCAGCUCUCGCCCGGUGGUGUUAAU-AU--CUC--ACUGGGGCCUCCAA-AAUGUUGUACCCA---GAC-GAGUUAGAGAAAAUGCCACAAUUUGAGACAAAUU-AA-GAGUCCUUUAUUAG
CABD02176942.1/3571-3679   AAGGCUCUUGCCCAGUGGUGUUAAU-AU--CUC--ACUGGGGCCUCCA--AAUGUUGUACCUG---AGU-AAGUUAGAGAAAACAUCACACUUUGAGAUGAAUU-AA-GAGUCCGUUUAUUU
AADA01022577.1/11805-11697 CCGGCUCUUGCCCGGUGGCAUUAAU-AU--CUC--ACUGGGGCCUCCA--AAUGUUGUACUUG---AGU-GAGUUAGAGAAAACGCCACACUUUGAGAGGAAUU-GA-GAGACCGUUUAUUU
CABD02176300.1/657-550     CCGGCUCUCACCUGGUGGGGAAUAU-AU--CUC--GCU-GGGUCCUCCA-AAUGUUAUACCC----GAGCGAGUUAGAAAAA-CGCCACACUUUGAGAUGAAUU-AA-GAGUCCUUUAUUUA
AADA01282684.1/2456-2346   CCGGCUCUCGCCUGGUGGCGUUAAU-AUAUCU--CGCUGGGGCAUCCAA-AAUGUUGUACCCG----AGCGAGUUAGAA-AAACAACACACUUUGAGACGAAUU-AA-GAAUCCUUUAUUAG
AADA01012176.1/2789-2898   CCAGCUCUUGCCAGGUGGCGUUAAU-AU--CUC--GCUGGGGCCUCCAU-UAUGUUGUACCCA---GGC-AAGUUAGAGAAAACACCACACUUUGAGAUGAAUU-AA-GAGUCCUUCAUUAG
CABD02204725.1/179-289     CCGGCUCUCGCCCGGUGGCGUUAAU-AUAUCUC--GCUAAGGCAUCCAA-AAUGUUGUACC-C---GAGCGAGUUAGAA-AAACACCACACUUUGAGAUGAAUU-AA-GAAUCCUUUAUUAG
CABD02255003.1/421-529     CCGGCUCUCGCCCAGUGGCGUUAAAAUU--CU--CGCUGGGGCCUCCA--AAUGUUGUACCCG----AGCAAGUUAGAA-AAACGCCACACUUUGAGACGAAUU-AA-GAGUCCUUUAUUAG
AACZ03022234.1/71930-72038 -CGGAUCUCACCCGGUGGUGUUAAU-AU--CUC--GCUGGGGCCUCCAA-AAUGUUGUGCCCA---GGG-GUGUUAGAGAAAACACCACACUUUGAGAUGAAUU-AA-GAGUCCUUUAUUAG
CABD02255003.1/7042-7150   CCGGAUCUC-CCCGGUGGUGUUAAU-AU--CUC--GCUGGGGCCUCCAA-AAUGUUGUACCCA---GGG-GUGUUAGAGAAAACACUGCACUUUGAGAUAAAUU-AA-GAGUCGUUUAUUAG
AACZ03099708.1/18269-18161 CCAACUCUCACCCAGUGGCAUUAAU-UU--CUC--GCUGGGGCCUCCAU-UAUGUUGUACCC----GGG-GUGUUAGAGAAAACGCCACACUUUGAGACGAAUU-AA-GAGUCCUUUAUUAG
#=GC SS_cons               ::::<<<<<<----<<<<<<<<<<<.<<..<<<..----<<<<______.________>>>>-...>>>.>>>>>>------>>>>>>>---->>>>>>:::::.::.::::::::::::::
#=GC RF                    CCGGcUCUcgCCcgGUGGcGuuaAc.cu..ccc..gCUGgGGcCUCCAa.AAUgUUGUgCCca...ggg.aggUuaGAaAAAaCgCCACACUUugAGAggAAUU.AA.GAGUCCUUUAUUAg
//
# STOCKHOLM 1.0

#=GF AC   RF02003
#=GF ID   group-II-D1D4-4
#=GF DE   Group II catalytic intron D1-D4-4
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Weinberg Z
#=GF SS   Predicted; Weinberg Z
#=GF GA   49.00
#=GF TC   49.00
#=GF NC   48.90
#=GF TP   Intron;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.36 -Z 549862.597050 CM SEQDB
#=GF CL   CL00102
#=GF DR   SO; 0000603; group_II_intron;
#=GF DR   GO; 0000373; Group II intron splicing;
#=GF RN   [1]
#=GF RM   11377794
#=GF RT   The ins and outs of group II introns.
#=GF RA   Bonen L, Vogel J
#=GF RL   Trends Genet 2001;17:322-331.
#=GF RN   [2]
#=GF RM   11726522
#=GF RT   Control of branch-site choice by a group II intron.
#=GF RA   Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM
#=GF RL   EMBO J 2001;20:6866-6876.
#=GF RN   [3]
#=GF RM   12870716
#=GF RT   Group II introns: structure and catalytic versatility of large natural
#=GF RT   ribozymes.
#=GF RA   Lehmann K, Schmidt U
#=GF RL   Crit Rev Biochem Mol Biol 2003;38:249-303.
#=GF CC   Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi,
#=GF CC   plants and protists, and also in mRNA in bacteria. They are large
#=GF CC   self-splicing ribozymes and have 6 structural domains (usually designated
#=GF CC   dI to dVI. This model and alignment represents only domains V and VI. A
#=GF CC   subset of group II introns also encode essential splicing proteins in
#=GF CC   intronic ORFs. The length of these introns can therefore be up to 3kb.
#=GF CC   Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing
#=GF CC   with two transesterification steps. The 2' hydroxyl of a bulged adenosine
#=GF CC   in domain VI attacks the 5' splice site, followed by nucleophilic attack
#=GF CC   on the 3' splice site by the 3' OH of the upstream exon. Protein machinery
#=GF CC   is required for splicing in vivo, and long range intron-intron and
#=GF CC   intron-exon interactions are important for splice site positioning. Group
#=GF CC   II introns are further sub-classified into groups IIA and IIB which differ
#=GF CC   in splice site consensus, distance of bulged A from 3' splice site, some
#=GF CC   tertiary interactions, and intronic ORF phylogeny [1].
#=GF WK   Group_II_intron
#=GF SQ   90


BABB01008120.1/763-624         UUGCCGGUGUAAGUCCGG--UCACGG-UAAU---CGCCAGUGAG----CCGUGUAGUUAA-ACUC-GGUGCG-UU-GU-A-GUAA--------------U-A-CAG-GGUG-CUAAG-C-GAGUG--G-A-UAAA--GUAA--CCUU-GAAA-----------------------------------------AAGG-UGC-GAGCAAUCAUGC-AGAC--------CGUAACAUAA
BABG01006529.1/541-401         UAGCCGGUGUAAGUCCGG--UCACGG-UAAU---UGCCAGUGAG----CCGUGUAGCUAA-ACUC-GGUGCG-UU-GC-A-GUAA--------------U-G-CAG-GGUA-CUAAG-C-GAGUG--G-A-UAAA--G--UAACCUC--GGUAA---------------------------------------GAGGGG-C-GAGCAAUUAUGC-AGAC--------CGUAACAUAA
AAOF01000003.1/29985-30124     CAGUCGGUGGAAGUCCGA--CCGGGGCUAAG---AGACUCA-AG----CCCUGUAGCUUGGGAGG-CGCCGU-GG-CG-C-GAGA--------------G-C-AAG-GCGG-UGGAG-C-CCUCC--G-A-CAAC--A--U--UCUC-AGAAAG---------------------------------------GAGG-A-U-GCGCAACGCACC-AGGU--------UGCAACGUGC
ABSP01038369.1/477-338         CAGCGGGUGUGAGUCCCG--CCCGGC-AACU---GUCGCUC-CA----GCCGGUAGCAAUCGGAG-CGUCGA-GG-GA-G-GCAA--------------C-G-AAC-UCGA-CGAAG-C-CUCUGGUG-U-AGAG--G--G--UCGC--CACUG---------------------------------------GCGA-C-UCG-GCGAGCAGGC-AGGC--------CGUAACGUGA
ABSN01004467.1/157-16          UCACAGGUGCAAGUCCUG--UCUGGG-GAGU---UGUCG---GGACACCCCAGUAGCUA-CCAAGACGAUCC-GA-AG-G-GCAA--------------C-U-GAC-UGGU-CGAAG-CUCUUGG--G-A-CAGA--G--G--CCCACCGUGGG---------------------------------------UGGG-U-C-A-GCAAGCCGGC-GGGC--------CGCAACAUGU
ACNE01000186.1/6164-6027       UAAUUGGUGAAAGUCCAA--UCGGGA-GAAU---AGACUCC-AC----UCCCGUAGCCUGAGAGG-CGCCAU-GA-AG-U-GAAA--------------G-C-GAC-AUGG-CGAAG-C-CCUCU--G-A-CAUC--A--C--AUGC--AAAAG---------------------------------------GCAU-G-U-GGGCAAAUCUCC-AGGU--------UGUAACGUAC
CP000471.1/2465947-2465813     CGGCGGGAGUCAGUCCUG--CAAGGG-UAAU---AACCAAA-U-----CCCUUUAGCUUGGAUGG-CGGGGU-GG-CG-G-GAGA--------------C-C-AAA-GCCU-CGGAG-U-CCAUC--G-A-CAAA--U--G--CCGC--UUUAG---------------------------------------GUGG-C-A---GCGAGUUAUC-AGGC--------CGUAACAACA
ABSN01015039.1/661-543         CAGCGGGCUAAAGUCCCG--UCCGGG-GAAU---UGUCUGU---GCACCCCGGUAGCACAGGGAA-GCGGCG-UC-GG-A-GUAA--------------U-C-AGG-GGUC-GUAAG-U-UUCCC--G-A----------U---------------------------------------------------------G-----GCAAAGCCGC-AGGC--------CGUAACACAA
ABSP01044018.1/701-839         CAGUGGGUGAAAGUCCCA--CCCGGCUAAAU---CGCUCCG-------GCCGGAAGCAAUCGGGG-CAGCUA-UG-GA-G-GUAA--------------C-A-AAA-UAGC-UGAAG-C-CUCCG--A-U-GUAA--G--GAGUCGC--UUUAG---------------------------------------GCGAUC-C-A-GCGAGUGUAC-AGGC--------CGUAAUGAGA
ACIH01000234.1/28-170          UAGCCGGUGAAAGUCCGG--UCGCGG-GAAG---GGCCAAG---C-CCCCGCGUAGCUAGGAUAC-CUACGU-AU-GG-C-GAAA--------------U-C-UGU-ACGU-AGAAG-C-GUAUC--G-ACGAAA--GUAC--CUGU--CAGAG---------------------------------------GCAG-GGC-GAGCAACAUACC-AGGC--------CGUAACAUGA
CP000820.1/3561875-3562010     UUGCCGGUGCGAGUCCGG--UCCGGG-UAGC---UGCCAGG-AG---GCCCGGUAGC-AGACUGG-CGGCUU-GG------UCGGGUAAC----UGGCC--------GGGU-CGAAG-C-CCAGU--G-U-CAAA-----A--GCCC--AAUAG---------------------------------------GGG------GAGCGACUGGAC-GGUC--------CGUAGCAUGA
CP000319.1/4265187-4265048     CUAUGGAGGAAGGUUCCA--UCCGGA-GAGU---UGUCGAUUGA----UCCGGAAGCU-GACGAG-CGGCG----------CGGCCGGGCAACUGGCCU---------CGU-CGAAG-C-CUCGU--G-A-CAAA--G--G--CCGC--CUUGG---------------------------------------GCGG-C-C-GAGCGAUCCAAC-GGGC--------CGUAACGUGA
ABSP01012693.1/203-342         CAGCGGGUGUGAGUCCCG--CCCGGC-AACG---GUCGCUC-CA----GCCGGUAGCAAUCGGAG-CGUCGA-GG-GA-G-GCAA--------------C-G-AAC-UCGA-CGAAG-C-CUCUGGUG-U-AGAG--G--G--UCGC--CACUG---------------------------------------GCGA-C-UCG-GCGAGCAGGC-AGGC--------CGUCACGUGA
ACML01001005.1/27-164          UAGUUGGUGAAAGUCCAA--UCGGGA-GAAU---AGACUCC-AC----UCCCGUAGCCUGAGAGG-CACCAU-GA-AG-U-GAAA--------------G-C-GAC-AUGG-CGAAG-C-CCUCU--G-A-CAUC--A--C--AUGC--AAAAG---------------------------------------GCAU-G-U-GGGCAAAUCUCU-AGGU--------UGUAACGUAC
CP000879.1/1386377-1386495     CAACCAGUGAAAGUCUGG--UCUGAG-GAAA---GGUUAGC-AACCACCUCAGUAGGGAACUCUG-CAUAGU-GG-GA-G-GUAA--------------C-G-AAC--CUA-UGAAG-C-CAGAG--G--------------------GAACAAGGUACC--------------------------GGGCUGC-------------------------------------AACGCAA
CP000473.1/3231903-3232020     GAACUGAAAGGAGUUC-A--CCAUGU-AAAU---UGCCUGUUCG---GACAUGUAGCCCAGCCAG-CGUUAG-AA-AG-A-GAAA--------------U-C-GAU-CUGG-CGGAG-C-CUGGU--G-A------------------------------------------------------------------------GGGCGAACUCGC-GAGC--------CGCAACGCAA
ABSP01010957.1/867-728         CAGCGGGUGUGAGUCCCG--CCCGGC-AACU---GUCGCUC-CA----GCCGGUAGCAAUCGGAG-CGUCGA-GG-GA-G-GCAA--------------C-G-AAC-UCGA-CGAAG-C-CUCUGGUG-U-AGAG--G--G--UCGC--CACUG---------------------------------------GCGA-C-UCG-GCGAGCAGGC-AGGC--------CGUAUUAACU
ACII01000059.1/4006-3878       CGGUGGGUGGAAGCCCCA--UCAAAU-AAGC---UGCUAAC-CACAGCAUUUGAAGCGAGUCUUG-AGUCUG-UC-GC-G-GAAA--------------C-G-UUG-CAGG-CUAAG-C-GUAGA--C-AGCAAG--A--U------AACAGGG--------------------------------------------A-U-A-GCUAUUGAGC---AC--------CGAAA-----
AAOF01000004.1/113128-113266   CGGUGGGUGCAAUUCCCA--CCCGGC-AACU---AUCGCUC-CA----GCCGGUAGCAAUCGGAA-CGGCUG-UG-GA-G-GUAA--------------C-G-AAG-CAGC-CGAAG-C-CUCUGGUG-U-AGAA--G--G--UCAU--UAUAG---------------------------------------GUGA-C-UUG-UCGAGCAUGC-AGGC--------CG-AACGAGU
CP000113.1/6511088-6510950     CGUAGGGUGAAAGUCCCG--AGGCGG-UAAC---AGGUCAA-GG----CCGCAUAGCUGGGGUGG-CGCCGA-CA-GG-G-GAGA--------------C-C-CCU-GCGG-UGAAG-C-CCACU--G-A-CAAA--G--C--CCCG-UUUCAG---------------------------------------CGGG-G-U-GAGCGAGUGCAC-GGGC--------CGUAACGGCG
CP000758.1/660551-660698       CAGUGGAGGAAGGAUCCC--CCCAGAUAAUU---GUCUAUA-GG----UCUGGUAGUUA-ACAAG-CGGCUU-GC-CG-G-GCAA--------------C-CGGUC-GGGC-UGAAG-C-CUCGU--G-A-CAAA--G--G--CCGC--CAUGG---------------------------------------GCGG-U-C-GAGCUAUGCCACCUGGAGGCCCUUGGGUAUUGGAA
AATO01000197.1/1470-1608       CAGCGGGUGCGAAUCCCG--UCCGGC-AACUU-UCGCUCCG-------GCCGGUAGCAACUGGAG-CAGCCG-UG-GA-G-GUAA--------------C-G-AAG-CGGC-UGAAG-C-CUCUG--G-UGUAGA--G--G--GUCU-UGUAAG---------------------------------------GGAC-U-U-G-GCGACCAUGC-AGGC--------CGUAAUGCGA
AM408590.1/3831875-3831739     CUGCCGGUGGGAGUCCGG--UCCGGG-UAGC---UGUCAGG-AG---GCCCGGUAGC-AGGCUGGCCGCUUG-GU-UU-G-GAAA--------------C-G-GGC-AGGGUCGAAG-C-CCAGC--G-U-CGAA--A--G--CCCC--GUUGG---------------------------------------GGG------AAGCAACUGAGC-GGUC--------CGUAACGCGA
ACLX01000102.1/4739-4619       UUGCUGGUGAAAAUCCAGUCUCUAAG-UAAG---AGCCAAGUCG----UCUAGUAGCU-GACAGG-CAGCUG-GU-GG-A-GAAA--------------U-C-CUA-AGGU-UG-AG-C-CCUGU--G-A-CAAA--GUAA-------UUUCUA--------------------------------------------UUU-A------------UAGA-----------AAUGCGA
CP000249.1/2568729-2568867     UUGCCGGUGAAAGUCCGG--UCCGGG-UAGC---UGCCAGG-AG---GCCCGGUAGC-AGGCUGG-CGGCUUCGU-CU-G-GAAA--------------C-G-GGCGGGGU-CGAAG-C-CCAGC--G-U-CAAA--G--G--CCCU--GUGAG---------------------------------------AGGG----GGAGCGAGAGCGC-GGUC--------CGUAGCAUAA
ACMM01000163.1/1945-1808       UAGUUGGUGAAAGUCCAA--UCGGGA-GAAU---AGACUCC-AC----UCCCUUAGCCUGAGAGG-CGCCAU-GA-AG-U-GAAA--------------G-C-GAC-AUGG-CGAAG-C-CCUCU--G-A-CAUC--A--C--AUGC--AAAAG---------------------------------------GCAU-G-U-GGGCAAAUCUCC-AGGU--------UGUAACGUAC
AM746676.1/9207268-9207131     CAUAGGGUGAAAGUCCCG--AAGCGG-CAGA---AGGUCGA-AG----CCGCGUAGCUUGGGUGG-CGCCCG-GC-GG-G-GAGA--------------U-C-CCC-CGGG-UGAAG-C-CCACC--G-A-CAAA--G--C--CCCG--CAUGG---------------------------------------CGGG-G-U-GAGCGAGCGCGC-GGGC--------CGCAACGAGG
ABSN01048009.1/208-347         CAGCCGGUGAGAGACCGG--CCGAGGCCAAA---AGACUCA-GG----CCUCGUAGCUUGGGAGG-CGCCGU-GG-CG-C-GAAA--------------G-C-AAG-ACGG-CGGAG-C-CCUUC--G-A-CAAC--A--U--GCUC-GGAAAG---------------------------------------GAGU-A-U-GCGCAACGCACC-AGGU--------UGCAAUGUAA
ACNK01000028.1/5593-5734       UUCCUGGUGAAAGUCCAG--CCUAGG-UAAG---AGCCAAGUCG----CCUCGUAGCU-GACAGG-CAACUG-GU-GG-A-GAAA--------------U-C-CUA-AGGU-UGAAG-C-CCUGU--G-A-CAAA--GUA--ACUUC-UACUUA---------------------------------------GAAGU-GC-GAGCGAAUCAGC-AGAC--------CGUAACAUAA
BABG01002563.1/823-956         UUGCCAGUGAAAGUCUGG--UCAAGG-UAAU---CGCCAGUGAG----CCUUGUAGCG-AACCUC-CAAUGC-UU-UUGG-GUGA--------------CCG-AUU-GUGU-UGAAG-C-GAGGU--A-U-------G--C--CUGU--GAGAA---------------------------------------ACAG-G-U---GCAAAAUAGC-AGUC--------CGUAACAUAA
ACMI01000921.1/50355-50218     UAGUUGGUGAAAGUCCAA--UCGGGA-GAAU---AGACUCC-AC----UCCCGUAGCCUGAGAGG-CGCCAU-GA-AG-U-GAGA--------------G-C-GAC-AUGG-CGAAG-C-CCUCU--G-A-CAUC--A--C--AUGC--AAAAG---------------------------------------GCAU-G-U-GGGCAAAUCUCC-AGGU--------UGUAACGUAC
AATO01001194.1/1054-1192       CCGCGGGUGCGAAUCCCG--CCCGGU-AACUU-UCGUUCCA-------ACCGGUAGCAACUGGAG-CAGACG-UG-GA-G-GUAA--------------C-G-AAG-CGGC-UGAAG-C-CUCUG--G-UGUAGA--G--G--GUUC-UGUAAG---------------------------------------GAAC-U-U-G-GCGAGCAUGC-AGGC--------CGUAACGUGA
ABSP01001703.1/748-882         CAGUGGGUGCAAGCCCCA--CCCGGC-GAAC---GCUCC---A-----GCCGGAAGCAACCGGAG---GUCA-UG-GA-G-GUAA--------------C-G-AAG-UGGC-UGAAG-C-CUUCG--G-A-UAGCGAG-----UCAC-AAAUUG---------------------------------------GUGA---CAGCGCGAGUGUGC-AGGC--------CGUAACGCGA
ACHP01000071.1/46509-46373     CUGCCGGUGGGAGUCCGG--UCCGGG-UAGC---UGUCAGG-AG---GACCGGUAGCA-GGCUGG-CCGCUU-GGUUU-G-GAAA--------------C-GGGCA-GGGU-CGAAG-C-CCAGC--G-U-CGAA--A--G--CCCC--GUU-----------------------------------------GGGG---G-AAGCAACUGAGC-GGUC--------CGUAACGCGA
CP001186.1/925704-925835       UUGCUGGUGAAAGUCCAG--CC----CCAAGU-CGCCUA-------------GUAGCU-GACAGG-CAACUG-GU-GG-A-GAAA--------------U-C-CUA-AGGU-UGAAG-C-CCUGU--G-A-CAAA--GUAA--CUUC-UAUUUA---------------------------------------GAAG-UGC-GAGCGAAUCAGC-AGAC--------CGUAACAUAA
AATO01010354.1/569-707         CAACGGGUGCGAAUCCCG--UCCGGU-AACUU-UCGUUCCG-------ACCGGUAGCAACUGGAG-CAGACG-UG-GA-G-GUAA--------------C-G-AAG-CGGC-UGGAG-C-CUCUG--G-UGUAGA--G--G--GUUC-UUUUAG---------------------------------------GAAC-U-U-G-GCGAGCAUGC-AGGC--------CGUAACGUGA
ABVL01000004.1/2287-2148       AUCCGGGUUCCAAUCCCG--GCGGGC-AACU---UCGCUCC-A-----GCCCGAAGCACUGGGAG-CGAUUC-AG-GA-G-GUAA--------------C-A-AAU-GAAU-UGAAGUA-CUACC--A-G-AAAA--G--G--GCCGUGCAAAG---------------------------------------CGGU-C-C-A-GCGAACCAUGCAGGC--------CGUAACGCGC
AATO01000843.1/251-116         CAGUGGGUGCAAAUCCCA--CCCGGC-AACU---AUCGCUC-CA----GUCGCUAGCAAUCGGAG-CAGC-----------CGAGAAGGA---UGGGUA----------GC-UGAAG-C-CUUCG--GCG-CAAU--G--G--UCAC--CUUGG---------------------------------------GUGA-C-U-UGAUGAGUGUGC-AGGC--------CGUUGCGAAG
ACBV01000191.1/2594-2460       UUGCGGGUGGAAGUCGCG--UCCCGG-UAGG---CACCGGAGCG----CCGGGUAGGG-GGCCCC-GGUUCG-UC-GU-U-GAGA--------------G-G-CGG-CGGG-CUAAG-C-GGGGU--G-U-CGAA-A---G--CCUC---UUUG---------------------------------------GAGG-----GAUCGAGUGCAU-GGGC--------UGUAGCGGUA
AP009048.1/4506012-4505873     CCGUCGGUGAAAGUCCGC--CCCGG-CUAACU-CUCGCUCCGA------CUGGAAGGACAAGAAG-CGGUCC-AG-GA-G-GUAA--------------C-A-AAA-GGGC-UGAAU-CUCUCCC--U-G-AAAC--G--A--CUUC--UUCAG---------------------------------------GAAG-U-C-A-ACGGGUUAUGCGGGC--------CGUAACGUGA
AAQK01010439.1/2809-2677       UUGCCAGUGAAAGUCUGG--UCAAGG-UAAU---CGCCAGUGAG----CCUUGUAGCG-AGCCUC-CAAUGC-UU-UUGG-GUGA--------------CUG-AUU-GUGU-UGAAG-C-GAGGU--A-U-------G--C--CUGU--GAGAA---------------------------------------ACAG-G-U---GCAAAAUAAC-AGUC--------CGUA-CACGA
CP001046.1/385421-385557       CAGCAGGAAAUAGACCUG--CCGGGG-UAGA---AGUCAGA-AG----CUCCGUAGCUUGGAUAG-CAGGGU-GG-CG-G-GAAA--------------C-C-AAG-ACUC-UGAAG-C-CUAUC--G-A-CGAC--C--G--UCUC--CUUGG---------------------------------------GGGA-C-G-U-GCGAGUCAUC-GGGC--------CGUAAUGAAG
ABSN01002206.1/716-577         CAGCGGGUGUGAGUCCCG--CCCGGC-AACU---GUCGCUC-CA----GCCGGUAGCAAUCGGAG-CGUUGA-GG-GA-G-GCAA--------------C-G-AAC-UCGA-CGAAG-C-CUCUGGUG-U-AGAG--G--G--UCGC--CACUG---------------------------------------GCGA-C-UCG-GCGAGCAGGC-AGGC--------CGUAACGUGA
ACMY01000132.1/2150-2013       UAGUUGGUGAAAGUCAAA--UCGGGG-GAAU---AGACUCC-AC----UCCCGUAGCCUGAGAGG-CGCCAU-GA-AG-U-GAAA--------------G-C-GAC-AUGG-CGAAG-C-CCUCU--G-A-CAUC--A--C--AUGC--AAAAG---------------------------------------GCAU-G-U-GGGCAAAUCUCC-AGGU--------UGUAACGUAC
CP000431.1/540653-540513       UUGCCGGUGUAAGUCCGG--UCCGGG-UAGC---UGCCAGG-AG---GCCCGGUAGC-AGGCUGG-CGGCUC-GG-UC-UGGAAAC------------GG-G-UCG-GGGU-CGGAG-C-CCAGU--G-U-CGAA--A--G--CCCU--GUAAU---------------------------------------AGGG-G-G-GAGCGAGGAUGC-GGUC--------CGCAGCGUCA
AP008981.1/651863-651999       CAGUGUGAGGAAAACUUA--CUAGAU-AAAG---AGUUAGA-A-----AUCUAUAGCUAGGAUAGGCAGCAU-AA-AG-A-GAAA--------------U-U-GAG-AUGU-UGAAA-C-UUAUC--A-A-CAAA--C--U--UAUC--GAAAG---------------------------------------GAUA-A-G-A-GCGACUUAUU-AAGC--------UGCAACAAAA
AAFX01066282.1/101-245         CAGCGGAUGAGAGAUCCG--CCAGAG-UAGU---UGUCGAUUCG---ACUCUGUAGCCACCCGAG-CGCUUA-CG-CG-GAGUGA-------------UC-C-AUG-UGAG-CGAAG-C-CUCGG--GGA-CAAU--G--C--CUGCCUUUUGG---------------------------------------GCGG-G-CCA-GCAAACCCAC-GGGC--------CGUAACGCGA
AAVO02000019.1/2195-2056       CAGUCGGUGAAAGUCCGA--CUAUGG-UAAU---CACCAGUGAG----CCAUAUAGUCAA-AUCC-GGUGCG-UU-GU-A-GUAA--------------U-A-CAG-GGUA-CUAAG-C-GGAUG--G-G-UAAU--GUAG--CUUC---AUAA---------------------------------------GAAG-UGC-UAACAAUCAUGC-AGAC--------CGCAACAUAA
ABSP01055982.1/212-347         CAGCAGGAGUAAGUCCUG--CCGGGG-UAAU---AGUCAA--AG----CCCCGUAGCUUGGAUAG-CAGGGU-GG-CG-G-GAAA--------------C-C-AAG-ACCU-UGAAG-C-CUAUC--G-A-CAAG--U--G--UUUC--CUUGG---------------------------------------GAAA-U-G-C-GCGAGUCAGC-GGGC--------CGUAACGAAA
U00090.2/518719-518855         CAGUGGAGGAAGGUUCCA--CCCAGA-UAGU---UGUCGAU-AG---G---GGUAGCU-AGCGAC-CGGUUC-GG-UUGG-GUAA--------------CUA-GCC-GGGU-CGAAG-C-CUCGU--G-A-CAAA--G--G--CCAC--CUUGG---------------------------------------GCGG-U-U-GAGCGAUCCGAU-GGGC--------CGUAAUGCGA
FM211192.1/1313224-1313358     UUGCCGGUGUAAGUCCGG--UCUGGG-UAGU---CGUCAGG-AG---GCCUGGUAGCA-GACUGG-UGACUU-GG-UC-UGGAAA--------------A-GGACC-GGGU-CGAAG-C-CCCGU--G-U-CGAA--A--G--CCUUUUACUAG---------------------------------------GGGGAC-U-GAGU---------GGUC--------AGUAGCAUGA
AM999887.1/1040422-1040556     CAGUAGGAAAUAGACCUA--CCAGGA-UAAA---AGUCGGA-A-----UCCUGUAGCUUGGGUAG-CAGCAU-AA-AG-G-GAAA--------------C-C-AAA-AUGU-UGAAG-C-CUACC--G-A-CAAC--A--U--UAUC--GUA-G---------------------------------------GAUA-A-U-G-GCGAAUUACC-AGGC--------CGUAGCGAAA
ACNF01000057.1/14559-14696     UAGUUGGUGAAAGUCCAA--UCGGGG-GAAU---AGACUCC-AC----UCCCGUAGCCUGAGAGG-CGCCAU-GA-AG-U-GAAA--------------G-C-GAC-AUGG-CGAAG-C-CCUCU--G-A-CAUC--A--C--AUGC--AAAAG---------------------------------------GCAU-G-U-GGGCAAAUCUCC-AGGU--------UGUAACGUAC
AAFY01005701.1/391-254         CAGCGGGAGUUAGUCCCG--CCAGGG-AAGG---AGUCAGG-AG----CCCUGUAGCUUGGGCCG-CACGGG-UG-GA-G-GAAA--------------C-G-AAG-CACG-UGAAG-C-CGGCC--G-A-CAAA--G--C--CGCC--UUUGG---------------------------------------GGCG-G-UGA-GCGAGUCAUC-GGGC--------CGCAACGCAA
AP008981.1/705714-705849       CAGUGUGAGGUAACCCUA--CUAGAU-GAAG---AGUUAGA-A-----AUCUAUAGUUAGGAUAG-CAGCAU-GG-AG-A-GAAA--------------U-U-GAG-AUGU-UGGAA-C-AUAUC--G-A-CAAA--C--U--UAUC--GAAAG---------------------------------------GAUA-A-G-A-GCAAAUUAUC-AAGC--------UGCAACGAAA
CP000432.1/24993-24857         UUGCCGGUGCAAGUCCGG--UCCGGG-UAAC---UGCCAGG-AG---GCCCGGUAGC-AGGCUGG-CGGCAU-CG-GGGG-GAAA--------------CGC-CCG-GUGU-CGAAG-C-CCAGC--G-U-CAAA--A--G--CCCU--UCAAG---------------------------------------GGGG-A-GCAACCGAGUGGUC-------------CGUAGCAUCA
ABSP01019015.1/146-285         CAGUGGGUGAAAGCCCCA--CCCGGC-GAAA---UGCUCCA-------GCCGGAAGCAACCGGAG-CAACUA-UG-GA-G-GUAA--------------C-G-AAA-UGGU-UGAAG-C-CUUCG--G-A-UAGCGGG--C--CACA-AAAUUC---------------------------------------GGUG-G-CAGCGCGAGUGUGC-AGGC--------CGUAACGCGA
ABSN01061672.1/751-607         CAGUGGGUGAGAGUCCCA--CCCGGC-AACU---GGUCGUUCCA----GCCGGAAGCAGUCGGGG-CGGUGAGAG-GA-G-GCAA--------------C-AAGUU-UCGC-UGAAG-CACUCCGAUGAA-GAAG--G--G--UCGC--GAGAG---------------------------------------GCGA-C-U-CAGCAAGCAUGC-AGGC--------CGUAACGUGA
ABIZ01000001.1/1038771-1038906 CACCGGGUGGAAGUCCCG--GCUGGC-UAUAU-CGCUCCG--------GCCAGAAGCACUGGGGG-CGGUUC-AA-GA-G-GUGA--------------C-A-AAU-GAAU-CGAAG-U-ACUUC--C-A-GAAA--A--G--GCUC-CGUAGG---------------------------------------GAGU-C-A---GCGAUCAUGC-GGGC--------UGCAAUGUAG
ABSQ01023076.1/400-256         CAGUGGGUGAGAGUCCCA--CCCGGC-AAAG---GGUCGCUCCA----GCCGGAAGCAGUCGGAG-CGGUGAGAG-GA-G-GUAA--------------C-G-AAUUUCGC-UGAAA-CACUCCGAUG-A-CAAA-GG--G--UCGC--UUAAG---------------------------------------GCGA-C-U-CAGCGAGCAUGC-AGGC--------CGUAACGCGA
AACY023786104.1/1062-916       CAGCGGGUGCAAGUCCCA-GCCGGGG-UAAG---AGCCAGGUCG----CCCCGUAGAU-GGCAGC-GGUCGU-UG-GG-A-GAGA--------------U-C-CCA-GCGG-CUAAG-C-GCUGC--G-A-CAAG--C--C--UUCG-GGGGCAGGAG-------------------------------GAACCGGA-G-G-C-GCGACCGGUC-GGGC--------CGCAACAUGA
BA000040.2/2117981-2118120     CAGUGGAGGAAGGAUCCA--CCCAGA-GAGU---UGUCGAUUGA----UCUGGUAGCU-GACGAG-CGGUUU-GG-AC-GAGCAA-------------UC-G-GAC-GGAU-CGAAG-C-CUCGU--G-A-CAAA--G--G--UCGC--UUUAG---------------------------------------GCGG-C-C-GAGCAAUCCAGC-GGGC--------CGUAACGUGA
DQ363750.1/30096-30233         UAGUUGGUGAAAGUCCAA--UCGGGA-GAAU---AGACUCC-AC----UCCCGUAGCCUGAGAGG-CGCCAU-GA-AG-U-GAAA--------------G-C-GAC-AUGG-CGAAG-C-CCUCU--G-A-CAUC--A--C--AUGC--AAAAG---------------------------------------GCAU-G-U-GGGCAAAUCUCC-AGGU--------UGUAACGUAC
CP001348.1/1476653-1476795     UUGCCAGUGUAAGAAUGG--CACGGG-UAAU---UACCAAGAAG----CCCGGUAGCCAA-UCCC-GGUGCA-UA-CU-A-GUAA--------------U-G-CUA-UGUG-CUGAA-C-GGGAG--G-A-UAAA--GUAC--UUGUCUAAACA---------------------------------------ACAG-GGC-GAGCGAAAAUGC-AGAC--------CGUAACAAAA
ACDL01000030.1/426-291         CAUGGGGUGAAAAUCCCA--CCAGGU-GACU---GUCGUUC-CA----GCCGGUAGCAGUCAAAG-CAGUCG-UG-UG-G-GUAA--------------C-A-AAG-CGGC-UGAUG-U-AUUUGGUG-A---A------GAAG--C--UGUAG---------------------------------------G--UGUU-UCAGUGAGUAUAC-AGGU--------CAUAAUGUGA
AM494475.1/1496374-1496510     CAGUGUGAGGUAAGCAUA--CUAGAU-GAAG---AGUUAGA-A-----AUCUAUAGUUAGGAUAG-CAGCAU-GG-AG-A-GAAA--------------U-U-GAG-AUGU-UGGAA-C-AUAUC--U-A-CAAA--C--U--UAUC--AAAAG---------------------------------------GAUA-A-G-A-GCAAAUUAUUCAAGC--------UGCAACGAAA
BAAU01013897.1/287-420         UUGCCAGUGAAAGUCUGG--UCAAGG-UAAU---UGCCAGUGAG----CCUUGUAGCGAG-CCUC-CAAUGC-UU-UUGG-GGGA--------------CUG-AUU-GUGA-UGAAG-C-GAGGU--A-U-------G--C--CUGU--GAGAA---------------------------------------ACAG-G-U---GCAAAAUAAC-AGUC--------CGUAACAUAA
CP000089.1/2435428-2435289     CAGUGGGUGAAAGCCCCA--CCCGGCGAAAUG-CUCCA----------GCCGGAAGCAACCGGAG-CAGUCA-UG-GA-G-GUAA--------------C-G-AAA-UGGC-UGAAG-C-CUUCG--G-A-UAGCGGG--C--CACA-AAUUCU---------------------------------------GGUG-G-CAGCGCGAGUGUGC-AGGC--------CGUAACGCGA
CU928162.2/3255893-3255740     UUGCAGGUGAGAGUCCUG--CCGCAGUAAUU---GGUUAGUUUG---ACUGCGUAGCGAUGGCGUAC-AUGU-GG-AG-G-GUGA--------------C-C-GAA-GCAU-GGGAG-CAACGCC--GGA-UAAA-C---G--UG--UCCCC--CGAUCCAG-----------------------ACAGUGGG--CG-C---GCGCAAAUACAC-AGCC--------CGUAACUGAC
ABSN01001442.1/480-618         CAGUGGGUGAAAGUCCCA--CCCGGCUAAAU---CGCUCCG-------GCCGGAAGCAAUCGGGG-CAGCUA-UG-GA-G-GUAA--------------C-A-AAA-UAGC-UGAAG-C-CUCCG--A-U-GUAA--G--GAGUCGC--UUUAG---------------------------------------GCGAUC-C-A-GCGAGUGUGC-AGGC--------CGUAACGUGA
AE009948.1/568841-569017       UAACAGGUGAAAGUCCUG--UCCUAACAAUU---AACCAGUUCG---GUUAGGUAGCUAUGGCAUAC-GUAU-GC-GG-A-GUAA--------------U-C-CAA-AUGC-GGAAG-CAAUGCC--G-A-CUAA--C--G--UU---AUCCCCAGUAGGCUGAUAUUCAUUGGUCUUAUCUCAGUCCGUGGG--AG-C-G-A-GCAAACCUAC-AGUC--------CGUAACGAAA
CP000673.1/3033490-3033353     UUACUGGUGAAAGUCCAG--UCUAGGUAAUU---ACCAAGA-AG----CCUAGUAGCCAA-UCAC-CAUGUG-CA-GU-A-GAAA--------------U-A-CUG-GGCA-UGAAG-C-GUGAA--G-G-UAAU--A--U--AUCC-CGAAAG---------------------------------------GGAG-A-U-A-GCGAAAAUGC-AGGU--------UGUAAUAUAA
CP000113.1/4209271-4209409     CGUAGGGUGAAAGUCCCG--AGGCGG-CAAC---AGGUCAA-GG----CCGCAUAGCUGGGGUGG-CGCCGA-CA-GG-G-GAGA--------------C-C-CCU-GCGG-UGAAG-C-CCACU--G-A-CAAA--G--C--CCCG-UUUCAG---------------------------------------CGGG-G-U-GAGCGAGUGCAC-GGGC--------CGUAACGGCG
AM494475.1/1448229-1448365     CAGUGUGAGGCAAACCUA--CUAGAU-AAAG---AGUUAGA-A-----AUCUAUAGCUAGGAUAGGCAGCAU-AA-AG-A-GAAA--------------U-U-GAG-AUGU-UGAAA-C-CUAUC--A-A-CAAA--C--U--UAUC--GAAAA---------------------------------------GAUA-A-G-A-GCGAAUUAUC-AUGC--------CGCAGUGAAA
CP000511.1/2360159-2360293     UAGCGGGUGGAAGUCCCG--UCCCGG-UAGG---UACCGGAGCG----CCGGGUAGCA-GGCCCC-GGUUCG-UC-GU-G-GAGA--------------C-G-CGG-CGGG-CUGAG-C-GGGGU--G-U-CGAG--A--G--CCUC---UUCG---------------------------------------GAGG-----GAGCAAGUGUGC-GGGC--------CGUAGCGUUA
CP000494.1/6512366-6512228     CAGUGGAGGCAGGUUCCA--CACGGA-CAAU---UGUCGAUUGG----UCGGUUAGCU-GACGAG-CGGUUC-AA-CCGG-GCGA--------------CUG-GUG-GGAC-CGGAG-C-CUCGU--G-A-CGAA--G--G--CCGC-GACAUG---------------------------------------GCGG-C-U---GAGAUCCCGU-GGGC--------CGUAACGCGA
U15186.1/31958-31825           UUGCCGGUGUAAGUCCGG--UCCGGG-UAGU---CGUCAGG-AG---GCCUGGUAGCA-GACUGG-UGACUU-GG-UC-UGGAAA--------------A-G-GAC-CGGU-CGAAG-C-CCCGU--G-U-CGAA--A--G--CCUU--UUACU---------------------------------------AGGG-----GGAC---UGAGU-GGUC--------AGUAGCAUGA
AB000735.1/13070-13204         CGGCGGGUGUGAGUCCCG--UCCCGG-UAGG---UACCGGAGCG----CCGGGUAGCA-GGCCCC-AGUUCG-UC-GG-A-GAGA--------------U-C-UGG-CGGG-UCGAG-C-GGGGU--G-U-CGAG--A--G--CCUC---UUUG---------------------------------------GAGG-----GAGCAACCGUGC-GGGC--------CGUAGCGUGA
CP000764.1/2577968-2577838     UUGCUAGUGAAAGACAAG--CUUAGG-UAAG---AGCCAAAUCG----CCUAGUAGCC-GACAGG-CAACUG-GU-GG-A-GAAA--------------U-U-CUA-AGGU-GGAAU-C-CUUGU--A-A-AAAA--G--U--AACG-GCUC-----------------------------------------CGUU-U-CCG-----UCUUUCUAGUC-----------UACUUUA
CP000721.1/2624463-2624599     UAAAUGGUGGAAAUCCAU--UCUGAA-AAGAUUAAGUCAAAUCA----UUCAGUAGCGAGUCAUU-GAAAUA-AA-UA-G-GUAA--------------C-U-AUU-UAUU-UUAAG-C-GUUGA--C-A-G-----U--U--AGGU--AGUAG---------------------------------------GCUU-G-A-AUGUGAAUGAGC---CU--------CGUAAUAAGU
CP001720.1/3486549-3486413     UAACGGGUGGAAAUCCCG--UCUGGU-AAGA---CUCUAGC-CAAGUCACCAGUAGCGAGUCUUG-GACUCG-AU-GG-A-GUAA--------------U-U-CAU-AGAG-UUAAG-C-GUAGA--C-A-G-----G--U--AGGU--AGUAG---------------------------------------GCCU-G-A-AUGUGAUUGAGC---CC--------CGUAAUGGGC
CP001634.1/1518541-1518677     CAGUGGGAGAUAAACCCA--CCAAGG-CAAA---AGCCAGA-A-----CCUUGUAGCUUGGUCAG-CAAGGG-GG-AA-G-GAAA--------------C-U-GAA-CUCU-UGAAG-C-CUGAC--G-A-CAAA--G--C--CAUC--GGAAG---------------------------------------GAUG-G-U-GAGGGAGUAUCC-GGGC--------CGUAACGAAA
CP001720.1/4217733-4217598     UAGUCGGUGAAAGUCCGA--CCGGGA-GAAA---AGACUUC-AC----UCCCGUAGCUUGAGAGG-CACCGU-GG-AG-U-GAAA--------------A-U-GAA-ACGG-UGAAG-C-CCUUU--G-A-CAAC--A--C--ACUC----AAG---------------------------------------GAGU-G-U-GAGCGAAACUCC-AGGU--------UGUAAUCACA
CP003056.1/595614-595481       UAACAGGUGAAAGUCCUG--UAGUGG-UAAA---GGUAGGGCAG----CCACUUAGUC-AGUAAC-CAGCGU-AU-GA-A-GCAA--------------U-U-UAU-GCGU-UGAAG-C-GUUAC--G-G---AA--U--G--CUCU--GAA-A---------------------------------------AGAG-C-A-G-ACAAACUGAC-GGGU--------CGUAACAUGA
CP001658.1/3840117-3839981     CUGCCGGUGGGAGUCCGG--UCCGGG-UAGC---UGUCAGG-AG---GCCCGGUAGCA-GGCUGG-CCGCUU-GG-UUUG-GAAA--------------CGG-GCA-GGGU-CGAAG-C-CCAGC--G-U-CGAA--A--G--CC-C-UGUUGG---------------------------------------G-GG-----AAGCAACUGAGC-GGUC--------CGUAACGCGA
CP002878.1/2006476-2006338     CAGUCGGUGAAAGUCCGA--CCGAGG-CAAA---AGACUCA-GU----CCUCGUAGCUAGGGAGG-CGUCAU-GG-CG-C-GAAA--------------G-C-AAG-AUGA-CGGAG-C-CCUCC--G-A-CAGU--A--U--GCUC-AGAAAG---------------------------------------GAGU-G-U-AUGCAACGCACC-AGGU--------UGCAACGUGC
CP001720.1/1927159-1927295     CAGCAGGGGAGAAACCUG--CCGAGG-UAAA---AGUCAGA-AA----CCUUGUAGCUAGGAUAG-CAGGGU-UA-AA-G-GAAA--------------C-U-GAG-AUUC-UGGAG-U-CUAUC--G-A-CAAU--A--U--UAUC--CAAGG---------------------------------------GAUG-A-U-A-GCGAGUUGCC-AGGC--------CGUAGCGAAA
CP001720.1/4468440-4468575     UAAUAGGUGAAAAUCCGA--CCGGGA-AAAA---AGGCUCC-AC----UCUCGUAGCUUAAGAGG-CACCGU-GG-AG-U-GAAA--------------A-U-GAA-ACGA-UAAAG-C-CCUCU--U-A-CAAC--A--C--ACUC----AAG---------------------------------------GAGU-G-U-GAGCGAAACUCC-AGUU--------UGCAACCACA
CP001814.1/3372085-3371956     UUGCCGGUGGAAGUCCGG--UCCGGG-UAGC---UGCCAGG-AG---GCCCGAUAGCA-GGCCGG-CGGCUU-CG-UCUG-GAAA--------------CGG-GCG-GGGU-CGAAG-C-CCGGC--G-U-CGAA--A--G--C--C--CUUAG---------------------------------------G--G-U-C-G----CUUCACU-UGGU-------G---AGCGGGU
CP001720.1/1704837-1704973     UAACGGGUGGAAAUCCCG--UCUGGU-AAGA---CUCUAGC-CAAGUCACCAGUAGCGAGUCUUG-GACUUG-AU-GG-A-GUAA--------------U-U-CAU-AGAG-UUAAG-C-GUAGA--C-A-G-----G--U--AGGU--AGUAG---------------------------------------GCCU-G-A-AUGUGAUUGAGC---CC--------CGUAAUGGGC
#=GC SS_cons                   ::::::::::::::::::..:<<<<<.____..._______.__....>>>>>,,,,,,,<<<<<.<<<<<<.--.-<.<.____..............>.>.---.>>>>.>>---.-.>>>>>..,.,.,,,,..<..<..<<<<.._____.......................................>>>>.>.>.,,<<<_______.____........>>>:::::::
#=GC RF                        cAGCgGGUGaAAGUCCcG..uccgGg.aAau...aGcCagu.aG....cCcggUAGCuAgggcgg.Cggcgu.gg.gg.g.GuAA..............c.c.aaa.acgc.cGAAG.C.ccgcc..G.A.CAAA..g..g..ccgc..uauaG.......................................gcgg.c.c.gagCgAaucugC.AGGC........cGuAACGuaA
//
# STOCKHOLM 1.0

#=GF AC   RF02004
#=GF ID   group-II-D1D4-5
#=GF DE   Group II catalytic intron D1-D4-5
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Weinberg Z
#=GF SS   Predicted; Weinberg Z
#=GF GA   43.00
#=GF TC   43.40
#=GF NC   42.50
#=GF TP   Intron;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00102
#=GF DR   SO; 0000603; group_II_intron;
#=GF DR   GO; 0000373; Group II intron splicing;
#=GF RN   [1]
#=GF RM   11377794
#=GF RT   The ins and outs of group II introns.
#=GF RA   Bonen L, Vogel J
#=GF RL   Trends Genet 2001;17:322-331.
#=GF RN   [2]
#=GF RM   11726522
#=GF RT   Control of branch-site choice by a group II intron.
#=GF RA   Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM
#=GF RL   EMBO J 2001;20:6866-6876.
#=GF RN   [3]
#=GF RM   12870716
#=GF RT   Group II introns: structure and catalytic versatility of large natural
#=GF RT   ribozymes.
#=GF RA   Lehmann K, Schmidt U
#=GF RL   Crit Rev Biochem Mol Biol 2003;38:249-303.
#=GF CC   Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi,
#=GF CC   plants and protists, and also in mRNA in bacteria. They are large
#=GF CC   self-splicing ribozymes and have 6 structural domains (usually designated
#=GF CC   dI to dVI. This model and alignment represents only domains V and VI. A
#=GF CC   subset of group II introns also encode essential splicing proteins in
#=GF CC   intronic ORFs. The length of these introns can therefore be up to 3kb.
#=GF CC   Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing
#=GF CC   with two transesterification steps. The 2' hydroxyl of a bulged adenosine
#=GF CC   in domain VI attacks the 5' splice site, followed by nucleophilic attack
#=GF CC   on the 3' splice site by the 3' OH of the upstream exon. Protein machinery
#=GF CC   is required for splicing in vivo, and long range intron-intron and
#=GF CC   intron-exon interactions are important for splice site positioning. Group
#=GF CC   II introns are further sub-classified into groups IIA and IIB which differ
#=GF CC   in splice site consensus, distance of bulged A from 3' splice site, some
#=GF CC   tertiary interactions, and intronic ORF phylogeny [1].
#=GF WK   Group_II_intron
#=GF SQ   139


BAAU01012577.1/612-414       UACAACUAAUAGAAUGU--UGCUC-AAAUGAGUGGCUAACA-----------CCACAAAGGGGCGCACAUA--AACUG--CCU-AC-GGCA--------UGAGUAGCAGCG-C--------------------------CAUGUGAAAAUGUC-GGAAAGCUAGGCUGGAG-AG---CAAAA-A-UUCGAC------------CCA------AA------C---------AG---------UUU-------UAG--------------------------------------CU-G-------UGGA------AAU-GUU-UGUA-GAGG-UAC-AGGCUGUCG-AAGAUU---AUGUAGUGG-GCUGUAUA
BABA01023444.1/885-685       UACAACUGAUAUGGUGUG--GUUC-AAAAGAAGGGGGAACG----------CCCUGAAGGG-ACACACGUAAACUCCU--UAC-AG-CGUGA-AAGU--UGUGCAAAAGCAAU--------------------------CGG----G---UUG-UC-AAAA-GUNAGGGUG-AAGAGCAAAA-A-GCAGGU------------CCU------AA------C--------AGG---------U-A-------AGG--------------------------------------CU-G-------AGGA------AAG-AUU-CACA-GAGG-UGU-GGGUUGCCU-GUGAUU---AUGUAGUGA-AGCUGUAU
BABF01012828.1/982-789       GAAAACUAAAUGGGUGA---AAUUUGAAAGAAGGGGUAAA-----------CCCCUAAAAG-UUACUUUAAUUCUCCCGGCGGCUG-GGA-A-UG------GGUUAA------------------------------------CAUUAAAUUU-CAAAAGC-CCGGGG--A-AUCUGGCAAA-G-AAAUUC------------CUU------AA---------------ACA---------AUG-------UAG--------------------------------------UG-G-------ACGA------AAC-CUU-UCCA-AAGG-GGG-AUGGUGGUU-UCCAUU---AGCCCGGGA-UUUUAAAA
BAAY01000078.1/7978-8176     GAGAACUGCAUAACUGAA-AUCUC-AAAUGACGGGGUAACG----------CCCUGAAGGG-GAUUCACUA-AUACUC--CGA-AU-AGCGU-CAGC--CGA----AUACAGA--------------------------CGGUUGGG---GUU-AU-AAGC-UCGGGG--A-AGUCGUGCGA-A-GCACAC------------CCU------AA------C---------GC---------UUA-------AUG--------------------------------------UC-G-------AGGA------AAG-AUU-CGUA-GAGG-UAC-GGGUUGUGU-GUGACA---GUGCGGGUG-GGGUUGCC
BAAZ01024708.1/566-355       CCUAACUGUAACCUUGAU-AGAUG-GAAUGAGGGGGUAACG----------CCCUGAAACG-UCUUCCCUG-AUACUC--CGA-UU-GGCGC-UGCA--AGA------CAGCA--------------------------CUUGCAGG---GUC-AA-GAGC-UCGGUG--A-AGUCGGCUGA-AUACACUCGCUGU-AUCGACAAC------AA------U--------CAU---------A-U-------UGU--------------------------------------AU-C-------GUUACGGCAAAAG-CAA-GCCA-GAGG-UGG-C-UGUGAGU-GUUA-----GGCCGGGGG-UCUACAAA
BAAZ01024707.1/829-1038      CCUAACUGUAACCUUGAU-AGAUG-GAAUGANGGGGGUACG----------CCCCUGAACG-UCCUCCCUG-AUACUC--CGA-UG-GNCGC-UGNC--AGA------CAGCA--------------------------CUUGCAGG---GUC-AA-GAGC-UCGGUG--A-AGUCGGCUGA-A-UACACU------------CG---------------------------CUG---UAUCGACCA-CAAUCAUAUG------------------------------GUAU------------CGAUACGGCAAAGCAA-GCAA--AAG-UGG-CUUGUAAUG-U---UA---AGGCGGGGG-UCUCAAAA
BABF01012829.1/273-471       GAGAACUGAAUGCGUGAA-UAGUC-GAAUGAAGGGGUAACG----------CCCUGAAAGG-CUA-CUCUA-AUACUC--CGG-CUCGGCA-UGGAA----AUGAGUAAACAU----------------------------UGAAAU---GUC-AG-AAAC-CCGGUG--A-AGUCGGCAGA-G-AGAUAC------------CGU------AA------C---------AA---------UAG-------UAG--------------------------------------UU-U-------ACGA------AAG-CUU-GUCC-AAGG-UGG-AAGGUGUAU-CCUAUA---UUCCGGGAG-UCUAAAAA
BAAY01002678.1/1230-1427     GUGAACUGGUAAUCCGAU-AGGUG-GAAUGAUGGGGUAACG----------CCCUGAAACG-UCUAUCCUU----GAC--GGA-CU-UGCGU-CAGC--UGU---------AA--------------------------UGGUUGGG---GUG-AG-AAGC-UCCGUGACA-AC--GACCGA-G-AGUAGU------------CGU------AG------G--------AAUCU----GCCA-A-------AAG-------------------------------------AUU-C-------UCGA------AAA-CGC-CCCAAAAGG-UGG-GGUGCCCUA-CCUAUA---GGUCUAGGA-UCUUUAAA
BAAY01025675.1/864-669       CUGUGAACUGUAAUCCGA-UAGUG-GAAUGAUGGG-UAACG----------NCCUGAAACGUCUAUCCUUG-----AC--GGA-CU-UGCGU-CAGC--UGU---------AA--------------------------UGGUUGGG---GUG-AG-AAGC-UCCGUGACA-AC--GACCGA-G-AGUAGU------------CGU------AG------G--------AAUCUG---CCAA---------AAG--------------------------------------AUUC-------UCGA------AAA-CGC-CCCA-GAGG-UGG-GGUGCGCUA-CCUAUA---GGUCUAGGA-UCUAUAAA
BAAZ01028647.1/215-15        AACAACUGAUAACCCGAU-AGGUA-GAAUGAAGGAGUAACG----------CCCUGAAAUG-CCUACUCUG-AUACUU--CGA-CC-GGCUU-CGGC--UGU---------AA--------------------------UGGCUGGA---GUC-UG-GAGC-UCGA--UAA-AGUCGGCGGA-A-GUUUGU------------CGU------AA------C--------AGCGUG---GCAA-C-------ACG--------------------------------------GCUG-------ACGA------AAG-UGC-AGUA-GAGG-UAC-UGUAUGCAG-AUGACA---CAUAAAUUU-CUACUUCU
BAAX01017955.1/276-76        AACAACUGAUAACCCGAU-AGGUA-GAAUGAAGGAGUAACG----------CCCUGAAAUG-CCUACUCUG-AUACUU--CGA-CC-GGCUU-CGGC--UGU---------AA--------------------------UGGCUGGA---GUC-UG-GAGC-UCGA--UAA-AGUCGGCGGA-A-GUUUGU------------CGU------AA------C--------AGCGUG---GCAA-C-------ACG--------------------------------------GCUG-------ACGA------AAG-UGC-AGUA-GAGG-UAC-UGUAUGCAG-AUGACA---CGCCGGGAU-GUCUAUAA
BAAW01000932.1/826-1025      GAGAACUAAUAAUCUGAG-GAAUG-GAAUGAAGGAGUAACG----------CCCCGAAACG-UUCCCACUG-AUACUC--CGA-CA-AGCAU-UAG----------UCAAAAG-----------------------------CUGGU---GUU-UG-AAGC-UCGGUG--A-AGUCGGCAGA-A-GAUUAC------------CGU------AA------UUUAUUCUUAUU---------A-G-------AGU--------------------------------------AA-A-------ACGA------AAU-UUG-UUCA-GAGG-UGA-AUGAUGUAA-UUGAUA---UGCCGGGUG-UCAAUUGU
BABD01022186.1/748-950       GAGAACUGAUAUUUCGAU-GGAUG-AAAUGAGGGGAGUACG----------CCCCGAAGCG-UCGGCACUG-AUACUC--CCA-CU-GGC-A-UAGG--CGC------GCACC--------------------------CGCCGAUG---GUC-AG-AAGC-UCGGUG--A-AGUCGGCAGA-A-AAAUUUCGUAGUUCUGGC-----------------------------CCG---CAAGGCAAA-GCCC------------------------------------------------------A------AAG-CUG-UCCA--AGG-GGG-ACCGGGCAU-CGGAAA---UCCCGGGUG-GCACCGCC
BAAX01005633.1/1175-1376     GAGAACUAAUAUUCCGAU-A-GUG-GAAUGAAGGGGUAACG----------CCCUGAAACG-CCUACCUUAUAAACUG--CGA-UA-UGCGG-CAGU--CCUC-UGUAACA-A--------------------------GGGCUACG---GUA-UA-ACGC-UCGC--UAA-AGUCGGCGGA-A-AUGUAC------------CCA------AA------C--------AGG---------U-U-------AUG--------------------------------------CC-G-------UGGA------AAG-CAU-CUCAAGCGG-UGG-GAUGUGUGC-AUGAUA---CGCCGGAGG-UCUAAAAA
BAAZ01000637.1/1268-1469     UAGAACUGAUAUUCCGAC-AGGUG-GAAUGAUGGGGUAACG----------CCCUGAAACG-CCUGCCCUA-AGACUG--CGC-CG-GGCAU-GGU---GCAAGCGCAAAGAC--------------------------GC-ACUGU---GUC-CGAGAGC-GCGCGG--A-AGUCGGCGGA-A-GUCUGC------------CCU------AA------C--------AGG---------U-C-------AAG--------------------------------------CC-G-------AGGA------AAG-CGC-CCC-AGCGG-UGG-GGUGUGCAG-AUGAUA---CGCCGGGGG-UCUAUAAA
BABA01014576.1/697-502       GCUAACUGAUAUUCCGAG-GAGUG-GAAUGAUGGGGUAACG----------CCCUGAAACG-CUCCCCUGG-AUACUA--CGA-CG-UGCA--AAGG--CGG--UGUAAA--A--------------------------CGCNGUAU---GUG-CG-AAGC-UCGUUG--A-AGUCGGCAGA-G-AGACAC------------CGA------AA------C--------A-----------U-U-------AAG--------------------------------------UU-G-------UCGA------AAG-CUG-UCCA-GAGG-UGG-AUGGUGUGU-CCUAUA---UGCCGGAGG-UCUAUAAA
BAAX01009471.1/988-790       UAGAACUGAUAUUCCGAG-CGGUG-GAAUGAUGGGGUAACG----------CCCUGAAACG-CCCCCUUUA-AAACUG--CGG-CA-GGCGA-UAAA--ACU--UGUGAC--A--------------------------GUUUUGUG---GUC-UG-AAGC-CCGCGG--A-AGUCGGCAGA-G-AGCCGC------------CCA------AA------C--------AGG---------U-C-------AAG--------------------------------------CU-G-------CGGA------AAG-CUG-UCCA-GAGG-UGG-ACGGUGCGG-CCUAUA---UGCCGGAGG-UCUAAAAU
ABDH01034038.1/443-643       GCGAACUGAUAACCCCAA-GAGUG-GAAUGAAGGGGUAACG----------CCCUGAAACG-CUCUCCCUG-AUACUC--CGA-CG-GGCGU-AUGUACAGG--------AAA--------------------------CUGGAUAU---GUC-UG-AAGC-UCGGUG--A-AGUCGGCUGA-G-AGCUGC------------CGU------AA----------------AGCAG---AGUAAU-------CUG--------------------------------------CU---------ACGA------AAG-CUA-UCCA-GAGG-UGG-AUGGUGCAA-CCUACA---GGCCGGGGG-UCUAUAAA
BABG01000124.1/1176-968      GAGAACUAACAAUCCAAG-AGGUG-GAAUGAUGGGAUAACG----------CCCUGAAACG-CCCCCUUAA--UACUC--CGA-CU-GGCGG-GU----GUAAGUGAA----A--------------------------ACUGACCU---GUC-AG-AAGC-UCGGUG--A-AGUCGGCUGA-G-AGUAGC------------CGU------AUGGAUUGC--------UGG---------A-U-------AAUUAC-------------------------------CAGCCC-C-------ACGA------AAG-CUG-UCCA-GAGG-UGG-ACGGUGCUA-CCUAUA---GGCCGGAGG-UCUACAAA
BAAZ01004027.1/874-1082      GAGAACUAACAAUCCAAG-AGGUG-GAAUGAUGGGGUAACG----------CCCUGAAACG-CCCCCUUAA--UACUC--CGA-CU-GGCGG-GU----GUAAGUGAA----A--------------------------ACUGACCU---GUC-AG-AAGC-UCGGUG--A-AGUCGGCUGA-G-AGUAGC------------CGU------AUGGAUUGC--------UGG---------A-U-------AAUUAC-------------------------------CAGCCC-C-------ACGA------AAG-CUG-UCCA-GAGG-UGG-ACGGUGCUA-CCUAUA---GGCCGGAGG-UCUACAAA
BABG01003233.1/2180-2367     GAGAACUAAACACACGAA-UAGUC-GAAUGACGGGGUAACG----------CCCUGAAAGG-CUA-CUUUAAUACUCC--CGA-CU-GGC-A-GAAA--CUUG-AGUAAACAA--------------------------AG-CUCU----GUC-AG-AAGC-UCGGUG--A-AGUCGGCAGA-C-UGACAC------------CGU------UA------C--------AGA---------U-A-------UUG--------------------------------------UU---------ACGA------AAG-AUC--CCA-GAGG-UGG--CGUUGUGU-UCUAAU---UUCCGGAAG---------
EU839837.1/395-596           GAGAACUCUUAACUUGAA-AAGUG-GAAUGAUAGGGUAACG----------CCUUGAAACG-CUUUCUCUA-AUACUC--CGA-CA-UGCAG-UAAC--U-A---UGUGUGAA---------------------------AGUUAUU---GUG-UG-AAGC-UCGGUG--A-AGUCGGCAGA-A-AAUUAC------------CGU------AA------U---------AGA------UA---AU---AUUAU--------------------------------------CU-A-------ACGA------AAG-UGU-UCUA-GAGG-UAG-AAUAUGUAG-UUGAUA---UGCCGGGAG-UCGUUAAA
ABDV01000020.1/17094-17300   GAGAACUCUUAACUUGAA-AAGUG-GAAUGAUAGGGUAACG----------CCUUGAAACG-CUUUCUCUA-AUACUC--CGA-CA-UGCAG-UAAC--UUU---GUGU--GA--------------------------AAGUUAUU---GUG-UG-AAGC-UCGGUG--A-AGUCGGCAGA-A-AAUUAC------------CGU------AG------C---------AGAU----AAU---AAAAUGUUAU--------------------------------------CU-A-------ACGA------AAG-UGU-UCUA-GAGG-UAG-AAUAUGUAG-UUGAUA---UGCCGGGAG-UCAUUAAA
ACNK01000130.1/2638-2441     GUGAACUAUCAUUCCGAG-AAGUC-AAACGAUAGGGUAACG----------CCUUGAAGGG-CUUCCUUUA-AUCCUU--CGA-CA-UGCAG-UGAA--GUU----AGCAAGA--------------------------ACCUUACU---GUA-UG-AAGC-UCGGUG--A-AGUCGGCUGA-G-AGUUAC------------CGU------AA------G---------UC---------U-U-------AGA--------------------------------------GA-C-------ACGA------AAG-CCG-UCCA-GAGG-UGG-ACGGUGUAA-CCUAUA---AGCCGGAAG-UCUAUAAA
ABYO01000253.1/71-272        GAGAACUAACAAUCUAAU-AGGUA-GAAUGAUGGAGUAACG----------CCCUAAAAUG-CCUACACUG-AUACUC--CGA-UU-GGCAA-UAAA-----UAUUAGACUAA----------------------------UUUAUU---GUC-AA-AAGC-UCGGUG--A-AGUCGGCAGA-G-AGUAGC------------CGU-----------------------AAAUAG---CUAU-A-------UAG--------------------------------------UUAU-------ACGA------AAC-CUG-UUUA-GAGG-UAA-AUGGUGCUA-CUUAUA---UGCCGGGUG-UCGAAUAC
ACMN01000047.1/56586-56787   GUGAACUCUUAACUCGAU-AGGUA-GAAUGAUAGGGUAACG----------CCUUGAAAUG-CCUACUCUA-AUACUC--CGA-CA-UGCGU-UAU---UCGAAUGUGUAUAA--------------------------GA-AUAGG---GUG-UG-AAGC-UCGGUG--A-AGUCGGCUGA-A-AGUUGU------------CGU------AG------U---------AC---------U-C-------AUG-------------------------------------AGUAA-------CCGA------AAG-CUA-ACCA-GAGG-UGG-UUGGUACAA-CUGAUA---GGUCGGGAG-UCGUGAAA
ABDX01000035.1/9072-9280     UAGAACUCUUAACUUGAA-AAGUG-GAAGGAUAGGGUAACG----------UCUUGAAACG-CUUUCUCUA-AUACUC--CGA-CA-UGCAG-UAAC----UUCUGUGUGAAA----------------------------GUUAUU---GUG-UG-AAGC-UCGGUG--A-AGUCGGCAGA-A-AAUUAC------------CGU------AG------C---------AG---------A-U-------AAUAAAAC---------------------------CCUUAUCU-A-------ACGA------AAG-UGU-UCUA-GAGG-UAG-AAUAUGUAG-UUGAUA---UGCCGGGAG-UCGUUAAA
ACMX01000209.1/9428-9631     GAGAACUACUAUUUCGAG-AAGUC-AAAUGAAAGGGUAACG----------CCUGGAAGGG-CUUCCUCUG-AUACUC--CGA-CA-UGCAU-GAUG--CAGUGGAUAAGAAC--------------------------UGUA-AGU---GUG-UG-AAGC-UCGGUA--A-AGUCGGCCGA-G-AGCUAC------------CGU------AA------A--------GUA---------UGG-------AAG--------------------------------------UA-C------UACGA------AAG-UUG-UCCA-GAGG-UGG-AUGAUGUAG-CCUAUA---GGCCGGGAG-UCUACAAA
ABCB02000015.1/25216-25412   GAGAACUGGUAAUUCGAU-GGGUG-AAAUGAAGAAGCAACG----------UUCGGAAGCG-CCCACCUUA-AUACUC--CGA-CU-GGCAG-UGUAAGCGG--------AAA--------------------------CGCUGACU---GUC-AG-AAGC-UCGGUG--A-AGUCGGCAGA-G-AGCAGC------------CGU------AU------U---------GC---------AGA-------AAU--------------------------------------GC-A-------GCGA------AAG-CGG-UUCA-GCGG-UGA-AUUGUGCUG-CCUAUA---UGCCGGAGG-UCUAUAAA
ACNG01000251.1/780-979       GAGAACUAAUAAUCCAAA-AAGUA-AAAUGAUAGGGUAACG----------CCUUGAAGGG-CUUUCUCUA-AUACUC--CGA-AU-AGCGU-UCUC----AUUGAUAAGAAU----------------------------GAGAGG---GUU-AU-AAGC-UCGGUG--A-AGUCGGCUGAGA-AUACAC------------CCU------AA------C---------AG---------GUC-------AAG--------------------------------------CU-G-------AGGA------AAGGCGA-ACCA-GAGG-UGG-U-CGAGUGU-AUGAUA---GGUCGGGAG-UCCAUAAA
ABHH01000027.1/15612-15815   GAGAACUGAUUAAUUGAA-AGCUG-GAAUGAGAGAGUAACG----------ACUUGAAACG-GCUUCCCUA-AUCCUC--CGA-UA-UGCGU-UUAA----AUAGGUGAAAAU----------------------------UUAAUC---GUA-UA-AAGC-UCGGUG--A-AGUCAGCUGA-A-AAAAGC------------CGU------AA------A--------UAA---------GAC-------AAG--------------------------------------UU--CU--UAUACGA------AAA-AGA-UCCA-GAGG-UGG-AUCUCGCUU-UUGAUA---GGCUGGGGG-UCUUAUAA
ABDW01000006.1/46534-46726   GAGAACUGAACACAAGAU-UAGUC-GAAUGAAGGGGUAACG----------CCCUGAAAGG-CUAUCCUAA--UACUC--CGA-CU-GGC----AUCAAUGUGAGCAAACACU--------------------------AAGGU------GUC-AG-ACGC-UCGGUG--A-AGUCGGCAGA-G-AGAUAC------------CGU------AA------C--------C-----------G-A-------UUG-----------------------------------------G-------UCGA------AAG-UCA-CUCA-GAGG-UGA-GUGAUGUAU-CCUAUA---UGCCGGGGU-CUAUAAA-
AF454824.1/13194-13409       GAGAACUCUUAUUUUGAG-AAUUG-GAAUGAUGGGGUAACG----------CCCUGAAACG-AUUCCCCUA--AUCUC--CGA-CA-UGCGU-UUAUCUCGU------GCAAA--------------------------AGAUAAAG---GUG-UG-AAGC-UCGGUA--A-AGUCGGCUGA-A-AGAUAC------------CGUACGGAAAU------CU------CUACG------UGA-AAUA-GAGAAG--------------------------------------GUAA-------ACGA------AAG-UGC-CUUA-GCGG-UAA-GGUAUGUAU-CUGAUA---GGUCGGGGG-UCGGAAAA
AM180355.1/596164-596370     GAGAACUGAUAAUUCGAA-AAGUC-GAAUGACGGAGUAACG----------CCCUGAAAGG-CUUUAGCUA-AAACUG--CGA-CA-GGCGA-UAAA--UUA---UUA--AGG--------------------------AUUUCAUG---GUC-UG-GAGC-UCGCAG--A-AGUCGACUGAGA-AGACGC------------CCU------AA------U---------CGUA-----UU---UUG-AGAAUA--------------------------------------CGAA-------AGGA------AAUGCGA-ACUA-GAGG-UAG-U-CGAGUGU-CCGAUA---GGUCGGGCU-UCCAUAAA
AB105543.1/53-264            AAUAACUUUACUAUCGAG-AAAUC-AAAUGACGGGGUAACG----------CCCUGAAGGG-UUUCCACUG-AUACUG--CGA-CA-UGC-G-UUAG--UAG---GAUGUGCA--------------------------UCCAAACG--CGUA-UG-AAGC-UCGCUG--A-AGUCGGCAGA-A-GGGUAC------------CGU------AA------G----------G--------A--A-------AGACACGAUA-----------------------CGUAUCUAC--C-------ACGC------AAG-UGC-UCUA-GAGG-UAG-GGUAUGUAC-CUGAUA---UGUCGGGUG-UCCUAAAA
CP000673.1/559567-559765     GAGAACUGAUAGUUUGAA-AAGUC-AAAUGAUGAGGUAACG----------CUUUGAAGGG-CUUUCUCUA--AUCUA--CGA-CU-GGCAU-UUAA--UGA------AUAAG--------------------------CAUUGAAG--UGUC-AGAUAGC-UCGUUG--A-AGUCGGCUGAGA-GUACAC------------CCU------AA------C---------GG---------AUU-------AUG--------------------------------------CU-G-------AGGA------AAUGUGA-ACCA-GAGG-UGG-U-CAAGUGU-AUGAUA---GGUCGGGAG-UCUAUAAA
ACNE01000126.1/69537-69738   UAGAACUAAUGAUUCGAG-AGACA-GAAUGAUAGAGUAACG----------UCUUGAAAUG-UUUCCCCUA-AGUCUC--CGA-CA-UGCAU-UAAA--UGG------UAGGA--------------------------CGUUUAAA--UGUG-UG-AAGC-UCGGUG--A-AGACGGCUAA-C-AGAUAC------------CGUAGUAAAAA------A---------UA-----------U-------AUU-------------------------------------UUA-A-------CCGA------AAA-UCC-UUUU--AGU-AAA-AGGAUGUAU-CCCAUA---GGCCGGGGG-UCCGUAAA
AAXG02000030.1/2195-2388     GAUAACUGGUAAUUCGAC-AGGUG-GAAUGACGGGGUAACG----------CCCUGAAACG-CCUGCCCUC----GGU--GGG-CG-UGCAU-CGGC----U------GCAAA----------------------------GCCGGU---GUA-CG-AAGC-CCCACGACA-AC--GGCUGA-G-AGCAAC------------CGU------AG------C--------CGC---------CGCC-----AACG--------------------------------------GCAG-------CCGA------AAG-CGG-UCUG-GAGG-CAG-ACUGUGUUG-CCUAUA---GGCCAAGGG-UCUACAAA
ACMS01000358.1/3194-3405     UAGAACUCUUAACUUGAG-AAGUG-GAAUGAUAGAGUAACG----------UCUUGAAACG-CUUCCCCUA-AUACUC--CGA-CA-UGCGC-CUUC--UAGUUUUGCGACAU--------------------------AAGAAGGG---GUC-UG-AAGC-UCGGUG--A-AGUCAUCUGAAA-AAUUAC------------CGA------AG------U---------ACCUA---UUU---U----AACAG--------------------------------------GCAA-------CCGA------AAA-GGAUCUCA-GAGG-UGA-GUCCCGUAG-UUGAUA---GGGUGGGGG-UCACAAAA
ABAX03000014.1/245028-244831 GAGAACUGCAUAACUGAA-AUCUC-AAAUGAUGGGGUAACG----------CCCGGAAGGG-GAUUCACUG-AUACUC--CGA-GU-AGCGU-CAGC--CAG-----AUACAG--------------------------UGGCUGGG---GUU-AU-AAGC-GCGGGA--A-AGUCGUGCGA-A-GCACAC------------CCU------AA------C---------GC---------UGA-------AAG--------------------------------------GC-G-------AGGA------AAG-AUU-CAUA-GAGG-UAU-GAGUUGUGU-GUGACA---GUGCGGGUG-GGGCUGCC
ACMW01000132.1/1514-1318     CGGAAGGAUUAUAUCGAA-GAGUC-GAAUGAUAGGGUAACG----------CCUUGAAAGG-CUCUCUCUG----CGU--CGA-AU-AGCAC-GACA--UUG----AGUAAGA--------------------------AGUUUCGU---GUU-AU-AAGC-UCGGCA--A-AUAGGCGUGAGA-AUUUAC------------CGU------AA------C---------AG---------UAU-------CGG--------------------------------------CU-G-------ACGA------AAA-CCUUACCC-GAGG-GGG-C-GGUGUAA-AUUAUG---AUGCUUGAG-UUGAACAA
ACMT01000363.1/23380-23574   UACAACUGAUAUACCGAU-GUCAG-GAAUGAAAGC----CGUCAU--GUUGAGCUGAAACU-GACAGUCUA-AUACUC--CUG-CA-UGCA------UUUAUCUUGAUAGAGAUA---------------------CAUUGCGUUAU---GUA-UG-AAAC-UAGGUG--A-AGUCGGCUGA-A-UCUAAU-----------------------------U--------C-----------U-A-------AAG-----------------------------------------C------C---A--------CUCUU-ACAGAGAGG---G-UAUG-GUUA-GAGAUA---GGCCGGGAC-GCUAUAAA
BABF01000534.1/4297-4494     GAGAACUGCAUAACUGAA-AUCUC-AAAUGAUGGGGUAACG----------CCCGGAAGGG-GAUUCACUG-AUACUC--CGA-GU-AGCGU-CAGC--CAG----AUACAG---------------------------UGGCUGGG---GUU-AU-AAGC-GCGGGA--A-AGUCGUGCGA-A-GCACAC------------CCU------AA------C---------GC---------UGA-------AAG--------------------------------------GC-G-------AGGA------AAG-AUU-CAUA-GAGG-UAU-GAGUUGUGU-GUGACA---GUGCGGGUG-GGGCUGCC
AATB01005478.1/536-741       GAGAACUGACAAUCCGAU-GGGUG-GAAUGACAGGAUAACG----------CCUUGAAACG-CUCACACUG-AUACUC--CGA-UU-GACG--------GCGA-UAUGCGACU--------------------------GCCUAACC---GUC-AA-AAGC-UCGGUG--A-AGUCGGCAGA-G-AGUGAC------------CGU------AA------G--------CGGG-------AU-U-------UUUUU---------------------------------UUACC-G------CACGA------AAC-CUG-UCCA-GAGG-UGGGAUGGCGUCA-CCUAUA---UGCCGGGUG-UCGGAUAC
AE016830.1/1836423-1836242   GACAACUAAUGUUUUGAG-AGAUG-GAAUGAAAG--CCUUCAAGU--UGAG--CUGAAACA-UCUCCGCUA-AUACUC--CUA-CA-UGC-U-CUAA--UCAA-UGAAGUA----------------------------GAUUGGUUUUGGUA-UG-AAGC-UAGGUG--A-AGUCGUCUGA-A-AUCUGC-----------------------------------------CUA---AGUGUUUGA-GCAUAA-------------------------------------G------------------------------------------------GCUG-ACUAUA---GGGCGGGCG-GCUGAAAA
CP000227.1/3416755-3416570   GAUAACUGUUCAGGCGAGUGAGAG-GAAUGAAGGAGUAACG----------CCCCGAAACU-CUCCCAGUG-AGAUUC--CCA-AC-UGCAU-ACAC--UCG--------GCA--------------------------GAGUGAGA--UGUU-GG-AAGC-AGGGUAAAACAUGCGGUUAC-G-GUU---------------CGU------AG------U---------GUC-------UAUA-------UGG--------------------------------------AUAA-------CCGA------AAG-CCA-G-------------CAGGA-----AUAAUA---AACCGGCUG-GAACUAAC
ACMI01001147.1/2532-2354     AACAACUGAUUGACUGAA-AGUAG-GAAUGAAAGC----CGUCAG--GUUGAGCUGAAACU-AGUUAUCUA-AUACUC--CUA-CA-UGCAA-GGCG--UGA----UAGUAGU--------------------------CACAAAUU---GUA-UG-AAGC-UAGGUG--A-AGUCGACUGA-A-CA-------------------------AA----------------AC---------C---------UAA--------------------------------------GU-G----------A---------GAAA-UCAU------AUG-AUUU------UGGAUA---GGUCGGGAU-GCUACAAA
AE017195.1/35525-35314       UAGAACUCUUAACUUGAG-AAGUG-GAAUGAUAGAGUAACG----------UCUUGAAACG-CUUCCCCUA-AUACUC--CGA-CA-UGCGC-CUUC--UAGUUUUGCGACAU--------------------------AAGAAGGG---GUC-UG-AAGC-UCGGUG--A-AGUCAUCUGAAA-AAUUAC------------CGA------AG------U--------ACC---------U-AUUU-UAACAG--------------------------------------GCAA-------CCGA------AAAGGAU-CUCA-GAGG-UGA-GUCCCGUAG-UUGAUA---GGGUGGGGG-UCACAAAA
ACMV01000321.1/12297-12493   CGGAAGGAUUAUAUCGAA-GAGUC-GAAUGAUAGGGUAACG----------CCUUGAAAGG-CUCUCUCUG------CGUCGA-AU-AGCAC-GACA----UUGAGUAAGAAG----------------------------UUUCGU---GUU-AU-AAGC-UCGGCA--A-AUAGGCGUGAGA-AUUUAC------------CGU------AA------C---------AG---------UAU-------CGG--------------------------------------CU-G-------ACGA------AAACCUU-ACCC-GAGG-GGG-C-GGUGUAA-AUUAUG---AUGCUUGAG-UUGAACAA
AAXG02000049.1/4632-4432     GAGAACUGACAAUCCGAU-GGGUG-GAAUGAAGGGGCAACG----------UCCGGAAACG-CCCACACUG-AUACUC--CGA-UU-GGCUU-UGAA----GUGUGCAACUAC----------------------------UUCAUG---GUC-AA-AAGC-UCGGUG--A-AGUCGGCAGA-G-AGUGGC------------CGU------AA------G--------CGG---------AGC-------AAU--------------------------------------CC-G------CACGA------AAC-CUG-CCCA-GAGG-UGG-GCGGCGUCA-CCUAUA---UGCCGGGUG-UCAGAUAC
BABA01022420.1/262-49        UACAACUGAUACUGCGAC-AGGUG-GAAUGAGGGAGUAACG----------CCCUGAAACG-CCUGACCUGAAAACUA--CGG-CU-GGCGU-UGGC--UGG--------AAA--------------------------CGGCCAGG---GUC-AG-AAGC-CCGUUA--A-AGACGGCUGA-CUGCGUUCGCUCUGUGCGCGGUA------AA------C--------A--------------------AUGGAAACAG--------------------------CGGCAG---G-------UGCA------UAG-CAA-GCCA-GAGG-UGG-C-UGUGAGC-GUUA-----GGCCNGGGGGUCUAUAAA
ACNF01000150.1/51-254        CAGAACUAUUAUUUCGAG-AAGUC-AAAUGAUAGGGUAACG----------CCUUGAAGGG-CUUCCUCUG-AUACUC--CGA-CA-UGCAG-CAUA--CAAA-AGAUAAGCC--------------------------UGUA-GUU---GUG-UG-AAGC-UCGGUG--A-AGUCGGCUGA-G-AGCUAC------------CGU------UA------A--------AGU---------AUC-------UCG--------------------------------------AUAC------UACGA------AAA-CUG-UCCA-GCGG-UGG-AUGGUGUAG-CCUAUA---GGCCGGGAG-UCUAAAAA
AAXA02000016.1/106752-106558 GAGAACUGGUAGUUUGAU-AGGUG-GAAUGACGGGGUAACG----------CCCUGAAACG-CCUACCCUU----GAU--GGG-CG-UGCAU-UAGC--UGU---------AA--------------------------UGGCUGGU---GUA-CG-AAGC-CCCAUGACA-AA--GGCUGA-G-AGUAAC------------CGU------AA------C---------CACUG---CCUA---------AAG--------------------------------------UG-G-------UCGA------AAG-CGG-UCUG-GAGG-CAG-ACUGUGUUA-CCUAUA---AGCCGAGAG-UCUAUAAG
AAVL02000027.1/57523-57719   GAGAACUAAACACACGAU-AUGUC-GAAUGAUGGAGUAACG----------UCCUGAAAGG-CA-ACCCUA-AUCCUC--CGA-CU-UGCAC-CUAA----GUUAGUAGAAAC----------------------------UAAAGU---GUA-AG-AAGC-UCGGUG--A-AGUCGGCAGA-G-AGAUAC------------CGA------AA------C---------AG---------A-U-------UAG--------------------------------------AU-G-------UCGA------AAG-CAU-UUCA-GAGG-UGA-GAUGUGUAU-CCUAUA---UGCCGGGGG-UCUAUAAA
BA000036.3/1890017-1889808   AGAAACUGUUUCAUUGAU-ACACA-GAAUGACGGAGUAACG----------CCCUGAAAUG-UGCACACCA--AGCUA--CGG-UA-UGCGG-UUUG----------AACAAA--------------------------AUAGAACU---GUA-UA-AAGC-CCGUUA--G-AGUCGGCAGAAG-GUCGGU------------CGU------AAAGGUGCU---------GGGA-----UUUGAUCA-CAGUAG--------------------------------------CU---------ACGA------AAG-CGU-CAGA-GUGA-UCU-GAUGUGCCG-CUGAUA---UGCCGGGUG-UCCAGAAA
CP000228.1/137163-136978     GAUAACUGUUCAGGCGAGUGAGAG-GAAUGAAGGAGUAACG----------CCCCGAAACU-CUCCCAGUG-AGAUUC--CCA-AC-UGCAU-ACAC--UCG--------GCA--------------------------GAGUGAGA--UGUU-GG-AAGC-AGGGUA--A-AA---------C-AU----GCGAUUACGGUUCGU------AG------U---------GUC-------UAUA-------UGG--------------------------------------AUAA-------CCGA------AAG-CCA-G-------------CAGGA-----AUAAUAAACCGGCUGGAA-CUAAC---
BAAU01004979.1/1791-1602     --------CAUAACUGAA-AUCUC-AAAUGACGGGGUAGCG----------UUAUGAAGGG-GAU-CACUA-AUACUC--CGA-AU-AGCGU-CAGC--CGA----AUACAGA--------------------------CGGUUGGG---GUU-AU-AAGC-UCGGUG--A-AGUCGUGCGA-A-GCACAC------------CCU------AA------C---------GC---------UUA-------AUG--------------------------------------GC-G-------AGGA------AAG-AUU-CGUA-GAGG-UAC-GGGUUGUGU-GUGACA---GUGCGGGUG-GGGUUGCC
AAVL02000036.1/304995-304799 GAGAACUAAACACACGAU-AUGUC-GAAUGAUGGAGUAACG----------UUCUGAAAGG-CA-ACCCUA-AUCCUC--CGA-CU-UGCAC-CUAA----GUUAGUAGAAAC----------------------------UAAAGU---GUA-AG-AAGC-UCGGUG--A-AGUCGGCAGA-G-AGAUAC------------CGA------AA------C---------AG---------A-U-------UAG--------------------------------------AU-G-------UCGA------AAG-CAU-UUCA-GAGG-UGA-GAUGUGUAU-CCUAUA---UGCCGGGGG-UCUAUAAA
CP001407.1/3678247-3678050   UAGAACUGCUAUUCUGAA-GUAUG-GAAAGAUGGAGUAACG----------UCCUGAAACA-UACUCACUG-AAGCUA--CGG-CA-AGCGA-UAGC--GAUAAUGCAAAC-A--------------------------UCAACAUC---GUU-UG-AAGC-CCGUUA--A-AGUAGGCUGA-A-GUUCAC------------CCU------AA------C---------GU---------A---------AAG--------------------------------------AC-G-------AGGA------AAG-GGA-GGUA-UAAA-U---CUUCUGUGA-AUGAUA---GGUCUGGUG-UCUAUAAA
ABDV01000012.1/19004-19211   UAGAACUGUUAUUGCGAA-AGGUA-GAAUGAUAGGGUAACG----------CCUUGAAAUG-CCUUCCUUG-AUACUC--CGA-AU-AGCGU-UU----UGUUGAGUAAACAA--------------------------CA--AAGG---GUU-AU-AAGC-UCGGUG--A-AGUCGGUUGAGA-GUACAC------------CGU------AA------G--------GUA---------UGUAGA-AAUACA--------------------------------------UACC-------ACGA------AAUGCGA-ACCA-GAGG-UGG-U-CGAGUGU-AUGAUA---GGCCGGAGG-UCUAUAAA
ABDU01000049.2/14192-14000   GAGAACUAAUACUCCGAG-CAAUU-AAAUGAGGAAGUAACG----------CUCCGAAGAA-UUGCCAUUA-AUACUA--CGA-UA-UGCAA-UGGAUUAAGUUAUUAUGAAG--------------------------UU---------GUG-UA-AAGC-UCGUUG--A-AGUCGGCAGAAA-AAUUAC------------CCU------AA------C---------GA---------GUU-------AAG--------------------------------------UC-G-------AGGA------AAG-GUU-----UGAUU------AGCCGUAA-UUGAUA---UGCCGGAUG-UCUAUGAA
AE016830.1/2252414-2252203   GAGAACUGAUAUUCCGAU-GGGUG-AAAUGAGGGGGUAACG----------UCCCGAAGCG-CCACCCUAAUACUCCG--AAU-------GG-CGGG--GAGCAUGCAACGGC--------------------------UCUCUCCAAAAGUU-UA-UAGA-GCUCGGUGA-AGUCGGCAGA-G-AGCAAC------------CGU-----AAG------A--------CUG---------G-U-------UUU--------------------------------------CA-GACCAGACACGA------AAG-CUG-UCCA-GAGG-UGG-AUGGUGUUG-CCUAUA---UGCCGGGGG-UCGGAUAU
CP001081.1/247764-247557     GAGAACUAAUAUUCCAAG-AUGUC-GAAUGAAAGGGUAACG----------CCUUGAAAGG-CA-CUACUA-AUACUC--CGA-UA-UGUGU-CAUG-----UAUAUAAGAAA----------------------------CAUGAG---AUA-UA-AAGC-UCGGUG--A-AGACAGUUGAGA-GUACAC------------CGU------AA------G--------UAGA------UGA-AAAA-CCAUUC--------------------------------------CUAC-------CCGA------AAUGCGA-ACCA-GAGG-UGG-U-CGAGUGU-AUGAUA---GACUGGGUA-UCUAUAAA
ABQR01000051.1/148965-149160 GCUAACUGAUAUUCCGAG-GAGUG-GAACGAUGGGGUAACG----------CCCUGAAACG-CUCCCCUUG-AUACUA--CGA-CG-UGCAA-AGGC--GGU------GUAAA--------------------------ACGCU--GUAUGUG-CG-AAGC-UCGUUG--A-AGUCGGCAGA-G-AGACAC------------CGA------AA------C--------A-----------U-U-------AAG--------------------------------------UU-G-------UCGA------AAG-CUG-UCCA-GAGG-UGG-AUGGUGUGU-CCUAUA---UGCCGGAGG-UCUAUAAA
AF333235.1/10781-10987       GAGAACUGAUAAUUCGAA-AAGUC-GAAUGACGGAGUAACG----------CCCUGAAAGG-CUUUAGCUA-AAACUG--CGA-CA-GGCGA-UAAA-----UUAUUAAGGAU----------------------------UUCAUG---GUC-UG-GAGC-UCGCAG--A-AGUCGACUGAGA-AGACGC------------CCU------AA------U--------CGU---------A-UUUU-GAGAAU--------------------------------------AC-GA-----AAGGA------AAUGCGA-ACUA-GAGG-UAG--UCGAGUGU-CCGAUA---GGUCGGGCU-UCCAUAAA
CP000040.1/462079-462257     AACAACGGAUUGACCGAA-AGUAG-GAAUGAAAGC-CGUCAAG-----UUGAGCUGAAACU-ACUUAUCUG-AUACUC--CUA-CA-UGCAA-GGCGUGAUAGUAGUUACAAA--------------------------UU---------GUA-UG-AAGC-UAGGUG--A-AGUCGGCUGA-A-CA---------------------------------------------AAG---CCUAAGUGA-GUAAUCAUAU-----------------------------GGUAA-----------------------------------------------------UGGAUA---GGUCGGGAU-GCUACAAA
ACNF01000063.1/9596-9418     AACAACUGAUUGACUGAA-AGUAG-GAAUGAAAGC----CGUCAG--GUUGAGCUGAAACU-ACUUAUCUG-AUACUC--CUA-CA-UGCAA-AGCGUGAUAGUAGUCACAAA--------------------------UU---------GUA-UG-AAGC-UAGGUG--A-AGUCGACUGA-A-CA-------------------------AA------A--------CCU---------A-A-------GUG--------------------------------------AG------------A------AAU-------CAUAUGG-UA------A-----UGGAUA---GGUCGGGAU-GCUACAAA
CP000817.1/3910429-3910247   CACAACUGAUUAACCAAA-AUUCG-GAAUGAAAGC-CGUCAUG-----UUGAGCUGAAACG-AAUUAUCUG-AUACUC--CUA-CA-UGCAU-GAAA--UGG----UAAUAGA--------------------------CAAGACAU---GUA-UG-AAGC-UAGGUG--A-AGUCGGCUGA-A-AAGUAC-----------------------------------------CUA---AGUCGCUAA-GAAAGGAU---------------------------------AUG------------------------------------------------GUUC-UCGAUA---GGUCGGGAU-GCUACAAA
ACNJ01000249.1/7764-7942     AACAACUGAUUGACUGAA-AGUAG-UAAUGAAAGC----CGGCAG--GUUGAGCUGAAACU-ACUUAUCUA-AUACUC--CUA-CA-UGCAA-GGCG--UGA----UAGUAGU--------------------------UACAAAUU---GUA-UG-AAGC-UAGGUG--A-AGUCGACUGA-A-CA-------------------------AA------A--------CCU---------A-A-------GUG--------------------------------------AG------------A------AAU-------CAUAUGG-UA------A-----UGGAUA---GGUCGGGGU-GCUACAAA
AATE01006454.1/546-754       UCUAACUGAUACUCCAAG-GAGUG-GAAUGAACGGGUAACG----------CCCUGAAACG-CUCCCCCUG-AUACUG--CUU------------------UUGGAGGAAACGGGGGCGCAAUCCCCUGCAACUGACAC-------------------AGC-ACGCUG--A-AGGCGGCUGG-ACUAACCC------------GCC------UU------U---------ACU------CGA-UGUA-AAGACG--------------------------------------GUAG-------GGCC------AAC-ACG-ACCC-GAAG-UGG-CCGUGGG----CGAUA---GGCCGGGGG-UUCUAACC
ACNI01000128.1/28382-28562   AACAACUGUUUGACUGAA-GGUAG-GAAUGGAAAC--ACCGCCAG--GUUGAGCUUAAACU-ACUUAUCUA-AUACUC--CUA-CA-UGCAA-GGCA--UGA----UAAUAGU--------------------------CACAAAUU---GUA-UG-AAGC-UAGGUG--A-AGUUAGCUGA-A-CA-------------------------AA------A--------CCU---------A-A-------GUG--------------------------------------AG------------A------AAU-------CAUAUGG-UA------A-----UGGAUA---GGUCGGGAU-GCUACAAA
ACNJ01000243.1/54084-54262   AACAGCUGUUUGACUGAA-AGUAG-GAAUGAAAGC----CGUCAG--GUUGAGCUGAAACU-ACUUGUCGG-AUACUC--CUA-CA-UGCAA-GGCG--UGA----UAGUAGU--------------------------CACAAAUU---GUA-UG-AAGC-UAGGUA--A-AGUCAGCUGA-A-CA-------------------------AA------A--------CCU---------A-A-------GUG--------------------------------------AG------------A------AAG-C----GUA------UA-----GUAA---UAGAUA---GGUCGGGAU-GCUACAAA
DQ889679.1/179031-179240     GAUAACUAUUCAGACGAG-AUAAG-GAAUGAUGGAGUAACG----------CCCUGAAACU-UAUCCAGUG-AGAUUU--CCA-CC-CGCAU-UAUA--CAG--------GCA--------------------------UGUAUAGA--UGUG-GA-AAGC-CGGAUA--A-AAUAUGCAAU-C-ACGAAC------------CG-------AA------G--------UGUCCG---AUAAGG-------AUA--------------------------------------AC-CGAAAGCC-CAAGGGAAUAAU-AAA-CCCG------UGG-GAAUUGUUC-AAGUAU---UGUAUGCUG-UCAACCGA
AAQL01006282.1/686-496       ----------------------UG-AAAUGAGGGGGUAACG----------UCCCGAAGCGC-C-ACCCUA-AUACUC--CGA-AU-GGC-G-GGGA--GCA--UGCAACGGC--------------------------UCUCUCCAAAAGUUUAUAGAGC-UCGGUG--A-AGUCGGCAGA-G-AGCAAC------------CGU------AA------G--------A--CUG---GUUUUC-------AGA-----------------------------------------CCA--GACACGA------AAG-CUG-UCCA-GAGG-UGG-AUGGUGUUG-CCUAUA---UGCCGGGGG-UCGGAUAU
BABA01029745.1/187-395       GAGAACUAACAAUCCAAG-AGGUG-GAAUGAUGGGGUAACG----------CCCUGAAACG-CC-CCCUUA-AUACUC--CGA-CU-GGCGG-GU------GUAAGUGAAAAC----------------------------UGACCU---GUC-AG-AAGC-UCGGUG--A-AGUCGGCUGA-G-AGUAGC------------CGU------AUGGAUUGC--------UGG---------A-UAAU-UACCAG--------------------------------------CC-C------CACGA------AAG-CUG-UCCA-GAGG-UGG-ACGGUGCUA-CCUAUA---GGCCGGAGG-UCUACAAA
ACMX01000066.1/11688-11492   CGGAAGGAUUAUAUCGAA-GAGUC-AAAUGAUAGGAUAACG----------CCUUGAAAGG-CUCUCUCUG------CGUCGA-AU-AGCAC-GACA----UUGAGUAAGAAG----------------------------UUUCGU---GUU-AU-AAGC-UCGGCA--A-AUAGGCGUGAGA-AUUUAC------------CGU------AA------C---------AG---------UAU-------CGG--------------------------------------CU-G-------ACGA------AAACCUU-ACCC-GAGG-GGG-C-GGUGUAA-AUUAUG---AUGCUUGAG-UUGAACAA
ACLT01000067.1/45633-45455   AAUAACUGAUUGACUGAA-AGUAG-GAAUUAAAGC----CGUCAA--GUUGAGCUGAAACU-ACUUAUCUG-AUACUC--CUA-CA-UGCAA-AGCGUGAUAGUAGUCGCAAA--------------------------UU---------GUA-UG-AAGC-UAGGUG--A-AGUCGGCUGA-A-CA-------------------------AA------A--------CCU---------A-A-------GUG--------------------------------------AG------------A------AAU-------CAUAUGG-UA------A-----UGGAUA---GGUCGGGAU-GCUACAAA
BABB01015796.1/486-681       GCUAACUGAUAUUCCGAG-GAGUG-GAAUGAUGGGGUAACG----------CCCUGAAACG-CUCCCCUUG-AUACUA--CGA-CG-UGCAA-AGGC--GGU------GUAAA--------------------------ACGCU--GUAUGUG-CG-AAGC-UCGUUG--A-AGUCGGCAGA-G-AGACAC------------CGA------AA------C---------AU---------U---------AAG--------------------------------------UU-G-------UCGA------AAG-CUG-UCCA-GAGG-UGG-AUGGUGUGU-CCUAUA---UGCCGGAGG-UCUAUAAA
BAAZ01010521.1/518-340       ----------------------UG-GAAUGAUAGGGGAACG----------CCUUGAAACGC--CUGCCUA-AAACUG--CGA-AU-GGCAU-GAUU----GUGAUUAAGCAC----------------------------AAGAUU---GUC-AUAAAGC-UCGCUG--A-AGUCGCCUGU-A-UGCACU------------UGC------UA------A--------GGU---------C-AA-----AAAGG-----------------------------------AUAC-A-------GCAA------AAC-CAA-GCCA-GAGG-UGG-CUGGGAGUG----AUA---GGGCGG-GG-UCUAUAAA
AAXG02000054.1/5652-5846     GAGAACUGAUAGUUCGAU-AGGUG-GAAUGACGGGGUAACG----------CCCUGAAACG-CCUACCCUU----GAU--GGG-CG-CGCAU-UAGC--UGU---------AA--------------------------UGGCUUUU---GUA-CG-AAGC-CCCAUGACA-AA--GGCUGA-G-AGUAAC------------CGU------AA------C---------CACUG---CCAA---------AAG--------------------------------------UG-G-------UCGA------AAG-CGG-UCUG-GCGG-CAG-ACUGUGUUA-CCUAUA---GGCCGAGGG-UCUAUAAG
ABWO01000042.1/58561-58772   GAGAACUGAUAUUCCGAU-UGGUG-AAAUGAGGGGGUAACG----------UCCCGAAGCA-CCA-CCCUA-AUACUC--CGA-AU-GGC-G-GGGA--GCA--UGCAACGGC--------------------------UCUCUCCAAAAGUUUAUAGAGC-UCGGUG--A-AGUCGGCAGA-G-AGCAAC------------CGU------AA------G--------ACU---------GGUUUU-CAGACC--------------------------------------AGAC-------ACGA------AAG-CUG-UCCA-GAGG-UGG-AUGGUGUUG-CCUAUA---UGCCGGGGG-UCGGAUAU
AAVL02000010.1/1228-1032     GAGAACUAAACACACGAU-AUGUC-GAAUGAUGGAGUAACG----------UUCUGAAAGG-CA-ACCCUA-AUCCUC--CGA-CU-UGCAC-CUAA----GUUAGUAGAAAC----------------------------UAAAGU---GUA-AG-AAGC-UCGGUG--A-AGUCGGCAGA-G-AGAUAC------------CGA------AA------C---------AG---------A-U-------UAG--------------------------------------AU-G-------UCGA------AAG-CAU-UUCA-GAGG-UGA-GAUGUGUAU-CCUAUA---UGCCGGGGG-UCUAUAAA
ACMF01000176.1/9325-9140     CACAACUAAUUAUUCGAA-AAGUG-GAAUGAAAGC----CGUCAU--GUUGAGCUGAAACA-CUUUCCCUA-AUACUC--CUA-CG-UGCGU-CAAA--CUG----UGAUAGC--------------------------GGUGAGAG---GUA-CG-AAGC-UAGGUG--A-AGUCGCCUGA-A-UUUAAU-----------------------------C--------UGG---------A-G------------------------------------------------CC------------A----------CUU-AAUGAGAAGG----UAUG-AUUA-AAGAUA---UGGCGGGGG-GCUAUAAG
ABDM02000005.1/295898-295701 UAGAACUGCUAUUCUGAA-GUGUG-GAAAGAUGGAGUAACG----------UCCUGAAACA-UACUCACUG-AAGCUA--CGG-CA-AGCGA-UAGC--GAUAAUGCAAAC-A--------------------------UCAACAUC---GUU-UG-AAGC-CCGUUA--A-AGUAGGCUGA-A-GUUCAC------------CCU------AA------C---------GU---------A---------AAG--------------------------------------AC-G-------AGGA------AAG-GGA-GGUA-UAAA-U---CUUCUGUGA-AUGAUA---GGUCUGGUG-UCUAUAAA
ACNC01000606.1/3569-3373     GAGAACUAUUAUUCCGAU-GAAUC-AAAUGAUAGGGUAACG----------CCUUAAAGGG-UUCACUCGA----UAC--CGA-AC-UGCGU-GGGA----AUAUGUAAGAGU----------------------------CGAAGC---GUA-GU-AAGC-UCGGUGUAA-AA--GUGGGAGA-GCUUAU------------CGU------AA------C---------AG---------AAG-------AAG--------------------------------------CU-G-------ACGA------AAG-ACU-UUCA-GAGG-UGA-AAGUUGUAG-GUCAUA---CCACAAGAG-UCGAGCGG
BABF01001649.1/550-753       GCAAACUAACAAUUCGAU-UGGUG-GAAUGAUGGGGUAACG----------CCCAGAAACG-CCAACCUUG-AUACUC--CGA-CU-GGC-U-CUGC----U-----CAAAAG----------------------------GCAGAU---GUUCAG-AAGC-UCGGUG--A-AGUCGGCAGA-G-AGUUAC------------CGU--------------C--------UUACAG---UUGUGAAAA-CAACUG--------------------------------------UA---------ACGA------AAG-CUA-UCCA-GAGG-UGG-AUGGUGUAG-CCUAUA---UGCCGGAGG-UCUACAAA
AATC01005780.1/717-566       UCUAACUGAUAUUCCGAG-AAGUG-GAAUGACGGGGUAACG----------CCCUGAAACG-CUUCCCUUG-AUACUG--CGU-UG--G-AA-GAAA--CAGGACGUAUUUCC--------------------------CGCGACUG-----A-CA-CAGC-ACGCUG--A-AGUCGGCUGU-C-UG---------------------------------C---------ACC------CGC-A-------ACU--------------------------------------GU-C-----------------------------------------------------UC---CUUUGGGGA-U------A
AATF01000088.1/656-453       UCUAACUGAUAUUCCGAG-AAGUG-GAAUGACGGGGUAACG----------CCCUGAAACG-CUUCCCUUG-AUACUG--CGU-UG--G-AA-GAAA--CAGGACGUAUUUCC--------------------------CGCGACUG-----A-CA-CAGC-ACGCUG--A-AGUCGGCUGU-CUGCACCC-------------GC------AA------C--------UGUCUC---CUUU-G-------GGG--------------------------------------AUAA------AGCAA------AAC-CGA-GCCA-GAGG-UGG-C-CGGGGGU-GUUA-----GGCCGGAGG-UCUAUAAA
ACIO01000228.1/1963-1764     GAGAACUGAUAAUCCGAU-AGGUG-GAAUGAUAGGGGAACG----------CCUUGAAACG-CCUGCCUAA--AACUG--CGA-AU-GGC-A-UGAU--UGUGAUUAAGCACA--------------------------AGAUU------GUC-AUAAAGC-UCGCUG--A-AGUCGCCUGU-A-UGCACU------------UGC------UA------A--------GGUC-------AA-A-------AAGG-----------------------------------AUAC-A-------GCAA------AAC-CAA-GCCA-GAGG-UGG-CUGGGAGUG----AUA---GGGCGGGGU-CUAUAAA-
ACMH01000138.1/9232-9441     GAUAACUGUUCAGAUAAGUGGUAG-GAAUGAAGGAGUAACG----------CCCCGAAACU-ACCCCAGUG-AGAUUC--CCA-AC-UGCAU-ACAC--UAG--------GCA--------------------------UAGCGUGA--UGUG-GA-GAGC-AGGGUA--A-AAUAUACGGU-CACGGU-------------------------------U--------CGU---------AGUGCA-CAACUGUAUAACCGAAAGCCAACAGGAGUAAUAAACCGGUUGGAACUA-----------A---CCAAG-----------------------U--AC----------CGUAUGCUG-UCAACCGA
CP001177.1/1742092-1741895   GUGAACUGUCAUUCCAAG-AAGUC-AAAUGAUAGGGUAACG----------CCUUGAAGGG-CUUCCUUUA-AUACUC--CGA-CA-UGCAG-UGAA----GUUAGCAAGAAC----------------------------UGAACU---GUA-UG-AAGC-UCGGUG--A-AGUCGGUUGA-G-AGUUAC------------CGU------AA----------------UC---------CUA-------UAG--------------------------------------GA-U-------ACGA------AAG-UCA-CUCA-GAGG-UGG-GUGGUGUAA-CCUAUA---AACCGGAAG-UCUAUAAA
BAAZ01001530.1/969-1172      GCAAACUAACAAUUCGAU-UGGUG-GAAUGAUGGGGUAACG----------CCCAGAAACG-CCAACCUUG-AUACUC--CGA-CU-GGC-U-CUGC----U-----CAAAAG----------------------------GCAGAU---GUUCAG-AAGC-UCGGUG--A-AGUCGGCAGA-G-AGUUAC------------CGU--------------C--------UUACAG---UUGUGAAAA-CAACUG--------------------------------------UA---------ACGA------AAG-CUA-UCCA-GAGG-UGG-AUGGUGUAG-CCUAUA---UGCCGGAGG-UCUACAAA
CP001216.1/34053-33844       GAUAACUGUUCAGAUAAGUGGUAG-GAAUGAAGGAGUAACG----------CCCCGAAACU-ACCCCAGUG-AGAUUC--CCA-AC-UGCAU-ACAC--UAG--------GCA--------------------------UAGCGUGA--UGUG-GA-GAGC-AGGGUA--A-AAUAUACGGU-CACGGU-------------------------------U--------CGU---------AGUGCA-CAACUGUGUAACCGAAAGCCAACAGGAGUAAUAAACCGGUUGGAACUA-----------A---CCAAG-----------------------U--AC----------CGUAUGCUG-UCAACCGA
ACMP01000083.1/181078-180900 AACAACUGUUUGACUGAA-AGUAG-GAAUGAAAGC----CGUCAG--GUUGAGCUGAAACU-ACUUAUCUA-AUACUC--CUA-CA-UGCAA-GGCG--UGA----UAGUAGU--------------------------CACAAAUU---GUA-UG-AAGC-UAGGUG--A-AGUCGGCUGA-A-CA-------------------------AA------A--------CCU---------A-A-------GUG--------------------------------------AG------------A------AAU-------CAUAUGG-UA------A-----UGGAUA---GGUCGGGAU-GCUACAAA
DQ321786.1/12527-12724       GAGAACUAAACACACGAA-UAGUC-GAAUGACGGGGUAACG----------CCCUGAAAGG-CUACUUUAAUACUCUG--A---CU-GGC---AGAA--ACUUGAGUAAACAA--------------------------GGCUCU-----GUC-AG-AAGC---UCGGUGA-AGUCGGCAGA-C-AGACAC------------CGU------AA------C--------AGA---------U-A-------AUG--------------------------------------CU-G-------ACGA------AAG-AUU-CCCA-GAGG-UGG-GCGUUGUGU-CCUAUA---UGCCGGAAG-UCUAUAAA
ABDL02000015.1/91966-91768   GUGAACUGUCAUUCCAAG-AAGUC-AAAUGAUAGGGUAACG----------CCUUGAAGGG-CUUCCUUUA-AUACUC-CCGA-CA-UGCAG-UGAA----GUUAGCAAGAAC----------------------------UGAACU---GUA-UG-AAGC-UCGGUG--A-AGUCGGUUGA-G-AGUUAC------------CGU------AA----------------UC---------CUA-------UAG--------------------------------------GA-U-------ACGA------AAG-UCA-CUCA-GAGG-UGG-GUGGUGUAA-CCUAUA---AACCGGAAG-UCUAUAAA
ACLZ01000063.1/28049-27848   GUGAACUCUUAACUCGAU-AGGUA-GAAUGAUAGGGUAACG----------CCUUGAAAUG-CCUACUCUA-AUACUC--CGA-CA-UGCGU-UAU---UCGAAUGUGUAUAA--------------------------GA-AUAGG---GUG-UG-AAGC-UCGGUG--A-AGUCGGCUGA-A-AGUUGU------------CGU------AG------U---------AC---------UUA-------UGA--------------------------------------GUAA-------CCGA------AAG-CUA-ACCA-GAGG-UGG-UUGGUACAA-CUGAUA---GGUCGGGAG-UCGUGAAA
ACLT01000219.1/19728-19906   AACAACUGUUUGACUGAA-GGUAG-GAAUGGAAAC----CGCCAG--GUUGAGCUUAAACU-ACUUAUCUA-AUACUC--CUA-CA-UGCAA-GGCA--UGA----UAAUAGU--------------------------CACAAAUU---GUA-UG-AAGC-UAGGUG--A-AGUUAGCUGA-A-CA-------------------------AA------A--------CCU---------A-A-------GUG--------------------------------------AG------------A------AAU-------CAUAUGG-UA------A-----UGGAUA---GGUCGGGAU-GCUACAAA
AARF01000049.1/30252-30069   CCUAACUGUAUAACCAAA-GAUCG-GAAUGACGGAACCAUGU--------UUCCCGAAACG-AUCUCGUCA-AUACUC--CUG-CG-UGCGU-UAUG--GGU------GACAG--------------------------CUCUUAGG---GUU-CG-AAGA-CAGGUG--G-AGUCGGCAGA-A-AGAGGC---------------------UA------U---------AG---------C-C-------ACU--------------------------------------CA-G----------A------AAG------AGA-AAGG-UA------UGCCUACUGAUA---UGCCGGGCG-GCUGAAAA
ACMU01000120.1/21873-21695   AACAACUGAUUGACUGAA-AGUGG-GAAUGAAAGC----UGUCAG--GUUGAGCUGAAACU-ACUUAUCUA-AUACUC--CUA-CA-UGCAA-GGCG--UGA----UAGUAGU--------------------------CACAAAUU---GUA-UG-AAGC-UAGGUG--A-AGUCGGCUGA-A-CA-------------------------AA------A--------C--C------UAAGU-------AAG----------------------------------------------------A------AAU-------CAUAUGG-UA------A-----UGGAUA---GGUCGGGAU-GCUACAAA
ACNI01000192.1/11831-12015   AAUAACUGAUUUAACGAGUGAGUG-GAAUGAAAGC----CUUCAU--GUUGAGCUGAAACA-CUCCCAAUA-AUACUC--CUA-CA-UGCAG-AGAA----AGUUGAUAGA-C----------------------------UGCACU---GUA-UG-AAGC-UAGGUG--A-AGACGCAUGA-A-GAAAGC-----------C---------UA---------------AGU---------A-C-------AUG--------------------------------------AC-------------------AAC-AUG-U-------------AUAUGGCAA-UUGAUA---AUGCGGUUG-GCUAUAAA
DQ889680.1/79607-79398       GAUAACUGUUCAGAUAAGUGGUAG-GAAUGAAGGAGUAACG----------CCCCGAAACU-ACCCCAGUG-AGAUUC--CCA-AC-UGCAU-ACAC--UAG--------GCA--------------------------UAGCGUGA--UGUG-GA-GAGC-AGGGUA--A-AAUAUACGGU-CACGGU-------------------------------U--------CGU---------AGUGCA-CAACUGUGUAACCGAAAGCCAACAGGAGUAAUAAACCGGUUGGAACUA-----------A---CCAAG-----------------------U--AC----------CGUAUGCUG-UCAACCGA
ABDV01000021.1/47135-46943   UACAACUGAUAGUUUGAG-AAGUG-GAAUGAUGGAGUAACG----------ACCUGAAACG-CUUCCCUUA-AUACCC--CGU-UA-GGCGA-GUGG--AUA---------AA--------------------------GUUCAU-G---GCC-UA-CAGC-ACGGAG--A-GGACGACCGA-A-GUAUAC------------CCA------AA------C---------AG---------AUA-------AAG--------------------------------------CU-G-------UGGA------AAA-AUU-AACA-GAGG-UGU-UAGUUGUGU-AUGACA---GGUCGGAGG-UCUAUAUA
AB236336.1/19883-20089       UAGAACUCUUAACUUGAA-AAGUG-GAAUGAUAGGGUAACG----------UCUUGAAACG-CUUUCUCUA-AUACUC--CGA-CA-UGCAG-UAAC-----UUUGUGUGAAA----------------------------GUUAUU---GUG-UG-AAGC-UCGGUG--A-AGUCGGCAGA-A-AAUUAC------------CGU------AG------CAGAUAAUAAAA---------UGU-------UAU--------------------------------------CU-A-------ACGA------AAG-UGU-UCUA-GAGG-UAG-AAUAUGUAG-UUGAUA---UGCCGGGAG-UCGUUAAA
AAXG02000040.1/15-198        GUGGAUUC---------C-AGGUG-GA-UGACGGGGUAACG----------CCCUGAAACG-CCUGCCCUC----GGU--GGG-CG-UGCAU-CGGC----U------GCAAA----------------------------GCCGGU---GUA-CG-AAGC-CCCACGACA-AC--GGCUGA-G-AGCAAC------------CGU------AG------C--------CGC---------CGCC-----AACG--------------------------------------GCAG-------CCGA------AAG-CGG-UCUG-GAGG-CAG-ACUGUGUUG-CCUAUA---GGCCAAGGG-UCUACAAA
ACNK01000147.1/8199-8016     AACAACUGAUUGACUGAA-AGUAG-GAAUGAAAGC----CGUCAG--GUUGAGCUGAAACU-ACUUAUCUG-AUACUC--CUA-CA-UGCAA-GGCG--UGA----UAGUAGU--------------------------CACAAAUU---GUA-UG-GAGC-UAGGUG--A-AGUCGGCUGA-A-CA-------------------------AA------A--------C--C-------UAAGUGA-GAAAAG----------------------------------------------------A------AA-------UCAUAUGG-UAA-----------UGGAUA---GGUCGGGAU-GCUACAAA
ABDV01000022.1/66578-66372   GAGAACUCUUAACUUGAA-AAGUG-GAAUGAUAGGGUAACG----------CCUUGAAACG-CUUUCUCUA-AUACUC--CGA-CA-UGCAG-UAAC-----UUUGUGUGAAA----------------------------AUUAUU---GUG-UG-AAGC-UCGGUG--A-AGUCGGCAGA-A-AAUUAC------------CGU------AG------CAGAUAAUAAAA---------UGU-------UAU--------------------------------------CU-A-------ACGA------AAG-UGU-UCUA-GAGG-UAG-AAUAUGUAG-UUGAUA---UGCCGGGAG-UCGUUAAA
AAQL01011977.1/504-715       GAGAACUGAUAUUCCGAU-GGGUG-AAAUGAGGGGGUAACG----------UCCCGAAGCG-CCACCCUAAUACUCCG--AAU-------GG-CGGG--GAGCAUGCAACGGC--------------------------UCUCUCCAAAAGUU-UA-UAGA-GCUCGGUGA-AGUCGGCAGA-G-AGCAAU------------CGUA----AGA------C--------UGGU------UUU-C-------AGG--------------------------------------CC-AG----ACACGA------AAG-CUG-UCCA-GAGG-UGG-AUGGUGUUG-CCUAUA---UGCCGGGGG-UCGGAUAU
ACNE01000197.1/28015-27837   AACAACUGAUUGAAUGAA-AGUAG-UAAUGAAAGC----CGGCAG--GUUGAGCUGAAACU-ACUUAUCUA-AUACUC--CUA-CA-UGCAA-GGCG--UGA----UAGUAGU--------------------------UACAAAUU---GUA-UG-AAGC-UAGGUG--A-AGUCGACUGA-A-CA-------------------------AA------A--------CCU---------A-A-------GUG--------------------------------------AG------------A------AAU-------CAUAUGG-UA------A-----UGGAUA---GGUCGGGGU-GCUACAAA
ACIY01000540.1/8689-8897     GAGAACUGAUAAUCUGAC-AGGUG-GAAUGAUGAAGUAACG----------CUCUGAAACG-CCUGCCCUG-AGCCUC--CGA-CA-AGC-A-UUGUAUGAG------GAAAC--------------------------UCAGAAU----GUU-UG-AAGC-UCGGUA--A-AGACGGCUGA-A-AGAUAC------------CGU------AA------U---------AGUUG---AUGAACAUA-UAUCUU--------------------------------------CU-A-------UCGA------AAA-CUA-UCCA-GAGG-UGG-GUAGCGUAU-CCAACA---GGUCGGGGG-UCUAUAAA
CP000040.1/205798-205988     CUGAAGGGUUAUAUCAAG-AAGUC-GAAUGAGGAAGUAACG----------CUCUGAAAGG-CUUCCCCUG------CGUCGA-AU-UGC-----ACGUUUUUCAGUAAGGAA--------------------------AAGC-------GUG-----AGC-UCGGUU--A-AUAGGCAUGAGA-AUUUAC------------CGU------AA------C---------AG---------UUU-------CGG--------------------------------------CU-G-------ACGA------AAG-CCU-ACCC-GAUG-GGG-U-GGUGUAA-AUCAUG---GUGCUUGGG-UUGAACAG
AB444205.1/10024-10230       GAGAACUCUUAACUUGAA-AAGUG-GAAUGAUAGGGUAACG----------CCUUGAAACG-CUUUCUCUA-AUACUC--CGA-CA-UGCAG-UAAC-----UUUGUGUGAAA----------------------------GUUAUU---GUG-UG-AAGC-UCGGUG--A-AGUCGGCAGA-A-AAUUAC------------CGU------AG------CAGAUAAUAAAA---------UGU-------UAU--------------------------------------CU-A-------ACGA------AAG-UGU-UCUA-GAGG-UAG-AAUAUGUAG-UUGAUA---UGCCGGGAG-UCAUUAAA
FM204884.1/1440779-1440574   GAGAACUGACAAUCUGAU-AGGUA-GAAUGAUGGGGUAACG----------CCUUGAAAUG-CCUACACUG-AUACUC--CGA-UU-GGCAA-UGAA-----UAUUAGACUAU----------------------------UUCAUU---GUC-AA-AAGC-UCGGUG--A-AGUCGGCAGA-G-AGUAGC------------CGU------AA------G--------A--CUG---AUAUUA-------ACA-----------------------------------------UCA--GACACGA------AAG-CUG-UUCA-GAGG-UGG-ACGGUGCUA-CCUAUA---UGCCGGGUG-UCGAAUAC
ABDW01000012.1/7531-7325     GAGAACUCUUAACUUGAA-AAGUG-GAAUGAUAGGGUAACG----------CCUUGAAACG-CUUUCUCUA-AUACUC--CGA-CA-UGCAG-UAAC-----UUUGUGUGAAA----------------------------GUUAUU---GUG-UG-AAGC-UCGGUG--A-AGUCGGCAGA-A-AAUUAC------------CGU------------------------AGUAG---AUAAUAAAA-CAUUAU--------------------------------------CU-A-------ACGA------AAG-UGU-UCUA-GAGG-UAG-AAUAUGUAG-UUGAUA---UGCCGGGAG-UCAUUAAA
ACMY01000188.1/4932-5134     UAGAACUAAUGAUUCGAG-AGACA-GAAUGAUAGAGUAACG----------UCUUGAAAUG-UUUCCCCUA-AGUCUC--CGA-CA-UGCAU-UAAA--UGG------UAGGA--------------------------CGUUUAAA--UGUG-UG-AAGC-UCGGUG--A-AGACGGCUAA-C-AGAUAC------------CGUA---GU------------------AA---------A-AAAA-UAUAUU--------------------------------------UUAA-------CCGA------AAA-UCC-UUUU--AGU-AAA-AGGAUGUAU-CCCAUA---GGCCGGGGG-UCCGUAAA
AATE01006681.1/531-737       UCUAACUGAUACUCCGAG-GAGUG-GAAUGAAGGGGUAACG----------CCCUGAAACG-CUCCCCCUG-AUACUG--CGU-UG---------------GAGGAAACGGGGCGCAAUCCC--------UGCGACUGA---------------CA-CAGC-ACGCUG--A-AGUCGGCUGG-ACACACCC------------GCC------UU------A--------CACGAG---GUAA-AA-----GACG--------------------------------------GUAG-------GGCA------AAGACGA-GCCA-GAGG-UGG-C-CGUGGGU-G--AUA---GGCCGGGGG-UUCAUAAC
AAXG02000036.1/8100-8293     GAUAACUGGUAAUUCGAC-AGGUG-GAAUGACGGGGUAACG----------CCCUGAAACG-CCUGCCCUC----GGU--GGG-CG-UGCAU-CGGC----U------GCAAA----------------------------GCCGGU---GUA-CG-AAGC-CCCACGACA-AC--GGCUGA-G-AGCAAC------------CGU------AG------C---------CGCCG---CCAA---------CGG--------------------------------------CA-G-------CCGA------AAG-CGG-UCUG-GAGG-CAG-ACUGUGUUG-CCUAUA---GGCCAAGGG-UCUACAAA
ACNH01000170.1/3164-2997     AACAACGGAUUGACCGAA-AGUAG-GAAUGAAAGC----CGUCAA--GUUGAGCUGAAACU-ACUUAUCUG-AUACUC--CUA-CA-UGCA-----------------AGGCG----------------------------UGAUA----GUAGUUAAAAA-UAGGUG--A-AGUCGGCUGA-A-CA-------------------------AA----------------GC---------C---------UAA--------------------------------------GU-G----------A----------UUA-AUCA-UA---UGG-U-AA------UGGAUA---AAUUGGGAU-GCUACAAA
CP000040.1/3890-4068         AACAACGGAUUGACUGCA-AGUAG-GAAUGAAAGC----CGUCAG--GUUGAGCUGAAACU-ACUUAUCUG-AUACUC--CUA-UA-UGCAA-GGCG--UGA----UAGUAGU--------------------------CACAAAUU---GUA-UG-AAGC-UAGGUG--A-AGUCGGCUGA-A-CA-------------------------AA------A--------CCU---------A-A-------GUG--------------------------------------AGAA----------A---------------UCAUAUGG-UAA-----------UGGAUA---GGUCGGGAU-GCUACAAA
AATF01004896.1/796-593       UCUAACUGAUAUUCCGAG-AAGUG-GAAUGACGGGGUAACG----------CCCUGAAACG-CUUCCCUUG-AUACUG--CGU-UG--G-AA-GAAA--CGGGACGUAUUUCC--------------------------CACAACUG-----A-CA-CAGC-ACGCUG--A-AGUCGGCUGU-CUGCACCU-------------GC------GA------C--------U--GUC---CCUUUUGGG-GAUAAA-------------------------------------------------GCAA------AAC-CGA-GCCA-GAGG-UGG-C-CGGGGGU-GUUA-----GGCCGGAGG-UCUAUAAA
CP001166.1/247033-247227     UACAACUGAUAUACCGAU-GUCAG-GAAUGAAAGC----CGUCAU--GUUGAGCUGAAACU-GACAGUCUA-AUACUC--CUA-CA-UGCA------UUUAUCUUGAUAGAGAUA---------------------CAUUGCGUUAU---GUA-UG-AAAC-UAGGUG--A-AGUCGGCUGA-A-UCUAAU-----------------------------U--------C-----------U-A-------AAG-----------------------------------------C------C---A--------CUCUU-ACAGAGAGG---G-UAUG-GUUA-GAGAUA---GGCCGGGAC-GCUAUAAA
ABQR01000056.1/131867-132064 GAGAACUGCAUAACUGAA-AUCUC-AAAUGAUGGGGUAACG----------CCCGGAAGGG-GAUUCACUG-AUACUC--CGA-GU-AGCGU-CAGC--CAG-----AUACAG--------------------------UGGCUGGG---GUU-AU-AAGC---GCGGGAA-AGUCGUGCGA-A-GCACAC------------CCU------AA------C--------GCU---------G-A-------AAG--------------------------------------GC-G-------AGGA------AAG-AUU-CAUA-GAGG-UAU-GAGUUGUGU-GUGACA---GUGCGGGUG-GGGCUGCC
ABDA02000013.1/60158-59980   AACAACUGUUUGACUGAA-AGUAG-GAAUGAAAGC-CGUCAUG-----UUGAGCUGAAACU-ACUUAUCUA-AUACUC--CUA-CA-UGCAA-GGCG--UGA----UAGUAGU--------------------------CACAAAUU---GUA-UG-AAGC-UAGGUG--A-AGUCGGCUGA-A-CA---------------------------------------------AAA---CCUAAGUGA-GAAAUCAUAU-----------------------------GGUAA-----------------------------------------------------UGGAUA---GGCCGGGAU-GCUACAAA
ACMO01000125.1/2891-2707     AAUAACUGAUUUAACGAGUGAGUG-GAAUGAAAGC----CUUCAU--GUUGAGCUGAAACA-CUCCCAAUA-AUACUC--CUA-CA-UGCA--GAGGAAGU---UGAUAGACCA------------------------CAC-----U---GUA-UG-AAGC-UAGGUG--A-AGACGCAUGA-A-GAAAGC-----------C---------UA---------------AGU---------A-U-------AUG--------------------------------------AC-------------------AAC-AUG-U-------------AUAUGGCAA-UUGAUA---AUGCGGUUG-GCUAUAAA
AATD01002042.1/709-506       UCUAACUGAUAUUCCGAG-AAGUG-GAAUGACGGGGUAACG----------CCCUGAAACG-CUUCCCUUG-AUACUG--CGU-UG--G-AA-GAAA--CGGGACGUAUUUCC--------------------------CACAACUG-----A-CA-CAGC-ACGCUG--A-AGUCGGCUGU-CUGCACCU-------------GC------GA------C--------UGUCCC---UUUU-G-------GGG--------------------------------------AUAA------AGCAA------AAC-CGA-GCCA-GAGG-UGG-C-CGGGGGU-GUUA-----GGCCGGAGG-UCUAUAAA
ABOO01000017.1/41884-41706   CACAACUGAAUAUUCGAU-AUUUG-GAAUGAUA---GUCAUCAUGUUGGCU---UGAAACA-AAUAGUCUG-AUACUC--CUA-CA-UGCA-----U--AGGAUUGUAACAGC--------------------------AUGAAUGU---GUA-UG-AAGC-UAGGUA--A-AGACGGCAGA-A-C----------------------------------------------AAU---GCCUAAGUG-AGAUAUCAUAC---------------------------GGCAAA------------------------------------------------------GGAUA---UGUCGGGAC-GCUAUAAA
CP003056.1/1756046-1756244   GAGAACUGAUGAUUCGAA-GAGUC-GAAUGAAGGAGUAACG----------CCCGGAAAGG-CUCUCCCUG-AUCCUC--CGA-AU-AGCGU-CAAG--AUA----GGUAAGG--------------------------AUCUUGAG---GUU-AU-AAGC-UCGGUG--A-AGUCGGCUGA-A-UGCUGC------------CGU------AA------C--------AAG---------U-C-------AAG--------------------------------------UU-G-------ACGA------AAG-CUU-UCCA-GAGG-UGG-AAGGUGCAG-CAAAUA---AGCCGGGGG-UCUAUAAA
FN668944.1/1876350-1876554   UAGAACUAUUACUUUGAG-AAAUC-AAAUGAGUGGGUAACG----------CCACAAAGGG-UUUCCUCUA-AUACUC--CGA-CA-UGCGG-GAAA--AGU--UGAUAUUAA--------------------------CAUGAACC---GUA-UG-AAGC-UCGGUG--A-AGUCGGUUGA-A-AGUGAC------------CGU------AA------A---------GCA------UU---AU---CAAAU--------------------------------------GC-U-------ACGA------AAU-CUG-CUCA-GAGG-UGG-GCGGUGUCA-CCCAUA---GACCGGGAG-UCUAUAAA
CP001910.1/95746-95549       GUGAACUAUCAUUCCGAG-AAGUC-AAACGAUAGGGUAACG----------CCUUGAAGGG-CUUCCUUUA-AUCCUU--CGA-CA-UGCAG-UGAA--GUU----AGCAAGA--------------------------ACCUUACU---GUA-UG-AAGC-UCGGUG--A-AGUCGGCUGA-G-AGUUAC------------CGU------AA------G---------UC---------U-U-------AGA--------------------------------------GA-C-------ACGA------AAG-CCG-UCCA-GAGG-UGG-ACGGUGUAA-CCUAUA---AGCCGGAAG-UCUAUAAA
FN668943.1/237763-237571     GAGAACUAAUACUCUGAG-CAAUU-AAAUGAUAAGGUAACG----------CUUUGAAGAA-UUGCCAUUA-AAAUUA--CGA-UA-UGCAA-UGGA--UUAA-GUUAUUAUG--------------------------AA---GUU---GUG-UA-AAGC-UCGUUG--A-AGUCGGCAGAAA-AAUUAC------------CCU------AA------C---------GA---------GUU-------AAG--------------------------------------UC-G-------AGGA------AAG-GUU-U-----AAU-----UAGCUGUAA-UUGAUA---UGUCGGAUG-UCUAUGAA
FP929044.1/1418452-1418659   GAGAACUAACAAUCCGAG-AGGUG-GAAUGAUGGGGUAACG----------CCCUGAAACG-CC-CCCUUA-AUACUC--CGA-CU-GGCAU-UUCA-ACAG--------AAA--------------------------UGUGACUU---GUC-AG-AAGC-UCGGUG--A-AGUCGGCUGA-G-AGUAGC------------CGU------AU------G--------G-AUUGCUGGAU---AAA-UACCAGC------------------------------------CU--C-------ACGA------AAG-CUG-UCCA-GAGG-UGG-ACGGUGCUA-CCUAUA---GGCCGGAGG-UCUACAAA
CP002491.1/2238445-2238264   GACAACUAAUGUUUUGAG-AGAUG-GAAUGAAAGC-CUUCAAG-----UUGAGCUGAAACA-UCUCCGCUA-AUACUC--CUA-CA-UGCUC-UAAU--CAAU-GAAGUAGAU--------------------------UGGUUUUG---GUA-UG-AAGC-UAGGUG--A-AGUCGUCUGA-A-AUCUGC------------CU-------AA------G---------UG---------UUU-------GAG--------------------------------------CA-U-------AAG----------------------------------GCUG-ACUAUA---GGGCGGGCG-GCUGAAAA
CP001904.1/53380-53176       GAAAACUAAUAUUCUGAA-AGGUA-GAAUGAGGAGGUAACG----------CUCUAAAAUG-CCUUCCCUG-AUACUC--CGA-UA-UGCAA-UCUU--GUU----GAUAAAG--------------------------ACAAGAUU---GUA-UA-AAGC-UCGGUA--A-AGUCGGUUGA-A-UGUUAC------------CCC------AG------U--------AUGCU----CUAA-A-------AGG--------------------------------------CAUA-------UGGA------AAA-CUG-CUCA-GAGG-UGA-GUGGCGUAG-CAGAUA---GACCGGGGG-UCUAUAAA
CP001910.1/84128-83925       CAGAACUAUUAUUUCGAG-AAGUC-AAAUGAUAGGGUAACG----------CCUUGAAGGG-CUUCCUCUG-AUACUC--CGA-CA-UGCAG-CAUA--CAAA-AGAUAAGCC--------------------------UGUA-GUU---GUG-UG-AAGC-UCGGUG--A-AGUCGGCUGA-G-AGCUAC------------CGU------UA------A--------AGU---------A-UC----UCGAU--------------------------------------AC-U-------ACGA------AAA-CUG-UCCA-GCGG-UGG-AUGGUGUAG-CCUAUA---GGCCGGGAG-UCUAAAAA
GQ484955.1/6756-6968         GAGAACUUUCAGUUUGAG-AGGUG-GAAUGAUAGGGUAACG----------CCUUGAAACG-CCUCCCUUA-AUACUC--CGA-CA-UGCCU-UUU---CUUA-CGUGUUAAA--------------------------AG-AAAUG---GUA-UG-AAGC-UCGGUG--A-AGUCGGCAGA-A-GGAUAC------------CGU------AA------G---------CAAGA---UUGA-A-------AAACAUG------------------------------GGUCUG-C-------ACGA------AAA-UUU-CCUA-GAGG-UAG-GAAACGUAU-CUAAUA---UGCCGGAGG-UCGCAAAA
CP001638.1/1239159-1239309   GUGAA---AGUCCGAGAC-AGGAA----UGAAGG-------------------UUGGCAUU-CCUGCCCUA-AUACCC--CGA-CG-UGCGG-UAAU--GGU------GCGCA--------------------------ACAUUACC---GUG-CG-AAGC-UCGGAG--A-GGACGGCGAA-A-AGCAGAC---------CU---------GA------G------------------------------AAG-------------------------------------------------------------------------UGG----------UUAG-CGAAGU---AGCCGGGGG-UCCAUAAA
AP007209.1/1700914-1700717   GUGAACUGUCAUUCCAAG-AAGUC-AAAUGAUAGGGUAACG----------CCUUGAAGGG-CUUCCUUUA-AUACUC--CGA-CA-UGCAG-UGAA--GUU----AGCAAGA--------------------------ACUGAACU---GUA-UG-AAGC-UCGGUG--A-AGUCGGUUGA-G-AGUUAC------------CGU------AA------U---------CC---------U-A-------UAG--------------------------------------GA-U-------ACGA------AAG-UCA-CUCA-GAGG-UGG-GUGGUGUAA-CCUAUA---AACCGGAAG-UCUAUAAA
ABYU02000011.1/391039-390841 GAGAACUGAUAUUCCAAA-GAGUG-GAAUGAGGGGGUAACG----------CCCCAAAACG-CUCUCCUUA-AUACUC--CUA-CA-UGCUG-UG----C-AACUGCUGAA-A--------------------------UG--CACA---GUA-UG-AAGC-UAGGUG--A-AGUCGGCAGA-G-AGAUAC------------CGU------AA------G---------GCA------UGA-A-------AAU--------------------------------------GC-C-------ACGA------AAG-CUG-UCCA-GCGG-UGG-GCGGUGUAU-CCUAUA---UGCCGGAGG-UCUAUAAA
ACBY02000013.1/28190-28391   GAGAACUAAUAUUCCGAU-AGGUG-GAAUGAAGGGGUAACG----------CCCUGAAACG-CCUACCUUAUAAACUG--CGA-UA-UGCGG-CAGU--CCUC-UGUAACA-A--------------------------GGGCUACG---GUA-UA-ACGC-UCGCUA--A-AGUCGGCGGA-A-AUGCAC------------CCA------AA------C---------GG---------AUU-------AUG--------------------------------------CC-G-------UGGA------AAG-UGU-CCCA-GAGG-UGG-GAUAUGUGC-AUGAUA---CGCCGGAGG-UCUAUAAA
#=GC SS_cons                 :::::::::::::::::<.<<<<<.------<<<<<_____..........>>>>>--->>.>>>>,,,,,.,,,<<<..<<<.<<.<<<-<.<<<<..<<_...________..........................>>>>>>>-...>>>.>>.----.>>>>>>..-.--((((((--.-.((((((............<<<......--......-........-<<........._._.......___......................................>>.-.......>>>,......,,<.<<<.<<<<.____.>>>.>>>>>)))).))----...)))))):::.::::::::
#=GC RF                      gAuAACUGaUaauucGAg.ggguG.GAAUGAcgGgGUAACG..........CcCcgAAACg.ccccCccUg.AuAcuc..Cga.cc.uGCAc.ucac..ugg...guaaaaaa..........................cagugagu...GUa.gg.AAGC.ucGgug..A.AGucGgcaGA.a.cgcuaC............cgu......AA......u........agc.........a.u.......aaG......................................gc.g.......acgA......AAg.ccg.ucca.GAGG.ugg.acgguGuag.cggAUA...ugcCggGgG.UCuauAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02005
#=GF ID   group-II-D1D4-6
#=GF DE   Group II catalytic intron D1-D4-6
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Weinberg Z
#=GF SS   Predicted; Weinberg Z
#=GF GA   49.00
#=GF TC   49.10
#=GF NC   48.90
#=GF TP   Intron;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00102
#=GF DR   SO; 0000603; group_II_intron;
#=GF DR   GO; 0000373; Group II intron splicing;
#=GF RN   [1]
#=GF RM   11377794
#=GF RT   The ins and outs of group II introns.
#=GF RA   Bonen L, Vogel J
#=GF RL   Trends Genet 2001;17:322-331.
#=GF RN   [2]
#=GF RM   11726522
#=GF RT   Control of branch-site choice by a group II intron.
#=GF RA   Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM
#=GF RL   EMBO J 2001;20:6866-6876.
#=GF RN   [3]
#=GF RM   12870716
#=GF RT   Group II introns: structure and catalytic versatility of large natural
#=GF RT   ribozymes.
#=GF RA   Lehmann K, Schmidt U
#=GF RL   Crit Rev Biochem Mol Biol 2003;38:249-303.
#=GF CC   Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi,
#=GF CC   plants and protists, and also in mRNA in bacteria. They are large
#=GF CC   self-splicing ribozymes and have 6 structural domains (usually designated
#=GF CC   dI to dVI. This model and alignment represents only domains V and VI. A
#=GF CC   subset of group II introns also encode essential splicing proteins in
#=GF CC   intronic ORFs. The length of these introns can therefore be up to 3kb.
#=GF CC   Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing
#=GF CC   with two transesterification steps. The 2' hydroxyl of a bulged adenosine
#=GF CC   in domain VI attacks the 5' splice site, followed by nucleophilic attack
#=GF CC   on the 3' splice site by the 3' OH of the upstream exon. Protein machinery
#=GF CC   is required for splicing in vivo, and long range intron-intron and
#=GF CC   intron-exon interactions are important for splice site positioning. Group
#=GF CC   II introns are further sub-classified into groups IIA and IIB which differ
#=GF CC   in splice site consensus, distance of bulged A from 3' splice site, some
#=GF CC   tertiary interactions, and intronic ORF phylogeny [1].
#=GF WK   Group_II_intron
#=GF SQ   174


BABE01000503.1/2186-1953       AAAAGC--CUAUC-AGG---UAAGG-U-CUAA--CCA-A-CCGCCU--GUA---CCGAG-U-CCUUGGAA-----C-UGAAG-UG-GUAA-CACCAG-G-UUU-AAGCGUAGG---A--C-A--------GG---GAG---------C-----AACAGAGC---------CGAAACGAAA------------------------------GUGA-AGC--------GAUUGAGCUGGG-AAAUUAGUA-----------------UGAGGUUGGA-AA-U-GG-UCGA-------UGUGU-UGU------AUUACA-C-AGUAGACAACACU-GCU-G-UA--ACCGCUACG----------GUGAGGU---UAUG-GC-GGC---A-UCC---------CCCAGUC--UGAGAGCU
ABDH01050529.1/621-390         AUAGUG--ACUAU-GGC----AAAG-U-CUAG--CAA-A-C-AGCC--AUA-CACCGAG-U-CUUGCGUG---G-U-GU-GC-UG-GCGA-CAGGCA-C-UGC-GAAGCGUAG---A--C-A--------GG---GGG---------AGU-GCAGGCCGGG---------CGAAGAGUAC------------------------------AGGA-C------------AUUAGCCCCGAAAUUGAC---------------------AUUGUCGA-GA-U-GG-CCGA-------CCAG---CUCCACAUA---CU-G-GGAAGGCAGCAAA-GAG-C-UG--ACCGUUAU-----------GCGAGGG---CAGC-GA-AAU---GUCUC---------CGGGGUU--CGAACCUG
ABDH01035009.1/907-691         CGUGCAUUCCAUC-CAG---AAGGG-C-GGAG--CAA-G-CCACUG--GAA---GCGAG-U-CUUGCAUG---G-G-UC--U-UG-GCGA-CAAGAU-U-UGU-GAAGCGUAG---A--C-A--------GC---GGG---------U-----A---CAAA---------AGCCGCGU-----------------------------------U-A------------UUGAGCCCCGAAAAAUUC---------------------AUAUUGCA-UG-A-GG-CUUU-------CACU---UUCGUGAU----AG-U-GGG-AGCGGUCGU-AUA-C-GC--AC-----GCC-------AGGCGA-GU---GCGA-AU-ACC---UCGGC---------CGGGGUC--GGAGAGCG
ABDH01013406.1/338-121         CGUGCAUUCCAUC-CAG---AAGGA-C-GUAG--CGA-G-UCACUG--GAA---GCGAG-U-CUUGCAUG---G-G-UC--U-UG-GCGA-CAGGAU-U-UAU-GAAGCGUAG---A--C-A--------GC---GGG---------U-----A---CAAA---------AGCCGCGU-----------------------------------G-A------------UAGAGCCUCG-AAGUAAUUA-----------------UUAUUGCAG---G-A-GG-CUUU-------CACU-----UUUCAUU--CAG-U-GGG-AGCGACCGU-GGA-C-G---GGCGACAA-----------GCGAGC----GCGC-AC-ACC---UCAGC---------CGGGGUC--CGAGAGCG
ABDH01028488.1/465-247         CGUGCAUUCCAUC-CAG---AAGGA-C-UUAG--CAA-G-UCACUG--GAA---GCGAG-U-CUUGCAUG---G-G-UC--U-UA-GCGA-UAAGGC-U-UGU-GAAGCGUAG---A--C-A--------GC---GGG---------U-----A---CAAA---------AGCCGCGU-----------------------------------G-A------------UUGAGCCACG-AAAUAGUCA-----------------AACAU-UGCA-UG-A-GG-CUUUC-----ACCGUG-UGGU------G-CGU-G-GG--AGCGACCGU-GGA-C-G---CGCGAUAA-----------GCGAGCG----UGG-AC-ACC---UCGGC---------CGGGGUC--UGAGAGCG
ABDH01007395.1/275-57          UGUGCAUUCCAUC-CAG---AAGGA-U-UUAG--CAA-G-UCACUG--GAA---GCGAG-U-CUUGCAUG---G-G-UC--U-UA-GCGA-UGAGGC-U-UGU-GAAGCGUAG---A--C-A--------GC---GGG---------U-----A---CAAA---------AGCCGCGU-----------------------------------A-A------------UUGAGCCACG-AAAUAGGUA-----------------AACAU-UGUA-AG-A-GG-CUUU-------CACCG-UUUGGU----G-C-G-U-GGG-AGCGAUCGU-GGA-C-G---CGCGAUAA-----------GCGAGUG----CGG-AC-ACC---UCUGC---------CGGGGUC--UGAGAGCG
ABDH01039692.1/1300-1082       UGUGCAUUCCAUC-CAG---AAGAA-C-UGAG--CAA-G-UUACUG--GAA-GC--GAG-U-CUUGCAUG---G-G-UC--U-UG-GCGA-CAAGAU-U-UGU-GAAGCGUAG---A--C-A-------------GC----------G-----AGUACAAA---------AGCCGCGU-----------------------------------G-A------------UUGAGCUCCGAAAUUAGG--------------------UAUCAUCGCAUG-A-GG-CUUU-------CACU---AUACUACC----AG-U-GGG-AGCGACCGU-GGG-C-GU---ACGAUAA-----------GCGAGU----GCGU-UC-ACC---UUGGC---------CGGGGUC--GGAGAGCG
ABDH01005930.1/540-772         AAACACCAUGUCC-GGC----AAAG-U-UUAG--CGA-A-C-AGCC--GGU-ACCA-AG-C-CUUGGAUC---U-G-AA--G-CC-GCGA-GG--UCAA-GAU-UAAGCGUAG---G--C-A--------UG---GGAGUGCGAGAGC-----CGCAAUGC---------GAAAGCGUGA------------------------------AGCG-A------------UUGAGCCUCG-UAAUAAA----------------------UUGGAGC-GG-A-AG-CCGA-------UGUA-----CUUCAGU--CUA-C-AGCAGGCAGCAA--UGC-G-UA--CUCGUAAAC----------GCGAGAG---UGCG-CA-GGU---UCCGU---------CGGGGUC--CGAGAGCG
ABDH01006449.1/253-485         AAACACCGCGUCC-GGC----AAAG-U-UUAG--CGA-A-C-AGCC--GGU-ACCA-AG-C-CUUGAAUC---G-G-AA--G-CC-GCGA-GGCCA--A-GAU-UAAGCGUAG---G--C-A--------UG---GGA---------G-----CGCAAGAGCCGCAAUGCGAAAGCGUGA------------------------------AGCG-A------------UUGAGCCUCG-UAAUAAA----------------------UUAGAGC-GG-A-AG-CCGA-------UGUA---UUGUUGUC----UA-C-AGCAGGCAGUAA--UGC-G-UA--CUCGUAAAC----------GCGAGAG---UGCG-CA-GGU---UCCGU---------CGGGGUC--AUAGAGCG
ABDH01039499.1/395-627         AAACACCACGUCC-GGC----AAAG-U-CUAG--CGA-A--UAGCC--GGU-ACCA-AG-C-CUUGAAUC---U-G-AA--G-CC-GCGA-GG--UCAA-GAU-UAAGCGUAG---G--C-A--------UG---GGA---------G-----CGUAAGAGCCGCAAUGCGAAAGCGUGA------------------------------AGCG-A------------UUGAGCCUCG-UAAUAAA----------------------CUGGAGC-GG-A-AG-CCGA-------UGUA-----CUGUUGU--CUA-C-AGCAGGCAGCAA--UGC-G-UA--CUCGUAAAC----------GCGAGAG---UGCG-CA-GGU---UCCGC---------CGGGGUC--AGAGAGCG
ABDH01005979.1/398-630         AAACACCGCGUCC-GGC----AACG-U-UUAG--CGA-A-C-AGCC--GGU-ACCA-AG-C-AUUGAAUC---U-G-AA--G-CC-GCGA-GGCCA--A-GAU-UAAGCGUAU---G--C-A--------UG---GGA---------G-----CGUAAGAGCCGCAAUGCGGAAGCGUGA------------------------------AGCG-A------------UAGAGCCUCG------UUAU-----------------AAUAAGAAGC-GG-A-AG-CCGA-------UGUG-----CUUCAGU--CUA-C-AGCAGGCAGCAA--UGC-G-UA--UUCGUAAUC----------GCGAGAA---UACG-CA-GGU---UCCGC---------CGGGGUC--AAAGAGCG
ABDH01019176.1/624-391         AGAUUCCAAAUCA-GGC----AAAG-U-UUAG--CGA-A-C-AGCC--UGU-ACUC-AG-U-CUUGAUGC---C-G-AA--G-CC-GCGA-GG--UCAG-GUA-UAAGCGUAG---A--C-A--------GA---GGAGUAUGCGAGC-----CGCAAUGC---------GAAAGCGUGA------------------------------AGCG-A------------UUGAGCCUCG------UUAU-----------------AACUGAAAGC-GG-A-AG-CCGA-------UGUG---UUCGUCCU----CA-C-AGCAGGCAGCAAU-GUA---CA--CUCGUUAUC----------GCGAGAG---UGUU-AC-AGG--UUCCGC---------CGGGGUC--AUAGAGCG
BAAV01013885.1/523-744         AAAAUC--CUGUC-AAA---UAAGCGG-CUAA--CCA-CAGCAUUU--GAA---GUGAG-U-CUUGGGUG---U-G-UC--G-CA-GUAA-UGCGGC-G-UGU-UAAGCGUAG---A--C-A--------GC---------------A-----AGGUAGUG---------GGGAUAGC-----------------------------------U-A------------UUGAACAUCG-AAAUACC--------------------AACAAACCA-GA-G-CG-UCGA-------CUCU---GUUGCCUGA---GG-A-G-AAGACAACAUG-UGG-GUUU--AUCGUUAAG----------GUGAGAU---UUCA-CA-CAG---UUCUG---------CGGUGUC--GGAAGGAA
BAAY01005042.1/819-1040        GGAUUCCGGUUUA-UCC----AAGG-U-UUAG--CCA-A-CCA-GA--UAA-UAGCGAG-U-CUUGGGAU---G-A-UG--C-CG-GUAA-CGGCAU-C-UGA-CAAGCGUAG---A--C-A--------GC---AAG---------A-----A-AGCA-----------GGGUUGAAUA-------------------------------GUG-A------------UUGAGCUUCG-AAACGUU----------------------AACUUCA-GU-C-GG-UCGA-------CGU----CUUAACUGG--U-G-C-GGAAGACAAUAUC-AUG-U-AA--UGCGAUAUG----------GCGAGUG---UUAU-GU-GAC----ACUG---------CGGAGUC--AGAGAAGC
BAAV01010738.1/534-752         GGAAUCCGGUUUA-UCC----AAGG-U-UUAG--CAA-A-CCA-GA--UAA-UAGCGAG-U-CUUGGGAU---G-A-UG--U-CG-GUAA-CG-CAU-C-UGA-CAAGCGUAG---A--C-A--------GC---AGA---------A-----AGCAGGGU---------UGAAUAGU-----------------------------------G-A------------UUGAGCUUCG-AAACGUU-----------------------ACUUCA-GU-C-GG-UCGA----------CG-UCUUAACUGGUGCG-----GAAGACAAUACC-AUG-U-AA--UACGAUAUG----------GCGAGUA---UUAU-GU-GGC----ACUG---------CGGAGUC--AGAGAACC
BABA01016158.1/522-743         CAAAUCCUGUCUG-UUU----AAGG-U-CUAA--CCA-A-CCA--G--CAG-UAGCGAG-U-CUUGCGUG---G-U-AA--U-CA-GUAA-UGAUUG-U-UGC-GAAGCGUAG---A--C-A--------GC---AAG---------C-----AAGUAG-----------GGUUG--CAA------------------------------UGCG-A------------UUGAGCCUCGAAAAGUUG----------------------AAUUUCA-GA-G-GG-CUGA-------CGU----CUUAACUGG--U-U-C-GGAAAGCAACAUC-GGC-U-AA--CUCGCUAUG----------GUGAGAG---UUCG-UC-GG----CACUG---------CGGGGUU--CAAGGGGC
ABEF01032066.1/170-396         AAAGUCCACCGCG-GAG---UAAGG-C-CUAG--CCA-G-CCGCUC--CGG-CCCCGAG-U-GAUGCGCG---G-C-AG--U-UC-GCGA-GGGCUG-A-CGU-GAAGCGUUC---A--C-A--------GG---GG----------------AGACCAUG---------GGCUG-GG-----------------------------------U-A------------UUGAGCUGCG-AAACUGG---------------------CUUUUCCA-AG-G-UG-CUGAUCUUUUUUCCG---UUG---------UG-G-AGAAGGCAACAUC-AUC-U-CA--UGCGAUGACU-------UGGCGAGUG---UGAG-AU-GGA---CCUUG---------CGCAGUC--GGAGACCC
ABEF01016589.1/1254-1044       AAAGUCAUCUGUG-UCG----AAGG-A-GUAG--CGA-A-CCACGA--CAG-CCCCGAG-U-CAUGCGUC---G-U-UG--C-GG-GCAA-UCGCAG-G-GGC-GAAGCGUUG---A--C-A--------GG---GG----------------AGGUGU-----------AAGUCCAG-----------------------------------U-U------------UUGAGCCGCGAAAAGCCAUG-----------------AACCACUCCA-GG-G-GG-CCGA--------------GC----------------GAAGGCCACAUC-CGG-C-GC--CGCGAUAUC----------GCGAGUG---GCGU-CG-GGC---CCCUG---------CGCGGUC--GGAGACCC
ABEF01040610.1/747-522         UAAGUCAUCCGUG-UCG----AAGG-C-GUAG--CGA-G-CCACGA--CAG-CCCCGAG-U-CAUGCGUC---G-U-UG--C-GG-GUAA-CCGCAG-G-GGC-GAAGCGUUG---A--C-A--------GG---GGG---------------AGGUGU-----------AGGUCCGG-----------------------------------U-U------------AUGAGCCGCG-AAAGACAUG-----------------AACCACUUUU-GG-G-GG-CCGAG-----ACGCU---GGAGUACG----AG-C-G-AAGGCUACAUC-CGA-C-GC--CGCGAUAUC----------GCGAGUG---GCGU-CG-GGC---CCUGG---------CGCGGUC--AGAGACCC
ABEF01049269.1/668-445         AGAGCC--AUACA-GAG----AAGG-A-GUAG--CGA-U-CCACUC--UGG-CCCUGAG-U-CAUGCGUU---G-U-UG--U-UC-GUAA-GGACCG-C-GGU-GAAGCGUUG---A--C-A--------GG---GGU---------A-----CGUCCA-----------GGCUG-GG-----------------------------------U-A------------UUGAGCCGCG-AAAUUGCUG-----------------AUAUGCUCCG-AG-G-GG-CCGA-------CGCUU-UAGCAG----G-AAG-C-GGAAGGCAACAAC-UGG-C-GC--GUCGAUAUC----------GCGAGAC---GCGU-GG-GAA---CCUCG---------CGCGGUC--UGAGACCC
ABEF01004477.1/823-603         AGAGCC--CCACA-GCG----AAAG-U-CUAG--CGA-A-CUACGU--UGA-CCUCGAG-U-CAUGCGCC---G-G-CG--G-UG-GCGA-CAUCGC-G-GGU-GAAGCGUUG---A--C-A--------GA---GG----------C-----A---CU-----------GGCGG--GCC------------------------------GAUU-A------------UCGAGCCGCG-AAAUACC---------------------UCU-UUUC-GG-G-CG-CCGA-------CCCU---GUGGACAGA---AG-G-GGAAGGCCACAUC-GAC-U-GU--CGCGUUAGC----------GCGAGCG---GCAG-CC-GAG---CCCGG---------CGCGGUCGCGGGAACCC
ABPP01002109.1/48-264          CGAGUCCCGAA-C-CGG---AAAGG-A-CUGG--CCG-U-CCACCG--GAA---UCGAG-U-GUUGCGUG--GU-G-CG--G-GA-GUGA-UCUCGC-C-UGC-GAAGCGUAC---A--C-A--------GA---GGG---------------CGUGUA-----------GGCCGUGU-----------------------------------G-A------------UUGAGCCCCG-AAAGUGG----------------------CACGUGC-GG-A--G-CCGA-------CGUU---GUUAAUGG----UG-C-GGAAGGCAACAGC-AUC-C-CC--AUCGCAAUG----------GCCUGGU---GAGG-AU-GC----UCCGC---------CGGGGUC--GAAGAGCA
ABPY01002352.1/365-133         CCAAUCCAGCGCA-UGC----AACG-G-UUAG--CAG-C-C-AGCA--UGG-AAUCGAA-C-CGCACGUA---U-G-AG--G-AG-GCAA-CAAAUC-A-UGC-GAAGCUGCG---G--UAA--------GAGCG--U---------C-----UCGUCAGC---------CGCAACGCAA-------------------------------GUG-AAG-------GUUAUAAGCCCCG-AAAUGUC--------------------CCUAUGUGC-GA-C-GG-GCCA-------AGGG-----UUUCAUU--CCC-C-CGAAGCCAGCAUC-GUG-C-CG--UCCGCUAC-----------GCGAGGA---CGGC-AC-GGC----ACGC---------CGGGGUC--CCAGACCG
CP000721.1/3720113-3719888     AAAUCC--AUUCU-GAA----AAGA-U-UAAG-UCAA-A-UCAUUC--AG--UAGCGAG-U-CAUGGAGA---U-A-AA--U-AG-GUAA-CUAUUU-A-UUU-UAAGCGUUG---A--C-A--------GC---UA-----------------GGUUGUA---------GGCUU--GAA------------------------------UGUG-A------------AUGAGCCUCG-UAAUAAGUA-----------------UAAAG-UUGG-GA-A-GG-CUGA-------CGGU---GUCGGUUC----UC-U-GAAAAGCAAUAUU-AUG-G-UA--GGCGAUAAU---------GACGAGUC---UACU-AU-AAC---UUCCC---------CGGGGGC--AAAGAGCC
ABPX01010171.1/601-369         CCAAUCCAGCGCA-UGC----AACG-G-UUAG--CAG-C-C-AGCA--UGG-AAUCGAA-C-CGCACGUA---U-G-AG--G-AG-GCAA-CGAAUC-A-UGC-GAAGCUGCG---G--UAA--------GAGCG--U---------C-----UCGUCAGC---------CGCAACGCAA-------------------------------GUG-AAG-------GUUAUAAGCCCCG-AAAUGUC--------------------CCUAUGUGC-GA-C-GG-GCCA-------AGGG-----UUUCAUU--CCC-C-CGAAGCCAGCAUC-GUG-C-CG--UCCGCUAC-----------GCGAGGA---CGGC-AC-GGC----ACGC---------CGGGGUC--CCAGACCG
CP001472.1/747303-747081       AGAGUC--GUACG-GUG----AGGG-C-CUAG--CCA-G-CCACAC--CGG-CUCCGAG-U-CUUGCGGA---U-G-UG--G-CC-GUAA-GGCCAU-G-UAC-GAAGCGUAG---A--C-A--------GG---AGG---------A-----ACUACA-----------GGCCAGGC-----------------------------------U-A------------UUGAGCCGCG-AAAUAUCC------------------CU-AACUUCA-GG-A-CG-CCGA-------CGCC---UUGACACAA---CG-C-GGAAGGCAACAUC-CUG-A-CA--AGCAGUAUG----------GCGAGCU---UGGC-AG-GAG---UCCUG---------CGCGGUC--UAUGACCC
BAAV01010106.1/407-647         AAACUCCUGACCU-GGU---AACUC-UUUGAG--CAA-A-GAGGCC--AGUA-U-CUAGUC-CUUGGGCA---U-U-GU--A-UC-GUGA-GGUACA-G-UGU-UAAGCGUAG---G---AA--------G----G-A---------A-----AGACUUAG---------AGCCCUAAAGCGAAAG-------------------CCUGAAGCA-A------------UCUAGCGUCG-UUAGUAC--------------------CGAUAAAGU-GG-U-GG-GUGA-------UGCU---CUCAUAUU----GG-C-CGCAACCAACAU-AGGU-U-GA--AUCGUUAU-----------GCCAGAU---UCAA-UCUGAC---ACCAC---------CGGCGUU--UUAAAGCA
ACII01000059.1/3997-3773       GAAGCC--CCAUC-AAA---UAAGCUG-CUAA--CCA-CAGCAUUU--GAA---GCGAG-U-CUUGAGUC---U-G-UC--G-CG-GAAA-CGUUGC-A-GGC-UAAGCGUAG---A--C-A--------GC---------------A-----AGAUAACA---------GGGAUAGC-----------------------------------U-A------------UUGAGCACCG-AAAUCCCA------------------AA-GUCACCA-GA-G-GG-UCGA-------CAUC---GUGGUCUG----GA-U-GGAAGACAACAUA-UGU-AUUU--AUCGUUAUG----------GUGAGAU---UUUA-CA-UAC---CUCUG---------CGGUGUUGGUUGGAACU
AM999887.1/355822-356055       AAAAUCCAACAUA-AAC----AAAG-U-CUAG--CCA-A-C-AGUU--UAG-AACAGAC-C-ACUAUGUU---G-C-AU--G-AG-GUAA-CGAGUG-U-AAU-AGAGCUAGU---G--GAA--------UG---GA----------C-----AAUGCA-----------GGGUA--CAACGAAA---------------------GUGAAGGG-A------------UUGAGUCCCG-AAAUACC--------------------UGAAGACAU-AG-A-GG-UCGA-------CAUU---UUCAUUUC----GG-U-GGAAGACAGCAUG-AGG-G-AU--AAUGCAAAG----------GCGAGUU---AUCA-CU-CAC---UCUAU---------CGGGAUC--UGAGACCG
BABE01001424.1/606-826         GAAUGC--CUGUC-UGG---UAAGG-U-CUAA--CCA-A-CCGCCA--GUA---GCGAG-U-CUUGGGUG---A-C-UG--C-CA-GUAA-UGGUAG-U-UGC-UAAGCGUAG---A--C-A--------GC---GAG---------A-----AAAUAGAG---------AGUGU--------------------------------------G-A------------UUGAGCCUCG-AAAUUUU---------------------GAUAUCUA-GA-A-GG-CUGA-------CGUU---UUAAUUCC----AG-C-GGAAAGCAACACA-AAC-C-A-----AAUCGUCA-------UGGUAAUCU---GUGU-UU-UCCACUUUCCC---------UGAAGCA--UCAGAAGC
CP001097.1/1564826-1564607     AGAGUC--UUACA-UGA----AAGG-C-AUAG--CCA-A-CCAUCA--UGG-CCCCGAG-U-CAUGCCUC---G-ACCU--U-CA-GCAA-UGGGG--U-GGG-GAAGCGUUG---A--C-A--------GG---GGA---------A-----CACACA-----------GGCAG-GC-----------------------------------C-A------------UUGAGCUCCG-AAAUCAC---------------------CUCAAUUC-GC-A-GG-CUGA-------CCCU---GUUCAACGA---AG-G-GGAAAGCAACAUC-GGA-C-GU--ACCGAUCAA---------GGCGAGGU---ACGA-AC-GGC---U-CGG---------CGGAGUC--AGGAAAGG
ABSP01059776.1/347-561         AAAGCC---CGUC-CGG---UAGUG-C-UUGA--CCA-G-CGGCCG--GAA---GCGAG-U-CUUGCGCC---G-U-AC--GUGG-GUAA-CCCGUC-C-GGC-GAAGCGUAG---A--C-A--------GU---------------C-----AGUCUGAA---------AGCCAUGC-----------------------------------U-A------------UUGAGCUUCG-AAAGACC-----------------------AGUUGC-GG-G-AG------------CCUCU-GUUUUUCCGACCCCU-G-GGU---CCACGCU-GCG-G-CA--CU--UUAUU---------GGUCU-GG---UGCCAGC-AGU---CCUGC---------CGGAGUC-GACUGAACA
ACMU01000057.1/15585-15356     GGAUUC--CCGUC-GAG---UAAGA-A-CUAG--CCA-U-UCGCUC--GUA---GCGAG-U-CUUGGAGG---G-C-UA--A-AG-GUAA-CUUUAG-U-CUU-UAAGCGUAG---A--C-A--------GUUAGG-------------------UGGC-----------GGAUUUGCUUUACUG---------------------AUCGUUCU-A------------UUCAUCCUGU-UAAUCAUUAUA-------------GGAUGUAGUUGU-UG-G--A-GCGG-------CGGU---AGCGGCGGA---UU-C-G---GUUACUAAA-AAA-A-GG--GGCACUCAU----------AAGAGUG---UCUU-UU-UUC---UCAAU---------A--------UAAGAACU
CP000473.1/9697852-9697636     AGAGUC--AUACA-GGA----AAGG-A-GUAG--CGA---CCAUCC--UGA-CCCCGAG-U-CAUGCGAG---G-G-CA--G-UC-GCGA-GGCUGC-A-CUU-GAAGCGUUG--GA--C-A--------GG---GG----------------CAUAUGUG---------GGCUG-GG-----------------------------------U-A------------AUGAGCUCCGAAAACGGC-----------------------AAUCCA-GG-G-AG-CCGA-------CG------GCGUCAGCCAGUA-C-GGAAGGCAACAGA-GCG-G-CA--CGCGAUCGC----------GCGAGUG---UGCC-GU---G---CCCUG---------CGGAGUC--GAAGACCC
ACII01000148.1/19745-19965     GAAUGC--CUGUC-UGG---UAAGG-U-CUAA--CCA-A-CCGCCA--GUA---GCGAG-U-CUUGGGUG---A-C-UG--C-CA-GUAA-UGGUAG-U-UGC-UAAGCGUAG---A--C-A--------GC---GAG---------A------AAAUA-----------GAGAGUGU-----------------------------------G-A------------UUGAGCCUCG-AAAUUUU---------------------GAUAUCUA-GA-A-GG-CUGA-------CGUU---UUAAUUCC----AG-C-GGAAAGCAACACA-AAC-C-AA--AUCGUCAUG----------GUAAUCU---GUGU-UU-UCCACUUUCCC---------UGAAGCA--UCAGAAGC
AAFX01072698.1/619-839         AGAGUC--GUACA-GGA----AAGG-A-UUAG--CGA-A-CCACCC--UGU-CCCCGAG-U-CAUGCACU---G-G-CA--G-UC-GUGA-GGCUGU-U-GGC-GAAGCGUUG---A--C-A--------GG---GGC---------A-----CCUGCG-----------GGCUG-GG-----------------------------------U-A------------UUGAGCUGCG-AAAUAAU---------------------CGCAAAUC-GG-G-UG-CCGA-------CGCU---GUUCAACAA---AG-C-GGAAGGCCACCUU-GAC-G-GG--AGCGUUAAG---------CGCCAGCG---ACCG-UC-GAA---CCCUG---------CGCAGUC--UGAAGCCC
ABSN01059230.1/362-139         --AGAGUCCUACG-AAG----AAGA-U-GUAG--CCC-A-UCACUU--CGG-CCUCCAG-C-GGAGGGGC---G-A-CU--G-CG-GUAA-CAACGUCG-UCU-UGAGCGUCCG-UG--C-G--------GA---GGG---------U-----CAAGCA-----------GGCUGUGC-----------------------------------U-A------------UUGAGCUCCG-AAAUCAC----------------------CACUCUC-GC-G-UG-CCGA-------CCAU---GUCCUGACA---AG-G-GGAAGGCCACAUC-GCG-G-GC--GUCGCUAUG---------GGCGAGAC---GCCA-GC-GGA---CGCGG---------CGGAGUC--UGAGAACC
ABYT01000157.1/39-279          AAACUCCUAACCU-GG----UAACUCUUGGAG--CAA-AGAGG-CC--AGUA-U-CUAGUC-CUUGGGCA---U-U-GU--A-UC-GUGA-GGUACA-G-UGU-UAAGCGUAG---G---AA--------G----G-A---------A-----AGACUUAG---------AGCCCUAAAGCGAAAG-------------------CCUGAAGCA-A------------UCUAGCGUCG-UUAGUUC--------------------CAACAAAGU-GG-U-GG-GUGA-------UGCU---CUCAUAUA----AG-C-CGCAACCAACAU-AGGU-U-GA--AUCGUUAU-----------GCCAGAU---UCAA-UCGGAC---ACCAC---------CGGCGUU--GUAAUGCA
ABSN01058947.1/63-283          CAAGUCCCCCACA-GCA----AAGG-U-GUAG--CGA-A-CCAUGU--UGU-CCCCGAG-U-CAUGCGUG---G-U-GC--A-UC-GCGA-GGUGCA-G-CGC-GAAGCGUUG---A--C-A--------GG---GGU---------A-----CGUGCA-----------GGCCA-GC-----------------------------------C-A------------UUGAGCCGCG-AAAGAGA---------------------UUCGAUCC-GG-G-UG-CCGA-------CGUU---GUCCGACU----CG-C-GGAAGGCAACACG-CAC-G-GG--CGCGCCAUC----------GCAAGCG---CCCA-UG-CGA---CCCGG---------CGUGGCC--GAAGACCC
ABPS01012783.1/522-296         CAAGCCCCGCCCG-GCG----AAGG-G-UGAG-CCCG-C-CCA-GC--CGG-UAGCGAG-C-CUUGCGAC---G-G-AG--A-CG-GCAA-CGCCUC-C-GGC-GAUGCGUAG---G--CAC--------GC---GAG---------------CGAGUG-----------GGCCGUGG----------------------------------GGAA------------AGCAGCCACGAAAACUAU---------------------GUCAUCCC-GG-G-UG-CCGA-------GGGU---GUUGCGUU----AC-C-UGAAGGCGACGGC-GGU-C-UG--UCCGCAACAG--------GGCGAGGA---CAGG-GC-GCA---CCCGG---------CGGGGUG--UACGACCA
AAFX01019973.1/46-267          AAAGAGCCGCACA-AGA----AAGG-A-GUAG--CGC-A-CCAUUU--UGG-CCCCGAG-U-CAUGCGCC---U-G-GG--U-UC-GUAA-GGAUGC-G-GGC-GAAGCGUUG---A--C-A--------GG---GAU---------A-----CGCACA-----------GGCCA-GG-----------------------------------U-A------------UGGAGCUCCG-AAAUCAC----------------------CACUUCG-GU-G-UG-CCGACCGUGUC-------UUGAUACGG--G------GAAGGCAAUAUG-AAG-G-GC--AGCGUUAGG---------CGCGAGCG---GUCC-UU-CGA---CACCG---------CGGAGUC--AGAGACCC
AAQF01000035.1/2744-2520       UAAGUCCCCCGCA-UGA---UAAAG-G-CUAG--CGA-C-CAGUCA--UGG-CCCCGAG-U-CAUGCGUC--GG-C-CC--G-UC-GUAA-GGCGGG-C-GGC-GAAGCGUUG---A--C-A--------GG---GGU---------A-----CUGGCA-----------GGCCGGGC-----------------------------------U-A------------UUGAGCUCCG-AAAUCAC---------------------CUCAUUCG-GG-U-UG-CCGA-------CCUU---GUUGUAUGA---UG-G-GGAAGGCAGCACU-CUG-G-AG--CGCGCUAUC----------GCAAGUG---CUCC-GG-CGG---ACCCG---------CGGAGUC--AUAGAACC
ABSQ01040172.1/767-543         --AGAGUCUUACA-GGA----AAGG-A-AUAG--CGA-A-CCAUCC--UGA-CCCCGAG-U-CAUGCACG---U-G-UC--U-UC-GCAA-GGGGGC-G-CGC-GAAGCGUUG---G--C-A--------GG---GGC---------A-----CAGGCA-----------GGCAG-GG-----------------------------------U-A------------UUGAGCUGCG-AAAUCAAUC-----------------UUUACGUCCG-GG-G-UG-CCGA-------CGCCG-UUCGGC----G-CAG-C-GGAAGGCCACAUU-AUG-G-GU--GACGAAACA---------CGCGAGCC---AUCC-AU-GAA---CCCUG---------CGCAGCC--AGAGACCC
ABSP01056812.1/340-548         GAAGAGCUUGGCC-------AGUCC-G-CCGG--AGG-C-GGA-----GAA---GCAAG-U-CUUGCGUG--GU-G-GU--G-GA-GCGA-UCCAUC-C-CGC-GAAGCGUAG---A--C-C--------GC---GA----------A-----UGCCCA-----------AGCCGUGU-----------------------------------G-A------------UUGAGCCUCG-AAAUACC-----------------------CAAUGC-CG-G-AG-CCUU-------CGUC---GUGGACAG----AG-C-GGG-GGCCACGUC-GGC-G-UA--CC--GUAUG----------GCCU-GG---UAUG-CC-GAU---CCUGC---------CGGGGUC--GUAGAGCA
ACMM01000163.1/1936-1680       AAAGUCCAAUCGG-GAG---AAUAG------A--CUC---C-ACUC--CCU-UAGCCUG--AGAGGCGCC---A-U-GA--A-GU-GAAA-GCGACA-U-GGC-GAAGCCCUCU-GA--CAUCA---CAUGC---AAA---------A-----GGCAUGUG---------GGCAA--AUCUCCAGGUUGUA--------ACGUACAGUGAACGU-AG----------AUGUAGCCUCG-UUACACG----------------------CAAUUCC-GG-U-GG-CUGA-------GACG---GUCGAUAA----CG-UGCGAAAGCAACAAG-AAC-U-G---ACCGAAAUG---------AGUCUGGAACGGCAG-UU-CUC---ACCGG---------CGGGGUA--UCAGCGGC
CP000724.1/1100219-1100447     GGAACC--CCGCU-GAG---AAAGA-U-UUAG--CAA-A-UCACUC----A-UAGCGAG-U-CUUGGACA---U-C-AU--C-GG-GUAA-CCUAUG-A-UGU-UAAGCGUAG---A--C-AGC----AAGU---UAG---------U-----AGGCCGAA---------AGCGAAAGUUG----------------------------AAGGG-A------------UUGAGCCUCG-AAAUCCC-----------------------CAUUGG-GA-A-GG-UUAA-------UACU---GUGAACCG----AG-U-AGAAAACAACAUC-AAU-A-UA--UUCGCUAA-----------GCGAGAA---UAUA-UU-GGC---UUCCC---------CGGGGUC--AGUGACCU
CP000473.1/8186380-8186164     AGAGUC--AUACA-GGA----AAGG-A-GUAG--CGA---CCAUCC--UGA-CCCCGAG-U-CAUGCGAG---G-G-CA--G-UC-GCGA-GGCUGC-A-CUU-GAAGCGUUG--GA--C-A--------GG---GG----------------CAUCUGUG---------GGCUG-GG-----------------------------------U-A------------AUGAGCUCCGAAAACGGC-----------------------AAUCCA-GG-G-AG-CCGA-------CG------GCGUCAGCCAGUA-C-GGAAGGCAACAGA-GCG-G-CA--CGCGAUAGC----------GCGAGUG---UGCC-GU---G---CCCUG---------CGGAGUC--GAAGACCC
BAAV01019113.1/322-82          AAACUCCUGACCU-GG----UAACUCUUGGAG--CAA-AGAGG-CC--AGUA-U-CUAGUC-CUUGGGCA---U-U-GU--A-UC-GUGA-GGUACA-G-UGU-UAAGCGUAG---G---AA--------G----G-A---------A-----AGACUUAG---------AGCCCUAAAGCGAAAG-------------------CCUGAAGCA-A------------UCUAGCGUCG-UUAGUCU--------------------CGAUAAAGU-GG-U-GG-GUGA-------UGCU---GUCAUAGG----AG-C-CGCAACCAAUAU-AGGU-U-GA--AUUGUUAU-----------GCCAGAU---UCAA-UCGGAC---ACCAC---------CGGCGUU--UUAAAGCA
ACMY01000132.1/2141-1885       AAAGUC--AAAUC-GGG------GG-A-AUAG--AC--U-CCACUCCCGUA---GCCUG--AGAGGCGCC---A-U-GA--A-GU-GAAA-GCGACA-U-GGC-GAAGCCCUCU-GA--C-AUCA--CAUGC---AAA---------A-----GGCAUGUG---------GGCAA--AUCUCCAGGUUGUA--------ACGUACAGUGAACGU-AG----------AUGUAGCCUCG-UUACACG----------------------CAAUUCC-GG-U-GG-CUGA-------GACG---GUCGAUAA----CG-UGCGAAAGCAACAAG-AAC-U-G-AU--CGAAAUG---------AGUCUGGAACGGCAG-UU-CUC---ACCGG---------CGGGGUA--UCAGCGGC
CP000647.1/1330966-1331191     AAAGUCCCCGACCAUUG----AAGG-A-CCAG--CAA-U-CCACAA--GGU-CCCCGAG-U-CAUGCGUU---G-C-AU--A-CC-GCGA-GGUAUG-G-GGC-GAAGCGUUG---A--C-A--------GG---GG----------------UGUUGACA---------GGCCA-GC-----------------------------------C-A------------UUGAGCCACG-AAAUGUAUA-----------------UUAAAUUACC-GG-G-UG-CCGA-------CGUU---GUACUGUU----AA-C-GGAAGGCAACAUC-AUA-G-GG--UGCGAUACU----------GCGAGUG---CCAC-AU-GGA---CCCGG---------CGGGGUC--UGAGACCC
ABSP01053373.1/518-757         AGAGUC-CCGUCA-GCA----AAGG-A-GGAG--CAA-U-CUAUGC--UGU-A-GCGAA-C-AUUGAGUG--AC-C-AAGCC-CG-GUGA-CGGGUA-A-CAC-UAAGCGUAU---G-G--A--------GC-----G---------A-----AUCCCGUA---------GGCCGAAAUGCAUUUA------------------GCGUGAAGCG-A------------UUGAGCUCCG-ACAGAUU---------------------AAUAUUCCACUUA-AG-AUGA-------UGGU---CUAUUCAA----GU-C-AGAAAUCGAAACU-GCA-A-AU--CCCGACAA-----------GCGAGGG---AUGG-GUGAAG---U--GG---------CGGAGUC--UAAGAGCU
CP000232.1/2324972-2325208     AAAGCC---CACC-UGG---UAAGG-U-CUAG--CCA-A-CCGCCA--GUA-GCC--AG-C-CUUGGAGC---C-U-GU--A-GG-GUAA-CCGGCA-G-GUU-UAAGCGUAG---G--U-A---------G---GCA---------A-----GGCAGCGG---------GCCGAAAGCCAUAGC--------------------GCUGAAGGG-A------------UUGAGCCUCG-AAAUAAAA-------------------UUUAGUUGG-GA-G-GG-CCGA-------UGCU---CUGACCCA----AG-C-AGAAGGCAACAUG-GCG-G-UA--AUCAUUAAA---------GGCGAGAC---UACC-GC-CAU---CUCCU---------CGGGGUC--GCAGACCU
AACY020310823.1/6209-5993      CAAGUCCCGAGCC-GGA----AAGG-A-UUGG--CCA-U-CCA-CC--GGA-ACC-GAG-U-GUGGCGUG---GUG-CG--G-GA-GUGA-UCCCGC-C-UGC-GAAGCGUAC---A--C-A---------G---GUG---------G-----CGUGCA-----------GGCUGUGU-----------------------------------G-A------------UAGAGCCUCG-AUACUGA-----------------------UGUCAG-CG-G-AG-CCGA-------CGUA---GUCGGAAGA--C---C-GGAAGGCAACAGC-CUC-G-AC--AUUGUAACG----------GCCUGAU---GGCG-AG-ACU---CCGC----------CGGGGUC--UGAGAGCA
ABSN01056386.1/298-76          AAAGAGCCCCACA-AAG---AAAGG-A-GUAG--CGA-C-CCACUU--UGG-CUGCGAG-U-CUUGCGCG---A-U-GU--C-CG-GCGA-CGGGCA-U-GGC-GAAGCGUAG---A--C-A--------GC---AGA---------A-----UCAGCG-----------GGCUGGGC-----------------------------------U-A------------AUGAGCUUCGAAAAGUAC------------------------CUCCC-GG-A-CG-CCGA-------CCUU---GUUCAUAUA---AG-G-GGAAGGCAACACG-GUG-C-GU--CUCGUAAAU---------CGCGAGAG---GCGC-GC-CGG---UCCGG---------CGUAGUC--AGUGAACC
CP001101.1/59992-60213         GAAGUUUCUUACA-UGA----AAGG-C-UUAG--CCA-G-CCAUCA--UGG-CCCCGAG-U-CAUGCCUC---G-A-UC-GU-CA-GCAA-UGGGAU---GGG-GAAGCGUUG---A--C-A--------GG---GGA---------A-----AACACAGG---------CGUCC--------------------------------------U-A------------AUGAGCUCCGAAAACACC---------------------ACG-AAUC-GC-A-GG-CUGA-------CCCU---AUACUACGG---AG-G-GGAAAGCAAUAUC-GUC-C-AU--CCCGAAAAG----------GCGAGGA---AUGG-GA-GAC---UGCGG---------UGGAGUC--AAAGAACG
AAOF01000003.1/254671-254889   CAAGUCCACGGCA-GUG----AAGG-G-UUAG--CGA-C-CCACGC--UGG-CCCCGAG-U-CAUGCGUC---G-A-UG--U-CC-GCGA-GGACAU-G-GGC-GAAGCGUUG---A--C-A--------GG---GG----------------AGCGUAUA---------GGCCA-GC-----------------------------------C-A------------UUGAGCGGCGAAAAGUUU------------------------UUCUG-GG-G-UG-CCGA-------UGCC---CUCGAAGU----GG-C-AGAAGGCAACACG-GAC-C-GG--CGCGUGAAC----------GCGAGUG---UCGG-CC-CGA---CCCUG---------CGUCGUC--UAAGACCC
ABSN01026997.1/564-776         AAAGCC---CGUC-CGG---UAGCG-C-CUGA--CCA-G-CAGCCG--GAA---GCGAG-U-UUUGCGUG---G-G-GC--G-GG-GCAA-CCCGCA-C-UGC-GAAGCGUAA---A--C-A--------GC-----G---------------AGUCCGAA---------AGCCAUGC-----------------------------------U-A------------UUGAGCGUCG-AAAGACC-----------------------UUUCGU-GG-G-A-----A-------CCUUUGCCUUUCGAGCACCAA-G-GGC----CACGUC-GCG---GC--ACUGUAAUG----------GUCUGGU---GUCC-GC-GGU---CCUGC---------CGGCGUC--GGAGUGGA
CP000448.1/177545-177775       GGAAUC--CCGUC-CGG---UAAGG-U--UAG--CCA-A-CCGCCG--GUA-AU--UAG-U-CUUGGAGG---G-C-AG--A-GG-GUAA-CCGCUG-U-CUU-UAAGCGUAG---A--C-AAA---CAAGC---AAA---------C-----GGGCCGAA---------AGCAGUAGCUG----------------------------AAGGU-G------------UUGAGCCCCG-AAAUACC---------------------GAACAUGG-GA-A-GG-CAGA-------UGCU---AUUGCCUG----AG-C-AGAAUGCAACAUC-CUG-G-AA--GUCGAUAAG----------GCUAGAC---G-AC-AG-GAC---UUCCC---------CGGAGUC--GGAGGCCU
ACII01000033.1/1141-921        GUGGUC--CCAUC-AAA---UAAGCUG-UUAA--CCA-CAGCAUUU--GAA---GCGAG-U-CUUGAGUC---U-G-UU--A-CG-GUAA-CGU-GA-A-GGC-UAAGCGUAG---A--C-A--------GC---AAG---------------AUAGCA-----------GGGAUAGC-----------------------------------U-A------------UGGAGCACCG-AAAUCCC--------------------AAAGUAUCA-GA-G-GG-UCGA-------CACC---GUGGUCAG----GG-U-GGAAGACAAUAUA-UGC-ACUU--AUCGUUAUG----------GUGAGAU---UUUG-CA-UGC---CUCUG---------CGGUGUU--GUUGAAAC
CP000249.1/2696740-2696963     UAAACC--GGCCU-UAGG-AUAAGG-A-GUAG--CGA-U-CCACGA--CGA-CCCCGAG-C-CAUGUGGC---U-G-CU--U-CC-GCAA-GGGGGC-G-GCU-GAAGCGUUG---G--U-A--------GG---GGC---------A-----CGUGUA-----------GGCCAGGC-----------------------------------U-A------------UUGAGCCGCGAAAUGAGA-----------------------AGACCG-GGUG-CG-CCGA-------CGUG---GUCGAAAG----CA-C-GGAAGGCAACACC-GUC-G-CG--AGCGCUAGA---------CGCGAGUU---CGGG-AC-GGG---CCCCG---------CGCGGUC--GGAGAACC
AAQK01004255.1/899-663         GGAAUC--CAGUC-UGG---UAAAA-C-CUAG--CAA-G-UUGCCA--GUA---CCAAGAC-CUUGGAGC---A-C-CA--A-AG-GCUAACAAUGG-U-GUU-UAAGCGUAG---G-AC-A--------GG---AA----------A-----CAGGAA-----------CGCCGUAAUGCGUAAG-------------------CGUGAAGUG-A------------UUGAGCUCCG-UUAGAAUU------------------AU-CGAUUGU-GU-G-GG-GUGG-------UCUA-----CUACUUU--CUU-G-GGUCACCAACAA--GGA-U-UA--GUCGCUAAA----------GCGAGAC---UAUG-AA--AA---CACAC---------CGGAGUC--CUAGAGCA
BABG01031395.1/279-58          GGAUUCCGGUUUA-UCC----AAGG-U-UUAG--CCA-A-CCA-GA--UAA-UAGCGAG-U-CUUGGGAU---G-A-UG--C-CG-GUAA-CGGCAU-C-UGA-CAAGCGUAG---A--C-A--------GC---AAG---------A-----A-AGCA-----------GGGUUGAAUA-------------------------------GUG-A------------UUGAGCUUCG-AAACGUU----------------------AACUUCA-GU-C-GG-UCGA-------CGU----CUUAACUGG--U-G-C-GGAAGACAAUAUC-AUG-U-AA--UGCGAUAUG----------GCGAGUA---UUAU-GU-GGC----ACUG---------CGGAGUC--AGAGAACC
AACY023748197.1/147-376        AAACACCUAAACUGACGGGGUAAGU-A-GAAG--AUC-U-ACCUGUAAAGU-GCCCGAG-U-CAUGCGCA---U-G-UG--G-GC-GUGA-GGCCAU-G-UGU-GAAGCGUUG---A--C-A--------GG---GU----------------UGCAAAUA---------GGCCA-AG-----------------------------------U-A------------UUGAGCCCCGUAAUAAAA---------------------CAAUUCCA-GG-A-UG-CCGA-------CGCCU-UAGGAG----G-CUG-C-GGAAGGCCACAAC-CGG-U-AG--UUCGCUUUG----------GCAAGAG---CUGC-UG-GUA---UCCUG---------CGGGGUC--UAAGACCU
ACMP01000084.1/64966-64737     GGAUUC--UCGUC-GAG---UAAGA-A-CUAG--CCA-U-UCGCUC--GUA---GCGAG-U-CUUGGAGG---G-C-UA--A-AG-GUAA-CUUUAG-U-CUU-UAAGCGUAG---A--C-A--------GU-----U---------A-----GGUGGC-----------GGAUUUGCUUUACUG---------------------AUCGUUCU-A------------UUCAUCCUGU-UAAUCAUUAUA-------------GGAUGUAGUUGU-UG-G--G-GCGG-------CGGU---AGCGGCGGA---UU-C-GGUUACUAAAAAA-AGG-G-GU--ACUCAUAAG--------------GGU---GUCU-UUUUUC---UCAAU---------A--------UAAGAACU
ABYT01000048.1/91171-90950     GGAUUCCGGUUUA-UCC----AAGG-U-UUAG--CCA-A-CCA-GA--UAA-UAGCGAG-U-CUUGGGAU---G-A-UG--C-CG-GUAA-CGGCAU-C-UGA-CAAGCGUAG---A--C-A--------GC---AAG---------A-----A-AGCA-----------GGGUUGAAUA-------------------------------GUG-A------------UUGAGCUUCG-AAACGUU----------------------AACUUCA-GU-C-GG-UCGA-------CGU----CUUAACUGG--U-G-C-GGAAGACAAUAUC-AUG-U-AA--UGCGAUAUG----------GCGAGUG---UUAU-GU-GGC----ACUG---------CGGAGUC--AGAGAACC
BA000040.2/2069375-2069595     AAAGUCCAUUGCG-AUG----AAGG-U-GUAG--CGA-A-CCACAU--CGG-CCCCGAG-C-CGUGCGCA---G-G-CG--U-CC-GCGA-GGGUGU-C-GGC-GAAGCGUCG---G--U-A--------GG---GG----------------AGCAUGCA---------GGCCA-GC-----------------------------------C-A------------UUGAGCCGCG-AAACAGU---------------------GUUAUCUC-GG-G-AG-CCGA-------CGCU---GUCCAAAG----AG-C-GGAAGGCAACAUG-GAU-G-AG--UGCGCAAUU----------GCGAGCA---CCCG-UC-CAA---CCCGG---------CGUGGUC--GUAGACCC
ABBM01001064.1/1918-1697       AAAGUCCUUUGCG-AUG----AAGA-A-CUAG--CGA-A-UCACAU--CGA-CCCCGAG-U-CAUGCGGG---G-G-CA--C-UC-GCGA-GAGUGU-C-ACC-GAAGCGUUG---A--C-A--------GG---GG----------------CGCACGUA---------GGCCA-GC-----------------------------------C-A------------UUGAGCGACG-AAAGACU--------------------UCCCAAUCG-GA-G-UG-CUGA-------UGCU-----UUCCAGU--CAG-C-AGAAGGCAAUACG-UCC-C-AC--CGCGAUAUC----------GCGAGCG---GUGG-G--CGG---CUCCG---------CGUCGUC-GGUAGACCC
AAQF01000035.1/6913-6690       CAAGUCCCCCGCA-UGA---UAAAG-G-CUAG--CGA-C-CAGUCA--UGG-CCCCGAG-U-CAUGCGUC--GG-C-CC--G-UC-GUAA-GGCGGG-C-GGC-GAAGCGUUG---A--C-A--------GG---GGU---------A-----CUGGCA-----------GGCCGGGC-----------------------------------U-A------------UUGAGCUCCG-AAAUCAC---------------------CUCAUCCG-GG-U--G-CCGA-------CCUU---GUGGUCUGA---GG-G-GGAAGGCAGCACG-CUG-G-AG--UGCGCUAAC----------GCAAGUG---CUCC-AG-CGG---ACCCG---------CGGAGUC--GUAGAACC
ABSP01001842.1/467-251         CCAAUC--CCAUC-CGG---CACAG-C-GGGU--CC--G-CAGCCG--GAA---CCGAG-U-GUUGCGCG--UG-C-CG--C-GG-GUAA-CUGCGG-G-CGU-CAAGCGUAC---A--C-A--------GG---GAG---------------CAUGCA-----------GGCCGCGU-----------------------------------G-A------------UUGAGCCUCG-AAAGCGU---------------------CACUGCGU-GG-G-AG-CCGA-------CGCC---GUCGGAACA---GG-C-GGAAGGCCGUGCU-GC--C-GU--GCCGAGAGG----------ACCGGGC---ACG--GC-GGU---CCCAC---------CGGGGUC--UGAGAGCG
ABSP01011098.1/441-217         AAAGAGCCCUACC-GGA----AAGG-A-GCAG--CGACU-CCAUCC--UGA-CCUCGAG-U-CUUGCGCC---G-G-UC--G-UC-GCGA-GGCGGC-A-GGC-GAAGCGUAG---A--C-A--------GA---GGC---------A-----UCGGUG-----------GGCUGGGC-----------------------------------G-A------------UUGAGCUCCG-AAAACAA-----------------------AGAACC-GG-G-CG-CCGA-------CCCU-----UUUCUGU--CAGCG-GGAAGGCCACACC-GGC-CGAU--GGCGCUAGAU--------CGCGAGUC---AUGG-CC-GGG---CCCGG---------CGUAGUC--GAAGACCC
CP000820.1/3622687-3622467     GAAGAGCUCUGCG-UCG----AAGG-G-CUAG--CGA-C-CCACGG--CGA-CCCCGAG-U-CAUGCGUC---G-A-CG--U-CCCGCGA-GGGCGU---GGC-GAAGCGUUG---A--C-A--------GG---GGC---------A-----CGUGCA-----------GGCCGGGC-----------------------------------U-A------------UGGAGCCGCG-AAAUGAA---------------------GCA-UCCG-GG-G-UG-CCCA-------CGCU-----GUACAAG--AGG-C-GGAAGGCCACACU-ACU-G-GC--GGCGCUAUC----------GCGAGUC---GUCG-GU-GGA---CCCUG---------CGCGGUC--AAAGAACC
ABPR01001428.1/263-48          CGACCCCCGUUCG-GUA----AAGG-C-GCAG--CCC-G-CCA-GC--CGG-AAGCGAG-U-CUUGCACG---G-A-CG--U-CG-GUGA-CGACGU-U-CGU-GAAGCGUAG---A--C-A--------GC---GGU---------------CGCUGA-----------AGCCGUGC-----------------------------------G--------------UC-AGCCUCG-AAAUCAU---------------------GGUCCUGU-CG-A-AG-CCUU-------CGGUG-UGUUG-----G-UCC-C-GGG-GGCAGCACC-GGA-A-AG--UCCGUCAUC---------GGCGAGGA---C-GA-CC-GGU---UCGAC---------CG-GGUC--UCGGACAC
BX571862.1/162169-161948       AAAGUC-CCUUCC-GGG---UAAGA-G-CUAG--CCA-C-UCACCU--GGC-CCUUUAG-C-UAUGCGCG---A-C-UG--U-GG-GUAA-CUCCUG-U-CGU-GAAGUGUUA---G--C-G--------AA---GGC---------A-----CUCACA-----------GGCCA-GG-----------------------------------U-A------------UUGAGCCACG-AAAUCGG---------------------UAAAUCGG-AG-G-UG-GUGAUGCAGUU-------AAGGUAAGC--A------GAAACCCACAAU-GGU-C-AG--GUUGUAUUG----------GCGAAAC---CUGA-CC-AUA---CCUCC---------CGGGGUC--GGAGACCC
ABSP01033910.1/582-364         AGAGUCCUGUCUG-GCC---AAAGC-C-GUAG--CG--G-GCAGGC--CAG-GACCGAG-U-CUUGCAGG---C-G-CU--G-CG-GUAA-CGCAGG-G-UCU-GAAGCGUAG---A--C-A--------GG---GGU---------------CGUGCA-----------GGGUG-CG-----------------------------------G-A------------GUAAGCCCCGAAAAGCUG---------------------AAUCUCGU-GG-A-GG-CCGA-------AUGG---GUUCCCGU----CC-A-UGAAGGCAGCAUG-UGC-A-UC--AUCGUUAC-----------GCGAGAU---GAUG-U--UGC---UCCAC---------CGGGGUC--GUGGACCG
ABSQ01017945.1/417-671         GAAGAUCCCGCCG-GGG---UAGCG-G-CUAG--CCA-C-CGGCCC--CGUAUCG--AG-U-CUUGCAGC---G-C-GG--G-CG-GCAA-CGGCCG-C-GUU-GAUGCGUAG---A--U-A---------C---GA----------A-----AGCAAGCGAGGACCAAUGGAGCUGGGCGGNCCCCA--------------GUCCGUGAAGGU-A------------UUGAGCCCCG-AAAUCUUG------------------UUCCUGACGG-AGCG-CG-CCGA-------GGUG---AUCUGCAU----CA-C-CGCAGGCAACACC-CUG-C-GC--CGCGCGGCG----------GCGAGUG---GCGU-GG-GGG---C-ACC---------CGGGGUC--GGAGGCCG
CP001390.1/1069306-1069527     AAAGUCUCAUACG-AUG----AAGG-A-GUAG--CGA-A-CCGCAU--CGG-CCCCGAG-U-CAUGCGCA---G-U-CG--U-CC-GUGA-GGACGG-C-UGC-GAAGCGUUG---A--C-A--------GG---GG----------------GGAUGU-----------GGGCCAGG-----------------------------------U-A------------UUGAGCCGCGAAAAGACC---------------------CUCAUCCG-GG-G-UG-CCGA-------CGCCA-UCGAGG----G-CAG-C-GGAAGGCAAAACG-GGA-U-GU--CUCGUAAGC----------GCGAGAA---GCAU-UC-CGA---CCCCG---------CGUGGUC--UUAGACCC
ABPP01011700.1/208-417         ACAUGCCAUCCUC--------CCUG-G-AUCC--CCG-C-CAC-----GAG-CUCC--G-C---CGCGUC---C-A-AC--A-GG-GGCU-CGAACU-U-CGU-GAAGC-------C--C-A--------GG---GGC---------A-----CGUGCA-----------GGCCG-GG-----------------------------------U-A------------UUGAACCGCGAAAAGUCC---------------------CACUUCCG-GG-A-CG-CCGA-------CGUC---GCUAGGGGU--CGA-U-GGAAGGCAACAUC-GGU-C-GC--ACCGUCAUC----------GCAAGGC---GCGA-CU-GAG---UCCCG---------CGCGGUC--UGAGACCC
CP000492.1/2465212-2464990     CAAGUC-CCUGCA-GUG---AAAGG-A-UUAG--CGA-U-CCGCAC--UGG-CCCCGAG-U-CAUGCGCG---C-A-UA--A-CC-GCGA-GGAUAU-G-CGC-GAAGCAUUG---A--C-A--------GG---GG----------------UGCAUAUA---------GGCCA-GC-----------------------------------C-A------------UUGAGCGGCGAAAAUGAG---------------------CAAAUAUG-GG-G-AG-CCCA-------UGC----CCUCCUAAA--A-G-C-AGAAGGCAAUACA-GACGA-AG--UGCGAUAAU----------GCGAGCA---CAAG-AC-UGU---CCCCA---------CGACGUC--AGAGAACC
CP000648.1/119297-119522       AAAGUCCCCGACCAUUG----AAGG-A-CCAG--CAA-U-CCACAA--GGU-CCCCGAG-U-CAUGCGUU---G-C-AU--A-CC-GCGA-GGUAUG-G-GGC-GAAGCGUUG---A--C-A--------GG---GG----------------UGUUGACA---------GGCCA-GC-----------------------------------C-A------------UUGAGCCACG-AAAUGUAUA-----------------UUAAAUUACC-GG-G-UG-CCGA-------CGUU-----GUACUGU--UAA-C-GGAAGGCAACAUC-AUA-G-GG--UGCGAUACU----------GCGAGUG---CCAC-AU-GGA---CCCGG---------CGGGGUC--UGAGACCC
AACY021965703.1/681-445        AGAGUCCUCAUAG-GAA----AGCG-G-UUCC--CG--C-CGUAUC--CUA-AAUCGAG-U-UUUGAGUG---U-A-UG--G-AG-GUGA-CGACAU-G-GAC-UAAGCGUAA---A--C-A--------GA-----G---------A-----UGAAGCAG---------GCCGUAAGGGGGUGUC------------------CCCUGAAGUG-A------------UUGAGCCUCGAAAAGUCG-----------------------AGAUAG-AA-U-GG-CCGA-------CACU---UUCGCAAU----AG-U-GGAAGGCAACAUC-GUU-A-UA--CCUGUAAUG----------GGUAGGG---UAUA-AU-GGC---AUUCU---------CGGGGUC--UUAGAGCA
CP001046.1/171975-171755       UGAGUCCACUACG-AUG----AAGG-C-AUAG--CGA-G-CCACAU--CGC-CCCCGAG-C-CGUGCGCG---G-G-CA--U-CC-GCGA-GGAGGU-C-AGC-GAAGCGUCG---G--C-A--------GG---GGA---------A-----UGUGUA-----------------GGCC------------------------------AGCC-A------------UGGAGCCACGAAAUGGUU---------------------UAUAUCCC-GG-A-UG-CCGA-------CGCG-----CUCCAGU--ACG-U-GGAAGGCAAUACG-AGC-G-GG--CGCGACAUC----------GCGAGUG---CCUG-C--CGA---UCCGG---------CGUGGUC--GUAGAACC
AAQL01011280.1/141-362         GGAAUCCGAUUUA-UCC----AAGG-U-CUAG--CCA-G-CCA-GA--UAA-UAGCGAG-U-CUUGGGAU---G-U-UG--U-UG-GUAA-CAGCAA-C-UGA-CAAGCGUAG---A--C-A--------GC---AAG---------A-----AAGCAG-----------GGUUG--CAA------------------------------UGCU-A------------UUGAGCCUCGAAAAGUUA-----------------------ACUUCA-GU-A-GG-CCGA----------CG-UCUUAACUGGUGCG-----GAAGGCAACAGC-ACA-C-AA--GUCAUUAUG----------GCGAGAA---UUGU-GU-GGC----GCUG---------CGGGGUC--AAAGGGCC
ABSN01002238.1/314-91          AAAGUCCCUGACG-ACC----AAGA-C-CUAG--CGA-G-UCAUGU--UGU-CCCCGAG-U-CAUGCGCA---G-U-GC--A-UC-GCGA-GGUGCG-C-GGC-GAAGCGUUG---A--C-A--------GG---GGU---------G-----CGUGUA-----------GGCCA-GC-----------------------------------C-A------------UUGAGCCACG-AAAUGUUU------------------AUUCAGACCC-GG-G-UG-CCGA-------CGCU---GUUACUGG----CG-C-GGAAGGCAACACG-UGA-G-GG--CGCACCAUC----------GCAAGUG---CCCG-CA-CGA---CCCGG---------CGGGGUC--ACAGACCC
BX571862.1/231587-231808       AAAGUC-CUUUCC-GGG---UAAGA-G-CUAG--CCA-C-UCGCUC--GGU-CCUUUAG-C-UAUGCGCG---A-C-UG--U-GG-GUAA-CUCCUG-U-CGU-GAAGUGUUA---G--C-G--------AA---GGC---------A-----CUCACA-----------GGCCA-GG-----------------------------------U-A------------UUGAGCCACG-AAAUCGG---------------------UAAAUCGG-AG-G-UG-GUGAUGCAGUU-------AAGGUAAGC--A------GAAACCCACAAU-GGU-C-AG--GUUGUAUUG----------GCGAAAC---CUGA-UC-AUA---CCUCC---------CGGAGUC--GGAGACCC
CP001108.1/85791-86013         CAAGUC-CCUGCA-GUG---AAAGG-G-UUAG--CGA-C-CCGCAC--UGG-CCCCGAG-U-CAUGCGCA---C-A-UA--G-CC-GCGA-GGGUAU-G-CGU-GAAGCGUUG---A--C-A--------GG---GG----------------UGCAUAUA---------GGCCA-GC-----------------------------------C-A------------UUGAGCGGCGAAAAUGAG---------------------CAAAUCUG-GG-G-AG-CCCA-------UGCC---CUCCUAAU----AG-C-AGAAGGCAAUACA-GUCGA-AG--UGCGAUAAC----------GCGAGCA---CAAG-AC-UGU---CCCCA---------CGACGUC--AGAGAACC
AAQF01000070.1/13340-13564     CAAGUCCCCCACA-UGA---UAAAG-G-CUAG--CGA-C-CAGUCA--UGG-CCCCGAG-U-CAUGCGUC--GG-C-CC--G-UC-GUAA-GUCGGG-C-GGC-GAAGCGUUG---A--C-A--------GG---GGU---------A-----CUGGCA-----------GGCCGGGC-----------------------------------C-A------------UUGAGCUCCG-AAAUCAC---------------------CUCAUCCG-GG-U-UG-CCGA-------CCUU---GUGGUCUGA---UG-G-GGAAGGCAGCACG-CUG-G-GG--CGCGCUAUC----------GCAAGUG---UUCC-GG-CGG---ACCCG---------CGGAGUC--GCAGAACC
BABG01001153.1/904-1121        ----UCCGGUUUA-UCC----AAGG-U-UUAG--CCA-A-CCA-GA--UAA-UAGCGAG-U-CUUGGGAU---G-A-UG--C-CG-GUAA-CGGCAU-C-UGA-CAAGCGUAG---A--C-A--------GC---AAG---------A-----A-AGCA-----------GGGUUGAAUA-------------------------------GUG-A------------UUGAGCUUCG-AAACGUU----------------------AACUUCA-GU-C-GG-UCGA-------CGU----CUUAACUGG--U-G-C-GGAAGACAAUAUC-AUG-U-AA--UGCGAUAUG----------GCGAGUG---UUAU-GU-GGC----ACUG---------CGGAGUC--AGAGAACC
AAQF01000022.1/13251-13475     UAAGUCCUCUACA-UGG---UAAAG-G-CUAG--CGA-C-CAGCCA--UGA-CCCCGAG-U-CAUGCGUC--GG-C-CA--U-CC-GUGA-GGAUGG-C-GGC-GAAGCGUUG---A--C-A--------GG---GG----------G-----UGUGCA-----------GGCCGGGC-----------------------------------U-A------------UUGAGCUCCG-AAAUCAC---------------------CUCAUCCG-GG-U-UG-CCGA-------CCUU---GUGGUCUGA---GG-G-GGAAGGCAUCACG-UUG-U-GC--CGCACUACU---------CGCAAGUG---GCCC-AG-CGG---ACCCG---------CGGAGUC--GAAGAACC
ABSR01035198.1/565-787         AAAGAGUCAUACG-GUG----AAGG-G-CUAG--CGA-C-CCACGC--CGG-CCCCGAG-U-CAUGCGGA---G-C-UG--C-CU-GCAA-GGGCAG-C-GUC-GAAGCGUUG---A--U-A--------GG---GGC---------A-----CGUGCG-----------GGCCG-GG-----------------------------------U-A------------UUGAGCCGCG-AAAGAAC--------------------AUGCCUUCG-GG-G-UG-CCGA-------CGCU---GUCAGGAGA---AG-C-GGAAGGCCCCACC-CGG-C-GC--AUCGAUAGC----------GCGAGAU---GCGG-CG-GGA---CCCCG---------CGCGGUC--AGAGACCC
CP000473.1/8176067-8175851     AGAGUC--AUACA-GGA----AAGG-A-GUAG--CGA---CCAUCC--UGA-CCCCGAG-U-CAUGCGAG---G-G-CA--G-UC-GCGA-GGCUGC-A-CUU-GAAGCGUUG--GA--C-A--------GG---GG----------------CAUAUGUG---------GGCUG-GG-----------------------------------U-A------------AUGAGCUCCGAAAACGGC-----------------------AAUCCA-GG-G-AG-CCGA-------CG------GCGUCAGCCAGUA-C-GGAAGGCAACAGA-GCG-G-CA--CGCGAUAGC----------GCGAGUG---UGCC-GU---G---CCCUG---------CGGAGUC--GAAGACCC
CP000820.1/4404640-4404862     GAAGAGCUCUACG-UCG----AAGG-A-GUAG--CGA-C-CCACGA--CGA-CCCCGAG-C-CAUGUGGC---U-G-CU--U-CC-GUAA-GGGGGC-U-GCU-GAAGCGUUG---G--U-A--------GG---GGC---------A-----CGUGUA-----------GGCCGGGC-----------------------------------U-A------------UUGAGCCGCG-AAAUGAA---------------------CAGUUCCA-GG-G-UG-CCGA-------CACG---UUCAGAUC----CG-U-GGAAGGCAACACC-GCC-G-GG--AGCGUUAGU---------CGCGAGUU---CCCG-GG-GGA---CCCGG---------CGCGGUC--AGAGAACC
ACNE01000186.1/6155-5899       AAAGUCCAAUCGG-GAG---------A-AUAG-ACUCCA----CUC--CCG-UAGCCUG--AGAGGCGCC---A-U-GA--A-GU-GAAA-GCGACA-U-GGC-GAAGCCCUCU-GA--C-AUCA--CAUGC---AAA---------A-----GGCAUGUG---------GGCAA--AUCUCCAGGUUGUA--------ACGUACAGUGAACGU-AG----------AUGUAGCCUCG-UUACACG----------------------CAAUUCC-GG-U-GG-CUGA-------GACG---GUCGAUAA----CG-UGCGAAAGCAACAAG-AAC-U-G---ACCGAAAUG---------AGUCUGGAACGGCAG-UU-CUC---ACCGG---------CGGGGUA--UCAGCGGC
AAQF01000035.1/29388-29164     UAAGUCCUCUGCA-UGA---UAAAG-G-CUAG--CGA-C-CAGUCA--UGG-CCCCGAG-U-CAUGCGUC--GG-C-CC--G-UC-GUAA-GGCGGG-C-GGC-GAAGCGUUG---A--C-A--------GG---GGU---------A-----CUGGCA-----------GGCCGGGC-----------------------------------U-A------------UUGAGCUCCG-AAAUCAC---------------------CUCAUCCG-GG-U-UG-CCGA-------CCUU---GUGGUCUGA---UG-G-GGAAGGCAGCACG-CUG-G-AG--UGCGCUAAC----------GCAAGUG---CUCC-GG-UGA---ACCCG---------CGGAGUC--GUAGAACC
ABBM01001155.1/212-1           CAAGUCCAUUACG-AUG----AAGG-U-GUAG--CGA-U-CCACAU--CGG-CCCCGAG-C-CGUGCGCA---G-G-CG--U-CC-GCGA-GGAUGU-C-GGC-GAAGCGUCG---G--C-A--------GG---GGA---------G-----CGUGCA-----------------GGCC------------------------------AUCC-A------------UUGAGCCGCGACAUCUAC---------------------GACAUCCU-GG-G-UG-CCGA-------CGUC-----GUUCUGA--AGA-C-GGAAGGCAACACG-GCG-G-GG--CGCGUCAUC----------GCAAGCG---CUUC-GA-CGA---CCCGG---------CGCG-------G-----
CP000492.1/3014517-3014295     CAAGUC-CCUGCA-GUG---AAAGG-A-UUAG--CGA-U-CCGCAC--UGG-CCCCGAG-U-CAUGCGCG---C-A-UA--A-CC-GCGA-GGAUAU-G-CGC-GAAGCAUUG---A--C-A--------GG---GG----------------UGCAUAUA---------GGCCA-GC-----------------------------------C-A------------UUGAGCGGCGAAAAUGAG---------------------CAAAUUUG-GG-G-AG-CCCA-------UGC----CCUCCUAAA--A-G-C-AGAAGGCAAUACA-GACGA-AG--UGCGAUAAC----------GCGAGCA---CAAG-AC-UGU---CCCCA---------CGACGUC--AGAGAACC
CP001157.1/2471442-2471664     AAAGUUCGAUACU-GGU----AAGA-A-AUGG--CGA-A-UCAACC--AGC-CCCCGAG-U-CAUGCACG---U-U-GC--A-CC-GUGA-GGUGCA-G-GGU-GAAGCGUUG---A--C-A--------GG---GG----------------AAACCGAU---------GGGCCAGC-----------------------------------C-A------------UUGAGCCGCGUAAUCAGA-----------------------AAUCCG-GG-A-CG-CCGA-------UGCU---GUUAAGCGA---AG-C-AGAAGGCAAUACG-GGG-C-AU--GGCGUUAUA---------CGCCAGUC---AUGC-CC-UGG---UCCUG---------CGCGGUC--GGAGACCC
AAQF01000095.1/15272-15496     GAAGUCCCCCGCA-UGA---UAAAG-G-CUAG--CGA-C-CAGUCA--UGG-CCCCGAG-U-CAUGCGUC--GG-C-CC--G-UC-GUAA-GGCGGG-C-GGC-GAAGCGUUG---A--C-A--------GG---GGA---------A-----CUGGCA-----------GGCCGGGC-----------------------------------U-A------------UUGAGCUCCG-AAAUCAC---------------------CUCAUCCG-GG-C-CG-CCGA-------CCCU---GUUGUACGA---AG-G-GGAAGGCAGCACG-CUG-U-AG--CACGCUAUC----------GCAAGUG---CUCC-AG-CGG---ACCCG---------CGGAGUC--AUAGAACC
CP000820.1/3393705-3393922     GCAUUUGUUUACG-CCG----CA-----CUAG--CGA-C-CCACGG--CGA-CCCCGAG-U-CAUGCGUC---G-A-CG--U-CCCGCGA-GGGCGU---GGC-GAAGCGUUG---A--C-A--------GG---GGC---------A-----CGUGCA-----------GGCCGGGC-----------------------------------U-A------------UGGAGCCGCG-AAAUGAA---------------------GCA-UCCG-GG-G-UG-CCCA-------CGCU-----GUACAAG--AGG-C-GGAAGGCCACACU-ACU-G-GC--GGCGCUAUC----------GCGAGUC---GUCG-GU-GGA---CCCUG---------CGCGGUC--AAAGAACC
CU928144.1/6288-6513           AAAGUCCCCGACCAUUG----AAGG-A-CCAG--CAA-U-CCACAA--GGU-CCCCGAG-U-CAUGCGUU---G-C-AU--A-CC-GCGA-GGUAUG-G-GGC-GAAGCGUUG---A--C-A--------GG---GG----------------UGUUGACA---------GGCCA-GC-----------------------------------C-A------------UUGAGCCACG-AAAUGUAUA-----------------UUAAAUUACC-GG-G-UG-CCGA-------CGUU---GUACUGUU----AA-C-GGAAGGCAACAUC-AUA-G-GG--UGCGAUACU----------GCGAGUG---CCAC-AU-GGA---CCCGG---------CGGGGUC--UGAGACCG
AAFX01094613.1/793-550         AAAGUUUCAUACA-GUG----AAGG-A-GUAG--CGA-U-CCACAC--UGG-CUCCGAG-U-CAUGUGCC---U-U-GG--U-UC-GCAA-GAGCGA-G-GGU-GAAGCGUUG---A--C-A--------GG---GGU---------A-----CGUGCA-----------GGCGA-GG-----------------------------------U-A------------UUGAGCCGCGAAAAUGAACCACCAUCGCGCAAGCGGUGGCCACUUCU-GG-G-UG-CCGA-------CGCUU-UUGAAC----G-GAG-C-GAAAGGCAAAACU-GGA-G-GC--GUCGCAAUG----------GCGAGAC---GCUC-UC-GGA---CCCGG---------CGCGGUC--UACGACCC
ABSP01001654.1/1357-1114       AAAGUUUCAUACG-UUG----AAGG-C-UUAG--CCA-G-CUACGG--CGG-CCCCGAG-U-CAUGCGUG---C-A-CA--U-UC-GUGA-GGGUGU-G-GGC-GAAGCGUUG---A--C-A--------GG---GGG---------A-----CGCGCG-----------GGCCG-GG-----------------------------------U-A------------UUGAGCUGCGCAAUCCAUGCCCUGGGCCGAGAGGCUCGGGACGAUCG-GG-G-UG-CCGA-------GGCA---GUGGAGAUA---UG-C-CGAAGGCCACACC-GUG-C-CU--GCCGCAUUG----------GCGAGGC---AGGC-AU-GGA---CCCCG---------CGCAGUC--ACAGACCC
CP000092.1/479295-479516       CAAGUCCACUGCG-AUG----AAGG-A-AUAG--CGA-A-CCACAU--CGG-CCCCGAG-C-CGUGCGCA---G-G-CC--A-CC-GUGA-GGUGGU-C-GGC-GAAGCGUCG---G--U-A--------GG---GAA---------A-----CGUGCG-----------------GGCC------------------------------AGCC-A------------UUGAGCUGCGAUAGUUGU---------------------GCAAUUCC-GG-G-UG-CCGA-------CGCG-----GUUGAGA--ACG-C-GGAAGGCAACAAG-AAG-G-GG--CGCGUGAAC----------GCGAGUG---CCUC-AA-CGA---CCCGG---------CGUGGUC--UAAGGCCU
AF027768.1/2532-2307           AAAGUCCCCGACCAUUG----AAGG-A-CCAG--CAA-U-CCACAA--GGU-CCCCGAG-U-CAUGCGUU---G-C-AU--A-CC-GCGA-GGUAUG-G-GGC-GAAGCGUUG---A--C-A--------GG---GG----------------UGUUGACA---------GGCCA-GC-----------------------------------C-A------------UUGAGCCACG-AAAUGUAUA-----------------UUAAAUUACC-GG-G-UG-CCGA-------CGUU---GUACUGUU----AA-C-GGAAGGCAACAUC-AUA-G-GG--UGCGAUACU----------GCGAGUG---CCAC-AU-GGA---CCCGG---------CGGGGUC--UGAGACCC
CP001097.1/2496440-2496221     AGAGUC--UUACA-UGA----AAGG-C-AUAG--CCA-A-CCAUCA--UGG-CCCCGAG-U-CAUGCCUC--GA-C-CA--A-CA-GCAA-UG--GG-GUGGG-GAAGCGUUG---A--C-A--------GG---GGA---------A-----CACACA-----------GGCAG-GC-----------------------------------C-A------------UUGAGCUCCG-AAAUCAC---------------------CUCAAUUC-GC-A-GG-CUGA-------CCCU---GUUCAACGA---AG-G-GGAAAGCAACAUC-GGA-C-GU--ACCGAUCAA---------GGCGAGGU---ACGA-AC-GGC---U-CGG---------CGGAGUC--AGAAAACU
ABPR01006620.1/235-473         ACAAUCCAGCCCA-UGC----AAAG-G-CUAA--CCA-C-C-AGCA--UGG-AAUAGAC-C-UACACGGC--UU-G-AU--G-AG-GUAA-CGAAUC-A-GUC-GAAGCUGUA---G--GAA--------UA-----G---------C-----GGUUUAUC---------AGCCA--CAA------------------------------UGCGAAAGCGUGAAGGUUACCAGCCCCG-AAAUAAU--------------------CAUCGUUGC-AC-A-UG-GCCA-------AGGG-----UUUCAUU--UCC-U-GGAAGCCAGCAUC-GUG-U-GG--AUCGACAAG----------GUGAGAG---CUAC-AC-GAA----GUGC---------CGGGGUC--UCAGACCG
AACY023784592.1/304-545        AAAGUC-CUCACA-AGA----AAGC-A-UUAU-CCGA-U-GCAUCU--UGA--AUCGAG-U-UUUGAGCU---U-A-UG--G-AG-GUGA-CGAAAU-G-AGU-UAAGCGUAA---A--C-A--------GA---GAG---------ACAAGCAGGCCAUA---------GGGAAACCGA------------------------------AGUG-A------------UUGAGCCCCGUAAACCUG-----------------------UUUUGG-AG-U-GG-CCGA-------CGUG---GUCGACAU----AG-C-GGAAGGCAAUAUC-AAU-A-AG--AAUGUUUUUUUUUUUUUGGGAUAGUU---CUUA-UU-GAC---ACUCC---------UGGGGUC--UGAGAGCA
AM999887.1/286776-286524       AUAGAC-CUACCA-GGA---UAAA------AG-UCGG--A--AUCC--UGUA--GCUUG--GGUAGCAGC---A-U-AA--A-GG-GAAA-CCAAAA-U-GUU-GAAGCCUACCGA---CAACA---UUAUC--G---UAG---GAUA-----AUGGCGAAUUA---CCAGGCCGUAGCGAAAGCG-------------------AAUGCACAG-A------------UU--GCCUCG-AAAGGAA-----------------------UAUUCU-GA-A-GG-UCGA-------GCCA----UCUUGGUA--CUG-G-CGAAGACAGAAUA-GAC-C-AG--ACGAAAAACGA------AUGAAACGA---UUGG-UC-UAC---UUCAG---------CGGGGUG--UUAGUAAC
AAXY01000018.1/76506-76285     AAAGUC-CCUACG-AGG---UAAGG-C-GG-G--CGG-G-CCGCUU--CGU-CCCCGAG-U-CAUGCGCG---A-C-UG--U-CC-GCAA-GGGCCG-C-CGU-GAAGUGUUG---A--C-A--------GG---GG----------------UGUCUGCA---------GGCGA-AG-----------------------------------U-A------------UCGAGCUGCG-AAAUCAC----------------------UAGUUGG-AG-A-GG-CAGA-------UGCU---GUUAAGCGA---AG-C-AGAAUGCAACAUG-ACC-C-GU--ACCGUCAAAC--------CGCAAGGU---AUGG-GC-CAC---UCUUC---------CGCAGUC--GUAGACCU
AACY023752507.1/609-369        ACAGUC-CCACCA-GUC---UAAUG-A-CUAA--CCA-U-CAGGAC--UGUACC--AAC-C-CCUCCGCG---U-A-CC--A-UG-GUGA-CAAGGU-A-CGU-GAAGCAGAG---G--G-C--------AA---GGG---------A-----AAUACCAG---------GCCAUAAGCC------------------------------AAAU-AAGGUUGAAGGUUGUUAGCCACG-AAAGUUA---------------------UUAAUUGC-GG-A-GG-UCAA-------UCGC-----GUUCAUA--UGC-G-GAAAGACAACAUU-ACC-C-UA--GACAUUAUG---------GGUGAGUC---UAAG-GU-AGC---UCUGC---------CGGGGUC--UUAAGACC
CP001110.1/2743975-2743757     CAAGUUACUCACA-UGA----AAGG-U-AUAG--CCA-A-CCAUCA--UGA-CCCCGAG-U-CAUGCCUC---G-A-UA-GC-CA-GCAA-UGG-AA-U-GGG-GAAGCGUUG---A--C-A--------GG---GGA---------A-----AACACAGG---------AGUCC--------------------------------------U-A------------UUGAGCUCCG-AAAUCACCA-----------------CAAUU-UUCA-G-----G-CUGA-------CCUC---GUAGGAUGA---GA-G-GGAAAGCAACAUC-ACC-C-AU--ACCGACAUG----------GCAAGGU---GUGG-UA-GG------CUG---------CGGCGUU--GGUUUAUA
ABSN01065010.1/839-616         CAAGUCCAGCCCG-GUC---AAAGC-C-GUAG--CG--G-GCAGGC--CGG-UAACGAG-U-GUUGCCAU---U-C-GC--U-GG-GCGA-CCGGCG-G-GUGCGAAGCGUAC---A--C-A--------GU---GAG---------------GAAGCA-----------GGCCGUGA-----------------------------------G-G------------AUCAGUUCCG-AAAUCGGA------------------UA-UCGUCGC-GA-U-CG-CCGA-------CACC---GUAACCCU----GG-U-GGAAGGCAGCAUC-CUG-G-CA--ACCGACAAG---------CGCGAGGU---UGCC-CG-GA----GUCGC---------CGGAAUC--CCUAGCCC
ABSN01015208.1/466-251         AAAGCC---CGUC-CGG---UAGCG-C-CUGA--CCA-G-CGGCCG--GAA---GCGAG-U-CUUGCGUG---G-U-GA--CCGG-GUAA-CCGGCG-C-UGC-GAAGCGUAG---A--C-A--------GC---------------C-----AGUCCGAA---------AGCCAUGC-----------------------------------U-A------------UUGAGCGUCG-AAAGCCC-----------------------UCUCGU-GG-G-AG-CCUU-------UGCU---GUGCACAU----AC-C-AAG-GGCCACGCU-GCU---GC--ACCGUAACG---------GGUCUGGU---GCAC-GC-AGU---CCUGC---------CGGCGUC-GGAAGAACA
ACLX01000072.1/517-288         GGAUUC--CCGUC-GAG---UAAGA-A-UUAG--CCA-U-UCGCUC--GUA---GCGAG-U-CUUGGAGG---G-C-UA--A-AG-AUAA-CUUUAG-U-CUU-UAAGCGUAG---A--C-A--------GUUAGGUG-------------------GC-----------GGAUUUGCUUUACUG---------------------AUCGUUCU-A------------UUCAUCCUGU-UAAUCAUUAUA-------------GGAUGUAGUUGU-UG-G--G-GCGG-------CGGU---AGCGGCGGA---UU-C-G---GUUACUAAA-AAA-A-GG--GGCACUCAU----------AAGAGUG---UCUU-UU-UUC---UCAAU---------A--------UAAGAACU
DQ363750.1/30143-30361         UGAGAG----GCG-CCA---UGAAG-UGAAAG--CGA---C-AUGG--CGA------AG-C-CCU--CUGACAU---C--AC-AU-GCAA-AAG----G-CAU------GUGG---G--C-A---------------A---------A-----UCUCCA-----------GGUUG--UAACGUACA------------------GUGAACGUAG-A------------UGUAGCCUCG-UUACACG----------------------CAAUUCC-GG-U-GG-CUGA-------GACG---GUCGAUAA----CG-UGCGAAAGCAACAAG-AAC-U-G---ACCGAAACG---------AGUCUGGAACGGCAG-UU-CUC---ACCGG---------CGGGGUA--UCAGCGGC
ABSN01003306.1/492-717         AGAGUUUCGUACG-GUG----AAGG-U-GUAG--CGA-G-CCACAU--CGG-CCCUGAG-U-CAUGCGCC---G-U-CG--C-CC-GUGA-GGGCGG-G-GGC-GAAGCGUUG---A--C-A--------GG---GGA---------A-----CGUGCG-----------GGCCG-GG-----------------------------------U-A------------UCCAGCCGCG-AAAUUUUGG-----------------GAUCACUCCG-CG-G-UG-CCGA-------CGCC---GUGGCUACA---GG-C-GGAAGGCCACACC-GGU-C-GC--GUCGCCAGC----------GCGAGAC---GCGA-AC-GGA---CCCCG---------CGCGGUC--UGAGGCCC
ABSQ01005528.1/199-418         AAAAUC--CCGCC-CGG---CAAAG-G-CUGG--CCA-C-CAGCCG--GAA---GCGAG-U-CUUGCGUG--GU-G-GU--G-GG-GCGA-CCCACC-C-UAC-GAGGCGUAG---A--C-A--------GC---GAG---------------AGUGAA-----------GGCCGUGU-----------------------------------G-A------------UAGAGCCUCG-AAAGGAC---------------------CGCAUUGA-CG-A-GG-CCAG-------CGUG---CUCAAGACG---AG-C-GCU-GGCAGCACC-CGA---GC--GCUGCGAACU--------GGCCAGGC---GCAU-UG-GGC---UCGUC---------CGGGGUC--UGAGAGCA
ABPV01012891.1/357-572         UCAAUC--CUGCC-CGG----AAGG-G-CCAG--CCC-C-CCGCCG--GAA---GCGAG-U-CUUGCCUA---G-U-CA--G-CA-GUGA-UGCUGG---CGG-GAAGCGUAG---A--C-A--------GC-----G---------A-----CUGUUAAA---------GGUAU--G-----------------------------------U-A------------UUGAGCCUCG-AAAGAUGU------------------UUAUGUUCAC-UG-G-AG-UCUU-------UGUU---UUUAACAU----UG-C-AGG-GACAACACC-AAA---GC--AGCGAUUAC---------GGCGAGUU---GC-G-GC-GGU---CCGGU---------CGGGGUC--GGAGACCA
ABPV01013350.1/352-567         GAAGUCCUGUACG--GC----AAAG-C-CUGA--CCA-G-C-AGC---CGG-GAGCGAG-U-CUUGCGUG---G-U-GU-AC-GG-GUAA-CCGGCA-C-UGC-GAGGCGUAG---A--C-A--------GC-----G---------------AGUUCGGA---------AGCCACGC-----------------------------------G-A------------CUGAGCCUCG-AAAGUAC-----------------------CGUCGU-CG-G-AG-CCUU-------CGUC---GUUGAAUG----AG-C-GGG-GGCAGCACG-GG--C-GU--UCCGCCAGU---------GGUCGGGA---ACG--CU-CGU---CCGGC---------CGGGGUC-GCGCGAGCG
ACFY01000094.1/3778-3999       GGAUUCCGGUUUA-UCC----AAGG-U-UUAG--CCA-A-CCA-GA--UAA-UAGCGAG-U-CUUGGGAU---G-A-UG--C-CG-GUAA-CGGCAU-C-UGA-CAAGCGUAG---A--C-A--------GC---AAG---------A-----AAGCAG-----------GGUUG--AAU------------------------------AGUG-A------------UUGAGCUUCGAAACGUUA-----------------------ACUUCA-GU-C-GG-UCGA----------CG-UCUUAACUGGUGCG-----GAAGACAAUAUC-AUG-U-AA--UGCGAUAUG----------GCGAGUG---UUAU-GU-GGC----ACUG---------CGGAGUC--AGAGAACC
AAFX01005343.1/1439-1222       GAAGUCCGGCCCA--AG---UAAGG-A-GUAG--CG--U-CCGCU---UGG-UAGCGAG-U-GUUGCGCA---G-C-CA--A-UG-GCGA-CAGGGG-U-UGC-GAAGCGUAC---A--C-A--------GC---GAU---------U-----G---CAUG---------GGGUGUGG-----------------------------------G-A------------UUGAGCCACG-AAAGAUCAG-----------------ACAUU---GC-AG-G-GG-CCGA-------GGGU-----UUUCAUU--CAC-U-CGAAGGCAACAUG-UGC-G-GU--ACCGCUAU-----------GCGAGGU---GCCG-U--CGC---CCUGC---------CGGGGUC--CAAGGCCA
AACY023938727.1/723-940        CAACUC--CCUCC-CGG---UAAAA-G-CUAA--CCA-C-UGGCCG--GAA---GCGAG-U-CUUGCAUG---G-A-CA--A-CG-GUAA-CGUUAU-U-CGU-GAAGCGUAG---A--C-A--------GC---AG-----------------GUGCUAA---------AGCCGCGG-----------------------------------G-A------------UUGAGUCUCG-AUAUCAU---------------------GUUCACGU-UG-G-AG-GCUU-------CAUUU-UGUUUG----G-GAA-U-GGG-GUCAGUACA-GUA-C-AU--AUCGUAAUG----------GUAAGAG---AUGU-AU-UGU---CCGAC---------GGGGAUCUAUGG--CCG
CP000492.1/1685153-1684932     AAAGUCCCUUACA-GUG----AAAG-A-GUAG--CGA-U-CUACAC--UGG-CCCCAAG-U-CAUGCGUG---G-G-UG--G-CC-GUGA-GGCCAU-A-CGU-GAAGCGUUG---A--C-A--------GG---GGU---------G-----CGUAUA-----------------GGCC------------------------------AGCC-A------------UUGAGCGGCGAAAAAUCA------------------------AUCUG-GG-G-GG-CCGA-------UGCU---CUCAAACU----UG-C-AGAAGGCAAUAUG-AAC-A-GG--UGCGAUAAUA-------AUGCGAGUG---CUUG-UU-UGC---CCCCA---------CGUCGUC--UGAGACCC
ACML01001005.1/36-292          AAAGUCCAAUCGG-GAG----AA------UAG-ACUCC----ACUC--CCG-UAGCCUG--AGAGGCACC---A-U-GA--A-GU-GAAA-GCGACA-U-GGC-GAAGCCCUCU-GA--C-AUCA--CAUGC---AAA---------A-----GGCAUGUG---------GGCAA--AUCUCUAGGUUGUA--------ACGUACAGUGAACGU-AG----------ACGUAGCCUCG-UUACACG----------------------CAAUUCC-GG-U-GG-CUGA-------GACG---GUCGAUAA----CG-UGCGAAAGCAGCAAG-AAC-U-G---ACCGAAACG---------AGUCUGGAACGGCAG-UU-CUC---ACCGG---------CGGGGUA--UCAGCGAC
BA000040.2/9009300-9009080     GAAGUCCAUUGCG-AUG----AAGG-U-GUAG--CGA-A-CCACAU--CGG-CCCCGAG-C-CGUGCGCA---G-G-CG--U-CC-GCGA-GGGUGU-C-GGC-GAAGCGUCG---G--U-A--------GG---GG----------------AGCAUGCA---------GGCCA-GC-----------------------------------C-A------------UUGAGCCGCG-AAACAGU---------------------GUUAUCUC-GG-G-AG-CCGA-------CGCU---GUCCAAAG----AG-C-GGAAGGCAAUAUG-GGC-G-AG--UGCGCAAAC----------GCGAGCA---CCCG-UC-CAA---CCCGG---------CGUGGUC--GUAGACCC
CP000923.1/1286666-1286898     AAACACCGAGCCC--GG---UAAAG-U-GAGG--CCA-A-CAGCC---GGUACCA--AG-C-CUUGGAGC---C-G-AA--G-CC-GCGA-GG-UUA-G-GUU-UAAGCGUAG---G--C-A---------U---GGG---------------AGUAAGCG---------AGCCG-CAAUGCGAAA------------------GCGUGAAGCG-A------------UACAGCCCCG-UUAGUUU----------------------AUGAAGU-CG-A-AG-CCGA-------UGCC---GUCCUUUC----GG-C-AGCAGGCAGCAA--UCC-G-CA--AACGAAAAG----------GCAAGAA---UGCG-GA-GGU---UCGGC---------CGGGGUC--AGAGAGCG
AACY020309388.1/3496-3281      AAAGUCCUGAC-C-CGG---UAAGG-A-UUGG--CCA-U-CCACCG--GAA-C--CGAG-U-GUUGCGUG---GUG-UG--G-GA-GCGA-UCCCGC-C-UGC-GAAGCAUAC---A--C-A--------GC---AGG---------C-----A---UGCA---------GGCUGUGU-----------------------------------G-A------------UUGAGCCUCG-AAAGCAG-----------------------AGUGGC-GG-A--G-CCGA-------CGUU-----GUUAAGU--AGG-C-GGAAGGCAACAGU-GCU-G-CC--ACCGAGAGG----------GCCUGGG---GGCA-GC-AC----UCCGC---------CGGGGUC--GAAGAGCA
CP000448.1/196547-196777       GGAAUC--CCGUC-CGG---UAAGG-U--UAG--CCA-A-CCGCCG--GUA-AU--UAG-U-CUUGGAGG---G-C-AG--A-GG-GUAA-CCGCUG-U-CUU-UAAGCGUAG---A--C-AAA---CAAGC---AAA---------C-----GGGCCGAA---------AGCAGUAGCUG----------------------------AAGGU-G------------UUGAGCCCCG-AAAUACC---------------------GAACAUGG-GA-A-GG-CAGA-------UGCU---AUUGCCUG----AG-C-AGAAUGCAACAUC-CUG-G-AA--GUCGAUAAG----------GCUAGAC---G-AC-AG-GAC---UUCCC---------CGGGGUC--GGAGGCCU
ABBG01000562.1/328-549         AAAGUCCUUUACG-AUG----AAGA-A-CUAG--CGA-A-UCACAU--CGA-CCCCGAG-U-GAUGCGGG---G-G-CA--C-UC-GCGA-GGGUGU-C-ACC-GAAGCGUUG---A--C-A--------GG---GG----------------CGCACGUA---------GGCCA-GC-----------------------------------C-A------------UUGAGCGACG-AAAGACU--------------------UCCCAAUCG-GA-G-UG-CUGA-------UGCU-----UUCCAGU--CAG-C-AGAAGGCAAUACG-UCC-C-AC--CGCGAUAUC----------GCGAGCG---GCGG-G--CGG---CUCCG---------CGUCGUC-UGUAGACCC
AAGA01002104.1/1486-1709       AAAAUCCUCUGCU-CGG---AAAGA-G-CUAG--CAA-C-UCGCCG--AGA-CUCCGAG-U-CAUGGGCU---G-U-UU--A-UC-GUAA-GGUAAC-C-GGU-UAAGCGUUG---A--C-A--------GG---GGA---------A-----AGUGCA-----------GGCUC-AG-----------------------------------U-A------------UUGAGCUCCG-AAAUCAU----------------------GACUUGA-GU-A-GG-CAGA-------CCUU---GUAGGGUGA---AG-G-GGAAUGCAAUAUU-AAC-U-GU--UGCGCUAUU---------UGCGAGCG---ACAAUUU-AGC---UGCUC---------CGGAGUC--CUAGACCU
ABSP01020810.1/511-274         -AAAUUCCCGCCC-CGG---CAAGAGGUGCAG--CCG-CCUCACCG--GGA--AUCGAG-U-CUUGGGUC---U-G-AA--G-AG-GUAA-CGAAUC-G-GAC-UAAGCGUAG---A--C-A--------GA---GCG---------A-----CGCGCG-----------AGCCG--UAACGAAA---------------------GUGAAGCG-A------------UUGAGCCUCGUAAAAUAC-----------------------UUAACC-GC-A-GG-CCGA-------CAGC---AUCGUAGUG---GC-U-GGAAGGCACCAGU-AGG-C-AC--ACCGCAAAC---------GGCGAGGU---GGCCGGA-GAC---UGCGG---------CGGGGUC--AGUGAGCA
ABSR01017210.1/162-385         CAAGUC--CUACC-CCG------GG-A-GGAG-UCCG-C-CCCCGG--GAA-GUCCAGU-C-CUUGCGUC---G-C-GC----GG-GUGA-CUUGCG-C-GGC-GAAGCGUAG---G----A--------GG---GCG---------------GAUGAGCG---------GGCCGGGC-----------------------------------A-A------------UCGAACCUCGAAAAUGCU---------------------GUCACCGU-GU-G-CG-CCAA-------CGCA---CUCCUGUAA---UG-C-GGAUGGCCAUGAC-GAU-G-C---GCCGACAAGUG-----CGGACGUGGA---AGCA-UC-GUG---CACAC---------CGGGGUC--UAAGAGUU
ABSQ01000319.1/1165-1388       CAAGUCCAGCCCG-GUC---AAAGU-C-GUAG--CG--G-ACAGGC--CGG-UAGCGAG-U-GUUGCCAU---U-C-GU--C-GG-GUGA-CUGGCG-G-GUGCGAAGCGUAC---A--C-A--------GU---GAG---------------UAAGCA-----------GGCCGUGA----------------------------------GG-A------------UUCAGCUCCG-AAAUCUUU------------------UCCUCGUUGC-G--A-UG-CCGA-------CGCC---GUUAUGAG----GG-C-GGAAGGCAGCAUC-CGA-G-CC--ACCGUUAU-----------GCGAGGU---GAACUCG-GGG---U-CGC---------CGGAGUC--CCUAGCCC
CP001391.1/602236-602468       AAAAUCCAACACG-GGU----AAAG-C-UUAG--CCG-G-C-AACC--UGG-AACAAAC-C-AUUAUGCU---G-C-GU--A-AG-GUAA-CGAGCG-U-AGU-AAAGCUAAU---G--GAA--------UG---GAC---------A-----ACAUAGGG---------UGCAACGAAAGU--------------------------GAAGGU-A------------UUGAGUCCCG-UAAUUCA---------------------CGCGUCAU-GG-G-GG-CUGA-------CACU-----UUACAUU--UGG-U-GGAAGGCAACAUG-GGU-A-AU--AACGCUAAG----------GCAAGAU---AUUA-CU-CAC---CUCAU---------CGGGAUC--GAAGGCCG
DQ449578.1/13927-13702         AAAGUCCCCGACCAUUG----AAGG-A-CCAG--CAA-U-CCACAA--GGU-CCCCGAG-U-CAUGCGUU---G-C-AU--A-CC-GCGA-GGUAUG-G-GGC-GAAGCGUUG---A--C-A--------GG---GG----------------UGUUGACA---------GGCCA-GC-----------------------------------C-A------------UUGAGCCACG-AAAUGUAUA-----------------UUAAAUUACC-GG-G-UG-CCGA-------CGUU-----GUACUGU--UAA-C-GGAAGGCAACAUC-AUA-G-GG--UGCGAUACU----------GCGAGUG---CCAC-AU-GGA---CCCGG---------CGGGGUC--UGAGACCC
AAFX01078195.1/400-622         AAAGUUUCAAACG-UUA----AAGG-U-CUAG--CCA-A-CCAUGA--CGA-CCCCGAG-U-CAUGCGGC---G-G-CA--U-UC-GUAA-GGGUGA-C-GUC-GAAGCGUUG---A--C-A--------GG---GGA---------A-----AGUGCA-----------GGCUG-GG-----------------------------------U-A------------UUGAGCCGCGAAAAACAA---------------------UUCAUUCG-GG-A-UG-CCGA-------CCCU---GUAAGGAGA---AG-G-GGAAGGCCACAAU-CAA-C-AC--UCCGCAUUG----------GCGAGGA---GUAU-UG-GUA---UCCCG---------CGAGGUC--AGAGACCC
ABSP01045733.1/44-267          AGAGAGCCAUACA-GGA----AAGG-GGGUAA--CGG-A-CCGUCC--UGG-CCCCGAG-U-CAUGCGUG---G-G-CG--A-CC-GUGA-GGGCGC-C-GGC-GAAGCGUUG---A--C-A--------GG---GGA---------A-----CGCGCA-----------GGCGA-GG-----------------------------------U-A------------UUGAGCCGCG-AAAUCAG---------------------GCUGAACCAGU-G-UG-CCGA-------CGCC---GUCUGAGUA---GG-C-GGAAGGCGAAACC-GGA-G-GG--GGCAUUAGC----------GUGAGUC---CUCA-UCUGGA---CG-GG---------CGCGGUC--GGAGACCC
CP001087.1/2996655-2996431     AAAGAGCCCUACA-UUG----AAGG-A-GAAG--CUGCU-CCAUCA--UGGU-CCCGAG-U-CAUGUGCG---G-G-UG--G-UC-GCGA-GGCUGC-A-CGU-GAAGCGUUG---A--C-AG------AGG---G-----------A-----AACGCA-----------GGCCA-AC-----------------------------------U-A------------UUAAGUUCCG-AAAUCAC----------------------CCAUCCG-GG-G-UG-GCGA-------CCCA---GUGGUCUGA---AG-G-GGAAGGCAACACG-UUG-UGG--CAACGGUAAAC--------AGCGAGUC--A-UAC-AA-CGG---CCACG---------CGGAGUA--UAAUAACC
AACY023816958.1/378-591        AGAAUC--CCGCC-CGG---AAAGG-G-UUGG--CCA-C-CCACCG--AAA---GCGAG-U-CUUGCGUG---G-C-GU--C-GG-GUAA-CCGCCG-C-UGC-GAAGCGGAG---A--C-A--------GC---GA----------G-----CGUGCA-----------GGCCCUGU-----------------------------------G-A------------UUGAGCCCCG-AAAUGACCG-----------------CACUG------GG-G--G-CCGAGGUUUUC-------GAGACGACG---------GAAGGC-ACUAC-CGA-U-GC--GCCGCACUG----------GCCUGGC---GCGG-AG-GU----CCCGC---------CGGGGUC--GAAGAGCA
AAFY01027505.1/228-14          ACAACC--CUGCC-CAG---AGAAG-G-UUGG--CCA-C-CAACUG--GAA---GCGAG-U-CUUGCGUG---GAA-CG--G-GG-GUAA-CCCCGG-C-UGC-GAAGCGUAG---A--C-A--------GC---GAG---------C-----A---GACA---------GGCUAUGU-----------------------------------G-A------------UAGAGCCCCG-AAAUCUA------------------------GUUGU-GG-G-AG-CAGA-------CGCG---GUCACAAU----CG-C-GGAAGGCAACACC-AAA-G-GG--UCAAGAAUG----------GCC-UGA---CCCU-GA-GGU---CCCAC---------CGGGGUC--CAAGAGCA
AACY020493875.1/2297-2081      CAACUC--CCUCC-CGG---UAAAA-G-CUAA--CCA-C-UGGCCG--GAA---GCGAG-U-CUUGCAUG---G-A-CA--A-CG-GUAA-CGUUAU-U-CGU-GAAGCGUAG---A--C-A--------GC---AG-----------------GUGCUAA---------AGCCGCGG-----------------------------------G-A------------UUGAGUCUCG-AUAUCAU---------------------GUUCACGU-UG-G-AG-GCUU-------CAUUU-UGUUG-----G-GAA-U-GGG-GUCAGUACA-GUA-C-AU--AUCGUAAUG----------GUAAGAG---AUGU-AU-UGU---CCGAC---------CGGGAUCUAUGG--CCG
BABG01003105.1/426-647         GGAUUCCGGUUUA-UCC----AAGG-U-UUAG--CCA-A-CCA-GA--UAA-UAGCGAG-U-CUUGGGAU---G-A-UG--C-CG-GUAA-CGGCAU-C-UGA-CAAGCGUAG---A--C-A--------GC---AAG---------A-----A-AGCA-----------GGGUUGAAUA-------------------------------GUG-A------------UUGAGCUUCG-AAACGUU----------------------AACUUCA-GU-C-GG-UCGA-------CGU----CUUAACUGG--U-G-C-GGAAGACAAUAUC-AUG-U-AA--UGCGAUAUG----------GCGAGUG---UUAU-GU-GAC----ACUG---------CGGAGUC--AGAGAAGC
ABSN01048999.1/390-617         CGAAACCCGCUCG-GCC----AAGG-G-UGAG-CCCG-C-CCGGGC--CGA-UAGCGAG-C-CUUGCGAC---G-G-CC--G-CG-GUGA-CAUGGU-C-GGC-GAUGCGUAG---G--UAC--------GC---GAG---------------CAUGUG-----------GGCCGUGG----------------------------------CA-G------------UGUAGCCUCGAAAACUAU---------------------GAGAUUCC-GG-G-UG-CCCA-------GGGU---GUAGAAAG----GC-C-UGAAGGCGACGGC-GGA-U-CC--UCCGCACAGC-------GGGCGAGGG---GGUU-CC-GCA---CCCGG---------CGGGGUC--UUUGAUCA
ACNF01000057.1/14568-14824     AAAGUCCAAUC---GGG------GG-A-AUAG--AC--U-CCACUC--CCG-UAGCCUG--AGAGGCGCC---A-U-GA--A-GU-GAAA-GCGACA-U-GGC-GAAGCCCUCU-GA--C-AUCA--CAUGC---AAA---------A-----GGCAUGUG---------GGCAA--AUCUCCAGGUUGUA--------ACGUACAGUGAACGU-AG----------AUGUAGCCUCG-UUACACG----------------------CAAUUCC-GG-U-GG-CUGA-------GACG---GUCGAUAA----CG-UGCGAAAGCAGCAAG-AAC-U-G---ACCGAAACG---------AGUCUGGAACGGCAG-UU-CUC---ACCGG---------CGGGGUA--UCAGCGGC
CP000492.1/2544307-2544088     AGAGUC--UUACA-UGA----AAGG-C-AUAG--CCA-A-CCAUCA--UGG-CCCCGAG-U-CAUGCCUC---G-A-CC--U-AC-AGCA-AUGGGG-U-GGG-GAAGCGUUG---A--C-A--------GG---GGA---------A-----CACACA-----------------GGCC------------------------------CAAU-A------------AUGAGCUCCG-AAAUCAC---------------------CUCAAUUC-GU-A-GG-CUGA-------CCCU---GUUGAGCGA---AG-G-GGAAUGCAACAUC-GGU-C-GU--AUCAUCAAG----------GCAAGAU---ACGA-CA-GGC---UACGG---------CGGAGUC--GUAGAACU
AAFX01074064.1/382-601         AGAGUC--GUACA-GGA----AAGG-A-AUAG--CAA-A-CCAUCC--UGG-CCCCGAG-C-CAUGCGAG---G-G-CG--G-UC-GAGA-GGCUGC-A-CUU-GAAGCGUUG---G-AC-A--------GG---GGU---------A-----UCUGUA-----------GGCUG-GG-----------------------------------U-A------------UAGAGCUCCG-AAAUCGC---------------------CCGUUGUG-GG-G-AG-CUGA-------CG-GC-GUCGGGC---U-GUA-C-GGAAGGCAACAAG-GUG-G-AC--CGCGAUAGU----------GCGAGUG---GGCU-AC-C-A---CCCGA---------CGGAGUC--GCAGACCC
CU633751.1/83053-82831         AAAGUUCGAUACA-GGA----AAGG-A-AUAG--CGA-A-CCACCC--UGG-CCCCGAG-U-CAUGCGGC---G-G-CA--C-CC-GCGA-GGGUGC-A-GCC-GAAGCGUUG---A--C-A--------GG---GGA---------G-----AGUGCA-----------GGCCA-GC-----------------------------------C-A------------UUGAGCCGCG-AAAUCAU---------------------UCUGUCUG-GA-G-CG-CCGA-------CGCU---GUUGAUCGA---AG-C-GGAAGGCAACAUC-GUC-G-AG--GGCGCUAAA---------CGCGAGUU---CUCG-GC-GGG---CUCCA---------CGCGGUC--GAAGACCC
AY691909.1/4303-4081           AGAGUC--UUAUG-GUG---GAAGG-U-UUAG--CAA-A-CCACAC--CAG-CCUCGAG-U-CAUGCGGC---A-A-UU--G-CA-GUAA-UGCAUU-G-GCU-GAAGCGUUG---A--C-A--------GA---GGG---------A-----AGCACA-----------GGCGG-GC-----------------------------------U-A------------UUGAGCUCCG-AAAUCAC---------------------UCAUUCUC-GG-G-UG-CCGA-------CCAC---GUGGUCCGA---UG-G-GGAAGGCAACACG-UUU-U-GC--CGCGUUAUUA--------UGCGAGCU---GUAA-GA-CGA---CCCGG---------CGGAGUC--CUAGAACC
AM747721.1/1155000-1154778     AAAGUCCCCGACA-UUG---CAAGA-A-CUAG--CGA-U-UCACGA--UUU-CCCCGAG-U-CAUGCGUG---G-C-CA--G-CC-GCGA-GGCGGG-U-UGC-GAAGCGUUG---A--C-A--------GG---GG----------------CGCUGAUA---------GGCCA-GC-----------------------------------C-A------------UUGAGCCACG-AAAUGGA--------------------UACAUUCCC-GA-G-UG-CUGA-------CGUA---CUACUGUA----UG-C-GGAAGGCAACAUC-GCG-C-GG--CGCGCUAUC----------GCGAGCG---CUGC-GC-GGA---CUCGG---------CGUGGUC--UGAGACCC
ABLD01000019.1/26500-26722     CAAGUCCACUGCG-AUG----AAGG-A-AUAG--CGA-A-CCACAU--CGG-CCCCGAG-C-CGUGCGCA---G-G-CA--U-CC-GCGA-GGAUGU-C-GGC-GAAGCGUCG---G--C-A--------GG---GGU---------A-----CGUACA-----------GGCCA-GC-----------------------------------C-A------------UUGAGCCACG-AUAGAAAA-------------------ACUGAUUCC-GG-G-UG-CCGA-------CGCU---GUCUGUGU----AG-C-GGAAGGCAAAACG-UCU-G-AG--CGCGCAAUC----------GCGAGCG---CCCG-GA-UGA---CCCGG---------CGUGGUC--GUAGAACC
EF066650.1/85074-84854         GAAGUCCGUCACG-AUG----AAGG-A-GUAG--CAA-A-CCACAU--CGG-CCCUGAG-C-CAUGCGCA---G-G-CG--C-UC-GCGA-GGGCGU-C-GGC-GAAGCGUUG---G--C-A--------GG---GGA----------------GCAUGUA---------GGCCA-GC-----------------------------------C-A------------UUGAGCCGCG-AAAUCGC---------------------CUCAUCUU-GG-A-UG-CCGA-------CGCC---GUUGUCAU----GG-C-GGAAGGCAACAUG-GGA-A-GG--UGCGCUACU----------GCGAGCA---CCCG-AC-CAA---UCCGG---------CGCGGUC--GUAGACCC
ABKW02000004.1/1031661-1031882 GAAAUCCUGUCUG-AAU----AAGG-U-CUAG--CCA-A-CCA--U--CAG-UAGCGAG-U-CUUGAGUU---G-U-UA--U-CA-GUAA-UGGUGA-G-AGC-UAAGCGUAG---A--C-A--------GC---AAG---------G-----AAGUAG-----------GGUUUAA-AA-------------------------------GCU-A------------UUGAGCCUCG-AAAUUUU---------------------GUCUAUCA-GA-U-GG-CUGA-------CGUC---UUAAUUGG----UG-C-GGAAAGCAACAUC-ACA-U-AG--GUUGGUAUG----------GCAAGAA---CUGU-GU-GGC---A-CUG---------CGGGGUC--AAAGGGCA
AF440524.1/60112-60334         CAAGUCCGAUACG-AGA----ACGA-A-GUGG--CGA-A-UCAUCU--UGG-CCCCGAG-U-CAUGCGUU---G-G-AC--G-UC-GUGA-GGCGGA-C-AGC-GAAGCGUUG---A--C-A--------GG---GGA---------A-----ACGACA-----------GGCCA-GC-----------------------------------C-A------------UUGAGCCGCG-AAAUCAU---------------------AAGUCCCA-GG-A-UG-CCGA-------CGCU---AUACAGAUG---AG-C-GGAAGGCGACACG-GAG-C-AG--GGUGUCAAU---------CGCAAGCC---CUGU-GA-CGA---UCCCG---------CGCGGUC--GAAGACCC
AY837591.1/493-246             GAACUCCCGCCUG-GGU----AAUC-G-CUAG--CCA-C-GAG-CC--CGG-UAUCGAG-C-CUUGCGGC---G-C-GG--C-UG-GUAA-CAGCCG-C-GUC-GAUGCGUAG---G--C-A-------CGA---CAG---------C-----AGGCGAGG---------UGCAAAGGUAACGGGUGGAG----------CCGACCUUGAAGGU-G------------UUGAGCCCCG-AAACAUU----------------------UGGUCGG-GA-G-UG-CCGA-------CGGG---UUUGUCCC----UC-C-GGCAGGCAACAGU-CCG-U-GU--CGCGUCAUG----------GCGAGUG---GCAC-GG-GUA---CUCCC---------CGGGGUC--CGAGGCCG
ABWO01000213.1/212-1           GGAAUCCGGUUUA-UCC----AAGG-U-UUAG--CCA-A-CCA-GA--UAA-UAGCGAG-U-CUUGGGAU---G-A-UG--U-CG-GUAA-CG-CAU-C-UGA-CAAGCGUAG---A--C-A--------GC---AAG---------A-----AAGCAG-----------GGUUGAAUA--------------------------------GUG-A------------UUGAGCUUCG-AAAUGUU-----------------------AACUUC-AG-UCGG-UCGA-------CGUC---UUAACUGG----UG-C-GGAAGACAAUACC-AUG-U-AA--UACGAUAUG----------GCGAGUA---UUAU-GU-GGC---ACUGG---------CGG--------AG----
AJ245436.1/17314-17098         ACAGUUCGAUACU-GGU----AAUA-A-AUGG--CGA-A-UCAACC--AGA-CCCCGAG-U-CAUGCAUG---U-U-GC--G-CC-GUGA-GGUUCA-G-GGU-AAAGCGUUG---A--C-A--------GG---GGA---------A-----A-CCGAUG---------GGCCA-GC-----------------------------------C-A------------UGGAGCCGCG-UAAUCAC---------------------AAAUUCGG-GA---UG-CCGA-------UGCU---GUUAAGCGA---AG-C-AGAAGGCUAUACG-GAG-C-AU--GACGAUAC-----------CCGAGGC---AGGA-GC-CGU--A--------------UGCGGUA--GUUCCGCA
ABVL01000009.1/196694-196480   CGAGUC--CCGUC-CGG---UAGAG-G-CUGG--CCA-C-CAGCCG--GAA---GCCAC-C-AUUGCGUC---G-U-CG--U-CA-GAGA-UGGCGG---CAC-GAAGCGUAU---G--G-G--------GC-----G---------------AGUCCAAA---------AGCCGUGU-----------------------------------G-A------------AUGAGUCCCG-AAAUAAA--------------------GAUGAACGU-UG-G-AG-CCUU-------CGC---GAUCGUUCAA--C---C-G-AGGGCCGCGCC-GA--C-AC--GCCGCGAAA----------GCCUGGC---GUG--AA-GGU---CCGAC---------CGGGAUC--UGAGAGCA
AM746676.1/11692161-11692384   AGAGUC-CCGCCC-GGC----AAGG-U--UGG--CCC-A-CCAGCC--GGA--AGUGAG-U-CUUGCGUG---G-U-GC--C-GG-GCGA-CCGGCG-U-CGC-GAAGCGUAG---A--C-A--------GC---GAG---------------CGUGCG-----------GGCCGUGG-----------------------------------G-A------------UAGAGCCUCG-AAAGAAC--------------------GGAGGUCGU-GG-G--G-CCGA-------CGUC---GUGAGCGU----AG-C-GGAAGGCAACAUC-GUC--------GCGUCAAG---------AGCGAGCC---UGGG-UA-GCC---CCCGCUCGCUCUGGCGGGAUC--CCUGACCG
ACMI01000921.1/50346-50093     AAAGUCCAAUCGG-GAG----AA------UAG--ACU---CCACUC--CCG-UAGCCUG-A-GAGGCGCC---A-U-GA--A-GU-GAGA-GCGACA-U-GGC-GAAGCCCUC---U--G-ACAUCACAUGC---AAA---------A-----GGCAUGUG---------GGCAAAUCUCCAGGUUGUAAC--------GUACAGUGAACGUAG-A------------UGUAGCCUCG-UUACACG----------------------CAAUUCC-GG-U-GG-CUGA-------GACG---GUCGAUAA----CG-UGCGAAAGCAAUAAG-AAC-U-G---ACCGAAACG---------AGUCUGGAACGGCAG-UU-CUC---ACCGG---------CGA---C--AUGGAGAG
CP001720.1/4217724-4217474     AAAGUCCGACCGG-GAG---AAAAG-A-CU--------U-C-ACUC--CCG-UAGCUUG-A-GAGGCACC---G-U-GG--A-GU-GAAA-AUGAAA-C-GGU-GAAGCCCUU---U--G-A---------C---AAC---------A-----CACUCAAG---------GAGUGUGAGCGAAACUCCAGGUUG--UAAUCACAAUGAACGUAG-A------------UGUAGCCUCG-UUACACG-----------------------AAAUCC-GG-U-GG-CUGA-------GACG---GUCGAUAA----CG-UGCGAAAGCAACAAG-UGC-U-G---ACCGAAAAGAG-----UCUGAAACGG----CAG-UG-CUC---ACCGG---------CGGGGUA--UCA--ACG
CP001720.1/4202978-4202723     AGAAACCUGCCGA-GGU----AA------AAG--UCA---GAAACC--UUG-UAGCUAG-G-AUAGCAGG---G-U-UA--A-AG-GAAA-CUGAGA-U-UCU-GGAGUCUAU---C--G-A---------C---AAU---------A-----UUAUCCAA---------GGGAU-GAUAGCGAGUUGCCAGGCCGUAGCGAAAGCGAACGCAU-A------------GGUGGCCUCG-AAAGUGC---------------------GUAGUCCC-GA-A-GG-CUGA-------GCCC---GCAACCGUA---GG-G-UGAAAGCAGCAUG-GA--C-AG--UUGAAAACUGA------CUGAUACAA---CUG-UUC-CAC---UUCGG---------CGGGGUG--GUAGCGAC
CP001720.1/4224356-4224159     GGAAUC-CCACUA-GAA----AAGG-U-UUAG--CCA-A-UCAUUC--UAU--AGCGAG-U-CUUGGGAA---G-C-AC--G-GG-GCGA-CCCGUG-U-UUC-UAAGUGUAG---A--C-A--------GC---AAA---------------CUAGUG-------------C---AC-----------------------------------G-A------------UGGCGC-----AAAUACAUG-----------------CACACCAAUA----A-CAACCAA-------UUAA---GU------A---UU-A-UGCAGCCAAGAGU-UUA-U-UU--GC--AUAUG----------UCCA-GC---AAAA-UG-GUU------UA-------------GCC--AAAUACUG
CP001804.1/1447391-1447609     CCAAUC--CCGCC-CGG---AAGAG-G-UUAG--CCG-C-CAGCCG--GAA---GCGAG-U-UUUGCGUG---GAC-CC--G-GA-GCGA-UCCGGG-C-UGC-GAAGCGUAA---A--C-A--------GC-----G---------------AGUGCGGA---------AGCCAUGA-----------------------------------G-G------------UUGAGCCCCG-AAAUAGAU-------------------ACGCAAUGC-AG-A-GG-CCUU-------CGUU---GUUGCACA----GU-C-GGG-GGCAGCACC-AA--C-GU--GCCGUGAAU---------GGCGAGGC---ACC--GA-GGC---UCUGC---------CGGGGUC--UGAGAGCA
CP002271.1/7347839-7347624     CGAAUCCUGC-CC-GGC---AAAGG----AGG--CCA---CCGGCC--GGA--AGCGAG-U-CUUGCGUG---GUG-CU--G-GG-GUAA-CCCGGG-C-UGC-GAAGCGUAG---A--C-A--------GC---GAG---------------UGGGCG-----------GGCCGCGU-----------------------------------U-A------------UUGAGCCCCG-AAAGGAA---------------------CUUGUCGC-GA-G-AG-CUGA-------CGCC---GUCGAAAC----AG-C-GGAAGGCCGCAUC-GGG-A-GA--UU-GAACGG----------GCCU-GC---UCUC-CC-GGU---CUCGC---------CGGGGUC--GAAGAGCG
CP001720.1/1704846-1705067     GAAAUCCCGUCUG-GUA----AGAC-U-CUAG--CCA-A-GUC-AC--CAG-UAGCGAG-U-CUUGGACU---U-G-AU--G-GA-GUAA-UUCAUA-G-AGU-UAAGCGUAG---A--C-A--------G------G---------U-----AGGUAGUA---------GGCCU-GAAU-------------------------------GUG-A------------UUGAGCCCCG-UAAUGGG----------------------CAAACGG-GA-A-GG-UUGA-------CGGU---UUCGAAAC----UC-C-GGAAAACUAUAUC-UUG-G-UA--CGCGAUAUG----------GCGAGUG---UAUU-GA-GAC---UUCCU---------CGGGGUC--UAAGAGCC
HM037272.1/29474-29218         AAAGUCCAAUCGG-GAG----AA------UAG--ACU---CCACUC--CCG-UAGCCUG-A-GAGGCGCC---A-U-GA--A-GU-GAAA-GCGACA-U-GGC-GAAGCCCUC---U--G-ACAUCACAUGC---AAA---------A-----GGCAUGUG---------GGCAAAUCUCCAGGUUGUAAC--------GUACAGUGAACGUAG-A------------UGUAGCCUCG-UUACACG----------------------CAAUUCC-GG-U-GG-CUGA-------GACG---GUCGAUAA----CG-UGCGAAAGCAACAAG-AAC-U-G---ACCGAAACG---------AGUCUGGAACGGCAG-UU-CUC---ACCGG---------CGGGGUA--UCAGCGGC
CP001634.1/1518551-1518803     UAAACC--CACCA-AGG---CAA------AAG--CCA---GAACCU--UGUAGCUUG---G-UCAGCAAG---G-G-GG--A-AG-GAAA-CUGAAC-U-CUU-GAAGCCUGA---CGA-CA--------AA---GCC---------A-----UCGGAA-----------GGAUG-GUGAGGGAGUAUCCGGGCCGUAACGAAAGUGAACGCAC-A------------GGUAGCCUCG-AAACCCU----------------------UAUUCCC-GG-A-AG-CCGA-------AUCC---AUGGUACAG---GG-A-UGAAGGCAACAUG-AAU-U-CA--CG--AAAACUG-----GAUGAAA-CG---UGGA-UU-CAU---UCUGG---------CGGGGUG--AUAGCGAC
CP002271.1/1796107-1796329     AAAGAGCCUCACA-UCG----AAGG-G-CCAG--CCA-C-CCACGA--UGG-CCCCGAG-U-CAUGCGCC---A-C-CA--C-CU-GUGA-GGGUGA-G-GGU-GAAGCGUUG---A--C-A--------GG---GGU---------A-----CGAGCG-----------GGCUG-GG-----------------------------------U-A------------UUGAGCCGCG-AAAUCAG---------------------CCAGUCCA-GG-G-CG-CCGA-------CGCG---GUUAAGUGA---CG-C-GGAAGGCAACACG-GAC-A-GG--GACGCUACU----------GCGAGUC---CCUG-GCUCGG---CCCUG---------CGCGGUC--GGAGACCC
CP001720.1/3075418-3075203     AUAUUC--AGAAG-GU----UAGAU-U-UAAAUUCAA-U-AUA---------------A-C-CUUGGUUG--CA-C-CU--G-GG-GCGU-UUCAUA-G-AGA-UAAGCGUAG---G--C-A---------------G---------G-----CAGGUA-----------GGUAGUGGGCCUG-------------------------AAUGUG-A------------UUGAGCCCCG-UAAUGGU----------------------CAAACGG-GA-A-GG-UUGA-------CGGU---UUCGAAAC----UC-C-GGAAAACUAUAUC-UUG-G-UA--CGCGAUAUG----------GCGAGUU---UAUU-AA-GAC---UUCCC---------CGGUGUC--UAAGAGCC
CP001699.1/3122585-3122800     UUAAUC--CUGUC-CGA---CAAGG-U-CUAG--UCA-A-CCACCG--GAA---GCGAG-U-CUUGCGUA---G-U-CA--U-UA-GAGA-UGAUGG---CAC-GAAGCGUAG---A--C-A--------GC-----G---------A-----CUGCUGAA---------GGUAU-GC-----------------------------------U-A------------UUGAGCCUCG-AAACUGU--------------------CCUGGACGU-UG-A-AG-CUUU-------AGUU---GUUCGAAA----AG-C-U-AAGGCAACAUC-AAA---CC--UGCGUUAUA---------GACGAGUG---GG-G-GU-GAU---UCGAC---------CGGGGUC--UAAGAACA
CP001734.1/747087-747309       AAAGAGCCUUACG-GUG----AAGG-G-UUAG--CGC-C-CCACAC--CGA-CCCCGAG-U-CAUGCGUU---G-A-CG--G-CC-GUAA-GGUCGG-C-GGC-GAAGCGUUG---A--C-A--------GG---GGC---------A-----CGCACG-----------GGCCA-GC-----------------------------------C-A------------UUGAGCUGCG-AAAUAAA---------------------AUGGUCCG-GG-A-CG-CCGA-------CGCU---GUUAAGACA---AG-C-GGAAGGCAACACC-AAG-G-AU--GGCGAUAUG---------CGCGAGCC---GUCC-GA-GGG---UCCCG---------CGCAGUC--GAAGACCC
CP002271.1/9441490-9441268     AAAGAGCCUCACA-UCG----AAGG-G-CCAG--CAA-C-CCACGA--UGG-CCCCGAG-U-CAUGCGCC---A-C-CA--C-CU-GUGA-GGGUGA-G-GGU-GAAGCGUUG---A--C-A--------GG---GGU---------A-----CGAGCG-----------GGCUG-GG-----------------------------------U-A------------UUGAGCCGCG-AAAUCAG---------------------CCAGUCCA-GG-G-CG-CCGA-------CGCG---GUUAAGUGA---CG-C-GGAAGGCAACACG-GAC-A-GG--GACGCUACU----------GCGAGUC---CCUG-GCUCGG---CCCUG---------CGCGGUC--GGAGACCC
CP001720.1/3486540-3486319     GAAAUCCCGUCUG-GUA----AGAC-U-CUAG--CCA-A-GUC-AC--CAG-UAGCGAG-U-CUUGGACU---C-G-AU--G-GA-GUAA-UUCAUA-G-AGU-UAAGCGUAG---A--C-A--------G------G---------U-----AGGUAGUA---------GGCCU-GAAU-------------------------------GUG-A------------UUGAGCCCCG-UAAUGGG----------------------CAAACGG-GA-A-GG-UUGA-------CGGU---UUCGAAAC----UC-C-GGAAAACUAUAUC-UUG-G-UA--CGCGAUAUG----------GCGAGUG---UAUU-GA-GAC---UUCCU---------CGGGGUC--UAAGAGCC
CP001699.1/7590039-7589824     UUAAUC--CUGUC-CGA---CAAGG-U-CUAG--UCA-A-CCACCG--GAA---GCGAG-U-CUUGCGUA---G-U-CA--U-UA-GAGA-UGAUGG---CAC-GAAGCGUAG---A--C-A--------GC-----G---------A-----CUGCUGAA---------GGUAU-GC-----------------------------------U-A------------UUGAGCCUCG-AAACUGU--------------------CCUAGACGU-UG-A-AG-CUUU-------AGUU---GUUCGAAA----AG-C-U-AAGGCAACAUC-AAA---CC--UGCGUUAUA---------GACGAGUG---GG-G-GU-GAU---UCGAC---------CGGGGUC--UAAGAACA
AAYG02000006.1/94955-94734     GGAUUCCGGUUUA-UCC----AAGG-U-UUAG--CCA-A-CCA-GA--UAA-UAGCGAG-U-CUUGGGAU---G-A-UG--C-CG-GUAA-CGGCAU-C-UGA-CAAGCGUAG---A--C-A--------GC---AAG---------A-----AAGCAG-----------GGUUGAAUA--------------------------------GUG-A------------UUGAGCUUCG-AAACGUU----------------------AACUUCA-GU-C-GG-UCGA-------CGUC---UUAACUGG----UG-C-GGAAGACAAUAGC-AUG-U-AA--UGCGAUAUG----------GCGAGUA---UUAU-GU-GGC----ACUG---------CGGAGUC--AGAGAACC
#=GC SS_cons                   :::::::::::<<.<<<....--<<.<.____..___.>.>>->>>..>>,.<<<<--<.<.<<<<<<<<...-.<.<<..<.<<.____.>>>>>>.-.>>>.--->>>->>...>..>.-........>>...>>-.........-.....--------.........---------................................---.-............-(--((((((.-------.....................------((.((.(.,<.<<--.......<<<<..._________...>>.>.>--->>>,,,,<<.<<<.<.<<..<<<______..........____>>>...>>>>.>>.>>,...))))).........))))))-..--):::::
#=GC RF                        AaAGUCCccuacc.ggg....AAgG.u.uUAG..CcA.a.CcAccc..gga.cccCGAG.u.cuuGCgcc...g.c.cc..c.cg.GuaA.cggggg.u.ggc.GAAGCgUag...a..C.A........Gg...ggg.........A.....aGugcaaa.........GGCcguGcu................................gau.A............UuGAGCccCG.AAAuaau.....................cuaaUucc.GG.g.gG.cCGA.......cgcu...gUcgucaua...ag.c.gGAAGgCAACAcc.gac.c.gg..ccCGauAug..........GCGAGgg...ccgg.uc.ggc...cCCgg.........CGggGUC..ugaGAgCc
//
# STOCKHOLM 1.0

#=GF AC   RF02006
#=GF ID   mir-1253
#=GF DE   microRNA mir-1253
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   84.40
#=GF NC   59.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.44 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000611;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   2


ABGA01182959.1/4315-4419 AGCAGCAAGAGGUAAAAUCCAAAAGAGGAGAAGAUCAGCCUGCAGAUGUGGACUGCUAAAUGCAGGCUGAUCUUCUCCUCUUUGGGAUUCUCUUAUGAGAGGCCA
AC005696.1/123507-123403 AGCAGCAAGAGAUAGAAUCCAAAAGAGAAGAAGAUCAGCCUGCAGAUGUGGACUGCUAAAUGCAGGCUGAUCUUCUCCCCUUUGGGAUUCUCUUAUGAGAAGCCA
#=GC SS_cons             :<<--<<-<<<<--<<<<<<-<<<<-<-<<<<<<<<<<<<<<<<----<<<____>>>-->>>>>>>>>>>>>>>>->->>>>->>>>>>>>>>->>---->>::
#=GC RF                  AGcAGcaAgaGgUAgaauccAaaaGAGaaGaaGaucaGccuGcaGAUGugGAcUGCcaAAugCaggCugauCuuCucCuCuuuGggauuccCucAugAGAagCcA
//
# STOCKHOLM 1.0

#=GF AC   RF02007
#=GF ID   mir-1237
#=GF DE   microRNA mir-1237
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   48.30
#=GF NC   40.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000585;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   17964270
#=GF RT   Mammalian mirtron genes
#=GF RA   Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC
#=GF RL   Mol Cell. 2007;28:328-336.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


AC200630.4/80537-80436   GUGGGGGGGCCCAGGCGCGGGAAGGGGUGGGGGUGGCAGAGCGCUGUCCCGGGGGCAGGGCUGAAGCGCGGCGACAGUAACUCUUUCUGCUCCGUCCCCCAG
AC163739.2/51314-51415   GUGGGAGGGCCCAGGCGCGGGCAGGGGUGGGGGUGGCAGAGCGCUGUCCCGGGGGCGGGGCCGAAGCGCGGCGACCGUAACUCCUUCUGCUCCGUCCCCCAG
AC175468.3/166036-166136 -UGGGAGGGCCCAGGCGCGGGCAGGGGUGGGGGUGGCAGAGCGCUGUCCCGGGGGCGGGGCCGAAGCGCGGCGACCGUAACUCCUUCUGCUCCGUCCCCCAG
#=GC SS_cons             :<<<<-<<<<---<<-<<<<<-<<<<<<-<-<<<-<<---<<<<<<<<<<<____>>>>>>--->>>>>->>->>>->->>>>>>>>>>>->>>>>>>>>>:
#=GC RF                  guGGGaGGgcccAGGcGcgGgaagGgGuGgGgGuGGcAGAGcGcuGccccGGGGGCggggCuGAagCgCGgCGaCcGcAaCcCcucCcgCUCCgcCCCCCaG
//
# STOCKHOLM 1.0

#=GF AC   RF02008
#=GF ID   mir-621
#=GF DE   microRNA mir-621
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   55.00
#=GF TC   65.40
#=GF NC   54.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000631;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [3]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF WK   MicroRNA
#=GF SQ   3


ABGA01215007.1/7101-7196   UAGAUUGAGGAAGGGGCUGAGUGGUAGGCAGUGCUGCUGUGCGUUGAUGAAGACCCAUGUGGCUGGCAACAGCUCUUACCUUUUGUCUCUGGGUCC
AJ309943.1/21168-21263     UAGAUUGAGGAAGGGGCUGAGUGGUAGGCGGUGCUGCUGUGCUCUGAUGAAGACCCAUGUGGCUAGCAACAGCGCUUACCUUUUGUCUCUGGGUCC
AACZ03170140.1/25830-25924 -AGAUUGAGGAAGGGGCUGAGUGGUAGGUGGUGCUGCUGUGCUCUGAUGAAGACCCAUGUGGCUAGCAACAGCGCUUACCUUUUGUCUCUGGGUCC
#=GC SS_cons               ::::::::<<<<<<<<<-<<<-<<<<<<<<-<<-<<<<<-<<-<--<<<______>>>-->>>>>>>>->>->>>>>>>>>>>->>>>>>--->>>
#=GC RF                    uAGAUUGAGGaaGgGgCUgagUGGuagGcgGuGcuGCugUGCucUGauGAAGAccCauGUgGCcaGCaACaGcgCcuaCCcucUGcCcCuGGGuCC
//
# STOCKHOLM 1.0

#=GF AC   RF02009
#=GF ID   mir-987
#=GF DE   microRNA mir-987
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   105.30
#=GF NC   48.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000859;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17989255
#=GF RT   Systematic discovery and characterization of fly microRNAs using 12
#=GF RT   Drosophila genomes
#=GF RA   Stark A, Kheradpour P, Parts L, Brennecke J, Hodges E, Hannon GJ, Kellis M
#=GF RL   Genome Res. 2007;17:1865-1879.
#=GF RN   [2]
#=GF RM   20037610
#=GF RT   Evolutionary flux of canonical microRNAs and mirtrons in Drosophila
#=GF RA   Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC
#=GF RL   Nat Genet. 2010;42:6-9.
#=GF RN   [3]
#=GF RM   17989254
#=GF RT   Evolution, biogenesis, expression, and target predictions of a
#=GF RT   substantially expanded set of Drosophila microRNAs
#=GF RA   Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC
#=GF RL   Genome Res. 2007;17:1850-1864.
#=GF WK   MicroRNA
#=GF SQ   3


AE013599.4/5200627-5200523 GAACAAUGUUGGACUGUGUUUAAAGUAAAUAGUCUGGAUUGAUGAAAGUUGCAUUCGAGAAUUCAUCAACAGGCAUUUACUUCAACUGCAGUUUGAACAAAAUGC
AC008341.3/60747-60643     GAACAAUGUUGGACUGUGUUUAAAGUAAAUAGUCUGGAUUGAUGAAAGUUGCAUUCGAGAAUUCAUCAACAGGCAUUUACUUCAACUGCAGUUUGAACAAAAUGC
AASS01002766.1/1118-1014   GAACAAUGUUGGACUGUGUUUAAAGUAAAUAGUCUGGAUUGAUGAAAGUUGCAUUCGAGAAUUCAUCAACAGGCAUUUACUUCAACUGCAGUUUGAACAAAAUGC
#=GC SS_cons               ::::::::<--<<<<<<--<<-<<<<<<<<-<<<<<---<<<<<<<--<<_______>>-->>>>>>>->>>>>>>>>>>>>->>-->>>>>>-->:::::::::
#=GC RF                    GAACAAUGuUGgaCuGcGUuuAaaGuaaauAGcCuGGAUuGauGaaAGcuGCAUUCGagAAuuCauCaACaGgCauuuaCuuCaaCUgCaGucUGaACAAAAUGC
//
# STOCKHOLM 1.0

#=GF AC   RF02010
#=GF ID   mir-3180
#=GF DE   microRNA mir-3180
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   74.80
#=GF NC   53.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000894;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20224791
#=GF RT   Discovery of novel microRNAs in female reproductive tract using next
#=GF RT   generation sequencing
#=GF RA   Creighton CJ, Benham AL, Zhu H, Khan MF, Reid JG, Nagaraja AK, Fountain
#=GF RA   MD, Dziadek O, Han D, Ma L, Kim J, Hawkins SM, Anderson ML, Matzuk MM,
#=GF RA   Gunaratne PH
#=GF RL   PLoS One. 2010;5:e9637.
#=GF RN   [2]
#=GF RM   20300190
#=GF RT   Characterization of the Melanoma miRNAome by Deep Sequencing
#=GF RA   Stark MS, Tyagi S, Nancarrow DJ, Boyle GM, Cook AL, Whiteman DC, Parsons
#=GF RA   PG, Schmidt C, Sturm RA, Hayward NK
#=GF RL   PLoS One. 2010;5:e9685.
#=GF WK   Mir-3180_microRNA_precursor_family
#=GF SQ   3


AC010488.7/42610-42497   GCCGACUCUACAGUGCGACGGGCGGAGCUUCCAGACGCUCCGCCCCACGUCGCAUGCGCCCCGGGAAAGCGUGGGGCGGAGCUUCCGGAGGCCCCGCCCUGCUGCCGACCCUGU
AC138932.4/127957-127844 GCCGACUCUACAGUGCGACGGGCGGAGCUUCCAGACGCUCCGCCCCACGUCGCAUGCGCCCCGGGAAAGCGUGGGGCGGAGCUUCCGGAGGCCCCGCCCUGCUGCCGACCCUGU
AC002039.1/16228-16341   GCCGACUCUACAGUGCGACGGGCGGAGCUUCCAGACGCUCCGCCCCACGUCGCAUGCGCCCCGGGAAAGCGUGGGGCGGAGCUUCCGGAGGCCCCGCCCUGCUGCCGACCCUGU
#=GC SS_cons             ::::::::::::::(((--((((((-((((((-((-((((((((((((((,<<____>><____>,,,))))))))))))))-))-))))))-)))))))))::::::::::::
#=GC RF                  GccGAcUcUAcAGUGCgAcGGGCGGAGCcuCCAGacGCuCCGCCCCaCGccGCAUGcGCCccGGGAAAgCGuGGGGCGGaGCUuCcGGagGCcCCGCCCcGCUGccGAcccUGU
//
# STOCKHOLM 1.0

#=GF AC   RF02011
#=GF ID   mir-575
#=GF DE   microRNA mir-575
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   73.20
#=GF NC   38.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000586;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [3]
#=GF RM   16505370
#=GF RT   The colorectal microRNAome
#=GF RA   Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O,
#=GF RA   Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H,
#=GF RA   Kinzler KW, Vogelstein B, Velculescu VE
#=GF RL   Proc Natl Acad Sci U S A. 2006;103:3687-3692.
#=GF WK   Mir-575_microRNA_precursor_family
#=GF SQ   3


AC073413.6/132554-132462     -AUUCAGCCCUGCCACUGGCUUAUGUCAUGACCUUGGGCUACUCAGGCUGUCUGCACAAUGAGCCAGUUGGACAGGAGCAGUGCCACUCAACUC
ABGA01388661.1/10721-10628   AAUUCAGCCCUGCCACUGGCUUAUGUCAUGACCUUGGGCUACUCAGGCUGUCUGCACAAUGGGCCAGUUGGACAGGAGCAGUGCCACUCAACUC
AADB02007055.1/191943-191850 AAUUCAGCCCUGCCACUGGCUUAUGUCAUGACCUUGGGCUACUCAGGCUGUCUGCACAAUGAGCCAGUUGGACAGGAGCAGUGCCACUCAACUC
#=GC SS_cons                 ::::::<<<<<<<<<<<<<<<<<<<<<<-<<<<<<<<<___>>>>>>-->>>>>->>->>>>>>>>>->>>->>>>->>:::::::::::::::
#=GC RF                      AAUUcAGCCCuGCCaCuGGCucauGuCaUGaCCcuGgGcUACcCagGcUGuCuGcaCAaugaGCCaGUuGGACaGGAGCAGUGccAcUcAAcUc
//
# STOCKHOLM 1.0

#=GF AC   RF02012
#=GF ID   group-II-D1D4-7
#=GF DE   Group II catalytic intron D1-D4-7
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Weinberg Z
#=GF SS   Predicted; Weinberg Z
#=GF GA   34.00
#=GF TC   34.20
#=GF NC   33.80
#=GF TP   Intron;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00102
#=GF DR   SO; 0000603; group_II_intron;
#=GF DR   GO; 0000373; Group II intron splicing;
#=GF RN   [1]
#=GF RM   11377794
#=GF RT   The ins and outs of group II introns.
#=GF RA   Bonen L, Vogel J
#=GF RL   Trends Genet 2001;17:322-331.
#=GF RN   [2]
#=GF RM   11726522
#=GF RT   Control of branch-site choice by a group II intron.
#=GF RA   Chu VT, Adamidi C, Liu Q, Perlman PS, Pyle AM
#=GF RL   EMBO J 2001;20:6866-6876.
#=GF RN   [3]
#=GF RM   12870716
#=GF RT   Group II introns: structure and catalytic versatility of large natural
#=GF RT   ribozymes.
#=GF RA   Lehmann K, Schmidt U
#=GF RL   Crit Rev Biochem Mol Biol 2003;38:249-303.
#=GF CC   Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi,
#=GF CC   plants and protists, and also in mRNA in bacteria. They are large
#=GF CC   self-splicing ribozymes and have 6 structural domains (usually designated
#=GF CC   dI to dVI. This model and alignment represents only domains V and VI. A
#=GF CC   subset of group II introns also encode essential splicing proteins in
#=GF CC   intronic ORFs. The length of these introns can therefore be up to 3kb.
#=GF CC   Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing
#=GF CC   with two transesterification steps. The 2' hydroxyl of a bulged adenosine
#=GF CC   in domain VI attacks the 5' splice site, followed by nucleophilic attack
#=GF CC   on the 3' splice site by the 3' OH of the upstream exon. Protein machinery
#=GF CC   is required for splicing in vivo, and long range intron-intron and
#=GF CC   intron-exon interactions are important for splice site positioning. Group
#=GF CC   II introns are further sub-classified into groups IIA and IIB which differ
#=GF CC   in splice site consensus, distance of bulged A from 3' splice site, some
#=GF CC   tertiary interactions, and intronic ORF phylogeny [1].
#=GF WK   Group_II_intron
#=GF SQ   244


BABA01000146.1/2452-2598       CCUAU-UG--UUCUGUCA-AU-AGUAGUCUA-AAG-AGG-CGUGCU-UUAC-CAAG---UCA-------------------------UGGUUUAGU--GCG-AAGC-CCUCUUGACAA-UGCAGUC--CUUUACA-GAAAUAU-------------------------------CCAAUG-UAUA-GG-----------CUGUUA--------GG---------C--UGACU-GA-UAUG-AGUA-AC-A---UA-UG--UGAAUCG
BABG01002401.1/429-583         CCUGU-UA--UUCCAUUA-GC-AGUAGUCUA-CUG-UCAACA-AAG-CAGC-UG-G---UAA-------------------------CGGCUGUGA----GGAAGCGUGACGGGACAAGGGUAGCC--C-CACCC-GAAA--------------------------------------GG-GU---UC-AAGC-UGAAACUGCGA--------GGUGAAAG-C-G--AUA-A-GC-UGCA-AGCA-AC-A--AUG-UGGUUGGGGAG
BAAZ01017280.1/390-540         CCUGU-UG--UUUCGUCA-AC-AGUAGCCUA-UGG-GAG-CGUGCG-AUAGUUA-G---CAA-------------------------UGAGGUCGU--GCGAUAGCAGAACC-AACAA-UGAAGC----CCUUCC-GAAA--------------------------------------GG-AGAA-GU-C-A----GAACCGCGA--------GGGAA----CGA--CAACU-GC-CGUU-AGUA-UC-G---AA-UGGCAGGGGAG
BABB01011740.1/601-458         -CUGU-----UUCGUCA--GC-AGUCUCCUA--CG-GUA-GGUGUA-UAAC-CA-A---UAA-------------------------GGUUCUUGU--ACU-AAGU-GGCUCGGACAA-UGAGGC----CCUUCC-GAAA--------------------------------------GG-AGAA-GU-U-U----GAACCGUGA--------GGGGA----AAG--CAACU-GC-UAUG-AGUG-UC-A---UA-UAGUUAGGGGA
BABA01032328.1/635-788         CCUG--UA--UGCCAUUA-GC-AGUAGUCUA-CUG-UCAACA-AAG-CAGC-UG-G---GUA-------------------------CGGCUGUGA----GGAAGCGUGACGGGACAAGGGUAGCC--CUACCCC-GAAA--------------------------------------GG-G----UU-N-CAGCUGAACCGCGA--------GGCGA-AN-GCA--AUA-G-ACUGGCA--GCA-ACGA---UG-CCGUCGGGGAG
BAAW01000739.1/43-153          UGCUC-UA--UCCAUUCA-GG-GUAACUCUA-UCA-UGA-CUAGCG-UGAA-UA-G---UAA-------------------------CGUUCGGGU--UAGAAAGC-UCAUGAGACAA-UGUGGA-------------------------------------------------------------------------------------------------------AG-U-CC-GAGU-AGCC-UA-A---AC-UGGGAUAACUG
BABG01005704.1/988-1136        CCUGC-AA--UUCCGUUU-GC-AGUAGUCUG-AGG-GUA-CGUGCA-UAAU-GA-G---UAA-------------------------UCAUUUUGU--GCG-AAGC-UGCCCUGACAA-AGUACC----CUUUCC-GAAA--------------------------------------GG-AAUA-GA-C-C----AAAGCGUGA--------GCCGA----GGU--CAA-UAGC-GGAU-AACA-UC-G---UU-CUGCCGAGGGG
BABB01001024.1/1564-1712       CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUCUCC-GAAA--------------------------------------GG-ACAA----G-AC-UGAA-CCGUGA--------GGGAA-CG-UCA--AGG-G-GC-GGUU-AGUA-UC-A---UA-CUGCCGAGUGG
BABD01035765.1/573-426         CCCGC-UG--UUCCGUCA-GC-GGCAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------GGGAA----UGU--CAA-GGAC-GGUU-AGUA-UC-A---GA-CCGUUGAGUGG
BAAU01002944.1/1762-1615       CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCU-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA----G-AC-UGAA-CCGUGA--------GGAAA-CG-UCA--AG--G-GC-GGUU-AGUA-UC-A---UA-CCGUCGAGUGG
BAAY01000702.1/2417-2270       CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------GGGGA----AGU--CAA-GGGU-GGUU-AGUA-UC-A---UA-CUGCCAAGUGG
BABB01001802.1/2526-2674       CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CC-G---UGA-------------------------CUGGGUUGU--GCU-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------AGGAA----CGU--CAA-CGGC-GGUU-AGUA-UC-A---UA-CCGUCAAGUGG
BABG01031736.1/46-193          CCUAU-UG--UUCCGUCA-AU-AGUAGCCUA-CGG-UCA-CGUGCG-UCGC----U---CAAA----------------------AG--GCGGGGU--GCG-AAGC-UGGCCGGACAA-AGUAGC----CCUUCC-GCAA--------------------------------------UG-AGAA-GC-C-C----GAACCGCGA--------UGGAA----CGG--CAACU-GC-UCUU-AGCA-CA-A---AA-GAGUCGGGGAA
BABD01032669.1/717-570         CCCGC-UA--UUCCGUCA-UC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCU-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA----G-AC-UGAA-CCGUGA--------GGGAA-CG-UCA--AG--G-GC-GGUU-AGUA-UC-A---UA-CCGUCGAGUGG
BAAX01014215.1/304-454         CCUGU-UA--UUCCAUUA-UC-AGUAGCCUA-UCG-UCA-CCGAAG-CGGC-UG-G---CAA-------------------------CGGCCGUGA--GGC--AGCAUGACGAGAAAA-GGUAGC----CCUCCC-GAAA--------------------------------------GG-G----UC-AAGC-CAAAACCGCGA--------GGCAGAGG-C-G--AAA-A-GC-UGGA-AGCA-AC-G---UC-CGGCUGGGGAG
BAAU01000472.1/2053-2192       CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CCG-ACC-GAUGCA-CCU---------UAA----------------------------UGUUGU--AUU-AAGC-GGUCGGGACAA-AGUACAC--U---UUC-GCAA--------------------------------------GA------CA-A-GA-CAGAACCGUGA--------GGGGAAGU-CAA--G---U-AC-GGUU-AGUA-UC-A---UA-CCGUAGAGUGG
BABD01002595.1/2257-2405       CCCGU-UG--UUUCGUCA-AC-GGUAGCCUA-UGG-ACA-GAUGCA-CCAA-UA-G---UAA-------------------------UAUA-CUGU--AUCAAAGC-UGUCCAGACNA-GGUAGC----CCUUCC-GAAA--------------------------------------GG-AGCA-GU-C-A----GAACCGUGA--------GGGAA----AGA--CAA-UGGC-UGUU-AGUA-UC-A---UA-CAGUCAGGGAG
BABD01024695.1/315-465         CCUGU-UA--UUCCAUUA-GC-AGUAGCCUA-UCG-UCA-CCGAAG-CGGC-UG-G---CAA-------------------------CGGCCGUGA--GGC--AGCAUGGCGAGAAAA-GGCAGC----CCUCCC-GAAA--------------------------------------GG-G----UC-AAGC-CGAAACCGCGA--------GGCAGAGG-C-G--AAA-A-GC-UGGA-AGCA-AC-G---UC-CGGCUGGGGAG
BAAX01002618.1/1039-894        CCUCU-UA--UUCCGUUA-AG-AGUAGCCUA-CCG-AAG-CGUGCG-UAGU-UG-G---CAA-------------------------CGACUGGGU--GCG-AAGC-CUUCGGGACAA-UAUGGCG-AGGUCUUGAACAUC------------------------------------ACA-AGAC-GC-A-G-------CUGUUA--------GG-------CUGACUGA-C-AA-GGAC-AACG-UA-A--AG------UAACCGC
BAAU01010920.1/619-769         CCUGU-UA--UUCCAUUA-GC-AGUAGCCCA-UCG-UCA-CCGAAG-CGGC-UG-G---CAA-------------------------CGGCCGUGA--GGC--AGCAUGACGAGAAUA-GGUAGC----CCUCCC-GAAA--------------------------------------GG-G----UU-AAGC-CGAAACCUCGA--------GGCAGAGG-C-G--AAA-A-GC-UGGA-AGCA-AC-G---UC-CGGCUGGGGAG
BABD01008324.1/247-93          CCUGU-UA--UUCCAUUA-GC-AGUAGUCUA-CUG-UCAACAAAGC-GG-C-UG-G---UAA-------------------------CGG-CUGUG--AGG-AAGCGUGACAGGACAAGGGUAGC----CCCACC-CGAAA------------------------------------AGG-U----UC-AAGC-UGAAACUGCGA--------GGUGAAAG-C-G--AUA-A-GC-UGCA-AGCA-AC-A--AUG-CGGUUGGGGAG
AF103902.1/305-453             UCCGU-UG--UUCCGUCA-AC-GGUAACCUA-CGG-ACA-GAUGCA-CCAA-UA-G---UGA-------------------------UAAUUCUGU--AUC-AAGC-UGUCUGGACAA-UGUACU----CCUUCC-GAAA--------------------------------------GG-AAAA-GA-C-A----GAGCCGUAA--------GGGAA----AGA--CAA-UAAC-UCUU-AGUA-UC-A---UA-GAGUUGGGAGG
ABFZ02000022.1/174605-174752   CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------GGGAA----UGU--CAA-GGAC-GGUU-AGUA-UC-A---UA-CCGUUGAGUGG
ABSO01000678.1/263-413         CCUGC-UA--UGCGACUA-GC-AGUAGCCUA-GGG-AGA-CGUGCG-UCAC-UG-G---UAA-------------------------CGGUGGGGU--AUG-AAGC-UCUCCUGACAA-UGUAGCC--C----CC-GCAAA------------------------------------GGG------UG-U-UC-AAGGAUCGCGA--------GGUCUUCG-GGC--AGA-G-AC-UCCG-AGCA-GC-A--ACG-GGGUCGAGGAG
ABQC02000024.1/368037-367894   C-----UG--UUCCGUCA-G-CGGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------GGGAA----UGU--CAA-GGGC-GGUU-AGUA-UC-A---UA-CCGUUGAGUGG
ABWZ01000028.1/26993-27140     CCUGC-UG--UUUCGUCA-GC-AGUAGCCUA--CG-GCA-GGUGCA-UAAC-CA-G---UAA-------------------------UGGUCUUGU--ACU-AAGC-UGCUCGGACAA-UGAAGC----CCUUCC-GAAA--------------------------------------GG-AGAA-G----U--UUGAACCGUGA--------GGGGA-AA-G----CAACU-GC-UAUU-AGUG-UC-A---UA-UAGUAGGGGAG
ABFZ02000019.1/461424-461274   CCUGU-UG--UUUCGUCA-AC-AGUAGCCUA-UGG-GAA-CGUGCG-AUAGUAA-G---CAA-------------------------UGAGGUCGU--GCGAUAGCAGAACC-AACAA-UGAAGC----CCUUCC-GAAA--------------------------------------GGAGAA--GU-C-A----GAACCGCGA--------GGGAA----CGA--CAACU-GC-CGUU-AGUA-UC-G---AG-UGGCAGGGGAG
AAJT02000075.1/22811-22921     CCAGC-UA--UCCCAUUA-GC-UGUAGCCUA-CCG-GGA-CAGGCG-CUGC-CG-G---CAA-------------------------CGGCGGGGU--CUG-AAGC-UCCCGGGACAA-CGAGAG----------CCG---------------------------------------------------------------------------------------------G-GC-UGCA-AGCA-UC-A---UG-CGGCAGGAGAG
AB255564.1/13708-13853         CUCGC-UA--UGCGACCA-GC-GAUAGCCUA-ACA-AGA-CAUGCA-UCAC-UG-G---UAA-------------------------CGGUGGGGU--GUG-AAGC-UCCUGCAACAA-UGUAGCC--C-----C-UUG-A------------------------------------UG-------UG-U-GU-AUUUGCUGCGA--------GGUGA-AG-CAC--AGA-U-GC-UCGG-AGCC-GU-A---CC-GGCUUGUGGCG
AP008981.1/1757381-1757231     UCUGU-UG--UUCUAUCA-AC-AUAAGCCUA-CUG-GUA-UAUGC----------AAAGAAGUGAUUUGA---------UGUAUAAA-------GU--AUA-AAGC-UAUCAGGACAA-UGUACU-----CGGCU-CAAA--------------------------------------AG-UGG--AU-C-A----GAAUCGUGA--------GAGGA----AGA--UUA-G-AC-UACU-AGUU-UC-A---UG-UGGUCAGAGGU
BA000039.2/2082748-2082897     CCGGU-UG--UUCCCCCA-AC-CGUAGCCUA-AGG-AGG-CAUGCG-UGAC-UG-G---UAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-UGAAGC----CCGAAC-CGGAA------------------------------------GGU-UGGA-GC-C-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-CACC-AGCG-UC-A---GG-UGAUAGGGAGC
AAZW01000003.1/136710-136849   CCAUC-UG--UAUCACCA-GA-UG-AACCUA-GGA-GCC----------------UGAAUUAA----------------------GU----------------AGC-GGCUCUGACAA-UGUAACG-AAGACAAGAAACUA------------------------------------UCU-UGUC-GG-GAG--CUAAAUCGCGA--------GAGAA-AG-CUC--C---U-CC-UGAU-AACC-AC-AUAAAU-CGGGUGAGUGC
BA000039.2/1148197-1148346     CCGAU-UG--UUCCCCCA-AC-CGUAGCCUA-GGG-AGG-CAUGCG-CGAC-UG-G---UAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-CGGAGC----CCGAAC-CGAAA------------------------------------GGU-UGAA-GC-C-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-UGCC-AGCG-UC-A---GG-CGAUAGGGAGC
AAOF01000010.1/5644-5795       UCCGG-UG--UUCUGCCA-CC-GGUACCCUA-CCG-GGC-CAUGCG-UCGG-GA-G---UAA-------------------------UCCCGGGGU--GCG-AAGC-GUCCGGGACAC-UGUGGCC--UCCGCCU-G---A------------------------------------UAC-GCGG-GC-A-AC-UGAA-CCGCGA--------GGGGA-CG-UUG--U---G-AC-UGCC-AGCC-UC-A--GGG-CGGUCGGGAGC
AAWO01000025.1/18480-18617     CCGGA-AC--UUCCCUGU-UC-CGUAGCCUA-UCG-UUG-CGUGCG-UGGU-GA-G---CAA-------------------------UC-CCGGGU--ACG-AAGC-CAACGAGACAA-CGUAACC--C--------UAUA------------------------------------A--------GC-C-G----AUCCUGCGA--------AGGAA----AGG--CGU-G-AC-UGCG-AGCA-UA-A---CG-CGGGAGGGUGC
BAAY01011046.1/145-299         CCUGU-UA--UUCCAUUA-GC-AGUAGUCUA-CUG-UCAACA-AAG-CGGC-UG-G---UAA-------------------------CGGCUGUGA----GGAAGCGUGACAGGACAAGGGUAGCC--C-CACCC-GAAA--------------------------------------GG-GU---UC-AAGC-UGAAACUGCGA--------GGUGAAAG-C-G--AUA-A-GC-UGCA-AGCA-AC-A--AUG-CGGUUGGGGAG
ABPQ01003269.1/619-463         UCCUG-UU--UUCUGCAA-CA-GGUAUUCUA-CCG-GGA-CGUGCU-UUCG-GA-G---UAA-------------------------UCUGAUGGU--GCG-AAGC-UUCCGGGACAA-UGAAGCC--CGUGGGG-ACUUG------------------------------------AUC-UCCA-GA-A-GA-GGAAACCGCGA--------GGGGACCU-CAA--C---U-UC-UGCC-AGCA-UC-G--GGG-CGGUAGGGGGC
CP000721.1/836503-836393       UGCCC-CA--UCCAUUCG-GG-GUAACUCUA-UCG-UGA-CUAGCG-UGAA-UG-G---UAA-------------------------CGUUUGGGU--UAGAAAGC-UCACGAGACAA-UGUGGA-------------------------------------------------------------------------------------------------------AG-U-UC-GAGU-AGCC-UA-A---AC-UGGAACAACUG
ABLD01000049.1/3908-3760       CCGGU-UG--UUCCAUCA-AC-CGUUCCCUA-CCC-GGA-CAUGCG-GGGC-UG-G---UAA-------------------------CAGCUCGGU--GUG-AAGC-UUCGGGGACAA-CGUAGC----CGCCGG-AUAU--------------------------------------CC-GGUA-CG-C-C----GAGCCGUGA--------GGCAA----GGC--GGA-A-UC-UGCC-AGCA-CG-A--AGG-CGGAGAGGAGC
BA000012.4/4898240-4898092     CCGGC-UG--UUUCAUCA-GC-CGUUCCCUA-CAC-GGA-CAUGCC-GAGC-CG-G---UAA-------------------------CAGCUCGGU--GUC-AAGC-UCUGGGGACAA-CGUAGC----UGCCGG-AU--U------------------------------------UCC-GGUA-CG-C-C----GAGCCGUGA--------GGCAA----GGC--GGA-A-UC-UGCC-AGCA-CG-A--AGG-CGGAGUGGAGC
ABSN01046413.1/475-626         CCUGA-UG--UUCUGCCA-UC-AGUAUCCUA-CCA-GGC-GGUGCG-UCGC-UG-G---UAA-------------------------CGGCGGGGU--GCU-AAGC-GCCUGGGACACGUGUAACC--UCAUCCU-UC----------------------------------------GG-GAUG-GC-A-AC-UUAA-UCGUGA--------GAAG-CGG-UUG--C---G-AC-UGCC-AGCA-UC-A--AGG-CGGUUGGGAAC
BA000039.2/1023518-1023667     CCGGU-UG--UUCCCCCA-AC-CGUAGCCUA-GGG-AGG-CAUGCG-UGAC-UG-G---UAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-CGGAGC----CCGAAC-CGAAA------------------------------------GGU-UGAA-GC-C-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-CACC-AGUG-UC-A---GG-UGAUAGGGAAC
AATD01006660.1/210-362         CCCAC-UA--UUCCGUUA-GU-GGUAGCCUA-GUG-CCA-CCUGCA-UCUG-CG-G---CAA-------------------------CAAGGAUGU-UGGG-AAGC-UGGCACGACAA-AGUAGC----CCUUUGCGAUAU------------------------------------GCA-AGAA--G-U-G---GAAACCGUGA--------GGUGG-A--AAC---AA-A-AC-UGCG-AGCA-UC-A--AUG-CGGUUAGGGAG
CR626927.1/4789716-4789861     CCUAU-UG--UUCCGUCA-AU-AGUAGUCUA-AAG-AGG-CGUACU-UUAC-CA-G---UAA-------------------------UGGUUUAGU--GCG-AAGU-CCUCUUGACAA-UGCAGUC--CUUUACA-AAAAUAU-------------------------------CCAAUG-UAUA-GG-U-U---------GUUA-----------------GGC--UGACU-GA-UAUG-AGUA-AC-A---UA-UG--UGAAUCG
ABPU01008502.1/193-333         CCUGA-UA--UGUUCCUA-UC-AG-ACUCUA-GGA-UGA-CAUGCU-ACCU-UU-GCGCAGA-------------------------UGAAGGGGU--GUG-AAGC-UCAUCCGACAA-UGUACC-----------GAAAU------------------------------------G--------GG-U-C---AAAGCUGCAA--------GGUAG-A--GAC--C---CUUC-CGGA-AAUC-CC-G---UC-CGGUUAAGGGC
AAFY01000746.1/409-545         CCAUU-UG--UAUCACCA-GA-UG-ACCCUA-GGA-UCC----------------UGAAUAAA----------------------GC----------------AGC-GGAUCUGACAA-UGUAACG-AAGUCCGGUAAAUU------------------------------------ACU-GGAC-GG-GAA--CUGAAUCGUGA--------GAGGA-UG-UUC--C---U-CC-UGAU-AACC-AC-A---AU-CGGGUAAGUGC
AE015928.1/2873429-2873279     CCUGU-UG--UUCCGUCA-AC-AGUAGCCUA-UGG-GAA-CGUGCG-GUAUUAA-G---CAA-------------------------UGAACCCGU--GCGGUAACAGAACC-AACAA-UGAAGC----CCUUCC-GAAA--------------------------------------GG-AGAA-GU-C-U----GAACCGUGA--------GGGGA----UGA--CAACU-GC-CGUU-AGUA-UC-G---AA-CGACAGGGGAG
ABPX01010118.1/134-278         CCCUA-UA--UGCUGCUA-UA-GGUAUCCUA-UCG-AUA-CAUGAG-GGGU-UG-G---CAA-------------------------CGACCCGGU--CUG-AAGC-UAUCGAGACAA-UGUCCC-----CGGCC-U---C------------------------------------UGA-CCC--UG-U-G----GAUUCGUGA--------GAAAA----AGC--AGG-U-CU-UGUC-AGUG-UC-A---GA-CAAGUAGGGGG
AF038459.1/665-813             UCCGU-UG--UUCCGUCA-AC-GGUAACCUA-CGG-ACA-GAUGCA-CCAA-UA-G---UGA-------------------------UAAUUCUGU--AUC-AAGC-UGUCUGGACAA-UGUACU----CCUUCC-GAAA--------------------------------------GG-AAAA-GA-C-A----GAGCCGUAA--------GGGAA----AGA--CAAUA-AC-UCUU-AGUA-UC-A---UA-GAGUUGGGAGG
AAFY01025956.1/394-530         CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-AGA-CUC----------------UGAAUAAA----------------------GC----------------AGC-GAGUCUGACAA-UGUAACA-AUAUUCGGCUUUAU------------------------------------GCC-GAAU-GG-G-AACUGAA-UCGUGA--------GAGGACGU-UCC--U-----CC-UGAU-AACC-AC-A---AU-CGGGUAAGUGC
AAQF01000163.1/6697-6545       CCUAC-UG--UAUCGUCA-GU-AGUUUCCUA-CCU-CGG-CAUGCA-UUGC-UG-G---UAA-------------------------CGGCUUUGU--GUG-AAGC-CCGAGCGACAA-UGAAGCC--CUCAGUC-AC--U------------------------------------CGA-CUGG-GA-G-A--GAAAAUCGCGA--------GAGGA----UCU--CAA-C-UC-UGGA-AGCA-UC-G--AUC-UGGAUGGGAGC
AACY020306371.1/2215-2077      CCGGC-UG--UACUUCCA-GC-CGUAGCCUA-CCG-GCA-CAUGCG-GGAU-UG-G---UAA-------------------------CGAACCCGU--GUG-AAGC-UGCCGGGACAA-CGCAAC----CUGUGA-AUAAA------------------------------------UCC-ACAA--------------GGCCGA--------CCCGU----------GA-A-AA-CCAG-ACCU-GU-C---CC-GGUUUUGAUCC
BA000039.2/246565-246416       CCAGC-UG--UUCCCCCA-GC-UGUAGCCUA-GGG-AGG-CAUGCG-UGAC-UG-G---CAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-CGUAGC----CUGAAC-CGUAA------------------------------------GGU-UGAA-GC-C-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-CACC-AGUG-UC-A---GG-UGAUAGGGAGC
AE017354.1/2313467-2313326     CCAUU-UG--UAUCGUCA-GA-UG-AACCUA-CGG-GAG-U--------------UAAU-----------------------------------------A-AAGC-CUCCCUGACAA-UGUAGUG--AAACUA-CAGCUGAAGG----------------------------GCUGA-U-AGUG-AG-AUGUUAACAUCCGAAA--------GGAAGUAA-AUC--U---A-CC-UGAU-AGCC-AA-A---AU-CGGGAUAGCUA
AACY020351447.1/700-847        CCUGC-UG--UUCUGCCA-GC-AGUAGCCUA-CUU-GAU-CGUGCG-UCAC-UG-G---CAA-------------------------CGGUGGGGU--GCG-GAGC-UUCAAGGACAA-CG-ACC----GGGGCG-UCA---------------------------------------UG-CCUA-GC-U-G----GAGCCGCGA--------GGCGA----AAG--CGACA-CC-UGCA-AGCA-UC-G--ACG-CGGGAGCCGGA
CP001108.1/688351-688494       CCAGC-UG--UACCGUCA-GC-UGUGCCCAC-CGG-CA--CAUGCA-GAGG-GA-G---UAA-------------------------UCCUUCUGU--GUG-AAGC--UGCC-GGAAA-CGUACC----CGCAGG-AUA-C------------------------------------CUG-U----AGGC-G----AACCCGUGA--------GG-GA---ACGC--UGA-G-UC-UGCC-AGUA-GC-----AGGCGGAGAGGGGC
BA000039.2/1578955-1578806     CCGGU-UG--UUCCCCCA-GC-UGUAGCCUA-GGG-AGG-CAUGCG-UGAC-UG-G---CAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-CGUAGC----CCGAAC-CGUAA------------------------------------GGU-UGGA-GC-U-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-CACC-AGCG-UC-A---GG-UGAUAGGGAGC
AACY020351085.1/47-199         UCGUACUG--UUCCAGCAG--CCGUUCCGUA-UCU-GGA-CAGAUG-GAAC-UU-G---CAA-------------------------CAGCCCGGU--GUG-AACC-UUCGGGGACAA-CAUGGCU--GUCGGUU-------------------------------------------AU-CUGC-UA-C-GA-CGGGGCCGUGA--------GGCAAGGU-GGA--CGA-G-CC-CAUG-AUAC-CG-A---CA-UCGGGCGUUGG
ACET01000012.1/29501-29629     CCAAC-UA--UUCCGUUA-GU-UG-AGCCGA-GUA-UCG----ACU-GCAC----U---UAG---------------------------GUGUGGU------AAGC-UGAUAUU--AA-AGUAGCC--C-------UA--C------------------------------------UUG-A----GG-U-A----AAACCGUGA--------GGAAA----UAC--CGA-A-AC-UGCC-AGCA-AC-A--AGG-UGGUUAGGGAG
CP000724.1/1470038-1470147     UGCUC-UA--UCCAUUUG-GA-GUAACCCUA-UCU-ACA-GGUGCG-UCAU-CA-G---CAA-------------------------UGAAGGGGU--UCU-AAGC-UGUAGAGACAA-UGUGAA-------------------------------------------------------------------------------------------------------AA-U-CC-UGCA-AGCC-UA-A---UG-UGGGUGAUUGC
CP000471.1/3417928-3418068     CCCGA-UA--UUCUGCUA-UC-GGUAACCUA-CCU-GGA-CAUGCA-UGGU-GA-G---CAA-------------------------UCA-CAUGU--GUG-AAGC-UCCAGGGACAA-CGGUACU--G--------UCAC------------------------------------C--------UG-C-CA-CCAAGCCGUGA--------GGUAAGGU-GGU--U-----AC-UGCC-AGCA-UC-A---GG-CGGUUAAGUAU
ACAV01000027.1/56193-56040     UAUUA-CU--UCCACUUG-UA-AUAUUCCUA-CCG-GUA-CAUGCG-UGAA-AA-G---UAA-------------------------UUUUUAGGU--GUGAUAGC-UACCGGGACAA-UGUGGUA-GA-ACAGUACUCAC------------------------------------AAC-UG----G-U-A----AUACUGCUA--------GGAAA-AG-UGC----A-C-AU-GGUU-AACA-UA-AGUGAA-CUACUGCUGGG
ABPV01010990.1/218-373         CCUGC-UG--UUCUGCCA-GU-AGUAUCCUA-CCG-C-CACGUGCG-CCGUGCA-A---GAA-------------------------UGGCGGAGU--ACG-GAGC-GUGCGGGACAA-CGUAACC--CCUGACC-GGAU--------------------------------------GG-UCAA-GA-G-AC-AGAA-UCGCGA--------GAAGA-CG-UC----AA-U-UC-UGCC-AGCC-UC-AGAAGG-CGGAGGGGAAC
BABD01000296.1/2562-2415       CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------GGGAA----UGU--CAA-GGAC-GGUU-AGUA-UC-A---UA-CCGUUGAGUGG
CP000539.1/1496155-1496007     CCUGG-UG--UUCCGUCA-UC-AGUAGCCUA-CCG-GCA-CAUGCA-GGAC-UG-G---UAA-------------------------CGGUCUUGU--GUG-AAGC-UGCCGGGACAA-UGUAGC---UGGGCCC-UC----------------------------------------GG-GCUG-CG-C-U---GAUGCCGUGA--------GG---CAA-GGC--GUU-A-UC-UGCA-AGCA-UC-A--AUG-CGGAUACGGCG
CP000139.1/4214122-4214272     CCUGU-UG--UUCCGUCA-AC-AGUAGCCUA-UGG-GAA-CGUGCG-GUAUUAA-G---CAA-------------------------UGAACCCGU--GCGGUAACAGAACC-AACAA-UGAAGC----CCUUCC-GAAA--------------------------------------GG-AGAA-GU-C-----UGAACCGUGA--------GGGGA-U---GA--CAACU-GC-CGUU-AGUA-UC-G---AA-CGACAGGGGAG
BABA01000062.1/4413-4556       C-----UG--UUCCGUCA-G-CGGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------GGGAA----UGU--CAA-GGAC-GGUU-AGUA-UC-A---UA-CCGUUGAGUGG
ACAA01000102.1/2352-2209       C-----UG--UUCCGUCA-G-CGGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCU-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-----UGAACCGUGA--------GGGAA-C---GU--CAA-GGGC-GGUU-AGUA-UC-A---UA-CCGUCGAGUGG
CP000875.1/6105704-6105852     CCUGC-UG--UUCCACCA-GC-AGUACCCUA--CU-CGG-UACUGC-GGGA-CG-G---UAA-------------------------CGUCCCGUG--G-A-AAGC-CCGAG-GACAA-CGUAUCC--ACGACCG-AC----------------------------------------UG-GUCG-GG-A-CA-AGGG-CUGUAA--------AGCG-CUU-GUC--A---A-UC-UGCA-AGCA-UC-AU-CAG-CGGAUAGGAAC
ABZY01000084.1/63-210          CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCU-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-----UGAACCGUGA--------GGGAA-C---GU--CAA-GGGC-GGUU-AGUA-UC-A---UA-CCGUCGAGUGG
ACFP01000160.1/309-162         UCAGA-UG--UUUUGCCA-UC-UG-AGUCUA-CGC-AUC-AAUGCG-AAUC-GG-G---UAA-------------------------CCGGUUGGU--GCC-AAGC-GAUGCGGACAA-UGAACC----UCCUCU-UGAAA------------------------------------AAG-AAGA-UG-C-----UCAAUCGUGA--------AAGGA-----GC--AUA-A-AC-UACA-AGCA-UC-A---UG-UGGUUGGAGAG
CP001064.1/104769-104918       CCCGC-UA--UUCCGGUA-GC-GGUAGCCUA-AUC-AGA-AUGGCG-UUGC-UG-G---UAA-------------------------CGGCAAGGU--CAU-AAGC-UCUGAUGACAA-CGUAC-----UCUCCC-UCA---------------------------------------GG-AAGG-GU-A-AG-UCGAGCCGUGA--------GGUGAGAC-GAU--C---G-UC-UGCA-AGCA-UC-A---UG-CGGACAGGAGG
CP000316.1/4881571-4881428     CCACG-UC--UGGAACGA-CG-UGACCUCGA--CC-GUA-CGUGCG-UCUG-GA-G---UAA-------------------------UCCGGGGGU--GCG-GAGC-UACGGUUAAAC----AAC----CCGUGC-GCAA--------------------------------------GC-ACAC-AA-G-GC-UG---ACGUGA--------GU---CAG-UCC--CAA-U-CC-CACG-AACA-AG-A---CG-CGGGAAGGUUG
CP000471.1/1415555-1415413     CCCGA-UA--UUCUGCUA-UC-GGUAACCUA-CCU-GGA-CAUGCA-UGGU-GA-G---CAA-------------------------UCA-CAUGU--GUG-AAGC-UCCAGGGACAA-CGGUACU--G----UC-AC--C------------------------------------UG-------CC-A-C---CAAGCCGUGA--------GGUAUGAU-GUG--G---C-AA-CACU-AAAACGG-A--CAG-UGUUUUACGC-
AM902716.1/1122133-1122279     CCUGG-UG--UUCCGUCA-UC-AGUAGCCUA-CCG-AUA-CAUGCA-GGAC-UG-G---CAA-------------------------CGGUCUUGU--GUG-AAGC-UAUCGGGACAA-UGCACU----CAGGCC-AU--U------------------------------------UGG-CC-G-CG-C-A----GAGCCGCGA--------GGCAA----GGC--GUC-C-AC-UGCA-AGCA-UC-A--AUG-CGG-GGUGAGG
ABJB010326724.1/3999-4128      CCAUC-UA--UGUCACUA-GA-UG-AAUCUA-AGG-GUA----------------UGAAAAA----------------------------------------GAGC-UACCCUGACAA-UGUGACG-AAAUACUC-UUAA--------------------------------------GC-AUAG-GG-AAA----AUCUCGUGA--------AAGCA-AU-UUC--U---U-UC-UAAU-AAUC-AC-A---AU-CAGAUAAGUUG
CP000821.1/2188793-2188922     CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-AGA-CUC-U--------------GAAUAAA--------------------------------------G-UAGC-GAGUCUGACAA-UGUAACG--AAGUCCA-U-----------------------------------------UG-GACG-GG-A-AC-AGAA-UCGUGA--------GAAGA-CG-UUC--U---U-CC-UGAU-AACC-AC-A--AGU-CGGGUAAGUGC
AP002086.1/136129-135981       CCGAC-CG--UUCCAUCG-GU-CGUUCCCUA-CCC-GAA-CAUGCG-AAGU-UG-G---CAA-------------------------CGACUCCGU--GUG-GAGC-UUCGGGGACAA-CGUAAC----CACCGG-GUGA--------------------------------------CC-GGUC-CA-C----CGAA-CCGUGA--------GG---CGA-AGU--GGA-A-AC-UGCC-AGCA-CA-A--AGG-CGGUGAGGUGC
BA000039.2/93690-93541         CCGGU-UG--UUCCCCCA-AC-CGUAGCCUA-GGG-AGG-CAUGCG-UGAC-UG-G---UAA-------------------------CGGUCAGGU--GUG-AAGC-CCUCCCGACAA-UGUAGC----CCGAAC-CGCAA------------------------------------GGU-UGAA-GC-U-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-CACC-AGUG-UC-A---GG-UGAUAGGGAAC
ACAA01000059.1/15688-15835     CCUGC-UG--UUUCGUCA-GC-AGUAGCCUA--CG-GCA-GGUGCA-UAAC-CA-G---UAA-------------------------UGGUCUUGU--ACU-AAGC-UGCUCGGACAA-UGAAGC----CCUUCC-GAAA--------------------------------------GG-A----GA-AGU--UUGAACCGUGA--------GGGGA-AA-G----CAACU-GC-UAUU-AGUG-UC-A---UA-UAGUAGGGGAG
ABSP01002357.1/341-471         CCACC-UA--UGCUACUG-GG-UG-AAUCUA-GGG-GCA----------------UGAAUAAA-----------------------G----------------AGC-UGCCCUGACAA-UGUGACG-AUAGAAAC-UUA---------------------------------------GU-UUCG-GG-G-A--ACGAAUCGUGA--------GAAAU-GU-UCC--U---U-CC-UAGC-AACC-AC-A---GC-UGGGUAAGUGC
AAXF02000049.1/211098-210959   CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CCG-ACC-GAUGCA-CCU---------UAA----------------------------UGUUGU--AUU-AAGC-GGUCGGGACGA-AGUACAC--U---UUC-GCAA--------------------------------------GA------CA-A-GA-CAGAACCGUGA--------GGGGAAGU-CAA--G---U-AC-GGUU-AGUA-UC-A---UA-CCGUAGAGUGG
AAGC01000009.1/2186-2334       CCAGA-UG--UUUUGCCA-UC-UG-AGUCUA-CGC-AUC-AGUGCG-AAUC-GG-G---CAA-------------------------CCAGUUGGU--GCC-GAGC-GACGCGGACAA-UGAACC----UCCUCU-UGAUA------------------------------------AAG-AAGA-UG-C-U----CAAUCGUGA--------GAGAA----AGC--AUA-A-AC-UACA-AGCA-UC-A---UG-UGGUUGGAGGG
AAYH02000041.1/217042-217189   CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------GGGAA----UGU--CAA-GGAC-GGUU-AGUA-UC-A---UA-CCGUUGAGUGG
CP000155.1/4095686-4095835     CCGGU-UG--UGUGACCA-AC-CGUAGCCUA--GG-GGC-AGCGCA-UUUC-UG-G---CAA-------------------------CGGAUUUGU--GUG-AAGC-GCCCU-GACAA-UGUACC----CCCGCU-UU----------------------------------------AG-CGG--UG-C-CG-UUUUAUCGUGA--------GGUGA-AC-GGU--AGA-U-AC-UGCC-AGUA-GC-AA-AGG-CGGUUAAGGGG
ABSO01000493.1/1505-1630       CCUGC-UA--UGCGACUA-GC-AGUAGCCUA-GGG-AGA-CAUGCG-UCAC-UG-G---UAA-------------------------CGGUGGGGU--GUG-AAGC-UCUCCUGACAA-UGUAGC----CCC-----CGAA------------------------------------A----GGG-UG-C-CG-UCCAGUCGUGA--------GACAG-GC-GGU--A--------------------------------GAGGCUC
AAGC01000457.1/85-235          CCAGA-UG-UUUUCGCCA-UC-UG-AGUCUA-CGC-AUC-AGUGCG-AAUUAGG-G---UAA-------------------------CCAGUUGGU--GCC-GAGC-GACGCGGACAA-UGAACC----UCCUCU-UGAUA------------------------------------AAG-AAGA-UG-C-U----CAAUCGUGA--------GAGAA----AGC--AUA-A-AC-UACA-AGCA-UC-A---UG-UGGUUGGAGGG
CP000891.1/1166711-1166574     CCAUC-UG--UAUCACCA-GA-UG-AACCUA-GGA-GCC----------------UGAAUAAA----------------------GU----------------AGC-GGCUCUGACAA-UGUAACG-AAGAUUGG-UCUUU-----------------------------------GACC-AAUC-GG-G-AU-AUGAACCGCGA--------GGGGAUGA-UCC--U-----CC-UGAU-AACC-AC-A--AAU-CGGGUGAGUGC
ACBW01000110.1/707-846         CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA--CCGACC-GAUGCA-CC------U---UAA---------------------------U-GUUGU--AUU-AAGC-GGUCGGGACGA-AGUACA----CUUUC--GCAA---------------------------------------G-ACAA-GA-C-A----GAACCGUGA--------GGGGA----AGU--CAA-GUAC-GGUU-AGUA-UC-A---UA-CCGUAGAGUGG
CP000254.1/2920134-2920243     CACCC-AA--UCCAUUCU-GG-GCGUCCCUA-CCU-GCA-CGUGCG-UGUU-UA-G---CAA-------------------------UAAACGGGU--GCG-AAGC-UGCAGGAACAA-CGUGGU-------------------------------------------------------------------------------------------------------GA-U-UC-CCAU-AGUC-UC-U---UU-GGGAUAAGCUG
CP001101.1/1470582-1470724     CCAGU-UG--UGCCGUCA-AC-UGCUCCCAC--CG-GCA-CAUGCA-GGAU-GA-G---UAA-------------------------UCGCCCUGU--GUG-AAGC-UGCCG-GA-AA-CGUACC----CGCAGG-AAA---------------------------------------CC--GUA-GG-C-U----GCUCCGCGA--------GGAAA----UGC--CGA-A-UC-UGCC-AGUA-GC-A---GG-CGGAGAGGGGC
AACY021362152.1/133-261        CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-UGG-UUC----------------UGAAUAAA----------------------GC----------------AGC-GAGCCAAACAA-UGUAACA--AAGCCAA-U-----------------------------------------UU-GGCG-GG-A-A--ACAAAUCGUGA--------GAGGC-GU-UUC--U---U-CC-UGAU-AACC-AC-A---AU-UGGGUAAGUGC
BAAV01001924.1/1029-882        CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------GGGAA----UGU--CAA-GGAC-GGUU-AGUA-UC-A---UA-CCGUUGAGUGG
CP000099.1/2122669-2122779     UACCU-UU--UCCAUUUG-AG-GUAAUCCUA-CUG-UGA-CAUGCA-UAAA-UG-G---UAA-------------------------CGUUUGUGU--GUG-AAGC-UCACAUGACAA---UAUC----------AA-------------------------------------------------------------------------------------------GAAC-UC-AAAG-AACC-UG-A---CU-UUGAUAAUUGG
AACY020558273.1/3080-2932      CCUGU-UG--UGCAACCA-GC-AGUAGCCUA--GG-GAU-AGUGCG-UCAC-CA-G---UAA-------------------------UGGUGGGGU--GCA-AAGC-UUCCU-GACAA-UGUACU----CCCCAU-UC----------------------------------------AU-UGGG-UU-U-GG-UUUUACCGCGA--------GGUAG-GC-CAA--AGA-C-UU-CGCC-AGUA-GC-A---GG-CGGAUGAGAGA
BAAX01001945.1/1866-2020       CCUGU-UA--UUCCAUUA-GC-AGUAGUCUA-CUG-UCAACA-AAG-CGGC-UG-G---UAA-------------------------CGGCUGUGA----GGAAGCGUGACAGGACAAGGGUAGCC--C-CACCC-GAAA--------------------------------------GG-GU---UC-AAGC-UGAAACUGCGA--------GGUGAAAG-C-G--AUA-A-GC-UGCA-AGCA-AC-A--AUG-CGGUUGGGGAG
BAAY01003657.1/1599-1452       CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------GGGAA----UGU--CAA-GGAC-GGUU-AGUA-UC-A---UA-CCGUUGAGUGG
AAUJ02000001.1/2380424-2380574 CCUUG-UG--UGCGACCG-CA-AGUAGCCUA-CGG-UGA-CGUGCA-AGAC-CA-G---UAA-------------------------UGGACUUGU--GCG-AAGC-UCACCCGACAA-AGUACC-----CCCGC-GCAA--------------------------------------GC-GG---CA-U-CU-CUUACCCGUAA--------GG-GCAGC-GGU--GGA-C-AC-UGCC-AGCA-GA-A--AAG-CGGUGAAGGGG
AAFY01020425.1/496-367         CCUGA-UG--UUCUGCCA-UC-AGUAGUCUA--CC-CAC-U--------------GA-AUAA--------------------------------------A-GUGC-GUGGG-GACAG-AGGAAGC--CUCAUCC-GUAA--------------------------------------GG-AUG--GU-C-AC-UAAA-CCGUGA--------GGGG-UGG-UGG--C---G-AC-UGCA-AGCA-CC-A--CUG-CGGUCGGGAGC
BA000039.2/1159143-1159292     CCGGU-UA--UUCCCCCA-GC-UGUAGCCUA-GGG-AGG-CAUGCG-UGAC-UG-G---CAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-CGUAGC----CCGAAC-CGUAA------------------------------------GGU-UGGA-GC-U-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-CACC-AGCG-UC-A---GG-UGGUAGGGAGC
AACY024059039.1/148-8          CCUGU-UA--UACGGCUA-AU-AGUAGCCUA--GG-GAU-AGUGCG-AUGC-UG-G---UAA-------------------------CGGCAUGGU--GCG-GAGC-UUCCU-GACAA-UGUACCU--C---UGC-GCAA--------------------------------------GC-A----GU-A-CU-UUAACCCGCGA--------GGGUG--G-GUA--U-A-G-CA-CACG-AACA-AU-A---CG-----GAGCUGG
BA000039.2/2169626-2169775     CCGGU-UG--UUCCCCCA-GC-UGUAGCCUA-GGG-AGG-GAUGCG-UGAC-UG-G---CAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-CGUAGC----CCGAAC-CGUAA------------------------------------GGU-UGGA-GC-U-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-CACC-AGCG-UC-A---GG-UGGUAGGGAGC
ABQC02000019.1/68372-68519     CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-----UGAACCGUGA--------GGGAA-U---GU--CAA-GGGC-GGUU-AGUA-UC-A---UA-CCGUUGAGUGG
AAGC01000030.1/2524-2376       CCAGA-UG--UUUUGCCA-UC-UG-AGUCUA-CGC-AUC-AGUGCG-AAUU-GG-G---UAA-------------------------CCAGUUGGU--GCC-GAGC-GACGCGGACAA-UGAACC----UCCUCU-UGAUA------------------------------------AAG-AAGA-UG-C-U----CAAUCGUGA--------GAGAA----AGC--AUA-A-AC-UACA-AGCA-UC-A---UG-UGGUUGGAGAG
AE017196.1/522584-522732       CCAGA-UG--UUUUGCCA-UC-UG-AGUCUA-CGC-AUC-AGUGCG-AAUU-GG-G---UAA-------------------------CCAGUUGGU--GCC-GAGC-GACGCGGACAA-UGAACC----UCCUCU-UGAUA------------------------------------AAG-AAGA-UG-C-U----CAAUCGUGA--------GAGAA----AGC--AUA-A-AC-UACA-AGCA-UC-A---UG-UGGUUGGAGGG
CP000947.1/617466-617322       CCUGU-UA--UAUGACUA-AC-AGUAACCUA--GG-GAU-AGUGCA-UAAU-UG-G---CAA-------------------------CGAUUUUGU--GCG-GAGC-UUCCU-GACAA-UGUACC--------CC-CGAUA------------------------------------AGG------UU-A-UU-AAUA-CUGUGA--------AGUA-UUA-AUA--AGA-G-AC-UCGA-AACG-AC-C--AUU-GGGUUGAGGGA
BABB01003440.1/277-138         CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CCG-ACC-GAUGCA-CCU---------UAA----------------------------UGUUGU--AUU-AAGC-GGUCGGGACAA-AGUACA--------CU-UUCGC------------------------------------AAG-ACAA-GA-C-A----GAACCGUGA--------GGGGA----AGU--CAA-G-UA-CGGUUAGUA-UC-A--UAC-CGUAGAGUGG-
BAAU01010415.1/548-433         UAC---CG------ACCG-AU-G-CACCUUA-AUG-UUG--------------------UAU-------------------------U--------------AAGC-GGUCGGGACGA-AGUACA----CUUUC--GCAA---------------------------------------G-ACAA-GA-C-A----GAACCGUGA--------GGGGA----AGU--CAA-GUAC-GGUU-AGUA-UC-A---UA-CCGUAGAGUGG
ABSP01041733.1/674-526         CCUGC-UG--UUCCUCCA-GC-AGUAGCCUA-AGA-GUG-CAGGCA-ACAU-UG-G---UAA-------------------------CAA-GUUGU--CUG-AAGC-CACUCUGACAA-UGUAAC----CCAAUC-CGAAA------------------------------------GGA-UGAA-GC-C-A----AGCCCGUGA--------GGGGG----AAG--CGG-A-AC-UGCG-AGCA-UU-A---CG-CGGUAGGGGGC
CU207211.1/1002485-1002637     CCGGA-UG--CACGACCA-UU-CGUAACCUA-CUC-AAG-CAUGCG-UCAU-CG-G---UAA-------------------------CGGUGGGGU--GUG-AAGC-CUUGAAGACAA-UGUACCC--CCAGCUU-CA--C------------------------------------AGG-GCGG-CU-A-UC-UC---AUGCGA--------AUGA-GUG-GUU--GGA-G-AC-UGCU-AGCA-GC-A--AAG-CGGUUGAGGGG
ACBW01000084.1/16881-17028     CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-----UGAACCGUGA--------GGGAA-U---GU--CAA-GGGC-GGUU-AGUA-UC-A---UA-CCGUUGAGUGG
CP000096.1/1578347-1578202     CCAGC-AG--UGCCGUCU-GU-UGCCCUCAC--CG-AGA-CAUGCA-AGCA-GG-G---UAA-------------------------CCAACUUGU--GUG-AAGC-UCUCGGAUAAA-CGUACC----CGCAGA-AAA---------------------------------------AC-UGUA-GG-C-C----GACCCGUGA--------GGGAA----CGC--UGA-A-UC-UGCC-AGUA-GC-A---GG-CGGAGAGGGGC
CP000681.1/4055237-4055100     CUAUC-UG--UAUCACCA-GA-UG-AACCUA-GGA-GCC----------------UAAAUUAA----------------------GU----------------AGC-GGCUCUGACAA-UGUAACG-AAGAUUGGUCUUUG------------------------------------ACC-AAUC-GG-G-AU-AUGAACCGCGA--------GGGGAUGA-UCC--U-----CC-UGAU-AACC-AC-A--AAU-UGGGUGAGUGC
CP000698.1/1005804-1005665     CCUGA-AG--UAUCCCCU-UC-AGCGCCCUA--GG-CGG-CGUGCU-GGGU-AC-GCGCUGU-------------------------GUACUUGGU--GCG-AAGC-CCGCU-GACAA-UGUACC-----------GAA-U------------------------------------C--------GG-G-U--UUGAAUGGCGA--------CAGGA-GA-ACC--C---C-UC-CGGA-AACU-CC-A---UC-CGGUUAAGGGC
AM494475.1/1836266-1836116     UCUGU-UG--UUCUAUCA-AC-AUAAGCCUA-CUG-GUA-UAUGC----------AAAGAAGUGAUUUGA---------UGUAUAAA-------GU--AUA-AAGC-UAUCAGGACAA-UGUACU-----CGGCU-CAAA--------------------------------------AG-UGG--AU-C-A----GAAUUGUGA--------GAGGA----AGA--UUA-G-AC-UACU-AGUU-UC-A---UG-UGGUCAGAGGU
CP000790.1/1882981-1883118     CCGUU-UG--UAUCACCA-GA-CG-ACCCUA-AGG-CUC----------------UGAAUAAA----------------------GC----------------AGC-GAGCCUGACAA-UGUAACG--AAGUUUG-GCACUG---------------------------------UGCCA-AACG-GG-A-G--CAGAACCGUGA--------GGGAA-UG-CUC--C---U-CC-UGAU-AACC-AC-G--AAU-UGGGUGAGUGC
AAWO01000025.1/3044-3193       CCUCC-CG--UUCCCUCG-GG-AGUAGCCUA-ACC-GGA-CGUGCG-AAGG-CG-G---UAA-------------------------CGCCUUGGU--GCG-AAGC-UUCGGUGACAA-CGUACCG--GCCUCCC-AAAG--------------------------------------GG-GA---CA-G-U---CAGACCGCGA--------GGAAU--G-ACU--GAG-G-CC-UGCG-AGCA-UC-A---CG-CGGACCCCGGG
CP000254.1/549450-549341       CACCC-AA--UCUAUUCU-GG-GCGUCCCUA-CCU-GCA-UGUGCA-UGUU-UA-G---CAA-------------------------UAAACGGGU--GCG-AAAC-UGCAGGAACAA-CGUGGU-------------------------------------------------------------------------------------------------------GA-U-UC-CCAU-AGUC-UC-A---UU-GGGACAAGCUG
BA000039.2/2565424-2565275     CCGGU-UG--UUCCCCCA-AC-CGUAGCCUA-GGG-AGG-CAUGCG-UGAC-UG-G---UAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-UGAAGC----CCGAAC-CGUAA------------------------------------GGU-UGGA-GC-U-G----AAUCCGCGA--------GGAGG----AAG--CAA-C-UU-CACC-AGCG-UC-A---GG-CGAUAGGGAGC
CP001391.1/1013867-1014014     CCAGA-UG--UUUUGCCA-UC-UG-AGUCUA-CGC-AUC-AGUGCG-AAUC-GG-G---CAA-------------------------CCGGUUGGU--GCC-AAGC-GAUGCGGACAA-UGAACC----UCCUCU-UGAAA------------------------------------AAG-AAGA-UG-C-UC-AA---UCGUGA--------GAG----G-AGC--AUA-A-AC-UACA-AGCA-UC-A---UG-UGGUUGGAGAG
ABSQ01001138.1/277-409         CCGCC-CG--UGUCACCG-GGUUG-AAUCUA-GGA-GUC----------------UGAAUAAA-----------------------G----------------AGC-GACUCUGACAA-CGUAGCG--AAGCACC-GCAA--------------------------------------GG-UGUG-GG-A-U--GCAACUCGCGA--------GAGGC-GC-AUC--C---U-UC-UGGU-AGCC-AU-A--GGC-UGGAUGAGCGC
AAXF02000054.1/107638-107777   CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CCG-ACC-GAUGCA-CCU---------UAA----------------------------UGUUGU--AUU-AAGC-GGUCGGGACGA-AGUACA----CUUUC--GCAA---------------------------------------G-ACAA-GA-C-A----GAACCGUGA--------GGGGA----AGU--CAA-GUAC-GGUU-AGUA-UC-A---UA-CCGUAGAGUGG
BABG01003053.1/544-414         U--AU-UG--UUCCAUCA-AU-AGUAGCCUG-AAG-AGG-CGUACG-UGAC-UG-G---CAA-------------------------CGGUCGGGU--GCG-AAGC-CCUCUUGACAA-CGACGUU-CCAACCUAAGCAUC------------------------------------AUA-GGCG-----------AA------------------------------GA-A-UG-UCAA-AGCU--G-A---CU-GAUAUGAGUAA
AAFY01027438.1/334-183         CCUAC-UG--UAUUACCG-GC-AGUUUUCUA-CUC-CGG-CAUGCA-UUAC-CA-G---UAA-------------------------UGGUUUUGU--GUG-GAGC-CCGGAUGACAA-UGAAGCC--CUUGGCC-AUA---------------------------------------AG-CCUG-AA-G-AG-AGAA-UCGUGA--------GAGGA-CC-UC----AA-C-UC-UGGG-AGCA-UC-A--ACC-UGGAUGGGAGC
CP001046.1/55041-55185         CCCGC-CG--UGCGACCG-GC-GGUAGCCUA-GGA-GCG-CGUGCA-UUGC-UG-G---CAA-------------------------CGGCGUUGU--GCG-AAGC-CGUUCCGAAAA-AGUUGUC--C--------GAAA------------------------------------G--------CA-U-G--UAGCGCUGCGA--------AGCGCUGC-CAU--GGA-G-GC-UCUG-AGCA-GC-A--ACG-GGGCUGAGACG
CP001044.1/2002012-2001865     CCUGU-UG--UGCGACCG-AC-AGUUGCCUA-UCC-AGA-CAUGCU-CAAC-UG-G---UAA-------------------------CGGCUGGGU--AUG-AAGC-UUUGGAGACAA-CGUGCC--------UC-UCGAU------------------------------------UGA-C----GG-C-UC-ACCC-CGGUGA--------CGGG-GCG-GGU--CGA-C-AC-UGCC-AGCC-GC-C--GUG-CGGUGUGAGGU
ABBM01001009.1/7246-7393       CCUGC-UG--UACGACCA-GC-AGUUGCCUA-CUU-GGA-CAGGCG-CGGU-GG-G---UAA-------------------------CUACCGGGU--CUG-AAGC-UCCAAGGACAA-UGUACUC--G----UC-CAAA--------------------------------------GA------CG-C-CA-CGACUCGGUGA--------CGAUGUGU-GGU--G-A-C-GC-UGCG-AGCC-GC-A--AUG-CGGCGUGGAGG
ABSN01017912.1/613-482         UCGCC-CG--UGUCACCG-GG-CGCAUCCAG--GG-GUC----------------UGAGUAAA-----------------------G----------------AGC-GACCCUGACAA-UGUAAUG--AAGCAUC-GAAA--------------------------------------GG-UGCG-GG-G-U--AUCAAUCGCGA--------GAGGC-GU-ACC--C---U-UC-UGGC-AGCC-AC-A--CGC-CGAAUGAGUGC
AM902716.1/4553000-4552852     CCUGA-UA--UUCCGCUA-UC-AGUAGCCUA-CCG-ACA-CAUGCG-ACUU-CG-G---CAA-------------------------CGAGGUGGU--GUG-AAGC-UGUCGGGACAA-UGUAGA----CCUCCC-AUGA--------------------------------------GG-GAAA-GG-U-CC-UU---CCGCGA--------GG---GAG-GGC--CAA-A-UC-UGCC-AGCA-UC-A--AGG-CGGAUGGGUCG
AAZW01000015.1/102153-102016   CCAUC-UG--UAUCACCA-GA-UG-AACCUA-UGA-GCC----------------UGAAUAAA----------------------GC----------------AGC-GGCUCAGACAA-UGUAACG-AAGAGCGGGAAUAU------------------------------------CCC-GUUC-GG-GAU--UUGAAUCGUGA--------GAAGA-AG-AUC--C---U-CC-UGAU-AACC-AC-A--AAU-CGGGUGAGUGC
ABSN01070113.1/166-17          CCUGA-UG--UUCAGCCA-UC-AGUGGCCUA--UG-GGCUGUGGCG-GCCU-CC-G---CAA-------------------------GG-GACCGU--CUA-GAGC-GCCCG-GACAA-UGUACC-----CCUGC-GCAA--------------------------------------GC-AG---CG-G-AA-UCUUUCUGUGA--------GGAAUGAU-UCC--GGA-G-UC-UGCC-AGCU-AC-A--ACG-CGGAUCAGGGU
BA000039.2/1683703-1683852     CCGGU-UG--UGCCCCCA-AC-CGUAGCCUA-GGG-AGG-CAUGCG-UGAC-UG-G---UAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-CGGAGC----CCGAAC-CGAAA------------------------------------GGU-UGGA-GC-U-G----AAUCCGCGA--------GGAGG----AAG--CAA-C-UU-UGCC-AGCG-UC-A---GG-CGAUAGGGAGC
ABIC01000011.1/97033-97162     CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-UGG-CUC-U--------------GAAUAAA--------------------------------------G-UAGC-GAGCCAGACAA-UGUAACG--AAGUCCA-U-----------------------------------------UG-GACG-GG-A-AC-AGAA-UCGUGA--------GAGGA-CG-UUC--C---U-CC-UGAU-AACC-AC-A--AAU-CGGGUGAGUGC
AASA01000116.1/13905-13757     CCUGU-UA--UAUGGCUA-AC-AGUAGUCUA--GG-GAU-AGUGCG-ACAC-CG-G---UAA-------------------------CGGUGUGGU--GCG-GAGC-UUCCU-GACAA-UGAACC----CCUGAU-GAAA--------------------------------------AU-CAG--UC-A-A--UGAAAUCGUGA--------GAGGACA--UUG--GGA-G-AA-AGUG-AAUA-GC-A---CA-CCUUCAAGGGG
AAGB01000380.1/557-704         CAGGA-UG--UUUUGCCA-UC-U-GAGUCUA-CGC-AUC-AGUGCG-AAUC-GG-G---CAA-------------------------CCGGUUGGU--GCC-AAGC-GAUGCGGACAA-UGAACC----UCCUCU-UGAAA------------------------------------AAG-AAGA-UG-C-UC-AA---UCGUGA--------GAG----G-AGC--AUA-A-AC-UACA-AGCA-UC-A---UG-UGGUUGGAGAG
AE017196.1/210728-210581       CCAGA-UG--UUUUGCCA-UC-UG-AGUCUA-UGC-AUC-AGUGCG-AAUC-GG-G---UAA-------------------------CCGGUUGGU--GCC-AAGC-GAUGCGGACAA-UGAACC----UCCUCU-UGAAA------------------------------------AAG-AAGA-UG-C-UC-AA---UCGU----------GAAAG--G-AGC--AUA-A-AC-UACA-AGCA-UC-A---UG-UGGUUGGAGAG
CP001391.1/219578-219431       CCAGA-UG--UUUUGCCA-UC-UG-AGUCUA-CGC-AUC-AGUGCG-AAUC-GG-G---UAA-------------------------CCGGUUGGU--GCC-AAGC-GAUGCGGACAA-UGAACC----UCCUCU-UGAAA------------------------------------AAG-AAGA-UG-C-UC-AA---UCGU----------GAAAG--G-AGC--AUA-A-AC-UACA-AGCA-UC-A---UG-UGGUUGGAGAG
CP000851.1/3790675-3790538     CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-GGA-GCC----------------UGAAUAAA----------------------GU----------------AGC-GACUCUGACAA-UGUAACG-AAGAUUGGUUAUAG------------------------------------ACC-AAUC-GG-G-AU-CUAAAUCGUGA--------GAGGACGA-UCC--U-----CC-UGAU-AACC-AC-A--AAU-CGGGUAAGUGC
ABZZ01000030.1/12396-12251     CCUAU-UG--UUCUGUCA-AU-AGUAGUCUA-AAG-AGG-CGUGCU-UUAC-CA-G---UCA-------------------------UGGUUUAGU--GCG-AAGC-CCUCUUGACAA-UGCAGUC--CUUUACA-GAAAUAU-------------------------------CCAAUG-UAUA-GG-----------CUGUUA--------GG---------C--UGACU-GA-UAUG-AGUA-AC-A---UA-UG--UGAAUCG
ABSN01001711.1/589-721         CCGCC-CG--UGUCACCG-GGUUG-AAUCUA-GGA-GUC----------------UGAAUAAA-----------------------G----------------AGC-GACUCUGACAA-CGUAGCG--AAGCACC-GCAA--------------------------------------GG-UGUG-GG-A-U--GCAACUCGCGA--------GAGGC-GU-AUC--C---U-UC-UGGU-AGCC-AU-A--CGC-CGGAUGAGCGC
CP000096.1/2030696-2030838     CCAGU-UG--UGCCGUCA-AC-UGCCCCCAC--CG-GCA-CAUGCA-GGAU-GA-G---CAA-------------------------UCGCCCUGU--GUG-AAGC-UACCG-GA-AA-CGUACC----CGCGGG-AA----------------------------------------AC-CGUA-GG-C-C----GACCCGUGA--------GGAGA----AGC--UGA-A-UC-UGCC-AGUA-GC-A---GG-CGGAGAGGGGC
CP000821.1/3279492-3279364     CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-AGA-CUC----------------UGAAUAAA----------------------GC----------------AGC-GAGUCUGACAA-UGUAACG--AAGUCCA-U-----------------------------------------UG-GACG-GG-A-A--CAGAAUCGUGA--------GAGGA-UG-UUC--C---U-CC-UGAU-AACC-AC-A---AU-CGGGUAAGUGC
ABJL02000008.1/3103022-3102872 CCUGU-UG--UUCCGUCA-AC-AGUAGCCUA-UGG-GAA-CGUGCG-GUAUUAA-G---CAA-------------------------UGAACCCGU--GCGGUAACAGAACC-AACAA-UGAAGC----CCUUCC-GAAA--------------------------------------GG-AGAA-GU-C-U----GAACCGUGA--------GGGGA----UGA--CAACU-GC-CGUU-AGUA-UC-G---AA-CGACAGGGGAG
AAPS01000002.1/275718-275855   CCGUU-UG--UAUCACUA-GA-CG-ACCCUA-AGG-CUC----------------UGAAUAAA----------------------GC----------------AGC-GAGCCUGAUAA-UGUAACG-AAGUUUGGUAUAGU------------------------------------GCU-AGAC-GG-GAG--CGAUACCGUGA--------GGUGA-UG-AUC--C---U-CC-UGAU-AACC-ACGA---AU-UGGGUGAGUUC
ABSR01018038.1/279-410         CCCUG-CG--UGUCGCCG-CA-GGUACUCCA-CGG-AAG-CAUGCG-UCUG-AC-GGGCCGCGGCCAAGUG-------GCCAUUACUGUCAGAGGU--CUG-AAGC-CUUCCCGGUAA-UGUAGC-------------------------------------------------------------------------------------------------------AA-A-CC-UGGC-AGCC-UC-A--AGC-CGGGUGCGCGC
CP000563.1/2701890-2701754     CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-AGG-CUC----------------UGAAUAAA----------------------GC----------------AGC-GAGUCUGACAA-UGUAACG-AUAUUUGGCUUUAU------------------------------------GCC-GAAU-GG-G-AACUGAA-UCGUGA--------GAGGACGU-UCU--U-----CC-UGAU-AACC-AC-A---AU-CGGGUAAGUGC
CP001157.1/2457091-2457240     CCGAU-UG--UUCCACCA-AC-CGUUCCCUA-CCC-GGA-CAGGCG-AAGC-CG-G---CAA-------------------------CAGCUUGGU--CUG-AAGC-UCUAGGGACAA-UGUAGC----CACCGA-CGU-C------------------------------------GUC-GGUA-GG-U-C----GAGCCGUGA--------GGCAA----GGC--CGA-A-UC-UGCC-AGCA-UC-A--AGG-CGGAGAGGCGC
CP000851.1/3571700-3571562     CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-GGA-CUC----------------UGAAUAAA----------------------GU----------------AGC-GAGUCUGACAA-UGUAACGAAGUUCAGU-ACCAU------------------------------------AAC-UGAG-CG-GGAGCUGAA-UCGUGA--------GAGAACGA-UCC--U-----CC-UGAU-AACC-AC-A--AAU-CGGGUGAGUGC
FM204884.1/1988432-1988322     UACUC-UA--UCCAUUUG-GA-GUAAUCCUA-CUA-CAG-CCUGCU-UGAC-UG-G---UAA-------------------------CGGUUAUGU-UGGG-AAGC-CUGUGGGACAA-UAUGGA-------------------------------------------------------------------------------------------------------AA-G-UC-UGAU-AGCC-UA-A---AU-CAGAUGGACUG
CP000438.1/642924-642777       CUCGU-UG--UGCGACCA-AC-GGUAGCCUA-GGG-AAA-CGUGCG-UUGC-UG-G---UAA-------------------------CGGCAGGGU--GCG-AAGC-UUUCCCGACAA-CGUAGC----CCC--------C------------------------------------GCG-AGGG-UG-C-GA-AUUCACCGUGA--------GGUGA-AC-CGC--AGA-G-GG-UCGG-AGUA-GC-A---CC-GACCCAAGGCG
AAFY01028012.1/378-241         CCAUC-UG--UAUCACCA-GA-UG-AACCUA-GGG-CUC----------------UGAAUAAA----------------------GU----------------AGC-GAGCCUAACAA-UGUAACG-AAGAUUGGUCAUGG------------------------------------ACU-AAUC-GG-G-AU-CUCAAUCGUGA--------GAGGACGA-UCC--U-----CC-UGAU-AACC-AC-A--AAU-CGGGUGAGUGC
AAFY01000487.1/1836-1699       CCAUC-UG--UAUCACCA-GA-UG-AACCUA-GGG-CUC----------------UGAAUAAA----------------------GU----------------AGC-GAGCCUGACAA-UGUAACG-AAGAUUGGUCAUGG------------------------------------ACU-AAUU-GG-G-AU-CUAAAUCGUGA--------GAGGACGA-UCC--U-----CC-UGAU-AACC-AC-A--AAU-UGGGUGAGUGC
CP001046.1/360354-360496       CCCG--UG--UACGACCA-GC-GGUAGCCUA-GGA-AGG-CAUCGG-AAGC-UG-G----AA-------------------------CGGCUUUCG--GUG-AAGC-CCUUCGGAAAGCCGUAGU--------CC-GAAA--------------------------------------G-------CG-U-G--UGCCGUCGCGA--------GGCGG-CA-UAU--GGA-G-GC-UCCA-AGCA-GCGA---CA-GGGCCAAGACG
ACHW01000024.1/158008-157860   CCUAU-UG--UUCAGCCA-AU-AGUAGCCUA--GG-GAU-AGUGCA-UCUG-CG-G---UAA-------------------------CGC-GGUGU--GCG-GAGC-UUCCU-GACAA-UGUACC-----CCCAC-GCAA--------------------------------------GU-GG---UU-A-AU-CCUUGCUGCGA--------AGUGAAGG-UUA--AGACA-AU-UGCC-AAUA-GC-A---GG-UGGUUGAGGGG
CR378668.1/97359-97496         CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-GGG-UUC----------------UGAAUAAA----------------------GC----------------AGC-GAACCCGACAA-UGUAACG-AAGUUCAGCAGUUU------------------------------------GCU-GAGC-GG-G-AA-UGGAAUCGUGA--------GAGGACGU-UCC--U-----CC-UGAU-AACC-AC-A--AAU-CGGGUAAGUGC
CP000352.1/270085-270234       CCUGU-CA--UGCGACUG-AC-AGUAGCCUA-GGG-AGA-CAUGCG-UCAC-UG-G---CAA-------------------------CGGUGGGGU--GUG-AAGC-UUUCCUGACAA-CGUAGC------CCCC-GCAA--------------------------------------GG-G----UG-C-GU-CAUUAUCGUGA--------GAUAAGGA-CGC--AGA-G-AC-UCCG-AGCA-GC-A--AUG-GGGUCAAGGAG
CP000949.1/403145-402997       CUCGU-UG--UGCGACCA-AC-GGUAGCCUA-CGA-CGG-CAUGCA-UCAC-UG-G---CAA-------------------------CGGUGGUGU--GUG-AAGC-CCGUCUGACAA-UGUAGCC--C----CC-ACCUC------------------------------------GGG------UG-C-AU-UCUCUCCGCGA--------GGAGA-GG-UGC--GGA-G-AC-UCGG-AGCA-GU-G---CC-GGGUUGAGGCG
CP000304.1/1274579-1274431     CCGAC-UG--UUCCACCA-CU-CGUUCCCUA-CCC-AGA-CAGGCG-UGGC-CG-G---CAA-------------------------CAGCCGGGU--CUG-AAGC-UCUGGGGACAA-UGUAAC----CGCCGA-UA--U------------------------------------UUC-GGUA-GG-U-C---GAA-CCGCGA--------GG---CCA-GAC--UGA-A-UC-UGCC-AGCA-UC-A--AGG-CGGAGAGGUGC
ABSN01006648.1/257-110         CCGAG-UA--UUUCCUUA-CU-CCGAGCCUA-UUG-GUA-CAUGCG-AUUC-UG-G---UAA-------------------------CGGAAAGGU--GUG-GAGC-UACCAAGACAA-UGAAGC----UUGACU-GCAA--------------------------------------AG-UCUA-GG-U-G----AAUCCGUGA--------GGAUA-----AC--CGA-ACUC-UCCC-AGCA-UC-A---GG-GGGUAUAAGCU
CU633751.1/441058-441201       CCCGC-CG--UGCGACCG-GC-GGUAGGCUG-GGA-GCG-CGCGUG-UUGC-UG-G---CAA-------------------------CGGCGGCGU--GCG-AAGG-UGCUCUGACAA-UGUAGUC--C--------GACA------------------------------------G--------UG-G-GC-AAUA-UCGCGA--------GGUG-UUG-CGU--AGA-G-GC-UCCG-AGCA-GC-G--AUG-UGGCUCAGACG
CP001068.1/3298789-3298937     CCUGC-UA--UGCGACUA-GC-AGUAGCCUA-GGG-AGA-CAUGCG-UCGC-UG-G---UAA-------------------------CGGCGGGGU--GUG-AAGC-UCUCCUGACAA-UGUAGC------CCCC-GCAA--------------------------------------GG-G----UG-U-CG-UCGCGCCGUGA--------GGCGCAAU-GGC--AGA-A-GACUCCG-AGCA-GC-A---CG-GGUCGAGGAG-
CP000447.1/4148540-4148677     CCAUC-UG--UAUCACCA-GA-UG-AACCUA-GGA-GCC----------------UGAAUAAA----------------------GU----------------AGC-GGCUCUGACAA-UGUAAUG-AAGAUUGGUUAUAG------------------------------------ACC-AAUC-GG-G-AUCUGAA-UCGUGA--------GAGAACGA-UCC--U-----CC-UGAU-AACC-AC-A--AAU-UGGGUGAGUGC
CP000472.1/5137626-5137491     CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-AGA-CUC----------------UGAAUAAA----------------------GU----------------AGC-GAGUCUGACAA-UGUAACG--AUAUUUG-GCUUAU----------------------------------GUCA-AAUG-GG-A-AC-UGAA-UCGUGA--------GAGGA-CG-UUC--U---U-CC-UGAU-AACC-AC-A---AU-CGGGUAAGUGC
ABSO01001142.1/214-362         CCUGC-UA--UGCGACUA-GC-AGUAGCCUA-GGG-AGA-CAUGCG-UCAC-UG-G---UAA-------------------------CGGUGGGGU--GUG-AAGC-UCUCCUGACAA-CGUAGC------CCCC-GCAA--------------------------------------GG-G----UG-C-UC-AAGGACCGUGA--------GGUCCGUG-GGC--AGC-A-GA-UCGA-AGUA-GC-A---UC-GGUCGAGGAGC
CP000270.1/790796-790653       CCCGC-UG--UGCGACCA-GA-GGUGGCCUA-GGA-AAG-CAUCUU-UCGU-UG-G---CGA-------------------------CGACGCUGG--AUG-AAGC-CUUUCCGACAA-CGUAGUC--C---------AAC------------------------------------U--------GU-A-UG-CGCCGCCGCGA--------GGUGACGU-GUA---GA-A-GC-UCUG-AGCA-GC-G--ACG-GGGCCGAGACG
CP000790.1/1614874-1615010     CCAUC-UG--UAUCACCA-GA-UG-AACCUA-GGA-CUC----------------UGAAUAAA----------------------GU----------------AGC-GAGUCUGACAA-UGUAACG-AAGGUUGG-CAUUU------------------------------------GCC-AAUC-GG-G-AU-CGAAAUCGUGA--------GAAGACGA-UCC--U-----CC-UGAU-AACC-ACGA---GU-CGGGUAAGUGC
ABJL02000008.1/129912-130060   CCCGU-UG--UUUCGUCA-AC-GGUAGCCUA-UGG-ACA-GAUGCA-CCAA-UA-G---UAA-------------------------UAUA-CUGU--AUCAAAGC-UGUCCAGACAA-GGUAGC----CCUUCC-GAAA--------------------------------------GG-AGCA-GU-C-A----GAACCGUGA--------GGGAA----AGA--CAA-UGGC-UGUU-AGUA-UC-A---UA-CAGUCAGGGAG
CP001110.1/1176910-1177053     UCAGU-UG--UUCAGUCA-GC-GG-AGCCCA-ACA-AUA-CAUUCA-GGAUAAA-U---AAA-------------------------UUGCGUUGU--GUG-AAGC-CGUCG-GA-AA-AAUACC----CGCAGG-AA----------------------------------------AC-UGUA-GA-C-A----AAUCCGUGA--------GGGAA----GGU--UGA-A-UC-UGCU-CGUA-AC-A---GG-UGGAGAAGUGC
CP000139.1/2750287-2750437     CCUGU-UG--UUCCGUCA-AC-AGUAGCCUA-UGG-GAA-CGUGCG-GUAUUAA-G---CAA-------------------------UGACCCCGU--GCGGUAACAGAACC-AACAA-UGAAGC----CCUUCC-GAAA--------------------------------------GG-AGAA-GU-C-U----GAACCGUGA--------GGGAA----UGA--CAACU-GC-UGUU-AGUA-UC-G---AA-UGGCAGGGGAG
CP000789.1/2246918-2247054     CCAUC-UG--UAUCACCA-GA-UG-AACCUA-AGA-CUC----------------UGAAUAAA----------------------GU----------------AGC-GAGUCUGACAA-UGUAACG-AAGGUUGG-CAUUU------------------------------------GCC-AAUC-GG-G-AU-CGAAAUCGUGA--------GAAGACUA-UCC--U-----CC-UGAC-AACC-ACGA---GU-CGGGUAAGUGC
CP000254.1/1523470-1523361     CCCCC-AA--UCCAUUCU-GG-GUGUCCCUA-CCU-GCA-CGUGCG-UGUU-UA-G---CAA-------------------------UAAAUGGGU--GCG-AAGC-UGCAGGAACAA-AGUGGU-------------------------------------------------------------------------------------------------------UA-C-UC-CCAU-AGUC-UC-A---UU-GGGAUAUACUG
BA000039.2/219808-219957       CCGGU-UG--UGCCCCCA-AC-CGUAGCCUA-GGG-AGG-CAUGCG-UGAC-UG-G---UAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-CGUAGC----CCGAAC-CGCAA------------------------------------GGU-UGAA-GC-C-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-CACC-AGCG-UC-A---GG-UGAUAGGGAGC
ABRV01000007.1/10738-10849     CCAGU-CCAGUGUCCAGG-AC-UGUUUCUAA-CAC-UCC-CAUGCG-UUGC-UG-G---CAA-------------------------CGGCAAGGU--GUG-AAGC-GGAGCGUA-AC----ACC-------------------------------------------------------------C---------AA-----------------------------GGA-A-GC-AUCA-AGCC-AA-C---UG-AUGUAACCAGG
CP001046.1/237422-237274       CCGGU-UG--UUCCAUCA-AC-CGUUCCCUA-CCU-GGA-CAUGCG-GAGC-CG-G---CAA-------------------------CAGCACCGU--GUG-AAGC-UCCGGGGACAA-AGUAGC----CGCCGG-GC--C------------------------------------ACC-GGUA-CA-C-C----GAACCGCGA--------GGGGA----GGU--GAA-A-UCUGCCU-AGCA-CG-A---AG-GCGUUGAGGCG
EF382672.1/192101-191954       CUCGU-UA--UUCAGCUA-AC-GGUAGCCUA--AG-GAU-AGUGCG-UCAC-UG-G---UAA-------------------------CGGUGAGGU--AUG-AAGC-AUCCC-UACAA-UGUAGU----CAUGUC-A---U------------------------------------CGA-CAU--CG-G-GU-GUCC-CCGCGA--------GGGU-AAA-CCU--GGA-U-UC-UACC-AGCA-AC-A---GG-UGGAUGAGACG
BAAU01000067.1/4370-4231       CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CCG-ACC-GAUGCA-CCU---------UAA----------------------------UGUUGU--AUU-AAGC-GGUCGGGACGA-AGUACA----CUUUC--GCAA---------------------------------------G-ACAA-GA-C-A----GAACCGUGA--------GGGGA----AGU--CAA-GUAC-GGUU-AGUA-UC-A---UA-CCGUAGAGUGG
AJ850063.1/220-72              UCCGU-UG--UUCCGUCA-AC-GGUAACCUA-CGG-ACA-GAUGCA-CCAA-UA-G---UGA-------------------------UAAUUCUGU--AUC-AAGC-UGUCUGGACAA-UGUACU----CCUUCC-GAAA--------------------------------------GG-AAAA-GA-C-A----GAGCCGUAA--------GGGAA----AGA--CAAUA-AC-UCUU-AGUA-UC-A---UA-GAGUUGGGAGG
ABLK01000569.1/1320-1464       CCUGC-UG--CACAACCA-GC-AGUUGCCUA-CCG-GGA-CGUGCG-UGAC-UG-G---CAA-------------------------CGGUCGGGU--AUG-AAGC-UCCCGGGACAA-AGUACCC--C----UC-GGAA--------------------------------------GA-C----GU-U-A---CAACCGGUGA--------CGGUA----UGA--CGA-C-GC-UGCA-AGCC-GC-G--AUG-CGGCGUGAGGG
CP000446.1/2528855-2528719     CCAUC-UG--UAUCACCA-GA-UG-AACCUA-GGA-GCC-U--------------GAAUAAA--------------------------------------G-UAGC-GGCUCUGACAA-UGUAACG-AAGGUUGG-UAUGC------------------------------------ACC-AAUC-GG-G-AU-CGAAAUCGUGA--------GAAGACGA-UCC--U-----CC-UGAU-AACC-AC-A--AAU-CGGGUGAGUGC
ABSP01036936.1/29-175          CCUAU-CG--UUCCUCCG-AU-AGUAGCCUA-AAG-GCA-CGGGCA-UCAA-CA-G---CAA-------------------------UGUA-AUGU--CCG-AAGC-UGUCUUGACGA-UGUAAC----CCAAUC-GAAA--------------------------------------GA-UGAA-GC-C-A----AACCCGCGA--------GGGCA----AAG--CGG-A-AC-UGCG-AGUA-UC-A---CG-CGGUAGGGUGC
CP001108.1/684229-684087       CCAGU-UG--UGCCGUCA-AC-UGCUCCCAC--CG-GCA-CAUGCA-GAGG-GA-G---UAA-------------------------UCCUUCUGU--GUG-AAGC-UGCCG-GA-AA-CGUACC----CGCAGG-AAA---------------------------------------CC--GUA-GG-C-U----GCUCCGCGA--------GGAAA----UGC--CGA-A-UC-UGCC-AGUA-GC-A---GG-CGGAGAGGGGC
AATD01002214.1/700-840         CCAUC-CA--UUCCGUUG-GA-UGAAGCCGU--UG-UCC-CCGGCU-CUGC-CA-G---UAA-------------------------UGGCACUGUUUCGG-AAGC-GGACA-UA-AA-CGUAAC----CCUA--CU--------------------------------------------UGGA-AU-C------AAACCGGUUGAG--GGGGGAGG-----GA--UGA-A-AC-UGCG-AGC---------UG-CAAUGGCGGGU
AAGB01000298.1/1057-1205       CCAGA-UG--UUUUGCCA-UC-UG-AGUCUA-CGC-AUC-AGUGCG-AAUU-GG-G---UAA-------------------------CCAGUUGGU--GCC-GAGC-GACGCGGACAA-UGAACC----UCCUCU-UGAUA------------------------------------AAG-AAGA-UG-C-U----CAAUCGUGA--------GAGAA----AGC--AUA-A-AC-UACA-AGCA-UC-A---UG-UAGUUGGAGGG
ABSO01010351.1/660-808         CCUGC-CA--UGCGACUG-GC-AGUAGCCUA-GGG-AGA-CAUGCG-UCAC-UG-G---UAA-------------------------CGGUGGGGU--GUG-GAGC-UCUCCUGACAA-UGUAGC------CCCC-GCAA--------------------------------------GG-G----UG-C-UC-AGGGACCGUGA--------GGUCCGUG-GGU--AGC-A-GA-CCGA-AGUA-GC-A---UC-GGUCGAGGAGC
AJ850062.1/241-93              UCCGU-UG--UUCCGUCA-AC-GGUAACCUA-CGG-ACA-GAUGCA-CCAA-UA-G---UGA-------------------------UAAUUCUGU--AUC-AAGC-UGUCUGGACAA-UGUACU----CCUUCC-GAAA--------------------------------------GG-AAAA-GA-C-A----GAGCCGUAA--------GGGAA----AGA--CAAUA-AC-UCUU-AGUA-UC-A---UA-GAGUUGGGAGG
AY057439.2/2005-2156           CCUUC-UG--UUCAGCCA-GAAAGUAGCCUA--GG-GAC-AGUGCG-UCGC-CG-G---UAA-------------------------CGGCGGGGU--GCG-AAGC-GUCCU-GACAA-UGUAGC----CCCAUG-AUG-U------------------------------------CUG-UGG--UG-C-GU-GGUCGCCGCGA--------GGCG-CCA-UGC--AGA-C-CC-UGCG-AGCA-AC-A---CG-CGGGCGAGGCG
ACOQ01000171.1/2450-2303       CUCGU-UG--UGCGACCA-AC-GAUAGCCUA-GGA-AGA-CAUGCG-UCAC-UG-G---UAA-------------------------CGGUGGGGU--GUG-AAGC-UCUUCCAACAA-UGUAGC------CCCC-GUAU--------------------------------------GG-G----UG-C-GU-CUUCGCCGUGA--------GGCGG-AG-CGC--AGA-U-GC-UCGG-AGCA-GU-A---CC-GGGUUGAGGCG
ACIC01000137.1/106917-106769   CCCAC-UG--UUCCGUCA-GU-GGUAGCCUA-CGG-GCA-CGUGCA-UUAC-GA-G---UAA-------------------------UUGUUUUGU--ACG-AAGC-UGCCCGGACAA-AGUAAC----CCACCC-GAAA--------------------------------------GG-GGAA-GC-A-A----AAGUCGCGA--------GGUGG----AUG--CAACG-AC-CGCC-AGCA-UC-A---GG-CGGUUAGGGAG
CP000891.1/5029896-5029759     CCAUC-UG--UAUCACCA-GA-UG-AACCUA-GGA-GCC----------------UGAAUAAA----------------------GU----------------AGC-GGCUCUGACAA-UGUAACG-AAGAUUGGUCUUUG------------------------------------ACC-AAUC-GG-G-AU-AUGAACCGCGA--------GGGGAUGA-UCC--U-----CC-UGAU-AACC-AC-A--AAU-CGGGUGAGUGC
ABSO01002779.1/786-934         CCUGC-UA--UGCGAUUA-GC-AGUAGCCUA-GGG-GGA-CAUGCG-UCAC-UG-G---CAA-------------------------CGGUGGGGU--GUG-AAGC-UCCCCUGACAA-UGUAGC----CCC--------C------------------------------------GUA-AGGG-UG-C-CC-UCUCGUCGUGA--------GAUCGGAG-GGU--AGA-A-AG-CCGA-AGCA-GC-A---UC-GGUUGAGGAGC
ABYL01000045.1/29453-29606     CCUGC-UG--UGCGACCA-GC-AGUAGCCUA-GGA-AGA-CAUGCG-UCAC-UG-G---CAA-------------------------CGGUGGGGU--GUG-AAGC-UCUUCUGACAA-UGUAGC----CCCCGG-ACG-U------------------------------------UUC-GGG--CA-G-AU-UGGUUCCGUGA--------GG-AACGA-UCU--GGA-G-AC-UCCC-AGCA-GC-A--AGG-GGGUUGAGGAG
CP000304.1/1962133-1962280     CCGGG-CA--UGUACCUG-CC-CGUUCAUUA-GAU-CGG-CAUGCG-UCAG-GG-G--CCAA-------------------------CCCUGGGGU--GUG-AAGC-CCGAUUAACAA-UGUCUC------GCUC-GCAA--------------------------------------GA-G----GG-U-G--UUAUCCGGUGA--------CGGAG-AA-CGCUUC---G-CG-UCCG-AAUU-GC-A---CG-GACGUGUCGAG
AP008981.1/404428-404555       CCUGU-UG--UUCUAUGA-AC-AGAAGCUUA-CUG-GUA-CA-------------CGCAA---------------------------------------UGGUAGC-UAUAAGGACAA-UAUACUUGAC----UC-GAAAU------------------------------------GGA------CU-C-G----AAAUCGUGA--------AAGGA----AGA--UUA-G-AC-UAUU-AGUA-UC-A---UG-UGGUCAGAAGC
ABPQ01011315.1/143-20          CCCUG-UU--UUCCGCAA-CA-GGUAUUUUA-CCG-AGA-CGUGCG-CCCG-GA-G---UAA-------------------------UCUGGGGGU--GCG-AAGC-UCUCGGGACAA-UGAAGC---------------C------------------------------------C--------GU-G-GA-AGAUU----GA----------GUUCUU-UCA--GGA-G-AG-------GAA-AC-C--G-------UGAGGGG
AP006841.1/4863986-4864131     CCUAU-UG--UUCCGUCA-AU-AGUAGUCUA-AAG-AGG-CGUACU-UUAC-CA-G---UAA-------------------------UGGUUUAGU--GCG-AAGU-CCUCUUGACAA-UGCAGUC--CUUUACA-AAAAUAU-------------------------------CCAAUG-UAUA-GG-U-U---------GUUA-----------------GGC--UGACU-GA-UAUG-AGUA-AC-A---UA-UG--UGAAUCG
CP000139.1/2745361-2745509     CCUCC-AG--UUCCGUCU-GG-AGUAGCCUA-CGG-ACA-CGUGCA-UUGG-GA-G---UAA-------------------------UCCUUUUGU--ACG-GAGC-UGUCCCGACAA-GGUAGC----CUUUCC-AAAA--------------------------------------GG-AGAA-GA-U-U----GAACCGUGA--------GGGGA----AAU--CAA-CGGC-UGAU-AACA-CC-A---UU-CAGCACGAGGA
BAAU01009686.1/856-1009        -CUGU-UA--UUCCAUUA-GC-AGUAGUCUA-CUG-UCAACA-AAG-CGGC-UG-G---UAA-------------------------CGGCUGUGA----GGAAGCGUGACAGGACAAGGGUAGCC--C-CACCC-GAAA--------------------------------------GG-GU---UC-AAGC-UGAAACUGCGA--------GGUGAAAG-C-G--AUA-A-GC-UGCA-AGCA-AC-A--AUG-CGGUUGGGGAG
CP000648.1/40066-40214         CCGAC-UG--UUCCACCA-CU-CGUUCCCUA-CCC-AGA-CAGGCG-UGGC-CG-G---UAA-------------------------CAGCCGGGU--CUG-AAGC-UCUGGGGACAA-UGUAAC----CGCCGA-U-A-U------------------------------------UUC-GGUA-GG-U-C---GAA-CCGCGA--------GG---CCA-GAC--UGA-A-UC-UGCC-AGCA-UC-A--AGG-CGGAGAGGCGC
CP000790.1/1339770-1339907     CCGUU-UG--UAUCACCA-GA-CG-ACCCUA-AGG-CUC----------------UGAAUAAA----------------------GC----------------AGC-GAGCCUGACAA-UGUAACG-AAGUUUGGCACUGU------------------------------------GCC-AAAC-GG-GAG--CAGAACCGUGA--------GGGAA-UG-CUC--C---U-CC-UGAU-AACC-ACGA---AU-UGGGUGAGUGC
BA000039.2/625012-625161       CCGGU-UG--UUCCCCCA-GC-UGUAGCCUA-GGG-AGG-CAUGCG-UGAC-UG-G---UAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-UGUAGC----CCAAAC-CGUAA------------------------------------GGU-UGAA-GC-C-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-CACC-AGUG-UC-A---GG-UGAUAGGGAAC
AE003849.1/1691335-1691482     CCUGA-UG--UUCCGUCA-UC-AGUAGCCUA-UCG-GUG-CAUGCG-UGGU-UG-G---CAA-------------------------CGACUGCGU--GUG-AAGC-CACCGAGACAA-UGUAGGU--C---GGC-GAAA--------------------------------------GC-CA---GG-U-G---GAGACCGCGA--------GG--UCGA-AAC--CGC-A-UC-UGCG-AGCG-CC-A--ACG-CGGAUGGAUCG
AM902716.1/2117115-2117269     CCCGU-CA--UACGACUG-AC-GGUAGCCUA-CAG-UGG-CGGGCA-GGAU-CG-G---UAA-------------------------CGGCCCUGU--CUG-AAGC-CCACUCGACAA-UGUACU----CCUGUG-UACUC------------------------------------CAA-CAG--UA-U-CC-ACUG-CCGUGA--------GGCU-GGG-GAU--GGA-U-UC-UGCC-AGCA-GCCA--GGG-CGGAUGAGAGG
ACIC01000218.1/2357-2210       CCCGC-UG--UUCCGUCA-GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUCUCC-GAAA--------------------------------------GG-ACAA----G-AC-UGAA-CCGUGA--------GGGAA-CG-UCA--AG--G-GC-GGUU-AGUA-UC-A---UA-CUGCCGAGUGG
ABPS01009315.1/325-148         CCCGG-CG--UUCUGCCG-CC-GGUACCCUA-CCC-GGA-CAUGCG-UCAC-UG-G---UAACCCUCCGACUUUGCUCAGGGCAGGCUGGUGGGGU--GUG-AAGC-UCCGGGGACAAAGGUAUCC--CUCAUUC-GAAG--------------------------------------GA-AUGG-CA-A-C---GAGACCGCGA--------GGCGA-U--GUU--G---UGAC-UGUC-AGCA-CC-A--AGA-CGGUCGGGGGC
AE010299.1/238445-238335       UACCU-UU--UCCAUUUG-AG-GUAAUCCUA-CUG-UGG-CAUGCA-UAAA-UG-U---UAA-------------------------CGUUUGUGU--GUG-AAGC-UCACAGGACAA---UAUC----------AA-------------------------------------------------------------------------------------------GAAU-UC-AAGG-AGCC-UG-A---CU-UUGACAUGCGU
AAUJ02000001.1/1482380-1482530 CCUUG-UG--UGCAACCA-CA-AGUAGCCUA-CGG-UGA-CGUGCA-AGAC-CA-G---UAA-------------------------UGGGUUUGU--GCG-AAGC-UCACCUGACAA-AGUACC-----CCCGC-GCAA--------------------------------------GC-GG---UA-C-AU-CCGACCUGCGA--------GG-GCGGA-UGU--AGA-C-AC-UGCC-AGCA-GA-A--GGG-CGGUAGAGGGG
CP000724.1/4402160-4402051     UGCUC-UA--UCCAUUUG-GA-GUAACCCUA-UCU-AUA-GGUGCG-UCAU-CA-G---CAA-------------------------UGAAGGGGU--UCU-AAGC-UGUAGAGACAA-UGUGAA-------------------------------------------------------------------------------------------------------AA-U-CC-UGCA-AGCC-UA-A---UG-UGGGUGAUUGC
CP001277.1/935058-935205       CGCAC-UG--UUUCCCCA-GU-GCUAGCCUA-CUG-AGC-CAAGCG-UUGC-UG-G---UAA-------------------------CGGCGAGGU--UUG-AAGC-GCUCAGGACAA-UGAAACG--C---UUC-GUAAG------------------------------------AGA-A----GG-A-A----GAACCGCGA--------GGUGA----AAC--CAACG-AC-UGCC-AGCA-UC-A--AAG-CGGUCAGCGAG
AM999887.1/1043133-1043280     CCAGA-UG--UUUUGCCG-UC-UG-AGUCUA-CGC-AUC-AGUGCG-AAUC-GG-G---CAA-------------------------CCGGUUGGU--GCC-AAGC-GAUGCAGACAA-UGAACC----UCCUCU-UGAAA------------------------------------AAG-AAGA-UG-C-UC-AA---UCGUGA--------GAG----G-GGC--AUA-A-AC-UGCA-AGCA-UC-A---UG-UGGUUGGAGGG
BA000039.2/1717130-1717279     CCAGC-UG--UUCCCCCA-AC-UGUAGCCUA-GGG-AGG-CAUGCG-UGGU-UG-G---CAA-------------------------CGACCAGGU--AUG-AACC-CCUCCCGACAA-UGUAGC----CCGAAC-CGCAA------------------------------------GGU-UAAA-GC-U-G----AAUCCGUCA--------GGAGG----AAG--CAA-C-UU-CACC-AGUG-UC-A---GG-UGAUAGGGAGC
AM494475.1/1732978-1732830     CCUGU-UG--UUCUACGA-AC-AGAAGUCUAAGUU-GUA-CAUACA-AUG--GA-G---UGA-------------------------UC-CUAUGU--AUG-AAGC-UAUCAUGGCAA-UGUCUA----CAGUUUGAAAGA------------------------------------GAU-AUCG-UG-U-----------AAAAAAACAGAA----------AC--AGAAACCC-AAUA-AAAA-UCUC---UA-UUGAUAAACUA
BABF01006568.1/145-284         UCCGU----------CA--GC-GGUAGCCUA-CUA-UAA-GGUGCA-UCUC-CA-G---UGA-------------------------UGG-GUUGU--GCC-AAGC-UUAUAGGACAA-AGUACA----CUUUCC-GAAA--------------------------------------GG-ACAA-GA-C-U----GAACCGUGA--------GGGAA----UGU--CAA-GGAC-GGUU-AGUA-UC-A---UA-CCGUUGAGUGG
ABPR01008080.1/238-87          CCUGC-UG--UAUUACCA-GC-AGUUUCCUA-UUC-CGG-CAUGCA-UCUC-CA-G---CAA-------------------------UGGAUUUGU--GUG-AAGC-CCGGAUGACAA-UGAAACC--CUCGGCC-U---C------------------------------------CGG-CCGG-AA-G-AG-AGAA-UCGCGA--------GAGAA-CC-UC----AA-C-UC-UGGG-AGCA-UC-A--ACC-CGGAUGGGAGC
AATO01000486.1/3084-3213       CCACC-GA--UGUCACUC-GG-UG-AAUCUA-GGA-GUC-UU-------------AU-A----------------------------------------AA-GAGC-GACUCUGACAA-CGUAACG--AAGCGCC-GCAA--------------------------------------GG-UGCG-GG-A-U--AUAAAUCGUGA--------GAAGC-AU-AUC--C---C-UC-UGGC-AGCC-AC-A---GC-UGGAAUAGUGC
CP000352.1/3135043-3135192     CCUGC-UA--UGCGACUA-GC-AGUAGCCUA-GGG-AGA-CAUGCG-UCAC-GG-G---UAA-------------------------CUGUGGGGU--GUG-AAGC-UCUCCUGACAA-CGAAGC------CCCC-GCAA--------------------------------------GG-G----UG-C-GU-AACUGCCGAGA--------GGUAGAGA-CGC--AGA-G-AC-UCCU-AGCA-GC-A--AUG-GGGUCGAGGAG
BAAY01000957.1/541-409         CCUAU-UG--UUCCAUCA-AU-AGUAGCCUG-AAG-AGG-CGUACG-UGAC-UG-G---CAA-------------------------CGGUCGGGU--GCG-AAGC-CCUCUUGACAA-CGACGUU--C--------CAAC------------------------------------C--------U---------AAGCAUCAU--------AGGCG---------AAG-A-AU-GUCA-AAGC-UG-A--CUG-AUAUGAGUAA-
ABSP01000685.1/370-240         CCACC-UA--UGCUACUG-GG-UG-AAUCUA-GGG-GCA----------------UGAAUAAA-----------------------G----------------AGC-UGCCCUGACAA-UGUAACG-AUAGAAAC-UUA---------------------------------------GU-UUCG-GG-G-A--ACGAAUCGUGA--------GAAAU-GU-UCC--U---U-CC-UAGC-AACC-AC-A---GC-UGGGUAAGUGC
AE010299.1/5711693-5711583     UACCU-UU--UCCAUUUG-AG-GUAAUCCUA-UUG-UGA-CGUGCA-UAAA-UG-G---UAA-------------------------CGUUUGUGU--GUG-AAGC-UUACAAGACAA---UAUC----------AA-------------------------------------------------------------------------------------------GAAA-UC-AAGG-AGCC-UG-A---CU-UUGAUAAUUGG
AAZW01000012.1/71028-70891     CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-GGU-UCC----------------UGAAUAAA----------------------GC----------------AGC-GGAACCGACAA-UGUAACG-AAACUCAGUCGUUA------------------------------------GCU-GAGU-GG-GAA--CGGAAUCGUGA--------GAAGA-UG-UUC--C---U-CC-UGAG-AACC-AC-A--GCU-CGGGUGAGUGC
CP001088.1/58758-58573         CCUGC-CG--UAUCACCG-GC-AGUUUCUUA-CCC-CGG-CAUGCA-UUAC-UG-G---UAA-------------------------CGGUUUUGU--AUG-AAGC-CCGGGGGACAA-UGAAGC----CCGGGG-GACAAUGAAGCCCGGGGGACAAUGAAGCCCUUGGUCGAAAGACC-UGGA-GA-G-C----AAGUCUUGA--------GGCAA----GCU--CAA-C-UC-UGGC-AGCA-UC-A--AGC-CGG-UUGGGAG
AAOJ01000008.1/4963-4826       CCAUC-UG--UAUCACCA-GA-UG-AACCUA-GGA-GCC----------------UGAAUAAA----------------------GU----------------AGC-GGCUCUGACAA-UGUAACU-AAGGUUGG-UAUUU------------------------------------UCC-AAUC-GG-G-AU-UGAAGUCGUGA--------GAGGACGA-UCC--U-----CC-UGAU-AACC-ACAA--CAU-CGGGUGAGUGC
CP000300.1/800585-800695       UAUCC-CU--UCCAUUUG-GG-AUAAUCCUA-CUA-UGA-UAUGCG-UCAA-UG-G---UAA-------------------------CGUUGGGGU--GUA-AAGC-UCAUAGGACAA-UGUGGA-------------------------------------------------------------------------------------------------------GAAA-UU-CGGA-AGUC-UA-A---UC-UGAAUCAUCUG
CP000444.1/646328-646476       CCUGU-UG--UGCAACCA-GC-AGUAGCCUA--GG-GAU-AGUGCG-CCAC-CA-G---UAA-------------------------UGGUGGGGU--GUG-AAGC-UUCCU-GACAA-UGUAUU----CCCCAU-UCA---------------------------------------CU-GGG--UU-U-GG-UUUUACCGUGA--------GGUAG-GC-CAA--AGA-C-UU-CACC-AGUA-GC-A---GG-CGGAUGAGAGA
AAUJ02000001.1/1569593-1569743 CCUUG-UG--UGCGACCA-CA-AGUAGCCUA-CGG-UGA-CAUGCA-AACC-UA-G---UAA-------------------------UGGGUCUGU--GUG-AAGC-UCACCUGACAA-AGUACC-----CCCGC-GCAA--------------------------------------GC-GG---UA-C-AC-CUAACCCGUGA--------GG-GCGGA-UGU--AGA-C-AC-UGCC-AGCA-GA-A--GGG-CGGUAGAGGGG
AE017354.1/1178263-1178108     CCUAU-GA--UUCCGUUC-AU-AGUAGCCUA-AUU-CGA-CGUGCG-UCAU-UG-G---UAA-------------------------CGAUGGCGU--GCG-AAGC-UCGAAUGACAA-UGUACUG--AAGUUUA-CGCAU------------------------------------GUA-AACG-UC-G-UGGAUUUGCUGAUA--------GGUAA-AC-ACG--A---A-UC-UGGA-AGCU-UC-A---UC-CGGAAUAAGGC
AM886293.1/20012-19863         CCAGC-UA--UCCCAUUA-GC-UGUAGCCUA-CCG-GGA-AAGGCG-CUGC-CC-G---GCA-------------------------CGGCGGGGU--CUG-AAGC-UCCCGGGACAA-CGAGAG----CCGGGC-GU--C------------------------------------AGC-CCGG-GU-A-AA-GCC--CCGUGA--------GGG--GCU-UUA--CCU-U-GC-UGCA-AGCA-UC-A---UG-UGGCAGGAGAG
Y16016.1/1129-983              CCUGA-UG--UUCCGUCA-UC-AGUAGCCUA-CUG-ACA-CAUGCG-UCAC-UG-G---UAA-------------------------CGGUGGGGU--GUG-AAGC-UGUCAGGACAA-UGAAAC----CGGAUC-U---U------------------------------------CGG-AUCG-CA-U-G----AAACCGUGA--------GGUUA----CAU--GUA-A-UC-UGCC-AGCA-UC-A---GG-CGGAGGAGGUC
AAUJ02000001.1/4219067-4219218 CCUUG-UG--UGCGACCA-CA-AGUAGCCUA-CGG-UGA-CAUGCA-AAUC-CA-G---UAA-------------------------UGGACUUGU--GUG-AAGC-UCGCCCGACAA-CGUACU----CCCGCU-AA----------------------------------------CG-CGG--UA-C-CC-CUCAUCCGCAA--------GG-AUAGG-GGU--AGA-U-GC-UGCC-AGCA-GA-AA-UGG-CGGUUGAGAGG
AM286690.1/701768-701914       CCUGU-UG--UUCGACCA-AC-AGUAGCCUA--UG-GGC-AGUGCG-UUGC-UG-G---UAA-------------------------CGGCAAGGU--GCG-AAGC-GCCCU-GACAA-UGUAGU-----CCCAC-U---C------------------------------------UGU-GG---UC-U-GG-UUUGCCCGUGA--------GGGUU-GC-CGG--GGA-U-UC-UGCC-AGCA-AC-A---GG-CGGAUGAGACG
CP001043.1/507282-507435       CCUGC-UG--UACGACCA-GC-AGUAGCCUA-GGA-AGA-CAUGCG-UCAC-UG-G---CAA-------------------------CGGUGGGGU--GUG-AAGC-UCUUCUGACAA-UGUAGC----CCCCGG-ACG-U------------------------------------UUC-GGG--CA-G-AU-UGGUUCCGUGA--------GG-GACGG-UCU--GGA-G-AC-UCCC-AGCA-GC-A--AGG-GGGUUGAGGAG
AAOE01000010.1/130075-130222   CCGAA-UG--UUCAGCCA-UU-CGUAGUCUA-CGG-AU--AGUGCG-UCAC-UG-G---UAA-------------------------CGGUGGGGU--GCG-AAGC--UUCCUGACAA-UGUAGCC--CUUCUUC-U-----------------------------------------GA-AG---CA-A-UC-AGAG-CUGUGA--------AGUUUCUG-AUC--GGA-U-UC-UGCG-AGCA-AU-A---CG-CGGAUGAGGCG
BA000039.2/1197012-1197161     CCGGU-UG--UUCCCCCA-AC-CGUAGCCUA-GGG-AGG-CAUGCG-CGAC-UG-G---UAA-------------------------CGGUCAGGU--AUG-AAGC-CCUCCCGACAA-CGGAGC----CCGAAC-CGAAA------------------------------------GGU-UGAA-GC-C-G----AAUCCGUGA--------GGAGG----AAG--CAA-C-UU-UGCC-AGCG-UC-A---GG-CGAUAGGGAGC
AM886293.1/14306-14157         CCAGC-UA--UCCCAUUA-GC-UGUAGCCUA-CCG-GGA-CAGGCG-CUGC-CG-G---CAA-------------------------CGGCGGGGU--CUG-AAGC-UCCCGGGACAA-CGAGAG----CCGGGC-GU--C------------------------------------AGC-CCGG-GU-A-AA-GCC--CCGUGA--------GGG--GCU-UUA--CCU-U-GC-UGCA-AGCA-UC-A---UG-UGGCAGGAGAG
CT573071.1/1199330-1199189     CCGGA-UG--UAUUUCCA-UC-UGUACCCUA-GGG-AGG-CAUGCUACCAU-UG-CG-CUGA-------------------------UGAUGGGGU--GUG-AAGC-CCUCCCGACAA-UGUACC-----------GAAA-------------------------------------C--------GG-G-U--AGAAACCGUGA--------GGUGA-AA-ACC--C---A-UC-CGGA-AAUU-CC-G---UC-CGGUUAAGGGC
CP002457.1/837896-837760       CCAUC-UG--UAUCACCA-GA-UG-ACCCUA-AGA-CUC-U--------------GA-AUAA------------------------A-------------G-CAGC-GAGUCUGACAA-UGUAACG--AUAUUUG-GCUUUA---------------------------------UGCCG-AAUG-GG-A-A--CAGAACCGUGA--------GAGGA-CG-UUC--U---U-CC-UGAU-AACC-AC-A---AU-CGGGUAAGUGC
FQ312004.1/2121603-2121735     CCUAU-UG--UUCCAUCA-AU-AGUAGCCUG-AAG-AGG-CGUACG-UGAC-UG-G---CAA-------------------------CGGUCGGGU--GCG-AAGC-CCUCUUGACAA-CGACGUUCCA----AC-CUAA--------------------------------------GC------A--------UCAUAGGCGA----------------------AGA-A-UG-UCAA-AGCU--G-A---CU-GAUAUGAGUAA
CP002121.1/847289-847417       CCAAC-UA--UUCCGUUA-GU-UG-AGCCGA-GUA-UCG-ACUGCA-CUU----------------------------------------AGGUGU--GGU-AAGC-CGAUAUU--AA-AGUAGC---C-C-----UAAU-------------------------------------U-----G-AGG-U-A----AAACCGUGA--------GGAAA----UGC--CGA-A-AC-UGCC-AGCA-AC-A--AGG-UGGUUAGGGAG
FN543502.1/3382802-3382950     CCCGU-UG--UUCAGCCA-AC-GGUAGCCUA--AG-GAU-AGUGCG-UCAC-UG-G---UAA-------------------------CGGUGAGGU--GCG-AAGC-UUCCU-GACAA-CGUACU-----CCCGC-GCAA--------------------------------------GC-GG---CG-G-CU-GGUAUCCGCGA--------GGACGCCA-UCU--GGA-U-UG-GUCU-AACG-AC-A---UG-ACCAUGAGAGG
CP001779.1/734706-734858       CCCUC-UA--UUCCGUUA-GA-GGUAGCCUA-AUA-CCA-CCUGCU-UUAU-CA-G---CAA-------------------------UGAUAAUGU-UUGG-AAGC-UGGUAUGAUAA-UGUAGC---CCUCCAC-GAAA--------------------------------------GU-GGUA-AA-G-U--CGAAGCCGUGA--------GGCUA-AG-GU----GA-A-UC-UGCU-AGCA-GC-A--AUG-CGGUUAGGGAG
CP001709.1/88882-89010         CCAAC-UA--UUCCGUUA-GU-UG-AGCCAA-GUA-UCG-ACUGCA-CUU----------------------------------------AGGUGU--GGU-AAGC-CGAUAUU--AA-AGUAGC---C-C-----UACU-------------------------------------U-----G-AGG-U-U----GAACCGUGA--------GGGAA----UAC--CGA-A-AC-UGCC-AGCA-AC-A--AGG-CGGUUAGGGAG
FP929032.1/3739299-3739151     CCCGU-UG--UUUCGUCA-AC-GGUAGCCUA-UGG-ACA-GAUGCA-CCAA-UA-G---UAA-------------------------UA-UACUGU--AUCAAAGC-UGUCCAGACAA-GGUAGC----CCUUCC-GAAA--------------------------------------GG-AGCA-GU-C-A----GAACCGUGA--------GGGAA----AGA--CAAUG-GC-UGUU-AGUA-UC-A---UA-CAGUCAGGGAG
ACDI02000039.1/35262-35406     GCUGU-U---UCGUCA---GC-AGUAGCCUA--CG-GCA-GGUGCA-UAAC-CA-G---UAA-------------------------UGGUCUUGU--ACU-AAGC-UGCUCGGACAA-UGAAGC----CCUUCC-GAAA--------------------------------------GG-AGAA-G----U--UUGAACCGUGA--------GGGGA-AA-G----CAACU-GC-UAUU-AGUG-UC-A---UA-UAGUAGGGGAG
ACAB02000041.1/9814-9669       CCUAU-UG--UUCUGUCA-AU-AGUAGUCUA-AAG-AGG-CGUGCU-UUAC-CA-G---UCA-------------------------UGGUUUAGU--GCG-AAGC-CCUCUUGACAA-UGCAGUC--CUUUACA-GAAAUAU-------------------------------CCAAUG-UAUA-GG-----------CUGUUA--------GG---------C--UGACU-GA-UAUG-AGUA-AC-A---UA-UG--UGAAUCG
ACDI02000039.1/39553-39700     CCUGC-UG--UUUCGUCA-GC-AGUAGCCUA--CG-GCA-GGUGCA-UUAC-CA-G---UAA-------------------------UGGUUUUGU--ACU-AAGC-UGCUCGGACAA-UGAAGC----CCUUCC-GAAA--------------------------------------GG-AGAA-G----U--UUGAACCGUGA--------GGGGA-AA-A----CAACU-GC-UAUU-AGUG-UC-A---UA-UGGUAGGGGAG
#=GC SS_cons                   :<<<<.<<..______>>.>>.>>,,,,,,,.,<<.<<<.<<<<<<.<<<<.<<._...___.........................>>>>>>>>>..>>>.----.>>>>>,,,,,,.,,,,,,....<<<<<<.____......................................>>.>>>>.<<.<.<....---<<____........>>---....>>>..>,,.,.<<.<<<<.____.__._...>>.>>>>:::::::
#=GC RF                        CCugc.uG..UuCcacCa.gc.aGUAgCCUA.ccg.ggg.cguGCa.ucac.cg.G...UAA.........................cggugauGU..acg.AAGC.ccccggGACAA.uGUAgC....cccucc.gaAA......................................gg.aggg.gg.c.c....aAacCGUGA........GgggA....ggc..caA.a.cC.ugcc.AGCa.uC.A...gg.cgGguggGggg
//
# STOCKHOLM 1.0

#=GF AC   RF02013
#=GF ID   mir-1280
#=GF DE   microRNA mir-1280
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   87.70
#=GF NC   49.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.88 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000648;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


AF196968.5/58781-58873  -CUGUCCCACCGCUGCCACCCUCCCCUCUGCCUCAGUGUGCCAGGCAUCAGCACUCACUCACAGAGGCAGGCUGGAUGGCGGGUGGGACAACAG
AL449210.5/98173-98266  UCUGUCCCACCGCUGCCACCCUCCCCUCUGCCUCAGUGUGCCAGGCAUCAGCACUCACUCACAGAGGCAGGCUGGAUGGCGGGUGGGACAACAG
AC092549.14/72588-72495 UCUGUCCCACCGCUGCCACCCUCCCCUCUGCCUCAGUGUGCCAGGCAUCAGCACUCACUCACAGAGGCAGGCUGGAUGGCGGGUGGGACAACAG
#=GC SS_cons            ::<<<<<<<<<-<-<<<<---<<<--<<<<<<<<-<<<-<--<<<<____>>->>-->->>>->>>>>>>>-->>>>>>>>>>>>>>>>>::::
#=GC RF                 ucuGucccaccGcUGccacccuccccccuGccucAGuGUGccaGGcAUcAgCACucACUCaCAgaggCaggcUggauggCgggugggaCaAcAG
//
# STOCKHOLM 1.0

#=GF AC   RF02014
#=GF ID   mir-1178
#=GF DE   microRNA mir-1178
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   75.00
#=GF TC   77.00
#=GF NC   73.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000601;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   17922033
#=GF RT   MicroRNA expression signature of human sarcomas
#=GF RA   Subramanian S, Lui WO, Lee CH, Espinosa I, Nielsen TO, Heinrich MC,
#=GF RA   Corless CL, Fire AZ, van de Rijn M
#=GF RL   Oncogene. 2008;27:2015-2026.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


ABGA01218732.1/20464-20574 AAGCCCAGGGGGGUUGGCUGGCAGAGGAAGGGAAGGGUCCGGGGUCGGCUGAGCAUGCCCUCAGGUUGCUCACUGUUCUUCCCUAGAAUGUCAGGUGAUGUGUCACCCCAA
AC079262.28/36467-36357    AGAAGCCCAGGCGUUGGCUGGCAGAGGAAGGGAAGGGUCCAGGGUCAGCUGAGCAUGCCCUCAGGUUGCUCACUGUUCUUCCCUAGAAUGUCAGGUGAUGUGUCACCCCAA
AACZ03087357.1/567-457     AGAAGCCCAGGGGUUGGCUGGCAGAGGAAGGGAAGGGUCCGGGGUCGGCUGAGCAUGCCCUCAGGUUGCUCACUGUUCUUCCCUAGAAUGUCAGGUGAUGUGUCACCCCAA
#=GC SS_cons               ::::::::::::<<<<-<<<<<<-----<<<<<<<--<---<<<<-<-<<<<<______>>>>>->->>>>--->-->>>>>>>---->>>>>>->>>>::::::::::::
#=GC RF                    AgaagCccaGGgguugGCuGgCaGAGGAaGGGaaGGGuCCgGgGuCgGCuGaGCAUGCCCuCaGGcUgCuCACUgUUCuuCCCuAGAAuGuCaGGugauGUGUCACCCCAA
//
# STOCKHOLM 1.0

#=GF AC   RF02015
#=GF ID   mir-1287
#=GF DE   microRNA mir-1287
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   46.00
#=GF TC   47.60
#=GF NC   44.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000725;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18945293
#=GF RT   Annotation of 390 bovine miRNA genes by sequence similarity with other
#=GF RT   species
#=GF RA   Strozzi F, Mazza R, Malinverni R, Williams JL
#=GF RL   Anim Genet. 2009;40:125.
#=GF RN   [2]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [4]
#=GF RM   19508715
#=GF RT   Identification and analysis of miRNAs in human breast cancer and teratoma
#=GF RT   samples using deep sequencing
#=GF RA   Nygaard S, Jacobsen A, Lindow M, Eriksen J, Balslev E, Flyger H, Tolstrup
#=GF RA   N, Moller S, Krogh A, Litman T
#=GF RL   BMC Med Genomics. 2009;2:35.
#=GF WK   MicroRNA
#=GF SQ   3


AL139243.11/40094-40005    GUUGUGCUG-UCCAGGUGCUGGAUCAGUGGUUCGAGUCUGAGCCUUUAAAAGCCACUCUAGCCACAGAUGCAGUGAUUGGAGCCAUGACAA
ABGA01175918.1/2390-2301   GUUGUGCUG-UCCAGGUGCUGGAUCAGUGGUUUGAGUCUGAGCCUCUAAAAGCCACUCUAGCCACAGAUGCUGUGAUUGGAGCCAUGACAA
AAFC03063226.1/56390-56480 GCUCUGCUUUCCCAGGUGCUGGAUCAGUGGUUUGAGUCUGAGCCUCUAAAAGCCACUCUAGCAACGGACGCAGUGAUUGGAGCUAUGACAA
#=GC SS_cons               <<<<<<<<-.-<<<<--<<<<-<<<-<<<<<<-<<<<--<-<<________>>>>>>>->>>>>>->>>->>>>-->>>>>>>->>>>>::
#=GC RF                    GucguGCug.uCCagGUgCuGGguCAGugGcuuGaGuCUGAGCCUcUAAAAGCCaCuCUagCcaCaGacGCaGcGAcuGGaGCcacgaCAA
//
# STOCKHOLM 1.0

#=GF AC   RF02016
#=GF ID   mir-1183
#=GF DE   microRNA mir-1183
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   97.00
#=GF NC   33.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.58 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000668;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   17922033
#=GF RT   MicroRNA expression signature of human sarcomas
#=GF RA   Subramanian S, Lui WO, Lee CH, Espinosa I, Nielsen TO, Heinrich MC,
#=GF RA   Corless CL, Fire AZ, van de Rijn M
#=GF RL   Oncogene. 2008;27:2015-2026.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


AC187735.3/112267-112180   -UUAUUCAAAUGCUCGGAGACACAGAACAUUAGAGAAGACAGGAGUUCACUGUAGGUGAUGGUGAGAGUGGGCAUGGAGCAGGAGUGCC
ABGA01071238.1/42987-43075 AUUAUUCAAAUGCUCGGAGACACAGAACAUUAGAGAAGAUAGGAGUUCACUGUAGGUGAUGGUGAGAGUGGGCAUGGAGCAGGAAUGCC
AC004595.1/61725-61813     AUUAUUCAAAUGCUCGGAGACACAGAACAUUAGAGAAGACAGGAGUUCACUGUAGGUGAUGGUGAGAGUGGGCAUGGAGCAGGAGUGCC
#=GC SS_cons               ::<<<<<---<<<<<-<-<-<<<----<<<<<--<---<<<<_______>>>>--->-->>>>>--->>>-->->->>>>>->>>>>::
#=GC RF                    AUuacuCAAAuGCuCGgAGACaCAGAACauuaGAgAAGacaGGAGUUCACuguAGGuGAugguGAGAGuGGGCAuGGaGCaGGagugCC
//
# STOCKHOLM 1.0

#=GF AC   RF02017
#=GF ID   mir-1912
#=GF DE   microRNA mir-1912
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   82.30
#=GF NC   58.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000768;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20413612
#=GF RT   Mammalian microRNAs: experimental evaluation of novel and previously
#=GF RT   annotated genes
#=GF RA   Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, Johnston
#=GF RA   WK, Russ C, Luo S, Babiarz JE, Blelloch R, Schroth GP, Nusbaum C, Bartel
#=GF RA   DP
#=GF RL   Genes Dev. 2010;24:992-1009.
#=GF RN   [2]
#=GF RM   19784364
#=GF RT   Ago2 immunoprecipitation identifies predicted microRNAs in human embryonic
#=GF RT   stem cells and neural precursors
#=GF RA   Goff LA, Davila J, Swerdel MR, Moore JC, Cohen RI, Wu H, Sun YE, Hart RP
#=GF RL   PLoS One. 2009;4:e7192.
#=GF RN   [3]
#=GF RM   18583537
#=GF RT   MicroRNA discovery and profiling in human embryonic stem cells by deep
#=GF RT   sequencing of small RNA libraries
#=GF RA   Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite
#=GF RA   A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R,
#=GF RA   Ruohola-Baker H, Tewari M
#=GF RL   Stem Cells. 2008;26:2496-2505.
#=GF RN   [4]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   13


AC007025.2/34347-34426     CUCUAGGAUGUGCUCAUUGCAUGGGCUGUGUAUAGUAUUAUUCAAUACCCAGAGCAUGCAGUGUGAACAUAAUAGAGAUU
AC233299.3/103621-103542   CUCUAGGAUGUGCUCAUUGCAUGGGCUGUGUAUAGUAUUAUUCAAUACCCAGAGCAUGCAGUGUGAACAUAAUAGAGAUU
AAFC03018986.1/1127-1206   CUCUAGGAUGUGCUCAUUGCAUGAGCUGUGUAUAUUGUUAUUCCAUACCCAGAGCGUGCAGUGUGAACAUAAUAGAGAUU
ABVD01865131.1/604-683     CUCUAGGAUGUGCUCAUUGCAUGGGCUGGGUAUAUUUUUAUUCAAUACCCAGAGCAUGCAGUGUGAACAUAAUAAAGAUU
ABRQ01091277.1/2521-2600   CUCUAGGAUGUGCUCAUUGCAUGGGCUGUGUAUCUUUCCAUUUAAUACCCAGAGCAUGCAGUGUGAACAUAAUAGAGAUU
AANN01763307.1/187-108     CUCUAGGAUGUACUAAUUGCAUGGGCUGUGUAUAUUUUUAUUUAAUACCCAGAGCAUGCAGUGUGAACAUAAUAGUGAAA
ABDC01305767.1/54-133      CUCUAGGAUGUGCUCAUUGCAUGGGCUGUGUAUAUUAUUAUUUAAUACCCAGAACGUGCAGUGUGAACAUAAUAGAGAUU
AAIY01019018.1/1306-1385   CUCUAGGAUGUACUCAUUGCAUGGGCUGUGUAUAUUUUUAUUUAAUACCCAGAGCAUGCAUUGUGGACAUAAUAGAGAUU
AAKN02039766.1/17807-17728 CUCUAGGAUGUGCUCAUUGCAUGAACUGUGUAUAUUUUUAUUCGAUACCCAGAGCAUGCAGUGUGAACAUAAUAGAGAUG
BX005219.12/56682-56761    CUCUAGGAUGUGCUCAUUGCAUGGGCUGUGUAGAUUUUUAUUUAAUACACAGAACAUGCAGUGAGAACUUGAUAGAGAUU
CU207399.3/51306-51385     CUCUAGGAUGUGCUCAUUGCAUGGGCUGUGUAUAUUUUUAUUCAAUACCCAGAGCGUGCAGUGUGAACAUAAUAGAGAUU
AAPE02002646.1/33646-33567 CUCUAGGAUGUGCUCACUGCAUGGGGUGUGCAUAUUUUUAUUCAAUACCCAGAGUAUGCAGUGUGAACAUAAUAGAGAUU
AAQR03176721.1/75364-75443 CUCUAGGAUGUUCUCAUUGCAUGGGCUGUGUAUAUCAUCACUCAAUACCCAGAGCGUGCAGUGUGAACAUAAUAGAGAUU
#=GC SS_cons               <<<<<--<<<<-<-<<<<<<<<<--<<<-<<<<___________>>>>->>>-->>>>>>>>>->->>>>-->>>>>:::
#=GC RF                    CuCuaGGauGugCUCacuGCauGGGCuGUGuauAUUuUUAUUuAauaCCCaGAGCauGCaguGUGAaCauAAuaGaGAUu
//
# STOCKHOLM 1.0

#=GF AC   RF02018
#=GF ID   mir-1207
#=GF DE   microRNA mir-1207
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   96.20
#=GF NC   62.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000596;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   18314482
#=GF RT   The identification of microRNAs in a genomically unstable region of human
#=GF RT   chromosome 8q24
#=GF RA   Huppi K, Volfovsky N, Runfola T, Jones TL, Mackiewicz M, Martin SE,
#=GF RA   Mushinski JF, Stephens R, Caplen NJ
#=GF RL   Mol Cancer Res. 2008;6:212-221.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


ABGA01186596.1/3317-3403   GCAGGGCUGGCAGGGAGGCAGGGAGGGGCUGGCUGGGCCUGGUAGUGGGCAUCAGCUGGCCCUCAUUUCUUAAGACAGCACUCCUGU
AC026248.7/31021-31107     GCAGGGCUGGCAGGGAGGCUGGGAGGGGCUGGCUGGGUCUGGUAGUGGGCAUCAGCUGGCCCUCAUUUCUUAAGACAGCACUUCUGU
AACZ03062653.1/43403-43318 -CAGGGCUGGCAGGGAGGCUGGGAGGGGCUGGCUGGGCCUGGUAGUGGGCAUCAGCUGGCCCUCAUUUCUUAAGACAGCACUUCUGU
#=GC SS_cons               <<<<<<<<<-----<<<<----<<<<<-<--<<<<<<<<<______>>>>->>>>>-->>>>>>--->>>>---->>>>--->>>>>
#=GC RF                    gCaGgGCuGGCAGGgaGgCuGGGaGGGGCUGGCuGgGcCcGGUAGUgGgCAcCaGCUGGCCCuCAUUcCucAAGACaGCACUcCuGc
//
# STOCKHOLM 1.0

#=GF AC   RF02019
#=GF ID   mir-1265
#=GF DE   microRNA mir-1265
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   80.50
#=GF NC   73.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000688;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


ABGA01122763.1/3022-2937 AUGGUUUGGGACUCAGGAUGUGGUCAAGUGUUGCUAAGGCAUGUUCAGUGACAAUACUUGACCACAUUUUGAAUCCCAAACCAUAU
AL139405.11/97021-97106  AUGGUUUGGGACUCAGGAUGUGGUCAAGUGUUGUUAAGGCAUGUUCAGGAACAAUACUUGACCACAUUUUGAAUUCCAAACCAUAU
AADA01001195.1/1918-1985 -CGGUUUGGGACUCAGGAUGUGGUCAAGUGUUGUUAAGGCAUGUUCAGCAACAAUACUUGACCACAUUU-----------------
#=GC SS_cons             <<<<<<<<<<<-<<<<<<<<<<<<<<<<<<<<<<<---<______>--->>>>>>>>>>>>>>>>>>>>>>>->>>>>>>>>>>::
#=GC RF                  auGGuuuGGgaCucaggauGuGGuCaaGuguuGuuAAGGCAUGUUCAGuaaCaacaCuuGaCCaCauccugaAucCCaaaCCauAU
//
# STOCKHOLM 1.0

#=GF AC   RF02020
#=GF ID   mir-25
#=GF DE   microRNA mir-25
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   56.70
#=GF NC   39.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000013;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20403161
#=GF RT   Small RNA expression and strain specificity in the rat
#=GF RA   Linsen SE, de Wit E, de Bruijn E, Cuppen E
#=GF RL   BMC Genomics. 2010;11:249.
#=GF RN   [2]
#=GF RM   17604727
#=GF RT   A mammalian microRNA expression atlas based on small RNA library
#=GF RT   sequencing
#=GF RA   Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S,
#=GF RA   Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V,
#=GF RA   Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B,
#=GF RA   Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G,
#=GF RA   Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di
#=GF RA   Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN,
#=GF RA   Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo
#=GF RA   JJ, Sander C, Zavolan M, Tuschl T
#=GF RL   Cell. 2007;129:1401-1414.
#=GF RN   [3]
#=GF RM   18392026
#=GF RT   Discovering microRNAs from deep sequencing data using miRDeep
#=GF RA   Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S,
#=GF RA   Rajewsky N
#=GF RL   Nat Biotechnol. 2008;26:407-415.
#=GF RN   [4]
#=GF RM   15652478
#=GF RT   Phylogenetic shadowing and computational identification of human microRNA
#=GF RT   genes
#=GF RA   Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E
#=GF RL   Cell. 2005;120:21-24.
#=GF RN   [5]
#=GF RM   16766679
#=GF RT   Identification and characterization of two novel classes of small RNAs in
#=GF RT   the mouse germline: retrotransposon-derived siRNAs in oocytes and germline
#=GF RT   small RNAs in testes
#=GF RA   Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N,
#=GF RA   Imai H
#=GF RL   Genes Dev. 2006;20:1732-1743.
#=GF WK   Mir-25_microRNA_precursor_family
#=GF SQ   3


AADA01162939.1/2400-2483   GGCCAGUGUUGAGAGGCGGAGACUUGGGCAAUUGCUGGACGCUGCCCUGGGCAUUGCACUUGUCUCGG-CUGAGACGCGCCCGCC
AY866339.1/648-731         GGCCAGUGUUGAGAGGCGGAGACUUGGGCAAUUGCUGGACGCUGCCCUGGGCAUUGCACUUGUCUCGGUCUGACA-GUGCCGGCC
AABR05031162.1/12939-12856 GGCCAGUGUUGAGAGGCGGAGACACGGGCAAUUGCUGGACGCUGCCCUGGGCAUUGCACUUGUCUCGGUCUGACA-GUGCCGGCC
#=GC SS_cons               <<<<-<<<<----<<<<-<<<<<----<<<<<-<<<<<______>>--->>>>>>>>---->>>>>->>>>----.>>>>->>>>
#=GC RF                    GGCcAGuguUGAGaGgCGGaGaCuuGGGCaauUGCuGGACGCUGCCCUGgGCauuGCACUUGuCuCGGcCuGAcA.gcgCCgGCC
//
# STOCKHOLM 1.0

#=GF AC   RF02021
#=GF ID   mir-3179
#=GF DE   microRNA mir-3179
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   90.00
#=GF TC   93.60
#=GF NC   83.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000900;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20224791
#=GF RT   Discovery of novel microRNAs in female reproductive tract using next
#=GF RT   generation sequencing
#=GF RA   Creighton CJ, Benham AL, Zhu H, Khan MF, Reid JG, Nagaraja AK, Fountain
#=GF RA   MD, Dziadek O, Han D, Ma L, Kim J, Hawkins SM, Anderson ML, Matzuk MM,
#=GF RA   Gunaratne PH
#=GF RL   PLoS One. 2010;5:e9637.
#=GF RN   [2]
#=GF RM   20300190
#=GF RT   Characterization of the Melanoma miRNAome by Deep Sequencing
#=GF RA   Stark MS, Tyagi S, Nancarrow DJ, Boyle GM, Cook AL, Whiteman DC, Parsons
#=GF RA   PG, Schmidt C, Sturm RA, Hayward NK
#=GF RL   PLoS One. 2010;5:e9685.
#=GF WK   MicroRNA
#=GF SQ   3


AC136427.3/102832-102749 CAGGAUCACAGACGUUUAAAUUACACUCCUUCUGCUGUGCCUUACAGCAGUAGAAGGGGUGAAAUUUAAACGUCUGUGAUCCUG
AC136618.3/8090-8007     CAGGAUCACAGACGUUUAAAUUACACUCCUUCUGCUGUGCCUUACAGCAGUAGAAGGGGUGAAAUUUAAACGUCUGUGAUCCUG
AC010488.7/52282-52199   CAGGAUCACAGACGUUUAAAUUACACUCCUUCUGCUGUGCCUUACAGCAGUAGAAGGGGUGAAAUUUAAACGUCUGUGAUCCUG
#=GC SS_cons             <<<<<<<<<<<<<<<<<<<<<<-<<<<<<<<<<<<<<<________>>>>>>>>>>>>>>>->>>>>>>>>>>>>>>>>>>>>>
#=GC RF                  CaGGauCaCaGaCGuuuaaauuACaCcCCuuCugCuGcGCCUUACAgCaGcaGaaGGgGuGAaauuuaaaCGuCuGuGauCCuG
//
# STOCKHOLM 1.0

#=GF AC   RF02022
#=GF ID   mir-1275
#=GF DE   microRNA mir-1275
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   71.50
#=GF NC   55.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000674;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   18285502
#=GF RT   Application of massively parallel sequencing to microRNA profiling and
#=GF RT   discovery in human embryonic stem cells
#=GF RA   Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL,
#=GF RA   Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA
#=GF RL   Genome Res. 2008;18:610-621.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   6


ABGA01022599.1/16760-16839   CCUCUGUUAGGAAGGGUG-UGGGGGAGAGGCUGUC---------------------UUGUGUCUGUAAAUAUGCAAAACUUAUCUUCCCCAAG--GCAGAGGGA
AL589941.6/62761-62682       CCUCUGUGAGAAAGGGUG-UGGGGGAGAGGCUGUC---------------------UUGUGUCUGUAAGUAUGCCAAACUUAUUUUCCCCAAG--GCAGAGGGA
AC193265.3/130181-130103     CCUCUGUGAGAAAGGGUG-UGGGGGAGAGGCUGUC---------------------UUGUGUCUGUAAGUAUGCCAAACUUAUUUUCCCCAAG--GCAGAGGG-
AADB02010022.1/904419-904521 CCUCUGUUAGGAAGGAUG-UAGGGGAGAGGCUGCCUCAAGUCGUGCUUGUCUCACAUUGUGUCUAUAAACAUGCAAAACUUGUUUCCCCCAAGCAACAGAGGGA
AANU01208069.1/6838-6918     CCUCUGUUAGGAAGGGUGUUGGGGGAGAGGUUGUC---------------------CUGUGUCUGUAAAUAUGCAAAACUUAUUUUCCCCAAG--GCUGAGGGA
AANU01208069.1/5405-5303     CCUCUGUUAGGAAGAGUG-UGGGGGAGAGGCUGCCUCAUGUCUUGUUUGUCUCACAUUGUGUCUAUAAACAUGCAAAACUUGUUUCCCCCAAGCAACAGAGGGA
#=GC SS_cons                 <<<<<<<-----------.<<<<<<<<<----<<-.....................<<<<<<________>>>>>>->>--->>>>>>>>>--..>>>>>>>::
#=GC RF                      CCuCuGuuAGgAAGggUG.uGGGGgagaGGcUGuC.....................uuGuguCUgUAAauaugCaaAaCUUaucucCCCCaAG..aCaGaGGGA
//
# STOCKHOLM 1.0

#=GF AC   RF02023
#=GF ID   mir-1208
#=GF DE   microRNA mir-1208
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   95.50
#=GF NC   66.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000628;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   18314482
#=GF RT   The identification of microRNAs in a genomically unstable region of human
#=GF RT   chromosome 8q24
#=GF RA   Huppi K, Volfovsky N, Runfola T, Jones TL, Mackiewicz M, Martin SE,
#=GF RA   Mushinski JF, Stephens R, Caplen NJ
#=GF RL   Mol Cancer Res. 2008;6:212-221.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   3


AC007860.6/97961-98032     -ACCGGCAGAAUCACUGUUCAGACAGGCGGAGACGGGUCUUUCUCGCCCUCUGAUGAGUCACCACUGUGGUGG
ABGA01186599.1/24346-24418 CACCGGCAGAAUCACUGUUCAGACAGGCGGAGACGGGUCUUUCUCGCCAUCUGAUGAGUCACCACUGUGGUGG
CT824641.5/53483-53411     CACCGGCAGAAUCACUGUUCAGACAGGCGGAGACGGGUCUUUCUCGCCCUCUGAUGAGUCACCACUGUGGUGG
#=GC SS_cons               <<<<<-<<<----<<<--<<<<<--<<<<<<<<______>>>>->>>>->>>>>-->>>----->>>>>>>>:
#=GC RF                    CaCCgGCaGAAUCaCuGUuCaGaCAGGCGGagaCGGGUCuuuCUCGCCcuCuGaUGaGuCACCACuGuGGuGG
//
# STOCKHOLM 1.0

#=GF AC   RF02024
#=GF ID   mir-1180
#=GF DE   microRNA mir-1180
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   74.70
#=GF NC   64.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000789;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19406225
#=GF RT   In silico detection and characteristics of novel microRNA genes in the
#=GF RT   Equus caballus genome using an integrated ab initio and comparative
#=GF RT   genomic approach
#=GF RA   Zhou M, Wang Q, Sun J, Li X, Xu L, Yang H, Shi H, Ning S, Chen L, Li Y, He
#=GF RA   T, Zheng Y
#=GF RL   Genomics. 2009;94:125-131.
#=GF RN   [2]
#=GF RM   17922033
#=GF RT   MicroRNA expression signature of human sarcomas
#=GF RA   Subramanian S, Lui WO, Lee CH, Espinosa I, Nielsen TO, Heinrich MC,
#=GF RA   Corless CL, Fire AZ, van de Rijn M
#=GF RL   Oncogene. 2008;27:2015-2026.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF RN   [4]
#=GF RM   19508715
#=GF RT   Identification and analysis of miRNAs in human breast cancer and teratoma
#=GF RT   samples using deep sequencing
#=GF RA   Nygaard S, Jacobsen A, Lindow M, Eriksen J, Balslev E, Flyger H, Tolstrup
#=GF RA   N, Moller S, Krogh A, Litman T
#=GF RL   BMC Med Genomics. 2009;2:35.
#=GF WK   MicroRNA
#=GF SQ   3


AL160492.5/61752-61684     GCUGCUGGACCCACCCGGCCGGGAAUAGUGCUCCUGGUUGUUUCCGGCUCGCGUGGGUGUGUCGGCGGC
AC124066.6/52207-52275     GCUGCUGGACCCACCCGGCCGGGAAUAGUGCUCCUGGUUGUUUCCGGCUCGCGUGGGUGUGUCGGCGGC
AAWR02013581.1/12615-12683 UCUGCCUGGCCCACCCAGCCGGGAAUAGUGCACGAGUUUGUUUCCGGCUCGAGUGGGUGUGUCGGAGGC
#=GC SS_cons               <<<<<<<<<<<<<<<-<<<<<<<<<<<<_________>>>>>>>>>>>>->->>>>>>--->>>>>>>>
#=GC RF                    gCugCcggaCCCACCCgGCCGGgAAuAgUGCuCcuGguUgUUuCCGGCuCGcGUGGGuGUGucgGcgGc
//
# STOCKHOLM 1.0

#=GF AC   RF02025
#=GF ID   mir-3017
#=GF DE   microRNA mir-3017
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   59.00
#=GF TC   59.30
#=GF NC   58.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.76 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0001107;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20444247
#=GF RT   Bioinformatic prediction, deep sequencing of microRNAs and expression
#=GF RT   analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon
#=GF RT   pisum
#=GF RA   Legeai F, Rizk G, Walsh T, Edwards O, Gordon K, Lavenier D, Leterme N,
#=GF RA   Mereau A, Nicolas J, Tagu D, Jaubert-Possamai S
#=GF RL   BMC Genomics. 2010;11:281.
#=GF WK   MicroRNA
#=GF SQ   36


ABLF02038620.1/9798-9872   GUCGUCGGUGCCGUGUUCUGUGACCGACUCGGCCCGC----------------------------------------GC-CCGCCGGUCUGUCACAGAACACGGGACCGGCCGCAG
ABLF02037893.1/63-152      GGCGUCGGUGCCAUGUUCUGUGACUGACUCAGCUGGC-----GCCGGACU-----GUCG---------------GACGC-CCGCCGGUCUGUCACAGAACACAAGACCGGCCGCAU
ABLF02024751.1/14352-14441 CGCGUCGGUGCCGUGUUCUGUGAAUGACUCGGCUGGC-----GCCGGACU-----GGCG---------------GGCGC-CCGUCGGUCUGUCAUGGAACACGAGACCGGCCCCAG
ABLF02008770.1/11823-11901 GGCGUCGGUGCCGUGUUCUGUUCCUGACCCGACCGGC-----------GG-----GC--------------------GC-CCACCGUUCCGUCACAGAACACGGGACCGGCCGAAU
ABLF02038629.1/37719-37789 CGCGUCGGUGCCGUGUUCUGUGACUGACUCGGCU---------------------GG------------------------CGCCGGUCUGUCACAGAACACGGGACCGGCCGCGU
ABLF02024629.1/12903-12992 GGCGUCGAUGCCGUGUUCUGUGACUGACUCGGAUGGC-----GCCGGACU-----GGUG---------------GGCGC-CCGCCGGUCUGUCACAGAACAAGAGACCGGACGCAA
ABLF02033058.1/85111-85041 CGCGUCGGUGCCGUGUUCUGUGACUGACUCGGCU---------------------GG------------------------CGCCUGUCCGUCACAGAACACGAGACCGGCCGCGG
ABLF02018735.1/4707-4778   GGCGUCGGUGCCGUGUUCUGUGACUGACUCGGCUGG--------------------------------------------CGUCCGAUCUGUCACAGAACAUGGGACCGGCCGCAU
ABLF02033848.1/32278-32194 CGCGUCGGUGCCGUGUUCUGUGACUGACUCGGCUGGC-----AACGGACU-----GA--------------------GC-CCUCCGGUCUGUCACGGAACACGGGACCGGCCGCAU
ABLF02017426.1/4304-4393   GCGGUCGGUGCCGUGUUCUGGUCCUGACUCGGCUGAC-----GCUGGAUU-----GGCG---------------GGCGC-CCGCUGGUCUGUCACAGACCACGGGACCGGCCGCAU
ABLF02038524.1/14008-14078 CGCGCCGGUGCCGUGUUCUGUGACCGACUCGGCU---------------------GG------------------------CGCGGGACCGUCACAGAACACGGGACCGGCCGCAU
ABLF02021808.1/14777-14705 AGCGCCGGUGCCAUGUUCUUUGACUGACUCGGCUGGC----------------------------------------GC-CCGUCGGUUUGUCACAGAAC--GGGACCAGCCGCAU
ABLF02014955.1/836-925     CGCGUCGGUGCCGUGUUCUGUGACUGACUGGGCUGAC-----GUCGGACU-----GGCG---------------GGCGC-CCGCUGGUCUGUCACAGAACCUGAGACCGGUCGCAU
ABLF02033839.1/10856-10772 CGCGUCGGUGCCGUGUUCUGUGACUGACUCGGCUGGC-----AACGGACU-----GA--------------------GC-CCUCCGGUCUGUCACGGAACACGGGACCGGCCGCAU
ABLF02018835.1/546-634     AGCGUCGGUGUCGUGUUCUGUUCCUGACUCGGCUGGC-----GCCAGACU-----GGC-----------------GGGCGCCGCCAGUCUGUCACAGAACACGGGACCGGACGAAU
ABLF02006227.1/12753-12679 UACGUCGGUGCCGUGUUCUGUUCCUGACUCAGCUGGC----------------------------------------GC-CCUCUGUUCUGUCACAGAACACGGGACCCACCGCAU
ABLF02032338.1/296-207     CGCGUUGGUGCCAUGUUCUGUGACUGACUCGGUUGGU-----GCCGGACU-----GGCG---------------GGCGC-CCGCCGGUCUGUCACGGAACACGAGACAGGCCGCAG
ABLF02037810.1/10195-10284 CGCAUCGGUGCCAUGUUCUGUGACUGACUGGGCUGGC-----GCCGGACUGGGGGGU--------------------GC-CCGCCGGUCGGUCACAGAGCACGGGACCGGCCGCAU
ABLF02018694.1/7084-6995   GGCAUCGGUGCCGUGUUCUGUGACUAACUCGACUGGC-----GCCGGACU-----GACG---------------GGCGC-CCGCCGGUCUGUCACAGAUCACGGGACCAGCCGCAU
ABLF02016156.1/1846-1757   CGCGUCGGUGCCGUGUUCUGUGACAGACUGGGCUGGC-----GCCGGACUGGCGGGU--------------------GC-CCGCCGGUCUGUCACAGAGCACGGGACCGGCUGCAU
ABLF02026093.1/21945-22018 GGCGUCGGUG-CGUGUUCUGUGACUGACUCGGCUGGC----------------------------------------GC-CCGCAGGUCUGUCACGAAACACGGGACCAUAGAAAA
ABLF02016826.1/4915-4841   CGCGUCGGUUCCAUAUUCUGUGACUGACUCCGCUGGC----------------------------------------GC-CCGCCGGUUUGUCACAGAACACGGGACCGGCCACAU
ABLF02010408.1/2001-2102   CGCGUCGGUGCCGUGUU-UGUGACUGACUGGGCUGGC-----GCCGGACU-----GGCUGCACGCCGGCUACGGCGCGC-CCGCCGGUCGGUCACAGAGCACGGGACCGGCCG--C
ABLF02038162.1/53024-52954 CGCGUCGGUGCCGUGUUCUGUGCCUGACUCGGCU---------------------GG------------------------CGCCGGUCUGUCACAGAACACGGGACCGACCGCAG
ABLF02023539.1/26570-26659 AGCGUCGGUGCCGUGUUCUGUGACUGACUCGGCUUGC-----GUCGGGCU-----GGCG---------------GGCGC-CCGCCGGUCCGUCACAGAACACGGGACCGGCCGCAU
ABLF02009007.1/684-610     GGCGUCGGUGCCGUGUUCUAUGAUAGACUCGGCUGGC----------------------------------------GC-CUGCCGGUCUGUCGCAGAACACGGCACCGCAUACGG
ABLF02024900.1/22656-22567 CGCGUCGGUUCCGUGUUCUGUGACUGACUGAGCUGGC-----GCCGGACUGGCGGGU--------------------GC-CCGCAGCUCGGUCACAGAGCACGGGACCGGCCGCAU
ABLF02017030.1/27450-27524 GACGUUGGUGUCAUGUUCUGUUACUGACUCGGCUGGC----------------------------------------GC-CCUCCGUUCCGUCACAGAACACAGAACCAACCGCAU
ABLF02023892.1/10072-10146 CGCGUCGGUGCCGUGUUCUGUGACUGACUCGGCUGGC----------------------------------------AC-CCGCCGGUCUGUCACAGAACACGGGACCGGCCGCGG
ABLF02010090.1/1948-1859   GGUGUCGGUGCCGUGUUCUGUUCCUAACUCGGCUGGCGCCAUAUUGGCAG-----GC--------------------GU-CCUUCGUUCCGUCACAGAACACGGGACCAGCCGCAU
ABLF02023791.1/4952-4878   CGCGUCGGUGCCGUGUUCUGUGACUGACUCGGCUGGC----------------------------------------GC-CUGCCGGUCUGUCACAGAACACGGGACCGGCCGCAU
ABLF02007019.1/14409-14487 CGCGUCGGUGCCGUGUUCUGUGACUGACUGGGCUGGC-----------GG-----GU--------------------GU-CCGCCGGUCUGCCACAGAACACGGGACCGGCCGCAA
ABLF02013625.1/792-881     UGCGACAGUGCCGUGUUCUGUGACUGACUAGGCUGGC-----GCCGGACU-----GGCG---------------GGCGC-CCGCUGGUCUGUCACUGAACACGAGACCGGCCGCAU
ABLF02039826.1/29244-29333 UUAGUCGGUGCCGUGUUCUGUGACUGACUCGGCUGGC-----GCCGGACUGGCGGGG--------------------GC-CAGCCGGUCUGUCACGGAACACGGGACCGGCCGCAU
ABLF02006524.1/1779-1868   CGCGUCGGUGUCGUGUUCUGUGGCUGACUGGGCUGGC-----GCUGGACU-----GGCG---------------GGCGC-CCGCCGGUCUGUCACAGAACACGAGACCGGCCGCAU
ABLF02031377.1/72575-72486 CGCGUCGGUGCUGUGUUCUGUGACUGAUUCGGCUGGC-----GCCGGACUGGCGGGA--------------------GC-CCGACGGUCUGUCACGGACCACGAGACCGGCCGCAG
#=GC SS_cons               ::::::::::<<<<<<<<<<<<<<-<<<-<<<--<<<.....________.....__....................>>.>-->>>>>>->>>>>>>>>>>>>>::::::::::::
#=GC RF                    cGCGUCGGUGcCGUGuUCuGUGaCUGAcUcgGCUGGC.....GccGGAcu.....Gg....................GC.CCGCcggUCuGuCACaGAaCACGgGACCGGCCGCAu
//
# STOCKHOLM 1.0

#=GF AC   RF02026
#=GF ID   mir-2833
#=GF DE   microRNA mir-2833
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   85.00
#=GF NC   35.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000886;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   20199675
#=GF RT   MicroRNAs of Bombyx mori identified by Solexa sequencing
#=GF RA   Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q
#=GF RL   BMC Genomics. 2010;11:148.
#=GF WK   MicroRNA
#=GF SQ   5


AADK01040104.1/1718-1790 -AGAA--UUCGCGGUAAACAGUGGAAACUGGUCCUCAUAUGUUGAGAGAUUGGAAAUGUACUUUUUAGUGAAUAAA-
BAAB01167795.1/319-245   AAGAA--UUCGCGGUAAACAGUGGAAACUGGUCCUCAUAUGUUGAGAGAUUGGAAAUGUACUUUUUGGUGAAUAAAG
BABH01058117.1/633-707   AAGAA--UUCGCGGUAAACAGUGGAAACUGGUCCUCAUAUGUUGAGAGAUUGGAAAUGUACUUUUUGGUGAAUAAAU
BABH01082483.1/16-86     AAGAA--UUCGCGGUAAACAG-GGAAACG-GUCCUCAUAUG-UGAGAGAUG-GAAAUGUACUUUUUAGUGAAUAAAG
BABH01039435.1/1413-1337 AAGUAGCUUCGCGGUAAACCAUGGAAGCUGGUCUUCAUAUGUUGAGAGAUUGGAAAUGUACUUUUUGGUGAAUAAAG
#=GC SS_cons             ::::<..<<<<<--<<<<-<<<<-<--<--<<<<<<<_____>>>>->>>-->--->->>>>->>>>>>>>>>::::
#=GC RF                  AAGAA..UUCgCGGuAAACaGugGAAACuGgUCcUCAUAUGUUGAgAGAuuGGAAAUGuaCuUUUUaGuGAAUAAAg
//
# STOCKHOLM 1.0

#=GF AC   RF02027
#=GF ID   MIR2907
#=GF DE   microRNA MIR2907
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   52.00
#=GF TC   52.00
#=GF NC   51.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.97 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000861;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19796675
#=GF RT   Identification of novel stress-regulated microRNAs from Oryza sativa L
#=GF RA   Jian X, Zhang L, Li G, Zhang L, Wang X, Cao X, Fang X, Chen F
#=GF RL   Genomics. 2010;95:47-55.
#=GF WK   MicroRNA
#=GF SQ   52


AC097280.8/88746-88810     GAGCAGCUCUCUCUCCGCCCACUUGGC-C-ACCACGCGGCA-GCC-GAGCGAG--GGC--------------CUCG--GGGCAGCUU
AC146939.2/23550-23614     CAGCGCCUCUCCCUCCGCCCACUCAGC-C-ACCACGUGGAA-GCC-GAGUGAG--GGC--------------CUCG--GGGCAGCAU
AAAA02011510.1/6970-6906   CAGCGCCCCUGUCUCCGCCCACUCAGC-U-GCAACGUGGCG-GCC-GAGUGAG--GGC--------------CUCG--GGGGGACGC
AAAA02017789.1/5897-5961   CAGCGCCCCUUCCUCCGCCCACUCAGC-G-GUGUCGUGGCA-GCC-GAGUGAG--GGC--------------CUCG--GGGCGACGU
AAAA02030917.1/28001-27937 UAGCGCCCUUUCCUCCACCCACUUGGC-U-GCCACGUGGCA-GCU-GAGCGAG--GGC--------------CUCG--GGGUGACGC
AP004794.3/136094-136030   UGGCGCCCCCUCCUCCGCCCGCCCAGC-C-GCCACAUGGCA-GCU-GAGCGGG--GGC--------------CUUG--GGGUGGCGC
AAAA02027275.1/5747-5684   CAGCGCCCCUUCCUCCGCCCACUCAGC-U-GCAACGUGGCA-GCC-GAGUGAG---GC--------------CUCG--GGGUGACGC
AP004267.3/81703-81639     CAGCGCCUCUCCCUCCGCCCACUCGAC-C-GCCACGUGGCA-GCC-GAGCGAG--CGC--------------CUCG--GGGCAGCGU
AAAA02020856.1/51375-51439 UAGCGCCCCUAUCUCCGCCCACUCAAC-C-GCCACGUGGCA-GCC-GAGUGAG--GGC--------------CUCG--GGGUAACGC
AP003339.4/6849-6785       GAGCACCCCUCUCUCCGCCCACUCGGC-C-ACCAUGUGGCA-GCC-GAGCGGG--GGC--------------CUUG--GGGCAGCUU
AC093919.2/14849-14913     CAGCGCCCCUUCCUCCACCCACUCAGC-U-GCGACGUGGCA-GCC-GAGCGUG--GGC--------------CCCG--GGGCGACGC
ABRL01000509.1/3235-3171   CAGCGCCUCUCCCUCCGCCCACUCGGC-C-GCCACGUGGCA-GCC-GAGUGGG--GGC--------------CUCG--GGGCAGCGC
AP005833.2/12365-12301     CAGCGCCCUUACCUCCGCCCGCUCGGU-C-GCCACGUGGCG-GCC-GAGCGAG--GGC--------------CUCG--GGGUAACGC
AP003217.3/53226-53162     CAGCGUCCCUUCCUCCGCCUACUCAGC-U-GCGACGUGGCA-GCC-GAGUGAG--GGC--------------CUCG--UGGUGAUGU
AC125780.2/3524-3460       CAGUGCCCCUUCCUCUGCCCACUCAGC-C-GCGACGUGGCA-GCC-GACUAAG--GGC--------------CUCG--GGGCGACGU
AAAA02006744.1/10968-11032 CAGCGCCCCUUCCUCCGCCCACUCAGC-U-ACAACGUGGCA-ACC-AAGUGAG--GGC--------------CUCG--GGGUGACGC
AC090482.3/148437-148501   CAGCUCCUCUUGCUCCGCCCACCCGGC-C-GCCACGCGGCA-GCC-GGAUAGG--GGC--------------CUUG--GGGCAACGC
AP005830.4/146068-146003   CAGCGCCUCUUGCUCUGCCCACUCACCCC-GCCACGUGGCG-GCC-GGGUGAG--GGC--------------CUCG--GGGCAGCAU
AAAA02003651.1/822-757     CAGCGCCUCCUGCUCCGCCCACUCAACCC-GCCACGUGGUG-GCU-GGGUGAG--GGC--------------CUCG--GGGCAGCAU
AP006524.3/10082-10146     CAGCGCCCCUUCCUCCGCCCACUCGGC-C-GCCACGUGGCA-GCC-GACUGAG--GGC--------------CUCG--GGGCGGCGC
AACV01023519.1/9076-9141   CCGCGCCUCCCUCUCCGCCCGCUCGAC-C-GCCACAUGGCA-GCCCGGAUGAG--GGC--------------CUCG--GGGCAACGC
AAAA02028983.1/24029-23965 CUCCUACUCCUGCUCCGCUUUCUCGGC-C-GCCACGUGGUG-GCC-GAGUGAG--GGC--------------CUCG--GGGCGGUAC
AAAA02028759.1/3196-3260   AAGCGCUUCCUGCUCUACCCACUUGGC-C-GCCACGUGGCG-GCC-GGCUGAG--GAC--------------CUCG--GGGCAACGC
AC117265.2/49258-49323     CAACGCCUCCUACUCCGCCCACUCACCCC-GCCACGUGGUG-GUC-GGGUGAG--GGC--------------CUCG--GGGCAGCAU
AC174464.1/33908-33844     CAGCGCCUCCUGCUCUGCUCACUCAGC-C-GCCACGUGGUA-GCC-GGGUGAG--GGC--------------CUCG--UGGCAUCGU
AAAA02027671.1/23039-22975 UAGCGCUCCUAUCUCUGCCCACUCGAC-U-GCCACGUGGCA-GCC-GAGUGAG--GGC--------------CUCG--GUGUGGCGC
AP005563.3/32124-32060     CGGCGCCCCCUCCUCCACCCACUUAGC-C-GCCGAGUGGCA-GCU-GAGCGGG--GGC--------------CUCG--GGGUGGCAC
AP004176.2/40286-40222     UAGCGCCCCUACCUCCGUCCACUCGGC-C-GCCACGUGGUA-GCC-GAACGAG--GGC--------------CUCG--GAGUGGAGG
AAAA02017378.1/13073-13137 CAGCGCUCCUUCCUCCACCCACUCAGC-U-GCGACGUGGCA-GCU-GAGCGUG--GGC--------------CCUG--GGGUGACGC
ABRL01002336.1/15997-15933 CAGCACCCCUGUCUCCGCCCACUCGGC-C-ACCACGUGGUG-GCU-GAGCGAG--GGC--------------CUCG--GGGUGACAC
AACV01006843.1/44477-44413 GAACACCUCUCCCUCCGCCCACUCGGC-C-ACCACGUGGCA-GCC-AAGCGAG--GGC--------------CUCG--AGGCAGCUC
AAAA02001440.1/37725-37660 CAGCAUCUUUCGCCCCGCCCGCUCUCC-CUGCCACGUGGUG-GCC-GGGCGAG--GGC--------------CUCG--GGGUAGCAC
AAAA02021825.1/11739-11675 CGGCGUCCCCUCCUCCGCCCACUCAGC-C-GCCACGCGGCA-GCU-GAGCGAG--GGC--------------CUCU--GGGUGACGC
AAAA02012223.1/67944-67879 CAGCGCCCCUUCCUCCGCCCACUAGGC-C-GCCACGUGGCAAGCC-GAGUGAG--GGC--------------CUCG--GGGCGGCAC
AC146939.2/4686-4750       CAGUGCCUCUCCCUCUGCCCACUCGGC-C-GCCACGUGGUA-GCU-AAGUGAG--GGC--------------CUUG--GGGCAGUGC
AP000399.1/44777-44713     CAGCGCCUCUUUCUCUGCCCACUCAGC-A-GCAACGUGGCA-GCC-GAGUGAG--GGC--------------CUCG--GGGCGACGC
AP003431.2/181742-181678   CGGCGUCCCCUCCUCCGCCCACUCAGC-C-GCCACGUGGCA-GCU-GAGCGAG--GGC--------------CUCG--GGGUAACAC
AP005541.3/84154-84090     CAGCGCCCCUUCCUCUGCCCACUUGGC-C-GCCACGUGGCA-GCC-GAGCGAG--GGC--------------CUCG--GGGCAGCGC
AP005676.3/7015-7079       UAGCGCUCCUAUCUCCGCCCACUCGAC-C-GCCACGUGGCA-GCC-GAGUGAG--GGC--------------CUCA--GGGUGGCGC
AP003538.2/47461-47525     CAGCGCCCCUUCCUCCGUCCGCUCGGU-U-GCAACAUGGCA-GCC-GAGUGAU--GGC--------------CUCG--GGGUGACGU
AC073166.7/88638-88701     GAGCACCUCUCUCUCUGCCCACUCGGC-C-ACCACGUGGCA-GCC-C--CGAG--GGC-------------CCUCG--GGGUGCGGC
AC105731.2/61950-62032     CAGCGCCUCUCCCUCCGCCCACUCGGC-C-GCCACGUGGCA-GCC-GAGUGGGGUGUCACGACCGGAAAUAACCCAACGGGCGUUCC
AP003077.3/69428-69492     CAACGCCCCUAUCUCCGCCCACUCGAC-C-GCCACGUGGCA-ACC-GAGUGAG--GGC--------------CUCG--GGGUGCGAC
AL713955.4/137906-137842   AGGCACCCCUAUCUCCACCCACGCGGC-C-GCCACAUGGCA-GCC-GAGCGAG--GGC--------------CUCG--GGGUAACUC
AP004069.2/40068-40004     CACGCCCGCUGACGGCUCCCGCUUGGC-C-ACCAAGUGGUG-GCC-GAGCGAG--GGC--------------CUCG--GGGGUGGUU
AL713955.4/87163-87099     AGACGCCCCUAUCUUCGCCCACUCGGC-C-GCCACGUGGUG-GCC-GAGCGAG--GGC--------------CUCG--GGGUAACUC
AL954826.3/54818-54754     CAGCGCCCCUAUCUCCGCCCACUCAGC-U-GCAACGUGGCG-GCC-GAGUGAG--GGC--------------CUCG--GGAGGACGC
AL713954.3/107270-107206   CAGCACCCCUUCCUCCGCCUACUCGGC-C-GCCAUGUGGCA-GCC-GAGUGAG--GGC--------------CUCG--GGGCGGCGC
AC135561.3/90907-90842     CAGCAUCUCCUGCGCCGCCCACUUACC-CUGCCACGUGGAG-GCC-AGGCGAG--GGC--------------CUUG--GGGCAGCAU
AL713954.3/88229-88165     CAGCGUCCCAUCCUCCGCCCACUCGAC-C-GCCACGUGGCA-GCC-GAGUGAG--GGC--------------CUCG--GCGCGGCGC
AC091302.5/25938-25874     CAGCACCUCCUGCUCUGCUCACUUGGC-C-GCCACGUGGCA-GCC-GGGUGAG--GGC--------------CUCG--GGGUGGUGU
AC147811.2/113342-113406   GAGCACCUCUCCCUCCGCCCGCUCGGC-C-ACCACGUGGCA-GCC-GAGCGAG--GGC--------------CUCG--GGGCAGCUC
#=GC SS_cons               ::::::::::::::::((((,<<<<<<.-.-<<____>>--.>>>.>>><<<<..___..............>>>>..)))):::::
#=GC RF                    CAGCGCCuCUucCUCCgCCCACucGGC.C.GCCACGUGGCA.GCC.gaGcGaG..GGC..............CuCg..GGGcggcgC
//
# STOCKHOLM 1.0

#=GF AC   RF02028
#=GF ID   mir-1827
#=GF DE   microRNA mir-1827
#=GF AU   Boursnell C; 0000-0002-3494-4451
#=GF SE   Predicted; ClustalW2
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   68.20
#=GF NC   52.30
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   MIPF; MIPF0000646;
#=GF DR   URL; http://www.mirbase.org;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   18760970
#=GF RT   Computational identification of novel microRNA homologs in the chimpanzee
#=GF RT   genome
#=GF RA   Baev V, Daskalova E, Minkov I
#=GF RL   Comput Biol Chem. 2009;33:62-70.
#=GF RN   [2]
#=GF RM   18392026
#=GF RT   Discovering microRNAs from deep sequencing data using miRDeep
#=GF RA   Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S,
#=GF RA   Rajewsky N
#=GF RL   Nat Biotechnol. 2008;26:407-415.
#=GF RN   [3]
#=GF RM   20214803
#=GF RT   Genome-wide comparative analysis of microRNAs in three non-human primates
#=GF RA   Brameier M
#=GF RL   BMC Res Notes. 2010;3:64.
#=GF WK   MicroRNA
#=GF SQ   6


AADA01308090.1/9228-9163   UCAGCAGCACAGCCUUCGGCCUAAAGCAAUGAGAAGCCUCUGAAAGGC-UGAGGCAGUAGAUUGAAU
AADA01153194.1/18299-18363 -CAGCAGCACAGCCUUCAGGCUAAGGCAAUGAGAAGCCUCUGAAAGGC-UGAGGCAGUCGAUUGAAU
AC010203.14/28663-28598    UCAGCAGCACAGCCUUCAGCCUAAAGCAAUGAGAAGCCUCUGAAAGGC-UGAGGCAGUAGAUUGAAU
AAWR02000886.1/57387-57453 UUAGCGGCACAGCCUUCAGCCUAAAACAAUGAGAAGCCUCUGAAAGGCUUGAGGUAGUGGAAUGAAU
ABRQ01651150.1/1997-2063   UAAGGAGCACAGCCUUCUGUCUAAGACAACAAGAAGCAUCUGAAAGGCUUGAGGUUGUGGAAUGAAC
AAGU03052084.1/61465-61399 UAAGGAGCACAGGCUUCUGUCUAAGGCAACAAGAAGUCUCUGAAAGGCUUGAGGUAGUGGACUGAAU
#=GC SS_cons               ::::<<<<<<-<<<<-<<<<<<----<<--<<<____>>>>>-->>>>->>>>>>->>->->>>:::
#=GC RF                    UaAGcagCACAgCCUUCaGcCUAAagCAAuGAGAAGCCUCUGAAAGgCUuGAGGcAGUgGAcugAAU
//
# STOCKHOLM 1.0

#=GF AC   RF02029
#=GF ID   sraA
#=GF DE   sraA
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Predicted; FSA; RNAalifold; Infernal
#=GF SS   Predicted; FSA; RNAalifold
#=GF GA   56.00
#=GF TC   58.30
#=GF NC   55.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11448770
#=GF RT   Novel small RNA-encoding genes in the intergenic regions of Escherichia
#=GF RT   coli.
#=GF RA   Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner EG, Margalit H,
#=GF RA   Altuvia S
#=GF RL   Curr Biol. 2001;11:941-950.
#=GF RN   [2]
#=GF RM   12654996
#=GF RT   A survey of small RNA-encoding genes in Escherichia coli.
#=GF RA   Hershberg R, Altuvia S, Margalit H
#=GF RL   Nucleic Acids Res. 2003;31:1813-1820.
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   20


U00096.2/458040-457945         AUGUACGUCAGUAUAUGGGGAUGUUUCCCCCA-CAUUCAACGCCGAGAAUAG-AGGAAAAAUUAAAGGGGAGAU-AAAAUCCCCCCUUUUUGG--UUAACU
L18867.1/1516-1421             AUGUACGUCAGUAUAUGGGGAUGUUUCCCCCA-CAUUCAACGCCGAGAAUAG-AGGAAAAAUUAAAGGGGAGAU-AAAAUCCCCCCUUUUUGG--UUAACU
CP000826.1/1206747-1206652     UGGUUAAUGAGUAUAUGGGGAUGAAUCUCUUA-CAUUCAACGGCAAGAACGC-AGGAAAUAA-AAAUGGGGGAU-AAAAUCCCCCAUUUUG-ACAUUAACU
BX950851.1/1303544-1303449     AGGUAUUUGAGUAUAUGGGGAUAAAUGUCUCA-CAUUCAACGACCAGCAUGCGUGUAAAAAACAAAUGGGGGAU-AAAAUCCCCCAUUUUU-A--UUUCUU
CU468135.1/2810017-2810111     AGGUACCUGAGUAUAUGGGGAUGAAUGGAAUA-GAUUCAAUGUCGAGGUUAU-GAGAAAAGUAAAAGGGGGGAA-UAUUUCCCCCCUGAGC-C--UUAACU
CP000647.1/442518-442424       AUGUAAUCCAGUAUAUGGGGAUGUAUUCCACA-CAUUCAACGGCGGGAAUGC-AGGAAAAAUAAAAGGGGAGAU-AAAAUCCCCCCUUUUU-G--UUAACU
CP000822.1/2523922-2524015     AUGUAUGUCAGUAUAUGGGGAUGUUUCCCACA-CAUUCAACGCCAUGUUUAC-G-GAAAAAUAAAAGGGGGGAU-AAAAUCCCCCUUUUUC-G--UUAACU
CAAQ01000897.1/914-820         AUGUACGUCAGUAUAUGGGGAUGUUUCCCACA-CAUUCAACGGCGUGUUUAC-AGGAAAAACGAAAGGGGAGAU-AAAAUCCCCCUUUUUG-G--CUAACU
CU928158.2/2646706-2646800     AUGUGUGUCAGUAUAUGGGGAUGUUUCCCCCA-CAUUCAACGCCGGGAAUAG-CGGAAAAAUAAAAGGGGAGAU-GUAUUCCCCCCUUUUU-G--AUAAAC
CP000783.1/2813866-2813960     AAGUAAAUCAGUAUAUGGGGAUGUUUCCCGGA-CAUUCAACGGCACGGAAGC-AGGAAAAAU-AAAUGGGGGAA-UAUUUCCCCCAUUUAU-U-GUUAACU
CP000653.1/1007140-1007047     AUGUAAC-CAGUAUAUGGGGAUGUUUCCCACA-CAUUCAACGCUAUGAAUAC-GG-AAAAAUAAAAGGGGAGAU-AAAAUCCCCCCUUUUUGA--UUAACU
ABHK02000001.1/3377659-3377571 AUGUACGUCAGUAUAUGGGGAUGUUU-CCCCA-CAUUCAACGCCGAGAAUAG-AGGAAAAUU-AAAGGG-AGAU-A-AAUC--CCCUUUUC-G--UUAACU
AP008232.1/1138801-1138709     AGGUAUUUGAGUAUAUGGGGUCGAAUCGCUUA-CAUUCAACGGCAGCCGGUG-AUGAAAAAAAA--CGGGGGAU-AAAAUCCCCCGCCUGG-A--CGCUGU
AAPH01000003.1/150889-150795   UCUUUAAUGAGUAUAUGGGGGU-AACCCACUAUUAUUCAACGGGAGAAGUAA-CAGAAAA-CAAAAAAGGAGGCCAAAGCCUCCUUUUUUU-A--UUCAUU
ABHP01000004.1/210574-210667   AUGUACGUCAGUAUAUGGGGAUGUUUCCCCCA-CAUUCAACGCCGAGAAUAG-AGGAAAAAUUAAAGGGGAGAU-AAAAUCCCCCCUUUUU-G--GUUA-A
AAOJ01000002.1/828677-828771   CUUAUAUUGAGUAUAUGGGGGU-AAAACAUGAUUAUUCAACGAAAGAAGUAA-CAGAAAA-UAAAAAAGGAGGCUUAUGCCUCCUUUUUUU-A--GCCUUU
CP002487.1/504957-504861       AUGUACGUCAGUAUAUGGGGAUGUUUCCCACA-CAUUCAACGGCGUGUUUAC-AGGAAAAACGAAAGGGGAGAU-AAAAUCCCCCCUUUUU-UGGCUAACU
ABWL02000009.1/18177-18271     AUGUAUGUCAGUAUAUGGGGAUGUUUCCCACA-CAUUCAACGCCAUGUUUAC-G-GAAAAAUAAAAGGGGAGAU-AAAAUCCCCCCUUUUU-A-AUUAAAU
ABWM02000017.1/136105-136011   AUGUAAUCCAGUAUAUGGGGAUGUAUUCCAUA-CAUUCAACGCCAUGAAUAA--GGAAAAAAUAAAGGGGAGAU-AAAAUCCCCCCUUUUUGA--UUAACU
AALC02000011.1/48347-48443     AGGUAAUUGAGUAUAUGGGGACGAAUGUCUUA-CAUUCAACGAUAACAAUGCGAGGAAAA-AGAAAUGGGGGAU-AAAAUCCCCCAUUGUC-AUACUAACC
#=GC SS_cons                   :::::::<-<<<---<<<<<_______>>>>>.->>>->-------------.----------<<<<<<<<<<<.___>>>>>>>>>>>::.:..::::::
#=GC RF                        AuGUaauUgAGUAUAUggGGAUGuaUcCCccA.cAUUCAACGacaagaaUaa.agGAAAAAuaAAAgGGGgGau.aAAauCcCCCcUUUUu.a..uUaAcU
//
# STOCKHOLM 1.0

#=GF AC   RF02030
#=GF ID   tp2
#=GF DE   tp2
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Predicted; FSA; RNAalifold; Infernal
#=GF SS   Predicted; FSA; RNAalifold
#=GF GA   50.00
#=GF TC   51.50
#=GF NC   45.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.70 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   11553332
#=GF RT   Computational identification of noncoding RNAs in E. coli by comparative
#=GF RT   genomics.
#=GF RA   Rivas E, Klein RJ, Jones TA, Eddy SR
#=GF RL   Curr Biol. 2001;11:1369-1373.
#=GF RN   [2]
#=GF RM   12654996
#=GF RT   A survey of small RNA-encoding genes in Escherichia coli.
#=GF RA   Hershberg R, Altuvia S, Margalit H
#=GF RL   Nucleic Acids Res. 2003;31:1813-1820.
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   24


AACY020346484.1/116-5          GGUAUUCCUUAUCUA-------UCUAAUA-CGUUG----AGU--UAUCUG-GAACCUGUCCCAUUACGUUCUC-----GCC----A-----------------------GAGAGCGUAAUAAGACAGGUUCUGCG---U-UUAGUUGCCGCGCACUUUAUAUG-
ACDJ01000024.1/237326-237214   GGUAUUCCUUAUCUA-------UCUAAUA-CGUUG----AGU--UAUCUG-GAACCUGUCCCAUUACGUUCUC-----GCC----A-----------------------GAGAGCGUAAUAAGACAGGUUCUGCG---U-UUAGUUGCCGCGCACUUUAUAUGG
CP000653.1/746257-746145       GGUAUUCCUUAUCUA-------UCUAAUA-CGUUG----AUU--UGUCUG-GAACCUGUCCCAUUGUAUUUUC-----GCC----A-----------------------GAAAAUACAAUAAGACAGGUUCUGCG---U-UUAGUUGCCGCGCUCUAAAAAAGG
CP000822.1/3028726-3028838     GGUAUUCCUUAUCUA-------UCUAAUA-CGUUG----AUU--UGUCUG-GAACCUGUCCCAUUGAGCUUUC-----GCC----A-----------------------GAAAGCGCAAUAAGACAGGUUCUGCG---U-UUAGUUGCCGCGCGCUAUAAUUUG
CP000886.1/170338-170228       GGUAUUCCUUAUCUA-------UCUAAUA-CGUUG----AGU--UAUCUG-GAACCUGUCCCAUUAAACUUUC-----GUC----A-----------------------GAAAGCUUAAUAAGACAGGUUCUGCG---U-UUAGUUGCCGCGCACAUUUU-UG-
U00096.2/123014-122903         GUUAUUCCUUAUCUA-------UCUAAUAACGUUG----AGU--UUUCUG-GAACCUGUCCCAUUGAACUCUC-----GCC----G-----------------------GAAAGCUCAAUAAGACAGGUUCUACG---U-UUAGUUGCCGCGC-UUUUA-UAUG
CP000647.1/137673-137544       GGUAUUCCUUAUCUA-------UCUAAU--CGUUG----AUU--AAUCUG-GAACCUGUCCCAUUGAACUCUUCGUUCUUC----ACGCUGG----------AACAACCAAAAAUUCAAUAAGACAGGUUCUGCG---U-UUAGUUGCCGCGCUCUAAAAAUGG
CP000826.1/4451302-4451410     GGUAUUCCUUAUCUG-------UCUAAU---GGU-------U--UGUUUUGGAGCCUGUCUUCCUGUGUUCUG-----A-G----G-----------------------CAAAACACACGAAGACAGGCCCAUCA---GUUUAGUUGCCGCUUACUUAAAUGCU
CU468135.1/910773-910651       GGUAUUCCUUAUCUGU-----GUCUAAUUUCGUUG----AAU--UGUCUG-GAACCUGUCUCUCUGUGCUCUG-----AUCCUCUG-----------------------CAAAACACAGAGAGACAGGUCCUUCGUGAG-UCACAUACCGUUAUCGGGUACGUG
AP008232.1/805453-805347       GGUGUUCCUUAUCUA-------UCUUUAA-UAUUG----GUU--UAGUUG-GAGCCUGUCUUCCUAUGCUCUG-----GCC----G----------------------UCAGAACAUACGAAGACAGGC-CCAUAG-CU-UCUGCUGCCGCGU--------GGG
AM286415.1/809472-809339       GGUAUUCCUUAUUUG-------UUUCUAA-UGGU-------U--UAUUUG-GAGCCUACCUUCCUGUGCUUUA-----ACC----CCAGGCUAAAGCACGUGCCCUGGUGAAAACACCGGAAGAUAGGCCCAUCA--GU-UUAGUUGCCGCGUUUCGUGCUCAA
ABVY01000104.1/11119-11246     GUUAUUCCUUAUCUU------CUCUAAU--CAGUU----AGU--U-UAUG-GAGCCUGUCUUCCUGCAUUCUG-----ACU----UAGGUUUC--------GUCCUAAGCAAAACGCAUGAAGACAGGCUCAUCG---UCGUCAUUACCGCAUUCAGAGCCCCA
BX950851.1/4236584-4236712     GUUAUUCCUUAUCUU------CUUUAAU--CAGUU----AGU--UUAUUG-GAGCCUGUCUUCCUGCAUUCUG-----GCU----UAGGUUUC--------GCCAUAAGCAAAACGCAUGAAGACAGGCUCAUCG---UCGUCAUUGCCGCAUUCAGAGCCCCA
ABVP01000024.1/81187-81301     UGUAUUCCUUAUCUG-------UUAU--C-UGUUUU--UAAUGGUUAUGG-GAGCCUAUCUUCCCGUUAUACC----CAUC----U-----------------------GAUAUGACGGGAAGAUAGGCCCUGCU---G-UUA-UUACCGCUUCCCCUGAAAAU
ABJD02000101.1/1889625-1889740 UGUAUUCCUUAUCUG-------UUAUCUA-UUUUUUAAUGUU--UAUGUG-GAGCCUAUCUUCGCGCUACUUU-----CUA----C-----------------------AAAAUAGCGAGAAGAUAGGCCCUG-C---U-GUUGUUGCCGCUAGAACUCUCACA
BX571871.1/107916-108044       UGUAUUCCUUAUCUGUUAUCUGUUUCUAA-UG-------AUU--GUUUUG-GAGCCUACCUUCCCGUCAUACC-----CUU----UGACGU-----------UCAGCCGGUCAUGACUGGAAGAUAGGCCCU-CA--CU-GUUGUUGCCGCUAGUGCCCUCAGU
CP002956.1/1936337-1936205     GGUAUUCCUUAUUUA-------UUUCUAA-UGGU-------U--UAUUUG-GAGUCCAUCUUCUAAUGCUUUA-----ACA----CAAGGGUAAAG-CACACGCCCUGGUGAAGAACAGAAAGAUAGGCCCAUCA--GU-UUAGUUGCCGCUAAUAAUUCUCAA
FR775191.1/114676-114565       GGUAUUCCUUAUCUA-------UCUAAUA-CGUUG----AGU--UAUCUG-GAACCUGUCCCAUUAAACUUUC-----GUC----A-----------------------GAAAGCUUAAUAAGACAGGUUCUGCG---U-UUA-UUGCCUGGCCCAUAAGGUGU
AM942759.1/2205334-2205448     UGUAUUCCUUAUCUG-------UU--AUC-UGUUUC-UA-AUGGUUAUAG-GAGCCUAUCUUCCCGUGAUACC-----ACG----G----------------------GGAUAUGACGGGAAGAUAGGCCCUGCU---G-UUA-UUACCGCUACCCCUGAAUAU
ABXV02000030.1/41961-42078     UGUAUUCCUUAUCUG-------UUAUCUA-UUUUAUAUGUUU--AAUAUG-GAGCCUAUCUUCCAGCUAUUUU-----GCU----G---------------------UAAAAACAGCUGGAAGAUAGGCCCUG-A---U-GUAGUUGCCGCUUUAACUCUCAGA
ACCI02000061.1/87070-87192     UGUAUUCCUUAUCUGU----UAUCUAUUU-UAUAU----GUU--UAUGUG-GAGCCUAUCUUCCUGCUAUUUU-----CCC----AGUC---------------GCUAUAAAACAGCGGGAAGAUAGGCCCUG-A---U-GUAGUUGCCGCUUUAACUCUCAAU
ABWM02000004.1/105479-105589   GGUAUUCCUUAUCUA-------UCUAAUA-CGUUG----AUU--UGUCUG-GAACCUGUCCCAUUGUAUUUUC-----GUC----A-----------------------GAAAACACAAUAAGACAGGUUCUGCG---U-UUAGUUGCCGCGCUCUAAAA-UG-
AALD02000021.1/18257-18386     GGUAUUCCUUAUCUG-------UUUCUAA-UGGU-------U--UAUUUG-GAGCCUAUCUUCCUGUGCUUUA-----ACU----CAAGGCUAAAGCACGUGCCCUGGUGAAAACACCGGAAGAUAGGCCCAUCA--GU-----UUAUCCCCGUCAUACUUCAA
AALF02000001.1/64143-64010     GGUAUUCCUUAUCUG-------UUUCUAA-UGGU-------U--UAUUUG-GAGCCUAUCUUCCUGUGCUUUA-----ACC----CCAGGCUAAAGCACGUGCCCUGGUGAAAACACCGGAAGAUAGGCCCAUCA--GU-UUAGUUGCCGCUAAUAAUUCUCAA
#=GC SS_cons                   <<<<-----------.......------<.<<<--....---..-----<.<<<<<<<<<--<<<<<-<<<<<.....___...._......................_>>>>>->>>>>-->>>>>>>>>>>>>...>.----->>>>:::::::::::::::
#=GC RF                        GGuAUUCCUUAUCUg.......UuUaaua.cGcUg....AuU..UaUuUg.GaGCCUgUCUUccuGugcUuuc.....acc....a......................ugaaAgcaCaggAAGAcAGGCcCugCg...u.uUAGUUgCCGCuuucauuauuaaa
//
# STOCKHOLM 1.0

#=GF AC   RF02031
#=GF ID   tpke11
#=GF DE   tpke11
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Predicted; WAR; Infernal
#=GF SS   Predicted; WAR; T-coffee consensus
#=GF GA   43.00
#=GF TC   44.70
#=GF NC   41.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF RN   [1]
#=GF RM   11553332
#=GF RT   Computational identification of noncoding RNAs in E. coli by comparative
#=GF RT   genomics.
#=GF RA   Rivas E, Klein RJ, Jones TA, Eddy SR
#=GF RL   Curr Biol. 2001;11:1369-1373.
#=GF RN   [2]
#=GF RM   12654996
#=GF RT   A survey of small RNA-encoding genes in Escherichia coli.
#=GF RA   Hershberg R, Altuvia S, Margalit H
#=GF RL   Nucleic Acids Res. 2003;31:1813-1820.
#=GF RN   [3]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   In Yersinia located in ICR upstream dnaJ (chaperone)gene. Has temperature
#=GF CC   responsive RNA structure.
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   28


CP000647.1/15539-15613       AACGGGUA--AA--ACACU-G--GC-ACGGGCGAAGAGG--UUUCCUCUCCGCCCGUGCACGCAUGUU-AAGGG-GCUGAAAAACAC
CU928158.2/12677-12754       AACGGGUA--AU-UAUACU-G--AC-ACGGGCGAAGAGGAAUUUCCUCUCCGCCCGUGCAUUCAU-CU-AGGGGCAAAUCAAAAAAG
CU928163.2/14047-14124       AACGGGUA--AU-UAUACU-G--AC-ACGGGCGAAGGGGUAUUUCCUCUCCGCCCGUGCAUUCAU-CU-AGGGGCAAUUUAAAAAAG
CP000653.1/651194-651270     UGCAGGGU--AA-UUAAUC-G--GC-ACGGGCGAAGAGG--UUUCCUCUCCGCCCGUGCUCGCAUGUU-AAGGGGCUGAAAAAACCA
CP000783.1/3259866-3259791   CAGGGUAG--AU-AACACU-G--GC-ACGGGCGUAGGAG--UUUCUCC-ACGCCCGUGCACGCAUGUC-AGGGGCAGAUAAAACAUG
CU468135.1/787164-787231     AA----UU--A--ACCA------GC-ACGGGCGUAGGAU--UUUAUCC-ACGCCCGUGCACGCAUGUU-AAGGGCAGGAUCAAUAAC
BX571860.1/308434-308511     AACUGUUGCUGA-UUAACC-G--GC-ACGGGCGUUGAGG--GAA-CUCUGCGCCCGUGCGCGCAUGUU-AAGGGUAAAAUAAGAGAU
AP008232.1/728266-728329     AAC-------------A---G--GC-ACGGGCGUCGGGG--AAACUCUG-CGCCCGUGCAAGCAUGUU-GAGGGCAGGAAGAGACAA
ABVX01000033.1/14366-14303   AA------------UCA------GC-ACGGGCGUCGAGG--AAA-CUCUACGCCCGUGCACGCAUGUU-GAGGGGCAGGAAAAGAAA
BX950851.1/4343561-4343497   AA------------UCA------GC-ACGGGCGUCGAGG--AAA-CUCUGCGCCCGUGCACGCAUGUUGAAGGGCAGGAAAAGAAAU
CP000964.1/4793539-4793465   AACGGGUA--AA--ACACU-G--GC-ACGGGCGAAGAGG--UUUCCUCUCCGCCCGUGCACGCAUGUU-AAGGG-GCUGAAAAACAC
U00096.2/14090-14167         AACGGGUA--AU-UAUACU-G--AC-ACGGGCGAAGGGGAAUUUCCUCUCCGCCCGUGCAUUCAU-CU-AGGGGCAAUUUAAAAAAG
CP000822.1/3143083-3143008   AACGGGUA--AA--AUACU-G--GC-ACGGGCGAAGAGG--GUUCCUCUCCGCCCGUGCACGCAUGUU-AGGGGCAGAUAAAAACAA
CP000880.1/2912194-2912120   AACGGGUA--AU---UACU-G--GC-ACGGGCGAAGAGG--UUUCCUCUCCGCCCGUGCAUGCAUGUU-AAGGGCAGAUAAAAAGAG
ABKX01000006.1/205904-205827 AACGGGUA--AU-UAUACU-G--AC-ACGGGCGAAGGGGAUUUUCCUCUCCGCCCGUGCAUUCAU-CC-AGGGGCAAAUAAAAAGAG
ABJD02000118.1/106029-106105 AAUGGUUA--CU-GAUACCGA--AC-ACGGGCGUCGAGG--AAA-CUCCACGCCCGUGUCGGCAUGUU-AAGGGUAAAAUAAAUGGC
ABVP01000025.1/412798-412722 AAUAGUUA--CUGAUACCG-A--AC-ACGGGCGUCGAGG--AAA-CUCAACGCCCGUGUGCUUAUGUC-AAGGGUAAUCUAGAAUGG
AM942759.1/20059-20136       AACAGUUA--CU-GAUACC-GAAAC-ACGGGCGUCGAGG--CAA-CUCUACGCCCGUGUGCUUAUGUC-AAGGGUAAUCCAGAAUGG
AE013218.1/162850-162775     AUUAGAGU--AUUUAAACC-A--GC-ACGGGCGUAGAAA--AAA--UCUACGCCCGUGUACUUAUUUU-GAAAGCAGGAAGAAUAGC
ABXW01000004.1/75427-75497   GACUGAU--------ACCG-G--AC-ACGGGCGUUGAGG--GAA-CUCUGCGCCCGUGUCUGCAUGUU-AAGGGAAAAAUAAAUGGC
CP000826.1/764446-764516     UACCGC--------AAACC-A--GC-ACGGGCGUCGAGG--CAA-CUCUACGCCCGUGCACGCAUGUU-AAGGGUUACAGAAAUAAU
CP001158.1/162206-162132     UAUAGACU--UU--AAACU-A--GC-ACGGGCGUAGAUA--AACU-UCUGCGCCCGUGUAAUUAUUUU-UAAAUCAGGUAGAGUAAG
CP000720.1/3906242-3906166   UACUGUUG--CUGGAAACC-A--GC-ACGGGCGUCGAGG--AAA-CUCUACGCCCGUGCACGCAUGUU-AAGGGUAGGAAAAAAGAG
ABWM02000004.1/208752-208678 AACGGGUA--AU---UACU-G--GC-ACGGGCGAAGAGG--UUUCCUCUCCGCCCGUGCACGCAUGUU-AGGGGCAGAUAAAACAAG
ACCI02000067.1/224286-224211 AAUGGUUA--CU-GAUACC-G--GAUACGGGCGUCGAGG--CAA-CUCUACGCCCGUUC-CGCAUGUU-AAGGGUAAAAUUAAAUGG
ABWL02000016.1/374933-375008 UGCAGGGU--AG-UUAAUC-G--GC-ACGGGCGUAGAGG--UUUCCUCUUCGCCCGUGCUUGUAUGUU-AAGGG-GCUUAAAAAAAC
AALC02000002.1/46140-46071   GCUGG---------AAACC-A--GC-ACGGGCGUCGAGG--AAA-CUCUACGCCCGUGCACGCAUGUU-AAGGGUAGGAAAAUAAGA
ABXV02000043.1/45137-45067   UACUGAU--------ACCG-G--AC-ACGGGCGUUGAGG--GAA-CUCUGCGCCCGUGUCUGCAUGUU-AAGGGAAAAAUAAAUGGC
#=GC SS_cons                 ::<<<___..__.____>>.>..<<.<<<<<<<-<<<<_..___.>>>>->>>>>>>>>:::::::::.::::::::::::::::::
#=GC RF                      aAcgGuUa..aU.uaaACc.g..GC.ACGGGCGUaGAGG..uaa.CUCuaCGCCCGUGCacGCAUGUU.AAGGGcAaaaaAAAaaag
//
# STOCKHOLM 1.0

#=GF AC   RF02032
#=GF ID   GOLLD
#=GF DE   Giant, ornate, lake- and Lactobacillales-derived (GOLLD) RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:12376536; Weinberg Z
#=GF SS   Published; PMID:12376536; Weinberg Z
#=GF GA   45.00
#=GF TC   45.90
#=GF NC   44.60
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19956260
#=GF RT   Exceptional structured noncoding RNAs revealed by bacterial metagenome
#=GF RT   analysis.
#=GF RA   Weinberg Z, Perreault J, Meyer MM, Breaker RR
#=GF RL   Nature. 2009;462:656-659.
#=GF WK   GOLLD_RNA_motif
#=GF SQ   35


AACY020652058.1/112-538      U-GAGGCGUGCGGCAUAGAGUGGCU-CAAAA--AGUCAUUCAACC-GCU--GGUAGAGCACGUCUU--UGUCAGUUCCUCGCUAGAGGGCAAACACUACGGAU------------------------------------------------------------------------GUUCUUGUUAAACGCC--AAGU-CUCUACC--CGCGAGCCGC---GAAAGCGGCAUA-AU-GCUCGG-GGC--UUCG-------GCCAA-C-CGAGU-CGGCGAC-GGUCCCGCAAGGGCCUAU--CUGUU-GAUCG-UGAAAUUG-UCG------GAGACGUUAGCG-CGUCUCGC--UGCC-CCGAA-GGCA-GA-----------------------------------------------CGGUG--AGGAAGUGAUCGUGUA-GUGGUUCGUCAGGGGUGAAACGCCACACCCUAA-AAAAGGC---AGUCGUGAU-GGC-UACGCCGGA-AGU--GAUGA---GCUACGGUUGUG-GACA-AG-CGGGAAGCCUCGGUGCC-----ACCGGGG-GAUAAUCCGA-CGAGAGGCC-AUCGAUGAAG-GGU---AUAGUCUCA---GCCC
ABAF01000010.1/42565-42956   -GCAGGCGCUGUGCAUUUUGUUCUU-CAAAA--GAGAAUGAAACA-CAU--GACGAUGCGUGUCUGUGAUAGAUGAAAGAUGAUUUUUAUAUUUUAAGGCUAUUCAAGAUAGAA-------------------------------------------------------------AAAACUCAAAAAAGCAA-AAGU-CAUCGCC--CGUCGUAAAC---GAAAGUGCACUU--C-GGCAA-------UUAGA--------------UUGCC-UGCUC-A-AGUCUCGCAAGGAU-GA-GAGUAA--AGUCA-AAGAGUAA-AGC-AGCUUAGACUUUUAGCG-GAGUCUUC-------------------------------------------------------------------GUUAAUUGAAAAAUGGCUUAGUA-GUUUGCGAUGUGAG---GAGUGAUUGG-UCUAA--CCAAUC---GUGCAUGAG-UGA-UACAAGUA-------G-GAA-------UAUUUGUG-GACA-AGAUAAUAA--------ACU--------------AUAAGUUAU-CAAAAGUCA-CUCGUUUAAA-GCA---GUAGUCUCA---UGCU
ABAA01000017.1/22131-22522   -GCAGGCGCUGUGCAUUUUGUUCUU-CAAAA--GAGAAUGAAACA-CAU--GGCGAUGCGUGUCUGUGAUAGAUGAAAGAUGAUUUUUAUAUUUUAAGGCUAUUCAAGAUAGAA-------------------------------------------------------------AAAACUCAAAAAAGCAA-AAGU-CAUUGCC--CGUCGUAAAC---GAAAGUGCACUU--C-GGCAA-------UUAGA--------------UUGCC-UGCUC-A-AGUCUCGCAAGGAU-GA-GAGUAA--AGUCA-AAGAGUAA-AGC-AGCUUAGACUUUUAGCG-GAGUCUUC-------------------------------------------------------------------GUUAAUUGAAAAAUGGCUUAGUA-GUUUGCGAUGUGAG---GAGUGAUUGG-UCUAA--CCAAUC---GUGCAUGAG-UGA-UACAAGUA-------G-GAA-------UAUUUGUG-GACA-AGAUAAUAA--------ACU--------------AUAAGUUAU-CAAAAGUCA-CUCGUUUAAA-GCA---GUAGUCUCA---UGCU
AACY021081069.1/931-436      --AUGUGGUGUCUGGUAUUUCGUGUUGAAA--GAUACGAAGUCAG--UG--AGGCCAGCACGUCAUGGUAGGUUACUAGCGGACUCAUACUCCGUUGGGUUGUAGCUCAUUUGGGUAGAGCACUCGUUUUUGGAACGAAUGGUAGCCGGUUCAAAUCCGGUCAACUCAUCCUUGAAAGAUGAAAAAACGCA--AAGA-CUGGCCUCACAGGUAGUAC---GAAAAUGGCUUA-AU-GCUUCA-GUC--CUUCG------GGCAA-U-GAAGC-CCUUC-G-AAGCUCGCAAGGCG-GA-CAAGGUU-AGUAG-CGAAGCGCACUA------UAGCGACGGCCA-UCGUUG---------------------------------------------------------------------UAGGUAGCAG-AACUACUGAGUA--CGCUACUUGAUACGUGAAUCGCCACACGUUAA-AAAAGGC---AGUCAUGCUGGCAGACUCAGGAG-CAUCCU-UGAUGGAUGG-CUUGGGU-GGAUAAGCUGGGAACCAAAGGGGUCGCA--CCCUACG-GAUAAUCCAG-CAAAGGUGUUAGCGGUGAA--GGU---GUAAUCUCA---GCCU
AACY020169428.1/1317-906     CGGAGUCGUCCAGUAUUCUUGAGUU-CAAAA--GAUUUGAGAGCU-GAG--AGGUGACCACGACUUCGACAAAUCUACACGGCACUAAAUUUCUAACUGUUAAUUGGAAACAUUU------------------------------------------------------------AAAAAAGAAGAAAUCGA-AAGU-GUUACCU--AGUUGUUGAC---GAAAGGUGUCUACAUAGUUAUGG-----GUUGU----------C-C-AUAGC-CA-CU-G-AAGCUCGAAAGGCC-GA-UG-UGAU-UUCAC-CUAAAAGC-UUAUA---------------------------GAGGGUCGAG-CCUC-GAA-UCAGUCCGGCA--------------------------GGGUUGAAUAAGUG-GAUUAAGU-GAGAGUA-GUUAACAACUUAAG---UAGUGAUUGG-UCUAA--CCAAUC---GACACUGACAGAA-UACUUCU--------C-AAAA-------GGAAGUG-GAUA-AGAAGGGAA--------ACC--------------AUAAUCUGA-CAAAAGUUCUGUCUUUAUAA-GGU---GUAAUCUCA---GCCC
AACY023425995.1/83-490       UCGGGGCGUUC--UAUCUAAACUUCUCAAAA-GGAAG-CAAGGUA-GAUGCGUGGUUGCGCGUCCUGA-----------AUUAUGGCAUUGUUUUCGGGUUAAAUCCCACUUAACA-----------------------------------------------------------AUUAAAAAAUUAAGCAA-AAGA-CAACCAC--CUUUCCCGCU---GACAAUAGCGUU-AU-CCCUCUGCAC--UUCG-------GU-AAUAUGAGGG-CACAGUA-AAUCCCGCAAGGAUGAGAAUGUGA--UGUGGAAUGAGUAA-AUCUA----AGGUGAGGAGGCAUCCUCUUU--AGUC-CGCAA-GACA-CU----------------------------------------------UGGUUGAAAAGAAAGCAUA-UAUA-AGCUGGAAAGUACA---UGGUAGU----UAGUCU----ACU---CGCUAUCCU-AGU-UACUUUG------GAG-UAA-UC-----UAAAGUGUGUGUAAACGGGC----------GAAA-----------------GUCUG-UAAAAUACU-GGGGACAUAG-GGU---CAACACUCA---GCCU
AACY022114434.1/570-988      AGAAGGAGCGCGGCAUUCGGCAUCUCGAAA--GGGGUGUCGAACC-GCA--GGUGACGCGCUUCU--CGAUCGGUUUCCUACACUGGGAAGUGGUU-------------------------------------------------------------------------------GCGAACCAUUAAAGCAA-AAGC-CGUCACC--CCUGGUCGAG---CGCAACGACUUA-AC-ACUGCG-GGC--GCAA-------GCCAA-C-GCAGU-CGGU--U-GAUUCUGCAAGGA---GUCACCGUU-GAUCU-CGGAGGAU-UCGG-----AGGGCGUAAGC--UGCCCUAG--CCGGACGCAAAGCGG-------------------------------------------------ACGGGUCCGAUG--AGGUCGAAAG-CAAGAUCAGCAGGGAUGAAAUGCCACAUCUUAA-AAAAGGC---AGUCGUGCU-GGA-UACGC-CGC-AGU--G-AGA---GCCGCGAGCGUG-GACA-AAGCGGGAACACCGGC-UAGCU----GCCGGGAGAUA-UCCGC-GCAAAGGCC-AGCGAUGAC--GGC---AUAGUCUCA---GCCC
ABOX02000006.1/193416-192978 --AAGGCGUGCAGUAUAGCGUGAUC-CAAAA--GAUCAUGAAGCU-GCA--AGACGCGCACGUCUUGGUAGGAUUGCUGCUGCAGGCAACUGUAGCACCUGACUGAA--------------------------------------------------------------------AAUCAGGCUAAACGCA--AAGU-CGCGUCUUCUGUUGGAUUG---GAAAGUAGCUUA-AU-CCCUGA-AUCC-UGCG------GGAUAA-U-CAGGG-CGUCC-GAUGCUCCGCAAGAGCUGA-GGACGU---UGGU-UGAAAUCG-CAU------GGUGGGUUCGCAGCCCUUUAC--UGCC-CGCAA-GGCA-GA----------CAGUAAGAGGACAGCCGAGCGAUCCAAUG--------GUGAACUGGCAAUGCCACCAGUA-UAAAACGGC-----------------------------------AGCUAUCGG-ACU-UACCAGAUU-GUGGCU-UCG-GCC-UGGUUUGGUG-GAAA-CGUUGGGAAGCCUUCC-CGCAU----GGAGGG-UAUAAUCCAA-UCAAAGAGU-CCGAACCAAA-ACU---GUAUUCUCA---GGUU
AACY023434052.1/501-43       -UUUGGUGAGUUGUAUACUGUAUGC-CAAAA--GCAUAUGGAGCA-ACU--GAGGCAGCUCAUCAAGGUAGGUUGCAACGUAGAUCAAUGGUAGAUCGUCUGUCUCUUAAACAGGAUGUUGCGGGUUCGAUCCCC----------------------------------------GCCGUAAUAAAAUGCA--AAGA-CUGCCUC--GGUUAUCAGU---GAAAAGCAUCUA-AU-GCUUGA-CAC--GCAA-------GUGAA-U-CAAGU-CCAUU-GUA-GCUCGCAAGGC-GAA-AGUGGUU-UGUGU-UAGAAGUU-UCGU----------------------------AGUU-CGCAA-GACU-UAA-UGG--CUCGCA--------------------------AGG-UCAACGGAG--AAGAAGACACAGAGUA-GCUGGUAACGACAAGCCUACUGCCUGGCUUUAAAAAC-GGC---GAUGCUGACAACA-GACAGUGAU-ACC--G-CAA---GG-GUCGCUGUG-GAUG-UCUAGAGAAGCAGUGC-UCGCAAG--GUGCUG-UAUAAUGCUA-G--AGGUGUUGUUGGCUUAA-GGU---GUAAUCUCA---ACCU
AACY023290448.1/464-41       GGGUGGUGUGAAGCAUUUUGUU-CU-CAAAA--GG-AACGGAACU-UCU--CCCGAAGCACAUCGUCCAUUUUUCCACAAUUGCUAAUUAUCCUGCAACGAUAAUGUUAC-----------------------------------------------------------------AUAAGAUAAUACAGCGA-AAGC-CUUCGGG--CGUUGACAGU---GAAAGGUGUCUA-AU-ACUUCA-GAC--AUUA-------GUCAA-U-GAAGU-CAUCAG-UUAGAACGCAAUUCU-C-CUGAUGUC-AAUCA-CGAAAUAC-CUGGU---------------------------GGGACGGCCA-UCCC-UUA-GAGAGUUCGCA--------------------------AGACUUUACAGAGUAGAGUAACGGUUGAGUA-GCUGGCAACGAAAA---GAGUGGUAAA-CUUAA--AUUACC---GACACUGACUCGA-UACUACGG-------G-CAA-------UCGUAGUG-GACAAUGUGAGGAACCG-----AUUCAA-------UG-GAUAAUCUCA-CGAAAGACGGGUCACAUAAA-CGU---GUAGUCUCA---GCGU
AACY020181262.1/483-77       GAGGGUAGUUUAGUAUCGUGUCGUU-CAAAA--GAUGACAUGGCU-GGU--GACGAGCCGCUACCUUCCUUAUCCGUAAACCAACUUUGGAAUUGCAAUGUCCAAAACAU-----------------------------------------------------------------UAAAAUUAACAAAGGAG-AAGU-GCUCGUC--AGUUGUGUGU---GACAGGUCACUACAUAGUCGUGA-----GAUGU----------U-C-ACGGC-CG-UG-A-AGGGUCCCAAGCCC-GA-CA-UGAG-UUUCG-AGAAAGUU-CUCUA---------------------------AUCC-CGCAA-GGAU-AAA-UUGGUGGGGCA--------------------------CCAUCGAAGAGUGAUAAGUACCGAGAGAGUU-GCAGACAACUUAAG---GAUUGGUUAA-UCUAA--UUGACC---GUGACUGAG-GGU-UACCGUU--------C-AAAA-------GACGGUG-GAAA-CGAAGGGAA--------UCAA-------------AUAAUCCUU-CCAAAGAUC-CUCACAAAAU-GGU---GUAUUCUCA---ACCU
AACY020054975.1/146-556      AGGUGUAGUUCAGUAUCGUCUCGUU-CAAAA--GAUGAGACAUCU-GGUUUGACGGACCGCUACAUCUAUUAUCCACAAAUCACAACUUUGUUAAUUAAGGUUUAACAACUU---------------------------------------------------------------AUAAAUCAAUAAAGGAA-AAGU-GUUCGUC--AGUCGUGGUA---GACAGGUCACUACUUAGUCAUGA-----GUUGU----------U-C-AUGGC-CG-UA-A-AGGGUCCCAAACCC-GA-UA-CGAU-UGUUU-UGAAAGUU-CUCUA---------------------------AUCC-CGCAA-GGAU-GAG-UUUGGGUGGCA--------------------------ACCUAGAAGAGUGAUGAGUAAGAAUAGAGUA-UAUUACCACUUUAG---GAUUGGUUAA-UCUAA--UUGACC---GUGACUGAG-AGG-UACUUCU--------C-AAAA-------GGAAGUG-GAAA-UCGGAGGAA--------ACA--------------AUAAUCUCCUGUAAAGUCU-CUCACAAGAU-GGU---GUAUUCUCA---ACCU
AACY021678619.1/249-654      GAGAGGUGUGAAGCAUUUUGUU-UU-CAAAA--GA-AACGAAACU-UCU--CCCGAAGCACAUCUUUCUCAUUUCCAUCGUUACUUUUACUA-----------------------------------------------------------------------------------AAACUAAAAGAGAGCAA-AAGUUCUUCGGG--CGUUGACAAC---GAAAGGUGUCUA-AC-ACUUCG-AGUC-AAUA------GACUAA-C-GAAGU-CAUCGGU--AGACCGCAAGUCU-CC-UGAUGUC-AAUUA-UCAAAUAC-CUGGU---------------------------GGGAUGGCCG-UCCC-UUAGU-GAACUCGCAA-------------------------GGUUUGA-CAGAGUAAAGUAGUAGUUGAGUA-GUUGUUAACGAAAA---GAGUGGUUCA-CUCAA--AUAACC---GACACUGACUUGA-UACUUUCG-------G-CAA-------CGAGAGUG-GAUA-CAUGAGCAACC------GAUAUA--------G-GGUAAUCUCA-CUAAAGACAAGUCACCAUAAACGU---GUAAUCUCA---GCGU
AACY020677266.1/810-406      CGGAGUAGUCUAGUAUUUGGUCGUU-CAAAA--GAUGACUAAGCUUAC---GACAGACCACUACUUCGACACAUCCACGACACACACUUAAAAUGAAUUUAAGUCAAAU------------------------------------------------------------------UAAAUACAAUUAAGCAA-GAGU-GUCUGUC--AGGUAUCAGU---GAAAGGUGACUACAUAGUAAUGA-----GCCGU----------U-C-AUUGC-AC-AU-G-AUGACCGCAAGUCU-GA-CU-GUAA-UCUUA-CCAAAGAC-CUCUA---------------------------UUCC-CGCAA-GGAA-GAG-UUGGGGAGGCA--------------------------UCCUCAAAGAGAGUUGAGUAAUUAGAGAGUA-AUUGAUACCUCAAG---GAGUGGUGUA-CCUAA--AAGACC---GUCAUUGAG-AAA-UACUUUC--------C-AAAA-------GAAAGUG-GAUA-UUAAGGGAA--------ACA--------------AUAAUCCUU-AUAAAGGUU-CUCACAAAUA-GGU---GUAAUCUCA---GCCU
AACY021411229.1/441-862      GGAGAUUGUUUACAGUAUUCUUGUCUGAAA--GGAUGAGAGCUGU-AAU--UUAAGAGCGCAAUCUUCACUUCGCCCCUUUUCUGCAUAAUCCUUGUUUAGCCAAAAGGCGUAGAUAACAAGUUC--------------------------------------------------AUUAACAAGAAAAGCAAAGAGU-CUCUUAA--CGGUUAAGAG---CAUAGGGCACUU--U-ACCUC-------UGAAACAAU----------GAGGUGCAUUA----AACCCGCAAGGUU----UGGUGUU-CAUGA-UGAAAGGU-CAGGU----UGGU--UCGU-----ACCCAU------------------UAG-ACG-GUCGGCA--------------------------GACUUGUACUGAACUGAGUAAUUGUGUAGAU-AACUUAACCGAUAA---GACUGAUGAG--CUAUA-CUCAUU---GUGCCUGAUACUG-UACUAAUC-------G-CAA-------GAUUGGUG-GACAAAAGAGGGAA--------UAG--------------AUAAUCCUC-UCAAAGUGGUAUCGC-AAAG-CCU---GUAGUCUCA---AGGC
AACY020167603.1/1020-1431    GAGAGUAGUUAAGUAUCGACUCAUC-CAAAA--GAUGGGUUGGCU-UGGUUGGCGGACCACUACUUUCACAAUCCACAACACAAAACUUAUGACUCUGAUUAAGUCAAAUUAAU-------------------------------------------------------------UAUUAUGAAGUAAGGAA-AAGU-GUCCGUC--AGGUUUGAAU---GAAAGGUGACUACAUAGUAAUGA-----GCCGU----------U-C-AUUGC-ACACA-A-A-GAUCCCAAGUC--GA-UGUGUAA-UUAUC-CCAAACAC-CUUUA---------------------------GUCC-CGCAA-GGAC-GAA-CUGGGAAGGCA--------------------------UUCUCAGAAAGAGUCAAGUAAGAUGAGAGUA-AUUUAAACCUUAAG---GAGUGGUAAA-CCUAA--AAGACC---GUCACUGAG-AAA-UACUUCU--------C-AAAA-------GGAAGUG-GAUA-GGAGUAGAA--------ACA--------------AUAAUGACU-CUAAAGGUU-CUCAAUCAAA-CGU---GUAAUCUCA---GCGU
AACY023435560.1/1014-602     GAGGGUAGUUUAGUAUCGUGUCAUU-CAAAA--GAUGAUUUGGCU-UGU--GACGAGCCGCUACCUUCCACAUCCGUAAACCAAACCUUAAUUGUUAAUUCUGGUUUAACAACUAU-----------------------------------------------------------UAAUUAAAAUCAAGGAA-AAGU-GCUCGUC--AGUCGUUGGA---AACAGGUGACUACUUAGUCUUGA-----GAUGU----------U-C-AUGAC-CGCGU-C--GGGUCCCAAGCCC-U--ACACGAU-UUUCA-CGAAAGUU-CUCUA---------------------------ACCC-CGCAA-GGGU-UCA-UCAGGGAGGCA--------------------------UCCUUGAAGAGUGAUGAGUAAGGAGAGAGUA-UUCAGCGACUUCACG--AA-UGGUUCAACGUAA-UUG-ACC---GUCACUGAG-AGU-UACUACU--------C-AAAA-------GGUAGUG-GAAA-CGGAGGGAA--------UCA--------------AUAAUCCUU-CUAAAGAUU-CUCAUCAGAA-CUU---GUAUUCUCA---GAGU
AACY023329291.1/454-42       CGUGGACGUGUUGUAUUUUGUGGGU-CAAAA--GCCUAUGAAGCA-AC---GGCGGCACGCGGACACAGACUAAAAAAUAACUUUCACGAUUA----------------------------------------------------------------------------------UGAAAAUAAACAUGCA--AAGU-UGUCGCC--AAGAAUUGAU---GAUAGAACCGUA-AU-GCUCAA-CGG--GUAA-------CCGAA-U-UGAGC-CAGUCCA-AGACUCGCAAGGUU-GAGGGUUGUU--GUGG-GAAAG----UCGCACGUU-----------------------UGGGGUCGAA-CCCU-UAA-CUG-CUCGCAA--------------------------GG--CAGGCGGUAGAUAGAA-CCAU-GAGUA-AUCAAUUCUUAUAGUGGAAAUGCCACCACUCAAAACAAGGC---CGGUUCGGU-UGA-UUCGUCC--------A-UGA--------GGACGAG-GAUA-AGGGUAGAACGUCUUA-CUAGCAC--UAGGAC-GAUAAUGACC-CGAAAGGCA-ACCUUCAAAU-GCU---UUAAUCUCA---AGCA
AACY020176744.1/891-482      GAGAGUAGUUCAGUAUCGAGUCGUU-CAAAA--GAUGACUUGUCU-GGUU-GGCAGACCGCUACUUUCACCAUCCACAGACCAAAAACUUUGCAUUUUUGAAGUAUGCAAAU---------------------------------------------------------------ACUAAGAGACAAAGGAA-AAGU-GUCUGUC--AGUCGUAGGC---GAAAGGUGACUACAUAGUAAUGA-----GAUGU----------U-C-AUUGC-CG-UU-GUGGGUUCCCAAGACC-CA-AA-CGAU-UCUUG-AGAACGUU-CUCUA---------------------------AUCC-CGCAA-GGAU-UCA-CUGGGGUGGCA--------------------------ACCUCGGAGAGUAACAAGUACAAAGAGAGUA-ACCGACGACUCAAG---GAAUGGUAAC-CCUAA--GUGACC---GUCACUGAG-AAU-UACUACU--------C-AAAA-------GGUAGUG-GAAA-CGGGAAGAA--------AAA--------------AUAAUGUCC-CCAAAGAUU-CUUAAUCAAA-GGU---GUAUUCUCA---ACCU
AACY022651301.1/330-755      GGGUGGUGUGAAGCAUUUUGUUCC--CAAAA---GGAACGAACCU-UCU--CCCGAAGCACAUCGUCCAUUCUUCCACAACUGCUAAUUAUCCUGCAACGAUAAUGUUACU----------------------------------------------------------------AAUAAUUAUGCAAGCGA-AAGU-CUUCGGG--CGUUGACAGU---GAAAGGUGUCUA-AU-ACUUCA-GAC--AUUG-------GUCAA-U-GGAGU-CAUCAG-GGAGACCGCAAGUCU-A-CUGAUGUC-AAUCA-CGAAAUAC-CUG-------------------------GU--GGGACGGCCA-UCCC-UUA-GAGAGUCCGCA-------------------------AGACUUUA-CAGAGUAGAGUAACGGUUGAGUA-ACUGGCAACGAAAC---GAGUGGUUCA-UCGUAC-UGAACC---GACACUGAUUCGA-UACUACGG-------G-CAA-------UCGUAGUG-GACAAUGUGAGGAACCG-----AAACAA-------UG-GAUAAUCUCA-CGAAAGACGGGUCACAUAAA-CGU---AUAGUCUCA---GCGU
ABHI01000002.1/126521-126020 AGGAGAAGGUUGGUAUUUUGUAGG--CAAAAA--UCUACGAAGCC-AUU--UUCGAAGCCCUUCUCCUAGGUCAAAGUUUUGAAGUCUAGGUUCGAUUCCUAGUAUCUCAACCGAAAAGGGGAUAUAGUUCAACUGGUAGAGCACUGUAUUUUU---------------------CAUACAGCGAAAGGCAC-AAGA-CUUCGAA--CAUUAUAGCAGUUAGUAGUUGCCUA-AA-CCCAU-------UGCAAUAU-----------AUGGG-ACAGUA--GAGGUCGCAAGCCU-A-UACUGUGC-GGUGA-ACAUUCUA-GUAGGCCGCCUCAACAGAGGACGUCUAUGAAUGGUGAGGGAG-CCAA-CCCUUGUAAUUGCAA---------AGCGUGGUUUUAAUACCACUAUGCAAGCCAAGUCUAAGUCGCUGAA--CAUCUAUAAUGUAUUA-----------------------------GGCAUCAGGUAAG-UACACAAUUCUCUAAG-CGA-U-GAGAAGCGUGUG-GAAA-AUUAGGGAAGGGC----UACG--------GCU--AUAAUCCUA-AGAAAGCUUAUCUACAA----GCGGAGGUAUUCUCAGAACGCU
AACY023325324.1/1159-749     AGGUGUAGUUCAGUAUCGUCUCGUU-CAAAA--GAUGGGAUGGCU-GGUUUGACGAACCGCUACAUCUAUUAUCCACAAAUCAAACUUUUACUUUCAAAUGGUGAAAAC------------------------------------------------------------------UAAUAAAUUAAAAGAAA-AAGU-GUUCGUC--AGUCGUGGUA---GAUAGGUCACUACUUAGUCAUGA-----GUUGU----------U-C-AUGGC-CG-UA-A-AGGGUCUCAAACCC-AA-UA-CGAU-UGUUU-UGAAAGUU-CUCUA---------------------------AUCC-CGCAA-GGAU-GAG-UUUGGGUGGCA--------------------------ACCUAGAAGAGUGAUGAGUAAGAAUAGAGUA-UAUUACGACUUUAG---GAUUGGUUAA-UCUAA--UUAACC---GUGACUGAG-AGG-UACUUCU--------C-AAAA-------GGAAGUG-GAAA-UCGGAGGAA--------AUCAAA-----------AUAAUCUCCUGUAAAGUCU-CUCACAAGAU-GGU---UUAUUCUCA---ACCU
AAJO01000044.1/12678-12304   -GUAGGCGUUGCGCAUUUUGUUGCU-CAAAA--GGCGACGAAACG-CAA--GGCAAUGCACGUCUGCGAUA-CACGAAAACAAUGCUAUUUGUUGAAA-----------------------------------------------------------------------------AUAUUGGAAUAAAGCAA-AAGU-CAUUGCC--CGUCGCAAAC---GAAAGUGUGCUU--C-GGUAG-------CUAGG--------------CUACC-UGCUA-G-AGUCUCGCAAGGAU-AA-UAGCAA--AGUCA-AAGAGUAA-AGC-AGCUUAGACCUUUAGCG-GGGUUUUC-------------------------------------------------------------------GUUAAUUGAAAAAUGGCUUAGUA-GUUUGCGGCGUAAC---GAGUGGUUAG-CGAUA--CUAACC---GCGCAUGGU-UGU-UACUUGAA-------G-GGA-------UUUGAGUG-GAUA-AAAAACUAA--------AAC--------------AUAAGGUUU-UGAAAGACA-ACUGACUAAA-CGU---GUAAUCUCA---GCGU
AACY023301467.1/619-1039     GAAAGUUGAGUGGCAUUUGCUUCUU-CAAAA--GAGAAGUUAACC-AC---CUCAGAGCUCAACUUUCAUUACACUCACUAUGUUGGAUUAAUUAAAAAUU--------------------------------------------------------------------------AAAACUACAGAAAGGAA-AAGU-CUCUGAG--CGGUUAAACU---GAAAGUCACCUA-AU-UCCUUG-GGUA-GAAA------UACUAA-C-AAGGA-GAUUGA-CAGGACCCCAAGUCC-U-UCAGUUUU-GACUA-AGAAAGUC-CUAGU---------------------------ACCUGGGCAC-GGGU-UUAGGGAGUC-CGCAA--------------------------GAUUCCAUAGAGAUGAGUAACAGUUGAGUA-GGGUUAACCGAAAC---GAGUGAUUGA-CGUAA--ACAAUC---GGUGAUGACUUGA-UACCUUUG-------G-CAA-------CAUCGGUG-GACA-CGGGAGGAACCCA----AUGUAGAA----UGG-GAUAAUCUCA-CAAAAGACAGGUCAACGAAA-CGU---AUAGUCUCA---GCGU
AACY022756534.1/925-515      GAGAGUAGUUGAGUAUUUCGUUGUU-CAAAA--GAUAACGAAGCC-CGU--GGCGGACCACUACUUUCACAAUCCACAACACAAAAACUUAUGACACUGAUUAAGUCAAAUUAAU------------------------------------------------------------UAUUAAGAAAUAAGCAA-AAGU-GUCCGUC--AGGUAAUAGU---GAAAGGUGACUACAUAGUAAUGA-----GCCGU----------U-C-AUUGC-AC-GA-A-AGGAUCGCAAGUCU-GA-UC-GUAU-UCUUA-CCAAACAC-CUCUA---------------------------AUCC-CGCAA-GGAC-UAG-UUGGGGAGGCA--------------------------UCCUCGAAGAGAGUCGAGUAAUAAGAGAGUA-ACUAUUAUCUCAAG---GAGUGGUACA-CCUAA--AAGACC---GUCACUGAG-AAA-UACUUCU--------C-AAAA-------GGAAGUG-GAUA-GGAGUAGAA--------ACA--------------AUAAUGACU-CUAAAGGUU-CUCACAAACA-GGU---GUAAUCUCA---GCCU
ABGE01000002.1/232092-232484 AGCAGGCGCUGUGCAUUUUGUUCUU-CAAAA--GAGAAUGAAACA-CAU--GGCGAUGCGUGUCUGUGAUAGAUGAAAGAUGAUUUUUAUAUUUUAAGGCUAUUCAAGAUAGAA-------------------------------------------------------------AAAACUCAAAAAAGCAA-AAGU-CAUCGCC--CGUCGUAAAC---GAAAGUGCACUU--C-GGCAA-------UUAGA--------------UUGCC-UGCUC-A-AGUCUCGCAAGGAU-GA-GAGUAAA--GUCA-AAGAGUAA-AGC-AGCUUAGACUUUUAGCG-GAGUCUUC-------------------------------------------------------------------GUUAAUUGAAAAAUGGCCUAGUA-GUUUGCGAUGUGAG---GAGUGAUUGG-UCUAA--CCAAUC---GUGCAUGAG-UGA-UACAAGUA-------G-GAA-------UAUUUGUG-GACA-AGAUAAUAA--------ACU--------------AUAAGUUAU-CAAAAGUCA-CUCGUUUAAA-GCA---GUAGUCUCA---UGCU
AACY021241093.1/652-232      GAAAGGUGAGUGGUAUUUACUUCUU-CAAAA--GAGAAGCUAUCC-AC---CUCAGAGCUCAUCUUUCAUCACACUCACUAUGUUGAUUUAUUAUGAAAAAAU------------------------------------------------------------------------AAACUACAGAAAAGGAA-AAGU-CUCUGAG--CGGUUAAACU---GAAAGUCACCUA-AU-UCCUUG-GGUA-GAAA------UGCCAA-C-AAGGA-AAUUGA-CAGGACCCCAAGUCC-U-UCAGUUUU-GACUA-AGAAAGUC-CUAGU---------------------------ACCUGGGCAC-GGGU-UUAGAGAGUC-CGCAA--------------------------GAUUCUAUAGAGGCAAGUAGUAGUUGAGUA-AGUUUGACCGAAAC---GUGUGAUUGU-CGUAA--ACAAUC---GGUGAUGACUUGA-UACUGAUG-------G-CAA-------CAUUAGUG-GAUA-CGAGAGGAAACC-----UUAGUCG------GG-UAUAAUCUCUACAAAAGACAGGUCACUUAAA-CGA---GUAAUCUCA---UCGU
AACY020178275.1/701-306      CGGAGUCGUCCAGUAUUCUUGAGUU-CAAAA--GAUUUGAGAGCU-GAG--AGGUGACCACGACUUCGACAAAUCUACAGGCACUAAAUUUCUAACUU-----------------------------------------------------------------------------UAAAAAGAAGAAAUCGA-AAGU-GUCACCU--AGUUACUGAC---GAAAGGUGUCUACAUAGUUAUGG-----GUCGU----------C-C-AUAGC-CA-CU-G-AAGCUCGAAAGGCC-GA-UG-UGAU-UUCAC-CUAAAAGC-UUAUA---------------------------GAGGGUCGAA-CCUC-GAA-UCAGUCCGGCA--------------------------GGGUUGAAUAAGCG-GAUUAAGUGGAGAGUA-GUUAGUAACUCAAG---UAGUGAUUGG-UCUAA--CCAAUU---GACACUGACAGAA-UACUUCU--------C-AAAA-------GGAAGUG-GAUA-AGAAGGGAA--------ACC--------------AUAAUCUAA-CAAAAGUUCUGUCUUUAUAA-GGU---GUAAUCUCA---GCCU
CP000416.1/1118883-1118471   CGGCCCAGUGAAGCAUUUGCUUUCU-CAAAA--GGAAAGCGAACU-UCU--GGCGAAGCACUGGGUUCCGAAUAAGAUGAAUUAUUCCUAGCUAAGGAAUAGUAUGUUAAACCAUUAAAUAUAA---------------------------------------------------CAUUAUCUAAAAUGCAA-AAGU-CUUCGCC--UGCUGUAUCU---GAAAGUAGUCUA-AU-GCUCCA-CACACAAGGG----GUGUGAA-U-GGAGCGUCGAU-G-A-ACUCGCAAGGU--GA-UUCGAUUCAGUAG-C-GAGUAG-UGC-AACCGAGUGGG-UAGCU-CCCAUUUA-------------------------------------------------------------------GUGAAUCGAAA-GCUGCUGAGUA-GGAUGCAGUAUGAAC--GGGUGGAA---CUCC-----UUCCACCGACUAUGGC-AGU-UACACGA--------G-GGA--------UCGUGUG-GAAA-CGCGACUAA--------GAA--------------AUAAGGUCG-UUAAAGACU-GCUGCUAACG-GAU---GUAUUCUCA---AUCU
AACY020168123.1/822-410      UCGGGUAGUUAAGUAUUCUGUCGUU-CAAAA--GGCGGCGGAGCU-UGU--GAUAGACCGCUACCUGAAACCACUGCAAAACCAAACUUAUAUUUGCAUUUAGGAUUGCAAAAUCAUA---------------------------------------------------------AAAAUCAAAAUAAGAAA-AAGU-GUCUAUC--AGUUUUGACC---GAAAGGUGUCUACAUAGUAAUGA-----GUUGU----------U-C-AUUGC-CA-CA-A-ACACUCUCAAGGUG-AA-UG-UGAU-UCUUU-CGAAAGGU-UUCUA---------------------------ACAC-CGCAA-GUGU-GAA-UCUGCUCGGCA--------------------------GGGUAGAAGAAAAU-AAGUAAGAAGAGAGUA-GGUUAAAACUCAAA---GAGUGGUUCA-CUUAA--AUAACC---GACAUUGGU-UGU-UACAUCU--------C-AAAA-------GGAUGUG-GAAA-CAAAGGGAA--------UAG--------------AUAAUCCUU-UUAAAGACA-ACUACAAUAU-GGU---GUAUUCUCA---GCCU
AACY020063107.1/600-1006     GAGAGGUGUGAAGCAUUCUGU-ACU-CAAAA--GGU-ACGGACCU-UCU--CCCGAAGCACAUCUUUCAUAAAUCCACAUUUGCUAACUUUUAAUUC------------------------------------------------------------------------------AAUGAUUAAAAAAGCAA-GAGU-CUUCGGG--CGUUGAUGAC---GAAAGGUGUCUA-AU-ACUUCG-GAC--CUUA-------GUCAA-C-GAAGU-CAUCCU-UUGAACCGCAAGUUC-G-GGGAUGUC-AAUUG-UGAAACAA-CUCGU---------------------------GGGUUGGCCG-ACCCUUUG-UGAGACCGCAA---------------------------GUCUUAAGAGAUUGGAGUAGUAGUUGAGUA-GUUAUCGACGAUAC---GAAUGGUAGC-CGUAA--GCGACC---GACACUGACCUGA-UACCUCU--------GUCAA--------UGAGGUG-GACA-AGUGGGGAACAA-----ACUAA--------UU--AUAAUCCCA-CAAAAGACAGGUUAUUCAAA-CGU---GUAGUCUCA---GCGU
AACY022755407.1/774-310      --GUGGUGAGUUGUAUUCAGCAUUC-CAAAA--GAUUGUUGAGCA-ACA--GUGGCAGCUCAUCGCGGUAGGUUGCAAUUAGCCUAAUGGUAAGGCAUCAGUCGCUUAAACUGGAGACUGUAGGUUCAAAUCCUACAUU------------------------------------GUAAAUCAAAAAUGCA--AAGA-CUGCCAC--GGUCAUGUGU---GAAAAGUAUCUA-AU-ACUUGA-CAC--GUAA-------GUGAA-U-CAAGUUUAGUG-A-A-GCUCGCAAGGU--GA-CACUAAUUUGUGG-AGGGGGGU-UCGUA-----AGUGGUUAGCA-CCACC-GAAUAGCU-CGCAA-GGCU-A-----------------------------------------------ACGGAAUGGAAU--CCGCAGAAUA-GCACAUGAUGACAAGACUACAGCCUGUCUUUAAAAAC-GGC---GAUACUGGUAACA-GACAUAGAU-ACC--G-AAA---GG-GUUUAUGUG-GAUG-UCAAGAGAAGGUAUGC-UCGCAAG--GUGUAC-UAUAAUGCUU-G--AGGUGUUACUGGUUAA--GAU---GUAAUCUCA---GUCU
AACY020183680.1/1963-1552    GAGAGUAGUUGAGUAUCAGGUCGCU-CAAAA--GGUGAUUUGGCU-CGGGUGGCGGACCACUACUUUCACAAUCCACGACACACAACUUAUGGAAACUAUUAAUUCCCAAAUUA-------------------------------------------------------------AAAAGAUCAUUAAGGAA-AAGU-GUCCGUC--AGGUCUAAUU---GAAAGGUGACUACUUAGUCGUGA-----GCUGU----------U-C-ACGGC-AC-AC-A-AGGAUCCCAAGUCU-GA-GU-GUAA-UUUUA-CCAAAGAC-CUCUA---------------------------AUCC-CGCAA-GGAC-GAG-CUGGGGAGGCA--------------------------UCCUCGGAGAGAGUUGAGUAAUGAGAGAGUA-GAUUAGACCUCAAG---GAGUGGUUUA-CCUAAA-UA-ACC---GUCACUGAG-AAA-UACUUCU--------C-AAAA-------GGAAGUG-GAUA-GGAGUAGAA--------UAA--------------AUAAUGACU-CUAAAGGUU-CUCACAAAAA-ACU---GUAAUCUCA---GGUU
AACY023432766.1/892-480      AGGAGUAGUUUAGUAUUCUGUUGUU-CAAAA--GAUAACGGAGCU-UAC--GGUGGACCACUACUUCUAUCAUCACGACACACAACUUUAUUUUACGUUCAGAAGUAAAAUUCAUG-----------------------------------------------------------AUAUAAACAUAAAGCAA-AAGU-GUCCAUC--AGGUUUUGAU---GAAAGUCGCCUACACAGUCAUGG-----GUUGU----------C-C-AUGGC-AC-AC-A-GAGACCGCAAGUCA-AA-GU-GUAU-UUUUA-CCAAAAAC-CUCUA---------------------------AGGGGUCGAA-CCCU-GAG-UCAGGUCGCAA---------------------------GCUUGAAGAGAGUUGAGUAAUGAAAGAGUA-GUUAAAACCUUAAG---AAGUGAUUGG-UCUAA--CCAAUC---GGCGAUGAG-AGU-UACCAUU--------C-AAAA-------GAUGGUG-GAAA-CGAAGGGAA--------CCAC-------------AUAAUCCUU-UAAAAGAUU-CUCAAAAUUA-GGU---GUAUUCUCA---ACCU
AACY020583117.1/670-250      GAAAGUUGAGUGGUAUUUCCUUCUU-CAAAA--GAGAAGCUAGCC-AC---CUCAGAGCUCAACUUUCAUGACUCUCACUAUGUUGAUUUAUUUAUGAAAAAA------------------------------------------------------------------------UAAACUACAGAAAGGAA-AAGU-CUCUGAG--CGGUUAAACU---GAAAGUCACCUA-AU-UCCUUG-AGUA-GAAA------UACUAA-C-GAGGA-AAUUGAU-AGGACCCCAAGUCC-U-UCAGUUUU-AACUA-AGAAAGUC-CUAGU---------------------------ACCUGGGCAC-GGGU-UUAGGGAGUCCGCAA---------------------------GAUUCCAUAGAGAUUAGUAGUAGUUGAGUA-GGGUUAACCGAAAC---GAGUGAUUGA-CGUAA--ACAAUC---GGUGAUGACUUGA-UACAGAUG-------G-CAA-------CAUUUGUG-GAUA-CGGAAGGAAACC-----UUAGUAC------GG-UAUAAUCUUCACAAAAGACAGGUCAGUUAAA-CGA---GUAAUCUCA---UCGU
#=GC SS_cons                 <<<<<<<<<<<<<<--<<<<<<<<<._____..>>>>>>>>>>>>.>>-..-------->>>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,.............................................................,,,,,,,,,,,,,,,,,.,,,,.,,,,,,,..[[[[[[[[[[...,,,,,,,,,,,,.,,.<<<<<<.<<<.._____......>>>--.>.>>>>>.<<<<<.-.-<<<<_____>>>>.--.>>>>>,,.(((((.--------.((((,....<<<<<<_____..>>>>>>....<<<<._____.>>>>.,,,.<<<.<<_____...........................>>->>>))))----------))))),,,,,.]]]]]]]]]],,,,...,,,,<<<<<<._____..>>>>>>...,,,,,,(((.(((.<<<<<<<<......._.___.......>>>>>>>>.,,,,.,<<<<<<---<<.....____.........>>..---->>>>>.>,,,,,))).))),,,,,,,.<<<..._________...>>>:
#=GC RF                      gggaGucGugcaGuAUuuugucuuu.CAAAA..gaagacaaagCu.gcu..ggcGaAGCaCgaCucccaaaauucaaaaauuaauaauuuuuuuuuauuuuauauauuAaauag.............................................................aAaAaaaAAaAAaGCAA.AAGU.CUucgcc..cguuguagcc...GAAAGuuGcCUA.AU.gCcucg.ggC..guugu......GccAA.c.gagGc.cguuc.a.AggcuCGCAAggcc.gA.gaacguU.uguga.agAAauau.cucuA....aggggguuAGC..cccccu....agcc.cGCAA.ggcu.uaa.ucg.gcuGGcA...........................gcUcgaagagaaaugAGuAaucacaGAGUA.ggcuacaacgaaAg...gAgUGguugg.cuUAA..ccaacC...GgcaaUGac.agu.UACuuccg.......g.aAA.......cggaaGUG.GAaA.agugGGGAAgcc.....uaag.........gg..AUAAUCCca.caAAAGacu.guCacuaAAA.Ggu...GUAaUCUCA...gcCU
//
# STOCKHOLM 1.0

#=GF AC   RF02033
#=GF ID   HEARO
#=GF DE   HNH endonuclease-associated RNA and ORF (HEARO) RNA
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:12376536; Weinberg Z
#=GF SS   Published; PMID:12376536; Weinberg Z
#=GF GA   32.00
#=GF TC   32.00
#=GF NC   31.70
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19956260
#=GF RT   Exceptional structured noncoding RNAs revealed by bacterial metagenome
#=GF RT   analysis.
#=GF RA   Weinberg Z, Perreault J, Meyer MM, Breaker RR
#=GF RL   Nature. 2009;462:656-659.
#=GF WK   HEARO_RNA_motif
#=GF **   seedtax: Bacteria; Viruses; Archaea; unclassified sequences
#=GF SQ   110


BABF01001490.1/2915-3043     GUCAAUAACCCACC-------AC----GAAA----GC--A------G-UGAGCUU-------AUAU--------AAG---------------------------------------------------------------------CUUUUAUUG--ACUAG-ACCCGGUGU----------AUAA-A---------------------------------------------------------GCACU---CCGUUAUG-------UAAG--------------------AAUAUAUA--GUU--ACCAGU-GGACG---------------UACAGC-CUAAUCCACUGCU-C-U-AAG
BABE01012960.1/454-650       GUCAAUAACCC-GCGC---CCGAG--GUAAAC--CUCGGA-----CG--GGGCUU-------GCAA--------AAGAAUAAAUUGUUUUAUUUCCACUUUUGUUUAGCUCCGUUACAGUUUACGGAAGGUGUUGGCCGAAAGGCC---UUAUUG--AUUAG-CCUUAGCA-----------GUAC------------------------------------------------------------UGCU---ACGUUAC--------CGAUA-------------------AA-----AUAGGC--ACCGUG-GGAUA----------------CUCCU-CAAGUCUCACGCU-C-U-GCG
BAAX01006901.1/977-846       GUCAACUACCC--CGG-----CC----UAAA----GA-------CCG--AGGCUUG-----UGAAAG------CAGG----------------------------------------------------------------------CCUGGUUG--ACCAG-CCUAAGUUU----------UUCG-A---------------------------------------------------------GAACU---ACGUUGCAG-----ACAGGUU----------------CAAG-----A--CCC--ACCUCG-GAAUG----------------CUUCC-UCAGUUCCGAGCU-C-U-GGA
CP000121.1/149539-149673     GUCAGUAACUC--AG------GG----ACAAA--GCC--A-----CU--GAGCUUGUA-AGAGAAAUCA--AGCAAG----------------------------------------------------------------------CUGUACUG--ACCAG-UCUAAGUC-----------UUAA-CU---------------------------------------------------------GACU---ACGUUUUU-------UGAGU-------------------CA-----C--GAC--ACCGGA-GAAUG----------------CGAAG-CUAGUUUUCCGCU-C-U-GUC
CP000529.1/2206036-2206189   GUCAACCACCC--C-----ACCC----UAAA----GGAU-------G--GGGCUUGAAAGGUGAAAGCC-UUGAAAG---------------------------------------------------------------------CCCAGGUUG--ACCAG-ACCCAGAAAGG-----AAUUUAA---AAA--------------------------------------------------ACCAAUCU---ACGUUGCC-------UACAGGUU------------AUCGGA-----C--CA---ACGGCA-GGAUG----------------CUUCU-CCAGUCCUGCCCU-C-U-UGA
AAVU01000064.1/5670-5810     GUCAGC-ACCC--CG-----CUC----UAAA----GA-GA-----CG--GGGCAUC---------------------AUGCCUC-------------------------------------------------------UCUUUUUAGGUAGCUG--ACCAG-CCUAAGUC-----------CCUU-GA-------------------------------------------------------A-GGCU---ACGUUAUCGGC-AAGAGUUA-------------------AA-----G--UUCCUACCCGG-AGAUG-----------------CGUGGCCAGUCUCCGGCU-C-UAGAA
BA000020.2/291979-291841     GUAAACUACCC-ACCAC--GGAUU-GCUAAAAGCAAUAUA---GUGG--GGGCUU-------UCA---------AAG--------------------------------------------------------------------CCCAGAGUUU--ACCCG-ACUAAGUGU----------UUCG-C---------------------------------------------------------GCACU---ACGAUUUU-------AAGGU-------------------CA-----U--CUU--ACCUGG-GAAUG----------------CGUAG-CCAGUUCCCAGCA-C-U-AGG
AP008972.1/169876-169737     GUCAAUUACCC--CA----CGAC----UAAA----GU-C-------G--GGGCUUG---------------------UCUUAA--------------------------------------------------------CAAACAGCCCUAGUUG--AUUAG-ACUAAGCAC----------UUAU-GUU-----------------------------------------------------AUGUGCU---ACGUUAC--------UUGUA-------------------AAUAUAUA--GUU--ACCAAG-GAAUG---------------UUUUAC-CUAGUUCCUUGCU-C-U-AAG
ABRS01000124.1/92937-92767   GUCAACUACCG-CACACCAACCC----UGAU---CGGGUAU-GGUGU--GGACUU-------GAAU-------AAAG-----------------------------------------------------------------------UCUGUUG--ACCAG-ACGGCUCACCUCGACUUCGCGGGCGUGAGCGGAGC--------------------------------------CGAACCGAGC--AG---CCGUUAAGACU-AAGAGUUA-------------------AA-----GUUCGU--ACCUUG-GGAUG-----------------CGUG-CCAGUUCCAAGCU-C-U-ACA
AAXW01000074.1/2655-2521     GUCACGAACCC-ACCA---CUAAU-CCAGUAG-GUAUAG-----UGG--GGGCUUG------AAAAGC----CCAAG-------------------------------------------------------------------------ACGUG--ACCAG-ACUAAGGUU----------CUAG-A---------------------------------------------------------GACCU---ACGUUAUU-------UGAGU-------------------CA-----A--GAC--ACCUUG-AGAUG-----------------CGUG-CCAGUCUCACGCU-C-U-GUC
ABYK01000021.1/61929-61792   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CAG--GGGCUUC---------------------GUGCCC--------------------------------------------------------CCCUUUCAGGUAGCUG--ACCAG-CUAUAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCC-C-UAGAA
CP000975.1/1397025-1396883   GUCAACCAUCC--C-----GCCC----UUUA----GGGC-------G--GGGCUUGC---GGGUAAGC----GCAGG---------------------------------------------------------------------CUCAGGUUG--ACCAG-GGAAAGCG-----------CUACCUAG-----------------------------------------------------UC-CGCU---ACGUUGCA--------UGGAG----------------AGCA-----AAAGACCGACGUUG-GGAUG----------------CUUCCUAAAGUCCCAACCU-C-UCGAA
AADL01001511.1/37237-37402   GUCAACUACUC--CUG-----GC----UCAC----GC--A-----GG--GGGCCUGUU--CCGUGAGG---AACAGC--------------------------------------------------------------------GUAAGAGUUG--AUUAG-AG--AGCUU----------UAAAAAAUAUAGUGAAAA----------------------------------ACAUGAAAGAAAAGCA--GAAGUUAGACAA-AAGAGAUA-------------------CA----UA--CAC--ACCCGC-GGAUG----------------CUCCA-CAAGUCCGUGGCAAC-U-GUG
CR954247.1/342323-342459     GUCAACUACUCAC-------CCC----UAAA----GG-GA--------UGAGCUU-------GUAA--------AAG---------------------------------------------------------------------CGCUUGUUG--ACCAG-ACCACUAAC----------UGAGGAUUAG-------------------------------------------------AAAUGUUAGUAAACGAUAAU-------UUAGA-------------------U------GUAGAA--ACCUUG-GAAUG----------------CCGCC-UCAGUUCCAAGCU-C-U-UUC
ABYK01000068.1/24308-24171   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CAG--GGGCUUC---------------------GUGCCC--------------------------------------------------------CCCUUUCAGGUAGCUG--ACCAG-CUAUAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCC-C-UAGAA
ABRS01000034.1/26295-26445   GUCAGGAACCCCACCG---C-------UAUA---A--------GCCG-GGGGCUU-------GAAU-------AAAG--------------------------------------------------------------------CCCGUACCUG--ACCAG-CCUAAGUGC----------CUAA-C---------------------------------------------------------GCACU---ACGUUAACGGC-AAGAGUUA-------------------AA-----G--UUCCUACCUUG-GGAUGCGUGCGCGUAGCGCGU--AAG-CCAGUCCCAUGCU-C-UAGAA
ABRS01000103.1/29482-29351   GUCAACGACCC-GUCG---C-------UAAA---A---G-----CGA--AGGCUU-------CUAA--------AAG---------------------------------------------------------------------CUCAAGUUG--ACCAG-CCUAAGUGC----------UACG-C---------------------------------------------------------GCACU---ACGUUAACGGU-AAGUGUUA-------------------AA-----G--UUCCUACCUUG-GGAUG-----------------CGUG-CCAGUUCCAAGCU-C-UAGAA
AAVU01000002.1/234448-234321 GUCAGC-ACCC--C-----GCUC----UAAA----GAGCA------G--GGGCCGAA----GCGCCUCU-CUCUUAG-----------------------------------------------------------------------AUAGCUG--ACCAG-CCUAAGUC-----------UUUG------------------------------------------------------------GACU---ACGUUUUU-------AGAGU-------------------UA-----U--GAC--ACCUAC-AAAUG----------------CUUGA-CC-GUUUGUAGCC-C-U-GUC
AAVU01000046.1/44330-44188   GUCAGC-ACCC--CG-----CUC----UAAA----GA-GA-----CG--GGGCAUC---------------------AUGCUUC-------------------------------------------------------UCUUUUUAGGUAGCUAGUACCCG-CCUAAGUCC----------CUUG-A---------------------------------------------------------GGGCU---ACGUUAUCGGC-AAGAGUUA-------------------AC-----G--UUCCGACCCGG-AGAUG-----------------CGUGGCCAGUCUCCGGCU-C-UAGAA
ABYK01000027.1/61956-61819   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCC--------------------------------------------------------CCCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---CCGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCU-C-UAGAA
CP000812.1/104833-104710     GUCAACUACCC-GCCG-----CC----UAUAG--AGG-------CGG--GGGCUU-------GAAA--------AAG---------------------------------------------------------------------CCCUGAUUG--ACUAC-CCUCAGCCA---------CAUAA----------------------------------------------------------GUGGCU---ACGUUAGA-------CAGGU------------------------------AC--ACCCUA-UGAUG----------------CUGCU-CAAGUUCCAGGCU-C-U-GUC
ABRS01000018.1/15775-15915   GUCAACAACUC-ACCGC-UAAGUU--CUAUCG--AAC-UAU-AGCGG--GAGCUUG------UAAAA-----ACAGG---------------------------------------------------------------------CUCUAGUUG--ACCAG-ACUAAGUUC----------UACG-A---------------------------------------------------------GAACU---ACGUUAUU-------UAGCU-------------------CA-----U--GAC--ACCCUA-AGAUG----------------CGU-G-CCAGUUUUAGGCU-C-U-GUC
ABRS01000085.1/18787-18922   GUCAGGAACCC--CA----CGGC----UAUA---AGC-C-------G--GGGCUU-------UGAA-------AAAG--------------------------------------------------------------------CCUAUACCUG--ACCAGUCCUAAGUGC----------UUAG-C---------------------------------------------------------GCACU---ACGUUAACGGC-AAGAGUUA-------------------AA-----A--GUCCUACCUAC-GGAUG-----------------CGUG-CCAGUCUGUAGCU-C-UAGAA
ABRS01000075.1/145280-145145 GUCAGGAACC---CCA---CGGC----UAUA---AGC-C------GG--AGGCUU-------GAAU-------AAAG--------------------------------------------------------------------UCUAUACCUG--ACCAG-CCUAAGUGC----------UUAG-C---------------------------------------------------------GCACU---ACGUUAACGGU-AAGCGUUA-------------------AA-----G--UUCCUACCUUG-GGAUG-----------------CGUG-CCAGUCCCAUGCU-C-UAGAA
ABYK01000024.1/58704-58842   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCCC------------------------------------------------------CCGCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----GUUCCU--ACCCUG-GAAUG----------------CGU-G-CUAGUUCCAGGCC-C-U-AGA
ABYK01000008.1/66741-66878   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCCC-------------------------------------------------------CGCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----GUUCCU--ACCCUG-GAAUG----------------CGU-G-CUAGUUCCAGGCA-C-U-AGA
AAVU01000071.1/5233-5375     GUCAGC-ACCC--CG-----CUC----UAAA----GA-GA-----CG--GGGCAUC---------------------AUGCUUC-------------------------------------------------------UCUUUUUAGGUAGCUAGUACCCG-CCUAAGUCC----------CUUG-A---------------------------------------------------------GGGCU---ACGUUAUCGGC-AAGAGUUA-------------------AA-----G--UUCCGAGCCUG-AGAUG-----------------CGUGGCCAGUCUCCGGCU-C-UAGAA
ABRS01000008.1/47129-47260   GUCAACGACCC-GUCG---C-------UAAA---A---G-----CGA--GGGCUCC---------------------UUA--------------------------------------------------------------UAGC-CCAAGUUG--ACCAG-CCUAAGUGC----------UACG-C---------------------------------------------------------GCACU---ACGUUAACGGC-AAGUGUUA-------------------AA-----A--AUCCUACCUUG-GGAUG---------------CGUG---CCAGUUCCAAGCU-C-UAGAA
CP000812.1/1146373-1146494   GUCAACUACCC-ACUG-----CC----UAUAG--AGG-------CGG--GGGCUU-------G-AA--------AAG----------------------------------------------------------------------CUUAGUUG--AUUAC-CCUCAGCCA---------CACAA----------------------------------------------------------GUGGCU---ACGUUAGA--------CAGU-----------------------------UAC--ACCCCG-GGAUG----------------CUGCU-CAAGUUCCAGGCU-C-U-GUC
ABRS01000093.1/29198-29060   GUCAGGAACCC--CAC---AGCU----ACA-----AGCU-----G-G--GGGCUUG---------------------GAAUU-----------------------------------------------------------UAGCC-CAUACCUG--ACCAG-AAG-ACCAG---------AGUAA----------------------------------------------------------UCUGGU--AGCCGUUAU-------GGGGAAGC------------GUUAAA-----G--UUCCGACCUAC-GGGUG----------------CGU-G-CCAGCCUGUAGCU-C-UCGAA
ABYK01000049.1/395-258       GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCC--------------------------------------------------------CCCUUUCAGGUAGCUG--ACCAG-CUAUAGCC-----------UUAA-CU---------------------------------------------------------GGCU---CCGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCU-C-UAGAA
CP000812.1/646151-646028     GUCAACUACCC-ACCG-----CU----UGUAG--AAG-------CGG--AGGCUU-------GAAA-------AAAG----------------------------------------------------------------------CCUGGUUG--ACUAC-CUUCAGCCA---------CAUAA----------------------------------------------------------GUGGCU---ACGUUAGA-------CAGGU------------------------------AC--ACCCUG-UGAUG----------------CUGCU-CAAGUUCCAGGCU-C-U-GUC
AAVU01000006.1/129564-129436 GUCAGC-ACCC--C-----GCUC----UAAA----GAGCA------G--GGGCCGA---------------------AGCGCCU-------------------------------------------------------CUCUCUUAGAUAGCUG--ACCUG-CCUAAGUCU----------UGUU-----------------------------------------------------------GGACU---ACGUUUUU-------AGAGU-------------------UA-----U--GAC--ACCUAC-AAAUG----------------CUUGA-CC-GUUUGUAGCU--A--GUC
ABYK01000007.1/165532-165393 GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------CUGCCCC------------------------------------------------------CCGCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCU-C-UAGAA
AAVU01000040.1/23488-23345   GUCAGC-ACCC--C-----GCCC----UAAA----GAGCA------G--GGGCCGA---------------------AGCGCCU------------------------------------------------------CUCUUUUUAGGUAGCUAGUACCCG-CCUAAGUCC----------CUUG-A---------------------------------------------------------GGGCU---ACGUUAUCGGU-GAGAGUUA-------------------AC-----G--UUCCGAGCGGG-AGAUG-----------------CGUGGCCAGUCUCCGGCU-C-UAGAA
ABYK01000067.1/4667-4530     GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCC--------------------------------------------------------CCCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---CCGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCU-C-UAGAA
CP001036.1/4028-4153         GUCAACUACCC-A------CGGC----UAAA----GCCGA---------GGGCUU-------GAAA--------CCC-----------------------------------------------------------------------UUAGUUG--ACUAG-CCUAAGCAC----------UGUG-A---------------------------------------------------------GUGCU---ACGUUAC--------CCGUG-------------------AAUAUAUA--GGU--AUCUUG-GGGUA----------------CUCCU-CCAGCUCCAAGCA-C-U-ACG
AADL01001524.1/11381-11217   GUCAACUACCC--C-----UCCC----UGAC----GG-AA------G--GGGCUUGUU--CCGUGAGG---GGCAUC--------------------------------------------------------------------GCAAGAGUUG--AUUAG-GGGGCUU------------GAAA-GACAUGGUGAAA-----------------------------------AACAUGAAAGA-GAAGCAGAAGUUAGA-------UUGGA-------------------GAAAUACAUACAC--ACCUAC-GGAUG----------------CUCCA-CAAGUCCGUGGCAAC-U-GUG
CP000812.1/1296076-1296197   GUCAACUACCC-ACCG-----CU----UGUAG--AAG-------CGG--GGGCUU-------G-AA--------AAG----------------------------------------------------------------------CCUGAUUG--ACUAC-CCUCAGCCA---------CAUAA----------------------------------------------------------GUGGCU---ACGUUAGA-------CAGGU------------------------------AC--ACCUUG-GGAUG----------------CUGCU-CAAGUUCCAGGCU-C-U-GUC
EU421841.2/52627-52779       GUCAACCACUC--CCCC-UAAGCC--CUGGUG--GGC-UGU-AGGCG--GAGCUUGUG--GGGAAGCU---CACAGG--------------------------------------------------------------------CUCCUGGUUG--ACCAG-GCUCAGUCCC--------GGAAU-C-C------------------------------------------------------GGGGCU---ACGUUGGU-------UAGGU-------------------CA-----G--GAC--ACCCUG-GGAUG---------------CGUGUG-CCAGUUCCAGGCU-C-U-GUC
CP000812.1/1419310-1419172   GUCAAUUACCC-ACCG-----CU----UGUAA--AAG-------CGG--GAGCUU-------GAAA--------AAA---------------------------------------------------------------------CCCUGAUUG--ACUAC-CCUCAGCC-AGGG--GAAGUUGAU--CUUC-----------------------------------------------CUAUCGGGCU---ACGUUAGA-------CAGUU------------------------------GC--ACCCUA-UGAUG----------------CUGCU-CAAGUUCCAGGCA-C-U-GUC
CP001291.1/3704030-3703891   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUCGU--GCCUCCCGC--AACAGG-----------------------------------------------------------------------AUAGCUA--ACCAG-CCUAAGCU-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CUUG-CUAGUUCCAGGCU-C-UAGAA
ABYK01000001.1/47034-46896   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCCC------------------------------------------------------CCGCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----GUUCCU--ACCCUG-GAAUG----------------CGU-G-CUAGUUCCAGGCA-C-U-AGA
ABRS01000025.1/224904-224769 GUCAGGAACCU-C--------UCGGCUUACAG-CCGU------------GGGCUU-------GAAA--------AAG--------------------------------------------------------------------CCCAUACCUG--ACGAG-CCUAAGACC----------UACA-U---------------------------------------------------------GGUCU---ACGUUAUGCCC-AAGAGUUA-------------------AA-----G--UUCCUACCUUG-GGGUG-----------------UGUG-CCAGCCCUAAGCUGC-UAGAA
CP000963.1/144664-144525     GUCAACUAACC-C--------ACG-AAUAAAU-UCGU--A---------GG-CUU-GUAGGAGCAAUCC-UAUUAAG----------------------------------------------------------------------CUUGGUUG--AUUAG-CCUAAGUA-----------UUAA-UU---------------------------------------------------------UACU---ACGUUAUA-------CAAGA--------------------AUAUAUA--GUU--AUCUUG-GGAUA----------------CUCCA-CAAGUCCCAUGCU-C-U-AAG
AADL01000519.1/1402-1544     GUCAACCACCC--C-----GCCC----UGAA----GGGC-------G--GAGCUUGA----AAGGAGGUUCGACAGG---------------------------------------------------------------------CUCGGGUUG--ACCAG-GGAAAGCGG----------UACC-CAA------------------------------------------------------CCCGCU---CCGUUGGC-------AACAGG----------------UACA-----AGACCC--ACCCCG-GGAUG----------------CUUCC-UCAGUCCCGGGCU-C-U-GGA
ABRS01000117.1/72674-72507   GUCAACUACCG-CACACCAACCC----UUAG----GGGUAU-GGUGU--GGGCUU-------GAAA--------AAG----------------------------------------------------------------------CCU-GUUG--ACCAG-ACGGCUCACCUCGACUUCGCUCGGUGAGCGGAGC---------------------------------------CGAACCGAGC--AG---CCGUUAAGACU-AAGAGUUA-------------------AC-----GUUCGU--ACCAAG-GGAUG-----------------CGUG-CCAGUUCCUUGCU-C-U-ACA
CP001022.1/1392346-1392469   GUCAAUUACCU-A------UCAC----UAAA----GUGAC---------GGGCU--------UAUA-------C-AG--------------------------------------------------------------------CUUGAAAUUG--ACUAG-UCUAGGUUC----------UCAC-----------------------------------------------------------GAACU---ACGUUGGU-------UGGGU-------------------CA-----U--GAC--ACCUCU-CGGUG---------------CCCGUU-CUAGCCGUUUGCC-C-U-GUC
AP008983.1/135254-135119     GUCAACUGCCA-ACUA----CCC----UAAA----GG-G-----UAG--UGGCUUGU---AAGAAAUU----GCAAG-----------------------------------------------------------------------UCGGUUG-AAU-AG-CCUAAGUC-----------UUAA-AU---------------------------------------------------------GACU---ACGAUUAU-------UAAGAAU---------------AUAU-----A--GGU--ACUUCA-AGAUA----------------CUUCU-CUAGUCUUGAACA-C-U-ACG
AADV02000153.1/7573-7431     GUCACAAACCC-GCCGUUAA-UUG--CUCAGG--CAA-UAU-AACGG--GGGCUU-------GAUUU------AAAGC-------------------------------------------------------------------CCAUGAUGUG--ACCAG-UUCA--CCUG--------AUUU----U------------------------------------------------------CAGG--UAAACGUUAUC-------UAAUU-------------------CA-----U--GAC--ACCUCU-UGGUA-----------------CGUG-CCAGCCUAGAGCAAC-U-GUC
AAQK01002334.1/258-410       GUCAAGAACCC-GCCACUUAAACU--CCGAAG--AGUUUUGAAGUGG--GGGCUUGU---GGAAAACA----ACAA----------------------------------------------------------------------ACCUGCUUG--ACUGC-CCUAAGUGC----------UUCG-G---------------------------------------------------------GCACU---GCGUUAC--------CCGGG-------------------AAUAGAUA--GGC--GCCGGC-GGACG---------------CGCAUC-CGAAUCUGCCGCU-C-U-GCG
ABRS01000081.1/81891-81742   GUCAACAACCC-ACCGUUAAAUCG--GAGUAC--CGAUUAU-AACGG--GGGCUG-------GUAAG------AUAG---------------------------------------------------------------------CCCGAGUUG--ACCCG-ACUCAGGCA----------GGAA-----------------------------------------------------------UGCCU---ACGUUAGUGGC-AAGUGUUU-------------------AA-----G--UUCUUACCUAC-GGAUG----------------CGUAG-CUAGUCUGUAGCU-C-UAAAA
ABYK01000014.1/34688-34551   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CAG--GGGCUUC---------------------GUGCCC--------------------------------------------------------CCCUUUCAGGUAGCUG--ACCAG-CUAUAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCGG-GAAUG-----------------CGUG-CUAGUUCCAGGCC-C-UAGAA
AAXY01000002.1/157923-158067 GUCAACUACCC--C-----GCCG----UGAA----CGAC-------G--GGGCUUGUA-GAGAACACCC--UACACG----------------------------------------------------------------------CCAAGUUG--ACCAG-GGAAAGCGG----------ACAC-CAA------------------------------------------------------CCCGCU---ACGUUUAC-------CACAGGUC------------GUUAAG-----A--CCC--ACUCCG-GUGUG----------------CUACC-UCAGCACCGGACA-C-U-GGA
ABYK01000062.1/9265-9403     GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCCC-------------------------------------------------------CGCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUGAGCGAGCAAGAGUUA-------------------AA-----GUUCCU--ACCCUG-GAAUG----------------CGU-G-CUAGUUCCAGGCA-C-U-AGA
AAXY01000008.1/96459-96603   GUCAACUACCC--C-----GCCG----UGAA----CGAC-------G--GGGCUUGUA-GAGAGCACCC--UACACG----------------------------------------------------------------------CCAGGUUG--ACCAG-GGAAAGCGG----------UAAC-CAA------------------------------------------------------CCCGCU---ACGUUUAC-------CACAGGUC------------GUUAAG-----A--CCC--ACUUCG-GUGUG----------------CUUCC-UCAGCACCGGACA-C-U-GGA
AAVU01000005.1/42194-42336   GUCAGC-ACCC--CG-----CUC----UAAA----GA-GA-----CG--GGGCAUC---------------------AUGCUUC-------------------------------------------------------UCUUUUUAGGUAGCUAGUACCCG-CCUAAGUCC----------CUUG-A---------------------------------------------------------GGGCU---ACGUUAUCGGC-AAGAGUUA-------------------AC-----G--UUCCGACCCGG-AGAUG-----------------CGUGGCCAGUCUCCGGCU-C-UAGAA
CP000812.1/21069-20949       GUCAACUGCCC-ACUA-----------UAGAA--A----G----CGG--GGGCUU-------GAAA-------AAAG----------------------------------------------------------------------CCUGAUUG--ACUAC-CCUCAGCCA---------CAUAA----------------------------------------------------------GUGGCU---ACGUUAGA--------CAGU-----------------------------UAC--ACCUUG-GGAUG----------------CUGCU-CAAGUUCCAGACU-C-U-GUC
ABHD02000059.1/31723-31845   GUCAACUGCCA-CC-----ACCC----UAAA----GGGUA------G--UAGCUU-------GUAA--------AAG-----------------------------------------------------------------------CUAGUUG-AAU-AG-CCUAAG-------------UUUA-CA-----------------------------------------------------------CU---ACGUUAUG-------UAAG--------------------AAUAUAUA--GGU--ACUUUA-GGAUA----------------CUUCU-CUAGUCCUAAACU-C-U-ACG
AADL01001534.1/23182-23018   GCCAACUACCC--C-----UCCC----UGAC----GG-AA------G--GGGCUUGUC--CCGUGAGG---GGCAUC--------------------------------------------------------------------GCAAGAGUUG--AUUAG-GGGGCUUU-----------GAAA--ACAUGGAGAAA-----------------------------------AAUAUGAAAGA-GAAGCAGAAGUUAGA-------CCGGA-------------------GAAAUACAUACAC--ACCUAC-GGAUG----------------CUCCA-CAAGUCCGUGGCAAC-U-GUG
AADL01001526.1/57-221        GUCAACUACCC--C-----UCCC----UGAC----GG-AA------G--GGGCUUGUU--CCGUGAGG---GGCAUC--------------------------------------------------------------------GCAAGAGUUG--AUUAG-GGGGCUUU-----------GAAA--ACAUGGUGAAA-----------------------------------AACAUGAAAGA-AAGGCAGAAGUUAGA-------UUGGA-------------------GAAAUACAUACAC--ACCUAC-GGAUG----------------CUCCA-CAAGUCCGUGGCAAC-U-GUG
AADL01001731.1/4150-3986     GUCAACUACCC--CUA-----GC----UCAC----GC--A-----GG--GGGCCUGUC--CCGUGAGG---AACAAC--------------------------------------------------------------------GCAAGAGUUG--AUUAG-GGGGCUUU-----------AAAU--ACAUGGAGAAA-----------------------------------AACAUGAAAGA-AAAGCAGAAGUUAGA-------UAGGA-------------------GAGAUACAUACAC--ACCUGC-GGAUG----------------CUCCA-CAAGUCCGUGGCAAC-U-GUG
AADL01001502.1/32784-32947   GUCAACUACCCUA--------GC----UCAC----GC--A-------GGGGGCAUGUC--CCGUGAGG---GACAAC--------------------------------------------------------------------GCAAGAGUUG--AUUAG-GGGGCUUU-----------AAAA--ACAUGGAGAAA-----------------------------------CAUAUGAAAGA-GAAGCAGAAGUUAGA-------UAGGA-------------------GAGAUACAUACAC--ACCUGC-GGAUG----------------CUCCA-CAAGUCCGUGGCAAC-U-GUG
CP000318.1/158631-158775     GUCAAUCACCC--C-----ACCC----UAAA----GGAC-------G--GGGCUUGGA-ACUGAAAGGA--ACCAAG----------------------------------------------------------------------CCAGGUUG--ACCAG-GGAAAGCGG----------UAAU-CAA------------------------------------------------------CCCGCU---ACGUUAGC-------AACAGGUC------------GUUCAG-----A--CAC--ACCAGC-GAAUG----------------CUUCC-UCAGUUCGCUGCU-C-U-GUA
CP000318.1/206041-205897     GUCAAUCACCC--C-----ACCC----UAAA----GGAU-------G--GGGCUUGGA-ACUGAAAGGA--GCCAAG----------------------------------------------------------------------CCAGGUUG--ACCAG-GGAAAGCGG----------UAAU-CAA------------------------------------------------------CCCGCU---ACGUUAGC-------AACAGGUC------------GUUCAG-----A--CAC--ACCAGC-GAAUG----------------CUUCC-UCAGUUCGCUGCU-C-U-GUA
ABRS01000008.1/48357-48491   GUCAGGAACCU--CA-----GCC----UAAA----GC-CA-----UG--AGGCUUGAA-AGAGCAAUCU--GACAAG----------------------------------------------------------------------CCAUUCUG--ACCAG-CCUAAGUC-----------UUAA-CU---------------------------------------------------------GACU---ACGUUUUU-------UGAGU-------------------CA-----C--GAC--ACCCUG-GAAUG----------------CGAAG-CUAGUUCCUUGCU-C-U-GUC
AAVU01000004.1/148866-148995 GUCAGC-ACCC--C-----GCUC----UAAA----GAGCA------G--GGGCCGA---------------------AGCGCCU-------------------------------------------------------CUCUCUUAGAUAGCUG--ACCAG-CCUAAGUCU----------UGUU-----------------------------------------------------------GGACU---ACGUUUUU-------AGAGU-------------------UA-----U--GAC--ACCUAC-AAAUG-----------------CUUU-CCAGUUUGUAGCC-C-U-GUC
AAVW01000151.1/2275-2106     GUCAGUAACCC--AG-----CCC----UAAA----GG-GA-----CU--GGGCUUGUA-AGAGUAAUCA--AGCAAG----------------------------------------------------------------------CCGUACUG--ACCAG-ACCACCCUGA-------GCGCAG-UCGUAAAGCCUACGG-----------------------------CAUAGCUCCCGGCU-AGGGUAGCCGUUAUU-------UGAGU-------------------CA-----C--GAC--ACCCUGUGGAUG----------------CGUAG-CUAGUCCCCUGCU-C-U-GUC
AAXY01000013.1/14326-14470   GUCAACUACCC--C-----GCCG----UGAA----CGAC-------G--GGGCUUGUA-GAGAACACCC--UACACG----------------------------------------------------------------------CCAAGUUG--ACCAG-GGAAAGCGG----------ACAC-CAA------------------------------------------------------CCCGCU---ACGUUUAC-------CACAGGUC------------GUUAAG-----A--CCC--ACUCCG-GUGUG----------------CUACC-UCAGCACCGGACA-C-U-GGA
AAXY01000008.1/90929-90785   GUCAACUACCC--C-----GCCC----UAAA----GGAC-------G--GAGCUUGUA-GAGAACACCC--UGCAAG----------------------------------------------------------------------CCAGGUUG--ACCAG-GGAAAGCGG----------ACAC-CAA------------------------------------------------------CCCGCU---ACGUCCGUGACAGGUCGCUA-------------------AG-----A--CCC--ACCGCC-GAAUG----------------CUUCC-UCAGUUCGGCGCU-C-U-GGA
AAVW01000046.1/19066-19196   GUCAGUAACUC--AG-----CCC----UAAA----GG-GA-----CU--GAGCUUGU---AAGAAAUU----ACAAG----------------------------------------------------------------------CUGUACUG--ACCAG-UCUAAGUC-----------UUAA-CU---------------------------------------------------------GACU---ACGUUUUU-------UGAGU-------------------CA-----C--GAC--ACCCUG-GAAUG----------------CGAAG-CCAGUUCCCUGCU-C-U-GUC
CP000812.1/1793370-1793247   GUCAACUACCC-GCCG-----CC----UAUAG--AGG-------CGG--GGGCUU-------GAAA--------AAG---------------------------------------------------------------------CCCUGAUUG--ACUAC-CCUCAGCCA---------CAUAA----------------------------------------------------------GUGGCU---ACGUUAGA--------CAGU-----------------------------UAC--ACCUUG-GGAUG----------------CUGCU-CAAGUUCCAGGCU-C-U-GUC
AADL01001579.1/3685-3521     GUCAACUACCC--C-----UCCC----UGAC----GG-AA------G--GGGCUUGUC--UCGUGAGG---AACAGC--------------------------------------------------------------------GCAAGAGUUG--AUUAG-GGGGCUUU-----------AAAA--ACAUGGAGAAA-----------------------------------CAUAUGAAAGA-GAAGCAGAAGUUAGA-------UAGGA-------------------GAGAUACAUACAC--ACCUAC-GGAUG----------------CUCCA-CAAGUCCGUGGCAAC-U-GUG
CP000412.1/64523-64713       GUCAAUGGUAACAC-------CUU-ACUGAAG-UAAG--A------G----ACCUGAA--GCGCAAGC---UUCAGGUCUCUUAUCUUUAGCAGG---------------------------------GAAGCUGGGGAAAUCCAGCUUUCAUUG--UCUAG-ACUAAGCAAUCCAGUCGGCUUCG---GCCAA----------------------------------------------CAGGAUUGCU---ACGUUAUC-------CAUGU--------------------A-----U--CAC--ACCCAA-GGAUG----------------AUGCC-CAAAUCUUUGGCU-C-U-GUG
CR954253.1/66072-66262       GUCAAUGGUAACAC-------CUU-ACUGAAG-UAAG--A------G----ACCUGAA--GCGCAAGC---UUCAGGUCUCUUAUCUUUAGCAGG---------------------------------GAAGCUGGGGAAAUCCAGCUUUCAUUG--UCUAG-ACUAAGCAAUCCAGUCGGCUUCG---GCCAA----------------------------------------------CAGGAUUGCU---ACGUUAUC-------CAUGU--------------------A-----U--CAC--ACCCAA-GGAUG----------------AUGCC-CAAGUCUUUGGCU-C-U-GUG
ABYK01000016.1/74467-74328   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCCC------------------------------------------------------CCGCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCU-CAU-GAA
AADL01001529.1/2525-2361     GUCAACUACCC--CCA-----GC----UCAC----GC--A-----GG--GGGCUUGUU--CCGUGAGG---GACAAC--------------------------------------------------------------------ACAAGAGUUG--AUUAG-GGGGCUUU-----------AAAA--ACAUGGAGAAA-----------------------------------AACAUGAAAGA-AAGGCAGAAGUUAGA-------UAGGA-------------------GAGAUACAUACAC--ACCUGC-GGAUG----------------CUCCA-CAAGUCCGUGGCAAC-U-GUG
ABYK01000042.1/23793-23932   GUCAGC-ACCC--CCG-----CC----UGAA----GC--A----CGG--GGGCUUCGU--GCCUCCCGCAACAGAA-------------------------------------------------------------------------UAGCUG--ACCAG-CUAUAGCC-----------GUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG----------------CGU-G-CUAGUUCCCGGCU-C-UAGAA
AAVU01000052.1/32776-32634   GUCAGC-ACCC--CG-----CUC----UAAA----GA-GA-----CG--GGGCAUC---------------------AUGCUUC-------------------------------------------------------UCUUUUUAGGUAGCUAGUACCCG-CCUAAGUCC----------CUUG-A---------------------------------------------------------GGGCU---ACGUUAUCGGC-AAGAGUUA-------------------AC-----G--UUCCGACCCGG-AGAUG-----------------CGUGGCCAGUCUCCGGCU-C-UAGAA
ABRS01000056.1/117550-117415 GUCAACAACCC-ACCA---CUGAC-CCUAGGG-GUACAG-----UGG--GGGCUU-------GAAAG------AAAG---------------------------------------------------------------------CCCUAGUUG--ACCAG-UCUAAGUAC----------UUUU-----------------------------------------------------------GUACU---CCGUUUUU-------UGAGU-------------------CA-----A--GAC--ACCUAC-AAAUA----------------CGACG-CCAGUUUGUUGCU-C-U-GUC
AAXY01000019.1/51520-51664   GUCAACUACCC--C-----GCCC----UAAA----GGAC-------G--GAGCUUGUA-GAGAACACCC--UGCAAG----------------------------------------------------------------------CCAGGUUG--ACCAG-GGAAAGUGG----------ACAC-CAA------------------------------------------------------CCCGCU---ACGUUUAU-------CACAGGUC------------GCUAAG-----A--CUC--ACCGCC-GAAUG----------------CUUCC-UCAGUUCGGCGCU-C-U-GAA
ABYK01000004.1/65195-65058   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CAG--GGGCUUC---------------------GUGCCC--------------------------------------------------------CCCUUUCAGGUAGCUG--ACCAG-CCUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCC-C-UAGAA
CP000879.1/1130450-1130638   GUCAACUACCC-ACCG-----UC----UAAA----GA-------CGG--GGGCUU-------GCAA--------AAG---------------------------------------------------------------------CCUUAGUUG--ACUAC-CCUCAGCC-GAU----UGAAGAAACGGGCUUCCGCCUCUUAAGGAAGAAGAAACGGGCUCACGCCUCUAAAGGAAGAUCAUCGGGCU---ACGUUAUA-------UAGGU-------------------CA-----U--AAC--ACCUUC-GGAUG---------------UUUCUC-CUAGUCUGUCGCU-C-U-GUU
CP000879.1/1238841-1239005   GUCAACUACCC-ACCG-----UC----UAAA----GA-------CGG--GGGCUUG-----UGAUGA-----ACAAG---------------------------------------------------------------------CCUUAGUUG--GCUAC-CCUCAGCCGUA-----UGAAGAAACGGGCUUCCAUCUCU-----------------------------AAAGGAAGAUCAUCGGGCU---ACGUUAUA-------UAGGU-------------------CA-----U--AAC--ACCUUC-GGAUG---------------UUUCUC-CUAGUCUGUCGCU-C-U-GUU
ABYK01000060.1/10738-10876   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCCC-------------------------------------------------------CGCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG----------------CGU-G-CUAGUUCCAGGCU-CAU-GAA
CP000530.1/245182-245324     GUCAAUCACCC--C-----ACCC----UGAA----GGGU-------G--GAGCUUGCG--GAGAAAUCC--AAAAAG----------------------------------------------------------------------CUAGGUUG--ACCAG-GGUA-GUGG----------UAGC-CAA------------------------------------------------------UCCACG---GCGUUAAU-------AACAGGUC------------CUUCAG-----A--CAC--ACCAGU-GAGUG----------------CUUCC-UCAGCUCGCUGCU-C-U-GUA
ABRS01000116.1/126537-126395 GUAAACUACCC-GCCGCUAAGUCG--GAGUAC--CGACUCU-AGCGG--GGGCUUU------UAAA-------GAAGC-------------------------------------------------------------------AAGCGAGUUU--ACCAG-GCUGAGUG-----------UUAA-UU---------------------------------------------------------CACU---ACGUUACG-------AAAGU-------------------CA-----A--GAU--ACCUAA-GAAUG----------------CGUAG-CCAGUUUUUAGCU-C-U-AUC
CP000119.1/70899-70759       GUAAACAACCC-ACCACCAAUUAU--UGCUAAGAGCAAUAU-GGUGG--GGGCUUU---------------------UAA---------------------------------------------------------------AGCCCAAAGUUU--ACCCG-ACUAAGUG-----------UUAA-AU---------------------------------------------------------CACU---ACGAUUUU-------UAGGU-------------------CA-----U--CCU--ACCUGC-AAAUG----------------CGUAG-CCAGUUUGUAGCU-C-U-AGG
CP000807.1/298700-298834     GUCACGAACCC-ACCA---CUAAU-CCAGUAG-GUAUAG-----UGG--GGGCUUG------AAAAGC----CCAAG-------------------------------------------------------------------------ACGUG--ACCAG-ACUAAGGUU----------CUAG-A---------------------------------------------------------AACCU---ACGUUAUU-------UGAGU-------------------CA-----A--GAC--ACCUUG-AGAUG-----------------CGUG-CCAGUCUCACGCU-C-U-GUC
CP000975.1/2021163-2021303   GUCAACCACCC--CCG-----AC----UGAA----UU-------CGG--AGGCUUGC----CUUACGG----CCAUG---------------------------------------------------------------------CCUGGGUUG--ACAAG-GAAAAGCGG----------UACC-CAA------------------------------------------------------CCCGCU---GCGUUGCAA----GGAGUAG-------------------AGGAGACC--CUC----GUCG-GGAUG----------------CUUCC-UCAGUCCCGACCU-C-UAGAA
AAXY01000015.1/18509-18653   GUCAACUACCC--C-----GCCC----UGAA----GGAC-------G--GGGCUUGU---AGAAAACACCCUGCAAG----------------------------------------------------------------------CCAGGUUG--ACCAG-GGAAAGCGG----------ACAC-CAA------------------------------------------------------UCCGCU---ACGUUUAUCACAGGUCGCUA-------------------AG-----A--CCC--ACCGUC-GAAUG----------------CUUCC-UCAGUUCGGCGCU-C-U-GGA
CP000879.1/839931-839787     GUCAACUACCC--CCG-----UC----UAAA----GA-------CGG--AGGCUU-------GAAG--------CCU----------------------------------------------------------------------CGGAGUUG--ACCAG-CCUAAGUUC----------GAAGACAGCCUCACGG-------------------------------------CAAAUUUGAAGAACU---ACGUUAUU-------CUGGU-------------------CA-----U--GAC--ACCUUG-GAAUG---------------CUGGAG-CCAGUUCCAAGCC-C-U-GUC
AAVW01000110.1/2377-2512     GUCAGAAACCU--CA-----GUC----UAAA----GG-CA-----UG--AGGCUUGAA-AGAGAAAUCU--AGCAAG----------------------------------------------------------------------CCGUUCUG--ACCAG-CCUCAGCAC----------UUCA-A---------------------------------------------------------GUGCU---AUGUUUUU-------UGAGU-------------------CA-----C--GAU--ACCGGA-GGAUA----------------CGUAG-CCAGUCUUCCGCU-C-U-AUC
AAXY01000028.1/17319-17175   GUCAACUACCC--C-----GCCC----UAAA----GGAC-------G--GGGCUUGUA-GAGAACACCC--UGCAGG----------------------------------------------------------------------CCAGGUUG--ACCAG-GGAAAGCGG----------UAAC-CAA------------------------------------------------------CCCGCU---ACGUUUAUCACAGGUCGCUA-------------------AG-----A--CUC--ACCGCC-GAAUG----------------CUUCC-UCAGUUCGGCGCU-C-U-GGA
AADL01000696.1/2135-1993     GUCAACCACCC--C-----GCCC----UGAA----GGGC-------G--GAGCUUGA----AAGGAGGUUCGACAAG---------------------------------------------------------------------CUCGGGUUG--ACCAG-GGAAAGCGG----------UACC-CAA------------------------------------------------------CCCGCU---ACGUUGGC-------AACAGG----------------UACA-----AGACCC--ACCCCG-GGAUG----------------CUUCC-UCAGUCCCGGGCU-C-U-GGA
AADL01001522.1/10871-11035   GUCAACUACCC--CCA-----GC----UCAC----GC--A-----GG--GGGCUUGUU--CCGUGAGG---AACAGC--------------------------------------------------------------------GCAAGAGUUG--AUUAG-GGGGCUUU-----------AAAA--ACAUGGAGAAA-----------------------------------AACAUGAAAGA-AAGGCAGAAGUUAGA-------UAGGA-------------------GAGAUACAUACAC--ACCCAC-GGAUG----------------CUCCA-CAAGUCCGUGGCAAC-U-GUG
AADL01001518.1/40322-40159   GUCAACUACCC-C------UCCC----UAAC----GG-AA---------GGGCAUGUC--CCGUGAGG---AACAGC--------------------------------------------------------------------GCAAGAGUUG--AUUAG-GGGGCUUU-----------AAAA--ACAUGGAGAAA-----------------------------------AACAUGAAAGA-AAGGCAGAAGUUAGA-------UCGGA-------------------GAGAUACAUACAC--ACCUGC-GGAUG----------------CUCCA-CAAGUCCGUGGCAAC-U-GUG
ABYK01000029.1/51480-51617   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCC--------------------------------------------------------CCCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---CCGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCCACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCC-C-UAGAA
AAVU01000004.1/134372-134232 GUCAGC-ACCC--CG-----CUC----UAAA----GA-GA-----CG--GGGCAUC---------------------AUGCCUC-------------------------------------------------------UCUUUUUAGGUAGCUG--ACCAG-CCUAAGUCC----------CUUG-A---------------------------------------------------------GGGCU---ACGUUAUCGGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-AGAUG-----------------CGUGGCCAGUCUCCGGCU-C-UAGAA
ABYK01000062.1/4012-3875     GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCC--------------------------------------------------------CCCUUUCAGGUAGCUG--ACCAG-CUAUAGCC-----------UUAA-CU---------------------------------------------------------GGCU---CCGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCC-C-UAGAA
AAXY01000023.1/15773-15628   GUCAACUACCC--C-----GCCC----UAAA----GGAC-------G--GGGCUUGUU--AGAGAACACCCUGCAAG----------------------------------------------------------------------CCAGGUUG--ACCAG-GGAAAGCGG----------ACAC-CAA------------------------------------------------------CCCGCU---AUGUUUAU-------CACAGGUC------------GAUAAG-----A--CUC--ACCGCC-GAAUG----------------CUUCC-UCAGUUCGGCGCU-C-U-GGA
AACY021009484.1/304-452      GUCAGCGACCC--CCG-----GC----UAAA----GC-------CGG--GAGCUU-------GUAA--------AGG---------------------------------------------------------------------CUCAUGCUG--ACCAG-CCUAUGUCUG--------CUUAA---G------------------------------------------------------CAGACG---CCGUUAC--------GGGUGAAUGGCAACCAUAGGUUGCU-UG-AUA--GGC--ACUCCG-GGGUG---------------ACUGAA-CCAGCCCCGGACC-C-U-GCG
ABYK01000036.1/23269-23408   GUCAGC-ACCC--CCG-----GC----UGAA----GC--A----CGG--GGGCUUC---------------------CUGCCCC------------------------------------------------------CCGCUUUCAGGUAGCUG--ACCAG-UUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---ACGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCA-C-UAGAA
AAVU01000002.1/65829-65969   GUCAGC-ACCC--CG-----CUC----UAAA----GA-GA-----CG--GGGCAUC---------------------AUGCUUC-------------------------------------------------------UCUUUUUAGGUAGCUG--ACCAG-CCUAAGUCC----------CUUG-A---------------------------------------------------------GGGCU---ACGUUAUCGGC-AAGAGUUA-------------------AC-----G--UUCCUACCCGG-AGAUG-----------------CGUGGCCAGUCUCCGGCU-C-UAGAA
ABYK01000039.1/3944-4081     GUCAGC-ACCC--CCG-----AC----UGAA----GC--A----CGG--GGGCUUC---------------------GUGCCC--------------------------------------------------------CCCUUUCAGGUAGCUG--ACCAG-CUUAAGCC-----------UUAA-CU---------------------------------------------------------GGCU---CCGUUCAGAGC-AAGAGUUA-------------------AA-----G--UUCCUACCCUG-GAAUG-----------------CGUG-CUAGUUCCAGGCU-CAU-GAA
CP002198.1/4111013-4110884   GUCAGC-ACCC--CG-----CGC----UAAA----GC-GA-----CG--GGGCAUC------------------AUGCCUCU-----------------------------------------------------------CCUUUAGGUAGCUG--ACCAG-CCUAAGUC-----------UUAG-CU---------------------------------------------------------GACU---ACGUUAGA-------UAAGU-------------------CA-----C--GAC--ACCCUA-GAAUG----------------CGUUG-CUAGUUCUCGGCU-C-U-GUC
CP001791.1/3062759-3062884   GUCAACAACCC-AACG-----AC----UAAA----GU-------CGU--GGGCUU-------GUAA--------AAG---------------------------------------------------------------------CCCCUGUUG--ACUAG-CCUAAGUCU----------UUCG-A---------------------------------------------------------GGACU---ACGUUGGA-------UUGGU-------------------CA-----C--GAC--ACCUUA-CGGUG---------------CGGAUU-CUAGCUGUAAGCC-C-U-GUC
CP001791.1/2931567-2931692   GUCAACAACCC-AACG-----AC----UAAA----GU-------CGU--GGGCUU-------GUAA--------AAG---------------------------------------------------------------------CCCCUGUUG--ACUAG-CCUAAGUCU----------UUCG-A---------------------------------------------------------GGACU---ACGUUGGA-------UCGGU-------------------CA-----A--GAC--ACCUUA-CGGUG---------------CGGAUU-CUAGCUGUAAGCC-C-U-GUC
CP002198.1/5933639-5933792   GUCAGC-ACCC--CGC-----AC----UGAA----GU--U----GCG--GGGCUAG------GCUACG----CCUCGCUGCGCGCCCGUG-------------------------------------------CCCCCCCCGUUUCAGUUAGCUG--ACCAG-CCUAAGUC-----------UUAA-AU---------------------------------------------------------GACU---ACGUUUUU-------AAGGU-------------------CA-----U--AAU--ACCUAC-GAAUG----------------CCUCG-CUAGUUCGUAGCU-C-U-AUU
CP001791.1/589528-589653     GUCAACAACCC-AACG-----AC----UAAA----GU-------CGU--GGGCUU-------GUAA--------AAG---------------------------------------------------------------------CCCCUGUUG--ACUAG-CCUAAGUCU----------UUCG----------------------------------------------------------AGGACU---ACGUUGGA-------UCGGU-------------------CA-----A--GAC--ACCUUA-CGGUG---------------CGGAUU-CUAGCUGUAAGCC-C-U-GUC
#=GC SS_cons                 (((((((,<<<.-<<<....-<<....____....>>.--....>>>..>>><<<_......____......._>>>....................................................................,,,,,)))))..)),,,.,,,,<<<<<..........____._........................................................_>>>>>...,,,,,,,,.......,,,,,...................,,.....,..<<<..<-<<<<.<<<<_................_____.___>>>>>>>>--.-.>.>>>
#=GC RF                      GUCAacuACCC.aCcg....ccc....UaAA....gg.uA....cgG..GGGCuUg......GaAA.......cAaG....................................................................cccuuaguUG..ACcAG.ccUaaGccc..........uuAa.c........................................................agggCu...ACGUUAuu.......uguua...................aA.....a..cgC..ACCcug.gGAUG................cuuug.CcAGUCccagGCU.C.U.Gcg
//
# STOCKHOLM 1.0

#=GF AC   RF02034
#=GF ID   IMES-1
#=GF DE   IMES-1 RNA motif
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:12376536; Weinberg Z
#=GF SS   Published; PMID:12376536; Weinberg Z
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   38.30
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19956260
#=GF RT   Exceptional structured noncoding RNAs revealed by bacterial metagenome
#=GF RT   analysis.
#=GF RA   Weinberg Z, Perreault J, Meyer MM, Breaker RR
#=GF RL   Nature. 2009;462:656-659.
#=GF WK   IMES-1_RNA_motif
#=GF SQ   219


ABEF01019263.1/859-1058   UCUCAAGAGACCGAUCG--GAAGGUGAGUGCAGAAACCGAA-----AGAAGAGUC-----GAAAA-GAGAAAGAGAC-C-UAAAGGGUGAAA-GCGAA--GACGGCUG------GAGAAGCUAGCAAUAACAAAAGCCGAC----UCCCACCAAACUCGAAAAGAGAAA-UCGAGUAAGG-AGCUGAAGAAAAAAUCUCA-CUUCAGAC-ACCUAAAGGA-CUCGA-CU-------GAGAA
ABEF01054392.1/547-746    UCUCAAGAGACCGAUCG--GAAGGUGAGUGCAGAAACCGAA-----AGAAGAGUC-----GAAAA-GAGAAAGAGAC-C-UAAAGGGUGAAA-GCGAA--GACGGCUG------GAGAAGCUAGCAAUAACAAAAGCCGAC----UCCCACCAAACUCGAAAAGAGAAA-UCGAGUAAGG-AGCUGAAGAAAAAAUCUCA-CUUCAGAC-ACCUAAAGGA-CUCGA-CU-------GAGAA
AACY022471452.1/369-178   AGAC----GACCGACUAGUGAC--CAACUGCAGA-C-GGAAU-ACCUAGAGAGAA-----G-UUA-GAGGGAGAGGC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAAAUCCACCAAG-GAUUCAAGAGAAAGGAUC-CAAGG-AGCUGAAG--AGAAUCUCG-CUUUAGAC-CCCUG-AGGAACUCGAUU------AAAGAAA
AACY020518344.1/736-548   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY020081936.1/1243-1051 GUAAC---GAG-AACUGG-AAAGGAACUGCAGAAC-CAAAG--AA-AGGAAACG------U-UACACAGGAAGAGACCU-GAA-GGGUGAAA-GUUCAAGAGAGCUUA--------GCAUG---CAAAA-----AAGCAAA-CUUGACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAAGAG--GUAAUCUCA-CUUUUGACACCCA--CAGAUCUCGAUUU---AUAAAAA--
AACY020520186.1/173-363   CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGUUAUUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-AUAACCCACCAAG-AAGGAAAGAGAAAGCCUU-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGACACCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY020434238.1/1656-1856 --UCUUGAGACCGACCC--GAAAGUAACUUAAGA-CGCGGAA----GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCGG-----GGAAGAUAAGCUAGCAGCAAAAAGGAA-----CC-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAAAAA
AACY023560009.1/1255-1063 AGGU----AACCGACUAGUGAC--CAACUGCAGA-CGGAAAA-AUCUAGAGAGAA-----G-CCA-GAAGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUACAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-UAAAUCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAA-UCGAACU-----AAGAAAA
AACY021360501.1/671-478   UAAU----UUUCGACUAGUGAC--CAACUGCAGA-CGGAAGA-UCCUAGAGAAAA-----A-UUA-AAGGAAGAGAC-C-AAA-GGGUGAAA-GCAUUUAUAAG---A--------GUCGAUGAUAAAAAACAG---CUUA-UAAAUCCACCAAG-AAUACAAGAGAAAGUAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGACCUCGAAUU-----AAAGAAA
AACY023108695.1/288-100   CGGA----GACCGAUAAGCGAA--CAACUGCAGA-C-GGGA--AC-UUAAGAGAA-----A-CCG-AAAGGAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-ACCUG-GGGAACUCGAACU------AAGAGA
AACY020563142.1/274-459   -----UU-AUCCGAUCCGGAAA--CAACUCGAGA-C-GGGAG-AA-GGAAGAGAU-A-AAA-AAG----UUAGAGAA-C-GGA-AGGUGAAA-GCUCUAAUAAA---G--------AAAGGUACCAAAAAAA-----UUUA-UUAGACCACCAAG-AUCAAAAGAGAAAUUGAU-CAAGG-AGCUAGAAGAAAAAACUCAACUCUAGAC-ACUUU-CGAA-CUCGAACU---------AAA
AACY020261033.1/1902-1710 CAGC----AACCGACUAGUGAC--CAACUGCAGA-CGGGAG--ACCUAGAGAGAA-----G-CUG-AAGGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUACAAG---A--------GUCGGCGAUAAAAAAGAG---CUUG-UAAAUCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGAACU-----AAGAAAA
AACY021602364.1/284-94    CGAC----AACCGACCAGGGAC--CAACUGCAGA-CGGAGA--AC-UGGAGAGAA-----A-GCG-AAGGAAGAGCC-C-UCA-GGGUGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-GAUGGA-GAGAUAGCAUC-CAAGG-AGCUAAAG-AGAAAUCUCA-CUUUAGAC-ACCUG-GGGAACUCGAAUG------AAAAGA
AACY020558761.1/896-1086  ----ACGAAACCGACUAGGGAC--CAACUGCAGA-CGGAGA--AC-UAGAGAGAAU-CGAA-AGG-----AAGAGUC-C-GAA-GGGCGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUUAAG--AGAAUCUCA-CUUAAGAC-CCCUU-CGAAACUCGGAUU------AGAAGA
AACY023210574.1/1309-1501 CUUGA---UUCCGACUAAAGAA--CAACUGCAGA-C-GGGA--CU-UAGAGAGAA----GC-AAG-AAGGUAGAGCC-C-AUA-GGGAGAAA-GCGUUUAUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-UAAACCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCCGGAG--AAAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACU-----AAAGAAA
AACY020013406.1/1516-1706 UCGC----AUCCGACUAAAGAC--CAACUGCAGA-C-GAGA--AU-UAGAGAGAG-----A-ACA-UAGAAAGAGAC-C-UGA-GGGUGAAA-GCGUUUUUAAG---A--------GUCGACGAUAAAAAAGAG---CUUAAAAAACCCACCAAG-AAUUCCAGAGAAAGAAUU-CAAGG-AGCUAGAG--AGAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGAACU------GAAGAA
AACY022815106.1/434-622   UGAG----GACUGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGGGAA-----A-UCA-UAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------GAAAGA
AACY022454024.1/377-190   CCGA----AACCGACUUGGAAA--CAACUGCAGA-C-GGGA--AC-AAGGGAGAA-----U-CGG-AAGGAAGAGAC-C-AAA-GGGAGAAA-GCGUUUCUAAG---A--------GUCGAUGAUAAAAAAUAG---CUUA-GAAACCCACCAAG-GAAAUCAGAGAAAAUUUC-CAAGG-CGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGACCUCGGACU--------AAGA
AACY022023721.1/693-505   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY022177340.1/325-125   --UCUUGAGACCGACCC--GAAAGUAACUUAAGA-CGCGGAA----GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCGG-----GGAAGAUAAGCUAGCAGCAAAAAGGAA-----CC-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY020278482.1/268-81    AAUU----AUCCGAUCUGGAAA--CAACUCGAGA-CGGUAG--AA-AGAAGAGAU-----A-AAU-AAGUUAGAGAA-C-GAA-AGUAGAAA-GCUCUAAUAAA-------------UAAAGGUACCAAAAAAA---UUUA-UUAGACCACCAAG-AUUAAAAGAGAAAUUAAU-CAAGG-CGCUAAAAGAAAAAACUCAAUUUUAGAC-ACUUU-CGAA-CUCGAACU---------AAA
AACY023647313.1/640-449   CUUGA---UUCCGACUAACAAU--CAACUGCAGA-C-GGGA--GU-UAGAGAGGU-----C-AAG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUAUUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AGUUCAAGAGAAAGAACU-CAAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-AGGAACUCGAACUU----AAAGAA-
AACY020934089.1/290-481   UGGC----AACCGACUAGUGAC--CACCUGCAGA-CGGGAA--ACCUAGGGAGAA-----G-CCA-GACGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGGUU------GAAGAAA
AACY020047544.1/1332-1523 UUGA----UUCCGACUAAAGAA--CAACUGCAGA-C-GGGA--CU-UAGAGAGAA-----UAAAG-GAGGUAGAGCC-C-AUA-GGGUGAAA-GCGUUUGUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-UAGACCCACCAAG-AAUUCAAGAGAAAGAAUU-CGAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACU-----AAAGAAA
AACY023857006.1/974-786   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY020131047.1/1711-1523 CUGA----AACCGACCAGGGAC--CAACUGCAGA-C-GGGA--GC-UGGAGAGAA-----U-CAG-AAGGAAGAGAC-C-GAA-GGGCGAAA-GCGUUACUAAG---A--------GUCGACGAUAAAAAAUAG---CUUA-GUGACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-CCCUU-CGAACCUCGACCU-------AAGAA
AACY023090540.1/689-501   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY020497314.1/2712-2905 GGUA----ACAAGAACU-GGAAAGGAACUGCAGAAC-CAAAG-AA-AGGAAAUGU-----U-ACA-CAGGAAGAGACCU-GAA-GGGUGAAA-GUUCAAGAGAGCUUA--------GCAUG---CAAAA-----AAGCAAA-CUUGACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAAGAG--GUAAUCUCA-CUUUUGACACCCA--CAGAUCUCGAUUU----AAAAGAA-
AACY023923153.1/478-288   CUGA----AACCGACUGAUGAC--CAACUGCAGA-C-GGAU--AUUUAGAGAGAA-----U-UAG-UAGUCAGAGCA-C-GAA-AGGAGAAA-GCGUUACUAAG---A--------GUCGACGAUAAAAAAUAG---CUUA-GUAGCCCACCAAG-AGGGAAAGAGAUAACCCU-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-CCUUU-CGUAUCUCGAAUU------AUAAAA
AACY023681261.1/1134-952  UCCG----AGCAGA-----AAA--CAACUCGAGA-C-GGAAG-AA-AGCAGAGAG-----A-GGA-UGAAUAGAGUA-CGGAA-GG-UGAAA-GCUCUAGAAAA---A--------AAAGGUACCAAAAAA--G---UUUU-CUAGACCACCAAGAUCUAAAAAGAAGAAUAGAUCAAGG-AGCCUGAA--AGUCUUCAA-GUCAGGAC-ACUUU-CGAA-CUCGAAACU--------AAA
AACY021830390.1/280-480   --UCUUGAGACCGACCC--GAAAGUAACUUAAGA-CGCGGAA----GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCGG-----GGAAGAUAAGCUAGCAGCAAAAAGGAA-----CC-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY020382539.1/2-193     UGGC----AACCGACUAGUGAC--CAACUGCAGA-CGGAAAA-UC-UAGAGAGAA-----G-CCA-GAAGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAGG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAAAUCCACCAAG-GGUUCAAGAGAAAGAAUC-CAAGG-AGCUGAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAA-UCGAACU-----AAGAAAA
AACY020001324.1/3130-3322 CUUGA---UUCCGACUAAAGAA--CAACUGCAGA-C-GGGA--CU-UAGAGAGAA-----UAAAG-AGGGUAGAGCC-C-AUA-GGGUGAAA-GCGUUUGUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-UAAACCCACCAAG-AAUUCAAGAGAAAGAAUU-CGAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACU-----AAAGAAA
AACY020395327.1/242-430   CGGG----GACUGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACAAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAGAG--AGAAUCUCA-CUCUAGAC-ACCUG-GGGAACUCGAACU------AAGAGA
AACY020375769.1/2794-2606 UGAG----GACUGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGGGAA-----A-UCA-UAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAGACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------GAAAGA
AACY023483054.1/325-516   CAGU----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAG-AUCUAGAGAGAA-----G-CUG-AAGGAAGAGCC-C-AAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGAUU------GAAGAAA
AACY020048942.1/1256-1072 ACCG---------ACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGUAACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUGACCCACCAAG-GAGGCAAGAGAAAACCUC-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY022739624.1/644-453   UGGC----AACCGACUAGUGAC--CACCUGCAGA-C-GGGAG-ACCUAGGGAGAA-----G-CCA-GACGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGGUU------GAAGAAA
AACY023656333.1/615-807   CAGC----AACCGACUAGUGAC--CAACUGCAGA-CGGGAG--ACCUAGAGAGAA-----G-CUG-AAGGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUACAAG---A--------GUCGGCGAUAAAAAAGAG---CUUG-UAAAUCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGAUCU-----AAGAAAA
AACY023724622.1/569-760   CUUGA---UUCCGACUAACAAU--CAACUGCAGA-C-GGGA--GU-UAGAGAGGU-----C-AAG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GCAACCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACUU----AAAGAA-
AACY022102568.1/183-374   CAAC----GACCGACUAGUGAC--CAACUGCAGA-C-GGAAU-ACCUAGAGAGAA-----G-UUG-GAGGAAGAGGC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-UAAGG-AGCUAGAG--AGAAUCUCG-CUUUAGAC-CCCUG-AGGAACUCGAUU------AAAGAAA
AACY020504103.1/227-35    CAGC----AACCGACUAGUGAC--CAACUGCAGA-CGGGAG--ACCUAGAGAGAA-----G-CUG-AAGGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUACAAG---A--------GUCGGCGAUAAAAAAGAG---CUUG-UAAAUCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGAACU-----AAGAAAA
AACY024081192.1/860-672   ACGA----AACCGACCAGCAAG--CAACUGCAGA-C-GGGA--GC-UGGGGAGAA-----U-CAG-GAGGAAGAGAC-C-GAA-GGGCGAAA-GCAUCACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUGAACCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-CCCUU-CGAAACUCG-UUU------GAGAAA
AACY022727350.1/375-559   AUCA----GACCGACUUGGAAA--CAACUCGAGA-C-GAAG--AA-AAGGGGGGA-----A-GAU-AGGUUAGAGAA-C-GGA-AGGUGAAA-GCUCUAAAAAAC--A--------GCUAG---CAAAAAAA----GUUUU-UUAGACCACCAAG-GUUGGAAGAGAAACCAAC-CAAGG-AGCUAAAC--AGAAUCUCG-GUUUAGAC-ACUUU-CGAA-CUCGAACU-------AAAGA
AACY021450808.1/557-745   CGGG----GACUGACGCGCAAC--CAACUGCAGA-C-GGGA--GC-GGGGGGGAA-----A-CCG-GAGGAAGAGUG-C-UCA-GGUAGGAAAGCGUAGCGAAG---A--------GCCGGCA-CAAAUAGCA----GUUC-GCUACCCACCGAG-GGUGAA-GGGAUACCACC-CGAGG-GGCCAGAC--GGAAUCCCG-GUCUGGAC-GCCUG-AGAGGCUCGAAAC-----AGAAAGA
AACY020934089.1/592-783   UGGC----AACCGACUAGUGAC--CACCUGCAGA-CGGGAA--ACCUAGGGAGAA-----G-CCA-GACGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGGUU------GAAGAAA
AACY020378071.1/737-925   CGGG----GACUGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACCUG-GGGAACUCGAAUU------GAAAGA
AACY020592008.1/386-574   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------GAAAGA
AACY024099317.1/364-173   CGGU----AACAGACUA-AGAAGGGAACUGCAGAACCCAAA--U--UAGAAAGAA-----A-CCA-CAGGCAGAGAACA-GAA-GGGUGAAA-GUUCAAGCAAGCU-A--------GCCGG---CAAAAA-----AGCAAA-CUUGACCACCAAG-GAUAAAAGAGAUCUUAUC-CAAGGAUGCAAAAG--AUAAUCUCA-CUUUUGACACCCA--CUGAUCUCGAACUU---AAAGAA--
AACY022312667.1/431-619   AUCG----GACUGACUUACAAU--CAACUGCAGA-C-GGGA--GU-AGGAGAGAA-----A-GAG-GAGGAAGAGAC---GAA-GGGUGAAA-GCGAUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-GAGGAAAGAGAAAGCCUC-UGAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CUAAUCUCGAUUG------AAAAGA
AACY024079769.1/362-162   --UCUUGAGAUCGACCCGGAAG--UAACUUAAGA-C-GCAG--AA-GGGAGAGUCGAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCAG-----GGAAGAUAAGCUAGCAGCAAAAGAGAA-----CU-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY020430362.1/75-267    -AGAU---AACUAGAUAGGAAAAGGAACUGCAGAACCUAGA--AC-UAGAAAGUU-----A-CUC--AGGAAGAGACCA-GAA-GGGUGAAA-GUUUAAGGUAGCUCA--------GUCGA---CAAUA-----GAGUAAA-CUUAACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAGAAG--GUAAUCUCA-CUUUUGACACCCA--CUGUUCUCGA-U-----AAGAAAAA
AACY020504287.1/1209-1400 AGGC----AACCGACUAGUGAC--CAACUGCAGA-CGGAAAA-UC-UAGAGAGAA-----G-CCA-GAAGAAGAGAC-C-GAA-GGGCGAAA-GCAUUUACAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-UAAAUCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAA-UCGAAUU-----AAGAAAA
AACY020435716.1/2254-2062 -AGAU---AACUAGAUAGGAAAAGGAACUGCAGAACCUAGA--AC-UAGAAAGUU-----A-CUC--AGGAAGAGACCA-GAA-GGGUGAAA-GUUUAAGGUAGCUCA--------GUCGA---CAAUA-----GAGUAAA-CUUAACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAGAAG--GUAAUCUCA-CUUUUGACACCCA--CUGUUCUCGA-U-----GAGAAAAA
AACY020900726.1/451-260   CAGU----AUCCGACUAGUGAC--CAACUGCAGA-C-GGAAG-ACCUAGAGAGAA-----G-CUG-AAGGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-CAAGUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGAUU------GAAGAAA
AACY023580016.1/695-883   CUCG----GACUGACCUACAAG--CAACUGCAGA-C-GGGA--GU-AGGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGUUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAGCCCACCAAG-GAGGAGAGAGAAGGCCUC-UAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAUUG------AAAAGA
AACY020561493.1/379-570   CAGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGGAG-ACCUAGAGAGAA-----G-CUG-AAGGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-CGGAA-UCGAUUU-----AAAGAAA
AACY023593210.1/311-502   ACGA----GACCGACUAGGGAC--CAACUGCAGA-CGGAGA--AC-UAGAGAGAA-----U-CGA-AAGGAAGAGUC-C-GAA-GGGCGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUGACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-CCCUU-CGAAACUCGGAUU-----AAGAAGA
AACY023999220.1/806-615   UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAA-ACCUAGAGAGAA-----G-CCA-GACGGAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAAGAGAAAGAGUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAA-UCGAUUU-----AAAGAAA
AACY020328778.1/925-735   ----AAGAAACCGACUAGGGAC--CAACUGCAGA-C-GGAAA-AC-UAGAGAGAAU-CAGA-GGG-----AAGAGUC-C-GAA-GGGCGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUUAAG--AGAAUCUCA-CUUAAGAC-CCCUU-CGAAACUCGGAUU------AGAAGA
AACY023216459.1/366-556   CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGUAGAGAC---GAA-GAGAGAAA-GCGAUACUAAG---A--------GUCGACAAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGCAAGAGAAUACCUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CUCUU-CUAAUCUCGAACUUU----AAGAAA
AACY020131266.1/823-639   AUCA----GACCGACUUGGAAA--CAACUCGAGA-C-GAAG--AA-AAGGGGGGA-----A-GAU-AGGUUAGAGAA-C-GGA-AGGUGAAA-GCUCUAAAAAAC--A--------GCUAG---CAAAGAAA----GUUUU-UUAGACCACCAAG-AUUGGAAGAGAAACCAAU-CAAGG-AGCUAAGC--AGAAUCUCG-GUUUAGAC-ACUUU-CGAA-CUCGAACU-------AAAGA
AACY022618134.1/803-612   UUGA----UUCCGACUAACGAU--CAACUGCAGA-CGGGAA--G--UAGGGAGAA-----UCGAA-GAGGUAGAGCC-C-AUA-GGGUGAAA-GCGUUUAUAAG---A--------GUCGGCGAUAAAAAAGAG---CUUA-UAAACCCACCAAG-AUUUCAAGAGAAAGAAAU-CAAGG-AGCUAGAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGAAUU-----AAAAAGA
AACY020224921.1/866-675   UGAC----GACUGACUAGUGAC--CAACUGCAGA-CGGGAA--AC-UAGGGGGAA----AG-UCA-AACGGAGAGAC-C-UAA-GGGUGAAA-GCAUUUGUAAG---A--------GUCGAUGUUAAAAAAUAG---CUUA-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAA-UCGAUUG-----AAAGAAA
AACY020392860.1/553-363   UGGC----AACCGACUAGAUAA--CAACUGCAGA-CGGGAU--AC-UAGAGAGAA-----G-CCA-AACGGAGAGAC-C-GAA-GGGAGAAA-GCAUUUACAAG---A--------GUCGGCGAUAAAAAAGAG---CUUG-UAGAUCCACCAAG-GGUUCAAGAGAAAGAACC-CAAGG-AGCUGAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAA-UCGAACU-----AAGAAAA
AACY024107103.1/304-115   CUCA----GACUGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGUUAUUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGGAAGAGAAAACCUU-CGAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----AAAAAGA
AACY020900726.1/763-572   UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAA-ACCUAGAGAGAA-----G-UCA-GACGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-CAAGUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGGUU------GAAGAAA
AACY022798897.1/177-365   CGGA----GACCGAUAAGUGAA--CAACUGCAGA-C-GGGA--AC-UUAAGAGAA-----A-CCG-GAAGGAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-ACCUG-GGGAACUCGAACU------AAGAGA
AACY020217031.1/301-113   UGAG----GACCGAUAAGAGAC--CAAAUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY023717221.1/282-471   CUGA----GACCGACUAACAAC--UAAAUGCAGA-C-AGAA--GU-UAGAGAGAA-----U-CAG-AAGGAAGAGAC-C-AGA-GGGAGAAAAGCGUUUCUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GAGACCCACCAAGGAAAUAA-GAGAAAAAUUUCCAAGG-AGCUAAAG--AAAUUCUCA-CUUUAGAC-CCCAA-AGGAACUCGAACU--------AAGA
AACY022952696.1/806-614   CUGGG---UGGGCACUAACAAU--CAACUGCAGA-C-GGGA--GU-UAGAGAGGU-----C-GAG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUGCUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAGCCCACCAAG-AGUUCAAGAGAAAGAACU-CAAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-UGGAACUCGAACUU----AAAGAAA
AACY023483054.1/10-201    UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAG-ACCUAGAGAGAA-----G-CCA-GCCAGAGAGAC-C-UAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CGAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGGUU------GAAGAAA
AACY023081900.1/722-910   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AAGAACUCGAACU------AAGAGA
AACY023604670.1/337-527   ----ACGAAACCGACUAGGGAC--CAACUGCAGA-C-GGAAA-AC-UAGAGAGAAU-CGAA-AGG-----AAGAGUC-C-GAA-GGGCGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUUAAG--AGAAUCUCA-CUUAAGAC-CCCUU-CGAAACUCGGAUU------AGAAGA
AACY023675129.1/393-582   CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGAUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGAAAGAGAAAACCUU-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY020399872.1/537-349   CGGA----GACCGAUAAGGGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY023529548.1/391-200   UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAA-ACCUAGAGAGAA-----G-CCA-AACGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CGAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGGUU------GAAGAAA
AACY020412681.1/486-686   --UCUUGAGAUCGACCUGGAAG--UAACUUAAGA-C-GCAG--AA-GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCAG-----GGAAGAUAAGCUAGCAGCAAAAGAGAA-----CU-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY022432296.1/519-709   ----ACGAAACCGACUAGGGAC--CAACUGCAGA-C-GGAAA-AC-UAGAGAGAAU-CGAA-AGG-----AAGAGUC-C-GAA-GGGCGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUUAAG--AGAAUCUCA-CUUAAGAC-CCCUU-CGAAACUCGGAUU------AGAAGA
AACY021219699.1/3-191     UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--UAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY020551096.1/199-15    AUCA----GACCGACUUGGAAA--CAACUCGAGA-C-GAAG--AA-AAGGGGGGA-----A-GAU-AGGUUAGAGAA-C-GGA-AGGUGAAA-GCUCUAGAAAAC--A--------GCUAG---CAAAAAAA----GUUUU-UUAGACCACCAAG-GUUGGAAGAGAAACCAGC-UAAGG-AGCUAAGC--AGAAUCUCG-GUUUAGAC-ACUUU-CGAA-CUCGAACU-------AAAGA
AACY022398967.1/792-602   CUUG----AACUGACCAGCAAC--CAACUGCAGA-C-GGAA--AC-UGGGGGGAA-----C-AAG-AAGGAAGAAGC-C-GAG-GGGCGAAA-GCGUUACUAAG---A--------GUCGAUGAUAAAAAAUAG---CUUA-GUAACCCACCAAGGAAAUAAAGAGAUA-AUUUCCAAGG-AGCUAGAG--AGAAUCUCA-CUUUAGAC-CCCUU-CGAACUUCGAACU------AAAAGA
AACY022380787.1/426-614   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY020109857.1/933-744   CGCA----GACCGACCAGGGAC--CAACUGCAGA-C-GAGA--AC-UGGAGAGAA-----A-GUG-AAGGAAGAGCC-C-UCA-GGGUGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-GAUGGA-GAGAUAGCAUC-CAAGG-AGCUAAAG-AGAAAUCUCA-CUUUAGAC-ACCUG-GGGAACUCGAAUG------AAAAGA
AACY020857154.1/618-426   CAGC----AACCGACUAAUGAC--CAACUGCAGA-CGGGAGA-CU-UAGAGAGAA-----G-CUG-GAGGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUACAAG---A--------GUCGGCGAUAAAAAAGAG---CUUG-UAAAUCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGAACU-----AAGAAAA
AACY023088657.1/661-461   --UCUCGAGACCGACCC--GAAAGUAACUUAAGA-CGCGGAA----GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCGG-----GGAAGAUAAGCUAGCAGCAAAAAGGAA-----CC-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----GAAGAAA
AACY021700335.1/535-348   CGGC----GACCGACGAGUGAC--CAACUGCAGA-C-GGGA--GC-GAGGGGGAA-----G-CCG-GAGGAAGAGUG-C-UCA-GGUAGAAAAGCGUGGCGAAG---G--------GCCGGC---ACAAACGCA---GUUC-GCUACCCACCGAG-GGUGAG-GGGAUACCACC-CGAGG-GGCCAGAU--GGAAUCCCG-GUCUGGAC-GCCUG-AGAGGCUCGAAUA-----AAAAAGA
AACY020427724.1/1141-1341 --UCUUGAGACCGACCC--GAAAGUAACUUAAGA-CGCGGAA----GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCGG-----GGAAGAUAAGCUAGCAGCAAAAAGGAA-----CC-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY020561667.1/5146-5340 AGAU----AACAAGAUCAGGAAAGGAACUGCAGAACCAAGA--AU-GAGAAAGUU-----A-ACU-UAGGAAGAGACCA-GAA-AGGUGAAA-GUUUAAGGAAGGUCA--------GCAUG---CAAAA-----GACCAAA-CUUAACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAGAAG--GUAAUCUCA-CUUUUGACACCUA--CUGAUCUCGAAUU----AAAAAAA-
AACY020101502.1/1162-974  UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AUGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGUUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY020146286.1/907-1089  AACA----GACCGACCCGGAAA--CAACUCGAGA-C-GAAG--AA-GGGAGAGAA-----A-GAU-AGGUUAGAGAA-C-GGA-AGGUGAAA-GCUCUAGAG-----G--------GAAGCUAGCAAAAAGAA------CU-CUAGACCACCAAGGCAGGAGAGAGAAA-CCGGCCAAGG-AGCUAAAC--AGAUUCUCA-GUUUAGAC-ACUUU-CGAA-CUCGAACU--------AAGA
AACY022982258.1/635-447   CUGA----AACCGACCAGGGAC--CAACUGCAGA-C-GAGA--GC-UGGAGAGAA-----U-CAG-GAGGAAGAGAC-C-GAA-GGGCGAAA-GCGUUACUAAG---A--------GUCGACGAUAAAAAAUAG---CUUA-GUGACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-CCCUU-CGAACCUCGACUU-------AAGAA
AACY021575514.1/864-676   CGGG----GACUGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-------CCGAAAGGAAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AGAAUCUCG-CUUUAGAC-ACCUG-GGGAACUCGAACU------AAGAGA
AACY020237302.1/2165-1981 CGGC----GACUGACGAGUGAC--CAACUGCAGA-C-GGAA--GC-GAGAGGGAA-----G-CCG-ACAGAAGAGUA-C-UCA-GGUAGAAA-GCGUGACAGAG---G--------GCCGGC-AUAGAA-AGCG---CUUU-GUUGCCCACCGAG-GACGGA-GGGAUAGCGUC-CGAGG-AGCUGAAG-GAAAGUCCCA-CUUCAGAC-GCCUG-AGGAACUCGAAC--------AAAA-
AACY023462828.1/265-74    UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAG-ACCUAGAGAGAA-----G-CCA-AACGAAGAGAC-C-UAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CGAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGGUU------GAAGAAA
AACY020218726.1/142-335   AGAU----AACCAGAUCGGAAAGGGAACUGCAGAACCCAGA--AC-GAGAAAGUU-----A--CU-CAGGAAGAGACCA-GAA-AGGUGAAA-GUUCAAGGUAGCUUA--------GCAUG---CAAAA-----AAGCAAA-CUUGACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAGAAG--GUAAUCUCA-CUCCUGACACCUA--CUGAUCUCGAUUU----GAAAAAA-
AACY020444567.1/1265-1065 --UCUUGAGACCGACCUGGAAG--UAACUUAAGA-C-GCAG--AA-GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCAG-----GGAAGAUAAGCUAGCAGCAAAAGAGAA-----CU-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY020565117.1/1934-1742 CAGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGGAG-ACCUAGAGAGAA-----G-CUG-AAGGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGGCGAUAAAAAAGAG---CUUG-CAGAUCCACCAAG-AGUUCAAGAGAAAGGACU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGAACU-----AAGAAAA
AACY023113618.1/241-53    CGGG----GACUGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AGAAUCUCG-CUUUAGAC-ACCUG-GGGAACUCGAAUU------GAAAGA
AACY023946693.1/622-434   CAAC----GACUGACGCAGGAA--CAACUGCAGA-A-GGGA--AU-GCGAGGGAA-----G-UUG-GAAGGAGAGUC-C-UCA-GGAAGAAA-GCGUUGUAGAGC--G---------CCGG---CAAAAAGAGA--GCUUU-ACGACCCACCAAG-GGUGAA-GAGAUACCACC-CGAGG-AGCUAAAG-AGAAAUCUCG-CUUUAGAC-GCCUG-GGGAACUCGGAUUAAAUUUA-----
AACY022580367.1/826-638   CGGA----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY023256204.1/732-921   CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGUGAAA-GCGAUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGAAAGAGAAAGCCUU-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY023359010.1/1488-1298 ----AAGAAACCGACUAGGGAC--CAACUGCAGA-C-GGAAA-AC-UAGAGAGAAU-CGAU-AGG-----AAGAGUC-C-GAA-GGGCGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUUAAG--AGAAUCUCA-CUUAAGAC-CCCUU-CGAAACUCGGAUU------AGAAGA
AACY022347161.1/568-380   CGGA----GACCGAUAAGCGAA--CAACUGCAGA-C-GGGA--AC-UUAAGAGAA-----A-CCG-AAAGGAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAGACCCACCAAG-GAUGGA-GAGAUAACAUC-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-ACCUG-AGGAACUCGAACU------GAAAGA
AACY020560493.1/1115-915  --UCUUGAGAUCGACCCGGAAG--UAACUUAAGA-C-GCAG--AA-GGGAGAGUCGAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCAG-----GGAAGAUAAGCUAGCAGCAAAAGAGAA-----CU-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY020215295.1/1664-1475 CGAC----GACUGACACAGGAA--CAACUGCAGA-C-GGGA--AU-GUGAGGGAA-----G-UCG-GAGGGAGAGCC-C-CCA-GGGAGAAA-GCGUUGUAAAG---A--------CCCGGUGAAAAAAGAGAG---CUUU-ACGACCCACCAAG-GAUGAA-GAGAUACCAUC-CAAGG-AGCUGAAG--AAAAUCUCA-CUUUAGAC-ACCUG-GGGAACUCGGAUAAAUUC-AA----
AACY021441208.1/216-27    CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGAUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGAAAGAGAAAACCUU-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY023067484.1/734-922   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY020223595.1/295-483   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY023245640.1/95-285    CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGUAGAGAC---GAA-GAGAGAAA-GCGAUACUAAG---A--------GUCGACAAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGCAAGAGAAUACCUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CUCUU-CUAAUCUCGAAUUUU----AAGAAA
AACY020514217.1/1674-1483 CUUGA---UUCCGACUAACAAU--CAACUGCAGA-C-GGGA--GU-UAGAGAGAU-----C-AGG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GCAACCCACCAAG-AGUUUAAGAGAAAAAACU-CAAGG-AGCCAGAG--AAAAUCUCA-CUUUGGAC-CCCUA-AGGAACUCGAACUU----AAAGAA-
AACY020266519.1/2257-2446 CUGA----GACCGACUAACAAC--UAAAUGCAGA-C-GGAA--GU-UAGAGAGAA-----U-CAG-AAGGAAGAGAC-C-AGA-GGGAGAAAAGCGUUUCUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GAGACCCACCAAGGAAAUAA-GAGAAAAAUUUCCAAGG-AGCUAAAG--AAAUUCUCA-CUUUAGAC-CCCAA-AGGAACUCGAACU--------AAGA
AACY023122438.1/489-301   CGGG----GACUGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAAUU------GAAAGA
AACY020550681.1/861-1053  GGUA----AACAAGAUCGGAAAAGGAACUGCAGAACCUAGA--AC-GAGAAAGUU-----A-ACC--AGGGAGAGACCA-GAA-AGGUGAAA-GUUCAAGGUAGGUUA--------GCUAG---CAUUA-----AACCAAA-CUUGACCACCGAG-GAUAAAAGAGAUCUUAUC-CAAGGAUGCAAGAG--GUAAUCUCA-CUUUUGACACCUA--CUGAUCUCGA-U-----AGAAAAAA
AACY024105131.1/1101-913  UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY020483406.1/474-662   CGGA----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY020049903.1/244-436   CUUGA---UUCCGACUAAAGAA--CAACUGCAGA-C-GGGA--CU-UAGAGAGAA----CC-AGG-AAGGUAGAGCC-C-AUA-GGGAGAAA-GCGUUUAUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-UAAACCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCCGGAG--AAAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACU-----AAAGAAA
AACY020432661.1/1304-1116 CGGA----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCU-AAGGAAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-ACCUG-GGGAACUCGAACU------GAAAGA
AACY023688380.1/1541-1352 CUCG----GACCGACUUACAAU--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGUUAUUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-GAGGAAAGAGAAAGCCUC-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY020189889.1/1257-1066 CUUGA---UUCCGACUAACAAU--CAACUGCAGA-C-GGGA--GU-UAGAGAGGU-----C-AAG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUUGUAAG---A--------GUCGAUGAUAAAAAAUAG---CUUA-CAGACCCACCAAG-AGUUCAAGAGAAAGAACU-CAAGG-AGCCAGAG--AAAAUCUCA-CUCAGGAC-CCCUA-AGGAACUCGACUU-----AAAGAAA
AACY021853345.1/300-107   GGUA----ACGAGAACU-GGAAAGGAACUGCAGAACCAUAG--AA-AGGAAACGU-----U-ACA-CAGGAAGAGACCU-GAA-GGGUGAAA-GUUCAAGAGAGCUUA--------GCAUG---CAAAA-----AAGCAAA-CUUGACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAAGAG--GUAAUCUCA-CUUUUGACACCCA--CAGAUCUCGAUUU---AUAAAAA--
AACY023354273.1/834-1023  CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGUAGAGAC---GAA-GGGCGAAA-GCGUUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUGACCCACCAAG-AAGGCAAGAGAAAACCUU-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY023028282.1/262-69    UAAU----UUUCGACUAGUGAC--CAACUGCAGA-CGGAAGA-UCCUAGAGAAAA-----A-UUA-AAGGAAGAGAC-C-AAA-GGGUGAAA-GCAUUUAUAAG---A--------GUCGAUGAUAAAAAACAG---CUUA-UAAAUCCACCAAG-AAUACAAGAGAAAGUAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGACCUCGAACU-----AAAGAAA
AACY022482481.1/242-51    UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGGAG-ACCUAGAGAGAA-----G-CCA-GAAGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUACAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-UAGAUCCACCAAG-GAUUCAAGAGAAAGAGUC-CAAGG-CGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAA-UCGAACU-----AAGAAAA
AACY020563141.1/1471-1656 -----UU-AUCCGAUCCGGAAA--CAACUCGAGA-C-GGGAG-AA-GGAAGAGAU-A-AAA-AAG----UUAGAGAA-C-GGA-AGGUGAAA-GCUCUAAUAAA---G--------AAAGGUACCAAAAAAA-----UUUA-UUAGACCACCAAG-AUCAAAAGAGAAAUUGAU-CAAGG-AGCUAGAAGAAAAAACUCAACUCUAGAC-ACUUU-CGAA-CUCGAACU---------AAA
AACY020011803.1/864-673   UUGA----UUCCGACUAACGAU--CAACUGCAGA-CGGGAA--G--UAGGGAGAA-----UCGAA-GAGGUAGAGCC-C-AUA-GGGUGAAA-GCGUUUAUAAG---A--------GUCGGCGAUAAAAAAGAG---CUUA-UAAACCCACCAAG-AUUUCAAGAGAAAGAAAU-CAAGG-AGCUAGAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGAAUU-----AAAAAGA
AACY020563601.1/3791-3982 UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAG-ACCUAGAGAGAA-----G-CCA-AACGGAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAGGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAA-UCGAUU-----GAAAGAAA
AACY023526629.1/1055-864  CAGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGGAG-ACCUAGAGAGAA-----G-CUG-AAGGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUACAAG---A--------GUCGGCGAUAAAAAAGAG---CUUG-UAAAUCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCUAA--GGAACUCGAACU-----AAGAAAA
AACY023590823.1/590-778   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY021122835.1/508-324   CGGC----GACUGACGAGCGAC--CAACUGCAGA-C-GGGA--GC-GAGAGGGAA-----G-CCG-ACAGAAGAGUA-C-UCA-GGUAGAAA-GCGUGACAGAG---G--------GCCGGCA-UAGAA-AGCG---CUUU-GUUGCCCACCGAG-GACGGA-GGGAUAGCGUC-CGAGG-AGCUGAAG-GAGAGUCCCA-CUUCAGAC-GCCUG-AGGAACUCGAAU--------AAAA-
AACY021775963.1/255-446   CUUGA---UUCCGACUAACAAU--CAACUGCAGA-C-GGGA--GU-UAGAGAGGU-----C-AAG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUGCUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUGACCCACCAAG-AGUUCAAGAGAAAGAACU-CAAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-AGGAACUCGAAUUU----AAAGAA-
AACY020389354.1/638-456   UCCG----AGCCGA-----AAA--CAACUCGAGA-C-GAAAG-AA-AGCAGAGAG-----A-GGA-UGAUUAGAGUA-C-GAA-GGGUGAAA-GCUCUAGAAAA---A--------AAAGGUACCAAAAAAG-----UUUU-CUAGACCACCAAGAUCUAAAAAGAAGAGUAGAUCAAGG-AGCCUGAA--AGUCUUCAA-GUCAGGAC-ACUUU-CGAA-CUCGAAACU--------AAA
AACY023685398.1/600-789   CUCA----GACUGACUUACAAG--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGUUAUUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGGAAGAGAAAACCUU-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----AAAAAGA
AACY022306888.1/160-349   CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGAUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGAAAGAGAAAGCCUU-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY022673568.1/227-46    AUCG----GACCGACUUGGAAA--CAACUCGAGA-C-GAAG--AA-GAGAGAGAA-----A-GAU-AGGUUAGAGAA-C-GAA-AGGUGAAA-GCACUAGAG-----G--------GAAGCUAGCAAAAAGAA------CU-CUAGACCACCAAG-GCAGGAAGAGAAACCGGC-CAAGG-AGCUAAAC--AGAAUCUCG-GUUUAGAC-ACUUU-CGAA-CUCGAACU--------AAGA
AACY021997040.1/367-555   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY023621300.1/956-768   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------GAAAGA
AACY023617732.1/362-171   UGAC----GACUGACUAGUGAC--CAACUGCAGA-CGGGAA--AC-UAGAGGGAA----AG-UCA-AACGGAGAGAC-C-UAA-GGGUGAAA-GCAUUUGUAAG---A--------GUCGAUGUUAAAAAAUAG---CUUA-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAA-UCGAUUG-----AAAGAAA
AACY020546617.1/1442-1630 CGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCG-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-UAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY021524383.1/318-518   --UCUUGAGAUCGACCCAGAAG--UAACUUAAGA-CGCAGAA----GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCAG-----GGAAGAUAAGCUAGCAGCAAAAGAGAA-----CU-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY023994458.1/589-777   CGGG----GACUGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACCUG-GGGAACUCGAAUU------GAAAGA
AACY020028399.1/1627-1818 UUGA----UUCCGACUAAAGAU--CAACUGCAGA-CGGGACG----UAGAGAGAA-----UCAAA-GAGGUAGAGCC-C-AUA-GGGUGAAA-GCGUUUGUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-UAAACCCACCAAG-AUUUCAAGAGAAAGAAAU-CAAGG-AGCUAAGG--AUAAUCUCA-CUUUAGAC-CCCUA-AGGAUCUCGAAUU-----AAAAAGA
AACY020564006.1/4741-4935 -AGAU---AACAAGAUCAGGAAGGGAACUGCAGAACCAAGA--AU-GAGAAAGUU----AA-CUU--AGGAAGAGACCA-GAA-AGGUGAAA-GUUCAAG---G---A------AGGUC-AGCAUGCAAAAGAU---CAAA-CUUGACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAGAAG--GUAAUCUCA-CUUUUGACACCUA--CUGAUCUCGAAUU----AAAAAAA-
AACY020472736.1/1252-1441 CUCG----GACCGACUUACAAU--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGUUAUUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-GAGGAAAGAGAAAGCCUC-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY022739624.1/341-152   UGGC----AACCGACUAGAGAC--CAACUGCAGA-C-GGAA--AC-UAGGGAGAA-----G-CCA-GACGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGGUU------GAAGAAA
AACY021532574.1/346-537   UGGC----GACUGACUAGCUAC--CAACUGCAGA-CGUGAA--GU-UAGAGGGAA-----AACCA-GACGGAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAGGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAA-UCGAUU-----GAAAGAAA
AACY020489190.1/1632-1445 CCGA----AACCGACUUGGAAA--CAACUGCAGA-C-GGGA--CC-AAGGGAGAA-----U-CGG-AAGGAAGAGAC-C-AAA-GGGUGAAA-GCGUUUCUAAG---A--------GUCGAUGAUAAAAAAUAG---CUUA-GAGACCCACCAAG-GAAAUAAGAGAAAAUUUC-CAAGG-CGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGACCUCGGACU--------AAGA
AACY021395533.1/140-329   CUGA----GACCGACUAACAAC--UAAAUGCAGA-C-AGAA--GU-UAGAGAGAA-----U-CAG-AAGGAAGAGAC-C-AGA-GGGAGAAAAGCGUUUCUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GAGACCCACCAAGGAAAUAA-GAGAAAAAUUUCCAAGG-AGCUAAAG--AAAUUCUCA-CUUUAGAC-CCCAA-AGGAACUCGAACU--------AAGA
AACY022304692.1/553-364   CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGUAGAGAC---GAA-GGGCGAAA-GCGUUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUGACCCACCAAG-AAGGCAAGAGAAAACCUU-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY020313783.1/382-569   CGGC----GACCGACGAGUGAC--CAACUGCAGA-C-GGAA--GC-GAGGGGGAA-----G-CCG-UGGGAAGAGUG-C-UCA-GGUAGAAAAGCGUAGCGAA----GG-------GCCGGC---ACAAACGCA---GUUC-GCUACCCACCGAG-GGUGAG-GGGAUACCACC-CGAGG-GGCCAGAU--GGAAUCCCG-GUCUGGAC-GCCUG-AGAGGCUCGAAAA-----AAAAAGA
AACY020255585.1/216-28    UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY020017256.1/979-1170  UUGA----UUCCGACUAACAAA--CAACUGCAGA-C-GGGA--GU-UAGAGAGAA-----U-CAAGAAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUUGUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-UAGACCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACU-----AAAGAAA
AACY021889085.1/159-351   UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGGAG-ACCUAGAGAGAA-----G-CCA-AACGGAGAGAC-C-GAA-GGGAGAAA-GCAUUUACAAG---A--------GUCGGCGAUAAAAAAGAG---CUUG-UAAAUCCACCAAG-GGUUCAAGAGAAAGAAUC-CAAGG-AGCUGAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGAUUUU----AAAGAA-
AACY020502004.1/984-1172  UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY023901079.1/1027-839  UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY021644063.1/208-17    CAGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAG-ACCUAGAGAGAA-----G-CUG-AAGGAAGAGCC-C-GAA-GGGAGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGAUU------GAAGAAA
AACY022408018.1/252-440   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAAUU------GAAAGA
AACY020393868.1/570-379   UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAG-ACCUAGAGAGAA-----G-CCA-GACAUAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAGGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAA-UCGAUU-----GAAAGAAA
AACY021556557.1/797-606   CUUGA---UUCCGACUAACAAU--CAACUGCAGA-C-GGGA--GU-UAGAGAGGU-----C-AAG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GCAACCCACCAAG-AGUUUAAGAGAAAAAACU-CAAGG-AGCCAGAG--AAAAUCUCA-CUUUGGAC-CCCUA-AGGAUCUCGAACUU----AAAGAA-
AACY023034076.1/722-534   UGAG----GACCGAUGAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--UAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY020421087.1/980-1171  UGGC----AACCGACUAGUGAC--UAACUGCAGA-C-GGGAG-ACCUAGAGAGAA-----G-CCA-GAAGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUACAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-UAGAUCCACCAAG-GAUUCAAGAGAAAGGAUC-UAAGG-CGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAAUCGAACU------AAGAAAA
AACY020400182.1/505-313   -AGAU---AACUAGAUAGGAAAAGGAACUGCAGAACCUAGA--AC-UAGAAAGUU-----A-CUC--AGGAAGAGACCA-GAA-GGGUGAAA-GUUUAAGGUAGCUCA--------GUCGA---CAAUA-----GAGUAAA-CUUAACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAGAAG--GUAAUCUCA-CUUUUGACACCCA--CUGUUCUCGA-U-----AAGAAAAA
AACY021955569.1/174-364   CUAA----UUCCGACUAAAGAC--CAAUUGCAGA-C-GAGA--AU-UAGAGAGAA-----AAAAG-CUGGCAGAGCC-C-AUA-GAGAGAAA-GCGUUUAUAAG---A--------GUCGGCGAUAAAAAAGAG---CUUA-UAGACCCACCAAG-AAUUCCAGAGAAAGAAUU-CAAGG-AGCUAGAG--AGAAUCUCA-CUUUAGAC-CUCUA-AGGAACUCGAAUU------AAGAAA
AACY024069994.1/73-265    CAGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGGAG-ACCUAGAGAGAA-----G-CUG-AAGGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGGCGAUAAAAAAGAG---CUUG-CAGAUCCACCAAG-AGUUCAAGAGAAAGGACU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGAACU-----AAGAAAA
AACY020564830.1/230-42    CGGA----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAGAG--AGAAUCUCA-CUCUAGAC-ACAUG-GGGAACUCGAACU------AAGAGA
AACY020500954.1/1125-1314 ACGAA----ACCGACUAGGAAA--CAACUGCAGA-C-GGGA--CC-UAGAGAGAA-----U-CGA-AAGGAAGAGUC-C-GAA-GGGCGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUUAAG--AGAAUCUCA-CUUAAGAC-CCCUU-CGAAACUCGGAUU------AGAAGA
AACY023094901.1/467-661   -AGAU---AACAAGAUCAGGAAGGGAACUGCAGAACCAAGA--AU-GAGAAAGUU----AA-CUU--AGGAAGAGACCA-GAA-AGGUGAAA-GUUCAAG---G---A------AGGUC-AGCAUGCAAAAGAU---CAAA-CUUGACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAGAAG--GUAAUCUCA-CUUUUGACACCUA--CUGAUCUCGAAUU----AAAAAAA-
AACY022741729.1/86-286    --UCUUGAGACCGACCC--GAAAGUAACUUAAGA-CGCGGAA----GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCGG-----GGAAGAUAAGCUAGCAGCAAAAAGGAA-----CC-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY021543506.1/484-672   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAAUU------GAAAGA
AACY020400221.1/950-759   UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAA-ACCUAGAGAGAA-----G-CCA-GAAGAAGAGAC-C-UAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CGAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGGUU------GAAGAAA
AACY022092045.1/216-406   CUAA----AACCGACUGAUGAC--CAACUGCAGA-CGGAUA--CU-UAGAGAGAA-----U-UAG-UAGUCAGAGCA-C-GAA-AGGUGAAA-GCGUUACUAAG---A--------GUCGACGAUAAAAAAUAG---CUUA-GUAGCCCACCAAG-AGGGAAAGAGAUAACCCU-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-CCUUU-CGUUACUCGUUUU------AUAAAA
AACY023149008.1/339-539   --UCUUGAGACCGACCC--GAAAGUAACUUAAGA-CGCGGAA----GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCGG-----GGAAGAUAAGCUAGCAGCAAAAAGGAA-----CC-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY020198623.1/460-643   AUCA----GACCGACUUGGAAA--CAACUCGAGA-C-GAAG--AA-AAGAGAGAA-----A-GAU-AGGUUAGAGAA-C-GAA-AGGUGAAA-GCUCUAAAAAAC--A--------GCUAG---CAAAAAAA----GUUUU-UUAGACCACCAAG-GUUGAAAGAGAAAUCAAC-CAAGG-AGCUAGAC--AAAAUCUCG-GUUUAGAC-ACUUU-CGAA-CUCGAACU--------AAGA
AACY022230445.1/429-240   CUCG----GACCGACUUACAAU--CAACUGCAGA-C-GGGU--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGUUAUUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-AUAACCCACCAAG-AAGGAAAGAGAAAGCCUU-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY020028407.1/1138-949  CUCA----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGCAGAGAC---GAA-GGGCGAAA-GCGAUGCUAAG---A--------GUUGACGAUAAAAAAGAG---CUUA-GUAUCCCACCAAG-AAGGCAAGAGAAAACCUU-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-CUCUU-CCAAUCUCGAACUU-----AAGAAA
AACY020454360.1/2283-2474 CUUGA---UUCCGACUAACAAU--CAACUGCAGA-C-GGGA--GU-UAGAGAGAG-----C-AAG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUUGUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-CAGACCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACU-----AAAAGAA
AACY023230226.1/1450-1261 CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGUAGAGAC---GAA-GGGCGAAA-GCGAUACUAAG---A--------GUUGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGCAAGAGAAAACCUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CUCUU-CCAAUCUCGAACUU----AAAGAA-
AACY020400221.1/636-445   CAGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAG-ACCUAGAGAGAA-----A-CUG-GAGGAAGAGCC-C-GAA-GGGUGAAA-GCAUUUGUAAG---A--------GUCGAUGAUAAAAAAUAG---CUUA-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGAUU------GAAGAAA
AACY020555885.1/411-599   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UUA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUA-AGGAACUCGAACU------AAGAGA
AACY024096912.1/672-480   GUAAC---GAG-AACUGG-AAAGGAACUGCAGAAC-CAAAG--AA-AGGAAACG------U-UACACAGGAAGAGACCU-GAA-GGGUGAAA-GUUCAAGAGAGCUUA--------GCAUG---CAAUA-----AAGCAAA-CUUGACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAAGAG--GUAAUCUCA-CUUUUGACACCCA--CAGAUCUCGAUUU---AUAAAAA--
AACY022978903.1/477-277   --UCUUGAGAUCGACCUGGAAG--UAACUUAAGA-C-GCAG--AA-GGGAGAGUCGAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCAG-----GGAAGAUAAGCUAGCAGCAAAAGAGAA-----CU-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY023363698.1/283-94    CUCG----GACCGACUUACAAU--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGUUAUUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-GAGGAAAGAGAAAGCCUC-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY023412721.1/1218-1028 ----ACGAAACCGACUAGGGAC--CAACUGCAGA-C-GGAAA-AC-UAGAGAGAAU-CGAA-AGG-----AAGAGUC-C-GAA-GGGCGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUUAAG--AGAAUCUCA-CUUAAGAC-CCCUU-CGAAACUCGGAUU------AGAAGA
AACY022674253.1/215-34    AUCG----GACCGACUUGGAAA--CAACUCGAGA-C-GAAG--AA-AAGAGAGAA-----A-GAU-AGGUUAGAGAA-C-GAA-AGGUGAAA-GCUCUAGAG-----G--------GAAGCUAGCAAAAAGAA------CU-CUAGACCACCAAG-GCAGAAAGAGAAACCUGC-CAAGG-AGCUAAAC--AGAAUCUCG-GUUUAGAC-ACUUU-CGAA-CUCGAACU--------AAGA
AACY023161256.1/159-359   --UCUUGAGACCGACCC--GAAAGUAACUUAAGA-CGCGGAA----GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCGG-----GGAAGAUAAGCUAGCAGCAAAAAGGAA-----CC-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY020008628.1/454-644   CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGUAGAGAC---GAA-GAGAGAAA-GCGAUACUAAG---A--------GUCGACAAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGCAAGAGAAUACCUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CUCUU-CUAAUCUCGAACUUU----AAGAAA
AACY024111588.1/1114-1303 CUGA----GACCGACUAACAAC--UAAAUGCAGA-C-GGAA--GU-UAGAGAGAA-----U-CAG-AAGGAAGAGAC-C-AGA-GGGAGAAAAGCGUUUCUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GAGACCCACCAAGGAAAUAA-GAGAAAAAUUUCCAAGG-AGCUAAAG--AAAUUCUCA-CUUUAGAC-CCCAA-AGGAACUCGAACU--------AAGA
AACY024042706.1/40-227    AAUU----AUCCGAUCUGAAAA--CAACUCGAGA-CGGUAG--AA-AGAAGAGAU-----A-AAU-AAGUUAGAGAA-C-GAA-AGAAGAAA-GCUCUAAUAAA-------------UAAAGGUACCAAAAAAA---UUUA-UUAGACCACCAAG-AUUAAAAGAGAAAUUAAU-CAAGG-CGCUAAAAAAAGAAACUCAAUUUUAGAC-UCUUU-CGAA-CUCGAACU---------AAA
AACY020064977.1/664-473   UUGA----UUCCGACUAAAGAA--CAACUGCAGA-C-GGGA--CU-UAGAGAGAA-----UAAAG-GAGGUAGAGCC-C-AUA-GGGUGAAA-GCGUUUGUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-UAGACCCACCAAG-AAUUCAAGAGAAAGAAUU-CGAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACU-----AAAGAAA
AACY022788058.1/294-105   CUCG----GACCGACUUACAAU--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGAAGAGAC---GAA-GGGCGAAA-GCGUUAUUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-GAGGAAAGAGAAAGCCUC-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY020397413.1/953-765   CGGG----GACUGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-GGGUGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--UAAAUCUCA-CUUUAGAC-ACCUG-GGGAACUCGAAUU------GAAAGA
AACY022432484.1/26-218    AGGC----AACCGACUAGUGAC--CAACUGCAGA-CGGAAGA-UCCUAGAGAGAA-----G-CCA-GAAGAAGAGAC-C-GAA-GGGCGAAA-GCAUUUACAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-UAAAUCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAA-UCGAAUU-----AAGAAAA
AACY020049903.1/581-773   CUUGA---UUCCGACUAAAGAA--CAACUGCAGA-C-GGGA--CU-UAGAGAGAA----CC-AGG-AAGGUAGAGCC-C-AUA-GGGAGAAA-GCGUUUAUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-UAAACCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCCGGAG--AAAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACU-----AAAGAAA
AACY022674159.1/644-453   CUUGA---UUCCGACUAACAAU--CAACUGCAGA-C-GGGA--GU-UAGAGAGGU-----C-AAG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUGCUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACUU----AAAGAA-
AACY023631486.1/249-58    UGGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAG-ACCUAGAGAGAA-----G-CCA-GACGAAGAGAC-C-UAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAGAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CGAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAACUCGGUU------GAAGAAA
AACY022544992.1/221-402   AUCG----GACCGACUUGGAAA--CAACUCGAGA-C-GAAG--AA-AAGAGAGAA-----U-GAU-AGGUUAGAGAA-C-GGA-AGGUGAAA-GCUCUAGAG-----G--------GAAGCUAGCAAAAAGAA------CU-CUAGACCACCAAG-GCAGGAAGAGAAACCGGC-CAAGG-AGCUAAAC--AGAAUCUCG-GUUUAGAC-ACUUU-CGAA-CUCGAACU--------AAGA
AACY021988464.1/265-65    --UCUUGAGAUCGACCCGGAAG--UAACUUAAGA-C-GCAG--AA-GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCAG-----GGAAGAUAAGCUAGCAGCAAAAGAGAA-----CU-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY022850433.1/337-531   GGUA-----ACGAGAACUGG-AAAGGAACUGCAGAACCAAAGAAA-GGAAACGU------U-ACACAAGGAAGAGCACU-GAA-AGGUGAAA-GUUCAAGAAAGCUUA--------GCAUG---CAAUC-----AAGCAAA-CUUGACCACCAAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAAAAG--AUAAUCUCA-CUUUUGACACCUA--CAGUACUCGAUUU----AAAAGAA-
AACY024002672.1/155-346   CAGU----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAA-ACCUAGAGAGAA-----G-CUG-AAGGAAGAGCC-C-GAA-GGGAGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGAUU------GAAGAAA
AACY023260634.1/754-942   CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A--GA-GAAGAAGAGAC---GAA-GGGCGAAA-GCGUAACUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUGACCCACCAAG-GAGGCAAGAGAAAACCUC-CAAGG-AGCUAAAG--AGAUUCUCA-CUUUAGAC-CCCUU-CCAAUCUCGAACU-----GAAAAGA
AACY022354394.1/146-335   CUUAAUU-AUCCGAUCCGGAAA--CAACUCGAGA-C-GGGAG-AA-GGAAGAGAU-A-AAG-AAG----UUAGAGAA-C-GGA-AGGUGAAA-GCUCUAAUAAA---G--------AAAGGUACCAAAAGA------UUUA-UUAGACCACCAAG-AUCAAAAGAGAAAUUGAU-CAAGG-AGCUAGAGAAAAAAACUCAAAUCUAGAC-ACUUU-CGAA-CUCGAACU---------AAA
AACY023359673.1/1342-1155 CCGA----AACCGACUUGGAAA--CAACUGCAGA-C-GGGA--CC-AAGGGAGAA-----U-CGG-AAGGAAGAGAC-C-AAA-GGGAGAAA-GCGUUUCUAAG---A--------GUCGAUGAUAAAAAAUAG---CUUA-GAAACCCACCAAG-GAAAUCAGAGAAAAUUUC-CAAGG-CGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGACCUCGGACU--------AAGA
AACY020239613.1/1898-2079 AUCA----GACCGACUUGGAAA--CAACUCGAGA-C-GAAG--AA-AAGAGAGAA-----U-GAU-AGGUUAGAGAA-C-GAA-AGGUGAAA-GCACUAGAG-----G--------GAAGCUAGCAAAAAGAA------CU-CUAGACCACCAAG-GCAGGAAGAGAAACCGGC-CAAGG-AGCUAAAC--AGAAUCUCG-GUUUAGAC-ACUUU-CGAA-CUCGAACU--------AAGA
AACY021309029.1/703-512   CAGC----AACCGACUAGUGAC--CAACUGCAGA-C-GGGAG-ACCUAGAGAGAA-----G-CUG-AAGGAAGAGAC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAGAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-CGGAA-UCGAUUU-----AAAGAAA
AACY023560069.1/1207-1014 GGUA----ACAAGAACU-GGAAAGGAACUGCAGAAC-CAAAG-AA-AGGAAAUGU-----U-ACA-CAGGAAGAGACCU-GAA-GGGUGAAA-GUUCAAGAGAGCUUA--------GCAUG---CAAAA-----AAGCAAA-CUUGACCACCGAG-AGUAAAAGAGAUCUUACU-CAAGGAUGCAAGAG--GUAAUCUCA-CUUUUGACACCCA--CAGAUCUCGAUUU----AAAAGAA-
AACY020392860.1/261-69    UGGC----AACCGACUAGUGAA--CAACUGCAGA-CGGGAU--AC-UAGAGAGAA-----G-CCA-AACGGAGAGAC-C-GAA-GGGAGAAA-GCAUUUACAAG---A--------GUCGGCGAUAAAAAAGAG---CUUG-UAGAUCCACCAAG-GGUUCAAGAGAAAGAACC-CAAGG-AGCUGAAG--AAAAUCUCA-CUUUAGAC-CCCUG-AGGAACUCGACUUU----AAAGAAA
AACY020158734.1/355-171   CGGC----GACUGACGAGUGAC--CAACUGCAGA-C-GGGA--GC-GAGAGGGAA-----G-CCG-ACAGAAGAGUA-C-UCA-GGUAGAAA-GCGUGACAGAG---G--------GCCGGC-AUAGAA-AGCG---CUUU-GUUGCCCACCGAG-GACGGA-GGGAUAGCGUC-CGAGG-AGCUGAAG-GAGAGUCCCA-CUUCAGAC-GCCUG-AGGAACUCGAAU--------AAAA-
AACY020214447.1/951-759   -GAUA---ACCAGA-UCAGAAAGGGAACUGCAGAACCCAGA--AU-GAAAAAGUU-A-----CUU-AG-GAAGAGAACA-GAA-AGGUGAAA-GUUCUAGAAAGCUUA--------GCUAG---CAAUA-----AAGCGAA-CUAGACCACCGAG-GAUAAAAGAGAUCUUAUC-CAAGGAUGCAGAAG--GUAAUCUCA-CUUUUGACACCUA--CUGAUCUCGA-UU----GAAAAAAA
AACY022354129.1/102-290   UGAG----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-UCA-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AGAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--UAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY020093121.1/1023-1214 AGAC----AACCGACUAGUGAC--CAACUGCAGA-C-GGAAU-ACCUAGAGAGAA-----G-UUA-GAGGGAGAGGC-C-GAA-GGGUGAAA-GCAUUUGCAAG---A--------GUCGAUGAUAAAAAAUAG---CUUG-CAAAUCCACCAAG-GAUUCAAGAGAAAGAAUC-CAAGG-AGCUGAAG--AGAAUCUCG-CUUUAGAC-CCCUG-AGGAACUCGAUU------AAAGAAA
AACY020051328.1/884-1074  ----ACGAAACCGACUAGGGAC--CAACUGCAGA-C-GGAAA-AC-UAGAGAGAAU-CGAA-AGG-----AAGAGUC-C-GAA-GGGCGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUUAAG--AGAAUCUCA-CUUAAGAC-CCCUU-CGAAACUCGGAUU------AGAAGA
AACY020862624.1/137-327   ----ACGAAACCGACUAGGGAC--CAACUGCAGA-C-GGAAA-AC-UAGAGAGAAU-CGAA-AGG-----AAGAGUC-C-GAA-GGGCGAAA-GCGUUAUAAAG---A--------GUUAACGAUAAAAAAUAG---CUUU-AUAACCCACCAAG-AGGAAAAGAGAGAAUCCU-CAAGG-AGCUUAAG--AGAAUCUCA-CUUAAGAC-CCCUU-CGAAACUCGGAUU------AGAAGA
AACY020421272.1/857-1057  --UCUUGAGAUCGACCCGGAAG--UAACUUAAGA-C-GCAG--AA-GGGAGAGUCAAAAAG-AGA-----AAGAGAC-C-UAAAGGGUGAAA-GCGAAUCAG-----GGAAGAUAAGCUAGCAGCAAAAGAGAA-----CU-GAUUCCCACCAAGUUCGGAAAGAGAUA-CCGGGCGAGG-CGCUGAAGAAAGAAUCUCG-CUUCAGAC-ACCCCAAGGA-CUCGA-CU-----AAAGAAA
AACY023205918.1/1132-1324 CUUGA---UUCCGACUAAAGAA--CAACUGCAGA-C-GGGA--CU-UAGAGAGAA----GC-AAG-AAGGUAGAGCC-C-AUA-GGGAGAAA-GCGUUUAUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-UAAACCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCCGGAG--AAAAUCUCA-CUCAGGAC-CCCUA-AGGAUCUCGAACU-----AAAGAAA
AACY023216776.1/295-485   CUCG----GACCGACUUACAAA--CAACUGCAGA-C-GGGA--GU-AAGAGAGAA-----A-GAG-AAGGUAGAGAC---GAA-GGGCGAAA-GCGAUGCUAAG---A--------GUUGACGAUAAAAAAGAG---CUUA-GUAACCCACCAAG-AAGGCAAGAGAAAACCUU-CAAGG-AGCUAAAG--AGAAUCUCA-CUUUAGAC-CUCUU-CCAAUCUCGAACUUU----AAGAAA
AACY023204447.1/874-1058  AUCA----GACCGACUUAGAAC--CAACUCGAGA-CGAAGA--AA-GAGAGAGAA-----A-GAU-AGGUUAGAGAA-C-GAA-AAGUGAAA-GCUCUAGAAAAC--A--------GCUAG---CAAAAAAA----GUUUU-UUAGACCACCAAG-AUUAAAAGAGAAAUUAAU-CAAGG-AGCUAAAC--AAAAUCUCA-GUUUAGAC-GCUUU-CGAA-CUCGAACU--------AAGA
AACY023699847.1/243-434   CUUGA---UUCCGACUAACAAU--CAACUGCAGA-C-GGGA--GU-UAGAGAGGU-----C-AAG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUGCUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-GUAGCCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCCAGAG--AGAAUCUCA-CUCAGGAC-CCCUA-AGGAACUCGAACUU----AAAGAA-
AACY022751166.1/170-358   CGGA----GACCGAUAAGAGAC--CAACUGCAGA-C-GGAA--AC-UUAAGAGAA-----A-CCG-AAGGAAGAGCC-C-UCA-AGGCGAAA-GCGUUUUAAAG---A--------GUAUACGAUAAAAAAUAG---CUUU-AAAACCCACCAAG-GAUGAA-GAGAUAGCAUC-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-ACUUG-AGGAACUCGAACU------AAGAGA
AACY020457582.1/561-752   UUGA----UUCCGACUAACAAA--CAACUGCAGA-C-GGGA--GU-UAGAGAGAA----AC-AAG-AAGGAAGAGCC-C-AUA-GGGUGAAA-GCGUUUGUAAG---A--------GUCGACGAUAAAAAAGAG---CUUA-UAAACCCACCAAG-AAUUCAAGAGAAAGAAUU-CAAGG-AGCUAAAG--AAAAUCUCA-CUUUAGAC-CCCUA-AGGAUCUCGAACU-----AAAGAAA
#=GC SS_cons              <<<<....------<<<<<___..__________._.____..>>.>>>------.....>.>>>.-----------.(.(((.((,,,,,,.,,<<<<<<<<<..._........__________________...>>>>.>>>>>,,,,,,,<.<<<<__________>>>>.>,,,,.,,<<<<<<.._________.>>>>>>,,.,)))).)):::::::::::.....:::::::
#=GC RF                   cggc....gACcGAcccgcgAa..cAACUgcAGA.C.ggaA..gc.gggAGAGaa.....g.ccg.aAGGaAGAGac.c.gca.GGGuGAAA.GCgcuugcaaG...A........GucgacgauAAAAAAuAg...Cuug.caagcCCACCAAG.ggugaAAGAGAuAgcacc.CAAGG.aGCugaAg..AaAAUCUCA.cUucaGAC.aCCug.cgGAaCUCGAauU.....AAAaAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02035
#=GF ID   IMES-2
#=GF DE   IMES-2 RNA motif
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:12376536; Weinberg Z
#=GF SS   Published; PMID:12376536; Weinberg Z
#=GF GA   30.00
#=GF TC   32.20
#=GF NC   29.20
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19956260
#=GF RT   Exceptional structured noncoding RNAs revealed by bacterial metagenome
#=GF RT   analysis.
#=GF RA   Weinberg Z, Perreault J, Meyer MM, Breaker RR
#=GF RL   Nature. 2009;462:656-659.
#=GF WK   IMES-2_RNA_motif
#=GF SQ   366


ABEF01040645.1/957-1063   AAUAAUCACAACGAUU-ACUU-AACGAGCACACU--------------------------------------GCAGAA-ACCUCACAUAG-UAGCGCUAAAAAUAGUGGGGUGGC--GGG-UCCAGCGGUAGCAU-UUACAACGACGGACCAA
ABEF01053338.1/230-337    AAUAAUCACAACGAUU-ACUU-AACGAGCACACU--------------------------------------GCAGAAAACCUCACAUAG-UAGUGCUAAAAAUAGUGGGGUGGU--GGG-UCCGGCUGUAGCAU-UUACAACGACGGGCCAC
ABEF01000673.1/517-656    UGAUGAC-UUAAGA-G-GCAA-CUCUUAACU-GGCCAGGUGGGGAA-AAACCGAGAGGUUCAAGCUUACCGGGCAGAAAACUGGGGUCAG-UAGUACUAAACA-GCCCUAGUGGC--AGU-GACGAAGGUAGUAC-UU-CAACAGCGUCACAA
ABEF01047612.1/1567-1707  AAAUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAGUUGAGGAA-AAACCGAGAGGUUCAAGCUCAGCGGGCAGAAAGUCUGAGACAG-UAGAACUAAACA-ACUCAGGUGAC--UGGUUACGAAGGUAGUUC-UC-UAACAGCGUACCAA
ABEF01001714.1/383-524    AUUUGAC-UUAAGA-G-GCAA-CUCUUAACU-GGCCAGGUAAGGAA-AAACCGAGAGGUUCAAGCUUAUCGGGCAGAAAGCCCUGCAAAG-UAGCGCUUAACAUGGUGGGGUGGC--GGG-UUCGGCGGUAGCGC-CUACAACGACGAACCAA
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AACY022672779.1/173-312   CUAUGAA-UUAAGG-G-GCAA-CUCUUAACU-GGCCAAUUGGAGAA-AAGCCGAGAGGUACAAUUCCAAGGGGCAGAAAGCUCUACAAAG-CAUCGCUGAACA-UGUAGAGCGGG--UGG-CAUGGCGGUAGCGC-AU-CAACGACGUGCCAA
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AACY020994739.1/405-264   AACUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAAGGAA-AAACCGAGAGGUUCAAGCUUGAAGGGCAGAAAGGUGAACCUAG-UAGCGCUAGAAU-AGUUCACCGGGA-UGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
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AACY022816197.1/276-415   AAAUGAA-UUAAGG-G-GCAA-CCCUUAACU-GGCCAUUUGGGCAA-AAGCCGAGAGGUACAAAUCCAAAGGGCAGAAAGUUCUGCAGAG-CAUCGCUGAACA-UGCAGAACGGG--AGG-CAUGGCGGUAGCGC-AU-CAACGACGUGCCAA
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AACY022178782.1/112-252   AGUUAAC-UUAAGA-G-GCAA-CUCUUAACU-GGCCAGCCAAAGAA-AGGUCGAGAGAUUUAAGUUUGGAGGGCAGAAAGCCUUGUAAAG-CAGCGCUAAACA-UACAGGGUGGU--CGG-UUCGGCGGUAGCGC-AUACAACGACGAACCAU
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AACY023484910.1/891-751   AUUUUAA-UUAAGA-G-GCAA-CUCUUAACU-GACCAUUUAAG-AA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUGAACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-UGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
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AACY021722227.1/337-197   AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAAUUGGGGAA-AAGCCGAGAGGUUCAAGCCCAGAGGGCAGAAAGUUCUGCAAAG-CAGCGCUAAACA-UGCAGAGCGGA--AGA-CACGGCGGUAGCGC-CUACAACGACGUGUCAA
AACY022543205.1/648-789   UUAUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAGGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUGAACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-AGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
AACY022629147.1/174-315   UUUUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAGGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUGGACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-AGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
AACY021104079.1/229-370   AAAUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAAGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGAUGGACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-UGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
AACY020380888.1/2695-2554 AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCGACUGGUGAA-AAACCGAGAGGUUCAAGACCAGGGGGCAGAAAGUUCUGCAAAG-CAGCGCUAAACA-UGCAGAACGGGA-CGA-CAUGGCGGUAGCGC-AUACAACGACGUGUCAA
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AACY020237372.1/887-746   AACUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAAUUAAGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUGGACCUAG-UAGCGCUAGAAU-AGUUCAUCGAUA-UGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
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AACY023856279.1/513-654   UAAUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAGGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUGAACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-AGG-CUUGGCGGUAGCGC-AUAAAACGACGAGCCAA
AACY023510195.1/778-638   AGAUGAA-UUAAGG-G-GCAA-CCCUUAACU-GGCCGACUGGGGAA-AGGCCGAGAGGACCAAGCCCAGGGGGCAGAAAGUCUUACGGAG-UAGCGCUAAAAU-CGUAGGGCGGA--AGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY020221966.1/797-936   UUAUGAU-UUAAGG-G-GCAA-CUCUUAACU-GGCCAAUUGGAGAA-AAGCCGAGAGGUACAAUUCCAGGGGGCAGAAAGCUUCACAAAG-CAUCGCUGAACA-UGUGGAGCGGG--AGG-CAUGGCGGUAGCGC-AU-CAACGACGUGCCAA
AACY020360713.1/91-233    AAAUGAA-UUAAGG-G-GCAA-CCCUUAACU-GGCCGAUUGGGGAA-AAACCGAGAGGUUCAAGCCCAGGGGGCAGAAAGUUCUACGGAG-UAGCGCUAAAAU-CGUAGAGCGGUCAUGG-CUUGGCGGUAGCGC-AUACAACGACGAGCCAA
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AACY020160151.1/3604-3463 AGAUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAAGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUGAACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-UGG-CUUGGCGGUAGCGC-CUACAACGACGAGCCAA
AACY021194104.1/246-105   AAUUAAC-UUAAGA-G-GCAA-CUCUUAACU-GACCGACUGGGGAA-AUGCCGAGAGGUUCAAGCCCAGGGGGCAGAAAACUCUGUUGAG-UAGCGCUAAAAU-GGCGGAGUGCAA-AGG-CAUGGCGGUAGCGC-CUACAACGACGUGCCAA
AACY020155965.1/1124-1264 AAAUGAA-UUAAGG-G-GCAA-CCCUUAACU-GGCCGACUGGGGAA-AGGCCGAGAGGACCAAGCCCAGGGGGCAGAAAGUCUUACGGAG-UAGCGCUAAAAU-CGUAGGGCGGA--AGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY022253829.1/522-662   AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAAUUGGGGAA-AAGCCGAGAGGUUCAAGCCCAGAGGGCAGAAAGUUCUGCAAAG-CAGCGCUAAACA-UGCAGAGCGAA--GGA-CACGGCGGUAGCGC-CUAAAACGACGUGUCAA
AACY024027476.1/229-89    AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GACCAGCUGGGGAA-AAACCGAGAGGUUCAAGCCCAGAGGGCAGAAAGCUCUACAGAG-UAGCGCUAAAAU-AGUAGAGUGGA--AGG-CAUGGCGGUAGCGC-AUAAAACGACGUGCCAA
AACY021477681.1/518-378   AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GACCAUCUGGGGAA-AAAUCGAGAGAUUCAAGAACAGAGGGCAGAAAACUCUACAGAG-UAGCGCUAAAAU-UGUGGAGUGAA--AGG-CAUGGCGGUAGCGC-AUAAAACGACGUGCCAA
AACY021433766.1/420-561   UCAUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAAUUAAGGAA-AAACCGAGAGGUUCAAGCUUAAGGGGCAGAAAGGUGGACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-CGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
AACY023708652.1/1273-1413 AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GACCAUCUGGGGAA-AAAUCGAGAGAUUCAAGAACAGAGGGCAGAAAACUCUACAGAG-UAGCGCUAAAAU-UGUGGAGUGAA--AGG-CAUGGCGGUAGCGC-AUAAAACGACGUGCCAA
AACY023648698.1/694-834   AUUUAAC-UUAAGA-G-GCAA-CUCUUAACU-GGCCAGCCAGAGAA-AGGCCGAGAGGCUCAAGUCUGGAGGGCAGAAAACCCUGUAAAG-CAGCGCUAAACA-UACGGGGUGGC--AGG-UUCGGCGGUAGCGC-AUACAACGACGAACCAA
AACY023525156.1/719-581   AAUUUAA-CUGAGG-GCGUAAGUUCUCAGCA-CUCAUCAAGAAGUA--GGC-UUAG-GCC-AAUUGCUUGGUGGUGAAAGUAGAGGGAAGGUAGCACUUCGAC-GCCUCUAAGUA--CGC-UGUGGGAGUAGUGC--UUAAAUCACACGGCAA
AACY022729684.1/566-427   AAUUGAA-UUGAGG-G-GCAA-CUCUCAACU-GGCCAGUUAAGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGUUCCGCUGAG-UAGCGCUAAAAU-AGUGGAACGGG--AGG-CUUGGCGGUAGCGC-AU-UAACGACGAGCCAA
AACY021926654.1/469-329   UAUUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAAGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUCAGCUGAG-UAGCGCUAAAAU-AGUUGACCGGG--GGG-UUCGGCGGUAGCGC-CUAAAACGACGAACCAA
AACY023496722.1/1109-1249 ACAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GACCAUCUAGGGAA-AAAUCGAGAGAUUCAAGCCUAGAGGGCAGAAAACUUCGCUGAG-UAGCGCUAAAAU-AGCGAGGUGGA--AGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY023721673.1/166-306   AACCGAC-UUAAGA-G-GCAA-CUCUUAACU-GGCCAGCCAGAGAA-AGGCCGAGAGGCUCAAGUCUGGAGGGCAGAAAACCCUGUAAAG-CAGCGCUAAACA-UACGGGGUGGU--AGG-UUCGGCGGUAGCGC-AUACAACGACGAACCAA
AACY021023837.1/602-736   AUAUUAA-UUGAGG-G-GCAA-CUCUCAACU-GACACACAAGGUGA--GGU-UUCG-GCCAAA-UAUUGUGUGCAGAAAGCCAGAGACAGGUAGCACGAGAAC--CUCUGGCGG---CGG-UUCGGCAGUAGUGC--UAAAAUGACGAACCAA
AACY021445850.1/154-13    AAAUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAGGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUGGACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-AGG-CUUGGCGGUAGCGC-CUACAACGACGAGCCAA
AACY021776120.1/155-16    AGAUGAA-UUAAGG-G-GCAA-CCCUUAACU-GGCCAAUUGGGCAA-AAACCGAGAGGUACAAAUCCAAGGGGCAGAAAGUUCUGCAAAG-CAUCGCUGAACA-UGCAGAACGGG--AGG-CAUGGCGGUAGCGC-AU-CAACGACGUGCCAA
AACY022167035.1/586-447   AAAUUAA-UUAAGG-G-GCAA-CCCUUAACU-GACCGGCUGGAGAA-AAACCGCAAGGAACAAAUUCAGAGGGCAGAAAGUUUCGCGGGG-GAUCGCUGAACG-CGCGAAGCGGG--UGG-CAUGGCGAUAGCGA-GU-CAACGACGUGCCUA
AACY022003034.1/836-695   AAUUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAGGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUGAACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-AGG-CUUGGCGGUAGCGC-CUACAACGACGAGCCAA
AACY023710606.1/586-726   AAACGAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCGAUUGGGGAA-AAGCCGAGAGGUUCAAGCCCAGGGGGCAGAAAGUUCUGCAAAG-CAGCGCUAAACA-UGCAGAGCGAA--GGA-CACGGCGGUAGCGC-AUACAACGACGUGUCAA
AACY020287560.1/1676-1534 AUAUGAA-UUAAGG-G-GCAA-CUCUUAACU-GGCCAUCUAGGGAA-AAACCGAGAGGUUCAAGCUUAGGGGGCAGAAAGUCUUGCAGAG-UAGCGCUAAAAU-UGUGAGGCGGUCACGG-CUUGGCGGUAGCGC-AUACAACGACGAGCCAA
AACY022381893.1/170-310   AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GACCGAUUGGGGAA-AAGCCGAGAGGUUCAAGCCCAGGGGGCAGAAAGUUCUGCAAAG-CAGCGCUAAACA-UGCAGAGCGAA--GGA-CACGGCGGUAGCGC-AUACAACGACGUGUCAA
AACY020854965.1/359-499   AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GACCGACUGGGGAA-AAAUCGAGAGAUUCAAGCCCAGGGGGCAGAAAACCUAGCGGAG-UAGCGCUAAAAU-CGUUAGGUGGA--AGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY023394561.1/995-857   -UAUUAACUUAAGA-G-GCAA-CUCUUAACU-G-CCAGCCAAAGAA--AGUCGAGAGAUUUAAGUUUGGAGGGCAGAAAGCCUUGUAAAG-CAGCGCUAAACA-UACAGGGUGGU--CGG-UUCGGCGGUAGCGC-AUACAACGACGAACCAU
AACY020213394.1/1879-2019 AGAUGAA-UUAAGG-G-GCAA-CCCUUAACU-GGCCGACUGGGGAA-AGGCCGAGAGGACCAAGCCCAGGGGGCAGAAAGUCUUACGGAG-UAGCGCUAAAAU-CGUAGGGCGGA--AGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY020279837.1/956-816   AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCGAUUGGGGAA-AAGCCGAGAGGUUCAAGCCCAGGGGGCAGAAAGUUCUGCAAAG-CAGCGCUAAACA-UGCAGAGCGGA--GGA-CACGGCGGUAGCGU-CUACAACGACGUGUCAA
AACY020141954.1/928-1068  UAAUUAA-UUAAGG-G-GCAA-CCCUUAACU-GGCCAACUGGGGAA-AGGCCGAGAGGACCAAGCCCAGGGGGCAGAAAGUCUUACGGAG-UAGCGCUAAAAU-CGUAAGGCGGA--AGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY022538728.1/42-182    AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCGAUUGGGGAA-AAGCCGAGAGGUUCAAGCCCAGGGGGCAGAAAGUUCUGCAAAG-CAGCGCUAAACA-UGCAGAGCGGA--AGA-CACGGCGGUAGCGC-CUACAACGACGUGUCAA
AACY021393059.1/888-747   AUAUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAGGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUGAACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-AGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
AACY022843217.1/153-12    AAAUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUGGGGAA-AAACCGAGAGGUUCAAGCUCAAAGGGCAGAAAGGUGAACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-CGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
AACY023726397.1/568-425   UUUUAAC-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUCCAGGGAAAAAACCGAGAGGUUCAAGCUUGGAGGGCAGAAAGCUUCACGGAG-UAGCGCUAAAAU-CGUGAGGUGGUCAUGG-CAUGGCAGUAGCGC-AUACAAUGACGUGCCAA
AACY022981883.1/301-162   AAAUGAA-UUGAGA-G-GCAA-CUCUCAACU-GGCCAGUUAAGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGUUCCGCUGAG-UAGCGCUAAAAU-AGUGGAACGGG--AGG-CUUGGCGGUAGCGC-AU-UAACGACGAGCCAA
AACY023668429.1/618-758   AAAUUAA-UUAAGG-G-GCAA-CCCUUAACU-GGCCGAUUGGGGAA-AAACCGAGAGGUUCAAGCCCAGGGGGCAGAAAGUCCUGCGGAG-UAGCGCUAAAAU-CGUGGGGCGGA--AGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY024064404.1/850-990   UAAUCAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAGGGAA-AAGCCGAGAGGUUCAAGCUUAAAGGGCAGAAAGAUCAGCUGAG-UAGCGCUAAAAU-GGUUGAUCGGG--AGG-UUCGGCGGUAGCGC-CUACAACGACGAACCAA
AACY020140548.1/963-824   AAUUGAA-UUAAGG-G-GCAA-CUCUUAACU-GGCCAAUUGGACAA-AAGCCGAGAGGUACAAUUCCAGGGGGCAGAAAGCUCUGUAAAG-CAUCGCUGAACA-UACAGAGCGGG--AGG-CAUGGCGGUAGCGC-AU-CAACGACGUGCCAA
AACY023546305.1/887-747   UUCUAAC-UUAAGA-G-GCAA-CUCUUAACU-GGCCAGCCAGAGAA-AAGCCGAGAGGCCCAAGUCUGGAGGGCAGAAAGCCCUGUAAAG-CAGCGCUAAACA-UACAGGGUGGU--AGG-UUCGGCGGUAGCGC-AUACAACGACGAACCAU
AACY020057953.1/328-188   AAUUGAA-UUAAGG-G-GCAA-CUCUUAACU-GGCCAGUUAAGGAA-AAACCGAGAGGUUCAAGCUUAACGGGCAGAAAGGUGGAAACAG-UAGCGCUUUACA-UUUCCAUCGAC--GGG-CUUGGCGGUAGCGC-CUACAACGACGAGCCAA
AACY022289122.1/630-770   AAAUGAU-UUAAGA-G-GCAA-CUCUUAACU-GACCAUCUGGGGAA-AAAUCGAGAGAUUCAAGCCCAGAGGGCAGAAAACCACGCAGAG-UAGCGCUAAAAU-UGCGGGGUGGA--AGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY021794956.1/148-9     UUAUGAA-UUAAGG-G-GCAA-CUCUUAACU-GGCCAAUUGGAGAA-AAGCCGAGAGGUACAAUUCCAGGGGGCAGAAAGCUCCACAAAG-CAUCGCUGAACA-UGUGGAGCGGG--AGG-CACGGCGGUAGCGC-AU-CAACGACGUGCCAA
AACY022990280.1/375-515   AGAUGAA-UUAAGG-G-GCAA-CCCUUAACU-GGCCGACUGGGGAA-AGGCCGAGAGGACCAAGCCCAGGGGGCAGAAAGUCUUACGGAG-UAGCGCUAAAAU-CGUAGGGCGGA--AGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY024092476.1/788-928   UCUUAAC-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUCCAGGGAA-AAGUCGAGAGACCUAAGCCUGGAGGGCAGAAAACCCUGCAAAG-UAGUGCUAAACA-UGUGGGGUGGC--CGG-UUCGGCGGUAGCAA-CUUCAACGACGGACCUA
AACY021530690.1/12-153    AAUUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUGGGGAA-AAACCGAGAGGUUCAAGCUCAAAGGGCAGAAAGAUGAACCUAG-UAGCGCUAGAAU-AGUUCAUCGUGA-CGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
AACY020122570.1/1066-1203 GUUUUAA-UUGAGG-G-GUGA-CCCUCAACU-GACAUACAAGGGGA--GGU-UUCG-GCCAAA-UGUUGUAUGCAGAAAGCGUGAGGAAGGUAGCACUUAGAC-ACUCACGAGUAG-CGG-UUCGGCAGUAGUGC--UAAAAUGACGAACCAA
AACY021172812.1/174-315   UAUUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAAUUAAGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGGUGAACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-AGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
AACY020123120.1/2462-2323 AAAUGAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCGAUUGGAGAA-AAGCCGAGAGGUACAAAUCCAGGGGGCAGAAAGCUCUACAAAG-CAUCGCUGAACA-UGUGGAGCGGG--AGG-CAUGGCGGUAGCGC-AU-CAACGACGUGCCAA
AACY020134665.1/2162-2023 AAUUGAA-UUAAGG-G-GCAA-CCCUUAACU-GGCCAAUUGGGCAA-AAGCCGAGAGGUACAAAUCCAAGGGGCAGAAAGUUCUGCAAAG-CAUCGCUGAACA-UGCAGAACGGG--AGG-CAUGGCGGUAGCGC-AU-CAACGACGUGCCAA
AACY020208594.1/1217-1358 UUUGUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUUUAAGGAA-AAACCGAGAGGUUCAAGCUUAAAGGGCAGAAAGAUGAACCUAG-UAGCGCUAGAAU-AGUUCAUCGGGA-UGG-CUUGGCGGUAGCGC-CUAAAACGACGAGCCAA
AACY020284538.1/1134-1274 AAGUGAA-UUAAGA-G-GCAA-CUCUUAACU-GACCAUCUGGGGAA-AAAUCGAGAGAUUCAAGCCCAGAGGGCAGAAAACCACGCAGAG-UAGCGCUAAAAU-UGCGGGGUGGA--AGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY022392294.1/378-238   GAGUUAA-UUAAGA-G-GCAA-CUCUUAACU-GACCAACUGGGGAA-AGGCCGAGAGGACCAAGCCCAGGGGGCAGAAAGCUUCGCGGAG-UAGCGCUAAAAU-CGUGAAGCGGG--AGG-CAUGGCGGUAGCGC-CUACAACGACGUGCCAA
AACY023952949.1/736-596   AAUUGAA-UUAAGA-G-GCAA-CUCUUAACU-GACCAGCUAGGGAA-AAACCGAGAGGUUCAAGCCUAGAGGGCAGAAAGCUCUGCAGAG-UAGCGCUAAAAU-UGCAGGGUGGA--CGG-CAUGGCGGUAGCGC-AUACAACGACGUGCCAA
AACY023726932.1/593-735   UUCUUAA-UUAAGA-G-GCAA-CUCUUAACU-GGCCAUCUGGGGAA-AAACCGAGAGGUUCAAGCCUAGAGGGCAGAAAGUCUUGCAGAG-UAGCGCUAAAAU-UGUAAGGCGGUCAUGG-CUUGGCGGUAGCGC-AUACAACGACGAGCCAA
#=GC SS_cons              :::::::.<<<<<<.<.____.>>>>>>><<.<-<<-<<<<<<---.-<<<<____>>>>---->>>>>>->>>>>,,,<<<<<<<<___.____________.>>>>>>>>,,,..,<<.<<<<<<<_______.______>>>>>>>>>::
#=GC RF                   aaaUuAA.uuaaGg.G.GCAA.CcCuuaaCu.GgCcaccugggGAA.AggcCGAgAGgcccAAgcccaggGgGCaGAAAgccccgccaAG.UAGCGCUaaAau.ggcggggcGga..aGG.cccGgcGGUAGCGC.aUAcAACgaCgggCCAA
//
# STOCKHOLM 1.0

#=GF AC   RF02036
#=GF ID   IMES-3
#=GF DE   IMES-3 RNA motif
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:12376536; Weinberg Z
#=GF SS   Published; PMID:12376536; Weinberg Z
#=GF GA   55.00
#=GF TC   57.00
#=GF NC   38.80
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19956260
#=GF RT   Exceptional structured noncoding RNAs revealed by bacterial metagenome
#=GF RT   analysis.
#=GF RA   Weinberg Z, Perreault J, Meyer MM, Breaker RR
#=GF RL   Nature. 2009;462:656-659.
#=GF WK   IMES-3_RNA_motif
#=GF SQ   32


AACY020666588.1/528-675   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---GGUCGUCGCAAGAUUGGCAAUUUA-GGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-UGCUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY020184545.1/512-365   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCGCU-CAGAA---UGUCAUCGCAAGAUUGACAAUCUA-AGCGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAGU-GAAAGGCAAA
AACY022278987.1/242-389   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUUACU-UAGAU---GGUCGUCGCAAGAUUGACAAUUUA-AGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY023906506.1/632-777   AGGAUAAAAACUGGGGGGUAUUAGAAGUCAAGAAAAUAAUAG---AUGC---GUCG----GCAUUUAUAGUUUUCGAACACGGACAAAACCAACUCCAGAUGUAUAGAGUUCAGAUCGUCCACAACCUUUCGGUUGGAUCGGAGCUCGAAGUUGGA
AACY022145704.1/89-236    AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUUGCU-CAGAA---UGUCAUCGCAAGAUCGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAGU-GAAAGGCAAA
AACY020498361.1/1001-854  AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCAUU-UAGAU---GGUCAUCGCAAGAUUGACAAUUUG-AGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY020337245.1/1393-1540 AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCGCU-CAGAA---UGUCAUCGCAAGAUCGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAGU-GAAAGGCAAA
AACY020257101.1/1740-1593 AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---GGUCGUCGCAAGAUUGACACUUUA-GGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAGCUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY023852264.1/707-854   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---CGUCGUCGCAAGAUUGACAAUUUA-GGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY021888837.1/709-563   AGGAUAAAAACUGGGGGGUAUUAGAAGUUUAGAAAUAUAUAA---UAA-GU-UUCG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAACUCGAAGUUGGA
AACY023885650.1/635-781   AGGAUAAAAACUGGGGGGUAUUAGAAGUUUGGAAAUAUAUAA---UAA-GU-UUCG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAACUUGAAGUUGGA
AACY021300597.1/306-453   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCACU-UAGAA---GGUUAUCGCAAGAUUGACAAUUUA-GGUGAAAA-ACGGACAAAACCAACUCUGGAUCAACA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCGGU-GAAAGGUGAA
AACY022356298.1/458-605   AGGAUAAAAACUGGGGGGUGCUAGAAGUUAAUCACU-UAAUG---GGUCAUCGCAAGAUCGACAAUGUA-GGUGAAAA-ACGGACAAAACCAACUCUGGAUCAACA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY023202785.1/871-726   AGGAUAAAAACUGGGGGGUAUUAGAAGUUUAGAAAGAUGCAG---AAGC---UUAG----GCGUUUGUAUAUUUCGAAUACGGACAAAACCAAACCCAGAAGUAUAGAGUUCAGAUCGUCCACAACCUUUUGGUUGGAUCGGAACUUGAAGUUGGA
AACY020854413.1/116-263   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-CAGAC---AGUCAUCGCAAGAUUGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUUAAUA-AACUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAGU-GAAAGGUAAA
AACY020508546.1/1794-1648 AGGAUAAAAACUGGGGGGUAUUAGAAGUUUAGAAAUAUAUAA---UAA-GU-UUCG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAACUCGAAGUUGGA
AACY020090496.1/1071-926  AGGAUAAACACUGGGGGGUAUUAGAAGUUAAGAAAAUUGUAG---GCGC---UUUA----GCAUUUACAGUCUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUCAGAUCGUCCACAACCUUACGGUUGGAUCGGAGCUUGAAGUUGGG
AACY020328555.1/1541-1691 AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAAACGGGUCGUCGCAAGAUGGACAAUCUA-GGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUAAA
AACY020224664.1/2056-1910 AGGAUAAAAACUGGGGGGUAUUAGAAGUUUAGAAAUAUAUAA---UAA-GU-UUCG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAACUCGAAGUUGGA
AACY021897919.1/485-338   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-CAGAA---GGUCGUCGCAAGAUUGACAAUCUA-GGUGAAAA-ACGGACAAAACCAACUUUGGAUCAAUA-AUCUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAG-UGAAAGGUAAA
AACY020092547.1/380-527   AAGAUAAAGACUGGGGGGUGUUAGAAGUUAAUUGCU-CAGAG---UGUCAUCGCAAGAUAGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUCUCGAGUUGGAUCGCAGU-GAAAGGCAAA
AACY023559001.1/557-704   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCGCU-CAGAA---UGUCAUCGCAAGAUCGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGGGAUCGUCCACAACUCUCGAGUUGGAUCGCAGCU-AAAGGCAAA
AACY021990316.1/291-438   AGGAUAAAAACUGGGGGGUAUUAGAAGUUAGUUACU-UAGAG---UGUCAUCGAAAGAUAGAUAAUUUA-AGUAAAAA-AUGGACAAAACCAACUCUGGAUUAAUA-AGCUGAGAUCGUCCACAACUCUCGAGUUGGAUCACAGU-AAAAGGUGAA
AACY020503557.1/1589-1736 AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCAUU-UAGAU---GGUCGUCGCAAGACUGACAAUUUA-AGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY020267093.1/346-199   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---GGUCGUCGCAAGAUUGACAAUUUA-GGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AGCUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY023713779.1/894-1041  AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---GGUCGUCGCAAGAUUGACAAUUUA-GGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AGCUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGCU-AAAGGUGAG
AACY021483546.1/235-90    AGGAUAAAAACUGGGGGGUAUUAGAAGUUAAGGAAAAUAUAG---AAGC---UUCG----GCAUUUAUAGUUUUCGAACACGGACAAAACCAACCCCAGAAGCAUAGAGUUCAGAUCGUCCACAACCUUUCGGUUGGAUCGGAUCUCGAAGUUGGA
AACY023357761.1/718-865   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCGCU-CAGAA---UGUCAUCGCAAGAUCGACAAUCUA-AGUGAAAA-ACGGACAAAACCAACUCUGGAUCAAUA-AACUGAGAUCGUCCACAACUCUUGAGUUGGAUCGCAGU-GAAAGGCAAA
AACY022322085.1/613-759   AGGAUAAAAACUGGGGGGUAUUAGAAGUUUAGAAAUAUAUAA---UAA-GU-UUCG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAUAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAACUCGAAGUUGGA
AACY021804107.1/46-192    AGGAUAAAAACUGGGGGGUAUUAGAAGUUUUGAAAUAUAUGA---UAA-GU-UUAG-GC--UU-UUAUAAAUUUCGAAUACGGACAAAACCAACCCCAGAAGCAAAGAGUUGAGAUCGUCCACAACCUUUUGGUUGGAUCGCAAUUUGAAGUUGGA
AACY020246597.1/967-1114  AGGAUAAAAACUGGGGGGUGUUAGAAGUUAAUCACU-UAGAU---AGUCAUCGCAAGAUUGACAAUUUA-AGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
AACY023888787.1/955-808   AGGAUAAAAACUGGGGGGUGUUAGAAGUUAGUCACU-UAGAA---GGUCGUCGCAAGAUUGACAAUUUA-AGUGAAAA-ACGGACAAAACCAACUCCGGAUCAAUA-AACUGAGAUCGUCCACAACUUUCGAGUUGGAUCGCAGUU-AAAGGUGAA
#=GC SS_cons              ::::::::::<<<<<<<<<-------<<<--<<<<<.<<<<<...-<<<<<<____>>>->>>->>>>>.>>>>>-->.>>------->>>-->>>>>>-------.<<<<<-<<<<-----<<<<<____>>>>>>>>>->>>>>::::::::::
#=GC RF                   AGGAUAAAAACcGGgGGGugUUAGAAGuuaagcacu.uagac...uguCguCguaaGacuGacagucua.agugcaAa.aCGGACAAAaCCAACcCCgGAucaAUA.agcugAGauCGUCCACaaCcuUuggGuuGGauCGcagcuuaAAGgUgaA
//
# STOCKHOLM 1.0

#=GF AC   RF02037
#=GF ID   IMES-4
#=GF DE   IMES-4 RNA motif
#=GF AU   Weinberg Z; 0000-0002-6681-3624
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:12376536; Weinberg Z
#=GF SS   Published; PMID:12376536; Weinberg Z
#=GF GA   48.00
#=GF TC   50.00
#=GF NC   42.60
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19956260
#=GF RT   Exceptional structured noncoding RNAs revealed by bacterial metagenome
#=GF RT   analysis.
#=GF RA   Weinberg Z, Perreault J, Meyer MM, Breaker RR
#=GF RL   Nature. 2009;462:656-659.
#=GF WK   IMES-4_RNA_motif
#=GF SQ   30


AACY023717910.1/1180-1101 CUUAUUACACGCAAAGGUAGUAAGCAAAUUAAAUAAAG-GAAACUUUAUUUAGUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY022456354.1/372-293   CUUAUUACACGCAAAGGUAAUAAGCAAAUUAGAUAAAG-GAAACUUUAUUUAGUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY021350860.1/35-114    AUUAUUACACGCAAAGGUAAUAAUCAAAUUAAUUUAAG-GAAACUUUUUUUAAUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY020281743.1/404-324   AUUAUUACACGCAAAGGUAAUAAU-AGAUUGUUUAGGG-GAAACUUUAAAUAAUUUAAAUCGGGGAGGAAAUGUCUUGAUUUA
AACY022857199.1/655-734   AUUAUUACACGCAAAGGUAAUAAUCAAUUUAAUAAAAG-GAAACUAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY020554210.1/1667-1746 AUUAUUACACGCAAAGGUAAUAAUCAAUUUAAUAAAAG-GAAACGAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY020399179.1/830-909   AUUAUUACACGCAAAGGUAAUAAUCAAUUUAAUAAAAG-GAAACGAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY024081964.1/650-729   AUUAUUACACGCAAAGGUAAUAAUCAAUUUAAUAAAAG-GAAACGAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY021872291.1/390-469   AUUAUUGCACGCAAAGGUAAUAAUCAAAUUAAAUAAAG-GAAACUUUUUUUAAUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY020374533.1/764-685   AUUAUUACACGCAAAGGUAAUAAUCAAAUUAAUUAAGG-GAAACCUUUUUUAAUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY022518432.1/45-124    CUUAUUACACGCAAAGGUAGUAAGCAAAUUAAUUAAAG-GAAACUUUAUUUAGUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY020272207.1/1744-1664 AUUAUUACACGCAAAGGUAAUAAU-AGAUUGUUUAGGG-GAAACUCUAAAUAAUUUAAAUCGGGGAGGAAAUGUCUUGAUUUA
AACY020359071.1/1170-1090 CUUAUUACACGCAAAGGUAAUAAGCAAAUUAGAUAAAGGGAAACUUUAUUUAGUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY023723514.1/1066-987  AUUAUUACACGCAAAGGUAAUAAUCAAUUUAAUAAAAG-GAAACUAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY021659028.1/88-167    AUUAUUUCACGCAAAGGAAAUAAUUGGAUUAAUUAAAG-GAAACUUUAUUUAAUUCAUAUCG-GGAGGAAAUGCA-CGAUAUA
AACY022232148.1/159-238   AUUAUUACACGCAAAGGUAAUAAUCAAUUUAAUAAAAG-GAAACGAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY023539002.1/198-119   AUUAUUACACGCAAAGGUAAUAAUCAAUUUAAUAAAAG-GAAACAAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY022514676.1/132-211   CUUAUUACACGCAAAGGUAAUAAGCAAAUUAAUAAAAG-GAAACUUUUGUUAGUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY022537670.1/552-631   AUUAUUACACGCAAAGGUAAUAAUUAGAUAUUUUUUAG-GAAACUGUUAAAUAUCUAUAUCG-GGAGGAAAUGCA-CGAUAUA
AACY024064178.1/388-467   CUUAUUACACGCAAAGGUAGUAAGCAAAUUAAAUAAAG-GAAACUUUAUUUAGUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY020348620.1/850-771   CUUAUUACACGCAAAGGUAGUAAGCAAAUUAAAUAAAG-GAAACUUUAUUUAGUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY021392475.1/284-363   AUUAUUACACGCAAAGGUAAUAACCAAAUUAAAUUAGG-GAAACUUAUUUUAAUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY023728127.1/1413-1492 CUUAUUACACGCAAAGGUAAUAAGCAAAUUAGAUAAAG-GAAACUUUAUUUAGUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY021471132.1/523-601   AUUAUUACACGCAAAGGUAAUAAUGAAAUUAAAAAUUG-GAAACUUUUUUUAAUUU-GAUAG-GGAGGAAACCAA-CUAUCAC
AACY020365535.1/1391-1470 AUUAUUACACGCAAAGGUAAUAAUCAAUUUAAUAAAAG-GAAACGAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY020826484.1/626-547   AUUAUUACACGCAAAGGUAAUAAUCAAUUUAAUAAAAG-GAAACAAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY021843497.1/506-427   AUUAUUACACGCAAAGGUAAUAAUCAAUUUAGUAAAAG-GAAACGAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY023733028.1/1460-1381 CUUAUUACACGCAAAGGUAAUAAGCAAAUUAAAUAAGG-GAAACUUUAUUUAAUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY021867220.1/146-225   AUUAUUACACGCAAAGGUAAUAAUCAAUUUAAUAAAAG-GAAACGAUUAUUAAAUUGUAUCG-GGAGGAAAUGCA-CGAUACA
AACY021778738.1/540-461   CUUAUUACACGCAAAGGUAAUAAGCAAAUUAGAUAAAG-GAAACUUUAUUUAGUUUGUAUCG-GGAGGAAAUGCA-CGAUACA
#=GC SS_cons              <<<<<<<<________>>>>>>>>,<<<<<<<<<<<<<.____>>>>>>>>>>>>><<<<<<.____________.>>>>>>:
#=GC RF                   aUUAuUaCACGCAAAGGuAaUAAucaaauuaauuagaG.GAAACucuaauuaauuuGuAUCG.GGAGGAAAUGcA.CGAUaCA
//
# STOCKHOLM 1.0

#=GF AC   RF02038
#=GF ID   SPRY4-IT1_1
#=GF DE   SPRY4-IT1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   72.80
#=GF NC   44.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.35 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005737; cytoplasm;
#=GF RN   [1]
#=GF RM   21558391
#=GF RT   The Melanoma-Upregulated Long Noncoding RNA SPRY4-IT1 Modulates Apoptosis
#=GF RT   and Invasion.
#=GF RA   Khaitan D, Dinger ME, Mazar J, Crawford J, Smith MA, Mattick JS, Perera RJ
#=GF RL   Cancer Res. 2011;71:3852-3862.
#=GF WK   SPRY4-IT1
#=GF SQ   23


AY538661.1/11657-11567       CCUCC-AGAGGCAGCUGUC-AACA-UCUGGGCCUGC-AGUUGAGGCCAGACAUG------GGGAUGGGAGCUUGGCCCACGAUGACUUGGCUCUCUGGGGA
ABDC01205569.1/2189-2279     CCCCC-AGAGGCAGCUGUC-AACA-UCUGAACCUGC-AGUUGAGGCCAGACGUG------GGGGUGGGAGCUUGGCCCACGAUGACUUGGCUCUCUUGGGA
ABRP01216483.1/4899-4989     CCUCC-AGAGGCAGCUAUC-AACA-UCUGGGACUGU-AGUUGGGGCCAGACAUA------GGGGUGGGAGCUUGGUCCACGAUGACUCAGCUCUCUUGGGA
ACBE01024843.1/8349-8439     CCUCC-AGAGGUAGCUGUC-AACA-UCUGGGCCUGU-AGUUGGGGCCAGACAUG------GGGUUGGGAGCUCAGUCCACGAUGACUCAGCUCUCUUGGGA
ABRT010405424.1/121-211      CCUCU-AGAAGCAGCUGUU-AACA-UCUGGGCCUGC-AGUUGAGGCCAGACGUG------GGGGUGGGAGCUUGGCCCACGAUGACUCGGCUCUGGUGGGA
AAQQ01129269.1/161-251       CACCC-AGAGGCAGCUGUC-AACA-UCUGGGCCUGC-AAUGGAGGCCAGACAUC------GGGGUGGGAGCUUGGCCUAUGAUGACUCAGCUCUCUCAGGA
ABRN01363047.1/5619-5709     UCUCC-AGAGGCAGCUGUC-AACA-UCUGGGCCUGC-ACUCAGGGCCAGACGUG------GGGGUGGGAGCUCAGUCCACGAUGACUCAGCUCUCUUGGGA
AANN01646741.1/5155-5245     UCUCC-AGAGGCAGCUGUC-CACA-UCUGGGUCUGC-AGUGGGGGCCAGACACU------GGGGAGGGAGCUUGGUCCACAAUGACUCAGCUCUCUUGGGA
AAKN02009940.1/57891-57982   UCUCC-AGAGGCAGAUGCC-AACA-UCUGGGCCUGGCAGGUGAGGCCAGACAUC------GGGGUGGGCACAUGGCCCGCAAUGACUCAGCUCUCCUGGGA
ABRO01087767.1/815-911       UUCCC-ACAGGCAGCUGUC-AACA-UCUGAACCUGC-AAGUGAGGCCAGCCAUGUAGUUGGGGGUGGGAGCUUGGCCCACAAUGACUCAGCUCCCUCGGGA
AAFC03072388.1/44125-44035   CCUCC-GGGGGCAGCUGUC-AACA-UCUGGGUCUGC-ACUUAGGGCCAGACAAG------AGGGUGGGAGCUGGGUCCCUGGUAACUCAGCUGUCUCAGGG
AAWR02002347.1/6299-6210     CCUCC-AGAGGU-GCUGUC-GACA-UCUGGGCCUGC-GGUUGGGACCAGACGCG------GGAGGGAGCGCUGGGUCCACGAUGACUCAGCUCUCUUGGGA
AAIY01553531.1/2051-1963     CCUGC-AGAGGCAGCUGUC-AACA-UCUGGGCCUGC-CACUGUGGCCAGAAGA-------GAGGAAGGCGCUUGGCCUGGGAUGACU-GGCACCUGUAACA
ABRR01306573.1/50-141        CGGGU-GGGCACAGCUGUC-AACA-UCUGGGUCCAC-AGUCAGGGCCAGACACG-----GCGGGUGGGAGCUUGGUCCGCAAUGACUCAGCUCUCCUGGGA
AAHX01094633.1/29040-28945   GCUCC-AGGGGCAGCUGUU-AACA-UCUGGGCUGAC-AGUCUAGGCCAGCCUUGAG-AAGAGUGUGGGAUCUCAGCCCCCAGUGACUCAGCUCUCUCAGGA
AALT01069440.1/1429-1340     CCCUC-CGAGGCAGCUGUC-AACA-UCUGAGAUGGC-CAGCAAAUGGGGGCC-G------GGCAUGGGAGCUUGGCCCACGGUGACUCAGCUCUCCUGGGC
AC206009.4/30668-30578       CCUCC-AGAGGCAGCUGUC-AACA-UCUGGGCCUGC-AGUUGAGGCCAGACAUG------GAGAUGGGAGCUUGGCCCACGAUGACUUGGCUCUCUGGGGA
AK024556.1/496-404           CCUCCAAGAGGCAGCUGUC-AACAUUCUGGGCCUGC-AGUUGAGGCCAGACAUG------GGGAUGGGAGCUUGGCCCACGAUGACUUGGCUCUCUGGGGA
AAPE02012854.1/7370-7281     CUUCC-AGAGGCAGCUGUC-AACA-UCUGGGCCUGC-AUUUAGGGCCAGACAU-------GGGGGUGGAGCUUGGUCCACAAUGACUCAGCUCUCUUGGGA
AAGU03004790.1/25378-25467   CCUCC-AGAGGCAGCUGU-CAACA-UCUAGGCCUGC-UGUUGAGGCCAGA-GUG------GAAGAAAGAGCUUGGCUUAUGAUGACUCGGCUCUGUUGGGA
AAQR03008926.1/6765-6677     CCUCC-AGGGGCAGCUGUC-AACA-UCUGAGCCUGC-AGUUAAGGCCAGACGUG------GGGGUGGGAGCUCAGGCCACAAUGACUUGGCUCUC--GGCU
AAEX03001405.1/193663-193753 CCUCC-AGAAGUAGGUGUC-AACA-UCUGGGCUUGC-AGUUGGGGCCAGACAUG------GAGGUGGGAACUUGGUCCACGAUGACUUAGCUCUCUUGGGA
AAGW02027634.1/20301-20211   GCUCC-AGAGGCAGCUGGC-AGCA-UCUGGGCCUGA-GGCUGAGUCCAGAGGUG------GGGGUGGGAGCCCGGCCCACGAUGACUCAGCUCUCUUGGGA
#=GC SS_cons                 :::::.:::::::::::::.::::.:::::::::::.:::::::::::::::::......:::::::::::::::::::::::::::::::::::::::::
#=GC RF                      cCUCC.AGAGGCAGCUGUC.AACA.UCUGGGCCUGC.aguuGaGGCCAGaCauG......GGGGuGGGAGCUuGGcCCaCGAUGACUCaGCUCUCuuGGGA
//
# STOCKHOLM 1.0

#=GF AC   RF02039
#=GF ID   SPRY4-IT1_2
#=GF DE   SPRY4-IT1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   43.00
#=GF NC   31.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.44 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005737; cytoplasm;
#=GF RN   [1]
#=GF RM   21558391
#=GF RT   The Melanoma-Upregulated Long Noncoding RNA SPRY4-IT1 Modulates Apoptosis
#=GF RT   and Invasion.
#=GF RA   Khaitan D, Dinger ME, Mazar J, Crawford J, Smith MA, Mattick JS, Perera RJ
#=GF RL   Cancer Res. 2011;71:3852-3862.
#=GF WK   SPRY4-IT1
#=GF SQ   24


AY538661.1/11440-11320       --------CCUCACCCCUCACCAGC--AGGG-ACCCUCCA-----AGAGC---CUCUGCUGAAUUUAUGUGGCUGAC----AAAGGAAAACAAUUUUCUGAGCUGCCUAUUU-AAGAA-CCCCUCAG--CACAGCUAAAUGAUGUCUC
AANU01185687.1/1668-1784     --------CCUCACCCCUCACCAGC--AGGG-ACCCUCAA-----AGAAC---CUCUGCUGAAUUUAUUUGGCUGAC----AAU----AACAAUUUUCUGAGCUGCCUAUUU-AAUAA-CCCCUCAG--CACUGCUAAAUGAUGUCUC
ABDC01205569.1/2410-2529     --------CAAGAACCCUCCACAGG--AGGG-CCCUCUAA------GAGC---CUCCGAUGAAUUUAUUUGGCUGAC----AAAGGAGAACAACUUCCUGAGCUGCCUGUUU-GAUAA-CCCCUCAG--CACAGCUAAAUGAUGUCUC
AAGV020145882.1/113-227      ------CC-----UCUCUCCACAG----AAG-GCCGCUAA------GAGC---CUUUGUUGAAUUUAUUUGGCUGAC----AAUGAAAAACAACUUCCUGAGCUGCCUUUUU-GAUAA-CCCCUCAG--CACAGCUAAAUGAUGUCUC
ABRT010405424.1/357-475      --------GCAGAGACCUUCACAGG--AGGG--CCUCUAA------GAGC---CUCAGCUGAAUUUAUUUGGCUGAC----AAAGAAAAACAACUUCCUGAGCUGCCUGUUU-GAUAA-CCCCUCAG--CAGGGCUAAAUGAUGUCUU
AAPY01617416.1/9-127         --------CAGGGGCCCUCCACAGU--GGGG-CUCUCUAA------GAGC---CUCUGCUGAAUUUAUUUGGCUGAC----ACAGAAAAACAACUUCCUGAACUGCCUGAU--GAUAA-CCCUUCAG--CACAGCUAAAUGAUGUCUC
AAWR02002347.1/6058-5939     -------CCUCACCUCCCCAUUAGC--AGGGACCCUCCAC-----AGGAG------GGUUGAAUUCACUUGGCUGAC----AAAGAAAAAUAACUUCCCGAGCAGCCUGUUU-GAUAA-CCCCUCAG--CACAGCUAAAUGAAGUCUC
AANG01342115.1/8574-8692     -------CCUCACCUCCCCAUUAGC--AGGG-ACUUCCAC-----AGGAG------GGUUGAAUUCAUUUGGCUGAC----AAAGAAAAACUACUUCCCGGGCAGCCUGUUU-GAUAA-CCCCUCAG--CAUAGCUAAAUGAAGUCUC
AALT01069440.1/1155-1049     --------CCAGGCUUCUCCACAGG--GGGGAUCCUCUAA------GAGGCCA-------------AGUUGAC--------AAAGGAAAACUAUUUCCUGAGCAGCCCAUUU-GAUAA-GCCCUCAG--CACAGCUAAAUGAAGUCUC
AAIY01553531.1/1831-1711     --------CCUGCCCCGUGAGCAGGGGACAG-CCCUCCAAA---GGAGGG---UUCUGUUGAAUGUAUGCGAC--------AAAGAAAAACAACUCCCUGAGCUGCCUGUUU-GAUAG-CCCUUCAG--CACAGCUAAAUGAUGUCUU
ABRN01363047.1/5842-5959     -------CCUCACCUCCCAAUUAGC--CGGGACCCUCCGC-----AGGAG------GGUGGAAUUCAUUUGGCUGAC---A--AGAAAAACAACUUCCCGA-UAGCCUGUUU-GAUAA-CCCCUCAA--CACAGCUAGACGGUGUCUC
AAQQ01129269.1/419-542       -AGGGACCCUUGCU------GUAGG--AGGG-CCCUCCGA------GAGC---CCCUGAUGAAUUUAUUUGGCUGGUAAGAAAAGAAAAACAA-UUCCCGUUCUUUCUAUUU-GAUAA-AUCACCAG--CACAGCUCCAUGAUGUCUC
ABRR01306573.1/293-409       -------CCUCACCUACCAAUUAGC--CAGA-CCCUUCAC-----AGGAG---GAU---UGAAUUCAUUUGGCUGAC---A--AGAAAAACAACUUCCCAAUCA-CCUGCUU-GAUAA-CCCCUCAG--CACAGUCAAAUGAAGUCUC
ABRO01087767.1/1012-1122     -------A--CAGACCCUCCACAGG--ACAG-CCCUCUAA------GAAC---CUUUAUUGAGAU----UGUCUGAU---GAAGAAAAAACAACUUCUGGUGCUGCCUAUUU-GAUAA-ACCCUCAG--CAUAGCUCUGUAUC-----
AANN01646741.1/5407-5526     ------CG-----CCACCAUUAAGC--AGGA-UCGUCUCCC---CAGGAG---UACCUCUAGAAGCUUCUGUUGGGGG--U--GGGGAGACAACUUCCUGAGCAGCCUGCCU-GAUAA-GGUCUCAG--CACUGCUAAAUGAAGUCUC
AAFC03058595.1/100838-100715 -------CUUCAUCUCCUAGUUAGC--UGGG-ACCGUCCCUCCACAGGAC------GGUUGAAUUCAUUUGACUCACA-UG--AAAAAAAAUACUUGCUGA-UAGCCUGAUA-GAUAA-CACUUCAG--CACAGCUAAGUGAAGUUUC
AC206009.4/30451-30353       --------CCUCACCCCCCAACAGC--AGGG-AC------------------------------CCAUUUGGCUGAC----AAAGAAAAACAAUUUUCUGAGCUGCCUAUUU-AAUAA-CCCCUCAG--CACAGCUAAAUGAUGUCUC
AC151580.2/207250-207368     --------CUUAGGCCUGCCCCAG----CCA-GCCUCUGA------GAGC---CUCUGCUGAACUGAUGUGGCUGAC----UGAGAAACACAAUUUCCUAGACAGCCUGUCUUGACAA-CCCCUCAG--CACAACCCUAGGUCUUCUC
AAGU03004790.1/25623-25742   ACUGGCCCCUUAGG------GGAGG--ACCU-CCCUUUGG----GAAGGC---CUCUGUUGAAUUUGUCUGGC--------AAAGAGAAACAACUUCCUGAGCUGCCUGUUU-GAUAA-CCCUUCAA--CACAGCUAAAUGAUGUCUU
AABR05069927.1/27030-27144   --------CUUAGGCCUGCCCCAG----CCA-GCCUCUCA------GAGC---CUCUGCUGAAUUGAUGUGGCUGAUUGAGAAAGUCAAACAACUUCCUAAACUGCAGGUCU-GACAA-CCGCUCGG--CACAACCU--ACUC-----
AAPE02012854.1/6500-6380     --------CUCCCCUCCCCAUUAGC--AGGG-ACCUCCAC-----AGGAG------GGCUGAAUUCAUUUGGCUGAC----AAAGAAAAACAACUUCCGGAACUACCAGUUU-GAUAAACCCCUCAGAGCACAGCUAAAUGAAGUCUC
AAQR03008926.1/6513-6394     --------CAGGAACCCUCCACAGG--AGGG-CCCUCGAA------GAGC---CUCUGAUGAAUUUAUUUGGCUGAC----AAAGGAAAACAACUUCCUGAGCUGCCUGGUU-GAUAA-CCCCACAG--CACAGCUAAAUGAUAUCUC
AAGW02027634.1/20062-19963   --------CUCACCUCCCCAUAAGC--AGGG-ACCCUCCA-----------------------------UGGCUGAC----AAAGACAAGCAGCUUCCUGAGUGGCCUGUCU-GAAGA-CCCCUCAG--CACGGCUAAAUGAUGUCUC
AAEX03001405.1/193905-194021 --------CUUACUUCCCCAUUAGC--AGGG-AUUUCUAG-----AGGAG------GGUUGAAUUCAUUUGGCUAAC----AAAGAAAAACUACUUCCCGGGCAGCCUGUUU-GAUAA-CCCCUCA---CAUAGCUAAAUGAAGUCUC
#=GC SS_cons                 ........:::::::::::::::::..::::.::::::::.....:::::...::::::::::::::::::::::::....:::::::::::::::::::::::::::::::.:::::.::::::::..:::::::::::::::::::
#=GC RF                      ........CuuagccCCucaucAGc..agGG.cCCUCuaa.....AGggc...cuCuGuUGAAUUuAUuUGGCUGAc....aAAGaaAAACAACUUCCuGaGCuGCCUGuUU.GAUAA.cCCCUCAG..CACAGCUaaAUGAuGUCUC
//
# STOCKHOLM 1.0

#=GF AC   RF02040
#=GF ID   HOTTIP_1
#=GF DE   HOXA transcript at the distal tip, conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   51.80
#=GF NC   41.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   21423168
#=GF RT   A long noncoding RNA maintains active chromatin to coordinate homeotic
#=GF RT   gene expression.
#=GF RA   Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR,
#=GF RA   Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA,
#=GF RA   Chang HY
#=GF RL   Nature. 2011;472:120-124.
#=GF WK   HOTTIP
#=GF SQ   7


AJ335286.1/133-189     GGGAGGGGAGGUGGGCGCGCGA-UUGGGUUGCGAUCUGGAGCAGUGGGGACAGGUCAG
AANU01289438.1/446-502 GGGAGGGGAGGUGGGCUCGCGA-UUGGGUUGCGAUCUGGAGCGAUGGGGACAGGUCAG
AAKN02039093.1/568-625 GGGAGGGGACGUGGGCGCACCGCUUGGGUUGCGACCUGAGGCCGUGGGGACAGGUCAG
ABVD01019942.1/296-352 GGGAGGGGAAGAGGGCGCACGG-UUGGGUUGCGACCCGUGGCGGUGAGGACAGGACAG
AAWR02014104.1/186-242 GGGAGGGGACUGGGGCGCGCUG-UUGGGUUGCGACCUGAGGCGGUGGGCACAGGUCAG
ABDC01121664.1/358-414 GGGAGGGGAGGUGGGUGCGCGG-UGGGGUUGCGACCUGAGGCGGCGGGGACAGGUCAG
AAQR03057534.1/538-593 GGGAAGGGAGGUGG-UGCGUGA-UUGGGUUGAGACCUAAGGCGGUAGGGACAGGUCAG
#=GC SS_cons           ::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::
#=GC RF                GGGAGGGGAgGuGGGCGCGCGG.UUGGGUUGCGACCUGaGGCGGUGGGGACAGGUCAG
//
# STOCKHOLM 1.0

#=GF AC   RF02041
#=GF ID   HOTTIP_2
#=GF DE   HOXA transcript at the distal tip, conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   80.00
#=GF TC   87.70
#=GF NC   71.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 15.68 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   21423168
#=GF RT   A long noncoding RNA maintains active chromatin to coordinate homeotic
#=GF RT   gene expression.
#=GF RA   Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR,
#=GF RA   Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA,
#=GF RA   Chang HY
#=GF RL   Nature. 2011;472:120-124.
#=GF WK   HOTTIP
#=GF SQ   25


AK093987.1/1307-1682         AGUGUGCCCUUUCCUUCUUGACUUUUUAG----CAGUUCUGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------UCUCCCUGAC-UGGCCAUUUGCAGACUCAGGAACUAGCCUC-UGUAGGGACUUGAUUUUUCUGUUACUUUCU-------GGCCGUUUCACC-----------------------A--CCCCCCUUCCUCCCUCCAAGUGGCAUUGUAAAACUC-ACAGUGACAAAGAGACAGAGUAGGGUUC-UAGGCCCCUGUUCCUGGGGACU--UGAAGGC-------GGUUUUACA-UACUGGUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCC-AGCCAG-CAU--GAG--AACUGCCAUGCGAGCGU-----AGAGACA--------CAGGCAGCAG-CA----AAAGGCCC-AUUGCCCACAUCCCCUCA
AANU01289438.1/1839-2212     AGUUUGCCCUUUCCUUCUUGACUUUUUAG----CAGUUCUGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------UCUCCCUGAC-UGGUCAUUUGCAGACUCAGGAACUAGCUUC-UGUAGGGACCUGACUUUUCUGUUCCUUUCU-------GGCCCUUUCACC-----------------------A--CCCCCCUUCCUCCUUCCAAGUGGCAUUGUAAAACU---CAGUGACAAAGAGACAGAGUAGGGUUC-GAGGCCCCUGUUCCUAGGGACU--UGAAGGC-------GGUUUUACA-UACGGGUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAG-CAU--GAG--AACUGCCAUGCAAGCGU-----GGAGACC--------CAGGCAGCAG-CA----AAAGGCCC-ACUGCCCGCAUGCCCUCA
ABRN01187573.1/151-523       AGUGUGCCCUUUCCCUCCUGCCUUUUUAG----UAGCUCCGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------CCUCCCUGAC-UGACCAUUUGCAGACUAAAGAACCAGCCUC-UGUAGGGACCUGAUUUUUGUGUUACUUUCC-------GGCCCGUUCG----------------------------CCCCCCUUCCUUCCUCCAAGUGGCAUUGUAAAACUC-AUGAUGACAAAGAGACAGGGUAGGGUUU-GAGGCCCCAGUUCCUGAGGACU--UAAGGGC-------UGUUUUACA-UACAGGUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAU-CUU--GAG--AACUGCCAUGCAAGCCU-----GGAGACC--------CAGGCAGCUC-CU----AAAGGCCC-ACUGCCCACCUACCCUCA
AAPY01584654.1/1562-1934     AGCAUGCCCUUUCCCUCUUGACUUUUUAG----CAGUUUUGGGUAAAUAUUGAUUUGCCCCCCAGUUUACCU------UCUCUUCCAC-UGGCCAUUUGCAGACUAAGGAACCAGCCUC-UGUAGGAACUUGAUUUUUGUGUUACUUUCU-------GGCCCUUUUACC------------A-------------CCUCCCCUCCUCCCUCCAAGUGGCAUUGUAAAACUC-ACGGUGACAAAGAGACAGAGUAGGGUCC-AAGGCCCUAGUUCCUGGGGACU--UGCAGGC-------GGCUUUACA-UACGGGUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGUCGUCU-AGCCAG-CGU--GAG--AACUG---UGCAAGCCU-----GGAGACC--------CAGGCAGCUG-CA----GAAGG-CC-GGCGCCCACCUCCCCUCA
AAWR02014104.1/1556-1928     AGUGUGCCCUUUCCCUCCUGCCUUUUUAG----UAGAUCCGGGUAAAUAUUGAUUUGC-UCCCAGUUUACCU------CCUCCCUGAC-UGGCCAUUUGCAGACUAAGGAACCAGCCUC-UGUAGAGAUCUGAUUUUUGUGUUCCUUUCC-------GGCCCGUUCA----------------------------CCCCCCUUCCUUCUUCCAAGUGGCAUUGUAAAACUC-ACGGUGACAAAGAGACAGGGUAGUGCUC-GAGACCCCAGUUCCUGAGGACU--CGAAGCC-------UGUUUUACA-UACGGGUCAGAC---GCGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAG-CGU--GAG--AACUGCCAUGCAAGCCU-----GGAGACC--------CAGGCAGCUG-CG----AAAGGCCC-ACCGCCCACCUCCCCUCG
ACBE01077434.1/1266-1639     AGUGUGCCCUUUCCCUCCUGCCUUUUUAG----UAGCUCCGGGUAAAUAUUGAUUUGC-CUCCAGUUUACCU------CCUCCCUGAA-UGGCCGUUUGCAGACUGAGGAACUAGCCUC-UGGAGCGACUCGAUUUUUGUGUUACUUUCC-------GGCCCGUUCG----------------------------CCCCCCUUUCUUCCUCCAAGUGGCAUUGUAAAACUC-ACAGUGACAAAGAAACAGGGUAGGGUUC-GAGGCCCCAGUUCCUGAGGAGU--UGAGGGC-------UGUUUUACA-UACAGGUCAGAC---ACGGCUAGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAG-CGU--GAG--AACUGCCAUGCAAGCCU-----GGAGACC--------CAGGCAGCUGCCG----AUAAGCCC-ACUGCUCACCUCCCUUGU
ABRR01258443.1/1381-1754     AGUGUCCCCUUUCCCUCCUGCCUUUUUAG----UAGCUCCGGGUAAAUACUGAUUUGC-CCCCAGUUUGCCU------ACUCCCUGAC-UGGCCAUUUGCUGACUAAAGAACCAGCCUC-UGUAGGGACCUGAUUUUUGUGUUACUUUCC-------GGCCCAUUCAC---------------------------UCCCCCUUCCUUCCUCCAAGUGGCAUUGUAAAACCC-AUGAUGACAAAGAGACAGGGUAGGGCUU-GAGGCCCCAGUUCCUGAGGACU--UAAGGGC-------UGUUUUACA-UACAGGUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAG-CGU--GAG--AACUGCCAUGCAAGCUU-----GGAGACC--------AAGGCAGCUU-UG----AAAGGCCC-ACCGCCUGCCUCCCCUCC
ABRP01099873.1/1125-1501     AGAGUGCCCUUUCUCUCCUGCCUUUUUAG----UAGCUCCAGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------CCUCCCUGAC-UGGCCAUUUGCAGACUAAGGAAGUGGCCUC-UGUAGGGACUUGAUUUUUGAGUUACUUUCU-------GGGGCAUUCAUU-----------------------CACCUCCCCUUCCUUCCUCCAAGUAGCAUUGUAAAACUC-ACGGUGACAAAGAGACAGGGUAGGGUUC-AAGGCCCCAGUUCCUGAGGACU--UGAGGGC-------UGUUCUGCA-UAUGGGUCAGAC---ACGGCUAGAGGCCAAGGUCAAGUUGAAAGUUGUAGUCU-AGUCUG-UUU--GAG--AACUGCCAC-CAAGCCU-----GGAGACC--------CAGGCAGCUG-UG----AAAGGCCC-ACCGCUCACCUCCUCUCA
AAFC03071412.1/120324-119951 AGUGUGCCCUUUCCCUCCUGCCUUUUUAG----UAGCUCCGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------CUUCCCUGACUUGGCCAUUUGCAGCCUAAAGAACCAGCCCC-UGUAGGGACUUGAUUUUUGUGUUACUUUCC-------GGCCCGUUCA----------------------------CCCCCCUUCCUUCCUCCAAGUGGCAUUGUAAAACUC-AUGAUGACAAAGAGACAGGGUAGGGUUU-GAGGCCCCAGUUCCCAAGGACU--UGAGGGC-------UGUUUUACA-UACAGGUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAU-GGU--GAG--AACUGCCCUGCAAGCCU-----GGAGACU--------CCGUACGCUU-CU----CAAGGAAU-ACCGCCCACCUCCCCUCA
ABDC01121664.1/1756-2128     AGUGUGCCCUUGCCUUCUUGACUUUUUAGAGCUUUAUUUCAGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------UCUCUCUGGC-CA---UUUUGCAGACUAAGGAACUGGGCUC-UGUAAGGACUUGAUUUUUGUGUUACUUUCC-------AGCCCUUUUGC---------------------------CCCUCCUUCCUCCCCCCAAGUGGCAUUGUAAAACUC-ACAGUGACAAAGAGACAGCAUAGGGUUC-GAGGCCCCAGUUCCUGGGGACU--UGAAGGC-------AGUUUUACA-UACGGGUCAGAC---AUGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAG-UGU--GAG--AACUGCCAUGCAAGCCU-----GGAGACC--------UAGGUGGCUG-C-----AAAGGCCC-ACCG-CAACCUCCCCGCA
AC184818.19/150114-149736    AGUGUGCCCUUUCCCUCCUGCCUUUUUAG----UCGCUCGGGGUAAAUAUUGAUCUGC-CUCCAGGUUACCU------CCUCCCUGAA-UGGCCAUUUGCAGACAUUUGCCCCAGCCUC-UGUAGGGACUUGAUUUUUGUGUUACUUUCC-------GGCCCCAUCA----------------------------CCCCCCUUCCUUCCUCCAAGUGGCAUUGUAAAACUC-ACGGUGACAAAGAGACAGGGUAGGGUUC-GAGGCCCCAGUUCCUGAGGACU--UGAGGGC-------UAUUUUACA-UACGGGUCAGAC---ACCGCUAGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAG-UGU--GAG--AACUGCCAUGCAAGCCUGGAGAGGAGAGU--------CAGGCAGCUGCCG----CAAGGCCC-ACUGCCCAUCUCCCUUCU
ABRO01036386.1/419-796       AGUGCGCCCUUUCCCUCUUGACUUUUUAG----CAGUUCUGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------UCUCCCUCAC-UGGCCAUUUGGAGACUACGGAACCAGCCUC----AAAGACUUAAUUUUUGUGUUGCUUUCC-------GGCCCUUUCGUC-----------------------CCCCACCCCUUCCUCCCUCCAAGUGGCAUUGUAAAACUC-UCAGUAACAAAGAGACAAAGUAGGGUUC-GGAGCUCUGGUUCCUGGGGACU--UCAGGGC-------AGUUUUACA-UACGGGUCAGAC---GCGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCUAAGUCAG-CGU--GAGAAAACUGCCCUGCAAACCU-----GGAGACC--------AAGGCAGCUU-CC----AGAGGCCC-ACUGCUCACCUCCCCUCA
AAKN02039093.1/1941-2323     AGUGUACCCUUUCCCUCUUGACUUUUUAG----UGGUUCUGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------UCUCUCC-AC-UAGCCAUUUGCAGACUAAGGAACUGGUCUC-UGUAAAGACUUGAUUUUUGCGUUACUUUCC-------GGCCAUUCAUCC-----------------------CCCACCCUCUCCCUUCCUCCAAGUGGCAUUGUAAAACUC-ACAGUGACAAAGAGACGGGGUAGGGUUC-GAGGCCUCAGUUCCUGGGGACU--UGAGGGC-------GGUUUUACA-UACGGGUCAGGC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGUCAG-CGUGAGAG--AGCUGCCAUGCAAGCCU-----GGAGACC--------ACCGCAGCUG-UACUGUGGCUGCUA-AACGCCCACCACCCAUCU
AAGV020195931.1/478-849      AGUAUGCUCUUUUUCUCUUGCCUCUUUAG----CAGCCCUGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------CCUCCCCAAC-UGGCCAUUUGCAGACUAAGAAACUGCCCUC-UGUAGAGACCCGAUUUUUGUGUUACUUUUC-------UGCCAUUU------------------------------GUCUCCCUUCCCCCUCCAAGUGGCAUUGUAAAACUC-AGAGUGACAAAGAGAGAGGAUAGGAUUG-GAGGCCCCAGGAACUGGGGCCU--UGAGAAC-------UGUUAUACACUACAGGUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAG-CCA--GAG--AACUGCCGGGCAAGCCU-----AGAGACC--------CAGGCAACGG-CA----AAAGGCCC-ACCGCCUACCUUCCCUCA
ABRQ01101206.1/1740-2108     CGUGUAUCCUUUUCCUCCUGCCUUUUUAG----CAGCUCCGGGUAAAUAUUGAUUUG--CCCCAGUUUACCU------CCU--CUGAC-UGGCCAUUUGCAGACUGAGGAAUUGGCCUC-UGUAGGGACCUGAUUUUUGAGUUACUUUCC-------GCCCGCUU------------------------------GCCUCCCUUCCCCCUCCAAGUGGCACUGUAAAACUC-AGGGCGACAAAGAGA----GCAGGGUUC-GAGGCUUCAGUUCAUGGGGCCU--GGAAGGC-------UGUUUUACG-UGUGGGUCAGACUCAACGGCCGGAGGCCAAGGUCAAGUUGAAUGUUGCAGUCC-AGCCAG-CGUCAGAA--AACUGCCAUGGAAGCCU-----GGAAACC--------UAGGCGGCUU-UG----AAAGAACU-UCUGCCUACUUUCCCUCA
AALT01189717.1/2632-2266     UCUGUGUCUGUUCCCUUCAGUCGUUUUAG----UAGAUCCAGGUAAAUAUUGAUUUAC-CCCCAGUUUGCCU------CCUUCCU--C-UGGCCAUUUGCAGACUAAGGAACUGGCCUC-CAAAGAGACUUGAUUUUUGUGUUACUUUCC-------AGCCCCUUCUC---------------------------CCCCCCUUUCAUCCUCCAAGAACCAUUGUAAAACUC-GCAGUGACAAAGAGAGUGGGUAGGGUUU-GAGGCCCCUGUUCCUGAGGACU--UGAGUGC-------UGUUUUACA-UACGGGUCAGAC---ACGGCUAGAGGCCAAGGUCAAGUUGAAAGCUGCAGUCU-AGCCAG-UGU--GCG--AAC-----UGCAAGCCC-----GGAGACU--------CAGGACCCCC-UG----UGCUGUAC-AAGGCCCACCUCGCUCUA
AAIY01389017.1/3950-3570     CAUG-----UCCAUGUCCGGCCUUUUUAG----CAGCUCUAGGUAAAUAUCGAUUUG--CCCCAAUUUACCA------CCUCCUUAAC-UGACCAUUUGCAGACUAAGAAACCGACCUC-UGUAGGGACCAGAUUUUUAUUUGACUUUCCACUCCCCAGCCCCGCCAG---------------------------UCUCCCUUCCUCCCUCCAAGUGGCAUUGUAAAACU---CAGUGACAAAGAGACCAAGUAAGGUGC-GAGGCCCCAGUUCCUGGGGCCU--UGAGGGC-------UAUUUUACA-UAUGGGUCAGAC---AGGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAAUCU-AGCCUU-UCU--GAG--AACUGCCCUGCAAACGC-----AGAGACCAAGGCCAGCCGGCCGCUG-GA----AAAGACCU-UCUGGCCACCUCCCCUCG
AANN01604110.1/4170-3805     AGUGUACUC---------UACUUUUUUAG----UAGAUCCGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCUAUCUAGCCCUAUUCCC-CAGCCAUUUGCAAGCUAAGGAACUGGCCUCUGGUAGGGACCUGAUUUUUGUCUUACUUUCC-------GGCCCAUUUG----------------------------CCCCCCUUCCUUCCUCCAAGUGGCAUUGUAAAACUC-CCAGUGACAAAGAGACAGGGUCGGGUUCUGAGACCUCAGUUCCUGAGGACU--UGAGUGC-------UGUUUUACA-UACAGGUUAGACGC-ACGGCUAGAGGCCAAGGUCAAGUUGAAUGUUGCAGUCU-AGCCUA-CGU--GAG--AACUGCC-UGAAAGCCU-----AAGGACU--------CAGACAUCUG-UG----AAAG--------GCCUACGUCCCCUCA
AC122669.6/132831-133205     AGUGUGUCCUCUCCCUUCUGAC--UUUAG----CAGUACUGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------UCUUACUGAC-UGGCCAUUUGCAGACUAAGGAAGCAACCUC-UGUGAAGACUUGAUUUUU--GUUACUUUGG-------AGCCCUUUUCAU-------------CCCCCCCAUCCCCCACUCCUUCCUCCCUCUAAGUGGCAUUGUAAAACUCAACAGUGACAAAGAGACGAAGUACGGUUC-CGGGCUCCAAUUCUUGGAGACU--GGAGGGUUUGAGGGCAGUUUACA-UACAGGUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCUGUCU-AGUCAG-CGU--GAGA-AACUACAAUG--AGCCC-----AGAGACU-----------------------------GCCG-ACUGCCCACCUCCCCUCU
AC015583.34/50779-50402      AGGGAGUCCUUUCUCUCCUGAC--UUUAG----CGGUCCUGGGUAAAUAUUGAUUUGC-CCCGAGUUUACCU------UCUUACUGCC-UGACCAUUUGCAGACUAAAGAACCAACCUC-UGUGAAGACUUGAUUUCUGUGUUACUUUGG-------AGCCCUUUUCAU-------------CCGUC----CCCCCACUCCUUCCUCCCUCUAAGUGGCAUUGUAAAACUCAACAGUGACAAAGAGACGAAGUACGGUUC-CAGGCUCCAAUUCUCGGAGACUCUCGGAGACUCGAGGGCAGUUUACA-UACAGGUCAGAC---AC-GCUGGAGGCCAAGGUCAAGUUGAAAGUUGCUGUCU-AGUCAG-CGU--GAGA-AACUACAAUGAAAGCCC-----AGAGAC---------------------------AGAGCCG-ACUGCCCACCUCCCCUCG
AAYZ01055301.1/1460-1855     CAUGUCCCCUGCACACC----CAUUUUAG----CCAUUCUCUGUAAAUAUUGAUCUGC-CCCCAGUUUACCU------UCUCCCUGAC-UGGCCACUGGCAGCAGUAGGAACCGGCCUC-AGCAGGGGCUUGGUUUUUGUGUUAGUUUCA-------GGCCCUCUCAGCUACCCGCCCACAACCGCCCCCCCCCCAAGCCUAUCCUGUCUCUAAAUAGCAUUGUAAAACUC-ACAGUGACAAAGAAAUCGAGUAGGGUUU-GAGGCUCCAGUUCCCAGGGAUU--CCAGGGC-------GGUUUUACC-UACAGGUCAGAU---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUGGCAGUCU-AGCCAG-CGU--GAG--AAUUUGGCUGCAAGCUU-----GAAGACC---------AGACUCCCG-CU----AAAGGCUG-GCCGCCCAGCUCCCCUCG
AAGU03015372.1/8859-8492     AGUGUACCCUUAUCCUCCUGACUUUUUAG----CAGCUCCGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------CCUCCCCCAC-UGGCCAUUUGGAGACUAAAGAACUGGCCUC-UGUAGGGACCUGAUUUUAGCAUUACUUUCC-------ACCGGAUUGC----------------------------CUCCCUU-CCCUCCUCCAAGUGGCAUAGUAAAAC---AGGGUGACAAAGAGACAGAAUAGGGUUC-GAGGCUCCAGUUCCU--GGCCU--UGAGGGC-------UGUUUUACA-UACGUAUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAG-CGU--GAG--AACUGCCAUGCAAGCCU-----UGAGACC--------CAGGCGGCUU-UG----AAAGACCC-UCUGCUUUCCUCCCCUCA
AAGW02035945.1/42879-42503   AAUGUGCCCUUUCUCUCUUGACAUUUUAG----CAGCUGUCAGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------GCUGCCUGGC-UGGCCACUGGCAGACUCGGGGACCGGCUUCGGGAAGGAACUUGAAUUUUGUAUGACUUUCA-------GGCCCUUUCAGC-----------------------UCUCCCUAAACCUUCCCUCUGAGUGGCAUUGUAAAAC---ACAGUGACAAAGAGACAGAGUAGGGCUU-GAGGCCCCAGUUCCUGGGGACU--GCAGGGC-------GGUUUCACA-UAC-GGUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAG-CGU--GAG--AACUUCCAUGCAAGCCC-----GGAGACC--------CUGGUGGCCG-CA----AAAGGCCCAAUCGCCCACCUCCCCUCA
AAQR03057534.1/1941-2315     AGUGUGCCCUUUCCUUCUUGACUUUUUAG----CAGUUCUGAGUAAAUAUUGAUUUGCCCCCCCGUUUACCU------UCUCUCUGGC-CA---UUUUGCAGACUAAGGAACCGGGCUC-U-UAGGGAUUUGAUUUUUGUGUUACUUUCC-------GGCCCUUUUGCU------------------------GCCCUCCCCUCCUCCCUCCAAGUGGCAUUGUAAAACUC-ACAGUGACAAAGAGACAGAGUAGGGUUU-GAGGCCCCAGUUCCUGGGGAUU--C-AAGGC-------AGUUUUACA-UACGGGUCAGAC---ACGGCUGGAGGCCAAGGUCAAGUUGAAAGUUGCAGUCU-AGCCAGUUGU--GAG--AACAGCCAGGCAAGCCU-----GGAGACC--------CAGGCAGCUG-GA----AAGGCCCACACUGCCCACCUCCUCUCA
AAPE02018004.1/31504-31137   AGUGUGUCCUUUCCCUGCUGCCU----------UAGCUCCGGGUAAAUAUUGAUUUGC-CCCCAGUUUACCU------CCUCCCUGAC-UGUCCAGUUGCAGACUAAAACACCGGCCUC-UGUAGGGACCUGAUUUUUGUGUGACUUUCC-------GGGGCCUGUUU---------------------------CCCCCCUUCCUUCCUCCAAGCGGCAUAGUAAAACUC-GAGGUGACAAAGAGGCAGGGUAGGGUUC-AAGGCCCCAGUUCCUGACGACU--UGAGGGC-------UAUUUUACA-UACGGGUCAGAC---AGGGCUGGAGGCCAAGGUCAAGUUGAACGUUGCAGUCU-AGCCAA-UCU--GAG--AACUGCCAUGCAAGCCU-----GGAGACC--------CAGGCAGCUG-UG----AAAGGCCC-ACCGCCCAUCUCCCCUCA
#=GC SS_cons                 :::::::::::::::::::::::::::::....:::::::::::::::::::::::::.:::::::::::::......::::::::::.::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::.......:::::::::::...........................::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::.::::::::::::::::::::::..:::::::.......:::::::::.::::::::::::...::::::::::::::::::::::::::::::::::::::.::::::.:::..:::..:::::::::::::::::.....:::::::........::::::::::.::....::::::::.::::::::::::::::::
#=GC RF                      aGUGUgcCCUuucccUCcuGcCuUUUUAG....caGuUCugGGUAAAUAUUGAUUUGC.CCCCAGUUUACCU......uCUccCUgaC.UGGCCauUUGCAGaCUaaGGaACcgGCCUC.uGuAGgGACuUGAUUUUUGugUUaCUUUcc.......gGCCcuuUcag...........................ccccCCuUCCuuCCUCcAAGUGGCAUUGUAAAACUC.acaGUGACAAAGAGAcaGgGUAGGGUUc.gAGGCcCCaGUUCCUGgGGaCU..ugAGGGC.......uGuUUUACa.UACgGGUCAGAC...AcGGCUGGAGGCCAAGGUCAAGUUGAAaGUUGCaGUCU.AGcCaG.cgU..GAG..AACUgCcaUGcAAGCcu.....gGAGACc........caGGcagCug.cg....aaaGGccc.acuGCCcAccUCCCCUCa
//
# STOCKHOLM 1.0

#=GF AC   RF02042
#=GF ID   HOTTIP_3
#=GF DE   HOXA transcript at the distal tip, conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   99.70
#=GF NC   39.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 16.13 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   21423168
#=GF RT   A long noncoding RNA maintains active chromatin to coordinate homeotic
#=GF RT   gene expression.
#=GF RA   Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR,
#=GF RA   Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA,
#=GF RA   Chang HY
#=GF RL   Nature. 2011;472:120-124.
#=GF WK   HOTTIP
#=GF SQ   23


AAWR02014104.1/2009-2361     UUUUGGGGCGGUGUUUACAGACUC------UUCUUCUCUGCCU----CCGCCCUGCUCU--UG-GCCCGGGCUUUG-AGCCUUUU-CUGUUUUC-CAGCCAGACCCG-------GAAAAA--CGAAAACACAGCUCGGGGAGCCCCCACC-AGCCGGCGCCUGUGCCAGCUCACCUCUGGCCAUGGC-----GCAGCUGCU----GGUGCAC------ACAGCG-GCCAAGGCCAGCUCCACAUUCCUCCCUCCAGCUCCC-CACUUCACCGGAGAC----CGAGCCCUGCAUGCAGAGGAAG---GGCCCCAG-CUCCACAGACUGCCAAAGUCGA--CAGGGUGCCUCCUCACCAAAAAUGGUGAGACAAGAUUUCA-UCUUGU--CUGCUGA-GGAGCAACAA-GCAG-
ABDC01121664.1/2209-2562     UUGGGGGACGAUGUUUACCGACUC------UUCUUCUCUGCCU----CGGCCCUGCUUU--UG-GCUGGGGCUUUG-AGCCUCUU-CUGUUUUC-CAGCCAGACCCG-------GAAAAA-ACGAAAACACAGUUUGGGGAGCCCCCACU-AGCCGGCGCCUGUGCCAGCUCCUCUCUAGCCAUGGC-----GCAGCUGCG----GGUGCAC------ACAGCG-GCCAAGGCCAGCGCCACAUUCUUCCCUCCCCCUCCC--ACUUCACCGAAACCCC---GAACCCUGCGCGCAGAGGAAG---GGCCUCAG-CUCCACUGACUGCCAAAGUCGA--CUGGGUCCCUCCUCGCCAAAAAUGGUGAGAUGAGAUUUCG-UCUUGU--CCGCUGA-GGAGCCACAA-GCAG-
ABRP01099873.1/1583-1937     UUUUGGGGCGGUGUUUACAGACUC------UUCUUCUCUGCCU----CCGCCCUGCUCU--UG-GCCCGAGCUUCA-AGCCUCUU-CUGUUUUC-UAGCCAGACCCG-------GAAAAA--CGAAAACACAGCUCUGGGAGCCCCCACC-AGCUGGCGCCUGUGCCAGCUCACCUCUGGUCACGGC-----GCAGCUGCC----GGUGCAC------ACAGCG-GCCACGGCCAGCUCCGCAUUCCUCACUCCCUCUCCC-CACUUCACCGGAGACCG--AGAGCCCUGCGUGCAGAGGAAG---GGCCCCAG-CUCCACAGACUGCCAAAGUCGA--CUGGGUCCCUCCUCACCAAAAAUGGUGAGACAAGAUUUCA-UCUUGU--CUGCUGA-GGAGCCGCAA-GCAG-
AAQQ01071881.1/162-513       UUUUGGGGCGGUGUUUACGGACUC------UUCUUCUCUUCCU----CCGCCCUGCUCU--UG-GCUGGGGUUUCGUAGUCUAUU-CUGUUUUC-CAGCCAGACCCA-------GAAAAA--CGAAAACACAGCUUGGGAAGCCCCCCUC-AGCCGGCGCCUGUGCCAGCUCACCUCUGGCCGUGGC-----GCGGUUGCU----GGUGCAC------GCAUCG-GCCAAGGCCAGCUCUACAUUCUUCCCUCCCCCGCCC--ACUUCACCCGAGCCGG---GAGACCAGCGAACAGAGGAAG---GGCCUCAG-CUU--CAGACUGCCAAAGUCGA--CUGGGUCCCUCCACACCAAAAAUGGUGAGACAAGAUUUCA-UCUUGU--CCUCUGA-GGAGCCACAA-GCAG-
ABRN01187573.1/607-955       UUUUGGGGCGGUGUUUACAGACUC------UUCUUCUCUGCCU----CCGCCCUGCUCU--UG-GCCCAGGCUUCG-UUCCUCUU-CUGUUUUC-CAGCCAGACCCG-------GAAAAA--CGAAAACACAGCUCGGGGAGCCCCCACC-AGCCAGCGCCUGUGCCAGCUCACCUCUGGCCAUGGU-----GCAGCUGCCUCCCGGUGCAC------ACCGCG-GCCAAGGCCAGCUCCACAUUCCUCCCUCACUCUCCC-CACUUCACCGGAGAC----CGAGCCCUGCAUGCAGAGGAAG---GGCCCCAG-CUCCACAGACUGCCAGAGCCAG--CUAGGUCCCUCCUCACCAAAAAUGGUGAGACA---------AGAUUU--CUGCUGA-GGAGCCCCAA-GAAG-
ABRO01036386.1/886-1230      UUUUGGGGCGGUGUUUACGGACUC------UUCUUCUCUGCUU----CCGCCCUGCACU--UG-GCCCCGGCUUUG-AGCCUCUC-CUGUUUUC-CAGCCAGACCCG-------GAAAAA--CGAAAACAAGACUUGGGAAGCCCCCACC-AGCCGGCGUCUGUGCCAGCUCACCUCUGGCUGUGGC-----U-GGCUGCG----GCUGCAC------AUCCCG-GCCAAGGCCAGCUCCACAU-CUUCCCUCCCCCUCCC--ACUUCACUGGAGCCGG---GAGCACUUCGCCCAGAGGAAG---GGCCUCAG---------ACUGCCAAAGUCGA--CUGGGUCCCUCUACUCCAAAAAUGGUGAGGCAAGAUUUCAAUCUUGU--UCACCGA-GAAGCCACAAAGCAG-
AAKN02039093.1/2412-2741     UUUUGGGGCAGUGUUUACGGACUC------UUCUUCUCUGCCU----CCACCCAGCUCU--UG-GCAGGGGCUUUG-AGCCUCUU-CUGUUUCU-CAGCCAGACCCG-------GAAAAA--CGAAAACACGGCUUGGGAAGCCCCCAGC-AACCGGCGCCUGUGCCAGCUCACCUCUGGCUGUGGC-----GAGGCUGCC----UGUGCGC------ACUGCC-GCCAAGGCCAGCUC-ACGUUCUUUC-UCCCCCUCCC--ACUUCACUGGAGCCGG---GAGCCUUGCAAGCAGAG------------------------ACUGCCAAAGUCGA--CUGG-UCCUUCCUCACCAAAAAUGGUGAGACAAGAUUUCG-CCUUGU--CCGCUGA-GGAGCCACAA-GCAG-
AAPY01584654.1/2016-2369     UUCUGGGGCGGUGUUUACCGACUC------UUCUUCUCUGCCU----CCGCCCUGCUCU--UG-GCUGGGGCGUCA-AGCCU-UU-CUGUUUUU-CAGCCAGAUCCG-------CGAAAA--CGAAAACACAGCUCGGGGAA-CCCCACC-AGCAGUCGCCUAUGCCAGCUCACCUCUGGCCGUGGU-----GCAGCUGCU----GGUGCAC------GCAGCCCGGCAAAGCUAGCUCCAUAUUCUUCCCUCCCCUUCCC--ACUUUACUGAAGCCCG---GAGCCCUGGAUGCAGAGGAAG---GGCCUCAG-CUCCACAGACUGCCAAAGUGGAGACCCGGUCCCUCCUCACCAAACAUGGUGAGGCAAGAUUUCA-UCUUGU--CUGCUAA-GGAGCCACAA-GCAG-
AAGV020195931.1/927-1280     UUUUCAGGCGACUUUUACCGACUC------UUC-UCGCUGCCU----CCGCCCUGCUCU--CC-GCCCGGGCUUCC-AGCCUCUU-AUGUUUUUGCAGCCAGAGCCG-------GAAAAA--UGAAAACACAGCUCGAGGAGCCCCCACC-AGCCGGCGCCCUUGCCAGUUCACCUCCGGCCAGGGC-----ACAGCUGCC----CUUGCAC------ACGGUG-GCCAAGGCCAGCUCCGAAUUCCUCCCUCCCCCUCCC-CACCUCGCCAGAGACCG---GAGCUCUGCGAGCAGAGGAAG---GGCCCCAA-GUCCACAGACUGCCAAGGUCGG--CUGGGUCCCUUCUCAUCAAAAAUGGUGAGUCAAGAUUUCA-UCUUGU--CCACUGA-GGAAACACAA-GCAG-
AALT01189717.1/2161-1805     UUUUGGGGCGGUGUUUACAGACUC------UUCUUCUCUGCCU----CCGCCCUGCUCU--UG-GCCCGAGAUUUG-AGCCUCCU-CUGUUUUC-CAGCCAGACCCG-------GAAAAA--CGAAAAUACAGCUCAGGGAGCCCCCAAC-AGCCAGCGCUUGUGCCAGCUCACCUCUGGCCAUGGC-----ACAGCUGCU----GGUGCAU------GCAGUGGGCCAAGGCUAACUCCACAUUCUUCCCGCCCUCUCUC-UGCUUCAC-GGAGACUGGCAGGAGCCUGCAUGCAGAUGGAGGAAGGGUUCAA-CUCGACCGGCUGCCCAAGUAAA--CUGGGUCUCUUCUCACCAUAA-UGCUACAACAAGAUU--A-UCUUGU--CUGCUGA-GGAGCUCUAA-GCAG-
AANN01604110.1/3721-3378     UUUUGGGGCGGUGUUUACAGACUC------UUCUUCUCUGCCU----CCGCCCUAUUCU--UG-GCCCAGACUUGG-AGCCUCUU-CUGCUUUC-CAGCCAGAUCCG-------GAAAAAUACGAAAACACAGCUCAGGGAGCCCCCACC-AGCUGGCGCCUAUGCCAGCUCACCUCUGGC----------------UGUU----GGUGCA--------CAAUG--CCAAGGCCAAAUCCACAUUCUUCCUUCUCUCUCCC-CACUUCUC-GGAGACCA---GAGACCAGAGCCCUGAAGAAGAAGGGCCCAAG-CUCUACAGACUG-CAAAACCAA--CUGGGUCCCUUCUCACCAAAAAUGGUAAGACAAGAUUUCA-UCUUGU--CCGUUGCGGGAGUCACAA-GCAG-
AAFC03071412.1/119854-119570 UUUGGGGGCAGUGUUUACAGACUC------UUCUUCUCUGCCU----CCGCCCUGCUCU--UG-GCCCGAGCUUCG-UGCCUCUU-CUGUUUUC-UAGCCAGACCCG-------GAAAAA--CGAAAACACUGCUCCGAGAGCCCCCACC-AGCUGGCGCCUGUGCCAGCUCACCUCUGGUCAUGGCAUGGCGCAGCUGCCUGCCGGUGCAC------ACCGCG-GCCAAGGCCAGCUCCACAUUCUUCCCUCAUUCUCCC-CAAUUCGCCGGAGACCA--AG--CCCUGAAUGCAGAGGAAG---GGCCCCAG-CUCCACAGACUG-------------------------------------------------------------------------------------
AC122669.6/133284-133639     UUUGGGGGCGGUGUUUACAGACUGGACUGAUUCUUCUCUGUCG----CCGCCCUGCUCU--AU-GCUGGGUUUCCG-AGCCACCG-AAGUUUUC-CAGCUAUGUUCA-------GAAAA---CGAAAACACAGCUCAGGAAGCCUCCACC-AGCAGUUGCCUAUGCCAGUUCACCUCUGGCAGUGGC-----UGUACUGCU----GGUCCAC------GCAGCA-GCCAAGACCAGCUCCACGUUCUUCCCUCCCCCUC----AGUUCACUGGAGCCGG---GAGCCCUGCACUCAGGGAAAG---GGCCUCAG-CUCUACAGACUGCCAAAGUCCG--CUGUGUCCCUCCGCUCCAAAAAUGGUGAGAAAGGAACCCA-UCUUUU--UCACAGA-GGAACCGGGA-ACAG-
AAYZ01055301.1/1954-2304     UUCUGGGGCGGUGUUUACUGGCUCC---UCUUCUUCCCUGCCU----CCGCCCUGCUCU--UG-GCCCGGGCGUGG-AGCUUCUUUCUGUUUCC-CAGCCAGACCUG-------GAAAAA--AAAAAAAAAAACGAAAA-----CGCAGC-UUGGGGAGCCCCCACCAGCUUGCCUCUGGCCACGGC------CAGCUGCU----GAUGCAC------ACUACA-GCCAAGGCCAGCUCCACAUUUUUCCCUCCCCCUCUC--ACUUCACCAGAGCCCGG-GGAACUCUG----CAGAGGAAG---GGCCUUGGACUGUGGGGACUGCCCAAGUCAA--CUGGGUCCCUCCUCAUCAAAAACAUUGAAAAGAAGUUUCA-UCCGGU-UUCCCCGA-AGAGCCACCC-GCAG-
AC015583.34/50313-50032      UUUGGGGGCGGUGUUUACAGGCUGGACUGGUUCUUUUCUGUCG---GCCGCCCUGCUCU--UA-GCUGGGUUUCUG-AACCUCCG-AAGUUUUC-CAGCUAGGUUCG-------GAAAAA-ACGAAAACACAGCUCAGGAAGGCUCCACC-AGCCGAUGCCUAUGCCAGUUCACCUCUGGCAGUGGC-----UGUACUGCU----GGUCCAC------ACAGCA-GCCAAGACCAGCUCCACGUUCUUUCCUCCCCCUC----AGUUCACUGGAGCCGG---GAGCCCUGCACUCAGGGGAAG---GGCCUCAG-CUCUACAGACUG-------------------------------------------------------------------------------------
ABRQ01101206.1/2191-2542     UUUUGGGGCGGUGUUAACCGACUC------UUCUUCUCAGCCU----CCACCCCGCGCU--CC-GCGGGG-CUUCC-AGUCUCUU-CCGUUUUC-CAUUCCAUUCGGAGCCCGGGAAAAAAAAGAAAACACAGCCCGGGAAGCCCCCAUC-AGCCGGCACCCAGCCUAGCUUAC---------GGAC-----GCAACUGCU----GAUUCAG------UGGGCG-GCCAAGGCCAGCUCCACAAUCUUCCUUUCACCUCCC-CACUUCACCAGCGACCG---GAGUCCCACACGCAGAGGAAG---GGCCCUAG-UUCCACAACCUGCCAAAUUCAG--CUGUGUCCCUCCUCCCCCAGAACGGUGAGAAA-GAUUGCA-UCUUCU--CUUCGGA-GCAGCCACAA-GAA-C
AAIY01389017.1/3491-3201     AUUUGGGGCGGUGUUAACGGACUC------UUCUUCUCUGUCUGUCCCCGCCCUGCUCU--CC-GCAGAG-CUUCA-AGCCUUCUUCUGUUUUC-CAGUCAGAGCUGGCAGGGGGAAAAA-AAGGGAAAACAGCCCAGGAAGCCCCCACU-GGCCGGCGCCCAUGCCAGCUCUCUUCUGGCCAGGAC-----GCAGCUGCUGCGCACUUCGC------GCGGGGGCCCACGGCAGGCAGCACAACCCUCCCUCCAUCUCCC--ACUCCACCGGCGGCCG---AAGCCCCACGCGCACUGGAAG---GGGCCCAG-GUCUACAGCU---------------------------------------------------------------------------------------
GU724873.1/1623-1959         UUUUGGGGCGGUGUUUACCGACUC------UUC---UCUGCCU----CCGCCCUGCUCA-----GCCAGGGCUUUG-AGCCUCUU-CGGUUUUC-CGGCCAGACCCG-------GAAAAA--CGAAAACACAGCUUGGGGAGCCCCCACU-AGCCGGCGCCUGUGCCAGCUCACCUCUGGCCAUGGC-----GCAGCUGCC----GGUGCAC------ACGGCG-GCCAAGGCCAGCUCCACAUUCUUCCCUCCCCCUCCC--ACUUCACCGUAGCCCC---GAACCCUGCGCGCAGAGAAAG---GGUCUCAG-CUCCACAG-------A---CGA--CUGGGUCCCUCCUCACCAAAAAUGGUGAGACAAGAUUUCA-UCU-GU--CGGCCGA-GGAGCCACAA-GCAG-
AC184818.19/149648-149293    UUUUGGGGCGGUGUUUACAGACUC------UUCUUCUCUGCCU----CCACCCUGCUCUCUUG-GCCCGGGCUUCG-AGCCUCUU-CUGUUUUC-CAGCCAGACCCA-------GAAAAA--CGAAAACACAGCUCGGGGAGCCCCCACC-AGCCGGCGCCUGUGCCAGCUCACCUCUGGCCAUGGC-----GCAGCUGCU----GGUGCAC------ACAGCG-GCCAAGGCCAGCUCCACAUUCCUCCCUCCCUCUCCCCCACUUCACCGGAGAC-G---GAGCCCUGCAUGCAGAGGAAG---GGCCCCAG-CUCCACGGACUGCCAAAGUCGA--CUGGGUCCCUCCUCACCAAAAAUGGUGAGACAAGAUUUCA-UCUUGU--CUGCAGA-GAAGCCACAA-GCAG-
AAGW02035945.1/42425-42072   UUUUGGGGCGGUGUUUACCGACUC------UUCUUCCCUGCCU----CCGCCCUGCUCU--UGG-CCGGAGCUUUG-AGCUUCUU-CUGUUUUC-CAGCCAGACCCG-------GAAAAA--CGAAAAUACAGUGUGGGGAGCCCCCACC-AUCCAGCGCCUGUGCCAGCUCACCUCUGGCCAUGGC-----GCGGCUGCU----GGUGCAC------ACAGCG-GCCAAGGCCAGCUCCACAUUCUUCCCUCCCC-UCCC--AUUUUACCGGAGCCCG---GAGCCCCGUGCGCAGAGGAAG---GGCCUCAG-CUACGCGGACUGCCAGAGUCGA--CUGGGUCCUUCCUCACCAAAAAGGGGGAGAGGAAAUUUCG-UCUUGUCCCCCCCGA-GGAGCCACUA-GCAG-
AAPE02018004.1/31056-30774   UUUUCGGGCGGUGUUUACAGACUC------UUCUUCUCUGCCU----CCGCCCUGCUCU--UG-GCUCAAGCUUCA-AGCCUCUU-CUGUUUUC-UAGCCAGACCUG-------GAAUAA--CGAAAACACAGCUCUGGGAGCCCCCACCGAGCCGGCGCCUGUGCCAGCUCACCUCUGGCCAUGGC-----GCAGCUGCC----GGUGCACGCAGCGGCCAAG-GCCAAGGCCAGCUCCACAUUCCUCCAUCCCUCUCCC-CACUUCACCGGAGAC----CGAGCCCUGCGUGCAGAGGAAG---GGCCCCAG-CUCCACAGACUG-------------------------------------------------------------------------------------
AAQR03057534.1/2396-2741     UUUUGGGGCGGUGUUUACCGGCUC------UUCUUCUCUGCCU----CCGCCCUGCUCU--UG-GCUG-GGCUUUA-AGGCUCUU-CUGUUUUC-CAGCCAGACCCA-------GAAAAA--CGAAAACACAGUUUGGGGAGCCCCCACU-AGCUGGCGCCUGUGCCAGCUCAUCUCUGGCCAUCGC-----GCAGCUCCG----GGUGCAC------ACAGGG-GCCAAGGCCAGCUCCGCAUUCUUCCC--CCCCUCCC--ACUUCUCUGGAGCCCC---GAACCCAG----CAGAAGAAG---AGCUUCAG-CUCCAUAGGCUGCCAGAGUCGA--CUGGGUCCCUCCUCACCAAAAAUGGUGAGAUGAGAUUUCG-UCUUGU--CCGCUGA-AGAGCCACAC-GCAG-
AAGU03015372.1/8412-8065     UUUUGGGGCGGUGUUAACCGACUC------UU-UUCUCUGUCU----CCGCC-UGCUCU--CG-GCGG-GUCUUCC-AGUCUCUU-C-----UC-CAUUCAGAGCUG-------GAAAAAAACGAAAACACAGCCCAGGAAGCCCCCAUC-AGCCAGCACCCAGGCCAGCUCACCUCGGCCCAGGGC-----ACAGCUGCC----CGUGCAC------UCCGUG-GCCAAGGCCAACUCCACUAUCUUCCCUCCACCUCCC-CACUUCACGGUCAACCG---CAGCCCCACAUGCAGAGGAAG---GGCCCCAG-CUCCGGAGCCUGCCAAAGUCGG--CUGGGUGCCUCCUCACCAAAAAUGGUGAGAAAAGAUUGCA-UCUUGU--CCGCUGA-GGAGCCACAA-ACAG-
#=GC SS_cons                 ::::::::::::::::::::::::......:::::::::::::....::::::::::::..::.::::::::::::.::::::::.::::::::.::::::::::::.......::::::..::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::.....:::::::::....:::::::......::::::.::::::::::::::::::::::::::::::::::::..::::::::::::::::...:::::::::::::::::::::...::::::::.::::::::::::::::::::::..::::::::::::::::::::::::::::::::::::::::.::::::..:::::::.::::::::::.::::.
#=GC RF                      UUUuGGGGCGGUGUUUACaGACUC......UUCUUCUCUGCCU....CCGCCCUGCUCU..ug.GCcggGgcUUcg.AGCCUCuU.CuGUUUUC.CAGCCAGacCcG.......GAAAAA..cGAAAAcACaGCucgGGgAGCCCCCAcC.aGCcGGCGCCuguGCCAGCUCaCCUCUGGCcauGGC.....gcaGCUGCu....GgUgCAC......aCaGcG.GCCAAGGCcAGCUCCACaUUCuUCCCUCCccCUCCC..AcUUCaCcGGaGaCcg...GAGcCCuGcgugCAGaGGAAG...GGcCucAG.cUccacaGaCUGCCaaAGUcga..CUGGGUCCCUcCuCaCCaAAAAuGGUGAGacaAGAUUuCa.UCuUgU..ccgCuGA.GGAGCCacaa.GCAG.
//
# STOCKHOLM 1.0

#=GF AC   RF02043
#=GF ID   HOTTIP_4
#=GF DE   HOXA transcript at the distal tip, conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   45.00
#=GF TC   45.80
#=GF NC   33.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.08 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   21423168
#=GF RT   A long noncoding RNA maintains active chromatin to coordinate homeotic
#=GF RT   gene expression.
#=GF RA   Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR,
#=GF RA   Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA,
#=GF RA   Chang HY
#=GF RL   Nature. 2011;472:120-124.
#=GF WK   HOTTIP
#=GF SQ   19


AAPY01584655.1/2416-2581   UGUCCCAUC-GCUCCAGCCCCGAUCGGCCCAACGCUCAGGGAAACGGAGCAGCUCAAUAAAAA-CUUUUGAUAUUAGUUUUU-AUGGGUAUUUACACUCUGGUGAGGGGAGCUGAGUACGGAAGCU---CCAUUAAUCAGCCCC-CAACCUUGGAUUUGGAUACUCAGUUUAU
ACBE01077435.1/3560-3725   UGUCCCGCU-GCUCCAGCCCCACUCAGCCCAACGCUCAGGGAAACGAAGCAGCUCAAUAAAAA-CUUUUGAUAUUAGUUUUU-AUGGGUAUUUACACUCUAGUCAGGGGAGCUGAGUACGGAAGCU---CCAUUAAUCAGCCCC-CAACCUCGGGUUUGGAUGCUCAGUUUAU
ABRT010251891.1/525-690    UGUCCGGCU-GCUCCAGCCCCGUUCGGCCCAACGCUCAGAGAAACGAAGCAGCGCCAUAAAAA-CUUUUGAUAUUAGUUUUU-AUGGGUAUUUACACUCUGGUGAGGGGAGCCGAGUGCGGAAGCU---CCAUGAAUCAGUCCC-CAACCUCGAGUUUAGAUACUCAGUUUAU
ABDC01121664.1/6087-6252   UGUCCAGCG-GCUCCAGCUUCGCUCGGCUCAACGCUCAGAGAAACGAAGCAGCUCAAUAAAAA-AAUUUGAUAUUAGUUUUU-AUGGGUAUUUACACUCUGGUGAGGGGAGCUGAGUGCGGAAGCU---CCAUUAAUCAGCCCC-CAACCUCAGGUUUGCAUACUGAGUUUAU
ABRN01187574.1/371-536     UGUCCCGCU-GCUCUGGCCCCGCUCCCCCCAACGCUCAGGGAAACGAAGCAGCUCAAUAAAAA-CUUUUGAUAUUAGUUUUU-AUGGGUAUUUACACUCUGGUCAGAGGAGCUGAGUACGGAAGCU---CCAUUAAUCAGCCCC-CAACCUCUGGUUCGGAUGCUCAGUUUAU
ABVD01739464.1/520-683     UGUCCCGUG-GCUUCAGCCCCGCUGGGCCCAACGCUCAGGGAAAUGAAGCGGCUCAAUAAAAA-CUUUUGAUAUUAGUUUUU-AUGGGUAUUUACACU--AGUCAGGAGAGCUGAGUACGGAAGCU---CCAUUAAUCAGCCCC-CAAACUCGGGUUUGGAUGCUCAGUUUAU
AAQQ01559862.1/2766-2933   UGUCCCCGGAGCUGGAGCCCGGCUUGGCCCAAUGCUCAGAGAAACGAAGCAACUCAAUAAAAA-CUUUUGAUAUUAGUUUUUUAUGGGUCUUUACACUCUGGUGAGGGGAGCCCAGUACGGAAGCU---CCAUUAAUCAGCCCU-CAACCUUGGGUUUGGAUACUCAGUUUAU
ABRQ01101207.1/2580-2739   UGUCCCUCA-GCUC---CAC---GCGGCCCAGGGCUCAGGGAAACGAAGAGGUUCAAUAAAAA-UUUUUAAUAUUAGCUUUU-AUGGGUAUUUGCACUUUGGUCAGGAGAGCUGAGUACGGAGGCU---CCAUUAAUCAGCCCC-CGACCUCAGGUUUGGAUACUCAGUUUAU
AALT01189718.1/2768-2604   UGUCCCGCU-GCGUCAGCCCCUCUCGGCCCAACACU-GGGGAAACGGAGCAGCUCAAUAAAAA-CUUUUGAUAUUAGUUUUU-AUGAGUAUUUACACUCUAUUCAGCGGGGUUGAAUAUGGAAGCU---CCACUACUCAGCCCC-UAACCUUGGGUUUGGAUGCUCAGUUUAU
AAIY01754188.1/1314-1149   GCCUCCUCG-GCUCCCGCCCCAUGCGGCCCAAGGCUCAGGGAAGCAAAGUGGCUCAAUAAAAA-CUUUUGAUAUUAGUUUUU-AUGGGUAUUUGCACUCUGGUCAGGAGAGCUGAGUACGGAAGCU---CCAUUAAUCAGCCAC-CAAGCUCAGGUUUGGAUGCUCGGUUGGU
AAKN02039093.1/6163-6328   UGUCCCUGG-GCUGGAAUUCCACUUGGCCCAAUGCUCAGGAAAACGAAGCAGCUCAAUAAAAAACGUUUGAUAUUAGUUUUU-ACAGACAUUUACAUUCUGAUGUGGGGGGCUGAGUACGGAAGC----CUGCUAAUCAGCCCC-CAGCCUUGGGUUUGGAUACUUGGUUUAU
ABRO01036387.1/1299-1461   UGUUCCUUU-GCUUU--CCUCACUUGGCCCAAUUUUCUGGGAAAUGAAACAGCUCAAUUAAAAAAAAUUGAUAUUAGUUUUU-AUGGGUAUUAACACUUUGGUGAAGGGAGCAGAACAUGGAAGCU---CCAUGAAUCAGCUC---AAGUUUGGAGUAGGGGAGGGAGCUCAC
AC113985.11/61294-61462    UGUCUGUGGGACUAGAUCCCUUCAUGGCCCAAUGCUCUGGGAAACGAAGCAGCUCAAUACAAA-CUUUUGAUAUUAGUUUUUUAAAGGUAUUUACACUUUGGUGAGAGUAGCUGGGUACGGAAGCUGCUUCGUUAAUCAGCCCC-CGACCCCGACCUUAG--GUUCGGCUGGG
AC122669.6/137003-137167   UGUCUGUGGGACUGGAUGCCUGCGCGGCCCAAUGCUCUGGGAAAUGAAGCAGCUCAAUAAAAA-CUUCUGAUAUUAGUUUUU-AUAGGUAUUUACACUUUGGUUUGGGUAGCUGGGUACGGAAGCU---UCAUUAAUCAGUCCC-CGACCUUGGGUUUGG--GCUGGGAAAAG
AC116608.1/56363-56199     UGUCCCGUG-GCUCCAGCCCCGUUCCGCCCAGCUCUCAGGGAAACGAAGC-GCUCAGUACGAA-CUUCUGAUAUUAGUUUUU-AUGGGUAUUUACACUCUGGUGAGGGGAGCUGACUACGGAAGCU---CCAUCAAUCAGCCCC-CAACCUUGGGUUUAGAUAUUCAGUUUAU
GU724873.1/3387-3551       UGUCCCGCG-GCUCCAGCCCCGUUCGGCCCAGCUCUCAGGGAAACGAAGC-GCUCAGUAAGAA-CUUUUGAUAUUAGUUUGU-AUGGGUAUUUACACUCUGGUGAGGGGAGCUGAGUACGGAAGUU---CCAUUAAUCAUACUC-CAACCUUGGGUUUAGAUAUUCAGUUUAU
AAPE02018004.1/27169-27003 UGUCCCGUG-GCUCCAGCCCCGCUCAGCCCAAGGCUCGGGGAAACGAAGCAGCUCAAUAAAAA-CUUUGGAUAUUAGUUUUU-AUGGGUAUUUGCACUCUGGUCCGAGGAGCUGAGUACGGAAGCU---CCGUUAAUCAGCCCCACAACCUCGCGUUUGGAUGCUCAGUUUAU
AAGU03015372.1/4572-4410   UGUUGCUCG-GCUCCAGUCC---ACGGCCCAAGGCUCAGGGAAACGAAGAGGCUUAAUAAAAA-UUUUUAAUAUUAGUUUUU-AUAGGUAUUUGCACUUUGGUCAGGAGAGCUGAGUACGGAAGCU---CCAUUAAUCAGCCCC-CAGCCUCGGGUUUGGAUGCUCAGUUUAU
AAQR03057534.1/6138-6298   UGUCCGGCG-GCUCCAGCUC-----GGCCCAACGCUCCGAGAAACGAAGCAGCUCAAUAAAAA-CUUUUGAUAUUAGUUUUU-AUGGGUAUUUACACUCUGGUGAGGGGAGCUGAGUACGGAAGCU---CCAUUAAUCAGCCCC-CAACUUCGGGUUUGCAUACUGAGUUUAU
#=GC SS_cons               :::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::...:::::::::::::::.::::::::::::::::::::::::::::
#=GC RF                    UGUCccucg.GCUccagccCcgcucGGCCCAAugCUCaGGGAAACGAAGcaGCUCAAUAaAAA.cuUUUGAUAUUAGUUUUU.AuGGGUAUUUaCACUcUGGUgaGGGGAGCuGAGUACGGAAGCU...CCaUuAAUCAGCCCC.CaAcCUcGGGuUUGGAUgcUcaGuUuAu
//
# STOCKHOLM 1.0

#=GF AC   RF02044
#=GF ID   CDKN2B-AS_2
#=GF DE   CDKN2B antisense RNA 1 convserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   53.60
#=GF NC   42.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   21151178
#=GF RT   Long non-coding RNA ANRIL is required for the PRC2 recruitment to and
#=GF RT   silencing of p15(INK4B) tumor suppressor gene.
#=GF RA   Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, Xiong Y
#=GF RL   Oncogene. 2011;30:1956-1962.
#=GF WK   CDKN2BAS
#=GF SQ   6


AALT01439542.1/1125-1080 AUCGUCACCUGACGCGGC--CCUACCAGGA-ACCGCCGCGCUCCCCUAG
AAWR02015923.1/40-85     UCCGUCACCUGACACGGC--CAAACCAGGA-ACCGCCGCGGCCCGGCGG
AAYZ01119082.1/881-927   UCCGUCACCUGACGACGCGGCCUACCAGGA-ACAGCCGCGCUGAGCGG-
ABDC01122116.1/8455-8501 CCGGUCACUUGACACGGC--CCUACCAGGAAACCGCCGCGCUCCCCCUC
ABRR01349555.1/413-458   UCCGUCACCUGACCCUGC--CAUAUCAGGA-ACCGCCGCGGUCCCGCUC
AB548314.1/8-53          UCCGUCACCUGACACGGC--CCUACCAGGA-ACAGCCGCGCUCCCGCGG
#=GC SS_cons             ::::::::::::::::::..::::::::::.::::::::::::::::::
#=GC RF                  UCCGUCACCUGACaCgGC..CCUACCAGGA.ACCGCCGCGCUCCCccgg
//
# STOCKHOLM 1.0

#=GF AC   RF02045
#=GF ID   CDKN2B-AS_3
#=GF DE   CDKN2B antisense RNA 1 convserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   57.00
#=GF NC   48.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.12 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0006342; chromatin silencing;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   21151178
#=GF RT   Long non-coding RNA ANRIL is required for the PRC2 recruitment to and
#=GF RT   silencing of p15(INK4B) tumor suppressor gene.
#=GF RA   Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, Xiong Y
#=GF RL   Oncogene. 2011;30:1956-1962.
#=GF WK   CDKN2BAS
#=GF SQ   18


AL354709.15/38344-38487      UUUGAUGAGAAGAAUAAGCCUCAUUCUGAUUCAACAGCAGAGAUCAAAGAAAAGA---CUUCUGUUUUCUGG-CCACC-AGAUAUAU-GUUAUCUGUGCUUAAAGAAUUGAAAAACACACAUCAAAGGAGAAUUUUCUUGGAAAGAGAGG
ABRR01116618.1/4084-4213     GAUGAGAAGAAGAAUAA-CUUCAUUCU-------------GAAUCAAUGAAAAGA---CUUCUGUCCUCUUG-CCAUU-GGAUAUAU-GUUAUCUGCACUUACAGAAUUGAAAUUUGUACAUCAAAGGAACAUUCUCUUGGGAAGAAAGA
ACBE01405412.1/1885-1746     GAUGAGAAGAAGAAUAAACCUCAUUCUUGUUCAGAUGUAGAGAUCAAGGAAAAGA---CUUCUGUCUUAUUG-GCUUC-AGAUA--U-GUUAUCAGCACCUAAAGAAUGGAAAGC--UGCACUAAAGGAGGUUUCCCUUGGGAAGAGAGG
AAFC03086665.1/29304-29176   GAUGAGAGGAAGAAUAG-CUUCAUUCU-------------GAAUCAAUGAAAAGA---CUUCUGUCUUCUUG-CCAGC-AGAUAUAU-GUUAUCUUCACUUAUAGAAUUGAAAGU-GUACCUCAAAGGAGCAUUCUCUUGGGAAGAAAGG
ABRP01140986.1/7141-7283     UUUGAUGAGAAGAAUAAACCUCAUUCUGUCUCAACUGUAGAGAUCAAUGAAAAGA---CUUCUGUCUUCUUG-CCACC-AGAUAUAU-GUUACCUGCACUUAAAGAAUUGAAAAC-ACGAAUCUAAGGAGUGUUCUCUUGGGAAGAGUAG
AANN01722443.1/605-459       UAAUAAAAUAAAGAGAAACCUCAUUCUGGUUCCAUAGUAAAGAUCAAUGAAAUGACUUUUUUUUUCCUUUUUUCCACC-AGAUACGU-GCUAUCUGUGCUUUAAGAAUAAAAAAU-ACACAUCAAAGGAGAAUUUAUUUGGGAAGAAGGG
ABDC01122126.1/2864-3008     UUGGAUGAGAAAAAUGAGCCUCAUUCUGCUUCAAUGGCAGAGAUCAAAUAAAAGA---CUUUUGUUUUUUUG-CCACC-AGAUAUGUUGUUAUCUGUGCUUACAGAACUGAAAAGCACACAUCAAAGGAGCAUUCCCUUGAAGAGACAGG
ABRT010055860.1/534-679      UUUGAUGAGAAAAAUAAGCCUCACUCUGGUUCAAUAGCAGAGAUAAAAGUAAAGAA-UUCUCUGUCUUCUUG-CCACC-AGAUACAU-AUUAUCUGCACUUAAAGAAUUGAAAAGCACUCAUGAAAGAAACAUUCCCUUGAAAAGAGAGG
ABRO01019636.1/5159-5302     UUUGAUGAGAAGAAUAAGCCUCGUUUUGAUUCAAUAGCAGAGAUCAAAGAAAAAG---CUUUUGUCUUCUGG-GCACC-AGAUAUAU-GUUAUCUGUGUUUAAAGAAAUGAAAAGCACACAUCAAAGAAGCAUUGGCUUGGAAAGAGAGG
AAWR02015923.1/44161-44302   GAUGCGAAGAAGAAUAAAUGUCAUUCUGGUUCAAUGGUAGAGAUCACUGAUAAGA---CUUCUGUCUUCUUG-CCACC-AGAUACAC-UUUAUCUAAACCUAAACAAUUAAAGUG--CACAUCAAAGAAGUGUUCUCUUGGCAAGAGAGG
ABRQ01212661.1/1623-1755     UUUGAGGAGA---ACACAUCGCACUCUGGUUCU-UAGUAGAGAUCAAUGACCAAA---UUCCUGUCCUUUUA-------AGGGA-AU-GUUAUCUGCAAUUAAAAAAUUGGAAAUGGCAAAUCAAAG-AGCAUUCCCUUGGAAGAAGGGA
AAGV020696513.1/3860-4003    GAUGAGAAGGAGAAUAAGCCUCAUUCUUGUUCAUAGUAAAGAAUCGAUGAAAAGA---CUUUUUACCUCUUG-CCACC-AGACAUGU-UUUAUCUGAGCUUAAAGAACUGGAAAACACACAUGAAAGAAGUGUUUCCCUGGAAGGAUGAA
ABVD01163001.1/2639-2782     UUUGAUGAGGAGAAUAAACCUCAUUAUAGUUCA-UAGUAAAGAUCAAUGAAAAGA--CUUUUUCUCCUCUUA-CUAUC-AGACUUAU-GUUAUCUGAGCUUAAAGAACUGGAAAGCACACAUCAAAGGAGCAUUCCCAUGGAAGAAGAGG
AAQQ01036565.1/346-486       CUUGAUGUGA---AUUACCAUAAUUCUGACUCAAUGGCACAAAUCAAAGAGAAGA---CUCGUGUCUUCUUG-ACACC-AUAUAUAU-GCUAUGUGCACUCAAAGAAUUGAGAAGCACACAUCAGAAAACCAUUCCUUUGGAAAAAGAGG
CT027658.2/21033-21173       UUUGAUGAGA---AUAAGCCUCAUUCUGAUUCAACAGCAGAGAUCAAAGAAAAGA---UUUCUGUUUUCUGG-CCACC-AGAUAUAU-GUUAUCUGUGAUUAAAGAAUUGAAAAACACACAUCAAAGGAGCAUUCCCUUGGAAAGAGAGG
AACN010024863.1/308-165      UGUGCUGGGAACUGUAUAU-UCAUUACUUCAUUUUAAAGUGGAUUAAAAAGUGAG--GCAUACAGUUUUUUU-CUUCCUAGUUAGAU-GCU-UGAGAGCUCAAAGCCUUGCAGAGACCCCAUCACAGAAGAAUUGUCUUGGAGGAAGAGG
AAGW02033080.1/161454-161594 UUUCAUGAGAGGAAUAAGCCUCACUCUGAUUCAAAAGCAGGGUUCAAAGAAAAGA---UGUCUAU-UUCUUG-CCACC-AGCUACGU-GUUAUCUGUGCUUA--GAACUGGAAAGCACACAUCAGAAGAGCACCAGCGUGGAGAGACAGA
AAQR03014003.1/17740-17619   UGCAAUGAGAAGAAUGAGCCUCA----------------GAGAUCAAGUACAAGA---CUU--AUUUUCUUG-CCACC-AGAUACAU-GUUAUCCGUG---AGCUGACUGAAAAACAUACAUCAAAGGAAC-UUCCCUUGAAGAGAGAGG
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::...::::::::::::::.:::::.::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      uuUGAuGaGAAgaAUAagCcUCAUUCUggUUCaauaGuAgaGAUCAAuGAaaaGA...CuUcUgUCUUcUUg.CCACC.AGaUAuaU.GUUAUCUGugCUUAaAGAAuUGaAAagcaCaCAUCAaAGgAGcaUUccCUUGGaaaGAgaGG
//
# STOCKHOLM 1.0

#=GF AC   RF02046
#=GF ID   Sphinx_1
#=GF DE   Sphinx_ conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   34.00
#=GF TC   34.00
#=GF NC   33.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.67 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0008049; male courtship behavior;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   11904380
#=GF RT   Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster.
#=GF RA   Wang W, Brunet FG, Nevo E, Long M
#=GF RL   Proc Natl Acad Sci U S A. 2002;99:4448-4453.
#=GF WK   Sphinx_(gene)
#=GF SQ   3


AC010838.12/46454-46565      ACGCGGUGUCAUUUGGUGACUAUCCAGGUGAGUACAACCCCAAGGUGCACGGGCCCUAAGACCCCGCUCGCUUCUACGGUAAAGCCUGGCUGGGACGCCGCAACAAGACGCC
AAKO01003069.1/18326-18227   GCGCGAUGGCAUUCGGUGACUAUCCAGCUGAGUACAACCCCAAGGUGCACGGGCCCUACGACCCCGCUCGCUUCUACGGCAAAGGUGAGC--AGGUUACGUA----------
AAEU02000402.1/220447-220348 GCGAGAUGGCAUUCGGUGACUAUCCAGCUGAGUACAACCCCAAGGUGCACGGGCCCUACGACCCCGCUCGCUUCUACGGCAAAGGUGAGC--AGAUUACGUA----------
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..::::::::::..........
#=GC RF                      gCGcGaUGgCAUUcGGUGACUAUCCAGcUGAGUACAACCCCAAGGUGCACGGGCCCUAcGACCCCGCUCGCUUCUACGGcAAAGgugaGC..aGauuaCGuA..........
//
# STOCKHOLM 1.0

#=GF AC   RF02047
#=GF ID   Sphinx_2
#=GF DE   Sphinx conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   34.00
#=GF TC   34.00
#=GF NC   31.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0008049; male courtship behavior;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   11904380
#=GF RT   Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster.
#=GF RA   Wang W, Brunet FG, Nevo E, Long M
#=GF RL   Proc Natl Acad Sci U S A. 2002;99:4448-4453.
#=GF WK   Sphinx_(gene)
#=GF SQ   37


AF433800.1/2284-2127         GUGGCCGGAGCCGUGAACCGUGCAUGCUGGCGCUGGCAG-UACAACUACGUGUUCCCGAAGCGCGCCGU---------GAUCGCUCCCUUCUUCCAGCUGACCGU------------CGCCAGCAUGACGUUCUUCUGUCUGAUUAACUACACCAAGUUGAAGCACCACAG---GAACUACAA
FJ158227.1/588-732           GCU--------CAAGAG-----CGUGGUGGCGUUGGCAA-CACAAGUACGUGCAGCCAAAGCGUACUGG---------AGUCGCUCCAUUCUUCCAGCUAACUUU------------UGCUGGAAUGGCAUUCUUCUACUUUCUUAAUUACGGACGCAUCAAGCACCACAA---GAACUACAA
AAGE02015032.1/44888-44739   G-CGCUGGAGCCGUGAGCCGUGCCUUUUAGAGAUGGCAA-GAGAAAUACUGGAAACACAAGCGGCUU----------------CCUCGUUCUUCCAGGUCAUCGU------------CGGCGGAAUGGUGUUUUUUUAUGCCAUCAACUGUGGCAAGCGGAAGCACCACAG---GAACUACAA
AAGE02016650.1/501-344       GCCGCUGGAGCCGUGAGCCGUACCUUUUGGAGAUGGCAA-CACAAAUAC-------CCAAGCGGAUGGGAAUUGCC--CCUUGCCCCGUUCUUCCAGGCUAUCGU------------CGGCGGAAUGGUGUUCUUCUAUGCCAUCAACUGCGGCAAACGGAAGCAUCACAG---GAACUACAA
BT023907.1/2945-2788         GUGGCCGGAGCUGUGAGCCGUGCCUGGUGGCGCUGGCAG-CACAAGUACGUGUUCCCAAAGCGCGCCGG---------GAUCGCUCCCUUCUUCCAGCUGACCGU------------CGCCAGCAUGACGUUCUUCUAUCUGAUUAACUACACCAAGUUGAAGCACCACAG---GAACUACAA
AAGE02004718.1/168409-168564 GUUGCAGCA------A--CAUGCUUUUUCGUGUCAUUAAAUAAAAACAAGAUUUCAUUAAACAUUUAAGGACCC----AAUUGCCCCAUUCUUCCAGGUCAUCGU------------CGGCGGAAUGGUGUUUGUCUAUGCCAUCAACUGCGGCAAACGGAAGCACCACAG---GAACUACAA
AAGE02001251.1/187260-187103 GCCGCUGGAGCCGUGAGCCGUGCCUUUUGGAGAUGGCAA-CACAAAUAUUGGAAACCCAAACGGAUGGG---------AAUUGCCCCGUUCUUCCAGGUCAUCGU------------CGGCGGAAUGGUGUUCUCCUAUGCCAUCAACUGCGGCAAACGGAAGCACCACAG---GAACUACAA
AAGE02020818.1/30316-30166   GCCGCUGGA-------GCCUUGCCUUUUGGAGAUGGUAA-CACAAGUACUGGAAACCCAAGCGGAUGGG---------AAUUGCCCCGUUCUUCCAAGCCAUCGU------------CGGCGGAAUGGUAUUCUUCUAUGCCAUCAACUGCGGCAAACGGAAGCACCACAG---GAACUACUA
AAPT01021584.1/84619-84776   AUGGGUGGUGCCAUUAGCCGUGCCUGGUGGCGUUGGCAG-CACAAAUAUGUGUUCCCCAAGCGUGCUGG---------CAUUGCACCAUUUUUCCAAUUGACCGU------------GGCCAGCAUGACGUUCUUCUAUCUGAUCAACUACUCCAAGUUGAAGCACCACAG---GAACUACAA
AAGE02022714.1/9244-9377     --GGCUG---------------CCUUUUGGAGAUGGAAA-CAGAAAUACUGAAAACCCAAGCGGCUGGG---------AAUUGCCCCGUUCUUCCAGGUCAUCGU------------CGGCGGAAUGAUGUU-------GCCAUCAACUGCGGCAAACGGAAGCACCACAG---GAACUACAA
AAGE02000027.1/12586-12729   GCCGCUGGA-------GCCGUGCCUUUUGGAGAUGGAAA-CAGAAAUACUGAAAACCCAAGCGGCUGGG---------AAUUGCCCCGUUCUUCCAGGUCAUCGU------------CGGCGGAAUGAUGUU-------GCCAUCAACUGCGGCAAACGGAAGCACCACAG---GAACUACAA
AAGE02001604.1/9044-9198     GCUGCUGGAGUCGUGAGCCGUGUCUUUUGGAGAUGGCAA-CACAAGUACUGAAAAUCCAAGCGGAUGGGAAUUGCCCGAAUUGCCCCGUUCUUCCAGGUCAACGU------------CGGCGGAAUGGUGUUAUUCUAUGCCA------------AAAUGAAGCAGCGCAG---GAACUACAA
AAGE02000802.1/82971-83126   GCCGCUUAAGCCGUGAGCCGUGGCUUUUGGAGAUAU--A-CACAAGUACUGGCAACCCAAGCGGAUGGG---------CAUUGUCCCGUUCUUCCAGGUCAUCGU------------CGGCGGAAUGGUGUUUCUGUAUUCCAUCAACUACGGCAAACUGAAGCAUUACAG---GAACUACAA
AAGE02003143.1/91392-91241   GCCGCUGGAGCCGUGAGCCGUGCCUUUUGGAGAUGGCAA-CAGAAAUACUGGAA------GCGGCUGGA---------AAUUGCCCUGUUCUUCCAGAUCAUCGU------------CGGCGGAAUGGUAUUUUUCUAUGCCAUCAACAGCGGCAAACAGUAGCACCACAG---GAACUACAA
ABKP02020555.1/1862-1705     AUAGCAGGAGUUUUUAGUCGCGCUUUUUGGAGAUGGCAG-CACAAGUAUAUGCAGCCGAAGCGAACGGG---------AAUUGCUCCGUUUUUUCAAGUCAUCGU------------CGGAGGAAUGGUGUUCUUCUAUACCAUUAACUAUGGAAAACUGAAGCAUCACCG---UAACUACAA
AAGE02019809.1/108477-108634 GCCGCUGGAGCCGUGAGCUGUGCCUUUUGGAGAUGGCAA-CACAAGUACUGGAAACCCAAGCGGAUAGG---------AAUUGCCCCGUUUUUUCAGGCCAUCUU------------CGGCGGAAUGAUGUUCUUCUAUGCCAUCAACUGCGGCAAACGGAAGCACCACAG---GAACUACAA
AAGE02012700.1/13761-13913   GCCGCUGGAGUCGUGAGCCGUGUCUUUUGGAGAUGGCA------AGUACUGAAAACCCAAGCGGAUGGG---------AAUUGCCCCGUUCUUCCAGGUCAACGUGUUCUUCUAUGCCAAUGGAAUGGUGUUCUUCUAUGCCA------------AAAUGAAGCACCGCAG---GAACUACAA
AAGE02008863.1/62712-62872   GCCGCUGGAGCCGUGAGCCGUACCUUUUGGAGAUGGCAA-CACAAAUACUGGAAACCCAAGCGGAUGGG---------AAUUGCCCCGUUCUUCCAGGCCUUUGU------------CGACGGAAUGGUGUUCUUCUAUGCCAUCAACUGCGGCAAACGGAAGCAUCACAGCAGGAACUACAA
AAPU01010130.1/187417-187574 AUCGCUGGCGCUGUCAGCCGUGCCUGGUGGCGUUGGCAG-CACAAGUAUGUGUUCCCGAAGCGUGCUGG---------CAUUGCACCCUUCUUCCAGUUGACCGU------------CGCCAGCAUGGCGUUCUUCUAUAUCAUCAACUACCCCAAGUUGAAGCACCACAG---GAACUACAA
AAGE02019324.1/17415-17572   GCCGCUGGUGCCGUGAGCCGUGCCUUCUGGAGAUGGCAA-CACAAGUACUGGCAGCCGAAGCGGAUGGG---------AAUUGCCCCGUUCUUCCAGGUCAUCGU------------CGGAGGAAUGGUGUUCUUCUACGCCAUCAACUAUGGCAAGCUGAAGCACCACAG---GAACUACAA
AAGE02002758.1/152662-152819 GCCGCUGGAGCCGUGAGCCGUGCAUUUUGGAGAUGGCAA-CAGAAAUACUGGAAACCCAAGCGGCCGGG---------AAUUGCCCCGUUCUUUCAGGCCAUCGU------------CGGCGGAAUGGUGUUUUUCUAUGCCAUCAACUGCGGCAAACGGAAGCACCACAG---GAACUACAA
AAGE02011040.1/38665-38810   GCCGCUGGAGUCGUGAGCCGUGUCUUUUGGAGAUGGCAG-CACAAGUACUGAAAACCCAAGCGGAUGGG---------AAUUGCCCCGUUCUUCCAGGUCAACGU------------CGGCGGAAUGGUGUUCUUCUAUGCCA------------AAAUAAAGCACCGCAG---GAACUACAA
AAGE02029956.1/20300-20457   GCCGCUGGAGCCGUGAGCCAUGCCUUUUGGAGAUGGCAA-CACAAGUACUGGAAACCCAAGCGGAUGGG---------AAUUGCCCCGUUCUUCCAGGCCAUCGU------------CGGCGGAAUGGUGUUCUUCUAUGCCAUGAACUGCGGCAAACGGAAGCACUACAG---GAACUACAA
AAGE02020038.1/89863-90014   GCCGCUGGAGCCGUGAGCCGUGCCUUUUGGAGAUGGCAA-CAGAAAUACUGGAAACCCAAGCGGCUGGG---------AAUUGCCCCGUUCUUCCAGAUCAUCGU------------CGGCGGAAUGG--UCUUGUGGUGUCAUCA----UUGUCGGCGGAAGCACCACAG---GAACUCCAA
AAGE02020438.1/41487-41644   GCCGCUGAAGCCGUGAGCCGUGCCUUUCGGAGAAGGCAA-CACAAGUACUGGGAACCCAAGCGGACGGG---------AAUAGACCCAUUCUUCCAGGUCAUUGU------------CGGCGGAAUGGUGUUCUUCUAUGCCAUCAACUACGGCGAACUGAAGCACCACAG---GAACUACAA
AAGE02020938.1/5030-5173     GCCGCUAGA-------GCCGUGCCUUUUGGAGAUGGAAA-CAGAAAUACUGAAAACCCAAGCGGCUGGG---------AAUUGCCCCGUUCUUCCAGGUCAUCGU------------CGGCGGAAUGAUGUU-------GCCAUCAACUGCGGCAAACGGAAGUACCACAG---GAACUACAA
AAIZ01008070.1/55248-55091   AUGGUUGGUGCCGUCAGCCGUGCCUGGUGGCGCUGGCAG-CAUAAGUACGUUUUUCCCAAGCGUGCUGG---------CAUUGCACCCUUUUUCCAGCUGACCGU------------GGCCAGCAUGACGUUCUUCUAUAUGAUCAACUACACCAAAUUGAAGCACCACAG---GAACUACAA
AAGE02030165.1/2924-2767     GCCGCAGGAGCCGUGAGCCGUGCCUUUUAGAGAUGGCAA-CACAAGUACUGGAAACCCAAGCGGAUGAG---------AAUUGCCCCGUUCUUCCAGAUCAUCGU------------CGGCGGAAUGGUGUUCUUCUAUGCCAUCAACUGCGGCAAACGGAAGCACCACAG---GAACUACAA
AAQB01006255.1/312129-312286 AUUGCCGGUGCAGUGAGUCGUGCAUGGUGGCGCUGGCAG-CACAAGUAUGUGUUCCCCAAACGUGCUGG---------AAUUGCACCCUUCUUCCAGUUGACCGU------------GGCCAGCAUGACGUUCUUUUACUUGAUUAACUACACCAAGUUGAAGCACCACAG---GAACUACAA
AAGE02016081.1/18355-18508   GCCGCUGGAGCCGUGAGCCGUGCCUUUUGGAGAUGGCAA-CAGAAAUACUGGAAAACCAAGCGGCUGGG-------------GCCCCGUUCUUCCAGGUCAUCGU------------CGGCGGAAUGGUGUUUUUUUAUGCCAUCAACUGCGGCAAACAGAAACACCACAG---GAACUACAA
AAWU01007454.1/82326-82169   GCCGUCGGUGCCGUGAGCCGUUCCUUCUGGAGAUGGCAA-CACAAGUACUGGCAGCCGAAGCGGAUGGG---------CAUUGCCCCGUUCUUCCAGGUCAUCGU------------CGGUGGCAUGGUCUUCUUCUACACCAUCAACUACGGCAAGCUGAAGCACCACAG---GAACUACAA
AAGE02000754.1/100522-100679 GCCGCUGGAGCCGUGAGCCGUGCCUUUUGGAGAUGGCAA-CACAAGUACUGGAAUCCCAAGCGGAUGGG---------AAUUGCCCCGUUCUUCCAGGUCAUCGU------------CGGCGGAAUGGUGUUCUUCUAUGCCAUCAACUACGGCAAACUGAGGCACCACAG---GAACUACAA
AANI01014883.1/315769-315926 AUUGCUGGCGCCGUUAGCCGUGCCUGGUGGCGCUGGCAG-CACAAAUACGUGUUCCCCAAGCGUGCUGG---------CAUUGCACCCUUCUUCCAACUGACCGU------------CGCCAGCAUGACGUUCUUCUACUUGAUCAACUACACCAAGUUGAAGCACCACAG---GAACUACAA
AAGE02007743.1/34961-34804   GUCGCUGGUGCCGUGAGCCGUGUCUUUUGGAGAUGGCAA-CACAAGUACUGGAAACCCAAGCGGAUGGG---------AAUUGCCCCGUUCUUCCAGGUCAUCGU------------CGGCGGAAUGGUGUUCUUCUAUGCCAUCAACUGCGGCAAUAGGAAGCACCACAG---GAACUACAA
AAPP01018796.1/442718-442561 GUUGCCGGAGCCGUGAGCCGUGCCUGGUGGCGCUGGCAG-CACAAGUAUGUGUUCCCCAAGCGCGCUGG---------UAUCGCUCCCUUCUUCCAGCUGACCGU------------CGCCAGCAUGACGUUCUUCUACUUGAUCAACUACACCAAGUUGAAGCACCACAG---GAACUACAA
AAGE02030191.1/28124-27970   GCCGCUGGAGCCGUGAGCCGUGCCUUUUGGAGAUGGCCA-CACAAUUAUUGGCAACCCGAGCCGAUGGG---------AAUUCCUCCGUUCUUCCGGGCCAUCGU------------CGGCGGAAUGGCGUUCUUCUAUGCC---AACUACGGCAAACUGAAGCACCACAG---GAACUACAA
AAGE02021407.1/95217-95361   GCCGCUGGAGCCGUGAGCCGUGCCUUUUGGAGAUGGCAA-CAGAAAUACUGGAAACCCAAGCGGCUGGG---------AAUUGCCCCGUUCUUCCAGGUCAUCGU------------CGGCGGAAUGGUGUUUCCCUGUGCCAUCAACU-------------GCACCACAG---GAACUACAA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::.........:::::::::::::::::::::::::::............::::::::::::::::::::::::::::::::::::::::::::::::::::::...:::::::::
#=GC RF                      GccGCuGGaGcCGUGAGCCGUGccUuuUGGaGaUGGCAa.CAcAAgUAcuggaaaCCcAAGCGgaugGG.........aAUUGCcCCgUUCUUCCAGgUcAuCGU............CGgcGGaAUGGuGUUcUUCUAUgccAUcAACUgCggcaAacuGAAGCAcCACAG...GAACUACAA
//
# STOCKHOLM 1.0

#=GF AC   RF02048
#=GF ID   STnc30
#=GF DE   Salmonella enterica conserved region STnc30
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Predicted; WAR; Burge, SW
#=GF GA   120.00
#=GF TC   159.80
#=GF NC   34.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



AE006468.1/58792-58923   AUCUUAAGAAUUUCUUUUGAUAUUCAAUGUGCGACAGGAAGAAUAAGGCGUAGUCGUCAUCCGUUGCUAAUGCCCCACCUUUUUGCUAUUCAUCUGAAAAACCAGCACAAUCGUUGCUGGUUUUUUGGUUGU
CAAT01000320.1/4899-5030 AUCUUAAGAAUUUCUUUUGAUAUUCAAUGUGCGACAGGAAAAAUAAGGCGUAGUCGUCAUCCGGUGCUAAUGCCCCACCUUUUUGCUAUUCAUCUAGAAAAACCGCACAAUCGUUGCUGGUUUUUGGGUUGU
#=GC SS_cons             :::::::<<<<-<<____>>->>>>,,,,,((((-(((,,,,,,,,<<<<____>>>>,,,,,,,<<____>>,,,,)))--))))-------<<<<<<<<<<<<<<_______>>>>>>>>>>>>>>::::
#=GC RF                  AUCUUAAGaauUuCUUUUGaUauuCAAUGUGCgaCaGGAAaAAUAAGgCGUAGUCGuCAUCCGuUGCUAAUGCCCCACCuUUuuGCUAUUCAUCuggaaaacCaGCaCAAUCGUuGCuGguuuuccgGUUGU
//
# STOCKHOLM 1.0

#=GF AC   RF02049
#=GF ID   STnc460
#=GF DE   Salmonella enterica sRNA STnc460
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Predicted; FSA
#=GF SS   Predicted; RNIE; RNAalifold
#=GF GA   70.00
#=GF TC   76.00
#=GF NC   38.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


AE006468.1/4758332-4758187 GUGUUGCGUGAAUAUUUACAUUAAAUAUAAAUGAUAAGCAAAGUAAAGAGGCUUGCGUAAUUAUGACGCUACUGACAAAGAGACCAUGGUCUUCGUAUCGGAUGAAACGUGAGAUCCCAUUAAUGAAU-GGGAUCUAUUUUAUUAUU
CP000880.1/3002394-3002531 GUGCUGAGUGGGUAUUUAUAUUCAAUACAGAUGAUAGACAAAGUAAAGAACCUUGCAUAUUUAUGACGAU---------GAGGCCGGAGUCUUCUUGUCAGAUAAAACGUUAGAUGCCAUUAAUGAAUUGAGAACUAUUCUAUUAUU
#=GC SS_cons               :<<<<<<<<--<<<<<<<___>>>>>>>-->>>->>>->><<<________>>><<<<-<<<<<<<<<<----------<<<<<____>>>>>->>>>>-->>>>>>>>>,<<<<<<<<<<____>>>.>>>>>>>:::::::::::
#=GC RF                    GuGcugcguGaguauuuauAUuaaauacAaaugAuagaCaaaGUAAAGAagCuugCguAuuuauGacgcUAcUGAcAAAgaGaCCauaGuCuuCguguCaGauaaaacGuuaGauccCauuAAUGaau.GggauCuAUUuUAUUAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02050
#=GF ID   STnc470
#=GF DE   Salmonella enterica sRNA STnc470
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Predicted; WAR; Burge SW
#=GF GA   80.00
#=GF TC   84.50
#=GF NC   58.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



AE006468.1/94548-94770     ACAUCAUCUUAAAACAG--CCCGCAAAACCGUCUUAUUCACGAAGGGCUUACUGCCUGCGCGCGCACAUUCCAACGGCUUGCCUGCCCCGGAUGAACUGUUGAUAAAAAAG-AGGGCCAGCAUCCGUUUCCAGACGGCCCUGAGUGGAUUGUGACGUAACAUGGCACCUUGCUGGCGCUCUCUUAUUAUUUCAUGCCAGUGCCCUCGUUAUGGCGCAAUCAGAGCU
CP000880.1/2862522-2862303 AUAUUACUUUAAAACAAGUUCCGGAAAACUAUCUUUCUGUCAAGAGACUCACUGCCUGCUCG------UUUUACUGGCUUACCUGCUUCAGAUAAGAUUUUAAUAAAAAAGGAGGGCCGGCAUCUCUUUCCAGACGGCCCUGAGCGGAUUGUGACACAACAUGGCACCUUGCCGGCGCUCUCUUAUUGUUUCAUGCGUGUGCCAUCGCUAUGGCGCAAUCAGAGCA
#=GC SS_cons               ::::::::::::{{-{{..,,,<--<<______>>-->,,,[[-[[[,((((---((((-(,,,,,,,,<-<<-<<<<______>>-->>-->>->,,,,,,,,,,,,,,,.<<<<<<_________________>>>>>>)-))))---)))),,,,,,,<<<<_____>>>>,,,,]]]-]],}}-}}--------<<<<<________>>>>>::::::::::
#=GC RF                    AuAUuAuuUUAAaaCaa..uCCggAaaACuaUCuuauugaCaaaaGaCucaCUGCCugCuCGcGcAcAUuucaacGGCUUaCCUGCuuCgGAugAaaUuUUaAUAAAAAAG.aGGGCCaGCAUCugUUUCCAGACGGCCCuGAGcgGAUUGugaCauAACAugGCACCUUGCcgGCGCuCuCuuAuuauuUCAUGCgaGuGCCaUCGuUAUGGCgCAAUCAGAGCu
//
# STOCKHOLM 1.0

#=GF AC   RF02051
#=GF ID   STnc450
#=GF DE   Enterobacterial sRNA STnc450
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   37.00
#=GF TC   37.40
#=GF NC   34.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   12


CP000857.1/4659978-4659923   CGCUAUACUAGCC-CUGAACUUAUCGGCUCACUG-C-UACGAGCCGGUUUUCAUUAAAC
ACDJ01000023.1/46840-46784   CGCUAUACUAGCUUCUGAAUUUACCGGCUCACUU-C-CACGAGCCGGUUUUCAAUGAAU
AACY020372851.1/538-481      CGCUAUACUAGCUUCUGAAAUUACCGGUCCACUC-CCUUCGGACCGGUUUUCAUUGAAU
BAAW01013988.1/721-664       CGCUAUACUAGCUUCUGAAAUNACCGGUCCACUC-CCUUCGGACCGGUUUUCAGGGAAU
CP000822.1/3365825-3365882   CGCUAUACUAGCGACUGAAAUUACCGGCCCACAUCC-UUCGGGCCGGUUUUCAAUGUGU
CP000653.1/447397-447341     CGCUAUACUACCCGCUGAAAUAAUCGGCUCAACG-C-UACGAGCGGGUGUUCAAUGUGU
CU928158.2/4381957-4381900   CGCUAUACUAGCCACUGAAAAUGCUGGUUCACUU-CCUUCGAACCAGUUUUCAAUGUGU
ABKX01000002.1/56698-56755   CGCUAUACUAGCCACUGAAAAUGCCGGUUCACUCUC-UUCAGACCGGCUUUCAAUGUGU
CP000647.1/5041940-5041883   CGCUAUACUAGCCAGUGUGACAGCCGGUCCAGCG-CCUUCGGACCGGUUUUUUAUGUAU
CP001671.1/4873579-4873522   CGCUAUACUAGCCACUGAAAAUGCCGGUUCACUUUC-UUCGAAUCGGCUUUCAAUGUGU
ABWM02000041.1/80106-80052   CGCUAUACUACCG-CUGAAAUAAUCGGCUCAACG-C-UACGAGCCG-UGUUCUAUGUGU
ABWL02000016.1/111125-111069 CGCUAUACUAGCUGCUGAAUUUACCGGCUCAACU-C-CACGAGCCGGUUUUCAAUGUGU
#=GC SS_cons                 :<<<<___>>>>---<<<<---<<<<<<<<____._.___>>>>>>>>->>>>::::::
#=GC RF                      CGCUAUACUAGCcaCUGAAAuuaCCGGcuCAcuu.C.UuCGagCCGGuUUUCAAUGUgU
//
# STOCKHOLM 1.0

#=GF AC   RF02052
#=GF ID   STnc630
#=GF DE   Enterobacterial sRNA STnc630
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   55.00
#=GF TC   60.10
#=GF NC   49.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   10


FM200053.1/4280093-4280258 AUUUCGCGCUUAAGGUUCGCUUAAUCUCUCGCGGGCAUACUCUCCUCCAUACCUUUGGAGGAGAGCGUCAUGAAAAGCUAUAUUUAUAAAAGUUUGACGACCCUGUGUAGUGUGCUGAUUGUCAGCAGUUUUAUCUAUGUGUGGGUCACGACGUAUUAAACGCCUG
CP000880.1/3273877-3273712 AUGUCGUGCUUAAGGUUCGCUUAAUCUCUUGCUGGCACGCUCUCCUCCAUACCUUUGGAGGAGAGCGUCAUGAAAAGCUAUAUUUAUACAAGUUUGACGACCCUGUGUAGUUUGCUGAUUGUCAGCAGUUUUAUCUAUGUGUGGGUCACUACGUAUUAAACGCCUG
ACDJ01000045.1/48040-48204 AUAUCA-ACUUAAGGUUGGCUUAAUCUGUGUCAGGCAAACUCUCAUCCAUAGUUCCGGAGGAGAGUGUCAUGAAAACCCGUAUUUAUGAAAGUUUGACCACCGUGUGCAGUGUGCUGAUCGUCAGCAGCUUUUUGUAUGUGUGGGUGAGCUCUUACUGAUCUUUCG
CP000822.1/3494436-3494275 ----AAAUCUUAAUGUUCGCUUAAUCUUCGUCAGGCAUACUCUCCUCCAGACCAUCGGAGGAGAGUGUGAUGAAAACGCGAAUGUAUGAAAGUCUGACAGCCCUGUUCAGUAUGCUGAUUGUCAGCAGUUUCCUGUAUGUCUGGGUCACGACUUACUGAUCUCUUU
BAAX01014454.1/1134-969    CGCGUGGCCUUAAGGUUGGCUUAAUAUCCUUCAGGCAAACUCUCCUCCAUAGUUUCGGAGGAGAGUGUCAUGAAAACCCGUAUUUAUGAAAGUUUGACCACCGUGUGCAGUUUGCUGAUCGUCAGCAGCUUUUUGUAUGUAUGGGUGAGCUCUUACUGAAUUUUCG
ABKX01000011.1/51296-51131 GUCUGGAUCUUAAGGUUCACUUAAGCUCUCAUACGCAUACUCUCCUCCAUUCGUCUGGAGGAGAGUGCCAUGAAAAAACGUAUUUAUGAAAGUUUAACCACCGUGUUCAGCGUGCUGGUCGUAAGCAGCUUUCUUUAUAUCUGGUUUACAACGUAUUGAUCUUUCU
CU928164.2/4739770-4739935 AUUGAACUCUUAAGGUUCACUUAAUCUCUGACGUGCAUACUCUCCUCCAGGUUAACGGAGGAGAGUGCAAUGAAAAACCGUGUUUAUGAAAGUUUAACUACCGUGUUUAGCGUGCUGGUGGUCAGCAGCUUUCUUUAUAUCUGGUUUACCACGUACUGAUCUUUCU
CU928158.2/4277377-4277542 GCUGCACGCUUAAGGUUCACUUAAUCUCCAGGAUGCAUACUCUCCUCCAGUUCAACGGAGGAGAGUGUCAUGAAAAACCGUGUUUAUGAAAGUUUAACGACUGUGUUUAGCGUGCUGGUGGUCAGCAGCUUUCUCUAUAUCUGGUUUGUGACUUACUGAUUUUUUU
M83089.1/1978-2135         AUUGAACUCUUAAGGUUCACUUAAUCUCUGACGCGCAUACUCUCCUCCAGGUUAACGGAGGAGAGUGCAAUGAAAAACCGUGUUUAUGAAAGUUUAACUACCGUGUUCAGCGUGCUGGUGGUCAGCAGCUUUCUUUAUAUCUGGUUUGCCACGUACUG--------
ABWL02000036.1/16106-15942 -ACCGCGACUUAAGGUUGGCUUAAUAUCCUUCAGGCAAACUCUCCUCCAACGUAUCGGAGGAGAGUGUCAUGAAAACCCGCAUUUAUGAAAGUUUGACCACCGUGUGCAGCGUGCUGAUCGUCAGCAGCUUUUUGUACGUUUGGGUGAGUUCUUACUGAUCUUUCG
#=GC SS_cons               :::::<_________>--------------[[,(((,<<<<<<<<<<<________>>>>>>>>>>><--<<____________>>-->,,))),,,,<<<<------<<--<<<<<_____>>>>>----->>--------->>>>,,,,,]]::::::::::::
#=GC RF                    auuuaaauCUUAAGGuUcgCUUAAUcUcuuacaggCAcaCUCUCCUCCAuauuuucGGAGGAGAGugucAUgAAAAacCGUAUUuAUGaAAGucUgACcacCgUGUucAgugUGCUGaUuGUCAGCAGcUUUcUuUAUgUcUGGgugAcuaCguAcUGAucuuUug
//
# STOCKHOLM 1.0

#=GF AC   RF02053
#=GF ID   STnc430
#=GF DE   Enterobacterial sRNA STnc430
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   47.00
#=GF TC   47.10
#=GF NC   45.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   7


AE006468.1/4442059-4441898 AAAAGACAUCAGCAUCCGUAUAAUCUGAAAAUAACGCAGAGUGAUUUUCUGGUUAUUGC--U-UAUUUUAGGAUUAAGCUCAAUAUAAAACUGUGGGGAUAAAGACGGACAAGC-GGAAUUAUCUUAUAAAAAAAGCCGAUGUGAAUAUCGGCCUUUUUAUUAUCU
CP000880.1/3390394-3390555 AAAAGAAGGCGACAUCCGUAUAAUCUGAAAAUAACGCAGAGUGAUUUUCUGGUUAUUGG--U-UAUUUUAGGAUUAAGCUCAAUAUAAAAUUAUAGGGGAAAAGACGGACAAGC-GGAAUUAUCUUAUAAAAAAAGCCGAUGUGAAUAUCGGCUUUUUUAUUAUCU
CP000822.1/3621029-3621187 ---AACAUUCAUUAUCCGUAUACUCUGAAAAUAACACCGAGUAACUUACGGGUUAUUCA--U-UAUUUUAGGAUUAAGCUCAAUAUAAAUUUUUGCGGAAUAGCACAGACAACC-GGAAUUAUCUUAUAAAAAAAGCCGAUAAUAAUAUCGGCUCUAAUUACAGAU
CP000653.1/275300-275142   AACAACGUUCACACUCCGUAUUUUCCUAAAAAAACCCGCAGUAAUUAACGGGGAAAUCA--G-GCUUUUCGGAUUAAACUCAUAAUAGAAAUUUGCGUCAGGUAACGGACAACC-GGAAUUAUCCGAUAAAAAAUGCCAGCAUUU-CGCCGGCAUGUAUUACGG--
BABF01004542.1/437-592     AACACAAUACCCGGU-----AAAUCUGAAAAUAUCAGAAACAGGAUAAC-GUUGAAUAA--AUUAUUUUAGGAUUAAGCUCAAU-UAAAGGGUGAAGUAAAAACAUAAAUAUCCUGGAGUAAUCUUAUAAA-AAAGCCGAUAUUAAUAUCGGCUUUUUUAUUUCAU
ACDJ01000044.1/32607-32447 AUUAAAAUGCAAUAUCCGGUAAAUCCGAAAACAUCAGAAAUUGAAUAACA--UUAAUAAAAU-UAUUUUAGGAUUAAGCUCAAUUAAGGUAUG-AAGUUAAAACGUAGAUAUCCUGGAGCAUUCUUAUA-AAAAAGCCGAUAUUAAUAUCGGCUUUUUAUUUCAUU
BAAW01001217.1/1598-1438   AUAAAAACACAAUACCCGGUAAAUCUGAAAAUAUCAGAAACAGGAUAAC-GUUGAAUAA--AUUAUUUUAGGAUUAAGCUCAAU-UAAAGGGUGAAGUAAAAACGUAGAUAUCCUGGAGUAAUCUUAUAAA-AAAGCCGAUAUUAAUAUCGGCUUUUUUAUUUCAU
#=GC SS_cons               ::::::::::::::<<<<<----<<<-<<<<<<<-----<<<<<<<____>>>>>>>--..>.>>>>>>->>>------------------------------->>>>>,,,,,.<<______>>,,,,,,,,<<<<<<<<<____>>>>>>>>>:::::::::::
#=GC RF                    AaaAaaauuCAauauCcGuauAaUCcGAAAAuaaCacaaAcugacuaACuggucagUaA..u.uaUUUUAgGAUUAAGCUCAAUAUAaAaauuuaaGuaAaAacaCgGacAacC.gGAaUuAUCuUAUAAAAAaaGCCGauaUUAAuauCGGCuuUUuUauUauaU
//
# STOCKHOLM 1.0

#=GF AC   RF02054
#=GF ID   STnc420
#=GF DE   Salmonella enterica sRNA STnc420
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   70.00
#=GF TC   78.00
#=GF NC   59.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


AE006468.1/4251539-4251480 UAUUGCCUGAUGAAGAAUACAUGAACGAAAAAAGCGCCUGAUCGGCGCUUUUUAUUGGCG
CP001120.1/4255606-4255549 UAUUGCCUGACGA--AAUACAUGAACGAAAAAAGCGCCUGAUCGGCGCUUUUUAUUGGCG
CAAQ01005189.1/124-67      UAUUGCCUGACGA--AAUGCAUGAACGAAAAAAGCGCCUGAUCGGCGCUCUUUAUUGGUG
#=GC SS_cons               ::::<<<------..-------------<<<<<<<<<<_____>>>>>>>>>>--->>>:
#=GC RF                    UAUUGCCUGAcGA..AAUaCAUGAACGAAAAaAGCGCCUGAUCGGCGCUuUUUAUUGGCG
//
# STOCKHOLM 1.0

#=GF AC   RF02055
#=GF ID   STnc380
#=GF DE   Enterobacterial sRNA STnc380
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   92.30
#=GF NC   41.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   5


CP001120.1/3898746-3898639     UGAGUAGGCUGUGGUAACUGGCUAAAAUUGGUAGGGCCAAUUGAGGGGAGAGGACAGCAAAGGGAAGUGAAAAGGCAAUGGCAUUAUGCCAUUGCCUUUGAUGUCGGG
ABFH02000001.1/1288107-1288214 UGAGUGGGUUGUGGUAACGGGUUAAAAUUGGUAGGGCCAAUUGAGGGGGGCGGGCAGCAAAGGGAAGUGAAAAGGCAAUGGCAUGAUGCCAUUGCCUUUGAUGUCGGG
CP001113.1/3858172-3858065     UGAGUGGGUAGUGGUAACGGGCUAAAAUUGGUAGGGCCAAUCAAGGGGUGGGGACAACAAAGGGAAGUGAAAAGGCAAUGGCAUAAUGCCAUUGCCUUUGAUGUCGGG
CP001127.1/3765162-3765055     UGAACAUGUGGCCGGAUUUAGCGGGAAUUGGUAGGGCCAAUUAAGGGGUGAGGACAACAAAGGGAAGUGAAAAGGCAAUGGCAUAAUGCCAUUGCCUUUGAUGUCGGG
ABWL02000023.1/264384-264277   UGAGAGGGUAUUCGGAUCUUGCUGGAAUUGGUAGGGCCAAUUACAAGGACAGGACAACAACAGAAAGUAAAAGGGCAACAGUACAAUACCAUUGCCCUGGACGAAGAG
#=GC SS_cons                   :::::::<<-<<---------<<--<<<<<<<___>>>>>>>---->>----->>->>-----<<-----<<<<<<<<<<<<<___>>>>>>>>>>>>>---->>:::
#=GC RF                        UGAguggGuagugGuAacugGccaaaauuGGuAGGgCCaauuaaggggagaGGacAaCAAagGgaAGUgAaagGGCaauGGcauaAugCCauuGCCcuuGAuGucGgG
//
# STOCKHOLM 1.0

#=GF AC   RF02056
#=GF ID   STnc390
#=GF DE   Salmonella sRNA STnc390
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   52.90
#=GF NC   46.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.72 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


ABEI01000011.1/139348-139290 GGGUCUC-UAUACGUUUCAUCGUAAAAGGUUGGUGUCAUUCACCAACCUUUUUUGUUAGG
CP000886.1/3851601-3851542   GGGUCUGAUAUACGUUUCAUCGUAAAAGGUUGGUGUCAUUCGCCAACCUUUUUUGUUAGG
#=GC SS_cons                 ::::::::::<<<<______>>>><<<<<<<<<<<_____>>>>>>>>>>>:::::::::
#=GC RF                      GGGUCUgAUAUACGUUUCAUCGUAAAAGGUUGGuGUCAUUCaCCAACCUUUUUUGUUAGG
//
# STOCKHOLM 1.0

#=GF AC   RF02057
#=GF ID   STnc40
#=GF DE   Salmonella enterica sRNA STnc40
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Predicted; LocARNA; Infernal
#=GF SS   Predicted; RNIE; LocARNA
#=GF GA   45.00
#=GF TC   46.00
#=GF NC   43.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   17


CP000880.1/2781072-2781004     AUGGCGCUACGCUUAUUCG--GCCUGGGUAUUGAACAC-----GGAUAAAAAGGCGCAGGCGACUGCGCUUUUUUU
AE006468.1/161464-161531       AGGGCGCUACGCUUAUUCG--GCCUGG-CAUUGAACAC-----AGAUAAAAAGGCGCAGGCGACUGCGCCUUUUUU
CP000822.1/3043277-3043209     ACAGUGCCACGGCCGUCUG--AGCUAAGGUCUGAAUAA-----AGACAAUGAGGCGCAGGUGACUGCGCCUUUUUU
CP000647.1/122806-122874       ACAGUGCCACGGCCGUCUG--AGCUAAGGUCUGAUAAA-----ACAAACAAAGGCGCAGAGUUCUGCGCCUUUUUU
CP000964.1/4673201-4673134     ACAGUGCCACGGCCGUCUG--AGCUAAGGCCUGAUAAA------AAAACAAAGGCGCAGAGUUCUGCGCCUUUUUU
CP000653.1/731936-732003       GUCGUGCCACGGCCGUUUA--AGCUAAGCACAGAGUAA------AUCGAAAAGGCGCAGAGAUCUGCGCCUUUUUU
ACDJ01000024.1/222657-222724   ACAGUGCCACGGCCGUCUG--AGCUAAGAAAAUAAC------UUACUGAAAAGGCGCAGAAUUCUGCGCCUUUUUU
CP000783.1/3162702-3162632     GCAGUGCCACGGCCGCUUA--AGCUAACCGGUUGUUAA---CCGACAUAAAAGGCGCAGAUAUCUGCGCCUUUUUU
CU928160.2/111367-111436       GCAGUGCCAUGGUCGCCUG--CAAUAAAAGCUAACAGU----UGAAGUAAAAGGCGCAGGAUUCUGCGCCUUUUUU
CP000243.1/113402-113471       GCAGUGCCAUGGCCGCCUG--CAAUAAAAGCUAACAGU----UGAAGUAAAAGGCGCAGGAUUCUGCGCCUUUUUU
AAKB02000001.1/1223381-1223312 GCAGUGCCAUGGCCGCCUG--CAAUAAAAGCUAACUGU----UAAAGUAAAAGGCGCAGGAUUCUGCGCCUUUUUU
BAAX01000839.1/2541-2472       GCAGUGCCAUGGCCGUCUG--AGCUAAGCUCAGAGCAU----GAAAAAUAAAGGCGCAGAUAUCUGCGCCUUUUUU
ABKX01000006.1/107125-107057   GCAGUGCCAUGGUCGCCUG--CAAUAAAAACUAAUCAA-----UAAAACAAAGGCGCAGGAAUCUGCGCCUUUUUU
CP000036.1/98963-99032         GCAGUGUCAUGGUCGCCUG--CAAUAAAAGCUAACUGU----UGAAGCAAAAGGCGCAGGAUUCUGCGCCUUUUUU
CU928158.2/132925-132998       GCAGUGCCAUGGCCGCCUG--CAGUAAUUAAAUAUUCACACAUAAGGUAAAAGGCGCAGGAUUCUGCGCCUUUUUU
CR628337.1/3065649-3065578     UUGUCUCUAUGGGGACGCAUCAAAUAAUAAAUCAGUUU----UAGAAUAAAAGGCGCAGCGUUCUGCGCCUUUUUU
AL627265.1/162886-162953       AGGGCGCUACGCUUAUUCG--GCCUAG-CAUUGAACAC-----AGAUAAAAAGGCGCAGGCGACUGCGCCUUUUUU
#=GC SS_cons                   :<<<-<<____>>--->>>..-----------------....------<<<<<<<<<<<____>>>>>>>>>>>::
#=GC RF                        gcagUgCCAuGGccGucug..aacUAAgaacUgAuuaa....UaaAaaAAAAGGCGCAGgauUCUGCGCCUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02058
#=GF ID   STnc400
#=GF DE   Gammaproteobacterial sRNA STnc400
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   102.30
#=GF NC   71.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


AF261825.2/44236-44359     UAGGGUUGCGCUAGAAAGUUUUCUACCGAUCCUAGAAGUCUCUAGGAUCGGUAGAAAACUUUCUAGCGCCUCCUCUAGUAAAGAGUAAAA-AACGAGCAAAAAACAUUGCUCGUUUUUUUCAUCA
CP000749.1/2734628-2734508 UUGGGCUGCGUUAGAUCUUCGUCUACCGCUCCUUCGUGCCUC-AGGAUCGAUAGACGAAGAUCUAACGCUUCCUCUAGUAAAGAGUCAGAUGAUGGGGUGAAAGCCCCAUUAUUUAUUAUAA---
#=GC SS_cons               ::<<<--<<<<<<<<<<<<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-->>>-------------<<<.<<<<<<<<____>>>>>>>>->>>::::::::::
#=GC RF                    UagGGuUGCGcuaGaucgucguCuacCGauCCuagaaGuCucuaGGauCGguaGacgacgauCuagCGCuUCCuCUAGUAAAGAGUaaaa.agcggggcaAAAgccccgcuauuuaUUaUaAucA
//
# STOCKHOLM 1.0

#=GF AC   RF02059
#=GF ID   STnc50
#=GF DE   Salmonella enterica sRNA STnc40
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Predicted; FSA; Infernal
#=GF SS   Predicted; RNIE; RNAalifold
#=GF GA   55.00
#=GF TC   55.00
#=GF NC   44.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


AE006468.1/182539-182458   UUUCGUUAUCCUUCGCCAUC-AUUUGACACAUCUGAUUUGCCAUGCAUAAAAAAAGCGGCUGUAAAGCCGCUU-UUUUGUAUCG
CP000880.1/2759977-2760060 UUUCGUUAUCCUUCGCCAUCUAUUUGACACAUCUGGUUUAUCACACAUAAAAAAAGCGGCUGCAAAGCCGCUUGUUCUGUAUUG
#=GC SS_cons               ::::<<<<________________>>>>-------------------------<<<<<<<<____>>>>>>>>:::::::::::
#=GC RF                    UUUCGuuaUCCUUCGCCAUCUAUUugaCACAUCUGaUUUauCAuaCAUAAAAAaaGCGGCuGuAAaGCCGCuuGUUuUGUAUuG
//
# STOCKHOLM 1.0

#=GF AC   RF02060
#=GF ID   STnc410
#=GF DE   Enterobacterial sRNA STnc410
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   52.10
#=GF NC   37.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   14


CP001144.1/4101065-4101222   AGGAUAAAACGCUCACCGGGAUAAAAUCCCCGCCUGCUAAUGAAUCAUU-UUCGUUCAUUACCGCGCCUCUUGUCUCCUGAAAAGUAAAAACACCCGCGUAUUGGCAACGUAGUCC-GAUGUUUUUGCUGUUUUUUUACUCCAUAAAUAAAGAAGAUAAC
CP000822.1/67167-67324       AAGAGAAAACGCUCAACGCGGGGUUUUCACCGCUUGUUAAUGGGAUAUU-UUCGUUCAUCGCCCUGCCUUUUGUCUUCAGAAAAGUCAGACUUACCUUUCAUUAAAGGCUUAGGUU-AAUGUUUUUGCUAUUUUUUUGACCCAUGAAUAAAGAUGAGACA
CP000034.1/3751309-3751152   AGGAUAAAUUGUUCAAUAACGGAUUAUCCCCGCUGACGAAAGCGCCAUU-UUCGACCAUCGUCACGCCUUUUGUCUGCAGAAAAUUAAGGCUGUACCUUCAUUUAAGCGUCAGGUG-GAUGUUUUUGCUCUUAUUUCGAUCAAUGAAUAAACGGGAAAAC
ABKX01000002.1/624746-624903 GGGAUAAAUUGUUCAAUACUGGAUUAUCCCCGCCUGCAAAAGAGCCAUU-UUCGGCUAUCGCCACGCCUUUUGUCUUCAGAAAAAUAAGGCACGGCCUUCAUUUAAGCGUCAGGCU-GAUGUUUUUGCUCUUAUUUCGAUCAAUGAAUAAACGGGAAAAC
AACY020948956.1/434-276      AGGAUAAAACGCACAAUCGCGAGAUUUCCCCAACGGAGAUAGAGACAUU-UUCGUCCAUUGCUGCGGCUUUUGUCUUCUGAAAAGUCACCUGAUACCGUGAUUAACACGCCAGGCCCAAUGUUUUUGCUCUUUUUUUGAUCCAUAAAGAAAGAUGACGCA
BAAW01002700.1/1428-1271     AAGAUAAAACGUUCAACAGGGGUAAUUCCCCAUCUGAUAACUCACUAUU-UUCGUCUAAAUCAGUGUCUUUUGUCUGCCAAAAACCUGGGGUCUGCUCUUAUUAAAGCCUUAGGUU-AAUGUUUUUGCUAUUUUUUUACCGCAUGAAUAAAGAGUUACAC
ACDJ01000026.1/413764-413921 AAGAUAAAACGUUCAACAGGGGGUAUUCCCCAUCUGAUAACUCACUAUU-UUCGUCUAUAUCUGCGUCUUUUGUCUCCCAAAAACCAGGAGUCUGCUCUUAUUAAAGCCUUAGGUU-AAUGUUUUUGCUAUUUUUUUACCGCAUGAAUAAAGCAUUACAU
BAAV01033811.1/736-892       AGGAUAACUUGUUCAAUAACGGAUUAUCCCCGCUGACGAAAGCGCCAUUUUUCGACCAUCGUCACGCCUU-UGUCUGGCGAACAUUAGCGCAGUACCUUCAUUUAAGCGUCGCGUG-GAUGUUAUGGCAC-UAUUUCGAUCAUUGAAUACACGGGAAACC
BAAW01007528.1/766-609       AGGAUNAAUNGUCAUNNACGGGAUUAUCCCCGCUGACGAAAGCGCCAUU-UUCGACNAUCGUCACGCCUUUUGUCUGCAGAAAAUAAGGGCAGUACCUUCAUUUUAGCGUCAGGUG-GAUGUUUUUGCUCUUAUUUCGAUCAUGAANUAAANCGGGAAAA
BABG01023150.1/711-868       AGGAUAAAUUGUUCAAUAACGGAUUAUCCCCGCUGACGAAAGUGCCAUU-UUCGACCAUCGUCACGCCUUUUGUCUGCAGAACAUUCAGGCAGUACCUUCAUUUAAGCGUACGGUG-CAUGUCGUCGCUCUAAUUUCGAUCAAUGAAUAACGGGGAAACA
X05968.1/360-203             AGGAUAAAUUGUUCAAUAACGGAUUAUCCCCGCUGACGAAAGCGCCAUU-UUCGACCAUCGUCACGCCUUUUGUCUGCAGAAAAUUAAGGCAGUACCUUAAUUUAAGCGUCAGGUG-GAUGUUUUUGCUCUUAUUUCGAUCCCCGCAUGCCUUCGCUACG
CU928162.2/4352088-4352245   AGGAUAAAUUGUUCAAUAACGGAUUAUCCCCGCUGACGAAAGCGCCAUU-UUCGACCAUCGUCACGCCUUUUGUCUGCAGAAAAUUAAGGCAGUACCUUCAUUUAAGCGUCAGGUG-GAUGUUUUUGCUCUUAUUUCGAUCAAUGAAUAAACGGGAAAAC
CP000819.1/3875650-3875807   AGGAUAAAUUGUUCAAUAACGGAUUAUCCCCGCUGACGAAAGCGCCAUU-UUCGACCAUCGUCACGCCUUUUGUCUGCAGAAAAUUAAGGCAGUACCUUAAUUUAAGCGUCAGGUG-GAUGUUUUUGCUCUUAUUUCGAUCAAUGAAUAAACAGGAAAAC
ABWL02000023.1/436807-436964 AAGAUAAAACGUUCAAUAAGGGUAAUCCCCCAUCUGAUAACUGUCUAUU-UUCGUCUAUAUCUACGUAUUUUGUCUCCCCAAAACCAGCAGUCUGCUCUUAUUAAAGCCUUAGGUG-GAUGUUUUUGCUAUUUUUUUGCCGCAUGAAUAAAGAGUUAGAU
#=GC SS_cons                 :<<<<<<--<-<______>->-->>>>>>,,,,,,<<-<<---<<____._______________>>-->>->>,,,,,,,,,,,,<<<_______>>>:::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      AgGAuaaAucGuUCAAuAaggGauuaUCcCCGcuggcgAaaGcgcCAUU.UUCGuCcAUcgccaCgcCUuUUguCUgCaGAAAAuUagggcagUaCccuuAUUuAAGCgUuAGGUg.gAUGUUUUUGCUcUUuUUUuGAUCcAUGAAUAAAgagGaaAac
//
# STOCKHOLM 1.0

#=GF AC   RF02061
#=GF ID   mir-301
#=GF DE   microRNA mir-301
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW; ENSDART00000115588;
#=GF SS   Predicted; WAR; Burge SW;
#=GF GA   56.00
#=GF TC   63.70
#=GF NC   50.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF RN   [1]
#=GF RM   12919684
#=GF RT   Embryonic stem cell-specific MicroRNAs.
#=GF RA   Houbaviy HB, Murray MF, Sharp PA
#=GF RL   Dev Cell. 2003;5:351-358.
#=GF WK   Mir-301_microRNA_precursor_family
#=GF SQ   17


AANH01000530.1/26334-26250 UGUUGGCGGGUGCUCUGACUUCAUUGCACUACUGUUUGAACACAG-CUAGCAGUGCAAUAGUAUUGUCAAAGCAUCUGAAAACUGC
AAQQ01354558.1/852-769     UGCUUACGAAUGCUCUGACUUUAUUGCACUACUGUAUUU-GACAG-CUAGCAGUGCAAUAGUAUUGUCAAAGCAUCUGAAAGCAGA
AAYZ01072680.1/3739-3656   UGCUAACAAAUGCUCUGACUUUAUUGCACUACUGUACUU-UACAG-CUAGCAGUGCAAUAGUAUUGUCAAAGCAUCUGAGAGCAGC
ABPJ01062999.1/150-233     UGUUGGCAGAUGCUCUGACUUCAUUGCACUACUGUAUCA-GACAA-CUAGUAGUGCAAUAGUAUUGUCAAAGCAUCUGAAAACUGC
ABQF01026522.1/1442-1359   UGCUAACGAGUGCUCUGACUUUAUUGCACUACUGUACUA-UACAG-AGAGCAGUGCAAUAGUAUUGUCAAAGCAUCUGAGAGCAGA
BX088525.4/83955-84038     UGUUAACAGGUGCUCUGACUUCAUUGCACUACUGUAUUG-GACAG-CUAGCAGUGCAAUAGUAUUGUCAAAGCGUCUGAGAGCAGC
AAVX01190178.1/648-731     UGUUGUCGGAGGCUCUGACGAUAUUGCACUACUGUCCUC-ACCGU-UAAGCAGUGCAAUAGUAUUGUCAAAGCGUCAGGCAACAGA
BAAE01282596.1/561-477     UGAGGUCAGCUGCUCUGACAAUGUUGCACUACUGUACCA-UCCAUUCUAGCAGUGCAAUAGUAUUGUCAUAGCAUUUGGCCUCAGC
AANN01291171.1/711-630     UGGCCGCAGGUGCUCUGACGAGAUUGCACUACUGUGCA---CCCA-GAAGCAGUGCAAUGAUAUUGUCAAAGCAUCUGGGACCAGC
AAKN02007371.1/58666-58747 UGGCUGCAGAAGCUCUGACGAGGUUGCACUACUGUGCU---CUGA-GAAGCAGUGCAAUGAUAUUGUCAAAGCAUCUGGGGCCAGC
ABRQ01300519.1/2745-2826   UGGGCGCAGGUGCUCUGACGAGGUUGCACUACUGUG--U-GCUGA-GAAGCAGUGCAAUGAUAUUGUCAAAGCAUCUGGGACCAGC
AL713917.6/125920-126003   UGCUAACGGCUGCUCUGACUUUAUUGCACUACUGUACUU-UACAG-CGAGCAGUGCAAUAGUAUUGUCAAAGCAUCCGCGAGCAGG
AC099350.8/217035-216952   UGCUGACGACUGCUCUGACUUUAUUGCACUACUGUACUG-UACAG-CUAGCAGUGCAAUAGUAUUGUCAAAGCAUCCGGGAGCAGG
AAWZ02031871.1/4158-4075   UGCGGACAAGGGCUCUGACUUCAUUGCACUACUGUACUU-CCCAA-CUAGCAGUGCAAUAGUAUUGUCAAAGCACUUGCAAGCAGA
CAAB02012615.1/15813-15897 AGAGGUCAGCUGCUCUGACGAUGUUGCACUACUGUACCG-UGCACUAAAGCAGUGCAAUAGUAUUGUCAUAGCAUCGGACCUUCGC
AAGW02071375.1/71553-71634 UGGCUGCAGGUGCUCUGACGAGGUUGCACUACUGUGCU---CUAA-GAAGCAGUGCAAUGAUAUUGUCAAAGCAUCUGGGACUAGC
AAQR03174393.1/7600-7681   UUGUCACAGGUGCUCUGACGAGGUUGCACUACUGUGCU---CUGA-GAAGCAGUGCAAUGAUAUUGUCAAAGCAUCUGGGACUAGC
#=GC SS_cons               :<<<--<<<<<<<<-<<<<---<<<<<<<<---<_____.__>--.----->>>>>>>>------>>>>->>>>>>>>-->>>:::
#=GC RF                    UgcugaCaGguGCUCUGACuuuaUUGCACUACUGUacuu.uaCaa.cuAGCAGUGCAAuAgUAUUGUCAAAGCacCuGagagcAGc
//
# STOCKHOLM 1.0

#=GF AC   RF02062
#=GF ID   STnc361
#=GF DE   Salmonella enterica sRNA STnc361
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   107.90
#=GF NC   37.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


AE006468.1/3780254-3780402 UUUAAAGUAAGGAAUAUCUUAUUAGCGCGAACAGCUAAGGCUAAUUUGAAUAUUAAUUUA-AUGAAGAGUACGCCUGGCGCGUCACAAAGGAAAUAUCUGCUUUUCGCCUGAUGUGUUACAAAAAAUAAAGUAGCACAUUUUGUUAAAAA
CP000880.1/3968200-3968051 UUUGACUUAAGGAACAUCUUAUUAUCACAAGCGAACAACGUUAAUUUGAAUAUUAAUUUAUAAGAAGAGUACGCCUGGCGCGCCACAAAGGAAAUAUCUGUCUCCCAUCUGGUAUGUUACAAAAUAUAAAUUGGCACACCAUGUUAAAAA
#=GC SS_cons               [[[[[[,,,(((,,,,<<--<<<<<<_____________>>>>>>-->>,,,,,,,,,,,,,,,,<<<-----<<<<<____>>---->>>----->>>,,,,,,,,)))<<<<<<<<<<__________>>>>>>>>>>,,]]]]]]::
#=GC RF                    uuuaacuUAaGgAAuAuCUUauuagCaCaAaCaaauAAgGcuaauUUGaAUAUUAAUUUAUAaGAaGaGUACGCCuGgCGCGcCACAAaGGAAAUAuCuGuuUuuCacCugguguGuuacAAAAaAUAAAguagCacaccaUguuaaaAA
//
# STOCKHOLM 1.0

#=GF AC   RF02063
#=GF ID   STnc350
#=GF DE   Salmonella enterica sRNA STnc350
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   87.50
#=GF NC   55.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


CP000026.1/3558109-3558042 AUGUACUGAGUACUGCGAAGAAGGGGGGAUAAACAAAACGCCCACAUAAGCGGGCGUUGUUGUUGAUA
CP000880.1/3988979-3989045 AUGUACUGAGAGCUGUGGAAAAGAGGGAAUAAA-AAAACGCCCACAUAAGCGGGCGUUAUUGUUGCUU
#=GC SS_cons               :::<-<________>->--------------<<-<<<<<<<<<________>>>>>>>->>->>::::
#=GC RF                    AUGuACUGAGuaCUGugaAaAAGaGGGaAUAAACAAAACGCCCACAUAAGCGGGCGUUaUUGUUGaUu
//
# STOCKHOLM 1.0

#=GF AC   RF02064
#=GF ID   STnc370
#=GF DE   Enterobacterial sRNA STnc370
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   54.00
#=GF TC   54.20
#=GF NC   53.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.31 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   10


ABEH02000004.1/254218-254148   AAUUAUUAGCGAAUCGACUGAUACUAUUUAUAUUAUAA-AAAAACCUGCC--CGAAAGCAGGUUUUUGUUUAAU-
ABFG01000002.1/215355-215284   AAUUAUUAGCGAAUCGACUAGCACUCUUUACGUUAUAAAAAAAACCUGCC--CGAAAGCAGGUUUUU-UUUAUUU
ABFH02000001.1/1335782-1335712 AAUUAUUAGCGAAUCAACUAAUACUAUUUACGUUAUAA-AAAAACCUGCC--CGAAAGCAGGUUUUU-UUUAUUU
ACBF01000002.1/183905-183835   AAUUAUUAGCGAAUCGACUGAUACUAUUUAUGUUAUAA-AAAAACCUGCC--CGAAAGCAGGUUUUU-UUUAAUU
AE017220.1/3793326-3793396     AAUCAUUAGGGGAUUCAUCAGUACUAUUUAUGUUAUAA-AAAAACCUGCC--CGAGAGCAGGUUUUUGUUUAUU-
CP000857.1/3777076-3777146     AAUUAUUAGCGAAUCAACUAAUACUAUUUAUGUUAUAA-AAAAACCUGCC--CGAGAGCAGGUUUUUGUUUAUU-
FM200053.1/3623316-3623386     AAUUAUUAGCGAAUCGACUAGCGCUCUUUACGUUAUAA-AAAAACCUGCC--CGAAAGCAGGUUUUUAUUUAUU-
CP000964.1/192732-192662       AAUUAUUAACGGUUCAUCUAUUUAUAUUUCCCGUAUAA-AAAAACCUGCC--CUGAGGCAGGUCUUUUAUUAUU-
CP000713.1/976751-976685       AAUAAUA-UCUAACCUU---AUCCGAUUUUAGGCAUAA-AAAAACCUGCC--AGAAAGCAGGUUUUUUUAUUGU-
AE014075.1/4585598-4585667     ACCGAAAGACGAUUAAU---UUCGUUUUUUAGUCAUAA-AAAAACCUGCCAGCGAUGGCAGGUUUUUUUUUGCC-
#=GC SS_cons                   :::<<<<<<________>>>>>>---------------.<<<<<<<<<<_.._____>>>>>>>>>>:::::::.
#=GC RF                        AAUuAuuaGCGAAUcaaCuaaUacUaUUUauGUUAUAA.AAAAACCUGCC..CGAaAGCAGGUUUUUuUUUAuU.
//
# STOCKHOLM 1.0

#=GF AC   RF02065
#=GF ID   STnc340
#=GF DE   Enterobacterial sRNA STnc340
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   80.00
#=GF TC   112.50
#=GF NC   52.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4


ABEH02000004.1/441959-442088 AAGAUCUAUUUAGCGUAUAGUACGAUAGCAAUUAAUAAACCAUGCAGGUAGUCCAAAUAAGGACUUCAUCUUUACCUGGAAAUCUGAUUUAAAAAAGGCCG-CUUAAUAAUAAGCGGCCUGUAUUAGUGUU
ABFG01000002.1/414881-415009 AAGAUCUAUUUAGCGUAUAGUACGAUAGCAAUUAUUAAACUAUACAGGUAGUCCAAAUAAGGACUUUAUCUUUACCAGGGGAUAUGAUUUAAAAA-GGCCG-CUUAAUAAUAAGCGGCCUUUAUUAGUGUU
AE006468.1/3635884-3635756   AAGAUCUAUUUAGCGUAUAGUACGAUAGCAAUUAAUGAAUCAUCCAGGUAGUCCAAAUAAGGACUUUAUCUUUACCAGGGGAUAUGAUUUAAAAA-GGCCG-CUUAAUAAUAAGCGGCCUUUAUUGUCUAU
CP000822.1/4397336-4397206   AAAAUCCAUUUUGCGGACGUUACCAUAUCAAUUAAUAAGGGAGUGAGGUAGUCCAGAUAAGGACUUCUUAUUCUGCGGGUAAUAUGCUUUGCGUAGACUCAACAUAAUAAAAAACGGCCUGGAGAUGAUGU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::<<<<<______>>>>>-----------------------------<-<<<<<.<<<<____>>>>>>>>>>:::::::::::
#=GC RF                      AAgAUCuAUUUaGCGuAuagUACgAUAgCAAUUAAUAAauuAuucAGGUAGUCCAaAUAAGGACUUuaUcUUuacCaGGuaAUAUGaUUUaaaaAaGGcCG.cuUaAUAAuAagCGgCCUuuAuuaguuuU
//
# STOCKHOLM 1.0

#=GF AC   RF02066
#=GF ID   STnc320
#=GF DE   Salmonella enterica sRNA STnc320
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   51.20
#=GF NC   46.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


ABEI01000008.1/131560-131614 UUGACGCAUAUCACAACAAAAAAGGGCGCACGUUGGUGCGCCCUUUUCUCAGCUU
AE006468.1/3404895-3404949   UUGACGCGUAUCACAACAAAAAAGGGCGCACUUUGGUGCGCCCUUUUCUCAACUU
CP001127.1/3312429-3312483   UUGACGCACAUCACAACAAAAAAGGGCGCACACUGGUGCGCCCUUUUCUCAGCUU
#=GC SS_cons                 :::::::::::::::::::<<<<<<<<<<<<____>>>>>>>>>>>>::::::::
#=GC RF                      UUGACGCAUAUCACAACAAAAAAGGGCGCACaUUGGUGCGCCCUUUUCUCAgCUU
//
# STOCKHOLM 1.0

#=GF AC   RF02067
#=GF ID   STnc310
#=GF DE   Salmonella enterica sRNA STnc310
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   40.00
#=GF TC   45.70
#=GF NC   37.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.60 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   8


AE006468.1/3393327-3393267 AUUGUGACAU-GUUAAACAAAAACG-CCCGACAGGUGUGCGCUGUCGGGCGUUUUUGACGGGG
FM200053.1/3199455-3199395 GUUGUGACAU-GUUAAACAAAAACG-CCCGGCAGGUGUGCGCUGCCGGGCGUUUUUGAUGGGG
CAAU01002608.1/533-577     AUUGUGACAU-GUUAAACAAAAACG-CCCGGCAGGUGUACGCUGCCG----------------
CAAQ01000523.1/996-935     AUUGUGACAU-GUUAAACAAAAACGACCCGGCAGGUGUACGCUGCCGGGCGUUUUGUAUGGGC
CP000880.1/4318546-4318606 AUUGUGACAU-GUUAAACAAAAAAG-CCCAACGGGUAUGCGCCGCCGGGCGUUAAUGACAGAG
CAAZ01000091.1/10490-10433 AUUGUGACAU-GUUAAACAAAA--A-CGCCGCAGGUGUACGCUGCCG-GCGUUUUUGAUGGGG
CAAX01001521.1/1144-1084   AUUGUGACAUAGUUAAACAAAAC-G-CCCGGCAGGUGUACGCUGCCGGGCGUUUUUGAUGGGG
CAAR01000235.1/14645-14589 AUUGUGACAU-GUUAAACAAAAACG-CC--GC-GGUGUACGCUGCCGGGCGUUUU-GAUGGGG
#=GC SS_cons               :<<<<_____._____>>>>-----.<<<-<<<<<____>->>>>->>>::::::::::::::
#=GC RF                    AUUGUGACAU.GUUAAACAAAAAcG.CCCgGCaGGUGUaCGCuGCCGGGCGUUUUUGAUGGGG
//
# STOCKHOLM 1.0

#=GF AC   RF02068
#=GF ID   STnc480
#=GF DE   Enterobacterial sRNA STnc480
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Predicted;WAR ;Burge SW
#=GF GA   72.00
#=GF TC   72.00
#=GF NC   70.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   6


AB115590.1/13295-13366   GAAUAAAAAAUGCCACGGUUCUCACCGUGGCAAAAUCCAACAUAGCUAAACAAAAAAAAUUUAUGCGA-------UGGG
AE006468.1/587848-587926 GCAUAAAAAAAGCCACGGUUCUCACCGUGGCAAAAUCCAACAUAGCUAAAUUAAAAAUAAUCAGGAGGGCUGCCCGCCG
BAAW01012546.1/529-589   GAAUAAAAAAUGCCACGGUUCUCACCGUGGCAAAAUCCAACAUAGCUUAACAAAAAAGGUG------------------
CAAY01000321.1/1134-1204 GUAUAAAAAAAUCCACGGUUCUCACCGUGGCAAAAUCCAACAUAGCUAAAUA-AAAAUAAUCAGGAGG-------GCUG
U82664.1/122636-122702   UUACAAAAAAAGCCACGGUAUAAACCGUGGCAAAAUCCAACAUAGCUA-----AAAAUAAUCAGGCGA-------GUGG
CU928164.2/509611-509677 CCGCAAAAAAAGCCACGGAAUAAACCGUGGCAAAAUCCAACAUAGCUA-----AAAAUAAUCAGGCGA-------GUGG
#=GC SS_cons             :::::::::::<<<<<<<<____>>>>>>>>:::::::::::::::::::::::::::::::::::::.......::::
#=GC RF                  guAUAAAAAAaGCCACGGuucucaCCGUGGCAAAAUCCAACAUAGCUAAAuaAAAAAuAaUCAGGaGa.......GugG
//
# STOCKHOLM 1.0

#=GF AC   RF02069
#=GF ID   STnc70
#=GF DE   Enterobacterial sRNA STnc70
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Burge SW
#=GF SS   Predicted; Pfold; Burge SW
#=GF GA   40.00
#=GF TC   40.20
#=GF NC   39.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Non-coding_RNA
#=GF SQ   2


AM933173.1/660477-660625   GAGCGCAACACUUAGCCAGCAUAUACGCUAUGGAUUUCGAGUUGCAGACAAUACGUCUGUAAUUUGCAAGACGAGUCGUACUGGCUCUGAAGUUACCUACGGGUAGUUCAGGUAAUGGGGCCGCCUGUCAGGCGGCCUUUUUACUUUAG
CP000880.1/2252604-2252456 GAGCGCAACACUUAGCCAGCAUAUACUCUGUGCAUUUCGAGUUGCAGACAACGGGUCUGUAAUUUGAAAGAGGAGUUGUACUGGCUCUGAAGUUACCUACGGGUAGUUCAGGUAAUGGGGCCGCCUGUCAGGUGGCCUUUUUACUUUAG
#=GC SS_cons               :::::::::::::<<<<<<---------------<<<<<<<<<<<<<<<_____>>>>>>>>>>>>>>>----------->>>>>>,,,,,,,,<<<____>>>,,,,,,,<<<--<<<<<<<<<<___>>>>>>>>>>-->>>:::::
#=GC RF                    GAGCGCAACACUUaGCCaGCAUAUACuCUaUGgAuuuCgaguugCaGaCAAuagGuCuGuaauuuGaaaGAgGAGUuGUACuGGCuCUGAAGUUaCCUACGGGuAGUUCAGGuaAUggGGCCgCCuGUCaGGcGGCCuuUUuaCUUUAG
//
# STOCKHOLM 1.0

#=GF AC   RF02070
#=GF ID   STnc300
#=GF DE   Salmonella enterica sRNA STnc300
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   83.30
#=GF NC   71.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4


CP001120.1/3276332-3276174 UUUUUUAUAACAUCUUGAAAAUAAAUGAUUUUAAUUUAAAUCCUGUCUGGUUUUCUAAAAAAUAAUUUAAAAUUAUUAAUAUGAUUUUUUUCUGUCGCGGUUGA-CUCAUCUCCUGAAAAUGCCGUGAGUUCUCGUCCUUCAGGACGAUAUUCUUUUGAG
CP001138.1/3200248-3200090 UUUUUUAUAACCGAUUGAAAAUAAAUGUUUUUAAUUUGAAUCUUGUCUGGAUUUCUAAAAAAUAAUUAAAAAUUAUUAAUAUAAUUUUUUUCUGUCGCGGUUGA-CUCAUCUCCUGAAAAUGCCGUGGGUUCUCGUCCUUCAGGACGAUAUUCUUUUGAG
ABEJ01000015.1/11211-11053 UUUUUUAUAACUAUUUGAAAUAAAACAGUUUUAAUUUAAAUCCUGUUUGGUUUUCUAAAAAAUAAUUAAAAAUUAUUAAUAUAAUUUUUUUCUGUCGCGGUUGA-CUCAUCUCCUGAAAAUGCCGUGGGUUCUCGUCCUUCAGGACGAUAUUCUUUUGAG
CP000880.1/4417788-4417947 UUUUUAAUAACUAAUUGAAAUUUAUUGUUUUUAUUUAAGGCCCCAUCUGAUUUUUAAAAAUGUCAUUAAAACUUAUUAAUAUAAUAUCUUUAUGUCGUGGUUGAACUCAUAUAAUGAAAAGGUCGACGGUUCUCGUUCCUCAGGACGAUAUCCUUUUGAG
#=GC SS_cons               ::::::::::::::::<<<<-----<<---<<______>>--->>------>>>>,,,,,,,,,,,,<<<<<<<<<____>>>>>>>>>,,,,,<<<<<<<---.-<<<_____>>>---->>>>>>>,,,,<<<<<<____>>>>>>::::::::::::
#=GC RF                    UUUUUuAUAACuaaUUGaaauuaAacguUUuuAaUUuAaauCccgUcUGguuuuCuAAAAaaUaAUUaaaaauuauUAAUauaauuuuuUUcUGucgcGGuUGA.CuCaUcUccuGaAAAugCCgcggGUUCuCGucCuUCAGgaCGaUAUuCUUUUGAG
//
# STOCKHOLM 1.0

#=GF AC   RF02071
#=GF ID   STnc280
#=GF DE   Salmonella enterica sRNA STnc280
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   80.00
#=GF TC   95.00
#=GF NC   53.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


ABEL01000005.1/206755-206838 CGCGGCAAGAAGUUCUGCGCUAUAACGAAAAAGGGGGGGUCUGUCACUGGCUUUGCCCUCGUGAUAGAGGGCUUUU-UAUAACGG
AE006468.1/3179540-3179622   CGCGGCAAGACGUUCCGCGCUAUAACGAAAAAGGGGG-UUCUGUCACUGGCUUUGCCCUCGUGAUAGAGGGCUUUU-UAUGACGG
CP000880.1/4536157-4536076   CGCGCCUGCAA--UACCCGUUACAACGAAAUAUGUGU-UUCUGUAACUGGCUUUGCCCUCUUGAUUGAGGGCUUUUUUAUGACGG
#=GC SS_cons                 <<<<<_________>>>>>------------------.----------------<<<<<<______>>>>>>::::.::::::::
#=GC RF                      CGcGgCaagAaGUUcCgCGcUAuAACGAAAaAgGgGg.uUCUGUcACUGGCUUUGCCCUCgUGAUaGAGGGCUUUU.UAUgACGG
//
# STOCKHOLM 1.0

#=GF AC   RF02072
#=GF ID   STnc590
#=GF DE   Salmonella enterica sRNA STnc590
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   100.00
#=GF TC   142.80
#=GF NC   60.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


AE006468.1/3010807-3010966     CUUUAACUUUUCAGAUUUAAUAUAUUGCCUGCAAAAAUAUGCCUCAAUGAUUGAGCCAGGCUACCAACCACCUCCGGAUGAUUAUAUAUAAGAAUUACUACUCAAAAAAUCUUUUUUAUAAUAAAAGCUCAACACAUGGUCAUAAAUGAUAAAAAAUAUU
ABEI01000005.1/40301-40460     CUUUAACUUUUCAGAUUCAAUAUAUUGCCCGCAAAAAUAUGCCUCAAUGAUUUAGCCAGGCAACCAAUCACCUCCAGAUGAUUAUAUAUACGAAUUACUACUCAAAAAAUCUUUUUUAUAAUAAAAGCUCAACACAUGGUCAUAAAUGAUAAAAAAUAUU
ABFH02000001.1/2176118-2175959 CUUUAACUUUUCAGAUUCAAUAUAUUGCCUGCAAAAACAUGCCUCAAUGAUUGAGCCAGGCUACCAGCCACCUCCGGAUGAUUAUAUAUAAGAAUUACUACUCAAAAAAUCUUUUUUAUAAUAAAAGCUCAACACAUGGUCAUAAAUGAUAAAAAAUAUU
#=GC SS_cons                   ::::::::::::::::::::::::::[[[,<<<______>>>,,,,,,,,((((((,,<<_______>>,,,,,,,,,,,<<<<<<---<<<<________________>>>>--->>>>>>,,,,)))))),,,,,]]]::::::::::::::::::::
#=GC RF                        CUUUAACUUUUCAGAUUcAAUAUAUUgCCuGCaAAAAuAuGCCUCAAUGAuugaGCCAGgCuACCAacCACCUCCgGAUGauuauaUAUaaGaAUUACUACUCAAAAAAuCuuUUUuauaauAAAAGCucaaCACAUGGuCAUAAAUGAUAAAAAAUAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02073
#=GF ID   STnc260
#=GF DE   Salmonella enterica sRNA STnc260
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   100.00
#=GF TC   137.00
#=GF NC   78.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


FM200053.1/2777436-2777610   UCAAUACACUCUGGCAUCGUGAGUUAUCCGCCU-UUUCUGUUUACCAGAUCACAUUUUAUUAUUUAACAGGCCAGGCAUUACUUAAUUUAAAAUGUAUUCUCGCCGCAAAUAUAAUAAACGCAAAUUAUAUUAAGCAAUAAAAAACCCCGGCCAUAAACCGGGGUUAAUUUAAAUA
ACDJ01000017.1/168123-168298 UCAAUACACUCUGGCAUCGUUAAUUAUCCACCUCUUUCUGCUUGCCAGAUCACAUUUUAUUAUUUAACAGGUCAGGCAUCAUUUAAAUUAAAAUAUAUUCUCGCCGCAAAUAUAAUAAACCCACAUUAUAUUAAGCAAUAAAAAACCCCGGACAUAAACCGGGGUUAAUUUAAAUA
#=GC SS_cons                 :::::::::<<<<<<---<<-<<-------------<<<<_____>>>>-------------->>->>-->>>>>>------((((,,,,,,,,,,,,,,,,,,,<<-<<<<<<<<________>>>>>>>>-->>,,,,,,,<<<<<<<<_______>>>>>>>>,,,)))):::
#=GC RF                      UCAAUACACuCuGgCAUCGuuaaUUAUCCaCCUcUUuCuGuUUaCCaGaUCACAUUUUAUUAUuuAaCAGGcCaGgCAUuAuuuaaaUUAAAAUaUAUUCUCGCCGCAaauauaauAAACgCAaauuauauuAAGCAAUAAAAaaCCCCGGaCAUAAACCGGGGuuAAUuuaaAUA
//
# STOCKHOLM 1.0

#=GF AC   RF02074
#=GF ID   STnc240
#=GF DE   Enterobacterial sRNA STnc240
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   55.00
#=GF TC   55.60
#=GF NC   53.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.65 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   15


BAAW01000093.1/15904-15981   AGUAAGUGUUGCAAAAUAC-GCGGCCUGAAAAAAUAGAA-ACUAGCCGACGCU--UUUUUAAAGUGUCGGUUAUUUUUUUGC
BAAX01035909.1/273-349       CCAAUUUAGUGCAAAAUAC-GCCGCUUGCAAAAAAUGAC-AUUAACCGACGUU---UUAAUACGCGUCGGUUAUUUUUUUGC
CP000266.1/2094763-2094689   CCCAUUUAG-GCACAAUGC-GCCGCUGUCAAAAAAUGAUUAAAAACCGACGUU---UAAUUA-GCGUCGGUUAUUUUUU-GC
CP000653.1/2827549-2827474   CAAAGAUGGGGCAAAAUGC-GCCGC-UGCAAAAAAUUAG-AAUAAUCGACGAU--AU-AAAAGGCGUCGGUUAUUUUUUUUU
CP000783.1/1173331-1173403   UUAAAGUGGUGCAAAAUAC-GCGCCCUGCAAAAUAAGAU-AUUAACCGACG-------UCAACGCGUCGGUUAUUUUUUUGC
CP000822.1/744757-744833     UUAAUUUAGUGCACAAUGC-GCCGCUUGCAAAAAAUGAC-AUUAACCGACGUU---UUAAUACGCGUCGGUUAUUUUUUUGC
CP001120.1/2195028-2194952   UCAAUUUAGGGCAGAAUAC-GCCGCUUGCAAAAAAUGAC-ACUAACCGACGUU---UUAAUACGCGUCGGUUAUUUUUUUGC
ABVY01000090.1/1902-1836     AUCGAGUGGUGCAGAAUAC-GCGCCUUGCAAA---------AUAACCGACG-----UCUAAUAGCGUCGGUUAUUUUUUUAC
CP000647.1/2697551-2697473   UGAAUUUGUUGCAAAAUAU-GCGGCCUGA-AAACCAGAG-ACUAGCCGACGCUUUUUUUUAAAGUGUCGGUUAUUUUUUUGG
CP001593.1/1843947-1844011   UCAAGUUAGGGCAAAAUAC-GCCGA----------AUGA-AAUAGCCGACG-----UUUAAACGCGUCGGUUAUUUUUUUUU
CU928160.2/2137500-2137426   CCCAUUUAG-GCACAAUGC-GCCGCUGUCAAAAAAUGACUAAAAACCGACGUU---UCAUCA-GCGUCGGUUAUUUUUU-GC
AALF02000015.1/92314-92378   UCAACUUAGGGCAAAAUAC-GCACC----------AUGC-AAUAACCGACG-----UUUAAACGCGUCGGUUAUUUUUUUGC
ABWM02000009.1/216483-216408 CUUGAAUAGGGCAAAAUGCCGCCGC-UGCAAACAAAU-G-AAUAAUCGACGAU---AUAAAAGGCGUCGGUUAUUUUUUUUU
AALE02000021.1/46560-46623   UCAAGUUAGGGCAAAAUAC-GCAC-----------AUGC-AAUAACCGACG-----UUUAAACGCGUCGGUUAUUUUUUUGC
AALC02000021.1/56264-56200   UCGAGUUAGGGCAAAAUAG-GCCCC----------AUGC-AAUAACCGACG-----UUUAAACGCGUCGGUUAUUUUUUUGC
#=GC SS_cons                 ::::::::::<<_______.>>-----------------.--<<<<<<<<<__...________>>>>>>>>>:::::::::
#=GC RF                      ucaAuuUaGuGCAaAAUAC.GCcgCuUGcAAAAAaagAc.AauAACCGACGuU...UUuaaAaGCGUCGGUUaUUUUUUUgc
//
# STOCKHOLM 1.0

#=GF AC   RF02075
#=GF ID   STnc230
#=GF DE   Enterobacterial sRNA STnc230
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   63.80
#=GF NC   44.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   11


AE017220.1/2137109-2137191   ---UUAUUACCAU--UAUCCU-G-GCCCUGAUAAAAA-GUACAAU-GACAAUAUCAAAAGUCUCCCAUUGCUGGGAGACG-UUUUGAUCAGUU
BAAW01001196.1/1134-1219     UUUUUAGCAUCAG---AUCCC-G-UCGACGAUAAAAAAGUGCAUU-GACAAUAACAAAAGUCUCCCACCCCGGGGAGACU-UUUUGAGCGGUU
CP000647.1/3514533-3514615   ---UUAGCAUCAG---AUCCC-A-UCGACGAUAAAAAAGUGCAUU-GACAAUAACAAAAGUCUCCCAACCCGGGGAGACU-UUUUGAGCGGUU
CP000822.1/770090-770007     ---UCAUCACCAU---ACUGU-A-UUAGUGAUAAAAAAGUAUAAGGGACAAUAACAAAAGUCUCCCAUCCGUGGGAGACG-UUUUGACCAGUU
BAAW01000983.1/1921-2001     ---UCAUCAUCAU---UUACC-G-CCAACGAUAAAAGAAUAU----UACGAUAGCAAAAGUCUCCCAUCCGUGGGAGACGUUUUUGGCCAGUU
AM498294.1/3774-3860         ---UUUUCACCCUGCCAUCCUGA-GCAUUGAUGAAAGUCGUAAUU-GAACAUAACAAAAGUCUCCCAUUCUUGGGAGACU-UUUUGGGCAGUU
BABF01013615.1/279-362       ---UCAUCUCGCG---AUCCA-GCGCUCUGAUGAAAGUCAGCAUU-GAACAUAACAAAAGUCUCCCAUUCUUGGGAGACU-UUUUAAGCCGUU
CU928158.2/2060013-2060095   ---GCGUUACCAU---UCCAU-U-UCAUUGCCAGAAAACAAAACG-GACAAUAACAAAAGUCUCCUUUUGAGGGGAGACU-UUUUGUUCAGUU
CP000800.1/2245619-2245702   ---ACAUCAUCCC--UGAUGA-U-UUACUGACGAGAAGCACAAAG-GACAAUAACAAAAGCCUCCGUGAAGCGGGAGACU-UUUUAAUAAGUU
AM236324.1/64735-64818       ---ACAUCAUCCU---UGAUGAU-UUACUGACGAGAAGCACAAAG-GACAAUAACAAAAGCCUCCGUGAAGCGGGAGACU-UUUUAAUAAGUU
ABWL02000002.1/645137-645054 ---UCAUCUCGCU--UUCCUG-A-GCACUGAUGAAAGUCAUCAUU-GAACAUAACAAAAGUCUCCCAUUCUUGGGAGACU-UUUUGGACGGUU
#=GC SS_cons                 ...::::::::::...:::::.:.:::::::::::::::::::::.::::::::<<<<<<<<<<<<______>>>>>>>-.>>>>>:::::::
#=GC RF                      ...UcAUCAuCau...auccu.a.uCacUGAUaAAAAacaaaAuu.GACaAUAACAAAAGUCUCCcAuucuugGGAGACU.UUUUGauCAGUU
//
# STOCKHOLM 1.0

#=GF AC   RF02076
#=GF ID   STnc100
#=GF DE   Gammaproteobacterial sRNA STnc100
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Predicted; CMfinder; Burge SW
#=GF SS   Predicted; CMfinder
#=GF GA   47.00
#=GF TC   47.10
#=GF NC   46.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.97 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   24


AE006468.1/975011-975224     ---CCAGCUAAAUUAUCAUGUUAUGUUA-C-UGCUGCUACAGUGAAUCCCCCUGUGCGGUGGGGUGUAAUUGGUUAUCAAUGG----AAACAGCUGUU--------UGUUUGC-CA------CACGAGUCACGGUAUAGCCA-GCCAAAGAUUCACCGGGA-GGCACCCGGCAC--U-GCAGCAUACUGAUAACAAAUAUAGC-GU-GUCCC---AAAGGCUCAC-UUCGGUGAGCCUUU-UUUACAGGC--
ABHR01000006.1/211014-210809 ---UCAGACUGAGCAUU-UGUUAAAAAA-A-UUUCGC-AUGGUGAAUCCCCCUGUGUGGAGGGGCG--ACUGGUGAAAAAUCC---UUGCUUGUGAUU--------CAUUAUC-GA------CACGGGUU-CGGUGGUACCA-GGCCGA-ACUCACCGGGA-GGCACCCGGCACCAU-GCAGUAUACAGA-GAUUAG----GC-AU-AUACC---AAGGCCUCUC-AUAGCAGGGGCCUU-UUUACAUGU--
AB028904.1/451-659           CUGUCAAACUGAGCAUU-UGUUAAAAAA-A-UUUCGC-AUGGUGAAUCCCCCUGUGUGGAGGGGCG--ACUGGUGAAAAAUCC---UUGCUUGUGAUU--------CAUUAUC-GA------CACGGGUU-CGGUGGUACCA-GGCCGA-ACUCACCGGGA-GGCACCCGGCACCAU-GCAGUAUACAGA-GAUUAG----GC-AU-AUACC---AAGGCCUCUC-AUAGCAGGGGCCUU-UUUACAUGU--
ABEJ01000006.1/45604-45802   ---CCAUGUAAAUUAUCAUGUUAUGGUA-A-UGAUGUUGCGGUGAAUCCCGUUA-GCACGGGGCAU--A--AAUGGUUAACCU---------GCUUAU--------CAUGUGU-GA------UGCGAGUCAUUGUAUAACCA-UUCAGUGGCUCACCGGGU-AGCG-UCGGCAC--U-GCAACAUCUACUCUACUCAU--UAC-UU-AACUC---AAGGCU-----ACUUCGGUAGCCUU-UUCUUUUCCAC
AE006468.1/976548-976765     ---CCAUGUAAACCACAGUGUUAUUAUG-C-AGGUGUUGCGGUGAAUCCCGUUA-GCACGGGGCAA--AUUGAUCAUCUACUUUUGUUAAUCAACGUUGCAGCAGACAUGAGC-GC------CGCGAGUCAUGGC-UGAUCA-ACCAAAGGCUCACCGGGU-AGCGAUCGGCAC--U-GCAGCACCUACUCUACCCAU--UAC-UU-AAAUC--AAAGGCU-----ACUUCGGUAGCCUU-UUCUUUUUCC-
ABEJ01000006.1/44765-44978   ---CAUGGUAAAUUAUCAUGUUAUGUUA-U-UGCGGUUGCAGUGAAUCCCCCUGGGCGGUGGGGCGUAACUGGUUUUCAAUGG----AAAUAGCUGUU--------UAUUUGC-UA------CGCGAGUCACGGUAUAGCCA-GCCAAAGAUUCACCGGGA-GGCACCCGGCAC--U-GCAGCAUACUGAUAACAAAUAUAGC-GU-GUCCC---AAAGGCUCAC-UUCGGUGGGCCUUU-UUUACAGGC--
AB028901.1/452-658           ---UCAGACUGAGCAUU-UGUUAAAAAA-A-UUUCGC-AUGGUGAAUCCCCCUGUGUGGAGGGGCG--ACUGGUGAAAAAUCC---UUGCUUGUGAUU--------CAUUAUC-GA------CACGGGUU-CGGUGGUACCA-GGCCGA--CUCACCGGGAAGGCACCCGGCACCAU-GCAGUAUACAGAAGAUUAG----GC-AU-AUACC---AAGGCCUCUC-AUAGCAGGGGCCUU-UUUACAUGU--
ABHT01000159.1/340-541       ---UCAGACUGAGCAUU-UGUUAAAAAA-A-UUUCGC-AUGGUGAAUCCCCCUGUGUGGAGGGGCG--ACUGGUGAAAAAUCC---UUGCUUGUGAUU--------CAUUAUC-GA------CACGGGUU-CGGUGGUACCA-GGCCGA-ACUCACCGGGA-GGCACCCGGCACCAU-GCAAUG-GCACA-----UA----GC-GC-CACUC--UCCAGCCCCUC-UCCGGAGGGGCUUU-CUUAUGGAC--
AJ271153.1/2772-2981         ---UCUGAUAAUAGAUG-UGUUAGAAAA-U-UUCUGC-AUGGUGAAUCCCCCUGUGCGGAGGGGCG--ACUGGUGAACGGUAUGAUCUCUUUGAUGAU--------CGUAAGC-GAGA-AUACGCGGGUU-UGGUGGCACCA-GGCCGA-ACUCACCGGGA-GGCACCCGGCACCAU-GCAAU-GGCACA-----UA----GC-GC-CACUC--UCCAGCCCCUC-UCCGGAGGGGCUUU-CUUAUGGAC--
ABHW01000120.1/1472-1680     ---ACAUGCUGAGCGUU-UGUUAAAAAA-A-UCCUGC-AUGAUGAAUCCCCCUGAGCGGCGGGGCA--U--AAUGACAGAUGU---UUGGUUGCGUAUU------GUAUAGGC-AAG----UUGCGGAUU-CUGUCUGGUCAUUGCAGA-AUUCACCGGGA-GGCACCCGGCAUCAU-GCUGUAUACAGA-GAUUAG----GC-AU-AUAUC---CAGGCUUCUC-AUCGCAGGAGCCUU-UUUACAUGC--
CU928162.2/1046252-1046457   ---UCAGACUGAGUAUU-UGUUAAAAGA-A-ACUGGC-AUGGUGAAUCCCCCUGUGCGGAGGGGCA-UAUCAGCGACAGGUGG---UUGGUUAUAUCC--------CUUAUCU-GG------UGCGGGUU-CAGG-UGCUGA-UACUGA-ACUCACCGGGA-GGCACCCGGCAUCAU-GCUGUAUACAGA-GAUUAG----GC-AU-AUAUC---CAGGCUCCUC-AUCGCAGGAGCCUU-UUUACAUGC--
AE005174.2/2995675-2995466   ---UCUGAUAAUAGAUG-UGUUAGAAAA-U-UUCUGC-AUGGUGAAUCCCCCUGUGCGGAGGGGCR--AYYRGYGAACGGUAKGAUMUMUKKGAURAU--------CGUAAGC-GAGA-WUACGCRGGUU-UGSUGGCACYA-GGCYGA-AYUCACCGGGA-GGCACCCGGCACCAU-GCAAU-GGCACA-----UA----GC-GC-CACUC--UCCAGCCCCUC-UCCGGAGGGGCUUU-CUUAUGGAC--
AAJV02000111.1/779-981       ---AUUUGCUGUUUAU----UAAAAACA-C-UUCUGC-AUGGUGAAUCCCCCUGUGCGGAGGGGCG--ACUGGUGUAGGUAGCAUUUAUUAUGUUAUA--------GGCAAGCCGA------CGCGGGUU-CAGUGACACC--GGCUGA-AUUCACCGGGA-GGCACCCGGCACCAU-GCAAGAAA---AAGAAUGU----GC-AU-GCAAA---CAUGCCCCUC-UCCGGAGGGGCAUU-UU-UUAUGG--
ABHS01000064.1/1682-1471     ---UCAGACUGAGCAUU-CGUUAAAAAA-A-UUC-GC-AUGGUGAAUCCCCCUGUGCGGAGGGGCG--ACUGGUGUAUAAGGU---GUCAUCUCUGACGAC--AACCUGGAGC-GAGA--UACGCGGGUU-CAGGGACACCG-GACUGA-ACUCACCGGGA-GGCACCCGGCACCAU-GUACAUGAUGAUACAGAUA----CG-CA-GUGUC---A--GCCCCUC-UCCGGAGGGGC--U-UUUUAUCUG--
ACGN01000130.1/12393-12184   ---UCAGACUGGGCAUU-UGUUAAAAAA-A-UUUCGC-AUGGUGAAUCCCCCUGAGCGGAGGGGCG--ACUGGUGACGGUAUA---AUCUCUGAUUAUCA---AAACGAGAAU-GA------CGCGGGUU-UAGUGGCACCG-GGCUGA-ACUCACCGGGA-GGCACCCGGCACCAU-GU-GCAUGAUGAUACAGAU----AC-GC-GGCUU----UAGCCCCUC-UCCGGAGGGGCUUU-CUUGUGGGC--
ACDM01000017.1/5708-5499     ---UCAGACUGGGCAUU-UGUUAAAAAA-A-UUUCGC-AUGGUGAAUCCCCCUGAGCGGAGGGGCG--ACUGGUGACGGUAUA---AUCUCUGAUUAUCA---AAACGAGAAU-GA------CGCGGGUU-UAGUGGCACCG-GGCUGA-ACUCACCGGGA-GGCACCCGGCACCAU-GU-GCAUGAUGAU--ACAG----AU-AC-GCGGC--UUUAGCCCCUC-UCCGGAGGGGCUUU-CUUAUGGAC--
CP001164.1/2963989-2963797   ---ACAUGCUGAGCGUU-UGUUAAAAAA-A-UUUCGC-AUGGUGAAUCCCCCUGUGCGGAGGGGCA--AUCA--------------GCAACCAGGUAU-----------AUGU-GAUA--AUCGCGGAUU-CAGG-UGCUGA-UACUGA-AUUCACCGGGA-GGCACCCGGCACCAU-GCAAGAAAAAGA---AUGU----GC-AU-GCAAA---CAUGCCCCUC-UCCGGAGGGGCUUU-UUUAUGGGU--
CP000034.1/1748636-1748431   ---CCCGGAUGAGAAUU-UGUUAGAAAA-A-AC-UGC-AUGGUGAAUCCCCCUGAGCGGAGGGGCG--ACUGGUGACGGUAUA---AUCUCUGAUUAUCA---AAACGAGAAU-GA------CGCGGGUU-UAGUGGCACCG-GGCUGA-ACUCACCGGGA-GGCACCCGGCACCAU-ACAAUGG-CACA-----UC----GC-GC-CACUC--UCCAGCCCCUC-UCCGGAGGGGCUUU-CUUAUGGAC--
AAMJ02000006.1/180919-180705 ---GCCGGAGGGAUAUU-UGUUAAAAAG-UGCGCCGU-GUGGUGAAUCCCCCUGUGCGGUGGGGCG--ACUGGUGUACAUAGC----AUUUAUUAUGU--------UAUGAGC-GAAGCCUACGCGGGUU-CAGUGACACC--GACUGA-AUUCACCGGGA-GGCACCCGGCACCAU-GCAACAGACGCA-AGUUAG----GC-UA-AGCCUUAUACCCCUGUAAGUUUUUUACAGGGGU-UUUUUGUGC--
ABKY02000005.1/221076-220884 ---UUUGUUUGCUGUUU-AUUAAAAACA-C-UUCUGC-AUGGUGAAUCCCCCUGUGCGGAGGGGCG--AUCA--------------GCAACCAGGUAU-----------AUGG-GAUA--AUCGCGGAUU-CAGG-UGCUGA-UACUGA-AUUCACCGGGA-GGCACCCGGCACCAU-GCAAGAAA---AAGAAUGU----GC-AU-GCAAA---CAUGCCCCUC-UCCGGAGGGGCUUU-UUUAUGGGU--
ABHU01000062.1/1730-1534     ---GCGGGGAG----UU-UGUUAAAAGA-A-ACUGGC-AUGGUGAAUCCCCCUGAGCGGAGGGGCA--UAUCAGCGCAGGUGU----UUCUACUCUAU--------CCUUU-C-UG------UGCGGGUU-CAGG-UGCUGA-UACUGA-ACUCACCGGGA-GGCACCCGGCACCAU-GC---AUAUGGU-UAACAG----AC-AC-GUAGC---GAAGCCCCUC-UCCGGAGGGGCUUUUUUUAUGGGC--
ABEI01000019.1/48136-47919   ---CCAUGUAAAUUAUCAUGUUAUGGCA-A-UGAUGUUGCGGUGAAUCCCGUUA-GCACGGGGCAA--ACUGAUCAUAUACUU---CUGUUAACCAAUGUC-GCAGCAGACGC-CA-----UAGCGGGUCAUGGC-AGGUUA-ACCAAAGGCUCACCGGAA-AGUACCCGGCACCGUAACAC--UCCAGUGAAAGCG---GGUAAU-UAAUC---AAAGGUUCAC-UACGGUGGGCCUUU-UCUGUAUAC--
ABKX01000022.1/1624-1817     ---GCUGCCGGAGAAUU-UGUUAAAAAUUA-CAUCGC-AUGGUGAAUCCCCCUCAGCGGCGGGGCA--U--CUGGCAAAGUGU----------AUGAU--------CCAGAGA-AC-----AUGCAAAUU-CAGU--AGACA-GGCUGA-AUUUACCGGGA-GGCCCCUGGCACCAU-GCGACAGACAGA-AAUUAG----GC-UAUACUUC-----AGCCCCUC-UCCGGAGGGGCU---UUUCUGUGC--
CP000880.1/3543688-3543870   ---UCAUAUUGUAAAAG-UAUUAUUCGG-A-UUGU-U-GUAGUGAAUCCCACUA-GCGUUGGGGCA---UAAAUGGUUAACCU---------GCUUAU--------CAUGUGU-GA------UGCGGGUCAUUGU-UAAUCA-UUCAGUGACUCACCGGGU-AGCGACCGGCACUGC-AA---CUCUACU-UAC-------AG-GU-AGAUU---GAAGA------UGACC----UCUUC-UCUUUAAUC--
#=GC SS_cons                 ...:::::::::::::(.((--------.-.----((.((((((,,,,<<<<<______>>>>>,,..,,,,<<<________...____________........>>>,,<<.<_......>>><<<<-.<<<________.__>>>-.>>>>,<<<<<_.____>>>>>)))))).))------)))-.------....<<.<<.-----...<<<<<<<<<_._____>>>>>>>>>.----->>>>..
#=GC RF                      ...uCagguuGaguAUc.ugUUAaaAaA.a.UuuuGc.auGGUGAAUCCCCCuGuGCGGaGGGGCg..AcUgaugaaaaaugu...uuauUuguuuaU........caugaGc.gA......cgCGGGUU.caGUguaacCA.gaCugA.ACUCACCGGGA.GGCACCCGGCACCau.gCAauAuacagA.aAuuaa....gc.au.auauC...aagGcccCuC.UccGgaGgggCcuu.UUUaUaugc..
//
# STOCKHOLM 1.0

#=GF AC   RF02077
#=GF ID   STnc220
#=GF DE   Salmonella enterica sRNA STnc220
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   69.00
#=GF NC   49.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4


AE006468.1/2079068-2078990 AUACAUUCGCUCAGGGCAGGUUCCGCCAGAUUUUAGAAAAUAAUUCAUAUUAGCUCCGUACAGGAGCUUUUUU--AUGCCC
CAAQ01000246.1/134-54      AUACAUUCGCUCAGGACAGGUUCCGCUAGAUUUUAGAAAAUAAUUCAUAUUAGCUCCGUACAGGAGUCUUUUUUUAUGCCC
CP000880.1/931506-931584   GUAUAUGUGCUCAGGACAGAUUCCGCCAGAUUUUAGAAAAUAAUUCAUAUUAGCUCCUUACAGGAGCUUUUUU--AUGCCC
CAAZ01000375.1/25444-25365 AUACAUUCGCUCAGGACAGGUUCCGCUAGAUUUUAAAAUA-AAUUCAUAUUAGCUCCGUACAGGAGCUUUUUUUAUUGCCC
#=GC SS_cons               ::::::::((,,,<<<_____>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<_____>>>>>>,,,,,,,,,))::
#=GC RF                    AUAcAUucGCUCAGGaCAGgUuCCGCuAGAUUUUAgAAaAUAAUUCAUAUUaGCUCCgUACAGGAGCuUUUUUUaaUGCCC
//
# STOCKHOLM 1.0

#=GF AC   RF02078
#=GF ID   STnc210
#=GF DE   Salmonella enterica sRNA STnc210
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   100.00
#=GF TC   148.20
#=GF NC   45.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


AE006468.1/2032404-2032580 GAUAAAAAUAAUUUUUUUGCAGGCAGUU-GGAUGGCAACCAUCAGGGGCCAGAUUAACACGAAAUGAGGAGGAUUCCGGAAGUUAACGCACAAAAGGAGGAUCAGGGCGCAGAUUUUCCGCCAGGAAGCGCUCGCC-CCACACAAAAGCGAGAGAUGGGUUUCUCGCUAUAUUAUACUC
CP000880.1/976393-976220   GAUAAAA-UAAUUUUU--GCAGGCAGUUUGGAUGGCAACCAUCAGAGGCCAGAUUAACACGAAAUGAGGAGGAUUCCGGAAGUUAAUGCACAAAAGGCGAAUCGGGAAGCAGUUUUUCCAAUAAGAAGCGCCCAAAGCCACACUAAAGCCAGACAUGUGAACCG-GCGUUAGCGCCCC-
#=GC SS_cons               ::::::::::::::::::((,<<<----.-<<<<<___>>>>>---->>>,,,<<<<<_______________________>>>>>,))---------------<<<<<<-----<<<______>>>>>>>>>:::.::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GAUAAAAAUAAUUUUUUUGCAGGCAGUU.GGauGGCAACCauCAGaGGCCAGAuuaaCACGAAAUGAGGAGGAUUCCGGAAGuuaauGCACAAAAGGaGaAUCaGggcGCAGaUUuuCCaauAaGaaGCgccCaaa.CCACACaAAAGCgAGAgAUGuGuuuCucGCuaUAuuauaCuc
//
# STOCKHOLM 1.0

#=GF AC   RF02079
#=GF ID   STnc180
#=GF DE   Enterobacterial sRNA STnc180
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   55.30
#=GF NC   40.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   10


AE006468.1/1807776-1807565   UGUCUUAUUACACCGCAGCAACCGUGUGCUGAG--CGCCUCUCAGUAUUGA---UUAAACACA-GUU-GGUGUC-GCCUAUGUUAACGUCAAAUAUA------AAGUAUUGGUCAUGGACUGGCGCGUUUAUAUUAUCGCUACUGUUCUGGGCCGAGUUAAUCUGGAUUGCCGU---CU-AAUCUCGUCAAA--------GCCCGAUAAUGCGUUAUUUAUCGGGCUUUUUCAUCUUC
CP000880.1/1209054-1209261   UGACUUUUUACACCGCAGCAGCCGUGUGCUGAG--CGCCUCUCAGUAUUGA---UUAAACACA-GUU-GGUAUC-GCCUAUGUUAACGUCAAAUAUA------AAGUAUUGGUCAUGGACUGGCGCGUUUGUAUUAUCGCUACUGUUUUGGGCCGAGUUAAUCUGGAUUGCCGU---CU-AAUCA----GAA--------GCCCGAUAAUGCGUUAUUUAUCGGGCUUUUUCAUGUCU
CP000822.1/1320698-1320907   UUUCCUUAUACACCACAGCAAU-AAGCGCUGAG--UACAUCUCAGCAUAAAGUAUUAAACAAAUGUC-GGUGUA-GCCUAUGCAAACUGUGAAUCUU------AAAUAUUGGUCAUGGAUUGGGGCGUUCUCAGUAUCGCUCUUGUUCUGGGCUCAACUUAUCUGGAUUGUCUCUUUCU-GAUCGUAUGCCGGUA--AAUGCCCGAUGGCGCAACG-UCAUCGGG-------------
CU928158.2/1726878-1726653   UUUACUCAUACACCACAGCAAU-ACACGUUGAG--AAUAUCUCAAUACUGGUCCUAAAAAUUGUCAU-GGUGUC-GCCGAUGAAUACGACAAAUAUG------AAGUACUGGUCAUGGAUCGGAGCGUUUUCGCUGUCAUUCCUUUUCUGGGCUGAAUUAAUCUGGUACGUCUCUCGCU-AAUUCUUCCAAAAUACUGCCGCCCGAUGGUGUAUCAACCAUCGGGCUUACUCCUGACA
CU928164.2/1686418-1686621   GCUUUUAAUACACCGCAGCAAUAACAGGUUGAG---UUAUCUCAA--CACAAAGUAAUAACCGUUAAGGGUGUA-GCCUAUGAUCAACACAAAUAUG------AAAUAUUGGUCCUGGAUGGGCGCGUUUUCUCUGUCAAUGCUCUUCUGGGCUGAACUCCUCUGGAUCAUUACUCACU-AAUC---CCUGA--------CCCCGCUG----------CGGCGGGGGUUUUCAUUUGC
AE014075.1/1579810-1580022   GCUUUUAAUACACCGCAGCAAUAACAGGUUGAG---UUAUCUCAA--CACAAAGUAAUAACCGUUAAGGGUGUA-GCCUAUGAUCAACACAAAUAUG------AAAUAUUGGUCCUGGAUGGGCGCAUUUUCUCUGUCGAUGCUCUUCUGGGCCGAACUCCUCUGGAUCAUUACUCACU-GAUC---CCUGA--------CCCCGCUGUUUGCUUU-GCCUCAAGGUUUCUCCUCUUU
CU928163.2/1587332-1587534   GCUUUUAAUACACCGCAGCAAUAACAGGUUGAG---UUAUCUCAA--CACAAAGUAAUAACCGUUAAGGGUGUA-GCCUAUGAUCAACACAAAUAUG------AAAUAUUGGUCCUGGAUGGGCGCAUUUUCUCUGUCGAUGCUCUUCUGGGCCGAACUCCUCUGGAUCAUUACUCACU-GAUC---CCUGA--------CCCCGCUG----------CGGCGGGGUU-UUCAUUUGC
CP000653.1/2383757-2383545   UUAAUAAAUACACAUCAGUAAUAAAGAAUCGGG-UUAUACCCCGACCGAGCAAAUAAAUAGAAUAUCUGGUGUCCGAUGAUGAAUACUCUACAAAACG---UUAAAUACUGGUCGUGGAUGGGCGCGUUUACCGUCUCCACUCUGUUCUGGUGUCAGCUUAUCUGGCUGGCCCUAAACU-AAAUC--UAAAA--------CCUCGCUG----------CGGCGAGGUUUUUUGUUUUA
BAAW01014869.1/682-895       UUAAUAAAUACACAUCAGCAAUAUAGAACUGAGGGCAAACCUCGGAGC-CUUUUUAAAAAUUAUGCCUGGUGUA-CCCUAUGAUGAAUACCAUGAUGUCUCAUAUAUUCUGGUCAUGGCUCGGCGUUUUUUCUGUGUCGAUCCUUUUCUGGUCUCAGCUCAUCUGGCUGGCCUUCCUGUUUAUC---CAAAA--------CCUCGCUU----------CGGCGGGGU-AUAAGUUUUC
ABWM02000007.1/191007-190797 UUAAUAAAUACACAUCGGCAAUAUAGAACUGAGGGCAAACCUCGGAAC-CUUAAUUAAUAAAGCCUGGUGUCCC-UAUGAUGAAUAACAUGACAACGC---UCAAAUACUGGUCAUGGAUCGGCGUUUUCUCCGUGUCGAUUCUGUUCUGGUGCCAGCUCCUCUGGCUGGCCGUCAACU-GAUC---CAAAA--------CCUCGCUU----------CGGCGGGGUUUUUCAUUUUC
#=GC SS_cons                 :::::::::<<<<<---<<---------<<<<<.._____>>>>>----------------->>---->>>>>,.,,,,,,,,,,,,,,,,,,,,,,......,,,,,,,,<<<--<-<<<<<<<_________>>>>>>>->------->>><<<-<<_____>>->>>,,,,,,,,,.,,,,,..,,,<<........<<<<<<<<<_______.>>>>>>>>>>>::::::::::
#=GC RF                      UuuaUuaAUACACcuCAgcAAUAaagagcuGAG..cauAUCUCaguacagaaaaUaAAAAaaguuuuggGUGUa.GCCuAUGauuAauacaAAuAUg......AAAUAuUGGuCaUGGaucGGcGCgUUUuCugUgUCgauuCUgUUCUGGgCcgAaCUcAUCUGGaUcguCuuucaCU.aAUCu..caaaA........cCcCGcuggUGcauua.ccagCGgGgUuuUUcaUuUuc
//
# STOCKHOLM 1.0

#=GF AC   RF02080
#=GF ID   STnc170
#=GF DE   Salmonella enterica sRNA STnc170
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   97.90
#=GF NC   28.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.58 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


AE017220.1/1644264-1643932   AGUUGAGGCCACAGCCCUUCUUAUUUUUGUGUAUAAUUUGUUACGUUUACAUUUAUUUUUAAAUUAGCGUUAUGAAAAUAUCAGUACUACUGAAAUAGCACUUCUUCGCUUCGUGUAUUUUUACUAUGGUUAAUUAUCACAUAGCGCAAACGGUCAUUUGUGUAUCACUAUUCAUAAGAUUAACUAUUUACCAGUGGUAAUAAAAAUAAAAGUAAGUCAAUGGACAACAACAAUACUGAAACUCUAAAUGUUGAUAUUUUGAGUCAUGCCGUUACAAACAAAUACGAUAUUCUUAAUUGCACUACUCCCUUUUCGGGGUAGUUUUAUAGAAGG
ABFG01000001.1/725023-725355 AGUUGAGGCCACAGCCCUUCUUAUUUUUGUGUAUAAUUUGUUACGUUUACAUUUAUUUUUAAAUUAGCGUUAUGAAAAUAUCAGUACUACUGAAAUAGCACUUCUUCGCUUCGCGUAUUUUUACUAUGGUUAAUUAUCACAUAGCGCAAACGGUCAUUUGUGUAUCACUAUUCAUAAGAUUAACUAUUUACCAGUGGUAAUAAACAUAAAAGUAAGUCAAUGGACAACAACAAUACUGAAACUCUAAAUGUUGAUAUUUUGAGCCAUGCCGUUACAAACAAAUACGAUAUUCUUAAUUGCACUACUCCCUUUUCGGGGUAAUUUUAUAGAAGG
FM200053.1/1405979-1406311   AGUUGAGACCACAGCCCUUCUUAUUUUUGUGUAUAAUUUGUUACGUUUACAUUUAUUUUUAAAUUAGCGUUAUGAAAAUAUCAGUACUACUGAAAUAGCAUUUCUUCGCUUCGUGUAUUUUUACUAUGGUUAAUUAUCACAUAGCGCAAACGGUCAUUUGUGUAUCACUAUUCAUAAGAUUAACUAUUUACCAGCGGUAAUAAAUACAAAAACAAAUCAAGGGACAACAACAAUCCUGAAACUCUAAAUGUUGAUAUUUUGAGUCAUGCCGUUACAAACAAAUACGAUAUUCUUAAUUGCACUACUCCCUUUUCGGGGUAAUUUUAUAGAAGG
#=GC SS_cons                 :<<<<______>>>>{{{{{{,,,,,,,[[[[[--[[[[[[[,<<<<---<<<<<____>>>>>->>>>(((((,,,,,,<<<<<___>>>>>,,,<<<________>>>,,,,<<<____>>>,,,<<<_____>>>,)))))<<<<<<______>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<-----------------------------------------<<<<-<<<<<____>>>>>->>>>-->>>>>>,,,,]]]]]]]--------------]]]]]<<<<<<______>>>>>>,,,,,,,}}}}}}
#=GC RF                      AGuuGAGgCCACagCCCuuCuUAUUUUUGuGuaUAauuuGuuACGuuUACauuuaUUUUuaaauUagCGuuauGAAAAUAuCaGuACUaCuGaAAUaGCAcUUCUUCGCuUCGuGuaUUUUuaCUAUGguUAAUUauCACauagCgCaaaCGGUCAuuuGuGUAUCACUAUUCAUAAGAUUAACUAUUUACCAgcGGuaAUAAAuAuAAAAguAAgUCAAuGGACAACAACAAUaCUGAAaCuCUaaaugUUGAuauuuUGaGuCAugCCguUACAaaCaaauACGAUAUUCUUAAUugCaCuaCuCCCUUUUCGGgGuaaUUUUAUaGaaGG
//
# STOCKHOLM 1.0

#=GF AC   RF02081
#=GF ID   STnc550
#=GF DE   Enterobacterial sRNA STnc550
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   48.00
#=GF TC   49.20
#=GF NC   46.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   11


CP001120.1/1514461-1514749   UACAUUUCACUCCAGACC-CUCGC---U-AAGC-UCCUG-AGAA-ACGCC----AGGUAAACGUUUGCCUACACACACCCUAAU--CGCAAC-A--UCAGGGUUGCGGCACGCCGGAAAA-ACGACACGGAACGUCAGGAAGGGGUCAAUGGCCGUUACGCUAAUUCAG-UAAGCCUGGAAUUUUGUCUGAUCUUGAGGAAAAGGGGAAGCGUUAAAAACAGUUAUCAAUAUAGAAUGUAUAAA----UUGUAUGUAAAU---CAACAUUUUG---------UUUGUGUUUUGGAGUAAAU-G-CGGAUCAA--UAAUAACUAACCCC---------------------------------------------------------------------------------
CP001144.1/1849102-1848715   UACAUUUCACUCCAGACC-CUCGC---U-AAGC-UCCUG-AGAA-ACGCC----AGGUAAACGUUUGCCUACACACACCCUAAU--CGCAAC-A--UCAGGGUUGCGGCACGCCGGAAAA-ACGACACGGAACGUCAGGAAGGGGUCAAUGGCCGUUACGCUAAUUCAG-UAAGCCUGGAAUUUUGUCUGAUCUUGAGGAAAAGGGGAAGCGUUAAAAACAGUUAUCAAUAUAAAACAUGAGAGAUUUUUGUGCGGGAAUGUGCAAAAAUGCGCUAUAUCACUUUUUGUGUGGGAAUAAAA-A-GGAGAAAACUUGAUGAGUACCGACCUGAAAUUUUCGUUGAUUACUACGCUGAUUGUUCUGGGCGUGAUUGUCGCAGGUGGAUUAACGGCCGCUCUGCACUGAUUU
CP000886.1/1612967-1612583   UACAUUUCACUCCAGACC-CUCGC---U-AAGC-UCCUG-AGAA-ACGCC----AGGUAAACGUUUGCCUACACACACCCUAAU--CGCAAC-A--UCAGGGUUGCGGCACGCCGGAAAA-ACGACACGGAACGUCAGGAAGGGGUCAAUGGCCGUUACGCUAAUUCAG-UAAGCCUGGAAUUUUGUCUGAUCUUGAGGAAAAGGGGAAGCGUUAAAAACAGUUAUCAAUAUAAAACAUGAGAGAUUUUUGUGCGGGAAUGUGCAAAAAUGCGCUCUCU---UUUUUUAGAGAGAUAGAAAAA-GGGGAAAGCCCAAUGACAAAAGACCGGAAAUUUUCGUUGAUUACUACACUAA-CGUUCUGGGCGUGAUUGUCGCAGGUGGAUUAACGGCCGCUCUGCACUGAUUU
CP000880.1/1507822-1507434   UAUAUUUCACUCCAGACCCCUCGC---C-AGAC-UCCUG-AGAA-ACGCC----AGGUAAACGUUUGCCUACACACACCCUAAU--CGCAAC-C--UCAGGGUUGCGGCACGCCGGAUAA-ACAACACGGAACGUCAGGAAAGGGUCAAUGGCCGUUAUGCUAAUUCAA-UAAGCCUGGAAUUUUGUCUCAUCUUGAGGAAAAGGGGAAGCGUUAAAAACAGUUAUCAAUAUAAAACAUGAGAGAUUUUUGUGCGGAAAUCUGUAAAAAUGCUCUAUAUCACUUUUUGUGUGGGAAUAAAA-A-GGAGAAAACUUGAUGAGUACCGACCUGAAAUUUUCAUUGAUCACCACGCUUAUUGUUCUCGGCGUGAUUGUCGCAGGUGGAUUAACUGCCGCACUGCACUGAUAU
ACDJ01000007.1/140140-140529 UACAUCUCACUCCAGACC-AUAUC--CU-AAGC-UCCUG-AGAAUACUCC----AGGUAAACGUUUGCCUUUACACACCCUUAU--CGCAAC-G--UAAGGGUUGCGGCACGCCGGGAAA-ACGACACGGAACGUCAGGAAGGGGUCAAUGGCCGGUACGCUAAUCAAG-UAAGCGUGGAAUUUUGUCUGAUCUUAACGAAAAGGGGAAGAGUUAAAAGCAGUUAUCAAUAUAAAUCGUGAGAGAUUUUUGCUUUCAAGUGUGUAAAAAUGCGCAAUAUCACUUUUUGUGUGGGAAUAAAA-A-GGAGAAAACUUGAUGAGCACCGAUCUGAAAUUUUCGUUAGUGACUACCAUAAUUGUUCUGGGAUUGAUCGUCGCGGGUGGCCUGACCGCAGCGCUGCAUUGAUUU
CP000822.1/1605311-1604922   UACAUCUCACUCCAGACC-AUA--UCCU-GAAC-UCCUG-AAAA--UACUG--UAAGUAAACGUUUGCCUUUACACACCUUGAU--CGCAAC-G--UCAGGGUUGCGGCACGCCGGGAAA-ACGACACGGAACAUCAGGAAGGGGGCAAUGGCCGGUACGCUAAUCAAG-UAAGCGUGGAAUUUUGUCUGAUCUUGACGAAAAGGGGAAGAGUUAAAAGCGCUUAUCAAUAUAAAUCAUGGGAGAUUUUUGCAUUCAAGUGUGUAAAAAUGCGCAAUAUCACUUUUUGUGUGGGAAUAAAA-A-GGAGAAAACUUGAUGAGCACCGAUCUGAAAUUUUCGUUAGUGACCACCAUUAUUGUGCUGGGCCUGAUUGUCGCAGGCGGUCUGACUGCCGCACUGAACUGAUUU
CU928158.2/1424052-1424440   UACAUCUCACUCCAGACC-CGAUC---C-AUAACUCC-A-UUAA-AUGCC----AGGUAAACGUUUGCCUUUACACACCCUGAG--CGCAAC-G--UCAGGGUUGCGGCACGCCGGAAAAUACGACACGGAACGACAGGAAGGGGUCAAUGGCCGGUACGCUAUACUUG-UAAGCGUGGAAUUUUGGCCGAUCUUGACCAAAAGGGGAAGUGCUAAAAACAGUUAUCACGCUAAAUGGCGGGAGAUUUUUAGCCAAAUGUAUGCAAAAAUGCGCUACAUCACUUUUUGUGUGGGAAUAAAA-A-GGAGAAAACUUGAUGAGCAAUGAUCUGAAAUACUCUUUAAUUACGACCUUAAUCGUCCUCGCUUUGAUCGUUGCGGGUGGUCUGACCGCAGCUCUGCACUGAUUU
CU928145.2/1886472-1886082   UCCAUUUCACUCCAGACC-CUAAC---UUCAGC-UCCUGCAAAA-UCGCA----AGGUAAACGUUUGCCUUUACACACCUUACG--CACAAC-A--AAAGUGUUGCGGUACGCCGGAAAA-ACGACACGGAGCGUCAGGAAGGGGUCAAUGGCCAGUACGCAAAUAGUG-UAAGCGUGGAAUUUUGGCCGAUCUUGACGAAAAGGGGAAGUGGUAAAAACACUUAUCAUUAUAAAUGACGGGAGAUUUUUUCAUCACAGUGUGUAAAAAUGCGUAAUAUCACUUUUUGUGUGGUAAUAAAAAA-GGAGAAAACUUGAUGAGCACCGACCUUAAAUUUUCACUGGUAACAACGAUUAUCGUCCUCGGUUUGAUCGUAGCCGUGGGUUUGACUGCCGCGCUGCACUGAUUU
CP000653.1/1948106-1948494   UAGCUGUCACUCCAGACC-AUAUC--CU-AAGC-UCCUG-AUAA-AU---UGAGAGGUAAACGUUUGCCUUCUCUCACCCUAAU--CUCGCA-AAUUGAAUUGCGA--UACGCCGGGAAA-ACGACACAGGACGUCAGGAGGGGGUCAGUGGCCGGUACGCUUAUAAAU-UUAGCGUGGAAUUUUGUCCUAUCUUGAUGAAAAGGGGAAGCG-CAAAAACGGUUAUGAGCCUAAAUCCAGGAAGAUUUUUGAGCGAAACUGUGUAAAAAUGAGCAAGCUCACUUUUCAUGUGGGGAUUAAA-A-GGAGAAAAAUUGAUGAAUACCGAUCUUAAGUUUUCGUUAACGACCACAAUUAUCGUGCUGGGUUUGAUUGUUGCGGCAAGUUUUACGGCUAUUCUGCACUGAUUC
BAAW01000456.1/1034-646      UACUUCUCACUCCAGACC-UU-GAC-CU-GAUC-GUCUG-AUUA-UCGAU----ACGUAAACGUUUGCCUAUACACACCCUGAA--UACAAUUU--UCAACAUUGCAUCACGUCGGGAAA-ACGACACAGAACGACAGGAAGGGGUCAAUGGCCGAUACGCU--UUCAAAUUAGCGUGGGAUUUUGUCCGAUCUUGCGGCAAAGGGGAAGAG-CAAAAAUGUGCAUCACCCUAAAACAUGGAAGAUUUUUGCGCUAUAUUGUGCAAAAAUGAGCAAGCUCACUUUUCAUGUGGGGAUAACU-GGGGGGAAAAAUUGAUGGAUACAGAUUUAAAGUUUUCGCUGACGACAACGAUUAUUGUCCUGGGUCUCAUCGUGGCCGCCGGCCUGACAGCGGUGCUGCACUGAUUU
ABWM02000005.1/250934-251323 UAAAUGUCACUCCAGACC-AUAUC--CU-AAGC-UCCUG-AUAA-UU---AUGAAGGUAAACGUUUGCCUUCUCUCACCCUUAUUCCGCAAU-C--UU-GAAUUGCGACACGCCGGGAAA-ACGACACAGGACGUCAGGAGGGGGUCAAUGGCCGGUACGCUAAUAAAU-UUAGCGUGGAAUUUUGUCCUAUCUUGAUGAAAAGGGGAAGAG-CAAAAGUGGAUAUCAGGUUAAAACCAGGAAGAUUUUUGACCUGAACUGUGUAAAAAUGAGCAAGCUCACUUUUCGUGGGGUGAUUAAA-A-GGAGAAAAAUUGAUGAGUUCCGAUCUGAAGUUUUCGCUGGUUACCACCGUUAUUGUGCUGGCAUUGAUUGUGGCCGGUGGUUUAACGGCUGCGCUGCACUGAUUC
#=GC SS_cons                 ::::::::::::::{{{{.{{,<<..._.__>>.[[[[[.[,,,.,,(((....<<<<<<____>>>>>>,,,,,,,,,,,,,,..,<<<<<._.._____>>>>>))),,,<<<_____.______>>>,,,,]]]]]],}}}}}},,,,,,,,,,(((((,,<<<<<._____>>>>>,,,,,,<<<--<<_____>>-->>>,,,))))),,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<--------------------------<-<-<<<______>>>->-.>.------------------->>::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UAcAUuUCACUCCAGACC.cuagc...U.aAgc.uCCUG.auAA.acgcc....AGGuAAACGUUUgCCUuuACACACCCUaAu..CgCaac.a..UcAGgguuGcggcACGCcGGaAAA.ACGACACgGAACGuCAGGaAggGGUCAAUGGCCGgUaCgCuAAuccag.UaAGCcuggaAUUUUGuCugAuCUUGAuGaAAaGgGGAaGcGuuAAAAACagUUAUCAauaUAAAacauGggAGAUUUUUGuacggaAaUgUGuAAAAAUGcGCaAuaUCACuUuUuguGUGGGAauaAaA.a.GGAGAAAAcUUGAUGAguAccGAuCUgAAaUUUUCguUgaUuACuACaaUuAUuGUuCUgGguuUGAUuGUuGCaGguGGuuUaACuGCuGcuCUGCACUGAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02082
#=GF ID   STnc540
#=GF DE   Enterobacterial sRNA STnc540
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   38.00
#=GF TC   38.30
#=GF NC   36.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


CAAV01001492.1/496-340     UCAGAUCCAGGCAUAACAUCCAUCAGGGUGUAUUGCGGCAGAUACGCUGCCAUCCCGAAAGUAGAUCAGCGGGAUGACAGCGUAUUUGUCAGCCUGAAAGAUGACCCGUAUAACUAAAAAGGCCGCUCUGCGGCCUUUUUUCUUUCAA-UAACCGAUU--------------------------------------------
CP001144.1/1938269-1938068 UCAGAUCCAGGCAUAACAUCCAUCAGGGUGUAUUGCGGCAGAUACGCUGCCAUCCCGAAAGUAGAUCAGCGGGAUGACAGCGUAUUUGUCAGCCUGAAAGAUGACCCGUAUAACUAAAAAGGCCGCAUUGCGGCCUUUUUUCUUUCAAGUAAAGGAUACCCACCGUAAAAUCACGCUACCUCUUUUCAGCUGAAUGGAUAAC
CP000880.1/1578208-1578007 UCAGAUCCAGGCAUAACAUCCAUCAGGGUGCAUUGCGGCAGAUAUUCUGCUCUCCUGAAAGUCGAUCUGCGGGAGGCGAGGGGAUUUGCCAGUCUGAAAGAUGACGCGUAUAACUAAAAAGGCCGCAUUGCGGCCUUUUUUCUUUCAAGUAUGGAAUACCCACCGUAAAAUCACGCUACCUCUUUUCAGCUGAAUGGAUAAC
#=GC SS_cons               ::::::::((((,,,<<<<<<____>>>>>>,,,,,<<<<<<<<<<<<<-<<<<<<<____________>>>>>>>->>>>>>>>>>>>>,))))<<<<<<--------------<<<<<<<<<<<___>>>>>>>>>>>>>>>>>::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UCAGAUCCaGgCAUAaCauCCAUCAGGguGuAUUGCGgCagauacgCugCccuCCcGAAAGUaGAUCaGCgGGaggacaGcguauuuGcCAGcCuGaaaGaUGACcCGUAUAACUaaaaaGGCCGCauUGCGGCCuuuuuuCuuuCAAGUAaaggAUaCCCACCGUAAAAUCACGCUACCUCUUUUCAGCUGAAUGGAUAAC
//
# STOCKHOLM 1.0

#=GF AC   RF02083
#=GF ID   OrzO-P
#=GF DE   OrzO-P RNA antitoxin family
#=GF AU   Barquist LE; 0000-0003-4732-2667
#=GF SE   Predicted; Barquist LE; FSA; Infernal
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   66.30
#=GF NC   42.60
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   20156992
#=GF RT   Abundance of type I toxin-antitoxin systems in bacteria: searches for new
#=GF RT   candidates and discovery of novel families.
#=GF RA   Fozo EM, Makarova KS, Shabalina SA, Yutin N, Koonin EV, Storz G
#=GF RL   Nucleic Acids Res 2010;38:3743-3759.
#=GF WK   Toxin-antitoxin_system
#=GF SQ   7


CP001164.1/2880285-2880358 CGAAAUGUUGCACAAUCAGCAAG-UU-AGCGUCACUGUAGUAAAUAAAAGAACCUGCCUCACCAGCAGGUUUUUUU
CP000243.1/2345635-2345708 CGCCAUGUUGCAUAAUCAGUAAC-UU-AACGUCAAAGUUGUAAAUAAAAGAACCUGCCUCACCAGCAGGUUUUUUU
CU928163.2/2506954-2507029 CACGAUGUUGCACAGGCUGCGGUGUUGGGCCUGAAAAUAGUAAAUAAAAGAACCUGCCUCACCAGCAGGUUUUUUU
CP000970.1/936313-936238   CACGAUGUUGCACAGGCUGCGGCGUUGGGCCUGAAAAUAGUAAAUAAAAGAACCUGCCUCACCAGCAGGUUUUUUU
CP002212.1/2433444-2433519 CACGAUGUUGCACAGGCUGCGGUGUUAGGCCUGAAAGUAGUAAAUAAAAGAACCUGCCUCACCAGCAGGUUUUUUU
CP001383.1/2253950-2254025 CACGAUGUUGCACAGGCAGUGGUGUUAGGCCUGAAAAUAGUAAAUAAAAGAACCUGCCUCACCAGCAGUUUUUUUU
AP010958.1/2615735-2615808 UGCCAUGUUGCACUAUCAGUAAC-UU-AACAUCAAAGUAGUAAAUAAAAGAACCUGCCUCACCAGCAGGUUUUUUU
#=GC SS_cons               ::::::<<<<<_______>>>>>----------------------<<<<<<<<<<<<_______>>>>>>>>>>>>
#=GC RF                    CaCgAUguuGCACAauCaGCaacGUUaagCcUgAAAgUAGUAAAUAAAAgAACCUGCCUCACCAGCAGGUUuUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02084
#=GF ID   STnc130
#=GF DE   Enterobacteria sRNA STnc130
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Predicted; WAR;Burge SW
#=GF SS   Predicted; WAR;
#=GF GA   55.00
#=GF TC   57.30
#=GF NC   48.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.17 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Bacterial_small_RNA
#=GF SQ   13


ABKX01000009.1/140038-140172 UACAUCGAAUAAUUUGAAAAUCAAC--AACAUAGGAAGAUCUUCACUCGAAAGUAGUAUUACGCGCAAAUGAGGAGUAAUUAUUGUUCGGUAUCAA---AUGGAGAGAAAAAA-AGCGCCCGCAGGCGCUUUAACGUUUC-U
ACDJ01000004.1/142871-142736 GAUACUGAAUUUGCGAAAAGACAGA--GAUAAAUACUGACUUUCAUUCGAAGGCAGUAUUACUCCUAUGGAGGUAGGCGUUAUUGUCCGACGUCAA---ACGGGCAUAAAAAA-AGCGCCCUGAGGCGCUUUUUUAGCAAAG
CP000034.1/2165685-2165819   UACAUCGAAUAAUUUGAAAAUCAAA--GAGAUAAGUAGAUUUUCACUCGAAAGUAGUAUUACGUGUAAGUGAGGAGUAAUUAUUGUUCGGUAUCAA---AGGGAGACAAAAAA-AGCGCCCGCAGGCGCUUUUUAGAUUC-A
CP000243.1/948597-948463     UACAUCGAAUAAUUUGAAAAUCAAA--GAGAUAGGUAGAUUUUCACUCGAAAGUAGUAUUACUUGUAAGUGAGGAGUAAUUAUUGUUCGGUAUCAA---AGGGAGACAAAAAA-AGCGCCCGCAGGCGCUUUAACGUUCA-U
CP000647.1/1040149-1040015   UAUAAUGCUUUGCGAUAUUAUUGGU--UUUUUAUGCUGGUUUAAUCCAAAGGG-AGUAUCACUGCAUUCGCGAAAAGGAUUAUUGCCCGGUAUCAA--UAAGGGCGUAAAAA-AAGCGCCCGCAGGCGCUUUUAAAAGAA-G
CP000653.1/1558622-1558486   UAUAGAGAAACAGUUAUUCAGACAC--AUAACGUGCUGGGUUUCAUUCAAAGG-AGUAUUACUACUUUAGGAGGAGCAGACAUUGCCUGGAGUCAAAGCAGAGGCAUAAAAA-AAGCGCCCUCAGGCGCUUUUUAUUUUU-A
CP000822.1/2018357-2018493   UAUAAUGAAUAUGAGAAAAAUCAGC--GAUAAAUGCUAAUCUUCAUUCGAAGGUAGUAUUACCCCCAAAGGGGUAACCAUUCUUGUCCGGUGUCAA---ACAGGCAUAAAAAAAAGCGCCCGGAGGCGCUUUUUAAGCAGAG
CP000964.1/3671387-3671520   UAUAUUGCUUUGAAAUAUUAUUGGU--UUUUUAUGCUGAUUUAAUCCAAAGGG-AGUAUCACUGCAUUCGUAGAAUGGAUUAUUGCCCGGUAUCAA--UAAGGGCGUAAAAA-AAGCGCCCGCAGGCGCUUUUAAAAG-A-G
CP001113.1/1005702-1005568   UAUAUCGAAAAAGUAGAAAAAUAGU--GUUAAAAACUGACCUUCAUUCGAAAUCAGUAUUACCCCUAAUAGGGUAGGGAUUAUUGUCCGGUAUCAA---ACUGGCAUAAAAA-AAGCGCCCGAAGGCGCUUUUUAGAAGA-G
CU928162.2/947361-947229     UACAUCGAAUAAUUUGAAAAUCAAA--GAGAUAGGUAGAUUUUCACUCGAAAGUAGUAUUACUUGUAAGUGAGGAGUAAUUAUUGUUCGGUAUCAA---AGGGAGACAAAAAA-AGCGCCCGCAGGAGAUUUAACACAC---
CAAV01000642.1/139-7         UAUAUCGAAAAAGUAGAAAAAUAGC--GUUAAAAACUGACCUUCAUUCGAAAUCAGUAUUACCCUAAU-AGGGUAGGGAUUAUUGUCCGGUAUCAA---ACUGGCAUAAAAA--AGCGCCCGCAGGCGCUUUUUAGAAGA-G
ABWL02000007.1/107130-107266 UAUAUCGCUAGUAUCACUAUACAGACAGGUAAAUACUGACUUUCAUUCGAAGGCAGUAUUACUCCUAUGGGGGUAGUGGUUAUUGUCCGGCGUCAA---ACGGGCAUAAAAAA-AGCGCCCGGAGGCGCUUUUUUAGCAGA-
ABWM02000004.1/479174-479038 UAUAACGAAGUACUUCGUUUUCAGC--GAGUUACGCUAAAUAUCAUCUACCGA-AGUAUUACUACUUUAGAGGGAGGGGUUAUUGCUUAGUAUCAAACGAGGGGCAUAAAAAA-AGCGCCGGGAGGCGCUUUUUACAUUA-C
#=GC SS_cons                 :::::::::::::::::::::::::..:::::::::::::::::::::::::::::::::::<<______>>------------------------...------------<<.<<<<<<____>>>>>>>>::::::::.:
#=GC RF                      UAUAucGAAuaauuuaaaaAucAga..gauAuAuGcUGAuUUUCAuUcgAAgGuAGUAUUACcccuauagggGgAGuaAUUAUUGucCGGUAUCAA...AggGGcAUAAAAAA.AGCGCCCGcAGGCGCUUUUuaaauua.g
//
# STOCKHOLM 1.0

#=GF AC   RF02085
#=GF ID   Yar_1
#=GF DE   Yellow-achaete intergenic RNA conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   77.90
#=GF NC   35.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.62 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005737; cytoplasm;
#=GF DR   GO; 0042749; regulation of circadian sleep/wake cycle;
#=GF RN   [1]
#=GF RM   21775470
#=GF RT   A Conserved Long Non-coding RNA Affects Sleep Behavior in Drosophila.
#=GF RA   Soshnev AA, Ishimoto H, McAllister BF, Li X, Wehling MD, Kitamoto T, Geyer
#=GF RA   PK
#=GF RL   Genetics 2011;0:0-0.
#=GF WK   Yar_(gene)
#=GF SQ   10


AAEU02002803.1/38409-38481   AACGAGCUGCUAAUUUUACGUUGGACGCCCUUUAAUUUCACGCUGCCAU------UUGUGGCUUCCGUUUCGUAU--GUUU
AAIZ01005649.1/2104-2174     AACGGG--GCUAAUUUCAUGUUAGACG--CUUUAAUUUCACGCUGCCAU------UUGUGGCUUCCGUUUCGCAUGAGUUU
AAPP01017309.1/2657-2730     AACGAGCUGAUAAUUUCAUGUUAGAUUCCCU-UAAUUUUACGCUGCCAU------UUGUGGCUUCCGUUUCGCAUGAGUUU
AAPT01021057.1/2394-2320     CUGCUGUUGCUAAUUUUAUGCUAGACGGGCGUUAAUAUCAAGCUGCCAU------UUAUGGCUUCCGUUUUGUAGAAUUAA
AAPU01007946.1/59490-59417   AACACUUUGCUAAUUUUAUGCUAGACGG-CGUUAAUAUCAAGCUGCCAU------UUAUGGCUUCCGUUUUGGGGCAGCAG
AC104286.11/127199-127273    AACGAGUUGCUAAUUUUACGUUAGACGCCCUUUAAUUUCACGCUGCCAU------UUGUGGCUUCCGUUUCGUAUAAGUUU
AF132809.1/2523-2596         AACCAAUUGCUAAUUUAAUGCUAGACGG-CGUUAAUAUCAAGCUGCCAU------UUAUGGCUUCCGUUUUGGGCCAGGCA
DQ992394.1/1291-1365         AACGAGCUGCUAAUUCCACGUUAGACGCCCUCUAAUUUCACGCUGCCAU------UUGUGGCUUCCGUUUCGUAUGAGUUU
AAQB01008767.1/141103-141031 UGUCCGGAGUUAAUUUUAUGUUAGAAG--CGUUAAUUUCAUGCUGCCAU------UUAUGGCUUCCGUUUCGCAUGGAUUG
DQ992393.1/719-798           AAACACUUGCUAAUUUACUGCUAGACGG-CGUUAAUAACAAGCUGCCAUUGCCAUUUAUGGCUUCCGCUCUUCUUGAUUAA
#=GC SS_cons                 ::::::::::::::::::::::::::::.::::::::::::::::::::......::::::::::::::::::::::::::
#=GC RF                      AacgaguUGCUAAUUUuAUGuUAGACGg.CgUUAAUuUCAaGCUGCCAU......UUaUGGCUUCCGUUUcGcaugAgUuu
//
# STOCKHOLM 1.0

#=GF AC   RF02086
#=GF ID   Yar_2
#=GF DE   Yellow-achaete intergenic RNA conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   86.40
#=GF NC   33.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.77 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005737; cytoplasm;
#=GF DR   GO; 0042749; regulation of circadian sleep/wake cycle;
#=GF RN   [1]
#=GF RM   21775470
#=GF RT   A Conserved Long Non-coding RNA Affects Sleep Behavior in Drosophila.
#=GF RA   Soshnev AA, Ishimoto H, McAllister BF, Li X, Wehling MD, Kitamoto T, Geyer
#=GF RA   PK
#=GF RL   Genetics 2011;0:0-0.
#=GF WK   Yar_(gene)
#=GF SQ   7


AE014298.4/260742-260816     CAAGUCAAUGUCAA-GUGUUGCUUCGG------CUGACUUACUACAAAAGUUAAUUGCACUGCACGCACAUGCCAAAAGGUA
AAIZ01005649.1/7238-7313     CCAGUCAAUGUCAA-GUGUUGCCCCGG-----ACUGACUUACUACAAAAGUUAAUUGCACUGCACGCGCACGCCAAGAGGCU
AAPP01017309.1/7366-7435     GAAGUCAAUGUCAA-GUGUUGC-----------CUGACUUACUACAAAAGUUAAUUGCACUGCACGCGCACGCCAAAAGGCC
AAPT01018945.1/76490-76422   CCAGUCAAUGUCAAAGUGUUGC------------UGCCUUACAACCAA-GUUAAUUGCACUGCACGCACACGCCAAGACGCA
AAPU01007946.1/52420-52347   CAAGUCAAUGUCAAAGUGUUGCCU--G-----CUUGCCUUACAACAAA-GUUAAUUGCGCUGCACGCGCACGCCAAGAUCCA
AAQB01008767.1/135946-135873 CCAGUCAAUGUCAA-GUGUUGCCCUGG------CUGCCUUACUACAAA-GUUAAUUGCACUGCACGCGCACGCCAAAAGGCC
AANI01016904.1/21708-21628   CAAGUCAAUGUCAAAGUGUUGCCUGGCUUGUUGUUGCCUUACAGCAAA-GUUAAUUGCGCUGCACGCGCACGCCACAAGACG
#=GC SS_cons                 ::::::::::::::.::::::::::::......:::::::::::::::.:::::::::::::::::::::::::::::::::
#=GC RF                      CaAGUCAAUGUCAA.GUGUUGCCucGg......cUGcCUUACuACAAA.GUUAAUUGCaCUGCACGCGCACGCCAAaAggCa
//
# STOCKHOLM 1.0

#=GF AC   RF02087
#=GF ID   Yar_3
#=GF DE   Yellow-achaete intergenic RNA conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   59.40
#=GF NC   38.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.89 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005737; cytoplasm;
#=GF DR   GO; 0042749; regulation of circadian sleep/wake cycle;
#=GF RN   [1]
#=GF RM   21775470
#=GF RT   A Conserved Long Non-coding RNA Affects Sleep Behavior in Drosophila.
#=GF RA   Soshnev AA, Ishimoto H, McAllister BF, Li X, Wehling MD, Kitamoto T, Geyer
#=GF RA   PK
#=GF RL   Genetics 2011;0:0-0.
#=GF WK   Yar_(gene)
#=GF SQ   4


AE014298.4/260895-260961   GACUCUGGCUACGAGGCGCGUGUGUGCAAUAUCAGGUUUCCGCAUCGACUUGCAUAGUGAUUC--GAGG
AAPQ01005758.1/54851-54917 GAGUCUGGCCACGAGGCGCGUGUGUGCAAUAUCAGGUUUCCGUGUCAACUUGCAUAGUGACUC--AAGG
AAPP01017309.1/7589-7655   GGCUCGGGCCAAGAGGCGCGUGUGUGCAAUAUCAGGUUUCCAUGUCAACUGGCACAGUGGUUG--GAGG
AAEU02001095.1/90591-90659 GAGUCUGGCCACGAGGCGCGUGUGUGCAAUAUCAGGUUUCCGUGUCAACUUGCAUAGUGAUUCAGGAUG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..::::
#=GC RF                    GagUCuGGCCAcGAGGCGCGUGUGUGCAAUAUCAGGUUUCCGUGUCaACUuGCAUAGUGaUUc..GAGG
//
# STOCKHOLM 1.0

#=GF AC   RF02088
#=GF ID   STnc510
#=GF DE   Enterobacterial sRNA STnc510
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Predicted; WAR; Burge SW
#=GF GA   80.00
#=GF TC   88.30
#=GF NC   27.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18725932
#=GF RT   Deep sequencing analysis of small noncoding RNA and mRNA targets of the
#=GF RT   global post-transcriptional regulator, Hfq.
#=GF RA   Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT,
#=GF RA   Hinton JC, Vogel J
#=GF RL   PLoS Genet. 2008;4:e1000163.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   5



AE006468.1/1331440-1332250   AGCACCUCCUGUUAUAUAUAAUGACUUGUGAAGUUCAUCUCCUGAAUUAUGGAACGUCAUUGACAUUUUUUAUUCAACGAAGAGUUAACCACUCUUAAUAAUAAUGGGUUUUAUAGCGAAAUAGACUUUUUUAUCGCGUGUUCAAUAUUUGCGUUAGUUAUUAUUUUUUUGGAAUGUAAAUUCUCUCUAAACACAGGUGAUAUUUAUGUUGGAAUUGUG-GUGUUGAUUCUAUUCUUAUAAUAUAACAAGAAAUGUUGUAACUGAUAGAUAUAUUAAAA-GAUUAAAUCGGAGCGGGAAUAAAGCGUG--------------------------CUAAGCAUCAUCGUGAA-UAUGAUUACAGCGCCUGCGAUGGCAUAUAACCGUAUUGCGGAUGGAGCGUCACGUGAGGACUGUGAAGCACAAUGCGAUAUGUUCUGAUUAUAUGGCGAGUUUGCUUAAUGA-CAUGUUUUUAGCCGAACGGUGUCAAGUUUCUUAAUGUGGUUGUGA-----GAUUUUCUCUUUAAAUAUCAAAAUGUUGCAUGGGUGAUUUGUUGUUCUAUAGUGGCUAAACACUUUAUGGUUU---CUGUUAAAUAUAUAUGCGUGAGAAAAAUUAGCAUUCAAAUCUAUAAAAGUUAGAUGACAUUGUAGAACCGGUUACCUAAAUGAGCGAUAGAGUGCUUCGGUAGUAAAAAUAUCUUUCAGGAAGUAAACACAUCAGGAGCGAUAGCGGUGAAUUAUUCGUGGUUUUGUCGAUUCGGCAUAGUGGCGAUAACUGAAUGCCGGAUCGGUACUGCAGGUGUUUAAACACACCGUAAAUAAUAAGUAGUAUUAAGGAGUUGUU
CP001138.1/1882020-1881214   AGCACCUCCUGUUAUAUGUAAUGACUUGUGAAGUUCAUCUAAUGAAUUAUGGAACGUCAUUGGCAUUUUUUAUUCAACGAAGAGUUAACCACUCUUAAUAAUAAUGGGUUUUAUAGCGAAAUAGACUUUUUUAUCGCGUGUUCAAUAUUUGCGUCCGUUAUUAUUUUUCUGGAAUGUAAAUUUUCUCUCAACACAGGUGAUAUUUAUGUUGGAAUUGUG-GUGUUGAUUCUAUUCUUAUAA-----CAAGAAAUGUUGUAACUGAUAGACAUAUUAAAA-GAUUAAAUCGGAGCGGGAAUAAAUCGUG--------------------------UUAAGCAUCAUUGUGAA-UAUGAUUACAGCGCCUGCGAUGGCAUAUAACGGUAUUGUGGCUGAAGCGUCACGUGAGGACUGUGAAGCACAAUGCGAUAUGUUCUGGUUAUAUGGUGAGUUUGCUUAAUGA-CAUGUUUUUAGCCGAUCGGUGUCAGGUCUCUUAAUGUGGUUGUGAU----GUUUUUUUCUUUAAAUAUCAAAGAGUUGUAUGGUGAGCUUGUUGUUCUAUAGUGGCUAAACACUUUAUGGUUU---CUGUUAAAUAUAUAUGCGUGAGAAAAAUUAGCAUUCAAAUCUAUAAAAGUUAGAUGACAUUGUAGAACCGGUUACCUUAAUGAGCGAUAGAGCGCUUUGGUAGUAAAAAUAUCUUUCAGGAAGUAAACGCAUCAGGAGCGAUAGCGGUGAAUUAUUCGUGGUUUUGUCGAUUCGGCAUAGUGGCGAUAACUGAAUGCCGGAUCGGUACUGCAGGUGUUUAAACACACCGUAAAUAAUAAGUAGUAUUAAGGAGUUGUU
CAAX01001393.1/1988-1184     AGCACCUCCUGUUAUAUGUAAUGACUUGCGAAGUUCAUCUAAUUAAUUAUGGGACGUCAUUGGCAUUUUUUAUUCAACGAAGAGUUAACCACUCUUAAUAAUAAUGGGUUUUAUAGCAAAAUAGACUUUUUUAUCGAGUGUUCAAUAUUUGCGUCCGUUAUUAUUUUUCUGGAAUGUAAAUUCUCUCUCAACACAGGUGAAAUUUAUGUUUGAAUUGUG-GUGUUGAUUCUAUUCUUAUAA-----CAAGAAAUGUUGUAACUGAUAGACAUAUUAAAA-GAUUGAAUCGGAGCGGGAAUAAAGCAUG--------------------------CUGAACAUCAUGGUGAA-UAGGAUUACGGUGCCAGCGAUGGCAUGUAACGGCAUUUCGUCUGGAGCGUCACGUGAGGACUGUGAAGCACAAUGCGAUAUGUUCUGGUUAUAUGGCGAGUUUGCUUAAUGA-CAUUUUUUUAGCCGAUCAGCGUCAGGCUUCUUAAUGUGGUUGUGAU----UAUUUU-UCUUUAAAUAUCAAAAGUUUGUAUGACGUGUUUGUUGUUUUAUAGUGGCUAAACACUUUAUGGUUU---CUGUUAAAUAUAUAUGCGUGAGAAAAAUUAGCAUUCAAAUCUAUAAAAGUGAGAUGACAUUGUAGAACCGGUUACCUUAAUGAGCGAUAGAGCGCUUCGGUAGUAAAAAUAUCUUUCAGGAAGUAAACGCAUCAGGAGCGAUAGCGGUGAAUUAUUCGUGGUUU-GUCGAUUCGGCAUAGUGGCGAUAACUGAAUGCCGGAUCGGUACUGCAGGUGUUUAAACACACCGUAAAUAAUAAGUAGUAUUAAGGAGUUGUU
ABEH02000010.1/190465-191270 AACGCCUCCUGUUAUACGCAAUGACUUGUGAAGUUCAUCUCCAGAAUUAUGGAACGUCAUUGGCAUUUUUUAUUCAACGAAGAGUUAACCAUUCUUAAUAAUAAUGGGUUUUAUAGAGAAAUAGACUUUUUUAUCGGGUUUUCAAUAUUUGCGUCCGUUAUUAUUUUUCUGGAAUGUAAAUUCUUUCUCAACACAGGUGAUAUUUAUAUUGUAAUUGUG-GUAUUGAUUCUAUUCUUAUAA-----CAAGAAAUGUUGUAACUGAUAGAUAUAUUAAAAAGGUUAAAUCGGAGCGGGAAUAAAGCGUG--------------------------CUGAGCAUCAUAGUGAA-UAUGGUUACGGCACCAGCGAUGGCAUAUAACGGUAUUUCGGCUGGAGCGUCAAGUGAGGGCUGUGAAGCACAAUGAGAUAUGUUCUGGUUAUAUGGCGAGUUUGCUUACUGA-UAUGUUUCUAGUCACGCGGCGUCAGUUCUCUUAGCAUGGUUGUUG-----GAUUUU-UCUUUAAAUAUCAAAAGGUUACGUGGUGAAUUUAUUGUUCCAUAGUGGCUAAACACUUUAUGGUUU---CUGUUAAAUAUAUAUGCGUGAGAAAAAUUAGCAUUCAAAUCUAUAAAAGUGAGAUGACAUUGUAGAACCGGUUACCUUAAGGAGCGAUAGAGAACUUCGGUAGUAAAAAUCUCUUUCAGGAAGUAAACGUAUCAGGAGCGAUAGUGGUGAAUUAUUCGUGGUUUUGUCGAUUCGGCAUAGUGGCGAUAACUGAAUGCCGGAUCGGUACCGCAGGUGUUUAAACACACCGUAAAUAAUAAGUAGUAUUAAGGAGUUGUU
CP000880.1/1666914-1666079   -AUACCUCCUGUUAUAUGUAAUGACUUAUGUAUUUCAUAUGCGGAAUUAUGGAUCGUCAUCACCAUCUUUUAUUAAACGAAGAGUUAACUAUUCUUAAUAUUAAUAUGUUUUAUAUAGAGAUAAGCAAUUUUAUUGAAUAUUCAAUAUUUGCGGUUGUUAUUAUUUUUGUGGAAUGUAAACUUUUUAUCAAUACAGGCGAUAUUUAUGUUGGGAUUGUGAGGGUUGAUUCUAUUCUUAUAA-----CAAGAAAUGUUGUAAUUGAUAGAUAUGUUAAAA-AAUUAAUUGGAGGAGGGAAUGAUGCAUGUUGUGAAAUUUUUGCAACCAAUAGUACUGGGCAUCAUAGUGAAACAUGUUUGCAGCGCCAACGAUGGCAUAUAACUGUAUUUCGUCUGGAGAGUCAAGUGAGGACUAUGAAGCACAAUGCGAUAUCUUCUGGUUAUAUGGCGAAUUUGCUUACUGGGCAUGUUUUGGGCUGGUCGGCGUCAGCUAUUUCGGUAUACGAGAGAUGCAGAAUAUUUUAUUUGAAUAUCAACGACUUAAAUCAU-AGUUGUUUUUUCUGUAGUGGCUAAAUACUUCAUAAUAGGGGCUCUUAAAUUCGUAUGUAUGAGAAAGAUUAGAAUCCACAUUUAUUAAUAUUAGAUGACCCUGGAGAGCUGGUUGUCUUAAUAAACGAUACGGGUCCUCGUUAGUGAAAAUAUCCUUAAGGAAGUAAACGCAUCGGGAGCGAUAGCGGUGAAUUAUUCGUGGUUUUAUCGAUUCGGCAUAGUGGCGAUAACUGAAUGUCGGAUCGGUACUGCGGGUGUUUAAACGCACCGUAAAUAAGAAGUAGUAUUAAGGCA-----
#=GC SS_cons                 {{{{-{{{{{{{{{{{,,<<<<<<<<<-<<-<<<<<_______>>>>>->>->>->>>>>>>{{{{{{{{{,,,,,,,,<<<<<<_____>>>>>>,[[[[-[[[[[[,<<<<<______>>>>>,,,,,,,,,,,,,,,,((((((<<<<<<<<<<--<______>-->>>->>>>>>>,,,,,,,,,,,<<<<<-<<<<<____>>>>>--->>>>>.,)))))),]]]]]]-]]]],,.....,}}}}}}}}}}}}}}}{{{{{-{{-{{{{{,,,.,,,,,,,,,,,,{{{{{{{{{{,,,,,,..........................,,,,,,,,,,,,<<<<_._____>>>>,,{{{{,,,{{{{,<<<<<<<<-<<<<<<<<--<<--<<-<<<<<_______>>>>>->>->>->>>>>>>>------>>>>>>>>,,,,[[[[[[[[--[[[.-[[[[[[[[[<<<____>>>,,,,,,,,,,,,,,,,,,,,,,,,,,....,,,,,,,,,,,,,,,((((,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<<-<<<<----<<<<<<<---...-<<<<<<---------<____>----->>>>>>------->>>>>>>-->>>>---->>>>>>>>>>><<-<<<______>>>->>,,,,,,,,,,,,)))),]]]]]]]]]---]]]--]]]]]]]],}}}},,,,<<____>>}}}},,}}}}}},,,,,,,,,<<<<<<<<<<<<<<<_______>>>-->>>>>>>>>>>>,,}}}},<<<<<______>>>>>,,,,,}}}}}-}}--}}}}}}}}}}-}}}}
#=GC RF                      agCaCcuCCuGuuauaUgcaauGaCuugcgaaguucAUcUacugaacuAugGaaCGuCauuggCauuuuuuAUUcAACGaaGaguUAACcacuCuuAauaaUaaugggUucuauAgagAaauagaCuuUUUUAUcGagUgUuCaacauuugCguccgUUaUUAUUUuUcuggAauGuaaauUuUuUcUcAAcaCagGcgacaUUUAuguuggaAuuGug.GuguuGaUuccauuCuuauAA.....CaagaaauGcuguaaCugauaGacAuauuaAAA.gAUUAAaUcGgaGcgGGaauaaagCaUG..........................cUgagCAUCAUaGugaA.uAuGauuaCaGcgCCagCGauGGCauauaaCuguauugcgucuGGAGcGuCacgUGAGGACuguGaAgCACaAugcgauaugUUCUGGuuauauGGcGAGuuugCuuAauga.cauguuuuuagccgauCggcGUCAggUuUcUuaaUaUgguuGugAU....gAUuUUuUcUUUaAAuacCAAaaagUUauAUgaugagUUugUUguucuauaguGGCuaaAcACuuuaugGUuu...CuguuaaAUauaUAUGcgUGAgAAAaAuuagcaUuCAaAUCcauaaaaguuaGAUGACacuguagaaccGGucacCUuAAugagCgAUAgaGugCuUcGguaGuaaaaacauCuUucaGGaaGuaaaCgCauCaGGAGCGAUAGCGGugAAuuauuCGUGGUUUUguCGauuCGGCauaGuGGCGAUAaCuGAauGCCGgauCGgUACcgCaGGuGuUUAAACaCaCCGUAAAuaauaAguAGuauuaaGGagUuGcu
//
# STOCKHOLM 1.0

#=GF AC   RF02089
#=GF ID   CLRN1-AS1
#=GF DE   CLRN1 antisense RNA 1 conserved region
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   48.00
#=GF TC   49.20
#=GF NC   43.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.77 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   11524702
#=GF RT   Mutations in a novel gene with transmembrane domains underlie Usher
#=GF RT   syndrome type 3.
#=GF RA   Joensuu T, Hamalainen R, Yuan B, Johnson C, Tegelberg S, Gasparini P,
#=GF RA   Zelante L, Pirvola U, Pakarinen L, Lehesjoki AE, de la Chapelle A, Sankila
#=GF RA   EM
#=GF RL   Am J Hum Genet. 2001;69:673-684.
#=GF WK   CLRN1-AS1
#=GF SQ   19


AAHX01017269.1/18577-18653   UAGAGUA-GGGGCAGCUCUGGGUUAUCUGAUAAAUUAUGAUUCUAGUGCUGAAAAGCAGAGU--GUGAGCUUGAUCAGU-A
AAKN02013480.1/8230-8306     GAAAGCU-UCAACAGCUCUGGGUUAGCUGACAAACU--GAUUUUGGUGCUACAAAGUUCAGUAGGUGACCCUGAUUAAG-A
AANU01195773.1/12052-12130   UAGAGCU-UGAACCACUCUGGGUAAGCUGACAAAAUAAGAUUCUGGUGUUGAGAAGCUGAGUACGUGACCAUGAUAUUA-A
AAPY01835884.1/4667-4744     UAGAACU--GACCAGCUCUGAGUAGGCGGACAAGAUAAGAUUCUGGUGCUAAAUAGCUAAGUAUAUGACCCUGAUUCAU-A
AAQQ01171490.1/2873-2950     UAGAGCU-UGGACUGUUCUGGAUUAGCUAACAAAUUAAGAUUCUGGUGCUG-AAAGUUGAAUAUGUGACCCUAAUUAAC-A
AAWR02009269.1/244832-244909 UAGAGCUUUGGGCAGCUCUGGGUAAGCUAACGAAAUAAAAUUCUGGUGCUGAAAAGCU--GUUUGUGACCCUGAUCAAC-A
ABRN01182279.1/14104-14183   UGGAGCUUUGAACAGCUCUGGGUGAGUGAACAAAAUAAGAUCCUGGUGCUGAAAAGCUGACUAUGUGACCCAGACAGUG-C
ABRR01192868.1/3094-3173     UGGAGCUUUAAACAGCUCUGGAUAAGCAAACAAAAUAAGAGUCUGGUGCUGAAAAGCUGAGUGUGUGACCCUGCUCGAC-U
ABRT010483457.1/373-451      UAGAGUU-UGAACUGCUCUGGGUACGCUGGCAAAACAAGAUCCUGGGGCUGAAAAGCUGAGUAUAUGACCCUGAUGAAC-A
ABVD01370355.1/2014-2090     UAGAGCU-UGAAUAGCUCUGAAUAAGCUGGUAAAAUAAGAUUCUGGAUCUGGAAAGCUGAGU--GUGACCCUGAUCUGC-A
AC108726.9/2215-2293         UAGAGAU-UGAACCACUCUGGGUCAGCUGACAAAAUAAGAUUCUGGUGCUGAAAAGCUGAGUAUGUGACCAUGAUAUUA-A
ACBE01322641.1/3658-3737     UGGAGCCUUAAACAGCUCUGAGUAAGCUAACAAAAUAAUACUCUGGUGCUGAAAAGCUGAGUAUGUGACCCUGAUCAUU-A
ABRQ01058783.1/5192-5270     CGGAUCU-GGGAGAGCUUGGAGCAGGCUAACAGAGUAACAUUCUGGGGCUGAAAAGCUGGGAGAGUGACCUUGAUCUAC-A
ABRP01048264.1/6286-6358     CUGAGCUUUGAACAACUCUGAGGAUGUUACCA-----AGAGUCUGGCGCUGAAAAGCUGAAUAUGUGAC--UAGCCAAC-A
AC115919.14/181435-181360    GAGAGUA-GUGGCAGCUCUGGGUUACCUGACAAAUUAUGAUUCUAGUGUUG-AAAGCAGACU--GUGAGCUUGGUCAAU-A
AAEX03013683.1/191514-191593 UGGAGCUUUAAACAGCUCUGAGUAAGCUAACAAAGUAAGAUUCUGGUGCUGAAAAGCUGAGGAUGUGACCCUGAUCAUC-A
AAQR03177923.1/532-460       UAGAGCU-UGGACAGUUCUGGGCAAGCUGACUAAAUAUGAUUCUGUUGCCC--AGGCUAAA---GUG-CCCUGUUGCCA-U
AAGU03062178.1/6501-6423     UAGAGCU-UGGAGAGCUCUGGGUAAGCUGACAAAAUAAGAUUCUGGGGCUGAAACGCUGAGUAUGUGACCUUGAUCUAU-A
AAPE02032099.1/4988-5067     UAGAGCUUUGAACAGCGCUGAGUAAGCUAACAAAAUAAGAUUCUGGUGCUGAAAAGCUAAAUAUGUGACC-AGCAAGUAGG
#=GC SS_cons                 :::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:
#=GC RF                      UaGAGCU.UGaACAGCUCUGGGUaaGCUGACAAAaUAAGAUUCUGGUGCUGAAAAGCUGAGUAuGUGACCcUGaUcaac.A
//
# STOCKHOLM 1.0

#=GF AC   RF02090
#=GF ID   DAOA-AS1_1
#=GF DE   DAOA antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   54.00
#=GF NC   44.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 36.49 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12647258
#=GF RT   Polymorphisms at the G72/G30 gene locus, on 13q33, are associated with
#=GF RT   bipolar disorder in two independent pedigree series.
#=GF RA   Hattori E, Liu C, Badner JA, Bonner TI, Christian SL, Maheshwari M,
#=GF RA   Detera-Wadleigh SD, Gibbs RA, Gershon ES
#=GF RL   Am J Hum Genet. 2003;72:1131-1140.
#=GF WK   DAOA-AS1
#=GF SQ   24


AAFC03117925.1/24558-24758   CAGAUUACUUUUAAGUCUGAAGGGUUCUAUUCAAAUCUUGAAAUGUC---UUUUGA-------CUUUAUAUUUGAAAACCUGUAUGCAUGUGCAUUCAUGAAGGGUAGAGACAUGAUGAAUGU-UCU-CACCUGAGUUAGAACCAAACCCAGCGCAGGCAGC--UGCCCUGAGCUUUGUUAUUACAAUUUUGGCCUGACAUGCGAGUUGGAAAA-U
AAGV020139836.1/6481-6675    UGGAUUACAUUUGUGUAUGAAGGUUUCUAUCCAAACUUUGAAAUAUC---UUUUGA-------CUUUAUAUUUUA---CAUGCAUGCAUGUGUGUUCAUGAUGGGGAGAGAAAGG---AAUGU-UCG-CAUUUGGGUUAGUACCAAGCAUGGUGUGGGUAAC--UGCUGUGAGCCUUUUUAUUACAAUUUUGUCCUGACAUAUGAGUUGGAAAA-U
AAIY01381897.1/1299-1095     UUUAUUACUUUUAAGUAUGAAGGAUCCUAUCCAAACUUUGAAAUGUGGUGUGUUUGUUUUUCAUUUUAAAUUUGUAAAUGUGCAAGCACGUGCAUUCAUGAAGGAAAGAGAAAUGGU-----U-UCU-CAUUUGGGGGAGAACCAAACACAGGCU-GGCAGC--UGCCGGGAGCUUUGUUAUUACCAUUUUGGACUGAUAUGUGAGUUGAAAAA-U
AANG01116959.1/1195-1389     CGAGUUACUUUUAAGUAUGA-G-AUUCUAUCCAAACCUUGAAAUAUC---UUUUGA-------CUUUUUAUUUGAAAAUGCGCAUGCAUGUGUAUUCAUGAAGGGCAAAGAAAUGAUAAAUGU-UCU-CAUCUGAGUUAGAACCAAAGACAGUGUAGGCAGC--UGCUGUGAGCUUCCUUAUUGC--UUUUGGCCUGACAU--GAGCUGGAAGA-U
AANN01184755.1/7269-7071     UGGAUUAUAGUUAUGUAUGCAGGAGUGCCCACAUACUUUGCGAUACC---UUAUGA-------CUUUAUAUUUGGAAAUGUGCACACAUGCACAUUCAUGAAAG--ACAGAGAUGAUGAAUGU-UCU-CAUUUGAGUUAGAACCAAACACAGGGAGAGCAAC--CGAUGGGAGUUUUGUUAUUACAGUUCUGGUCUGACAUAGGCACUGGAAAA-U
AANU01261897.1/134520-134320 UUUCUUACAUGUAAGUAUGAAAGAUUCCAUCCAAACUUUGAAAUGUC---UUUUGC-------CCUCAUAUAUGAAAAUGUGCACGCAUGUGCAUUCAUGAAGGAGAGAGAAAUGAUCGAUGC-UCU-AAUUAGAGCUGGCACAAAACCCGGACUAGGCAGC--UGCUGUGAGCUUUGUCAUUACAAUUUUGACGUGACAUAUGAUUUGGGAAA-U
AAPY01171848.1/1957-2152     AUUACUUUUUUUA--UGUGAAGAAUUUCAUUCAAAUUGUAAACUGUU---UUUUGG-------CUUUUUAUU-GAAAAUAUGCAUGCACACACAUUCAUGAAGAGAAGAGAAAUGGUGAGUGU-UCC-CAUUUGAGUGAGAACCACC--CAGUGCAGGUAGC--UGCUGUGAGCUUUGCAAUUACAAUUUGGGCCUGACAUAUGAGAUGGAAAA-U
AAWR02011203.1/35406-35606   UGAAUUACUUUUAAGUAUGAAGGAUUCAAUCCAAACCUUGAAAUGUC---UUUUGA-------CUUUAUAUUUGAAAAUGGGCAUGCAUGUGCAUUCAUGAAGGGCAGAGAAAUGAUAAAUGU-GCU-CAUUUGAGUUAGGAACAAACACAGUGUAGGCAGC--UGCUGUGAGCUUUGUUAUUACGAUUCUGGCUUGACAUAUGAGUUGGAAAA-U
AAYZ01159253.1/8164-8352     CAAGUUACUUUUAAGUAUGA-GGAUUCUAUCCAAU---------GUC---UUCUGA-------CUUUAUAUUUGGAAAUGUGCAUGCAAGAACACUCACAAAGGG-AGAGCAGUGAUAAAUGU-GCU-CAUUUGAGUUAGAGCCAAAUGCAGCACAGGCUAC--UGCUGUGGGCUU-GUUAUUACAGGCUUGGCCUGACAUAUGAGCUGGAAAA-U
ABDC01124513.1/5798-5997     UAGAUUACUUUC-AGUAGGAAGGAUUCUAUUCAAACUUUGAAAUGUC---UUUUGA-------CUUUAUAUUUGAAAAUAUGCAUGCAUGUGCUUUCAUGAAGUAGAGAGAAAUGAUACAUGC-UUU-CAUCUGAGUUAGAACCAAACACAUUAUAGGCAGC--UGCUCCGAGCUUUGUUAUUACAAUUUUGACCUGACAUAUGAGGUGGAAAA-U
ABRN01441980.1/888-1088      UGGAUUAAUUUUAAGUCUGAAGGAUUCCAUUCAAAUCUUGAAAUGUC---UUUCGA-------CAUUAUAUUUGAAAACGUGCGUGCAUGUGCAUUCAUGAAGGGCAGAGACAUGAUGAAUGU-UCU-CAUCUGAGUUACAACCAAACACAGCAUAGGCAGC--UGCCGUGAGCUUUGUUAUUACAGUUUUGUCCUGACAUACGAGUUGCAAAA-U
ABRO01046282.1/565-761       UGGAUUACUUUCAAGUACAAAGGAUUUCAUUGAACCUUAGAAAUGAC---UUUAGU-------CUUUGUGUUC-AAUAGGUGAAUGCUUGUGUACUUAUCAAUGUGAGGAAAAUGUUUAAUUGCUCU-UAUUUACAUUAAAACCAA---CAGCAUAGGCU-C--UGCAGAGACCUCAAUUAUUACAGUUUUGGUCUGAUACCUGAAUUGGAAAA-C
ABRP01072732.1/2333-2532     UGGAUUACUUUUCAGUAUGAAGGAUUCGAUCCAAACCUUGAAAUGUC---UUUUGA-------CGUUAUAUUUGAAAAUGUGCAUGCAUGUGUAUUCAUGAAGGGCAGAGA-AUGAUAAAUGU-UCU-CAUUUGAGUUAAAACCAAACACAGUGUAGGCAGC--UGCUGUGAGCUUUGUUAUUACAAUUUUGGCCUGACAUAUGAGUUGGAAAA-U
ABRQ01301253.1/605-802       UGGAUUAC-UUUAAGUGUAAAGAAUCUUAUCCCAACUUUGAAAUGUAU--UUUUUA-------CUUUAUAUUUGAAAAUGUGCAUGCAUGUGCAUGAACGAAGGGGAGAGAGG-GAUAAAUGC-UCU-CGUGGGAGCUAGAAUCCACCGCGGUGU-GGUGGC--UUCUCGGA-CUUCAUCAUUACCAUUUUGGCCUGACACACGAGUUGGAAGA-C
ABRR01094712.1/4095-4293     UGGACUAGUUUUAGGUAUGAAGGAUUCCAUCCACAUCUUGCAACGUC---UUUGGA-------CUUUAUAUUUGAAAAUGUGCACGCAUGUGCAUUCAAGAAAGGCAGAG--AUGAUGCAUGU-UCU-CAUGUGAGUGAGUCCGAAACACUGAGGAGGCAGC--UGCAGUGAGCUUUGUUAUUACAAUUUUGGCCUGACCUACAAGGUGGAAAA-U
ABRT010071868.1/4320-4510    UGGAUUACUUUUAAAUAUGAAGGAUUCUAUCCAAAUAUUGAAAUGUC---UUUUGA-------CUUUACAUUUGAAA----------AUGUGUAUUCAUGAAGGAAAGAAAAAUGAUAAAUGC-UUU-CAUUUGACAUAGAAACAAACCUAAUGCUGGCAGC--UGCCAUGAGUUUUGUUACUGCAAGUUUGACCUGACAUG-AAAUUUAAAAAUG
ABVD01019220.1/354-557       UGGAUCACAUUUAUGUAUGAAGGAUUCUAUCCAAACUUUGAAAUGUC---UUUUGA-------CUUUAUAUUUUAAAAUGUGCAUGCAUGUGCAUUCAUGAAUGAGAGAGAAAUGAUGAAUGU-UAGAUCAUUGGGUUAGAACCAAACACAGUGUGGGCAGCUCUGCUGCAAGCUUUGUUAUUACAGUUUGGGCCUGACAUAUGAGUUGGAAAA-U
AL359751.12/9985-10185       UUUAUUACUUCUAAGUAGGAAAGAUUCCAUCCAAACUUUGAAAUGUC---CUUUGC-------CCUUAUAUAUGAAAAUGUGCACUCAUGUGCAUUCAUGAAGGGGAGAGAAAUGAUCAAUGC-UCU-AAUUAGAGCUGGCACCAAACCUGGCGUAGGCAGC--UGCUGUGAGCUUUGUCAUUACAAUUUUGACGUGACAUAUGAUUUGCGAAA-U
AY143165.1/8601-8799         GGCAUUGCUUUUAAGUAUGAUGGGUUCUAUGCAAACUUUGAAAUGCC---UUUUUA-------CCUCAUAUUUCAGAAUGCGUGUGCCUAUGCAUUCAUAAUGG--AGAGAGAUGAUAAAGGU-UCU-CAGUUGCAUUAAAACUAAACACAAUAUAGGCAGC--UGCUGUGAGCUAGACUAUUAUAGUUUUAUCCCGAUAUAUAAAAUGGAAAA-U
AAQR03066307.1/14865-15061   ---UUUCUGUUUAAGACAGAAGGAUUCUAUACAAACUU-GAAAUGUC---UUUUGA-------CUUUAUAUUUGAAAAUGUGUGUGCAUGUGCAUUCAUGAAGUGGAGAGAAAUGAUAAAUGC-UUU-CAUUUGAGUCAGAGUCGUACACAUCACAGGCAGC--UGCUGUGAGCGCUGUUAUUACAGUUUUGACCUGACAUAUGAGGUGGAAAA-U
AAPE02014045.1/58670-58472   UGGAUUACUUUUCAGUAACAAGGAUUCUAUCCAAAGCUUGAAAUGUC---UUUUGA-------CUUUAUAUUUGAAAAUGUGCAUGCAUGUGCAUUCAUGAAGGACAGAGAAAUGAUAAAUGU-UCU-CAUUUGAGUUAGAACCAAA--CAGUGCAGGCAGC--UGCUGUGAGCUUUGUUAUUACAAUUUUGUCCUGACGUAUGAGUUGGAAAA-U
AABR05061235.1/5092-4894     GGCAUUGCUUUUAAGUAUGAUGAAUUCUAUGCAAGCUUUGAAAUACC---UUUUUA-------CUCUAUAUUUGAAAAUGUGUGUGCCUGUGCAUUCAUAAUGA--GGAGGGAUGAUAAAGGU-UCU-CAGCUGCAUUAAAACUAAACACAAUAUAGGCAGC--UGCUGUGAGCUAGACUAUUAUAGUUUUAUCCUGAUAUAUGAAAUGGAAAA-U
AAGW02021481.1/26617-26815   UUGGUCACUUUUAAGUAUGA-GGAUUCUAUCCAAACUUUGCCAAGUC---UUCUAA-------CUUUAUAUUUGAAAAUGUGCAUGCAUGAGCAUUCGCAAAGGG-AGAGAAGUGAUAAAUGU-GCU-CAUUUGAGUUAGAGCCAAAUGCAGUGCAGGCAGC--UGCUGUGAGUUUUGUUAUUACAGUCUGGGGCUGACAUAUGAGCUGGAAAA-U
AAEX03013359.1/491114-491311 GGGGUUACUUUUAAGUAUGA-GGAUUCUAUCCAAACCUUGAAGUGUC---UUUUGA-------CUUUUUAUUUGAAAAUGCACAUGCAUGUGCAUUCAUGAAGGGCAGAGAGAUGAUGAAUGU-UCU-CAUCUGGGUUAGAACCAAAUACAGUGUAGGCAGC--UGCUGAGAGCUUUCUUAUUACAAUUUUGGCCUGACAU--GAGUUGGAAAA-C
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::...::::::.......::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::.::::::::::::::::::::::::::::::::::..::::::::::::::::::::::::::::::::::::::::::::::::::.:
#=GC RF                      uggaUUacuUUUAaGUauGAAGGAUUcuAUcCAAacuUUGAAAUGuc...UUUUGa.......CUUUaUAUUUGaAAAuGUGcAuGCaUGUGCAUUCAUGAAGGggAGAGAaAUGaUaAAUGu.UCU.CAuuUGaGuuAGaaCCAAaCaCaGuguaGGCaGC..UGCuGuGAGCUuugUUAUUACagUUUUGgcCUGACAUauGAguUGGAAAA.U
//
# STOCKHOLM 1.0

#=GF AC   RF02091
#=GF ID   DAOA-AS1_2
#=GF DE   DAOA antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   43.00
#=GF TC   43.60
#=GF NC   40.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.43 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12647258
#=GF RT   Polymorphisms at the G72/G30 gene locus, on 13q33, are associated with
#=GF RT   bipolar disorder in two independent pedigree series.
#=GF RA   Hattori E, Liu C, Badner JA, Bonner TI, Christian SL, Maheshwari M,
#=GF RA   Detera-Wadleigh SD, Gibbs RA, Gershon ES
#=GF RL   Am J Hum Genet. 2003;72:1131-1140.
#=GF WK   DAOA-AS1
#=GF SQ   24


AL359751.12/12472-12675      -UUGAGAAAGAGUGGCGGGGGUAGCACAUCUCUC---CAGCCUCAA---ACUAUUCCUUCCUC-AGGGCAGAAUUUCCCCGU--GACGCUCUCUUGUCAUCAUCACCUUCUUCUU--GUCUGAACUCAUCAACAUUUC--AGCCAAAUUACUGUGCUGCUAAGUCACUGGGAAGAU--CAGGACCCCACACCAAGAUGAUCAUCUUAGAGAUGCACAAAA
ABRT010071869.1/2462-2665    -UUGAGAAACCGUGGCAGGGGUAGCACAUCUCUU---CAGCCACAA---ACUAUUUCUUCCCC-AGGGCAGUAUUUCCCAAU--UAUGCCAUCCUGUCAUCAUCACCUCCUUCUU--GUCUGAACUCAUCAACAUUUC--AGCCAAAUUACUGUGCUGCUAAGUCACUGGGAAAAU--CAGGACCCCACACCAAGACGAUCAUCUUAGAAAUGCACAAAC
ABVD01019221.1/1039-1243     -UUGAGAAACAGAGGCCAGGGUAGCGCUUCUCUCU--UGGCCACAA---ACUAUUUCUUCCUC-AGGGCAGUAUUUCCCAAU--UACACUUUCCUGUCAUCAUCACCUCUUUCUU--AUCUAGGUUCAUCAAGAUUUU--UGCCAAGUUUCUAUGCUGCUAAGUCACUGGGAAAAU--UGGGACCCCACACCAAGAUGAUCAUCUUAGAAAUGCACAAAA
AAWR02011203.1/38970-39170   -UUGAGAAAAAGUGGUCAAG-CACUUC---UCUCC--CAGCCACAA---ACUAUUUCUUCCCC-AGGGCACUAUUUCCCAAU--UAUCCUUUCCUGUCAUCAUCAACUUCUUCUU--GUCUGGGCCCAUCAGCGUUUC--AGCCAAGUUACUGUGCUGCAGAGUCACUGGGAAACU--CAGGACCCCACACCAAGGAGAUCAUCUCGCAAAGGCACAAAA
AAGV020139837.1/3994-4192    -UUGAGAAAGAGUGGCCAAUGUAGCGCUUCUCCC----AGCCACAA---ACCCUUUCUUCCCC-AGGGCAGUAUUUCUCAAU--UACACCUUCCUGUCAUCAUCAUCU---UCUU--GUCUGGGCUCAUCAAGCUUUC--UGCCAGGUUUCCAUGCUGCUAAGUCACUGGGAAAAU--UAG-ACCCCACACCAAGAUGAUCAUCUUAGAAAUGCACAAAA
AAQQ01605126.1/3173-3375     -UGGAGAAAGAGCGGCUGGG-GAGCACCUCUCUC---CAGCCUCAA---ACUAUUUCUCCCCC-AAGGCAAUGUUUCCCAAU--UACACUUUGCUGUCAUCAGCACCUUCUUCUU--GUCUGGGCUCAUCAACCUUCC--AGCCCAGUUACCACGGUGCUGCAUUGCUGGAGAAUU--CAGGACCCCACACCAAGAUGAUCAUCUUAGAAAUGCACAACA
AAIY01459802.1/998-796       -CAGAAAAAGGGUGGUCAGAGAAGCACAUCUUCUC--CAGCCACAA---ACUAUUUCUCCCC--AGGGCAGUAUUUCCCAAU--CAUGC-UCCCUGUCACGAUCACCUCCUUCUU--GUCUGGGCUCAUCAAUAUGUC--AGCUGAGUUCCUGUGCUGUGAAGUUACUAAGAAAAU--GUGGACCCCACACCGAGAUGAUCAUCUUAGAAAUACGCUAAA
ABRR01094713.1/722-919       -UUGAGAAAGAGUGGUCAAG-CCCUUC---UCUCC--CAGACACAA---ACUAUUUCUUCCCC-AGGGCAGUAUUUCCCAAU--UAUCCCUUCCUGUCAUCAUCUCCU---UCUU--AUCUGGGCUCAUCAGCAUUUC--AGCCAAGUUACUGUGCUGCAAAGUCACUGGGAAAAU--UGGGACCCCACACAGAGGUGAAUAUCUCCGAGACACAUGAAA
ABRN01441980.1/4440-4643     -UUGAGAAAGAGUGGUCAAG-CCCUUCUUCUCUCC--CAGACACAA---ACUAUUUCUUCCCC-AGGGCAGUACUUCUCAAU--UAUCCUUUUCUGUCAUCAUCUUCUCCUUCAU--GUCUGGGCUCAUCAACAUUUC--AGCCAAGUUACUAUGCUUCAAAGUCACUAGGAAAAU--CAGGAGCCCACACAGAGGUGAUCAUCUCACACACACACAAAA
AAFC03117925.1/28114-28314   -UUGAGAAAGAAUGGUCAAG-CCCUUC---UCUCC--CAGACACAA---ACUAUUUCUUCCCC-AGGGCAAAACUUCCCAAU--UAUCCUUUUCUGUCAUCAUCACCUCCUUCAU--GUCUGGGCUCAUCAACAUGUC--AGUGAAGUCACCGUGCUUCAAAGUCCCUGGGAAAAU--CUGGACCCCACACAGAGGUGAUCGUCUCACACACACACAACC
ABRQ01301254.1/3312-3521     -UUGAGAAACAGUGGCUGGGGGAGCCGAGCUCUCUGCCAGCCACAACCCAGUGCUUCUUCCCC-AGGGCAGGAUUUCCCAAU--UACGCGACCCUGUCACCGUCACAUCCUUCUU--GUCCGGGCUCAUCAAGAUUUC--AUCCCAGUUACCCUGCUCCGAAGUCACUAGGAAAAC--UGGGGCCCCACACCAAGAUUAUCAGCUUAGAAAUGUACUCAC
AAKN02008532.1/158477-158276 -UUGAGAAAGAGUGGCUGGGGUAACACAUCUCUC---CAGCCUCGA---AGCAUUUCUUCCCC-AGGGCAGUAUUUCCCAAC--CACACUCCUCAGUCUUCCUUACCUCUUGCUU--GUCUGGACCCAUCCAC-UACC--AGCCUACUUCCUGUGUAGCUCAGUUCUUGGAGAAAG--CAGGACCCCACAGUAAGAUGAGCG-CUGAAAAAUGCACAGCU
AALT01656191.1/30740-30936   -UUGAGAAAAUGUGGUCAAGGUAGUUCAUCUCUCC--CAGACACAA---ACUGUUUCUUGCCC-AGAGCGGAAUUUCUCAAU--UAUGC-UUCCUGUCAUCAUCGGCU---UCUU--GUCUGGGCUCAUCAACAUUUC--AGCCAAGUUACUCUGCUGUGAAGUCACUGGAAAGAG--CAG-ACCCCACACCACGCUGCUCUUCUCAGAGCCGUGAA---
ABRP01339926.1/65-252        UUGAAAAUAAAGCGGUCAAG-CACUUC---UUUCC--CAGACACAA---ACUAUUUCUUCCCC-AGGGCAGUAUUUCCCAAU--UAUCCCUUCCUGUCAUCAUCACCU---UCUU--GUCCGUGCUCAUCAGCAUCUC--AGACAAGUUACUAUG-----------CUGGGAAAAU--CAGGACCUCACACUUAGAUGAUCUUCUUAGAACCACAAAAAA
AANN01184755.1/3367-3170     -GAAAAAAAAAAUGGUCAAGGUAACACAUCUCCUG--CAGACACCA---ACUAUUUCUUCCCC-AGGGCGGGAUUUCUCAAU--UAGAC-CUCCUGUCAUCAACCUCU---UCUU--GUCUGGGCCCAUCAACAUUUC--AGUCAAGUGACUGUGCUGUGAAGUCCCUGGAAGACU--AGG-ACCCCACACUGAGAAGCUCAUCUCACAAGCCCAUCA--
AAPY01636758.1/433-634       UUGGGAGAACAGUGGC-AUGGUACCACAUCUCACG---AGUCACGA---GCUCUUCCUUCCCC-AGGGCAGCAUAUCCCAAU--UAUGCAUUCCUGUCAUCAUCCUCUCCCUCUU--GUCUGGGCUCAUCC-CCCUUC--AGACAAGCUACAGUGCUGCUAAGUCCCUAAAGAAAU--CAA-GCGCCCCCUCAAAAAGAACAUCUUAGCAGUGCAAAAUG
ABRO01046283.1/111-309       -UGGAGAAAGAAGGAAGGGGUUUGUAAAUCUCCA---CAGCGUCAG---AAUCUUUCUCCCCC-AGAGCAGUAUUCCCCAAU--UAUACUUCUCAGUCAUCAACACCUCUUUCUU--GUCUGGGCUCAUCAACCUUCC--AGCCCAGUU--AGCACAUCCG--UCACUGCAGAAAG--CUGUACCCCACACCAAGUCUAUCAUCUUAGA-AUGCGGACAG
AAFR03020033.1/17343-17137   -CUACAACACAGUAACCAGGAAAGCACAAUUCUCU--CAGCCACAA---AGUAUUUCUUCCUCUAGGGCUAUAUUUUUCAAU--UAUGACUUGCUGUCAUCAUCAUCUCCUUCUAC-AUCUGUGUUGAUCAAGCACUU--AGCCAUGUUACUCUCUUCUUGAAUUACUGGAAGAGU--UGAGACCGCACACAAUGAGGAUAAUUCUAGAAAGACUUAAGG
ABGA01265037.1/21866-22052   -UCAAGAAACAGUAGA---------------------CAACUACAA---AAUGUUUCUGUCCC-AGGGAAAGAUUUUUCAAUACCUUUCUUUUUUGUCAUCUAUACUUUGUUUUA--AGCUAAACGUAUUAAG-AUUU--CAUCAAGUUACUUUGCCUCCAAGACUCUGGAAAAGU--UGAGACCUCACACAAAGAUAUUCAUCUUAGAAGUUCACAAAC
AAYZ01159253.1/10339-10544   -UUGAGAACGUGUGGCUGGAGCAAAGUAUCUCUC---CAGCCAUGC---ACCACUUCU--CCC-AGGGUAGCCUUUCCCAUC--CUCCCUCCCAAGGCACUCUU-UGUGCUUCUCUCCUCU-GGUCCAUCCUCACCUUGUAGCCCAGUUUCCACGUGACUAACACACGGAGGAAAUCAUGGCCCCCCACACAAAGGUGCUUCUCUUCAACAGACACAACA
AAPE02014045.1/55427-55227   -AAAAAAAAAAGCGGUCAAG-AACUUC---UCUCC--CAGACACAA---ACUAUUUCUUCCCC-AGGGCAGUAUUUCCCAAU--UAUCCUUUCCUGUCAUCAUCACCUUCUUCUU--GUCUGGGCUCAUCAACAUUUC--AGCCAAGUUAUCAAGCUGCGAAGUCACUGGGAAAAU--CAGGACCUCACACCAAGAUGAUCAUCUUUGAACCACAGAAAA
AABR05061235.1/820-619       -UUGAGGAG--GAGGUGGGGGUGGUAAGCCUCAG---CAGCCCUAG---CUUUCUUCUUCCCC-UGGGCAGUAAUUCCCAAU--UAUGCCUCUCUGUCAUCAACACCUCCUUCUU--GUCUGGACCCAUCAGCCUUCC--AGACCAGUUCCUGCAUAGCUAAAUCACCAGAGAAAG--CAGGACCCCACACCUAGAUGAUCUUCUUAACCAUGCUCAACA
AAEX03013359.1/494519-494716 -UUGAGAAAAAGUGGUCAAG-CACUUC---UCUCU--CCGUC--AA---AGUAUUUCUUCCCC-GGGGCACUAUUUCCCAAU--UAUCCUUUACUGCCAUCAUCACCU-CUUCUU--GUCUGGACUCAUCAACAUUUC--AGCCAAGUUCCUGUGCUGCAAAGUCACUGGGAAAGU--CAGGACCCCACACCAAGAUUAUCAUCUCCCAAACACACAAAA
AAQR03066308.1/2117-2318     -UCGAGAAAUAGGGGUGGGG-UAGCACAAAUCUC---CAGCCACAG---ACUCUUUCUUCCCC-AGGGCA-AAUUCCCCAAU--UAUGUUUUCCUGUCAUCGUUGCCUCCCUCUU--GUCUGAGCUCAUCAACAUUUC--AGCCAAAUUACUGUGCUGCUAAGUCACUGGGAAAAU--CAGGACCCCACACCAAGAUGAUCAUCUUAGAAGUGCACAAAA
#=GC SS_cons                 .::::::::::::::::::::::::::::::::::..:::::::::...::::::::::::::.::::::::::::::::::..:::::::::::::::::::::::::::::::..:::::::::::::::::::::..::::::::::::::::::::::::::::::::::::..::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      .UuGAGAAAgaGuGGccggGGuagcacauCUCucu..CAGcCaCaa...AcUaUUUCUuCCCC.AGGGCAGuAUUUCCCAAU..uAugCuuucCUGUCAUCauCaccUccUUCUu..GUCUGGGCuCAUCAacauuUC..AGcCaAGUUaCugUGcugCuaAGUCaCUGGgaAAau..cgGGaCCCCACACcaAGauGaUCaUCUuagAaaugCacaAaa
//
# STOCKHOLM 1.0

#=GF AC   RF02092
#=GF ID   mir-2970
#=GF DE   mir-2970 microRNA precursor
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:21627805
#=GF SS   Published; PMID:21627805
#=GF GA   50.00
#=GF TC   55.50
#=GF NC   42.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   21627805
#=GF RT   Song exposure regulates known and novel microRNAs in the zebra finch
#=GF RT   auditory forebrain.
#=GF RA   Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB,
#=GF RA   Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S,
#=GF RA   Clayton DF
#=GF RL   BMC Genomics. 2011;12:277.
#=GF RN   [2]
#=GF RM   20360741
#=GF RT   The genome of a songbird.
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF WK   MicroRNA
#=GF SQ   5


ABQF01037869.1/1025-1108   CUCCUGC----CCUGCGGACAGUCAGCAGUUGGUCUGGUGUGAGCAGCAAUUCUCAGAUCACCUCUUGGCUGUGGGUGGUGCAGGGAG
ABQO010558253.1/489-576    CUCUUCCUGUCACUGCAGACAGUCAGUAGUUGGUCUGGCGUGAGCAGGAAUUCUCAGAUCACCUCUUGGCUGUGAGUGGUGGAGAGAG
AAPN01354696.1/850-937     CUCUUCCUGUCACUGCAGACGGUCAGUAGUUGGUCUGGUGUGAGCAGCAAUUCUCAGAUCAUCUCUUGGCUAUGGAUGGUGGAGAGAG
AAFR03030218.1/14427-14514 CUCUUCCUGUCACUGCAGACAGUCAGUAGUUGGUCUGGUGUGAGCAGGAAUUCUCAGAUCACCUCUUGGCUGUGAGUGGUGGAGAGAG
AAWZ02016383.1/3231-3157   C------UGUCACUGCAGACAGUCAGUAGUUGGUCUGGCAUAAGCAGAAAGUUUCAGAUCACCUCUUGGCUGUGAGUAGU-------G
#=GC SS_cons               <<<<<<<-----<--<--<<<<<<<<-<<-<<<<<<<<<<<_____>>>---->>>>>>>>->>->>>>>>>>-->-->->>>->>>>
#=GC RF                    CuCcucCUGUCaCUGCAGaCaGuCaguaGUuGguCuGgugugAGCAgcaAuUcuCaGauCacCuCuuGgCuGuGaGUgGUGgaGgGaG
//
# STOCKHOLM 1.0

#=GF AC   RF02093
#=GF ID   mir-2968
#=GF DE   mir-2968 microRNA precursor
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:21627805
#=GF SS   Published; PMID:21627805
#=GF GA   70.00
#=GF TC   83.50
#=GF NC   51.60
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   21627805
#=GF RT   Song exposure regulates known and novel microRNAs in the zebra finch
#=GF RT   auditory forebrain.
#=GF RA   Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB,
#=GF RA   Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S,
#=GF RA   Clayton DF
#=GF RL   BMC Genomics. 2011;12:277.
#=GF RN   [2]
#=GF RM   20360741
#=GF RT   The genome of a songbird.
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF WK   MicroRNA
#=GF SQ   12


ABQF01011073.1/6857-6962     GCUGCCCUGCGAGUUGCUAUCCUCCAGGUCGCUCUGGCAGCCCUCGUCGUUGAGCGAGCUCUGCUUGGUG-ACCUUGGGCGACAGCAGCUUCACCAGGUCGCCCAGC
ABRP01185955.1/4956-5061     GCUUCCCUGAGAGACGUUGUCCUCCAGGUCGCUCUGGCAGCCCUCGUCGUUAAGCGAGUUCUGCUUGGUG-ACCUUGGGCGACAGCAGCUUGACCAGGUCAGUCAGC
ABQO010769703.1/2675-2570    GCUGCCCUGAGACAGGUUGUCCUCCAGGUCGCUUUGGCAGCCCUCGUCGUUGAGCGAGCUCUGCUUGGUC-ACCUUGGGCGACAGCAGCUUGACCAGGUCGCCCAGU
AANU01230676.1/10556-10661   GCUACCCUGCGAGACGUUGUCCUCCAGGUCGCUCUGGCAGCCCUCGUCGUUGAGCGAGUUCUGCUUGAUG-ACCUUGGGCGACAGCAGCUUGACCAAGUCGGUGAGC
AAFR03034753.1/114702-114807 GCUGCCCUGAGACAGGUUGUCCUCCAGGUCGCUCUGGCAACCCUCGUCGUUGAGCGAACUCUGUUUGGUC-ACCUUAGGCGACAGCAGCUUAACCAGGUCGCCCAGU
AAPE02017191.1/686-581       GCUGCCCUGCGAGAGGUUGUCCUCCAGGUCGCUCUGGCAGCCCUCGUCGUUGAGCGAGUUCUGCUUGGUG-ACCUUGGGCGACAGCAGCUUGACCAGGUCGGGCAGC
AAWZ02018787.1/21072-21177   GCUGCCCCCGGCGCUGCCUUCCUCCAGGUCGCUCUGGCAGCCCUCGUCGUUGAGCGAACUCUGCUUGGCC-ACCUUGGGCGAGAGCAGCUUGGCGAGCUCGGGCAGU
AAEX03009026.1/406796-406901 GCUGCCCUGGGAGCCGCUGUCCUCCAGGUCGCUCUGGCAGCCCUCGUCGUGGAGCGAGCCCCGCCUGGUG-ACCUUGGGCGCCAGCAGCUUGACCAGGUCGGCCAGC
AAGW02010782.1/83294-83399   GCUGCCCUGCGAAACGUUGUCCUCUAGGUCGCUCUGGCAGCCUUCGUCGUUGAGCGAGUUCUGCUUGGUG-ACCUUGGGCGACAGCAGCUUGACCAGGUCGGUGAGC
AAQR03112917.1/15345-15450   GCUGCCCUGCGAGACGUUGUCCUCCAGGUCGCUCUGGCACCCCUCGUCGUUGAGCGAGUUCUGCUU-GGUGACCUUGGAUGACAGCAGCUUCACCAAGUCGGUGAGC
AADN03004253.1/270515-270620 GCUGCCCUGCGAGGUGCUGUCCUCCAGGUCGCUUUGGCAGCCCUCGUCGUUGAGCGAACUCUGCUUGGUG-ACCUUGGGCGAGAGCAGCUUCACCAGGUCGCCUAGC
AAGU03040474.1/89954-90059   ACUGCCCUGCGAGACGUUGUCCUCCAGGUCGCUCUGGCAGCCCUCGUCGUUGAGCGAGUUCUGCUUGGUG-ACCUUGGGCGACAGCAGCUUGACCAGGUCAGUGAGC
#=GC SS_cons                 <<<<-<<<<-<<<<<<<<-<<<<<-<<<<<<<<--<<<<<--<<<<<______>>>>>-->>>>>->>>>.>>>>->>>->>->>>>>>>>--->>>>----->>>>
#=GC RF                      gCugCCCugagagccGcuguCCuCcaGGucgCccUgGCagCCcuCGuCGUuGAgCGaguUcuGCcUgGcg.aCCuUGgGcGacagCggcuugACcaGGUCggucaGc
//
# STOCKHOLM 1.0

#=GF AC   RF02094
#=GF ID   mir-1803
#=GF DE   mir-1803 microRNA precursor
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:21627805
#=GF SS   Published; PMID:21627805
#=GF GA   64.00
#=GF TC   64.10
#=GF NC   63.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   21627805
#=GF RT   Song exposure regulates known and novel microRNAs in the zebra finch
#=GF RT   auditory forebrain.
#=GF RA   Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB,
#=GF RA   Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S,
#=GF RA   Clayton DF
#=GF RL   BMC Genomics. 2011;12:277.
#=GF RN   [2]
#=GF RM   20360741
#=GF RT   The genome of a songbird.
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF WK   MicroRNA
#=GF SQ   6


ABQF01031421.1/75836-75924   GGACUUAGGGCAUGAUCCAGAGCCCAUUGUAGUCAAUGGGAGACUUUUUCCAUUGACUUCAUCGGGGUUUGGAUCAGGCCUUUACUACC
AB125492.1/804-885           AUAUUU--GGCCUGAUCCAAAGUCCAUCAA-GUCCAUGGAAGU--AUUUCCAUUGACAUUACUGGGCUUUGGGUCAGGCC--CCUUCAU
DQ483797.1/114-196           AUAGCU-GGGUCUGACCCCAAGCUCACUGAAACCAAUGGAG-UC--UUUCCAUUGCCUUCACAGGGCUUUGAAUCAAGCC--UUUAAAU
DQ917767.1/654-571           ACAUU--GGGAAUGAUCCGAAGCCCACUGAAGUCAAUACCAGUC--UUUCCACUGAUGCCAAUGAGCUUUGGAUCAGAUCC-ACGGCGU
AADN03005573.1/260448-260533 GCAAUUAGGGUGUGAUCCAAAGCCCAUUAAAGUCAUUGGGAAUCAG--UCCACUGACUUAAACAGGCUUUGGAUCAAGCCC-AUAUUGC
AAWZ02010769.1/22549-22632   -G-CUUAGGUCCUGAACCAAAGCCCCUCGAGGACAAUGUGAGUC--UUUCUAUUGACUUCAGUGGGCUUAGGAUCAGGCCCUUAAUGC-
#=GC SS_cons                 <<----.<<<<-<<<<<<<<<-<<<--<<-<<<<<<<<<<<<__..>>>>>>>>>>>>->>-->>>->>>>>>>>>->>>>.----->>
#=GC RF                      gcAuUU.GGgcaUGAuCCaaAGCcCAuugAaGuCAaUGgaagUC..uuucCAuUGaCuUcaauGgGCUuuGGaUCAggcCC.uuuuagc
//
# STOCKHOLM 1.0

#=GF AC   RF02095
#=GF ID   mir-2985-2
#=GF DE   mir-2985-2 microRNA precursor
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:21627805
#=GF SS   Published; PMID:21627805
#=GF GA   65.00
#=GF TC   66.60
#=GF NC   64.80
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   21627805
#=GF RT   Song exposure regulates known and novel microRNAs in the zebra finch
#=GF RT   auditory forebrain.
#=GF RA   Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB,
#=GF RA   Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S,
#=GF RA   Clayton DF
#=GF RL   BMC Genomics. 2011;12:277.
#=GF RN   [2]
#=GF RM   20360741
#=GF RT   The genome of a songbird.
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF WK   MicroRNA
#=GF SQ   20


ABQF01006516.1/5391-5471     AGGGUUCUCCAUUAAGGUGGGUGGAAUAGUAUAACAAUAUAA--AAUGUGUUGUUAUAGUAUUCCACCUUCCCUGAUGU----CCCU
ABRR01237905.1/1607-1527     AGGGCUCUUCAUUAAGGUGGGUGGAAUAAUAUAACAAUAGAA--CGCGUGUUGUUAUAGUAUUCCACCCUCCCUGAUGU----CCCU
ABQO011184433.1/694-774      AGGGUUCCUCAUUAAGGUGGGUGGAAUAGUAUAACAAUAUAA--CAUGCGUUGUUAUAGUAUUCCACCUUCCCUGAUGU----CCCC
AALT01500699.1/4056-3976     AGGGGUCUUCAUUAAGGUGGGUGGAAUAGUAUAACACUAGAA--CACGUGUUGUUAUAGUAUUCCACCUUCCCUGAUGG----CCCU
ABRO01083327.1/1068-988      AGGGCUCCUCAUUAAGGUGGGUGGAGUAGUAUAACAAUGUGA--UCUGUGUUGUUAUAGUAUUCCACCCUCCCUGAUGU----CCCC
CAAE01014573.1/830212-830292 AAGGCUCAGCAUUAAGGUGGGUGGAAUAAUAUAACAAUAUUC--UCCAUGUUGUUAUAGUAUUCCACCUACCCUGAUGU----CCCU
AAVX01192266.1/1027-946      AGAGCUCCCCAUUAAGGUGGGUGGGAUAGUAUAACAAUAUAU-CAUUGCGUUGUUAUAGUAUUCCACCUUCCCUGAUGC----CUUU
AAFR03056060.1/56137-56060   AAGGCUCAACAUUAAGGUGGGUGGAAUAAUAUAACAAUAUC-----CAUGUUGUUAUAGUAUUCCACCUACCCUGAUGU----ACUU
AANG01312935.1/2137-2218     AAGGAUCUUCAUUAAGGUGGGUGGAAUAGUAUAACAAUAUGC--UAAAUGUUGUUAUAGUAUCCCACCUACCCUGAUGU---AUCUU
AF201354.1/71-153            AAGGCUCUGCAUUAAGGUGGGUGGGAUAUUAUAACAAUAUCC--UCCAUGUUGUUAUAGUAUUCCACCUACCCUGAUGUU--UCCUU
BX324225.7/13605-13685       AGGGCUCACAGUUAAGGUGGGUGGAGUAGUAUAACAAUAUGC--CACGUGUUGUUAUGGUAUUCCACCUUCCCUGGCGU----GCCU
AF159274.1/262-338           AAGGCUCAGCAUUAGGGUGGGUGGAAUAAUAUAACAAUAUC-----CGUGUUGUUAUAGUAUUCCACCUACCCUGAUG-----CAUU
BAAF04035238.1/29072-29151   AAGGCUCUGCAUUAGGGUGGGUGGGAUAAUAUAACAAUCUC-----CAUGUUGUUAUAGUAUUCCACCCUCCCUGAUGUU--UCCUU
AAPY01592049.1/96-171        AGGCUCC-UCAUUAAGGUGGGUGGAAUAGUAUAACAAU--AG--CAC--GUUGUUAUAAUAUCCCACCUACCCUGAUGU----GUCU
BC168009.1/2484-2565         AACAAUCUCCAUUAGGGUGGGUGGAAUAGUAUAACAAUGUGC--UCAAUGUUGUUAUAGUAUCCCACCUACCCUGAUGU---AUAUU
ABPK01035929.1/509-423       AGGGUUCACAGUUAAGGUGGGUGGAAUAGUGUAACAAUAUGUUCUACGUGUUGUUAUGGUAUUCCACCUUCCCUGGUGUGCCGCCUU
AF166373.1/352-429           AAGGCUCAGCAUUAAGGUGGGUGGAAUAAUAUAACAAUAUC-----CGUGUUGUUAUAGUAUUCCACCUACCCUGAUGC----AUUU
AC144489.2/157878-157958     AAGGCUCAGCAUUAAGGUGGGUGGAAUAAUAUAACAAUAUCC--UCCAUGUUGUUAUAGUACUCCACCUACCCUGAUGU----CCCC
AAEX03003527.1/67523-67443   AGGGCUCCUCAUUAAGGUGGGUGGGAUAGUAUAACAAUGUCG--CGUGUGUUGUUAUAAUAUUCCACCUUCCCUGAUGG----CCCC
CAAB02000555.1/16686-16768   AAGGAUCCCCAUUAAGGUGGGUGGAAUAGUAUAACAAUGUGU--CCAAUGUUGUUAUAGUAUCCCACCUACCCUGAUGUA--GCUUU
#=GC SS_cons                 <<<<-----<<<<<-<<-<<<<<<<<<<-<<<<<<<<<<<__..___>>>>>>>>>>>->>>>>>>>>>->>->>>>>-....>>>>
#=GC RF                      agggcUCuuCauuAAGGUgGGUGGaaUAguaUAACAAuauau..uacaugUUGUUAuaGUAuuCCACCuuCCCUgauGu....cccu
//
# STOCKHOLM 1.0

#=GF AC   RF02096
#=GF ID   mir-2973
#=GF DE   mir-2973 microRNA precursor
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:21627805
#=GF SS   Published; PMID:21627805
#=GF GA   61.00
#=GF TC   61.00
#=GF NC   60.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.94 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   21627805
#=GF RT   Song exposure regulates known and novel microRNAs in the zebra finch
#=GF RT   auditory forebrain.
#=GF RA   Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB,
#=GF RA   Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S,
#=GF RA   Clayton DF
#=GF RL   BMC Genomics. 2011;12:277.
#=GF RN   [2]
#=GF RM   20360741
#=GF RT   The genome of a songbird.
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF WK   MicroRNA
#=GF SQ   7


AACV01021033.1/30811-30888 GACU-GCAUGGGAUAAUCGAUUAUCAUGUGCGCUCGGUAUAACUGGACCGCACGGGAUAAUCGAUUAUCCCAUGCAGUU
CR855037.1/53819-53896     GACC-GUACGGGAUAAUCGAUUAUCCCGUGCGAUCGGCAUAAAUCAACCGCACGGGAUAAUCGAUUAUCCCGUGCGGUU
AAAA02006271.1/2367-2444   GACC-GCAGGGGAUAAUCGAUUAUCCCGUGCGGUCGGGUUAUACGGACCACACGGGAUAAUCGAUUAUCCCGUGCGGUC
AC232156.1/17736-17659     AACC-GCACGGGAAGAUCGCUUAUCCCGUGCGGGCGGCUUAAGCGACCCGCACGGGAUAAGCGAUCUUCCCGUGCGGUC
FJ032633.1/123484-123407   GACC-ACACGGGAUAAACGAUUAUCCCGUGCAGUCGAGUUAAGUGGACCGCACGGGAUAAUCGAUUAUCCCGUGCGGUC
ABRL01002367.1/1543-1619   AACC-GCACGGGAUAAUC-AUUUUCCCGUGCGGUCGUGUUAAGUGGACCGCACGGGAUAAUCGAUUAUCCUGUGCGGUC
AC225085.1/31339-31416     GGCUCGCACGGGAUAAUGCAUUAUUCCGUGCGGGUGCUUAA-GCGGACCGCAUGGGAUAAUGCAUUAUCCCGUGCAGUC
#=GC SS_cons               <<<<.<<<<<<<<<<<<<<<<<<<<<<<<<<---<<_______>>---->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
#=GC RF                    gaCc.GCAcGGGAuaAucgaUUaUcCCGUGCGgucgguuUAAgcggACCGCACGGgAuAAucgaUuaUCCCgUGCgGuc
//
# STOCKHOLM 1.0

#=GF AC   RF02097
#=GF ID   mir-1662
#=GF DE   mir-1662 microRNA precursor
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:21627805
#=GF SS   Published; PMID:21627805
#=GF GA   65.00
#=GF TC   68.00
#=GF NC   57.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001244; pre_miRNA;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   21627805
#=GF RT   Song exposure regulates known and novel microRNAs in the zebra finch
#=GF RT   auditory forebrain.
#=GF RA   Gunaratne PH, Lin YC, Benham AL, Drnevich J, Coarfa C, Tennakoon JB,
#=GF RA   Creighton CJ, Kim JH, Milosavljevic A, Watson M, Griffiths-Jones S,
#=GF RA   Clayton DF
#=GF RL   BMC Genomics. 2011;12:277.
#=GF RN   [2]
#=GF RM   20360741
#=GF RT   The genome of a songbird.
#=GF RA   Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A,
#=GF RA   Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP,
#=GF RA   Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan
#=GF RA   CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J,
#=GF RA   Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B,
#=GF RA   Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin
#=GF RA   DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente
#=GF RA   XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer
#=GF RA   MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J,
#=GF RA   Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H,
#=GF RA   Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T,
#=GF RA   Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
#=GF RL   Nature. 2010;464:757-762.
#=GF WK   MicroRNA
#=GF SQ   2


ABQF01044481.1/14404-14339 UGGGCUUGACAUCAUCAUACUUGGGAUGUA---UGACACGAAGUCCCAAGCAGGCUGAUGUCAGGCCCA
AAWZ02017349.1/4059-4127   UGGGCUUGACAUCAUCCUACUUGAGAUGUAAUGUAAUGCAAAGUCCCAAGUAGGUUGAUGUCUGGCCCA
#=GC SS_cons               :<<<<<<<<<<<<<-<---<<<<<<<<_______________>>>>>>>>--->->>>>>>>>>>>>>:
#=GC RF                    UGGGCuuGACAUCAUCaUACUUGgGAuGUAAUGUaAuaCaAAgUCcCAAGuAGGuUGAUGUCagGCCCA
//
# STOCKHOLM 1.0

#=GF AC   RF02098
#=GF ID   DGCR5
#=GF DE   DiGeorge syndrome critical region gene 5 conserved region
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   60.10
#=GF NC   38.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.91 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   8659529
#=GF RT   Identification of a novel transcript disrupted by a balanced translocation
#=GF RT   associated with DiGeorge syndrome.
#=GF RA   Sutherland HF, Wadey R, McKie JM, Taylor C, Atif U, Johnstone KA, Halford
#=GF RA   S, Kim UJ, Goodship J, Baldini A, Scambler PJ
#=GF RL   Am J Hum Genet. 1996;59:23-31.
#=GF WK   DGCR5
#=GF SQ   4


AB051434.1/395-443       AUCUGUGACAAUUACUAAAAACUUCCCCAAAUAAAAAGGACAUGAAAAG
AANU01129535.1/7428-7476 AUCCAUGACAGUUACUAAAAACUUCCCCAAAUAAAAAGGACAUGAAAAG
ABRT010560813.1/698-746  CACCAUGCCAAUUACUAAAAACUUCUCAAAAUAAUAGGGACAUGAAAAG
AADA01164929.1/4214-4262 AUCCAUGACAAUUACUAAAACCUUUCCCAAAUAAAAAGGACAUGAAAAG
#=GC SS_cons             :::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  AUCCAUGACAAUUACUAAAAACUUCCCCAAAUAAAAAGGACAUGAAAAG
//
# STOCKHOLM 1.0

#=GF AC   RF02099
#=GF ID   rivX
#=GF DE   rivX sRNA
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:18005100
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   301.70
#=GF NC   51.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18005100
#=GF RT   RivR and the small RNA RivX: the missing links between the CovR regulatory
#=GF RT   cascade and the Mga regulon.
#=GF RA   Roberts SA, Scott JR
#=GF RL   Mol Microbiol. 2007;66:1506-1522.
#=GF WK   RivX_sRNA
#=GF SQ   2


CP000017.1/194056-193809 AGCCUUGCACCAGAACCACUACCAAAAACGUUUAGAAGAACUUUGGAGAGUUCCUUCUUAAUUUUUUGACAGUCCCUCCUAGAUACUUUCACAGUCUAGGAGGGUCUUUAAGGUUGUCACUUGCAACCUUGAUAAGCUCUCUUUUUAGCCAUUGCUAUUUGCUUAGAAACAGAACUGGAACUGUUAUAGCGGUUCAACUCCUCUUGUAGGAUCUUCUUCCCUUUUUUGAAGGUCUUAUCUGAAAUUUG
CP000262.1/193939-193692 AGCCUUGCACCAGAACCACUACCAAAAACGUUUAGAAGAACUUUGGAGAGUUCCUUCUUAAUUUUUUGACAGUCCCUCCUAGAUACUUUCACAGUCUAGGGGGGUCUUUAAGGUUGUCACUUGCAACCUUGAUAAGCUCUCUUUUUAACCAUUGCUAUUCGCCUAGAAACAGCACUGGAACUGUUUUAGCGGUUCAACUCCUCUUGUAGGAUCUUCUUCCCUUUUUUGAAGGUUUUAUCUGAAAUUUG
#=GC SS_cons             ::::::::::::{{{{{-{{{,,,,,,,,[[[[--[[[,,,,,,((((((((,,,,,,,,,,,,,,,,,,<<-<<<<<<<<<<<_________>>>>>>>>>>>->><<<<<<<<<<_____>>>>>>>>>>,,)))))))),,,<<<<____>>>>,,,,]]]--]]]],,<<<_______>>>,}}}-}}}}}------<<--<<<<<<<<<<<___________>>>>>>>>>>>-->>::::::
#=GC RF                  AGCCUUGCACCAGaaCCACuaCCAAAAACGuuuAGagGAACUUUgGaGaGuuCCUUCUUAAUUUUUUGACaGUCCCuCCuaGauACUUUCACAguCuaGGaGGGUCuuuaaGGuuGuCACUUgCaaCCuugaUAagCuCuCuUUUuagCCAUUGcuaUUuGCcuAGaaaCAGaaCUGGAACUGuuauaGCGGuuCAACUCCuCUUguaggauCuuCUUCCCUUUUUUGaaGgucuuauCUGaAAUUUG
//
# STOCKHOLM 1.0

#=GF AC   RF02100
#=GF ID   tfoR
#=GF DE   Translational regulator of tfoXVC
#=GF AU   Moore B; 0000-0002-4074-1933
#=GF SE   Published; PMID:21317321
#=GF SS   Predicted; WAR
#=GF GA   70.00
#=GF TC   80.10
#=GF NC   52.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   21317321
#=GF RT   Identification of a chitin-induced small RNA that regulates translation of
#=GF RT   the tfoX gene, encoding a positive regulator of natural competence in
#=GF RT   Vibrio cholerae.
#=GF RA   Yamamoto S, Izumiya H, Mitobe J, Morita M, Arakawa E, Ohnishi M, Watanabe
#=GF RA   H
#=GF RL   J Bacteriol. 2011;193:1953-1965.
#=GF WK   Sxy_5'_UTR_element
#=GF SQ   10


AAND01000024.1/44297-44397 AU---UCCAGAGGUGAUGUGGCUU-GCCAUAUCACUCCGGCAGCAAGCGAAGGUGUCAUUGGCACCCGUGGUAUAGUCCCCCCGGCUAUACCACGAUAUUUUUUU
ABCH01000040.1/28749-28650 AU---UCCAGAGGUGAUGUGGGUA-ACCGCAUCACUCCGGCAGCAAGCGAAGGUGUCAUUGGCACCCGCGGUAUGGUCCCCC-GGCUAUGCCGCGAAUUUUUUUU
ABGR01000010.1/15041-15138 UU---UCCAGAGAUGGCAUGGAAA---CAUGUCAAUC-GGCAGCAAGCGAAGGUGUCUUUUACACCCGUGGUACAGUCACCCCGGCCGUACCACGUUUUUUUAUU
ACCV01000112.1/51188-51285 AU---UCCAGAGGUGGCGCAUCCA----GCGUCACUCCGGCAGCAAGCGAAGGUGUCAUUGGCACCCGUGGUAUAGUCCCCCCGGCUAUACCACGAUAUUUUUUU
BA000031.2/890615-890517   AU---UCCAGAGGUGGCAUGGCAA---CAUGUCACUCCGGCAGCAAGCGAAGGUGUCAUUGACACCCGUGGUAUAGUCCCCCCGGCUAUACCACGAUAUUUUUUU
CP000020.2/917861-917758   AUUCUAAUAGAAGUAACAAGAAGU-AUCUUGUUACUUCGGCAGCAAGCGAAGGCGUCUUUGGCGCCCGUGGCGUAGUCCCCCCGGCUACGUCACGAUCUUUUUUU
FM178379.1/2430470-2430367 AUUCUAUAAGAGGAAACAAGAGAA-AUCUUACUUCCUCGGCAGCAAGCGAAGGUGCCUUUGGUACCCGUGGCGUCGUCCCCCCGGCGACGCCACGAUCUUUUUUU
CP002555.1/2072018-2072119 AU---UCCAGAGGUGGUAUGACCAUGUCAUACCACUCCGGCAGCAAGCGAAGGUGUCGUUGACACCCGUGGUAUAGUCCCCCCGGCUAUACCACGAUAUUUUUUU
AE016795.3/135127-135228   AU---UCCAGAGGUGACGUGACGAUGUCGCGUCACUCCGGCAGCAAGCGAAGGUGUCAUUGACACCCGUGGUAUAGUCCCCCCGGCUAUACCACGAUAUUUUUUU
AB598400.1/1-102           AU---UCCAGAGGUGGUAUGACCAUGUCAUACCACUCCGGCAGCAAGCGAAGGUGUCGUUGACACCCGUGGUAUAGUCCCCCCGGCUAUACCACGAUAUUUUUUU
#=GC SS_cons               ::...::::::<<<<<<<<<<___._>>>>>>>>>>,,,<<_____>>,,,<<<<<<___>>>>>><<<<<<<<<<<<_____>>>>>>>>>>>>::::::::::
#=GC RF                    AU...uccAGAgguggcgcGgaaa.acCgcgccacccCGGCAGCAAGCGAAGGuGccaUUggCaCCCGuGGcgugGuCcCCCCGgCcacgCCaCGAUaUUUUuUU
//
# STOCKHOLM 1.0

#=GF AC   RF02101
#=GF ID   HULC
#=GF DE   Highly up-regulated in liver cancer conserved region
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   45.00
#=GF TC   47.40
#=GF NC   44.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005840; ribosome;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   17241883
#=GF RT   Characterization of HULC, a novel gene with striking up-regulation in
#=GF RT   hepatocellular carcinoma, as noncoding RNA.
#=GF RA   Panzitt K, Tschernatsch MM, Guelly C, Moustafa T, Stradner M, Strohmaier
#=GF RA   HM, Buck CR, Denk H, Schroeder R, Trauner M, Zatloukal K
#=GF RL   Gastroenterology. 2007;132:330-342.
#=GF WK   HULC_(gene)
#=GF SQ   19


AL161437.13/445-684          UCUUUGGAAGAAACUCUG-AAGUA-AAGGCCGGAAUAUUCUUUGUUUAAAACAUUAAAA--ACAAAACAGACCAAAGCAUCAAGCAAG----AAGUUUCCUGGCAAUAAACUAAGCACAGCAUUAUUUUUU-AAGGAACACAAAUUAAGUGUUCAACCUGUGGCAAAUUUGUACUUUCUCCCUGAAUUAUGUUGUUAUCAAAGAAAAAAA--UUGGGAAGCA-UGGCAAAAUAUCAUCAAAACUGAAACUAG
AANU01226948.1/923-684       UCUUUGGAAGAAACUC-G-AAGUA-AAGGCGAGAAGAUUCUUUGUUUAAAACAUUAAAA--ACAAAACAGACCAAAACAUCAAGCAAG----ACGUUUUCUGGCAAUAAACUAAGCACAGCAUUAUUUUUU-AAGGAAUACAAACUAAAUGUUCAACCUGUGGCAAAUUUGUACUUUCUCCCUGAAUUAUGUUGUUAUCAAAGAAAAAAA--AUGGAAAAGGCUGGUGAAAUAUCAUCAAAACUGAAACUAG
ABRT010046075.1/361-594      GCUUUGGAAGAAAUUCUG-AAGU--AA-------AGAUUCCUCAUUUAAAAAAUUUAAA--ACAAAACAAGCAAAAAUAUCAAACAGG----AAGUUUUGUGGCAAUGAACUAAAUACAGAUUUUUUUUUUUAAGGAAACCAAAUUAAGUCUAAAACCUGUGGCAAAUUUGUACUUUCUCCUUAAAUUACAUUGCUUUCAAAGAAAAUGU--UUGAAAAGGACUGGUAAAUCAUUAUCAAAACUGAAAUGGG
ABVD01293866.1/2401-2616     ACUUUGGAAGAGACCCCA-AAGUAAAAGGUAAGAGGACUCUUUGUUUAAAACAUUAAAA--AAAAAA---------AAGUCAAGCAAG----AAAUUUUGUGGCAACAAUCUAAGCUCAGAGUUA-CUUAU-AAGGAAUAUAAAUAAAG--UUCAACCUGUGGCAAAUUUGCACUUUCUCCUUGAACUAUGUUGCUCUCAAAGAAAAAGG--UUUGAAAGG--------------AUCAAAACUAAAACUAG
AAPY01273060.1/1078-1311     GCUUUAAAAGAAAACCUG-GAGUA-AAGAUGAGAAAAUGCUUUGUGUGGAACAUUAAAC--AUAAAACAGAGAAAAAAAUCAAACAGG----AUGUUCUGUGGUAACAAACGAAACA--CAGUUAUUUUUC-AAGGAACAUGAAUUAACUACUCCAU----GGCAAGU-UGUACUUUCUUGGUGAAUUAUGUUGCUCUCUAAGAACAGGG--UUGGAAAGAACUGAUUAAAUACCAUCGAAACCAAAAUUAG
AAWR02009544.1/222632-222856 GCUUAGGAAGACACUCUG-AAGAA-UAGGGGAGAAGAUUUUUUGCUUAAAACGUUAAAA--ACAACAA-------AAGACAAGUCAAG----ACGUUUUAUGGCAACAGACUAAACACAUAGUUAUUUUCU-AAGGAAAACACAUU--GUGUUCAAU-------GUCUUUGUACUUCCUCCUUGAAUUAUAUUGCUUGCAAAGAACAAGG--UUUGAAAGGACUAAUCAAACACCAUCAAAACUAAUACUAG
ABRR01028187.1/731-956       GCUUUGGAAGACACCCUG-AAGUA-UAAGCAAGAAGAUUCUUUGCUUAAAACGUUAAAA--CCACCACUGCCACCAAAAACAACAAAA--------CCCAAGUCAAGAAGUCA---GCAGAGUUAUUUUUU-AUGAAACACAAAUUAAGUGUUCCAC-------UUGUUUGCACUUGCUAUUUGAAUUAUGCUGCUUGC-AAGAAAAAAG--UUUGAAAGGAUGAAUAAAACACCAUCAAAACUGAAACUAG
ABRP01201152.1/5635-5867     GCACUAGAAGACACACUA-AACUA-UAGGUGAGAAGAUGCUUU-CUUAAAACAUUAAAA--AUAACAACAAGAACAACUCAAGUCAAGCAGGAAGUUUUAUGUCAACAAACUA-GUGCACAAUUAUAUUUU-AAGGAUUAUGAAUUAAGUGUGCAAC-------UUGUUUGUACUUUCUUCUUGAACUAUGUUGCUUAUGAAGAAAAAGG--UUUGAAAGGACUAAUAC---AUCAUCAAAACUAAAACUAG
AAGV020064911.1/1681-1901    GCUUUGGAAGAGACCCUG-AAGUAGAAGGUGAAAGGACUCUUUGUUUAAAACUUUUUUU------UUUUUUUUUUAAUGUCAAGCUAG----AAGUUUUGUGACAACAAACUAAGCUCACAGUUAGUUUUU-AAGGAAUAUAAAUGAAG--UUCAGC-UAUAGCAAAUUUGCACUCUUUCCGUGAAUUAAGUUGCUCUCAAAGAAAAAGG--AUCGAAAGG--------------AUUAAAACUAAAACUAG
AACN010057538.1/2469-2677    GCUUUGGAAGACACUCUG-AAGUA-AAGGUGAGAAG-UUCUUUGUUCGAAAUGUUAACA--ACAGCUGUGGCC------CUAGACAAG----------CAAAUGAAG----------CAUAGUUAUUUUUU-AAAGAACACAAUUUAAAUGUUCAAA-----------CUGCACCUUUCCCUUGAAUUAUGUUGCUCACAAAGAAAAAAAAAUUUGAAAGGAUUGAUAAAACACCAUCAAAACAAAAUCGAG
AANG01350834.1/626-828       GCUUUGGGAGACACCUUG-AAGGA-AAGGUGAC----UUCUUUGUUUGAAAC--UAACA--ACCAUC---------ACAUGAGACAAA----------CAAAUUAAG----------UACAGUUAUUUUUC-AAAGAACACAAAUUAAGUGUUCGAA-------GAGUUUGCACUUUCUCCUUGCAUUGUGUUGCUCAUGAAGAAAGAAG--UUUGAAAGGAUGGAUAAAACACCAUCAGAACAAAAGCUGG
AAKN02037029.1/25847-26080   AUUUUAAAAGAAGGUGUG-GAGU--AAUAUGAAAAGUUGUUUUGUUUAAAAUGUUUUUA--A--AAACUAAUCAAAGUUUUGGCAAAA----AA--UUUGUGGUAACAAUAUAAUUCCAGAGUUAUUUCUU-AAGUUGCAGAAAUUAAGUGUUCAACCUGUGGCAAACUUAUAUUUUUCCCUUAUAUUAUUUUGCGUUAGAAGGAGAAAG--UUGAAAAGG-CAAAUCAAACACCAUUAAAACUAAACUAA-
ABRQ01105875.1/420-634       ACUUUAGACGGGGCC-UG-AAGAA-AAGGUGAGAGGAC--UGUGUUUGAAGUAGUGAUU--U--------------AAGUAUAUCAAA----GAGUUUCAUG-CAGCAAACUAAGCACUGAGUUAUUUUUU-AAGGAACAGAAA------GUUCAGCUUGUUGCAAGUUUGCCCUUUCUUCUUCAGUUGGAUAAUUUUCAAAGCAAAAGC--CUUGAAAGGACUGA--AGGUACCACCAGAACUAAAACUAG
AAYZ01260466.1/2937-3157     GCUUUGGGCGAAAUUCUGCAAGG--GAAGUGAGAAGAUCCUCCAUUUUGCUCAUCAAAC--A--------------AAGCAUGCAAAC----AA----UGUGGCCAUCACCAAAGCACAGGAAUAUAAUUU-ACAGCAUGUAAACUG-UCGUUCAACCUGUAUCAAGUUUUCAUAUUCCGUUUGAAUAACUUUGUUCUCAAAGGAAAGA---ACAGAAAAGACUCAUGAAACACUGCCAGUACUUAACAUUG
AAQR03055378.1/13227-13451   GCUUUGGAAGAAACUCUA-AAGUC-AAAGUGGAAAGGU--UGGGUUGUGAACAUUAAAA--AUGAA-----CAAGAAACUCAAGCAAG----AGGUUCUGUGACAGUAGACUAAGUAUGCAGUUAUUUUUU-AAGGAACACGAAUUAAGCAUUCCAUCUGUGGAAAAUGUGUACUUUCUCACUGCGUUAUGUCGCUCUUCAAGAAAAAGG--CUGGA--UG-------AAACACCACCCAAACUGAAACUGG
AAGU03069309.1/56454-56676   GCCUUAGAAAGCACCCUC-AGGUC-AAGGUGGGAGGACUCUUUGUUUAAAAUACUUAC------------------ACGUAUAGCAAA----AAAGUUCAUGGCAACAAGCUAAGCACCAAGUUAUUUUUU-AAGGCACACAAAUUAAGUGUUCAAUCUGUGGCGGAUUUGUACUUCCUUUCUGAAUUGUAUUGUUCUCAGAGAAAAACG--UUUGAAAGCACCGA--AAGCACCAUCAGAACUGAAACAAG
AAPE02025580.1/188146-187923 ACAUUGGAAGACCC--UG-AAGUG-UAGGUGAGAAGAUGCUUUGCUUCAGUCAUCACAAUGACAACAACGAUAGUAACUCAAGUCAAGCAAGAAGUUU-AUGUCAACAAACUAAGAACAGAGUUGUUUUUU-AAGAAUCA-------------CAAC-------UUAUUUGCACUUUCUUCUUGAAUUAUGAUGCUUGCAAAGAGCAAGG--UUUGAAAGGACUAAUACUACAUUACCAAAAUUAAGACUAG
AAGW02052255.1/90529-90295   GCCUUGGAAGAAAUCCUG-AAGA--AAGGUGAGAAGAUUCUUUGUUUUACACAUUAAAC--ACAAAAC--------AAACCAACCGAGUGAGAGUUGCCAUGGCAAUAAUGGAAGUAUGGCAUUGUUUUUU-AAGGCACACAAUUUAAGUGUUCAGUUUGUCACAAGUUUUUACCUUCUUUUUGAAUAAUGCUGUUCUCAAGGAAAAUA---UUGGAAAGGACUCAUAAAACACUAUCAGUAUUUAAACUGA
AY914050.1/196-435           UCUUUGGAAGAAACUCUG-AAGUA-AAGGCCGGAAUAUUCUUUGUUUAAAACAUUAAAA--ACAAAACAGACCAAAGCAUCAAGCAAG----AAGUUUCCUGGCAAUAAACUAAGCACAGCAUUAUUUUUU-AAGGAACACAAAUUAAGUGUUCAACCUGUGGCAAAUUUGUACUUUCUCCCUGAAUUAUGUUGUUAUCAAAGAAAAAAA--UUGGGAAGCA-UGGCAAAAUAUCAUCAAAACUGAAACUAG
#=GC SS_cons                 ::::::::::::::::::.:::::.::::::::::::::::::::::::::::::::::..:::::::::::::::::::::::::::....:::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..::::::::::::::::::::::::::::::::::::::::
#=GC RF                      gCUUUGGAAGAaacuCUG.AAGua.aAGGUGAGAAGAUuCUUUGUUUaAaacaUUaaaa..AcaaaacugacaaaAAaaucaagCAAg....AaGUUUugUGgCAAcaAacuAAGcaCagaGUUaUUUUUU.AAGGaacAcAAAUUAAGUGUUCaAcCUGUgGCaagUUUGuACUUUCUccuUGAAUUAugUUGcUcuCaAAGaAaAagg..uUuGAAAGGACugAUaAAaCACCAUCAaAACUaAAacuaG
//
# STOCKHOLM 1.0

#=GF AC   RF02102
#=GF ID   DISC2
#=GF DE   Disrupted in schizophrenia 2 conserved region
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   100.00
#=GF TC   100.80
#=GF NC   83.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 45.21 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   10814723
#=GF RT   Disruption of two novel genes by a translocation co-segregating with
#=GF RT   schizophrenia.
#=GF RA   Millar JK, Wilson-Annan JC, Anderson S, Christie S, Taylor MS, Semple CA,
#=GF RA   Devon RS, St Clair DM, Muir WJ, Blackwood DH, Porteous DJ
#=GF RL   Hum Mol Genet. 2000;9:1415-1423.
#=GF WK   DISC2
#=GF SQ   5


AC202673.8/78875-79075   AAGCUAUAACCUAUUUCCUAAAGUUGUGAUGACAUUCAAAGGUGAGAAAGUUUGUAGCUAUUAUUGUGAUUAUAGUUACUAUAAAUUCUUAGAAAACAUAGUGGGGUUUUCUAAC--------ACUA--AUUUGUGGGGCACUCAUUAAUGUUAUAUAUUUAGUAAUUUAUUGUUCAGUGUUCAUACUUUAAAAUUUCCUAAUUUUUCCUC
AF222981.1/9966-9762     AAGAUAUAACCUGUUUCCUAAAGUUGUGAUGACAUUUAAAGGUGAGAAAGUUUGUAGCUAUUAUUGUGAUUAUGGUUACUAUAAAUUCUGAGAAAACACAGUGGGGUUUUCUAAUUAACACUAACUA--AUUUAUGGGACACUCAUUAAUGUUAUAUAUUUA----UUUAUUGUUCAAUGUUCAUGCUUAAAAAUUUCUUAAUUUUUCCUC
AF222983.1/2009-2213     AAGAUAUAACCUGUUUCCUAAAGUUGUGAUGACAUUUAAAGGUGAGAAAGUUUGUAGCUAUUAUUGUGAUUAUGGUUACUAUAAAUUCUGAGAAAACACAGUGGGGUUUUCUAAUUAACACUAACUA--AUUUAUGGGACACUCAUUAAUGUUAUAUAUUUA----UUUAUUGUUCAAUGUUCAUGCUUAAAAAUUUCUUAAUUUUUCCUC
AF222987.1/23235-23439   AAGAUAUAACCUGUUUCCUAAAGUUGUGAUGACAUUUAAAGGUGAGAAAGUUUGUAGCUAUUAUUGUGAUUAUGGUUACUAUAAAUUCUGAGAAAACACAGUGGGGUUUUCUAAUUAACACUAACUA--AUUUAUGGGACACUCAUUAAUGUUAUAUAUUUA----UUUAUUGUUCAAUGUUCAUGCUUAAAAAUUUCUUAAUUUUUCCUC
ABDC01061326.1/9612-9811 AAGGUUUAAAUCUAUUAUUAUUGUUGU--UGUUAUUAGCAGAAG-------UAGUAGCUAUUUUUGUGAUUAUGGUUACAAUAAAUUCUUAGAAAACAUAGUGGAGCCCUUUAGU-AACAGUAACUAUCAUUUAUGGGGCACUCUUUAAUGUGAUAUAUCUAUUAAUUUAUGGUUUAAUUUUCAUAUAUACA-UUUUUCUAAUUCCCCCCC
#=GC SS_cons             :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..:::::::::::::::::::::::::::::::::....:::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  AAGaUaUAAccuguUUccUAaaGUUGUGAUGacAUUuaaAGguGAGAAAGUUuGUAGCUAUUaUUGUGAUUAUGGUUACuAUAAAUUCUgAGAAAACAcAGUGGgGuuuUcUAauuAACAcUAACUA..AUUUaUGGGgCACUCaUUAAUGUuAUAUAUuUA....UUUAUuGUUcAaUgUUCAUgcuUaaAAaUUUcuUAAUUuuuCCuC
//
# STOCKHOLM 1.0

#=GF AC   RF02103
#=GF ID   DLEU1_1
#=GF DE   Deleted in lymphocytic leukemia 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   30.00
#=GF TC   30.10
#=GF NC   29.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.65 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9395242
#=GF RT   Cloning of two candidate tumor suppressor genes within a 10 kb region on
#=GF RT   chromosome 13q14, frequently deleted in chronic lymphocytic leukemia.
#=GF RA   Liu Y, Corcoran M, Rasool O, Ivanova G, Ibbotson R, Grander D, Iyengar A,
#=GF RA   Baranova A, Kashuba V, Merup M, Wu X, Gardiner A, Mullenbach R, Poltaraus
#=GF RA   A, Hultstrom AL, Juliusson G, Chapman R, Tiller M, Cotter F, Gahrton G,
#=GF RA   Yankovsky N, Zabarovsky E, Einhorn S, Oscier D
#=GF RL   Oncogene. 1997;15:2463-2473.
#=GF WK   DLEU1
#=GF SQ   26


AL137060.13/75754-75943    -UGUGGGGCCGAGGG--GUCGUCUUAUAGC--UACC--AG-CCCACA--GGCA-UUUA--GUCUAC-GUUGGAGGUAAACAA-AUACGG----GUCCUG-CUUAGGAGA-AAAG-AAAAACGUCUUACAGCCAGUGUCUAAACUCCAAACAACGGAAUGUAUCAA-UGAGACCUUGUAU-----AUGGAUACACGUGCAU-UUAAAACCGCCCUGCCGG
AF328925.1/7723-7913       -UGUGGGGCCGAGGG--GUCGUCUUAUAGC--UACC--AG-CCCACA--GGCG-UUUA--GUCUAC-GUUGGAGGUAAACAA-AUACGG----GUCCUG-CUUAGGAGA-AAAGAAAAAACGUCUUACAGCCAGUGUCUAAACUCCAAACAACGGAAUGUAUCAA-UGAGACCUUGUAU-----AUGGAUACACGUGCAU-UUAAAACCGCCCUGCCGG
AF279660.2/85239-85428     -UGUGGGGCCGAGGG--GUCGUCUUAUAGC--UACC--AG-CCCACA--GGCA-UUUA--GUCUAC-GUUGGAGGUAAACAA-AUACGG----GUCCUG-CUUAGGAGA-AAAG-AAAAACGUCUUACAGCCAGUGUCUAAACUCCAAACAACGGAAUGUAUCAA-UGAGACCUAGUAU-----AUGGAUACACGUGCAU-UUAAAACCGCCCUGCCGG
AANU01125899.1/6146-6334   -UGUGGGGCCGAGGG--ACCA-CUUAUAGC--UAUC--AG-CCCACA--GGCA-UUUA--GUCUAC-GUUGGAGGUAAACAA-AUACGG----GUCCAG-CUUAGGAGA-AAAG-AAAAACGUCUUACAGCCAGUGUCUAAACUCCAGACAACGGAAUGUAUCAA-UGAGACCUUGCAU-----AUGGAUACACGUGCAU-UUAAAACGGCCCCGCCGG
ABGA01025383.1/17459-17652 -GUUGGGGCCAAGGGGUCCCU-CUUAUAGC--UAUC--AGCCCCACA--GGCA-UUUA--GUCUACGUUGGAGGGUAAACAA-AUACGG----GUCCAGCCUUAGGAGA-AAAC-AAAAACGUCUUACAGCCAGUGUCUAAACUCCAAACAACGGAAUGUAUCAA-UGAGACCUUGUAU-----AUGGAUACACGUGCAU-UUAAAACCGCCCUGCCGG
ABRR01275127.1/8632-8444   -UGCGGGCCCGAGGG--UCCA-UAGAUGAC-ACAUC--AG-UCGGUA--GGCA-UUUA--UUCUACUGUUCAAGGAAAACAA-AUAAGG----GUGCAG-CUUAGGCAA-AAAG-AAAAACAUAUUAUUGCCAGUGUCUAAACUCCUAACAACGGAAUGUG--UC-UGAGACCGUGUGU-----AUGGAUACAUGUGUAC-UUAAAACAGCUCCGCCGG
AAWR02010525.1/12600-12411 -UGCGGGCCCUAGGG--UCCA-CAGAUGAC-AUAUC--AG-UCGAUA--GGCA-UGCA---UUUACUGUUCGAGGGAAACAA-AUAAGG----GUGCAG-CUUAGGCGA-AAAG-AAAAUCGUCUUAUUGCCAGUGUCUAAACUCCUAACGACGGAAUGUGUCUC-UGAGACUAUGAGU-----GUGGAUACACGUGUAC-UUAAAACAGCCCCGCCUG
ABRN01179174.1/5846-5662   -UGUGGGCCCGAGGG--UCCG-UAGAUGAC-GUAUC--AG-UCGAUA--GGCA-UUUA--UUCUACUGUUCAAGGAAAACAA-AUAAGG----GUGCAG-CUUAGGCGA-AAAG-AAAAACAUCUUAUUGCCAGUGUCUAAACUC----CAACGGAAUGUG--UC-UGAGACCGUGUGU-----AUGGAUACACGUGUAC-UUGAAUCAACCCCGCCUG
AANG01107290.1/887-1073    -UGUGGGCCCGAGGG--UCCA-UAGAUGAC-UUGUC--AG-UCGAUC--GGCA--UUA--UUUUACUGUUCGAGGAAAACAA-AUAUGG----GUGCAG-CCUAGACGA-AAAG-AAAAACGUUUUAUUGCCAGUGUCUAAA---CUAACAACGGACUGUGUCUC-UGAGACCCUGUGU-----AUGGAUACACGUGUAC-UUAAAACAGCCCCGCCUG
ABRT010201399.1/4796-4613  -UGUGGGCCCGAGGA--UGCA-CAGAUAUC--UAGCAGAG-UCGACA--GGCA-UUUA--GUCUACUGUUCGAGGUCAACAA-AUAAAG----GUCCAG-UUUCGGCGA-AAAU-AAAAAUGUCUUAUAGCCAGUGUCUAUACUGCAAACAACGG--------UC-UGAGUCCAUGGGU-----AGGGAUACACGUGCAC-UUAAAACAGUCCCACCAG
AAPY01162169.1/688-499     -UCUGAGCCCGAAGG--UCCG-GAGAUAUG--UGUC--AG-UUGACA--GGCA-UUUA--GCCUGUUAUUUGAAGUAGACAA-GUAACG----GUCCAG-CUUAGGCUA-AAAG-AAGAACGUGUUACAUCUAGUGUCUAAACUUCAAACAACGAAAUAUAUUUC-UGAGACCUUGUGU-----AGAGACACACAUGUCC-UUCAAACAGCCCCACCAG
AAFC03089644.1/11022-11212 -UGUGGGCCUGAGGG--UCCA-UAGGUGACAUUAUC--AG-UCGGUA--GACA-UUUA--UUCUACUGUUCGACGAAAACAA-ACAGGG----GUACAG-CUUAGGUGA-AAAG-AGAAACAGCUUAUUGCCAGGGUCUAAACUCCUAACAACGGAAUGUG--UC-UGGGAGCGUGUGU-----AUGGAUACACGUGUACUUUAGAGCAGCCCCGCCUG
AAQQ01377439.1/198-377     -UGUGGGCCCGAGAG--UCCA-CAGAUGCU--UGUC--AG-GAGACA--GGCA-GUCA--GUCUACCGUUGGAGGUAAACAA-AUUAGG----GUACAG-CUUAGGCUA-GAAG-AAAAACGUCCUG----------CUAAACUACGGACAACGGAAUGUGCCUCUUGAGAUCAUGUGU------UGGAUACACGUGUUC-UUAAAACAGCCCCGCCGC
AAYZ01196145.1/2396-2213   -UGUGGGCCUAAAAG--CCUA-CAUCUACC--UAUU--GG-CUGACA--UGCA-UUUA--GUAUACCGUUCAAGGUAAAUCA-AGGAUU----GUCCAA-CUUAGGCAG-AAUG-AAUUAUAUGUUACAGCCAGUAUCUAAACUCCAGAU--CAGAAUG----CC-UAAGACCAUGUUU-----AUGGAUAUUUGUGUGC-AUAAAACAGCCCUGCCAG
ABRQ01105888.1/3782-3593   -UGUGAGCCCGAGGG--UCCA-CAAGUCCC-GUACC--UA-CAAACGUUGACA-CUUA--AUCCACUGUUCGAGGUAAACAA-ACAAGGAAGAGUUCAG-C-UAAGCGA-AAAG-AAAAAUA------AGCCAGUGCCUAAAAUCCAAAGAGCGGAAUUUGUCCG-UCAGACCUUGUGU-----ACGGAUACACGUGUAC-UUACAACAGCUCCGAAGU
AANN01750438.1/583-765     -UUUGGGACUGUAGG--UCCU-UAGG------UGUC--AG-UCGAUA--UGCA-UUGA--UUCUUCUGCUUGGGAAAAAGAA-ACAAGG----GCCCAU-CUUAGACGA-AAAA-AAAACCAUCUCACCGUCAGUG---AAAUUCCUAGCCCCAGACUGUGUUUC-UGAGACCCUGUAC-----AUUGAAACACGUGUCC-UUAAAGCAGUCCUGCUUG
AAKN02011212.1/4481-4659   UUGCUGGCCAUAAAC--UCCA-CAAAUACC--UAUC--AG-ACUACA--GGCA-UUUA--AUCUACAGUUGAAGGUAAACAAAACUGGG----GUCUAG-UUUAGGCGA-AAAG----AACGUUUUACA----------AAACUCCAAACCACCGGAUGUGCCUC-UGAAAACAUGUGC-----CUGGACACACAAGUGC-GUAAAACAACCCGCCAGU
AAGV020803108.1/703-526    CUUUGGGCCCAAGGG--UCUA-CAGAGAGU--UAUC--AA-AGGAAA--AGCU-UUUAUUUUCUAUUGUGCAAGGUAAGCAA-AAAAGG----AUCCAG-CUUAGGUAA-AAAG-AAACAUGUCUUACAGCCAGAGUUUACACUCCAUAAAAUGGAGUAUGUUCU---------------------GAGUCCAGGUGAAC-UCACCACAGCCUCACAAG
ABVD01165160.1/1603-1433   -UGUGGACCCGGGGG--UCUG-CAGACACU--UAUC--AA-UGCAUA--GGCAUUUUU--UUCUGCAGUGCGAGAUAAACAA------G----GUCCAG-CUUAGGCGA-AAAG-AGAAACGUCUUACAGGCAGCAUCUACACUCCAGACAACGGAGCGUGUUCU---------------------GAGUCCACGUUAAG-UCACCAGGCCCCCGCUGG
ABRP01194832.1/157-11      -UGUGGGCCCGAGGG--UCCA-UAGAUGACGUUAUC--AG-UUCAUA--GGCA-UUUA--GUCUGGUGUUCGAGGAAAACAA-----GG----GUGCAG-CUUAAGCGA-AAAG-AAAAACGUCUUAUUGCUAGUGUCUAAACUCAUAACAGCAGAAUG------------------------------------------------UGUUCCGACUAU
AAQR03165215.1/8415-8248   -CGUGGGCUUGAGGG--UGCG-CAAACACC--UAUC--AA-UUGGCA--GGUA-UUUA--GUAUACUCCUGGAGGUAAACAA------G----AUACUC-CUGGAGCUC-CAGA-GGAAAACUCUUACAGCCUUUGUCUAAAUUCCCAACGAGGGAAUGUGUCUU-CAGACGCUUGUA-----------------------UUAAAACGGCCCCACCAG
AAPE02005599.1/22162-22354 -UGUGGGCCUGAAGG--UCCA-UAGACGAU-AUAUC--AG-UCUAUA--AGCA-UUUA--GUCUACUGUUCGAGGAAAACAG-AUAAGG----GUGCAG-CUUAAGCGA-AAAG-AAAAAUGUCUUAUUGCCAGUGUCUAAA---CCAACAACGGAAUGUGUCUC-CGAGACCAUCUAUAUUGGAUGGACACACGCGUAC-UUAAAACAACCCGGCCUG
AAEX03013095.1/15931-15739 -UGCGGGGACCCGGG--GCCG-CGGGGGGGCCUGUC--AG-CCGAUG--CGCG-CUGA--UCCUACUGUCCGGGGAAAGCAAAACGGGG----GUGCAG-CUUGGGCGGAAAAG-AAAACCGCUCGGUGGGCAGGGGCUGACCUCCCGAGUGCGGAGUGGGUCUC-UAACACCCGGUGG------GCGCUACACGUGUGC-UUAGGGCAGCCCCGCCCG
AJ412038.1/125-314         -UGUGGGGCCGAGGG-GUCGU-CUUAUAGC--UACC--AG-CCCACA--GGCA-UUUA--GUCUAC-GUUGGAGGUAAACAA-AUACGG----GUCCUG-CUUAGGAGA-AAAG-AAAAACGUCUUACAGCCAGUGUCUAAACUCCAAACAACGGAAUGUAUCAA-UGAGACCUUGUAU-----AUGGAUACACGUGCAU-UUAAAACCGCCCUGCCGG
Y15227.1/125-315           -UGUGGGGCCGAGGG-GUCGU-CUUAUAGC--UACC--AG-CCCACA--GGCA-UUUA--GUCUACGUUGGGAGGUAAACAA-AUACGG----GUCCUG-CUUAGGAGA-AAAG-AAAAACGUCUUACAGCCAGUGUCUAAACUCCAAACAACGGAAUGUAUCAA-UGAGACCUUGUAU-----AUGGAUACACGUGCAU-UUAAAACCGCCCUGCCGG
AF440619.1/132942-133131   -UGUGGGGCCGAGGG-GUCGU-CUUAUAGC--UACC--AG-CCCACA--GGCA-UUUA--GUCUAC-GUUGGAGGUAAACAA-AUACGG----GUCCUG-CUUAGGAGA-AAAG-AAAAACGUCUUACAGCCAGUGUCUAAACUCCAAACAACGGAAUGUAUCAA-UGAGACCUNGUAU-----AUGGAUACACGUGCAU-UUAAAACCGCCCUGCCGG
#=GC SS_cons               .::::::::::::::..::::.::::::::..::::..::.::::::..::::.::::..::::::::::::::::::::::.::::::....::::::.:::::::::.::::.::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::.....::::::::::::::::.::::::::::::::::::
#=GC RF                    .UGUGGGcCcgaGGG..uCCa.cagauagc..UAUC..AG.ucgAcA..gGCA.UUUA..gUCUaCuGUucGAGGuAAACAA.AuaaGG....GUcCAG.CUUaGGcGa.AAAG.AAAAAcGUcUUAcaGCCAGuGUCUAAACUCCaaAcaaCGGAaUGUGUCuc.UGAGAcCuUGUgu.....auGGaUACACGUGuac.UUAaaACaGCCCcGCcgG
//
# STOCKHOLM 1.0

#=GF AC   RF02104
#=GF ID   DLEU1_2
#=GF DE   Deleted in lymphocytic leukemia 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   100.00
#=GF TC   100.00
#=GF NC   83.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.10 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9395242
#=GF RT   Cloning of two candidate tumor suppressor genes within a 10 kb region on
#=GF RT   chromosome 13q14, frequently deleted in chronic lymphocytic leukemia.
#=GF RA   Liu Y, Corcoran M, Rasool O, Ivanova G, Ibbotson R, Grander D, Iyengar A,
#=GF RA   Baranova A, Kashuba V, Merup M, Wu X, Gardiner A, Mullenbach R, Poltaraus
#=GF RA   A, Hultstrom AL, Juliusson G, Chapman R, Tiller M, Cotter F, Gahrton G,
#=GF RA   Yankovsky N, Zabarovsky E, Einhorn S, Oscier D
#=GF RL   Oncogene. 1997;15:2463-2473.
#=GF WK   DLEU1
#=GF SQ   16


AL137060.13/98292-98633    AAAAGGAGACAGAAGAUUGAAGCCU---UUGCCAGCCAUUCUUUCCCUUUUUGCU-UCCAAACUCCUCAACUGGGAACCUUCAUAUGUGCAGUA-----UUUAUAUUGGAUCAUACUGGUGAUUAUAAAAGUU--CCUAGGAGGCUAGAAGA-GCCAACC-AACA---GAGAAGGGAAAGCAGUCUGUUCUGA-ACAUAGGGACAUA---AGUUCAUUC--AUGCCAAGUAUCUUUCCAGCAUGUUUC-----UC-CCAUUUAGAAU---AUCUAGCAUGUAAGGCCUUUCAAUAUUAAUAUAAGCCCAAUAUCAGCUCUUU-CUCUUUGUAUUUCAUCUCUUUCUACUCUCCUAUUUGUAUU-UUGUGUUCCUA
AF279660.2/107776-108117   AAAAGGAGACAGAAGAUUGAAGCCU---UUGCCAGCCAUUCUUUCCCUUUUUGCU-UCCAAACUCCUCAACUGGGAACCUUCAUAUGUGCAGUA-----UUUAUAUUGGAUCAUACUGGUGAUUAUAAAAGUU--CCUAGGAGGCUAGAAGA-GCCAACC-AACA---GAGAAGGGAAAGCAGUCUGUUCUGA-ACAUAGGGACAUA---AGUUCAUUC--AUGCCAAGUAUCUUUCCAGCAUGUUUC-----UC-CCAUUUAGAAU---AUCUAGCAUGUAAGGCCUUUCAAUAUUAAUAUAAGCCCAAUAUCAGCUCUUU-CUCUUUGUAUUUCAUCUCUUUCUACUCUCCUAUUUGUAUU-UUGUGUUCCUA
ABRT010980224.1/1025-690   AAAAGGAGACAGAAGAUUGAAGCUC---UUGCUAGCCAUUCAUUUCCUUUUUGCUCUCUACCCACCUCACCUGGGAACCUUUAUCUGUGCAAUA-----UGUGUACUGUGUCACACUGGUGAUUAUAAUGGAG--GCUAGGAG---------UGCUGACC-AAC-----AGAGAGGAAAGCAGU--GUUAUGA-CUGUAGUGACAUA-GGAGUUCAGUU-CACACCAAACAUCUUUCAAGCAUGUUUCCAGUUUCUCCAUUUAGAAA-CAUCCUAGCACUUACAGCCUUUCAGU------ACAAGCCCAAUACUAGCUUUUU-CCAUUUGUAUUUCAUUUCUCUCGACUCUCUUAUUCGUAUU-CUGUGGUCCAC
ABRN01179171.1/8411-8110   AAAAGGAGCCAUAAAAUUCAA-CUU---CUGCUAGCCAUUCUUUCCCUUUUUGCUCUCCAUACACCUCAGCUGGGAAUCUUUAUAUGUGCAGUA-UUUAUUUGGCUUGUGUUAUCCUGGUCAUUAUAAAGUUA--UCUAGGAGGCUAAGAGA-GCUGACC-AACU---GAGAAGGGAAAGCAGUCUGUUCUGA-CAGUGAUGACAAAAGGAGUUCAAGU--------CAUACC----AAACAUCUUUC-----UC-CCAUUUAGAAA-CAUCCUAGUAUUUAAGACCU--------------------------AGU--------------AUUUCAUUUCUCUCUACUCCCAUAUUUGUGUU-CUCUGUUCUUA
AAGV020165551.1/7227-6882  AAACGGAGACA-AAGAUUUAAGCUU---UUCCUAGCCAUUCUUUCCCUUUUUGCUCUUCACAC--CGCAGUCGAGGAUCUUUCUAUGUGCAGUA--UUAUUUUGUUUGUUUUAGCCUGGUAAUUUUAAAGAUA--CCUAGGAGGGUAGGAGA-GCUGACCCAACA---GAGAAGGGAAAA-AUUCUCUUCUGA-CCAUAGUGACAUAAGGAGGUCAGUU-CACACCAGAUACCUUUACAGCAUGUGUC-----UUUCUGUUUAAAAA-CAUCUUAGUACUUAAGGUAUUUUAAU------AUAAGCCCAUAACUAGCUCUUUACCCUUUUUAUUUCAUUUCUCACUAUUCUCAUUUAUCUGUUUCUGUGCUCCUU
AAWR02010524.1/17521-17198 AAAAGGAGACAUAAAAUUCAA-CUU---UUGCUAGCCACUCUUUCCCUUUUUGCUCUCCAUAUACCUCA--------------UAUGUGCAGUA-UUUAUUUUGUUUGUCUUAUUCUGGUCAU---AAAGUUA--UCUAGGAGGCUAGGAGC-GCUGACC-ACCAUCAGAGAUGGGAAAGUAGUCUGUUCUGA-UUGUAGUGACGAAAGGAGUUCAAUU--------CACACC----AAGGGUCUUUC-----UC-GCAUUUAGAAA-CAUCCUAUUAUUUAAGGCCUUUCGCUC---AUAUAAGCUCAUCACUAGUUCUUU-ACCUUUCUAUUUCAUUUCUCUCUACUCUCAUGUUUGUGUU-CUCCGUUCCUA
AANG01107293.1/241-574     AAAAGGAGAUAUGAAAUUCAA-CUU---UU----UGCUUUCUUUCCCUUUUUGCUUUUCACAUUGUUCAGUUGGGAAUCUUUCUAGGUGCAGUA-UUUAUUUUGUUUGUGUUAGUCUGGUCAGUAUAAAGUCA--UCUAGGAAGCUAGGAGA-GCUGACC-AGCAG-AAGGGAAAAAAAGCAGUCUAUUCUGA-CUACACUGACCAAAGGAGUUCAAUU--------CAUACC----AAACAUCUUUC-----UC-CCAUUUAGAAAACAUCCUAGCAUCUAAGGCCUUCUACU------AUAAGCCCAUUACUAGGUCUUU-UCCUUUCUCUUUCAUUUCUCUCUACUCUCAUAUUUGUGUC-GACUGUUCCUA
ABVD01914036.1/325-639     AAAAGGAGACAGAAGAUAUAAGCUU---UUAUUAGUCAUUCUUUCCCUUUUUGCUCUCCACACACCUCAGUUGAGACUCUUU-------------------------GUUACAUCCUGGUAAUUAUA--GUUA--UCUAGGAGGCUAGGAGAUGCUGACC-AACA---GAGAAGAGAAAACAGUCCAUUCCAA-CCAUAGUGACAUAAAGAGUUCAGUU-CACACCAGACAUCUUUACAGCAUGUUUC-----U--CUGUUUAGAAA-CAUACUAGUAUUUAAGGUCUUUUAAU------GCAAGCUCAUAACCUGGUCUUU-UCCUUUCUAUUUCAUUUCUCUCUACUC---CUUGUUUAU--CUG--UUUCUG
AAKN02011212.1/27032-27359 AAAAGGAGAUAGAACAUUCAAGCUUGUUUUGCUCAGUAUCCUUUCCCUUUUUGCUCUUCACACACACUAGCUGGGAACCUUUAUGUGUACAGUA-----UUUAUUUUGUAUUAUACUAGUAAUUACAAAGUUA--CCUAUGAGGCUAGAGAG-GCAGCCA-A-------GAUAAGGAGCACAUCUGACUGUGAUCUGCAGUGACU---GGUAUUUACUG-CAUAUCAAAUAUUGUCCCAGAAUGAUUC-----UC-CCACUUAGAAA-CAUCUGAGCACCUAAGACCUUUUAAU------AUAAGCCAAAUACCAGCUCUUU-UGAUUUUAAUUUCA--UCUUUAUGCUCUCGUA---------UUA--UUCCUA
ABRP01175984.1/3916-3615   AAAAGGAGACAUAAAAUUCAA-CUC---UUGGUAGCCAUUCUUUCCCUUUUCGCUCUCCACAUACCUCAGCUGGGAAUCUAUAAAUGUGCAGUA------CUUGUU--UGUUAUACUGGUCAUUAUUAAGUUA--UCUAGGA---------------------------GGCUAGGAGAGCAAUCUGUUCUGA-CUGUAGUGACAAAAGGAAUUCAAGU--------CACACC----AAAUAUCUUUA-----UC-CUGUUUAGAAA-CAUCCUAGCAUUUAAGGCCUCUUAAU------UUAAGCCCAUUACAAGUUAUUU-UCCUUUCUAUUUCAUUUUUCUCUACUC----UCUUAUGUU-CUGUGUUCUAU
AANU01125897.1/9237-9577   AAAAGGAGACAGAAGAUUGAAGUCU---UUUCCAGCCAUUCUUUCCCUUUUUGCU-UUCAAACUCCUCAACGGGGAACCUUCAUAUGUGCAGUA-----UUUAUAUUGGAUCACACUGAUGAUUAUAAAGGUU--CCUAGGAGGCUAGAA---GCCAACC-AACA---GAGAAGGGAAAGCAGUCUGUUCUGA-ACAUAGGGACAUA---AGUUCAUUC--AUGCCAUGUAUCUUUUCAGCAUGUUUC-----UC-CCACUUAGAAA-CAU-CUAGCAUGUAAGGCCUUUUAAUAUUAAUAUAAGCCCAAUACCAGCUCUUU-CCCUUUGUAUUUCAUCUCUUUCUGCUCUCCUAUUUGUAUU-UUGUGUUCCUA
AAFC03089646.1/9898-9569   AAAAGGAGCCAUAAAAUUGAA-CUU---CCACUAGCCAUUCUUUCCCUUUUUGCUGUCUGCACACUUCAGCUGGGAAUCUUUAUGUAGGUAGUA-GUUAUUUGACUUGUGUUAUUCUGGUUGUAAUAAAGUUAUAUCUAAGAGGCUAAGAGA-GCUGACC-AACU---GAGAAGGGAAAGCAGUUCGUUCUGA-CCAUAAUGACAAAAGGAGUUCAAGG--------CGCACC----AAACAUCUUUC-----UC-CCAUUUAGAAA-CAUCCUAGUAUUUAAGCACAUAAAUA------CUUGGGC--UUCCCAGGUGGCG-CAGAUGGUAAAGCGUGUGCCAGCA-----AUGCGGGAGAC-CUGGGUUCAAU
AAQR03165214.1/412-78      ---AUAUGGCAAAAGAGAAGAAGCU---CUGCUAGCUGUUCUUUCCCUUCUUACCCUU-ACAUACUUCAUCUGGGAGACUUUACAUAUGUGAUA--UU--UAUGAUCUUGUUAGACUGGUAAUUACAAAGUGC--CCUAGGAGGCUAGGAGG-ACUGACC-AAGA---GAGAAGGGAAAGCAUUUUGUUCUGA-CCAUAAUGACAUAAGGAGUUCAUUU-CACACCAAACAUCUUUCCAGCAUGUUUC-----UC-CCAUUGAGAAA-CAUCCUAGCAUUUAAGGCCUCUUAAUGU-AAGAUAAGCC-------GGGUACUA-UCUCUUUUACUUC---UCUCUCUACUAUCUUCUUUGUGUU-CUGUUUUCCUA
AAGU03046469.1/58026-58335 AAAAGGAGACAGAAAAUUCAAUCUU---UUGCUGGCCAUCCUUUCCCUUUCUGUUCUCCACAUACUUCACUUGGGAAUCUUUCUAUGUGCACUAAUUUAUUUGGUUUGUGGUAUACUGUUAAUUAUAAUGUUA--CCUAGGAGGCCAGGAGA-GCUGACC-AACA---AAGAAGAGAAAGCAGUAUAUUCUGA-CCACAGUGA--------------------------UAC-----AAACAUCU-------------GUUUAGAAA-CACUCUAGCACUUAAGGUCUUUUAGU------AUAAGCCCAUUAUCAGCUCUUU-UUCUUU-UAUUUCAUGUCUCUCUACCUUCUUACUUCAGUU-CUGUGUUCCUA
AAEX03013094.1/17820-17496 AAAAGGAGAGAUAAAAUUCAA-CUU---UUGCUACCCAUUCUUUCUCUUUUUGCUUUCCAUACACUUCAGAUGGGAAUUUUUCUGUGU---GUA-UUUAUUUUGUUUGUGUUAUCUUGGUAACUAUAAGUUUA--U-----------------GCUGACU-GACAG-GGGGGAAAAAAAGCUGUCUAUUCUGA-CUGCAGUGACCAAAGGAGUUCAAUUGUUCAAUUCACACCC---AAACAUCUUUC-----UU-CCAUUUAGAAA-CAUCCUAGUAUUUAAGGCCUUCUACU------AUAAGCCCAUUACUAGUUCUUU-UCCUUUCUAUUUCAUUUCUGUAUGCUC--AUAUUUGUGUU-CUCUGUUCCUA
AJ412023.1/517-858         AAAAGGAGACAGAAGAUUGAAGCCU---UUGCCAGCCAUUCUUUCCCUUUUUGCU-UCCAAACUCCUCAACUGGGAACCUUCAUAUGUGCAGUA-----UUUAUAUUGGAUCAUACUGGGGAUUAUAAAAGUU--CCUAGGAGGCUAGAAGA-GCCAACC-AACA---GAGAAGGGAAAGCAGUCUGUUCUGA-ACAUAGGGACAUA---AGUUCAUUC--AUGCCAAGUAUCUUUCCAGCAUGUUUC-----UC-CCAUUUAGAAU---AUCUAGCAUGUAAGGCCUUUCAAUAUUAAUAUAAGCCCAAUAUCAGCUCUUU-CUCUUUGUAUUUCAUCUCUUUCUACUCUCCUAUUUGUAUU-UUGUGUUCCUA
#=GC SS_cons               :::::::::::::::::::::::::...::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..::.::::::::::::::::::::::::::::::::::..:::::::::::::::::.:::::::.::::...:::::::::::::::::::::::::.:::::::::::::::::::::::::..:::::::::::::::::::::::::::.....::.:::::::::::.::::::::::::::::::::::::::......::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::.:::::::::::
#=GC RF                    AAAAGGAGacAgAAgAUUcAAgCuU...UUgCUaGcCaUUCUUUCCCUUUUUGCUcUcCAcAcaCcUCAgcUGGGAauCUUUaUaUGUGCAGUA..UU.UUUuguUUGUgUuAuaCUGGUaAUUAUAAaGuua..uCUAGGAGGCUAGgAGa.GCuGACC.AaCa...GaGaaGGGAAAGCAgUcugUUcUGA.ccauAGUGACauAAGGAGUUCAauu..acacCaaauAuCuUucaAgcAUgUUUC.....UC.CCaUUUAGAAA.CAucCUAGcAuuUAAGGcCUUuuAaU......aUAAGCCCAuuACcaGcUcuUu.uccuUUgUAUUUCAUuUCUcUcUaCUCUCaUaUuugUgUU.cUguGUUCcua
//
# STOCKHOLM 1.0

#=GF AC   RF02105
#=GF ID   DLEU2_1
#=GF DE   Deleted in lymphocytic leukemia 2 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   52.00
#=GF TC   54.00
#=GF NC   51.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 41.46 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9395242
#=GF RT   Cloning of two candidate tumor suppressor genes within a 10 kb region on
#=GF RT   chromosome 13q14, frequently deleted in chronic lymphocytic leukemia.
#=GF RA   Liu Y, Corcoran M, Rasool O, Ivanova G, Ibbotson R, Grander D, Iyengar A,
#=GF RA   Baranova A, Kashuba V, Merup M, Wu X, Gardiner A, Mullenbach R, Poltaraus
#=GF RA   A, Hultstrom AL, Juliusson G, Chapman R, Tiller M, Cotter F, Gahrton G,
#=GF RA   Yankovsky N, Zabarovsky E, Einhorn S, Oscier D
#=GF RL   Oncogene. 1997;15:2463-2473.
#=GF WK   DLEU2
#=GF SQ   27


AY455757.1/890-771           ACUAGAGCCAAA-UCUA-UCUCAAAAGUUU-AGGUCAUU---UUUUUU-UCCUUUUUGAUAGUAUUCAA-UGA-GAAA-UAACACUUUA--AAUAAAACUUU--UUC---C-AUGA-G-GAA-GGUACAGUAAU-------UAUCCAC
AL137060.13/38108-38227      ACUAGAGCCAAA-UCUA-UCUCAAAAGUUU-AGGUCAUU---UUUUUU-UCCUUUUUGAUAGUAUUCAA-UGA-GAAA-UAACACUUUA--AAUAAAACUUU--UUC---C-AUGA-G-GAA-GGUACAGUAAU-------UAUCCAC
AL109925.11/127996-128115    ACUAGAGCCAAA-UCUG-UCUCAAAAGUUU-AGGUCAUU---UUUUUU-UCCUUUUUGAUAGUAUUCAA-CGA-GAAA-UAACACUUUA--AAUAAAACUUU--UUC---C-AUGA-G-GAA-GGUACAGUAAU-------UAUCCAC
AF279660.2/47646-47765       ACUAGAGCCAAA-UCUA-UCUCAAAAGUUU-AGGUCAUU---UUUUUU-UCCUUUUUGAUAGUAUUCAA-UGA-GAAA-UAACACUUUA--AAUAAAACUUU--UUC---C-AUGA-G-GAA-GGUACAGUAAU-------UAUCCAC
AF380424.1/780-661           CCUAGAGCCAAA-UCUA-UCUCAAAAGUUU-AGGUCAUU---UUUUUU-UCCUUUUUGAUAGUAUUCAA-UGA-GAAA-UAACACUUUA--AAUAAAACUUU--UUC---C-AUGA-G-GAA-GGUACAGUAAU-------UAUCCAC
AAWR02010526.1/29031-28911   ACUAGAGCCAAA-UCUA-UCUCAAAAGUUU-AGGACAUUAA-UUUUUC-UCCUUUUUGUUAAUACUCAA-CGA-GAAA-CAACACUUAG--AAUACAACUUU--UUC---C-AUGA-A-UAA-GGGAUAGUAAU--------AUCCAC
AAQQ01600879.1/4109-3989     ACUAUUGCCAAA-UCUA-UCUCAAAAAUUU-AGGACAAUAA-UUUUUC-UCCUUUUUGAUAAUACUCAA-UGA-GAAA-CAACACUUAG--AAUAAAACAUU--UUC---C-AUGA-G-GAA-GGGAUAGUAAU--------AUCCAC
ABRR01275135.1/2340-2220     ACUAGAGCCAAA-ACUA-UCUCAAAAGUUU-AGGGCAUUAG-UUUUUC-UCCUUUUUGAUAAUAUUCAA-UGA-GAAA-UGACACUUAG--AAUAUAACCUU--UUC---C-AUGG-A-UAA-GGAUUAGUAAU--------AUCCAC
ABRT010133259.1/11603-11725  ACUAGAGCCAAAAUCUA-UCUCAAAAGUUU-AGAAUAUUAA-UCUUUC-UCCUUUUAAAUAAUAUUCAA-UAA-GAAA-UAACAUUUAG--AAUAAAACUUU--UUC---C-AUGA-G-GAA-GGAAUAGUAAU-------UAUCCAC
ABVD01299549.1/2864-2740     ACUAGAGCCAAA-UCUA-UCUCAAAAGUUU-AGAACAUUCA-UUUUUC-UCUCUUUUGUUAAUAUUCAA-UAA-GAAAACAACAUUUAA--AAUAAAACUUU--UUUUUCC-AUGA-G-GAA-GGGAUGGUAAU--------AUCCAC
AAFC03089645.1/13318-13197   ACUACAGCCAAA-UCUAAUCUCAAAAGAUU-AGGAUAUUAA-UUUUUC-UCCUUUUUGCUAAUACUCAA-UGA-AAAA-CAACACUUAG--CAUAAAACUUU--UUC---C-AUGA-A-UAA-GGGCUAGUAAU--------AUCCAC
ABRO01260383.1/790-668       AUUAGUAUCAGA-CCUA-UCUCAAAUGGUU-AGGUCAUUAAUUUUUUC-ACCAUUCUGAUAAUGCUCAA-AGA-GAAA-UAACACUUAA-GAAUAAAACUUU--UUC---C-AUGA-G-GUA-CAGAUAGUAAU--------AUCCAC
AAGV020165561.1/804-689      UCUACAGCCAAC-UCUA-CCUCAAAAAUUU-AGGACAUUAA-CUUUUC-UCCCUCUCGUUAAUAUUCAA-UGC-GAAA-CAACACUUA-------AAACAUU--UUC---C-AUGA-G-GAA-GGGAUGGUUAU--------AUCCAC
ABRQ01105896.1/3360-3246     ACUAGA-UCAAA-UCUA-UCUUAAUAGUUU-AGGACAUUAA-UUUUUC-UCCU--UUGCU---AUUAAA-UGA-GAAA-UACUGCUCAG--AAUAAAAUGUU--UUU---C-ACGG-U-GAA-GGGAUGGCAAU--------AUCCAC
AAPY01631686.1/5136-5020     ACUAGA-CCAAA-UCUA-UCUCAAAAGUUUUAAGACAUUAA-UUUUUC-U-UCUUUUGAUAACAUUCAA-UGA-GG----AACAUUUAA-AAAUAAGACUUU--UUU---C-AUGA-G--AA-GAGAUAGUAAU--------AUCCAC
AAKN02011211.1/24815-24923   AUUACAGCCAAG-UCUA-UCUAAAAAUUUU-AGAACAUUAA-UUUUUC-UCCUUUUUAAUAUUAUUUAA-UGA-GA-----ACACUUA-------AAACUUU--UUC---C-AUGA-----A-GGGAAAGUAAU--------AUCCAC
AAYZ01277512.1/47-168        ACUAGAACCAAA-UAUA-ACUUAAAAAUUA-AGGCAACCA--CUUUUC-UCCCUUUUUAUAAUACUCAAAUGA-GAAA-UAAAAUUUCGGAAUUAAGACUUU--UUC---C-AUCA-G--AA-GAGACAGUAAU--------AUCCAC
CAAA01192847.1/9232-9118     UGCUGAUCCAAA-UCUA-UUUAAAACAAUUAAGGACAUU---UUCUUU-UCUUUUUGGAUGGUAUUUAA-UGA-GAAA-CAACACUGAG--A---AAAAAUA--UAU---C-AUAC-----A-AGGAUAGUAAU-------AUUCCUU
ABVD01171437.1/671-795       CUUAGAGCCAAA-UAUA-UCUCAGAAGUUU-AUAACAUUCA-UUUUUCUCUCUUUUUGUUAAUAUUCAA-UAG-GAAAACAACACUUAA--AAUAAACCUUUUUUUC---C-ACGA-G-GAA-GAGAUGGUAAU--------AACCAU
ABVD01873795.1/989-873       ACUAGAGCCAAA-UCUA-UCUCAGAAAUUU-AGAACAUUCA-UUUUUC-UCUAUUUUGUUAAUGUUCAA-UGA-GAAAACAACACUUA-------AAACUUU--UUC---C-AUGA-A-GAA-GGGAUGGUAAU--------AUCCAC
ABRP01205680.1/2705-2590     UCUAGAGC-AAU-UUUA-UAUCAAAUUUAU-AAGAUAUAA--AUGUUC-UCUUUAUUAAU---AUUUAG-UGA-GAAAUGAACACUCCA--GAUAAAACAUU--UUU---C-AUGU-A-GAA--GGAUGGUAAU--------AUAAAC
AACN010177803.1/1143-1022    ACUAGAGCCAAA-UCUA-UCUCAAAAGUUU-GGGACAUUAA-UUUUUC-UCCUUUCUGUCAAUACUCAA-UGA-GAAAUUAACACUUAG--AAUAAAACGUU--UUC---G-AUGA-A-UAA-AGGAUAGUAAU--------AUCCAC
AAQR03165218.1/6758-6639     ACUAGAGACAAA-UCUA-UCUCAAAAGUUU-AAAACACUAA-UUUUUC-UCCUUUUUGAUAAUAUUCAA-GGA-GAUA-UAACAAUUAG-AA--AAAACUUU--UUC---C-AUGA-G-GAA-GGGAUAGUAAU--------AUCCAC
AAGW02061188.1/108033-108155 AAUAAAUCUUAA-AAAA-AAAAAAAAUUUU-AAGGCAGUAU-UUUUAU-UCCAUUUUCAUAUUAUUCAA-CGACAAAA-CAAGACUCAG-AAUUAAAACUUU--UUC---C-ACAA-G-GAA-GAAACAGUAAU--------AUCCAC
AAGW02046027.1/82376-82257   ACUGAAGCCAAA-UCUA-GCUAAAAAGUUC-AAUACAAU---UUUUAU-CCUUUUUUCAUAAUAUUCAA-UGA-GAAA-UAACACUUAG-GAAUAAAACAUU--UUC---G-AUGA-G-GAA-GAAAUAGUA-U-------CAUCCAC
AAEX03016987.1/215466-215344 ACUAGAGCCAAA-UCUA-UCUCAAAAGUUU-GGGAUAUUAA-UUUUUC-U-----UUGUUAAUAUUAAA-UGA-GAAAUGAACACUUAG--AAUAAAACUUU--UUCG-G-GACGCC-UGAGUGGCUCAGUGGUUGAACGUC------
Y15228.1/521-403             ACUAGAGCCAAA-UCUA-UCUCAAAAGUUU-AGGUCAUU---UUUUUU-UCCUUUUUGAUAGUAUUCAA-UGA-GAAA-UAACACUUUA--AAUAAAACUUU--UUC---C-AUGA-G-G-A-GGUACAGUAAU-------UAUCCAC
#=GC SS_cons                 ::::::::::::.::::.::::::::::::.::::::::::.::::::.::::::::::::::::::::.:::.::::.::::::::::..:::::::::::..:::...:.::::.:.:::.:::::::::::........::::::
#=GC RF                      acUAGAGCCAAA.UCUA.UCUcAAAagUUU.AGGacAuUAa.UUUUUC.UCCuUUUUGaUAaUAUUcAA.UGA.GAAA.uAACACUUaG..AAUAAAACuUU..UUC...C.AUGa.g.GAA.GGgauaGUAAU........aUCCAC
//
# STOCKHOLM 1.0

#=GF AC   RF02106
#=GF ID   DLEU2_2
#=GF DE   Deleted in lymphocytic leukemia 2 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   45.00
#=GF TC   46.50
#=GF NC   42.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.17 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9395242
#=GF RT   Cloning of two candidate tumor suppressor genes within a 10 kb region on
#=GF RT   chromosome 13q14, frequently deleted in chronic lymphocytic leukemia.
#=GF RA   Liu Y, Corcoran M, Rasool O, Ivanova G, Ibbotson R, Grander D, Iyengar A,
#=GF RA   Baranova A, Kashuba V, Merup M, Wu X, Gardiner A, Mullenbach R, Poltaraus
#=GF RA   A, Hultstrom AL, Juliusson G, Chapman R, Tiller M, Cotter F, Gahrton G,
#=GF RA   Yankovsky N, Zabarovsky E, Einhorn S, Oscier D
#=GF RL   Oncogene. 1997;15:2463-2473.
#=GF WK   DLEU2
#=GF SQ   18


AY455757.1/745-656           CUGAGUAAGCUCCAAAC---UCAAUCCGUAAUCC-AAGUA-ACAGACUUAAGAUGUUCAAUAUUGGAACUCUUUGGC-AUCAAUUAAAAAAGAAAC
AL137060.13/38602-38691      CUGAGUAAGCUCCAAAC---UCAAUCCGUAAUCC-AAGUA-ACAGACUUAAGAUGUUCAAUAUUGGAACUCUUUGGC-AUCAAUUAAAAAAGAAAC
AF279660.2/48140-48229       CUGAGUAAGCUCCAAAC---UCAAUCCGUAAUCC-AAGUA-ACAGACUUAAGAUGUUCAAUAUUGGAACUCUUUGGC-AUCAAUUAAAAAAGAAAC
ABRR01275135.1/1851-1762     CUGAGUUAGCUCCAAAC---UCAAUCCAUACUCC-AAGUA-ACAGAUUUAAGAUGCUCAAUAUUGGAAUUAUUUGGC-AUCAACUUAAAAAGAAAC
AAWR02010526.1/28540-28451   CUGAGUUAGCUCUAAAC---UCAAUCCAUACUCG-AAGUA-ACAGAUUUAAGAUGCUCGAUAUUGGAAUGAUUUGGC-AUCAACUUAAAAAGAAAA
AAFC03089645.1/12839-12750   CUGAGUUAGCGCCAAAC---UCAAUCCAUAAUCC-AAGUA-ACAGAUUUAAGAUGCUCAAUACUGGAAUUAUUUGGC-AUCAACUUAAACUUGAAU
ABRP01194837.1/4703-4614     CUGAGUUAGCUACAAAC---UCAAUCCAUACUCC-AAACA-GCAGAUUUAAGAUGCUCAAUACUGGAAUUAUUUGGC-AUCAACUUAAAAAGAAAC
AACN010177803.1/660-582      CUGAGUUAGUUCCAAAC---UCAAUCCAUA-------------AGAUUUAAUAUGCUAAAUAUUGAAAUUAUUUUGC-AUCAACUUAAAAAGAAAC
AALT01128162.1/721-811       CAGAGUUAGCAGCAAAC---UUAAUCAAUAUUCC-AAGUA-ACAGAUUUAACAUGCUUAAUACUGGAAUUCUAUGGCUCUCAACUUAAAAACAAAC
AAPY01631686.1/4646-4556     CUGAGUUAUCUCUAAAC---UCAAUCCAUACUCCAAAGCA-AUUGAUUUAACAUGAUUAAUGUUAUAAUUUUUUAGC-AUCAACAUAAAAAAAUUA
ABVD01873795.1/862-777       CUGAG----CUCCAAAC---UCAAUCCAUACUCA-AAGUAUACAGAUUUAAGAUGC-UGAUAUUGGAAUUAUUUGGC-AUGAACUUAACAAGAUAA
ABRT010468198.1/316-255      CUGAGUUAGCUCCAAGC---UCAAGUUCAUAUUC-AAGAA-GCAGAUUUAAGAUGCUCAAUAUU-----------------------------AGC
AAYZ01277512.1/512-594       C----UCCAUUCCAAAC---UCAUCUCAAACUUC-AGCUA-ACAGUUUGAAGAUUCUCAAUACCAGA---AUUUGGC-AUUAACUUAAAAGGAAAA
AANN01027737.1/1725-1803     CAGAGUUAGCUGCAGAU---UUAAUUCACAUUCC-AAGUA-ACA-----------AUAAACAUUAGAAUUUCUUUUG-CAAAGAUGAAGAAGAAAA
AANU01125901.1/11505-11594   CUGAGUAAGCUCCAAAA---UCAAUCCAUAUUCC-AAAUA-ACAGACUUAAGAUGUUCAAUAUUGGAACUCUUUGGU-AUCAAUUAAAAAAGAAAC
AAPE02005598.1/14472-14559   CUGAGUUAGCACCAAAC---UCAAUCUAUACUCC-AAAUA-AC--AUUUAAGAUGAUCAAAGCUGGAAUUAUUUGGC-AUCAACUUAAAAAAAAAA
AAGW02061188.1/108517-108605 C----UCAGCUCCAAACCCAUCAUCUCACAAUCC-AACUA-ACAGUUUGAAAAUGAUCAAUACCAGAAUUAUUUGGG-AUUAACUUAAAAGAAAAA
AL109925.11/128141-128230    CUGAGUAAGCUCCAAAC---UCAAUCCAUACUCC-AAGUA-ACAGACUUAAGAUGUUCAAUAUUGGAACUCUUUGGC-AUCAACUAAAAAAGAAAC
#=GC SS_cons                 :::::::::::::::::...::::::::::::::.:::::.::::::::::::::::::::::::::::::::::::.::::::::::::::::::
#=GC RF                      CUGAGUuAGCUCCAAAC...UCAAUCCAuAcUCC.AAGUA.ACAGAUUUAAgAUGcUcAAUAuUGGAAUUaUUUGGc.AUcAAcUuAAAAagAAAa
//
# STOCKHOLM 1.0

#=GF AC   RF02107
#=GF ID   DLEU2_3
#=GF DE   Deleted in lymphocytic leukemia 2 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   60.90
#=GF NC   56.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.92 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9395242
#=GF RT   Cloning of two candidate tumor suppressor genes within a 10 kb region on
#=GF RT   chromosome 13q14, frequently deleted in chronic lymphocytic leukemia.
#=GF RA   Liu Y, Corcoran M, Rasool O, Ivanova G, Ibbotson R, Grander D, Iyengar A,
#=GF RA   Baranova A, Kashuba V, Merup M, Wu X, Gardiner A, Mullenbach R, Poltaraus
#=GF RA   A, Hultstrom AL, Juliusson G, Chapman R, Tiller M, Cotter F, Gahrton G,
#=GF RA   Yankovsky N, Zabarovsky E, Einhorn S, Oscier D
#=GF RL   Oncogene. 1997;15:2463-2473.
#=GF WK   DLEU2
#=GF SQ   24


AL137060.13/43050-43122    AAAGGAG-AAUUUACAAA---CAUUUUGUUCCUUGCAGUACACCUUUCAAAAGACAUCUUCAUCAAA-UAGGUAAGAC
AL109925.11/128238-128310  AAAGCAG-AAUUUACAAA---CAUUUUGUUCCUUGCAGUACACCUUUCAAAAGACAUCUUCAUCAAA-UAGGUAAGAA
AF279660.2/52588-52660     AAAGGAG-AAUUUACAAA---CAUUUUGUUCCUUGCAGUACACCUUUCAAAAGACAUCUUCAUCAAA-UAGGUAAGAC
AF380424.1/653-581         AAAGGAG-AAUUUACAAA---CAUUUUGUUCCUUGCAGUACACCUUUCAAAAGACAUCUUCAUCAAA-UAGGUAAGAA
AY455757.1/648-576         AAAGGAG-AAUUUACAAA---CAUUUUGUUCCUUGCAGUACACCUUUCAAAAGACAUCUUCAUCAAA-UAGGUAAGAA
ABDC01614677.1/551-623     AAAGCUG-AAUUUACAAA---CAUUUUGUUCCUGGCAGUACGUCUUUCAAAAGACAUCUUCAUCAAG-UAGGUCAGAC
AY866302.1/72-1            AAAGCAG-AAUUUACGAA---CAUUUUGUCCCUUGCAGUACAACUUUCAAAAGACAUCUUCAUCAAG-UAGGUAAGA-
ABRN01179179.1/5823-5748   AAAGCAU-AAUUUACAAACAGCAUUUAAUUCCUUGCAGUACACCAUUCAAAUGACAUCUUCAUCAAG-UAGGUAAGAC
ABRR01275134.1/5167-5092   AAAGCAU-AAUUUACAAACAGUAUUUCACUCCUUGCAGUACACCAUUCAAAAGACAUCUUCAUCAAG-UAGGUAAGAC
AAWR02010526.1/25823-25749 AAAGCAU-UAUUUACAAACAGCGUUUCAUUC-UUGUAGUACAUCUUUCAAAAGACAUCUUCAUCAAG-CAGGUAAGAC
ABRT010452149.1/3315-3240  AAAGCAG-AAUUAAUAAAUAACGUGUUGUUCCUUGCAGUAUACUUUUCAGAUGACAUCUUCAUCAAG-UAGGUAAGAC
AAPY01631686.1/1863-1789   AAAGCAG-AAUUUACAAACUUCAUCUUUUUCCUUGCAG-ACACCUUUCAAAAGACAUCUUCAUCAAG-GAGUAAAGAC
AAFC03089645.1/10115-10040 AAAGCAU-UAUUUACAAACAGCAUUUAACUCCUUGCAGUACACCUCUCAAACGACAUCUUCAUCAAG-UAGGUAAGAU
ABRO01260382.1/928-852     AGAGCAG-AAUUUACAAAUAGCUUUUUGUUCCUUGUAGUACAUCUUUCAAAAAGCAUCUUCAUCAAGGCAGGUAAGAC
ABVD01299548.1/3028-2953   AAAGCAG-AAUUUACAAAUAGCAUUCUGUUCCUUGUAGUACAUCUUUCAAAAGAUAUCUUCAUCAAG-CAGAUAACAU
ABRP01194837.1/2212-2137   AAAGCAU-AAAUUACAAACGGCACUUCAUUCCUUGAAACACAUCUUUCAAAAGACAUCUUCAUUAAG-UAGGGAGGAC
ABRQ01105896.1/181-107     UAAGCAG-AAUUUACAAACUACAGUUUGCUCCUGGUAGUAUACCUUUCACAAAAUAUCUUCAUCAAG-CAG-UAAGAC
AAGV020295888.1/1405-1334  AAAGCAGACUUUGACAAG----AUUUUGUUCCUUGCCAUACACCUUUCA-AAGACAUUUUCAUCUAGUUAU-UCAGAG
AAQQ01600879.1/1210-1134   AGAGCAG-AAUUUACAAAUAGCAUUUUGUUUCUUUUAGUAUAUCUUUCAAAAGACAUGUUUAUCAGGGUAGAUAAGAC
AAIY01323892.1/583-511     AAAGCAA-AAUUUACAAACUGCAGCCUGUUC-UUG-UGUAUACCUUUCAAAAGACAUAUUCAUCAAG--AGCUCACUU
AAPE02005599.1/1635-1708   ACAGCAU-AUAUUAUAAACAGCA--UCAUUCCUUGAAGUACACUUUUCAUAAGACAUCUUCAUUAAG-AAGGUAAGAC
AAQR03165218.1/3169-3097   AAAGUAG-CAUUUACAGA---CAUUUUGUUCCUUGCAGUACACCUUUCAAAAGACAUCUUCAUCAAG-UAGGACUGAG
AAEX03013096.1/23721-23645 AAAGCAUUAAUUUACAGAUGGCACUUCAUUCCUUGCGGUACACCUUUCAAAAGACCUCUUCAGCAAG-UAGGUAAGAA
AAGU03046468.1/42681-42753 AAAG----AAUUCACAAACUGCAGUUUGUUCCUUGUAGUGCAUCUUUCAAAAGAAAUCUUCAUCUAG-UAGGUAAGAC
#=GC SS_cons               :::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::
#=GC RF                    AAAGCAg.AAUUUACAAAcaGCAuUUUGUUCCUUGcAGUACAcCUUUCAAAAGACAUCUUCAUCAAG.uAGGUAAGAc
//
# STOCKHOLM 1.0

#=GF AC   RF02108
#=GF ID   DLEU2_4
#=GF DE   Deleted in lymphocytic leukemia 2 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   40.90
#=GF NC   39.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.82 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9395242
#=GF RT   Cloning of two candidate tumor suppressor genes within a 10 kb region on
#=GF RT   chromosome 13q14, frequently deleted in chronic lymphocytic leukemia.
#=GF RA   Liu Y, Corcoran M, Rasool O, Ivanova G, Ibbotson R, Grander D, Iyengar A,
#=GF RA   Baranova A, Kashuba V, Merup M, Wu X, Gardiner A, Mullenbach R, Poltaraus
#=GF RA   A, Hultstrom AL, Juliusson G, Chapman R, Tiller M, Cotter F, Gahrton G,
#=GF RA   Yankovsky N, Zabarovsky E, Einhorn S, Oscier D
#=GF RL   Oncogene. 1997;15:2463-2473.
#=GF WK   DLEU2
#=GF SQ   21


AL137060.13/61566-61623     UUGCUGAG-CUAAGUAGAGGU-CU-CUUUUAUUGUGGUCUUCAUUC-UAUCAUUAUUAAACC
AF279660.2/71053-71110      UUGCUGAG-CUAAGUAGAGGU-CU-CUUUUAUUGUGGUCUUCAUUC-UAUCAUUAUUAAACC
AF380424.1/571-514          UUGCUGAG-CUAAGUAGAGGU-CU-CUUUUAUUGUGGUCUUCAUUC-UAUCAUUAUUAAACC
AY455757.1/566-509          UUGCUGAG-CUAAGUAGAGGU-CU-CUUUUAUUGUGGUCUUCAUUC-UAUCAUUAUUAAACC
ABGA01212113.1/1175-1118    UUGCUGAG-CUAAGUAGAGGU-CU-CUUUUUUUAUGGUCUUCAUUC-UAUCAUUAUUAAACC
AAWR02010526.1/13443-13386  UUGCUGGG-CUAAGUAGGGGG-CU-GUUUUAUUAUGGUCUUCAUUU-UAUCAUUAUUAAACC
AAQQ01153890.1/1256-1200    UUCCUGGG-CUA-GUAGGGGG-CU-GUUUUAUUGUGGUCUUCAUUU-UGUCAUUAUUAAACC
ABRT010133259.1/11818-11875 UUUCUGGG-CUAAGCAAGGGA-UU-AUUUUAUUAUGGUCUUCAUUU-UACCACUAUUAAAUC
AALT01467626.1/1548-1605    UUGCUGGU-UUAAGUAGAGGG-UU-GCUUUAUUAUGAUCUUCAUUC-UACUAUUAUUAAGUC
ABRP01194835.1/1877-1819    CUGUUGAAAUUUAGUAGGGGG-CU-GUUAUAUUAUGGUCUUCAUUU-CAUCAUUAUUAAACC
ABVD01171437.1/806-862      UUGCUAGG-UUAAGUA-GGGG-CU-GUUUUAUUAUGGUCUUUAUUU-UAUUGUUAUUAAACC
ABRN01179176.1/8562-8505    UUGCAGGG-CUAAGUAGGGGG-CU-UGUUUUAUAUGGUCUUCAUUU-UGUUGUUAUUCACCU
ABRR01399352.1/68-10        CUGCUGGG-CUACGUAAGGGG-CUUGUUCUAUUAUUGUCUUCAUUU-UAUUGUUACUAAACC
AAFC03089641.1/1601-1547    CUGCAGGG-CUAAGUAGGGGG-CUUGUUAUACUAUGGUCUUCAUUU-UAUUAAU----AACC
AAIY01579408.1/1388-1332    UUGUUGUU-CUAAAUAGGGGG-CC-UUUUUAUUAUGCUCUUCAUU--UAUCGUUACUAAGGC
AAGW02011693.1/21165-21223  CUAUUAUG-CUAAGUUGAGGG-CU-GUUUUAUUAUUAUCUUCAUUUUUAUCAUUAUUAAACC
AAGU03046469.1/306-363      UUGCUGGG-CUAAAUAGGGGG-CU-GUUUUAUUAUGGUCUUCAUUU-UAUUGUUACAAAACC
AAQR03165215.1/22857-22801  CUGCUAGG-CUAAGUGGAAGG--U-GUUUUAUUAUGAUCUUCAUUU-UAUCAUUAUUAGAUC
AAPE02005599.1/7600-7657    CUGAUGAA-CUAAGUACGAGG-CU-GUUUUAUCAUGGUCUUCAUUU-UAUCGUUAUAAACCU
AL109925.11/128320-128377   UUGCUGAG-GUAAGUAGAGGU-CU-CUUUUAUUAUGGUCUUCAUUC-UAUCAUUAUUAAACC
AAEX03008745.1/15501-15443  UUGCUGGG-CUAAGUAGGGGAACU-GUUCUAUUAUGGUCUUCAUCC-UAUCAUUAUUAAACC
#=GC SS_cons                ::::::::.::::::::::::.::.:::::::::::::::::::::.:::::::::::::::
#=GC RF                     UUGCUGgG.CUAAGUAGGGGG.CU.gUUUUAUUAUGGUCUUCAUUU.UAUCAUUAUUAAACC
//
# STOCKHOLM 1.0

#=GF AC   RF02109
#=GF ID   DLEU2_5
#=GF DE   Deleted in lymphocytic leukemia 2 conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   40.00
#=GF TC   41.90
#=GF NC   38.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.88 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9395242
#=GF RT   Cloning of two candidate tumor suppressor genes within a 10 kb region on
#=GF RT   chromosome 13q14, frequently deleted in chronic lymphocytic leukemia.
#=GF RA   Liu Y, Corcoran M, Rasool O, Ivanova G, Ibbotson R, Grander D, Iyengar A,
#=GF RA   Baranova A, Kashuba V, Merup M, Wu X, Gardiner A, Mullenbach R, Poltaraus
#=GF RA   A, Hultstrom AL, Juliusson G, Chapman R, Tiller M, Cotter F, Gahrton G,
#=GF RA   Yankovsky N, Zabarovsky E, Einhorn S, Oscier D
#=GF RL   Oncogene. 1997;15:2463-2473.
#=GF WK   DLEU2
#=GF SQ   30


AY455757.1/324-241           GUC-AUGUUCC-A-AUGCAUUAUG-UAAGUAUUCAA-UCAAAGAAG-UGAGGCUGUUCUCCAGAAUUGGUUCUCUGCU----ACAGGUCAAAAC
AF328925.1/1029-1112         GUC-AUGUUCC-A-AUGCAUUAUG-UAAGUAUUCAA-UCAAAGAAG-UGAGGCUGUUCUCCAGAAUUGGUUCUCUGCU----ACAGGUCAAAAC
AL137060.13/69029-69112      GUC-AUGUUCC-A-AUGCAUUAUG-UAAGUAUUCAA-UCAAAGAAG-UGAGGCUGUUCUCCAGAAUUGGUUCUCUGCU----ACAGGUCAAAAC
AF279660.2/78515-78598       GUC-AUGUUCC-A-AUGCAUUAUG-UAAGUAUUCAA-UCAAAGAAG-UGAGGCUGUUCUCCAGAAUUGGUUCUCUGCU----ACAGGUCAAAAC
AF380424.1/503-420           GUC-AUGUUCC-A-AUGCAUUAUG-UAAGUAUUCAA-UCAAAGAAG-UGAGGCUGUUCUCCAGAAUUGGUUCUCUGCU----ACAGGUCAAAAC
ABRT010133259.1/11886-11969  AUC-AUGUUCC-A-AUGCAUUAUA-UGAGUAUUCAA-UCAAAGAAG-UUAGGUUGUUCUCCAGAACUGGCUCUCUCCU----ACAGGUCAAAAC
AALT01467627.1/851-934       AUA-AUGUUCC-A-AAGCAUUAUG-UGAGUGUUCAA-UCAAAGAAG-UUAGGCUGUUCUCCAGAACUGGCUCUCUCCU----AAAGGUCAAAAC
AAQQ01600877.1/1751-1668     AUC-AUGUUCC-A-AAGCAUUAUG-UGUGUAUUCAA-UCAAAGAAG-UUAGGUUGUUUUCCAGAAUUGGCUCUCUCCU----AAAGGUCAAAAC
ABRP01256841.1/5505-5588     AUC-AUGUUCC-A-AUGCAUUAUG-UGAGUGUUCAA-UCAAAGAAG-UUAGGUUGUUCUUCAGAACCUGUUCUCUCCU----CAAGGUCAAAAC
AAPY01162170.1/287-204       AUC-AUGUUCC-A-GCACAUUAUG-UGAGUAUUGAA-UCAAAGAAG-UUAGGUUGUUCUCCGGGACUAGCUCUCUCCU----AAAGGUCAAAAC
ABRQ01105890.1/812-728       AUC-AUGUUCC-A-GUACAUUAUGUUGAGUAUUCAA-CCAAAGAAG-UUAGGCUGUUCUCCAGAAUUGGCCCUCUCCU----AAAGGUCAAAAC
ABVD01165163.1/976-892       AUU-AUGUUCCUG-GUGCAUUACG-UAUGUAUUCAA-UCAAAGAAG-UUAGGUUGUUCUCCAGAAUUGGCUCUCUCCU----AAAGGUCAAAAC
AAFC03089644.1/4570-4649     AUU-AUGUUCC-A-AUGCAUUAU-----AUGUUCAA-UCAAAGAAG-UUAGCUUGUUCUCCAGAACUGGCUCUCUCCU----AAAGGUCAAAAC
AAIY01173663.1/4679-4599     AUC-AUGUUCC-A-AUUGAU-----UGAGUAUUCAAGUCAAAGAAG-UUAGGUUGUUCUCCAGAAUUGGCUCUCUUCU----AAAGGUCAAAAC
AANN01693923.1/2305-2377     GUC-AUGUUCC-A-ACACA------------UUCAA-UCAAAGAAG-UUAGGUUGUUCUUCUGAAUUGGUUCUCUCCU----AAAGGUCAAAAC
ABRO01260378.1/98-18         AUC-AUGUUCC-A-AUGCAUUAU----AAUGUUGAG-UAUUCAAAG-UUAGGUUGUUUUCCAGAACUGGUUCUCUCUU----AAAGGUCAAAAC
AAKN02011211.1/45926-46004   AUC-AUGUUCC-A-AUGCAU---G-CGAGUAUUCAA-UCAAAGAAC-UUUGGUUGUUUUCCAGAACUGGCUCACU--U----AAAGGUCAAAAC
AF380423.1/326-242           AUC-AUAUUCC-A-AUGCAUUACA-UGGGCAUUCAA-UCAAAGAAACUUUGGUUGUUUUCCAGAACUGGUAUUCUUCU----AAUGGUUAAAAU
AAGV020377696.1/1723-1639    AUC-AUGCUGC-A-ACAUAUUGCA-UGAGUAUUCAA-UCAAAGAAGGUAUGUUUGUUCUUCAGAAAUGACUCUCCCUG----AAAGGUCAAAAU
AAFR03025973.1/13379-13291   AUC-UUUUUCC-AUAUAUAAUAUG-GGGGUUUUCAA-UCACAGAAG-UUAAGUUGUUCUCCAGAAUCAGUUCUCCUCUACAAAAAGGUCAAAAC
ABQO010856561.1/79-167       AUC-UCUUUUC-ACAUAGAAUAUA-GAGGUUUUCAA-UCACAGAAG-UUAAGUUGUUCUCCAGAAUCAGUUCUCCUCUACAGAAAGGUCAAAAC
AAPN01007038.1/6376-6288     AUCCAUUUUCC-CCAUAGGAUGCA-UGACUUUUCAAAUCACAGAAG-UG-CGUUGUUCUCUAGAAUCAGCUCUCUCUUU-UGAAAGGUCAAAAC
ABQF01007226.1/47105-47180   UCA-ACCUUCC-A-GAGAGU---------UUUUCAA-UCACAGGAG-U-AAGCCAUUCUCCAAAAUCAGCUCUCUAUU---GAAAGGUCAAAAC
AACN010500885.1/178-261      AUC-AUGUUCC-A-AUGCAUUAUG-UGAAUGUUCAA-UCAAAGAAG-UUAGGUUGUUCUCCAGAAUUGGCUCUCUCCU----AAAGGUCAAAAC
AAGW02061188.1/131749-131832 AUC-AUGUUCC-C-GUGUGUUUUG-UGAGUAUUCAG-UCAAAGAAG-UUAGGUUGUUCUCCAGAAUUGGCUCUCUCCU----AAAGGUCAAAAC
AAHX01083321.1/13563-13482   AUC-AUAUUCC-A-AUGUAUUACG-UGGGUAUUCGA-UCAAAAAA---CUGGUUGUUUUCCACAACUGGCUCUCUUCU----AAAGGUUAAAAU
AAGU03046469.1/7890-7973     AUC-AUGUUCC-A-AUGCAUUAUG-UGAGUAUUCAA-UCAAAGAAG-UUAGGUUGUUCUCCAAAAUAGGCUCUCUCCU----AAAGGUCAAAAC
AADN03000560.1/4465-4388     UCA-ACCUUCC-A-GAAAGA-------GUUUUUCAA-UCACAGGAC-U-AAGCCGUUCUCCAAAAUCAGCUCUCUAUU---GAAAGGUCGAAAC
AACZ03001550.1/6037-6118     --G-UUGUUCC-A-AAGCAUUAUG-UGAGUAUUCAA-UCAAAGAAG-UGAGGCUGUUCUCCAGAAUUGGUUCUCUGCU----ACAGGUCAAAAC
AAPE02005599.1/15764-15847   AAC-AUGUUCC-A-GUGCAUUAUG-UGAGUGCUCAA-UCAAAGAAG-UUAGGUUGUUCUCCAGAACUGGCUCUCUCCU----UAAGGUCAAAAC
#=GC SS_cons                 :::.:::::::.:.::::::::::.:::::::::::.:::::::::.:::::::::::::::::::::::::::::::....::::::::::::
#=GC RF                      aUC.AUgUUCC.A.AuGcAUUaUG.UGaGUaUUCAA.UCAaAGAAG.UuAGGUUGUUCUCCAGAAuUGGcUCUCUcCU....AAAGGUCAAAAC
//
# STOCKHOLM 1.0

#=GF AC   RF02110
#=GF ID   DLEU2_6
#=GF DE   Deleted in lymphocytic leukemia 2 conserved region 6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   60.00
#=GF TC   62.60
#=GF NC   58.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.89 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9395242
#=GF RT   Cloning of two candidate tumor suppressor genes within a 10 kb region on
#=GF RT   chromosome 13q14, frequently deleted in chronic lymphocytic leukemia.
#=GF RA   Liu Y, Corcoran M, Rasool O, Ivanova G, Ibbotson R, Grander D, Iyengar A,
#=GF RA   Baranova A, Kashuba V, Merup M, Wu X, Gardiner A, Mullenbach R, Poltaraus
#=GF RA   A, Hultstrom AL, Juliusson G, Chapman R, Tiller M, Cotter F, Gahrton G,
#=GF RA   Yankovsky N, Zabarovsky E, Einhorn S, Oscier D
#=GF RL   Oncogene. 1997;15:2463-2473.
#=GF WK   DLEU2
#=GF SQ   32


AL137060.13/75302-75437      AAGCUCCGC---C-GACUGC-CCUUUGCUCCAA-GUAA---UUUUUGGC--GAUUUUUA----AAGUAAU--UUUUCC-GGCGGA-GUCAUAGUGG--CGCU-AUACUCU-CGGACAGGUUAUCCUG--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
AF328925.1/7274-7409         AACGUCCGC---C-GACUGC-CCUUUGCUCCAA-GUAA---UUUUUGGC--GAUUUUUA----AAGUAAU--UUUUCC-GGCGGA-GUCAUAGUGG--CGCU-AUACUCU-CGGACAGGUUAUCCUG--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
AF279660.2/84787-84922       AAGCUCCGC---C-GACUGC-CCUUUGCUCCAA-GUAA---UUUUUGGC--GAUUUUUA----AAGUAAU--UUUUCC-GGCGGA-GUCAUAGUGG--CGCU-AUACUCU-CGGACAGGUUAUCCUG--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
ABRT010201399.1/5255-5119    AAGCUCCGC----CGACUGC--CCUUUGAUCCGAGUAA---UUUUUGGCGAUUUUUUU------AGUGAU--UUUUUCCGGCGGA-GUCCUAGUGG--UGCU-AUACUCU-CGGACAGGUUAGCCCG--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
ACBE01544446.1/500-634       AAGCUCCGC----GGGCUGC--CCUUUGCACGAAGUAA---UUUUUGGCAAUUUUUUA-----A-GUGAU--UUUUCG--GCGGA-GUCCUAGCGG--CGCU-AUAAUCU-CGGACAGGUUAUCCCG--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
ABDC01270114.1/3857-3993     AAGCACCG----CCGACUGC--CCUUUACUCCAAGCGA---UUUUUGGCGAAUUUUUU------AGUGAU--UUUUUCUGGCGGA-GUCCUAGUGG--CACU-GUACUCU-CGGACAGGUUAUCCCG--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
ABRP01194832.1/610-476       AAACUCCGC----UGACUGC--CCUUUGCUCGAAGUAA---UUUUUGGCGAUUUUUUUAGUGAU--------UUUUCU--GUGGA-GUUCUAGUGG--CGAU-AUACUCU-CGGACAGGUUAUCCCG--CCUCACCCG----CUAGAUU-GAUGAGAUCAGGCAUC
AAWR02010525.1/13047-12915   AAGCUCUGC----GGACUGC--CCUUUGCUUCAAGUAA---UUUU--GCGAUUUUUUU------AGUGAU--UUUUCG--GCGGA-GUCCUAGCGG--CGCU-AUACUCU-CGGACAGGUUAUCCCG--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
ABRR01275127.1/9085-8952     AAGCUCCGC----CAACUGC--CCUUUGCUCGAAGUAA---UUUUUGACGAUUUUUUU------AGUGAU--UUUUU--GGCGUA-GUCCUAGUGG--CGCU-AUACUCU-CG-ACAGGUUAUCCCG--UCUCUUCAG----CUAGAUU-GAUGAGAUCAGGCAUC
AAFC03089644.1/10568-10702   AGGCUCCGC----CAAGUGC--CCUUUGCUCUAAGUAA---AUUUUUGGGAUUUUUUU------AGUGAU--UUUUCG--GCCGA-GUCUUAAAGG--CGCU-GUAGUCU-CGGACAGGUUACUCCG--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
AAKN02011212.1/4061-4195     AAGUUCCGC----GGGCUGC--UCUUUUCUCUAAGUUA---UUUUUGGUGAUUUUUUA-------GUGAU--UUUUUU-GGCGUG-GUCUUAGUGG--UGCU-AUACUCC-CGGACAGGUUAUCCAG--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
ABVD01165160.1/2057-1925     AAGCUCCAC----CGGCUGU--CCAGUGGUGGGAGUAA---UUUUUGGCGAUUUUUUA-------GUGAU--UUUU-G--GCGAA-GUCCUAGCGG--CGCU-AGAGUAU-CGGACAGGUUAUCCCG--GCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
ABRQ01105888.1/4247-4114     AAGCUCUGC----GGACUGC--UCUUUGCUAGAAGUAA---U-UUUGGAAAUUU--AAAUUAUU--------UUUUCU--GCAGA-GACCUAGUGGGCCAAU-AUACUAC-CGGACAGGUUAUCCCG--UCUCUCUCG----CUAGAUU-GAUGAGAUCAGGCAUC
AAQQ01600874.1/3159-3019     AAGCUUCGC----GGAUUGU--CUUUUGCUCCAAGUUA---UUUUUGGUGAUUUUUUUUUUUUUAGUGGU--UUUUCG--GCGGA-GCGCUAGUGG--CACU-AUACUUU-CAGACAGGUUAUCCCG--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
AAGV020165555.1/246-113      AAACUCCAC----CGGCUGC--CCUAUGUUAGGAAAAA---UUUUUUGCAAUUUUUUA-------GUGAU--UUUUCG--GCGAA-GUCCUAACGG--CGCU-GGAGUCU-CCGACAGGUUAUCCCG--UCUCUCCCG----CUAGAUU-GAUGAGCUCAGGAAUC
AF380425.1/151-15            AAGCCCCAC---C-GACUGC--CCUCUGCUCUAAGUUAAUUUUUUUGAUGAUUUUUGG-------GGGAU--UUUCCG--GCGUG-AUCCUAGCGU--CGCG-CUAGGCU-CGGACAGGUUAUCCCU--UCCCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
ABGA01025383.1/16958-17107   AAGCUCCGGC--CGAACUGCUCCUUUGCUCCAAAGUAA---UUUUUGGGCGGAUUUUUUA--AAAGUAAU--UUUUCCCGGCGGNAGUCAUAGUGG--CGCU-AUACUCUUCGGACAGGUUAUCCCUGUUCUCUCCCG----CUAGAUUUGAUGAGAUCAGGCAUC
AALT01467628.1/648-780       GAGCUCCGC-----GGCCUC--UCUCGGGUCAAAGUAA---UUUUUAGCGAUUUUUUG-------GCGAU--UUUUCG--GCGGA-CUUCGAGUGG--CGCU-GGGCUCU-CGGACAGGUUACGCCG--UCUCUCCGG----CUAGAUU-AAUGAGAUCGGGCAUC
AAPY01352997.1/326-189       --UUUCUAAG--ACGACUGCACCAACCCUUACAACUAA---UUUUCAGC--AAUUUUUUU--UUAGUGAU--UUUUC--GGUGGA-GUCCUGUUGG--UGUU-AUACUCU-CGGACAGGUUAUCGGU---CUCUCCCA----CUAGAUU-GAUGAGAUCAGGCAUC
AAIY01579408.1/1231-1098     AAACUCCAU----GCACUGC--CCUAUGAUAAAGGUAA---UAUUUGGAGAUUUGAAAAUUAUU--------UUUUG---GUGAA-GUUUUAGUGG--UGAU-GUACUCU-CAAAUUUGUUAUCUCA--UUUCUUCCC----CUGGAUU-AAAGAGAUCAGGCAUC
AAYZ01539185.1/153-298       AAGCACCGGCCGUGGAUUGC--CUUUUGCUCCAAAGAA---UUUUUUGCUGAUUUUUUUUUUUUAGCGAU--UUUUCC--GCGGA-GUCCCACUGG--CGCUUAGACUCU-CGGACAGGUUGUCCCG--UCCCUCCCG----CUAGAUU-GAUGAGAUCUGGGAUC
AANN01750438.1/130-267       AAGCUCCAC----GGGCUCC---UCUGGUUCGAUAAAA---UUUUUGACAAUUUUUUU-----CAGUGAU--CUUUUUCAGGUCGAGUCCGAGCGA--CUCU-GUGCCCU-CAGACAGGUUAUAUAA--UUCCUCCCG----CUAGAUG-GAUGAGAUCAUGCAUC
ABQO010856887.1/45-179       AAGCUCCCC----GAACCGC--CUCCAUCUACAGAAAA---UUUUUAAAAAUUUUUUG-------GUGAU--UUUUCG--GCGGG-UUAUCAAUGGGGUUCU-CCACCCG--GAUCAGAGUGACCAG--UCUCUCCCG----CUGAAUU-GAUGCGAUCAGGCAUC
AAFR03025973.1/6942-6808     AAGUUCCAC----GUACUGC--CUCCAUCUAGAGGAAA---UUUUAAAAGAUUUUUUG-------GCGAU--UUUUCA--GGGGG-UUCCCCAUGGGGCUUU-CCACCCG--GAUUAGGGUGCCCCG--UUUCUCCCG----CUGAAAU-GAUGCGAUCAAGCAUC
AAPN01007036.1/46381-46248   CGGCUCCGC----GGGCCAC--CCCGGGGCCGGGAGAA---UUUUUUAGGAUUUUUUG-------GCGAU--UUUUUG--ACGGG-UGUCCGACGG--GGGU-AUCCGCC-AGUUCAGGGUGUCCCC--UCUCUCCCG----CUGGAUU-GAUGCGAUCGGGCAUC
AADA01002428.1/530-641       GAGCUCUGU----GGACU----------------------------AGAGAUGUUUCU------CAUGAU--UUUUCA--GUGAG-UUCUUAGGGG--UCCC-AGCCUCU-CAGGCAGGUUAUCAUG--ACUCUCCCU----CUGAGCU-GAUGAGAUCGGACAUC
ABRN01136772.1/1944-1837     AAGCUCCAU----GGACUGC----------------------------AGAUACUUUU------CAUGAUUUUUUUCU--GUGAC-AUCUUAGGGA--UGCU-AUCCUCU-CAGGCAAGUUAUAACU--CUCU----------GGAAUU-GAUGAGAUUAGGUAUU
AAPE02006755.1/27052-26944   AAGCUCCA-----GGACU----------------------------AGAGAUACUUUU------UAUGAU--CUUUCA--GUAAU-UUCUUCAGAG--CAAU-AUCCUCU-CAGGCAGGUUAUUGCU--GCUCUCU------CAGAAUU-UAUGAUAUUAGGCAUC
AABR05051046.1/20835-20970   AAGCCCCAC---C-GACUGU--CCUUUGGUCUAAGUUAU-UUUUUUGAUGAUUUUUGG-------GGGAU--UUUCCG--GCGCG-AUCCUAGCGU--CGCG-CUACUCU-CGGACAGGUUAUCCCU--UCUCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
AAGW02061188.1/137789-137922 AAGCACCA----UGGACUGC--CCUUUGCUCCAAGUAA---UUUUUGG-UGAUUUUUU------AGCGAU--UUUUUG--GCGGA-GUCCUAAUGG--CGCU-AUACUCU-CGGACAGGUUGUCCCG--UCCCUCCCG----CUAGAUU-GAUGAGAUCAGGCAUC
AAQR03016951.1/64169-64278   AAGCUGCAU----GGACU----------------------------GGAAAUAUUUUU------CAUGAU--UCUA-A--GUGAG-GUUUUAGGGA--UGCU-AACCUCU-CAAGCAGGUUACUGGG--ACUUU-CUU----CUGAGAU-GAUGAGAUCCGACAUC
AAEX03009929.1/394512-394396 GAGACUCAU----GGACU-----------------------------GAGAAUGUUUU------CACAAU--UUUUCA--CUGAG-GUCUUGGUGG--CACU-AUUCUCC-CAGGUAGGUUACUGAGAUUCUCUCCCUCUGUCUCAGUU-AAUGAGAUUAAGCAUU
#=GC SS_cons                 :::::::::....:::::::..::::::::::::::::...:::::::::::::::::......::::::..::::::..:::::.::::::::::..::::.:::::::.::::::::::::::::..:::::::::....:::::::.::::::::::::::::
#=GC RF                      aAGCUCCgc....gGACUGC..CcuuugcUcgAaGuaA...UUUUUgGagAuuUUUUu......aGuGAU..UUUUCg..GcGgg.gUCcUaGuGG..cgcU.auaCUCU.CGGaCAGGUUAUcccg..uCUCUCCCG....CUaGAUU.GAUGAGAUCaGGCAUC
//
# STOCKHOLM 1.0

#=GF AC   RF02111
#=GF ID   IS009
#=GF DE   IS009
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Predicted; CMFinder; Burge SW
#=GF GA   117.00
#=GF TC   117.20
#=GF NC   114.30
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   21665928
#=GF RT   Genome-wide detection of novel regulatory RNAs in E. coli.
#=GF RA   Raghavan R, Groisman EA, Ochman H
#=GF RL   Genome Res. 2011;21:1487-1497.
#=GF RN   [2]
#=GF RM   12069726
#=GF RT   A bioinformatics based approach to discover small RNA genes in the
#=GF RT   Escherichia coli genome.
#=GF RA   Chen S, Lesnik EA, Hall TA, Sampath R, Griffey RH, Ecker DJ, Blyn LB
#=GF RL   Biosystems. 2002;65:157-177.
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   11


ACDM01000017.1/143-2       UGAAGGAUACGGA-AGCAGAAAAACUGUUCCGGAUCCGGGAGGCGGAAGAA--ACAAAAAACAACCUGAUGCAGGUAGCCAGUGAGCAUAUUGCGCCGCUUCAGGAUGCUGCAGAUCUGGAAAUUGCAACGGAGGAAGAAACCUC---------------------------------------------------------
CP000946.1/3655900-3655701 UGAAUGAUAAAAAUGGCGCAAAUACAGCGCCAUUUUUAUAGGUUAAAAACAUUGCUUUUUAUAUUCUGAUGCAGAUAGUCAGUGAGUAUAUCGCGCUACUUCAGGAUGAUGUAGAUCCGAAGAACGCUACAGAAGA-GAGGCAUUGUUGCUGGCAA-AUAGAAGAAGUAUCGGGUUUUGUUACCCCUGAAAAACGAAGCCCC
CU928164.2/443783-443583   UGAAUGAUAAAAAUGGCGCAAAUACAGCGCCAUUUUUAUUGGUUAAAAACAUUGUUUUUAACUUUCUGAUGCAGAUAGCCAGUGAGUACAUCGCGCUACUUCAGGAUGCUGUAGAUCCGGAGAACACUAUAGAGGAAGAGGCAUUGUUGCUGGCAG-AUGGAAGAAGUUUCGGGUUUUGUUAUCCCUGAAAAACGAAGCCCC
ACGN01000011.1/51529-51329 UGAAUGAUAAAAAUGGCGCAAAUAUAGCGCCAUUUUUAUAGGUUAAAAACGUUGCUUUUCAUAUUCUGAUGCGGACAGUCAGUGAUCAUAUCGCGCUACUUCAGGAUGAUGUAGAUCCGGAGAACGCUACAGAAGAAGAGGCAUUGUUGCUGGAAA-AUGGAAGAAGUUUCAGGUUUUGUUGUCCCUGAAAAACGAAGCCCC
ACDL01000051.1/39401-39597 UGAGAUCCCUUUA-GGCUCAA--ACAGAUAAUGCAUUGAAUGAUAAAAACAUUGCUUUUUAUAUUCUGAUGCAGAUAGUCAGUGAGUAUAUCGCGCUACUUCAGGAUGAUGUAGAUCCGAAGAACGCUACAGAAGA-GAGGCAUUGUUGCUGGCAA-AUAGAAGAAGUAUCGGGUUUUGUUACCCCUGAAAAACGAAGCCCC
CP000802.1/2799327-2799129 UGAAGGAUACGGA-AGCAGAAAAACUGUUCCGGAUCCGGGAGGCAGAAGAA--ACAAAAAACAGCCUGAUGCAGGUAGCCAGUGAGCAUAUUGCGCCACUUCAGGAUGCUGUAGAUCUGGAAAUCGCAACGGAGGAAGAAAUCUCGUUGCUGGAAGCAUGGAAGAAGUAUCGGGUGUUGCUGAACCGUGUUGAUACAUCAAC
CU928145.2/864560-864758   UGAAAGAUGCAGA-AGCAGAAAAACUGUUCCGGAUCCGGGAGGCGGAAGAA--ACAAAAAACAGCCUGAUGCAGGUAGCCAGUGAGCAUAUUGCGCCGCUUCAGGAUGCUGCAGAUCUGGAAAUUGCAACGGAGGAAGAAACCUCGUUGCUGGAAGCCUGGAAGAAGUAUCGGGUGUUGCUGAACCGUGUUAAUACAACAAC
AAJW02000001.1/70236-70428 UGAAAGAUGCAGA-AGCAGAAAAACUGUUCCGGAUCCGAGAGGCGGAAGAA--ACAAAAAACAGCCUGAUGCAGGUAGCCAGUGAGCAUAUUGCGCCACUUCAGGAUGCUGUAGAUCUGGAAAUCGCAACGGAGGAAGAAACCUCAUUGCUGGAAGCCUGGAAAAAGUAUCGGGUGUUGC------UGAACCGUGUUGAUAC
BABF01012618.1/788-590     UGAAGGAUACGGA-AGCAGAAAAAAUGUUCCGGAUCCGGGAGGCGGAAGAA--ACAAAAAACAACNUGAUGCAGGUAGCCAGUGAGCAUAUUGCGCCGCUUCAGGAUGCUGCAGAUCUGGAAAUUGCAACGGAGGAAGAAACCUCAUUGCUGGAAGCCUGGAAAAAGUAUCGGGUGUUGCUGAACCGUGUUGAUACAUCAAC
CP000800.1/853218-853416   UGAAGGAUACGGA-AGCAGAAAAACUAUUCCGGAUCCGGGAGGCGGAAGAA--ACAAAAAACAGCCUGAUGCAGGUAGCCAGUGAGCAUAUAGCGCCACUUCAGGAUGCUGUAGAUCUGGAGAUCGCAACGGAGGAAGAAACCUCAUUGCUGGAAGCCUGGAAAAAAUAUCGGGUGUUGCUGAACCGUGUUAAUACAACAAC
CU928158.2/2755306-2755108 UGAAAGAUGCAGA-AGCAGAAAAACUGUUUCGGAUACGGGAGGCGGAAGAA--ACAAAAAACAGCCUAAUGCGGGUAGCCAGUGAGAAUAUUGCGCCACUUCAGGAUGCGGUAGAUCUUGAGAUCGCAACGGAGGUAGAAACCUCAUUGCUGGAAGCCUGGAAAAAGUAUCGGGUGUUGCUGAACCGUGUUGAUACAUCAAC
#=GC SS_cons               :::::::<--<--.-<-<_________>->---->-->-------------..------------(((--((,,,<-<<--<<<<_____>>>>>>->,<<<-<<<<_______>>>>>>>,,,,))--)))::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UGAAaGAcacagA.aGCggAAAaAcuGcuCCggauuugggaGguagAAgaA..aCaaaaaAcAuuCuGAUGCAGguAGcCAGugAGcAUAUcgCgCuaCUuCAgGAUGcUGUAGAUCcGgAgAucGCaACaGAgGAAGAaaCaUugUUGCUGGaAg.aUGGAAgAAGUAUCGGGUuUUGuUgaaCCugaauaAugaAgCaaC
//
# STOCKHOLM 1.0

#=GF AC   RF02112
#=GF ID   DLG2-AS1_1
#=GF DE   DLG2 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   96.40
#=GF NC   75.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 43.12 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   13130513
#=GF RT   Novel putative nonprotein-coding RNA gene from 11q14 displays decreased
#=GF RT   expression in brains of patients with schizophrenia.
#=GF RA   Polesskaya OO, Haroutunian V, Davis KL, Hernandez I, Sokolov BP
#=GF RL   J Neurosci Res. 2003;74:111-122.
#=GF WK   DLG2-AS1
#=GF SQ   21


AF525782.1/3822-4034         UUAACUUGUUA-AUCAUAAA---UUGCUCUAC--AAAUAGUAUACUGGAAACAUCCGGAUGUGAGGUUAUAAUUAAAAAUG---AAAGCA----AAACAGCUUCCCUGAAAAGAAAGAAAA--CUCUUAAUUCAAACCUA-CCAGAUAGCUGAUUUAUGAAAGUGAAAAUGCUGGCAUGUAUAGA--UAUUGGGAAGUCUUGGGAUCUGGAUUUU-AUCACU-GACCAUCUGG-----
ABRP01085163.1/1770-1556     UUAACUUGUUA-AUCAUAAAAA-UUGCUCUCC-AAAGAAGUAUACUGGAAACAUCCGGAUGUGGGGUUAUAAUUAAAAAUA---AAAGCA----AAACAGCCUCCUUUAAAAGAAGUACAA--CUCUUAAUUCAGAUUUA-CUGGAGAGCUAAUA-AUGAAAGGGAAAAUGCUGGCAUCUAUAGA--UAUUGGGAAGUCUUGUGAUUUGGGUUUU-AUCACU-GACCAUCUGG-----
AAWR02018020.1/66855-66643   UUAACUUGUUA-AUCAUAAAAA-UUGCUCUUC--AAGAAGUACACUGGAAACAUCCGGAUGUGGAGUUAUAACUCAAAAUG---AAAGCA----GAACAGCUUCUCUUAAAAGAAGUGAAA--CUCUUAAUUCAAACUUA-CUGGAUAGCU-AUA-AUGAAAGCGAAAAUGCUGGCAGCUAUAGA--UAUUGGGAAGUCUUUGCAUUUGGAUGUU-AUCACU-GACCAUCUGG-----
AAFC03090425.1/17188-17402   UUAACUUGUUA-AUCAUAAAAA-UUGCUCUAC-AAGGAAGUAGACUGGAAACAUCCGGAUGUAGGGUUAUAAUUUAAAAUA---AUAGCA----AAACAGCCGCCCUUAAAAGAAGUAGAA--CUCUUAAUUCAAACUUA-CUGGAGAGCUGAUA-AUGCGAGUGAAAAUGCUGGCAUCCAUAGA--UAUUGGGAAGUGUUGGGAUUUGAAUUUU-AUCAUU-GACCAUCUGG-----
ABRT010009120.1/2188-1975    UUAACUUGUUA-AUCAUAAAAA-UUGCUCUCC-AAAAAAGUAUACU-GAAACAUCCGGAUGUGAGAUUAUAAUUAAAAAUG---AAAGCA----AAACAGCCUCUAUGAAAAGAAAUGAAA--CUAUUAAUUCAAAUGCA-GUGGAUAGUUGAUA-AUGAAAGUAAAAACACUGGCAUAUAUAGA--UAUUGGGAAGUCUUGGGAUUUGCAUUUU-AUCACU-GACCAUCUGG-----
ABVD01129166.1/1724-1511     UUGACUUGUUA-AUCAUAAAAC-UUGCUCUCU--AAGAAGUAUACUGGAGACAUCCGGAUGUGGGGUUAUAAUUAAAAAUG---AAAGCA----ACAAACCAU-CAUUAAAAGAAGUGAAA--CUCUUAAUUCAAAUUUA-CUGGAUAGCUGACA-AUGAAAGUGAAAAUGCUGGCAUGUACAGA--UAUUGGGAAGUCUUGGGAUUUGGAUUUUUAUCACU-GACCAUCUGU-----
ABRN01284461.1/6272-6058     UUAACUUGUUA-AUCAUAAAAA-UUGCUCUAC-AAGGAAUUAGACUGGAAACAUCCGGAUGUAGGGUUAUAGUUUACAAUA---AAAACA----AAACAGCCUCCCUUAGAAGAAGUAAAA--CUCUUAAUUCAAACUUA-CUGGGUAGCUGAUA-AUGCAAGUGAAAAUGCUGGCAUCUAUAGA--UACUGGGAAGCCUUGGGAUUUGAAUUUU-AACGUU-GACCAUCUGG-----
AAPY01156262.1/2481-2266     UUAACGUGUUA-AUCAUAAAAAGUCACUCUCC-AAGGAAGUAUACU-GAAACAUCCGGAUGUGAGGUUAUAAUUUAAAACA---GAAGCA----AAAGAGCUCUUCUUAAAAGAAGUAAAA--CUCUUAAUUCAAACUUAACUAGAUAGCUAAUA-AUGACAGUGAAAAUGCUGGCAUGUAUAGA--UAUUGGGAAGUCUUGGGAUUUGGAUUUU-AUUACU-GACCAUCUGG-----
ABRQ01458408.1/272-59        CUGUCUGGCUA-AUCAUAAAAAAUUGCUCUCC-AGAGAG-UAUAUUGGAAACAUCCGGAUAUGGGGUUAUAAUUAAAAAUG---AAAGCA----AAACAGCAU-CCUUAAAAGAAGUGAAG--CCCUUAAUUCAAAUUUA-CCAGAUAGCUGAUA-AUGUAAGUGAAAAUGCUGGCAUACACAGA--UAUUGAAAAAUCUUGGAAUUUGAACUUU-AUCACU-GACCAUCUGU-----
ABRR01144011.1/20340-20123   UUAACUUGUUA-AUCAUAAAAA-CUGCUCUGC-AAAGAAGUACACUAGAAACAUCCGGAUGUGGGGUUACAAUUUUUUUUUUUUAAAGUG----AAACAGCCUCCCUUAAAAGAAGUAAAA--CUCUUAAUUCAGACUUA-CUGGAUAGCUGAUA-AUGCAAGUGAAAAUGCUGGCAUCUACAGA--UACUGGGAAGUCUCUGGAUGUGAAUUUU-AUCAGU-GACCAUCUGG-----
AAIY01127316.1/5724-5937     CUGUCUGAUUA-AUCAUAAAAA-UUGCUCUCC-AAAGAGGUAUACUGGAAACAUCCGGAUGUGAGGUUAUGAUUACAAAUG---AAAGCA----AAGUAGUAU-CCUUAAAAGAAGUGACA--CUCUCAAUUCAAGCGCA-CUAAAUAGCUGAUC-AUGAAAGUGAAAACGCUGGCAUCUGUAGA--UACCCGGAGUUCUUGGGUGUUGGACUUC-AUCACU-GACCAUCUGG-----
AAYZ01150310.1/240-451       UUAACUUGUUA-GUCAUAAAAA-UUGCUCUCC-UAAGAAAUAUGCUGGAAAUAUCCGGAUGUAGAUUUAUAAUUAAAACUG---AAAGCA----AAACAGCCUUCUUUAAAAGAAGUGAAA--UUAUUAAUUCAUAU----CUGCAUAGCUUAUA-AUGAAAGUGAAAAUGCUGGCAUGUAUGAA--UACUGGGAAGUUCUGGGAUUUGAAUUUC-AUCAUU-GACCAUCUUG-----
AAKN02037870.1/21589-21380   UUAACUUGUUA-AUCAUAAAAA-UUGCUCUCCCAAAAAAAUAUACUGGAAACAUCCGGAUGUAGG-UUAUAAUUAAGAAUG---AAAGCA----AAACAGCCUUCCCUAAAAGAACUGAAA--UUCUUAAUUCAAACAUA-UAGCAUGGUUGAUA-AUGAAAGUAAAAAUGCUGAUAUAUAUUGA--AAUUGAGAAGUUUAGAGAUU-----UUU-AUUACU-GGCCAUCUGG-----
ABDC01223973.1/7050-7262     UUAACUUGAUA-AU----AAAAUUUGUUCUCU-GAGGAAGUAUACUAGAAACAUCAUGAUUUGGGGUUAUCAUUUAAAAUG---AAAACAAAACAAACAGAAUCCCUUCAAACAAAUAAAA--CUCUUAAUUCAAACUUA-CCAGAUAGUUGAUA-AUAAAAUUGAAAAUACUGGCAUGUAUAGA--CAUUGAGAAGUCUUGGAAUUUGGAU----AUCACU-GAACAUCUGG-----
ABRO01204500.1/1107-896      UUAACUUGUUA-AUCAUAAAAA-UUGUUCUCC-AAAAAAGUAUACUCGAUACAUCCGGAUGGAGGAUUAUAAUUAUAAAUG---AAAGCA----AAAUAGCCUUUCCUGAAAGAAGUGAAA--UUCCU--UUCUAACUAG-CAGUAGAGGCAAUA-GUAGAAAUGAAAAUACUG-UUUGUAAAGA--CAUGGAGAAGUGUGAGAAUUGGGAUUUU-AUCACU-GACCAUCUGG-----
AAHX01007143.1/51775-51981   UUAACUUGUUAGAUCAUAAAAAAAUUCUUUCC-AAAAAA-UAUACUGGAAACAUGUGGAUGUGCAGUUAUAAUUAAAAAUG---AAAGCA----AAACAGCCUUCCCCCAAAACAGAGGAAGCCCCACAAGUCAAAGCUA-CAGCUAAACUGAUG----AGAGCCAAAA---------AUAGGGGGUUACUGAAAAGUCUUGGAAUAUGG--UCACAUCACU-GA-----UGGUAUUC
AAPE02025456.1/142197-141983 UUAACUUCUUA-AUUAUAAAAA-UUGCUCUCC-AAAGAAGUGUAUUGGAAACAUCCGGAUGUGGGGUUAUAAUUAAAAAUG---AAAGCA----AAACAGCCUCCCUUAAAAGAAGGGAAA--CUCUUAGCUCAGACUUA-CUGGAGAGCUGAUA-AUGAGAGGGGAAAUGCUGGCAUCUAUAGA--UACUAGGAAGUCUUGGGAUUUGGAUUUU-AUCACU-GACCAUCUGG-----
AAEX03012754.1/496055-495841 UUAACUUCUUA-AUCAUAAAAA-UUGCUCUCC-AAAGAAGUAGACUGGAAACAUCCGGAUGUGAGGUUAUAAUUUAAAACA---AAAGCA----AAACAGCCUCCCUUAAAAGAAGUGAAA--UGCUUAAUUCAAACUUA-CUGGAUAGCUGAUA-AUGAAAGUGAAAAUGCUGGCAUCUAUAGA--UAUUGGGAAGUCUUGGGAUUUGAAUUUU-AUCACU-GAGCAUCUGG-----
AAQR03000688.1/111760-111554 UUAACUUGUUG-AUCAUAAACU-UUGCUCUCA-GAAAAAGUAUACUGGAAAUGCCCUGAUUGGGGGUUAUAAUUAAAAAUG---AAAACA----AAACAGCCUUUCUUAAAA-AAAUAAAA--UUCUUAACUAAGAC----UUGGAUAGCUGAUG-AUGAAAAUGAAAACACUGGCAUGUGAAGA--UACAGGGAAG-GUUGGAAUUUGGAU----AUUACU-GACCGUCUGG-----
AAGW02008491.1/36537-36748   AAAUUUUGUUA-AUCAUAAAAA-UUGUUCUCC-CAAGAAGUAUACUGGAAAUAUCCAGAUGUGGAGUUAUAAUUAAAAAUG---AAGGCA----AAAUAGCUUCCCUUAAAAGAAGUGAAA--CUAUUAAUUCCAAU----CUGCAGAGCUGAUA-AUGAAAGUGAAAAUGCUGUCAUGUAUAGA--UACUGAGAAGUGUUGGGAUUUGAAUUUC-AUCACU-GACCAUCUGG-----
AAGU03072873.1/79513-79728   CUGUCUGGCUA-AUCAUAAAAA-UUACUCUCC-AAAGAA-UAUACUGGAAACAUCUGGAUGUGGGGUUAUAAUUAAAAAUG---AAAGCA----AAACAGCAC-CCUUAAAAGAAGUGGAA--CUCUUAAUUCAAAUCUA-CCAGAUAGUUGACA-AUGAAAGUGAAAAUGCUGGCAUAUAUAUAGCUAUUGGAAAAUCUUGAGAUUUGGACUGU-AUCACUUGACCAUCUGG-----
#=GC SS_cons                 :::::::::::.::::::::::.:::::::::.::::::::::::::::::::::::::::::::::::::::::::::::...::::::....:::::::::::::::::::::::::::..:::::::::::::::::.::::::::::::::.:::::::::::::::::::::::::::::..::::::::::::::::::::::::::::.::::::.::::::::::.....
#=GC RF                      uUaaCUUGUUA.AUCAUAAAAa.uUGCUCUcC.aAagAAGUAuACUGGAAACAUCcGGAUGUGgGGUUAUaAUUaaaAaUG...AAAGCA....AAAcAGCcUccCUuaAAAGAAGugaAA..cuCuUAAuUCaaAcuuA.CuGgauAGcUGAUa.AUGaaAGuGAAAAUGCUGGCAUgUAuaGA..uAuuGgGAAGUcUuGGgAUuUGgAuUuu.AUCAcU.GACCAUCUGG.....
//
# STOCKHOLM 1.0

#=GF AC   RF02113
#=GF ID   DLG2-AS1_2
#=GF DE   DLG2 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   70.00
#=GF TC   86.30
#=GF NC   64.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.03 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   13130513
#=GF RT   Novel putative nonprotein-coding RNA gene from 11q14 displays decreased
#=GF RT   expression in brains of patients with schizophrenia.
#=GF RA   Polesskaya OO, Haroutunian V, Davis KL, Hernandez I, Sokolov BP
#=GF RL   J Neurosci Res. 2003;74:111-122.
#=GF WK   DLG2-AS1
#=GF SQ   23


AP001825.4/191918-192135     GAGCUGUCUGUCUUUUCCAUUUGGGCUGUGGCAGACUGAGCUGAGUAGG--UCAGGGAUAUGUUUUAC----AGGCAUUACGCA--GGCCAGUCUUCAGAGGCCAGUGUGCAUGGU------GGGU-CCAGCCAUCCUCAGA-----CAUACUCUGCACAUGUCAU---------------GCUGGGGG-ACAGAGCAGCGUGUGUG---CUGUCUGGAUGAUUCCUCUUGGAAUGUUGGUUGCCUAGCAACAAGAU
AANU01189030.1/803-1020      GAGCUGUCUGUCUUUUCCAUCUAGGCUGCAGGAGACUGAGCUGAGUAGG--UCAGGAAUAUGUUUUAC----AGGCAUUACACA--GGCCAGUCUUCAGAGGCCAGUGUGCAUGGU------GAGU-CCAGCCAUCCUCAAA-----CACACUCUGCACAUGUCAC---------------GCUGGCGG-ACAGAGCAGCCUGUGUG---CCGUUUGGAUAUUUCCUCUUGGAAUGUUGGUUGCCUAGCAACAAGAU
AAPY01628483.1/350-137       GGGCUGUCUGUCUUUUCCAUCUGUGCUAC---AAAGUGAGCUGAGAAGG--UCAGGGGUAAGUUCUAC----AGGCAAUACACA--UGCCAGACUUUGGAGGCCAGUGUGCACAGC------GAGU-CCAGCCAUUCUCACA-----A-CACUAUGCACAUGUCAU---------------GCUGGAGG-GCAGAACAGCGGGUGUG---CUGUCUGGAGGUCUCCUCCUGGAAUUUCAGUUGCCUAGCAACGAGAU
AAWR02018020.1/63128-62914   GAGUUGUCUGUCUUUUCUAUCUGGGCUGC---AGACUGAGCUUAGAAGG--UGAGGAGCAUGUUCUAG----AGGCAGGACACA--UGCCGGACUUUGGAGGCCAGUAUGCACAGA------AAGU-CCAGCCAUCCUCACAA---A--CACUCAGCACAUGUCAU---------------GCUAGGGG-GCAGAGAAGAGGAUGCG---CUGUCUGGAGGUCUCCUCCUGGAAUGCUGGUUGCCUAGCAACAAGAU
ABRP01085162.1/17243-17029   GACCUGUCUGUCUUUUCCAUCUGGGCUGC---AAACUGAGCUGAGAAGG--UCAGGGGCAUAUUCUAU----GGGCAGGACACA--UGCUGGACUUUGGAGGCCAGUUUGCAUAAG------GAGC-UGAGCCAUCCUCACA-----AACACUCAGCACAUGUCAC---------------UCUGGGGG-GCAGAGCAGUGGGUGUA---CUGUCUGGAGGUCUUCUCCUGGAAUGCUGGUUGCCUAGCAACAAGAU
ABRR01144011.1/16728-16509   GAGCUGUUUGUCUUUUCCAUCUGGGCUGC---AGACUGAGCUGAGAAGG--UCAGGGACACAUACUAC----GGGCAGGACGCA--UGCUGGGCUUUGGAGGCCAGUGUGUAUAGG------GAGU-CCAGCCAUCCUCACAGAACAAACACUCAGCACGUGUCAC---------------GCUGGGGG-GCAGAACAGCGGGUGUA---CUAUCUGGAGGUCUCCUCCUGGAAUACUGGUUGCCUAGCAACAAGAU
ABRT010009119.1/3796-3598    GAGCUGUCUGUCUUUUCCAUCUGGGCUGC---AGACUGAGGUAA---GG--UCAGGGGCAUGUUCUAC----GGGCAGAACACA--GGCCAGUCUUCAGAGACCAGUGUGCAAGG-------GAGU-CCAGC----------------ACACUGUGCACAUGUCAU---------------GCUGGGGG-ACAGAGCAGCAUGUGUG---CUGUCUGGA-GGUCUGUCUUGGAAUGUUGGUUGCCUAGCAACAAGAG
ABRN01284461.1/2161-1942     GAGCUGUUUGUCUUUUCCAUCUGGGCUGC---GGACUGCGAUGAGAAGG--UCAGGGGCACAUUCUAU----GGGCAGGACACA--UGCCGGACUUUGGAGGCCAACGUGCAUAGG------GGGU-CUAUCCAUCCUCACAAAAUAAACACUCAGCACACGUCAC---------------GCUGGGGG-GCAGAAUAGCGGGUGUG---CUGUCUGGAGGUCUCUUCCUGGAAUGCUGGUUGCCUAGCAACAAGAU
ABDC01223973.1/10371-10584   GGGCUAUCUGUUUUUUUCAUCUGGGCUGC---AGACUGAGCUGAAAAGG--ACACGAGCAUGUUCUAC----GGGCAGUCCACA--GGCCAGUCUUCAGAGGCUAGUGUACACAGG------GAGU-CCAGCGAUUCUCACC-----AACAC--UGCACAUGUCAC---------------GCUGGGGGGACACAGAAAGAGAUGUG---CUGUCUAGAGGUCUCCUCCUGAAAUGCUGGUUGCUAAGCAACAAGAU
AAYZ01150311.1/1305-1516     GAGUUGUCUGUCUUUUCCAUCUGGACUGC---ACACUGAACUGAGAAGG--UCAGGGUCAUGAUCGAU----GGGCAGUAUACU--UGCCAGAC--UGAAAGCCAGUAUUCAUAGA------GAGA-CCAACAAUUCUCACA-----AGCACUCUGCACAUGUUAU---------------GCCCAGGG--UAGAGCAGCAGGUGAG---CUAUCUGGAGCUCUCCUCCUAGAAUGGUAGUUGCCUAGCAACAAGAU
ABVD01129165.1/4784-4587     GAGCUGUCUGUCUUUUCCAUCUAGGCAGC---ACACUGAGCUGAGAGGA--UUAGGGGUAUGUUCUAC----AGGCAGGACACA--UGCCAGACUUUGGGGGCCAAUGAGCAUAAU------GAGUUCCAGCCAUCCUUACA-----AACAUUCAACACUUGUCAC---------------UCUGGGGGCACAGAGCAGCAGGUGUG---CUGUCUAGAGGUCUCCUAGCAACAGAGC-------------------
AAIY01406486.1/716-934       GUGCUGUCUGUCUUUUCCAUCUGAACAUC---ACACUGAUCUGAGAAGG--UCUGGGCCAUGGUCUACUGAUGGGCAGAACAUG--GGCCAGACCGGGGAAGUCGGUGUGCACAGG------UAGUUCUAGCCAUCC-CCAA----ACACACUCAGC-UGUGUCAU---------------GCUGGAGGGGCAGAGCAGCCAGGGUG---CUGUCUGGAAGUUUCCUCCUGG-AUGGUAGUUGCCUAGCAACAAAAU
AAKN02037870.1/13940-13730   GAGCUGUCUGUCUUUUCCAUCUGGGCUAC---ACAGUGAGCUGAGAAGG--UCAAGUGUACUAUCUAU----GGGCAGCACACA--UGCUGGGACUUGGAGGCCAGUUUACGUGUA------GAAA-CCAGUUAUUGUCACA-----AACACUCUGAGCAUGUCAU---------------GCUGAGGG--CAAAGCAGCAAGCGU----CCAGUUGGAGGUCUCCUGCUAGAAUGUUUGUUGCUUAGCACAGAU--
ABRQ01458407.1/1548-1336     GAGCUGCCUAUUUUUCCCAUGUGAGCAGU---ACAUCAGGCUGGGAAGU--UCUGGGGCACAUACUAC----AGGCAGAACACA--GGCAGGAUUUUGGAGGACAGUGUAUGUAGA------GAAUUCUAGCCAUCCUCCCC----ACACACUCAAUAUGUAUCAC---------------ACUGGA-GGACACAGCAGCCAGUGUG---CUGUCUGGAAG---UCUCCUGG-AUGUUGGUUGCCUAGCAACAAAAU
AAFC03090425.1/20968-21182   GAGUUGU-UGCCUUUUCCAUCCAUGCUAC---AGCCUGAGCUAAGGCGA----GGGGGCAUGUGCUGU----GGGCAGCACACU--GGCCAGACUUUG-AGGCCAGUGUGCACGGG------GAGC-CUGGCCAUCCUCACAAAACAAACACUCAGCACAUGUCAC---------------GCCAGGGG--CAGCACAGUGGGGGAG---CUGUCUGGAGGUCUCCUCCUGAAAUGCUGGUUGCCUAGCAACAGGAU
CAAA01004439.1/16293-16084   GAACUGUCUGUCUUUUCCAUCUGGGCUGC-----ACUGAGCUAAGAUGG--UCAGGGACAUACUGUAU----GGACAAUACACA--UGCCAGAUGUUAUAAAUCACUGAGUAAAG-------GAGUUUUCCUCAGCUACAUA-------UUCUGAACACAUGUUAU---------------GCUAUGGG--CAGAGCAAAGGGCACC---CUAUGAGGAAGACCUUUCUUAGACUUUUGGUUGCCUAGUAACCAGAC
AALT01232049.1/749-962       AUCCCGGGGCUCUUUUCCAUCUGGGCUAU---AGAUCAAGCUGAGAAGG--CCAGGGGCCAGCCCUGU-----GGAAAGACACC--UGCUGAAGAGUGGAGGCGAGGGUGCCCAGA------AAGU-CCAGCUGUCCUCAGA-----GAUGCUCAGAAUAGGGAGG----------------CUAGGGGUGCAGAGAACAGAGUCUG---CUGUCUGGAGGAAUCUUCCUGGAAUGCUGGUUGCUUAGCAACAAGCU
AANN01457332.1/808-1031      GAGCAGUC----UUUUCCAUCUGGGUUCC---AGACUGAGUUGAGAAGG--U-UGGGGUAAGCUUUAU----AGGAAGGACAUA--GGUUGAAUUUGGGAGGCCAGUAUGUGUAGG------AAGC-CCAGCCAUUCUCAUA-----AACACUCAGCACAUGUCAGACCAGGGGGCUGGGAGGUGGGGG-GUAGAGCAGCAGGUGUG---CUGCCUGCACUGUUCCUCCUGGAAUGCU-GUUGCUUAGCAACAAGAU
ABRO01204499.1/2779-2548     UGUCUGUGUGUCUUUUCCAUCUG-GCCGC---ACACUGAGCUGAGAAGG--UCAGGGGCAUGUUCUAC----AGGCGGCAUACA--UGCCACACUGUGGAGACCAGUUUGCAUAGGGUGGGGGAGU-CCAGUCAUUUUCUCA-----CAC--AGUAUGUUUCUCAUGGGUGUG-GGGGCGGGGAGGAGG-GCAAAGCAGUGGGCGUU---CUAUCUGAAGGUCUCUUCCUUGAAUAUCGGUUGCUUAGCAACCAGAU
AAEX03012754.1/492656-492441 GAGCUGUCUGUCUUUUCCAUCUGGGCUGC---AGACUGAGCUGAGGAGG--GCAGAGGCAUGUUCCA-----GGGCAGGGCACA--UGCUGGACUUCUGAGGCCAGUGUGCAUAGA------GAGU-AUAGCCAUCCUCGCA-----AAAACUCAGCACAUGUCACA-------------UGCUGGGGG-GCAGAACAGCGGGUGUG---CUGUCUGGAGGUCUCCUCCUGGAAUGCUGGUUGCCUAGCAACAAGAU
AAGU03072873.1/82725-82937   GAGUUGUCUAUCUUUUCCAUCUGGGCAGC---ACACCAAGCUGAGAAGGGGUCUGGGGUGUAUACUAC----AGG-AGGACACA--GGCUGGACUUUGGAGGCCAGUGUGCAUAGG------GAGUUCCAGCCAUCC---CC----ACACACUCAGUAUGUAUCAC---------------ACUGG--GGACAGAGCAGCCGGUGUG---CUGUCUGGAUGGCUCCUCCUGG-ACAUUGGUUGCCUAGCAACAAAAU
AAPE02025456.1/139261-139045 GAGCUGUCUGUCUUU-CCAUCUGGGCUAC---AGACUGAGCUGAGAAAG--UCAGGGGCAUGUUCUCC----GGGCAGGACACA--UGCUGGAGUUUGGAGGCCAGUGUGCAUAGG------GAGU-CUAGCCAUCCUCACA-----ACUGCUCAGCACAUGUCUC---------------GCUGGGGG-GCAGAACAGUGCAUGUCUGUCUGUCUGGAGGUCUCCUCCUGGAAUGCUGGUUGCCUAGCAACAAAAU
AAGW02008491.1/41246-41462   GAGCUGUCUGUCUUUUCCAUCUGGGGGGC---ACACUGAGCUGAGAAGG--UCAGAGUCAUGUUCUAC----GGGCAGUACACAAACGCCCGACUUUGGAGGUCAGUAUGCAUAGG------GUGG-CCAGCCAUUCUCACA-----AGCUUUCUGCACAUGUCAU---------------GCUAGGGG-ACAAAGCAGCAGGUGUG---CUGUCUGGAGGUCUCCUCCUGGAAUGGUGGUUGCCUAGCAACAAGAU
#=GC SS_cons                 :::::::::::::::::::::::::::::...:::::::::::::::::..:::::::::::::::::....::::::::::::..::::::::::::::::::::::::::::::......::::.:::::::::::::::.....:::::::::::::::::::...............::::::::.:::::::::::::::::...:::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      GagCUGUcUGUCUUUUCCAUCUGGGCugC...AgACUGAGCUGAGaaGG..UCaGGGgcAuGuucUac....gGGCAGgACACa..uGCcgGacuuuGGAGGCCAGUgUGCauAGg......GAGu.CcAGCcAUccUCacA.....aacaCUcaGcAcaUGUCAu...............GCUGGGGG.gCAGAGCAGcggGuGUg...CUGUCUGGAgGucUCcUCCUGGAAUguUGGUUGCcUAGCAACaAGAU
//
# STOCKHOLM 1.0

#=GF AC   RF02114
#=GF ID   FAM13A-AS1_1
#=GF DE   FAM13A antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   70.00
#=GF TC   77.90
#=GF NC   63.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.29 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   15234000
#=GF RT   Cloning and characterization of FAM13A1--a gene near a milk protein QTL on
#=GF RT   BTA6: evidence for population-wide linkage disequilibrium in Israeli
#=GF RT   Holsteins.
#=GF RA   Cohen M, Reichenstein M, Everts-van der Wind A, Heon-Lee J, Shani M, Lewin
#=GF RA   HA, Weller JI, Ron M, Seroussi E
#=GF RL   Genomics. 2004;84:374-383.
#=GF WK   Long_non-coding_RNA
#=GF SQ   10


AAFC03128838.1/5061-4947     AGACUUGGAGGAACCAUAAUAAAAC-UGUGGAUAA-CUUACUAA-AGUCUUAGGAGGAACUUG-GUCAUAGU-UGAUAUUGAAU---AGAGAGAACAAGUGUCUGGGACUUUCUGCCACCGGU
AAKN02040788.1/159306-159419 AAACUUGUAGGAAUUAUAGUAACAG-AGUAGGUAACUUCA---A-AAUCUUGUGAUGAGCUU-GUUGUAAUU-UGCUACUGAACC--AGAGAAGACAAUUCUUUUGGCUUUUUGGCCAUGUAG
AAPY01833016.1/275-390       AGACUUGCAGGGCCUGCGGUAACCG-AGCAGAACGCCUUCCUGA-AGCCCUCAGAGGACCUCGAGUCAUACU-U--UGUGGAACU--GGAGAAAACGAGUGUUUGGGCCUUUCUUCCAGGUAA
AAWR02004794.1/160960-160851 AGACGUGCAGGAAUCACAAUGACAG-AGUGGCUGACCUCACUGA-AGUCUUAGAGGGA--------CUUAGUUGGACGUUGAACC--AGAGAGAACA-GUGUUUGGACCUUUCUGCCACAGGG
ABDC01220640.1/1285-1406     AGACUUGGAGGAAUCCUAAUAAACUGAGUGGAUGAUCUUCCUGA-AGUUUUAGGAAGAACUCGAGUCAUAAUUUGACACUGAAUCAGGGAGAAAACAAGUGUUUGGAUUUUUCUGCUACAGAG
ABRQ01141839.1/3197-3315     AGGCUAACAGGGAUCACAGCAAUAAAAGUGGGUAACCUCAGCAA-AGGCAUGUGAGGAAAGUAGGUCAAACU-UAAUGCUGAACC--AGAGAGAACAAGCAGAUGGGUUUUUCUGACAAAAAC
ABRR01224949.1/462-577       AGACUUGCAGGAAUCAUAACAACAG-AGCUGGUAA-CUUGCUGA-AGUCUUAGGAGGAACGUG-GUCAUAGC-UGACACUGAACC--AGAGAGAACAAAUGUGUGGGCCUUUCUGCCACAGGG
AK126217.1/359-477           AGACUUGCAAAAAUUACAGUAACAG-AGUGAAAAACCUUCUUGA-AGUGUUAGGAGGAACUUGAGUCAUAAUUUGAUGUUGAAUC--AGAGAGAACAACUGUUUGGGCUUAUUUGCCUCAGAG
AANN01464110.1/3906-4022     AGAUUGGCAAGAGUCACAGCGACAA-AGUGGGUGGCCUUGGCCAGUGGCCUGC-AGGAAUGUGGGUCAUUAU-UGACGUUGACCC--AGUGAGAGCA-GUGUCUAGACCUUCCUGACAAAAAG
AAGU03053900.1/926-811       AGACUAGCAGGGAUCACAGUAAUAA-AGUAGGUA--CUCACUGA-AGUCGUAUGAGGAACGUGGGUCAAAUC-UGAUGCUGAACC--AGAGAGAACAAGUGUGUGGGCUUUUCUGACACAGGG
#=GC SS_cons                 :::::::::::::::::::::::::.::::::::::::::::::.:::::::::::::::::::::::::::.::::::::::::..::::::::::::::::::::::::::::::::::::
#=GC RF                      AGACUuGcAGGaaUCacAGUAAcAg.AGUgGgUaaCCUuacUgA.AGuCuUagGAGGAacuUGgGUCAuAaU.UGAuGuUGAACC..AGAGAGAACAAgUGUuUGGGcuUUUCUGcCAcagag
//
# STOCKHOLM 1.0

#=GF AC   RF02115
#=GF ID   FAM13A-AS1_2
#=GF DE   FAM13A antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   38.00
#=GF TC   39.90
#=GF NC   36.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.96 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   15234000
#=GF RT   Cloning and characterization of FAM13A1--a gene near a milk protein QTL on
#=GF RT   BTA6: evidence for population-wide linkage disequilibrium in Israeli
#=GF RT   Holsteins.
#=GF RA   Cohen M, Reichenstein M, Everts-van der Wind A, Heon-Lee J, Shani M, Lewin
#=GF RA   HA, Weller JI, Ron M, Seroussi E
#=GF RL   Genomics. 2004;84:374-383.
#=GF WK   Long_non-coding_RNA
#=GF SQ   10


AC108065.3/60853-60960       GAUUCAGAAUCCAUGGCUGGAAGAGGUAGU---AAGGCCAUUGGGAGG-----GCAUGCCUCUCCUCAGCC-----CACCCC--CACCCUGUGUG--GGUCUCCAUUCUGAAAUUUC-CAUUCAGG
AANU01104240.1/2911-2805     GAUUCAGAAUCCAUAGCUAGAAGAGGUAAU----AGGCCAUUGGGAGG-----GCCUGCUUCUCCUCAGCC-----CGCCCC--CACCCCGCGUG--GGUCUCCAUUCUGAAAUUUC-CAUUCAGG
AAWR02004794.1/151522-151411 GACUCAGAAUCCAUUUCUAGAAGAGGUAAUACUGAGGCCAUUGACAGG---GACUGCCUCUGCCCCUCAGC-----CUCCUC--CCCGGGC-GUA--GGUCCCCAUUCUGAGACUCC-CAUUCAGC
AAFC03126434.1/10358-10470   AAUUCAGAAUCCAUUUCUAGAGGAGGUAAU---GAGGCCAUUGAGAGGCCUGAUAAGGACUGUCCCUCUCC-----CCUAGC--CUACGCCUGUU--GGUUCCUGUUCUGAAAUUCC-CAUUCAGG
ABRT010044670.1/1674-1785    GAUUCAGAAUCCAUUUCGAGAAGAGGUAAU---GAGCCCAUGGAGAGGG--GGCUGCCUCUUCUCCUCAGC-----CCGCCC--CACCCCAUAUG-UGGGUCCUGUUCUGGCCUUUC-CAGGUAGC
ABRN01149944.1/2226-2341     GAUUCAGAAUCCAUUUCUAGAGGAGGUAAUAAUGAGGCUAUUGAAAGGAGCGACGAGGACUGUCCUUCUCU-----CCCAAC--CUCCCCCCGUC--GGUCCCUGUUCUGAAAUUCC-CAUUCAGU
AAGV020057930.1/1192-1294    GAUUCAGAAUCUAUUCCUAGAAGAGAA-------AUGCCUUCUAC--------CUCCCACUCCCCGCCGAC-----CCC-UC--CACCCUGUGUUUAGGUCACCAUUCUGAAAUCCCCCUUUCAGG
AAEX03016754.1/104107-104220 GAUUCAGAAUCCAUUUCUAGAAGCAGUGAUAAUGAGGCCAUUGAAAGAACUGAAAGGGACCGCCUCUCUUC-----CCU-GC--ACAGCCCUGUA--GGUCCCCAUUCUUAAAUUCC--AUUCAGG
AAPE02007756.1/74010-74111   GAUUCAGCAUCCAUUA---GAAGUGGUUAUCAUGAGCCCCUUGAAUGA-------AAGGCACUGCCUCUUC-----CCCCGC--A----CGCGCG--GGUCCCGGCUCUGAAACUCC-CACUCAGG
AAGU03053899.1/68952-68832   GAUUCAGACUCUAUUUCUAGAAGAGGUAAUAGUGAGGCCAUUGAAAGUA-CUGCCUCUCCUACUCCUCAACUUUUGCCCCCCACUCCCGAGUGUA--GGUCCCCAUUCUGAAAU-CC-CAUUCAGG
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::..::::::::::::::::::::.....::::::..:::::::::::..::::::::::::::::::::.::::::::
#=GC RF                      GAUUCAGAAUCCAUUuCUAGAAGaGGUaAUaaUGAGGCCaUuGAgAGga..ggcuacgaCUgccCcUCucC.....CccCcC..caCCccgUGUg..GGUCcCcaUUCUGAaAUUCC.CAUUCAGg
//
# STOCKHOLM 1.0

#=GF AC   RF02116
#=GF ID   FAS-AS1
#=GF PI   SAF
#=GF DE   FAS antisense RNA 1 conserved region
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   55.00
#=GF TC   59.00
#=GF NC   46.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   15829500
#=GF RT   Identification and characterization of a novel gene Saf transcribed from
#=GF RT   the opposite strand of Fas.
#=GF RA   Yan MD, Hong CC, Lai GM, Cheng AL, Lin YW, Chuang SE
#=GF RL   Hum Mol Genet. 2005;14:1465-1474.
#=GF WK   FAS-AS1
#=GF SQ   19


AY450925.1/2908-3077         CAAUGUUGGCUGCUU-UGAAAAUCUCAU--------AGUUUUUGGA-CAGCAGUAUU---AGUAAAGUGUAAGAAAAUUGUCAAAGCUUGGA-GCUAUGCUUGUUGAA-CUUUUGUACCAAUAGCACCUUUACCAGAGGCUGCG-UGU--UUAAAGCCCGAAGAAAACUUUGCUUUUCUGAAAGAAUA----
AANU01192721.1/41656-41827   CAAUGUUGGCUGCUU-UGAAAAUCUCUU--------AGUUCAUGGA-CAGCAGUAUU---AGCAAAGUGUAAGAAAAUUGCCAAAGCUUGGA-GCUAUGCUUAUUGAA-CUAUUGUACCAAUAGCACCUUUACCAGAGGCUGCG-UGUGUUUAAAGCCCGAAGAAAACUUUGCUUUUCUGAAAGAAUA----
ABRT010121123.1/268-438      CAGCUUUGGUUGCUU-UCAAAAUCUCUCUU------AGUUCUUGGA-CAACAGUAUU---AGCAAAGUGUAACAAAAUUAUCAAAGCAUGGA-GACGUGCUGGUUUAA-CUUUUGUAC-AAUAGCAUCUUUACCCGAGGCUGA---AUGUUGAGAGCACCAAGAAAACUUUGCUUGUCUGAAGGAAUG----
ABDC01116622.1/2510-2682     CAGUGUUGGUUGCUU-UGAAAAUCUCUUUUAUUAAUAGUCCUUGGA-CAGCAGUAUU---AGCAAAGUGUAGUCAAAUUGUCAAAGCAUGGA-GCUAUGCU----GAA-CUUUUAUAC-AAUAGCAUCUUUAUCAGAGGAUCAU-UGU--UUGAAGUACCAAGGAAACUUUGCAUUUCUGAAAGAAUA----
AAWR02007878.1/27819-27650   CAGUGGUGGUUGCUU-UGAAAAUAUCUCUU------AGAUCUUGGGACAGCAAUACU---AGUAA-GUAUAGCAAAGUUAUCAAAGCCUGGA-GCUAUGCUUAUUUGA-CUUUUAUAU-UAUAACAUCUUUACCAGAGG-UGC---AUAUUUAAAGCACCAAGAAAACUUUGCUCUUCUGAAAGAAUG----
ABVD01398987.1/2360-2530     CAGUGUUGGCUCCUU-UGAAAA-----UCUU----UAGUUCUUGGGGCAGCACUAAU--UAUCAAAGUGUAGCAAAAAUAUUGCGGCCUGGA-GCUAUGCUUGUUGUAACUUUUGUAC-AAUAGCAUCUUUACUAGAUAAUAC---AUGUUUAAAGCACCAAGGAAACUUUGCUUUUCUUAAAGAACG----
AAQQ01377132.1/742-905       CAAUGUGGGCUGCUU-CCACAA----UCUCC----CAGUUCUU-----AGCAGUAUU---AGCAAAGUGUAACAAAACUGUCAAGGCCUGGGAGCUAUGCUUGUUUAA-UUUAUGUGC-AAUUGUAUCUAUACCAGAGAAUGC---AUGUCCAAAGCACCAAGAAAGGG--GCUUUUCCAAAAGAAUG----
ABRN01309671.1/162-323       CAGUGUUAGUUGCUU-UGACAGUCUCUUA--------GCUCUUGGAACAACAAUACU---AAUAA-GUGUAGCAAAAUUAUCAAGGCCCAGA-GCUAUGCUUAACUUUUAUA------CUAUAGCAUCUUUACCAGAGG-UGC--A-UGUUUAAAGCACCAAGGAAAC--UGCUUUUCUGAAAGAAUG----
AAGV020324854.1/1295-1470    CAGUGUUGGCUGUUU-UUAAAAAAAAUCCCU----UAGGUCUUGGGGCAGCACUAAU--UAGCAAAGUGUAGUAAAAGGAUUGCAGCCUAGG-GCUAUGCUUGUUGUAACUUUUGUAC-AAUAGCACCUUUACUAGAUAAUAC---GUGUUUAAAGCACCUAGGAAGCUUUGCUUUUCCGAAAGACUG----
ABRR01180822.1/1322-1487     CAGUGUUGGUUGAUU-UGAGAAUCCCUCUU------AGUUUUGGGA-CAAAAGUAUU---AGUAA-GUGUAGCAAAAUUGUCAAAGCUCAGA--GC-UACU-CAUUAA-CUUUUAUAC-CAUAGGAUUUUUACC-UGAUGUGC---AUGUUUAAAGCAUCAAGGAAUCUCAGCUUUUCCAAAAGAAUG----
AAFC03127381.1/21815-21648   CAGUCUUGGUUGCUU-UGACAAUCUCUUC--------GUUCUAGGAACAACAAUUCC---AACUA-GUAUAGCAAAAUUAUCAAAGCCCAGA-GCUACACUUUACUUUUAUAAUAAUGCUAUAGUGUCUCUACCAGGGG-UGC--C-UGUUUAAAACAGCAAGGAAAC--UGCUUUUCUGAAAGAAUG----
AAKN02020737.1/1283-1450     GAGUGUCCCUUGCUC-UGA-ACUACCACUU------AGUUCUUGGA-CAGCAGGAUU---AGCGAUGUGUAAUGACAACAUCAAAGUUUGGC--CCAUGCUUCUUUAA-CCUGUGUAU-CAUGGCAUCUUUACCCUAACAUGC---AUGCUUAAAGCACCAAGGGGA--CGGCUUUU---AAGGAAUGCACA
AAYZ01037727.1/3434-3605     -----CAGAUCCCUU-UGAAAAAAAAAAGCU----UAUUUCUUGGA-CAACAUUACUAACAGCAAAGUGUCAUAAAACUGC-GAGGCGCAGC-CCUUGGCUUGUUUAACCUUUUGU---CACAGCAUCUAUACCAGGGAAUGCUGCAUGUGUGCAGUACCAAGAAAACAUUGCUAUUCUAUAAGAACG----
AC186993.25/130178-130328    GGGUGUUGGUUACUU-UGAAAAA---UCUC------AGCUCUGGGGACAGCAAUAUG----GUAA-GUGUAGCAGAAUUAUCAAAGCCCAGA--GGGAGCUACCCUUG-----------UUCAACUUUUCUGCUAGGCC-UGU-----AUUUAAAACACCAGGGACACUUUGUAUGUACCGAAUA-------
ACBE01549560.1/8513-8363     CAGGGCCGGUUGCUU-UUGCAAAAUCUCUCC----CAGUUCUUGGGACAGCAGCACU---AGUGA-GUGUAGCAAAGUUACCCAAACCCAGAAGGGCUUCGUUUUUUAACUUGUAUAC-UAUUGCAUCUUUUCCAGAAGUUUU--U-------------------------GCUUUUCUGAAAGAAUG----
CAAA01020746.1/16171-16013   UAGUAUGGGUGGCCU-GGAAAAGC--UCUC------AGCUCUUAGAGUAACAUUAAUG-AAGU-------AACAGGAGGCAAAAGGCCUGGA-GCUAUGCUCAG-----CUUAGGGGU-AGCUGUGUCUUUACCACAGGAUGU---GUGCCUCAAGCACCCAGGAAACA--GCCUUUCUAAAAGAAGA----
AABR05016229.1/5765-5923     UUGUGUGAGUGGCUU-GGAAACA--CUCUC------AGCUCUUAG---AGUCCUAUU---CGUGAA--GGAACAGAAUGCGAACGGCCUGGA-GCUAUGCU----CAA-CUUAGGAGU-AGCUGUGUCUUUACCACAGGAUGU---GUGCCUUGAGCACCCAGGAAACA--GCCUUGCUAAAAGAAGG----
AAPE02032846.1/57480-57313   CAAUGUUGUUUGCUU-UGGAAAUGUCUCCU------AGUUCAGGGA-GAGCAAUACU---AGUAC-AUGUAGCAACAUUAUCAAAGCCGGGA-GCUAUACUUACUUAA--CUUUAUAC-UAUAGCAUCUUUACCAGAGG-UGC---AUAUUUAAAGCACAAAGGAAACCUUGCUUUUCUGAAAGAAUG----
AAQR03020007.1/265089-265240 CAGUGUUGGUUGCUUUUGAAAAUCUCCUUU------UGUUCUUGGA-UAGCAA-------------AGGAAAUAGAAUUGUGAAAGCCUGGA-GCUAUGCU----UCC-CUUUUGCAC-AAUAGCAUCUUUACCAGAGGCUGAUGU-AUAUUAAAGCACCAAGGAAGC--UGCAUUUCU----GAA------
#=GC SS_cons                 :::::::::::::::.::::::::::::::......::::::::::.::::::::::...::::::::::::::::::::::::::::::::.:::::::::::::::.:::::::::.::::::::::::::::::::::::...::::::::::::::::::::::::::::::::::::::::::....
#=GC RF                      cAGUGUuGGUUGCUU.UGAaAAucuCucuu......AGuUCUuGGa.CAGCAgUAuU...AGuaAaGUGUAgcAAaAuuaucaAaGCcuGGa.GcuauGCUuguUuaa.CUUuUGuac.aaUaGcaUCUuUACCAGAggaUGc...aUGuuUaaAGCACCaAGGAaaCuUuGCuUUUCUgaAAGAAuG....
//
# STOCKHOLM 1.0

#=GF AC   RF02117
#=GF ID   FMR1-AS1_1
#=GF DE   FMR1 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   41.60
#=GF NC   33.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.58 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0043066; negative regulation of apoptotic process;
#=GF RN   [1]
#=GF RM   17921506
#=GF RT   An antisense transcript spanning the CGG repeat region of FMR1 is
#=GF RT   upregulated in premutation carriers but silenced in full mutation
#=GF RT   individuals.
#=GF RA   Ladd PD, Smith LE, Rabaia NA, Moore JM, Georges SA, Hansen RS, Hagerman
#=GF RA   RJ, Tassone F, Tapscott SJ, Filippova GN
#=GF RL   Hum Mol Genet. 2007;16:3174-3187.
#=GF RN   [2]
#=GF RM   18213394
#=GF RT   A novel RNA transcript with antiapoptotic function is silenced in fragile
#=GF RT   X syndrome.
#=GF RA   Khalil AM, Faghihi MA, Modarresi F, Brothers SP, Wahlestedt C
#=GF RL   PLoS One. 2008;3:e1486.
#=GF WK   FMR1-AS1_gene
#=GF SQ   20


EU251067.1/765-710           UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
L29074.1/12293-12348         UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
S76590.1/130-185             UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
EU251068.1/661-606           UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
EU251065.1/1307-1252         UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
EU048202.1/1404-1349         UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
EU048200.1/1946-1891         UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
EU048204.1/1862-1807         UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
EU048203.1/1300-1245         UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
EU251066.1/925-870           UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
EU048201.1/1564-1509         UAGUCCAAAAGGUCUUUCCUGUUUGCUAUGGCCUUGAGGAAUGUGGCCCUAGAUCC
AAPY01387897.1/898-953       UAGUCCAAUGGGUCAUUCCUGUUUACUAUGGCCUCAAGGAAUGUGGCCCUUGACCC
ABRR01160656.1/1096-1151     UAGUUCAAUAGGUCAUUCCUGUUUACCGUGGCCUCAAGGAAUGUGGCCCUUGAUCU
AAHX01006829.1/49696-49641   UAGUUCAAUGGGUCAUUUCUGUUUACUAUAGCCUCAAGGAAUAUGGCCCUUGAUCC
ABDC01376791.1/857-912       UAAUCCAAUGGGUCACUCCUGUUUACUAUGACCUUAAGGAAUGUGACCCUUGAUCU
ABRP01270137.1/1706-1761     UAGUCCAAAGGGUCAUCCCUGUUUACUGGGGCCUCAAGGAAUGUGACCCUUGAUCU
ACBE01510376.1/2136-2191     UAUUCCAAUGGGUCACUCCUGUGUACUGUGGCCUCAAGGAAUGUGGCCCUCGAUCC
AAKN02048760.1/1433-1378     UAAUCCAAUGGGUCACUUCUGUUUACUAUGGUCUCAAGGAUUGUAGUCCUUGACCC
AAEX03027029.1/301027-301082 UAUUCCAAUGGUUCAUUUUUGUGUACUGUGGCCUCAAGGAAUGUGGCCUUUGAUCC
AAPE02015618.1/29221-29166   UAGUCCAAUAAGUCAUUCUUAUUUACUGUGGCCUCAAGGAAUGUGACCCUUGGUCU
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UAGUCCAAugGGUCaUUCCUGUUUaCUAUGGCCUcaAGGAAUGUGGCCCUuGAUCC
//
# STOCKHOLM 1.0

#=GF AC   RF02118
#=GF ID   FMR1-AS1_2
#=GF DE   FMR1 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   88.80
#=GF NC   61.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 44.76 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0043066; negative regulation of apoptotic process;
#=GF RN   [1]
#=GF RM   17921506
#=GF RT   An antisense transcript spanning the CGG repeat region of FMR1 is
#=GF RT   upregulated in premutation carriers but silenced in full mutation
#=GF RT   individuals.
#=GF RA   Ladd PD, Smith LE, Rabaia NA, Moore JM, Georges SA, Hansen RS, Hagerman
#=GF RA   RJ, Tassone F, Tapscott SJ, Filippova GN
#=GF RL   Hum Mol Genet. 2007;16:3174-3187.
#=GF RN   [2]
#=GF RM   18213394
#=GF RT   A novel RNA transcript with antiapoptotic function is silenced in fragile
#=GF RT   X syndrome.
#=GF RA   Khalil AM, Faghihi MA, Modarresi F, Brothers SP, Wahlestedt C
#=GF RL   PLoS One. 2008;3:e1486.
#=GF WK   FMR1-AS1_gene
#=GF SQ   25


EU048202.1/635-509           GGCGGGGCCGAGGGG--CUGAGCCCGCGGGGGGAGGGAACAGCGUUGAUCACGUGACGUGGUUUCAGUGUUUACACCCG-CAGCGGGCCG--GGGGUUCGGC-------CUCAGUCAG----GCGCUCAGCUCCGUUUCGGUU
L29074.1/13604-13730         GGCGGGGCCGAGGGG--CUGAGCCCGCGGGGGGAGGGAACAGCGUUGAUCACGUGACGUGGUUUCAGUGUUUACACCCG-CAGCGGGCCG--GGGGUUCGGC-------CUCAGUCAG----GCGCUCAGCUCCGUUUCGGUU
EU048204.1/551-425           GGCGGGGCCGAGGGG--CUGAGCCCGCGGGGGGAGGGAACAGCGUUGAUCACGUGACGUGGUUUCAGUGUUUACACCCG-CAGCGGGCCG--GGGGUUCGGC-------CUCAGUCAG----GCGCUCAGCUCCGUUUCGGUU
EU048200.1/635-509           GGCGGGGCCGAGGGG--CUGAGCCCGCGGGGGGAGGGAACAGCGUUGAUCACGUGACGUGGUUUCAGUGUUUACACCCG-CAGCGGGCCG--GGGGUUCGGC-------CUCAGUCAG----GCGCUCAGCUCCGUUUCGGUU
EU048203.1/635-509           GGCGGGGCCGAGGGG--CUGAGCCCGCGGGGGGAGGGAACAGCGUUGAUCACGUGACGUGGUUUCAGUGUUUACACCCG-CAGCGGGCCG--GGGGUUCGGC-------CUCAGUCAG----GCGCUCAGCUCCGUUUCGGUU
EU048201.1/635-509           GGCGGGGCCGAGGGG--CUGAGCCCGCGGGGGGAGGGAACAGCGUUGAUCACGUGACGUGGUUUCAGUGUUUACACCCG-CAGCGGGCCG--GGGGUUCGGC-------CUCAGUCAG----GCGCUCAGCUCCGUUUCGGUU
AANU01202631.1/13495-13367   GGCGGGGCCGAGGGG--CUGAGCCCGCUGGGGGAGGGAACAGCGUUUAUGACGUGACGUGGUUUCAGUGUUUACACGCG-CAGCGGUCUUUUAGGGUUCGGC-------CUCAGUCAG----GCGCUCAGCUCCGUUUCGGUU
ABRP01270137.1/3081-3207     GGCGGGGCUGAGGGG--CCGAACCCGCGGGGGGGAGGGGCGGCGUCGGUCACGUGACGAGGUUUCAGUGUUUACACGCG-GAGCGGCCAG--AGCGUUCGGC-------CUCAGUCAG----GCGCUCGCCUCCGUUUCGGUU
AAFC03039350.1/29361-29486   GGCGGGGCCGAGGGG--CCGAACCC-GCGGGGGGAGGGGCGGCGUCGGUCACAUGACGCGGUUUCACUGUUUACACGCG-GAGCGGCCGG--AUCCUUCGGC-------CUCAGUCAG----GCGCUCGGCUCCGUUUCGGUU
AAKN02048760.1/159-33        GGCGGGGCCGAGGGG-GCCGAGCCC-GCGGGGGAAGGGGCGGUGUGUGUCACGUGACGCGGCUUCACUGUUUACACGAG-GAGCAGGCCG--AGCGUUCGCC-------CUCAGUCAG----GCGCUCAGCUCCGUUUCGGUU
AAGV020291878.1/2299-2423    GGCGGGGCCGAGGGG-CCU-AGCCG-GCGGGGGGAGGGGCGGCGCCGGUCACAUGACGCCGUUUCACUGUUUACACGCG-GAGCAGCCGG---GCGUUCGGC-------CUCAGUCAA----GCGUUCGGCUCCGUUUCGGUU
AANG01461939.1/3424-3551     GGCGGGGCCGAGGGGGGCCAAGCCC-GCGGGGGGAGGGGCGGUGUCGGUCACGUGACGCUGUUUCACUGUUUACACGCG-GAGCGGCCGG--AGCUUUCGGC-------CUCAGUCAG----GCGCUCGGCUCCGUUUCGGUU
ABRO01306181.1/671-797       GGCGGGGCCGAGGGG-GCUGAGUCC-GCGGGAGGAGGGGCGGCGCCGGUCACGUGACCCGGUUUCACUGUUUACACGAG-GAGCGGCCCC--AGCCUUCGGC-------CUCAGUCAG----GCGCUCGGCUCCGUUUCGGCU
ABRQ01341770.1/482-613       GGCGGGGCCGAGGUG--CCAAGCCC-GCGAGGGGAGGGGCGGUGAGGGUCACGUGACGCGGCUUCACUGUUUACACGCG-GAGC-GGCCG--AGCGUUCGGCUUUCGGCCUCAGUCAG----GCGCUCCGCUCCGUUUCGGUU
AAIY01330092.1/1840-1709     GGCGGGGCCGAGGGG-GCUGAGCUA--GGGGGGGAGGGGCGGCAUGGGUCACGUGACGCGGCUCUACUGUUUACACGCG-GAUCUGCCCG---GCGCUCGCCGUUUCGCCUCAGUCAG----GCGCUCGGCUCCGUUUCGGUU
AANN01248869.1/1126-1004     GGCGGGGCGCAGAGG------AGCAGCCUGGGGGAGGGGCGGCUCCAGUCACGUGACACGACGGCGGUGUUUACACGCG-GGGCGGCUGA--GGCGUCCGGC-------CUCAGUCAG----GCGCUCGGCUCCGUUUCGCUU
AAFR03054339.1/16805-16928   GGCGGGG-CGGGGG---CGGAGAGAGGGCGGCGAGGGCGCGGCCUGGGUCACGUGACGGGAUUUCAGUGUUUACAUUCG-GAGCGGGACA--AGCCCACGGC-------UCUGUCCGC----CCGUUUGG-UCCCUUUCGGUU
ABQO010005013.1/1524-1399    GGCGGGGGCGGGGG---CGGAGGGAGGGCGGUGAGGGCGCGGCCUGGGUCACGUGACGGGAUUUCAGUGUUUACAUUCG-GAGCGGGACA--AGCCCACGGC-------UCUGUCCGC----CCGCUCGGGUCCCUUUCGGUU
AF251350.1/122-250           GGCGGGGCCGAGGGG--CUGAGCCCGCUGGGGGAGGGAACAGCGUUGAUCACGUGACGUGGUUUCAGUGUUUACACGCGCGAGCGGGCCG-GAGGGUUCGGC-------CUCAGUCAG----GCGCUCAGCUCUGUUUCGGGU
AY007232.1/88-215            GGCGGAGCGGAGAGG-GCGGGG-CCAAAGG--GGAGGGGCUGCGCGGGUCACGUGACAUCGUUUGACUGUUUACAGGAG-GCGCAG-CGG--AGCCCUUGGCCU---CAGUCAGUCAG----GCGCUGGGGAGCGUUUCGGUU
AAGW02055954.1/121539-121665 GGCGGGGCCGAGGGG-GCCGAACCC-GCGGGGGGAGGGGCGGUGUCGGUCACGUGACUCGGUUUCACUGUUUACACGCG-GAGCGGGCCG--AGCUUUCAGC-------CUCAAUCAG----GCGCUCGGCUCCGUUUCGGUU
AAPE02015618.1/27884-27758   GGCGGGGAUGAGGG--GCCGAACCCUGGGGGGGGAGGGGCGGUAGCGAUCACGUGACGCGGUUUCACUGUUUACACGCG-GAACGGCCGG--AGCGUUUGGC-------CUCAGUCAG----UCGUUGGGCUCCGUUUCGGUU
AF251348.1/124-249           GGCGGGACCGUGGGG--CCAAGCCC-GCGGGGGGAGGGGCGGUGUCGGUCACGUGACGCGGUUUCACUGUUUACACGCG-GAGCGGUCGG--AGCUUUCGGC-------CUCAGUCAG----GCGCUCGGCACCGUUUCGGUU
AY630337.1/384-512           GGCGGAGCGAAGGGG-GCGGAG-CCCAUGG-GGGAGGGGCCGCCAGGGUCACGUGGUGUCGUUUGACUGUUUACAGGAG-GCGCGG-CAG--AGCCCUCGGC-------CUCAGUCAGUCUUGCGCUGGGGAGCGUUUCGGUU
AY630338.1/535-662           GGCGGAGCGGAGAGG-GCGGGG-CCAAAGG--GGAGGGGCUGCGCGGGUCACGUGACAUCGUUUGACUGUUUACAGGAG-GCGCGG-CGG--AGCCCUUGGCCU---CAGUCAGUCAG----GCGCUGGGGAGCGUUUCGGUU
#=GC SS_cons                 :::::::::::::::..::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::..::::::::::.......:::::::::....:::::::::::::::::::::
#=GC RF                      GGCGGGGCcGaGGGG..CuGAGcccgggGGGGGgaGGgGCgGCgugGGUCACGUGACGugGUUUcAcUGUUUACAcgcG.GaGCGGgCcG..aGcguuCGGC.......cUCAGUCAG....GCGCUcgGcuCCGUUUCGGUU
//
# STOCKHOLM 1.0

#=GF AC   RF02119
#=GF ID   FTX_1
#=GF DE   FTX transcript, XIST regulator conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   50.00
#=GF TC   52.10
#=GF NC   36.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.63 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   12045143
#=GF RT   Comparative sequence analysis of the X-inactivation center region in
#=GF RT   mouse, human, and bovine.
#=GF RA   Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, Jones L, Eggen A,
#=GF RA   Avner P, Duret L
#=GF RL   Genome Res. 2002;12:894-908.
#=GF RN   [2]
#=GF RM   21118898
#=GF RT   Ftx is a non-coding RNA which affects Xist expression and chromatin
#=GF RT   structure within the X-inactivation center region.
#=GF RA   Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C
#=GF RL   Hum Mol Genet. 2011;20:705-718.
#=GF WK   Ftx_(gene)
#=GF SQ   11


AAFC03076268.1/57467-57537 ACUGAGAUCCCUGUUAUUAGGUCCAGAUCACAUUUUGAGACAUCAAUGGGAGGAUUAAUUCCUCCUAAUCC
AAWR02034181.1/1610-1680   GAUGAGAUACCUGUUCCUUUGUCCAGAUCCCAUUUUGAGGUAUCAACGGAACAAUUAAUUCCUCCUAAUCC
ABRN01177567.1/70-140      ACUGAGAUCCCUGUUACUUUGUUCAGAUCACAUUUUGAGACAUCAAUGGAAGGAUUAAUUCCUCCUAAUCC
ABRR01305997.1/4511-4581   ACUGAGAUCCCCGUUACUUUGUACAGAUCACAUUUUAAGACAUCAACGGAAGGAUUAAUUCCUCCUAAUCC
AC004386.1/60941-61011     CCUGAGAUACCUGUUCCUUUGUCCAGAUCACCUUUUGAGAUAUCAGUGGAAGAAUUAAUACUUCAUAAUCC
ACBE01497856.1/985-1055    ACUGAGAUGGCUGUUCCUUUGUCCAGAUCUCAUUUUUACAUAGCAAUGGAAGGAUUAAUUCCUCCUAUCCU
CAAA01213123.1/14807-14737 AGUGAGAUAACUGUUCGUUUGUCCACAUCUCCUUCUGAGAUAUUCAUGGAAACAUUAACUCCUCAGAAUCC
AAHX01111729.1/1026-956    AGUGAGAUACCUGUUCCUCUGUCCAUGUCUCCUUCUGAGAUAGUCAUGGCAACAUUAACUCCUCUGAAUCC
AAEX03026520.1/39264-39334 ACUGAGAUAUCUGUUCCUUUGUCCAGAUCACAUUUUUGGGUAUCACUGGAAGGAUUAAUUCCUCCUAUCCC
AAQR03189636.1/24672-24740 ACUGAGAUACCUGCUUCUUUGUCC--AUCACCUUUUGAGAUAUCAAUAGAAGAAUUAAUUCUUCCUAAUCC
AJ421478.1/241201-241131   AGUGAGAUAACUGUUCGUUUGUCCACAUCUCCUUCUGAGAUAUUCAUGGAAACAUUAACUCCUCAGAAUCC
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    AcUGAGAUacCUGUUccUUUGUCCAgAUCaCaUUUUGAGAUAUCAAUGGAAGgAUUAAUUCCUCcUAAUCC
//
# STOCKHOLM 1.0

#=GF AC   RF02120
#=GF ID   FTX_2
#=GF DE   FTX transcript, XIST regulator conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   48.00
#=GF TC   49.80
#=GF NC   42.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.02 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   12045143
#=GF RT   Comparative sequence analysis of the X-inactivation center region in
#=GF RT   mouse, human, and bovine.
#=GF RA   Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, Jones L, Eggen A,
#=GF RA   Avner P, Duret L
#=GF RL   Genome Res. 2002;12:894-908.
#=GF RN   [2]
#=GF RM   21118898
#=GF RT   Ftx is a non-coding RNA which affects Xist expression and chromatin
#=GF RT   structure within the X-inactivation center region.
#=GF RA   Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C
#=GF RL   Hum Mol Genet. 2011;20:705-718.
#=GF WK   Ftx_(gene)
#=GF SQ   18


AK057701.1/569-476         CUGAGAGGACC-CUCCUUCUUUUGCUGCAUGGUCACUCACAUGGAUGAUCUGGUGGACUCU---AAAAUACUUUUCAA-A--UAU-CCUUCACAAUCCAGCC
ABDC01480889.1/1408-1502   CUGAGAAGACU-CCCC-UCUUCUGCUGUGCAGUCGCUAACAUAGAAGAUCUGGUGGACUGU---AAAACACUUUUCAA-AGAUAU-CCUUCACAGUCCAGCC
AAPY01379554.1/510-604     CUAAGAGGAAU-GCCC-UCUUCUACUGUGCAGUUACUUACAUGGAAGAUCUGGUAGAUUCU-C--AAAUACUUUUCAA-AGAUAU-CCUUCAUAAUCUAGCC
ABRN01177567.1/3397-3492   CUGAGAAGACC--CCC-UCUUCUGCUGCACAUGCACUCACGUGGAAAAUCUGGUAGACUCU-CUAAAACACUUUUCAA-AGAUAU-CCUUCAAAAUUCAGCC
AAWR02034182.1/2106-2201   CUGAGAGGCAC--CCC-UCUUCUGUUGCACAUUCACUCACAUGGCAGAUCUGGUGGACUCU-CUAAAAUGCUUUUCAA-ACAUAU-CUUUCAUAAUUCAUCC
AAFC03076268.1/59551-59646 CUGAGAAGACC--CAC-UCUUCUGCUGCACAGGCACUCACAUGGCCAAUCUGGUAGACUCU-CUAAAACACUUUUCAA-AGAUAU-UCUCCACAGUUCAGCC
ABRR01305998.1/772-864     CUGAGAGGACC--CCC-UCUUCUG---CACGUGCACUCACAUGGAAGAUCUGGGAAACUCU-CUAAAACACCUUUGAA-AGAUAU-CGUUCACAAUUCAGCC
ABRQ01725521.1/564-660     CUGAAAAGGCU-CUCU-UCCUCUGCUGUAUGUUCACUCACAUGGAAGGUCUGGGGAGUUCU-CUAAAAUGCUUUUCAA-AGAUGC-CCUUCACAGUUCAGCC
AAGV020483722.1/1814-1720  CUGAGA--GCC-UCCC-UCUUCUGGUGCAAGUUCACUCACAUGUAAUAUCUAGUGACCUCU-UUAAAACACUGUUCAA-AAACAU-CCUUUGCAAUUCAGCC
AAQQ01367844.1/198-293     CUGCAAACCCC-CCUC-UCUUCUUCUAUGUGGUCACUCACAUGUAACAUUUGCUGGACUCU---GAAACACUUUUCAA-AGAUAUGCCUUCACAAUCCAGCC
ACBE01497858.1/354-258     CUGAGAGGAUC--CUC-UCUUCUGCUACACGUUCACUCAUGUGGGAAAACCAGUAGACUCU-CUAGAACACUUUUCAAAAGACAU-CCUUCACAAUUUAGCC
AANN01604272.1/1828-1739   CUUAAG------UCAC-UCUUCUG---CAUGCUCACUCAAGUGGAAGGUCUUCUGCACUCAACUAAAAUGCUUUUCAC-AGAUAU-CAUUCACAAUUCAAUC
AAGU03047889.1/7046-6950   CUGAAAGCGCU-CUCC-UCUUCUGCUGGAUGUUCAGUCACAUGGAAAAUCUGAUGAUCUCU-CUAAAAUGCUUUUCAA-AACUAU-CCUUCACAGUUCAGCC
AAGW02068487.1/16375-16285 CAGAAGUCACC--ACC-UCUUCCACUGCACCAUCACUCACAUG-AAGAUCUGGUGGACUCU---AAAAC--UUUUCAA-AGAUAC-CCUUCACAGUCCAACC
AAQR03189636.1/30987-31080 CUGAGAAGACC--CUC-UCUUUUGGUUUAUAGUCAUUCACAUAGAAGAUCUGGUGGACUCU---AAAACACCUUUCAU-AGAUAU-CCUUCACAAUCCAGCC
AAEX03026520.1/44243-44339 CCAAGAAUAUC--CCC-UCUUCUGCUACACGUGGACUCAUGUAGAAGAGCUGGUAGACCUU-CUAAAACACUUUCCAAAAGACAU-CUUUCAGAAUUCAGUC
AC002418.1/102522-102429   CUGAGAGGACC-CUCCUUCUUUUGCUGCAUGGUCACUCACAUGGAUGAUCUGGUGGACUCU---AAAAUACUUUUCAA-A--UAU-CCUUCACAAUCCAGCC
AJ421478.1/231906-231814   UUGAGAAGUACCCUCC-UCUUCUCUUUUGAGGUCACUCACGCAUAGGAUCUGGCAAACGCU---AAACCCUUUUUCAA-AAAUAU-CUUCCCUA---GAGCC
#=GC SS_cons               :::::::::::.::::.::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::.::::::.::::::::::::::::
#=GC RF                    CUGAGAagacC.cccC.UCUUCUGcUgcAcGuUCACUCACaUGGAaGAUCUGGUGgACUCU.CUAAAAcaCUUUUCAA.AGAUAU.CcUUCAcAaUuCAGCC
//
# STOCKHOLM 1.0

#=GF AC   RF02121
#=GF ID   FTX_3
#=GF DE   FTX transcript, XIST regulator conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   55.00
#=GF TC   56.40
#=GF NC   48.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.82 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   12045143
#=GF RT   Comparative sequence analysis of the X-inactivation center region in
#=GF RT   mouse, human, and bovine.
#=GF RA   Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, Jones L, Eggen A,
#=GF RA   Avner P, Duret L
#=GF RL   Genome Res. 2002;12:894-908.
#=GF RN   [2]
#=GF RM   21118898
#=GF RT   Ftx is a non-coding RNA which affects Xist expression and chromatin
#=GF RT   structure within the X-inactivation center region.
#=GF RA   Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C
#=GF RL   Hum Mol Genet. 2011;20:705-718.
#=GF WK   Ftx_(gene)
#=GF SQ   14


AC004386.1/67536-67682     ----CUUCCCAA-CUGCCUCACAAGGAC--AUUCAUGGC-AACCGUAA----UUCAUCCUCGCCCUCUGA-UGAACUUGCUGGGCAGGAAGC-------AUCAGUAUGAGUAACAGGCAGAUCUUAAU----GUUGCUCUUGAC---CAAUGACAAGUUUUCUGGCCAUCCAGG-
ABDC01357403.1/3005-3155   ----CUUUCCAA-CUGCUUCACAAGGAC--AUCCAUAGU-AACAGUGAUUCAUUCAUCCCGGCUCUCUGG-UGAAUUUGCUGGGCAGGAAGC-------GUCGCUAUGAGUAACAGGCAGUUAUUUAU----GUUGCUCUUAAC---CAAUGACAAGAUUUCUGGGUACCCAGG-
AAWR02034182.1/2630-2775   ----CUUCCCGG-CUGCCUCACAAGGAU--AUCCAUGGC-AACAGUGA----UUCAUUCUGGCUCACUGG-UGAACCCACUGGGCAGGAAGC-------CUCAAUAUAAGUGACAGGUAG-UCUUAGU----GUUGCUCUUGAC---CAACGACAAGGUUUCUGGCUGCCCAAG-
ABRR01305998.1/1266-1412   ----CUUCCCAG-CUGCCUCACAAGGAU--AUCCAUGAC-AGCAGUGA----UUCAUGCUGGCUUGCUGG-UGAACUCACUGGGCAGGAAGC-------CUCAAUACAAGUGACAGAUAGGUCUUAGU----GUUGCUCUUGAC---UAAUGACAGGGUUUCUGGCUGCCCAGG-
ABRT010478266.1/513-656    ----CUUCUCAC-CUGCCUCACAAGGCC--AUCCACGAC-AACAGUGA----UUCACGUUGGCUCUCUGGAUGAGCUUGCUGGGCAAGAAGC-------AUCAGUAUAAAU---AGGCAGAUCUUAAU----GUUGCUCUUGAU---CAAUGACA-GGUUUCUGACUGCCCAGG-
ABRN01177567.1/3933-4080   ----CUUCCUAA-CGGCUUCACAAGGAC--AUCCAGGGC-AAUGAUGC----UUCAUUCUGGCUUGCUGG-UGAACCCACUGGGCAGGAAGC-------CUCAGGAUAAGUGACAGGUAGGUCUUAGU----GUUGCUCUUGAC--UCAAUGACAAGGUUUCAGGCUGCCCAGG-
AANG01453982.1/271-418     ----CUUCCCAG-CUGCCUCACAAGGAUCCACACACAGC-AAUGGUGA----UUCAUUCUGGCUUGCUGA-UGAACCCACCGGGCAGGAAGC-------CUCAAUAUAAAUGACAGGUGGGUCUUAGU----GUUGCUCUUGAC---UAGUG-CAAGGUUUCUGGCUGCCCAGA-
ABRQ01725521.1/1494-1640   ----CUUCCUAG-AUUCCUCCCAAGGAU--GUCCAUGGC-AAUGGUAA----UUCAUUCUGACUCUCUGG-UGAACCCACUGGUCAGAGAGU-------CUCAGUGUAACCGACAGGCGGGUCUUAAG----GCUAGGCUUGAC---AAAUGACAAGAUUUCUGCAUUUUCAAA-
AAGV020483722.1/254-109    ----CUUCCCAA-CUCCCUCACAAGGAU--GUCCAUGGC-AACGGCUA----UUCAU--UGUUUCUUUGG-UAAACUCAAUGAGCAGGAAGCAGGAAGCCUCAGUGUA----ACAGGCUAGUCUUAAU----GUUGCUCUUGAC---CAAUGAUAAGGUUU--GACUGC-CAAGG
AAFC03117240.1/23521-23671 ----CUUCCCAA-CCAUCUCACAAGGAC--AUCCAGGGC-AAUGAUGC----UUUAUUCUGGUUUGCUGG-UAAACCCACUGGGCACGAUGC-------CUCAGGAUAAGUGACAAGUAGGUCUUGUUACUUGUUGCUCUUGAC---CAGUGACAAGGUUUCUAGCUGCCCAAG-
ABRO01401819.1/2225-2373   ----UUUCCGAG-UUGCUUUACAAGGAC--AUCCACAGC-AACAGUGA----UUCAUCCUGGAGCACUGG-UGAACUUUCUGAGUCAGAAGC-------CUUAGUGAAAAGAACAGGAAGAUCUUAAA---AACUACUCUUAAA--UCAAUAAAAAGGCUUUUUGCUACACAGG-
AACN010230879.1/1227-1089  ----CUUCC------ACCUCACAAGGAC--AUCUAUGGC-AAUGGAGGAGA-UUCAUUCUGGCUUGCUGA-UGAACCCACUGGGCAGGAAGC-------CGCAAUAUAAGUGACAGGUAGGU----------GGUAGUGUUGAC---CAAGGACAAGGUUUCUGGCUGCCCAGG-
AAQQ01367844.1/958-1101    ----CUUCCAGA-CUGCCUCACCAGGAC--AUUCUCAGA-AAUAGUGA----UUGAUGCUGGCACUCUGG-UGAAUUUGCUGAGCAGGAAGG-------CUCAGUAUAAGUAUCAGGCAGAGCCAUGU--GUGGUGAUAUACACUUGUAAUCGCAGCAACUC--------CAGA-
AAQR03189636.1/31499-31646 CUGA-----UACCUUGCCUCACAAGGAC--AUCCAUGGUUAACAGUGA----UUUAUCCUGGCUCUCUGG-UGAACUUACUAGGCAAGGAGC-------AUCAGUCUAAGUAACAGGUGGUUAUUAAU----GUUGCUCUUAAC---UAAUGACAAUGUUUCUGGCUACCCAGG-
#=GC SS_cons               ....::::::::.:::::::::::::::..:::::::::.::::::::....::::::::::::::::::.:::::::::::::::::::::.......:::::::::::::::::::::::::::::....::::::::::::...:::::::::::::::::::::::::::.
#=GC RF                    ....CUUCCcAa.cUgCCUCACAAGGAc..AUcCAuGGc.AAcgGUGa....UUcAUuCUGGcucuCUGG.UGAACucaCUGGGCAgGAAGc.......cUCAgUaUAAgugACAGGuaGgUCUUaau....GuUGcUcUUgAC...cAAUGAcAAGguUUCUGgcUgCcCAGG.
//
# STOCKHOLM 1.0

#=GF AC   RF02122
#=GF ID   FTX_5
#=GF DE   FTX transcript, XIST regulator conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   45.00
#=GF TC   48.10
#=GF NC   36.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.75 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   12045143
#=GF RT   Comparative sequence analysis of the X-inactivation center region in
#=GF RT   mouse, human, and bovine.
#=GF RA   Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, Jones L, Eggen A,
#=GF RA   Avner P, Duret L
#=GF RL   Genome Res. 2002;12:894-908.
#=GF RN   [2]
#=GF RM   21118898
#=GF RT   Ftx is a non-coding RNA which affects Xist expression and chromatin
#=GF RT   structure within the X-inactivation center region.
#=GF RA   Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C
#=GF RL   Hum Mol Genet. 2011;20:705-718.
#=GF WK   Ftx_(gene)
#=GF SQ   14


AC004386.1/79957-80174     GGUUGAAUUCAGUGUCGUAGCAGGAAUUCUUAGAGCUGGCCGUCCCAAGAUGGGGUGGA-GAGAGCGGCAUGAAAGAGAGAGAGAGAGAGAGACACGCCUGAAUGGCAGCAGCAG-GCCUUAGCGGCAAUGGACAGCAGGCACA-GGACCAGCUUUGCCUCGAGCCGCAACGCUGAUGCCAGAAAA-GGACAACCUCUCCAGAAUCGCCGCAGUGUGCUUCC
AANU01175069.1/6188-5977   GGUUGAAUUCAGUGUCGUAGCAGGAAUUCUUAGAGCCGGCCGUCCCAAGAUGGGGUGGA-GAGAGCGGCAUGAAAGAGAGAGAGAGA------GACGCCUGAAUGGCAGCAGCAG-GCCUUAGCGGCAAUGGACAGCAGGCACA-UGACCAACUGUGCCUUGAGCCGCAACGCUGAAGCCAGAAAA-GCACAACCGCUCCAGAAUCGCCGCAGUGUGCUUCC
ABDC01357404.1/4492-4695   GGCUGAAUCGAGUGUCGUAGCAGGAAUUCUUAAAGCCAGCAGUCCCAAGAUUGGGUGGA-GAGAGCGGCGGGACAGACAGAGAGC---------GCGCCUGAGUGGCAGCAGCAG-GCCUUAAUGGCAGUGGACAGCAGGCAGG-GGACCGG---UGGCUCAAGCCGCAGCCCUGAUGCCAGAAAA-GGACAUCC--UCCUAGAUCGCCGCACUGUGCUUCC
AANG01529120.1/248-454     GGCUGAAUCGAGUGUCGUAGCAUGAAUUCUUAGCGCUCGCCGCCGCAAGAUAUGGUGGA-CGGAGCAGCUGCACAGAGUUCGCAG----------AUCCAGGGUGGUUGCA-CAA-GCCCAGGUGGAACUGGACAGCAGGCAGA-GAACCAGCCGCGCCUCCAGCCGCAGCGCUGAUGCCAGUUAA-GAUCUGCCUCUCAGGGAUCGCCGCAGUGUACUUCU
AAWR02034182.1/13344-13543 GGCUGAAUCGACUGUCGUAGCGAGAAUUCUUAGCGCCGGCCGUCCCAAGACAGGGUGGA--GGCACAGCGGCACAGAGUUCGCGU----------CGCCAGGGUGGCAGCAGCAG-GCCAAGGUGGCAACGGACA-------GA-CGACCAGCCGCGCUUGCAACUGCACCGCUGAAGCCAGUAAA-GGACUGCCUCUCCAGGGUCGCCGCAGUGUGCUUCC
AAPY01776549.1/1334-1133   CGGUGAAUCAAGCGUUGAAACA--AUUCUUAAAAGCCGACCGUCUCAAAACAGGGUGAA-GAGAGCAGCGGAAGAGAGAGA--------------CGCUUGGAUGGCAGCAGCAG-GCCUGAGCAACAGCUGACAGCAGGCAGG-GGACAAGCUGUGCCUGCAGCCACAGCACCAACGGCAGAGAA-GGGGAGCCUCUUCCAGAACUCCGCAGUGUGCUUCC
ABRR01306003.1/595-802     GCCUGAAUCGAAGGUCAUAGCAUAAAUUCUUAGCGCCGGCCGUCCCAAGACAGGGCGAA-GGGAGCGGCGGCACACGGUUCGCGG----------CGCCAGGGUGGCAAGAGCAG-GCCAAGGUGGCAGUGGACAGCACGCAGA-ACAUCAGCCGCGCCUCCAGCCGCAGCGCUGAUGCCGGGAAA-GAACCGCCUCUCCGGGAUCGCCGCAGUGUGCUUCA
AAFC03073181.1/7435-7632   GGCUGAAUCGAAGGUCAUAGCAUAAAUUCUUAGCGCCGGCCGUCCCAAAAUAUGGUGAAAGGGAACGACGGCACAGAGUUCGCGG----------CGC---------AAGAGCAG-GCCAAGGUGGCAGUGGACAGCAGGCUGA-GGACCAGCCCUGCCUCCAGCCGCAACGCUGAUAUCCAGAGA-GGACCGCC--UCCAGGAUAGCUGCAAUGUGCUUCA
AAHX01111730.1/22628-22830 UGCUGAAGAGAGUGUCGUAGCAAAAAUUCUUACUGCUGGCAGUGCCGAGA--GGGUAGA-GGGAGCGGCGGGAUAGAG--CCG------------CGCCUGGGUGGUAGCAGCGAUGACUUAACGGCGAUGAACACCGGGUACG-AAACCUGCUACACUUGCGGCCGCUGCGCGGAUGCCACGAAC-CCACAGCCUCUCCAGGAGCGCUGCACUGUGCUGCA
AAHY01215359.1/2984-2780   UGCUGAAGCGAGUGUCGCAGUUAAAAUUCUUACGGCAGGCAGUGCCUAGA--GGGUGGA-GGGAGCGGCGGCAUAGAGAGCCG------------UGCCUGGGUGGCAGCAGCGAUGACUUAACGGCGAUGAACACCAGGUACG-AAACCUGCUAUACUUGCGGCCGCGGCGCGGAUGCCACGAAC-CCACAGCCUCUCCAGGAGCGCUGCGCUGUGCUGCA
ABRQ01771181.1/473-270     AGCUGAAU-GAGUGUCCUAACUUG-AUUCUUAGAGCAGGCUGUCCCAAGUCAGGGUGGA-GGGGGCGGCAUCACUGAGCUCUCGG----------CGCCAUGGUGGCAGUA-UGA-GCUAUGGCGGCAGUGGAGAGCAGGCAGC-CGACCUGCCCGGACUCCAGCCGCAACGCA-AUGCCGUAAGG-AUCCUGCCUCUCCAGUAUUGCCGCGGUGUGCUUCC
AAEX03026520.1/55787-55994 GGCAGAAUCGAGUGUCGUAGCAUGAAUUCUUAGCGCUUGCUGCCUCAAGACAGGGUACA-GGGAGCGGCGGCACAGAGUUCGCAG----------AUCUAGGGCUGCUGCA-CAG-ACCAAGGUAGAACUGGACAGUCAACUGA-GCGACACCCGCGCCUCCAGCCGCAGCGCUGAUGCCAGUUAAAGGACUGCCUCUCCAGGGUCGCCGCAGUUUGCGUCU
AJ421478.1/213585-213381   UGCUGAAGCGAGUGUCGCAGUUAAAAUUCUUACGGCAGGCAGUGCCUAGA--GGGUGGA-GGGAGCGGCGGCAUAGAGAGCCG------------UGCCUGGGUGGCAGCAGCGAUGACUUAACGGCGAUGAACACCAGGUACG-AAACCUGCUAUACUUGCGGCCGCGGCGCGGAUGCCACGAAC-CCACAGCCUCUCCAGGAGCGCUGCGCUGUGCUGCA
CU469472.9/34460-34668     GGCUGAAUCGAAGGUCAUAGCAUGAAUUCUUAGCGCCAGCCGUCCCAAGACUGGGUGAA-GGGUGCGGCGGCACAGAGUUCGGGG----------CGCCAGGGUGGCAAAAACAG-GCCAAGGUGGCAGUGGACAGCAGACAGGAGCACCAGCAGUGCCUCCAGCCGCAGCGCUGAUGCCAGGAGA-GCACCGCCUCCGCCGGAUCGCCGCAGUGCGCUUCA
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::..........::::::::::::::::::::.::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::
#=GC RF                    gGcUGAAucgAGuGUCguAGCaugAAUUCUUAgaGCcgGCcGUccCaAGAcaGGGUGgA.GGGaGCGGCgGcAcAGAGuucgcGg..........cGCCuGGGUGGCaGcAGCaG.GCCuugGcGGCagUGGACAGCaGGCagg.ggACCaGCuguGCcUccaGCCGCagCGCuGAuGcCaggaaa.ggaCaGCCUCUCCaGGAuCGCcGCagUGUGCUuCc
//
# STOCKHOLM 1.0

#=GF AC   RF02123
#=GF ID   FTX_4
#=GF DE   FTX transcript, XIST regulator conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   96.90
#=GF NC   44.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.19 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   12045143
#=GF RT   Comparative sequence analysis of the X-inactivation center region in
#=GF RT   mouse, human, and bovine.
#=GF RA   Chureau C, Prissette M, Bourdet A, Barbe V, Cattolico L, Jones L, Eggen A,
#=GF RA   Avner P, Duret L
#=GF RL   Genome Res. 2002;12:894-908.
#=GF RN   [2]
#=GF RM   21118898
#=GF RT   Ftx is a non-coding RNA which affects Xist expression and chromatin
#=GF RT   structure within the X-inactivation center region.
#=GF RA   Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C
#=GF RL   Hum Mol Genet. 2011;20:705-718.
#=GF WK   Ftx_(gene)
#=GF SQ   13


AC004386.1/68303-68449     AAGACUUCACAAUGGUUUGAUAACUAGGUGCAGGAUGCUGAUUUGAGCCUCUCCCAAUUCUCUAAUAACCUCA-CUGGAGGUUAACCAGGCAGGGCUC--AAUAUACCUCUU-CAGCAGUAGCAUAGUUUCUGAUUGAGUGUGGCAUCACC
ABRN01177567.1/4519-4659   AAGACUUCACAAUGGUUUGAUAACCAUGUGCAGGAUGCUGAUUUGAGUCUCUUCCAAUUCUCUAGUAACCUCA-CUGGG------CCAGGCAGGGCUC--AAUAUACCUCUU-CACCAGUGGCAUGGUUUCUGAUCGAGUUUGGUGUCACC
ABRR01305998.1/1870-2011   AAGACUUCACAAUGGUCUGAUAACCACGUGCAGGAUGCUGAUUUGAGCCUCUUCCAAUUCUCUAGUAACCUCAACUGGG------CCAAGCAGGGCUC--AAUAUACCUCUU-CACCAGUGGCACGGUUUCUGAUCGAGUUUGGUGUCAUC
AAWR02034182.1/3235-3375   GAGACUUCACAAUGGUUUGAUAACCAUGUGUAGGAUGCUGAUUUGAGCCUCUCCCAAUUCUCUAGUAGCCUCA-CUGGG------CCAGGCAGCACUC--AAUAUACCUCUU-CACCACUGGCAUGAUUUCUGAUCACAUUUGGUGUCACC
AAQQ01367844.1/2293-2432   AAAAUUUCACAAUAGUUUGAUAACCAUGUGCAGCAUGCUGAUUUGAGCCUCUCCCAAUUCACUAAUAACCUCA-CUGGA------CCAAGCAGGGCUC--AAUGUAUCUCUU-CACCAGCAC-AUGCUUUCUGACAGCAUUAUGCAUCACC
ABDC01357403.1/4449-4590   AAGACUUCACAAAGGUUUCAUAACCACACUCGAGACGCUGAUUUGAGCCUCUCCCAAUUCUCUAAUAACCUUG-UUAGAGGUUAACCAGGCAGGGCUU--AAUAUGGCUCUU-CACCAG-----UGGUUUCUGGCUGCAUUUGGUGUCACC
ACBE01497859.1/3107-3247   AAGACUUUACAAUGAUUUGAUAACCAUGUGCAGGAUACUUAUUUAAGCCUUUCCCAAUUCUCUAGUAACCUCA-CUGGG------CCAGGCCGGGUUC--AGUAUACCUCUU-CACCAUGGGCAUGGCUUCUGAUCACAUUUGGUGUCACC
AAPY01006408.1/2276-2148   AAGACUUCACAAUAGUUUGAUAGCCAUGUGCAGAAUGCUGAUUUGAGCCUCUCCCAAU------------UCU-CUGGA------CCAGGCAGAGCUC--AACAUUCCACUU-UACCAUUUCCAUGGUUUCUGAUGGCAUUUGGCAUCACC
AANN01604272.1/606-469     AAGACUUCACAAU---CUGACAGCCACAUUCAGGAUGCUGAUCUAUGCCUCCACCAAUUUUCUAGUAAUCUCA-CUGGG------CCAGGCAGGGUUC--AAUAUAUCUCUU-UAUCAGCACUAAGGUUUCUGAUCACAUUUAGUUUUACC
AALT01404790.1/399-531     GAAAGUUCACAAUGGUUUGAUAACCACAUUUAAGAUGAUGAUCUGAGCUUCUUCCAAUUUUCUAGCAACGUCA-CCGGG------CCAGACAGGGAGC--AAUAUACCCCUGGUAUCUGC---------UUUUAUCACAUUUGACAGUACC
AAGW02068487.1/15000-14882 GAGAGUCCCCAAU--------GAC-------------UUGAU---AACCUUUCUCAAUUCUCUAGUAACCUCA-CUUGA------CCAGGCAGGGCUCUCAAUAUACCUCUU-CACCAGUGGCAUGGUUUCUGAUUACAUCUGGUGUCACC
AAQR03189636.1/32075-32221 AAAACUUCAUAAAUGUUUGAUAACCAUAUGCAAGAUGCCGACUUGAGCCUCUCCCAAUUCUCUAAUAACCUUG-CUAGAGGUUAGCCAGGCAGGGCUC--AAUAUACCUCUU-CACCAAUGGAAUAGUUUCUGAUUGCAUUUGCUGUCACC
AAEX03026520.1/45805-45945 CAGACUUCACAACGAUUUGAUAACCAUGUGCAGGAUGUUGGUUUAAGCCUCUCCCAAUUUUCUAGUAACCUCA-CUGGG------CUAGACGGGGCUC--AAUAUACCUCUU-CACCAAUGGCAUGGCUUCUGAUCACAUCUGGUGUCACC
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::......:::::::::::::..::::::::::::.::::::::::::::::::::::::::::::::::::::
#=GC RF                    aAGAcUUCACAAugGUUUGAUAACCAugUgCAGGAUGcUGAUuUGAGCCUCUcCCAAUUcUCUAgUAACCUCa.CUgGg......CCAGGCaGGGcUC..AAUAUacCuCUU.cAcCAguggcAuGGUUUCUGAUcgcaUuUGGugUCACC
//
# STOCKHOLM 1.0

#=GF AC   RF02124
#=GF ID   JPX_1
#=GF DE   JPX transcript, XIST activator conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   55.00
#=GF TC   59.90
#=GF NC   49.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.42 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   21029862
#=GF RT   The long noncoding RNA, Jpx, is a molecular switch for X chromosome
#=GF RT   inactivation.
#=GF RA   Tian D, Sun S, Lee JT
#=GF RL   Cell. 2010;143:390-403.
#=GF WK   Jpx_(gene)
#=GF SQ   14


AL353804.22/127735-127869  UAGGGCUAGUGGAAGACUUAAGAUGGCGGCGUUUGCACGGAGUGCA--AUCACUGCGUCCUUA-CGGGGGUUGCAAGGCGUCCG-AAGUAUG--AGUCCACUAACAAAAGUCCAGAAACUCGCCAGUUAAUAGUAUUGUGG
AANU01175094.1/9357-9233   UAGGGCUAGUGGAAGACCUAAGAUGGCGGCGUUUGUACGGGGUGCA--ACCGCUGCG------------GUUGCAAGGCGUCCG-AAGUAUGUGAGUCCACUAACAA-AGUCCAGAAACUCGCCAGUUAAUAGUAUUGUGG
ABRT010698935.1/997-1131   CUAGACUAGUGGCAGACUUAAGAUGGCGGCGUUUGCAUGGGAUGUA--GUAGCCGCAUGCUUACCGGGAGUGGCAAGGCGGCUA-AAGAAUA--AAUCUACUAACGAAAGUCCAGAAACUCGUCAGAUUUU-CAGUUGUGG
ABVD01472675.1/1542-1677   UAGAGUUAGGGCAAGACCUAAGAUGGUGGCGUUUGCGCAGCGUCCA--AUUACUGCAUGAGUAGUGAGGUUGCUAAGACGGCCAAAAAGAUG--GAUCUACUAACGAAAGCCCAGAAACUCGUCAAUUUUU-GUGCUGUGA
ACBE01497838.1/1026-892    UAGGGCUCAUCUAAGACCUAAGAUGGCGGCGUUUGUACCGAGGGAA--AGUCCUGACCAAGUACUGGGUGUGGAAA-GCAGCCA-AUGGACA--AAUCUAUUAAGGAAGGUACAGAAACCCGCUAAUUUUUUGUUUUGUGG
ABRR01418325.1/303-435     GAGGGUUUAUCUGAGACCUAAGAUGGCGGCGUUUGCAUAGGGUGCA--AAUACUGCAGGCAUACGAGAUGUGGAAAGGCGGCCA-AAGGACG--AAUCUUCUAAGGAAAGUCCAGGAACU--CCAAUAUUU-GUGUUGUGG
ABRN01131321.1/2205-2339   UAGGGCUCAUCUAAGACCUAAGAUGGCGGCGUUUCCAUGGCGUGUA--AGCGCUGCAGGCGUACCAGAUAUGGAAAGGCGGCCA-AAGGACG--AAUCUACUAAGGAGUGUCCAAGAACUCGCCGAUAUUU-GUGUUGUGG
AAFC03027146.1/13000-13132 UAGGGCUCAUCUAAAACCUAAGAUGGCGGUAUUUGCAUAGGGUGUA--AGCGCUGCAGGCAUACUUUAUGUGAAAAGACGGCCA-AAGGACG--AGUCUCCUAAGGAAUGUCCAGAAACG--CGGAUAUUU-GUGUUGUGG
AAWR02034176.1/38434-38568 UAGGGCGCAUCUAAGGCCUAAGAUGGCGGCGUUUGCGCCGGAGGCA--AGUACUCCAGGCGAACCAGGGGUGGAAACGCGGCCA-AAGCACA--AAUCUACGAAGGGAAGUCCAGAGACUGGCCCAUUUUU-GUGUUGUGG
AAPE02004043.1/21316-21182 CACGUUUUAUUUAAGACCCAAGAUGGCGGCGUCCGCUCCGUGCCAA--AAUACGGCCUGGGUACCAGGUGUGGAAAGGCGUCCA-AAGGACG--AAUUUACUGAGGAAAGUGGUGAAACUGGACAGUUUUU-GUGUUGUGG
AAQR03188588.1/1811-1682   UAGGUUUGGUGGAAGACCUAAGAUGGCGGCCUUUUCUUG-----AA--ACUGCUGCGUGCUUACCCCGUGUAGCUGGGAGACCA-AAGGAUG--AAUCUACUAACGAAAGUCCAAAAACGCCCCAGUUUUU-GUGUUGUGG
AAEX03026517.1/79813-79945 UAGAGCUCAUCUAAAACCUAAGAUGGCGGCUUUCGUACUGAGAGGGUGAGUACUGCCAGCUUACUAGGUUUGGAAA-GCAGCCA-AUGAACA--AAUCU---GAGGAAAGUACAGAAACUCGCCAACUUUU-GUUUUGUGG
AAGW02057585.1/13100-13225 GAGAGCUGGUGUGAGGCUUGAGAUGGUGGCAUUUACAGAGGGUA-----------CCUGCUUAUCAGAGGUGGCAAGGCAGCCA-AAGGAUG--AAUCUACUAAUGAAAAUCCAGAAAUUUGCUAGUUUUU-GUGUUAUGG
AJ421481.1/78382-78250     UAGGGCUCAUCUAAAACCUAAGAUGGCGGUAUUUGCAUAGGGUGUA--AGCGCUGCAGGCAUACUUUAUGUGAAAAGACGGCCA-AAGGACG--AGUCUCCUAAGGAAUGUCCAGAAACGC--GGAUAUUU-GUGUUGUGG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::..::::::::::::::::::::::::::::::::::::.:::::::..:::::::::::::::::::::::::::::::::::::.:::::::::
#=GC RF                    uAGGGcUcgUguaAGACCUAAGAUGGCGGCgUUUGCacgGgGuguA..AgugCuGCauGcgUAccagGuGUGGaAAGGCGgCCA.AAGgAcG..AaUCUaCUAAgGAAaGUcCAGAAACucGccagUUUUU.GUgUUGUGG
//
# STOCKHOLM 1.0

#=GF AC   RF02125
#=GF ID   JPX_2
#=GF DE   JPX transcript, XIST activator conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; Pfold;
#=GF GA   48.00
#=GF TC   49.10
#=GF NC   44.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.63 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   21029862
#=GF RT   The long noncoding RNA, Jpx, is a molecular switch for X chromosome
#=GF RT   inactivation.
#=GF RA   Tian D, Sun S, Lee JT
#=GF RL   Cell. 2010;143:390-403.
#=GF WK   Jpx_(gene)
#=GF SQ   11


AK056172.1/136-204         UAUCGGAGAAUAAUUUCUUUCUCGCUGAUCGCCUAACUUCUACUGACGAAGCUUGGAAGUUGCAGAAGG
ABGA01241190.1/1091-1159   UAUCGGAAAAUAAUUUCUUUCUCGCUGAUCGCCUAACUUCUACUGACGAGGCUAGGAAGUUGCAGAAGC
ABRT010698935.1/1254-1322  UAUCGGAGAACAAUUUAUCUCUCUUUGCUUACUUUACCUCCACCGAUGAGGUUGGGAGGUUGCGGAAGC
ABRR01418325.1/566-634     UAUCAGAGAAUAAUUUCUCUCUCCUUAAUCACCUUUCUGCCAUGGAUGAGGCUAGGUGGUUACAGAAAC
AAFC03027149.1/550-618     CAUUGGAGAGUAAUUUCUCUCUCCUUAAUCACUUUACUAUCACGGAUGAGGAUAGGUGGUUGCAGAAAC
AAKN02029932.1/12261-12195 UAUCUGAAAAUAAUUCUGCCUUU--UAAUCGUCGUAUUUAUACUGAUGAACCUAGGAAGUUUCAGAAAG
AAPY01783752.1/364-296     UAGCGGGGAACAGUUUCUCUCUCCCUGAUCACCUUACCUCCACUGAUGAGGCUAGAAGGUUGCGGAAGC
ABRN01131321.1/2471-2536   UAUCGGAGA---AUUUCUCUCUCCGUAAUCACCUUACUGUCACGGAUGAGGAUAGGUGGUUGCACAAAC
AAPE02004043.1/21037-20969 UAUCAGACAAUAAUUUCUCUCUCCUUAAUCACCUUACCACCACUAACGAGGCUAGGUGGUUGCGGACAC
AJ421481.1/78125-78057     CAUUGGAGAGUAAUUUCUCUCUCCUUAAUCACUUUACUAUCACGGAUGAGGAUAGGUGGUUGCAGAAAC
AL353804.22/127998-128066  UAUCGGAGAAUAAUUUCUUUCUCGCUGAUCGCCUAACUUCUACUGACGAAGCUUGGAAGUUGCAGAAGG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UAUCGGAGAAUAAUUUCUCUCUCcuUaAUCaCCUUACUucCACuGAUGAGGcUaGGaGGUUGCAGAAaC
//
# STOCKHOLM 1.0

#=GF AC   RF02126
#=GF ID   GHRLOS
#=GF DE   Ghrelin opposite strand RNA conserved region
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   48.00
#=GF TC   48.50
#=GF NC   40.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.38 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   17727735
#=GF RT   Revised genomic structure of the human ghrelin gene and identification of
#=GF RT   novel exons, alternative splice variants and natural antisense
#=GF RT   transcripts.
#=GF RA   Seim I, Collet C, Herington AC, Chopin LK
#=GF RL   BMC Genomics. 2007;8:298.
#=GF RN   [2]
#=GF RM   18954468
#=GF RT   Complex organisation and structure of the ghrelin antisense strand gene
#=GF RT   GHRLOS, a candidate non-coding RNA gene.
#=GF RA   Seim I, Carter SL, Herington AC, Chopin LK
#=GF RL   BMC Mol Biol. 2008;9:95.
#=GF WK   GHRLOS
#=GF SQ   16


AANU01289926.1/47573-47504 GGGAGAGCUCCCCAUCUCUCCCG-UUUUCCAGGCGUUCC-UG-AGAUGAUUUUCUGGAGCUCAAAGCUUUAAG
ABGA01254661.1/11554-11623 GGGAGAGUGCCCCAUCUCUUCCA-UGUUCCAGGCAUUCC-UG-AGAUGACUUAUUGGAGCUCAAAGCUUUGGG
ABRP01080144.1/26682-26612 GGGAGAGCACCCCUUUCUCCCUA-CUUUCUCGGCAUUCUGUG-AGAUGAUUUAUUGUAGCUAAAAGCUUUGGG
EU789535.1/239-308         GGGAGAGCGCCUCAUCUCUUCCA-UUUUCCAGGUAUUCC-UG-AGAUGAUUUAUUGGAGCUCAAAGCUUUGGG
EU789536.1/239-308         GGGAGAGCGCCUCAUCUCUUCCA-UUUUCCAGGUAUUCC-UG-AGAUGAUUUAUUGGAGCUCAAAGCUUUGGG
EU789538.1/156-225         GGGAGAGCGCCUCAUCUCUUCCA-UUUUCCAGGUAUUCC-UG-AGAUGAUUUAUUGGAGCUCAAAGCUUUGGG
EU789539.1/156-225         GGGAGAGCGCCUCAUCUCUUCCA-UUUUCCAGGUAUUCC-UG-AGAUGAUUUAUUGGAGCUCAAAGCUUUGGG
EU789541.1/156-225         GGGAGAGCGCCUCAUCUCUUCCA-UUUUCCAGGUAUUCC-UG-AGAUGAUUUAUUGGAGCUCAAAGCUUUGGG
EU789542.1/156-225         GGGAGAGCGCCUCAUCUCUUCCA-UUUUCCAGGUAUUCC-UG-AGAUGAUUUAUUGGAGCUCAAAGCUUUGGG
EU789543.1/335-404         GGGAGAGCGCCUCAUCUCUUCCA-UUUUCCAGGUAUUCC-UG-AGAUGAUUUAUUGGAGCUCAAAGCUUUGGG
EU789545.1/239-308         GGGAGAGCGCCUCAUCUCUUCCA-UUUUCCAGGUAUUCC-UG-AGAUGAUUUAUUGGAGCUCAAAGCUUUGGG
EU789546.1/156-225         GGGAGAGCGCCUCAUCUCUUCCA-UUUUCCAGGUAUUCC-UG-AGAUGAUUUAUUGGAGCUCAAAGCUUUGGG
ABDC01299934.1/1227-1294   GGGAGCG---CCUGUCUUUCCUG-UUUUCUGGGCAUCCUCUG-AGAUGAUUUAUUGGAGCUCAGAGUUUUGAG
ABRN01369365.1/527-459     GGGAGAGCACCCCAUUUCCCCUG-CUUUCGUGGCAGCCU-AUGAGAUGAUUUACUGGAGCUC--AGUUUUGGG
AAQR03036031.1/11919-11849 GGGAGAGCACCCUGUCUUUGCUG-UUUUCUAGGCAUUCUCUG-GGAUGAUUUAUUGGAGCUCAGAGUUUUGAG
AAEX03012077.1/63398-63327 GGGACAGCACCCCAUUUUUCCCUCCUUUCUCAGCACCCUUGG-AGAUGAUUUAUUGGAGCUCAGAGUUUUGGG
#=GC SS_cons               :::::::::::::::::::::::.:::::::::::::::.::.::::::::::::::::::::::::::::::
#=GC RF                    GGGAGAGCgCCcCaUCUCUuCCa.UUUUCcaGGcAUUCc.UG.AGAUGAUUUAUUGGAGCUCAaAGcUUUGGG
//
# STOCKHOLM 1.0

#=GF AC   RF02127
#=GF ID   GNAS-AS1_1
#=GF DE   GNAS antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   45.00
#=GF TC   46.20
#=GF NC   36.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.08 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10749992
#=GF RT   An imprinted antisense transcript at the human GNAS1 locus.
#=GF RA   Hayward BE, Bonthron DT
#=GF RL   Hum Mol Genet. 2000;9:835-841.
#=GF WK   GNAS-AS1
#=GF SQ   21


AJ251760.1/2772-2874         -AGGGGCCGG---CGGCUCCGGCAGCCUUG----------GGGAGGGGAGGCGAGGC-----GGCGUGCU-----CCGGCCAUUUUCA-G---CACGG-----GUAGAGUUAAGUUUA--AUCU-GUAAC----CUGGAGGGG
AL132655.13/108650-108752    -AGGGGCCGG---CGGCUCCGGCAGCCUUG----------GGGAGGGGAGGCGAGGC-----GGCGUGCU-----CCGGCCAUUUUCA-G---CACGG-----GUAGAGUUAAGUUUA--AUCU-GUAAC----CUGGAGGGG
AJ251759.1/726-624           -AGGGGCCGG---CGGCUCCGGCAGCCUUG----------GGGAGGGGAGGCGAGGC-----GGCGUGCU-----CCGGCCAUUUUCA-G---CACGG-----GUAGAGUUAAGUUUA--AUCU-GUAAC----CUGGAGGGG
AANU01258066.1/6004-5905     -AGGGGCCGG---CGGCUUCGGCAGCCUUG----------GGGAGGGCA-----GGC-----GGCGUGCU-----CCGGCCAUUUUCA-G---CUCGG-----GUGGAGUUAAGUUUAGAAUCU-GUAAC----CUGGAGGGG
ABGA01236543.1/23343-23234   -AGGGGCCGG---CGGCUCCGGCAGCCUUG----------GGGAGGGGAGGCGAGGCAAGGCGGCGUGCU-----CCGGCCAUCUUCA-G---CUCGG-----GUGGAGUUAAGCUUAGAAUCU-GUAAC----CUGGAGGGG
AAWR02038939.1/28183-28282   -CGGCGCCGG---CGGCUUCUCCAGCCUCG----------GGGAGGGGA-----GGC-----GGCGCGCA-----CCGGCCAUUUUCA-G---CUUGG-----GUGGAGCUAAGUUUGGAAUCU-GUAAC----CUGGAGGAG
AAFC03013468.1/14271-14167   -AAGGGCCAG---AGGCUACGGCAGCCUCA----------GGGAGGGGAGGGCAGGC-----GGCACGUA-----CCGGCCAUUUUUG-G---CUCGG-----GUGGGGCUAAGUUUGGAAUCU-GUAAC----CUGAAGGCA
AAQQ01179621.1/2326-2425     -AGGGGCUGG---CGGCUUCGGCAGCCUUU--------------GGGGAGGAGAGGC-----GGCGCGCU-----CCGGCCAUUUUUG-G----UCGG-----GUAGAGCUAAGUUUGGAAUUU-GUAAC----CUGGGGGAA
CR956413.12/21924-22033      -AGGGGCCGG---UGCCUUCGGCAGCCUCG----------GGGAGGGGAAGGGAGGC-----GGCGCACA-----CCGGCCAUUUUCA-G---CUGGGCUCCCGUGGAGCUAAGUUUGGAAUCU-GUGAC----CUGGAGGUG
ABRT010063641.1/1039-1140    -AGGGGCCCA---UGGCUUCGGCAGUCUC--------------AGGGAAGGGGAGGC-----GGCGGGUU-----CCGGCCAUUUUCA-G---CUUGG-----GUGGAGCUAAGUUUGGAAUCUUGUUAC----CUGGAGGGG
ABVD01502572.1/1262-1365     -AGGAGCCUG---CGGAUGAGACGGCCUCA----------GGGAGGGAA-----GGU-----AGCGCGCAAC-UACCGGCCAUUUUCA-G---CUCGG-----GUGGAGCUAAGUUUGGAAUCU-GUAAC----CUGGAGGGG
AANN01425009.1/508-409       -GGGGGCUGG---CAGCUUCAGCAGCCUC---------------GGGGCAGGCAGGU-----GGUGCGCA-----UCAGCCAUUUUUA-G---CUCAG-----GUGGAGUUAAGUUUGGAAUGU-GUAAC----CUGGAGUUG
ABDC01114723.1/72-175        AGGACCUGCG---CGGCUUCAGUAGCUGC---------------GGGAGGGGGAGGC-----AGCGUGCUC---CCGCACAAUUUUCAAG---CUCGG-----GUGGAGCUAAGUUUGGAAUCU-GUAAC----CUGGAGGGG
AAPY01188918.1/658-746       -GCGGGCCGG---CGGCUCCGGCAGCCUGG----------CGAAGGG-------GGA-----GGCACGCU-----CCGGCCAUUUUCA-G---CCCAG-----C--GGGCUAAGUUUGGAGUCU-G---G----CGGGA----
ABRN01244655.1/383-497       -AGGAGCCGG---CGGCUACGGCAGCCUUGAGGAGGGGAGGGGAGGGGAGGGGAGGC-----UGCGCGCA-----CCGGCCAUUUUCA-G---CUCCG-----GUGGAGCUAAGUUUGGAAUCU-GUAAC----CUGGAGGCG
ACBE01090672.1/2760-2860     -AGGGGCCGGCAGCGGCUUCGGCAGCCUCG----------GGGAGGGGA-----GGC-----G--GCGCA-----CCGGCCAUUUUCG-G---CUCGG-----GUGGAGCUAAGUUUGGAAUCC-AUAAC----CUGGAGGUG
ABRP01270782.1/2310-2414     -CCGGGCCGG---UGGCUUCCGCAGCCUCG----------GGCAGUGGCGGGGAGGU-----GGCUGGCA-----CGGGCCAUUUUCG-G---CUCCG-----GUGGCGCUAAGUGUGGAAUGC-GUAAC----UUGGAGGGA
ABRQ01520820.1/1478-1584     -CAGGGGCGG---CGGCUAAGACAGUCUCG----------GCGAGGGGA-----GGC-----UGCGCGCA-----CCGGCCAUUUUCA-GCAGCUUUG-----GCGCAGCUAACUUUGGAACCU-GUAACCAGGCUGGAAAAA
AAEX03014051.1/129851-129948 -AGGGGCCGG---CGGCUUGGGCAGCCUCG----------GGGAGGGGA-----GGC-----G--GCGCA-----CCGGCCAUUUGCA-G---CUCGG-----GUGGAGCUAAGUUUGGUAUCU-GUAAC----CUGGAGGUG
AAGW02068306.1/45267-45360   -CGGGGCUGG--------AGGGGAGA---G----------GGGAGAG---GGGAGGC------GCGC---GCGUUCCGGCCAUUUUCA-G---CUCUG-----GUGGAGCUAAGUUUGGAAUC--GUAAC----CUGGAGGAG
AAPE02030481.1/101597-101693 -AGGGGCCGG---CGGCUUCGGCAGCCUCG----------GGGAGGGGA-----UGC-----GGCGCACA-----CCGGCCAUUUUCA-G---CU-CG-----GUGGGGCCAAGUUUGGAAUC---UAAC----CUGGAGUUA
#=GC SS_cons                 .:::::::::...:::::::::::::::::..........:::::::::::::::::.....::::::::.....:::::::::::::.:...:::::.....:::::::::::::::::::::.:::::....:::::::::
#=GC RF                      .aGGGGCcGG...CGGCUucGGCAGCCUcG..........GGGAGGGGaGGgGAGGC.....gGCGcGCa.....CCGGCCAUUUUCA.G...CUcgG.....GUGGaGCUAAGUUUGGAAUCU.GUAAC....CUGGAGGgG
//
# STOCKHOLM 1.0

#=GF AC   RF02128
#=GF ID   GNAS-AS1_2
#=GF DE   GNAS antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   47.00
#=GF TC   48.50
#=GF NC   41.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10749992
#=GF RT   An imprinted antisense transcript at the human GNAS1 locus.
#=GF RA   Hayward BE, Bonthron DT
#=GF RL   Hum Mol Genet. 2000;9:835-841.
#=GF WK   GNAS-AS1
#=GF SQ   16


AAFC03013468.1/13876-13759   CUUAAGGGGUCUUCCUUCCAGGUCUCCGCC-C-GGGGGAAGGCGUCACGCAGCCC-CAAAACUUA-GCUCUGGUGGGCUGCGG----CGCUG------ACUAAUAGCUCUUGGAUGCUGCCCUGAUCUUAC-C
AANG01240621.1/3195-3306     UUUUCUUGGUCCUCCUUCCAGGUCUCUUCU-C-UGGGAAAGGCGUCGUGGCGCGC-CAGAACUUA-GUUAUGCUG-GCUGCGG----CGC----------AAAUGGCUGCUGGACGCCUGUGU-GUCUUCA-C
AANU01258066.1/5608-5495     CUUAAAUGGUCUUCCUUCCAGGACCUAUUC-CGUAGGAAAGGCGUCGCGGCGC-C-CAAGACUUA-GUUCUGCUGGUCUGCAA----GGC----------AAACUGUGGUUAGAUGCCUUUGUGGUCUUCC-G
AAWR02038939.1/28583-28699   UUUAAAUGGUCUUCCUUCCAGGUGUCUUCC-C-UGAGAAAGGCGUCGCAGAGUCC-CAGAACUUA-GUUAUUUUGGGCUGCGG----CGCUG------ACGGAUGGCUGCUGGA-GCCGUUGUGGUGUUCC-C
ABDC01114723.1/477-574       AAUAAACGGUCUUCCUUCCCGGACCUAUUC-CGUAGGAAAGGCGCUACAGCGCCC-CAGAACUUA-GUUAUGCGA--CGGU-----------------------------UGGAUGCCUUUGUGGUCUUCG-G
ABRN01244655.1/803-920       GUUAAAGGGUCUUCCUUCCAGGUCUCUUCC-C-UGGGCAAGGCGUCGCGGAGCCC-CAGAACUU-----CUUCUGGGCUGCGGCGCUCGCUG------ACUAAUGGCUGUUGGAUGCUGUUCUGGUCUUCA-C
ABRT010063641.1/1433-1528    UUUCAGUGGUCAUCCUUCCAGGUCCGGUUC-C-UAGGAAAGGCGUUGCAGCACUC-CAGAACUUA-GUUCAGCGG--CUGU------------------------------GGUGGGAACAGUGGUCUUCA-G
ABVD01502572.1/1681-1790     UUAACACGGUCUUCCUUCCAGGACCGUUUA-CCUAGGAAAGGCG--ACGGAGCGU-CU---CCCA-CCUUAG-GG--CUGUGG----UGCUG------GCUAAUGAUAGUUG-AUGCCUU-AGGGUUUUCACC
AJ251759.1/526-413           CUUAAAUGGUCUUCCUUCCAGGACCUAUUC-CGUAGGAAAGGCGUCGCGGCGC-C-CAAGACUUA-GUUCUGCCGGGCUGCAG----CGC----------AGACUGUGGUUGGAUGCUUUUGUGGUCUUCC-C
AJ251760.1/3175-3288         CUUAAAUGGUCUUCCUUCCAGGACCUAUUC-CGUAGGAAAGGCGUCGCGGCGC-C-CAAGACUUA-GUUCUGCCGGGCUGCAG----CGC----------AGACUGUGGUUGGAUGCUUUUGUGGUCUUCC-C
AL132655.13/109053-109166    CUUAAAUGGUCUUCCUUCCAGGACCUAUUC-CGUAGGAAAGGCGUCGCGGCGC-C-CAAGACUUA-GUUCUGCCGGGCUGCAG----CGC----------AGACUGUGGUUGGAUGCUUUUGUGGUCUUCC-C
CR956413.12/22314-22428      GUUAAAGGGUCUUCCUUCCAGGUCA----G-C-UAGGAGAGGCGUGGCGGCGUCC-CGGAACUUAAGUUAUGCUGGGCUGCGG----CGCUG------ACUAACGACUGUUGGAUGCGGUUCUGGUGUUGG-C
ABRQ01520820.1/1888-1998     UUAAAAGGGGCUCUC--CCGGGACCCUUCC-C-U-GGGAAGGCGCGGCAGCGUCC-CCGAACUCG-GCGCUGUGGGGCCGCGG----CGC----------UUAGGGUGCGUGGAUGCCUCUCUGGUCCCCA-C
AAGV020495917.1/433-550      AAGGAUCAGUCUGCCUUGCUGCGCCCCUUC-CCUAGGAAAGGCGUCACCGCGUCCCCCCCACUUC-GUUAUCUUGGGCUGUGG----CGCC-------GGCUAAAGAUGCUGGAUGCCUG-CUGGUCUUCA-C
AAKN02054782.1/86242-86366   UGUCGAUGGUCCUCCUUGCAGGGCGUCUUCUCUUGGGAG--GAGUCGCAGCGUCC-CAGGACUUA-GUUCCGCUGCGUUGCGG---GCGCCGAUGGUGGUGAACCCUGAUCCGAGGCCGGUGUGGCCUUUA-G
AAEX03014051.1/130251-130363 UUGCCACGGUCUUCCUUCCAGG-UCUCCUC-CAUAGGAACCGCG--ACGGUGCCC-CCA-ACUUA-GUUCGCCGG--CUGCGG----CGCUG------ACUAACUACCGUUGGAUGCCUUUAAGGUCUUAA-C
#=GC SS_cons                 ::::::::::::::::::::::::::::::.::::::::::::::::::::::::.:::::::::.:::::::::::::::::....:::::......:::::::::::::::::::::::::::::::::.:
#=GC RF                      uuuaaauGGUCUUCCUUCCaGGuCcuuUUC.CgUaGGaAAGGCGUcGCgGcGccC.CagaACUUa.GUUcuGcuGGGCUGCGG....CGCuG......gcuaAcgguuguUGGAuGCcuuUgUGGUCUUca.c
//
# STOCKHOLM 1.0

#=GF AC   RF02129
#=GF ID   GNAS-AS1_3
#=GF DE   GNAS antisense RNA 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   42.00
#=GF TC   43.70
#=GF NC   41.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.77 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10749992
#=GF RT   An imprinted antisense transcript at the human GNAS1 locus.
#=GF RA   Hayward BE, Bonthron DT
#=GF RL   Hum Mol Genet. 2000;9:835-841.
#=GF WK   GNAS-AS1
#=GF SQ   9


AJ251759.1/412-375           UAAAGGACUUAGGUUUUUCAGAGUCUGGUAGCCAGUCA
AJ251760.1/9624-9661         UAAAGGACUUAGGUUUUUCAGAGUCUGGUAGCCAGUCA
AL132655.13/115500-115537    UAAAGGACUUAGGUUUUUCAGAGUCUGGUAGCCAGUCA
ABDC01114725.1/371-408       AAAAGGAUUUAGGGUUUUCAGAUUCUGGUAGCCAGUCA
ABRT010063643.1/1651-1688    UAAGGGAUUUGGGAUUUUCAGAUUCUGGUAGCCAGUCA
AAFC03013468.1/7737-7700     CAAGAGAUUUGGGGUUUUCAGAUUCUGGUAGCCAGUCA
ABRP01270785.1/1119-1156     CAAGCGAUUUGGGGUUUUCAGAUUCUGAUGGCCAGUCA
AAWR02038939.1/34891-34928   CAAGUGAUUCAGGGUUUUCAGAUUCUGGUGGACAAUCG
AAQR03050726.1/103898-103935 AAAAGGGUUUAGAGUUGUCAGAUUCUGGUAGCCAGUCA
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::
#=GC RF                      uAAgGGAUUUAGGGUUUUCAGAUUCUGGUAGCCAGUCA
//
# STOCKHOLM 1.0

#=GF AC   RF02130
#=GF ID   GNAS-AS1_4
#=GF DE   GNAS antisense RNA 1 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   51.50
#=GF NC   43.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.70 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10749992
#=GF RT   An imprinted antisense transcript at the human GNAS1 locus.
#=GF RA   Hayward BE, Bonthron DT
#=GF RL   Hum Mol Genet. 2000;9:835-841.
#=GF WK   GNAS-AS1
#=GF SQ   18


AJ251760.1/11274-11385       CUUCCACUU-GUGCAGG-CUCAGCAUCCCUGGGGCCUCAACUCCUUAUCCAUCCUGGGCUGCUCCUC---------GCAGUAAGCC-CU---C----U----CCUUGGGGUCCUGGCC-CUCUACCUCCCAGCCCU
AL132655.13/117150-117261    CUUCCACUU-GUGCAGG-CUCAGCAUCCCUGGGGCCUCAACUCCUUAUCCAUCCUGGGCUGCUCCUC---------GCAGUAAGCC-CU---C----U----CCUUGGGGUCCUGGCC-CUCUACCUCCCAGCCCU
ABRT010063644.1/285-396      CUUCCACUU-GUGCAGGGCUCAGCAUCCCUGAGGCCUCAACUCCUUAUCCAUCCUGGGGUGCUG-UC---------GCAGUAAACC-CU---C----U----CCUCAGGGUCCUGGCC-UUCUACCUCCAGGCCCU
ABDC01114725.1/2038-2149     CUUUCACUU-CCGCAGGGCUCAGCAUCCCCGGGGCCUCAACCCCUUAUCCAUCCUUGGC-GCUCCUC---------GCAGUAAGCC-CU---C----U----CCUCAGGGCCCCGGCC-CUCUACCUCCAGGCCCU
AAKN02054782.1/94213-94333   CUUCCACGU-GUGCAGGGUUCAGCAUCCUUGGGGCCUCAACUGCUUAUCCAUCCUGGGUCGAUCCUCUGCAUAUGAGCAGUAAGCU-CU---C----C----CCUCAGGGUCCUGGCC-C-CUACCUCUAAGCCCU
AANN01579945.1/4784-4665     CUUCCUCUU-CAGUAGGACUCGGCAUCUCUGGGGCCUCAAUUCUUUAUCCCUCUGAAGUUGUU--UUGGCAUUGCGGCAAUUAGCC-CU---C----U----CCUUGGGACGCUGGCC-CCCUACCUCCAAGCCCU
ABRP01270785.1/2654-2754     CUUCCACU--CGGUAGAGCUCAGCAUCUCUGGGGCCUCAACUCCUUAUCCAUCUGGGGCUGCUGCUCUGCAUCGGGGCAGUGAGCU-CU---C----U----CCUCCU-ACGCCCU--------------------
ABVD01612417.1/717-810       CUUCCACUU-CUGCAGGUCUCAGCAUCCCCGGGAAC--AAC------UGCAUC----GG-G---------------GCGGGAAGCC-CU---C----U----CCUCAGGGUCCUGGCC-CUCUACCUCCAGGCCCU
ABRO01055397.1/226-343       CUUCCAUUUUGUACAGGGCUCAGCAUCUCUGGGUUUUCAAUUCCUUGUGAGUCAUGGGCGGCUCCUCCGCU-CUGGGCGGGAAGUC-CU---C----A----CCU---GGUUCUGGCC-CACUAC-UCCAGGCCCU
AAQQ01179622.1/6983-7104     CUUCCACUU-GUGCAGGGCUCAGCAUCCCUGGGGCCUCAACUCCUUAUUCAUCCUGGACUGCUCCUCUGCAUCGGGGCAGUAAGCU-CU---C----U----CCCCAGGGUCCCGGCC-CACUACUUCCAGGCCCU
ABRN01244656.1/5935-6057     CUUCCACUU-CGGCAGGGCUCAGCACCCCCGCGACCUCAACUCCUUAUCCAUCUGGGGCCGCUCCUCUGCAGCGGGGCAGCGAGCCCCU---C----U----CCUCAGGGUCUGGGCC-CUCUACCUCCAGGCCCU
AAFC03013468.1/6132-6007     CUUCCACUU-CGGCAGGGCUCAGCAUCCCCACGACCUCAACUCCUUAUCCAUCUGGGGCUGUUCCUCUGCAUCGGGGCAGUGAGCC-CC---CUCUCU----CCUCAGGGUCUUGGCC-CUCUACCUGCAGGCCCU
ACBE01090673.1/5071-4945     CUUCUACUU-CGGCAGGGCGCAGCAUCCCUGGGGCCUCAACUCCUUUUCCGUCUGGGACUGCUCCUCUGCAUCGGGGCAGUGAGCC-CU---C----UCCCUCCUCAGGGUCCUGGCCCCUCUACCUCCAGGCCUU
AAWR02038939.1/36519-36643   CUUCCACUU-UCGCAGGGCUCGGCAUCCCUGGGGCAUCAACUCCUUAUCCAUCUGAGGCUGCUGCUCUGCAUUGGGGCAGUAAGCC-CU---C----UCCCUCCUCGGGAUCAUGGUC-CUUUGC-CCCAGGCCCU
CR956413.12/30134-30258      CUUCCACUU-CGGCAGGGCUCGGCAUCCCCGGGACCUCAACUGCUUAUCCAUCUGGGGCUGCUCCUCUGCAUCGGGGCAGCGCGCC-CCCCUC----G----CCUCGGGGUCUGGGCC-CUCUACCUCCGGGCCCG
AAGV020495918.1/4610-4728    CUUCCACUU-UCGCGGGGAUCAGCAUCCCUGGGGCCUCAUCCCCUUAUC-UUCCUGGGCUGCUGCUCUGCAUCGAGGCACCGAGCC-CU---C----U----CCUCAGGGUCCUCACC-CUCUACCUCCAGG--CC
AAPY01645884.1/3931-4037     CUCACGCUC-CCGCAGGGCUCAGCAUCCCCGGGGCCUG---GCCU-GAUCUUCCUGGGCCGCUGGUCUAC---AGGGCAGAACGCC-CU---C----U----UCA-GGGGUGCCUACA-C------UGCAGGC-CU
AAQR03050726.1/105447-105559 CUUCCACUU-CUGCAUGGCUCAGCAUCCCCGGGGCCUCAACCCCUUAUCCAUCCAUGGCUGCUCCUC---------GCAGUAAGCC-CU---C----U----CCUGUGGGUCCUGGCC-CUCUACCUCCAGGCCCU
#=GC SS_cons                 :::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::...:....:....::::::::::::::::.:::::::::::::::::
#=GC RF                      CUUCCaCUU.cuGCAGGGCUCAGCAUCCCuGGGgCCUCAACuCCUUaUcCaUCuuGGGcuGCUcCUCuGCaUcgGGGCAGuaAGCC.CU...C....u....CCUcgGGGUccuGGCC.CuCUACCUCCaGGCCCU
//
# STOCKHOLM 1.0

#=GF AC   RF02131
#=GF ID   GNAS-AS1_5
#=GF DE   GNAS antisense RNA 1 conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   70.00
#=GF TC   77.50
#=GF NC   43.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 40.12 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10749992
#=GF RT   An imprinted antisense transcript at the human GNAS1 locus.
#=GF RA   Hayward BE, Bonthron DT
#=GF RL   Hum Mol Genet. 2000;9:835-841.
#=GF WK   GNAS-AS1
#=GF SQ   22


AJ251760.1/11527-11647       UGA--CCCCACGGCGCUAGCGGUCCUCGUGGUCUUCCAGGCCUAGCCGCCAUACACC-----CGCCCC----CCAC-CGGCUUCC-AACCACCCCAGC-AGC---ACCUCUUCGGGCGUUCCAAC-GCGGCGCCCCCUA
AL132655.13/117403-117523    UGA--CCCCACGGCGCUAGCGGUCCUCGUGGUCUUCCAGGCCUAGCCGCCAUACACC-----CGCCCC----CCAC-CGGCUUCC-AACCACCCCAGC-AGC---ACCUCUUCGGGCGUUCCAAC-GCGGCGCCCCCUA
AJ251759.1/121-1             UGA--CCCCACGGCGCUAGCGGUCCUCGUGGUCUUCCAGGCCUAGCCGCCAUACACC-----CGCCCC----CCAC-CGGCUUCC-AACCACCCCAGC-AGC---ACCUCUUCGGGCGUUCCAAC-GCGGCGCCCCCUA
ABRT010063644.1/543-666      UGA--CCCCACGGCGCUAGCAGUCCGCGUGGCCUUCCAGGCCUAGCCGCCAUACGCC-----CGCCCA----CCAG-CGGCCUCC-AACCACCGGAGC-AGCACAACCUCUUUGGGCGUUCCAAC-GCGGCGCCCCCUA
AAQQ01179622.1/7254-7377     UGA--CCCCACGGCGCUAGCUAUCCUCGUGGCCUUCCAGGCCUGGCCGCUGUACGCC-----CGCCCA----CCAA-CCGCUUUC-AACCACCCCAAC-AGCACAACCUCUUUGGGCGUUCCAAC-GCGGCGCCCCCUA
AACN010211161.1/432-309      UGA--CCCCACGGCGCCAGUGAGCCUCGUGGCGUCCCAGGCCUGGCCGCCAUACGCA-----CGCCCA----CCAA-CCGCUUCC-AACCACCCCAGC-AGCACAACCUCUUGGGGCGUUCCAAC-GCGGCGCCCCCUA
ABRO01055397.1/467-589       UGA--UCUCCCGGCGCCAUCGGUCCUCUUGGCCUCCUAGGCCUGGCCGCCAUACGUC-----GGCCCG----CCAA-CUGCUUCC-AACCACCCAAGC-AACCCAACCU-UUUGGGCGUUCCAAC-GCGGCGCCCCCUA
AAGV020495918.1/4878-5002    UGA--CCCCACGGCGCUAGCCGGCCUGGUGGCCUCUCAGGCCUGGCCGCCAUACACC-----CACCCA----CCAA-CGGCCACCAAACCACCCCGGC-GGCACAAUCUCUUCGGGUGUUCCAAC-GCGGCGCCCCCUA
ABDC01114725.1/2296-2410     UGA--CCUCAGGGCGCCAUCGGUCCUCGUGGCC---------UAGUCGCCAUACACG-----CGCCCC----CCAA-GGCCUUAA-AAUCACCCCCGC-AGCAUAACCUCUUAGGGCGUUCCAAC-GCGGCGCCCCCUA
AAKN02054782.1/94486-94609   UGA--ACCCUCAGCGCCAGCGGUCCUCGUGGUCCUCUCGGCCUGGCCGCCAUGCACU-----CACACA----CCAA-CAUUUCCU-AAGCACCCGAAC-UGCAUAACCCCUUUGGGCGUUCCAAC-GCGGCGCCCCCUA
AAFC03013468.1/5872-5749     UGA--CCCCACAGCGCCAGCCGGCCUCGUGGCAGCCCAGGCCUGGCCGCCAUACGCC-----CGCCCA----CCAA-CCGCUCUU-AACCACCCCAGC-GGCACAACCUCUUAGGGCGUUCCAAC-GCGGCGCCCCCUA
AANN01579945.1/4586-4465     UGA-CCCCCAUGGCGCCUACUGGCCUCGUGGUGUUCCAGGCCUAGUCGCCAUACUCC-----CGCCCA----C----CGCCUUCC-UUCUACUCCAGC-AGCACAAUCUCUUCGGUAGUUCUAAC-GCGGCGCCCCCUA
AAPY01645884.1/4157-4277     UGA--CCCCACGGCGC--GCGGUCCUCGUGGCUUGCCGGGCCUGACCACCAUACAC------CGCCAU----CCAA-CCGCAUCC-AACCAACCCAGC-GGCACAACCUCUUCGGGUGUUCCAAC-GCGGCGCCCCCUA
AAWR02038939.1/36791-36915   UGA-CCCCCACGGCACCAGCCAGCCUCGUGGCGUCCCAGGCCUGGCCGCCAUACGCC-----CGCCCA----CCAA-CCGCUUCC-AACCACCCCAGC-AACACAAUCUCUUAGGGCUUUCCAAC-GCGGCGCCCCCUA
ABVD01612417.1/958-1081      UGA--CCCCACGGCGCUAGCCGGCCUCGUGGCCCCCCAGGCCUGG-CGCCAUACAUC-----CGGCCA----CCAA-CGGCUUCC-AACCUCCCCAAC-AGCACAACCUCUUUGGGGGUUCCAACGGCGGCGCCCCCUU
AL593857.10/151496-151620    GGC--CCCCAAGGCACUCACGGCGACCGUGGCCUUCUAGGCCUGGCCGCCAUACGCC-----CGCCCG----CCAA-CCGCUUCC-AACCAACCCAGCAAGCACAACCUCUUUGGGCGUUCCAAC-GCGGCGCCCCCUA
ABRN01244656.1/6199-6323     CGA--CCCCACGGCGCCACCCAGCCUCGUGGCGGUCCAGGCCUGGUCGCCAUACGCC-----CGCCCA----CCAAUCCGCUUCU-AACCACCCCGGC-CGCAUAACCUCUUAGGGCGUUCCAAC-GCGGCGCCCCCUA
CR956413.12/30400-30523      UGA--CCCCACGGCGCCCACCGGCCUCGUGGCAUCCCAGGCCUGGCCGCCAUACGCC-----CGCCCA----CCGA-CCGCUCCA-ACCCACCCCAGC-CUCACAACCUCUUAGGGCGUUCCAAC-GCGGCGCCCCCUA
ABRQ01176517.1/1082-1209     UGA--CCCCAAGGUGCCAGGCGGCCUCGUGGCUUCUCGGGUCUAGCCGCCAUGCACC-----CGCCCAACCACCAG-CGCCUGCC-UGCCACCCCAGC-AGGCCAACUUCUUGGGGCGUUCCAAC-GCGGCGCCCCCUG
AAIY01739346.1/747-641       UGU--CCCCAUGGGGCGAGCG-GCCUCGAGGUUUCUCAGGUCUGGCCGCCAUACCA-------GCCCG----CCAA-CAACAG----------------CGCACAACUUCUUGGGGCAUUCCAAC-GAGGCGCCCCCUA
AABR05108926.1/3003-3129     UGAUCCCCCAAGGAACUUACGGCGACCGUGGCCUUCUAGGCCUGACCGCCAUACGCC-----CGCCCG----CCAA-CUGCUUCC-AACCAACCCAGCAAGCACAACCUCUUUGGGCGUUCCAAC-GCGGCGCCCCCUU
AAQR03050726.1/105702-105831 UGA-CCCCCAUGGCGCUGGCGGUCCUCGUGGCCUUCUGGGCCUAGCCGCCAUACGCCCCCCACCCCCA----CCAA-CGGCUUCC-AACCACCCCUGC-AGUUUAACCUUUUUGGGCGUUCCAAC-GCGGCGCCCCCUA
#=GC SS_cons                 :::..::::::::::::::::::::::::::::::::::::::::::::::::::::.....::::::....::::.::::::::.::::::::::::.::::::::::::::::::::::::::.:::::::::::::
#=GC RF                      UGa..CCCCacGGcGCuagCgGgCCUCGUGGccuuCcaGGCCUgGCCGCCAUACgCc.....CGCCCa....CCAa.CggCuuCc.aaCCACCCcaGC.aGCacAACCUCUUuGGGcGUUCCAAC.GCGGCGCCCCCUa
//
# STOCKHOLM 1.0

#=GF AC   RF02132
#=GF ID   HOXB13-AS1_1
#=GF DE   HOXB13 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   65.30
#=GF NC   57.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.73 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12746837
#=GF RT   PRAC2: a new gene expressed in human prostate and prostate cancer.
#=GF RA   Olsson P, Motegi A, Bera TK, Lee B, Pastan I
#=GF RL   Prostate. 2003;56:123-130.
#=GF WK   HOXB13-AS1
#=GF SQ   12


ABRR01223724.1/168-314     CUUUAUACCCCCUAUAC---CAUAGAGGGACUCUUC---UAGUGGGUGAG---AAUACGGUAUACGUUU-CUUUCAAAAAAAAAAAAAAAAAAAACGGAA--CCUCGUC-U--UUCGCCCCCUC-GGCAGCUGU-UGC--CUCUGCGC-UUUAUU-CCAAG--UUUACGG
ABRP01067034.1/4697-4832   UUUCUUCUCCCCUUUCC---CAGAGAGGGACUAUUC---AGGUGAGUGAG---AGUAUGAUAUACAUUU-CUUUCAAAAAC------------AGCAGAC--CCUCCUCCU--UUCGCGCCCUC-UGAAACAGU-UGC--CUUUGCGC-UUUGUU-ACAAG--UUGACGG
AAFC03034539.1/13010-13144 UCUGCUUUUCCCUUUCC---CCGAGAGGGAGUAUUC---AGGUGGGUGAG---AAUGUACUAUAAAUUU-CUUUCAAAAAC------------AACGGAA--CC-UCUCCC--UUUGCCCCCUC-CGCAGCAGU-UGC--CUCUGCGC-UUUAUU-GCCAG--UUUACGG
AAGV020493267.1/1387-1523  CUUUCCACCCUCUUUUC---CGGAGAGGGACUGUUUUUUAGGUGGAUGAG---AAUAUGGUAUAAUUUU-AUUUCAAAAAC------------AACGAAA--UCUUCUG-U--CGCUCCCCCCA-CGCAGCAGU-CGC--CUCCGCGC-UUU-UC-GCAAA--CUAACGG
ABRO01194076.1/3074-3193   UUUUCUC-CCUCGUG-----CCGGGAGGGAAUGUCC---AGGUGGGAGAG---ACUAUGAUAUAGAUUU-CACCCCAAAAC------------GACGAAA--UCUCCU--U--UCAGCCGACUC-CGCCGCAGU-CGC--CUCUGCGC-UUUUUG-G-------------
ABDC01167017.1/2424-2578   CCUCUCCCCCUCUUGCUCGGAAGAGAGCGACUGCUC---AGGUGGGGUGAAGAAAUAUAGUAUAAAUUUUUUUUCAAAAAA------------AACGAAAACCCGGCUCCUUUUCAUCCCCCUCCCGCGGCAGUGUGCUACCCGGCGCUUUUAUUUGCAAGCCUUUACCG
AAQQ01353107.1/1059-1196   AUUUCUCCCCUCGUGAAA-ACAGAGAGCAACUGUUC---AGGUGGGUGAA---AAUAUCAUAUAAAUUU-CUUUCAAAAAC------------GACGAAA--CCUCCUCCU--UUCACCCCUUC-CACAGCAGU-CGC--CUCCAUGC-UUUAUG-GCACG--UUUACGG
ABRN01424954.1/4207-4341   CUUUCUCCCCACUUUCC---CGGAGAGGGACUAUUC---AGGUGGGUGAG---AAAGUGGUAUAAAUUU-CUUUCAAAAAC------------AACGGAA--CC-UCUCCU--UUCGCCCCCUC-CGCAGCAGU-UGC--CUCCGCGC-UUUAUU-GCCAG--UUUACGG
ABRT010363059.1/1228-1360  CUGGCUCCCCUCUUUCC---UGGAGCGCGACUGUUC---AAGUGGGUGAG-----CAUGGUACACGGUU-CUUUCGAAAUC------------AAGGACA--CCUCCUCCU--GCCGCCGCCUC-CGCAGCAGU-CGC--U-CCGCGC-UUUAUU-GCAAG--UUUACGG
AC068531.9/18396-18522     CUUUCUCCCCUCUUCCC---UGGAGAGCGACUGUUC---GGGAGGGUGAG---AAU--GGUAUAA-----AUUUCAAAAAC------------AACGAAA--CCUUCU-----UUUGCCCCCUC-CGCAGCAGU-CGC--CUCCGGGC-UUUAUU-GCAAG--UUUACGG
AAQR03043344.1/6161-6288   CUUUCUCCCAGCUUUCU---CAGAGAAUGACUGUUC---AGGUGGGUGAG---ACUACAGUAAAAAUUU-CUUUCAAAAAC------------AAA---------UUUC-U--UGCACCCGCUC-UGCUGCAGU-UGC--UACUGCGC-UUUAUU-GCAAG--GUUACGG
AACN010072409.1/652-520    CUUCCUC-CCCCUCUCC---UGGAGAGGAACCGUUC---AUGGCGGGGAG---AAUAGGAUAUAAAUUU-CUUCCAGAA-C------------AGCAGAA--CCGUCUCCU--UUUGCCCC-GG-UGCAGCAGG-CAC--CUCCGCGC-UCCAUU-GCAGG--UUUACGC
#=GC SS_cons               :::::::::::::::::...::::::::::::::::...:::::::::::...::::::::::::::::.:::::::::::............:::::::..:::::::::..:::::::::::.:::::::::.:::..::::::::.::::::.:::::..:::::::
#=GC RF                    cUUucUcCCCuCUuucc...caGAGAGgGACUgUUC...aGGUGGGuGAG...AaUAuggUAUAaaUUU.cUUUCaAAAAc............AACGgAA..CCuucUCCU..UucgCCCCCUc.cGCaGCAGU.uGC..CuCuGCGC.UUUaUu.GCAaG..UUuACGG
//
# STOCKHOLM 1.0

#=GF AC   RF02133
#=GF ID   HOXB13-AS1_2
#=GF DE   HOXB13 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   40.00
#=GF TC   43.00
#=GF NC   35.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.77 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12746837
#=GF RT   PRAC2: a new gene expressed in human prostate and prostate cancer.
#=GF RA   Olsson P, Motegi A, Bera TK, Lee B, Pastan I
#=GF RL   Prostate. 2003;56:123-130.
#=GF WK   HOXB13-AS1
#=GF SQ   14


AAQQ01353107.1/1599-1679   AAAGGCCCUAACCACGGAGCCUCGCAAUCGUUCUCCGCUUUGCCGUGGCCGAAAUCUAGAUUCAAAAA-GAGCUCCCGGAGG
ABVD01690044.1/120-200     AAGGACCCCGGAGCUGGAGUCUCGGGUUCGCUCUCCGCAGAGUCGCUGCCGGAACCUUAAUUCGAAAA-CAGCUUCCGGAGG
ABRN01424954.1/4734-4814   AAGGACCCCGGAGCCAGAGCCUCGGGUUCGCUCUCCGCUGGGCUGCUUGGAGAACCUAGAUUCGAAAA-GAGCUUCCGGAGG
ABDC01167017.1/2966-3042   AAAGACGUGAAAGAUGGAGCCUUAGGUUAGCUCCCCAC-UUUCUGCUGCCAGAACCUAGAUUCAA--A-GAGCUUCAGAGG-
AAGV020493267.1/1859-1940  AAGGACCCCGGAGCUGGAGUCUCUGGUUCGCUCUCCGCUGAGCUGCUGCCGGGACCUUGAUUCGAAAAACAGCUUCCGGAGG
ABRP01067034.1/5189-5269   AAGGACCCAGGAACUGGAGCCUCGGGUGGACUCUCUACUGGGUUGCUGCGGGAACCCAGAUUCGAAAA-GCGUUUCCGGAGG
AAHY01095565.1/20534-20455 AAAGGCCGGAACUUGAAAGCCUGGGGGUCACCCUUCGCUUUGCUGUGGCUGGGACCUAGAUUCAAAA--GAGCUUCCGGAAG
AAFC03034539.1/13564-13644 GGGGACCCCGGAGCUGGGGCCCCGGGUUCGUUGUCUGCGGGGCUGCUUCGAGAACCUAGAUUCGAAAA-GAGCUUCCCGAGG
ACBE01423658.1/5900-5820   AAGGACCCCAGGGCUGGAGCCCCGGCCUGGCCCUCCUCUGGGCGGCCUCGGGAAUUUAGAUUCGAAAA-GAGCUUCCGGAGG
ABRR01223724.1/698-777     AAGGACCCUGGAGCUGGGGCCUCGAGUUCG-ACUCCGCUGGGCUGCUUCGGGAAGGGAGAUUCGAAAA-GAGCUUCUGGAGG
AAWR02012784.1/20913-20989 AGGGACCCCGGAGCUGGAGCCCC--GUUCGCUCUCC--UGGGCUACUGCGGGAACCGAGAUUCGAAAA-GAGUUUCCGCAGG
AACN010072409.1/182-102    GAGGACCCCAGGGCCGGAGCCCCCGCCUGGCUCUUCGCUAGGCUGCAGCGGGGAUUUAGAUUCGAAAA-GAGCUUCCGGAGG
AAGU03054990.1/20390-20310 AAGGACCCCGGAGUUGGAGUCUCAGGUUUGCUCUCCUUUGGGCCGCUGCGGGAACAGAGAUACGAAAA-GAGCUUCAAGGGG
AC068531.9/18900-18980     UAAAACCCGAAAGAUGGAGCCUCAGGUUCGCGCUCUGCGUUGCGGGUGCUGGAACCGAGAUUCAAAAA-GAGCUUCCGGAGG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::
#=GC RF                    AAGGACCCcgGaGcUGGAGCCUCgGGuUcGCuCUCCGCUggGCuGCuGCgGGAACcuAGAUUCGAAAA.GAGCUUCCGGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF02134
#=GF ID   HTT-AS1_1
#=GF DE   HTT antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   200.00
#=GF TC   241.10
#=GF NC   57.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21672921
#=GF RT   A natural antisense transcript at the Huntington's disease repeat locus
#=GF RT   regulates HTT expression.
#=GF RA   Chung DW, Rudnicki DD, Yu L, Margolis RL
#=GF RL   Hum Mol Genet. 2011;20:3467-3477.
#=GF WK   HTT-AS1
#=GF SQ   3


Z68756.1/25278-25049     GGUCUCUGCACUGGCCAGGCAUGCAGAACAUUCUGUUCAGUAGCACUGGACAGAAGGCCCCAUCUAGAUGAGACAGAGCUGGUGGGGCAGGACAAAGACUCCUGGCAGCUCAAACGGCCUGGCAGAUGCUUGGAGAGAGGGGGCUUCUUGAGACAGCACCAUUUCUGGGAAGAGAGUCACCUGGGAGGGAUGAGGCCACGCUCCGGCUUGGAGGUGAAGAGAGGGGCUGC
ABGA01203367.1/1333-1562 GGUCUCUGCACUGGCCAGGCAUGCAGAACAUUCUGUUCAGUACCACUGGACAGAGGGCCCCAUCUAGAUGAGACAGAGCUGGUGGGGCAGGACAAGGACUCCUGGGAGCUGAAAUGGCCUGGCAGAUGCUUGGUGAGAGGUGGCUUCUUGAGACAUUCCCAUUUCUGGGAAAAGAGUCACCUGGGAGGGGUGAGGCCAUGCUCCGGCUUGGAGGUGAAGGGAGGGGCCAC
AANU01223710.1/5131-4903 GAUCUCUGCGCUGGCCAGGCAUGCAGAACAUUCUGUUCGGUCCCACCGGACAGA-GGCCCCAUCUAGAUGAGACCAGGCUGGUGGGGCAGGACAAGGACUCCUGGGAGCUGAAAUGGCCUGGCAGAUGCUUAGUGAAAGAGGGCUUCUUGAGACAGCACCAUUUCUGGGGAGAGAGUCACCUGGGAGGGGUGAGGCCAUGCUUUGGCUUGGAGGUAAAGGGAGGGGCCAC
#=GC SS_cons             ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  GgUCUCUGCaCUGGCCAGGCAUGCAGAACAUUCUGUUCaGUacCACuGGACAGAgGGCCCCAUCUAGAUGAGACagaGCUGGUGGGGCAGGACAAgGACUCCUGGgAGCUgAAAuGGCCUGGCAGAUGCUUgGuGAgAGggGGCUUCUUGAGACAgcaCCAUUUCUGGGaAgAGAGUCACCUGGGAGGGgUGAGGCCAuGCUccGGCUUGGAGGUgAAGgGAGGGGCcaC
//
# STOCKHOLM 1.0

#=GF AC   RF02135
#=GF ID   HTT-AS1_2
#=GF DE   HTT antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   100.00
#=GF TC   126.70
#=GF NC   37.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.30 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21672921
#=GF RT   A natural antisense transcript at the Huntington's disease repeat locus
#=GF RT   regulates HTT expression.
#=GF RA   Chung DW, Rudnicki DD, Yu L, Margolis RL
#=GF RL   Hum Mol Genet. 2011;20:3467-3477.
#=GF WK   HTT-AS1
#=GF SQ   3


Z68756.1/18770-18596       CCUGGUCUCGGGUCGGGGCUGCUCCCGCUUACUGCCCCCUGCCCAGGCUGGUGUGCACCCCCUCUGGCUGCUUUCAAGGCCUCUUCUCUCUUCUCGGCAGGACAGGCACA-------GGCAGGUGGCCAGGUGUCAUGCUUAGCUCCCCGCCCAGUGAGAUUCUUUCAUUUAACAAUCUUCC
ABGA01275948.1/365-184     CCUGGUCUUGGGUCGGGGCUGCUCCUGCUUACUGCCCCCUGCCCAGGCUGGUGUGCACCACCGCUGGCUGCUUUCAACGCCUCUUCUCUCUUCUCGGCAGGACAGGCACAAGGCACAGGCAGGUCGCCAGGUGUCAUGCUUGGCUCCCCGCCCGGUGAGAUUCUUUCAUUUAACAAUCUUCC
AANU01223709.1/12042-11915 CCUGGUCUUGGGUUGGGGCUGCCCCCGCUUACUGCCCCCUGCCCAGGCUGGUGUGCACCCCCUCUGGCUGCUU-CAGCGCCUUCUCUCUCUCCUUGGCAGGACAGGCGCA-------GACAUGUUACCAGGUGUUA----------------------------------------------
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.......:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    CCUGGUCUuGGGUcGGGGCUGCuCCcGCUUACUGCCCCCUGCCCAGGCUGGUGUGCACCcCCuCUGGCUGCUUUCAacGCCUcuUCUCUCUuCUcGGCAGGACAGGCaCA.......GgCAgGUugCCAGGUGUcAUGCUUgGCUCCCCGCCCgGUGAGAUUCUUUCAUUUAACAAUCUUCC
//
# STOCKHOLM 1.0

#=GF AC   RF02136
#=GF ID   HTT-AS1_3
#=GF DE   HTT antisense RNA 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   70.00
#=GF TC   76.70
#=GF NC   35.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.50 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21672921
#=GF RT   A natural antisense transcript at the Huntington's disease repeat locus
#=GF RT   regulates HTT expression.
#=GF RA   Chung DW, Rudnicki DD, Yu L, Margolis RL
#=GF RL   Hum Mol Genet. 2011;20:3467-3477.
#=GF WK   HTT-AS1
#=GF SQ   4


AC005516.1/197134-197075 UCUCCGUUGAGCCCCGCGCCUUCGCCCGGGUGGGGCGCUGCGCUGUCAGCGGCCUUGCUG
ABGA01203369.1/341-400   UCUCCGUUGAGCCCCGCGCCUUCGCCCGGGUGGGGCGCUUCGCUGUCAGAGGCCUUGGUG
AANU01223709.1/7309-7250 UGUCCGUUGAGCCCUGCUCCUUCGCCCAGGUGGGGCGCUGCGCUGUCAGAGGCUUUGGUG
ABRT010687680.1/665-606  UCUUCGCUGAGCCCCGCGCCUUCCCCCGGGUGGGGCACUGCGUUCCCUGCGGUCGCGGCA
#=GC SS_cons             ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  UCUCCGUUGAGCCCCGCGCCUUCGCCCGGGUGGGGCGCUGCGCUGUCaGcGGCCUUGGUG
//
# STOCKHOLM 1.0

#=GF AC   RF02137
#=GF ID   HOXA11-AS1_1
#=GF DE   HOXA11 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   50.90
#=GF NC   32.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   9745033
#=GF RT   Evolutionary conservation and tissue-specific processing of Hoxa 11
#=GF RT   antisense transcripts.
#=GF RA   Potter SS, Branford WW
#=GF RL   Mamm Genome. 1998;9:799-806.
#=GF RN   [2]
#=GF RM   12050232
#=GF RT   HOXA11 silencing and endogenous HOXA11 antisense ribonucleic acid in the
#=GF RT   uterine endometrium.
#=GF RA   Chau YM, Pando S, Taylor HS
#=GF RL   J Clin Endocrinol Metab. 2002;87:2674-2680.
#=GF WK   HOXA11-AS1
#=GF SQ   15


AF039307.1/1506-1409       GUCACUCGGUGUUCUCACCGAAAGCAC-GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCCGGCGCGCGCGGAGAGGCUGGGGUGCGCCCCC
AF071164.1/3661-3758       GUCACUCGGUGUUCUCACCGAAAGCAC-GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCCGGCGCGCGCGGAGAGGCUGGGGUGCGCCCCC
U20366.1/599-694           GUCACUCGGUGUUCUCACCGAAAGCAC-GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCCC--GCGCGCAGAAAGGCUGGGGUGCGCCCCC
AANG01383131.1/987-1082    GUCACUCGGUGUUCUCACCGAAAGCAC-GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCCG--GCGCGCGGCGAGGCUGGGGUGCGUCCCA
AALT01189713.1/2453-2358   GUCACUCGGUGUUCUCACCGAAAGCAC-GUAAUCGCUGGUGUAACUCAUGUUGGCUGAGGGGCCUCCCG--GUGCGCCGCGAGGCUGGGGUGCGCCCCC
ABRO01036384.1/15346-15439 GUCACUCGGUGUUCUCACCGAAAGCAC-GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCCG--GCGCG--GUGAGGCCGGGGUGCGCCCGC
ABVD01019939.1/8392-8487   GUCACUCGGGGUUCUCACCGAAAGCAC-GUAAUCGGCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCCG--GAGCGCUGCGAGGCUGGGGUGCGCCCUC
ABRQ01101202.1/1237-1332   AUCACUCGAUGUUCUCACCGAAAGCAC-GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCUG--GCGCACGGCGAGGAUGGGGUGCGCUCAG
AAIY01684959.1/779-685     GUCACUCGGUGUUCUCACCGAAAGCAC-GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGG-CCUCCCG--GCGCGCGACCAGGCUGGGGUGUGCCCCU
ABRP01099870.1/2232-2328   GUCACUCGGUGUUCUCACCGAAAGCAC-GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCCC-GGCGCGCGGCAAAGCUGGGCCGCGCCCCG
AANN01604113.1/187-93      CUCACUCGGUGUUCUCACCGAAAGCAC-GUAAUCGCUGGUGUAACUCAUGUUGGCUGGGGGGCCUCCUG--GCGCGCUGCGAAC-UGGGGUGCGCCCCU
AAYZ01682622.1/810-889     GUCACUCCGCGUUCUCACCGAAAGCGC-GUAAUCGCCGGUGUAACUCAUGUUAGCUGGGGG------------------CGAGGGAGGGGGGCUCCCGG
ABQO010579153.1/124-29     GGCACUUGGUAUUCUCACCGAAAGCUCAGUAAUCUCCAGUGUAACUCAUGUUCGCUGGGGCACCCUCCGAGGACCGC--CGGACGCGUGACAGACCUU-
AAFC03071410.1/14191-14096 GUCACUCGGUGUUCUCACCGAAAGCAC-GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCCG--GCGCGCGGCGAGGCUGGGUGCUACCCCG
AAGW02035946.1/13789-13694 GUCACUCGGCGUUCUCACCGAAAGCAC-GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCCG--GCGCGCGGCGAGGCCGCGGUGCGCCCCG
#=GC SS_cons               :::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::..::::::::::::::::::::::::::::
#=GC RF                    GUCACUCGGuGUUCUCACCGAAAGCaC.GUAAUCGCCGGUGUAACUCAUGUUGGCUGGGGGGCCUCCCG..GcGCGCgGcGAGGcuGGGguGcGCCCcg
//
# STOCKHOLM 1.0

#=GF AC   RF02138
#=GF ID   HOXA11-AS1_2
#=GF DE   HOXA11 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   66.60
#=GF NC   41.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.35 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   9745033
#=GF RT   Evolutionary conservation and tissue-specific processing of Hoxa 11
#=GF RT   antisense transcripts.
#=GF RA   Potter SS, Branford WW
#=GF RL   Mamm Genome. 1998;9:799-806.
#=GF RN   [2]
#=GF RM   12050232
#=GF RT   HOXA11 silencing and endogenous HOXA11 antisense ribonucleic acid in the
#=GF RT   uterine endometrium.
#=GF RA   Chau YM, Pando S, Taylor HS
#=GF RL   J Clin Endocrinol Metab. 2002;87:2674-2680.
#=GF WK   HOXA11-AS1
#=GF SQ   21


AF071164.1/4060-4246       GGAUGUGCCUGCCUGGUGGCUUGUCCGAUUUGCACGGUGACUUGAUUACACUCUCUCAUUCAUGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCUAAACCGCC-AACAGCCA-G-AACGGCUUCUCCC--CGCGGUUU-------GUCAC-U---GAUCC-GCAGGGCCCG-GAAGGGCCUUCGUCUUACCCGGGAUCCAC
AF039307.1/1106-920        GGAUGUGCCUGCCUGGUGGCUUGUCCGAUUUGCACGGUGACUUGAUUACACUCUCUCAUUCAUGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCUAAACCGCC-AACAGCCA-G-AACGGCUUCUCCC--CGCGGUUU-------GUCAC-U---GAUCC-GCAGGGCCCG-GAAGGGCCUUCGUCUUACCCGGGAUCCAC
AAFC03071410.1/13806-13621 GGAUGUGACUGCCUCGUGGCUUGCCCGAUUUGCACGGUGACUUGAUUACACGCUCGCAUUCAUGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCUAAACCGCC-AACAACCA-G-GGCGGCUU-CCCC--CGCGGUUU-------GUCAG-G---GAUCC-GCAGGUCCCG-GAAGGGCCUUCGUCUCACCCGGGAUCCAC
U20371.1/4028-3842         GGAUGUGCCGGCCUCGUGGCUUGUCCGAUUUGCACGGUGACUUGAUUACACGCUCUCAUUCACGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCCAAACCGCC-AACAGGCA-A-AGCGGCUUCCCUC--CGCGGUUU-------GUCAA-U---AAUCC-GCGCUGUCCG-GAAGGGCCUUCGUCUUACCCGGGUUCCAC
AAQQ01071875.1/1053-1238   GGAUGUGCCCGCCUCGAGGCUUGUCCGAUUUGCACGGUGACUUGAUUACACGCUCGCAUUCACGGUCACUUCCGAAGCGCUUUAGUGUCUUCCGUCCCUAAACCGCC-AAGAACCA-A-GGCGGCUU-CCCC--CGCGGUUU-------GUCAA-U---GAUUC-GCGGGGUCCG-GAAGGUCCUUCGUCUUACCCGGGAUCCAC
AAKN02039092.1/11891-12075 GGAUGUGCUGGCCUCGUGGCUUGUCUGAUUUGCACGGUGACUUGAUUACACGCUCGCAUUCAUGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCUAAACCGCC-AACAGCCA-G-GGCGGCUU-UCCG--CGCGGAUU-------GUCAG-U---GAUCC-AC-GGGUCCG-GAAGGGCCUUCGUCUUACCCGGGAUCCAC
AALT01189713.1/2056-1870   GGAUGUGCCUGCCUCGUGGCUCUCCCGAUUUGCACGGUGACUUGAUUACACGCUCGCAUUCACGGGCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCUAAACCGCC-AACAACCC-G-GGCGGCUUCCCCC--CGCGGUUU-------GUCAG-G---GAUCC-GCAGGUCCCU-GAAGGGCCUUCGUCUUACCCGGGAUCCAA
ABRO01036384.1/15763-15949 GGAUGUGCCGGUCCCGUGCUUUAUCCGAUUUGCACGGUGACUCGAUUACACGCUCGCAUUCAUGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCUAAACCGCC-AACAGCCU-G-GGCGGCUUCCCCC--CGCGGUUU-------GUCAA-U---AAUCC-GCGGGGUCCG-GAAGGGCCUUCGUCUCACCCGGGAUCCAU
AC184818.19/166437-166251  GGAUGUGCCUGCCUCGUGGCUUGCCUGAUUUGCACGGUGACUUGAUUACACGCUCGCAUUCAUGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCUAAACCGCC-AACAACCA-C-GGCGGCUU-CCCC--CGCGGUUU------UGUCAG-G---CAUCU-GCAGGUCCCG-GAAGGGGCUUCGUCUUACCCGGGAUCCAC
ABRQ01101202.1/1601-1787   GGAUGUGCCGGCCUUGUGGCCUACCCGAUUUGCACGGUGACUUGAUUACACGCUAGCAUUCAUGGUCACUUCCGAAGCGCUUUAGUACCUUCCGUACCUAAACCGCC-AACAGCCCUG-AGCGGCUU-CCCC--UGCGGUUU-------GCCUG-G---GAUCC-GCAGGGCCCG-GAAAGACAUUCGUCUCACCCGGGAUCCCC
AAGV020458988.1/192-377    GGAUGUGCCGGCCUGGUGGCUUGCCCGAUUUGCACGGUGACUUGAUUACACGCUCGCAUCCAUGGUCACUUCCGAAGAGCUUUAGUGCCUUCCGACUCGAAACCGCC-AACCGUCG-C-GGCAGCUU-CCCC--CGCGGUUU-------GCCUG-G---GAUCC-GCAGGGCCCG-GGAGGGCGUUCGUUUUACCCGGGAUCCUC
ABRT010410211.1/4-181      UGA-----AGCUCCAAUG--UGGUGGAAUUC---CGGUGACUUGAUUACACGCUCGCAUUCAUGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCCAAACCGCC-AACAGCCA-G-GGCGGCCUCUCCC--CGCGGUUU-------GUCAAAU---GAUCC-GCAGGGCCCG-GAAGAGCCUUCGUCUCACCCGGGAUCCAC
AAIY01684959.1/401-213     AGAUGUGCCGGCCUCGUGGCUUGCCUGAUUUGCACGGUGGCUUGAUUACACGCUCGCAUUCACGGUCACUUCCGAAGCGCUUUAGUACCUUCCGUCCCGAAACCGCC-AACUGCCC-G-GGAGGCUUUAUAC--CCGCGCUU------GGUCGG-G---GAUCCACAGGGCCCCG-GAAGGGCAUUCGUCUCACCCGGGAUCCCC
AAYZ01055296.1/762-947     GGAUGUGCUCGCCCCGUGGCUUGUCCGAUUUGCACGGUGGCUUGAUUACACGCUCGCAUUCAGGGUCACUUCCGAAGCGCUUUAAUACCUUCCGUCCCUAAACCGCC-GACAGCC--G-GGCGGCUU-CCCC--CGUGGUUU-------GGGGA-G---GAUCUUGCGGGGUCCG-GAAGGGCCUUCGUCUCACCCGGGAUCCAC
ABQO010902588.1/128-321    GAAUGUGCCGGGCUCGGGGCUUGUCUGAUUUGCACGGUGGCUCCAUUACACGCUCGCAUUCACGGUCACUUCCGAGGCGCUCCAAUAACUCCCCUCCCU---UUACU-AGAAGCCU-C-AGCAAUCCCCCAA--GGCGGUUUGCACCCGGGCUU-UGCAGACCU-GCUCAGUCAG-GCAGGGCGUUCGUCUCACCCGGGAUCUUU
AAQR03057533.1/76157-76343 GGAUGUGCUGGUCUCAUGGCUUGUCCGAUUUGCACGGUGACUUGAUUACACGCUCGCAUUCAUGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCUAAACCGCU-AACAGCCA-G-GGCGGCUUCUCCC--UGCGGUUU-------GUCAA-U---GAUCC-GCAGGGCUGA-GAAGGGCCUUCGUCUCACCCGGGAUCCAC
AAGW02035946.1/13417-13232 GGAUGUGCCCGCCUCGUGGCUUGUCCGAUUUGCACGGUGACUUGAUUACACGCUCGCAUUCAUGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCUAAACCGCC-GACAGCC--G-GGCGGCUUCCCCU--CGUGGCUU-------GUCGA-U---GAUCC-GCAGGGUCCG-GAAGGGCCUUCGUCUCACCCGGGAUCCAC
AAPE02018006.1/6511-6326   GGAUGUGCCUGCCUCGUGGCUCGCCCGAUUUGCACGGUGCCUUGAUUACACGCUCGCAUUCAUGGUCACUUCCGAACCGCGUUAGUGCCUUCCGUCCCUAAACCGCC-AACGACCC-AGGGCGGCUU-CCCU--CGCGGUUU-------GUCAG-G---GAUCC-GCAGGUCC--CGGAGAGCCUUCGUCUUACCCGAGAUACAC
U20366.1/875-1058          GGAUGUGCCGGCCUCGUGGCUUGUCCGAUUUGCACGGUGACUUGAUUACACGCUCUCAUUCACGGUCACUUCCGAAGCGCUUUAGUGCCUUCCGUCCCCAAACCGCC-AACAGGCA-A-AGCGGCUUCCCUCCGCGGGGUUC-------GGAGU-G---ACUCC-UCA-GAGCCA-GA-GGCACUUCUGCUCAC-CGG--UCCGC
AF071166.1/1-76            ------------------------------------------------------------------------------------------------------CCGCC-AACAGCCA-G-AACGGCUUCUCCC--CGCGGUUU-------GUCAC-U---GAUCC-GCAGGGCCCG-GAAGGGCCUUCGUCUUACCC---------
AF327372.1/7641-7466       GAAUGUGCCAGGGUCAAGUCUGCACUGAUUUUCAUGGUGAAUAGAUUACAUGCUUGCAUUCAUGUUCACUUCCGAAGCGCU-UAGUGUCUUCCUUCCCUCCCUUACAUAUUAACCU-C----AAAUACCCCG--UGCGGCUCC-----AGCC-------AAGCC-UCAC----CA-GAGG-UACUUAG--CAAUAUUGGAUUCCC
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::.:.:::::::::::::..::::::::.......:::::.:...:::::.::::::::::.:::::::::::::::::::::::::::::
#=GC RF                    GGAUGUGCcgGcCUcGuGGCUuguCcGAUUUGCACGGUGaCUuGAUUACACGCUcGCAUUCAuGGUCACUUCCGAAGCGCUUUAGUGcCUUCCgUCCCuaaaccGCc.AacaGcCa.g.gGCGGcUuCcCcc..cGcGGuUU.......GuCag.u...gAuCC.gCagGgcCcg.GaAGGgccUUCGUCUcACCCGGGAUcCac
//
# STOCKHOLM 1.0

#=GF AC   RF02139
#=GF ID   HOXA11-AS1_3
#=GF DE   HOXA11 antisense RNA 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   62.10
#=GF NC   34.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.69 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   9745033
#=GF RT   Evolutionary conservation and tissue-specific processing of Hoxa 11
#=GF RT   antisense transcripts.
#=GF RA   Potter SS, Branford WW
#=GF RL   Mamm Genome. 1998;9:799-806.
#=GF RN   [2]
#=GF RM   12050232
#=GF RT   HOXA11 silencing and endogenous HOXA11 antisense ribonucleic acid in the
#=GF RT   uterine endometrium.
#=GF RA   Chau YM, Pando S, Taylor HS
#=GF RL   J Clin Endocrinol Metab. 2002;87:2674-2680.
#=GF WK   HOXA11-AS1
#=GF SQ   24


AF039307.1/772-675         UGCCU-GGUCUUCUGGAGCUGAGGACUCGGGAAA-CCAUGCAAUUGAGGCAAGCCUUGGGCUGCUUUAGAGGCGCUGACAUCCGAGGAGACUUCUCCUGG
AF071164.1/4394-4491       UGCCU-GGUCUUCUGGAGCUGAGGACUCGGGAAA-CCAUGCAAUUGAGGCAAGCCUUGGGCUGCUUUAGAGGCGCUGACAUCCGAGGAGACUUCUCCUGG
ABDC01121663.1/1550-1647   UGCCU-GGUCUUCUGGAGCUGAGGACUCAGGAAA-CCAUGCAACUGAGGCAAGCCUUGGGCUGCUUUAGAGGCGCUGACAUCCGAGGAGACUUCCCCUGG
AAKN02039092.1/12223-12320 UGCCU-GGUCUUCUGGAGCUGAGGAAUCGGGAAA-CCAUGCAAUUGAGGCAAGCCUUGGGCUGCUUUAGAGGAGCUGACAUCCGAGGAGCCUUCUCCUGG
AAQQ01071875.1/1385-1482   UGCCU-GGUCUUCUGGAGCUGAGGAAUCGGGAAA-CCAUGCAAUUGAGGCAAGCCUUGGGCUGUUUUAGAGGCGCUGACAUCCGAGGAGCCUUCCCCUGG
ABRN01187570.1/4630-4727   UGCCU-GGUCUUCUGGAGCUGAGGACUCGGGGAA-CCAUGGAAUUGAGGCGAGCCUUGGGCUGCUUUAGAGGCGCUGACAUCCAAGGAGACUUCUCCUGG
AAWR02014102.1/1502-1596   CGCCU-GG---UCUGGAGCUGAGGACUCGGGAAA-CCAUGCAGUUGAGGCGAGCCUUGGGCUGCUUUAGAGGCGCUGAUAUUCGAGGAGGCUUCUCCUGG
ABRQ01101202.1/1932-2029   UGCCU-AGUCUUCUGGCGCCGAGGACUCGGGAAA-ACAGGCAGCUGAAGGGAGCCUAGGGCUGAUUUAGAGGCGCUGACAUCCGAGGAGCCUUCUCCUGG
AAPY01076971.1/208-302     UGCCU-GGUGUUCUGGAGCU---GACUCGGGAAA-CCGUGCAGUUGAGGCGAGCCUUGGGCUGCUUUAGAGGCGCUGACAGCCGAGGAGACUUCUCCUGG
ABRP01099870.1/2939-3036   CGCCC-GGUCUUCUGGAGCUGAGGACUCGGGAAA-UCAAGCAGUAGAGGCGAGACUUGGGCUGUUUUAGAGCCGCUGACAUCCGAGGAGCCUUCUCCUGG
AC184818.19/166100-166004  CGCCG-GGUCUUCUGGAGCUGAGGACUCGGGAAA-CCAUGCAGUUGAAGCGAGCCUUGGGCUGC-UUAGAGGCGCUGACAUCCGAGGAGCCUUUUCCUGG
ABRT010410211.1/328-426    CGCCU-GGUCUUCUGGAGCCGAGGACUCGGGAAACCCGUGCAGUUGAGGCAAGCCUCGGGCUACUUCAGAGGCGCUGACAUCCGAGGAGCCCUCUCCUGG
AAFC03071410.1/13477-13380 CUCCG-GGUCUUCCGGAGCUGAGGACUCGGGAAA-CCAUGCGGUUGAGGCGAGCCUUGGGCGGCUUCACAGGCGCUGACAUCCGAGGAGACUACUCCUGG
ABRO01036384.1/16096-16194 UGCCUGGGUCUUCAGGAGCUGAAGAACCGGGAAA-CCAUGCAACUGAGGCAAGCCUUGGGCUGUUUUAGAGGCGCUAACAUCCGAAGAGCCUGUUCCUGG
ABVD01019940.1/178-275     CGUCU-GGUCUUCUGGCGCCGAGGACUCGGGAAA-CCGUGCGGUUGAGGCGAGCCUGUGGCUGCUUUAGAGGCACUGACAUCCGAGGACCCUUCUCCUGG
AAGV020458988.1/521-618    CGCUU-GGUCUUCUGGCGCCGAGGGCUCGGAGAA-CCGUGCAGUUGAGGCGAGCCUGGGGCUGCUUUAGAAACGCUGACAUCCGAGGAGCCUUCUCCUGG
AC122669.6/117109-117199   UGCCU-GGUCUGCUGAAGCUGACGAAUCGGGAAA-CCAUGCAAUUGAGGCGAACCUUGGGCUGCUUUAGAGGCGCU-------GAGGAGCCUUCUCCUGG
U20371.1/3709-3619         UGCCU-GGUCUGCUGAAGCUGACGAAUCGGGAAA-CCAUGCAAUUGAGGCGAACCUUGGGCUGUUUUAGAGGCGCU-------GAGGAGCCUUCUCCUGG
ACBE01077432.1/1728-1825   UGCCU-GGUCUCAUGGAGCUGAGGACCCGGGAAG-CCGUGCGGUUGAGGCGAGCCUUGGGCUGCUUUAGGGGCGCUGACAGCCGAGGAGCGUUUUCCUGG
AALT01189713.1/1706-1609   GGCUG-GGUCUUUUGGAGCUGAGGACUCGGGAAA-UGCAGCAGCAAAGGCGAACCCUGGGCUGCUUUGAAGGCGCUGCCAUCUGAGGAGCCUUCUCCUGG
AAYZ01055296.1/1110-1207   UGCCU-GGUCUUCGGGGAGCGGAGGCGUCGGAAA-CCCAGCACUUUAGGCGCGCGCUGCGCGGCUUUAGAGGCGCUGACAAUCGAAGAGGCUUCCCCAGG
AAPE02018006.1/6179-6084   CGCCU-GGCCUUGUAAAGCUGAGGACU-GGGGAG-CCGGGCGGCAGAGGCGAGCCC-GAGCUGCGUCAGAGGCGGUGACAGCCGAGGGGUCUCCUCCUAG
AAGW02035946.1/13079-12983 UGUCU-GGUCUUCUGCGGCGGAGGCGUC-GGACA-CCGCGCAGUUGAGGCGCGCCCGGGGCCGCUUUAGAGGCGCUGACAUCCGAGGAGACUUCUCCUGG
AAQR03057533.1/76493-76587 AGCCU-GGUCUUUUGGAGCUGAUGACUCAGGAAA-CCAUGCAAUUGAGGCAAGCCUUGGGCUGCUUUAGAGGCGCUGACAUCCGAGGAG---UCUUCUGG
#=GC SS_cons               :::::.::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    uGCCU.GGUCUUcuGGaGCuGAGGacUCGGGAAA.CCauGCAgUUGAGGCGAGCCUuGGGCUGCUUUAGAGGCGCUGACAuCCGAGGAGcCUUCUCCUGG
//
# STOCKHOLM 1.0

#=GF AC   RF02140
#=GF ID   HOXA11-AS1_4
#=GF DE   HOXA11 antisense RNA 1 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   87.90
#=GF NC   66.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 45.48 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   9745033
#=GF RT   Evolutionary conservation and tissue-specific processing of Hoxa 11
#=GF RT   antisense transcripts.
#=GF RA   Potter SS, Branford WW
#=GF RL   Mamm Genome. 1998;9:799-806.
#=GF RN   [2]
#=GF RM   12050232
#=GF RT   HOXA11 silencing and endogenous HOXA11 antisense ribonucleic acid in the
#=GF RT   uterine endometrium.
#=GF RA   Chau YM, Pando S, Taylor HS
#=GF RL   J Clin Endocrinol Metab. 2002;87:2674-2680.
#=GF WK   HOXA11-AS1
#=GF SQ   20


AF071164.1/5119-5351       GUUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCAAUAACAAA-UCUAAUCGUGUAUUGCACUG-GAAAA-GAAAUAUUCUUAUUAUGUAUUUUCUCC-AAAUAAUGGCCUACCAUUGCAUUUGAAUACCUGCUGUAAAUAU--CAAUAAUAUGAAGUAA-UUACU
ABVD01019940.1/888-1120    AGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACGCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUCAUUUAUUGCUGAGCUGACUGUAACUGACUCAGUAACAAA-UCUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUCCCC-AAAUGAUGGCCCACCAUUGCAUUUGAAUACCUGCUGUCAAUAU--CAAUAAUAUCGAGUAA-UUACU
ABRP01099870.1/3626-3858   GGUAUUUAUAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGUGGACUGUAACUGACUCAAUAACAAA-UCUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUCUCC-AAAUGAUGGCCCACCAUUGCAUUUGAAUGCCCACUGUAAAUAU--CAAUAAUAUCAAGUAA-UUACU
AAPY01076971.1/894-1126    GGUAUUUACAUAUCUCAGGGCGAUUU--AGAGAAUAAACUCUA-----GGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCAAUAACAAA-UCUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUCUCC-AAAUAAUGGUCCACCAUUGCAUUUGAAUACCCGCUGUAAAUAU--CAAUAAUAUCGAGUAA-UUACU
AAHY01053339.1/13083-12851 GGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACGCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCAAUAACAAA-UUUAAUCAUGUAUUGCUCUG-GAAAA-GAACUACUCUCGUUAUGUAUUUUCUCC-AAAUAAUGACCCACCAUUGCAUAUGAAUGCCCACUGUAAAUAU--CAAUAAUAUCAAGUAA-UUACU
AANN01604120.1/4844-4612   GGUAUUUAUACAUCUCGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAGCAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCAAUAACAAA-UCUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUUGCC-AAAUGGUGACCCACCAUUGCAUUUGAAUACCGGUUGUAAAUAU--CAAUAAUAUCCAGUAA-UUACU
AAKN02039092.1/12920-13152 GGUAUUUACAUAUCUUGAGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGCAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUUAAUAACAAA-UUUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUCUCC-AAAUAAUGACCUGCCAUUGCAUUUGAAUACUCACUGUAAAUAU--CAAUAAUAUCGAGUAA-UUAUU
ABRN01187570.1/5318-5551   GGUAUUUAUAUAUCUCGGGGAGAUUU--AGAGUAUAACCUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUAACUGUAACUGACACAAUAACAAAAUCUAAUCGUGUAUUGCACUG-CAAAA-GAAAUAUUCUCAUUAUGUAUUUUCUCU-AAAUGAUGGCUCACCAUUGCAUUUGAAUACUCGCUGUAAAUAU--CAAUAAUAUCGAGUAA-UUACU
AAIY01705046.1/1523-1291   GGUAUUUACAUAUCUCGGGGAGAUUU--AGAGUAUAAUCUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUCGCUGAGCUGACUGUAACUGACUCAAUGGCAAA-UCUAAUCGUGUAUUGCACUG-GAAAA-GGAAUAUUCU-AUUAUGUAUUUCCCCCCAAAUGAUGGCUUACCACUGCAUUUGAAUGCCCGCAGUAAAUAU--CAAUAAUAUCAGGUAA-UUAUG
ABRQ01101202.1/2639-2874   GGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUUUAUUUAUUUAUUGCUGAGCUGACUGUAACCGACUCAGUCACAAA-UCUAAUCGUGUAUUGCACUG-GAAAA-GAAAUAUUCUUAUUACAUAUUUUCCCC-AAAUGAUGUUGCACCAUUGCUUUUGAAUACCUGUUGUAAAUAUAUCAAUAAUAUUAGGUAA-UUACU
ABRO01036384.1/16802-17035 AGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCAAUUU-AUUUAUUUAUUGCUGAGCUGACCAUAACUGACUCAAUAACAAA-UUUAAUCAUGUAUUGCACUG-GAAAAAGAAAUAUUCUCGUUCUGUAUUUUCUCC-AAAUAAUAACCCACCAUUCUAUUUGAAUACCCACUGUAAAUAU--CAAUAAUAGUGAGUAA-UUAUU
AAGV020458989.1/269-494    GGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAAUGUCAUCAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCGGUAACAAA-UCUAAUCAUGUAUUGCACUG-GAAAA-GAAAUAUUCUCAU---GUAUUUUCCUC-AAAUGAUGGCGCGCCAUUGCAUUU----ACCUGGUGUAAAUAU--CAAUAAUAUCGAGUAA-UUACU
AAPN01063703.1/15252-15484 GGUAUUUACAUAUCUGGGGAAAAUUU--CGAUUAUAAAUUUUA-----AGAUCUUC-UGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGAUCGUAACUGACUCAAUAACAAA-UCUAAUCAUGUUUUGCCCUG-GAAAA-GAACUAUCCUCAUUAUGUAUUUUCGCC-AAAUUAUAGCACACUAUUCCACUUGAAUACCAGCUGUAAAUAU--CAAUAAUAUCAAGUAA-UUACU
AAYZ01055296.1/1799-2024   GGUAUUUACAUAUCUUGGGGAGAUUU--AGAGCAUAAACUCCA-----AGAUCUUG-GGUAUUUAAGUGUCAGCAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACGGACUCAAUAACAAA-UCUAAUCAUGUAUUACCCUG-GAAA------UAUUCU---UAUGUAUUUUCUCC-AAAGAAUGGCUCACCAUUGCAUUUGAAUGCCCGCUAUAAAUAU--CCAUCAUAUCGAGUAAAUUACU
AAFR03047692.1/44711-44480 GGUGUGUAUAUAU-----GAAGAUUU--GCAGCCUAAAUUCCAUCCAAAGAUCUUC-AGUAUUUAAAUGUCAACAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACCGUAACUGACUUAAUAACAAA-UCUAAUCAUGU-UUGCUCCG-GGAAA-GAAAUAUUCUCAUUAUGUAUUUUCACC-AAAUGAUGGCUCACCAUUCCAUUUGAAUACCGGCCAUAAAUAU--CAAUAAUACGCAGUAA-UUACU
AAQQ01071885.1/63-291      AUUCUUUAUAUAUGU-AGAGAGAUUUUAGAAGUAUAAACUCUA----AAGGUCUUUUGGUAUUUAAGUGUCAACAUCGAUUAAAUGUAUUUAUUGCUGAGCUGACUGUAACCGACUCAAUAACAAA-UUUAAUCAUGUAUUGCACUG-GAAAA-AAAAUAUUCUCAUUAUGUCUUUUCUCC-AAAUAAUGACCCACCAUU------GAAUACC--CUGUAAAUAU--CAAUAAUAUCAAGUAA-UUACU
ABQF01013713.1/13270-13498 AGUAUUUAUAUAUCCGGAGAAAGUUC---UCUAGUAAAUUCUG----GAGAUCCUC-GGUAUUUAAAUGUCAACAUCGAUUU-GUUUAUUUAUUGCUUAGCUUAUCGUAACCGACUCAAUAACAAA-UCUAAUCAUGUUAUGCAGAGAGAAA-----AUAUUCUCAUUAUGUAUUUCCCCU-ACAUUAUAGUUAACUAUUGCGUUUGAAUUCAAGCUGUAAAUUC---AAGAUUAUCAAGUAA-UUACU
AF327372.1/6683-6451       AGUAUUUAUACGUCCGGAGAAAGUUC---UAUAGUAAAUUCGG----GAAAUCUUC-GCUAUUUGAAUAUCAACGUCGAUUU-GUUUAUUUAUUGCUCGGCUUAUCGUACCAGACUCCGUAACAAA-UCUAAUCAUGGUGCUCGCAG-GAAAAGAAAAUAUUCUCAUUAUGUAUUUUCCCU-CCAUUAUAGUUAACUGUUACAUUUGAAUUCGAGCUGUAAAUUC---AAUAUUAUCAAGUAA-UUACU
AAGW02035946.1/12410-12186 GGUAUUUACAUAUCUUGGGGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUG-GGUAUUUAAGUGUCAGCAUCGAUUU-AUUUAUUUAUUGCUGAGCUGACUGUAACUGACUCAAUAACAAA-UCUGAUCUUGUAUUAUACUG-GAAA------UAUUCU---UAUGUAUUCUCUCC-AAAUAAUGGCUCACUAUUGCAUUUGAAUGCCCACUAUAAAUAU--CAAUAAUAUCGAAUAA-UGACU
AAGU03015373.1/12862-12630 GGUAUUUACAUAUCUUGGAGAGAUUU--AGAGUAUAAACUCUA-----AGAUCUUU-GGUAUUUAAGUGUCAACAUCGAUUU-AUUUAUUUAUUGCCGAGCUGACUGUAACUGACUCAGUAACAAA-UCUAAUCGCAUAUUGCACUG-GAAAA-GAAAUAUUCUCAUUAUGUAUUUUUCCC-AAAUGAUGGCCCACCAUUGCAUUUGAAUACCUGCUGUAAAUAU--CAAUAAUAUUAGGUAA-UUACU
#=GC SS_cons               ::::::::::::::::::::::::::..:::::::::::::::.....::::::::.:::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::.:::::.:::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::..::::::::::::::::.:::::
#=GC RF                    gGUaUUUAcAUAUCuuGGGGAGaUUU..agAguaUAAacUCua.....AGAUCUUu.GGUAUUUAAGUGUCAaCAUCGAUUU.aUUUAUUUAUUGCUGAGCUgAcuGUAaCuGACUCaaUaACAAA.UcUAAUCaUGUauUGCaCuG.GAAAA.GAAaUAUUCUCAUUAUGUAUUUUCuCc.aaAUgAUGgcucACcAUUgCaUUUGAAUaCccGcUGUAAAUaU..CAAUAaUAUcaaGUAA.UUACU
//
# STOCKHOLM 1.0

#=GF AC   RF02141
#=GF ID   HOXA11-AS1_5
#=GF DE   HOXA11 antisense RNA 1 conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   53.20
#=GF NC   49.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.96 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   9745033
#=GF RT   Evolutionary conservation and tissue-specific processing of Hoxa 11
#=GF RT   antisense transcripts.
#=GF RA   Potter SS, Branford WW
#=GF RL   Mamm Genome. 1998;9:799-806.
#=GF RN   [2]
#=GF RM   12050232
#=GF RT   HOXA11 silencing and endogenous HOXA11 antisense ribonucleic acid in the
#=GF RT   uterine endometrium.
#=GF RA   Chau YM, Pando S, Taylor HS
#=GF RL   J Clin Endocrinol Metab. 2002;87:2674-2680.
#=GF WK   HOXA11-AS1
#=GF SQ   28


AF071164.1/6046-6248       CUAG-GAAAACCGAAAACA---GUUCUAGACAGACCUGCGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGACGGGGUUGUGGUGGCCCGCCAGC-----GGGGGAUGCCAGGCCAC----------CUCCCCCAGCG----GCACG-CAGCCCCUCUCUUAAUUAGAUCGGU--UUUCCCC---U------------------GGUGUCCG---------GGA-GAGCGG----UCCCGGCAGAAAGG
ABDC01121663.1/3177-3380   CUAG-GAAAACCGAAAACA---GUUCUAGACAGACCUGCGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGGCUGAGC--AGACUGGGCCGUGGUGGCCCGCCAGC-----GGGGGACGCCAGGCCGC----------CUCCCCCGGCU----GCACG-CAGCCCCUCUCUUAAUUAGAUCGGU--UUUCCCC---U------------------GGUGCCAG---------GGA-GAACGG---GUCCCCGCGGAAAGG
AANG01383132.1/860-1063    CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGGGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGACCGG-CUGCGGUGGCCCGCCAGC-----CGGGGACGCCAGGCUAC----------CUCCCCCAGCU----GCACG-CAGCCCCUCUCCUAAUUAGAUCGGC-UUUCCCCU---U------------------AGUGCCAG---------GGA-GAGGGG---GUACCGGCAGAAAGG
AAKN02039092.1/13829-14030 CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGCGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGUGGGG-CCGAAGUCGCCCGCCAGC-----GGGGGAUGCUAGACCAC----------CUCCCCCAGCU----GCAUG-CAGCCCCUCACUUAAUUAGAUCGGC---UUCCUC---U------------------GGUGCCAA---------GGA-GAGGGU---GUCCCCACAGAAAGG
AAPY01076971.1/1789-1991   CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGCGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGU--AGACUGG-CCGCGGUGGCCCGCCUGC-----GGGGGACGCCUGGCCGC----------CUUUCCUGGCU----GCACG-AAGUCCCUCUCUUAAUUAGAUCGAU--UUCUUCC---U------------------GGUGCCAG---------GAA-GAGGGG---GUCCCUGCAGAAAGG
ABRP01099870.1/4524-4725   CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGGGGUUUUAUAGCACUUUUGGCAGUCAACUUCAGGUUGUGCCUGAGC--AGACCGG-CUGCGGUGGCCCGCCAGC-----GGGGGACACCA-GCCGC----------CUCCCCCAGCU----GCACG-CAGCCUCUCUCCUAAUUAUAUCGGU--UUCCCCU---G------------------GGUGCCAA---------GAA-GAAGGG---GUUCCCACAGAAAGG
ABRN01187570.1/6231-6436   CUAG-GAGAACCAAAAACU---GUUCUAGACAGACCUGGGGUUUUAUAGCAGUGUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGACCGG-CUGCAGUGGCCCUCCAGC-----GGGGGACGCCAGGCUAC----------CUACCCUAGCU----GCACA-CAGCCCCUCUCCCCAUUAGAUCGGU-UUUCCCCU---U------------------GGUGCCAG---------GGA-GAGGGGG-GGUCACCACAGAAAGG
AAQQ01071885.1/981-1182    CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGCGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGUCUGAGC--AGUGGGG-CCACGGUGGCCCACCAGC----UGGGGGACGCCAAGCUAC----------CUCCCCAGGCA----GAAUA-CAGCCCCUCUCUUAAUUAGAUCGGU--UUCCCU-----------------------GGUGCCAG---------GGG-AAAGGA---GUUCUUGCAGAAAGG
AAWR02014102.1/3113-3310   CUAG-GAGAGCCGAAAACA---GUUCUAGACAGACCUGGGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGACCGG-CUGCGGUGGCCCGCCAGC-----GGGGGACGCCAGGCCGU----------CUCCCCCAGCU----G--------CACCUCUCCUAAUUAGAUCGGGGUUUCCCCU---U------------------GGUGCUAG---------GGA-GAGGGG---GUCCCCGCAGAAAGG
ABVD01019940.1/1825-2027   CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGCAGUUUUAUAGCCGUUUUGGCAGUCAACUUCAGCUUGUGUCUGAGC--AGACAGG-CUGCGGUGGCCCUCCCUUCA-GCUGGGGAAUCCAGGCUGC----------CUCCCCAGGCU----GCGUG-CAGCCCCUCUCCUAAUUAGCUUGUU--UCCCC------------------------GGUGCCU----------GGA-GAGGGG---GUCCUGGCAGAAAGG
AC113985.11/43047-43250    CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGUGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGUGGGGCCCGAGGUGGCUCAGCCGC-----GGGGGACGCCAGGCCGC----------CUCCCCUGACU----ACAUGGCAGCUUCUCUCAUAAUUAACUCGAC---UUCCCG---G------------------GAUGCCAG---------GGA-GAAGGG---GUACCCACAGAAAGG
AAYZ01055296.1/2733-2915   CUAG-GAGAACCGAAAACA---GCUCUAGACAGACCUGCGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGACUGG-CCGCGGUGGCCCGCCAGC-----GGGGGAUGCCG-GCAGC----------CUCCCCCAGC---------------CCCUCUCUUAAUUAGAUCGGU--------------------------------GCACCAG---------ACA-GAGGGG---GUCCCCGCAGGAAAA
AC122669.6/118712-118916   CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGUGGUUUUAUAGUAGUUUUGGCAGUCAACUUCAGCUUGUGCCUUAAC--AGUGGGG-CCGAGGUGGCCCAGCCGC-----GGGGGACGCUAGGCCGC----------CUCCCCUGACUC--UACAUGGCAGCUUCUCUCAUAAUUAACUCGAC---AUCCUG---G------------------GAUGCCAG---------GGA-GAAGGG---GUACCCGCAGAAAGG
ABRQ01101203.1/183-384     CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGCGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGCCCAGACAG--UCG--GUGACCUGUCCGCC--AGCCGGGGCCCCAAGCAGC----------C-UCCCAGGAU----GCUUG-CAACCCCUCUCCUAAUUAAGUCGUU--UUCCCCU----------------------GAUGCCA----------GGA-GAGGGG---GACCCUGCAGAAAGG
AANN01604120.1/3903-3696   CUAG-AAGAACCAAAAACA---GUUCUAGACAGACCUGGGGUUUUAUAGUAGUUUUGGCAGUCAACUUCAGCCUGUGUCUGUGC--AGACUGA-CUACAGUGGCCUGCCAGC-----GGGGGGCACAACAUUG-AGACACCUCCCCCCCCCAGCU----GCACU-UAGACUCUCUCCUAAUUAGAUUGGU-CUCUCCAC---C------------------CCUCCCCA---------AUG-CCUGGG---A-----GAAGAACGG
AAIY01705046.1/575-368     CUAGGGGGAACCGAAAACA---GUUCUAGACAGACCUGUGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUAAAC--AGACGG--CCACGGUGGCCUGGCCGCCU-GCGGGGGACGCCCAGCCCCUU-----CCCCUCCCCAGGCU----GC-UG-CAGCCCCUC--CUAAUUAGGCCAUU--UCCCCCU---U------------------GGUGCGGG---------CUU-UGCGGG----UGCCCGCAGAAAGG
ABQF01013713.1/14285-14484 CUAG-GGGAACCGAAAACA---GUUCUAGACUGACCUGCGGUUUUAUAGCA-CUUUGGCAGUCAACUUCAGCUUGUGUCAGAGC--AGACAUGACAGAGCUG-CCCAACACUUAAUCGCGGGACGCCA-----C----------CUCCUCGGACUCACUGCA-G-CUG-CCCUCUUGCAUUUCAAUAAAUUUCAAACCU---U------------------GGGGCUAG---------AAA-UGGGGA---------GCAGAGCUG
AAFR03047692.1/43828-43636 CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUCCGGCUUUAUAGCC-CUUUGGCAGUCAACUUCAGCUUGGGGUAGAGC--AGACAAGCCCGCGUUG-CUCAGCAGUGA-GAUGGAUGCGCCAGCCUGU----------C---CACAACU----CCUAG-CCGUCACUUU-UUAAUUAACUGCAC-----CCCU---------------------------------------AUA-GAGGGAAGAGUGACCCCGAAAAGG
ABQO010315400.1/1088-899   CUAG-GAGAACCGAAAACU---GUUCUAGACAGACCUCUGGCUUUAUAGCC-CUUUGGCAGUCAACUUCAGCUUGUGGUAGAGC--AGACAAACUCGCGGUG-CUCAGCAGUGA-GAUGGAUGCGCCACUCUAC----------C---CACAACU----CCUGG-CUGUCCCGUU-UUAAUUAACUGCCC-----CCCC---A------------------UCCCCCA----------UUA-AAGGGA-----------AGAAUGA
AAFC03071410.1/11867-11658 CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGGGGUUUUAUAGCAGUGUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGACCGG-CUGCGGUGGCCCGCCAGC-----GGGGGACGCCAGGCUAU----------CAACCCUGGCU----GCA----AGCCCCUCUCCCAAUUAGAUCAGU-UUUCCCCU---U------------------GAUGCCAGGGAGGGCGGGGG-GGGGGG---GUCAUCGCAGAAAAG
ABRO01036384.1/17701-17926 CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGUGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGUGGGGCCCGAGGUGGCCCGCCGGC----GGGGGGAUGCCAGACCAC----------CUCCCCUAGCU----GCACA-CAACCCUUCUCUUAAUUGGAUCGGC--UUCCUCUGUU-GCGGGGGGUGGGGGGUGGGGGGUGGG---------GGAGGAAGGG---GUUCCUGCAGAAAGG
AC165369.3/85308-85490     CUAG-GAGAACCGAAAACA---GUUCUAGACUGACCUGCGGUUUUAUAGCA-CUUUGGCAGUCAACUUCAGCUUGUGUCAGAGC--AGACACGACAGGGCUG-CCCGGCCCC-----GGG--ACGCCA-CCUAC----------UUGGCCCGGCU----GA------GGCCCCCCCCGCACU-------------CACC---C------------------CAUGGCAG---------AGC-UGGGGC---AGCGCUGGCACAAGG
AAPE02018006.1/4547-4347   CUAG-GGGAACCGAAAACA---GUUCUAGACAGACCUGGGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGACCGG-CUGCGGUGGCCCGCCAGC------GGGGACGCCAGGCUGC----------CUCCCCCAGCU----GCCUG-CAGCCCCUCUUCUAAUUAGCUCGGU---UUCCCU---U------------------GGUGCCAG---------GGA-GAAGGG---GUCCCCACAGGAAGG
AAGU03015373.1/11950-11751 CUAG-GAGAAGC-AAAACA---GUUCUAGACAGACCUGUGGUUUUACAGCAGUUUUGGCAGUCUACUUCAGCUUGUGCCUAAGC--AGGCAG--CCA--GUGGCCUGUCGGCCA-GCCGGGGACACCAAGCAGC----------CUCCCCAGGUU----GCUUG-CAGCCACUCU-CUAAUUAAAUCAUU--UUCCCCG----------------------GGUGCCAG---------GAG-UGGGGG----UCCCCGCAGAAAGG
AC184818.19/164475-164273  CUAG-AAGAACCGAAAACA---GUUCUAGACAGACCUGGGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGACCGG-CUGCGGUGGCCCACCAGC-----GGGGGACGCCAGGCCGC----------CUCCCCCAGCG----GC-CG-CAGCCCCUCUCCUAAUUAGAUCGCU-UUUCCCCU---A------------------GGUGCCAG---------GGA-GAGGGG---GUCCCCGCUGAAAGG
AAGW02035946.1/11502-11333 CUAG-GAGAACCGAAAACA---GUUCUAGACAGACCUGCGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGACUGG-CCGCGGUAGCCUGCC------------------------C----------C------GGCU----GAGUG-CAGCCCCUCUUCUAAUUAGGUCCGG-------------------------------UGCGCCAG---------AAA-GAGGGG---GUCCCCGCCGAAAGG
AF071169.1/147-345         CCAG-GAGCUGUUCUUUCUCAGGAGCUCCACAGCGCGGGCCAUCUCCAGAA-----AACUGUC--UUUCAGCUUGUGCCUGAGC--AGACGGGGUUGUGGUGGCCCGCCAGC-----GGGGGAUGCCAGGCCAC----------CUCCCCCAGCG----GCACG-CAGCCCCUCUCUUAAUUAGAUCGGU--UUUCCCC---U------------------GGUGUCCG---------GGA-GAGCGG----UCCCGGCAGAAAGU
AF071165.1/191-387         CCAG--AAAACUGU---C-----UUCUAGACAGACCUGCGGUUUUAUAGCAGUUUUGGCAGUCAACUUCAGCUUGUGCCUGAGC--AGACGGGGUUGUGGUGGCCCGCCAGC-----GGGGGAUGCCAGGCCAC----------CUCCCCCAGCG----GCACG-CAGCCCCUCUCUUAAUUAGAUCGGU--UUUCCCC---U------------------GGUGUCCG---------GGA-GAGCGG----UCCCGGCAGAAAGU
#=GC SS_cons               ::::.::::::::::::::...::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..:::::::.::::::::::::::::::.....:::::::::::::::::..........:::::::::::....:::::.:::::::::::::::::::::::::..:::::::...:..................::::::::.........:::.::::::...:::::::::::::::
#=GC RF                    CUAG.GAGAACCGAAAACa...GUUCUAGACAGACCUGcGGUUUUAUAGCAGuUUUGGCAGUCAACUUCAGCUUGUGcCuGAGC..AGacgGG.CuGcGGUGGCCCgcCaGC.....gGGGGacGCCaggCugc..........CucCCCcgGCu....GCacg.CaGcCcCUCUCuuAAUUagaUcggu..UucCCCu...u..................gguGccaG.........gga.gagGGG...GUccCcGCaGAAaGG
//
# STOCKHOLM 1.0

#=GF AC   RF02142
#=GF ID   HOXA11-AS1_6
#=GF DE   HOXA11 antisense RNA 1 conserved region 6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   57.20
#=GF NC   38.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.78 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   9745033
#=GF RT   Evolutionary conservation and tissue-specific processing of Hoxa 11
#=GF RT   antisense transcripts.
#=GF RA   Potter SS, Branford WW
#=GF RL   Mamm Genome. 1998;9:799-806.
#=GF RN   [2]
#=GF RM   12050232
#=GF RT   HOXA11 silencing and endogenous HOXA11 antisense ribonucleic acid in the
#=GF RT   uterine endometrium.
#=GF RA   Chau YM, Pando S, Taylor HS
#=GF RL   J Clin Endocrinol Metab. 2002;87:2674-2680.
#=GF WK   HOXA11-AS1
#=GF SQ   21


AF071164.1/7043-7221       UUCCUUUUAUCGUCAACCCAGAGCCCCACCGCGGCUAAUGCAAGAGGCCAAAAAAUGUUU-GGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCCUGACG-GUGCGU----GUGUGUCUGCAGAGAA-GGGAGGGAGC---------CGGCUC-A-------------------GUCUCUUC---UUGUUUUUCC-AAACUUCAAGGU---CCAGGCAG
AAWR02014102.1/4088-4266   UUCCUUUUAUCGUCAACCCGGAGCCCCUCGGCAGCAAAUGCAAGAGGCCAAAAA-UGUUUUGGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCCUGACG-GUGCGU----GUGUGUCUGCGGAGAA-GGGAGGGAGC---------CGUUUC-A-------------------AUCUCUU---GUUGUUUUUCC-AAACUUCAAGGU---CUAGGCAG
ABRN01187570.1/7200-7378   UUCCUUUUAUCGUCAACCCGGAGCCCCAUGGCAGCUAAUGCAAGAGGCCAAAAA-UGUUUUGGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCUUGACG-GUGCGU----GUGUGUCUGCGGAGAA-GGGAGGGAGU---------CAUUUC-A-------------------AUCUCUUC---UUGUUUUUCC-AAACUUCAGGGU---CCAGGCAG
ABRR01276337.1/667-845     UUCCUUCCAUCGUCAACCCAGAGCCCCACGGCAGCUAAUGCAAGAGGCCAAAAA-UGUUUGGGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGACUGACG-GUGCGU----GUGUGUCUGCGGAGAA-GGGAGGGAGU---------CGUUUC-A-------------------AUCUCAUC---UUGUUUUUCC-AAACUUCAGGGU---CUAGGCAG
AAPY01076971.1/2763-2943   UUCCUUUUAUCGUCAACCCGGAGCCCUACAGCGGCUAAUGCAAGAGGCCAAAAA-UGUUU-GGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCCUGACG-GUGCGUG--UGUGUGUCUGUGGAGAA-GGGAGGGAGC---------CGGUUC-A-------------------AUCUCUCC---UUGUUUUUUCCAAACUUCAAGGU---CUAGGCAG
ACBE01077432.1/4325-4506   UUCCUUUUAUCCUCAACCCAGAGCCCCACGGCAGCUAAUGCGAAAGGCCAAAAA-UGUUUUGGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCCUGACG-GUGCGU----GUGUGUCUGCGGAGAA-GGGAGGGAGC---------CGUUUC-A-------------------AUCUCUUCUUGUUGUUUUUCC-AAACUUCAAGGU---CUAGGCAG
ABRO01036384.1/18739-18916 UGCCUUUAAUCGUCCACCCGGAGCCCCACGGCGGCUAAUGCAAGAGGCCAAAAA-UGUUU-GGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCCUGACG-GUGCGU----GUGUGUCUGUAAAGAA-GGGAGGGAGC---------CGGUUC-A-------------------AUCGCUUC---UUGUUUUUCC-GAACUUCAAGGU---CUCGGCGG
ABRP01099870.1/5493-5669   UUCCUUUUAUCGUCAACCCGAAACCCCACGGCAGCUAAUGCAAGAGGCCAAAAA-UAUUUGGGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCAGCCUGAUG-GUGCGU----GUG--UCUGCGGAGAA-GGGAGGGAGC---------CGUUUC-A-------------------AUCUCUUC---UUGUUUUUCC-AAACUUCAAGGU---UUAGGCAG
AAKN02039092.1/14814-14988 UUCCUUUAAUCGUCAACCCGGAGCCCCAGGGCGGCUAAUGCAAGAGGCCAAAAA-UGUUU-GGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCUGCCUGACG-GUGUGU----GUGUGUCUGCAAAGAA-GGGAGGGAGC---------CAGUUC-A-------------------AUCUC------UUGUUUUUCU-GAACUUCAAGGU---CUAGGCAG
AAQQ01559864.1/435-612     UUCCUUUAAUCGUCCAUCCGGAGCUCCACGGCGGCUAAUGCGCGAGGCCAAAAA-UGUUU-GGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCCUGACG-GUGCGU----GUGUGUCUGUAAAGAA-GGGAGGGAGC---------CGGUUC-A-------------------AUCUCUCC---UUGUUUUUCC-GAACUUCAAGUU---CUAGGCGG
AC122669.6/119677-119855   UUCCUUUAAUCGUCAACCCGGAGCCCUACGGCGGCUAAUGCGAGAGGCCAAAAA-UGUUU-GGAGGAAGAAAAACAAAGGCAGGAAGUGGCCGCGGCCUGACG-GUGCGU----GUGUGUCUGUAAAGAA-GGGAGGGAGC---------CGGUUC-A-------------------AUCUCUUC---UUUUUUUCCCCGAAUUUCAAGGU---UUAGGCAG
U20369.1/574-750           UUCUUUUAAUCGUCG-CCCGGAGCCCUAAGGCGGCUAAUGCAAGAGGCCAAAAA-UGUUU-GGAGGAAGAAAAACAAAGGCAGGAAGUGGCCGCGGCCUGACG-GUGCGU----GUGUGUCUGUAAAGAA-GGGAGGGAGC---------CGGUUC-A-------------------ACCUCCCC---UCGUUUUCCC-GAACUUCAAGGU---CUAGGCAG
ABRQ01101203.1/1105-1287   UUCCUUUAAUCGUCAAGCCGGAGCCCCACGGAGGCUAAUGCAAGAGGCCAAAAA-UGUUUUGAAGGAAGAAAAACAAAGGCAGGAAGUAGCGGCUGCCUGACG-GUGCGU----GUGUGUCUGCGGAGAA-GGGAGGCAGG--------ACCUUUC-A-------------------AUCUCUUCUAGCUGUUUUUCC-AAACUCGAAGGU---CUAGGCGG
AANN01604120.1/2915-2737   UUCCUUUUAUCGUCAUCCUGGAGCUCUAGGGCAGCUAAUGCAAGAGGCCAAAAA-UGUUUUGGAGGAAGAAAAACAAAGGCAGGAAGUGGUGGCGGCCUGACG-GUGCGU----GUACAUCUUUGGAGAA-GGGAGGGAGC---------CUUUUC-A-------------------AUCUC------UUGUUUUUGC-AAACUUCAAGGUGCUCCACACAG
AAYZ01055297.1/172-352     UUCCUUCCACCGUCACCCCGGAACCCCACGGCAGCUCAUACAAGACGCCAAAAA-UGUUU-GGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCCUGACG-GUGCGCACGCGUGUAUCUCCGCAGAA-GGGAGGGAGA---------CGGUUCCA-------------------GUCUC--C---UUGUUUUUCC-AAACUUCAAGGU---CUAGGCCG
AALT01041412.1/825-1012    UUCCUUUCAUCGUCAUCCCCGCGGCCUCGGGCCGCUAAUGCAAGAGGCCAAAAAAUGUUUUGGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCCUGGCG-GUGCGU----GUGUGUCUGCGGAGAA-GGGAGGGGGC---------CUUUUU-UUU--------------UUCAUCUCUUCCAGUUGUUUCCCC-AAAUUUCAGGGU---CUAUGCAG
AAPN01063703.1/17462-17649 UGCUUUUCUUUUUCAACAUGGAGCCAC-CAGCUACUUCUAUAAAAUGCCGAAAAAUGCUUUGGAGGAAGAAAAACAAAGCCAGGAAGUCUCCUCUGUCUGACAUGUGUGUGUGUGUUUAUGUGUGAUGAGCGGGAGGGAAA---------UAUUGC-A-------------------AUUUCUUCUUGUUGUUUUGAA-AAAUAUCAAGGU---CUCCGUGA
ABDC01121663.1/4174-4360   UUCCUUUUACCGUCAACCCGGAGCCCCACGGCGGCUAAUACAAGAGGCCAAAAA-UGUUU-GGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCCUGACG-GUGCGU----GUGUGUCUGUGGAGAA-GGGAGAGAAGGGAGGGAACCGGUUC-A-------------------AUCUCUUC---UUGUUUUUCC-UAACUUCAAGGU---CCAGGCAG
AAGW02035946.1/10597-10418 UUCCUUUCAUCGUCCACCCGGAGCCCCACGGCGGGUAAUGCAAGAGGCCAAAAA-UGUUU-GGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGCCUGACG-GUGCGU----GUGUGUCUCUGCAGAA-GGGAGGAGGGAU-----CCGGGCCC-A-------------------AUCUC--C---UUGUUUUUCC-AAACUUCAAGGU---CCAGGCAG
AAPE02018006.1/3581-3381   UUCCUUUUAUCGUCAACCCGGAGCCCCACGGCAGCUAAUGCAAGAGGCCAAAAA-UGUUUUGGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGACUGACG-GUGCGU----GUGUGUCUGCGGAGAA-GGGAGGGAGC---------CGUUUC-AAUCUCUUGUUUUUCCAAACUUCUCUUCUUGUUGUUUUUCC-AAACUUCAAGGU---CUAGGCAG
AAGU03015373.1/10949-10768 UUCCUUUUAUCGUCAACCCGGAGCCCCACAGAGGCUAAUGCAAGAAGCCAAAAA-AGUUUUGGAGGAAGAAAAACAAAGGCAGGAAGUGGCGGCGGGCUGACG-GUGCGU----GUGUGUCUGCGGAGAA-GGGAGGGAGC---------CCUUUC-A-------------------AUCUCUUCUUGUUGUUUUUCC-AAACUUCAAGGU---CUAGGCGG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::.::::::....::::::::::::::::.::::::::::.........::::::.:...................::::::::...::::::::::.::::::::::::...::::::::
#=GC RF                    UuCCUUUuaUCGUCaaCCcGGAGCCCcacGGCgGCUaaUGCAAGAgGCCAAAAA.UGUUUuGGAGGAAGAAAAACAAAGGCAGGAAGUGGCgGCgGcCUGACG.GUGCGU....GUGUGUCUgcGgaGAA.GGGAGGGAGc.........cguUuC.A...................aUCUCuuC...UUGUUUUucc.aAAcUUCAaGGU...CuagGCaG
//
# STOCKHOLM 1.0

#=GF AC   RF02143
#=GF ID   HYMAI
#=GF DE   Hydatidiform mole associated and imprinted conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   80.00
#=GF TC   112.60
#=GF NC   52.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.46 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10936046
#=GF RT   A novel imprinted gene, HYMAI, is located within an imprinted domain on
#=GF RT   human chromosome 6 containing ZAC.
#=GF RA   Arima T, Drewell RA, Oshimura M, Wake N, Surani MA
#=GF RL   Genomics. 2000;67:248-255.
#=GF WK   HYMAI
#=GF SQ   16


AF241534.1/1504-1267         CUUACCAUGUGCUAAGUAAGCAAUCUCUGAGCCCAG--CGAGACCGGUGGGUUAAUACGCGG----AGGGGC-------------UGCG-GGGGAGGACUUAGGGGACCAGGACCUCAGUGAGGCCCCA-GAAAGCACCCGGGAGGGGCCUCCGAUCCU-GCCUG-GGAGGG---AGGGGUUAGAGGAGGAUUCCUGGAAGAAGGAGGACCUAAGCUGGGUGUUUCUAUUUUUGA--UUUUUAUUGGUUUCCUAAAACAUGAAAGU
BC059359.1/1025-799          CUUACCAUGUGCUAAGUAAGCAAUCUCUGAGCCCAG--CGAGACCGGUGGGUUAAUACGCG-----------------------------GAGGAGGACUUAGGGGACCAGGACCUCAGUGAGGCCCCA-GAAAGCACCCGGGAGGGGCCUCCGAUCCU-GCCUG-GGAGGG---AGGGGUUAGAGGAGGAUUCCUGGAAGAAGGAGGACCUAAGCUGGGUGUUUCUAUUUUUGA--UUUUUAUUGGUUUCCUAAAACAUGAAAGU
ABRR01019192.1/1201-1438     CUUACCAUGUGCCA----AGUAUCCACUGGGCUCAGACCGAGACUGAUGGGUUAAUACAUGG----GGGGGUU-----------GGGGG-GGGGGGACAUA-AGGAACCAGGACCUCAGUGAGGCCCCA-GAAAGCUCACAGGAGGGGCCUCCGAUCCU-GCCUGGGGAGGG---AGGGGUUAGAGAAGGAUUCCUGGAAGAAGGAGGACCUAAGCUGAGUGUUUCUAUUUUUAA--UUUUUAUUGGUUUCCUAAAACAUAAAAGU
AAFC03106602.1/27937-27701   CUUACCAUGUGCUA----AGUAGCCACUGGACUCCGAGCGAGAUUGAUGGGUUAAUACACGCG---AGGAG--------------GGUA-GGGGGAGGACAUAGGGACCAGGACCUCAGUGAGGCCCCA-GAAAGCUCACAGGAGGGGCCUCCGAUCCU-GCCUGGGGAGGG---AGGGGUUAGAGAAGGAUUCCUGGAAGAAGGAGGACCUAAGCUGAGUGUUUCUAUUUUUAA--UUUUUAUUGGUUUCCUAAAACAUAAAAGU
AANG01374483.1/344-576       CUUACCAUGUGCUA----UGUAUCCACUGGACUCCGAGCGAGACUGAUGGGUUAAUACAC------AGGGG--------------GGUG-GGGAGGACAUA-AGGGACCCGGACCUCAGUGAGGCCCCA-GAAAGCUCACAGGAGGGGCCUCCGAUCCU-GCCUGGGGAGGG---AGGGGUUAGGGAAGGAUUCCUGGAAGAAGGAGGACCUAAGCUGAGUGCUUCUAUUUUUAA--UUUUUAUUGGUUUCCUAAAACAUAAAAGU
AAWR02036690.1/834-602       CUUACCAUGUGCUA----AGUAGCCAGUGAGCUCUGAGCGAGACUGAUGGGUUAAUACAC------CGGGG--------------GGUG-GACAGGACAGA-AGGGACCAGGACCUCAGCGAGGCCCCA-GAAAGCUCACAGGAGGGGCCUCCGAUCCU-GCCUGGGGAGGG---AGGGCUUAGGGUAGGAUUCCUGGAAGAAGGAGGACCUAGGCUGAGUGUUUCUAUUUUUAA--UUUUUAUUGGUUUCCUAAAACAUAAAAGU
ABRQ01647567.1/162-402       CUUACGGUAUGCUA----AGUGACCACUGGACCCCAAAAAAUACUGACGGGUGAAUACACAGGGGUGAGGG--------------GGUU-GGAAGGACAUUGAAGGACCAGGAUCUCAGUGAGGCCCCAAGAAUGCUCACAGGAGGGGCCUCGGAUCCU-GACUGCGGAGGG---AGGGGCCAAGGAAGGAUUCCUGGAAGAAGGAGGACCUAAGCUGAGUGUUUCUAUUUUUAA--UUUUUACUGGUUUCCUAAAACAUAAAAGU
AAQQ01005476.1/2788-3020     CUUACCAAGUGCUGAGCCAGCGACCACUGGAUUCCCAGCAAGACAGACGGGUUAAUACGCGGAGGCAGGGGG------------CGCAGAGGGGAGAACUUCAGGGACCCGGACCUCGGGGAGACCCAG--AAAGAUCACAGGAGGGUC-UCCGAUCCU-GCCUG-GGCAGG---AGAGGUUACAGGAGGUUUCCUGGAAAAAGGAGGACUUAGUUGGA---UUUCUAUUUUUAU---------UGGUUUCCUAAAACAUACAGU-
AAKN02045704.1/24902-24663   CUUACCACGUGCUAG-UAAGCACUGACUGGCCCCAGAGCCAGAC-GUUGGAUUCAUCUGUG-----AAGGACCCG------CAGAGAAA-AGGAAGAACUUGGGGAACCAGGACCUCAGGAAAACCCCA--GAAAAUCACAGGAUGGCCCUUGGGUGCU-ACCUG-GGUGGA---AGGGGUUAGAAAAGGUUUCCUGGA---AGGAGGACCUAAACUGGCUGUUUUUAUUUUUAA--UUUUUAAUGAUUUACUUUAGCAUAAAAGU
AL691505.12/38677-38913      CUUACCACACGCCAAGGAAGCAGGCACAGACUCCAA-CCCAGACCUAUGGAUUAA--AACGCAGAGAGAAGGGGAAAG-AAUGGGGG---GGGGGGCGCUUCGGGGAGCAGCACCUCGGCGAGGCCCCA-GAGAGCUAACAGCCG------------CU-GCCUUGGAGGGC---GAGGU-UAGCUGAAGAUUCCUAGAAGAAGAAU--CUACUCUGGGACAUUUCUAUUUUUAA--UUUUUACUCGAUUCCUAAAACACCAAAGU
AALT01662935.1/7812-8054     CUUACCAUGCGCCGC-CAAGGGUCCGCCGAGCUCAGAGCGCAGCCGAUGAG--GAGUAGGGGG---AGGAAUCGAGGUGGGGAGGGGUG-UGCCGGAGCCACGGGGAUAGGGACCU-GGUGAAACCCCG-GGGAGCACUCAGCCU------------CUGGCCUGGGGAGGAAGGAGGGGUUAGGGAAGGAUUCCUGGAAGAAGGAGGACCUAAGUUGCAGGUUGCUAUUUUUAA--AUUUUAUUGGUUUCCUAAAACACAAAAGU
AAEX03000236.1/137127-137357 CUUACCAUGUGCUA----UGUAUCCACUGGACUCCC--CGAGACGGAUGGGUUAAUUCGC------AGGGG--------------GGUG-GGGAGGACACA-AGGGACCCGGACCUCAGGGAGGCCCCA-AAAAGCUCACAGGAGGGCCUUCCGAUCCU-CCCUGGGGAGGG---AGGGGUUAGGGAAGGAUUCCUGGAAGAAGGGGGCCCUAAGCGGGGGGCUCCUAUUUUUAA--UUUUUAUGGGUUUCCUAAAACAUAAAAGU
AAPE02007348.1/1272-1025     CUUACCAUGUGCUG----AGGAUCCACUGGGCUCCGAGCCAGACGGAUGGGUUAAUACACGGGCGUGGGGGUGGGGUG-GGGUGGGG------AGGACCU-UAGGGACCAAGACCUCGGUGAGGCCCCA-GAAAGCUCACAGGAGGG-CCUCGGAUCGU-GCCUGGGGAGGG---ACGGGGGAGGGAAGGAUUCCUGGAAGGAGGAGGACCUAAGUUGAGUGUUUCUAUUUUUAACUUUUUUAUUGGGUUCCUGAAACAUAAAAGU
AABR05000762.1/4020-3788     CUUACCACACGCCAAGCAAGCAGGCACAGACUCCAA-CC-AGACCUGUGGAUUAA--AAC--AGAGAAAAGGGAAAAG-GGUGAGGG---GGGGGGCGCUUCGGGU-GCAGCACCUCGGCGAGGCCCCG-GACAGCUAAUAGGAG------------CU-GCCUUGGAGGGU---GGGGU-UAGCGGAAGAUUCCUAGAAGAAGAAU--CUACCCUGGGAUGUUUCUAUUUUUAA--UUUUUACUCGAUUCCUAAAACAUCAAAGU
AAGU03000328.1/51651-51413   CUUACCAUGUGCUA----AGUAACCACUGGAUCCCGAAGGAGACUGAUGGGUUAAUACACUGGGGUGGGGG--------------AGUG-GGGAGGACAU-AAGGGACCAGGACCUCAGUGAGGCCCCA-GAAUGCUCACAGGAGGGGCCUCCGAUCCC-GACUGCGGAGGG---AGGGGCCAAAGAAGGAUUCCUGGAAGAAGGAGGACCUAAGCUGAGUGUUUCUAUUUUUAA--UUUUUACUGGUUUCCUAAAACAUAAAAAG
AAGW02028471.1/14534-14336   CUUACCAUGUUCCAAGCAAGCCCACCAGUGAUUCCGGGCGCACCCGACGGGUUCAGGCGC--------------------------------GGAGGGCUGUGGGGAAGAGAGGGUUGG---GGCUACG---------GAAGGGGGGAC------------CCCG---GGGC---CCAGGUUGUGGGAG---UCCUGGAAGCAGGCGGACCUAAGGAAAUUGCUUCUACUUUUAU--UUUUUAUUGGUUUCCUAAAACAUAAAAGU
#=GC SS_cons                 :::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::...::::::............:::::.:::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::.::::::::::::...::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..:::::::::::::::::::::::::::::
#=GC RF                      CUUACCAuGUGCuaa.caAGcaucCaCuGggcuCcgagCgaGaCcGaUGGGUUaAuacgcGgg...aGGgGu............gGGug.GGGgGGagcuuugGGGAccaGgACCUCgGuGAGGCCCCa.GaaAGCuCaCAGGaGGGgCCUCcGaUcCU.GCCUGgGGaGGg...agGGGuuAggGgAGGaUUCCUGGAAGaAGGaGGACCUaagcuGgguGUUUCUAUUUUUAa..UUUUUAuUGGuUUCCUaAAACAUaAAAGU
//
# STOCKHOLM 1.0

#=GF AC   RF02144
#=GF ID   rsmX
#=GF DE   rsmX
#=GF AU   Moll S
#=GF AU   Schneider DJ
#=GF AU   Stodghill P
#=GF AU   Myers CR
#=GF AU   Cartinhour SW
#=GF AU   Filiatrault M
#=GF SE   Moll S, Schneider DJ, Stodghill P, Myers CR, Cartinhour SW, Filiatrault M
#=GF SS   Predicted;
#=GF GA   56.00
#=GF TC   66.50
#=GF NC   52.60
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00106
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   21060253
#=GF RT   Construction of an rsmX co-variance model and identification of five rsmX
#=GF RT   non-coding RNAs in Pseudomonas syringae pv. tomato DC3000.
#=GF RA   Moll S, Schneider DJ, Stodghill P, Myers CR, Cartinhour SW, Filiatrault MJ
#=GF RL   RNA Biol. 2010;7:508-516.
#=GF WK   RsmX
#=GF SQ   16


CP000076.1/4774103-4773991 -----CACAACUGCAGCGCAGGAAGCGCUCAGG--AUCAGGGAAGGUCGACCAUU-AGCACGGAU-GCUGCAGACAGGAAGUCAU-AAUGGUC---UUGGAAAA----AACCCGCUUCGGCGGGUUUUUU-
AE016853.1/6145122-6145235 -----AUCAAGUGGUGAACAGGGAGUUCACCAG-GAUCAAGGAUGAUCGACCAUC-GCCUCGGAG-GCGGCCGACAGGAUGUCGG-GAUGGUU---CUUGGAAA----AACCCGCUUCGGCGGGUUUUUU-
ABSM01000028.1/34936-34823 -----AACAACUGGUGAACAAGGAGUUCACCAG-GAUCAGGGACGAUCGACCAUC-GCCGGGAAG-GCAGCCGACAGGGAGUUGG-AAUGGUC---UUGGUACA----AACCCGCUUCGGCGGGUUUUUU-
ABZR01000765.1/44722-44611 -----AUCAAGUGGUGAACAGGA-GUUCACCAC-GAUCAAGGAUGAUCGACCAUC-GCCUCGGAG-GCAGCCGACAGGGAGUCGG-GAUGGUC----UUGGAAA----AACCCGCUUCGGCGGGUUUUUU-
AY135187.1/3374-3485       -----ACCAACUGCAGCGCAGGAUGCGCUCAGG--GUCAUGGAAGACCGACCAUU-GCAAGGAUU-GC-AACGACAGGAUGUCGU-AAUGGUC---UUGAAAAA----AACCCGCUUCGGCGGGUUUUUU-
CP000058.1/2002611-2002728 -----AACAGCUGCAGCGAAGGA-ACGCCGCAGCGAUCAGGGAAGAUCGACCAUU-GCC-AGGAG-GCUACUGACAGGAUGUCGG-AAUGGUCAUGUUGCAAAA---CCACCCGCUUCGGCGGGUUUUUUG
CP000075.1/3053360-3053480 -----AUCAACCGUUGCGCAGGAGGCGCUUCGGAGGUCAAGGAUGAUC-ACCAUU-GCCGGGAUG-GCUACUGACAGGAUGUUGG-AAUGGUAUUGAUAGAAAAAAACGACCCGCUUCGGCGGGUUUUUU-
CP000304.1/357143-357250   CAUCU-----CUGCAGCGCAGGACGCGCUCGGG--AUCAUGGAUGAUCGACCACU-GCCAGGAGGCGC-GCCGA-AGGAU-UCGG-AAUGGUC------ACAAA----AACCCGCUUCGGCGGGUUUUUU-
CP000680.1/3581176-3581069 -----AUCCCCUGCAGCGACGGA-GCGCUGAGG--AUCAAGGAAGAU-GACCAG--GCCACGAUG-GCUACCGACAGGAUGUUGG-A-UGGU-----UGGGAAG---AAACCCGCUUAGGCGGGUUUUUU-
AE016853.1/6198149-6198038 -----AUCAACUGGUGAACAGGA-GUUCACCAG-GGUCAAGGAUGACCGACCAUU-GCCUUGGAG-GCAGCCGACAGGGAGUCGG-GAUGGUC---UUGGGAAA-----ACCCGCUUCGGCGGGUUUUUU-
AE016853.1/4170369-4170253 -----AACAGCUGCAGCGAAGGA-ACGCCGCAGCGAUCAGGGACGAUCGACCAUU-GCC-AGGAG-GCUACUGACAGGACGUUGG-AAUGGUCAUGUUGCAAUA---CCACCCGCUUCGGCGGGUUUUUU-
AE016853.1/6144830-6144943 -----AACAACUGGUGAACAAGGAGUUCACCAG-GAUCAGGGACGAUCGACCAUC-GCCGGGAAG-GCAGCCGACAGGGAGUUGG-AAUGGUC---UUGGUACA----AACCCGCUUCGGCGGGUUUUUU-
AE016853.1/3244374-3244256 -----AUCAACUGCAGCGCAGGAAGCGUUGCAGAGGUCACGGAUGAUC-ACCAUU-GCCGGGAUG-GCUACUGACAGGACGUCGG-GAUGGUAUUGAUAGAAAAA--CGACCCGCUUCGGCGGGUUUUUU-
AEAD01000347.1/12673-12561 -----AUCAAGUGGUGAACAGGGAGUUCACCAG-GAUCAAGGAUGAUCGACCAUC-GCCUGGGAG-GCGUCCGACAGGAAGUCGG-GAUGGUC----UUGGAAA----AACCCGCUUCGGCGGGUUUUUU-
CP000094.2/4402504-4402389 -----AUCAACUGAAGCACAGGGAGUGUUUCAG-GAUCACGGAUGAUCGACCAUU-AGCAAGGAUCGCUGCCGACAGGGAGUCGAUAAUGGUC---UUGGGAAA----AACCCGCUUCGGCGGGUUUUUU-
DQ137846.1/6-118           -----CACAACUGCAGCGCAGGAAGCGCU-CAG-GAUCAGGGAAGGUCGACCAUUAGCA-CGGAU-GCUGCAGACAGGAAGUCAU-GAUGGUC---UUGGAAAA----AACCCGCUUCGGCGGGUUUUUU-
#=GC SS_cons               .....:::::<<<<<<<<<_____>>>>>>>>>.<<<<______>>>>(((((((.<<<_____>.>>,,<<<<<_____>>>>>.)))))))...,,,,,,,<....<<<<<<<____>>>>>>>>:::.
#=GC RF                    .....AuCAacugggGcgcAGGaagcgCcccag.GauCAaGGAuGauCGaCCauc.GCcaaGaag.GCuaccGaCAGGauGuCgg.gauGGuC...uUggaAAa....aaCCCGCUUcGGCGGGuuuUUU.
//
# STOCKHOLM 1.0

#=GF AC   RF02145
#=GF ID   MEG8_1
#=GF DE   Maternally expressed 8 exon 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   70.00
#=GF TC   76.80
#=GF NC   35.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.80 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005634; nucleus;
#=GF RN   [1]
#=GF RM   11481034
#=GF RT   Identification of a new imprinted gene, Rian, on mouse chromosome 12 by
#=GF RT   fluorescent differential display screening.
#=GF RA   Hatada I, Morita S, Obata Y, Sotomaru Y, Shimoda M, Kono T
#=GF RL   J Biochem. 2001;130:187-190.
#=GF RN   [2]
#=GF RM   11337479
#=GF RT   Human-ovine comparative sequencing of a 250-kb imprinted domain
#=GF RT   encompassing the callipyge (clpg) locus and identification of six
#=GF RT   imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8.
#=GF RA   Charlier C, Segers K, Wagenaar D, Karim L, Berghmans S, Jaillon O, Shay T,
#=GF RA   Weissenbach J, Cockett N, Gyapay G, Georges M
#=GF RL   Genome Res. 2001;11:850-862.
#=GF WK   MEG8
#=GF SQ   23


AC226390.3/19317-19221       UUGCAAAUUUGUAGAUUCUUU-----AGAAUAGAACUAACUCAAGCCCUUCAUUCUGCAGCUG---AGGCUCACUGCCCCCA-----GUGGGC-AGUGGGUCCAGGGGGUU
AAQQ01697070.1/589-684       UUGCAAAUUUGUAAACUUCUU-----AGAAUGGAACUAACUUAAGCCCUCCAUUUUGCAGCUG---GGGCUCACUGCCCCCA-----GUGGGC-AGUGAG-UCAGCGGGUU
ABRT010568605.1/331-426      UUGCAAAUUUGUAGCCUCCUU-----AGGAUGGAACUAACUAGAGUUCUUCUCUCUGCAGCUG---AGGCUCACUGCCCCCG-----GUGGGC-AGUGAG-UUGGUGGGUU
ABDC01493542.1/774-871       UUGCAAAUUUGUAAAUUCUUC-----AGAAUGGAACUAAUGGGAGCCCUUCUUUCCGCAGCGG---CGGCUCACUGCCCCCUG---GCUGGGC-AGUGAG-UCUGUGGGUU
AAWR02020062.1/13963-14060   UUGUAAAUGUGUAGACUCCUC-----AGAAUGGAACUAACUUGAGCCCUUCGUUCCCCAGCCG---AGGCUCACUGCCCCCCG---GAUGGGC-AGUGAG-UCGGUGGGUU
AANG01132980.1/2059-2156     UUGCAAAUGUGUGGACCCCUC-----AGAAUGGAACUAACCUGAGCCUUUUAUUUUGCAGUUG---AGGCUCACUGCCCCCUG---GAUGGGC-AGUGAG-UCAGUGGAUU
AAKN02051948.1/28057-28150   UUAAAAAUUUGUAGAUUUCUU-----AGAAUGGAACUAAGUCAAGCCCUUCGUUUCA-GCU-G---GGGCUCACUGCCCAUC-----GAGGGC-AGUGAG-UGAGUGGGAU
AAYZ01216249.1/1119-1211     UUGUGA-UUUGUAGAUUUCUU-----GGGAUGGAACUAACAGAUGCCCUUCUCUAUGCAGCCA---AGGCUCACUGCCC--A-----AUGGGC-AGUGAG-CCAGUGGGUU
CAAA01088145.1/11496-11399   UUGCAAAUUUGCAGAUUUUCC----CAGAAUGGAACUAACUGGAACUCUUCAUUUUACAGCUA---UGGCUCACUGCCCCUCA----GGGGGC-AGGGGG-CUGGUGAUUC
AAFC03050876.1/66645-66741   AUGUAAACAUGUAGUGUCCUC-----AGGAUGGAUCUAACCUGAGCUCUUUGUCCUGCAGCCG---UGGCUCACUGCCCGCCG----GCGGGC-AGUGAG-UCAGUGGGUU
ABRR01449614.1/1194-1296     UUGUAAAUGUGUAGACUCCUC-----AGGAUGGAACUAACUUGAGCCUUUUGUCCCGUAGCUGCUGAGGCUCACUGCCCCCCAC-CAAUGGGC-AGUGAG-UCAGUGGGUC
ABRP01223357.1/3162-3257     UUGUGAAUGUGU-GCACCUUC-----AGAAUGGGACUAAUUCGAGUCCUUUGUUCCGUAGCUG---AGGCUCACUGCCCCGAG---G-UGGGC-AGUGAG-CUCGUGGCCC
AAHX01046580.1/1463-1363     UUGCAAAUUUGUAGAUCCCCCCC-CCAGAAUGGAAUUAACUGGACCUCUUCAUUUUGCAGCUA---AGGUUCCCUGCCCCUUA----GUGGGC-AGGGGG-CUAGUGAGGG
AAPY01359948.1/3622-3718     UUGUAAAUCUGUAGGCCCCUC-----AGAAUGGAGCUAACUCCCAUCCUUCGUUCUGCAGCCG---AGGCUCGCUGCCCCAGG----ACGGGC-AGUGAG-UCAGUGGGCC
ABRQ01576113.1/653-754       UUGUAAAUUUAUACAUGAAGCUCCGUGGAGUGGAACUAACUCAGGCUCUUCAUGUUGCAGCUG---AGGCUCGCUGCCCCUGG-----GGGGC-AGUGAGCAGGGUCGGGC
ABRO01195545.1/3264-3364     UUUCACAUUUGUUAGUUUCUC-----AGAAUGGAACUAACUCAAGCCCUCCAUUCCACAGC-C---CGGCUCACUGCCCUCCUCCCGGAGGGCCAGUGAG-UUGAUGGGUC
AAGV020261369.1/319-412      AUUUCUACCUGA-AACUCCCC-----AGGAUGGA-CUAACUUGAGCCCUUUGUUUCACAGCCG---AGGCUCGCUGCCCCUC-----GUGGGC-AGUGAG-UCGGUGGGUA
ABVD01661371.1/400-494       AUGUAUGCAUGCA-AGUCCUU-----AGGAUGGAACUAACCCGAGCCCUUUCCUUCACAGCCG---AGGCUCACUGCCCCCG-----CUGGGC-AGUGGG-UCGGUGGAUG
AAEX03006004.1/434923-435020 UUGUAAGUGCGUAGCCCUCUC-----AGGAUGGAACUAACCUGAGCUCUUUAUUCUGCAGCUG---AGGCUCACUGCCCCCUG---GAUGGGC-AGUGAG-UUGGUGGGUU
AAQR03046506.1/28719-28816   UUACAAAUUUGUAGAUUCCUU-----AGAAUGGAACUAACUCGAGCCCUUCUUUCUGCAGCUG---AGGCUCACUGCCCCCUG---GAUGGGC-AGUGAG-UCUUUGGGUU
AAPE02047295.1/113257-113161 UUGUAAAUGUGUGAACCCUUC-----AGAAUGGAACUAACUUGAGCCUUUGGUUCUACAGCCG---AGGCUCGCUGCCCCCCG---GA-GGGC-AGCGAG-UCGGUGGGUU
CABD02116352.1/509-604       UUGCAAAUUUGUAGAUUCUUU-----AGAAUGGAACUAACUCAAGCCCUUCAUUCUGCAGCUG---AGGCUCACUGCCCCCA-----GUGGGC-AGUGGG-UCCAGGGGUU
HQ407410.1/65-161            AAGUAAACAUGUAGUGUCCUC-----AGGAUGGAUCUAACCUGAGCUCUUUGUUCUGCAGCCG---UGGCUCACUGCCCGCCG----GCGGGC-AGUGAG-UCAGUGGGUU
#=GC SS_cons                 :::::::::::::::::::::.....:::::::::::::::::::::::::::::::::::::...:::::::::::::::::....::::::.::::::.::::::::::
#=GC RF                      UUGuAAAUuUGUAGauuccUC.....AGaAUGGAACUAACucgaGCCCUUcgUUcuGCAGCuG...aGGCUCaCUGCCCcccg....guGGGC.AGUGAG.ucgGUGGGuu
//
# STOCKHOLM 1.0

#=GF AC   RF02146
#=GF ID   MEG8_2
#=GF DE   Maternally expressed 8 exon 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   45.00
#=GF TC   46.30
#=GF NC   41.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.10 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005634; nucleus;
#=GF RN   [1]
#=GF RM   11481034
#=GF RT   Identification of a new imprinted gene, Rian, on mouse chromosome 12 by
#=GF RT   fluorescent differential display screening.
#=GF RA   Hatada I, Morita S, Obata Y, Sotomaru Y, Shimoda M, Kono T
#=GF RL   J Biochem. 2001;130:187-190.
#=GF RN   [2]
#=GF RM   11337479
#=GF RT   Human-ovine comparative sequencing of a 250-kb imprinted domain
#=GF RT   encompassing the callipyge (clpg) locus and identification of six
#=GF RT   imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8.
#=GF RA   Charlier C, Segers K, Wagenaar D, Karim L, Berghmans S, Jaillon O, Shay T,
#=GF RA   Weissenbach J, Cockett N, Gyapay G, Georges M
#=GF RL   Genome Res. 2001;11:850-862.
#=GF WK   MEG8
#=GF SQ   12


AC226390.3/15172-15051       AGCCCUGGGCUCCCCCAGUGUUGCCUGGGUCUGACUUUGCCUCAGUGAAAACUGCCUCGAAUUCUUUCUUGCACCGAUGGGCAGAUGGGCAGUGUCGGAGGAUCGUGUCAUCUGUCCCGUGG
AANU01197810.1/7192-7313     AGCCCUGGGCUCCCCCAGUGUUGCCUGGAUCUGACUUUGCCUCAGUGAAAACCACCUCGAAUUCUUUCUUGCACCGAUGGGCAGAUGGGCAGUGUCAGAGGAUCGUGUCGUCUGCCCUGUGG
ABGA01039457.1/23902-24023   AGCCCUGGGCUCCCUCAAUGUUGCCUAGAUCUGACUUUGCCUCAGUGAAAACCACCUCAAAUUCUUUCUUGCACUGAUGGGCAGAUGGGCAGUGUCAGAGGAUCGUGUCAUCUGUCCUGUGG
ABRT010568606.1/2221-2325    AGCCCGGGGCUCCCCC-GUGUUGCCUGGAUCUGACUUCUCUUAACCGAAAACCGCCUCGUAUUCUCUCUUG----------CAC------UGUGUUGGAGGAUCGAGUUGCCUGCCCUGUGG
AAWR02020062.1/17797-17907   UGUCCCUGGCUCCC---GUGUUGCCUGCAUCUGAUGUUCCCUAACUGAAACCUGCCUCAUGUUCCUCCCUGGGCCGAUGGGCA--------GUUUCAGAGGACAGAGCUGUCUGCUCUGCGG
ABRN01400946.1/3485-3593     UGCCCUUGGCUCCC---AUGUCGCCUGGAUCCAACUUCCCCUAACUGAAAACCGCCUCAUAUUCCCCCG--GGCCCAUGGGCA--------GCUCCAGAGGACUGAGCCGUAUGCUCUGUGG
ABRP01223358.1/1792-1900     GUCCCUUGGCUCCA----UCUUGCCUGGAUAUGACGUCCCCGGACUGAAAACCGCCUCACAUUCUUCCCUG-GCCGACGGGCU--------GUGUCGGGGGGCUGGGCUGUGCGCGCUGUGG
AAFC03050876.1/70475-70582   UGACCUCGGCUCCC---GUGUUGCCAGGAUCCGACCUCUCCUAGUUGAAAACAGCCUCGUGUUCC--CCUGGGCCGAGGGGCA--------GCUCCAGAGGACUG-GCUGAGUGCUCCGCGG
AAQQ01350185.1/606-715       AGCCCCCAUCUCCACC-GUGU-GCUGGG-UCUGACUUCCCCUCACUGAGACCA-GGUCAUGUUCUCUUUGGGUCUGAUGGGCC--------GUGGCAGAGGGUCGUGUUUCCUGCCCUGUGG
AAPE02047295.1/109902-109794 AGCCGCCGGCCCCU---GCCUUGCCUGAAUCUGACGUCCCGUCACUGAAAACCGCCUCAUAUUGUUCCC--GGCCGAUGGGCA--------GUGUCGGAGGUCGGAGCUGUGUGCUCUGCGG
HQ407421.1/1-107             GACC-UCGGCUCCC---GUGUUGCCAGGAUCCGACCUCUCCUAGUUGAAAACAGCCUCGUGUUCC--CCUGGGCCGAGGGGCA--------GCUCCAGAGGACUG-GCUGAGUGCUCCGCGG
HQ407414.1/219-316           UGACCUCGGCUCCC---GUGUUGCCAGGAUCCGACCUCUCCUAGUUGAAAACAGCCUCGUGUUCC--CCUGGGCCGAGGGGCA--------GCUCCAGAGGACUGG----------CUGAG-
#=GC SS_cons                 ::::::::::::::...::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::........:::::::::::::::::::::::::::::::
#=GC RF                      aGCCCucGGCUCCc...GUGUUGCCuGGAUCUGACuUccCCUaAcUGAAAACcGCCUCguaUUCuuuCuUGggCCGAuGGGCa........GUguCaGAGGacuGuGuugucUGCuCUGuGG
//
# STOCKHOLM 1.0

#=GF AC   RF02147
#=GF ID   MEG8_3
#=GF DE   Maternally expressed 8 exon 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   40.00
#=GF TC   41.20
#=GF NC   37.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005634; nucleus;
#=GF RN   [1]
#=GF RM   11481034
#=GF RT   Identification of a new imprinted gene, Rian, on mouse chromosome 12 by
#=GF RT   fluorescent differential display screening.
#=GF RA   Hatada I, Morita S, Obata Y, Sotomaru Y, Shimoda M, Kono T
#=GF RL   J Biochem. 2001;130:187-190.
#=GF RN   [2]
#=GF RM   11337479
#=GF RT   Human-ovine comparative sequencing of a 250-kb imprinted domain
#=GF RT   encompassing the callipyge (clpg) locus and identification of six
#=GF RT   imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8.
#=GF RA   Charlier C, Segers K, Wagenaar D, Karim L, Berghmans S, Jaillon O, Shay T,
#=GF RA   Weissenbach J, Cockett N, Gyapay G, Georges M
#=GF RL   Genome Res. 2001;11:850-862.
#=GF WK   MEG8
#=GF SQ   10


AANU01197810.1/14355-14420 UUGGCUUGGUCAAAUCAGUGUUCAAACUAUCUCCUGCCGU-UUCA--AGAGGAUCUAGGGCUCUAGAAG
ABRT010202750.1/280-345    UUGACUUGUUCCAGUCAGUGUUCAAACUAUCUCCUGCACU-UUGA--AGGGGCCCUGGGGUUCUGGGAG
ABDC01401091.1/182-246     UUGGCUUGUUCAAGUCAGCGUUCAGACCAUCUCCUGCAGU-UUC---AGGGGCACUGGGGUUCUGGAAG
ABRN01400949.1/767-832     UUGGCUUGUUCAAAUCAGUGUCCAAGUUCUUUCCUGCACU-UUCA--GCGGGCACUGGGAUUAUAGAAG
AAFC03050875.1/1173-1240   UCGGCUUGUUCAAAUCAGUGUCCAGAUUCUUUCCUGCACU-UUCAAGGGGGGCACCGGGAUUGUAGGAA
ABRP01215028.1/65-131      UUGGCUUCUCUAAGUCAGUGUCCAAACUCUUUCCCACACUCUUCA--GGGGCCACCGGGGUUACAGAAG
AANG01662489.1/898-965     UUGGCGCGUUCGAAGCAGUGUCCAAAAUCUUUCCUGCAUU-UUCAGGGGGGGCGCUGGGCUUACAGAAG
AAQR03046506.1/39666-39731 UUGGCUUGUUCAAGUCAGUGUUCAAACUAUCUCUUGCACU-UUCA--AGGGCCACUGGGAUUCUCAAAG
AAEX03006005.1/4105-4171   UUGGCUUGUUCAAGUCAGUGUCCAAAUUCUUACCUGCAGU-UUCA-AGGGGGCACUGGGAUGUCAGCAG
AC226390.3/8017-7952       UUGGCUUGGUCAAGUCAGUGUUCAAACUAUCUCCUGCUCU-UUCA--AGGGGAUCUGGGGCUCUAGAAG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::.::::..::::::::::::::::::::::
#=GC RF                    UUGGCUUGUUCAAGUCAGUGUcCAAAcUcUuUCCUGCAcU.UUCA..GGGGGCaCUGGGgUUcUaGaAG
//
# STOCKHOLM 1.0

#=GF AC   RF02148
#=GF ID   MESTIT1_1
#=GF DE   MEST intronic transcript 1, antisense RNA conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   54.60
#=GF NC   47.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.38 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12095916
#=GF RT   Identification and characterization of an imprinted antisense RNA
#=GF RT   (MESTIT1) in the human MEST locus on chromosome 7q32.
#=GF RA   Nakabayashi K, Bentley L, Hitchins MP, Mitsuya K, Meguro M, Minagawa S,
#=GF RA   Bamforth JS, Stanier P, Preece M, Weksberg R, Oshimura M, Moore GE,
#=GF RA   Scherer SW
#=GF RL   Hum Mol Genet. 2002;11:1743-1756.
#=GF WK   MESTIT1_(gene)
#=GF SQ   16


AF482998.1/2816-2677       UGUCAUUUAGGUUCAUCUUAUUUGGGUAAGAGAUU-AUUCAGUUCCACUGCUU-CCCUCGUCUGCCACUCAUCUUUUGAG--C-----------UUUUUACAGCCAAA-CACUUUUACUCAAAAAUGGGCCUGAAG-----AGGAACACACCAGUAGCUUC-
AANU01033463.1/1093-1232   UGUCAUUUAGGGUCAUCUUAUUUGGGUAAGAGGUU-AUUCAGUUCCACUGCUU-CCUUCGUCUACCACUCAUCUUUUGAG--C-----------UUUUUACAGCCAAA-GACUUUUACUCAAAAUUGGGCCUGAAG-----AGGAAGACACCAGUCGCUUC-
ABRN01099754.1/4181-4038   AGUCUCUUAGGUUUAUCUUAUCUGGUUAAUGGGUU-AUCCAGCUCCCUUGCUU-CUCUCCUCUCCCACUUAUCUUUUGAA--C-----------UUUUUUCAGCCAAA-GAUUUUUACCCAAAAACGAGCCUGAAG-AGGAAGGAAGACACCAGUCGCCUU-
ABRP01251556.1/3260-3116   UGCCACUUAGGUUCAUUUUAUCCGGUUAAUGGAUU-UUUCAGCCCCAUUGCUU-CCCUGCUCUACCACUCAUCUUUUGAA--C-----------UUCUUGCACUCAAA-GACUUUUACCCAAAAAUGAGGAUAAAAGAGGAAGGAAGAUACCAGUCACUUU-
ABDC01335509.1/126-264     UGUCAUUGAGCUGCAUC-----UGGAUACGGGAUA-AUUCUGCUCUGGUGCUU-CCCUCCUCUACCGUUCAUCUGUUGAG--C-----------UUUUUGCAGCCAAA-GACUUUUACCCAAAAAUGAACCUGAAA-AGGGAGGAAGACACCAGUCACUUC-
ABRR01314427.1/2379-2236   UGUCUGUGAAGUUUAUCUUAUCUGGUUAAUGGGUU-AUUCAGCUCCCUUGCUU-CUCUCCUCUCCCACAUUUCUUUUGAACUC-----------UUUUUUCAGCCAAA-GACUUUUACCCAAAAAUGAGCUUU--G-AAGAGGAAAGACACCAGUUGCUUU-
ABVD01564453.1/953-814     UGUCAUUUAGGUUUAUUUUAUCUGCUGAGUGGAUU-AUCCAUUUCCUUUGCUU------CUUUACCACUCAUCUUUUGAG--C-----------UUCUUGCGGUCAAA-GACUUUUACCCAAAAAUGAGCCUGAAGAGGGAAGGAAGAUACCAGUCACUUU-
ABRQ01225307.1/11473-11332 UGUCACUUAGGGUCAUCUUAUCUUGCUCAUGGAAU-AUUCAGCUCGUUUGUUU-CUCUUGUUUGCCAUUCAUCUCUUGAG--C-----------UUUUCACAGCCAGG-CAAUUUUAUCCAG--AACAACCUGAAG-AGGUAGGAAGACUCCAGUCGCUUC-
AAWR02014504.1/35946-36090 UUUCACUUAGAUUCAUGGGAUCUGGUUCAUGCAGU-CUUCUGCUCCCUUGCUUUCUCUCCUCUACCACUCAUCUUAUGAA--C-----------GUUUUGCAGCCAAA-GACUUUUACCCAAAAAUGAGCCUGAAG-GGGAAGGAAGACACUAGUCACUUU-
ACBE01084549.1/1440-1309   UGUCGCUUAGGUUCGUUUUCUCUGGCUAACGGAUU-AUUCA-CCUUGAUGCUU------CUCUAC--CACACCUUUUGAA--C-----------UUUCUGCAGCCAAA-GACUUUUACCCAGACAUGAGCCUGAAG-AGGAAAAAAAAAAAAAAAAA-----
AAGV020321980.1/3248-3120  --UCAUUUAGGUUUAUUUUAUCUGGUUAAUGGAUU-AUGCAGUUCCUUUGCUU------CUUUACCACUUAUCUUUUGAG--U-----------UUUU----GUCAAA-GAUUUUAUCCCAAAAACCAGUCUGAAG-AAGGAGGAAGACAAC----GCUUU-
ABRO01035231.1/14282-14134 UGUCCUUUGGGUUCAUCUCAUCUGGCUGAGAGAUU-AUUUCAUUCCUUUGCUG-CUGCU-UCUAACACU-ACCUUUGGAU--UUCCCCCCCACCUUUUUUUAUGCAAA-GAAUUCUACCCCUAAAUGAGACUGAAG-AGGGAGGA-AACAUUAGUCA----U
AAKN02017560.1/9880-10011  UAUUCUUUGAGUUUGUUUUAUGUAGUUAAG---UA-AUUCAGCUGUGUUGCUU-CCCUUCUCUACCAUUCAUCUUUGGAGU-U-----------UUUUUUUUUU--------UUUAACCCAAAAAUGAACCUGAAA-GGGAAGGAGAACAUUAAUUGC----
AAEX03009252.1/23249-23116 UGUCACUUAGGUUCAUUUUAUCUGGUUAAUGGAUU-AUUCA--CUUUUUGCUU------CUCUGCCGCACAUCUUUUGAAA-C-----------UUUCUGCAGCCAAA-GACUUUUACCCAAAAAUGAGCUUGAAG-----AGGAAAAUACCAGUCACUUU-
AAQR03184722.1/12928-12786 UGCCAUUUAGAUUCAUCCUGUCUGGAUAAGGGGGUUAUUCAGCUC-AGUGCUU-CCCUCCUCUACCACUUAUUUGUUGAA--U-----------GUUUUGUAGCCA--AGACUUUUACCCAAA-AAUGAGCCGGAAGAGGGAGAAUGACACGAGUCACUUC-
AAGW02039137.1/31744-31877 UGCCAGUUAGGCUCCUCUUAUUUGGUUACAGGCGG-AGUUAGCACCUUCGCUU-----CCUCUACCACUCAUCCUUGGAG--C-----------UUUUUGCAGCCAAA-AAUGUAUACCAAAAAAUGAGCGUUGAA-------GAAGGUGCCAUUCCCCUU-
#=GC SS_cons               :::::::::::::::::::::::::::::::::::.:::::::::::::::::.::::::::::::::::::::::::::..:...........::::::::::::::.:::::::::::::::::::::::::::.::::::::::::::::::::::::.
#=GC RF                    UGUCauUUAGGuUCaUcUuaUcUGGuUaauGGauu.AUUCaGcuCcuuUGCUU.CucUcCUCUaCCACUcAUCUUUuGAg..c...........UUUUUgcAgcCAAA.GAcUUuUACCCAaAAAuGAGccUGAAG.aGGgAGGAagAcaccAGUcgCUUu.
//
# STOCKHOLM 1.0

#=GF AC   RF02149
#=GF ID   MESTIT1_2
#=GF DE   MEST intronic transcript 1, antisense RNA conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   133.90
#=GF NC   55.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.92 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12095916
#=GF RT   Identification and characterization of an imprinted antisense RNA
#=GF RT   (MESTIT1) in the human MEST locus on chromosome 7q32.
#=GF RA   Nakabayashi K, Bentley L, Hitchins MP, Mitsuya K, Meguro M, Minagawa S,
#=GF RA   Bamforth JS, Stanier P, Preece M, Weksberg R, Oshimura M, Moore GE,
#=GF RA   Scherer SW
#=GF RL   Hum Mol Genet. 2002;11:1743-1756.
#=GF WK   MESTIT1_(gene)
#=GF SQ   16


AF482998.1/1995-1761       GGAAAAUUCUUUAUGUUGAAUCGACAUCUGUUU-CUCUACAAUUUGCACUC-----AUUGGAGCCAUACAGAAUAAAAUGUCUAA--------UGCUGCUUCCACAAAUAUUUGAGGACUGCUAACACAUUUCCUUCUUCUACUUACUCCACAAGGCUUCUUUUCUUCAAACC-AAACAUGCCCAUCUAUUUCAAACAGGGAGGCAGUGUGGAGUAGUGGAAAGAAGGCCAACUUUGGAGCCAGG-CACAU
ABDC01335509.1/646-880     GGAAAAUUCUUUAUGUUGAAUCGACAUCUGUUU-CUCUACAAUUUGCACUC-----AUUGGAGCCACACAGAAUUAAAUGUCUAA--------UGUUGCUUCCACAAAUAUUUGAGGACUGCUAGCACAUUUCCUUCUUCCAUUUACUCUACAAGGCUUCUUUUCUUCAAACU-AAACAUGCCCAGUUAUUUCAAACAGGGAGGCAGUGUGGGGUAGUGGAAAGAACGCCAGCGUGAGAGCCAGA-CACAU
ABVD01564453.1/462-228     GGAAAAUUCUUUAUGUUGAAUCGACAUCUGUUU-CUCUACAAUUUGCACGC-----AUUGGAGCCAUACAGAAUAAAAUGUGUAA--------UACUGUUUCCACAAAUAUUUGAAGACUGCUAGCACAUUUCCUUCCUCCACUCACUCCACAAGGCUUCUUUUCUUUAAACU-AAACAUGCCCGGUUAUUUCAAACAGGGAGGCAGUGUGGUGUAGUGGAAAGAAUGCCAGCUUUGGAGCCAGA-CACAU
AAGV020321980.1/2762-2528  GGAAAAUUCUUUAUGUUGAAUCAACAUCUGUUU-CUCUAUAAUUUGCACUC-----AUUGGAGCCAUACAGAAUAAAAUGUCUAA--------UACCGCUUCCACAAAUAUUUGAAGACUGCUAACACAUUUCCUUCCUCCACUCACUCCACAAGGCUUCUUUUCUUCAAGCU-AAAUAUGCCCCGUUAUUUCAAACAGGAAGGCAGUGUGGUGUAGUGGAAAGAAUGCCAGCUCUGGAGCCAGA-CACAU
AAFC03096495.1/11054-10811 GGAAAAUUCUUUAUGUUGAAUCGACAUCUGUUU-CUCUACAAUUUGCACUC-----AUUGGAGCCAUACAGAAUAAAACGUCUAAACAUCUAAUGCUGCUUCCACAAAUAUUUGAGCACUGCUAACACAUUUCCUUCUUCCACUCAUUCCACAAGGCUUCUUUUCUUCCAACU-AAAUAUGCCCGGUUAUUUUAAACAGGGAGGCAGUGUGGGGUAGUGGAAAGAACGCCAGCUUUGGAGCCAGAACGCAU
AAKN02017560.1/10369-10602 GGAAAAUUCUUUAUGUUGAAUCCACAUCUGUUU-CUCUACAGUUUGCACUC-----AUUGGAGCUGUACAGAAUAAAAUGUUUAA--------UACUGCUUCCACAAAUAUUUGAGGACUGCUAAUACAUUUCCUUUUCCCACUCAUUCCACAAGCCUCCUUUUCUUCAAACU-AAACAUGCCU-GUUAUUUCAAACAGGAAGGCAGUGUGGGGUAGUGGAAAGAUCACCAGCUCUGGAGCCAAA-CACAU
ABRO01035231.1/13781-13546 GGAAAAUUCUUUAUGUUGAAUCGACAUCUGUUU-CUCUGCAGUUUGCAUUC-----ACUGCAGCCACACAGAAUGAAAUGUCUAA--------UGCUGCUUCCACAAAUAUUUGAGGAUUGCUAAUAUAUUUCCUUCUUCCACUCACUCCACAAGGCUCCUUUUCUUCAAACUCAAACAUGCCCAGUUAUUUCAAACAGGGCAUCAGUGUAGGGCAGUGGAAAGCACGCCAGCUCUGGAGCCAGA-CACAU
ABRQ01225307.1/10977-10744 GGAAAAUUCUUUAUGUUGAAUCAACAUCUGUCU-CACUAGAAUUUGCACUC-----AUUGGAGACAUACAGAAUAAAAUGCCCAG--------UACUGCUUCCACAAAUAUUUGAGGACUACUAACACAUUUCCUUCCUCCGCUCCUUCCACAAGGCUUCUUUUCUUCCAGUG-AAGCCUGCCCAGUGAUUUCAAACAGGGAGACAGUGUAGUGUAGUGGAAAGAACGCUACCUGGGCAACCAG--CACGU
AANN01534930.1/1049-1289   GGAGAAUUCUUUAUGUUGAAUCGACAUCUGUUUUCCCUACAAGUUGCUCUCUACAAGUUGGAGACAUACAGAACCUAAUGUCUAA--------CGCUGCUUCCACAAAUAUUUGAGGACCACUAACACAUUUCCUUCUUCCACUUGCUCCACAAGGCUCCUUUUCUUCCAGUA-AAGCAUGCCUGGUUAUUUUAAACAGGGAGGCAGUGUGGGGUAGUGGAAAGAACGCCAACUUUGAAACUAGA-CACAC
AALT01061449.1/1162-929    UGCCAGUUCUUUAUGUUGAAUCCACAUCUGUGU-CUCUGCAACUCACACUC-----CUUGGAGCCGUGCAGAGCAAAAUGUCUAA--------UGCUGCUUCCACAAAUAUUUGAAGGCCACAAACACAUUUCCUCCUUCCACUCACUCCACAAGGCU-CUUUUCUUCCAGCU-CAGCAUGCCCAGUGGUUUUGAACAGGGAGGCAGUGUGGGGUAGUGGAAAGAAGGCCAGCUUCGGAGCCAGA-CAUCU
AAHX01029309.1/1828-1606   GGAAAAUUCUUUAUGCUGAAUGGAUUUUUGUUU-CUGUGCCGUUUGCGCUC-----CUUGGAGCCAUAUGGAAUAAAAUGUCUAA--------CACGGCUUCCACAAAUAUUUGAAGACUGCGAACACAUUUCCUCCUUCCACAUACUCCACAAGGCUCCUUUUCUUUAGACU-AAACAUGCCCAGUUAUUUCAAACAGCGAGGUAGUGUGGGGCGGUACAAAGAACUCCAG-----G--------CGCAU
AAHY01052390.1/74244-74473 GAAAAAUUCUUUAUGCUGAAUGGAUUUCUGUUU-CUGUGCCGUUUGUGCUC-----CUUGGAGCCAUAUGGAAUAAAAUGUCUAA--------CACCGCUUCCACAAAUAUUUGAAGACUGUGAACACAUUUCCUCCUUCCACUCACACCACAAGGCUCCUUUUCUUUAGACU-AAACAUGCCCAGUUAUUUCAAACAGCGAGGUAGUGUGGGACCGUGCAAAGAACUCCAG-----GAGCAAGA-GGGUU
AAYZ01073938.1/35-266      GGGAACUGGCUGCUGUUGCCUCCACAUCUGGUC-CUCUAGCAUUUGCACUC-----GUUGGCGCCGUGCAGGAUGAAAUGUCUCA--------UGCCGCUUCCACAAACAUUUGAGAACUGCUAACACAUUUCC---UUCCACUCACUCCACAAGGCUGCUUUUCUUCCACUU-AAGCACGCCCAGCUCUCUCAAACCGGGAGGCUGUGAGGGGUAGUGGAAAGAAGGGUAGCCCCUGAGCCAGA-CACCC
AAQR03184722.1/12438-12204 GGAAAAUUCUUUAUGUUGAAUCACCAUCUGUUU-CUCUACAAUUUGCAAUC-----AUUGGAGCCAUACAGAAUAAAAUGUCUAA--------UGCUGCCUCCACAAAUAUUUGAGGACUGCUAACACAUUUCCUUCUUCCACUCACUCCACAAGGCUUCUUUUCUUCAAACU-AAACAUGCCCAGUUAUUUCAAACAGGCAGGCAGUGUAGGGUAGUGGAAAGAACGCCAGCUUUAGAGCCAGA-CACAU
AAEX03009252.1/22761-22527 GGAAAAUUCUUUAUGUUGAAUCGACAUCUGUUU-CUCUACAAUUUGCACUC-----AUUGGAGCCAUACAGAAUAAAAUGUCUAA--------UGCUGCUUCCACAAAUAUUUGAGGACUGCUAACACAUUUCCUUCUUCCACUUACUCCACAAGGCUUCUUUUCUUCCAACU-AAACAUACCCGGUUAUUUUAAACAGGGAGGCAGUGUGGGGUAGUGGAAAGAACGCCAGCUUUGGAGCCAGA-CACAU
AAGW02039137.1/32520-32754 GGAAAAUUCUUUAUGUUGAAUCGACAUCUGUUU-CUCUACGAUUUGCACUC-----ACUGGAGCCAUACAGAGUAAAACGUCUAA--------UGCUGCUUCCACAAAUAUUUGAGAACUGCUAACACAUUUCCUUCUUCCACUCACUGCACAAGGCUCCUUUUCUUCAAGCU-ACACAUGCCCAGUUAUUUCAAACUGGGAGGCAGUGAGGGGUAGUGGAAAGAAAGUCAGCACUGGAGCCAGA-CACCU
#=GC SS_cons               :::::::::::::::::::::::::::::::::.:::::::::::::::::.....:::::::::::::::::::::::::::::........::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::
#=GC RF                    GGaaAaUUCUUUAUGUUGAAUcgACaUCUGUuU.CucUacaauUUGCaCUC.....aUUGGAGcCaUaCAGAAUaAAAUGUCUAA........ugCuGCUUCCACAAAUAUUUGAggACUGCuAACACAUUUCCUuCUUCCACUcacUCCACAAGGCUuCUUUUCUUcaAacu.AAaCAUGCCCaGUuaUUUcAAACaGGGAGGCAGUGUGGgGuaGUGGAAAGAAcGcCAGCuuugGAGCcAGA.CacaU
//
# STOCKHOLM 1.0

#=GF AC   RF02150
#=GF ID   MESTIT1_3
#=GF DE   MEST intronic transcript 1, antisense RNA conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   60.00
#=GF TC   66.10
#=GF NC   36.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.85 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12095916
#=GF RT   Identification and characterization of an imprinted antisense RNA
#=GF RT   (MESTIT1) in the human MEST locus on chromosome 7q32.
#=GF RA   Nakabayashi K, Bentley L, Hitchins MP, Mitsuya K, Meguro M, Minagawa S,
#=GF RA   Bamforth JS, Stanier P, Preece M, Weksberg R, Oshimura M, Moore GE,
#=GF RA   Scherer SW
#=GF RL   Hum Mol Genet. 2002;11:1743-1756.
#=GF WK   MESTIT1_(gene)
#=GF SQ   18


AF482998.1/431-333         UGGGUAGACAUGUUCCA--------UGGCCUUC-AGAAUAAGAUCUUUUGUGGGGUACUCAGUCCA-U--AAACAGAAAAUUGCCUUCAUCUUGGAUG-CUG-GUGUUUCUGG
ABGA01200454.1/21337-21435 UGGGUAGACAUAUUCCA--------UGGCCUUC-AGAAUAAGGUCCUUUAUGGGGCACUCAGUCCA-U--AAACAGAAAAUUGCCUUCAUCUUGGAUG-CUG-GUGUUUCUGG
AAQQ01065895.1/762-663     UGGGUAGAUAUGUUCUG--------UGGCCUUC-AGAAUAGGAUCCUUUGUGGGGCAUUUAGUCCAUU--AAUUAGAAAAUUGCCUUCAUCUUGGAUG-CUG-GUGCUUCUGG
ABRN01099754.1/2160-2062   UGGGUGGACAUGUUCCA--------UGGCUUUC-AGAAUAAGAUCCUUUGU-GAGCACUCAGUCCAUU--AAAUACAAAAUUGCCUUCAUCUCGGAUG-CUG-GUGCUUCUGG
ABRR01314427.1/385-287     UGGGUGGACAUAUUCCC--------GGGCUUUC-AGAAUAAGAUCCUUUGU-GAGCACUCAGUCCAUU--AAAUACAAAAUCGCCUUCAUCUUGGAGG-UUG-GUGAUUCUGG
AAHY01052390.1/75790-75888 UGGGUAGAC-UGUUCCC--------CGGCCUUC-AGAAUGAGAUCCAUUGUGGGGCACUCAAUCCAUU--AAUUAGAAAAUUGCCUUCAUCUUAGAUG-CUG-GUGCUUCGGC
ABDC01335509.1/2204-2302   UGUGUGAGCAUGUUCUG--------UGGCCUUC-AGAAUAAGAUCCUUUGU-GGGCACUCACUCCAUU--AAAUAGAAACUUGCCUUCAGCUUGGAUG-CUG-GUACUUUUGG
ABRO01035231.1/12277-12176 UGGGUAGACAUGUUCCA--------AGGCCUUCAAAAAAAAGAUCCUUUGUGGGGUACUUAGUCCAUU--AAUUAGAAAAUCGUUUUCAUCCCCGACA-CUGCGUGCUUCUGU
AANN01534930.1/2601-2702   UGGGCAGACAUGCUCCA--------UGGCUUUC-AGAAUAAGGUCCUUUGU-GCGCACUCAGACCCUUACAAAUACAAAAUCGCCUUCAUCUUGGAUGCCCG-GUGCUUCUGG
ABRP01251556.1/1307-1209   UGGGUGGACAUGUCCUC--------UUGCUUUC-AGAAUCAGAUCCUUUGU-GAGCACUCUGUCCAUU--AAAUACAAAAUUGCCUUCAUCUUGGAUG-CGG-GUGUAUGGUG
AAWR02014504.1/38001-38098 UGGGUGGACGUGUUCCA--------UGGCUUUC-AGAAUAAGAUCCUUUGU-GUGCACUCAAUCCAUU--AAAUCCACAAUUGCCUUCAUCUUGUG-G-CUG-AUCCUUCUGG
AANG01398330.1/29-126      UAUCUACCACUGUUCUG--------UGGCUUUC-AGAAUAGGAUCCUUUGU-GAGCAUUCAGUUCA-U--AAAUACAAAACCGGCUUCAUCUUGGGUG-CUG-GUGCUUCUGG
AAGV020321980.1/1239-1141  CCUGCUUGCUUGUUCUG--------UGACUUUC-AGAAUAAGAUCCUUUGUGCAGUGCCCAGUUCAUU--AAAUAGAAAAUUGCCUUCAUCUUGGAUG-CUG-UUG-UUCUGG
ABRQ01225307.1/9047-8949   UGAGUAGACCUG-UCCG--------UGGCCUUC-AGAAUGAGACCCUUUAUGCGGUACUCAGGCCAUU--AAAGAGAAAAUUGUCUUCACUUUGAAUA-CUG-AAAGCAAGGA
AACN010967834.1/532-629    UCUGCCCACUUGUUCUG--------UGGCUUUC-AGAAUAAGAUUCUUUGU-GAGCUCUCAGUCCAUU--AAAUACAAAACUGCCUU-GUCUUGGAUA-CUG-GUGCUUCUGG
AAPE02016897.1/20294-20196 UGGGUGGAAAAGUUCAC--------UUACGUUC-AGAAUCAGAUCUUUUGU-GAGCACUCGGUCCAUU--AGCUACAAAAUUGCCUUCAUCUUGGAUG-CGG-GUGCUGCUGG
AAQR03184722.1/10902-10796 UGGGUGGACAUCUUCCUGUGGCCUUUGGGCUUU-GGGAUAAGAUCCUUUAU-GGACAUUAAGUCCAUU--AAAUAGAAACUUGCCUUCAUCUUGAAUG-CGG-GUGCUUUUGG
AB007765.1/2046-2144       UGGGUAGAC-UGUUCCC--------CGGCCUUC-AGAAUGAGAUCCAUUGUGGGGCACUCAAUCCAUU--AAUUAGAAAAUUGCCUUCAUCUUAGAUG-CUG-GUGCUUCGGC
#=GC SS_cons               :::::::::::::::::........::::::::.:::::::::::::::::.::::::::::::::::..::::::::::::::::::::::::::::.:::.::::::::::
#=GC RF                    UGGGUgGACaUGUUCcg........UGGCcUUC.AGAAUaAGAUCCUUUGU.GgGCACUCAGUCCAUU..AAaUAgAAAAUUGCCUUCAUCUUGGAUG.CuG.GUGcUUcUGG
//
# STOCKHOLM 1.0

#=GF AC   RF02151
#=GF ID   MIMT1_1
#=GF DE   MER1 repeat containing imprinted transcript 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; RNAz; Eberhardt R
#=GF GA   45.00
#=GF TC   47.80
#=GF NC   40.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.86 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001641; lincRNA gene;
#=GF RN   [1]
#=GF RM   17509818
#=GF RT   Genomic organization and imprinting of the Peg3 domain in bovine.
#=GF RA   Kim J, Bergmann A, Choo JH, Stubbs L
#=GF RL   Genomics. 2007;90:85-92.
#=GF WK   MIMT1
#=GF SQ   21


ABRN01180214.1/4550-4465     ACGAAGCC-CAUGCUAGGGGCCCUGAGGAAGGGUCUGGAAAAGGG--------GGAGGGGG--AGU-------------GAGUGUGCGACCCCCAAACAA---AGAAG--GGGGG
AAPY01017500.1/1201-1121     ACCAAGCC-AACGCAAGGGGUCCUGAAGUGGGGUCUGGAAAAG-------------CGGUAUGGAG-----------UGUGAGGUGUAGCCCCCGAA-------GAAC--GGGGA
ABDC01508070.1/664-739       ACCGUGCC-AGCGUGAGGGGCCCCGAAAG-GGG---------------------AUGGGGGUGGGC-----------GGUGGGGUGCAGCCCCCAAACAA---AGAAA-UGG-GG
ABRP01093371.1/1758-1674     ACUGAGCC-CACGCGAGGGGCCCCAGAGAGGGGUCUAGAUAAG------------CGGGGGUGGGG---------AUGCGGGGGUGCAACCCCCAAAGAA------AA--GGGAG
ABGA01258517.1/14103-14017   -GGGAGUG-GCCGUGAGGGACCCCAAAGCCAGGUCUGGAAAAG-------------GGGGGUGGGUU----GG-GUGGUGGGGGUGCAGCCACCAAA-------GAAA-UGGGGG
AAWR02030955.1/626-717       ACUGAGCU-GAGGCGAGGGGCCUCAAAAAGGGGUCUAGAAAAA-------------GGGGGG-GGCGG-GUGA--GUGGCUGUGAGCGACCCCCAAACAA---AGAAA--GGGGG
AF229257.1/16-109            ACGGAGUC-AGUGUUAGGGGCCCCCAAGCAGAGUCUGGAAAAG-------------GGGGAUGGGAUG--UGGGUGUGAAGGGAUGCAGCCCCCCCAA-A---AGAAA-UCGGGG
AC006115.1/163717-163803     -GGGAGUG-GCCGUGAGGGACCCCAAAGCCAGGUCUGGAAAAG-------------GGGGGUGGGUU----GG-GUGGUGGGGGUGCAGCCCCCAAA-------GAAA-UGGGGG
ABRT011054967.1/305-378      AACAGGCG-GAUGCGGGGGUC--------------UGCAAGAG-------------GGGGGCA-GC------G--GGGUGGGGGUGCAGCCCCCAAACAA---AGACA-UGGGGG
ABRQ01141854.1/1891-1806     AUCGUGCA-GACGCAAGGGGCCCAAAAGAGGGGUCUCGAAAAG-------------GAGGGUGU--------------UGUGGGUGCUACCCCCAAAGAAAAAAAAAA-UGGGUG
AAYZ01191454.1/466-562       -GCCACUG-GACACCAGGGGCCCCG-AGCAGGGUCUGGAAAAGUGGGGGUGGGGUGGGGGGAUAGC------A--CUGGUGGGGAGCAUCUCCCCAAAGU---CGAGGGGG----
AAFC03057657.1/129671-129595 ACAGAGCC-AACGCGAGGGGCCCUGAGGAAGGGUCUGGGGGG-------------UGGGGGU-------------------GUGUUCGACCCCCAAACAA---AGAAG--GGGGG
AANU01181344.1/21862-21952   -GGGAGUG-GCCGUGAGGGACCCCAAAGCCGGGUCUGGAAAAG-------------GGGGGUGGGUU----GG-GUGGUGGGGGUGCAGCCCCCAAACAA---AGAAA-UGGGGG
EU746669.1/336-243           ACGGAGUC-CGUGGUAGGGGCCCCGAAGCAGGGUCUGGAAAAG-------------GGGGAUGGGAUGUGGG--UGUGAAGGGAUGCAGCCCCCCCAAA----AGAAA-UCGAGA
EU746668.1/129-35            ACGGAGUCCGUGGUANGGGGCCCCGAAGCAGGGUCUGGAAAAG-------------GGGGAUGGGAUGCGGG--UGUGAAGGGAUGCAGCCCCCCCAAA----AGAAA-UCGAGG
AAQQ01016402.1/311-232       CGGGCGCG-GGAGCUAGGGGCC--GAAGCAGGGUCUGGAAAUG-------------GGGG-CGGGG---------UGGGGAAGGUGCA-CCCCCAAA-------GAAA-UGGGUG
AABR05005289.1/3544-3451     ACGGAGUC-CGUGUUAGGGGCCCCCAAGCAGAGUCUGGAAAAG-------------GGGGAUGGGAUG--UGGGUGUGAAGGGAUGCAGCCCCCCCAA-A---AGAAA-UCGGGG
EF110915.1/5-91              -GGGAGUG-GCCGUGAGGGACCCCAAAGCCAGGUCUGGAAAAG-------------GGGGGUGGGUU----GG-GUGGUGGGGGUGCAGCCCCCAAA-------GAAA-UGGGGG
AAEX03000703.1/94529-94452   ACUGAGCU-GACACUAGGGGCCCCAGAGA-GGGUCUGGGGGGG------------AGGGGG----C-----------GAGUGGAUGUGACCCCCACACAA---AGGGG--GG---
AAGW02071590.1/69393-69480   ACCAAGUG-GACGCCAGGGGCCCCGAAGCAGGGUCUGGAAAAG-------------GGGGGUGGGC---------UUGGUGGGGAGUAGCCCCCAAACAA---AGACA-UGGGGG
AAGU03012401.1/1098-1176     ACCUAGCG-GACGCAAGGGGCCCGGAAGAGGGUUCUGGAAAAG-------------GGGGGUGUG--------------GUGGGUGCUACCGCCGAA-------GAAA-UGGGGG
#=GC SS_cons                 ::::::::.::::::::::::::::::::::::::::::::::.............::::::::::.........:::::::::::::::::::::::::...:::::.::::::
#=GC RF                      AccgAGcg.GacGCgAGGGGCCCcgAAGcaGGGUCUGGAAAAG.............GGGGGuGGGc.........guGggGGGGUGCagCCCCCaAAaAA...AGAaa.UGGGGG
//
# STOCKHOLM 1.0

#=GF AC   RF02153
#=GF ID   NBR2
#=GF DE   Neighbour of BRCA1 gene 2 converved region
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   40.50
#=GF NC   39.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.04 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9215675
#=GF RT   Isolation and characterisation of the NBR2 gene which lies head to head
#=GF RT   with the human BRCA1 gene.
#=GF RA   Xu CF, Brown MA, Nicolai H, Chambers JA, Griffiths BL, Solomon E
#=GF RL   Hum Mol Genet. 1997;6:1057-1062.
#=GF RN   [2]
#=GF RM   15777733
#=GF RT   Model of transcriptional regulation of the BRCA1-NBR2 bi-directional
#=GF RT   transcriptional unit.
#=GF RA   Suen TC, Tang MS, Goss PE
#=GF RL   Biochim Biophys Acta. 2005;1728:126-134.
#=GF WK   NBR2
#=GF SQ   26


DQ190454.1/58870-58808       GUAAAAGUUUCAUUUGAUCUGAAUAGUAUUAAAAUAAAAUACCUGGAUGAGGAAGAUGAAGAG
U88573.1/162-224             GUAAAAGUUUCAUUUGAUCUGAAUAGUAUUAAAAUAAAAUACCUGGAUGAGGAAGAUGAAGAG
DQ190452.1/62355-62293       GUAAAAGUUUCAUUUGAUCUGAAUAGUAUUAAAAUAAAAUACCUGGAUGAGGAAGAUGAAGAG
DQ190452.1/15620-15558       GUAAAAGUUUCAUUUGAUCUGAAUACUAUUCAAAUAAAAUACCUGGAUGAGGAAAAUGAAGAG
DQ190455.1/66018-65956       GUAAAAGUUUCAUUUGAUCUGAAUAGUAUUAAAAUAAAAUACCUGGAUGAGGAAGAUGAAGAG
DQ190455.1/19287-19225       GUAAAAGUUUCAUUUGAUCUGAAUACUAUUCAAAUAAAAUACCUGGAUGAGGAAAAUGAAGAG
DQ478408.1/66348-66286       GUAAAAGUUUCAUUUGAUCUGAAUAGUAUUAAAAUAAAAUACCUGGAUGAGGAAGAUGAAGAG
DQ478408.1/19615-19553       GUAAAAGUUUCAUUUGAUCUGAAUACUAUUCAAAUAAAAUACCUGGAUGAGGAAAAUGAAGAG
DQ190450.1/63299-63237       GUAAAAGUUUCAUUUGAUCUGAAUAGUAUUAAAAUAAAAUACCUGGAUGAGGAAGAUGAAGAG
DQ190450.1/16557-16495       GUAAAAGUUUCAUUUGAUCUGAAUACUAUUCAAAUAAAAUACCUGGAUGAGGAAAAUGAAGAG
DQ190451.1/62428-62366       GUAAAAGUUUCAUUUGAUCUGAAUAGUAUUAAAAUAAAAUACCUGGAUGAGGAAGAUGAAGAG
DQ190451.1/15693-15631       GUAAAAGUUUCAUUUGAUCUGAAUACUAUUCAAAUAAAAUACCUGGAUGAGGAAAAUGAAGAG
DQ190456.1/63449-63387       GUAAAAGUUUCAUUUGAUCUGAAUAGUAUUAAAAUAAAAUACCUGGAUGAGGAAGAUGAAGAG
DQ190456.1/16712-16650       GUAAAAGUUUCAUUUGAUCUGAAUACUAUUCAAAUAAAAUACCUGGAUGAGGAAAAUGAAGAG
DQ190457.1/63413-63351       GUAAAAGUUUCAUUUGAUCUGAAUAGUAUUAAAAUAAAAUACCUGGAUGAGGAAGAUGAAGAG
DQ190457.1/16682-16620       GUAAAAGUUUCAUUUGAUCUGAAUACUAUUCAAAUAAAAUACCUGGAUGAGGAAAAUGAAGAG
DQ190453.1/64718-64656       GUAAAAGUUUCAUUUGAUCUGAAUAGUAUUAAAAUAAAAUACCUGGAUGAGGAAGAUGAAGAG
DQ190453.1/17974-17912       GUAAAAGUUUCAUUUGAUCUGAAUACUAUUCAAAUAAAAUACCUGGAUGAGGAAAAUGAAGAG
ABRP01214784.1/3280-3218     GUAAAAGUUUCAUUUGACCUGUACACUAUUCAAAUAAAAUAUCUGGAUGAGGAAAAUGAAGAG
AAIY01641832.1/1123-1185     GUAAAAGUGUCGUUUGAUCUGAACACUAUUCAAAUAAAAUACUUGGAUGAGGAAAAUGAAGAG
ABQO010497260.1/1671-1733    GUAAAAGUUUCAUUUGAUCUGAACACCAUUCAGAUAAAAUACCUGGAUGAGGAUAGUGAAGAG
AAHY01095770.1/129123-129185 GUAAAAGUUUCAUUUGAUCUGAAUACUAUCCAGAUAAAAUACCUGGAUGAGGAGAACGAGGAG
BC149979.1/203-265           GUAAAAGUUUCGUUUGAUCUCAACACUGUUCAAAUAAAAUAUUUGGAUGAGGAAAAUGAAGAG
AAQQ01352197.1/820-758       GUGAAAGUUUCAUUUGACCUGAACACUAUUCAAAUAAAAUACCUAGAUGAAGAAAAUGAAAAG
BX933274.1/182-244           GUUAAAGUUUCAUUUGACCUGGAUGAUAUUCAGAUAAAAUACAUUGAUGAGGAUAAUGAUGAG
AAQR03042605.1/1782-1720     GUAAAAGUGUCAUUUGAUUUGAACACUAUUCAGAUAAAAUACCUGGAUGAGGAAAAUGAAGAG
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      GUAAAAGUUUCAUUUGAUCUGAAUAcUAUUcAAAUAAAAUACCUGGAUGAGGAaaAUGAAGAG
//
# STOCKHOLM 1.0

#=GF AC   RF02154
#=GF ID   NCRUPAR_1
#=GF DE   Non-protein coding RNA, upstream of F2R/PAR1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   44.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 40.56 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   12084570
#=GF RT   A noncoding RNA regulates human protease-activated receptor-1 gene during
#=GF RT   embryogenesis.
#=GF RA   Madamanchi NR, Hu ZY, Li F, Horaist C, Moon SK, Patterson C, Runge MS,
#=GF RA   Ruef J, Fritz PH, Aaron J
#=GF RL   Biochim Biophys Acta. 2002;1576:237-245.
#=GF WK   NCRUPAR
#=GF SQ   9


AC025188.8/53778-53910    -UAAGAGCACAUAAACAU---AGGAACUUUGUGAAGUCUA-AGGACAAAACAAAAAACA--ACAUCACUAACAGACCAUAA-----AAUUAGAAAUCAGUCACAAAAA-GCCAGUCAAAAUAUCCAAGAAUUUAU-GG-UUGAAGAUU
ABGA01158148.1/1753-1631  -UAAGAGCACAUAAACAU---AGGAACUUCGUGAAGUCUG-AGGACAAAACAAAAAACA--UCAUCACUAACAGACCAUAA-----AAUU----------CACAAAAA-GCCAGUCAAAAUAUCCAAGAAUUUAU-GG-UUGAAGAUU
ABDC01212228.1/2289-2420  -GAAGAGUGUAUAAACAU---AGGAAUUUUGUAAAGUCUG-AGGACAAAACAGACAACA-AAGACUACCACCAGACCAUAAAACAAAAUUAGAAAUCAAUCACAAA------AGUCAAAAUUUCCAAUA---UAUCAG-UUGAAGAUU
ABRP01058420.1/1959-1819  -AAAAAGCAUACAAAUAU---AGGAACUUUGUAGAGUCUG-AAGAGAAAACAGAAAGCAGAACACCACCAAUAGUUUAUAACACAAAAUUAGAAACCAAUCACAAAAA-GCCAGUUAAAACUUUCAAUAAUUUAGGGG-UUAAAGAAG
AAWR02003127.1/3262-3119  -AAAGAGCACACAAAUGUUAUAGGAACUUUGUAGAGUGUG-GGGAAAAAACAGAAAACAGAACAUCACCAACAGACCAUAACACAAAAUGAGAACUCAAUCACAAAAA-GUGUGUCAAAACUUCCAAUAACUGAUGGG-AUGAAGAAG
ABRT010217459.1/208-69    UAAAGAG-ACCUAGACAU---GGGAACCUGGUGAAAUUUA-AGGACCAAAGAGAGAA---AACAACAUCAACAGAUCCUAAAACAAAAUUAGAAACUAGUCACAAAAGAGCCAGACAAAACUUCCAAUAAUUUAUGGGAUUCAAGAUU
ABRN01397986.1/1086-957   -AAACAGCACACGAAUAUUACAGGAACUUU------UGUA-GAGAAAA---------CAGAACAUCACCAACAGACCAUAACACAAAACUGGAAAUUAAUCACAAAAAAGCCAGUCAAAACUUCCAAUAACUUAUGGA-UGGAAGAAG
AACN010242927.1/1376-1518 -AAGGAGCACACAAACAUUACGGGAAUUUUGUAUAAUAUGCAGAAAAAAACAGAAAACAGAACAUUGUCAUCAGACCGUAACAUAAAAUUAGAAAUUAAUCACAAA---GCCAGUCAAAACUUCCAAUCAUGUAUGGG-UUGAAGAAG
U36755.1/1342-1474        -UAAGAGCACAUAAACAU---AGGAACUUUGUGAAGUCUA-AGGACAAAACAAAAAACA--ACAUCACUAACAGACCAUAA-----AAUUAGAAAUCAGUCACAAAAA-GCCAGUCAAAAUAUCCAAGAAUUUAU-GG-UUGAAGAUU
#=GC SS_cons              .:::::::::::::::::...:::::::::::::::::::.::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::.:::::::::
#=GC RF                   .aAAgAGCAcauAAAcAU...aGGAAcUUuGUgaAgUcUg.aGGAcaAAAcAgAaAaCA.AACAucAccAaCAGacCaUAAcAcAAAAUUAGAAaucAaUCACAAAAa.GCcaGUCAAAAcuUCCAAuaAuuUAUgGG.UUgAAGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF02155
#=GF ID   NCRUPAR_2
#=GF DE   Non-protein coding RNA, upstream of F2R/PAR1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   93.90
#=GF NC   45.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 38.02 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   12084570
#=GF RT   A noncoding RNA regulates human protease-activated receptor-1 gene during
#=GF RT   embryogenesis.
#=GF RA   Madamanchi NR, Hu ZY, Li F, Horaist C, Moon SK, Patterson C, Runge MS,
#=GF RA   Ruef J, Fritz PH, Aaron J
#=GF RL   Biochim Biophys Acta. 2002;1576:237-245.
#=GF WK   NCRUPAR
#=GF SQ   3


U36755.1/1906-2004       AUGCUAAAGAGUAAACUCAAAGAAAGUAGAGGAAAAGAAUGAAUUAAAAAUCUGUGUUUAUAAAUAAAAAUAAAAGUAACGGAGCAAAAAGACGGGCAU
AANU01151923.1/631-729   AUACUAAAGAGUAAACUCAAAGAAAGUAGAGGAAAAGAAUGAAUUAAAGAUCUGUGUUUAUAAAUAAAAAUAAAAGUAACAGAACAAAAAGAUGGGCAU
ABGA01158148.1/1184-1088 ACAUGAAAGAGUAAACUCAAAGAAAGUAGAGGAAAAGAAUGAAUUAAAGAUUUGU--UAAUAAAUAAAAAUAAAAGUAAUGGAGCAAAAAGAUGGGCAU
#=GC SS_cons             :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  AuacuAAAGAGUAAACUCAAAGAAAGUAGAGGAAAAGAAUGAAUUAAAgAUcUGUGUUuAUAAAUAAAAAUAAAAGUAAcgGAgCAAAAAGAuGGGCAU
//
# STOCKHOLM 1.0

#=GF AC   RF02156
#=GF ID   NPPA-AS1_1
#=GF DE   NPPA antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   45.00
#=GF TC   47.20
#=GF NC   39.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   19671135
#=GF RT   Natural antisense transcript of natriuretic peptide precursor A (NPPA):
#=GF RT   structural organization and modulation of NPPA expression.
#=GF RA   Annilo T, Kepp K, Laan M
#=GF RL   BMC Mol Biol. 2009;10:81.
#=GF WK   NPPA-AS1
#=GF SQ   19


FJ706071.1/968-1140        AGGAAGUUGCCCCAC-ACACAGAUUGCCCCGAUGUCCAACCAGAAGA-AGUGAAACUGCUGCUGGGUCUGGAGAG----GUGAAGACCC-GUGGCCAGCUUCUGUUGUUGCCAUCGGCCAUUGCUUUUU----GUUC---GCUUGCUUUUGGUUUUGCAAGAAGA-GCGGCCU-CUGUCUCUG------AUCUGC-----
FJ706073.1/412-584         AGGAAGUUGCCCCAC-ACACAGAUUGCCCCGAUGUCCAACCAGAAGA-AGUGAAACUGCUGCUGGGUCUGGAGAG----GUGAAGACCC-GUGGCCAGCUUCUGUUGUUGCCAUCGGCCAUUGCUUUUU----GUUC---GCUUGCUUUUGGUUUUGCAAGAAGA-GCGGCCU-CUGUCUCUG------AUCUGC-----
FJ706074.1/315-487         AGGAAGUUGCCCCAC-ACACAGAUUGCCCCGAUGUCCAACCAGAAGA-AGUGAAACUGCUGCUGGGUCUGGAGAG----GUGAAGACCC-GUGGCCAGCUUCUGUUGUUGCCAUCGGCCAUUGCUUUUU----GUUC---GCUUGCUUUUGGUUUUGCAAGAAGA-GCGGCCU-CUGUCUCUG------AUCUGC-----
FJ706070.1/998-1170        AGGAAGUUGCCCCAC-ACACAGAUUGCCCCGAUGUCCAACCAGAAGA-AGUGAAACUGCUGCUGGGUCUGGAGAG----GUGAAGACCC-GUGGCCAGCUUCUGUUGUUGCCAUCGGCCAUUGCUUUUU----GUUC---GCUUGCUUUUGGUUUUGCAAGAAGA-GCGGCCU-CUGUCUCUG------AUCUGC-----
FJ706072.1/435-607         AGGAAGUUGCCCCAC-ACACAGAUUGCCCCGAUGUCCAACCAGAAGA-AGUGAAACUGCUGCUGGGUCUGGAGAG----GUGAAGACCC-GUGGCCAGCUUCUGUUGUUGCCAUCGGCCAUUGCUUUUU----GUUC---GCUUGCUUUUGGUUUUGCAAGAAGA-GCGGCCU-CUGUCUCUG------AUCUGC-----
AL021155.1/29326-29498     AGGAAGUUGCCCCAC-ACACAGAUUGCCCCGAUGUCCAACCAGAAGA-AGUGAAACUGCUGCUGGGUCUGGAGAG----GUGAAGACCC-GUGGCCAGCUUCUGUUGUUGCCAUCGGCCAUUGCUUUUU----GUUC---GCUUGCUUUUGGUUUUGCAAGAAGA-GCGGCCU-CUGUCUCUG------AUCUGC-----
FJ706075.1/231-403         AGGAAGUUGCCCCAC-ACACAGAUUGCCCCGAUGUCCAACCAGAAGA-AGUGAAACUGCUGCUGGGUCUGGAGAG----GUGAAGACCC-GUGGCCAGCUUCUGUUGUUGCCAUCGGCCAUUGCUUUUU----GUUC---GCUUGCUUUUGGUUUUGCAAGAAGA-GCGGCCU-CUGUCUCUG------AUCUGC-----
AANU01225053.1/6810-6986   AGGAAUUUGCCCCACCAAACAGAUUGCCCUGAUGUCCAACCCGAAGA-AGUGAAACUGCUG-UGGGUCUGGAGAG----GUGAAGCCCC-GUGGCCAGCUUCUGUCACCGCCAUCUGCCAUUGCUUUUU----GUUC---CCUUGCUUUUGGUUUUGCAAGAAGC-AUGGCCU-CUGUCUCUG--UCUGAUCUGC-----
AAGV020236958.1/4589-4423  AGGAAUUUGCCCCAC-AGA----UUCCCCUGAGAUCCAGCCAGAAGA-AAUGAAAUUGACGCCAGGUCUGUAGAU----GUUUGGACCUGGUGACUGGCUUCUGUCAGUGCCAGCUGUCACUGCUUUCU----GUUA---GCUUGCUUUUUGUUUUGCAAGAAAU-GGGACUGCCUUUGU---------------UCUCU
ABDC01246908.1/22606-22777 AGGA-ACUGACCCAC-AGACACAGUCCCCUGAUGUCCGACCAGAAGACAACGAAAUCCGUGCUGGG-CUGCAGCU----GGUGAGACCU-GUGGCUAGCUUCUGUCUUUGCCAUCUGCCGUGGCUUUG-----AUCC---ACUCGCAUUUAUUUCUGCAAGAAGU-GUGACUUUCUGUCUCUG------AUCUGC-----
ABRR01308492.1/2700-2521   AGGAAAUUGCCCCAC-AAGGAGUUUCCUCUGAUAUCCAACCAGAAGA-AAUGGACUUGGCCCCGGGCCUAAGGGU----AUUUAGAUCUUGUGGCCAGCUUCUGUCCCUGCCAUUGGUCAUUGCUCUUU----GCUCUUUGCUCAUUUUUUGUUUUGUCAGAAAU-GUGACUUUCCUGGUCUC----UAAU----GAUC-
ABRP01086364.1/6242-6067   AGGAAUUUGCCCCAC-AAACAGAUUCCCCCAGUAGCCGAC-AGAGGA-AACGAAAUCCAUGCUGAGUCUGUAGAUCCAUGCUGAGACCCCGUGCCUGGCUUCUGCUGGUGCCAUCUGUCACUGCUUUUU----CUUC-------ACUCCCGAGUUUGCCAGAAAU-CUGGCUGGCUUUGUCUC----UAAUCUGC-----
ABVD01778980.1/534-361     AGGAAUUUGUC-CAC-AGA----UUCCCCUGAGAUCUGACCAGAAGAAAUGAAAAUUGAUGGCAGGUCUGUAGAU----GUUCAGACUUUGCAGCUGGCUUCUGUCA--GCCACCUGUCAUUGCUUUUUAUUUGUUC---ACUUGCUUUGGGUUUUGCAAGUGACUGUCUCUGUCCCUAUUUG------AUCUGC-----
ABRN01129462.1/11991-11826 AGGAGGCUGACCCAC-AGGCAGCUUUCCCCGAUGUCCAACCAGAACA-AAUGGACGUGGUGCUGGGCCUGAGGAC----GUUUAGCCCUUGCAACCGGCUUCCGUCGCUGCCACCUGCCACGGCUCUUU----GCUC-------ACAUUUUAUUUCGCCGGAAAC-GUGAUGUUCUUGGUCUC-----C-----------
AAWR02037340.1/50955-50783 AGGAGUUUGCCCCAU-CAGCAGAUUCCCCUGACAUCCAAC-CG--GA-AGUGAAACCGCUGCUGAGCCUGUGGAU----AUUUGGACAU-GGGGCUGGCUUCCGUCGGUGCCGUCUGUCGUUGGUUUCU----GCUC-----U--CUUCGUGUUUUGCCAGAAAU-GGGACUUUCUGUGUCUCUAGUUGAUCUGC-----
AAFC03122056.1/48365-48540 AGGAUACAGCCCUGC-GGGCAGAUUCCCCCAGUGUCCAACCAGAAGA-AAUGGACCCGGUGCUGGGCCUAAGGAC----UUUCAGACCUUGGUGCCAGCCUCCAUCACUGCCACCUCUCAGGGCUUUUG----GGUC-------ACAUUGUGUUUUGCCGGAAAU-GUGAUUU-CUUGGUCUCUGGGUGAUCUGC-----
AANG01001886.1/47-208      AGGACUUCGCCCCGC-CGACAGGUUCCCC-GACACCCAGC-AGAAGA-AGUGAGAUCCAUACUGAGUCUGUAGAU----GUUUAGACCUUGGGGCCGGCUUCC-CUGGUGCCAUCUGUCAUU--------------C-----U--CUU--UGCUCUGCCAGAAAC-AGGAUUCUCUUUGUCUCUGGCUGAUCUGC-----
AAGU03049869.1/43526-43357 AGGAAUUUGUCUCAC-AAACACAUUCCCCUGAGAUUUAACAAGAAGAAAUAAAAAUCAUUGCUGCAUCUGUAGAU----GUUUAGAUUUUGUGGCUACCCUCUGCCAAGGCCA--UUUCACUGGUUUUU----GUUC---GUUUGCCUUUUGUUUUACAAGAAAC-GUAACUGUCUUUGUCUC-----U------C----
AAPE02047954.1/36234-36403 AGGAAUUUGCCCCAC-AAACAGAUUCCCCUGAGAACCAACCAGAGGA-AAUGAAGUCGAUGCUGAGCCUGUAGAG----GUCUGGCCU--GUGGC-AGCUUCUGCCGGUACCAUGUGCCGUUGCUUUGU----GUUC-------ACUUCGGGUCUUGCCAGAAAC-GUGCCUU--UUUCUCUA--ACUGAUCUGC-----
#=GC SS_cons               :::::::::::::::.:::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::....::::::::::::::::::::::::::::::::::::::::::::::::::....::::...:::::::::::::::::::::::::.:::::::::::::::::.....:::::::.....
#=GC RF                    AGGAauUUGcCCCAC.agaCAGaUUcCCCuGAuguCCaACCAGAAGA.AguGaAauugaUGCUGgGuCUGuaGau....GUuuAGaCcuuGuGGCcaGCUUCUGucguUGCCAuCuGuCAuuGCUUUuU....GuUC...gCUugCuUUugGUUUUGCaAGAAau.GuGaCuuuCUuugUCUg.....gAUCUGC.....
//
# STOCKHOLM 1.0

#=GF AC   RF02157
#=GF ID   NPPA-AS1_2
#=GF DE   NPPA antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   64.20
#=GF NC   56.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.11 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   19671135
#=GF RT   Natural antisense transcript of natriuretic peptide precursor A (NPPA):
#=GF RT   structural organization and modulation of NPPA expression.
#=GF RA   Annilo T, Kepp K, Laan M
#=GF RL   BMC Mol Biol. 2009;10:81.
#=GF WK   NPPA-AS1
#=GF SQ   16


FJ706079.1/38-186          -GUGGAAUUUG-AGGCCUCCCCAAC-CACCUAC-CAAAAAAGGA------GGGUGAAAUGAAAGGAAGAA--GAAAAACUCAGCAUUCUUUCCUCUGACAAAG--AGUAAAACGACAAGGAAUAUCG----GCCUGAAUUCUCUUCCCA-AGAAGAAAGAAAGCACAC--
FJ706073.1/676-824         -GUGGAAUUUG-AGGCCUCCCCAAC-CACCUAC-CAAAAAAGGA------GGGUGAAAUGAAAGGAAGAA--GAAAAACUCAGCAUUCUUUCCUCUGACAAAG--AGUAAAACGACAAGGAAUAUCG----GCCUGAAUUCUCUUCCCA-AGAAGAAAGAAAGCACAC--
FJ706074.1/579-727         -GUGGAAUUUG-AGGCCUCCCCAAC-CACCUAC-CAAAAAAGGA------GGGUGAAAUGAAAGGAAGAA--GAAAAACUCAGCAUUCUUUCCUCUGACAAAG--AGUAAAACGACAAGGAAUAUCG----GCCUGAAUUCUCUUCCCA-AGAAGAAAGAAAGCACAC--
EU326308.1/2841-2989       -GUGGAAUUUG-AGGCCUCCCCAAC-CACCUAC-CAAAAAAGGA------GGGUGAAAUGAAAGGAAGAA--GAAAAACUCAGCAUUCUUUCCUCUGACAAAG--AGUAAAACGACAAGGAAUAUCG----GCCUGAAUUCUCUUCCCA-AGAAGAAAGAAAGCACAC--
FJ706070.1/1262-1410       -GUGGAAUUUG-AGGCCUCCCCAAC-CACCUAC-CAAAAAAGGA------GGGUGAAAUGAAAGGAAGAA--GAAAAACUCAGCAUUCUUUCCUCUGACAAAG--AGUAAAACGACAAGGAAUAUCG----GCCUGAAUUCUCUUCCCA-AGAAGAAAGAAAGCACAC--
FJ706072.1/699-847         -GUGGAAUUUG-AGGCCUCCCCAAC-CACCUAC-CAAAAAAGGA------GGGUGAAAUGAAAGGAAGAA--GAAAAACUCAGCAUUCUUUCCUCUGACAAAG--AGUAAAACGACAAGGAAUAUCG----GCCUGAAUUCUCUUCCCA-AGAAGAAAGAAAGCACAC--
AL021155.1/31063-31211     -GUGGAAUUUG-AGGCCUCCCCAAC-CACCUAC-CAAAAAAGGA------GGGUGAAAUGAAAGGAAGAA--GAAAAACUCAGCAUUCUUUCCUCUGACAAAG--AGUAAAACGACAAGGAAUAUCG----GCCUGAAUUCUCUUCCCA-AGAAGAAAGAAAGCACAC--
FJ706076.1/209-357         -GUGGAAUUUG-AGGCCUCCCCAAC-CACCUAC-CAAAAAAGGA------GGGUGAAAUGAAAGGAAGAA--GAAAAACUCAGCAUUCUUUCCUCUGACAAAG--AGUAAAACGACAAGGAAUAUCG----GCCUGAAUUCUCUUCCCA-AGAAGAAAGAAAGCACAC--
AANU01225053.1/8553-8702   -GUGGAAUUUG-AGGCCUCCCCAAC-CACCCAC-CAAAAAAGGA------GGGUGAAAUGAAAGGAAUAG--GAAAACCUCAGCAUUCUGUUCUCCGACAAAG--AGUAAAAUGACAAGGAAUAUCGAUCGGCCUGAAUUCUCUUCCCCAAGAAGA----AAUCACAC--
ABRT010604666.1/880-723    -CUGCAGUCUG-AAGCUUCCCCACCCUCCACAAAAAAGAGAGGAAG-CCAGGGAGAGACAAAAGGAAAGA-CAAAGAACAGAGCGUUCUUUU-UCUGACAAAG--GGUGAAAUGACAAGGAACAUCA----GGCUGAAUUCUCUUCCCC-UGGAAGCACAGAAAUCACGC
AAFC03122056.1/50630-50773 -------------GUGAACCUAAAACUGCUCCCCCAAACAAGUUA----AUUCCUUUAAAAAAAGAAUGAAAAAGGAACUGAGAAUUCUUCUCUCCAACAAAA--GGUAAAAUGACAAGGAGUAUCA----GGCUGAACUCCCUUCC---GGAAAUGAAAGAAAUCACAC
ABRN01129462.1/9934-9772   GUUCAAUUUUGCUGUGAACCUCUAACUGCUCCC-CAAAAUAAGUUUGUUAUUUUUUUAAAAAAGGAGGAAGAAAAGAACUGAGCAUUAUUCUCUUUGACAAAA--GGUAAAAUGACAAGGACUAUCA----GGCUGACCUCCCUUCCCCAGGAAAUGAAAGAAGUCACAC
AAPY01622222.1/605-466     UUUGAGGUCCC-CGGUCCCCCCACCACACACAUACACACGGAGA------UGGGGAAAUAAAACGAACAA--AAAGAA---AACAUUCUUUUCUCUGACGAAG--AGUAAAGCG-CAAGGAAUAUCA----GACCGAAUUC---------AGAAAUGACAACGCAAUC--
AAGV020236958.1/2975-2821  -CUGUAGUUUG-AGGAAAAUAAUAAUUUUAAAAAGAAGGGAGGG-----CAAGGGAAACAGAGGGAUGAAGGAGGAAACGGGGCAUUC-UCU--CUGACAAAGGAGAUAAUAUGACAAGGAAUAUUG----GACUGACUUCUCUUCCCC-UGAAAACGAAAGAAUCACAC
FJ706077.1/132-264         -CUCAACUCUG-GGGAAUGCUACCAUUUUUUUUCCAAAGUAGAA------AGGAAGCAC---------UU--CUGAGCCAGUGAC-------CACUGA--AAG--AGUAAAACGACAAGGAAUAUCG----GCCUGAAUUCUCUUCCCA-AGAAGAAAGAAAGCACAC--
ABGA01237639.1/4835-4980   -GUGGAAUUUG-AGGCCUCCCCAAC-CACCCAC-CAAAAAAGGA------GGGUGAAAUGAAAGGAAGAA--GAAAAACUCAGGAUUCUUUCCUCUGACAAAG--AGUAAAACGACAAGGAAUAUCG----GCCUGAAUUCUCUUCCCCAAGAAGA----AAUCACAC--
#=GC SS_cons               .::::::::::.:::::::::::::::::::::.::::::::::......::::::::::::::::::::..:::::::::::::::::::::::::::::::..::::::::::::::::::::::....::::::::::::::::::.::::::::::::::::::..
#=GC RF                    .gUGgAaUuUG.aGGccucCccaacuuaCccac.cAAaaaAGGa......ggGugaaAugAAAGGAagaa..gaaaAACugaGcaUUCUUuuCUCUGACAAAG..aGUAAAAcGACAAGGAaUAUCg....GcCUGAaUUCUCUUCCCc.aGAAgaaAgAaagcaCAC..
//
# STOCKHOLM 1.0

#=GF AC   RF02158
#=GF ID   NPPA-AS1_3
#=GF DE   NPPA antisense RNA 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   55.00
#=GF TC   55.70
#=GF NC   43.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.11 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   19671135
#=GF RT   Natural antisense transcript of natriuretic peptide precursor A (NPPA):
#=GF RT   structural organization and modulation of NPPA expression.
#=GF RA   Annilo T, Kepp K, Laan M
#=GF RL   BMC Mol Biol. 2009;10:81.
#=GF WK   NPPA-AS1
#=GF SQ   24


FJ706078.1/185-292         UUAGAAAAGGAA-AAUACAGGGA-AAGGGAUAAACCUCACUGACUUGGAGGAAAUCAAGAGGAGUGAGCACAGCAUCAGAAAGCCCCCUGG--CCCCAGACUGCACCCGCUU-----
FJ706071.1/1365-1472       UUAGAAAAGGAA-AAUACAGGGA-AAGGGAUAAACCUCACUGACUUGGAGGAAAUCAAGAGGAGUGAGCACAGCAUCAGAAAGCCCCCUGG--CCCCAGACUGCACCCGCUU-----
EU326308.1/4734-4841       UUAGAAAAGGAA-AAUACAGGGA-AAGGGAUAAACCUCACUGACUUGGAGGAAAUCAAGAGGAGUGAGCACAGCAUCAGAAAGCCCCCUGG--CCCCAGACUGCACCCGCUU-----
FJ706070.1/1488-1595       UUAGAAAAGGAA-AAUACAGGGA-AAGGGAUAAACCUCACUGACUUGGAGGAAAUCAAGAGGAGUGAGCACAGCAUCAGAAAGCCCCCUGG--CCCCAGACUGCACCCGCUU-----
AL021155.1/32956-33063     UUAGAAAAGGAA-AAUACAGGGA-AAGGGAUAAACCUCACUGACUUGGAGGAAAUCAAGAGGAGUGAGCACAGCAUCAGAAAGCCCCCUGG--CCCCAGACUGCACCCGCUU-----
AY091942.1/141-34          UUACAAAAGGAA-AAUACAGGGA-GAGGGAUAAACCUCAUUGACUUGGAGAAAAUCAAGAGGCGUGAGCACAGCAUCAGAAAGCCCCGUGG--CCCCAGACUGCACCCGCUU-----
AY091943.1/140-34          UUGACAAAGAAA-AAUACAAGGA-AAGGGAUAAGCCUCAUUGACUUGGAGAAAAUCAAGAGGAACGAGAACAGCAUCA-AAAGCCCUCUGG--CCCCAGACUGCACCCACUU-----
AAPY01145649.1/1356-1249   UUACAAAGGGAA-AACACAAGGA-AAGCGAGAGGCCUCAUUGACUUGGAGAAAAUCAAGAGGAGUGGGCUCAUUAUCAGGAAACUCCCUGG--CCCCAGAGUGUGUCCCCUC-----
ABDC01246909.1/2306-2412   UUACAAAAGGAA-AAUACAAGGA-AAGCGAGAGGCCUCGCUGACUUGGGGGAAAUCGACAGGAAUGGGCACAGUGUCAGAAAGCCCCC-GA--CCCCAGACCGUGCCCCUUC-----
ABRQ01214571.1/1660-1553   UUACAAAAGGAA-AAUAUAGGGA-AAGGGACAAGUGUCAUGAGCUUGGAGAAAAUCACCAGAAAUUGGUGCAGUAUAACAAAGCCCCUUGA--UCCCAGACUGAGCCCCCUU-----
AAGV020236958.1/1611-1510  UUACAAAGGGAA-AAUACAG-------GGAGAGAGCUCACCGACUUAUGGAAAAUCAACAAGAAUGGGCCCAAUGUCAGAAACCCCCCUGG--UACCAGAAUAAACCCCUUU-----
AAQQ01592265.1/465-357     UCACAAAAGGAA-AAUACAGGGGGAAGGGAGGGGUCUCGUUGACUUGGAGAGAAUGGAAAAGAACCAGCCCAGCACUGGAAAGCCCCCUGG--UGCCAGGCUGUACCUCCUU-----
ABRO01208187.1/2088-1976   UAAAAAAAAAAA-AAAACAGGGA-AAGGGAGAGACCUCACUGAUCCAGAGAAGAUGGAGAGGAGGAGGCCCAGUACCAGAAAGCCUCCCGC--UUCCUAUCUGGGUAUCCCCCGCUU
AAIY01668037.1/2126-2233   UGACCAAAAGGA-AACAGAGGGA-GAGGGGGAGGUCUGAGGGGCUUGGAGAAAAUCAACAGGAAUGGGCACGGGGUCUGAAAGCCUCUUGG--UCCCCGGCUGAGCCCCCUC-----
AANG01623314.1/1406-1492   UUACAAAAGGAA-CACACAGGGA-AAGGGAGAGGUCUCAGUGACC---------------------GGCACAGUGUCACAAAGCCCCCUGG--UCCCAGACUGUGGCCCCUG-----
ABRN01129462.1/8607-8523   UUACAAAAGGAA-AACA--GGGA-AAGGGAGACGUCUCACUGCCU---------------------GGCACAGCAUCACAAAGCCCCCUCA--UCCCAGACCGUGCCCCUUU-----
AAYZ01228997.1/939-1047    UCACCGAGGGAA-AACAUAGAGG-AGAGGAACAUGCUCAUUGACUUGGAGAAAAUCGAGGGGGAAGAGCA-AGGAUCCAAAAGCCCCCGGGAGCCCCCCACUUCUUAGUCCU-----
AAFC03122056.1/51940-52022 UUACAAAAGGAA-AACA--GGGA-AAGGGAGAGGUCUCGCUGCCU---------------------GGCACAAUGUCACAA--CCCCCUCA--CCCCAGACCAUGCCGCUUC-----
AANN01240314.1/1823-1741   UUACAAAAGGAAAAACACAGGGA-AAUGGAGAGGUCUCAC-------------------------GUGCACAGUGUCACCGAGCCUCG-GG--UCCCAGGCUGUGCCCCCUG-----
AF037465.1/1047-967        UUACAAAAGGAA-AA----UGGA-AAGGGAGAAGUCUCGCUGCCU---------------------GGCCCAAUGUCACAA--CCCCCUCA--CCCCAGACCAUGCCGCUUU-----
AAEX03001913.1/36710-36624 UUACAAAAGGAA-CACACAGGGA-AAGGGAGAGGUCUCACUGACC---------------------GGCACAGCAUCACAAGGCCCCCUGG--CCCCACACUGUGGCCCCUG-----
AAGU03049869.1/39998-39891 UUACAAAAGGAA-AAUACAGGGA-AAGGUAAAGUUCUCAUGGGCUUGGAGAAAAUCACCAGAAAUAGGCACAGUAUCAGAAAGCCCCUUGG--UCCCAGGCUAAGCCCCCUU-----
AAQR03101503.1/11261-11368 UUACAAGAGGAA-AAUACAAGAA-AAGGGAGCGGUCUCACUGAUUUGGGGGGAACCAAGUGGAAUGAGCACAGUAGCAGAAAGCCCCCUGG--UCCCAGACUGUGCCCCCUU-----
AAGW02066754.1/41645-41540 UUACCAAAGGAA-AACACAAGGA-AAAGGAGAGUGCUCACUGACUUGG-GCAAAUCGAGAGGAACGGGCG-AGUAUCUAAAAGCGCCCCGG--CCCCAGACUGUGCCCCCCU-----
#=GC SS_cons               ::::::::::::.::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..:::::::::::::::::::.....
#=GC RF                    UuAcAAAAGGAA.AAuACAGGGA.AAGGGAgAGguCUCAcUGaCUUGGAGaAAAUCaAgaGGAauGgGCaCAGuAUCagAAAGCCCCCuGG..uCCCaGaCUGugcCccCUu.....
//
# STOCKHOLM 1.0

#=GF AC   RF02159
#=GF ID   PART1_1
#=GF DE   Prostate androgen-regulated transcript 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   65.00
#=GF TC   70.50
#=GF NC   53.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.48 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10706094
#=GF RT   PART-1: a novel human prostate-specific, androgen-regulated gene that maps
#=GF RT   to chromosome 5q12.
#=GF RA   Lin B, White JT, Ferguson C, Bumgarner R, Friedman C, Trask B, Ellis W,
#=GF RA   Lange P, Hood L, Nelson PS
#=GF RL   Cancer Res. 2000;60:858-863.
#=GF WK   PART1
#=GF SQ   22


AC091922.2/130372-130588     AAACAGCCUCCUUCAAAAUGCAGCUU-GACUGUGAUUCA-UGGCACAAAG----------------------------------CUGGAAUAACCCUGCCAGUUCU------UAGAAGCUUU--AAGAUUCAUCGUCUUGAACUUGAUACAC-AUAGUA-UAGCACCUUAAAAA-CGAAUCAUCUGCUAG-UUCAGUAUUUUCUACUUACAAUCA--CUCCCUCCCAGGGCAUGUAAUUAAUUUACUGAGCUUAAAAAAAAAAUAUC--
AANU01256163.1/30636-30420   AAACAGCCUCCUUCAAUAUGCGGCUU-GACUGUGAUUCG-UGGCACAAAG----------------------------------CUGGAAUAACCCUGCCAGGUCU------UAGAAGCUUU--AAGAUUCAUCGUUUUGAACUUGAUACAC-AUAGUA-CCGUGCCUUAAAAA-CGAAUCAUCUGCUAG-UUCAGUAUUUUCUACUUACAAUCA--CUCCCUCCCAGGGCAUGUAAUUAAUUUACUGAGCUUAAAAAAAAAAAAAA--
ABDC01308808.1/2945-3163     GAACAGCCUCCUUCAAAAUGCGGCUUUGACUGUGAUUCA-UGGCAAAAAA--------------------------------G-CUGGAAUAACCCUGCCAAGUCU------UAGAAGCUUU--AAGAUUCAUCGCAUUGAACUUGAUACGU-AUAGUA-CAGCACCUUGAAAA-CAAAUCAUCUGCUAG-UUCAGUAUUUUCUACUUACAAUCA--CUCCCUCCCAGGGCAUGUAAUUAAUUUACUGAGCUUA-CAAAAAAAAAGUC-
AAWR02016308.1/97678-97462   GAACAUCCUCCUUCAAAAUGCAGCUU-GACUGUGAUUCA-UGGCAAAAA----------------------------------GCUGGAAUAAUCCUGCCAGGUCU------UAGAAGCUUU--AAGAUUAAUAGCAUUGAACUUGAUACAU-AUAAAA-CAGCACCUUGAAAA-UGAAUCAUCUGCUAA-UUCAGUAUUUUCUAAUCACAAUCA--CUCCCUCUGGGGGCAUGUAAUUAAUUUACUGAGUUUAAAAAAA-AAGUCAG-
ABRN01417205.1/12794-13010   GAAGAGCCUCCUUCAAAAGGCAGCUU-GCCUGUGAGUCG-UGGCAAAAA----------------------------------GCUGGAAUGACCCUGCCAGGUCU------UAGAAGCUUU--AAGAUUAACUGCAUUGAACUUGAUACAU-AGAAAA-CAGCACCUUGAAAA-UGAAUCAUCUGCUAC-UUCAGUAUUUUCUAAUUGCAAUCA--CUCCCUCUCGGGGCAUGUAAUUAAUUUACGGAGUUUAAAAAAAAGAAGUC--
ABRP01041883.1/67973-68187   GAACAGCCACCUUCAAAAUGCAGCUU-GAUUGUGAUUCA-UGGCAAAAA----------------------------------GCUGGAAUAACCCUGUCAGGUCU------CAGAAGCUUU--AAGAUAAAUCGAAUUGAACUUGUUACAC-AUAAAA---GCACCUUGAAAA-UGAAUCAUCUGCUAA-UUUAGUAUUUUCUAAUUACAAUCA--CUCUCUUUCAGGGCAUGUAAUUAAUUUACUGAGUUUAAAAAAAUAAGUCA--
ACBE01026868.1/548-764       GAACAGCUUCCUUGAAAAUGCAGCUU-GACUGUGACUCG-UGACAAAAAU----------------------------------CUCAAAUAACCGUGCCGGGUUU------UACAAGCUUU--AAGAUUAAUUGCACUGAACUUGAUACAU-AUAGUA-UAGCACCUUGAAAA-UGAAUCAUCUGCUAA-UUCAGUAUUUUCUAAUUACAAUCA--CUCCCUCCUGGGGCAUGUAAUUAAUUUACUGAGUUAAAAAAAAAAAGAGU--
AAGV020014918.1/385-600      GAACAGCCUCCUUCAAAAUGCAGCUU-CACUG--AUUCA-UGGCAAAAA----------------------------------GCUGGUAUAAGCCUGCCAGGUCU------UAGAAGCUUU--CAAAAUAAUCAUAUUGAACUUGAUACAUUAGAGUA-CAGCACCUUGAAAA-UGAAUCAUCUGCUAG-UUCAGUAUUUUCUAAUUACGAUCA--CUCCCUCUCAGGGCAUGUAAUUAAUUUACUGAGCCAAAAAAAAAAAAAAA--
AAKN02031374.1/128127-127912 AAACAGCCUCCUCCAAAAUGCAGCUG-GACUGUGAUCCA-UGGCAAAACA----------------------------------CUGGAAUAACUCUGCCAGGUCC------UAGAAGCUUU--AAGAUUCAUCCCAUUAAACUUGAUACAU-ACA--A-CAGCACCUUGAAAA-CGAACCAUCUUCUGGGUUCAGUGUUUUCUCCUUAUAAUCA--CUCCCUCCCAGGGUAUGCAAUUAAUUUACUGAGCUU--UAAAAGAAAAAGUC
AAFC03014129.1/106097-106319 GAAGAGCCUCCCUCAAAAUACAGCUU-GACUCUGAUUCG-UGGCAAAAAAUA----------------------------AAAGCUGGAAUAAUCCUGCCAGGUCU------UAGAAGCUUU--ACGAUUAAUUGCAUUGAACUUGAUACAC-AGAAAA-CAGCACCUUGAAAA-UGAAUCAUUUGCUAC-UUCAGUAUUUUCUAAUUACCAUCA--CUCCCUCUUGGGGCAUGUAAUUAAUUUACGGAGUUUUAAAAAAAAAAAAA--
AAIY01345145.1/574-792       GAACAGCCUCCUUCAAACUACAGCGA-GAUUGCGAUGCA-UGGGCCAAC----------------------------------CCUGGAAGAACCCUGCCAGCUCU------CAGAAGCGUU--AAGAUUAAUCUUACUGCCCUUGAUAGAU-AUAGUG-CAGCACCUUGAAAA-UGAAUCAUCUGCUAG-GUCGGUAUUUUCUAAUUACAAGCA--UUCCCUCUCGGGGCAUGUAAUUAAUUUACUGAGUUUGGAGGAAAAAAAAAUC
AAHX01012898.1/11486-11277   -GGCCGGCUGCCUUCAAAUGCAGCUU-GGCUGUGACACA-CAGUGGGAAAA-------------------------------AGCAGGACUAACCCUGCCAGGUCC------UAGAAGCUUU--CAGAUUCAUCGCAUAGAAUUUGAUACAU-ACGGCA-AAGCACCUUGAAAA-UGAAUCAUCU----------GUAUUUUCUCCUUACAAUCA--CUCCCUCCCAGGACAUGUAAUUAAUUUCCUGAGCUUUGAAAAAAAAAAUC--
AAYZ01152318.1/1360-1586     AAACAGCCUCCUUCAAAG-GCAGCUU-GACUGUAAUUCA-UAGCAAAAGACUGGGGG------------------AAAAGAAAAAAAUAAAAAAC-CACCAGAUCU------UAGAAGCCUUAGAAGAUUCAUGGCAUUGAAUUUGAUACAG-AUAGCA-CAGCACCUUGAAAA-CGAAUCAUCUGCUAG-UUCAAUAUUUUCUACUCACGAUCA--CUCCCUCCCAGGGCAUGUAAUUAAUUUACUGAGUUUUUUGUAUU--------
ABRO01092102.1/1509-1733     GAACAGCCUCCUUCAAAAUGCAACUU-GACUGUGAUUCA-UGGUAAAAAAAAAU------------------------UAAUAAUAAUAAUAAAUGUACCAGGUCC------UAGAUACUUU--CAGAUCCGAG---UUGAACUUGAUACCA-GCAGUAAUAGCACCUUGCAAA-GGAAUUACCUGCUAG-UUUAGUAUUUUCUUCUUACAAUCG--CUCCUUCUCUGGGCAUGGAAUUAAUUCACUGAGCUUUAUAAACAGACAAA--
AANN01089400.1/83-306        GAACAACUUCCUUCAAAAUGCAGUUG-GUCUGUGAUUAA-CAGCCAAAAA--------------------------------AAAAAUAAUAACCUUGCCAGAUCCAGAUCACAGAAGCUUU--AAGAUUAACUC--UUGAACUAGAUUCAUAAUAGAA-CAGCAACUCAAAAG-UGAAUCAUUUGCUAA-UUCAGUCCUUACUAAUUAUAGUCA--CUCCCUCUCAGGUCAUGUAAUUAACUUAUUGAAUUCAAAAAAAAAAAAAA--
AC164877.2/47534-47729       -----------UAACAAAUGC--CUC-CAACG-GGCA-G-CUGUGAGGAAG-------------------------------AGCAAGACUAACCCUGCCAGGUCC------UAGAACCUUU--CAGAUUCACCGCGGUGAAUUUGA-ACAU-AAGGCA-AAGCACCUUGAAAAAUGAAUCAUCU----------GUAUUUUCUCCUUAUAAUCA--CUCCCUCCCGGGGCAUGUAAUUAAUUUCCUGAGGUUUGAAAAAAAAAAAA--
ABVD01115871.1/324-573       UAACAGUCUCCUUCAAAAUGCAGCUU-AACUG--AUUCA-UGGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGCUGGAAUAAGCCUGCCAGGUAU------UAAAAGCUUU--AAAAUUAAUCAUCUUGAACUUGAUACAAUAUAGUA-CAGCACUUUGAAAA-UGAAUCAUCUGCUAG-UUCAGUAUUUUCUAAUUACAAUCA--CUCCCUCUCAAGGCAGGUAAUUAAUUUAUUGAGCUUUAAAAAAAAAAAAA--
AALT01573415.1/1412-1628     GAACAACCUCUUGCAAAAUGUAGCUU-AACCAUGAUUCA-UGGCCAAAA----------------------------------GCUGGAAUAACCCCUGCCAGGCU------UAGAAUCUUU--AAGAUUAAUUGCAAUGAACUUGAUGCAUAAUAGUA-UAACACCUUGAAAA-UGAAUCAUUUGCUAA-UUCCAUAUUUUUUAAUUACAAUCA--CUUCAUCUCAGGGCAUGAAAUUUAUUGA-GGUUUUUUUUUUUUAAAGAAA--
AAPE02000884.1/57722-57506   GAACAGCCUCCUUCAAAAUGCAGCCU-GAUUGUGAUUCA-UGGCAAAAA----------------------------------GCUGGAAUAGCCCUGCCAGGUCG------UAGACGCAUU--AAGAUAAAUUGCAUUGAAUGUGAUACAU-AUAAAA-CAGCACCUUGAAAA-UGAAUCAUCUGCUAA-UUCAGUAUUUUCUAAUUACAAUCA--CUCCCUCUCAGGGCAUGUAAUUAAUUUACUGAGUUUAAAAAAAAAAAAAA--
AAQR03013098.1/45670-45460   CAGAUGCAUCCUUCCAAAGGCAGCUU-AACUGUGAUUCA-AGGCGAAAGC----------------------------------CUGGAAUAACCCUGCCA------------AGAAGCUUU--AAGAUUCAUCACAUCGAACUUGAUACAU-ACAGUA-CAGCACCUUGAAAA-CAAAUUAUCUGCUAG-UUCAGUAUUUUCUACUUAUAAUCA--CUCCCUCCCAGGGCAUGUAAUUAAUUUACUGAGCUUACCAAAAACAAAAA--
AAGU03021008.1/72468-72679   GAACAGCCUCCUUCAAAAUGCAGC-----UUGUAAUUC--UGGCCAAAA----------------------------------GCUGGAGUAACCCUGCCAGAUCU------UAAAAGCUUU--ACGAUUAAUCAUUCUGAAGUUGAUACAU-ACAGUA-UAGCACCUUGAAAA-UGAAUCAUCUGUUAG-UUCAGUACUUUCUAAUUACAAUCA--CUCCCUCUCAGGGCAGGUAAUUAAUUUAUUGAGUU--AAAAAAAAAAAAGUC
AAEX03001456.1/461656-461879 CAACAGCCUCCCAGAAACAGCAGCUU-GCCCGUGACCCCGUGGCACCAA----------------------------------GCUCCAAUAACCCUGCUGGGCCUUC--CAAGCAAGCUUC--AAGAGUCGUUGCCCUGAACUUGAUACAU-AGAGCA-CAGCACCUCGAAAA-UGAAUCAUCUGUUAA-GUCAGUAUUUUCUAAUUGCAAUCACUCUCCCUCUCAAGGCAUGUAAUUAAUUUACUGAGGUGUUUUUUUUUUUUUU--
#=GC SS_cons                 ::::::::::::::::::::::::::.::::::::::::.::::::::::.................................:::::::::::::::::::::::......::::::::::..::::::::::::::::::::::::::::.::::::.::::::::::::::.:::::::::::::::.::::::::::::::::::::::::..::::::::::::::::::::::::::::::::::::::::::::::::::..
#=GC RF                      gAACAGCCUCCUucAAAauGCAGCUu.gacUGUGAuuCa.UGGcaaaAaa.................................gcuggAaUAAcCcUGCCaGgUCu......uAGAAGCUUU..aAGAUUaAucgcauUGAAcUUGAUaCAu.AuAGuA.cAGCACCUUGAAAA.uGAAUCAUCUGCUAg.UUCaGUaUUUUCUaaUUACaAUCA..CUCCCUCuCaGGGCAUGuAAUUAAUUUACUGAGuUuuaaaaAaaaAaaaa..
//
# STOCKHOLM 1.0

#=GF AC   RF02160
#=GF ID   PART1_2
#=GF DE   Prostate androgen-regulated transcript 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   55.00
#=GF TC   57.10
#=GF NC   48.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.90 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10706094
#=GF RT   PART-1: a novel human prostate-specific, androgen-regulated gene that maps
#=GF RT   to chromosome 5q12.
#=GF RA   Lin B, White JT, Ferguson C, Bumgarner R, Friedman C, Trask B, Ellis W,
#=GF RA   Lange P, Hood L, Nelson PS
#=GF RL   Cancer Res. 2000;60:858-863.
#=GF WK   PART1
#=GF SQ   29


AF163475.1/147-396           -UCGUA-CGCU-GGGCUAUAAUCUAUGAAA-CUGAGCUCCAGAGCCAGCCAAUCACUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCACUGGAACAACACAGAUGAG-AUAUUCUACACAUUAAUCUACUUAUCUGGAAUCACUUUGCCUCUAAAGG-CCAGAG---------------------------------AAAAAUCACAGCUUC-CUUGUCG-GAGGGGAAAA---GGACAGGUGAUCUGGGGAAAACGCAGC-UACACCUGGAGCAA---------------------
ABRT010140880.1/200-455      -UCGUA-CGCU-GGGCUAUAAUCUAUGAAA-CUGAGCCCCAGAUCCAACCAAUCACUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGUGCUGGAAAAACAUAGAUGAG-AUAUUCCACACAUUAAUCUGCUUAUCUGGAAUCACUCUGCCUCAAAAGG-CCAGAGGAA---------------------------AAAAAAAAUCACAGCUUC-AUUGUCU-GGGGGGAAAA---GGACAGGUGAUCUGGGAAAAUCACAGC-UACAACUGGAGCAA---------------------
ABRP01041883.1/68336-68581   -UCGUA-CGCC-GGGCUAUAAUUUAUGAAA-CUGAGCCCCAGAUCCAGCCAAUCACUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCACUAGAACAACAAAGAUGAG-AUAGUCCACACAAUAAUCUGCUUAUCUGGAAUCACUUUCCUUCACAAGA-CCAGGG---------------------------------AAAAAUCACAGCUUC-AUUGACU-GAAGAAAG------GACAGAUGGCCUGGGAAAA-UGCAAC-UACACCUGGAGCAA---------------------
AAGV020014918.1/753-1001     -UCGUC-UGCC-GGGCUCUAAUUUAUGAAA-CUGAGCCCCAGAUCCAGCCAAUCAUUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCACUAGAACAACAUAGAUGAG-AUAUCCCACACAAUAAUCUGCUUAUCUGGAAUUGCUUUCCCCCUCAAGG-CCAGAG---------------------------------UAAAAUCGCAGCUUC-AUUGUCU-GAGGGAAGAA---GGACAGGUGACCUGGAAAAA-CGUGAC-AGUACCUGGAGCAC---------------------
AALT01573415.1/1789-2039     -UUGUA-UGCUUGGGCUAUAAUUUAUGAAA-CUGAGCCCCAGAUCCAGCCAAUCAUUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCACUAGAACAACAAAGAUGAG-AUAUUCCACACAAUAAUCUGCUUAUCUGGAAGAACUUUCCCUCGAAAGG-CCAGAG---------------------------------AAAAAUCACAGCCCCCAUUGUCU-GAGGAAAGA----GAAUAGAUGAACUGGGAAAAACGCAAC-UCUACCUGGAGACA---------------------
ACBE01026868.1/915-1163      -UAGUG-CACG-GGGCUAUAAUUUAUGAAA-CUGAGCCCCAGAUCCAGCCAAUCACUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------ACUGCACUAGAACAACAAAGAUGAG-AUAUUCCACACAAUAAUGUGCUUAUGUGGAAUCACAUUUCCCUGCAAGG-CCAGAG---------------------------------AAAAAUCACAGCUUC-GCUGUCG-GAGGGAAGGA---GAACAGAUGACCUGGAAGAA-UGUGAC-UAGAUCUGGAGCAA---------------------
AAWR02016308.1/97316-97067   -UCGUA-CGCU-GGGCUAUAAUUUAUGAAAACUGAGCCCCAGAUCCAGCCAAUCAUUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------ACUGCGCUAGAACAACAACGAUGAG-AUAUUCCACACAAUAAUCUGCUUAUCUGGAGUCACUUUCCCUUGCCAGG-CCAGAG---------------------------------AGAAAUCGCAGCUUC-AUCGUCU-GAGGAAAGGA---GGACAGAUGACCCUGGAAAA-CGCAAC-GACACCUGGAGCAA---------------------
AAPY01139042.1/5491-5735     -UCGUAAUGCU-GGGCUAUAAUCUCUGAAA-CUGAGCCCCAGAUCCAACCAAUCAUUUGGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------ACUGUACUGGAACAACACAGAUGAG-AUAUUCCCCACAAUAAUCUGCUUAUCUGGAAUCACUGUGCCUCAAAAGG-ACAGAG---------------------------------AAAAUUUACAGCUUC-AUUGUCU-GAGGGAAG------GACAGGUGA-CUGGGAAA--CACAAC-AGCACCCAGAGCAA---------------------
ABRR01161449.1/90-338        -CCGUA-CGCU-GGGCUGUAAUUUAUGAAA-CUGAUCCCCGGAUCCAGCCAAUCACUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCAGAAAGG--------GCUGCACUAGAGCAACAAGGAUGAG-AUAUUCCACACAACAACCUGCUUAUCUGGAAUCACUUUCCCUUGCAAGG-CCAGAG---------------------------------AAAAAUCCCAGCUUC-AUUGUCU-GAGAGAAGCA---GGACAGAGGAGCUGCAGAAA-UGCGAC-UUCACCUGGAGUCU---------------------
ABVD01115871.1/726-963       -CCGAA-CGCU-GGGCUAUAAUUUAUGAAA-CUGAGCCCCAGAUCCAGCCAAUCACCUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCACUAGAACAACAUAAAUGAG-AUAUCCCACACGAUAAUCUGCUUAUCUGGAAUCACUUUCCCUC-CAAGG-CCAG--------------------------------------------AGCUUCAUUUGUCU-GGGGGAAGAA---GGACAGGUGACCUGGGAAAA-CACGAC-AAUACCUGGAGCAA---------------------
AAFC03014129.1/106476-106722 -UCGUA-CGCU-GGGCCAUAAUUUAUGGAA-CUGAGCCCCAGAUCCAGCCAAUCAUUUAGCU----CCUCAUAACAAGUCUGA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCACUAGAACAACAGAGAUGAG-AUAUUCCACAUAACACUCAGCUUAUCUGGAAUCACUUUCCCUUGCAAGG-CCAGAA---------------------------------AAAAAUCAUAGCUUU-ACUGCCC-AAGGGAAGCA---CGACAAAGGA-CUGGGAAA--UGCGAC-UUCACCUGGAGCAA---------------------
AANN01089400.1/464-710       -UCGUA-UGCU-GGGCUAUAAUUUAUGAAA-CUGAGCCACAGUCCCAGCCAAUCAUUUAGCU----UCUCAUAACAAGUCUAAACUGGCUCUGGAAAGCUGAAAAG--------GCUGCACUAGAACAACAAAGAUGAG-AUAUUCUGCACAAUGAUCUGCUUAUCUGGAAGUGCUUUCCCUCGAAAGG-CCAGAG---------------------------------AAAAAAUAUAGCUUC-ACUGUGU-GAGGGAAG------GACAGAUGAUUUGGGGAAA-UAGGAC-UCUGUGUAGAGCAG---------------------
ABRQ01140638.1/74-319        -UUGUA-CGCU-AGGCUGUAAUUUAUGAAA-CCGAGCCCCAGACCCAGCCAAUCAUUUAGCU----CCUCAUAACAAGUCUAA-CAGGCUCGGGAAAGCUGGAAGG--------GCUGUGCUAGAACAACAUAGAUGAG-AUAUUUUGCACGAUAAUCUGCUGAUCUGGAGUCGCUUUCUCUCCCGAGG-CCAGAG---------------------------------AAAAAUCACAGCUGC-AUUGUCU-GGAGGAAG------GACAGGUGACCUGGGAAGA-GACAGC-AGCACCUGGGACGA---------------------
AAKN02031374.1/127766-127522 -UCAAC-UGCC-GGGCUAUAAUCUAUGAAA-CUGAGCCC-AGAUCCAGCCAAUCAGUUUGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCACUGGAGCGGCAUAGAGGA-UAUACUCCACACAGCAAUCUGUUUAUCUAGAAUCACUCUGCCUGGAAAAA-AUGGAG----------------------------------AAAAUCACAGCUUC-AGUAUCU-GAGGGGAG------GACAGGUGAUCUGGCAGAAACACAUC-UGAACCUGAAGCAG---------------------
AAIY01345145.1/935-1179      A-UGUA-CGCC-GGGCUGUCAUUUAUGAAA-CUGAGCCC-AGAUCCAGCCAAUCGUUCACCU----CCUCAUAACAAGUCUAA-CUGGCUCGGGGAAGCUGAAAGG--------GCUGCACUAAAAUAACAUAGAUGAG-AUAUUUCGCAUGAUAAUCUGUUGAUCUGGACACACUCUCCCUCUCGGGG-CCAGAG---------------------------------AAAAAUCACAGCUUC-AUUGUGU-GGAGGAAG------GACAGGUGACCCUGGAAAA-GAUGGU-AGCCCCCGGAGCAA---------------------
AAYZ01152318.1/1751-1998     -CUGGA-CGCU-UGGCUAUAAUCUCCGAAA-CGGAGUCCCAGCCCCAGCCAAUCACUCAGCU----CCUCUUAACAAGUCUAA-CUGGCUCUGGGAAGCUGAGCGG--------GCUGCGCUGGAACA-CAGAGAUGAG-AUAUUCCACACAAUAAUCUGCUUAUCUGAAAUUGCUUUGCCUGAAGAAA-CCAGAG---------------------------------AGAAGGCACAGCCUC-AUUGUCU-GGGGAGAAAAAAGAGGCAGGUGAUCCCGGGGGGAAACG-----CACCUGGAGCAA---------------------
ABRO01092102.1/1891-2146     -CCGAC-CGCA-GGGCUAUAAUCUAUGAGA-CUGAGCGC-AGAUCCAGCCAAUCAGUCAGCU----UCUCAUAACUAGUCGAA-CUGGCUCUGGAAAGCUAAAGGGUUCUCUCAGUUGCACUGGAGCAAGGCAGAUGAG-AUAUUCCACA-AAUAAUCUGCUUAUCUACGCUCACUUUGCCUCGUAAGG-CCAGAG---------------------------------AAAAAUCACAGUUUC-AUUGUCU-GAAAGAAGAA---AGACAGAUGAUCUGGCAAAA----------------------AAAAAAAAAAAAAAAGACUUA
AAHX01012898.1/11143-10891   -CCAAC-CGCC-GGGCUAUAAUCUAUGAAA-CUGAGCCC-GGAUCCAGCCAAUCAGUUAGCU----CCUCAUAACAGGUCUAA-CUGGCUCUGGACAGCUG-AAGG--------GCUGCGCUGGAGCACAGCAGAGGAGUAUACUCUCCACAACA--CUGCAUGUCUACAGUCACUUUGCCUGCAAAGG-CCAGAGGG----------------------------GGAAAAAUUCACAGCUUC-AUUGUCU-CGGGGAGGGA---GGACAGGUGAUCUGGCACAGACGGAGUCCGAAGCUGGAGCAA---------------------
ABQO010933014.1/746-990      G-UGCA-AGGC-GGGCCAUAAUUUAUGAAA-CUGAGCUCCAGUCUCAGCCAAUCACUUAGCU----UCCCAUAACAAGUCUAA-CUGGCUCAGAAGAGCUAGCUGU--------GCCGCAAUAAAACCACAUGGAGGAG-AUAUCCCACUUGAUAAUCUAUUUAUCUGGGCUCGAUUUCUGGCAGGGAGGCCAAAG---------------------------------AGAAAUUCUAACUUC-AUUGUCU-UCAGGGAGGG--AGGGCAGAUGACCUGCGUCAG--------UAAAACUCGAGCAC---------------------
CT030256.13/47989-48243      -CCAAC-CGCU-GGGCUAUAAUCUAUGAAA-CUGAGCCG-GGAUCCAGCCAAUCAGUUAGCUAGCUCCUCAUAACAGGUCUAA-CUGGCUCUGGACAGCU--AAGG--------GCUGCGCUGGAACACAGCAGAGAAG-UGACUCUACACAACA--UUGCAUAUCUACAGUUACUUUGCCUGCAAAGA-CCAGAGAGG--------------------------GGAAAAAAAUCCCAGCUUC-AUCAUCU-CGGGGAGGGA---GGACAGGUGGUCUGGCACAG-ACCGAG-UGAGUCUGAGGCUG---------------------
AAFR03035516.1/49349-49592   -UAGGG-UGCC-AGGCCAUAAUUUAUGAAG-CCGAGCUCCAGCCUCAGCCAAUCACCUAGCU----GCCCAUAACUAGUCUAA-CUGGCUCAGAGGAGCUAGCUGU--------GCUGCAAUAAAGCCACAUGGAGGAG-AUAUCCCACCUGAUAAUCUGUUUAUCUGGGCUGCCUUUCUGUGGGAAGG-CCAAAG---------------------------------AGAAAUCCUAACUCC-AUUGUCU-GCAGGGAGGG--AGGACAGAUGACCUGCGUCAA--------UAACACUGGAGCAC---------------------
AC187109.2/187194-187417     A-UGCA-UGCU--GGCUAUAAUUUAUGAAA-CGGAGCCCAGGAAACAACCAAUCAGUUAGCU----CCUCCUAACAAGUCCAA-CUGGCUACGAAAAGCUGGAAGU--------GCGGCGC-AGAACAAUGAAGAGGAG-CUAUCCCACAUAUUAAUCUGCUUAUCUGGGAUUGCUUUCUGUGUGGAGA-----AGGAAACAUGAA-------------ACAAGGAGGGAAA----------------------AGGAAAAU-----CACAGCUCCACAGUUGAAA----------------------UAA------------------
ABQF01033351.1/51084-50806   -AUGCA-UGCU-GGGCUAUAAUUUAUGAAA-CGGAGCACAGGAAACAACCAAUCGCUUAGCU----UCUCCUAACAAGUCCAA-CUGGCUAGGAAAAGCUGUAAGU--------GCUGCAC-AGAACAAUGAAGAGGAU-CUAUCCCACAUAUUAAUCUGCUUAUCUAGGAUUGCCUUCUGUGUAGAGA-GA--AGGAAGCAUGUAAAAAGAGAGGGAAAAAAAAAAAGAAAAAUCACCGUUCC-AUUGUUAACAGAAUA-AA---UUCCAGUCAACAUGAAAAUC-CUCCAU-UGCAGUCAGAUGGC---------------------
AAGU03021008.1/72829-73074   -UCGUA-CGCU-AGGCUAUAAUUUAUGAAA-CUGAGCCCCAGAUCCAGCCAAUCGUUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCGGGCAAGCUGAAAGG--------GCUGCGCUAGAACAGCAUAGAUGAG-AUAUUUCGCACAAUAAUCUGCUGAUCUGGGAUCGCUUUCCCUCACGAGG-CCAGAG---------------------------------AAAAAUCACAGCUUC-GUUGUCU-GGAGGAAG------GACAGGUGACCUGGGAAUA-GAUGGC-AACACCUGGGGCAA---------------------
AAEX03001456.1/462066-462314 -UUGUA-CACG-GGGCUAUAAUUUAUGAAA-CGGAGCCCCAGAUCCAGCCAAUCAUUUAGCU----CCUCAUAACAAGUCUGA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCGCUAGAGCAACAAGGAUGAG-AUAGUCCACACAAUCGUCGGCUUCUCCGGAAUCACUUGGCCCUGAGAGG-CCAGAG---------------------------------AAAAAUCACAGCUUC-GCUGUCA-CAGGGAAGGA---GGGCAGAUGACCCGGAAAAA-CGUGAC-UGGAUCUGGAGCGA---------------------
AAPE02000884.1/57353-57107   -UCGUA-CGCU-GGGCUAUAAUUUAUGAAA-CCGAGCCCCAGAUCCAGCCAAUCAUUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCACUAGAACAACAAAGAUGAG-AUAGUCCACACAAUAAUCUGCUUAUCUGGAAUCACUUUCCCUCACAAGGGCCAGAG---------------------------------AAAAAUCACAGCUCC-AUUGUCU-GAGGGCAG------GACAGCUGACCUGAGAAAA-UGCGAC-UACACCUGGAGCAA---------------------
AAGW02030941.1/28253-28503   -CCCAG-CGCG-GGGCUAUAAUCUCUGAAA-CCGAGCCCCAGACCCAGCCAAUCACUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGGAAGCUGGAAGG--------GCUGCGCUGGAACA-CAUAGAUGAG-AUAUUCCACACAAUAAUCUGCUUAUCUGGAAUCGCUUUGCCUGAAGAGG-CCAGAG--------------------------------GAAAAAGCACAGCUUC-AUUGUCU-CGGGGCAAGA--GGUGCAGGUGAUCUGGGAUCAACGCGGC-CGCACCUGGAGCAG---------------------
AAQR03013098.1/45307-45058   -UAGUA-CGCU-GGGCUAUAAUCUAUGAAA-CUGAGCCCCAGAUCCAGCCAAUCACUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCACUGGAACAACAUAGAUGAG-AUAUUCCACACAAUAAUCUGCUUAUCUGGAAUCGCUUUGCUUUGAAAGG-CCAGAG---------------------------------AAGAAUCACAGCUUC-AUUGUCU-GAGGGGGAGA---GGACAGGUGAUCUGGGAGAAACACAGC-UACACCUGGAGCCA---------------------
BC096727.1/147-396           -UCGUA-CGCU-GGGCUAUAAUCUAUGAAA-CUGAGCUCCAGAGCCAGCCAAUCACUUAGCU----CCUCAUAACAAGUCUAA-CUGGCUCUGGAAAGCUGAAAGG--------GCUGCACUGGAACAACACAGAUGAG-AUAUUCUACACAUUAAUCUACUUAUCUGGAAUCACUUUGCCUCUAAAGG-CCAGAG---------------------------------AAAAAUCACAGCUUC-CUUGUCG-GAGGGGAAAA---GGACAGGUGAUCUGGGGAAAACGCAGC-UACACCUGGAGCAA---------------------
#=GC SS_cons                 .:::::.::::.::::::::::::::::::.:::::::::::::::::::::::::::::::....:::::::::::::::::.::::::::::::::::::::::........:::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::.::::::.................................:::::::::::::::.:::::::.::::::::::...::::::::::::::::::::.::::::.::::::::::::::.....................
#=GC RF                      .ucGua.cGCu.GGGCUAUAAUuUAUGAAA.CuGAGCcCcaGaucCAGCCAAUCAcUUAGCU....cCUCaUAACaAGUCuAA.CUGGCUCuGGaaAGCUGaaaGg........GCUGCaCUaGAaCaacauaGAuGAG.aUAuuCCaCAcAaUAAUCUGCUUAUCUGgaaUcgCUUUcccUcgaaAGG.cCAGAG.................................AAAAaUCaCAGcUuC.aUUGUcu.gaGGGaAGga...ggaCAGgUGauCuGggaaaa.cgcgac.ugcaccugGAGcaa.....................
//
# STOCKHOLM 1.0

#=GF AC   RF02161
#=GF ID   PART1_3
#=GF DE   Prostate androgen-regulated transcript 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   43.50
#=GF NC   39.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.59 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10706094
#=GF RT   PART-1: a novel human prostate-specific, androgen-regulated gene that maps
#=GF RT   to chromosome 5q12.
#=GF RA   Lin B, White JT, Ferguson C, Bumgarner R, Friedman C, Trask B, Ellis W,
#=GF RA   Lange P, Hood L, Nelson PS
#=GF RL   Cancer Res. 2000;60:858-863.
#=GF WK   PART1
#=GF SQ   3


AK094518.1/519-649         CUUUGCAAAGUAUCCAAGACCAACA-----AGAAAGUAAUUUCCCACCUCACCCUACCACCACCC-AGAAAA---------------GGAGCACAGAGAUGGGGAAGAGAGUGGCUGCAUCUGGCAUCCAGCCAGAGGAGUCCGUGCAGGGA
AANU01256159.1/24320-24195 CUUUACUAAGUAUCCAAGACCAACA-----AG-----AAUUUCCCAUCUCACCCUACCACCACCC-AGAAGA---------------GGAGCACAGAGAUGGGGGAGAGAGUGGCUGCAUCUGGCAUCCAGCCAGAGGAGUCCGUGCAGGGA
AAQR03013097.1/27735-27585 CUUGGUAAAGUGACUGAGACAAACACAAGAGGAAAACAAUAUCCCACCUCACCCUCCCAUCACUCCAGAAAAGAAAAAGAUUUUUCUGUAGUAGAGAAUGGGGGAAAAGAGUGGCUGCAUCUGACAUCUAGGCUGAGGAGUCCACGU-AGGG
#=GC SS_cons               :::::::::::::::::::::::::.....:::::::::::::::::::::::::::::::::::.::::::...............:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    CUUugcaAAGUguCcgAGACcAACA.....gGAAAgcAAUuUCCCAcCUCACCCUaCCAcCACcC.AGAAaA...............GgAGcAcAGAgauGGGGaAgAGAGUGGCUGCAUCUGgCAUCcAGcCaGAGGAGUCCguGcAgGGg
//
# STOCKHOLM 1.0

#=GF AC   RF02162
#=GF ID   XIST_A_REPEAT
#=GF PI   XIST
#=GF DE   XIST RNA A repeat
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Duszczyk MM, Wutz A, Rybin V, Sattler M, Burge SW;
#=GF SS   Predicted; CMFinder;Burge SW
#=GF GA   33.00
#=GF TC   33.10
#=GF NC   32.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000726; repeat_unit;
#=GF DR   GO; 0016458; gene silencing;
#=GF RN   [1]
#=GF RM   21947263
#=GF RT   The Xist RNA A-repeat comprises a novel AUCG tetraloop fold and a platform
#=GF RT   for multimerization.
#=GF RA   Duszczyk MM, Wutz A, Rybin V, Sattler M
#=GF RL   RNA 2011;17:1973-1982.
#=GF WK   XIST
#=GF SQ   54


EU086094.1/497-529         UGGUCCAUCGGGACCUCGGAUACCUGCGUUU---A-----G-
M97168.1/608-642           UGGCCCAUCGGGGCUUCGGAUACCUGCUUU-----UUUUU--
AF104906.5/650-686         UUGCCCAUCGGGGCCUCGGAUACCUGCUUUA---AUUUUU--
ABDC01412462.1/1593-1561   UGGCCCAUCGGGGCUUCGGAUACCUGCUUUU---AU------
AAPY01379542.1/1953-1917   UGGCCCAUCGGGGCUUCGGAUACCUGCUUUA---AUUUUU--
ABRN01131313.1/617-581     UGGCCCAUCGGGGCCUUGGAUACCUGCUUUG---AUUUUU--
AADA01036560.1/1221-1185   UGGCCCAUCGGGGCCGCGGAUACCUGCUUUG---AUUUUU--
AJ310129.1/9034-9068       UGGUCCAUCGGGACCUCGGAUACCUGCUAGU----UU---AG
ABRR01407567.1/1407-1373   UGGCCCAUCGGGGCAACGGAUACCUGCUUU-----UUUUA--
AANG01523518.1/1387-1422   UUGCCCAUCGGGGCCUUGGAUACCUGCUUU----AUUUAU--
ABRP01195257.1/1801-1762   UUGCCCAUCGGGGCCUCGGAUACCUGCUUUCACUAUUUUU--
U50910.1/1530-1566         UGGCCCAUCGGGGCCCCGGAUACCUGCUCUG---AUUUUU--
AJ310130.1/12382-12417     UUGCCCAUCGGGGCCUUGGAUACCUGCUU-A---AUUUUU--
AANN01200569.1/1569-1605   UUGCCCAUCGGGGCCACGGAUACCUGCUUAG---AUUUUU--
AALT01486907.1/919-954     UUGCCCAUCGGGGCCUCGGAUACCUGCUCGC----UUUUU--
AAKN02029935.1/42514-42550 UUGCCCAUCGGGGCCUCGGAUACCUGCCCUA---AUUUUU--
AANU01175104.1/38293-38330 UCGCCCAUCGGGGCCGCGGAUACCUGCUUUU--UAUUUUU--
AAHX01111727.1/40962-40998 AUGCCCAACGGGGCCUCGGAUACCUGCUUUA---AUUUUU--
AJ421479.1/106796-106828   UAGCCCAUCGGGGCCAUGGAUACCUGCUUUU---------UG
AAIY01358820.1/951-987     UUGCCCAUCGGGGCCUCGGAUACCGGCUCUG---AUUUUU--
AAGV020511993.1/1505-1469  UUGCCCAACGAGGCCUCAGAUACCUGCUUUA---AUUUUU--
ABRT010581361.1/119-87     UCACCCAUCGGGGUCACGGAUACCUGCUUUU---AU------
ABGA01241178.1/1628-1596   UUGCCCAUCGGGGCUGCGGAUACCUGGUUUU---AU------
L10734.1/371-408           UUGCCCAUCGGGGCUGUGGAUACCUGCUUUA---AAUUUUU-
AF138745.1/1968-1936       AUGCCCAACGGGGCCUCGGAUACCUGCUGUU---AU------
L10730.1/44-76             UUGCCCAUCGGGGCCACGGAUACCUGUGUGU---------CC
FJ361197.1/331-367         -UGCCCAUCGGGGCUGUGGAUACCUGCUUUA---AAUUUUU-
AJ310127.1/13329-13364     UUGCCCACCGGGGCCGUGGAUACCUGCUUC----AUUUUU--
AAVX01126796.1/700-665     AUGCCCAUCGGGGCCUCGGA-AUCUGUACUU---CUUUUA--
AAPE02004049.1/4919-4953   UGGCCCACCGGGGCCUAGGAUACCUGCUUU-----UUUUU--
AGCE01104057.1/2893-2927   UUGCCCAUCGGGGCCGCGGAUACCUGCUUU-----UUAUU--
CU855548.6/128407-128372   UUGCCCAUCGGGGCCUCGGAUACCUGCUUU----AUUAUU--
AF104906.5/487-523         UUGCCCAUCGGGGCCACGGAUACCUGCUUUU---AAUUUU--
M97168.1/456-493           UCGCCCAUCGGGGCCGCGGAUACCUGCUUUU--UAUUUUU--
M97168.1/368-404           UUGCCCAUCGGGGCUGCGGAUACCUGGUUUU---AUUAUU--
AL353804.22/35456-35420    UGGCCCAUCGGGGCCGCGGAUACCUGCUUUG---AUUUUU--
AF104906.5/693-729         UUGCCCAUCGGGGCCUCGGAUACCUACUUUA---AUUUUU--
FJ156095.1/1619-1583       UGGCCCAUCGGGGCUGCGGAUACCUGGUUUC---AUUAUU--
FJ156095.1/1573-1535       UUGCCCAACGGGGCUGUGGAUAGCUGCUUUUU-AAUUCUU--
M97168.1/560-591           UGGCCCAUCGGGGUGACGGAUAUCUGCUUUU----U------
U29341.1/1642-1673         UAGCCCAUCGGGGCCAUGGAUACCUGCUUUU----U------
FJ156095.1/1519-1484       UUGCCUAUCGGGGCCGUGGAUACCUGCUUUU----UUUUU--
M97168.1/698-734           CUGCCCAUCGGGGCCGCGGAUACCUGCUUUG---AUUUUU--
FJ156095.1/1324-1288       UUGCCCAUCGGGGCCUCGGAUACCUGCUUUU---AUUAUU--
AF104906.5/437-474         UUACCCAACGGGGUCAUGGAUACCUGCCUUU--UAUUUUA--
AF104906.5/587-622         UGGCCCAUCGGGGCAAUGGAUACCUGCCUCU----UUUUU--
L04961.1/549-585           CGGUCCAUCGGGACCUCGGAUACCUGCGUUU---AGUCUU--
AF104906.5/735-771         UUGCCCAUCGGGACCGCGGACACCUGCUUAG---AUUUUU--
AF104906.5/536-567         UAGCCCAUCGGGGCCUCGGAUACCUGCUGUG----U------
FJ156095.1/1280-1244       UUGCCCAUCGGGGCCUCGGAUACCUGCUCUA---AUUUUU--
AF104906.5/358-389         UUGCCCAUCGCGGCUGUGGAUACCUGGUUUU---A-------
L04961.1/435-471           UUGCCCAUCUGGGCUGUGGAUACCUGCUUUU---AUUCUU--
CU855548.6/128656-128618   UUGCCCAACGGGGCCGUGGAUACCUGCCUUUU-AAUUCUU--
FJ156095.1/1368-1332       UGGCCCAUCGGGGCCUCGGAUACCUGCUUUU---AUUAUU--
#=GC SS_cons               ::<<<<____>>>>--<<<____>>>:::::...::::::..
#=GC RF                    UUGCCCAUCGGGGCCuCGGAUACCUGCUUUU...AUUUUU..
//
# STOCKHOLM 1.0

#=GF AC   RF02163
#=GF ID   sR-tMet
#=GF DE   Small nucleolar RNA sR-tMet
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; PMID:21654217; Eberhardt R
#=GF SS   Predicted; PMID:21654217;
#=GF GA   50.00
#=GF TC   53.50
#=GF NC   43.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0030488; tRNA methylation;
#=GF RN   [1]
#=GF RM   21654217
#=GF RT   2'-O-methylation of the wobble residue of elongator pre-tRNA (Met) in
#=GF RT   Haloferax volcanii is guided by a box C/D RNA containing unique features.
#=GF RA   Joardar A, Malliahgari SR, Skariah G, Gupta R
#=GF RL   RNA Biol. 2011; [Epub ahead of print]
#=GF WK   Small_nucleolar_RNA_sR-tMet
#=GF SQ   2


CP001365.1/2074171-2074240 GGCCGAUGACGAUGCACCGCUCCGAGCCGCCUCGGC--ACCGGCGAUGACGAGCCCUAUGAGUGCCGAGGCC
CP001687.1/2637902-2637831 GGCCGAUGACGAGCGACUGGGCCGAGCCGGGGUGACUCCCCGGUGAUGACGAGCCCUAUGAGUGCCGAGGCC
#=GC SS_cons               <<<<---<<<<----------<<<<<<<<<_________>>>>>>>>>---------------->>>>>>>>
#=GC RF                    GGCCGAUgacGAuggACuGguCcgagCCGgguuGaCUCacCGGcgauGACGAGCCCUAUGAGUGCcgaGGCC
//
# STOCKHOLM 1.0

#=GF AC   RF02164
#=GF ID   PVT1_1
#=GF DE   Pvt1 oncogene conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   85.80
#=GF NC   79.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 61.36 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   17503467
#=GF RT   The PVT-1 oncogene is a Myc protein target that is overexpressed in
#=GF RT   transformed cells.
#=GF RA   Carramusa L, Contino F, Ferro A, Minafra L, Perconti G, Giallongo A, Feo S
#=GF RL   J Cell Physiol. 2007;213:511-518.
#=GF WK   PVT1
#=GF SQ   17


AY336081.1/1737-1906       CCGAGCACAUGGGCCC--GCGGGCCGGGCGGGCUCGGGGCGGCCGGGACGAGGAGGGGCGACGACG--AGCUG--CGAGCAAAGAUGUGCCCCGGGACCC--------CCGGCAC-C-UUC-CAGUGGAUUUCCUUGCGGAAAGGAUGUUGGCGGUCCCUGUGACCUGUGGAGACACGGCCAGAUCU--------
M26714.1/90-266            CCGAGCACAUGGGCC---GCGGGCCGGGCGGGCUCGGGGCGGCCGGGACGAGGAGGGGCGACGACG--AGCUG--CGAGCAAAGAUGUGCCCCGGGACCC--------CCGGCAC-C-UUC-CAGUGGAUUUCCUUGCGGAAAGGAUGUUGGCGGUCCCUGUGACCUGUGGAGACACGGCCAGAUCUGCCCUCCA
ABDC01028845.1/408-584     CCGAGCACAUGGGCCC--GCGGGCCGGUCGCGCUCGGGGCGGCCCGGGCGAGGAGGGGCGGCCGGG--AGCCG--CGAACGAGGAUGGGCCCUGGCACCC--------C-GGAAC-C-CCC-AAGUGGAUUUCCACGCGGAAAGGAUGUUGGCGGCCCCGGUGACCUGUGGAGAUACGGCGGGAUCCACCCUCCA
ABVD01506303.1/484-664     CCGAGCACAUGGGCCC--GCGGGCCAGGCGGGCUCGGGGCUGCCUGGACGAGGAAGACUGGCCAGG--AGCCGGAGGAACACGGUGGUCCCC-GGCACCCC------UCGGCCAA-C-CCC-GAGUGGAUUUGCAAACGGAAAGUAUGUCCGCGGCCCCGGUGACCUUUGGAGACACGGCUGGAUCCACCCUCCA
AAYZ01075585.1/274-450     CCGAGCACAUGGGCCC--GCGGGCCAGCCGGGCUCGGGGCGGCCGGGACGAGGAGGAGCAGCGAGG--AGCCG--CUAGCAGCCGCGGGUCUGGGCUCUC--------CCGGCAC-C-AGC-GAGUGGAUUUCCACGCGGAAAGGAUGCGGGC-GCCUGGGUGACCCGUAAAGACACGGCAGGAGCCACCUUCCA
ABRN01096386.1/1247-1067   CCGAGCACAUGGGCCC--GCGGGCCGGGCGGACUCCGGGCGGCCGGGACCCGGAGUAUCAGCGAGG--GGCCG--CGAGCGAGGGUGGGCCCCGGCACGCG------CCCGGAAC-C-CCCUGAGUGGAUUUCCACGCGGAAAGGCUGUUGGCGGCCCCGGUGACCUGCGGAGACACGGCUGAAUCCACCUUCCA
AC153008.4/68565-68721     CCGAGCACAUGGACCC--ACUGGUCAAGCGGGCUCGGCAAGGCCAGGAUGAAGAGAAGCUACGAAC---------UUAGCA--UU---CCCAGAGCCCCC--------C-------------GAGUGGAUAUCCGCGUGGAAAGGAUGUUGGCAGCCCCGGUGACCU-CGGAGUCACGGCUGGAUCCACCCUCUU
AAHX01051111.1/26053-25895 CCGAGCACAUGGACCC--GCUGGUCAAGCGGGUUGUACAAGGCCAGAAUGAAGAGAAGCUGCGA-G---------UCAGUAUGGAA--CUCAGAGGUCCC--------C-------------GAGUGGAUAUCCACGUGGAAAGGAUGUUGGCAGCCCGGGUGACCU-CGGAGUCACGGCUGGAUCCACCCUCCC
AAQQ01353359.1/3840-4021   UAGUUUUGAU-AAUCC--ACGUACCGGGCGGGCUUGGAGCUACCGGGUUGAGGAGGAGCAGAGAGCAGCUCGA--GUAAGGAUGGGCUCUCACACCUCCUGG----AGCCAGCAC-C-CUC-CAGGAUAUUUCCAUGAGGAAAGGAUGGUGGCAGCCCUAGUGACCCAUGG-GACACGGCUGGAUCCACGUUCCA
AAIY01758172.1/1226-1056   CCGAGCACAUGGGCCC--GCGGUCCGGGCGGGCGCGGGGUGGCCGGGUCGGGCAGAGCCCGCGAGGAGCAGCG--UGGCCGGGAUAGUCCCGGAGCUCC---------GCAACGG-A-GCC-GCGUGGAUUUCCACGCGGA-GGGAUGCGGC-------GGUGACCUGUGGCGACGCGGCUGGAUACACCCCCCC
CU468566.24/24251-24072    CCGAGCACAUGGGCCC--GCGGGCCGGGCGGACUCG-GGCGGCCUGGACCGGGAGGAACAGCGAGG--GGCGG--CGAGCGAGGCUGGGUCCCGGCACGCC------CCCGGAGC-CCCCC-GAGUGGAUUUCCACGCGGAAAGGAUGGUGGCCGUCCGGGUGACCUGCGGAGACACGGCCGGAUCCACCUUCCA
AAFC03009717.1/23370-23186 CCGAGCACAUGGGCCC--GCGGCCCGGGCGGACUCGGGGCGGC-GGGGCCCGGGGGAACGGCGAGG--GGCCG--CGAGCGAGGAUGAGUCCCGGCACGCCCCCGCCCCGGACCC-C-CUC-GAGUGGAUUUCCACGCGGAAAGGAUGUUGGCGGUCCCGGUGACCUGCGGAGACACGGUUGGAGCCACCUUUCA
ABRP01224730.1/1449-1620   CCGAGCACAUGGGCCCGCGCGGGCCGGGC-CGCUCGGAGCGGCCUGGUCUGCAGGGAGCAGCGAGG--GGCCG--CGAGCGAGGAUGGACCCCGGUACCC-------CCCAGAAG-C-CCCUCAGUGGAUUUCCACGCGGAAAGGAUGUUGGCGGCCCCGGUGACACG---------GCUUGGAUCCACCUUCCA
ABRQ01213433.1/1336-1511   CCGAGCACAUGGGCCG--GC-GGCUGGGCGGGCGCGGGGCGGCCUGGACCGGGAGGCACGGCCGGG--AGCCG-CGGAGCCAGGAUGGGCCC-GGCGCCC--------CCGGCCUGU-CCC-GCGUGGAUUUCCACGUGGA-AGGAUGUGGGC-GUCCCUGUGACCUUUGGCGGCACGGCUGGAUGUACCCUCCA
CABD02371170.1/6054-6231   CCGAGCACAUGGGCCC--GCGGGCCGGGCGGGCUCGGGGCGGCCGGGACGAGGAGGGGAGACGAGG--AGCUG--CGAGCAAAGAUGUGCCCCGGGACCC--------CCGGCAC-C-UUC-CAGUGGAUUUCCUUGCGGAAAGGAUGUUGGCGGUCCCUGUGACCUGUGGAGACACGGCCAGAUCUGCCCUCCA
AAPE02026190.1/31158-30988 CCGAGCACAUGGGCCC--UCGGGCCGGGCAGGCGCGGGGCGGACCGGACCCGGAGGAACAGCUCCG-GGGCCG--CGAACCAGGACGGGCCC-GGCUCCCC------CUGGGCUC-C-CCC-GAGUGGAUUUCCGCGCGGCAAGGAUGUUGGCGGCCCCGGUGCCACG---------GCUUGGAUCCACCUUCCA
AAGU03023647.1/16561-16736 CCGAGCACAUGGGCCC--GCGGGCUGGGCGGGCGCGGGGUGGCCUGG-CGGGGAGGCACGGCGAGG--AGCCG-CGGAGCUGGGAUGGGCCC-GGCACUG--------CCGGAGUGU-CCC-GCGUGGAUUUCCACGGGGG-AGGAUGUGGGCGGC-CCGGUGACCUUUGGCGACACGGCUGGAUCCCCCCUCCG
#=GC SS_cons               ::::::::::::::::..::::::::::::::::::::::::::::::::::::::::::::::::..:::::..:::::::::::::::::::::::::........:::::::.:.:::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    CCGAGCACAUGGGCCC..GCGGgCCGGGCGGGCucGGgGcGGCCgGGaCgaGGAGGagCgGCgaGG..aGCcG..cgAgcgagGauGggcCccGGcaCcc........CcGgcac.c.ccC.gaGUGGAUUUCCacGcGGaAAGGAUGuuGGCgGcCCcgGUGACCuguGGaGaCACGGCuGGAUCCaCCcUCCa
//
# STOCKHOLM 1.0

#=GF AC   RF02165
#=GF ID   PVT1_2
#=GF DE   Pvt1 oncogene conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   47.00
#=GF TC   48.40
#=GF NC   40.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.62 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   17503467
#=GF RT   The PVT-1 oncogene is a Myc protein target that is overexpressed in
#=GF RT   transformed cells.
#=GF RA   Carramusa L, Contino F, Ferro A, Minafra L, Perconti G, Giallongo A, Feo S
#=GF RL   J Cell Physiol. 2007;213:511-518.
#=GF WK   PVT1
#=GF SQ   17


AC084123.9/59124-59288     GACCAUAGCUGUCUGCAGUGC----AGGAAGCCAACUAUUA-AGGGGAAACAAAAGUGUUCUUAGGAGUCCUGCUGU-CACUGUGGAUUGAGC---CG----GUGAAGCC------C-----------UGAG------------GG--AUUUCAUCGCUGAGGUGGA----------------UGGAGAAGCAGCUGGGGGCCUUGGCU---GUAAGGACCCCUAAGG
ABGA01172063.1/1883-1719   GACCAUAGCUGUCUGCAGUGC----AGGAAGCUAACUGUUA-AGGGGAAACAAAAGUGUUCUUAGGAGUCCUGCUGU-CAUUGUGGAUUGAGA---UG----GUGAAGCC------C-----------AGAG------------GG--AUUUCAUCGUAGAGGUGGA----------------UGGAGAAGCAGCUGGGGUCCUUGGCU---GUAAGGACCCCUAAGG
AANU01124519.1/6095-6262   GACCAAAGCUGUCUGCAGUGC----AGGAAGCCAACUAUUA-AGGGGAAACAAAAGUGUUCUUAGGAGUCCUGCUGU-CAUUGUGAAUUGAGC---CG----GUAAAGCC------C-----------CGAG------------GG--GUUUCAUCGUGGAGGUGGA----------------UGGAGAAGCAGCUGGGGGCCUUGACUUUAGUAAGGACCCCUAAGG
ACBE01483200.1/2672-2505   GAUGGCAGCUGUCAGCCUUGC----AGGAAGCCCACUAUUA-AAAGGAAACAAAAGUGUCAUUAGGAGCCCUGCUGU-CGCUGUGGAUUGAGC---CUG--CAUGCUGCC------C-----------UGAG------------GG--CUG-GACCGCAUUCGCAGGG--------------CUGAGAAAGCAGCUGGAGGCCUUGACC---GUGAGGGCCUCUGAAA
ABVD01678581.1/664-830     GACUGUAGCUUCCAGCAAAGC----AGGAAGCUGACCAUAA-AGGGGAAACAAAAG-GGCCUGAGGAGCCCUGCUGUGCUCUGUGGAUUGAGC---CACACUGCUGAGCC------C-----------UGAG------------GG--CUGUGAACCCGUCCUCAG------------------GAGAGAGCAGCUGGAGGCCUGGGCA---GUGAGGAGCCCUAGGG
ABRQ01415900.1/53-195      GAAGGUAGCUGUCCACAGUAC----AGGAAGCCUCAUCUGA-AGGGGGAACAGAAGUGCCAUUGGGGU-CCUGCUGCUGACUGUGA-UUGAGC--UCUGCAU-CAGAGAU------G-----------GAGA------------AA--GCAGCUGGGAGGCGUUGAC----------------CUGAAGGCCCCCUGAGG----------------------------
ABRP01224740.1/2387-2568   GAAGUCAGCUGUCAGCAGUGC----AGGAAGCAGACUAUUA-AGAGGAAACAAAGGCGUCAUUAGGAGCCCUGCUGU-CACUGUGGAUUGAGC---CUGCAUGCUGAGCC------C-----------UGAG------------GG--CACGCUGCGCAGUGGGCCUCCUAGG---CAGGGAUGGAGAAGGCAGCUGGAGGCCUUGGCA---GUGAGGACCCCUAAAG
AAWR02021559.1/7307-7490   GAAGGCAGCUGUCAGCAGUGC----AGGAAGCUGACUAUUAAAGAGGAAACAAAAGUGUCACUAGGAGUCCUGCUGU-CACUGUGGAUUGAGC---CUGCCUGCUGAGCC------C-----------UGAG------------GG--CA--CACUGGGGCAGUGGCCCUUUUCUGCAGGGAUGGAGAAAGCCUCUGGAGGCCUCCACA---GUGAGGACCCUAAGGG
AAYZ01075590.1/1561-1744   GAGAGCAGCUGUCAGCGGAGC----AGGAAGCCGGCUAUUA-AGGAGAAACAAAAGUGUCAUUAGGAGCCCUGCUGU-CAUUGUGGAUUGAGC---CUGCCUGGAGAGCC------G-----------GGAGGCAG---GCUCAGG--AGUGUGGG---------G-CCUCCACCUCUGGGGUAGCUGGAACAGCUGGAGGCCUUGGCA---GUGAGGAGGCCUAAGG
ABDC01028852.1/4056-4242   UAGGGCAGCUGUCAGCAGUGC----AGGAAGCUGACUAUUA-AGGGGAAACAAAAGUGUUAUUAGGAGUCCUGCUGU-CACAGUGGUUUGAGCAUCCUGAGCCCUGAGGCUGUUUCU-----------GGUGG---------UGGA--CCUCCUCCUCCUCAGUAGGGAU---------GGGUAGAGGAAGCAGCUAGAGGCCUUGGCA---GUGAGGAACCCUAAG-
ABRO01556930.1/283-465     GGUGGCAGCUGUCUGCAGCAC----AGGAAGCUGCCUAUUA-AGGGCAAACAAAAGUGUCAUUAGGAGCCCUGCUGU-CACUGUGGAUUGAGCC-CGUACUGGCUGAGCC------C-----------CGAG------------GC--UGUCUCUGGUGGCGGCGGGCAUCCG---CUGGGAAGUGGCAAGCAGCUGGG-GAAUUGGCA---GUGGGGACCCCUGGGG
ABRT010128715.1/1410-1587  GACCACAGCUGUAGGCAAAGC----AGGAAGCCGGCUAUUA-AGGGGAAACAAAAGCAUCACAAAGAGUC--GCUGU-CUCUGUGGAUUGAGC--U--GCUUGCUGAGCC------CCAGGCAGGCUCUGAU------------GG--GAACC-UCCUGGCUGGGAGGG------------GUGGAGGAAGCUGAUGGAGGUCUUGGCA---GCCUG--ACCCUAAGG
AAFC03009720.1/55397-55214 GAAGGCAGCUGUCAGCUGUGUUAAGGGGAAGCC-ACUGUUA-AGGAGAAACCAAAGUGGUGUUUGGAGUCCUGUUGU-CAGUGUGGGUUCAGC---CUGCAGGCUGAGCC------C-----------UGGGAGCA---AACUGGG--CAUUGACUCCAUCCACUGGG-------------AUGGAGAGAGAAGCCAGAGGCCUUGACA---GUGAGGACCCCCAGGG
AAGW02013344.1/81276-81412 GAUAGCAGCUGUCAGCAGUGC----AGGAGGCUGGCUAUUA-AGGGGAAACAAAAGUGUCAUUAGGAGUCCUGCUGU-CACCGUGGGUUGAGU---CUGCCUGCUGAGCC------C-----------UGAG------------GG---UGGAGGCCUGGCAGUGG----------------------GGACCCCUAAGG----------------------------
AAQR03010387.1/10688-10504 GACCUCCGCCCUCAGCAAUGC----AGGAAGCUGACUAUUA-AGGGCAAACAAAAGUGUUAUUAAGACCCCUGCUGU-CGCUGUGGAUUGUGC---CCUCAUCCUGCGCC------C-----------UGGGGCUGCCUCCCAUGG--ACCUCCCCUUGGUGGGGACUG------------GUAGGGGAAGCCGUUGGAGGCCUUGGCU---GUGAGGACCCCUAAGU
AAPE02026189.1/46686-46519 GAAGGCAGCUGUCAGCCCAGC----AGGAAGCAGACGAUUG-AG-----A--------------GGCGUCCUGCUGU-CCCUGUGGCUGGAGC---CUGCCCGCUGAGCC------C-----------UGAG------------GGCGCUGGGGCGGCGACCUCAGCGCCUGGAUGGAGGGAUGGAGAAAGCAGCGGGAGGGCUGGGCA---GUGAGGACCCCUAAGG
AAGU03023649.1/12023-12167 GAGGGUAGCUGUCUGCAGUGC----AGGAAGCUGACUAUGA-AGGGUAAAGAGA-GUGCCGUUAGGGUUCCUGCUGUUCGCUAUGAAUUGAGC--UCUGCAUGCUGAGAU------G-----------GUGA------------AA--GCAGUGGGGUGGCCUUGAC----------------AUGAAGACCCCCUAAAG----------------------------
#=GC SS_cons               :::::::::::::::::::::....::::::::::::::::.:::::::::::::::::::::::::::::::::::.:::::::::::::::...::::::::::::::......:...........::::............::..:::::::::::::::::::::............::::::::::::::::::::::::::::...::::::::::::::::
#=GC RF                    GAaggcAGCUGUCaGCaguGC....AGGAAGCugaCUaUuA.AGGGGAAACAAAAGUGucaUUaGGaGuCCUGCUGU.CacUGUGGaUUGAGC...CuGCauGcuGaGcC......c...........uGaG............GG..cuuucaucguggcgguggggg............gugGgggaAGCaGCUGGaGGcCUuGGCa...GUgaGGAcCCCUAaGG
//
# STOCKHOLM 1.0

#=GF AC   RF02166
#=GF ID   PVT1_3
#=GF DE   Pvt1 oncogene conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   45.00
#=GF TC   46.00
#=GF NC   39.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   17503467
#=GF RT   The PVT-1 oncogene is a Myc protein target that is overexpressed in
#=GF RT   transformed cells.
#=GF RA   Carramusa L, Contino F, Ferro A, Minafra L, Perconti G, Giallongo A, Feo S
#=GF RL   J Cell Physiol. 2007;213:511-518.
#=GF WK   PVT1
#=GF SQ   25


AC103705.5/32657-32751     CCCUCAAGAUG-GCUGUGCCUGUCAGCUGCAUGGAGC--UUCGUUCAAGUAUUUUCU-GAGCCUGAUGGAUUUACAGUGAUCUUCAGUGGUCUGGGGAA
AANG01541995.1/1375-1281   CCCUCACGAUG-GCCGUGCCUGUCGGUUACAUGGAGC--UCCAUUCAAGGAUUUUCG-GAGCCUUUUGGAUUUACAGUGAUAUUCAGCUGCCUGGGGAA
AAFC03046547.1/46341-46248 CU-UCAUAAUG-ACUAUACCUGUCAGUUGUGUGGAGC--UACAUUGAAGAUUUUUCU-GAGCCUGAUAGAUUUACAGUGAUAUGCAGCUGCCUGGGGAA
ABRP01042655.1/8732-8639   CC-UCAUGGUG-ACUGUGCCUGUCAGCUGCAUGGAGC--AUCGUUCAAGGAUUUUCU-GAGCCUGAUGGAUUUAUAGUGAUAUUUGGCCAUGUGGGGAA
AAWR02021559.1/33435-33529 CUGUCAUGCUG-GCUGCGCCCGUCAGCUGCAUGCAGC--UUCGUUCAAGGAUUUUUG-GAGCCCUGUGGAUUUACAGUGAUACUCGGCCGCCUGGGGGA
ABVD01506303.1/709-804     CCCUUGCGAUG-GCUGAACCUGUCAGUUGCCUGGAGC--CAAGUCCAAGGAUUUUUCUGAGCCUGAUGGAUUUACAGUGAUCGUUGGUGGCCUGGGGAA
ABRN01401776.1/594-501     CC-UCGUGAUG-ACUGCAUCUGUCUGUUGCAUGGAGC--UUCACUGAAGGACUUCCU-GAGCCUGAUGGAUUUACAAUGAUACUCAGGUGCCUGGGGAA
ABDC01485147.1/1245-1149   CCCUCAUGAGG-ACUGUGCCUGUCAGCUGCAUGAAUCCUUCCAUUCCAGGAUUUUCG-GAGCCUGAUGGAUCUGCAAUGAUAUUUGGCUGCCUGGGGAA
AAGV020411855.1/961-1055   CCCUCGCGAUG-GCCAUGCCUGUCAGUCGCCCGGAGC--UUCGCUUGAGGAUUUUCU-GAGCCUGAUGGAUUUACAGUGACCGUGGGCCGCCCGGGGAA
ABRR01414933.1/772-865     CCCUCAAGAUG-GCCGCACCUGUCAGCUGCUUGGAAC--GUCCUUCAAGGCUAUGCU-GAACCUUAUGGAUUUACAGUGAUACCCGGCCGCCUG-GGAA
AAPY01762735.1/1414-1507   CCAUCGUGAUG-GCUGUGCCCGUCAUUUGUGUGGAGC--UUCUGUCAAGGAUUUUCA-GAGCCUGAUGGAUUUACAGUGACACUCAACCACCUG-GGAA
ABRT010462759.1/1803-1712  CCCUCAUGAGG-ACUGUUCCUGUCAGUUGCAUGAAAA--UUCAUUCAAGAAUUUUCU-GAGCCUGAUGGAUUUACA---AUACUUGGCUGUCAGAGGAA
AAQQ01353359.1/4059-4151   UGCUCAACACA-GCUGCGC-UGCCAGUCGCAAGGGCC--UCCCUCUAGAUUUUUCCU-GACC-UGAUGGAUUUGUGGUGAUGUUCAGUCUCCUGGGGAA
ABGA01149833.1/1040-1134   CCUUUAUAAUG-GUUAUGGCUGUCACUCGCCUGCAG---UUUGUUCAAGUAUUUUUCUGAGCCUGGUGUAAUUACAGUGAUAUUCUGUGGCCUGGGGAA
AAKN02041847.1/35193-35101 CC-UCAAGACU-GCUGAGCCUGCCAGUUGCACAGAGC--UGUGUCUAGAGGUUUUCU-GAGCACAGUGGAUUUACAGCGAGAUUCAACUGCCUGGGGG-
ABRQ01432567.1/1524-1601   ---U---------------CUGCCAGUUGCACAGAGC--AUUGUUCACGGAUUUUCC-GAGCCUGAUGGAUUUACAGUGAUAGUCGGCUACCUGGGGAC
AAHX01051114.1/29063-29155 CC-UCCAGGAG-GCUGUGCUUGCAGACUCCACGGAGC--CUCUCUCAA-GAUUUCCU-GAACCUUGUGGAUUUACAGUAAGACGAAGUUCCCUGGGGAG
ABQO010461830.1/3037-2947  GCCUCCCGACA-GUUUUCC-UG--UGUUUUCUGGAGC-UGCUGCUCAAGGCUUUCCC-AGACCUG-UGGAUUUACAGACAUACUGAGCUGCCUGGGGG-
AAHY01122720.1/3525-3610   UCCAUCAGCAG-GCCGUGUCUGC--------UGGGAC--CUCUCUGGA-GACUUCCU-GAACCCUGUGGAUUUACAGUAAGAUGCAGUUUCCUGGGGAG
AAYZ01185222.1/2430-2341   -CACAGUGAGG-ACAGUGCCUGUCAGCAACACGGAGC--UUCAUUCAG----ACUCU-GGGUCUGACAGAGCUGCAGUGAUGUUUUUUCAUUAGUGUGA
AAPE02026189.1/23420-23328 CCUACCCCGUG-GCCAUACCUGUCCGCUGCAUGGAGC--GUCACUCGAGGAUUUCCC-GCGC-GUGUGGAUUUACAGAGAUGUCCAGCUGC-UGCGGAA
AAEX03016758.1/3204-3110   CC-UUGUGAUGAACUGUGCCUAUCAGUUGCAUGGAGC--UUCAUUCAAGAAUUUUCU-GAGCCUGAUGGAUGUACAACGAUACUCAACCACCUGGUGAA
AAQR03010386.1/18628-18534 AUCUCGUGAUG-GCUGUGCCUGUCAGUUACGUGGAGC--UUUGCCCAGGGAUUUCCU-GAGCCUGCUGGAUUUACAGGGAUAUUUGGCCAUCUGAGGAU
AAGU03023649.1/45561-45638 ------------------CCUGCCAGUUGUGUGGAGC--CUUGUUCACGGAUUUUCU-GAGCCUGAUGGAUUUACAGUGAUAUUUGGUUGCCCGGGGAA
AAGW02022553.1/67224-67315 UU-UCAUGAGA-ACUGUGCCUGUCAGCUGCAUGGAGU--UUGAUUCAA--ACAUUCU-GAGCCUGAUGAGUUUACAGUGAUGCUGGGCUUCCUGGGUAA
#=GC SS_cons               :::::::::::.:::::::::::::::::::::::::..::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::
#=GC RF                    CCcUCauGAuG.GCUGUGCCUGUCAGUUGCaUGGAGC..uUcgUUCAAGGaUUUUCu.GAGCCUGaUGGAUUUACAGUGAUauUcaGcugCCUGGGGAA
//
# STOCKHOLM 1.0

#=GF AC   RF02167
#=GF ID   PVT1_4
#=GF DE   Pvt1 oncogene conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   60.00
#=GF TC   64.10
#=GF NC   49.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.42 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   17503467
#=GF RT   The PVT-1 oncogene is a Myc protein target that is overexpressed in
#=GF RT   transformed cells.
#=GF RA   Carramusa L, Contino F, Ferro A, Minafra L, Perconti G, Giallongo A, Feo S
#=GF RL   J Cell Physiol. 2007;213:511-518.
#=GF WK   PVT1
#=GF SQ   10


AAFC03094311.1/32598-32776 AUUACCCCACUUCCCAAAGCCAUGUCCUGAGGUG-CCCGUGU-GUCCUUGGCACAUACCAUCCAUCACGGUGGUUCUUGUCAUGU-----AGGGAUUGAAUCCAUAGGAUCUCCACUUUGAACUGCACAGUAGGCAGCCUCCUUGGG-GUCUGCAUUUUGCCA-CGGGGGACACUGAGAUUUGGAGAA
AANU01124523.1/16000-16169 CUGACCACGCUCCCUGGAGCCUUCUCCCGAGGUGGCGCAGGU-GUCCUUGGCACAUAC-AGCCGUGGUGAUGGUACUU--UAAGU-----GGAGGCUGAAUCA------UUUCCCCUUUGAGCUGCAUGGCACAUGGCUCCCUUGGU-GUUCCCAUUUUA-CA-GCCAGGACACUGAGAUUUGGAGAG
AAPY01063171.1/5537-5712   CUCAUCACACCUCACGGAGCCUGUUUCUGAGGUG-CCAGGGU-GGCCCUG-CACGUGC-UGCCAUCAUGA-GGCACUUGUUACGU-----AGGGGCUGAACCAACAGGUCCUUUCCUUCGAGCCGCUGGGCAGGCGGCUUCCUGGGC-CUCUCUGUUUUAGCA-CUUGGGACACUGAGAUGUGGAGAA
AAWR02021560.1/18452-18610 CUGACCCCACUUCGUGGACCCCUGACCCGAGGUG-CCCGGGU-GUCCU-GGCACACACCAGUCACCACGAUGGUUCUUGUUAAGU-----GGCGGCUG------------------AAUGAGCUGCAUGGCAGGAAGCCUUCUUGCU-GUUUGCACAUUACCA--CAGGGACACUGAAAUUUGAAGGA
ABDC01028869.1/1387-1547   CUGACCACACUGC-CAGAUCCUUCUCCCGAGGCG-CCUGGGU--UCCUUGGCACAUAC-AGUUGUCGAGAAGGUGCUUGCUGACU-----UGGGGCUCA---------------UUCGAUAGGUGCACAACAGGCGGCUCCCCAGGU-GUUCCCAUUUUGCUG-CCAUGGACUCUAAGAUUUGGAGAC
ABGA01172054.1/9892-9724   CUGACUACACUCCCUGGAGCCUUCUCCCGAGGUG-CACAGGU-GACCUGGGCACAUAC-AGCCAUUGUGAUGGUACUU--UGAGU-----GGAGGCUGAGUCA------UCUCCCCUUUGAGCUGCUUGGCACGUGGCUCCCUUGGU-GUUCCCCUUUUA-CU-GCCAGGACACUGAGAUUUGGAGAG
ABRP01177235.1/10947-11086 CUGACCACACUUCAGGGAGCUUUGUCUCAAGGUG-CCUGGGG--AC--------ACACCAGCCAUCGUGAUGGCUCUCG------------------------------------CUUUGAGCUGCACGGCAGGUGGCCCUCUCGGC-GUUUGCAUUCUAUCACUGAGGGACUCUGAGGUUUGGAGAC
CR812473.1/31228-31396     CUGACCAUACUCCCUGGAGCCUUCUCCCGAGGUG-CGCGGGU-GACCUUGGCACAUAC-AGCCAUCAUGAUGGUACUU--UAAGU-----GGAGGCUGAAUCA------UCUCCCCUUUGAGCUGCUUGGCACGUGGCUCCCUUGGU-GUUCCCCUUUUA-CU-GCCAGGACACUGAGAUUUGGAGAG
AAGU03023652.1/21409-21595 UUGCUCACCCUUCACAGCGCCCUCUCACAAGGUGGUGUGGGCAGUCUUUAGCACAUACCAGUGGUCACAACGGUUCUUGUUAAGUUCAGAGGUGACUGAAUAAAUAGGUCCUCUCCUUUGAGCUGCGGGACAGACAGCCCUGUUGGCUGUUUUCAUUUUACAG-CAAGGGAAGCUGAGAUUUGGAAAG
AACN010020724.1/1281-1458  CUGACCACACUCCACCGGGCCUUGUUCCGAGGUA-CCUGGGU-GUCUUUGGCACACACCAGUCAUCAUGAUGGUUCUUGGUAAGG-----GGGGGCUGGGCUCCCAGGUUCUCUCCUUUGAGGGGC-CAGUUGGCAGCCCUUUUGGU-GUUUGCAGUUUGCCA-UGAGGGACACUGAGAGUUGAAGAU
#=GC SS_cons               ::::::::::::::::::::::::::::::::::.:::::::.::::::::::::::::::::::::::::::::::::::::::.....:::::::::::::......::::::::::::::::::::::::::::::::::::::.:::::::::::::::.::::::::::::::::::::::::
#=GC RF                    cUgAcCaCaCUuCacgGaGCCuUcUCcCGAGGUG.CcuGGGu.GuCcUUGGCACAuACCAGccaUCauGAuGGUuCUUGuUaaGU.....gGgGGCUGAauca......uCUcucCuuuGAGcuGCauGGCAGGcgGCccccUuGGu.GUUugCauUUUacca.ccagGGACaCUGAGAUUUGGAGAg
//
# STOCKHOLM 1.0

#=GF AC   RF02168
#=GF ID   PVT1_5
#=GF DE   Pvt1 oncogene conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   63.40
#=GF NC   56.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.08 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   17503467
#=GF RT   The PVT-1 oncogene is a Myc protein target that is overexpressed in
#=GF RT   transformed cells.
#=GF RA   Carramusa L, Contino F, Ferro A, Minafra L, Perconti G, Giallongo A, Feo S
#=GF RL   J Cell Physiol. 2007;213:511-518.
#=GF WK   PVT1
#=GF SQ   23


AK129745.1/486-615           AAUCCUGUUACACCUGGGAUUUAGGCACUUUCAAUCUGAAAAAA------UACAUAUCCUUUCAGCACUCUGGACG-GAC-UUGAGAACUGU-CCUUACGUGACCUAAAGCUGGAGUAUUUUGAGAUU-G--GAGAAUUAAG-------
AANU01124526.1/23747-23874   AAUCCUGUUACACUUGGGAUUUAGGCACUUUCAAUCUGAAAAAA--------CAUAUCCCUUCAGCACUCUGGAUG-GAC-UUGAGAAUUGU-CCUUACCUGAACUAAAGCUGGAGUAUUUUGAGAUU-G--GAGAAUUAAG-------
AAWR02021560.1/59810-59941   AAUCCUGUUACACCUGGGAUUUAGGUGCCUUCAAUCUG-GAAAA----AAUACAUAUCCGUUCAGCACUCCAGAGG-GAC-UUCAGAGCUGU-CCUUCCCUGAACUAAAGCUGGAGUAUUUUAGGAUUUG--GAGAAUUAAG-------
ABDC01028873.1/10792-10925   AAUCCUGUUACACCUGGGAUUUAGGUCCUUUUAAUCUGAAAAAAA--AAAUACAUACUCCUUCAGCAUUCCAGAAG-GAU-UUGAGAACAAU-CCUUCCCUGAACUAAAGCUGGAAUACUGUGGGAUU-G--GAGAAUUAAG-------
ABRT010710007.1/522-651      AAUCCUGUUCCACCUAGGAAUUAGGUGCUUUUACUCUGAGAAAA------UACAUAGCCCUUCAGCACUCCAGAAA-GAC-UUGAGAACUGU-UCUUCCCUGGACUAAGCCUGGAACAUUUGGGGACU-G--GAGAAUUAAG-------
ABRQ01037090.1/12780-12907   AAUCCUGUUAUACCUAGGAGUUAGGUACUUUGAAUCUGACAAGA------CACGUGUCUGUUCAGCACUCCAGAGG-GAU-UCGAGAACUGU-CCUUCCUUGAAGAAU-GCUGGAAUA-UUGGAGUUU-A--GAGAACUAAG-------
ABVD01898602.1/170-39        AAUCCUGUUAUACCUGGGAUUUAAGUACUGUAGAUCCG-AAAAG----CAUGUGUGUCCUCUCAGCACUUCACAGG-GAC-UUGAGAAAUGC-CCUUCCCUGAACUAAAGCUGGAUUUUCUUGGGAUUUG--GAGAAUUAAG-------
AAFC03094310.1/34367-34498   AAUCUUGUUACACCUGGGAUUUUGGUGCCUUUAAUCUGAGAAAA----AGUACAUAUCCAUUCAGUAAUCCAAAAG-GAC-UUGAAA-CUCU-UCUUCUCUGAACUAAAGCUAGAGUAUCAUGGGAUUUA--AAGAAUCAAG-------
AAKN02041846.1/188770-188640 AAUCCUGUCACACCUGAGAUUUAAGUGCUUACAACCAG-AAAAA----UCUGCAUAUUCAUUCAGCACUGCAGAAG-AAC-UUGUGGACU-U-CUUUGCCUGAGUUAAAGCUGGAAUAUUUGGGAGUUUG--GAGAAUCAAG-------
ABRN01339755.1/27562-27698   CAUCCUGCUCCACCUGGGAUUUAGGUGCCUUUAAUUUGACAAAAGAAGAAUACGUAUCCAUUCAGUACUCCAGAGG-GAC-UUGAAAACUGU-UCUUCCCUGAACUAACGCUGGACUAUCAUGGGAUGUG--AAGAAUCAAG-------
AANG01423812.1/5336-5467     AGUCCUGUCCUACCUGAGAUUUUGGUGCCUUCAAUCUG-AAAAA----AAUACGCAUCCCUCUGGUACUCUAGAGG-AAC-UUGAGAACAGU-CCUUCCCUGAACUAAAGCCAGACCAUUGUGGGAUUUG--GAGACUAAAG-------
ABRP01177240.1/8111-8238     AAUCCUGAUAUACCUGGGAU-UAGGUGCUUUUAACCCG-AAAAA----UGUACAUAUCCAUUCGACACUCCUGAGG-GAC-UUGAGAAC-GU-CCUUCUC--AAGUAAAGUUGUGAUGUCUUAAGAUUUG--GAGAAUUAAG-------
AAYZ01075606.1/1190-1315     AAUCCUGUUAUACCAGUGAUUUAGAUUAUUUGAAUCUAAAAAAA---ACCUGCCCAUUCACUCAGUGCUCCAGAAG-GAC-UUGAGAGCUGU-CCUUCCCUGGACAGAAGCUGAAACAUUUGGAGAAUUA---AG--------------
ABRR01450788.1/179-312       AAUCCUGCUGUGCUUGAGAUUCACGGGCCUUUCAUCUGAAAAAA---AAAUACAGCUCCAUUCAAGACUCCAGAAG-GAU-UUGAAAACUGU-CCUUUUUUGAGCUAAAGCUGGAGUAGCAUGGGAUUCG--GAGGGCCACG-------
AACN010982509.1/479-611      AAUCCUGUCAUACCUCGGAUUUUGGUGCCUUCAGUCUG-AAAAA----UACACACAUCCAUUUGGUACCCUAGAGG-AAC-UGGAGAAUUGU-CUUCCCCUGAAUGAA-GCUGGACCAUUCUGGGAUUUGGAGAAAGGUAAG-------
ABGA01029396.1/1164-1043     AAUCC---------UAUGAUUUAGGUCCUCUGAGUCUG-AAAAA----AAUAUGUGUUCACUCAAUACUC-AAAGG-GAC-UUGAGAAAUGU-UCUUCCCUGAACUAUACCUGGAAUACCUUGUGAUUUG--GAGAAUUCAG-------
ABRO01134620.1/3634-3768     AAUCCUGUUACACCUGGGAUUUCCAUACUUACAACCUGCAAAAA----CAAAAAAGUGUUGUAAGCCCUCCAGAAGCAAA-UCUAGGAC-AU-CCUUCCCUGAAUGAACGCUGGGGUAUCUGGAGAACUGACGUGAGGUAAG-------
AALT01028797.1/1476-1608     UUUCUUGUAACUCCAUAGACCUGGGUGUCUUGGAUCUGAAUAAA----AUUACAUGACCAUUCAACUCUCCAGAGG-AAC-UUGAGAAUCAUUCUUUUCUUGAGCUGAAG-UGGGAUAUUUUGGAAUUUU--GAGAGUUAAG-------
AAGV020253241.1/242-370      CAUCC--UCAUACCUGGGAUUUAAGCUCAUUGGAUCUGAGCAAC---GGCUG--UAUCCAUUCAGCACUCCAGAGG-GUC-UUGAGAACCGC-CCUUCCCUGGACUGAAUUUGGAGACUCAAGGUAAG-G--GAG-------CUUCUCC
AABR05147329.1/23773-23903   CAUAUUGAUAC---UGAUAAGUCUCUCUCCUUUAUUUGCAUUUU----CUAGCAUAUCCUUUAAGCAUUCCAGAAG-GAUUUUGAGAACCAU-CCUUUCCUAAAUCAAAGCUAGAAUAUUUGGAGAUUUG--GAAAAUUGAG-------
AAQR03010384.1/7855-7729     AAACGUAUUACACCUGGGAUUUAGGUGCUUU-AAUCUGAAAAAG------UACAUAUUCCCUCAGCAUUCUAGA-G-GAU-UUGAGA-CUAU-CCUUCCCUGAACUAAAGCUAGAAUCUUUCAGGAUU-G--GAGAAUUAAG-------
AAGW02013345.1/85946-86075   AAUCCUGUUAGACCUGGGAUUUCGACACUUUCAGUCUGAAAAAC------UGCGCGUCCACUCAGAACCCCAGAAG-GAC-UUAGGCACUGC-CCUUUCCUGCUGAGAAGCUGGAACA-UUUGGCAUUUG--GAGCAUUGAG-------
AAPE02026186.1/14829-14709   GAUCC---------UGGGAUUUAGGUGCCUUUCGCCUGAAAACA------CACGUGUCCAUUCAACACUCCAGAGG-AAC-CCGAGCGCUGG-CCUUCCCUGGACUCCAGUGGUAACGCCUUGAGCUU-G--GAGGAGGGAG-------
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::....::::::::::::::::::::::::::::.:::.:::::::::::.:::::::::::::::::::::::::::::::::::::..::::::::::.......
#=GC RF                      aAUCCUGUuacACCUGGGAUUUagGUgCuUUuaaUCUGAaaAAa....aauaCauaUCCaUUCAGcACUCCAGAgG.GAC.UUGAGaACuGU.CCUUcCCUGaacuaAAGCUGGAauaUuuuGGGAUUUG..GAGaauuaAG.......
//
# STOCKHOLM 1.0

#=GF AC   RF02169
#=GF ID   PVT1_6
#=GF DE   Pvt1 oncogene conserved region 6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   45.00
#=GF TC   47.40
#=GF NC   39.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.58 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   17503467
#=GF RT   The PVT-1 oncogene is a Myc protein target that is overexpressed in
#=GF RT   transformed cells.
#=GF RA   Carramusa L, Contino F, Ferro A, Minafra L, Perconti G, Giallongo A, Feo S
#=GF RL   J Cell Physiol. 2007;213:511-518.
#=GF WK   PVT1
#=GF SQ   7


AC007860.6/18009-18121     AGCCAGUCUUGGUGCUCUGUGUUCACCUGGUUCAUCUGAGGAGCUGCAUCUACCCUGCCCAUGCCAUAGAUCCUGCCCUGUUUGCUUCUCCUGU-UGCUGCUAGUGGACAUGAG
AANU01107823.1/10843-10955 AGCCAGUCUUGGUGCUCUGUGUUCACCUGAUUCAUCUGAGGGACUGCAUCUACCCUGCCCUUGCCAUAGUUCCUGCCCUGUUUGCUUCUCCUGU-UGCUGCUAGUGGACAUUGC
AANG01423833.1/3416-3527   AUCCAGUCUUGGUGCACGGUUUACACUUAGCUCAUAAGAGGG-CUGCGUCUGCCCUUCCGUCGCUGCAGAUCCUGCCCUGUUCACUUCUCUUGU-CCCUGCAGAUGGACACUAG
ABRP01234926.1/706-816     AUCCAGUCUGGUGGUUCUGCGUACACCUAGCUCGUCAGAGGGGCUGCAUCGACCCG--CCUUGCCAUUGGUCCUGCCACGUUUUCCUCUCUCGU-CCCUGUUGAGGGACACGAA
AACN010003212.1/2969-2857  AUCCAGUCUUGGUGCACAACGUACGGGUAGCUCACCGGAGGGGCCGCAUCUGGCCUUCCCUUGCCUCGGGUCUUGCCCUCUCCGCUUCUCUGGU-CCCUGGAGGUGGACACUAG
ABDC01028886.1/1691-1790   AUAUAGUCUUGGUGCUCUGUGUACACCUGGCUCACCUG--------------CCUGUCCUCUGUCGUAGGUCCUGCCCUGUUUAAGUCCCCUGUGCCCUGCUGGGGGACACUAG
AAGV020253253.1/1920-2018  ACCCAGCCCUGCUGCUCUGUGUACCCCCGGUUCAUCUG---------------CCACCCCCUGCCCUAGGUCCCUCCCUCUUUACUUCUCUGGUGGCCCGCUGAUAGACACCAG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::
#=GC RF                    AuCCAGUCUUGgUGCuCuGuGUaCaCcUgGcUCAUCuGAGGGGCuGCaUCugCCCuuCCcuUGCCaUaGgUCCUGCCCUgUUUgCuUCUCuuGU.ccCUGcuGguGGACACuAG
//
# STOCKHOLM 1.0

#=GF AC   RF02170
#=GF ID   PVT1_7
#=GF DE   Pvt1 oncogene conserved region 7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   93.30
#=GF NC   77.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.77 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   17503467
#=GF RT   The PVT-1 oncogene is a Myc protein target that is overexpressed in
#=GF RT   transformed cells.
#=GF RA   Carramusa L, Contino F, Ferro A, Minafra L, Perconti G, Giallongo A, Feo S
#=GF RL   J Cell Physiol. 2007;213:511-518.
#=GF WK   PVT1
#=GF SQ   8


AC007860.6/44367-44503       AAGGACA-GAAUAACGGGCUCCCAGAUUCACAAGCCCCACCAAGAGGAUCACCCCAGGAACGCUUGGAGGCUGAGGAGUUCACUGAGGCUACUGCAUC-UUGAGACUCAGGA---UGAAGACCCAGCUUGGGGCUGUCAAAG
AANU01107823.1/36720-36855   AAGGACA-GAAUAAUGGGCUCC-AGAUUCGCAAGCCCCACCAAGAGGAUCACCCCAGGAACCCUUGGAGGCUGAGGAAUUCACUGAGGCUAGUGCAUC-UCGAGACUCAGGA---UGAAGACCCAACUUGGGGCUGUCAAAG
ABRP01127593.1/2711-2843     AAGGACC-AAACGACAGGCUCCCAGAUUCCUAAGCCCCAAUAAGAGGACCA-CCCAGGUAGCACUGAAGGCU---GAGUUCACCAAGGCGAGUGCAUC-CUCGGGCUCAGGA---CAGGAGCCCGUCUCUGGGCUGGCAGAG
AAWR02021560.1/157967-158099 AAGGACA-GAACGACAAGCCCCCGGAUUCCUAAGCCCCAACGAGAGGACCA-UUCAGGAACCACUGAAGGCU---GAGUUCACCAAGGUGAGUGCAUC-CUUGCAACCUGGA---CAGGAGCCCAGCUCUGAGCUAACAAAC
AAPY01577453.1/1297-1418     ---AACAUGAACAACAGACUCCCAGAUGUCUAAGCCCUGACCAGAGGACCAGUCUGGGAACCAGUAAAGGCUCAUGAGUUUACUGUGGCAAGUGCACC-C----------------AAGAGCCCAGCAUGGGGCUGGCAAAG
AC210209.2/185141-185003     AAAGACA-AAACAACAGCGUCCCAGAUUCCUAACCCCUGAUGAGAGGACUUCUCCAGAAACCACAGAAGGCUGAAGAAUUCACACAGACAAGCACAUC-CCAGUGACUCUCAGA-UAGGAGUUCAGCUCCAGGCUAGCAAAC
AANG01748875.1/12986-13119   AAAGACA-GAAUAACAGGCUUCCAGGUCCCUACGCCCCAAGGAAGAGACUG-ACCAGGAACCCAUGAAGGCU---GGGUUCAAUGAGACAAGUACAUC-CUUGCAACUAAAGGUGCAGGAAGUCAGC-CAGGACUUCCAGG-
AAGW02013349.1/16245-16384   GAGGACA-GAGUUACAGGCACCCAGGCCCUUAAGCCCCAACCAGACGAUUGCCCCAGGAAUGAGUGAAGAUGGAGGGGUUCAGCAAGGCCCCCCUGCCACCCCAGACUCACACAUGUAGAUUCUGGCCCCAGUCUCGUAAG-
#=GC SS_cons                 :::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::...:::::::::::::::::::::::::::
#=GC RF                      AAGGACA.GAAuaACAGGCuCCCAGaUuCcUAAGCCCCaacgAGAgGAccaccCCAGGAAccagUGAAGGCUgAgGaGUUCAcugAGGCaAGugCAuC.CuugggacuaggA...uagGAgcCCaGCucgGGgCUggCAaag
//
# STOCKHOLM 1.0

#=GF AC   RF02171
#=GF ID   RFPL3-AS1_1
#=GF DE   RFPL3 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   70.00
#=GF TC   109.70
#=GF NC   53.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.66 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10508838
#=GF RT   Duplications on human chromosome 22 reveal a novel Ret Finger Protein-like
#=GF RT   gene family with sense and endogenous antisense transcripts.
#=GF RA   Seroussi E, Kedra D, Pan HQ, Peyrard M, Schwartz C, Scambler P, Donnai D,
#=GF RA   Roe BA, Dumanski JP
#=GF RL   Genome Res. 1999;9:803-814.
#=GF WK   RFPL3-AS1
#=GF SQ   4


AL021937.1/51514-51601   CUUCAUGUGAGUGCACCCGGUGGUUUGCCCAGAGUCCAGGUUGUGUCAUGUGCCUCUUGGUGUAGAGGCUAUAUCUUCUUAAAAUUUC
AC188069.1/2291-2378     CUUCACGUGAGUGCGCCCGGUGGUUUGCCCAGAGUCCAGAUUGUGUCAUGUGCCUCUUGGUGUAGACGCUAUAUCUUCUUAAAUUUUC
AANU01294791.1/3391-3304 CUUCAUAUGGGUGCACCCGGUGGUUUGCCCAGAGUCCAGGUUGUGUCACGUGCCUCUUGGUGUAGAUGCUGUAUCUUCUUAAAGUCUC
ABGA01087082.1/3717-3630 CUUCAUGUGGGUGCACCUGGUGGUUUGCCCAGAGUCCAGGUUGUGUCAUGUGCCUCUUGGUGUAGACACUGUGUCUUCUGAAAGUCUC
#=GC SS_cons             ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  CUUCAuGUGgGUGCaCCcGGUGGUUUGCCCAGAGUCCAGGUUGUGUCAuGUGCCUCUUGGUGUAGAcGCUgUaUCUUCUuAAAgUuUC
//
# STOCKHOLM 1.0

#=GF AC   RF02172
#=GF ID   RFPL3-AS1_2
#=GF DE   RFPL3 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   41.20
#=GF NC   39.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.84 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10508838
#=GF RT   Duplications on human chromosome 22 reveal a novel Ret Finger Protein-like
#=GF RT   gene family with sense and endogenous antisense transcripts.
#=GF RA   Seroussi E, Kedra D, Pan HQ, Peyrard M, Schwartz C, Scambler P, Donnai D,
#=GF RA   Roe BA, Dumanski JP
#=GF RL   Genome Res. 1999;9:803-814.
#=GF WK   RFPL3-AS1
#=GF SQ   3


AJ010233.1/158-88       CUUGGUAACAGAGAAGGGGUCCUCACUUGCCCACUCUUUGGAAUCCACCUUCCAUUGAUCUUCUGGGGGAA
AANU01294782.1/439-509  CUUGGUAAUAGAGAAGGGGUCCUCACUUGCCCAGUCUUUGGAAUCCGCCUUCUGUUGAUCUUCUGGGGAAC
ABRT010789798.1/681-751 CUUGGUAAUAUAGUUGGGCUCCUCAUUUCCCCACUCUUUGGAAGUCAUCUUCUCCUCAACUUCUGGGGGAA
#=GC SS_cons            :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                 CUUGGUAAuAgAGaaGGGgUCCUCAcUUgCCCAcUCUUUGGAAucCacCUUCuguUgAuCUUCUGGGGGAa
//
# STOCKHOLM 1.0

#=GF AC   RF02173
#=GF ID   SMAD5-AS1_1
#=GF DE   SMAD5 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   45.00
#=GF TC   47.80
#=GF NC   38.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.96 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10049768
#=GF RT   An antisense transcript to SMAD5 expressed in fetal and tumor tissues.
#=GF RA   Zavadil J, Svoboda P, Liang H, Kottickal LV, Nagarajan L
#=GF RL   Biochem Biophys Res Commun. 1999;255:668-672.
#=GF WK   SMAD5-AS1
#=GF SQ   18


AC009014.5/74842-74577       GGAAAGGAAGCUUUAUUGUUUCCAAGGACUCUG-CUGGAGGAGUCAUACAAACUUCGCCAUUUCUUCCUCUGAUGUCCAUGUGCCAUGAUUGUCUGAGGAAGGGAGAAAAAGUCUUUGAAGUGGCUACCAGG----AUCCUUUGCAGAUCUCUGGGAUG----UCAUUCACUCAUGCU-UCUAUGCUGGGUG----ACUCCUACCAUCAUCACAUUCUUCCAAUUCUCCCAGUAGGGUAUGCAGUAGUCAUGUA-GGCAGAGCCUUCUGAGCUACAGCAAA---
ABDC01055301.1/12098-12366   GGAAAGGAAGCUCCAUUGUUUCCAAGAACCCUGUCUGGAGGAGUCACACAAAUUUAGACAUUUCUUCCUCUGAUGUCCAUGCACCGUGAUUGUCUGAGGAAGA--AGAGAAGUCCUUGAGGUAGCCACCAGG----ACACUUUAUGGCUCUUUGUAAUG----UCAUUCACCGAUGCU-CCUACCCUGGGUGGACUCUUCCUAACAUCAUCACCUUCUUCCGAUUCUCCCAGGAAUGUAUGCGGUAGUCAUUUA-GGGAGAACCUUCUGAGCUACAGCAAA---
ABRR01145896.1/4990-5252     UGAAACACAGCUUUCUUGUUUCC-AGGAUACUGUCCAGAGAAGUCACACAAACUUAGACAUUUCUUCUUCUGAUGUCCACUUGCCAUGACUGUGUGAGGAAGG---GAGAGGUCUCUGAAGUGGCUACCAGG----GCCCCUUGUAGAUCUCUGUGAUG----UCAUUCACUAAUGCU-UUUACACUGGGUG-ACUCCUUCUAACAUCACCACAAUCUUCCAGUUCUAUGGA----GAAUGCACUGAUUAGUUAUGGAAAAAUACUCUGAGCUACAGCAAA---
ABVD01168129.1/1239-1495     GGAAAGGCAGCCUUAUUGUUUCCAAGGACAAUAUCCGGAGGAGUCACACAAACUUUGGCAUUUCUUUCUCUGAUGUCCACUUGCCAUGACAGUCUGAGGAAGU---GAGAAGUCUUUGAGGCAGCAACCAGA----AACUUUUAUGG-----UGGGAUG----UCAUUCACUGAUGCU-UCUAGGCUGGGUG-ACUUUCUCCAACAUCACUACAUUCUUCCAAUCCUACUGG----GUA-GCACUAAACAUUUA-GGGAGAAUCUUCUAAACUAUAGCAAG---
ABRN01383331.1/5239-5500     GGAAAGGUGGCUUUAUUGUUUCC-UGGACAAUGUCCAGAGGAGUCACACAAACUUAGACAUUUCUUCUUUUGAUGUCCACUUGCCACGACUGUGUGAGGAAGU---GAGAGGUUUCUUAGGUGGCUACCAGG----ACCCUUUAUGGAUCUCUGUGAUG----UCAUUCACUGAUACU-UCCACACUGGGUG-ACCCCUCUGAACAUCACCACGUCCUUCCACUUCUACUGG----GUGUGCACUGGUCAUUUA-GGGAGAAUCUUCUGAGCUAUAGCAAA---
ABRT010053602.1/3897-4152    GGAAAGGAAGCUUUAUUUCUUCCAAGAACCCUAUCUGGAGGAAUUAUGCAUACUUAGACAAUUCUUCUUCU-------AUUUGCCAUGAUUGCCUGAGGAAG----GAGAAGUCUCUGAGAUAGCUACCAAG----ACCCUUUAUGGAUCUCUGUGGUG----UUAUUCACUGAGGCUUCCUAGGAUGGGUG-ACUCCUCCUACCAUCAUUGUAUUCUUCCAAUUCUCCCAGUAGGGUAUGCAGUAGUCAUUUA-GGGAAAACCU----GACUAUGGCAAA---
AAWR02002460.1/279360-279099 GGAAAGGCAGCUUGACUGUUUCC-CGGACACUGUCUGGAGGAGUCACACAAACUUAGACAUUUCUUCCUCUCGUGUCCACUUGCCAUGACUAUCUGAGGCAGA---GAGAAGUCUUUGAGAUAGCUACCGGG----ACCCUACAUGGAUCUCUGUGAUG----UCAUUCACUGAUCCU-UCUAGGCCAGCCG-ACUCCUCUAAACAUCACCAUAUUCCUUCAAUUCCACUAG----GUGUGCCCUGGUCAUUUA-GGGAGAAUCUUCUGGGCUACAGCAAA---
AAFC03075338.1/29529-29790   GGAAAGACAGGUUUAUUGUUUCC-CAGACAUUGUCGAGAGGGGUCACACAAACUUAGACAUUUCUUCCUUUGAUGUCCACUUGCCAUGGCUGUGUGAGAAAGU---GAGAUGUCUCUGAGGUGGCUACCAGA----UCCCUUUAUGGAUUUCUGUGAUG----UCAUUCAUUGAUCCC-UCUACACUGGGCA-ACUCUUUGGAACAUCACCACAUUCUUCCAAUUCUACUGG----AGGUCCACUGGUCAUUUA-GGGAGAAUCUUCUGAACUACAGCAAA---
ABRP01033331.1/9134-9399     GGGAAAGCAGUUUUAUCAUUUCC-AGGACACUGUCUAGAGGAGUCAUACAAACUUAGAUAUUUCUUGCUCUGAUGUCUACUUGCCAUGUCUGUGUGAGGAAGU---GAAAAGCCCUUGAGGAGGCUCUUAGG----ACCCUUUAUGGAUCUCCAUGAUGUCAUUCAUUCACUGCUCCU-GCUAUGCUGGGUG-ACUCCUCCAAACGUCAUCACAUUCUUUCAUUUCUACUGG----GUGUGCACUGGUCAUUUC-AGGAGAAUCCUCUGAGCUACAGCCAA---
ACBE01024211.1/3098-3358     GGAGAGGAAGCUUUAUCAUUUCC-AGGACACUGUCCAGAGGAGUCACUCAAACUCAGGCAUUUCUUCCUCUGAGGUCCACUUGCCAUGACUUUCGGAGGAAGU----GAGUGUCUCGGAGGUGGCUAUGAGGUGGGACCCUUCGCA--UCUCUGUGGU------CACUCACUGAUCCU-UUUAUGCCGAGUG-ACUCCUCGAAACACCAUCACGUUCUUCCAAUUCUAGUGG----GUGUGCGUUGGGCAUUUA-GGGAGAAUCUUCUGAGCUGUAGCAAA---
AAPY01647327.1/586-844       GAAAAGGAAGCUUUAUAAUUCCCAAGGGCCCUGUCUGAAAAAGUCAUGCAAACUCAGGUAUUUCUUCCUCUGAUGUCCGCUCAUCACGA----CUGAAAAAGU---GAGAAGUCUUUGAGUUCACUACCAGG----ACUCUAUCUAGAUCUCCAUGGUA----UCAUUCACUGAUGGCUUUCAUACUGGGUG-ACUUCUCCGA-UAUCGUCACAUUCUUCCGAUGCUAUUUG----GCCUGCAGUAAUUCUUUG-GAGAGAACCAUAUGAGCUACAGAAAG---
ABRQ01183941.1/1348-1608     GACAAGGCAACUUUAUUGUUUCCAAGGAUAAUAUCUGGAGGAAUCUCGUAUACUUGGGCAUUU-UUCCUCUGAUGUCCACUUGCUAUGCCCAACUAAGGAAGU---AAAAAGUCUUUGAGGCAGCUACCAGG----ACUCAUUAGGGGUCUCUGUGAUG----CUGUUUUCUGAUACU--CUAGGCUGAGUG-ACUUCUCCAGAUUUCCCCACAUUCUUCCAGUUUUACUGG----GUACAGAUUAGUUAUGAA-GGGAGACUCUUCCAAGCUACCGCAAA---
AAQQ01033829.1/1760-2009     GGGAUGGAAGUUUUAUUGUUUCUAAGGAUCCUGUCUGGAGGAGCCAUACAAAC-----------------UGAUGUCCACUUUUUAUGGCUGUCUGUAGAUGU---GAGGUGUCUUUGACUUAUCUACCCAG---AGCCCUUUGAGGAACCUUGUGAUG----UCAAUUGCUGAUACA-UCUAUGCUGUGCAAUGUCCCCCAAAUGCCAUUGCAUUCUUCCGGCUCUACUGG-----GGCCUGAGAGUUAUUUA-GGCAGAAUCUUCUGAGCUAUUACAGCAAU
CAAA01017758.1/118-366       GAAACGGGAGCUUUAUUCUACCGUAGGAUCCUGUCUGCGGAACGCAUAUAAACUUAGGCAUUUCUUCCUCUGGUGCCCACGUUCCAUAA----CUGAGGAUGG--C-GGGUGUCUCUGGGG-GGCUAUGAAG---------GUGUGGAUGCCUGUGAUAA-UGUCACUCCUUGAUGCU---UCUGUUGGGUG-AUGCCACCAAA---CCCUGGAUUCUUCUAGCUCCACUGG------AUGUGUAGGUAUAUUA-GGGAGGGUCUUCUGAGUUAAAGCAAA---
AAGU03004546.1/6191-6451     GGAAAGGCGGCGUUAUUAUUUCCGAGGACAAUGUCUGGAGGAGUCACAUACCUUUAGGCAUUU-UUCCUCUGAUGUCCAAUUGCCAUGACCAUCUGAGGAGGU---AAAAAAUCUUUGAGGCAGUUACCAGG----ACUCUUUAUGGGUCUCUGUGAUA----UCAUUUACUGAUACC--AUAGGCUGGGUG-ACUUCUCCAGACAUCCUCACAUUCUUCCAAUUCUACUGG----GUACACACUAGUUACUUA-GGGAGAAUGUUAAGAGCUACAGAGAA---
AAEX03007799.1/84457-84717   GAAAAGGCAGCUUUAUUGUUUCC-AGGACCCUGUCCAGAGGAGUCACUCAAGCUCAGACAUUUCUUCCUCUUGUGUCCACUUGCCACGACUGUCUGACAAAGU----GGGAGUCU--GAGGUGGCUACUAGGUAGGACCAUUUGCAGAUCUCUGUGAU------CAUUUGCCGAUCCU-UCUACAGUGGGUA-GCUCCUCCAGACAUCAUCAUGUUCUUCCAGUUCUACUGG----GUGUACGAUGGUUCUCAA-GAGAGAAUCUUCUGAGCUAUAGCAAA---
AAHX01089885.1/55639-55404   GAAAUGGAGGUUUUCUUCUACCUAAGGAUCCUGUCUGCAGAACAUAUUUAAACUGGGGUGUUUCUCCCUCUG---------UUCCAUAACUGUUUGAGGAUGG---CAGGUGUCUCUUGGG-GGCUGUGAAG---------GUCUGGAUGCCUGUGACAA-UGUCACUCCCUGAUGCU---UCUGUUGGGUG-AUACCGCCAAA---CCCUGAAUUCUUCCACU--------------GUAUGUAGGUAUAUUA-GGGAGAGUCUUCUGAGUUACCGCAGA---
AAPE02012974.1/32726-32468   GAAAAGGCAGCUUUG---UUUCC-AGGACACUGUCUGAAAGAGUCAUACAAAC--AGAUAUUUUUUGCUCUGAUGUCCACUUGCCAUGACUGUCUGGGGAAGU---GAGAAGUCUUUGAGGUGGCUACCAG-----ACACUUUAUGAGUCUCCCUGAUGCCAUUCAUUCACUGAUCCU-UCUACGCUGGGUA-ACAC-UCCAAACAUGAUCACAUUCUUCCAGUUCUACUGG----GUGUGUACUGGUCAUUUG-GGGAGGAUCUUCUAAGCUUCAGCUAA---
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::...::::::::::::::::::::::::::....:::::::::::::::::::::::....:::::::::::::::.:::::::::::::.:::::::::::::::::::::::::::::::::::::::....::::::::::::::::::.::::::::::::::::::::::::::...
#=GC RF                      GGaAaGGaAGcUUUaUUgUUUCcaaGGAcacUGUCuGGAGGAGuCAuaCAaACUuaGgCAUUUCUUCCUCUGAUGUCCAcUUgCCAUGaCUGUcUGAGGAaGu...gAGaaGUCUuUGAGGugGCUACcAGG....aCcCUuUauGGaUcUCUGUGAUG....UCAuUCaCUGAUgCu.ucUAuGcUGGGUG.acucCuCCaAACaUCaucacaUUCUUCCAaUUCUaCuGG....GugUgcauugGUcauUUa.GGGAGAaUCUUCUGAGCUAcaGCaAa...
//
# STOCKHOLM 1.0

#=GF AC   RF02174
#=GF ID   SMAD5-AS1_2
#=GF DE   SMAD5 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   51.40
#=GF NC   47.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.89 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10049768
#=GF RT   An antisense transcript to SMAD5 expressed in fetal and tumor tissues.
#=GF RA   Zavadil J, Svoboda P, Liang H, Kottickal LV, Nagarajan L
#=GF RL   Biochem Biophys Res Commun. 1999;255:668-672.
#=GF WK   SMAD5-AS1
#=GF SQ   20


AF071109.1/347-475           UAUUCCAGUCUCUUCCCCUCCCCUUUUCCCCUCUCCU-------CCUUUCAGCUGCUGUUACUACGUGG--AGUUUGGAGCC-U-AAGCU-UUGAAAACUCCCAUGUGGCGCGCCCGUCUUAA-GUCUGAGCAUGCUCAGUA
ABRP01033332.1/2854-2980     UUUUCCAGUCUCUCCCCCUCCCUUUUCCCUCUCUUCC-------CCUUUCAGCUGCUGUUAUUACGUGG--AGUUUGGAGCC-U-AAGCU-UUGAAAACUCCCAUGUGGCGC--CCGUCUUAA-AUCGGAGCAUGCUCAGUA
AAPY01035600.1/2651-2778     UAUUCCAGUCUCUUCCCCCUCCCC-----CUUUCCUCUCUUC-CCCUUUCAGCUGCUGUUAUUACGUGG--AGUUUGGAGCC-U-UAGCU-UUGAAAACUCCCAUGUGGCGC--CUGUCUUAA-GUUAGAGCAUGCUCAGUA
AAWR02002460.1/275215-275083 UAUUCCGGCCUCUCUCCCUCCCCCGCCCUUUUUCCUCUCUUC-CCCUUUCAGCUGCUGCUAUUACGUGG--AGUUUGGAGCC-U-AAGCU-UUGAAAACUCCCAUGUGGCGC--CUGUCUAAA-GUCGGAGCAUGCUCAGUA
AAFC03075338.1/33749-33875   ------UGCCCCCUCCCCAUGCUCUCCCUCUUUCCUCUCUUC-CCCUUUCAGCUGCUGUUAUUACGUGG--AGUUUGGAGCC-U-AAGCU-UUGAAAACUCCCAUGUGGCGC--CUGUCUUAA-GUCGGAGCAUGCUCAGUA
ACBE01024212.1/541-673       UAUUCCGGGCUCUCCCCCUCCCCCGCCCGUUUUCCUCUCUUC-CCCUUUCAGCUGCUCUUAUUACGUGG--AGUUUGGAGCC-U-AAGCU-UUGAAAACUCCCAUGUGGCGC--CUGUCUUAA-GUUGGAGCAUGCUCAGUA
AAQQ01033872.1/493-621       ----UUUUCCAGACCCCCGCCACCUUCCCUUUUUCCUUCUUC-CCUUUUCAACUGCUGUUAUUACGUGG--AGUUUGGAGCC-U-AAGCU-UUGAAAACUCCCUUGUGGCGC--CUGUCUUAA-GUCCGAGCAUGCUCAAUA
ABRN01383331.1/9219-9351     UAUUCCGGUCUGUCCCCCUCCCCCUCCCUCUUUCCUGCCUUC-CCCUUUCAGCUGCUGUUAUUACGUGG--AGUUUGGAGCC-U-AAGCU-UUGAAAUCUCCCAUGUGGCGC--CUGUCUUAA-GUCGGAGCAUGCUCAGUA
ABRQ01183941.1/5632-5758     ------CACGGCUCUUCCCUCCCCCCACUUUUUCCCCCUCUU-CCCUUUCAGCUGCUGUUAUUACGUGG--AGUUUGGAGCC-U-AAGCU-UUGAAAAUUCCCAUGUGGCGC--CUGUCUUAC-GUCGGAGCAUGCUCAGUA
AAKN02022958.1/9419-9545     -------UCUUUUUGUCCUUUACCACCCGGUUUCCUCUCCUCCCUUUUUCAGCUGCUGUUACUACGCAG--AGUUUGGAACC-U-AAGCU-UUGAAAACUCUCAUAAGGCGC--CUGUCUAAA-GUCAGAGCAUGCUUAGUA
ABRT010053604.1/1724-1848    UAUUCCAGCCUCUUCCCCUCCUCCUCCCCCUUUUCCCUAUUC-CCCUUUCAGCUGCUGUUAUUACGUGG--AGUUUGGAACC-U-AAGCU-UUGAAAACUCCCAUGUGGCGC--CUGUCUUAA-GUCUGAGGAA--------
AAIY01523265.1/4393-4510     -----------UAUCCACGGCGCCUCCC---UCCCCCUCUUC-CCUUU-CAGCUGCUGUUAUUACGUGG--AGUUUGGAGCC-U-AAGCU-UUGAAACCUCCCAAGUGGCGC--CUGUCUUAA-GUCGGAGCAUGCUCCGUU
ABVD01168131.1/114-240       ------AUGUCCCCCUUCCUCGGUUCCC-CUCUUCUCCAUUUUCCCUUUCAGCUGCUCUUAUUACAUGG--AGUUUGGAGCC-U-AAACU-UUGAACACUCUCAUAUGGCGC--CUGUCUUAA-AUCGGAGCAUGCUCAGUA
AAYZ01609777.1/414-540       ------UACUCAGAGCUGGACUCCAGGCCCCCUGCCCCCUCCCCCCUUCCAGCCGCUGUUGUUACGUGG--AGUUUGGAGCU-U-AAGCU-UUGAAAACUC-CAAGUGGCGC--CUGUCUGAA-GUCGGAGCAUGCUCAGUA
AAGV020384958.1/212-339      ------UUCUCCACCCCACUCGCCACCCACCUUUCUCCUCUUCCGAUUUCAGCCACUCUUAAUUCCGGG--AGUUGGGAACC-U-AAGCU-UUGAAAACUCCCAUGUGGUCC--UUGUCCUAA-AUUGGGGCAUUCUCAGUA
ABDC01055302.1/753-880       ----CCAGUCUCCUCCCCUCCUCCUCU--UUUCCCCCUCGUUUCCCUUUCAGCUGCUGCUGUUACGUGG--AGUUUGGAGCC-U-AAGCU-UUGAAAACUCCCAUGUGGCGC--CUGUCUUGA-GUCUGAGCAUGCUCAGUG
CAAA01017758.1/3829-3955     ----CAAGUUCAGACUCCAUCCCCUCCCCCUGCCCUUU------CUCCUCUGCGCUUCUGGCUGCGCCG--AGCCGGGAACCCU-AAGCUCUGGGAACUUCCCCGGUGGCGG--CCGUCUUAGGGUCAGAGCAUGCUCAGUG
ABQO010020562.1/3113-2986    ----AAAGCACAGCCCCCUUUCCAAUUCUGUGGGGUCUGUGU-CCCCCUCAGCUGCUGCUAAGAGCUGGAGAAGUGGAAUCC-U-AAG---UUGA-AACUCCAAUGUGGUUC--UAGUACAGA-AACUGGGCAUGCUCAGUA
AAQR03009545.1/7988-7858     ----CUAGUCUCUUCCCCUCCUCCUCCCCCUUUCCCCUCUUUUCCCUUUCAGCUGCUGUUAUUACGUGG--AGUUUGGAGCC-UUAAGCU-UUGAAAACUCCCAUGUGGCGC--CUGUCUUAA-GUCUGAGCAUGCUCAGUA
AAHX01089885.1/52074-51959   ------------------UACUCCACUCCCUCCCCCUACCCUUUCUCCUCUGCGCUGGUGGCAGCGCUG--AGCCGGGAGCC-U-GAGCU-UUGAGAACUCCCCUGUGACGG--CCGUCUUCG-GUCAGAGCAUGCUCACUG
#=GC SS_cons                 ....::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::..:::::::::::.:.:::::.:::::::::::::::::::::..:::::::::.::::::::::::::::::
#=GC RF                      ....ccagcuucuccCCCuuCcCcuccCccUuucCucucuuu.CCcUUUCAGCuGCUGUUauUaCGuGG..AGuUuGGAgCC.U.AAGCU.UUGAAAACUCCCaUGUGGCGC..CuGUCUuaa.GUCgGAGCAUGCUCAGUa
//
# STOCKHOLM 1.0

#=GF AC   RF02175
#=GF ID   SMAD5-AS1_3
#=GF DE   SMAD5 antisense RNA 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   60.00
#=GF TC   69.00
#=GF NC   43.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.42 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10049768
#=GF RT   An antisense transcript to SMAD5 expressed in fetal and tumor tissues.
#=GF RA   Zavadil J, Svoboda P, Liang H, Kottickal LV, Nagarajan L
#=GF RL   Biochem Biophys Res Commun. 1999;255:668-672.
#=GF WK   SMAD5-AS1
#=GF SQ   18


AF071111.1/979-856         GUUCUGGUGGUGAU---GGCAUUGGAGAAUGGGG---CU-UAGGCAAGCCUGUAGGUGAGGAAUGGCUGAACA-CCCUGAGCCAGAUGU--UUAUCUUGAUUGUAAA-GACAAUGUUUCCUGACCAGCUGGAGCU
ABDC01055302.1/976-1099    AUUCUGGUUGCGAU---GGCAUUGGAG---AAGGGAGCU-CAGGCCGGCCUGUAGGUGAGGAAUGCCUGAACA-CCCUGGGCCAGAUCU--UUAUCUCGACUGUAAA-GACAAUGUUUCCUGACCAGCUGGACGU
AAPY01035600.1/2868-2991   AAUCUGGUUCUGAU---GGUAUUGGAG---AAUGGAGUU-GAGGCCGGCCCGGAGGUGAGGAAUGCCUGAACA-CCCUGGGCCAGAUCU--UUAUCUUGAUUGUAAA-GACAAUGUUUCCUGACCAGCUGGAGGU
AAQQ01033872.1/711-834     AUUCUGGUCUUGAU---GACAUUGGAG---AAUGGAGCG-UAGGCCAGCCUAGAGGUGAGGAAUUCCUGAACA-CCCUAUGCCAGAUUU--UUAUCUGAACUGUAAA-GACAAUGUUUCCUGACCAGCUGGAGGU
ABRP01033332.1/3068-3192   AUUCUGGUUUUGAU---GGCUGUGGAG---AAUGGAGUUGUAGGCCAGCCUGGAGGUGAGGAAUGCCUGAACA-CCCUGGGCCAGAUCU--CUAUCUUGAUUGUAGA-GACAUUGUUUCCUGACCAGCUGGAGGU
AAFC03075338.1/33964-34088 AUUCUGGUUUGGAU---GGCAUUGGAG---AGUGGAGCUGUAGGCCAGCCCAGAGGUGAGGAAUGCCUGAACA-CCCUGGGCCAGAUCU--CUAUCUUGAUUGUAGA-GACAUUGUUUCCUGACCAGCUGGAGGU
AAGV020384958.1/420-544    AUUCUGGUUUUGAU---GGUAUAGUAG---AAUGGGGCUGUAGGCCAGCCGGGAGGUGAGGAAUGCCUGAACA-CCCUGGGCCAGAUCU--CUAUCUUGAUUGUAGA-GACAUUGUUUCCUGACCAGCUGAAAGU
ABRQ01183941.1/5848-5972   AUUGUCGUUUUGAU---AGCAUUGGGG---AAGGGUGCUGUAGGCCAGCCUGGAGGUGAGGAAUGCCCGAACA-CCCUGAGCCAGAUCU--CUAUCUUGAUUGGAGA-GACAUUGUUUCCUGACCAGCUGGAGGU
AAKN02022958.1/9635-9761   AUUCUAGUUUUGAUAUGGGUAUUGGAGAAUAGAG---CC-UAGAUCAGCUAGGAGGUGAGGAAUGCCCAAACA-CCCUAAGCCAGAUCU--UUAUCUUGAUUAUAAA-GACAAUGUUUCUUGUCCAGCUGGAGGU
ABVD01168131.1/327-450     AUUCUGGUUUUGAU---GGCAUAGUUG---AGUGGAGCUGUAGACCAGCCUGGAGGUGAGGAAUGCCUGAACA-CCC-GGGCCAGAUCU--CUAUCUUGAUUGUAGA-GACAUUGUUUCCUGACCAGCUGAAGGU
AAIY01523265.1/4599-4722   AUUUUGCUUUCGAU---CGCGUUGUAG---AAUGGCGCUGUAG-CCAGCCCGUAGGUGAGGAAUGCCUGGACA-CCCUGGGCCAGAUCU--CUAUCUUGAUUGUGGA-GACUUUGUUUCCUGACCAGCUGGAGGU
CAAA01017758.1/4069-4193   GUCCGGUUUGUGAU---GGCCCCGGCG---AAAGGAGUCCC-GGCCAACCUGGAAGGCAGGAACGGCCGAACA-CUGUAGGCUAGAUCU--UUAUCUUGAUCGUAAAAGACAGUGUUUCCUGAGCAGCUGGAGGG
AAYZ01609777.1/658-786     GUUCUGGCUUGGGU---GGCAUUGGAGAUUGGUCGUUCU-UCGUCGGGCCUGGAGGUGCGGAAUGCCCGAACA-CCCCGAGCCUAGUGGGGUUAUCUCAUUGUGAGA-GACAGUGUUUCCUGACCAGCUGGAGGU
ABQO010070138.1/2425-2305  ------GUUUUGAU---AGAAAGAGGACAACACAUUGCAAUAGUCGGGCCAGGAGGUGAGGAAUGCCUGGAUAACUCUGGGCCAGAUCU--CUAUCUUGAUUGUAGA-GACG--GUUUCCUGACCAGCUGGGGAU
AAFR03013964.1/1430-1321   AUUCUGGUUUUGAU---GGAAAGAGA-----AUAUUGCUACAGUCUGUCCAGGGGGUGAG-AAUGCCUGAUUAAUUCUGGGCCAGAUCU--CUAUCUUGAUUGUAGA-GAC-------------CAGCUGGGGAU
AAQR03009545.1/7770-7647   AUUCUGGUUUUGAU---GGCUUUGGAGAGUGGCG---CU-UAGGCCAUCCAGUAGGUGAGGAAUGCCUGAACA-CCCUAGGCCAGAUCU--UUAUCUUGAUUGUAAA-GACAAUGUUUCCUGACCAGCUGGAGGU
AAEX03007800.1/164-282     AUUCUGGUUUUGAU---GG------AG---CUUGGAGCUGUAGGCCAUCCUGGAGGUGAGGAAUGCCCGAACA-CCCUGGGCCAGAUCA--CUAUCUUGAUUGCAGA-GACAUUGUUUCCUGACCAGCUGGAGGU
AABR05062355.1/61332-61216 ACUCCGGGGGUGAU---GGCACCGGCG---UAAGGAGUCCCCGGCCAACCU---GG------AUGGCCGAGCG-CUCUAGGCUAGAUCU--UUAUCGCGAUUGUAAAAGACGAUGUUUCCUGAGCAGCUGGAGGU
#=GC SS_cons               ::::::::::::::...::::::::::...:::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::..::::::::::::::::.:::::::::::::::::::::::::::
#=GC RF                    aUUCuGGUuuuGAU...GGcauuGGaG...aauGGaGCuguaGgCcagCCuGGAGGUGAGGAAUGCCuGAaCA.CcCUGgGCCAGAUcU..uUAUCUuGAUuGuAgA.GACaaUGUUUCCUGACCAGCUGGAGGU
//
# STOCKHOLM 1.0

#=GF AC   RF02176
#=GF ID   SMAD5-AS1_4
#=GF DE   SMAD5 antisense RNA 1 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   64.50
#=GF NC   34.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.36 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10049768
#=GF RT   An antisense transcript to SMAD5 expressed in fetal and tumor tissues.
#=GF RA   Zavadil J, Svoboda P, Liang H, Kottickal LV, Nagarajan L
#=GF RL   Biochem Biophys Res Commun. 1999;255:668-672.
#=GF WK   SMAD5-AS1
#=GF SQ   19


AF071111.1/809-643           UGCUUGUGCAUUUAAAUGGG-UGUGGCGCUAAGUAUAUCUUGUUUACCUUAUCUUUCU-GUGGAAAA-GUUUUGAUGUCUA---GG-UUUGUCAC-----AUCAUGCCUGUUGCCUAGCAC-UACCA-AAAGGGUUGUUAUC-UAGCAGCAAA-GAUUGA----AUAGGUGG-AGGUCGUGGCUUGGC
AAPY01035600.1/3026-3196     UGCCGGUGCGUUUGAA-UGGGUGUGGUGCUAAGUGUAUCUUGUUUACCUUAUCUUUCU-GUGGAAAAAGUUCUGAAGUC-GGUUGGGUUUGUCAC-----AUCAUGCUUGUUGCCUAGCAC-UACCA-AAAGUGUUCUUAUC-UAGUAACAAA-GACUGG----GUAGGUGG-AGGUUGUGGCAUGGC
AANG01340942.1/25-194        UGCUUGUGCGUUUAAAUGGG-UGUGGUGCUAAGUAUAUCUUGUUUACCUUAUCUUUCU-GUGGAAAAAGUUUUGAAGUCUGGUUGGGUUUGUCAC-----AUCAUGCCUGUUGCCUAGCAC-UGCCU-AAAGUGCUCUUAUC-UAGCAAC--A-GGCUGG----GUAGGUGG-AGGUCGUGGCUUGGC
AAQQ01033872.1/866-1039      UGCUUUUGCGUUUAAA-UGGGUGUGGUGCUAAGUAUAUCUUGUUUACCUUGUCUUUCUAUUGGAAAAAGUUUUGAAGUCUGGUUGAGUUUGUCAC-----AUCAUGCCUGUUGCCUAGCAC-UACCA-AAAGUAUUCUUAUC-UAGUAACAAA-GACUGG---AAUAGGUGG-AGAUUGAGGCUUGGC
ABRR01145897.1/358-529       UGCCAGUGCGUUUACA-UGGGUGUGGUACUAAGUGUGUCUUGUUUACCUUAUCUUUCU-UUGGAAAAAGUUUUGAAGUCUGGUUGGGUUUGUCAC-----AUCAUGCCUGUUGCCUAGCAC-CACCA-AAAGUGUUCUUAUC-UAGCAACAGA-GACUGG----AUAGGUGGA-GGUUGUAGCUUGUC
AAWR02002460.1/274828-274657 UGCUUGUGCGUUUAAA-UGGGUGUGGUGCUAAGUAUAUCUUGUUUACCUUAUCUUUCU-GUGGAAAAAGUUUUGAAGUCUGGUUGGGUUUGUCAC-----AUCAUGCCUGUUGCCUAGCAC-UACCG-AAAGUGUGCGUAUC-UUGCGAGGAA-GACUGG----AUCAGUGG-AGGUUGUGGCUUGGC
ABRN01383331.1/9603-9775     UGCCUGUGAGUUUAUA-UGGGUGUGGCACUCCCUGUAUCUUGUUUACCUUAUCUUUCU-GUGGAAAAAGUUUUGAAGUCUGGUUGGGUUUGUCAC-----AUCAUGCCUGUUGCCUAGCAC-CACCA-AAAGUGUUCUUAUC-UAACAACGAA-GACUGG----AUAGGUGGAAGGUUGUGGGUUGGC
ABVD01168131.1/484-650       UGCUUGUGAGUUUAAAUGGG-UGGGGUGCUAAGUAUAUCUUGUUUACCUUAUCUUUUA-GUGGAAAAAGUUUUGAAGUCAAGAUGGGUUUGUCAC-----AUCAUGCCUGUUGCCUAGCAC-UACCA-AA-GUGUCCUUAUC-UAGCAACAGA-GA--------AUAGGUUG-AGGUUCUAUCUUGGC
ABRQ01183941.1/6012-6183     UGCUUAUGCGUUUAAAUGGG-UGUGGUGCUAAGUAUAUCUUGUUUACGUUACCUUUCU-UUGGAAAAAGUUUUGAAGUCUGGUAGGAUUUGUCCC-----AUCUUGCCUAUUGCCUGACAC-UACUG-AAAGGGUCCUUAUC-UAGCAGCAAG-GACUGG----AUAGGCAG-AGGCUGUGGUUUAGU
ABRP01033332.1/3225-3400     UGCCUGUGCGUUGAAACUGGGUGUGGUGCUAAGUAUAUCUUGUUUACCUUAUCUUUCU-UUGGAAAA-AUUUUCAAGUCUGGUUGGGUUUGUCACUGAGCAUCACGCCUGUUGCUUAGUAC-UACCA--AAUUGUUCUUAUC-UAGCAACAAA-GACUGA----AUAGGUGG-AGUUUGCGGCUUGGC
AAIY01523265.1/4768-4940     CGGUUGUGCGUUUAAA-UGGGUGUGGUGCUAAGUAUAUCUUGUUUACCUUAUCUUUCU-UUGGAAAACGUUUUGAAGUCUGGUUGGAUUUGUCAC-----AUCAUGCCUGUUGCCUAGCAC-UGCCA-CAGAUGUCCUUAUC-UCACAACAAAAGACUGC----AUAGGUGG-AGGUUAAUGCUCAGG
AAGV020384958.1/594-770      UGCUUUUGAGUUUAAAUGGGGUGGGGUGCUAAGUAUAUCUUGUUUACCUUAUCUUUCC-GUGGAAAAAGUUUUGAAGUCUAGUUGGGUUUUUCAU-----AUCAUGCCUGUCGCCUAGCAC-UACCA-AAAGUGUCCUUGUC-CAGCAACAAU-GACUGAAUUAAUAGGUUG-AGGUUCUAUCUUGGU
AAFC03075338.1/34122-34294   UGCCCGUGCAUUUGUA-UGGGUGUGGUGCUAAGUGUAUCUUGUUUACCUUAUCUUUCU-GUGGAAAAAGUUUUGAAGUUUGGUCGGGUUUGUCAC-----AUCAUGCCGGUUGCCUAGUAC-CCCCCCAGAGUGUUCUUAUU-UAGCAA-AAA-GACUGG----AUAGGUGGGAGGUUGUGGCUUGGC
AAKN02022958.1/9796-9966     UGCUUUAGUGUUUGGA-UGGGUGUGGUGUUAAAUAAAUCGUGUUUACCUUAUCUUUAU-GUAAAAAAGGUUUUGAAGUCUGAUAUGGUUUGUCAC-----UUUAUGCAUGUUGCCUAGCAC-UAUCA--UAAUGCUCUUAUC-UAGCAACAGA-GACUGG----AUAGGUGG-UGCUUGUGGCUUGCU
AAHX01089885.1/51731-51568   UGCUUUUGCAGUUUAAAUGGGUGUGGUGCUAAGUAUAUCUUGUUUA-----UCUUUCU-GUGGAAAAAGUUUUCAAGUCUGGUGGAGUUUGUCAC-----CUCAUGCCGGUUGCCUAGCAC-UAUCA-AGUGGAUCCCUACC-UAGCAACAGA-GAGUGGG-UGAUCGCGGG-AGCUUGUU-------
CAAA01017758.1/4218-4387     UGCUGCUGC-GUUUAGAUGGGUGUGGUGCUAAGUAUAUCUUGUUUA-----UCUUUCU-GUGGAAAAAGUUUUGAAGUCUGGUGGAGUUGAUCAC-----AUCAUGCCUGUUGCCUAGCAC-UAUCA-AGUGUAUGCCUACC-UAGCAACGGA-CACUGGG-CGAUCAAUGG-AAUUUGUUGGUUGCU
ABQO010070138.1/2267-2104    UGCUUGUGCAUAUAAAAUGGGCGUGGUGCUAACUAUAUCUUGUUUACCUUAUCUUUCU-UUGGAAAAAGUUUUGAAGUCUGUUUGGGGU-GUCAC-----AUCUUGCCUUUUGCCCAGCAC-UG--A-AGAGUGUUGUUAGCUUAGCAGCAAA-CACUAG-----------C-ACACUCUUUUAUGGA
AAEX03007800.1/338-510       UGCCUGUGCCUUUCAAUGGG-UGUGGUGCUAAGUAUAUCUUGUUUACCUUAUCUUUCU-GUGGAAAAAGUUUUGAAGUCUGGUUGGGUUUGUCAC-----AUCGUGCGUGUUGCCUAGCACCUACCA-AAAGUGCCCUUAUC-UAGCAGCCGA-GGCUGA----AUAGGUGG-AGGUCGUGGCUUGGC
AAQR03009545.1/7619-7448     UGCUUGUGCUUUUAAA-UGGGUGUGGUGCUAAGUAUAUCUUGUUUACCUUAUCUUUCU-GUGGAAAAAGUUUUGAAGUCUGGUUGGGUUUGUCAC-----UUCGAGCCUGUUGCCUAGCAC-UACCC-AAAGUGUUCUUAUC-UAGCAACAAA-GACUGG----GUAGGUGG-AGGUUGUGGCUUGGC
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::.....:::::::::::::::::::::.:::::.::::::::::::::.::::::::::.::::::....::::::::.:::::::::::::::
#=GC RF                      UGCuugUGcgUUUaaAuuGGGUGUGGUGCUAAGUaUAUCUUGUUUACCUUAUCUUUCU.gUGGAAAAaGUUUUGAAGUCUGGUuGGGUUUGUCAC.....aUCaUGCcUGUUGCCUAGCAC.UacCa.AaaGuGUuCuUAuC.UaGCAaCaaa.GACUGg....AUaGGuGG.AGgUUgugGcUUGgc
//
# STOCKHOLM 1.0

#=GF AC   RF02177
#=GF ID   SMCR2_1
#=GF DE   Smith-Magenis syndrome chromosome region, candidate 2 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   50.00
#=GF TC   51.60
#=GF NC   47.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.51 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   11997338
#=GF RT   Genes in a refined Smith-Magenis syndrome critical deletion interval on
#=GF RT   chromosome 17p11.2 and the syntenic region of the mouse.
#=GF RA   Bi W, Yan J, Stankiewicz P, Park SS, Walz K, Boerkoel CF, Potocki L,
#=GF RA   Shaffer LG, Devriendt K, Nowaczyk MJ, Inoue K, Lupski JR
#=GF RL   Genome Res. 2002;12:713-728.
#=GF WK   SMCR2
#=GF SQ   6


AC078903.11/76693-76537    CUGCUCCCUCUCUUCUCUCUGCUAGAGACCAGAGGCCUUGAAGGAAGGAAGCCCAAGGGUCUCUCCUGGC--UCUGCUUCCCCAUCACUGCCUCCACUU------------------CCCCGCAUCCCUUU-CCCUGGCAGAGGCUUCUUGCCACAGGGCUCUGGGCACUCACAAGAC
AANU01105355.1/1144-988    CUGCUCCCUCUCUUCUCUCUGCUAGAGACCGGAGGCCUUGAAGGAAGGAGGCCCCACGGUCUCUUCUGGC--UCUGCUUCCCUAUCACCGCCCCCACUU------------------CCCCGCAUCCCUUU-CCCUGGCAGAGGCUUCUUGCCAUAGGGCUCUGGGCACUCACAAGAC
ABRT010425597.1/623-455    GUCCUCACUUUCUUCUCUUGGCUGUAGAUCAGAAGCCUCAAAGGAAG----CCCAAGGGU----CCAAGCAUCUCGCUCUCCUCUCUCUGCUCCCUGCUCACCCUCCCCUCCCAGGCCUCUGCAUCCCUUU-CCCUGGUGGAGCCAAACUACCGCAGGGCUCUGAGCACUCACAAGAC
AAQR03079824.1/6159-6316   UACCUCAUUCUCUUUUUUCUGCUGAAGCUCAGAUGCCUUGCAGGAAG----CCCAAAGUUCUCUCCU--C--CCUGCACCCCCGUUGCUGCUCCCCUCAAAA------------GGGCCUCUUAUCCCUUUUCCCUGGUGGAGUCUUCCUACUAUCGGGCUUUGAGCACUCAUAAGAC
AAGW02073333.1/26928-26759 ACCCCCUCACUCUGCUCUCUGCUGGAAGUCAGAGGCCUCCCAGGAAG----CCCCAGGGCCCCUCUUCAC--CCUGCUGGUCUAUCCGUGGCACCUCCCACCAAGUG-AAAGCG-GCUUCCCCAUCCCUCUCCCCUGGCAAUGUCCUCCUUCUCCAGGGCUCUAAGUACUUACAAGAC
AAGU03083231.1/9269-9412   ----CUGUUCUCAACUUUCUCCUGGAGAUAGGCAGCCUCACAAGAAG----CCCAAGGAUAUCUGCCUGC--UCUGACUCCCACU--CUGAGAUGGCUG-------------------CCC---UCCCUUUUCCUUGGCCAUGCCUUCCUGCUGCAGGGCUCUGAGCACUUGUAAGAC
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::....:::::::::::::::::::..::::::::::::::::::::::::::::::.............:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    uucCuCacuCUCUuCUcUCuGCUGgAGauCaGagGCCUcgcAGGAAG....CCCaAgGgUcuCUcCugGC..cCUGCuucCCuaUcucUGcucCcuccuaac.............GcccCCgcAUCCCUUUuCCCUGGcggaGuCuuccUgCugcaGGGCUCUGaGCACUcacAAGAC
//
# STOCKHOLM 1.0

#=GF AC   RF02178
#=GF ID   SMCR2_2
#=GF DE   Smith-Magenis syndrome chromosome region, candidate 2 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   55.00
#=GF TC   56.50
#=GF NC   50.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.01 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   11997338
#=GF RT   Genes in a refined Smith-Magenis syndrome critical deletion interval on
#=GF RT   chromosome 17p11.2 and the syntenic region of the mouse.
#=GF RA   Bi W, Yan J, Stankiewicz P, Park SS, Walz K, Boerkoel CF, Potocki L,
#=GF RA   Shaffer LG, Devriendt K, Nowaczyk MJ, Inoue K, Lupski JR
#=GF RL   Genome Res. 2002;12:713-728.
#=GF WK   SMCR2
#=GF SQ   5


AC020558.4/182113-182273 UGGCCACAGUAAACGCCCU-UGCAUCCUAUUGAGUGAGCCAAGGAUAA----GCGUGGUCCCUGGCAGGGUGCAGGAUUCUAUCCUGAAAUACACCCCCUCCACUU-UCUCCUAUUCCAGUCCACCGGG------GCCUCUCCUCCAGGCAGGAAACAUGAUCUCCUUUUGAC
AANU01105355.1/294-134   UGGCUACAGUAAGUGCCCU-UGCAUCCUAUUGAGUGAGUCAGGGAUAA----GCCUGGUCCCUGGCAGGAUGCAGGAUUCUAUCCUGAGAUACACCCCCUCUGCUU-UCCCCUAUUCCAGCCCACCAGG------GCCUCUCCUCCAGGCAGGAAACAUGAUCUCCUUUUGAC
ABDC01273248.1/1729-1892 UGGCCGCAGUGGGCACCCUCUGCGUUCUGCUGAGCAGUCCAAGGGCAA----GCCUGGUCCCUGGCAGGGUGUGGGAUUCUGUCCUGAGAUAGCUCCUCUCCCCUU-UCCUGUCUUCCAGCCCGAGGGGCG---UGUCUGUCCUGAAGGCAGGAAACUU-AUCUCCUUCUGAC
ACBE01418270.1/1516-1350 UGG---UGAAAGGCUCGCUUUGUAUUCUGUUGAGUGAGCAAAUGAUAAAUAAGGCUGUUCGCU--CAGGAUGCUCGAUCCAAUCUUGAGAAAGAUCCUUCCCCUUU-UCCUGUCCUCCAGCCCACAAGGGUCUUUCUCCCUCCCCUAGGUAGAGGUCUUUGUCUCCUUUCAAC
AAQR03079824.1/6984-7144 UGACUGUAGCAAGCACCCUUCACAUUCUGCUAAAUGGAACAAGGGUA----------AUCCCUGGCAGGGUGCAGGAUUCUAUCCUGAGAGAGAUCCUCUCCCCUUGCCCUGUCUUCCAGUCCACAGGGGA--CUUUUUGUCCUGGAGACAGGAAACAGUCUCUUCACCUGUG
#=GC SS_cons             ::::::::::::::::::::::::::::::::::::::::::::::::....::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::...:::::::::::::::::::::::::::::::::::::::
#=GC RF                  UGGCugcaGuagGCgCcCUuuGcaUuCUguUGAGUGagccAagGaUAA....GccUGgUCcCUGGCAGGgUGCagGAUuCuaUCcUGAGAuAgauCCucuCCccUU.uCCugUcuUCCAGcCCacagGGgu...UgucucUCCucuAGGcAGGaaaCauuaUCUcCuuuuGac
//
# STOCKHOLM 1.0

#=GF AC   RF02179
#=GF ID   ST7-AS1_1
#=GF DE   ST7 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   45.00
#=GF TC   46.10
#=GF NC   42.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.60 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-AS1
#=GF SQ   25


AF400039.1/1637-1522       AAUUAUCCCAGAGAAU--------UGUU-UAUAU---UAAAAACAGGCUGAGAAUAGUUUGACCUCUGAUCACCAAA----------AA-ACCUGGAGGAUAAACA----UUCAUCU-GUCAAGAU--UUCUCUGG-AAAAUCCCUG
AC166602.2/29801-29917     AAUUAUCCCAGAGAAU--------UGUU-UCUAU---UAAAAACAGGCUGAGAGUACUUUGAACUGUGACCAUCAAA----------AA-AACUGGAGGAUAAACA----UUCACCUUGUCAAGAU--CUCUGUCG-AAAACCCCUG
AC146316.3/134034-134150   AAUUAUCCCAGAGAAU--------UGUU-UAUAU---UAAAAACAGGCUGAGAGUAGUUUGAACUGUGACCACCAAA----------AA-AAUUGAAGGAUAAACA----CUCACCUUGUCAAGAU--AUCUUUUG-AAAACCCUUG
AC182539.4/16954-17058     AAUUACCCCAGAGAAU--------GGUU-UAUAU---UAAAAACAGGCUGAGAAUAGUUUGACUUGUAAUCACC-------------------UGGAGGAUAUUCA--------GCUUGUCAAGAU--UACUAUGG-AAAAUCCCUG
AC124157.4/33454-33570     AAUUAUCCCGGAGAAU--------UGUU-UAUAU---UAAAAACAGGCUAAAAGUUGUUCGAACUGUGAUUGCCCCA----------AA-AAUUGGAGGAUAAACA----UUCCUCUUGUCAAUAU--UUCUUUGG-AAAUCCUCUG
ABRR01087119.1/2121-2237   AAUUAUCCCAGAGAAU--------UGUU-UAUAU---UAAAAACAGGCUGAGAGUUGUUGGAACUGUCAUCACCCCC----------CA-AAUUGGAAGACAAACA----UUCUUCUUGUCAGGAU--UUCUUCAG-AAAUCCCCUG
ABRN01307492.1/16098-16214 AAUUAUCCCGGAGAAU--------UGUU-UAUAU---UAAAAACAGGCUGAGAGUUGUUUGAUCUGUCAUCACCCCC----------CA-GAUUGGAUGAUAAACA----UUCUUCUUGUCAAGUU--GUCUUUGG-AAACCCCCUG
AC152893.4/28582-28686     AAUUACUCCAGAGAAU--------UGUU-UAUAU---UAAAAACAGGCUGAGAAUCGUUUGACUUGUAAUCACC-------------------UGGAGGAUAGUCA--------GCUUGUCAAGAU--UACUAUGG-AAAAUCCCUG
ABVD01643133.1/843-960     AAUUAUUUCAGAGAAAA------UUGUU-UACAU---UAAAAACGG-CUGAGAGUUGUUUGAACUGUGAUUGCCAAA----------AG-AAUUGGAGGAUAAACA----UUCAACUUGUCAAGAU--UUCUUUGGAAAAAUCCCU-
AC163242.3/29706-29807     AAUUACCCCAGAGAAU--------UGUU-UAUAU---UAAAAACGGGCUGAGAAUAGUUUGACUUGUAAUCACC-------------------UGG-------CCA----UUCAGCUUGUCAAGAU--UACUAUGG-AAAAUCGCUG
AC149571.3/114850-114968   AACUAUCCCACAGAAU--------UGUU-UGUAU---UAAAAACAGGGCAAGAGUUGUAGGAAUUAUGAUCACCAAA----------AA-AAUUGGAGGAUAAACA----UUCUUCUUGUCAAGACACUUCUUUGG-GAAACCCCGU
AC161329.3/112964-113082   AAGUAUUCCAGAGAAUA------UAGUU-UAUAU---UUAAAACGGUCUAAGAGUUGUUUGAACUGCGAUUGCUAAA----------GG-AAUUGGAGGAUAAACA----CUCAUCUUGUCAAGAU--UUCUUUGGGAAAACCCCU-
AC146920.3/72952-73066     AAUUAUAUCAAAGGGU--------CAUU-CAUAU---UAAAAACAGGCUAAGAGUAGUCUGA-CUGUGAUCGCCU-A----------AA-AACUGGAAGAUAAGUA----UUCACGUUGUGAAGAU--UUCUUUGG-AAAACCCCUG
AC153775.3/39354-39463     AACUAUUCUAAAGAAC---------------UAU---UAAAAACAGGCUAAGAGUUGUUUUAACUGUGAUCGUCA-A----------AA-AAUUGUAUGAUAAACA----UCCAUCUUGUCAAGAU--UUCUUUGG-AAAACCCCUG
ABRP01280183.1/685-803     AAUUAUCCAAGAGAAU--------UGUU-UAUAU---UAAAAACAGGUGGAGAGUCCUUUGAACCAUGAUUGCCCCA----------AA-AAUUGGAGGAUAAAUA----UUAUUUUUGUCAAAACCCUUCUUUGG-ACAAUCUCGA
AC147928.3/151231-151346   AAAUUUCCCAGAGAAC--------UGUU-UAUAU---UAAAAACAGGUUGAGAGUUUUU-GAACUAUCAUUGCCCUC----------CA-AACUGGAAGAUAAACA----CUCUUCUUGUGAAGAU--UUCUUUCA-AACCCCCCGG
ABRT010186621.1/1678-1798  AGUUAUCCCAGAGAAG--------C-UU-UAUAU---UAAAAACAGGCUGAGAGUGGCUUGAACCGUGAUCACCAAA----------AAGACCCGGAGGAUAAGUCAACUUUCAUCUUGUCAAGAU--UUCUACGG-CAGACCCCCC
AC089991.2/63331-63448     AAUUAUCCCAGAAAAC--------UGUUAUAUAU---UAAAAACAGGUUGAGAGUUUUUUGAACUGUCAUCGCCCCC----------GA-AAUUCGAAGAUAAACA----CUCUUUUUGUGAAGAU--UUCUUUCA-AAACCCCCGG
AC139728.3/107529-107647   AAUUAUCCCAGAGAAU--------UGUU-UAUAU---UAAAACUGGGCUAGGAGUUGUUUGAACUGCAAUUGCCCCC----------AA-AAUUGGGGGAUAAAUA----AACAUUUUUUGAAGACAUUUCUUUGG-GAAACCCCGU
AC182002.3/161158-161275   GAUCAUCCCAGAGAAU--------UGUU-UAUAUCAUUAAAAGCGGGCCAAGCAUGGUUUGAACUGUGAUUGCUCCC----------CA-AAUUGGAGGAUAAACA--------UUCUUUAAAGACAUUUCUUUGG-GAAACCCCCG
AC153100.3/25794-25908     -----CCCACGGGAAU--------UGUU-UAUAU---UCAAAGCAGGCUGAAAGUUGUUUCAACUGUGAUGGCUA-A----------AA-GAUUGGAGGACAAAUAAACAUUUAUGUUGUCCAGAU--UUCUUUGG-AAAACCCUUU
CU633802.4/92044-91943     AAUUAUCCCAGAGAGU--------UGUU-UA--------AAAAUAGGCUG----UUAUUUGAACUGUCAUCACCCCC----------UG-AAUUGGAAGAUAAACA----UUCUUCUUGUCAAGAU--UUCUUAUU-CAAG------
AC156348.3/56202-56318     AAUUACCCCAGAGAAC--------UGUU-UAUGU---UAAAAACAGGCUGAGAAUAGUUUGACCUCUGAUCACCAAA----------AA-ACCUGGAGGAUAAACA----UUCAUCUUGUCAAGAU--AUCUCUGG-AAAAUCGCUG
AC090033.2/111184-111310   AAUUAUCCCAGAAAAU--------UGUU-UAUAU---UAAAAACAGGCUGAGAGUUGUUUGAACUGUGAAUCCCCCCCCCCCCCCCGCA-AAUUAGAGGAUAAACA----UUCUUCUUGUUAAGAU--UUCUUUGG-AAAACCCCUG
AC087067.3/67422-67547     AGUUAUCCUAGGGAAUGACUUAGAUGUU-AAAAA---CAAAAACAAGACAAGACUUGUUUGAAUGGUGAUCACUUGG----------AA-AAUAGGAAGAAAAAGAAAUAUGUAUGUUGUCA---G--UUUCUUUG-CAAAGCCCUU
#=GC SS_cons               ::::::::::::::::........::::.:::::...::::::::::::::::::::::::::::::::::::::::..........::.::::::::::::::::....::::::::::::::::..::::::::.::::::::::
#=GC RF                    AAUUAUCCCAGAGAAU........UGUU.UAUAU...UAAAAACAGGcUGAGAgUuGUUUGAACUGUGAUcgCCcca..........aA.AAUUGGAgGAUAAacA....UuCaUcUUGUcAAGAu..UUCUuUgG.aAAacCCCug
//
# STOCKHOLM 1.0

#=GF AC   RF02180
#=GF ID   ST7-AS1_2
#=GF DE   ST7 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   55.70
#=GF NC   40.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.67 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-AS1
#=GF SQ   24


AF400039.1/1121-1011       CCUUCGGCGCG-CCACUUGGCCUUCUCUUUCUAAAUAUUA----GCAUAAUAAAUAUAAAUGGACCCAGAACGCGAGGGGGCAGGGGCCACGUG----AUCGCUCCACGAAAGCCACUUG
AC146768.3/94628-94738     CCUUCUGCUAG-CCAUUUGGCCUUGUCUUUCUAAAUAUUA----GCAUAAUAAAUAUAAAUGGACCCAGAACGCGAGGGGGCAGAGGCCACGUG----AUCGCUCCACGAAAGCCACUUG
AC171368.3/17543-17652     CCCUCGGCGCG-CCGCGUGGC-CUGUCUUUCUAAAUAUUA----GUAUAAUAAAUAUAAAUGGCAUCAGAACGUGAAGGGGCAGGGGCCACGUG----AUCGCUCCACGAAAGCCACUCG
AC090033.2/111708-111817   CCCUCCGCGCC-CCAGUUGGC-CUGUCUUUCUAAAUAUUA----GCACAAUAAAUAUAAAUGGCAUCAGAACGUGAGGGGGCAGGGGCCACGUG----AUCCCUCCACGAAAGCCACAUG
AC166602.2/30320-30427     CCUUCAACGC---CACUUGGC-CAGUCUUUCUAACUAGUA----GCAUAAUAAAUAUAAAUGGCAUCAGAACGUGAGGGGACAGGGGCCACGUG----AUCGCUCCACGAAAGCCACUUG
AC124157.4/33965-34074     CCCUCAGCGCG-CCACUUCGC-CUGUCUUUCUAAAUAUUA----CCAUGAUCAAUAUAAAUGGCAUCGGAAUGCGAGGGGGCAGGGGCCACGUG----AUCCCUUCACGAAGGCCACUUG
ABVD01643133.1/1380-1488   CCUUCAGGGCG-CCACAAGAC-CUGUCUUUCGAAUUUUA-----ACAUAAUAAAUACAAAUGGGAUCAGAACGUGAGGGGGCAGGGGCCACGUG----AUCCCUACACGAAAGACACUUG
AC153775.3/39874-39983     CCUUCAGUGAGGCCACUUGGC-CUGUCU-UUUAAAUGUUA----GCAUAAUAAAUAUAAACGGCAUCAGAAGGUGAGGGGGCAGGAGCCACGUG----AUCCCUGCACGAAGGCCACUUG
AC146920.3/73465-73570     CCUUCUGCGC--CCACUUGGC-CUGUC---CUAACUGGUA----GCUUAAUAAAUAUAAAUGGCAUCAGAACGUGGGGGGACAGGGGCCACGUG----AUCGCACCACGAAAGCCACUUG
ABRQ01336256.1/719-828     CCUUCAGUGAGGCCACUUGGC-CCGUUUUUCCAAUGUUA-----GCCUAAUAAAUAUAAAUGGCACCAGAAGGUGAGGGGGCAGGGGCCACGUG----AUCCCGGCACGAAAGCCACUUG
ABRN01307492.1/16593-16697 CCCUCAGCGCG-CCACUUGGC-UUGUCUUUCUAAGUAUUA----GCAUAAUAUA----AAUGGCAUCAGAACGUGAGGGG-CAAGGGCCACGUG----AUCCUUCCACGAAGGCCACUUG
AAFC03098364.1/18271-18167 CCCUCAGUAGG-CCACUUGGC-UUUUCUUUCUAAAUAUUA----GCAUAAUAUA----AAUGGCAUCAGAACGUGAAGGG-CAGGAGCCACGUG----AUCCUUCCACGAAAGCCACUUG
AC153100.3/26290-26403     CCUGAAGCAGG-CCACUUGGC-CUGUCUCCCUAAAUGAGAGUCCGUAUAAUAAAUAUAAGUGGCAUCCGAACGAGAGCGGGCAGGGGCCACGUG----AUCGCUCCACGAAAGCCACUUG
AC186278.3/93577-93684     CCUUCAGCGCU-CCCCUGGGC-CUGUCUUUCCAAAUUUGA----GUAUAAUAAAUAUAAAAGGCAUCCCAACGCGGGGC--AGGGGGCCACGUG----AUCGCUCCACGCAAGCCACUUG
ABRP01280183.1/1190-1298   CCCUCAGUGAU-CC-CUUGGC-UUGUCUUUCUAAAUAUGA----CUAUAAUAAAUAUAAAUGGCAUCGGACCAUCAGGGGUCAGGUGCCACGUG----AUCUCCCCACGAAAGCCACUUG
AC147455.3/43888-43996     CCCUCACCCUA-CCACUGGGC-CUAUCUGUCUAAGUAUCA----GGAUAAUAAAUGGAAAUGGCCCCAGAACUUGAGGGGGCAGGAGCCACGUG----A-CCAUCCACGAAAACCACUUG
AC147928.3/151694-151794   CCCUCAGUACG-CCACUUGGC-UU----UUCUAAGUAUCC----GCAUAAUAUA----AAUGGCAUCAGAACGUGAGGGG-CAGGAGCCACGUG----AUCCUUCCACGAAAGCCACUUG
AC161329.3/113163-113263   CUUCUAGGACG-CCACCUGGC-CCGUCUUUCACAUUUUA-----GCAUAAUAAAUAUAAAUGGGAUCAGAACGUGAGGGGGCAGGCGCCACGUG----AUCCCUGC--------CACUCG
AC139728.3/108007-108106   CCCUUAGUGCC-CC-CUGAAC-UA-----UCUAAAU---A----GUAUAUUAAAAAUAAAUGGCAUCAGACCGUGAGGGGGCAGG-GCCACGUG----GUCCCUCCACGAAAGCCACUUG
AC149571.3/115338-115438   CC---AGUGC--CC-CGUGGC-CGGGCUUUCUCCGU--GA----CCAUAAUAAAUAUGAAUGGCACCAGAGCCCGCGGG-GCAGGGGCCACGUG----AUCCCUCCGCGAAAGC-ACUUG
ABRO01223603.1/534-643     CUCCCGGCUGG-CCACCUGGC-CCGUCCCUCCCGCUGCUA----GUAUAAUAAAUAUAAAUGGCAGCCGAUCGUGAAGGGGCCGAGCCCACGUG----AUCAGGCCACGAAAGCCGCUGG
AC087160.2/95475-95579     CCCCCAGGGUG-UCACUUGGC-CUGU----CUAAAUAUUA----GCAUAAC----AUAAAUGGCAUCAGAACGUGAAGGG-CAGGGGCCACUGGUAGGAUUCUGCCAGGAGAGCCACUUG
AC153836.5/21794-21902     CCCUCGGCGGC-GC-CCGGGC-UGUCCUCCUAAAAUACUA----GUACAAGAAGUAUAAAUGGCCCGGGAGAGUGCAGGGACCGGGCCCACGUG----ACCGCUCCACGAAGGCCACCGG
AAHX01028813.1/6355-6250   CCCUCGGCGGC-GC-CCGGGC-UGUCCUCCUAAAAUACUA-------GUAGAAGUAUAAAUGGCCCGGGAGUGUGCAGGGACCGGGCCCACGUG----ACCGCUCCACGAAGGCCACCGG
#=GC SS_cons               :::::::::::.:::::::::.::::::::::::::::::....::::::::::::::::::::::::::::::::::::::::::::::::::....::::::::::::::::::::::
#=GC RF                    CCcuCaGcgcg.CCACuuGGC.cuGUCUuUCuAAaUauuA....GcAUAAUAAAUAUAAAUGGCAuCaGAacGuGaGGGGGCaGGGGCCACGUG....AUCccuCCACGAAAGCCACUuG
//
# STOCKHOLM 1.0

#=GF AC   RF02181
#=GF ID   ST7-AS2_1
#=GF DE   ST7 antisense RNA 2 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   94.10
#=GF NC   61.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.74 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-AS2
#=GF SQ   4


AF400045.1/553-482       GACUCCCUUCUAGAUCCAUGGUGUGUAAAUUUAUCAUUCCUGAGCUUUCUUCUUUUAUGCAAAAUCCCAUUC
AC145355.3/74745-74813   GACUCCCUUCUAGAUCCAUGGUGUGUAAAUUUAUCAUUCCUGAGCUUUCU---UUUAUGCAAAAUCCCACUC
AC148205.3/117038-117109 GACGCCCCCCUAGAUCCAUGGUGUGUAAAUUUAUCAUUCCCAAACUUUCUUCCUUUAUGCAAAAUCCCAUUC
AC148186.3/115517-115588 ACCCCCCACCCCGAUCCAUGGUGUGUAAAUUUAUCAUUCCCAAACUUUCUUCCUUUAUGCAAAAUCCCAUUC
#=GC SS_cons             ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  GaCuCCCuuCUaGAUCCAUGGUGUGUAAAUUUAUCAUUCCugAgCUUUCUUCcUUUAUGCAAAAUCCCAUUC
//
# STOCKHOLM 1.0

#=GF AC   RF02182
#=GF ID   ST7-AS2_2
#=GF DE   ST7 antisense RNA 2 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   45.00
#=GF TC   50.80
#=GF NC   43.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.34 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-AS2
#=GF SQ   8


AF400045.1/481-435          CAGUGUGUUUCAAGCCAUGAUCUGGAGUCAAGGUGUUAGUGAUUCCU
AC150597.4/87298-87344      CAGUGUGUUUCAAGCCAUGAUCUGGAGUCAGAAUGUUAGUGAUUCCU
AC165378.3/118697-118743    CAGUGUGUUUCAAGCUGUGAUCUGGAGUCAGGGUGUUAGUGAUUCCU
AC146884.3/173902-173948    CAAUGUGUUUCAAGCCAUAAUCUGGAGUCAGAGUGUUAGCGAUUCCU
ABDC01046490.1/2633-2679    CAGUGUAUUUGAAGCCAUGAUCUGGAGUCAGUGUGUUAGUGACCACU
ABRT010057108.1/11642-11688 CAGCAUGUUUCAAGCCAUGAUCUGGAGUUAGUAUGUUAUUGACUCCU
AC182032.3/42779-42825      CAGUGUGUCUCCAGCCAUGAUCUGGAGUCAGUGUGUUCAUGACCCCU
BAAE01009315.1/2051-2097    CAUUGUGGAUGCAGCCAUAAUCUGGAGUCAGAGUGACUGUGAUCUCU
#=GC SS_cons                :::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                     CAGUGUGUUUCAAGCCAUGAUCUGGAGUCAGuGUGUUAGUGAUUCCU
//
# STOCKHOLM 1.0

#=GF AC   RF02183
#=GF ID   ST7-OT3_1
#=GF DE   ST7 overlapping transcript 3 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   54.60
#=GF NC   40.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.63 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-OT3
#=GF SQ   28


AF400044.1/67-140          AAAACAUUUCUAUAAAACAUAA-GAUGGCAAAGAGGUGGAAGAAAAAUUAA-----UGCCAGCAGUUCAGCUUUGACUAA
AC183847.3/2461-2534       AAAACAUUUCUAUAAAACACAA-GAUGGCAAAGAGGCAGAAGAAAAAUUAA-----UGCCAGCAGUUCAGCUUUGCCUAA
AC165378.3/177136-177209   AAAACAUUUCUACAAAACAUAA-GAUGGCAAAGAGGUGGAAGAAAAAUUAA-----UACUGGCAGUUCAGCUUUGCCUAA
AC148137.3/32106-32179     AAAACACUUCUAUAAAACAUAA-GAUGGCAAAGAGUUGGAAGAAAAAUUGA-----UGCGAGCAGUUCAGCUUUGCCUAA
AC151541.4/49076-49149     AGAACACUUCUAUAAAACAUAA-GAUGGCAAAGAGGUGGAAUAAAAAUUGA-----UGCUAGCAGUUCAGCUUUGCCUAA
AC148115.3/58891-58964     AAAGUAUCUAUAUGAAGCACAA-GAUGGCAAAGAAGUGGAAGGAAAAGUAA-----CGCCAGCAGCUCAGCUUUGCUUAA
AC090031.2/173656-173729   AAAGGAUCCAUAUGAAGCACAA-GAUGGCAAAGAAGUGGAAGGAGAAUUAA-----CGCCAGCAGUUCAGCUUUGCUUAA
AC148119.4/26004-26077     AAAGGAUCUAUAUGAAGUACAA-GAUAGCGAAGAAGUGGAAGGAAAAUUAA-----CGCCAGCAGUUCAGCUCUGCUUAA
AC123544.4/12404-12482     AAAGGGCUUGUAUGAAACACAA-GAUGGCAAAGAAGUGGAAGAAAAAUUAAAUUAAUGCCAGCAGUUCAGCUUUGCUUGA
ABDC01046495.1/17642-17720 AAAGGACUUAUAUGAAACACAA-GAUAGCAAAGAAGUGGAAGAAAAAUUAAAUUAAUGCCAGCAAUUCAGCUUUGCUUAA
AC165192.3/11577-11655     AAAGGACUUAUAUGAAACACAA-GAUGGCAAAAAAGUGGAAGAAAAAUUAAAUUAAUGCCAUCAGUUCGGCUUUGCUUAA
AALT01590550.1/1180-1104   AACCAACAUGUAUGAAAUAUAA-GAUGGCAAAGACAUGAAAGGAAAAUUACG--AAUGCCAGCAGUUCAGCUUUGCUUAG
ABRR01087158.1/3311-3389   AAAAGAACCAUAUGAAACACAA-GAUGGCAAACAUGUAGAAGGAAAAUUAAACUAAUGCCAGCAGCUCAGUUUUGCUUAA
AAPY01079829.1/1680-1758   AAAGGGCUUGUAUGAAACAUGA-GAUGGCAAAGACAUGGAAGAAAAAUAAAGCUAAUGCCAGGAAUUCCGCUUUGCUUAA
ACBE01081549.1/1173-1095   AAAGGACCUGUAUAAAACAAAA-GAUGGCCAAGAAGUAGAAGGAAAAUUAAACUAAAGCCGGGAGUUCAGCUUUGCUUAA
AC206087.3/111678-111755   AAAGGACCUGUAUGAA-CACAA-GAUGACAAAGAAGUGGGAGGAAAAUUAAACUCAUGCCAGCAGUUCAUCUUUGCCUAA
AC124909.3/69592-69670     AAAGGACCUGUAUGAAACACAA-GAUGGCAAAGAGGGGGACAGAAAACUAAACUAACACCAGCAGUUCGUCUUUGCUUAA
AC153102.3/12422-12499     AAAGGACCUAUAUGAAACACAA-AAUGGCAAAGAAGUGGAAGGAAAAUGAAAUGAAUGCCAGCAGCUCAGCUU-GCUUAA
ABVD01010020.1/2049-2127   AAAGGAUGUGUAUGAAACACAA-GAUGGCCAAGAAGUAUAUGAAAAAUUAAACUAACACUAUCAGUUCAGCUUUGCUUAA
ABRN01248939.1/18172-18249 AAAGGAUCUGUAUGAAACACAA-GGUGG-AAAGAAAUGGAAGGAAAAUUAAACUAACGCCAACAGUUCAGCUUUGCCAAA
ABRT010121723.1/499-577    AAAAGGACUAUGUGAAACACAA-AGUGGCAAAGAAGUGGAAAGAAAUUUAAAUUUAUACUAGCAGUUCAGCUUUGCCUGA
AC150241.3/64089-64166     AAAGGACCUGUAUGAAACACAA-GAUGGCGAGGAAGUGGAAGGAAAAAUGAACUAAUGCCGGUAGUU-AGCUUUGUCAAA
ABRQ01148775.1/499-568     AAAGG---------AAAUACAA-GAUAGCAAAAAACUGGAAGGAAAAUUAAAAUAAUGCCAGCAGUCCAGCUUUGCUUAA
AANN01603841.1/16503-16582 AAAAAAUAUGUAUGAAACACAAAAAUGGCAAAGAAGUAGAAGGAAAAUUAAACUAACACCGGCGGUUAAACUUUGCUCAA
ABRO01073152.1/1078-1155   AAGGGGCUUGUUUGAU-UACAA-GAUGGCCAAGAACUAGAAGGAAAACUCAGCUAAUAUCAGCAGUUCAACUUUGCUUCA
AC139341.3/129661-129740   AAUAAAUAUGUAUGAAACACAAAAAUGGCAAAGAAGUAGAAGGAAAAUUAAACUAACACCAGCGGCUAAACUCUGCUCGA
AC188936.4/163198-163276   AAAGGGCCUGUAUGAAACAAAA-GAUGGCCAAGAGGUGGAAGGAGAUUUAAACUGAAGCCAGGAGUUCAGCUUUGCUUAA
AC147580.3/149167-149244   AAAGGAUUUGUAUGAAACACAA-GGUGGCAAAGAUGUAGAAGAAAAAUUAAAUUAAUGCCAACAGUUCAGCUU-GUUUAA
#=GC SS_cons               ::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    AAAGgAcuUgUAUGAAACACAA.GAUGGCaAAGAaGUGGAAGGAAAAUUAAAcUaAuGCCAGCAGUUCAGCUUUGCUUAA
//
# STOCKHOLM 1.0

#=GF AC   RF02184
#=GF ID   ST7-OT3_2
#=GF DE   ST7 overlapping transcript 3 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR; Eberhardt R
#=GF SS   Predicted; WAR;
#=GF GA   100.00
#=GF TC   139.90
#=GF NC   54.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.52 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-OT3
#=GF SQ   5


AC130185.3/56080-56217         AUCGCCAGUACCUACUGCAACAUCUUUCCUCCCUACACAGUGACUCCAGCUUGGGAGGGGCAGGGCUAGGCUGAGCCAGCACUCCCUGUGGUGUCUGCCUGCCACGUGCAGCUCUGGAGUUAGCCGUGGGGUGUGAGG
AF400044.1/214-350             AUCGCCAGUACCUACUGCAACAUCUUUUCUCCCUACACAGCGACUCCAGCUUGGGAGGGCAGGGCCAGGGUUGUCACAGCUUCCCCUGUGGUGUCUGCCUGCCAAGCACAGCUCUGGAGUUAGCCCUGGG-UGUGAGA
BL000001.1/115854638-115854774 AUCGCCAGUACCUACUGCAACAUCUUUUCUCCCUACACAGCGACUCCAGCUUGGGAGGGCAGGGCCAGGGUUGUCACAGCUUCCCCUGUGGUGUCUGCCUGCCAAGCACAGCUCUGGAGUUAGCCCUGGG-UGUGAGG
AC159212.3/135378-135241       AUCGCCAGUACCUACUGCAACAUCUUUCCUCCCUACACAGCGACUCCAGCUUGGGAGGGCAGGGCUAAGGUUGUCACAGCUUUCCCUGUGGUGUCUGCCUGCCAAGUACAGCUCUGGAGUUAGCCGUGGGGUGUGAGG
AAWZ02000034.1/11116-10979     AUCGCCAGUACCAACUGCAACAUCUUUCCUCCCUACACAGCGACUCCAGCUUGGGAGGGCAGGGCUAGGUUUGUCACAGCUUUCCCUGUGGUGUCUGCCUGCCAAGUACAGCUAUGGAGUUAGCCGUGGGUUGUGUGA
#=GC SS_cons                   ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                        AUCGCCAGUACCuACUGCAACAUCUUUcCUCCCUACACAGcGACUCCAGCUUGGGAGGGcaGGGccagGguUGucaCAGCuuuCCCUGUGGUGUCUGCCUGCCAaGuaCAGCUcUGGAGUUAGCCgUGGGgUGUGaGg
//
# STOCKHOLM 1.0

#=GF AC   RF02185
#=GF ID   ST7-OT3_3
#=GF DE   ST7 overlapping transcript 3 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   58.00
#=GF NC   40.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-OT3
#=GF SQ   21


AF400044.1/462-579         GCUGUAUU-ACGUAAUU-AUCAUCUUCUCUGAGGGAGGAAAAAAAGUAGCUGAGAG-CCACUUUCAGUCCC-----GCUAUU-AAGUACAUUUUGGCCUCU-AAGAAAC--U--U--CGUGUGGUUCACCUCAG
AC148137.3/39310-39423     UGUUUACC--UGUAUCUAACUACCUGCUCUGUGAUAGGCAUGAAGC----CAAGAG-GCACUUUCACUCUC-----GCUAUU-AAGUACAUUUUGACCUCU-AAGAAAC--U--U--AUUGUAGUUUACAUCAG
ABDC01046495.1/23296-23409 GACUUACC--UGUAUUUGAGUACCUGCUAUGUGAUAGGCACAUGGC----UGAGGG-CCAUUUGCAGUCUC-----ACUAUU-AAGCACACUUUGACCUCU-AAGAAAC--U--U--CCUGCAGUUCACAUCAG
AC183695.3/20785-20898     UAUUUACC--UAUAUUUAACUACCUGCUCUGUGAUAGGCAUGAAGC----CAAGAG-GCAUUUUCACUCUC-----GCUAUU-AAGUACAUUUUGACCGCU-AAGGAAC--U--U--ACUGUAAUUUACCUCAG
AC165192.3/17236-17349     GACUUACG--UGUAUUUCAGUACCUGCUGUGUGAUAGGCACACGGC----UGAGGG-CCAUUUACAGUCUC-----ACUAUU-AAGCACACUUUGACCUCU-AAGAAAC--U--U--CCUGCAGUUCACAUCAG
AC151541.4/56247-56360     UAUUUACC--UAUAUUUAACUACCUGCUCUAUGAUAGGCAUGAAAC----CAAGAG-GCACUUUCACUCUC-----GCUAUU-AAGUACAUUUUGACUGCU-AAGAAAC--U--U--ACUGUAAUUUACCUCAG
AC152017.3/31067-31181     UAUUUACC--UAUGUUUAGCUACCUGCUCUGUGUUAGGCAUGAAGC----UGAGAG-GCACUUUGACUCUC-----GCUAUUUAAGUACAUUUUGACCUCU-AAGAGAC--U--U--AUUGUAAUUUACCUCAG
ABRT010121725.1/3039-3153  AAUUUACC--UGUGUUUGAAUGCCUGCUCUAUGAUAGACAUGUGAA---AUGAGUG-CCAUUUUCAGUCUC-----ACUAUU-GAGCACAUUUUGACCUCU-AAGAAAC--U--U--UCUGCAAUUCACAUCAU
ABRN01248940.1/201-319     GACUUACC--CGUAUUUGAGUACCUACUACGUGAUAGGCACGUGGC----UGAGGG-CCAUUUUCAGUUUCUUGAUAUUAUA-AAACACAUUUUGACCUCU-AGGAAAC--C--U--CCUGCAGUUCACAUCAG
AC123544.4/18033-18144     GACUUACA--UGUAUUUGAGUACUCGCUGUGUGACAGGCACACGGC----UGAGGG-CCAUUUACAGUCUC-----ACUGUU-AAGCAC--UUUGACUCCU-AAGAAAC--U--U--CCUACAGUUCACAUCAU
ACBE01081553.1/2004-1886   UAUUUACC--UAUAUUUGAGUACCUGCUAUGUGAUAGGCACAUUGC----UGAGGG-CUAUUUUCAGUUUCUCGAUAUUAUA-AAGUGCAUUUUGACCUCU-GGGAAAC--U--U--CAUACAAUUUACAUCAG
AC183690.3/91042-91159     AGUUUACC--CGUGUUUGAGUACCUGUUCCGUGAUAGAUAGGAAGC----UGAGAG-CCAGUUUCUGUUUCU---UGAUACU-AAACAUAUUUUAACCUCU-AAGAAACUCU--U--GCUGCAGUUCAUAUUAG
ABRR01087160.1/113-232     GAUUUACC--UGUGUUCGAGUA-CUGCUUUGUGAUAGGCAAGUCGC----UGAGGG-CCAUUUUGAGUUUCUUGUUAUUAUA-AAGCACAUUUCAACCUCU-AAGAAAC--UAUU--CCUGCGGUGCACAGCAG
ABRO01336613.1/477-594     AAUUCACC--UGUAUUUGAGUAACUGUUGUAUGAUAGAUAUGUAGC----UAAGGG-UCACGUUCAGUCUCU---GGAUAUU-AAGCACAUUUUUGUCUCU-AAAAAACGAU--U--CACGCUGUUUAUACCAG
AC182032.3/109921-110038   GAUUUACC--UGUGUUUGAGUACCUGCUCUGUGGUAGGUAUCUAGA----UUAGGG-UCAAUUUCAAUCUCU---UGACAUU-AAGCACAUCCUAACUUGU-AAGAAAC--UAUU--CCUACAAUUCAUAUUGG
AC145508.3/71789-71910     AUAACACC--UCUUUUUGAGGAAUUGCUCUGCGAUAGAAACAUAUG---CUAAGGU-CCACUUUCCAUUUCUGGAUAUUAUA-AAGCACAUUUUGACCUCU-AAGAAACCAU--U--CUUGAAAUUCACAUCAG
AC068561.2/52899-53018     UAUUUAGGGUUUUCCUGAAGUAUCUGCUCUGUGGUAGGUAUUUAGC----UGUGGGUCCAUUUUCAGUCUGU---UGAUAUU-AAGCACAUUUAG-CCUCU-AAGAAAU--UAAU--CCUGCAGCUCACAUCUG
AC087066.3/103003-103121   UAUUUAGGGCUUCCCUGAAUUAUCUGCUCUGUGGUAGGUAUUUAGC----UGUGGG-UCCAUUUCAGUCUGU---UGAUAUU-AAGCACAUUUAG-CCUCU-AAGAAAU--UAAU--CCUGCCACUCACAUCUG
AC139341.3/136641-136758   GAUUUACC--UGCACUG-AGUUUCUGCUAUGUGACAGACACACUGC----UGAAUG-ACAGUUUUAGCUUAUAAAUACUAUG--ACUGCAU-UUGACCUCU-AACAAAC--U--UUCCCUCCAAUUUAUAUUAG
AC188936.4/172016-172135   GAUUUGCC--UCUAUUUGAGUACCUGCUAUGCGAUAGGCACAUGGC----UGAGGG-CUAUUUUCAGUUUCUCGAUAUUAUA-AAGCACAUUUUGACCUGGGAAAACUA--U--U--CAUACAGGGUACUACAG
AC147583.3/3991-4099       AAUUUAGG--AGUAAAU-----GCAGUUAUGUGACAGGCACACAGC----GGAAGG-CCACAUCCCAUCGC-----ACUGUU-AAGCACACUUUGACCUCU-AAGGCAC--U--U--CCUGCAGUUCCCAUCAG
#=GC SS_cons               ::::::::..::::::::::::::::::::::::::::::::::::....::::::.:::::::::::::::...:::::::.::::::::::::::::::.:::::::..:..:..:::::::::::::::::
#=GC RF                    gaUUUACc..UgUauUUGAgUAcCUGCUcUGUGaUAGGcAuauaGc....UGAGgG.cCAuUUUCAGUcUCU...UgcUAUu.AAGCACAUUUUGACCUCU.AAGAAAC..U..U..ccUGCaGUUcACaUCAG
//
# STOCKHOLM 1.0

#=GF AC   RF02186
#=GF ID   ST7-OT3_4
#=GF DE   ST7 overlapping transcript 3 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   80.00
#=GF TC   92.90
#=GF NC   41.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.08 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-OT3
#=GF SQ   8


AF400044.1/801-873       GGGUACUUCU-ACCAAUUGGAGCUGGGCUGUUGGAGUCAUCUCCACUGCCUACCACCAGGACAAGCAGAGAAGU
AC189856.1/105659-105587 GGGUACUUCU-ACCAGUUGGAGCUGGGCUGUUGGAGACAUCUCCACUGCCUACCACCAGGACAAGCAGAGUGGU
AC165378.3/192077-192149 GGGUACUUCU-ACCAAUUGGAGUUGGGCUGUUGGAAUCAUUUCCACUGCCUACCACCAGGACAAGGAGAGCGGU
AC183695.3/28127-28199   GGGUUCUGCU-ACCAGUUGGAGUUGGGCUGUUGGAAUGAUCUCCACUGCCUACCACCAGGCAAAGGGGAACAGU
AC151541.4/63840-63912   GAGUUUUGCU-ACCAAUUGGAGUUGGGCUGUUGGAAUGAUCUCCACUGCCUACCACCAGGCAAAGGGGAAUGGU
AC148137.3/46648-46720   CAGUUCUGCU-ACCAAUUGGAGUUGGGCUGUUGGAAUGAUCUCCACUGCCUACCACCAGGCAAAGGGGAGCGGU
AC152017.3/38735-38808   GAGUACUGCUUACCAAUUGGAGUUGGGCUGUUGGAAUGAUCUCUACUGCCUACCACCAGGCAAAGAGGAACGGU
AC158411.4/29622-29694   GGGUACUUCU-ACCAAUUGGAGUUGGGCUGUUGGAGUCAUUUCCACUGCCUACCACCGGGACAAGGAGAGCAGU
#=GC SS_cons             ::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  GGGUaCUgCU.ACCAaUUGGAGUUGGGCUGUUGGAaUgAUCUCCACUGCCUACCACCAGGcaAAGggGAGcGGU
//
# STOCKHOLM 1.0

#=GF AC   RF02187
#=GF ID   ST7-OT4_1
#=GF DE   ST7 overlapping transcript 4 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   53.20
#=GF NC   49.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.67 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-OT4
#=GF SQ   24


BC043268.2/231-430         --GCCGCGUGCCUCCCAUCCUUGGUCGGUGGUAAAUGCAG-GAGGUAAUUA--ACAGGAUCUUCA-CAAACUUGGAGCCGGCCCACUGAGUCGUUAAAAAA--------ACACCCGCAAAGA-------AAA-C--ACAC---GAGCCUUAACACUCCAGAGAGUUC----CGAAACACAAAGUAAAUUUC-GAGCUAAGGGUUACAGUC-------CUUUAAAUCUGGAAAUUUCAAG------
AC156348.3/57972-58173     --GCCGCGUGCCUCCCAUCCUUGGUCGGUGGUAAAUGCAG-GAGGUAAUUAGAACAGGAUCUUAA-CAAACUUGGAGCCAGCCCACUGAGUCGUUAAAAAA--------ACACCCGCAAAGA-------AAA-C--ACAC---GAGCCCUAACACUACAGAGGGUUC----CGAAACACAAAGUAUAUUUU-GAGCUAAGGGUUACAAUC-------CUUGAAAUCUGGAAAUUUCAAG------
AC163242.3/31481-31682     --GCCGCGUGCCUCCCAUCCAUGGUUGGUGGUUAAUGCAG-GAGGUAAUUAGAACAAGAUCCUAA-CAAACUUGCAGCCAGCCCACUGAGUCGUUAAAAUA--------ACACUCGCAAAGA-------AAA-C--ACGC---CCGCCCUAACGCUCCAUAGAGUUC----CAAAACACAAAGUAUAUUUC-GAACUAAAGGUUACAAUC-------CUUGAAAUGUGGAAAUUUCAAG------
AC182539.4/18715-18912     --GCCGCGUGCCUCCCAUCCAUGGUCGGUGGUUAAUGCAG-GAGGUAAUUAGAACAAGAUCCUAA-CAAACUUGCAGCCAGCCCACUGAGUCGUUAAAA------------ACCCGCAAAGA-------AAA-C--ACGC---CAGCCCUAACGCUCCAGAGAGUUC----CAAAACACAAAGUAUAUUUC-GAACGAAGGGUUACAGUC-------CUUGAAAUGUGGAAAUUCCAAG------
AC159917.3/63003-63203     --GCCGCGUGCCUCCCAUCCAUGGUCGAUGGUUAAUGCAG-GAGGUAAUUAGAACAAGAUCCUAA-CCAAAUUGCAGCCAGCCCACUGAGUCGUUAAAAAA---------CACCCGCAAAGA-------AAA-C--ACGC---CAGCCCUAACGCUCUAGAGAGUUC----UAAAACAUAAAGUAUAUUUC-GAACUAAGUGUUUCAGUC-------CUUGAAAUGUGGAAAUUCCAAG------
AC152893.4/30358-30567     --GCCGCGUGCCUCCCAUCCGUGGUCGGUGGUUAAUGCAG-GAGGGAAUUAGAACAAGAUCCUAA-CAAACUUGCAGCCAGCCCACUGAGUCGUUAAAAAA---------CACCCGCAAGGAUGUUAAAAAA-CACACGC---CAACCCUAACGCUCCAGAGAGUUC----CGAAACACACAGUAUAUUUC-GAACUAAGGGUUACAGUC-------CUUCAAAUGUGGAAAUUCCAAG------
AC146768.3/95912-96108     --GCCGCGUGCUUCCCAUCCAUGGUCGGUGGUUAAUGCAG-GUGGUAAUUAAAACAAGAUCCUAA-CAAACUUGCAGCCAGCCCACUGGGUCGUUAACAAA---------CACCCGCAAAGA-------AAG-C--ACGC---CAGCCCUAACGCUCCAGAGAGUUC----CAAAACACAAAGUGUAUUUC-GAACU----GUUACAAUC-------CUUGAAAUGUGGAAAUUCCAAG------
AC146316.3/135856-136054   --CCCGCGUGUCUCGUAUC-AUGGUCGGUGGUAAGUGCAG-GAGGUAAUUAGAGCAGGAUCUUAA----ACUUGCAGCCAGCCGACUGAAUCGUUAAAAAA---------CAGCCACAGAGA-------AAA-CUCACAC---CAACAGUAACACUUGAGAGACAAUU--CAGAAACAC--AGUAUAUUUU-AAAGGAAGGAUUACAGUC-------CUUGACGUCUGGAAAUUGUUGU------
AC138559.3/136100-136298   --CCCGCGUGUCUCGUUUC-AUGGUCGGUGGUAAGUGCAG-GAGGUAAUUAGAGCAGGAUCUAAA----ACUCGCAGCCAGCCAACUGAAUCGUUAAAAAA---------CAACCACAGAGA-------AAA-CUCACAC---CAACAGUAACACUUCAGAGACAAUU--CAGAAACGC--AGUAUAUUUU-AAAGGAAGGGUUACAGUC-------CUUGACGUCUGCAAAUUGUUGU------
ABRN01307492.1/17951-18145 --GCCGUGUGUCCU--CUCCACGGUCG----UAAGUGCAG-AAGGUAAUUA-AACAGGAUCUUAA----ACUUGCAGUCAGACAACUGAAUCAUUAGAAAG---------CAACCACAGAGA-------AAA-CUCACAC---CAACAGUGACACUCCGGAGACAAAU--CAAAAACGCAAAGUAUAUUUU-GCAGGAAGGGUUACAGUU-------CUUGAAGUCUGGAAAUAGUUGU------
AANG01396076.1/561-761     --CCCGCAUGUCUCAUACCCACGGUCG----UAAGUGAAG----GUGAUUAGAACAGGACCUUAA-UAAAUUGGCAGCCAGCCGACUGAAUCCUUAAAAAA---------CAGCCACAAAGA-------AAA-UCCACAC---CGACAGAAACACUCCAGGGACAAUU--CAGAAACACAAAAUAUAUUUU-GAAGGAAGGGUUACGGUC----CUUUUCGAAGUCUGGAAAUAGUUGU------
AAFC03098364.1/16923-16726 --CCCGCAGGUCUUGUAUCCACGGUUG----UAAGUGCCC-AAGGUAAUUAGAACAGGAUCUUAA----ACUUGCAACCAGCCAACUGAAUCAUUAAAAAA---------CAACCACAAAGA-------AAA-CAGACAC---CAGCAGUAACACCCCAGAGACAAAU--CAAGAACCCAAAGUAUAUUUU-GCAGGAAGGGCUAUAGUU-------CUUGAAGUCUGGAAAUACUUGU------
AC147928.3/153046-153239   --CCCGCAGGUCUUGUAUCCCCGGUCG----UAAGUGCCA-GA------UAGAACAGGAUCUUAA----ACUUGCAACCAGCCAACUGAAUCAUUAAAAAA---------CAACCGCAAAGA-------AAA-CACACAC---CAGCAGUAACACCCCAGAGACAAAAAUCAAGAACACAAAGUAUAUUUU-GCAGGAAGGGCUAUAGUU-------CUUGAAGUCUGGAAAUAGUUGU------
AC146920.3/74770-74955     --CCCGCAUGUCUCCUGUCCAUGGCCGGUGGUGAGUGCAG-GAGGUGAUUAGAGCAGGAUCUUAA----ACCUGCAGCCGGCCAACUGAAUCAUUAAAA-A---------CAACCUCAGAGG-------AAA-C----------AAUAGUAACACUCGUGAAACAAUU--CAGAAACA----GUAUAUUUU-AAAGGAAGGGUUACAGUG-------CUUGACGUCGGGAAAUAG----------
AAWR02014325.1/563-763     --CCCCCGAGGCUCGGGUCCGCGGUCG----GAACUGCAG-AGGGUAAUUGGAACAGGAUGUUAA-UAAACCUGCGAGCGGCCAACUGAAUCCUGGAAAAG---------CAACCACAGGGA-------AAA-CCCACAC---CACGUGUAACACGCCAGAGACAAUU--CAGAAACACGAAGUAUAUUUU-GCGGGAAGGGUUGCAGUC-------CUUGAAGUCUAGAAAUAGAUGU------
AC087160.2/96835-97035     --CCCGCACGUCUCGUAUCCAGUGUUG----UAAGUGCAG-AAUGUAAUUGGAAAGGGAUCUUAA----ACUUGCAGCCAGCCAGCUGAAUCAUUAAAAAG---------CAACCACAAAGA-------AAA-CUCACAC---CAAUAGUAACGCUCCAGAGACAAAU--CAAAAACCCAAAGUCUAUUUU-GCAGGAAGGGUUAUAGUU----CCUCUCGAAAUCUGGCCAUGGUUGU------
AAKN02017194.1/596-789     GCCCCGCGCAUCUCCUCUCCGCAGUCG----CAAGAGCGG-AGGGUAAUUAGGACAGGAUCCUAA-UAAACCUGCGAGU--------GAGACGUUAAAAAA--------ACUUCCACUGGCA-------AAA-CGCAGGC---CAACAGUAACACUCCAGAGACAGA----UUAGAAGUAAAGUAUAUUUU-GAAGGAAGGGUUACAGUC-------UUUGAAGUCGGGAAGUAAUAGU------
ABRP01243925.1/446-621     --CCCGCAUGGCUCAUAUCCAUGG-------CAAAUACAG-AAAGUAAUGAGAACAGGAUCUUAA-UAAACGUGCAGCCAGCCAACCGAAUCAUUAAAAAA---------CAACCACAAAAU-------AAA-C----------AAAAACCUCACUC---------UU--CAGGAACAAAAAUUAUAUUUU-GCUGGAAAGGUUACAGUC-------CUUGAGUUGU------------UUUGAG
AC139728.3/109300-109490   GCCCUGCAAGUGUC--UUCUAGGGUCG----CAAGUACAG-AAAGUAAUUAUAAUAGGAUCUUAA-UAAACUUGCAGUCCACCAACCGAGUCAUUAGAAAA---------CAAUCACAAAGA-------AAA-CUGACAC---CAACAGUAACUC---------------CAGAGCCGCAAAGUAUAUUUU-GCAAGAAGGGUAACAGCC----UUUCUUGAAGUCUGGAAAUAGUGGG------
AC161329.3/114519-114729   GCCCCGCUUCUUUCAUACCCACAGUUG----UAAUUGGAG-AUGGUAAUUAGAACAGGAUCUUAA-AACACAUGUUGCCAGCCAAAUGAAUCAUUAAAAAAAACCCAACACAACCACAAAGA-------AAA-GUCACGA------CAGUAACAAUCUAGUAGCGACU--CAGAUACACAAGGUGUAUUUU-GAAGGAAGGAU-ACAGUA----CUAUUUGGAAUCUGGAAAUAGGUAU------
AC149571.3/116655-116851   --CCCGCGUGGCUCAUAUCCACAGUCU----CAAGUGCAG-AAAAUAAUUAGAGUAGUCUCUUAA-UAAACGUGCAGCCAGCCAAC-GAAUCAUGAAAACA---------CAACCACAAAGA-------AAA-CUCACAC---CGACAGUAACACUCCAGAGACAGUU--CAGAAACA---AGUAUAUUUU-GCAGGAAAGCUUACCUGCCAUCUUUCUUGAAGUCUGGAAG-------------
AAQQ01561278.1/327-511     --CCCGCGUGUCUCAUGGCCACGGUCU----UCGGUGCAG-AA-GCAACUAGGACAG--UGUUAA-UAAACUUGGAGCU--------GAGUCGAUAAACAG---------CCACUACAGACA-------AGA-C-UACGC---CAACAGUAACACUCCAGGGACAAUG--CAGAAACA--AAGUAU--UUC-AAAGGAAGUGUUACAAUC-------CUUGAAAUGUGAAAAUAAUCAU------
AC153775.3/41296-41492     --CCUGCUUGUCCUGCAUCCACGGUCA----UGAUUGCAGGAAGGUAGUGAGAACAGGAUCUUAA----ACAUGCAGUCAGCC----GAAUCAUUAAAAAG---------CAGCCACAAGGA-------AAA-CUCAUAA---AAACAGUACCACCCCCGAAGCGACU--CAGAAACUCAAGGUAUAUUUU-GAAGGAAGAGC-GCGAUC----CUUCUUGAAGUCUGGCAAUAGUUGU------
AC147455.3/45158-45369     --CCCCCACCGCUCAGAUCUGCGGUCU----UCCGUGCAC-AAGGUAAUUGGGACUGGAUCUUAAGUCAACUUGCUGCCAGCCAGCCGGCUCGUUAAAAUA---------CAACCGCAAAGA-------AAAACUCACGCUGACAGUAGUGACACCCGAGGGACCAUUCGAAGAAAAACAAAGUAUAUUUUUGCAGGAAGGGUUACGGUC----UUAAGUGAUUGCAGGAAGAUGCAAC------
#=GC SS_cons               ..:::::::::::::::::::::::::....:::::::::.::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::.........::::::::::::.......:::.:::::::...:::::::::::::::::::::::::..:::::::::::::::::::::.::::::::::::::::::.......::::::::::::::::::::::......
#=GC RF                    ..cCCGCguGuCUCauaUCCacGGUCG....uaAgUGCAG.aaGGUAAUUAGAACAGGAUCUUAA.uaAACuUGCaGcCaGCCaACuGAaUCgUUAAAAaA.........CAaCCaCAaAGA.......AAA.CucACgC...CaacagUaACaCuCcaGaGAcaauu..CaGAaACaCAAAGUaUAUUUU.GaagGAAGGGUUACaGUc.......cUUGAagUcUGGAAAUaguugu......
//
# STOCKHOLM 1.0

#=GF AC   RF02188
#=GF ID   ST7-OT4_2
#=GF DE   ST7 overlapping transcript 4 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   55.00
#=GF TC   62.80
#=GF NC   36.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.30 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-OT4
#=GF SQ   29


AC142297.1/5454-5283       -----GGAUCGUGUCCCUGGGAGGCGG------AUAGGAUUCAGCACUCU----AGAAUUGUCUCACCAUUU-GAAUAGGUGCUGCUCAGCCCUUUUGAGUCUGUCAUCGGAAAGA-CCAUGGCUUUCUCGCUUUUCA--UCUUUUU-GGAUGGCUGCUUGUCG------CAAUA-UUGUCUUCUUCGCUUUAGACAAG
BC043268.2/440-611         -----GGAUCGUGUCCCUGGGAGGCGG------AUAGGAUUCAGCACUCU----AGAAUUGUCUCACCAUUU-GAAUAGGUGCUGCUCAGCCCUUUUGAGUCUGUCAUCGGAAAGA-CCAUGGCUUUCUCGCUUUUCA--UCUUUUU-GGAUGGCUGCUUGUCG------CAAUA-UUGUCUUCUUCGCUUUAGACAAC
AC087215.5/55518-55689     -----GGAUAGUGUCCCUGGGAGGCGG------AUAGGAUUCAGCAGUCU----AGAAUUGUCUCACUAUUU-GAAUAGGUGCUGCUCAGCCCUUUGGAAUCUGUCAUCGGAAAGA-CCAUGGCUUUCUGGCUUUUCA--UCUUUUU-GGAUGGCUGCUUGUCA------CAAUA-UUGUCUUCUUCGCUUUAAACAAA
AC182539.4/19196-19364     -----GGAUGGUGUCCCUGGGAGGUGG------AUAGGAUUCAGCACUAU----AGAAUUGUCUCACCAUUU-GAAUAGGUGCUGCUCAGCCCUUUGGAGUCUGUCUUCGGAAAGA-CCAUGGCUUUCUGACUUUUCA--UCUUUUU-GGGUGGCUGCUUGUUG------CAGUA-UUGUCU---UUGCUUUAGACAAG
AC156348.3/58477-58641     -----GGAUAGUGUCCCUGGGAGGCGG------AUAGGAUUCAGCACUCU----AGAAUCGUUUCACUAUUU-GAGUAGGUGCUGCUCAGCCCUUUGGAAUCUGUCAUCGGAAAGA-CCAUGGCUUUCUGGCUUUUCA--UCUUUUU-GGAUGGCUGCUUUUUG----GACAAUA-UUGUGAUCC---------AAAAA
ABDC01071171.1/294-464     -----GGAUAGUAUCCCUGGGAGGCAG------AUAGGAUGCUGUGCCCU----GGAAUUGUCUCACCAUUU-GAAUUGGUAUUGCUCAGCCCUGUGGAUUCAA-CAUCCCAGGGA-CCAUGGCUUUCUGGCUUUUUG--UCUUUUU-GGAUGGCUGCUUAUCA------CAAUA-UUGUCGUAUUUGCUUUAGGCAAA
AC166602.2/32145-32320     -----GGAUAGUAUCCCUGGGAAUCAG------AUAGGAUGCUGCACCCCAGAUAGAAUUGUCUCACCAUUU-GAAUAGGUAUUGCUCAGCCUUGUGGAUUCAAUCAUCCCAGGGA-CAUUGCCUUUCUGGCUUUUUG--UCUUCUU-GGAUGGCUGCUUGUCA------CAAUA-UUGUCUUCUUUACUUUAGGCAAA
AC138559.3/136604-136776   -----GGAUAGUAUCCAUGGGAAUCAG------AUAGGAUGCUGCACCCUAGACAGAAUUGUCUCACCAUUU-GAAUAGGUAUUGCUCAGUC---UGGAUUCAGUCAUCCCAGGGA-CGUUGGCUUUCUGGGUUUCUG--UCUUCUU-GGAUGGCUGCUUGUCA------CAAUA-UUGUCUUCUUUGCUUUAGGCAAA
AC124157.4/35834-36004     -----UCAUAGUAUCCCUUGGAGGCAG------AUAGGAUUUUGCACCUU----AGAGUCAUCUUACUACUU-UAAUAGGUGCUGCUCAGCC-CUUGGAUUCAGUUAUCUCAGAGA-CCGUGGCUUUCUGGCUGUUCA--UCUCUUA-GAGUGGCUGCUUGUCA------CAAUA-CUGUCUUCCUUGCGUUAGGCAAA
AC153775.3/42084-42254     -----UGGUAGUGUUAUUGGGAGGCAG------AUAGGAUUUGGCACCCC----AGAACCUUCUCACCAUUU-UAUUAGACGCCGCUCAGCACUGUGGAGUCAGUCAUCCCAGAGG-UCAUGGCUUCCUGGCUUUUCA--UCGUUUA-GGGUGGCUGCUUGUCA-----A--AUG-CUGUCUUCUUUGCUUUAGGUGAA
AC149571.3/117176-117345   -----GGCUGGCACCGCUGCCAGGCAG------AUAGGAUUCUGCACCCU-----AAUUCACCUUACCUUUU-UAACAGGCGCUGCUCAGCC-CUUGGAUUCAGUCAUCCCACAGA-CCAUCGCUUUCUGGCUUUUCU--UCUUUUA-GAGUGGCUGCUUGUCA------CGAUA-CUGCCUUCCUUGCUUUAGCCAAA
ABRR01087120.1/36-207      -----GGAUGAUGUCUUUAGGAUGCAG------AUAGGAUUAUACACCCC----AGAAUCGUCUUGCCAUUU-UAAUAGGAGCUGUUCAACC-CUUGGAUUCAUUCACCCUAGUGA-UGAUGUCUUUGUGGCUGUUCA--UCUUUUA-GAGUGGCUGCUUAUCA------CAAUACUUAUCUUCCUUGUUUUAGGCAGA
AAKN02017194.1/1053-1222   -----GGAUAGUAACACU-GAAAGGUG------AUAAGAUUCCGUGCCCC----AGAAUUCUAUCACAGUUG-AAA-AGGCACAGCUCAGCCCUUUGAAUUGAGUCAUUCUGGAGA-CACUAGCGUUUGGGUUUUUCA--UUUUUUA-GGACCGCUGCUUGUCA------CAAUA-UCAUCUUCCUUGCUCUAGGCAAA
CU633802.4/89449-89282     -----CUGUGGUAUUCCUGGGGCCCAG------AUAGGAUCCUGUACCUU----AGAAUCAUCUUAUCAUUU-UUAGAGGAGAUGCACAGCC-CUUGGAUUCAGUCAUCCCAGU---UAAUGGCUUUCUG-CUUUUCA--UCUUUUA-GAGUGGCUGCUUAUCA------AAAUA-CUGUCUUCCUUGCUUUUGGCAAA
AANG01802794.1/59-225      -----UCAUAGUGACCCUGGGAGACA----------GGAUCCUGCACCCU----AGAAUCAUCCUGCCAUUUUUAAUAACUUUUGCUCAGCC-UUUGGAUUUAGUCACCUCAAAGA-CCAUGGCUUUCUGGCUAUUUU--UCAUUUA-GAGUUGCUGAUUGUCA------CAAUA-C-AUCUUCCUUGUUUUAGGCGAA
AC153100.3/27948-28110     -----GGAUACUAUCCCUAGGAGGCAG------GUGGGAUUCUGCACCCC----AGA---AUCUCACUGUUU-UAAGAGGUGCAGCUUGGCCCUUUGGGUUCAGUCAUCCCAGAGA-CUGAC-UUUUCUGAGUUUUCU--U-----A-GGGUGUUUGCUUAUCG------CAGUU-UUGUCUUCCUUGCUUUAGGCAAG
ABRP01243925.1/950-1120    -----GGCUAGCACCCCU-CAAGGCAA------AUAGGCUUCUGCACUGU----AGAAUAAUCUUACCAUUU-UAAUAGGUGCUGCUCUACC------CUUCAGUCAUUCCACAGA-UCAUGGCUUUCUGGCUUUUCC--UCUUUUA-GAGUGUCUGCUUCUCACAAUCACAAUA-CUAGCUUCCCUGUUUUAGGCAAA
AC186278.3/95292-95471     -----GGAUUGUAUCCCUCAGAGGAUACUAUCUGUAGGAUUCUGUACCCA----AGAAUUCUCUCCCCAUUU-ACAUAGAUACUGCUUAGCCCACUGGAUCCAGUCUUUCUAGAGA-CUCUAGCUUUCGGAUUUUUCA-UUCUUU-A-GGGUGGCUACUUGUCA----UAUAAUA-UUGUCUUCCUUGCUUCAGGCAAA
ABRN01307492.1/18806-18972 -----GGAAGGUACUCCUGGGGUGCAG------AUAGGACUCUGCACCCG----AGAAUCAUCUUGCCAUUU-UUAUAGGAGCUGCUCAGCC-CUUGGAUGCAGUCAUCCUAGUGA-UGAUGGCUUUCUGGCUUUUCC-AUCUGUUA-GAGUGGUUGCUUAUCA------GAGUA-UU--CUUCCUUGCUUUUGGU---
AAFC03007187.1/1029-1199   -----GGAUGUUAUUCCUGGGCUGCCCC-----GUGGAAU-CUGCGUUGU----AGAAUCAUGUUGCCAAAU-GGAUAGGAGCUGUUCAGCC-CUUGGAUUCAGUUUUCCUAGUGA-UAAUGGCUUUCUGGCUUUUCA--UCUAUUAUGAGUGGCUGCUCAUUA------CAAUA-CUGGCU-CCUUGCUUGUGGCAAA
AAGV020207641.1/1618-1779  -----CCAUAUGGUAGACAGGAGUCC---------AAACGCUUGAGCCACA---UCACUUCCCUCACUAUUU-UAAUAGGUGCUUCUCAGCCCUGUGGAGUCAG--------GAGU-UCAUGGCUUCCCUGCUUUUCC--UCUUUUA-GGGUGGCUGAUUGCCA------CAAUA-CUGGCUUCUUUGCUUUAUGCAAG
AC147928.3/153545-153705   AGAAU-----------CU-----GCCCC-----GUAGAAUUCUACACCGU----AGAAUCAUCUUGCCAAAU-UUAUAGGAGCUGUUCAGCC-CUUGGAUUCAGUUUUCCUAGUGA-UAAUGGCUUUCUGGCUUUUCA--UCUAUUAUGAGUGGCUGCUUAUCA------CAAUA-CUGUCU-CCUUGCUUGUGGCAAA
AC139728.3/109811-109972   ----------GGACCCCUGCCACGUACAAAG--AUAGGAUUCUGCACCCC----AGAAUCA-CUUACCAUUU-UAAUA--UGC---UUAGCC-CUUGGAUUCAGUCAGACCGCAGA-CCAUGGUUUUCUGGCUUUUCA--UCUUU-A-GCGUGGCUGCUUGUCA------GGACA-CUGUCUUC-UUGCUUUAUAUAAA
AAYZ01112118.1/1030-1195   -----GGUUAGUACCCCUGAAAGGCAG------GUGAAAGUCUGCACCUC-----AAUUAGUGUCAUUGUCU-UAAUAGGCGCAGCUCAGCCCUUUGGAGUCAGUCAUCCCAGAAC-GUGUAGCUUUUGGGGGGUUU-----UCUCA-GGGUGCC----UGUCA----CAAAAUA-UUGUCCUCUUUGCUUUAGACACA
ABVD01886406.1/269-403     -----UGAUGGUAUCCCU-----ACAGA-------AGGAUUCUGCACCCC----AGAAUCAUCUCACUGUUU-UAAUAGGUUCUGCUCAGUCCCUUGGAGUCAG--------GAGU-CCAUGGCUUCCAGGCUUGUUA--CCUUUCU-----GGC---------------------UU-----CCUUGCUUUAGGCAAA
AC153836.5/23211-23387     -----GGAUGGUCUUUUUGGGAGGCAG------ACAGAAUUCUGCAC-AU----AGAAUCAGCUCAUCCUA--AUGUAGAGGAUGCUAAGCUGUUUGGCUCUGAUUAUUCCGAAGA-UCCCACCUUUUUUUUUUUUUUAAUCUGUUA-GCGUGACUGCUUGUCA-CAUUGUAAUA-UUGUGUUCCUUGCCUUAGGACAG
AC182512.4/194165-194323   -----GUGUGGUGCUGU-GGGAGGCAG------GUGGGAUGCUGCACCCCC---AGAAUCUUCUCACCAAUU-GACUGGAUGCUGCUCAGCAUCUUGGAGCCAGCCCUCCCCCAGG-CUGGGGCUUCCUGGCUUUU----------A-UAGGGGCUGCAUGUCA------------CCACCUUCCCUGCUUUCAGUGAG
AC182003.3/547-714         -----GCUGAGUACCCCUGCCGAGCAG------AUAGGGUUCUGCACCCU----GGAGUCA-CUUAUUGCUU-UAAUGGUCACUGCUCAGUC-CUUGGAUUCAGUCACCCCAUGGA-CCAUGGCUUUCGGGCUUUUCA----UGUUA-GAGUGGCUGCUUGUCA------CAGUA-CUGUCUUCCUUGCUUUAUGUAAG
AC146920.3/75276-75423     -----GGAUAGUAUCCCAGCGAGGCAG------AUGGGAUCCUGUG----------------------------AAUAGGUUUU--UCAGCCCCGUGGAUUCAGUCAUCCCAGAAAGCCAGCACUUUCUGGCUUUUUG--GCUUACU-GGAUGGCUGCUUGUCA------CAAUA-UUGUCUUUUUUGCUUUCAACAAC
#=GC SS_cons               .....::::::::::::::::::::::......:::::::::::::::::....::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::..:::::::.::::::::::::::::......:::::.:::::::::::::::::::::::
#=GC RF                    .....GGaUaGUaucccUGgGAgGCaG......aUAGGAUuCUGCACCcu....AGAaUcaUCUcaCcaUUU.uaaUAGGuGcUGCUCAGCCcuuUGGAuUCaGUCaUcCcagaGa.ccaUGGCUUUCuGGcUUUUCa..UCUuUUa.GgGUGGCUGCUUGUCA......cAAUA.uUGuCUUCcUUGCUUUaGGcaAa
//
# STOCKHOLM 1.0

#=GF AC   RF02189
#=GF ID   ST7-OT4_3
#=GF DE   ST7 overlapping transcript 4 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   50.00
#=GF TC   51.00
#=GF NC   43.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.91 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-OT4
#=GF SQ   20


BC043268.2/619-911           UGCUUACUCUU--CCUGUGAUGAAGGCAAG-----UGUGUUCCUGGAGAGGUUACUGAAUCUGGAGCUGCUUUUAGG-GAGUUGCAGAUGGCGCAGGCCUCCCUUCCUCCUCAAGGAAGCCAAAGACACCAUCACAAU------------------CAGGCAGC---------------CAGGAGCC-AGGGCUUCCAU-----AGGCCCAGCUCUGUACCUGUAGGG--GGAUGGAA-UCUGCUAAAAG-UGUUCUGGAGUCGUUCUUGGAUAUCUGCUUGGUAU---CUUCUCAAUAUCUUGACCAUCUGUGA-CAAU-------UUU-AAUCCUCAUUUGAUCAUAUUUUAUG
AC153073.3/94383-94675       UGCUUACUCUU--CCUGUGAUGAAGGCAAG-----UGUGUUCCUGGAGAGGUUACUGAAUCUGGAGCUGCUUUUAGG-GAGUUGCAGAUGGUGCAGGCCUCCCUCCCUCCUCAAGGAAGCCGAGGACACCAUCACAAU------------------CAGGCAGC---------------CAGGAGCC-AGGGCUUCCAA-----AGGCCCAGCUGUGCCCCUGUAGGG--GUAAGGAA-UCUGGUAAAAG-UAUUCUGGAGUCGUUCUUGGAUAUCUACUCAGUAU---CUUCUCAAUAUCUUGACCAUCUGUGA-CAAU-------UUU-AAUCCUCAUUUGAUCAUAUUUUAUG
AC182539.4/20652-20927       UGCUUACUCU----CUGUGAUGAAGGCAAG-----UGUGUUCCUGGAGAGGUCACUGACUCUGGAGCUACUUUGAGG-GAGUUGCAGAUGGCAAAGGCCUCCCUUC----UCAAGGAAGCCCAGGACACCAUCACAGU------------------CAGGCAGC---------------CAGGAGCC-AGGGCUUCCAU-----AGGCCCAGCUCUGCACCUGUAGGG--GAAUGGAA-UUUGGUAAAAG-UGUUCUGGAGUCAUUCUUAGAUAUCUGCUUGGUAU---CUUCUCAAUAUCUUGACCAUCUGUGA-CAAUUUUUUUUUUU-------------------UUUUUUU
AC146768.3/97851-98126       UGCCUACUCU----CUGUGAUGAAGGCAAG-----UGUGUUCCUGGAGAGGUCACUGACUCUGGAGCUACUUUGAGG-GAGUUGCAGAUGGCACAGGCCUCCCUUC----UCAAGGAAGCCCACGACCCCAUCACAAU------------------CAGGCAGC---------------CAGGAGCC-AGGGUUUCCGU-----AGGCCCAGCUCUGCACCUGUAGGG--GGAUGGAA-UCUGGUAAAAG-UGUUCUGGAGUCAUUCUUGGAUAUCUGCUUGGUAU---CUUCUCAAUAUCUUGACCAUCUGUGA-CAAUUUUUAUUUUU-------------------UUUUUUG
AC152893.4/32309-32583       UGCCUACUCU----CUGUGUUGAAGGAAAG-----UGUGUUCCUGGAGAGGUAACUGACUCUGGAGCUACUUUGAGG-GAGUUGCAGAUGGCACAGGCCUCCCUUC----UCAAGGAAGCCCAGGACACCAUCACAAU------------------CAGGCAGC---------------CAGGAGCC-AGGGCUUCCAU-----AGGCCCAGCUCUGCACCUAUAGGG--GUAUGCAA-UCUGGUAAAAG-UGUUCUAGAGUCAUUCUUGGAUAUCUGCUUGGUAU---CUUCUCAAUAUCUUGACCAUCUGUGA-CAAUUU-----UUUAUAU---------------UUUUUUG
AC163242.3/33425-33694       UGCCUACUCU----CUGUGAUGAAGGCAAG-----UGUGUUCCUGGAGAGGUCACUGACUCUGGAGCUACUUGGAGG-AAGUUGCAGAUGGCACAGUACUCCCUUC----UCAAGGAAGCCCAGGACACCAUCACAAU------------------CAGGCAGC---------------CAGGAGCC-AGGGCUUCCAU-----AGGCCCAGCUCUGCACCUGUAGGG--GGAUGAAA-UCUGGUAAAAG-UGUUCUGGAGUCGUUCUUGGAUAUCUGCUUGGUAU---CUUCUCAAUAUCUUGACCAUCUGUGA-CAAUU------UUU-------------------UUUUUUG
AC159917.3/64949-65219       UGCCUACUGU----CUGUGAUGAAGGCAAG-----UAUGUUCCUGGAGAGGUCACUGACUCUGGAGCUACUUUGAGG-GAGUUACAGAUGGCACAGGCCUCCCUUC----UCAAGGAAGCCCAGGACACCAUCACAAU------------------CAGGCAGC---------------CAGGAGCC-AGGGUUUCCAU-----AGGCCCAGCUCUGCACCUGUAGGG--GGAUGGAA-UCUGGUAAAAG-UGUUCUGGAGUCAUUCUUGGAUAUCUGCUUGGUGU---GUUCUCAAUAUCUUGACCAUCUGUGA-CAAUUU-----UUU-------------------UUUUUUG
AC166602.2/33663-33967       UGGUUGCCCUU--CCUGUGAUGAAGGCAGG-----UGUGUCCCUGGAGAGGCCACUGAGUCUAGAGCUGCUUUUAGG-GAGCUGCCAAUGGCACAGCCCUCCCUAC----UCAGGGAAGCUGAGGGCACCAUCACAGU------------------GAGGCAGC---------------CAGGAGCC-AGGGCUUCCAUGACAUAGGCCUAGCUCUGUACCUGCAGGG--GGGCAGAA-UCUGGUAAAAG-UGUUCCAGAGUUGUUCUUGGGUGUUUGCUUGGCAUAUUCUUCUCAAUAUCUUGAUUACUUGGGG-CAAUUUUAAUAUUUUUAACCUCAUUUGAUCAUAUUUUAUG
ABRT010186623.1/516-809      UGCUUGCUCUU--UCUGUGAUGAAGGCAAG-----UGUGUCCCUGGAGAGGCCACUGAAUCUAGAACUGCUUUUAGG-GAGUUGUGAAUGGCACAGGCCUC---------UCAGAGAAGCUGAGGACACUGUCACAGU------------------GAGGCAGU---------------CAAGACCC-AGGGCCUCCGUGACACAGGCCCAACUCUGUAUCUGUGGGG--GGAUGGAA-UCUGGUAAAAA-UGUUCCUGAGUUGCUCUUGGAUGUCUACUUAGCAU---CUUCCUAGGAUCUUGAC-ACCUGUGA-CAGU--UAAUAUUUUAAAACUCAUUUGAUCAUAUUUUGUA
AC146920.3/76775-77075       UGCUCACUCUU--UCUGUGAUGGACACAGG-----UAUGUAGCGAGAGAGAC-AUUGAGUCUAGAGCUGCUUUUAGG-GACCUGCUGAUGGCAUAGCCCUCUCUCU---CUCUGGGAGGCUGAGUGCACCAUCACAGU------------------GAGGCAGU---------------CAGGAGCC-AGGGCUUCCAUGACACCUGCCUAGCUCUGUACCUGGGGGGAGGGGCGGAA-UCUGGUAAAAA-UGUUCCAGAGUUGCUCUUGGGUACCUACUUGGCAUAUUCUUCUCAAUGUCU-----AA-UGUGG-UAAUUUUAGUAUUUAUAACCUCAUUUGAUCAUAUAUUUUG
AAWR02014325.1/1989-2302     UGCUUGCUCUU--CCUGUGACGGUGAAGGU--------GUCCCUGGAGAGGCAGCCGAGUCUAGAGCUGCUUUUAGG-GAGCUGCGGGUGGCGCGGGCCUCCUUCC----UCAGGGAAGCUGAGGACGCUAUCACAGU------------------GAGGCAGACGGGUGAGACAGCAGGAGGAGUC-AGGGCUUCCAUGACACAGGCCCAGCUCUGCACUUGUAAGA--UUGUGGAA-UUUGGUAAAAAAUGUUCCAGAGUUGUU-UUGAAUAUCUACUUGGCGU--G-UUCUCAAUAGCUUGAUUACCUGUGA-CAACUUUGAUAUAUCUAAUCUCAUGUGAUCAUAUUUUGUG
AANG01802794.1/948-1251      UGCUUGCUCUU--CCUGUGGCGGUGAAGGCGAGUAUGUAUCCCUGCGGUUGCCACUGAGUCUAGAGCUGCCUUUAGG-GAGCUGUGGGUAGCACAGGCCUCCUUCC----UCAGGGAUGGUGAAGACAUCAUCACAGUUGGGCA-----GACUGGUGAGGCAGC---------------CAGGAGCCCAGGGCUUCCAUGACACAGCCCCAACUCUGUACUUU---------GUGGAA-UCUGGUAAAAA-UGUUCCAGAGUUGUU-UUGGAUACCUGCUUGGCAU---GUUCUUAAUAGAUUGAUUACCAAUGA-CAACUUUAAUAUUUCUGACCUCAUUUGAUC---------U
AC186278.3/96642-96925       UCCUUGUUCUU--CCUAUGAUGAAGGCAAG-----UAUGUUCUUGGAAAGGCUG-UGAAUCUAGAACUGCUUUUAGGUGAUCUGCAGGUGACACAGGCCUC---------CC-------------ACACCAUCACAGU------------------GAGGCAGAGCUA------UGAGACAGGAGCC-AGGGCUUCUGUGAUGCAGAAACUGCUCUGCACCUGUAGGG----GUGGAA-UCUAGUAAAAA-UGUUCU-GAGUUGUUCUUAGAU--CAACUUGGUGUGUUCUUCUUAAUAUCUUGAUUAUCUAUGG-CAAUU------UUUAAAAAAAUAUUUAUUUAUUUAUUUA-
AC087160.2/98258-98551       UGCCUGUUCUU--CCUGUGAUGGUGAAAGC----ACAAGUCUCUGGAGAGGCUACUGAAUCUAAAGCUACUUUGCAG-GAGCUGUGGGUGGCAGAGACCUCCUUCC----UCAGGGAAGCCAAGGACAUAAUCACAGUGAGGAG------AUCUGUGAGGCAGC---------------CGGGAGCC-AGGGCUUCCAUGACACGGGCCCAGCUCUGUACCUUUAAGG--UUGUGAAAAUCUAGUAAAAA-UGUUCCUGAGUUGCU-UUGGGUGUCUACUUGGCAU---GUUCUCAAUAGCUUGAUUACCUGUGAACAACUUUAAUAUUUCUAG----------------------
AC149571.3/118048-118353     UGCUUGCUCUU--CCUGUGA-GGUGAAGGC----AAGUGUCCCUGCAGAGUCUACUGUGUCUAGAGAUGCUUUUAGA-GAGCUGUGGGU---------UUUCUUCC----UCAGGAAAGCUGAGGACACCAU------UGAGGGAGGCAGAUCCGUAAGGCCAC---------------CAGGAGCC-AGAGCUUCCAUGACCCAGGCCCAGCUCUGCUCUUGUAAGG--UUGUGGAA--CUGGUAAAAA-UGUUCCAGAGUUGUU-CUGGGUAUCUGUUUGGCUUGCUCUUCUCAAUAUCUUGAUCACUUAUGG-CAUCUUUAAUAUUCCUAACCUUAUUUGAUCAUAUUUUGUG
ABRP01243925.1/1845-2138     UGUUUACUCUU--CCUGUGA-AUUGAAGGC--------CUCCCUGGAGAGGCCGCUGAAUCUAGAGCUGCUUUUAGG-GAGCUGUGAGUGGUGCCGGCCUUCUUCC----UUAGGAAAGCAG----------------GCAGA--------UGGGUGAGGCGGA---------------UGGAAGAC-AAGGCUUCCGUGACACAGACCCAGCUCUGCUGUUCUGAGG--UUGUGGGA-UCUGGUAAAAA-UGGUCCAGAGUUGUU-CUGGAUGUCUACUUGGCUUGCUCUUCUCAUUCUUUUGGUCAGUUAUGU-CAUCUUUAAUAUUUUUAACCUCAUUAGAUCAUAUUUUGUG
AC139728.3/110938-111212     UGCUUGCUCUU--CCUGGGA-GGUGAAGGC----AAGUGGCCCU------------------AGA-----------------UG---------CAGGCCUUCUUCC----UCAGAAAAGCUGAGGACACCACUGCAGUGGGGGUA----GGUCUAGGAGGCAGC---------------CAGGAGCC-AGGGCUUCCAUGACACAGGCCCAGCUAUGCUCUUACAAGG--UUGUGGAA-UCUGGUAAAAA-UGUUCCUGAAUUGUU-CUGGAUGUCUGCUUGGCUUGUUUUUCUACAUACCUUUGUCACUGACGG-AGCUUUUAAUAUUUCUAACAUCAUUUGAUUAUAUUUUGUG
AAKN02017194.1/1878-2145     UGUUUGCCCUU--CUUGUGGUGAGUGCAAG-----UACGACCCUGGAAAGGU---GGAGUCUAGAGCUGCUUUUAGGAGAGUGGUAGGUGGUUCACAUCUCCCACA----UUAUCACAGUGA--GGCAGAGUUACAG---------------------GGUAGC---------------CAGAAGCU--GGAUUUCAGUGAUAUAGACCCAGCUCUAAAG-----UGG--AGGUAAAA-CCUGGUAAAG---------GAGGUACU-UUGGAUAACUGUUUGACAUGUUCUCCUCAAUAUCUUGAUUACCUGGGG-GAAUUACGCUAUUGGUAU---------------UUUUGUG
AC153775.3/43520-43811       UGCUUGCCCUUUUCCUGUGUAGGUGAAGGU----GCGUGUCCCUGGGGAAGCUGCUG-UUCUAGCACUGUUUUUAGG-GAGCUGCAG-UAGCGCAGGCCUCGCUUC----UCAGGAAAGGUGAGGACACAAACUCAGUGAGGCA-----GAUCAGCGAGGCAGC---------------CAAGUGCC-AGGGCUUCUGUGACGCAGGCCCAGCUCUGCACUUUUCAGG--UUAUGGGA-UAUGAUGAAAA-UGUUCCAGUGUUCUU-CUCGAUAUCU--UUGUUGU---CUU---------------------GG-UAAUUUUAAUAUUUUUAACCUCAUUUGAUCAUGUUUUGUG
AAEX03009455.1/816214-816482 UGCUCACUCUU--UCUGUAGCAGUGAAGGC--------A-----AGAGAGGCCCCCGAGUCUAGAGCUGCUCUUAAG-GAGCUGCUGGGAGCACCGGCCUCCUUCC----UCGGCAGAGGUGAGGACAC-AUCGCGGG------------------GAGGCCGC---------------CGGGAGCCCAGGC----------------CCAACUCUGUACUUUGUGCG-AUUGUGGAA-UCUGCUAAAAA-UGUU------------UCGGAUACUUGCUUGGCACGAUCUUCUCAAUAGCUUGAUUA-CUACGA-CGACGUUCAUAUUUACAACCUCAUUUGAUCUUAUUUUUUG
#=GC SS_cons                 :::::::::::..:::::::::::::::::.....::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::....::::::::::::::::::::::::::::..................::::::::...............::::::::.::::::::::::::::::::::::::::::::::::::::..::::::::.:::::::::::.:::::::::::::::.:::::::::::::::::::..:::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UGCUUgCUCUU..CCUGUGauGguGgaggg.....uguGucCCUGGAGAGGcuaCuGAgUCUaGAGCUGCUUUuAGG.GAGcUGcgGgUGGCaCaGgCCUCCcUcC....UCagggaaGcugAGGACAccAUCaCAGU..................gAGGCaGc...............CAGGAGCC.AGGGCUUCcaUGAcacaGgCCCAGCUCUGcaccUguagGG..uuGUGGAA.UCUGGUAAAAa.UGUUCcaGAGUuguU.UUGGaUauCUgCUUGGcaU..ucUUCUcAAUauCUUGAuuAccUguGg.cAauUUUaaUAUUUuuAaccUcAUUUGaUcaUaUUUUgUG
//
# STOCKHOLM 1.0

#=GF AC   RF02190
#=GF ID   ST7-OT4_4
#=GF DE   ST7 overlapping transcript 4 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   70.00
#=GF TC   76.20
#=GF NC   49.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   12213198
#=GF RT   The RAY1/ST7 tumor-suppressor locus on chromosome 7q31 represents a
#=GF RT   complex multi-transcript system.
#=GF RA   Vincent JB, Petek E, Thevarkunnel S, Kolozsvari D, Cheung J, Patel M,
#=GF RA   Scherer SW
#=GF RL   Genomics. 2002;80:283-294.
#=GF WK   ST7-OT4
#=GF SQ   26


BC043268.2/1352-1564       UUUGCAGCUUUAGAUUGUGGUCAGAGGCUGUUACAAGAUCUUAUA-UAUUCUA-UGAUGGGCCAUAUGCAUC---UAAAGCAUGGUGGUUCAGUUUAUGAAUAUAU-AAAAGGACAAUUUUUU----------------------GAUUAAUGUCAGCUUUGAGUUUAGAAUGUAUCCCAGACAUCUU-AGUUGCCCUUAAU------U-AUUUUUGGAGAUAUUUUUCUCAGCCAUUAAUAAAGCAAU-----
AC159917.3/70200-70410     UUUGCAGCUUUAGAUUGUGGUCAGAGGCUAUUACAAAAUCUUGU---AUUCUA-UGAUGGGUCAUAUGCAUC---UAAAGCAUGGUGGUUCAGUUUAUGAAUGUAU-AAAAGGACAAUUUUUU----------------------GAUUAAUGGCAGCUUUGAGUUUAGAACAUAUCCCAGACAUCUU-AGUUGCCCUUAGU------U-AUUUUUGGAGAUAUUUUUCUCAGCCAUUAAUAAAGCAAU-----
AC087215.5/60099-60310     UUUGCAGCUUUAGAUUGUGGUCAGAGACUGUUACAAAAUCUUCUG-UGUUCUA-UGAUGGGUCAUGUGCAUC---GAAAGCAUGGUGGUUCAGUUUAUGAAUAUAU-AAAAGGGCAAUUUUUU----------------------GAUUAAUGUCAGCUUUGAGUUUAGAAGGUAUCCCAGACAUCUU-AGUUGCCCUUAAU------U--UUUUUGGAGAUAUUUUUCUCAGCCAUUAAUAAAGCAAU-----
AC146768.3/101811-102024   UUUGCAGCUUUAGAUUGUGGUCAGAGGCUGUUACAAAAUCUUAU---AUUCUA-UGAUGGCUCAUAUGCAUCAUCUAGAGCAUGGUGGUUCUGUUUAUGAAUGUAU-AAAAGGACAAUUUUUU----------------------GAUUAAAGUCAGCUUUGAGUUUAGAACGUAUUCCAGACAUCUU-AGUUGCCCUUAGU------U-AUUUUGGGGGAUAUUUUUCUCAGCCAUUAAUAAAGCAAU-----
AC124157.4/39320-39531     UUUUCAGCUUUAGAUCGAGGUCAGAAGCUGUCACAAAAACGUAA---AUUCUA-UGAUGGGUCGUAUGCAUC---UCAUUCAUGGUGGUCUAGUUUACGAACACAUGAAAAGGACAAUUUUCU----------------------GAUUAACGUCAGCUUUGAGUUUAGGAUAUAUUCCAGACAUCUU-AGUUGCCCUUACU------U-AUUUUUGGAGACAUUUCUCUCAGCCAUUAAUGAAGCAAU-----
ABRT011102227.1/18-228     UUUUCAGCUUUAGAUUGAGGUCAGAGGCUGUCACGAAACUUUAG---AUUCUG-UGAUUGGUCCUAUGCAUC---AAAUACAUGUUGGUCCAGUUUAUAAACAAAU-AAAAACAUAAUUUUUA----------------------AAUUAAUGUCAACUUUGAAUUUGGGAUGUAUCCCAGACAUAUU-AGUUGCCCUUACU------U-AUUUUUGGAAAUGUUUCUCUCAGCCGUCAGUGAAGCAAU-----
ACBE01081492.1/2908-3117   UUUUUAGCUUCAGAUCCAGGUCAGAGGUUGACACAAAAACUUAA---AUUCUG-UGAUUGGUCAUAUGCGUG---UGAUUCAUGGUGGUCCAGUUCAUGAACACAU-GAAAGGAUAAUUUUCU----------------------AAUUAAUGUCAGCUUUGAGUUUAGGAUAUAUCCCAGACAUUUU-AGUUGUCCUUACU------U-AUU-UUGGAGACAUUUCUCUCAGCCAUUAAUGAAGAAAU-----
AC146316.3/141823-142023   UUUUCAGCUUUAGAUUGAGGUCAGAAACUGUCACAAAGUCUUAA---AUUCUA-UUAUGAGUCAUAUGCAUC---CAAUGCGUGGUGGUCCAGUUUAUGACCACAU-AAAAGGACAAUUUGUU----------------------GUUUAAUGUCAGCUUUGAGUUUAGGAUGCAUCCCAGACA-----------UAUUACU------U-AUUUUGGGAGAUGUUUCUCUCAGCUGUUAAUGAAGCAAU-----
AC166602.2/37647-37847     UUUUCAGCUUUAGACUGAGAUCAGGUGCUGUCACAAAAUCUUAA---AUUCUA-UGAUGAGUCAUAUGCAUC---UAAUGAAUGGUGGUCCAGUUUAUAACCACAU-GAAAGGACAAUUUGUU----------------------GUUUAAUGUCAGCUUUGAGUUUAGGAUAUAUCCCAGACA-----------UCUUACU------U-AUUUUGGGAGAUGUUCCUCUCAGCUGGUAAUGAAGCAAU-----
AC149571.3/119997-120210   UUUUCAGUUUUAGAUCGAUGUCAAAAGCUGUUACAAAAACUUAAAAAAUUCUC-UGAUGGGUCAUAGGCAUC---UAAUUUGUGGUGGUCCAUUUUAUGAACAUAU-GAAAGGAAAGUUAUCU----------------------GUUUAACAUCAGCUUUGAGUUUAGGAUAUAUCCCAGAUAUCUU-AGUUGCGCUUACU------U-UUUUUUGGAGAUGUUUCUCGUAUCCAUUAACGAAGCAAU-----
AC147928.3/156556-156766   UUUUCAGCUUUAGAUAGAAGUCAGAAACUGUCACAAAAAUUUAAGAAAUUCCA-UGGUGAGUCAUAAGUAUC---UAAUCCAUGGUGGUUCAAUUUAUGAACACAU-AAAAGGACAAUUUUAU----------------------GGUU---GUCAGCUUUGAGUUGAGGAUAGAUCCCAGACAUCUU-AGUUGCCUUUACU------UUACUUUUGGAGACAUUUCUCUCAGCCGU-AAUGAAGCAAU-----
AC138559.3/142103-142303   UUUUCAGCUUUAGAUUGAGAUCAGGUUUUGUCACAAAGUCUUAA---AUUCUA-UGAUGAGUCAUAUGCAUC---UAAUGCAUGGAGGCCCAGUUUAUGACCACAU-GAAAGGACAAUUUGUU----------------------GUUUAAUGUCAGCUUUGAGUUUAGUAUAUAUCCUAGACA-----------UCUUAUU------U-AUUUUGGGAGAUGUUUCUCUCAGCCGGUAAUGAAGCAAU-----
AC182002.3/166974-167184   UUUCCAGUUUUAGAUGGAGGUCUAAAGCUGUCACAAAAACUUAAAAAAUUUUCCUGAUAGGUCAUGUGCAUC---UAAUUCAUGGUAAUCCAGUGUAUGAACACGU-ACAAGGACAAUUUCCU----------------------GAUUAAUGUCAGCUUUGAGUUGAGGCUAUAUCCUAGACAUCUU-AGUUGCUCUUAUU-----------UCUGGAGACAUUUUUCUUGGCCAUUAAUGAAGCAAU-----
ABRP01243926.1/1174-1386   UUUUCAGCUUUAGAUAAAGGUCAAAAACUGUCACAAAAACUUAAAAAAUUAUC-UGAUGGGUCAUCUGCAUC---UAAUUCAUGAAGGUGCAGUUUAUAAACACAU-GAAAGGACAAUUAUCU----------------------GCUUAAUGUCAGCUUUGAGUUUAGGGUAUGUCCCAGACAUGUU-AGUUGCUCCAACU------C-GUU-UUAGAAACGUUUCUCUCAUCCAUUAAUGAAGCAAU-----
AC139728.3/113109-113310   UUUUCAGCUUUAGAUCGA--------GCUGUCACAAAAGCUUAAAAAAUCCUC-UAAUGGGUCAUAUGCAUG---UAAUUCAUGGUGAUCCAGUGUGUGAACAUAC-AAAAGGAUAAUUUUCU----------------------GAUUAAUGUCAGCUUUUAGUUGAGGAUAUAUCCCAGACAUUUU-AGUUGCUCUUAUU-----------UUUGGAGAUGUUUUUCUCAGUCACCAAUGAAGCAAC-----
CU633802.4/82853-82646     CUUUUAGCUUUAAACCGAGGUCAGAAACUGUCACAGAAACUUAA---GUUCUU-UGGCGGGUUAGAUGAAUC---UAAUCCAUGGUCAUCCACUUUAUAAAUACAU-AAAAGGACAGUUUUAU----------------------GAUU---GUCAGCUUUGAGUUGAGGAUAUGUUCCAGACAUCUU-AGUUUCCCUUACU------U-AUUUUUGGAGACAUUUCUCUCAGCUAUUAGUGAAGC---UGA--
ABVD01540098.1/137-344     AUUUCAGUUUUAGAUUGAGGUCAGGGGCUGUUAAAAGAU-AUAAGAAAUUUUA-UAAUGGGUCAUAUGCAUU---UAGUUC---GUGGCCCAGUUUAUGACCACAU-AAA-GGACAUUAUUUUC--------------------UGAUUAAUGCCAACUUUGAGUUUAGGAUAUGUUCUGGACA---U-ACUUGCCCUUAAU------U-AUUUUUGUAGAUGUUUCUGUUAGCCAUUAAUGAAACAAU-----
ABRR01087121.1/980-1170    UUUUCAGCUUUAGAGCAAAAUCAGAAACUGUCACAAAAACUUAAGAAUUUCUU-UAAUGGAUCAUAUG-----------------------AGUUUAUGAACACAU-AAAAGGACAAUUUUGU----------------------GAUU---GUCAGCUUUGAGUUGAGGAUAUAUCACAGGCAUCUU-AGUUGCCCUUACU------U-AUUUUUGGAGACAUUUCUCUCAGCCAUUAAUGAAGCAAU-----
AAQQ01074767.1/512-708     UUGUCAAUUUUAA-UCGAGGUCAGAGGCU---------------C-AAUUCUA-UGGUGGAUCAUAUGUAUC---UCACUCAUGGUGGUCCAGUUUGUGGACACAG-AAAAUGACAUUUUUCU----------------------GAUUAAUGUCAGUUUUGAGUUUACAAUGUAUUUCAUAUACCUU-AGUUGCCUUUACU------U-ACUGUUGGAGAUAUUUCGUUUAGUCAUUAAUGAAGCAAU-----
AAGV020575780.1/789-574    UUUUCAGAUUUAGAUUGAGUUCAGUGGCUGUCACAAAAUCAUAAGAAAUUCUA-UGAUUGGUCAUAUGCAU----UAAUUCACUGU---CCAGUUUAUGACCACAU-AAAUAGACUUUUUUUUUUU---------------CCCUGCUUAAUGUCUGCUUUGAGUUUAGGGUAUAUCCCAGAUAU-UU-AGUUCCCCUUAAU------U-ACUUUUGGAGAUGUUUCUCAUAGCCAUUAAUGAAACAAU-----
AC171368.3/23159-23371     UGCUAUGCUUUACAUUGAGGUCAGAGGCCAUUGCUAAAAGUUGA---AUUGUU-UGAUUGGUGUUAUUUAUC---UAAUUCAUGGUGGUUCAGCUUAUGAACACCU-AAAAGGACAAUUUUUC---------------------CAAUUAACUUUAAUUUUGAGUUUAAGGUAUAUCCCAGAUUCCUU-AGUUU-GCUAAGUUGCUCUU-ACUCUUGGAGGUAUUUCAGC--------AAUGAA-CAAUUUAAG
AC087067.3/77465-77654     UUUUUAGCAUUUGAUUGAGGUCAGAGGCUGCUAUAAAAACUUAA----UUUUU-UCAUAGGUGUUACAAAUC---UA----------------UUCAUUGAUGUAU-AAAAGCACACUUUUCU----------------------AAUUCAGGUCAGAUUUGAGAUUAGCAGGUAGCUCAUACAGCUU-CAUGUCCUUCAGU-----------UUUGGGAAUAUCUGCCCCACACAGGAAUGCAGCAAU-----
AC146920.3/83829-84001     --UUCAAAUAU---UUAAGUUACUGUGCUGUCACAAAACCUUAA---AUUCUG-UGAUGGGUCACAUGCAUC---UA-------------------AUGAAUACAU-ACA-GGACAAUUUGUU----------------------GUUUAUUGUCAGCUUUGAGUUUAGGAUGUAUCAUAGGCA-----------CCAUACU------U-AUUUUUGGAGAUGUUUCCCUCAACUGUUAAUGCAAU--------
AAHY01051747.1/24739-24553 UUUUUAGCUUUUG----AGGUCAGAGGCUGCCAUGAAAACUUAA---AUUUUU-UGAUAGGUGUUGCAAAUC---UA----------------UUCAUUGAUGUAU-AAAAGCACGGCAUUCU----------------------AAUUCAAGUCAGCUUUGAGUUUUGCAUGUAACUCAUACAUCUG-CAUCUCCUUUACA-----------UUUGGAAAUAUUUCUCUCACACAUUAAUGCAGCAAU-----
AACN010494501.1/506-274    UUUCCAGUUUUAGAUCGAGGUCGGAAACUGACACGAAAACUUAA---AUUCUG-UGAUGGGUCACAUGCAUG---UAAUUCAUGGUGUUCCAGUUCGCGAACACAU-AAAAGGACAAUUUUCUUUUUUUUUUUUGACAAUUUUCUAAUUAACGUCAGCUUGGAGUUUAGGAUACAUCCCAGACAUCUU-AGUUGCCCUUAUG------U-AUUUUUGGAGACAUUUGUCUCAGCCAUUAAUGAAGCAAC-----
AACZ03161076.1/506-294     UUUGCAGCUUUAGAUUGUGGUCAGAGGCUGUUACAAGAUCUUAUA-UAUUCUA-UGAUGGGUCAUAUGCAUC---UAAAGCAUGGUGGUUCAGUUUAUGAAUAUAU-ACAAGGACAAUUUUUU----------------------GAUUAAUGUCAGCUUUGAGUUUAGAAUGUAUCCCAGACAUCUUUAGUUG-CCUUAAU------U-AUUUCUGGAGAUAUUUUUCUCAGCAUUUAUAAAAGCAAU-----
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::...::::::.::::::::::::::::::...:::::::::::::::::::::::::::::::.::::::::::::::::......................:::::::::::::::::::::::::::::::::::::::::::.:::::::::::::......:.:::::::::::::::::::::::::::::::::::::::.....
#=GC RF                    UUUucAGcUUUAGAUuGAGGUCaGagGCUGucACaAAAacUUaa...AUUcUa.UGAUgGGUcaUaUGcAUc...UAAuuCAUGGUGgUcCAGUUUAUGAAcAcaU.AAAAGGACAaUUUUuU......................GaUUAAuGUCAGCUUUGAGUUUAGgaUaUAUCcCAGACAucUU.AGUUgCcCUUAcU......U.AuUUUUGGAGAuaUUUcuCuCAgcCaUUAAUGAAGCAAU.....
//
# STOCKHOLM 1.0

#=GF AC   RF02191
#=GF ID   TCL6_1
#=GF DE   T-cell leukemia/lymphoma 6 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   60.00
#=GF TC   70.10
#=GF NC   43.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10588720
#=GF RT   Genomic analysis of human and mouse TCL1 loci reveals a complex of tightly
#=GF RT   clustered genes.
#=GF RA   Hallas C, Pekarsky Y, Itoyama T, Varnum J, Bichi R, Rothstein JL, Croce CM
#=GF RL   Proc Natl Acad Sci U S A. 1999;96:14418-14423.
#=GF RN   [2]
#=GF RM   10851082
#=GF RT   Identification of the TCL6 genes within the breakpoint cluster region on
#=GF RT   chromosome 14q32 in T-cell leukemia.
#=GF RA   Saitou M, Sugimoto J, Hatakeyama T, Russo G, Isobe M
#=GF RL   Oncogene. 2000;19:2796-2802.
#=GF WK   TCL6
#=GF SQ   9


AB035338.1/1052-1164       AAUGGACCUGUGUAAGGAGGU--AUGUGUGGGAGAAGAUUCCAGAAGGUCUUGAGACACUCCAGAUGAAGGUUGGUGUGGGGCUGUGCUGCUGGAGCACCAGAGAGUGAAAAGAG---
AB035346.2/2269-2381       AAUGGACCUGUGUAAGGAGGU--AUGUGUGGGAGAAGAUUCCAGAAGGUCUUGAGACACUCCAGAUGAAGGUUGGUGUGGGGCUGUGCUGCUGGAGCACCAGAGAGUGAAAAGAG---
AB035337.1/1052-1164       AAUGGACCUGUGUAAGGAGGU--AUGUGUGGGAGAAGAUUCCAGAAGGUCUUGAGACACUCCAGAUGAAGGUUGGUGUGGGGCUGUGCUGCUGGAGCACCAGAGAGUGAAAAGAG---
AAWR02019957.1/47134-47246 GAAGGACCAGAGUGAGGACAU--AUGUGUGGGAGAAGAUUCUAGAAGCUCUUGAGAGAAUCCAGAUGAAAGUCAGCGAGGAGCUGUACUGCUGGAGCUGCAGAGAAAAUGGAAAG---
ABVD01559622.1/53-161      AACUGACCCGAG-AAAGAGGU--AUGUGUGGGAGAAGUUUCCAGAAGCUUUUGAGACAGUCCAGAUGAAAGUGAGGG---GGCUAUACUGUUGAAGCAACAGAGAAAAUAAUAAG---
ACBE01215578.1/790-676     AAUGGACCAGAGAGAGGACAU--ACGUGAGGGAGAAGAUUCUGGAAGCUCUUGAGAAAAUCCAGAUGAAAGUCAGGGAGGGGCUGUGCUGC-UGAGCAGCAGAGAAAAUGGAAAAGAG
ABRP01149292.1/7411-7527   AAUGGAUCCGGGUGAGGAUGUGUAUGUGUAGGAGAAGAUUCCAGAAUCUUUAGAGAUAAUUCAGAUGAAAUCCAGUGAGGACAGGUACUUCUGGAGAAGCAGAGAAAAUGGAAAGAA-
AAFC03028527.1/56805-56907 AACAGAGAAGAGUGAGGACAU--AUGUGUAAGAGAAGAUUCUAGAAGCUCUUGAGGCAAUCCAUAUGAAAGUCAGUGAGGGG----------GGAGCAGCAGAGAAAAUCACUCU---
AAEX03005961.1/89084-89191 AAUGGACCAGAGCAUGGACAC--ACGUGUGGUAGAAGAUUCUGGAAGCUCUUGAGACAGUCCAGAUGAAAGUCAGUGAAUGGCUGUACUGC-UGAGCAGCAGAGAAAAUAG-------
#=GC SS_cons               :::::::::::::::::::::..::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::...
#=GC RF                    AAuGGAcCaGaGugAGGAcgU..AUGUGUGGGAGAAGAUUCcaGAAGcUcUUGAGAcAaUCCAGAUGAAaGUcaGuGaGGGGCuGUgCUGCUGGAGCAgCAGAGAaaauggaaag...
//
# STOCKHOLM 1.0

#=GF AC   RF02192
#=GF ID   TCL6_2
#=GF DE   T-cell leukemia/lymphoma 6 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW; Eberhardt R
#=GF SS   Predicted; RNAalifold;
#=GF GA   45.00
#=GF TC   47.00
#=GF NC   37.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10588720
#=GF RT   Genomic analysis of human and mouse TCL1 loci reveals a complex of tightly
#=GF RT   clustered genes.
#=GF RA   Hallas C, Pekarsky Y, Itoyama T, Varnum J, Bichi R, Rothstein JL, Croce CM
#=GF RL   Proc Natl Acad Sci U S A. 1999;96:14418-14423.
#=GF RN   [2]
#=GF RM   10851082
#=GF RT   Identification of the TCL6 genes within the breakpoint cluster region on
#=GF RT   chromosome 14q32 in T-cell leukemia.
#=GF RA   Saitou M, Sugimoto J, Hatakeyama T, Russo G, Isobe M
#=GF RL   Oncogene. 2000;19:2796-2802.
#=GF WK   TCL6
#=GF SQ   12


AB035346.2/4084-4202       UUAUUUUAUUCUUAUGAGCUUGUGGGCUCCAUCUACC-AACCUCUGGGCAAAUGCUCAUCUGACUUCCAU---AGACACACAGC----AAGCAGACAACCACACAAAGAG---GAAGA-GGGAGAAUAUUU
AB035337.1/1283-1401       UUAUUUUAUUCUUAUGAGCUUGUGGGCUCCAUCUACC-AACCUCUGGGCAAAUGCUCAUCUGACUUCCAU---AGACACACAGC----AAGCAGACAACCACACAAAGAG---GAAGA-GGGAGAAUAUUU
AANU01198095.1/1206-1322   UUAUUUUAUUCUUAUGAGCUUGUGGGCUCCAUCUACCCAGCCUCUGGGCAAAUGCUCAUCUGACUUCCAU---AGAUACACAGC----AAGCAGACAGCUACACAAAGA------AGA-GGGAGAAUAUUU
AAWR02019957.1/52341-52458 UUACUUUAUUCUCCUGAGCUUGUGGGUUCCAUCCCCCCAUCCAGAGGGCAACUGCCCAUCUGACUUCCAUUACAGUCAUGCAAC----AAG--AAAGACAGCAAGAGUAA----AAUG-AGGAACAUAG--
ABRP01149294.1/552-667     UUACUUCAUUGUUGUGAGCUUGUUGGCUCUACCUGCCCAUCUUCUUGGCAAACGCCCAUCUAACUUCUAUUAUGG------AAG--AAAAGA---CAACAGUAAUAA-AA---UAAUGUAGAAGAACAUUU
AAFC03028527.1/62608-62734 UUACUUCAGUCUCACGAGCUUGUGG-CUCCACCUGCCCAUCCUCUAGGUAAAUGCCCAUCUGACUGCCAUUCAGGCCAUUUAACAGGAAAGACAGCAACCAUCAAAAUAA---UAAUCUAGCAGAAUAUUU
AANG01131935.1/507-629     UCGCUUUACUCUCACGAGCUUGUGGGCUCCACCUGCCCAGCGCCCAGGCCAAUGCCCAUCUGACUUCCAUCGUGGCCACGGAAC--GAGAGA---CAACAAUGACACUAA---UAAUACAGAAGAAUGUUC
AAGV020761136.1/910-1039   CCACUUUAUUUAUCUGCGCCUAUGAGUUACAAUCACCCAUCCUCUGCGUAAAUGCCCAUUUGACUUCCAGGAUAGCCACGUAACAAGGAAGCUGACAACAGCAAAAAUAACAGUAAUA-AGAAAAAAACUU
CT867964.5/114485-114606   UUACUUUACUCUCACGUGCUUGCCGGCUCCACCUGCCCAU---UUAGGCAGAUGCCUGUCUGCCUUCCAUUAUGGCCGUAUAAC--AAGAAA-GACAACAGUCAAACUGA---AAAUACGCCAGAAUCUUU
AAIY01140199.1/744-860     AUACUGAAUUUUCCUGUGCUCAUGGGCUCCGUCCACAUAUCCUCUGGU--AAUGGCCAUUUGACUUCCAUUAAAGCCAAGUAAC----AAG----AAACACAAACAG-AA---GAAGGUUGGAGAGGAAGU
AAQR03046300.1/5454-5578   UUACUUUAUUCUCAUGUGCUUGUGGGCGCCAUCCACCCAUCCUCUGGGCAAAUGCCCGUCUGACUUCUGUUGUAGUCACAUAACCA--AAAAAGACAACAACAAUAAAAA---UAAGA-AGGAAAAUAUUU
AAEX03005961.1/94444-94568 UCGCUUUACUCUCAUGAGCUUGUGGACUCCACUUGCCCAUCCUCCAGGCAAAUGCCCAUCUGCCUUCCAUUAUAGCCAUAUAAC--GAGAGAUUGCACCAAUAACACUAA---UAAUACAGAGGAACGUU-
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..::::::::::::::::::::::::...::::::::::::::::::
#=GC RF                    UUACUUuAuUcUcaUGaGCUUGUGGGCUCCAuCugCCCAuCCUCUgGGCAAAUGCCCAUCUGACUUCCAUuauaGcCAcguAAC..gaAAGaugaCAACaguaAaAauAA...uAAuauaGgAGAAuauUU
//
# STOCKHOLM 1.0

#=GF AC   RF02193
#=GF ID   TCL6_3
#=GF DE   T-cell leukemia/lymphoma 6 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder; Eberhardt R
#=GF SS   Predicted; CMfinder;
#=GF GA   40.00
#=GF TC   43.90
#=GF NC   38.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.67 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   10588720
#=GF RT   Genomic analysis of human and mouse TCL1 loci reveals a complex of tightly
#=GF RT   clustered genes.
#=GF RA   Hallas C, Pekarsky Y, Itoyama T, Varnum J, Bichi R, Rothstein JL, Croce CM
#=GF RL   Proc Natl Acad Sci U S A. 1999;96:14418-14423.
#=GF RN   [2]
#=GF RM   10851082
#=GF RT   Identification of the TCL6 genes within the breakpoint cluster region on
#=GF RT   chromosome 14q32 in T-cell leukemia.
#=GF RA   Saitou M, Sugimoto J, Hatakeyama T, Russo G, Isobe M
#=GF RL   Oncogene. 2000;19:2796-2802.
#=GF WK   TCL6
#=GF SQ   26


AB035343.1/1888-2024         GAGAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AB035339.1/2-136             --GAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AB035342.1/1888-2024         GAGAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AB035338.1/1729-1865         GAGAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AB035332.1/3311-3447         GAGAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AB035335.1/1888-2024         GAGAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AB035346.2/12058-12194       GAGAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AB035334.1/2343-2479         GAGAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AB035340.1/2276-2412         AAGAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AB035341.1/2343-2479         GAGAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AB035337.1/1534-1670         GAGAGACAACAGAUUUGCAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCUUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AADA01358963.1/15591-15461   GAGAGACAACAGAUUUACAUCCCAGACA------CACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCGAGUCACGUCCUUUUUUCCCUC--------C-UUCUCCUU---CUUGGAGU--UACAACA--GAAGCUGGGGAGGUGAG-AGUGCAG
AAWR02019957.1/59171-59308   GAGAGACAACAGAUUUACAUCCCAGACACUUUC---CCUGGGCCAGAGCAGCUGCCACUGCAGAAUCUACUCACGUACUUUUUUUCUUC--------C-CUCUCCUU---CUUGGAGUUGAUCAGAAUAGAAGUUGGGGAGGUGAG-GGGGGAG
AAPY01359119.1/3022-3161     GAGAGACGACGGAUUUACAUCCCAGACACAUUCGCUCUGGGCCAAGAGCAGCUGCCCUUGCAGAGUCCAGUCACGUACGUUCCCCCUCC--------C-U-CUCCUG---UUAGGAAUUGUCCAGAACAGAAGCUGGGGAGGUGGG-GGUGGAG
ABRN01352191.1/972-1117      GAGAGACUGUGGAUUUACAUCGCAGACGCUGUCACACUGGGCCAGGAGCAGCUGCCGUUGCAGAAUCUAGACACGUACUUUCCCCCCCUUC---CUCC-UUCUCCUU---CUUGGAGUUGGUUGGAAGAGAAAUCGGGGAGGUGAG-GGGGCAG
AANG01662174.1/1402-1536     CAAAGACAACGGAUUUACAUCCCAGACACAUUCACGCAGGGCCCAGAGCAGCUGCCACUGUGGAAUCGAGUCGUGUAUUUUCCAC------------U-CCGCCCUU---CUUGGGGUUGAUCAGAA--GACAGGUUGGGGCGGCG-AGGGUGG
AAGV020445990.1/452-570      GAGAGACAACAGAUUUAUAUCCCAGACACAUUCACCCUGGCCCCAGAGCCACUGCCACUGCAGGAUUGAGGCACAUACUUCUAUUGGCU--------CCUUCUUCUU---CCUGGAGU----------------UG-------GUC-AGAGCAG
AAFC03028527.1/71522-71660   GAGAGACCGGGGAUUUACCUCCCAGGCACGGUCACGCUGGGCCAGGAGCAGCCGCUAUUACAGAAUCUAGGCACGUACUCUCCCCAUCC--------U-CCUUCUUC---C-UGGAGUCAUUCAGAA--GAGAAGUUGGGGCUCUGAAGGGCAG
CT867964.5/119213-119356     --GAGAUGACGGAUUUACAUCCCAGACAGUGUCACUCGGGUCGAGGAGCAGCUGCUGUUGCAGAAUCUAGGCACGUAUUUCUUUCCCCUCCUUCCUUC-UUCUCCUU---CUUGGAGGCAGUCAGAA--GAGAAGG-UGGGAGGUG-AUGGGGA
ABDC01193447.1/3633-3742     GAGAGACAGCGGAUUUACAUCC--------------------------CAGCUGCCGUUGCAGAAUCUAGUCAUGUACUUUUUUCCCUUU------CC-UUCUCUUU---CUCGGA----GUCAGAA--CAGA-GCUGAGGGGGCG-AAGGAGG
AAFR03013275.1/215008-215127 UAGUGACAAUAGAUUUACAUCCCAGGCACAAUCACACUGCAGCUAC-GUGGCUGCCUUUGCAGAACCGAGUCACACAUUUUUUUCUUUC----------UCCUUUCUAAGUGUGAAAU--UUUGAAA--UAGAAU-------------------
AAIY01060236.1/7545-7673     GAGAGACCAGGGAUUUACUUUCCAG-CACAUCCCCACUGGGCUAAGUAGAGAUGCCUUUCCAGAAUCUCAUUA---------UUUUUUCCCC--CUCC-UCCUCUCC---CUUGGAGUUGUUCAGAU--CAGAAGGCUCCAGCUUA-A------
AANU01198094.1/8666-8529     GAGAGACAACAGAUUUACAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAUUCCAGUCAUGUCCUUUUUUUCCCU-------CC-UUCUCCUU---CUUGGAGU--UACAAUA--GAAGCUGGGGAGGUGAG-AGUGCAG
AAGU03025848.1/13024-13167   GAGAGACAACGGGUUUAUAUCC-AG-CACACUCACACCAGGCCAGGAGCAGAUGCCCUUGCUCAGUCUCCUCAGGUAUUAGGUUUUUUUUUUUUUCCC-CUCUCCUU---CUUGCAGCUGGUCAGAU--CAGAAGG-UCCAGAUUA-AUGGGGA
AAGW02069995.1/9645-9789     GAGAGACGCCAGAUUUAUAUCCCAGACACACGCUCCCCGGGCUAGGAGCGGCUGCCGCUGCAGAGUCGAGUCACGGACUGCCUCUGCCUUG---UCUU-CCUUCCCU--UCUUGGAGCUGGUCAGAG--CAGGAGUCGGGGGCGGG-GGUAAGG
AAQR03046300.1/16845-16972   GAGA-------G----ACAUCCCAGACACAUUCACACUGGGCCAAGAGCAGCUGCCAUUGCAGAAUCCAGCCAUGUCCUUCCGUCACAC--------C-UUCUCUUU---CUUGGAGUUAGUCAGAA--CAGAAGCUGGGGAUGUG-GGGGAAG
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::........:.::::::::...:::::::::::::::::..:::::::::::::::::.:::::::
#=GC RF                      GAGAGACaacgGAUUUACAUCCCAGACACauUCaCaCuGGGCCaaGAGCaGCUGCCaUUGCAGAaUCgAGuCAcGUacUuuuuuccuuc........C.UuCUCCUU...CUUGGAGUuGuuCAGaa..gAggauggGGgGGuGuG.aGgGcaG
//
# STOCKHOLM 1.0

#=GF AC   RF02194
#=GF ID   HPnc0260
#=GF DE   Bacterial antisense RNA HPnc0260
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Predicted; CMFinder
#=GF GA   59.00
#=GF TC   59.00
#=GF NC   58.80
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF RN   [1]
#=GF RM   20164839
#=GF RT   The primary transcriptome of the major human pathogen Helicobacter pylori.
#=GF RA   Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A,
#=GF RA   Chabas S, Reiche K, Hackermuller J, Reinhardt R, Stadler PF, Vogel J
#=GF RL   Nature. 2010;464:250-255.
#=GF WK   Antisense_RNA
#=GF SQ   31


CP000891.1/2753645-2753511   -AGGACAUAACUAUGU----GUUUUAAA----GA--CGGUUUG-A-------UUUA-----AU---------UUUUUAUUGAUAAUU------GGAUU---AGU-AACU---AGGCGAA------------U----AGAUGAAAUGCAGAAAAA--GAAAUGGUACACCCGAGUGGACUCGAACCACCGACCCCUACCA
AE000511.1/78090-78244       -AGUGUUAUAUCUUUGAAGCGCUAUAAA----AUCGUUAUUAG-AAGUG-CGUUUA-----AU------ACCCCUUUAG-A--AUUU-AUAAA-GAUC---AAA-AACU---CGCAAAA---------AAAUGAGAAUUAAAAUUGGAGUGAU-----AAUGGUGGCCACGACUGGACUUGAACCAGCGGCCACUACCA
CP001072.2/65890-66057       -AGUGUUAUAGUUUUGGAGUGCCAUAAA----AGCGUUACUUGUAAGCG-CGUUUA-----AU------ACCUUUUGGA-AUCAUUUGACAAA-GAUC---AAA-AACC---CACAAAAAACAAGAAUUAAUGAGAACUAGGAUUGGAGUAAU-----AAUGGUGGCCACGACUGGACUUGAACCAGCGGCCACUACCA
AM260522.1/1332501-1332352   ---------AGUGUUA---UCUUUUAAG----GGCGUUAUUUU--AGCG-UGUUUA-----AC------GAUUUUUGAAUAUCAUUUUAGAGGCAAUC---AAA-AAUU---UGCAAAA------------UGAGAAUUAAAAUUGGAGUAAUGUAAUAAUGGUGGCCACGACUGGACUUGAACCAGCGACCACUACCA
AE001439.1/75594-75713       -AGUAUUAUAGUUUUAAAGUGCUAUCAA----AGCGUUAUUAG-GAGCG-CGUUUA-----AU------ACCCUUUAAA-AUCAUUUGAUAAA-AAUC---AAA-A-CC---UAUAAAA----------A-UGAGAACUAGAAUUGGAGUUAU-----AAUGAG-----------------------------------
AE017125.1/1703851-1703967   --------------------AAUUUUUA----ACCUUG--CUG---AUG-UGCUCA-----UU------GA--UAUAAGUGUGGUGU------UGAUG---A-----UU---UAUCAAA------------U----GUUACAAGAAAAAAGA------AAUGGUGGCCACGACUGGACUUGAACCAGCGACCACUACCA
ACFU01000005.1/103590-103447 GAUGAAUAAACUUUGACGCGAAUUUUGC----AUUUUGGUUUG---CAA-UGCGAA-----UU----------UUUGAAUGAAAUUU------UGAUG---AGA-G-UU---UGAAAAA------------UCCGGACUUUAAAAGAAGCGA------AAUGGUGGCCCCGAAUGGACUCGAACCAUCGACCACUACCA
AY078177.1/214-61            -AGUGUUAUAGUUUUGAAGCGCUAUAAA----AGCGUUAUUAG-AAGCG-CGUUUA-----AC------ACCCUUUAGA----AUUU-AUAAA-GAUC---AAA-AACC---CACAAAA---------AAAUGAGAAUUAAAAUUGGAGUGAU-----AAUGGUGGCCACGACUGGACUUGAACCAGCGGCCACUACCA
CP001217.1/77766-77921       -AGUGUUAUAGUUUUGAAGUGCUAUAAA----AGCGUUAUUGA-AAGCG-CGUUUA-----AU------ACCCCUUUAG-A--AUUU-AUAAA-GAUC---AAA-AACU---CGCAAAAA--------AAAUGAGAAUUAAAAUUGGAGUGAU-----AAUGGUGGCCACGACUGGACUUGAACCAGCGGCCACUACCA
ABSX01000024.1/3863-3696     -AGUGUUAUAGCUUUGAAGCGCUAUAAA----AGCGUUAUUUGUAAGCG-CGUUUA-----AU------ACCCUUUAGA-AUCAUUUGACAAA-GAUC---AAA-AGCC---CACAAAAAACAAGAACUAAUGAGAAUUAGGAUUGGAGUAAU-----AAUGGUGGCCACGACUGGACUUGAACCAGCGACCACUACCA
CP001252.1/2528306-2528440   -AUGACAUAACUAUGU----GUUUUAAA----GA--CGGUUUG-A-------UUUA-----AU---------UUUUUAUUGAUAAUU------GGAUU---AGU-AACU---AGGCGAA------------U----AGAUGAAAUGCAGAAUAA--GAAAUGGUACACCCGAGUGGACUCGAACCACCGACCCCUACCA
CP000563.1/2488897-2489031   -AGGACAUGAUGAUGU----GUUUUAAA----GA--CGGUUUG-A-------UUUA-----AU---------UUUUUAUUGAUAAUU------GGAUU---ACU-AACU---AGGCGAA------------C----AGAUGAAAUGCAGAACAA--GAAAUGGUACACCCGAGUGGACUCGAACCACCGACCCCUACCA
CP000792.1/20883-20761       -AAAAUUUAAAAAUGGCAGAGUUACAAA----AAAUAUUUUUA-AAUUU-UAUUUA-----UU------------------UGAUUU----------U---AGG-U-UU---UGGGAAA------------UUUGAAAUAG----------A------AAUGGUGGCCCCGAAUGGACUCGAACCAUCGACCACUACCA
BX571659.1/81767-81634       -ACGAUUUCAUUUU------ACCUUGGU----GUCUAUUUUCG----GG-UGUCUA-----UU----------UCAAAAAAUUGGUUUAGAUU-UUUU---AAC-U-----------------------GUUGUUGCAAAGAACCUGAAGAA------AAUGGUGGCCACGAGAGGACUCGAACCUCCGACCACUACCA
AP009179.1/2506666-2506547   -UGUAUUAGAUGAUAAAUAUGCUUUAAA----UCCCGUAUUUA--AGGG-GCUUUG-----UU------AGGUUUUGUU--------------AGAUU----------G---GGUUAAA-----------UU-----------GUGG-----------AGUGGUGAUCACGAUUGGACUUGAACCAACGACCACUACCA
CP000447.1/2405050-2404925   -AUUUUUUAAUUAUUUAGAAGAUAUGAA----AA-----UUUG-A-------UUUA-----AU----------UCGAAG---GAUUU-AUUUU-GAGC---AGG-UAAG---UGA----------------U----UUUGUAAUUUUU--GA------AAUGGUACACCCGAGUGGACUCGAACCACCGACCCCUACCA
ABSN01012789.1/430-585       -CGUAUAAAAUGUUUACAGGCGCUGUUACGCUAGAGACUAAUG-AGUUUCCGAGAU-----UU------AAAUUUUUAG-GAAAUAU------AUUUG---AAA--AAU---CACCAAA---------AAUUGUAUGAUUCAACUUAUUGGAG-----AAUGGUGGGCCCGGCAGGACUUGAACCUGCGACCACU-CCG
CP000753.1/2651712-2651575   -AAUUUCAAAGAUGAA----GAGGGACA----ACUUGCUCAAG-AACAG-AGAAUC-----AU------UGGUUUUGAG-UAAAU-----AUA-UAGG-------AAUU---AGCACAA----------A-U-GGAGAUAAAACA--AG--A------AAUGGUACACCCGAGUGGACUCGAACCACCGACCCCUACCA
ACDP01000001.1/83710-83568   -AGCACGAAAUCUCCC---CACUACG-------CUCUUUUUCG-AAAUA-UGAACG-----AU------------CCAA-AAGAUUU-AGAAU-AAGG---AAA----C---AGAAAAAC-------AGAAAGGUGGGGUGAACCCAAAAGA------AAUGGUAGGCACGAUUGGACUCGAACCAACGACCCCUACCA
ABVP01000026.1/453670-453538 -UUUUUAAACGUUUUGUUGCGCAAUAAA----AU-AUUGCAAG-CAAA----AUUA-----AU------UAUUUUGUAG-GGUAGGU----AA-GAUG---AGU-----------AAAA-----------AUUAGGAA-------AAAGAGA------AAUGGUGCGUCCAAGUGGACUCGAACCACCGACCCCCACCA
CP000776.1/1402335-1402223   -UGAAUUAAAAUUUUC-------UUAAA----AUCUCGAUUUA-UAGGG-GGUUU------------------UUUGAA-GUGAUUU--------------GAA-C-GU---UUAAGAA------------U---------------AGUG-------UAUGGUGGCCCCGAAUGGACUUGAACCAUCGACUUCCACCA
CU928164.2/1460531-1460694   -UGUAACAAAGUUGCCAUAGCGAUUCUC----CUUCUGAUAAC-GCAUA-CGAAGA-----AAGU-GUAAAUCUUUUAA-CGUAUUGGAUACA-GAGA---AGA-AACA--GAGGGAAA---------AAAGGAGAAGACCAGAUUAAGAAAA-----UCUGGUGCGUCCGAGUGGACUCGAACCACCGACCCCCACCA
CP000034.1/1727776-1727614   -UGUAACAAAGUUGCUAUAGCGAUUCUC----CUUCUGAUAAC-GCAUA-CGAAGACAGUGUA------AAUCUUUUAA-CGUAUUGGAUACA-GAGA---AGA-AGCA---GAGGGAA---------AAAGGAGAAGACCAGAUUAAGAAAA-----UCUGGUGCGUCCGAGUGGACUCGAACCACCGACCCCCACCA
CP001393.1/1621903-1622035   -AUUAUUCAACAAUGAAA--AUUUGCAA----AAAAAAAUAAC--CCUU-CUUUUC-----UU------GACUUUUUAA----AUCU--------AUC---AUA-AACA---AUUAAAA------------U------------UGUCAAUAAC--CAAAUGGAGCCCACGACCGGGCUCGAACCGGCGACCUCCGCCU
CP000647.1/2199606-2199451   -UGUGGACUAGUAUGG----ACUAUGCA----AGGAAAACGCU-UUGCC-AAUACA-----CA------ACAUUUUAAU-GUCAGCA-AUACC-AACGGGGAGC-AG-G---UGAUAAA---------AUUCAGGAAUUACAGAAGGAAAAAU----GAUUGGUGCGUCUGAAUGGACUCGAACCAUCGACCCCCACCA
FM180568.1/1818140-1817974   -UGUAACAAAGUUGCCAUAGCGAUUCUC----CUUCUGAUAAC-GCAUA-AGGAGACAGUGUA------AAUCUUUUAA-CGCAUUGGAUACA-GGGA---AGA-AACAG-AGGAAAA-AA------GAAGAGAGAAGACCAGAUUAAGAAAA-----UCUGGUGCGUCCGAGUGGACUCGAACCACCGACCCCCACCA
CU928158.2/1416627-1416790   -UGUAAUAAAGUUGCCAUCGCUUAUCUC----CUUCGUUAAAG--AACA-UGAAGG-----GUAGUGUAAGACUAUUAA-UGCUUUGAAUAUA-GAGG---AGA-AAAA---AGG--AA----------UUUUAGAAGUGGCACCAGAUUGAAUA-AAUCUGGUGCGUCCGAGUGGACUCGAACCACCGACCCCCACCA
ABJO01000003.1/6127-6281     -AGCAUUAUAGUUUUGAAGCGCUAUAAA----AUCGUUAUUGG-GAGCG-CGUUUA-----AU------ACCCCUUUAG---AAUUU-AUAAA-GAUC---AAA-AAUU---CGCAAAA---------AAAUGAGAAUUAAAAUUGGAGUGAU-----AAUGGUGGCCACGACUGGACUUGAACCAGCGGCCACUACCA
ABKX01000007.1/155924-155761 -UGUAAUAAAGUUGCCAUUGCUAUUUUC----CUUCUGAUAAC-ACAUA-CAGAAACA-GU--G---UAAAUCUUUUAA-CGCGUUGAAUACA-GAAG---AUA-AAUAG-AGGAAAA----------AGAAGAGGAGACCAGACUAAGAUAA-----UCUGGUGCGUCCGAGUGGACUCGAACCACCGACCCCCACCA
CU928162.2/1824208-1824046   -UGUAACAAAGUUGCCACAGCGAUUCUC----CUUCUGAUAAC-GCACA-CGAAGACA-GU--G---UAGAUCUUUUAA-CGUAUUGGAUACA-GAGA---AGA-AACAGAGGGACAA------------AGAAGAAGACCAGAUUAAGAAAA-----UCUGGUGCGUCCGAGUGGACUCGAACCACCGACCCCCACCA
ABQU01000070.1/17962-18080   -GGAAUUAUAUAUAUAUCUUAGCUUAAA----AU-----UAUU---------UUUG-----AU------AAAUUGAUAG---AAU-----UU-UGGAG-----AUAAUU---UGGAGAA------------U---------------CAAAA------AAUGGUGGCCACGACUGGACUUGAACCAGCGACCACUACCA
#=GC SS_cons                 .:::::::::::::::::::::::<<<-....--<<<<_____._>>>>.--->>>.....,,......,,,,,,,,,,.,,,,<<<._____.____...>>>.----...-------..........------------------------.....--<<<<<<---<<-<<<<_______>>>>>>->>>>>>:::
#=GC RF                      .aGUAuuAaAgUUUuaAagggcuuuaaA....aucguuaUuug.aaacg.cGuuua.....aU......AauUUUUuAa.auuAuuu.AUAaA.GAug...aaa.AAcu...uGaaAAA..........AaUGaGAAuuagAAaUgaAGaaAa.....AAUgGuGGgCcCGAgUGGACUCGAACCAcCGACCaCuACCA
//
# STOCKHOLM 1.0

#=GF AC   RF02195
#=GF ID   TP53TG1_1
#=GF DE   TP53 target 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   40.00
#=GF TC   44.90
#=GF NC   35.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9713990
#=GF RT   Isolation of a novel TP53 target gene from a colon cancer cell line
#=GF RT   carrying a highly regulated wild-type TP53 expression system.
#=GF RA   Takei Y, Ishikawa S, Tokino T, Muto T, Nakamura Y
#=GF RL   Genes Chromosomes Cancer. 1998;23:1-9.
#=GF WK   TP53TG1
#=GF SQ   16


BC061927.1/364-213           GAGCCCAAGUAGGAAUCUGUGUGAUCA-CUGUUCUUUUGCCAAGACACGGGGUGGACA--AUAAGAUUCCUUUACA-AAGCACUGGUGUAAGUGUUC-GCCUGGUG-CUGCAAAAAGCG-GCUCA-CUGGGAAUGG--GGAGGAGCGUGUG----GUAAGCCAGAC
BC068535.1/445-294           GAGCCCAAGUAGGAAUCUGUGUGAUCA-CUGUUCUUUUGCCAAGACACGGGGUGGACA--AUAAGAUUCCUUUACA-AAGCACUGGUGUAAGUGUUC-GCCUGGUG-CUGCAAAAAGCG-GCUCA-CUGGGAAUGG--GGAGGAGCGUGUG----GUAAGCCAGAC
AANU01287884.1/12564-12413   GAGCCUAAGUAGGAAUCCGUGUGAUCA-CUGUUCUUUUGCCAAGACACGGGGUGGACA--AUAAGAUUCCUUUACA-AAGCACUUGUGUAAGUGUUU-GUCUGGUG-CUGCAAAAAGCA-GCUCA-CUGGGAAUAG--GGAGGAGCGUGUG----GUAAGCCAGAG
ACBE01070274.1/370-519       GAGAUUAAGCAGAUAUCUGUGUGGUCA-CUACUCUCUUGCCAAGACACAGGGUG---A--ACAAGAUUCCUUUAAA-AAGCAAUGGUAUAAAUUAUU-GCUUGAGGGUUGCAAAAAGAG-UCGCA-CUGGUAAGGG--GAAGGAGCGGCUG----GCAAGACAGAA
ABRN01432346.1/2305-2458     GAGGUCAAGUAGGGAUUUAUGUGGUUA-CUGUUCUCUUCCUAGGACACGGAGUGAAAA--AUAGGAUUCCUUUUUA-AGGCGCUGGUAUAAAUUCUUA-CUUGGGGGUUACAAAAAGCGUCA-CA-CGGGGAACGG-GGUAAGAGCGGCUG----GUAAGCCAUAG
AAGV020392316.1/642-793      GGGACCAAGUAGAGAUCUGUGUGGUCA-CUGUUCUCUUGUCAGGAUGCGG-GUGGACA--AUAAAGUUCCUCUAUA-AAGCUUUGGCAAAGGUUUUG-ACUUGGCGGCUGCAAAAAGCG-CGGCC-CUGGGAACGC--GGAGGAAAGACUGGUAAGCGAGCG----
ABDC01159779.1/1246-1384     GAGGCCAAGUAGGGAUCUGUGUGGUCA-CUGUUCUCUCGCCAGGACA-AGA---------------UUCCUUUGUA-AAGCACUGGUGUAAGUUCUU-GCUUGGGGGCUGCAAACAGCG-UCACA-CCGGGGAGAG--GAAGGAGCUGGUG----GCACGCCGGAG
ABRP01045128.1/909-1054      GAGGUCAAGUCGGUGUCAGUGUGAUCA---GUUUUAUUGCCAGGACAUAGGGUG---A--ACAAGAUUUCUUUAAA-AGCCAUUGGAAUAACUCCUU-GAUUCCGGGCUGCGAAAAAGA-UCGCA-CUGGGAGGG----GAGGAGCGGCUG----GUAAACCAGAA
AAQQ01557720.1/144-300       GAGGUCGAGGAGGGAUCCGUGUGGUCA-CCGUGCUCUUGCCAGAACACAGGGCGGACA--ACGAAAUUCCUUUCUA-AAACUCUGGGCUGAGUUCUUUGCUUGGGUGAUGCAAAAAGCA-UCGCC-CUGGGAAAAG---GGAGGAGAGCAACGGGGCGCGCAAGAA
AACN010011568.1/3324-3174    GGGAUUAAAUAGACAUCUCUGAGGCCA-CCGCUCUCUUGCCAAGACACUGGGCG---A--ACUAAAUUCCUUUCAG-AGGCAUUGGUAUAAAAUCUU-GCUUGGGGGCUGCAAAAAGAACUCUCA-CAGGUAAGGG--GGAGGAGUGGCUA----AUAAGCCGGAG
AAWR02013730.1/178097-178229 CAGGUCAACUAGGAAUCUGUGUGGUCAACUGUUCUCUUGCCAGGACACAGG-----------------------AA-ACGCGUUGGUAUAAAUUCUU-GUUUGGAGGCUGCAAAAAGCG-UCGCA-CAGAGAAGGG--GGAGGAGUGGCUG----AUAAGUCAGAG
AAPY01071599.1/1314-1465     AGCCUCAAGCAGGGAUCUGCGUGCUCA-CUGUUCUCUUGCCAAGACACGGAGUGGACA--GUAACUCGCCUUUACACGGGCGUUGGUAUCAGUUCUU-GCUUCGAAGCUGCGAAUAGCG-UCGCA-CUGGAAAGAC--CGGCGGAGAUCUG------GCGCGAGAA
AAFC03103647.1/4947-4791     GAGACCAAGUGGGGAUUUAUGUGGUUA-CUGUUCUCUUGGUAGGACACGGAGGGAACG--ACAGUAUUCCUCCUUA-AGGCACUGGUAUAAAUUCUUA-CUUGGGAGUUACAAAAAUGACAAGGAAUUCUUCACUUUGGGAAGAGCGGCUG----CUAAGUAGGAG
AAQR03012492.1/8358-8509     AAAGGCAAGCAGGGAUCUGUACGGUCA-CUGUUCUCUUGCCAGGACA-AGGGUGUACA--AUAAGUUUCCUUUAUA-AAGCACUCGUGUAAGUUCUU-GCCUGGAGGCUGCAAAAAAAG-UAACC-UCAGGAAGGG--CAAGGAGCGAGUG----AUAAGCCAGAU
BT009845.1/270-146           CUGUUC---------------UUUU-------------GCCAAGACACGGGGUGGACA--AUAAGAUUCCUUUACA-AAGCACUGGUGUAAGUGUUC-GCCUGGUG-CUGCAAAAAGCG-GCUCA-CUGGGAAUGG--GGAGGAGCGUGUG----GUAAGCCAGAC
U26034.1/587-738             GAGGCCAAACCGGAUCCAUUCUGCUG--CUAUUCUCUUGCCAGCACACAGGGUAGACAAAAUAAAAUGUCUCAGUA-CAACUCCAGUAAAAAUUCUU-GCUUGGGCCAUGCAAAGGAGGCUCGCA-CUCGCAAGGG-----GGAGCGACUG----GGAAGAAAGAA
#=GC SS_cons                 :::::::::::::::::::::::::::.::::::::::::::::::::::::::::::..::::::::::::::::.::::::::::::::::::::.:::::::::::::::::::::.:::::.::::::::::..:::::::::::::....:::::::::::
#=GC RF                      GaGguCAAGuaGGgaUCugUGUGgUcA.CUGUUCUCUUGCCAGGACACgGGGuGgACA..AuaAgaUUCCUuUauA.aaGCacUGGuaUaAgUucUU.GCUUGGggGcUGCAAAaAgcG.ucgCa.CuGGgAAggg..GGAgGAGcGgcUG....guaaGccaGAg
//
# STOCKHOLM 1.0

#=GF AC   RF02196
#=GF ID   TP53TG1_2
#=GF DE   TP53 target 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   75.00
#=GF TC   78.90
#=GF NC   67.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 48.22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9713990
#=GF RT   Isolation of a novel TP53 target gene from a colon cancer cell line
#=GF RT   carrying a highly regulated wild-type TP53 expression system.
#=GF RA   Takei Y, Ishikawa S, Tokino T, Muto T, Nakamura Y
#=GF RL   Genes Chromosomes Cancer. 1998;23:1-9.
#=GF WK   TP53TG1
#=GF SQ   12


BC068535.1/222-41            CUUCGUGGGCGGAGCGCGGCCUG----------CCCAGAGUGCCUUCUAGAUCCUGG-GUC-AGGCGCCAAGCUCCCC-AGCAUCAUGCAGGAAGCUGCAGCC-CCGCAGAGUUAGGACAGCUCAUUU--GGCACCCGGCGAGCCCUUCCCAGG-CCCGCAGC-CCAGAAUAGAGCC-----GGGGCCCAAGACGCCCACUGGAG
AANU01287884.1/12341-12162   CUUCGUGGGCGGAGCGCGGCCUG----------CCCAGAGUGCCUUCUAUAUCCUGG-GUC-AGGCGCCAAGUUCCCC-AGCAUCAUGCAGGAAGCUGCAGCC-CCGCAG--UUAGGACCGCUCAUUU--GGCACUCGAGGAGCCUUUCCCAGG-CCAGCAGU-CCAAAAUAGAGCC-----GGGACCCAAGACGCCCACUAGAG
ABDC01159779.1/1489-1661     CUUCGUGGGCG-----CGGCCU---------------------CCUCCGUGUCCCGG-GUCUGGGCGCCUAGCUCCCCCAGCACCAGGCUGGAAGCUGCGGCC-CCACAGAGUUCGGACCGCUCAUCC--CGUACAGAGAAAGCCUUUUCCAGG-CCCACAGC-CCAGAAUCGAGCACCCCAGCGGCCAAGAACGUCCACGAGAG
AAWR02013730.1/178335-178519 CUGCGUGGGCGGAGCACCGCCGA----------CCCAGAAGCCCCGCCGUAUCUCGG-GCCAGGGCGCUGUGCUCCACCUGCGGCAAACAGUUAACUGCUGCC-CGACAGUGUUCACACAGUCCAUGU--GCCAUCCCGCGAGCCCGUCCCAGG-CCCACAGC-CUAGAAUCCAACCC----CGCGCAGAGGACACCCACGGGAA
AAPY01071599.1/1554-1735     CUGUGUGAGCCGAGCAUGGCCCG---------G-CUGCGGCCCCUGCCAAGUAACAG-AUUUGAACGCCGAGUUCGUCCAUCAGCGCCCAGGAAGCUGGAGCC-CUGCAGAGUCCAGGGCCCUGGCC---GGUGCCUGGCAAGCCUUUCCUAUG-CCCACAGC-CCAGAAUCGAGCCC------GGGCCAAGGCCCCGGCGGGAG
ABRN01432346.1/2528-2704     CUGCGUGAGCGGAGCACGGCC-----------CUUAGAGCCCUCCG---UGUCCCUG-GCA-AUGCGCUGAGCUCCACCGGCAGCAAGUAGUUGACUGCUCCC-GGGCUGUAUUUGGACUGUUUCUCUUGUCCGCCCAGCCGAGCCUUGCCAGCGCCCGCAGC-CUAGAACCCUGCCC----GCAACAGACGAC--UAGAG----
AAQQ01557720.1/394-571       UUCCGUGGGCGGAGGA--GUC-----------CCCAGAUAGCUCAG----GUCGGGGCGUCGGGGCAUUGAGCUCCCACAGCGUCAGGCAGGUCACCGAGGCU-GCGCGGACUUGGGGAGCUAGCUU---GGUGCGAGGCAAGUCUUUCCCAGG-CCCGCAGC-CCAGAAUCCUACCC----CAGGCCUAGAACGCUCGAGGCAG
AANG01739183.1/735-920       CUGCGUAGGCGGAGGGCUGCCUG---------CCCGGAGUCUCCCGCUGUAUCCCUG-GCCCGGGCGCUGGGCUCCACCUGCUGAAAGCAGUCAACCGCUGUC-CAGCAGGGCUGGGGCCGUUUCUC--GGACGUCGGGGAAGCCUCUCCCAGC-CCUGCAGC-CUGGAACCCAGCCU----CCGGCAGAGGACGCCCGAGUGAG
AANN01405433.1/8021-7841     UUGCUUGGACGCAGCGCAGC-GG----------CGCGGAACCCCAG-UGUAUCCCGA-GACACAGCGCUGUGCUCUCACAGCAG----CAGUUACCUUCUGCUUUCGUAGGUUUUGAAUCGUUCCACA--GGUGUCCA-CAAGCCUUCCCAAGG-CCCGCAGCCCCAAAAUCGAGCCU---CAAGAUCCAAGACACAGGCGGGAG
AAQR03012492.1/8608-8801     CUUCGUGGGCGGAGCGCGGCCCCACCCCCACCCCCCGAAGCCUUCUCCAUGGCCCAG-GUCUGGGUGCCGAGCUCCCACAGCAUCAAGCAGGAAGCUGCGGCU-CCGUAGAGUUCGGACCGCUCUCUGCGGGUACUGAGUAAGCCUUUCCC-GG-CCCACAG--CCAGAACCGACCC-----CUAGCCGAGGACGUCCGCGAGAG
BC103631.1/152-4             -----UGGGCGGAGCGCGGCCUG----------CCCAGAGUGCCUUCUAGAUCCUGG-GUC-AGGCGCCAAGCUCCCC-AGCAUCAUGCAGGAAGCUGCAGCC-CCGCAGAGUUAGGACAGCUCAUUU--GGCACCCGGCGAGCCCUUCCCAGG-CCCGCAGC-CCAGAAUC---------------------------------
BC061927.1/131-1             ----------GGAGCGCGGCCUG---------C-CCAGAGUGCUUUCUAGAUCCUGG-GUC-AGGCGCCAAGCUCCCC-AGCAUCAUGCAGGAAGCUGCAGCC-CCGCAGAGUUAGGACAGCUCAUUU--GGCACCCGGCGAGCCCUUCCCAGG-CCC-----------------------------------------------
#=GC SS_cons                 :::::::::::::::::::::::.........:::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::..::::::::::::::::::::::::.::::::::.::::::::::::::....:::::::::::::::::::::::
#=GC RF                      CUgCGUGGGCGGAGCgCgGCCug.........cCccGgagcccCcgCugugUCccgG.GuCuggGCGCcGaGCUCcccCaGCagCAaGCAGgaagCUGcuGCc.ccGCaGagUUcGGaccGcUcauuu..GGugCccgGcaAGCCuUUCCCAGG.CCCgCAGC.CcAGAAuCgagCCc....gcgGccgAgGACgcccGcGgGAG
//
# STOCKHOLM 1.0

#=GF AC   RF02197
#=GF ID   TP73-AS1
#=GF DE   TP73 antisense RNA 1 conserved region
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   75.00
#=GF TC   82.50
#=GF NC   56.20
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.98 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   20477830
#=GF RT   KIAA0495/PDAM is frequently downregulated in oligodendroglial tumors and
#=GF RT   its knockdown by siRNA induces cisplatin resistance in glioma cells.
#=GF RA   Pang JC, Li KK, Lau KM, Ng YL, Wong J, Chung NY, Li HM, Chui YL, Lui VW,
#=GF RA   Chen ZP, Chan DT, Poon WS, Wang Y, Mao Y, Zhou L, Ng HK
#=GF RL   Brain Pathol. 2010;20:1021-1032.
#=GF WK   TP73-AS1
#=GF SQ   4


AL136528.11/32288-32128    -AAGGAGGGCUGGGCGGUGGUGGGCCCACCCCCUCAUAGCCG--CAGGACUCUGGAUCAUGAAGGUGUUGAGGCCUCAAACUAGACAGGAAGUGGAGGGAUUCUGGAUGUUCCCUCGGCAAGAGGGUGCCACAUAGAACGUAGAAACGGGGACUCUAAAACGCC
AC196671.6/131470-131630   -AAGGAGGGCUGGGCGGCGGUGGGCCCAGCCCCUCACAGCCA--CAGAACUCUGGAUCACCAAAGUGCUGAGGCCUCAAACUAGACAGGAAGUGGAGGGAUUGGGGAUGUUCCCUCGGCAAGAGGGUGCCAUGUAGAACGUAGAAACGGGGACUCUAAAACGCC
ABDC01497515.1/37-198      CGUGAGGGUUGAGUAGGCUGCGCCUCCCCCCACACACACCAAGACAGAACUCUGGGUCACAAAAGGGCCAGCACCUCAGAACCGACGGGAAGC--GAGGAUUUGGGACAUUUCAUCAGAAAGACAGUGCCACACAGAACAUAGACACUGGGACUUAAAAAAAAU
AACZ03010219.1/22341-22186 -----UAGGAGGGAAGAUGAUCGUCCCACCCUCUCAUAGCCA--CAGGACUCCGGAUCAUGAAGGUAU-GAGGCCUCAAAUUAGACAGGAAGUCGAGGGAUAGGGGAUGUUCCCUCGGCAAGAGGGUGCCACAUGGAAGGCCUAAACGGGGAGUGUGAAAGGCC
#=GC SS_cons               .:::::::::::::::::::::::::::::::::::::::::..::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    .gaGggGGguggGgaGGcgGugggcCCacCCcCuCAcAgCca..CAGgACUCuGGaUCAcgAAgGuGcugaggCCUCAaAcuaGACaGGAAGugGagGGAUuggGGAugUUcCcUCgGcAAGAggGUGCCAcauaGAAcguagAaACgGGGAcUuuaAAAcgcc
//
# STOCKHOLM 1.0

#=GF AC   RF02198
#=GF ID   TTC28-AS1_1
#=GF DE   TTC28 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   70.00
#=GF TC   73.70
#=GF NC   67.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 54.33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   11258795
#=GF RT   Identification of novel transcribed sequences on human chromosome 22 by
#=GF RT   expressed sequence tag mapping.
#=GF RA   Hirosawa M, Nagase T, Murahashi Y, Kikuno R, Ohara O
#=GF RL   DNA Res. 2001;8:1-9.
#=GF WK   Long_non-coding_RNA
#=GF SQ   14


AL031591.19/148093-148254  -CCCCGGGCACACGAGGCCUCCACUGCGGUUGCGCAGCCUGC-CGAAGAGCGUG--CGGCUUCUACUGCGGCUGCGCAAGCUCGACGCGCGCAC--UCUUGUCUGCUUACGAGGGCUCCUCCCUUC-AGCUUUGGUCCCUCGGGGCGUCUG-GGCAGCCUACGCUUUCCG--
AANU01252520.1/34666-34827 -CCCCGGGCACACGAGGCCUCCACUGCGGUUGCGCAGCCCGC-CGAAGAGCUUG--CGGCUUUUACUGCGGCUGCGCAAACUCGACGCGCGCAC--UCCUGUCCGCUGACGAGGGCUCCUCCCUUC-AGCUUCAGUCCCUCGGGGCGUUUG-GGCAGCCUACGCUUUCCG--
ABDC01114144.1/1935-2098   -CCCCAGGCACACGAGGCCUCUACUGCGGCUGCGCGGCCCGC-UGGAGCACGUG--CGGCUUCUACUGCGGCUGCGCGACCUCGGCGCGCGCGCAUGCUCGUCGGCGUCCUAGGGCUCCUCCCUCC-AGCCUAAGUCCCUCGGGGCGACUG-UGCUGCCUACGCUUUCCG--
AAPY01200935.1/1139-1303   -CCCCGGGCGCACGAGGCCUCAAAUGCGGCUGCGCAGAACGC-UGAAGCGCGCGCGCGGCUACUACUGCGGCUGCGCGAACAGGACACGCGCAC--AGGCGUGUGUUUGCUAGGGUUCCUCCCUCU-GGCCGAGGUCUCUCGGGGCAUCUGGUACAGCCUACGCUUUCCG--
ABRT010029259.1/3985-4146  ACCCCGGG-GCACGAGGCCUCCACUGCGGCUGCGCCGCCUGC-CGGCGCGCGUC--CGACUUCUACUGCGGCUGCGCACGGUCGGCGCGCACAC--GCUCUUCUGCUUUCUGGGGCUCCUCCCUCC-AGCCGAGGUCCCUCGGGGCGUCUG-UGCAGUCUGGGCUUUCCG--
ACBE01381697.1/4448-4287   -CCCUAGGCUCACGGAGCCUCCACUGCGGCUGCGCGACUAGU-UGGAAAGCGUG--CACCUUCUACUGCGGUUGCGCAAACUGGGCUCGCGCUC--GCACGUCCCUUAGGUGCCACUCCUCCCUAC-AGUCUAGUUUCCUCGGGUCCUGUG-UGCAGCCUACGGUUUCUG--
ABRO01291941.1/385-544     -UCCUCGGCACACGAGGUCUCCAGUGCGGCUGCGCGGUCGGC-GGAAGCCCGUG--AGGCUUGUACUGCGGCUGCGCAGACUCCG-GCGCGCAC--GCUCUGUGGCUUCCGGCGGCUCCUCCCUUC-AGCCUGGGCCCCUCGGGGCGC-CG-UGCAGCCUACGCUUUCCG--
ABVD01161616.1/5586-5747   -GCCUAGGAGCACGAGGACUCCAUUGCAGCUGCGCUGUCUGG-CUGGCCGAGGG--CUGCUUCUACUGCGGCUGCGCAACCUCGGCGCUCGUUC--GUUUCACUUCUGCCAAAGGCUACUCCCUCA-CGCCGAGUUCCCUCGGGGCGUCUU-UGUAGCGUACGGUUUCUC--
AAQQ01192276.1/1953-2112   -CAAGGGGCGCACGAGGCCUCCCCGGCAUCUACGCAGAGCGC-UGGAGAGCCAG--UGCCUUCUAUUGCGCCUGCGCGAGAGGAGGGCGCAAGC----CUGCCUGCUUUCAGUGACUUCCUCCCACCAGCGCCGG-CGCUCUAGGCACGUG-UGCAGCCUACGCUUUCCG--
CAAA01027192.1/19355-19196 -CUCACGGAGCACGAGGCCUCCACUGCGGCUGCGUGGCCCCU-UGGCGCGCUGGUGAGCCUUGGAGCGCGCCUGCGUACUCUCGGCGAGCA-----GUGGGGCAGCAAGCGCGGCGUCCUCCUGCC-AGCGUUAGUCUCUCACGGCGC-UG-UGCAGCCUAUGGUUUCCA--
AAKN02007306.1/48819-48659 -UCCGGAGGACACGAGGUCUCUAUUGCACCUGCGCGGUUCGC-CCGCGUGCGCGCGCGG-UUCUGCCGUGCCUGCG-AAUCUCGGCGCGCGCAC---GCCGACGGGUCUGGUGGGCUCCUCCCUAC-AGCCUGAAUCGGUCUGAGCAUCUG-UGUAGUCUGCGGCGAGUG--
ABRR01522118.1/160-318     -CGCGAGAGAGGCUGGCUCCCCC---CAGUUGCGCGCCCCACCCAGGACGCGCG--AGGCUGCCACUGCGGCUGCGCGAACUCGGCGCGCGCUC--GCCCGUGCCCU-GCGCGGGCUCCUCCCUCC-AGUCAAGUUGUCUCGCGGCGUCUG-AGCAGCCUGCGCUCUGUG--
AAPE02038459.1/57832-57681 -CCCCGGGCGCACGAGGCCUCCACUGCGGCUGCGCGGGCGGC-GGGAGGGCGUG--CGGCUUCUACUGCGGCUGCGCAAACUCCGCGCCCGGCC--GCUCGUCUCCUCCCUCAGGCUCCUCCUUCCCAGUCGAGUUCCCUCGGGGCG---GCUGCUUUC-----------CG
AAQR03069579.1/7159-7299   -CCCCAGCCCCGCGAGGCUUCGC---UGCCUCUGCGAGCCCC-UCGGAAGCGUGUGCGACUUCUACUGCGGCUGUGCAAGCUCGC-------------------ACA----GGGGCUCCGCCCGCCAAGUCCGAGUCCGUCGGGGAAUCUG-UACAGCUUACGCUUUCCG--
#=GC SS_cons               .:::::::::::::::::::::::::::::::::::::::::.:::::::::::..::::::::::::::::::::::::::::::::::::::..::::::::::::::::::::::::::::::.::::::::::::::::::::::::.::::::::::::::::::..
#=GC RF                    .ccCcgGGcgCACGAGGcCUCcacUGCGgCUGCGCgGcccGc.ugGagcGCGuG..cGgCUUCUACUGCGGCUGCGCaaaCUCGGCGCGCGcaC..GcucGucugcuugCgggGGCUCCUCCCucC.aGccuaGgUCcCUCGGGGCgucUG.UGCAGCCUaCGcUUUCcG..
//
# STOCKHOLM 1.0

#=GF AC   RF02199
#=GF ID   TTC28-AS1_2
#=GF DE   TTC28 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   50.00
#=GF TC   52.70
#=GF NC   43.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 39.12 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   11258795
#=GF RT   Identification of novel transcribed sequences on human chromosome 22 by
#=GF RT   expressed sequence tag mapping.
#=GF RA   Hirosawa M, Nagase T, Murahashi Y, Kikuno R, Ohara O
#=GF RL   DNA Res. 2001;8:1-9.
#=GF WK   Long_non-coding_RNA
#=GF SQ   8


BC028176.2/5-161           AAAAUGGCAGAAUGAAAGAAUUAUGAGU-GGAACUAGAGAAUAGGAAAGACAUGAACCAACGCCCAAAAUGAGAAAGAAGGACAUA-UAAAGAAAAAGACAAAUACAAGUGAAAAAAAUAGACUAAUGGAUUAACGUCCCUGUCGUGUGACAUUUUCUG
AANU01252520.1/37262-37418 AAAAUGGCAGAAUGAAAGAAUUAUAAGU-GGAACUAGAGAAUAGGAAAGCCACGAACCAGUGCCCAAAAUGAGAAAGAAGGACAUA-CAAAGAAAAAGACAAAUACACGUGAAAAAAAUAGACUAGUGGAUUUAUGUCCCUGUUGUGUGACAUUUUCUU
ABDC01114145.1/1026-1176   AAAAUGGCAGAACAAAAGAAUUAUGAGG-GGAACUGGAAAGUAGGAAAGACG--AACCAACACUCAAAAUGAGAAAGAAGGACAUA-UAAGGAAAAAGAC---UACUCAUGAUAAAAA-AGACUAAUGGAUUAACAUCUCCAUUGUGUGACAUUUUCUU
ABRP01150307.1/516-658     AAAAUGGCAGAAUGUGGGAAUAUUGAAG-AGGACUAGAGAGUAGGAAAGACAUGAACCAUCACUCCAAA---AUAAGAGGGACAUG-UAAAGAAAAAGACAAUUACACUUGAAAAAAA-----UUACAGAGU------UCGAUUGUGUGGUAUCUUCUU
ABRQ01802201.1/766-917     AAGAUGACAGAGAGACUGAAUUAUGUA--AAGAUUGGAGAGUAGUCAAGACAU-GAGUGGCUAUCUUAA-GAUAAGGAAGGAUAUG-UAAAGAAAAAGAC--ACACAACUGAAGAAAAUAGACUGAUGGAUUAAGGUGUUCACUGUGUCACAUUUUCUU
ABRR01155982.1/1851-1997   CUCAUUCUCAAAUGAGGGAAUG-------AAGACUA--GAGUAGGAAAGACAUGAACUGUCACCCCAAA--AUGAGAAAGGACAUU-UGAAGAAAAAAACUAUUACAUGUGAAAAAAAUAAGCUAAUGGUUACCCCCCCCCAUAAGCUAAUGGAUAGUC
AAGV021059036.1/432-583    AGAAUAUCAGA--GAAGAAAUUAUAAGG-AGGACUAGAGAAUAGGAAAGAUAUAAACUGACACCCCAAG--GUGAGAAAAGACAUA-UAAAGAA-AAGACAAAUGCGCAUGAAAAAAAUAGACUGAUGGGUUAACAUCUCCAUUGUGUGGCAUUUUCUU
AAQR03069579.1/13443-13600 AAAAUGGCAGAAAGAAAGAAUUAUGAAGGAAGACCAGAAAGUACGACAGACAA-AACCAACAAUCAAAAUGAGAAAGUAGGACAUAACAAAGAAAAAGACUGACACUCAUGAACAAAGUAGACUAAUAGACGAACAUCUACAUUGUGUGACGUUUUCUU
#=GC SS_cons               ::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::.::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    aaaAUggCaGAauGAagGAAUuaUGagg.agGACUaGAGAGUAGGaAAGACAuGAACcgaCacuCaaAA.GAgaAgGAAGGACAUa.uAAAGAAAAAGACaaauACacgUGAAaAAAAUAGaCUaAUGGauuaacgUcuccaUuGUGUgacaUuUUCUu
//
# STOCKHOLM 1.0

#=GF AC   RF02200
#=GF ID   TTC28-AS1_3
#=GF DE   TTC28 antisense RNA 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; Pfold
#=GF GA   55.00
#=GF TC   56.50
#=GF NC   51.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.02 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   11258795
#=GF RT   Identification of novel transcribed sequences on human chromosome 22 by
#=GF RT   expressed sequence tag mapping.
#=GF RA   Hirosawa M, Nagase T, Murahashi Y, Kikuno R, Ohara O
#=GF RL   DNA Res. 2001;8:1-9.
#=GF WK   Long_non-coding_RNA
#=GF SQ   6


AL033538.1/33518-33698       AAACACUGGGAUGCCGGAGCUCAGGCAUCCCAGACAGGAGGAAGUGUGUA-CUCACACCA--GCCAGGAGGAAACAAGCCUGCCUGGG-AGGACAGAC-GAUCAGCC--CUGGCUGUCCC-UCAGGAGCGGGGGGCCUCCAAGGCACACUG----CCCACUGGG-UCA----AGGAGUAUCCAGGA--GGAGUUAGAAGG
AANU01252521.1/51386-51563   AAACACUGGGAUGCCGGAGCACAGGCGUCC-AGACAGGAGGAAGUGUGUA-CUCACAUCA--GCCAGGAGGAAACAAGCCUGCCCGGG-AGGACAGAA-GAUCAGCC--CUGGCUGUCAC-UCAGGCAGGGCGGGCCUCCAAG--ACACUG----CCUACUGGA-UCA----AGGAAUAUCCAGGA--GGUGUUAGAAGG
ABRT010501874.1/3613-3784    AUACACCCUGGUCCUGGUGCUCAGGGCUGGCAAGCAGGAGGAAACAUGCG-CUCACAUCA--GCCUGGAGGAAGUGAACGUUCCUGGGCAGGAUAGAC-AGCCAGCUCCCUGGCUGCCCC-UCAGGCUGGAAGGGCCUUGGAGA--CAUUG----UCCACUGGGGUCA----AGGAAGAAGAGAG---GG----------
AAWR02038392.1/259932-259775 -------------------------------AAACCCUGGGAUGCGGGGGACUGACAUCACAAACGGGAGGAAAUGAGCAUUCCCGGGCAGGACAGACCAGCCAGCUGGCUGUCCAUCAGGCUGGGCUGGAAGGACCUUGGAGAGACACUG----CCCACUGGGGUCA----AGGGGCACCCAGG---GUAGUUAGAAGG
ABDC01114148.1/19475-19652   --ACACAGG-AUACGAGGGCCCGGGUGUCUC-GGCAGGAGGAAGUGUGCA-CUCGCACCC---CCACAAGGAAGCGAGCCUUCCUGGACAGGACAGGU-GACCAGCCCCUG---UGACCC-CUGGGCCAGAAGGGCCUUGGAGACAAGCUG----CCCACCGGAGCG-----AAAGAGACCCAGGGUAGCAAGCAGAAGG
AAQR03069599.1/30158-30349   AAACACAGGGAUAGUGGGGCCCAGGUGUCCCAGGCAGGAGGAAGUGUGCA-CUCAUACUA---GCCAAGAGGAAAGAGCCUUCCUGGGCAUGACAGGU-GACCAGCCCCUAGGCUGUCCC-UCAGGCAAGAAUGGCCUUGGAGACAUGCUGGAGACCCCUUGGAGCAUAGCCAAGGAGACCCAGG--AGUAGUUAGAAGA
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::..::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::.::::::::::::::::::::::::::::::....:::::::::::::....:::::::::::::...::::::::::::
#=GC RF                      AaACACuggGaUgcuGGgGCuCaGGugUccCAggCaGGaGGAaGuGuGca.CUcaCAuCa..gcCaggaGGaAauGAGCcUuCCuGGGCAGGACAGac.gacCAGCccccuGgCUGuCcc.ucaGGCugGaaGGGCCUugGAGacAcaCUG....CCCaCUGGgGuca....AgGgagAccCaGG...GgaGuuAGAAGG
//
# STOCKHOLM 1.0

#=GF AC   RF02201
#=GF ID   TTC28-AS1_4
#=GF DE   TTC28 antisense RNA 1 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   48.80
#=GF NC   40.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.96 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   11258795
#=GF RT   Identification of novel transcribed sequences on human chromosome 22 by
#=GF RT   expressed sequence tag mapping.
#=GF RA   Hirosawa M, Nagase T, Murahashi Y, Kikuno R, Ohara O
#=GF RL   DNA Res. 2001;8:1-9.
#=GF WK   Long_non-coding_RNA
#=GF SQ   18


AL033538.1/41528-41639       UGUGCUCGCUUGACCCGUCUGAUGUGCUGCCGUGGGCACUUGACUGAGAGUGGCAG--AGCACUAGGCUAACCCAAAGUGAC-ACAUGCCUGGCGGGAUGUUCAGUCUCUGUAAA
AANU01252521.1/59775-59886   UGUGCUUGCUUGACCCGUCUGAUGUGCUGCCGUGGGCACUUGGCUGAGGGUGGCAG--GGCACUCAGCUAACCCAAAGUGAC-ACAUGCCUGGCGGGACGUUCAGUCUCUGUAAA
AAPY01652395.1/727-839       UGUGCUCGCCUGACCCGUCUGAUGUGCCGCCGUGGGCGCUCGGCGGAGGGUGGCGGC-AGCGCUCAGCUAACCCAAAGUGAC-ACGUGCCUGGCGGGACGUUCAGCCUUUCCAAA
AAWR02038392.1/251829-251716 UGUGCACGCCUAAUCCGUCUGACGCACUGCUGUGGGCGCUUCGCUGAGGGUGGCAGACGGCACUCAGCUAACCCAAAGUGAC-AAGUGCCUGGCGGGACAUUCAGUCUGUACAAA
ACBE01381674.1/5679-5567     UGUGCGCGCCUAAUCCGUCUGACGUGCUGCUGUGGGCGCUCGACCGAGGCUG-CAGAAGGCACUCAGCUAACCCAAAGUGAC-AUGUGCCUGGCGGGACAUUCAGUCCGUACAAA
AAKN02007305.1/60748-60636   CAUGCUUGCCUGACCCAGCUGCCCUGCUGCCCUGAGCACUUGGCUGAGGGUGGCAGA-AGCACUCAGCUAACCCAAAGUGAC-ACAUGCCUGGUGGGACAUACAGGAUACACAAA
AAQQ01192278.1/886-998       CGUGCUCGCCUGGCCCGUCUGCCACGCUGCCCCGGGCACUUGGCUGACGGUGGCAUA-GGCACUCGGCUAACCUAAAGUGAC-ACAUGCCUGGCGGGACAGUCAAGCCCUACAAA
ABRP01111219.1/630-743       UAUGCACGCCUCAUCUGGCUGACAUACCGCUGUGGGCACUUGGCUGAGGGUGGCAGAAGACACUCAGCUAACACAAAGUGAC-ACGUGCCUGGCAGGACAUUCAGCGUGUCUAAA
CAAA01027183.1/2451-2341     UGUGCUCAUGUGACCCAUCUG-CCUGCUGCCAGAGGCACCUGGCUGAGGGUGGCAGA-AAUGCU-GGCUAACCCAAAGUGAC-AAGUGUCUGGUGGGAAGCUCAGGCUUCUCGGG
AAHX01073183.1/53235-53125   UGUGCUCAUUGGACCCAGUUG-CCUGCUCCUGGGGGCACCUGGCCGAGGGUGGCAGG-AAUGCU-GGCUAACCCAAAGUGAC-AUGUGCCUAGUGGGAAGCUCAGGCUUCCCAGC
AAGV020063793.1/469-581      AGUGUGUACAUCCUCUUGCUGACUUGCUGCUGGGGGCACUUGGCUGAGGGUGGCAGGAGGCGCUCAGCUAACCCAAAGUGAC-AAGUGUCUGGCAGGACAUU-AGUCUAAAUGAC
AAYZ01009372.1/896-1000      UGCUCGUGCCUGACCCAUCUGCUGGGCUGCCCUGGGCGCAUGGCUGAGAGUGGCAGA-AGCACUCAACUAACCCGAAGUGACAACGUGCCUUGCGGG---------CCCGAUAGA
ABRN01249058.1/6547-6659     UGGAGGAGCGAGUGUCCACGGCCGCGCUGCUGUGGGCACUGGGCUGAGGGUG-CAGAGGGCAUUCAGCUAACCCAAAGGGAC-ACGCGCCUGGUGGGACAUUCUGUCUGUACAAA
ABDC01114150.1/541-629       CGUGCCCGCCUGACCCAUCUGCCAGGCCGCUGUGGGCGCUUG------------------------GCUAACCCAAAGUGAC-ACGUGCCCGGC-GGACAUUCAGGCUCUACAGA
AAFR03071970.1/2247-2356     AGUGUCUCUCUAAUCCGUUUGACUUCCUGCUCCAGGAAUUGGGCUGAGGGCAACAGG-AU--CU-CGCUAAGCCAGAGUGGC-AUGUGCCUAGCAGAAUUGUCAGGCUAUAUGGA
ABRQ01263922.1/72-173        UGUCCA-------UUCAUCUGACCCACUGCACUGGGCCUGGGGCUGCAGGCGGCAGA-GGCAUUCCACUAGCCCACAGUGAC-AC-UGCCUGGUGGGACAGU---UCUCUGCAGC
AAGU03075228.1/18554-18445   UGUGCACAUCCG-CUCGUCUGACCCACUGCUCUGGGCCUGGGGCUGUGGGUGGCAGA-GGUGCUCCACUAACCCACAGUGAC-AC-UGCCUGGCGGG-UGUUCAGUCUGUGCAAA
AAEX03014780.1/74925-75037   UGUGCACGCCUAAUCCGUCUGACGUGCUGCUGUGGGUGCUGCGCUGAGGCCGGCAGCAGUCACUCAGCUAACCCAAAGUGAC-AC-UGCCUGGCGGGCCAUUCAGUCUGUGCAAA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::.::::::::::::::::::::::::::::::::
#=GC RF                      uGUGCucgCcugacCCguCUGaCguGCUGCuguGGGCaCuuGGCUGAGGGUGGCAGa.ggCaCUCaGCUAACCCAaAGUGAC.AcGUGCCUGGCGGGAcauUCAGuCUguacAaa
//
# STOCKHOLM 1.0

#=GF AC   RF02202
#=GF ID   UCA1
#=GF DE   Urothelial cancer associated 1 conserved region
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   93.50
#=GF NC   32.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.22 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   18501714
#=GF RT   UCA1, a non-protein-coding RNA up-regulated in bladder carcinoma and
#=GF RT   embryo, influencing cell growth and promoting invasion.
#=GF RA   Wang F, Li X, Xie X, Zhao L, Chen W
#=GF RL   FEBS Lett. 2008;582:1919-1927.
#=GF WK   UCA1
#=GF SQ   5


EU334869.1/724-798       AGGCCGAGAGCCGAUCAGACAAACAACCUACAACCCUUAAGCUCCUGGCAGCGCCCAGCCAAGGCCAUGCUUCCA
DQ249310.1/671-745       AGGCCGAGAGCCGAUCAGACAAACAACCUACAACCCUUAAGCUCCUGGCAGCGCCAAGCCAAGGCCAUGCUUCCA
DQ343132.1/723-797       AGGCCGAGAGCCGAUCAGACAAACAACCUACAACCCUUAAGCUCCUGGCAGCGCCCAGCCAAGGCCAUGCUUCCA
AC225834.3/110065-109991 AGGCCAAGAGCCGACCAGACAAACAACCUACAACCCUUAAGCUCCUGGCAGCGCUCAGUCAAGGCCAUGCUUCCA
ABGA01052491.1/3008-3080 AAGCCGAAAGCCGAUCAGACAAACAACCUACAACCCUUA-GCUCCUGACAGUGCCCAGUCAAG-CUAUGCUUCCA
#=GC SS_cons             :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  AGGCCGAGAGCCGAUCAGACAAACAACCUACAACCCUUAAGCUCCUGGCAGCGCCCAGcCAAGGCCAUGCUUCCA
//
# STOCKHOLM 1.0

#=GF AC   RF02203
#=GF ID   WT1-AS_1
#=GF DE   WT1 antisense RNA conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   40.00
#=GF TC   43.40
#=GF NC   36.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.85 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   2173145
#=GF RT   Tissue, developmental, and tumor-specific expression of divergent
#=GF RT   transcripts in Wilms tumor.
#=GF RA   Huang A, Campbell CE, Bonetta L, McAndrews-Hill MS, Chilton-MacNeill S,
#=GF RA   Coppes MJ, Law DJ, Feinberg AP, Yeger H, Williams BR
#=GF RL   Science. 1990;250:991-994.
#=GF RN   [2]
#=GF RM   8406502
#=GF RT   Sequence of the WT1 upstream region including the Wit-1 gene.
#=GF RA   Gessler M, Bruns GA
#=GF RL   Genomics. 1993;17:499-501.
#=GF RN   [3]
#=GF RM   17210670
#=GF RT   A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS and
#=GF RT   exhibits sequential epigenetic defects during Wilms' tumourigenesis.
#=GF RA   Hancock AL, Brown KW, Moorwood K, Moon H, Holmgren C, Mardikar SH,
#=GF RA   Dallosso AR, Klenova E, Loukinov D, Ohlsson R, Lobanenkov VV, Malik K
#=GF RL   Hum Mol Genet. 2007;16:343-354.
#=GF WK   WT1-AS
#=GF SQ   10


X74840.1/1233-1125         CAACCCAACACGCGCUCUCAGCUGGCCGGUGUGGCACAACCCUCC-CCCCACCUCCCCUUCUUGGCCUUCGCCAGUGUGGGAGCCUCGUCUCACUG-GAGAGUCCGUUCAG
U06486.1/1586-1479         CAACCCAACACGCGCUCUCAGCUGGCCGGUGUGGCACAACCCUCC-CCCCACCUCCCCUUCUUGGCCUUCGCCAGUGUGGGAGCCUCGUCUCACUG-GAGAGUC-GUUCAG
X77549.1/2206-2099         CAACCCAACACGCGCUCUCAGCUGGCCGGUGUGGCACAACCCUCC-CCCCACCUCCCCUUCUUG-CCUUCGCCAGUGUGGGAGCCUCGUCUCACUG-GAGAGUCCGUUCAG
S77896.1/958-850           CAACCCAACACGCGCUCUCAGCUGGCCGGUGUGGCACAACCCUCC-CCCCACCUCCCCUUCUUGGCCUUCGCCAGUGUGGGAGCCUCGUCUCACUG-GAGAGUCCGUUCAG
AY245105.1/1692-1584       CAACCCAACACGCGCUCUCAGCUGGCCGGUGUGGCACAACCCUCC-CCCCACCUCCCCUUCUUGGCCUUCGCCAGUGUGGGAGCCUCGUCUCACUG-GAGAGUCCGUUCAG
AANU01216576.1/2029-1921   CAACCCCACACCCGCUCUCAGCUGGCCGGUGUGGCACAACCCUAC-CCCCACCUCCCCUUCUUGGCCUACGCCAGUGUGGGAGCUUCGUCUCACUG-GAGAGUCCCUUCAG
AAQQ01112620.1/3627-3519   CUACCCGCCACGCGCUCCAAACUGGCCUAUAUGGCACAGCCCUCC-CCCUACCUCCCCUACUGGGCCUUGGAGAGUGUGGGCGCCCCGCGGCACUG-GCAAGUCCCUCCAG
AAFC03041825.1/3941-3832   CUACCCGCCACGCGCUCUUCGCUGGCCUGUGGGACACAGGCCUCCCCCCCACCUCCCCUUCUCGGCCUUCGCGAGUGUGGGCGCCUCGGGGCACUG-GCGAGCCGCUCCAG
ABRP01285284.1/3861-3761   CUAUCAGCCACG-GCUCUUAGCUGGCCAGUGGGACGCAACCCUGC-CCCCGCCUCCCCUUCUCGGCCAUCGCGAGUGUGGGAGCC-------ACUG-GCAAGUCUCUCCAG
ACBE01540146.1/14481-14379 CUACCCGCCACGCGCUCCCAGCUGGCCUGUGGGACACAGCCCUCC-CCCCACCUCCCCUUCUCGGCCUUCUCAAGUGUGGGCGCCU-------CUGGGAGAGCCUCUCCAG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::
#=GC RF                    CuACCCgaCACGCGCUCucAGCUGGCCgGUGuGgCACAaCCCUcC.CCCCACCUCCCCUUCUuGGCCUUCGCcAGUGUGGGaGCCUCGucuCACUG.GaGAGuCccUuCAG
//
# STOCKHOLM 1.0

#=GF AC   RF02204
#=GF ID   WT1-AS_2
#=GF DE   WT1 antisense RNA conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   45.00
#=GF TC   49.80
#=GF NC   37.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.87 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   2173145
#=GF RT   Tissue, developmental, and tumor-specific expression of divergent
#=GF RT   transcripts in Wilms tumor.
#=GF RA   Huang A, Campbell CE, Bonetta L, McAndrews-Hill MS, Chilton-MacNeill S,
#=GF RA   Coppes MJ, Law DJ, Feinberg AP, Yeger H, Williams BR
#=GF RL   Science. 1990;250:991-994.
#=GF RN   [2]
#=GF RM   8406502
#=GF RT   Sequence of the WT1 upstream region including the Wit-1 gene.
#=GF RA   Gessler M, Bruns GA
#=GF RL   Genomics. 1993;17:499-501.
#=GF RN   [3]
#=GF RM   17210670
#=GF RT   A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS and
#=GF RT   exhibits sequential epigenetic defects during Wilms' tumourigenesis.
#=GF RA   Hancock AL, Brown KW, Moorwood K, Moon H, Holmgren C, Mardikar SH,
#=GF RA   Dallosso AR, Klenova E, Loukinov D, Ohlsson R, Lobanenkov VV, Malik K
#=GF RL   Hum Mol Genet. 2007;16:343-354.
#=GF WK   WT1-AS
#=GF SQ   18


U77682.1/333-197           ACGGUUAAGCCGGGAAAA--CAG-----CGGCUAGUUU-AGGAGGG--AAGAAAACCCUUGGGCAAACGCCC-AAAGCCUGC-GUAUAUUCCGGCCGGAGCAUCCUGGCGCCCAGUUUGGGGAGGAGGGGUGAAGG------GGAGGGUUUGGAU-----
DQ289488.1/273-409         ACGGUUAAGCCGGGAAAA--CAG-----CGGCUAGUUU-AGGAGGG--AAGAAAACCCUUGGGCAAACGCCC-AAAGCCUGC-GUAUAUUCCGGCCGGAGCAUCCUGGCGCCCAGUUUGGGGAGGAGGGGUGAAGG------GGAGGGUUUGGAU-----
AL049692.13/53131-52995    ACGGUUAAGCCGGGAAAA--CAG-----CGGCUAGUUU-AGGAGGG--AAGAAAACCCUUGGGCAAACGCCC-AAAGCCUGC-GUAUAUUCCGGCCGGAGCAUCCUGGCGCCCAGUUUGGGGAGGAGGGGUGAAGG------GGAGGGUUUGGAU-----
X77549.1/1637-1502         ACGGUUAAGCCGGGAAAA--CAG-----CGGCUAGUUU-AGGAGGG--AAGAAAACCCUUGG-CAAACGCCC-AAAGCCUGC-GUAUAUUCCGGCCGGAGCAUCCUGGCGCCCAGUUUGGGGAGGAGGGGUGAAGG------GGAGGGUUUGGAU-----
AY245105.1/1119-983        ACGGUUAAGCCGGGAAAA--CAG-----CGGCUAGUUU-AGGAGGG--AAGAAAACCCUUGGGCAAACGCCC-AAAGCCUGA-GUAUAUUCCGGCCGGAGCAUCCUGGCGCCCAGUUUGGGGAGGAGGGGUGAAGG------GGAGUGUUUGGAU-----
ABDC01041565.1/1140-1277   ACGGUUAAGCCGGGAAAA--CAA-----CUGAUGGUUUCAGGAGGG--AAGAAACCCCUUGGGGAAACGCCC-GGAGCCUGC-AUAUAUUCCAGCCG-AGCAUCCUGGCGCCUGUUUUCGGGAGGGAGGGGUAGCG-----GGGAGAGUUUGGAU-----
AAQQ01112620.1/3091-2957   ACGGUUAAACCGGGAAAA--CAG-----UGGCUAGUUU-GGGGGGG--GGGA---CUCCUGGGGAAACGCCC-AGUGCCUGCGCUCUUUUCCGGCUGGAGCAUCCUGGCGCCCAGUUGAGGGAGGAAGGGAAAUGG------GAAGGGUUUGGGC-----
ABRP01285284.1/3310-3186   ACGAUGAAGU-GAGAAAA--CAG-----CAGCUAGUUU-AGGAGGU--AAUAAAACUC--AGGGAAGCGCCC-AGAGCCUGC-UUAUAUUCCUGCCGGAGAAUCCUGGCGUCCAGUUU---------GGAGGGUGG------GCAGGGUUUGGAU-----
ABVD01084533.1/598-496     ACGGCGAAAUCGGGAAGA--UAC-----UGGCUAGUCU-AUGAGGG--AAGAAUACCCUUGGGGAAAUGGCC-AGAGCCUGC-GUAUAUUCCAGCUGGAGCAUCCUGGCGC-----------------------CG-------------------CU---
AAFC03041825.1/3381-3253   ACGGUGACGCCGGGAAAA--CAGAAUGGCGGCUAGUUU-GGGAGGA--AAGAAAACCCUUAGGGAAAUGCCC-AGAUUCCGG------U------UGGAGAAUCCUGGCGCCGAAUGUGGAGGGUAGGGGGUGAGG--------AAGGUUUGGAU-----
ACBE01540146.1/13935-13807 AUCUUCCUUUCCAGUGAA--CAG-----CGGCUAGUCU-GGGAGGG--AAGAAUACCCUUAGGGAAACACUC-AGAGCCUGC-ACAUAUUCUGACUGGAGAAUCUCAGAGCCCGUUUUGGAGGGUAAGGGGUGGAA--------AGGAU-----------
AAPY01606765.1/2315-2189   ACGGAUAAGCCGGGAAAA--CCG-----CGGUCAGCUU-GGGAGGG--AGGAAAACCUUCGAGGAAACGCUCGAGGACCUGG-G----CUCC--C--AGGCGUGCCGGCGCCCAG---AUGGAGAGGGAGGCCUGG------GGAGUGUUUGGAC-----
ABRQ01001651.1/684-561     ACUGUGGAGUAGGGGAAA--CA------CAGCUAGUUU-GGGAGGG--AAGAAUAUCCUUGG-GAAAUUGUC-AGAGCCUGA-GUGUAAUCCUGCAGGAGCGUCCAAGAAUUCAGC----------UGGAUUGCUG------GGGAGACU-AGAU-----
AAWR02018627.1/25-161      AGUGAAAGCCUGGGAAAAACCAG-----CAGCUGGUUUGGGGAGGGGCAAUUAAACCCUUAGGG-AACGCUC-AGCGGGUGC-ACACAUCCCGGCCAGAGAA-CCCGGUGCCCACUGU---GGGGGUGGGACGUGG------GGAGGGUUUGAAU-----
AAQR03002375.1/1230-1364   ACGGUUAAGCCGGGAGAA--CAA-----CUGCUGGUUU-AGGAGGG--UAGAAACCCC--GGAGAAAAGCCC-AGGGCAUGC-GUACAUUACCGCCGGAGCAUCCUGGCGCCCAUUUUCGGGGGGAGGGGCGAAGG------GGAGGGUUU----GAUA-
AAEX03011404.1/45551-45435 ACGGUGAAGCCGGGAAAA--CAG-----CGGCUAGUUC-GGGAGGG--AGGAAAACUCCU-------------AGGGCCUGC-ACGUACCCCGACCGGGGAAUCCUGGAGCCCAGUUUGGUGGGUGAGCGGUAGGG--------AGGAU-----------
AAGU03043695.1/2955-2829   ACGGUGAAGCUGGGGAAA--CCC-----CCGCUAGUUU-GGGAGGG--AAGCACACCCCUGGG-AAAUGCUC-AGAGCCUGC-GUAUAUUCUGGCGGGACCGUCCUGGAACCGAG---CUGGAUUGU----UGAGG------GG-------GGACUAGGU
AAGW02037545.1/940-1083    GCGGUUAAGCCGGGAAAA--GCG-----AGGCUAGUUU-GGGAGGA--AAGAGAACCCUUGGGGAAAACACCCGGAGCCUGC-CUAUACUCUGGCCGGAGCAUCCCGGCGCCCAGUUGAGGGAGAAAGAGGAAUGGAAAUGGGGAGGGUUCGGAU-----
#=GC SS_cons               ::::::::::::::::::..:::.....::::::::::.:::::::..::::::::::::::::::::::::.:::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::......:::::::::::::.....
#=GC RF                    ACGGuuaagCcGGGaAAA..CaG.....CgGCUAGUUU.GGGAGGG..AAGaAaACCCUUGGGGAAAcgccC.AGaGCCUGc.gUaUAuUCCgGCcGGAGcAUCCuGGcGCCcAgUuugGgGgGgagGGGgugugG......GGAGGGUUUGGAu.....
//
# STOCKHOLM 1.0

#=GF AC   RF02205
#=GF ID   WT1-AS_3
#=GF DE   WT1 antisense RNA conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   55.00
#=GF TC   66.70
#=GF NC   49.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 35.78 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   2173145
#=GF RT   Tissue, developmental, and tumor-specific expression of divergent
#=GF RT   transcripts in Wilms tumor.
#=GF RA   Huang A, Campbell CE, Bonetta L, McAndrews-Hill MS, Chilton-MacNeill S,
#=GF RA   Coppes MJ, Law DJ, Feinberg AP, Yeger H, Williams BR
#=GF RL   Science. 1990;250:991-994.
#=GF RN   [2]
#=GF RM   8406502
#=GF RT   Sequence of the WT1 upstream region including the Wit-1 gene.
#=GF RA   Gessler M, Bruns GA
#=GF RL   Genomics. 1993;17:499-501.
#=GF RN   [3]
#=GF RM   17210670
#=GF RT   A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS and
#=GF RT   exhibits sequential epigenetic defects during Wilms' tumourigenesis.
#=GF RA   Hancock AL, Brown KW, Moorwood K, Moon H, Holmgren C, Mardikar SH,
#=GF RA   Dallosso AR, Klenova E, Loukinov D, Ohlsson R, Lobanenkov VV, Malik K
#=GF RL   Hum Mol Genet. 2007;16:343-354.
#=GF WK   WT1-AS
#=GF SQ   19


AL049692.13/52645-52412    --AAGGAGAAGAACCGGGGGCC-GGAGCG--GAGCGUGUUUCAG--AGGUGCGUAUAAAAUC--CCAGGGGCGCCAGGAGGCAGCAGCGACGGCGC-AGCGUGGGACGGCCAGGCGCGACGGGAGGGAAGCAACCGGUUGCAGUCCGGCCUCCUGUACCUGGCUGGCCCGGGCUGGGGCUGCAAGCUUUCCAGCCAAACUUAUGU----GAAG-------CAAAGUAGUUGCAGUUUGACAAAGAAU----GGCGUUUC-
L25110.1/2734-2967         --AAGGAGAAGAACCGGGGGCC-GGAGCG--GAGCGUGUUUCAG--AGGUGCGUAUAAAAUC--CCAGGGGCGCCAGGAGGCAGCAGCGACGGCGC-AGCGUGGGACGGCCAGGCGCGACGGGAGGGAAGCAACCGGUUGCAGUCCGGCCUCCUGUACCUGGCUGGCCCGGGCUAGGGCUGCAAGCUUUCCAGCCAAACUUAUGU----GAAG-------CAAAGUAGUUGCAGUUUGACAAAGAAU----GGCGUUUC-
DQ289488.1/759-992         --AAGGAGAAGAACCGGGGGCC-GGAGCG--GAGCGUGUUUCAG--AGGUGCGUAUAAAAUC--CCAGGGGCGCCAGGAGGCAGCAGCGACGGCGC-AGCGUGGGACGGCCAGGCGCGACGGGAGGGAAGCAACCGGUUGCAGUCCGGCCUCCUGUACCUGGCUGGCCCGGGCUGGGGCUGCAAGCUUUCCAGCCAAACUUAUGU----GAAG-------CAAAGUAGUUGCAGUUUGACAAAGAAU----GGCGUUUC-
X77549.1/1152-921          --AAGGAGAAGAACCGGGGGCC-G-AGCG--GAC--UGUUUCAG--AGGUGCGUAUAAAAUC--CCAGGGGCGCCAGGAGGCAGCAGCGACGGCGCGAGCGUGGGACGGCCAGGCGCGACGGGAGGGAAGCAACCGGUUGCAGUCCGGCCUCCUGUACCUGGCUGGCCCGGGCUGGGGCUGCAAGCUUUCCAGCCAAACUUAUGU----GAAG-------CAAAGUAGUUGCAGUUUGACAAAGAAU----GGCGUUUC-
ABRP01285284.1/2879-2637   --AAGGAGAAGCGCCGGGAACCCGAACUA--GAGUGCGUUUCAG--GG-UGCAUGUAAACGC--CCAAGACAGCCAGGAGGCAGCGGCGACGGCGC-AGCCUAGGACCGUCGCUAGCUCCCGGCAGGAAGCGGCCGGUUGCCGCCAGGCCUUUUACACCGGGCUGGCCCAGGAUGGGGCCCGCAGCUUUCCAGCCAAGCCAGUGU----GAAGCAACAGUCAAGGUAGUUGCAGUUUUACAAAGAAGUC--AGCGUUUU-
ABVD01084533.1/285-45      --AAGGAGAAGCGCCGGGACUCCGGAGUG--GUGUGCAUUUCAG--GGGCGCGUGGAAACGC--CCAGCAGUGCCAGGUGGCAGAAACGA---CUA-AAGCUGGGACUGUGAGGCGCACCGGGUGGGAAGCGGCGGGUUGCACCA-GGUCUCACGCACCAGGCUAGCCCGGGUUAGGGCCCACGGCUUUCCAACCAAGCUUUCCU----GAAGUAACAAUCAAGAUAGUUGCAGUUUUACAAAGGCAUC-GAGCGUUUU-
ABRN01427349.1/2518-2281   UAGGCUAGAAGAGCCGUGAACCUGAAUGG--GAAUGCGCUUCAG--GGGCGCGUGGAAAC----------GC-CCAGGAGGCAGCGGCGACGGCGC-AGCCUGGGACUGCCAGGAGCGCCGGGCGGGAAGCGGCCUGUGGCCGCCUGGCCUCUGACACGAGGCUGGCCGGGGAUGGCGCCCGAAGCUUUUCACCCAAGCCCAUGU----GAAGCAACAAUCAAGGUAGUUGCAGUUUUAUAAAGAAGCC-GGAAGUUUU-
AAGV020131545.1/2352-2125  --AAGGAGAAGCGCCGGGACUCCUGAGUG--GUGUGCCUUUCAG--GGGCGCGUGGAAACGC--CCAGCAGCGUCAGGUGGCAGAGACGAUGACUC-AAGCUGGGACCGCGAGGCGCAUCCGGAGGGAAGCGGCCGGGUGCAUCG-GG---CU-----------AGCCGGGGAUCCGGCCCGCAGCUUUCCAGCCAAACUCUUGU----GAAACAACAGUCAAGGUAGAUGCAGUUUUACAAAGAAAC---AGCGUUUU-
ABDC01041565.1/1621-1848   --AGCAAGAAGCGCUGGGAGCCCGGAGUG--AAGUGCGUUUCAG--GGGCUCGUGGAAACUC--CCAGGAGCGCAAGGGGGCAGCGCGGACAGUGC-AG-----------------CC-UGGGAGGAAAGUAGCCGACUGCAGUCCGGCCUGUCGCACCAAGCUGGCCAGGGAUGG-ACCCGCAGCUUUCCAGCCAAGCCUAUCUAUGUGAAGCGACAGUCAAGGUAGUUGCAGUUUUACAAAGACAC---AGCGUUUC-
AAFC03041825.1/2932-2699   UAGGCUAGAAGCGCCGGGAACCUGGAUUG--GAGUGCGCUUCAG--GGGCGCGUGGAAAC----------GC-CCAGGAGGCAGCGGCGACGGCGC-AGCCUGGGACUGCCAGGAGCGCCGGGCGCGAAGCAGCCGGGUGCCGCUUGGCCUCUGACGUGAGACUGGCCGCGGAUGGGGCCCGAAGAUUUUCAGCCAAGCUCUCU--------GCAACAAUCAAGGUGGUUGCAGUUUUAUAAAGAACCU-GGGCGUUUU-
ABRO01046980.1/9267-9033   --AAGGAGAAACGCCAGGCGUCUGGCCUG--AAGUGCGUUUCUG--GG-CGCGUGGAAACGC--CCAGGAGCGCCGGGAGGCAGCGGCGAUGGCGG-AGCCUGGGACUGCCAGGCGCGCCGGGCAGGAAAAGACCGAUUCCAGCCAGG--------ACAA--CUGCACCAGGCUGUCUGGGCAACUUUUCUAGUCAAACCUAACGACGCAAAGCAACAAUGGAGGCAAUUGCUGUUUUACAAAUAAAAA-GAUCAU----
AAPY01606765.1/1887-1682   ---ACGGGCCGGGUCGAGAGCCCGGAGUA--GAGCGCAUUUCAG--CGGCUGGUGGAAAC----------GC-CCAGGAGGC---GGCGACGGCGC-AGCCUGGGACCGCCAGGCGCGCGGGGCGGGAAGCUGCCAGUUGCAGCCCGGCCCCGGAC---------------------CCC--AGGCUUUCCUGCCAAACCUGCGU----GAAGCAGCAGU-GAAGUAGUUGCAGUUUCACCAAAACACC-GAACUU---C
AAWR02018627.1/483-718     --AAGGAGAAACGCCGAGAACC-GGAUUG--GAGUGCGUUUCAG--GGGCGCGCGGAAACGCCCCGGGGAGAGCCGGGAGGCAGCGGCGACGGCGC-AGCCUGGGACGGCCAGGAGCGCGGGGCGGGGAGCGGCCGGUGGCCGUG-GGCGUCUCACCAAAGC--GGCCCUGGAGGGGCCC--CCGGCUCCCAGCCAAGCCCACGU----GAAGCAGCA-UCAGGGCAGUUGCAGCUG--UAGAGGAACC-GCGCGU---C
AAYZ01200691.1/243-472     --AGGGAGCAGGGGCGGGAGCCCGGAGUGCGGGGAGCGUUUCAGGGGGGCGCGUGGGAUCUC--CCGGGAGCGCCCGGAGGCAGCGGCGAUGGCGC-AGCCUGGGACUGCCAGG--CGCGGGGCAGGAAGCGGCAGGCUGCAGGGAGGCCCCGCACCCCAG----GCCAGGGCGGGGACCUGCCGCUCUCCAGCUGAGCCUGAGC----GAAG----------GGUAGUUGCAGUUGGGCGAAGAAGCC-CAGUAC----
AANU01216576.1/975-745     --AAGGAGAAGAACUGGGAGCCCGGAGCG--GAGCGUGUUUCAG--AGGUGCGUAUAAAAUC--CCAGGGGCGCCAGGAGGCAGCAGCGACGGCGC-AGCGUGGGACAGCCAGGCGCGACGGGAGGGAAGCAACCGGUUGCAGUCCGGCCUCCUGUACCUGGCUGGCCCGGGCUGGGGCUCCAAGCUUUCCAGCCAAACAU--GU----GAAG-------CAAAGUAGUUGUAGUUUGACAGAGU------GGCGUUUC-
ACBE01540146.1/13463-13234 --AAGGGGAAGCGCUGGGAACCCGGGUGG--GAGUGCGUUUCGG--GG-CACGUGGAAAAGC--CCGGGAGAGGCAGGGGGUAGCGGCGACGGCGC-AACCUGGAACCGCCUGGAGCG-CGGGCGGGCAGCGGCCGGUUGCCGCCAGGCCUCUUAUUCCAGGCUGGCCGCGGAUGGGGCCCGCAGC--UCCAGC---------G------AAGCGACAACCAAGGUAGCCACAGUUUUACAAAGAAACA-GAACGUUUU-
AAGW02037545.1/1395-1630   --AAGGAGAAGGGCCGGGAGCCCGAAGCG--GGGAGCGCCUCAG--CGGCGCACAGACACGC--A---GAGCGCCAGGAGGCAGCGGCGAUGGCGC-AGCCUGGGACUGCCAGGCGCGCGGGGCAGGAAGCAGCCGGUUGCUGAGAGGCCUCGCGCGGGA----GGCCGGGGCUGGGGCCCGCGGC--UCCAGCGGCGCCUAAGU----GAAGCGACCAUGGAGGUCGUCGCAGUUGGUCAAAGAAGCC-GAGUGCUCC-
AAPE02023626.1/1901-2145   --AGGGAGAAGCGCCGGGAACCCUGGUUA--GAGUGCGUUUCAG--GGGCGCUUGGAAACGC--CGGGGGGAGCUAGGAGGCAGCGGGGAUGGCGC-AGCCUGGGACAGACAGCAGCUCCCGGCAGGAAGCCGCGGGUUGCUGCCAGGCCUCUUACACCAGGCGGGUCGGAGGUGGGCCCCGCAGCUUUCCAUCCAAUCUCACGU----GAAGCGACAGUCAAGGCAGUAGGAGUUUUACGAAGAAACC-GAACGUUUU-
AAQR03002375.1/1689-1895   --AAGGAGAAGUGCAGGGAGCCCAGAAUG--AAGUGCGUUUCAG--GGGCGCGUGGAAACGC--CCAGGCGCGCAAGGGAGCAGCUCCGGCAGCGG-CAGCGCAGCCUG-------AGACUGGAAGAAAGCAGCGGGUUGCAGUCCGG---CU-----------GGCUGGGGAUGGGACACGAAGCUUUCCAGCCA----------------------GUCAAGACAGUUUCAGUUUUAUGGAGAAACAAGAGCGUUUC-
#=GC SS_cons               ..:::::::::::::::::::::::::::..:::::::::::::..::::::::::::::::..::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::....::::::::::::::::::::::::::::::::::::::::.:::::::::.
#=GC RF                    ..AaGGAGAAGcGCcGGGagCCcGGaguG..GaGuGCGUUUCaG..gGGCGCGUGGAAAcgC..CcaGGaGcGCCaGGaGGCAGCgGCGAcGGCGc.AGcCUGGGACuGcCaGGcGCgccgGGcgGGAAGCgGCcGGuUGCaGccaGGCCUCuugcaccaGgCUGGCCggGGaUGGGgCccgcaGcUUUCCAGCCAAgCcuaugu....GAAGCaaCagUCaAGGuAGUUGCAGUUUuaCaAAGaaacc.GagCGUUUu.
//
# STOCKHOLM 1.0

#=GF AC   RF02206
#=GF ID   WT1-AS_4
#=GF DE   WT1 antisense RNA conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   62.70
#=GF NC   51.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.67 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   2173145
#=GF RT   Tissue, developmental, and tumor-specific expression of divergent
#=GF RT   transcripts in Wilms tumor.
#=GF RA   Huang A, Campbell CE, Bonetta L, McAndrews-Hill MS, Chilton-MacNeill S,
#=GF RA   Coppes MJ, Law DJ, Feinberg AP, Yeger H, Williams BR
#=GF RL   Science. 1990;250:991-994.
#=GF RN   [2]
#=GF RM   8406502
#=GF RT   Sequence of the WT1 upstream region including the Wit-1 gene.
#=GF RA   Gessler M, Bruns GA
#=GF RL   Genomics. 1993;17:499-501.
#=GF RN   [3]
#=GF RM   17210670
#=GF RT   A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS and
#=GF RT   exhibits sequential epigenetic defects during Wilms' tumourigenesis.
#=GF RA   Hancock AL, Brown KW, Moorwood K, Moon H, Holmgren C, Mardikar SH,
#=GF RA   Dallosso AR, Klenova E, Loukinov D, Ohlsson R, Lobanenkov VV, Malik K
#=GF RL   Hum Mol Genet. 2007;16:343-354.
#=GF WK   WT1-AS
#=GF SQ   12


DQ289488.1/1032-1159      -----CUUGCAUUGCAUAAACG-UUGUCGCCAUUAAAUUCUGGCUG-CGGACCCGAAGUGUGUGCGGGCCCAGGACUUACUCGAAGG-GCGCA-------CUUCUUGGGAAUGCGCAU-CCCGUAGGCGCAGGAGACCCUGAGG
U06486.1/255-127          -----CUUGCAUUGCAUAAACGAUUGUCGCCAUUAAAUUCUGGCUG-CGGACCCGAAGUGUGUGCGGGCCCAGGACUUACUCGAAGG-GCGCA-------CUUCUUGGGAAUGCGCAU-CCCGUAGGCGCAGGAGACCCUGAGG
X77549.1/881-754          -----CUUGCAUUGCAUAAACG-UUGUCGCCAUUAAAUUCUGGCUG-CGGACCCGAAGUGUGUGCGGGCCCAGGACUUACUCGAAGG-GCGCA-------CUUCUUGGGAAUGCGCAU-CCCGUAGGCGCAGGAGACCCUGAGG
AY245105.1/357-230        -----CUUGCAUUGCAUAAACG-UUGUCGCCAUUAAAUUCUGGCUG-CGGACCCGAAGUGUGUGCGGGCCCAGGACUUACUCGAAGG-GCGCA-------CUUCUUGGGAAUGCGCAU-CCCGUAGGCGCAGGAGACCCUGAGG
AANU01216576.1/705-578    -----CUUGCAUUGCGUAAACG-UUCUCGCUAUUAAAUUCUGGCUG-CGGACCCGAAGUGUGUGCGGGUCCAGGACUUAGUCGAAGG-GCGCA-------CUUCUUGGGGAUGCGCAU-CUCGUAGGCGCAGGAGACCCUGAGG
AAQQ01112620.1/2365-2232  -----CUUGCAUGGUGUAAACA-CAACCGCUG-UAAAUUCUGGCUGAAGGAUCCGAAGUAUGUGCAGGUUCAGGAAGUCCCGUGU---GCGCGAUCCUCUUCCUCUUGGGCUGCGCAUCCCCUUAGGCACAAGAGACCUUGAGG
ABRN01427349.1/2234-2103  -----UUUCCACUACGUAAA---CGGUAGCCA-GGAGUUCUCGCUG-CGGACCAGAAGCGUGUGCCAGCUCAAGACCUACACGCUAA-GUGCAUUUCCCUCCUCUUGGGGUCGCUUGU-CUUGGAGGCGCAGGAAACCGUGAGG
ABDC01041565.1/1900-2033  -----CGUGUA-AAAAAAAAUG-CCGUCGCUG-UAAAUUCCGGUUU-CGGUCCCAAAGCGUUUGGGGGCUCGGGGCGUACCCGCGGGCUUGCAGUUCCCUCCUCUUUGGGUUGCGCAU-CCAGUGGGCGCAGCAGACCCUGAGG
AAGV020131545.1/2080-1948 -----UUUGCACUGAGUAAACC-CAGUCGCCG-UCAG-CCCAGCUG-CCGACCCCAAGCGUGUGCGGGCUCAGGACCUACACAAUGC-AAGCAAUUCUCUCCUUUCGGGAUCUCGCGG-CGGCGAGGUGCAGGAGACCCAGACC
AAFC03041825.1/2661-2535  AUUAAUUCGCACUAAGUAAA-------AGCCA-GGAGUUCUGGGUG-CGGACCCGCAGCGUGUGUG------GCACCUACACGCUAA-GUACAGGUCCUUCCUCUGGAGGUCGCUUGU-CCUGGAGGCGCAGGAAACCUUGAGG
AAGU03043695.1/2212-2078  -----AUUUCCACAAGCAAACG-CAGUCGCGG-UGAGUUCGGGCUG-ACGACCUGAAGCGUGUGCUGGUUUAGGAAACACAAGCUGGCACGCGAUUCCCCCCUUUUGGGGCAGUGGGU-CCAGGAGGCGCAGGAGACCCUGAGA
AAQR03002375.1/1927-2057  -----CUUUUGUU---UGAACU-UGCUUGCCUGUAAAUUCCGACUG-AGGUCCUAAAGCAUUUGCGGGCUCAACACCUACUUGCCAC-ACGCAACUUCCUCCU-UUGCGGCUCCUGGU-CCAGUAGGCACAGAAGACCCCGGGG
#=GC SS_cons              .....:::::::::::::::::.:::::::::.:::::::::::::.::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::.:::::::::::::::::::::::::
#=GC RF                   .....cUUgCauugaGUAAACg.cugUcGCcg.UaAaUUCuGGcUG.cGGaCCcGAAGcGUGUGcgGGcuCAGGACcUACucGcuGg.gcGCAauUCcCUCCUcUuGGGGuuGCgcgU.CccGuAGGCGCAGGAGACCcUGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF02207
#=GF ID   WT1-AS_5
#=GF DE   WT1 antisense RNA conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   89.00
#=GF NC   47.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.44 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   2173145
#=GF RT   Tissue, developmental, and tumor-specific expression of divergent
#=GF RT   transcripts in Wilms tumor.
#=GF RA   Huang A, Campbell CE, Bonetta L, McAndrews-Hill MS, Chilton-MacNeill S,
#=GF RA   Coppes MJ, Law DJ, Feinberg AP, Yeger H, Williams BR
#=GF RL   Science. 1990;250:991-994.
#=GF RN   [2]
#=GF RM   8406502
#=GF RT   Sequence of the WT1 upstream region including the Wit-1 gene.
#=GF RA   Gessler M, Bruns GA
#=GF RL   Genomics. 1993;17:499-501.
#=GF RN   [3]
#=GF RM   17210670
#=GF RT   A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS and
#=GF RT   exhibits sequential epigenetic defects during Wilms' tumourigenesis.
#=GF RA   Hancock AL, Brown KW, Moorwood K, Moon H, Holmgren C, Mardikar SH,
#=GF RA   Dallosso AR, Klenova E, Loukinov D, Ohlsson R, Lobanenkov VV, Malik K
#=GF RL   Hum Mol Genet. 2007;16:343-354.
#=GF WK   WT1-AS
#=GF SQ   4


AL049692.13/51819-51741 GGCACUUUUAGCGGGGGGAGAGGAGGUUAUCUGAAGGGA----GGCUGGCUUGAAUGUGAGUCGUUGUGUUUGUGAAACCCAG
L25110.1/3560-3638      GGCACUUUUAGCGGGGGGAGAGGAGGUUAUCUGAAGGGA----GGCUGGCUUGAAUGUGAGUCUUUGUGUUUGUGAAACCCAG
X77549.1/328-250        GGCACUUUUAGCGGGGGGAGAGGAGGUUAUCUGAAGGGA----GGCUGGCUUGAAUGUGAGUCGUUGUGUUUGUGAAACCCAG
AANU01216576.1/178-102  GGCCCUUUUAGCGGGGGGAGAGGAGGUUAUCUGAAGGGAGGGAGGCAGGCUUGAAUGUGAGUC------UUUGUGAAACCCAG
#=GC SS_cons            :::::::::::::::::::::::::::::::::::::::....::::::::::::::::::::::::::::::::::::::::
#=GC RF                 GGCaCUUUUAGCGGGGGGAGAGGAGGUUAUCUGAAGGGA....GGCuGGCUUGAAUGUGAGUCgUUGUGUUUGUGAAACCCAG
//
# STOCKHOLM 1.0

#=GF AC   RF02208
#=GF ID   WT1-AS_6
#=GF DE   WT1 antisense RNA conserved region 6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT
#=GF SS   Predicted; RNAalifold
#=GF GA   80.00
#=GF TC   83.90
#=GF NC   58.00
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 41.00 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   2173145
#=GF RT   Tissue, developmental, and tumor-specific expression of divergent
#=GF RT   transcripts in Wilms tumor.
#=GF RA   Huang A, Campbell CE, Bonetta L, McAndrews-Hill MS, Chilton-MacNeill S,
#=GF RA   Coppes MJ, Law DJ, Feinberg AP, Yeger H, Williams BR
#=GF RL   Science. 1990;250:991-994.
#=GF RN   [2]
#=GF RM   8406502
#=GF RT   Sequence of the WT1 upstream region including the Wit-1 gene.
#=GF RA   Gessler M, Bruns GA
#=GF RL   Genomics. 1993;17:499-501.
#=GF RN   [3]
#=GF RM   17210670
#=GF RT   A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS and
#=GF RT   exhibits sequential epigenetic defects during Wilms' tumourigenesis.
#=GF RA   Hancock AL, Brown KW, Moorwood K, Moon H, Holmgren C, Mardikar SH,
#=GF RA   Dallosso AR, Klenova E, Loukinov D, Ohlsson R, Lobanenkov VV, Malik K
#=GF RL   Hum Mol Genet. 2007;16:343-354.
#=GF WK   WT1-AS
#=GF SQ   19


DQ289489.1/2040-2160       CAGCCGCAACCCCAGGGACCAGUGCGCA---CGCC-UGGGC--CGCCCUCCGG-GAGUCA-CCCAGCGGCCGCGGACAACUGAAUAAACACCCCAAAGCGCUGCGGUCGGUCAAGGGCGGGGACAGCCA
DQ289490.1/1287-1407       CAGCCGCAACCCCAGGGACCAGUGCGCA---CGCC-UGGGC--CGCCCUCCGG-GAGUCA-CCCAGCGGCCGCGGACAACUGAAUAAACACCCCAAAGCGCUGCGGUCGGUCAAGGGCGGGGACAGCCA
AL049692.13/50356-50236    CAGCCGCAACCCCAGGGACCAGUGCGCA---CGCC-UGGGC--CGCCCUCCGG-GAGUCA-CCCAGCGGCCGCGGACAACUGAAUAAACACCCCAAAGCGCUGCGGUCGGUCAAGGGCGGGGACAGCCA
AANU01216577.1/1151-1271   CAGCCGCAACCCCAGGGACCAGUGCGCA---CGCC-CGGGC--CGCCCUCCGG-GAGACA-CCCUGCGGCCGUGGACAACUGAAUAAACACCCCAGAGCACUGCGAUCGGUCAAGGGCGGUGACAGCCA
ABRN01427348.1/2977-2857   CAGCCGCGGCCCCAGGGACCAGCGCGUA---CUCC-CGAGC--CGCGCUCCGG-GCGUCA-CCCCGCGGGCGCCGACAACUGAAUAAACACACCGUAGCGCUGUGAUCUGUCAAGGGUUGGGGCCGCCU
ABRP01285284.1/573-453     CAGCCGCGGCCUCAAGGGCCAGCGCGUA---CUCU-CCAGC--UUCGUUCUGG-GAGUCA-CCCCGGGGCUGCCGACAACUGAAUAAACACACCAAAGCGCUGCGAUCUGUCAAGGGCUGGGGUCGCCU
ABRR01094885.1/2428-2309   CAG-CGCGGCCCCAGGGACCAGCGCGUA---UUCC-UGAGC--UGCGCUCCGG-GCAUCA-CCCCGCGGCCGCCGACAACUGAAUAAACACACCGAAGCGCUGCGAUCUGUCAAGGGCUGGGGCCGCCG
AAQQ01112620.1/312-189     CAGCCACGGCCCCAGGGACCAACGCGCACGCCGCC-GGGGC--CGCGCUCUGG-CGGUCA-CCCGGCGGCUGCUGACAACUGAAUAAACACUCCGAAGCACUGCGAUCUGUCAAGGGCUGGGGCCGCCA
AAFC03041822.1/2192-2071   CAGCCGCGGCCCCAGGGACCAGACCGUA---CUCC-GGAGC--CGCGCUCCGG-GCGUCACCCCCGCGGCCGCCGACAACUGAAUAAACACACCGAGUCGCUGCGAUCUGUCAAGGGCUGGGGCCGCCU
ABDC01041566.1/1555-1675   CAGCCGCGGCCCAGGGGACCAGCCCGCA---CGCU-CUGGC--AGCGCUCCGG-GCGUCU-CCUCGCGGCCGCCAACAACUGAAUAAACACGCCAGAGCGCUGCGAUCUGUCAAGGGCCGGGGCUACCC
ABRQ01001649.1/4395-4276   AGGCCGCGGCCCCUGGGACCAGCGCGCA---CGCC-GGGGC--AGAGCUCUAG-GCGUCA-CCCCGAGGCCGCCGACAACUGAAUAAACAAGAUGUAGCGCUGCGAUCUGUCAAGGGCU-GGGCCGCAU
CAAA01042818.1/3877-3998   CAGCCGUGGCCCCAGGGACCGGCGCGCA---CGCC-AGGGC--CGCGCUCUGGCGGGUCA-CCCCGAGGCUGUUGACAAUUGAAUAAACACGCUGUAGCCUUGCGAUCUGUCAGUGGCUGAGGCCGCCA
ABRO01046980.1/7145-7030   CAACCGCGACUCCAGGGACCAGCGCGCA---CUUC-CCGGCCGUGCGCGCCGG-CAGUCA-CCCCGCGGCCGCGGACAACUGAAUAAACAUACCGAAGGGCAAGG-------AAGGACUGGGGCCACCA
AAIY01350831.1/805-925     AGGCCGCGGCCCCAGGGACCGGCGCGCA---CGCCGGGGGC--UGAGCUCCGG-GCGUCA-CCCCA-GGCCGCGGACAACUGAAUAAACACGCCGCCGCGCUCCGAUCUGUCAAGGGCUGGGGCCUCCU
AAYZ01200691.1/2234-2354   CAGCUCGGGCCCCAGGGACCAGAGCGCU---CGCC-CUGGC--UGCGCUUCAG-GCGUCA-CCCGGCGGCAGGCAACAACUGAAUAAACACGCUGAAGUUCUGCCGGUUCUCCCGGCCGCAGUCGUCUA
AANG01575001.1/5876-5756   CAGCCGCGGCCCCAGGGGGCAGCGCAUA---CUCC-CAGGC--UGCGCUCCGG-GCGUCA-CCCCGCGGCCGCCGACAACUGAAUAAACACACCGAAGCACUGCGAUCUGUCAAGGGCUGGGGCCGCAG
AABR05104440.1/978-857     CAGCCGUGGCCCCAGGGACCAAAGCGCA---CGCC-AGGGC--CGCGCUCUGGCGGGUCA-CCCCGAGGCUGUUGACAGUUGAAUAAACACGAUUAAGCCUUCCGAUUUGUCAGUGGCUGAAGCCGCCA
AAEX03011404.1/42848-42728 CAGCCCGGGCCCCAGGGGGCAGCGCGGA---CGCC-CAGCC--UGCGCUCCCG-GCGUCA-CCCCGAGGCCGCGCACAACUGAAUAAACACGCCGCAGCGCUGCGACCUGCCAGGAGCUGGGGCCGCAG
AAGU03043695.1/264-144     AGGCCACGGCUCCAGGGACCAGUGCGCA---CGCC-GGGGC--UGCGCUCCGG-GUGUCA-CCCCGAGGCCGCGGACAACUGAAUAAACACGCUGCAGCGCUGCGAUCUGUCAAGGGCUGGGGCCGCCU
#=GC SS_cons               ::::::::::::::::::::::::::::...::::.:::::..::::::::::.::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    CAGCCGcGGCCCCAGGGACCAGcGCGcA...CgCC.cgGGC..uGCGCUCcGG.GcGUCA.CCCcGcGGCcGcgGACAACUGAAUAAACACgCcgaAGCgCUGCGauCUGUCAaGGGCuGGGGCcgCca
//
# STOCKHOLM 1.0

#=GF AC   RF02209
#=GF ID   WT1-AS_7
#=GF DE   WT1 antisense RNA conserved region 7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   58.20
#=GF NC   45.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   2173145
#=GF RT   Tissue, developmental, and tumor-specific expression of divergent
#=GF RT   transcripts in Wilms tumor.
#=GF RA   Huang A, Campbell CE, Bonetta L, McAndrews-Hill MS, Chilton-MacNeill S,
#=GF RA   Coppes MJ, Law DJ, Feinberg AP, Yeger H, Williams BR
#=GF RL   Science. 1990;250:991-994.
#=GF RN   [2]
#=GF RM   8406502
#=GF RT   Sequence of the WT1 upstream region including the Wit-1 gene.
#=GF RA   Gessler M, Bruns GA
#=GF RL   Genomics. 1993;17:499-501.
#=GF RN   [3]
#=GF RM   17210670
#=GF RT   A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS and
#=GF RT   exhibits sequential epigenetic defects during Wilms' tumourigenesis.
#=GF RA   Hancock AL, Brown KW, Moorwood K, Moon H, Holmgren C, Mardikar SH,
#=GF RA   Dallosso AR, Klenova E, Loukinov D, Ohlsson R, Lobanenkov VV, Malik K
#=GF RL   Hum Mol Genet. 2007;16:343-354.
#=GF WK   WT1-AS
#=GF SQ   21


DQ289490.1/1917-2210       AGAUGGUCCCCGAGCUCCCCGAGAGUCCUCAGUGAAAGGA-UUCCGCGGCACUGC-CUCUAUUAUUAUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUGGAGGCCAGGCCGUGGCCAGAGCAGAUAC-GUAGGCCCAUGAAAUUGAUGAACUGAGAG--UUGCUUCCAGUCCUGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
AL049692.13/49726-49433    AGAUGGUCCCCGAGCUCCCCGAGAGUCCUCAGUGAAAGGA-UUCCGCGGCACUGC-CUCUAUUAUUAUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUGGAGGCCAGGCCGUGGCCAGAGCAGAUAC-GUAGGCCCAUGAAAUUGAUGAACUGAGAG--UUGCUUCCAGUCCUGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
U82757.1/25966-25684       -----------GAGCUCCCCGAGAGUCCUCAGUGAAAGGA-UUCCGCGGCACUGC-CUCUAUUAUUAUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUGGAGGCCAGGCCGUGGCCAGAGCAGAUAC-GUAGGCCCAUGAAAUUGAUGAACUGAGAG--UUGCUUCCAGUCCUGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
ABRN01427348.1/2380-2087   AGAUGGUCUCCGAGCUCCGAGAGAGUCCCCAAAGAAAGGA-UUGCGCGGCGCUGC-CUCUAUUAUUAUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACGGUGGGGAUGGAGGCCGGGCUGUGGCCAGAGGAGAUAC-GCAGGCCCAUGAAAUUGAUGAGCUGAGAG--UUGCUUCCAGUCCUGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUACUGACCCCAGAUUCAACUUUGCAAACAAC
AAIY01350831.1/1406-1699   AGAUGGUCCCCAAGCUCCCAGAGAGUCCCCAGUGAAAGGA-CUCCACAGCGCUGC-CCCUAUUAUUAUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUGGAGGCCGGGAUGUGGCCGGAGCAGAUAC-AUAGGCCCAUGAAAUUGAUGAACUGAGAG--UUGCUUCCAGUCCUGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAAAUUCAACUUUGCAAACGAG
AAGV020131544.1/3530-3239  AGAUGGUUCUCGAGCUCCCA--GAGUCCCCAAUGAAAGGA-UUCCGCAGUUCCGU-CUCUAUUAUUAUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGCUGGAGGCCGGGCCGUAGCCAGAGCAGAUAC-AUAGGCCCAUGAAAUUGAUGAACUGAGAG--UUGCUUCUAGUCCUGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
ABRO01046980.1/6508-6226   AGAUGGUCCCCGA-----------GUCCCCAAUGAAAGGA-UUCCGCAGCGAGGC-CUCUAUUAUUAUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUAGAGGCCAGGCCGUGGCCAGAGCAGAUAC-GUAGGCCCAUGAAAUUGAUGAACUGAGAG--UUGCUUCCAGUCCUGGGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
AAYZ01200691.1/2847-3133   AGAUGGUCCCUGAG---------AGUCCCCAGCGACAGGA-UCCCGCAGCACUGC-UUCUAUUAUGAUAUCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUGGCGGCCAGGCCGUGGCCAGAGCAGAUAC-GGAGGCCCAUGAAAUUGAUGAACUGAGAGACUUGCUUCCAGUCCUGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
AAFC03041822.1/1604-1317   ---UGAUGCC---ACCGCGAGAGGGUCCCCAAUGAGAGGA-UUCCGCAGCGCUGC-CUCUAUUAUUAUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUGGAGGCCGGGCCGUGGCCAGAGCAGAUAC-GCAGGCCUAUGAAAUUGAUGAGCUGAGAG--UUGCUUCUAGUCCUGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
AAWR02018627.1/3176-3468   AGAUGGUCCCCGAGCUCCCACAGAGUCCCCGGUGAAAGGA-CGCUGCAGCGCCGC-CUCUAUUACGAUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUGGAGGCCGGGCCGUGGCCGGAGCAGAUAC--UCGGCCCAUGAAAUUGAUGAACUGAGAG--CUGCUUCCAGUCCCGGGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUCUGCAGACAAC
ABRQ01001649.1/3785-3493   AGAUGGUCCCCAAGCACCCAAAGAGUCCCCAUUGAAAGAA-C-CCUCGGUGCCGC-CUCUACGAUUAUACCGUAAAUCUGCUUAAAUUCUGGAACUAAUUAUACAGAGGAUAUGUCUCAAUUUGUUCUGCACUAAUGCCACAGCGGGACUGGAGGCCUGGCCAUGGCCAGAGCAGAUAC-GUAGGCCCAUGAAAUUGAUGAACUGAGAG--UUGUUUCCAGUCCUGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACACC
AAKN02048412.1/2848-3138   GGGUGAGCGCCUGCCCGCCU--GGAGUCGCAUUGAGAGGA-UUCCACUACGCUGC-CUCUAUUAUUAUACCGUAAAUCUCUUUAAAUUCUGGAACUAAUUACGUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUGAUGCCGCAGCGGGGACGGGGGCCAGGCCAUGGCU-GCUCAGAUAC-AUGGGCCCAUGAAAUUGAUGAACUGAGAG--CUGCUUCCAGCCCUGCGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
AAFR03017974.1/13339-13632 AGACGUUCCCGGGUCCCGGGGAGAAACCCUAAAUAAAAGAAUCAGGCAGAGUC-CAGGCUAUUAUUUUACCGUAAAUCU-UGUAAAUUCUGGAACUAAUUACAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACUUUGGGAAUGGAGUCGAGGCCAUAACCAGAACAGAUCC-UCCAGCUCGUGAAAUUGAUGAACUGAGAG--CUGCUUCCAGUCCUGAACA--CGCCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAAAUUCAACUUUGCAAAGAAC
ABQO010577855.1/566-860    GAAAGUUCCCAGGUCCCCUGGAGAAGCCCUAAAUAAAAGAAUCCGGCAGAGUC-CAAGCUAUUAUUUUACCGUAAAUCU-UGUAAAUUCUGGAACUAAUUACAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUUAUGCCACAUUGGGAAUGGAGUCGGGGCCGUAACCAGAACAGAUCCCUCCAGCUCGUGAAAUUGAUGAACUGAGAG--CUGCUUCCAGUCCUGGACA--CGCCAUCUGGAAUUCCAGUCUGAGACUACA-AUUAGAACUCCUGACCCCGGAUUCAACUCUGCAAAGAAG
AAPN01115953.1/1683-1391   GGUAGCAAUCGGG-CCCGAGGAGAAGCUCCGCAUCAAAGCCUUCGGUGGAGUUGCGCGCUAUUAUUUUACCGUAAAUCU-UUUAAAUUCUGGAACUAAUUACCUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAUUGGGGAUGGAGCCGGGGCCACAACCAGAGCAGAAUC-UCGAGUCCACCAAAUUGAUGAGCUGAGAG--UUGCU-CCAGCCCCGAGCC--CGCCAUCUGGAAUUCCUGUCUGAGGUUACA-GCUACAACUCUUGACCCCUCAUUCAACUUUGCAACGAAC
AAVX01033539.1/1934-2217   ----AAACUCUCACUUUGUG------AACCAUGAAACGGCCUUGUAUGGU-CCACUGAACAGUCUUUCUCGUUAAAUCU-CUAUGAUUCUGGAACCAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUCCAUUAAUGCCACAUUGGG-AUGUGAGGC-GUCCCUACCCGGAGCAGAUAUUCCAAGCACAUGAAAUUGAUGAACUGAGAC--CUACUACUAGUCCUGACUU--UACCAUCUGGAAUUCCAGACUGAGGUUACAGAAAAGAGCUUUUGACCCAAGAUUCAACUUUCACAAGUAC
AC146873.3/58290-58566     AGUUUCACCUUCAACUUGAGC-CAAAAAGAAUGAAGCGGUUAUUUGUAGC-CCACU--CUAUUAUUUUACCGUAAAUCU-UCUAAAUUCUGGAACUAAUUACACCGAGGAUAUGUCUCAAUUUGUUCUGCUUUAAUGCCGCAGUCGG-A---------GCCACCACC-AGACCUGAU-UCUCAGCAUCAUGAAAUUGAUGAAGUGAGAC--UUGCGG--AGUCCUAAAUA---ACCGUGCGGAAUUCCAGACUGGGGUUACC-AGGAGAGGCGCUGACCCCAUCCUCAACUUCCCUGGGAGC
AANG01575001.1/5234-4943   UGAUGGUCCCCAAGCUCCCA--GAGUCCCCAUUGGAAGGA-UUCCGCAGCGCUGC-CUCUAUUAUUAUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUGGAGGCCGGGCCGUGGCCAGAGCAGAUAC-GUAGGCCCAUGAAAUUGAUGAACUGAGAG--UUGCUCGCAGUCCUCAGCG--CACCAUCUGGAAUUCUAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
AANN01446529.1/371-665     AGAUGGUCCCGAG-CUCCCA--GAGUCCCCAGUAAAAGGA-UUCCGCCGCCCUGC-CUCUAUUAUUGUGCCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUAGAGGCCGGGCCGUGGCCAGAGCAGAUAC-GUAGGCCCAUGAAAUUGAUGAACUGAGAGAGUUGCUUCCAGUCCUGAGCGCACACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
AABR05104440.1/330-37      CACGGGUUCCCCAGCUCCCCAAGAGCCCCCAAUGAAAGGA-UUCAGCAGCGCUGC-UUCUAUUAUUAUCCCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACAGUGGGGAUGGAGACCAGGCCGUGGCCAGAGCAGAUAU-GGAAGCCCAUGAAAUUGAUGAACUGAGAG--UUGCUUCCAGUCCAGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUAGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAG
AAGW02037545.1/4117-4401   AGAUGGUCCCCGGG---------AGUCCCCGGUGAAAGGAUUUCCGCAGCGCUGC-CUCUAUUAUUGUACCGUAAAUCUUUUUAAAUUCUGGAACUAAUUAUAUAGAGGAUAUGUCUCAAUUUGUUCUGCAUUAAUGCCACGGUGAGGAUGGCGGCCAGGCGGUGGCCAGAGCAGAUAC-G-AGGCCCAUGAAAUUGAUGAACUGAGAG--UUGCUUCCAGUCCUGAGCG--CACCAUCUGGAAUUCCAGUCUGAGGUUACA-AUUGGAACUCCUGACCCCAGAUUCAACUUUGCAAACAAC
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::.::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::..:::::::::::::::::::..::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::
#=GC RF                    aGauGguccCcgagCucccggAGAguccccAuugaaaGGa.uuccGcaGcgcuGC.cuCUAuUAUUaUaCCGUAAAUCUuUuUAAAUUCUGGAACUAAUUAuaUaGAGGAUAUGUCUCAAUUUGUUCUGCAUUaAUGCCaCagUGGGGAUGGaGgCcgGgCcgUggCCaGAgCAGAUac.guaGGccCAUGAAAUUGAUGAACUGAGAG..uUGCUuCcAGUCCUGagcg..CaCCAUCUGGAAUUCCAGuCUGAGGUUACa.AuuAGAaCUcCUGACCCCagaUUCAACUUUGCaAacaaC
//
# STOCKHOLM 1.0

#=GF AC   RF02210
#=GF ID   WT1-AS_8
#=GF DE   WT1 antisense RNA conserved region 8
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   70.00
#=GF TC   80.40
#=GF NC   58.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 48.44 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   2173145
#=GF RT   Tissue, developmental, and tumor-specific expression of divergent
#=GF RT   transcripts in Wilms tumor.
#=GF RA   Huang A, Campbell CE, Bonetta L, McAndrews-Hill MS, Chilton-MacNeill S,
#=GF RA   Coppes MJ, Law DJ, Feinberg AP, Yeger H, Williams BR
#=GF RL   Science. 1990;250:991-994.
#=GF RN   [2]
#=GF RM   8406502
#=GF RT   Sequence of the WT1 upstream region including the Wit-1 gene.
#=GF RA   Gessler M, Bruns GA
#=GF RL   Genomics. 1993;17:499-501.
#=GF RN   [3]
#=GF RM   17210670
#=GF RT   A CTCF-binding silencer regulates the imprinted genes AWT1 and WT1-AS and
#=GF RT   exhibits sequential epigenetic defects during Wilms' tumourigenesis.
#=GF RA   Hancock AL, Brown KW, Moorwood K, Moon H, Holmgren C, Mardikar SH,
#=GF RA   Dallosso AR, Klenova E, Loukinov D, Ohlsson R, Lobanenkov VV, Malik K
#=GF RL   Hum Mol Genet. 2007;16:343-354.
#=GF WK   WT1-AS
#=GF SQ   24


AL049692.13/49333-49059    ACACAAUCUUAAAAUCUUUCC-GUCUUAGACAAUU-CUUUCCAAGUAUUUCUUU-UGUGU-------------UUUUUAACCUAUAAAAGA-----UAAUGGAAU--GUUUUAUAGACUGGAUUUU-AUCUCAUCCCCUUUCCCUCUC-CCAACUGCCCUCAGUUU-AAUAGUUGUCAG------------------UUUUACCUCA-----------------GUGUUGAAUUUAAUUAUAUAGGAACAAAAUA--UUCCU---CAGUAA-AUUUGCUUG--CUAAAUAUUCU-GUCACAU-----UU---ACUUCC-CCUUUGAGAAAUGGCUUAAUUAUAGAAAUCUACCU
U82757.1/25583-25309       ACACAAUCUUAAAAUCUUUCC-GUCUUAGACAAUU-CUUUCCAAGUAUUUCUUU-UGUGU-------------UUUUUAACCUAUAAAAGA-----UAAUGGAAU--GUUUUAUAGACUGGAUUUU-AUCUCAUCCCCUUUCCCUCUC-CCAACUGCCCUCAGUUU-AAUAGUUGUCAG------------------UUUUACCUCA-----------------GUGUUGAAUUUAAUUAUAUAGGAACAAAAUA--UUCCU---CAGUAA-AUUUGCUUG--CUAAAUAUUCU-GUCACAU-----UU---ACUUCC-CCUUUGAGAAAUGGCUUAAUUAUAGAAAUCUACCU
ABDC01041566.1/2489-2781   ACACAAUCUUAAAAUCUUUCC-AUCUUAGAAAAUU-CAUUCCAAGUAUUUCUUU-UGUGUGUGUGUGUGUGUUUUUUUUGCCUAUAAAAGA-----UAAUGGAAUAUGUUUUAUAGACUGGAUUUU-AUCUCAUCCCCCUUCCCUCUC-CGGACUGCACUCUGUUU-AAUAGUUGUCAG------------------UUUUUCUUCA-----------------GUGUUGAAUUUAAUUAUAUAGGAACAAAAUA--UUCCU---CAGUAA-AAUAGCUUG--CUAAAUAUUCU-GCAACGU-----UUGUGAUUUCC-CGUUUGAGAAAUAGCUUAAUUACAGAAAUCUACCU
AAPY01606771.1/1008-729    ACACAAUCUUAAAAUCUCCCC-AUUUUAGAAAUGU-CUUUCCAAGUAUUUCUUU-UGUGU------------UUUCUUAACCUAUAAAACA-----UAAUGGAAUAUAUUUUAUGGAGUGUAUUUU-AUCUCAUCCCCUUUCUCCCUC-CGGACUGCACUCAGUUU-AAGAGUUGUCAG------------------UUUUUCCUCA-----------------GAGUUCAAUUUAAUUAUAUGGGACCAAAAUA---UCCA--UCAGUUA-AUUAGCUUG--CUAAAUAUUCU-GUCACUU-----UUGUGAUUUCC-C-UUUGAGAAAUAGCUUAAUUACAGAAAUCUACCU
ABRN01427348.1/1982-1704   GCACAACCUUAAAAUCUUUCC-AUCUUAGAAGAUU-CUUUCCAAGUAUUUCUUU-UGUGU------------UUUUUAAACCUAUAAAAGA-----UAAUGGAAUAUAUUUUAUAGAUUGGAUUUU-AUCUUAUCCCCUUUCCCUCUC-CCGAGUGCACUCAGUUU-AACUGUUGUCAG------------------UUUUUACUCA-----------------GUGUUGGAUUUAAUUAUGUAGGACCAAAACA--UUCCU---CAGUAA-AUUAGCUUG--CUAAAUAUU---GUUACUU-----UUGUGAUUCUG-CCUUUGAGAAACAGCUUAAUUACUGAAAUCUAUCU
ABRR01094885.1/1447-1171   ACACAAUCAUAAAAUCUUCCC-ACCUUAAAAGAUC-UUUUCCAAGUAUUUCUUU-UGUGU-------------UUUUUAACCUAUAAAAGA-----UAAUGGAAUAUAUUUUAUAGAUUGGAUUUU-ACCUUAUCCCCUUUCCUUCUC-CCAACUGCACUCAGCUU-AAUAAUUGU--G------------------UUUUUCCUCA-----------------GUGUUGAAUUUAAUUAUAUAGGACCAAAACA--UACCU---CAGUAA-AUUAGCUUG--CUAAAUAUUCU-UUCACUU-----U-GUGAUUCUG-CCUUUGAGAAACACCUUAAUUACAGAAAUCUAUCU
AAWR02018627.1/3545-3821   ACACAAUCUUAAAAUCU-----AUCUUAGAGAAUU-CUUUCCAAGUAUUUCUUC-UGUGU------------UUUUUUAACCUGUAAAAGA-----UAAUGGAAUAUAUUUUAUAGACUGGAUCUU-AUCUUAUCUCUUUUUCCUCUC-CUGACUGCACUCAGUUU-AAUAGUUGUCAG------------------UUUUUCCUCA-----------------GUGUUGGAUUUAAUUAUGUAGGACCAAAAGA--UUCCU---CAGUAA-AUUAGAUUG--CUGAAUAUUCU-GUUGUUU-----GUGUGAUUUCG-CCUUUGAGAAACAGCUUAAUUACAGAAAUUUAUCU
ABRT010557018.1/755-485    ACACAAUCUUA--GUCUUUCC-AUCUUAAAGGAUU-CCUUCCAAGUAUUUCUUU-UGUGC-------------UUUUUAACCUAUAAAAGA-----UAAUGGAAUAUGCUUUAUAGACUGGAUUUU-AUCUCGU------UCCCUCUC-CCAACUGCACUCAGUUU-AAUAGUUGUCAG------------------UAUUUCCUCC-----------------GUGUUGAAUUUAAUUAUAUAGGAACAAAAAA--AUUUC--UCAGUGA-AUUAGCCUG--CUACAUCUUCU-C--ACAU-----UUGUCAUUUCC-CCUUUGAGAAAUAGCUUCAUUACCGAAAGCUACCU
AAFC03041822.1/1217-946    ACACAAUCUUAAAAUCUUCUC-AUCUUAGAAGAUU-CUUUCCAAGAAUUUCUUU-U----------------------AACCUAUAAAAGA-----UAAUGGAAUAUAUUUUAUAGAUUGGAUUUU-AUCUUAUCCCCUUUCCAUCUC-CAGGCUGCACUCGAUUUUAAUAGUUGUCAG------------------UUUUCCCUCA-----------------AUGUUGGAUUUAAUUAUAUAGGAACAAAACU--UUCCU---UAGUAA-AUUAGCUUG--CUAAAUAUUCU-GUCACUU-----UUGUGAUUCUG-CCUUUGAGAAAUAGCUUAAUUACGGAAAUCUAUCU
AAGV020131544.1/3173-2900  ACACAAUCUUAAAAUCUUGUCCAUCUUAGAAAAUUUCUUUCCAAGUAUUUCUUU-UGC---------------UUU-------UUAAAAAAACUUAUAAA--AAU--AUUUUAUAGACCGAAUUUU-AUCUCCUCCCCCUUCCCUCUC-CCGGCUGCUCUCAGUUU-AAUAGUUAUCAG------------------UUUUCCCUCA-----------------GUGUUGGGUUUAAUUAUGUAGGACCAAAAUA--UUCCC---CAGUAA-AUUAGCUUG--CUAAAUAUUCU-GUCACUA-----UUGUGAUUACC-CCUUAGAGAAAUAGCUUAAUUACACAAAUCCUAUU
ABRO01046980.1/6119-5842   AAGGAAGGGGGAAAUCCCGAU-GUCUUAGAAAUUU-CUUUCCAAGUAUUUCGUU-UGUGU-------------UUUUUAACCUAUAAAAGA-----UAAUGGAAUGUAUUUUAUAGGCUGGAUUUU-AUCUUGUCUCCUUUCACUCUU-CUGACUGCACUCGGUUU-UGUAAUUGUCAU------------------UUUCCCCUCA-----------------GCGUUGGGUUUGAUUAUAUAGGACCAAAACA--AUCCU---CAGUAA-AUUAGUUUG--AUAAGUAUU---GCCACUC-----UCAUGAUGUCC-UUUUUGAUAAAUAGCUUAAUUAUAGAAAUCUACCU
AAIY01350831.1/1775-2058   CCACAAUCUUAAAAUCGUUUC-AUCUUAGAAAAUG-CUCUACAAGUAUUUCUUU-GGUGGUU---------GUUUUUUAACCUAUAAAAGA-----UAAUGGAAUACAUUUUAUAGACUGGAUUUU-AUCU-GUUCCCUUGGCCUCUC-CUGGCUGUACUCAGUUU-AAUAGUCGUCAG------------------UUUUUCUCC------------------GUGUUGGAUUUAAUUAUGUAGGUCCAAACUA--UUCCCCCCCAGUAG-GUUAGCUUG--CUAAAUAUUCU-GUCACUU-----UUGCGAUCCCA-UCGCU-AGAAAUAGCUUAAUUUAAAAAAUCUGCCA
AAQQ01112619.1/3104-2826   ACACAAUCUUAAAGUGUUUCC-AUCUUAGAAAAAU-CUUUUCAAGUAUUUCUUU-UGUGU-------------UUUUUAACCUAUAAAAAAGA-GAUGAUGGAAUAUAUUUUGUAAACUGAAUUUU-GUCUUACUCCUUUUCACUCUC-CCAACUGCAAU----UU-AAUAGUUGUCAG------------------AUUUCCCUGA-----------------GCAUUGGAUUUAAGUAUAUAGAACCCAGAUA--UUCCU---CAGUAA-AUUAGUUUG--CUAACUACUUU-GUCACUU-----UUGUGAUUUCA-CAUUUGAGAAAUAGGUUAAU-ACAGAAAUCUACCU
ABVD01084531.1/907-630     ACACAAUCUUAAAAUCUUUUCCAUCUUAGAAAAAU-UUUUCCAAGUAUU-CUUU-UGCUUU-----------UAUUAAAACUUAUAAAAGA-----UAACGGAAUGUAUUUUAUAGACUGGAUAUU-AUCUACUCCCCCUUCCUCCUC-CAGGCUGCUCUCAGUUU-AGUAGUUAUCAG------------------UUUUU----A-----------------CUGUUAGAUUUAAUUAUGCAGUAUCAAAAUA--UUCCC---UAGUAA-AUUAGCUUG--CUGAAUAUUCU-GUCACUA-----UUAUGUUUACC-CCUUUGAUAAAUAGCUUAAUUACAGAAAACUAUUU
AAKN02048412.1/3220-3489   ACACGAUCUUAAAAUCUGUCC-AUCUUAGCAAAUU-CUUUCCAAGUGUUUCUUU-UGUGU-------------UUU-UAACCUAUAAAAGA-----UAAUGGAGUAUAUUUUAUAGGCUGGGUUUU-AUCUCAUCCCCUUU------C-CCAACUGCACUCGGC------ACUUGUCAG------------------CUUUCUCUUG-----------------GCCUUGGAUUUAAUUACACAGAACCAAAACA--UUCCC---CAGUAG-AUUAGCUCG--CUAAAUAUUUUUGGCACUU-----CUAUGGUUUCCCCCCUUGAGAAUUGGAUUAAUCCCGGAUAUCUACCU
ABRQ01001649.1/3410-3139   ACACAAUCUUAAAAUCUUUUC-AUAUUAGAAAAUU--UCUACAAGCUUUUUUUC-AAU----------------------CCUAUAAAAAA----ACAAAGGAAUCUAUUUUAUGGACUGGAUUGU-AUCUCGUUCCUUUUCCCUCUC-CCGGCUGCACGCAGUUU-AAUAGUUGUCAG------------------UUUUUCUGAA-----------------GUGGUAGAUUUAACAAUAUAAGACCUAAAUA--UUUCU--CCAGUAG-AUUAGCUUG--UUAAAUAUUCU-GUCACUU-----UUGCGAUUCCU-UCCUUGAGAAAUAGCUUAAUUACAGGAAUCUGUCU
AAYZ01200691.1/3226-3489   ACAAAAUCUUAGCAUCUUUCC-UCCUUAGAAAAUU-CUUUCCGACUAUUUCUGU-U-----------------UUUUUAAUCUUUGAAAGA-----UAAUGGAAGAUGUUUUCUAUACUGGCAUUU-AUGUCAUCCCCUCUACCACUC-AUAAAAGCAUUCAGCUU-GAUAACUGCCUG------------------CUAUUUCUCA-----------------GUGUUGGAUUUAAUUA-AUAGGACUGAAAUC--UUCCA---CAGUGA-AUUCGUGGG--CUAAAUAUUCU-GUCAUCU-----UCAUAGUUCCGCUCUUUGAGAAA----------AAAAAAAUU--CCU
AANN01446529.1/759-1026    ACACAAUCUUAAAAUCUU---------AGAAGGUU-CUUUCUAAAUAUUUAUUU-UGA---------------UUUUUAAUCUAUAAAGA------UAAUGGAAUGUGUUUAUUAGACUGAAUUUU-AUCUUAUCCUCUUU----CUC-CCAAGUGUACUC---UU-AAUAGUUGUCAG------------------UUUUCCCUCA-----------------GUGUUGGAUUUAAUUAAACAGGACUAAAAUA--CUUCU---CAGUAAUACUACUCUG-GCUAAAUAU-CU-GUCACUAAAUAGUUGUGGUUCUG-ACUGUAAGAAGCAGCUUAAUUACAAAAAUCUUAUU
AALT01228987.1/920-651     UCACAAUCUUAAAAUUUUUUCCAUCUUCGAGGAUU-CUAGCCAAGUAUCUCUUU-UGUGU------------GUGUUUAACGUAUACAAUA-----UAAUGGAAUAGAUUUUAUAGACUGGAUUUUUAUCAUAUUCCCCUUUUCCCUCUCUUGUACUAUUUGCUAU-AAUAGUUGUCAG------------------UUUUUCUUUA-----------------GUGUUGGAUUUAA-----UGAGAUCAAAAUA--UU------CAGUAA-AUUA-UUUG--CUAAAUGUUAU-GU----------UUGAGAUUCCA-UCUUUAAGAAACAACUUAAUCAUAAAAAUCUAUCU
AL512584.13/81330-81071    ACAGAGACUUUA-AUCUUCUC-ACCUUAGAAAAUU-CUUUCAAAGUAUUUGUGUUUUUAU------------GUUUUUAACCUAGAAAUGA-----U-----AACAUCCUUUAUAGGCAGGGCUUC-AUCUCAUCCC---CCUCACUC-CUGGCUACACUC--------CGG--GUCAC------------------UUUUCUGUCA-----------------ACACUGGAAUUAAUUAAAUAUGAAUGAAUUA--UUCCU---CAGAAA-ACUAGCUAAAUCUAAAUAU------CACUU-----U-GUGAUUUCC-CUUUUGAUAAGUAGUGUAACUGCAGAACAUUAUAU
ACBE01540146.1/10195-9896  ACACAAUCUUAAAAUCUUCCC-AGCUUAGAAGAUU-CUUUCCAAGUAU-UCUUU-UGUGUU----------UUUUUUUAACCUAUAAAAGA-----UAAUGGAAUAUAUUUUAUAGACUGGAUUUU-AUCUUAUCCC-UUUCUCUCUC-CCGGCUGCACUCAGUUU-AAUAGUUGUCAGGGCUUUUUUUCCCCCGUGUUUUUCCUAA-----------------GUGUUGGAUUUAAUUAUAUGGGACCAAAAUAUAUACCU---CAGUAA-AUUAGCUUG--CUAAAUAUUCU-GUCAUUU-----U-GUGAUUCUG-CCUUUGAGAAGCAGCUUAAUUACAGAAAUCUAUCU
AAPE02023626.1/4980-5259   ACAUAAUCUUAAAAUCUUUCC-AUCUUAGAAAACU-CUUUCCAAGUAUUUUUGUGUGUGU------------GUUUUUAACCUAUAAAAGA-----UAAUGGAACAUAUUUUAUAGACUGGAUUUU-AUCUUAUCCCCUUUCCCUCUC-CCAACUGCACUCAAUUU-AAUAGUUGUCAG------------------UUUCUCCUCG-----------------GUGUUGGAUUUAAUUAAAUAGGACCGAAAUA--UUCUU---CAGUAA-AGUAGUUUG--CUGAAUAUU---GUCACUU-----UUGUUAUUCUG-CCUUUGAGAAACAGCUCAAUUACAGAAAUCUAUGU
AAEX03011404.1/41773-41478 ACACUAUCUUAAAAUCUUUCC-AUCUUAGACGAUU-CUUUCCAAGUAU-UCUUU-UGAGUU-----------UUCUUUAACCUAUAAAAGA-----UAAUGGAAUAUCUUUUAUAGAUUGGAUUUU-AUCUUAUCCC-UUUCCCUCUC-CCGAUUGCACUCAGUUU-AAUAGUUGUCAG------------------UUUUUUCUCACAGUGUUUUUUUGUUACGUGUUGGAUUUAAUUAUAUGGAACCAAAAUA--UUCCU---CAGGAA-AUUAGCUUG--CUAAAUAUUCU-GUCAUUU-----U-GUGAUUCUG-CUUUUGAGAAACAGCUUAAUUACAGAAAUCUAUCU
AAGW02037545.1/4519-4797   ACACAAUCUUAAAAUUUUUCC----UUAGAAAAUU-UUUUCCAACUAUUUCUUU-UGUGUGU---------UUUUUUUAACCUAUAAAAGA-----UAAUAGAAUAUCUUUUAUGGACUGGAUUUUUAUCUCAUCCC-UCUGCCUCUC---AAAGGCACUCAGUUU-AAUAGUUGCCUA------------------UUAUUUCUCA-----------------GCGUUGGAUUUAAUUA-AUAGGACCAAAAUG--UUCCA---CAGUGA-AUUCGUUUG--CUAAACAUUCU-GUCACUU-----CUGUGAUUUCUGCCUUUGAGAAAUUGCUUCAUUACAGAAAUCUAUCU
#=GC SS_cons               :::::::::::::::::::::.:::::::::::::.::::::::::::::::::.:::::............:::::::::::::::::::.....::::::::::::::::::::::::::::::.:::::::::::::::::::::.:::::::::::::::::.::::::::::::..................::::::::::.................:::::::::::::::::::::::::::::::..:::::...::::::.:::::::::..:::::::::::.:::::::.....:::::::::::.:::::::::::::::::::::::::::::::::::
#=GC RF                    aCAcAAUCUUAAAAUCUUucC.auCUUAGAaaaUU.CUUUCCAAGUAUUUcUUU.UGuGU............uUUUUUAACCUAUAAAagA.....UAAUGGAAUaUaUUUUaUAGACUGGaUUUU.AUCUuaUCCCCUUUccCuCUC.CcgacUGCaCUCaGUUU.aAUAGUUGUCAG..................UUUUuccUca.................GuGUUGGAUUUAAUUAuaUaGGAcCaAAaua..UUCCu...CAGUaA.AuUaGcUuG..CUAAAUAUUcU.GUCACuu.....UUGUGaUUucg.ccUUUGAGAAauaGcUUAAUUacaGAAAUCUaucU
//
# STOCKHOLM 1.0

#=GF AC   RF02211
#=GF ID   ZFAT-AS1_1
#=GF DE   ZFAT antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   83.10
#=GF NC   37.10
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.30 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   15294872
#=GF RT   SNPs in the promoter of a B cell-specific antisense transcript, SAS-ZFAT,
#=GF RT   determine susceptibility to autoimmune thyroid disease.
#=GF RA   Shirasawa S, Harada H, Furugaki K, Akamizu T, Ishikawa N, Ito K, Ito K,
#=GF RA   Tamai H, Kuma K, Kubota S, Hiratani H, Tsuchiya T, Baba I, Ishikawa M,
#=GF RA   Tanaka M, Sakai K, Aoki M, Yamamoto K, Sasazuki T
#=GF RL   Hum Mol Genet. 2004;13:2221-2231.
#=GF WK   ZFAT-AS1
#=GF SQ   3


AB167741.1/4942-4864       GAGACCUACCAAGAACCAUGUGGUUGCUGUUAAUGACCAACUACAACAAAAUGGGCAACCCCAGGCAGUGGUGAGAAUG
AB167742.1/1-79            GAGACCUACCAAGAACCAUGUGGUUGCUGUUAAUGACCAACUACAACAAAAUGGGCAACCCCAGGCAGUGGUGAGAAUG
AANU01107532.1/43791-43713 GAGACCUACCAAGAACCAUGUGGUUGAUGUUAAUGACCAACUACAACAAAAUGAGCAGCCCCGGGCAGUGGUGAGAAUG
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GAGACCUACCAAGAACCAUGUGGUUGcUGUUAAUGACCAACUACAACAAAAUGgGCAaCCCCaGGCAGUGGUGAGAAUG
//
# STOCKHOLM 1.0

#=GF AC   RF02212
#=GF ID   ZFAT-AS1_2
#=GF DE   ZFAT antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   70.00
#=GF TC   72.30
#=GF NC   44.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.81 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   15294872
#=GF RT   SNPs in the promoter of a B cell-specific antisense transcript, SAS-ZFAT,
#=GF RT   determine susceptibility to autoimmune thyroid disease.
#=GF RA   Shirasawa S, Harada H, Furugaki K, Akamizu T, Ishikawa N, Ito K, Ito K,
#=GF RA   Tamai H, Kuma K, Kubota S, Hiratani H, Tsuchiya T, Baba I, Ishikawa M,
#=GF RA   Tanaka M, Sakai K, Aoki M, Yamamoto K, Sasazuki T
#=GF RL   Hum Mol Genet. 2004;13:2221-2231.
#=GF WK   ZFAT-AS1
#=GF SQ   11


AB167742.1/248-448         CAGCAGCUGUUCCUUCCCUUUCCCCCAACAUGUAUUUCCCCAGAUGCCAUCCUACAUGUUCACAUUGAAGAGAUAAGCCUCUCAGAAGGAAGAU----AACCA----------------------UAGAAAGUUGAAAAGAGAAACCUCUUUAGAUGCUGGUUUAUUAAGAAGAAUGAAGGCAGAUGUGACUGGGGCCAAAG---AUCUCAGUGCACAUUCCUGACACUC
AB167741.1/4695-4495       CAGCAGCUGUUCCUUCCCUUUCCCCCAACAUGUAUUUCCCCAGAUGCCAUCCUACAUGUUCACAUUGAAGAGAUAAGCCUCUCAGAAGGAAGAU----AACCA----------------------UAGAAAGUUGAAAAGAGAAACCUCUUUAGAUGCUGGUUUAUUAAGAAGAAUGAAGGCAGAUGUGACUGGGGCCAAAG---AUCUCAGUGCACAUUCCUGACACUC
AANU01107532.1/42931-42727 CAGCAGCUGUUCCUUCCCUUUCCCCCAACAUGUAUUUCCCCAGAUGCCAUCCUACAUGUUCACACUGAAGAGAUAAGCCUCUCAGUAGGAAGAUUCAUAACCA----------------------CAUAAAGUUGAAAAGAGAAACCUCUUUAAAUGCUGGUUUACUAAGAAGAAUGAAGGCAGAUGAGACUGGGGCCAAAG---AUCUCUGCACACCUUCCUGACACUC
ABDC01016599.1/2251-2453   CAGCAGCUGUCUCUUCUCUUUCUCCCAACACAUACUUCCC-AGAUGCCUUCAGAAGUGUUGAUAAGGAAUAGAUAAGCCUCUCCUAAGGCUUAU-CAAAACCA----------------------UGGAAAGUUGAAAAGAGAAACUUCCUUAAAUGCCAGUUUAUUAAGAAGAACGAAAGUGUAUGAAAUCAGGAUCAAAG---AUCUCAGCGCACAUUCCUGGCACUG
AAWR02021640.1/65408-65612 CAGCAACCGUUACUUCCCUUUCCCCCAACACACAUUCCCCUGGGUAUCCUCUCAAGUGUCGAUAUCGAAGAGAUAAGCCUCUUUGAAAAAAGAUUCAUAGCUA----------------------UAGAAAGAUGAAAAGAGAAGCUUCUUAAAACACCAGUUUAUCAAGAAAAAUGAAAGCAUGUGAAAUUGGGGCUGAAG---GUCUUAGAGCAUGUCCCUGACACUC
ABRP01197930.1/3738-3940   CAGCAACUGCUACUUUCCUUUCUCCCAACACACGCUUCCUUGGACGCCUUCUCAAACAUCAAUACUGAAGAGAGA-GCCUCUUUGAAGGAAGACCCAUAACCA----------------------CAGAAAGUUGAAAAGGAAAAGCUCUUUCGGUGCCAGAUUACCAAGAAAAAUAAAAGCCUAUGGAAUUGGG-CUGAAG---AUCUCAGAGCACGUCCCCCACGCUC
AANG01749074.1/2150-2349   CAGAAACCGUUCCUUCCCUU--CCCCAGCACCCACUUCCCCAG---CUGCCUCAGGUGUCCACAGUAGAGAGAGAAGCCUCUCAGAAGGAAGAGUCGCAACCA----------------------CAGGGAGUUGGAAAGAGAAGCUUCUCUAAGUGCUGGAUUAUCAAGAUAAAGGAAAGCACGUGAAAUUGGGGCUUAAG---AUCUUAGGACAUGUUCCCGACAUGG
AAKN02041738.1/18239-18050 UAGCAAUC--UAUGUCUCUUUACCCCCAC-CUUGACUCACCAGAUGGCUUCCUAAGUAUUGACAUUGAUGUGAUAAAU-UCUUUGAAAGAAGUUUCAUGACCA----------------------UGAAAAG-UGAAAAGAG----------AAAUGGUAACUUAUCAGGAAGAAAGGAAGCAGAUGGAAUUGAGGCCAAAG---AUCUAAACACCUGCUCCUGACACUC
ABVD01825248.1/321-98      CAGCAACUGCUACUUCCCCUU-CCCCUGU--CCCCUUCCCUGGGUGCCUCCUCAAGUACCAGUUUUGAAGAGAGAAGCCUCUUUGGAGGAAGACUCGUAACUAAAUUAAGGGAGGGACUGGGUUCUAGGAAGUUGAAAGAGAACUGUCUC-UAAAUGCCAAUUUAUCAAGGAAAAUGAAAGCACGUGAAGUUGGGACUGAAGGAAACUUUAACUCACGUUCCAGA--AGC
AAGV020076165.1/486-681    AGGCACCUGCUGCUCACCUUUCCCCCAACACCUUCUUCCCCGG--UGCCUCCCAGGUGUCGAUGCUGAAGGGCUAAGU-CCUUUGAAGGAAGGGUCAU-ACUA----------------------UGUAAGG---AAGGGA-UUUGGUUUUAGGAAGCCAAUUUAUUAAGAUAAGUGAAAGCACAUGAAGUCAGGAUUCACG---UUCCGGAAGCUCCU-GCUGACCGUG
AAEX03008840.1/43729-43916 CAGACAUCGUCAC--CCCUUUUCCCCAACACGC--------------CUUCUUAAGUGUCAACACUGGAGAUAGAAGCCUCCCUGAAGGAAGGUUCACAACCG----------------------UAGAAAGUUGAAAAGAGAAGCUUCUUUAAAUGCCAGUUUAUCAAGAUAAAUGAAAGCAUAUGACAUUGGG-CUUAAG---AUCUUAUGACACGUCUCUGAUGGGC
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::......................:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::...:::::::::::::::::::::::::
#=GC RF                    cAGCAaCuGuUaCUUcCCUUUcCCCCaaCAccuacUUCCCcgGaUGcCuUCucAaGUGUcgAuauUGAAGaGAuAAGCCUCUuuGaAGGAAGauUCauAACcA......................UagaAAGUUGAAAaGaGAaucuUcuUuaaAuGCcaguUUAUcAAGAaaAAuGAAAGCauaUGaaaUUGGGgCugAAG...aUCUuagcgCaCgUucCuGACacuc
//
# STOCKHOLM 1.0

#=GF AC   RF02213
#=GF ID   ZFAT-AS1_3
#=GF DE   ZFAT antisense RNA 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   77.30
#=GF NC   57.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.82 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   15294872
#=GF RT   SNPs in the promoter of a B cell-specific antisense transcript, SAS-ZFAT,
#=GF RT   determine susceptibility to autoimmune thyroid disease.
#=GF RA   Shirasawa S, Harada H, Furugaki K, Akamizu T, Ishikawa N, Ito K, Ito K,
#=GF RA   Tamai H, Kuma K, Kubota S, Hiratani H, Tsuchiya T, Baba I, Ishikawa M,
#=GF RA   Tanaka M, Sakai K, Aoki M, Yamamoto K, Sasazuki T
#=GF RL   Hum Mol Genet. 2004;13:2221-2231.
#=GF WK   ZFAT-AS1
#=GF SQ   5


AB167742.1/507-586         GACUCUUGCUGUGA-AAGGAACCUGGG--AAGCCU-CUGCCACGUGCACAGCUGUGUAAGGAGAAGGAUCUCUCUAUGUUUUCA
AB167741.1/2756-2677       GACUCUUGCUGUGA-AAGGAACCUGGG--AAGCCU-CUGCCACGUGCACAGCUGUGUAAGGAGAAGGAUCUCUCUAUGUUUUCA
AANU01107532.1/40987-40907 GACUCUUGCUGUUAGAAAGAACCUGGG--AAGCCU-CUGUCACGCGCACAGCUGUGUAAGGAGAAGGACCUCUCUAUGUUUUCA
ABDC01016600.1/309-389     GACUCUUGCUGUGA-AAGGAACCGGGGUGAAGCCUUCUGUACAGGGAAAAGCUGUUUCAGGAGAAGGCCCUCUCU--GUUUUCA
AAPY01064125.1/637-717     GACUCUCACUGUGA-AAGCAACCUGGGUGAAGCCUUCAGGAAAGGGAGCA-CUGUUUAGAGAGAAGGCCUUCUCUACGU-GUCA
#=GC SS_cons               ::::::::::::::.::::::::::::..::::::.::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GACUCUUGCUGUGA.AAGGAACCUGGG..AAGCCU.CuGucacGgGcaCAGCUGUgUaaGGAGAAGGacCUCUCUAuGUUuUCA
//
# STOCKHOLM 1.0

#=GF AC   RF02214
#=GF ID   mir-56
#=GF DE   microRNA mir-56
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   70.00
#=GF TC   90.70
#=GF NC   47.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.65 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   GO; 0050779; RNA destabilization;
#=GF RN   [1]
#=GF RM   20421599
#=GF RT   The conserved miR-51 microRNA family is redundantly required for embryonic
#=GF RT   development and pharynx attachment in Caenorhabditis elegans.
#=GF RA   Shaw WR, Armisen J, Lehrbach NJ, Miska EA
#=GF RL   Genetics. 2010;185:897-905.
#=GF RN   [2]
#=GF RM   12672692
#=GF RT   The microRNAs of Caenorhabditis elegans.
#=GF RA   Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB,
#=GF RA   Bartel DP
#=GF RL   Genes Dev. 2003;17:991-1008.
#=GF WK   MicroRNA
#=GF SQ   4


CAAC02000466.1/111135-111037 ACAUCAGUU-UCUGUUCUCAGGGGAUCCAGUUCCGGUUGUGCCUCAUCUCAAUACCCAGAUGGCACCCGUAUUGCUUCCUCUGAGAAUCGACUGCGUACC
ABEG02000165.1/125297-125387 GAGACAGUU-UCUGUUCUCGGCCGAUACAUUUCUGG-UGUACCUCA----AAA---CUGAUGGUACCCGUAAUGUUUCCGCCGAGAACCGACUGCGCUCA
ABLE03020788.1/20651-20562   -AUGCGGUACUCUGUUCUUGGCAGAUCCAUUUUAGG---UACCUCAUC----A--UUUGACGGUACCCGUAAUGCUUCUGCUGAGAGCCGACCGUGAGCC
Z69788.1/18337-18241         GAGCCAGUG-UCUGUUCUUGGCGGAUCCAUUUUGGGUUGUACCUCAUCCUAAA--UUUGACGGUACCCGUAAUGUUUCCGCUGAGAACCGACUGUGCACC
#=GC SS_cons                 :::::::::.:::::::::::::::::::::::::::::::::::::::::::..:::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      gaguCaGUu.UCUGUUCUuGGcgGAUcCAuUUuuGGUUGUaCCUCAUCucAAa..uuuGAuGGuACCCGUAaUGcUUCCgCUGAGAacCGACUGuGcaCc
//
# STOCKHOLM 1.0

#=GF AC   RF02215
#=GF ID   ZNFX1-AS1_1
#=GF DE   ZNFX1 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   78.00
#=GF NC   62.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 40.54 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005634; nucleus;
#=GF DR   GO; 0005737; cytoplasm;
#=GF RN   [1]
#=GF RM   21460236
#=GF RT   SNORD-host RNA Zfas1 is a regulator of mammary development and a potential
#=GF RT   marker for breast cancer.
#=GF RA   Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru
#=GF RA   K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA,
#=GF RA   Dinger ME, Mattick JS
#=GF RL   RNA. 2011;17:878-891.
#=GF WK   ZNFX1-AS1
#=GF SQ   15


AL049766.14/55677-55874    GCGGACAAGCCCGGGUGGCCCGGCGUGUAGAGGGAAGGGGGCGGGGCUAGAC---GCGGCCUGGACAACUACUAGAGCGCCUCGGGCUGUGCUGCUCG-AGACUACAUUUCCCAGAGCGACGCGCG-CGGAGCGG-------GCGGGAAAGA--GAGCG--UUUCGGGUCCAGUGCGCAGGUGCGAAAG-CCAUCUUUGG--UUAUAUAAGGGAGGU
ABGA01124293.1/9658-9855   GCGGACAAGGCCGGGUGGCCUGGCGUCUACAGGGAAGGGGGCGGGACUAGAC---GCGGCCUUGACAACUAGUAGAGCGCCUCGGGCUGUGCGGCUCG-AGACUACAUUUCCCAGGGGGCCCCGCG-CGGAGCGG-------GCGGAAAAGA--GAGCG--UUUCGGGUCCAGUGCGCAGGUGCGAAAG-CCAUCUUUGG--UUAUAUAAGGGAGGU
AANU01258745.1/1098-901    GCAGACGAGCCCGGGUGGCCCAGCGUGUACAAGGAAGGGGGCGGGGCUAGAU---GCGGCCUUGACAUCUACUAGAGCGCCUCGGGCUGUGCGGCUCG-AGACUACAUUUCCCAGGGGGUCCCGCG-CGGAGCGG-------GCGGAAAAGA--GAACG--CCUCGGAUCCAGUGCGCAGGUGCGAGAG-CCAUCCUUGG--UUAUAUAAGGGAGGU
ABRP01092641.1/9676-9841   GCCGACGAGCCCGGGAAGCCCAGUGUGUACGGGGAGGGGGGCGGGGCUAGA----GCGGCCUUGACAACCAUUGGAUCGCCUCGG----------------------UUUCCC----------GCG-AGGCGCCG-------GGGGAACCGG--AAACG--CCUCGGGUCCAGUGCGCAGGCGCAAGAGCCUCCCUAUGG--U-AUAUAAGGGAAGU
AAWR02026844.1/371-554     GCCGACGAGCCCGGCUGGCCCCGUGCGUACGGGAAAGGGGC--AGGCUAGA----GCUUCCUUGACGACCAUUAGGUACCUUCGGA--------------GACUACAUUUCCCAGAUGGCCCCGCG-CGGCGCGG-------GGCUGAUGGGGGAAGCG--CCGAGGGCCCAGUGCGCAGACGCGAGAG-CCCCCUCUGG--UUAUAUAAGGGAGGG
AAYZ01103176.1/952-1142    GCCGGGGAGCUCGGGUGGCCCCCAGUGUACCAGGAAGAGGGCGGGGCUAGAU---GCCGCCCUGGCAACCAUUAGAGCGCUCCGAGCUGGGCGGCACGGGGACUACAUUUCCCAGGGGUCCCCGCG-CAUCGGGC-------GC------GG-----CG--C-UCAAGCCCGGUGCGCAGGCGCAAAUC-CCCCUUCUGGGCUUAUAUAAGGGCGGC
AAIY01540491.1/185-378     GCCGAGGUGCUCGA-UGGUCUUGCGUGUUGGAUGGAGGGGGCGGGCCUAGACUUGGCGC--CCGACAACCAAGAGAUCGCCUCGAG-UGGGCGGUUCGGAGACUACAUCUCCCAAGGGCCCCUGCG-CGGCGCGA-------AAGGGGAAGC---ACUG--C---GGACCCACUGCGCAGGCGCGGGAG-UCUCCAUUGU--CUAUAUAUGCGAGCU
AAKN02039581.1/335-531     ACCGAGUUGCCU---CAGUGUUAUACGGGGGAAGAAGGGGCGGGGGCCAGGCCUCCCGCUUCCGACAACCAUUGGAGCGCCUCGUGCUGGGCGGGCCUAAAACUACAUUUCCCAAGGAUCACAGCA--GGCACUA-------ACCGGAAGGG---GCGG--CCUCAAAUCCAUUGCGCACGCGCACCAG-GAGUCUGUCC--UUAUAUAAGAGAGGU
AALT01363455.1/119-313     GCCGGCGGGCCCUGGCGGCCCCUCGCGUGCGGG--AGGGGGCGGGGCGAGGC---GCGGCCCGGCCGACGACGGAAGUUCUUUCUGCCGGGCGGCGCCGGGACUAAACUGCCCAUAUGGCCCUGUG-CGCUGUGC-------GAGACAAAAA---UACA--CUUCCGGCGCAGUGCGCAGGCGCGAGAG--UUCCGCCUG--CUAUAUAAGGCAAGU
ABRN01156570.1/170-371     GCCGACGAGCCCGGGGGGCCUCGUGUGUACCGGGAAG-GGGCGGGGCUAGU----GUCGCCUUGACAACCAUUAGGCCUCCUCCGCCUGGGCGGCGCGGCGACUACAUUUCCCAGAGGGCCUCGCG-UGGCGCGGCUUGGGGGGCGGGGAGG--AAGCG--CCUCGGGCCCAGUGCGCAGGCGUGA--G-UCCCCUCUGG--UUAUAUAAGGGAGGC
AAHY01012690.1/29834-30022 GCCGAGAAGCCCCGGAGGCCCAGUGAGCAC-------GGGGAGGGGCUAGAC---ACUGGCUGGACAACCAUUAGCUAGC-UGGGGCCGGGCGGCUCGGGGACUACAUUUCCCAGGACGCCAAGCG--GUCGCGC-------CCGGAAGCGA---CGCG--CCAUGGGCACAGUGCGCAGGCGCACGCG-CCGCCAAGGU--CUAUAUAAGGAAGGU
AAHX01026503.1/1184-996    GCCGAGAAGCCCUGGAGGCCCAGUGAGCAC-------GGGGAGGGGCUAGAG---ACUGGCUGGACAACCAUUAGAGAGC-UGGGGCCGGGAGGCUAGGGGACUACAUUUCCCAGGACGCCAAG--CGGUCGGGU-------CCGGAAACGA---CG--GACUUUGGGCUAAGUGCGCAGGCGCACGCG-CCGCCGUGGU--CUAUAUAAAGAAGGU
AAEX03013993.1/167-364     GCCGACGAGCCCCGGGGGCCCCG-ACGUACGGCGAAGGGGGCGGGGCUAGA----GCGGCCUUGGCAACCAUUAGAUCGCCUCGGGCUGGGCGGCUUGCAAACUACAUUUCCCAGAGGGCCUCGCG-UGCCGCGG-------GACGGAAGGG-GAAGCG--CCUCGGGUGCAGUGCGCAGACGCGAGAG-CUUCUUCUGG--UUAUAUAAGAGCGGU
AAGW02065227.1/468-639     GCCGAGAAGCCCGGGCGGCCCGCUGUGUCCAGAGAAGGGGGCGGGGCUAGAC---GCGGCCUUGCCGACCAUUAGAGCGCUGAGCG-------ACCCGGAGACUACAUUUCCCAGGGGGCCCCGCG-CGGCG-------------------------CG--UUUCGAGCCGAGUGCGCAGGCGCACGAA--GCUCUAUGA--UUAUAUAAGGGC---
AAPE02035274.1/15900-15728 GCGUAAGAGUCCGGGCGGUCCAAUGUGUAUGGGGAAGAGGGCGGAGCUAGA----GCGGCCUGGACUACCAUUAGGUAUAGUCGGA--------------GACUACAUUUCCCA----------UG-CUGCGCCG-------GG--AACCGG--AAGCA--CCUCGGCGCCAGUGCGCAGGCGCAAAAAGCCCCCUCUGG--UUAUAUAAGAGAGAU
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::...:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::.......::::::::::...::::..::::::::::::::::::::::::::::.::::::::::..:::::::::::::::
#=GC RF                    GCcGAggaGCCCgGGuGGCCcaguGuGuacgggGAAGGGGGcGGGGCuAGac...GCggcCuuGaCaACcAuUaGagcgCcUcGgGCuGGGCGGcucggaGACUACAUUUCCCAgggggCCccGCG.cGgcGcgg.......gcgGgaaaGg...agcG..CcUcGGgccCAGUGCGCAGGCGCgagaG.ccccCuuuGg..uUAUAUAAGgGaGGu
//
# STOCKHOLM 1.0

#=GF AC   RF02216
#=GF ID   ZNFX1-AS1_2
#=GF DE   ZNFX1 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   45.00
#=GF TC   48.90
#=GF NC   42.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.93 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005634; nucleus;
#=GF DR   GO; 0005737; cytoplasm;
#=GF RN   [1]
#=GF RM   21460236
#=GF RT   SNORD-host RNA Zfas1 is a regulator of mammary development and a potential
#=GF RT   marker for breast cancer.
#=GF RA   Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru
#=GF RA   K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA,
#=GF RA   Dinger ME, Mattick JS
#=GF RL   RNA. 2011;17:878-891.
#=GF WK   ZNFX1-AS1
#=GF SQ   18


AY339614.1/54-146          AGCGGGUACAGAAUGGAUUUUGGAAGAGGGAG----UCACC-ACUGGACCUCCAAGGAAGCCACGUG-CAGACAUCUACAACCUUCGAUCUCC-UGACGA
ABRN01156570.1/851-943     ACAGCAUACAGAAUGGAUCUUGGAGGAAGGGG----UCCCU-GCUGGGCCUUCAAGGAAACCACGUG-UAGACAUGAACAACCUUCAAUCUCC-UGACCU
AAWR02026844.1/1020-1112   AGAGGGUACGGAAUGGAUCUUGGAGGAGGGGG----UCGCU-GCUGGGCCUCGACGAGAACGCCGUG-UAGACAUCUACAGCCUUCAGUCUCC-UGAUCU
AAPY01187610.1/644-736     AGAAGGUACACAGCGACUGUUGGAGGAGGAAG----UCACU-UCUGGGCGUGUAGGGGAGCCCCGUG-UAGACAUCUGCAGCCUUGGAUCUCC-UGACCA
AAFC03014094.1/16973-17063 AGAUGGUACAGAAUGAAUCUUGGAGGAGGG-G----UCCCU-GCUGGGGCUCCAAG-GAACCACGUG-UAGACGUGCACAACCUUCAGUCUCC-UGACCU
AANG01528073.1/1597-1501   AGAGGGUACCGAAUGGAUCUUGGAGGAGGGAGGCACUCGCU-GCUGGGCCUCCAAGAGACCCCCACG-UAGACGUCUCCAGCCUUCGGUCUCC-UGACUU
AAKN02039581.1/973-1065    AGGGAGUAUAGCAUGGAUGUGAGAGAACGGAG----UCACC-UCUGGGCCUAUGAGAGAUUCCGAUU-UAGAUCUCUCCAACCUUGGAUCUCU-UGACCU
ABRO01394468.1/1754-1662   CCCAGGCUUAGAAUGGAUAUUGGGAGAAGGAG----CCACC-CCUGGAAUAUCAGAAAAAUCCUAUU-UGGUCAUCCACAACCUCUGAUCUCC-UAAGCU
ABRT010490067.1/561-650    UGGCCAAACAACAUGGAUGAUGAAGGAAGAAC----UCACC-CCUGGGCCUCCAAGAGAACUACAUG-CAGACGUCUGCGGUUUUUGAUC----UGACCA
AAGV020924726.1/642-729    --AGUCGGGAGAAUGGAUGUUGGAGGAGGAGG----AGUCU-GCUGGGCCGCCGAG-GAACCUCGCG-CAGACAUCU-CAACCUU-GGUCUCU-UGACUC
AANN01122270.1/923-829     GAAAGGUACCAGAUGGAUCUUGAAGCAGGGAA---AUGACUGCUUGGGCCUCUCAGGGAACCCUGUG-UAAACAUCUGCAGCCUUGGGGCUCC-UGAGCU
ABRR01228250.1/3816-3905   AGGGUGGGCAGAAUGGAUCCUGGAGGAGGG-G----CCGCU-GCCGGGCCUCCCGGGGAGCCGCGUG-UAGCCCUCGGCAGCCUU--GUCUCC-UGACCU
AC152409.8/45089-44997     AACCAGUGCAGAAUGGAUGUUGGAGGAGAGGGA-GGUCACC-UCUGGGCUUCUGGGAAAACCA---G-AAGACAUAUAUGAUCCUCAACCUCG-UAACUU
AAEX03013993.1/824-916     ACGGGGUACGGAAUGGAUCUCGGAGGAGGGCG----UCGCU-GCUGGGCCUUCAAGAGAGCCCGCGG-UAGAUCCCUAGAGCCAUCGGUCUCC-UGAUCC
AAPE02044001.1/10284-10376 CAAAGGUACAGAAUGGAUCUUGAAGGAAAGGG----UCGUU-GCUGGGCCUCCAAAAGAACCCCGUG-UAGACAUUGAGAACCUUCGGCCUCC-UGACCU
AAGU03041983.1/708-797     GGAGCGUGCAGGAUGGCUGUUGAAGUGGGACG-------CC-GCUGGGCCACCGAAGGCACCCGGUG-CGGACUUUUCCAGCCUUCGGUCUCC-UGACCU
AAQR03137585.1/46983-47074 AGAGUAUACAGAAUGUACACUAAAACAGGG-G----UGACC-ACUGGGCCUUCAAAGGAACCACAUG-CAGACACAUAUAAUCUUCCAUCUCU-UGACUU
AAGW02042283.1/62272-62183 AGAGGGGACAGAAUAGAUGUUGGAGGAAGGA---------C-UCUGGGUUUCCAUGAGAACUCCAUGGAAGAGACCUACAACCUGUGAUCUCCUUGAUCU
#=GC SS_cons               ::::::::::::::::::::::::::::::::....:::::.:::::::::::::::::::::::::.:::::::::::::::::::::::::.::::::
#=GC RF                    aGaggGuaCAGAAUGGAUgUUGGAGGAGGGaG....UCaCu.gCUGGGCCUcCaaGaGAaCCccgUG.uAGACaUcUaCAgCCUUcGgUCUCC.UGACCU
//
# STOCKHOLM 1.0

#=GF AC   RF02217
#=GF ID   ZNFX1-AS1_3
#=GF DE   ZNFX1 antisense RNA 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   60.00
#=GF TC   71.70
#=GF NC   44.90
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0005634; nucleus;
#=GF DR   GO; 0005737; cytoplasm;
#=GF RN   [1]
#=GF RM   21460236
#=GF RT   SNORD-host RNA Zfas1 is a regulator of mammary development and a potential
#=GF RT   marker for breast cancer.
#=GF RA   Askarian-Amiri ME, Crawford J, French JD, Smart CE, Smith MA, Clark MB, Ru
#=GF RA   K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA,
#=GF RA   Dinger ME, Mattick JS
#=GF RL   RNA. 2011;17:878-891.
#=GF WK   ZNFX1-AS1
#=GF SQ   3


AY513723.1/326-412         GUUUAUUGUUGGCCAAAACCAGGCUUUGAUUGAACCAGGAUGAAUGCGGGUGUUGGAAGUAGAAUAUAUAUAUA--CAUAUAAAAUUGG
AANU01258744.1/12032-11946 GUUUAUUGUUGGCCAAAACCAGGCUUUGACUGAACCAGGAUGAAUGCGGGUGUUGGGAAUAGAAUAUAUAUAUA--CAUAUAAAACCGG
ABGA01335474.1/1567-1643   GUUUAUUGUUGGCUAAAACCA------------ACCAGGAUGAAUGCGGGCGUUGGAAGUAGAAUAUAUAUAUAUACAUAUAAAAUUGG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..:::::::::::::
#=GC RF                    GUUUAUUGUUGGCcAAAACCAGGCUUUGAuUGAACCAGGAUGAAUGCGGGuGUUGGaAgUAGAAUAUAUAUAUA..CAUAUAAAAuuGG
//
# STOCKHOLM 1.0

#=GF AC   RF02218
#=GF ID   ZNRD1-AS1_1
#=GF PI   HTEX4
#=GF DE   ZNRD1 antisense RNA 1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   43.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.32 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9553157
#=GF RT   HTEX4, a new human gene in the MHC class I region, undergoes alternative
#=GF RT   splicing and polyadenylation processes in testis.
#=GF RA   Lepourcelet M, Coriton O, Hampe A, Galibert F, Mosser J
#=GF RL   Immunogenetics. 1998;47:491-496.
#=GF RN   [2]
#=GF RM   11130983
#=GF RT   Transcriptional analysis of the 69-kb sequence centromeric to HLA-J: a
#=GF RT   dense and complex structure of five genes.
#=GF RA   Coriton O, Lepourcelet M, Hampe A, Galibert F, Mosser J
#=GF RL   Mamm Genome. 2000;11:1127-1131.
#=GF WK   ZNRD1-AS1
#=GF SQ   8


BA000025.2/1906285-1906218 UUUUGCUCUUCACUGUAUCUUCAGGGUCUAGUAGAUCACAUGAUUCAUCAGAGGACUUGAAAUACAUG
AB202082.1/4488-4555       UUUUGCUCUUCACUGUAUCUUCAGGGUCUAGUAGAUCACAUGAUUCAUCAGAGGACUUGAAAUACAUG
AB210195.1/4487-4554       UUUUGCUCUUCACUGUAUCUUCAGGGUCUAGUAGAUCACAUAAUUCAUCAGAGGACUUGAAAUACAUG
AB210196.1/4487-4554       UUUUGCUCUUCACUGUAUCUUCAGGGUCUAGUAGAUCACAURAUUCAUCAGAGGACUUGAAAUACAUG
AL671859.3/15477-15544     UUUUGCUCUUCACUGUAUCUUCAGGGUCUAGUAGAUCACAUGAUUCAUCAGAGGACUUGAAAUACAUG
AAWR02009842.1/2919-2984   UUUUGCUCUUCACUGUAUCUCGAGAGUCUAGCUGAUCC--UGAUUCACUGGAGGCCUUGAAAUAUACA
ABRT011055274.1/753-819    UUUAGCCCCUCU-UGUAUCUUCAGUGUCUAGCCAAUCUCUUGGUUCACCAGAGGCCUUGACAUAUACA
AP009553.1/203684-203748   UUUCACUUCUAAUUUUAUCUCCAGUGUCUAGCAGAUCU---GAUUCAAAGGAGACCUUGAAAUAUACA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UUUuGCUCUUCACUGUAUCUUCAGgGUCUAGuaGAUCaCaUGAUUCAucaGAGGaCUUGAAAUAcAug
//
# STOCKHOLM 1.0

#=GF AC   RF02219
#=GF ID   ZNRD1-AS1_2
#=GF PI   HTEX4
#=GF DE   ZNRD1 antisense RNA 1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   60.00
#=GF TC   62.80
#=GF NC   53.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.89 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9553157
#=GF RT   HTEX4, a new human gene in the MHC class I region, undergoes alternative
#=GF RT   splicing and polyadenylation processes in testis.
#=GF RA   Lepourcelet M, Coriton O, Hampe A, Galibert F, Mosser J
#=GF RL   Immunogenetics. 1998;47:491-496.
#=GF RN   [2]
#=GF RM   11130983
#=GF RT   Transcriptional analysis of the 69-kb sequence centromeric to HLA-J: a
#=GF RT   dense and complex structure of five genes.
#=GF RA   Coriton O, Lepourcelet M, Hampe A, Galibert F, Mosser J
#=GF RL   Mamm Genome. 2000;11:1127-1131.
#=GF WK   ZNRD1-AS1
#=GF SQ   34


BX927229.6/89400-89475     CAAGAUCUUUU-UUUCCAGUGGAGACUGCUGACCUGCAGCAAUCCUAGGAUCUUUAGAUG--AUGUACCCCAGGCCAAU
AB158486.1/124957-125032   CAAGAUUUUUU-UCUCCAGAGGGGACUGUUGACCUGCAGCAAUCCUAGGGUCUUUAGAUA--CUUUAGCCCAGGCCAAU
AB202082.1/26744-26819     CAAGAUCUUUU-UUUCCAGUGGAGACUGCUGACCUGCAGCAAUCCUAGGAUCUUUAGAUG--AUGUACCCCAGGCCAAU
AB210195.1/26694-26769     CAAGAUCUUUU-UUUCCAGUGGAGACUGCUGACCUGCAGCAAUCCUAGGAUCUUUAGAUG--AUGUACCCCAGGCCAAU
AL671859.3/37718-37793     CAAGAUCUUUU-UUUCCAGUGGAGACUGCUGACCUGCAGCAAUCCUAGGAUCUUUAGAUG--AUGUACCCCAGGCCAAU
ABDC01385912.1/1808-1883   CAAGAUCUUUU-UCUCCAGUGGGGACUGCUGACCUGCAGCAAUCCGAGGAUCUUUAGAUG--AUUUAGCCCAGGCCAAU
AAPY01795997.1/566-491     CAAGAUCUUUU-UCUCCAGUGGGGACUGCUGACCUGCAGCAAUCCUAGGAUCUUCAGAUA--CUUUAGCCCAGGCUAAU
AAQQ01488059.1/1679-1754   CAAUAUCUUUU-UCUCCAGUGGAGAAUGUUGAUCUGCAGCAAUCCUAGGGUCUUUAGAUG--CUUUAGCCCAAGCCAAU
AAWR02009834.1/39363-39438 CAAAAUUUUUU-UCUCCAGUGGGGACUGCUGACCUGCAGCAAUCCUAGGGUCUUUAGUUG--CUUUAGCCCAGGCCAAU
AAGV020611706.1/1022-1097  CAAGAUCUUUU-UCUCCAGUGGGGACUGUUGGCCUGCAGCAAUCCUAGAGUCUUUAGAUG--CUUUAGCCCAGGCCAAU
AAFC03022489.1/49217-49292 CAAUAUUUUUU-UCUCCAGUGGAGACUGUUGACCUGCAGCAAUCCUAGGGUCUUUUGAUA--CUUUAGCCCAGGCCAAU
ABRR01324132.1/3538-3613   CAAGAUUUUCU-UCUCCAGUGGGGAAUGCUGACCUGCAGCAAUCCUGGGAUCUUUAGAUA--CUUUAGCCCAAGCCAAU
AAKN02056639.1/16137-16062 CAAGAUUUUUU-UCUCCAGUGGGGACUGCUGACCUACAGCAACCCUCGGGUCUUUCGAUG--UUUUAGCCCAGGCCAAU
AAYZ01329398.1/8214-8289   CAAGAUCUUCU-UCUCCAGUGGAGACUGUUGACCUACAGCAACCCUAGGGUCCUUAGAUG--CUUUCACCCAGGCGAAU
ABRQ01145254.1/2995-3070   CAAAAUCUCUU-UUUCCAGUGGAGAGUGUUGGCCAGGAGCAAUUCUAGGGUCUUUAGAUG--CUUUAGCCCAGGCUAAU
ABVD01584167.1/2072-2147   CAAUAUCUUUU-UCUCCAGUGGGGACUCUUGGCCUGCAGCAAUCCUAGAGUCUUUAGAGG--CUAUAGCCCAGGCCAAU
AALT01150796.1/1716-1641   CAAUAUUUUUU-UCUCCAGUGGAGAUUGCUGACCAGCAGCUAUUCUAGGGUCUUUAGAUG--AUUUAGCCCAAAUCAGU
ABRP01143455.1/10603-10679 CAAUAUUUUUUUUCUCCAGUGGAGACUGCUGACCUGAAGCAGUCCUAGGGUCUCUAGAUG--CUUUAGCCCAGAUCAAU
ACBE01158275.1/13794-13869 CAAGAUUUUCU-UCUCCAGUGGGGACAGCUGACCUGUAGCAAUCCUGGGGUCUGUAGACA--UUUUAGCCCAGGACAAU
CU463334.13/59668-59593    CAGGAUCUUCU-UCUCCAGUGGAGACUGCUGGCCUUCUGAAAUCCUAGGGUCUCUGGAUU--CUUUUGCCCAAGCCAAU
AAHX01099545.1/2312-2387   CAGGAUCCUUU-UCUCUAGAGGAGACCGUUGACCUUCUGAGAUCCUAGGGUCUUUGGAUU--CUUUUGCCCAAGCCAAU
ABQO011070168.1/1023-1098  CAAGAUCUUUU-UUUCCAGAGGAGAUUGGAGACCCCUGGCAAUCCAAGGGUGCUGAGUAU--UUUUGACCCAGGCUAAC
ABRO01143486.1/395-320     CUUAAUCUUCU-UUUCUAGUGGGGAAUAAGAACCUACUGCAAUCCGAGGGUCUUGAAUAU--UUUUAGCCCAGGCCAAU
AAFR03024661.1/17133-17058 CAAGAUCUUUU-UCUCUAGAGGGGAUCGGAGACCUCUGGCAAUCCGAGGGUCUUGAGUAU--UUUUGACCCAGGCUAAC
AAIY01339795.1/2447-2372   CUGGAUCUUCU-UUUCCAGUGGGGACUGAGAGCCCAUUGCGAUCCGAGAGUCUUGAGUAU--AUCUGGCCCAGGCCAAC
ABRT010452027.1/1937-1862  CUUAAUCUUCU-UUUCUAGUGGGGAAUAGGAGCCUACUACAAUUCAAGGGUCUUGAGUAU--UGUUAGCCCAGGCCAAU
ABRN01149097.1/2721-2644   CUUCAUCUUCU-UUUCUCAUGGGGACUGGGAACCUACUGCAAACCGAGGGUCUUGAGUAUUUUUUUGGCCCAGGCCAAU
AANN01596763.1/735-810     CUCAAUCUUCU-UUUCUAGUGGUGACUGGAAUCCUGGUGCGAUCCGAGGGUCUUGGAUGU--GUCUGACCCACGCCAGU
AC234889.2/53699-53774     CGAGAUCUUUU-UCUCCAGUGGAGACUGUUGACCUACAGCAACCCUAGGGUCCUUAGACG--AUUUCGCCCAGGCCAAU
AAPE02059329.1/35545-35620 CAAUAUUUUUU-UCUCCAGUGGGGACUGCUGACCUGAAGCAAUCCUAGGGUCUCUAGAUG--CUUUAACCCAGGCCAAC
AL731566.7/58444-58369     CUGAAUCUUCU-UUUCUAAUGGGGAAUAGGACCCUACUGCAAUCUGAGGGUCUUGAGUAU--UUUUAGCCCAGGCCAAU
AAQR03060021.1/3762-3837   CAAAAUCUUUU-UUUCCAGUGGGGACUGUUGGCCUGCAGCAAUCCUAGGAUCUUUAGAUG--AUUUAGCCCAGGCCAAU
AAEX03017624.1/44793-44868 CAGGAGUUUUU-UCUCCAGUGGGGACUGUUGGUCUACGGCAAUCCUAGGGUCUGGUGAUG--CUUUAGCCCAGGCCAAA
AAGU03087280.1/57524-57599 CCGAAUCUUCU-UUUCUAAUGGGGAUUGGGGACCCACUGCAAUCCGAGGGUCUUGAAUAU--AUUUGGCCCAGGCCAAU
#=GC SS_cons               :::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::..:::::::::::::::::
#=GC RF                    CaagAUCUUUU.UcUCCAGUGGgGAcUGuuGaCCUgcaGCAAUCCuAGGGUCUUuAGaug..cUUUaGCCCAGGCCAAU
//
# STOCKHOLM 1.0

#=GF AC   RF02220
#=GF ID   ZNRD1-AS1_3
#=GF PI   HTEX4
#=GF DE   ZNRD1 antisense RNA 1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   74.70
#=GF NC   54.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   9553157
#=GF RT   HTEX4, a new human gene in the MHC class I region, undergoes alternative
#=GF RT   splicing and polyadenylation processes in testis.
#=GF RA   Lepourcelet M, Coriton O, Hampe A, Galibert F, Mosser J
#=GF RL   Immunogenetics. 1998;47:491-496.
#=GF RN   [2]
#=GF RM   11130983
#=GF RT   Transcriptional analysis of the 69-kb sequence centromeric to HLA-J: a
#=GF RT   dense and complex structure of five genes.
#=GF RA   Coriton O, Lepourcelet M, Hampe A, Galibert F, Mosser J
#=GF RL   Mamm Genome. 2000;11:1127-1131.
#=GF WK   ZNRD1-AS1
#=GF SQ   9


DQ976748.1/83-186          AAUUUUGGCCUCAACGUCUCAGUACUAAGGUGAAAGUGGAGCCGCAAACCCUCUUCGAAGAGGUUAGGCUCCAUCUCUGAGGCUCCCGAGACAAGGUUCGCAAU
DQ977202.1/62-165          AAUUUUGUGCUCAACCUCUCAGUACCAGGGUGAAAGUGGAGACGCAAUCUCCCUUGGAAGACGUUAGUCUCCAUCUCUAACGCUCCCGAGACACGGUUCGCAAU
AB210195.1/29663-29761     AAUUUUGUG--C---CUCUCAGUACCAGGGUGAAAGUGAAGACGCAAUCUCCCUUGGAAGACGUUAGUCUCCAUCUCUAACGCUCCCGAGACACGGUUCGCAAU
DQ976608.1/86-189          AAUUUUGUGCUCAACCUCUCAGUACCAGGGUGAAAGUGGAGACGCAAUCUCCCUUGGAAGACGUUAGUCUCCAUCUCUAACGCUCCCGAGACACGGUUCGCAAU
DQ977091.1/84-187          AAUUUUGUGCUCAACGUCUCAGUACCAGCCUGAAAGUUGAGCCCCAACCUCCCUUAGAAGAGCUGACUCUCCAUCUCUAAGGCUUCCGAGACACGGUUCGCAAU
DQ976469.1/84-187          AAUUUUGUGCUCANNNUCUCAGUACCAGGGUGAAAGUGGAGACGCAAUCUCCCUUGGAAGACGUUAGUCUCCAUCUCUAACGCUCCAGAGACACGGUUCGCAAU
AL671859.3/40683-40786     AAUUUUGUGCUCAACCUCUCAGUACCAGGGUGAAAGUGGAGACGCAAUCUCCCUUGGAAGACGUUAGUCUCCAUCUCUAACGCUCCCGAGACACGGUUCGCAAU
DQ977497.1/85-188          AAUUUUGUGCUCAACCGCUCAGUACCAGGGUGAAAGUGGAGCCGCAAUCUCCUUUGGAACACGCCAGUCUCCAUCUCUAAGGCUCCCGAGACACGGUUCGCAAU
BA000025.2/1881082-1880979 AAUUUUGUGCUCAACCUCUCAGUACCAGGGUGAAAGUGGAGACGCAAUCUCCCUUGGAAGACGUUAGUCUCCAUCUCUAACGCUCCCGAGACACGGUUCGCAAU
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    AAUUUUGUGCUCAaCcUCUCAGUACCAGGGUGAAAGUGGAGaCGCAAuCUCCCUUgGAAGAcGUuAGUCUCCAUCUCUAAcGCUCCCGAGACACGGUUCGCAAU
//
# STOCKHOLM 1.0

#=GF AC   RF02221
#=GF ID   sRNA-Xcc1
#=GF PI   sX1; sX10
#=GF DE   sRNA-Xcc1
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published; PMID:21941121
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   21941121
#=GF RT   sRNA-Xcc1, an integron-encoded transposon- and plasmid-transferred
#=GF RT   trans-acting sRNA, is under the positive control of the key virulence
#=GF RT   regulators HrpG and HrpX of Xanthomonas campestris pathovar campestris.
#=GF RA   Chen XL, Tang DJ, Jiang RP, He YQ, Jiang BL, Lu GT, Tang JL
#=GF RL   RNA Biol. 2011;8:947-953.
#=GF RN   [2]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF RN   [3]
#=GF RM   8870269
#=GF RT   HrpG, a key hrp regulatory protein of Xanthomonas campestris pv.
#=GF RT   vesicatoria is homologous to two-component response regulators.
#=GF RA   Wengelnik K, Van den Ackerveken G, Bonas U
#=GF RL   Mol Plant Microbe Interact. 1996;9:704-712.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   74


AM920689.1/396887-396974       GGCCGGGCG-GCGCG-CAGC-UAUACAACACCC-GAAA-GGGGAAAUCUGCG-GGCC-G------UCU-------UCGAGCGGUGUUCAAGCGCCCGGCCGCCUCUCU
AE008922.1/409481-409568       GGCCGGGUG-GCGCG-CAGC-UAUGCAAUACCC-GAAA-GGGGAAAACUGCG-GGCG-GC------CC-------UACGACCGUGUUCAAGCACCCGGCCGCCUCUCU
FM866940.1/153-240             GGCCGGGUA-GCGCG-CAGC-CAUACAACACCC-GAAA-GGGGAAAACUGC--GGNCCGU------CU-------GAUAGCGGUGUUCAAGUACCCGGCCGCCCCUCU
AP008232.1/3378542-3378629     GGUCGGGUA-GCGAG-UAGU-GAUACAACACCC-UUAG-GGGGAAAGCUGCU-GGCC-GA------CU-------UUGCACGGUGUUCAAGUACCCGACCGCCCCACU
AM260479.1/3486192-3486280     GGCCGGGCA-GCGCG-CAUC-GAUACAAGACCC-GAAA-GGGGAAACAUGCG-GGCC-GA-----UCU-------GCGGGCGGUGUUCAAGUGCCCGGCCGCCCUGCU
ABSO01007042.1/74-160          AGCCGGGUA-GCGCG-CAUU-GAUACAAGACCC-GAAA-GGGGAAA-AUGCG-GGCC-GU------CU-------GUGAGCGGUGUUCAAGUACCCGGCCGCCCUCUG
ABXW01000012.1/16194-16280     GGUCGGGUA-GCGUG-CAAUACAUACAAUACC--GAAA--GGGAAAAUUGCA-GGCC-GU------CU-------CGUAGCGGUGUUCAAGUGCCCGACCGCCCUCUG
AAKB02000001.1/3307218-3307130 GGUCGGGUA-GCGCG-UAUACCGAAAAACAGCC-GAAA-GGCUAAGGAUACG-GGCC-GA------CU-------UGCUGCGGUGUUCAAGUACCCGACCGCCCUGCU
AAJW02000017.1/30970-30882     GGUCGGGUA-GCGCG-UAUACCGAAAAACAGCC-GAAA-GGUUAAGGAUACG-GGCC-GA------CU-------UUGCACGGUGUUCAAGUACCUGACCGCCCUGCU
AAAL02000004.1/2712-2797       GUCGGGAGG-GC-GG-CAGC-CAUACAACACCC-GCAA-GGGGAAAGCUGCC-CGCC-GU------CU-------GAGUUCGGUUUCUAA-CCUCCCGACACCCAUAG
AAAM03000063.1/2-88            GUCGGGAGG-GC-GG-CAGC-GAUACAACACCC-GCAA-GGGGAAAACUGCC-CGCC-GU------CC-------GAGUUCGGUUUCUUAGCCUCCCGACACCCACAG
CP001011.1/1323860-1323774     GUCGGGAGG-GC-GG-CAGC-CAUACAACACCC-GCAA-GGGGAAAGCUGCC-CGCC-GU------CU-------ACUUCCGGUUUCUUAGCCUCCCGACACCCACAG
AE009442.1/1215344-1215430     GUCGGGAGG-GC-GG-CAGC-GAUACAAGACCC-GCAA-GGGGAAAGCUGCC-CGCC-GU------CU-------AUGUCCGGUUUCUUACCCUCCCGACACCCACAG
AE016825.1/141711-141801       GGCCGGGUA-GCGCGUCUGU-CGAACAACAGCCCGAAAGGGCUAAGGCAGCG-GGCC-GU------CU-------AGUGUCGGUGUUCAAGUACCUGGCCGCCCCUCC
CP000941.1/1236708-1236623     GUCGGGAGG-GC-GG-CAGC-GAUACAAGACCC-UU-U-GGGGAAAGCUGCC-CGCC-GU------CU-------UUGUCCGGUUUCUUAGCCUCCCGACACCCACAG
AE003849.1/2020989-2021073     GUCGGGAGG-GC-GG-CAGC-GAUACAAGACCC-UU-U-GGGGAAAGCUGCC-CGCC-GU------CU-------GUUUCCGGUUGUUAA-CCUCCCGACACCCACGA
AACY021332711.1/106-21         GGUCGGGUA-GCGCG-UAGC-CAUACAAGACCU-U--C-GGGAAAAGC-GCGUGGCC-GU------CU-------GAUAGCGGUGUUUAACUGCCCGACCGCCCUAAU
BAAU01012267.1/286-204         GGCCGGGAG-UG-GG-C--U-AAUAGAAUACCC-UUCG-GGGGAAUA-UGCC-CGCC-GU------CU-------CGCAACGGU-UUCUAGCUCCCGGCCUUUUCCAU
AM181176.4/5253901-5253985     UGCCGGGAG-UG-GG-C--U-AAUACAAGACCC-GAAA-GGGGAAUAUGUCC-GGCC-CU------CU-------GUGUGGGGUUUCUUAACUCCCGGCACCCAGCCC
CP000614.1/1369093-1369010     GGGCGGGAG-UGCGA-C--G-GAUACAAGACCC-GAAA-GGGAAAGA-AGUC-CGCC-GU------CU-------GUGUGCGGUU-UUGAGCUCCCGCCCGCCCUCUC
AAZG01000021.1/15717-15803     GCCGAGAGG-GCGGA-GA----AUACAACACCC-GAAA-GGGGAAUAAUCCC-GGCC-GUU----CUU-------UGUUUCGGUUUACGAACCUCUUGGCGACCCUAU
CP000438.1/4401602-4401685     GCCGGGAGU----GG-ACG--AAUACAAGACCC-GAAA-GGGAAAUAUGUCC-GGCC-CU------CU-------GCGUGGGGUUUUCUUAACUCCCGGCACCCCAGC
CP001321.1/272620-272704       GCCGAGGGG-GCGAG----G-AAUACAACACCC-GAAA-GGGGAAUAACUCC-AGCC-GU------CU-------UUGUAGGGCUUUCGAACCCCUUGGCACCCUAUU
ABXU01000030.1/22578-22665     UGCCGGGCUGAUAGC-UCCC-AAUACAAGACCC-UUCG-GGGGAAUAAGAGC-AGCG-CA------CC-------GUGUGGCGUAGUUGAG-GCCCGGCAUUUCCUCA
AM421808.1/850144-850228       GACCGCGUG-GGCGA-C--G-AAUACAAGACCC-GAAA-GGGGAAUA-AGUC-CGCC-CU------CC-------UAUGUGGGUUCUUAACCGCGCGUCCGCCCAUUU
AAZI01000014.1/17063-17150     GUCGGGCGG-GCGGA-GA----AUACAACACCC-GAAA-GGGGAAUAAUCCC-AGCC-GUU---UCUU-------UUGGUCGGCUUUCGAACCACCUGGCACCCUUAA
CP000947.1/1032328-1032412     GUCGAGAGG-GCGGA-GA----AUACAAUACCC-GAAA-GGGGAAUAAUCCC-GACC-GU------CU-------GUUUGCGGUUUUCGAACCUCUCGGCACCCUAUU
ABHR01000028.1/1791-1708       GACCGGGCG-UGCGG-C--U-AAUACAACACCA-GCAA-UGGGAAUA-UGCC-CGCC-GA------CU-------ACUUGCGGU-UUUGAGCGCCCGGUCACCCUCUC
CP000746.1/1376775-1376859     GUCGAGAGG-GCGGA-GA----AUACAAUACCC-GAAA-GGGGAAUAAUCCC-AGCC-UA------CU-------UGUUGAGGCUUACGAACCUCUCGACACCCUAUU
AAMJ02000007.1/125127-125210   GGUCGGGCG-UGCGG-C--U-AAUAAAACACCC-GCAA-GGGAAAUA-UGCC-CGCC-GU------CU-------AUCGCCGGU-UUUGAGCGCCCGACCACCCUCUC
AE013598.1/4919226-4919144     GCCGGGAGG-GC-GG-C--G-AAUACAACACCC-GCAA-GGGGAAUA-AGCC-CGCC-GG------CU-------GUGUGCGGU-UUCUAGCCUCCCGGCAUCCCGCU
CP000050.1/2760973-2760891     GUCGGGAGG-GC-GG-C--U-AAUACAACACCC-GCAA-GGGGAAUA-CGCC-CGCC-GG------CU-------GUGUGCGGUU-UCGAACCUCCCGACAUCCCGUC
AE008923.1/5030744-5030826     GCCGGGAGG-GC-GG-C--G-AAUACAACACCC-GCAA-GGGGAAUA-AGCC-CGCC-GU------CU-------GUUUGCGGUUGCUAA-CCUCCCGGCAUCCCGCC
AP008229.1/3694898-3694816     GUCGGGAGG-GC-GG-C--U-AAUACAACACCC-GCAA-GGGGAAUA-CGCC-CGCC-GG------CU-------GUUAGCGGU-UUCGAGCCUCCCGACUUCCCGUC
CP000038.1/2936202-2936119     GACCGGGUG-UGCGG-C--U-AAUACAAUACCA-GCAA-UGGAAAUA-CGCC-CGCC-GA------CU-------UUCGACGGU-UUUGAGCGCCCGGUCACCCUCUC
BX571872.1/151514-151430       GUCGGGAGG-GC-GA-C--U-AAUACAACACCC-GCAA-GGGGAAUA-AGUC-CGCG-GUU----UCU-------UACUGCCGU-UUUGAGCCUCCCGACACCAUAUU
CP000436.1/1601874-1601960     GUCGAGAGG-GCGGA-GA----AUACAAUACCC-GAAA-GGGAAAUAAUCCC-AGCC-GUU----CUA-------UGUUUCGGUUUUCGAACCUCUUGACGCCACUGU
AAZJ01000029.1/3648-3732       GCCGAGUGG-GC-GA-C--U-AAUACAAUACCC-GAAA-GGGGAAUA-UGUCCAGCU-GA------CU-------UACUGCAGCCUUCGAACCACUUGGCGCCCAACU
CP000967.1/148352-148270       GUCGGGAGG-GC-GG-C--U-AAUACAACACCC-UUCG-GGGAAAUA-CGCC-CGCC-GG------CU-------ACGUGCGGUUUCUAA-CCUCCCGACAUCCCGUC
ABEW01000010.1/115609-115692   GUCGGGAGG-GC-GA-C--U-AAUACAAUACCC-GUAA-GGGAAAUA-AGUC-CGCG-GU-----UCU-------UUAGGCCGUUCUGAA-CCUCCUGACACCACUAU
CP000749.1/2805028-2804944     GUCGGGAGG-GCGAG-G----AAUAAAAUACCC-GCAA-GGGAAAUAACUCC-GCCU-GG------AC-------UUGUGCAGGUUUCGAACCUCCCGGCACCCUUCU
AACK01000018.1/13896-13980     GUCGAGAGG-GCGGA-GA----AUGCAAUACCC-UUCG-GGGGAAUAAUCCC-GACC-GA------CU-------UUUGGCGGUUUUCGAACCUCUCGGCACCCUAUG
AM039952.1/155852-155934       GUCGGGAGG-GC-GG-C--U-AAUACAACACCC-UUCG-GGGAAAUA-CGCU-CGCC-GC------CU-------CUCUGCGGUUUCUAA-CCUCCCGACAUCCCGUC
ABKM01000033.1/25380-25464     ACCGAGGGG-GCGAG-G----AAUACAACACCC-GAAA-GGGAAAUAACUCC-AGCC-GU------CU-------UUGUGUGGCUUACGAACCCCUUGGCACCCUAUU
CU928162.2/1163305-1163220     GUCGGGAGG-GC-GA-C--G-AAUACAACACCC-GCAA-GGGGAAUA-AGUC-CGCG-GUA---UCUU-------UUGGGCCGU-UUCGAGCCUCCCGGCACCACAUU
BA000007.2/1308311-1308223     GGUCGGGUG-GAGAG-GCGU-AAUACAACACCC-GCAA-GGGGAAUAUGCCCAGAGC-UU------CU-------UAUUUGGCUCAGUUGACACCCGACCGCCAGCUA
ABVY01000196.1/913-997         GUCGGGAGG-GC-GA-C--U-AAUAGAAUACCC-GCAA-GGGGAAUA-AGUC-CGCG-GUU----UCG-------UUAAGCCGU-UUCGAGCCUCCCGGCACCACACC
ABEJ01000006.1/19217-19133     GUCGGGAGG-GC-GA-C--G-AAUACAACACCC-UUAC-GGGGAAUA-AGUC-CGCG-GUC----UCA-------CUGAGCCGUU-UCGAACCUCCCGGCACCACUCC
CP000569.1/589673-589757       GUCGAGAGG-GCGGA-GA----AUACAAUACCC-UUUG-GGGGAAUAAUCCC-GGUC-UA------CU-------UGUGAAGGCUUCUGAACCUCUCGGCACCCUAUU
CP001164.1/3293012-3293101     GGUCGGGUG-GAGAG-GCGU-AAUACAAUACCC-GCAA-GGGGAAUAUGCCC-GGAG-CAU----CUU-------UGAAGGCUCUAGUUGACACCCGAUCACCAGCCA
AAKV01000001.1/130739-130648   UGCCGGGAG---UGG-AC-U-AAUAAAAAACCC-GAAA-GGGAAAUAUGUCC-GGCC-CU------CUAGCUAGGUAGUAGGGUUUCUUAGCUCCCGGCGCCCAGCUU
AAZD01000009.1/15169-15251     GCCGAGAGG-GCGAG-G----AAUAAAAGACCU-UC---GGGGAAUAACUCC-AGCC-GA------CU-------UUGGACGGUUUACGAACCUCUUGGCACCCUAUU
ABZR01000211.1/2031-1946       GUCGGGAGU----GG-AC-C-AAUACAAGACCC-GCAA-GGGGAAUACGUCC-GGCC-UUU---UCUA-------CAUUGGGGUUUCUUAG-CUCCCGACGCCUAGCU
L42023.1/1509724-1509641       GACCGACGG-UGCGA-G--G-AAUACAAUACC--GAAA--GGGAAUAACUCC-GCCA-GA------UU-------GUGUACUGGUUUUGAGCCGUUGGUCGCCCAAUU
AAUR01000002.1/1715-1803       GUUGGGAGG-GC-GA-C--G-AAUACAAUACCC-UUCG-GGGAAAUA-AGUC-CGCG-GCGUUUAUCC-------UUAGGCCGUU-UCGAACCUCCCAACACCAAUCU
AAKI02000002.1/26074-25986     GUUGGGAGG-GC-GA-C--G-AAUACAAUACCC-UUCG-GGGAAAUA-AGUC-CGCG-GCGAUUUUCC-------UUGAGCCGUU-UCGAACCUCCCAGCGCCAAAUU
AASA01000007.1/1180-1266       GUCGGGAGG-GC-GA-C--U-AAUACAAGACC--GAAA--GGAAAUA-CGUCCAGCC-CUUA--CCUU-------AGAGUGGGUUUUCGAACCUCCCGACGCCACUGU
AJ576011.1/759-671             GGUCGGGUG-GAGAG-GCGU-AAUACAAUACCC-GUAA-GGGGAAUAUGCCCAGAGC-UU------CU-------UGUAAGGCUCAGUUGACACCCGACCAACCAGCU
CP000155.1/2965094-2965182     GGCCGGGAG-UU-CU-GCCG-AAUACAAUACCC-GCAA-GGGGAAUAGGCAA-AGCG-GUC----UCG-------UAGAGCCGUUGUCACCCUCCCGGUCGCCUUCUC
AE017143.1/385715-385797       GACCGACAG-UGUGA-G--G-AAUACAAUACC--GCAA--GGGAAUA-ACUC-CGCU-GU-----UCA-------UACUACAGU-UUUGAGCUGUCGGUCGCCCUAAU
AJ566110.1/3784-3701           GAUCGAGAG-UGCGA-G--G-AAUACAAUACC--GCAA--GGGAAUAACUCC-GCUA-GA------GU-------UUCGACUAGUUUUGAGCUCUCGAUCACCCUAAU
CP000672.1/156419-156335       GGUCGGCGG-UGCGA-G--G-AAUACAACACC--GCAA--GGGAAUA-ACUCCGCUA-GC-----UAA-------UAGAUCUAGUUUUGAGCCGCCGACCACCCGAUU
AAZF01000016.1/25482-25399     GACCGACAG-UGCGA-G--G-AAUAUAAUACC--ACAA--GGGAAUA-ACUCCGCUG-UU------CA-------UCUUUACAGUUUUGAGCUGUCGGUCGCCCUACU
CP000057.2/1447819-1447735     GAUCGACAG-UGCGA-C--U-AAUACAAUACC--GCAA--GGGAAUA-CGUCCG-CU-GGA---UUAU-------CUGACCAG-UUUUGAGCUGUCGAUCGCCCUAAC
AF148496.1/14698-14785         GGCCGGGUA-GCGCG-CAGC-UAUACAAGACCC-UUCG-GGGGAAAUCUGCG-GGCG-GU------CC-------UGACACCGUGUUCAAGUACCCGGCCCGUCCUCU
FM866756.1/158-74              --CCGGUUA-GCGCG-CAGC-UAUACAACACCC-UUUG-GGGGAAAUCUGCG-GGCG-GU------CC-------UGACACCGUGUUCAAGUACCGGGCC-GCCCUCU
AE004091.2/3087685-3087772     GGCCGGGUG-GCGCG-CAGC-CAUACAAGACCC-UUCG-GGGGAAAACUGCG-GGCC-GU------CC-------UAGAGCGGUGUUCAAGCGCCCGGCCGCCUCUCU
AF148496.1/12662-12749         GGCCGGGUA-GCGCG-CAGC-UAUACAAGACCC-UUCG-GGGGAAAUCUGCG-GGCG-GU------CC-------UGACACCGUGUUCAAGUACCCGGCCCGUCCUCU
CP000050.1/410075-410162       GGCCGGGUG-GCGCG-CAGC-UAUGCAAUACCC-GAAA-GGGGAAAACUGCG-GGCG-GC------CC-------UACGACCGUGUUCAAGCACCCGGCCGCCUCUCU
AF148496.1/13680-13767         GGCCGGGUA-GCGCG-CAGC-UAUACAAGACCC-UUCG-GGGGAAAUCUGCG-GGCG-GU------CC-------UGACACCGUGUUCAAGUACCCGGCCCGUCCUCU
AF148496.1/4597-4684           GGCCGGGUA-GCGCG-CAGC-UAUACAAGACCC-UUCG-GGGGAAAUCUGCG-GGCG-GU------CC-------UGACACCGUGUUCAAGUACCCGGCCGCCUCUCU
AF421314.1/431-344             GGCCGGGUG-GCGCG-CAGC-CAUACAAGACCC-GAAA-GGGGAAAACUGCG-GGCC-GU------CC-------UAGAGCGGUGUUCAAGCGCCCGGCCGCCCCUCU
CP003057.1/4197433-4197515     GUCGGGAGG-GC-GG-C--U-AAUACAACACCC-UUCG-GGGAAAUA-CGCC-CGCC-GU------CU-------GUCUGCGGUU-UCGAACCUCCCGACAUCCCGUC
CP000057.2/1590260-1590343     GUUCGACAG-UGCGA-C--U-AAUACAAUACC--GAAA--GGGAAUA-AGUCCGCUG-GA------UU-------CUUGACCAGUUUUGAGCUGUCGAACGCCCGAUU
#=GC SS_cons                   (((((((((.,,,<<.<<.-.---------<<<.____.>>>------>>>>.,<<<.<_......__......._____>>>>,,,,,,,)))))))))::::::::
#=GC RF                        GgCcGGggG.GcggG.cc.u.aAUACAAuACCC.GaAA.GGGGAAUAaggCc.gGCc.gu......CU.......uugugcgGUuUUcaAgCccCCgGcCaCCcuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02222
#=GF ID   sX2
#=GF DE   Xanthomonas sRNA sX2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   40.00
#=GF TC   40.40
#=GF NC   31.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   9


AM920689.1/90601-90706   ACCAGCUGUGCAGCCCUAGAGCAUCUAGGCAGCUUAAAGGGUGCAGGCAUCCGCAGUUGGACCACUUUCUU----CGACAGACCCCGUGCAG-GCAUGGAGGUCUGUCGCG
AM039952.1/85087-85196   ACCAGCUGUGCAGCCCUAGAGCAUCUAGGCAGCUUAAAGGGUGCAGGCAUCCGCAGUUGGACCACAUUCGCUCACCGACAGACACCGCGCACCGCGCGGUGUCUUCGUUU-
CP000967.1/44669-44567   ACCAGCUGUGCAGCCCUAGAGCAUCUAGGCAGCUUAAAGGGUGCAGGCAUCCGCAGCUGGACCACAUUCGCUCACCGACAGACACCGCGCGGUGUCUGUCGGU--------
AE008922.1/89757-89862   ACCAGCUGUGCAGCCCUAGAGCAUCUAGGCAGCUUAAAGGGUGCAGGCAUCCGCAGUUGGACCACUUUCUU----CGACAGACCCCGUGCAG-GCAUGGAGGUCUGUCGCG
AE013598.1/46007-45905   ACCAGCUGUGCAGCCCUAGAGCAUCUAGGCAGCUUAAAGGGUGCAGGCAUCCGCAGCUGGACCACAUUCGCUCACCGACAGACACCGCGCGGUGUCUGUCGGU--------
AE008923.1/118491-118600 ACCAGCUGUGCAGCCUUAGAGCAUCUAGGCAGCUUAAAGGGUGCAGGCAUCCGCAGUUGGACCAUCUUCGCUGACCGACAGGCACCGCGCAUUGCGCGGUGUCUUCGUUU-
AP008229.1/130044-130146 ACCAGCUGUGCAGCCCUAGAGCAUCUAGGCAGCUUAAAGGGUGCAGGCAUCCGCAGCUGGACCACAUUCGCUCACCGACAGACACCGCGCGGUGUCUGUCGGU--------
CP000050.1/89756-89861   ACCAGCUGUGCAGCCCUAGAGCAUCUAGGCAGCUUAAAGGGUGCAGGCAUCCGCAGUUGGACCACUUUCUU----CGACAGACCCCGUGCAG-GCAUGGAGGUCUGUCGCG
CP003057.1/184260-184153 ACCAGCUGUGCAGCCCUAGAGCAUCUAGGCAGCUUAAAGGGUGCAGGCAUCCGCAGCUGGACCACAUUCGCUCACCGACAGACACCGCGCGGUGUCUGUUGGU--GAUGU-
#=GC SS_cons             :((((((((<<-<<-<<<<_____>>>>>>->>,,,,,<<<<<____>>>>>))))))))----------------<--<<<<-<<<<<_____>>>>>-->>>>-->::.
#=GC RF                  ACCagCuGuGCAGCCcuaGAGCAUCuagGCAGCUUAAAGGguGCAGGCauCCgCaGcuGGACCAcaUUCgcUcAcCgACaggcacCgcgCaguGcgcGguGgccugucgu.
//
# STOCKHOLM 1.0

#=GF AC   RF02223
#=GF ID   sX4
#=GF DE   Proteobacterial sRNA sX4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   70.20
#=GF NC   65.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   5


AM920689.1/3837482-3837316 ACCGGGGACC-AUCUGGAGAGGUGGCAGAGCGGUUGAAUGUACCUGACUCGAAAUCAGGCAGGCGUUUAUAGCGCCUCGGG-GGUUCGAAU---CCCCCCCUCUCCGCCAGAUUGUGGUGACGCGUUGUGCCAAUGCCGCGUGAGUUUCGCCGGCGUCAUUGGGGGGUGAGA
AM039952.1/1235373-1235528 ---------------GUAGGGGACACUUCCCACUGAGGGUUUCCCGGCGUAAGUUCCUGAACA-AUUUGCGGAAAUUGGUGUGGGUCGUAUUGUCCCCCCCUCUCCGCCAGAUUGAGGCGAGUAGGUGCGCCAGUGCCGCGUGGGUUUCGCCGGCGGCAUUGGGGGGUGAGA
CP000050.1/3896546-3896380 ACCGGGGACC-AUCUGGAGAGGUGGCAGAGCGGUUGAAUGUACCUGACUCGAAAUCAGGCAGGCGUUUAUAGCGCCUCGGG-GGUUCGAAU---CCCCCCCUCUCCGCCAGAUUGUGGUGACGCGUUGUGCCAAUGCCGCGUGAGUUUCGCCGGCGUCAUUGGGGGGUGAGA
AE008923.1/1246268-1246435 ACUGGGGACCCAUCUGGAGAGGUGGCAGAGCGGUUGAAUGUACCUGACUCGAAAUCAGGCAGGCGUUUAUAGCGCCUCGGG-GGUUCGAAU---CCCCCCCUCUCCGCCAGAUUGAGGCGAGCAGUUGUGCCAGUGCCGCGUGAGUUUCGCCGGCGGCAUUGGGGGGUGAGG
AE008922.1/1144003-1144169 ACCGGGGACC-AUCUGGAGAGGUGGCAGAGCGGUUGAAUGUACCUGACUCGAAAUCAGGCAGGCGUUUAUAGCGCCUCGGG-GGUUCGAAU---CCCCCCCUCUCCGCCAGAUUGUGGUGACGCGUUGUGCCAAUGCCGCGUGAGUUUCGCCGGCGUCAUUGGGGGGUGAGA
#=GC SS_cons               :((((((,,,.,<<<<_________>>>><<---<<<<<<<-<<<<<_______>>>>>--->>>>>>>-->>,))))))-.---------...-((((((,,,,<<<<_______>>>>,,,,,,,,,,,,,,<<<<<-<<<_____>>>>>>>>,,,,,)))))):::::
#=GC RF                    ACcGgGGACC.AuCuGgAGaGGuggCaGagCggUugaacGcaCcuGaCucgAaauCagGcAggCguucauaGcgCCcCgGG.GGuUCGaAU...CCCCCCCUCUCCgCCAGAUUGuGGcGAguaGuUGuGCCAauGCCGCGuGaGUUUCgCCGGCguCAUUGGGGGGUGAGA
//
# STOCKHOLM 1.0

#=GF AC   RF02224
#=GF ID   sX5
#=GF DE   Xanthomonadaceae sRNA sX5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   61.60
#=GF NC   45.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   10


AM920689.1/3085438-3085486 CGAAGUCCGUUUGCUCCCCUCCCCUCACGGCUUC-GGACUGGCGGGUCUU
AM039952.1/1899085-1899037 CGAAGUCCGUUUGCUCCCCUCCCCUCACGGCUUC-GGACUGGCGGGUCUU
CP000967.1/2196602-2196554 CGAAGUCCGUUUGCUCCCCUCCCCUCACGGCUUC-GGACUGGCGGGUCUU
AE008923.1/1894987-1894939 CGAAGUCCGUUUGCUCCCCUCCCCUCACGGCUUC-GGACUGGCGGGUCUU
AE008922.1/1853354-1853306 CGAAGUCCGUUUGCUCCCCUCCCCUCACGGCUUC-GGACUGGCGGGUCUU
AE013598.1/2551964-2552012 CGAAGUCCGUUUGCUCCCCUCCCCUCACGGCUUC-GGACUGGCGGGUCUU
AP008229.1/2530105-2530153 CGAAGUCCGUUUGCUCCCCUCCCCUCACGGCUUC-GGACUGGCGGGUCUU
CP001111.1/2837797-2837845 CGGCUGCCGUUUG-UUCCCUCCCCUCACGGCUUCAGGAUUGGCGGGUUUU
CP000050.1/3188911-3188959 CGAAGUCCGUUUGCUCCCCUCCCCUCACGGCUUC-GGACUGGCGGGUCUU
AM743169.1/3139706-3139754 CGGCUGCCGUUUG-UUCCCUCCCCUCACGGCUUCAGGAUUGGCGGGUUUU
#=GC SS_cons               ::::::<<<<--<-<<<-----<<____>>----.>>>>-->>>>:::::
#=GC RF                    CGAAGUCCGUUUGCUCCCCUCCCCUCACGGCUUC.GGACUGGCGGGUCUU
//
# STOCKHOLM 1.0

#=GF AC   RF02225
#=GF ID   sX6
#=GF DE   Proteobacterial sRNA sX6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT
#=GF SS   Predicted; RNAalifold
#=GF GA   40.00
#=GF TC   42.00
#=GF NC   39.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   8


AM920689.1/2972365-2972031 UCACCGAACCAGGAGCAGAC-CCAUGAAGUUCAAGCACAUUCUGAUGCUCACCCUGGGCGCCGCCGCGAUUGCAGCACUGCCGGCCAUCGCGCAGACCGCUCCGCCACAG---GGGCAAGGCGCCAGCGCGCAGAAGGCCAAUGACGAGAAGGCCAAGACCGAGGCCGAGCGCAAGGCCGAGCGCCGCGCCGCUGCCGCCAAGGCCAGGCCGGAAGCCGGCCAGGCCCCGCGCGAAGAAGAGGAAGAAGAGAAGCCGUCGCGCUGA--GGACAGC---GCAGGUUUCGCCCGCAGACGCCCCGGCUCCGGCCGGGGCGUCUGCAUUUGCACGGUGUGCGUGCAU
AM039952.1/1971505-1971845 UCACCGAAGCCAAAGAGGACGCCAUGAAGUUCAAGCACAUCCUGAUGCUCACCCUCGGUGCGGCCGCAGUCGCAGCGCUUCCCGCCAUGGCCCAGGCCGCUCCGCAGCAGACCGGACAGGGCGCCGCGGCUCAAAAGGCCGAUGACGCGAAGGCCAAGACCGAAGCCGAACGCAAAGCCGAACGCCGCGCUGCCGCCGCUGCGCAGAAGCCCAAGGCCGACAGCGCCCCGCGCGAGGAAGAGGAAGAAGAAAAGCCUGCACGCUGAUCGCGCGGCCUAGCGGCCAGGUGCUACCGACGCCCCGGCAUU-GCCGGGGCGUUCGCUUUUGG--GGUAGCUGUGUAA
CP000967.1/1699097-1699436 UCGACGAAGCUAAGGAGGACGCCAUGAAGUUCAAGCACAUCGUGAUGCUCACCCUCGGUGCGGCCGCAGUCGCAGCGCUCCCCGCCAUGGCCCAGGCCGCUCCGCAGCAGACCGGGCAGGGCGCCACCGCGCAGAAGGCGGGCGACGCCAAGGCCAAGAGCGAAGCCGAGCGCAAGGCCGAACGCCGCGCCGCCGCUGCCGCGCAGAAGCCCAAGGGCGACGUGUCACCGCGUGAGGAAGAGGAAGAACAGACGCCGGCGCGCUGAUUUUUUCGCAUCGCUUGAGUGAUACGCAGACGCCCCGGCUCAGGCCGGGGCGUCUGCAUUUGC--GGC--CCGCGCAA
AE008922.1/1973962-1974296 UCACCGAACCAGGAGCAGAC-CCAUGAAGUUCAAGCACAUUCUGAUGCUCACCCUGGGUGCCGCCGCGGUUGCAGCACUGCCGGCCAUUGCGCAGACCGCUCCGCCACAG---GGGCAGGGCGCCAGCGCGCAGAAGGCCAAUGACGACAAGGCCAAGACCGAGGCCGAGCGCAAGGCCGAGCGCCGCGCCGCUGCUGCCAAGGCCAAGCCGGAAGCAGGCCAGGCCCCGCGCGAAGAAGAGGAAGAAGAGAAGCCGUCGCGCUGA--GGACAGC---GCAGGUUUCGCCCGCAGACGCCCCGGCUCCGGCCGGGGCGUCUGCAUUUGCACGGUGUGCGUGCAU
AE008923.1/1976875-1977215 UCACCGAAGCCAAAGAGGACGCCAUGAAGUUCAAGCACAUCCUGAUGCUCACCCUCGGUGCGGCCGCAGUGGCAGCGCUUCCCGCCAUGGCCCAGGCCGCUCCGCAGCAGACCGGACAGGGCGCCGCCGCUCAAAAGACCGACGACGCGAAGGCCAAGACCGAAGCCGAGCGCAAGGCCGAACGCCGCGCCGCCGCUGCCGCGCAGAAGCCCAAGGCCGAUAGCGCCCCGCGCGAGGAAGAGGAAGAAGAAAAGCCUGCACGCUGAUCGCGCGGCCUAGCCGCCGGAUCUUAACGACGCCCCGGCAUU-GCCGGGGCGUUUACUUUUGG--AACAUGUCAGACC
AE013598.1/3174425-3174086 UCGACGAAGCUAAGGAGGACGCCAUGAAGUUCAAGCACAUCGUGAUGCUCACCCUCGGUGCGGCCGCAGUCGCAGCGCUCCCCGCCAUGGCCCAGGCCGCUCCGCAGCAGACCGGGCAGGGCGCCACCGCGCAGAAGGCGGGCGACGCCAAGGCCAAGAGCGAAGCCGAGCGCAAGGCCGAACGCCGCGCCGCCGCUGCCGCGCAGAAGCCCAAGGGCGACGUGUCACCGCGUGAGGAAGAGGAAGAACAGACGCCGGCGCGCUGAUUUUUUCGCAUCGCUUGAGUGAUACGCAGACGCCCCGGCUCAGGCCGGGGCGUCUGCAUUUGC--GGC--CCGCGCAA
AP008229.1/3167098-3166759 UCGACGAAGCUAAGGAGGACGCCAUGAAGUUCAAGCACAUCGUGAUGCUCACCCUCGGUGCGGCCGCAGUCGCAGCGCUCCCCGCCAUGGCCCAGGCCGCUCCGCAGCAGACCGGGCAGGGCGCCACCGCGCAGAAGGCGGGCGACGCCAAGGCCAAGAGCGAAGCCGAGCGCAAGGCCGAACGCCGCGCCGCCGCUGCCGCGCAGAAGCCCAAGGGCGACGUGUCACCGCGUGAGGAAGAGGAAGAACAGACGCCGGCGCGCUGAUUUUUUCGCAUCGCUUGAGUGAUACGCAGACGCCCCGGCUCAGGCCGGGGCGUCUGCAUUUGC--GGC--CCGCGCAA
CP000050.1/3066163-3065829 UCACCGAACCAGGAGCAGAC-CCAUGAAGUUCAAGCACAUUCUGAUGCUCACCCUGGGUGCCGCCGCGGUUGCAGCACUGCCGGCCAUUGCGCAGACCGCUCCGCCACAG---GGGCAGGGCGCCAGCGCGCAGAAGGCCAAUGACGACAAGGCCAAGACCGAGGCCGAGCGCAAGGCCGAGCGCCGCGCCGCUGCUGCCAAGGCCAAGCCGGAAGCAGGCCAGGCCCCGCGCGAAGAAGAGGAAGAAGAGAAGCCGUCGCGCUGA--GGACAGC---GCAGGUUUCGCCCGCAGACGCCCCGGCUCCGGCCGGGGCGUCUGCAUUUGCACGGUGUGCGUGCAU
#=GC SS_cons               :::::::::::::::::::::{{,,,,,[[[[--[[------[[-[[[[[,,,,,,<<<<<-<<_______>>->>>>>,,,((((,,,,,,,,,,<<--<<<__________>>>-->><<<<____>>>>,,,,)))),,,,,,,,,,,<<<__________>>>]]]]]]]--]]-]]]],,(((((,,,,<<<__________>>>,,,,,<<_______>>,,,))))),,,,,,,}}----------------((((,,,,,,,,,,<<___>>,,,,,,,,,,,<<<<<<<<<<<<<<____>>>>>>>>>>>>>>,,,,,,..,,,,,,,))))::
#=GC RF                    UCacCGAAgCuaaaGagGACGCCAUGAAGuuCAAGCACAUccuGAuGCuCACCCUcgGcGCgGCCGCaGUuGCAGCgCuuCCgGCCAUgGCcCAGgCCGCcCCGCagCAGACCGGgCAGGGcGCCaccGCgCAgAAGGCcgauGACGccAAGGCCAAGAcCGAaGCCGaGCgCaAGGCCGaaCGCCGCGCcGCcGCuGCcgcGcagAaGCCcaAgGccGacaaggCcCCGCGCGAgGAAGAGGAAGAAgAgAaGCCggCgCgCUGAUuguacaGCaUaGCugguuugauacGcaGaCGCCCCGGCucuGGCCGGGGCGuCugCaUUUGc..GGuaugcGcGcAa
//
# STOCKHOLM 1.0

#=GF AC   RF02226
#=GF ID   sX7
#=GF DE   Xanthomonas sRNA sX7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT
#=GF SS   Predicted; RNAalifold
#=GF GA   55.00
#=GF TC   57.20
#=GF NC   47.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   8


AM920689.1/2945220-2945125 AGUUUUCCCUAUCGCGGGGACGGCGGAGUCAGUGCCGUCGCUCCUCGCGGUAGUUCUAUCGAAAGCCAGGAGGGCGGGCGCCACGGACGGCGCAUU
AM039952.1/1995660-1995754 AGUUUU-UCUAUCGCGGGGACGGCGGAGUCAGUGCCGUCGCUUCUCGCGGUAGAUCUAUCGAAGGCCAGGAGGGCAGGCGCCAUGGACGGCGCAUU
CP000967.1/1723554-1723648 AGUUUU-UCUAUCGCGAGGACGGCGGAGUCAGUGCCGUCGCUUCUCGCGGUAGAUCUAUCGAAGGCCAGGAGGGCAGGCGCCACGGACGGCGCAUU
AE013598.1/3150074-3149980 AGUUUU-UCUAUCGCGAGGACGGCGGAGUCAGUGCCGUCGCUUCUCGCGGUAGAUCUAUCGAAGGCCAGGAGGGCAGGCGCCACGGACGGCGCAUU
AE008922.1/2001108-2001203 AGUUUUCCCUAUCGCGGGGACGGCGGAGUCAGUGCCGUCGCUCCUCGCGGUAGUUCUAUCGAAAGCCAGGAGGGCGGGCGCCACGGACGGCGCAUU
AE008923.1/2001102-2001196 AGUUUU-UCUAUCGCGAGGACGGCGGAGUCAGUGCUGUCGCUUCUCGCGGUAGAUCUAUCGAAGGCCAGGAGGGCAGGCGCCAUGGACGGCGCAUU
AP008229.1/3142767-3142673 AGUUUU-UCUAUCGCGAGGACGGCGGAGUCAGUGCCGUCGCUUCUCGCGGUAGAUCUAUCGAAGGCCAGGAGGGCAGGCGCCACGGACGGCGCAUU
CP000050.1/3038998-3038903 AGUUUUCCCUAUCGCGGGGACGGCGGAGUCAGUGCCGUCGCUCCUCGCGGUAGUUCUAUCGAAAGCCAGGAGGGCGGGCGCCACGGACGGCGCAUU
#=GC SS_cons               ::::::.:<<<<<<<<<<<<<<<<<<________>>>>>>->>>>>>>>>>>>,,,,,,,,,,,<<<_____>>>,,<<<<<______>>>>>:::
#=GC RF                    AGUUUU.uCuacCGCGgGgaCGgCGGAGUCAGUGCCGcCGCucCcCGCGguaGaUCUAUCGAAgGCCAGGAGGGCaGGCGCCAcGGACGGCGCAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02227
#=GF ID   sX8
#=GF DE   Proteobacterial sRNA sX8
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   50.00
#=GF TC   72.50
#=GF NC   33.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   12


AE003849.1/1705273-1705354     CUUCGCUGACCACCUCGGCGAAGAAAGUGUUCGGGAAACAACGACUUACGCGCCUAGUAAAUGUCUCGUUUCCCGCUCCAAU
AM039952.1/2740875-2740956     CUUCGCUGGCCACCUCGGCGAAGAAAGGGUUUGGGAAACAACGACUUAUGCGCCUAGUGCAAGUCUCGUUUCCCGCUCCAAA
CP000270.1/3559500-3559419     CUUCGCUGGCCACCUCGGCGAAGAAAGAGCUUGGGAAUCAACGACUUACUGCCCUAGUAAACGUCUCGUCUCCCGCUCCAAA
CP000539.1/1516345-1516426     CUUCGCUGGCCACCUCGGCGAAGAAAGGGUUUGGGAAACAACGACUUAUGCGCCUAGUGCAAGUCUCGUUUCCCGCUCCAAA
AM902716.1/1493620-1493539     CUUCGCUGGCCACCUCGGCGAAGAAAGAGCUUGGGAAUCAACGACUUACUGCCCUAGUAAACGUCUCGUUUCCCGCUCCAAU
CP001392.1/1241889-1241970     CUUCGCUAGUCAAGCCAGCGAAGAAAGUGAUUGGGAAACAACGGCUUACGGUCUUAGUAAACGUCUCGUUUCCCGCUCCAAA
AAQW01000001.1/3494121-3494040 CUUCGCUGCUCACCACAGCGGAGAAAGUGAUUGGGAAACAGAGACUUAUCGCUCUAGUGCAUGACUCGUUUCCCGCUCCAAA
AE008922.1/2465860-2465779     CUUCGCUAAGCACCGAGGCGAAGAAAGUAAUUGGGAAUCAACGACUUAGCGCUCUAAAGCAUGACUCGUUUCCCGCUCCAAA
AAKW01000022.1/158662-158581   CUUCGCUGAUCACCACAGUGGAGAAAGUGAUUGGGAAACAGAGACUUAGCGCUCUAGUGCAUGACUCGUCUCCCGCUCCAAU
CP000774.1/3615044-3614963     CUUCGCUGCUCACGGCGGCGAAGAAUGUGAUUGGGAAACAAGGAUUUAGCGCCCUAGUGCCUGUCUCGUUUCCGGCUCCACA
ABMY01040726.1/95-19           -----CUGAUCACCACAGUGAAGAAAGUGAUUGGGAAACAGAGACUUAGCGCUCUAGUGCAUGACUCGUUUCCCGCUCCAGA
CP001616.1/2621241-2621160     CUUCGUUGAAGCCCUCAGCGAAGAAAAGAGUUGGAAAACAUACGCUUAGCGCGUCAGUGCUAGUCCCGUCUCCCGCUCCAAU
#=GC SS_cons                   <<<<<<<<<_____>>>>>>>>>-----<<-<<<<<<<<---<<<----<<<____>>>--->>>-->>>>>>>>->>::::
#=GC RF                        CUuCGCugcuCACcgcaGCGaAGAAAGuGaUuGGGAaaCAaaGaCUUAgcgccCUAgugcAuGuCUCGuuUCCCgCuCCAAa
//
# STOCKHOLM 1.0

#=GF AC   RF02228
#=GF ID   sX9
#=GF DE   Xanthomonas sRNA sX9
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   44.00
#=GF TC   44.10
#=GF NC   43.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   16


AM039952.1/2929816-2929890   AGGCGCUGCUCGGACACCCCGGCUCC-GCUGCGCCGGCCAUG-CCAGCUGACGGCUGGUCGCGGUGUGAUGUCGACC-
AE008923.1/2798898-2798972   AUGUGCUACUCGUACACUCCGGUUCC-GCUGCGCGGGCAAUG-CCAGCUGACGGCUGGUCGCUCUGUGGUGUCGACC-
AE013598.1/1973885-1973959   AUGUCCCACUCGAACACUCCGGUUCC-UCUGCGCCGUCCGCAGCCAGCUGACGGC-GCUCGCUACGUGUU-UUAGCCG
CU694975.3/24187-24112       AUGUACCACCCGUACACUCCGGUUCC-UCCGCGCCGUCCACACCCACCUGACGACUGCUCGCUACGUUUUGUUAGCC-
AM920689.1/458839-458914     AUGUACCACUCGUACACUGCGGUUCC-UAGGCUCCUUCCGCGCCCACCUGACGGCUGUUCGCUAUGUUUUGUCAGCC-
AP008229.1/4403283-4403358   AUGUACCACGCGUACACUGCGGUUCC-CCCGCGCCGUCCACACCCGCCUGACGGCUGCUCGCUACGUUCUGUUAGCC-
AE008922.1/1724182-1724108   AUGUGCC-CACGUACACUCCGGUUCC-UCCGCGCCGUCCGCACCCACCUGACGGCUGCUCGCUACGUUUUGUUAGCC-
CP000967.1/2402615-2402539   AUGUGCCACUCGUACACUGCGGUUCUGACCGCGCCGUCCGCGCCCACCUGACAGCGGCUCGCUACGUUGUGUUAGCC-
AY010120.2/7073-6997         AUGUACCACGCGUACACUCCGGUUCUGAGUGCGCCGUCCGCACCCACCUGACGACUGCUCGCUACGUUUUGUUAGCC-
CP000050.1/184667-184741     AUGUACC-GACGUACACUGCGGUUCC-UCCGCGCCGUCCGCACCCAGCUGACGACUGCUCGCUACGUUUUGUCAGCC-
AF303107.1/1745-1818         AUGUACC--CCGUACACGCCGGUUCC-UCCGCGCCGUCCGCACCCACCUGACGGCUGCUCGCUACGUUUUGUUAGCC-
AY228335.1/24031-23956       AUGUGCCACCCGCACAUUUCGUUUCC-UUCGCGCCGUCCGCACCCACCCGACGACUGCUCGCUACAUAGUGUUAGCA-
AJ586576.1/1612-1538         AUGUACCACUCGUACACACCGGUUCC-UGCGUGCUGCGCGGU-ACGCCUGAGAGUCGCUCGCUAUGUUUUGUUAUCC-
ACIS01000003.1/401658-401583 AUGGACUACGUGUCCAUUCCGGUUCC-UGAGCUCCAGCCGCCCCUCGCUGACGACCGCUCGUUACACUUUGAGAGCC-
FJ827773.1/140-208           AUGCG-------UACAGUGGGGCGCG-CGAGCGCCAUCCACACCCACCUGAUCGCUGCUCGCUCCGUUUUGUUAGCC-
CP003057.1/1871786-1871710   AUGUGCCAGUCGUACACUCCGGUUCUGCGCGCGCCGUCCGUGCCCACCUGACAGCUGCUCGCUACGUUUUGUUAGCC-
#=GC SS_cons                 :<<<<<_____>>>>>,,,<<<<-<_.___>->>>>-----------<<<<<<<______________>>>>>>>::.
#=GC RF                      AUGuaCCACuCGuaCACUccGGuUCC.uccGCgCCguCCGcaCCCAcCugACgaCUGCUCGCUACGUUuuGUuaGCC.
//
# STOCKHOLM 1.0

#=GF AC   RF02230
#=GF ID   sX11
#=GF DE   Proteobacterial sRNA sX11
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   70.00
#=GF TC   71.50
#=GF NC   38.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   10


AM920689.1/1028434-1028297   ACGCCAGUCGCAGCCCCCCUU-UGGUCCUACUCCCCAAGAGGCCAAAUCCCCAGGGAGCUCAUGCUGU-GGGGCUUUGAGCAAGCUCAUUACUGGCGCCAUU---ACUGCCCCGGUCGU----CAUGU-----ACGACCGGGGUUUUUCUUU
AM039952.1/4069950-4070087   ACGCCAGUCGCAGCAUCCCUU-UGGUCCUACUCCCCAAGAGGCCAAAUCCCCAGGGAGCUCAUGCUGUUGGGGCUCUGAGCAAGCCUACUACUGGCGUUAUU----CUGCCCCGGGCGU----CUUGU-----ACGUCCGGGGUUUUUCUUU
CP000967.1/4434236-4434373   ACGCUAGUCGCAGUAUCCCUU-UGGUCCUACUCCCCAAGAGGCCAAAUCCCCAGGGAGUUCAUGCUGUUGAGGCUCUGAGCAAGCCUACUACUGGCGUUGUU----CUGCCCCGGACGU----CUUGU-----ACGUCCGGGGUUUUUCUGU
AE008923.1/4047263-4047400   ACGCCAGUCGCAGUAUCCCUU-UGGUCCUACUCCCCAAGAGGCCAAAUCCCCAGGGAGCUCAUGCUGUCGGGGCUCUGAGCAAGCCUACUACUGGCGUUAUU----CUGCCCCGGGCGU----CUUGU-----ACGUCCGGGGUUUUUCUUU
AE013598.1/996627-996490     ACGCUAGUCGCAGUAUCCCUU-UGGUCCUACUCCCCAAGAGGCCAAAUCCCCAGGGAGUUCAUGCUGUUGAGGCUCUGAGCAAGCCUACUACUGGCGUUGUU----CUGCCCCGGACGU----CUUGU-----ACGUCCGGGGUUUUUCUGU
AE008922.1/3907502-3907639   ACGCCAGUCGCAGCACCCCUU-UGGUCCUACUCCCCAAGAGGCCAAAUCCCCAGGGAGCUCAUGCUGU-GGGGCUUUGAGCAAGCUCAUUACUGGCGCCAUU---ACCGCCCCGGUCGU----CAUGU-----ACGACCGGGGUUUUUCUUU
AP008229.1/965395-965258     ACGCUAGUCGCAGUAUCCCUU-UGGUCCUACUCCCCAAGAGGCCAAAUCCCCAGGGAGUUCAUGCUGUUGAGGCUCUGAGCAAGCCUACUACUGGCGUUGUU----CUGCCCCGGACGU----CUUGU-----ACGUCCGGGGUUUUUCUGU
CP000050.1/1052672-1052535   ACGCCAGUCGCAGCACCCCUU-UGGUCCUACUCCCCAAGAGGCCAAAUCCCCAGGGAGCUCAUGCUGU-GGGGCUUUGAGCAAGCUCAUUACUGGCGCCAUU---ACCGCCCCGGUCGU----CAUGU-----ACGACCGGGGUUUUUCUUU
ACDV01000026.1/115588-115441 CUGCCAGCCGCAGUACCCGAACCGGUCCUACUCCCCAAGAGGCCA-UCCCCAAGGGAGCUCAUGCUGC-GGGGCCCUGAGCAAGCCCUCUGCUGGCGCCUAUCAAACGACACAGGCCUGA-UCCUCGCGG-ACCAGGCCUGUGUUUUUUUGC
CP001111.1/3703939-3704087   CUGCCAGCCGCAGUACCCGAACCGGUCCUACUCCCCAAGAGGCCA-UCCCCAAGGGAGCUCAUGCUGC-GGGGCCCUGAGCAAGCCCUCUGCUGGCGCCUAUG-AAACGACACAGGCCUGAUCCUCGCGGACCAGGCCUGUGUUUUUUGCGC
#=GC SS_cons                 [[[[[[[[,(((((((,,,<<.<<<<<<<________>>->>>>>>><<<____>>>,,,,))))))).,<<<<<_______>>>>>,,,]]]]]]]]----...---<<<<<<<<<<<...._____.....>>>>>>>>>>>::::::::
#=GC RF                      gcGCcaGcCgCaGcacCCcuu.uGGuCCuACUCCCCAaGAGgCCaaauCCCcAGGGaGcUCgugCuGc.GgGGCucUGAGCAaGCCcacUgCugGCgcuauU...AcugccccGGgCgu....CuuGu.....acGcCCggggcUUUUcUgu
//
# STOCKHOLM 1.0

#=GF AC   RF02231
#=GF ID   sX12
#=GF DE   Xanthomonas sRNA sX12
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   70.00
#=GF TC   102.90
#=GF NC   38.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0009405; pathogenesis;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   8


AM920689.1/4309963-4310040 GAGGCCUGCACAUCCUCGUCGAAAGGUUCCACUGCAGGCUGCGUCUAGGAGCCCUGGGAGACCGGGGCUCCUGCUUUU
AM039952.1/4358796-4358873 GAGGCCUGCACAUCCUCGUCGAAAGGUAGCGCCGCAGGCCGCGUCUGGGAGCCCUGGGAGACCGGGGCUCCUGCUUUU
CP000967.1/4689093-4689170 GGCGCCUGCACAUCCUCGUCGAAAGGUAUCGCCGCAGGCCGCGUCUAGGAGCCCUGGGAGACCGGGGCUCCUGCUUUU
AE013598.1/744496-744419   GGCGCCUGCACAUCCUCGUCGAAAGGUAUCGCCGCAGGCCGCGUCUAGGAGCCCUGGGAGACCGGGGCUCCUGCUUUU
AE008923.1/4334636-4334713 GAGGCCUGCACAUCCUCGUCGAAAGGUACCGCCGCAGGCCGCGUCUAGGAGCCCUGGGAGACCGGGGCUCCUGCUUUG
AE008922.1/664027-663950   GAGGCCUGCACAUCCUCGUCGAAAGGUUCCACUGCAGGCUGCGUCUAGGAGCCCUGGGAGACCGGGGCUCCUGCUUUU
AP008229.1/714023-713946   GGCGCCUGCACAUCCUCGUCGAAAGGUAUCGCCGCAGGCCGCGUCUAGGAGCCCUGGGAGACCGGGGCUCCUGCUUUU
CP000050.1/4372195-4372272 GAGGCCUGCACAUCCUCGUCGAAAGGUUCCACUGCAGGCUGCGUCUAGGAGCCCUGGGAGACCGGGGCUCCUGCUUUU
#=GC SS_cons               ::<<<<<<<---------------<<_____>>>>>>>>>-----<<<<<<<<<<<<____>>>>>>>>>>>>:::::
#=GC RF                    GagGCCuGCACAUCCUCGUCGAAAgGUauCgCcGCaGGCcGCGUCuaGGaGCCCuGGGAGACCgGGGCuCCugCUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02232
#=GF ID   sX13
#=GF DE   Xanthomonadaceae sRNA sX13
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   50.00
#=GF TC   66.70
#=GF NC   41.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   12


AM920689.1/4756283-4756169 AACGCCUGUC-GGCAGAUCUC-UCC-CAUCCCCUGGAGCAGAUCU--CGGAGCGGAAACUCCUCCCCAAGUUUCCGUUCCCUGGCCCCGCCGACCU--CCCCCUGGUCUGCGGGGCUUUUUA
AM039952.1/4810196-4810082 AACGCCUGUC-GGUAGAUCUC-UCC-CAUCCCCUGGAGCAGAUCU--CGGAGCGGAAACUCCUCCCCAAGUUUCCGUUCCCUGGCCCCGCCGACCU--CCCCCUGGUCUGCGGGGCUUUUUA
CP000967.1/575770-575884   AACGCCUGUC-GGCAGAUCUC-UCC-CAUCCCCUGGAGCAGAUCU--CGGAGCGGAAACUCAUCCCCAAGUUCCCGCUCCCUGGCCCCGCCGACCU--CCCCCUGGUCUGCGGGGCUUUUUA
AE013598.1/4515226-4515112 AACGCCUGUC-GGCAGAUCUC-UCC-CAUCCCCUGGAGCAGAUCU--CGGAGCGGAAACUCAUCCCCAAGUUCCCGCUCCCUGGCCCCGCCGACCU--CCCCCUGGUCUGCGGGGCUUUUUA
AE008923.1/4814948-4814834 AAUGCCUGUC-GGCAGAUCUC-UCC-CAUCCCCUGGAGCAGAUCU--CGGAGCGGAAACUCCUCCCCAAGUUUCCGUUCCCUGGCCCCGCCGACCU--CCCCCUGGUCUGCGGGGCUUUUUU
AE008922.1/4765833-4765719 AACGCCUGUC-GGCAGAUCUC-UCC-CAUCCCCUGGAGCAGAUCU--CGGAGCGGAAACUCCUCCCCAAGUUUCCGUUCCCUGGCCCCGCCGACCU--CCCCCUGGUCUGCGGGGCUUUUUA
AP008229.1/4512673-4512559 AACGCCUGUC-GGCAGAUCUC-UCC-CAUCCCCUGGAGCAGAUCU--CGGAGCGGAAACUCAUCCCCAAGUUCCCGCUCCCUGGCCCCGCCGACCU--CCCCCUGGUCUGCGGGGCUUUUUA
CP000050.1/4839952-4839838 AACGCCUGUC-GGCAGAUCUC-UCC-CAUCCCCUGGAGCAGAUCU--CGGAGCGGAAACUCCUCCCCAAGUUUCCGUUCCCUGGCCCCGCCGACCU--UUCCCUGGUCUGCGGGGCUUUUUA
CP001111.1/4436013-4435900 AACGCCUGUU-G-UGGAUCUC-UCC-CAUCCCCUGGAGCAGAUCU--CGGAACGGGGACUCCUCCCCAAGUGCCCGUUCCCCGGCCCCGUUGACCU--CCCCCUGGUCAGCGGGGCUUUUUA
AM743169.1/4710929-4710816 AACGCCUGUU-G-UGGAUCUC-UCC-CAUCCCCUGGAGCAGAUCU--CGGAACGGGGACUCCUCCCCAAGUGCCCGUUCCCCGGCCCCGUUGACCU--CCCCCUGGUCAGCGGGGCUUUUUA
AE003849.1/1055829-1055946 AAUGCUUGCCUGUAGGAUCUC-UCCUAAUCCCCUGGAGAAGAUCGU-UGGAGCGGGGAUUCAUCCCCAA-UCCCCGCUUC-UGGCCUCGCCGACCUAAUCCCCUGGUCAGCGAGGCUUUUUA
AATO01005714.1/691-804     AACGCCUGUC-G-CGGAUCUCCUCC-CUUCCCCUGGAGCAGAUCCACCGGGGCCGG-ACUCCUCCCCAAGU--CCGGCUCCCCGCCCCGCCCGGCU--CCCCCUGCCCGGCGGGGCUUUUUU
#=GC SS_cons               :::<<<____.>>><<<<<<<.<<<.________>>>>->>>>>>..,<<<<<<<<<<<<________>>>>>>>>>>>>,,<<<<<<<<-<<<<_..______>>>>->>>>>>>>:::::
#=GC RF                    AAcgccUGUc.ggcgGauCuC.uCC.cAUCCCCUGGaGcaGauCc..cGGagCGGggaCuCcUCCCCAaGuccCCGcuCCCugGCCcCGccGacCU..ccCCCUGguCugCGgGGCcUUUUa
//
# STOCKHOLM 1.0

#=GF AC   RF02233
#=GF ID   sX14
#=GF DE   Xanthomonas sRNA sX14/Xoo3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   106.10
#=GF NC   53.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF RN   [2]
#=GF RM   21276262
#=GF RT   Identification and functional characterization of small non-coding RNAs in
#=GF RT   Xanthomonas oryzae pathovar oryzae.
#=GF RA   Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT
#=GF RL   BMC Genomics. 2011;12:87.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   8


AM920689.1/4930438-4930347 GUCCGAUGUCAGUCGGAAGUUGUGCCACGCAUUGUCCACCGGGCUUGUCCCGGUUUUUGAAGGGAUCGGGCCUUGUGCCCGAUCCUUUUUUU
AM039952.1/5040690-5040599 GUCCGAUGUCAGUCGGAAGCUGUGCCACUCAUUGUCCACCGGGCUUGUCCCGGUUUUCGAAGGGAUCGGGCCUUGUGUCCGAUCCUUUUUUU
CP000967.1/250669-250760   GUCCGAUGUCAGUCGGAAGCUGUGCCACUCAUUGUCCACCGGGCUUGCCCCGGUUUUCGAAGGGAUCGCGCCUUGUGCCCGAUCCUUUUUUU
AE013598.1/260825-260916   GUCCGAUGUCAGUCGGAAGCUGUGCCACUCAUUGUCCACCGGGCUUGCCCCGGUUUUCGAAGGGAUCGCGCCUUGUGCCCGAUCCUUUUUUU
AE008922.1/4927229-4927138 GUCCGAUGUCAGUCGGAAGUUGUGCCACGCAUUGUCCACCGGGCUUGUCCCGGUUUUUGAAGGGAUCGGGCCUUGUGCCCGAUCCUUUUUUU
AE008923.1/5051592-5051501 GUCCGAUGUCAGUCGGAAGCUGUGUCACUCAUUGUCCACCGGGCGUGUCCCGGUUUUCGAAGGGAUCGCGCCUCGUGCCCGAUCCUUUUUUU
AP008229.1/247574-247665   GUCCGAUGUCAGUCGGAAGCUGUGCCACUCAUUGUCCACCGGGCUUGCCCCGGUUUUCGAAGGGAUCGCGCCUUGUGCCCGAUCCUUUUUUU
CP000050.1/5001412-5001321 GUCCGAUGUCAGUCGGAAGUUGUGCCACGCAUUGUCCACCGGGCUUGUCCCGGUUUUUGAAGGGAUCGGGCCUUGUGCCCGAUCCUUUUUUU
#=GC SS_cons               :<<<<<<____>>>>>>,,,,<<<_____>>>,,,,,<<<<<<_____>>>>>>----<<<<<<<<<<-<<_____>>->>>>>>>>>>:::
#=GC RF                    GuCCGauGUCAguCGGaAGuUguGcCACuCauUGUCCaCCGGGCuUGuCCCGGuUUUugaagGGauCGgGCCUUGUGCCCGauCCuuuuUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02234
#=GF ID   sX15
#=GF DE   Xanthomonadaceae sRNA sX15
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   55.00
#=GF TC   56.00
#=GF NC   51.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   14


AM743169.1/3623545-3623388 GUCGAGAGC-UCCCCC-GCUUGCCCAGUCUUAUCGCUUCGAGUGUCAGCUCCAGCAACUGUUCGGGCGGAUCAAGGGAGAUUCCGGCGUGGGCGCCAA-GCUACAUGGCGAUCG--UCGA-GAUCCAGGCUCGUACGGCGGCCCACGCCGG-CUCUCGACACCUA
AM743169.1/2293027-2292870 GUCGAGAGC-UCCCCC-GCUUGCCCAGUCUUAUCGCUUCGAGUGUCAGCUCCAGCAACUGUUCGGGCGGAUCAAGGGAGAUUCCGGCGUGGGCGCCAA-GCUACAUGGCGAUCG--UCGA-GAUCCAGGCUCGUACGGCGGCCCACGCCGG-CUCUCGACACCUA
AM743169.1/2371563-2371405 GUCGAGAGC-UCUCCCCGCUUGCCCAGUCUUAUCAGUUCGAGCGCCAACUCAACCAACUGUUCGGGCGGUUCA-GGGAGAAUCCGGCGUGGGGACCCAAGCUACUUCUCGGUCG---CAA-GACCUGGAUCCACACGGUCGCCCACGCCGGGCUCUCGGCACCCA
AM743169.1/1143908-1144065 GUCGAGAGC-UCCCCC-GCUUGCCCAGUCUUAUCGCUUCGAGUGUCAGCUCCAGCAACUGUUCGGGCGGAUCAAGGGAGAUUCCGGCGUGGGCGCCAA-GCUACAUGGCGAUCG--UCGA-GAUCCAGGCUCGUACGGCGGCCCACGCCGG-CUCUCGACACCUA
AM743169.1/1775461-1775304 GUCGAGAGC-UCCCCC-GCUUGCCCAGUCUUAUCGCUUCGAGUGUCAGCUCCAGCAACUGUUCGGGCGGAUCAAGGGAGAUUCCGGCGUGGGCGCCAA-GCUACAUGGCGAUCG--UCGA-GAUCCAGGCUCGUACGGCGGCCCACGCCGG-CUCUCGACACCUA
CP001111.1/564203-564361   GUCGAGAGC-UCCCCCCGCUUGCCCAGUCUUAUCACUGCGAGUGUCAGCUCCAGCAACUGUUUGGGCGGAUCAAGGGAGAUUCCGGCGUGGGCGCCAA-GCUACAUGGCGAUCG--UCGA-GAUCCAGGCUUGUACGGCGGCCCACGCCGG-CUCUCGGCACCUA
AM743169.1/2395109-2395267 GUCGAGAGC-UCUCCCCGCUUGCCCAGUCUUAUCAGUUCGAGCGCCAACUCAACCAACUGUUCGGGCGGUUCA-GGGAGAAUCCGGCGUGGGGACCCAAGCUACUUCUCGGUCG---CAA-GACCUGGAUCCACACGGUCGCCCACGCCGGGCUCUCGGCACCCA
AM743169.1/370108-370266   GUCGAGAGC-UCUCCCCGCUUGCCCAGUCUUAUCAGUUCGAGCGCCAACUCAACCAACUGUUCGGGCGGUUCA-GGGAGAAUCCGGCGUGGGGACCCAAGCUACUUCUCGGUCG---CAA-GACCUGGAUCCACACGGUCGCCCACGCCGGGCUCUCGGCACCCA
AM743169.1/730628-730785   GUCGAGAGC-UCCCCC-GCUUGCCCAGUCUUAUCGCUUCGAGUGUCAGCUCCAGCAACUGUUCGGGCGGAUCAAGGGAGAUUCCGGCGUGGGCGCCAA-GCUACAUGGCGAUCG--UCGA-GAUCCAGGCUCGUACGGCGGCCCACGCCGG-CUCUCGACACCUA
AM743169.1/478358-478200   GUCGAGAGC-UCUCCCCGCUUGCCCAGUCUUAUCAGUUCGAGCGCCAACUCAACCAACUGUUCGGGCGGUUCA-GGGAGAAUCCGGCGUGGGGACCCAAGCUACUUCUCGGUCG---CAA-GACCUGGAUCCACACGGUCGCCCACGCCGGGCUCUCGGCACCCA
AM039951.1/116378-116536   GUCGAGAGC-UCCCCU-GCCUGCCCAGCCUUACGUCUACGCGUGGCAACACUGGCAACUGUUCGGGCGAUACGGGGGAGAAACCGGCGUGGGCACCCA-GCUACACGACGAUCG--GUAACGAUCCAGGCUCUCACGGUGGCCCACGCCGG-CUCUCGACGCCCA
AM743169.1/687536-687693   GUCGAGAGC-UCCCCC-GCUUGCCCAGUCUUAUCGCUUCGAGUGUCAGCUCCAGCAACUGUUCGGGCGGAUCAAGGGAGAUUCCGGCGUGGGCGCCAA-GCUACAUGGCGAUCG--UCGA-GAUCCAGGCUCGUACGGCGGCCCACGCCGG-CUCUCGACACCUA
AAFX01021086.1/797-958     GUCGAGAGCAUCGCGCCCGUGGCCCACGCUUAUCGGUUCGAGGGAAACCUCGUCCAACUGUUCGGGCGCAAGGCGCGAGA-UCCGGCGUGCGGCCCCU-GCUGAAUUACGGUGGUGCUGA-CACCGAGGCGUUAUCGGGCGCGCACGCCGGGCUCUCGGCUCUUA
ABWE01005100.1/547-706     GUCGAGAGCAUCGCGCCCG-GGCCCACGCUUAGCAGUUCGAGGGAAACCUCGUGCAACUGUCCGGGCGCAGGGCGCAAGA-UCCGGCGUGUGGCCCCU-GCUGAAUUACGGUGCUG-CUA-CACCGAGGCGUUAUCGGGCGCACACGCCGGGCUCUCGGCGCCUA
#=GC SS_cons               ((((((((<.<<<<<<-<<<<<--<<<<-------<<--<<<<____>>>>->>-->>>>-->>>>>>>----->>>>>,,,<<<<<<<<<<<<<<--.----------<<<<_..____.>>>>----------->>>>->>>>>>>>>>.)))))))):::::
#=GC RF                    GuCGaGaGC.uCcCcCcgcccGCCCaguCUUAucacuuCGaGcGucAgCuCaagCAacuGUUCgggcGgaucaaGgGaGAuUCCGGCGuGgGggCCaa.GCUAcaUuaCGgucg..ucaA.gacCuaGgcucuuaCGGccGCcCaCGCCGG.CuCuCGaCaCcuA
//
# STOCKHOLM 1.0

#=GF AC   RF02235
#=GF ID   asX1
#=GF DE   Xanthomonadaceae sRNA asX1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22080557
#=GF SS   Predicted; CMfinder
#=GF GA   70.00
#=GF TC   81.40
#=GF NC   49.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   15


AE009442.1/956107-956224   CACCUGCCGCAGCAUUUGCGGCUACAGGCGCAAAGGUCGGGAUUGGAAUAGGGGCUGGC-CACGCGUGCGGUGGGGAAGCA-AGGGGCUGGCAGGUCAGAGGGCUGCCAGCCUUUGAUGU
AM920689.1/440232-440346   CACCCGUCGUGGCAUU-GCGAC-AUGGGCGCAA-GGCUGGAAUUGGAACAGGGGCCAGC-CGCGCGUGCGAUGGGGUAGCGUAAGGGCCGGUAG-UCGGGGGACUGCCGGCCCUUAGUUU
AM039952.1/447108-447223   CACCCGUCGUGGCAUU-GCGAC-AUGGGCGCAAAGGCUGGAAUUGGAACAGGGGCCAGC-CGCGCGUGCGAUGGGGUAGCGUAAGGGUCGGUAG-UCGGGGGACUGCCGACCCUUAUUUU
CP000967.1/231228-231343   CACCCGUCGUGGCAUU-GCGAC-AUGGGCGCAAAGGCUGGAAUUGGAACAGGGGCCAGC-CGCGCGUGCGAUGGGGUAGCGUAAGGGUCGGUAG-UCGGGGGACUGCCGACCCUUAAUUU
AE013598.1/241384-241499   CACCCGUCGUGGCAUU-GCGAC-AUGGGCGCAAAGGCUGGAAUUGGAACAGGGGCCAGC-CGCGCGUGCGAUGGGGUAGCGUAAGGGUCGGUAG-UCGGGGGACUGCCGACCCUUAAUUU
AE008923.1/449836-449951   CACCCGUCGUGGCAUU-GCGAC-AUGGGCGCAAAGGCUGGAAUUGGAACAGGGGCCAGC-CGCGCGUGCGAUGGGGUAGCGUAAGGGUCGGUAG-UCGGGGGACUGCCGGCCCUUAUUUU
AE008922.1/452391-452505   CACCCGUCGUGGCAUU-GCGAC-AUGGGCGCAA-GGCUGGAAUUGGAACAGGGGCCAGC-CGCGCGUGCGAUGGGGUAGCGUAAGGGCCGGUAG-UCGGGGGACUGCCGGCCCUUAGUUU
AP008229.1/228139-228254   CACCCGUCGUGGCAUU-GCGAC-AUGGGCGCAAAGGCUGGAAUUGGAACAGGGGCCAGC-CGCGCGUGCGAUGGGGUAGCGUAAGGGUCGGUAG-UCGGGGGACUGCCGACCCUUAAUUU
AE003849.1/2001956-2001840 CACCUGCCGCAGCAUU-GCGGCUACAGGCGCAAAGGUCGGGAUUGGAAUAGGGGCUGGC-CACGCGUGCGGUGGGGAAGCA-AGGGGCUGGCAGGUCAGCGGGCUGCCAGCCUUUGAUGU
CP001111.1/4317597-4317482 CACCCACCGUGGCUGGCGCCGU-AGGCGCCCGU-GACCGGAAUUGGAACAGGGGCCGGUACAGGCGCAUGGUGGGGGAGCA-GGGGGCCGGCAG-UCGGGGGACUGUCCGGCCCUGUUUU
CP000050.1/452985-453099   CACCCGUCGUGGCAUU-GCGAC-AUGGGCGCAA-GGCUGGAAUUGGAACAGGGGCCAGC-CGCGCGUGCGAUGGGGUAGCGUAAGGGCCGGUAG-UCGGGGGACUGCCGGCCCUUAGUUU
CP000941.1/995184-995301   CACCUGCCGCAGCAUUUGCGGCUAUAGGCGCAAACGUCAGGAUUGGAAUAGGGGCUGGC-CACGCGUGCGGUGGGGAAGCA-AGGGGCUGGCAGGUCAGAGGGCUGCCAGCCUUUGAUGU
CP001011.1/965626-965743   CACCUGCCGCAGCAUUUGCGGCUACAGGCGCAAAGGUCGGGAUUGGAAUAGGGGCUGGC-CACGCGUGCGGUGGGGAAGCA-AGGGGCUGGCAGGUCAGAGGGCUGCCAGCCUUUGAUGU
AM743169.1/4588470-4588355 CACCCACCGUGGCUGGCGCCGC-AGGCGCCCGU-GACCGGAAUUGGAACAGGGGCCGGUACAGGCGCACGAUGGGGGAGCA-GAGGGCCGGCAG-UCGGGGGACUGUCCGGCCCUGUUUU
AATO01001136.1/1094-982    CACCCAUCGCGGCAC--GCGCCGGGGGGCGC--AGACUGGAAUUGGAACAGGGGCCAGU-CAUGCGCGCGACGGGGAAGCC-AGGGGUCGAUGG-UCGGGGGACCAUCGGCCCCAUUUUU
#=GC SS_cons               ::(((((((((((,<<.<<<__._____>>>>>,<<<<<<--<<______>>-->>>>>.>,,))-)))))))))------.<<<<<<<<<<<<.<<____>>>>>>>>>>>>>>:::::
#=GC RF                    CACCcgcCGcgGCauu.GCgac.AuggGcGCaaAGgccgGaAuuGGAAcAggGGCcggc.CacGCGcgCGgcgGGGuAGCa.agGGgccGgcaG.uCgGgGGaCugcCggcCCcuaaUuU
//
# STOCKHOLM 1.0

#=GF AC   RF02236
#=GF ID   asX2
#=GF DE   Xanthomonas sRNA asX2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   70.00
#=GF TC   96.90
#=GF NC   46.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   2


AM039952.1/3290997-3290913 UCGAAGGUUGUUGGGUGGUCUGCGCAGCGAGUGAU-GAUCCAUCGCGUUGCCAAACCGCAA-AAAAAAGCCCCGACAAGCGGGGCUU
AE008923.1/3207472-3207386 UCGAACGUCCCUGGGUGUCCGUUGUCGCGAGCGAAAGAUCCACCGCGUUGCCAAGCCGCAACAAAAAAGCCCCGACACGCGGGGCUU
#=GC SS_cons               ::::::::::::::<<<-<----<<-<<--<<<__________>>>>>->>--->->>>--------<<<<<<<_____>>>>>>>:
#=GC RF                    UCGAAgGUuguUGGGuGucCuuuGcagCGAGcGAaAGAUCCAuCgCGuUgCCAAgCCgCAAcAAAAAaGCCCCGACAaGCGGGGCuU
//
# STOCKHOLM 1.0

#=GF AC   RF02237
#=GF ID   asX3
#=GF DE   Xanthomonas sRNA asX3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   40.00
#=GF TC   44.00
#=GF NC   34.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   4


AP008229.1/605165-604984   AUCGGCGAUCAGCCGUGGUGCUGAGCGGCUUUGGCAACGCGAGCGAUUGCACUGCUCAAUUCAAUGACGACGACCACGUUCGGCAAGGCGUCGCCGAUCAUCACCCCCGCGCUCGAUACGGCGGAUCGUGCUCAGCGUUGCGCCGGUCCCCAGUAGCCCAACUCGCGACGGAUCUGCAACCC
AM039952.1/4498825-4499001 AUCCGCGAUCAGCCUUGGUGCUGCUCGUCAGUCGCAAUCCGGGUCAGUGAUCUGAUCAAU--GACAAGGACG--UAAGUUCGGCAAAACGUCGCCGAUCAUCACCACC-CGCUCGUUGCCGCUGAUCGCGCUCAGCGCUGCGCCGGCCCCCAGUAGCCCAACUCGCGACGGAUCUGCAACCC
CP000967.1/709789-709608   AUCGGCGAUCAGCCGUGGUGCUGAGCGGCUUUGGCAACGCGAGCGAUUGCACUGCUCAAUUCAAUGACGACGACCACGUUCGGCAAGGCGUCGCCGAUCAUCACCCCCGCGCUCGAUACGGCGGAUCGUGCUCAGCGUUGCGCCGGUCCCCAGUAGCCCAACUCGCGACGGAUCUGCAACCC
AE013598.1/617186-617005   AUCGGCGAUCAGCCGUGGUGCUGAGCGGCUUUGGCAACGCGAGCGAUUGCACUGCUCAAUUCAAUGACGACGACCACGUUCGGCAAGGCGUCGCCGAUCAUCACCCCCGCGCUCGAUACGGCGGAUCGUGCUCAGCGUUGCGCCGGUCCCCAGUAGCCCAACUCGCGACGGAUCUGCAACCC
#=GC SS_cons               (((((((((--(((----(((((((((<<----<<<<<<____>>->>>>--->><<________>>,,,,,,,,,)))))))))-))))))))))))--------((((((,,,,,,,<<-<<<<<<<<<________>>>>->>>>>>>,<<______>>,,)))-))):::::::::::
#=GC RF                    auCgGCGauCAGccgUGGuGCuGagCggCuuUggCaacgCGaGcgAuuGcaCUGcucAAUUcaAugacGACGAccAcGcuCgGCaAggCguCGCcGauCAUCACCcCCGCGCUCGaUaCgGCgGauCGcGCUCAGCGuUGCgCCGguCcCcAGuAGCCCAaCUCGCGACGGAUCUGCAACCC
//
# STOCKHOLM 1.0

#=GF AC   RF02238
#=GF ID   asX4
#=GF DE   Xanthomonas sRNA asX4/Xoo4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   100.00
#=GF TC   155.70
#=GF NC   27.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF RN   [2]
#=GF RM   21276262
#=GF RT   Identification and functional characterization of small non-coding RNAs in
#=GF RT   Xanthomonas oryzae pathovar oryzae.
#=GF RA   Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT
#=GF RL   BMC Genomics. 2011;12:87.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   8


AM920689.1/4650065-4649754 GUCAGGCACGGUGCUCAAUCGUGUAGCGUUUGAGCGACGCUUUACUGACUUCAAGGAUGAAGGACGCGUCGCCGCCACCCUAGAGGCGGCAUCCCCCGCGUGACGCCCUCUGCAGGCACCGUCGUGACCGGAUUCCUUGACUCACUUUGUGUGCGCG------UUGAUUGCGCACGGCCACCUUCCGCUCAGACCGGCGCGGAGGUGUAGCGAUAGGACAGCAGCGUUUUCACCAGGAAGGUGAUCUGGGUGGCCGAGCGCGCAUCCACGCGCAUGACCGGGAUGCGGAAGCCUUCGACCACCAGCGCCUCGCGGAAC
AM039952.1/4701994-4701686 GUCAGACACACUGCACGCGCAUCUCGCGACUGAGUCGUGUUUU--UGGCUUCAAGGAAGACGGACGCGUCGCCGCCACCCUAGAGGCGGCAUCCCCCGCGUGACGCCCGCU-CAGGCACCGUCGUGACCAGAUUCCUUGUCUUGCUGGCCGUACCCA------GCGCCGGCGCCAGGCGCGCUUUCGAUCAACUGGUCGCCGAGGUGUAGCGAUAGGACAGCAGCGACUUCACCAGGAAGGUGAUCUGGGUGGCCGAGCGCGCAUCCACGCGCAUGACCGGUACGCGGAAGCCUUCGGCCACCAAGGUCUCGCGAAAC
CP000967.1/4955968-4955654 GUCAGACACGAGGCAGAUUUGUACUACGACCGAGUCUUGUUUC--UGGCUUCAAGGAAGACGGACGCGUCGCCGCAACCCUAGAGGCGGCAUCCCCCGCGUGACGCCCUUU-CAGGCACCGUCGUGACCGGAUUCCUUGUCUUACUCACCGCGUCGACUGCAUAUGCACGCGUCACGCGCGCUGGCGAUCAGCUGGUCGCCGAGGUGUAGCGAUAGCACAGCAGCGACUUCACCAGGAAGGUGAUCUGGGUGGCCGAGCGUGCAUCCACCCGCAUGACCGGGAUGCGAAAGCCUUCGGCCACCAAGGCAUCGCGAAAU
AE008923.1/4704917-4704609 GUCAGACACACUGCACACGCACAUCGCGACUGAGUCGUGUUUU--UGGCUUCAAGGAAAACGGACGCGUCGCCGCCACCCUAGAGGCGGCAUCCCCCGCGUGACGCCCUCU-CAGGCACCGUCGUGACCAGAUUCCUUGUCUUGCUUGCCGUGCCCA------GCGCCCGCGCCAGGCGCGCUUUCGAUCAGCUGGUCGCCGAGGUGUAGCGGUAGGACAGCAGCGAUUUCACCAGGAAGGUGAUCUGGGUGGCCGAGCGCGCAUCCACGCGCAUGACCGGCACGCGGAAGCCUUCGGCCACCAGGGCUUCGCGAAAG
AE013598.1/440506-440820   GUCAGACACGAGGCAGAUUUGUACUACGACCGAGUCUUGUUUC--UGGCUUCAAGGAAGACGGACGCGUCGCCGCAACCCUAGAGGCGGCAUCCCCCGCGUGACGCCCUUU-CAGGCACCGUCGUGACCGGAUUCCUUGUCUUACUCACCGCGUCGACUGCAUAUGCACGCGUCACGCGCGCUGGCGAUCAGCUGGUCGCCGAGGUGUAGCGAUAGGACAGCAGCGACUUCACCAGGAAGGUGAUCUGGGUGGCCGAGCGUGCAUCCACCCGCAUGACCGGGAUGCGAAAGCCUUCGGCCACCAAGGCAUCGCGAAAU
AE008922.1/4660613-4660302 GUCAGGCACGGUGCUCAAUCGUGUAGCGUUUGAGCGACGCUUUACUGACUUCAAGGAUGAAGGACGCGUCGCCGCCACCCUAGAGGCGGCAUCCCCCGCGUGACGCCCUCUGCAGGCACCGUCGUGACCGGAUUCCUUGACUCACUUUGUGUGCGCG------UUGAUUGCGCACGGCCACCUUCCGCUCAGACCGGCGCGGAGGUGUAGCGAUAGGACAGCAGCGUUUUCACCAGGAAGGUGAUCUGGGUGGCCGAGCGCGCAUCCACGCGCAUGACCGGGAUGCGGAAGCCUUCGGCCACCAGUGCUUCGCGGAAC
AP008229.1/428428-428742   GUCAGACACGAGGCAGAUUUGUACUACGACCGAGUCUUGUUUC--UGGCUUCAAGGAAGACGGACGCGUCGCCGCAACCCUAGAGGCGGCAUCCCCCGCGUGACGCCCUUU-CAGGCACCGUCGUGACCGGAUUCCUUGUCUUACUCACCGCGUCGACUGCAUAUGCACGCGUCACGCGCGCUGGCGAUCAGCUGGUCGCCGAGGUGUAGCGAUAGGACAGCAGCGACUUCACCAGGAAGGUGAUCUGGGUGGCCGAGCGUGCAUCCACCCGCAUGACCGGGAUGCGAAAGCCUUCGGCCACCAAGGCAUCGCGAAAU
CP000050.1/4735291-4734980 GUCAGGCACGGUGCUCAAUCGUGUAGCGUUUGAGCGACGCUUUACUGACUUCAAGGAUGAAGGACGCGUCGCCGCCACCCUAGAGGCGGCAUCCCCCGCGUGACGCCCUCUGCAGGCACCGUCGUGACCGGAUUCCUUGACUCACUUUGUGUGCGCG------UUGAUUGCGCACGGCCACCUUCCGCUCAGACCGGCGCGGAGGUGUAGCGAUAGGACAGCAGCGUUUUCACCAGGAAGGUGAUCUGGGUGGCCGAGCGCGCAUCCACGCGCAUGACCGGGAUGCGGAAGCCUUCGGCCACCAGUGCUUCGCGGAAC
#=GC SS_cons               <<<<<<-<<<<<<<-<<--<<<___>>>-->>->>>>>>>->>..>>>>,,(((((((---((-((((,,<<<<<<________>>>>>>,,,,,,,<<-<<<_______>.>>->>,,,,,))))-))---))))))),,,,,,,,,,,,,(-(,,......,,,,,,<<_____>>,<<<<<-<<<<<____>>>>>->>-->>>,,,,)-),,,,,,,,,((((,,<<<<<_____>>>>><<<-<<<<<<<<<<<-<<<<<<----<<______>>->>>>>>--->>-->>>>>>>>>->>>,,)))):::::
#=GC RF                    GcCagaCaCgcggCacguucGcauugCgaccgAGccgcGuUuc..uGgCUUCaaGGaaGAaGGACgCGUCGCCGCcACCCUAGAgGCGGCAUCCCCCGCGuGaCGCCCucu.CaGGCACCGUCGuGACCgGAuuCCuuGuCUuaCUuaccGugccca......auGauuGCGcaagGCgcgCuguCGcucAGaugggCGCcgAGGcgUAGCgAuAGgACAGCAGCGauUuCaCCAGGAAGGuGaucuGGGuGGCCGaGCGcGCaucCACgCGCAUGACCGGgauGCggAAGCCUuCGGCCaCCAaggcuuCGCGaAAu
//
# STOCKHOLM 1.0

#=GF AC   RF02239
#=GF ID   asX6
#=GF DE   Xanthomonas sRNA asX6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   50.00
#=GF TC   58.50
#=GF NC   36.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   22080557
#=GF RT   Genome-wide transcriptome analysis of the plant pathogen Xanthomonas
#=GF RT   identifies sRNAs with putative virulence functions.
#=GF RA   Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J,
#=GF RA   Stadler PF, Bonas U
#=GF RL   Nucleic Acids Res. 2011;0:0-0.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   3


AY228335.1/27728-27819   CCACCUACUGAUGUGUCACAUGGUCUGUUUC-UUGUACAAGUUCGCACCGGGUUAGGCGAGGU-GUAGGGCGGCUCCUUCAACCUCGCCGCUUG
AM039951.1/109851-109943 AGCCCUACGGAUGUGCCACAUGGUCUGUUUCCUUGUACAAGUUCGCAC-GGGUUAGGCGGGGUUGUAGGGCGGCUCCUUCAACCUCGCCGCUUA
AE008925.1/50049-50141   AGCCCUACGGAUGUGCCACAUGGUCUGUUUCCUUGUACAAGUUCGCAC-GGGUUAGGCGGGGUUGUAGGGCGGCUCCUUCAACCUCGCCGCUUA
#=GC SS_cons             <<<<<--<<<<<-<<--<<<-<<_______>>->>>->>->>>>>---.>>>>>-<<<<<<<<<<-<<<<____>>>>->>>>>>>>>>:::::
#=GC RF                  agcCCUACggacGuGcCaCaUGGUCUGUUUCCUuGuACaAguccGCAC.GGgcuAGGCGgGGuuGUaGGgCGGCcCCuUCaaCCcCGCCGCUUa
//
# STOCKHOLM 1.0

#=GF AC   RF02240
#=GF ID   Xoo1
#=GF DE   Xanthomonadaceae sRNA Xoo1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   70.00
#=GF TC   80.50
#=GF NC   58.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   21276262
#=GF RT   Identification and functional characterization of small non-coding RNAs in
#=GF RT   Xanthomonas oryzae pathovar oryzae.
#=GF RA   Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT
#=GF RL   BMC Genomics. 2011;12:87.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   5


AE013598.1/978955-978861   GUUGCU---UCCUAAUGACAGGC---GGCAGCGUCAGGCUCUCUCUCUCUCGCCGACGAAUUCAAAUAAUUACGACGUAUCCUUCGCGCCUUCUGGCGCGA
AE008922.1/3941051-3941141 GUUGCU---UCCUA-UGACAGGC---GGCGACGUCAGGCUCUCUCUCU--CGCCGAAGAAUUCAAACAAUUACGACGUACCCUUCGCGCCU-CUGGCGCGA
CP000967.1/4451914-4452008 GUUGCU---UCCUAAUGACAGGC---GGCAGCGUCAGGCUCUCUCUCUCUCGCCGACGAAUUCAAAUAAUUACGACGUAUCCUUCGCGCCUUCUGGCGCGA
AE008923.1/4062113-4062206 GUUGCU---UCCUA-CGACAGGC---GGCAGCGUCAGGCUCUCUCUCUCUCGCCGACGAAUUCGAAUAAUGACGACGUACCCUUCGCGCCUUCUGGCGCGA
AACY021048318.1/738-643    GCCGGUUAACCGCGCCUACGCGCGUGGCCGACAACAGGCUCUCUCU----CGCCGACGAAUUCCCAUAAAU-UGAUUCAGCAUUCGCGCCUUCGGGCGCGA
#=GC SS_cons               <<<<<<...-<<<______>>>-...>>>>>>(((,<<<____________>>><<_____>>,,,,,,,,,,))),,,,,,,<<<<<<<____>>>>>>>
#=GC RF                    GccGcu...uCccaaugACggGC...ggCggCguCAGGCUCUCUCUCUcUCGCCGacGAAUuCaaAUAAuuAcGacguAuCcUuCGCGCCUUCuGGCGCGa
//
# STOCKHOLM 1.0

#=GF AC   RF02241
#=GF ID   Xoo2
#=GF DE   Xanthomonadaceae sRNA Xoo2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   45.00
#=GF TC   46.40
#=GF NC   39.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   21276262
#=GF RT   Identification and functional characterization of small non-coding RNAs in
#=GF RT   Xanthomonas oryzae pathovar oryzae.
#=GF RA   Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT
#=GF RL   BMC Genomics. 2011;12:87.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   3


CP000967.1/3205976-3206053 AGGCGAAGUAA--CGCCAUAGGCCGCAACCGGACGCAGCCACUGAGCGGCGGACUACCUCGUCGGGUCCGCCGCUUUUUU
AM920689.1/1515082-1515003 AGGCGAAGUGACGCGCCACCGGCCGCACCAGGACGCGGCCACUGAACGGCGGACUACCUCGUCGGGUCCGCCGUUUUUUU
AM039952.1/3603640-3603716 AGGCGAAGUAA--CGCCACAGGCUGCAACCGGACGCAGCCACUGAGCGGCGGACUAC-UCGUCGGGUCCGCCGCUUUUUU
#=GC SS_cons               :<<<<______..>>>>,,,<<<<<<________>>>>>>-----<<<<<<<<<<_________>>>>>>>>>>::::::
#=GC RF                    AGGCGAAGUaA..CGCCAcaGGCcGCAaCcGGACGCgGCCACUGAgCGGCGGaCuACCUCGUCGgGuCCGCCGcUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02242
#=GF ID   Xoo5
#=GF DE   Xanthomonadaceae sRNA Xoo5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   65.90
#=GF NC   42.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   21276262
#=GF RT   Identification and functional characterization of small non-coding RNAs in
#=GF RT   Xanthomonas oryzae pathovar oryzae.
#=GF RA   Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT
#=GF RL   BMC Genomics. 2011;12:87.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   3


CP000967.1/2045785-2045908 CUAUGCAAGCAAACGCCUUUCAGCACGACACCAGCGCCGCCCGGAUGGCCUCCGGCAUGACAUCGCGUGCCCGCCGACCGGAAUCCCACAUUUUCGCUGGGUAAGCCGGGGCGUU-UGCUGUUCC
CP000050.1/2262883-2263006 CUAUGCACGCAAACGCCUUUCAGCACGACAGCAGCGCCGCCCGGAUGGCCUCCGGCAUGACGUCGCGUGCCCGCCAACCGGAAUCCCACAUUUUCGCUGGGUAA-CCGGAGCGUUUUGCUGCCUG
AATO01000195.1/985-1108    UCAUGAACGCCGACCUGCAGCCACACGCCGCCAGCGCCGCCCGGAUGGCCUCCGGGAUGACCUCGCGCGCGCGCCGACCGGAACCCCGCCAUUCCGCUGGGUGA-CCGGGGCGUCCUGCCGUCCG
#=GC SS_cons               ::::::::::::::::::::::::::::::((((((-(((((<<-<<<<----<<<<<<______>>>>>>->>>>->><<---<<<<<______>->>>>---.>>))-)))---)))))):::
#=GC RF                    cuAUGcAcGCaaACgccuuuCagCACGaCagCaGCgCCGCCCGGAcGGCCUCCgGcauGACaUCGCgugCcCGCCgACCGGAAuCCCaCauUUuCGCuGGGUaA.CCGGgGCGUuuuGCuGcccg
//
# STOCKHOLM 1.0

#=GF AC   RF02243
#=GF ID   Xoo8
#=GF DE   Proteobacterial sRNA Xoo8
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   90.00
#=GF TC   99.40
#=GF NC   88.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   21276262
#=GF RT   Identification and functional characterization of small non-coding RNAs in
#=GF RT   Xanthomonas oryzae pathovar oryzae.
#=GF RA   Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT
#=GF RL   BMC Genomics. 2011;12:87.
#=GF WK   Xanthomonas_sRNA
#=GF SQ   4


CP000967.1/1067954-1068276 GCCAGGCCGACUAAGGAGCGUCGGCCGCGUCGCUACGGUGACGCAGCCCGUCUUGCCCCGGAGUCCGCUUCGGGGUGCAUUGCCAUGCCAUGUCAUUUCUGCCGGAUCGGUGCCGAUCCGGCAGCUUUUGUAACAGCGUGACCGGGUGAUGACAGUUUCCGUCACGCGCGACUUGUUAAAAUACUGAUAAUCUCAGCGGGCCAGGCAGUCGAUUCAGCGUCUGUCUGCAUUGUUCAGCCAGACUUCGCAUAUGACCCAGCAACGCACGCUCAAGAACACCAUUCGCGCCACCGGCGUCGGCCUGCAUAGCGGCGACAAGGUGU
AE008923.1/931224-931546   GCCAGGCCGACUGAGGAGCGUCGGCUGCGUCGCCACGGUGACGUAGCCCGUCCUACCCCGAAGCCCGCUUCGGGUUGCACCACCAUGUCAUGUCAUUUCUGCCGGAUCGGUGCCGAUCCGGCAGCUUUUGCCAUCGCGUGACUGACUGAUUACGGUUGCCGUCACGCGCGACUUGUUAAAAUUCGGAUAAUCUCAGCGGAAUAGACAGCCGGUUCAGCGUCUGUCUGCAUUGUUCAUCCAGACUUCGCAUAUGACCCAGCAACGCACUCUCAAGAACACCAUUCGCGCCACCGGCGUCGGCCUGCACAGCGGCGACAAGGUGU
AM039952.1/953236-953556   GCCAGGCCGACUGAGGAUCGUCGGCUGCGUUGCUACGGUGACGUAGCCCGUCC--GCCCGGGGCCCGCUUCGGGUUGUACUGCCAUGUCAUGUCAUUCCUGCCGGAUCGGUGCCGAUCCGGCAGCUUUUGUUAUCGCGUGACUGACUGAUUACCGUUGCCGUCACGCGCGACUUGUUAAAAUUCGGAUAAUCUCAGCGGAUUAGACAGUCGGUUCAGCGUCUGUCUGCAUUGUUCAUCCAGACUUCGCAUAUGACCCAGCAGCGCACUCUCAAGAACACCAUUCGCGCCACCGGCGUCGGCCUGCACAGCGGCGACAAGGUGU
AE008922.1/876753-877065   GCCAGGCCGACUGACCGCCCCACGCUGCG-CGCGGUU-CGGCGCAGCG-GCAAUGCCCCGGCAGCCGC--CGGGGCGC-CUGUCCUGUCCU----UUUCUGCCGGGUCGGUGCCGACCCGGCAGCUUUUGCAGCGGCGUGUAUGGUGCGUUACAGUCUCCGUCACGCGUGAUUUGUUAAAAUUCGGCUAAUCUCCCCCGAUUAGACAGCCGGUUCAGCGUCUGUCUGCAUUGCUCAUACAGACUUCGCCCAUGACCCAGCAACGCACUCUCAAGAACACCAUCCGCGCCACCGGCGUCGGCCUGCAUAGCGGCGACAAGGUCU
#=GC SS_cons               {{{[[[[[[[[,,,,<<-----<<<<<<<<<<<____>>>>>>>>>>>-->>,,<<<<<<<<<____>>>>>>>>>((,,,,,,,,<<----------<<<<<<<<<<<____>>>>>>>>>>>----->>,,,,<<<<<<<-<<<________>>>--->>>>>>>,<<<___________>>><-<<-<<______>>->>----->,,,,<<-<<<---<<<<<___________>>>>>-->>>---->>,,,,,,,,,)),,,,,,,,,,,,,,,,,,,,,<<<___>>>]]]]]]]]<<___>>}}}::::::::::
#=GC RF                    GCCaGGCCGaCUgAggguCgucgGCugCGucgCuacgGcgaCGcaGCcCGccuUgcCCCGgaguCCGcucCGGGgcGcAcugcCaUgcCaUGUCAUUuCuGCCGGguCGGUGCCGacCCGGCaGCUUUUgcaauaGCGuGacugacugaUuACagucuCCguCaCGCGcGacUUGUUAAAAUuCggauaAuCUCagCgGauuaGaCAGcCGgUuCAGCGUCUGuCuGCAUUGuUCAucCaGaCUUCGCauAUGaCCCAGCAaCgCACuCUCAAGAACACCAUuCGCGCCACCGGCGuCGGCCuGCAuAGCGGCGACAAGGUgU
//
# STOCKHOLM 1.0

#=GF AC   RF02244
#=GF ID   mir-785
#=GF DE   microRNA mir-785
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   70.00
#=GF TC   78.60
#=GF NC   61.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF WK   MicroRNA
#=GF SQ   4


AAGD02000048.1/2868-2778     UCUUUUUU----GUCCGUCAGCGCAGAAUUUUUUC-GCUUACACGA-GUA-----AUGUAAACGAUGUAAGUGAAU-AUUCUGUGUCGAUGGGUAUAAAAA-GA
CAAC02000521.1/485008-485104 GCUCUU--UCGCAACCGUCAGCACAGAGU-GCUUCGACUUACACAGAAUUCGUAAAACCAACUGAUGUAAGUGAAU-ACUCUGUGUUGAUGGUGA---UGAUGC
FO081792.1/58385-58478       GCUCUUUUUCUCACCCAUCAGCACAGAAU-UUUUC-GCUAACAGAAACCU-----CAAAACA--AUGUAAGUGAAUUGUUUUGUGUAGAUGGUGGAAAUGA-GC
ABEG02000018.1/13364-13455   GCUCUUUU-CUCUCCCGUUAGCACAAAAU-AUUUU-ACUUACACAUAACA-----AAACAUAUGAUGUAAGUGAAU-ACUUUGUGUUAAUGG--AAAAAGG-GC
#=GC SS_cons                 <<<<-<<<------<<<<<<<<<<<<<-<.--<<<.<<<<<<<_______.....__________>>>>>>>>>>-.>->>>>>>>>>>>>>--->>>->>.>>
#=GC RF                      gCucUuuuUCuCauCCgUcagCaCAgAAu.uuUUc.aCUuACAcAaAauu.....aaauAaauGAUGUaAGugAAU.auUcUGuGuugAuGGugAaaauga.Gc
//
# STOCKHOLM 1.0

#=GF AC   RF02245
#=GF ID   mir-788
#=GF DE   microRNA mir-788
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   70.00
#=GF TC   73.50
#=GF NC   49.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   17174894
#=GF RT   Large-scale sequencing reveals 21U-RNAs and additional microRNAs and
#=GF RT   endogenous siRNAs in C. elegans.
#=GF RA   Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP
#=GF RL   Cell. 2006;127:1193-1207.
#=GF WK   MicroRNA
#=GF SQ   4


AAGD02008354.1/131552-131474 ACUUACGUCUCCGCUUCUAA--CUUCCAUUUGCAGAGUUCAUCAAUUCU--CUGGAAAUGGA-UUAGAACCGUG-AAAUGUUAGU
CAAC02000603.1/469330-469248 ACUAACUUUUCCGCUUCUCAAUGCUCCAUUUGCAAAAUCAAAUUGAUUUUCUUGCAAAUGGGAUGAGAACCGG--AAACGUUUGA
ABLE03033251.1/2548-2625     CCCUACUUUUCCGCUUCUAG--CUUCCAUUUGCAAAG--CAGUAAGUCU--CUGAAAAUGGA-CUAGAAACGUGAAAAAGUUGGU
FO081164.1/16886-16809       GCUCACUUUUCCGCUUCUAA--CUUCCAUUUGCAGAGUUCA--AGUAAU--CUGGAAAUGGA-UUAGAAUCGUGGAAAAGUUAGU
#=GC SS_cons                 :<<-<<<<<<-<<-<<<<<<..--<<<<<<<-<<<<<__________>>..>>>->>>>>>>.>>>>>>->>--.>>>>>>->>:
#=GC RF                      aCcuACuUuUCCGCUUCUaa..cuuCCAUUUGCAgAgUucAauaauUcU..cUGaAAAUGGa.uuAGAAcCGuG.AaAaGUUgGu
//
# STOCKHOLM 1.0

#=GF AC   RF02246
#=GF ID   Six3os1_1
#=GF DE   Six3os1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   42.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21936910
#=GF RT   The long noncoding RNA Six3OS acts in trans to regulate retinal
#=GF RT   development by modulating Six3 activity.
#=GF RA   Rapicavoli NA, Poth EM, Zhu H, Blackshaw S
#=GF RL   Neural Dev. 2011;6:32.
#=GF WK   Six3OS1
#=GF SQ   9


AY589790.1/604-517         UCCUUGGCUUCCUGUACAUCUCUGUGCGUGUCU-GGGCGUCACUCCA--AG--CGGACAUGGUAGCUUUUGUCUGCAUCU-GGACAACAAGGUG
ABRR01379223.1/276-356     ----UGGCUUCCUGCACAUCUGCC--UGUGGCU-AGG-GUCACUCCG--CG--CGGGCACUGUGGCUUUUGUCUGCAUCU-GCACAACUAGAUG
AAWR02004034.1/5244-5162   ----UGGCUUCCUGCACAUCUGCUCGCGUGGCU-GGG-GUCACUCUG--CG--CGGGCACUGCCGCUUUCGUCUGCAUCU-GGACAACUGGGUA
AAFC03054895.1/55173-55259 UAUGUGGCUUCCUGCACACCUGCCUG--UGGCU-GGG-UUCACUCCGAG--CGCGGGCACUGCGGCUUUUGUCUGCAUCU-GCACAACUGGGUG
AANU01292492.1/7077-7163   UUCGCGGCUUCCUGUACAUCUGCCCUUGUGGUU-GGG-GUCACUCCU--CG--CGGGCACUGUGGUUUUUGUCUGCAUCU-GGACAACUGGGUG
AAKN02023921.1/63796-63883 UGCGCAGCUUCCUGUACAUCUGCCUGCAUGUGU-GGG-GUCAAUCCA--UG--UGGGCACUGAGCCUUUUGUCUGCGUCUUAGACAACUGAGAG
ABRN01211795.1/141-225     UAGGUGGUUUCCUGCACAUCUGCC--UGUGGCU-GGG-GUCACUCCG--CG--CGGGCACUGCGGCUUUUGUCCGCAUCU-GGACAACUGGAUG
AC012354.11/89894-89980    UUCACGGCUUCCUGUACAUCUGCCCUUGUGGUU-GGG-GUCACUCCU--CG--CAGGCACUGUGGCUUUUGUCUGCAUCU-GGACAACAGGGUG
AAGU03061906.1/13962-14048 GGUGCGGUUUCCUGUAAGUCGGCCCGUGUGGCUGAGG-GUCACUCCG--CG--CGGGCACUGCAGCUUUUGUCAGCAUCU-GGACA-CCUGCCU
#=GC SS_cons               :::::::::::::::::::::::::::::::::.:::.:::::::::..::..:::::::::::::::::::::::::::.:::::::::::::
#=GC RF                    UgcguGGCUUCCUGuACAUCUGCcuGuGUGGcU.GGG.GUCACUCCg..cG..CGGGCACUGugGCUUUUGUCUGCAUCU.GGACAACugGguG
//
# STOCKHOLM 1.0

#=GF AC   RF02247
#=GF ID   Six3os1_2
#=GF DE   Six3os1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   119.40
#=GF NC   59.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21936910
#=GF RT   The long noncoding RNA Six3OS acts in trans to regulate retinal
#=GF RT   development by modulating Six3 activity.
#=GF RA   Rapicavoli NA, Poth EM, Zhu H, Blackshaw S
#=GF RL   Neural Dev. 2011;6:32.
#=GF WK   Six3OS1
#=GF SQ   15


BC065087.1/1944-1722       GUGAGGGGCUGGGCGAAAGGAAGGAGGGGAGGGGAUGGGGG-G----GGACGCGCGCCCCAGGAGCGAAAGCAAACUGCUAGCUGCAGAGGCGCUAC-CGCAGUUCAGGCUUCCCAACAGGUUAGCUAGCCUAGGAUCCACCCGGUAUUUCGCAGGAAGGGGGGGGGGG-------CGUUGAGAUAGCUAGAGGAGGGGA-AGCCUUCCUGGAGGACAGAGGGAGGGAGAGAAAGAG
AAQQ01026224.1/199-417     GUGAGGGGCUGGGCGAGAGAAGGGAGGGGAAAGGAUGGGGGA-------ACGCACGCCCCAAGAGCGAAAGCAAACAGCUAGCUGUGGAGGCGCCGCCCGCAGUUCAGGCUUCCCAACAGGAUAGCUGGACUGGGAUCCACCCGGUAUUUCGCAGGAAAGGGGGGGUG---------GGA--CGAAGCAAGAGGAGGAGAGUGCAUUACUAGAGGACAGAAGGAGGGAGGGAAGGAG
ABDC01085241.1/5510-5719   GUGAGGGGCUGGGCAAAAGGAGGGAGGGGAGAGGAUGGGGGA-------ACGUGCGCCCCAAGAGCGAAAGCAAAC----UGCUGUGGAGGCGCUGCCCGCGGCUCAGGCUUCCCAACAGGUUAGCUAUACUGAGAUCCACCCGGCAUUUCGCAGGAAGGG-----GG---------GGAGAC--AGCCAGAGGGGGAGAGAGCCUCACAAGAGGACAGAGCGAGCGAGGGAAAGAG
ABRO01159317.1/2847-3007   GUGAGGGGCUGGGCGAAAGAAGGGAGGGGAGAGGAUGGGGAA-------ACGCGCGCCCCAAGAGCGAAAGCAAACAGCCAGCUAGGGAGGCGCUGCCGGCAGCUCAAGCUUCCCAACAGGUUAGCUAGACUGGGAUCCACCCGGUAUUUCGCAGGAAGGGG----GG---------GGU-------C-------------------------------------------------
AAFC03054895.1/56890-57104 GUAAGGGGCUGGGCGAAAGGAG----G---AAGGAUGGGGA--------ACACGCGCCCCAAGAGCGAAGGCAAAC----AGCUGUGCAGGCGCUGCCCGCAGCUCAGGCUUCCCAACAGGUUAGCUAGACAGGGAUCCACCCGGCAUUUCGCAGGAAAGGGUGGGGGUUG---GGGGGAGACUGAGCGAGAGGGGGAGAGAGCCUCACAAGAGGACAGAGGGAGGGAGAGAGAUAG
ABRP01066958.1/1299-1515   GUGAGGGGCUGGGCGACUGUAGAGAAG---GCGAAUGGGGA--------AUGCACGCCCCAAGAGCGAAGGCAAAC----AGCUGUGGAGGCGCUGCCCGAGGCUCAGGCUUCCCAACAGGUUAGCUAGACGAGAAUCCACUAGGCAUUUCGCAGGAAAGGGGGGGUGGG-----GAAGAGACUGAGCGAGACGAGGAGAGAGCCUCACAGGAAAACAGAGGGAGGGAGGGAAAGAG
AACN010734315.1/271-61     GUGAGGGGCUGGGCGAAAGGAGGGAGG---GAGGAUGGGGA--------ACGCGCGCCCCAAGAGCGAAGGCAAAC----AGCUGUGGAGGCGCUGCCCAGGGCUCAGGCUUCCCAACAGGUUAGCUAGACGGGGAUCCACCCGGCAUUUCGCAGGAAAGGGGGGGGG-----------AGACUGAGCGACAGGGGGAGAGAGCCUCAGAAGAGGACAGAGGGAGGGAGGGAGAGAG
AANG01197538.1/480-689     GUGAGGGGCUGGGCGAGAGAAGGGAGG---GUGGAUGGGGA--------ACGCGCUCCCCAAGAGCGAAGGCAAAC----AGCUGUGGAGGCGCUGCCCAGGGCUCAGGCUUCCCAACAGGUUAGCUAGACGGGGAUCCACUCGGCAUUUCGCAGGAAAGGGGGGGG------------AGGCUGAGUGAGAGGGGGAGAGAGCCUCAGAAGAGGACAGAGGGAGGGAGGGAAAGAG
ABRQ01283046.1/2291-2496   GUGAGGGACUGGGCAAAAGAA---------GAGGAUGGGGAC-------AAACGCGCCCCAAGAGCGAAGGCAAAC----AGCUGAGGAGGUGCUGCCCGCAGCUCAGGCUUCCCAACAGGUUAGCUAGGCGCCGAUCCAACCGGCAUUUCGCAGGAAAGGGUGGGGG---------GAAGAC--AGCGAGAGGGAGAGUGCGCCUCACAGGAGGACAGAGGGAGGGAGGGAAAGGG
AAPY01027907.1/545-754     GUGAGGGGCCGGGCAAAUGGAGGGAGGGGAGAGGACGGGGGA-------GCUUGCGCCCCAGGAGCGAAG-CAAAC----AGCUGUGGAGGCGCUGCCCAGGGCUCAAGCUUCCGAACAGGUUAGCUAGACUGGGAUCCACCCGGUAAUUCACAGGAGGGGG----GG-----------AGACAGAGGGAGAGGGGGAGAGAGCCUCACUAGAGGACAGAGGGAGGGAGGGCGAGAG
AC012354.11/91629-91845    GAGAGGGGCUGGGCAAAAGGAGAGAGGGGAGAGGAUGGGGAA-------ACGCGCGCCCCAAGAGCAAAAGCAAAC----AGCUGUGGAGGCGCUGCCCGCGGCUCAGGCUUCCCAACAGGUUAGCUAUACUGGGAUCCACCCGGCAUUUCGCAGGAAGGGGUGGGGG---------GAAGACAGAGCGAGAGGGGGAGAGAGGCUCACAAGAGGACAGAGGGAGGGAGGGAAAGAG
AAGU03061906.1/15706-15917 GUGAGGGGCUGGGCAAGAAGAAGAACG---GAGGAUGGGGGC-------ACUCGCGCCCCAAGAGUGAAGACAAAC----AGCUGUGGAGGCGCUGCCCGCGGCUCAGGCUUCCCAACAGGUUAGAUAGACCGGGAUCCAACCGGCAUUUCUCAGUAAAGGGUGGGGG---------GAAGGC--AGCGAGAGGGAGAGAGCGCCUCACAAGAGGACAGAGGGAGGGUGGGAAAGAA
AAQR03051360.1/26108-26319 GUGAGGGGUUGGGCAAAAGGAGGGAGGGGAGAGGGUGGGGA--------ACGCAUGCCCCAAGAGCGAAGGCAAAC----AGCUGUGGAAACGCUGCCCGAGGCUCAGGCUUCCCAACAGGUUAGCUAUACCGGGAUCCACCCGGCAUUUCGCAGGAGGGAG----GG---------GAGUGCAGAGCGAGAGGGGGAGAGAGCCUCACCAGAGGACAGAGGGAGGGAGGGAGAGAG
AAHX01041599.1/428-194     GUGAGGGGCUGGGCGAAAGGAAGGAGGGGAGAGGAUGGGGGUGGGGGGGACGCGCGCUCCAGGAGUGAAAGCAAACUGCUAGCUGUCGAGGC-UUGC-GGCAGUUCAGGCUUCCCAACAGGUUAGCUAGCCUAGGAUCCACCCGGUAUUUCGCAGGAGGGGGUGGGGGGGGAGCGGCGUUGAGAUAGCUAAAGGAGGGGAGAGCCUUCCUGGAGGACAGAGGGAGGGAGAGAAAGAG
ABGA01092200.1/7628-7412   GAGAGGGGCUGGGCAAAAGGAGAGAGGGGAGAGGAUGGGGAA-------ACGCGCGCCCCAAGAGCAAAAGCAAAC----AGCUGUGGAGGCGCUGCCCGCGGCUCAGGCUUCCCAACAGGUUAGCUAUACUGGGAUCCACCCGGCAUUUCGCAGGAAGGGGUGGGGG---------GAAGACAGAGCGAGAGGGGGAGAGAGCCUCACAAGAGGACAGAGGGAGGGAGGGAAAGAG
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::.......:::::::::::::::::::::::::::....::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.........::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    GUGAGGGGCUGGGCgAaaGgAgGGAgGGGAGaGGAUGGGGga.......AcgCGCGCCCCAaGAGcGAAgGCAAAC....AGCUGugGAGGCGCUGCCcGcgGcUCAGGCUUCCCAACAGGUUAGCUAgaCugGGAUCCAcCCGGcAUUUCGCAGGAagGGGuGGGGG.........GgaGacagAGcgAGAGGgGGaGaGaGCCUcacaaGAGGACAGAGGGAGGGaGgGaaAGAG
//
# STOCKHOLM 1.0

#=GF AC   RF02248
#=GF ID   Six3os1_3
#=GF DE   Six3os1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   40.00
#=GF TC   43.70
#=GF NC   32.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 19.57 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21936910
#=GF RT   The long noncoding RNA Six3OS acts in trans to regulate retinal
#=GF RT   development by modulating Six3 activity.
#=GF RA   Rapicavoli NA, Poth EM, Zhu H, Blackshaw S
#=GF RL   Neural Dev. 2011;6:32.
#=GF WK   Six3OS1
#=GF SQ   10


CAAA01010790.1/5892-5819     AGAAUCAGUCUGGGGUCGGCCAGCUCCGGAUCUGCUCGAGGUGGACACACAAAAGCAAAAGCC-AAGCUGGGAAA
ABGA01092200.1/6393-6319     AGAAUCCAUGUGGGGUCGACUGGCUCCGGAGUUGCGCAAGGUGGACACACAAAACCAAAAGCCGGAGUUGGGAAA
AAKN02023921.1/66774-66847   AGAAUCCAUCUGGGGUCGGCCAGCUCCCAGGCUGCACGAGGUGUACACAGAAAACCCAAAACA-AAGUUGGCAAA
AAHX01041598.1/6020-5947     AGAAUCAGUCUGGGGUCGGCCAGCUCCGGAUCUGCUCGAGGUGGACACACAAAAACAAAAGCC-AAGCUGGGAAA
ACBE01098576.1/3433-3359     GGAAUCCAUUUGGGGUCGGCCAGUUCCGGAGCUGCUCCAAGUGGACACACAAAACCAAAAGCCGAAGUUGGAAAA
AAFC03054895.1/58113-58187   AGAAUCCAUGUGGGGUCGGCCGGCUCCGGAGCUGCGCGUGGUGGACACACAAAACCAAACGCCCAAGUUGGAAAA
ABBA01075117.1/25436-25510   AGAAUCCAUGUGGGGUCGGCUGGCUCCGGAGUUGCGCAAGGUGGACACACAAAACCAAAAGCCGGAGUUGGGAAA
AAWR02004034.1/2257-2183     AGAAGCCAUUUGGGGUCGGCUGGCUCCGGAGCUGUGCGAGGUGGACACACAAAACCGAAAGCCGAAGUUGGAAAA
AY590888.1/385-311           AGAAUCAGUCUGGGGUCGGCCAGCUCCGGAUCUGCUCGAGGUGGACACACAAAAGCAAAAGCCAAGACUCUGCAG
AAEX03007479.1/117423-117497 GGAAUUCAUUUGGGGUCAGUCGGCUCCAGAGCUGCUCCAAGUGGACACACAAAAUCAAAAGCCGAAGUUGGAAAA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      AGAAUCcaUcUGGGGUCGGCCgGCUCCGGAGCUGCuCgAGGUGGACACACAAAAcCaAAAGCCgAAGUUGGgAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02249
#=GF ID   Six3os1_4
#=GF DE   Six3os1 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   79.80
#=GF NC   59.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.13 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21936910
#=GF RT   The long noncoding RNA Six3OS acts in trans to regulate retinal
#=GF RT   development by modulating Six3 activity.
#=GF RA   Rapicavoli NA, Poth EM, Zhu H, Blackshaw S
#=GF RL   Neural Dev. 2011;6:32.
#=GF WK   Six3OS1
#=GF SQ   7


AY589789.1/390-68            UAAGCCCUGCUCAGAAGUCAAGAGCAGCAGCGCCGCC-GCUCCUCGCAGCCUUUCACGCUGCAGCCGCUUCUUAUUCUUGUGCCUCGGCCUUUCUGGGCGCCCCCGGACAAAGCCCCCAGAACCCGGUCGCUCCCUUCCCGCUAAAUCCCCUUCGGGGUCAGUGCGCUACCAGCACAGGGCCGCACGCCUCUCCUGCUAGCCGUGUGGCUCUUAAAGAGCCCCACAC----------CCCUCCGCCCUGCGUGCUCCUCCGACCCCCGCCACCC---CUCCCCUCUCCUCCGGAUCUAGCCCCC-CACGCCGUCGCCUGAAGUCCCUGCUGCCCCGAC
AAKN02023921.1/67044-67357   UAAACCCCACUCAGAAGUCAAGAGCAGCAGCGCCGCC-GCUCCGCGAGGCCUUUCAAGCUGCAGUCGCUCCUUAUUCUUGUGCUUGGGCCUCUCCGGGUGCCC-------------CCCGAGACCGGCCGCUCCCUUCCCACUAAAUCCCCUUCGGGGUCAGUGCGCUACCAGCACCGGGCCGCUCGCCUCUCCUGCCAGCAGAGUGGCUCUUAAAGAGCUGCGCCC---------CCCCUCCGCCCAACGCGCUCCUCAGACCCCCGCCCCCCCCCCGCCCCUCGCCUUCGGAUCUAGCCCCC-CACGCCGACGCCUGAGGUCCCUGCUGCCCCGAC
ABDC01085242.1/62-387        UAAGCCCUGCUCAGAAGUCAAGAGCAGCAGCGCUGCC-GCUCUGCGCGGCCUUUCAUGCCUUCGACUCUCCUUAUUCUUGCGCCUCGGCCUCUCCGGGCGCCCUCGGACAAAACCCCCAGAGCCCGGCCGCUCCCUUCCGGCUAAAUCCCCUUCGGGGUCAGUGAGCUACCAGCACCCGGGCGCGCGCCUCUCCUGCCAGCCGUGUGGCUCUUAAAGAGCCGCACCC-------CCCCCCUCCGCCCUGCGCGCUCCCUUGACCCCCGCCUCCC---CGCCCCUCUCCUCCUGAUCUAGCCCCC-CACGCCGACGCCUGAGGUCCCUGCUGCCCCGAC
AAXN01005891.1/250-572       UAAGCCCUGCUCAGAAGUCAAGAGCAGCAGCGCCGCC-GCUCCUCGCAGCCUUUCACGCUGCAGUCGCUUCUUAUUCUUGUGUCUCGGCCUUUCUGGGCGCCCCCGGACAAAGCCCCCAGAACCCGGUCGCUCCCUUCCCGCUAAAUCCCCUUCGGGGUCAGUGCGCUACCAGCACAGGGCCGCACGCCUCUCCUGCUAGCCGUGUGGCUCUUAAAGAGCCCCACAC----------CCCUCCGCCCUGCGUGCUCCUCCGACCCCCGCCACCC---CUCCCCUCUCCUCCGGAUCUAGCCCCC-CACGCCGACGCCUCAAGUCCCUGCUGCCCCGAC
AC012354.11/93159-93482      UAAGCCCUGCUCAGAAGUCAAGAGCAGCAGUGCUGCC-UCUCCUCGCCGCCUUUCAUGCCGCGGCCGCUCCUUAUUCUUGUGUCUCGGCCUCUCCCGGCCCCCUCGGACAAAACCCCCAGAGCCCGGCCACUCUCUUCCCGCUAAAUCCCCUUCGGGGUCAGUGCUCUACCAGCACCGGGCCGCGCGCCUCUCCUGCCAGCCGUGUGGCUCUUAAAGAGCUGCACCCCUCCUCCGCCCUGCGCGAUCCCCCGACCCCCG-CCUCCCCUCCCCUC---UCCUC-CGGAUCUAGCCCCCCACGCCGACGCCUGAGGUCCCUGCUGCCC-CGAC-------
AAGV020928460.1/116-446      UAAGCCCUGCGCAGAAGUCAAGAGCCGCGGUACCGCCGCCUUCGCGCGGCCUUUCAUGCUGAGGCCGCUC-UUAUUCUUGUGCCUCGGCCUCUCCGGGCACCCGGCGACAAAGCCCCCGGAGCCCGGCCGCUCUCUUCCCGCUAAAUCCCCUUCGGGGUCAGUGCGCCACCAGCCCCGGGCCGCGCGCCUCUCCUGCCAGCCCAGUGACUCUUAAAGAGCCGCACCCUGCACCCCCCACCCCCGCCCUGCGCUCUCCCC-GACCCCCACCUCUU---CGCCC-UCUCCUCCGGAUCAACCCCCCCCACGUCCACGCCCGAGGACCC-GUUGCCCCGAC
AAEX03007479.1/117718-118031 UAAGCCCUGCUCAGAAGUCAAGAGCAGCAGCGCCGCCGCCUUGGCGCGGCCUUUCAUGACGCGGUCGCUCCUUAUUCUUGUGCCUCGGCCUCUCUGGUCGCCCCCGGACAAAGCCACCGGAGCCCGACCGCUCCCUUCCCGCUAAAUCCGCUUCGGGGUCAAUGCGCUACCAGCACCGGGCCGCGCGCUUCUCCUGCCAGCCGUGUGGCUCUUAAAGAGCCGCACCC-----CCCCCCCCUCCGUCCUGCGCGCUCCCCCGACCCCCGCCUCCC---CGCCCCUCUGCUCUGGAUCUAGCCUUAGGUCCCUGCUGCCCCGAC----------------
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.......::::::::::::::::::::::::::::::::::::::::...:::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::
#=GC RF                      UAAGCCCUGCuCAGAAGUCAAGAGCaGCaGcGCcGCC.gCUccgCGcgGCCUUUCAuGcuGcgGuCGCUcCUUAUUCUUGUGcCUcGGCCUcUCcgGGCgCCCucgGACAAAgCCcCCaGAGcCCGGcCGCUCcCUUCCcGCUAAAUCCcCUUCGGGGUCAGUGcGCUACCAGCaCcGGGcCGCgCGCCUCUCCUGCcAGCcGuGUGGCUCUUAAAGAGCcgCaCcC.......cCCcccucCGccCugCgcgCuCCcccgacCCCCgCCuCcC...cgCcCCucuccuccGgauCuagCcCCc.caCgccgacGCCugagguCCCUgcugCCCCGAC
//
# STOCKHOLM 1.0

#=GF AC   RF02250
#=GF ID   Six3os1_5
#=GF DE   Six3os1 conserved region 5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   50.00
#=GF TC   52.00
#=GF NC   43.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 18.81 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21936910
#=GF RT   The long noncoding RNA Six3OS acts in trans to regulate retinal
#=GF RT   development by modulating Six3 activity.
#=GF RA   Rapicavoli NA, Poth EM, Zhu H, Blackshaw S
#=GF RL   Neural Dev. 2011;6:32.
#=GF WK   Six3OS1
#=GF SQ   15


AC166821.2/74615-74886       CGG-GGCUCAUUAGGCAGAGCGGGGUGCCGAGAGGUGCGCGC-UGCCGGCCCCAGAGG--CCG-CCUUUGAGCCGUCGGGGCGGCUUCAUUAAGCAGCGCUAACAAGGCGUACAAAUGC-CGGGCCCAGCAGCUUUUUU---GCAAUGGUGGGGCCUUAGCAGGGCGCCAG-GCUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCC-CCU-CACGCCGGGAACUUUU---AUGCACCAGGAAAGUUGAGGCAACUGAGCUGUGUUUACUGUCCAG
AC151334.2/12225-11963       UGG-CUUUCAUUAGAGGUGACCAGUUGACAUAAGGUAAAAUC-UACA---UUGUGCAG--CUC-UUAUUGUGUGUGAGGGUUGGCCUCAUUAACCAGCGCUAACAAGCCGUGCAAAUGCUCUGAUUGGGCAGCUUUUAUUGGAUAGUACCAGGCCCUUAGCAGGAUACCCA-CUUAAUGAGGGUCACCACAAGAGAAUGAUAAAAUAUUCAA---------------CGGGGGACUUUUCAUAUGGAACGAUAAAGUUGCAGCGACUUGACCGUUUAAAACAUAAUC
AC012354.11/95000-95270      CGG-GGCUCAUUAGGCAGAGCAGGGUGCCGAGAGGUGCGCGU-CGCCGGCCCCUGAGG--CCG-CCUUUGAGCCGUCGGGGCGGCUUCAUUAAGCUGCGCUAACAAGGCGUACAAAUGC-CGAGCCCAGCAGCUUUCUU---GCAAUGCCCGG-CCUUAGCAGGGCGCCGG-ACUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCC-CCG-CACGCCAGGAACUUUU---AUGCAUGGAGAAAGUUGAGGCAACUGAGCUGUGUUUACUGUCCGG
AAQQ01538745.1/1867-2138     UGG-GGCUCAUUAGGCAGAGCGGGGUGCCGAGAGGUGCGCGC-UGCCGGCCUCUGAAG--CCG-CCUUUGAGCCGUCGGGGCUGGUUCAUUAAGCGGCGCUAACAAGGCGUACAAAUGC-CUGGCCCAGCAGCUUUCUU---GCAAUGCCGGGGCCUUAGCAGGGCGCCAG-GCUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCC-CCG-CACGCCAGGAACUUUU---AUGCACCGAGAAAGUUGAGGCAACUGAGCUGUGUUUAUGGUCCUG
AAFC03054895.1/60301-60571   UGG-GGCUCAUUAGGCAGAGCGGGGUGCCGAGAGGUGUGCGC-CGCCAG-CCGGGAGG--CCG-CCUUUGAGCGGUCGGGGCGGCUUCAUUAAGCGGCGCUAACAAGGCAUACAAAUGC-CGGGCCCAGCAGCUUUCUU---GCAAUGUCGGGGCCUUAGCAGGGCGCCAG-GCUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCC-CCG-CACGCCGGGAACUUUU---AUGUAUGGAGAAAGUUGAGGCAACUGAGCUGUGUUUACUGUCCUG
AAKN02023921.1/68799-69070   UGG-GGCUCAUUAGGCAGAGCGGGGUGCCGAGAGGUGCGCGC-UGCCGGCCUCCGAGG--CCG-CCUUUGAGCCGACCGGGCGGCUUCAUUAAGCGGCGCUAACAAGGCGUACAAAUGC-CGGGCCCAGCAGCUUUCUU---GCAAUGCCGAGGCCUUAGCAGGGCGCCAG-GCUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCC-UCG-CACGCCGGGAACUUUU---AUGCACGGAGAAAGUUGAGGCAACUGAACUGUGUUUACGGUUCGG
ABRO01159317.1/6238-6509     CAG-GACUCAUUAGGCAGAGUGGGGUGCGGAGAGGUGCGCGC-CGCCGGCCCCUGAGG--CCG-CUUUUGAGCCGUCGGGGCAGCUUCAUUAAGCGGCGCUAACAAGGCGUACAAAUGC-CUGGCCUAGCAGCUUUCUU---GCAAUGCCGGGGCCUUAGCAGGGCGCCAG-GCUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCC-CCG-CACGCCGGGAACUUUU---AUGCAAGGAGAAAGUUGAGGCAACUGAGCUGUGUUUAUGGUUCGG
ABDC01085242.1/1903-2168     CGG-AGCUCAUUAGGCAGAGCGGGGUGCCGAGAGGUGCGCGC-UGCCGGCCCCUGAGG--CCG-CCUUUGAGCGGCCGGGGAGGCUUCAUUAAGCGGCGCUAACAAGGCGUACAAAUGC-CAGGCCCAGCAGCUUUCUU---GCAAUGCUGGGGCCUUAGCAGGGCGCCGG-GCUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCCCCCG-CACGCCAGGAACUUUU---AUGCAUGGAGAAAGUUGAGGCAACUGAGCUGUGUU-------ACG
AAGV020976255.1/277-547      CAG-GGCUCAUUAGGCGGAGCGGGGUGCCUAGAGGUGCACGC-CGCCGG-CCGGGAGG--CCG-CCUUUCAGCGGUCGGGGCGGCUUCAUUAAGCGGCGCUAACAAGGCGUACAAAUGC-CGGGCCCAGCAGCUUUCUU---GCAAUGCCGGGGCCUUAGCAGGGCGCCGG-GCUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCC-CCG-CACGCCGGGAACUUUU---AUGCGCGGAGAAAGUUGAGGCAACUGAGCUGUAUUUACUGUCGGG
AAIY01735224.1/759-1032      CGG-GGCUCAUUAGGCUGAGCGGGGUGCCUUGAGGUGCGCGC-UGCCGGCUCCGGAGG--CCG-CCUUUGAGCCGGUAGGGCGGCUUCAUUAAGCAGCGCUAACAAGGCGUACAAAUGC-AGGGCCCAGCAGCUUUCUU---GCAAUGCCUGCGCCUUAGCAGGGCGCCGGGGCUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCC-CCGGCACGCCGGGAACUUUU---AUGCGGGGCGAAAGUUGAGGCAACUGAGUUGUGUUUACUGUCCUG
ABRQ01283046.1/5589-5860     AGG-GGCUCAUUAGGCAGAGCGGGGUGCCUCGAGGUGCGGGA-CGCCGACCCCGGAGG--CCU-CCUUUGAGUCGAUGGGGCGGCUUCAUUAAGCGGCGCUAACAAGGCGAACAAAUGC-AGGGCCCAGAAGCUUUCUU---GCAGCGCCGGCGCCUUAGCAGGGCGCCAG-GCUAAUGAGGGUCACUCAAAGAGGCUGAUCAAAUAUUCAAAUUUCC-CGG-CACGCCGGGAACUUUU---AUGCCAGGAGAAAGUUGAGGCAACUGAGCUGUGUUUACUGUUCAG
AAFR03002773.1/3914-4185     UGC-GGCUCAUUAGAAGUAACCAGUUGCCGUAAGGUGCGUGUAUACA---CCGGGAGG--CCUUCCUUUCAGCAGUCGGGGAGGCUUCAUUAAUCGGCGCUAACAAGGCGUGCAAAUGCAGAGACUGGGCAGCUUUCUU---GCAACGCCCGGGCCUUAGCAGGGCGCCAG-GCUAAUGAGGGUCACUAAAAGGGGCUGAUCAAAUAUUCAAAUUUCC-CCG-CGCACCAGGAACUUUU---AUGAGGGGAGAAAGUUGAGGCAACUGAGUAGUGUUUACUCACGGG
AADN03003231.1/1035-764      AUGCGAUUCAUUAGAAGUAACGAGUUGACAUAAGGUAA-AUC-UACA---UCGAGGGGGCCUU-UCUUUGAGUGCGCGGGGAAGCUUCAUUAAGCAGCGCUAACAAGGCGUGCAAAUGCUCUGAUUGGGCGGCUCGCUC---GGAACGCCGGGGCCUUAGCAGGAUGCCCA-CCUAAUGAGGGUCACCACAAGAGACUGAUAAAAUAUUCACAUUUUC-CAU-CGCACCGGGAACUUUG--CACUGAAGGAGAAAGUUGGGGCAACUGCG-CGGCUGUAUGCCCCGG
AAPE02005217.1/1429-1160     UGG-GGCUCAUUAGGCAGAGCAGGGUGCGG--AGGUGCCCGC-CGCCAGCCCCGGAGG--CCA-CCUUUGAGCCGUGGGGGCGGCUUCAUUAAGCGGCGCUAACAAGGCUUACAAAUGC-GGGGCCCAGCAGCUUUCUU---GCAGUGGCGGGGCCUUAGCAGGGCGCCAG-GCUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCA-CCG-CGCGCCGGGAACUUUU---AUGUGCGGAGAAAGUUGAGGCAACUGAGCUGUGUUUACUGUCCCC
AAEX03007479.1/119548-119819 UGG-GGCUCAUUAGGCAGAGUGGGGUGCCGAGAGGUGCGCAG-CGCCGGCCCCGGAGG--CCG-CCUUUGAGCCGUCGGGGCAGCUUCAUUAAGCGGCGCUAACAAGGCAUACAAAUGC-CUUGCCCAGCAGCUUUCUU---GCAAUGCCGGGGCCUUAGCAGGGCGCCAA-GCUAAUGAGGGUCACUCAAAGGGGCUGAUCAAAUAUUCAAAUUUCC-CCG-CACGCCAGGAACUUUU---AUGUGCGGAGAAAGUUGAGGCAACUGAGCUGUGUUUACUGUCCGG
#=GC SS_cons                 :::.::::::::::::::::::::::::::::::::::::::.:::::::::::::::..:::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::...:::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::.:::.::::::::::::::::...:::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      ugG.ggcUCAUUAGgcggagCggGgUGcCgugAGGUGcgcgc.ugCcGGCcccgGaGG..Ccg.ccuUUGaGcggucGGGGcgGCUUCAUUAAgCgGCGCUAACAAGGCGUaCAAAUGC.cgGgcccaGCAGCUUUcuU...GcAauGcCgGGGCCUUAGCAGGGcGCCag.gCUAAUGAGGGUCACucaAAGgGGcUGAUcAAAUAUUCAaAUUUCC.Ccg.CaCGCcGGGaACUUUU...AUGcaagGaGAAAGUUGaGGCaACUGaGcuGUgUuuAcuguccgg
//
# STOCKHOLM 1.0

#=GF AC   RF02251
#=GF ID   Six3os1_6
#=GF DE   Six3os1 conserved region 6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   85.70
#=GF NC   76.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 57.23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21936910
#=GF RT   The long noncoding RNA Six3OS acts in trans to regulate retinal
#=GF RT   development by modulating Six3 activity.
#=GF RA   Rapicavoli NA, Poth EM, Zhu H, Blackshaw S
#=GF RL   Neural Dev. 2011;6:32.
#=GF WK   Six3OS1
#=GF SQ   4


AC166821.2/75980-76178  AGGCAGCA-UAGGGCUUCCGGCCUGGGCUGGAGAAGCGCAGGCAGCGUUGUGGCCAGGAGGUGGGCUCAGAGGGCGGCGCAGAGCCUUGCU-UGGGGAGAGGCUCUCGGACAGUCGGGGUUG-CUGCGGGCCCGAGCCGGGUAGGGUCGCGCUCAGAG-CUGUGCGCCCUGCCUGCGCCCUCCUCCCGGCUUAGCGCUUACAA
AC012354.11/96407-96602 AGGCGGGAGUACUGCUUCAGGCCAGAGCCGAA-AGGCGCUGGCGGCGGCUGGACCGCGAGGUGGGCUCGGUGGGCGGCGCCGAGCUCGGCUCUGCUGGGAGGCGC--GGACAGCCCGGGGCUGCCACCUGCCCCA-CCGGGUC--CUGGCGCACAAAG-CUACACGCCUCUCUGCAGCCCUCUGCCCUGCUUCGCGUUCCGGA
AY590889.1/158-1        AGGCAGCA-UAGGGCUUCCGGCCUGGGCUGGAGAAGCGCAGGCAGCGUUGUGGCCAGGAGGUGGGCUCAGAGGGCGGCGCAGAGCCUUGCU-UGGGGAGAGGCUCUCGGACAGUCGGGGUUG-CUGCGGGCCCGAGCCGGGUAGGGUCGCGCUCAGAG-CUA-----------------------------------------
AY590888.1/160-1        AGGCGGCA-UAGGGCUUCCGGCCUGGGCUGGAGAAGCGCAGGCAGCGUUGUGGCCAGGAGGUGGGCUCAGAGGGCGGCGCAGAGCCUUGCU-UGGGGAGAGGCUCUCGGACAGUCGGGGUUGGCUGCGGGCCCGAGCCGGGUAGGGUCGCGCUCAGAGGCUA-----------------------------------------
#=GC SS_cons            ::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                 AGGCgGcA.UAggGCUUCcGGCCuGgGCuGgAGAaGCGCaGGCaGCGuuguGgCCagGAGGUGGGCUCaGaGGGCGGCGCaGAGCcuuGCU.UGggGaGAGGCuCUCGGACAGuCgGGGuugGCugCggGCCCgAGCCGGGUaGGgUcGCGCuCAgAG.CUacgCGCCucuCuggaGCCCUCugCCCuGCUUcGCGuUccggA
//
# STOCKHOLM 1.0

#=GF AC   RF02252
#=GF ID   Six3os1_7
#=GF DE   Six3os1 conserved region 7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   50.00
#=GF TC   54.90
#=GF NC   37.50
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.99 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21936910
#=GF RT   The long noncoding RNA Six3OS acts in trans to regulate retinal
#=GF RT   development by modulating Six3 activity.
#=GF RA   Rapicavoli NA, Poth EM, Zhu H, Blackshaw S
#=GF RL   Neural Dev. 2011;6:32.
#=GF WK   Six3OS1
#=GF SQ   5


AC166821.2/77138-77330  UGUACCCGGCGCCGCGCCCCCAGAUCUGCAUCGGAAUGUAGAAAAGAUCUUUUUAAAAAAA-----------GUUUUGAAUUCCUCAAUGAUUUUUCUUCUGGAAAGGCAGCUUAGGAUAAUUAUUUCAGCUUUAUUGAGGGCAGAUUAGUUGAAGUCUGGGCGCUGCGUUUCAAUACGCGUUGUACAUGGGCCGACAAUGUGG
AC151334.2/6887-6696    CGGGCGCUGCGCC-UGCCCCCAGAUCUCCAUCGGAAUGCAGAAAACAUCUUAGAAAAAAAGU----------AGUUUGAAUUCCUGAAUGAUUUUUCCUGUAGAAAGG-GGCUUAGGAUAAUGAUUUCAGCUUUAUUGAGGGCAGAUUAGUAGCAGUCUCGAUGCUGCCUCUCAAUACGCGCUGUACAUGCCUUUACAAUGUGC
AY589792.1/187-1        UGUACCCGGCGCCGCGCCCCCAGAUCUGCAUCGGAAUGUAGAAAAGAUCUUUUUAAAAAAA-----------GUUUUGAAUUCCUCAAUGAUUUUUCUUCUGGAAAGGCAGCUUAGGAUAAUUAUUUCAGCUUUAUUGAGGGCAGAUUAGUUGAAGUCUGGGCGCUGCGUUUCAAUACGCGUUGUACAUGGGCCGACA------
AC236461.1/25148-24947  AGUGCUCUGCACC-UGACCCCAGAUCUCCAUCAGAAUGCAGAAAAGAUUUUAUAAAAAAAAAGAAAACAAGAAGUUUGAAUUCCUGAAUGAUUUUUUUCUGCAGAUAGGGGCUUAGGAUAAUGAUUUGUGCUUUAUUG-GGGCAGAUUAGUCACAGUGUCACUACUGUCUCUCAAUGUGCCCUGUACAUGUCUCUUCAAUGUGC
AC012354.11/97619-97819 UGGACACGGCGCCUUGCCCCCAGAUCUGCAUCGGAAUGCAGAAAAGAUCUUUAAAAAAAAAAAAAAAAA---GUUUUGAAUUCCUCAAUGAUUUUUCUUCUGGAAAGGCAGCUUAGGAUAAUUAUUUCAGCUUUAUUGAGGGCAGAUUAGUUGAAGUCUGGGCGCUGCGUUUCAAUACGCGUUGUACACGGGCCGACAAUGUGG
#=GC SS_cons            ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..........::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                 uGugCuCgGCGCCguGcCCCCAGAUCUgCAUCGGAAUGcAGAAAAgAUcUUuuaAAAAAAaa..........guUUUGAAUUCCUgAAUGAUUUUUcuucugGaAaGGcgGCUUAGGAUAAUuAUUUcaGCUUUAUUGAGGGCAGAUUAGUuGaAGUcUgGgcGCUGcgUuUCAAUacGCguUGUACAuGggccgaCAAUGUGg
//
# STOCKHOLM 1.0

#=GF AC   RF02253
#=GF ID   IRE_II
#=GF PI   Model1_new
#=GF DE   Iron response element II
#=GF AU   Stevens S
#=GF AU   Gardner P; 0000-0002-7808-1213
#=GF AU   Brown C
#=GF SE   Leipuviene, R. and Theil, E.C.
#=GF SS   Published; PMID:17849083
#=GF GA   27.00
#=GF TC   27.00
#=GF NC   26.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.45 -Z 549862.597050 CM SEQDB
#=GF DR   GO; 0010039; response to iron ion;
#=GF DR   SO; 0004725; regulatory_region;
#=GF RN   [1]
#=GF RM   2498873
#=GF RT   A cytosolic protein binds to structural elements within the iron
#=GF RT   regulatory region of the transferrin receptor mRNA.
#=GF RA   Koeller DM, Casey JL, Hentze MW, Gerhardt EM, Chan LN, Klausner RD,
#=GF RA   Harford JB
#=GF RL   Proc Natl Acad Sci U S A. 1989;86:3574-3578.
#=GF RN   [2]
#=GF RM   14568251
#=GF RT   The role of the iron responsive element in the control of
#=GF RT   ferroportin1/IREG1/MTP1 gene expression.
#=GF RA   Lymboussaki A, Pignatti E, Montosi G, Garuti C, Haile DJ, Pietrangelo A
#=GF RL   J Hepatol. 2003;39:710-715.
#=GF RN   [3]
#=GF RM   8530520
#=GF RT   Succinate dehydrogenase b mRNA of Drosophila melanogaster has a functional
#=GF RT   iron-responsive element in its 5'-untranslated region.
#=GF RA   Kohler SA, Henderson BR, Kuhn LC
#=GF RL   J Biol Chem. 1995;270:30781-30786.
#=GF RN   [4]
#=GF RM   11741608
#=GF RT   Iron-dependent regulation of the divalent metal ion transporter.
#=GF RA   Gunshin H, Allerson CR, Polycarpou-Schwarz M, Rofts A, Rogers JT, Kishi F,
#=GF RA   Hentze MW, Rouault TA, Andrews NC, Hediger MA
#=GF RL   FEBS Lett. 2001;509:309-316.
#=GF RN   [5]
#=GF RM   16412980
#=GF RT   A novel iron responsive element in the 3'UTR of human MRCKalpha.
#=GF RA   Cmejla R, Petrak J, Cmejlova J
#=GF RL   Biochem Biophys Res Commun. 2006;341:158-166.
#=GF RN   [6]
#=GF RM   8643505
#=GF RT   Translational regulation of mammalian and Drosophila citric acid cycle
#=GF RT   enzymes via iron-responsive elements.
#=GF RA   Gray NK, Pantopoulos K, Dandekar T, Ackrell BA, Hentze MW
#=GF RL   Proc Natl Acad Sci U S A. 1996;93:4925-4930.
#=GF RN   [7]
#=GF RM   2050126
#=GF RT   Identification of a novel iron-responsive element in murine and human
#=GF RT   erythroid delta-aminolevulinic acid synthase mRNA.
#=GF RA   Dandekar T, Stripecke R, Gray NK, Goossen B, Constable A, Johansson HE,
#=GF RA   Hentze MW
#=GF RL   EMBO J. 1991;10:1903-1909.
#=GF RN   [8]
#=GF RM   16760464
#=GF RT   Iron regulation and the cell cycle: identification of an iron-responsive
#=GF RT   element in the 3'-untranslated region of human cell division cycle 14A
#=GF RT   mRNA by a refined microarray-based screening strategy.
#=GF RA   Sanchez M, Galy B, Dandekar T, Bengert P, Vainshtein Y, Stolte J,
#=GF RA   Muckenthaler MU, Hentze MW
#=GF RL   J Biol Chem. 2006;281:22865-22874.
#=GF RN   [9]
#=GF RM   17417656
#=GF RT   Iron-regulatory proteins limit hypoxia-inducible factor-2alpha expression
#=GF RT   in iron deficiency.
#=GF RA   Sanchez M, Galy B, Muckenthaler MU, Hentze MW
#=GF RL   Nat Struct Mol Biol. 2007;14:420-426.
#=GF RN   [10]
#=GF RM   16110529
#=GF RT   Deficiency of glutaredoxin 5 reveals Fe-S clusters are required for
#=GF RT   vertebrate haem synthesis.
#=GF RA   Wingert RA, Galloway JL, Barut B, Foott H, Fraenkel P, Axe JL, Weber GJ,
#=GF RA   Dooley K, Davidson AJ, Schmid B, Paw BH, Shaw GC, Kingsley P, Palis J,
#=GF RA   Schubert H, Chen O, Kaplan J, Zon LI
#=GF RL   Nature. 2005;436:1035-1039.
#=GF RN   [11]
#=GF RM   10468622
#=GF RT   Bacillus subtilis aconitase is an RNA-binding protein.
#=GF RA   Alen C, Sonenshein AL
#=GF RL   Proc Natl Acad Sci U S A. 1999;96:10412-10417.
#=GF RN   [12]
#=GF RM   9891009
#=GF RT   Molecular cloning of mouse glycolate oxidase. High evolutionary
#=GF RT   conservation and presence of an iron-responsive element-like sequence in
#=GF RT   the mRNA.
#=GF RA   Kohler SA, Menotti E, Kuhn LC
#=GF RL   J Biol Chem. 1999;274:2401-2407.
#=GF RN   [13]
#=GF RM   11313346
#=GF RT   Regulation of the 75-kDa subunit of mitochondrial complex I by iron.
#=GF RA   Lin E, Graziano JH, Freyer GA
#=GF RL   J Biol Chem. 2001;276:27685-27692.
#=GF CC   IRE, TFRC, SLC40A1, SDHB, SLC11A2, CDC42BPA, ACO2, ALAS2_H.SAPIENS,
#=GF CC   CDC14A, EPAS1, ALAS2, qoxD, Hao1, NDUFS1, transferrin, Aconitate.
#=GF WK   Iron_response_element
#=GF SQ   29


DQ496099.1/33592-33622       UAAUUAUCGGGAACAGUGUUU-CCCAUAAUUU
DQ496099.1/33076-33106       UAAUUAUCGGAAGCAGUGCCU-UCCAUAAUUA
DQ496099.1/33026-33056       UAUUUAUCAGUGACAGAGUUC-ACUAUAAAUG
BC002592.2/1805-1836         UAGCCAUCAGAGCCAGUGUGUUUCUAUGGUUU
U87926.1/193-223             ACCUCAUCUUUGUCAGUGCAC-AAAAUGGCGC
DQ496099.1/33480-33510       ACAUUAUCGGGAGCAGUGUCU-UCCAUAAUGU
AC096777.1/125476-125507     GUACAAUCCUCGGCAGUGUCCUGAGACUGUAU
DQ065759.1/122-152           CCAACUUCAGCUACAGUGUUA-GCUAAGUUUG
BT072252.1/999-1029          UAAUUAUCGGGAGCAGUGUCU-UCCAUAAUUA
ABQO010331002.1/2885-2915    ACAUUAUCGGAAGCAGUGUCU-UCCAUAAUGA
AANH01009495.1/10595-10625   ACGUUAUCGGGAGCAGUGUCU-CCCAUAAUGC
AAPY01264792.1/6848-6818     UAAUUAUCGGGAACAGCGCUU-CCCAUAAUUU
AAFR03033680.1/6556-6526     UAAUUAUCGGGGACAGCGUUU-CCCAUAAUUU
CAAE01012432.1/1092-1062     CCAUUAUCGGGAGCAGUGUCU-UCCAUAAUGA
AAVX01293942.1/615-585       AAGUUAUCGGGAACAGAGAUU-CCCAUAAUUU
ABQF01023485.1/2300-2270     UAAUUAUCGGGGACAGUGUUU-CCCAUAAUUG
AJ851647.1/104-134           CCGACUUCAGCUACAGUGCUA-GCUAAGUCGG
AANN01734046.1/1792-1822     UGAUUAUCGGGGGCAGUGUCU-CCCAUAAUCC
CT030428.1/3683-3713         UAUUUAUCAGUGACAGCGAUC-ACUAUAAAUG
BAAF04049161.1/677-707       ACGUUAUCGGAAGCAGUGCCU-UCCAUAAUUA
AAPN01033802.1/214-244       GGAUUAUCGGAAGCAGUGACU-UCCAUAAUUU
ABRT010089884.1/134-104      CCGACUUCAGCUACAGUGUUG-GCUAAGUUUG
ABPK01066404.1/64-34         UUUUUAUCGGGAGCAGUGCCU-UCCAUAAUAA
ABJB010839612.1/1641-1672    AUGCAAUCCUCGGCAGUGUCCUGAGACUGCGU
AF428141.1/386-416           ACUUCAUCUUUGUCAGUGCAC-AAAAUGGCGC
AAWZ02031527.1/19065-19095   CCGACUUCAGCUACAGUGCUA-GCUAAGUUUG
AAEX03017890.1/298469-298439 CCGACUUCAGCUACAGUGUUA-GCUAAGUUAG
CAAB02011656.1/4642-4612     UCAUUAUCGGGAGCAGUGUCU-CCCAUAAUGU
BC108025.1/2966-2996         UAAUUAUCGGAAGCAGUGCCU-UCCAUAAUUG
#=GC SS_cons                 <<<<<<<-<<<<<<___>->>.>>>>>>>>>>
#=GC RF                      caauuAUCgGcggCAGUGUcc.gCcAUaauug
//
# STOCKHOLM 1.0

#=GF AC   RF02254
#=GF ID   mir-35
#=GF DE   microRNA mir-35
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   69.00
#=GF TC   69.40
#=GF NC   68.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00088
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   11679671
#=GF RT   An abundant class of tiny RNAs with probable regulatory roles in
#=GF RT   Caenorhabditis elegans.
#=GF RA   Lau NC, Lim LP, Weinstein EG, Bartel DP
#=GF RL   Science. 2001;294:858-862.
#=GF WK   Non-coding_RNA
#=GF SQ   2


AAGD02001682.1/66884-66789   UCCUCGGUCGGAUCGGACCUACACUGGUUUUCGCUGCGGUGAUACUUC-GAGAAUGAUUAUCACCGGGUGAAAAUCAGGGCAGGUCCGAUUCCACCG
ABEG02001577.1/118515-118419 UAUUCGGCCGGAUCGGACCUAUGCUGGUUUUCACCGCGGUUAUACUUCUAACAAUAAUUAUCACCGGGUUAAAACUUGCAGAGGUCCGGUCCGGCCU
#=GC SS_cons                 :::::<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<-<<<<<<<<-<<________>>->>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>:
#=GC RF                      UauUcGGccGgaccGGaccugcgcugguuuucgccGcGGugauacuccuaAgAAUgaUuaucaCCgggcgaaaaccagcgcagguCCggucCggCCu
//
# STOCKHOLM 1.0

#=GF AC   RF02255
#=GF ID   adapt33_1
#=GF DE   Adaptive response 33 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   60.00
#=GF TC   65.30
#=GF NC   52.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 37.93 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   8806733
#=GF RT   adapt33, a novel oxidant-inducible RNA from hamster HA-1 cells.
#=GF RA   Wang Y, Crawford DR, Davies KJ
#=GF RL   Arch Biochem Biophys. 1996;332:255-260.
#=GF RN   [2]
#=GF RM   12837039
#=GF RT   Characterization of adapt33, a stress-inducible riboregulator.
#=GF RA   Wang Y, Davies KJ, Melendez JA, Crawford DR
#=GF RL   Gene Expr. 2003;11:85-94.
#=GF WK   Adaptive_response_33
#=GF SQ   3


AC107744.8/42816-42743     CUUAUAUAAAUCUUCAAAUUAAUGAAUAUUUCUGUAAGUGUUACUCUUACA---AAAAACAUCCUUUGAUUUCAUUC
U29660.1/522-447           CUUAUAUAAAUCUCCAAAUUAUUGAAUGAAUUUGCAAAUGGCAUACUCUUA-AGCAAAACAUCCUUUUACUUCUUUC
AABR05042275.1/39958-39882 CUUAUAUAAAUCUUCACAUUACUGAAUACAUGUGUAAACAUUACUCUAUCAUGGAAAAACAUCCUUUGAUUUCACUC
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::::::::
#=GC RF                    CUUAUAUAAAUCUuCAaAUUAuUGAAUauaUuUGuAAauGuuAcuCUuucA.gGaAAAACAUCCUUUgAuUUCauUC
//
# STOCKHOLM 1.0

#=GF AC   RF02256
#=GF ID   adapt33_2
#=GF DE   Adaptive response 33 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   60.00
#=GF TC   79.80
#=GF NC   53.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.02 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   8806733
#=GF RT   adapt33, a novel oxidant-inducible RNA from hamster HA-1 cells.
#=GF RA   Wang Y, Crawford DR, Davies KJ
#=GF RL   Arch Biochem Biophys. 1996;332:255-260.
#=GF RN   [2]
#=GF RM   12837039
#=GF RT   Characterization of adapt33, a stress-inducible riboregulator.
#=GF RA   Wang Y, Davies KJ, Melendez JA, Crawford DR
#=GF RL   Gene Expr. 2003;11:85-94.
#=GF WK   Adaptive_response_33
#=GF SQ   2


AC107744.8/38048-37980     CUUUCCUGUAU--UUCGUAAUCAUCUUCCAACGUCACGCAUCUCUUCCAGGCAUCACCGAGAACACAAUUC
AABR05042275.1/36961-36891 CUUUCCUGUAUAUUUCAUAAUCUUCUUUCAAAGCCACACAUUUCUUUCAGACAUCGCCAAGAAUACAAUUC
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    CUUUCCUGUAUAUUUCgUAAUCuUCUUuCAAaGuCACgCAUuUCUUuCAGgCAUCgCCgAGAAuACAAUUC
//
# STOCKHOLM 1.0

#=GF AC   RF02257
#=GF ID   adapt33_3
#=GF DE   Adaptive response 33 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   70.00
#=GF TC   82.50
#=GF NC   54.80
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.25 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   8806733
#=GF RT   adapt33, a novel oxidant-inducible RNA from hamster HA-1 cells.
#=GF RA   Wang Y, Crawford DR, Davies KJ
#=GF RL   Arch Biochem Biophys. 1996;332:255-260.
#=GF RN   [2]
#=GF RM   12837039
#=GF RT   Characterization of adapt33, a stress-inducible riboregulator.
#=GF RA   Wang Y, Davies KJ, Melendez JA, Crawford DR
#=GF RL   Gene Expr. 2003;11:85-94.
#=GF WK   Adaptive_response_33
#=GF SQ   3


AC107744.8/35683-35546 UUUCAUUAGCCACCUCCCAUCUUCAGAAAAAGCGUUCUCUCA-UGAGGACAGCGGAGCAGUCCCACUCAAGCUGCUGUG-CAUCACAUCCACAGCGCCAGGUCACAUCGAGAGCUCCUGUGCCCCCUCGCCAUCCGUGAC
U29660.1/310-175       ---CACCACUUC-ACACCUCAUCGAAGCAAAAGGUUCGCUGAAUUAUGAUUGCGUGGCACGCUCGGUCAAGCUCGUGUGGUAUCACACACAUGGCGCCAGGUCACACCAAAAGCUCCUCCGUCACCUCCACAUCAGUGAG
U29661.1/303-164       CAUCACCAACACGAUGCCUCAUCGAAGCAAAAGGUUCGCUGAAUUAUGAUUGCGUGGCACGCUCGGUCAAGCUCGUGUGGUAUCACACACAUGGCGCCAGGUCACACCAAAAGCUCCUCCGUCACCUCCACAUCAGUGAG
#=GC SS_cons           ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                uuUCAccAgcucgaugCCucaUcgAagcAAAagGUUCgCUgAAUuAuGAuuGCGugGCAcgCuCggUCAAGCUcgUGUGGuAUCACAcaCAugGCGCCAGGUCACAcCaAaAGCUCCUccGuCaCCUCcaCAUCaGUGAg
//
# STOCKHOLM 1.0

#=GF AC   RF02258
#=GF ID   adapt33_4
#=GF DE   Adaptive response 33 conserved region 4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   119.40
#=GF NC   38.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 37.29 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF RN   [1]
#=GF RM   8806733
#=GF RT   adapt33, a novel oxidant-inducible RNA from hamster HA-1 cells.
#=GF RA   Wang Y, Crawford DR, Davies KJ
#=GF RL   Arch Biochem Biophys. 1996;332:255-260.
#=GF RN   [2]
#=GF RM   12837039
#=GF RT   Characterization of adapt33, a stress-inducible riboregulator.
#=GF RA   Wang Y, Davies KJ, Melendez JA, Crawford DR
#=GF RL   Gene Expr. 2003;11:85-94.
#=GF WK   Adaptive_response_33
#=GF SQ   2


AC107744.8/35455-35277 UUUGGCGCCAUUCUCCAAUCAGUCCUUCCCGGCGCGCGCCACCAUCGCCAGGGUCAGGCAGGCGUCAGCUCGGUUUCCACCUCUCUACUCCCCAUGGCCAUGCUCGCCCAAAGCGCGAUGGCGCCGGAUUGCGCGGGAGCUGGCGUAGACAUGAUGCCAGAGCGUUAACAAAAGGAGGA
U29660.1/170-4         CCUGGCGCUGGUCUCCGAUCGGUCCUCCAGAGCGCGCGCCACCAUCGCCAAAGCCAGGUCGGCCUCCGCUCGGCUGCCGCCUCUCUACUACCCAUUACAAUGCUCGCCCAAAGCGCGAUGGCGGCGGAUUGCACGCGAGCAGG--UACACACGGUA--GAAACACCAGAGA--------
#=GC SS_cons           :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                uuUGGCGCuguUCUCCgAUCgGUCCUuCcggGCGCGCGCCACCAUCGCCAggGuCAGGuaGGCgUCaGCUCGGuUuCCgCCUCUCUACUcCCCAUggCcAUGCUCGCCCAAAGCGCGAUGGCGgCGGAUUGCgCGgGAGCuGGcGUAgACAuGgUgccggAgCguuAgcgAaaGGaGGa
//
# STOCKHOLM 1.0

#=GF AC   RF02259
#=GF ID   Vax2os1_1
#=GF DE   Vax2os1 conserved region 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   100.00
#=GF TC   178.00
#=GF NC   81.70
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.04 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0051726; regulation of cell cycle;
#=GF RN   [1]
#=GF RM   22128341
#=GF RT   The long noncoding RNA Vax2os1 controls the cell cycle progression of
#=GF RT   photoreceptor progenitors in the mouse retina.
#=GF RA   Meola N, Pizzo M, Alfano G, Surace EM, Banfi S
#=GF RL   RNA. 2012;18:111-123.
#=GF WK   Vax2os1
#=GF SQ   3


AY589787.1/1733-1547       GCAUCCAGGGCCUGCAGCUCGGAAGCAUUCCAGAGAAGUCGCGGGAGCCGCCCGGGGACUCCACAGCCCAGGCCUCUCCCAAGCCACCUCCGCUUUCCACAGCUCCUUGCCACC-----UUCCGUACUUUCCCCAG---------AGCUGGAAGUAGGAAACUUCUCCCCUGCAGGGAUCGGAU-AGGCUUACUCCGUGAAG
AY589788.1/1183-999        GCAUCCAGGGCCUGCAGCUCGGAAGCAUUCCAGAGAAGUCGCGGGAGCCGCCCGGGGACUCCACAGCCCAGGCCUCUCCCAAGCCACCUCCGCUUUCCACAGCUCCUUGCCACC-----UUCCGUACUUUCCCCAG---------AGCUGGAAGUAGGAAACUUCUCCCCUGCGUGGGUCG-AU-GUAUUUAUCUGGUCAG-
AAHX01031257.1/14005-13805 GCAUCCAGGGCCUGCAGUGCGGAAGCAUUCCAGAGAGGUCGCGGGAGCCGCCCGGGAACUCCACAGCCCAGGCCUCUCCCAAGCCACCUCCUCUUUCCACCGCUCCCUGCCACCGCGGUUUCUGUGCUUUUCCCAGUCCUCAGAGAGCUGGGAAGAUGAAACU-CUCCCCUGCAGGGAUCCAGUCGAACUUUCUCCGUGCAA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.....:::::::::::::::::.........:::::::::::::::::::::::::::::::::::::::.:::::::::::::::::
#=GC RF                    GCAUCCAGGGCCUGCAGcuCGGAAGCAUUCCAGAGAaGUCGCGGGAGCCGCCCGGGgACUCCACAGCCCAGGCCUCUCCCAAGCCACCUCCgCUUUCCACaGCUCCuUGCCACC.....UUCcGUaCUUUcCCCAG.........AGCUGGaAguAgGAAACUUCUCCCCUGCagGGaUCggaU.ggacUUacuccGUgaag
//
# STOCKHOLM 1.0

#=GF AC   RF02260
#=GF ID   MAT2A_A
#=GF DE   MAT2A 3'UTR stem loop A
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published; PMID:21994249
#=GF SS   Published; PMID:21994249
#=GF GA   40.00
#=GF TC   40.60
#=GF NC   38.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   21994249
#=GF RT   New families of human regulatory RNA structures identified by comparative
#=GF RT   analysis of vertebrate genomes.
#=GF RA   Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R,
#=GF RA   Pedersen JS
#=GF RL   Genome Res. 2011;21:1929-1943.
#=GF WK   S-adenosylmethionine_synthetase_enzyme
#=GF SQ   20


AANH01001932.1/45985-45920   CU-UUUUCCCCCCAGGCCUGUUGGUGUAUACUACAGAGAAGCCUCCAAGGUUCCGGGGGUGAAAUGC
AB070266.1/1283-1347         GCCUUUUUUCCCCAGACUUGUUGGCGUAGGUUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
BC001686.2/1304-1368         GCCUUUUUUCCCCAGACUUGUUGGCGUAGGCUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
AAPN01391386.1/5170-5234     GGCUUCUUUCCCCAGACUUGUUGGCGUAGGUUACAGAGAAGCCUUCAAGCUCUGCGGGA--AAGGGC
L43509.1/1197-1261           GCCUUUUUUCCCCAGACUUGUUGGCGUAGGCUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
AAFR03050370.1/27806-27870   GGCUUUUUUCCCCAGACUUGUUGGCGUAGGUUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
AC207174.3/17678-17742       GCCUUUUUUCCCCAGACUUGUUGGCGUAGGCUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
AAGV020304924.1/3018-2954    GCCUUUUUUCCCCAGACUUGUUGGCGUAGGCUACAGAGAAGCUUUCAAGCUCUGAGGGA--AACGGC
ABRP01178874.1/882-818       GCCUUUUUCCCCCAGACUUGUUGGCGUAGGCUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
AAIY01292066.1/4756-4820     GCCUUUUCUCCCCAGACUUGCUGGCGUGGGCUACAGAGAAGCCUGCAAGCUCUGAGGGA--AAGACC
AB000717.2/6730-6794         GCCUUUUUUCCCCAGACUUGUUGGCGUAGGUUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
AC016753.9/110740-110804     GCCUUUUUUCCCCAGACUUGUUGGCGUAGGCUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
BC058360.1/1880-1944         GCCUUUUUUCCCCAGACUUGUUGGCGUAGGUUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
ABRT010239600.1/4676-4740    GACUUUUCUCUCCAGACUUGUUGGCGUAGGCUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGA
BT030708.1/1302-1366         GCCUUUUUUCCCCAGACUUGUUGGCGUAGGCUACAGAGAAGCCUUCAAGCUCUGCGGGA--AAGGGC
BC001854.2/1304-1368         GCCUUUUUUCCCCAGACUUGUUGGCGUAGGCUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
BT044899.1/1318-1381         GC-UUUU-CCCCCAGGCCUGUUGGUGUAUACUACAGAGAAGCCUGCAUGGUCUUGGGGU-GAAAGGC
AB168273.1/1351-1415         CCCUUUUUUCCCCAGACUUGUUGGCGUAGGCUACAGAGAAGCCUUCAAGCUCUGAGGGA--AAGGGC
CAAB02003344.1/269460-269526 GCUUUUUCCCCCCAGGCCUGUUGGUGUAUACUACAGAGAAGCCUCCAGGGUUCCGGGGGUGAAAUGC
AAPE02053540.1/30750-30686   GCCUUUUUUCCCCAGACUUGUUGGCGUAGGCUACAGAGAAGCCUUCAAGUUCUGAGGGA--AAGGGC
#=GC SS_cons                 <<<<---<<<<-<<<<--<<--<<<<<_____>>------>>>-->>--->>>>->>>>..-->>>>
#=GC RF                      GccuUUUuuCCCcaGaCUUGUUGGCGUAGGCUACAGAGAAGCCUuCAAGcuCugaGGga..AAgggC
//
# STOCKHOLM 1.0

#=GF AC   RF02261
#=GF ID   MAT2A_B
#=GF DE   MAT2A 3'UTR stem loop B
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published; PMID:21994249
#=GF SS   Published; PMID:21994249
#=GF GA   45.00
#=GF TC   47.00
#=GF NC   43.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   21994249
#=GF RT   New families of human regulatory RNA structures identified by comparative
#=GF RT   analysis of vertebrate genomes.
#=GF RA   Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R,
#=GF RA   Pedersen JS
#=GF RL   Genome Res. 2011;21:1929-1943.
#=GF WK   S-adenosylmethionine_synthetase_enzyme
#=GF SQ   28


L43509.1/1988-2051           ACAGGCACUUGGCAGCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
AALT01193755.1/245-307       ACAGGCACUUGGCAGCCUUGUGAUGUCAUACAGAGAAGUCAC-GGGGCAGUACCUGA-GGUCUGU
BT030708.1/2105-2168         ACAGGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
AAPY01600731.1/2315-2253     ACAGGCACUUGGCA-CCCUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
AY603043.1/98-161            ACAGGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
BC001686.2/2094-2157         ACAGGCACUUGGCAGCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
AAFR03050370.1/28606-28669   GCGGGCACUUGGCAGCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCGGUAUCUGAGGGUCUGU
AAWR02003557.1/104626-104563 ACAGGCACUUGGCACCCUUGUGAUGUUAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
AAYZ01081944.1/5452-5515     ACGGGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
BC058360.1/2670-2730         ACAGGCAUUUGGCACCCUUGUGAU---AUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
ABRR01311502.1/2361-2298     ACAGGCACUUGGCACCCUUGUGAUGUGAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
AAGV020304924.1/2231-2168    ACAGGCACUUGACUUCCUUGUGGCGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
BC001854.2/2094-2157         ACAGGCACUUGGCAGCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
AAQQ01101557.1/1519-1456     ACAGGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
AAPN01391386.1/6027-6090     ACGGGCGCUUGGCACUCUUGCGAUGUCCUACAGAGAAGUCGC-GGGGUGGUGCCAGAGGGUCUGU
AANN01466464.1/6112-6173     AUAGCCACUUGGCACCCUUGUGAU---AAACAGACAAGUCACAGGGGCAGUACCUGAGGGUCUGU
AAHX01074269.1/59413-59476   ACAGGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCAC-AGUGCAGUACCCGAGGGUCUGU
ABRT010239600.1/5455-5517    ACAGGCACUUGGCA-CCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
ABRP01178874.1/83-21         ACAUGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCAC-AUGGCAGUACCUGA-GGUCUGU
ABDC01214652.1/875-938       ACAGGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGAAGUACCUGAGGGUCUGU
AAFC03063288.1/5554-5617     ACAGGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
BC062394.1/2652-2715         ACAGGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCCCAGGGUCUGU
AC048334.21/82720-82783      ACAGGCACUUGGCAGCCUUGUGAUAUCAUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
AB000717.2/7499-7562         ACAGGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCAC-AGGGCAGUACCCGAGGGUCUGU
AC164538.4/22511-22451       ACAAGCAUUUGGCACCCUUGUGAU---AUACAGAGAAGUCAC-AGGGCAGUACCUGAGGGUCUGU
AAPE02053540.1/29951-29888   ACAGGCACUUGGCACCCUUGUGAUAUCAUACAGAGAAGUCAU-AGGGCAGUACCUGAGGGUCUGU
AAGU03081186.1/62880-62816   ACAGGCACUUGGCACCCUUGUGAUGUCAUACAGAGAAGUCACAGGGGUGGUACCUAAGGGUCUGU
AAGW02007264.1/5656-5719     ACAGGCACUUGGCACCCUUGUGACGUCAUACAGAGAAGUCAC-AGGGCAGUCCCCGAGGGUCUGU
#=GC SS_cons                 <<<<<<-<<--<--<<<<<<<<<<<<___>>------>>>>>.>>>>>----->-->>->>>>>>
#=GC RF                      ACaGgCACUUGGCAcCCuuGuGAuGUCAUACAGAGAAgUCaC.agGGgAGUACCUGAGGGuCuGU
//
# STOCKHOLM 1.0

#=GF AC   RF02262
#=GF ID   MAT2A_C
#=GF DE   MAT2A 3'UTR stem loop C
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published; PMID:21994249
#=GF SS   Published; PMID:21994249
#=GF GA   47.00
#=GF TC   48.00
#=GF NC   43.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   21994249
#=GF RT   New families of human regulatory RNA structures identified by comparative
#=GF RT   analysis of vertebrate genomes.
#=GF RA   Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R,
#=GF RA   Pedersen JS
#=GF RL   Genome Res. 2011;21:1929-1943.
#=GF WK   S-adenosylmethionine_synthetase_enzyme
#=GF SQ   18


AC190303.9/101932-101881   GCUU--UCUGAACAGCUGGUGUAGCUACAGAGAAACCAGCUUCCUUCAGAGAGC
BC001854.2/2284-2335       GCUU--UCUGAACAGCUGGUGUAGCUACAGAGAAACCAGCUUCCUUCAGAGAGC
AY603043.1/288-339         GCUU--UCUGAACAGCUGGUGUAGCUACAGAGAAACCAGCUUCCUUCAGAGAGC
BC001686.2/2284-2335       GCUU--UCUGAACAGCUGGUGUAGCUACAGAGAAACCAGCUUCCUUCAGAGAGC
ABRT010239600.1/5642-5693  GCUU--UCUGAACAGCUGGUGUAGCUACAGAGAAACCAGCUUCCUUCAAAGAGC
BC062394.1/2837-2888       GCUU--UCUGAACAGCUGGUGUAGCUACAGAGAAACCAGCUUCCUUCAGAGAGC
BC058360.1/2851-2902       GCUU--UCUGAACAGCUGGUGUAGCUACAGAGAAACCAGCUUCCUUCAGAGAGC
AC207174.3/18658-18709     GCUU--UCUGAACAGCUGGUGUAGCUACAGAGAAACCAGCUUCCUUCAGAGAGC
AAFR03050370.1/28792-28843 GCUU--UCUGAGCAGCUGGUGUAGAUACAGAGAAACCAGCUUUCUUCAGAGAGC
ABGA01073367.1/2769-2718   GCUU--UCUGAACAGCUGGUGUAGCUACAGAGAAGUCAGCUUCCUUCAGAAAGC
AALT01193755.1/435-486     GCUU--UCUGAGUAGUUGGUGUAGCUACAGAGAAACCAGCUUCCUUCAGAGAGC
AAIY01648805.1/14956-15009 GCUUUUUCUGAACAGCUGGUGUAGCUACAGAGAAACCAGCUCCCUUCAGAGAGC
ABRP01178872.1/24320-24270 GCU---UCUGAACAGCUGGUGUAGCUACAGAGAAACCAGCUUCGUUCAGACAGC
AAPN01213645.1/1538-1589   GCUU--UCUGAACAUCUGGUGUAGCUACAGAGAAACCACGUCCCUUCAGAGAGC
ABQO010159685.1/1818-1869  GCUU--UCUGAGCAGUUGGUGUAGAUACAGAUAAAUCAGCUUCUUUCAGAGAGU
AAQQ01512580.1/1438-1387   GCUU--UCUGAACAGCUUGUGUAACUACAGAGAAACCAGUUUCCUUCAGAGAAU
AAYZ01662450.1/113-63      GCU---GCUAAAGGGCUGGUGUAGUUACAGAGAAACCAGUUUUCUUCAGAGAGC
AAWZ02030028.1/3913-3862   GCGU--UCUGAAGUCCUGGUGUAGCUACAGAGAAACCAGUUCUCUUCAGAAUGC
#=GC SS_cons               <<<<..<<<<<--<<<<<<<<<____>>------>>>>>>>---->>>>>>>>>
#=GC RF                    GCUu..UCUGAACAgCUGGUGUAGCUACAGAGAAACCAGcUUCCUUCAGAgAGC
//
# STOCKHOLM 1.0

#=GF AC   RF02263
#=GF ID   MAT2A_D
#=GF DE   MAT2A 3'UTR stem loop D
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published; PMID:21994249
#=GF SS   Published; PMID:21994249
#=GF GA   32.00
#=GF TC   32.00
#=GF NC   31.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   21994249
#=GF RT   New families of human regulatory RNA structures identified by comparative
#=GF RT   analysis of vertebrate genomes.
#=GF RA   Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R,
#=GF RA   Pedersen JS
#=GF RL   Genome Res. 2011;21:1929-1943.
#=GF WK   S-adenosylmethionine_synthetase_enzyme
#=GF SQ   35


AADD01036532.1/25137-25097   UCUGGGGUAUGGCGU-AAGUACAGAGAA-GCCAUCACCUCAGA
AAIY01413108.1/115-155       UCUGGGGCAUGGUGU-AAGUACAGAGAA-GCCAUCGCCUCAGA
AAPN01391386.1/6339-6379     UCUGGGGUGUGGCGU-GAGUACAGAGAA-GCUAUCACCUCAGA
BAAF04060906.1/485-525       UCUGGAACUCGGCGU-GGAUACAGAGAA-GCCGAUGUUUCAGA
AAHX01033174.1/21764-21724   UCUGGGAUAUGGUGU-AAAUACAGAGAA-GCCAUCACCUCAGA
AAYZ01314226.1/2704-2664     UCUGAGGUAUGGUUU-AAGUACAGAGAA-GCCAUCACCUUAGA
AAWR02022626.1/22707-22747   ACUGGGAUAUGGCAU-AAGUACAAAGAA-GCCAUCACCUCAGA
CAAE01014999.1/739530-739570 UCUGAGGCCCGGCGU-GGAUACAGAGAA-GUCGGGCUUUCAGG
AANU01209281.1/27885-27845   UCUGGGGUAUGGCAU-AAGUACACAGAA-GGCAUCACCUCAGA
ABQO010224520.1/1811-1851    UCUAGGGUGUGGCAU-GAGUACAGAGAA-GCUAUCAUCUCAGA
AADA01039591.1/220-179       UCUGGGGUAUGGCGUUAAGUACAGUGAA-GCUAUCACCUCAAA
AC164538.4/22211-22174       UCUGGGGUAUGGCAU-AAGUACAGAGAA-GCCAUGA---CAGG
AANN01466464.1/6421-6461     UCUGAGGUAUGGCGU-AAGUACAGAGAA-GCCAUCACCUCAGA
ABRN01335285.1/1307-1347     ACUGAGGUAUGGCAG-AAGUACAAGGAA-UUCAACAUCUCAAA
BC080342.1/2125-2162         GCUAGGCUUGGGCGU-AAGUACAGAGUA-GCCUUUGCCUU---
BC058360.1/2971-3011         UCUGGGGUAUGGCGU-AAGUACAGAGAA-GCCAUCACCUCAGA
AAFR03050370.1/28915-28955   UCUGGGGUGUGGCGU-GAGUACAGAGAA-GCUAUCACCUCAGA
AAKN02036536.1/211964-211924 UCUGGGGUAUGGCGU-AAGUACAGAGAA-GCCAUCGCCUCAGA
BAAE01005449.1/2392-2352     UCUGGAACUCGGCGU-GGAUACAGAGAA-GCCGAUGUUUCAGA
AANH01001932.1/45031-44991   UCUGAGACGCAGCGU-GGAUACAGAGAA-GCUGUGGUUUCAGA
L43509.1/2298-2338           UCUGGGGUAUGGCGU-AAGUACAGAGAA-GCCAUCACCUCAGA
AY603043.1/408-448           UCUGGGGUAUGGCGU-AAGUACAGAGAA-GCCAUCACCUCAGA
ABVD01282125.1/176-136       UCUGGGGUAUGGUGU-AAGUACAGAGAA-GCCGUCACCUCAGA
BT030708.1/2419-2459         UCUGGGGUAUGGCGU-AAGUACAGAGAA-GCCAUCACCUCAGA
AAQQ01101557.1/1211-1171     UCUGAGGUAUGGUGU-AAGUACAGAGAA-GCCAUCACCUCAGA
AAIY01292066.1/5079-5118     U-GGGGGUAUGGCUU-AAGUACAGAGAA-GCCCUCACCUCAGA
ABRR01179265.1/6700-6739     ACUGAGGU-UGGCAU-GAGUACAAGGAA-GCUAUCAUCUCAAA
ABQO010470677.1/775-815      UUUUGGGUGAGGUGU-GAGUACAGAAAA-GCUAUCACCUCAGA
AAQQ01512580.1/1318-1278     UCUGGGAUAUGGCAU-AAGUACAGAGAAUGUCAUUG-CUCAGA
AAIY01360048.1/860-900       UCUGGGGUGUGGCCU-AUGUACAGAGAA-GCCCUCACCUCGUA
AAGW02007302.1/51152-51192   UCUGGGGGAUGGCGU-AAGUACAGAGAA-GCCAUCUCCUCAGA
CAAB02003344.1/270480-270520 UCUGAGGCCCGGCGU-GGAUACAGAGAA-GUCGGGCUGUCAGG
AAWZ02030028.1/3779-3739     UUUGGGACCGGGUGU-GAGUACAGAGAA-GCCCUUGUCUCAAA
AAEX03002783.1/176649-176609 UCUGCAGUAGGGUGU-AAGUACAGAUAA-GCUAUCACCUCAGA
AB168273.1/2451-2491         UCUGGGGUAUGGCGU-AAGUACAGAGAA-GCCAUCACCUCAGA
#=GC SS_cons                 <<<<<<<<<<<<<__.____________.>>>>>->>>>>>>>
#=GC RF                      UCUGGGGUauGGCGU.AAGUACAGAGAA.GCCauCACCUCAGA
//
# STOCKHOLM 1.0

#=GF AC   RF02264
#=GF ID   MAT2A_E
#=GF DE   MAT2A 3'UTR stem loop E
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published; PMID:21994249
#=GF SS   Published; PMID:21994249
#=GF GA   46.00
#=GF TC   47.10
#=GF NC   45.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   21994249
#=GF RT   New families of human regulatory RNA structures identified by comparative
#=GF RT   analysis of vertebrate genomes.
#=GF RA   Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R,
#=GF RA   Pedersen JS
#=GF RL   Genome Res. 2011;21:1929-1943.
#=GF WK   S-adenosylmethionine_synthetase_enzyme
#=GF SQ   28


BC001686.2/2508-2574         CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
BC062394.1/3055-3121         CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
BC001854.2/2508-2574         CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
BC064879.1/2134-2200         CAUGUGCUCUCUGCCAGCUCAAGGUGUAGUACAGAA-AAACCUUGGCUGUAUUCUGC-AGGGGUCCUGG
ABRN01335285.1/1411-1478     UCAGCAUUCAUGAAAAGGUCAAGGCAUCCUACGAAAUAAACCUUGAGUGAGAUCUAU-AGGCAGUCUGG
AAPY01600731.1/1903-1837     CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGUCCUAC-AGGGGGUCUGG
AK054569.1/1969-1903         CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
L43509.1/2400-2466           CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
BC058360.1/3071-3137         CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
AC190303.9/101712-101646     CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
BT030708.1/2517-2583         CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGUUCUGG
AAYZ01081944.1/5861-5927     CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUGGACCUAC-AGGGGGUCUGG
AC016753.9/111944-112010     CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
AY603043.1/512-578           CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
AC207174.3/18882-18948       CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
AC154002.8/25365-25299       CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
AC116115.11/197181-197115    CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
AAWR02003557.1/104194-104128 CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-GGGGGGUCUGG
AAPN01391386.1/6451-6517     CCAGCAUUCCCAGGUAGGCCAGGGUGUCCUACAGAA-AAACCUUGGGUCGCACCUUU-GGGGGUUCUGG
ABRP01178872.1/24102-24036   CCAGCGUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
ABGA01395032.1/6677-6743     CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
ABRT010239600.1/5863-5929    CCAGCAUUCCCAGGUAAGCCAAGGUGCCCUACAGAA-AAACCUUGGGUUAGACCUAG-AGGGGGUCUGA
ABGA01114179.1/13946-14012   CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
AB168627.1/1632-1698         CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
ACBE01106865.1/3510-3444     CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
AAIY01292066.1/5180-5244     CCAGCAUUCCCAGGUAGGCCGAGGUGUCCUACAGAA-AAGCCUUGGGUUAGACCUAC-A-GGGGUCU-G
AB168273.1/2551-2617         CCAGCAUUCCCAGGUAGGCCAAGGUGUCCUACAGAA-AAACCUUGGGUUAGACCUAC-AGGGGGUCUGG
AAWZ02030028.1/3687-3620     CCAGCACUCCCUGGUAGGCCAAGGUGUCCUACAGAA-AAGCCUUGGGUCCCAUCCGCCAGGGGGUCUGG
#=GC SS_cons                 <<<<-<<<<<<--<<<<<<<<<<<<<<___>>----.-->>>>>>>------>>>>>.->>>>>>>>>>
#=GC RF                      CCAGCauuCcCaGguAGgcCAAGGuGUCCUACAGAA.AAaCCUUGgGUuagAcCUac.AGgGgguCUGG
//
# STOCKHOLM 1.0

#=GF AC   RF02265
#=GF ID   MAT2A_F
#=GF DE   MAT2A 3'UTR stem loop F
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published; PMID:21994249
#=GF SS   Published; PMID:21994249
#=GF GA   51.00
#=GF TC   52.00
#=GF NC   50.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.17 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   21994249
#=GF RT   New families of human regulatory RNA structures identified by comparative
#=GF RT   analysis of vertebrate genomes.
#=GF RA   Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R,
#=GF RA   Pedersen JS
#=GF RL   Genome Res. 2011;21:1929-1943.
#=GF WK   S-adenosylmethionine_synthetase_enzyme
#=GF SQ   26


AY603043.1/620-685         CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
ABRT010239600.1/5971-6036  CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAAAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AAIY01292066.1/5286-5350   CAUGGAG-AG-GCUGACUUGGCCGGUGUGCUACAGAGAAGCCAGCUUGUUGACAUGCUCCUCCAUUG
BC001686.2/2616-2681       CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AAYZ01081944.1/5969-6034   CAUGGAGGAA-GCGGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
BC062394.1/3163-3228       CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
BT030708.1/2625-2690       CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AAPN01391386.1/6556-6622   CGUGGGGAGACGCUGACUUGGCUGGUGUUGUACAGAGAAGCCAGCUUGUUUACAGGCUCAUCCCAUG
AALT01193755.1/758-823     CAUGGAGAAA-GCGGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AC016753.9/112052-112117   CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AC116115.11/197073-197008  CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AANN01466464.1/6628-6693   CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUGCUCCAUG
AAFR03050370.1/29132-29197 CAUGGAGGAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCCUACUCCAUG
AC190303.9/101604-101539   CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
BC001854.2/2616-2681       CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AC154002.8/25257-25192     CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
BC058360.1/3179-3244       CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AK054569.1/1861-1796       CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AC207174.3/18990-19055     CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AAQQ01101557.1/1002-938    CGUGGAGAGA-GCGGACUUGGCUGGCGUGGUACAGAGAAGCCAGCUUGUUUACAUGC-UACUCCAUG
ABBA01166058.1/319-254     CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
L43509.1/2508-2573         CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
AB168627.1/1740-1805       CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
ABRP01178872.1/23996-23931 CAUGGAAAAA-GCAGACCUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUUCAUG
AAGW02007302.1/51363-51428 CAUGGAGAAA-GCGGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUCAUCCAUG
AAWZ02030028.1/3579-3514   CCUGGGAGGG-GCUGACUUGGCCGGUGUGGUACAGAGAAGCCGGCUUGUUUACUUACCCGUCCCACG
#=GC SS_cons               <<<<<<<-<<.<<-<<<--<<<<<<<<<___>>------>>>>>>>->>>----->>>>->>>>>>>
#=GC RF                    CaUGGagAaa.GCUgACUUgGCuGGuGUGGUACAGAGAAgCCaGCuUGUuUACAUGCuuAcuCCAuG
//
# STOCKHOLM 1.0

#=GF AC   RF02266
#=GF ID   XIST_intron
#=GF DE   XIST 3' intron conserved motif
#=GF AU   Daub J; 0000-0001-6022-563X
#=GF SE   Published; PMID:21994249
#=GF SS   Published; PMID:21994249
#=GF GA   70.00
#=GF TC   80.10
#=GF NC   58.40
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   21994249
#=GF RT   New families of human regulatory RNA structures identified by comparative
#=GF RT   analysis of vertebrate genomes.
#=GF RA   Parker BJ, Moltke I, Roth A, Washietl S, Wen J, Kellis M, Breaker R,
#=GF RA   Pedersen JS
#=GF RL   Genome Res. 2011;21:1929-1943.
#=GF WK   XIST
#=GF SQ   20


AAHX01111727.1/62311-62378 UUGACCCUUUCG-AUUUUUCUUUCACUC-ACA-GAGGGUGGGACAGGAGGACGAGUGAAAGAAAGGGUCAA
ABRP01195253.1/6212-6145   UUGACCUUUUCU-AUUUUUAAAUCACUC-ACA-GAGGGCGGGAUAGGAGGAAGAGUGAAAGAAAAGGUCAA
AAYZ01604181.1/1268-1201   UUGACCUUUUCU-AUUUUUAAAUCACUC-ACAAGAGGGUGGGACAGGAGGAAGAGUGAAGGAAA-GGUCAA
AAQQ01705612.1/1217-1150   UUGGCCUUUUCC-AUUUUUAAAUCACUC-ACA-GAGGGUGGGACAGGAGGAAGAGUGAAGGAAAAGGUCAA
AANN01657536.1/1371-1436   UUGACCUUUUUU-A-UUUUAAAUCACUC-ACA-GAGGGUGGGU-AGGAGGAGGAGUGAAAGAGAAGGUCAA
AAWR02034174.1/23031-22964 UUGACCUUUUCU-AUUUUUAAAUCACUC-ACA-GAGGGUGGGAUAGGAGGCAGAGUGAAAGAAAAGGUCAA
AADA01036556.1/9937-9870   UUGACCUUUUCC-AUUUUUAAAUCACUC-ACA-GAGGGUGGGACAGGAGGAAGAGUGAAGGAAAAGGUCAA
AAIY01677296.1/375-443     UUGACCUUUUCU-AUCUUUAAAUCACUCUGAA-GAGGGUGGGCUAGGAGGAAGAGUGAAAGGAAAGGUCAA
ABRQ01340283.1/1022-955    UUGACCUUUUCU-AUUUUGAAAUCACUC-AAA-GAGGGUGGGCUAGGAGGAAGAGUGAAAGAAAAGGUCAA
ABRR01331034.1/1820-1753   UUGGCCUUUUCU-AUUUUUAAAUCACUC-ACA-GAGGGUGGGAUAGGAGGAAGAGUGAAAGAAAAGGUCAA
ABRO01250281.1/7546-7481   UUGACCUUUUCC-AUUUUUAUU-CACUC-ACA-GAGGGUGGGCCAGGAGGA-GAGUGAAGGAAAAGGUUAA
ABDC01374820.1/328-261     UUGACCUUUUCC-AUUUUUAAAUCACUC-ACA-GAGGGUGGGACAGGAGGAAGAGUGAAGGAAAAGGUCAA
AAKN02029936.1/20607-20674 UUGAUCUUUUCU-AUUUUGCAAUCACUC-ACA-GAGGGUGGGGCAGGAGGAAGAGUGAAGGAAAAGGUCAA
AAPY01379537.1/6535-6468   UUGACCUUUUCU-AUUUUAAAAUCACUC-AUA-GAGGGUGGGACAGGAGGAAGAGUGAAAGAAAAGGUCAA
AJ421481.1/150048-150115   UUGGCCUUUUCU-CUUUUUAAAUCACUC-ACA-GAGGGUGGGAUAGGAGGAAGAGUGAAAGAAAAGGUCAA
ABRN01368090.1/1053-985    UUGGCCUUUUCUAUUUUUUAAAUCACUC-ACA-GAGGGUGGGAUAGGAGGAAGAGUGAAAGAAAAGGUCAA
U41394.1/12649-12716       UUGACCCUUUCC-AUUUUUCUUUCACUC-ACA-GAGGGUGGGACAGGAGGCCGAGUGAAGGAAAGGGUCCA
ACFV01154005.1/363-296     UUGACCUUUUCC-AUUUUUAAAUCACUC-ACA-GAGGGUGGGACAGGAGGAAGAGUGAAGGAAAAGGUCAA
AAGW02057584.1/21932-21866 UUGACCUUUUCU-AUUUUUAAAUCACUC-ACA-GAGGGUGGGACAGGAGGGAGAGUGAAGGAAA-GGUCAA
AAGU03047922.1/27926-27993 UUGACCUUUUCU-AUUUUUAAAUCACUC-AAA-GAGGGUGGGCUAGGAGGAUGAGUGAAAGAAAAGGUCAA
#=GC SS_cons               <<<<<<<<<<<<.---------<<<<<<.___.___________________>>>>>>->>>>>>>>>>>>
#=GC RF                    UUGaCCuUUUCc.AUUUUUAAAUCACUC.AcA.GAGGGUGGGauAGGAGGAaGAGUGAAgGAAAaGGuCAA
//
# STOCKHOLM 1.0

#=GF AC   RF02267
#=GF ID   Vax2os1_2
#=GF DE   Vax2os1 conserved region 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   55.00
#=GF TC   57.60
#=GF NC   49.30
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 13.33 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0051726; regulation of cell cycle;
#=GF RN   [1]
#=GF RM   22128341
#=GF RT   The long noncoding RNA Vax2os1 controls the cell cycle progression of
#=GF RT   photoreceptor progenitors in the mouse retina.
#=GF RA   Meola N, Pizzo M, Alfano G, Surace EM, Banfi S
#=GF RL   RNA. 2012;18:111-123.
#=GF WK   Vax2os1
#=GF SQ   3


AC090647.6/93356-92891     CUUCCUGCAGAUCGCUCGAGCCAGCCUUUGCCAGGGACCUUGACCUAGCACGGACUUGGUCGCCACGCUUAGCUCCCCCUGACCUGCUUUUGAACCCGCUAAUCCACCCCAACUCUUGCCCCGACGUUCACUCCACGCGCUAAUUCCCGGGGGCCCCACAGCCCCCACACUCCCUCUCGGCCCGAGGCUCUGAAGGGCACAACCAGGGCUCCACACUGAAGCAA-UGGCCUCAGCUACAAAUAUCCCUCUCCUUGGUUCCCCUUAAUUUAAUUCGUUUUCUUUUUUUCAAAACAAUAACCAUACAAAUACCAAUCUUCCGGAACGGAAACGAAUCUGACACACUGGUGGUCUGGCAAAGCAGUGGUCACAGUGGCUGGCCAGGGACGAGAGCCGAGAGCCGGGGAAGGGUAAGCCAGAAUCUAGUGUCCUGCCAAAGCC-AGAGAGGCUGGAAGAACCGCAGACACAA
AY589788.1/699-237         CUUCCUGCAGAUCGCUCGAGCCAGCCUUUGCCAGGGACCUUGACCUAGCACGGACUUGGUCGCCACGCUUAGCUCCCCCUGACCUGCUUUUGAACCCGCUAAUCCACCCCAACUCUUGCCCCGACGUUCACUCCACGCGCUAAUUCCCGGGGGCCCCACAGCCCCCACACUCCCUCUCGGCCCGAGGCUCUGAAGGGCACAACCAGGGCUCCACACUGAAGCAA-UGGCCUCAGCUACAAAUAUCCCUCUCCUUGGUUCCCCU---UUUAAUUCGUUUUCUUUUUUUCAAAACAAUAACCAUACAAAUACCAAUCUUCCGGAACGGAAACGAAUCUGACACACUGGUGGUCUGGCAAAGCAGUGGUCACAGUGGCUGGCCAGGGACGAGAGCCGAGAGCCGGGGAAGGGUAAGCCAGAAUCUAGUGUCCUGCCAAAGCC-AGAGAGGCUGGAAGAACCGCAGACACAA
AABR05115646.1/15114-15570 CUCCCUGCAGAUCGCCCGAGCCAGCCUUUGCCAAGGACCUUGACCUAGCAUGGACUUGGUCGCCACGCUUAGCUCCCCCUGACCUGCUUUUGAACCCGCUAAUCCACCCCAACUCUUGCCCCAACGUUCACUCCACGCGCUAAUUCCCGCUGGCCCCACAGCCCCCAC--UCCCUCUCGGCCCGAGGCUCUGAAGGGCACCACCGGGGCUCCGAACUGAAGCAAAUGGCCUCAGCUACAAACAUCCCUCUCCUUGGCUGCCCUUAAUUUAAUUCGUUU--UUUUUUUCAAAAUAAUAACCAGACGAAUAUCAAUCUUCUGGAACGGAGACGAACCUAGCAAACUGGUGGUCCGGUAAAGAAGUGGCCACCUUGGCUGACCAGCGACCAGGGCC-------UGGGAAGGAAAAGCCAGAAUCUGGUGCCCUGCAAGAGCGGAAAAAGGCCGGAAGAACCGCAGACACAA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::
#=GC RF                    CUuCCUGCAGAUCGCuCGAGCCAGCCUUUGCCAgGGACCUUGACCUAGCAcGGACUUGGUCGCCACGCUUAGCUCCCCCUGACCUGCUUUUGAACCCGCUAAUCCACCCCAACUCUUGCCCCgACGUUCACUCCACGCGCUAAUUCCCGggGGCCCCACAGCCCCCACAcUCCCUCUCGGCCCGAGGCUCUGAAGGGCACaACCaGGGCUCCacACUGAAGCAA.UGGCCUCAGCUACAAAuAUCCCUCUCCUUGGuUcCCCUUAAUUUAAUUCGUUUucUUUUUUUCAAAAcAAUAACCAuACaAAUAcCAAUCUUCcGGAACGGAaACGAAuCUgaCAcACUGGUGGUCuGGcAAAGcAGUGGuCACagUGGCUGgCCAGgGACgAGaGCCGAGAGccgGGGAAGGguAAGCCAGAAUCUaGUGuCCUGCcAaAGCc.AgAgAGGCuGGAAGAACCGCAGACACAA
//
# STOCKHOLM 1.0

#=GF AC   RF02268
#=GF ID   MtlS
#=GF DE   MtlS RNA
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   PMID 22101846
#=GF SS   Predicted; WAR; Burge SW
#=GF GA   80.00
#=GF TC   91.60
#=GF NC   52.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.34 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0015797; mannitol transport;
#=GF RN   [1]
#=GF RM   22101846
#=GF RT   The Vibrio cholerae mannitol transporter is regulated
#=GF RT   post-transcriptionally by the MtlS small RNA.
#=GF RA   Mustachio LM, Aksit S, Mistry RH, Scheffler R, Yamada A, Liu JM
#=GF RL   Journal of Bacteriology. 2012;194:1-12.
#=GF RN   [2]
#=GF RM   25826566
#=GF RT   A cis-regulatory antisense RNA represses translation in Vibrio cholerae
#=GF RT   through extensive complementarity and proximity to the target locus.
#=GF RA   Chang H, Replogle JM, Vather N, Tsao-Wu M, Mistry R, Liu JM
#=GF RL   RNA Biol. 2015;12:136-148.
#=GF WK   MtlS_RNA
#=GF SQ   6


FM178379.1/3046315-3046195   UUCCCCGUUUGAGGUUUUUAUU---AAA--CUGU--C-UAA-AAAUGACUCGCCAA-AGUCAU-UGGUUAAUUUCUAAGUACAGACAUAAUUUACC-AUAGAUUUUUUAAUUGAACCGAUAACGGGAAAUUCG
CR378676.1/60481-60604       UUCCCCGUUUGAUGUU-CUAUUUUUAUA--UUUUGUUGUAAGUAACGGUUCGCCAA-AACCG-----UCGAUUGCUUAGUACCCAAUUAAUUUACCAUAGAUAUUUAAAUUAGAACUGAUAACGGGUUUUUUG
AE003853.1/994876-994755     UCCCCCGUUGGAUGUU-CCGUU--UGAA--UUUAAUCGUAG-UAACGGUUCGGCAAAAACCG-----UUGAUUGCUUAGUACACAAUCACUCUACCACACAAAUUUCGAAUGGAAUCACCAACGGGUUUUUUG
CP002469.1/2842639-2842522   UUCCCCGUUUGAUGUU-CUGAU---GAA--UGUUGUAGUA----ACGGUUCGCCAA-AACCG----UUUGAUUGCUUAGUUCUCAAUCAAUCUACCACAUAUUUUUCUAUUAGAACUGAUAGCGGGUUUUUCG
ACCV01000146.1/2554-2435     UUCCCCGUUCGAUGUU-CUGAU---GAA--UAUUGUAGUAG--UACGGUUCGCCAA-AACCG----CUUGAUUGCUUAGUUCUCAAUCAAUUUACCACACAAAUUCAUUCUGGAACUGACGACGGGUUUUUUG
ACFO01000016.1/355731-355855 UUCCCCGUUCGAUGUU-CUGAU---GAAUAUGUUGUCGUAA---ACGGUUCGCCAA-AACCGCUUGUUUGAUUGCUUAGUACCCAAUCAAUUUACCACACAUUUUCCAAUUGGAACUGACGACGGGUUUUUCG
#=GC SS_cons                 :::((((((----(((.(((((...(((..(((-((-((((.,,,<<<<<______.>>>>>....,<<<<<<<_________>>>>>>>,))))-)))))--)))--))))))))----)))))):::::::
#=GC RF                      UUCCCCGuuuGAuGuu.ccagu...gaa..uguugucGuag.uaAcGGuuCGcCAA.aaCCg....uuugauugCUuAGUaCacaaucaaUcuaCCacacaauuucuuacuggaaCuGAuaaCGGGuuuUUuG
//
# STOCKHOLM 1.0

#=GF AC   RF02269
#=GF ID   HPnc0580
#=GF DE   Heliobacter pylori small RNA HPnc0580
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Predicted; MAFFT
#=GF SS   Predicted; RNAalifold
#=GF GA   37.00
#=GF TC   37.90
#=GF NC   36.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20164839
#=GF RT   The primary transcriptome of the major human pathogen Helicobacter pylori.
#=GF RA   Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A,
#=GF RA   Chabas S, Reiche K, Hackermuller J, Reinhardt R, Stadler PF, Vogel J
#=GF RL   Nature. 2010;464:250-255.
#=GF WK   Bacterial_small_RNA
#=GF SQ   7


AAUQ01092265.1/347-449     UUGAUUUUGUA---ACGGUAGGAACUAUCGAAAGUUACGCC--UGUCAGAUAUGAUAAGUGAAACCCUGCGAGGAUAAGAAGUUGGAGUUCGAACUCUGUAAAAUCCU
ABSX01000011.1/4251-4147   AUACAUUUGUAUCUAGCACAGGAAGUGUGCAAAGUUACGCCUUUAUAAGAUAUGAUGUGUGAGACC---UGUAGGGAAUGCGUUGGAGCUCAAACUCUGUAAAAUCCC
CP001072.2/1532260-1532156 AUGCAUUUGCAUCUAGUGCAGGAAGUGCACAAAGUUACGCCUUUAUAAGAUAUGAUGUGUGAGACC---UGUAGGGAAUGCGUUGGAGAUCAAACUCUGUAAAAUCCC
AF315502.1/434-537         AUACAUUUGUAUCUAGCGUAGGAAGUACGCAAAGUUACGCCUUUG-GAGAUAUGAUGUGUGAGACC---UGUAGGGAAUGCGUUGGAGAUCAAACUCUGUAAAAUCCC
AE001439.1/1191504-1191607 AUACAUUCGUAUCUAGUGCAGGAAGUGCGCAAAGUUACGCCUUUG-GAGAUAUGAUGUGUGAGACC---UAUAGGGAAUGCGUUGGAGCUCAAACUCUGUAAAAUCCC
CP001173.1/934778-934881   AUACAUUUGCAUCUAGCGUAGGAAGCACGCAAAGUUACGCCUUUAU-AGAUAUGAUGCGUGAGAGC---UGUAAGGAAUGCGUUGGAGCUCAAACUCUGUAAAAUCCA
AE000511.1/968980-969084   AUACAUUUGCAUCUAGCGUAGGAAGUGCGCAAAGUUACGCCUUUAU-AGAUAUGAUGCGUGAGAGC--UUGUAAGGAAUGCGUUGGAUUUCAAACUUUGUAAAAUCCA
#=GC SS_cons               :::::::::::::::<<<<<_____>>>>>,,,<<<-<<<---<<<<<____>>>>>->>>->>>-...---------------<<<<______>>>>::::::::::
#=GC RF                    AUacAUUUGuAUCUAgcgcaGGAAgugcgcAAAguuACgCCUUuaucaGAUAugauguGuGAgacC...UGuAgggAAugcGUUgGaGuUCAAACuCuGUAAAAUCCu
//
# STOCKHOLM 1.0

#=GF AC   RF02270
#=GF ID   nse_sRNA
#=GF DE   Neisseria sigma-E sRNA
#=GF AU   Gardner PP; 0000-0002-7808-1213
#=GF SE   Gardner PP
#=GF SS   Published; PMID:22194974; Gardner PP
#=GF GA   75.00
#=GF TC   79.30
#=GF NC   39.50
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22194974
#=GF RT   Deep Sequencing Whole Transcriptome Exploration of the sigma Regulon in
#=GF RT   Neisseria meningitidis.
#=GF RA   Huis In 't Veld RA, Willemsen AM, van Kampen AH, Bradley EJ, Baas F,
#=GF RA   Pannekoek Y, van der Ende A
#=GF RL   PLoS One. 2011;6:e29002.
#=GF WK   Neisseria_sigma-E_sRNA
#=GF SQ   7


AE002098.2/1919694-1919766 ACUAGUUUGAUAGUCCUUUA----UAUCUAUCAAUACUCCUUGGGAAGCCUCCGCCA---UACGGCAGGAGGCAUUUUUU
CP000381.1/409892-409820   ACUAGUUUGAUAGUCCUUUA----UAUCUAUCAAUACUCCUUGGGAAGCCUCCGCCA---CACGGCAGGAGGCAUUUUUU
AL157959.1/618027-617955   ACUAGUUUGAUAGUCCUUUA----UAUCUAUCAAUACUCCUUGGGAAGCCUCCACCA---CACGGUAGGAGGCAUUUUUU
CP001050.1/87346-87274     ACUAUUUUGAUAGUCCUUUA----UAUCUAUCAAUACUCCUUGGGAAGCCUCCGCCA---CACGGCAGGAGGCAUUUUUU
ACKO02000013.1/29625-29703 ACUAGUUUCAUAGUUCUUUAGGG-UUACUUUUAAAACUCCUUGGAUAGCCUCCGCCAGCUCCCGGCAGGAGGCGUUUUUU
ACDY02000005.1/74847-74919 ACUAGUUUGGUAGUACUUUA----UAUCUAUCAAUACUUCUUGGGAAGCCUCCGCCA---UACGGCAGGAGGCAUUUUUU
ACDX02000003.1/73835-73756 ACUAGUUUCAUAGUUCUUUAGGGUUAUUUUUUAAAACUCCUUGGAUAGCCUCCGCCAGCUCCCGGCAGGAGGCGUUUUUU
#=GC SS_cons               :::<<<<<<<<<<_______....___>>>>>>>->>>---------<<<<<<<<<_...___>>>->>>>>>:::::::
#=GC RF                    ACUAGUUUgauAGUuCUUUA....UAUCUaucAAuACUCCUUGGgaAGCCUCCGCCA...caCGGCAGGAGGCaUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02271
#=GF ID   uc_338
#=GF DE   TUC338
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Predicted; WAR; Burge SW
#=GF GA   120.00
#=GF TC   120.00
#=GF NC   119.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 20.50 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; noncoding RNA;
#=GF RN   [1]
#=GF RM   21187392
#=GF RT   Expression and functional role of a transcribed noncoding RNA with an
#=GF RT   ultraconserved element in hepatocellular carcinoma.
#=GF RA   Braconi C, Valeri N, Kogure T, Gasparini P, Huang N, Nuovo GJ, Terracciano
#=GF RA   L, Croce CM, Patel T
#=GF RL   Proc Natl Acad Sci U S A. 2011;108:786-791.
#=GF WK   TUC338
#=GF SQ   34


AC023509.42/158050-157869  UUGACAGCCCUGGAGACUGAAAUCCUCUA-UUUAUCCACAGGA----CAGGUAC---AGCACA-G-G-CAGCGACAGUGCGAGCUUUCCCCACACCACCCCGUCCA--U---GUGCCUCAA-CCCU-GACCUGGAGGGA-----CCACCUCUAG-A-G-GUGAGAGG-GG-AUG-----UUCAGUCUC--CAAGGCUCACUCA-AUCCUUCCGCCUCA
AACN010300665.1/189-3      UUGACAGCCCUGGAGACUGAAGUCCUCUA-UUUAUCCACAGAG----CAGACACUGCAGCACG-G-G-CAGCGGCAGUGCCAGCUUCGCCCACACUGCCCCUCCGC--CAGCGGGCGUCAA-CCCC-GACUUGGAGGAG-----CCACCUCUAA-A-G-GUGAGAGG-GG-UAG----GUUCAGUCUC--CA-UGCCCAUUCA-AUCCUCG-GCUUCU
ABQF01071627.1/1039-1214   UUGACAGCCCUGGAGACUGAAUCCCUGUG-UUUAUCCACAGAG----CAGACAG---AGCGCG-G-G-CAGUGGCAG------CUUCCCCCACGCUGCCUCCUCCC--U---GUGCCUGGG-CGCU-GAGUCGGAGGAA-----GCACCUCUAA-A-G-GUGAGCGG-GG-UCG-----UUCAGUCUC--CACUGCCCAUUCA-AUCCUCCCGCCAGC
AAFR03049215.1/8557-8375   UUGACAGCCCUGGAGACUGAAGUCCUCUA-UUUAUCCACAGAG----CAGACAC---AGCACG-G-G-CAGCGGCAGUGCAAGCUUCGCCCACACUGCCCCUCCGC--CAAUGUGCCUCAA-CCCU-GACUUGGAGGAA-----CCACCUCUAA-A-G-GUGAGAGG-GG-UAG-----UUCAGUCUC--CA-UGCCCAUUCA-AUCCUUG-GCUUCU
AAHX01053601.1/30667-30481 UUGACAGCCCUGGAGACUGAAGUCCUGUA-UUUAUCCACAGAG----CAGACACUGCAGCACG-G-G-CAGCGGCAGUGCCAGCUUCGCCCACACUGCCCCUCCGC--CAGCGGGCGUCAA-CCCC-GACUUGGAGGAG-----CCACCUCUAA-A-G-GUGAGAGG-GG-UAG-----UUCAGUCUC--CA-CGCCCACUCA-ACUCAGCUUCUUGC
AAPY01797385.1/601-417     UUGCCAGCCC-GGAGACUGAAGUCCUCUA-UUUAUCCACAGAG----CAGACACUGCAGCACG-G-G-CAGCGGCAGUGCCAGCUUGGCCCACACUGCCCCUCCGC--CGGCGGGCGUCAA-CCCC-GACCUGGAGGAG-----CCACCUCUAA-A-G-GUGAGCGG-GG-UAG-----UUCAGUCUC--CA-CGCCCAUUCA-GUCCUCG-GCGUCG
ABRO01334200.1/2222-2037   UUGACCGCCCUGGAGACUGAAGUCCUGUA-UUUAUCCACAGAG----CAGACACUGCGGCGCG-G-G-CAGCGGCAGUGCCAGCUUCGCCCACUCUGCCCCUCCGC--CAGCGGGCGUCCC-CCCC-GACAUGGAGGAG-----CCGCCGCUAA-A-G-GUGAGAGG-GG-UAG-----UUCAGUCUC--CA-CGCCCGCUCA-AUCCUCG-GCUCCU
AC151571.1/101252-101072   UUGAUAGCACCAGAGACUGAAGUCCUCUA-UUUAUCCACAGGA----CAGGUAC---AGCACGGG-G-CAGCAGCAGUGCAGGCUUC-CCCACAUUG--UCCUGCCAAU---GUGCCUCAA-CCCU-GCCCUGGAGGGA-----UCACCUCUAG-AGG-GUGAAAGG-GG-UAG-----UUCAGUCUC--CA-UGCCCAUUCG-AUCCUUG-GCCUCU
AAPN01300052.1/16976-16797 UUGACAGCCCUGGAGACUGAAGUCCUCUA-UUUAUCCACAGAA----CAGGUGC---AGCACG-G-G-CAGCAGCAGUGCAAGCUUUCCCC-UACCGCCCCACCAA--U---GUGCCUCAG-UUCU-GUUCUGGAGGGU-----CCACCUCUAA-A-G-GUGAGAG--GG-UAG-----CUCAGUCUCUUCA-CGUCCAGUAA-AUCCUUG-GUUUCU
ABQO010093652.1/2720-2893  UUGAA-GGCCUGGAGACUGAAGUCCUCUC-UCUAUCCACAGAA----CAGGUAC---GGCACA-G-A-CAGCGGCAGUGCAAGCUUUUCC---ACUGUCCCAUUAU--U---GUGCCUCAG-CCCU-GGCCUGGAGGGA-----CCAUGGUUAG-G-G---GGAAGA-GGGUUG-----UUCAGUCUC--CACGCCCU--UCA-AUCCUUG-GCUGCU
ABGA01257126.1/24212-24041 UUGAA-GGCGUGGAGACUGAAGUCCUCUC-UAUAUCCACAGAA----CAGGUAU---GGCACA-G-G-CAGCGGCAGUGCAACUUUUCC----ACUGUCCCACCAA--U---GUGCCUCAG-UCCU-AGCCUAGGGGGA-----ACACGUUUAG---G-AUAAGAG--GG-CUG-----UUCAGUCUC--CAUGCCCU--UCA-AUCCUUG-GCUACU
AAGV020151289.1/933-1105   UUGAA-GGCGUGGAGACUGAAGUCCUCUC-UAUAUCCACAGAA----CAGGUAU---GGCACA-G-G-CAGCGGCAGUGCAG-CUUUUUCC--ACUGUCCCACCAA--U---GUGCCUCAG-UCCU-GGAUUAGGGGGA-----AUAUAUUUAG---G-GUAAGAG--GG-CUA-----UUCAGUCUC--CAUGCCCU--UCA-GUCCUUG-GCUACU
ABRQ01128951.1/8604-8774   UUGAA-GGCGUGGAGACUGAAGUCCUCUC-UAUAUCCACAGAA----CAGGUAU---GGCACA-G-G-CAGCGGCAGUGCAG-CUUUUC---CACUGUCCCACCAA--U---GUGCCUCAA-UCCU-AGCUAGGGG-GA-----AUG-CGUUUA-G-G-GUAAGAG--GG-UUA-----UUCAGUCUC--CAAGACCU--UCA-AUCCCUG-GCUACU
ABRN01432335.1/8795-8965   UUGAA-GGCGUGGAGACUGAAGUCCUCUC-UAUAUCCACAGAA----CAGGUAU---GGCACA-G-G-CAGCGGCAGUGCAG-CUUUUC---CGCUGUCCCACCAA--U---GUGCCUCAG-UCCU-AGCCAAGAGGGA-----CCA--UGUUG-A-G-G-GUAAGA-GG-GCU-----AUCAGUCUC--CAUGCCCU--UCA-AUCUUUG-GCUACU
AANU01287879.1/12756-12924 UUGAA-GGCGUGGAGACUGAAGUCCUCUC-UAUAUCCACAGAA----CAGGUAU---GGCACA-G-G-CAGAGGCAGUGCAG-CUUUUC---CACUGUCCCACCAA--U---GUGCCUCAG-UCCU-AUAAGG---GGA-----ACACG--UUU-A-G-G-AUAAGAUGG-CUG-----UUCAGUCUC--CAUGCCCU--UCA-AUUCUUG-GCUACU
ABDC01218542.1/1907-2091   UAGACGGCCAAG-AGACUGAAGUCCUCCA-UUUUUUCACAGAA----CAGGUAG---AACAUG-G-A-CAACAGCAAUUCAAGUUUUCCCCACACUGCCCUGCCAA--U---GUGCCUCGA-UCCU-GACCUGGGGGGG-----CCACCUCUGG-G-GUGAGAGGGU-GG-CUCAUUCAUUCAGUC----CUUGGC-CAUUCUUCUGAAACAGCCAAC
AANN01373355.1/6047-6217   UUGAA-GGCGUGGAGACUGAAGUCUUCUG---UAUCCACAGAA----CAGGUAC---GGCACA-U-G-CAGCGGCAGUGCAG-CUUUUC---CACUGUCCCACCAA--U---GUGCCUCAGGUCCU-ACCUUAAGGAGA-----CCAUG-UUGA-G-G-GUA--AGA-AG-GCU----GUUCAGUCUC--CAUGCCCU--UCA-AUCUUUG-GCUACA
AAQQ01557671.1/2283-2451   UUGAA-GGCGUGGAGACUGAAGUCCUCUA---UAUCCACAGAA----CAGGUAU---GGCACA-G-G-CAGCGGCAGUGCAG-CUUUUC---CACUGUCUCACCAA--U---GUGCCUCAG-UCCUAGCC-UAGG-GGU-----ACAUGUUUA--G-G-GUAAUAGA-G--CUG-----UUCAGUCUC--CAUGCCCU--UCA-AUCCUUG-GCUACU
AAFC03081541.1/46490-46320 UUGAA-GGCGUGGAGACUGAAGUCCUCUC-UCUAUCCACAGAU----CAGGUGU---GGCACA-G-G-CCGCGGCAGUGCA-GCUU--CCCACUGUGCC-CCGCCC--C---GUGCCUCAG-UCCU-GGCUGAGAGGGG-----CCAUGU-UGA-G-G-GUA--AGA-GG-GCU-----GUCAGUCUC--CAUGCCCU--UCA-AUCUUUG-GCUACU
AAIY01226831.1/1978-2148   UUGAA-GGCGUGGAGACUGAAGUCCUCUC-UAUAUCCACAGAA----CAGGUAU---GGCACA-G-G-CAGCGGCAGUGCA-GCUUGUC---CACUGUC-CCACCA--U---GUGCCUCAG-UCCUCGUCUAGAGGGAA-----CGUGC--UUA-G-G-GUAAGAG--GG-UUA-----UUCGGUCUC--CAUGUUCU--UCA-AUCUGUG-ACUUCU
AAWR02013730.1/56615-56785 UUGAA-GGUGUGGAGACUAGAGUCCCUUC-UAUAUCCACAG-A----CAGGUAC---GGCACA-G-G-CAGCGGCAGUGCAG-CUUUUC---CACUGUCCCACCAG--U---GUGCCUCAG-UCCU-AGCCUAGGAGGA-----CCACGGUGAG---G-GUA-AGAG-AG-CUG-----UUCAGUCUC--CAUGCCCU--UCG-AUCUUUU-AAUACU
AAWZ02008214.1/16496-16669 UUGACAGCCCUGGAGACUGAAGUCCUCUA-UUUAUCCACAGGA----CAGGUAC---AGC---------AGCGGCAGUGCAAGCUACCCCCACACCGCCCCAUCAA--U---GUGCCUCAA-CUCU-GACCUGGAGGGA-----CCACCUCAAG-A-G-GUGAGAGG-GG--AG-----UUCAGUCUC--CAUGGCCCAUUCA-AUCCUUG-GCCUCU
ADDD01071070.1/4869-5046   UUGACGGCUGUGGAGACUGAAGCCCUCUU-UUUAUCCACAGAA----CAGGUAC---AGCACA-G-G-CAGCGGGAGUGCAAGCUUCCCCCAGACUGCCCCACCAA--U---GUGCCUCAA-CCCU-GACCUGAAGGGA-----CCACUUCUAG-G-G-AUGAGAGG-GG-A-------UUCAGUCUC--CA-UGCUCAUUCA-AUUCUUG-GCCUCU
AAGW02061958.1/92760-92935 UUGAA-GGUGUGGAGACUGAAGUCCUGUC-UAUAUCCACAGAA----CAGGUAU---GGCACA-G-G-CCGCGGCAGUGCAG-CUUUUC---CACUGUCCCACCAA--U---GUGCCUCUG--UCU-GAGUUAGCCUAAGGGGAACAUGGCUAG---G-GUAAGA-G-GG-CUG-----UUCAGUCUC--CACACCCU--UCA-AUCUUUG-GCUGCU
AAGU03016019.1/10793-10622 UUGAA-GGCGUGGAGACUGAAGUCCUCUC-UAUAUCCACAGAA----CAGGUAC---GGCACA-G-G-CAGCGGCAGUGCAG-CUUUUC---CACUGUCCCACCAA--U---GUGCCUCAG-UCCU-AGCCUAGGGGGA-----ACGCAUUUAG-A-G----UAAGA-GG-GUU----AUUCAGUCUC--CAAGCCCU--UCA-AUCCAUG-GCUACU
AAQR03012484.1/16090-16261 UUGAA-GGCGUGGAGACUGAAGUCCUCUC-UGUAUCCACAGAA----CAGGUAC---GGCACA-G-G-CAGCGGCAGUGCAG-CUUUUC---CACUGUCCCACCAA--U---GUGCCUCAG-UCCU-AGCCUCUGGGGA-----ACAUGUUUAG-G-G-CUA--AGA-GG-GCU-----AUCAGUCUC--CAUGCCCU--UCA-AUCCUUG-GCUACU
FJ497007.1/301275-301095   UUGAUAGCACCAGAGACUGAAGUCCUCUA-UUUAUCCACAGGA----CAGGUAC---AGCACG-GGG-CAGCAGCAGUGCAGGCUUC-CCCACAUUGUCCUGCCAA--U---GUGCCUCAA-CCCU-GCCCUGGAGGGA-----UCACCUCUAG-AGG-GUGAAAGG-GG-UAG-----UUCAGUCUC--CAUGCCCA-UUCG-AUCCUUG-GCCUCU
EU284132.1/105967-106146   UUGAUAGCACCAGAGACUGAAGUCCUCUA-UUUAUCCACAGGA----CAGGUAC---AGCAUG-G-G-CAGCAGCAGUGCAGGCCUC-CCCACAUUGCUCUGCCAA--U---GUGCCUCAA-CCCU-GCCCUGGAGAGG-----CCACCUCUAC-AGG-GUGAGAGG-GG-UAG-----UUCAGUCUC--CAUGCCCA-UUCA-GUCCUUG-GCCUCU
AC192206.3/92386-92557     UUGAA-GGCGUGGAGACUGAAGUCCUCUG-UAUAUCCACAGAA----CAGGUAU---GGCACA-G-G-CAGCGGCAGUGUAG-CUUUUC---CACUGUCCCACCAA--U---GUGCCUCAG-UCCU-AGCCUAGGGGGA-----ACACGUUUAG---G-AUAAGAG--GG-CUG-----UUCAGUCUC--CAUGCCCU--UCA-AUCCUUG-GCUACU
FJ497006.1/250071-249892   UUGAUAGCCACAGAGACUGAGGUCCUCUA-UUUAUCCACAGAA----CAGGCAU---GGCAUG-G-G-CAGCAGCAGUGCAGACU-CCCCCACAUUGCCCCAGCAA--U---GUGCCUCAA-CCCU-GCUCUGGAGGGA----AUCUCUUCUGG-A-G-A-GUGAGA-AG-CUA----AUUCAGUCUC--UAAGACCA-UUCA-AUCCUUG-GCCUCU
FJ497007.1/290543-290363   UUGAUAGCACCAGAGACUAAAGUCCUCUA-UUUAUUCACAGGA----CAGGUAC---AGCACG-G-GACAGUGGCAGUGCAGGCUUCUC-CACACUGCCCUGUCAA--U---GUGCCUCAA-UCCU-GCCCUGGAGGGA-----CCACCACUAU-AGG-GUGAGAGG-GA-UAG-----UUCAGUCUC--CAUACUCA-UUCA-AUCCUUG-GCCUCU
EU284132.1/44642-44460     UUGAUAACAUAAGAGACUGAAGUCCUUUA-UUUAUCCACAAGACAGACAGAUAC---AGCAUG-G-G-CAGUGGCAGUUCAGGCU-CCCCCACACUGUCGCACCAA--U---GUGCCUCAA-CUCU-GCCCUGGAGGGA-----CCACCUCUAC-A-GCGUGAGAG--GG-UAG-----UUCAGUCUC--CAUGC-CCAUUCA-GUCCUUG-GCCUCU
FJ497005.1/245864-245687   UUGAUAGCACCAGAGACUGAAGUUCUCUA-UUUAUCCACAGAA----CAAGUAC---AACAUG-G-A-CAGUGAUAGUGCAGGCU-CCCCCACAUUGUCC-UACAA--U---AUGCCUCAA-CUUU-GCUCUGGAGGGA-----CCAUUUCUAGAA-G-GUGA-AGU-AA-UGG-----UUCAGUCUC--UAUCCCCA-CUCC-AUCCUUG-GUCUAU
FJ497008.1/237427-237247   UUGAUAGCACCAGAGACUGAAGUCCUCUAUUUUAUCCACAUGA----CAGGUAC---AGUAUA-G-G-CAGUGGCAGUACAGGCUUC-CCCACACUGCCCUGCCAA--U---GUGCCUCAA-CCCU-GCCCUGGAGGGA-----CCACCUCUAC-AGG-GUGAGAGG-GG-UAG-----UUCAGUCUC--CAUGCCCA-UUCA-AUCCUUG-GCCUCU
#=GC SS_cons               :(((--((--(((((((((((--(((((-.((((((,,<<<-<....-----<-...-<<<<<.<.-.----<<<<<_________________>>>>>------>..>...>>>>->---.>->>.>,,<<<<<<<__.....___>>>>>>>.,.).)))))))).)).---.....)))))))))..))--))--.-))).:::::::.::::::
#=GC RF                    UuGAaaGcccuGGAGACUGAaGUCCcCua.uuuauCCACaGAg....CAGGUAc...aGCacg.g.G.CAGcGgCaGUGCAgGCUUuuCCCACACuGcCCCacCac..c...guGCCUCAa.ccCu.GaccuggaggGa.....cCAccuccag.a.G.gugagaGg.GG.uug.....uUCAGUCUC..CauggCCu.uUCa.AUCcUUg.GCuucU
//
# STOCKHOLM 1.0

#=GF AC   RF02272
#=GF ID   Vax2os1_3
#=GF DE   Vax2os1 conserved region 3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; MAFFT
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   57.20
#=GF NC   41.60
#=GF TP   Gene; lncRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.19 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001463; lincRNA;
#=GF DR   GO; 0051726; regulation of cell cycle;
#=GF RN   [1]
#=GF RM   22128341
#=GF RT   The long noncoding RNA Vax2os1 controls the cell cycle progression of
#=GF RT   photoreceptor progenitors in the mouse retina.
#=GF RA   Meola N, Pizzo M, Alfano G, Surace EM, Banfi S
#=GF RL   RNA. 2012;18:111-123.
#=GF WK   Vax2os1
#=GF SQ   5


AC090647.6/86135-85942   CUUUUCUGCCGGGUCGAGUCAGGGUCGCC-UCCUCGAGC-UCUGAGUUUUCCAUCAAGCGGAGCCAGACUGAAAGCUAGG--UGCAUUUCCCUGGAGAUAUAGGGAACAGAGGGAAGAG-GGCGAGAGGGACCAAUGG-----GUAGGGAGUAAUAAAGUUUAUGAG-AGGGUGUGGGGCGGUCUUCUGUACCACGGGGCUGUCC
AAHX01031257.1/5609-5415 GUUUUCUGCCGAGUCGAGCCGGGGUCGCCUUCCUCGAAC-UCUGGGUUAUCCAUCAGGCGGAGCUAGCCUGAAAGCUAGG--UGCAUUUCUCUGGGGACACAGGGAACAGAGAGAAGAGGGGCGAGAGGGAUCAAUAG-----AUGGGAGAUAAUAAAGUUUAUGAG-A-GGUAUGGGGCGGUCUUCUGUACGACGGGGCCGUCC
ABDC01264062.1/2177-2380 GUUCUCUGCUAGAUCUCUCCGGGAUCGCCUUCCUUGCGCACUUUGGUUAUUGAUCUUGCUGAACCGGCCUGAGCGCAGAGGCUGCGCUGCUCUGGGGACGAAGGGAGGGGGGAGAUGAGUAGGCUAGGGAAAUGGUGGUGGGAGGAGAGGUUAAUAAACUUUAGGAG-AGGGUGUAGGGCGUUCCUCAGUAGCCCAGAGCCGCCC
AAQQ01797201.1/3938-4136 GUUCUCUGCUCAAUCUCGCCUGGGUCGCCUUCCUCGCGCACUUUGGUUAUUGAUCCAGCUGAACCGGCGGGAGCGCGGA-ACUGCGCUUCCCUAGGGACGAAGAGAGUGGGGAGGGGAGUAGACUAAGGGGGUAGUGA-----GGGGAGGUUGAUAAACUUUAGGAGAAGGGUGUAGGGUGUUCCUCAGAACCCCAAGGCAGACC
AAFC03120959.1/6811-6616 GUUUUCUGCUCGGUCUCGCCGGGGUCGCCUUCCUGGAACACUUUGGUUAUUGAUUCCGCUGAAAGAGCCGGAGUGCGAAGACUGCGCUUCCCAGGGGACGAAGGGAGUGGGGAGGAGAGCAGGCUGGCGG--UUACGG-----GAGGGAGUUGAUAAACUUUAGGAG--GGAUGCAGGGCGUUCCUCGGUACCCUAGGGCCUCCU
#=GC SS_cons             ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.....::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::::::
#=GC RF                  gUUuUCUGCugggUCucgcCgGGGUCGCCUUCCUcGagCAcuUuGGUUaUugAUcaaGCuGAaccgGccuGAgaGCggaGaCUGCgcUuCcCuGGGGAcgaAGGGAgugGgGaGaaGAGuaGgcuggGGGauuaguGG.....GggGggGuUaAUAAAcUUUAgGAG.AGGGUGuaGGGcGuUCcUCuGuAccccaGGGCcGuCc
//
# STOCKHOLM 1.0

#=GF AC   RF02273
#=GF ID   FsrA
#=GF DE   FsrA
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Predicted; WAR; mafft_alifold
#=GF GA   80.00
#=GF TC   108.50
#=GF NC   39.90
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; non-coding RNA gene;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   22427629
#=GF RT   The FsrA sRNA and FbpB Protein Mediate the Iron-Dependent Induction of the
#=GF RT   Bacillus subtilis LutABC Iron-Sulfur-Containing Oxidases.
#=GF RA   Smaldone GT, Antelmann H, Gaballa A, Helmann JD
#=GF RL   J Bacteriol. 2012;194:2586-2593.
#=GF WK   FsrA
#=GF SQ   6


CP002906.1/1457980-1458063 AUAGAGAGAAGCUACUCUCUGUUCCCCAACCCCUCUAUCAGAUCAAGAUCCGAAAAAACUUGGCGCUACCCCCGCCAAGUUUUU
CP000002.3/1588759-1588841 AUAGAGAGAUGAACCUCUCUGUUCCCCAACCCCUCUAUCAGAUCAAGAUUUAAAAAA-CUUGGCGCUGCCCCCGCCAAGUUUUU
CP002207.1/939109-939191   AUAGAGAGAAGCUACUCUCUGUUCCCCAACCCCUCUAUCAGAUCAAGAUCCGAAAAA-CUUGGCGCUACCCCCGCCAAGUUUUU
CP000813.1/1367069-1367151 AUAGAGAGAAGCUACUCUCUGUUCCCCAACCCCUCUAUCAGAUCAAGAUCCAAAAAA-CUUGGCGCUACCCCCGCCAAGUUUUU
FN597644.1/1493166-1493249 AUAGAGAGAAGUUACUCUCUGUUCCCCAACCCCUCUAUCAGAUCAAGAUCCGAAAAAACUUGGCGCUACCCCCGCCAAGUUUUU
CP002183.1/1436090-1436173 AUAGAGAGAAGCUACUCUCUGUUCCCCAACCCCUCUAUCAGAUCAAGAUCCGAAAAAGCUUGGCGCUACCCCCGCCAAGUUUUU
#=GC SS_cons               <<<<<<<<______>>>>>>>>------------------------------<<<<<.<<<<<<<_______>>>>>>>>>>>>
#=GC RF                    auaGaGaGAAGcuACuCuCuguUCCCCAACCCCUCUAUCAGAUCAAGAUccgaaaaa.CuuGGCGCUACCCCCGCCaaGuuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02274
#=GF ID   AniS
#=GF DE   AniS
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Predicted; WAR; CMFinder
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   46.20
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; non-coding RNA gene;
#=GF RN   [1]
#=GF RM   21338417
#=GF RT   A novel Hfq-dependent sRNA that is under FNR control and is synthesized in
#=GF RT   oxygen limitation in Neisseria meningitidis.
#=GF RA   Fantappie L, Oriente F, Muzzi A, Serruto D, Scarlato V, Delany I
#=GF RL   Mol Microbiol. 2011;80:507-523.
#=GF WK   Non-coding_RNA
#=GF SQ   5


CP002419.1/1099947-1099843 AUGAAAUUCAGGGUGCUUGUUUGCUGUUUUCCAAUCUGUCU-GAUUUUAUCUCUUUCCUCUUGAUGUGUGUG--UGUUUGGGUGUGGCUGCCGCCACCCCUUUUUUUU
FN995097.1/1060951-1060846 AUGAAAUCUAGAUUGCUUGUUUGCUGUUUCCCAAUCUAUCUUGAUUUUAUCUCUUUCCUCUUGAUGUGUGUG--UGUUUGGGUGUGGCUGUCGCCACCCCUUUUUUUU
CP002440.1/804237-804130   AUGAAAUCUAGAUUGUUUGUUUGCUGUUUCCCAAUCCGUCUUGAUUUUACCUCUUUCCUCUUGAUGUGUGUGUGUGUUUGGGUGUGGCUGCCGCCACCCCUUUUUUUU
CP002420.1/1121117-1121222 AUGAAAUCUAGAUUGCUUGUUUGCUGUUUCCCAAUCUGUCUUGAUUUUACCUCUUUCCUCUUGAUGUGUGUG--UGUUUGGGUGUGGCUGCCGCCACCCCUUUUUUUU
CP001050.1/828351-828250   AUGAAAUCUAGAUUGUUUGUUUGCUGUUUCCCAAUCCGUCUUGAUUUUACCUCUUUCCUCUUGAUGUG------UGUUUGGGUGUGGCUGCCGCCACCCCUUUUUUUU
#=GC SS_cons               :<<<<<<<-<<<<---<<<____________>>>--->>>>->>>>>>>-----------------------..-----<<<-<<<<<____>>>>>>>>::::::::
#=GC RF                    AugaaaucuaGacUGuuuGUUUGCUGUUUcCCaaUCuguCuUgauuuuauCUCUUUCCUCUUGAUGUGUGUG..UGUUUGGGUGuGGCUGcCGCCaCCCCUUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02275
#=GF ID   Hammerhead_HH9
#=GF PI   Hammerhead_RECK
#=GF DE   Hammerhead ribozyme HH9
#=GF AU   de la Pena M
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Burge SW
#=GF SS   Published; PMID:20651741; Burge, SW
#=GF GA   52.00
#=GF TC   52.40
#=GF NC   51.90
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00010
#=GF DR   SO; 0000374; ribozyme;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   20651741
#=GF RT   Intronic hammerhead ribozymes are ultraconserved in the human genome.
#=GF RA   de la Pena M, Garcia-Robles I
#=GF RL   EMBO Rep. 2010;11:711-716.
#=GF WK   Hammerhead_ribozyme
#=GF SQ   33


ABQF01059171.1/305-384     UUGGGCCG-UUACCUACAGCUGAUGAGCUCCAAGAAGAGCGAAACCUGCU-AAGCAAGGUCCUGUAGUAUUGGCCUGAACCC---
AADN03003451.1/4511-4593   CUGGGCCG-UUACCUACAGCUGAUGAGCUCCAAGAAGAGCGAAACCUUGU-AAAAUAGGUCCUGUAGUAUUGGCCUGAUGAGCUC
AAWZ02032198.1/15823-15741 UGAGGCCG-UUACCUACAGCUGAUGAGCUCCAAAAAGAGCGAAACCUGUU-AAAAUAGGUCCUGUAGUAUUGGCCGACUGAGCCG
AGAI01055016.1/63287-63205 UUAGGCCG-UUACCUACAGCUGAUGAGCUCCAAGAAGAGCGAAACCUUUU-AAGAUAGGUCCUGUAGUAUUGGCCUGAAAACCAU
AANN01066007.1/588-511     CUGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--GCUAGGUCCUGCAGUACUGGCUUAAGAGGCUA
AAQR03161315.1/4048-3972   UUGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--AUUAGGUCCUGCAGUACUGGCUUAAGAGAAU-
ABRN01375670.1/21703-21777 UUGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--AUUAGGUCCUGCAGUACUGGCUUGAGAUA---
ABRP01270906.1/1966-2043   UUGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--AUUAGGUCCUGCAGUACUGGCUUAAGAUAAUA
ACTA01058962.1/24761-24837 AUGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--AUUAGGUCCUGCAGUACUGGCUUAAGAUAUA-
AAKN02030441.1/10428-10505 UUGGGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--ACUAGGUCCUGCAGUACUGGCUUAAGAUAAUG
AEYP01022184.1/5895-5972   GUGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--AUUAGGUCCUGCAGUACUGGCUUAAGAUGGAA
AFTD01093388.1/13316-13239 CUGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--GUUAGGUCCUGCAGUACUGGCUUAUGACAGUA
AAPN01231077.1/15198-15121 UCCUGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----A--ACCAGGUCCUGCAGUACUGGCGAAAGGAGCUU
AAGU03018532.1/57571-57497 UUGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----G--AAUAGGUCCUGCAGUACUGGCUUAAGACA---
AAFR03027197.1/99742-99816 UUAGGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----A--AUUAGGUCCUGCAGUACUGGCUUUAGCAU---
AAQQ01544543.1/2644-2721   UAGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----G--AUAAGGUCCUGCAGUACUGGCUUAAGACGGUA
ABRQ01056532.1/2019-2096   CUGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----G--AACAGGUCCUGCAGUACUGGCUUAAGAUAGUG
ADDD01012933.1/19585-19662 UUGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----A--GUUAGGUCCUGCAGUACUGGCUGAAAUCUUUC
AAWR02025218.1/31065-31139 CCGAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----G--GUUAGGUCCUGCAGUACUGGCUUAAGAUA---
AEKR01154328.1/10424-10501 UCUGGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--GUUGGGUCCUGCAGUACUGGCUUACCAUAGUA
AALT01643156.1/444-367     UCCAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--ACGAGGUCCUGCAGUACGGGCUUAGGGGAGCA
AFYH01089550.1/2099-2023   -CAAGCAAGUUACCUACAGCUGAUGAGCUCCAAGAAGAGCGAAACC----U--UAUAGGUCCUGUAGUACUGGCUUGUUACCAU-
AAIY01498693.1/2014-1937   CCGAGCCG-UUGCCUGCAGCUGAUGAGCUCCAACAAGAGCGAAACC----G--AACAGGUCCUGCAGUACGGGUGGGGUCAGCAG
AADN03002802.1/91438-91372 --GAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----A--GUUAGGUCCUGCAGUACUGGCUG---------
AGCE01141575.1/4443-4377   --GAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--AUUAGGUCCUGCAGUACUGGCUU---------
ACIV010818800.1/185-250    --GAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAG-GCGAAACC----U--AUUAGGUCCUGCAGUACUGGCUU---------
ABQO010129822.1/1187-1253  --AGGCCG-UUACCUGCAGCUGAUGAGCUCCAAUAAGAGCGAAACC----A--AUUAGGUCCUGCAGUACUGGCUU---------
ABQF01023900.1/7348-7414   --GAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----A--GUUAGGUCCUGCAGUACUGGCUA---------
AAHX01036414.1/22499-22433 --GAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--GUUAGGUCCUGCAGUACUGGCUU---------
AGAI01061309.1/24394-24460 --GAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----A--GUUAGGUCCUGCAGUACUGGCUA---------
AFEY01454121.1/10166-10232 --AGGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----A--AUUAGGUCCUGCAGUACUGGCUU---------
AGTP01043633.1/33547-33613 --GAGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----G--AUAAGGUCCUGCAGUACUGGCUU---------
AL773539.18/161561-161627  --UGGCCG-UUACCUGCAGCUGAUGAGCUCCAAAAAGAGCGAAACC----U--GUUGGGUCCUGCAGUACUGGCUU---------
#=GC SS_cons               :::(((((.----((((((,,,,,,,<<<<______>>>>,,,<<<...._..____>>>,))))))---))))):::::::::.
#=GC RF                    uuggGCCg.UUACCUGCAGCUGAUGAGCUCCAAaAAGAGCGAAACC....u..auuAGGUCCUGCAGUACuGGCcuaagauaau.
//
# STOCKHOLM 1.0

#=GF AC   RF02276
#=GF ID   Hammerhead_II
#=GF DE   Hammerhead ribozyme (type II)
#=GF AU   de la Pena M
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   de la Pena M; Burge SW
#=GF SS   Predicted; WAR
#=GF GA   37.00
#=GF TC   37.20
#=GF NC   36.90
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00010
#=GF DR   SO; 0000380; hammerhead ribozyme;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   21573207
#=GF RT   Identification of hammerhead ribozymes in all domains of life reveals
#=GF RT   novel structural variations.
#=GF RA   Perreault J, Weinberg Z, Roth A, Popescu O, Chartrand P, Ferbeyre G,
#=GF RA   Breaker RR
#=GF RL   PLoS Comput Biol. 2011;7:e1002031.
#=GF WK   Hammerhead_ribozyme
#=GF SQ   24


FP929049.1/3216698-3216766 AGCCGAAACGCUCCACC----------CUGGAG-CGUCAGCCGCGGGAUGAUCGCC-CGGCUCUGAUGAUGGCAGAUCAAA
ABBO01000909.1/30753-30820 AUGCGAAACGCCCGCGC----------AAGCGGGCGUCUAUUCGG-CGUGGCGGCC-GAGUACUGACGA-UGCAGCCGAGG
EU822883.1/15732-15799     AUGCGAAACGCCCGCGC---------GAGCGGG-UGUCUAUCCGG-CGUGGUGGCC-GGGUACUGACGA-UGCAGCCGAGG
AECZ01000006.1/72490-72555 AAGCGAAACCGCCCCGC----------GUGGGC-GGUC-GUCCGGGCGUGGCGGCC-CGGGCCUGAUGA--GCAGCCAAAG
CP002431.1/2631417-2631481 AAGCGAAACCGCCCUGC-----------GGGGC-GGUC-GCCGGGGCGUGGCGGCC-UCGGCCUGAUGA--GCAGCCAAGG
BX640448.1/36812-36876     GUGCGAAACCGCCCUCC-----------GGGGC-GGUC-UGCCGGGCGUGGUGGCC-GGGCACUGAUGA--GCAGCCAUAC
FP929062.1/2627211-2627146 AGCCGAAACGCCCUU-------------GUGGG-CGUCCACCGUGGGAUGGUCUCC-CGGUGCUGAUGAUGGCAGACCAGA
FP929049.1/3977641-3977709 AGCCGAAACGCUCCACC----------UUGGAG-CGUCAGCCGCGGGAUGAUCGCC-CGGCUCUGAUGAUGGCAGAUCAAA
FP929050.1/3256692-3256760 AGCCGAAACGCUCCACC----------CUGGAG-CGUCAGCCGCGGGAUAAUCGCC-CGGCUCUGAUGAUGGCAGAUUAAA
CP001616.1/802639-802703   CCGCGAAACCGCCUGAA-----------AAGGC-GGUCUGCCCGA-UGUGGUGAUC-GGGCACUGAUGA--GCAGCCACGG
AM747720.1/1750820-1750753 AUGCGAAACGCCCGCGC---------GAGCGGG-UGUCUAUCCGG-CGUGGUGGCC-GGGUACUGACGA-UGCAGCCGAGG
ABBI01002348.1/74-141      AUGCGAAACGCCCGCGU---------AAGCGGG-CGUCUAUUCGG-CGUGGCGGCC-GAGUACUGACGA-UGCAGCCGAGG
FP929049.1/3976834-3976903 AGCCGAAACGCUCCGAU----------CUGGAG-CGUCAGCUGCGGACCGGUCGCCGCGGCUCUGACGAUGGCAGACCAAC
BX640448.1/37265-37328     AAGCGAAACCGCCCAUG-----------AGGCG-GUCUGCCCAC--CGUGGUGGCU-GGGUACUGAUGA--GCAGCACCAA
FP885897.1/1749548-1749483 GUGCGAAACGCCCGCGA----------UGCGGG-CGUCUGCCUGG-CGUGGUGGCC-GGGUACUGAUGA--GCAGCCGAAA
CP002607.1/1980217-1980286 CUGCGAAACAGGGCGGCAA------UGCCGCCU-UGUCUACCCGG-UGUGGUGGCC-GGGUACUGAUGA--GCAACCAAAC
CP002457.1/4228190-4228119 AAGCGAAACCCGCCUCAAU-----CUUGAGGCGUGGUCUAUCCAG-CGUAGUGGCU-GGGUACUGAUGA--GCAGCUAACA
AE017285.1/2805967-2806034 UUGCGAAACCGCCCCCAU--------GCGGGGC-GGUCGUCGGAG-CGUGGCGGCU-CCGGCCUGACGA--GCAGCCGAAG
AE016825.1/2338135-2338209 AAGCGAAACCGCGCACAUUGA-AAUAUGUGCGC-GGUCUGCCCGG-CGUGGUUGCC-GGGUACUGAUGA--GCAGCCAACG
FM209186.1/1691949-1692020 GAGCGAAACCGCCCCGGCCU----GGCCGGGAC-GGUCUGCCGGA-CGUGGUGGUC-CGGUACUGACGA--GCAGCCAACC
CP001339.1/1761142-1761074 GAGCGAAACGCCCGCCUG-------CGGGUGGG-CGUCUGCCGGG-CGUGGUGGCC-CGGCACUGAUGA--GCAGCCAGAG
FP929056.1/1749292-1749367 UUGCGAAACGCCCUCGACCAAGGCGGUUGAGGG-CGUCAUCCCGG-AGCGGCGUCC-GGGGUCUGAUGA--GCAGCCGAAG
CP000112.1/3331688-3331763 AUGCGAAACCGUCCUCCGUGCGGGAGCGGAGGC-GGUCGUCCGGC-GGUGGCGCGU-CGGACCUGAUGA--GCAGCCAAGC
CP001921.1/1469248-1469180 AAGCGAAACACAGGCAUU-------CGUGCCUG-UGUCUGCCGGG-UGUCGUGACU-CGGUACUGACGA--GCAGCGAGAU
#=GC SS_cons               :((,,,,<<<<<<____.........____>>>.>>>,<<<<<<<.<<___>>->>.>>>>>,,,,,,,..))::::::::
#=GC RF                    AgGCGAAACgccCccgc.........uuggGgg.cGUCugCCggG.cgUGGcgGCc.cGGcaCUGAUGA..GcAGCCaAag
//
# STOCKHOLM 1.0

#=GF AC   RF02277
#=GF ID   Hammerhead_HH10
#=GF DE   Hammerhead ribozyme HH10
#=GF AU   de la Pena M
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   de la Pena M; Burge SW
#=GF SS   Predicted; WAR; mafft_alifold
#=GF GA   75.00
#=GF TC   83.00
#=GF NC   68.00
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00010
#=GF DR   SO; 0000380; hammerhead ribozyme;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   20651741
#=GF RT   Intronic hammerhead ribozymes are ultraconserved in the human genome.
#=GF RA   de la Pena M, Garcia-Robles I
#=GF RL   EMBO Rep. 2010;11:711-716.
#=GF WK   Hammerhead_ribozyme
#=GF SQ   18


DAAA02059264.1/10059-10184 UGAAGAGUGUUUCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCACUUCUCACU-----C-U-GCUGAAACAGUUUUGAAGUGCGAAUUGGUCCUGUAGUACUGUGUCAGAAACAGAAA
ABDC01016136.1/1645-1521   AAAAAAUUGUUUCUUGACAAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC------C-U-ACUGAAACAAUUUUGAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACAGAAA
AC022023.7/76347-76471     AAAAAAUUGUUUCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC------C-C-ACUGAAAUGAUUUCGAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACAGAAA
ABRT010035571.1/1210-1086  UAAAAAUUGUUUCUUGACCGGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC------C-C-GCUGAAACAAUUUUGAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACAGAAA
AAWR02007510.1/95228-95353 UAAAAAAUGUUUCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCACU-----C-C-ACUGAAACAGUUUUGGAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACAGAAA
AAGU03026496.1/1499-1624   AGGCUAAUGUUUCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC-U----C-C-ACGGAUGCACUUUUGAAGUGUGGCUUGGUCCUGUAGUACUGUGUCAGAAACAACUG
AAKN02016348.1/4290-4412   UGAAAAAUGUUCCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGCAAGAGCGAAACCAGUUCUCAC------G-U-ACUGAA--AGUUUUGAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACAACUG
AACZ03072024.1/84930-85054 AAAAAAUUGUUUCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC------C-C-ACUGAAAUGAUUUCAAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACAGAAA
AANU01125296.1/31012-30889 UAAAAGUUGUUUCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC--------C-ACUGAAAUGUUUUCGAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACAGAAA
ABRO01075407.1/4297-4173   AAAAAAUUGUUUCUUGACCAGUUACCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC------C-U-GUUGAAAUAAUUUUGAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACGGAAA
AAPY01660575.1/1490-1366   UAAAAAAUGUUUCUUGACCAGUUGCCUGCAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC------C-C-ACUGAAAUGAUCUUGAAGUGCGAAUUGGUCCUGUAGUACUGUGUCAGAAACAACUC
ABRN01381274.1/4843-4718   AAGUAAAUGUUUCUCGACCAGUUGCCUACAGCUGACGAGCUCCAGUAAGAGCGAAACCACUUCUCAC--U---C-C-ACUGAAACAAUUUUGAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACAGAAA
AANN01835346.1/6695-6820   UAUAAAAAGUUUCUGGACCAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC---U--C-C-GCUGAAACAAUCUUAAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAGCAGAAA
ABRP01180546.1/5965-5840   CAAGAAAUGUUUCUUGACCAGUUGCCUGCAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC----U-C-C-ACUGAAACAAUUUUGAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACAACUC
ABRR01225530.1/1389-1264   UAAAAAGUGUUUCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCACUUCUCAC------U-CGAUUGAAACAAUUUUGAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAAAAGAAA
AACN010833217.1/254-131    AGAUAAAUGUUUCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAAUUCUCACU-----U-U-ACUGAAACAGUAUUGAAGUGUGAAUUGGUCCUGUAGUACU--GUCAGAAACAACUC
AAPE02016436.1/88673-88548 UAAAAAAUGUUUCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGUAAGAGCGAAACCAGUUCUCAC------UUC-ACUGAAACAAUUUAGAAGUGUGAAUUGGUCCUGUAGUACUGUGUCAGAAACAAACA
ABVD01205953.1/236-113     UAAAAAGUGUUUCUUGACCAGUUGCCUACAGCUGAUGAGCUCCAGUCAGAGCGAAACCAGUUCUCAC-----UC-C-ACAGAAACAAUUUUGAAGUGUGAAUUGGUCCUGUAGUACU--GUCAGAAACAACUC
#=GC SS_cons               :::::::(((((((-(((<<<<<<____>>>>>>,,,,,,,,<<<<<---<<<--<<<<-<<<-<<<......_._._________________>>>->>>->>>>-->>>-->>>>>,))))))))))::::
#=GC RF                    uaaaAAauGuuuCuuGaCCaGuuGCCUACagCuGAUGAGCUCCaGuaAGAgCgAAaCCaguuCUCaC......c.c.AcuGAAAcAaUuUuGAAGuGUGaaUuGGuCCuGuAGuaCuGUGuCaGaaaCagaaa
//
# STOCKHOLM 1.0

#=GF AC   RF02278
#=GF ID   Betaproteobacteria_toxic_sRNA
#=GF DE   Betaproteobacteria toxic small RNA
#=GF AU   Levy A
#=GF AU   Burge SW; 0000-0002-2506-927X
#=GF SE   Levy A; Burge SW
#=GF SS   Predicted; WAR; Burge SW
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   49.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.71 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   22300632
#=GF RT   A vast collection of microbial genes that are toxic to bacteria.
#=GF RA   Kimelman A, Levy A, Sberro H, Kidron S, Leavitt A, Amitai G, Yoder-Himes
#=GF RA   DR, Wurtzel O, Zhu Y, Rubin EM, Sorek R
#=GF RL   Genome Res. 2012;22:802-809.
#=GF RN   [2]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF CC   Overexpression in amino aid rich medium attenuates growth, suggesting role
#=GF CC   in repressing amino acid intake and metabolism.[2]
#=GF WK   Toxic_Small_RNA
#=GF SQ   51


CP000440.1/3546030-3546096     UGUCUCCUCCAUGUCUCCUC--CUGA-UAUGGAUUA---AGC-CCGUUCCGCUCUGCGUGAACGG-GCUUUUUUU-
CP000958.1/319934-319993       UGUCUCCUCCAUGUCUCCUC---UGA-UAUGGAUUC---AGC-CCGCCAC-------UUAGGCGG-GCUUUUUUUU
CP000086.1/89328-89266         UGUCUCCUCCAUGUCUCCUC--CUGA-UAUGGAUUA---AGC-CCGUUCGAA----UGUGAACGG-GCUUUUUUU-
CP000378.1/3074662-3074604     UGUCUCCUCCAUGUCUCCUC---UGA-UAUGGAUUC---AGC-CCGCCAC-------UUAGGCGG-GCUUUUUUU-
CP001043.1/3468448-3468511     UGUCUCCUCCAUGUCUCCUC--CUGA-UAUGGAUUC---AGC-CCGCUCCAC----GUCGAGCGG-GCUUUUUUUU
CP001025.1/273177-273236       UGUCUCCUCCAUGUCUCCUC---UGA-UAUGGAUUC---AGC-CCGCCUC-------UUAGGCGG-GCUUUUUUUU
ABBE01000190.1/3783-3721       UGUCUCCUCCAUGUCUCCUC--CUGA-UAUGGAUUA---AGC-CCGUUCCAA-----GUGAGCGG-GCUUUUUUUU
AP009385.1/85296-85234         UGUCUCCUCCAUGUCUCCUC--CUGA-UAUGGAUUA---AGC-CCGUUCCGC-----GUGAACGG-GCUUUUUUUC
CP000614.1/3642563-3642630     UGUCUCCUCCAUGUCUCCUC--CUGA-UAUGGAUUA---AGC-CCGCUCCGCAUUGCGUGAGCGG-GCUUUUUUUC
AAMM02000050.1/1-64            GGUCUCCUCCAUGUCUCCUC--CUGA-UAUGGAUUA---AGC-CCGUUCGAA----CAUGAGCGG-GCUUUUUUUC
ABBG01000292.1/25323-25263     UGUCUCCUCCAUGUCUCCUC---UGA-UAUGGAUUC---AGC-CCGCCUUUU------CAGGCGG-GCUUUUUUUU
CP000269.1/87474-87410         UGUCUCCUCUAUGUCUCCUCCUUUGA-UAUAGAUUC---AGC-CCGCCUCCU-----UUGAGCGG-GCUUUUUUUU
ABLK01000420.1/4316-4377       UGUCUCCUCCAC-UCUCCUC--CUGA-GGUGGAUUA---AGC-CCGAACCAG-----CCGUUCGG-GCUUUUUUUU
ABYL01000011.1/92050-91992     CGUCUCCUCCAUGUCUCACC---UGA-UGUGGAUUC---AGC-CCGCCAA--------UGAGCGG-GCUUUUUUCU
CU207211.1/66782-66719         UGUCUCCUCUAUGUCUCCUCCUUUGA-UAUAGAUUC---AGC-CCGCCUU-C-----UUGUGCGG-GCUUUUUUUU
AM747721.1/2089714-2089771     UGUCUCCUCCAUGUCUCC-----AAA-CAUGGAUUC---AGC-CCGCUCCAG-------CAGCGG-GCUUUUUUAU
ACFD01000014.1/69813-69752     UGUCUCCUCCACCCUCCUCC---UAA-GGUGGAUUA---AGC-CCGAACCAG-----CCGUUCGG-GCUUUUUUUC
AAKY01000117.1/13557-13497     UGUCUCCUCCACC--UCCUC--CUAU-GGUGGAUUA---AGC-CCGAACCAG-----CCGUUCGG-GCUUUUUUUC
ABBD01000514.1/1786-1847       UGUCUCCUCCACCC-UCCUC--CUUU-GGUGGAUUA---AGC-CCGAACCAG-----UGGUUCGG-GCUUUUUUUU
AAKX01000049.1/7-63            UGUCUCCUCCAUGUCUCCUC---UGA-UAUGGAUUC---CGC-UCGCCAC-------UUAGGUG----GUUUUUUU
ABMY01013182.1/39-104          UGUCUCCUCCAA-UCUCCUU--AAGAAAUUGGAUUC--AAGC-CCGCACCUC---UUGGUCGCGG-GCUUUUUNUU
ABLC01000085.1/5947-6004       UGUCUCCUCCAUGUCUCC-----AAA-CAUGGAUUC---AGC-CCGCUCCAG-------UAGCGG-GCUUUUUCUU
CP000152.1/1175498-1175440     UGUCUCCUCCAUGUCUCC-----AAA-CAUGGAUUC---AGC-CCGCUCAAU------GCAGCGG-GCUUUUUCUU
AACY020347747.1/192-252        UGUCUCCUCCACC--UCCUC--CUUU-GGUGGAUUA---AAC-CCGAACCAC-----UCGUUCGG-GUUUUUUUUC
AM902716.1/4261276-4261212     UGUCUCCUCCACCC-UCCUC--CUUU-GGUGGAUUU---AGC-CCGAGAUCGC--AAGAUCUCGG-GCUUUUUUUU
AATO01015090.1/573-509         UGUCUCCUCCAC-CCUCCUCCUUUGG-UGUGGAUUU---AGC-GCGAUUCCA----ACGAAUCGC-GCUUUUUUUU
CP001013.1/3800215-3800277     UGUCUCCUCCACCC-UCCUC--UAAA-GGUGGAUUA---AAC-CCGGGGUUC----AUCCCCCGG-GUUUUUUUUC
AAHN02000004.1/150529-150590   UGUCUCCUCCACCC-UCCUC--CUUU-GGUGGAUUA---AGC-CCGAACCAG-----CGGUUCGG-GCUCAGAUUG
AAUJ02000001.1/4829926-4829989 UGUCUCCUCCACC--UCCUC--UAAU-GGUGGAUUC---AGC-CCCUAGCUCC--UGAGCUAGGG-GCUUUUUUUC
CP000555.1/3325575-3325639     UGUCUCCUCCACCC-UCCUC--CAAA-GGUGGAUUC---AGC-CCAGGGCCUC--ACGGCCUUGG-GCUUUUUUAU
CP000089.1/711354-711417       UGUCUCCUCCAC-CCUCCUCCUUUGG-UGUGGAUUU---AAC-GCGGCUCAG-----CGAGCCGC-GUUUUUUUUG
AL646052.1/527123-527187       UGUCUCCUCCACCC-UCCUC--CUUU-GGUGGAUUCA-AACC-CCAAGCCAA----ACCGCUUGG-GGUUUUUUUU
ABCT01000013.1/1117-1183       UGUCUCCUCCACCC-UCCUC--CUUU-GGUGGAUUA---AAC-CCAAGCACCUCACAGUGCUUGG-GUUUUUUUUA
AM406670.1/3042379-3042315     UGUCUCCUCCAC-CCUCCUCCUUUGG-UGUGGAUUU--AACG-CAGUCCCAA-----ACGGACUG-CGUUUUUUUU
CP000090.1/513434-513497       UGUCUCCUCCACCC-UCCUC--CUUU-GGUGGAUUC--AAAC-CCAGGCUAA----ACCGCCUGG-GUUUUUUUUC
CU633749.1/448639-448702       UGUCUCCUCCACCC-UCCUC--CUUU-GGUGGAUUC--AAAC-CCAAGCUCA----AACGCUUGG-GUUUUUUUUC
CP000352.1/436937-437000       UGUCUCCUCCACCC-UCCUC--CUUU-GGUGGAUUCG-AACC-CAAGUCCAA-----CCGACUUG-GGUUUUUUUU
CP001068.1/391402-391465       UGUCUCCUCCACCC-UCCUC--CUUU-GGUGGAUUC--AAAC-CCAAGCUUG----AUGGCUUGG-GUUUUUUUUC
CR555306.1/32466-32533         UGUCUCCUCCAC-CCUCCUCCUUUGG-UGUGGAUUU--CAGC-CCGGGCCCGA--AAGUGCUCGG-GCUUUUUCUU
CP001281.2/1366049-1366113     UGUCUCCUCCAC-CCUCCUCCUUUGG-UGUGGAUUU---AAC-GCAGUCCGA----UCGGACUGC-GUUUUUUUUG
CP001392.1/682297-682234       UGUCUCCUCCAUC--UCCUC--AAAG-GAUGGAUUC---AGC-CCCAGGCUUU--ACCGCUUGGG-GCUUUUUUUU
CU914168.1/35-95               UGUCUCCUCCAC----CCUC--CU-U-GGUGGAUUG--CGGC-CCGAGCACC---AAGUGCUCGG-GCCUUUUUUC
CP000529.1/683733-683669       UGUCUCCUCCACC--UCCUC--AAAG-GGUGGAUUUAUAGGU-CCAGACCGC----AUGGUCUGG-GCCUUUUUUU
CP000316.1/759861-759798       UGUCUCCUCCAC---UCCUC--UAAG-GGUGGAUUUACAGGC-CCAGACCGC----AAGGUCUGG-GUCUUUUUUC
CP000116.1/910327-910392       UGUCUCCUCCAAUCCUCCUCCUUUGG---UGGAUACU-CUGC-CCGGCUCUC----GCGAGCUGG-GCAUUUUUUU
CP000542.1/587077-587015       UGUCUCCUCCAUC--UCCUC--AAAG-GAUGGAUUG--AGCC-CCGGACCGC----AAGGUCCGG-GGCUCUUUUU
CP000884.1/6323027-6323089     UGUCUCCUCCACC--UCCUC--UAUU-GGUGGAUUC--AGCC-CCCGGCUUU----ACAGCCUGG-GGCUUUUUUU
CP000512.1/1011515-1011452     UGUCUCCUCCAUC--UCCUC--AAAG-GAUGGAUUC---GGCUCCGGAUCUC----ACGAUCCGGGGCCGUUUUUU
ABSR01021248.1/512-450         UGUCUCCUCCACCU-UCCG---AAAG-GGUGGAUUC--GGCC-CAAGGCAGC----AAUGCCUUG-GGCUCUUUUC
CP001644.1/3454936-3454996     UGUCUCCUCCAC----CCUC--CU-U-GGUGGAUUG--UGGC-CCGAGCACC---UGGUGCUCGG-GCUUUUUUCU
CP001635.1/1190002-1189940     UGUCUCCUCCACCCUUCC----AAUU-GGUGGAUUU--AGCC-CCGAGCUGC----AAGGCUCGG-GGCUUUUUUC
#=GC SS_cons                   :::::::<<<<<<<<_____..__>>.>>>>>>---...<<<.<<<<<____....____>>>>>.>>>:::::::
#=GC RF                        UGUCUCCUCCAccuCUCCUC..uUGa.ggUGGAUUc...aGC.CCggcccac....auuggccGG.GCuUUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02279
#=GF ID   TtnuCD1
#=GF DE   Tetrahymena snoRNA TtnuCD1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   70.00
#=GF TC   84.00
#=GF NC   38.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.62 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909302.1/1-63              UCUGAUGACAAUCUCAUUACAUGAAUCAUACAUGUUUAUAAAUUAUCCAUCUUUCGGCUGAAA
AFXY01001373.1/273286-273348 UCUGAUGACAAUCUCAUUACAUUAAUCAUCCAUGUUUAUAAAUUAUCCAUCUUUCGGCUGAAA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UCUGAUGACAAUCUCAUUACAUgAAUCAUaCAUGUUUAUAAAUUAUCCAUCUUUCGGCUGAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02280
#=GF ID   TtnuCD3
#=GF DE   Tetrahymena snoRNA TtnuCD3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   70.00
#=GF TC   104.00
#=GF NC   41.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


JF909303.1/1-72              AAUAUUGUUUUGAUGAAAAUUUAAGAUCAUUACUCUUCGGAGAUUGAUGAAAUUAAUUCUGCUUCCCUGAUU
AFXY01000473.1/88470-88399   UGACUUGUUUUGAUGAAAAUUUAAGAUCAUUACUCUUCGGAGAUUGAUGAAAUUAAUUCUGCUUCCCUGAUU
AFXF01000011.1/353283-353212 UAAUUUGUUUUGAUGAAAAUUUAAAAUCAUUACUCCUCGGAGAUUGAUGAAAUUAAUUCUGCUUCCCUGAUU
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      uaauUUGUUUUGAUGAAAAUUUAAGAUCAUUACUCuUCGGAGAUUGAUGAAAUUAAUUCUGCUUCCCUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02281
#=GF ID   TtnuCD4
#=GF DE   Tetrahymena snoRNA TtnuCD4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   60.00
#=GF TC   74.80
#=GF NC   35.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.54 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


EF503648.1/1-60              UAACAUCCAGCUCACUUUGAAGGC-UCGCCUUCUGAAA-AAAACC-UUUCCUAUACUCUGACA
AFXF01000011.1/357712-357651 UAACAUCCAGCUCACUUUGAAGGU-UCGCCUUCUGAAAAAAAACCAAUUCCUAUUACCUGACA
AEDN01001543.1/15726-15667   UAACAACCAGCUCACUUUGAAGGUUUAUCCUUCUGAA--AAUACA-AUCCAAAUUAUCUGAAC
#=GC SS_cons                 ::::::::::::::::::::::::.:::::::::::::.::::::.:::::::::::::::::
#=GC RF                      UAACAuCCAGCUCACUUUGAAGGU.UcgCCUUCUGAAA.AAaACc.aUuCcuAUuauCUGAca
//
# STOCKHOLM 1.0

#=GF AC   RF02282
#=GF ID   TtnuCD5
#=GF DE   Tetrahymena snoRNA TtnuCD5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   70.00
#=GF TC   104.90
#=GF NC   43.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.74 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909304.1/1-76              UAAUGAUGAGAUUAGAAACGCUGAUUAUAACUCUCUUGAAAGAA-AUUUGAAAACAACCUUCUUUCCCCUACUGACU
AFXY01000199.1/335010-334934 UAAUGAUGAGAUUAGAAACGCUGAUUAUAACUCUCUUGAAAAAAAAUUUGAAAACUACCUUCUUUCCCCUACUGACU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UAAUGAUGAGAUUAGAAACGCUGAUUAUAACUCUCUUGAAAgAAAAUUUGAAAACuACCUUCUUUCCCCUACUGACU
//
# STOCKHOLM 1.0

#=GF AC   RF02283
#=GF ID   TtnuCD6
#=GF DE   Tetrahymena snoRNA TtnuCD6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   50.00
#=GF TC   63.90
#=GF NC   33.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.11 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909305.1/1-70            UGCUGAUGAUA-UUUCUUAGGACGCCUUCUGAAACGACUUUUCGUUUGUGAGAAUAA-CCAAGAAACUGACG
AEDN01001333.1/96508-96579 UAUGGAUGAAAUAUACUUAGGACGCCUUCUGAAACGAUUUUUCGUUUGUGAGAACAAAACUGGUACCUGAAC
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UgugGAUGAuAUuUuCUUAGGACGCCUUCUGAAACGAuUUUUCGUUUGUGAGAAuAAAaCugGuAcCUGAag
//
# STOCKHOLM 1.0

#=GF AC   RF02284
#=GF ID   TtnuCD7
#=GF DE   Tetrahymena snoRNA TtnuCD7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   90.00
#=GF TC   127.70
#=GF NC   42.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 39.82 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909306.1/1-108           UUCAUGAUGAUAUAAAUAUGGAAUUACCGUCUGAAUUUAGAUUGAUGGAAAAAUUUUGCUAAACUGAUAGAAUAUUCAAACAUUUCUCACAGUUAAAUGACUGAAGAA
AFXF01001532.1/87951-88057 UUCAUGAUGAUAUAAAUAUGGAAUUACCGUCUGAAA-UACAUUGAUGCAAAAUUUUUGCAAAACUGAUAGAAUAUUAAAACAUUUCUCACAGUUAAAUGACUGAAGAA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UUCAUGAUGAUAUAAAUAUGGAAUUACCGUCUGAAuUUAgAUUGAUGgAAAAuUUUUGCuAAACUGAUAGAAUAUUcAAACAUUUCUCACAGUUAAAUGACUGAAGAA
//
# STOCKHOLM 1.0

#=GF AC   RF02285
#=GF ID   TtnuCD8
#=GF DE   Tetrahymena snoRNA TtnuCD8
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   70.00
#=GF TC   75.70
#=GF NC   37.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503645.1/1-59              UAAAUAUUCCAGUUCUGCUGCUGAAAACAGCUUGAAGAUAACUUUGCUUACCUUUCUGA
AEDN01002082.1/104168-104111 GUAACAUACCAGUUCUGCUGCUGAAAACAGCUUGAAGA-AAUUUUACUUACCAUUCUGA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      guAAuAUuCCAGUUCUGCUGCUGAAAACAGCUUGAAGAUAAuUUUgCUUACCuUUCUGA
//
# STOCKHOLM 1.0

#=GF AC   RF02286
#=GF ID   TtnuCD9
#=GF DE   Tetrahymena snoRNA TtnuCD9
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   70.00
#=GF TC   78.60
#=GF NC   37.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.17 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909307.1/1-55            UAUGAUGAUUUAACAACGCUCGUAUGAUUAUGAUUACAUUUAACUGCAAGCUGAA
AFXF01001532.1/88790-88844 UAUGAUGAUUUAACAACGCUCGAAUGAUUAUGAUUACAUUUAACUGCAAACUGAA
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UAUGAUGAUUUAACAACGCUCGuAUGAUUAUGAUUACAUUUAACUGCAAgCUGAA
//
# STOCKHOLM 1.0

#=GF AC   RF02287
#=GF ID   TtnuCD10
#=GF DE   Tetrahymena snoRNA TtnuCD10
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   85.00
#=GF TC   108.90
#=GF NC   42.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.49 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4


JF909308.1/1-117             GCUAUGAAGAUA-CGAUGACGAGAAUGA-CGGUUUUCUUCGAUUUGGGUACCAAAGUUCUUUUGGUAUUUGAUGAGAAGCGACC---UCAACGUGAUUCUAAAUGAGGCAUUUGACAGAGCA
AFXY01000862.1/264886-265002 GCUAUGAAGAUA-CGAUGACGAGAAUGA-UGGUUUUCUUCGAUUUGGGUGUCAAAGUUUUUUUGAUAUUUAAUGAGAAGAUACC---UCAAUGUGAUUCUAAAUGAGGCAUUUGACAGAGCA
AFXF01001532.1/89042-89159   GCCAUGAAGAUAAAGAUGACGAGAAUGA-CGGUUUUCUUUGAGUUGGAUGCCAAAGUUUUUUUGGUAUUCAAUGAGAAGAGACC---UCUAAGUGAUUCUAAAUGAGGCAUUUGACAGAGCA
AEDN01002082.1/103675-103555 GCGAUGAAGAAA-CGAUGACGAGAAUGACUGGAAAAUUGUCAUGUUUUUUUCAAAGUUUUUUUGAUUAAAAUUUGAUUUUUUUCUGUUUUCCGUGAUUCUAAAUGAGGCAUUUGUCAGAGCA
#=GC SS_cons                 ::::::::::::.:::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::...:::::::::::::::::::::::::::::::::::
#=GC RF                      GCuAUGAAGAuA.cGAUGACGAGAAUGA.uGGuuuucUuugAuuUgggUguCAAAGUUuUUUUGgUauuuaaUgaGaagauacC...UcuacGUGAUUCUAAAUGAGGCAUUUGaCAGAGCA
//
# STOCKHOLM 1.0

#=GF AC   RF02288
#=GF ID   TtnuCD11
#=GF DE   Tetrahymena snoRNA TtnuCD11
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   70.00
#=GF TC   78.90
#=GF NC   32.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.39 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


JF909309.1/1-74              UGUUUUUUCUGAUGACUGAUAUAGCCGCCCCAGUAAUAUGCCUCCAGGCGUUGAUUAUAGGCU--UGGU-UCUGAUA
AFXF01001532.1/89408-89481   UUUAAAAUCUGAUGACUGAUAUAGCCGCCCCAGUAAUAUGCCUCCAGGCGUUGAUUAUAGGCU--UGGU-UCUGACU
AEDN01002082.1/103029-102956 UAUUAUUAUUGAUGACUAAUUAG-CCGCCCCAGUAAUACGCUAC--GGCAUUGGUUAUAGGCUUAUGGACCUGAAUA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::..::::.:::::::
#=GC RF                      UaUuauuucUGAUGACUGAUauaGCCGCCCCAGUAAUAuGCcuCCAGGCGUUGaUUAUAGGCU..UGGu.ucuGAua
//
# STOCKHOLM 1.0

#=GF AC   RF02289
#=GF ID   TtnuCD13
#=GF DE   Tetrahymena snoRNA TtnuCD13
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   75.00
#=GF TC   88.60
#=GF NC   40.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.53 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909311.1/1-63            UGAUGAGAAACUUCUAGUCUCCUGAACUAAACUGAAGAAGAAAAUUUUCGCUCCUAUCUGACA
AFXF01001532.1/90024-90086 UGAUGAGAAACUUCUAGUCUCCUGAACUAAACUGAAGAACAAAAUUUUCGCUCCUAUCUGACA
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UGAUGAGAAACUUCUAGUCUCCUGAACUAAACUGAAGAAgAAAAUUUUCGCUCCUAUCUGACA
//
# STOCKHOLM 1.0

#=GF AC   RF02290
#=GF ID   TtnuCD14
#=GF DE   Tetrahymena snoRNA TtnuCD14
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   75.00
#=GF TC   95.50
#=GF NC   36.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909312.1/1-73            UUAAAUGAUGUUUUUAGUGUGUAAUCUCUCUCAUUAGAUCCUCGGAUCUAUGUAGAAAAUUU-AUCC-UUACUGA
AFXF01001532.1/90383-90456 UCGAAUGAUGUU-UUAGUGUGUAAUCUCUCUCAUUAGAUCCUCGGAUCUAUGUAGAAAAAUUCAUCCAUCACUGA
#=GC SS_cons               ::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UugAAUGAUGUU.UUAGUGUGUAAUCUCUCUCAUUAGAUCCUCGGAUCUAUGUAGAAAAuUUCAUCCAUuACUGA
//
# STOCKHOLM 1.0

#=GF AC   RF02291
#=GF ID   TtnuCD15
#=GF DE   Tetrahymena snoRNA TtnuCD15
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   75.00
#=GF TC   79.30
#=GF NC   48.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.76 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909313.1/1-61              UGAUGAAUAUAUUUGACUAGAGUUUCUGAUCUUUA----UGAUUACAUAACCCUUAGCUGCCUGA
AEDN01002082.1/102224-102160 UGAUGAUAUUAUUUGACUAGAGUUUCUGAUAAUUUUAAUUGAUUACAAAACCCUUAGCUGCCUGA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UGAUGAuuuUAUUUGACUAGAGUUUCUGAUauUUuUAAUUGAUUACAuAACCCUUAGCUGCCUGA
//
# STOCKHOLM 1.0

#=GF AC   RF02292
#=GF ID   TtnuCD16
#=GF DE   Tetrahymena snoRNA TtnuCD16
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   75.00
#=GF TC   83.40
#=GF NC   37.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 24.66 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503644.1/1-58            UCAUGACUGACACCUCUUGAGCGAGCCUUCGGGCAUUGAUCUUAACCAGUCCCUGAUU
AFXF01001532.1/91063-91120 UUAUGACUGACACCUCUUGAGCGAGCCUUCGGGCAUUGAUCUUAACCAGUCCCUGAUC
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UuAUGACUGACACCUCUUGAGCGAGCCUUCGGGCAUUGAUCUUAACCAGUCCCUGAUu
//
# STOCKHOLM 1.0

#=GF AC   RF02293
#=GF ID   TtnuCD17
#=GF DE   Tetrahymena snoRNA TtnuCD17
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   75.00
#=GF TC   91.40
#=GF NC   38.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.90 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909314.1/1-68            AUGAUGAUUAAAGUUAUCCCUGUCCUAAAACGUUUGUUUGCGGAAAAACUUUAAGGUAAAAUCUGACU
AFXF01001470.1/15860-15926 AUGAUGAUUAAAGUUAUCCCUGUCCUAAAACGUUUGUUUGCGGAAAAACUUUAAGGUA-AAUCUGAAC
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    AUGAUGAUUAAAGUUAUCCCUGUCCUAAAACGUUUGUUUGCGGAAAAACUUUAAGGUAAAAUCUGAcu
//
# STOCKHOLM 1.0

#=GF AC   RF02294
#=GF ID   TtnuCD18
#=GF DE   Tetrahymena snoRNA TtnuCD18
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   55.00
#=GF TC   64.80
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.32 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909315.1/1-56        UUGAUGAGC-AUUUGUGUCCGUGUUUAUGAAAACGUGAUUA-AUACACAUUUCUGAAA
AEDN01002204.1/600-657 UUGAUGAUUAAUUUGUGUCCGUGUUUAUGAAUACGUGAUUACUUACACAAUACUGAUA
#=GC SS_cons           ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                UUGAUGAguAAUUUGUGUCCGUGUUUAUGAAuACGUGAUUACuUACACAuUuCUGAuA
//
# STOCKHOLM 1.0

#=GF AC   RF02295
#=GF ID   TtnuCD19
#=GF DE   Tetrahymena snoRNA TtnuCD19
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   70.00
#=GF TC   80.50
#=GF NC   39.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 36.27 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909316.1/1-68            ACUGAUGCAUAACUAUGAAUAUGAUU---UCUGAUUAAAUUGUUCAUAAAUACCAUCUUUCGGGACUGACA
AEDN01001751.1/49163-49094 UAUGAUGCAUAAAUAUGAUUAUGAUUAACUAUGAUUUAAUUUAUCAUA-AUACCAUCUUUCGGGACUGAUU
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::
#=GC RF                    uaUGAUGCAUAAaUAUGAuUAUGAUUAACUaUGAUUuAAUUguUCAUA.AUACCAUCUUUCGGGACUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF02296
#=GF ID   TtnuCD20
#=GF DE   Tetrahymena snoRNA TtnuCD20
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   80.00
#=GF TC   92.60
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.13 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909317.1/1-66              AGUUUAAUGAUGAUAAAAGCCAAAAACGUGACCAUAUUCUGGACGUAUACAAUGAUAGGCCUGAUU
AFXY01000643.1/417458-417523 AGUUUAAUGAUGAUCAAAGCCAAAAACGUGACCGUAUUCUGGACGUAUACAAUGAUAGGCCUGAUU
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      AGUUUAAUGAUGAUaAAAGCCAAAAACGUGACCgUAUUCUGGACGUAUACAAUGAUAGGCCUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02297
#=GF ID   TtnuCD21
#=GF DE   Tetrahymena snoRNA TtnuCD21
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   70.00
#=GF TC   78.20
#=GF NC   35.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.38 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909318.1/1-63          GAUGAUGAGUUUAUUUUAACGGCUUAUG--AUUCAUGAUUAUAAUCUGUGCAUCACCACUCUGAA
AEDN01001090.1/9999-9935 AAUGAUGAUAUAUAUACAACGGCUUAUGAAAUUAAUGAUUAUAAACUGUGCAUCACCACUCUGAU
#=GC SS_cons             :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                  gAUGAUGAguUuuuUuuAACGGCUUAUGAAAUUaAUGAUUAUAAuCUGUGCAUCACCACUCUGAu
//
# STOCKHOLM 1.0

#=GF AC   RF02298
#=GF ID   TtnuCD22
#=GF DE   Tetrahymena snoRNA TtnuCD22
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   85.00
#=GF TC   108.60
#=GF NC   34.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.48 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909319.1/1-77              AAAUUGAUGACUUUUAAUGAGUACGAAGUAGUUUGGGUCAAACCAAGCUGCUGAUGAACUUAUUUCGCAGCCUGAAA
AFXF01001162.1/347516-347441 AAGUUGAUGACUUUUAAUGAGUACGAAGUAGCUUGGGU-AAACCAAGCUGCUGAUGAACUUAUUUCGCAGCCUGAAA
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      AAgUUGAUGACUUUUAAUGAGUACGAAGUAGuUUGGGUCAAACCAAGCUGCUGAUGAACUUAUUUCGCAGCCUGAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02299
#=GF ID   TtnuCD23
#=GF DE   Tetrahymena snoRNA TtnuCD23
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   70.00
#=GF TC   91.20
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.45 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503641.1/1-72              UAAAUGAUGAUUCAAGAUAGGGACAACAGACUUUAAUUCAACUGUUGACAUAAUCGAUAGUAGAUCCUGAUA
AFXY01000473.1/182193-182264 UAAAUGAUGAUCCUAGAUAGGGACAACAGACUUUAAUUCAACUGUUGACAACAUUGAUAGUAGAUCCUGAUA
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      UAAAUGAUGAUuCuAGAUAGGGACAACAGACUUUAAUUCAACUGUUGACAuaAUuGAUAGUAGAUCCUGAUA
//
# STOCKHOLM 1.0

#=GF AC   RF02300
#=GF ID   TtnuCD24
#=GF DE   Tetrahymena snoRNA TtnuCD24
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   75.00
#=GF TC   84.20
#=GF NC   36.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.13 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909320.1/1-58              GAUUGAUGAUACAUUUGGAUCAACCACCUGAUUUCUGAUGUUCUACUGGCGACUGAAU
AFXF01000634.1/109183-109126 GAUUGAUGAUACAUUUGGAUCAACCACCUGAUUACUGAUGUUCUACUGGCGACUGAAU
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      GAUUGAUGAUACAUUUGGAUCAACCACCUGAUUuCUGAUGUUCUACUGGCGACUGAAU
//
# STOCKHOLM 1.0

#=GF AC   RF02301
#=GF ID   TtnuCD25
#=GF DE   Tetrahymena snoRNA TtnuCD25
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   85.00
#=GF TC   98.00
#=GF NC   32.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.94 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


EF503642.1/1-87              UUCAACUGAUGAUUAAUUAGUUUCUCUAAAUUCGCAGUGACCCCCCUACUAGU---CCGAAAGGC--GCUGUAGGUUAGAGCCGUGUCUGAU
AFXF01000643.1/293393-293305 UUCACCUGAUGAUUUAUAAGUUUCUCUAAAUUCGCAGUGACCCCCCUACCAAU--GCCGAAAGGC-UGCUGUAGGUUAGAGCCGCGUCUGAU
AEDN01000208.1/43033-43121   AAAAAAUGAUGAUUAAU---UUUCUCUAUAUUCGCAGUAACCCCCCUACUAACUACCUAUUAGGUAUGCUGUAGGUUAUAGCCGCGUCUGAU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::..::::::::::.::::::::::::::::::::::::::
#=GC RF                      uucAacUGAUGAUUaAUuAGUUUCUCUAaAUUCGCAGUgACCCCCCUACuAau..gCcgaaAGGc.UGCUGUAGGUUAgAGCCGcGUCUGAU
//
# STOCKHOLM 1.0

#=GF AC   RF02302
#=GF ID   TtnuCD26
#=GF DE   Tetrahymena snoRNA TtnuCD26
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   90.00
#=GF TC   108.20
#=GF NC   36.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.26 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503643.1/1-98            CAUCAGUAGGUAAUCCUUACCUAUAUAUUUCUAAUGAUGAAGGAGAUGGCCAUAUCCCUCG----GGAUUGAAAAUCA--UGAAAAACUGGCUGC----AAUGCUGAU
AEDN01000513.1/93696-93589 CAUCAGUAGGUAAUCCUUACCUAUAAAUUUUCAAUGAUGAUGGAGAUGGCCAUAUCCCUUAACUGGGAUUGAUUAUUUUAUGAAAAACUGGCUACUCAUAUCGCUGAU
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    CAUCAGUAGGUAAUCCUUACCUAUAuAUUUuuAAUGAUGAuGGAGAUGGCCAUAUCCCUugACUGGGAUUGAuuAUuuUAUGAAAAACUGGCUgCUCAUAuuGCUGAU
//
# STOCKHOLM 1.0

#=GF AC   RF02303
#=GF ID   TtnuCD28
#=GF DE   Tetrahymena snoRNA TtnuCD28
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   70.00
#=GF TC   83.50
#=GF NC   46.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.37 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909321.1/1-64              AACUGAUGAACAAUUAUACAAGCAUAUGUCAGAAUACUGUUGUUGACAACCUUCAUGACUGAUU
AFXF01000574.1/197215-197277 AACUGAUGAACAAUU-UACAAGCAUAUGUCAGAAUUCCUUUGUUGACAACCUUCAUGACUGAUU
#=GC SS_cons                 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      AACUGAUGAACAAUUAUACAAGCAUAUGUCAGAAUuCugUUGUUGACAACCUUCAUGACUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02304
#=GF ID   TtnuCD29
#=GF DE   Tetrahymena snoRNA TtnuCD29
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   90.00
#=GF TC   110.30
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909322.1/1-77            UAAUGAUGACAAAAU-UCCCAAAAUGCCUAUUUGAAGCUUGCUUCAAAAAUGAAGGUUAAUCCAAUUUGCCACUGAUA
AFXF01000451.1/57048-57125 AAAUGAUGACAAAAUAUCCCAAAAUGCCUAUUUGAAGCUUGCUUCAAAAAUGAAGGUUAAUCCAAUUUGCCACUGAUA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    uAAUGAUGACAAAAUAUCCCAAAAUGCCUAUUUGAAGCUUGCUUCAAAAAUGAAGGUUAAUCCAAUUUGCCACUGAUA
//
# STOCKHOLM 1.0

#=GF AC   RF02305
#=GF ID   TtnuCD31
#=GF DE   Tetrahymena snoRNA TtnuCD31
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   75.00
#=GF TC   86.40
#=GF NC   32.80
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.59 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503640.1/1-66            UCUUAAUGAUGAUAUUUAGAGUCUCACGACGUCUGAU-AAAAUGUGACGCAACUACACUCUCCUGAU
AFXF01000365.1/95265-95199 UCUUAAUGAUGAUAUUUAGAGUCUCACGACGUCUGAACGAAAUGUGACGCAACUACACUCUCCUGAU
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UCUUAAUGAUGAUAUUUAGAGUCUCACGACGUCUGAuCgAAAUGUGACGCAACUACACUCUCCUGAU
//
# STOCKHOLM 1.0

#=GF AC   RF02306
#=GF ID   TtnuCD32
#=GF DE   Tetrahymena snoRNA TtnuCD32
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   128.10
#=GF NC   34.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.39 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


JF929905.1/1-98            AACAUGAUGUAUAAAACGCAUGGAAAGAGGUUUGUAGUUAACCCUACUGAACCCAGGGUUAAGCCAUCCCUCGAUGAAUCCAUACCAAUCGUCUGAUU
AFXF01000848.1/17725-17628 UACAUGAUGUAUAAAACGCAUGGAAAGAGGUGUGUAGUUAGCCCUACUGAACCCAGGGCUAAGCCAUACUUCGAUGAAUCCAUACCAAUCGUCUGAUU
AFXY01000819.1/52447-52544 AACAUGAUGUAUAAAACGCAUGGAAAGAGGUAUGUAGUUAACCCUACUGAACCCAGGGUUAAGCCAUACUUCGAUGAAUCCAUUCCAAUUGUCUGAUU
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    aACAUGAUGUAUAAAACGCAUGGAAAGAGGUgUGUAGUUAaCCCUACUGAACCCAGGGuUAAGCCAUaCuUCGAUGAAUCCAUaCCAAUcGUCUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02307
#=GF ID   TtnuCD33
#=GF DE   Tetrahymena snoRNA TtnuCD33
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   80.00
#=GF TC   103.70
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.73 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909323.1/1-74            UAUAAGGAUGAUUUAUUUGCAACAGCGAGAUCUAUAUGAUCCAUGAAAACUUCAUUUACGUCGAUAAUCUGAUU
AFXF01000848.1/18075-18002 UUCAAGGAUGAUUUAUUUGCAACAGCGAGAUCUAAUUGAUCUAUGAAAACUUCAUUUACGUCGAUAAUCUGAUU
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    UuuAAGGAUGAUUUAUUUGCAACAGCGAGAUCUAuuUGAUCuAUGAAAACUUCAUUUACGUCGAUAAUCUGAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02308
#=GF ID   TtnuCD34
#=GF DE   Tetrahymena snoRNA TtnuCD34
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   80.00
#=GF TC   89.40
#=GF NC   32.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.18 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909324.1/1-64            AAAUUGAUGACAACUCGCGUCCAUACUCUUCACCGAGAUUGAUGACUUUGUUCUGCAAUCCUGA
AFXY01000473.1/88226-88163 UGAUUGAUGACAACUCGCGUCCAUACUCUUUACGGAGAUUGAUGACUUUGUUCUGCAAUCCUGA
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    ugAUUGAUGACAACUCGCGUCCAUACUCUUuACgGAGAUUGAUGACUUUGUUCUGCAAUCCUGA
//
# STOCKHOLM 1.0

#=GF AC   RF02309
#=GF ID   TtnuHACA1
#=GF DE   Tetrahymena snoRNA TtnuHACA1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   137.40
#=GF NC   50.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503649.1/1-113           AGUCAUUAACUAUAUCUCCAUAUGUUGUUAAUGCUUGCGUUAUCUAUAGUGAAACUUCUCUUAGGCUCUUAUCAUAUGUUCAUAUGUGAAAAGAUACCAAGAUAAGGACAUUU
AFXF01000629.1/60824-60712 AGUCAUUAACUAUAUCUCCAUAUGUUGUUAAUGCUUGCGUUAUCUAGAGUGAAACUUCUCUUAGGCUCUUAUCAUAUGUUCAUAUGUGAAAAGAUACAAAGAAAAGGACAGUU
#=GC SS_cons               <<-<<<<<<<-<<<<______>>>>->>>>>>>>>------------<<<<---<<<-<<<<-<<-<<<<-<<<<<<<____>>>>>>>->>>>-->>>>>>->>>-->>>>:
#=GC RF                    aGUCauuaaCUacauCUCCAUauguUGuuaauGCuUGCGUUAUCUAuaguGAAACuuCuCuuAgGCuCuuAuCacaugUUCAcauguGaAaaGaUACcaaGaaaaGGACacuU
//
# STOCKHOLM 1.0

#=GF AC   RF02310
#=GF ID   TtnuHACA2
#=GF DE   Tetrahymena snoRNA TtnuHACA2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   139.00
#=GF NC   38.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


EF503650.1/1-121           AAUCAUUUCUACAAAAUUAUUUGUUUAAAUGACCUUGUGGGGAUGCAAAAUAAAAACUUAAAGAUUGUCCAGGUCGUUAUAGAUCAUAAUUUUAUAGCGAUGGUUCCAAGAUCUUACAAUU
AFXY01000699.1/60017-60136 AAUCAUUUCUUCAAAAUAAUUUGUUUAAAUGACAUUGUGGGGAUGCAAAAUAA-AACUAUAAGAUUAUCCAGGUCGUUAUAGAUCAUUAUUUUAUAGCGAUGGUUCCAAGAUCUUACAAUU
AFXF01000377.1/50392-50275 AAUCAUUUCUACAAAAUCAUUUGUUUAAGUGACCUUGUGGGGAUGCUAAAUCAAACC--AAAGAUUAUCCAGGUCGUUAUAGA-CUUUAUUUUAUAGCGAUGGUUCCAAGAUCUUACAACU
#=GC SS_cons               :::<<<--<<<<<<--<<<<<<____>>>>>>-->>>>>>-->>>---------------<<<<<<--<<<--<<<<<<<<<<_______>>>>>>>>>>>>>------>>>>>>::::::
#=GC RF                    AAUCauUUCuaCaaAAucauuuGUUUaaaugaCcuuGugGGGauGCaAAAUaAAAaCUaaaaGauuaUCCaGGuCGuuauagaUCaUuAUuuuauagCGauGGUUCCAAgauCuuACAAuU
//
# STOCKHOLM 1.0

#=GF AC   RF02311
#=GF ID   TtnuHACA3
#=GF DE   Tetrahymena snoRNA TtnuHACA3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   177.40
#=GF NC   41.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909326.1/1-152 AGGAUGUUGUCAUCAUUAAUACAAUUUAUUAAUAGGAUAGCUAUACAAAUAGUAGCAACAUCUAGAGCAUCUUAGCUUAAGUAUAUGUGUCUGUGAUUAUAUGAUUGAAAACAACUCUUUUUAGCUCUACUUUGACACUCAGUUGCAUAAUA
JF909327.1/1-152 AGGAUGUUGUCACUAUUAAUUCAAUUUAUUAAUAGGAUAGCUAUACAAAUAGUAGCAACAUCUAGAGCAUCUUUGCUUAAGUAUAUCUAUUUGCGAUUAUAUGAUUUAAAAUAACUGUUUUUAGCUCUAAUUUGACGCUCAGUUGCAUAAUA
#=GC SS_cons     :::::<<<<<<---<<<<<<<_____>>>>>>>-->>>>>>-------------(((((,,<<-<<<<______>>>>->>,,,,,<<<<<-----------<<<<<<<<<______>>>>>>>->>------>>>>>,,,)))))::::::
#=GC RF          AGGAUGuuguCAuuauuaauaCAAUUuauuaauAGGauagCUAUACAAAUAGUAGCaaCAUCuAgaGCAUCUUaGCuuAaGUAUAUgugucUGuGAUUAUAUGauugaaaauAACUguuuucagCuCUAaUUUgacacUCAGuuGCAUAAUA
//
# STOCKHOLM 1.0

#=GF AC   RF02312
#=GF ID   TtnuHACA5
#=GF DE   Tetrahymena snoRNA TtnuHACA5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   150.70
#=GF NC   37.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909328.1/1-132             UGAGCACCUAUGGUUUGAUUACUAGAUUCUAAUAUGACUAUGUAAUCCAUGCAGGAUGCUUAAAUUGAAUUUUGGUUAAACGGGAGUAUUAAAUUCAUUUUAAUAAACCUUCUUUUCCAACCAAAGACAUUU
AFXF01000020.1/128557-128427 UGAGCACCUAUGGUUUGAUUACUAGAUUCUUA-AUGACUAUGUAAUCCAUGCAGGAUGCUUAAAUUGAAUUUUGGUUUAACGGGAGUAUUAAAUAUAUUUUAAUAAACCUUCUUUUCCAACCAAAUACAUAU
#=GC SS_cons                 <<<<<<<<<---<<--<<<<<<<<<--<<______>>>>>->>>>>>--->>>>>->>>>>>-------<<<<<<<<-<<-<<<<<<<<<<<<_____>>>>>>>--->>>>>->>-->>>>>>>>::::::
#=GC RF                      ugaGCaCCuAUGGcUUGauuaCuaGAUuCUaAuAUGaCuaUGuaauCCAUgCaGGAuGCucaAAUUGAAcuuuGGuuaaaCgGgaGuauuaaaUauAUuuuaauaAACCucCcUuuCCaaCCaaagACAUaU
//
# STOCKHOLM 1.0

#=GF AC   RF02313
#=GF ID   TtnuHACA6
#=GF DE   Tetrahymena snoRNA TtnuHACA6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   150.20
#=GF NC   45.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909329.1/1-130             CCAUGCAUCUUUUGCGACAGACAACGUUUAUAUAUUAAACAAA-UGUCUUACUAUAGAUGCUAUAGUAAAUAUCUCUAUCCGUAUUGAACCACAAAUCAAUAGAAGGUUUAAUUUAUUUGAGAUGAAAUCU
AFXF01000010.1/272708-272578 CCUUGCAUCUUUUGCGACAGACUAUGUUUAUCUAUUAAGCAAAUAGUCUUACUAAUGAUGCUAUAGUAAAUAUCUCUAUCCGUAUCGGACCACUAAUAAAUAGAUGGUUUGAUUUAUUUGAGAUGAAAUCU
#=GC SS_cons                 :::<<<<_____>>>>,,<<<<<--<<<<<_____>>>>>---->>>>><<<<<<<<___>>>>>>>>--<<<<<<-------<<<<<<<<______________>>>>>>>>------>>>>>>::::::
#=GC RF                      CCauGCaUCUUUuGCgACaGaCuAuGuuuaUaUAUuaaaCAAAuaGuCuuaCuauaGAUGCuauaGuaAAuauCuCUAUCCGUaucgaaCCACaAAUaAAUAGAaGGuuugauUUAUUUGaGaugAAAUCU
//
# STOCKHOLM 1.0

#=GF AC   RF02314
#=GF ID   TtnuHACA7
#=GF DE   Tetrahymena snoRNA TtnuHACA7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   129.70
#=GF NC   32.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AAGF03001292.1/36463-36591 CAAAGUAACUUAGGUUGAGGUUGAGCUUGCUCCCUCGCCCAAGAGUUAGCCAAUCUAUAUUCCUGCGCCCUGAACAUAACGGACCUAAUGGACCUGUUGGUCUUGGGCUAAACCAUA-GGAAGGACAUCA
AEDN01000872.1/37808-37931 AAAAGUAU--UGGUUUGAGGUUGAGCUUGCUCC----CUCACUAAUAUACCAUACUAUAUUCCUACGCCUGGAUCAUAUAGGACCUCAUGGACCUGUUGGUUUCAGGCCAAACCAUAGGAAAGGACAAAC
#=GC SS_cons               ::::::::((((((((,,<<<<<<-<<<<__________>>>>-->>>>>>,,,,,,,,,,,,,,,<<<<---<<-<<<<<<-<<____>>-->>>>>>>>--->>>>,,))))-)).))::::::::::
#=GC RF                    aAAAGUAaccuaGguuGAGGuugaGcuuGCUCCcUcGCuCaagAaucaaCCAauCUAUAUUCCUaCGCCcuGAaCAuaacgGACCUaAUGGACCuguugGuuUugGGCuAaacCAua.ggAAGGACAuaa
//
# STOCKHOLM 1.0

#=GF AC   RF02315
#=GF ID   TtnuHACA8
#=GF DE   Tetrahymena snoRNA TtnuHACA8
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   50.00
#=GF TC   63.10
#=GF NC   36.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


JF909330.1/1-130             GGCAGUUAUGUGUACUUGCACUGAU-A-UUGUGAUUUGUAAGAUUACGGAAACUGCCAAAAACAAAUUAGAUUAUAUAAAGAAAUGUCUUAUUCUAGUUAAUCUGUUUUGGACUCUUUGUAUACUCAUAUUU
AFXY01000417.1/558034-558164 GGCAGUUAUGUGUACUCAUUUUGAUCA-AUGUGAUUUAUGAGAUUACGGAAACUGCCAAAAACAAAUUAGAUUAUAUAAAGAAAUGUCUUAUACUAGUUAAUCUGUUUUGGACUCUUUGUAUACUCACAUUU
AFXF01000112.1/364891-364761 GGCAGUUAUGUGUACUCAUUUUGAU-CUCUGUGAUUUAUGAGAUUACGGAAAUUGCCAACAAUAAAUUAGAUUAUAUAAAGAAAUGUCUUAUCUUAGUUCAUCUAAUUAGGGCUCUUUGUAUACUCACAUCA
#=GC SS_cons                 (((((((,,<<<<____>>>>,,,,.,.<<<<<<<<_____>>>>>>>>,)))))))------------<<-<<<<<<<<<<---<<<<-----<<<_____>>>---->>>>>>>>>>>>>>->>::::::
#=GC RF                      GGCaguuAUguguACUcacacUGAU.a.cuGugauuUaUgAgauuaCggAaacuGCCAAaAAcAAAUUAGaUuauauaaaGaAAUGuCuUAUuccaGUUaAUCuguUUugGaCuCuuuguauaCuCAcAUuu
//
# STOCKHOLM 1.0

#=GF AC   RF02316
#=GF ID   TtnuHACA9
#=GF DE   Tetrahymena snoRNA TtnuHACA9
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   127.30
#=GF NC   47.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


X66431.1/1-135               NAGGAUCUAUCGAAGCUGGUACAAUGAU--UUUAUCAUUGUAGAAGUCAAAACAAUCCAAAAGAAACCGUCAAAUAGUGAUUCGGGUGGCACUUUUAUU-UUCCAUA-AAUAAUC-GUGUCUA-UCGAAUUUCUAACACUU
AFXF01000011.1/357419-357290 AAGGAUCUAUCGAAGCUUGUGCAUUGAU--AUUAUCUUUGCAGAAGUCAAAACAAUCCAAAAGAAAAU-----UCAGUGAUUCGGGUGGCACUUUUAUU-UUUCAUA-AAUAAUC-GUGUCUA-UCGAAUCUCUUACACUC
AEDN01001712.1/46408-46546   AAGGAUUUAUCGAAGCUUGUGUAGUGUCAACAAAUCACUACAGAAGUCAAAUCAAUCCAAAAUUAAAUUUAAA--UGAUUUUCGGGUGGCAUGUUUAUUCUUUUAAAUAAUAAUCAAUGUCUAAUCGAAUAUCAAACAAAC
#=GC SS_cons                 ::<<<<--------<<<--<<<<<<<<<..___>>>>>>>>>-->>>------->>>>----------------<<<-<<<<<<<--<<<<<--<<<<<.<_____>.>>>>>--.>>>>>--.>>>>>>>->>>::::::
#=GC RF                      aAGGaucUAUCGAAgCuuGugcaguGau..uuuauCacugcaGAaGuCAAAaCAauCCAAAAgaAAauuUaAAacaGugauuCGgGUGgCacuUuuauu.uUucAua.aauaaUC.guGuCUA.uCGaaucUCugACAcuc
//
# STOCKHOLM 1.0

#=GF AC   RF02317
#=GF ID   TtnuHACA10
#=GF DE   Tetrahymena snoRNA TtnuHACA10
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   126.30
#=GF NC   42.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


EF503653.1/1-104           CUUUAUAGUACCUAUUCCAGUCCGAUUGCGACAUUAAAUUUAACUAUAUUUCUGCAUUUAAGAUGCUAUAAUAAAUUAUGGCAUCUUGUGGAAAGAUAGUACAU
AFXY01000467.1/5487-5384   CUUUAUAGUACCUAUUCCAGUCAGAUUGCGAGAUUAAACUUCACUAUAAUUCUGCAUCUAAGAUGCUAUAAUGUAUUAUGGCAUCUUGUGGAACGAUAGUACAA
AFXF01000011.1/41222-41119 CUUUAUAGUACCUAUUCCAGUCCGAUUGCGAGAUUAAAAUUAGCUAUAAUUCUGCAUAUAAGAUACCAAAAUCUAUUCUGGUAUCUUGUGGGGUGAUAGCACAA
#=GC SS_cons               :::::::::::::::::::<<<_______>>>----------<<<<<--<<<--<<----<<<<<<<<-<<____>>->>>>>>>>>>-->>>-->>>>>::::
#=GC RF                    CUUUAUAGUACCUAUUCCAguCcGAUUGCGacAUUAAAuUUagCuauAauuCUGCaUuUAaGaugCcauaaUauAuuaugGcauCuuGUGGaauGauaGcACAa
//
# STOCKHOLM 1.0

#=GF AC   RF02318
#=GF ID   TtnuHACA11a
#=GF DE   Tetrahymena snoRNA TtnuHACA11a
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   160.30
#=GF NC   48.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909331.1/1-141             AUCUUGUCAAAGGUUUUGCUGCCUUGUUAAUAGCUAUCCAUUAUUUAUUGACUAACUGUUAAAACCUAAAGAACCUGUGCUCCUCCACAUUUAGUAUCCUAACUAUGGGUAUCUUAAUACUAUCAGAGCACUUCAUUUUUA
AFXF01000514.1/142369-142509 AUAUUGUCAAAGGUUUUACUGCCUUGUUGAUAGCUUUACAUAAUUUAUUGACUAACUGUUAAAACCUAAAGAACCUGUGCUCCUCCACAUUUAGUAUCCUAACGAUGGGUAUCUUAAUACUAUCAGAGCACUUCAUUUUUG
#=GC SS_cons                 ::::::::::<<<<<<<<-------<<<<<<<<-<<_____>>->>>>>>>>------->>>>>>>>---<<<---<<<<<<--------<<<<<<<<<_______>>>>>>-->>>-------->>>>>>>>>:::::::
#=GC RF                      AUaUUGUCAAaGGuuuuaCUGCCUUGuuaauagCuuUaCAUaaUuuauugaCUAACUGUuaaaaCCuAAAGaaCCUGuGCuCCUCCACAUuuaguauCCUAACuAUGGguauCUuaaUACUAUCAGaGCaCuuCAUUUUUa
//
# STOCKHOLM 1.0

#=GF AC   RF02319
#=GF ID   TtnuHACA12
#=GF DE   Tetrahymena snoRNA TtnuHACA12
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   80.00
#=GF TC   89.50
#=GF NC   51.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.03 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909333.1/1-131             AACUAAAAAAAAUUAUUAAAAUUUAAAUUAGAUUUUACUUAUUGGAAUUUAAUUAAUUUUGGUAAAAAUAUAAUAAACCAUUUCUAGCUAUAUGAUUAUGCAAACCAUAAAGCUGCGAAGGGGUUUAAUUG
AFXF01000574.1/343563-343470 AAUGAUAAAAAUUUU-------------------AUUAUUUCAGC------------------AAAAAUAUAAUAAACCAUUUCUAGCGAUAUGAUUAUGUAAACCAUAAGGCUGCGAAGGGGUCUAAUUG
#=GC SS_cons                 ::::::::::::<<<<<<<<<<<--<<<<<<<<<-<<_____>>->>>>>>>>>>>>>>>>>>>>--------<<<<<<-<<<<<<<<--<<<<___________>>>>-->>>>->>>>->>>>>>::::
#=GC RF                      AAuuAaAAAAAauuaccaaaauuUAaauuagauuuuaaUUauuggaaucuaauuaauuuugguaaAAAUAUAAuagaCCAuuuCuaGCuAuauGAUUAUGuAAACCauaAaGCugCGaagGGGucuaAUUG
//
# STOCKHOLM 1.0

#=GF AC   RF02320
#=GF ID   TtnuHACA13
#=GF DE   Tetrahymena snoRNA TtnuHACA13
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   156.90
#=GF NC   45.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909334.1/1-134             UAAACCACAAUUACUUCAAUUCUGUUAAUUGCUCUAAAUCAAUUGAUAGAAAGUAAGAGUGGUAAAUUAAAAAUUGCCACCUAAGAAGAUAGAAUAAUUAAUUUACCUACCUUCAAACGAGGGAAUUGACAAUC
AFXF01001532.1/135585-135718 AUAACCAUAAUUACUUCUAUUCUGUUAAUUGCUCUUAAUCAAUUGAUAGAAAGUAAAAGUGGAAGAAUAAAAAUUGCCACCUAAGAAGAUAGAAUAAUUUAUUUACCUACCUUCAAACGAGGGAAUUGACAAUC
#=GC SS_cons                 :::::::(((((-((((,,<<<<<<<<<<<<________>>>>>>>>>>>>,,,,<<-<<<<<<<________>>>>>>>>>,,<<<<-<<<______________>>>->>>>,,,,))))-)))))::::::
#=GC RF                      aaAACCAcaauuACuuCaAuuCuguuaauuGCUCUaAAUCaauugauaGaaAGUAagAGuGGcagAaUAAAAAcugCCaCcuAAGaaGAuaGAAUAAUUaAUUUACCuaCCuuCAAACGagGGaauugACAAUC
//
# STOCKHOLM 1.0

#=GF AC   RF02321
#=GF ID   TtnuHACA14
#=GF DE   Tetrahymena snoRNA TtnuHACA14
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   159.40
#=GF NC   49.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


JF909335.1/1-133             CAAGCGAGAACUACUAAUAGUUUGUUCAGACUAGUUCUGUAUAAGCAAAACAGUUUUCGCAAAAACAGCCUGAGUUUCUUACUACCCAUUUAGCACAAAUAUUGCU-GAUGGUAAUUUCCGAAUUCAGACAUUA
AFXF01001355.1/514018-514150 UAAGCGAGAACUAUUCAUAGUUUGUUCAGACUAGUUCUGUAUGAGCAAAACAGUUUUCGCAAAAAUACCCUGAGUUUCUUACUACCCAUCUAGCACAAAUAUUGCU-GAUGGUAAUUUCCGAAUUCAGACAUCU
AFXY01000080.1/264156-264289 CAAGCGAAGACUACUCAUAGUUUGUUCAGACUAGUUCUGUAUAAGCAAAACAGUUUUCGCAAAAUCAGCCUGAGUUUCUUACUACCCAUUUAGCACUUAUAUUGCUGAAAGGUAAUUUCCGAAUUCAGACAUUA
#=GC SS_cons                 :::<<<<<<<<<-------<<<<<<-<<<<_____>>>>->>>>>>----->>>>>>>>>---------<<<<<<<<--------<<<<<-<<<<_______>>>>.>>>>>-------->>>>>>>>::::::
#=GC RF                      cAAGCGagaaCuAcUcAUAGuuuguUCaGaCUAGUuCuGUauaagCAAAACaGuucuCGCAAAAacAgCCuGaguuuCUUACUACCCaucUaGCaCaaAUAUuGCu.gauGGUAAUUUCCgaauuCaGACAUua
//
# STOCKHOLM 1.0

#=GF AC   RF02322
#=GF ID   TtnuHACA15
#=GF DE   Tetrahymena snoRNA TtnuHACA15
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   148.00
#=GF NC   47.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503656.1/1-117           AGCCUGGACUGCAUAAUUCAUUUAUGCAUUCCAUUUUUCAAGUCCAAAAGAAAUCCACUCUUGUUUAGAGAUGAAACUUCUUCAUAGUUUUUUCUUCAGACGGAGAGCGAUACAUUU
AFXY01000709.1/48955-48839 AGCCUGGACUGUGUAAUUCAUUUAUGCAUUCCAUUUUUCAAGUCCGAAAGAAAUCCACUCUUGUUUAGAGAUGAAACUUCUUCAUAGUUUUUUCUUCAGACGGAGAGCGAUACAUUC
#=GC SS_cons               ::::<<<<-<<<<<<<_____>>>>>>>->>>>-------------------<<<--<<<<<<<<<--<<<-<<<<<<_______>>>>>>->>>-->>>>->>>>>->>>::::::
#=GC RF                    AGCCuGGaCuGcguaaUUCAUuuacgCaUuCCaUUUUUCAAGUCCaAAAGAAauCCACuCuuGuuuAGaGaUgaaaCuUCUUCAUaGuuuuUuCuUCagaCGgaGaGCGauACAUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02323
#=GF ID   TtnuHACA16
#=GF DE   Tetrahymena snoRNA TtnuHACA16
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   148.60
#=GF NC   38.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503658.1/1-117             CAACGAUAUCACAUAUAUAGUGUAUUGUUAACAAAUUUAUGCAGACAUUGAAUAUUGAGAGUCUACACAUGUUCCUCCUCUUAAUGAAGGAACGUGCAAAAAAAUCAAUUACAAUUU
AFXF01001255.1/360816-360932 CAACGGUAUCACAUACAUAGUGUAUUGUUAACAAAUUUAUGCAGACAUUGAAUAUUGAGAGUCUACACAUGUUCUUUCUCUUCAUGAAAGAACGUGCAAAAAAAUCAAUUACAAUUU
#=GC SS_cons                 :<<<<<<<-<<<_______>>>>>>>>>>-----------------<<<<---<<<<<---------<<<<<<<<<--<<_____>>>>>>>>>>>-------->>>>>-->>>>::
#=GC RF                      CaaCgguaUCaCAUAuAUAGuGuacuGuuAACAAAUUUAUGCAGACauuGAAUauuGaGAGUCUACACauGuuCcuuCuCUUaAUGaagGaaCguGCAAAAAAAuCaauUACaauUU
//
# STOCKHOLM 1.0

#=GF AC   RF02324
#=GF ID   TtnuHACA17
#=GF DE   Tetrahymena snoRNA TtnuHACA17
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   127.40
#=GF NC   41.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


JF909336.1/1-118           CAACUACAAAAUUUUCUUAUCAAAUAAUUUUGAUCAAAGCCAGUGGAUAAAGCAUCUCAGAUGGUUUUUUAUUCUUUUCUCUAUAUGAGAUUGCGAAUUAUACGCCCAUCUUACAACU
AFXY01000049.1/70570-70687 AAAUUCCAAAAUUUUUAUUUUUAAUAAUUUUGAUGAAAGUCAAUGGAUAAAGCAUCUCAGAUGGUUUUUUAUUCUUUUCUCUGAAUGAGAUUUCGAAUUAUACGCCCAUCUUACAACA
AFXF01001075.1/49144-49258 AUACCA--AAAUUUUAAUUUUAAAUAAUUUUGA-CAUAGCCUGUGGAUAAAGCAUCUCAGAUGGUUUUUUAUUCUUUUCUCUUAAUGAGAUUUUGAAUUAUACGCCCAUCUCACAUUU
#=GC SS_cons               :::<<<<----<<<----<<<<<<____>>>>>>->>>---->>>>------------<<<<<<------<<<<---<<<<_____>>>>---->>>>------->>>>>>:::::::
#=GC RF                    aaAccacAAAAuuuUuaUaucaaaUAAUuuugaucaaaGcCaguggAUAAAGCAUCUCaGauGGUUUUUUauuCUUUuCuCUaaAUGaGaUUucGaauUAUACGCCCauCuuACAacu
//
# STOCKHOLM 1.0

#=GF AC   RF02325
#=GF ID   TtnuHACA18
#=GF DE   Tetrahymena snoRNA TtnuHACA18
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   143.90
#=GF NC   43.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


JF909337.1/1-130           UCCUAGUAUCUCCCUCUGAUUCAUUCAUGUAUUAGCGGGUCGUAAAGGUUGCUAAAUAAAUAUGAAUUCUUUUUUUAUUUAAUUAUCAAACAAUAAAUUUGUUUAAUAAUUACUUAAGAAUGCUACAAUU
AFXY01001580.1/24723-24594 UCCUAGUAUCUCCCUCUAAUUCAUUCAUGUCUUAGCGGGUCGUAAAGGUUGCUAAAUAAAUUUGAAUUCUUUUUUUAAAUAAUUACUUUACACUAAAUUUGUAUGGUAAAUAUUUAAGAAUUCUACAAUU
AFXF01000934.1/47183-47055 UCCUCGUAUCUCCUUCUGAUUCAUUCAUGUCUUAGCGGGUCGUAAAGGAUGCUAAAUAAAUAUGUAUUCU-UUUUUCAUUAAUUGUUAAACAAUAAAUUUGAUUAUCAAUUAAUAAAGAAUGCUACAUUA
#=GC SS_cons               :<<<--<<<--<<<-<<<<<-<<____>>->>>>>->>>-->>>->>>-----------------------<<<<<---<<<<<<<-<<<<<<_____>>>>>>->>>>>>>--->>>>>::::::::::
#=GC RF                    UCCuaGuauCUCCcUCugacUCaUUCAuGUgucaGCgGGUCguaAaGGuUGCUAAAUAAAUaUGaAUUCUUuuuuuaauuaauugcuaaaCaaUAAAUuuGuuuagcaauuauUuaagaaUgCUACAaUu
//
# STOCKHOLM 1.0

#=GF AC   RF02326
#=GF ID   TtnuHACA19
#=GF DE   Tetrahymena snoRNA TtnuHACA19
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   154.90
#=GF NC   38.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503651.1/1-121           ACUAUCCUUGCUCAUUCAGGAACUAGCUGAAUGGUCACCAGAAUUGUUUGCGAAAUUACCUGAAUUUUCUUACCAUCACAAGCACUUCGAUUACUUGUGGUAAUUGCAUGUUCAGACAUUU
AFXF01001656.1/36761-36881 ACUAUCCUUGCUCAUUCAGGAAUUAGCUGAGUGAUCACCAGAAUUGUUUGCGAAAUUAGCUGAAUUUUCUUACCAUCACAAGCACUACGAUUACUUGUGGUAAUUGCAUGUUCAGACAUUU
#=GC SS_cons               :::::::((((,<<<<<<<_______>>>>>>>,<<____>>,,,,,,,))))------<<<<<<---------<<<<<<<<___________>>>>>>>>-------->>>>>>::::::
#=GC RF                    ACUAUCCuuGCUCauuCaGGAAuUAGCuGaauGauCACCAGaAUUGUUUGCgaAAUUAgCuGaauUUUCUUACCauCaCaaGCACUaCGAUUACuuGuGguAAUUGCAUguuCaGACAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02327
#=GF ID   TtnuHACA20
#=GF DE   Tetrahymena snoRNA TtnuHACA20
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   143.80
#=GF NC   39.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503652.1/1-123           AAAGCAUGGAUAAUUGGAUUUCAGCAAAUAUUCGUGAAGAUUUCUGCAGAAAUUGAAGUAAAUAGCAGUUUAUGAAUUAAACGACAUUCAUGAUGUUUAAAUCACUGGCCUGCGCUUACAUUU
AFXF01001718.1/14690-14568 AAAGCAUGGAUAAUUGGAUUUCAGCAAAUAUUCGUGAAGAUUUCUGCAAAAAUUGAAGUAAAUAGCAGUUUAUGAGCUAAACGACGUUAAUGAUGUUUAUAUCACUGGCCUGCGCUUACAUCU
#=GC SS_cons               ::::<<<<<<<<-<<<________>>>->>>>>>>>,,<<<<<<____>>>>>>---<<<<---<<<<--<<<<<--<<<<<<-<<____>>->>>>>>-->>>->>-->>>>-->>>>::::
#=GC RF                    AAAGCacGgauaAuuGGAUUUCAGCaaAuaucCguGAAgauuucUGCAgaaaucGAAGuaaAUAGCaGUUcauGaauuaaaCgACgUUaAcGAcGuuuaaAuCaCugGCCuGCGCuuaCAUuU
//
# STOCKHOLM 1.0

#=GF AC   RF02328
#=GF ID   TtnuHACA21
#=GF DE   Tetrahymena snoRNA TtnuHACA21
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   164.70
#=GF NC   43.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


X66430.1/1-130             NUUCCCUUAAGUGUUGCCGCUAUGACUUAAAUAGUUGAAGUGGAGUCAAACGAGGGAUAAAGAGAAAUGGGGUAUUCAAGAUAUACUCUCCUAAUAUCAUGGAGAACUAUAUAGCUAUACCUGAAUAAUU
AFXF01000952.1/14797-14926 AUUCCCUUUAGUGUUGCCGCUAUGACAUAAAUAGUUGAAGUGGAGUCAAACAAGGGAUAAAGAGAAAUGGGGUAUUCAAGAUAUACUCUCCUAAUACUAUGGAGAACUAUAUAGCUAUACCUGAAUAUUU
#=GC SS_cons               ::<<<<<<---<<---<<<<<-<<<<<_____>>>>>->>>>>--->>--->>>>>>------------<<<<<<-----<<<<<-<<<<<_________>>>>>-->>>>>---->>>>>>::::::::
#=GC RF                    aUuCCCuuaAGuGUUGCCgCuAugaCuUAAAUaGuugAaGuGGAGUCaAACaaGGGaUAAAGAGAAAUGgGGuauUCAAGauauaCuCuCCUAAUAuuAUGGaGaACuauauAGCUauaCCuGAAUAaUU
//
# STOCKHOLM 1.0

#=GF AC   RF02329
#=GF ID   TtnuHACA22
#=GF DE   Tetrahymena snoRNA TtnuHACA22
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   90.00
#=GF TC   115.10
#=GF NC   40.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503654.1/1-103             UUCAUUUAGAAUUAGGUUUGAUUCUGUUGAUCUUAAAAUAAAAGGUUAAUUAGUUGGUCGGUUAGCUUUAAUGCUGAUUUGACCUAGUUAGUUUUCCAACAUG
AFXF01000514.1/263351-263253 UUAAUUUAGAAUU----AGGAUGCUGUUGACCUUAAAAUAAAAGGUUAAUUAGUUGGUCGGUUAGCCUUAAUGCUGAUUUGACCUAGUUAGUUUUCCAACAUG
#=GC SS_cons                 :<<<--<<<<<<<<____>>>>>>>>->>>-------------<<--<<<<<--<<<<<<<<<<<<______>>>>>->>>>>>->-->>>>>-->>::::::
#=GC RF                      UucaUUuaGaauuagguuugauuCugUugauCUUAAAAUAAAAGGUUaauuaGUuGGuCgguuaGCuUUAAUGCugaUuuGaCCUaGUuaguuUUCCAACAUG
//
# STOCKHOLM 1.0

#=GF AC   RF02330
#=GF ID   TtnuHACA23
#=GF DE   Tetrahymena snoRNA TtnuHACA23
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   130.00
#=GF NC   41.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


JF909338.1/1-133           UGCUUUGUUCGCUUAGAUAAA-AUAAGU-UAUUAUCUUAUUUUAACUCCUAAUAAUAAAGCUAAAUAAAACUUAUUGCUUAUCGAACAUUAAAUCACACUUCAUUGUGGUUUAAUUUUGCAAUUCUCAAACAUAA
AEDN01000401.1/54714-54582 AGCUUUGUUCGCUUCGAUAGUUUCAAGUAUAUUAUCUUGAGUUAUCACCUAA-AACAAAGCAAAAUUAAAAUA-AUGUUUUUCGAACAUCAAGUUACACAAAAUUGUAAUUUGAUUUUGCAAAAUUCAUACAAAC
#=GC SS_cons               :<<<<<<<<------<-<<<<-<<<<<________>>>>>>>>>->------->>>>>>>>------------<<<<<-----<<<-<<<<<<<<<<<______>>>>>>>>>>>>>>>>>>>::::::::::::
#=GC RF                    aGCuuuguuCGCUUaGAuaacUucaaGUAUAUUAUCuugaguuaaCaCCUAAUaacaaaGCaAAAUaAAAaUaauuGcUUaUCgaaCaucaaaucaCaCaaaAUuGugauuugauuuugCaauauUCAaACAaAa
//
# STOCKHOLM 1.0

#=GF AC   RF02331
#=GF ID   TtnuHACA24
#=GF DE   Tetrahymena snoRNA TtnuHACA24
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   154.10
#=GF NC   40.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


X66432.1/1-127               AGUCUGUAUAUCCCGAGUGCAAAGUAAUUCAUGUCUUUGUACCGUUUACAAUAUAGAUAAAGAAGAGUGAAGAACCUUAAUUCUCUUACUGUCUUCAUUGGUAAGCGAAUCCAUUCUUCCAACAACU
AFXF01000573.1/209997-210123 AGUCUAUAUAUCCCGAGUGCAUAGAAAUACAUAACUUUGUACCGUUUACAAUAUAGAUAAAGAAGAGCGAAGAACCUUAAUUCUCUUACUGUCUUCAUUGGUAAGCGAAUCCAUUCUUCCAACAGCA
#=GC SS_cons                 :<<<<<<<<----<<-<<<<<<<<__________>>>>>>>>>>------>>>>>>>>---<<<<<<<<----------<<<<-<<<<<<<_______>>>>>>>->>>>->>>>>>>>::::::::
#=GC RF                      AguCuguauAUCCCGAGugCaaaGaAAUaCAUaaCuuuGuaCCGUUUACAauacaGauAAAGaaGagcGAAGAACCUUAauuCUCuuaCugUCUUCAUugGuaaGCGaauCCguuCuuCCAACAaCa
//
# STOCKHOLM 1.0

#=GF AC   RF02332
#=GF ID   TtnuHACA25
#=GF DE   Tetrahymena snoRNA TtnuHACA25
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   100.00
#=GF TC   135.60
#=GF NC   44.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503655.1/1-111         AGAAUUUCGACAAUAAUAUUGAUAUUCUCAUGAAGUAGGCAAAGAAUAAAAUCACUAGCAAGCUGGUAUAGUAAUUUCAUAUUACUACGCUUGAUGAGCAGUGAGAUACUU
AFXY01002219.1/5941-5831 AGAAUUUCGACAAUAAUAUUGAUAUUCUCAUGAAGAAGGCAAAGAAUAAAUUCACUAGCAAGCUGGUAUAGUAAUUUCAUAUUACUACGCUUGAUGAGCAGUGAAAUACUU
#=GC SS_cons             [[-[[[[[,,<<<<___>>>>,,,,,(((((-((((,,,,,,,,,,,,,,,,,<<<<<____>>>>>,<<<<<<<_____>>>>>>>,))))-))))),,,,]]]]]-]]:
#=GC RF                  aGAaucuCGACaauAAUauuGAUAUUCuCauGaaGcAGGCAAAGAAUAAAaUCaCcaGCAAGCugGuAuaGuaauUUCAUauuaCuaCgCuuGauGaGCAGUGagauACuU
//
# STOCKHOLM 1.0

#=GF AC   RF02333
#=GF ID   TtnuHACA27
#=GF DE   Tetrahymena snoRNA TtnuHACA27
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   80.00
#=GF TC   106.00
#=GF NC   43.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


EF503659.1/1-86              AACUUAUGUAUGGACAAAUAAAUUACCAUUUCAAUAAUCCCUAUAAUAUUUUUAUAUAAUUUAGGAUUCGCUAAAUGGAAACAAAA
AFXF01001075.1/173331-173247 AACUUAUGUAUGGAGAAAGAAAUUACCAUUUCA-UAAUCCCUAUAAUAUUUUGAUAUAAUUUAGGAUUCGCUAAAUGGAUACAAAA
#=GC SS_cons                 :::::::::::::::::::::::::<<<<<<----<<<<<--<<-<<<<____>>>>->>--->>>>>---->>>>>>::::::::
#=GC RF                      AACUUAUGUAUGGAgAAAuAAAUUACCauuuCAAUaauCCCUauAauauUUUuauauAauUUAGGauuCGCUaaauGGAaACAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02334
#=GF ID   TtnuHACA28
#=GF DE   Tetrahymena snoRNA TtnuHACA28
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   130.00
#=GF TC   170.60
#=GF NC   55.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   21967850
#=GF RT   Experimental identification and analysis of macronuclear non-coding RNAs
#=GF RT   from the ciliate Tetrahymena thermophila.
#=GF RA   Andersen KL, Nielsen H
#=GF RL   Nucleic Acids Res. 2012;40:1267-1281.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


X66429.1/1-134               NACUUAUGACAUGCCAUGAAGGUCUUGUACUUAAUGAUACAUUCCUUCGCCAGCUCAUAAUAAGAAAAAACAGAAGGAUCUCUAUAGGAAGCAAAUCGGAAAACAAUGAUGAGUUUGCGCCAAAUGAAAUCUAC
AFXF01000019.1/160920-160787 AACUUAUGACAUGCCAUGAAGGUCUAGUACUUAAUGAUACAUUCCUUCGCCAGCUCAUAAUAAGAAAAAACAGAAGGAUCUCUAUAGGAAGCAAAUCGGAAUUUGAUGAUGAGUUUGCGCCAAUUGAAAUCUAC
#=GC SS_cons                 ::<<<<<-----<<--<<<<<<---<<<<________>>>>-->>>>>>--->>----->>>>>-----------<<<<-<<----<<--<<<<<<<<___________>>>->>>>>->>---->>->>>>::
#=GC RF                      aACuuauGACAUGCCAuGaaGGUCUuGuaCUUAAUGAuaCaUUCCuuCgCCAGCUCAUAauaaGAAAAAACAGAAgGauCuCUAUAGGAAGCaaauCgGAAaauaAUGAuGaGuuuGCGCCAAaUGaAauCuAC
//
# STOCKHOLM 1.0

#=GF AC   RF02335
#=GF ID   GlsR2_miR4
#=GF DE   Giardia snoRNA GlsR2/miRNA miR4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22028939
#=GF SS   Predicted; PMID:22028939
#=GF GA   90.00
#=GF TC   120.30
#=GF NC   33.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   22028939
#=GF RT   Gene regulation in Giardia lambia involves a putative microRNA derived
#=GF RT   from a small nucleolar RNA.
#=GF RA   Li W, Saraiya AA, Wang CC
#=GF RL   PLoS Negl Trop Dis. 2011;5:e1338.
#=GF WK   Small_nucleolar_RNA-derived_microRNA
#=GF SQ   3


AY820283.1/1-104           UGUAGCGAACCCACGCGCAAGCGUUGCUACGAGGCGAUGGAGACAAAAGCAGUUACGUUCGCAACUCUCUGAGGGUUCCUGAUGCUUCCUUGGAUGUCCGAGCC--
L27110.1/23-125            UGUAGCGAACCCACGCGCAAGCGUUGCUACGAGGCGAUGGAGACAAAAGCAGUUACGUUCGCAACUCUCUGAGGGUUCCU--UGCUUCC-UGGAUGUCCGAGCCUU
AACB02000005.1/19712-19607 UGUAGCGAACCCACGCGCAAGCGUUGCUACGAGGCGAUGGAGACAAAAGCAGUUACGUUCGCAACUCUCUGAGGGUUCCUGAUGCUUCCUUGGAUGUCCGAGCCUU
#=GC SS_cons               :<<<<<<-----<<<<____>>>>>>>>>>---<<--<<<<--<<<<<<<<-<<<-------<<<<<_____>>>>>-->>>>>>>>-->>>---->>>>->>:::
#=GC RF                    UGuaGCgAACCCaCGCGCAAGCGucGCuaCGAGGCGAcGGaGACaaaaGCaGucaCGUUCGCaaCcCUCUGAGgGuuCCugauGCuuCCuuGGAUGuCCgAGCCUU
//
# STOCKHOLM 1.0

#=GF AC   RF02336
#=GF ID   GlsR1_miR6
#=GF DE   Giardia snoRNA GlsR1/miRNA miR6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22568619
#=GF SS   Predicted; PMID:22568619
#=GF GA   70.00
#=GF TC   106.90
#=GF NC   33.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   22568619
#=GF RT   The profile of snoRNA-derived microRNAs that regulate expression of
#=GF RT   variant surface proteins in Giardia lamblia.
#=GF RA   Li W, Saraiya AA, Wang CC
#=GF RL   Cell Microbiol. 2012;0:0-0.
#=GF WK   Small_nucleolar_RNA-derived_microRNA
#=GF SQ   2


AY820282.1/1-85        GUCCACUGGCCUCUCCUGAGGCAGAUGAUGACUUUGCGACGGGCGGACGGAGGGACGCGUGACGAAGUUUGUCGUAUUCUGAAUU
ACGJ01002434.1/552-636 AUCCACCAGUCUCUCUGGAGACAGAUGAUGACUUUGCGACGGGCGGACGGAGGGACACGUGACGAAUUCUGUCGUAUUCUGAAUU
#=GC SS_cons           ::::::::::::::::::::::::<<<<<<<<<<<<---<<<<<<--<_____>->>>>>>->>>>>->>>>>>>::::::::::
#=GC RF                aUCCACuaGuCUCUCuuGAGaCAGauGaugacuuuGCGACggGcGGACGGAGGGACgCguGACgaagUuuguCguAUUCUGAAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02337
#=GF ID   GlsR8_miR10
#=GF DE   Giardia snoRNA GlsR8/miRNA miR10
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22568619
#=GF SS   Predicted; PMID:22568619
#=GF GA   70.00
#=GF TC   103.30
#=GF NC   33.20
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   22568619
#=GF RT   The profile of snoRNA-derived microRNAs that regulate expression of
#=GF RT   variant surface proteins in Giardia lamblia.
#=GF RA   Li W, Saraiya AA, Wang CC
#=GF RL   Cell Microbiol. 2012;0:0-0.
#=GF WK   Small_nucleolar_RNA-derived_microRNA
#=GF SQ   3


AY820289.1/1-70              CGUAGAUGAAGAGAGAUAAAUCAGCUACCGCUGAGCCCAACGUGAGGAAGAAACCGCCUUUCGUCUGACC
AACB02000018.1/139734-139803 CGUAGAUGAAGAGAGAUAAAUCAGCUACCGCUGAGCCCAACGUGAGGAAGAAACCGCCUUUCGUCUGACC
ACGJ01002439.1/4478-4547     CUUAGAUGAAGAGAGAUAAAUCAGCUACCGCUGAGCCCAACGUGAGGAAGAAACCGCCUUUCGUCUGAUC
#=GC SS_cons                 :::<<<<<<<<<<<<-<---<<<<-<---<<___>>-->->->>>------->->>>>>>>>>>>>::::
#=GC RF                      CgUAGAuGAAgaGaGAUAAAUCAGCUACCGCUGAGCCCAACGUGAGGAAGAAACCgCcuUUCgUCUGAcC
//
# STOCKHOLM 1.0

#=GF AC   RF02338
#=GF ID   GlsR16_miR3
#=GF DE   Giardia snoRNA GlsR16//miRNA miR3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:19043559
#=GF SS   Predicted; PMID:19043559
#=GF GA   70.00
#=GF TC   103.60
#=GF NC   32.40
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19043559
#=GF RT   snoRNA, a novel precursor of microRNA in Giardia lamblia.
#=GF RA   Saraiya AA, Wang CC
#=GF RL   PLoS Pathog. 2008;4:e1000224.
#=GF WK   Small_nucleolar_RNA-derived_microRNA
#=GF SQ   3


AY820297.1/1-77            UAAAACUAUGAUGAGGUUAGCGAUCCCAAGCGGGGCCUGGCCCUGCGUUGCAGACAACGCAUCACCGCUCUGACCUU
ACVC01000187.1/13496-13420 AAAAAUUAUGAUGAGGUUAGCGAUCCCAAGCAGGGCCUAGCCCUGCGUUGCAGACAACGCAUCACCGCUCUGACCUU
ACGJ01002367.1/360-284     UAAAAUUAUGAUGAGAUUAGCGAUCCCAAGCGGGGCCUUGCCCCGCUCUGCAGACAACGCAUCACCGCUCUGACCUU
#=GC SS_cons               ::::::::<<<<<--<<<-<<<<<-----<<<<<<<___>>>>>>>>>>>>->>>---->>>>>:::::::::::::
#=GC RF                    uAAAAuUAuGauGAGGuuAGCgacCCCAAGCgGGGCCUaGCCCcGCguuGCAgaCAACGCauCaCCGCUCUGACCUU
//
# STOCKHOLM 1.0

#=GF AC   RF02339
#=GF ID   GlsR17_miR2
#=GF DE   Giardia snoRNA GlsR17/miRNA miR2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:19043559
#=GF SS   Predicted; PMID:19043559
#=GF GA   40.00
#=GF TC   169.80
#=GF NC   33.00
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF RN   [1]
#=GF RM   19043559
#=GF RT   snoRNA, a novel precursor of microRNA in Giardia lamblia.
#=GF RA   Saraiya AA, Wang CC
#=GF RL   PLoS Pathog. 2008;4:e1000224.
#=GF WK   Small_nucleolar_RNA-derived_microRNA
#=GF SQ   4


AACB02000045.1/26253-26397 GUUUCUAG-AC--CUCCUGGGAUAAUGCGCUUCUUUGAGCCGCGGGUUUACUCGUGGUGAGGAUCCGGGGCACUGAGCAAUCCCCAGGACACAGGCGGAGCGGAAGGCACGGCUGCGCCACGCAGCCUAAUCACCGCCCCUAUAGUCC
ACGJ01001410.1/76610-76755 GUUUCUAGCAC--CUCCUGAGUUAAUGCGCUUCUUUGAGCCGCGGGUUUACUCGUGGUGAGGAUCCGGGGCACCGAGCAAUCCUCAGGACACAGACGGAGCGGAAGGCACGGUUGUGUGACGCAACCUAAUCACCGCCCCGACAGUCC
L27108.1/40-185            AGUCCUAG-ACGCGUCCUGGGAUAAUGCGCUUCUUUGAGCCGCGCGUUUACUCGUGGUGAGGAUCCGGGGCACUGAGCAAUCCCCAGGACACAGGCGGAGCGGAAGGCAACG-UGCGCCACGCAGCCUAAUCACCGCCCCUAUAGUCC
AY820298.1/1-144           GUUUCUAG-AC--CUCCUGGGAUAAUGCGCUUCUUUGAGCCGCGGGUUUACUCGUGGUGAGGAUCCGGGGCACUGAGCAAUCCCCAGGACACAGGCGGAGCGGAAGGCACGGCUGCGCCACGCAGCCUAAUCACCGCCCCUAUAGUC-
#=GC SS_cons               ::::::::.::..:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<---<<-<<-<<<<--<<---<<<<<<<___>>>>>>>--->>->>>>>>>>--->>>>
#=GC RF                    guUuCUAG.AC..cUCCUGgGaUAAUGCGCUUCUUUGAGCCGCGgGUUUACUCGUGGUGAGGAUCCGGGGCACuGAGCAAUCCcCAGGaCACAgGCGGAGCGGAAGgCAcgGcuGcGccACgCagCcUAAuCACCGCCCCcAuAGuCC
//
# STOCKHOLM 1.0

#=GF AC   RF02340
#=GF ID   DENV_SLA
#=GF DE   Dengue virus SLA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:19004935
#=GF SS   Published; PMID:19004935
#=GF GA   34.00
#=GF TC   34.00
#=GF NC   33.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19004935
#=GF RT   Structural and functional studies of the promoter element for dengue virus
#=GF RT   RNA replication.
#=GF RA   Lodeiro MF, Filomatori CV, Gamarnik AV
#=GF RL   J Virol. 2009;83:993-1008.
#=GF RN   [2]
#=GF RM   21994804
#=GF RT   Functional RNA elements in the dengue virus genome.
#=GF RA   Gebhard LG, Filomatori CV, Gamarnik AV
#=GF RL   Viruses. 2011;3:1739-1756.
#=GF WK   Flavivirus
#=GF SQ   4


GQ398255.1/1-71 AGUUGUUAGUCUACGUGGACCGACAAGAACAGUUUCGAAUCGGAAGCUU-GCUUAACGUAGUUCUAACAGUU
DQ863634.1/1-71 AGUUGUUAGUCUACGUGGACCGACAAGAACAGUUUCGACUCGGAAGCUU-GCUUAACGUAGUGCUGACAGUU
GQ398276.1/1-72 AGUUGUUAGUCUACGUGGACCGACAAAGACAGAUUCUUUGAGGGAGCUAAGCUCAACGUAGUUCUAACAGUU
GQ398256.1/1-71 AGUUGUUAGUCUGUGUGGACCGACAAGGACAGUUCCAAAUCGGAAGCUU-GCUUAACACAGUUCUAACAGUU
#=GC SS_cons    :::((((((-((((((,,,<<<<---<<<____>>>--->>>><<<___._>>>,))))))--)))))):::
#=GC RF         AGUUGUuAGUCUacGUGGACCgaCAAGgACAGuUcCgaaucGGgAGCUu.GCUcAACguAGUuCUaACAGUU
//
# STOCKHOLM 1.0

#=GF AC   RF02341
#=GF ID   ncrMT1302
#=GF DE   Mycobacterium sRNA ncrMT1302
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   45.00
#=GF TC   46.30
#=GF NC   43.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22446041
#=GF RT   A screen for non-coding RNA in Mycobacterium tuberculosis reveals a
#=GF RT   cAMP-responsive RNA that is expressed during infection.
#=GF RA   Pelly S, Bishai WR, Lamichhane G
#=GF RL   Gene. 2012;500:85-92.
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   7


ABIN01000073.1/238558-238450 AAGCGACCAAUUCGAAGCGCCGGAACACGGGGUAGGAAUCCGGCCGCGUAGGACACGCGUAAGACGG-AGUCAGACGCCCCC-UGGAGUCGCACCGGGCCUG-CCCAUAUUG
ACBV01000110.1/1568-1675     AAGCGACCGAACUCAAGUGCCGGAAAUCGGGGU-GAGAUCCGGCAGCGCAGGAUCCGCGUAAGACGG-AGCCAGACGCCCCC-GAGAGUCGCUCCGGGCCUG-CCCAUAUGC
ADNV01000348.1/4629-4523     GAACGACCAAUUCGAAGCGCCGGAAGUCAGGGUAGAAAACCGGCCGCGUAGGACCCGCGCAUGACGG-AGCCC-ACGCCCCC-UAGAGUCGU-CCGGGCCUG-CCCAUGUCC
AE000516.2/1412696-1412588   UAGUGACCAAUCGAAAGUGCCGGAAGACGGGGU-GAAGGCCGGCCGCGCAAGACCCGCAGAAGACGG-UGUCAGACGCCCCCCGAGAGUCACGCCGGGUCUG-CCCAUGUGU
AFVW01000014.1/121121-121013 AAGCGACCAAUUCGAAGUGCCGGAACACGGGGUAGGAAUCCGGCCGCGUAGGACACGCAUAAGACGG-AGUCAGACGCCCCC-UGGAGUCGCGCCGGGCCUG-CCCAUGUGC
CP000325.1/4956666-4956772   AACAGACCGAACUCAAGUGCCGGAGAAUGGGGU-GGAAUCCGGCCGCGUAAGCGCCGCGUAAGACGG-A-CCAAACGCCCCC-GGGAGUCGCUCCGGGCCUG-CCCAUAUGA
AL583920.1/286853-286746     AAGCAACCCAUCCAAAGUGCCGAAAAACGGG--AGAGAACCGGCCGUAUAGGACUAAUGCAGGAUGGCAGUCAGACGUCCCC--AGAGGCGCUCCGGGCCUGGCCUACUUGU
#=GC SS_cons                 ::(((((,,,,,,,,,,,,<<<<----<______>---->>>>,,<<<<-----<<<_______>>>.------>>>>,,,,.,,,,)))))---<<<____.>>>::::::
#=GC RF                      aAgcGaCCaAuccaAAGuGCCGGAAaaCGGGGUAGaaAuCCGGCcGcGuAgGAccCGcguAaGACGg.AGuCAGaCgCCCCC.uaGAGuCgcuCCGGGCCUG.CCCAUaUgu
//
# STOCKHOLM 1.0

#=GF AC   RF02342
#=GF ID   ar7
#=GF DE   Alphaproteobacterial sRNA ar7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22418845
#=GF SS   Predicted; PMID:22418845
#=GF GA   60.00
#=GF TC   77.40
#=GF NC   47.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.83 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22418845
#=GF RT   A survey of sRNA families in alpha-proteobacteria.
#=GF RA   del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N,
#=GF RA   Jimenez-Zurdo JI
#=GF RL   RNA Biol. 2012;9:119-129.
#=GF WK   %CE%91r7_RNA
#=GF SQ   29


AM236080.1/192753-192620     GAUCGC------------GUCGCGGGUCUGAUU--ACCGGCUUGUCCCCCGCCG--CGUCAGG--CUUGGACAAAGGCCUUAU--CC-CCCUCUCCGGGCCUUUGUCCCCACUU---UAA--AGUCGCCAUGGCC----AACCUCCA-GGCCAUGGCGACUUUUG
CP000390.1/4251581-4251722   UAUCGGCAAUAUUU-UUCGCCGAA-G--UCCGG--AAAGGCUCGUCCCCCGCCGAACCGGACA--UAAAAGCGGCAGCCUUAU--CC-CCCUCUCCGGGCUGCCG---CACAUAAUAUAA--GGCCGCCGUGGU-U---CCCCUCC---ACCACGGCGGCACUUU
CP001191.1/4280653-4280520   GAUCGC------------GCCGCGGGUCUGAUU--ACCGGCUUGUCCCCCGCCG--CGUCAGG--CUUGGACAAAGGCCUUAU--CC-CCCUCUCCGGGCCUUUGUCCCCACUU---UAA--GGUCGCCAUGGCC----AACCUCCA-GGCCAUGGCGACUUUUG
CP000738.1/3585152-3585302   GAGCGGCAGUCAUAAAAUGCCGUGUGUCUGGUG--AUUGGCCUGUCCCCCGCCCG-CACCAGA--UAAGGACAAAGGCCUCAU--CC-CCCUCUCCGGGCCUUUGUCCCGCUUUCAAAAA--AACCGUCACGGCGC---CGCCUCCG-CGCCGUGACGGUUUUUU
CP000133.1/163895-163762     GAUCGC------------GUCGCGGGUCUGAUU--ACCGGCUUGUCCCCCGCCG--CAUCAGG--CUUGGACAAAGGCCUUAU--CC-CCCUCUCCGGGCCUUUGUCCCCAUUUU---AA--AGUCGCCAUGGCC----AACCUCCA-GGUCAUGGCGACUUUUG
CP002997.1/134716-134574     CAUCGACACUUC------GUCGGU-CUCCGGUU-UUCCGACCCGUCCCCCGUCGGAAACCGGA--UGGUAGCGGUAGUCUCAU--UC-CCCUCUCCGGGCUGCCGCUGUGUAGUGACAUG--G-CCGCUGUGGUAA---UC--CCCU-CACCACAGCGGCCAAUC
CP001622.1/4553697-4553564   GAUCGC------------GUCGCGGGUCUGAUU--ACCGGCUUGUCCCCCGCCG--CGUCAGG--CUUGGACAAAGGCCUUAU--CC-CCCUCUCCGGGCCUUUGUCCCCACUU---UAA--AGUCGCCAUGGCC----AACCUCCA-GGCCAUGGCGACUUUUG
CP000633.1/255869-256019     CAGCGGCGCAUGAUUAGCACCGCA-GUCUGAAA--GUUGGCUCGUCCCCCGCCG--CUUCAGACUUCAGGACAAAGGCCUUAU--CCCCCCUCUCCGGGCCUUUGUCCCCUGUUACGAAA--AGUCGUCACGGCGC---CGCCUCC-A-GCCGUGACGACUUUUU
AM040264.1/132458-132316     CAUCGACACUUC------GUCGGU-CUCCGGUU-UUCCGACCCGUCCCCCGUCGGAAACCGGA--UGGUAGCGGUAGUCUCAU--UC-CCCUCUCCGGGCUGCCGCUGUGUAGUGACAUG--G-CCGCUGUGGUAA---UC--CCCU-CACCACAGCGGCCAAUC
CP000887.1/134477-134335     CAUCGACACUUC------GUCGGU-CUCCGGUU-UUCCGACCCGUCCCCCGUCGGAAACCGGA--UGGUAGCGGUAGUCUCAU--UC-CCCUCUCCGGGCUGCCGCUGUGUAGUGACAUG--G-CCGCUGUGGUAA---UC--CCCU-CACCACAGCGGCCAAUC
BA000012.4/2648390-2648245   CAUCGGCAGUUUU----CGCCGAA-GUCCGGAG--CAAGGCCCGUCCCCCGCCUA-UCCCGGA--CAAUUGCGGCAGCCUAUC--CC-CCCUCUCCGGGCUGCCGCAUCGUUUCGAGUAU--GAGGCCGCCGUGGUU-CCCCCUCCA-CCACGGCGGUCUUUU--
AM939557.1/1-150             GAGCGGCACUCAUACAAUGCCGUGAGUCUGGUG--AUUGGCCUGUCCCCCGCCCG-CACCAGA--UGAGGACAAAGGCCUCAU--CC-CCCUCUCCGGGCCUUUGUCCCGCUUUCAAAGA--G-CCGCCACGGCGC---AGCCUCCG-CGCCGUGGCGGUUUUUU
CP001074.1/205811-205678     GAUCG------------UGCCGAGGGUCUGAUC--ACCGGCUUGUCCCCCGCCG--CAUCAGG--CUUGGACAAAGGCCUUAU--CC-CCCUCUCCGGGCCUUUGUCCCCAUUUU---AA--GGUCGCCAUGGCC----AACCUCCA-GGCCAUGGCGACUUUUG
CP000872.1/134715-134573     CAUCGACACUUC------GUCGGU-CUCCGGUU-UUCCGACCCGUCCCCCGUCGGAAACCGGA--UGGUAGCGGUAGUCUCAU--UC-CCCUCUCCGGGCUGCCGCUGUGUAGUGACAUG--G-CCGCUGUGGUAA---UC--CCCU-CACCACAGCGGCCAAUC
CP000911.1/135050-134908     CAUCGACACUUC------GUCGGU-CUCCGGUU-UUCCGACCCGUCCCCCGUCGGAAACCGGA--UGGUAGCGGUAGUCUCAU--UC-CCCUCUCCGGGCUGCCGCUGUGUAGUGACAUG--G-CCGCUGUGGUAA---UC--CCCU-CACCACAGCGGCCAAUC
CP001488.1/134697-134555     CAUCGACACUUC------GUCGGU-CUCCGGUU-UUCCGACCCGUCCCCCGUCGGAAACCGGA--UGGUAGCGGUAGUCUCAU--UC-CCCUCUCCGGGCUGCCGCUGUGUAGUGACAUG--G-CCGCUGUGGUAA---UC--CCCU-CACCACAGCGGCCAAUC
CP000628.1/243377-243240     GAUUG-------AU-UACGCCGAGGGUCUGACA--ACCGGCCUGUCCCCCGCCA--UGUCAGA--CUUGGACAAAGGCCUA-U--CC-CCCUCUCCGGGCCUUUGUCCUCCUUUU--CUA--AGCCGCCAUGGCG----CCCCUCCA-GGCCAUGGCGGCUUUUC
CP001578.1/136309-136167     CAUCGACACUUC------GUCGGU-CUCCGGUU-UUCCGACCCGUCCCCCGUCGGAAACCGGA--UGGUAGCGGUAGUCUCAU--UC-CCCUCUCCCGGCUGCCGCUGUGUAGUGACAUG--G-CCGCUGUGGUAA---UC--CCCU-CACCACAGCGGCCAAUC
AE017223.1/136091-135949     CAUCGACACUUC------GUCGGU-CUCCGGUU-UUCCGACCCGUCCCCCGUCGGAAACCGGA--UGGUAGCGGUAGUCUCAU--UC-CCCUCUCCGGGCUGCCGCUGUGUAGUGACAUG--G-CCGCUGUGGUAA---UC--CCCU-CACCACAGCGGCCAAUC
CP001389.1/3727450-3727302   GAGCGGCACUCAAACGAUGCCGUC-GUCUGGUG--AUUGGCCUGUCCCCCGCCCG-CACCAGA--UGUGGACAAAGGCCUCAU--CC-CCCUCUCCGGGCCUUUGUCCCGCUUUCACGAA--G-CCGCUACGGCGC---CGCCUCCG-CGCCGUAGCGGUUUUUG
CP000708.1/135029-134888     CAUCGACACUUC------GUCGGU-CUCCGGUUUC--CGACCCGUCCCCCGUCGGAAACCGGA--UGGUAGCGGUAGUCUCAU--UC-CCCUCUCCGGGCUGCCGCUGUGUAGUGACAUG--G-CCGCUGUGGUAA---UC--CCCU-CACCACAGCGGCCAAUC
AE008917.1/1868345-1868487   CAUCGACACUUC------GUCGGU-CUCCGGUU-UUCCGACCCGUCCCCCGUCGGAAACCGGA--UGGUAGCGGUAGUCUCAU--UC-CCCUCUCCGGGCUGCCGCUGUGUAGUGACAUG--G-CCGCUGUGGUAA---UC--CCCU-CACCACAGCGGCCAAUC
CP002447.1/1781903-1782047   CAUCGGCAGUUUU----CGCCGA--GUCCGGAG--CAAGGCCCGUCCCCCGCCUA-UCCCGGA--CACCUGCGGCAGCCUAUC--CC-CCCUCUCCGGGCUGCCGCAUCGUUUCGAGUAGAAGGCCGCCGUGGUUC---CCCCUCC---ACCACGGCGGUCUUUU
ABIA02000001.1/222769-222919 CAUCGGCGCACUAA-CAAGCCGUU-GUCUGGAUUUUUCGGCUCGUCCCCCGCCGC-UUCCAGA-CGAAGGACAAGGGCCUCCCCGCC-CCCUCUUAUGGUCCUUGUCCUGCCAA---UAU--G-CCGCCAUGGCCCU-UCCCCUCCG--GCCAUGGCGGCUUUUC
ABRC01000789.1/83-227        CACCGGCGCUUGAU-CGCGCCGCGGGUCUGAUU--ACCGGCUUGUCCCCCGCCG--CAUCAGG--CUUGGACAAAGGCCUUAU--CC-CCCUCUCCGGGCCUUUGUCCCCAUUUU--AAA--G-UCGCCAUGGCC----AACCUCCA-GGCCAUGGCGACUUUUG
AFSD01000001.1/795064-794933 GAUCAC------------GCCGUA-GUCUGAUU--GUAGGCUCGUCCCCCGCCG--CAUCAGA--CC-GGACAAAGGCCUU-U--CC-CCCUCUCCGGGCCUUUGUCCUCCAAUA---CG--A-CCGCCAUGGCCG--ACCCCUCCC-GGCCAUGGCGGUUUUAU
ABRA01002131.1/2293-2151     UAACGUGGUGUGAC--CC-UUGAAAAACCGAUC--ACCGGCUUGUCCCCCGCCG--CAUCAGG--UUUGGACAAAGGCCUUAU--CC-CCCUCUCCGGGCCUUUGUCCCCAUUUU---AA--GGUCGCCAUGGCC----AACCUCCA-GGCCAUGGCGACUUUUG
CP002248.1/112655-112523     GAUCAC------------GCCGUA-GUCUGAUU--GUAGGCUCGUCCCCCGCCG--CAUCAGA--CC-GGACAAAGGCCUUUC--CC-CCCUCUCCGGGCCUUUGUCCUCUUAUA---UG--A-CCGCCAUGGCCG--UCCCCUCCC-GGCCAUGGCGGUUUUUA
CP000758.1/149962-149814     CAUCGACAGUUC------GUCGGUCGCCGGUU--UUCUGACCCGUCCCCCGUUGGA-UGCCGG-AUGCUAGCGGUAGCCUCAU--UC-CCCUCUCCGGGCUACCGCUUUGAGUGUAGUGA--CAUGGCCGUUGCGGUACCCCCUCAC-CGUAACGGCCAAUUCAU
#=GC SS_cons                 :::::::::::::....:::::::.:<<<<<<<..---<<<_________>>>--.>>>>>>>..,,,<<<<<<<<<<<____..__._________>>>>>>>>>>>-----------<..--<<<<<<<<<<<<..._______>.>>>>>>>>>>>->::::
#=GC RF                      cAUCGaCAcuuua....cGcCGau.guCcGgug..accGGCucGUCCCCCGCCgg.cacCgGa..uaagggCggcgGCCUuAU..cC.CCCUCUCCGGGCcgccGcccuguuuuuAauag..ggccGCcguGGcgg...ccCCUCCc.cgCCacgGCggccuuUu
//
# STOCKHOLM 1.0

#=GF AC   RF02343
#=GF ID   ar9
#=GF DE   Alphaproteobacterial sRNA ar9
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22418845
#=GF SS   Predicted; PMID:22418845
#=GF GA   45.00
#=GF TC   46.90
#=GF NC   43.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.71 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22418845
#=GF RT   A survey of sRNA families in alpha-proteobacteria.
#=GF RA   del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N,
#=GF RA   Jimenez-Zurdo JI
#=GF RL   RNA Biol. 2012;9:119-129.
#=GF WK   %CE%91r9_RNA
#=GF SQ   28


AM236080.1/1803079-1802936   ACAAAACAGGCAGGGA---G-UUAAA--UUCUUGCCGAA-UUCGCGGUC-A--AGUCUUGGGAGGAUCAGAUCUUAGGCGCGCUCGU--CGCAGCC-CCG------G--CAA-CGG-UUACAGAUC--ACGCGAUACUUA--AAACAGGGCUUU-UA-GCCUUGUUUUUUUUU
CP000887.1/818045-817898     AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUG-A--AGUCUUGGGAGGAUG-GAUCC-AGGCGCGGUUUC--CGCAGCCGCCA------GUAAAA-UGGAAAACGGAUCGAACGCGUAUUCAA-UUGGCAGGGCGAA--A-GCCUUGCUUUUUUUU
CP002248.1/1215726-1215580   ACAAAAGAGGCAGGAA---GUCUAAA--UUCUUGCC-GUUUUCGCGGUC-A---GUCUUGGGAGGAUUCGAUCUUAGGCGCGCUUGU--CGCUGCC-CCG------G--UAA-CGG-UUACAGAUC--ACGCGAAACCUGAAAAACAAGGCUGA-AAUGCCUUGUUUUUUUUU
AE007869.2/1275443-1275297   ACAAAAGAGGCAGGAA---GUUUAAA--UUCUUGUC-AUUUUCGCGGUC-A---GUCUUGGGAGGAUCAGAUCUUAGGCGCGCUCGU--CGCUGCC-CCG------G--CAA-CGG-UUACAGAUC--ACGCGAAACCUGAAAAACAAGGCUGA-AAUGCCUUGUUUUUUUUU
CP000911.1/817909-817762     AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUG-A--AGUCUUGGGAGGAUG-GAUCC-AGGCGCGGUUUC--CGCAGCCGCCA------GUAAAA-UGGAAAACGGAUCGAACGCGUAUUCAA-UUGGCAGGGCGAA--A-GCCUUGCUUUUUUUU
CP002447.1/3449786-3449639   AUAACCGAGAGGGCAG---AAAAAAA-UCUGCUCUC---CUACGCGGUC-A-AAGUCUUGGGAGGAUGCGAUCU-AGGCGCGGUUAC-UCGCUGCCGCCG------G--AAACCGG-AAACAGAUCGGACGCGUU--UAA-AUUGCAAGGCCUC-GU-GCCUUGCAUUUUUUU
AM939558.1/1-149             ACAAAACAGGCAGGAA---GACCAAA--UUCUUGCCGAAAUUCGCGGUC-A--AGUCUUGGGAGGAUAAGAUCUUAGGCGCGCUUGU-UCGCUGCCGCCG------G--AAA-CGGAUUAAAGAUC--ACGCGACACUUA-AAAACAAGGCUUU--G-GCCUUGUUUUUUUUU
CP000633.1/1448659-1448510   ACAAAACAGGCAGAAA---GCUUAAA--UUUCUGCCGAU-UUCGCGGUUAA--AGUCUUGGGAGGAUCAGAUCUUAGGCGCGGUCAU-UCGCAGCC-CCU------U--AAU-UGG-UGAAAGGUC--ACGCGACAUUUCAAUAACAAGGUCUU-CGGGCCUUGUUUUUUUUU
AE014291.4/798064-797917     AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUG-A--AGUCUUGGGAGGAUG-GAUCC-AGGCGCGGUUUC--CGCAGCCGCCA------GUAAAA-UGGAAAACGGAUCGAACGCGUAUUCAA-UUGGCAGGGCGAA--A-GCCUUGCUUUUUUUU
CP000708.1/822859-822712     AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUG-A--AGUCUUGGGAGGAUG-GAUCC-AGGCGCGGUUUC--CGCAGCCGCCA------GUAAAA-UGGAAAACGGAUCGAACGCGUAUUCAA-UUGGCAGGGCGAA--A-GCCUUGCUUUUUUUU
CP001191.1/1296650-1296506   ACAAAACAGGCAGGAA---GGAUAAA--UUCUUGCCGAA-UUCGCGGUC-A--AGUCUUGGGAGGAUCAGAUCUUAGGCGCGCUCGU--CGCUGCC-CCG------G--CAA-CGG-UUACAGAUC--ACGCGAUACUUA--AAACAAGGCUUU-UA-GCCUUGUUUUUUUUU
CP001074.1/1685072-1684929   ACAAAACAGGCAGGAA---G-CUAAA--UUCUUGCCGAA-UUCGCGGUC-A--AGUCUUGGGAGGAUCAGAUCUUAGGCGCGCUCGU--CGCAGCC-CCG------G--CAA-CGG-UUACAGAUC--ACGCGAUACUUA--AAACAAGGCUUU-UA-GCCUUGUUUUUUUUU
CP001389.1/1130150-1130001   ACAAAACAGGCAAGAA---GACCAAA--UUCUUGCCGAUUUUCGCGGUC-A--AGUCUUGGGAGGAUAAGAUCUUAGGCGCGCUCGU-UCGCUGCCGCCG------G--CAA-CGGUUGAAAGAUC--ACGCGAAACUUGAAAAACAAGGCUUU--G-GCCUUGUUUUUUUUU
CP000133.1/1703345-1703203   ACAAAACAGGCAAGGA---AGUUAA---UUCUUGCC--AUUUCGCGGUC-A--AGUCUUGGGAGGAUCAGAUCUUAGGCGCGCUCGU--CGCAGCC-CCG------G--CAA-CGG-UUACAGAUC--ACGCGAUACUUA--AAACAAGGCUUU-UA-GCCUUGUUUUUUUUU
CP001578.1/802225-802078     AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUC-A--AGUCUUGGGAGGAUG-GAUCC-AGGCGCGGUUUC--CGCAGCCGCCA------GUAAAA-UGGAAAACGGAUCGAACGCGUAUUCAA-UUGGCAGGGUGAA--A-GCCUUGCUUUUUUUU
CP000738.1/979902-979753     ACAAAACAGGCAGGAA---GACCAAA--UUCUUGCCGAAACUCGCGGUC-A--AGUCUUGGGAGGAUAAGAUCUUAGGCGCGCUCGU-UCGCUGCCGCCG------G--AAA-CGGAUUAGAGAUC--ACGCGAAACUUAGAAAACAAGGCUUU--G-GCCUUGUUUUUUUUU
CP001488.1/819523-819377     AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUG-A--AGUCUUGGGAGGAUG-GAUCC-AGGCGCGGUUUC--CGCAGCCGCCA------GUAAAA-UGGAAAACGGAUCGAACGCGUAUUCAA-UUGGCAGGGCGAA--A-GCCUUGCU-UUUUUU
CP000758.1/2529108-2529255   AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUC-A-AAGUCUUGGGAGGAUG-GAUCC-AGGCGCGACUUU--CGCAGCCGCCA------GUCAAA-UGG-AAACGGAUCGAACGCGUAUUUGA-UUAGCAAGGCGAA--A-GCCUUGCUUUUUUUU
CP000872.1/796428-796281     AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUG-A--AGUCUUGGGAGGAUG-GAUCC-AGGCGCGGUUUC--CGCAGCCGCCA------GUAAAA-UGGAAAACGGAUCGAACGCGUAUUCAA-UUGGCAGGGCGAA--A-GCCUUGCUUUUUUUU
AE017223.1/819744-819597     AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUG-A--AGUCUUGGGAGGAUG-GAUCC-AGGCGCGGUUUC--CGCAGCCGCCA------GUAAAA-UGGAAAACGGAUCGAACGCGUAUUCAA-UUGGCAGGGCGAA--A-GCCUUGCUUUUUUUU
CP000628.1/1482119-1481975   ACAAAAGAGGCAGGAA---GGCUAAA--UUCUUGUC--GUUUCGCGGUC-A--AGUCUUGGGAGGAUCAGAUCUUAGGCGCGCUCGU--CGCUGCC-CCG------G--CAA-CGG-AUAAGGAUC--ACGCGAUACUUA-AAAACAAGGCUUA-CC-GCCUUGUUUUUUUUU
AE008917.1/1187596-1187743   AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUG-A--AGUCUUGGGAGGAUG-GAUCC-AGGCGCGGUUUC--CGCAGCCGCCA------GUAAAA-UGGAAAACGGAUCGAACGCGUAUUCAA-UUGGCAGGGCGAA--A-GCCUUGCUUUUUUUU
CP000390.1/1141933-1141776   ACAAAAUAAGAGGGUGGAACAAUGAAUCCGCUCUC---AUUACGCGGUC-AAAAGUCUUGGGAGGAUACGGUCCU-GGCGCGGUUAC-UCGCCGCCGCCGUUUAAA-AAAAA-CGG-AAGCGGAUCGGACGCGU--UCUA-GUUGCAAGGCUUC--U-GCCUUGCUUUUUUUU
AM040264.1/816022-815875     AUAAGAGCAACAACGG---AAUAAAA--CCGUUGGU--UUCACGCGGUG-A--AGUCUUGGGAGGAUG-GAUCC-AGGCGCGGUUUC--CGCAGCCGCCA------GUAAAA-UGGAAAACGGAUCGAACGCGUAUUCAA-UUGGCAGGGCGAA--A-GCCUUGCUUUUUUUU
BA000012.4/1127217-1127363   AUAACCGAGAGGGCGG---AGAAAAA-UCUGCCCUC---CUACGCGGUC-A-AAGUCUUGGGAGGAUGCGAUCU-AGGCGCGGUUAC-UCGCUGCCGCCG------G--AAACCGG-AAACAGAUCGGACGCGU---UUA-AUUGCAAGGCCUC-GU-GCCUUGCAUUUUUUU
CP001622.1/1354736-1354593   ACAAAACAGGCAGGAA---G-UUAAA--UUCUUGCCGAA-UUCGCGGUC-A--AGUCUUGGGAGGAUCAGAUCUUAGGCGCGCUCGU--CGCAGCC-CCG------G--CAA-CGG-UUACAGAUC--ACGCGAUACUUA--AAACAAGGCUUU-UA-GCCUUGUUUUUUUUU
ADGO01196589.1/206-362       AUAAAAUAAGAGGGUGGAACCUUAAAUCCGCUCUCA--CUUACGCGGUC-A-AAGUCUUGGGAGGAUACGAUCCU-GGCGCGCAUGU-UCGCUGCCGCCGUU-UGA--AAAA-CGG-AAACGGGUCGGACGCGU---UUA-GUUGCAAGGCGUACCU-GCCUUGCUUUUUUUU
ABIA02000005.1/121279-121432 ACUAAAGAGGCACAUC---UUACGGG--AAAGUGCC-CAAUUCGCGGUC-A-AAGUCUUGGGAGGAUAGGAUCUCAGGCGCGCUUUGUUCGCAGCCCCCG------GGCAAC-CGGGAAACAGAUC--ACGCGACACCUGAACAACAAGGCUUU-CA-GCCUUGUUUUUUUUU
#=GC SS_cons                 ::{{{{,,,,<<<<<<..._______..>>>>>>,,..,,,,[[[[,,,.,..,<<<<_____>>>>,,(((((,,<<<<<<_____..>>>->>>,<<<......_.____.>>>.,,,,))))),,,]]]],,,,,,,.,,<<<<<<<<___.__.>>>>>>>>,,,}}}}
#=GC RF                      Auaaaagaagcagggg...aauuAAA..ccccugcc..uuuaCGCGGUc.A..AgUCuUGGGAgGAuaaGauCcUAGGCGCGgUuuu..CGCaGCCgCCg......G.aaAA.cGG.aaAcgGauCGaACGCGuaauuuA.auggCaaGGCuua.ua.GCCuuGccUUUuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02344
#=GF ID   ar14
#=GF DE   Alphaproteobacterial ar14
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22418845
#=GF SS   Predicted; PMID:22418845
#=GF GA   52.00
#=GF TC   52.00
#=GF NC   51.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.54 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0044403; symbiont process;
#=GF RN   [1]
#=GF RM   22418845
#=GF RT   A survey of sRNA families in alpha-proteobacteria.
#=GF RA   del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N,
#=GF RA   Jimenez-Zurdo JI
#=GF RL   RNA Biol. 2012;9:119-129.
#=GF RN   [2]
#=GF RM   28401641
#=GF RT   A conserved alpha-proteobacterial small RNA contributes to osmoadaptation
#=GF RT   and symbiotic efficiency of rhizobia on legume roots.
#=GF RA   Robledo M, Peregrina A, Millan V, Garcia-Tomsig NI, Torres-Quesada O,
#=GF RA   Mateos PF, Becker A, Jimenez-Zurdo JI
#=GF RL   Environ Microbiol. 2017;19:2661-2680.
#=GF CC   Smr14C2 was renamed NfeR1 (Nodule Formation Efficiency RNA) highly
#=GF CC   expressed in salt stress and during the symbiotic interaction on legume
#=GF CC   roots.[2] 
#=GF WK   %CE%91r14_RNA
#=GF SQ   118


CP002781.1/3627045-3626927     CCUUGUCGAAGCGCUG-----UACCUCCUCCC--A----CGGC-GCC-CGGCAUUCGGUC-GGU-UC---AC--UCCUCCUCCCA--GA--ACCGAUCAAGU----UU-----AA--GACCCCGA-GCC-A------CCU---CCUCCC-GGCUCGGGGUCUUUCU
CP000634.1/598556-598433       GUCUCUCGG-ACGACCC--A-CUCCUCCUCCC--U-AG-GGGC-GU-CCGAU---GGAAC-GGUGGC---AC--UCCUCCUCCCA--GCC-GCUGUUCACUC----UUU--UAAA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUUG
CP001622.1/107063-107184       AUCUUCGUAAGCAGCGC--A-CUCCUCCUCCC--A--G-UGCU--CUUACAU--CGGACU-GACAAC---AC--UCCUCCUCCCA--GUU-GUCAGUCAGGA----UC-----AA--GAGCCCGG-CGC-A------CCU---CCUCCC-GCGUCGGGCUUUUUUC
AE017223.1/359925-360032       AUACAUCGAGU----U-----CGCCUCCUCCC--A--G-A-----ACUCGAU-AAGGA-A-UACGGC---AC--UCCUCCUCCCA-AGCC-GUAU-UCAAGA----UC---------AGGCCGCG-CAU-C-------CU---CCUCCC---GUGCGGCCUUUUUC
CP000137.1/443129-443009       GAUAUGCA-GGCG-CUC--C-AUCCUCCUCCC--A--G-GGAC-GUC-UG-C--GGGAAC-GACCGC---AC--UCCUCCUCCCA--GCU-GUCGUUCGGUU----UUC---CGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUUC
CP000738.1/3590417-3590299     CCUUGUCGAAGCGCUG-----UACCUCCUCCC--A----CGGC-GCC-CGGCAUUCGAUC-GGU-UC---AC--UCCUCCUCCCA--GA--ACCGAUCAGGU----UU-----AA--GACCCCGA-GCC-A------CCU---CCUCCC-GGCUCGGGGUCUUUCU
CP001074.1/513993-514114       AUCUCCGUAAGCAGCGC--A-CUCCUCCUCCC--A--G-CGCU--CUUACAU--CGGACU-GACAAC---AC--UCCUCCUCCCA--GUU-GUCAGUCAGGA----UC-----AA--GAGCCUGG-CGC-A------CCU---CCUCCC-GCGCCAGGCUCUUUUC
CP001192.1/607636-607759       CGUGUUAG--GCGACCC--G-CUCCUCCUCCC--A-AG-GGCC-GC--CUUA--CAGAAC-AGCGGC---AC--UCCUCCUCCCA--GCC-GUUGUUCAAUUC--U--UU-CGAA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
CP000911.1/888831-888713       GUUCGUCGCAAAGCUCU--C-CACCUCCUCCC--A--G-G--C-UUUGCGAU--AACAAG-ACCGGU---UC--UCCUCC-CAAU--GCC-GGUCUUCCCCU----AA-----UG--GCAUCCGU-CGC-C-------CU---CCUCCC-GCGACGGAUGCCAUUU
AE008917.1/1116661-1116779     GUUCGUCGCAAAGCUCU--C-CACCUCCUCCC--A----GA-C-UUUGCGAU--AACAAG-ACCGGU---UC--UCCUCC-CAAU--GCC-GGUCUUCCCCU----AA-----UG--GCAUCCGU-CGC-C-------CU---CCUCCC-GCGACGGAUGCCAUUU
CP001193.1/50814-50936         GAUAUGCA-GGCGCCCC----AUCCUCCUCCC--A--G-GGUC-GUC-UG-C--GGGAAC-GGCAGC---AC--UCCUCCUCCCA--GCU-GUCGUUCGGUU----UUUU-UCGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
U80928.5/77668-77794           AAGUUUAG--ACGGCCC--A-CUCCUCCUCCC--AAAG-GGAC-GU--CUGU--GGGAAC-AGCGGC---AC--UCCUCCUCCCA-GGUC-GCCGUUCGGUUCUUU--U--AGGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUCUA
CP003128.1/868918-868800       GUUCGUCGCAAAGCUCU--C-CACCUCCUCCC--A--G-G--C-UUUGCGAU--AACAAG-ACCGGU---UC--UCCUCC-CAAU--GCC-GGUCUUCCCCU----AA-----UG--GCAUCCGU-CGC-C-------CU---CCUCCC-GCGACGGAUGCCAUUU
CP000633.1/115126-115249       AAUCAUCGAAGCGACGC--A-CUCCUCCUCCC--A--G-UGUC-GCUUUGAA--GGGAUC-GGCGAU---AC--UCCUCCUCCCA--AUU-GCCGAUCAAGU----UC-----AA--GAGCCCGA-CGC-A-----UCCU---CCUCCC-GCGUCGGGCUCUUUUG
AM040264.1/356293-356400       AUACAUCGAGU----U-----CGCCUCCUCCC--A--G-A-----ACUCGAU-AAGGA-A-UACGGC---AC--UCCUCCUCCCA-AGCC-GUAU-UCAAGA----UC---------AGGCCGCG-CAU-C-------CU---CCUCCC---GUGCGGCCUUUUUC
CP000633.1/2793936-2793811     CGAAUUCAGACG-GCCU--A-CUCCUCCUCCC--A--G-GGCA-CGUCUG-U--CGGAAC-UGCGGC---AC--UCCUCCUCCCA--GCC-GUUGUUCGGUUC-UU--UU-CGGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
CP002997.1/338018-338125       AUACAUCGAGU----U-----CGCCUCCUCCC--A--G-A-----ACUCGAU-AAGGA-A-UACGGC---AC--UCCUCCUCCCA-AGCC-GUAU-UCAAGA----UC---------AGGCCGCG-C---A-----UCCU---CCUCCC---GCUCGGCCUUUUUC
CP001074.1/1173512-1173639     GAGAUUCAG-AUGGCCC--A-CUCCUCCUCCCGAA--G-GGAC-GU-CUG-U--UGGAAC-AGCGGC---AC--UCCUCCUCCCA-AGUC-GCUGUUCGGUUCUUU--U--AGGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUCUA
CP000738.1/1258431-1258311     GGAAUUCGAAGCAGCGC--A-CUCCUCCUCCC--A--G-CGCC-GCUUUGAU--AGGAUU-GGCAGC---AC--UCCUCCUCCCG--GUU-GCCAAUCGCCU----UU-----GU-GACGCCCGC-CGG----------U---CCUCCC-CCGGCGGGCGUUCUCU
CP000740.1/338866-338990       GUGAUUCAG-GCGGCCC--A-CUCCUCCUCCC--A--G-GGAC-GU-CUGAA---GGACC-AGCGGC---AC--UCCUCCUCCCU--GUC-GCUGAUCGGUUCUUU--U--AGGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
AM939559.1/1-123               AUCGAUCGG-GCAGCGC--A-CUCCUCCUCCC--A--G-CGC--GC-CCGAU-ACGGAUU-GGCGAC---AC--UCCUCCUCCCG--GUU-GCCAAUCAGAU----CAA---GCA--ACGCCCGC-UGG-A------CCU---CCUCCC-CCAGCGGGCGUUGUUU
CP001622.1/1697156-1697038     GAGAUUCGCAGCUGCGC--A-CUCCUCCUCCC--A--G-CGC--GCUGCGAU--A-GACU-GACAAC---AC--UCCUCCUCCCA--GUU-GUCAGUCACCA----UA-----AC--ACGCCCGC-CGG-A--------U---CCUCCC-CCGGCGGGCGUUUUUG
CP000629.1/957686-957810       GAAUUUCAG-ACGGCCC--A-CUCCUCCUCCC--A--G-GGAC-GU-CUG-U--AGGAAC-AGCGAC---AC--UCCUCCUCCCA--GUC-GCUGUUCGGUUC-UU--UU-CGAA--AAACCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGUUUUUUCG
AE006469.1/1220690-1220808     CCUUGUCGAAGCGCUG-----UACCUCCUCCC--A----CGGC-GCA-AGAC--GCCGAU-CGGUUC---AC--UCCUCCUCCCA--GGA-CCGAUCUAGUU----CA-----GA--GACCCCGA-UGC-A------CCU---CCUCCC-GCAUCGGGGUCUUUCU
CP002782.1/574162-574045       AACUGUCG--AUGGAAC--A-CUCCUCCUCCC--A--G-UUCC-AU--CG-C--GGGAUC-GGCAAC---CC--UCCUCCUCCCA--GUU-GCCGGUCAGGA----UC-----GA--AAGCCCGG-CGC-A------CCU---CCUCCC-GCGCCGGGUUUUCUCU
CP001622.1/4296749-4296632     ACUCAUCGA-ACGGCU---U-CUCCUCCUCCC--A--U-AGCC-GU-UCGAU--AGGGUC-GACAAC---AC--UCCUCCUCCCA--GUU-GUCGAUCGAGU----UU-----AU--AAGCCCGA-CGG-A--------U---CCUCCC-CCGUCGGGCUUUCUCG
CP001578.1/339699-339806       AUACAUCGAGU----U-----CGCCUCCUCCC--A--G-A-----ACUCGAU-AAGGA-A-UACGGC---AC--UCCUCCUCCCA-AGCC-GUAU-UCAAGA----UC---------AGGCC--G-CGC-A-----UCCU---CCUCCC-GCGC--GGCCUUUUUC
CP000911.1/355557-355664       AUACAUCGAGU----U-----CGCCUCCUCCC--A--G-A-----ACUCGAU-AAGGA-A-UACGGC---AC--UCCUCCUCCCA-AGCC-GUAU-UCAAGA----UC---------AGGCC--G-CGC-A-----UCCU---CCUCCC-GCGC--GGCCUUUUUC
CP000133.1/462566-462687       AUCUUCGUAAGCAGCGC--A-CUCCUCCUCCC--A--G-CGCU--CUUACAU--CGGAUU-GACAAC---AC--UCCUCCUCCCA--GUU-GUCAGUCAGGA----UC-----AA--GAGCCUGG-CGC-A------CCU---CCUCCC-GCGCCAGGCUCUUUUC
CP000758.1/448505-448614       CUUCAUCGA----GUUC--A-CUCCUCCUCCC--A--G-AAC-----UCGAU-AAGGAAU--GCGGC---AC--UCCUCCUCCCA-AGCC-GU-AUUCAAGA----UC---------AGGCC--G-CGC-A-----UCCU---CCUCCC-GCGC--GGCCUUUUUC
CP002997.1/868951-868833       GUUCGUCGCAAAGCUCU--C-CACCUCCUCCC--A--G-G--C-UUUGCGAU--AACAAG-ACCGGU---UC--UCCUCC-CAAU--GCC-GGUCUUCCCCU----AA-----UG--GCAUCCGU-CGC-C-------CU---CCUCCC-GCGACGGAUGCCAUUU
CP002447.1/5265891-5266009     GGUUGUCGGC----CAU----CUACUCCUCCC--A-GA-UGCG-AUGCCGAC-GCUGAAU-GGGGUG----C--ACCUCCUCCCG--CGC-CACAUUCGAAA----AU-----CG--AGCCCGCU-GCC-A------CCU---CCUCCC-GGCAGCGGGCUUUUUU
AE008917.1/1644273-1644167     AUACAUCGAGU----U-----CGCCUCCUCCC--A--G-A-----ACUCGAU-AAGGAA--UACGGC---AC--UCCUCCUCCCA-AGCC-GUA-UUCAAGA----UC-----A---GGUC---G-CGC-A-----UCCU---CCUCCC-GCGC---GGCCUUUUU
CP002448.1/241531-241412       GAUUGUCGGC----CAU----CUACUCCUCCC--A-GA-UGCG-AUGCCGGC-GCUGAAU-GAGGCG----C--ACCUCCUCCCG--CGC-CACAUUCGAAA----AU------C--GAGCCCGC-UGCCA------CCU---CCUCCCGGCAGCGGGCUUUUUUU
CP001389.1/1434293-1434171     AUCGGUCGGC--AGCGC--A-CUCCUCCUCCC--A--G-CGCU---CCCGAU-ACGGAUU-GGCGAC--AAC--UCCUCCUCCCG--GUU-GCCAAUCAGAA----CAG---GCA--ACGCCCGC-UGG-A------CCU---CCUCCC-CCAGUGGGCGUUGUUU
AE007870.2/1230297-1230418     AAUCAUCGAAGCGACGC--A-CUCCUCCUCCC--A--G-UGUC-GC-UCGAU-GUGGAUC-GGUGGU---AC--UCCUCCUCCCA--AUC-GCCGAUCAAGU----UU-----G---AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCC
AM236086.1/407202-407316       ACGGACCGAAGCG------C-UUUCCCCUCCU--A-G----CC-GCUUCGGU--CCGACG-GACAGC---AC--UUCUCCUCCCA--GCU-GUCGGUCACUU----UC-----G---AAGCCCGG-CGC-A-------UC---UCUCCC-GCGCCGGGCUUUUGUC
CP001626.1/119313-119435       CGCUUUCAGC-CGACCC--A-CUUCUCCUCCC--A-UG-GGAC-G-UCUGUA---AAAAC-AGCGGC---AC--UCCUCCUCCCA--GUC-GCUGUUCGAUC----UUC---AGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUUG
BA000012.4/890941-891061       AGAUUUCGUCAAAGCCG--A---CCUCCUCCC-----C-GGCG-AUGACGAA-UACGGUC-GAUCUU----C--ACCUCCUCCCG--AGG-AUCGACCCCCA----AA-----AC-GACACCCGC-CGG-A------CCU---CCUCCC-CCGGCGGGUGUUGUUG
CP000636.1/7318-7437           UUGUUACAAGGCCGCCC--A---CCUCCUCCC-----G-GGCC-GCUUUG-U--CCGACU-GGCAGC---AC--UCCUCCUCCCA-AGUU-GUCAGUCAUAA----UC-----GA--AAGCCCGG-UGC-A------CCU---CCUCCC-GCACCGGGUUUUUUCG
CP000874.1/2205311-2205428     AUUUAUCGAC--GAAGC--A-CUCCUCCUCCC--A--G-CUUC---AUCGAG---GGAUC-GGCGAC---CC--UCCUCCUCCCA--GUU-GCCGAUCAGGA----UC-----GA--AGGCCCGG-CGC-A------CCU---CCUCCC-GCGCCGGGCCUUCUCU
BA000012.4/5350767-5350882     AAUACCCGGCGAGUGGA--A---CCUCCUCCC-----U-CUGC-UCCCCGGG--GUGACC-AGCCAG----C--UCCUCCUCCCG--CUG-GC---UCGUAA----CA-----GG--AAAAGGCC-GGC-A------CCU---CCUCCC-GCCGGCCUUUUUCUUU
CP000739.1/679160-679043       GAUUGUCG--AUGGAAC--A-CUCCUCCUCCC--A--G-UUCC-AU--CG-C--GGGAUC-GGCAAC---CC--UCCUCCUCCCC--GUU-GCCGGUCAGGA----UC-----GG--AAGCCCGG-CGC-A------CCU---CCUCCC-GCGCCGGGCUUUCUCU
CP000887.1/358310-358417       AUACAUCGAGU----U-----CGCCUCCUCCC--A--G-A-----ACUCGAU-AAGGA-A-UACGGC---AC--UCCUCCUCCCA-AGCC-GUAU-UCAAGA----UC---------AGGCCGCG-CAU-C-------CU---CCUCCC---GUGCGGCCUUUUUC
CP000887.1/888995-888877       GUUCGUCGCAAAGCUCU--C-CACCUCCUCCC--A----GA-C-UUUGCGAU--AACAAG-ACCGGU---UC--UCCUCC-CAAU--GCC-GGUCUUCCCCU----AA-----UG--GCAUCCGU-CGC-C-------CU---CCUCCC-GCGACGGAUGCCAUUU
CP000759.1/1275649-1275772     GAAUAUCACCGGGGUGCUUU-CUCCUCCUCCC--A--U-UUCC-UCGGUGAU--U-CAAG-ACCGGA---UG--UCCUCCUCCCAAGUCC-GGUCUUCCCCA----UA-----AA--ACACCCGU-CGC---------CU---CCUCCC-GCGACGGGUGUUUUCG
AE007870.2/1831482-1831606     UAAUGCGGGUG-AUCCU--A-CUCCUCCUCCC--A-AA-GGAU--UGCCC-C--GGGGAC-AGCGGU---UU--UCCUCCUCCCA-UAUC-GCUGUUCAUCU----UUU--CAGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUUG
CP000628.1/1693409-1693286     GGAAUUCGGGGCCGCAC--A-CUCCUCCUCCC--A--G-UGC--ACUCCGAU--A-GAUU-GACGAC---AC--UCCUCCUCCCA--GUC-GUCAAUCACCA----CA-----AAUGACGCCCGC-CGC-A-----UCCU---CCUCCC-GCGGUGGGCGUUAUUU
CP000708.1/895867-895749       GUUCGUCGCAAAGCUCU--C-CACCUCCUCCC--A--G-G--C-UUUGCGAU--AACAAG-ACCGGU---UC--UCCUCC-CAAU--GCC-GGUCUUCCCCU----AA-----UG--GCAUCCGU-CGC-C-------CU---CCUCCC-GCGACGGAUGCCAUUU
CP002248.1/109372-109493       AAUCAUCGAAGCGACGC--A-CUCCUCCUCCC--A--G-CGUC-GCC-CGAU--UGGACU-GACAAU---AC--UCCUCCUCCCA--AUU-GUCAGUCAGUU----UC-----AA--GAACCCGG-CGC-A------CCU---CCUCCC-GCGCCGGGUUUUUGCU
CP000390.1/3977208-3977086     AAGUUCUCGACGGGGCU--C-CUCCUCCCAAA--A--A-UCCC-UGUCGGGU--CGCGGU-UAGCCU----U--UCCUCCUCCCU--AGG-CUGACCGACUU----CA----AAA--GCACCCGC-UGG-A------CCU---CCUCCC-CCAGCGGGUGCUUUUU
CP000628.1/3945639-3945517     GAGCAUCGGAACGGCGA--U-CUCCUCCUCCC--A--A-UGCC--UUCCGAU-AACGAUC-GGCAAC---UC--UCCUCCUCCCU--GUU-GCUGGUCAGGU----UU-----GA--AAGCCCGA-CGG-A------UCU---CCUCCC-CCGUCGGGCUUUUCAU
CP000634.1/901035-901159       AUACACCGGGCCAGCUU----CUCCUCCUCCC--A--G-AGC--GGCCCG-U--CGGAAU-GACGGA---AC--UCCUCCUCCCA--GCC-GUCGUUCGGUUC-UU--UU-CGAA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUCGU
CP001191.1/4019446-4019326     ACCUAUCGAAACGGCUU--U-CUCCUCCUCCC--A-UA-AGCC-GU-UCGAC--AGGGUC-GACAAC---AC--UCCUCCUCCCA--GUU-GUCGAUCGAGU----UU-----AU--AAGCCCGA-CGG-A--------U---CCUCCC-CCGUCGGGCUUUCUCG
CP002783.1/252065-252190       CGAUAUGCGAGCGACCU----UUCCUCCUCCC--G--A-GUUC-GCUUGC----GGGAUC-AGCGCU---AC--UCCUCCUCCCG-GAAU-GCUGAUCGGUUC-UU--UU-GGAA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
AE017223.1/890694-890576       GUUCGUCGCAAAGCUCU--C-CACCUCCUCCC--A----GA-C-UUUGCGAU--AACAAG-ACCGGU---UC--UCCUCC-CAAU--GCC-GGUCUUCCCCU----AA-----UG--GCAUCCGU-CGC-C-------CU---CCUCCC-GCGACGGAUGCCAUUU
CP000872.1/338021-338128       AUACAUCGAGU----U-----CGCCUCCUCCC--A--G-A-----ACUCGAU-AAGGAAU-AUGGC----AC--UCCUCCUCCCA--AGC-CGUAUUCAAGA----UC---------AGGCC--G-CGC-A-----UCCU---CCUCCC-GCGC--GGCCUUUUUC
CP000738.1/1258160-1258038     AUCGAUCGG-GCAGCGC--A-CUCCUCCUCCC--A--G-CGC--AC-CCGAU-ACGGAUU-GGCAGC---AC--UCCUCCUCCCA--GUU-GCCAAUCAGAA----CA-----AGCGACGCCUGC-UGG-A------CCU---CCUCCC-CCAGCGGGCGUUGUUU
CP001830.1/2001057-2001179     AGAAUUCGAAGCAGCGC--A-CUCCUCCUCCC--A--U-CGCC-GCUUCGAU---GGAUU-GGCAAC---AC--UCCUCCUCCCG--GUU-GCCAAUCGCCU----UU-----AU-GACGCCCGC-CGG-U------CCU---CCUCCC-CCGACGGGCGUCAUUU
CP002447.1/3675142-3675022     AGUUUUCGUCAAAGCCG--A---CCUCCUCCC-----C-GGCG-AUGACGAA--UCGGCCCGAC-CU---UC--ACCUCCUCCCG--AGG-GUUGGCCACAA----AA-----AC-GGCGCCCGC-CGC-A------CCU---CCUCCC-GCGGCGGGCGCUGUUU
CP001851.1/359224-359330       AUACAUCGAGU----U-----CGCCUCCUCCC--A--G-A-----ACUCGAU-AAGGAA--UACGGC---AC--UCCUCCUCCCA-AGCC-GUA-UUCAAGA----UC-----A---GGUC---G-CGC-A-----UCCU---CCUCCC-GCGC---GGCCUUUUU
CP000390.1/1916694-1916817     AAGAGUUUC-GUCGAGA--U-AUCCUCCUCCC--G--U-CUCG-ACGGAUAA--ACGGCC-GGC-UU---UC--UCCUCCUCCCG--AAACGCCGGUCGAUC----AA-----AACGACACCCGC-CGG-A------CCU---CCUCCC-CCGGCGGGUGUUGUUU
CP002447.1/2545673-2545788     AAUACCCGGUGAGUGGA--A---CCUCCUCCC-----U-CUGC-UCCCCGGG--GUGACC-AGCCAG----C--ACCUCCUCCCG--CUG-GC---UCGUAA----CA-----GG--AAAAGGCC-GGC-A------CCU---CCUCCC-GCCGGCCUUUUUCUUU
CP001624.1/28646-28767         GAUAUACAG-GCGCCCC--A--UCCUCCUCCC--A--G-GGUC-GU-CUG----UGGAAU-GACAGC---AC--UCCUCCUCCCA--GCU-GUCGUUCGGUU----UUUU-ACGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
CP000138.1/22818-22935         GUGACGAGCCGAAGCGC--U-GUAUUCUUCUU--A--GCCGCU-UCCGCC-----UGAUG-GACAGC---AC--UCCUCCUCCCA-UGCU-GUCGGUCACUA----UC-----G---AAGCCCGG-CGC-A-------CU----CUCCC-GCGCCGGGCUU-CUGC
AM040264.1/886972-886854       GUUCGUCGCAAAGCUCU--C-CACCUCCUCCC--A----GA-C-UUUGCGAU--AACAAG-ACCGGU---UC--UCCUCC-CAAU--GCC-GGUCUUCCCCU----AA-----UG--GCAUCCGU-CGC-C-------CU---CCUCCC-GCGACGGAUGCCAUUU
CP000629.1/1921242-1921118     -AUGAUGCAGGCGCUCU--U-AUCCUCCUCCC--A--A-GGUC-GCCUGC----GGGAAC-AGCAGC---AC--UCCUCCUCCCA--GCU-GCUGUUCGGUUC-UU--UU-CGAA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
CP000708.1/359682-359789       AUACAUCGAGU----U-----CGCCUCCUCCC--A--G-A-----ACUCGAU-AAGGAA--UACGGC---AC--UUCUCCUCCCA-AGCC-GUA-UUCAAGA----UC---------AGGCC--G-CGC-A-----UCCU---CCUCCC-GCGC--GGCCUUUUUC
CP000740.1/316304-316428       AUAUGUGGGCG----AC--C-UUCCUCCUCCC--G-GG-UUCU-UCGCUCAC--GAGAUC-AGCGCC---AC--UCCUCCUCCCG--GGCUGCUGAUCGGUU---C-UUU-CGGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCGGGCUUUUUCG
CP001074.1/4445016-4444894     ACUCAUCGAAACGGCUU--U-CUCCUCCUCCC--A-UA-AGCC-GU-UCGAC--AGGAUC-GACAAC---AC--UCCUCCUCCCA--GUU-GUCGAUCGAGU----UU-----AU--AAGCCCGA-CGG-A------UCU---CCUCCC-CCGUCGGGCUUUCUCA
CP001488.1/890461-890343       GUUCGUCGCAAAGCUCU--C-CACCUCCUCCC--A----GA-C-UUUGCGAU--AACAAG-ACCGGU---UC--UCCUCC-CAAU--GCC-GGUCUUCCCCU----AA-----UG--GCAUCCGU-CGC-C-------CU---CCUCCC-GCGACGGAUGCCAUUU
CP002447.1/3674963-3674843     GAAUUUCGUCAAAGCCG--A---CCUCCUCCC-----C-GGCG-AUGACGAA-UAUGGCC-GGCCUU----C--ACCUCCUCCCG--AAG-GUCGACCCCAA----AA-----AC-GACACCCGC-CGG-A------CCU---CCUCCC-CCGGCGGGUGUUGUUG
CP001623.1/112604-112720       AUGGACUGAAGCG---C--U-UAACCCCUCCG--A--G---CC-GCUUCGGU--CCGACG-GACAGC---AC--UCCUCCUCCCA-GGCU-GUCGGUCACUA----UC-----G---AAGCCCGG-CGC-A-------CC---UCUCCC-GCGCCGGGCUUUUGUC
CP000628.1/597900-598022       CCCCUCGAAGGCAGCGC--AUCUCCUCCUCCC--A--G-CGCU--CCUUCAU--C-GAUU-GGCAAC---UC--UCCUCCUCCCU--GUU-GCCAAUCCGGA----UC-----AA--GAGCCCGA-UGC-A-----UCCU---CCUCCC-GCAUCGGGCUCUUCUU
AM236080.1/4988158-4988038     ACUCAUCGACACGGCU---U-CUCCUCCUCCC--A--U-AGCC-GU-UCGAU--AGGGUC-GACAAC---AC--UCCUCCUCCCA--GUU-GUCGAUCGAGU----UU-----AU--AAGCCCGA-CGG-A------UCU---CCUCCC-CCGUCGGGCUUUCUCG
CP001074.1/1912597-1912478     GAGAUUCGCAGCCGCGC--A-CUCCUCCUCCC--A-AG-CGC--GCUGCGAU---GGACU-GGCAAC---AC--UCCUCCUCCCA--GUU-GCCAGUCACUA----UA-----AU--GCGCCCGC-CGG-A--------U---CCUCCC-CCGGCGGGCGUUUUAU
CP001191.1/1534621-1534501     GAGAUUCGCAGCCGCGC--A-CUCCUCCUCCC--A-AG-CGC--GCUGCGAU--AAGACU-GGCAAC---AC--UCCUCCUCCCA--GUU-GCCAGUCAUCA----UA-----AU--GCGCCCGC-CGG-A--------U---CCUCCC-CCGGCGGGCGUUUUAU
CP002447.1/3675318-3675197     GGAAUUUCGCCAGGGUC--G--ACCUCCUCCC--C--G-ACCU-UGACGAAU--ACGGUC-ACCCCU----U--ACCUCCUCCCA--AGG-GUUGACCACCA----AA-----AC-GGCGCCCGC-CGC-A------CCU---CCUCCC-GCGGCGGGCGUUGUUU
CP001623.1/265945-266069       UGGUUUCAG-GCGACCC--A-CUCCUCCUCCC--A-AG-GGGA-GC-CUGAC---GGAAC-AGCGGC---AC--UCCUCCUCCCA--GCC-GUUGUCCAAUC----UUUU-GGAA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCGGGCUUUUUCA
AE007869.2/109473-109594       AAUCAUCGAAGCGACGC--A-CUCCUCCUCCC--A--G-CGUC-GCC-CGAU--UGGACU-GACAAU---AC--UCCUCCUCCCA--AUU-GUCAGUCAGUU----UC-----AA--GAACCCGG-CGC-A------CCU---CCUCCC-GCGCCGGGUUUUUGCG
BA000012.4/6092540-6092423     GGUUGUCGGC----CAU----CUACUCCUCCC--A-GA-UGCG-AUGCCGAC-GCUGAAU-GGGGUG----C--ACCUCCUCCCG--CGC-CACAUUCGAAA----UC-----G---AGCCCGCU-GCC-A------CCU---CCUCCC-GGCAGCGGGCUUUUUU
BA000012.4/890760-890880       AGAUUUCGUCAAAGCCG--A---CCUCCUCCC-----C-GGCA-AUGACGAA--UAGGCC-CAACCU---UC--ACCUCCUCCCG--AGG-GUUGGCCAACC----AA-----AC-GGCGCCCGC-CGC-A------CCU---CCUCCC-GCGGCGGGCGUUGUUU
CP001389.1/3720579-3720700     CCUCAUCGAAGCGCUGC--A---CCUCCUCCC-----G-CGGC-GCC-CGAU-GCGGGUC-GGUUUC---AC--UCCUCCUCCCA--GGA-ACCGGCCAAGU----UU----GAA--GACCCCGACGCC-A------CCU---CCUCCC-GGCUCGGGGUCUUUUU
CP000133.1/4314505-4314384     AUCCAUCGAAACGGCUU--U-CUCCUCCUCCC--A--U-AGCC-GU-UCGAC--AGGAUC-GGCAAC---AC--UCCUCCUCCCA--GUU-GUCGGUCGAGU----UU-----AU--AAGCCCGA-CGG-A------UCU---CCUCCC-CCGUCGGGCUUUCUCG
CP000633.1/2043913-2044036     CAGUUUCGGCGCCGCAU--A-CUCCUCCUCCC--A--A-UGC--GCGCCGAA--CGGGCU-GACAAC---CC--UCCUCCUCCCA--GUU-GUCGCCCAUUU----CA-----AAUGACGCCCGC-CGG-A------UCU---CCUCCC-CCGGUGGGCGUUAUUG
CP001578.1/873167-873049       GUUCGUCGCAAAGCUCU--C-CACCUCCUCCC--A--G-G--C-UUUGCGAU--AACAAG-ACCGGU---UC--UCCUCC-CAAU--GCC-GGUCUUCCCCU----AA-----UG--GCAUCCGU-CGC-C-------CU---CCUCCC-GCGACGGAUGCCAUUU
CP001389.1/1434586-1434463     GGAAUUCGAAACAGCGC--A-CUCCUCCUCCC--A--G-CGCU-GUUUCGAU--AGGAUU-GGCAAC---AC--UCCUCCUCCCG--GUU-GCCAAUCAUUC----UU-----AU-GACGCCCGC-CGG-A------UCU---CCUCCC-UCGGCGGGCGUCGUUC
BA000012.4/890582-890702       GAAUUUCGCUGGGGUC-----GACCUCCUCCC--C----GACCUCCAGCGAA--C-GGUC-AGCCCU---UA--UCCUCCUCCCG--AGG-GUUGGCCAACC----AA-----AC-GGCGCCCGC-CGC-A------CCU---CCUCCC-GCGGCGGGCGUUGUUU
AM236080.1/512658-512779       AUCUUCGUAAGCAGCGC--A-CUCCUCCUCCC--A--G-CGCU--CUUACAU--CGGACU-GACAAC---AC--UCCUCCUCCCA--GUU-GUCAGUCAGGA----UC-----AA--GAGCCCGG-CGC-A------CCU---CCUCCC-GCGUCGGGCUUUUUUC
AM236085.1/574592-574471       -GAUAUACAGGCGCCCC--A--UCCUCCUCCC--A--G-GGUC-GUCUGU-----GGAAU-GACAGC---AC--UCCUCCUCCCA--GCU-GUCGUUCGGUU----UUUU-ACGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
CP001075.1/346021-345900       GAUAUGCA-GGCG-CCC----AUCCUCCUCCC--A--G-GGUC-GCC-UG-C--GGGAAC-AACAGC---AC--UCCUCCUCCCA--GCU-GUCGUUCGGUUCUUUU-----CGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
CP001192.1/306454-306339       GUGGACCGACGCG---C--U-CACCCCCUCCG--A--G---CC-GCUUCGGU--UCGACG-GACAGC---AU--CCCUCCUCCCA-GGCU-GUCGGUCACUA----UC-----G---AAGCCCGG-CGC-C-------CU----CUCCC-GCGCCGGGCUUUCGUU
CP000631.1/138626-138502       GAAUUUCAG-ACGGCCC--A-CUCCUCCUCCC--A--G-GGAC-GU-CUG-U--AGGAAC-AGCGAC---AC--UCCUCCUCCCA--GUC-GCUGUUCGGUUC-UU--UU-CGAA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
AM236080.1/2175074-2174956     GAGAUUCGUAGCCGCGC--A-CUCCUCCUCCC--A--G-CGC--GCUGCGAU--A-GACU-GGCAAC---AC--UCCUCCUCCCA--GUU-GUCAGUCACCA----UA-----AC--GCGCCCGC-CGG-A--------U---CCUCCC-CCGGCGGGCGUUUUUG
CP000133.1/1926358-1926239     GAGAUUCGCAGCCGCGC--A-CUCCUCCUCCC--A-AG-CGC--GCUGCGAU---GGACU-GGCAAC---AC--UCCUCCUCCCA--GUU-GCCAGUCGCUA----UA-----AU--GCGCCCGC-CGG-A--------U---CCUCCC-CCGGCGGGCGUUUUAU
CP001191.1/98050-98171         AUCUCCGUAAGCAGCGC--A-CUCCUCCUCCC--A--G-CGCU--CUUACAU--CGGACU-GACAAC---AC--UCCUCCUCCCA--GUU-GUCAGUCAGGA----UC-----AA--GAGCCUGG-CGC-A------CCU---CCUCCC-GCGCCAGGCUCUUUUC
CP001076.1/112292-112418       AAGUUUAG--ACGGCCC--A-CUCCUCCUCCC--AAAG-GGAC-GU--CUGU--GGGAAC-AGCGGC---AC--UCCUCCUCCCA-GGUC-GCCGUUCGGUUCUUU--U--AGGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUCUA
ABRC01002556.1/2222-2346       GUGUUUCAG-GCGACCC--A-UUCCUCCUCCC--A-AA-GGGC-GC-CUGAC---GGAAC-AGCGGC---AC--UCCUCCUCCCA--GCC-GUUGUUCAAUU----CUUU-CGAA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
AFSD01000003.1/1193499-1193621 CGAAUUGAGGCGACCCU--A--UCCUCCUCCC--A--A-GGGU-UGUCUUGU----GAAC-AAUGGC---AC--UCCUCCUCCCA--GCC-GUUGUUCGAGU----UUU--UGAA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCGGGCUUUUUCG
ABQZ01000022.1/48-170          GAUAUGCAG-GCG-CCC----AUCCUCCUCCC--A--G-GGUC-GC-CUGCG--UGGAAC-GACAGC---AC--UCCUCCUCCCA--GCU-GUCGUUCGGUU---C-UUU-UCGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
AGVZ01000006.1/161917-162039   CGGAUUGAGAUGACCCU--A--UCCUCCUCCC--A--A-GGGU-UGUCUUGU----GAAC-AAUGGC---AC--UCCUCCUCCCA--GCC-GUUGUUCGAAA----UUU--CGGA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCGGGCUUUUUCG
ABQY01001266.1/48-171          CGAUAUGCAGGCGCCC-----GUCCUCCUCCC--A--G-GGUC-GCCUGC----GGGAAC-GACAGC---AC--UCCUCCUCCCA--GCU-GUCGUUCGGUU----CUUUUCGAA--AAGCCUGC-CGC-A------CCU---CCUCCC-GCGGCAGGCUUUUUCG
AB032242.1/1025-1145           AUCAUCCGAAGCGACGC--A-CUCCUCCUCCC--A--G-UGUC-GC-UCGAU-GUGGAUC-GGUGGU---AC--UCCUCCUCCCA--AUC-ACCGAUCAAUU----UU-----G---AAGCCUGC-CGC-A------CCU---CCUCCC-GCGG-AGGUUUUUCCU
ABRB01000056.1/343-470         GAAAUUCAG-ACGGCCA--A-CUCCUCCUCCC--GAAG-GGAC-GU-CUG-U--CGGAAC-AGCGGC---AC--UCCUCCUCCCA-GGUC-GCUGUUCGGUU----CUUUUAGAA--AAGCCUGC-CGC-A------CCU---CCACCC-GCGGCAGGCUUUUCUA
ABIA02000005.1/16560-16686     AGAAUUCGGAGCGGCCU--C-CUCCUCCUCCC--A-AU-AGCC-GCUUCGAU--GUGACU-GACGUU---CA--UCCUCCUCCCG--AGC-GUCAGUCUUCC----AA-----AAUGGCGCCCAC-CGG-A-----UCCU---CCUCCC-CCGGUGGGCGUUAUUU
AGSN01000128.1/201468-201347   AGAAUUUCGCCAGGGUC----GACCUCCUCCC--C--G-ACCC-UGACGGAU--ACGGCC-AACCUU----C--ACCUCCUCCCG--AGG-GUUGACCAGCA----AA-----AC-GGCGCCCGC-CGC-A------CCU---CCUCCC-GCGGCGGGCGUUGUUU
ACQA01000001.1/1034034-1033915 GUUCAUCGC--CAAACC----AUCCUCCUCCC--A--G-GUUU-G--GCGAU--AACAAG-ACCGGU---UC--UCCUCCUCCCAACACC-GGUCUUACUAU----AA-----UG--GCAUCCGU-CGC-U------CCU---CCUCCC-GCGACGGAUGCCAUUU
AGIX01000001.1/372706-372828   GGAAUUUCGCUGGGGUC----GACCUCCUCCC--C--G-ACCC-AAGCGAAU--ACGGUC-CGCCCU---UA--CCCUCCUCCCA--AGG-GCUGACCAUCA----AA-----AC-GGCGCCCGC-UGC-A------CCU---CCUCCC-GCGGCGGGCGUUGUUU
ACXD01000073.1/113959-113837   GAAUAUCGCCGGGUGUU--U-CUCCUCCUCCC--A--U-UCCC-UCGGCGAU--CAAAGA-CCGGAC---AC--UCCCCCCCCAA--GUC-CGGUCUUUUCC---AUA-----AA--ACACCCGU-CGC---------CG---CCUCCCGGCGACGGGUGUUUUGU
ADFB01000015.1/6603-6477       GAAUAUCGCCGGGGUGU-UU-CUCCUCCUCCC--A--U-UCCC-UCGGCGAU--CAAAGA-CCGGA-CACUC--UCCUCCUCCCAAG-UC-CGGUCUUUUCC---AUA-----AA--ACACCCGU-CGC---------CU---CCUCCCGGCGACGGGUGUUUUGU
AAPJ01000003.1/273428-273309   GACUUUCGCAAGGGUCC--A-CUCCUCCUCCC--A--G-GACC-CAAGCGGA--UCGGAA-ACUGCC---AC--UCCUCCUCCCA--GGC-AGUUUCCACCC----AG---------ACGCCCGC-CGGG---------U---CCUCCCCCCGGCGGGCGCCCAGA
ADEZ01000033.1/272602-272476   GAAUAUCGCCGGGGUGU-UU-CUCCUCCUCCC--A--U-UCCC-UCGGCGAU--CAAAGG-CCGGAC---ACUUUCCUCCUCCCA-AGUC-CGGUCUUUUCC---AUA-----AA--ACACCCGU-CGC---------CU---CCUCCCGGCGACGGGUGUUUUGU
ACBO01000020.1/11259-11385     GAAUAUCGCCGGGUGUU--U-CUCCUCCUCCC--A--U-UCCC-UCGGCGAUCAAAGACC-GGACAC---UC--UCCUCCCCCCC--AAG-UCCGGUCUUUUC-CAUA-----AA--ACACCCGU-CGC---------CG---CCUCCCGGCGACGGGUGUUUUGU
AL672113.1/48134-48252         UGUUGUCGGC----CAU----CUACUCCUCCC--A-GA-UGUG-GUGCCGAC-GCUGAAU-GGGGCG----C--ACCUCCUCCCG--CGU-CUCAUUCGAAA----UC---------GAGCCCGC-UGCCA------CCU---CCUCCCGGCAGCGGGCUUUUUUA
AATP01000007.1/157109-156986   AGGGUUUCGCUUCGGGC--U-CACCUCCUCCC--G-GGCUUCG-AAGCGGAU--CAAGGG-GCCUAC---AC--UCCUCCUCCCAACGUA-GGCUCCGUUCA----UA-----CG--ACACCCGC-CGG----------U---CCUCCC-CCGGCGGGUGUUGUUC
ABRD01000625.1/697-812         GCGGACUGAAGC---GC--U-UAACCCCUCCG--A--G-C--U-GCUUCGGC--UUGACG-GACAGC----A--UCCUCCUCCCA-GGCU-GUCGGUCACUA----UC-----G---AAGCCCGG-CGC-U------CCU----CUCCC-GCGCCGGGCUUUCGUU
AEYZ01000051.1/13533-13653     AUGAGCUGAAGC-GCU---G---CACCCUCUU--A----AGCG-GCUUCGGC--CCGACG-GGCAGC---AC--UUCUCCUCCCA-GGCU-GUCGGUCACUA----UC-----G---AAGCCCGG-CGC-A------UCUCUCCCCCCC-GCGCCGGGCUUCUGCC
ABRA01002512.1/2841-2718       AUGAGCUGAAGC-GCU---G---CACCCUCUU--A----AGCG-GCUUCGGC--CCGACG-GGCAGC---AC--UUCUCCUCCCA-GGCU-GUCGGUCACUA----UC-----G---AAGCCCGG-CGC-AUCUCUCCCC---CCCCCC-GCGCCGGGCUUCUGCC
#=GC SS_cons                   ::::::<<<-<<<<<<<.._.___________.._..>.>>>>.>>->>>,,..,,<<<<.<<<<<<...__..___________..>>>.>>>>>>>----....--.....--..<<<<<<<<.<<<._......___...______.>>>>>>>>>>>:::::
#=GC RF                        aaauuUcggagcggccc..a.cuCCUCCUCCC..A..g.ggcc.gcuccgAu..aggacc.ggcggc...aC..UCCUCCUCCCa..gcc.gccggucaauu....ua.....aa..acgCCcGc.CGc.A......CCU...CCUCCC.gCGgCgGGcguUuUuu
//
# STOCKHOLM 1.0

#=GF AC   RF02345
#=GF ID   ar15
#=GF DE   Alphaproteobacterial ar15
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22418845
#=GF SS   Predicted; PMID:22418845
#=GF GA   40.00
#=GF TC   40.60
#=GF NC   36.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00108
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   22418845
#=GF RT   A survey of sRNA families in alpha-proteobacteria.
#=GF RA   del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N,
#=GF RA   Jimenez-Zurdo JI
#=GF RL   RNA Biol. 2012;9:119-129.
#=GF RN   [2]
#=GF RM   22690807
#=GF RT   Identification of two small regulatory RNAs linked to virulence in
#=GF RT   Brucella abortus 2308.
#=GF RA   Caswell CC, Gaines JM, Ciborowski P, Smith D, Borchers CH, Roux CM, Sayood
#=GF RA   K, Dunman PM, Roop Ii RM
#=GF RL   Mol Microbiol. 2012;85:345-360.
#=GF RN   [3]
#=GF RM   17971083
#=GF RT   Identification of differentially expressed small non-coding RNAs in the
#=GF RT   legume endosymbiont Sinorhizobium meliloti by comparative genomics.
#=GF RA   del Val C, Rivas E, Torres-Quesada O, Toro N, Jimenez-Zurdo JI
#=GF RL   Mol Microbiol. 2007;66:1080-1091.
#=GF RN   [4]
#=GF RM   21320185
#=GF RT   Small RNA-mediated control of the Agrobacterium tumefaciens GABA binding
#=GF RT   protein.
#=GF RA   Wilms I, Voss B, Hess WR, Leichert LI, Narberhaus F
#=GF RL   Mol Microbiol. 2011;80:492-506.
#=GF RN   [5]
#=GF RM   20205931
#=GF RT   The Sinorhizobium meliloti RNA chaperone Hfq influences central carbon
#=GF RT   metabolism and the symbiotic interaction with alfalfa.
#=GF RA   Torres-Quesada O, Oruezabal RI, Peregrina A, Jofre E, Lloret J, Rivilla R,
#=GF RA   Toro N, Jimenez-Zurdo JI
#=GF RL   BMC Microbiol. 2010;10:71.
#=GF RN   [6]
#=GF RM   23869210
#=GF RT   Independent activity of the homologous small regulatory RNAs AbcR1 and
#=GF RT   AbcR2 in the legume symbiont Sinorhizobium meliloti.
#=GF RA   Torres-Quesada O, Millan V, Nisa-Martinez R, Bardou F, Crespi M, Toro N,
#=GF RA   Jimenez-Zurdo JI
#=GF RL   PLoS One. 2013;8:e68147.
#=GF WK   Ar15_RNA
#=GF SQ   61


CP001389.1/1612626-1612514   GGUUGGUGCACCUG--GCGG-C-UUCC-UCCUCCCC-GGCCGUCGCAUCAGCUGUUCCCCUCUGGAGGUUUCC--------A-ACCUUCACAACUG-ACAGGGCCCAAGUUCG--CUUGUGGCCCUCUUUU
CP000638.1/198928-199036     AGCUGAUGCACGCG--AUGG-C-CU---UCUACCAG-UGCUAUCGCAUCAGCUGUUCCCCUCUGGAGGUUUUA----------ACCUUCACACUUC--AAGGGCCUCGGUUUU--CCGAUGGCCCUAUUUU
CP000738.1/1337331-1337215   AGCUGAUGCAUCUU-GGUGG-C-UUCU-CCUCCCAG-UGCCACCGCAGCAGCUGUUCCCCUCUGGAGGUUUAAA-------UUACCUUCACAACUA-UAAGGGCCCAAGUUCU-UCUUGUGGCCCUCUUUU
AE017223.1/1471191-1471076   AUCUCAG---UGCU--GCGU-U-UCCU-CCUCCCAUUUUGCGCAGGCUGAG-UGUUCCCCUCUGGAGGUUUGCCUCA-AUGGCACCUUCAAAAUUC--AAAAGCCGGACGUUU--GUC-UGGCUUUUUUUU
CP000633.1/2608532-2608644   AGCUGAUGCACACG--GUGG-C-UUCC-UC-CCAGU-UCCCACCGCACCAGCUGUUCCCCUCUGGAGGUUUUU--------A-ACCUUCACACUUU--AAGGGCCCUGGAGUAAUCCGGUGGCCCCUUUUU
AE014291.4/1453129-1453014   AUCUCAG---UGCU--GCGU-U-UCCU-CCUCCCAUUUUGCGCAGGCUGAG-UGUUCCCCUCUGGAGGUUUGCCUCA-AUGGCACCUUCAAAAUUC--AAAAGCCGGACGUUU--GUC-UGGCUUUUUUUU
CP001074.1/3155217-3155329   AGCUGAUGCACAUG--GUGG-C-UUUU-CCUCCCAG-UUCCACCGCAUUAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACACUUA-UAAGGGCCCUGGUUUU--CCGGUGGCCCUCUUUU
CP001389.1/1612830-1612714   AGCUGAUGCAUCUUUGGUGG-C-UUCU-CCUCCCAG-UGCCACCGCAGCAGCUGUUCCCCUCUGGAGGUUUUAA-------UUACCUUCACAACUA-CAAGGGCCCAAGUUUU--CUUGCGGCCCUCUUUU
CP000637.1/52397-52289       AGCUGAUGCACGCG--ACGG-C-C--U-CCUCCCAG-UGCCAUCGCAUCAGCUGUUCCCCCCUGGAGGUUUUA----------ACCUUCACACUUC--AAGGGCCUCGGUUUU--CCGGUGGCCCUAUUUU
CP000633.1/2608739-2608836   AGUUGC-----GGA--GAAA-C-UAUC-AUUGGUAG-UUUUUUG----UAGCUGUUCCCCUCUGGAGGUUUGA--------CGACCUUCACACUUG-AAGCAUCC---GUUCG--C----GGGUGCUUUUU
CP000911.1/1473909-1473794   AUCUCAG---UGCU--GCGU-U-UCCU-CCUCCCAUUUUGCGCAGGCUGAG-UGUUCCCCUCUGGAGGUUUGCCUCA-AUGGCACCUUCAAAAUUC--AAAAGCCGGACGUUU--GUC-UGGCUUUUUUUU
AL591688.1/1698937-1698820   AGCUGAUGCAUCUUUGGUGG-C-UUCU-CCUCCCAG-UGCCACCGCAGCAGCUGUUCCCCUCUGGAGGUUUUAA-------UUACCUUCACAACUA-CAAGGGCCCAAGUUUU-UCUUGUGGCCCUCUUUU
CP000134.1/157296-157406     AGCUGAUGCACAUG--GCGG-C-U-UU-CCUCCCAG-UUCCGCCGCAGCAGCUGUUCCCCUCUGGAGGUUUAU--------UGACCUUCACACUUC--AUGGGCCGCGGUUU---CCGCUGGCCCAUUUUU
CP000887.1/1469525-1469410   AUCUCAG---UGCU--GCGU-U-UCCU-CCUCCCAUUUUGCGCAGGCUGAG-UGUUCCCCUCUGGAGGUUUGCCUCA-AUGGCACCUUCAAAAUUC--AAAAGCCGGACGUUU--GUC-UGGCUUUUUUUU
CP000709.1/709415-709521     ACUUACCGUU------GUGC-C-U-----CCUCCCA-UUGCGC-ACGGUAAGUGUUCCCCUCUGGAGGUUUGCCCAA-GUGGCACCUUCAUAACUU-------GGCCGGACUU-CCCAGUCCGACUCUUUU
BA000013.4/65154-65047       AGCUGAUGCACGCG--AUGG-U-U----UCCUCCCA-UUCCAUCGUAUCAGCUGUUCCCCUCCGAAGGUUUUG----------ACCUUCACACCUA--AAGGGCUUCGGUUUU--CCGAUGGCCCUGUUUU
CP000872.1/1452087-1451972   AUCUCAG---UGCU--GCGU-U-UCCU-CCUCCCAUUUUGCGCAGGCUGAG-UGUUCCCCUCUGGAGGUUUGCCUCA-AUGGCACCUUCAAAAUUC--AAAAGCCGGACGUUU--GUC-UGGCUUUUUUUU
CP000708.1/1460624-1460509   AUCUCAG---UGCU--GCGU-U-UCCU-CCUCCCAUUUUGCGCAGGCUGAG-UGUUCCCCUCUGGAGGUUUGCCUCA-AUGGCACCUUCAAAAUUC--AAAAGCCGGACGUUU--GUC-UGGCUUUUUUUU
CP000761.1/22208-22317       AGCUGAUGCAUUUU-GACGG----UCA-CCUCCCAG-UUCCGUCGCAUCAGCUGUUCCCCUCUGGAGGUUCAA---------GAUCUCCACACUUC--AUGGGCCGCGGUUU---CCGACGGCCCAUUUUU
CP002248.1/2112823-2112936   AGUUGAUGCACACG--GUGG-C-UUUU-CCUCCCAG-UUCCACCGCAUCAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACACUUA--AAGGGCCCUGGAUUUAUCCGGCGGCCCUCUUUU
AM939560.1/1-112             AGCUGGUGCAUCUA--GCGG-C-UUUC-UCCUCCCC-AGCCGCUGCAGCAGCUGUUCCCCUCUGGAGGUUUGA--------A-ACCUUCACAACUG-AAAGGGCCCAAGUUU---CUUGUGGCCCUCUUUU
CP001622.1/2981499-2981610   AGCUGAUGCAUCUU--GUGG---UUUC-UCUCCCAG-UACCACCGCAUUAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACAAUUA-CAAGGGCCCUGGUUUU--CCGGUGGCCCUCUUUU
AM236085.1/567166-567056     AGCUGAUGCAACAC-GGCGG-C-U-UU-CCUCCCAG-UUCCGUCGUUUCAGCUGUUCCCCUCUGGAGGUUUAU----------ACCUUCACAAUUA--AUGGGCCACGGUUCU--CCGUCGGCCCUUUUUU
AM236080.1/3605714-3605826   AGCUGAUGCAUCUU--GUGG---UUUC-UCUCCCAG-UACCACCGCAUUAGCUGUUCCCCUCUGGAGGUUUUU--------UGACCUUCACAAUUA-UAAGGGCCCUGGUUUU--CCGGUGGCCCUCUUUU
CP001076.1/188041-187930     AGUUGAUGCAGUCG--AUGG---UUUU-CCUCCCAG-UGCCAUCGUAUCAGCUGUUCCCCUCUGGAGGUUAUU---------GACCUUCACACCUU-AAAGGGCCCUGGUUUU--CCAGCGGCCCUAUUUU
CP001191.1/2770612-2770724   AGCUGAUGCACAUG--GUGG-C-UUUU-CCUCCCAG-UUCCACCGCAUUAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACACUUA-UAAGGGCCCUGGUUUU--CCAGUGGCCCUCUUUU
CP001624.1/36176-36286       AGCUGAUGCAACAC-GACGG-C-U-UU-CCUCCCAG-UUCCGUCGUUUCAGCUGUUCCCCUCUGGAGGUUUAU----------AUCUCCACAAUUA--AUGGGCCACGGUUUA--CCGUCGGCCCUCUUUU
U80928.5/172874-172763       AGUUGAUGCAAUCG--AUGG---UUUU-CCUCCCAG-UGCCGUCGUAUCAGCUGUUCCCCUCUGGAGGUUAUU---------GACCUUCACACCUU-AAAGGGCCCUGGUUUU--CCAGCGGCCCUAUUUU
CP000636.1/122736-122627     AGCUGAUGCACGCG--AUGG-C-UU---CCUCCCAG-GUCCAUCGUAUCAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACAAUUA--AAGGGCCUCGGUAUU--CCGAUGGCCCUAUUUU
CP000133.1/3117667-3117779   AGCUGAUGCACAUG--GUGG-C-UUUU-CCUCCCAG-UUCCACCGCAUUAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACACUUA-UAAGGGCCCUGGUUUU--CCAGUGGCCCUCUUUU
CP002250.1/211807-211701     AGCUGAUGCACGCG--AUGG-C-CUCU---UCCCAG-UGCCAUCGCAUCAGCUGUUCCCCUCUGGAGGUUUUA----------ACCUUCAC---UU-CAAGGGCCUCGGUUUU--CCGAUGGCCCUAUUUU
CP000133.1/3117890-3118001   AGCUGAUGCAUUUC--GUGG---UUUC-UCUCCCAG-UUCCACCGCAUUAGCUGUUCCCCUCUGGAGGUUAUU---------GACCUUCACAAUUC-AAAGGGCCCUGGUUUU--CCGGUGGCCCUCUUUU
AE006469.1/552873-552981     AGUUGAUGCGCAUG--GCAG---UUUU-CCUCCCAG-UUCCGCUGCAUCAACUGUUCCUCUCUGGAGGUUCAU----------ACCUUCAAACUCA---UGGGUCGCGGUUUU--CCGACGGCCCUUUUCU
AM236080.1/3605490-3605602   AGCUGAUGCACAUG--GUGG-C-UUUU-CCUCCCAG-UUCCACCGCAUUGGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACACUUA-UAAGGGCCCUGGUUUU--CCAGUGGCCCUCUUUU
CP000741.1/40165-40057       AGUUGAUGCACAUG--GCGG----UUU-CCUCCCAG-UUCCGCAGCAACAACUGUUCCCCUCUGGAGGUUCAU----------ACCUUCAAAACUA--AUGGGCCGCGGUUUU--CCGACGGCCCUUUUUU
AM040264.1/1468345-1468230   AUCUCAG---UGCU--GCGU-U-UCCU-CCUCCCAUUUUGCGCAGGCUGAG-UGUUCCCCUCUGGAGGUUUGCCUCA-AUGGCACCUUCAAAAUUC--AAAAGCCGGACGUUU--GUC-UGGCUUUUUUUU
CP000738.1/1337126-1337014   AGCUGGUGCAUAUA--GCGG-C-UUUC-UCCUCCCC-AGCCGCUGCAGCAGCUGUUCCCCUCUGGAGGUUUGA--------A-ACCUUCACAACUG-AAAGGGCCCAAGUUUU--CUUGUGGCCCUCUUUU
CP001622.1/2981275-2981387   AGCUGAUGCACAUG--GUGG-C-UUUU-CCUCCCAG-UUCCACCGCAUUAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACACUUA-UAAGGGCCCUGGUUUU--CCAGUGGCCCUCUUUU
CP000629.1/1011624-1011514   AGUCAACGCGAUCG--GCGU-U-UCCCUCCUCCCGG-UCUCGCUGCGUUGGCUGUUC-CCUCUGGAGGUUU-----------GACCUUCAAACUUA-AAGGGCUCCGGUUCAU--GCCGAGAGCCCUUCUU
CP000758.1/1751482-1751595   AUCUCAGC---GCU--GCGU-U-UCCU-CCUCCCAU-UUGCGCAGGCUGAG-UGUUCCCCUCUGGAGGUUUGCCUCA-AAGGCACCUUCAAAACUC---AAAGCCAGACAUUU--GUCU-GGCUUUUUUUU
CP001191.1/2770835-2770946   AGCUGAUGCAUCUU--GUGG---UUUC-UCUCCCAG-UACCACCGCAUUAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACAAUUA-CAAGGGCCCUGGUUUU--CCGGUGGCCCUCUUUU
CP000874.1/134190-134081     AGUUGAUGCACAUG--GCGG---UUUU-CCUCCCAG-UUCCGCUGCAACAGCUGUUCCCCUCUGGAGGUUCAU----------ACCUUCAAACUCA---CGGGCCGCGGUUUU-UCCGGCGGCCCUUUUUU
CP000628.1/2506215-2506328   AGCUGAUGCAUACG--GUGG-C-UUUU-CCUCCCAG-UUCCACCGCAUUGGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCAUACCUA--UAGGGCCCUGGUUUACUCCGGAGGCCCUUUUUU
CP001578.1/1461416-1461301   AUCUCAG---UGCU--GCGU-U-UCCU-CCUCCCAUUUUGCGCAGGCUGAG-UGUUCCCCUCUGGAGGUUUGCCUCA-AUGGCACCUUCAAAAUUC--AAAAGCCGGACGUUU--GUC-UGGCUUUUUUUU
CP001074.1/3155440-3155552   AGCUGAUGCAUUUC--GUGG---UUUC-UCUCCCAG-UACCACCGCAUUAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACAAUUA-UAAGGGCCCUGGUUUU-UCCGGUGGCCCUCUUUU
AE007869.2/2163254-2163367   AGUUGAUGCACACG--GUGG-C-UUUU-CCUCCCAG-UUCCACCGCAUCAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACACUUA--AAGGGCCCUGGAUCUAUCCGGCGGCCCUCUUUU
CP001077.1/941345-941449     CGAGCCGGCUUUCG--AUGG-A-UU---CCUCGGGG-UUCCAUGGUCAGC-CGUUUUUCCUA--GAGGUCUAU--------UUACCUC--CACCUA---AGGGCCCUGGUUUU--CCAGUGGCCCUAUUUU
AE007869.2/2163454-2163551   AGCUGUCACGCUUG---------------CCCACGG-CA----CGCGACAGCUGUUCCCCUCUGGAGGUUUUG----------ACCUUCAAACUUG-UCAGGCCGCGGAGCAA--UCCAGCGGCCUUCUUU
AM236084.1/138799-138909     AACUGAUGCACAUG--GCGG----UCU-CCUCCCAG-UGCCGCCGCAACAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACACUUC--AUGGGCCUCGGUUCU-UCCGACGGCCCAUUUUU
CP000628.1/2506418-2506531   AGCUGAUGCACAUG--GUGG-C-UUUU-CCUCCCAG-UUCCACCGCAGCAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACACCUA--UAGGGCCCUGGUUCAUUCCGGUGGCCCUCUUUU
CP000759.1/1270083-1270188   ACUUACCGCU------GUGC-C-U-----CCUCCCA-UUGCGC-GCGGUAAGUGUUCCCCUCUGGAGGUUUGCCCAAUGUGGCACCUUCAUAACUU-AGCCGGAC----UUCC-C----AGUCCGGCUCUU
AP002086.1/116716-116828     AGCUGAUGCACAUG--GCGG-A-U-UU-CCUCCCAG-UGCCGCCGCAGCAGCUGUUCCCCUCUGGAGGUUUAAA-------UUACCUUCACAUCUA--AAGGGCCCGAGUUUU--CUCGUGGCCCUCUUUU
AFSD01000008.1/322059-321949 AGCUGAUGCAUAUG--GCGG----UCA-CCUCCCAG-UUCCGCCGCAUCAGCUGUUCCCCUCUGGAGGUUAGUU-------UGACCUUCACACUUC--AUGGGCCGCGAUAU---UCGCAGGCCCAUUUUU
ABRC01001985.1/1309-1198     AGCUGAUGCAUAUG--GCGG-C-CCCU-CCUCCCAG-UGCCGCCGCAGCAGCUGUUCCCCUCUGGAGGUUUAU--------UGACCUUCACACUUC--AUGGGCCGCGGUCU---CCGCUGGCCCAUCUUU
AECL01000024.1/10088-9979    AGCUGAUGCACAUG--GCGG-C-UU---CCUCCCAG-UUCCGCCGCAGCAGCUGUUCCCCUCUGGAGGUCCAU---------GACCUUCACACUUU--AUGGGCCGCGGUUUU--CCGUCGGCCCUUUUUC
ABIA02000019.1/52-168        AGCUGAUGCACCUUUGGUGG-CCUACU-CCUCCCAG-UGCCACCGCAUGAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCAUACCUA--UUGGGCCCGAGAGAAAUCUCGCGGCCCAUUUUU
AAGA01007206.1/671-789       AGCUGAUGCACCUUUGGCGGNC-UACU-CCUCCCAG-UGCCGCCGCAUGAGCUGUUCCCCUCUGGAGGUUUUU---------GACCUUCACACUUUGAUUGGGCCCGAGAGCAAUCUCGCGGGCCAUUUUU
AGVZ01000003.1/210720-210815 AGCUGUCACGCCUG----------------CCUAUG-CA----CGCGACAGCUGUUCCCCUCUGGAGGUUUUA----------ACCUUCAAACUCA--UUGGCCGCGGAGAAA--UCCGGCGGCCAUUUUU
Y13942.1/578-675             GGCUGUCACGCUCG----------------CUCAGG-CA----CGCGACAGCUGUUCCCCUCUGGAGGUUUUG----------ACCUUCAAACUUA-UCAGGCCGCGGGAAAU-AUCCAGCGGCCUUUUUU
AGSM01000003.1/250495-250398 GGCUGUCACGCUCG---------------CCCAAGG-CA----CGCGACAGCUGUUCCCCUCUGGAGGUUUUG----------ACCUUCAAACUUG-UCAGGCCGCGGAGACA--UCCAGCGGCCUUCUUU
ACEJ01000013.1/80301-80197   ACUUACCGUU------GUGC-C-U-----CCUCCCA-UUGCGC-ACGGUAAGUGUUCCCCUCUGGAGGUUUGCCCAA-AUGGCACCUUCAUAACUU-GGCCGGAC----UUCC-C----AGUCCGGCUCUU
#=GC SS_cons                 <<<<<-<<<-----..<<<<._.____.________.__>>>>->>>->>>>>,,,,,,,,,<<<<<<<____........__>>>>>>>,,,,,,..,<<<<<<<<<<____..>>>>->>>>>>:::::
#=GC RF                      aGcugacGCauaug..GcGg.c.Uuuu.cCUcCcag.UucCgCcGCgucagCuGUUCCCCUCUGgAGGUUUuu........ugACCUuCAcAauUa..aagGgcCccGguUuu..cCgguGgcCcuuUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02346
#=GF ID   ar35
#=GF DE   Alphaproteobacterial sRNA ar35
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22418845
#=GF SS   Predicted; PMID:22418845
#=GF GA   45.00
#=GF TC   45.20
#=GF NC   44.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22418845
#=GF RT   A survey of sRNA families in alpha-proteobacteria.
#=GF RA   del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N,
#=GF RA   Jimenez-Zurdo JI
#=GF RL   RNA Biol. 2012;9:119-129.
#=GF WK   %CE%91r35_RNA
#=GF SQ   13


CP000759.1/1587279-1587135   AUAGGCAUUGCUUAAGAGCGCUGGAACGCGUCUGUCGCUCGCAAUAGCCU-U-CAUCGCUUGAU-GCUUUUGACCACGGAUGUACUGGCACUGGUA-GGAAAGCGAUGAUCA-GGAAGGUCGGUGCGUUUUCGCCCCGGCCUUU-UUUGUU
AE007870.2/132595-132736     AUAGCAACUGCUGGUGAGCG-CGAAUGAAA-UUGUCGUUCGCAGU-UGUU-U-UGUCGCUUCAG-ACUUUUGACCACGGAUGUACUGGCACUGGUGUUAAGAGCGAU-AUGA-GGAAGGUCGGUGCAAUAUUGCCCCGGCCUUU-UUUGUU
CP000138.1/136368-136511     AUCGGCAUCGCUGAUGAGCGCUGGAAAACAUCUGUCGCUCGCAAUUGCCG-C-AAUCGCUUUCU-GCUUUUGACCACGGAUGUACUGGCACUGGUACGG-CAGCGAU-GUGA-GGAAGGUCGGCGCGGUCUCGCCCCGGCCUUU-UUUGUU
AM236080.1/2256716-2256856   AUCGGCGUUGCUGGUGAGUG-CUCCAUGC--GAG-CGUUCGCGACUGCCG-A-AGUCGCUUAUC-UCUUUUGACCACGGAUGUACUGGCACUGGUGUGAAGAGCGAU-GUUG-GAAAGGUCGGUGCGAUUUCGCCCCGGCCUUU-UUUAUU
AL591985.1/577730-577871     AUCGGCAUUGCUUAUGAGCGCUGAUAA-C--UCGCCGCUCGCAAUUGCUG---CAUCGUUUUCG-ACUUUUGACCACGGAUGUACUGGCACUGGUUUGGUAAGCGAUGAUGA-GGAAGGUCGGUGCGGUUUCGCCCCGGCCUUU-UUUGUU
AFSD01000004.1/81384-81526   GUAGCAGCUGCUGGUGAGCGCAAGU-UAAA-UUGUCGUUCGCAGU-UGUUUU-AGUCGCUUUGG-ACUUUUGACCACGGAUGUACUGGCACUGGUGUUAAGAGCGAU-AUGA-GGAAGGUCGGUGCAAUAUUGCCCCGGCCUUU-UUUGUU
CP001626.1/114385-114244     AUCGGCGUUGCUGGUGAGCGCUCCACGA---GAG-UGUUCGCGACUGCCG-A-AGUCGCUUAUCUGCUUUUGACCACGGAUGUACUGGCACUGGUGUGAAGAGCGAU-GUUG-GAAAGGUCGGUGCGGUUUCGCCCCGGCCUUU-UUUAUU
AGSM01000013.1/19205-19063   AUGGCAACUGCUGGUGAGCG-CGAAUGAAA-UCGAUGUUCGCAGU-UGUUUU-AGUCGCUUUAG-ACUUUUGACCACGGAUGUACUGGCACUGGUGUUGAGAGCGAU-AUGG-GGAAGGUCGGUGCAAUAUUGCCCCGGCCUUU-UUUGUU
AGVZ01000009.1/223511-223650 ACAGCAACUGCUGGUGAGCGCA-AA---AU-AUGUCGUUCGCAGU-UGUU-UCCGUCGCUUUAG-ACUUUUGACCACGGAUGUACUGGCACUGGUGUUAAUGGCGAU-AUGA-GGAAGGUCGGUGCAAUAUUGCCCCGGCCUUU-UUUGUU
AGTN01581443.1/193-338       AUCGGCAUUGCUGAUGAGCGCUGAAAACCU-UCUACGCUCGCAAAUGCCG-C-CGCUGCUUUUA-ACCUUUGACCAUGGAUGUACCGGCACUGGUGGACAAAGCGGCGAUGA-GAGAGGUCGGAGCAACAUAGCCCCGGCCUUUUUUCGUC
CP002742.1/741206-741075     AAGCGCAUU---UGUCGGCGGGGGGAU-------ACGUUGGCAAUUGCGC-A-U--UGCUUUCG-ACUUGUGACCACGGAUGUACUGGCACGAGUUUUGAGAGCGAAAAGAC-AGAAGGCCGGGGCCAACGUGCCUCGGCCUUU-U--UUU
CP001832.1/1152387-1152254   AAGCGCAUU---UGUCGGCGGGGGGAU-------ACGUUGGCAAUCGCGC-A-U--UGCUUUCG-ACUUGUGACCACGGAUGUACUGGCACGAGUUUUGAGAGCGAA-AAGACAGAAGGCCGGGGCCAACGUGCCUCGGCCUUU-UUGUUG
CP002781.1/814035-814172     AAGCGCAUU---UGUCGGCGCGGAAGAAC--UACAUGCCGACAAUCGCGC-A-U--UGCUUUCG-ACUUGUGACCGCGGAGGCACUGGCUCAAGUUUUGAGAGCGAA-AAGACAGAAGGCCGGGGCCAGGU-GCUCCGGCCUUU-UUGUUA
#=GC SS_cons                 ::<<<<<<<------<<<<<__________.____>>>>>-->>>->>>>.,.,<<<<<<<--<.<<<--<<-<<<_________>>>>>-->>>>---->>>>>>>.<<<<.<<<<<<<<<<-<<<____>>>->>>>>>>>>.>>>>>:
#=GC RF                      AugggcauuGCUggUgagCGcugaaaaaca.uugaCGcucGCaauugccc.u.ugucGCucuuc.aCcUuuGACCaCGGAUGUACuGGCaCugGuguuaAgaGCgac.acga.ggaAGGcCGGuGCgauaUcGCCCCGgCCUuu.uucguu
//
# STOCKHOLM 1.0

#=GF AC   RF02347
#=GF ID   ar45
#=GF DE   Alphaproteobacterial sRNA ar45
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22418845
#=GF SS   Predicted; PMID:22418845
#=GF GA   40.00
#=GF TC   44.70
#=GF NC   34.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22418845
#=GF RT   A survey of sRNA families in alpha-proteobacteria.
#=GF RA   del Val C, Romero-Zaliz R, Torres-Quesada O, Peregrina A, Toro N,
#=GF RA   Jimenez-Zurdo JI
#=GF RL   RNA Biol. 2012;9:119-129.
#=GF WK   %CE%91r45_RNA
#=GF SQ   36


BX897700.1/1185319-1185173     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCUGG--UUCUCAAAU---GGUGAGAUU--AACCGGUACGGUACAUGGAAUUAAC--CACUCCAGUCAU-UCUUACGGCCAACCG-AAAGAGUGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
AE007870.2/205782-205635       GCCCAAAGUCGCACGUGCCCAUGUGUGUCC-------GCCGA-GUCCUCGAUG--UGGUGAGG-A--UUUAGGUAAGGUACCUGGAACUAAC--CCCUCCAGUCGC-UAUUCCGGCCAACCGGGAAAUGCGAGGACAUAU-GAAGCAACGACGGUGCGGGCCUUU
CP002998.1/97128-97273         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGAUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP000709.1/96814-96959         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGAUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
AM260525.1/1866022-1865876     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCUGG--UUCUCAAAU---GGUGAGG-U-CAACCGGUACGGUACCUGGAACUAAC--CGCUCCAGUCAU-UCUUACAGCCAAUUGUAAGA-AUGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
BA000012.4/2390867-2390721     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGGGA--AAUCGGUAAGGUAACUGGAGCUAAC--CCCUCCAGUCGG-UCUAGCGGCCAACCGCCA-GCCCGAGGACACCUUGAAGCAACGACGGUGCGGGCCUUU
CP002447.1/1999110-1999256     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGGGA--AAUCGGUAAGGUAACUGGAGCCAAC--CCCUCCAGUCGG-UCUAGCGGCCAACCGCCA-GCCCGAGGACACCUUGAAGCAACGACGGUGCGGGCCUUU
AM040265.1/96950-97095         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGAUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP000628.1/3124442-3124296     GCCCAAAGUCGCACGUGCCCGUGGGUGUCC-------GCCGA--UCCUCGAUG--UGGUGAGA-A--AAUCGGUAAGGUACCUGGAACUAAC--CCCUCCAGUCGC-UAUUUCGGCCAACCGAAAAAUGCGAGGACAUCU-GAAGCAACGACGGUGCGGGCCUUU
BX897699.1/1422014-1421868     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCUGG--UUCUCAAAU---GGUGAGAUU--AACCGGUACGGUACCUGGAACUAAC--CGCUCCAGUCAU-UCUUACGGCCAACCG-AAAGAAUGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP001489.1/97129-97274         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGAUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP001389.1/3069275-3069128     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--CCCUCGAUU--AGGUGAGG-A--UCUCGGUAAGGUACCUGGAACUAAC--CCCUCCAGUCGC-UAUUCCGGCCAACCGGGAAAUGCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP000873.1/97148-97293         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGAUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP000390.1/2952752-2952897     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGG--GCCUCGAAA--UGGCGAGG-A--AACCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUUACGGCCAACCG--AAGAUCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP000633.1/3167147-3167000     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAUG--UGGUGAGG-A--AAUCGGUAAGGUACCUGGAAUUAAC--CCCUCCAGUCGU-UAUCCCGGCCAACCGGGAAAUGCGAGGACACCUUGAAGCAACGACGGUGCGGGCCUUU
CP001622.1/3739551-3739404     GCCCAAAGUCGCACGUGCCCAUGGGUGUCC-------GCCGA-ACCCUCGAAU--UGGUGAGG-A--AAUCGGUAAGGUACCUGGAAUUAAC--CCCUCCAGUCGC-UAUUCCGGCCAACCGGAAAAUGCGAGGACGCCU-GAAGCAACGACGGUGCGGGCCUUU
CP000888.1/96948-97093         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGAUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
FN645454.1/1277776-1277630     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCUGG--UUCUCAAAU---GGUGAGAUU--AACCGGUACGGUACCUGGAACUAAC--CGCUCCAGUCAU-UCUUACGGCCAAUCG-AAAGAAUGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP001074.1/3953936-3953789     GCCCAAAGUCGCACGUGCCCAUGGGUGUCC-------GCCGA-ACCCUCGAAU--UGGUGAGG-A--AAUCGGUAAGGUACCUGGAAUUAAC--CCCUCCAGUCGC-UAUUCCGGCCAACCGGAAAAUGCGAGGACGCCU-GAAGCAACGACGGUGCGGGCCUUU
CP000759.1/1673683-1673538     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGUUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP000738.1/2892909-2892762     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--CCCUCGAUU--AGGUGAGG-U--UAUCGGUAAGGUACCUGGAACUAAC--CCCUCCAGUCGC-UAUUCCGGCCAACCGGGAAAUGCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP001191.1/3504389-3504242     GCCCAAAGUCGCACGUGCCCAUGGGUGUCC-------GCCGA-ACCCUCGAAU--UGGUGAGG-A--AAUCGGUAAGGUACCUGGAAUUAAC--CCCUCCAGUCGC-UAUUCCGGCCAACCGGAAAAUGCGAGGACGCCU-GAAGCAACGACGGUGCGGGCCUUU
CP002932.1/97052-97197         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGAUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP000133.1/3841158-3841011     GCCCAAAGUCGCACGUGCCCAUGGGUGUCC-------GCCGA-ACCCUCGAAU--UGGUGAGG-A--AAUCGGUAAGGUACCUGGAAUUAAC--CCCUCCAGUCGC-UAUUCCGGCCAACCGGAAAAUGCGAGGACGCCU-GAAGCAACGACGGUGCGGGCCUUU
CP001579.1/97102-97247         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGAUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
AE017224.1/96885-97030         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGAUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
AM236080.1/4405390-4405243     GCCCAAAGUCGCACGUGCCCAUGGGUGUCC-------GCCGA-ACCCUCGAAU--UGGUGAGG-A--AAUCGGUAAGGUACCUGGAAUUAAC--CCCUCCAGUCGC-UAUUCCGGCCAACCGGAAAAUGCGAGGACGCCU-GAAGCAACGACGGUGCGGGCCUUU
AL591688.1/3105445-3105298     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--CCCUCGAUU--AGGUGAGG-U--UAUCGGUAAGGUACCUGGAACUAAC--CCCUCCAGUCGC-UAUUCCGGCCAACCGGGAAAUGCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP001562.1/1761567-1761421     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCUGG--UUCUCAAAU---GGUGAGAUU--AACCGGUACGGUACCUGGAACUAAC--CGCUCCAGUCAU-UCUUACAGCCAAUUGCAAG-AAUGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP000524.1/1120229-1120083     GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCUGG--UUCCCAAAU---GGUGGGAUU--AACCGGUACGGUACCUGGAACUAAC--CGCUCCAGUCAU-UCUUGCGGCCAAUCG-AAAGAAUGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
CP000912.1/97254-97399         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--UCCUCGAAU---GGUGAGG-A--AUUCGGUACGGUACCUGGACCUAAC--CGCUCCAGUCGA-UCUGAUGGCCAACCGCCAGA-UCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
AATO01010394.1/305-451         GCCCAAAGUCGCACGUGCCUGUGGGUGUCC-------GCCGA--CCCUCGAAU--UGGUGAGG-A--AAUCGGUAAGGUACCUGGAAUUAAC--CCCUCCAGUCGU-UUCUCCGGCCAACCGGA-AGAGCGAGGACAUCUUGAAGCAACGACGGUGCGGGCCUUU
ABEF01036345.1/1274-1420       GCCCAAAGUCGCACGUGCCUGUGGGCGUCC-------GCCGG-UCCCUCGAAU---GGCGAGG-A--CAUCGGUAAGGUAACCGGAGUUAAC--CCCUCCGGUCGG-UUCGACGGCCAACCGCCGA-UCCGAGGACGCCUUGAAGCAACGACGGUGCGGGCCUUU
AATP01000001.1/1123291-1123438 GCCCAAUGUCGCACGUGCCGAUGGGCGUCC-------CCCGG--UCCUCACGA--UAGCGAGGA-UGAACCGGGACGGUACCUGGACGUAAC--ACACCCAGUCGG-UUUCGCGAGCCG-CGCGACAACCGAGGACGCUU-GAAGCAACGACGGUUCGGGCCUUU
AAPJ01000002.1/198038-197897   GCCCCAAGUCGCACGUGCCUGUGGGCGUCC-------CCCGG--UCCUCGAAU---G-CGAGGGU--UGCCGGGACGGUACCUGGAUCUGAC---GAUCCAGUCGG-UUUCGCUGC---UGGCGAAA-UCGUGGACGCCUUGAAGCAACGACGGUCCGGGCCUUU
CP001016.1/1241498-1241346     GCCCAAA-UCGCACGUGCCUGUGGUCGUG-GUCGAUUGGUGGGGAUCCGGACAAGAGGCCGGU-U--AACCACCUUAAAAGGAUCGACAGCCGGAGGCGAACCGGCGAACCCCG-CCAAACGGGGAAC---G---CGACUUAAAGCAACGACGGACCGGGCUUUU
#=GC SS_cons                   ((((---((((----(((----((((((((.......<<<<<..-<<<<<___..___>>>>>.-..-->>>>>,,,,,,,<<<<<______..___>>>>><<<<.--<<<<<<____>>>>>>--->>>>))))))))----)))-))))-----))))::::
#=GC RF                        GCCCAAAGuCGCACGuGCCugUgGgcGuCC.......gccGg..ucCucgAau..aGGcgaGg.a..AacCggcAagguAccugggacuAAC..cgccccaguCGc.uaucgcgGcCAACcgcgaaAugCGaGGaCgcCuUgAAGCaACGaCGGugCGGGCcUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02348
#=GF ID   tracrRNA
#=GF DE   Trans-activating crRNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22745249
#=GF SS   Predicted; PMID:22745249
#=GF GA   74.00
#=GF TC   76.80
#=GF NC   62.80
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   22745249
#=GF RT   A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial
#=GF RT   Immunity.
#=GF RA   Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E
#=GF RL   Science. 2012;337:816-821.
#=GF RN   [2]
#=GF RM   21455174
#=GF RT   CRISPR RNA maturation by trans-encoded small RNA and host factor RNase
#=GF RT   III.
#=GF RA   Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA,
#=GF RA   Eckert MR, Vogel J, Charpentier E
#=GF RL   Nature. 2011;471:602-607.
#=GF WK   Trans-activating_crRNA
#=GF SQ   35


AP010655.1/737198-737108       UGUUGGAACUAUUCGAAACAACAC-AGC---A-AGUUAAAAUAAGG--U-UU-A-UCCGUAUUCAA-CUUG----A-AA-AAGUGCGCACCGA-UUCGG-UGCUUUUUUA
AEUW02000001.1/849316-849406   UGUUGGAAACAUUCGAAACAACAC-AGC---A-AGUUAAAAUAAGG--U-UU-A-UCCGUAUCCAA-CUUG----A-AA-AAGUGAGCACCGA-UUCGG-UGCUUUUAUU
ACRJ01000085.1/10909-10818     UGUUGGAACUAUUCGAAACAACAC-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUACACAA-CUUG----A-AA-AAGUGAGCACCGA-UUCGG-UGCUUUUUAU
AEQQ01000063.1/19451-19541     UGUUGGAAUUAUUCGAAACAGCAC-AGC---G-CGUUAAAAUAAGG--C-UA-G-UCCGUAUUCAG-CUUG----A-AA-AAGUGAGCACCGA-UUCGG-UGCUUUUUUA
AFIM01000053.1/5077-5167       UGUUGGAAUCAUUCGAAACAACAC-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUACUCAA-CUU-----A-AA-AAGUGCGCACCGA-UUCGG-UGCUUUUUUA
AEVC01000007.1/325692-325784   UUUUGGAACCAUUCGAAACAACAC-AGC---A-AGUUAAAAUAAGGCUU-UU-G-UCCGUACACAA-CUUG----A-AA-AAGUGCGCACCGA-UUCGG-UGCUUUUUAU
AEDT01000029.1/16072-15980     CGUUGGAACUAUUCGAAACAACAC-AGC---AAAGUUAAAAUAAGG-CU-UU-G-UCCGUACACAA-CUUG----A-AA-AAGUGCGCACCGA-UUCGG-UGCUUUUUUG
AECT01000063.1/6663-6753       UGUUGGAACCAUUCGAAACAACAC-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUAUCCAA-CUUG----A-AA-AAGUG-GCACCGA-UUCGG-UGCUUUUUUC
CP000261.1/812792-812703       UGUUGGAACCAUUCAAAACAGCAU-AGC---A-AGUUAAAAUAAGG--C-UA-G-UCCGUUAUCAA-CUUG----A-AA-AAGUG-GCACCGA-GUCGG-UGCUUUUUUU
AFUO01000001.1/1088695-1088604 AGUUUGAACCAUUCGAAACAACAC-AGC---G-AGUUAAAAUAAGG-CU-UU-G-UCUGUACACAA-CUUG----A-AA-AAGUGAGCACCGA-UUCGG-UGCUUUUUAU
CACF01000009.1/10498-10406     UUUUGGAACCAUUAGAAACAACAU-AGC---AAAGUUAAAAUAAGG-CU-UU-G-UCCGUACACAA-CUUG----A-AA-AAGUGCGCACCGA-UUCGG-UGCUUUUUUG
AEVB01000025.1/19651-19742     UGUUGGAACUAUUCGAAACAACAC-AGC---G-AGUUAAAAUAAGG-CU-UU-G-UCCGUACACAA-CUUG----U-AA-AAGUGGCACCCGA-UUCGG-GUGCAUUUUU
AEUU02000001.1/165198-165106   UAUUGGAAUUAUUCAAAAUAACAU-AGCAACA-AGUUAAAAUAAGG--U--U-A-UCCGUAAACAA-CUUG----U-AA-AAGUGCGCACCGA-UUCGG-UGCUUUUUUG
ACRI01000034.1/5085-5175       UUUUGAAACCAUUCGAAACAAGAC-AGC---G-AGUUAAAAUAAGG--C-UU-AGUCCGUAUUCAA-CUUG----A-GA-AAGUG-GCACCGA-UUCGG-UGCUUUUUUU
ADME01000001.1/158721-158629   UUUUGGAACCAUUCGAAACAACAC-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUACUCAAGCUUG----C-AA-AAGCGUGCACCGA-UUCGG-UGCUUUUUUC
AGFN01000186.1/1088-1178       UUUUGGAACCAUUCGAAACAACAC-AGC---U-AGUUAAAAUAAGG--C-UU-AGUCCGUACUCAA-CUUG----A-AA-AGGUG-GCACCGA-UUCGG-UGUUUUUUUU
AEVI01000020.1/127-36          UAUUGAAACCAUUCAAAACAAUAC-AGC---G-AGUUAAAAUAAAG--C-UU-AGUCCGUAUACAA-CUUG----A-AA-AAAGUGGCACCGA-UUCGG-UGCUUUUUUG
CP003068.1/774585-774496       AAUGGAGACCAUUCAAAACAGCAU-AGC---A-AGUUAAAAUAAGG--C-UA-G-UCCGUUAUCAA-CUUG----A-AA-AAGUG-GCACCGA-GUCGG-UGCUUUUUUU
CP001129.1/1373630-1373722     CUAUGGAACUAUUCAAUACAGCAU-AGC---AAAGUUAAAAUAAGG-CU-UU-G-UCCGUAAUCAA-CCUG----A-AA-AGGGGAGCACCGA-AUCGG-UGCUUUUUUA
FR720602.1/132808-132900       UUUUGGAACCAUUCGAAACAACAC-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUGCACAA-CUUG----A-AA-AAGCGAGCACCGA-CUCGGUUGCUAAUAAG
ACLO01000062.1/107643-107734   GAGUGAAACCAUUCGAAACAAUAC-AGC---AAAGUUAAAAUAAGG--C-UU-AGUCCGUAUUCAA-CUUG----A-GA-AAGUG-GCACCGA-UUCGG-UGCUUUUUUU
BA000034.2/1153816-1153905     AAUUUUUCUUUUUCAAAACAGCAU-AGC---A-AGUUAAAAUAAGG--C-UA-G-UCCGUUAUCAA-CUUG----A-AA-AAGUG-GCACCGA-GUCGG-UGCUUUUUUU
CP002651.1/1297534-1297618     UGUUGAAACCAUUCGAAACAACAC-AGC---G-AGUUAAAAUAAGG-CU-UU-G-UCCGUACUCAU-UUU-------------UGCGCACCGA-UUCGG-UGCUUUUUUG
FR873481.1/489592-489501       GGGUGAAACCAUUCGAAACAAGGC-AGC---AAAGUUAAAAUAAGG--C-UG-AGUCCGUAUUCAA-CUUG----A-GA-AAGUG-GCACCGA-AUCGG-UGCUUUUUGG
ACAI01000050.1/53384-53472     UUUUGGGACUAUUCUAAACAACAU-AGC---A-AGUUAAAAUAAGG--UUUU-A-ACCGUAAUCAA-CUGU----A-AA---GU-GGCGCUGU-UUCGG-CGCUUUUUUU
AEUY02000005.1/1692633-1692725 UAUUGGAAUUAUUCAAAAUAACAU-AGCAACA-AGUUAAAAUAAGA----CU-A-UUCGUCAACAC-CUUG----U-AA-AAGUGCGCACCGA-UUCGG-UGUUUUUUUU
AEEL01000016.1/82271-82354     UGUUGGAACUAUUCGAAACAACAC-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUACACAU-UUU--------------GGCACCCGA-UUCGG-GUGCGUUUUU
AEPV01000075.1/20555-20642     UGUUGGUAGCAUUCGACUCAACAU-AGC---A-AGUUAAAAUAAGG--U-UU-A-ACCGUAAUCAA-CUUU----U-UA---GU-GGCGCUGU-CUCGG-CGCUAUUUUU
AEPO01000006.1/10251-10159     UUUUGGAACCAUUCGAAACAACAC-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUGCAUAA-CUUG----A-AA-AAUCGAGUACCGA-UUCAGUUGCUAAUAAG
ACBA01000078.1/12285-12195     UCGUGGAAGUAUCCAAAACAACGU-AGC---A-AGUUAAAAUAAGG--C-UU-AGUCCGUCAUCAG-CUUU----U-CA-AAGA-AGCACUGU-CUCGG-UGCUUUUUUU
AADQ01000049.1/15499-15591     UAUUGUUAGUAUUCAAAAUAACAU-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUUAUCAA-CUUU----U-AAUUAAGUAGCGCUGU-UUCGG-CGCUUUUUUU
ADXG01001843.1/1-90            UGUUAG---UAUUCAAAAUAACAU-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUUAUCAA-CUUU----U-AAUUAAGUAGCGCUGU-UUCGG-CGCUUUUUUU
AEOF01000020.1/106699-106796   UAGUGGAGUUAUACAAAACAACAUUAGC--GA-AGUUAAAAUAAGG--U-UUAA-UCCGUAAUCAA-CAAGUUUUA-UC-UUGCGCGCGCCGU-UUCGG-CGCUUUUUUU
ADMM01000076.1/70123-70215     UAUUGGUAGCAUUCAAAUCAAUAU-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUCAUCAG-CUUU----U-UU-AAAGCAGCGCUGUUCUCGG-CGCUUUUUUU
AM263198.1/2589713-2589805     UUAAACUAUCAUUCAAAAUAACAU-AGC---A-AGUUAAAAUAAGG-CU-UU-G-UCCGUUAUCAA-CUUU----UCAU-UAAGUAGCGCUGU-UUCGG-AGCUUUUUUU
#=GC SS_cons                   ::::::::::::::::::::::::.:::...:.:::::::::::::..:.::.:.:::::::::::.::::....:.::.:::::<<<<<<<_.__>>>.>>>>::::::
#=GC RF                        UauUGgAAcuAUUCaAAACAACAu.AGC...A.AGUUAAAAUAAGG..U.UU.g.UCCGUaauCAA.CUUG....a.aA.AAGuGaGCgCcGa.UUCgG.cGCuUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02349
#=GF ID   psRNA2
#=GF DE   Proteobacterial sRNA psRNA2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:20840601
#=GF SS   Predicted; PMID:20840601
#=GF GA   65.00
#=GF TC   70.00
#=GF NC   62.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20840601
#=GF RT   Computational prediction and transcriptional analysis of sRNAs in
#=GF RT   Nitrosomonas europaea.
#=GF RA   Gvakharia BO, Tjaden B, Vajrala N, Sayavedra-Soto LA, Arp DJ
#=GF RL   FEMS Microbiol Lett. 2010;312:46-54.
#=GF WK   Bacterial_small_RNA
#=GF SQ   7


CP000103.1/2391894-2392092 GGGUUACUCCUUUGCGCUUUCAGCGCUCAAUUUGAUAAAGAUUCGCACCUCUAUCAAACCGGGUAACCCCACCU-UUGGCAAG-G-CC-U-ACUGUCAGAUUAAAUCUGAACUACUACAAAUGAA---------------C----------A---------------GAUACU-UAGUCC--AGCUCGACUUCA-UCUCCUUUAUAAAAUU----CAAC-------UCGUUGUC-GUUCUGUUGCGCC----AAUACGCUGUUU
AL954747.1/1278292-1278486 GGAUUACUCCUUUACGCUUUC-GCGUUUGGUU-GAUAAAGAUUCGCACCUCUAUCAAACCGGGUAAUCCCACCUCUUGGCAAG-A-CC-U-GCUGUCAGAUCAAAUCUGAACUACUACACCUCAU---------------C----------AU-------------UGCAAAUGUAGUGA--AG-UC-A-UCCA-UUUU-UCUAUGAUAAA----CAUC--------CGGGCUCUGUUCUGA-GCCCG----GAUAUUC-GUUU
CP001507.2/87472-87678     GGGUUACUCCUUGGCGCUUGC-GCGCU-GUUUUGAUGAAGAUUCGCACCUCUAUCAAAACGGGUAACCCCGCCUCUUGGCAAG-G-CCUU-ACUGUCAGAUCAAGUCUGAACUUCUACACGUUAGGCACGCUGGCGCGGCC----------CG-------------CGGAGAUGCGGAAC--A--CCGAUAUCA-UGUCCUUCAAGCUAGA----CGAC-------------UGAGAGGACAUCG-------AUUGCGCAGCCG
CP002600.1/1077984-1077773 GGGUUACCCCUUGGCGCCUGC-GCGCU-GUUUUGAUGAAGAUUCGCACCUCUAUCAAAACGGGUAACUCCACCUCUUGGCAAGGC--C-UUGCUGUCAGAUCAAGUCUGAACUUCUACACUUCAA---------------U----------AC-------------CU-ACAUGCAGUGGCCA--GCGAGGCCG-GUUG-ACAAAAAGAGG----GCGUUUUCAGUUCUGUCGCUAAAUGGCCGAUAGAGCGUCGAAUGUGUCU
CP002745.1/4356997-4357206 GGGUUACUCCUUGGCGUUUAC-GCGCU-GGUUUAAUAAAGAUUCGCCCCCCUAUCAAACUGGGUAACCCCACCCUUUGGCAAG-G-CC-U-UCUGUCCGAUCAAGUCGGAACUACUACACCUGAAGCCA------GCCUA-UAUCAAUCUGAU-------------UACUAC-----UGU--AG-UCGU-UCGG-UGAACGAUUUCAUCAU----CAAC-------UGCUAAGU-UGACUAC-UUUGC----AUUGCCC-GUUA
CAEE01000080.1/201-415     GGGUUACUCCUGCUC--UUUCA-CGC-UGUCUUGAUGAAGAUUCGCACCUCUAUCAAAACGGGUAACCCCGCCUCUCUGCAAG-GCCU-G-ACUGUCAGAUCAAAUCGGAACUUCUACACUUCAG---------------A----------ACUCGGCACUUUACCUUCCAAU-AGGAGC--CACUCCAUGCUU-UUUCCAACAUUCAAAUCUUGCGUU-------UGUUGCUACGCUCAUC-GCAAC----GAUAACC-GCCU
CP002552.1/1780388-1780200 GGAUUACCCCUUUGAGCUUUC-GCGCUGUGUU-GAUAAAGUUUCGCAUCUCUAUCAAAUCGGAUAAUCCCACCC--GCAAGAC-U-CU-G--CUGUCAGAUCAAGUCUGAACUACAGCAGAUAAA------------------------------------------GUUCAU-UAGUCU--CAC--UUCUUGCUUAUUUAUUGUAAAUUU----CUUA--------AUAUUUCCGCUCCGAUGG-------UAAUAUCAGUUG
#=GC SS_cons               (((((((-((,,,<<<<____.>>>>,,<<<<<<<<<-<<________>>->>>>>>>>>)))))))))-[[,,,,(((---(.(.-(.(.,,,<<<<<<<___>>>>>->>,<<<<-<______..............._..........__.............______>.>>>>,,..)).))----))).,,,,,,,,,,,,,,,,....,<<<.......-<<<<<<<______>>->>>>>....>>>,,,,,]]::
#=GC RF                    GGGUUACUCCUUugCGcUUuC.gCGcUugguUUGAUaAaGAUUCGCACCuCuAUCAAaccGGGUAACCCCgCCUcUuggCAAG.g.Cc.u.aCUGUCaGAuCAAaUCuGAACUaCugCAcuUuAa...............u..........Au.............ugcuaAU.caGugu..ag.cCgauucca.UuUucauuauaaaaau....cggc.......Ugcggcgcugaucugcugccgc....gccaaucaGcuu
//
# STOCKHOLM 1.0

#=GF AC   RF02350
#=GF ID   psRNA6
#=GF DE   Nitrosomonas sRNA psRNA6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:20840601
#=GF SS   Predicted; PMID:20840601
#=GF GA   60.00
#=GF TC   63.60
#=GF NC   35.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20840601
#=GF RT   Computational prediction and transcriptional analysis of sRNAs in
#=GF RT   Nitrosomonas europaea.
#=GF RA   Gvakharia BO, Tjaden B, Vajrala N, Sayavedra-Soto LA, Arp DJ
#=GF RL   FEMS Microbiol Lett. 2010;312:46-54.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


CP000450.1/1340453-1340774 UUUGAUCUGUUUUUUGAUCCAUUUGGUCUGGCAUUGAAUCACGUUCCAUCAUCAGGCUCGGCGGAUAGUUG-CCGGGUUUAUCCGUAUCAAGACACCCGGUCAAGACAGUUGAAGCUACUAACAGGGUGGCGACAGUAAGUAUGAGUUUCAUUUUUUAGUCUCCUAUAAGAAAAA-UAUAUUGACAAUAUAACUCUUCUAGCUGGUUUGACUUAUUGCCUCCCUUCUCAGGA-GACAGUUAUUUAAUAACAAAUAUUUUAUUUAUUGUCAAUA-UUUUUUA-AU-UGU-CUC-ACUUAAUAAAAUUAUAA-AAUA-AUCUUUAUGUU-AUAAA
AL954747.1/1519925-1520248 UUUGUUCUGCUUUAUC-UACAUU-G-UCAGGCAUGGAAUCACGUUCCAUUGACAUGCUUGGAGGAUA-UUGACCUGGUUUGG--G-AUCCAUACAUGCAGUCAAUGUAGUAGCUGCGAACAACAGUGUUGAGAUGACGAGUACGAGUUUCAUUUUC-AGUCUCCUAUAAGAAAAAGUACAUUCACAAUAUAGUUCUUCCAACAGUUCUGACUUACUGUC-CCCUUUUUAGAAAGACAUCUAUUUGAUACCAGAUACGAUAUGCCCUGUCAAGAAUUUUUUAGACGUAUGCUUGACAGCAUCUGAUUACCAUAAGACAACUAUAUUUUUAUAAA
#=GC SS_cons               :::{{{(((((---((.,,,<<<.<.<<<<<<<<<<<<<___>>>>>>>------>>>>>>>->>>,.<<<<<<<<<<<<<<.._.__>>>>>>-->>>>>>>>,,,,<<____>>))--)))))[[[[[[[[[[-[[,<<<-<<<-<<_______.>>->>>->>>,,((((((((---((((((((((((,<<<<<<<<-<<<---<<<_____>>>.->>>->>->>>>->>,,,,<<<<<<____>>>>>>))))))----))))))-)))))))),,,]]]]]-]]]]]]],,,,,,,,,,,,,,,,,,,,}}}::::::::::::::
#=GC RF                    UUUGuuCuGuuUUauc.UaCauu.g.uCggGCaugGaauCACguuCcauuaaCAuGCucGgcGgauA.uuGaCcggGucugg..G.AUccagaCAuccgGuCaauauAGuaGaagCgaauaaCaGgGucgaGacaacgAguauGaGUuuCAUUUUu.agUCuCCuauAAgaaaaaguAuAuugaCaauauaguuCuuCuagCaGgUuUGgCUUAuUGcC.CcCuUcuuaGaaAGaCAuuuauuugAUAacaaauacuauauuuauuGucaauacuuuuuuAGAcguguGCucgaCcuaAUaaaAUUAuaAUAAuAcaaCUaUAUuUUUAUAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02351
#=GF ID   psRNA14
#=GF DE   Proteobacteria sRNA psRNA14
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:20840601
#=GF SS   Predicted; PMID:20840601
#=GF GA   60.00
#=GF TC   79.50
#=GF NC   54.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20840601
#=GF RT   Computational prediction and transcriptional analysis of sRNAs in
#=GF RT   Nitrosomonas europaea.
#=GF RA   Gvakharia BO, Tjaden B, Vajrala N, Sayavedra-Soto LA, Arp DJ
#=GF RL   FEMS Microbiol Lett. 2010;312:46-54.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


CP000450.1/1451274-1451356 UGAAA-UAAAUAACUAUUGGUUAAAAUCAGUGGUUGUUUAGUCUGGCUGACAGUUGUAAAAAAUAAAACUGUCAGCCAACGUCA
AL954747.1/2604951-2605032 UGAAACUAAACAACCACCGGCUAAAGCCGGUGGUUGUUUAGUUUGG-UCUCAUUAUUGAAAAAUCAAAUUUGCCGUCC-CGGCA
FN667741.1/2234864-2234787 GUUAACUCAACAACCACCGACUAAAGUCGGUGGUUGUUGAGUUAUGACAAGGUAAAAAAAUAAAUUUUACU------GAAAUAU
#=GC SS_cons               ((<<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>>>>>>>><<<<<<<<<<<-<<<____>>>>>>>>>>>>>>,,,,,))
#=GC RF                    ugaaACUcAAcAACcAccGgcUAAAgcCggUgGUUgUUgAGUuuGgcugccgguuaugaAaAAucaaaccggcagcCaAcguca
//
# STOCKHOLM 1.0

#=GF AC   RF02353
#=GF ID   BjrC68
#=GF DE   Bradyrhizobiaceae sRNA BjrC68
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22258152
#=GF SS   Predicted; PMID:22258152
#=GF GA   39.00
#=GF TC   39.40
#=GF NC   37.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22258152
#=GF RT   Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their
#=GF RT   analysis.
#=GF RA   Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J,
#=GF RA   Hess WR, Fischer HM, Evguenieva-Hackenberg E
#=GF RL   RNA Biol. 2012;9:47-58.
#=GF WK   Bacterial_small_RNA
#=GF SQ   12


BX572593.1/304163-304242   CCAGACCUACGGUU-CGGGCAACUA-CCCGGCAAUGUCCGAACCGUCGAGGGGUCCCAGCGCAAGCUGGGGCCCCUUUC--UUU
CP001096.1/298214-298293   CCAGACCUACGGUU-CGGGCAACUA-CCCGGCAAUGUCCGAACCGUCGAGGGGUCCCAGCGCAAGCUGGGGCCCCUUUC--UUU
BA000040.2/657248-657329   CCACAACUACGGUU-UGGGCACAUA-CCCGGCAAUGCCCCGACCGUUGAGGGGCUCCAGCGCAAGCUGGAGCCCCUUUCUUUUU
CP000494.1/297449-297368   CCGCAACUUCGGUU-CGGGCAAAUA-CCCGGCAAUGCCCUGACCGUUGAGGGGCUCCAGCGCAAGCUGGGGCCCCUUUCUUUUU
CP000250.1/414808-414884   -----ACUACGGUU-CGGGCAGAUA-CCCGGCACUGUCCGAACCGUCGAGGGGUCCUGGCGCAAGCCGGGGCCCCUUUCUUUUU
CU234118.1/319006-318925   CCGCAACUUCGGUU-CGGGCAAAUA-CCCGGCAAUGCCCUGACCGUUGAGGGGCUCCAGCGCAAGCUGGGGCCCCUUUCUUUUU
CP000283.1/516184-516106   ----AACUACGGUC-CGGGCAAAUACCCCGGCAAUGUCCGGACCGUCGAGGGGUCCCAGCGCAAGCUGGGGCCCCUGUCUUUUU
CP000463.1/443722-443653   ---------CGGAU-CGGGCACGU--CCCGGCAAA-CCCGAUCCGACCAAGGGCCCCCGCGCAAGCUGGGGCCCUUUUC-UUUU
AP012206.1/602566-602648   CCACGACUACGGUUUGGGGCACAUA-CCCGGCAAUGUCCCGACCGUUGAGGGGCUUCAGCGCAAGCUGAAGCCCCUUUCUUUUG
CP002418.1/388291-388210   CCGGACCUACGGUU-CGGGCAGAUA-CCCGGCAAUGCCCGAACCGUCGAGGGGUCCCAGCGCAAGCUGGGACCCCAGACCGCUG
AFOF01000013.1/89367-89286 CAAGGACAACGGUU-GGGGCACAAA-CCCGGCAAUGCCCCGUCCGUCGGAGGGCUCCAGCGCAAGCUGGAGCCCUUUUUCUUUG
AGTN01262265.1/335-416     GAAGAGAUACGGUU-AGGGCGGAUA-CCCGGCACCGCCCUUGCCGUCGAGGGGCCCUGGAGUGAUCCAGGGCCCCUCACUUUUU
#=GC SS_cons               :::::::::<<<<<.<<<<______.__________>>>>>>>>>----<<<<<<<<-<<____>>->>>>>>>>:::::::::
#=GC RF                    ccagAacUACGGuc.cGGGCAaAUA.CCCGGCAAUGCCCggaCCGUcGAGGGGccCcaGcGCAAgCUgGggCCCCUuUCUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02354
#=GF ID   BjrC80
#=GF DE   Bradyrhizobiaceae sRNA BjrC80
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22258152
#=GF SS   Predicted; PMID:22258152
#=GF GA   80.00
#=GF TC   94.90
#=GF NC   69.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22258152
#=GF RT   Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their
#=GF RT   analysis.
#=GF RA   Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J,
#=GF RA   Hess WR, Fischer HM, Evguenieva-Hackenberg E
#=GF RL   RNA Biol. 2012;9:47-58.
#=GF WK   Bacterial_small_RNA
#=GF SQ   15


CP000115.1/1303083-1303235   AGAUGGAAAGCGUCG-CCGGCAUCAGUCGCC-CCCCGCCGG-CGGCACUUUCCGGGGACGGGUC---AA---AAGUCCGUUCCCUUGAUU--GCCUUCCGAUCGGAAU--AGCCCCCCUCCGUCGGAAGGACUA--GGGCGGUGGAGUU--GCCCCAAGCUUCACCGCCC------
CP001096.1/2311502-2311656   -------GAGUGUCG-CCGGCAAUCGUCGCC-CCCAGCCGA-CGGCGCUAUCCCGGGGACGGGUCGUAAC-CCGCUCGUCCCCGCCUUUA-CACCUUCCGGAAGGAGUUCAGCCCCCCUCCGUCGGAAGGUCUAGGCGGGCGGUGGAGU--CCCCCAGCUCCAUCGCCC-------
BA000040.2/3457470-3457618   ---------GUCGCC-GGCAUCA--GUCGCC-CCAGCCGCC-GGCGCCCUU-CGGGGGAGCAGCGUAAC---AUUCGCUUCCCCAAUCUA---CCUUCCGGU-GGAAUUACGCCCCCCUCCGUCGGAAGGCCUA---GGGCGGUGAGGU-CCCCCCAGCUUCACCGCCCGC-CUUU
BX572599.1/72200-72355       -------GAGUGUCG-CCGGCAAUCGUCGCC-CCCAGCCGA-CGGCGCUGUCCCGGGGACGGGUCGCAACCCCGCUCGUCCCCGCCUUUA-CACCUUCCGGAAGGAGUUCAGCCCCCCUCCGUCGGAAGGUCUAGGCGGGCGGUGGAGU--CCCCCAGCUCCAUCGCCC-------
CP000494.1/3220512-3220667   GAGAUGGAGAGUCGC-CGGC---AUGUUGCC-CCCGCGUCG-GCGGCUCUUCCUGGGGGCGGGCAU-AA---GUCCCGCUCCCGC--AA---ACCUUCCGGUAGGAACAACGCCCCCCUCCGUCGGAAGGAACU--CGGGCGGUGAAGU--CCCCCAGCUUCACCGCCCAC-UUUC
CP000250.1/3948636-3948477   -AGUUGGAGAGUGUC-GCCGGCAAUGUCGCC-CCCGCUGAC-GGCGCUUUC-CGGGGGACGGG-UGAAC---AGCUCGUCCCCACCUUCU--ACCUUCCGGCCGGAGU-AAGCCCCCCUCCGUCGGAAGGACCAGGCGGGCGGUGGAGU-UCCCCCAGCUCCAUCGCCCGC-UU--
CU234118.1/2947755-2947911   GAGAUGGAGGGUUGC-CGGC---CUGUUGCC-CCCGCGCCG-GCGGCUCUCCCAGGGGGCGGGUUUCAA---AUUCCGCCCCCGC--AAC--ACCUUCCGUCAGGAAC-AUGCCCCCCUCCGUCGGAAGGAACU--CGGGCGGUGAAGU--CCCCCAGCUUCACCGCCCAC-UUUC
CP000283.1/2251087-2251246   -AGUUGGAGAGUGUC-GCCGGCAAUGUCGCC-CCCGCUGGC-GGCGCUUUC-CGGGGGACGGG-UGAAC---AGCCCGUCCCUGC-UUAU--ACCUUCCGUCCGGAGC-AAGCCCCCCUCCGUCGGAAGG-UCAGGCGGGCGGUGGAGU-UCCCCCAGCUCCAUCGCCCGC-UUUC
CP000463.1/2152649-2152803   AGAUGGAGCACGUCG-CAGGCUA---UCGCC-CCC-GCCG--CGACGUGUU-CCGGGAACGGG-CGAA----GGUCCGUUCCCAC-CGAU--ACCUUCCGGAAGGAGA-AUGCCCCCCUCCGUCGGAAGG-UGCGGCGGGCGGUGAGGU-CCCCCCAGCUUCACCGCCCGUACUU-
AFOF01000024.1/171274-171418 AAUGGGGAGUUGUCG-CCGGCUC--GUAGCC-CCC-GCCGA-CGGCUCCUCCCCGGGGACGGG-CCAAA---AGCCCGUCCCUUG-AAUU--GCCUUC-GAU-GGAAA-ACGCCCCCCUCCGUC-GAAGGUGG--CGCGAUCG-----C--ACUCCAGU----CGGUCGUGCAAU-
CP000301.1/1998478-1998634   GAAUGGAGUGCGUCG-UCGG-CA-UGUCGCC-CCCG-CCGA-UGGCGCGCUCCGGGGGACGGG-CUUA----GGCCCGUCCCCAC-GGAU--ACCUUCCGGU-GGAGA-AUGCCCCCCUCCGUUGGAAGG-CGCGGCGGGCGGUGAGGU-UCCCCCAGCCUCACCGCCCGU-UUCU
AAMY01000009.1/36976-37135   AGAUGGGAAGCGUCG-CCGGCAUCAGUCGCC-CCC-GCCGA-CGGCACUUUCCGGGGGACGGGUCA-AA---AGCCCGUUCCCUUGAGUU--ACCUUCCGAUCGAAAC--AGCCCCCCUUCGUCGGAAGGACUA---GGGCGGUGGAGUUGCCCCAAGCUUCACCGCCCGC-UUUU
CP000319.1/1626393-1626552   AGAUGGGAAGCGUCG-CCGGCAUCAGUCGCC-CCC-GCUGA-CGGCACUUUCCGGGGGACGGG-CCAAA---AGCCCGCCCCCUUGAGUU--GCCUUCCGAUGGAAAC--AGCCCCCCUUCGUCGGAAGGAUUA---GGGCGGUGGAGUCGCCCCAAGCUCCACCGCCCGC-UUUU
AP012206.1/6790380-6790222   -AGAUGAGGGGUGUCUUCGGCAUCAGUCGCC-CCC-GCCGCCGACGCCCUU-CGGGGGAGCAGCGCAAG---GCCCGCUCCCCCA-GCCU--ACCUUCCGGU-GGAAU-UACGCCCCCUCCGUCGGAAGGCCUA---GGGCGGUGAGGU-CCCCCCAGCUUCACCGCCCGC-CUUU
CP002418.1/3828315-3828147   GCUUGGAGAGUGUCG-CCGGCAAUCGUCGCCCCCCAGCCGA-CGGCGCUGUCCCGGGGACGGGUCGUAAC-CCGCUCGUCCCCGU-CUUUACACCUUCCGGAAGGAGUUCAGCCCCCCUCCGUCGGAAGGUUCAGGCGGGCGGUGGAGU--CCCCCAGCUCCAUCGCCCGU-CCCC
#=GC SS_cons                 ::::::::<<<<<<<.-<<<<__________.____>>>>-.>>>>>>>,,,,,<<<<<<<<<-<<___...>>>>>>>>>>><<.--<<..-<<--<<<<--<<<<_.________>>>>->>>>-->>-->>.>><<<<<<<<<<<<..______>>>>>>>>>>>>::.::::
#=GC RF                      aaaugGaaggcgccg.ccggcaauuGUcGCC.CCCagccga.cggcgccuUCCgGGGGgcGgguccaAa...ggccCgcCCCCgc.uauc..ACCUUCCGguaGGAgu.aaGCCCCCcUCCGcCGGAAGGacga.gcGGGcGguGgggu..cCCCCAgcccCacCgCCCgc.uuUu
//
# STOCKHOLM 1.0

#=GF AC   RF02355
#=GF ID   BjrC174
#=GF DE   Bradyrhizobiaceae sRNA BjrC174
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22258152
#=GF SS   Predicted; PMID:22258152
#=GF GA   45.00
#=GF TC   50.60
#=GF NC   39.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22258152
#=GF RT   Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their
#=GF RT   analysis.
#=GF RA   Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J,
#=GF RA   Hess WR, Fischer HM, Evguenieva-Hackenberg E
#=GF RL   RNA Biol. 2012;9:47-58.
#=GF WK   Bacterial_small_RNA
#=GF SQ   15


BX572593.1/224291-224494     CUCACGCCUUCGUUAGCCGAAUUCUUAUUGCCGCCC-GAUUUUCGCC-CAGCGC--GCGCCAAGCCCGCUUGCGAUAACGCUAUCACUGCGUUGGCCCGGUCCCUUCGGCUUCGGAUUCCUCAGCCCCCAGCCCCCCGAA-GCAGUCGGGAUCGGGCCUG----UACGCAGAA-CCUCGAUCCCCCU-----CCUGGGCCGACGCAAGUUGGUCC-UUUU
BA000040.2/504009-504142     ----------------------------------CC-UGCACUGCGAAAAGAGC-----------------------------UGUGUGCGUUGACCCGGUCCUUUCGGUUCCGGAUUCCUCAGCCCCCAGCCCCCCGGG-GUCGACGGGAUCGGGUCUG----UACGCGCGA--CAAGG--------------AGGGCCAACGCGAGUUGGUCCUUU-U
CP000494.1/383513-383319     GUCACGGGAUCGUUAGCAGAAUCAUAAUCGCGCCGU-CUUUCCGCCC-AGGGAC--CGCCCC-CGAUCUUGGGCAUAAGA-UUCGUGUGCGUUGGCCCGGUCCUUUCGGUUCCGGAUUCCUCAGCCCCCAGCCCCCCGGG-GUCGUCAGGAUCGGGUCU------AUUCACAA----GUGAUGGCA-------AAGGGCCAACGCAAGUUGGUCC-UUUU
CU234118.1/400893-400699     GUCACGGGAUCGUUAGCGGAAUCAUAAUCGCGCCGU-CUUUCCGCCC-AGGGAG--CGCCCC-CGACGUUAGGCAUAAGA-UUCGUGUGCGUUGGCCCGGUCCUUUCGGUUCCGGAUUCCUCAGCCCCCAGCCCCCCGGG-GUCGUCAGGAUCGGGUCU------AUUCACAA----GUAAUGGCA-------AAGGGCCAACGCGAGUUGGUCC-UUUU
CP000250.1/327537-327735     CUCACGCCUUCGUUAGCCGAA-UCUUAUUACCGCCA-GAUUUUCGCC-CAUCGA--ACGCCCGGUCGACUUGCGAAAAC---AUCCUGGCGUUGGCCCGAUCCAGGCGGUCUCGGAUUCCUCAGCCCCCAGCCCCCCGAG-GUCGUCGGGGUCGGGCCUG-----ACGCAGCA-ACCAAUCCCCCAG-----CCUGGGCCAACGUGAGUUGGCCUUUUU-
CP000319.1/447155-447228     ---------------------------------------------------------------------------------------UGCGAUGGCCCGGUCCUUUCGGUGCCGGA-UCCUCAGCCCCCAGCCCCCCGGG-GCCAUCAGGAUCGGGCCUA----UUC-----------------------------------------------------
CP000283.1/598794-598675     ---------------------------------------------------------------------------------------UGCGUUGGCCCGGUCCUUUCGGUCUCGGAUUCCUCAGCCCCCAGCCCCCCGAG-GCGGUCGGGAUCGGGCCUU-----UCGCAGCA-GCCAAAUCCCCAU-----ACUGGACCAACGCGAGUUGGUCCUUUU-
CP000301.1/221579-221781     GUCACACGAUCGUUAG-UGAAAUCAUAUUGCCGCCC-GAUUUCCGCCAAGCCGC--GGCCCUGCU-GGGCUGCGAGAGAU-GAUACUUGCGUUGGCCCGGUCUUGUCGGCGUCGGAUUCCUCAGCCCCCAGCCCCCCGGG-GUCUUCAGGAUCGGGCCUG----UUCGCAACAAUCAAUCCCCACAC-----UGAGGGCCAACGCGAGUUGGUCC-UUUU
CP000463.1/349940-350018     ---------------------------------------------------------------------------------------UGCGUUGGCCCGGUCCUUUCGGCACCGGAUUCCUCAGCCCCCAGCCCCCCGGG-GUCGUCGGGAUCGGGCCUG----UUCGCAA-------------------------------------------------
CP000115.1/362829-362677     -------GAACGUUAGGUAAAAUCAUAAUGCAGCCC-AAAUUCCGACAAGCAAC--CGCCCCGCUGAACU-GCGAAAAAACAUUCUCUGCGAUGGCCCGAUUCUUUUGGAACCGG-UUCCUCAGCCCCCAGCCCCCCGGG-GCCAUCAGGAUCGGGCCUA----UUCGCA--------------------------------------------------
AACY022416544.1/542-734      GUCACGGGAUCGUUAGCAGGAAUCAUAGUAUCGCCG-CUUUUCCGCCAAGCGC---CCGCCGCCCUGAAUUGGGAAAAGA-GUUGCGUGCGUUGACCCGGUCCUCUCGGCUCCGGAUUCCUCAGCCCCCAGCCCCCCGGG-GCCGUCAGGAUCGGGUCUG----UACGCACAA-CAAG-G--------------AGGGCCAACGAAAGUUGGUCC-UUUU
CP002418.1/473387-473184     CUCACGGCUUCGUUAGCCGAAUUCUUAUUGCCGCCC-GAUUUUCGCC-AACCGC--GCGCCAAGCCCGGUUGCGAUAACACCACCACUGCGUUGGCCCGGUCCCCUCGGUUUCGGAUUCCUCAGCCCCCAGCCCCCCGAA-GCAGUUGGGAUCGGGCCUG----UACGCAGAA-CCUCAAUCCCCCU-----CCUGGGCCGACGCAAGUUGGUCC-UUUU
AP012206.1/457470-457661     GUCACGGGAUCGUUAGAAGGAAUCUUGAUAUCGCCGCUUUUCCGCCA-AGCGC---CUGCCGCCCUGCAUUGCGAGAAGA-CCUGUGUGCGUUGACCCGGUCCUUUCGGUUCCGGAUUCCUCAGCCCCCAGCC-CCCGGG-GCCGUCAGGAUCGGGUCUG----UACGCGCGA--CAAGG--------------AGGGCCAACGCAAGUUGGUCC-UUUU
AFOF01000011.1/175259-175464 AUCACGCGGACGUUAGACAAACCAUAAUGCCGCCC---GAUUUCGGU-CAAUUCCCCGCCCU-UGUGGACUGCGAUCAAGUCUCUACUGCGUUGACCCGGUCCUUUCGGCACCGGAUUCCUCAGCCCCCAGCCCCCCGGG-GUCGUCAGGAUCGGGUCUAGUUCUUCGCAGCA--GA--AUCCCCAUC---CUUCGGGCCAGCGAGAGCUGGCCU-UUUU
AAMY01000001.1/59906-60112   UUAACAAGAAGGUUUGCCGAAAUCAUAAUGCAGCCC-AAAUUCCGUCAAGCAAC--CGCCCC-GCUGAGCUGGGAGAAAGCAUUCUCUGCGAUGGCUCGAUCCUUUUGGGACCGGA-UCCUCAGCCCCCAGCCCCCCGGGACUCAUCAGGAUCGGGCCUU-----UCGCAAGA--CUUGAGUUCCGACCUUUUUCGAGCUGGCCAAAGCCGGUCC-UUUU
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::(.(<<-<<____._>>->>..,,,,,,.,,,,,,,,,,,,,,,,,.,,,,<<<<<<<-<<<<<<<<<<<--<<<<<<<<<--------<<_____>>--->>>>>.>>>>-->>>>>>>>>>>--....->>>>>>>,..,,))--------.....---<<<<<<<<____>>>>>>>>.::::
#=GC RF                      gUcACGggauCGUUAGccGAAaUcuuAuugCagCCc.cgcUcccgcc.Aggagc..cgcCCu.cuugaauUGcGAuAAaa.uuuuccuGCGuUGgCCCGgUCCuUUcggcccCGGAUUCCUCAGCCCCCAGCCCCCCGgg.gccgUCaGGAuCGGGcCUg....UaCGCaggA..caggaucccCau.....uuaGGgCCaaCGcaAGuuGGcCC.UUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02356
#=GF ID   BjrC1505
#=GF DE   Alphaproteobacterial sRNA BjrC1505
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:22258152
#=GF SS   Predicted; PMID:22258152
#=GF GA   50.00
#=GF TC   54.20
#=GF NC   46.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22258152
#=GF RT   Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their
#=GF RT   analysis.
#=GF RA   Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J,
#=GF RA   Hess WR, Fischer HM, Evguenieva-Hackenberg E
#=GF RL   RNA Biol. 2012;9:47-58.
#=GF WK   Bacterial_small_RNA
#=GF SQ   25


CP000301.1/877729-877864     -----------C-------AUUUAC--GCGAUAUUAAGCUUUCC---AGCGUA--UUAC-UCU-GA-UUGUCC-A---UC--UU--U-GGACG----CCGAGUGGC---UCCUGUCCACUCUGCUUUGACG-CCUCCCUGUUAUCAACU-U--CAAAGCCGCCGGC--AA-CGGCGGCUCUUUUUUU
CP000283.1/4807986-4807848   ---U-CGC--UC-------AUUUAC--GAGCGAUUAAGCUUUCC---GGGGUA--UUAC-UUU-GA-UUGUCC-A---UC--UU--U-GGAC------CGAGUGGC---UCCUGUCCACUCUGUUUUGACG-CCUCCCUGUUAUCAACU-U--CAAAGCCGCCGGA--AA-CGGCGGCUCUUUUUUU
CP001096.1/1052457-1052590   -----------C-------AUUUAC--GCGCGAUUAAGCUUUCC---CGCCUA--UUACUGUG-GA--UGUCC-A---UC--UU--U-GGAC------CGAGUGGC---UCCUGUCCACUCUGUUUUGACG-CCUCCCUGUUAUCAACU-U--AAAAGCCGCCGGA--AA-CGGCGGCUCUUUUUUG
CP000319.1/3901825-3901696   --------------------UUUAC--GAUUGGUUAAGCUUUCU---CGAUUA--UGA--CUG-GA-AUGUCC-U---UG--AU--U-GGACG----CCGAGUGGC--UUCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAUCAAC-----UCAGGCCGCCGGA--AA-CGGCGGCUUUUUUUU-
BX572595.1/321077-321216     --UU-CGC--UC-------AUUUAC--GCGCGAUUAAGCUUUCC---CGCCUA--UUACUGUG-GA--UGUCC-A---UC--UU--U-GGAC------CGAGUGGA---UCCUGUCCACUCUGUUUUGACG-CCUCCCUGUUAUCAACU-U--AAAAGCCGCCGGA--AA-CGGCGGCUCUUUUUUG
CP000250.1/5080800-5080663   ---U-CGC--UC-------AUUUAC--GAGCGAUUAAGCUUUCC---GGUGUA--UUAC-UUC-GA-UUGUCC-A---UC--UU--U-GGAC------CGAGUGGC---UCCUGUCCACUCUGUUUUGACG-CCUCCCUGUUAUCAACU-U--CAAAGCCGCCGGA--AA-CGGCGGCUCUUUUUU-
CU234118.1/1177565-1177706   -UUC-CUG--CC-------AUUUAC--GGUUGAUUAAGCUUUCG---CGUUUA--CAAC-CGG-UA-CCGUCC-U---CG--UU--U-GGACA----CUGAGUGGC---UCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAUCAACU-U--CAAAGCCGCCGGC--AA-CGGCGGCUCUUUUUUU
CP002026.1/3196528-3196666   -----GCA--GG-------CUUAAC--CCCGCAUUAAGCUUUCC---GAUCUA--UUAC-UGGGGA-CGGUCC-A---GU--UU--U-GGCC-----GCGAGUGGC---UUCUGUCCACUCUGU-UUGACG-CAUCCCUGUCUAUGACUCA--UCGAGCCGCCUU---AC-GGGCGGCUCUUUUUUC
AAUW01000002.1/231908-232047 ---A-UUU--ACU-----CGUUUACCUGU--UAUUAAUCUUUCC---AAAUUAUA--AACAGA-GG-UAUCCA-G---UC--AU--C-UGGAU----GUGAGUGGC---UCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAAAGAC--U--CAGAGCCGCAACC--AA---GCGGCUCUUUUUUU
AAAP01001778.1/545-691       ---CGCUG--UG-------CUUAAC--CGGCCAUUAACCUUUCC---GGUCCA--CGAA-UAG-GG-AUAUCC-AGAUUG--UC--U-GGAUC----CUGAGUGGGAACUCUUGUCCACUCUGU-UUGAUG-CCUCCCUGUAGACUCGU-G--ACAAGCCGCUCUC--UG-GAGCGGCUUCUUUUUU
BA000040.2/1641162-1641306   --AU-UCG--CU------CGUUUAC--CGUCGAUUAAGCUUUCG---GCUUUA--UGAC-UGG-AA-CUGUCC-U---CG--UU--U-GGACA----CCGAGUGGC---UCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAUCAACU-U-UCAAAGCCGCCGGUCUUC-CGGCGGCUCUUUUUUG
AAFX01119212.1/371-520       --UA-CCG-AUCGUUUUGCAUUUAA-GGAGUCUUUAAGCUUUCC---CCGGUA--UUAC-UGG-CG-GCGUCC-A---UC--UU-CU-GGACA----UCGAGUGGC---UCCUGUCCACUCUGU-UUGACGCCCUCCCUGUUAUCCAC-----UUGAGCCGCCGGC--AA-CGGCGGCUCUUUUUUG
ADVZ01000003.1/187859-188002 -AUU-CGU--UC-------AUUUAC--GGCACAUUAAGCUUUCG---GGUUUA--UGAC--CA-GA-CUGUCC-U---UG--UU--U-GGACA----CCGAGUGGC---UCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAUCAACU-UUCAAAAGCCGCCGGU--UUCCGGCGGCUCUUUUUUU
AFOF01000015.1/278226-278369 --AA-UCG--UU------AAUUUAC--GGCGUAUUAAUCUUUCG---CGUUUA--UGAC-UGA-GC-UUGUCC-U---UG--UU--U-GGACA----CCGAGUGGC---UCCUGU-CACUCUGU-UUGACG-CCUCCCUGUUAUCAACU-UUCAAAAGCCGCCGGU--UUCCGGCGGCUCUUUUUUU
ACCU01000015.1/536630-536767 --UU-UAU--U-------CAUUUAC-C-AAUCAUUAAUCUUUCC---AAAUUA--UAAA-UUU-AU-GCAUCCAG---UC--AU--CUGGAU-----AGGAGUGGU---U-CAGACCACUCUGU-UUGACG-CCUCCCUGUUAAAGAC--U--UAGAGCCGCA-GC--CG--UGCGGCUCUUUUUUU
CP000390.1/3451882-3451742   -----AGU--UC-------GUUAAC--UCCGGAUUAAGCUUUACAGGCGUUUA--CUGU-----GU-GUAUCCAG---AG--AU--CUGGAUUCUGACCGAGUGGC---UGGAG-CCAUUCUGU-UUGACG-CCUCCCUGUUAACUCC--U--GAGAGCCGCAGUC-----CCGCGGCUCUUUUUUU
CP000463.1/736113-735972     --AC-GGU--UC-------AUUUAC--UAGGCGUUAAGCUUUUU---CACCUA--UUAC-UUU-GG-UCGUCC-A---UC--UU--U-GGACG----CCGAGUGGC---UCCUGUCCACUCUGCUUUGACG-CCUCCCUGUUAUCAACU-U--CAAAGCCGCCGGC--AA-CGGCGGCUCUUUUUUU
CP000115.1/2987672-2987531   -AUU-CGU--UC-------GUUUAC--GAUUGAUUAAGCUUUCC---UGACUA--UGAC--UG-AA-AUGUCC-U---UC--AU--U-GGACA----CCGAGUGGC--UUCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAUCAACU-U--CAAGGCCGCCGGC--AA-CGGCGGCUUUUUUUUG
CP002568.1/956986-956847     ---U-UUA-GUC-------GUUUAC--UUCUUGUUAAGCUUUCU----GAUUG--AUAACUAA-AA-CGUCCA-G---UC--AU--C-UGGAU---UUCGAGUGGC---UCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAAUGAC--U--UCGAGCCGCGGGU--U--CCGCGGCUCUUUUUUU
AAMY01000003.1/212732-212592 -AUU-CGU--UC-------GUUUAC--GAUUAAUUAAGCUUUCC---CGUCUA--UGAC--UG-AA-AUGUCC-U---UC--AU--U-GGACA----CCGAGUGGC--UUCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAUCAACU-U--CAG-GCCGCCGGA--AA-CGGCGGCUCUUUUUUU
AP012206.1/8642581-8642442   ---G-CUC-----------GUUUAC--UUCCAAUUAAGCUUUCG---GGUUUA--UGAC-UGG-AA-CUGUCC-U---CG--UU--U-GGACA----CCGAGUGGC---UCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAUCAACU-U-UCAAAGCCGCCGGU-CUC-CGGCGGCUCUUUUUUU
AEFL01000066.1/113305-113165 ---U-UUUAGUC-------GUUUAC--UAGUUAUUAAUCUUUCC---AAAUUA--UAAACAGA-GU-CAUCCA-G---UC--AU--C-UGGAU---UUGGAGUGGC---UCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAAAGAC--U--UCGAGCCGC-GGU--AA-C-GCGGCUCUUUUUUU
CP000494.1/7276273-7276132   --UU-UCG--CC-------AUUUAC--GGUUGAUUAAGCUUUCG---GGUUUA--CAAC-CGG-AA-CCGUCC-U---CG--UU--U-GGACA----CCGAGUGGC---UCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAUCAACU-U-CAAAAGCCGCCGGA--AA-CGGCGGCUCUUUUUUU
AGTN01453150.1/288-144       ---A-UUU--ACG----UCCUUAAC--GCGCCAUUAAGCUUUCC---UGCCUA--UUAC-UAA-UACUUGUCC-A---UC--UUCAU-GGACU----UUGAGUGGC---UCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAUCUAAC----UUGAGCCGCCGGC--AA-CGGCGGCUCCUUUUUU
ADGO01147999.1/280-139       ACGU-GCC--AG-------GUUAAC--CGACCGUUAAGGUUUCC---GAUUUA--UAAC-AAC-AA-CCAUCC-A---GUCUUC--U-GGAUG----CCGAGUGGC---UCCUGUCCACUCUGU-UUGACG-CCUCCCUGUUAUCACU-----UCGAGCCGCCCCU---C-GGGCGGCUCUUUUUUU
#=GC SS_cons                 ...(.(((..<<.......______..>><<---<<<<<<____...>>>>>>..>>,,.))).),.,,<<<<._...__..__.._.>>>>,....,,<<<<<<_...______>>>>>>,,,.,,<<<<.______>>>>,,,,,,,.,..<<<<<<<<<<<__..__.>>>>>>>>>>>:::::
#=GC RF                      ...c.ccc..cc.......aUUuAC..ggccuAUUaacccUUCc...ggguuA..ggAc.ggg.ga.uuguCc.a...uc..uU..U.gGaca....ccGAGUGGc...UCcUGUCCACUCUGU.UUgACg.CCUCCCuGUuAucaAcU.u..aagAGCCGCcggc..aa.cgGCGGCUcuuUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02357
#=GF ID   RNaseP-T
#=GF DE   RNaseP truncated form
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:21135215
#=GF SS   Predicted; PMID:21135215
#=GF GA   60.00
#=GF TC   78.00
#=GF NC   41.50
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.31 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF RN   [1]
#=GF RM   21135215
#=GF RT   Discovery of a minimal form of RNase P in Pyrobaculum.
#=GF RA   Lai LB, Chan PP, Cozen AE, Bernick DL, Brown JW, Gopalan V, Lowe TM
#=GF RL   Proc Natl Acad Sci U S A. 2010;107:22493-22498.
#=GF WK   Ribonuclease_P
#=GF SQ   9


AE009441.1/542976-543182   GGGGCGCCGAGGGGACGGGGGG-AGC-C-CGGAGACGGGCCC-CUUCUGGAACCUCCCGCACCGCCCGCGGAGGCUCUCGGCGGGCCGCCGAAAGGCGGGGGUAAAAA---CCAGCCGGGGGCGCGGCCCCCAAGCAGGGCCUGUGA-GGCCGCGGC-GAGGCCCGGGUAGGGGGUGAGAUAGAU-ACC-GAACAGAAGCGGGGGUACGCGGCGCCCC
CP000504.1/1063783-1063576 GGGGUGCCGAGGGGACGGGGGG-CGC-C-CGGAGACGGGCCC-CCUCUGGAACCUCCCGCACCGUCCGCGGAGGGUGCCGGCGGGCCGCCGCAAGGCGGGGGUAAAAA---CCAGCCGGCGCCACGGCCCCCAAGCAGGGCCUAUGA-GGCCGCGGC-GAGGCCCGGGUAGGGGGUUAGAUUGAU-ACCCCAACAGAAGCGGGGGUAUGCGGCACCCC
CP002590.1/1810975-1810769 GGGGCGCCGAGGGGACGGGGGC-GGC-U-CGGAGACGGCCGC-CCUCUGGAACCUCCCGCACCGCCCGCGGAGGCUCCCGGCAGGCCGCCGAAAGGCGGGGGUAAAAA---CCAGCUGGGGGCGCGGCCCCCAAGCAGGGCCUGUGA-GGCCGCGGC-GAGGCCCGGGUAGGGGGUUAGAUCGAU-ACC-GAACAGAAGCGGGGGUAUGCGGCGCCCC
CP000660.1/124150-124357   AGGGCGCCGAGGGGACGGGAGG-AGC-C-CGGAGACGGGUCC-CCUCUGGAACCUCCCGCACCGCCCGCGGAGGCCCCCGGCAGGCCGCCGAAAGGCGGGGGUAAAAA---CCAGCCGGGGGUGCGGCCCCCAAGCAGGGCCUAUGA-GGCCGCGGC-GAGGCCCGGGUAGGGGGUUAGAGAAAU-ACCCCAACAGAAGCGGGGGUAUGCGGCGCCCC
CP001014.1/115020-114812   GGGGCGCCGAGGGGACGGGGGGGCUC-C-CGGAGACGGGGCC-CCUCUGGAACCUCCCGCACCGCCCGCGGAGGGCGCCGGCGGGCCGCCGCAAGGCGGGGGUAAAAA---CCAGCCGGCGCUGCGGCCCCCAAGCAGGGCCUGUGA-GGCCGCGGC-GAGGCCCGGGUAGGGGGCUAGAUCGAU-ACCCCGACAGAAGCGGGGGUAUGCGGCGCCCC
CP000561.1/104313-104106   GGGGCGCCGAGGGGAACGGGGCAAGC-C-CGGAGACGGGCCG-CCCCUGGAACCUCCCGC-CCGCCCGCGGAGGUCCCCGGCGGGCCGCCGAAAGGCGGGGGUAAAAA---CCAGCCGGGGACGCGGCCCCCAAACAGGGCCAAUGA-GACCGCGGC-GAGGCCCGGGUAGGGGGCAAGAUCAAUACCC-CAACAGAAGCGGGGGUACGCGGCGCCCC
FN869859.1/1226851-1226646 CGCCCGCGGAGGGGACGGGGG--CCGUC-CGGAGACGGCGG-CCCUCUGGAACCUCCCGC-CCGCCCGCGGAGGCUCCCGGCGGGCCGCCGAAAGGCGGGGGUAAAAA---CCAGCCGGGGGCGCGGCCCCCAAGCAGGGCCUGUGA-GGCCGCGGC-GAGGCCCAGGUAGGGGGCUAGACCGAU-ACC-GAACAGAAGCGGGGGUAUGCCGCGGGCG
CP003098.1/1981693-1981486 GGGGCGCCGAGGGGAC-GGGGC-UGG-CUCGGAGACGGCCAG-CCUCUGGAACCUCCCGCACCGCCGCGGGGAGCCUCCAGCGGGCCGCCGAAAGGCGGGGGUAAAAA---CCAGCUGGAGGCGCGGCCCCCAAGCAGGGCCUGUGA-GGCCCGCGC-GAGGCCCGGGUAGGGGGAUAGACACAU-ACCCCAACAGAAGCGGGGGUACCCGGCGCCCC
CP002100.1/706409-706207   CAGCCACGGCGAACAACCGGGC-GAG-CCCGGCAACGGCUCG-CCUGAGGAAACUUCCCCACG--ACACCGUGGGUCCCC-----GCGGGGCAACCCGCCGACCGAGAGGUCG-CUGGGGAACAACGGCCCAAAUAGGGACCUGUGAUCUCCACGGGUGAGGUCCGGGUAGGGCCUUAGACGAAU----AGUACAGAAGGGGAGUUAUGCCGUGGCUG
#=GC SS_cons               [[[[[[[[[-[[[,,,,<<<<<.-<<.<.<<____>>>>>->.>>>>,,,,,,,,,,,,,,((((--------(((((((((,,,<<<<<____>>>>><<_______...>>,))))))))))))),,<<<-----<<<<<---<<.<_______>.>>>>>>>----->>>,,,,,,,,,,,,.]]]--------------------]]]]]]]]]
#=GC RF                    gGGgCGCcGaGGggAcgggGGg.agg.C.CGGagACGGcccc.CCccuGGAAcCUcCCgCACcGcccgcgGaGGcccCCgGCgGGcCGccGaAAggCGggGguaAAAA...CcAGCcGGgggCgCgGcCCCcAAgcAGGGCCUgUga.ggCCgcGGc.gaGGCCCGGGUAgGGgguuAGAuaaAU.cCCagaACAGAAGcGGgGgUAuGCgGCGcCCc
//
# STOCKHOLM 1.0

#=GF AC   RF02358
#=GF ID   hsp17
#=GF DE   Hsp17 thermometer
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:21131278
#=GF SS   Published; PMID:21131278
#=GF GA   45.00
#=GF TC   52.80
#=GF NC   32.10
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.49 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   21131278
#=GF RT   Translation on demand by a simple RNA-based thermosensor.
#=GF RA   Kortmann J, Sczodrok S, Rinnenthal J, Schwalbe H, Narberhaus F
#=GF RL   Nucleic Acids Res. 2011;39:2855-2868.
#=GF WK   Hsp17_thermometer
#=GF SQ   3


AP012205.1/460734-460688 AU-UCAAGGGUAAUCAAUUCCUUCCACACAUCAGGA-GUUAACAUUAUG
BA000039.2/889417-889465 AUCCCGCGGGCAAUCUAAAACUAAAACGAUACAGGAGGAUAAGCGUAUG
AB002666.1/390-432       AUCCCGCGGGCAAUCUAAAACU------AUACAGGAGGAUAAGCGUAUG
#=GC SS_cons             :::::::::<<<<<-<<<<<<<__________>>>>->>>--->>>>>:
#=GC RF                  AUCcCgcGGGcAauCuaaucCUuaaACaauaCAGgaGgauAAgagUaUG
//
# STOCKHOLM 1.0

#=GF AC   RF02359
#=GF ID   MS2
#=GF DE   Bacteriophage MS2 operator hairpin
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:11095669
#=GF GA   40.00
#=GF TC   44.30
#=GF NC   35.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.56 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   11095669
#=GF RT   Deletion of a single hydrogen bonding atom from the MS2 RNA operator leads
#=GF RT   to dramatic rearrangements at the RNA-coat protein interface.
#=GF RA   Grahn E, Stonehouse NJ, Adams CJ, Fridborg K, Beigelman L, Matulic-Adamic
#=GF RA   J, Warriner SL, Stockley PG, Liljas L
#=GF RL   Nucleic Acids Res. 2000;28:4611-4616.
#=GF WK   Bacteriophage_MS2
#=GF SQ   5


EF108464.1/1729-1764 AGAUUCCGUCCAUUCCAACAUGAGGAUUACCCAUGU
HQ332507.1/1662-1697 AGACGCCGGCCAUUCAAACAUGAGGAUUACCCAUGU
FJ799541.1/1686-1721 AGACNCCGCCCAUUCAAACAUGAGGAUUACCCAUGU
M38325.1/22-57       AAACCCGUGCCAUUCCAACAUGAGGAAUACCCAUGU
AF195778.1/1729-1764 AGAUACCGGCCAUUCAAACAUGAGGAUUACCCAUGU
#=GC SS_cons         :::::::::::::::::<<<<<-<<____>>>>>>>
#=GC RF              AGACuCCGgCCAUUCaAACAUGAGGAUUACCCAUGU
//
# STOCKHOLM 1.0

#=GF AC   RF02360
#=GF ID   Yfr8
#=GF DE   Cyanobacterial functional RNA 8/9
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   40.00
#=GF TC   43.20
#=GF NC   39.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.29 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18769676
#=GF RT   The challenge of regulation in a minimal photoautotroph: non-coding RNAs
#=GF RT   in Prochlorococcus.
#=GF RA   Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR
#=GF RL   PLoS Genet. 2008;4:e1000173.
#=GF WK   Non-coding_RNA
#=GF SQ   5



AACY021889802.1/369-594   UUUAAAGUCUAUUUACUCAUAAACCUAGAA-UACGUGAAUUCGGGGAUUUCUCUCGAUAAUUUCA-GUCCCUAGUGUCGCUAGUAAUUAUAAAGCGAAGUCUUAUCAGACUAAUUGAUUGAACUUUAAUUUUCGGAUAAUCCCAUUCUCAGGAAUACGCUUCCUAUAUUUUGGAAUUUGCUAAAUUUCAGGCGGACUAUCAAUCAUUUAGAUUGCCUCCGAACUCAAC
CP000551.1/348179-347954  UUUAAAGUCUAUUUACUCAUAAACCUAGAA-UACGUGAAUUCGGGGAUUUUUCUCGAUAAUUUCA-GUCCCUAUUGUCGCUAGUAAUUAUAAAGCGAAGUCUUAUCAGACUAAUUGAUUGAACUUAAAUUUUCGAAUAAUCCCAUUCUCAGGAAUACGCUUCCUAUAUUUUGGAAUUUGCUAAAUUUCAGGCGGACUAUCAAUCAUUUAGAUUGCCUCCGAACUCAAC
AACY020114721.1/1297-1072 UUUAAAGUCUAUUUACUCAUAAACCUAGAA-UACGUGAAUUCGGGGAUUUCUCUCGAUAAUUUCA-GUCCCUAUUGUCGCUAGUAAUUAUAAAGCGAAGUCUUAUCAGACUAAUUGAUUGAACUUUAAUUUUCGAAUAAUCCCAUUCUCAGGAAUACGCUUCCUAUAUUUUGGAAUUUGCUAAAUUUCAGGCGGACUAUCAAUCAUUUAGAUUGCCUCCGAACUCAAC
BX548174.1/340177-339952  UAUAAAGUUUAUUUACACAUAAGCUUUAAA-UACGUGGGUUAGGGGAUUCUUGUCGCUAAGUUUA-GUCCCUUUUGUCGCUGGUAAUUAUAGAGCGAAGUCUUAUCAGACUAAUUGAUUGAACUUUACUUUUCGAGAAAUCCCAUUGUCAGGAAUACGCUUCCUAUAUUUGUAAAUUUGCUAAAUUUCAGGCGGACUAUCAAUCAUUUAGAUUGCCUCCUAACUCAAC
CP000552.1/359787-359560  UAUAAAGUUGAUUUACUCAUAAACUUUAAAAUAUGUGAGUUAAGGGAUAUUUUUCGAUAAAUUCAAGUCCCGUUUGUCGCUAGUAAUUAUAAAGCGAAGUCUUAUCAGACUAAUUGAUUGAACUUUAUUUUUCGAAUAAUCCCAUUGUCAGGAAUACGCUUCCUAUAUUUGUAAAUUUACUAAAUUUCAGGCGGACUAUCAAUCAUUUAGAUUGCCUCCCAACUCAAC
#=GC SS_cons              ::<<<<<<<____________>>>>>>>--.----[[[[[[--[[[[,,,,,,,,,,,,,,,,,,.((((-(((((----((((((((((((((((,<<<<<____>>>>>,,<<<<<------<<<<<<___>>>>>>------->>>>>,,,,,))))--------))))))--))))))-----))))))))),,,<<<<<_____>>>>>,,]]]]]]]]]]::
#=GC RF                   UucaagGucuAUUUACuCAUAgaCcuugAA.UAcGuGaguuaggGGaUuuuUuUCGaUAAuUUcA.GuCCCgccuGUCGCuaGcaaucacaaaGCGAaGuCuUAUCaGaCuAAuuGacUGAACUuuacuuUUCgaguaaUCCCAUUguCagGAAUACGCuUCCUAUAUuugugaAUuugCuaAAUUUCaggcGGaCUAUCaauCAUUUAGauuGCCuCCcaacuCaAC
//
# STOCKHOLM 1.0

#=GF AC   RF02362
#=GF ID   Yfr10
#=GF DE   Cyanobacterial functional RNA 10
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   43.00
#=GF TC   43.20
#=GF NC   42.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.41 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18769676
#=GF RT   The challenge of regulation in a minimal photoautotroph: non-coding RNAs
#=GF RT   in Prochlorococcus.
#=GF RA   Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR
#=GF RL   PLoS Genet. 2008;4:e1000173.
#=GF WK   Non-coding_RNA
#=GF SQ   6


AACY022141642.1/164-241    AUCAGAAACUCCUCACACACUAAUUUCUGAUAAU-CAGGCAC-CCUUAUCUCUAAAUUAGGGUGUUUU-UUAUUGACAUAA
CP000111.1/1173516-1173439 AUCAGAAACUCCUCACACACUAAUUUCUGAUAAU-UAAACAC-CCUUUUCUCUAAAUUAGGGUGUUUU-UUAUUGCCAUAA
CP000576.1/133283-133206   AUCAGAAACUCCUCACACACUAAUUUCUGAUAAC-CAAACAC-CCUUUUCUCUAAAUUAGGGUGUUUU-UUAAUGCAACUA
BX548174.1/383217-383296   AUCAGAAACUCCUCAUAUACAAAUUUCUGAUCAC-UAAACACUCCGAUUCUUAAGAAUUGGGUGUUUUUUUAAUGCAAUUA
DQ366735.1/6280-6357       AUCAGAAACUCUUCACACGUUAAUCUCUUAUAAG-UAAAUUC-CUUUUUCUCUGAAUUAGGGUAUUUC-UUUAUGUCCAGA
CP000552.1/977591-977513   GUCAGAAACUCCUCACACACAUUUUUCUGAUAAUGCGAAGUA-CUCAAGCGAUCGUUUGAGUACUUUU-UAUUUAACCUUG
#=GC SS_cons               <<<<<<<<_______________>>>>>>>>---.-<<<<<<.<<<____________>>>>>>>>>:.::::::::::::
#=GC RF                    AUCAGAaACUCCUCACACACuAAUuUCUGAUAAu.uAAAcac.CcuuuUCUcUaaAUUagGgugUUUU.UUauUGacaUuA
//
# STOCKHOLM 1.0

#=GF AC   RF02363
#=GF ID   Yfr11
#=GF DE   Cyanobacterial functional RNA 11
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   44.00
#=GF TC   44.70
#=GF NC   42.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.84 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18769676
#=GF RT   The challenge of regulation in a minimal photoautotroph: non-coding RNAs
#=GF RT   in Prochlorococcus.
#=GF RA   Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR
#=GF RL   PLoS Genet. 2008;4:e1000173.
#=GF WK   Non-coding_RNA
#=GF SQ   4


BX548174.1/358754-358606   AAUCAAAUGGAGGGAUCAGAAAUGAUUGAUAGUCCACCAGAGAAUUUAAUGAGAUUGGUUUAAACAGCCAAAUCCUAUUAAAUAAAAAUAAGCUAAGUAUUCC------UAAAGAGGUUGUUUUCAUUUAAAGGCUGAGUUCAACCUCUUUUUUG
CP000552.1/1533584-1533717 ACUAAAAAGGAGGGAUUAGAAAUGAUCGAUAGUCCACCAGAGAAUUUAAUUGGAUUGGUUUAAACAGCC-AGUUUUACUACACA-----UAACUAAGUU------------AGGAGAUUAAUUUCU---AAAGGCGGAAGUUAAUCUCUUUUUUU
AACY022486491.1/72-220     AAUCGAAUGGAGGGAUUAGAAAUGAUUGAUAGUCCACCAGAGAAUUUAUUAAGAUUGGUUUAAGCAGCCAG--CCUAUUAGA-AAAAAAUUACUAGCAAUUAAAUAAGUGAAUUAGAUUGGCUCCUU---GAGGAUGGAGUCAAUCUCUUUUUUA
ADHP01001127.1/42790-42926 AUUAAUAUGGAGGGGUUAGAGAUGAUCGAAAGUCCACCACAGAAUCUUAACUGAUUGGUUUAAACA-------CCAGUAACACAAAUCAAAGUUGACAGCUAA------UCAAAAAACAUUGAGGGU--AUAAAGCCCUCU---UUUUUUGUAAA
#=GC SS_cons               ::::::::((((,<<<<<____>>>>>,,<<<<----------<<<<<<<<-<--<<<<<_____>>>>.>..>->>>>>>>>-------->>>>,,,,))))......-<<<<<<<<<<--<<<<_..______>>>>-->>>>>>>>>>::::
#=GC RF                    AaUaAaAuggagGgaUcAGAAAUgAucGAuAGuCCACCAgAGAgUcUaaucaGAUuGGuUUAAACAgCC.a..CcgauuAgAcAAAaaaaaaCUaAcaacucc......ucAagAGauuguuuccgU..AaAggacggauUcaauCUcuUgUuua
//
# STOCKHOLM 1.0

#=GF AC   RF02364
#=GF ID   Yfr13
#=GF DE   Cyanobacterial functional RNA 13
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   39.00
#=GF TC   39.00
#=GF NC   34.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.27 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18769676
#=GF RT   The challenge of regulation in a minimal photoautotroph: non-coding RNAs
#=GF RT   in Prochlorococcus.
#=GF RA   Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR
#=GF RL   PLoS Genet. 2008;4:e1000173.
#=GF WK   Non-coding_RNA
#=GF SQ   7


BX548174.1/621701-621601   GAGGCCAAACCUCAAUGAGUUGAAUAUAUGUUUAACUCCAAGACAUAGAUUGAUUACGUAUAGUAG-UGUAUUCAAUUUAAUAACCCUUCUGGUAGUGGGAA
CP000825.1/1106569-1106472 GAGGCCAAACCUCAAUGAGUACAAUCUUCGUU-UACUCCAAGACAUAGAUUGACUUUAUAUAGUAC---GAGUCAAUUUAAUAACCUCUCUUGUAGUUGGAA
ACDW01000003.1/2829-2732   GAGGCCAAACCUCAAUGAGCACACUCUUC-GUUUGCUCCAAGACAUAAAUUGACUUUAUAUAGUAC---GAGUCAAUUUAAUAACCUCUCUGGUAGUUGGAA
CP000552.1/1116918-1116820 GAGGCCAAACCUCAACGAGUUAACUCUACGUUCAACUCCAAGACAUAGAUUGGUUCAAUAUAGUAC---GAAUCGAUUUAACAACCUCUCUGGUGAUUGGAA
ADHP01001050.1/11553-11650 GAGGCCAAACCUCAAAGAGUCAACUCUGC-GUUUACUCCAAGACAUAAAUUGGUUCUAUAUAGUAC---GAUCCAAUUUAAUAACCCCUGUAGUAGUUGGAA
CP000111.1/1130396-1130299 GAGGCCAAACCUCAAUGAGUACGCUCUAC-GUUUACUCCAAGACAUAGAUUGACUUUAUAUAGUAC---GAGUCAAUUUAAUAGCCCUUUCAGUAGUUGGAA
CP000576.1/1071080-1071177 GAGGCCAAACCUCG-UCAGCACACUCUAC-GUUUGCUGCAAGACAUAGAUUGAUUCAAUAUAGUUGC--GAGUCAAUUUAAUAACCCUUUCAGUAGUUGGAA
#=GC SS_cons               <<<<_____>>>>,,,<<<<<<<<_____.>>>>>>>>,,,,,,,<<<<<<<<-<<__________...>>->>>>>>>>,,,,<<<__________>>>::
#=GC RF                    GaGGCCAAACCuCAAugaGucgacUcUac.gucgaCucCAAGACAuagauuGauucuAUAUAGUAc...gaguCaaucuaAUAACCcuUuuaGUAGUgGGAA
//
# STOCKHOLM 1.0

#=GF AC   RF02365
#=GF ID   Yfr17
#=GF DE   Cyanobacterial functional RNA 17
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   50.00
#=GF TC   52.00
#=GF NC   43.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.53 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18769676
#=GF RT   The challenge of regulation in a minimal photoautotroph: non-coding RNAs
#=GF RT   in Prochlorococcus.
#=GF RA   Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR
#=GF RL   PLoS Genet. 2008;4:e1000173.
#=GF WK   Non-coding_RNA
#=GF SQ   3


BX548174.1/664667-664930 AAAACCAACUUUGAUCUUAUCGUUCCUAAAAGAAUUCCGCGUGACAUUUUUUACAAAA-AA-GCUUAUAUUUUAUUUCGCACAUAGAAAAGUGAAUUAAAUCUACAACUUGUGGAAAAACCUGUUGAAAAAUGGUUAAAAAGUGGAUAACUCAUGGGGAUCAUGAUAAAAACAGGGUUUUUUGGCUUAUUUUCUGAGUAUUAAUACUGCAUCAAUAAAUUAUUAAAUGUAGUUUAAUAAUCAAUAAAACUUACUGAAACAACAAUG
CP000552.1/786071-785807 AAAAACAGAUUUGAUCUUAUCGUUCCUUAAAAAAUUCUGCGUGACAUAUUUUACAAAAAAA-ACUUAUAUUUUAUUUCGCUCAUAGAAAAGUGAAUUAAAUCUACAAGCUGUGGAAAAACCUGUUGAAAAAGCCUCAAAAAGUGGAUAACUCUUUGGGAUCAAGGUAAAAACUGGGUUUUAAUGCUUAUUUUCUAAGUAUUAAUACUUCAUCAAUAAAUUAUUAAAUAUAGUUUAAUAAUCAAUUAAACUAACUGAAAUAACAAUG
AACY021378008.1/484-748  UAACUGAUCUUUGAUAUUAUCGUUUCAUGACAAAAUCCGCGGUACAUUUUUUACAAAA-AAUACUAAUAUUUUAUUUCGCACAUAGAAAAUUAAAUUUAAUCUACAAGCUGUGGAAAAACCUGUUGAAAAAGGCUCAAAAAGUGGAUAACUUGCUGGGAUCAAGGUUAAAACUGGGUUUUUCGGAUGUUUUCCUAAGUAUUAAUACUUCAUCAAUAUAUGGUUAAAUAUAGUUUAAUAAUCAAUUAAACUAAUUGAAAUAACAAUG
#=GC SS_cons             ::::::(((((((---((((((((((((--((---(((((----(((((((((((,,,.,,.,,,,,,,,<<<<-<<<<<__________>>>>>->>>><<<<<_____>>>>>,,,,,,)))-))))))))--------)))))---))--)))))))---)))))---)))))))<<<--<----<<<--<<<-<<<<<<-<<<<<<<______________>>>>>>>>>>>>>->>>-->>>----->-->>>::::::::
#=GC RF                  aAAaucagcuuuGAUcuuacCguucCcgaAagAAuuCcgCGugAcauuuuuuaCaAAA.AA.aCUuAUAUuuuaUuucgcaCAUAGAAAAgugaaUuaaauCuaCAAgcUGugGaAAAACCuGuUgaaaaaugcUcAAAAAGugGaUAAcucacgGggauCAaGguaaAAACagggcuuuuugGcUuauuuuCugaGuauuaaUaCugcauCAAUAaAUuaUUAAaugcaGuuuaauaAucaAUaaaACUaACUGaaauAACAAUG
//
# STOCKHOLM 1.0

#=GF AC   RF02366
#=GF ID   Yfr19
#=GF DE   Cyanobacterial functional RNA 19
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   70.00
#=GF TC   72.50
#=GF NC   46.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.05 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18769676
#=GF RT   The challenge of regulation in a minimal photoautotroph: non-coding RNAs
#=GF RT   in Prochlorococcus.
#=GF RA   Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR
#=GF RL   PLoS Genet. 2008;4:e1000173.
#=GF WK   Non-coding_RNA
#=GF SQ   6


BX548174.1/1086162-1086081 GCUUACUUGAAAUUAUUCUUGUGAGAAUUAGGUAA-UGAGAGUUCGUUUUCAGCUAAAAAUCGAACUCUUU----UUUUAUUAAAAA
AACY021813985.1/9-89       GCUUACUUGAUAUUAUUCUCGUGAGAAUUAGGUUA-UGAGAGAUCGUUUUCAGCUAAAAAAUGAUCUCUUU----U-UUUUUAAGAA
CP000551.1/1087672-1087591 GCUUACUUGAAAUU-UUCAUGUAAGAAUUAGGUAAUUGAGAGAUUGUUUUUAGCUAAGAAACAAUCUCUUU----UUUUUUUACAAG
DQ366735.1/33757-33838     GCUUACUUGAAAUU-UUCAUGUAAGAAUUAGGUAAUUGGGAGAUUGUUUUUAGCUAAUAAACAAUCUCUUU----UUUUUAUAAAUA
CP000111.1/1145677-1145592 GCUUACUUGAAAUU-UUCAUGUAAGAAUUAGGUAAUCUAGAGAUUGUUUUCAGCUAAGAAACAAUCUCUUUUUUUUUUUUUUAAUAU
ACDW01000003.1/29926-29844 GCUUACUUGAAAUU-UUCAUGUAAGAAUUAGGUAAUUGAGAGAUUGUUUUUAGCUAAGAAACAAUCUCUUU---UUUUUAUUUUUCU
#=GC SS_cons               :<<<<<--<<<___.>>>-->>>>>--<<<<--<<--<<<<<<<<<<<<<______>>>>->>>>>>>>>-....>>--->>>>:::
#=GC RF                    GCUuaCUUGaaAUU.uuCaUGuaAGAAuuagGUaaUUgaGaGaUcGUUcUuAGCUAAgAAACgAuCuCuuU....uuUUuuuaaaaa
//
# STOCKHOLM 1.0

#=GF AC   RF02367
#=GF ID   Yfr20
#=GF DE   Cyanobacterial functional RNA 20
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   44.00
#=GF TC   44.00
#=GF NC   38.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.13 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18769676
#=GF RT   The challenge of regulation in a minimal photoautotroph: non-coding RNAs
#=GF RT   in Prochlorococcus.
#=GF RA   Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR
#=GF RL   PLoS Genet. 2008;4:e1000173.
#=GF WK   Non-coding_RNA
#=GF SQ   7


BX548174.1/1336435-1336523   AAGCAUUUAGGAAGUGCUUAGCUGGUUAAGCUCAGUCAAUCUGAAUUUAACUUUAUCGUCAUGAG--AGUUUGCUAGU-----AGGG---A---UGCGAGCA
CP000552.1/1383739-1383827   UGGCAUUUAGGAAGUGCUUAGCUGUUUAAGCUCAGUUCAUCUGAAUUUAACUUAUUCGUCAUGAG--AGUUUGCUAGU-----AGGG---A---UACAAGCA
AACY023403472.1/399-487      AGGCAUUUAGGAAGUGCUUAGCUGGUUAAGCUUAGAUUAUUUGAAGCUAACUUAAUCGUCAUGAG--AGUUUGCUGGU-----AGGG---A---UACAGGCA
CP000111.1/1389686-1389777   UAGCAUUUAGGAAGUGCUUAACUGGUUAAGAUCAAAAAAUCUGAAUUUAACUAGGUCGUCAUG----AGUUUGCCAGUGGUAUAUAC---U---UGCAAGCU
ACDW01000003.1/283050-283139 UAGCAUUUAGGAAGUGCUUAGCUGGUUAUAGUAAGAAAACCUUAAUUUAACCUGUUCGUCAUG----AGCUUGCCUGU-----GGGAUACA---UGCAAGCU
CP000551.1/1359515-1359602   AAGCAUUUAGGAAGUGCUUGCCUGGUUAAA-UCAC-AAAUCUGAAUUUAACUAGUUCGUCAUG----AGCUUGCCUGU-----GGGA---UACCUGCAAGCU
CP000576.1/1332702-1332785   UAGCAUUUAGGAAGUGCUUAGCUGGUUAA-AUCAGGUAAUCUGAA-UUAAUUAGGUCGUCAUGAGCUUGCAGGU----------GGG---A---UACUUGCA
#=GC SS_cons                 <<<<<<<<___>>>>>>>>,,,,<<<<<<<-<<<<_____>>>>->>>>>>>-------------..-<<<<<<____.....____..._..._>>>>>>:
#=GC RF                      aaGCAuUUAGGAAgUGCuuAgCUggUUAagaUcAgaaaAUcUgAAcuUAAcuuguUCGUCAUGAG..AGcuuGcuaGU.....aGGg...a...UgCaagCa
//
# STOCKHOLM 1.0

#=GF AC   RF02368
#=GF ID   Yfr21
#=GF DE   Cyanobacterial functional RNA 21
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   100.00
#=GF TC   222.90
#=GF NC   39.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.28 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   18769676
#=GF RT   The challenge of regulation in a minimal photoautotroph: non-coding RNAs
#=GF RT   in Prochlorococcus.
#=GF RA   Steglich C, Futschik ME, Lindell D, Voss B, Chisholm SW, Hess WR
#=GF RL   PLoS Genet. 2008;4:e1000173.
#=GF WK   Non-coding_RNA
#=GF SQ   2


BX548174.1/1069757-1069553 GGAAUUUUCUUUUUGGAUUCGAAACCUUUCAUGAUCUUAAACAUAACCUCUCAUUCAGAAAUUUUGUCAUGAUUUAAUAAAUCAAUUGGCUUGCUUAACCCUUAUUUAAAAAACAAAUCUUUUUUAAUUGGACACAAAUAAUAUCGGCACAACAUGUUGCAAUAAAAUUAAUGUUUAAAUUUUAUCCUCAAAAACCACUGCUAUG
AACY021878637.1/63-266     GGAAUGUUCUUUUU-UAUUUUAUUCCUUUCAUCAUCUCAAACAUAACCUCUCAUCCAGGAAUUUUGCCAAGAUUUAAUAAAUCAAUUGUCUUGCUUAACCCUUAUAUAAAAAGCAAAUCUUUUUUAAUUAGACACAAAUAAUAUCGGCACAACAGGUUGCUAUAAAAUUAAUGCAUAAAUUUUAUCCUUGAAAACCAUUGCUAUG
#=GC SS_cons               {{{,,,,,,,,,,,<<<<<-<<<____>>>-->>>>>[[[[[[[,,,,,,,,,,,,,((,,,,,,<<<<<<<<<<___>>>>>>-->>>>,,,,,,,,,<<----<<<<<<<<______>>>>>>>>-->>,,,,,,,,,,,,)),<<<________>>>,,,,,,,,,,]]]]]]],,,,,,,}}}::::::::::::::::::
#=GC RF                    GGaAUuUUCUUUUUggaucugaaaCCUuucAUgauccuaagCauAACCUCUCAUuCAGaAAUUUUGcCauGauuuAAUaaauCaAUuGgCUUGCUUAACCcUUAUuuaaaaaaCAAAUCuuuuuuaaUUgGACACAAAUAAUAuCGGCaCAACAuGUuGCaAUAAAAUUAauGcuuaAAUUUUAuCCUuaAAAACCAuUGCUAUG
//
# STOCKHOLM 1.0

#=GF AC   RF02369
#=GF ID   h2cR
#=GF DE   h2cR sRNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23082228
#=GF GA   70.00
#=GF TC   82.30
#=GF NC   48.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.73 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23082228
#=GF RT   The Novel Cis-Encoded Small RNA h2cR Is a Negative Regulator of hfq2 in
#=GF RT   Burkholderia cenocepacia.
#=GF RA   Ramos CG, da Costa PJ, Doring G, Leitao JH
#=GF RL   PLoS One. 2012;7:e47896.
#=GF WK   H2cR_sRNA
#=GF SQ   7


CP000614.1/1613873-1614008  GUCAGAG-AUGUGUUGUGCGUGUGUGUGGCG--UGAUCGCUCACCAA-GUAUUUAGCGGGAUUCUACCCUGUUCGUUCCGCCCGCGCGUGAUCGCGAUUGUGUCGAACCGUAACCCACUAUAGACGCUCCAGGACAUUUU
AACY020561250.1/13671-13807 GUCAGAGAAUAUGUUGUGCGUGUGUGUGGCG--UGUUCGUCCACAAG-GUGUUUGGCGGGAUUCUACCCUGUUCAAUCGGGGAGCGCGUAGUCGUGAUUGUGUCGAACCGUAACCCACUAUAGACGUUCCAGCGCAUUUU
AM747720.1/1704623-1704759  GUCAGAGAAUAUGUUGUGCGUGUGUGUGGCG--UGUUCGUCCACAAG-CCGUUUGGCGGAAUUCUACCCUGUUCGAUAGGGGAGCGCGCAGUCGUGAUUGUGUCGAACCGUAACCCACUAUAGACGUUCCGGCGCAUUUU
CP001025.1/1617383-1617519  GUCAGAGAAUAUGUUGUGCGUGUGGAUGGCG--UGGUCGCCCACCAG-GUGUUUGGCGGGAUUUUACCCUGUUCGUUCCAGCAGCGCGCGCUCGUGAUUGUGUCGAACCGUAACCCACUAUAGACGUUGCAGCGCGUUUU
ABLC01000233.1/10106-9970   GUCAGAGAAUAUGUUGUGCGUGUGGAUGGCG--UGGUCGCCCACCAG-GUGUUUGGCGGGAUUUUACCCUGUUCGUUCCACCAGCGCGCGGUCGUGAUUGUGUCGAACCGUAACCCACUAUAGACGUUCCAGCGCGUUUU
AEXE01001954.1/968-830      GUCAGAGAAUAUGUUGUGCGUGUGUGUGGCGUGUGUUCGUCCACAAG-GUGUUUGGCGGGAUUUUACCCUGUUCGUUCAGGAAGCGCCCAGUCGCGAUUGUGUCGAACCGUAACCCACUAUAGACGCUCCCGUCCGUUUU
CP000868.1/1903013-1902879  GUCAGAGAAUAUGUUGUGCG--UGUGUGGCG--UGGUCGU-CACAAAUCUGUUUGGCGGGAUUCUACCCUGUUCGAUCGGGAAGCGCCCAGUCGCGAUUGUGUCGAACCGUAACCCACUAUAGACGCUAACGCGCAUUUG
#=GC SS_cons                :::::<<<<<<<<<<<-<<<<-<<<<<<<<<..-<<<<<--<<<<<-.-<<-<<<<<<-----<<<<<<<<<___>>>>>>>>>>>>->>>->>--->>>>>->>>>>>>---->>>>->>>->>>>-->>>>>>>>>>>
#=GC RF                     GUCAGagaaugcguugUgCGuGuguguGGCG..UGuuCGucCaCaag.gcGUcugGCGGgAUUcucccccguUCgaugggggagCGCgcagUCguGAuuGuGUCGaaCCGUAACCCacUauaGaCGcUccagcgcauuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02370
#=GF ID   Trp_leader_2
#=GF DE   Bacillus tryptophan operon leader
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:14712717
#=GF GA   100.00
#=GF TC   119.90
#=GF NC   39.00
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   14712717
#=GF RT   Role of RNA structure in transcription attenuation in Bacillus subtilis:
#=GF RT   the trpEDCFBA operon as a model system.
#=GF RA   Babitzke P, Schaak J, Yakhnin AV, Bevilacqua PC
#=GF RL   Methods Enzymol. 2003;371:392-404.
#=GF RN   [2]
#=GF RM   11566976
#=GF RT   Posttranscription initiation control of tryptophan metabolism in Bacillus
#=GF RT   subtilis by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and
#=GF RT   RNA structure.
#=GF RA   Babitzke P, Gollnick P
#=GF RL   J Bacteriol. 2001;183:5795-5802.
#=GF WK   Tryptophan_operon_leader
#=GF SQ   9


AEFO01000035.1/194959-194814 AGCUUAGAAAUACACAAAAGUGUGUAUAAAGC------AGAAGUU-A-GA-----A-C---------AGUUGAGUUAGAGAAUAGGGUAG-CUGAGAAUGAGUUUAGUUGAGCUGA----------GGACAA---AUUUGUUAAUUCCUACCCAAAAGAAGUUU-AUUCUUUUGGGUUUAUUUU
CP002627.1/1123061-1123212   AGCUUAGAAAUACACAAGAGUGUGUAUAAAGC------U---GAUAA-GC-----AAGAUAUUGAACAGUUGAGUU-UAGAAUAGGGUAG-CAGAGAAUGAGUUUAGCUGAGCUGA-----------GAU-AAACACGUUUUUAUU-CUGCCCAAAAGAAGCCU--UUCUUUUGGGUUUAUUUC
AM295011.1/2654-2805         AGCUUAGAAAUACACAAGAGUGUGUAUAGAGCUG-GUA----AGU-AAGAUAUUGAAC---------AGUUGAGUU-UAGAAUAGGGUAG-CAGAGAAUGAGUUUAGCUGAGCUGA-----------GAU-AAACACGUUUUUAUU-CUGCCCAAAAGAAGCCU--UUCUUUUGGGUUUAUUUC
ACWC01000001.1/483169-483321 AACCUUGAAAUACACAGGAGUGUGUAUGGGGUU---UUA---GUU-U-AG-----AAA---------AGCUGAGUAUGAGACUAGGGUAGAUUGAGAAUGAGUUGAGAUGAGCUG-AGUUGAGACAAAAC-G---UU-UAUUCAUU-CUACCCAAAAGACGCUG--UUCUUUUGGGUUUGUUUC
EF191544.1/8405-8266         AGCUUAGAAAUACACAAGAGUGUGUAUAAAGC------G----AU-U-GA-----AUG---------AGUUGAGUUAGAGAAUAGGGUAG-CAGAGAAUGAGUGUAGUUGAGCUGA-----------GAC-A--UGUAUGUUUAUU-CUACCCAAAAGAAGCCU--UUCUUUUGGGUUUAUUUG
ABRX01000005.1/167547-167700 AGCCGAAGUUUACACACAG--GUGUAAACGGCAUUGCAA---GUU-U-AG-----AGA---------AGAUGAGAAUGAGACUAGGGUAG-UUGAG-AUGAGUAGAGUUGAGCAGAGAU----ACGAUAC-GUCUAUUUCAUCAUA-CUGCCUAAAAGAGUACC-CCUCUUUUAGGCUUAUUUC
AGBY01000140.1/51393-51239   AGCCGAAGUUUACACACAG--GUGUGAACGGCAUUGCAA---GCU-U-AG-----AGA---------AGAUGAGAAUGAGACUAGGGUAG-UUGAG-AUGAGUAGAGUUGAGCAGAGAU----ACGAUAC-UUCUAUUUAAUCAUA-CUGCCUAAAAGAGCGAAGCCUCUUUUAGGCUUAUUUC
EF191536.1/8403-8264         AGCUUAGAAAUACACAAGAGUGUGUAUAAAGC------A---AUU-A-GA-----AUG---------AGUUGAGUUAGAGAAUAGGGUAG-CAGAGAAUGAGUUUAGUUGAGCUGA-----------GAC-A---UUAUGUUUAUU-CUACCCAAAAGAAGUCU--UUCUUUUGGGUUUAUUUG
M14027.1/51-204              AGCCGAAGUUUACACACAG--GUGUAAACGGCAUUGCCA---GCU-U-AG-----AGA---------AGAUGAGAAUGAGACUAGGGUAG-UUGAG-AUGAGUAGAGUUGAGCAGAGAU----ACGAUAC-UUCUAUUUAAUCAUA-CUGCCUAAAAGAGCAAC-CCUCUUUUAGGCUUAUUUC
#=GC SS_cons                 :<<<-----<<<<<<______>>>>>>-->>>-...---...---.-.--.....---.........-----------------<<<<<<.-<<<<<<<<<<<<____________.........._>>>.---->>>>->>>->>.>>>>>>:::::::::::..::::::::::::::::::
#=GC RF                      AGCcuAgaaauACACAagaGUGUGUauAagGCa...uaa...GuU.u.aa.....Aaa.........AGuUGAGuuugAGAaUAGGGuAG.uagagaAcgaGUcuAGuUGAGCuGA..........AgAC.auauucgUauuuAuu.CUaCCCAAAAGAagucu..uUCUUUUgGGuUUAUUUc
//
# STOCKHOLM 1.0

#=GF AC   RF02371
#=GF ID   PyrG_leader
#=GF DE   PyrG leader
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:17302819
#=GF GA   65.00
#=GF TC   71.40
#=GF NC   50.00
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.69 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   17302819
#=GF RT   Regulation of pyrG expression in Bacillus subtilis: CTP-regulated
#=GF RT   antitermination and reiterative transcription with pyrG templates in
#=GF RT   vitro.
#=GF RA   Jensen-MacAllister IE, Meng Q, Switzer RL
#=GF RL   Mol Microbiol. 2007;63:1440-1452.
#=GF WK   PyrG_leader
#=GF SQ   10



AEFO01000028.1/125706-125628         GGGCUCUUCAAAAAAGAAGA---GGAAUUCA-----UA-CGAAUGCUACGCUCCCUUUCAAG-AAAUUGAAAGGGAGC-UUUCUUAUUUU
CP002627.1/3574054-3573978           GGGCUCUUCAAAAA-GAAGA---GAAU-UCA-----UA-AGAGUGCUACGCUCCCUUUCAAG-AAAUUGAAAGGGAGC-UUUCUUAUUUU
AEFW01000008.1/145237-145314         GGGCUCUUCAAAAAGAAGAG---GAAU-UCA-----UA-CGAAUGCUACGCUCCCUUUCAAG-AAAUUGAAAGGGAGC-UUUCUUAUUUU
ACWC01000017.1/164827-164747         GGGCUCUUCAA-AACGAAGA---GAUU-CGAGUGAUAC--GGACUAUCAGCUCCCUUUCAAG-AAAUUGAAAGGGAGC-UUUCUUGUUUU
AGBY01000032.1/88505-88584           GGGCUCUCUAAAAAAGAGUA--CGUAA-AGA-----UACGUUCAUUUACGCUCCCUUUCAUU-UAUUUGAAAGGGAGC-UUUCUUAUUUU
CP000813.1/3336893-3336815           GGGCUCUCUAAAAAGAGUAC---GUAA-AGA-----UACGUUCAUUUACGCUCCCUUUCAUU-UAUUUGAAAGGGAGC-UUUCUUAUUUU
ADGO01204330.1/13-95                 GGGCUCUUAAAAAAGCAAUCGUUGUAU-AAA----UUA-UACAUUUAACGCUCCCUUUCAACUUGUUUGGAAGGGGGC-UUUCUAUUUUU
ADLY01000031.1/57017-57096           GCACUCUUGAAAAAGAGUCA---GAAAGUGA-----UU-UAGAAUUUUCGCUCCCUAUUCAU-UUAUGGAUAGGGAGCUUUUCUUAUUUU
ACAL01000027.1/65483-65561           GCACUCUUUAC-AAGAGUCA---GAAAGUGA-----UU-UAGAAUUUUCGCUCCCUAUUCAU-UUAUGGAUAGGGAGCUUUUAUUAUUUU
CP002906.1/3615649-3615573           GGGCUCUUCAAAAACGAAGA---GAGA-ACA-----UA--GUACGUUAUGCUCCCUUUCAAG-AAAUUGAAAGGGAGC-UUUCUUAUUUU
#=GC SS_cons                         ::::::::::::::::::::...::::.:::.....::.::::::::::<<<<<<<<<<<<_.___>>>>>>>>>>>>.:::::::::::
#=GC RF                              GGGCUCUUuAAAAAgaAauA...GaAa.ugA.....Ua.uauAuuuUaCGCUCCCUuUCaAu.uaaUuGAaAGGGAGC.UUUCUUAUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02372
#=GF ID   PyrC_leader
#=GF DE   PyrC leader
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:18535147
#=GF GA   50.00
#=GF TC   60.90
#=GF NC   43.90
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   18535147
#=GF RT   Regulation of pyrimidine biosynthetic gene expression in bacteria:
#=GF RT   repression without repressors.
#=GF RA   Turnbough CL Jr, Switzer RL
#=GF RL   Microbiol Mol Biol Rev. 2008;72:266-300.
#=GF WK   PyrC_leader
#=GF SQ   9



AGTJ01000238.1/62221-62270           UAUCCUUUGUGUCCGGCAAAAAC-AUC---CCUUCAGCCGGAGCAUA-GAG-AUUA
AFCJ01001248.1/554-605               UAUCCUUUGUUUCCGGCAAAAAG-ACUU-UUCCUCAGCCGGAGCUUA-UUA-AUGA
FR877557.1/1111657-1111607           UAUCCUUUGUUUCCGGCAAAAGACUAC---CCCUCAGCCGGAGCAUA-UUA-AUGA
CP000822.1/1863926-1863978           UAUCCUUGGUUUCCGGCAAAAAU-GACUAUCCCCCAGCCGGAGCAUA-UUA-AUGA
CP000880.1/1763272-1763322           UAUCCUUUGUUUCCGGCAAAAGAUUAU---CCCUCAGCCGGAGCUUA-UUA-AUGA
BAAY01008612.1/75-126                UAUCCUUUGUUUCCGGGGAAAAAGACU--AUCCUCAGCCGGAGCAUA-UUA-AUGA
AEVY01000021.1/71316-71367           UAUCCUUUGUGCCCGGCAAAAAC-AUU---CCCACAGCCGGAGCUAAUAAGUAAUG
ABWL02000006.1/667527-667578         UAUCCUUUGUUUCCGGCAAAAAA-GACU-AUCCUCAGCCGGAGCAUA-UUG-AUGA
FN543502.1/1219902-1219852           UAUCCUUGGUUUCCGGCAAAAAUGACA---CCCUCAGCCGGAGCAUA-UUG-AUGA
#=GC SS_cons                         ::::::::::::<<<<<______.___...______>>>>>::::::.:::.::::
#=GC RF                              UAUCCUUUGUUUCCGGCAAAAAa.aau...CCCUCAGCCGGAGCaUA.UUa.AUGA
//
# STOCKHOLM 1.0

#=GF AC   RF02373
#=GF ID   PyrD_leader
#=GF DE   PyrD leader
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:7510398
#=GF GA   47.00
#=GF TC   49.00
#=GF NC   46.30
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   7510398
#=GF RT   Conformational heterogeneity in the Salmonella typhimurium pyrC and pyrD
#=GF RT   leader mRNAs produced in vivo.
#=GF RA   Sorensen KI
#=GF RL   Nucleic Acids Res. 1994;22:625-631.
#=GF WK   PyrD_leader
#=GF SQ   27



FR877557.1/978595-978668               AUUCCCUUUUUCAA-CGAUAUCGCCCAUAAUACGCCCCCGGUUUGCAUACCGGGAAUCCAGGAGAGUUCAUGUAC
FN543502.1/1116251-1116324             AUUCCCUUUUUGUG-CGAUAUCGCCCAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
CACD01000018.1/3151-3224               AUUCCCUUUUUGCU-CGCGAUCGCACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
AEJY01000055.1/19435-19362             AUUCCCUUUUGCUC-UGAACUCGCACAUAAUACGCCCCCGGUUUGCAUACCGGGAAUCCAGGAGAGUUCAUGUAC
CP000822.1/1964347-1964274             AUUCCCUUUUCGCU-GGAUAUCGCACAUAAUACGCCCCCGGUCUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
ADUD01000192.1/11365-11438             AUUCCCUUUUGGUC-CGAUCUCGCACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
AEME01000001.1/1208620-1208693         AUUCCCUUUUUGGC-UGAACUCGCACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
CU928158.2/1124982-1125055             AUUCACUUUUGAAC-CGAACUCGCACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
AGFT01013185.1/1104-1031               AUUCCCUUUUUGUG-CGCAAUCACACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
CP000964.1/3619469-3619396             AUUCCCUUUCAGCU-GCGGAUCGCACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
AFQK01000064.1/24675-24602             AUUCCCUUUCCGCA-ACAGAUCGCACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
AFVS01000867.1/54-128                  AUUCCCUUUUGGGUCCGAACUCGCACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
CP002824.1/3294994-3295067             AUUCCCUUUCGGGC-GCGGAUCGAACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
CP002272.1/3028558-3028485             AUUCCCUUUCUGCG-CCGGAUAGAACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
AEXB01000041.1/4416-4489               AUUCCCUUUCCGGG-CGGGAUCGCACAUAAUCCCCUCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
CP001655.1/1917144-1917216             AUUCCCUUUCGCCC-GGUGAUGGACGAUAAUACGCCCCCGGUUUAUA-ACCGGGAAUCCAGGAGAAGUCAUGUAU
CP002038.1/2931036-2930964             AUUCCCUUUCGCCU-GACGAUGGACGAUAAUACGCCCCCGGUUUGUA-ACCGGGAAUCCAGGAGAAGUCAUGUAU
CP000783.1/2338907-2338834             AUUCCCUUUGUGAA-GUGGAUCGCAGAUAAUAGCGCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
CP000653.1/1610383-1610455             AUUCCCUUUCACGC-CGCGAUCGCUGAUAAUCCGUGUCCGGUUUGCACACCGGA-AUCCAGGAGAGUUCAUGUAU
CP000826.1/1917045-1917117             AUUCCAAUUGGUCA-GGGGAUACCGGAUAAUACGCCCCCGGUUUGCA-ACCGGGAAAUCAGGAGAGUACAUGUAC
CP001654.1/1940384-1940456             AUUCCCUUUCAUUC-GAUGAUGCAGGAUAAUACCGCCCCGGUUUGC-CACCGGGAAUUCAGGAGAAUUCAUGUAC
CP002773.1/1858934-1859006             AUUCCAAUUGAUCA-GGGGAUGCCGGAUAAUCGGCCCCCGGUUUGCA-ACCGGGAAAUCAGGAGAGUACAUGUAC
BAAX01020672.1/1-72                    --UCCCUUUCAGGC-GUCGAUCGAACAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
ADGK01000071.1/15405-15475             AUUCCAAUUCGUCG-CGACUUACCCGAUAAUAGCGCCCCGUUUGGC--AACGGGAAU-CAGGAGAUCUCAUGUUC
CP001135.1/1358628-1358698             AUUCCAAUUGAUGA-CGACUUCCCUGAUAAUAGCGCCCCGUUUGGC--AACGGGAAU-CAGGAGAUCUCAUGUUC
CP001600.1/1364550-1364620             AUUCCAAUUGAGGU-CAACUUACCUGAUAAUAACGCCCCGUUUGGC--AACGGGAAU-CAGGAGAUCUCAUGUUC
X55636.1/171-244                       AUUCCCUUUUGCCU-UGUUAUCGCCCAUAAUACGCCCCCGGUUUGCACACCGGGAAUCCAGGAGAGUUCAUGUAC
#=GC SS_cons                           ::::::::::::::.:::::::::::::::::::::<<<<<<______>>>>>>:::::::::::::::::::::
#=GC RF                                AUUCCCUUUuaguu.cgagaUcgCacAUAAUAcGcCCCCGGUUUGCACACCGGGAAUCCAGGAGAgUUCAUGUAC
//
# STOCKHOLM 1.0

#=GF AC   RF02374
#=GF ID   YenS
#=GF DE   Yersinia YenS sRNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   80.00
#=GF TC   102.30
#=GF NC   36.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0009372; quorum sensing;
#=GF RN   [1]
#=GF RM   21362062
#=GF RT   The quorum-hindered transcription factor YenR of Yersinia enterocolitica
#=GF RT   inhibits pheromone production and promotes motility via a small non-coding
#=GF RT   RNA.
#=GF RA   Tsai CS, Winans SC
#=GF RL   Mol Microbiol. 2011;80:556-571.
#=GF WK   Quorum_sensing
#=GF SQ   7



AALE02000015.1/22232-22398           GCUUUACAGAAUUAGUUUUAA-AUAUAAUAGAGCUAAUAUCUUAGCGCACUAAUGCUAAGAAAGUUAGACUGCAAAGAAUAUAUUUUCGCCAACACCAGGGGAC--UUUUGUC-C--ACCAACACCAGGUUUUACCCUGCCAUCUGGAUGGCUUUACAUUCAGAUGGCGACUA
AALC02000078.1/10597-10430           GCUUUAAACAAUUAGCUUUGA-AUAUAAUUGAACUAAUAUCUUAGCGCACAGAUGCCAAGAAAGUUAGUCUGAAAAGAAUAUAAUUUCGCCAAUACCAGGGGACUUUUUAAGUCC--AAUA-GUAC-CGUUUUACCCCGCCAUCUGGAUGUCUUUACAUUCAGAUGGCUGUAA
AALD02000004.1/33982-33814           GCUUUAAACAAUUAGCUUUGA-AUAUAAUUGAACUAAUAUCUUAGCGCACAGAUGCCAAGAAAGUUAGUCUGAAAAGAAUAUAAUUUCGCCAAUACCAGGGGACUUUUUUGAGUCCAAC--AGUAC-CGUUUUACCCCGCCAUCUGGAUGCCUUUACAUUCAGAUGGCCGUAA
AALF02000003.1/253045-253210         GCUUUAAAUAAUUAGCUUUAA-AUAUUAUAGAACUACUAUAUUAGCGCACAGACGCUAAGAAAGUCAGUCCCAAAAGAAUAUAUUUUCGCCAACACCAGGGGAC-UUUUAGUCCC--GCAGAU---CUGUUUUACCCCGCCAUCUGGAUGCCUUUACAUUCAGAUGGCUGUAA
ACCD01000001.1/400286-400452         GCUUUAUAGAAUU-GAUUUAACUUAUAAUAGAACUAGUAUAUUAGCGCACUGCCGCUAAAAAAGUUAGUCUGAUCAUAAUAUAUUUUCGCCAACACCAGGGGAC--UUUUAGUCC--ACCC-GUCUCAGCUUUACCCCGCCAUCUGGGUGCUUUUACAUUCAGGUGGCGAUUA
ACCB01000005.1/119796-119629         GCUUUAGAAAAUAAAUAUUGA-AUAUAAUAGAACUAAUAUCUUAGCUUACUAUUGCUAAGAAAGUUAGUCUGAAAAGAAUAAAUCUUCGCCAUCACCAGGGGACUUUUUAGUC-C--AC-AGUUAGUCGUUUUACCCCGCCAUCUGGAUGCCUUCACAUUCAGAUGGUCGUAA
AM286415.1/1797931-1797764           GCUUUGCAGAAUUAGAUUUUA-AUAUAAUAGAACUAGUAUCUUAGCGCACUGCCGUUAAGAAAGUUAGUCUGAAAAGAAUAUAUUUUCGCCAACACCAGGGCAC--UUCAGAUUC--ACCAAGUACAAGUUUCACCCUGCCAUCUGGAUGUUUUUACAUUCAGAUGGCCAUCA
#=GC SS_cons                         [[[[[[[,,,<<<<<-<<<<<.______>>>>>>>>>>,<<<<<<<<______>>>>>>>>,,((-((((((((,,<<<______>>><<<________>>>,,.,))))))))-..)),,,]]]-]]]]--------<<<<<<<<<<<<<____>>>>>>>>>>>>>:::::
#=GC RF                              gCcuuacAaAauuaGuuuuca.AUAUAAuggaaCuaauAucuuaGCgcACugacGCuaagaAAGuUggccugaaAAgaaUAUAuUuucgCCAAcACCAGGGcAC.UuucaggccC..aCcaaguacagGcUUUACCCcGCCauCuGgauGccUUUgCauuCaGauGGCuaUaA
//
# STOCKHOLM 1.0

#=GF AC   RF02375
#=GF ID   Aar
#=GF DE   Aar sRNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   60.00
#=GF TC   69.70
#=GF NC   41.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0006521; regulation of cellular amino acid metabolic process;
#=GF RN   [1]
#=GF RM   20559624
#=GF RT   The small RNA Aar in Acinetobacter baylyi: a putative regulator of amino
#=GF RT   acid metabolism.
#=GF RA   Schilling D, Findeiss S, Richter AS, Taylor JA, Gerischer U
#=GF RL   Arch Microbiol. 2010;192:691-702.
#=GF WK   Aar_small_RNA
#=GF SQ   13



ACVR01000020.1/129184-128998         UUUAACGUGAUUUAACACUUGUUAACGUGAAUACCAAGG-----AA--------GUUACUCAGGU--AUUC-AAAUAUUA---UACUU-UCAUGAUU--U------AGAAAGCUUCUAAAUUCAUGACAUUU-CUCCUUA---A--CCGAAGCUGU-G-UAU--ACAGAUUCGUUGUUCUGCGCAAUGAUCACCCCAAUCAUUGCGUAUUUUUUU-GUCU--A--UAAAA---
AFIE01000009.1/93042-92852           GCUUACGAGAGUUAACACUUAUUUACGUGAAUACCAAUGA----AA-UUAC--AGAUGAGAACAU--CUAC-UAUCUACU---UAAGU--UAUGAAUCUUCCCCAA------------AAUUCAUAACAU-UUCUCCUUA---A--CCGAA-CUGU-G-AAA--GCAGAUUCGUUGUUCUACGCAAUGAUCACCCCAAUCAUUGCGUAUUUUUUUUGUCU--U--UGUUUUCA
AERZ01000074.1/117538-117352         UUUAACGUGAAGUAACACUAAUUAACGUGAACCUUAAUGAAC--AAAUAAGAAUGCAUCACUAAU--AUAA-CUU--GAG---UAGGU--UG--------------AUAUGAACCUCA------CGACAU-U-UCUCCUU---AAGCCGAAACUGU-U-UUU-AACAGAUUCGUUGUUCUACGCAGUGAUCACCCCAAUCAUUGCGUAUUUUUUUUGUCU--U--UUUUAA--
ADGZ01000383.1/68-255                UUUAACGUGAAGUAACACUAAUUAACGUGAAGCUUAAUGAAC--AA-AUAA--GAAUGCAUCACU--AAUA-UAACUUGA--GUAGGU--UG--------------AUAUGAACCUCA------CGACAU-U-UCUCCUU---AAGCCGAAACUGU-U-UUU-AACAGAUUCGUUGUUCUACGCAGUGAUCACCCCAAUCAUUGCGUAUUUU-UUUGUCU--A--UAAUAAUG
BAEB01000065.1/6981-7171             AUUAACAUCUAUUAACAGUAGUUAACAUGAAUACCUAUGAACUUAG-UCA---GGUUUUUUU-AU--AAUA-UAGCGAUG---UAGGU--UAGGUAA----CACUA------------AUCUCAUGACAU-U-UCUCCUUUCAA--CCGAAACUGU-UUUAA--ACAGAUUCGUUGUUCAACGCAAUGACAACCCCAAUCAUUGCGUUUUU-UUUCGCCU--A--AAGAAUA-
ADMT01000206.1/3469-3660             AUUAACAUCCAUUAACAUCUAUUAACACGAAUAUGCAUGAACUAGA-UCAA--AGUUUU--AAAU--AUUA-UAGCGAUG---UAGAU--UA-GCAA--ACACUAA------------UCU-CAUGACAU-UUCUCCUUUUCAA--CCGAAACUGUUU-UAU--GCAGAUUCGUUGUUCAACGCAAUGAUCACCCCAAUCAUUGCGUUUUUU--UUGCUU--A--UAAUAUUG
ABYN01000035.1/3520-3713             AUUAACAUCUAUUAACAGUAAUUAACAUGAAUACCUAUGAACUUGG-UCA----GGUUUUUAAAU--AAUA-UAGCGAUG---UAGAU--UA-GCAA--A-CACUA------------AUCUCAUGACAU-U-UCUCCUUUCAA--CCGAAACUGU-UUUAA--ACAGAUUCGUUGUUCAACGCAAUGAUCACCCCAAUCAUUGCGUUUUUUUUGCAUCU-CA--UAAUAUUA
CP002177.1/2331050-2331241           AUUAACGUGAAGUAACACUUAUUAACGCUAAUAGCGAUGAAG--AA-UA----UCUUAACUUUAU--CUAU-UAUCCUUUAUGUAGGU--UA--CAU--CAUAUGA------------GCCUCACGACAU-U-UCUCCUUA-A--ACCGAAACUGU-U-UUU--ACAGAUUCGUUGUUCUACGCAAUGAUCACCCCAAUCAUUGCGUAUUUUU-UUGCCU--A-AAAAUUUUA
CP002080.1/802589-802399             AUUAACGUGAAGUAACACUUAUUAACGCUAAUAGCGAUGAAG--AA-UUUC----UUAACUAUCUCUAUUAUUCAUCAUG---UAGGUUACAUGAU------AUGA------------ACCUCACGACAU-U-UCUCCUUA-A--ACCGAAACUGU-U-UUU--ACAGAUUCGUUGUUCUACGCAAUGAUCACCCCAAUCAUUGCGUAUUUUUUU-GCUU--A--AAUAUUUA
ACPK01000060.1/254263-254071         AUUAACGUGAAGUAACACUUAUUAACGCUAAUAGCGAUGAAG--AA-UU----UCUUAACUAUCUCUAUUAUUUACUAUG---UAGGU--UA--CAU--CAUAUGA------------ACCUCAGGACAU-U-UCUCCUUC-AA--CCGAAACUGU-UUUUU--ACAGAUUCGUUGUUCUACGCAAUGAUCACCCCAAUCAUUGCGUAUUUUU-UUGCUUAAA--CAUUUUA-
ACPM01000014.1/37039-36850           AUUAACACUUGAUAACACUCGUUAACACGAAUAUCUAUGAACACAG-UCAA---GUUUUU-UAUU--AGUA-UAGCCAAG---UAGGU--UA-GAUA--A-CACUA------------AUCUCAUGACAU-U-UCUCCUUUCAA--CCGAAACUGU-U-U-U--ACAGAUUCGUUGUUCAACGCAAUGACAACCCCAAUCAUUGCGUUUUUU--UUGCUU-UA--AAUAUUUA
ACPL01000061.1/27088-26894           GUUAACCUAAAUUUACAGUAAUUAACGUGAAUACUCAUGAAA--UA-AGAA--UGCACAGCCCUU--AUGA-UGA---GUCCAUAGCU--UAGAU-U--AACCCU-------------GAGAUAUAACAU-U-UCUCCUUUUUA--CCGAAACUGU-G-UAACAACAGAUUCGUAGUUCUACGCAAUGAAUACCCCAAUCAUUGCGUAUUUUU-UUGCCU--AAAAUUUGUCA
CR543861.1/2812240-2812430           UUUAACGUGAUUUAACACUUAUUAACGUGAAUACCAAUGAAC--AA-UGAG--UGUUACCCUAUU--AUUA-UGACGGAA---UAGGU--UAUGCAC--UCCCCCA------------AGUUCAUAACAU-U-CUACUUU---A--CCGAAGCUGU-G-AAU--ACAGAUUCGUUGUUAUGCGUAAUGAUCACCCCAAUCGUUACGCUUUUUUUUUGCCU--G--UUUUAUUA
#=GC SS_cons                         ::::::::::::<<<<<<<<<<<--<<<________>>>---..>>.>>>>..>>>>>-------..----.(((--(((...(((((..<<.<-<<..<._____............>>>->->>,,,,.,.,,,,,,,,.,,..,<<<<-<<<<._.___..>>>>->>>>,,,,,,,<<<<<<<<<<_______>>>>>>>>>>,,,,,,,,,))))..)..)))--)))
#=GC RF                              aUUAACgUgaauuaaCacucauuAACguGAAUAucaauGAAc..aa.ugag..uGuuaauuaaaU..AuuA.uggcuuug...uAggu..cg.Gagc..c.cacuA............ggcUCAcgACAU.U.ucuCcUUu.AA..CCGAAACUGu.u.Uau..aCAGAUUCGUUGUUCuaCGCAaUGAucACCCCAaUCAuUGCGuaUUUUUUUUgccU..a..caauacca
//
# STOCKHOLM 1.0

#=GF AC   RF02376
#=GF ID   SR1
#=GF DE   SR1 sRNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:17576690
#=GF GA   45.00
#=GF TC   45.90
#=GF NC   44.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0045947; negative regulation of translational initiation;
#=GF DR   GO; 0000900; translation repressor activity, mRNA regulatory element binding;
#=GF RN   [1]
#=GF RM   17576690
#=GF RT   In vitro analysis of the interaction between the small RNA SR1 and its
#=GF RT   primary target ahrC mRNA.
#=GF RA   Heidrich N, Moll I, Brantl S
#=GF RL   Nucleic Acids Res. 2007;35:4331-4346.
#=GF WK   SR1_RNA
#=GF SQ   6



AEFP01000007.1/448577-448780         AACAAA-AGAAAUUAAGCGUUUUCAAAA-AAAGAG--AAAU----GGGGAAUGAGAGAUGGGAACGAUUGUUUGCCAAGACUGUAACGAAGCCAUUCAUUACUUUGAGGAUGAGAAGGUUACAACGUUUUAUGGAACGUGCUGCGGACAAUGUCAGUG---UCAUCUUGAAGA---AGAAUAA---UAAAAGCAUGCGGU---GUAAAA---------------------GCCGCAUGCUUUUUU
CP000560.1/1452065-1452284           AACAAGUAAAAAUUAAGCGUUUUCAAA-UUCUGAG--AAAU----GGGGAAUGACAGAUGGGUACAAUUGUUUGCCAAGACUGUAACGAAGCGAUUCAUUACUUUGAGGAUGAGAAGGUCACGACGUUAUACGGAACAUGCUGCGGACAAUGCCAGUG---UCAUCUUGAAGA---AGAGUAA--AAAGCGUAAAAAGGC---C-----CGAAACGAUUUCGUUUCGG--GCUUCUUUAUGUUUA
ACWC01000004.1/416894-416689         ----AA-CAAAUUUAAACGCUUCCAUUUUGAAAAG--AAAA----GGGGAAUGAAAGAUGGGCACGAUCGUUUGUCAAGACUGCAAUGAAACCAUUCAGCAUUUUGAAGAUGAGAAAGUGACGAUACUUUACGGAACGUGC---GGACAGUGCAACUGCCAUCUUAAAGAGGA---AGAAUAG--AAAAAAGCAUGCGGCCAUUUA-CA-------------------GUGCCGCAUGCUUUUAU
AGBY01000072.1/2089-1874             UAUGAA-AUAGAUUAAACGCUUUCAAACUUUGAGU--AAAGAAAAGGGGAAUGUACUGUGGGUACAAUUAUUUGUCAAGAUUGCAAUGAAACCAUUGAUCAAUUUGAAAAUGAAAAAGUGACAACACUUUAUGGAACAUGUGGU---CACUGUCAUUG---CUGUGAUGAAGCCUCUGAAUAAAUAAAAAAGCAUGCAGC---UC----CAAU-----------UGGG--GCUGCAUGUUUCUUU
ABRX01000001.1/435735-435521         UGUGAA-AUAAAUUAAACGCUUUCAAAUAUUGAAUGAAGAAA--AGGGGAAUG-UACGUGGGUACAAUUAUUUGUCAAGAUUGCAAUGAGACCAUUGAUCAAUUUGAAAAUGAAAAAGUGACAACACUAUACGGAACGUGUGGU---CACUGUCAUUG---CUGUGAUGAAGCCUCUGAAUAAAUAAAAAAGCAUGCAGC---UC----CAUU-----------UGGG--GCUGCAUGUUUCUUU
AF012285.1/39173-39377               AACAAA-AGAAAUUAAGCGUUUUCAAAUUUCAAAG--AAAU----GGGGAAUAAGAGAUGGGUACGAUUGUUUGCCAAGAUUGCAACGAAGCCAUUCAUUACUUUGAAGAUGAGAAAGUGACAACAUUAUAUGGAACUUGCUGCGGACAAUGUCAAUG---UCCUGUUGAUGA---AGAGUAA--AAAAAAGCAUGCGGC---UUA-AA---------------------GCCGCAUGCUUUUUA
#=GC SS_cons                         ::::::.:::::::::<<-<<<<<<<--<<<<<<<..-<<<....-------------<<<-<-<<----<<____________>>>>->->>>--->>>->>>>>>>-->>>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<_______>>...>>>,,,,,,,,,...,,,,,,,..,,<<<<<<<<<<<<<...__....____...........____..>>>>>>>>>>>>>::
#=GC RF                              aAuaAA.AaAAAUUAAaCGcUUccaaAuuucaaag..Agau....GGGGAAUGAaAgaUGGGuACgAUUgUUUGuCAAGAuUGcAAcGAaaCCAUUcaucAcuuugaagAugagAAgGugACaACauUaUAuGGAACaUGcuGugGaCAaUGucAuUG...uCcUgaUGAaGa...aGAaUAA..AAAaaagcAuGcgGC...uu....Caau...........UgGG..GCcgCaUgcuuuUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02377
#=GF ID   SurA
#=GF DE   SurA sRNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   100.00
#=GF TC   118.80
#=GF NC   55.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16385044
#=GF RT   Genes for small, noncoding RNAs under sporulation control in Bacillus
#=GF RT   subtilis.
#=GF RA   Silvaggi JM, Perkins JB, Losick R
#=GF RL   J Bacteriol. 2006;188:532-541.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



AEHM01000036.1/43949-43666           CUUCAAGGAAUGGAGCAAACGGCGGAGCAGGGAUACUUUGGCCGGUUUCAUCUACUCCGCCUCUAAGUCCAAAUAAACAGGAUGUUGGUUUCUUUGAGGCUUUAGCACGAAUUCUCUCAUCCUCCUUGUUAAAUUUUUGUUAAAUUCACAAUAUUAUAUACCAUUAGCCCGGGCGCUGUUCUUCUCAUUUUUGAAUUUAUGAAAAGUAAGUUGGCACCACCUUUUC------CCAAUUCCC-------------AUAUCAAACAGAAAAAAA--CGCACCUGCCCUUUGGCCUGUGCG-UUUUUAC
CP002905.1/2018201-2017913           CUUCAAGGAAUGGAGCAAACGGCGGAGCAGGGAUACUUUGGCCGGUUUCAUCUACUCCGCCUCUAAGUCCAAAUCAACAGGAUGUCGGUUUCUUUGAGGCUUUAGCACGAAUU-UCUCGUCCUCCUUGUUAAAUUUUUGUUAAAUUCACAAUAUUAUAUACCAUUGGCCCGGGCGCUGUUCUUCCCAUUUCUGAAUUUAUGAAAAGUAAGUUGGCACCAACU---A------CCUUUUUCCCAAUUCGCAUAUCAAACAGAA----AAAAAA--CGCACCUGCCCUUUGGCCUGUGCA-UUUUUAU
ADGS01000013.1/239891-239607         CUUCAAGGAAUGGAGCAAACGGCGGAGCAGGGAUACUUUGGCCGGUUUCAUCUACUCCGCCUCUAAGUCCAAAUCAACAGGAUGUCGGUUUCUUUGAGGCUUUAGCACGAAUU-UCUCGUCCUCCUUGUUAAAUUUUUGUUAAAUUCACAAUAUUAUAUACCAUUAGCCCGGGCGCUGUUCUUCCCAUUUCUGAAUUUAUA-AAAGUAAAUUGGCACCAACUG-CCUUUUUCUCAAUUCCC-------------AUAUCAAA----CAAAAAAACGCACCUGCCCUUUGGCCUGUGCA-UUUUUAU
AL009126.3/1915271-1914992           CUUCAAGGAAUGGAGCAAACGGCGGAGCAGGGAUACUUUGGCCGGUUUCAUCUACUCCGCCUCUAAGUCCAAAUCAACAGAAUGUAGGUCUCUUUGAGGCUUUAGCACGAAUUCUCUCGUCCUCCUUGUUAAAUUUUUGUUAAAUUCACAAUAUUAUAUACCAUUAGCCCGGGCGCUGUUCUUCUCAUUUUUGAAUUUAUGAAAAGUAAGCUGGCACCACCUC-CC------CCAUUUUCC-------------AUACAAAA----CAAAAA--UGCACCUGCCCUUUGGCCUGUGCACUUUUUAU
#=GC SS_cons                         ::::::{{{{{{{,[[,,,,<<<<<<<-<<<<<-<<<______>>>->>->>>->>>>>>>,,,,,,,,,,,,,,(((((((,,,<<<<<<<___>>>>>>>,<<-<<<<___.__>>>>->>,,,,,,,,,,,))))))),,,,,,,,,,,,,,,,,,,,,,,,,]],,<<<<<<<---<<<-<<<<__________>>>>->>>-->>>-->>->>,,,,,.,,......}}}}--}}}.............--------....-<<<<<..<<<<<--<<<____>>>-->>>>>.>>>>>::
#=GC RF                              CUUCAAGGgauGGAGCAAACGGCGGaGCaGgGaUaCuUUGGCCgGuUuCAuCuACuCCGCCUCUAAGUCCAAAUcaaCaggaUGUcgGucuCUUUGaggCugUaGCacGaAUU.UCuCguCCuCCUUGUUAAAUucuuGuuAAAUUCACAAUAUUAUAUACCAUUaGCCCGGGCgcuGUUCuuCucauUUuUGAAUUUaugaAaaGUAagcUGGCACCAaCUu.cc......CCauUUcCC.............AuAuaaAA....aaaaaa..cGCaCCUGCCCUUUGGCCUGuGCg.uuuuuAu
//
# STOCKHOLM 1.0

#=GF AC   RF02378
#=GF ID   SurC
#=GF DE   SurC sRNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   80.00
#=GF TC   120.10
#=GF NC   56.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.69 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16385044
#=GF RT   Genes for small, noncoding RNAs under sporulation control in Bacillus
#=GF RT   subtilis.
#=GF RA   Silvaggi JM, Perkins JB, Losick R
#=GF RL   J Bacteriol. 2006;188:532-541.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



CP002905.1/2606967-2607127           GUAUCAUUUUGAAUUAUGAUUUUUCAAUUCCUUUUAUCCCGGGCAAGAAAAAAAGUCAAAGCCAAGAGAUGCCUGACUUUGACUUUCUAAUCAUUGAAUCAGAUUAUGAAAUGUGCUCUUUUCGGUCAGCCCCAAAAGCG-GGACUGACUCGGAGAAGAACU
CP002183.1/2481930-2482088           GUAUCAUUUUGAAUUAUGAUUUUUCAAUUCCUUUUAUCCCGGGCAAGAAAAAAAGUCAAAGCCAAGAGAUGCCUGACUUUGACUUUCUAACCAUUGAAUCAGAUUAUGAAAUAUGUUCUUUUCAGCCAGCCCAAAAAC---GGGCUGACUCAGAAAGAAACU
AEFR01000003.1/378345-378504         GUAUCACUUUGAAUUGUAUUUUUUCAAUUCCUUUUAUCCCGGGCAAGAAAAAAAGUCAAAGCCAAGAGAUGCCUGACUUUGACUUUCUAACCAUUGAAUCAGUUUGUGAAAAGCAGUUCUUUUGGAUGCCCGCCGGAUGGACGGGCUUCC--GAAAAAACUU
M84964.1/3927-3767                   GUAUCAUUUUGAAUUAUGAUUUUUCAAUUCCUUUUAUCCCGGGCAAGAAAAAAAGUCAAAGCCAAGAGAUGCCUGACUUUGACUUUCUAAUCAUUGAAUCAGAUUAUGAAAUGUGUUCUUUUCGGUCAGCUCCGGAAGCG-GGGCUGACACUAAAAAGAACU
#=GC SS_cons                         :::(((((((((-((((((((<<<<----<<<________>>>--->>>>,<<<<<<<<<<---<<______>>-->>>>>>>>>>,,))))))-))-)))))--))))-----<<<<<<<<--<<<<<<<<<<____>>.>>>>>>>>---->>>>>>>>:
#=GC RF                              GUAuCacuuuGaAuuaugguuuuuCAAUUCCuUUUAUCCCgGGCAAGaaaAaaaGuCaaaGCCAaGAGAUGCCuGACuuuGaCuuuCUaaccauUgaAuCagaUUguGaAAugugcuccuuucgGccggccccgaaAucg.gggccggCucagaaaggagcU
//
# STOCKHOLM 1.0

#=GF AC   RF02379
#=GF ID   csRNA
#=GF PI   csRNA1; 
#=GF DE   Cia-dependent small RNA csRNA1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:17725562
#=GF GA   57.00
#=GF TC   57.90
#=GF NC   55.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   17725562
#=GF RT   Identification of the genes directly controlled by the response regulator
#=GF RT   CiaR in Streptococcus pneumoniae: five out of 15 promoters drive
#=GF RT   expression of small non-coding RNAs.
#=GF RA   Halfmann A, Kovacs M, Hakenbeck R, Bruckner R
#=GF RL   Mol Microbiol. 2007;66:110-126.
#=GF WK   Cia-dependent_small_RNAs
#=GF SQ   48



AEDU01000019.1/54213-54307             AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUG--A-A-A-UCCUAA-AACU--U-----U-----U-----UUUCAUCAUAAUCUC-C------U-----AAU-GA-AGCCACC-CAAUCA--GGUGGCUUUUUU
AFQV01000006.1/197666-197759           AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUG--A-A-A-UCCUAAAA--C--U-----U-----U-----UUUCAUCAUAAUCUC-C------U-----AAU-AA-AGUCACC-CAAUCA--GGUGACUUUUUU
AFUB01000055.1/11920-11824             AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUG--A-A-A-UCCUAA-A--C--U-----U-----UUC-UUUUUCAUCAUAAUCUC-C------U-----AAA-GA-AGUCACC-CAAUCA--GGUGGCUUUUUU
CP002925.1/321341-321435               AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUG--A-A-A-UCCUAA-A--ACUU-----U-----U-----UUUUAUCAUAAUCUC-C------U-----AAU-GA-AGUCACC-UAAUCA--GGUGGCUUUUUG
AEGF01000038.1/286-196                 --AAAAUAAAGACCUCCUAA---CUUUAUUUAAUA--A-A-A-UCCUAA-A--C--U-----U-----U-----UUUCAUCACAAUCUC-C------U-----AAU-GA-AGCCACC-CACAGG--GGUGGCUUUUGC
AFUO01000001.1/1431069-1431166         AUUAGAUAAAGACCUCCUAA---CUUUAUUUAAUG--A-A-A-UCCUAA-U--C--C-----UUU-CUU-----UUUCAUCAUAAUCUCCC------U-----AAA-GA-GGCCACC-CAAUCA--GGUGGCUUUUUU
AEDX01000018.1/44739-44834             AUUAAGUAAAGACCUCCUAA---CUUUAUUUAAUA--A-A-A-UCCUAA-A--C--U-----U-----UUC-UUUUUCAUAAUAAUCUC-C------C------UU-GA-CUCCACC-CAAUCA--GGUGGAGUUUUU
AEVF01000001.1/71818-71910             AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUA--G-A-A-UCCUAA-A--C--U-----U-----U-----UUUCAUAAUAAUCUC-C------G-----ACA-AA-AGCCAUU-CUUAUG--AGUGGCUUUUGU
AEVD01000014.1/73224-73322             AUUAAGUAAAGACCUCCUAA---CUUUAUUUAAUA-GA-A-A-UCCUAA-A--C--U-----U-----UUC-UUUUUCAUAAUAAUCUCCC------U-----AAA-GA-AGCCACC-AAAUCA--GGUGGCUUUUUU
AEVC01000021.1/50657-50564             AUCAAAUGAAGACCUCCUAA---CUUUAUUUGAUA-GA-A-A-UCCUAA-A--A--C-----U-----U-----UUUCAUAAUAAUCUC-C------C-----AUA-AG-AGCCACC-AAAUUC--GGUGGCUUUUUU
AEWY01000010.1/62489-62397             AUCAAAUGAAGACCUCCUAA---CUUUAUUUGAUA-GA-A-A-UCCUAA-A--C--U-----------U-----UUUCAUAAUAAUCUC-C------C-----AUA-AA-GGCCACC-CAAUCC--GGUGGUCUUUUU
AFUQ01000012.1/193054-193151           AUUAAGUAAAGACCUCCUAA---CUUUAUUUAAUA-GA-A-A-UCCUAA-C--U--U-----UU--CUU-----UUUCAUAAUAAUCUCCC------U-----AAA-GA-AGCCACC-AAAUCA--GGUGGCUUUUUU
AEQR01000003.1/70619-70712             AUCAAAUGAAGACCUCCUAA---CUUUGUUUGAUAGAA-A-A-UCCUAA-A--C--U-----U-----------UUUCAUAAUAAUCUC-C------C-----AUA-AA-GGCCACC-AAAUCA--GGUGGCUUUUUU
AFNN01000024.1/22887-22796             AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUA--A-A-A-UCCUAA-A--C--U-----U-----------UUUCAUAAUAAUCUC-C------G-----ACA-AA-AGUCACU-CGUAAG--AGUGACUUUUGU
AFXN01000009.1/192083-191992           AUCAAAUGAAGACCUCCUAA---CUUUAUUUGAUG--A-A-A-UCCUAA-A--C--U-----U-----------UUUCAUAAUAAUCUC-C------C-----UAU-AA-AGAUCAC-CAAAAG--GUGAUCUUUUUG
AFUU01000003.1/821989-821898           AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUA--G-A-A-AUCCUA-A--A--U-----U-----U-----UUUCAUAAUAAUCUC-C------U-----AGG-GA-AGCUACC-A-UGAG--GGUAGCUUUUCU
AFNM01000001.1/2859-2768               AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUA-GA-A-A-UCCUAA-A--C--U-----------U-----UUUCAUAAUAAUCUC-C------U-----AGG-GA-AGCUACC-A-UGAG--GGUAGCUUUUCU
ADME01000011.1/531-439                 AUCAAAUGAAGACCUCCUAA---CUUUAUUUGAUG--A-A-A-UCCUAA-A--A--C-----U-----U-----UUUCAUAAUAAUCUC-C------C-----UAU-AAGGGUCACC-AA-AGA--GGUGGCCUUUUU
AECT01000040.1/11682-11590             AUCAAAUGAAGACCUCCUAA---CUUUGUUUGAUA-GA-A-A-UCCUAA-A--C--U-----------U-----UUUCAUAAUAAUCUCCC------U-----AAU-AA-AGUCACC-CAAUU---GGUGGCUUUUUU
AFXO01000006.1/67837-67741             AUCAGAUGAAGACCUCCUAA---CUUUAUUUGAUA--A-A-A-UCCUAA-A--C--U-----U-----UUC-UUUUUCAUAAUAAUCUC-C------C-----UAUAAG-AGCCACC-UAAUU---GGUGGCUUUUUU
AFUC01000017.1/89441-89535             AUCAAAUAAAGACCUCCUAA---CUUUGUUUGAUAGAA-A-A-UCCUAA-A--C--U-----U-----------UUUCAUAAUAAUCUC-C------C-----UAUAAG-AGCCACC-AAAACC--GGUGGCUUUUUC
BAAZ01007206.1/170-78                  AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUA-GA-A-A-UCCUAA-A--C--U-----------U-----UUUCAUAAUAAUCUC-C------U-----ACA-AA-AGUCGCU-CGUAAG--AGUGGCUUUUGU
AEDY01000032.1/35860-35951             AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUU--A-A-A-AUCCUA-A--C--U-----U-----------UUUCAUAAUAAUCUC-C------U-----ACA-AA-AGUCACU-CCAAAG--GGUGACUUUUGU
ACRK01000007.1/102886-102977           AUUAAAUAAAGAUCUCCUAA---CUUUAUUUAAUU--AGA-A-UCCUAA-A--C--U-----U-----------UUUCAUAAUAAUCUC-C------U-----AGA-AA-AGCUACC-A-UGAG--GGUAGCUUUUCU
CP002843.1/1645110-1645203             AUCA-UCAAAGACCUCCUAA---CUUUGAAUGAUA--A-A-ACUCCUAA-A--A--C-----U-----U-----UUUCAUAAUAAUCUC-C------C-----UAUAAG-AGCCACC-AAAACC--GGUGGCUUUUUU
ACNV01000054.1/76-171                  AUUAAAUAAAGACCUCCUAA---CUUUAUUUACAA--A-U-A-UCCUAA-A--C--U-----U-----UUC-UUUUUCAUAAUAAUCUC-C------C------UU-AA-CUCCACC-CAAUCA--GGUGGAGUUUUU
AFAZ01000006.1/140465-140377           AUCAAAUGAAG-CCCCCUAA---CUUUGUUUGAUA------A-UCCUAA-A--C--U-----U-----------UUUCAUAAUAAUCUC-C------C-----AUA-AA-GGCCACC-CAAUCU--GGUGGUCUUUUU
AEVH01000004.1/143978-143891           CAUAAACAAAGACCUCCUAA---CUUUGUUUA--A--A-A-A-UCCUAA-A--C--U-----U-----U-----UUUCAUAAUAAUCUC-C------U-----G---AA-AGUCACC-CUAGU---GGUGGCUUUCUU
AFGS01000002.1/8826-8730               GUUACAAGAAGACCUCCUAA---CUUGUUGUAACA--A-AUA-UCCUAA-A--C--U-----U-----UUC-UUUUUCAUAAUAAUCUC-C------C------UU-AA-CUCCACC-CAAUCA--GGUGGAGUUUUU
AFUP01000009.1/21475-21383             AUCAAAUGAAGACCUCCCAA---CUUUAUUUGAUA-GA-A-A-UCCUAA-A--C--U-----------U-----UUUCAUAAUAAUCUC-C-----CU-----AAUAAA-AGUCACC-CAUU----GGUGGCUUUUUU
AFIM01000079.1/6611-6708               AUCAGAUGAAGACCUCCUAA---CUUUAUUUGAUA--AAA-A-UCCUAA-A--C--U-----U-----UUC-UUUUUCAUAAUAAUCUC-C------C-----UAUAAG-AGUCGCC-CAAUC---GGCGGCUUUUUU
AEKM01000005.1/35823-35727             CAUAAACAAAGACCUCCUAA---CUUUGUUUAGAA--A-A-A-UCCUAA-A--A--CUUUUCU-----U-----UUUCAUAAUAAUCUC-C------C-----UA--AG-AGUCGCC-CAAUCA--GGCGGCUUUUUU
AEDT01000020.1/2260-2357               GUUACAAGAAGACCUCCUAA---CUUGUUGUAACA--A-AUA-UCCUAA-A--C--U-----U-----UUC-UUUUUCAUAAUAAUCUC-C------C-----UAU-AA-AGUCACC-GCAUUC--GGUGGCUUUUUU
AEVE01000049.1/11135-11047             CAUAAACAAAGACCUCCUAA---CUUUGUUUA--A--A-C-C-UCCUAA-A--C--U-----U-----------UUUCAUAAUAAUCUC-C------C-----AUA-AG-AGUCGCC-CAAUC---GGCGGCUUUUUU
AEEP01000016.1/1986-2083               GUUACAAGAAGACCUCCUAA---CUUGUUGUAACA--AGU-A-UCCUAA-A--C--U-----U-----UUC-UUUUUCAUAAUAAUCUC-C------C-----UAU-UA-AGUCACC-CCAUUG--GGUGGCUUUUUU
AFBA01000002.1/181855-181950           CAUAAACAAAGACCUCCUAA---CUUUGUUUA-GA--A-A-U-CCUAAA-A--C--U-----UUU-CUU-----UUUCAUAAUAAUCUC-C------C-----UAUAAA-AACCGCC-CAAUU---GGCGGUUUUUUU
AFFO01000018.1/45832-45746             CAUAAACAAAGACCUCCUAA---CUUUGUUUA--A--A-A-A-UCCUAA-A--C--U-----U-----------UUUCAUAAUAAUCUC-C------U-----G---AA-AGUCACC-CCAGU---GGUGGCUUUUAC
AEXA01000004.1/171311-171406           UAUAAACAAAGACCUCCUAA---CUUUGUUUA--G--A-A-A-UCCUAA-A-AC--UUU-UCU-----U-----UUUCAUAAUAAUCUC-C------C-----UAUAAG-AACCGCC-CAAUU---GGCGGUUUUUUU
ACOI01000013.1/64770-64684             AUCAAAUAAAAA-CUCCUAA---UUUUAUUUGAUA--G-U-A-UCCUAA-U--C--U-----U-----------UUUCAUAAUAAUCUC-C------C-----CA--AA-AGUCACC-A--UC---GGUGGCUUUUUU
AFQU01000001.1/1288687-1288780         CAUAAACAAAGACCUCCUAA---CUUUGUUUA--G--A-A-A-UCCUAA-A--A--C-----U-----U-----UUUCAUAAUAAUCUC-C------A-----AAA-CA-CCGCUGUUCUAUUAUGACAGUGGUGUUU
AGOC01000002.1/250-348                 GUUACAAGAAGACCUCCUAA---CUUGUUUUAACA--A-AUA-UCCUAA-A--C--U-----UUACCUU-----UUUCAUAAUAAUCUC-C------C-----UAU-AG-AGUCACC-GCAUUC--GGUGGCUUCUUU
AFUT01000008.1/123108-123020           AUUGAGUAA-----------CCU--UUAUUUAAUA--AAA-A-UCCUAA-A--C--U-----U-----UUC-UUUUUCAUAAUAAUCUCCC------U-----AAA-GA-AGCCACC-AAAUCA--GGUGGCUUUUUG
CP000725.1/2038880-2038787             CAUAAACAAAGAUCUCCUAA---CUUUGUUUA-GA--A-A-U-CCUAAA-A--C--U-----UUU-CUU-----UUUCAUAAUAAUCUC-C------C-----G---AA-AACCACC-UUGAAA--GGUGGUUUUCUU
ADMV01000003.1/158381-158291           CAUAAGUUAAGAG----AAA---CUUAACUU---A--A-A-C-UCCUAA-A--A--C-----U-----U-----UUUCAUAAUAAUCUC-CCU-AUAA-----AAU-UA-AGUCGCC-CAAUCA--GGCGGCUUAUUU
AFUF01000020.1/26674-26582             CAUAAGUUAAGAAGA-------CCUUAACUU---A--A-A-C-UCCUAA-A--A--C-----U-----U-----UUUCAUAAUAAUCUC-CC---UA-UAAAAAAU-UG-AGUCGCC-CAAUCA--GGCGACUUAUUU
CP001015.1/230778-230869               CAUAAGUUAAGAAAAC-------CUUAACUU---A--A-A-C-UCCUAA-A--A--C-----U-----U-----UUUCAUAAUAAUCUC-CCUAUAAA-----AAU-AA-AGUCGCC-CAAUCA--GGCGGCUUAUUU
AFBF01000020.1/12223-12128             CAUAAACAAAGACCUCCUAA---CUUUGUUUA--G--A-A-A-UCCUAA-A--A--C-----U-----UUUCUUUUUCAUAAUAAUCUCUC------U-----AUA-AG-AACCGCC-CAAUU---GGCGGUUUUUUU
CP000921.1/263767-263859               AUUAAAUAAAGACCUCCUAA---CUUUAUUUAAUA--A-A-A-UCCUAA-A--C--U-----U-----U-----UUUCAUCACAAUCUC-C------U-----AAU-GA-AGCCACC-CAAUCA--GGUGGCUUUUUU
#=GC SS_cons                           <<<<<<<<<<<............>>>>>>>>>>>.........................................................................<<.<<<<<<<.........>>>>>>>>>...
#=GC RF                                auuAaauaAAGAcCUCCUAA...CUUuauuUaauA..A.A.A.UCCUAA.A..c..U.....U.....U.....UUUCAUAAUAAUCUC.C......u.....aau.ga.agcCgCC.caAuca..GGcGgcuucUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02384
#=GF ID   FasX
#=GF DE   FasX small RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:21143309
#=GF GA   100.00
#=GF TC   155.40
#=GF NC   65.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 28.24 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   21143309
#=GF RT   The group A Streptococcus small regulatory RNA FasX enhances streptokinase
#=GF RT   activity by increasing the stability of the ska mRNA transcript.
#=GF RA   Ramirez-Pena E, Trevino J, Liu Z, Perez N, Sumby P
#=GF RL   Mol Microbiol. 2010;78:1332-1347.
#=GF WK   FasX_small_RNA
#=GF SQ   8



AEGO01000002.1/1921072-1920866         GUAAAUAAAGAUCUACGAAAUC-AUCGGUCUAUUAGGCGAUCAAUCCCCAAUUCAAUCAAAAUAUUGUUUUCUCUC--UC--UCUCCAUA--A-ACAAAUAGUAUUUUUGAUAUGACAGCCUAAUAGAUGAUAUGAUUAUUU-CAGUUGUCUUUGUUUGGAUAUCACAUUAACUGAUUGUAAAAUCAGUG---U---C-AAAGCCCGG--CUUG------CCGGGUUUUUU
CABY01000008.1/11102-10896             AUGAAUAAAGAUUUACGAAAUC-AUUAGGUAAUGGAGUGGUCCAUCCCCAAUUCAAUCAAAAUAUUGUUUUCUCU----C--UCUCCAUA--A-ACAAAUAGUAUUUUUGAUAUGACUGCUU-GUUAUUAAAAUGAUUGUUU-CAGUUGUCUUUGUUUGGAUAUCAUAUUUGCUGAUGCUCAAGUCAGCGGAGA---U-AAAGCUCGG--UUUA------CCGGGCUUUAU
AEUX02000007.1/249448-249656           GUAAAUAAAGAUCUACGAAAUC-AUCAGUUUAUUAAGUGAUCAAUCCCCAAUUCAAUCAAAAUAUUGUUUUCUCUC--UC--UCUCCAUA--A-ACAAAUAGUAUUUUUGAUAUGAUUGCUUUCUAUCCCCAAUGAUAAUUU-CAGUUGUCUUUGUUUGGAUAUUACUU-CACUGGUUAUUCAAUCAGUA---AUCAU-AAAACUCAG--GAAA------CUGAGUUUUAU
CP002471.1/1942763-1942559             GUAAAUAAAGACUUAA--CGUC-ACUAGUUU--AUAAGAGUCAAUCCCCAAUUCAAUCAAAAUAUUGUUUUCUCUC--UC--UCUCCAUA--A-ACAAAUAGUAUUUUUGAUCUGACUCUUCUG-AAACUAA-UGAUUAAUU-CAGUUGUCUUUGUUUGGAUAACAUAUUGACUGAUUUUUACAUCAGUA---A---A-AAAACUCGG--AA--UCCCAUCCGAGUUUUUU
AM946015.1/1648882-1648675             AUAGAUAAAGACGUCAUUUUGUUUCUAU---CUUAAGAAGUUAAUCCCCAAUUCAAUCAAAAUAUUGUUUUCUCUCUCUC--UCUCCAUA--AAACAAAUAGUAUUUUUGAUCUAACUUCUCAAGCAGAAUAGAACAAAACU-UAAUUGUCUUUGUUUGGAUAUGAUAACAACUGAUUG---UAUCAGUU---G---AAAAAACUCGGAGCAUU------CCGAGUUUUUU
AEUY02000005.1/851752-851939           AUAGAUAAAGACUGAGGUCGUU-UUAAAUCAG----AAAGUUAUUCCCCAAUUCAAUCAAAAUAUUGUUUUCUCU----C--UCCAUAAA--A-ACAAAUAGUAUUUUUGAUUUAGCUUUA---CUGAU--GGUUACGAUUAGAAUUUGUCUUUGUUUGGAUAUGA----AACUGAUUU---UAUCAGUG---------AAGCCUAGA--UUAU------UCUAGGCUUUU
AEUU02000001.1/1187331-1187140         AUAGAUAAAGACUG---AAGUC-GUCUCAA-AUCAUGAAGUUAUUCCCCAAUUCAAUCAAAAUAUUGUUUUCUCU----CUCUCUCCAUAAAA-ACAAAUAGUAUUUUUGAUUUAGCUUUACUGA--UGGUUACGACUAG---AAUUUGUCUUUGUUUGGAUAUGA----AACUGAUUU---UAUCAGUG---------AAGCCUAGA--GUAU------UCUAGGCUUUU
BA000034.2/199338-199542               GUAAAUAAAGAUUUACGAAGUC-AUGAGUUUAUCGAGCAAUCAAUCCCCAAUUCAAUCAAAAUAUUGUUUUCUCU----C--UCUCCAUA--A-ACAAAUAGUAUUUUUGAUAUGAUGGCUCGGCAGACAAAAUGACGAUGU-CAGUUGUCUUUGUUUGGAUAUCACAUUAGCUGAUUGUAAAAUCAGUA---U---U-AAAGCCCGG--CUUG------CCGGGUUUUUU
#=GC SS_cons                           :<<<<<<<<<<<--<<<<<<<<.<<--<<<<<<<<<<<<<<<<------------<<<<<<<<<<<<<<<______..__..________.._.__>>>>>>>>->>>>>>>->>>>>>>>>>>>>>>>--->>>>>>>>>>.----->>>>>>>>>>>,,,,,,,,,,,,<<<<<<<____>>>>>>>,...,...,.<<<<<<<<<..____......>>>>>>>>>::
#=GC RF                                auaaauaaaGacuuacgucguc.guuagucugccgagcagucaaUCCCCAAUUCAaUCaaaaUauUgUUUUCUCUc..UC..UCUcCAUA..A.ACAAAuAguAUuuuuGAuaugacugcucggcagacaaaacgacgacgu.cAgUUguCuuuguuugGAUAUuAuAuuaaCUGauuuUuaaauCAGua...a...u.aaggCucGG..uuuu......CCgaGccuuuU
//
# STOCKHOLM 1.0

#=GF AC   RF02385
#=GF ID   sau-13
#=GF DE   Staphylococcus sRNA sau-13
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   55.00
#=GF TC   58.70
#=GF NC   51.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   6



FR821777.2/2657646-2657543           CCGGUAAUAUCGUUGACAUGUGCUGAUUUAUCUAUAGAAGCACCUUCGACCAUUAAAAAGAAUCCUUUUUUAUUAUGUUCUAAUUUACUAAGUGCACUUUGUUG
AP006716.1/416867-416970             CCAGUAAUGUCGUUAGGGUGUCCUGAUUUAUCGAUAGACGCACCUUCGACCAUUAAGAAGAAACCUUUAUCAUUCUUUUCUAGUUUAGAUAAGGCACUGUUUUC
FR870271.1/357477-357580             CCAGUAAUAUCGUUAGGGUGACCAGAUUUAUCAAUAGAGGCACCUUCAACCAUUAAGAAGAACCCUUUAUUAUUUUUUUCAAGUUUAGAUAAUGCACUAUUUUC
ACRH01000037.1/278018-277915         CCAGUAACAUCAUUUGGAUGUGCAGCUUUAUCGAUAGAAGCACCUUCAACCAUUAAGAAGAAGCCUUUAUUGUUCUUAUCUAAUUUACUUAAUGCACUUUGUUC
AGGR01000615.1/444-547               CCAGUGAUAUCAUUAGGGUGUGCAGCUUUAUCAAUUGAAGCACCCUCAACCAUUAAAAAGAAUCCUUUAUUAUUUUUACUUAAUUUAUUAAGUGCACUGUUUUG
AJ938182.1/2644234-2644131           CCUGUAAUAUCGUUGGAAUGCGCUGAUUUAUCUAUAGAAGCACCUUCGACCAUUAAAAAGAAACCUUUUUUAUUACGCUCAAGCUUACUAAGUGCACUUUGUUG
#=GC SS_cons                         :::((((((,,<<<<<<-<<<----<<______>>---->>>-->>>>>>,,,,<<<<<<____>>>>>>))))))------<<_________>>:::::::::
#=GC RF                              CCaguaAuaUCGUugggaUGcgCuGaUUUAUCaAuAGAagCACCcucaACCAUUAaaAAGAAuCCUUuuUuaUuacuuUCuAguUUAcuaAaUgcACUuUuUUg
//
# STOCKHOLM 1.0

#=GF AC   RF02386
#=GF ID   sau-19
#=GF DE   Staphylococcus sRNA sau-19
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   80.00
#=GF TC   97.50
#=GF NC   52.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



ACHH02000004.1/11544-11470           GUUCUUUAGACAUUAAAAGCUUCUAACAUGAUAUGGAAUCCGAGGUUCCGAUAUCACAUUAGAAGCUUUUUUGUU
AM990992.1/2620746-2620820           GUUCUUUAGACAUUAAAAGCUUCUAACAUGAUACGGAAUUUGAGAUUCCCAUAUCACAUUAGAAGCUUUUUUGUU
ACKI01000038.1/123063-122989         GUUCUUUAGACAUUAAAAGCUUCUAACAUGAUAUGGAAUCCAAGAUUCCGAUAUCAUGUUAGAAGCUUUUUUGUU
CP001844.2/2558472-2558546           GUUCUUUAGACAUUAAAAGCUUCUAACAUGAUACGGAAUAUGAGGUUCCUGUAUCACAUUAGAAGCUUUUUUGUU
#=GC SS_cons                         ::::::::<<<<--<<<<<<<<<<<<--<<<<<<<<<<<_____>>>>>->>>>>>-->>>>>>>>>>>>->>>>
#=GC RF                              GUUCUUUAgaCaUUaaaaGCuuCuaaCAuGauacGGaauuugAGauuCCuguauCacAuuaGaaGCuuuuUuGuu
//
# STOCKHOLM 1.0

#=GF AC   RF02387
#=GF ID   sau-27
#=GF DE   Staphylococcus sRNA sau-27
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   80.00
#=GF TC   98.70
#=GF NC   39.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



CP002114.2/1265850-1265941         UCACAAAUUAGUGAGGGAGCUUUU--UUUAAGUUGUAGUCUCAAUCUAGUUAGACAGCACUUUAUUGGUAAUAACUAUAUUAAACAGUAGUUAU
AECP01000009.1/5-98                CCACCCGUUCACACGGGUGGUUUUGAUUUAAGUUGUAGUCUUAAUCUAGUUAGACAGCACUUUAUCGGUAAUAACUAUAUUAAACAGUAGUUAU
FR714927.1/1241998-1242088         UCACAAAUUAGUGAGGGAGCUUUU---UUAAGUUGUAGUCUCAAUCUAAUUAGACAGCACUUUAUCGGUAAUAACUAUAGUAAACAGUGGUUAU
#=GC SS_cons                       ::::::<<--<<<<<<--<<<-<<..-<<<--<<<______>>>-->>>--->>->>>->>>>>>-->>-<<<<<<<<________>>>>>>>>
#=GC RF                            uCACaaauUaauaagGGaGcuUuu..UcuaAGuuGUAGUCUCaaUCuagUUAgaCagCACuuuaucGguAauaaCuauAuUAAACAguaGuuau
//
# STOCKHOLM 1.0

#=GF AC   RF02388
#=GF ID   sau-30
#=GF DE   Staphylococcus sRNA sau-30
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   70.00
#=GF TC   88.60
#=GF NC   42.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



AEUN01000020.1/91-28               CUCAACAAACUUAUGAUGGGGUGCGCGCUUUUUUAUUGUACAAGAUAACGGAUUUGUAGACAUU
CP001781.1/2310790-2310727         CUCAACAAACUUAUGAUGGGGUGCGCGCUUUUUUAUUGAAUAAGAUAUCGGACUUAUGAACAGA
#=GC SS_cons                       :::::::::<<<<<<<<<<<<_________>>>>>>>-->>>>>::::::::::::::::::::
#=GC RF                            CUCAACAAACUUaUGAUGGGGUGCGCGCUUUUUUAUUGuAuAAGAUAuCGGAuUUaUaaACAuu
//
# STOCKHOLM 1.0

#=GF AC   RF02389
#=GF ID   sau-31
#=GF DE   Staphylococcus sRNA sau-31
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   50.00
#=GF TC   54.80
#=GF NC   42.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


CP001781.1/2309685-2309750 GGUCGAAAAUUUCAGUCGCUGUGCCUUCUUUAUAGACAGUCCCUUUAUUCAUAACGAUAACAUGAU
AJ938182.1/2243464-2243529 GGUCAAAAAUUUCAAUCGCUGUGCCUUCUUUAUAGACAGUCCCUUUAUUCAUAACGAUAACAUGAU
CP001996.1/2323100-2323165 GGUCAAAAAUUUCAAUCGCUGUGCCUUCUUUAUAGACAGUCCCUUUAUUCAUAACGAUAAGAUGAU
#=GC SS_cons               :<<<<--------<<--<<<<<_____________>>>>>-->>---------->>>>::::::::
#=GC RF                    GgUCgAAAAUUUCAgUCgCUGUGCCUUCUUUAUAGACAGuCCcUUUAUUCAUAAcGAuAAcAUGAU
//
# STOCKHOLM 1.0

#=GF AC   RF02390
#=GF ID   sau-41
#=GF DE   Staphylococcus sRNA sau-41
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   80.00
#=GF TC   101.20
#=GF NC   38.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



FR821777.2/448378-448223         UUCAAAUAACAUACAGGAGGACAAAACAAUGGCUAUUGUAGGUACAAUUAUUAAAAUCAUCAAAGCAAUUAUCGACAUUUUCGUAAAAUAAUUUAAACGAAUUGAAUACUUAAAAUUCUCAGGCCACUGUACCAAUAGGGAUGGUGGCUUUGCUUU
CP002120.1/489557-489402         UUAAAUCAACAUACAGGAGGACAAAACGAUGGCUAUUGUAGGUACUAUCAUUAAAAUCAUCAAAGCAAUUAUCGACAUUUUCGCAAAAUAAUUUAAGCGAAUUGAAUACUUAAAAUUCUCAGGCCACUAUACCAAUAGGGAUGGUGGCUUUGCUUU
#=GC SS_cons                     :::::::::::::::::::::::::::<<<<<-<<<_____>>>>>>>>------------(((((((,,,<<<<----<<<<<____________>>>>>>>>>,,,,,,,,,,,,,,,,<<<<<<<<<-<<____>>->>>>>>>>>)))))))
#=GC RF                          UUaAAauAACAUACAGGAGGACAAAACgaugGCuauUGUAGguaCcaucAUUAAAAUCAUCaaaGCaaUUAuCgaCAUUuuCGcAAAAUAAUUUAAgCGaauuGaAUACUUAAAAUUCUCAgGCCaCuauACCAAUAGGGaugGuGGCuuuGCuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02392
#=GF ID   sau-53
#=GF DE   Staphylococcus sRNA sau-53
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   100.00
#=GF TC   211.20
#=GF NC   37.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



ACST01000042.1/55063-55254           CAGCCAGGGUUAGAAAUGAGUUUCGUUCCAUUGUUAUCUAAAGAUUGCCAUUCUGAAAUGCUGUAAAUAGCAUGAUUCAAAUCAUCUUGUGCUGCAGCAGUUUCUUUGUAAUAUGCUUCAUAUAUUUCACGGUUUUUAAUUCUGAAUGCACCAGAUAAAUCAAUAACAUGAAUUCCUUUUUCUACUAAAGGA
ACKI01000028.1/118434-118625         CAGCCAGGAUUAGAAAUGAGCUUCGUUCCAUUGUUAUUAAACGAUUGCCAUUCUGAAAUGCUAUAGAUAGCGUGAUUUAAGUCGUCUUGUGAUGCAGCAGUUUCUUUGUAAUAUGCUUCAUAUAUUUCACGGUUUUUAAUUCUGAAUGCACCAGAUAAAUCAAUAACAUGAAUUCCUUUUUCUACUAAAGGA
FR821777.2/186061-186252             CAACCUGGAUUGGAAAUCAGUUUUGUUUCUUUGUUAUCAAAUGAUUGCCAUUCUGAAAUGCUAUAGAUAGCAUGAUUUAAGUCGUCUUGAGAUGCAGCUGAUUCUUUGUAAUAUGACUCAUAUACUUCACGAUUUUUAAUUCUAAACGCACCGGAUAAAUCGAUAACAUGAAUACCUUUUUCAACUAAAGGG
CP000730.1/215144-215335             CAGCCAGGAUUAGAAAUGAGCUUCGUUCCAUUGUUAUCAAACGAUUGCCAUUCUGAAAUGCUGUAAAUAGCAUGAUUCAAAUCAUCUUGUGCUGCAGCAGUUUCUUUGUAAUAUGCUUCAUAUAUUUCACGAUUCUUAAUUCUAAAUGCGCCAGAUAAAUCGAUAACAUGAAUACCUUUUUCUACUAAGGGA
#=GC SS_cons                         ::::::<<<---<<<______>>>-->>>,,(((((((-----(((((((((--(((,<<<<<<<-<<<<-<<<<<____>>>>>->>>>-->>>>>>>,,,,,,<<<<<<<<<<_____>>>>>>-->>>>,,,,,,,)))--))))-))--)))-----))))))),,,,,,<<<<<_______>>>>>:
#=GC RF                              CAgCCaGGaUUaGaaAUgAGuuuCGUuCCaUuGuuaucaAAuGauuGcCauuCUGaaAuGCuguaaauagCauGauUuAAauCauCuuguGaugcaGCaGuUUCUuuGuaauaugcuUCAuauauuUCaCgaUUuUUAAuuCUaaauGCgCCagauAAAUCgauaaCaUGAAUaCCuuuUUCuACUaaaGGa
//
# STOCKHOLM 1.0

#=GF AC   RF02393
#=GF ID   sau-59
#=GF DE   Staphylococcus sRNA sau-59
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   80.00
#=GF TC   82.80
#=GF NC   65.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 33.90 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



AEUN01000307.1/84765-84638         UCAUCCUCUUGAAUAUCUACAAUGUUUUUAACUUUUUGUUUAAACUUAUCACGUUUAGCUCUGAUUUUAUCUAAAUCGACACUUCUUCUUGUCUUACGAGCAUAUUCUGUUGUCUUAUCUUGGAGUUG
AFEC01000021.1/367-240             UCAUCUUCUUGAAUAUCAACAAUAUUUUUUACUUUUUCUUUAAAUUUAUCCCUUUUAACUCUAAUUCUUUCUAAAUCAACACUUCUUCUUGUUUUACGUGCAUAUUCUGUUGUCUUAUCUUGUAGUUG
CP001781.1/1069087-1068960         UCGUCUUCUUGAAUAUCGAUAAUAUCAUUAACUUUCUUUUUGAAUUUAUCUCUUUUAGCUCUAAUUUUAUCUAAAUCGACACUUCUUCUUGUCUUACGUGCAUAUUCUGUAGUCUUAUCUUGGAGUUG
#=GC SS_cons                       :::::::::::::::::<<<<<--<<<--<<_____>>-->>>-->>>>>-----(((((((((,,,,,,,,,,,,,<<<<________>>>>,,,,,<<<<_____>>>>,,,,,,,,)))))))))
#=GC RF                            UCaUCuUCUUGAAUAUCgacaaUaucaUUgaCUUUuucUUugaAuuugucuCuUUuaaCucuaaUUuUaUCUAAAUCgaCaCUUCUUCUuGucUUACGcgCaUAUUCuGugGUCUUAUCuuggaGuug
//
# STOCKHOLM 1.0

#=GF AC   RF02394
#=GF ID   sau-63
#=GF DE   Staphylococcus sRNA sau-63
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   100.00
#=GF TC   124.90
#=GF NC   51.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


CP001844.2/434660-434563   ACAAAUUCCCGGUAACCAUUCCGGCUUCAUUCUCUUGAAGAAUGACAUAUUCUCAGCGUUUUAGCUGAAGGUCAGAUGAUACGUCAUCUGGCCUCUUU
AFTQ01000021.1/10468-10565 ACAAAUUCCCGGUAACCAUUCCGGCUUCAUUCUCUUGAAGAAUGACAUAUUCUCAGCGUUUUAGCUGAAGGUCAGAUGAUACGUCAUCUGGACUCUUU
AM990992.1/498976-498879   ACAAAUUCCCGGUAACCAUUCCGGCUUCAUUCUCUUGAAGAAUGACAUAUUAUCAGCGUUUUAGCUGAAGGUCAGAUGAUACGUCAUCUGGCCUCUUU
#=GC SS_cons               ::::::::<<<<________>>>>,,<<<<<<<_____>>>>>>>,,,,,,,<<<<<______>>>>>,<<<<<<<<<<____>>>>>>>>>>:::::
#=GC RF                    ACAAAUUCCCGGUAACCAUUCCGGCUuCauuCuCUUGAaGaauGaCAUAUUcuCaGCGUUUUAGCuGaAGgcCaGauGaUACGuCauCuGgcCUCUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02395
#=GF ID   sau-66
#=GF DE   Staphylococcus sRNA sau-66
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   80.00
#=GF TC   110.40
#=GF NC   46.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


FR714927.1/729299-729220   GCGUAUACAAGGAUAAAGCUUAUAACAGUAGUAAUUGUUACUAUCAAACGAACAACAUAUAUUCUAUUUUCAGAUAGCAA
AFTT01000025.1/84513-84592 GCGUAUACAAGGAUAAAGCUUAUAACAGUAGUAAUUGUUGCUAUCAAACGAACAACAUAUAUUCUAUUUUCAGAUAUCAA
AM990992.1/827126-827047   GCGUAUACAAUGAUAAAGCUUAUAACAGUAGUAAUUGUUGCUAUCAAACGAACAACAUAUAUUCUAUUUUCAGAUAGCAA
#=GC SS_cons               ((-(((---((((((,,,,,,,<<<<<<<____>>>>>>>,,,<<____>>,,,,,,,,,,,,,))))))---)))))::
#=GC RF                    GcGuauACAaggauaAAGCUUAcaaCaguAGUAauuGuugCUAuCAAACGaACAACAUAUAUUCuauucuCAGauagCAA
//
# STOCKHOLM 1.0

#=GF AC   RF02396
#=GF ID   sau-5949
#=GF DE   Staphylococcus sRNA sau-5949
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   56.00
#=GF TC   57.40
#=GF NC   52.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   7



CP002114.2/1169486-1169544         UUAUCUCAUUUAGUUAAUUGUUUAGGCACUUUUAAUUAUAGAGAUAAUUGCGCUUUUUU
AJ938182.1/1156335-1156393         UUAUCUCCAUUAGUUAUUUGUUUAGGCACUUUUAAUUAUAGGGAUAAUUGCGCUUUUUU
AEUN01000001.1/150-92              UUAUCUCCUUAGAUUAUUUGUUUAGUCACUUUUAAUUAUAGAGAUAAUUGCGCUUUUUC
AM295250.1/1402905-1402848         UUAUCUCCUUUAAUUU-UGGUGUGGUUACUUUAAAUUAUAGAGAUAAUUGCGCUAUUUU
AM990992.1/1904927-1904984         UUGUCUCCUUUAGUUU-AGGUUUGGUCACUUUAAAUUAUAGAGGCAAUAGCGCUUUUUU
ABWY01000052.1/1402-1459           UUGUCUCCUUUAGUUU-GGGUUUGGUCACUUUAAAUUAUAGAGGCAAUUGCGCUUUUUG
CP000253.1/1771670-1771728         UUAUCUCCUUUAGUUAUUUGUUUAGUCACUUUUAAUUAUAGAGAUAAUUGCGCUUUUUU
#=GC SS_cons                       <<<<<<<---<<<<<<---<<______>>--->>>>>>-->>>>>>>::::::::::::
#=GC RF                            UUauCUCCUUuAgUUauuuGUUUaGUCACUUUuAAuUaUAGAGauAAUUGCGCUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02397
#=GF ID   sau-5971
#=GF DE   Staphylococcus sRNA sau-5971
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   90.00
#=GF TC   108.20
#=GF NC   52.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


CP000255.1/420142-420047     GAGGAAAGAGACUUAUAGGUCUCGCGAGUUAUUUUAAUUCGUAUGCA-AGAAAAAGAAGAGCUAUGCAUUUUAUUUAAAAUGCGUAGU-UCUUUUUUU
FR821777.2/393358-393263     GAGGAAAGAGACUUAUAGGUCUCGCGAGUUAUUUUAAUUCGUAUGCA-AGAAAAAGAAGAGCUAUGCAUUUUAUUUAAAAUGCGUAGU-UCUUUUUUA
ACSS01000018.1/250912-250815 GAGGAAAGAGACUUAUAGGUCUCGCGAGUUAUUUUAAUUCGUAUGCAAAGAAAAAGAAGAGCUAUGCAUUUUAUUUAAAAUGCGUAGUUUCUUUUUUU
#=GC SS_cons                 :::::::<<<<<<____>>>>>><<<<<<<<___>>>>>>>>-----.---<<<<<<<<<<<<<<<<<<<<<____>>>>>>>>>>>>.>>>>>>>>>
#=GC RF                      GAGGAAAGaGaCcUAUAgGuCuCgCGaguuaUUUuaacuCGcAUGcA.AGAaaaagaaGagCuacGCauuuuAUUUaaaauGCguaGc.uCuucuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02398
#=GF ID   sau-6072
#=GF DE   Staphylococcus sRNA sau-6072
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   50.00
#=GF TC   82.40
#=GF NC   38.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20151104
#=GF RT   Identification of differentially expressed small non-protein-coding RNAs
#=GF RT   in Staphylococcus aureus displaying both the normal and the small-colony
#=GF RT   variant phenotype.
#=GF RA   Abu-Qatouseh LF, Chinni SV, Seggewiss J, Proctor RA, Brosius J,
#=GF RA   Rozhdestvensky TS, Peters G, von Eiff C, Becker K
#=GF RL   J Mol Med (Berl). 2010;88:565-575.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



FR821777.2/2562707-2562759         ACAUGGAGUCACAUCAUCUCAUGUUAGCGCUCUACUCGUAGGGCGCUAUUUUU
FR821779.1/2559810-2559862         ACAUGGAGUCACAUCAUCUCAUGUUAGCGCUCUGAUUGCAGGGCGCUAUUUUU
#=GC SS_cons                       <<<<<--<<______>>-->>>>><<<<<<<<<<____>>>>>>>>>>:::::
#=GC RF                            ACAUGGAGUCACAUCAUCUCAUGUUAGCGCUCUgaUuGcAGGGCGCUAUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02399
#=GF ID   NsiR1
#=GF DE   Nitrogen stress-induced RNA 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:20227418
#=GF GA   39.00
#=GF TC   39.50
#=GF NC   38.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.20 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20227418
#=GF RT   Heterocyst-specific transcription of NsiR1, a non-coding RNA encoded in a
#=GF RT   tandem array of direct repeats in cyanobacteria.
#=GF RA   Ionescu D, Voss B, Oren A, Hess WR, Muro-Pastor AM
#=GF RL   J Mol Biol. 2010;398:177-188.
#=GF WK   Bacterial_small_RNA
#=GF SQ   17



AAVW01000047.1/14070-14009           UGGUAGAUGCACCCUGAUAACUAA-CU---CCCCUGACUGGCUAACA--CCCGUUGGGGGAUUUUUUU
AF288130.1/689-628                   UGGUAGAUGCACCCUGAUAACUAG-CU---CCCCUGGUUGGCUAACA--CCCACUGGGGGUUUUUUUA
BA000019.2/4271891-4271831           UGGUAGAUGCACCCUGAUAACUAA-CU---CCCCUAGUUGGCUGCCA--CC-ACUAGGGGUUUUUUAU
CP002059.1/26306-26245               UAGUAGAUGCACCCUGAUAACUAA-UU--UCCCCUAGUUGGCUAACA--CCG-CUGGGGGUUUUUUUU
ACYA01000038.1/84016-84077           UGGUAGAUGCACCCUGAUAACUAAUCC---CCCCUAGUCGGCUAAAA--CC-UCUGGGGGUUUUUUCU
AGIZ01000001.1/135297-135358         UGGUAGAUGCACCCUGAUAACUUG-CU---CCCCUAGUUAACUGUCG--GUUGCUAGGGGAUUUUUUU
ACYB01000006.1/74382-74445           UGGUAGAUGCACCCUGAUAACUAA-AUCUCCCCCUAGUCGGACAAAA--CCG-CUGGGGGUUUUUUCU
ABRS01000025.1/335729-335788         UGGUAGAUGCACCCUGAUU--GAC-GU---UCCCUGGCUCACUGAUU--UGGGCUAGGGAUUUUUUUU
AEPQ01000219.1/68550-68492           UGGUAGAUGCACCCUGAUU---GA-CA---CCCCCGGUUCACUUUGG--UGAGCUGGGGAUUUUUUUU
AFJC01000010.1/18368-18424           UGGUAGAUGCACCCUGAUUAAUUA-AC---UCCCGA-CCAAU----U--UUGGUUCGGGGUUUUUUUU
CACA01000082.1/85-31                 UGGUAGAUGCACCCUGAUU--GAU-CG---CCCCCGGCCAAAU------UUGGCUGG-GGUUUUUUAU
ABME01039189.1/40-90                 UGGUAGAUGCACCCUGAAU---UC-AA---UCCCUGGCU--------UC--GGCUGGGGAUUUUUUUG
AAVU01000007.1/56616-56668           UGGUAGAUGCACCCUGGUU----G-AA---GCUCCAGAUUUC-------AAAUCUGGGGCAUUUUUUU
ACSK01000113.1/15047-15098           AAGUAGAUGCACCCUGAUG--GUU-UU---CCCCCGGCU--------UC--GGCUGGGGGAUUUUUUU
ABYK01000050.1/18242-18186           UGGUAGAUGCACCCUGGUU----G-AU---GCCCUGGAGAAA-AACA-A-ACUCCGGGGUCUUUUUUU
CP000393.1/310886-310833             AAGUAGAUGCACCCUGAUA--UAC-GA---CCUCCACCG-UC-------AUAGGUGGGGGUUUUUUUU
CP000117.1/4378248-4378187           UGGUAGAUGCACCCUGAUAACUAA-CU---CCCCUAGCUGGCUAACA--CCGACUGGGGGCUUUUUUU
#=GC SS_cons                         :<<<______>>>------..---.--...<<<<<<<<<<<______..>>>>>>>>>>>::::::::
#=GC RF                              UGGUAGAUGCACCCUGAUa..Uaa.au...cCCCcaGccggcUaAca..ccggCugGGGgUUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02400
#=GF ID   Hsp83_3_UTR
#=GF DE   Heat shock protein 83 3' UTR
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   90.00
#=GF TC   121.60
#=GF NC   78.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   20040590
#=GF RT   Preferential translation of Hsp83 in Leishmania requires a thermosensitive
#=GF RT   polypyrimidine-rich element in the 3' UTR and involves scanning of the 5'
#=GF RT   UTR.
#=GF RA   David M, Gabdank I, Ben-David M, Zilka A, Orr I, Barash D, Shapira M
#=GF RL   RNA. 2010;16:364-374.
#=GF WK   Leishmania
#=GF SQ   5


FR799585.1/112337-111866 GCCGGUACGGCAGCGCGCACACGCACACAGUGCGCCGUUAUCUUCUCCGGCUUGCGUGCAUGCUGCCU-UCCGCAAAGCUGC-AGCGCG-GCGCUCUGG-AGGCCUUGCCCCGCGCACUGCUCUUUACAUGGCCCGACGUGAGGGCACUUCGCGGGCAGUGCUGCGGCCUCGUGUGGGAUCGCGUCAGGACUGAAGGAGAGCGAAUCCCGGGGCUCGGUGUGG-AGAAGGAGG----UGCCAAGUAGCCCCGUUGCGGAGAG---UGUGU--CAGCCCCAUCG-CAGUGCACCUCACUGCCCUCC-CGCUUCCCCGGCCACUUGGC-ACUCACUACCCCCUCCCCUUCCCUUCUCCC-CC----------------GUACCCCCCCC-CUCUCUUUCUCGCAUCCUCUGCCCUCUCACCGC-CGCGCCGGGCGCACCGGCGCUCUUUUCC------------------GUUUUGAUUUCGCGUGUCCCAACACACAGUUGGAUCGUUUUUCUUCUCUCCCUAACGA
X87770.2/2171-2642       GCCGGUACGGCAGCGCGCACACGCACACAGUGCGCCGUUAUCUUCUCCGGCUUGCGCGCACGCUGCAUUC-CGCAAAGCUGCAG-CGCGGGCGCUCUGG-AGGCCUUGUCCCGCGCACUGCUCUUUACAUUGCCCGACGUGAGAGCACUUCGCGGGCAGUGCUGCGGCCUCGUGUGGGAUCGAGUCAGGACUGAAGGAGAGCGAAUCUCAGGGCUCGGUGUGGAAGAAGGAGGU---G-UCAAGUAGCCCCGUUGCGGAGAGC-GUCUCA--GC--CCCAUCA-CAGUGCACCUCACUGGCCUCC-CGCCUCCCCGGCCACUUGC-CACUCACUACCCCCUCCCCUUCCCUUCUCCC-CC----------------GUACCC-CCUCUCUCUCUUUCUCGCACUCUCUGUCCUCUCACCGC-CGCGCCGGGCGCACCGGCGCUCUUUUCC------------------AUUUUGUUUUUGCGCGUCCCAACACACAGCUGGGUCGUUUUUCUUUUCU--CUAACGA
FR796429.1/135708-135204 GCCGGUACGGCAGCGCGCACACGCACACAGUGCACCGAUAUCUUCUCCGACUUGCGCGCACGCUGCAU-UCCGCAAAGCUGCA-GCGCG-GCGCUCUGGAGG-CCUUGUCCCGCGCACUGCUCUUUGCAUAGCCCGACGUGAGAGCACCUCGCGGGCAGUGCUGCGGCCUCGUGUGGGAUCGAGUCACGACUGAAGGAGAGCGAAUCUCAGGGCUCGGUGUGG-AGAAGGAGGU---G-UCAAGUAGCCCCGUUGCGGAGAG---CGUCUCAGA--CCCAUCA-CAGUGCACCUCACAGACCUCCCCGCCUCCCCGGCCACUUGC-CACUCACUACCCCCUCCCCUUCCCUUCUCCCCC-GUACCCCCCCGCCCCAAUCUCUCUCUCUCUCUCUUUCUCGCAGCCUCUGCCCUCUCACCGC-CGCGCCGGGCGCACCGGCGCUCGUUUCCGUUUUUUUUUGUGUUUUUGUUUUGUU-UUGCGCGUUCCAACACACAGCCGGAUCGUUUUUCUUCUCU--CUAACGA
M92925.1/1-468           GCCGGUACGGCAGCG-GCACACGCACACAGUGCU-CG-UAUCUUCUCCGGCUUGCGUGCAUGCUGCCU-U-CGCAAAGCUGCGGACGCG-GCGCUCUGG-AG-CCUUGCCCCGCGCACUGCUCUUUACAUAGCCCGACGUGAGGGCACUUCGCGGGCAGUGCUGCGGCCUCGUGUGGGAUCGCGUCAGGACUGAAGGAGAGCGAAGCCCGGGGCUCGGUGUGG-AGAAGGAGCGUUCGUCCAAGUAGCCCCGUUGCG-AGAG---UGUGU--GA--CCCAUGC-CAGUGCACCUCACUGCCCUCC-CGCUUCCCCGGCCACUUGGGCACUCACAUCCCCCUCCCCUUCCCUUCUCCCCCC----------------GUACUCCCCCCUCUCUCUUUCUCGCAUCCUCUGCCCUCUCACCGG-CGC----GGCGCACCGGCGCUCUUUUCC------------------GUUUUGAUUUUGCGUGUCCCAACACACAGUUGGAUCGUUUUUCUUCUCUCCCUAACGA
M73492.1/1360-1789       GCCGGUAUGGCAGCGCGCAC-----------------------------------------GCCGCAC-UCCGCAAAGCUGC-AGCGCG-GCGCUCUGG-AGGCCUUGUCCCGCGCACUGCUCUUCGCGUUGCCCGACGUGAGAGCACAUCGCGGGCAGUGCUGCGGCCUCGUGUGGGAUCGAGUCAGCGU-GAAGGAGAGCGAAUCCCAGGGCUCGGUGUGG-AGAAGGAGGU---G-UCAAGUAGCCCCGUUGCGGAGAGCGUGCUCA--GC--CCCAUGCACAGUGCACCUCACUGGCCUCC-CGCUUCCCC-GCCACUUGC-CACUCACUACCCCCUCCCCUUCCCUUCUCCG-CC----------------GUGCCC-CCUCUCUCUCUUUCUCGCAUCCUCUGCCCUCCCACCGCCCGCGCCGGGCGCACCGGCGCUCUUUUCC------------------GUUUUGUUUUUGCGCGUCCCAACACACAGUUGGAUCGUUUUUCUUCUCU--CUAACGA
#=GC SS_cons             :{{{{,,,(((-(((-((((,,<<<<-<<<-<<--<<__________>>>>>>>->>>>,,<<<<<-<.<-<<<<____>>>>>>->>>.>><<<<<<<.<<----<<<<<<<<<----<<<________>>>---->>>>->>>>>>>>>>->>>>,)))))))-))),,[[[[[[[[[[[[[[[[[[[[-[[[[-[[[[[[,,,,,,(((((--((--(((.((((((((,,...<.<<<<<<-<<<-----<<<--<<<...-<<<<..<<..----<<<.____>>>-->>>>->>->>>-.>>>------>>>->>>>>>.>,,,,<<________________________.__................>>,,,,,,,,,,,,)))))))))-))--))--))))),,,,<<<<.-<<_______>>->>>>]]]]]]]]]]-..................]]]]]]]]---]]]-]]]]]-]]]],,,,}}}}-<<<<<__________..__>>>>>
#=GC RF                  GCCggUAcGGCAGCgcGCaCAcGCgCACagUGcacCGuUAUcUUcUcCGgCcuGcGcGCAuGCcGCac.cccGCaAAGCuGCgggCGCg.GCGCuCuGg.gGgCCUuGccCCgCGCACUGCuCUUuaCAUaGCCCGACGuGAGggCaCcuCgCGgGCAGuGCuGCGGCCUCGuGuGGGauCGcguCaggacUGaagGaGaGCGAAuCuCaGGGCUCgGUGuGG.aGaagGaGgu...G.cCaaGuAGCCCCGUUGCGGAGaG...ugugu..ga..CCCAugc.CAGUgcaCCucacugcCCuCC.CGCuUCCCCGGCCaCuuGg.CACUCacuaCCCCCUCCCCUUCCCUUCUCCc.Cc................guacccccCuCUCUCuCuuuCuCGCaucCuCUGCCCuCuCACCGg.CGCGccGGGCGCAcCGGCGCuCuuuuCC..................guccuGauUUugCGuguCCCAaCaCACAGccGGAuCGuuUUUCUUcUCU..CUaaCGa
//
# STOCKHOLM 1.0

#=GF AC   RF02401
#=GF ID   ClpQY_promoter
#=GF DE   ClpQY promoter
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:19440251
#=GF GA   42.00
#=GF TC   42.10
#=GF NC   39.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0048255; mRNA stabilization;
#=GF RN   [1]
#=GF RM   19440251
#=GF RT   Regulation of clpQ(+)Y(+) (hslV(+)U(+)) gene expression in Escherichia
#=GF RT   coli.
#=GF RA   Lien HY, Yu CH, Liou CM, Wu WF
#=GF RL   Open Microbiol J. 2009;3:29-39.
#=GF WK   HslVU
#=GF SQ   39


CU468135.1/135524-135470     CCCCACAC-----------U----------GACGUGUGGG---GCCGUCUUUUUG----ACUGUAAC-AAGGGGUCUGCCCGUG
CP000668.1/4369910-4369974   CUCCGUACU-----GUUUUUUAA----CAGGCAGUACGGG---G-ACUCAUUCAG----UCUGCAACGA--GGGUCCGCUCGUG
CU928145.2/4504096-4504039   CCCCGUAC-------UUUU--------------GUACGGG---GUUUGUACUCUGUA--UUCGUAACCAAGGGGUCAGCUCGUG
CP000964.1/5521395-5521451   -CCCCGCG-------GACA-------------GCGCGGGG---CC-CCUGUUCCGCU--UUUGCAACCAAGGGGUCUGCUCGUG
CP000826.1/5312035-5312102   CCUCGUAGUGUCUGCGCAAGCA-------GAUACUGCGAG---G-GCUUCUUUCCGU--CUU-CAACGA--GGGUCUGCUCGUG
CP001144.1/4328033-4327977   CCCCGUAC-------GCC---------------GUACGGG---GCCGCAAUUCAGCA--UUAGUAACCAAGGGGUCUGCUCGUG
CP000822.1/2843817-2843873   CCCCGUAC-------CGC---------------GUGCGGG---GCCUGUAUUCUGCA--UUUGUAACCAAGGGGUCUGCUCGUG
CP000653.1/4395627-4395684   CCCUGAGU-------AUCA--------------GCUCAGG---GCAUCUGUUUCG-A-AUUUGUAACCAGGGGGUCUGCUCGUG
CP001383.1/4177093-4177036   CCCCGUAC-------UUUU--------------GUACGGG---GUUUGUACUCUGUA--UUCGUAACCAAGGGGUCAGCUCGUG
FN543502.1/4021530-4021586   CCCCGUAC-------ACC---------------GUGCGGG---GCCUUUAUUCUGCA--UUUGUAACCAAGGGGUCUGCUCGUG
ABWL02000013.1/97790-97734   CCCCGCAC-------CCU---------------GUGCGGG---GCCUGUAUUCUGCA--UUUGUAACCAAGGGGUCUGCUCGUG
FR877557.1/3959398-3959342   CCCCGUAC-------GCC---------------GUACGGG---GCCCGAAUUCUGCU--UUUGUAACCAAGGGGUCUGCUCGUG
BAAW01000341.1/2915-2971     CCCCGCGU-------GAA---------------GCGCGGG---GCCCCUAUUCCGCU--UUUGUAACCAAGGGGUCUGCUCGUG
AEWW01037258.1/6977-7033     CCCCGCGU-------AAC---------------GCGCGGG---GCCCCUAUUCCGCU--UUUGCAACCAAGGGGUCUGCUCGUG
CACD01000100.1/49836-49892   CCCCGCAU-------ACU---------------GCGCGGG---GCCUGUGUUUUGCA--UUUGUAACCAAGGGGUCUGCUCGUG
AEIA01000018.1/50077-50134   CCCCGCAC-------AAUU--------------GUGCGGG---GUUUGAAUUCUGUA--UUCCUAACCAAGGGGUCUGCUCGUG
AEQT01000001.1/84205-84149   CCCCGCAU-------ACU---------------GUGCGGG---GCCUGUACAUUGCA--UUUGUAACCAAGGGGUCUGCUCGUG
CP000880.1/3500933-3500989   CCCCGUAC-------GCA---------------GUACGGG---GCCGGAAUUCUGCA--UUAAUAACCAAGGGGUCUGCUCGUG
CAAQ01000691.1/1106-1052     -CCCGUAC-------GCC---------------GUACGGG---CC-GCAAUUCAGCA--UUAGUAACCAAGGGGUCUGCUCGUG
FP236843.1/166947-166893     CCCCGCAG-------GUGA-------------ACUGCGGG---G-ACAUCUUCUG----ACUGCAAC-AAGGGGUCUGCCCGUG
AFCM01000240.1/21-76         -UCCGUAC-------GCA---------------GUACGGG---GCCGCAAUUCAGCA--UUAGUAACCAAGGGGUCUGCUCGUG
AEXB01000128.1/27139-27080   CCCUGAGC-------ACUG--------------GCUCAGG---GCUUCUGUUUCCCGAAUCUGUAACCAGGGGGUCUGCUCGUG
AGQO01000036.1/40387-40451   CCCCAUACUG--UUU----UUCUG---AAUUCAGUAUGGG---G-ACUCAUUCAG----UCUGCAACGA--GGGUCCGCUCGUG
ACCD01000008.1/88773-88708   CCCCAUACUG---UU----UUUCUG-AAAGACAGUAUGGG---G-ACUCAUUCAG----UCUGCAACGA--GGGUCCGCUCGUG
AALF02000029.1/4567-4631     CCCCGUGCUG---UU----UUUUG--ACAGGCAGUACGGG---G-ACUCAUUCAG----UCUGCAACGA--GGGUCCGCUCGUG
CP002206.1/3326665-3326719   CUCCGCGC-------CCCG-------------UGCGCGGA---G-UCCUUUUCCG----ACUGCAAC-AAGGGGUCUGCCCGUG
ADBY01000022.1/29605-29672   CCUCGUAGUG---CC----GGUGCCGACCGGCGCUGCGAG---GGCUUCUUUCCG----UCUGCAACGA--GGGUCUGCUCGUG
ACCA01000030.1/23409-23344   CCCCGUGUU-----G--UUUUGCUG-CAAGGCAAUACGGG---G-ACUCAUUCAG----UCCGCAACGA--GGGUCCGCUCGUG
AALC02000076.1/2390-2455     CCCCAUACUG---UU----UUUCUG-AAAGACAGUAUGGG---G-GUCCAUUCAG----UCUGCAACGA--GGGUUCGCUCGUG
ACCC01000012.1/42407-42471   CCCCGUCUUGU-GUU----GAAC----AACACAAGACGGG---G-ACUCAUUCCG----UCUGCAACGA--GGGUUCGCUCGUG
CP003085.1/193694-193641     CUCCGCGC-------CCUA-------------GGCGCGGA---G-CUUUUUUCCG----ACAGUAA--AAGGGGUCUGCCCGUG
ADCU01000025.1/153682-153629 CCCCACAC-------AAAG--------------GUGUGGG---GUUCUUAUUUCG----UCAGCUACGG--GGGUCUGCUCGUG
CP002433.1/4226153-4226206   CUCCGCGC-------UGAG-------------UGCGCGGA---G-UCCUUUUCU-----ACUGCAAC-AAGGGGUCUGCCCGUG
FN666575.1/151612-151558     CCCUGCGC-------GAAU--------------GAGCAGG---GCCGUUUUUUUG----ACUGUAAC-AAGGGGGCUGCCCGUG
AFCW01000383.1/1-68          -CACACACUU---AA----UUA------AUUAAGUGUGUGNNNGCCGCAAUUCAGCA--UUAGUAACCAAGGGGUCUGCUCGUG
BABY01000105.1/20942-20996   CGCCGCGC------C-CGC-------------UGCGCGGA---G-UCUUUUUUCC----ACUGCAAC-AAGGGGUCUGCCCGUG
FP236842.1/156502-156447     CCCUGCGC-------GAAU--------------GAGCAGG---GCCGUUUU-UUUUG--ACGGUAAC-AAGGGGUCUGCCCGUG
AENX01000108.1/13409-13477   CCUCAUAGUC---UC----UGCAUAAGCAGAGACUAUGAG---GGCUUUCUUUCUGU--CUU-CAACCA--GGAUCUGCUCGUG
CP002272.1/4697124-4697177   CCCCGUAC-------GCU---------------GUGCGGG---GCCCCUAUUCUG-C--UUUGUA-CCAGGGGGUCC-UUCGUG
#=GC SS_cons                 <<<<<<<<.......___.............._>>>>>>>...>:::::::::::::..:::::::::::::::::::::::::
#=GC RF                      CCCCGcac.......gcu..............agugCGGG...GCccuUaUUCcGca..UcUGcAACcAAGGGGUCUGCUCGUG
//
# STOCKHOLM 1.0

#=GF AC   RF02402
#=GF ID   Afu_263
#=GF DE   A. fumigatus snoRNA Afu_263
#=GF AU   Osuch I
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   INFERNAL
#=GF SS   Predicted;
#=GF GA   60.00
#=GF TC   60.30
#=GF NC   55.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00070
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   19


AM921926.1/1-96                UAAUAUGAUGAUUA-CCA-U-UACCAAUAAGCAUAGUUCAACUG-AA-AUCUUCG-GAUUGCUGAACGACA--A--CCUUCUACCAU---CUUUCACCCCUAUCUGAUA
AP007161.1/1645458-1645553     UUUUAUGAUGAUCA-CCA-U-AAGUUAUAAGCAUAGUUCACCUG-AG-GUCUUCG-GACCGUUGAACGACA--A--CCUUAUACCAU---CUUUCACCUUUGUCUGAUA
ACJE01000001.1/1049987-1049893 CACAAUGAUGAACA-CCA-U--ACCAAUAAGCAUAGUUCACCUG-AG-AUCUUCG-GAUUGUUGAACGAAA--A--CUGUAUACCAU---CUUUCACCUUUAUCUGAUA
AAJN01000109.1/294816-294721   UUCGAUGAUGAACA-CCA-U-AAU-CCAAAGCAUAGUUCACCUG-AGUGUCUUCG-GACCGCUGAACGACA--A--CCUUAUACCAU---CUUUCACCUUUAUCUGAUG
ABAR01000033.1/224364-224455   ---UAUGAUGAACA-ACA----AAUUUAAAGCAUAGUUCACCUG-AA-AGUCUUGGACUUCAUGAACGACA--A--ACAUUUACCAU---CUUUCACCUUUAUCUGAUA
ABAS01000035.1/216863-216960   CUUUUUUGUGAUGA-GCAAC-AAAUUUAAAGCAUAGUUCACCUG-AA-AGUCUCGGACUUCAUGAACGACA--A--ACCUUUACCAU---CUUUCACCUUUGUCUGAUA
ABQE01000021.1/182056-181962   CUCUAUGAUGAUCC-CCA-UGUAC---AAAGCAUAGUUCAACUGAAG-GUCUUCG-GAUCGCUGAACGAGA-AA--CCCAUCACCAU---CUUUCAUC-CUAUCUGACA
ABVF01000006.1/121662-121756   CUCUAUGAUGAUCC-CCA-UGUAC---AAAGCAUAGUUCAACUGAAG-GUCCUCG-GAUCGCUGAACGAUA-AA--CCCAUCACCAU---CUUUCACC-UUGUCUGAUA
ABWI01000214.1/12251-12345     CUACAUGAUGAUCU-CCA-UGUA---UAAAGCAUAGUUCAACUGAAG-GUCUUCG-GAUCGCUGAACGAGA-AA--CCCAUCACCAU---CUUUCAUC-AUAUCUGAUC
ACPH01000030.1/46609-46514     CUACAUGAUGAUCU-CCA-UGUAC---AAAGCAUAGUUCAACUGAAG-GUCUUCG-GAUCGCUGAACGAGA--AACCCCAUCACCAU---CUUUCAUC-AUAUCUGAUC
AAIW01000006.1/115111-115019   UUUGAUGAUGAAUC-CCA----GUUUUUAAGCAUAGUUCACCUGAAG-GUCUUCG-GAUCGCUGAACGACA--A--CCAA-CACCAU---CUUUCACC-UUUUCUGAAU
ACYE01000154.1/10530-10435     CUACAUGAUGAUCC-CCA-UGUAC---AAAGCAUAGUUCAACUGAAG-GUCUUCG-GAUCUCUGAACGAGAAAA--CCCAUCACCAU---CUUUCAUC-AUAUCUGAUC
AM920428.1/3789865-3789956     UUUUGUGAUGAACAAACA-A-UAU-UUAAAGCAUAGUUCACCUG-AG-AUCUUCG-GAUUGUUGAACGAAA--A--CAUA-UUCCAU---CUUUCAU---UUUCUGAUC
AEII01000185.1/56457-56547     UUUCAUGAUGAACC-CCA----AUUCAUAAGCAUAGUUCAACUGAAG-GUCUCCG-GAUC-CUGAACGACA--A--CCUA--UCCAU---CUUUCACU-UUUUCUGAAA
ABKI01000368.1/11871-11780     CUUUAUGAUGAUUC-CCA----AGUUUUAAGCAUAGUUCAACUGAAG-GUCUCCG-GAU-AUUGAACGACA--A--ACCU-UACCAU---CUUUCAUC-CUUUCUGAAC
AAJI01000368.1/3741-3833       UUUCGUGAUGAUC---CA-A-AAUUUAUAAGCAUAGUUCAACUGAAG-AUCUCCG-GAUC-CUGAACGACA--A--AACAUUUCCAU---CUUUCAUU-UUUCCUGAGC
ABBB01000067.1/388587-388684   UCUUGUGAUGAUUC-CCA----AUUCUUAAGCAUAGUUCACCUGAAG-GUCCCUG-GACCACUGAACGACA--A--CCCAUCAUCAUUUUCUUUCACCUUUGUCUGAGU
ABRJ01000330.1/109661-109751   UUUCGUGAUGAUC---CA-A-AAUUUAUAAGCAUAGUUCAACUGAAG-AUCUCCG-GAUC-CUGAACGAUA--A--ACAU-UUCCAU---CUUUCAU--UUUCCUGAAC
AFPA01000204.1/184651-184737   CUUUAUGAUGAAC--CCA-U-AAC-CCAAAGCAUAGUUCAACUG-AG-GCAUUCG-UGUCAUUGAACGAAA--A--AU---UACCAU---CAUCAA----AUUCUGAAC
#=GC SS_cons                   :::::<<<<<____._>>.>.>>------------<<<<<------<.<<<____.>>>>-->>>>>::::..:..:::::::::::...::::::::.::::::::::
#=GC RF                        uUuuaUgaUGAuca.cCA.u.cAuUuuaAAGCAUAGUUCAaCUGAAG.gucUUCG.gacCgcUGAACGAcA..A..ccuauuACCAU...CUUUCAcC.uUaUCUGAua
//
# STOCKHOLM 1.0

#=GF AC   RF02403
#=GF ID   Afu_328
#=GF DE   A. fumigatus snoRNA Afu_328
#=GF AU   Osuch I
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   INFERNAL
#=GF SS   Predicted;
#=GF GA   70.00
#=GF TC   84.20
#=GF NC   60.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 31.85 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   18346967
#=GF RT   Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a
#=GF RT   novel mechanism for regulation of protein synthesis.
#=GF RA   Jochl C, Rederstorff M, Hertel J, Stadler PF, Hofacker IL, Schrettl M,
#=GF RA   Haas H, Huttenhofer A
#=GF RL   Nucleic Acids Res. 2008;36:2677-2689.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4



AACD01000109.1/203504-203433 UUGCAUGAUGAGCAA---UCCAUUAU----UAGUUAUCCCUGUCAGAAAUAU------ACUGU--UGAUAACA-UACAACUCUGAUUU
AAKD03000010.1/312115-312193 UUUUAUGAUGAGCAGU--UUUAUUAC----UAGUUAUCCCUGGCAGAAACUAUACAACCCUGU--UGAUAACA-CAAACCUCUGAAAA
AAJN01000176.1/28338-28263   UUCAAUGAUGAGCAAU--UUUAUUAUAAACUAGUUAUCCCUGGCAGAACUAC------ACUGU--UGAUAACC-UAA-CCUCUGAAAU
AM921932.1/1-76              CUACGUGAUGAGCAAUUCUUUAUUAC----UAGUUAUCCCUGGCAGAACUA--------CUGUGUUGAUAACAUUACAACUCUGAAUC
#=GC SS_cons                 ::::::::::::::::..::::::::....::::::::::::::::::::::......:::::..::::::::.::::::::::::::
#=GC RF                      UUucaUGAUGAGCAaU..UUUAUUAc....UAGUUAUCCCUGGCAGAAcUau......aCUGU..UGAUAACa.UAaAcCUCUGAauu
//
# STOCKHOLM 1.0

#=GF AC   RF02404
#=GF ID   P33
#=GF DE   Pseudomonas sRNA P33
#=GF AU   Osuch I
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; Clustal_alifold;
#=GF GA   45.00
#=GF TC   46.70
#=GF NC   44.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   3


AE004091.2/5775061-5775220 CCGCCCGGCACCACCGGUCAAACCAUGGCGUAGGGCGAAUAACCGCAUCGCGGUUAUCCGCCGGCUGUGCAGGGCAGCGGCCCUUGCCCGGAUUUUGGGCAGCGUGCACCAGCAGGCGACAAAUCGGCAUCAAUCGCUGGCGGAAAAGCCCGCUCCGUCA
CP000744.1/6057604-6057747 CCGCCCGGCACCGCCCGCCGAACCGUGGCGCAGGCCA----------------AUAUCCGCCGGUUCGGCGGGGCUGCGGUCCUUGCCCGGAUUUUGGGCAGCGUGCACCAGCAGGCGACAAAUCGGCAGGAAUCGCUGGCGGAAAAGCCCGCUCCGUCA
AAKW01000064.1/31090-30931 CCGCCCGGCACCGUCGAUCAAACCGUGGCGUAGGGCGAAUAACCGCAUCGCGGUUAUCCGCCGGUUCGGCAGGGCUGCGGCCCUUGCCCGGAUUUUGGGCAGCGUGCACCAGCAGGCGACAAAUCGGCAUCAAUCGCUGGCGGAAAAGCCCGCUCCGUCA
#=GC SS_cons               :<<<<<<<______________>>>->>>>--[[[[,,,<<<<<<<___>>>>>>>(((((((((---((<<<<<____>>>>><<<<<<_____>>>>>><<-<<<____>>>->>,,,,,,,,,))-------))))))))),,,]]]]:::::::::
#=GC RF                    CCGCCcGGCACCgcCgguCaAACCgUGGCGuAGGgCgAAuaaccGcAUcgCgguuauCCGCCgGcUcgGCaGGgCuGCGGcCCuuGCCCgGAUUUcGGGCaGCGuGCACCAGCaGGCGACAAAUCGGCAucAAUCgCcGGCGGaAAAGcCCGCUCCGUCA
//
# STOCKHOLM 1.0

#=GF AC   RF02405
#=GF ID   P34
#=GF DE   Pseudomonas sRNA P34
#=GF AU   Osuch I
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   INFERNAL
#=GF SS   Predicted; WAR; cmfinder;
#=GF GA   44.00
#=GF TC   46.30
#=GF NC   37.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   16870723
#=GF RT   Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of
#=GF RT   sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool
#=GF RT   sRNAPredict2.
#=GF RA   Livny J, Brencic A, Lory S, Waldor MK
#=GF RL   Nucleic Acids Res. 2006;34:3484-3493.
#=GF WK   Pseudomonas_sRNA
#=GF SQ   5


CP000438.1/6107695-6107297   CCGCCCAAGGCGCCGCCGAUGGCCGCGCGGGUGUUGUCGCCUGCGAAGGCGGUACCACCGACCAGACUCAGGGACAACAGGAGUAUCGAGGAAUACUUCAUAGAGAGUUUCUCUCUGUGGGGAUGACGGCUGCGAUGCUGGGGUUGGCCCAAACCGCUGACAAGCGUCAGCCGACGAUUGGUAGAACAAACUCGAAAUAUUCCAAGUGCUUGUUUUUUAUGGGGAACUUUCUUCGGCG---GAGGCG-GUCUUAAACCGAAUGCGAAACGCGAUUUCAGGGUCGAAAUCGGUAUUUUUGCUGG-CGGGAUGCUGGCCAUUCUAACGCCGACGAGCGGCCUGCCUUCAAGGCCUUUCAUCGACUUUUUCCUUAAGACGCCGCCUCCUGUUGCAGGAGGCGGCGUU
AE004091.2/5835480-5835082   CCGCCCAAGGCGCCGCCGAUGGCCGCGCGGGUGUCGUCGCCUGCGAAGGCGGUACUACCGACCAGACUCAGGGACAACAGGAGUAUCGAGGAAUACUUCAUAGAGAGUUUCUCUCUGUGGGGAUGACGGCUGCGAUGCUGGGGUUGGCCCAAACCGCUGACAAGCGCCAGCCGACGAUUGGUAGAGCAAAUUCGAAAUAUUCCAAGUACUUGUUUUGUAUGGGGAACUUUCUUAAGUA---GAGGCG-GUCGUAGACCGAAUGUGAAGCGCGAUUUCAGGGUCGAAAUCGGUAUUUUUGCUGG-CGGGAUGCUGGCCAUUCUAACGCCGACGAGCGGCCUGCCUUCAAGGCCUUUCAUCGACUUUUUCCUUAAGACGCCGCCUCCUGUUGCAGGAGGCGGCGUU
CP000744.1/6117984-6117586   CCGCCCAAGGCGCCGCCGAUGGCCGCGCGGGUGUCGUCGCCUGCGAAGGCGGUGCCACCGACCAGACUCAGGGACAACAGGAGUAUCGAGGAAUACUUCAUAGAGAGUUUCUCUCUGUGGGGAUGACGGCUGCGAUGCUGGGGUUGGCCCCCAUCGCUGACAAGCACCAGCCGACGAUUGGUAGAGCAAAUUCGAAAUAUUCCAAGUGCUUGUUUUUUAUGGGGAACUUUCUUCAGUG---GCGGCG-GUCGUAGACCGAAUGCGAAACGCGAUUUCAGGGCCGAAAUCGGUAUUUUUGCUGG-CGGGAUGCUGGCCAUUCUAACGCCGACGAGCGACCUGCCUUCAAGGCCUUUCAUCGACUUUUUCCUUAAGACGCCGCCUCCUCUUGCAGGAGGCGGCGUU
AEAZ01000003.1/118029-118399 CCGCCCAAUGCGCCGCCUACACCGGCUUCGGUGGUGCCACCGGCCAUGGCUGCGCCACUGACCAGGCCAAGGGACAACAAGAGAAUCGAGGAAAGCUUCAUUCAGGUA-AACCUCAA-GGGGAUGACGGCGC-GAUCCUGAGGCCGUAUUGACAUGCUGACAAUAGAAAUCCGACCAGUAACACGAGUUGUACACAAUUCUCUAAGUUACUGUUUUAACUGCGGAA----CUUAAGUGAUUUUUGCGAGUCAUUAGCU-CUUCGGAACGGCCGCUUUUAUGCAAAAGCGGCCUUUUUUUGUGUCCAAAAUGAU-------CGAUC-AGGCCGAGC--------GCGA-----CAUGAUCAAACCGCUC--UCGCUCGCGGC--UUCCAGGCGAAUCGCCACGAA
CP002585.1/372972-373256     CCGCCCAAUGCGCCGCCCACACCUGCUUCGGCAGUACCGCCGGCAGAAGCGAUGCCACUGGCCAGGCUAAGGGACAACAAGAGAAUGGAGGAGAACUUC--------AUA--------GAGG-----AGCCUCAAA----GGGAUGACG----GCGCGAUCCU----GAGGCUGGCUUCGCUUGGUUACAAUAGAA-----------------AUCCGACGAGUAACACGACU----U---GU-GCAC-----AAU----UCUCUAA-----------GUUAU-------UGUUUUUUGGUGG----GAA----------CUUAA----------GGC---AAAUUG--GCCGGUCUUUAGCUACUUC--GGACAGGCCGUUUUCUUU---GGAAAACGGCCUU
#=GC SS_cons                 :::<<<--<<-<<<<<<--------<<<<<<<<____>>>>>>>>-->>>>>>->>-------------->>>,,,,,,,[[[--[[[[,,,,,,<<<<-<<<<<<<___>>>>>>>.>>>>(((((-(((-(--(((((,,<<--<<_______>>-->><<<<<<--<<<<_____>>>>----------------------->>>>>>,,,,,,,,,,,<<______>>,)))))...)-)))--))))),,,<<.---<<---<<-<<<<<<<______>>>>>>>>>------>>---.->>,,,<<<......._____.______>>><<<...______..>>>,,,,,]]]]----]]]..,,,<<<<<<<<<<<<<_____>>>>>>>>>>>>>
#=GC RF                      CCGCCCAAgGCgCcGCCuAuagCuGcgccGGcGuuGuCgCCggcgAaGGCgGcgCcACuGACCAGaCUaAGGGACAACAaGAguAucGAGGAAuACuuCAcagaGgguUuccCucug.GggGacGaCGGCcuCGAcgCuggGGuUGgcucaAaacgcuGaCaagcgcaAgcCgAcgAucGgcAgaauaaAuucgAAAUauUCcAAgugcuuGUuUUuuAUGgggAACuuuccUcaGcg...GugGCGaGuCguaaacc.auUgcgAAgcGCggcuucagugucgaagccGgcuUUUUUgcUGg.CgggAuGcu.......CuAac.ccGaCGagCGGC...ccuUuA..GCCuuUcAUCgacUuucUC..uaAcacGCcGccucccuuuGCgggaggCgGCgug
//
# STOCKHOLM 1.0

#=GF AC   RF02406
#=GF ID   snoR120
#=GF DE   Small nucleolar RNA snoR120
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; mfold
#=GF GA   55.00
#=GF TC   79.70
#=GF NC   41.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 34.19 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4



ADBK01001495.1/70498-70425     GAAAAUGAGGAACAAAUAACUCAUCCGUGAAUCAA-----------------ACCAUGAACCAAAUUUUGCUUAUUGAUAUUCUGAUUCCA
AENI01009318.1/96185-96101     GAAAAUGAGGAACAAAUA----AAAUGUGAAUCAAGACAAAUG--UUUUGAAACAAUGUACCAAAUUUUGCUUAUUGAUAUUCUGAUUCCA
AFAN01000032.1/9627848-9627934 GAAAAUGAGGAACAAAUA----CAAUGUGAAUCAAGACUUAAUGUUCUUGGAACCGUGUACCAAAUAUUGCUUAUUGAUAUUCUGAUUCCA
AP002544.1/11447-11374         GAAAAUGAGGAACAUAUAACUCAAACGUGAAUCAA-----------------ACCAUGUACCAGUUUUUGCUUAUUGAUAUUCUGAUUCCA
#=GC SS_cons                   ::::::::::::::::::....:::::::::::::::::::::..::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                        GAAAAUGAGGAACAaAUA....aaauGUGAAUCAAGACuuAuu..UuUUGgAACcaUGuACCAaaUuUUGCUUAUUGAUAUUCUGAUUCCA
//
# STOCKHOLM 1.0

#=GF AC   RF02407
#=GF ID   snoR122
#=GF DE   Small nucleolar RNA snoR122
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; mfold
#=GF GA   36.00
#=GF TC   36.20
#=GF NC   35.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 29.69 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4



ADBK01000045.1/89712-89640     UGCCAAUGAUGUGCCUUAACAAUUGCACGUAUUAUCAGAU-UUUCAGUGAUGAGU-AUCACUUAUUUCUGAGGCA
AFAN01000001.1/6002742-6002671 UGCCAAUGAUGAUC-UUUACAAUUGCACGUAUUAUCAGA-UUUUCAGUGAUGAAU-AUCACUAAUCUCUGAGGCA
AENI01008624.1/73075-73149     UGCCAAUGAUGAUAUUACAAAAUUGCACGUAUUAUCAGAUAUUUCCGUGACGAAUUAUCACUAAUGUCUGAGGUA
AC011809.2/64001-64074         UGCCAAUGAUGUGCCUAAACAAUUGCACGUAUUAUCAGAUUUUUCAGUGAUGAAU-AUCACUUAUGUCUGAGGCA
#=GC SS_cons                   :::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::::::::::::
#=GC RF                        UGCCAAUGAUGuuccUuaAcAAUUGCACGUAUUAUCAGAUuUUUCaGUGAUGAaU.AUCACUuAUgUCUGAGGCA
//
# STOCKHOLM 1.0

#=GF AC   RF02408
#=GF ID   snoR124
#=GF DE   Small nucleolar RNA snoR124
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; mfold
#=GF GA   70.00
#=GF TC   92.60
#=GF NC   38.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.41 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5



ADBK01001983.1/287723-287648   UACCAAUGAUGGAAUUCAA-AUAAUCAUCAGAUCUGAUGUGU-UAUACAUACA--UGAUUACAAUCUUGACGCUGAGGUA
AC232542.1/85172-85095         UACCAAUGAUGGAAUUCAAAUAAAUCAUCAGAUCUGAUGUGUAACAACAUAUG--UGAUUACAAUCUUGAUGCUGAGGUA
AENI01002604.1/10661-10586     UACCAAUGAUGGAUUC--AAAUAAUCAUCAGAUCUGAUGUGUAAAAACAUAUG--UGAUUACAAUCUUGAUGCUGAGGUU
AFAN01000008.1/2227657-2227733 UACCAAUGAUGGAAUUCAA-AUAAUCAUCAGAUCUGAUGUGU--AAAAACACAUUUGAUUACACUCUUGAUGCUGAGGUA
AB010073.1/79699-79632         UACCAAUGAUGGAUUUCAAAAUAAUCAUCAGAUCUGAU----------AUACA--UGAUUACAAUCUUGACGCUGAGGUA
#=GC SS_cons                   <<<<______________________________________.__________.._____________________>>>>
#=GC RF                        uACCAAUGAUGGAaUUCAAAAUAAUCAUCAGAUCUGAUGUGU.aaaAcAUAca..UGAUUACAAUCUUGAuGCUGAGGUa
//
# STOCKHOLM 1.0

#=GF AC   RF02409
#=GF ID   snoR125
#=GF DE   Small nucleolar RNA snoR125
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; mfold
#=GF GA   100.00
#=GF TC   183.50
#=GF NC   66.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5



AC068602.2/61774-61577                 --AAGUUGAUUAAAAAGAGAGAGGCUUUAGAGAGGAGUGUGAACAAAACUCUCAUGGCA--UGGAGAAA---AAAAACUCAAAUUGAAAUCGAAGGAGAAAUAACAUUUGAU-----AAAUGUU--UUUUUCCCCUUUUUGAUUUAGGGUUC--UUUCUUUCAUCCCAUUUCCCUCGAUGACGGUCCUUCCAAGU-UACAC--UUGAUAUGAGCCCU
ADBK01001126.1/71340-71543             GGGUGAUGAUUAAAAAGAGAGAGGCUUGAGUGGGGAGUGUGAACAAAACUCUCAUGGGA--UGAAGAAAAAAAAAAGCCCAAAUCGAAAUCGAAGGAGAAAUAACAUUUGAUU----A-AUGUUUUUUUUCCCUUUUUAUGAUUUAGGGUUC--UUUCUUUCAUCCC-UAUCCCUCGAUGACGGUCCUUCCAAGU-UACAC--UUGAUAUGAGCCCU
AFAN01000020.1/4183674-4183865         GGGCGAUGAUUAUAAAGAGAGAGGAUUGAGUGGGGAGUAUGAACA-AACUCUCAUGGGA-UUGGAGAAA----AAAACUCAAAUCGAAAUCGAAGGAGAAAA-----------UAGU------UUUUUUUUCCCUUUUUCGAUUUUGGGCACUUUUUUCUUCAUCCC-UAACCCUCGAUGAAGGUCCUUCCAAUU-CGUACACUUGAUAUGAGCCCU
AENI01003131.1/43685-43490             GGGCGAUGAUUAUAAAGAGAGAGGAUUGAGUGGGGAGUGUGAACAAAACUCUCGUGGGAAUGGAGAAAA---CUAAACUCUAAUCGAAAUCGAUGGAGAAAA--UA-----UA-------UUUUAUUUUUUCCCUUUUUCGAACUAGGUUUU-UUUUUCUUCAUCCC-UUACCCUCGAUGACGGUCCUUCCAAAUGUACAC--UUGAUAUGAGCCCU
AL132975.1/53995-54194                 GGGCGAUGAUUAAAAAGAGAGAGGCUUGAGAGGUGAGUGUGAACAAAACUCUCAUGGGA--UGGAGGAA----AAAAUUCAAAUCGAAAUCGAAGGAGAAAU-ACAUUUAAUA----AAAUGUUUUUUUUUCCCUUUUUUGAUUUAGGGUUC--UUUCUUUCAUACC-UUUCCCUCGGUGACGGUCCUUCCAAGU-UACAC--UUGAUAUGAGCCCU
#=GC SS_cons                           [[[[----[[[[[,,,,,,,((((,,<<<<<<-----<<____>>--->>>>>>,<<<-..<<<<<<<<...---<<<<<<<<<<<<<<-----<<<<<<<-.<<<<-<____....>.>>>>--->>>>>>>--->>>>>>>>>->>>>>-..>>>>>>--->>>>.>,,,)))),<<<<<<<_____>>-->>.>>>,,..]]]]]----]]]]:
#=GC RF                                GGGcGaUGauuaaAAAGAGAGaGGaUugaGaGggGAGuGUGAACaAAACuCucaUgGgA..gggggaaa...aaAagccCaaaucgaaaUCGAaGGagaaau.acauUugAUa....a.auguUuUuuuuuCCcuUuuucgauuuaGggcuc..uuucccUCAuccC.uuuCCCuCGgugacGGUCCUUCCAAgu.cacAC..uugauAUGAgCCCU
//
# STOCKHOLM 1.0

#=GF AC   RF02410
#=GF ID   snoR136
#=GF DE   Small nucleolar RNA snoR136
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; mfold
#=GF GA   43.00
#=GF TC   43.80
#=GF NC   42.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8



CT963106.2/109334-109194               GUGGCUUCAGAUUUU-GAUUUUAAUUAUGC--UUGCACCUAAUUUAUU---GU-GUUUGCA-AUGUUC-UA---UGAAGCCUAUAAU----UGUGUUCCCCUCGCUAUCCACUACUGCAAAU-CUAAUGCUGUA--UAUGGACGUCGGGGAACAAAAUUU
BABX01073478.1/2260-2117               AUGGCUUCAUGUUUU-AUGUAAGCUUACAGCUGUAUGCUAAGUUUAAU-UAGUUAAUGCUG-CUAAUU-A----UGAAGCCUAAA--AAGUUGUGUUUCCCUCGCUAUCCAGUGCUGUAAUU---AAUGCUGU---AUUGGACGUCGGGAAACUACAUUU
CACC01011386.1/29905-29765             AUGGCUUCUUUGUCU----UAAGCUUAAAACUUA--AUUUUAAUAAUUAUUUU-UGAGCUU-UUUU-U-UAUAAAGGAGCCUAAAUCG---AUCGUUCUCCUCGCUAUCCAGUGUCUCGAUU-A---UGUAGCA--UUUGGACGUUGGAGAACUAUAACU
AGQN01031781.1/5472-5330               UUGGCUUCAUUUUUUUUUUCAUUAAUUAGCAUAC--AUUAAAUUAAAU-UAAU-GUA------UGUUG-UUAAAUGAAGUCGAAUAUAAA--AUGUUCCCCUCGCUAUCCAGUGU-CUACUU-UUUAUGUUGCAU--UUGGACGUUGGGAAACUACAUCU
AFAN01000020.1/1148380-1148530         GUGGCUUUUACAUGU-UUUAAAGAUUCAUGCUUUGAAUA--AUUCAAA--UGU-GAAGCUU-GUUAUG-AAUGUAUCAGCCUACAUUAAAUUUAGUUUCCCUCGCUAUCCUGUUCGUCAAUU-ACGAUGAUGUUACUUAGGACGUCGGGGAACAAUAUUU
AENI01005026.1/20260-20109             GUGGCUUUAACAUCU-UAACUAGAAUCAUGCUUUGAAUG--AUUAACA--UGU-GAAGCAUUGUUGUG-UAUGUUUUAGCCUACAGUGAACAUAGUUCCCCUCGCUAUCCUGUUCAUCAAUU-UAAAUGAUGUUACUUAGGACGUCGGGGAACAAUAUGU
CP002686.1/17445498-17445652           GUGGCUUUUACAUGA-UAGAAAGAUUCAGGCUUUGAAUAUAUUUUAGA--UGU-GAAGCUU-GUUGUGAAGUGUAAUUGCCUACAUUGAAUUUAGUUUCCCUCGCUAUCCUGUUCUUCAAUUUUCAAUGAUGUUUCUUAGGACGUCGGGGAACAAUAUGU
ACUP01001139.1/2316-2460               AAGGCUUCU-GGUUU-AUUUAAGAUUUUUGCUUUGCACUUUUUUCAUU-GUGU-AUGGCAA--UGUUU-AAUU--GAAGCCGAUAUG----UGUGUUCCCCUCGCUAUCCGUUGUUGCAAUU-UUGAUGCUGCAU-UUUGGACGUCGGGGAACUAAAUCA
#=GC SS_cons                           <<<<<--<<<<<<--.<<-<<-----<<<<<<<<--<<<_________._>>>.>>>>>>>.>>>->>.->>>>>>-->>>->>------.---<<<<<<<-<<---<<<<<----<<<___.____>>>-----.->>>>>>>-->>>>>>>:::::::
#=GC RF                                guGGCUUcaucguuU.gaucaAgAuUccggCuucGaAcuuaaUUuAuu.uagU.gaaGccg.guguuc.uacgaugaAGCCuacAuuaAA.uuuGUUcCCCUCGCUAUCCacUgcugcaAUU.uuaAugcUGuau.UguGGACGUcGGGgAACuAuAUuU
//
# STOCKHOLM 1.0

#=GF AC   RF02411
#=GF ID   snoR138
#=GF DE   Small nucleolar RNA snoR138
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; mfold
#=GF GA   44.00
#=GF TC   44.30
#=GF NC   43.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   7



EU379009.1/172-328                   AUAGCCU-CCGAAUAACGAGAAGGUGAAAUAUAGGAA------CACCUUCUGGUUCAGACAGAGGCUUAUAUCAAA--ACUCGAAUCAGUUUUUGUGAG-UG-AAAAAGCUCUCCCCUUU-UUUG------CUCUUC--AGAUUCCAAUAUCC-UUCA-AUGG-AUAGAUUCGAAUAUCU
AENI01002408.1/123894-123737         AUAGCCU-CCGAAUAACGAGAAAGUGAAAUAUAGGAA------CACUUUCUGGUUCAGACAGAGGCUUAUAUCAAA--ACUCGAAUCA-GUUUUUGAGGGUG-AAAGAGCUUUACUCUUUUUUUG------CUCAUC--AAAUCCAU-CAUCCGUUUC-UUGG-AUAGAUUCGAAUAUCU
AFAN01000028.1/556194-556354         UUAGCCU-CCGAAUAACGAUAAAGUGAUAUAUAGGAA------CACUUUCUGGUUCAGACAGAGGCUUAUAUCAAAAAACUCGAAUCA-GAUUUGAGGG-UGAAAAAAGCUUUACUCUUU-UUUG------CCAUCCAAAUCUUCA-UUUUCC-UUUACUUGG-AUAGAUUCGAAUAUCU
ACYM01102254.1/4052-3899             UUUGCCCUCCGAAUAACCAGAAGGCGAGAUGCAA---AUCCGACGCCGUUUGGUUCAGACAGGGGCACACAGCG----AUCCGAAGCC-GUUUUGUGGG-CG-AAGAU-CUGAUUAUUUC-UUCG------UCCUUU--AUUUCAUU----UU-UUCA-AAAACUUUGCUUCGAACAUUU
AEKW01011406.1/14938-15087           CUUGCCCUUCGAAUAACCAGAAGGCGAGAUGCAAGUCC---GACGCCGUUUGGUUCAGACAGGGGCAUAUAGUG----UUUCGAAGCA-AU-CUGAGGG-U--GAUGAGCUUUCAAUUCU-UCAU------CCUC----AAUUAAGUU----U-UUUU-AUAC-UUAGCUUCGAAAAUGC
AEMH01015574.1/12700-12555           UCUGCCC-ACGAAUAACCAAUCUGUGAAACG-----A------UACCGUUUGGUUCAGACAUGGGCGCACAGCG----AUUCGAAGCC-AUCUAAGGGA-UG-ACCAA-CUCUACUAUUC-CUUGUGUUCAUCCUUU--U--------GUUGU-UUUA-CAAC-UCCGCUUCGGACAUUU
AL161492.2/110463-110618             AUAGCCU-CCGAAUAACGGGAAUGUGAAAUAUAGGAA------CACCUUCUUGUUCAGACAGAGGCUUAUAUCAAA--AUCCGAAUCA-GUUUUGGGUG-UG-AAAAAGCUCUCUCCUUU-UUUG------CCCUUC--AAUUCCAAAUAUCC-UUCA-AUGG-AUAGAUUCGAAUAUCU
#=GC SS_cons                         ::<<<<<.<-----<<<<<<<<-<<<___________......>>>->>>>>>>>------>>>>>>-------....---((((((,.<<<--<<<-<.--.<<<<<<_______>>>>.>>--......>>>>--..>>>,,,,,,<<<<<.____.__>>.>>>)))))):::::::
#=GC RF                              uUcGCCc.cCGAAUAACcagaaaGuGAaAUauAgGaA......CaCcuucugGUUCAGACAggGGCguAuAuCa....AuUCGAAgCa.guuUUggGgG.UG.aagaaGCUuUacuCuuc.uuuG......CCccUu..aacUuaauuugucc.UUua.augg.acaGcUUCGAAuAUuU
//
# STOCKHOLM 1.0

#=GF AC   RF02412
#=GF ID   snoR144
#=GF DE   Small nucleolar RNA snoR144
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; mfold
#=GF GA   100.00
#=GF TC   140.80
#=GF NC   43.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   4



AFAN01000032.1/11034289-11034145         AAGGCAACUUUUUGCCGAGUGAAUCGAACAUCGAUCUCUCUCUUUUUCCCAGUUGCCAAAAUC-AUGUAA-UGGCCGCGUGAGGA--AUACGUUGAUCGGUUAUGUAAUUUCUAAUGUAACCGAUCUUUUAUUCUUUGCUGCUAAAUAU
ADBK01001148.1/251947-252094             UAGGCAACUUUUUGCCGAGUGAAUCGAACAUCGAUAUCUCUCUUUUUCCCAGUUGCCUAAAUCCAUGUAAUUGGCUGCGUGAGGAAUUU-UUUUGAUCUGUUAUUUAAUUCUCGAUAUAACCGAUCUUUUCCUCUUUGCUGCUACAUUU
AENI01001182.1/87183-87325               AAGGCAACUUUUUGCCGAGUGAAUCGAAUAUCGAUAUCUCUCUUUUUCCCAGUUGCCUAAAUC-AUCUUA-UGGCUGUGUGAAGA--AUACUUUGAACGGUUAUGUAUUUUUCUAAAUAACCGAUCUUUUCUUC--UGCUGCUACAUUU
AL161746.2/30547-30404                   AAGGCAACUUUUUGCCGAGUGAAUCGAACAUCGAUCUCUCUCUUUUUCCCAGUUGCCCAAAUC-AUGUAA-UGGCUGCGUGAGGA--UU-UUUUGAUUGGUUAUUCAAUCUUUUAUAUAACCUAUCUUUUCCUCUUUGCUGCUACAUAA
#=GC SS_cons                             ::<<<<<<<-------<<<-<<<<<<_____>>>>->>->>>-------->>>>>>>------.<<<<<-.-<<<-----<<<<<..--.----<<<-<<<<<<--<<____>>-->>>>>>->>>--->>>>>--->>>-->>>>>::
#=GC RF                                  aAGGCaaCuUUUUGCCGaGUGaauCGAAcAUCGauauCUCuCUUUUUCCCaGuuGCCuAAAUC.auguaA.UgGCuGcGUGagga..aU.uuUUGaucgGuuauuuagUuuucuAuauaaCcgauCUUUuccuCUUUGCuGCuacauuu
//
# STOCKHOLM 1.0

#=GF AC   RF02413
#=GF ID   snoR145
#=GF DE   Small nucleolar RNA snoR145
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; mfold
#=GF GA   57.00
#=GF TC   60.10
#=GF NC   52.90
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19357091
#=GF RT   Mining small RNA sequencing data: a new approach to identify small
#=GF RT   nucleolar RNAs in Arabidopsis.
#=GF RA   Chen HM, Wu SH
#=GF RL   Nucleic Acids Res. 2009;37:e69.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   19



AFSP01066114.1/1322-1172             AUGCGAAGG-UCCCAGCAGGGAGGC-GAGU-U--ACUC-UUAUUGUUGAGGCCUCUCUAACA---AU--GAAAUUUGAU-ACCCUUCGCAGAGUUAU---UUGCCGAAUC-GUAAGAUGUCCAGAU------UUUUC---AUUUUUG-GUG-CAUCUGGAACCCUCGGCUAUAUUUUA
AASG02003814.1/14641-14787           AAGCGAAGG-UCCCAGCAGGGAGGC-AGGA-----CUC-UG-AA-UUGAGGCCUCUCUAACAACAAU---AGAAAUUA----CCUUCGCAGAUUAAU---CUGCCGAAUC-GUAGGAUGCCCUGAA-----U-UUUCC-AUUUUUGU-G-G-CGUCCGGAACCCUCGGCUAUAUCUUU
ACYM01129633.1/2287-2137             AAGCGAAGG-UCCCAGCGGAGGGGC-AAGC-C--ACUC-AGA-A-AUGAGGCCUCUCUAACAU-UAU---UCAAUAAAA-AACCUUCGCAGAGUUAC---UUGCCAAAUC-GUACGGCGUCCAGAAA----U-CUUUC--ACUUCUG-A-G-CGUCUUGAACCCUUGGCUACAUUUUU
AEKV01000424.1/18275-18422           AUGCGAAGG-UCCCAGCGGAGGGGC-AAGC-U--ACUC-AGA-A-AUGAGGCCUCUCUAACAU-UAU---CAAUUAAA----CCUUCGCAAACUCAC-----GCCAAAUC-GUACGACGCCCAGAUUU--CU-C--UUUCACUUCUG-U-G-CGUCUUGAACCCUUGGCUACAUUUCU
AARH01006065.1/328881-329029         AUGCGAAGG-UCCCAGCAGAGGGGU-AAGG-A--ACUC-UAUAAAUUGAGGCCCCUCUAACA---AU--CAUAA-AAAU--UCCUUCGCAGAUUAAU---UUGCCGAAUC-GUAGGAUGCCCUGAA-----UUUCUC---AUGACGG-G-C-CGUCUUGAACCCUCGGCUAAAUAUCA
CACC01003539.1/16225-16075           UGGCGAAGG-UCCCAGCAGGGAGGU-GAGU----GCUCUAUGAU-UUGAGACUUCUCUAACG---AU---GAAACAAAAAUGCCUUCGCAAAUGAAUU--UAGCCGAAUC-GUAGGAUGCCCAAUUA----GUCCA-----UUUUUG-GAG-CGUCUGGAACCCUCGGCAACAUCCAA
AFSA01099187.1/1765-1617             UAUCGAAGG-UCCCAGCAGGGAGGUUGA-UUU--ACUC-UUA---ACGAGUCCUCUCUAACA--CAU---UUUAAUUA----CCUUCGAAGAUAUAUU--UUGCCGAAUC-GUAGGAUGCUCUAAA-----GUUUUCC--AUUUUAG-U-GAUGUCUUGAAAUCUCGGCUAUAAUCUA
ABIM01003718.1/16615-16465           GAGCGAAGU-UCCCAGCAGAGGGGU-GAAAAU--GCUC-UGGAA-UUGAGGCCCCUCUAACA---AU---AAUCCAAAA-CUACUUCGCAGAGUAAU---CUGCCGAAUC-GUAGGAUGCCCAUUAC---UA-UCUA----UUUUUG-GAG-CAUCUGGAACCCUCGGCUAAAUUUAU
ACYN01000498.1/25079-25227           GAGCGAAGG-UCCCAGCAGAGGG---GAGGAU-AACUC-UGAGA-UUGAGACCCCUCUAACU---UU---UAAUUAAA---UCCUUCGCAGAUUUAG---CUGCCGAAUC-GUAGGACGCCCAAAUC---GU-UAUU---AGUUUUG-GAU-CGUCUUGAACCCUCGGCAACAUUCGU
AEMH01013253.1/19512-19661           AUGCGAAGG-UCCCAGC-GGAGGGC-AAGC-U--GCUC-UUUAA-UUGAGGCCUCUCUAACA---UUU-GAAAACAAA----CCUUCGCAGAAUCAC---UUGCCAAAUC-GUACUACUCUCAGAGUUCUGUU---UC--UUUUCUG-A-G-UGUCUUGAACCCUUGGCUACAUUUUU
AGFK01039246.1/1863-1713             AUGCGAAGGUACCCAGCGGAGA----GGGUAAAAACUC-UUGA--ACGAGACCUCUCUAACA---CU---AUAAACAAU--ACCUUCGCAGAUUUAACAUUUGCCGAAUC-GUAGGAAGCUCCAUA-----U-UUUCC--AUUAUGG-U-G-CUUCUUGAACCCUUGGCUAAAUUUGU
AGQN01250368.1/1005-857              CAGCGAAGG-UCCCAGCGGAG-----GGGUAUGGACUC-UUUAA-UUGAGGCCUCUCUAACA--CAUAAAACAUUAAA----CCUUCGUAGAUUCAU---GAGCCGAAUC-GUAGGAUGCCCGGAA-----UUUCUG----UUUCUG-GAA-CAUCUUGAACCCUCGGCUAAAUUUCA
BABX01005872.1/9499-9647             AUGCGAAGG-UCCCAGCAGAGAGGC-AAGG----ACUC-U-GAA-UUGAGGUCUCCCUAACA---ACAGUUCAAUCAA---AUCUUCGCAAACUAAU---UUGCCGAAUC-GUAGGAUGACCAAGA-----U-UUUCC--AUUUUUGUG-G-CAUCCGGAACCCUCGGCUAUAUACGA
ADBK01000947.1/99765-99908           AAGCGAAGG-ACCCAGCAGGGAAGC-GAGUAA--ACUC-AUGAA-AUGAGGCUUCUCUAACA---AU---UUAUUUAA----CCUUCGUAGAUUGAGU--CUCCAAGAGCUCUUUGAUGAUCUAUC------UUCU------UGUGG-A-U-UGUCUUGUGU-UUUUGGUGUAUACUU
AFAN01000192.1/22210-22063           AAGCGAAGG-ACCCAGCAGGGAAGC-GAGUAU--ACUC-AUGAA-AUGAGGCUUCUCUAACA---AU---UUAAUUAA----CCUUCGUAGAUUUAGU--CUCGAGGAACUCUUUGAGGAUCUGUUU----CUUUUU----UCGCAG-A-U-UGUCUUGUGU-UCUUUGUGUAUAGUC
AC241033.1/20656-20796               AAGCGAAGG-ACCCAGCAGGGAAGC-GAGUAU--ACUC-AUGAA-AUGAGGCUUCUCUAACA---AU--UUUAUUUAA----CCUUCGUAUAUUUAGU--CUCCAAGUGAUAAUUGAUGAUCUGUU----------------AUCGG-A-U-UGUCGCGAGUU-CUUGGUGUAUAUAU
AENI01003767.1/44838-44692           GAGCGAAGG-ACCCAGCAGGGAAGC-GAGUAA-UGCUC-AUGAA-AUGAGGCUUCUCUAACA--AAU---UUAUUUAA----CCUUCGUAGAUUAAGUCUCUCCAAGAGAUCGUUGAUUAUCU-GU------UGUU------AUAGG-A-U-UGUCGUGAG-UUCUUGGUGUAAAGUU
DQ108765.1/429-573                   AAGCGAAGG-ACCCAGCAGGGAAGC-GAGUAA--ACUC-AUGAA-AUGAGGCUUCUCUAACA---AU---UUAUUUAA----CCUUCGUAGAUUGAAU--CUCCAAGAGCUCUUUGAUGAUCUACG------UUUU------CGUGG-G-U-UCUCUUGUGUUUUUUGGUGUAUAGCU
ACUP01009292.1/133174-133021         AUGCGAAGG-UCCCAGCAGGGAGGC-GAGU-U--ACUC-AUAUUGUUGAGGCCUCUCUAACA---AU--GAAAUUUAAC-ACCCUUCGCAGAGUUAU---UUGCCGAAUC-GUAAGAUGCCCAAA-U---UUUUCUUU-CAU-UUUG-GUG-CAUCUAGAACCCUCGGCUAUAUUUUU
#=GC SS_cons                         ::(((((((.,<<<____>>>,,,,.<<<---..-<<<.<<___.>>>>>---->>>,,,,,...,,...,,,,,,,,....)))))))--------...--<<<<<<<-.----<<-<<<<<<<<.....______...__>>>>>.>.>.>->>------>>>>>>>:::::::::
#=GC RF                              aagCGAAGG.uCcCAGCAGgGAgGc.GaGuAu..ACUC.augAA.auGAGGCcUCuCUAACA...AU...uuAauuAA....CCUUCGcAGAuUuAu...uUgCcgaagC.gUAgGAugccCcgaa.....uUuuUu...AUuucgG.g.g.cgUCUuGAAcccucgGcUAuAUuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02414
#=GF ID   rli60
#=GF DE   Listeria sRNA rli60
#=GF AU   Osuch I
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   INFERNAL
#=GF SS   Predicted;RNAalifold
#=GF GA   60.00
#=GF TC   66.90
#=GF NC   56.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF RN   [2]
#=GF RM   25442865
#=GF RT   The roles of noncoding RNA Rli60 in regulating the virulence of Listeria
#=GF RT   monocytogenes.
#=GF RA   Peng YL, Meng QL, Qiao J, Xie K, Chen C, Liu TL, Hu ZX, Ma Y, Cai XP, Chen
#=GF RA   CF
#=GF RL   J Microbiol Immunol Infect. 2016;49:502-508.
#=GF RN   [3]
#=GF RM   27032404
#=GF RT   The Regulatory Roles of ncRNA Rli60 in Adaptability of Listeria
#=GF RT   monocytogenes to  Environmental Stress and Biofilm Formation.
#=GF RA   Peng YL, Meng QL, Qiao J, Xie K, Chen C, Liu TL, Hu ZX, Ma Y, Cai XP, Chen
#=GF RA   CF
#=GF RL   Curr Microbiol. 2016;73:77-83.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   11



ADXK01000969.1/3567-3750           UGAUAUUCAUUGUUUUCAAAAAUGUGCGACUAAUCGAAAAUC--UA-AAACCAUUUGAUGAAGGGG---AUAAUGACUUAUGA-----------------------AAACGACUAA--------------------------AUCCGUCAUUACAAUUUUAUUA--CUCUAAAAGGACUUUGAACACUGUAGCAAA-----UUACAGUAGU--UUGAGUCCUGUUUACAUUAAAUGGGAUUCUUGCAA
AEUN01000493.1/11312-11108         GUUUAUCAAA-UUUUUAGACAA--UUCAAAUAAUUAAUACGAUAUA-AACCAUUCAAGGAAGGAGU---AUAAUA--AAAUGACUAAUCUUAA--UACGCAACAUCAACCAACAAC--------------------------AUCAAAUAUUAUUAUUUUAUUA-UACUCUUUAGGACUCGAACGUUAGUAAGAUU-----UUACUAAACGCUUUAAGUCCUAUUUCUGCUUGAAUGGGACUUAUAAA
AEQA01000019.1/43447-43653         GUUUAUCGAA-UUUUAAAACAAUUCAAACUAUUGAAACAAAU--UAUAACCAUUCAAGAAAAGAGGAGUAUAAUAAUGACUAAUCACACAU------UUCUAUAUCAACCGACAAA--------------------------UGUAAAUAUUAUUAUUUUAUUA-UACUCCAAAGGGCUGGAACUUUAGUAUCACU----UGUACUAAAUG-UUUAAGUCCUAUUUCUAAUUGAAUGGGACUUAUCAG
AFEC01000063.1/26148-26356         AGUUUAUAAA-UUUUAAAACAAUUCAAACUAUU-UAGAAUAA--AU-AACCAUUCAACGAAAGGAG--UAUAAUA----AAAUGAGACAUUAUACAACUCAACAUUCAACGACAAC--------------------------UUCAAAUAUUAUUAUUUUAUUAUACUC-UCAAGGGCUCGAACUUUAGUAAUUAUUUCAUUUACUAAAUG-UUUAAGUCCUAUUUGUAAUUGAAUGGGACUUAUUGA
AM295250.1/1574474-1574677         AUUUAUCAAA-UUUUUAGACAAU-UCAAUUUAAUGAU----A--UA-AACCAUUCGAAAGGAGAUA---AUUAAAAUGACUAACAC-----------------CAC-------A--ACUGCAAACACUCUACCGACAACAACAAAUAUUUUAGUCAUUUUAAUU--AUUUGCUAGGACUCGAACUUUAGUAAUUGUA---UCUACUAAAUG-UUUAAGUCCUAUUUCCGAUUGAAUGGGACUUUUGAA
AL591981.1/301124-301308           UGAUAUUAAUUUUUUUCAAAAAUGUGCGACUAAUCGAAAAAA-AUA-AAACCAUUUAACGAAGGAG---AUAAUGACUUAUGA-----------------------AAACGACCAA--------------------------AUCAGUCAUUACAAUUUUAUUA--CUCUAGAAGGACUUUGAGCACUGUAGAAAU-----UUACAGUAGU--UUGAGUCCUGUUUACGUUAAAUGGGAUUCUAGCAA
AADR01000028.1/13813-13996         UGAUAUUAAUUUUUUUCAAAAAUGUGCGACUAAUCGAAAAAA--UA-AAACCAUUUAACGAAGGGG---AUAAUGACUUAUGA-----------------------AAACGACCAA--------------------------AUCAGUCAUUACAAUUUUAUUA--CUCUAGAAGGACUUUGAGCACUGUAGAAAU-----UUACAGUAGU--UUGAGUCCUGUUUACGUUAAAUGGGAUUCUAGCAA
AADQ01000028.1/19200-19383         UGAUAUUAAUUUUUUUCAAAAAUGUGCGACUAAUCGAAAAAA--UA-AAACCAUUUAACGAAGGAG---AUAAUGACUUAUGA-----------------------AAACGACCAA--------------------------AUCAGUCAUUACAAUUUUAUUA--CUCUAGAAGGACUUUGAGCACUGUAGAAAU-----UUACAGUAGU--UUGAGUCCUGUUUACGUUAAAUGGGAUUCUAGCAA
AM263198.1/2028266-2028448         UGAUAUUAAU-UUUUUCAAAAAUGUGCGACUAAUCGGAAAUC--UA-AAACCAUUUAACGAAGGGG---AUAAUGACUUAUGA-----------------------AAACGACCAA--------------------------AUCAGUCAUUACAAUUUUAUUA--CUCUAGAAGGACUUUGAGCGCUGUAGAAAU-----UUACAGUAGU--UUGAGUCCUGUUUACGUUAAAUGGGAUUCUAGCAA
CP000046.1/2100785-2100964         AACUAUUAAA-GUGAUAUAUACCAUUCACGGAAGGAGUAUAA--UA-AAAUGCUUAAUCAAU-------AUACUG----AACAU---------------------CAACCGACAAC--------------------------UUCAAAUAUUAUUAUUUUAUUA-UACUCUUUAGGACUCGAACGUUAGUAAAUAU-----UUACUAAACGCUUUAAGUCCUAUUUCUGUUUGAAUGGGACUUGUAAA
AP006716.1/989644-989451           GUUUAUCGAA-UUUUUAAACAAUUCUAACUAUUCUAAUAUAA--C-----CAUUCAAGGAAGGAGUA-UAUUAAAAUGACAAAUCAA---------------ACAUAUAACCCAAC--------------------------UGACAAUUUAAUUAUUUUAUUA-UACUCGCAAGGGCUGGAACUUUAGUAAUUAUC--UGUUACUAAAUG-UUUAAGUCCUAUUUCUCAUUGAAUGGGACUUAUAGA
#=GC SS_cons                       ::::::::::.:::::::::::::(((---------------..--.---((((((((((,,<<<<...-<<<<<<<<-<<_____................._____________..........................>>->>>>>>>>-----------.->>>>,,,<<<<<-<--<<<<<<<<<<____.....>>>>>>>->>.->-->>>>>>,,,,,))))))))))-------))):
#=GC RF                            auuUAUuAAa.UUUUUAaAcAAUuugcAauuaauuAaaAaaA..UA.AAaCauUcaAacgAAgggg...AuaAugacuaauaAuaa.................aucAAaCgACaAa..........................aucagucaUuaUuAUUUUAUUA.uccccauaAGGaCUugAAccuuaGUAguaaU.....cUACuaaAgg.UUUAaGuCCUAUUUccguUugAauGGGacUUagcaA
//
# STOCKHOLM 1.0

#=GF AC   RF02415
#=GF ID   rliG
#=GF DE   Listeria sRNA rliG
#=GF AU   Osuch I
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   55.00
#=GF TC   55.60
#=GF NC   54.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.42 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19448609
#=GF RT   The Listeria transcriptional landscape from saprophytism to virulence.
#=GF RA   Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H,
#=GF RA   Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy
#=GF RA   M, Vergassola M, Nahori MA, Soubigou G, Regnault B, Coppee JY, Lecuit M,
#=GF RA   Johansson J, Cossart P
#=GF RL   Nature. 2009;459:950-956.
#=GF WK   Listeria_monocytogenes_non-coding_RNA
#=GF SQ   5


AL591982.1/286992-286715     AGUGAGAAGUGAAGAUGAUUACAAAAAUAAAAUCUUAUAUUGAGUCUGCGCUCCACUUCUCAUUUAUAAUCUUAUGAUGAUAUAGCAGGAGAUUGCUAUGUUGCCCGGCAGAGGCUUUGUAUCUGGGCACUAGUCUCAA--CAGAUGACGACACUUCUGUUCAAU-CUCAUAUCCUAUCCAUACUGGAUGUAAAACACGCAUGUGGCGCUGACUGGUGCGUUAAC-----------CAGUUUUUUAAAUAUAUAGCCCUUUCCAUCUGUUGAAAAUUGAGCAGGUGGUUUUU
AL596163.1/92283-92561       AUUGAAUUAGCAACAACACU-UGGGAUUGAAGUGCUAAAUUGAAAAUGG----CACUUUUC---UGGCACUUUUUGAGCAAAAAAAGGU-GAUAAA-AUGUUAUUAGUGAGAAG---UGAAGAUGAUUACAAAAAUAAAAUCUUAUAUUGAGUCUGCGCUCCACUUCUCAUUAAGUAUUAAAAGUGAUUUGUUAAAUCUUGAGCAAUAUUUUUAUGUUUGUUAAAAUAAAAGCGAACAAAAAUAAAAAUAUUGGAGGGAUUUUAAUGAAUGAAAAAGAAAAAAUUGAUUUUG
AARJ02000004.1/58925-59191   AUUGAACUAGCGACAACACU-UGGGAUUGAAGUGUUAAAUUGAAAAUGG----CACUUUUC---UGGCACUUUUUGAGUAAAAAAAGGU-GAUAAA-AUGUUAUUAGUGAGAAG---UGAAGAUGAUUACAAAAAUAAA-UCUUAUAUUGAGUCUGCGCUCCACUUCUCAUAUCCUAUCCACACUGGAUGUAAAACACGCAUGUGGCGCUGACUGGUGCGUUAAC-----------CAGUUUUUUAAAUAUAUAGCCCUUUCCAUCUGUUGAAAAUUGAGCAGGUGGUUUUU
AARI02000041.1/1397-1140     ---------GCGACUACUUU-AGGAAUUGAAGUGUUAAAUUGAAAAUGG----CACUUUUC---UGGCACUUUUUGAGUAAAAAAAGGU-GAUAAA-AUGUUAUUAGUGAGAAG---UGAAGAUGAUUACAAAAAUAAA-UCUUAUAUUGAGUCUGCGCUCCACUUCUCAUAUCCUAUCCACACUGGAUGUAAAACACGCAUGUGGCGCUGACUGGUGCGUUAAC-----------CAGUUUUUUAAAUAUAUAGCCCUUUCCAUCUGUUGAAAAUUGAGCAGGUGGUUUUU
AARU02000002.1/514619-514367 AGAAAAAAUACAACAACAAA-UCGACG-GAAGUU-UG--UUCUGCAUGG----CAAUUUAG---U--AAUUUUU-GCCG-CACACCUGC-CA-------CCUAUAUAUGAGAAG---UGAAGAUGAUUACAAAAAUAAA-UCAUAUAUUGAGUCUGCGCUCCACUUCUCAUAUCCUAUCUGCACUGGAUGUAAAACACGCAUGCGGCGCUGACUGGUGCGUUAAC-----------CAGUUUUUUAAAUAUAUAGCCCUUUCCAUCUGUUGAAAAUUGAGCAGCUGGUUUUU
#=GC SS_cons                 ::::::::::::::::::::.:::::::<<<<<<<<<----<<<<<<<_....>>->>>>>...>>>>>>>>>,,,,,,,,,,,,,,,,.,,,,,,.,,,,,,,,,((((((((...,,,,,,,,,,,,,,,<<<<<__.___>>>->><<<<____>>>>,,)))))))),,,,,,,,,,,((((,<<<<_______>>>>,<<<<<<________>>>>>>,,...........)))),,,,,,,,,,,,,,,,,,,,,<<<<<<<<<________>>>>>>>>>:::::
#=GC RF                      AuUGAAaaagcAAcAAcAuU.ugGaAuUgAagUgcuaaAUUGagaaUGg....CAcuucuC...uggcAcuUuuUGAguAaAaAaagGu.GAUaaa.AUGUUAUuaguGAGaaG...UGAAgAUGAuUACAAaaaUaAA.UCuuAuAuuGAguCUgCgcUCCACuuCUCauAuccUAUccAuacUGGauguAAAAcACgcauGuggcGcUgAcugGUgCguuaAc...........CAguuuUuuAAAUAUAuAGcccuUUccAccuguUGAAAAuuGAgcaggUggUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02416
#=GF ID   TCV_H4
#=GF DE   Turnip crinkle virus 3'UTR
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:19656866
#=GF GA   50.00
#=GF TC   57.10
#=GF NC   36.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19656866
#=GF RT   The 3' end of Turnip crinkle virus contains a highly interactive structure
#=GF RT   including a translational enhancer that is disrupted by binding to the
#=GF RT   RNA-dependent RNA polymerase.
#=GF RA   Yuan X, Shi K, Meskauskas A, Simon AE
#=GF RL   RNA. 2009;15:1849-1864.
#=GF WK   Turnip_crinkle_virus_(TCV)_hairpin_H4
#=GF SQ   2


AY312063.1/3856-3905 AGAAAACAAAAACCCCCAGGUCGCUU-UAUUUUGACCUGUGUUAGGGACCA
L16015.1/3846-3896   AACACAAAAAUACCCCCAGCUCGCUUUUGUUUUGAGCUGUGUUAGGGACCA
#=GC SS_cons         ::::::::::::<<<-<<<<<<___________>>>>>>----->>>::::
#=GC RF              AaaAaAaAAAuACCCCCAGgUCGCUUUUaUUUUGAcCUGUGUUAGGGACCA
//
# STOCKHOLM 1.0

#=GF AC   RF02417
#=GF ID   VR-RNA
#=GF DE   VR-RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   100.00
#=GF TC   396.20
#=GF NC   46.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19835966
#=GF RT   Identification of a two-component VirR/VirS regulon in Clostridium
#=GF RT   perfringens.
#=GF RA   Ohtani K, Hirakawa H, Tashiro K, Yoshizawa S, Kuhara S, Shimizu T
#=GF RL   Anaerobe. 2010;16:258-264.
#=GF WK   VR-RNA
#=GF SQ   3


CP000246.1/1369398-1369002 GUAAUAUUUCUUAAGUAAAUAUUUAUUUUUAUUAAGCAAGGGGUGAUUUUUUUGAAACAUACAAAAAGGAUUUUAACAAGUGCAAUUUUAAUUACAUUAAUAACUCUUUUUUCUCCCUUAAUACUUAAAAAUAGCAUAGCUUUAUAUAUUGAACAAAGAGUAUCUUAUUUUACAUCUUUAGAAGUUGUUUCAAGUAUUAUAAGUCCCAUACUUGCUUUAAUAUCAAUAUUUUCAAUUGCAUAUUCCAUAAUUGUAAUUAAAAAUAAAUAAUUACUUAUUAAUGAUUUUACUUUAAUUUAGUAAAAAACCUUACAUAAAAUUACCACCAUAACUAUUGAUCCUAGAAAUAGAACUGUCCACUCUAUUUUUAGGAUUUUUAUUUUUUUCUUCUUUAUGU
AB004104.1/755-1151        GUAAUAUUUCUUAAGUAAAUAUUUAUUUUUAUUAAGCAAGGGGUGAUUUUUUUGAAACAUACAAAAAGGAUUUUAACAAGUGCAAUUUUAAUUACAUUAAUAACUCUUUUUUCUCCCUUAAUACUUAAAAAUAGCAUAGCUUUAUAUAUUGAACAAAGAGUAUCUUAUUUUACAUCUUUAGAAGUUGUUUCAAAUAUUAUAAGUCCCAUACUUGCUUUAAUAUCAAUAUUUUCAAUUGCAUAUUCCAUAAUUGUAAUUAAAAAUAAAUAAUUACUUAUUAAUGAUUUUACUUUAAUUUAGUAAAAAACCUUACAUAAAAUUACCACCAUAACUAUUGAUCCUAGAAAUAGAACUGUCCACUCUAUUUUUAGGAUUUUUAUUUUUUUCUUCUUUAUGU
CP000312.1/1171261-1170868 GUAAUAUUUCUUAAGUAAAUAUUUAUUUUUAUUAAGCAAGGGGUGAUU-UUUUGAAACAUACAAAAAAGAUUUUAACAAGUGCAAUUUUAAUUACGUUAAUAGCUCUUUUUUCUCCCUUAAUACUUAAAAAUAGCAUAGCUUUAUAUAUUGAACAAAGAGUAUAUUAUUUUAUAUCUUUAGAGGUUGUUUCAAAUAUUAUAAACCCCAUACUUGCUUUAAUAUCAAUAUUUUCAAUUGCAUAUUCCAUAAUUGUAAUUAAAAAUAAAUAAUUACUUAUUAAUAAUUUUACUUUAAUUUAGUAAAA-ACCUUACAUAAAAUUACCACCAUAACUAUUGAUCCUAAAAAUAGAACUGUCCACUCUAUUUUUAGGAUUUUUAUUU-UUUCUUCUUUAUGU
#=GC SS_cons               ::::[[[[---[[[[[[[-[[[[[[[[[[[[,,((((((((((--((---(((((((((------((((((,,,,,,,<<<<-<<<____>>>->>>>,,,,<<<<<<<-<<<-----<<<--<<____________>>-->>>------>>>->>>>>>>,,,,,,,,,,,,))))))------)))))))))----))----)))---))))))),,,,,,,,,,,,,,,,,<<<<<<___________>>>>>>]]]]]]]]]]]]-]]]]]]]--]]]],<<<<<<<_______>>>>>>>,,,,,,<<<<<<<-----------<<-<<--<<<<<<<<<<<<<<<_________>>>>>>>>>>>>>>>-->>->>-------->>>>>>>
#=GC RF                    GUAAcauuUCUuaaGuaaAuauuuauuuuuaUUaaGCaaGGGGUGauUUUuuuGaaaCaUACAAAaagGauUUUAACAaguGCaauUUUAauuACauuAAUAaCuCuuuUuuCUCCCUuaaUACuUAAAAAUAGCAUaGCUuuaUAUAUUGaaCaaaGaGuAUcUUAUUUUAcauCcuuAGAaGUuGuuuCaaaUAUUauAAguCCCAUACuuGCuuUAAUAUCAAUAUUUUCAauugCaUAUUCCAUAAUuGuaauuaaaaauaaauaAuuaCuuaUUaaugAuuuuaCuUUAAUUUaGuaaaaAACCUUaCauaaaAUUACCACCAUaaCuaUUgauCCuagaaauaGaACUGUCCACuCuauuucuaGGauuUUuaUuuUUUUCUUCuuuauGu
//
# STOCKHOLM 1.0

#=GF AC   RF02418
#=GF ID   Spd-sr07
#=GF DE   Streptococcus sRNA Spd-sr07
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   55.00
#=GF TC   61.60
#=GF NC   42.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19854910
#=GF RT   Identification and characterization of noncoding small RNAs in
#=GF RT   Streptococcus pneumoniae serotype 2 strain D39.
#=GF RA   Tsui HC, Mukherjee D, Ray VA, Sham LT, Feig AL, Winkler ME
#=GF RL   J Bacteriol. 2010;192:264-279.
#=GF WK   Streptococcus_sRNA
#=GF SQ   3


CP000936.1/940677-940739 UACAGAAGAUUUGGAAUAAGCAAAA-AGCUUUAAAUCAAUAGUCUAAACUGCUUGAUUUAAAGC
CP002121.1/897968-898031 UACAGAAGAUUUGGAAUAAGCAAAAAAGCUUUAAAUCAAUAGUCUAAACUGCUUGAUUUAAAGC
CP000920.1/841930-841992 UACAGAAGAUUUGGAAUAAGCAAAA-AUCUUUAAAUCAAUAGUCUAAACUGCUUGAUUUAAAGC
#=GC SS_cons             :::::::::::::::::::::::::.:<<<<<<<<<<<<<<<<____>>>>->>>>>>>>>>>>
#=GC RF                  UACAGAAGAUUUGGAAUAAGCAAAA.AgCUUUAAAUCAAuAGUCUAAACUgCUUGAUUUAAAGc
//
# STOCKHOLM 1.0

#=GF AC   RF02419
#=GF ID   Spd-sr37
#=GF DE   Streptococcus sRNA Spd-sr37
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   45.00
#=GF TC   46.30
#=GF NC   36.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   19854910
#=GF RT   Identification and characterization of noncoding small RNAs in
#=GF RT   Streptococcus pneumoniae serotype 2 strain D39.
#=GF RA   Tsui HC, Mukherjee D, Ray VA, Sham LT, Feig AL, Winkler ME
#=GF RL   J Bacteriol. 2010;192:264-279.
#=GF WK   Streptococcus_sRNA
#=GF SQ   25



AEVE01000054.1/14045-13980             --CAAUAGAAAUGAUGGUCAAAGCUCAUGGAUGUUGCAGGCUUUUUUGUCCUGCACUUCUC-AGAGUUU
AFFN01000008.1/71751-71686             --CAAUAGUCAUGAUGGUCAAAGCUCAUGGAUGUUGCAGGCUUUUUUGUCCUGCACUUCUGGAGACUU-
CP000387.1/2362710-2362645             --CAAUACCUAUGAUGGUCAAAGCUCAUGGAUGUUGCAGGCUUUUUUGUCCUGCACUUCUAGAGAUUU-
ADME01000012.1/40416-40352             --CAAUAACUAUGAUGGUCAAAGCUCAUGGAUGUUGCAGGC-UUUUUGUCCUGCACUUCUAGAG-GUUU
AAJO01000062.1/2432-2366               --CAAUAACUAUGAUGGUCAAAGCUCAUGGAAUUUGUAAGUCUUUUUGACGUACAAUUUUCGAGAGUUU
ACRI01000041.1/35092-35157             --CAAUAGUCAUGAUGGUCAAAGCUCAUGGGAGUUGUGCGUUUUUUUG-CGUACAGUUUUCUGGAGUUU
AGLG01000120.1/16733-16668             --CAAUAAUCAUGAUGGUCAAAGCUCAUGAGAAUUGUUGGU-CUUUUGACCUACAAUUUUCGAGGGUUU
ABJK02000015.1/63198-63134             --CAAUAAUCAUGAUGGUCAAAGCUCAUGAGAAUUGUGCG--UUUUUGUCGCACAGUUUUCGAGGGUUU
AEKO01000010.1/46411-46474             --CAAUAGUCAUGAUGGUCAAAGCUCAUGGGAAUUGUGCGUU--UUUG-CGUACAGUUUUCUAGAGUUU
AP012054.1/2068650-2068586             --CAAUAAUCAUGAUGGUCAAAGCUCAUGAGAAUUGUGCGU--CUUUGCCGCACAAUUUUCGAGGGUUU
CABY01000001.1/6899-6833               --CAAUAACGAUGAUGGUCAAAGCUCAUGGGAAUUGUAAGUCUUUUUGGCUUACAGCUUUCUCAGGUUU
CP002471.1/2118862-2118797             --CAAUA-UCAUGAUGGUCAAAGCUCAUGGAGAUUGUAGGUCUUUUUGACAUACACUUUCCUCGGGUUU
AEUV02000002.1/362949-362885           --CAAUAAUCAUGAUGGUCAAAGCUCAUGAGAAUUGUGCGCCUUU-UG-CGUACAGUUUUCGAGAGUUU
AEUU02000001.1/1332386-1332321         --UAAAAACUGUGAUGGUCAAAGCUCAUGGAAAUUGUAAGCCUUUUUGU-GUACAAUUUUCGAGGGUUU
AEKN01000012.1/45137-45201             --CAAAUAUCAUGAUGGUCAAAGCUCAUGAGGAUUGUGCGUCUUU-UG-CGUACAGUUUUCGAGAGUUU
AM946015.1/1826505-1826440             --AUAUUUCGAUGAUGGUCAAAGCUCAUGGGAAUUGUAGGU-CUUUUGGCGUACAAUUUUCGAGGGUUU
AEDW01000009.1/63052-63120             AGCAAUAGAAAUGAUGGUCAAAGCUCAUGGAUGUUGCAGGCUUUUUUGCCCUGCACUCCUUACGAGUUU
AEVD01000011.1/40430-40362             AGCAAUAGAAAUGAUGGUCAAAGCUCAUGGAUGUUGCAGGUCUUUUUGUCCUGCGCUUCUUACGAGUUU
AEYY01000041.1/46473-46538             ---AAGAACUAUGAUGGUCAAAGCUCAUGGGAAUUGUAGGCUUUUUUGUCCUGCAAUUUUCGAGAGUUU
AFUT01000007.1/103744-103809           --CAAUAGUCAUGAUGGUCAAAGCUCAUGGAUGUUGUAGGC-UUUUUGUUCUGCACUUCUUACGAGUUU
AP010935.1/2078452-2078388             --CAAUAGCAAUGAUGGUCAAAGCUCAUGAAUAUUGUAGGU-UUUUUGUCCUGCAAUUUUCUAGGGUU-
CP000261.1/1828451-1828387             --CAAUCGGAAUGAUGGUCAAAGCUCAUGAAAGUUGUAGGUUUUUUUGUCCUGCAAUCUUCUAGGGU--
CP002340.1/1806432-1806367             --CAAUAGUCAUGAUGGUCAAAGCUCAUGGAUGUUGCAGGU-UUUUUGUCCUGCACUUCUUGCGAGUUU
CP002651.1/2007839-2007774             ---AAUUAUCAUGAUGGUCAAAGCUCAUGGGAAUUGUAGGCUUUUUUGUCCUGCAAUUUUCGAGAGUUU
FQ312030.1/116541-116609               AGCAAUAGAAAUGAUGGUCAAAGCUCAUGGAUGUUGCAGGCUUUUUUGUCCUGCACUUCUUUGUAGUUU
#=GC SS_cons                           ..::::::::::::::::::<<<<<<--------<<<<<<_________>>>>>>-------->>>>>>
#=GC RF                                ..CAAUAaucAUGAUGGUCAAAGCuCAUGGaaaUUGcagGuuUUUUUGuCcugCAaUUUUcgaGaGUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02420
#=GF ID   Bp1_162
#=GF DE   Burkholderia sRNA Bp1_Cand612_SIPHT
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   50.00
#=GF TC   50.30
#=GF NC   36.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23282220
#=GF RT   Computational discovery and RT-PCR validation of novel Burkholderia
#=GF RT   conserved and Burkholderia pseudomallei unique sRNAs.
#=GF RA   Khoo JS, Chai SF, Mohamed R, Nathan S, Firdaus-Raih M
#=GF RL   BMC Genomics. 2012;13:S13.
#=GF WK   Bacterial_small_RNA
#=GF SQ   11



CP000614.1/1571480-1571382          AAAAAAAAUGGGCG---GAACGCCCAUCUUCUCUUA-CUGGUGGUCGCACCU-GAGCCGCACAUUGA-----AU-CCGUACGCCCAGCGACUCCGCGAUUAUAGCGUUUU
CP003087.1/1843500-1843596          AAAAAAAAUGGGCG---CAACGCCCAUCUUUUUCAA--CCGAGAUCGCACUC-AGGGCAGAAAGAAA-----A--CUACGUGCCCAGCGACUUCAUGAUUUUAGCCAUUU
CP000570.1/1711991-1711895          AAAAAAAAUGGGCG---CAACGCCCAUCUUGUUACC---GGUGGUCGCACCU-GAGCUACACAUCGA-----AU-CCGUACGCCCAGCGACUCCGCGAUUAUAGCGAUUU
CP001043.1/1976666-1976764          AAAAAAAAUGGGCG---AAACGCCCAUCAUCUUAUUGCCGGUGGUCGCACCU-GAGCCGCACAUAAA-----A--CCGCACGCCCAGCGACUUUGUGAUUGUAGCCAUUU
CP001503.2/2197502-2197600          AAAAAAAAUGGGCG---AAACGCCCAUCUUCUCACUCCGG-UGGUCGCACCU-GAGCCGCACAAAAA-----AC-CUGUACGACCAGCGACUCAGCGAUUAUAGCGUUUU
CP001052.1/1837653-1837553          AAAAAAAAUGGGCU---AAACGCCCAUCAUCUUAUUACCGGUGGUCGCACCU-GAGCCGCACAUAAA-----AAGCCGCACGCCCAGCGACUCCGCGAUUGUAGCCAUUU
CP002013.1/1325353-1325255          AAAAAAAAUGGGCU---GAACGCCCAUCAUCUUAUUGCCGGUGGUCGCACCU-GAGCCGCACAUGAA-----A--CCGUACGCCCAGCGACUUCGCGAUUGUAGCCAUUU
CP002599.1/2026023-2025925          AAAAAAAAUGGGCG---AAACGCCCAUCUUCUUACUCUGG-UGGUCGCAUCU-AGGCCGCACAUUAA-----AC-CCGUACGCCCAGCGACUUUGCGAUUAUAGCGUUUU
AACY020561249.1/38944-38848         AAAAAAAAUGGGCG---GAACGCCCAUCUUCUUACU---GGUGGUCGCACCU-GAGCCGCACAUUGA-----AU-CCGUACGCCCAGCGACUCCGCGAUUAUAGCGAUUU
FR687359.1/1319378-1319269          AAAAAAAAUGGGCGCCAACACGCCCAUCUUCUUUUUACCGGUGGUCGCGCCUCGAGCCGCACCUUAACUAAUAAGACGUGUGCCCAGCGACUGCGAAAUUAUAGCGUUUU
AEXE01000781.1/318-220              AAAAAAAAUGGGCG---CAACGCCCAUCUUCCCUUACUGCCUGGUCGCACCU-GAGCCGCACAU-AA-----AU-CCGUACGCCCAGCGACUUUGUGAUUAUAGCGUUUU
#=GC SS_cons                        :::::::<<<<<<<...___>>>>>>>--------------<<<<<<<----.<<<-<<<_______.....__.___________>>>->>>->>>>>>>:::::::::
#=GC RF                             AAAAAAAAUGGGCG...aAACGCCCAUCuUcUUauuaccgGuggUCgCACCU.gaGcCGCAcAuuAA.....Au.ccGuacGCCCAGCGACuccGcGAuuaUAGCgaUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02421
#=GF ID   Bp1_684
#=GF DE   Burkholderia sRNA Bp1_Cand684_SIPHT
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   44.00
#=GF TC   44.30
#=GF NC   43.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23282220
#=GF RT   Computational discovery and RT-PCR validation of novel Burkholderia
#=GF RT   conserved and Burkholderia pseudomallei unique sRNAs.
#=GF RA   Khoo JS, Chai SF, Mohamed R, Nathan S, Firdaus-Raih M
#=GF RL   BMC Genomics. 2012;13:S13.
#=GF WK   Bacterial_small_RNA
#=GF SQ   14


CP000124.1/3038708-3038821    AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCUGAUAGACCGUUAGCGCAACAGGUUCAACGACGAAG-CGCGGA---UCACCGACAAAAAACCCACGCCCCCGCGAGCCACUCC
ABBP01000489.1/4627-4740      AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCUAAUGGACCGUUAGCACAGCAGGUUCAACGACGAGG-CGCGGA---UCACCGACAAAAAACCCACGUCCCCGCGAGCCACUCC
AACY020561174.1/104990-104877 AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCUAAUAGACCGUUAGCAAAACAGGUUCAACGACAGAG-CGUGGA---UAACAAACAAAAAACCCACGCCCCCGCGAGCCACUCC
AAKX01000083.1/18365-18253    AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCUAAUAGACCGUUAGCGCAACAGGUUCAACGACAGGG-CGAGGA---UCACAGACAUCGACCCCACGCCCCCGCGAGCCACUC-
CP000440.1/2385521-2385633    AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCCAGCAGACCGUUAGCGAAACAGGUUCAACGACGAGG-CAUGGA---UGACCGACAUAAACCCCACGCCCCCGCGAGCCCCUC-
ABBH01000593.1/1093-981       AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCUAAUAGACCGUUGGCAAAACAGGUUCAACGACGGGG-CAUGGC---GAACCGACAAACAACCCACGCCCCCGCGAGCCACUC-
CP000958.1/2394810-2394924    AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCUAAUAGACCGUUAGCGCAACAGGUUCAACGACAAGG-CGUGGACAAAAACCGAACAGAAACCCACGCCCCCGCGAGCCCCA--
AM747720.1/2436126-2436237    AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCUAGCAGACCGUUAGCGCAACAGGUUCAACGA-AAGGGCGUAGA---GAACCAAAAACAAACCCACGCCCCCGCGAGCCACC--
ABLC01000329.1/4562-4673      AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCCAGCAGACCGUUAGCGAAACAGGUUCAACGACAGGG-CGAGGC---GGACCGACAA-AAAACCACGCCCCCGCGAGCCCCUC-
ABLK01000167.1/1038-928       AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCCAGCAGACCGUUAUGAAAGCAAGUUCAACGACGAGG-CGUGGA---UGACCGACAGAAACCCCACGCCCCCGCGAGCCUC---
ABBE01000425.1/1089-979       AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCAUGCAGACCGUCAGGAAAGCAAGUUCAACGACGAGG-CGCGGA---UAACCGACAGAAAACCCGCGCCCCCGCGAGAAAC---
CP000458.1/2368976-2369089    AGAAAAGUAACCGCCGCCCCGCGCAGGGGCGACGCUGGCAGACCGUUGGCAAAACAGGUUCAACGACAAGGGCGUGGA---GAACCAAAAACAAACCCACGCCCCCGCGAGCCCCUC-
AEXE01002472.1/423-535        AGAAAAGUAACCGCCGCCCCGCGCAGGGGCGACACCAAUAGACCGUCAAGCCAACCAGUUCAACGACGGAG-CGCGGA---UCACCGACUCCAAACCCGCGCCCCUGCGAGCCCCUC-
CP000615.1/2377875-2377986    AGAAAAGUGACCGCCGCCCCGCGCAGGGGCGACGCUAGCAGACCGUAUGCAAAACAGGUUCAACGACAGUA-AGAGGC---GCACCGACAA-AAACCCACGCCCCCGCGAGCCCCUC-
#=GC SS_cons                  ::::::::::((((<<<<<<_____>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,<<<____>>>,,,,.,))))-...------------------<<<____>>>::::::::.
#=GC RF                       AGAAAAGUGACCgCCGCCCCGCGCAGGGGCGACGCuAauAGACCGUuAGcaaAACAgGuuCAACgaCaagG.CGcGGA...uaACcGAcAaaAAACCCACGCCCCCGCGAGCCaCuC.
//
# STOCKHOLM 1.0

#=GF AC   RF02422
#=GF ID   Bp1_738
#=GF DE   Burkholderia sRNA Bp1_Cand738_SIPHT
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   45.00
#=GF TC   47.10
#=GF NC   35.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23282220
#=GF RT   Computational discovery and RT-PCR validation of novel Burkholderia
#=GF RT   conserved and Burkholderia pseudomallei unique sRNAs.
#=GF RA   Khoo JS, Chai SF, Mohamed R, Nathan S, Firdaus-Raih M
#=GF RL   BMC Genomics. 2012;13:S13.
#=GF WK   Bacterial_small_RNA
#=GF SQ   21


CP001408.1/3106014-3106222   CAAAAAACCAGCGUCGACUGGGCGCUGGCGAGG-ACGACAUAC--AAACCGUCAGA--AGGCCGUGCAGGU-AUCGGCGGACGGCGACGCGA-UGCGUCUAUAGGGCCGGGGAUUAAUGGUUCAAC--UACUGGGGCCUGCAACCAAUGUGAGCGGAUUCUAG--CAGGGUUUUAUAGAUCGUCAACACUAUAGAAAUUCGUUUCUAUAACAAAAAGUAA
ABBM01000471.1/12437-12645   CAAAAAACCAGCGUCGACUGGGCGCUGACUAGG-ACAACAAAC--AGACCGUCAGA--AGGCCGUGCAGGU-AUCGGCGGACGGCGACGCGC-UGCGUCUAUAGGGCCGGGGAUUGAUGGUUCAAC--UACAGGGGCCUGCAACCAAUGUGAGCGGAUUCUAG--CAGGGUUUUAUAGAUCGUCAACACUAUAGAAAUGCAAUUUCAUAACAAAAAGUAA
CP000958.1/1012815-1012607   CAAAAAACCAGCGUCU-GGUAGCGCUGGCUAGG-ACUACGACAAAAG-CCGUCGAA-GACGCCGUGCAGGG-UUCGGCGGACGGUGACGCGC-UGCGUCAAA-G-AUCGGUGAUUGGUGGCUCGAA-GCCUUUUACCCUGCAACCAAUGUGAGCGGAUUCUAG--CAGGGUUUUAUAGAUCGUCAACACUAUAAAAACUCAAAUCUAUAACAAAAAGUAA
AM747720.1/3351131-3351339   CAAAAAACCAGCGUCU-GGUGGCGCUGGCUGGG-ACUACGAC-AAAGGCCGUCGAA-GACGCCGUGCAGGA-UUCGGCGGACGGUGACGCGC-UGCGUCAAA-G-AUCGGUGAUUGGCGGCUCGAA-GCCUUUUACCCUGCAACCAAUGUGAGCGGAUUCUAG--CAGGGUUUUAUAGAUCGUCAACACUAUAAAACCUCGAAAUUAUAACAAAAAGUAA
AAKY01000111.1/29638-29847   CAAAAAACCAGCGUCU-GGUGGCGCUGGCAGGG-ACUACGACUCAAGGCCGUCGAA-UACGCCGUGCAGGU-AUCGGCGGACGGUGACGCGC-UGCGUCAAA-G-AUCGGUGAUUGGCGGCUCGAA-GCCUUUUACCCUGCAACCAAUGUGAGCGGAUUCUAG--CAGGGUUUUAUAGAUCGUCAACACUACAAAACUUCAAAAUUAUAACAAAAAGUAA
AEXE01000895.1/1011-804      CAAAAAACCAGCGUCA-GGAGGCGCUGGCCGGG-ACUACGACU-AAGACCGUCGAA-UACGCCGUGCAGGU-UGCGGCGGACGGUGACGCGC-UGCGUCAAA-G-AUCGGUGAUUGGCGGCUCGAA-GCCUUU-ACCCUGCAGCCAAUGUGAGCGGAUUCUAG--CAGGGUUUUAUAGAUCGUCAACACUAUAAACCGUCAAAUCUAUAACAAAAAGUAA
ACFB01000008.1/147583-147791 CAAAAAACCAGCGUCA-GGAGGCGCUGGUCGGG-ACUACGACUCAAGACCGUCGAA-CACGCCGUGCAGGU-UUCGGCGGACGGUGACGCGC-UGCGUCAAG-G-AUCGGUGAUUGGCGGCUCGAA-GCCUUU-ACCCUGCAACCAAUGUGAGCGGAUUCUAG--CAGGGUUUUAUAGAUCGUCAACACUACAAAACCUUCAAAUUAUAACAAAAAGUAA
CP000614.1/948585-948375     CAAAAAACCAGCAUCA-GGUGGCGCUGGCCGAG-ACUACAACUAAAGACCGUCGAAAGACGCCGUGCAGGA-UUCGGCGGACGGUGACGCGC-UGCGUCGAA-G-AUCGGUGAUUGGCGGCUCGAA-GCCUUUUACCCUGCAACCAAUGUGAGCGGAUUCUAG--CAGGGUUUUAUAGAUCGUCAACACUAUAAAACCCCGAAAUUAUAACAAAAAGUAA
CP000151.1/977151-976944     -AAAAAACCAGCGUCU-GGUGGCGCUGGCCGGG-ACUACAACUCAAG-CCGUCGGA-UACGCCGUGCAGGA-UUCGGCGGACGGUGACGCGC-UGCGUCAAA-G-AUCGGUGAUUGGCGGCUCGAA-GCCUUUUACCCUGCAGCCAAUGUGAGCGGAUUCUAG--CAGGGUUUUAUAGAUCGUCAACACUAUAAAACAUUGAAAUCAUAACAAAAAGUAA
ABLC01000253.1/4948-5156     CAAAAAACCAGCGUGU-GGUAGCGCUGGCUGGG-ACUACUACAAAAG-CCGUCGAA-UACGCCGUGCAGGU-AUCGGCGGACGGUGACGCGC-UGCGUCAAA-G-AUCGGUGAUUGGCGGCUCGAA-GCCUUUUACCCUGCAGCCAAUGUGAGCGGAUUCUAG--CAGGGUUUUAUAGAUCGUCAACACUAUGAAAUCUCAAAAUUAUAACAAAAAGUAA
CP002599.1/944469-944263     CAAAAAACCAGCGUCGCGAAGGCGCUGGCUAGG-ACGACUAC----AACCGUCGAG---UGCCGUGCAGGU-CGCGGCGGACGGCGACGCGG-AGCGUCUGAGGAACCGGAGCGGACUGGCUGGCU-GCCAGGG-CCCGGCGAUCAAUGUGAGCGGAUUCUAGG-GACGGUUUUAUAGAUCGUCAACACUAUAAAGUCCCGAAAUCAUAACAAAAAGUAA
CP001503.2/849753-849551     CAAAAAACCAGCGUCGCGAAGGCGCUGGCUCGG-ACGACAAC----AACCGUCA-----UGCCGUACAGGU-CACGGCUAACGGCGACGCGA-AGCGUCUGGAAGACCGGAG---ACUGGUUGUCA-GCCAGGGGUCCGGCAAACAAUGUGAGCGGAUUCUAGG-GAGGGUUUUAUAGAUCGUCAACACUAUAAAAUCGAGAAAACAUAACAAAAAGUAA
ABBE01000379.1/5333-5124     CAAAAAACCAGCGUCA-GGAGGCGCUGGCUGUG-ACUACGACUAGAG-CCGUCGGA-CAGGCCGUGCAGGU-UUCGGCAGACGGUGACGCGC-UGCGUCAAA-GGAUCGGUGAUUGGCGGCUUGAA-GCCUUGUACCCUGCAACCAAUGUCAGCGGAUUCUAA--CAGGGUUUUAUAGAUCGUCAACACUAUAAAACAUAAAAAUCAUAACAAAAAGUAA
CP001052.1/3498696-3498902   --AAAAACCAGCGUCA-GUUGGCGCUGGCGAGG-ACAUCAAU--AAGACCGUUAGA---UACCGUGCAGGGACUCGGUAAGCGGUGACGCGU-UGCGUCUGAUGGGACCGGGGGCAGUGGUAAAAA-GGUUCACGCCCUGCAACCAAUGUGGACGGAUUCUAUG-CAGGGUUUUAUAGAUCGUCAACACUAUAGAUAGGCAAAUGUAUAACUAAUUGUA-
CP002217.1/3161626-3161832   --AAAAACCAGCGUCA-GAUGGCGCUGGCGAGG-ACAGCAAU--AAGACCGACGAA---UACCGUGCAGGGCUUCGGUAAGCGGUGACGCGU-UGCGUCUAAUGGGACCGGGGGCAGUGGUAAAA--GGUUCACGCCCUGCAACCAACGUGGACGGAUUCUAGGGCACGGUUUUAUAGAUCGUCAACACUAAAACCAGUCAAAUGUAUAACUAAUUGUA-
CP002519.1/3106541-3106747   --AAAAACCAGCGUCA-GUAGGCGCUGGCGAGG-ACUUCAAU--AAGACCGACGAA---UACCGUGCAGGGCUUCGGUAAGCGGUGACGCGU-UGCGUCAGAUGGGACCGGGGGCGGUGGUAAAA--GGUUCACGCCCUGCAACCAAUGUGGACGGAUUCUAGGGCACGGUUUUAUAGAUCGUCAACACUACAAACAGGCAAAUGUAUAACUAAUUGUA-
CP001043.1/691240-691039     --AAAAACCAGCGUCG-AAGUGCGCUGGCGAAG-ACUAC-AU--GUGACCGUCA-A---UACCGUGCAGGG--GCGGUAAG-AGCGACGCGU-UGCGUCUGAAGGACCGGAGGACGGUGGUAAAAACUAUCAAUUCCCUGCAACCGAUGUGACCGGAUUUUAU--CAGGGUUUUAUAGAUCGUCAACACUAUAAGGCCGCAAAACUAUAACCAAUUGUA-
CP002013.1/2598871-2599070   ---AAAACCAGCGUUG-AUGGACGCUGGUGAGGGACUUCAAU--AAUGCCGUUC-----UACCCUGCAGGGAAGUA--AAACGGUGACGCGU-UGCGUCUGA--GGACCGGGGGCGACGGUAAAAA-GGUUAACGCCCUGCAACCAAUGUGGACGGAUUCUAUG-CACGGUUUUAUAGAUCGUCAACACUAUAGAAUGCAAUAACUAUAACUAUUUGU--
ABYL01000023.1/53601-53401   -AAAAACUCAGCGUUA-GUGGACGCUGGUGAGGGACUUCUAU--AAGGCCGUUC-----CACCCUGCAGGGAAGUG--AAACGGUGACGCGU-UGCGUCUUA--GGACCGGGG-CGACGGUAAAAA-GGUUAACGCCCUACAACCAAUGUGGACGGAUUCUAUG-CACCGUUUUAUAGAUCGUCAACACUAUAGAAUAUUAAAACUAUAACUAUUUGU--
CAFE01000201.1/6438-6635     --AAAAACCGGCGUGU--CAAAUGCCGGCAACG-ACAACCUA---CAGCCAUGAGU---CGCCGGGCAGGA--GCGGCGCA-GGCGACGCAUGUGCGUUUGAAAGCACCUGAGGCAGAGGUAAAAA-GUUUCAAAACCUGCAAUUAAUGCCAAUGGAUUCUAG--CAGGGUUUAAUAAUCCGUCAAUGCUAUAGACUUUU--UUCAAUUACUUACAG---
CP003087.1/795789-795589     --AAAAACCGGCGUGC--AAAACGCCGGCCGUG-ACAACCAAA--CAGCCAUGAAU---CGCCGGGCAGGA--GCGGCGCA-GGCGACGCAUGUGCGUCCGAA-GAACCUGAGGCUAAGGUAAAAA-GUUUAAGAACCUGCAGUCAAUGCCAAGCGAUUCUAC--CAGCGUUUAAUGAUCCGUCAAUGCUAAAGACUUCUGUUUCAAUUACUUACAGU--
#=GC SS_cons                 :::::::<<<<<<<__.____>>>>>>>,,,,,.,,,,,,,,..,,,,(((((,,,...<<<<<_______.__>>>>>,,,,,,<<<<<__._>>>>>,,,,,,,,,,,,,,,,)))))------.--------------------<<<--<<<<--<<<<_..__________>>>>>>>>-->>>::::::::::::::::::::::::::::::::
#=GC RF                      CAAAAAACCaGCGuca.gaaggCGCuGGCuagG.ACuACaAu..AagaCCgucaaa...cGCCgUGCAGGu.uucGGCgaACGGuGACGCGu.UGCGUCuaAaGGauCgGgGauugacGGuuaaAA.GuuUuauacCCUGCAAcCAAuGuGAaCGgAUUCUAg..CAgGGUUUUAUAGAuCGuCAaCaCUAUAaAauuucaAAauuAUAACaAAaaGUAA
//
# STOCKHOLM 1.0

#=GF AC   RF02423
#=GF ID   Bp1_781
#=GF DE   Burkholderia sRNA Bp1_Cand871_SIPHT
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   170.40
#=GF NC   34.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0097311; biofilm matrix;
#=GF RN   [1]
#=GF RM   23282220
#=GF RT   Computational discovery and RT-PCR validation of novel Burkholderia
#=GF RT   conserved and Burkholderia pseudomallei unique sRNAs.
#=GF RA   Khoo JS, Chai SF, Mohamed R, Nathan S, Firdaus-Raih M
#=GF RL   BMC Genomics. 2012;13:S13.
#=GF RN   [1]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   15


CP000526.1/3314513-3314740   UCGCCCAAAAUGC-CUCUCACGGUUUC-AACACGGAUGCGGUCUCG--UGUGCAGCGUGUGAGCGGACACAAGCACGAAUGACGAGCCCGUCGGUCUCGUACCGAAUCCCU--UCC-CAGGGGCAUCCUUGUUGGAGUCGUCGUCGGC-----------CCAU--GCCGAUGCG-UUCCACCUUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCUCAUCAGCCCGCUUUUUUUCG
CP002599.1/101017-100788     UCGCCCACAAUGG-CUCUCACGGUUUC-AACACGGAUGCGGUCUUUCUUGUGCCUUGUGUGAGCGGAUACGAAGCACGCUGAAUAGUCCGUCGGUCUCGUACCGAAUCCCU--UCC-CAGGGGCAUCCUUGUUGGAAUCGUGAUCGGC-----------CCAC--GCCGAUUGC-UUCCACCUUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCUAAUAAGCCCGCUUUUUUUCG
CP001503.2/81667-81437       UCGCCCACAAUGG-CUCUCACGGUUUC-AACACGGAUGUGGUCUUUCUAGUGCGGCGUGUGAGCGGAUACGAUGCACUUCGAAUAGUCCGUCGGCUUUGUGCCGAAUCCCU--UGC-CAGGGGCAUCCCUGUUGGAAUCGUGACCGGC-----------CCAC--GCCGGUUGCGUUCCACCUUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCUCUUAAGCCCGCUUUUUUUCG
AAKY01000015.1/8690-8917     UCGCCCACAAUGC-CUUCAACGGUUUC-AACACGGAUGCGGUCUCG--UGUGCCAAGUGUGAGCGGACGCGAAGCGCUGCGAGC--C-AGUCGGUCACGUACCGAAGCCCU--UCC-GAGGGGCAUCCCUGUUGGAGUCGUUUCCGGC-----------UCCCCGCCGGAUUCGGUUUCAACUUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCUCAUAAGCCCGCUUUUUUUCG
ABBE01000613.1/3152-3380     UCGCCCACAAUGCCUUUCAACGGUUUC-AACACGGAUGCGGUCUCG--UGUGCCAAGUGUGAGCGGACGCAAAGCACUGCGAGC--CC-GUCGGUUAUAUGCCGAAGCCCU--UCC-GGGGGGCAUCCUUGUUGGAGUCGUUUCCGGU-----------CUUCGGACCGGACGCGUUCCAUCUUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCUAAUAAGCCCGCUUUUUUUCG
ABLK01000007.1/20716-20942   -CGCCCACAAUGGGCCUCAACGGUUUC-AACACGGAUGCGGUCUCG--UGUGCCAAGUGUGAGCGGACGCGAAGCGCUGCGAGC--C-AGUCGGUCACGUACCGAAGCCCU--UCC-GAGGGGCAUCCCUGUUGGAGUCGUUUCCGGC-----------CCCC-GCCGGACUCGGUUUCAUCUUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCUAAUAAGCCCGCUUUUUUUCG
CP000614.1/128165-127937     UCGCCCACAAUGG-CCUCAACGGUUUC-AAGACGGAUGCGGUCUCG--UGUGCCAAGUGUGAGCGGACGCGAAGCGCUGCGAGC--CCAGUCGGUCACGUACCGAAGCCCU--UCC-CAGGGGCAUCCCUGUUGGAGUCGUUUCCGGC-----------CCCCCGCCGGAUCCGGUUUCAACUUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCUAAUAAGCCCGCUUUUUUUCG
ABYL01000007.1/65221-65444   UCGCCCACAAUGC-CCUCAACGGUUUC-AACACGGAUGUGGCCG----GGUGCGUGGUGUGAGCGGAUACGAUGCACUU------GCCGAUCGGCGCU-UGCCGAAGCCCU--GUG-AAGGGGCAUCCCUGUUGGGGCCGUAGUCGACGCAGGG-----UCGUCGUGAUAACCG-UCCCAUCUUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCU-CCAGGCCCGCUUUUUUU--
ADNR01000005.1/193657-193881 UCGCCCACAAUGC-CCUCAACGGUUUC-AACACGGAUGUGGCUG----GGUGCGUGGUGUGAGCGGAUACGAUGCACUU------GCCGGUCGGCGUA-UGCCGAAGCCCU--GUG-AAGGGGCAUCCCUGCUGGGGCCGUAGUCGGCGCAGGG-----UCGCCGUCUCAGUCGGUUCCUUCUUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCU-CCAGGCCCGCUUUUUUU--
CP002013.1/3426452-3426675   UCGCCCACAAUGC-CCUCAACGGUUUC-AACACGGAUGUGGCUG----UGUGCGUGGUGUGAGCGGAUACAAUGCACUU------GCCGGUCGGCGCU-UGCCGAAGCCCU--GUG-AAGGGGCAUCCCUGCUGGGGCCGUAAUCGACGCAGGG-----UCGUCGGCGUAACCG-UCCCAUCAUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCU-CCAGGCCCGCUUUUUUU--
CP001043.1/3398466-3398673   UCGCCCACAAUGC-CUUUCACGGGUUC-AGCAAGGAUGCGGCCG-----GGUAGUUUCCUGAUCGGUCGAUGCAAAC--------GUC-G--------------AAGCUCU--UCA-AAGGGGCAUCUCUGCUGGAGUCGUGAUCGGCUUAGAUCA---UGCC--GAUUAUCCGGUUCCUCCAAUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCU-CCAGGCCCGCUUUUUUU--
FR687359.1/141117-140898     -CCCCCAAAAUGC-UUCCAUUGGUUUCCAACACGGAUGCGGUCU----ACUGUGUCGUAUGAGCGGAUGCGACGCGU---GAAC-ACCGGUCGGCACU--GCCGACGCUCUGCUGCGCAGGGACAUCUUUGUUGGCACCGCGUCAGAC-------------GC--GGUAACACAAUGCCACCCAUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCU-CCGAGCCCGCUUUUUUUU-
ADIG01003932.1/610-390       UCGCCCACAAUGCCUUUCAACGGUUUC-AACACAGAUGUGGGUU-----GGC-GUGCAUUGAUUGGACGCUUCCUAC-------------UCGGCGGU--GCCGAAUCCCC--CAU-GGGGGGCCUCUCUGUUGGAGUCGUUGCCGAUGCCCGGUUCGGGUGA--UCUUCUUCGGCUCCUUCAGUGGUCUCCUCGCGCUAACCCA-GUAGCGUGUGGUUUUUAGCGGGCUAUCAAGCCCGCUUUUUUUU-
CP003087.1/3006659-3006879   -CGCCCACAAUCUGUUCAAACGGUUUC-AACACGGAUGUAUUCG----GGCGCGCUGUGCAAAAGCCGCGUGU--CCGGUGGCAGACU-------UUUGGUCCGAGCUCUC--UUACCGGGGGCAUCCGUGUUGGGAUCGUU-CUUCGAAUG-------GAAAGGCAUUCGAACAUCCCACGAUUGGUCUCCUCGCGCUAACCCC-GUAGCGUGUGGUUUUUAGCGGGCU-CCAGGCCCGCUUUUUUU--
CAFE01000251.1/2562-2335     -CGCCCACAAUCUAUUUAAACGGUUUC-GACACGGAUGUGUUGG----GGCGCGCUGUGCGACAGCUGCGUGUUUCCGAUGGUCGGCUGGUCGACUUUG-GUCGAAGCUC----AAAUUGGGGCAUCCCUGUUGGGGUUGUUUCUUCGAGUG-------UACUCGCUCGGAAGCAUCCCACGUUUGGUCUCCUCGCGCUAACCCCCGUAGCGUGUGGUUUUUAGCGGGCU-CAAGGCCCGCUUUUUU---
#=GC SS_cons                 ::::[[[,,,,,,.,,,,(((((((((.((((-((((((<<<-<....-<<<<<<-<<<<______>>>>->>>>>>---->--.>>>,,<<<<<_____>>>>>,,<<<<..___._>>>>))))))-))))))))))))),<<<<<____.......______>>>>>,,,,,,,,,,,,,,]]],,,<<-<<<<<<<_____._>>>>>>>->>,,,,,<<<<<<<<.___>>>>>>>>:::::::.
#=GC RF                      UCGCCCAcAAUgc.uUuccaCGgcuuC.aaCACGGAuGcGgccu....ugugcgcugcguGAgcGgacgcugcgcacuuuGaac.gcCaGuCGGcuuuGugCCGaAgCcCu..uua.aaGgGgCaUCCcUGuuGgagcCGuguccggcauag.......ucaccGgccgguucggUuCCAucuuUGGUCUCCUCgCGCUAACCCC.GUAGCGuGUGGUUUUUAGCGGGCu.cuAaGCCCGCUUUUUUUc.
//
# STOCKHOLM 1.0

#=GF AC   RF02424
#=GF ID   Bp2_287
#=GF DE   Burkholderia sRNA Bp2_Cand287_SIPHT
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   70.00
#=GF TC   146.30
#=GF NC   51.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23282220
#=GF RT   Computational discovery and RT-PCR validation of novel Burkholderia
#=GF RT   conserved and Burkholderia pseudomallei unique sRNAs.
#=GF RA   Khoo JS, Chai SF, Mohamed R, Nathan S, Firdaus-Raih M
#=GF RL   BMC Genomics. 2012;13:S13.
#=GF WK   Bacterial_small_RNA
#=GF SQ   14



AAKY01000134.1/11265-11093             -AAAAAGCCCGCU-A--------------UGCAUCGGCAUCAGCGGGCUUCG-GUGCGGUAC-GACAGCGAUCGACUCGGGCCGGC--------UGCCGCCGGCCUUCGCUUUAGCUGUUUCGGGA-AGUUGCCCCGCGUCCGCAAGCUGAAAUCAAAUCGACGCAAGGCGCCAUCCUAGCACGCUUCGGAAG---------AGCGUGC----
ACFC01000001.1/1027058-1027231         -AAAAAGCCCGCC-A--------------UGCGUCUGCAUCAGCGGGCUUCG-GUGCGGUAC-GACAGCGAUCGACUCGGGCCGGC--------UGCCGCCGGCCUUCGCUUUAGCUGUUUUGGGA-AGAAGCCCCGCGUCCGCAAGCUGAAAUCAAAUCGACGCAAGGCCACAUCCUAGCACGCUUCGGCACA--------AGCGUGC----
AEXE01001637.1/2208-2038               -AAAAAGCCCGCC-A--------------UGCGUAUGCAUCGGCGGGCUUCG--UGCGGUAC-GACAGC--UCGACUCGGGCCGGC--------UGCCGCCGGCCUUCGCUUUAGCUGUUUGGGGU-AUUCGCCCCGCGUCCGCAAGCUGAAAUCAAAUCGACGCAAGCCCACAUGCUAGCACGCUUCGGCAAA--------CGCGUGC----
CP002600.1/2295288-2295462             -AAAAAGCCCGCG-A--------------CGCGUCGGCAUCAGCGGGCUUCA-GUGCGGUAC-CACAGCCUG-GACUCCAGCCGGC---------GGUGCCGGCCUUCGCUUUAGCUGUUUCGGGGCGAUUGCCCCACGUCCGCAAGCUGA-AUCAAAUCGACGCAAGGCG-CAUCGUAACACGCGAGCG----CGAAACGAUGCGCGC----
CP000011.2/1873350-1873536             CAAAAAGCCCGCUCA--------------UGCGUCGGCAUCAGCGGGCUUGGUGUGCGGUACGAACAGCUAUCGACUCGGGCCGGCAUGGCGCUGCUCGCCGGCCUUCGCUUUAGCUGUUUCGGG----UUGCCCCGCGUCCGCAAGCUGAAAUCAAAUCGACGCAAGGCCCCAUCGUAUCACGCCUUUUUGGC--------GACGUGCGCGG
AECN01000095.1/2585-2404               CAAAAAGCCCGCUCA--------------UGCGUCGGCAUCAGCGGGCUUGGUGUGCGG----AGCAGCUAUCGACUCGGGCCGGCAUGGCGCUGCUCGCCGGCCUUCGCUUUAGCUGUUUCGGG----UUGCCCCGCGUCCGCAAGCUGAAAUCAAAUCGACGCAAGGCCCCAUCGUAUCACGCCUUUUCGGU--------CGCGCGCGCG-
ABBE01000049.1/2526-2354               -AAAAAGCCCGCC-A--------------UGCGUCAGCAUCAGCGGGCUUCG--UGCGGUAC-GACAGCGGUCGACUCGGGCCGGC--------UGCCGCCGGCCUUCGCUUUAGCUGUUUUGGGA-UGAAGCCCCGCGUCCGCAAGCUGAAAUCAAAUCGACGCAAGGCCACAUCCUAUCACGCCUGUACGGC--------GGCGUGC----
AM747721.1/1106587-1106411             CAAAAAGCCCGCU-A--------------UGCGUCGGCAUCAGCGGGCUUCG-GUGCGGUAC-GACAGCGAUCGACUCGGGCCGGC--------UGCCGCCGGCCUUCGCUUUAGCUGUUUUGGGA-AGUUGCCCCGCGUCCGCAAGCUGAUAUCAAAUCGACGCAAGGCCACAUCCUAUCACGCCUCGAUCGA--------AGCGUGCGC--
CP000441.1/149635-149460               CAAAAAGCCCGCU-A--------------UGCGUCGGCAUCAGCGGGCUUCG-GUGCGGUAC-GACAGCGAUCGACUCGGGCCGGC--------GCUCGCCGGCCUUCGCUUUAGCUGUUUUGGGA-AGUCGCCCCGCGUCCGCAAGCUGA-AUCAAAUCGACGCAAGGCCACAUCCUAGCACGCUUCGUCGGA--------AGCGUGCGC--
CP000615.1/1308771-1308596             CAAAAAGCCCGCU-A--------------UGCGUCGGCAUCAGCGGGCUUCG-GUGCGGUAC-GACAGCGGUCGACUCGGGCCGGC--------UGCCGCCGGCCUUCGCUUUAGCUGUUUUGGGA-GAUCGCCCCGCGUCCGCAAGCUGA-AUCAAAUCGACGCAAGGCGCCAUCCUAUCACGCUUCGUCGCA--------AGCGUGCGC--
CP001504.2/1029372-1029203             -AAAAAGCCCGCG-A--------------UGCGUCGGCAUCGGCGGGCUUCAGGUGCGG------CAGCUUUCGACUCGGGCCGGCAU------UCGGGCCGGCCUUCGCUUUAGCUGUUUCGGGU-GACUGCCCCGCGUCCGCAAGCUGAGAUCAAAUCGACGCAGCGCC-CAUCCUAACAUGUGUCACGACG--------GGCGCG-----
CP000271.1/179142-178964               -AAAAAGCCCGCUUU--------------UGCGUCGGCAUAAGCGGGCUUCAUGUGCGGGGG--AAAGCUGG-AGCGGAGGCGGAUGAGUGCGGCUUUUCCACCCUUCGCUUUAGCUGUUUCGGG----UUGCCCCGCGUCCGCAAGCUGAGAUCAAAUCGACGCAAGCCGCCAUGCUAACACGCUCCCGGCGC--------GGCGUGC----
CP001053.1/3183647-3183825             -AAAAAGCCCGCUUU--------------UGCGUCGGCAUAAGCGGGCUUCAUGUGCGGGGG--AAAGCUGG-AGCGGAGGUAGAUGAAUGCGGCUUUUCCACCAUUCGCUUUAGCUGUUUCGGG----UUGCCCCGCGUCCGCAAGCUGAGUUCAAAUCGACGCAAGCCGUCAUGCUAACACGCUCCCGGCGC--------GGCGUGC----
ABLD01000002.1/474853-474663           --AAAAGCCCGCUUUGCGCCGGCGCUUUUUGCGUCGGUACAAACGGGCUUCAUGUGCGGGG---AAAGCUGG-AGCGGAGGCGGACAAGUGCGGCUUUUCCACCAUUCGCUUUAGCUGUUUCGGG----UUGCCCCGCGUCCGCAAGCUGAGAUCAAAUCGACGCAAGCCAUCAUGCUAACACGCUCGCGGCGC--------GGCGUGC----
#=GC SS_cons                           .:::<<<<<<<<<.-..............<<<____>>>-->>>>>>>>>,,.,[[[[,,,,.,,,<<<----<<--<-<<-<<<_........__>>>>>->-->>->>>((((((,,,,,<<<_.______>>><<____>>,)))))),,,,,,,,,,,]]]]--------------<<<<<<________........>>>>>>:....
#=GC RF                                .AAAaaGCCCGCu.a..............uGCGUCgGCaUcaGCGGGCuuca.GuGCGGuac.gAcaGCuauCgaCucgGGCcggc........uuccgCCggCcuuCGCuuuaGCuGUUUcGGGa.aauuGCCCCGCGUCCGCAaGCugaaAUCAAAUCGACGCaAGgCauCAUccUAaCaCGCcucuguaga........gGCGuGC....
//
# STOCKHOLM 1.0

#=GF AC   RF02425
#=GF ID   SpF01_sRNA
#=GF DE   Streptococcus sRNA SpF01
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   55.00
#=GF TC   57.10
#=GF NC   51.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   13



AGPO01000001.1/76753-76832           AUUUUAUUGAAUAAGAUAGGCUUU--GAGGCCUUGAUAUUAAG--CACUUUGGGACGUUCUCCCUUAGUGCUUUU-UUGAUUUCU
AEDU01000022.1/84997-85076           AUUUUAUUGAAUAAGAUAGGCUUU--AGAGCCUUGAUAUUAAG--CACUUUGGGGCGUUUUCCCUUAGUGCUUUU-UUUGUUUUU
CP002925.1/145771-145849             AUUUUAUUAAAUAAGAUAGGCUGU--AAAGCCUUGAAAUUAAG--CACUUUGGGGCGUUUUCCCCUAGUGCUUU--UUGAUUUCU
ACRL01000039.1/63311-63233           AUUUUAUUAAAUAAGAUAGGCUGU--AAAGCCUUGAUAUUGAG--CACUUUGGGGCGCUUUCCCUUAGUGCUU-U-UUGAUUUCU
FN568063.1/106345-106423             AUUUUAUUGAAUCAGAUAGGCUUU--AGAGCCUUGAUAUUAAG--CACUUUGGUGCGCUUUCCUUUAGUGCUU-U-UUGAUUUCU
AGQI01000002.1/99467-99546           AUUUUAUUAAAUAUGAUAGGCUGU--AAAGCCUUGAAACUAAG--CACUUUAGGCCUCUAUCCUAGAGUGCUUUU-UUGAUUUCU
AEDW01000013.1/65379-65458           AUUUUAUUGAAUAAGAUAGGCUAU--AAAGCCUUGAAAUUAAG--CACUUUAGGCCUCUAUCCUAGAGUGCUUUU-UUUGAUUUU
CP002644.1/500721-500800             AUUUUAUUGAAUAUGAUAGGCUGU--AAAGCCUUGAAAUUAAG--CACUUUAGGCCUCUUUCCUAGAGUGCUUUU-UUGAUUUUA
CP000260.1/1888212-1888133           AUUUUAUUGAAUAGGAUAGGCUUA--AAAGCCUUGAUACUAAG--CACUUUGGGGCAUUAUUCCAAGGUGCUUUU-UUUGAUUUU
CP002215.1/2123266-2123187           AUUUUAUUGAAUAAGAUAGGCUUA--AAAGCCUUGAUACGAAG--CACUUUGGAGGGUUAUUUCAAGGUGCUUUUCUUGAUUUU-
AEGF01000061.1/3123-3200             AUUUUAUUGAA--AGAUAGACUUUGUGAGGCCU--AUAUUAAGCGCACUUUGGGAC--UCUCCCUUAGUGCUUUU-UUGAUUUCU
AGPS01000006.1/118862-118939         UCUUUAUGUGAUU--AUAGGCUAU--AAAGCCUUUGAAAUAAG--CACUUUGGGGCGCUUUCCCUUAGUGCUUUU-UAUAAUUUA
AFGR01000001.1/69155-69226           AUUUUAUUGAAUAAGAUAGGC----------CUUGAUAUUAAG--CACUUUGGGACGUUCUCCCUUAGUGCUUUU-UUGAUUUCU
#=GC SS_cons                         :::::::::::::::::<<<----..------<--<----<<<..<<<<--<<<<_____>>>>-->>>>>>>--.>-->-->>>
#=GC RF                              AUUUUAUUgAAUAAGAUaggCUuU..AAAGCCuUGAuAuUAAG..CACuUUGGGgCguUuuCCCuuaGUGCUUUU.UUgaUUucu
//
# STOCKHOLM 1.0

#=GF AC   RF02426
#=GF ID   SpF03_sRNA
#=GF DE   Streptococcus sRNA SpF03
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   50.00
#=GF TC   71.40
#=GF NC   39.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   3


AGPS01000003.1/108824-108929 AUUGCUCGAAUUUAUCGGA--CUUUUC--UAUAAAGAAUAGUUUGGACUUGAACUGUAUCUAAAAAC-AGAGGUUGGUAGAUUAUCAGCCUCUUUCUUGUCGUU-GAAAAGA
FQ312029.1/118922-119029     AUUGCUCGAAUUUAUCGGACUUUUUUC--UAUAAAGAAUAGUUUGGACUUGAACUGUAUCUAAAAAC-AGAGGUUGGUCGAUUAUCAGCCUCUUUCUUGUCGUU-GAAAUUA
AGNY01000003.1/93001-93109   AUUGCUCGAAUUUAUAGGA--CUUUUUUCUAUAAAGAAUAGUUUGGACUUGAAAUGUAUUUAAAAACAAGAGGUUGGUAGAUUAUCAGCCUCUUUCUUGUCGUUGAAAAAG-
#=GC SS_cons                 :::::<<<<_____>>>>-..((((((..,,,,,<<<<<<<<<<______>>>>>>>->>>,,,,,,.<<<<<<<<<<<___>>>>>>>>>>>,,,,,,,,,,,.)))))):
#=GC RF                      AUUGCuCgaAUUUAucGgA..cuuuuc..UAUAAagaauaguuuGGACUUgaacuguAucuAAAAAC.aGaGGuuGguaGAUuauCagCCuCuUUCUUGUCGUU.gaaaagA
//
# STOCKHOLM 1.0

#=GF AC   RF02427
#=GF ID   SpF10_sRNA
#=GF DE   Streptococcus sRNA SpF10
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   60.00
#=GF TC   81.40
#=GF NC   38.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   2



AEGF01000034.1/2433-2487         CAGAGAGAACAUU--AUUCAGAAUAAUGAAAAACGCAUCAAAAAUGGUGCGUUCUGU
FQ312027.1/313736-313792         CAGAUAGAACAUUGCAUUCAGAAUAAUGAAAAACGCAUCAAAAAUGGUGCGUUCUGU
#=GC SS_cons                     :::(((((((,,,,,,<<<<______>>>>,,,,<<<<<<____>>>>>>)))))))
#=GC RF                          CAGAcAGAACAUUGCAUUCAGAAUAAUGAAAAACGCAuCAAAAAUGgUGCGUUCUgU
//
# STOCKHOLM 1.0

#=GF AC   RF02428
#=GF ID   SpF11_sRNA
#=GF DE   Streptococcus sRNA SpF11
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   54.00
#=GF TC   54.00
#=GF NC   52.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   3



CP002925.1/1876736-1876642         UAUUUGUUAUCAUUGGUCACAUUGAAAAUGUGAAAUAAGUAGCUACAACAUAGACUUUACAACACUUCAUGUUUCAUAUCAUGGGGUGUUUUUCU
ADHN01000059.1/29661-29755         CAUUUGUUAUCAUUGGUCACAUUGAAAAUGUGAAAUAAGCACCUACAACAUAGACUUUACAACACUUCAUGGUUCGAUCCGUGAGGUGUUUUUCU
CP001033.1/309320-309414           UAUUCGUUAUCACUGGUCACAUUGAAAUUGUGAAAUAAGCACCUACAACAUAGACUUUACAACACUUCAUGUUUCAUAUCAUGGGGUGUUUUUCU
#=GC SS_cons                       :::::<<-----<<--<<<<<_______>>>>>---->>----->>--------------<<<<<<<<<<<________>>>>>>>>>>>:::::
#=GC RF                            uAUUuGuUAUCAcuGGuCaCaUUGAAAauGuGaAAUAagcAcCUaCAACAUAGACUUUACaaCaCucCauGuUUCauauCauGggGuGuuUUUCU
//
# STOCKHOLM 1.0

#=GF AC   RF02429
#=GF ID   SpF14_sRNA
#=GF DE   Streptococcus sRNA SpF14
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   100.00
#=GF TC   107.80
#=GF NC   37.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   4



AEGF01000069.1/9500-9619           CACACAUAUAAAUUUGUAAUACCGUUCAUUUGGUAUUAUUUUUGGACAGUAGUUGUAUUU--CAUGAUCAAUUGGAAUUAUAUAUACGAAUACACUAAGAAGAGACAAAUAUAUAAAAAUAU
CP002925.1/1710548-1710430         CAAAAACCAGAAUUUAUAAUAUCGUUUAUAAUGGGCAUGAUUUGGGUUGUCGGUGUAUUCCUUCUAAUCUAUUGGAAUUUUAUA-GCAAAUAC--UAAGAAGAGACAAAAAUAUAUAAAUAU
AEDX01000005.1/54531-54649         CAAAAACCAGAAUUUAUAAUAUCGUUUAUAAUUGGCAUGGUUUGGGUUGUCUGUGUUUUCCUUCUAAUCUAUUGGAAUUUUAUA-GCCAAUAC--UAAGAAGAGACAAAAAUAUAUAAAUGU
CP000919.1/468632-468751           CAAACAUAUAAAUUUGUAAUACCGUUCAUAAUUGGUAUGAUUUGGACAGUAGUUGUAUUUCUUAUGAUCAAUUGGAAUUAUAUAGGCAAAUAC--UAAGAAGAGACAAAAAUAUAUAAAUAU
#=GC SS_cons                       :::::(((((--(((((,,<<<-<<<<<-<<<<_____>>>>>>>>>->>>,,,<<<<<<<<<<<<-<<_____>>---->>>>>>->>>>>>..,,,,,,,,,)))))--)))))::::::
#=GC RF                            CAaAaauauaAAuuuguAAuacCguucaUaaucgguaugauuuggacaguaguUGuauucCcuauaAuCaAUUGGaAUUauauagGCgaauaC..UAAGAAGAGacaaaaAuauauAAAUAU
//
# STOCKHOLM 1.0

#=GF AC   RF02430
#=GF ID   SpF19_sRNA
#=GF DE   Streptococcus sRNA SpF19
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   60.00
#=GF TC   89.10
#=GF NC   53.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   3



AAFA03000004.1/83317-83220         AAAUAAAAGGAUGUUAUCGCU--UUAAGGCGAGCAGGAACCUAUUUAAAUGAAUCGAUACGAUAUAUGUCGAUUUCUUUUAAGUAGGUUC-UUUUAUUUUA
AARD01000216.1/4451-4353           GAAAUAAAAGAUGUUAUCGCU--UUAAGGCGAGCAGGAACCUAUUUAAAUGAAUCGAUACGAUAUAUGUCGAUUUCUUUUAAGUAGGUUCUUUUAUUUUAA
CP002925.1/559026-559124           AAAUAAAAGGAUGUUAUCACUAAUACAAGUGAGCAGGAACCUAUUUAAUCACAUCAGAAGAAGUUUC-UUGAUG-UUUUUAAGUAGGUUCCUUUUAUUUUA
#=GC SS_cons                       (((((((,,,,,,,,,<<<<<..____>>>>>,,<<<<<<<<<<<<<<--<<<<<<<<<<___>>>>-->>>>>->-->>>>>>>>>>>>>>)))))))::
#=GC RF                            aaauaaaAgGAUGUUAuCgCc..UuaAgGcGaGCagGaaCCuauuuaaaugcauCgguacgAuguacGUcGaugUcUUuuaaguaGGuuCcuuuuauuuuA
//
# STOCKHOLM 1.0

#=GF AC   RF02431
#=GF ID   SpF22_sRNA
#=GF DE   Streptococcus sRNA SpF22
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   55.00
#=GF TC   59.60
#=GF NC   43.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   22



AFQV01000023.1/77720-77859           UGAGAUCGGCGCGUGCUUGCCAAUUCUUAUCAGAAC--AAGGUUAUGAGGUUAUCGAUGUCCAAGGUGGCAUGAU--GUCCUUUGAAGAACUUUAAA---------------AAUU-UG---------------CA----U------------U-UCUCCUACUUGGUGUGG------------ACUGGGUAGGAGAAUGUUAU
AFUF01000022.1/10543-10404           UGAGAUCGGCGCGUGCUUGUCAAUUCCUAGCUGAAC--AAGGUUAUGAGGUUAUCAAUGUUCAGGGUGGCAUGUU--AGCCUUUGAAGAACUUUAAA---------------CAGU-AG---------------AU----U------------U-UCUCCUACUCGGUAUGG------------ACUGGGUAGGAGAGUUUUAU
ACRL01000033.1/98931-99070           UGAGAUCAGCGCGUGCUUGCCAAUUCUUAUCAGAAC--AAGGUUAUGAGGUUAUCAAUGUUCAAGGUGGUAUGAU--GGCCUUUGAAGAACUUUAAA---------------AAUU-UG---------------CA----U------------U-UCUCCUAAUUGGUGUAG------------ACUGAGUAGGAGAGUUUUAU
FN568063.1/1617470-1617331           UGAGAUCAGCGCGUGCUUGCCAAUUUUUAGCUGAAC--AAGGCUAUGAGGUUAUCAAUGUUCAAGGUGGCAUGUU--AGCCUUUGAAGAAUUGUAAA---------------CAUU-AG---------------AA----U------------U-UCUCCUACUUGGUGUGG------------ACUGGGUAGGAGAAUUUUAU
AEDX01000019.1/224089-224228         UGAGAUCGGCGCGUGCUUGCCAAUUCCUAUCAGAAC--AAGGUUAUGAGGUUAUCAAUGUACAGGGUGGCAUGUU--AGCCUUUGAAGAACUUUAGA---------------CAUU-AG---------------AA----U------------UUUCUCCUACUUGGCGUGG------------ACUGGGUAGGGGA-UUUUAU
AEDT01000002.1/98387-98527           UGAGAUCAGCGCGUGCUUGCCAAUUCUUAUCAGAAC--AAGGUUAUGAGGUUAUCAAUGUACAAGGUGGCAUGAU--GGCCUUUGAAGAACUUUAAA---------------CAGUACA---------------AU----U------------U-UCUCCUACUUGGUGUGG------------ACUGGGUAGGAGAAUUUUAU
CP002925.1/610853-610993             UGAGAUCGGCGCGUGCUUGCCAAUUCCUAUCAGAAC--AAGGCUAUGAGGUUAUCAAUGUACAAGGUGGUAUGAC--UGCCUUUGAAGAACUGUAAA---------------CAGUACA---------------AU----U------------U-UCUCCUGCUUGGUGUGG------------ACUGGGUAGGAGAAUUUUAU
AGQG01000002.1/100482-100620         UGAGAUCAGCGCGUGCUUGCCAAUUCUUAUCAGAAC--AAGGUUAUGAGGUUAUCAAUGUUCAAGGUGGUAUGAC--UGCCUUUGAAGAACUCUAGA---------------CGUA-AG---------------AA----U------------U-UCUCCUACUUGGCGUGG------------ACUGGGUAGGGGA-UUUUAU
AFUU01000003.1/521713-521574         UGAGGUCAACUCGUGCUUGCCAGUUCUUGGAGGAGU--AUGGAUACAAGGUCAUCAAUGUUCAAGGUGGCAUGAC--GGCCUUUGAAAAUCUUUAAA---------------AUUU-UG---------------CA----U------------U-UCUCCUACUUGGUGUGG------------ACUAGGUAGGAGAAUUUUGU
AFUO01000001.1/753675-753536         UGAGAUCAGCUCGUGCUUGCCAGUUUUUAGAGGAGC--AUGGAUAUAAGGUCAUCAAUGUUCAAGGUGGUAUGAC--GGCCUUUGAAAAUCUUUAAA---------------AUUU-UG---------------CA----U------------U-UCUCCUACUUGGUGUGU------------ACUAGGUAGGAGGAUUUUGU
AEGF01000277.1/5727-5588             UGAGAUCGGCGCACGUGCUUCAAUACCUGUUAGAACAAAAGGAUAUAAUGUUAUCAAUGUCCAG--UGGCAUGUUUAAGCCAUUGA--AACUUUAAA---------------AAUU-UG---------------CA----U------------U-UCUCCUACACUUUGUGG------------ACUCUGGGGGAGAGUUUUAU
AEVF01000004.1/103530-103667         AGCGUUCGGCACGUGCUUGCCAAUUUCUAUCAGAAC--AAGGCUAUGACGUUAUCAAUGUCCAAGGUGGCAUGGA--UGCUUUAGAAUAAGA------------------------------------------AA----A------------C-UCUCUUUGGAGCCG---AAAUUAAGAAAAGGUCCCAAAGGGAAUUUUUU
AEPO01000012.1/30097-30251           UGAGGUCAGCGCGUGCUUGUCAAUUUCUAGCUGAAC--AGGGUUAUGACGUUAUCAAUGUCCAAGGUGGAAUGAU--GACCUUUGAAAAUCUUUAAACCUCUAUGGUGAUAGAUCC-UA---------------AU----C------------U-UCCCUUGCUCGGUUCCA------------ACUGAGUGAGGGAUUUUGUU
ACRJ01000023.1/15194-15042           UGCGUUCAGCGCGUGCUUGUCAAUUUCUAGUUGAAC--AGGGUUAUGAAGUUAUCAAUGUCCAAGGUGGAAUGAC--GGCCUUUGAAAAUCUUUAAA---------------UAUA-UAGUGACA--GAUCCUAAC----C------------U-UCCCUUGCUCGGUUCCA------------ACUGAGUGAGGGAUUUUGUU
FR720602.1/1419767-1419613           UGCGUUCAGCGCGUGCUUGUCAGUUUCUAGCUGAAC--AGGGUUAUGACGUUAUCAAUGUCCAAGGUGGAAUGAC--GGCCUUUGAAAAUCUUUAAA---------------GCUA-UA---------------UAGCGU-UAGAUCCUAAUCU-UCCCUUGCUCGGUUCCA------------ACUGAGUGAGGGAUUUUGUU
AFUT01000004.1/1582-1444             UGCGUUCAGCACGCGCUUGUCAAUUUUUAGCAGAAC--AAGGCUAUGAGGUUGUCAAUGUCCAAGGUGGCAUGGA--UGCCUUUGAAUAAGAAAAAA--------------------------------------------------------C-UCCCUUUAAGACCG---AAAAU-AAGAACGGUUUUAAAGGGAGUUUAUU
AEVD01000004.1/154818-154955         UGCGUUCAGCACGCGCUUGUCAAUUUUUAGCAGAAC--AAGGAUAUGAGGUUAUCAAUGUCCAAGGUGGCAUGGA--UGCCUUAGAAUAAG---AAA--------------------------------------A----U------------C-UCCCUUUAAGACCG---AAAAU-AAGAAAGGUUUUAAAGGGAGUUUAUU
ADMV01000012.1/303231-303385         UGAGGUCAGCGCGUGCUUGUCAAUUUCUAGCUGAAC--AGGGUUAUGACGUUAUCAAUGUCCAAGGUGGAAUGAC--GGCCUUUGAAAAUCUUUAAA---------------CCUA-UGUGGCGAUAGACCCUAAU----C------------U-UCCCUUGCUCGGUUCCA------------ACUGAGUGAGGGAUUUUGUU
AGAE01000029.1/25252-25406           UGAGAUCAGCUCGUGCUUGUCAAUUUCUAGCUGAAC--AGGGUUAUGACGUUAUCAAUGUUCAAGGUGGAAUGAC--GGCCUUUGAAAAUCUUUAAA---------------CCUA-UAUGACGAUAGAUUCCAGU----C------------U-UCCCUUGCUCGGUUCCA------------ACCGAGUGAGGAAUUUUGUU
AEDY01000079.1/6853-6993             UGCGUUCAGCACGCGCUUGUCAAUUUUUAUCAGAAC--AAGGAUAUGAGGUUAUCAAUGUCCAAGGUGGCAUGGA--UGCCGUUGAAUAAGA---A----------------------A---------------AA----U------------U-UCCUUCGAAACCUUUAAAAAAA--UGGGAAGGCUUCGAAGGAUUUUUUU
AFNN01000010.1/164706-164571         UGCGUUCAGCACGCGCUUGUCAAUUUCUUGCAGAAC--AGGGCUACGAAGUUAUCAAUGUCCAAGGUGGCAUGGA--UGCCUUAGAAUAAGAA-----------------------------------------AA----A------------C-UCCCUUUGAGACCAAAAUAA------AAAAGUUUCAAGGGGAAUUUAUU
FQ312039.1/1743791-1743930           UGAGAUCGGCGCGUGCUUGCCAAUUCCUAUUAGAAC--AAGGUUAUAAUGUUAUCAAUGUCCAGGGUGGCAUGUU--AGCCUUUGAAGAACUUUAAA---------------AUUU-UG---------------CA----U------------U-UCUCCUACUUGGUGUGG------------ACUGGGUAGGAGAGUUUUAU
#=GC SS_cons                         :::::::<<<<______>>>>---------((((((..,<<<<<<--<<<<<<<<_________>>>>>>>>-->..>>>>>,,,,,,,,,,,,,,,...............,,,,.,,...............,,....,............,.<<<<<<<<<--<<____............>>-->>>>>>>>>)))))):
#=GC RF                              UGaGaUCggCgCGUGCUcGccAAUUucUAgccgAAc..AgGGccaUGAcguuAuCAAUGUcCAAGgUggcgUGau..ggCCcUUGAAaAacUuUAAA...............aauu.ua...............aa....u............U.UCcCcugcuugguuuga............acUgagcagGgGAgUUuggU
//
# STOCKHOLM 1.0

#=GF AC   RF02432
#=GF ID   SpF25_sRNA
#=GF DE   Streptococcus sRNA SpF25
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   48.00
#=GF TC   48.90
#=GF NC   43.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   20



CP000918.1/1269860-1269759             GCAUG-GG-AUAGCCUUUCUAAA-UGGUUU---AUUGGGCAAUUCUAUUUUACCAAGACUAUCGCAACCAU-G-CAAAAA-AGCAAC-GG-CA---A-AUCCGCUUC-U--UUUUUG-G-AG
FQ312039.1/1774386-1774488             GCAUG-GG-AUAGCCUUUCUAAA-UGGUUU---AUUAAGCAAUUCUAUUUUACCAAGACUAUCGCAACCAU-G-CAAAAA-AGCAAC-GG-CA---A-AUCCGUUGC-C-UUUUUUG-G-AG
AGOA01000003.1/18673-18775             GCAUG-GG-AUAGCCUUUCUAAA-UGGUUU---AUUAAGCAAUUCUAUUUUACCAAGACUAUCGUAACCAUGC-AAAAAA-AGCAAC-GG-CA---A-AUCCGUUGC-U--UUUUUU-GGA-
AECT01000043.1/1575-1676               GCAUG-AG-AUAGCCUUUCUAAA-UGGUUU---AUUAAGCAAUUCUAUUUUACCAAGACUAUCGCAACCAU-G-CAAAAA--GCAAC-GG-CA---A-AACCGUUGC-U-UUUUUUU-G-AU
AFQT01000010.1/82131-82028             GCAUG-GG-AUAGCCUUUCUAAA-UGGUUU---AUUGGGCAAUUUUAUUUUACCAAGACUAUCGCAGCCAU-G-CAAAAAAAGCAAC-GG-AU---U-UGCCGUUGC-UUUUUUUUG-C-A-
AGHP01000093.1/8093-7992               GCAUG-GG-AUAGCCUUUCUAAA-UGGUUU---AUUUUGCACUUCUAUUUUACCAAGACUAUCGCAACUAU-G-CAAAAA-AGCAAC-GG-CA---A-AUCCGUUGC-UUUUUUUUG-G---
ABAF01000001.1/315439-315339           GCAUG-GG-AUAGCCUUUUUAAA-UGGUUU---AUUAAGCAAUUCUAUUUUACCAAGACUAUCGUAACCAU-GCGAAAAA-AGCAAC-GG-CA---A-AUCCGUUGC-U--UUUUUU-U---
AFNM01000058.1/50978-50879             GCGUG-GG-AUAGCCUUUCUAAA-UGGUUU---AUUGAGCAAUUCUAUUUUAGCAAGACUGUCGCAAUCAU-G-CAAAAA--GCAAC-GG-CA---A-AUCCGUUGC-U-UUUUUUG-U---
ACRK01000014.1/444735-444632           GCAUG-AGAAUAGCCUUUCUAAA-UGCUUU---AUUGAGCAAUUCUAUUUUACCAAGACUAUCGCAACCAU-G-CAAAAA-AGCAAC-GG-UA---A-AUCCGUUGC-C-UUUUUUG-A-AG
FR873481.1/765140-765241               GCAUG-GG-AUGGCCUUUCUAAA-UGGUUU---UUUGGCCAAUUCUAUUUCACCAAGACUAUCACAAUCAU-G-CAAAAA--GCAAC-GG-CAU-AA-AACCGUUGC----UUUUUG-G-AG
AEGF01000052.1/9748-9852               GCAUG-GG-AUAGCCUUUCUAAA-UGGUUU---AUUAAGCAAUUCUAUUUUACCAAGACUAUCGUAACCAU-G-CAAAAA-AGCAACUCGGCA---A-ACGCGUUCUUU--UUUUUG-U-AU
AEVC01000006.1/118688-118791           GCAUG-GG-AUAGCCUUUCUAAA-UGUUUUUUUUUUGAGCAAUUCUAUUUUAGCAAGACUAUCGCAACCAU-G-CAAAAA--GCAAC-GG-CA---A-AUCCGUUGC-UUAUUUUUG-U---
AEUT02000001.1/1107825-1107926         GCAUG-AG-GUAGCCUUUCUAAAGUGUUU-----UUAGACAAUUCUAUUUUAUCAAGACUAUCGCAACCAU-G-CAAAAA--GCAAC-GG-CA---AAAACCGUUGC-U--UUUUUGUU-AU
AEUY02000005.1/202629-202528           GCAUGGGG-AUAGCCUUUCUAAAGUGUUU-----CUGGACAAUUCUAUUUUAUCAAGACUAUCGCAACCAU-G-CAAAAA--GCAAC-GG-CA---AAAACCGUUGC-U--UUUUUG-U-UU
AFUJ01000016.1/86314-86416             GUAUAAAA-GUGGCAUCUGUAAA-UGGUAU---AUGGGGCGAUUCUGGUUUAGCAAGACUAUCGCAACUAU-G-CAAAAA-AGCAAC-GG-CA---A-AUCCGUUGC-U--UUUUUG-A-GA
AEUV02000002.1/2255461-2255561         ACAUG-GG-GUAGCCUUUCUAGU-AGGUU-----UUAGUCAACUCUAUUUUAUCAAGGCUAGCUCACUAAA-G-CAAAAA--GCAAC-GG-CAUCAA-AACCGUUGC----UUUUUG-U-CU
AEKN01000009.1/36244-36344             ACAUG-AG-GUAGCCUUUCUA---UUAUUU---UUUGUC-AACGAUAUUUUAUCAAGACUACCU-AUGUCA-A-GCAAAA-AGCAAC-GG-CAUCAA-AACCGUUGC-U--UUUUCG-U-UG
AGGK01000206.1/123-22                  ACAUG-AG-GUAGCCUUUCUA---UUAUUU---UUUUGUCAACGAUAUUUUAUCAAGACUACCUAUGUAAA-G-CAAAAA--GCAAC-GG-CAUCAA-AACCGUUGC-U--UUUUCG-U-UG
AGGJ01000267.1/469-570                 ACAUG-AG-GUAGCCUUUCUA---UUAUUU---UUUUGUCAACUAUAUGUUAUCAAGACUACCU-AUGUCA-A-GCAAAA-AGCAAC-GG-CAUCAA-AACCGUUGC-U--UUUUCG-U-UG
AAGY02000050.1/7964-8065               GCAUG-GG-AUAGCCUUUCUAAA-UGGUUU---AUUGGGCAAUUCUAUUUUACCAAGACUAUCGUAACCAU-C-CAAAAA-AGCAAC-GG-CA---A-AUCCGUUGC-C--UUUUUG-G-AU
#=GC SS_cons                           :::<<.-<.<<<<----<<<---.<<<<--...--<<<<____>>>>---->>>>>>>>>>>>->>---<<.<.<<<<<<.-<<<<<.<<.__..._.__>>>>>>>.-..>>>>>>.>.>>
#=GC RF                                gCAug.gG.guaGCCUUuCuAAA.ugguUU...aUugggCAAUcccaUUUUaccaaGaCuacCgcaacccu.g.caaaaa.AGCaaC.GG.cA...A.AuCCGuuGC.U..uuuuug.c.ag
//
# STOCKHOLM 1.0

#=GF AC   RF02433
#=GF ID   SpF36_sRNA
#=GF DE   Streptococcus sRNA SpF36
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   45.00
#=GF TC   46.60
#=GF NC   44.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   4



CP002925.1/954676-954727           CGAUA-AAAAUCUGAUUACAAGAUGUAGUCAGAUUUUUUUU--UUAGAAAAAUAU
AEDT01000014.1/31511-31559         CGAUAAA-AAUCUGAUUACAAGAUGUAGUCAGAUUUUU-----UUAGGAAAAUGU
CP002121.1/975352-975404           CGAUA-A-AAUCUGAUUACAAGAUGUAGUCAGAUUUUGGUAACUUCUAAAACUAA
AFQV01000013.1/63793-63840         CGAUA-A-AAUCUGAUUACAAGAUGUAGUCAGAUUUUU-----UUAGAAAAUUAU
#=GC SS_cons                       :::<<.<.<<<<<<<<<<<_____>>>>>>>>>>>>>>:::..::::::::::::
#=GC RF                            CGAuA.A.AAUCUGAUUACAAGAUGUAGUCAGAUUUUuuUa..UUAGAAAAaUAU
//
# STOCKHOLM 1.0

#=GF AC   RF02434
#=GF ID   SpF39_sRNA
#=GF DE   Streptococcus sRNA SpF39
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   60.00
#=GF TC   64.50
#=GF NC   53.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   13



CP000936.1/1042675-1042794           AAUUAG-CAUACC-AAUGAAUUUAAAGAUUCUUUA-AAGAUUCUUUAAAGAGUCUUAUUUUGUGAUGAAAAUUUAAUAUGUAAAUCUCAGACGAUAGA--AA-UUAAAAACUCUGUCGUCUUUUUU
AFUI01000002.1/474805-474913         AAAUAG-CAUACC-AAUAAAACAAAGGAUUCUUUAA------------AGAGUCUUAUUUUGUGAUGAAAAUUUAAUAUGCAAAUCUCAGACGAUAGA--AA-GUAAUAAUUCUGUCGUCUUUUUU
AEXJ01000002.1/13718-13610           AAAUAG-CAUACC-AAUAAAAGUAAAGAUUCUUUAA------------AGAGUCUUAUUUUGUGAUGAAAAUUUAAUAUGUAAAUCUUAGACGAUAGA--AA-GCAAUAAUUCUGUCGUCUUUUUU
AECM01000019.1/118-9                 AAAUAG-CAUACC-AAUAAAACUAAGGAUUCUUUAA------------AGAGUCUUAUUUUGUGAUGAAAAUUUAAUAUGUAAAUCUCAGACGAUAGA--AAAUCAAAAAUUCUGUCGUCUUUUUU
ABYO01000196.1/82916-83021           AAAUAG-CAUACC-AAUAAAACUAAAGAUUCUUUAA------------AGAGUCUUAUUUUGUGAUGAAAAUUUAAUAUGUAAAUUUCAGACGAUAGA--AA-GUAA---UUCUGUCGUCUUUUUU
CP001709.1/61977-62085               AAAUAG-CAUACC-AAUAAAACUAAGGAUUCUUUAA------------AGAGUCUUAUUUUGUGAUGAAAAUUUAAUAUGUAAAUUUUAGACGAUAGA--AA-AUAAAAAUUCUGUCGUUUUUUUA
AEGF01000293.1/9089-8981             AAUUAG-CAUACC-AAUGAAUUUAAAGAUUCUUUAA------------AGAGUCUUAUUUUGUGAUGAAAAUUUAAUA--UAAAUCUCAGACGAUAGAUAAA-UUAAAAACUCUAUCCUUUUUUUU
AFUH01000001.1/7246-7143             AAACAA-UAUU---AGUGGAUGAAAAAGAGUUUUUA------------AGG---UUAUCUAAUGAUGAAAAUUUAAUAUGUGAAUCUCAGACGAUAGA--AA-GUAAUAAUUCUGUCGUCUUUUUU
ABES01000001.1/122239-122130         AAAUAG-CAUACC-AAUAAAAAUAUGGAUUUUUUAA------------AGAGUCUUAUUUUGUGAUGAAAAUUUAAUAUUUAAAUUUUAGACGAUAGA--AAAUCAAAAAUUCUACCCUCUUUUUU
AEXN01000042.1/683-580               ----AGACAAUAUUAGUGGAUGAAAAAGAGUUUUUA------------AGG---UUAUCUAAUGAUGAAAAUUUAAUAUGUGAAUCUCAGACGAUAGA--AA-GUAAUAAUUCUGUCGUCUUUUUU
AEUY02000003.1/194737-194840         AGACAA-UAUU---AUUGGAUGAAAAAGAGUUUUUA------------AGG---UUAUCUAAUGAUGAAAAUUUAAUACACAUAUUUUAGACGAUAGA--AA-AUAAUAAUUCUGUCGUCUUUUUU
AFUG01000040.1/19843-19735           AAAUCC-CCUACC-AAUAAAAGUAAAUAUUUUAAAA------------AGCAUCUCAUUUUGUGAUAAAAAUUGAAUAUGUAAAUUUUAGACGAUAGA--AC-GUAAUAAUUCUGUCGUUUUUUUG
AE005672.3/972498-972607             AAGCAG-CACACCUAAUGAAUUUAAAGAUUCUUUAA------------AGAGUCUUAUUUUGUGAUGAAAAUUUAAUAUGUAAAUCUCAGACGAUAGA--AA-UUAAAAACUCUAUCGUCUUUUUU
#=GC SS_cons                         :::<<-.<<<<--.---<<<<---<<<<<<<<____............>>>>>>>>>>>>>>>>->>---------------------<<<<<<<<<<..__.________>>>>>>>>>>:::::
#=GC RF                              AAacag.cacacc.AaUagauuuAaagacucuUUaA............agagucuuaucuugugAugAAAAUUUAAUAUgUAAAUcUcaGaCGauaGa..AA.uUAAaAAuuCuguCGuCuUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02435
#=GF ID   SpF41_sRNA
#=GF DE   Streptococcus sRNA SpF41
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   52.00
#=GF TC   53.60
#=GF NC   50.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   9



AFGR01000002.1/126189-126291         AAAGCACAAUGAGUAGUAUAUAGGGAUUGCACCUUAAUUGAGGAGAUUCCGGUUCGAAUCCGGGCUAUUGUGCU--A-----GCAUCUAG--GAAACUAGGUGCUUUUUGUU
CP002651.1/1321428-1321323           AAAACGCAAGGGAUAGUAUAGAAGGAGUACACCUUGAUAGAGGUAGCCACGGUGCGAAUCCGUGUCAUUGCGUU--ACA-UCUAGCCCCU--UAAUUGGGGCU-UUUUAAUU
AFFN01000019.1/549-651               AAAGUACAAUGAGUAGUAUAUAGUGCUUGUGCCUUGAUUGAGGAGAUUCCGGUUCGAAUCCAGGCUAUUGUGCU--A-----GCAUCUAG--GGAACUAGGUGCUUUUAUGA
ACDZ02000005.1/165323-165430         UAAACGUAAGGAGUAGUAUAUAGGGAUUGCGCCUUGAUGGAGGAGAUUCCGGUUCGAAUCCGGGCUAUUACGUCUA-A---GACAUCUAUUUGUAAAUAGGUGUCUUUUUUU
AEEN01000007.1/4925-5032             GAAACGUAGGGAGUAGUAUAUAGGGAUUACGCCUUGAUGGAGGAGAUUCCGGUUCGAAUCCGGGCUACUACGUU--ACAUCUUAGCCCCU--UAAUUGGGGCUUUUUUUGUU
AFIN01000196.1/30401-30295           GAAACGCAAGGAGUAGUAUAGAGUGAGUACACCUUGAUGGAGGAGGCUCAGGUUGAAAUCCUGACUAUUGCGUU--ACAUCUUAGCCCCU--UAAUUGGGGUU-UUUUUGUG
ACRO01000019.1/4045-3938             AUGACGUAAGGAGUAGUAUAGAGUGAGUACGCCUUGAUGGAGGAGGCUCAGGUUGAAAUCUUGGCUAUUACGUCUA-A---GACAUCUAUUUAUGAAUAGGUGUCUUUUUUC
AEUT02000001.1/200486-200589         UUAACACAA-GAGUAGUAUAUAGAGAUUGCCCCUUUAUUGAUGGGAUGCCGAUUCGAAUCCUGACUAUUGUGUU--AA---UGCAUCCAG--AUAACUGGGUGCUUUUAAAA
AAGY02000021.1/17692-17794           AAAGCACAAGGGAUAGUAUAGAAGGAGUACACCUUGAUAGAGGUAGCCACGGUGCGAAUCCGUGUCAUUGUGCU--A-----GCAUCUAG--GAAACUAGGUGCUUUUUAUU
#=GC SS_cons                         ::(((((((--((,,,,,,,,,,,,,,,,,<<<<<____>>>>>,,,<<<<<_______>>>>>))-)))))))..--...-<<<<<<<<..____>>>>>>>>::::::::
#=GC RF                              aAagCgcAagGaGUAGUAUAuAGgGAuUaCcCcUugAUugAgGgGaucccGGUucGAAUCCgggCuAuUgcGcu..Aa...ugcgcCccg..uaAacggGgcgcUUUUuauu
//
# STOCKHOLM 1.0

#=GF AC   RF02436
#=GF ID   SpF43_sRNA
#=GF DE   Streptococcus sRNA SpF43
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   70.00
#=GF TC   76.40
#=GF NC   54.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   5



AEVF01000006.1/27729-27631           AGCAAUAUUCGGAGGUAAGGGAGACAUGAACAACUAAG-UCUAU--CAAAUAAAGAACCUUUAUUUAGUAGAU--CUUGUUUCUGUCUCUUUUUGUGUACUCUU
AFUO01000002.1/122223-122126         ACUAAUACUCGGAGGUAAGGGAGACAUGAACAACUA-A-UCUAU--CAAAUAAAGAAUCUUUAUUUAGUAGAU--CUUGUUUUUGUCUCUUUUUGCAUGCUCUU
AEGF01000236.1/10494-10396           AUUAAUACUUGGAGAGGUAAGUGACAUGAACAACUAAG-UCUAUCUCAAAUAAAGAACCUUUAUUUAGUAGAU--CUUGUUUUUGUC-UUUUU-GUGUGCUCUU
AFUC01000003.1/147470-147372         AAUUACAUUCGGAGGUAA-GGAGAUAUGAACAACUAAGUUUCGU--UAAAUAA-GAUACUUUAUUUAGUGGACUGCUUGUUC-UAUCUCUUUUUGUGUGCCCUC
FQ312045.1/254313-254411             ACUAAUACUCGGAGGUAAGGGAGACAUGAACAACUAAG-UCUAU--CAAAUAAAGAACCUUUAUUUAGUAGAU--CUUGUUUUUGUCUCUUUUUGUGUGCUCUU
#=GC SS_cons                         ::::::::::<<<<--<<<<<<<<<<-<<<<<<----<.<<<<<..-<<<<<<<<___>>>>>>>>->>>>>>..->>>>>>->>>>>>>>>>------>>>>:
#=GC RF                              AuuaAuAuUcgGaGguaaggGaGacaUgaaCaaCUAAg.ucuau..caaauaaaGAacCuuuauuuAguagac..CuuGuucuuguCuCccuuUGugUgCuCuu
//
# STOCKHOLM 1.0

#=GF AC   RF02437
#=GF ID   SpF44_sRNA
#=GF DE   Streptococcus sRNA SpF44
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   70.00
#=GF TC   85.20
#=GF NC   45.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   12



CP002925.1/1222436-1222530           AUGUCAUCCCGUGAGGUGACGAAGACGCAGAAAUACUUGAAAC-UCUCUAAAAUCUAG-----------------AUUUUAGA-GAAGUCUUACUCUGAGGGCCUAUUGCUGUA
CP001015.1/1155118-1155212           AUGUCAUCCCGUGAGGUGACGAAGACGCAAAAAUAUUUGAAAC-UCUUUAAAGUCUAG-----------------AUUUUAGA-GAAGUNUUACUCUGAGGGCCUAUUGCUGUA
AFUO01000002.1/117955-117854         AUGUCAUCCCGUGAGGUGACGAAGACGCAGAAAUAUAUGAAGU-UCUUUAAGAA----UGGAA------UAAUCUUUUUUAAA-GAAGUCUUACUCUGAGAGCCUGUUGCUGUA
ACRK01000017.1/14168-14268           AUGUCAUCCCGUGAGGUGACGAAGACGCAGAAAUAUAUGAAAU-UCUUUAAUGA----GAUAC-------CCCUCUCUUUAAA-GAAGUCUUACUCUGAGAGCCUGUUGCUGUA
AFUT01000001.1/277028-276926         AUGUCAUCCCGUGAGGUGACGAAGACGCAGAAAUAUAUGAAAU-UCUUUAAGAAU---GAGAUA-----AUCCUCUUUUUAAA-GAAGU-CUACUCUGAGAGCCUAUUGCUGUA
AEEP01000010.1/153198-153301         AUGUCAUCCCGUGAGGUGACGAAGACGCAGAAAUAUAUGAAAU-UCUUUGAGAAU---GAGAUC-----AUCCUCUUUUUAAU-GAAGUCAUACUCUGAGGGCCUAUUGCUGUA
AFNN01000018.1/98124-98226           AUGUCAUCCCGUGAGGUGACGAAGACGCAGAUAUACAUAACAU-UCAUUAAAA-----UGUGGUC---AAUUGUU-UUUUAAU-GAAGUCUUACUCUGAGAGCCUAUUGCUGUA
AFUQ01000001.1/523273-523170         AUGUCAUCCCGUGAGGUGACGAAGACGCAGAUAUAUAUGAAAU-UCUUUAAA------UAUUGGGAUAACCAUGU--UUUAAA-GAUGUCUUACUCUGAGAGCCUAUUGCUGUA
AFUU01000003.1/359808-359903         AUGUCAUCCUGUGAGGUGACGAAGGCGCAGAUUUAUAUAAAUU-UUUAAAAGAUAGCU-----------------AUUUUUUAAAAAGUCUUACUCUGAGGGCCUAUUGCUGCA
AGAE01000033.1/15814-15717           AUGUCAUCCCGUGAGGUGACAAAGACGCAGU-AUA--CGAAAU-UCUUUAAGAA----UGGAA-------UAGUUUUUUUAAA-GAAGUCUUACUCAGAGAGCCUAUUGCUGUA
AEVF01000006.1/24405-24304           AUGUCAUCCUGUGAGGUGACAAAGACACAGAAACUUAUCGUUCUUUAAUGAAGACU--AACA---------AUGUUUUUUAAU-AAAGUCUUACUCUGAGAGCCUGUUGCUAUA
CP000918.1/1255421-1255515           AUGUCAUCCCGUGAGGUGACGAAGACGCAGAAAUAUUUAAAAC-UCUUUAAAAUCUAA-----------------AUUUUAAA-GAAGUCUUACUCUGAGGGCCUAUUGCUGUA
#=GC SS_cons                         :<<<<<--<<____>>>>>>>-----((((-((((,,,,,,,,.<<<<<<<<<<_..._____......._____>>>>>>>>.>>,<<<<<______>>>>>,))))-)))):
#=GC RF                              AuGuCaUCCcGUGAgGuGaCgAAGACgCaGAaauaUaUgAaau.ucuuuaaaaau...uauaa.......uauuuuuuuuaaa.gaAGuccuACUCUGagggCCuauuGCuGcA
//
# STOCKHOLM 1.0

#=GF AC   RF02438
#=GF ID   SpF51_sRNA
#=GF DE   Streptococcus sRNA SpF51
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   50.00
#=GF TC   51.20
#=GF NC   37.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   8



AFUF01000014.1/63606-63650         AGUGUAGUCUCCUAAAUACAUUUAGCCCUUAUUAU-----AGGGCUUUUU
AEEN01000008.1/43457-43413         AGUGUAGCCUCCUAAAUGCACUUAGCCCUUAUUAA-----AGGGCUUUUU
AFUT01000007.1/45851-45807         AGUAUAGUCUCCUAAAUACACAAAGCCCUUGUUAA-----AGGGCUUUUU
ABAE01000013.1/42152-42108         AGUUUAGUCUCCUAAAUACAAUUGGCCCUUAUUAU-----AGGGCUUUUU
ACRL01000036.1/44169-44128         AGUGUAGUCUCCUAAAUGCACGUAGCCCUUAU--------AGGGCUUUUU
AEDY01000036.1/35148-35191         AGUAUAGUCUCCUAAAUACACUAAGCCCU------AUACAAGGGCUUUUU
AEVD01000011.1/84984-85028         AGUAUAGUCUCUUAAAUACACAAAGCCCUUU----AA-CAAGGGCUUUUU
FM211187.1/2193462-2193506         AGUAUAGUCUCCUAAAUGCACUUAGCCCUUAUUAU-----AGGGCUUUUU
#=GC SS_cons                       :<<<<__________>>>>----<<<<<<______.....>>>>>>::::
#=GC RF                            AGuaUAGUCUCCUAAAuaCACuuAGCCCUUAUUAu.....AGGGCUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02439
#=GF ID   SpF56_sRNA
#=GF DE   Streptococcus sRNA SpF56
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   80.00
#=GF TC   107.30
#=GF NC   37.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   2



AGOL01000005.1/173129-173227         UGAUAGGUAUGAAAAGUGGCGUUGAAGCUGGAUAAGUUUAUAAAGAGUUUGAAUGAAGAAAUGAAAAGUAAAUAAGUUGAUGAUGAAUUGCAAAAAUAG
AGPS01000003.1/150629-150726         UGAUAGGUAUGAAAAGUGGCGUUGAAGCUGAAUAAGUUUAUAAAGCGUUUGAAUGAAGAAAUGGAAAGUAAAUAAGUUGACGAUGAAUUACA-AAAUAG
#=GC SS_cons                         :::::::::::::::<<<<<<<<<-<<<<------<<<<<<----<<<<<________>>>>>---->>>>>>->>>>-->>>>>-->>>>::::::::
#=GC RF                              UGAUAGGUAUGAAAAGuggCguugAagCuGaAUAAguuuauAAAGcguuuGAAUGAAGaaaugaAAAguaaauAaGuuGAcgauGAAuuaCAAAAAUAG
//
# STOCKHOLM 1.0

#=GF AC   RF02440
#=GF ID   SpF59_sRNA
#=GF DE   Streptococcus sRNA SpF59
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   60.00
#=GF TC   88.40
#=GF NC   43.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   4



AEVF01000008.1/169798-169879         UAUAAACCCGAGUAAAAAAUACCUACGGACAGGUUGGGUUGAAUGCCGAAGCGUGGCUGGGAAGCCACAUUAUUGAUAGGGU
AM946015.1/1310066-1309991           UAUAGACCUUUAUAA----UGCCUACGGACAGGC-GGGUCGAAUGCCGAAGCGUGGUU-AAAAGCCACAUUAUUGAUUGAGU
CP002644.1/1419923-1419848           UAUUGAUCA---UAACCAAAGCCUACGGACAGGC-GGGUCGAAUGCCGAAGCGUGGC-GUAA-GCCACAUUAUUGAUAGGGU
FQ312029.1/853698-853779             UAUAAACCCGAGUAAAAAAUGCCUACGGACAGGCAGGGUUGAAUGCCGAAGCGUGGUUGAAAAGCCACAUUAUUGAUAGGGU
#=GC SS_cons                         :::::((((---(((,,,,,<<<<______>>>>.,<<<_____>>>,,,,,<<<<<<____>>>>>>,,,,)))---))))
#=GC RF                              UAUaaacCcgaguaaaaAAuGCCUACGGACAGGC.GGGuuGAAUgCCGAAGCGUGGcuGaAAagCCACAUUAuugAUagGgu
//
# STOCKHOLM 1.0

#=GF AC   RF02441
#=GF ID   SpF61_sRNA
#=GF DE   Streptococcus sRNA SpF61
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   60.00
#=GF TC   82.10
#=GF NC   49.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   3



AEHQ01000087.1/3722-3665         AAUAAAGAUAUGGAGGUGCUUGAACUUGCUUGUGGGUUUCGUGUCAUAAUAGUGAUAG
CP001709.1/48521-48578           AAUAAAGACAUGGAGGUGCUUGAAUUUGCUUGUGGGUUUCGUGUUAUAAUUAUGACAA
FQ312041.1/925550-925607         AAUAAAGAUAUGGAGGUGCUUGAACUUGCUUGUUGGUUUCGUGUCAUAACAGUUAUAG
#=GC SS_cons                     ::::::<<<<<<<<<-<<<________>>----->->>>>>>>>>:::::::::::::
#=GC RF                          AAUAAAGAcAUGGAGGUGCUUGAAcUUGCUUGUgGGUUUCGUgUCAUAAUagUgAUAg
//
# STOCKHOLM 1.0

#=GF AC   RF02442
#=GF ID   SpF66_sRNA
#=GF DE   Streptococcus sRNA SpF66
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   42.00
#=GF TC   42.10
#=GF NC   41.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   9



ABAD01000008.1/1107-1345             GUUACCGAUUACGUUCCUA-UGGGUUCGUGAGA--GGAGGUGAAACUAAUGAGCCUUAUACCAGAGCUUGCUCUUACUAUUAUAACAG--AUGUUAUAGCUGGAAUUAUCUUGUAUUUCGUCUGCAAAUGGCUAGAUGGUAAGAAGUAGACCGACUGACUAGCCUAUAAACACCCGUUAAAUC-GCUAAGAUACGUCAAAAAAGCCCUUAACUAUGGCACUAGU--UAGGGGCUUUGGUGU---UCUAAU
ABWC01000005.1/96509-96747           GUUACCGAUUACGUUCCUU-ACGGUUCGUGAAA--GGAGGUGAAACUAAUGAGCCUUAUCCCAGAGCUCGCUCUUACUAUUAUAGCAG--AUGUUAUAGCUGGAAUUAUCCUAUAUUUUGUUUGCAAAUGGCUAGAUGGUAAGAAGUAGACCGACUGACUAGCCUGUAAACACCCGUUAAAUC-GCUAAGAUACGUCAAAAAAUCCCUUAACUACGGCCAUAGU--UAAGGGAUUUGGUGU---UCUAAU
FN568063.1/2078653-2078891           GUUACCGAUUACCUUCCUU-ACGGUUAGUGAGA--GGAGGUGAAACUAAUGAACCUUGCCCCAAAGCUCGCUCUUACUAUUAUAGCGG--AUGUCAUAGCAGGAAUUAUCUUGUAUUUCGUCUGCAGAUGGCUAGAUAGUAAGGAGUAGACCGACUGACUAGCCUAUAAACACCCGUUAAAUC-GCUAAGAUACGUAAAAAAAGCCCUUAACUACGGCCAUAGU--UAGGGGCUUUGGUGU---UCUAAU
AFQV01000029.1/4783-5021             GUUACCGAUUACGUUCCUU-ACGGUUCGUGAAA--GGAGGUGAAACUAAUGAGCCUUAUCCCAGAGCUCGCUCUUACUAUUAUAGCAG--ACGUCAUAGCUGGAAUCAUCUUGUAUUUCGUUUGCAAAUGGCUAGAUGGUAAGAAGUAGACCGACUGACUAGCCUAUCAACACCCGUUAAAUC-GCUAAGAUACGUCAAAAAAGCCCUUAACUAUCGCAGUAGU--UAGGGGCUUUGGUGU---UCUAAU
AEDT01000032.1/170791-171029         GUUACCGAUUACGUUCCUU-ACGGUUCGUGAGA--GGAGGUGAAACUAAUGAACCUUGCCCCAGAGCUCGUUCUUACUAUUAUAGCGG--ACGUCAUAGCAGGAAUUAUCUUGUAUUUCGUCUGCAAAUGGCUAGAUGGUAAGAAGUAGACCGAGUGACUAGCCUAUCAACACCCGUUAAAUC-UCUAAGAUACGUCAAAAAAGCCCUUAACUAUGGCAGUAGU--UAGGGGCUUUGGUGU---UCUAAU
CACG01000004.1/291491-291253         GUUACCGAUUACGUUCCUU-ACGGUUCGUGAGA--GGAGGUGAAACUAAUGAACCUUGCCCCAGAGCUCGUUCUUACUAUUGUAGCGG--ACGUCAUAGCAGGAAUUAUCUUGUAUUUCGUCUGCAAAUGGCUAGAUGGUAGGAAGUAGACCGAAUGACUAGCCUGUAAACACCCGUUAAAUC-GCUAAGAUACGUCAAAAAAUCCCUUAACUACUGCAAUAGU--UAAGGGAUUUGGUGU---UCUAAU
AEGF01000243.1/386-146               GUUACCACGUACGUUCCUA-UGGGUUCGAGUGAGAGGAGG--UAACUAAUGAGCCUUAUCAUAGAGCUCGCUCUUUCUAUUAUAGCGGAGAUGUUAUAGCUGGAAUUAUCUUGUAUUUCGUCUGCAUGGCGAUAGAUAGUAAGGAGUAGACCGACUGACUAGCCUAUAAACACCCGUUAAAU---CUAAGAUACGUCAAAAAAAAGCCCUACUACGGCCAUAGUUAGGGGCUUUUUGGUGU---UCUAAU
AEQQ01000115.1/7049-6819             UAAACCGGUCGUAUCUCCAAAAGAGAUAUGAAA--GGAGGUGAUGGUUUUGAGUUACCUUUUCGAGCUCUUACUUAGUGUCCUGGCAA--AUGUAUUGGCC-----UAUUUCA-------UUUGCAAAUGGCUAGACGCUAAGGACAAAAGCGAUAG-CUAGCCUGUAAACACCCGUUAAAUCUAAUUAGAUACGUCAAAAAAUCCCAAGAGAACGGCCAUUCU--CUUGGGAUUUGGUGUAGUUUUAAG
FQ312045.1/1035033-1035271           GUUACCGAUUACGUUCCUA-UGGGUUCGUGAGA--GGAGGUGAAACUAAUGAGCCUUAUCAUAGAGCUCGCUCUUACUAUUAUAGCGG--AUGUUAUAGCUGGAAUUAUCUUGUAUUUCGUCUGCAGAUGGCUAGAUAGUAAGGAGUAGACCGACUGACUAGCCUAUAAACACCCGUUAAAUC-GCUAAGAUACGUCAAAAAAGCCCUUAACUACGGCCAUAGU--UAGGGGCUUUGGUGU---UCUAAU
#=GC SS_cons                         ::::<<--<<<<<--<<__.__>>-->>>>>--..>>,[[[[[,,,,,,,<<<<<<______>>->>>>,,,,,,,,,,,,,((((((..-((((,<<<-<<<<<<________>>>>>>->>>,,,,,<<<<<<-<<<<--<<______>>->>>>->>>>>>,,,,))))-)))))),,]].]]]-<<<-<<--<<<---<<<<<<<<<<<<______>>>>..>>>>>>>>>>>-->>...>>>:::
#=GC RF                              guuACCGaucacgUUcCUa.aaGguucgugagA..GGAggcGaAAcUAAUGaGccuUauccuagAgCuCguuCUUAcUAUUauagCgG..AuGuuAuagCcGgaauUAUcUUgUauuuCgUcugCAaAuGGCuaGAcgguAAGgAguAgAcCGaccgACuaGCCUaUAaaCaCCcGuuaAAuC.gcuAaGaUaCGUCaaAAAagccCcugacuacgGCcauagu..cagGggcuuuGGUGu...uCuAAu
//
# STOCKHOLM 1.0

#=GF AC   RF02443
#=GF ID   SpR08_sRNA
#=GF DE   Streptococcus sRNA SpR08
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   80.00
#=GF TC   104.40
#=GF NC   39.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   3


CP001993.1/2066445-2066373 AAAAAACGGAUAUAAUGUAUUUGAAGAUGUUGCUAGCAGAAAGAACUUAAUAAGCUUCUUAACAUCGCAGUGA
AFQV01000009.1/33920-33992 AAAAAACGGAUAUAAUAUAUUUGAAGAUGUUGCUAGCAGAAAGAACUUAAUAAGCUUCUUAACAUGGCAGUGA
CP000920.1/1849663-1849591 AAAAAACGGAUAUAAUGUAUUUGAAGAUGUUGCUAGUAGAAAGAACUUAAUAAGCUUCUUAACAUCGCAGUGA
#=GC SS_cons               ::::::<<<<<<<___>>>>>>>--<<<<<<<--<<<________________>>>--->>>>>>>:::::::
#=GC RF                    AAAAAACggAUAcAAUgUAUuuGAAgAUGUUgCUAGcAGAAAGAACUUAAUAAgCUUCUuAACAUcGCAGUGA
//
# STOCKHOLM 1.0

#=GF AC   RF02444
#=GF ID   SpR10_sRNA
#=GF DE   Streptococcus sRNA SpR10
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   50.00
#=GF TC   66.30
#=GF NC   35.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   5



CP002925.1/1998066-1998020           GGAGUUGCUCUCAAGACUUAUUUUUGACAAGGAGAGACGGACAAUGG
EF452717.1/1-44                      ---GUUGCUCUCAAGACUUAUUUUUGAAAAGGAGAGACAGAAAAUGG
ADMV01000003.1/219070-219024         GGAGUUGCUCUCAAGACUUAUUUUUAGCAAGGAGAGACGGAAAAUGG
AEGF01000097.1/241-195               UGGGUUGCUCUCUCGACUUAUUUUUGAAAAGGAGAGACAGAAAAUGG
FQ312030.1/1971353-1971307           GGAGUUGCUCUCAAGACUUAUUUUUGAAAAGGAGAGACAGAAAAUGG
#=GC SS_cons                         ::::<<<<<<<<-----<<<____>>>---->>>>>->>>:::::::
#=GC RF                              GGAGUuGCUCUCAAGACUuAUUUUUgAaAAGGAGAGACaGAAAAUGG
//
# STOCKHOLM 1.0

#=GF AC   RF02445
#=GF ID   SpR14_sRNA
#=GF DE   Streptococcus sRNA SpR14
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   50.00
#=GF TC   80.70
#=GF NC   44.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   5



AFGD01000007.1/81456-81377         UUGACAAAGAGC--CAAAAAAUUCUCUUUUCAUACUCAUUUAAAAUCAAAAAGGGAAAUUAUC--GUUUUACGGACAUACAUAU
CP002925.1/1027161-1027086         ----UUUCUAAU--GAAAAAAUUCUCUUUUCAUACUCAUUUAAAAUCAAAAAGGGAAUUUAUC--GUUUUACGGACAUGUAUAU
FQ312041.1/1004868-1004794         UUCUCAUGAA-------AAAAUUCUCUUUUCAUACUCAUUUAAAAUCAAAAAGGGAAUUUAUC--GUUUUACGGACAUGUAUAU
AEGF01000337.1/11864-11783         UUGACACAAAGACACAAAAAAUUCUCUUUUCAUACAUAUUUAAUAUC-AAAA-AGAAUUUAUCGUUUUUUACGGAUAUGUAUUA
CP002121.1/1044076-1044155         UUGACAAAGAGC--CAAAAAAUUCUCUUUUCAUACUCAUUUAAAAUCAAAAAGGGAAUUUAUC--GUUUUACGGAUAUGUAUAU
#=GC SS_cons                       :::::::<<<<<..----<<<<<<<<<<<<__________________>>>>>>>>>>>>---..>>>>>::::::::::::::
#=GC RF                            UUgaCAuaaAgc..cAAAAAaUUCuCUUUUCAUACucAUUUAAAAUCAAAAAGgGAAuUUAUC..guUuuACGGAuAUGUAUAu
//
# STOCKHOLM 1.0

#=GF AC   RF02446
#=GF ID   SpR18_sRNA
#=GF DE   Streptococcus sRNA SpR18
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   60.00
#=GF TC   63.30
#=GF NC   51.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   23



AEXM01000031.1/44882-44751           UUCAACGGUUACAG-----AAGAUAAAAAACUGUAACUG---GGAUUAAAAUGG-GAACAUUUGUUAAAAAGAAUAAAUCGAAUAAUAGUUCCAAGUGGUUUACAUUUGGGCAAAAAAUUAGACCGUAGUCUUUAGGCUGC
AEAA01000021.1/32046-31916           AUCAACAGUUACAG-----AAGAUUAAAAACUGUAACUG---GGAUUAAAAUGG-GAACAUUUGUUAAAAAGAAUAAAUUGAAUAAUUCUUCCAAGUGGUUUGCAUUUGGACAAAAAAUAAGACCGUAGU-UUCUAGCUGC
ADGP01000023.1/102717-102847         AUCAACGGUUACAG-----AAGAUGAAAAACUGUAACCG---GGAUUAAAAUGG-GAACAUUUGUAAAAAAGAAUAAAUUGAAUAAUCGUUCCAAGUGGCGUACAUUGGGACAAAAAAUUAGACCGUAGU-UUCAGGCUGC
ABYO01000191.1/4317-4187             AUCAAUAGUUACAG-----AAGAUUAAAAACUGUAAAUG---AGAUUAAAAUGG-GAACAUUUGUUAAAAAGAAUAAAUUGAAUAAUAGUUCCAAGUGGUUUACAUUCGGACAAAAAAUUAGACCGUAGU-UUCAAGCUGC
AEEH01000040.1/8108-8238             UUCAACGGUUACAG-----AAGAUGAAAAACUGUAACUG---GGAUUAAAAUGG-GAACAUUUGUAAAAAAGAAUAAACUAAACAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAAAUUAGACCGUAGUUA-AAAGCUGC
AENP01000027.1/10099-10229           AUCAAUGGUUACAG-----AAGAUUAAAAAUUGUAACUG---GGAUUAAAAUAG-GAACAUUUGUAAAAAAGAAUAAAUUGAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAUAUUAGACCGUAGU-UUCAAGCUAC
CP001849.1/699515-699644             AUAAAUGGUUACAG-----AAGAUGAAAAACUGUAACUG---GGAUUAAAAUGG-GAACAUUUGUAAAAAAGAAUAAAUUGAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAA-AAAUUAGACCGUAGUU-UAAAGCUGC
ACNV01000013.1/8204-8330             AUCAACGGUUACAG-----AGGAUUAAAAACUGUAACUG---GGAUUAAAACGG-GAACAUUUACUAAAAAGAAUAAAUUGAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAAAUGGCUCU----UUGUCAA-CUGU
AFUG01000021.1/14527-14657           AUCAAUGGUUACAG-----AAGGUAAAAAAUUGUAACUG---GGAUUAAAAUGG-GAACAUUUGUAAAAAAGAAUAAAUUGAAUAAUAGUGCCAAGUGGUUUACAUUUGGACAAAAAAUUAGACCGUAGUUA-AAAGCUGC
ADDO01000017.1/49963-49833           AUCAACGGAUACAG-----AAAAUGAAAAACUGUAACUG---GGAUUUAAAUGG-GAACAUUUGUUAAAAAGAAUAAACUUAAUAAUAGUUCCAAGUGCUCUACAUUUGGACAAAAAAUUAGGCCGUAGUUA-AAAGCUGC
AFUH01000001.1/239900-239770         UUCAACAGUUACAG-----AAGAUGCAAAACUGUAAUUG---GGAUUAAAAUGG-AAACAUUUAUAAAAAAGAAUAAAUUGAAUAAUUCUUCCAAGUGAUUUACUUUUAGGCAAAAAAUUAGACCGUAGU-UUCAAGCUAC
AEXN01000047.1/38216-38086           AUCAACGGUUACAG-----AAGAUGAAAAACUUUAACUG---GGAUUAAAAUGG-GAACAUUUGUAAAAAAGAAUGAAUUGAAAAAUAGUUCCAAGUACUUUACAUGAGGACAAAAAAUUAGACCGUAGUU-UAAAGCUAC
AEDP01000028.1/28717-28587           AUUACAAGCUAUAU-----AG-AGAAUAAAAUAUGGCUACUGGUACUCAAAUGG-UACUGGAAGUAAAAAAGAAUAAAUUAAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAAA--AGACCGUAGUUUU-AAGCUGC
CP001850.2/698195-698313             ----AAUAGAAUCC-----AGUAUUUUGAAUGGUU---U---GGGAUAUAUUGG---ACGUUUGG--AAAAGAAGAAUGGGAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAAA--AGACCGUAGUUUUUAGACUGC
AP008971.1/364491-364616             UUUAUUUC---CAC-----AA-AUUAGACAGUGCU-GCG---GGAUUAAAAUGG-GAACAUUUAUAAAAAUUAAUAAAUUGAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAAAUUAGACCGUAGU-UUCAAGCUGC
ACXU01000019.1/3192-3059             AUUACAAGCUAUAU-----AG-AGAAUAAAAAAUGGCUACUGGUACUCAAAUGG-UACUGGAAGCAAAAAAGAAUAAUUAAAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAAAUUAGACCGUAGUUUUUAAGCUGC
AEHO01000007.1/175702-175570         AUUACAAGCUAUA------AAUAUAAUGAAAAAUGGCUACUGGUACUCAAAUGG-UACUGGAAGUAAAAAAGAAUACAUUGAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAAAUUAGACCGUAGAUUU-AAGCUGC
ACGC01000072.1/19305-19434           UUCGAGAGGAAAGU-----GAUAUGAAAAACUGUAACUG---GGAUUAAAAUGG-GAACAUUUGUUAAAAAGAAUAAAUUGAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAAAUUAGAUCAUAACU-UAAGUGUU-
ABXA01000014.1/18882-19015           AUUACAAGCUAUA------AAGAGAAUGAAAAAUGGCUACUGGUACUCAAAUGG-UACUGGAAGUAAAAAAGAAUAAUUAAAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAAAUUAGACCGUAGUUUCAAUGGUUC
AFUI01000010.1/204917-204790         UUUGAAUCUUGAUA-----AAGAAAAUAAA----AAGAU---GCGAGCGAAUAGCGUGCAUUUGUUAAAAAUAAUAAAUUGAAUAAUAGUUCCAAGUGGUUUAUAUUUGGACAAAAAAUUAGACCGUAGUUUC-AAGCUGC
ACGK02000001.1/586846-586975         AUUGAGUGGGAGUA-----AUCGCAUAAAAUAAUUCCUU---GUAUUCAAAUGA-UGCGAGAAGCUAAAAAGAAUAAAUUGAGCAGUAGUUCCAAGUGGU-UAUAUUUGGGCAAAAGAUAAGACCGUAGCGUU-UAGCUGC
AFBB01000019.1/18024-18154           CUUAAUACAAGCUAUAAAGAAAAUGAAAAAUGGCUACUG---GUACUCAAAUGG-UACUGGAAGUAAAAAAU---AAUUGAAAUAAUAGUUCCAAGUGGUUUAUAUUUGGACAAAAAAUUAGAUCAUAAC-UUAAGUGU--
AGPR01000003.1/454153-454284         AUCAACGGUUACAG-----AGGAUUAAAAACUGUAACUG---GGAUUAAAACGG-GAACAUUUGCUAAAAAGAAUAAAUUGAAUAAUAGUUCCAAGUGGUUUACAUUUGGACAAAAAAUUAGACCGUAGUUUUCAAGCUGC
#=GC SS_cons                         :::::<<<<<<<<<.....___________>>>>>>>>>...-((-----((((.,,,,<<<<________>>>>,,,,,,,,,,,,,<<-<<<<<<<_____>>>>>>>>>,,,,,,,,,,,))))-----)):::::::
#=GC RF                              aUuAAcgguuacag.....AagAuaAaAAAcuguaaccg...GgauUaAAAuGG.gAacauucGUaAAAAAgaauAAAUugAAUAAUAGuUCCaAGUGGUUUACAUUuGGaCAAAAAAUUAGACCgUAGUUUucAaGcUgC
//
# STOCKHOLM 1.0

#=GF AC   RF02447
#=GF ID   SpR19_sRNA
#=GF DE   Streptococcus sRNA SpR19
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   79.00
#=GF TC   79.10
#=GF NC   77.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 27.53 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   23


AFUO01000002.1/76867-76988   GC-GU--U-CU--UCAAGCGAGCUUGGGGUAGUGGGAGCUAAGUAG-AAC-AAGGUA-AGAAAC---UGGCGCUUUCUGU---CGUA-----------U--UUU--UAAA-AACAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCUGACG
AEGF01000004.1/18200-18077   GC-GU--U-CU--UCAAGCGAGCUUGGGAUAUUGGGAGCCAAGUAG-GGC-AAAAUA-AUGAGC---UGGCGCUUUCUGU-AAAGUA-----------U--UAU--CAA---ACAA-----------------------------------------UGAAAAGAAAUAAAUUAGGGUGG--CCGCGUAUUUCAGACG
AEVF01000008.1/59380-59500   ---GUAA-AUC--CUAAGCGAGCCUGAGAUAGUGAGAGUCAGGUG--AUU-GAGAGA-UAAGUG---UGGCGCUUUCUGU---AGUA-----------U--UUU--CAAA-AACAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCUGACG
CP002888.1/1629808-1629675   GC-GU--U-UU--UCUAGCGAGCUUGGGAUAGUGAAAGCCAAGUAG-AGC-AAAAUG-AGCAG----UGGCGCUUUCUAU--CAGCA-------AAUAG--CUGAAGACA-AACA-----------------------------------GAUAAAAUGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCUGACG
FR873481.1/1676309-1676175   GC-GU--U-UU--UCUAGCGAGCUUGGGAUAGUGAAAGCCAAGUAG-AGC-AAAGUA----GGCAAGUGGCGCUUUCUCU--CAGCA---------AAGAGCUGAGUACA-AACA-----------------------------------GAUAAAAUGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCUGACG
CP000419.1/484617-484750     GC-GU--U-UU--UCUAGCGAGCUUGGGAUAGUGAAAGCCAAGUAG-AAC-AAAGUA----GGCA-AUGGCGCUUUCUCU--CAGC---------GAAGAGCUGAGUACA-AACA-----------------------------------GAUAAAAUGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCUGACG
CP000725.1/616173-616295     GU-CU--A-CU-UUUUAGCGAGUCUGGGAUAGUGUGAGCCAGAUAG-GGA-AGCAGA--GCAGA---UGGCGCUUUUGGU--UAACA-----------U--UUU--UAAA-CGUAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUUUGACG
AEDY01000133.1/2551-2430     ---GUAA-AUC--CUAAGCGAGCCUGUGGUAGUGAGAGUCAGGUG--AUU-GAGAGA-UGAGUG---UGGCGCUUUU--U---GGUAU--------AUU--UUU--UAUA-AAUAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCUGACG
AAJS01000001.1/612-738       GCUGU--U-UU--UUUAGCGAGCUCAAGGUAGUGAAAGUUGGGUAG-AAU-AGGAUG-AAU-AU---UGGCACUUUUUAG-UGAGUA-----------AAAGUA--CAAUCAAAAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UCUUUGACG
CP002176.1/766641-766762     GC-GU--U-CU--UCAAGCGAGCUUGGGAUAGUGGGAGCCAAGUAG-GGC-AAAAUA-AAGGGC---UGGCGCUUUCUGU---AGUA-----------U--UUU--CAAA-AACAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCUGACG
AEDX01000002.1/68960-68838   GC-GU--U-CU--UCAAGCGAACUUGGGAUAGUGGGAGCCAAGUAG-GGC-AAAAUA-AAGAAC---UGGCGCUUUCUGU---AAUA-----------U--UUU--UAAAAACAAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCUGACG
ACLO01000092.1/238019-237886 GC-GU--U-UU--UCUAGCGAGCUUGGGAUAGUGAAAGCCAAGUAG-AGC-AAAGUA-AGCAAG---UGGCGCUUUCUCU--CAGCAAAGAGCUGAGUA--CAA--CAGA-UAAAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCUGACG
AGMQ01000011.1/6820-6955     GC-GU--U-UC--UGCAGCGAACCUGAGAGAGUGUAAGUCAGGUGA-AAC-AAAAUA-AAGGAC---UGGCACUUUCUCU--UGGCU--------AAUAGCCAAGCUAACAAUCAGAUA------------------------------------AAUGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCAAACG
AGKJ01000013.1/6820-6955     GC-GU--U-UC--UGCAGCGAACCUGAGAGAGUGUAAGUCAGGUGA-AAC-AAAAUG-AAGGAC---UGGCACUUUCUCU--UGGCU--------AAUAGCUAAGCUAACAAUCAG------------------------------------AUAAAUGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCAAACG
AFBA01000004.1/53885-54005   GU-CU--A-CU-UUUUAGCGAGUUCGGGAUAGUGUGAGCCGGAUAG-GGA-AGC-AG-UGCAGA---UGGCGCUUUCGGU---UAUA-----------A--UUU--CAAA-AGUAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUU-UGACG
AFUT01000001.1/362365-362484 ---GUAAA-UC--CUAAGCGAGCCUGUGGCAGUGUGAGUCAGGUG--GUU-AAGAGA-UAAGUG---UGGCGCUUUU------GGUA-----------U--UUUAAUAAA-AAUAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCUGACG
AFFL01000010.1/71064-71184   GU-CU--A-CU-UUUUAGCGAGUUCGGGAUAGUGUGAGCCGGAUA--AGG-AAGCAG-UGCUGA---UGGCGCUUUCGGU---UAUA-----------A--UUU--CAAA-AGCAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UCU-UGACG
AFXO01000006.1/164557-164413 GC-AU--U-UC--UCAAGCGAGCCUGAGAUAGUGGAAGUCGGGUGA-AAU-AAAGUA-UG-AAC---GGGCGCUUUC------GGUA-----------A-GUUU--UA--------GUCGGUAGAUUAUUAAUUAAGACUAUAUUAACAA-------UGAAG--UAAUAAACUAGGGUGGAACCGCG--UUU-UGACG
AFXN01000007.1/222744-222601 GC-AU--U-UC--UCAAGCGAGCCUGAGAUAGUGGAAGUCGGGUGA-AAU-AAAGUA-UG-AAC---GGGCGCUUUC------GGUA-----------A-AUUU--UAG-------UCCUUGAUGUUAUCUU--AAGGCUAUAUUAACAA-------UGAAG--UAAUAAACUAGGGUGGAACCGCG--UUU-UGACG
AEKN01000016.1/65809-65941   ---GU--U-CUUCUCAAGCGAGUCUAGGAUAGUGGAAGCUAGAUGG-GAG-AUAGGGUAAUAAU---UGGCACUUUCGUAAUGAGCCUAGC---UCAAU--UUU--UUAA-ACAAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUU-UGACG
AP012053.1/431043-431174     GU-GU--U-UC--UU-AGCGAGUCCGAGGUGGUGAAAGUCGGAUGAAACU-GAAGUG-AGUCGC---UGGCGCUUUCGCU--UAGCA-----------A--GGC--UAAG------UU------------------------AAAAUCAG--AUAAAUGAAG--UAAUAAAAUAGGGUGGAACCGCG--UUU-UAACG
AGGI01000158.1/2834-2968     ---GU--U-CUUCUCAAGCGAGUCUAGGAUAGUGGAAGCUAGAUGG-GAG-AUAGGGUAAUAAU---UGGCACUUUCGUAAUGAGCCUAGCU-CAAUUU--UUU--UUAA-ACAAA-----------------------------------------UGAAG--UAAUAAAUUAGGGUGGAACCGCG--UUUCA-ACG
ABJK02000010.1/49302-49433   GU-GU--U-UC--UU-AGCGAGUCCGAGGUGGUGGAAGUCGGAUGG-AACUGAAAUG-AGUCGC---UGGCGCUUUCGCU--UAGCU-----------A--GGC--UAA-------GUU-----------------------AAAAUCAG--AUAAAUGAAG--UAAUAAAAUAGGGUGGAACCGCG--UUU-UAACG
#=GC SS_cons                 ((.((..(.((..((,,,,,,<<<--<<<-<<<<--<<<<---<<_.___.____>>.--->>>...>-->>>>->>>--..->>>,...........,..<<<..<<__._____.........................................>>>>>..,,,,,,,,,,,))-)))))-)):..:::::::::
#=GC RF                      Gc.gU..u.cc..ucaAGCGAgccUGgGaUAGuGaaagccagguag.Aau.AAAaua.aguggc...uGGCgCUUuCcuu..uggca...........a..cuu..cAaa.AacAA.........................................Ugaag..UAAUAAAuUAGggUggaAcCgCG..UUUcUGACG
//
# STOCKHOLM 1.0

#=GF AC   RF02448
#=GF ID   SpR20_sRNA
#=GF DE   Streptococcus sRNA SpR20
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   45.00
#=GF TC   47.70
#=GF NC   38.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22807675
#=GF RT   Control of virulence by small RNAs in Streptococcus pneumoniae.
#=GF RA   Mann B, van Opijnen T, Wang J, Obert C, Wang YD, Carter R, McGoldrick DJ,
#=GF RA   Ridout G, Camilli A, Tuomanen EI, Rosch JW
#=GF RL   PLoS Pathog. 2012;8:e1002788.
#=GF WK   Streptococcus_sRNA
#=GF SQ   7



AEEN01000015.1/76113-76069           UGGCACAGCCCUUGUUCUCGUGGCUAUCUGGUAAGGAUGGCCAAA
CP002925.1/1451231-1451187           UGGCGCAGCCCUCGUUCUCGUGGCUAUCUGGUUAGGAUGGCCCAA
AEDU01000001.1/27645-27689           UGGCCUAGCCCUUGUUCUCGUGGCUGUCUGGUUAGGAUGGCCAAA
CP000410.1/1398057-1398013           UGGCAUAGCCCUUGUUCUCGCAGCUGUCUGGUUAGGAUGGCCCAA
AFUU01000004.1/161093-161137         UGGCACAGCCCUUGUUCUCGCGGCUAUCUGGUUAGGAUGGACAAA
AEDT01000003.1/29291-29335           AGGCAUAUCCCUUGUUCUCGUGGCUGUCUGGUUAGGAUGGCCGAA
FQ312027.1/1378644-1378600           UGGCACAGCCCUUGUUCUCGUGGCUGUCUGGUUAGGAUGGCCCAA
#=GC SS_cons                         :<<<___>>>-----------<<<<<<<<_____>>>>>>>>:::
#=GC RF                              UGGCAcAGCCCUUGUUCUCGUGGCUgUCUGGUUAGGAuGGCCaAA
//
# STOCKHOLM 1.0

#=GF AC   RF02449
#=GF ID   ncr1015
#=GF DE   Bacillus sRNA ncr1015
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:20525796
#=GF GA   60.00
#=GF TC   67.90
#=GF NC   51.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 32.56 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20525796
#=GF RT   Identification of regulatory RNAs in Bacillus subtilis.
#=GF RA   Irnov I, Sharma CM, Vogel J, Winkler WC
#=GF RL   Nucleic Acids Res. 2010;38:6637-6651.
#=GF WK   Bacterial_small_RNA
#=GF SQ   16



CP002468.1/178695-178814             UUAUAAUAU-G-GA-UAUCUAUAACUUUUUAACUGGAAAGCGCACGUAGUGUGAUUAUAUCACCGUGUCUGUUUUUGUGCAAUAUAAAAAGAACCUGGGCAAUUUCA-------CCAGGUUCUUUCUUAA
CP002627.1/1590038-1590156           AUAUAAGAU-G-GA-CAUAUAUAACUAUUUAUCAAGAAAGCGCACGUAGACUGAUUAUAUCACCGUGUCUGUUUUUGCGCAAUAUAAAAAGAACCUGGCCUAAUUGG-------CCAGGUUCUU-UCUUA
AEHM01000045.1/69243-69361           AUAUAAGAU-G-GA-UAUCUAUGCACUU-UUAUAAGGAAACAGACGUAGUCUGAUUAUAUCACCGUGUCUGUUUUUGUGCAAUAUAAAAAGAACCUGAGUAAUUUUA-------CCAGGUUCUUUCUUAA
CP000560.1/1804532-1804413           AUAUAAGAU-G-GA-UAACUAUGACUUUUCACACAAAAAGCGCGCGUGUUCUGAUUAUAUCACCGUGUCUGUUUUUGUGCAAUAUAAAAAGAACCUGGCCAAUUUGG-------CGAGGUUCUUUCUUCA
CP000002.3/2129018-2128900           AUGUAAGAU-GGGA-UAUUUAUGUCGUUU--AAUUGAAAACAUGCGUGAUUUGAUUAUAUCAUCGCGUCUGUUUUUGUGCAAUACCAAAAGAACCUGGAUGUUAUUA-------CCAGGUUCUUUUUUCU
ADHJ01000025.1/202129-202246         UUAUAAGAU-G-AACUAACUUUGACUUUUUA--UAAUACAUAGUCGUGAUCUGAUUAUAUCAUCGGGUCUGUUUAUACGCAAUAAAAAAAGAACCUGUU-CAUUUAU-------CCAGGUUCUUUUUUUU
CP003107.1/3532036-3531919           UUGUAAGAU-GCAA-UAACUUUGCUCAUGAAACUUAUAAAAGU-CGUAAUCUGAUUAUAUCAAUGUGUCUGUUUAUGUGCAAUAU--AAAGAACCUGGUAAAACUGU-------CCAGGUUCUUUUUUGA
AP008955.1/3993705-3993822           AUAUAAGAU-GCAA-UAACUAUGAUCUCAUAUACAAUAA-CAGUCGUGAACUGAUUAUAUCAUCGCGUCUGUUUAUGUGCAAU--AAAAAGAACCUGGCGGAAAAAU-------CCAGGUUCUUUUUUGA
AFDH01000073.1/12810-12928           GUAUAAGAU-G-UA-GUUACUAUGCCUUUAAUUAAAAAAAGAGUCGUAAACCGAUUAUAUCAUCGUGUUUGUUUAUAUGCAAUAUU-AAAGAACCUGGUAAAGCUAC-------CCAGGUUCUUUUUUGA
CP001656.1/3640378-3640261           UUGUAAGAU-AAGA-UACUUAUGACUUUUUACUUAAAAUCAG-UCGUAAACCGAUUAUAGCAUCGUGU--UUAUUUAAGCGCAAUAAAAAGAACCUGAGCCAUUUGC-------CCAGGUUCUUUUUUGU
AGBD01001697.1/1188-1304             GUGUAGGAU-GCGU-UAUCUUUGAAAAUAUGACU-AUAGACGGUCGUGAUUUGAUUAUAUCAUCGUGUUUGUUCAUGUGCAAUAU-AAAAGAACCUGGAGGU--UUU-------CCAGGUUCUUUUUUUU
AGIP01000002.1/160970-161088         AUGUAAGAUAA-GA-UAUUUAUGACCUUUUACACAAUC-UCAGUCGUGGUCUGAUUAUAUCACCGCGUCUGUUUAUAUGCAAUAC-AAAAGAACCUGGUCCAUCGAC-------UCAGGUUCUUUUUUUU
AFHW01000177.1/6410-6525             GUGUAAGAU-GAAA-CAACUAUGACCACAUGA-UGGCGAAUAGUCGUGAUCUGAUUAUAUCAUCAUGUCUGUUUAUGUGCAAUAU-AAAAGAACCUGAA---ACUGU-------UCAGGUUCUUUUUUGA
CP002869.1/4671307-4671422           UUGUAAGAU-AGAA-UAAUUGUGUACGUUAA--UAACG--AAGAUGUAAUCUGAUUAUAACAUCGUGUUUGUUUAUAUGCAAUAU-AAAAGAACCUGAUGAAACAAC-------UCAGGUUCUUUUUUGA
CP001793.1/4012679-4012798           UUGUAAGAU-GACA-UAUUUAUACCCUUAUACCCG-AUUGUAU-CGCAUUCAGAUUGUAUCAUCGUGUCUAUGUAAUUGCAAUAAU-AAAGAACCUGAAAUC-----AGAGGAUUCAGGUUCUUUUUUGG
AF027868.1/33983-34102               UUAUAAGAU-G-GA-UAUCUAUAACUUUUUAACUAGAAAGCGCACGUAGUGUGAUUAUAUCACCGUGUCUGUUUUUGUGCAAUAUAAAAAGAACCUGGGAAAUUUCA-------CCAGGUUCUUUUCUUA
#=GC SS_cons                         :::::::::.::::.::::::::::::::::::::<<<<<<<<<<<_________________>>>>>-->>>>>>----------<<<<<<<<<<<<_________.......>>>>>>>>>>>>::::
#=GC RF                              uUgUAAGAU.GagA.UAuuUaUgaccuUuUAacuaauaaacacgCGUaaUcUGAUUAUAUCAuCGcguCUguuuaugUGCAAUAuaaAAAGAACCUGguaaauuUau.......cCAGGUUCUUUuUUga
//
# STOCKHOLM 1.0

#=GF AC   RF02450
#=GF ID   ncr1175
#=GF DE   Bacillus sRNA ncr1175
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:20525796
#=GF GA   60.00
#=GF TC   61.40
#=GF NC   48.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20525796
#=GF RT   Identification of regulatory RNAs in Bacillus subtilis.
#=GF RA   Irnov I, Sharma CM, Vogel J, Winkler WC
#=GF RL   Nucleic Acids Res. 2010;38:6637-6651.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



CP002905.1/2722560-2722668         AGGCCGGCGCGAUACUCCCUAUAAC-AUCCUUUU---CAGUAGAUUUCAU-UAUCGUGCCGGUUUUC-------UCACAUGCAAAGCAAUCCCGCCAAUCUA----AUUGAUGGCGGGAUUUGAU
AEHM01000050.1/11467-11575         AGGCCGGCGCGAUACUCCCUAUAAC-AUCCUUUU---CAGUAGAUUUCAA-UAUCGUGCCGGCUUUU-------UCAUAUGCAAAAUAACCCCGCCAUUCUG-AUUGAU---GGCGGGGUUUGAU
AEFY01000063.1/59296-59175         AGGCCGGCGCGAUACUCCCUAUAACUAUCCUUUUAAUCAGUAGAUUUCAAAUAUCGCGCCGGUUUUUUAUACUUUUAUACGAUAAAAAAUCCCGCCAUCUUCAUCAGAUC--GGCGGGUUUUAU-
AL009126.3/2773781-2773886         AGGCCGGCGCGAUACUCCCUAUAAC-AUCCUUUU---CAGUAGAUUUCAU-UAUCGUGCCGGUUUUC-------UCAUAUGCAAAGCAAUCCCGCCAAUCAG----AUU---GGCGGGAUUUUAU
#=GC SS_cons                       <<<<<<<<<<<<<<----<<<<___.________...__>>>>-------.>>>>>>>>>>>>>>--.......-------------<<<<<<<<<<<<___.___>>>-..>>>>>>>>>::::
#=GC RF                            aggCCGGCgCGauaCUCCCuauAAC.AUCCUUUU...CAguaGAUUUCAa.uauCGcGCCGGcuuUu.......UcAuAuGcaAAauaacCCCGCCauccua.uuagauc..GGCGGGguuUaaU
//
# STOCKHOLM 1.0

#=GF AC   RF02451
#=GF ID   ncr1241
#=GF DE   Bacillus sRNA ncr1241
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:20525796
#=GF GA   60.00
#=GF TC   64.70
#=GF NC   39.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20525796
#=GF RT   Identification of regulatory RNAs in Bacillus subtilis.
#=GF RA   Irnov I, Sharma CM, Vogel J, Winkler WC
#=GF RL   Nucleic Acids Res. 2010;38:6637-6651.
#=GF WK   Bacterial_small_RNA
#=GF SQ   8



AE017333.1/3179758-3179821         ACUAAGGCUUUCUAGUAUUCCCCCCUUAUG---UU-G-AUGCGGACCU---UUCAGGUGCGCAUUUUUUUAU
ACMQ01000197.1/2566-2628           CACAUGGCUUUCUAGUAUUCCCCCCCUUUU---AU-GGACAAAACGUAUUA-----CGUUUUGUCCUUUUUU
AAES01000037.1/8058-8119           CACAUGGCUUUCUAGUAUUCCCCCCUUUUA---U--GGACAAAACGUAUUG-----UGUUUUGUCCUUUUUU
ACPC01000020.1/24344-24408         AUCAAGGCUUUCUAGUAUUCCC-CCUUUUG---UUAGGACCAAAUCCACGUU---GGAUUUGGUCCCUUUUU
ACWD01000017.1/5705-5768           UGUAAGGCUUUCUAGUAUUCCCCCCUUUUUGAAGU-UGACAAUCUGU--UG-----CGGAUUGUCCUUUUUU
AL009126.3/3225711-3225773         CCAAAGGCUUUCUAGUAUUCCCCCCUUUUA---UU-GGAUGCGAACAAAAG-----GUUCGUAUCUUUUUUU
CP000560.1/2969063-2969124         ACGAAGGCUUUCUAGUAUUCCCCCCUUUUA---UUUGGAUGCGAACC--GG-----GUUCGUAUCUUUUUUU
AEFP01000013.1/50292-50353         CCAAAGGCUUUCUAGUAUUCCCCCCUUU-A---UU-GGAUGCGAACUGACA-----GUUCGUAUCUUUUUUU
#=GC SS_cons                       ::<<<<<________________>>>>>--...--.<<<<<<<<<<_____.....>>>>>>>>>>::::::
#=GC RF                            acuAaGGCUUUCUAGUAUUCCCCCCuUaUa...UU.gGAcgcgaccuauug.....ggucgcgUCcUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02452
#=GF ID   ncr1575
#=GF DE   Bacillus sRNA ncr1575
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:20525796
#=GF GA   60.00
#=GF TC   69.70
#=GF NC   50.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20525796
#=GF RT   Identification of regulatory RNAs in Bacillus subtilis.
#=GF RA   Irnov I, Sharma CM, Vogel J, Winkler WC
#=GF RL   Nucleic Acids Res. 2010;38:6637-6651.
#=GF WK   Bacterial_small_RNA
#=GF SQ   29


AEFY01000060.1/10854-11054 UUAAUAACAUGAGAAGGGA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AACGUUUGAAAU-U-G-AU--AUUU--CAAAU--CAU--ACAAA-AUA-GGAUUAGUCUGCCCAUU-UUCUAUAU-------ACGUAAGC------GCUAUUUCUGAA-----------------------------GAAUAGC-UUAUUUGAUCAUGGCAAA--G--GC--A-CGGCUAAUCCUUCCA-A--AA-CA--UUUGGGAGGAUUUUUUG
CP000560.1/574422-574226   UAA--CAAAUACGAAGGGA-UGAUGGGUGGACAAUGAUUAACUAAUCU-UAUUUUG-ACCGUUUGAAAU-C-AAAU--AUUU--CAAAU--CAG--AAAAA-AUA-GGAUUAGUCUGCCCAUU-UUCUAUACGA----UACGAAA--------GCUAUGUA---A-----------------------------AAAUAGC-UUAUUUGAUCAUG-CACA--G--GU--A-CGGCUAAUCCUUCCA-A--AU-CA--AUUGGGAGGAUUUUUUU
AAOX01000024.1/57078-56873 CAACUAAGUGCGAAAGGAA-UGAUGGGUGGACGAUGGAUAACUGAUCU-UAUUUUUUCUUGAUUGAAAU-AGC-AU--AUUU--CAAUU--CACACAAAAA-AUA-GGAUUAGUCUGCCCAUU-UUUCACUU-A----UACAUCAUUC----AGCCAUUA-UG-A-----------------------------UAAUGGU-UUAUUUGCUGAUG-CAAA--G--GU--A-CGGCUAAUCCUUCCA-A--UU-CA--AUUGGGAGGAUUUUUUU
CP000227.1/2437378-2437587 UAUUAACGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUUC-A-AUACAUUU--CAAUUUCUA----AAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAU---GUU-----------------------GCGCAAUAGC-UUAUUUGGGUAUA-AAUA--UUUUA--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACMD01000088.1/8944-9153   UACUAACGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUUC-A-AUAAAUUU--CAAUU--U-A-UAAAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCUUAC-A-----ACGGUAUU------GCUAUUUAUU-AUG-------------------------CGUAAUAGC-UUAUUUGGGUAUA-AAUA--U--GUUAA-CGACUAAUCCUGCCA-A--AUUAA--UUUGGGAGGAUUUUUUU
CP001176.1/2494406-2494615 UAUUAACGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUUAAAUGUUGAAAUU-C-A-AU-AAAUU--UCAAU--UUC-UAAAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAUA-UUG-------------------------CGCAAUAGC-UUAUUUGGGUAUA-AAUAAUG--UA--A-UGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACLT01000056.1/51155-51364 UAUUAAUGACAGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUUAAAUGUUGAAAUU-C-A-AU-AAAUU--UCAAU--UUC-UAAAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAG-A-----ACGGUAUU------GCUAUUUAU--GUU------------------------ACGUAAUAGC-UUAUUUGGGUGUG-AAUA--UUUUA--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACMY01000063.1/95493-95702 UACUAAUGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUGA-A-AUAAAUUU--CAAUUUCUA----AAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAUA-UUG-------------------------CGCGAUAGC-UUAUUUGGGUAUA-AAUA--UUUUU--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACNK01000052.1/72455-72664 UACUAAUGAGGGGAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUUAAAUGUUGAAAUU-C-A-AU-AAAUU--UCAAU--UUC-UAAAAA-AUA-GGAUUAGUCUGCCCGAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAU---GUU-----------------------GCGUAAUAGC-UUAUUUGGGUGUA-AAUAUUU--UA--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACMF01000050.1/21045-21254 UAUUAAUGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUUAAAUGUUGAAAUU-C-A-AU-AAAUU--UCAAU--UUC-AAAAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAU---GUU-----------------------GCGCAAUAGU-UUAUUUGGGUAUA-AAUA--UUUUA--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUA
ACNC01000090.1/185-394     UACUAACGAUGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUUAAAUGUUGAAAUU-C-A-AU-AAAUU--UCAAU--UUC-UAAAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUUUU------GCUAUUU-----GAUU---------------------UGCGUAAUAGC-UUAUUUGGGUAUA-AAUAAUG--UA--A-UGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUA
ACMU01000051.1/2518-2309   UACUUAUGACGGAAAGGAU-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUUA-A-AUAAAUUU--CAAUUUCUA----AAAA-AUA-GGAUUAGUCUGCCCAAU-UUCCAUAC-A-----ACGGUAUU------GCUAUUUAU--GUU------------------------GUACAAUAGC-UUAUUUGGGUAUA-AAUA--UUUUA--A-UGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
ACMJ01000045.1/2590-2799   UACUAACGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUUA-A-AUAAAUUU--CAAUUUGUA----AAAA-AUA-GGAUUAGUCUGCCCAA--UUCCAUUC-A-----ACGGUAUU------GCUAUUU-----GAUU---------------------UGCGUAAUAGC-UUAUUUGGGUAUA-AAUAAUG--UA--A-UGACUAAUCCUGCCA-A--AA-UUACUUUGGGAGGAUUUUUUU
ACLS01000064.1/23579-23787 UACUAAUGACGGAAAGGAA-UGAUGGGUGGACGAUGAUUAACUAAUCU-UAUUUUU-AAAUGUUGAAAUGA-A-AUAAAUUU--CAAUUUAUA----AAAA-AUA-GGAUUAGUCUGCCCAA--UUCCAAAC-A-----ACGGUUUU------GCUAUUU-----GAUU---------------------UGCGUAAUAGC-UUAUUUGGGUAUA-AAUA--UUUUA--A-CGACUAAUCCUGCCA-A-AUU-UA--UUUGGGAGGAUUUUUUU
AGIP01000011.1/90019-90227 GAACAUAAUGAUGAGAGGACUGAUGGAUGGACAAUGGUUAACUAAUCU--AUAUUU-U-UAUUUGAGUU-G-A-AU--AACUUCCAAAU-ACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UCUAUAA-A----UCAGU----------G-UACAUG-------UCAUGAAUUUAAUGGCAAACU-----ACAAACU----UAUUU--AUG-AAAA--U--UA--A-CGGCUAAUCCUUCCAUA--UC-CA--UUUGGGAGGAUUUUUUA
CP000817.1/2916920-2917132 -UAUACAAUUAUGAGAGGACUGAUGGAUGAACAAUGAUGAACUAAUCU--AUAUUU-UAAG-UUGAAAU-C-A-AU-UACUU--CAAACUACA----AAAU-AUA-GGAUUAGUCUGUCCAUU--UUUAUUC-A----UCAGUUUAU------ACUUUAU-------UUGUCAUUU------UCCUAUGGCA--AAAAGGUCCUUUAUUAUU----ACCU--G--UA--ACCGACUAAUCCUUCCA-A--UG-AA--AUUGGGGGGAUUUUUUU
AL009126.3/606606-606407   UAAUCAAAACAAGAAGGGA-UGAUGGGUGGACAAUGAUUAACUAAUCU-UAUUUUU-ACCGUUUGAAAU-C-A-AU--AUUU--CAAAU--CA----AAAA-AUA-GGAUUAGUCUGCCCAUU-UUCUAUAU-A----UACGACACU------GCUAUUUAUAAA-----------------------------AAAUAGC-UUAUUUGAUCAUG-CACA--G--GC--A-CGGCUAAUCCUUCCA-A--CA-CA--UUUGGGAGGAUUUUUUU
AFRV01000003.1/54844-55060 AAAUACAAUUAUGAGAGGACUGAUGGAUGGACAAUGAUUAACUAAUCU--AUAUUU-U-UAUUUGAAAU-G-A-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-A----UCAG--UUU------ACACUUUAU---UUGUCAUGAUU-------CCAAUGGCAAAAAAGAGC-UUAU-UUACUAU---AAG--U--GA--A-AGACUAAUCCUUCCA-A-UUACAA--AUUGGGAGGAUUUUUUA
AJ293027.1/6225-6003       UACUAUUAAUCGAAAGGAG-AGAUGGGUGGACAAUGAAGAACUAAUCU-AAUUUUU-AACAAAUGAAAU-AGU-AU--AUUU--CAGUU--UA----AAAA-CUUAGGAUUAGUCUGCCCAUUUUUCCAUAU-AC---UAAAUAAAU------GUAAGACUG---AAUAGCUAAA--------AAGGCUAAAUAGUUUUAU-UUGAGUCCUUAAA-AAGU--G--AC--A-UGACUAAUCCUUCCA-A-CAU-UA--UUUGGGAGGAUUUUUUA
AAXV01000013.1/57287-57073 AUAUACAAUUAUGAGAGGACUGAUGGAUGAACAAUGAUGAACUAAACU--AUAUUU-UAAG-UUGAAAU-C-A-AU-UACUU--CAAACUACA----AAAU-AUA-GGAUUAGUCUGUCCAUU--UUUAUCA-A----UCAGUUUAU------ACUUUUUUC---GUCAUUUU------------CCUAUGGCAAAAAAGU-CCUUAAU-CAAUA-CCUG--U--AA--C-CGACUAAUCCUUCCA-A-UGA-CA--AUUGGGGGGAUUUUUUU
ACMV01000132.1/9772-9988   AAAUAGAAUUAUGAGAGGACUGAUGGAUGAAUAAUGAUUAACUAAUCU--AUAUUU-UAA-UUUGAAAU-U-A-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-A-----UCA-----------GUUCAUACU---UUAUUUGUCAUGA---UUCCAAUGAUUAAUAAGAAC-UUAU-UAAGUAUA-AG----U--GA--G-AUACUAAUCCUUCCG-A-UUACAA--AUUGGGAGGAUUUUUUU
ADJR01000035.1/12266-12474 AAAGACAAUUAUGAGAGGACUGAUGAAUGGACAAUGAAGAACUAAACU--AUAUUU-U-UAUUUGAAUU-G-A-AU-GAUUU--CAAAC-ACA----AAAU-AUA-GGGUUAGUUUAUCCAUU--UUUAACA-A-----UCAGUU-U------GCAUUGUAU---UUGUC------------------AUGACACAAAUGG-CAAAUCGUAUUUA-UUUA--G-UGA--A-AGACUAAUCCUUCCA-AUGCA-CA--AGUGGAGGGAUUUUUUC
ACMZ01000088.1/41335-41548 AAUAGAAUUAUGAAAGGAA-UGAUGGAUGAAUAAUGAUUAACUAAUUU--AUAUUU-UAAG-UUGAAUU-U-U-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU-UUUAAAAU-U-----CAGUUCAU------ACUUUAUUU----GUCAUGAU----------UCAAAUGAUUAAUAAGU-ACUUAUUAA-GUA-UAGA--C--GA--A-AGACUAAUCCUUCCG-A-UUA-CA--AUUGGG-GGAUUUUUUU
ACLW01000071.1/41842-42052 AAAUAGAAUGAUGAAAGGAAUGAUGGAUGAAUAAUGAUUAACUAAUUU--AUAUUU-UAAG-UUGAAUU-U-U-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-UU---CAUUUCAUA-----CUUUAUUUAU---CAUG---------------------AUUCAAAUGAU-UAAUAAGUACUUA-CUUA--AGCGA--C-AGACUAAUCCUUCCG-A-UUA-AA--AAUCGGGGGAUUUUUUU
CP002508.1/3357927-3358143 AAAUAGAAUGAUGAAAGGAAUGAUGGAUGAAUAAUGAUUAACUAAUUU--AUAUUU-UAAG-UUGAAUU-U-U-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-------UUCAUUUC------AUACUUUAU---UUGUCAUGAUU-------CAAAUGAUUAAUAAGUAC-UUACUUAAGUAUA-AGC------GA--C-AGACUAAUCCUUCCG-A-UUA-AA--AAUUGGGGGAUUUUUUU
ABCZ02000041.1/1982-2197   AAAUAGAAAUAUGAAAGGAAUGAUGGAUGAAUAAUGAUUAACUAAUUU--AUAUUU-UAA-UUUGAAUU-U-U-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-U----U--CAUUUC------AUACUUUAU---UUGUCAUGAUU-------CAAAUGAUUAAUAAGUAC-UUAUU-AAGU--A-UAAG--A--GA--C-AGACUAAUCCUUCCG-AUUAA-UA--AUUGGG-GGAUUUUUUU
CP000001.1/2406369-2406154 AAAUAGAAUGAUGAAAGGAAUGAUGGAUGAAUAAUGAUUAACUAAUUU--AUAUUU-UAAG-UUGAAUG-U-U-AU-AACUU--CAAACUACA----AAAU-AUA-GGGUUAGUCUAUCCAUU--UUUAUAA-U----U--CAUUUC------AUACUUUAU---UUGUCAUGAUU-------CAAAUGAUUAAUAAGUAC-UUAU---UAAGUA-UAAA--A--GA--C-AGACUAAUCCUUCCG-A-UUA-AA--AAUUGGGGGAUUUUUUU
HQ128580.1/8169-7952       UCUUCAAAUAUGAAUGGAC-UACUGGGUGGAAGAUAAUUAACUAAUCUGUAUUCUU-CUAAUUUGAAAU-G-A-AUAAGUUU--CAAAG--UAC--UAAGAUAUA-GGAUUAGUC-AUCCAUU-UUUUUUAA-A----UCAGUUUAACUAGAUGUUUUGU-U------UGUCG-------------AAUGA-C-AAAAAAC-UCUUA-UUUAGUA-UAAA--U--GA--A-UAGAUAAUCCUUCCA-A-UAA-UA--AUUGGGAGGAUUUUUUA
AJ579365.1/3731-3942       AAAUAAAUAGACGAAAGGACUGACUGUAUAAUAAUGAUUUACUAAUUC----AACU-U--AUUUGAAAU-A-A-AU--AUUU--CAAACUCUA----AGUU-AUA-GGAUUAGUCUGAUCAUU--UUUAUAA-GUCGGUUUGUGACA------CCUAUUGCG---U--CAAAUG-----------CUGUUGGUACAAUAGGGACUUUUAAAUAUG-A-----G--AC--C-AGAUUAAUCCUUCCA-A--AU-UC--UUUGGAAGGAUUUUUAU
#=GC SS_cons               :::::::::::::::<<<<.---<<<<--<<<----------<<<<<<.<<<<<<<.---<<<<<<<<<._._.__._>>>>..>>>>>.---....>>>>.>>>.>>>>>>>>>-->>>>--.>>>>,,,,.,....,,<<<----......<<<<<<<__...________.............___.____>>>>>>>.---->>>,,,,,,.,,,,..,..,,..,.,,,,,<<<<<<<<<<.<.___.__.._>>>>>>>>>>>:::::
#=GC RF                    uAaUAaaaauaugAAggaa.UGAUGGgUGGAcaAUGAUUAACUAAuCU.uAUuuUU.uAaguUuGAAaU.a.a.AU.AAuUU..CaAac.auA....AAaa.AUa.GGaUUAgUCUgcCCAUU.uuccAUAa.A....Uacguuauu......gcuauuuaU...uuuuaaua.............auu.uauaaaauagc.UuaUacgauuAUA.aAuA..u..ga..A.aGACUAAUCCuuCCA.A.uuu.uA..uUUGGgaGGAUUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02453
#=GF ID   ncr952
#=GF DE   Bacillus sRNA ncr952
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:20525796
#=GF GA   100.00
#=GF TC   140.30
#=GF NC   37.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20525796
#=GF RT   Identification of regulatory RNAs in Bacillus subtilis.
#=GF RA   Irnov I, Sharma CM, Vogel J, Winkler WC
#=GF RL   Nucleic Acids Res. 2010;38:6637-6651.
#=GF WK   Bacterial_small_RNA
#=GF SQ   6


AL009126.3/1780406-1780550   GGGGGUGGAAACAUAUGGCAUGUGGUCCGAAGAUCAUUAUCUUUUUGGAUGAACUUGAUGAUCCAAAUGUGAGAAUCAUUUUAGAAUGCAGAAUUUAAAUUAC-AACAU--UGUGUUUUGCUCCCUGUUC-GUGUGAACAGGGAGAUUU
AEHM01000035.1/449233-449376 GGAGGUGGGAACA--UGACAUUCGAUUCAAAUAGAAUCAUCCUUUUGGAUGAGCUUGAGCAUGAGAUGGAAGGAAUUAUUUAUGAAUGCAGAAUCUAAAUCAAAUCAAC--AUUGUUUUGCUUCCUGUUU-UUAUGAACAGGGAGUUUU
CP002183.1/1737019-1737163   GGAGGUGGGAACA--UGACAUUCGAUCCGAAUAGAAUCAUCCUUUUGGAUGAGCUUGAGCAUGAGAUUGAAGGAAUUAUUUUUGAAUGCAGAAUUUAAAUCAA--ACCUUCAUUGUUUUGCUUCCUGUUUUUUAUGAACAGGGAGUUUU
CP002905.1/1884091-1884233   GGGGGUGGGAACA--UGGCAUGUGGUCCAAAUAUGAUUAUCGUUUUGAAUGAACUCGAUGAUCCGAAUGUAAGAAUAAUUGUAGAAUGCAGAAUUUAAAUUAA-AUCAU--UGUGGUUUGCUUCCUGUUC-AUGUGAACAGGGAGUUUU
CP002906.1/1754888-1755024   GGGGGUGGGGACAUAUGGCAUGUGGUCCGAAGAUCAUUAUCUUUUUGGAUGAACUUGAUGAUCCGAAUGUAAGAAUCAUUUUAGAAUGCAGAAUUUAAAUU------GU-----GUUUUGCUCCCUGUUC-GUGUGAACAGGGAGUUUU
CP002468.1/3990898-3991041   GGGGGUGGAAGCACAUGGCAUGUGGUCCGAAGAUCAUUAUCUUUUUGGAUGAACUUGAUGAUCCGAAUGUAAGAAUCAUUUUAGAAUGCAGAAUUUA-AUUAC-AACAU--UGUGUUUUGCUCCCUGUUC-GUGUGAACAGGGAGUUUU
#=GC SS_cons                 :::::::::::::..:::::::::<<<<<<<<<________>>>>>>>>>,,,<<-<<<<<<<<<____>>->>->>>>>-->>,,,,,,,,,,,<<<<-<<<.<____..>>>>->>>><<<<<<<<<<.____>>>>>>>>>>::::
#=GC RF                      GGgGGUGGgAACA..UGgCAUguGaucCaaagguaAUuAUCccuuuGgauGAaCuUgaugauccgAauGcgagaAucauuuuaGAAUGCAGAAUUuaaaUcac.aacaU..uguguuuugCucCCuGuuc.uUgUgaaCaGGgaGUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02454
#=GF ID   ncr982
#=GF DE   Bacillus sRNA ncr982
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Published; PMID:20525796
#=GF GA   50.00
#=GF TC   53.30
#=GF NC   37.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   20525796
#=GF RT   Identification of regulatory RNAs in Bacillus subtilis.
#=GF RA   Irnov I, Sharma CM, Vogel J, Winkler WC
#=GF RL   Nucleic Acids Res. 2010;38:6637-6651.
#=GF WK   Bacterial_small_RNA
#=GF SQ   6



AEHM01000036.1/46492-46571           GGUGUAAACAUGAUGUUCU-UUUUCCUCCUAUUCAGGCUCGCACCUAAAAGUUAGGGCGGGCCUGCUUUUUUUGAACAAUA
CP002183.1/1870100-1870178           GGUGUAAACAUGAUGUUCU-UUUUCCUCCUAUUCAGGCUCGCACCCAAAAGUCAGGGCGAGCCUGCUUU-UUUGUACAAUA
AEFS01000009.1/864766-864844         GGUGUAAACAUGAUGUAAUUUUUUCCUCCUUUUCAGGUUCGUUUCU--AAGCCAGGGCGAACCUGCUUUUUUUGUUUUGUU
CP002627.1/1562344-1562266           AAUGUAAGCAUGAUGUAAGUUUUUCCUCCUUAGCGGGUUCGUUUCU--AAGCCAGGGCGAACCUGCUCUUUUUUAUGCAAA
AGBY01000033.1/4390-4316             GGUGAAAACAUGAUGUAGU--UUUCCUCCUUCACAGGUUCGU-UC--CAAGCCA-AGCGAACCUGCUUUUUUUAUGCAAUU
AL009126.3/1917502-1917581           GGUGUAAACAUGAUGUUCU-UUUUCCUCCUAUUCGGGCUCGCACCCAAAAGUCAGGGCGAGCCUGCUUUUUUUGAACAACA
#=GC SS_cons                         :<<<____>>>--------.-------------<<<<<<<<<-<<_._______>>>>>>>>>>>::::::::::::::::
#=GC RF                              GgUGUAAACAuGAUGUaaU.UUUUCCUCCUuuuCaGGcuCGcacCu.aAAGuCAGggCGagCCuGCUUUUUUUgaacaAua
//
# STOCKHOLM 1.0

#=GF AC   RF02455
#=GF ID   Virus_CITE_1
#=GF DE   Dianthovirus RNA2 cap-independent translation element
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:20561661
#=GF GA   80.00
#=GF TC   111.40
#=GF NC   32.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20561661
#=GF RT   A Y-shaped RNA structure in the 3' untranslated region together with the
#=GF RT   trans-activator and core promoter of Red clover necrotic mosaic virus RNA2
#=GF RT   is required for its negative-strand RNA synthesis.
#=GF RA   An M, Iwakawa HO, Mine A, Kaido M, Mise K, Okuno T
#=GF RL   Virology. 2010;405:100-109.
#=GF WK   Cap-independent_translation_element
#=GF SQ   2



S46027.1/1091-1183         AGAAGGAGACAAGAAUUGCGUUGGCUUCGGCGAGCGACGAAAUGGUUUAAAUACAGGCUACGAGUUCUCCUCGUAGGGUCUCUUGCCUCCGGC
X08021.1/1092-1184         AAAAGAGAAAGAGAAUUGCUUUGGCUUCGGCGGAAGACGAAAAGGUUUAAAUACAGGCUACGAGUUCUCCUCGUAGGGUCUCUCUUUCUUGGC
#=GC SS_cons               :::::(((((((((,<<<<<<<-<<____>>->>>>->>>,,,,<<______>>,,,<<<<<<<_____>>>>>>>,,,,)))))))))::::
#=GC RF                    AaAAGggggcgaGaAuuGCguuGGCUUCGGCGaacGACgaAAaGGuUUAAAUaCAGGCuaCGaGUUCUCCuCGuaGGGUCuCucgccccuGGC
//
# STOCKHOLM 1.0

#=GF AC   RF02456
#=GF ID   Diantho_3_UTR
#=GF DE   Dianthovirus RNA2 3'UTR stem loops
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:20561661
#=GF GA   100.00
#=GF TC   205.00
#=GF NC   33.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20561661
#=GF RT   A Y-shaped RNA structure in the 3' untranslated region together with the
#=GF RT   trans-activator and core promoter of Red clover necrotic mosaic virus RNA2
#=GF RT   is required for its negative-strand RNA synthesis.
#=GF RA   An M, Iwakawa HO, Mine A, Kaido M, Mise K, Okuno T
#=GF RL   Virology. 2010;405:100-109.
#=GF WK   Red_clover_necrotic_mosaic_virus_translation_enhancer_elements
#=GF SQ   2


X08021.1/1247-1448 CUAUCGUAGUGUGUGCGAUAGCAUUGCGUUAGGGGUUACUUUC-GAGAGAUU-UGGAGGGGUUGGUCCCUCCG-GUGAGAGAAGAAAACUCAUCCCAAACAAAAAACAGGGUUUCUGAUAACCGGUGCGACAAUAUGCCCUUCCAAGGCACUGACCGGCACGGAGAAAAACUAUAAUGCCAUGUCGUAUAACGGCUAGGCACCCC
S46028.1/1247-1448 UAGACAGGGUGUUUGCGAUAGCAUCCUGUUCUAGGUUGGUUUCUUAGCGAUUAUGGAGGGGUUGGACCCUCCUGGUGUGAGAAGGAAACACAUCA-AAACAAAAAACAGGGUUC-U-GUAACCGGUGCGACAAUAUGCCCUUCCAAGGCACUGACCGGCACGGAUAAAACUUUAUUUGCCUAGUCGUAUAACGGCUAGGCACCCC
#=GC SS_cons       ::::<<<<<<<<________>>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<____>>>>>>><-<<<<<_________>>>>->>---------------------------------------------------------------------------------<<<<<<<<<<<___>>>>>>>>>>>::::
#=GC RF            uaaaCgggguGuuUGCGAUAgCaucccGUUauaGGUUagUUUCUuAGaGAUUAUGGaGGGgUUGGcCCCuCCgGGuGuGAGAAGaAAACaCaUCccAAACAAAAAACAGGGUUucUGaUAACCGGUGCGACAAUAUGCCCUUCCAAGGCACUGACCGGCACGGAuAAAAauUaaaauGCCuaGuCGuAUAaCGgCuaGGCaCCCC
//
# STOCKHOLM 1.0

#=GF AC   RF02457
#=GF ID   Virus_CITE_2
#=GF DE   Tombusvirus 3' cap-independent translation element
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23192876
#=GF GA   100.00
#=GF TC   116.70
#=GF NC   29.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   23192876
#=GF RT   Tombusvirus Y-shaped translational enhancer forms a complex with eIF4F and
#=GF RT   can be functionally replaced by heterologous translational enhancers.
#=GF RA   Nicholson BL, Zaslaver O, Mayberry LK, Browning KS, White KA
#=GF RL   J Virol. 2013;87:1872-1883.
#=GF WK   Cap-independent_translation_element
#=GF SQ   9



Z68899.1/618-782             UGUUGGGUUCUAGAUGUUA-UGAUGACGAGUCGGUCGG--CUCCGCGCUAGGUUUGGUCGCCUAGGGGAUGGAGAUAUGGAAAGGGUCU-CGUGUGCUGUCAGUCG-GUCGAAAGACG-CGCUUGCAACAUGGGCCUAUAACCGGAUAAGUCAUAGCAAUACUAGCCAACA
X62493.1/4487-4650           UGUUGGGUUCUAGAUGUUA-UGAUGACGAGCUGG-UCGGGCUCCGCAC-GGGUUUGGUCGCCC-GGGGAUGGAGAUAUGGAAAGGGUCU-CGUGUGCUGUUAGUCA-GUCGAAAGACG-UGCUUGCAACAUGGGCCUAUAACCAGAUAAGUCAUAGCAAUACUAGCCAACA
AJ288928.1/584-750           CACUGGCAUGCAGCCGUUA-UGAUGACGAGUCAGGUCGGGCUCCGCGGUGGGUUUGGUCGCCCAUGGGACGGAGAUAUGGAAAGGGUCU-CGUACGCUGUAAGACU-AACUUCGGUUG-AGCUUGCGAUAUGGGCCUAUGCCUGGAUAAGUCAUAAUGUUACUGCCCAGUG
X15511.1/4428-4594           UAGUGAGACUAGGUUCGUG-UGAUGACGAGUCAGGUCGGGCUCCGCGCUGGGUUUGGUCACCCAGGGGAUGGAGAUAUGGAAAGGAUCU-CGUGCGCUAUAAGUCU-AACGAAAGUUG-AGCUUGCAACAUGGGUCUAUGCCUGAAUAAGUCACGUGAGUUGCCACCACUA
AY370535.1/1808-1973         CGUAUUGUUCGGU-CUACA-UAAUGACGAGUCAGGUCAGGCUCCGCACUAGGUUCGGUCACCUAGGGGAUGGAGACAUGGAAGGGAUCU-CGUGCGCUAUAAGUCU-AACGAAAGUUG-AGCUUGCGACAUGGGUCUAUGCCUGGAUAAGUUGUGUAGGUUGCCGCAUACG
AY830918.1/4428-4591         AGUAUGAUU-AGGUCUACG-UGAUGACGAGUCAGGUCAGGCUCCGCACUGGGUUUGGUCGCCCAGGGGAUGGAGACACGGAAAGGACAU-CGUGUGCUAUAAGUCU-GACGUAAGUCG-AGCUUGCAACAUGGGUCUAUGCCUGGAUAAGUCACGUGGUUGCC--CCUACU
M25270.1/4407-4576           UCAUGGGUUCCUUCCCAUA-CGAUGACGAGUCAGGUCGGGCCCUAUCUUAGGUUUGGUCACCUAGGGGACGGGGAUAUGGAAAUCACUUUCGCUUGCUGUCAGUCUAGUGGAAACACUUAGCUUGCAAUGUGGGUGUAUGCCUGGAUAAGUCGUAUGGAUGCUGGCCAUGA
DQ011234.1/4462-4626         UGUCAGGUUGGAACCCACACUAAU--UGAGCUAGGCCGGGCCCCGUCGUAGGUUUGGUCACCUACGGAAUGGGGAUAUGGAAAGGAUCU-CGUACCCUGUGAGUCA-AACGAAAGUUG-UGCUUGGGAUAUGGGUCUAU-GCCUAGUAGGUUAUGUGGUGUGUCUCUGACU
X85215.3/4459-4625           UGUUGGGUUCUAGAUGUUA-UGAUGACGAGUCGGUUCGGGCUCCGCACUAGGUUUGGUCACCUAGGGGAUGGAGAUAUGGAAAGGGUCU-CGUGUGCUGUUAGACG-GUCGUAAGACG-CGCUUGCAACAUGGGCCUAUGACCGGAUAAGUCAUAGCAAUACUAGCCAACA
#=GC SS_cons                 ((((((---((((-(((((.((((--((-(((,,<<<<--<<<<<--<<<<<<______>>>>>>---->>>>>--->>>>,,<<<<<-.<<<<<--<<<-<<-<<.<<<____>>>-.>>>>->>>>>>>>>>>>>,,)))))-----)))))))))---))))))))))
#=GC RF                      cguuggguUcggguccgca.uGauGAcgAGccaGccCgGGCuCcgcacugGGuUUGGUCaCCcagGGGAcgGaGAUAcGggAAgggccU.CgugugCuguaaGuCg.gacGaAAgucG.cGCuUgcaacauGggccuAUggCcggAUAAguCaugcggauacccgccaacg
//
# STOCKHOLM 1.0

#=GF AC   RF02458
#=GF ID   Virus_CITE_3
#=GF DE   Aureusvirus cap-independent translation element
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23192876
#=GF GA   100.00
#=GF TC   117.30
#=GF NC   34.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   23192876
#=GF RT   Tombusvirus Y-shaped translational enhancer forms a complex with eIF4F and
#=GF RT   can be functionally replaced by heterologous translational enhancers.
#=GF RA   Nicholson BL, Zaslaver O, Mayberry LK, Browning KS, White KA
#=GF RL   J Virol. 2013;87:1872-1883.
#=GF WK   Cap-independent_translation_element
#=GF SQ   2



X87115.1/4173-4291           AAGCCUAAUGGCCAUAGUAGGAGGGGUAAUCUAUCUGGGGAAGUUGGUGGUUCUUCUUCCUCCU---UGCCCUCAGGUGCACAGACUGGGGAGUGGAUAGAUAAUGACUAUGGAGACAGCUU
EU127904.1/4197-4318         AAGCCUAAUGGCCUAGAUCGGAGGGGUCGUGGUAAUAGCACCGUUGGUGGUUCUUCGGAUGCUUCUCAGUCCCAAGGCGCACAAGCAUGGGGGGGUUACCAUAACGAUCUAGGAGACAGCUU
#=GC SS_cons                 ((((-------(((((((((--------((((((((,<<<<<<--<<____>>-->>>->>>,,,,,,,<<<<---<<______>>--->>>>,))))))))--)))))))))-----))))
#=GC RF                      aaGCCUAAUGGCCuuggucgGAGGGGUaaugguucuaGcgccGUUGgUGGUuCUUCggacgCuUcUcaGccCcaAGGcGCACAagCauGgGgguggaaccauAAcgaccaaGGAGACAGCuu
//
# STOCKHOLM 1.0

#=GF AC   RF02459
#=GF ID   Virus_CITE_4
#=GF DE   Necrovirus cap-independent translation element
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23192876
#=GF GA   40.00
#=GF TC   44.50
#=GF NC   34.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   23192876
#=GF RT   Tombusvirus Y-shaped translational enhancer forms a complex with eIF4F and
#=GF RT   can be functionally replaced by heterologous translational enhancers.
#=GF RA   Nicholson BL, Zaslaver O, Mayberry LK, Browning KS, White KA
#=GF RL   J Virol. 2013;87:1872-1883.
#=GF WK   Cap-independent_translation_element
#=GF SQ   5



GQ221829.1/3489-3569         UGG---AGAUGGAUGCUGGAUCCUGGAAAACAGGUUU-AACGGGUAGGGGGUGGUGCCCCUACCGACGCAUCAC-UCCAGAUA---CCA
DQ083996.1/3504-3585         GCG---GUAAGCAAGACGGAUCCUGGGAAACAGGUUU-AACGGGCUGGGGGUGGUGCCCCGGCCGUCGCAUCACUUGCUGAUACAA---
FN543467.1/3454-3532         GAG---GUAUCGAUGCUGGAUCCUGGGAAACAGGCUU-GACAGGUUUG-GGUGGUUC-CAAACCGCUGCAUCAC-UCGAGAUA---CUC
AY616760.1/3484-3572         UGGGCGGUAAGCAAGAGGGAUCCUGGGAAACAGGCUUCGACGGGUUGGGGGUGGUGCCCCGGCCGACGCAUCACUUGCUGAUACAACCA
D00942.1/3577-3660           UUG---ACGUACAAGCCGGAUCCUGGGAAACAGGUUU-AACGGGCUCACUGUGGUGG-UGGGCCGUCGAUACACUUGUAUGUGCCCCAA
#=GC SS_cons                 (((...(((((((((-((,,,<<<<_____>>>>,,,.,,,,<<<<<<__________>>>>>>,,))-----)))))))))----)))
#=GC RF                      ugG...augugcAaGccGGAUCCUGGGAAACAGGuUU.aACGGGccgGggGUGGUGcCCcggCCGuCgcAuCACuUgcacauACaaCca
//
# STOCKHOLM 1.0

#=GF AC   RF02460
#=GF ID   Virus_CITE_5
#=GF DE   Satellite tobacco necrosis virus cap-independent translation element
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:18031280
#=GF GA   90.00
#=GF TC   108.30
#=GF NC   37.60
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   18031280
#=GF RT   The amazing diversity of cap-independent translation elements in the
#=GF RT   3'-untranslated regions of plant viral RNAs.
#=GF RA   Miller WA, Wang Z, Treder K
#=GF RL   Biochem Soc Trans. 2007;35:1629-1633.
#=GF WK   Cap-independent_translation_element
#=GF SQ   2


M64479.1/655-746 AGGACGCUGAAAGAUGCGUAGCUACCCUCC-UGGUGCACUUCCUGGUGCAAAGCAGA-ACCAAAGGGUACGGUGGUACGGCGGACAGUAGUCCU
L06057.1/646-739 UGGGCGCUGAAAGAUGCGUAGCUACCCUUCUGGAGCCACUUCCUGGUGGUAAGCAGAAAUCCAAGGGUACGGUGGUACGGUGGAAAGCAGUCCC
#=GC SS_cons     <<<<<<<<<-----<<<<<<<<<<<<<<---<<<<<<<<<____>>>>>--------->>>>->>>>>>-->>-->>>>->>-->>>>->>>>>
#=GC RF          gGGgCgCugAAAGAcgCGuagCuaCCCuuCugGgugCaCcUCCUgGuGcaAAGCAGAAacCcAaGGGuaCGGcGGuaCGGcgGAcaGcAGcCCc
//
# STOCKHOLM 1.0

#=GF AC   RF02461
#=GF ID   Virus_CITE_6
#=GF DE   Blackcurrant reversion virus cap-independent translation element
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:18031280
#=GF GA   41.00
#=GF TC   41.50
#=GF NC   37.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 26.47 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   18031280
#=GF RT   The amazing diversity of cap-independent translation elements in the
#=GF RT   3'-untranslated regions of plant viral RNAs.
#=GF RA   Miller WA, Wang Z, Treder K
#=GF RL   Biochem Soc Trans. 2007;35:1629-1633.
#=GF WK   Cap-independent_translation_element
#=GF SQ   3


AF020051.3/5006-5120 CGCAAGUACAUCUGCUAGUGCUCCCAACGAAAGUUGAUAGCGAUGUGCACGUUUAGGAGAUAAAUAGCUAGUAUCUUUCUACUCGGAUUCCCCUCUGUCGUCAUAGAGGGGUUUC
AY210891.1/1341-1443 CGCAAGCACAUCCGCUAGUGCUCCCAACGCAAGUUGAUAGCGGCGUGCACGUCUAGGAGUUAAAUAGCUGGUAUCUUUCUACCCGGAUU-------CCCCUCUG-----CCGUCA
EF143983.1/516-630   CGCAAGCACAUCAGCUAGUGCUCCCAACGAAAGUUGAUAGCGAUGUGUACACCUUGGAGUUAAAUAGCUAGUAUCUUUCUACUCGGAUUCCCCUCUGCCGUCAUAGAGGGGUUUC
#=GC SS_cons         :<<<________>>>,,,,,,(((<<<<____>>>>,<<<-<<<<<<<--<<<<<_____>>>>>->>-->>>>>--->>>,,,)))--<<<<<<<<<____>>>>>>>>>::::
#=GC RF              CGCgAGcACAUCcGCUAGUGCuCCCaaCGaAAGuuGAuaGCGauguGcACgucuaGGAGuuagacAgCUaguauCUUUCuaCuCGGaUUccccucugcCgUCgcagagggguUuc
//
# STOCKHOLM 1.0

#=GF AC   RF02462
#=GF ID   Telomerase_Asco
#=GF DE   Ascomycota telomerase RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23093598
#=GF GA   30.00
#=GF TC   31.30
#=GF NC   29.80
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000390; telomerase_RNA;
#=GF DR   GO; 0007004; telomere maintenance via telomerase;
#=GF DR   GO; 0003720; telomerase activity;
#=GF DR   GO; 0000333; telomerase catalytic core complex;
#=GF RN   [1]
#=GF RM   23093598
#=GF RT   The common ancestral core of vertebrate and fungal telomerase RNAs.
#=GF RA   Qi X, Li Y, Honda S, Hoffmann S, Marz M, Mosig A, Podlevsky JD, Stadler
#=GF RA   PF, Selker EU, Chen JJ
#=GF RL   Nucleic Acids Res. 2013;41:450-462.
#=GF WK   Non-coding_RNA
#=GF SQ   4



CP003014.1/2215735-2213952           CAACAUCCAA------------ACAUCUCAAGUUCCCAAACCC--CCGGAAGUUGCCCGCACAGCGUCCAUCUUGGAACCGUCUCGAUCCAAGGCA--------CGCCAAACCUCUGGAACCCACCCGAGAGGCAUUUCUCGUCAAUCUAUAUCGCACUGUGCAAGCCAGCAGUCGCCUUCCCG-U--CGUCGACCCGCGCCG-UUCCAGC------UUCCACUCUUUC-G--CUC-ACACGCACGGCGCCUCCCCCACAGUUCUCCGAUUCCAAUUUUCCG--CAAGGAAUGUCAU-CGCGACCGCCCCGCCGGUGUCUGGA-CACCCGCAGUACGUCGCAGCUUCGA-UCCCGUAUCGGGUGCC-UCUCAAGCC-UGCCGCGCCUGG-AUUACUGCG---GUU---CAGUUCUUGUCCGCCGGGCAAGCCAGUCCC-GCGGGGCGAAUUGGUCUCGGAACUUAACCCUAAGUAUACCUUUGGU-U---CUGAAAAGUCUUGCGCUCCU--AUAGUCG-UUCGGAC---CGCCUUCUAUGCUCGCGUCUUUCGAGGGGUACGUCGCCAC--------UGGCCGCUGAAAAGUGGUGUGG-CACUGCUCCGG----------CGAGGACGUGGGCGGACCGGCGGGAUG---GGC-UCCAGUCACCGG-----------------CUCGGUGGGCGAC-CGUCCCUUCCCAUGAGUCCACA--CGGUAAGCGCCUCUGGCCCGAGGCCGCUCGUCGGGAAUCGGACACUGGAACUAGUACUCUGGUCAA---UGCGGAUUGC------------CUGUGGCGGUGUUGGCUGG-A----------CGACCGAGUGUCGGCGGAU----------ACCUCCGGGCAGCU-UGUCUGCUUGCAUGCUCCCAUGGGCUGGCUCCU-GCUUGCAGUCCCAGCUUCCGGAAUGAGA-GGGAGAGCGCAGCAUCUGGCUCCACACGAUCAUCCAGUACAUUUCACCACAU-UGUCUGCAGCUCACCUCGCAGGAAUCACUUC--------GGUGAGCGAGGGCUGUUCGACUCCACGCGGAAAUGUCGAAGGAUGAUGUCC----ACCACGCCGUGCUGUCACGUUCUCGGUACCCUCGA-UUUCCGUCUCUUCUU--GCAUGCGUA------------------UCCAACCGCCUCGCGGC-----UCCGCCGACCCCCAUGGACCGCGCUGCGGCACCAU-----G-CCCACGCGUCAUGAA--------ACCAUGAGGUC--CGACCAGGCGCAUUAACUUGU--CCUCGUAGGCGUCCGUCCUACGUC-CGAC-AAGACGACCAAAACACC-------C-CGUGUCUCGCUGUGCCUUCGGGUGCCGAG---CACU------CCCUCCCUCCG--CCGGG-UC---UGAAAGAACGAUUUUCGGC-UGGAGAUGACAGCGCGGUU-UUUGAGGACGUCUUUUGUCCGUGCGGUAC--CGCCCUCCUUG--------GUCGGCUCCGCCUACUCGGCGGUCGGCAGUGGAGAGGAAUCAAAAACUAGUCCCAGUUGGCAGUGCGAC--ACACACGGAGAGCAG------------------------UGGCU--GGCUCGGCGUCUCGGCACGGGG------------AAGUGCACCGCUGGCUGCCGAGUUUGACGAGAUCUG--CAUCAAUGACG-GUCGGCUUCUGCUUAAAGGUUGGGCGUUGCGGAGGAUCCUGA-----------C-ACUCUGUGGGGGGUUGGGGGUUG-------------------------GGACUUAG-------UU------GGCUGAUUGAGGAACAAUGCGU----CAACCUGGGUUCUCCUGAUGAAGGCGGCA--------GGUGGAGACGGAUCC-GGGUCCGGGACCCAUCUCGAGUUGGAGUCAAAGCUUUGUGCUUGUCUGGCGCUCGGAUUCUGUCU---------CCUUCGGCUCUCCAGAGUCGGAGCUC-UCCAG-GGAGCGCUUUGUUGUUCGAUGCC---GGCUGGUUGGAAAA-GGACGGGCCCUU--GGGGGCGGUC-CUGGUUG-UCUUCUCUCCAGAA--AUGGCGGGAAG-ACAACCCCUCA----UUUUGGAGG
CABT02000003.1/521099-523170         CACCAACAAA--------GACAAUACCUUCGACCUCCAACGCCCAACCAUAUUGAUCCUCGCAAUGCCCG------AAUGGGCCCAGCCUCAAGUCGGUCUCUGUUUCGAUCCUUGGAAACCCACGCGAAAUACAGUCAGAACUCGAUCCUGUCGAGAUACAC-AGCCAAAACGCGCUGGCCCGAA--CGACGACGACAGCCAUUCCCAUCGAGUCUUUCAACCCUCU-----CUCU--GAGCACGACGCCUCCCCUACAGUUCUCCGAUUCCGGUUUUCCCGUAAAGGAAUGUCCUUCGUGGCCGCUCGG---AUGUCCGGUUCUUCCGCAGUACGUCGCAGCUUCGAGUCCUGCAUCAGGAGCCUUCUCAAGCUUUGCCGCGCAUGGGAUUACUGCG---GAUUUCGGGAUUU---AUCCUACCCUUGCCGGCGCC--CAGAGUGAAUUGGUCUCGGAACUUAACCCUACGUAUA-CGCUGGUUACACAUUACAAGUCUUGCGCGCUUCGGCAGUCAAAUCGACCCUUCGCCUUCUACGUCCGCGUUAUCGUG-GUGUUUACUUUCGGGGUCUAUGGCGCCGCUGAAAAGUUGCGUCCUCUAGAUUCUUGGUAUUCUGCUUGAUGGCAAGGACUGACCGGCAAGGAGAGAAGU-UCCAGUCAUCUUGGUUGCACUUCGGUGCGCCUGAUGGGCGAGGUGUCUGGUCCCAUGAGUCAAAAGCUGGUGAGAACCUCUGGCCUGAGGUCGCUCGUCAGGACUGGAUCACUGGACGCAGUACUCUGGUCACCAUAGCGGAUUGCUUUGCAGAUGUCCCGUGGCUAGGUACACCG---CGUUGGGGAAGGAUACAUUUUGGGUGCCCUGCCAUGCCUGUCAUCCGGAAGUUCUUUCUG---GCUCUGACUCUUGGAGCUUUACGUUUCGCGACGCAUGCUCUGUGGAGUGACGAGGGGAGAGCGAAG-AUACGGCUACAUACGAUCACAUCCCUCAUUUCAUCUUUCGCGUCUUCAGCUUGCCUCGCCUGAAUCACUGCACUUGUGUGGUGAGCUGGGGCUGUACGACUACAAACGGAAAUGUUGG-GAAGGAUUCUU----UUCACGCCUGUCUGUCGCGCUCUCUGCACCCUCAGAUCUC--UCUUGUAUC--GCAUGCGCAGGAGCGGAUACCCACUUGUACGCUUUUCUCCCGGAUAACCUCCACUGACUCUGUGGAACCGCGUUCGGCAA-CAUAC--CG-UCAACGUGUCAUUGGCUGUUGUGUCAUUGAGAUCCCCGGCCAGGCGCAUCAACCGAUUUACACGUAUGGCUUUGUCCUACGUCGCGAAUUGGAC-GCCAGAACCA-CGUUUGUUUCAAAUCUUU--GAUCCGAAAGGAGAGGAGCUCUUUGGCAGACACUUUCCUUUCGACUGGAGUGCGCUGAAAAGUUCACUUUCGGGAGAAAGAUGAUAGCACGGUU-UUUGAGGACGCAUUUUGUCCGUGCGGAAA--UGCCCUCCUU----------CACACUUUCUCGGUUGGUACGAGAGUGC-GGAGAGGAUACAAAAGCUAGUCUCAGUUGGCCGUGCUC-U-ACACACGGAAAGACUCGUGGGACGGCUAUCUCGACGAUCCGGCUAUCGAUUUGGCUGCCGACACUUGACGACUGCUGUGUUAAUGACGGUGCGGUUUCUUUUGGGGGAUUGAGCAGGUCCGCCAUGGCUUGCUGGUUUGGACUGUGAGAGUG-GUGGUUGGGUGUUUAGUGUCCUGUGGGAGUGUCCAUUCUGGGGGUGUCCGCGUCCGUGUUGGUGUCCGUGUCCGUUCGGGGGAAGAAGCGUGUCUUUGGGCCACACUCGUUGAGAACCAAUGCUUUUGCAGCCCCUGGAUUUUCAGAGGAUGGUGGUUGUGGAC-UCUGGGGAAGAGAACCAAAAGUCGGGACCCAUCUCGAGUUGGAGUCAAAGUUUCGUACUUGUCUGGCCUUCGGAUCCUCUCUUUCUUGGUCUUCGCUUCUGGCC-GAAUCUGCGUCCUUGCGGAGGCUAGCUUUGUUGUUUGGAGUUCUGGCCCUUUAGGAUAGGGGACUGGCUUCCUGGAAGGUGGUCCCCGGUUGUUCCUCGUUCCUGAAAGAUGGCGGGAGGAACAACCCCUCUGCACUUUUUGAGG
AL355930.2/32605-30557               AACCAACAAACUGAAGUCAACAACACCUUCGACCUCCAACGCCCGACCAUAUUGAUCCUCGCAAUGCCCG------AAUGGGCCCAACCACAAGUCGGUCUCUGUUUUGAUCCUUGGAAACUCACCCGAAAUACAGUCAGAAGUCAAGCCUGUCGAGUUUCAC-AGUCAAGACGCGCUGGCCCGAA--CGGCGACGACAGCCAUUCCCAUCGAGUCUUUCAGCCCUCUC-G--CUCA--GAGCACGGCGCCUCCCCCACAGUUCUCCGAUUCCAGUUUUCCCGUAAAGGAAUGUCCUUGGUGGCCGCUCAG---GUGUUCGGUUCUUCCGCAGUACGUCGCAGCUUCGAGUCCUGUAUCAGGAGCCUUCUCAAGCUUUGCCGCGCAUGGGAUUACUGCG---GAUUUCGGGGUUUUUAACCCCACCUUUUCCGGCGCC--UAGAGUGAACUGGUCUCGGAACUUAACCCUAAGUAUA-CACUGGU--CACAUCCCAAGUCUUGCGCGCUUCGGCAGUCAAAUCUACCCUUCGCCUUCUACGUCUGCGUCAUCGUG--UGUUUGCCUUCGGGGUCUAUGGCGCCGCUGAAAAGUUGCGUCCUCUGGGCUCUUGGUAUUCUACUGGGUGGCAAGGGCUGACCGGCAAGGGAAGAAGUUUCCAGUCAUCUUG-UGCCACUUCGGUGCGC-AGAUGGGCGAGGUGUCCGGUCCCAUGAGUCAAAAGCCGGUAAGAACCUCUGGCCCGAGGUCGCUCGUCAGGACUGGACCACUGGACGCAGCACUCUGGUCACCAUAGCGGGUUGUUCUGCACAUGUCCCGUGGCUAGGUAUACCG---CGUUGGGGUAAGACACAUU-UGGGUGCCCUGCCAUGCCUGUCAUCCAGAAGUUCUUUCUG---GCACUGACUCGUGGGGCUUUGCGU-UCGCAACGCAUGCUCUGUGGAGUGACGAGGGGAGAGCGAAG-ACAUGGCUACACACGAUCACAUCCCUCAUUUCAUCUUUCGGGUCUUCAGCUUGCCUCGCCUGAAUCACUGCACUCGUGUGGUGAGCGGGGGCUGCAUGGCUACAAACGGAAAUGCUGG-GAAGGAUUUUU----UCCCUGCCUGUCUGUCGCGCUCUCUGCACCCUCCGAUCUCUCUCUUCUAUC--GCAUGCGCAGGAGCGGAUACCCACUUGUACGUCUUCCUCCCGGAUAACCUCCACCGACUCUGUGGAACCGCGUUCGGCAA-CAUAC--CG-UCAACGUGUCAUUGGCUUGUGUGUCAUUGAGAUCCCCGGCCAGGCGCAUUAACCGAUCUGCACGUAUGGCUUCGUCCUACGUCGCGAUUUGGAC-GCCAGAACCA-UGUUUGUU-CAAAUCUUC--GGUCCGCAAGGAGAGAAGCUCUUUGGCAAACACCUUCCUUUCAACUGGGGUGCGCUGAAAAGUUCACUUCCGGGAGAGAGAUGAUAGCACGGUU-UUUGAGGACGCAUUUUGUCCGUGCGGUAA--UGCCCUCCUU----------UACACUUUCUCGCAUGGUGCGGGAGUGU-GGAGAGGAAACAAAAGCUAGUCUCAGUUGGCAGUGUUC-U-ACACACGGAAAGACUCAUGGGACGGUUAUCUCGACGAUUUGGCUAUCGAUUUGGCUGCCGACACUUGACGACUACCAUGUUAAUGACGGUGCGGUUUCUUAUGGAGGGCUGAACAAGUCCGCCAUGACUUGCUGGUUUGGACUGUGAGAGUG-GUGGUUGGGUGUCUCA-----------AGUAUCC--UCUGGGGGUGUCCGUGUCCGU-----------------UCCGGGGGAAGAAGGGUGUUUUUGGACCAAACUCGUUGAAAACCAAUGCUUUUGCUGCCCUUGGAUU-UCGGGGGAUGGUAGUUGUGGAUUUCUAGGGAAGAGAACCAAAGGUCGGGACCCAUCUUGAGUUGGAGUCAAAGUUUCGUACUUGUCUGGCCUUUGGACCCCCUCUUCCUUGGUCUUCACUCCUGGCC-UAGUCUGUGUCCUUGCGGAGGCUGGCUUUGCUGUUUGAGGUUUUGGUCCUUUAGGACAGGGGACUGCCUUCCUGGAAAGUGGUCUCCGGUUGUUCCUCGUUCCUGGAAGAUGGCGGGAGGAACAACCCCUCA-CAUUUUUUGAGG
CP003008.1/2390583-2392406           CACUCUUCAA---------------CCUUCAAUCGCCAAAAG----------CUGCCUUCGCAAUAUCCGGC-AGGAAACGUCUCAACCUAACGCA--------CAUCGAACCCAGGAAUCCGGUUCGAGAUGCAGAUUUGGCCAAUUCACAUCGAGAUAUAC-AGCCACUGACCGCACGUACCAAGCCGACGCGCCCUCCCAGCUCCAAA-GGUCUUUCGCCUCGAGCAGCCCUU--CUCGCACCGCGCCUCCCCCACAGUUCUCCGAUUCCGGUUUUCCG--CAAGGAAUGUCGC-CCCGACCGCUCCC--CGGGACUGGAAACCCCGCAGUACGUCGCAGCUUCGA-UCCCGUAUCGGGUGCC-UCUCAAGCU-UGCCGCGUUCGGAUCUACUGUGGCCGAUUCCUUGCCCUUUUCACCUCGGCAAGCCAGUCCCGCGGGAGCGAAUCGGUCUCGGAACUUAACCCUAAGCAGAUCUUUGGU-----CCGUCAAGUCUUGCGCUGCU-GAUAGUCA--UCCGGCCCUCACCUUCUAUGCCCGCGCCGUCCGA-CGAGCUGCAGCUGC--------GGGCCGCUGAAAAGUGGUGCAGUCUCCGCUCUGG----------CGACGGCAGGGGCUGACCGGCGAGGUCCGAG-C-UCCAGUCACCCGC----------------CAGGGUGGGCGAC-CGUCUCUUCCCAUGAGUCCACA--CGGUAAGCGCCUCUGGCCUGAGGCCGCUCGUCGGGAACGGGACACUGGAACUAGUACUCUGGUCACGAU---GGAUUGU------------CCGUGGCGGUGUUGGCCAGACGGUCGAGG-------CAAGGCGGGCGCAU--------------UCGAGCAGCUCGGUCUGCUCGCAUGCUCUUUUGUGGUU----GUCUCCCGUCGGAGCAGCCUUCGGGAGGAGA-GGAAGAGCGCAG-UCUCGGCUACACACGAUCAACCAAGGCGUUUCACUCCUC-CACCAGCAGCUCGCCUCGCAGGAAUCACCCCUUCUG-GGAGUGAGCGAGGGCUGUCAGGUUACACACGGAAACGCCGACGGAUGAUACUACCCCUUCUCGCCGUGCUGUUACGCUCUCGGUACCUCGACUUCCACCUUUUUCACCCUGCAUGCGCA--------------------CCUAGUCCUCCUGAC-GAC-CCAGCCGACCCUCGCGGACCGCGCCGGGGCA-AAUACAUCGCCCGACGCGUCAUGGAACCCAAC-ACCAUGAGAUC-CCGACCAGGCGCAUUAACCCGU--CCUCGUA-GGCUCCGUCCUACGUUACGAC-GGGAC-GCCAAAGCCCCUGC----C-CGUGU----------CUCUAG-----------CACG----GCCCUUUCCUCCG--CCGGGGGCC--UGAAACAUGGUCGAUCGGCACGGAGAUGAUAGCGCGGUUUUUUGAGGAUGUAUUUUGUCCGUGCGGUUACCUGCCCUCCUUUUUUUCCUGCCCAUCCU-UCGGGGUGGUGCCGGCGAUG-GGAGAGGAAACAAAAACUAGUCCCCGUUGGCAGUGCGAC-AACACACGGAGAGACC------------------------UGGCU-UGGGUUGGGCUGUCGACUCUUGG-------UAUGUU---GCGGCUUUGGUUGCCGAUUUUGGCCGGAUCUG--CCUCGACGACG-ACCGGAUUCGGCUGCGGGCUUG-GUGCUGUGGCAGGUUUUGA-----------C-UCGUUGUGGGGG---CCGGGUUU-----------------------------GAAGGU------UGGGUC-GACCGGCUGAAAACCAAUGCGU----CGAACUGGGUGCUCCGGAUGAAGG-------GGCCUGCACGGGGACGGGCCGAGUCGCCGGGACCCAUCUCGAGUUGGAGUCAAAGCUUCGUGCUUGUCUGGUGCCUGGAGCUCGUCC---------CCUGCAGCUGUCCGGAUUCUGGGUUCCUUCAG-GGAGGGCUUUG-UGUUUGCGGUUC--GACCGUUUGGAAAA-GGACGGGCCCGUUGGUGGGUGGUC-CUGGUUG-UCCUCUCUCCAGAA--AUGGCGGGAGG-GCAACCCCUCU----UUUUGGAGG
#=GC SS_cons                         ::::::::::............:::::::::::::::::::::..:::::::::::::::::::::::::::.:::::::::::::::::::::::........:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::..:::::::::::::::::::::::.:::::::::::::::::.:..:::..:((((((---(((,,,,,,,,<<<---<<<<_____________.._____________._____________..____________________________________.________________._________.______________________...____________________________________.________________>>>>->>>,,,,,,,,,,,,,,,,,<<<<<._...____________________.________.___________________________________.______________........__________________________________.........._________________________________._____________................_____________.______________________.._______________________________________________________________________________............___________________._________..___________________.........._____________________________________________________________________________.____________._______________________________________.____________________________________._____________________________________________________....___________________________________________________.._________.................._________________.___._______________________________._____..__.______________________.___________.______________________.._____________________________._____.>>>>>,,,,,,<<<....-.<<<<-<<<<..--<<<____>>>-->>>>...>>>>....>>>,,,<<<<<<<..<<<<<<<<-..<____>--->>>>->>>>-->>>>>-->>,,,,,,,,,,.,,,,,,<<<<<-<<<<<<-----------..--<<<<<<---........--<<<<--<<<<<<<___>>>>>>>>>>>.>>>>->>-->>>>>>>>-->>>,,,,,,)))-)))))),..,,,,,,,,,,,,,,,........................,,,,,.,,,,,,,,,,,,,,,,,,,,,,,.......,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,...........,.,,,,,,,,,,,,,,,,,,,,,,,.........................,,,,,,,,,,.....,,,,,,,.,,,,,,,,,,,,,,,,,,,,,,....,,,,,,,,,,,,,,,,,,,,,,,,,,,,,..,,,,.,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>->>>,<<<<_____>>>>::::::::::::::::::::::.........::::::::::::::::::::::::::::::::.::::::::::::::::::::::::..::::::::::::::.::::::::::::::::::::::::.:::::::.::::::::::::::..:::::::::::.:::::::::::....:::::::::
#=GC RF                              cAccAucaAA............AcAcCUUcaAucuCCAAagcC..aCcauAuUuauCcuCGCAAUGuCCGuC.aGGAAugGuCuCAAcCuaAaGua........uuUcGAuCCUugGAAACccAcuCGAaAuaCAgUuauaauuaAuucaUaUCGAGaUauAC.AGcCAauAauCGCuugccCgAA..CGaCGAcgacagCCAuUuCCAuc.aGUCUUUCaaCuCucuC.G..CUc..CgcGCACgGCGCCUCCCCcACAGUUCUCCGAUUCCaGUUUUCCg..aAAGGAAUGUCaU.cguGaCCGCUCag..gGuGUcuGGuucuuCCGCAGUACGUCGCAGCUUCGA.UCCuGUAUCaGGuGCC.UCUCAAGCU.UGCCGCGcaUGGgAUUACUGcG...GAUUuCugGuUuUUuuaccCuaggcuugCCaGugCC.gcaGAGuGAAUUGGUCUCGGAACUUAACCCUAAGUAuAuCucUGGu.a...aUgacAAGUCUUGCGCucuU.GauAGUCA.aUCgaaCCuUCGCCUUCUAuGuccGCGUcaUcgua.guGuuUGccuucGg........ggGCCGCUGAAAAGUuGuGUagUCUauGcUCUuG..........uGAuGGCAaGGGCuGACCGGCaAGGugaGAaGu.UCCAGUCAuCuug................CuuGaUGGGCGAg.uGUCuguUCCCAUGAGUCaAaA..cGGUAAGaaCCUCUGGCCuGAGGuCGCUCGUCaGGAaUgGaaCACUGGAaguAGUACUCUGGUCAccAUaGCGGAUUGu............CcGUGGCuauGUugaCcGG.acGUuGgGG..aGAcacAuugUgGGuGcau..........guCaUCgaGaAGuUCuuUCUGCUuGCAuuguCUcuUGgGguuuuaCgUuuCucGacGuAugauCUuUgGaGugaaGA.GGGAGAGCGaAG.AuauGGCUACAcACGAUCAcauaauuCAUUUCAucuuUc.uGUCUuCAGCUuGCCUCGCauGAAUCACUuCacuuG.GuGGUGAGCgaGGGCUGUacGacUACAaACGGAAAUGuuGaaGaAuGAUuuUu....UuCacGCCuuuCUGUcaCGcUCUCuGuACCcUcagaUcUcccUcUUuUAUc..GCAUGCGcA..................UaCgucuucCUCccGGa.aAC.UCcaCcGACuCUguuGaACCGCGuUggGgaA.cAUAC..CG.uCaACGuGUCAUuGacuuuugu.uCauUGAGAUC.CCGaCCAGGCGCAUUAACcuaU..aCuCGUAuGgcUucGUCCUACGUcgCGAc.uGGAC.gCCAgAACcaCuGc....u.cgugUCUcc..GauCCucaAGGaGaggAG...cacg....gCaCuUuCCUccg..CcGggGugC..uGAAAaaUucaCcUcCgGgAcggAGAUGaUAGCaCGGUU.UUUGAGGAcGcAUUUUGuCCGUGCGGUAA..UGCCCUCCUUu........guccgCUUccccgccUgGggcggggGcgg.GGAGAGGAAaCAAAAgCUAgUCuCAGUUGGCAGUGCgcC..ACACACGGAaAGAcu........................UGGCU.UgGaUUuGgcUguCGACACuuGa.......uaUGUUAaUGaagguuuGGUUuCuuAuuuuGGauuGAuCuG..CcuCaAUGACu.GcuGGuUUggaCUguGAGauUG.GUGuUuuGGuGuuUcuUGa...........a.cCauUgUGGGGGugUccGgGUuu.........................GGAagAAGgg.....UUGGgcC.gACUgGUUGAaAAcCAAUGCuU....cGacCUuGGuuuUuCgGAuGAuGGugGuu..GGac.ucuuGGGaAgaGAaCcAaagguCGGGACCCAUCUcGAGUUGGAGUCAAAGcUUcGUgCUUGUCUGGcguUuGGAuccugUCU.........uuugCugCUguCCagAgUCuGuGUuCuUuCaG.GGaugGCUUUGuUGUUUGagGUUc..GuCcuuUuGGAaAa.GGACuGgCuuuuUGGaaGGUGGUC.CuGGUUG.UCcUCuuUCCuGAA..AUGGCGGGAGG.ACAACCCCUCu....UUUUuGAGG
//
# STOCKHOLM 1.0

#=GF AC   RF02463
#=GF ID   Ms_AS-1
#=GF DE   Mycobacterium sRNA Ms_AS-1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23169799
#=GF GA   37.00
#=GF TC   37.00
#=GF NC   35.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23169799
#=GF RT   Identification of small RNAs in Mycobacterium smegmatis using heterologous
#=GF RT   Hfq.
#=GF RA   Li SK, Ng PK, Qin H, Lau JK, Lau JP, Tsui SK, Chan TF, Lau TC
#=GF RL   RNA. 2013;19:74-84.
#=GF WK   Bacterial_small_RNA
#=GF SQ   5


CP000656.1/4627575-4627672 GUCGGGUU-CGGGAUGAAGUGGUUGAUCACACCACCGAACACCGCGUACGUGCGCUUGCCGUCGUUGAGCAUCUGCACCCCGCGGCUGCGGAACUCCUU
CP002329.1/3598675-3598772 CUCGGGUU-CGGGAUGAAGUGGUUGACGACCCCGCCGAACACCGCCAGGGUGCGAUUGCCGUCCUGCACCAUCUGGACACCGCGGCUGCGGAAUUCCUU
CP000511.1/2128977-2128879 GGUGGGAUUGGGGAUGAAGGUGUUGACCCGCCCGCCCAUCACCGCCCAGGUGCGCUUGCCGUCCUGGUACAUCUGCACGCCGCGGCGGCUGAAUUCUUU
CP000480.1/2308051-2307954 GACGGGUU-CGGGAUGAAGUGGUUGACCACGCCGCCGAACACCGCGUACGUGCGCUUGCCGUCGGUCAGCAUCUGCACUCCGCGGCUGCGGAACUCCUU
CP000518.1/1931632-1931535 GUCGGGUU-CGGGAUGAAGUGGUUGACGACGCCACCCAUGACGGCGAAGGUGCGUUUGCCCUCGGUCAGCAUCUGCACGCCGCGGCGCUUGAACUCCUU
#=GC SS_cons               :::::<<<.<<<--<<--<<<<____>>>>-->>>>>>>>,,,<<<<____>>>>-----------------------<<<<<____>>>>>:::::::
#=GC RF                    gucGGGuU.cGGGAuGAAgugGUUGACcacaCCaCCgAaCACcgCgcAgGUgcGcUUGCCgUCguucagCAUCUGcACcCcGCGGCuGCgGgAuUCcUU
//
# STOCKHOLM 1.0

#=GF AC   RF02464
#=GF ID   Ms_AS-4
#=GF DE   Actinobacteria sRNA Ms_AS-4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23169799
#=GF GA   50.00
#=GF TC   51.00
#=GF NC   48.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23169799
#=GF RT   Identification of small RNAs in Mycobacterium smegmatis using heterologous
#=GF RT   Hfq.
#=GF RA   Li SK, Ng PK, Qin H, Lau JK, Lau JP, Tsui SK, Chan TF, Lau TC
#=GF RL   RNA. 2013;19:74-84.
#=GF WK   Bacterial_small_RNA
#=GF SQ   9



ACBV01000035.1/18602-18683         CUUGGCGUCGGUGUAUCGA--UUCGGGUCGUCCCCGA-ACUCACCAAGCACCCGGGCGCCGAGU-ACGACACCAAGUCCU-GGCAGG
ADNV01000179.1/357-438             CUUGGCGGUGGUGUAUCUG--UUCGGGUCGUCCCCGA-ACUCACCGAGCACCCGGGCGCCGAGC-GCAACACCAAGUCCU-GGCAGG
AP011117.1/59578-59659             CUUGGCGGUGGUGUAGCGG--UCGGGGUCGUCCCCGA-ACUCACCGAGCACCCGGGCGCCGAGC-ACAACACCAAGUCCU-GGCAGG
ADGO01110529.1/172-253             CUUGGGAUUGGCGUAACGG--UCGGGGUCAUCCCCGA-ACUCGCCGAGCACCCGGGCGCCGAGC-ACAUCGCCGAGUCCU-GGCUGA
CP000433.1/309170-309088           CUUGGCGGUGGUGUAGCGA--UCGGGGACGUCCGAAGAACUCACCGAGCACCCGGGCGCCAAGG-AUGACACCAAGUCCU-GGCAGG
ABSR01009339.1/531-450             UCUGGCAUCCUUGUAGCGG--UUCGGCGCGUCGCCGA-ACUCGCCAAGCACCCGGGCGCCGAGG-ACGAGACCUAGUCCG-GGAAGA
ADGX01000119.1/109-26              UUUGGCGUCGGUGUAGCGC--UUCGGGUCGUCCCCGA-ACUCGGCGAGCACCCGGGCAGCGAGGACCGUGCCCCAGGCCGGGCGUGG
CP001814.1/5216397-5216478         UUUGGCGUUGACGUAGCGGCCUUCGGC--GUCGCCGA-ACUCUGCGAGCACCCGGGCGCCGAGG-ACCAGUCCCAGCCCC-GGCUGC
CP000480.1/4156013-4155932         CUUGGCGUUGGUGUAUCGG--UUCGGGUCGUCCCCGA-ACUCACCGAGCACCCGGGCGCCGAGG-AUGACACCAAGUCCU-GGCAGG
#=GC SS_cons                       :::::::<<<<<<----<<..<<<<<<_____>>>>>.>>>>>>>>>----------<<<-<<<.<<________>>>>>.>>>:::
#=GC RF                            cUUGGCGucGguGUAgCgg..UucGGguCGUCcCCga.AcuCacCgaGCACCCGGGCgcCGaGg.aCgAcaCCaAGucCu.GgcaGg
//
# STOCKHOLM 1.0

#=GF AC   RF02465
#=GF ID   Ms_AS-5
#=GF DE   Mycobacterium sRNA Ms_AS-5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23169799
#=GF GA   46.00
#=GF TC   46.30
#=GF NC   45.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23169799
#=GF RT   Identification of small RNAs in Mycobacterium smegmatis using heterologous
#=GF RT   Hfq.
#=GF RA   Li SK, Ng PK, Qin H, Lau JK, Lau JP, Tsui SK, Chan TF, Lau TC
#=GF RL   RNA. 2013;19:74-84.
#=GF WK   Bacterial_small_RNA
#=GF SQ   9



CP000384.1/989416-989460               AUCCGGGUACUGGCCGGUGAAGAUCGUCGGCCGGCUCGGCACGCA
CP000325.1/3834944-3834900             GUCGGGGUACUGGCCGGUGAAGAUCGUCGGGCGACUCGGCACACA
AGIQ01000002.1/958507-958551           GUCGGGAUACUGGCCGGUGAAGAUCGUGGGCCGGCUCGGCACGCA
AGVE01000046.1/593658-593702           AUCCGGGUAGUGCCCGGUGAAGAUGGUCGGCCGACUGGGCACACA
AFVW01000001.1/251966-252010           AUCGGGAUAGUGCCCGGUGAAAAUCGUUGGGCGGCUGGGCACGCA
BX842581.1/320716-320672               AUCCGGAUAUUGGCCGGUGAAAAUCGUCGGGCGGCUGGGCACGCA
CP000656.1/2471109-2471153             GUCCGGGUAGUGGCCGGUGAAGAUGGUCGGACGGCUGGGGACGCA
AGIO01000001.1/1115603-1115647         AUCGGGGUACUGACCGGUGAAAAUCGUUGGGCGACUGGGCACGCA
CP000480.1/1377204-1377248             AUCGGGGUAGUGGCCGGUGAACAUGGUCGGCCGGCUCGGCACACA
#=GC SS_cons                           :::::::::::<<<<<<<_______>>>>>>>:::::::::::::
#=GC RF                                AUCgGGGUAgUGgCCGGUGAAgAUCGUCGGcCGGCUgGGCACGCA
//
# STOCKHOLM 1.0

#=GF AC   RF02466
#=GF ID   Ms_AS-8
#=GF DE   Actinobacteria sRNA Ms_AS-8
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23169799
#=GF GA   48.00
#=GF TC   49.40
#=GF NC   43.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23169799
#=GF RT   Identification of small RNAs in Mycobacterium smegmatis using heterologous
#=GF RT   Hfq.
#=GF RA   Li SK, Ng PK, Qin H, Lau JK, Lau JP, Tsui SK, Chan TF, Lau TC
#=GF RL   RNA. 2013;19:74-84.
#=GF WK   Bacterial_small_RNA
#=GF SQ   10



CP000511.1/645152-645080             CAUGAUCGGACCUUCGGAUA-UUC-----AGAUCAUCCUCGGGAAGGUGCGCCCACUUUCACGCC-CCCACACCGAGGCU
ADGO01079120.1/673-745               CAUGAUCGGACCUACUGACA-UUC-----AGAUCAUCCUCGGGAAGGUGCGCCCACUUUCACGCC-CCCACCCCGAGGCU
AGIQ01000009.1/106372-106445         CUUGAUCAGAGCUACUGGAC-UUU----CAGAUCAUCCUCGGGAAGGUGCGCCCACUUUCACGCC-GCCCCACCGAGGCU
CP002385.1/4834087-4834014           CUUGAUCAGAGAACCUUGGACUUC-----AGAUCAUCCCCGGGAAGGUGCGCCCACUUUCAUGCC-GCCCCACCGAGGGU
CP000325.1/2665003-2664930           CUUGAUCAGAGUUUCUGGAC-UUU----CAGAUCAUCCACGGGAGGGUGCGCCCACUUUCACGCC-CCCUCACCAAAGCU
AACY023322092.1/644-573              CUUGAUCAGAGCUACUGGAC-UUU----CAGAUCAUCCUCGGGAAGGUGCGCCCAUUU--ACGCC-GCCUCGCCGCGGGU
AJ716150.1/421-350                   CCUGAUCAGAGCUGAUGGAA-UUU----CAGAUCAUUCCCGGGAAGGUGCGCCCAC--UCACGCC-GCCUCGCCGAGAAC
AJ716149.1/422-350                   CCUGAUCGGAGCUGAUGGAAUUUC-----AGAUCAUUCCCGGGAAGGUGCGCCCAC--UCACGCCCGCCUCGCCGAGAAC
CP001686.1/71653-71579               CCUGAUCCAGAACUUCGAUU-CCGU--GUAGAUCAUCCUCGGGAAGGUGCGCCCGCU-UCACGUC-ACCCCGCCGAGGGC
M69182.1/100-26                      CUUGAUCGAA--UACCUGA--UUCCGUGAAGAUCAUCCCCGGGAAGGUGCGCCCAUCUUCACGCC-CCCACACCGAGGCU
#=GC SS_cons                         ::<<<<<<<<__________.>>>....-->>>>>-------<<<<<<<____>>>>>>>:::::.::::::::::::::
#=GC RF                              CuUGAUCggagcUacuGgaa.uuc....cAGAUCAUCCuCGGGAagGUGCGCCCACuuUCACGCC.gCCuCaCCGAGGcU
//
# STOCKHOLM 1.0

#=GF AC   RF02467
#=GF ID   Ms_IGR-2
#=GF DE   Mycobacterium sRNA Ms_IGR-2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23169799
#=GF GA   45.00
#=GF TC   55.30
#=GF NC   32.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23169799
#=GF RT   Identification of small RNAs in Mycobacterium smegmatis using heterologous
#=GF RT   Hfq.
#=GF RA   Li SK, Ng PK, Qin H, Lau JK, Lau JP, Tsui SK, Chan TF, Lau TC
#=GF RL   RNA. 2013;19:74-84.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


CP000480.1/417847-417929 CUGAGGGGUACCCGAGGCGUACGAUCGUUCGUACGACGGGUUCGGGAGUGGCUUGAUCCAAAGAGUCGGUUCAGGGGUGAAAA
AGSZ01000926.1/2476-2557 UUGAGGGGUACCCGAGGCGUACGAUCGAGCCUACGACGGGUUCGGGAGUGAC-UGAUCCAAAGAGUCGGCAUUGGGGUGAAAG
CP000656.1/423161-423087 CUGAG-------CCAGGCGUAGCAUCGUUCUCACGACGGGUUCGGGAGUGAC-UGAAUCAAAGAGUCGGCAAAGGGAUGAAAG
#=GC SS_cons             :::::::::::::::::<<<<<<<____>>>>>>>----------------<.<<<-<<_________>>->>>->:::::::
#=GC RF                  cUGAGGGGUACCCgAGGCGUacGaUCGuuCguACGACGGGUUCGGGAGUGaC.ugaucCAAAGAGUCGGgaucgGGgUGAAAg
//
# STOCKHOLM 1.0

#=GF AC   RF02468
#=GF ID   Ms_IGR-4
#=GF DE   Mycobacterium sRNA Ms_IGR-4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23169799
#=GF GA   55.00
#=GF TC   61.00
#=GF NC   37.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23169799
#=GF RT   Identification of small RNAs in Mycobacterium smegmatis using heterologous
#=GF RT   Hfq.
#=GF RA   Li SK, Ng PK, Qin H, Lau JK, Lau JP, Tsui SK, Chan TF, Lau TC
#=GF RL   RNA. 2013;19:74-84.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


CP000480.1/6570040-6570077 GAGCGGCGGCAACUACCCUGCGGCCACGGCUGCUGCCU
AGSZ01000617.1/20812-20775 GAGCGGCGGCAACUACCCUGCGACCACGGCUGCGGCCU
#=GC SS_cons               ::<<<<<<<<-----<<____>>----->>>>>>>>::
#=GC RF                    GAGCgGCGGCAACUAcCCUGCGgCCACGGCUGCuGCCU
//
# STOCKHOLM 1.0

#=GF AC   RF02469
#=GF ID   Ms_IGR-7
#=GF DE   Actinobacteria sRNA Ms_IGR-7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23169799
#=GF GA   45.00
#=GF TC   45.40
#=GF NC   44.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23169799
#=GF RT   Identification of small RNAs in Mycobacterium smegmatis using heterologous
#=GF RT   Hfq.
#=GF RA   Li SK, Ng PK, Qin H, Lau JK, Lau JP, Tsui SK, Chan TF, Lau TC
#=GF RL   RNA. 2013;19:74-84.
#=GF WK   Bacterial_small_RNA
#=GF SQ   14



AFAQ01001960.1/4293-4412             UGGAAGUGC-CUUU-CUUGAAC-UGGACUGGUUUGUGCGU-GAAGAACAUCAAUCAUCCCAGUUCAGGGGGCGCUUUCUUUAUUUCG---ACACGCC-GCUAC-CCGCCGGG--G-GCA-UCGGUGGAUUCAG
CP000854.1/3843116-3843234           CGGAAGUGCCGUUC-U-CGAAC-UGGACCGAUUGUUGCCU-GAACAAUAUCAAUCUUCCCAGCUCAGAACGCACUUUCCUUAUCCCG---ACACCCCGACAAA-CAG-UCCA--U-U-G-UCAGUGGAUCGAG
CAFW01000025.1/44348-44232           CAGAGGUGC-CUUU-C-UGAUCCUAGAA--AUAGUGGCGU-GAACAACUACUAUUAUUCCAGGUCAAAAGGCACUUCUUCAGUUAAA---CCGCCGA-ACUCA-CAC-CAAA--U-UUA-UCGGUGGAUCCAG
CP000667.1/3059689-3059577           -CGAGGUGC-CCUC-U-CGAAC-CGGC-UGAUAGAAGCGU-CG-UAACUCCGAUCUUCCCAGUUCAGAGGGCACUUCUAUC-UCCGG---GGUCCCG-UCGA----G-CCGAGCU-UCG-UCGGUGGAUCGAG
CP002047.1/10314482-10314600         CGGAGAUGU-ACCU-C-CGAAC-UGGUCGAGUAGAAGCCU-AGAGAACUCCUAUUCUCCCAGGUCAGAGUGCAUCUCCACUUUCAUGUCCAAACACU--GGAC-CAA-CCG-----UCACCCGGUGGAUCGAG
CP000480.1/1402449-1402332           CGGAAGUGC-CUUU-C-UGACCGUGGGCUGAUCGAAGUGU-GG-UAACUCCAAUCAUCCCAGCUCAAAGGGCACUUUCCUUAUAUCA---ACACCCU-CCGAC-CAG-GCGA--U-UCA-UCGGUGGAUCGAG
AGSZ01000509.1/1542-1659             CGGAAGUGC-CUUU-C-UGACC-UGGACUGAUUAGUGCGUCGA-GAACACCAAUCUUCCCAGUUCAAAGGGCACUUUCCUCAUUCCG---ACACCCU-GCGAC-CAG-CCGA--U-ACA-UCGGUGGAUCGAG
CP000479.1/1447034-1447152           CGGAAGUGC-CUUU-C-UGACCA-GGACUGAUUGUUGCGU-AGAGAACAUCAAUCUUUCCAGCUCAGAGGGCACUUUCCUCGUUACG---ACACCCGGUCAAC-GAG-CCCG--U-UCA-UCGGUGGAUUCAG
CP002385.1/875738-875855             CGGAAGUGC-CUUU-C-UGAAC-UGGCCUGAUUGAUGCGU-AGAGAACACCAAUCCUCCCAGCUCAAGGGGCACUUUCCUCAUUCCG---ACACCCC-ACGAC-CAA-CCAA--U-UUA-UCGGUGGAUCGAG
CP000511.1/5931006-5930889           CGGAAGUGC-CUUU-C-GGAGU-UGUGUCGAUAAGUGCGU-AGAGAACACUCAUCAUCACAGCUCAGAGGGCACUUUCCUCGUUACG---ACACCCG-AUGAC-CAG-CUGA--U-UCA-UCGGUGGAUCGAG
CP000656.1/4916615-4916498           CGGAAGUGC-CUUU-C-CGAGU-UGUGCCGAUAAGUGCGU-AGAGAACACUCAUCAUCGCAGCUCAGAGGGCACUUUCCUCAUUCCG---ACACCCC-ACGAC-CAG-CCAA--U-UCA-UCGGUGGAUCGAG
CP000385.1/10110-9992                UGGAAGUGC-CUUU-C-UUAAC-UGGCCUGAUUGAUGCGU-AGAGAACACCAAUCCUCCCAGCUCAAGGGGCACUUUCCUUAUAUCG---ACACCCA-CCUACACAG-GCAA--U-UCA-UCGGUGGAUCGAG
AACY022400814.1/578-461              CGGAAGUGC-CUUU-CUUGUGC-UGAAACGAUUUUAGUGU-GA-GAACUCAAAUCAUCCCAGCUCAGAGGGCACUUUCUUUACUCCG---ACACCCG-CCCGG-AA--CCUA--UCUCA-UCGGUGGAUCGAG
AGVE01000027.1/548-430               CGGAAGUGC-CUUUUC-GGAGCCGGGUCCGAUUAAUGCGU-GA-GAACAUCAAUCAUCCCAGCUCAGAGGGCACUUUCCUCAUUCCG---ACACUCG-AUGAA-CAG-CUAA--U-UCA-UCCGUGGAUUCAG
#=GC SS_cons                         :<<<<<<<<.<<<<.-.<<<-<.<<<<-<<<<-<-<<<__._____>>>->->>>>->>>>>->>>>>>>>>>>>>>>---------...-------.-----.---.-<<<..<.<<<.____>>>>>>>::
#=GC RF                              CggAaGUGC.ccuc.C.uGAaC.uGggccGaUugauGcGU.agAgAaCaccaAuCgUccCaGcUCagaggGCACuUcccUuaUuacG...AcACcCu.acgAc.cAg.ccga..U.uCa.UCGGuGgAucgAG
//
# STOCKHOLM 1.0

#=GF AC   RF02470
#=GF ID   Ms_IGR-8
#=GF DE   Mycobacterium sRNA Ms_IGR-8
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23169799
#=GF GA   44.00
#=GF TC   44.00
#=GF NC   43.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23169799
#=GF RT   Identification of small RNAs in Mycobacterium smegmatis using heterologous
#=GF RT   Hfq.
#=GF RA   Li SK, Ng PK, Qin H, Lau JK, Lau JP, Tsui SK, Chan TF, Lau TC
#=GF RL   RNA. 2013;19:74-84.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



CU458896.1/1324579-1324517         CUAUAGCACUGUCGCGAGCGUGAAGCUGCUGUGGGAAAUCAGUGGAUUUGUCGCAGCAGCUUC
AGIO01000006.1/25005-24943         CUGACUUCCUGCCGCGAAUGUGAAGCUACUGCGAAUUCUCGGCUGAAUUUCCGCAGUAGCUUC
CP000480.1/1634985-1634923         AACGAGAAAUGCCGCGAGUGUGAAGCUGUUGCGAGUAUGCGGGUCAAUCGUCGCAACAGCUUC
#=GC SS_cons                       :::::::::::::::::::::<<<<<<<<<<<<<<---<_____>--->->>>>>>>>>>>>>
#=GC RF                            cuaaAguAcUGcCGCGAGUGUGAAGCUGCUGCGaguauuCGGuugAaUcguCGCAGCAGCUUC
//
# STOCKHOLM 1.0

#=GF AC   RF02471
#=GF ID   Ms_IGR-5
#=GF DE   Actinobacteria sRNA Ms_IGR-5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23169799
#=GF GA   45.00
#=GF TC   45.10
#=GF NC   40.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23169799
#=GF RT   Identification of small RNAs in Mycobacterium smegmatis using heterologous
#=GF RT   Hfq.
#=GF RA   Li SK, Ng PK, Qin H, Lau JK, Lau JP, Tsui SK, Chan TF, Lau TC
#=GF RL   RNA. 2013;19:74-84.
#=GF WK   Bacterial_small_RNA
#=GF SQ   21


AGSZ01000296.1/14276-14104   ACACAGGGAAGGAGGU-GGUCCGAC---------------------------AAAUUGAGUGAUUUAUGGACAUGUGAGGUGGCUGCCCGCUAGCAGCGC-CGGGGUA-AAG-------------------------------CCUG-CGCGC-GCUG-GCGAAUUCCCCGCAGUCACCCGGCCCCCGAGCCCUCCGGUC----UGUCCAACCAGG--UA-CC--AA-----------------------GGCUCGGGGGCUGCCCCAU
CP000518.1/4846918-4846735   ACACAGGGAAGGAGGU-GGUCCGAC---------------------------AAAUUGAGUGACUUAUGGACAUGUGAGGUGGCUGCCCGCUAGCAGCAC-CGGGG----AAGUCGAG-------------------CACCGACCUGUCGUGC-GCUG-GCGAAUUCCCCGCAGUCACCCGGCCCCCGAGCCCCUCGGUC----CGUCCAACCAGG--AACCA--AC-----------------------GGCUCGGGGGUCGCCCAUA
CP002385.1/1046661-1046843   ACACAGGGAAGGAGGU-GGUCCGAG---------------------------AAAUUGAGUGACUUAUGGACAUGUGAGGUGGCUGCGAGCUAGCAGCGC-CGGGA----GAGCGCUC-------------------GUCGCACCUG-UGCGC-GCUG-GCGAAUUCCCCGCAGUCACCCGGCCCCCGAGCCUCUUGGUC---UUGUCCGACCGGG--AA-CG--AC-----------------------GGCUCGGGGGCCGCUCCAU
AGVE01000046.1/729417-729238 ACACAGGGAAGGAGGU-GGUCCGG----------------------------AAAUUGAUUGAUCCAUGGACUUGUGAGGUGACUGCGCGCUAGCAGCUG-CGCA-------UGCGAGG-----------------AAUCACCUG---CGCGC-GCCG-GCGAAUUCCCCGCAGUCACCCGGCCCCCGAGCCCCUUGGUC----CGUCCAACCAGGGAAC-CA--AC-----------------------GGCUCGGGGGCCGCUCCAU
AGIQ01000001.1/358639-358822 ACACAGGGAAGGAGGU-GGUCUGCG---------------------------AAAUUGAUAGCUUCUAGGACAUGUGAGGUGGCUGCCAGCUAGCAGCAC-CAGGU-----GCGGUGGAUU-------------CACCUGCGUCCUG-CGCGC-GCUG-GCGAAUUCCCGGCAGCUACCCGGCCCCCGAGCUC--UGGUU----UGUCCAACCAGG---U-GA--AC-----------------------GGCUCGGGGGCCGCCCCAU
ABIN01000123.1/6509-6328     ACACAAGGAAGGAGGU-GGUCCGAG---------------------------AAAUUGAUAGCUUCAUGGACAUGUGAGGUGGCUGCGCGCUAGCUGCAU------------CGGCUCGGAAGA------GCUGGCGAUACAG------AUGC-GCUG-GCGAAUUCCCCGCAGUCACCCGGCCCCCGAGCUUCCGGUUU----UGUCCGACCUGG--AA-U---AC-----------------------GGCUCGGGGGCCGCUCCAU
AGIO01000003.1/297588-297768 ----ACGUAUGGGCGCUGGCAUGUCUU-----------------------CGAAAUUGAUUGACUUAUGGACAUGUGAGGUGGCUGCGAGCUAGCAGCGC-CAGGGG--ACUUGU------------------------CGCACCUG-AGCGC-GCUG-GCGAAUUCCCCGCAGUCACCCGGCCCCCGAGCCCUCGGUUU----UGUCCAAACUGG--AA-CA-CAU-----------------------GGCUCGGGGGCCGCUCCAU
AFVW01000006.1/10265-10447   ACACAAGGAAGGAGGU-GGUCCGCG---------------------------AAAUUGAUAGCUUCAUGGACAUGUGAGGUGGCUGCGCGCUAGCAGCAC------------CUGCUCGGAAGA------GCUGGCGUCACAA------GUGC-GCUA-GCGAAUUCCCCGCAGUCACCCGGCCCCCGAGCUUCCGGUUU----UUGUCCGACCAG--GA-AC--AC-----------------------GGCUCGGGGGCCGCUCCAU
CP000854.1/5927715-5927539   ACACAGGGAAGGAGGU-GGUCCG-C---------------------------GAAUUGAGUACUUCAUGGACAUGUGAGGUGGCUACGCGCUAGCUGCAU-UGGC-------UCGGAAG-----------------AGCUGGCGUUA-CGCGC-GCUG-GCGAAUCCCCCGUAGCCACCCGGCCCCCGAGCU-UUCGGUC----UGUCCAACCGGA--AC-U---U------------------------CGCUCGGGGGCCGCUCCAU
ACFI01000032.1/6096-6279     ACACAAGGAAGGAGGU-GGUCCGCG---------------------------AAAUUGAUAGCUUCAUGGACAUGUGAGGUGGCUGCGCGCUAGCUGCGC------------CGGCUUUCGAAGA-----GCCGGCGUUAUUU------GUGC-GCUG-GCGAAUUCCCCGUAGUCACCCGGCCCCCGAGCUUCCGGUUU----UUGUCCGACCAG--GA-AC--AC-----------------------GGCUCGGGGGCCGCUCCAU
AGQU01000008.1/64743-64907   ACACAAGGAAGGAGGU-GGUCCGAC---------------------------AAAUUGAUUGCUUAUGGGACAUGUGAGGUGGCUGCCCGCUAGCUGCAG------------CCA------------------------UGCG------CUGCGGUGG-GCAAAUCCACGGCAGCCACCCGGCCCCCGAACC-CUCGAUG----AGUCCGAUCGAG--CC-GA--AC-----------------------GGUUCGGGGGCCGCCCCUU
ACBV01000154.1/8754-8575     ACACAGGAAAGGAGGU-GGUCCGCG---------------------------AAAUUGAUAGCUUCAUGGACAUGUGAGGUGGCUGCGCGCUAGCUG---------------CAAUGGCUCGGAAGAGCCGGCGUUCUACGCA---------C-GCUG-GCGAAUCCCACGUAGCCACCCGGCCCUCGAGCU-UCCGGUC----UGUCCAACCGGA--AA-AG---------------------------CGCUCGGGGGCCGCUCCAU
ADNV01000206.1/20828-20649   ACACAGGAAGGGAGGU-GGUCCGGG----------------------------AAUUGAUAGCUUCAUGGACAUGUGAGGUGGCUGCGCGCUAGCUGCAG-UG---------GCUCGGAAGA-----------GCUGGCGAUU--CA-CGCGC-GCUA-GCGAAUUCCCCGCAGUCACCCGGCCCCCGAGCU-UCCGGUU----UGUCCAACCAGG--AG-CA--UU------------------------GCUCGGGGGCCGCGCCAU
CP002786.1/753141-753325     ACACGAGGAAGGAGGU-GGUCCA-G---------------------------AAGAUGAUUGGCUUUAGGACACGUGAGGUGGCUGUCCGCUAGCUGC--------------CAGCUGCGCCAGGAUUCACCCCCUGCCAUUG--------GCAGCGA-GCGAAUACCAGGCAGCUACCCGGCCCCCGAACCACCGGCUA----AGUCC-AGUCGG--UA-CA-CAC-----------------------GGUUCGGGGGCUGUCCGUU
AFAQ01001981.1/57143-56965   ACACGAGGAAGGAGGU-GGUCUGG-----------------------------AAGUGAUUGAUAUUCGGACGCGUGAGGUGGCUACCCGCUAGCUGCU-------------CGAGACGACGGAA-----UUCACCGACCGCG-----C--GCGGCUG-GCGAAUCCCAGGUAGUCACCCGGCCCCCGAGUC-CCCGGUC----CGUCCGAUCGGG--AC-CG--CC-----------------------GACUGCGGAG-CGAUCCGU
CP000480.1/5862639-5862466   ACACAGGGAAGGAGGU-GGUCCGAC---------------------------AAAUUGAGUGACUUAUGGACAUGUGAGGUGGCUGCCCGCUAGCAGCGC-CGGGAGAAUAG-------------------------------CCCG-CGCGC-GCUG-GCGAAUUCCCCGCAGCCACCCGGCCCCCGAGCCCCUUGGUC----AGUCCAACCAGG--AA-CA--AC-----------------------GGCUCGGGGGCCGCCCCAU
AP006618.1/611482-611687     ACACGAGGAAGGAGGU-GGUUCGAA---------------------------GAAUGGAUAGU-UCUAGGACACGUGAGGUGGCUGUCCGCUAGCGCCAC-CGCU---------GCAGGUG-------------GUAUCCGCCCGCG-CGAGC-GCUGAGCGAAUACCAGGCAGUCACCCGGCCCCCGAGCC-CCCGGUC---CUGUCCGACCGGG--AC-CC--GUGCAGGCACCCGCCGCACCGGUACGGCUCGGGGGCCGUUCCCU
CP000509.1/787290-787483     ACACGGGAAAGGAGGU-GGUCCGA----------------------------AGAAUGAGUUCUUCCAGGACGCGUGAGGUGGCUGCCCGCUAGCAGCCCACCAG-------CAACACCCGGG--------GUGGAAGUGCCCCGGG-ACGGCUGCUG-GCGAAUCCCAGGCAGUCACCCGACCCGCAGGCGAUCCGGUCAUCACGUCC-ACCGGA--GC-GG--UC-----------------------UCCUCGGAGGCCGGCGCCU
AFIF01000138.1/34887-35097   ACACAAGGAAGGAGGU-GGUCCGCGAAAUUGAUAGCUUCAUGGACAUGUGCGAAAUUGAUAGCUUCAUGGACAUGUGAGGUGGCUGGGCGCUAGCUGCGC------------CGGCUUUCGAAGA-----GCCGGCGUUAUUU------GUGC-GCUG-GCGAAUUCCCCGUAGUCACCCGGCCCCCGAGCU-UCGGGUUG--UUGUCCGACCAGG--AA-CA--C------------------------GGCUCGGGGGCCGCUCCAU
AGVD01000112.1/116426-116228 ACACGAGGAAGGAGGU-GGUCUGA-----------------------------AAUUGAAUGACAGACGGACACGUGAGGUGGCUGCCAGCUAGCCGCUA-CCGC-------UGACGGAAU-------------UCACUGACCGCG--CGAGCGGCGA-GCGAAUCCCAGGCAGCUACCCGGCCCCCGAGCCCCCGGUCU----GGUCCAGAUCGG--AC-CCGG--UGCACAAG-------CACCGGAAGGCUCGGGGGCCGUUGUGC
ACNO01000001.1/346604-346407 ACACAAGGAAGGAGGU-GGUCUGA-----------------------------AAUUGAAGUACAGACGGACGCGUGAGGUGGCUGCCAGCUAGCCGCAA-UCGC-------UGAUGGAAU-------------UCACUUACCGCG--UGAGCGGCCG-GCGAAUCCCAGGCAGCCACCCGACCCCCGAGCC-CCCGAUC----AGUCCGACCGGG--AU-CC--GCGCGAAAGC-------GUGGGUGUGGCUCGGGGGUCGCUUCGU
#=GC SS_cons                 :::::::::::::<<<.<<<_____...........................______________________________>>>>>><<<<<<<-<<<<.-<<<......._________............._________>>>..->>>>.>>>>.>>>-----------------<<<<<<<<<<<<<-<<<<<<_....______>>>>>>..--.--..--.......................>>>>>>>>>>>>>::::::
#=GC RF                      ACACAaGGAAGGAgGu.gGuCcGag...........................AAAUUGAuuGauUuauGGACAuGUGAGGUGgCugCccGCuaGCuGCgc.cggg.......cgacagaau.............uuauuaucuccc..cgcGC.GCug.GCgAAUuCCacGcAGuCACCCGGCCCCCGAGCcucccGguu....uGUCCaacCggg..aa.ca..ac.......................gGCUCGGGGGCCGcuccaU
//
# STOCKHOLM 1.0

#=GF AC   RF02472
#=GF ID   Gl_RNase_MRP
#=GF DE   Giardia RNase MRP
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   149.20
#=GF NC   32.90
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000385; RNase_MRP_RNA;
#=GF DR   GO; 0006364; rRNA processing;
#=GF DR   GO; 0000171; ribonuclease MRP activity;
#=GF DR   GO; 0000172; ribonuclease MRP complex;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   RNase_MRP
#=GF SQ   2


AACB02000011.1/93895-93777 UCUGGAUUCCGGGGAGUGUCUGGUGCCGAUCGGACACUCCCUAGCCGCCACACUGACAGUUAUGGUUGCAGGACAAGCUUAGCGAGUCCGAACUCGACAGGGAUACUCUACAGCGUUCC
ACGJ01002287.1/25883-26001 UCUGGACUCCGGGGGGUGUCUGGUGCUAAUCGGACACCCCCUAGCCGCCACACUGACAGUUAUGGUUGCAAGACGAGCUUAGCGAGUCUGAACUUGACAGGGAUACUCUGCGGCGUUCC
#=GC SS_cons               ::::::::::<<<<<<<<<<<<<<____>>>>>>>>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<___________>>>>,,,,,,,,,<<<<___>>>>::::::::::
#=GC RF                    UCUGGAuUCCgGGGgGuGuCuGguGCuaauCgGaCaCcCCCuAGCCGCCACACUGACAGUUAUGGUUGCAgGaCaAGCUUAGCGAGuCcGAACUuGACaGgGAUACuCuaCaGCGUUCC
//
# STOCKHOLM 1.0

#=GF AC   RF02473
#=GF ID   GlsR4
#=GF DE   Small nucleolar RNA GlsR4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   70.00
#=GF TC   76.10
#=GF NC   36.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.55 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AACB02000005.1/294322-294382 AGUCUCCAUGACGAGAAUUACGCCGCCCCAGUCUGACCCCUGACGAACGGCUUCUCUGAUC
ACGJ01001410.1/70516-70576   AGUCUCCAUGAUGAAAGUUACGCCGCCCCAGUCUGACGUCUGACGAACGGCUUUUCUGAUC
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      AGUCUCCAUGAuGAgAgUUACGCCGCCCCAGUCUGACguCUGACGAACGGCUUuUCUGAUC
//
# STOCKHOLM 1.0

#=GF AC   RF02474
#=GF ID   GlsR5
#=GF DE   Small nucleolar RNA GlsR5
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   114.10
#=GF NC   31.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.23 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


ACGJ01002910.1/40910-40824 --UUAAAAGCUGUGAUGACAGGUUCUUGCCCCGUAUGACCCUGCGAUGAGUUAUACAAAAGAACGCACUCAAGCCAACCGACUGAGCUC
AY820286.1/1-89            AAUUAAAAGCUGUGAUGACAGGUUCUUGCCCCGUAUGACCCUGCGAUGAGUUAUACAAAAGAACGCAUCCAAGCCAACCGGCUGAGCUC
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    AAUUAAAAGCUGUGAUGACAGGUUCUUGCCCCGUAUGACCCUGCGAUGAGUUAUACAAAAGAACGCAuuCAAGCCAACCGgCUGAGCUC
//
# STOCKHOLM 1.0

#=GF AC   RF02475
#=GF ID   GlsR6
#=GF DE   Small nucleolar RNA GlsR6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   75.00
#=GF TC   87.90
#=GF NC   34.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.97 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ACGJ01002918.1/30690-30632   AAUGAUGGCUUGUUAUCCCUGUCUGAGGCCAAUGGCUUGAUUAGAUGAUUUGACAGAGC
ACVC01000099.1/120002-119944 AAUGAUGGCUUGUUAUCCCUGUCUGAGGCUAACCUCCUGAUUAGACGAUUUGGCAGAGC
AY820287.1/1-59              AAUGAUGGCUUGUUAUCCCUGUCUGAGGUCAAUACCUUGAUUAGACGAUUUGACAGAGC
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                      AAUGAUGGCUUGUUAUCCCUGUCUGAGGccAAuguCuUGAUUAGAcGAUUUGaCAGAGC
//
# STOCKHOLM 1.0

#=GF AC   RF02476
#=GF ID   GlsR7
#=GF DE   Small nucleolar RNA GlsR7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   75.00
#=GF TC   88.90
#=GF NC   33.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.15 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ACGJ01002422.1/30167-30109 -CGCAAUGAUUACUACAUCACAGCGAUAUAGAAUGAAGCGUUCAUAGUUACUCUGAGCGG
ACVC01000035.1/64374-64316 -CGCAAUGAUUACUGAAUCACAGCGACACAUGAUGAAGCGUUCAUAGUUACUCUGAGCGG
AY820288.1/1-60            CCGCGAUGAUUACCGAAUCACAGCGAUACACGAUGAAGCACUCAUAGUUACUCUGAGCGG
#=GC SS_cons               .<<<____________________________________________________>>>:
#=GC RF                    .CGCAAUGAUUACUgaAUCACAGCGAUAcAugAUGAAGCgUUCAUAGUUACUCUGAGCGG
//
# STOCKHOLM 1.0

#=GF AC   RF02477
#=GF ID   GlsR9
#=GF DE   Small nucleolar RNA GlsR9
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   95.00
#=GF TC   107.70
#=GF NC   33.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.10 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


ACGJ01002928.1/11866-11792 ----AACCCAUGAUUUGCAAUGCUUAGUCCGUGUUUCGAAGUGUUUUGCACGCUGGUGAGUGAAAGCACACAUGAGGUU
AY820290.1/1-79            UAGCAACCCGUGAUUUGCAACGCUUAGUCCGUGUUUCGGAGUGUCUUGCACGCUGAUGAGUGAAAGCACACAUGAGGUU
#=GC SS_cons               ::::<<<<___________________________________________________________________>>>>
#=GC RF                    UAGCAACCCaUGAUUUGCAAuGCUUAGUCCGUGUUUCGaAGUGUuUUGCACGCUGaUGAGUGAAAGCACACAUGAGGUU
//
# STOCKHOLM 1.0

#=GF AC   RF02478
#=GF ID   GlsR10
#=GF DE   Small nucleolar RNA GlsR10
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   75.00
#=GF TC   86.30
#=GF NC   33.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.93 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


ACVC01000208.1/27609-27542 AGAAUGAUGAGACGUGUUCCUCUCUCCUACAGACCUCCUGGGGAUGCUAUGUACACCUUACUGAUUUA
AY820291.1/1-68            AGAAUGAUGAGACGUGUUCCUCUCUCCUACAGACUCCCUGGGGAUGCUAUGUACACCUUACUGAUUUA
#=GC SS_cons               :<<<____________________________________________________________>>>:
#=GC RF                    AgAAUGAUGAGACGUGUUCCUCUCUCCUACAGACuuCCUGGGGAUGCUAUGUACACCUUACUGAUUuA
//
# STOCKHOLM 1.0

#=GF AC   RF02479
#=GF ID   GlsR13
#=GF DE   Small nucleolar RNA GlsR13
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   128.50
#=GF NC   32.40
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 23.82 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ACGJ01002906.1/52907-52808 AUCCAUUCGUGUGAGAUAUGAUGAUUGGGAGCGACCUAUGUUGAGGAUGGCGGCUGCCCGUCUUACCUUGUGACUUCUGCCGUCUUGCAAUGCUCUGACC
ACVC01000232.1/20832-20931 AUCCAUUCGUAUGAGAUAUGAUGAUUGGGAGCAACCUAUCUUGAGGAUGGCGGCCGCCCGUUUUACCUUGUAACGUUUGCCGUCUUACAAUGCUCUGACC
AY820294.1/1-100           AUCCAUUCGUAUGAGAUAUGAUGAUUGGGAGCGACCUAUCUUGAGGACGACGGCCGCCCGUCUUACCUUGUGACGUUUGCCGUCUUACAAUGCUCUGACC
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF                    AUCCAUUCGUaUGAGAUAUGAUGAUUGGGAGCgACCUAUcUUGAGGAuGgCGGCcGCCCGUcUUACCUUGUgACgUuUGCCGUCUUaCAAUGCUCUGACC
//
# STOCKHOLM 1.0

#=GF AC   RF02480
#=GF ID   GlsR14
#=GF DE   Small nucleolar RNA GlsR14
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   90.00
#=GF TC   99.70
#=GF NC   34.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 21.64 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ACGJ01002915.1/13449-13382 AAAUGAUGAUAAUGCGCAUUUGUCGGAAGGCUCACUUCUGACGAUUCCUUUGUCCAUUCCCCUGACC-C
ACVC01000045.1/79812-79879 AAAUGAUGACAAUGCGCAUUUGUCGGAAGGCUUACUUCUGAUGAUUCCUCUGUCCAUUCCCCUGACC-C
AY820295.1/1-69            AAAUGAUGACAAUGCGCAUUUGUCAGAAGGCUCACUUCUGAUGAUUCCUCUGUCCAUUCCCCUGAUCCU
#=GC SS_cons               :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:
#=GC RF                    AAAUGAUGAcAAUGCGCAUUUGUCGGAAGGCUcACUUCUGAuGAUUCCUcUGUCCAUUCCCCUGAcC.c
//
# STOCKHOLM 1.0

#=GF AC   RF02481
#=GF ID   GlsR18
#=GF DE   Small nucleolar RNA GlsR18
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   126.90
#=GF NC   31.50
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AACB02000045.1/26369-26517 ACGCAGCCUAAUCACCGCCCCUAUAGUCCUUUUCUAAACGC-GUGGCCGGUGCAGCUGCCCGCUGGCGCUUGCGAGCGUGCACAGGCCUACAUCCAGGGUCAUAGGUGGGGAGCGGAUCCCGUCCAUCCUCAAUCCGGGCCCGCACAGUC
ACGJ01001410.1/76727-76873 ACGCAACCUAAUCACCGCCCCGACAGUCCUUCGCUUAAUUAUGCGGCCGGUGCGGCUGCCCACUGGUACCUUUGGGCGCGCACAGGCCCACAGCCGGGGUCAUAGGUGGGGAGCGGAUACUGUCCAUCCUCAAUCCGGGCCCUCACA---
ACVC01000024.1/8383-8527   --GCAGCCUAAUCACCGCCCCUAUAGUCCUUUUCUAAACCUUAUGGCUGGUGCAGCCGCCCGCCAGUGCUUGCGGGUGUGCACAGGCCUACAUCUAGGGUCAUAGGUGGGGAGCGGAUCCUGUCCAUCCUCAAUCCGGGCCCGCACA---
#=GC SS_cons               ::((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<-<<<<<--<<<<<<<________>>>>>>>>>>>>->>>>,,,,,,,,,,,,,,,,<<<<<<<<--<<<<___>>>>->>>>>>-->>,,,,,,)):::...
#=GC RF                    AcGcAgCCUAAUCACCGCCCCuAuAGUCCUUuuCUaAAcuuUguGGCcGGuGCgGCcGCcCgcugGugCuUgcGgGCgcGCaCAgGCCuACAuCcaGGGUCAUAGGuGgGGaGCGGaucCuguCCAuCCuCaAUCCGGGCCCgCACA...
//
# STOCKHOLM 1.0

#=GF AC   RF02482
#=GF ID   GlsR19
#=GF DE   Small nucleolar RNA GlsR19
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   180.40
#=GF NC   30.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ACGJ01001859.1/18807-18659 UGGAGGUCUGACGUCCCGUUCUGGGAGGGGAGGAUGGAAGCCUAGCUUGGUCACUACCAGUGUGCACAUGUGUGUAGACUAGUCAAGCAUCGUUGAUACAAGCUGCUCUUGGUCACCGGAGGGCCUUCGGUUUCAUAUGCAGAGACAUC-
ACVC01000193.1/33186-33335 UGGAGGCUUGGCAUCCCGUUCUGGGAAGGGCAAGCGGAGAUCCAGUCUGGUCUCUACCAGCGUAUGCAUGUGCGUAAGCUGGUCAAGCAUCGUUGAUAGAAGCUGCUCUUGGUCACCGGAGGGUCUCCGGUUUCAUACGCAGAGACAUCC
AY820300.1/27-176          UGGAGGCUCGGCGUCUCGUUCUGGGAAAAGCAAGCAGAAGCCCAGUUUGGUCUCUACCGGCGUAUGCAUGUGCAUAGGCUGGCCAAGCAUCGUUGAUAGAAGCUGCUCUUGGUCACCGGAGGGUCUCCGGUUUCAUACGCAGAGACAUCC
#=GC SS_cons               :::::<<<<______________________>>>>,,,,,,,,,,,,,,,,,,,,,<<<<<-<<<<<____>>>>>->>>>>--------------------------------<<<<<<<___>>>>>>>:::::::::::::::::::
#=GC RF                    UGGAGGcccGgCgUCcCGUUCUGGGAaggGcgggCgGAagcCcAGuuUGGUCuCUACcaGcGuacgCAUGUGcguaggCugGuCAAGCAUCGUUGAUAgAAGCUGCUCUUGGUCaCCGGaGGGuCuCCGGuUUCAUAcGCAGAGACAUCC
//
# STOCKHOLM 1.0

#=GF AC   RF02483
#=GF ID   GlsR20
#=GF DE   Small nucleolar RNA GlsR20
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   128.20
#=GF NC   31.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


ACGJ01000491.1/21078-21184 AAAAAUGCCAGCUAAGUUACGUCUGUAUGUACAGGCGCGUCAGAGGUUGGCUAGAGCGUGACUGGUUGAGUUCCUGGGGAAGCCUGGGUGAUUAACAGUCAUAUAGU-
ACVC01000234.1/36443-36337 AAAAAUGCCAGCUAAGUUACGUCUGUAUAUACAGACGCGUCAGAGGCUGGCUAGAACGCGACUGAUUGAGUUCCCAGAGCAAUCUGGGUGAUUGGCAGUCAUACAAU-
AY820301.1/1-108           AAAAAUGCCAGCUGAGUUACGUCUGUGUGCACAGGCGCGUCAGAGGCCGGCUAGAGCGCGACUGGUUGAGUUCCCAGAGCGAUCUGGGUGAUUAGCAGUCAUACAGUC
#=GC SS_cons               ::::::<<<<<<<------<<<<<<<____>>>>>>>------->>>>>>>--------<<<<<-<<<<---<<<<<<____>>>>>>--->>>>>>>>>:::::::.
#=GC RF                    AAAAAUGCCggCuaAGUUACGcCuGuaUguaCaGgCGCGUCAGAgGccGGCUAGAgCGcGaCuGgcugaGUUCCcaGgGcaacCugGGUGAuuagCaGuCAUAcAgU.
//
# STOCKHOLM 1.0

#=GF AC   RF02484
#=GF ID   GlsR21
#=GF DE   Small nucleolar RNA GlsR21
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   119.40
#=GF NC   35.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AACB02000002.1/624760-624649 AAAACCAAUAUUACUACCAUCGGUCCUCACCACUAGAUCGGUGUUAUGCUUUGUUGGGAUAGCAGGCCGUGCCAGUUGGACAGCCAAGGUCCACCU-CUGGUUCGGCACACAU
ACGJ01002311.1/35790-35679   AAAACCAAUAUUACUACCAUCGGUCCUCACUACUAGAUCGGUGUUAUGCUUUGUUGGGAUAACAUGCCGUGCCAAUCAGGCAGCUAGUGUCUCUCUACUGGUGCGGCAUACA-
ACVC01000189.1/15300-15411   AAAACCAAUAUUACUACCAUCGGUCCUCACCACUAGAUCGGUGCUAUGCUUUGUUGGGACAGCAGGCUGUGCCAGUUGGACAACUAAGGUCCAUCUACUGGUCCAGCACACA-
#=GC SS_cons                 ::::<<<<<<----<<-<<<<<<<<__________>>>>>>>>->>----->>>>>>--------<<<<-<<<<<<<<<<<_______>>>>>--->>>>>>->>>>:::::.
#=GC RF                      AAAACCaauaUUACuaCCauCGguCCUCACcACUAGauCGguGuuaUGCUUuguuGGGAuAgCAgGCcGUgCCaguugGaCAgCuAagGuCcauCUacuGGuuCgGCAcACA.
//
# STOCKHOLM 1.0

#=GF AC   RF02485
#=GF ID   GlsR22
#=GF DE   Small nucleolar RNA GlsR22
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   179.00
#=GF NC   37.30
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AACB02000001.1/458263-458113 GUCAAUUCUAUCAUAUUUUUUUGACAGCCUGCGACGCAAGCCCUCUAGCAAGAUGCAGGCCGGAGCCUGUGUCUCGUUCCCUGGGGCGAUAGCUCUUGCUGGCAGGUCUUGCAGUGUCCAUACCCGGGCAACACGUUUUCCAGCUACACCU
ACGJ01002895.1/16336-16188   -UAAAUUCUAUAGCAUUUCUUUGACAGCCUGUGACGCAAGCCCUCCAGCAAGGUGCAGACCGGAGUCUGUGCCUCGUUCCCUGGGGCGAUAGCUACUGCUGGAGGGUUUUGCAUUAUCCGUAUCUGGAUAACACGUCCCCCAGCUAUACC-
ACVC01000104.1/1962-1813     GUCAAUUCUAUCGUAUUUUUUUGAUAGCCUGAGACGCAAGCCCUCUAGCAAGAUGCAGGCCGGAGUCUGUGCCUCGUUCCCUGGGGCGAUAGCUCUUGCUGGCAGGUCUUGCAGUGUCCAUGCUUGGGCAACACGUUCUCCAGCUAUACC-
#=GC SS_cons                 :::::::::::::::::::::::::[[[----[[[(((((-(((((((((,<<<<<<<<<____>>>>>>>>><<<<<<____>>>>>>,,,,,,,))))))-)))-))))),,<<<<<______>>>>>,,,,]]]-----]]]:::::.
#=GC RF                      GUcAAUUCUAUcguAUUUuUUUGAcaGCCUGugaCGCaagCCCuCcaGCaAGgugCaGgCCGGAGcCuGugcCuCGuuCCCUGGggCGaUAGCUcuuGCugGcaGGUcuuGCAgugcCCaUaccuGGgcaACACGuccuCCAGCuAuACC.
//
# STOCKHOLM 1.0

#=GF AC   RF02486
#=GF ID   GlsR23
#=GF DE   Small nucleolar RNA GlsR23
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   121.40
#=GF NC   38.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


ACVC01000147.1/10980-10834 ---CUGGAUACUGACA-ACCGCGGCUGGUAACAAAAAAAUCGCCUUGUCGUCUCAUGCCUACGAUGGGCUAAAGAAGCACUGUGGCGAAACAUGCACUGGGUGGCCAUUGCGUCUGCGGUAGACCCGCCGAUUCCACAGCCCAGAAACAUC
U65017.2/251-103           GACUUAGAUACUGACAUACUGCAGCUGCGAU--AAAAAAUCGUCUGGCCGCCUCGUGCCUACGAUGGGCUAGGGAAAUGCCGUGACGAGACACGCACUGGGUGGCCAUUGCGUCUGCGGUAGAUCCGCCGAUUCCACAGCCCAGAAACACC
#=GC SS_cons               :::::::::::::::::<<<<<<<-------..------<<<<<--<---------<<<<_____>>>>---------->--->>>>>------------------------->>>>>>>:::::::::::::::::::::::::::::::
#=GC RF                    GAcuUaGAUACUGACAUaCcGCaGCUGguAu..AAAAAAuCGcCUuGuCGuCUCaUGCCuACGAUgGGCUAaaGAAauaCuGUGgCGaaACAuGCACUGGGUGGCCAUUGCGUCuGCgGuAGAuCCGCCGAUUCCACAGCCCAGAAACAuC
//
# STOCKHOLM 1.0

#=GF AC   RF02487
#=GF ID   GlsR24
#=GF DE   Small nucleolar RNA GlsR24
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   135.10
#=GF NC   37.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AACB02000040.1/79498-79351 ACCGCCUGUAAACG-----CCUUC-----CCCGAAUAAUUUCGG-GCAGUCCUUGCCCGCGGAGGGCACUUAAGGCUCCGGGGCCCGGGGCAGAGUCGGCCCUCCCAGAGCCCGCCGACGCCCCCGAGCGCCAGCCCGGCGCAGGGGCCCGGCCACACU
ACGJ01002360.1/10522-10369 ----CCUGUAAACGGCGCGCCUCCGCGGCUCCAAUUUAUUUCGGGGCAGUUCUUGCCCGGGGAGGAUACUUAAUGCUCGGGUCCGCGCAGCAGAGUCAGUCCUCCCAGAGCCCGCCGGGACCCCCAUGCGUCUGGCAGGCGC-GGGGGCCGGCCACAUU
ACVC01000173.1/37394-37537 -CCGCCUGUAAACG-----CCUUC-----CCCAA---AAUUCGG-GCAGUCCUUGCCCGCGGAGGAUCCUUAAUGCCCCGGGGCCCGGGGCAGAGUCGGCCCUCCCAGAGCCCGCCGGCGCCCCCGAGCGUCAGCCCGGCGCAGGGGGCCGGCCACACU
#=GC SS_cons               .:::::::::::::.....:::::.....::::::::::::<<<.<<<<___>>>>>>>,<<<<<<<-------<<<<<<_____>>>>>>------->>>>>>>--------<<<<<--<<<<<--<<<<<_____>>>>>->>>>>>>>>>::::::
#=GC RF                    .ccGCCUGUAAACG.....CCUuC.....cCCaAuUuAuUUCGG.GCagUcCuuGCCCGcGGaGGgcaCUUAAuGCcccGGggCcCgggGCAGAGUCggcCCuCCCAGAGCCCGCCGgcgcCCCCgaGCGcCaGcCaGgCGCAGGGGgcCGGCCACAcU
//
# STOCKHOLM 1.0

#=GF AC   RF02488
#=GF ID   GlsR25
#=GF DE   Small nucleolar RNA GlsR25
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   143.80
#=GF NC   33.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AACB02000068.1/10221-10367 CUUUGCAACGGCACUUGUAACGAAAAAGUAAAUCGAGGCUGCUAAAACACAGGGCUGCACAGCAUCCUUGCACCUGCGUAGCCGAUAGGUACGGGUGACCGUUUAUCCCGGGCUCGUGUGGGCCCGGGUAGGCACGGUCAAAGAGUU
ACGJ01001903.1/4369-4514   CUUUGCAACGGCAUUUAUAACGAAAAAGUAAAUUGAGGCUGCUAAAACACAGGGCUGCACAGCAUCCUUGCACCUGCGUAGCCGAUAGACGCAUUUGGCUGUUUAUCUAGGAUCUGCGUGGGUCUGAACAGGCACGGUCAAACAGU-
ACVC01000007.1/18935-19080 CUUUGCAACGGCACUUGCAACGAAAAAGUAAAUUGAGGCUGCUAAAACACAGGGCUGCGCAGCAUCCUUGCACCUGCGCAGCCGACAGGUACGGGUGACCGUUUAUCCCGGGCCCACGUGGAUCCGAGCAGGCACGGUCAAAGACU-
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::<<<<<<-------<<<<<-<<<___>>>->>>>>------->>>>>>-------------<<<<<<----<<<<<<<<<____>>>>>>>>>----->>>>>>:::::::.
#=GC RF                    CUUUGCAACGGCAcUUguAACGAAAAAGUAAAUuGAGGCugCUAAAACACagGGCuGCaCAGCaUCCuuGCACCUGCGcaGCCGAuAGguaCgggUGaCcGuUUAUcccgGgcccgcGUgggcCcgggcAGGCaCgGuCAAAgAgU.
//
# STOCKHOLM 1.0

#=GF AC   RF02489
#=GF ID   GlsR26
#=GF DE   Small nucleolar RNA GlsR26
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   125.80
#=GF NC   31.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3


AACB02000068.1/10395-10508 GGCGCACGUUACGAGGCCUGGCUCCCGGUCCGGCCCUACCUUGCGUGCGCAUAUCUCCGGGAUCUGCGCCGCGUCUGCUCGCGGCGAUUUCGGUUAUGCCGGCCCGAACACUCC
ACGJ01001903.1/4544-4655   GGCGCACGUUACGAGGCUAUGCUUCCGGCCUGGCCCUACCUUGCGUGCGCAUAGCUCCGGGACAUACACUACGUCUGGUCGUGACGACUGCGACUGUACUGACCCGAACAUU--
ACVC01000007.1/19109-19222 GGCGCACGUUACGAGGCCUGGCUUCCGGUCCGGCCCUACCUUGCGUGCGCAUAGCUCCGGGAUAUGCGCCGUGUCUGCUCACGGCGAUUUCGGCUAUGCCGGCCCGAACACUCC
#=GC SS_cons               :<<<<<<<<-----<<<<-<<<_____>>>->>>>------->>>>>>>>-------<<<<-----<<<<<<<______>>>>>>>---------------->>>>::::::::
#=GC RF                    GGCGCaCGuUACGAGGCcuggCUuCCGGcccgGCCCUACCUUgCGuGCGCAUAgCUCCGGGAuaUgCgccgcGUCUGcUCgcggcGAuUuCGgcUaUgCcGgCCCGAACAcUcc
//
# STOCKHOLM 1.0

#=GF AC   RF02490
#=GF ID   GlsR27
#=GF DE   Small nucleolar RNA GlsR27
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   139.00
#=GF NC   34.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   2


AACB02000004.1/98546-98434 AGCUCACCCAAAGUCAACGGAGCGCCAGCUACGUGUUAUGGGCAGCGAAAGUACCAGAGCCAAAGAGUUCCUCUGAUCGCCUGGCCGGAGCACAUUUGUGAUCUCCUAUACCU
ACGJ01002332.1/21997-21886 AGCUCACCCAAAGUCAACGAAACGCUAGCUUCGUGUUAUGGGCAGCGAAAGUGCCAGAGCCAAAGAGUUCCUCUGAUCGCCUGGCUGGAGCACACAUGUGACCUCCUACACC-
#=GC SS_cons               :<<<--<<<<------<<<<<<<____>>>>>>>---->>>>->>>,,,,,,,<<<<-<<---<<<<___>>>>---->>>>>>,,<<<<<<<____>>>-->>>>:::::::
#=GC RF                    AGCuCACCCaAAGUCAaCGaagCGCuAGcuuCGuGUUAuGGGCaGCGAAAGUaCCaGAGCCAAaGaGUUCCuCuGAUCGCCuGGCuGGaGCaCAuaUGuGAuCuCCUAuACCu
//
# STOCKHOLM 1.0

#=GF AC   RF02491
#=GF ID   Gl_U1
#=GF DE   Giardia U1 spliceosomal RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23019220
#=GF GA   100.00
#=GF TC   141.60
#=GF NC   32.20
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF CL   CL00005
#=GF DR   SO; 0000391; U1_snRNA;
#=GF DR   GO; 0000395; mRNA 5'-splice site recognition;
#=GF DR   GO; 0030627; pre-mRNA 5'-splice site binding;
#=GF DR   GO; 0005685; U1 snRNP;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   U1_spliceosomal_RNA
#=GF SQ   2



ACGJ01002471.1/10991-11110         ACUUACCUUAAGGGUGGCGAUGAGCCAUUGUUCAGGCC-GGCUAAUGCUGCGCAUACCGCGCUGGUGUUUGUCACAGAGCAGUGCUCUCAGACCUGCUACUGUACCCUUUUAAUUUUUCCU
AACB02000054.1/49489-49369         ACUUACCUCAAGGGUGGCGACGAGCCAGUGUUCGGGCCAGGCUGGUGCUGCGCAUACCGCGCUGGCACUGGUCACGGGGCAGUGCUCUCAGACCUGCUACCGUACCCUUUUAAUUUUUCCU
#=GC SS_cons                       :::::::::((((((<<<--<<<<<____>>>>>->>>,<<<<<<<<<<<<<<_____>>>>->>>>>>>>>><<<<<<<<<___________>>>>>->>>>))))))::::::::::::
#=GC RF                            ACUUACCUuaaGGGuGGCGAcGagCCAuUGcuCgGGCCAGgCcggcgCcGCGCAUACCGCGCUgGcgccgGcCaCgGgGCaGUGCUCUCAGACCuGCcACcGuaCCCuuUUAAUUUUUCCU
//
# STOCKHOLM 1.0

#=GF AC   RF02492
#=GF ID   Gl_U2
#=GF DE   Giardia U2 spliceosomal RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23019220
#=GF GA   100.00
#=GF TC   172.00
#=GF NC   30.90
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000392; U2_snRNA;
#=GF DR   GO; 0000395; mRNA 5'-splice site recognition;
#=GF DR   GO; 0030627; pre-mRNA 5'-splice site binding;
#=GF DR   GO; 0005685; U1 snRNP;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   U2_spliceosomal_RNA
#=GF SQ   2


AACB02000002.1/54704-54569 CAGAGUCGGCUUCGACUUUAGUGUAGUUACUGUUUCGUCGGCUUAACCGCCGAUCCACUACAUGCAAGGGGCAGCCGGGCUGUGAGGCAGCUGCCAGGAUGGUCCUGCCCUUGUCCCGGCUGGCGCCGUCCACCUU
ACGJ01002726.1/93842-93977 CAGAGUCGGCUUCGACUUUAGUGUAGUUACUGUUUUGUCGGCUUAACCGCCGAUCCAUUACAUUCAAGGGGCAGUCGGGCUGUGAGGCAGCUGCCAGGAUGGUCCUACCCUUGUUCCGGCUGGCGCCGUCCACCUU
#=GC SS_cons               ::::::::::::::::::::::::::::::::::::<<<<<<______>>>>>>,,,,,,,,,,,,,,,<<<<<<---<<<____>>>->>>>>>-<<<<<<<<<-<<<________>>>->>->>>>>>>:::::
#=GC RF                    CAGAGUCGGCUUCGACUUUAGUGUAGUUACUGUUUuguCGGCUUAACCGCCGauCCAuUACAUuCAAGGGGCaGcCGGGCuGUGAgGCAgCuGCCAGGauGGuCCUgCCCUUGUuCCGGcUGGCgCCguCCACCUU
//
# STOCKHOLM 1.0

#=GF AC   RF02493
#=GF ID   Gl_U4
#=GF DE   Giardia U4 spliceosomal RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23019220
#=GF GA   100.00
#=GF TC   126.20
#=GF NC   34.80
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000393; U4_snRNA;
#=GF DR   GO; 0000395; mRNA 5'-splice site recognition;
#=GF DR   GO; 0030627; pre-mRNA 5'-splice site binding;
#=GF DR   GO; 0005685; U1 snRNP;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   U4_spliceosomal_RNA
#=GF SQ   2



ACGJ01002266.1/10941-10847         CUAGACCGAAGCUGCCAAGGUGCGUGAUCCCUCGGUGAUGCCUUGAGUGUUGCUUCGCCAAAAAACAACCACACGGCCUAGCCGAAUUUCUCAUU
AACB02000006.1/75591-75497         CUAGGCUGAAGCUGCCAAGGUGCGUGAUCCCUCGGUGAUGCCUUGAGUGUUGCUUCACCAAAGAACAACCACACGGCACAGCCGAAUCUCUCAUU
#=GC SS_cons                       :::::::::::::::<<<<<<<------<<___>>--->>>>>>>----------------------------<<<<___>>>>:::::::::::
#=GC RF                            CUAGaCuGAAGCUGCCaaGGugCGUGAUCCCUCGGUGAugCCuuGAGUGUUGCUUCaCCAAAaAACAACCACACGGCauAGCCGAAUuUCUCAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02494
#=GF ID   Gl_U6
#=GF DE   Giardia U6 spliceosomal RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23019220
#=GF GA   100.00
#=GF TC   133.40
#=GF NC   33.00
#=GF TP   Gene; snRNA; splicing;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000396; U6_snRNA;
#=GF DR   GO; 0000395; mRNA 5'-splice site recognition;
#=GF DR   GO; 0030627; pre-mRNA 5'-splice site binding;
#=GF DR   GO; 0005685; U1 snRNP;
#=GF RN   [1]
#=GF RM   23019220
#=GF RT   Evolutionarily divergent spliceosomal snRNAs and a conserved non-coding
#=GF RT   RNA processing motif in Giardia lamblia.
#=GF RA   Hudson AJ, Moore AN, Elniski D, Joseph J, Yee J, Russell AG
#=GF RL   Nucleic Acids Res. 2012;40:10995-11008.
#=GF WK   U6_spliceosomal_RNA
#=GF SQ   2


AACB02000012.1/102610-102509 GUUAACAAAAACAGAGACAGUUAGCACCAGCUUCAGUCUAGAGUCGCUGGGGGACCUCUGGUUUCGCGGGAGCCCGUUGGCGCGUGCUUGCACCCCGCUCCU
ACGJ01001509.1/9098-9199     GUUAACAAAAACAGAGACAGUUAGCACCAGCUUCGGUCUAGAGUCGCUGGGGAACCUCUGGUUUCGCGGGAGCCUGUUGGCGCGUGCUUGCACCCCGCUCCU
#=GC SS_cons                 ::::::::::::::::::::::::::<<<<<<<<______>>>-->>>>>---------------(((((,<<<____>>>,,<<<____>>>)))))::::
#=GC RF                      GUUAACAAAAACAGAGACAGUUAGCACCaGCuuCaGUCUAGagUCGCuGGGGaACCUCUGGUUUCGCGGGAGCCuGUUGGCGCGuGCUUGCaCCCCGCUCCU
//
# STOCKHOLM 1.0

#=GF AC   RF02495
#=GF ID   ohsC_RNA
#=GF PI   RyfC
#=GF DE   Oppression of Hydrophobic ORF by sRNA
#=GF AU   Gardner P; 0000-0002-7808-1213
#=GF SE   Gardner P
#=GF SS   Published; PMID:19052321
#=GF GA   50.00
#=GF TC   51.60
#=GF NC   45.10
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   URL; http://ecoliwiki.net/colipedia/index.php/ohsC:Quickview;
#=GF RN   [1]
#=GF RM   19052321
#=GF RT   Small toxic proteins and the antisense RNAs that repress them.
#=GF RA   Fozo EM, Hemm MR, Storz G
#=GF RL   Microbiol Mol Biol Rev. 2008;72:579-589.
#=GF RN   [2]
#=GF RM   18710431
#=GF RT   Repression of small toxic protein synthesis by the Sib and OhsC small
#=GF RT   RNAs.
#=GF RA   Fozo EM, Kawano M, Fontaine F, Kaya Y, Mendieta KS, Jones KL, Ocampo A,
#=GF RA   Rudd KE, Storz G
#=GF RL   Mol Microbiol. 2008;70:1076-1093.
#=GF RN   [3]
#=GF RM   19239884
#=GF RT   Regulatory RNAs in bacteria.
#=GF RA   Waters LS, Storz G
#=GF RL   Cell. 2009;136:615-628.
#=GF RN   [4]
#=GF RM   23182878
#=GF RT   New type I toxin-antitoxin families from "wild" and laboratory strains of
#=GF RT   E. coli: Ibs-Sib, ShoB-OhsC and Zor-Orz.
#=GF RA   Fozo EM
#=GF RL   RNA Biol. 2012;9:1504-1512.
#=GF WK   Toxin-antitoxin_system
#=GF SQ   34


AP010960.1/3261102-3261178     GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
AEHS01000021.1/26265-26189     GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCUUUACCAG-UUCGGGGGUUUUACUUU
AELA01000016.1/28251-28175     AUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
CU928163.2/2992041-2992117     GUUGAGGGUGCGUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
AE005674.2/2697735-2697811     GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCCG-UUCGGGGGUUUUACUUU
AEZT01000049.1/62339-62264     GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUA-AAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
ABKX01000003.1/41392-41316     GUUGAGGGUGCGUGCUGCACAAAAUUA---AAGUUGUAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
ACXF01000048.1/47259-47335     GUUGAGGGUGCGUGCUGCACUAAAUUA---AAGUUACAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
AFAC01000012.1/379471-379396   GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGU-UUACUUU
AEZI01000040.1/47928-47852     AUUGAGGGUGCGUGCUGCACAAAAUUA---AAGUUGUAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
AFST01000001.2/28384-28309     GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGG-GGUUUUACUUU
AFGE01000046.1/207052-207127   AUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGU-UUACUUU
AEZJ01000069.1/422080-422155   GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAA-U-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
ADUR01000045.1/63442-63367     GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-UCCGUUCCUUACCAG-UUCGGGGGU-UUACUUU
AFSO01000013.1/177189-177263   GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGG--UUUACUUU
ADTP01000295.1/46114-46190     GUUGAGGGUGCGUGCUGCACAAAAUUA---AAGUUGUAAAGU-A-AA-CCC-CCUGUUCCUUACCAG-UUCGGGGGUUUUACUUU
AEMF01000001.1/45109-45188     GUUGAGGGUGCGUGCUGCACAAUAUUAUUUAAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
AEJW01000128.1/13993-13914     GUUGAGGGUGCGUGCUGCACAAUAUUAUUUAAGUUAUAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
AFPN02000010.1/177199-177274   GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAGGUUCGGGG--UUUACUUU
AETZ01000067.1/828-904         GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
CU928158.2/511044-510968       GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUGUAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
AEJZ01000030.1/5549-5473       GUUGGAAUCGUGUGCUGCAAAAUUUUA---AAGUUGUAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
ADUZ01000768.1/25357-25282     GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGG-GGUUUUACUUU
ADUG01000129.1/22451-22528     GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUGUAAAGUGA-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
ADBC01000131.1/169381-169458   GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUGUAAAGU-G-AAUACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
AEJY01000177.1/28069-27994     GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUGUAAAGU-A-AA-ACC-C-CGUUCCUUACCAG-UUCGAGGGUUUUACUUU
AEJU01000003.1/35180-35106     GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUGUAAAGU-A-AA-ACC--CCGUUCCUUACCAG-UUCGG-GGUUUUACUUU
CU928164.2/2875040-2875117     GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUGUAAAGUGA-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGGUUUACUUU
CP003034.1/3060858-3060934     GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUGUAAAGU-GAAA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUU-ACUUU
ADTR01000086.1/16574-16651     GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUGUAAAGU-G-AA-CCCCCCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
ADUS01000037.1/28435-28358     GUUGGAAUCGUGUGCUGCACAAAAUUA---AAGUUGUAAACUGA-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
AEME01000001.1/2988958-2988883 GUUGGAAUCGUGUGCUGCACAAUAUUA---AAAUAGUAAAG--A-AA-CCC-CCUGCUCCUUACCUG-UUCGGGGGUUUUACUUU
ACZW01000034.1/20449-20379     GUUGAAAUUUAUUUCAUAAC--AAUUA---A----GUAAAGC-A-AA-AGC-UCCGAUUUAUUCAAA-AUCGGAGCUUUUGCUUU
U00096.2/2698542-2698618       GUUGAGGGUGCAUGCUGCACAAAAUUA---AAGUUAAAAAGU-A-AA-ACC-CCCGUUCCUUACCAG-UUCGGGGGUUUUACUUU
#=GC SS_cons                   :<<<<--<<<<<___>>>>>---->>>...>------<<<<<.<.<<.<<<.<<<<___________.__>>>>>>>>>>>>>>>
#=GC RF                        GUUgaaaguGcgUGCcgCacAAAAuuA...AAGUUauAAAGu.A.AA.AcC.CCCGUUCCUUACCAG.UUCGGGGgUUUUaCUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02496
#=GF ID   Atu_At1
#=GF DE   Rhizobiales sRNA Atu_At1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   60.00
#=GF TC   70.40
#=GF NC   55.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   33


AE007872.2/55272-55165       UUCCAGGCC-GUGUCAACCGGACGUGGC-AGG-GA--UGACGAACGCG-AU-G--GUUUUUCCGGUUUCUCAUCGCG--GC--C---AACGAAACGGCA-GUCGA--G--CGUCCAA-CCUGUCC-GGCCG
AGSM01000015.1/84286-84179   AGGGCCGCC-GUGUCAAACGGACACGAU-GGU-GC--CGAAGAACACC-GG-G--AUUUUUCCGUUUUCUCCCGGUG--GC--C---AACGAAAUGGCA-GCCGA--G--CUUCUUA-CCCAUCC-GGCGC
ABRD01001128.1/1-108         GCGUGAGCC-GUGUUAACCGAACGCGAC-AGG-GA--UGAUGAACACA-GG-G--GUUUUUUCGGUUUCACCCUGUG--GC--C---GACGAAUUGGCA-GGCGA--G--CGUCCCA-CCUGUCC-GGCUC
CP000133.1/2167020-2166913   UUGCGGGCC-GCGCCAAGCGGACGCGGC-AGU-GC--UGGAGAACAUC-GG-G--AUUUUUCCGCUUUCUCCCGGUG--GC--C---AACGAAACGGCA-GGCGA--G--CUCCCUA-CCCGCCC-GGUCC
ABRB01002290.1/2052-2159     UUGCGGGCC-GCGCCAAGCGGACGCGGC-GGU-GC--UGGAGAACAUC-GG-G--AUUUUUUCGCUUUCUCCCGACG--GC--C---GACGAAAUGGCA-GACGA--G--CUCCCUA-CCCGCCC-GGUCC
AGIX01000001.1/925074-925182 CUGCGGGCC-GCGUCAACCGGGCUCGGC--GG-UA--CGGUGAACAGG-AU-GUCUUUUUCCCGGUUUCUCAUCCUG--GC--C---AACGAAAUGGCA-GACGA--G--CAUCUGU-CCCGCCC-GGCCC
AGTN01289841.1/286-181       CCGCAAGCC-GUGUUAACCGGACGUGGC-AGG-GA--UGAUGAACGAA-GG-G---UUUUUCCGGUUUCUCCUUGCG--GC--C---G-CGAAAUGGCA-GGCGA--G--CAUCCAA-CCUGUCC-GGCUU
CP000115.1/1134600-1134489   ACACGCCGG-GUGACAACCGGCCACGAC-GGG-GA--UGAUGGACGUA-GC-C-UAUUUUGCCGGUUUCAGGCUGCG--GCACC---AACGCAUUGGCA-CGCGU-UU--UGUCUAA-CCCGUUC-CCGGC
CP000463.1/4987281-4987394   GCACGCCGG-GUGACAACCGGCCGCAAC-GGA-GA--UGGCGGACGCAAGC-C-AAUUUUGCCGGUUUCUGGCUGCG--ACAUC---AACGCAUCGGUA-CGCGCUAA--CGCCUAA-CCCGUUC-CCGGC
CP000283.1/4683872-4683986   GCAUGCCGG-GUGACAACCGGCCGUAAC-AGG-GAAUUGGCGGACGCA-GC-U-CAUUUUGCCGGUUUCUGGCUGCG--ACAUC---AACGUAUCGGUA-CGCGCUGA--CGCCUAA-CCUGUUC-CCGGC
CU234118.1/6776504-6776617   GCAUGCCGG-GUGACAACCGGCCGCAAU-GGGGAA--CGGCGGACGCA-GC-U-GAUUUUGCCGGUUUCUGGCUGCG--ACAUC---AACGUAUUGGUG-CGCGCUGA--CGCCUAA-CCUGUUC-CCGGC
CP002083.1/1793874-1793763   ACGCGC-CG-GUGGUAACCGGCCACAAC-AGGGAA--UGAUGGACGCA-GC-C--AUUUUGCCGGUUUCUCGCUGCGACAC--C---AACGCAUCGGUA-CGCGUGGA--CAUCUAA-CCUGUUC-CGAGC
ADGO01075640.1/243-354       ACGCGCCGG-GUGUCAACCGGCCGCAAC-GGA-GA--AGAUGGACGCG-GU-U-GAUUUUGCCGGUUUCUGACCGCG--GCAGC---AACGUAUUGGUA-UGCGU-GG--CAUCUAA-CCCGUUU-CCGGC
CP001096.1/5375611-5375723   GCAUGCCGG-GUGACAACCGGCCGCAAC-GGG-GA--UGGCGGACGUG-GC-U-CAUUUUGCCGGUUUCUGGCCACGACAC--C---AACGCAUCGGUA-CGCGCUGA--CGCCUAA-CCCGUUC-CCGGC
CP002826.1/3164264-3164375   UCACGCCGA-GUGACAACCGGCCGUAAC-AGG-GA--CGAUGGACGCG-GC-U--AUUUUGCCGGCUUCUGGUCGCG--ACAUC---AACGCAUCGGUA-CGCGCUGA--CAUCUAA-CCUGUUC-UUGGC
CP001622.1/803158-803265     GGUCGCGGC-GUGCCAAUCGGACGUGAC-GGA-GA--UGGUGAACGCA-CC-G--GUUUUUCCGAUUUCUCGGUGCG--GG--C---AACGAAGCGCCA-GGCGA--G--CACCUUA-CCCGUUC-GCCGC
CP000250.1/4906572-4906684   GUAUGCCGG-GUGACAACCGGCCGUAAC-AGG-GA--UGGCGGACGCA-GC-U-CAUUUUGCCGGUUUCUGGCUGCGACAC--C---AACGCAUCGGUA-CGCGCUGA--CGCCUAA-CCUGUUC-CCGGC
AB016260.1/130370-130478     GCAGGGGCU-GUGUCAACCGGACGUGAU-AGG-GA--UGGUAGACGCA-GC-G--GUUUUUCCGGUUUCACGCUGCG--GC--CUAAAACGCCUAGGUU-AGAAA--G--CA--UUA-CCUAUCC-GGCCC
ABSQ01033941.1/431-537       GCGGUCCGU-GUAUCAACCGGAUGUGAC--GG-CA--GAAGGAACGCU-GC-G--GUUUUUCUGGUUUCCCGCUACG--GC--C---GAAGAAAUGGCA-GUCGA--G--CCUUUUC-CCCGUCC-ACGGA
ABLY01027024.1/114-6         CUGGGAGCC-GUGUUAACCGGACGCGAC-AGG-GA--UGGUGAACGCA-GC-GGCUUUUUCCCG-UUUCACCCUGCG--GC--C---AACGAAAUGGCA-GUCGA--G--CAUCCAA-CCUGUCC-GGCUC
CP001622.1/1876836-1876729   UUGCGGGCC-GCGCCAAGCGGACGCGGC-GGU-GC--UGGAGAACAUC-GG-G--AUUUUUCCGCUUUCUCACUCUG--GC--C---AACGAAAUGGCA-GUCGA--G--CUCCCUA-CCCGCCC-GGUCC
CP001074.1/2101714-2101610   UUGCGGGCC-GCGCCAAGCGGACGCGGC-GGU-GC--UGGAGAACAUC-GG-G--AU-UUUCCGCUU--UCUCGGUG--GC--C---GACGAAACGGCA-GGCGA--G--CUCCCUA-CCCGCCC-GGUCC
CP002447.1/3083905-3083797   CUGCGGGCU-GCGUCAACCGGGCCUGGU--GG-UA--CGGUGAACAGG-AU-GUCUUUUUCCCGGUUUCUCAUCCUG--GC--C---AACGAAACGGCA-GACGA--G--CAUCUGU-CCCACCC-GGCCC
CP001219.1/2354115-2354004   GUGUGAGUGGGUGUCAACCGGACGCGAU-GGG-GA--UCGAGAACUCG-A---GGAUUUUUCCGGUUUCUAAUCGAG--AC--CU-UAAGGAGUUGGUAUGCCUG--A--CCCGUAA-CCCAACC-CACUC
AAMS01000009.1/94914-94810   CGGCAGGCC--UGUCAAUCAGACCUGAC-GAC--A--CAAGGAACGGG-CA-A--AUUUUUCUGAUUUCUUUUCCCG--AC--C---AACGCAACGGUA-GUCGA--G--CCUUUAU-CUCGCC--GGUUU
FQ859181.1/1891260-1891148   ACGCGCCCG-GUGGCAACCGGCCGCAACAGGG-AA--UGAUGGACGUA-GC-U--AUUUUGCCGGUUUCUCGCUGCGACAC--C---AACGCAUUGGUA-CGCGC--UGACAUCUAA-CCCGUUC-CGGGC
AGSN01000085.1/16341-16234   ACGCGGGCC-GCGUCAGCCGGACCAGGU--GG-CA--AAGGGAACAGG-GUUG--GUUUCUCCGGCUUCACACCCUG--GC--C---AACGAAAUGGCA-GUCGA--G--CUCUUGU-CCCACCC-GGCCC
CP000738.1/2920507-2920401   GUGCGGUCU-GUGGCAACCGGACGCGAC-GGA-AC--AGGAGAGCACG-GG-A-A--CUUGCCGCUUUCUUUCCGUG--GC--C---CAUAAACUGGCA-GACGA--G--UUCCUGA-CCCGUCC-AGGCC
CP002279.1/6759348-6759242   CUGCGGGCC-GCGUUAGUCGGACCUGGU--GG-UA--AAGAGCACAGG-GU-G--GUUUUUCCGGCUUCACACCUUG--GC--C---AACGAAAAGGCA-GUCGA--G--CUCUUGU-CCCACCC-GGCCC
CP001389.1/3100514-3100406   ACGCGGACU-GUGGCAACCGGACGCGAC-GGA-AC--UGGAGAAUACG-GG-A--AUUUUGCCGGUUUCUUCCCGUG--GC--C---AACGAAAAGGCA-GGCGA--G--CUCCUGACACCGUCC-AGUCC
CP001191.1/1736441-1736333   UUGCGGGAC-GCGCCAAGCGGAUGCGGC-GGU-GC--UGGAGAACAUC-GG-G--AUUUUUCCGCUUUCUCCCGAUG--AC--C---AACGAAACGGCA-GGCGA--G--CUCCCUA-UCCGUCCGGUCCG
ADVZ01000003.1/502953-502842 UCGCGCCGG-GUGACAACCGGCCACAAC-GGG-GA--CGAUGGACGCG-GU-C--AUUUUGCCGGUUUCUGACCGCGACAC--C---AACGCAUCGGUA-CGCGCUGA--CAUCUGA-CCUGUUC-UCGAC
CP000629.1/833365-833258     CUGUAGGCC-GUGUCAAACGGACAUGAU-GGU-GC--UGAAGAACAGG-GA-G--AUUUUUCCGUUUUCUCUCCAUG--GC--C---AACGAAACGGCA-GCCGA--G--CUUCCUA-UCCAUCC-GGCCU
#=GC SS_cons                 :::::[[[[.,<<<<_____>>>>,(((.(((.--..-((((,,<<<<.<<.<.._______________>>>>>>>..<<..<...________>>>,.,,,,,..,..))))---.)))))),.]]]]:
#=GC RF                      augcGggcc.GcGuCAAcCGGaCgcGgc.gGg.gA..uGgcGaACgcg.gc.g..aUUUUuCCGgUUUCUcgccgcG..gC..C...AACGaAuuGGcA.ggCGa..g..CgcCUaA.cCcgcCC.ggccc
//
# STOCKHOLM 1.0

#=GF AC   RF02497
#=GF ID   Atu_C10
#=GF DE   Rhizobiales sRNA Atu_C10
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   60.00
#=GF TC   120.00
#=GF NC   42.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


AE007869.2/2667194-2667282 UUGUCAAUUGAUGCCUAGGCACCAAGAUGACCCGGUCCGGUGCAUUGACCCUUUACCCCCAGCCCCCAAUGCCCGGAUCGGAUCUUCCA
CP002248.1/2647711-2647799 UUGUCAAUUGAUGCCUAGGCACCAAGAUGACCCGAUCCGGUGCAUUGACCCUUUACCCCCAGCCCCCAAUGCCCGGAUCGGAUCUUCCA
#=GC SS_cons               ::<<<<-<<<-<<<____>>>->>>-->>>><<<<<<<<<-<<<<<<___________________>>>>>>>>>>>>>>>::::::::
#=GC RF                    UUGuCaAuuGAuGCCUAGGCaCCaaGAuGaCCCGauCCGGUGCauuGACCCUUUACCCCCAGCCCCCaauGCCCGGauCGGAUCUUCCA
//
# STOCKHOLM 1.0

#=GF AC   RF02498
#=GF ID   Atu_C3
#=GF DE   Rhizobiales sRNA Atu_C3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   100.00
#=GF TC   169.40
#=GF NC   41.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


AE007869.2/317175-317330 UCCAACAAGGGGUGCGGAGCUCAGUCCACAGAUUAUCUCGAUGAUCAUAUCGACGAUAUUCACCUUCUUGCUAGCGGAUCUUUCGAGAUCCGUUUUUUCAGGUCAUGGAGCUUUUUGUGCCGUUUCGGUCUCGGAACGGGAAGGAGCUUUUUGUCC
CP002248.1/312893-313047 -UCAACAAGGGGUGCGGAUCUCAGUCCACAGAUUAUCUCGAUGAUCGUAUCGACGAUAUUCACCUUCUUGCUGGCGGGCCUUUCGAGGUCCGUUUUCUCAGGUCAUUGAGCUUUUUGUGCCGUUUCGGUCUCGGAACGGGCUGGAGCUUUUUGUCC
#=GC SS_cons             :::::(((((((<<-<<<______>>>->><<-<<<<<<<<<<____>>>>>>->>>>->>,))-))))),,<<<<<<<<<____>>>>>>>>>,,,,,,<<-<<--<<<<<<<---<-<<<<<<<<____>>>>>>>>>-->>>>>>>-->>->>
#=GC RF                  uucAACaaGgGGuGcGGaucUcAGuCCACaGaUuauCuCGaugAUcacauCGacGauaUuCACCUcCuuGcUggCGGgcCuUUcGaGgcCCGccUUuUcAGGUCaUugaGCuccUUGcGCCGuucCGGUcUCGgaaCGGgaaggaGCucUUuGUCC
//
# STOCKHOLM 1.0

#=GF AC   RF02499
#=GF ID   Atu_C4
#=GF DE   Rhizobiales sRNA Atu_C4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   99.90
#=GF NC   36.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2


CP002248.1/947909-947840 AGGUCAUUUUCAUGACCGCGCAUCUCCAGUCAGGGCAGGCCGUUCCCAUACGGUCUUGCCCUUUUUUCUG
AE007869.2/998103-998034 AGGUCAUUUUCAUGACCGCGCAUCUCCAGUCAGGGCAGACCGUUCCCAUACGGUCUUGCCCUUUUUUCUG
#=GC SS_cons             :<<<<<<____>>>>>>---------<<<--<<<<<<<<<<<<______>>>>>>->>>>>>----->>>
#=GC RF                  AGGuCauUUUCauGaCCGCGCAUCUCCaGUCaGGGCaGaCCGuUCCCAUaCGGuCUuGCCCuUUUUUCuG
//
# STOCKHOLM 1.0

#=GF AC   RF02500
#=GF ID   Atu_C6
#=GF DE   EcpR1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   60.00
#=GF TC   61.70
#=GF NC   54.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0045786; negative regulation of cell cycle;
#=GF DR   GO; 0000499; base pairing with mRNA;
#=GF DR   GO; 0043555; regulation of translation in response to stress;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF RN   [2]
#=GF RM   25923724
#=GF RT   A stress-induced small RNA modulates alpha-rhizobial cell cycle
#=GF RT   progression.
#=GF RA   Robledo M, Frage B, Wright PR, Becker A
#=GF RL   PLoS Genet. 2015;11:e1005153.
#=GF RN   [3]
#=GF RM   20398411
#=GF RT   A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing
#=GF RT   alpha-proteobacterium Sinorhizobium meliloti.
#=GF RA   Schluter JP, Reinkensmeier J, Daschkey S, Evguenieva-Hackenberg E, Janssen
#=GF RA   S, Janicke S, Becker JD, Giegerich R, Becker A
#=GF RL   BMC Genomics. 2010;11:245.
#=GF RN   [4]
#=GF RM   24710299
#=GF RT   Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.
#=GF RA   Reinkensmeier J, Schluter JP, Giegerich R, Becker A
#=GF RL   Genes (Basel). 2011;2:925-956.
#=GF RN   [5]
#=GF RM   17971083
#=GF RT   Identification of differentially expressed small non-coding RNAs in the
#=GF RT   legume endosymbiont Sinorhizobium meliloti by comparative genomics.
#=GF RA   del Val C, Rivas E, Torres-Quesada O, Toro N, Jimenez-Zurdo JI
#=GF RL   Mol Microbiol. 2007;66:1080-1091.
#=GF CC   Perviously named SmelC291, SmrC10, or Sra33.[3][4][5] According to its
#=GF CC   overproduction phenotype it was renamed Elongated Cell Phenotype RNA1.[2]
#=GF CC   Induced by stress,EcpR1 negatively regulates cell cycle master regulatory
#=GF CC   genes dnaA and gcrA at post-transcriptional level by base pairing between
#=GF CC   its strongly conserved GC-rich loop and the target mRNAs. It's regulation
#=GF CC   is hfq-independent but requires RNase E to regulate dnaA.[2]
#=GF WK   EcpR1_sRNA
#=GF SQ   32



CP000628.1/1499310-1499419           -AUACCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGG-U--C-GUGGGG-UC-GGUCGGCUGGCA---GGCAAUUU-CAAGC---GG-UUCCUCGUGC-CGUU-UU-GCA--G-----------GCUAGCCGGCCCCCGA--
CP000633.1/1463226-1463337           -AUACCCCAUG---GUGCUCAGGUCCGCCGCAUCUCCUGGG-U--C-GUGGGG-UU-GGUCGGCAGGUG---UGCGAUUAUCAAGC---GG-UUCCUCGUGC-CGUUAUU-GCA--U-----------GCCCGCCGACCCCCAU--
CP000738.1/1002551-1002658           -UUACCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGG-U--C-GUGGGG-UC-GGUCGGCUGGCC-----UCGGAU-UUGCG---GA-UUCCUCGUGC-UGCAACC-GGA--A------------CCAGCCGACCCCCAU--
CP000390.1/1442043-1442153           -AUACCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGG-U--CCGUGGGG-UU-GGCCGGUUGGUG--CUGGUGUUA-GUGGC------CUCCUCGUAC-CGCAGCC-AGU--U-----------GCCAGCCGGCCCCCAA--
ACQI01022875.1/594-709               -AUACCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGG-UUCC-GUGGGG-UC-GGCCGGCCGGCGGCUGGCUCAAA-GUGGC------CUCCUCGUAC-CGCUGCC-AGUUCC-----------GCCGGUCGGCCCCUUU--
ABIA02000004.1/346729-346839         -AUGCCCCAUG---AUGUUCAGGUCCGCCGCAUCUCCUGGG-U--C-GUGGGG-U--GGCCGGUCAAGA---UUAAGUGC-ACAGU---GGCAUCCUCGUUC-CACGCUC-UUG--U-----------UUUGACCGGCCCUCGA--
CP001280.1/466473-466582             -UUACCCUACG-GAGUGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUAGGG-UC-GGCCGGCGCGCA---AGUAGUUG-GAGUG---GC-CUCCUCGAAA-CGCUA----CU--U-----------GC-CGCCGGCCACCUU--
AACY020886535.1/58-163               -UUGCCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGUCU--C-GUGGGG-UC-GACCGGCUGAC-----GGUAACC-G-------GC-UUCCUCGUGC-CGCUGCC-GUU--A-----------GCCGGUCGGUCUCGUG--
AATP01000008.1/148570-148681         -CACCCCAUGG--AAUGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-CGUGGG-GC-GGUCGGUCAGCC---UCGCUCGU-AUACG---GU-GUCCUCGUGC-CGUU-GA-GCA--G-----------GCUGGCCGGCCACUUU--
AAPJ01000003.1/487117-487230         --UACCCCAUG-GAAUGCUCAGGUCCGCCGCAUCUCCUGGG-UCCC-GUGGGG--C-GGUCGGUCGGUC---AAGUGCAA-UGGCG---GU-UUCCUCGUAC-CGUCGCACGAA--G-----------ACCGGCCGGCCACUUU--
AGTN01720617.1/284-395               -AUACCCUGCG-GAAUGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUAGGG-UC-GGCCGGCGCGCAA-UUGGUCCUG-GAGUG---GC-CUCCUCGAAA-CGCCA----AU--A-----------GC-CGCCGGCCGCCUU--
AEVM01000017.1/34048-34154           -AUACCCUGCG-GAGUGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUGGGG-UU-GGCCGGCUGGCG----GUGGUUG-GAGUG---GC-CUCCUUGAA----------------GCC-----AUCGUCAGUCGGCCGCCUU--
ADVE01000035.1/35456-35562           -AUACCCUGCG-GAGUGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUGGGG-UU-GGCCGGCUGGC-----GUUGGUU-GGAGU---GGCCUCC---------------------UUAAAGCCAGCGUCAGUCGGCCGCCUU--
CP002568.1/1929301-1929414           -AAUCCCUACG-GAGCGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUGGGG-UA-GGCCGGCGAGGA---AGGGAGCC-GAAGAGUGGC-CUCCUCGUGU-CGUU----CGC--U-----------UCCCGCCGGCCGCCUC--
ABXL01000052.1/24276-24388           -ACUCCCUACG-GAGCGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUGGGG-UU-GGCCGGCGAGUAA-ACGGGUUCU-GAGUG---GC-CUCCUCGUGU-CAU---C-CGG--U-----------UCUCGCCGGCCACCAA--
AEFL01000083.1/40074-40186           -UUUCCCUACG-GAGUGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUGGGG-CA-GGCCGGCGCGAA---AGCAAGUC-GAAGA---GU-GGCCUCCUCG-AAUGCUU-GCC--U-----------UC-CGCCGGCCUCCUA--
AAUW01000008.1/93016-93126           --UUCCCCUCG-GAGUGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUGGGG-CA-GGUCGGCAGGGAA-CCGGCCGAU-GAGUG---GC-CUCCUCGAA-----UGCC-GUG--U-----------UCCCGCCGACCACUAA--
ACCU01000009.1/18863-18751           -UUUCCCCUCGGGAUUGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUGGGG-UA-GGUCGGCAGGGAA-CCGGUCGAA-GAGUG---GC-CUCCUCGAA-----UACC-GUG--U-----------UCCCGCCGACCACUAA--
CP001016.1/1408693-1408804           -CUGCCCUGCG--GAGUGCCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUAGGG-UU-GGCCGGCGCGCAA-AUGGCUUAG-GAGUG---GC-CUCCUCGAAA-CGGC--C-AUC--U-----------GC-CGCCGGCCACCUU--
CP000781.1/4276631-4276737           -CAACCCUGCG-GAGUGCUCAGGUCCGCCGCAUCUCCUGGG-U-CC-GUGGGG-UU-UGGCCGGUGGGU---GAGCUUGC-GGGAG---GC-CUCCCCGCUU---------UCU--C-----------CCCACCGGCCAGCCUA--
CP000774.1/3020237-3020355           -UGUCCUCGUG-GGGCGCUCAGGUCCGCCGCAUCUCCUGAG-U-CC-GCGGGGCAC-GGCCGGCCGGGUCCGUGGUUGUG-GAGUG---GC-CUCCUCUGAUAAGCCGCG-AUU--C-----------CCUGGCCGGCCACUAU--
CP002026.1/1561100-1561205           -UUGCCCUGCG-GAAUGCUCGGGUCCGCCGCAUCUCCUGGG-C-CC-GCAGGU-CU-GGUCGGCGGGCG---A-UGGCUC-GGAAG---GC-CUCUCCGUCC-CAUC---------------------GCCCGCCGAUUCCAGA--
AAFX01080464.1/650-542               -ACCCCUACGG-UUCUCCUCAGGUCCGCCGCAACUCCUGGG-U--C-CGUAGG-GA-GGCUGGUUCGCA---GCGGGCAA-GAGUG---GC-CUCUUCGACA-UGCC-----GC--A-----------GCGGACCAGCCGCUUC--
AP009384.1/2121549-2121656           -UAGCCCUGCG-GAGUGCCUAGGUCCGCCGCAUCUCCUGGG-U-CC-GUGGGG-UUCGGCCGGCGGGUG--GACGAUCAC-GGGUG---GC-CUCCCCGUCC---------GUC--C-----------A-CCGCCGGCCACCUC--
CP003075.1/1614655-1614549           -AAACCCUACG---GUUUUCAGGUCCGCCGCAACUCCUGA--U-CC-GUAGGG--C-GGCUGGCCCGGU--AUCGGACAA-GAGUG---GC-CUCUUCGACA-AA----C-CGG--A-----------CCGGGUCAGCCAACCC--
ABRD01002513.1/1018-1127             -AUACCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGG-U--C-GUGGGG-UC-GGUCGGCUGGUA---CGCAAAUU-AUAGC---GG-UUCCUCGUGC-CGUU-UU-GCA--U-----------GCUGGUCGACCCCCUU--
AE007869.2/1288585-1288697           AAUGCCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGAA-U--C-GUGGGG-UC-GGUCGGCUGAC-----GAUGUCC-GAAUC---GG-UUCCUCGUGC-CGUAAUC-ACA-UC-----------GUUGGCCGACCGCCUUCU
BA000012.4/686046-685933             -AUACCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGG-U--CCGUGGGG-UC-GGCCGGCCGGCGC-UGGCACAUA-GUGGC------CUCCUCGUAC-CGCUGCC-AAA--C-----------GCCGACCGGCCCCCUUCU
CP001074.1/1700123-1700232           -AUACCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGG-U--C-GUGGGG-UC-GGUCGGCUGGUA---GGCAAGUC-AUAAC---GG-UUCCUCGUGC-CGUU-UU-GCA--U-----------GCUGGCCGACCCCCUU--
CP001389.1/1145517-1145625           ---ACCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGG-U--C-GUGGGG-UC-GGUCGGCUGGAUU-CCGACGUCC-G--CG---GA-UUCCUCGUGC-CGCAGUC-GGA--G-----------CCCAGCCGACCCCCUU--
CP001622.1/1369771-1369880           -AUACCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGG-U--C-GUGGGG-UC-GGUCGGCUAGUA---GGCAAGUU-AUAGC---GG-UUCCUCGUGC-CGUU-UU-GCA--U-----------GCUGGCCGACCCCCUU--
CP002279.1/4209508-4209618           -AUACCCCAUG---AUGCUCAGGUCCGCCGCAUCUCCUGGG-U--CCGUGGGG-UC-GGCCGGCCGGCGC-UGGCAAAUA-GUGGC------CUCCUCGUAC-CGCUGCC-AAA--C-----------GCCGACCGGCCCCCU---
#=GC SS_cons                         .::<<<<<<<<.-----<<<<<<____________>>>>>>.-.->.>>>>>>.>-.<<<<<<<<<<<_...________._____...__.__________.____.__.___.._...........>>>>>>>>>>>:::::..
#=GC RF                              .augCCCcgcG.GAaUGCuCAGGUCCGCCGCAUCUCCUGgG.U.CC.gcgGGG.cu.GGcCGGccgGca...ugguauuu.gagug...Gc.cUCCUCGuac.cGuu.uc.aua..u...........gCcggCCGgCCaCcuu..
//
# STOCKHOLM 1.0

#=GF AC   RF02501
#=GF ID   Atu_C7
#=GF DE   Rhizobiales sRNA Atu_C7
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   45.00
#=GF TC   50.80
#=GF NC   33.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



AACY023244673.1/230-73               CGGUUUUUAACGGUUGUGGCCCGCAGCGGGUCCGGCGCUCAAAACCCUCUCCGGUUCUCCCGGUGCGCACUUGAGGGCUCGCAGGUGUUUCCUCCCUCGCCUGCAUGCUGCGUACCCGCCUCGCCCCGCUCUCCUCUACCUGGUGAGCGGGGCUUUUU
AFSD01000002.1/949399-949555         CGGUUUGGAACGGUCGCUGCCCGCAGC-GGGUCGGGCGUUUUAACCGUCUCCGGUUCUCCCGGUGCGCACUUGAGGGCUCGCAGGUGUUUCCUCCCUCGCCUGCAUGCUGCGUACCCGCCUCGCCCCGCUCCCCGCUACCAGGUGAGCGGGGCUUUUU
AE007869.2/1345809-1345653           CGGUUUGGAAUGGUUGCGGCCCACGGC-GGUCCGACGGUUGCAACCGUCUCCGGUUCUCCCGGUGCGCACUUGAGGGCUCGCAGGUGUUUCCUCCCUCGCCUGCAUGCUGCGUACCCGCCUCGCCCCGCUCCCCACUACCAGGUGAGCGGGGCUUUUU
#=GC SS_cons                         :::::::::::::::::::::::::::.:::::::::::::::::::::::::::::::::<<<<<<<<-----------<<<<<<<__________>>>>>>>---->>>>>>>>------<<<<<<<<<-<<_______>>->>>>>>>>>:::::
#=GC RF                              CGGUUUggAAcGGUuGcgGCCCgCaGC.GGucCGgcggUuauAACCgUCUCCGGUUCUCCCGGugCGCaCUUGAGGGCUCGCaGGuGUUUCCUCCCUCgCCuGCAUGCuGCGuaCCCGCCUCGCCCCGCuCcCCaCUACCaGGUGaGCGGGGCUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02502
#=GF ID   Atu_C8
#=GF DE   Rhizobiales sRNA Atu_C8
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   50.00
#=GF TC   54.40
#=GF NC   48.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   27



ABQZ01002409.1/1146-1026             GAAAAUGGCAACGGCUCUUAUCGUGGUGGGAAAGCGCAUGGG--CAGGAUGGUGUAA---------CCAUCCGGCGAC-AGCCACCCAUGCGCUAG-AUGACAGGCUCCUC-C-GGGGCCUUUUUUUG-UGCCCGAA
AAPJ01000003.1/68728-68848           GACAAAGAUCAACA---UUCUCGUAGUAGGACGGCGCACACG--CGAGGCGGUCUA-GG-----GACCGCCCGGCGAG-AGCCACGUGUGCGCAAC-UCA-AAGGGCCCCA-GC-GGCCCUUUUUUAUUGCGCCGAG
AGTN01740502.1/35-155                CGCCAUGACGAGCACCAUUCUCCUCGUAGGAACGCGCACCAG--CCGGGCGG-----CCGCAUGGGUCGCCGGAAGCA----AGCUGGUGCGCGAA-AAA-CAGGCCCUUC-C-GGGGCCUUU-UUAUUGGCCGAAA
AFSD01000002.1/297214-297333         GAAAAAUCUUAACGUACUUAUCGUGGUGGGACGGCGCAUGGG--CAGGAUGGUGUAA---------CCAUCCGGCGAA-AGC-ACCCAUGCGCUGA-ACG--AGGCUCCUU-AAGGGGCCUUUUUUUAUGUCUUCAA
CP002740.1/1991453-1991333           GAAAAAUUUCGCGGUUAUUCUUGUGGUGGGACGGCGCAUGGG--CAGGGUGGUGUAA---------CCAUCCGGCGGU-AGCCACCCAUGCGCUGA-ACG--AGGCUCCUG-ACGGGGCCUUUUUUUAUGCCUUCAA
CP000628.1/2297110-2296988           GAAAAACUCGACGGUUCUUAUUGUGGUGGGACAGCGCAUGGG--CAGGAUGGUGUAA---------CCAUCCGGCGAU-AGCCACCCAUGCGCUAG-AUGACAGGCUCCCC-AAGGAGCCUUUUUUUAUGCCCGAAA
ABRD01002827.1/360-480               GAAAAUCGCAAUGGUUCUGGCAGUGGUGAUAGGGCGCAUGGG--CAGGGUGGUGUAA---------CCAUCCGGCGAA-GGC-ACCCAUGCGCGGU-AAG-CAGGCUCCCG-ACGGGGCCUUUUUUUAUGCCCUGCA
CP001622.1/2771191-2771071           GAAAAUCGCAACGGCUCUUAUCGUGGUGGGAAAGCGCAUGGG--CAGGAUGGUGUAA---------CCAUCCGGCGAU-AGCCACCCAUGCGCUAG-AUGACAGGCUCCUC-A-GGGGCCUUUUUUUA-UGCCCGAA
CP002447.1/3356627-3356747           GAUGAUCGCAACGGCUCUCGUGGUGGUAGGAAAGCGCAUGGG--CAGGAUGGUGUAA---------CCAUCCGGCGAU-AGCCACCCAUGCGCGGU-AAA-CAGGCUCCUG-ACGGGGCCUUUUUUUA-UGCCCGAA
ADGO01038458.1/181-299               GAUCAAGUUUGCGAACAUUCUUGUAGUGGGUAGGCGCAUGGG--CAGGAUGGUGUAA---------CCAUCCGGCGGA-AGCCACCCAUGCGCAGA-ACG--AGGCUCCUC-CGGGGGCCUUUUUUA--UGCCUCCA
AM236080.1/2575794-2575675           GAAAAUCGCAAUGGUUCUCGUAGUGGUGAUAUCGCGCAUGGG--CAGGACGGUCUGA---------UCGUCCGGCAAU-AGCCACCCAUGCGCCGA-AAA-CAGGUCCCUG-ACGGGGCCUUUUUUUAUGCCCCG--
CP000633.1/2335037-2334915           GAUCAAUUUUAACAUUCUUCUCGUGGUGGGUACGCGCAUGGG--CAUGACGGUGUGA---------CCGUCAGGCAAU-AGCCUCCCAUGCGCGAC-AGA-CAGGCUCCUUCCAGGGGCCUUUUUUUAUGGCCAAAA
CP000758.1/1894819-1894938           CAUGAACACGAUUAUUAUUCUUGUGGUACGGGCGCGCAUGGG--CAGGAUGGUGUAA---------CCAUCCGGCGAA-AGC-UCCCAUGCGCGAA-AGA-CAGGCUCCCU-CGGGGGCCUUUUUUAUUAUCCAAA-
ABIA02000004.1/37578-37698           GAACAGUUUUGCGAACAUUCUCGUAGUACGAAGGCGCAUGGG--CAGGGUGGCGUAG---------CCAUCCGGCGAA-AGC-UCCCAUGCGCGAA-ACA-CAGGCUCCUC-CGGGGGCCUUUUUUUAUGGCUUGAA
AE008917.1/643185-643305             CAUGAACACGAUCAUUAUUCUUGUAGUACGGGCGCGCAUGGG--CAGGGUGGUGUAA---------CCACCCGGCGAA-AGC-UCCCAUGCGCGAA-AGA-CAGGCUCCCU-CGGGGGCUUUUUUAUUAUCCAAAUC
ABRA01001125.1/734-614               GAAGAUCGCAAUGGUUCUUGUCGUGGUGAUAAAGCGCAUGGG--CAGGAUGGUGUAA---------CCAUCCGGCGAUCAGC--CCCAUGCGCGGU-AGUUCAAGCUCCUG-ACGGGGCUU-UUUUUGUGCCCUGAA
CP000133.1/2557551-2557432           GAAGAUCGCAAUGGUUCUUGUCGUGGUGAUAAAGCGCAUGGG--CAGGAUGGUGUAA---------CCAUCCGGCGAUCAGC--CCAAUGCGCUGU-AGAUCAAGCUCCUG-ACGGGGCUUUUUUUG--UGCCCCGA
ABQY01001254.1/167-49                GGAAACGAUGACGAUUGUCGUAGCGGUGAUAUCGCGCAUGGG--CAGGAGGGAAUAG---------CCCUCCGGAAAC-CGCCGCCCAUGCGCCGA-AAC--AGGUCCCUG-ACGGGGCCUUUUUUUAUGCCCCG--
CP002279.1/3742700-3742814           GAAAAAGGCACUCAUUCU------CGUAGGAAGGCGCGUGGG--CAAGGCGGUGUAA---------CCGCCGGGCGAA-AACCUCCCAUGCGCAAC-ACA-CAGGCUCCCU-CGGGGGCCUU-UUUUAUUGCCUAAA
ABRC01001853.1/1740-1621             GGAAACGAUGACGAUUGUCGUAGUGGUGAUAUCGCGCAUGGG--CA-GAGGGUAUAG---------CCCUCCGGCAAC-CGCCGCCCAUGCGCCGA-AAA-CAGGUCCCUG-ACGGGGCCUUUUUUUU-GUGCCCCG
AGIX01000001.1/655853-655740         GAAAACGGCACUCAUUCU------CGUAGGAAGGCGCGUGGG--CAAGGCGGUGUAA---------CCGCCGGGCGAA-AACCCCCCAUGCGCAGA-CAC--AGGCUCCCU-CGGGGGCCU-UUUUUAUUGCCUGAA
CP000390.1/1584883-1585004           CAUGAUUAAGAAGAUCAUUCUCGUAGUAGGAAGGCACAUGGG--CAAGGCGGCGUAG---------CCGCCAGGCGAC-AGCCGCUCAUGUGCAGA-AGA-CAGGCUCCCU-CGGGGGCCUUUUUUAUUGGGCCGAA
CP003075.1/1918053-1917937           ---GCAGACGGCACUUAUUCUUGUAGUAGGCAGGCGCAUCGCAACAUGAGGGCAUAA---------CCCUCGUGCG---AAU-UGCGGUGCGCCGA-ACA-CAGGUCCCUC-AGGGGGCCUU-UUUUAUUAUCCAAA
AATP01000008.1/11343-11464           GACGAACACGACCAUUCUCGUAAUCGUACGAAGGCGCACACG--ACCGGCAGCGUAG---------CUGCCAGGCGAA-UGCCACGUGUGCGCGAAGACA--GGGGCCCUC-CAGAGGCCCUUUUUUUAUGCUUGCA
CP001389.1/2074821-2074701           GAAAAACUUCGCGGUUAUUCUUGUGGUGGGACGGCGCAUGGG--CAGGAUGGUGUGA---------CCAUCCGGCGGU-AGCCACCCAUGCGCUGA-ACG--AGGCUCCUG-AUGGGGCCUUUUUUUAUGUCUUCAA
AE007869.2/1995973-1995854           GAAAAAUCUUAACGUACUUAUCGUGGUGGGACGGCGCAUGGG--CAGGAUGGUAUAA---------CCAUCCGGCGAA-AGC-ACCCAUGCGCUGA-ACG--AGGCUCCUC-UAGGGGCCUUUUUUUAUGUCUUCAA
CP001191.1/2338394-2338275           GAAAAUCGCAAUGGUUCUGGCAGUGGUGAUCGGGCGCAUGGG--CAGGAUGGUGUAA---------CCAUCCGGCGAA-AGC-ACCCAUGCGCGGU-AAG-CAGGCUCCUG-ACGGGGCCUUUUUUUA-UGCCCUGA
#=GC SS_cons                         ::::::<-<________________>->[[[[((((((((((..,,<<<<<<_____.........>>>>>>,<<___._>>,,)))))))))),,.,,<.-<<<<<<<__.__>>>>>>>>,,,,,,,]]]]::::
#=GC RF                              gAaaAacacaAugaUUaUUcUuGUggUgggcccGCGCAuggG..CAgGgcGGUgUAA.........CCgcCcGGCGAa.AGCcaCccaUGCGCgaa.Aaa.CAGGccCCUu.aaGGggCCUuUUUUuaUggccuaaA
//
# STOCKHOLM 1.0

#=GF AC   RF02503
#=GF ID   Atu_C9
#=GF DE   Rhizobiales sRNA Atu_C9
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   40.00
#=GF TC   41.30
#=GF NC   36.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   9


AE007869.2/2087200-2087379 UGUCAACAACAGGAGGCACCCAUGGGACUUACAAAAUCUCUCAAUGCCUUGGCAGUCGGUUUGGCGUUUUUGUUCGUAGCGAUGAUGCUUUUCAUCUGACGCGAC----------GUGAAGACCAAACGCAGUUAAGAACCGUAGAUGACACG----------------AAUUUAAAAAGCGCAGGCCC-CGAGGGACCUGCGCUUU
CP001191.1/2661405-2661594 --UUAACGCGAGGAGACAGACAUGGGACUCACGCAAUCCUUGAAUGUUCUGUUGGUCAGUGCAGCGUUUGCUUUCGUCUUGUCCAUGCUCUUCAUCUGAGCUGGCU--------GGGGAAAGCGGAAUGACUGGUAGUACCUGAACUCCCCUGAUCAA------UCCGCCAAUGAAAAAGCGCAUGUCC-CGCCCGACAUGCGCUUU
CP002248.1/2040426-2040605 UGUCAACAACAGGAGGCACCCAUGGGACUUACAAAAUCUCUCAAUGCCUUGGCAGUCGGUUUGGCGUUUUUGUUCGUAGCGAUGAUGCUUUUCAUCUGACGAGAC----------GUGAAGACCAAACGCAGAAAAGAACCGUAGAUGACACG----------------AGUUUGAAAAGCGCAGGUCC-UGUCGGGCCUGCGCUUU
CP000628.1/2404795-2404987 GGUUGACUA-AGGAGGAAGACAUGGGAUUGACACGAUCCAUCAACGUCCUAGUGGUCGGAGCAGCCUUCGUAUUCGUCGUGACGAUGCUUUUCAUCUGACGAAGAACGAUCACCGCAGACAACCGAACUCCUGAAAGCAAACA----------AAACAG---CCUAUUCCAUUUAAAAAGCGCAUGCCGAAGAUCGACAUGCGCUUU
AM236080.1/3495092-3495289 GGUUAACGCGAGGAGACAGACAUGGGACUCACGCAAUCCUUGAAUGUUCUGUUGGUCAGUGCAGCGUUUGCUUUCGUCUUGUCCAUGCUCUUCAUCUGAGCUGGCC--------GACGAAAGUGUAAUGACUGAUAGUGCCUAAACUCCUGAAUAGCUGAUCAAUCCGCCAACGAAAAAGCGCAUGUCC-CGCCCGACAUGCGCUUU
CP000133.1/3000301-3000487 GGUUAACGCGAGGAGACAGACAUGGGACUCACGCAAUCCUUGAAUGUUCUGUUGGUCAGUGCAGCGUUUGCUUUCGUCCUGUCCAUGCUCUUUAUUUGAGCUGAC----------GGGC---CGGUAAUGCUGAUAGUGCCUAAACUCCCCUGAUCAA------UCCGCCAACGAAAAAGCGCAUGUCC-CGCCCGACAUGCGCUUU
ABRD01002595.1/1336-1140   GGUUAACGCGAGGAGACAGACAUGGGACUUACGCAAUCCUUGAAUGUUCUGUUGGUCAGUGCAGCGUUUGCUUUCGUCCUGUCCAUGCUCUUUAUCUGAGCCGGAU--------CACGAAGGCGUAACGACUGAUAAUGCCUAAACUCCUGAAGAACUGA-UCAUCCGCCAACGAAAAAGCGCAUGUCC-CGCCCGACAUGCGCUUU
ABQY01001836.1/1010-819    GGUUAACGCGAGGAGACAGACAUGGGACUCACGCAAUCCUUGAAUGUUCUGUUGGUCAGUGCAGCGUUUGCUUUCGUCUUAUCCAUGCUCUUCAUCUGAGCCUGGA-------UGACGGACGCGUAACGUU-GAUAGUGCCUAAACUCCCCUGAUCAA------UCCGCCAAUGAAAAAGCGCAUGUCC-CGCCCGACAUGCGCUUU
ABRB01001498.1/479-289     GGUUAACGCGAGGAGACAGACAUGGGACUCACGCAAUCCUUGAAUGUUCUGUUGGUCAGUGCAGCGUUUGCCUUCGUCCUGUCCAUGCUCUUUAUCUGAGCUGGC---------CGGCGGGGUGUGACGACUGGUAGUACCUGAACUCCCCUGAUCAA------UCCGCCAAUGAAAAAGCGCAUGUCC-CGCCCGACAUGCGCUUU
#=GC SS_cons               ::::::::::::::<<<<-----<<<<_________>>>>---->>>>----------------------------------------------------------........--------------------------------------------......------------<<<<<<<<<<<<<.____>>>>>>>>>>>>>
#=GC RF                    gGUUAACgagAGGAggCagACAUgGGACUuACgcAAUCCcUgAAuGccCUGuUGGUCaGUGCAGCGUUUGcuUUCGUcuUGuCcAUGCUcUUcAUCUGAgcuggca........gguGAaaaCguAAcgacugauAGuaCCuaAAcUcccauGaaaaa......UccgCcAaUgAAAAAGCGCAuGuCc.cGccgGaCaUGCGCUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02504
#=GF ID   Atu_L1
#=GF DE   Rhizobiales sRNA Atu_L1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   60.00
#=GF TC   70.50
#=GF NC   35.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4


AGSM01000014.1/130526-130699 CUUGCAGAAUGACCGCACAGAUGAGGGUCUGGAUGAAUGCCGUAUAGAAGGAGCCGUGGAUAAAAUAUGUCGCAACCGCAAAGGCAAGCAAUGCACCGAUCAUGCUGAAAAAAACACGAGGUGCAUACAUGGUGCUCUCCUCCCGAGAACGAUUUCUCCAUUUUUGACUGCGCU
AE007870.2/1179740-1179913   CCUGCAGAAUGACGGCACAGAUGAGGGUCUGGAUGAAGGCGGUAUAGAACGAUCCGUGGAUGAAGUAUGUGGCAACCGCAAAAGCAAGCAAUGCACCGAUCAUGCUGAAAAAAACACGAGGUGCAUACAUGGUGCUCUCCUCCCGAGAACGAUUUCUCCGUUUUUGGCUGCGCU
AFSD01000003.1/586430-586603 UUUGCAGAAUGACGGCGCAGAUGAGGGUCUGGAUAAACGCCGUAUAGAACGACCCGUGAAUGAAAUAUGUGGCAACCGCAAAGAUAAGCAACGCACCGAUCAUGCUGAAAAAAACACGAGGUGCAUACAUGGUGCUCUCCUCCCGAGAACGACUUCUCCAUUUUUGGCUGCGCU
CP002249.1/1563868-1564041   UUUGCAGAAUGACGGCGCAGAUGAGGGUCUGGAUGAAUGCCGUAUAGAACGACCCGUGGAUGAAAUAUGUAGCGACCGCAAAGGCAAGCAAUGCACCAAUCAUGCUGAAAAAUACACGAGGUGCAUACAUGGUGCUCUCCUCCCGAGAACGAUUUCUCCGUUUUUGGCUGCGCU
#=GC SS_cons                 :::[[[[,,,,,,((--(,,,,,,<<<<<-<<_______>>--------->>>>>,,,,,,,,,,,,<<<-<___>->>>,,,,,,,,,,,,)--)),,,,,,,,,,,,,,,,,,,,<<<<-<<<<_____>>>>--->>>><<<<<<<-<_______>->>>>>>>]]]]:::
#=GC RF                      uuUGCaGAAUGACgGCaCAGAUGAGGguCUgGAUgAAuGCcGUAUAGAAcGacCCGUGgAUgAAaUAuGuaGCaACCgCaAAggcAAGCAAuGCACcgAUCAUGCUGAAAAAaACACGaGGUGCauACAUGguGCUCUCCuCcCgagaaCGAuUUCUCCauuuuuGgCuGCGCU
//
# STOCKHOLM 1.0

#=GF AC   RF02505
#=GF ID   Atu_L6
#=GF DE   Rhizobiales sRNA Atu_L6
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   100.00
#=GF TC   122.50
#=GF NC   39.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


AECL01000014.1/126110-126233 GAUAGACCAAGGCCAUGCGAUACCAAGGGCCAUUGAGAUUGAGGCGCGGCGGUUUUCAUCUCAGGCGAGGGGAC-CGACGGAUCGUUCGUUACUCCAUGAGUGGCGAGCGGUCUGUGGUUCCGUU
AE007870.2/1966571-1966694   AAUAAAUCAAGGCCAUGCGAUACCACGGGCCAUUGAAAUUCAGGCUCGGCGGUUUUCAUUUCAGGCGAGGGGAC-CGACGGAUCGUUCGUUACUCCAUGAGUGGCGAGCGGUCUGUGGUUCCAGU
CP002249.1/439402-439280     AAUAAAUCGGGGGCAUG-GGCACCUUGCGGCAUUGAGAGCCGUGCCCAUUCUUUUUCAUUUC-GGCGAGGGGACCCGACGGAUCGUUCGUUACUCGGUGAGUGGCGAGCGAUCUGUGGUUCCAGU
#=GC SS_cons                 ::::::::::::<<-<<______>>->><<<--<<<<<____________________>>>>>>>>---<<<<<.<-<<<<<<<<<<<<<<<<<<___>>>>>>>>>>>>>>>>>>>>>>>>:::
#=GC RF                      aAUAaAuCaaGGcCAuGcGauACCauGgGcCAUuGagauucagGCuCggcggUUUUCAucuCaGgCGAGGGgaC.CGaCgGacCGuuCGuuaCuCcaUGaGuggCGagCGguCuGuGGuuCCagU
//
# STOCKHOLM 1.0

#=GF AC   RF02506
#=GF ID   Atu_Ti1
#=GF DE   Rhizobiales sRNA Atu_Ti1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   55.00
#=GF TC   60.10
#=GF NC   41.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   14



U00090.2/517427-517336               GUCC-AGUUUGCGGCGGACCAAAGCCAAAAGCCUGUGAAGGCGAUUGCGACAGCCGGCC-ACAUGCGGGUUACGAGGCCCAU-GAGGCCGGCUGU
CP002245.1/164945-164853             GUCCCAGGUUGCGGCGGACCAGAUCCAAAAGCCUGCCAGGACAAUCGCGACAGCUGGCC-ACAUGCGGGUUACGAGGCCCAU-GAGGCCGGCUGU
AE007871.2/148374-148283             GUCC-ACGUAGCGGCGGACCAGAACCAGAAGCCUCCCAGGGCAAUGGCAGCAGCCGGCCAGUAUCGCGAUGUCAUCAUCGCG-A-GGCCGGCUGU
AGSM01000016.1/28446-28355           GUCC-ACGUUGCGGCGGACCAGAGCCAGAAUCCUGCGAGGAUGAUGGCGGCGGCCGGCCAAAGCCUCGUCGUCAUGACGGUG-A-GGCCGGUCGC
EF066650.1/162300-162209             GUCC-AGAAUGCGGCGGACCAGAGCCAGAGCCCUGCAAAGGUGAUGGCAGCAGCCGGCCAAUAGCGCGUCGUCAUGAUGGCG-A-GGCCGGCUGC
AECL01000064.1/15328-15237           GUCC-ACGUCGCGGCGGACCAAAGCCAGAAUCCCCCAAGGAUGAUGGCUGCGGCCGGCCAACGCCUCGUUGUCAUGAUGAGC-A-GGCCGGUCGC
EU186381.1/111162-111071             GUCC-AGAUUGCGGCGGACCAUAGCCAAAAGCCGGUCAAGGCGAUGGCGACAGCUGGCC-AUAUGCGGGUUACGAGGCCCGC-AAGGCCAGCUGU
AFSD01000008.1/89363-89454           GUCC-ACGUUGCGGCGGACCAGAGCCAGAAGCCUCCGAGGCCAAUGGCGGCAGCCGGCCGAUAUCUCGUCGUGAUAGUGAUC-A-GGCCGGCUGC
AFSD01000008.1/291049-291140         GUCG-CCAAUGCAGCCGACCCAAGCCAUAGGCCUGCGAAGGCGAAGGCCGCAACUGGCCAGCAUCGCGUCGACAUAAUCGCG-A-GGCCGGCCGC
CP000630.1/62736-62645               GUCC-ACGUGGCAGUGGACCAGAGCCACAACCCUCCCAGAACGAUGGCGGUUGCCGGCCAAUAUCGCGAUGUCAUCAUCGCG-A-GGCCGGCUGU
AM236082.1/131223-131132             GUCC-AGAAUGCGGCGGACCAGAGCCAGAAGCCUGCAAGGGUUAUGGCUACAGCCGGUCGAUAUUGCGUCGUCAUGAGCGCG-A-GACCGGCUGU
CP000637.1/91444-91353               GUCC-AUGUUGCGGCGGACCAGAGCCAGAACGCCCCGAGCGUAAUGGCAGCGGCCGGCCAGAAUCUCGUCGUCAU-GACGAGCA-GGCCGGCCGU
AGVZ01000012.1/62275-62184           GUCC-ACGAAACGGCGGACCAGAGCCAGAAUCCUCCCAGGACGAUGGCGGUUGCCGGCCAAUAUCGCGAUGUCAUCAUCGUG-A-GGCCGGCUGU
AF010180.1/7629-7538                 GUCC-ACGUAGCGGCGGACCAGAACCAGAAGCCUCCCAGGGCAAUGGCAGCAGCCGGCCAGUAUCGCGAUGUCAUCAUCGCG-A-GGCCGGCUGU
#=GC SS_cons                         <<<<.__________>>>>,,,,<<<<----<<_____>>---->>>>-<<<<<<<<<<----<<<<<<<______>>>>>>.>.>>>>>>>>>>
#=GC RF                              GUCC.AcguuGCGGCGGACCAgAgCcagAAgCcUgCaAgGgcgAugGcggCgGCcGGCCAAuAucgcGgcguCAuggcCgcg.a.GGCCgGCcGc
//
# STOCKHOLM 1.0

#=GF AC   RF02507
#=GF ID   Atu_Ti3
#=GF DE   Rhizobiales sRNA Atu_Ti3
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   50.00
#=GF TC   51.30
#=GF NC   43.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



CP000637.1/162445-162535         AGAUCUCUCUGUUCGGCUUCUUUUCGGCGAGCAGCGGCAAUGUCGGCAGGAUAAGUGAACUGCACGCUGUAGUAGAGGUCAGACUGCUCUU
X53264.1/7182-7094               AG-CCU-UCUCUUGUGCCGCCUUCUGGCGAGCCGCUGCGUCAUCGGCAGGGUAAGCGAAUUGUACGCUAUAGUAGAGAUCGGCCUGCUCUU
CP000134.1/54480-54393           -G-CCU-UGUCCUGCGCCUCCUUUCGGCGGGCCGCCGCUUCAUCGGCAGGAUAGGCGAAUUGUACGCUGUAGUAGAGAUCAGGCUGUUCCU
J03216.1/7555-7467               AG-CCC-UCUGUUGUGCCUCCCUUCGCCGAGCCGCCGCAUCGUCGGCGGGGUAGGCGAAUUGGACGCUGUAAUAGAGAUCGGGCUGCUCUU
#=GC SS_cons                     :<.<<<.-----------------------------------------------<<<_______>>>------------->>>>:::::::
#=GC RF                          AG.cCc.UcUgUUguGCcuCcUUUcGgCGAGCcGCuGCaucaUCGGCAGGaUAaGcGAAUUGuACgCUGUAGUAGAGAUCgGgCUGcUCUU
//
# STOCKHOLM 1.0

#=GF AC   RF02508
#=GF ID   Atu_Ti4
#=GF DE   Rhizobiales sRNA Atu_Ti4
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   40.00
#=GF TC   42.50
#=GF NC   37.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   22336765
#=GF RT   Deep sequencing uncovers numerous small RNAs on all four replicons of the
#=GF RT   plant pathogen Agrobacterium tumefaciens.
#=GF RA   Wilms I, Overloper A, Nowrousian M, Sharma CM, Narberhaus F
#=GF RL   RNA Biol. 2012;9:446-457.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


AE007871.2/194399-194505 GAAAAACUCAGCACUGCGGAGUGAUUGGAUGGGUCCUAUCUUUUGAGAGAUCAGCUGUUCGUUGCCUUCUCCCGAGCAAAGAAACAUGCAAGCGCUGCGGUAGCCAG
X12867.1/208-307         ------AGCAGUGCUGCGCAGUGAUCGGAUAGGCCCUCUCUUUUGAGGGAUCAUCUUUUAGUUGUCUUCUCCCCAGCAAAGAAAGAUGCAAGCGCGGCGGUAGCUA-
Y00535.1/1829-1935       GAAAAACUCAGCACUGCGGAGUGAUUGGAUGGGUCCUAUCUUUUGAGAGAUCAGCUGUUCGUUGCCUUCUCCCGAGCAAAGAAACAUGCAAGCGCUGCGGUAGCCAG
#=GC SS_cons             ::::::::::<<<<<<<<<-<<----------------------<<<<<--<<<<_____>>>>-->>>>>-------------------->>->>>>>>>->>:::
#=GC RF                  GAAAAAcuCAGcaCuGCggAGuGAUuGGAUgGGuCCUaUCUUUUGaGagAUCagCUgUUcGcuGcCuuCuCCCgAGCAAAGAAAcAUGCAAgCGccGCgGuAgCcAG
//
# STOCKHOLM 1.0

#=GF AC   RF02509
#=GF ID   PYLIS_2
#=GF DE   Pyrrolysine insertion sequence mtbB
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   36.00
#=GF TC   39.30
#=GF NC   31.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001268; recoding_stimulatory_region;
#=GF DR   GO; 0030631; pyrrolysine incorporation;
#=GF RN   [1]
#=GF RM   23557142
#=GF RT   Effects of using coding potential, sequence conservation and mRNA
#=GF RT   structure conservation for predicting pyrroly-sine containing genes.
#=GF RA   Theil Have C, Zambach S, Christiansen H
#=GF RL   BMC Bioinformatics. 2013;14:118.
#=GF WK   PYLIS_downstream_sequence
#=GF SQ   23


AE008384.1/2036681-2036780 UAGAUCGGGGUCGGCG-ACCCUCUGGGUAUGCCGAUCUCCCACAUAAUGGCCUCAGGCAUGACAGGAAUGAGAGCAGCAGGAGACCUUGUUGCAAGGAUGC
CP001994.1/1665285-1665190 ----UAGGAGUUGGCG-ACCCAAUCGGUAUGCCAAUCUCACAUAUCAUGGCAUCCGGUCUUACAGGAAUGCGUGCAGCCGGUGACCUUGUUGCCAGGAUGC
CP000099.1/4626052-4626151 UAGAUCGGAGUCGGCG-ACCCGAUGGGUAUGCCGAUUUCCCAUAUAAUGGCUUCAGGUAUGACUGGAAUUAGAGCUGCAGGUGACCUUGUUGCAAGAAUGG
CP002069.1/1959665-1959566 UAGGUAGGAGUCGGCG-ACCCAGUGGGUAUGCCGAUAGCACACGUAUCCGCAUCCGGUAUGACCGGUAUGCGUGCAGGUGGAGACCUUGUUGCAAGAAUGC
CP002105.1/1355639-1355540 UAGGUAGGUGUAGGUG-ACCCUAAUGGAAUGGUCAUCAGUCACGCAUUAGCUUCGGGCAUGGGCGGAGUACGUACUGCCGGAGACCUGGUAGCGCGCAUGC
CP003108.1/1150084-1150183 UAGAUUGGUCAUGGUG-AUCCUUAUGGUAUGGCUAUAACUCAUGAAAUGUCUGCAGGCAUGGGCGGCAUACGUACUGCCGGAGAUCUGGUAGCACGGAUGC
CP002101.1/653163-653262   UAGAUAGGAGUCGGCG-ACCCAAUGGGUAUGCCGAUUUCCCACAUAAUGACCUCCGGAAUGAGCGGUAUCAGAGCAGCAGGGGAUCUUGUUGCAAGGAUGC
AE010299.1/621688-621787   UAGAUCGGGGUCGGCG-ACCCUCUGGGUAUGCCGAUUUCCCACAUAAUGGCUUCAGGUAUGACCGGGAUCAGAGCAGCAGGCGACCUUGUUGCAAGGAUGC
CP000099.1/1863702-1863801 UAGAUCGGGGUCGGCG-ACCCAAUGGGUAUGCCGAUCGCACACAUAAUGGCUUCAGGUAUGACAGGAAUGAGAGCUGCAGGAGACCUUGUUGCAAGAAUGG
AE010299.1/1112233-1112134 UAGAUCGGGGUCGGCG-ACCCUCUGGGUAUGCCGAUUUCCCACAUAAUGGCCUCAGGUAUGACCGGGAUCAGAGCAGCCGGCGAUCUUGUUGCAAGGAUGC
CP000300.1/1455796-1455697 UAGAUUGGUGUUGGUG-ACCCAAUGGGUAUGCCAAUCUCACACAUCAUGGCUUCCGGUAUGACCGGUAUGAGAGCAGCUGGUGACCUUGUUGCAAGGAUGC
AE008384.1/3575182-3575281 UAGAUCGGGGUCGGCG-ACCCUCUGGGUAUGCCGAUUUCCCACAUAAUGGCUUCAGGUAUGACAGGAAUGAGAGCAGCAGGAGACCUUGUUGCAAGGAUGC
CP002069.1/1431427-1431328 UAGGUAGGAGUCGGCG-ACCCGGUGGGUAUGCCGAUAGCACACGUAUCCGCAUCCGGUAUGACCGGUAUGCGUGCAGGUGGAGACCUUGUUGCAAGAAUGC
CP000300.1/2416420-2416519 UAGAUCGGUGUUGGUG-ACCCAAUGGGUAUGCCAAUCUCACACAUCAUGGCUUCCGGUAUGACCGGAAUCAGGGCAGCUGGUGACCUUGUUGCAAGGAUGC
AE010299.1/3005185-3005284 UAGAUCGGGGUCGGCG-ACCCUCUGGGUAUGCCGAUUUCCCACAUAAUGGCUUCAGGUAUGACCGGGAUAAGAGCUGCAGGCGACCUGGUCGCAAGGAUGG
AE008384.1/2446620-2446521 UAGAUCGGGGUCGGCG-ACCCUCUGGGUAUGCCGAUCUCCCACAUAAUGGCUUCAGGUAUGACAGGAAUGAGAGCAGCAGGAGACCUUGUUGCAAGGAUGC
CP001994.1/518780-518879   UAGAUAGGAGUUGGCG-ACCCCAUAGGUAUGCCAAUCUCACAUAUCAUGGCAUCCGGUCUUACAGGAAUGCGUGCAGCCGGUGACCUUGUUGCCAGGAUGC
AF153453.1/922-1021        UAGAUCGGAGUCGGCG-ACCCAAUGGGUAUGCCGAUUUCCCACAUAAUGGCUUCAGGUAUGACUGGUAUGAGAGCUGCAGGAGACCUUGUUGCAAGAAUGG
AASZ01001188.1/7285-7384   UAGCUGGGCGUGGGAG-AUCCAUUCGGGAUGUCUGUCGCCCACAUAAUGGCUGCCGGGAUGGGGGGCAUCCGAACCGCUGGAGAUCUGGUGGCUUGGAUGC
AGTN01189397.1/107-206     UAGGUUGGGGUCGGCG-ACCCGAUGGGUAUGCCGAUCUCACACAUCAUGACCUCUGGGAUGAGCGGCAUCAGGGCGGCGGGCGACCUCGUUGCCAGGAUGG
ABSO01008050.1/630-531     UAGGUGGGUGUGGGCG-AUCCCUUCGGGAUGUCCCUUACGCACGCGAUUGCCUCCGGAAUGGGUGGCAUUCGUACCGCUGGAGAUCUAGUGGCGCGGAUGC
ABLU01108090.1/105-6       UAGGUGGGUGUGGGUG-AUCCCUACGGGAUGCCCAUCGCCCACGGGGUCGCUGCCGGGAUGGGUGGCAUUCGGACGGCCGGAGAUCUGGUCGCCCGCAUGC
AASZ01001188.1/26705-26606 UAGCUGGGUGUCGGCGAUGCCUUUGGCA-UGCCGAUAGCCCAUAUUAUGGCGGCUGGCAUGGGCGGCAUUCGGACCACCGGAGAUCUGGUGGCCUGGAUGC
#=GC SS_cons               ::::::<--<<<<<<<.<<<_____>>>->>>>>>>-->----------------------------------<<<<<-<<____>>->>>>>::::::::
#=GC RF                    UAGaUaGGugucGGcG.acCCuaUgGguAUgCCgauuuCaCAcaUaAUgGCuuCaGGuAUGaccGGaAUuaGaGCcgCuGGaGAcCUuGugGCaaGgAUGc
//
# STOCKHOLM 1.0

#=GF AC   RF02510
#=GF ID   PYLIS_3
#=GF DE   Pyrrolysine insertion sequence mttB
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   38.00
#=GF TC   38.00
#=GF NC   37.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001268; recoding_stimulatory_region;
#=GF DR   GO; 0030631; pyrrolysine incorporation;
#=GF RN   [1]
#=GF RM   23557142
#=GF RT   Effects of using coding potential, sequence conservation and mRNA
#=GF RT   structure conservation for predicting pyrroly-sine containing genes.
#=GF RA   Theil Have C, Zambach S, Christiansen H
#=GF RL   BMC Bioinformatics. 2013;14:118.
#=GF WK   PYLIS_downstream_sequence
#=GF SQ   23


AE010299.1/1110303-1110204 UAGGCUGACGCCAAGAUCCCGGAUAACCAGACAGGACACGAAAAGACAAUGACCUGCUUCCUGCCUGCCCUUGCCGGUGCCAACACCAUCUAUGGCGCCG
CP002028.1/33107-33008     UAGACUGACAGUAAAGUUCCUGAUCCCCAGCAAGCUUUCGAGUUUGCCCUUACCGGAAUUAUACCAGCGUUAGCAGGAGCUAACAUGAUAUAUGGUCUGG
AE008384.1/2032367-2032466 UAGUCUGAUGCAAAGAUCCCGGACAACCAGGCAGGACACGAAAAGACAAUGACCUGUCUCCUUCCAGCUCUUGCAGGUGCAAACACCCUGUACGGUGCCG
CP003108.1/1152166-1152265 UAGGCAGACAGUAAAGUACCCGAUGCACAAGCCGCCCACGAAAAAACCAUAACGGGAUUAUUAGCUGCUCUAGGCGGAGCAAACUUAAUCUAUGGUUUGG
CP002105.1/386129-386228   UAGGCGGACAGCAAGUUAUGUGACGUACAAUCCGGAUAUGAAAAGACUAUGACUUAUAUGCUGCCAGCUAUGGCAGGUGCUAACGUGCUUUACGGCUCAG
CP001336.1/5191561-5191462 UAGGUAGACAGCAAGAUUCCCGAUGCCCAGGCAAGUCAUGAAUUUACUCUGACUGGGUUCUUAACCGCCUUAGCCGGUGCCAAUCUGAUUUAUGGCGCCG
CP003108.1/1162704-1162803 UAGGCAGACAGCAAACUUCCUGAUGGACAGGCUACUCAUGAAUCGACUCUAAGUGCUCUGCUUACCUCUUUAUCCGGAGCAAAUCUUAUCUAUGGACUCG
CP003108.1/1713214-1713313 UAGACAGACAGCAAAGUACCGGAUGCCCAAGCAGCUCACGAGUUUACCUUGACCGCUUUAUUACCAGCGUUGGCAGGCGCCAACAUGAUAUAUGGUCUUG
CP002101.1/512851-512950   UAGGCAGACGCCAAGAUACCUGACGGCCAGGCUGGCCAUGAGAAGACAAUGACCACUCUUCUACCAGCUCUUUCCGGUGCAAACACCCUCUAUGGUGCAG
AE008384.1/2444656-2444557 UAGUCUGAUGCCAAGAUCCCGGACAACCAGGCAGGACACGAAAAGACAAUGACAUGUCUCCUCCCGGCGCUUGCCGGAGCAAAUACCAUCUACGGAGCCG
AE010299.1/617396-617495   UAGUCUGAUGCAAAGAUCCCGGACAACCAGGCAGGGCACGAAAAAACAAUGACCUGUCUCCUGCCAGCCCUUGCAGGCGCAAACACUCUGUACGGCGCCG
CP002069.1/1964372-1964273 UAGGCAGACUCCAAGGUACCUGAUGCUCAGGCAGGUCAUGAGAAGACAAUGACAACACUUCUCCCAGCACUCUCGGGUGCAAAUACCCUGUACGGCUCAG
CP000300.1/2439107-2439206 UAGACUGAUGCUAAAGUUCCUGAUGGCCAAGCAGGUCAUGAAAAAACCUUGACCAACCUCCUUCCUGCACUGGCUGGUGCAAAUACGCUGUACGGUGCAG
CP003108.1/1819562-1819661 UAGGUAGACAGCAAACUCCCGGAUGCCCAAGCAUCUCAUGAGUUCACUAUUACCGCUAUGCUGACAGCGUUGGCAGGGUCCAACCUGAUUUACGGUGCGG
CP000099.1/1859474-1859573 UAGUCUGAUGCCAAGGUUCCGGACGACCAGGCAGGCCACGAAAAAACCAUGACCACCCUUCUGCCUGCUCUUUCCGGUGCCAACACCAUCUACGGAGCUG
CP001994.1/1669950-1669851 UAGGCUGAUGCCAAGGUCCCAGAUGGCCAGGCAGGUCAUGAAAAGACCAUGACAACCCUGCUUCCAGCGCUUUCAGGAUGUAACACCCUUUAUGGUGCGG
CP003108.1/4286012-4285913 UAGGCAGACAGUAAAAUACCCGAUGCUCAAGCUGCUCAUGAAAAAACUCUGACAGGUCUCCUCGCUGCCCAGGGCGGCGCGAAUCUGAUCUAUGGAGCGG
CP000300.1/1460496-1460397 UAGUCAGAUUCAAAGGUCCCAGAUACACAGUCAGGCCACGAGAAGACAAUGACAACCCUCCUUCCAGCAUUCGCCGGAUGUAACACCAUCUACGGUGGAG
AGJA01000014.1/31303-31402 UAGACUGAUAGCAAAGUACCGGAUGCCCAAGCAGCUCAUGAGUUUACCCUAACCGCUUUAUUACCAGCGUUAGCAGGCGCUAACAUGAUAUAUGGUUUAG
AACY023145179.1/174-273    AUGACGGAUUCCAAAUUACCCGAUGCUCAAUCGGGUUACGAAAAAGGAUAUACCGUCACCCUUGCGGCUCAUUCGGGAGCAAAUCUGAUUUAUGAAUCUG
AASZ01001188.1/10356-10455 UAGGCUGACGCCAAGAUAUCCGACGCCCAGGCGGGACACGAGAAGACGAUCAGCGCGUUGCUCUCGGCCCUGGCAGGCGCCAAUCUCAUAUACGGAGCGG
AGBJ01000515.1/1623-1524   UUGACCGAUUCUAAAAUACCAGAUGCCCAGGCAGGCUGGGAAAAGGCAUUUACAACCCUUCUGACAGCCAUGGGUGGUUCUAACUAUAUCCAUCACGCAG
CP001751.1/1263270-1263171 AUGGCUGACGCUAAAAUGCCUGAUGCACAAUCAGGCUAUGAAAAAGGCAGCACAUUGGUCAUGGCAGGCCUAUCAGGGCUGAAUAUGGUUUAUGAAGCGG
#=GC SS_cons               ::<________>,,,,,,,,,,,,<______><<<________________________>>>--------------<-<<______________>>->::
#=GC RF                    UAGgCuGAcacCAAaaUaCCuGAUGccCAggCagguCAuGAAAAgACaaUgACcgcucUccuucCaGCucUaGCaGGugCaAAcaugAUuUAUGGcgCaG
//
# STOCKHOLM 1.0

#=GF AC   RF02511
#=GF ID   PYLIS_4
#=GF DE   Pyrrolysine insertion sequence TetR
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   50.00
#=GF TC   56.10
#=GF NC   38.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001268; recoding_stimulatory_region;
#=GF DR   GO; 0030631; pyrrolysine incorporation;
#=GF RN   [1]
#=GF RM   23557142
#=GF RT   Effects of using coding potential, sequence conservation and mRNA
#=GF RT   structure conservation for predicting pyrroly-sine containing genes.
#=GF RA   Theil Have C, Zambach S, Christiansen H
#=GF RL   BMC Bioinformatics. 2013;14:118.
#=GF WK   PYLIS_downstream_sequence
#=GF SQ   2


AE010299.1/3625967-3626066 UAGUUCAUAGGUGAGUACCCCGAUUAUAGUCGGAUGUACUCAUAUUUCCAUUCGGGAAGGUUCAACCUGGAAGAUAGCGAAGAUAUGGAUGAGGUUGCAA
CP000099.1/4234546-4234447 UAGUUCGUAGCUCAGUAUCCAGAUUAUAAUCGGAUGUACCUCUAUUUCCGAUCUGGAAGGUUCAAUCUGGAAGAUUAUGAAAAUAUGGAUGAAGCUGCAA
#=GC SS_cons               ::::::::::::::::::<<<<<--------<<<-<<<____>>>->>>-->>>>>--<<_____>>:::::::::::::::::::::::::::::::::
#=GC RF                    UAGUUCaUAGgUgAGUAuCCcGaUUAUAaUCGGaUguaCuuauauUuCCauuCgGGAAGgUUCAAcCUGGAAGAUuauGAAaAUAUGGAUGAaGuUGCAA
//
# STOCKHOLM 1.0

#=GF AC   RF02512
#=GF ID   PYLIS_5
#=GF DE   Pyrrolysine insertion sequence transposase 1
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   60.00
#=GF TC   78.50
#=GF NC   40.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001268; recoding_stimulatory_region;
#=GF DR   GO; 0030631; pyrrolysine incorporation;
#=GF RN   [1]
#=GF RM   23557142
#=GF RT   Effects of using coding potential, sequence conservation and mRNA
#=GF RT   structure conservation for predicting pyrroly-sine containing genes.
#=GF RA   Theil Have C, Zambach S, Christiansen H
#=GF RL   BMC Bioinformatics. 2013;14:118.
#=GF WK   PYLIS_downstream_sequence
#=GF SQ   17


AE008384.1/3079218-3079119 UAGGUAAUAGAACAUUCUUUGACCUGCUGCAAAGAAUGCGGAUCUACCCUUGAGAAUGUUGAAGUUGAAGCUUAUGAGAGAAGACAGGUCUUUGACAUUC
AE008384.1/3214050-3214149 UAGGUAAUAGAACAUUCUUUGACCUGCUGCAAAGAAUGCGGAUCUACCCUUGAGAAUGUUGAAGUUGAAGCUUAUGAGAGAAGACAGGUCUUUGACAUUC
AE008384.1/1495554-1495653 UAGGUAAUAGAACAUUCUUUGACCUGCUGCAAAGAAUGCGGAUCUACCCUUGAGAAUGUUGAAGUUGAAGCUUAUGAGAGAAGACAGGUCUUUGACAUUC
AE008384.1/965836-965935   UAGGUAAUAGAACAUUCUUUGAGUUGCUGCAAAGAAUGUGGCCAUACUCUUGAGAAUGUUGAAGUUGAAGCCUAUGAGAAAAGACAGGUCUUUGAUAUUC
AE008384.1/3843675-3843576 UAGGUAAUAGAACAUUCUUUGACCUGCUGCAAAGAAUGCGGAUCUACCCUUGAGAAUGUUGAAGUUGAAGCUUAUGAGAGAAGACAGGUCUUUGACAUUC
AE008384.1/509923-509824   UAGGUAAUAGAACAUUCUUUGAGUUGCUGCAAAGAAUGUGGCCAUACUCUUGAGAAUGUUGAAGUUGAAGCCUAUGAGAAAAGACAGGUCUUUGAUAUUC
AE008384.1/2076792-2076891 UAGGUAAUAGAACAUUCUUUGAGUUGCUGCAAAGAAUGUGGCCAUACUCUUGAGAAUGUUGAAGUUGAAGCCUAUGAGAAAAGACAGGUCUUUGAUAUUC
AE008384.1/3945829-3945730 UAGGUAAUAGAACAUUCUUUGACCUGCUGCAAAGAAUGCGGAUCUACCCUUGAGAAUGUUGAAGUUGAAGCUUAUGAGAGAAGACAGGUCUUUGACAUUC
AE008384.1/2134627-2134726 UAGGUAAUAGAACAUUCUUUGAGUUGCUGCAAAGAAUGUGGCCAUACUCUUGAGAAUGUUGAAGUUGAAGCCUAUGAGAAAAGACAGGUCUUUGAUAUUC
AE008384.1/2899226-2899325 UAGGUAAUAGAACAUUCUUUGACCUGCUGCAAAGAAUGCGGAUCUACCCUUGAGAAUGUUGAAGUUGAAGCUUAUGAGAGAAGACAGGUCUUUGACAUUC
AE010299.1/1695199-1695100 UAGGAAAUAGAACACUCUUUGAGUUGCUGCAAAGAAUGUGGACACACUCUUGAGAAUGUUGAAGUUGAAGCUUAUGAGAAAAGACAGGUCUUUGAUAUUC
AE008384.1/334605-334506   UAGGUAAUAGAACAUUCUUUGAGUUGCUGCAAAGAAUGUGGCCAUACUCUUGAGAAUGUUGAAGUUGAAGCCUAUGAGAAAAGACAGGUCUUUGAUAUUC
AE008384.1/887313-887214   UAGGUAAUAGAACAUUCUUUGACCUGCUGCAAAGAAUGCGGAUCUACCCUUGAGAAUGUUGAAGUUGAAGCUUAUGAGAGAAGACAGGUCUUUGACAUUC
AE008384.1/2183147-2183246 UAGGUAAUAGAACAUUCUUUGACCUGCUGCAAAGAAUGCGGAUCUACCCUUGAGAAUGUUGAAGUUGAAGCUUAUGAGAGAAGACAGGUCUUUGACAUUC
AE008384.1/2910327-2910228 UAGGUAAUAGAACAUUCUUUGAGUUGCUGCAAAGAAUGUGGCCAUACUCUUGAGAAUGUUGAAGUUGAAGCCUAUGAGAAAAGACAGGUCUUUGAUAUUC
AE008384.1/1935805-1935904 UAGGUAAUAGAACAUUCUUUGACCUGCUGCAAAGAAUGCGGAUCUACCCUUGAGAAUGUUGAAGUUGAAGCUUAUGAGAGAAGACAGGUCUUUGACAUUC
AAFX01064130.1/817-718     UAGGUGAUAGAGCAUUCUUUGACUUGCUGCAAAGAAUGUGGACAUAUUCUUGAGAACGUUGAAGUUGAAGCUUAUGAGAGAAGACAGGUCUUUGACAUUC
#=GC SS_cons               ::<<<<------<<<<<<<<<________>>>>>>>>>------>>>>-----<<<<<<--<<<_________________________>>>-->>>>>>
#=GC RF                    UAgGuaAUAGAACauuCuuuGAcuUGCUGCaaaGaauGuGGauauaCcCUUGAGaauguUGaaGUUGAAGCuUAUGAGAaAAGACAGGUCuuUGacauuC
//
# STOCKHOLM 1.0

#=GF AC   RF02513
#=GF ID   PYLIS_6
#=GF DE   Pyrrolysine insertion sequence transposase 2
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; WAR
#=GF SS   Predicted; WAR
#=GF GA   80.00
#=GF TC   136.50
#=GF NC   42.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 1001268; recoding_stimulatory_region;
#=GF DR   GO; 0030631; pyrrolysine incorporation;
#=GF RN   [1]
#=GF RM   23557142
#=GF RT   Effects of using coding potential, sequence conservation and mRNA
#=GF RT   structure conservation for predicting pyrroly-sine containing genes.
#=GF RA   Theil Have C, Zambach S, Christiansen H
#=GF RL   BMC Bioinformatics. 2013;14:118.
#=GF WK   PYLIS_downstream_sequence
#=GF SQ   3


AE010299.1/3429991-3429892 UAGAUAAAAUACCAUUCGCCGGAAUACUGCGAUCAUUGUGGUCAUCAUCUUGAAGAUACUGAAGUUCAGGACUAUGAACGUAGGCAAGAAGCUGAAAUUC
AE010299.1/4365854-4365953 UAGAUAAAAUACCAUUCGCCGGAAUACUGCGAUCAUUGUGGUCAUCAUCUUGAAGAUACUGAAGUUCAGGACUAUGAACGUAGGCAAGAAGCUGAAAUUC
AE010299.1/4734177-4734078 UAGAUAAAAUACCAUUCGCCGGAAUACUGCGAUCAUUGUGGUCAUCAUCUUGAAGAUACUGAAGUUCAGGACUAUGAACGUAGGCAAGAAGCUGAAAUUC
#=GC SS_cons               ::::::::::::::::::::::::::<<<<<--------<<<<----------------<<_____>>->>>>----->>>>>:::::::::::::::::
#=GC RF                    UAGAUAAAAUACCAUUCGCCGGAAUACugCGAUCAUUGUgGuCAUCAUCUUGAAGAUACuGAAGUUCaGGaCuAUGAACGuaGGCAAGAAGCUGAAAUUC
//
# STOCKHOLM 1.0

#=GF AC   RF02514
#=GF ID   5_ureB_sRNA
#=GF DE   5' ureB small RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold;
#=GF GA   40.00
#=GF TC   40.00
#=GF NC   39.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   23104809
#=GF RT   Helicobacter pylori 5'ureB-sRNA, a cis-encoded antisense small RNA,
#=GF RT   negatively regulates ureAB expression by transcription termination.
#=GF RA   Wen Y, Feng J, Sachs G
#=GF RL   J Bacteriol. 2013;195:444-452.
#=GF WK   5_prime_ureB_sRNA
#=GF SQ   13



AY368262.1/937-646                   CGGUAGGGAUUUGUUGGGGAGAGAUAAAGUGAAUGUGUGUGUCAAUACCACCCGCHGUUACGAUCAAACCUUCACCGGCUAAGGCUUCAGUAGCAGGRC-CCACGCAAAGAUURUUUUUAACGCCAUCUUGCAUGUCUUUGUUACC-GCCUUUACCAAUGCCAGCGAUUUUG-CCRUCUUUAAUACCAAUAUCCGCUUUAUAAAUACCGGUGUAAUCCACGAUUAAAGCGUUAGUGAUAAUCAAAUCCAGU-UCU--UCUUU--GCUAGGGUUGUUGGAU--UGGCUCAUGCCUUCUCU--UAG
AP011940.1/86970-87261               CUGUAGGGAUUUGUUGAGGGGAGAUGAAGUGGAUGUGUGUGUCAAUACCACCAGCAGUUACGAUCAAACCUUCACCAGCUAGUGCUUCAGUAGCAGGGC-CCACGCUAAGAUUGUUUUUAACGCCAUCUUGCAUGUCUUUGUUACC-GCCUUUGCCAAUGCCAGCGAUUUUG-CCAUCUUUAAUACCAAUAUCCGCUUUAUAAAUACCGGUGUAAUCCACGAUUAAAGCGUUAGUGAUGAUCAAAUCCAGU-UCU--UCUUU--GCUAGGGUUGUUGGAU--UGGCUCAUGCCUUCCCU--CAA
AM260522.1/1333793-1333502           CUGUAGGGAUUUGUUGGGGUGAAAUGAAGUGGAUGUGUGUGUCAAUCCCACCAGCAGUUACGAUCAAGCCUUCACCGGCUAGCGCUUCAGUAGCAGGAC-CCACGCUAAGAUUGUUUUUAACGCCAUCUUGCAUGUCUUUGUUACC-GCCUUUACCAAUACCAGCGAUUUUG-CCAUCUUUAAUGCCAAUAUCCGCUUUAUAAAUACCGGUGUAGUCAAUGAUCAAAGCGUUAGUGAUGAUCAAAUCCAAU-UCU--UCCUU--GCUAGGGUUGUUAGAU--UGACUCAUGCCUUCUCU--UAA
AF508018.1/940-649                   CUGUAGGGAUUUGUUGWGGAGAAAUGAAGYGGAUGUGUGUGUCAAUACCACCAGCAGUUACAAUCAAGCCUUCACCAGCUAAUGCUUCAGUAGCAGGAC-CUACAGAAAGAUUGUUUUUAACACCAUCUUGCAUGUCUUUGUUUCC-GCCUUUGCCAAUACCAGCGAUUUUG-CCAUCUUUAAUACCAAUAUCAGCUUUGUAAAUACCAGUAUAAUCUACAAUUAGAGCGUUAGUAAUGAUUAAAUCUAAC-UCU--UCCUU--GCUAGGGUUGUUAGAU--UGGCUCAUCCCUUCUCU--UAA
AY368266.1/947-654                   CUGUAGGGAUUUGUUGGGGUGAAAUGAAGUGGAUGUGUGUGUCAAUACCACCAGCCGUUACGAUCAAACCUUCACCGGCUAAGGCUUCAGUAGCAGGAC-CCACGCUAAGAUUGUUUUUAACGCCAUCUUGCAUGUCYUURUUGCC-UGCUUUACCAAUGCCUGCAAUUUUG-CCAUCUUUAAUUCCAAUGUCGGCUUUGUAAAUACCGGUAUAGUCCACGAUCAAAGCAUUGGUGAGCACCAAGUCCAAC-UCA--UAAGA--GCUGGGGCUGUUGGUU--UGACUCAUCCCAUCGCGGAUAG
AB462258.1/950-657                   CUGUGGGGAUUUGUUGGGGAGAAAUGAAGUGGAUGUGUGUGUCGAUCCCGCCAGCUGUUACAAUCAGUCCCUCACCCGCGAGCGCUUCGGUGGCAGGCC-CCACGCAUAGAUUGUUGUCUACACCAUCUUGCAUGUCUUUGUUGCCAGC-CUUGCCAAUGCCCGCAAUCUUG-CCAUCCUUAAUGCCAAUAUCGGCUUUGUAAAUGCCGGUAUAAUCCACGAUCAGAGCAUUGGUGAUGACCAAAUCCAAC-UCA--UAGGA--GCUAGGGCUGUUAGUU--UGCCCCAUCCCAUCUCGAAUGG
EF070340.1/751-462                   CAGUAGGAAUUUGUUGGGGGGAAAUAAAGUGGAUGUGAGUAUCAAUACCGCCAGCUGUAACAAUAAGCCCUUCGGCCGCUAGUGCUUCAGUAGCAGGAC-CUACACAAAGAUUGUUGUGUACACCAUCUUGAAUGUCUUUGUUGCCCGC-UUUACCAAUGCCAGCAAUUUUG-CCAUCUUUAAUGCCAAUGUCAGCUUUGUAAAUACCGCUGUAAUCUACAAUCAAGGCAUUGGUAAUAACCAAAUCUAAC-UCU--UGAGU--GCUAGGACUAUUAGUU--UGGCCCAUCCCA--UCA--CGG
AF508003.1/949-656                   CUGUGGGGAUUUGUUGGGGAGAAAUAAAGUGGAUGUGGGUGUCAAUCCCACCAGCUGUAACAAUCAGCCCUUCAGCGGCCAAAGCCUCAGUAGCAGGGC-CCACGCAAAGAUUGUUGCAAACGCCAUCUUGCAUGUCUUUAUUGCCUGC-UUUGCCAAUGCCAUGGAUUUUG-CCAUUUUUAAUGCCAAUAUCGGCUUUAUAAAUGCCGGUGUAAUCCACAAUCAAGGCGUUGGUGAGCACGAGAUCGAGU-UCA--UGGCU--GCUGGGGCUGUUGGUU--UGUGCCAUCCCAUCGCGAAUGG
ADGY01000059.1/92405-92698           CGGUGGGGAUUUGUUGUGGAGAAAUAAAGUGAAUGUGGGUAUCAAUCCCGCCAGCUGUAACAAUUAAACCUUCACCAGCUAGUGCUUCUGUAGCAGGAC-CUACACAAAGGCGGUUGCAAACGCCGUCUUGAAUGUCUUUAUUGCC-GGCUUUACCAAUGCCAUGGAUCUUG-CCAUCUUUAAUGCCAAUGUCGGCUUUGUAAAUCCCGGUGUAGUCUACAAUUAGGGCGUUAGUAAUCACUAAAUCUAAC-UCA--UGGCU--GCUGGGGCUAUUGGUU--UGGCCCAUCCCAUCGCGGAUAG
AY368259.1/979-686                   CAGUAGGGAUUUGUUGGGGAGAGAUAAAGUGAAUAUGCGUAUCGAUGCCACCAGCGGUUACAAUCAAGCCCUCAGCUGCCAAAGCCUCUGUAGCAGGAC-CUACGCAAAGAUUAUUAUCUACGCCAUCUUGCAUGUCCUUAUUGCCCGCCUU-GCCAAUGCCUGCAAUCUUG-CCAUCCUUAAUCCCAAUGUCGGCUUUGUAAAUGCCCGUAUAGUCCACAAUGAGGGCGUUAGUGAGCACCAAAUCUAAC-UCA--UAAGA--GCUAGGGCUAUUGGUU--UGACUCAUCCCAUCACGGAUAG
AP012224.1/2128992-2128708           -UUCUUCGAUCUGCUGCGGGCAGAUGAAGUGGAUGUGGGUGUCGAUGCCGCCGGCGGUGACGAUCAUGCCUUCGCCGGCGAUGAUCUCGGUGGC--GGC-G---CCGAUAAC-GAUGUCGACGCCGGGCUGGAUGUCCGGGUUGCC-GGCCUUGCCGAUGGCGGCGAUGCGG-CCGUUCUUGAGCGCGAGGUCGGCCUUGACGAUGCCCCAGUGGUCGAGGAUCAGGGCAUUGGUGAUGACGGUGUCG-GC-CAC--UUCUUCGGCCAA---CCUUUGGCCCUGACCCAUGCCGUCGCG--GAU
AANO01000003.1/292109-291823         CCGUUUCGAUCUGCUGCGGGCAGAUGAAAUGGAUGUGGGUGUCGAUGCCGCCGGCGGUGAGGAUGUGGCCCUCCCCGGCGAUCGCCUC-GGUGCCGGGCCCCACCA--CGAUCG----UCACCCCGUCGGUGAUGUCGGGGUUCCCUGC-CUUGCCGAUGGC-GCAGAUGCGUCCGUCGCGCAGGCCCACAUCGGCCUUGACGAUCCCCCACCAAUCGAGGAUGAGGGCGUUGGUGAUCACCGUGUCCACCGCCCCGUCGGC--GCGGGAGGUCUGGGCC--UGGCCCAUGCCGUCG----CGG
FM991728.1/71118-71409               CUGUAGGGAUUUGUUGGGGUGAAAUGAAGUGGAUGUGUGUGUCAAUACCACCAGCCGUUACGAUCAAACCUUCACCGGCUAAGGCUUCAGUAGCAGGAC-CCACGCUAAGAUUGUUUUUAACGCCAUCUUGCAUGUCUUUGUUACC-GCCUUUACCAAUGCCAGCGAUUUUG-CCGUCUUUAAUACCAAUAUCCGCUUUAUAAAUACCGGUGUAAUCCACGAUUAAAGCGUUAGUGAUGAUUAGAUCCAGU-UCU--UCUUU--GCUAGGGUUGUUAGAU--UGGCUCAUGCCUUCUCU--UAG
#=GC SS_cons                         {{{-{{{{{,[[[[[[[((((((,,,,,,<<<-<<-<<<<____>>>>>>>>>,,,<<<_______>>>,))))))<<--<<<<<----<<<<<<<<<<.----<<-<<<<<-<<_______>>->>>>>>>-->>>->>>>>>>-.>>>>>-->>,,,,]]]]]]],,,,(.(((--(((((((((,,,,,,<<<<<<<--------<<______>>----->>>>>>>,<<<--<-<<--<<<______.>>>..>>->-..->>>,))-)))))))-..)))),,,,,,,,}}}}}..}}}
#=GC RF                              CugUcGcGAUuuGcuGgGGcGAgAUgAAGuGGAuGUGcgUGUCaAugCCaCCaGCuGuuAcgAUcAaaCCcUCgCCgGCuAgggcuUCaGcagCagGaC.ccACgcaaagauuGcUuUuaACgCCaucuugcAUGuCuuuGuugCC.gcccUUgCcAAUGcCagCaaUuuuG.cCaUccuuaAcgCCaAuaUCcGCcuUguaAAUaCCgGugUAaUCcAcgAUcAagGCgUugGUGaucAccgggUCuAac.ccc..Ugauu..GCcaGGGucgUuaggU..uGgCuCAUgCCaUCgCg..caG
//
# STOCKHOLM 1.0

#=GF AC   RF02515
#=GF ID   AfaR
#=GF DE   AfaR small RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:23563153
#=GF SS   Predicted; PMID:23563153
#=GF GA   100.00
#=GF TC   295.60
#=GF NC   58.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010629; negative regulation of gene expression;
#=GF RN   [1]
#=GF RM   23563153
#=GF RT   The AfaR small RNA controls expression of the AfaD-VIII invasin in
#=GF RT   pathogenic Escherichia coli strains.
#=GF RA   Pichon C, du Merle L, Lequeutre I, Le Bouguenec C
#=GF RL   Nucleic Acids Res. 2013;0:0-0.
#=GF WK   AfaR_small_RNA
#=GF SQ   2


ADTK01000078.1/5754-5987 UAGCUACAUAUGUUCCAUAACAGACGUCCACUUUUUGAUGAAAAGGUGGACACUACAUCACCAAUACAAGUUUAAUGGCUACAUACGGCACUCAGUUUACACUUACAUUACAUAUGCAUUUUAACACAUCAACUAUAACACCUUUAUUUAAGUCUGUUGUGGACCAUAGAAUAUGGUAAAUUACAACAAGCAAAAUAAAGUUAUAUAUGCUUUUAUAAAAUAACAUGCUAUUUU
GQ497943.1/56562-56329   UAGCUACAUAUGUUCCAUAACAGACGUCCACUUUUUGAUGAAAAGGUGGACACUGCAUCACCAAUACAAGUUUAAUGGCUAUAUACGGCACUCAGUUUACACUUACAUUACAUAUGCAUUUUAACACAUCAACUAUAACACCUUUAUUUAAGUCUGUUGUGGACCAUAGAAUAUGGUAAAUUACAACAAGCAAAAUAAAGUUAUACAUGCUUUUAUAAAAUAACAUGCUAUUUU
#=GC SS_cons             ::::::::((((-((((((((((((<<<<<<<<<<<____>>>>>>>>>>>,,<<<<<----<<<--<<<<-<<<--<<<______>>>------->>>->>>>-->>>---->>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,))))))))))))-))))----------------------------------------<<-<<<<_____>>>->->>::::::
#=GC RF                  UAGCUACAuauGUuCCauaaCaGaCGuCCaCuuuuuGAUGaaaagGuGGaCACugCauCACCaauACaaGuUuaaUGGCuAuAUACgGCACUCAGUuuaCaCuuACauuACAUauGcaUUUUAACACAUCAACUAUAACACCUUUAUUUAAGuCuGuuguGGaCCauaGAAUAUGGUAAAUUACAACAAGCAAAAUAAAGUUAUAuAUGCUuuuaUAAAAuaaCaUGCUAUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02516
#=GF ID   mir-393
#=GF DE   mir-393 microRNA precursor family
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   miRBase
#=GF SS   Predicted; miRBase
#=GF GA   60.00
#=GF TC   60.10
#=GF NC   59.90
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   MIPF; MIPF0000083;
#=GF DR   URL; http://www.mirbase.org;
#=GF RN   [1]
#=GF RM   22647959
#=GF RT   Role of microRNAs and other sRNAs of plants in their changing
#=GF RT   environments.
#=GF RA   Kruszka K, Pieczynski M, Windels D, Bielewicz D, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Vazquez F
#=GF RL   J Plant Physiol. 2012;169:1664-1672.
#=GF WK   MicroRNA
#=GF SQ   27


AC147434.12/80936-80818        -----AGGCAUCCAAAGGGAUCGCAUUGAUCC--CA---------AAUCUAAUUAAG--------UCCCUAGCUACUUAAUUAACAACUUAAU------UUCCUUAAUAUC-----UCAUAAUAU----UUGGGAUCA-UGCUAUCCCUUUGGAUUCAU------
FN595243.1/2576236-2576360     GGUGGACAGUUCCAAAGGGAUCGCAUUGAUCC-----CAUGGUUAUCUUCCACC------------UCUCUUACCAGACUAUCAUAACAAAGUCUGGCCUUUUU--------------CCCA--------UUGGAUCA-UGCUAUCCCUUAGGAACUCUCCAUCA
ACUP01012050.1/26300-26182     AGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCC-----------CAAAUCCAAGCUUCAA---------UGUUCUUCUCUCUUUCUCACUCAA---------AAUG------------UUAAUUUUAUU--UGGGAUCA-UGCUAUCCCUUUGGAUGUCUCCUU--
ACUP01010273.1/128067-127950   GGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCC-----------CAAAUCCAAGCUUUAA---------UAUUUUUCUCUCUU-CUCACUCAAU--------AAUA------------UUAAUUU-AUU--UGGGAUCA-UGCUAUCCCUUUGGAUUUCUCCUU--
ACUP01005817.1/11632-11752     AGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCC-----------CAAAUCCAAGCUUCAA---------UGUUCUUCUAUCUUUCUCACUCAA---------AAUA------------UUAAUUUUAUU--UGGGAUCA-UGCUAUCCCUUUGGAUUUCUCCUUUA
AL161667.1/79735-79894         AGAGAAAGGAUCCAAAGGGAUCGCAUUGAUCC---UAAUUAAGCUGAUUUAUUCCCCAAUAAUUGUUUUUUUUUUCCUUCUCAAUCGAAAGAUGGAAGAAAAACAAAUUCCAAACAUUUUGCUUACUUUUCCGGAUCA-UGCGAUCUCUUUGGAUUCAUUCUUU-
AARH01014631.1/367-473         GUUGGAGUGUUCCAAAGGGAUCGCAUUGAUCU-----AAUGA-CUUUUGAUGUC---------------------UAUAUGAUGUU--AAUGUUUAGUCAU-----------------UUCA--------UUGGAUCA-UGCGAUCCCUUAGGAAUUUUCCA---
ACUP01008067.1/154284-154424   GGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCCCAAAUUUCAGAUUUAUAAAUUUGUC---------UUUCUCUUCCCUUGUCAAUAUUUGGGAUCAUUUCUCUUC------------CCUUCUCAAUAUUUGGGAUCA-UGCUAUCCCUUUGGAUUCCUCCUU--
ABXC01004479.1/156-73          ----------UCCAAAGGGAUCGCAUUGAUCU-----CACCUGCCGC---CCGCCGCUG------------------CGCCUG-----CG-CGCGAGGGGACA----------------AG-------------AUCAGUGCAAUCCCUUUGGAA----------
ACUP01012175.1/220009-219874   GGUGGAGAGUUCCAAAGGGAUCGCAUUGAUCU-----AAUUC-UUG-AUCUUCCUGCAUGCA-----UU------UGCUUGCAGUUC-UGCUUUUGAGCCAUAUUUUA------CCGGUUCA---CUGACUUGGAUCA-UGCGAUCCCUUAGGAAUUCUCCAUCG
ACYM01117972.1/14961-15079     -GUGGAGGCUUCCAAAGGGAUCGCAUUGAUCU-----AAUUGAUCAUAUAUGUC---------AAACAUCGUCCGUACAGACA--UGGCAGGUUAUAU-------------------AUGUAG-------UUGGAUCA-UGCGAUCCCUUCGGACGUUUCCAU--
ACUP01005431.1/175515-175655   GGUGGAGAGUUCCAAAGGGAUCGCAUUGAUCU-----AAUUC-UUGUAGAUGUUUACACUUGCAAGCUU------UGCAUGCAAUUCCUGGAUUCAGAUGUGAUUCA-------GUGGUUCA---CUUA-UUGGAUCA-UGCGAUCCCUUAGGAACUUUCCAUCA
AARH01003540.1/1541031-1541115 AGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCC------------CAAGUGUCUGUC----------------CCCCAUAAUU------------------------------------------------UUGGAUCA-UGCUAUCCCUUUGGAUUCCUCCU---
ACYM01036249.1/248-378         GGUGGAGGCUUCCAAAGGGAUCGCAUUGAUCU-----AAUUGAUCAGAUAUGUC---------AAACAUCAUCCGCAUAGACAUAUGGUGGGUUAUGUUUUCGU-----------CUGUGUAG-------UCGGAUCA-UGCGAUCCCUUCGGACGUUUCCAUC-
ACUP01009649.1/3909-4056       GGUGGAGAGUUCCAAAGGGAUCGCAUUGAUCU-----AAUUC-UUGUAGAUGCCUGAACUUGCAAUCUUGAAUCUUGCAUGCAAUUCCUGGAUUUAGGUUUGCUUUAA------GGGGUUCA---GUUA-UUGGAUCA-UGCGAUCCCUUAGGAACUUUCCAUCA
HQ234502.1/1449-1545           ---------CUCCAAAGGGAUCGCAUUGAUCU-----AACCUGCCGA---UCGACGCCGA---------------CGUACGUA-----CG-UGCCCGAGGACA----------------AGCAG------AUCAGUCAGUGCAAUCCCUUUGGAAUU--------
ACUP01001170.1/58605-58493     GGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCCCAAAUUUCAGAUUUAUAAAUUUUUC---------UCU----------------------------UUCCCUCC------------CCUUCUCAAUAUUUGGGAUCA-UGCUAUCCCUUUGGAUUCCUCCUU--
ACYM01036248.1/11328-11458     GGUGGAGGCUUCCAAAGGGAUCGCAUUGAUCU-----AAUUGAUCAGAUAUGUC---------AAACAUCAUCCGCAUAGACAUAUGGUGGGUUAUGUUUUCGU-----------CUGUGUAG-------UCGGAUCA-UGCGAUCCCUUCGGACGUUUCCAUC-
HM139751.1/279-393             UGGGGAAGCAUCCAAAGGGAUCGCAUUGAUCC-----UUCAUCGCUCUCGCUCGCU--UC---------------CAUGGCGG----UCGUCGUCUACAAGCAG----------------CUUG------ACGGAUCA-UGCGAUCCUUUUGGAGGCUUCCUCU-
AARH01006572.1/305458-305352   GCUGGAGUGUUCCAAAGGGAUCGCAUUGAUCU-----AAUGA-CUCUCGAUGUC---------------------UAAAUCAUAUU--AAUGUUUAGUUUU-----------------UUCG--------UUGGAUCA-UGCGAUCCCUUAGGAAUUUUCCA---
ACUP01006201.1/28080-28213     GGUGGAUAGUUCCAAAGGGAUCGCAUUGAUCU-----AAUUC-UU-UAUCUUCCUGCAUGUA-----UU------UACUUGCAGCUC-UGGUUUUGGACCU--UUUUA------CCGGUUCA---CUGACUUGGAUCA-UGCGAUCCCUUAGGAAUUUUCCAUCG
AM451712.1/45205-45124         GGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCC------------CAAACUCUC----------------------------------------------------------------CAUGUCU------UUGGAUCA-UGCUAUCCCUUUGGAUUCCUCCUUUG
ACUP01006718.1/47245-47364     GGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCC-----------CAAAUCCAAGCUUCAA---------UAUUCUUCUCUCUUUCCCACUCAA---------AAUA------------UUAAUUUUAUU--UGGGAUCA-UGCUAUCCCUUUGGAUUUCUCCUUU-
AASG02007234.1/12892-12999     -----AAAGUUCCAAAGGGAUCGCAUUGAUCU-----AAUG--UCGUU---------------GGGUACC-----UAAAUGAGUU---AAUUAUAAAUCUAU---AAU------CCAAUUCA--------UUGGAUCA-UGCGAUCCCUUAGGAAGUCUCC----
ACUP01000423.1/343786-343671   AGAGGAGGCAUCCAAAGGGAUCACAUUGAUCC-----------CAAAUCCAAGCUUCAA---------UGUUCUUCUCUCUUUCUCACUCAA---------AAUA------------UUAAUUUUAUU--UGGGAUCA-UGCUAUCCCUUUGGACUUCUC-----
FM163994.1/1-133               AGAGGAAGGAUCCAAAGGGAUCGCAUUGAUCC---UAAUUAAGGUGAAUUCUCCCCA-----------UAUUUUC--UUUAUAAUUGGCAAAUAAAUCACAAAAA------------UUUGCUUGGUU--UUGGAUCA-UGCUAUCUCUUUGGAUUCAUCCUUC-
AARH01004386.1/205486-205403   AGAGGAGGCAUCCAAAGGGAUCGCAUUGAUCC------------CGAGUGUCCCUGG-----------------CCAUAAUU------------------------------------------------UUGGAUCA-UGCUAUCCCUUUGGAUUCCUCCU---
#=GC SS_cons                   :<<<<<-<<<<<<<<<<<<<<-<<<<-<<<<<.....---<_.______________._........______________________________________............______>......-->>>>>>.>>>->>>>>>>>>>>>>>->>>>>..
#=GC RF                        ggaGGAggcaUCCaAAGGGAUCGCAUUGAUCc.....aaUga.uuaauuauuucuuc.a........uUuuuuuucauauuuaaUuacugaauuuaguuuuaauu............uUuuauc......UugGAUCA.UGCuAUCCCUUuGGAugcuUCCuu..
//
# STOCKHOLM 1.0

#=GF AC   RF02517
#=GF ID   mir-1017
#=GF DE   mir-1017 microRNA precursor family
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   miRBase
#=GF SS   Predicted; miRBase
#=GF GA   50.00
#=GF TC   54.30
#=GF NC   38.10
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   URL; http://www.mirbase.org;
#=GF RN   [1]
#=GF RM   21712066
#=GF RT   Mirtrons: microRNA biogenesis via splicing.
#=GF RA   Westholm JO, Lai EC
#=GF RL   Biochimie. 2011;93:1897-1904.
#=GF WK   MicroRNA
#=GF SQ   7



AFFG01008128.1/648694-648764         GUGAGUUUAGUGGAGUUU-AAUGCUUCCCAUCGCCGACA-----AUUACGCGA---------------AAGCUCUACCCAAACUCAUCCCCU
AFFH01006953.1/220862-220932         GUGAGUUUAGUGGAGUUU-AAAGCCUCCAAUCGCCGGCA-----AUUGCGCGA---------------AAGCUCUACCCAAACUCAUCCCCU
AFFD01006950.1/669964-670031         GUGAGUUUAGUGGAGUUU-AAAGC---CCAUCGCCUGCA-----AUUACGCGA---------------AAGCUCUACCCAAACUCAUCCCCU
AFFE01007555.1/306085-306155         GUGAGUUUAGUGGAGUUU-AAUGCUUCUCAUCGCCGGCC-----CUUUCGCGA---------------AAGCUCUACCCAAACUCAUCCCCC
AAIZ01001676.1/3499-3424             GUGAGUUUUGUGGAGUUU-AAAGUUUACAAUCGCCGACAAUCAAAUUACGCGA---------------AAGCUCUACCCAAACUCAUCCCUC
AAQB01008982.1/939175-939093         GUGAGUUUUGUAGAGUUUUAAAGCUAUAAAUCGCCGGUA-----AAUAG----ACGUUAAAGACGCGAAAGCUCUACCCAAACUCACCCCGG
AC008366.3/111838-111908             GUGAGUUUAGUGGAGUUU-AAAGCUUCCCAUCGCCAGCA-----AUUACGCGA---------------AAGCUCUACCCAAACUCAUCCCCC
#=GC SS_cons                         <<<<<<<<-<<<<<<<<<.____________________....._________...............>>>>>>>>>-->>>>>>>>:::::
#=GC RF                              gUGAGUUUaGUgGAGuUU.AAAGCUuucaAUCGCCGGcA.....AuUAcGCGA...............AAgCUCuACCCAAACUCAcCCCcu
//
# STOCKHOLM 1.0

#=GF AC   RF02518
#=GF ID   mir-2494
#=GF DE   mir-2494 microRNA precursor family
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   miRBase
#=GF SS   Predicted; miRBase
#=GF GA   50.00
#=GF TC   51.30
#=GF NC   45.50
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   URL; http://www.mirbase.org;
#=GF RN   [1]
#=GF RM   21712066
#=GF RT   Mirtrons: microRNA biogenesis via splicing.
#=GF RA   Westholm JO, Lai EC
#=GF RL   Biochimie. 2011;93:1897-1904.
#=GF WK   MicroRNA
#=GF SQ   10



AAEU02000024.1/13434-13318           UGCAUCUUCCGCCCGGCGAUCAGUAAGUG---CACCAGAU-U-G---GGAUUAACCUUCAA----AAGCUGCAG-CUUAACUAUUCC---CAGUAAUGUCCACUUACAAGGAGCCCCUGGAUGGCUGGGUGGA
AAKO01002387.1/13542-13423           UGCAUCUUCCGACCGGCGAUCAGUAAGUG---CACCAUAG-U-AAAUGGAAUAACCUUCAA----AAUCUGCAA-CUUAAAUAUUCC---CAGUAAUGUCCGCUUACAAGGAGCCCCUGGUUGGAUGGGUGGA
AAPQ01006453.1/32569-32453           UGCAUCUUCCGCCCGGCGAUCAGUAAGUG---CAACAGAU-U-G---GGAGUAACCGUCAA----AAGCUACAA-CUUCAAUAUUCC---CAGUAAUGUCCACUUACAAGGAGCCCCUGGUUGGCUGGAUAGA
AFPQ01006450.1/37538-37422           AGCAUCUUUCGACCAGCGAUCAGUAAGUC---CACCAGAU-U-G---GGAUUAAUCUUCAA----AAGUUGCAA-CUUAAAUAUUCC---CAGUAAUGUCCACCUACAAGGAGCCUCUGAAUGGGUGGGUGGA
AFPP01030176.1/6614-6499             UGCAUCUUCCGACCGGCAAUCAGUAAGUG---CACCAGAU-U-G----GGGUGGACCUUAA----ACGCUGCAA-CUUAAAUAUUCA---CAGUAAUGUCCACCUACAAGGAGCCUUUCGACGGGUGGGUGGA
AFFF01006997.1/561794-561910         UGCAUCUUCCGACCGGCGAUCAGUAAGUG---CUCCCGAU-U-G---GAAUUGACAUUCAA----A-GCUACAACCACAAAUAUUCC---CAGUAAUGUCCACCUACAAGGAGCCACUGCGUGGGUGGGUGGA
AFFI01008326.1/100338-100215         UCCAUCUUCCGGCCGGCGAUCAGUAAGUGCUUUACCCCGCAU-G---GGAUUAACCUUCAA----AAGCUGCAA-CUUGAAUAUUCCAUCCAGUAAUGUCCACCUACAAGGAGCCACUGAAUGGGUGGGUGGA
AFFG01007793.1/117879-117762         UGCAUCUUCCGACCGGCGAUCAGUAAGUG---CACCAAAC-UUA---UAUUGUCUCUUCAA----AGGCUGCCA-CUUGAAUCUUUA---CAGUAAUGUCCACCUACAAGGAACCCCUGCAUGGCUGGGUGGA
AFFH01007288.1/105751-105633         UGCGUCUUCCGACCGGCGAUCAGUAAGUU---AAUA-AAU-U-----AGGAUACCCCAGAAUCUGGCGCUGCAA-CUAACUUAUCCU---UAGUUAUGCCUACCUACAAGGACCCCGUCGUUGGAUGGACGGA
AC011616.5/101542-101658             UCCAUCUUCCGACCGGCGAUCAGUAAGUG---CACCAGAU-U-G---GGAAUAACCUUCAA----AAGCUGCAA-CUUAAAUAUUCC---CAGUAAUGUCCACUUACAAGGAGCCCCUGGUUGGAUGGGUGGA
#=GC SS_cons                         <<<<<<<<<<<<<<<<-<-<<-<<<<<<<...-<<---<<.<.<...<<<<<<________...._________.______>>>>>>...>>>>--->>->>>>>>>--->>-->->>>>>>>>>->>>>>>>
#=GC RF                              ucCauCucCCgccCggCGAuCAGuagGug...caccaaac.u.G...gGgauaacCuUcAA....AaGCUGCAA.CUuaAauaucCc...CaguAAUguCcaCcuaCAAGGagCCccuGgguGGgUgGguGga
//
# STOCKHOLM 1.0

#=GF AC   RF02519
#=GF ID   ToxI
#=GF DE   ToxI antitoxin
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:23267117
#=GF SS   Published; PMID:23267117
#=GF GA   50.00
#=GF TC   54.50
#=GF NC   46.00
#=GF TP   Gene; antitoxin;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   23267117
#=GF RT   Selectivity and self-assembly in the control of a bacterial toxin by an
#=GF RT   antitoxic noncoding RNA pseudoknot.
#=GF RA   Short FL, Pei XY, Blower TR, Ong SL, Fineran PC, Luisi BF, Salmond GP
#=GF RL   Proc Natl Acad Sci U S A. 2013;110:E241-E249.
#=GF WK   Toxin-antitoxin_system
#=GF SQ   4



CP000905.1/47243-47276             AAAUUGGUGUAGCCUUACCGUAGUAGGCACAAAA
ACNL01000295.1/1429-1396           AAAUUGGUGUAUCCUUACCCUAGUAGGAACAAAA
AAEP01000052.1/71937-71904         AAAUUGGUGUAGCCUUACCGUAGUAGGCAUUCAU
DQ025752.1/63481-63448             AAAUUGGUGUAGCCUUACCGUAGUAGGCGCUAAA
#=GC SS_cons                       :::::::::::<<<<_________>>>>::::::
#=GC RF                            AAAUUGGUGUAGCCUUACCGUAGUAGGCACuAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02520
#=GF ID   mir-965
#=GF DE   mir-965 microRNA precursor family
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   miRBase
#=GF SS   Predicted; miRBase
#=GF GA   60.00
#=GF TC   61.30
#=GF NC   54.70
#=GF TP   Gene; miRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 25.44 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000276; microRNA;
#=GF DR   GO; 0035068; micro-ribonucleoprotein complex;
#=GF DR   GO; 0035195; gene silencing by miRNA;
#=GF DR   MIPF; MIPF0000708;
#=GF DR   URL; http://www.mirbase.org;
#=GF RN   [1]
#=GF RM   23189562
#=GF RT   The regulation of silkworm fibroin L chain production by miRNA-965 and
#=GF RT   miRNA-1926 in insect cells.
#=GF RA   Huang Y, Zou Q, Song F, Wang X, Shen XJ
#=GF RL   Bioorg Khim. 2012;38:477-481.
#=GF WK   MicroRNA
#=GF SQ   32



AAEU02000355.1/17084-16979             -GACAAAAUUGCUCAAC-AUUUUAGG-GGGUUAAACUGUA-CGUUAUAUGU-GCCCUUUUGUAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUGAAGCAACAGCAA
AFPQ01006168.1/574450-574556           -GACAAUAUUGCUCAAC-AUUUUAGG-GGGUUAAACUGUA-CGUUAUAUGUGCUAUUCUAUGAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUAAAGCAACAGCAG
AFFE01007033.1/67269-67375             -GACAAUAUUGCUCAAC-CAUUUGGG-GGGUCAAACUGUA-CGUUGUAUGUGCCAAACUAUGAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUGAAGCAAAGCCAG
AAPU01010477.1/19927-19824             -AACAAAACACUCAAAU--GUUUAGG-GGGUCAAACUGUA-CGUUGUAUGU-GUAAACAAUGAAAU-CCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUU-GAAGUGGAAUCA
AAPQ01007317.1/124747-124641           -GACAAAAUUGCUCAAC-AUUUUAGG-GGGUGAAACUGUA-CGUUAUAUGUGUCCUUCUGUAAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUACAGCAACAGCAA
AGBW01008102.1/166813-166714           -CUAGGAGAUGCUUUAU--AACUAAC-GGGAGAAGUUAUAACGCUGUAUGU---AUCUAU----AA-CCAUAAGCGUAUAGCUUUUCCCCUUGGUUAUACAAGCAAAGAUCU
AADG06002331.1/24822-24736             --------UGGACAUAU--UCCAAGG-GGGAAAGGUUAUAGCGAU-UAUG--AGAAAUUA---A--GCCAUAAGCGUAUAGCUUUUUCCCUUUGGCAUUUGUUAUU------
AAGH01024246.1/17099-17189             --------GCUCAACAU--UUUGGGGGGUGAA--ACUGUA-CGUUAUAUGUGCCCUUCUGUGAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUAGAGCU-------
AC008371.4/67161-67057                 -CAAUAUUGCUCAACAU--UUUGGGGGGUAAA--ACUGUA-CGUUAUAUGUGCCCUUCUGUGAUAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUAGAGCUAUUGCAA
ABKP02001353.1/203-102                 -AAGUAAAUCGACGAAU--UCUGAAAGGGGAA-UGCUGUA-CACUCUAUGU---GCUAAA-AAUAU-CCAUAAGCGUAUAGCUUUUCCCAUUUAGCGUUCGUUGCGAGCAAA
AAGE02003410.1/87416-87494             --------------GAU--UCUGAAGGGGGAAAUCCUGUA-CGCUGUAUGUUGUAUUUGA-AUAAU-CCAUAAGCGUAUAGCUUUUCCCAUUCGGCGU--------------
AAJJ01000024.1/136630-136528           -GCGCGCUCCGAUUGGA--CCCUGGG-GUGGAAAGUUGUACCGCU-GAUG--GUGAUUUUUCUA--CACAUAAGCGUAUAGCUUUUCCCCUUUGGUUCCAAUCACGACGAUC
AAIZ01002360.1/6699-6609               --------GCUCAAAAA--UUUGAGGGGUCAA--ACUGUA-CGUUCUAUGUGACAAUAUUCGAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAAACUUGAUGCA-------
AAAB01008964.1/1298298-1298197         -AAGUAAAUCGACGAAU--UCUGAAAGGGGAA-UGCUGUA-CACUCUAUGU---GCUAAA-AAUAU-CCAUAAGCGUAUAGCUUUUCCCAUUUAGCGUUCGUUGCGAGCAAA
ABLF02036837.1/20149-20209             -------------------------G-AGGAAAAGUUAUAACGGU-UAUG-UUCAUA-AUAACA--GUCGUAAGCGUAUAGCUUUUCCCCUU--------------------
AAWU01004674.1/45158-45249             --------CUGGCAGAU--UCUGAAGGGGGAAAUCCUGUG-CGCUCUAUGUUGCAUUUUA-UCGAC-CCAUAAGCGUAUAGCUUUUCCCAUUCAGCGUGUGCCCA-------
ADOQ01008839.1/2122-2221               -GCAAAUUGAGAUAUAU--UUCGAGG-GGGAAAAGUUAUGGCGAU-UAUG---AGAAAUU---GAA-CCAUAAGCGUAUAGCUUUUCCCCUUUGGCGUAUAUCAACCUCGAC
ADIH01023041.1/1755-1854               -ACAAGCUGGGAUAUAU--UCCGAGG-GGGAGAAGUUAUGGCGAU-UAUG---AGAAAUU---GAA-CCAUAAGCGUAUAGCUUUUCCCCUUUGGCGUGUGUCACUUCAACG
AANI01016191.1/108031-108134           -AAACACACACACAAAU--GUUUAGG-GGGUCAAACUGUA-CGUUGUAUGU-GCAAAUGAUGAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAACGUU-GAUGUGACGACA
AFFD01006163.1/14053-14158             --ACGAUAUUGCCCGAC--AUUUUGGGGGGUGAAACUGUA-CGUUAUAUGUGCCAUUCUAUGAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAGAAGUUGGUGCAACAGCAA
AEAC01020242.1/7014-7113               -AUAAACUGAGAUGUAU--UCCGAGG-GGGAGAAGUUAUUGCGAU-UAUG----AAC--AAUUAAA-CCAUAAGCGUAUAGCUUUUCCCCUUUGGCGUAUGUCACCUCAACG
AEAB01023888.1/6989-7088               -GCGAGCUGAGAUGUAU--UCCGAGG-GGGAAAAGUUAUGGCGAU-UAUG----AAAAAU-GU-AA-CCAUAAGCGUAUAGCUUUUCCCCUUCGGCGUAUGUCACUUCAACG
AAPP01015987.1/377067-377174           -UUUCUGGAAGCUCAACCCUUUUGGG-GGGUCAAACUGUA-CGUUCUAUGUGGCAAUCUUAGAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUGAAGCAAAGUCAA
AFFI01005186.1/237124-237228           ---CAAUAUUGCUUAAC--AUUUUGGGGGGUGAAACUGUA-CGUUAUAUGUGCCAUUCUAUGAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUAAUGCAAAAGCAA
AAPT01021772.1/162955-162852           -AAAAUAACACUCAAAU--GUUUAGG-GGGUCAAACUGUA-CGUUAUAUGU-GUAAAUGAAGAAAU-UCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUU-GAAGUGAUAGCA
AEQM02010263.1/44628-44529             -UCAUAUUAGGACAUAU--UCCAAGG-GGAAAAGGUUAUAGCGAU-UAUG---AGAAAUU---AAG-CCAUAAGCGUAUAGCUUUUUCCCUUUGGCAUUUGUCAAUGUCAUC
AFFG01008093.1/276787-276681           -GAUUUUAUUGCUCAAC--AUUUUGAGGGGUGAAACUGUA-CGUUGUAUGUGCCCUAUUAUAAAAA-CCAUAAGCGUAUAGCUUUUCCCCUUAAAAGUUGAUGCAACACCAA
AEVX01011027.1/13769-13669             UUGCAAGCUGGAUAUAU--UCCGAGG-GGGAAAAGUUAUGGCGAU-UAUG--AGGAAUUG----AA-CCAUAAGCGUAUAGCUUUUCCCCUUUGGCGUAUGUCGCUCCAACG
AEAQ01007964.1/21336-21237             -ACAGGCUGGGAUAUAU--UCCGAGG-GGGAAAAGUUAUGGCGAU-UAUG--AGGAAUUG----AA-CCAUAAGCGUAUAGCUUUUCCCCUUUGGCGUAUGUCGUUCCAACG
BABH01005086.1/4530-4427               -AUAUAAAUGGCUGCAU--AGCUAAACGGGAGAAGCUAUAGCGCUAUAUG--UCAAUAUUA--AAA-UCAUAAGCGUAUAGCUUUUCCCCUUGGUUAUGCAUGCAUAUUCUC
AFJA01001346.1/23128-23029             -AUAAAUGAGGACAUGU--UCCAAGG-GGGAAAGGUUAUAGCGAU-UAUG---AGAAAUU---AAG-CCAUAAGCGUAUAGCUUUUCCCCUUUGGCAUUUGUCAUUAUCAUC
ADMH01000202.1/34559-34460             -UUAACGUCUGACGAAU--UCUGAAC-GGGAAUGGUUGUG-CGCUCUAUG---UGCUAUG---AAA-UCAUAAGCGUAUAGCUUUUCCCAUUUAGCGUUCGUUCAUCAUCAU
#=GC SS_cons                           .:::::::::<<<<<<<..<<<<<<-.<<<<<<<<<<<<<.-<<<-<-<<-.-<<___________._>>>>>>>>>>>>>>>>>>>>>->>>>>>>>>>>->>::::::::
#=GC RF                                .aaaaauauugcccaAc..uccuagG.GGGaaAaGcUgUA.CGgUaUAUGU.augauuUuugaAAu.ucaUAAGcGUAuAgCuUuuCCCCuuaggagUuggugcaaaaaaaa
//
# STOCKHOLM 1.0

#=GF AC   RF02521
#=GF ID   Virus_CITE_7
#=GF DE   Pea enation mosaic virus-2 cap-independent translation element
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23682606
#=GF GA   80.00
#=GF TC   105.80
#=GF NC   33.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   23682606
#=GF RT   3' Cap-Independent Translation Enhancers of Plant Viruses.
#=GF RA   Simon AE, Miller WA
#=GF RL   Annu. Rev. Microbiol. 2013;0:0-0.
#=GF WK   Cap-independent_translation_element
#=GF SQ   2


AY714213.1/3822-3906 UAGAACACGUGGGAUAGGGGAUGACCUUGUCGACCGGUUAUCGGUCCCCUGCUCCUUCGAGCUGGCAAGGCGCCCAAAGGUUCUA
JF713436.1/3827-3911 UAGAACUUGUGGGAUAGGGGAUGAUCUUGUCGACCGUUUCUCGGUCCCCUGCUCCGUUGAGCUGGCAAGGCGCCUAUAGGUUCUA
#=GC SS_cons         ((((((--(((((-----------(((((((<<<<<_____>>>>>,,,,<<<<____>>>>,)))))))--)))))--))))))
#=GC RF              uaGaaCaugugGGAUAGGGGAUGAcCuuGuCGaCCGuUUaUCGGuCCCCUGCuCCuUuGaGCUGgCaaGgCGCCcacAGGuuCua
//
# STOCKHOLM 1.0

#=GF AC   RF02522
#=GF ID   Virus_CITE_8
#=GF DE   Pea enation mosaic virus-2 cap-independent translation element
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; PMID:23682606
#=GF GA   80.00
#=GF TC   101.30
#=GF NC   35.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   23682606
#=GF RT   3' Cap-Independent Translation Enhancers of Plant Viruses.
#=GF RA   Simon AE, Miller WA
#=GF RL   Annu. Rev. Microbiol. 2013;0:0-0.
#=GF WK   Cap-independent_translation_element
#=GF SQ   2


AY714213.1/3742-3812 CGCAGGUGUCGGAGGGAUCGCCAGCCCUCAGGAUAGUGAGCUCCCGCAGAGGGAUAAGCUAUCUCCCUGCG
JF713435.1/3723-3793 CGCAGGUGUUUGAGGGAUCGCCAGCCCUCAGGAUAGUGAGCUCCCGCAGAGGGAUAAGCUGUCCCCCUGCG
#=GC SS_cons         ((((((,,,,,<<<<<________>>>>>,,<<<<<<----<<<<_____>>>>--->>>>>>,,))))))
#=GC RF              CGCaGGUGUuuGaGGGAUCGCCAGCCCuCAGGauaGuGAGCuCCCGCAGAGGGaUAAgCuauCuCCCuGCG
//
# STOCKHOLM 1.0

#=GF AC   RF02523
#=GF ID   ROSE_3
#=GF DE   Repression of heat shock gene expression (ROSE) element
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:23741480
#=GF SS   Predicted; PMID:23741480
#=GF GA   43.00
#=GF TC   43.30
#=GF NC   41.50
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   23741480
#=GF RT   Short ROSE-Like RNA Thermometers Control IbpA Synthesis in Pseudomonas
#=GF RT   Species.
#=GF RA   Krajewski SS, Nagel M, Narberhaus F
#=GF RL   PLoS One. 2013;8:e65168.
#=GF WK   Repression_of_heat_shock_gene_expression_(ROSE)_element
#=GF SQ   16



AEWE01000693.1/596-529             UACGCGAUGCCGAAUUCGGGUCGCGCA-AU--GAU-UUA-CUUGCUGAUAC---UCAGGAG---UUUAUGACCAUGACU
CT573326.1/1712655-1712723         UACGCGAUGCCGAAGUCGGGUCGCGUA-GU--GAC-UUAACUUGCUGAAUC---UCAGGAG---UUCAUGACCAUGACU
AGFS01074928.1/18-86               UACGCGAUGCCGAAUUCGGGUCGCGCA-GU--GACUUUA-CUUGCUGAAUC---UCAGGAG---UUUAUGACCAUGACU
CP002727.1/3297127-3297060         CGUGGGAUGCCGAAGUCGGGUCCCGCA-AC--UUA-UCA-CUCGCUGACUA-AUUCAGGAG---AUUA--ACCAUGAGC
AACY023936647.1/161-227            UGCGGGAUGCCGAAGUCGGGUUCCGCG-AU--AUG-AAC-CUUGCUGAAAU--UUCAGGAG---AAUA--CUCAUGAGC
Y11280.1/1592-1658                 UGCGGGAUGCCGGAGCCGGGUCCCGCG-AC--AGA-AUG-CUCGCUGAUCU--AUCGGGAG--AC---UGACGAUGUCC
AEAZ01000032.1/24229-24162         UACGCGAUGCCGAAUCCGGGUCGCGUA-UU--AAA-UCA-CUUGGAGAAAA--CUCAGGAG-AUU-UU--GCAAUGGCU
CADX01000007.1/20354-20287         UACGCGAUGCCGAAUUCGGGUCGCGGA-GA--UAA-CCA-CUCGCUGAAUA--AUCAGGAG----AAACACCCAUGAGU
CP002881.1/1746579-1746643         AGCGGGAUGCCGAAGUCGGGUCCCGCC-CG--UUU-CAA-CUCGCUGAUU----UCAGGAG---GUUU--AUCAUGAGU
AFOY01000083.1/61144-61073         UACGCGAUGCCGAAUUCGGGUCGCGGAGAC--AAA-AAA-CUUGCUGAUUGUUUUCAGGAG--AU-UUGAAUCAUGAGU
CP002585.1/4735082-4735011         UACGCGAUGCCGAAUUCGGGUCGCGGA-GACAAAA-AAA-CUUGCUGAUUU-UUUCAGGAG--AU-UUGAAUCAUGAGU
AGSX01000198.1/10013-9948          CACAGGAUGCCGAAUUCGGGUCCUGUA-U---GAA-CCA-CUCGCUGAAUG---UCAGGAG--AU--AGCAAAAUGACU
CP001157.1/3905282-3905216         UGCGGGAUGCCGAAGUCGGGUCCCGAG-CU-UAAC-AAA-CUCGCUGAUAU---UCGGGAG--AU---UGAACAUGGCU
AGTN01523214.1/95-28               UAAGGGAUGCCGAAGUCGGGUCUCUGU-CU-CAAU-GAA-CUUGCCGAUAA--UUCGGGAG--AU---UGAAUAUGGCU
CP000712.1/4238354-4238287         UACGCGAUGCCGAAGCCGGGUCGCGUA-AU--GAC-UUA-CUUGCUGAAUC---UCAGGAG---UUUAUGACCAUGACU
AE004091.2/3509227-3509161         UGCGGGAUGCCGAAGACGGGUUCCGCA-UC--AGA-GUA-CUUGCUGAUAA--UUCAGGAGAUUC-----GCAAUGAGC
#=GC SS_cons                       <<<<<<<<-<<<____>>>>>>>>>>>.--..-<<.---.<<<-<<<<___.._>>>>>>>..>>.:::::::::::::
#=GC RF                            ugCGgGAUGCCGAAgUCGGGUCcCGca.au..aac.uuA.CUuGCuGAuua..uUCaGgAG..gu.UaugAccAUGAcU
//
# STOCKHOLM 1.0

#=GF AC   RF02524
#=GF ID   sagA
#=GF DE   Streptococcus sRNA sagA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   60.00
#=GF TC   76.90
#=GF NC   47.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23762235
#=GF RT   Novel Regulatory Small RNAs in Streptococcus pyogenes.
#=GF RA   Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH
#=GF RL   PLoS One. 2013;8:e64021.
#=GF WK   Bacterial_small_RNA
#=GF SQ   6


AE014074.1/529786-529944       CAACUAA-GUUAUCUUUGGUAACUUCUG-AUUA-UAGAUGAAUGGCAUAGAGGUGUUA-GAAAACAUGAGACAAAAGUAAUCUUCUUGAUGCUAGCGUCUC-AGGUAAUUAGCAGGUACU-----AGACAGUACCUGCUAAUUACUAUAUGUUUAGUAAAAUGAGAUAG
AB520742.1/180-337             CGACUAG-GUUACCUAUCGUAACAGUUG-GUGA-GACUAGUAUUAAAUGGAGGUGUUA-GGA--CAUGAGGCAGUGGUAAUCGUCUUGGUUCUAGUGUCUCGAGGUAAUUAGCAGGUACU-----AAGUGGUACCUGCUAAUUACUAUAUGUUUGGUAGAAUAAGAUAG
AENS01000034.1/150927-151089   CGACUCA-AUUACUAUUAGUAAUGUCUGUGUGA--UAUUAUCUGGCAUAGAGGUGUG--GGACGUAGGGGGCAGUA-UAAUUAUUUUGGUUUUAGUGUCCCUUGGUAGUUAGCAGGUACUAUUUAGUUUAGUACCUGCUAAUUACUAUAUGUUUUGUAGAAUAAGAUAG
CABY01000004.1/243111-243271   CGACUAAGAUUACAGUUUGUAAUUGAUG-GUGUUAGCUGGUGUUGGAUAGGGGUGUUA-CAUGACAAGAGACGAAGACAAUCAGCUUGAUGUCAACGUCUUGUAGUAAUUAGCAGGUACU-----AGUCGGUACCUGCUAAUUACUA-UUAUUUAUUAAUAUAUUACAG
AF465842.1/1401-1558           UAACUAU-ACUGCAUCUA--ACUUGUGAUGUCA--GCUCAUUUUGAAUAGGGAUGUUACAUGU-CACGAGACUGUUGUAAUCAUCUUGGUUCUCAUGUCUCAAGGUAAUUAGCAGGUACU-----AGUCAGUACCUGCUAAUUACUAUAUGUAUACUAGAAUAAUGUAG
AEUU02000001.1/1586390-1586549 CGACUAC-GUUACUAUUAGUAAUAACUCUGUUGAUUGUGAUUUGCCAUAGAGAUGUGA-GGACAUAUGAGGCAAGA-UAAUCAUUUUGGUUAUGGUGUCUCUAGGUAGUUAGCAGGUACU-----GAACAGUACCUGCUGAUUACCA-AUGUUUUAUAGAAUGAGAUAG
#=GC SS_cons                   :::::::.<<<<<_____>>>>>,,<<<--<__.__________>-->>>--------.(((-(,,,<<<<<<--<--<<<<_____>>>>->-->>>>>>,,<<<<<<<<<<<<<<<<<.....____>>>>>>>>>>>>>>>>>,,,)-))):::::::::::::::
#=GC RF                        CgACUAa.guUAcuuuUagUAacugcugUGcua.uacUuaUuUugaAuagaGgUGUuA.ggauacAuGaGaCgauggUaAuCaUcUUGgUuucagcGuCuCuagGUAaUuAGCAGGUACu.....agucaGUACCUGCUaAuUACcAUAuGucuagUAgAAUAAgAUAG
//
# STOCKHOLM 1.0

#=GF AC   RF02525
#=GF ID   SSRC30
#=GF DE   Streptococcus sRNA SSRC30
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   100.00
#=GF TC   182.70
#=GF NC   37.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23762235
#=GF RT   Novel Regulatory Small RNAs in Streptococcus pyogenes.
#=GF RA   Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH
#=GF RL   PLoS One. 2013;8:e64021.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


CP003068.1/1229328-1229478 AUAGUGACUCCACUCUAGCUAGUUAAGCUUGCUAAGAGAAUAACGGUAUCCUGGAACUCCUAAAACAUGUUACUACAAGACAAGUCUUGAUAACAAUAUAACUUUUAGCUAAGAAUAACUAACAGCAACAUCAAAAAGAGGAUUUAUGAAA
AE009949.1/1313179-1313328 AUAGUGACUCCACCCUAGCUAGUUAAGCUUGCUAAGAGAAUAACGGUAUCCUGGAACUCCUAAAACA-GUUACUACAAGACAAGUCUUGAUAACAAUAUAACUUUUAGCUAAGAAUAACUAACAGCAACAUCAAAAAGAGGAUUUAUGAAA
AM295007.1/582206-582057   AUAGUGACUCCACCCUAGCUAGUUAAGCUUACUAAGAGAAUAACGGUAUCCUGGAACUCCUAAAACAUGUUACUACAAGACAAGUCUUGAUAACAAUAUAACUUUUAGCUAAGAAUAACUAACAGCAACAUCAAAAAGAGGAUUUAUGGA-
#=GC SS_cons               :::[[[[-[[[,,,,,,((((((((--(((((((((((,,<<<<<-------<<____>>------->>>>>,,,<<<<<____>>>>>,,,,,,,,,,,,))))))))-)))--)))))---))),,,,<<_____>>]]]-]]]]::::
#=GC RF                    AUAgugaCuCCACcCUAGCuaGuuaAGCuugCuaagaGAAuaaCgGUAUCCUGGAACUCCUAAAACAcGuuaCUACaaGaCAAGuCuuGAUAACAAUAUAACucuuaGcUaaGAAuaaCuAACaGCAACAuCAAAAAGaGGaUucacGaAA
//
# STOCKHOLM 1.0

#=GF AC   RF02526
#=GF ID   SSRC34_1
#=GF PI   SSRC34;
#=GF DE   Streptococcus sRNA SSRC34
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   64.00
#=GF TC   65.70
#=GF NC   60.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23762235
#=GF RT   Novel Regulatory Small RNAs in Streptococcus pyogenes.
#=GF RA   Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH
#=GF RL   PLoS One. 2013;8:e64021.
#=GF CC   It is based on computationally predicted coordinates (RNAz). 
#=GF WK   Bacterial_small_RNA
#=GF SQ   16


AP012053.1/392234-392108       UGAAAACGUUUUACAAUAAUAUCGUUCUUA-AAUUUCCUUGAAACGGAAAAGAAUUGCCAAGUUCGC--------------UUGGAAGGAGAUUAUUCUUUUUUGUUUCAACGAAAAAUAUUUAAA--AGGAGGAAGAACAAGA
AE009948.1/373841-373713       UGAAAACGUUUUAAAAUAUAUCUGUUCUAU-AAUUUCGUUGAAAUGAAAAAGAAUGGCCAAUUUUACG------------AUUGGAAGGAGAUUAUUCUUCUUUAUGUCAACGAAAAAAUUUUUUA--AGGAGGAAGAACAAGA
AE014074.1/1503278-1503407     UGAAAACGUUUUAAAAUAGAAACGUUCUUG-AAUUUCGUUUAAGUGAAAAAGAAUUGCCAAAAUUUAGU-----------UUUGGAAGGAGAUUAUUCUUCUUCAUUUCAACGAAAAAUAUUUUAA--AGGAGGAAGAACAAGA
AENS01000010.1/24724-24864     UGAAAACGUUUUAAAAUAGAGACGUUCUUG-AAUUUCGUUUAAAGGGAAAAGAAUUGCCAAAUACCCCACAAGA-GGGCCGUUGGAAGGAGAUUAUUCUUUUUCAUUUCAGCGAAAAAAUUUUUAA-AAGGAGGAAGAACAAGA
AEUT02000001.1/1178435-1178564 UGAAAACGUUUUAAAAUAAAGACGUUCUUG-AAUUUCGUUUUUUUGAAAAAGAAUUGCCAAAAUUAAU------------UUUGGAAGGAGAUUAUUCUUCUUCAAGUUAACGAAAAAAAAUAUUA-AAGGAGGAAGAACAAGA
AEUW02000001.1/1313018-1313140 UGAAAACGUUUUAAAAUAAUAUCGUUCUUA-AAAUUUCUUUAAAGAAAGAAGAAUGG-UAUUUCUUCU-------------AUA----AAGUUCCUUCUUCUUUUGUCUAAGAAAAAAAUAUUAUA--AGGAGGAAGAACAAGA
AEUX02000001.1/289934-289806   UGAAAACGUUUUAAAAUAGAGACGUUCUUG-AAUUUCGUUUAAGUGAAAAAGAAUUGCCAAAUUUAUU-------------UUGGAAGGAGAUUAUUCUUCUUCAUUUCAACGAGAAAUAUUUUAU-AAGGAGGAAGAACAAGA
CP001129.1/451169-451040       UGAAAACGUUUUAAAAUAGAGACGUUCUUG-AAUUUCGUUUAAGUGAAAAAGAAUUGCCAAAUGCUAU-------------UUGGAAGGAGAUUAUUCUUCUUCAUUUCAACGAAAAAUAUUUUAAUAAGGAGGAAGAACAAGA
ABJK02000010.1/18147-18020     UGAAAACGUUUUACAAUAAUAUCGUUCUUAAAAUUUCCUUGGAACGGAAAAGAAUUGCCGGACUUGU--------------CCGGAAGGAGAUUAUUCUUUUUUGUUUCAACGAAAAAUAAUAAUA--AGGAGGAAGAACAAGA
AM946015.1/1475905-1476033     UGAAAACGUUUUAAAAUAGAGACGUUCUUG-AAUUUCGUUUAAAAGGAAAAGAAUUGCCAAAUGAUU--------------UUGGAAGGAGAUUAUUCUUUUUCAUUUCAACGAAAAAAAAAUAUAUAAGGAGGAAGAACAAGA
AB114606.1/996-1123            UGAAAACGUUUUACAAUAAUAUCGUUCUUAAAAUUUCCUUGGAACGGAAAAGAAUUGCCGGACUUGU--------------CCGGAAGGAGAUUAUUCUUUUUUGUUUCAACGAAAAAUAAUCAUA--AGGAGGAAGAACAAGA
AEVB01000039.1/6784-6911       UGAAAACGUUUUACAAUAAUAUCGUUCUUAGAAUUUCCUUGGAACGGAAAAGAAUUGCCAAGCUUGC--------------UUGGAAGGAGAUUAUUCUUUUUUGUUUCAACGAAAAAUAAUCAUA--AGGAGGAAGAACAAGA
AEUU02000001.1/1005660-1005801 UGAAAACGUUUUAAAAUAGAGACGUUCUUG-AAUUUCGUUUAAAUGGAAAAGGAUUGCCAACUGUCAGACAAAAAUAACAGUUGGAAGGAGAUUAUUCUUUUUCAUUUUAGCGAAAAAAUUUUUAA-AAGGAGGAAGAACAAGA
AEUZ02000001.1/339175-339048   UGAAAACGUUUUAAAAUAGUUAUGUUCUUG-AAUUUCGUUAAAUUGAAAAAGAAUUGCCAAUUUUUUA-------------UUGGAAGGAGAUUAUUCUUCUUCAGUUCAGCGAAAAAUAUAAUAU--AGGAGGAAGAACAAGA
CP002471.1/241746-241619       UGAAAACGUUUUAAAAUAAAGACGUUCUUG-AAUUUCGUUU-UUUGAAAAAGAAUUGCCAAAAUUAAU------------UUUGGAAGGAGAUUAUUCUUCUUCAAGUUAACGAAAAAAAUAUUAA--AGGAGGAAGAACAAGA
FM204883.1/481172-481043       UGAAAACGUUUUAAAAUAGAGACGUUCUUG-AAUUUCGUUCAAGUGAAAAAGAAUUGCCAAAUGCUAU-------------UUGGAAGGAGAUUAUUCUUCUUCAUUUCAACGAAAAAUAUUUUAAUAAGGAGGAAGAACAAGA
#=GC SS_cons                   :::::<<<<<<<______>>>>>>><<<<-.--<<<<<<<-<<<<<<<<<<<<<<--<<<<_______.............>>>>--------->>>>>>>>>>>>>>->>>>>>>----------..------>>>>::::::
#=GC RF                        UGAAAaCGucuuAaAAUAaagaCGuuCuug.AAuuuCguuuaagcgaagaaGaauuGCCaaauuuuuu.............uuGGAAGGAGAUUauuCuucuucgcuucaacGaaaAAaauuuuaA..AGGAGGaaGaACAAGA
//
# STOCKHOLM 1.0

#=GF AC   RF02527
#=GF ID   SSRC38
#=GF DE   Streptococcus sRNA SSRC38
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   123.30
#=GF NC   58.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23762235
#=GF RT   Novel Regulatory Small RNAs in Streptococcus pyogenes.
#=GF RA   Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH
#=GF RL   PLoS One. 2013;8:e64021.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3


AY464086.1/106-271         UAGAGAGAACCAAUUUGGUUCUCUCUAUUUUUUUAUAUGUGCUACCUCAUCAAAAAGAAGUUAGGACAAAUAGCUGUCAACAAUUGCCUUUUGCUUAUCCCUUCAGUUGAUGUGAU----------------AAAAGAUGGUAGUUGCCCUUGACAAAGCAUUGAUAAAGGAGUAAAAUUAA
AE014074.1/1742292-1742111 UAGAGAGAACCAAUUUGGUUCUCUCUAUUUUUUUAUAUGUGCUGCCUCAUCAAAAAGAAGUUAGGACAAAUAGCUGUCAACAAUUGCCUUUUGCUUAUCUCUUCAGUUGCUGUGAUUUUAUCAUACAGUGAUAAAAGAUGGUAGUUGCCAUUGACAAAGCAUUGAUAAAGGAGUAAAAUUAA
AE004092.1/1675642-1675477 UAGAGAGAACCAAUUUGGUUCUCUCUAUUUUUUUAGAUGUGCUGCCUCAUCAAAAAGAAGUUAGGACAAAUAGCUGUCAACAAUUGUCUUUUGCUUAUCUCUUCAGUUGCUGUGAU----------------AAAAGAUGGUAGUUGCCAUUGACAAAGCAUUGAUAAAGGAGUAAAAUUAA
#=GC SS_cons               :<<<<<<<<<<_____>>>>>>>>>>((((((((((--(((((,,,,,,,,,,,,,,,,,,<<<<-<<<<--<<___________>>-->>>>>>>>,,,,,,<____>,,,<<--................----<<<<<<____>>>>>>-->>,)))))--))))))))))::::::::
#=GC RF                    UaGaGaGaaCCAAUUUGGuuCuCuCuauuuuuuuauAUguGCugCCUCAUCAAAAAGAAGUuagGACaaaUAgCUGUCAACAAUUGcCUuuuGCuuaUCuCUUCAGUUGcUGuGAU................AAAAgauGGuAGUUgCCauuGACaAaGCauUGauaaaggaguAAAAUUAA
//
# STOCKHOLM 1.0

#=GF AC   RF02528
#=GF ID   SSRC41
#=GF DE   Streptococcus sRNA SSRC41
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   60.00
#=GF TC   60.40
#=GF NC   44.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23762235
#=GF RT   Novel Regulatory Small RNAs in Streptococcus pyogenes.
#=GF RA   Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH
#=GF RL   PLoS One. 2013;8:e64021.
#=GF WK   Bacterial_small_RNA
#=GF SQ   8


CP002215.1/2071424-2071314     AAGCUCUU--CUGGAGCUUUUUUUCG-UACCUUCUUGACUUGAAAUUCUUGUUUAUUAUUAAAAAAUGAGCUAUAAUAAAGCAUAGCACUUAAUUUUAGAAAGAAGGUGUAAGU
FM204884.1/2063424-2063315     AAGCUCGA--ACAGAGCUUUUUU--AAUAUCCUAACAAAUCUGAUUUCUUGUUUAUUCAAUAAAAAUAAGCUAUAAUAGAGCGUAGCACUUAAAGUUAGAAAGAAGGUGUAAGU
CP000017.1/1765339-1765228     AAGCUCUU--GUAGAGCUUUUUUUAAAUACCUUCUUCGCUUGAAAUUCUUGUUUAUUUAAUAGAAAUAAGCUAUAAUAAAGCAUAGCACUUAAUUUUAGAAAGAAGGUGUAAGU
FM204883.1/2160295-2160185     AAGCUCUG--UCAGAGCUUUUUUU-AAUAUCCUAACAAAUCUGAAUUCUUGUUUAUUCAAUAAAAAUAAGCUAUAAUAGAGCGUAGCACUUAAAGUUAGAAAGAAGGUGUAAGU
AEUX02000003.1/88122-88228     AAGCUCCU--A-GGAGCUUUUUU--AUUUUCCCAUUAC--UUGAAUUCUUGUUUAUUCCUAAAAAAUAGGCUAUAAUAAAGCAUAGCAUUUAAUUUUAGAAAGAAGGUGUAAGU
AM946015.1/1763488-1763382     AAGCUCAU--AU-GAGCUUUUUUUGA--UUGUUCAUAACUA-GAUUUCUUGUUAAAUCUCAAAAAAUAAGCUAUAAUUAAUCAUAGCACUUA-GUUUAGAAAGAAGGUGUAAGU
AENS01000022.1/68512-68405     GCUCUAUU--UAUGAGCUUUUUUU--AUGUUCUAAUAACUA-GAUUUCUUGUUAAUUAUCAAAAAAUAAGAUAUAAUAUAUGAUAGCACUUA-GUUUAGAAAGAAGGUGUAAGU
AEUU02000001.1/1290061-1289952 AAGCUCUGUUUAGGAGCUUUUUUU--AUGUUCUAAUAACUA-GAUUUCUUGUUAAUUAUCAAAAAAUAAGCUAUAAUAUAUCAUAGCACUUA-GUUUAGAAAGAAGGUGUAAGU
#=GC SS_cons                   ::<<<<<<..----<<<<<-<<<<.--------<<<<____________>>>>--------->>>>->>>>>---->>>>>>---<<<<<<_____________>>>>>>::::
#=GC RF                        AAgcUcug..uuaGAGCuuUUUUu.AAUaUccUaacaacUuugAuUUCUuguuuAUUauaaAaAAAUaaGCUAUAAcagAgcAUAgCACuUAAuuUUAGAAAGAAgGUGuAAGU
//
# STOCKHOLM 1.0

#=GF AC   RF02529
#=GF ID   SSRC8_1
#=GF PI   SSRC8;
#=GF DE   Streptococcus sRNA SSRC8
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; CMfinder
#=GF SS   Predicted; CMfinder
#=GF GA   80.00
#=GF TC   89.00
#=GF NC   43.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   23762235
#=GF RT   Novel Regulatory Small RNAs in Streptococcus pyogenes.
#=GF RA   Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH
#=GF RL   PLoS One. 2013;8:e64021.
#=GF CC   It is based on computationally predicted coordinates (RNAz). 
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



AM295007.1/1492343-1492492         CAGUUUGGCUUGCUUUUAUGGUCUUUAUGUCUGUUUCUUACUUUGCUCAACUCUUUAACUUUUGUUAAGAAAUGAUCAUCUGCCAGCUCAAUUUCAAAGAAAGGUCCGACUGUUAAAAGGGAUGAUUUGUUGUCUCUUUGCGUUUUGUUA
AE014074.1/339703-339554           CAAACUGGCUUGCUUUUAUGGUCUUUAUGUCUGUUCCUUACUUUGCUCAACUCUUUAACUUUUGUUAAAAAAUGAUCAUCUGCCAGCUCAAUCUCAAAGAAAGGUCAGACUGUUAAAAGGGAUGAUUUGUUGUCUCUUUGCGCUUUGUUA
CP000003.1/379254-379105           CAAACUGGCUUGCUUUUAUGGUGUUUAUGUCUGUUCCUUACUUUACUCAACUCUUUAACUUUUGUUAAGAAAUGAUCAGCUGCCAGCUCAAUCUCAAAGAAAGAUCCGACUGUUAAAAGGGAUGAUUUGUUGUCUCUUUGCGUUUUGUUA
#=GC SS_cons                       ::(((-(((--((,,,,,,,,,,,,,,,<<<-<---<<<-<<<<--<<<----<<<<<<____>>>>>>--->>>-------------------->>>>->>>-->->>>,,,,,<<<<<<<<<<____>>>>>>>>>>)))))--))):
#=GC RF                            CAaacUggCUUGCUUUUAUGGUcUUUAUGuCUGUUcCuuACuuugCuCaACUCcuuaaCUUUUGuuaagAAAuGaUCAuCUGCCAGCUCAAUcUCaaaGAaaGgUCcGaCUGUUAaaaGgGaugaUUUGuuguCuCuuuGCGcuUUguuA
//
# STOCKHOLM 1.0

#=GF AC   RF02530
#=GF ID   URE2_IRES
#=GF DE   Ure2 internal ribosome entry site (IRES)
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:15314170
#=GF SS   Published; PMID:15314170
#=GF GA   70.00
#=GF TC   100.50
#=GF NC   44.30
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   18460470
#=GF RT   A small stem loop element directs internal initiation of the URE2 internal
#=GF RT   ribosome entry site in Saccharomyces cerevisiae.
#=GF RA   Reineke LC, Komar AA, Caprara MG, Merrick WC
#=GF RL   J Biol Chem. 2008;283:19011-19025.
#=GF WK   Ure2_internal_ribosome_entry_site_(IRES)
#=GF SQ   5


M35268.1/386-490           CAAAAUAAUGAUAACGAGAAUAAUAUCAAGAAUACCUUAGAACAACAUCGACAACAACAACAGGCAUUUUCGGAUAUGAGUCACGUGGAGUAUUCCAGAAUUACA
ABPO01000267.1/13719-13823 CAAAAUAAUAACAACGAGAACAAUAUCAAAGAUACUCUAGAACAGCAUCGACAACAGCAGCAGGCAUUCUCGGAUAUGAGUCAUGUGGAGUAUUCAAGAAUUACA
AABZ01001021.1/234-130     CAAAAUAAUGACAACGAAAAUAACAUCAAGGAGACAUUGGAACAGCAUCGGCAACAGCAACAGGCCUUUUCAGGUAUGAGUCACGUGGAAUAUUCCAGAAUUACA
AACI02000253.1/4811-4707   CAAAAUGAUGACAACGAAAACAACAUCAAAGAUACAUUGGAACAACAUCGACAACAACAGCAGGCGUUUUCUGAUAUGAAUCGCGUGGAGUACUCAAGAAUUACA
AABY01000018.1/18868-18764 CAAAGUAAUGACAACGGAAAUAACAUCAAGGAUACCUUAGAACAACAUCGACAACAACAACAGGCAUUUUCGGAUAUGAGUCACGUGGAGUAUUCCAGAAUUACA
#=GC SS_cons               :::::::::::::<<<-<<---<<<<<-<<<<<<<<<________________________>>>>>>>>>-->>>>>--->>->>>:::::::::::::::::::
#=GC RF                    CAAAAUAAUgAcAaCGAgaAuAauauCAaggauaCcuUaGAACAaCAUCGACAACAaCAaCagGcauucuCgGauauGAgucACGuGGAgUAUUCaAGAAUUACA
//
# STOCKHOLM 1.0

#=GF AC   RF02531
#=GF ID   NRF2_IRES
#=GF DE   Nrf2 internal ribosome entry site (IRES)
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:19934254
#=GF SS   Published; PMID:19934254
#=GF GA   50.00
#=GF TC   52.60
#=GF NC   44.20
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   19934254
#=GF RT   An internal ribosomal entry site mediates redox-sensitive translation of
#=GF RT   Nrf2.
#=GF RA   Li W, Thakor N, Xu EY, Huang Y, Chen C, Yu R, Holcik M, Kong AN
#=GF RL   Nucleic Acids Res. 2010;38:778-788.
#=GF WK   Nrf2_internal_ribosome_entry_site_(IRES)
#=GF SQ   20



ACFV01059192.1/6065-5938           UGAGC--CGC-C-C-UGUCC---------------GCGCCGCACCUCGGCAGCCGGAACAGGGCAGCC-GUCGGGG-AGCC-CCAACGCA-CA-GU--CC---------UCAG-CUCAGCAUGAUGGACUU-GGAGCUGCCGCCGCCG-GGACUCCCGUCCCAGCAG
ACBE01583330.1/253-380             UGUGC--CGC-C-C-AGUCC---------------GCGCCGCGCCUCGGCACCUGGGACAAGGCUGCC-GUCGGGG-AGCG-CCACACCA-CG-GU--CC---------CCAG-CUCAUCAUGAUGGACUU-GGAGCUGCCGCCGCCC-GGACUGCCGUCCCAGCAG
AGTP01035618.1/20905-20780         AGUGC--UGC-C-C-UGUCC---------------GCGCCGCGCUUUGGCAGCCGGGACAGGGUCGCC-GUCGAGG-AGCC-CCAACG---CA-GU--CU---------CCAG-CUCAGCAUGAUGGACAU-GGAGUUGCCGCCGCCA-GGACUGCCGUCCCAGCAG
AEYP01083926.1/6303-6176           GCCGC--CGC-C-C-GGUCC---------------GCGCCGCGCCUCGGCAACUGGGACACAGCCGCC-GUCGGGG-AGCG-CCAGAACA-CG-GU--CA---------CCAG-CUCAUCAUGAUGGACUU-GGAGCUACCGCCGCCC-GGACUGCCGUCCCAGCAG
BT030494.1/9-136                   AGUAC--CGC-C-G-UGUCC---------------GCUCCAAGCCUCGGCAGCCGGAACAGGGCCGUC-GUCGGGG-AGCC-UCAAAGCA-CC-GU--CC---------UCAG-CUCAGCAUGAUGGACUU-GGAGCUGCCGCCGCCG-GGACUGCCGUCCCAGCAG
ABRN01280247.1/722-595             --AGUACCGC-C-C-UGUCC---------------UCACCGCGCCUCGGCAGCCGGGACAGGGCCGCC-GUCGGGG-AGCC-UCAGAGCA-CC-GU--CC---------CUAG-CUCAGCAUGAUGGACUU-GGAGCUGCCGCCGCCG-GGACUGCCGUCCCAGCAG
AAPY01822907.1/1150-1281           AGUGC--UGC-C-C-UGUCC---------------GCGCCGCGCCUCGGCAGCCGGGACAGGGUCGCC-GUCGGGG-AGCU-ACAGCGCA-CG-GC--CCCA-----GCCCAG-CCCAGCAUGAUGGACUU-AGAGCUGCCGUCGCCG-GGACUAGAGUCCCAGCAG
AAGV020659894.1/2529-2402          ACCGC--CGC-C-C-CGUCC---------------GCGCCGCGGCUCGGCAGCCGGAACAGGCCCGCC-GUCGAGG-AGCC-GCAGCGCA-CG-GU--CG---------GCAG-CUCGGCAUGAUGGACUU-GGAGCUGCCGCCGCCG-GGACUGCCGUCCCAGCAG
AAQR03082811.1/11-138              UGUGC--UAC-C-C-UGUCC---------------ACGCCUCGCCUCGGCAGCCAGGGCAGGGCCGCC-GUCGAAG-AGCC-CCAAUACA-CG-GU--CC---------CCAU-CUCAGCAUGAUGGACUU-GGAGCUGCCGCCGCCG-GGACUGCCGUCCCAGCAG
ABRR01575001.1/1010-883            AGUGC--CGC-C-C-UGUCC---------------GAACCCUGCCUGGGCAGCCGGGACAGGGCCGCC-GUCGCGG-AACC-CCAGAGCA-CG-GU--CC---------CCAG-CUCAGCAUGAUGGAUUU-GGAGCUGCCACCGCCG-GGACUGCCGUCCCAGCAG
ACTA01178145.1/221-95              UCCGC--AGC-C-G-GGUCC---------------GCGCCGCGCCUCGGCAGCUGGGACAGGGCCGCC-GUCGGGG-AGCG-CCAGAGCA--G-AU--CC---------CCAG-CUCAUCAUGAUGGAUUU-GGAGCUGCCGCCGCCC-GGACUGCCGUCCCAGCAG
ABRP01048301.1/1286-1159           AGUGC--CUC-C-G-GGUCC---------------UCGCCGCGCCUCGCCAGCCGGGACAGGGUCGCC-GUCGGGG-AGCU-CCAGAGCA-CG-GU--CC---------CCAG-UACAGCAUGAUGGACUC-GGAGCUACCGCCGCCG-GGACUACCGUCCCAGCAU
AAYZ01649973.1/533-404             AGUGC--CGC-C-C-UGUCC---------------GCGCCGCGCCUCUGCAGCCGGGACAGGGUCGCC-GUCGGGA-AGCC-UCAGUACC-GG-GUUCCC---------CUGA-UUCAGCAUGAUGGACUU-GGAGCUGCCGCCGUCG-GGACUACAGUCCCAGCAG
AAGU03010213.1/33415-33537         ----A--GUG---C-CGCCC---------------UGUCCGCACUUCGGCAGCCGGGACAGGGCCGCC-GUCGGGG-AGCC-CCAGCGCA-CA-GU--CC---------CCAG-CUCAACAUGAUGGAUCU-GGAGCUGCCGUCGCCG-GAACUACCGUCCCAGCAG
AAGW02003945.1/87921-88043         GGAGC--CGC-C-A---------------------GCGCCGCUCCUCGGCAGCUGGGGCAGGGUCGCC-GUCGGGA-AGCC-CCAGCGC--CGCGU--CC---------CCAG-CUCAGCAUGAUGGACUU-GGAGCUACCGCCGUCG-GGACUGCAGUCCCAGCAG
ABRO01173918.1/6836-6706           GGAGC--CGC-CGC-CGUCC---------------GCGCCGCGCCUCAGCCGCCAGCGCAGGGUCGCC-GUCGGGGGAGCCGCCAGCACA-CG-GG--CC---------UCGG-CUCAGCAUGAUGGACCU-GGAGCUGCCGCCGCCG-GGACUGCCGUCCCAGCAG
ABRQ01668956.1/783-652             ----A--CCG----------CUGCCACUACCGCCCUGUCCACACUUCGGCAUCUGGGACAGGGCCGCC-GUCGGGG-AGCG-CCAGCGCA-UA-GU--CC---------UCAG-CUCAGCAUGAUGGAUUU-GGAGCUGCCGUCGCCA-GAACUGCCUUCCCAGCAG
AFTD01070349.1/15198-15322         ----C--GGGCC-CCUGCCG---------------CCGCCGCACCUCGGCAGCCAACGUAGCGUCGCC-GUCGGGG-AUCC-UCAGUGCAGCG-UU--CG---------UC---CUCAGCAUGAUGGACUU-GGAGUUGCCGCCGCCA-GGACUACAGUCCCAGCAG
AALT01281544.1/1069-1208           CGUGC--AAC-C-C-UGUCC---------------GCGCCGCGCUUCGGCCGCCGGGACGGGGUAGCCCGUCGGGA-AAGC-CUAGAGCA-CG-GG--CUUGCCUCUACCCAGAUUCAGCAUGAUGGACUUUGGAGCUGCCGCCGGCGGGGACUGC-GUCCCAGCAG
BC011558.1/31-158                  AGAGC--CGC-C-C-UGUCC---------------GCGCCGCGCCUCGGCAGCCGGAACAGGGCCGCC-GUCGGGG-AGCC-CCAACACA-CG-GU--CC---------ACAG-CUCAUCAUGAUGGACUU-GGAGCUGCCGCCGCCG-GGACUCCCGUCCCAGCAG
#=GC SS_cons                       :::<<..-<<._._._____...............>>>>,<<-<<<<<<<__________________.>>>>>>>.->>,.,,,,,,,,.<<.<<..--.........-<<<.<<<______________._>>>>>>-->>>>,,,.<<<<____>>>>::::::
#=GC RF                            aguGc..cgc.C.c.uGUCC...............gcgCCgcgCcuCGgCAgCcGGgACAGGGucGCC.GuCGggG.Agcc.cCAgagCA.cg.gc..Cc.........ccaG.CuCAGCAUGAUGGAcUU.GGaGCugCCgccgcCg.GGAcUgCcgUCCCAGCAG
//
# STOCKHOLM 1.0

#=GF AC   RF02532
#=GF ID   MNV_3UTR
#=GF DE   Murine norovirus 3'UTR
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Published; PMID:20053745
#=GF SS   Published; PMID:20053745
#=GF GA   70.00
#=GF TC   73.30
#=GF NC   56.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   20053745
#=GF RT   Functional analysis of RNA structures present at the 3' extremity of the
#=GF RT   murine norovirus genome: the variable polypyrimidine tract plays a role in
#=GF RT   viral virulence.
#=GF RA   Bailey D, Karakasiliotis I, Vashist S, Chung LM, Rees J, McFadden N,
#=GF RA   Benson A, Yarovinsky F, Simmonds P, Goodfellow I
#=GF RL   J Virol. 2010;84:2859-2870.
#=GF WK   Murine_norovirus
#=GF SQ   10



EU004681.1/7161-7389         ACAUCCCCUCUACCGAUCUCGGGUGGACGCUUGCCCUCCCUUCGUGGAGGUUCCUGGUCUCCGCGCGAUUACACGCCGGCGACUCAAGGCACCUACACGAACGGACGGUUCGUGUCUCUCCCUA-AGAUCGGGAGUAGCAGGGCAUAGGUUGGAAGAGAAAC-C--UUU-UGUGAAAAUGAUUUCUGCUUACUGCUUUCU----UU-UU---CCCUCAUUUUGUAGUAAUUAGAUGCAUUUU
AB435515.1/7161-7382         ACAUCCUCUCUGCCAAUCUCGGGUGGACGCUUGCCCUCCCUUCGUGGAGGUUCCUGGUCUCCGCGUGAUUACACGCCGGCGACUCAAGGCACCUACACGAACGGACGGUUCGUGUCCUUCCCUA-AGAUAGGGAGUAGCAGGGCAUAGGUUGGAAGAGAAAC-C--UUU-UGUGAAAAUGAUUUCUGCUUACUGCUUUCU----UU-CCUUU----------GUAGUAAUUAGAUGCAUUUU
EU004680.1/7164-7386         ACAUCCCCUCUGCCAGUCUCGGGUGGACGCUUGCCCUCCCUUCGUGGAGGUUCCUGGUCUCCGCGUGAUUACACACCGGCGACUCAAGGCACCUACACGAACGGACGGUUCGUGUCCUUCCCCA-AGAUUGGGAGUAGCAGGGCAUAGGUUGGAAGAGAAAC-C--UUUCUGUGAAAAUGAUUUCUGCUUACUGCUUCUU----UC-UUUUA----------GUAGUAUUUAGAUGCAUUUU
EU004674.1/7161-7382         ACGUCCCCCUUGCCAGUCUCGGGUGGGCGCUUGCCCUCCCUUCGUGGGGGUUCCUGGUCUCCGCGUGAUCACACGCCGGCGACCCAAGGCACCUACACGAACGGACGGUUUGUGUCCUUCCCAA-AGAUUGGAAGUAGCAGGGCAUAGGUUGGAAGAGAAAC-C--UUU-UGUGAAAAUGAUUUCUGCUUACUGCUUCUU----UU-CUUUU----------GUAGUAAUUAGAUGCAUUUU
EU004676.1/7161-7383         ACAUCCCCUCUACCGGUCUCGGGUGGACGCAUGCCGUCCCUUCGUGGAGGUUCCUGGUCUCCGCGUGAUUACACGCCGCAGACCCAAGGCACCUACACGAACGGGCGGUUUGUGUCCUUCCCAA-AGAUCGGGAGUAGCAGGGCAUAGGUUGGAAGAGAAAC-C--UUUCUGUGAAAAUGAUUUCUGCUUACUGCUCUUU----UC-UUUUG----------GUAGUAUUUAGAUGCAUUUU
FJ446720.1/7161-7384         ACAUCCCCUCUACCGGUCCCGGGUGGGCGCGUGCCGUCCCUUCGUGGAGGUUCCUGGUCUCCGCGCGAUUACACGCCGCAGACUCAAGGCACCUACACGAACGGUCGGUUCGUGUCCUUCCCAA-AGAUCGGGAGCAGUAGGGCAUAGGUUGGAAGAGAAACCC--UUU-UGUGAAAAUGAUUUCUGCUUACUGCUUCUU----UUCUUUUG----------GUAGUAUUUAGAUGCAUUUU
EU004663.1/7164-7390         ACAUCCCCUCUACCGGUCUCAGGCGGGCGCUUGCCGUCCCUUCGUGGAGGUUCCUGGUCUCCGCGUGAUUACACGCCGCAGACCCAAGGCACCUACACGAACGGGCGGUUUGUGUCCUUCCCAA-AGAUCGGGACUAGCAGGGCAUAGGUUGGAAGAGAAAC-A--UUUCUGUGAAAAUGAUUUCUGCUUACUGCUUUUUCUCUUU-UAGUA----------GUAGUAUUUAGAUGCAUUUU
EU004666.1/7161-7380         ACAUCCCCUCUACCGGUCUCAGGUGGGCGCUUGCCGUCCCUUCGUGGAGGUUCCUGGUCUCCGCGUGACUACACGCCACAGACCCAAGGCACCUACACGAACGGGCGGUUUGUGUCCUUCCCAA-AGAUCGGGAGCAGCAGGGCAUAGGUUGGAAGAGAAAC-C--UUUCUGUGAAAAUGAUUUCUGCUUACUGCUUUUC----UU-UC-------------UUAGUAUUUAGAUGCAUUUU
EU004683.1/7158-7381         ACAUCCCCUCUACCGGUCUCGGGUGGACGCACGCCGUCCCUUCGUGGAGGUUCCUGGUCCCCGCGUGAUUACACGCCACAGACCCAAGGCACCUACACGAACGGUCGGUUCGUGUCCUUCCCAAAAAAUCGGGAGUAGCAGGGCAUAGGUUGGAAGAGAAAC-CCUUUU-UGUGAAAAUGAUUUCUGCUUAUUGCUUUUC----U--UUUUA----------GUAGUAUUUAGAUGCAUUUU
EU004656.1/7161-7382         ACAUCCCCUCUACCGAUCUCGGGUGGACGCUUGCCCUCCCUUCGUGGAGGUUCCUGGUCCCCGCGCGACCAUACGCCGGCGACUCAAGGCACCUACACGAACGGACGGUUCGUGUCUCUCCCUA-AGAUCGGGAGUAGCAGGGCAUAGGUUGGAAGAGAAAC-C--UUU-UGUGAAAAUGAUUUCUGCUUACUGCUUUCU----UU-UCUUU----------GUGGUAGUUAGAUGCAUUUU
#=GC SS_cons                 :::::<<<<<<<<<<<<<<-<<<-<<<<<<--<<<-<<<-<<<<<<-<<<<-<<<<<<<-<<<-<<<______>>>>>>->>>>-->>>->>>>->>>>>>->>>->>>-->>>>>>-->>>--.>>>>>>>--->>>->>>>,,,<<<<<________>>>.>..>,,.,,,,<<<<<<---<<<<-<<<<<<<_____....__._____..........>>>>>>>->>>>-->>>>>>
#=GC RF                      ACAUCCcCucugCCgguCuCgGGUGGaCgCuUgCCguCCCuuCGuGGaGGuUCCugGuCuccGCGcGAuuAcACgCCggaGaCcCAaGGCaCCuACaCGaaCGGaCGGcUuGcGuCCuUCCcaA.aGaccGGGAgcagcaGgGCAUagGuuGGAAGAGAaaC.c..uUU.UGUGaaaauGAUUuCugCcuacugcUUuuu....Uu.uuuUa..........gcaguagUcaGaUGCauuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02533
#=GF ID   HAV_CRE
#=GF DE   Hepatitis A virus (HAV) cis-acting replication element (CRE)
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   PMID:18684812
#=GF SS   Published; PMID:18684812
#=GF GA   55.00
#=GF TC   55.40
#=GF NC   44.50
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   18684812
#=GF RT   Identification of a conserved RNA replication element (cre) within the
#=GF RT   3Dpol-coding sequence of hepatoviruses.
#=GF RA   Yang Y, Yi M, Evans DJ, Simmonds P, Lemon SM
#=GF RL   J Virol. 2008;82:10118-10128.
#=GF WK   Hepatitis_A_virus_cis-acting_replication_element
#=GF SQ   2



D00924.1/5890-6003         CAGAGGAUAAUGAAAGUGGAAUUCACUCAGUGUUCAAUGAAUGUGGUCUCCAAAACGCUUUUUAAAAAGAGUCCAAUUCAUCAUCACAUUGAUAGGAACAUGAUUAAUUUUCCU
M14707.1/5946-6059         CAGAGAAUUAUGAAAGUGGAGUUUACUCAGUGUUCAAUGAAUGUGGUCUCCAAAACGCUUUUUAGAAAGAGUCCCAUUUAUCAUCACAUUGAUAAAACCAUGAUUAAUUUUCCU
#=GC SS_cons               ::<<<<<<<<-----<<<<--<<<<-<<<<<<<---<<<<<<<-<<-<<<__________________>>>->>>>>>>>>---->>>>>>>>>>>->>>>--->>>>>>>>::
#=GC RF                    CAGaggauuaUGAAAguGgAauucaCuCaguGuUCAaugaaugUGGUCuCCAAAACGCUUUUUAaAAAGaGUCCcauucauCAUCaCauuGaugaaAcCauGAUuaaucuuCCU
//
# STOCKHOLM 1.0

#=GF AC   RF02534
#=GF ID   Noro_CRE
#=GF DE   Norovirus cis-acting replication element (CRE)
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   PMID:19735574
#=GF SS   Published; PMID:19735574
#=GF GA   35.00
#=GF TC   36.60
#=GF NC   34.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   19735574
#=GF RT   Phylogenetic prediction of cis-acting elements: a cre-like sequence in
#=GF RT   Norovirus genome?.
#=GF RA   Victoria M, Colina R, Miagostovich MP, Leite JP, Cristina J
#=GF RL   BMC Res Notes. 2009;2:176.
#=GF WK   Norovirus_cis-acting_replication_element
#=GF SQ   21



HM802552.1/355-406           AGUGGUCACCCGCACCACAUGCGGAAAAACGACUGCUGGAACGGGGAAUCCU
AB044366.2/3926-3977         AGCGGCCACCCGCACCACAUGCGGAAGAACGACUGCUGGAACGGGGAGUCCU
AB447432.1/3924-3975         AGUGGCCAUCCGCACCAUAUGCGGAAAAACGACUGCUGGAACGGGGAGUCCU
AY587987.1/3926-3977         AGUGGCCAUCCGUAUCACAUGCGGAAAAACGACUGCUGGAACGGGGAAUCCU
AB541318.1/3922-3973         AGUGGCCACCCGCAUCACAUGCGGAAAAACGACUGCUGGAACGGGGAGUCCU
FJ537136.1/3926-3977         AGUGGCCACCCGCACCACAUACGGAAAAAUGACUGCUGGAACGGGGAAUCCU
GQ845368.1/355-406           AGUGGCCAUCCGCACCACAUGCGGAAAAAUGACUGUUGGAAUGGGGAGUCCU
AB541232.1/3922-3973         AGCGGCCAUCCACACCACAUGCGAAAAAACGACUGCUGGAACGGGGAGUCCU
AB541321.1/3922-3973         AGCGGCCAUCCGCACCAUAUGCGGAAGAAUGACUGUUGGAACGGGGAGUCAU
U07611.2/3926-3977           AGUGGCCACCCACACCACAUACGGAAGAAUGACUGCUGGAAUGGGGACUCUU
EU921388.2/3926-3977         AGCGGCCACCCUUACCACAUGCGGAAGAACGAUUGCUGGAAUGGGGAGACUU
EU921353.2/265-316           AGUGGCCACCCACACCACAUAAGGAAAAAUGACUGCUGGAACGGGGACUCCU
AB242256.2/355-406           AGCGGCCAUCCUCACCACAUGCGGAAGAACGAGUGCUGGAACGGGGAGACUU
AY134748.1/3926-3977         AGCGGCCACCCCCACCACAUACGGAAGAACGAUUGCUGGAAUGGGGAGUCUU
FJ537135.1/3926-3977         AGUGGCCAUCCACACCAUAUACGGAAGAAUGAAUGCUGGAAUGGAGAUUCCU
DQ456824.1/3926-3977         AGUGGGUACCCCCACCACGUGCGCAAAAACGAGCACUGGAAUGGGGAAUCUU
FJ537138.1/3926-3977         AGUGGUCACCCACACCACAUACGGAAGAAUGAAUGCUGGAAUGGAGAUUCCU
DQ379714.1/1-50              --UGGCCACCCGCACCACAUGCGGAAGAAUGAAUGUUGGAAUGGAGAGUCCU
GQ845370.2/3932-3983         AGUGGCUACCCGCACCACGUGCGGAAGAAUGAACAUUGGAAUGGGGAAUCUU
EU424333.1/3923-3974         AGUGGCAGUCCCCACCACCUGAAGAAGAACGACCACUGGAAUGGAGACUCUU
EU794702.1/239-290           AGCGGCCAUCCGCACCACAUGCGGAAAAACGACUGCUGGAACGGGGAAUCCU
#=GC SS_cons                 :::<<---<<<<--<<<---<<<<________>>>>>>>-->>>>---->>:
#=GC RF                      AGUGGCCAcCCgCACCACAUGcGgAAgAAcGAcUgCUGGAAcGGgGAgUCCU
//
# STOCKHOLM 1.0

#=GF AC   RF02535
#=GF ID   ODC_IRES
#=GF DE   ODC internal ribosome entry site (IRES)
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Eberhardt R
#=GF SS   Predicted; mfold
#=GF GA   44.00
#=GF TC   44.30
#=GF NC   42.80
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   15905964
#=GF RT   Alternative splicing facilitates internal ribosome entry on the ornithine
#=GF RT   decarboxylase mRNA.
#=GF RA   Pyronnet S, Pradayrol L, Sonenberg N
#=GF RL   Cell Mol Life Sci. 2005;62:1267-1274.
#=GF WK   ODC_internal_ribosome_entry_site_(IRES)
#=GF SQ   13



ACFV01178186.1/6341-6215             AUUGUCACUGCUGCUCCAAGGGCACAC------G-------C------AG------AGGGAUUUGGAGU--UCCUAGAGA-----GUUGCCUUUGUGAAAAGCUGGA---AAU-G--C-U-UC-UUUC-------AAAUCCAUCUCUUAGUUUUCCAUA----------------GGAA--CAUGAAGAAAUC
CABD02350425.1/1188-1329             GUUUCCACUGCUGCUCUGAGGGCACAA------G-------A------GG------CAGGAUUUGGAAU--UCCUGGAGA-----ACUGUCUUCGUGAGAAGCUGGA---AAU-A--U-U-UC-UUUC-------AAUUCCAUCUCUUAGUUUUCCAU-UUUGUUGUGUUUCAGAGGAA--CAUCAAGAAACC
AGCE01007380.1/6420-6279             AUUUCCACUGCUGCUCUGAGGGUACAA------G-------A------GG------CAGGAUUUGGAAU--UCCUGGAGA-----AGUGUCUUUGUGAGAAGCUGGA---AGU-A--U-U-UC-UUUC-------AAUUCCAUCUCUUAGUUUUCCAUUCUGUUGU-GUUUAAGAGGAA--CAGCACGAAACC
ACBE01427778.1/3118-2986             AUUUCCACUGCUGCACUGAGGGCACAC------ACAU-UUUC------AG------UGGGACUUGGAAU--UCC-AGAGA-----AUUGCCUUUGUGAAAAACUGGC---AAUAG--U-U-UC-UUUA-------AAUUCCAUCUCUUAGUUUUCCAUA----------------GGAA--CAUCAAGAAACA
ABDC01534052.1/112-240               GUUUCCACUGUUGGUCUGAGGGCACGC------G-------A------UU------C------------CU----GGAGA-----AUUGCCUUUGUGAGAAGCUGGA---AAU-A--U-U-UC-UUUU------AAAUUCCAUCUCUUAGUUUUCCAAUUUGUUGC-AUUUUAGAGGAA--CAUUAAGGAACC
ABRN01282650.1/6008-5859             AUUUUCACUGCUGCACCGAGGGCACACGUAUCUU-------C------AG------CGGGACUUGGAAU--UCCUGGAGAAUUCAAUUGCCUUUGUG-AAAGCUGGC---AUA-A--U-U-UC-UUUA-------AAUUUCAUCUCUUAGUUUCCCAUUUUGUU-----GUUUCAGAAAGAUAUCAAGAAACC
ABVD01286055.1/5423-5572             GUUUCCACUGCUGCACCAAGGGCACAA------GUCUUAUUC------AG------CAGGAUUUGGGAU--UCCUGGAGA-----ACUGUUUUCAUGAAAAGUCAGA---AAUAA--U-U-UC-UUUA-------UAUUCCAUCUCUUAGUUUUCUGUUUUGUUGC-AUUUCAGAGGAA--CAUCAAGAAACC
AAGV020377958.1/7922-8073            AUGCACUCUGCUGCACCAAGGGCACAA------GGAUGAUUC------AU------CGGGAUUUGGAAU--UCCUAGAGA-----AUUGUCUUCGUGAAAAGCUGGGGAAAAA-A--U-C-CC-UCUA-------AAUUCCAUCUCUUAGUUUUCCAUAUUGUUGC-AUUUCAGAGGAA--CAUCAAGAAAUC
AAWR02017968.1/115190-115041         AUUUCCACUGCUGCUCUGAGGGCACACGUAUCUU-------C------AG------CGGGACUUGGAAU--UUCUGGAAA----AAUUGCCUUUGUGAAAAGCUGGC---AGU-A--C-U-UCCUUUG-------AAUGUCAUCUCUUAGUUUUCCACUUCGGUGC-GUUUCAGAGGAA--AAUCAAGAAACG
AEYP01059957.1/11419-11566           UUUUACACUGCUGCACUGAGGGCACAU------G-------CAUCUUUAG------UGGGACUUGGAA---UUCUGGAGA-----GUUGUCUUUAUGAAAAACUGGU---UAU-AAUU-U-UC-UUUA-------AAUCCCAUCUCUUAGUUUUCCCUUUUGUUAU--AUUUCGGGGAA--CAUCGAGAAACC
ACTA01000079.1/21900-21758           AUUUCCACUGCUGCACCGGGGGCACAC------G-------C------AUCUUCCCCAGGACUUGGAAU--UCC-GGAGA-----AUUGCCUUUGUGAGAAGCUGGC---AGU-A--AUU-UC-UUUA-------AAUUCCAUCUCUUAGUUUUCCAUGUAAGU------AUUCGUGGU--UGUUAAGAAUUA
AAQQ01517481.1/186-328               AUUUCCACUGCUGGUCCAAGGACAC--------------------------------GGGAUUUGGAAA--UCCUGGAGA-----AUUACCUUUGUAAGAAGCUGGG---AAU-A--A-UUUC-UUUAAAUUUUAAAUUUCAUCUCUUAGUUUUCCAUUUUGUUGC-AUUUCUGAGGCA--AAUGGAGAAUCC
AK292352.1/308-434                   AUUGUCACUGCUGUUCCAAGGGCACAC------G-------C------AG------AGGGAUUUGGAAU--UCCUGGAGA-----GUUGCCUUUGUGAGAAGCUGGA---AAU-A--U-U-UC-UUUC-------AAUUCCAUCUCUUAGUUUUCCAUA----------------GGAA--CAUCAAGAAAUC
#=GC SS_cons                         ::::<<---<<<-<<<<<<<<<<<-<<......-.......-......--......-<<<<________..>>>>-----.....>>>>>>>>>>->>>->>>-->>...---.<..<.<.<<.<<--.......--<<<<_________________________.________>>>>..---->>>>>>>:
#=GC RF                              aUUUcCACUGcUGcuCcgagGgCACac......g.......c......Ag......cgGGAuUUGGAAU..UCCuGGAGA.....guUGcCuucgUGagAAgCUGGg...AaU.g..u.u.uC.UuUa.......AAuucCAUCUCUUAGUUUUCCAUuUuguUgc.auuUuagAGgaa..cAUcaAGaaacc
//
# STOCKHOLM 1.0

#=GF AC   RF02536
#=GF ID   AEV_CRE
#=GF DE   Avian encephalitis virus (AEV) cis-acting replication element (CRE)
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   PMID:18684812
#=GF SS   Published; PMID:18684812
#=GF GA   100.00
#=GF TC   164.90
#=GF NC   54.10
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF RN   [1]
#=GF RM   18684812
#=GF RT   Identification of a conserved RNA replication element (cre) within the
#=GF RT   3Dpol-coding sequence of hepatoviruses.
#=GF RA   Yang Y, Yi M, Evans DJ, Simmonds P, Lemon SM
#=GF RL   J Virol. 2008;82:10118-10128.
#=GF WK   Avian_encephalitis_virus_cis-acting_replication_element
#=GF SQ   2


AJ225173.1/5433-5567 GCACAAUGUAGUAGGAUAUGGAAGACUGAGUUUGUGGAAGAGAAGAUAUCUGUGGGGUCUAAAACGAAGUACCACAAGUCCCCUUUAUAUGAUUUUUGUCCACAGGAGGUUAUUAAAUGUCCCACUAAGUUGUUC
AY517471.1/5432-5566 GCACAAUGUAGUAGGAUAUGGAAGACCGAGUUUGUGGAAGAGAAGAUAUCUGUGGGGUCUAAAACGAAGUAUCACAAGUCCCCUUUAUAUGAUUUUUGUCCACAGGAGGUUGUUAAAUGUCCCACUAAGUUGUUC
#=GC SS_cons         ::<<<<<-<<<<-<<<<<<----<<<<---<<<<<<<<-<<<<<--<<<-<<-<<<<-<<________________>>->>>>-->>->>>->>>>>->>>>>>>>->>>>----->>>>>>->>>>->>>>>::
#=GC RF              GCaCaacGuaGuAGGacauGGAAgaCcGAGccuGuGGaAgagaaGAcauCugUGGGGUCuAAAACGAAGUAuCACAaGUCCCCUUcaUaugAuucucGuCCaCaggAgGucaUUAAauguCCCaCuaAguuGuUC
//
# STOCKHOLM 1.0

#=GF AC   RF02537
#=GF ID   TarA
#=GF DE   Vibrio ToxT activated RNA TarA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   PMID:22546941
#=GF SS   Published; PMID:22546941
#=GF GA   80.00
#=GF TC   121.50
#=GF NC   37.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   22546941
#=GF RT   Non-coding sRNAs regulate virulence in the bacterial pathogen Vibrio
#=GF RT   cholerae.
#=GF RA   Bardill JP, Hammer BK
#=GF RL   RNA Biol. 2012;9:392-401.
#=GF WK   Vibrio_cholerae_ToxT_activated_RNAs
#=GF SQ   2


CP003069.1/366148-366050 GGUUUAGCACUCCCCCCUAUAGUGCCUAUUCCAUAUCUAUUAACUUGGUUACAUUAUCUUUCCUGUGACAUUUUGCCCCUUACGUUUGGGGCUUUUUUU
AF319653.1/262-165       GGUUUAGCACUCC-CCCUAUAGUGCCUAUUCCAUAUCAAUUAACUUGGUUACAUUAUCUUUCCUGUGACACUUUGCCCCUUCCGUUUGGGGCUUUUUUU
#=GC SS_cons             <<<<<<<<<<<_________>>>>>-->>>>>>,,,,,,,,,,,,,,<<<<<<__________>>>>>>,,,,,<<<<<________>>>>>:::::::
#=GC RF                  gGguuaGCaCuCCcCCCUAUaGuGCCUauucCaUAUCaAUUAACUUGGuuaCaUUAUCUUUCCuGugaCAuUUUGCCCCUUaCGUUUGGGGCUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02538
#=GF ID   TarB
#=GF DE   Vibrio ToxT activated RNA TarB
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   PMID:22546941
#=GF SS   Published; PMID:22546941
#=GF GA   80.00
#=GF TC   111.90
#=GF NC   36.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -E 1000 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   22546941
#=GF RT   Non-coding sRNAs regulate virulence in the bacterial pathogen Vibrio
#=GF RT   cholerae.
#=GF RA   Bardill JP, Hammer BK
#=GF RL   RNA Biol. 2012;9:392-401.
#=GF WK   Vibrio_cholerae_ToxT_activated_RNAs
#=GF SQ   2


CP001235.1/933467-933389     AUGAGCGGUUACCUCAUGUAUUGUUACAAGCUGACGAUUAAGCACUUUUUGGCGCACUGCGGUGCGCCUUUUUUUUGUU
ADOO01000003.1/555073-555151 AUGAGCGGUUACCUCAUGUAUUGUUACAAGCUGACGAUUAAGCACUUUUUGGCGCACUGCGGUGCGCCUUUUUUUAAAA
#=GC SS_cons                 <<<<<_______>>>>><<<____>>>,,<<<________>>>,,,,,,,<<<<<<<____>>>>>>>:::::::::::
#=GC RF                      auGaGCGGUUACCuCauGuaUUGUuaCAAGCuGACGAUUAaGCACUUUUUGGCGCaCUGCGGuGCGCCUUUUUUUuauu
//
# STOCKHOLM 1.0

#=GF AC   RF02539
#=GF ID   SNOR75
#=GF PI   U15
#=GF DE   Plant small nucleolar RNA SNOR75
#=GF AU   Griffiths-Jones SR; 0000-0001-6043-807X
#=GF SE   Griffiths-Jones SR; Plant snoRNA database, PMID:12520043
#=GF SS   Predicted; PFOLD; Griffiths-Jones SR, Daub J
#=GF GA   50.00
#=GF TC   50.20
#=GF NC   46.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 22.42 -Z 549862.597050 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; Mus_musculus300760;
#=GF DR   snoopy; Homo_sapiens300742;
#=GF RN   [1]
#=GF RM   8319909
#=GF RT   A small nucleolar RNA is processed from an intron of the human gene
#=GF RT   encoding ribosomal protein S3.
#=GF RA   Tycowski KT, Shu MD, Steitz JA
#=GF RL   Genes Dev 1993;7:1176-1190.
#=GF RN   [2]
#=GF RM   7984408
#=GF RT   Different forms of U15 snoRNA are encoded in the introns of the ribosomal
#=GF RT   protein S1 gene of Xenopus laevis.
#=GF RA   Pellizzoni L, Crosio C, Campioni N, Loreni F, Pierandrei-Amaldi P
#=GF RL   Nucleic Acids Res 1994;22:4607-4613.
#=GF RN   [3]
#=GF RM   11469857
#=GF RT   Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive
#=GF RT   gene duplications generated multiple isoforms predicting new ribosomal RNA
#=GF RT   2'-O-methylation sites.
#=GF RA   Barneche F, Gaspin C, Guyot R, Echeverria M
#=GF RL   J Mol Biol 2001;311:57-73.
#=GF RN   [4]
#=GF RM   12520043
#=GF RT   Plant snoRNA database.
#=GF RA   Brown JW, Echeverria M, Qu LH, Lowe TM, Bachellerie JP, Huttenhofer A,
#=GF RA   Kastenmayer JP, Green PJ, Shaw P, Marshall DF
#=GF RL   Nucleic Acids Res 2003;31:432-435.
#=GF CC   U15 is a member of the C/D class of snoRNA which contain the C (UGAUGA)
#=GF CC   and D (CUGA) box motifs. U15 is encoded within the introns of ribosomal
#=GF CC   protein S1 in Xenopus and S3 in human and Fugu. snoR75 from Arabidopsis
#=GF CC   [3] and homologues in rice and other plants are alternatively known as
#=GF CC   U15, and, despite a significantly shorter sequence length, appear to be
#=GF CC   related [4].
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6



AF318003.1/3-90        UCUCAGUGAUGAAGAAACAAUAGAUGACGAGUCCGAUGAAAUCCAUUCA-UAAAAUCGUGGGGACAAACGAGGCAUUUGUCUGAGAGGA
AB013389.1/56436-56523 UCUCAGUGAUGAAGGAACAAUAGAUGACGAGUCCGAUGAAAUCCAUUCAUUAAAUCAU-GGGGACAAACGAGGCAUUUGUCUGAGAGGA
AF318001.1/3-87        UCUCAGUGAUGAAUACACA---GAUGACGAGUCCGAUGAAAUCCAUUCAUUAAAUCAU-GGGGACAAACGAGGCAUUUGUCUGAGAGGA
AJ309198.1/702-616     UCUCCGUGAUGACGAACACA--GAUGACGAGUCCGAUCUAAUCCAUUCCAUUAAACCAUGGGGACAAUCGAGGCAUUUGUCUGAGAGAA
AJ489948.1/3-90        UCUCUGUGAUGACGAAAAACA-GAUGACGAGUCCGAUCCAAUCCAUUCCAUUAAACCAUGGGGACAAUCGAGGCAUUUGUCUGAGAGAA
AY103184.1/20-105      UCUCCUUGAUGAACACACA---GAUGACGAGUCCGAUCUAAUCCAUUCCAUUAAACCAUGGGGACAAUCGAGGCAUUUGUCUGAGAGAA
#=GC SS_cons           <<<<_________________.______________________________________________________________>>>>:
#=GC RF                uCUCaGUGAUGAagAaAcAau.GAUGACGAGUCCGAUgaAAUCCAUUCaaUuAAaCcaUGGGGACAAuCGAGGCAUUUGUCUGAGAGaA
//
# STOCKHOLM 1.0

#=GF AC   RF02540
#=GF ID   LSU_rRNA_archaea
#=GF DE   Archaeal large subunit ribosomal RNA
#=GF AU   Gutell RR
#=GF AU   Nawrocki E; 0000-0002-2497-3427
#=GF SE   Published; PMID:11869452
#=GF SS   Published; PMID:11869452
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17.38 -Z 549862.597050 --mxsize
#=GF SM   512--noali CM SEQDB
#=GF CL   CL00112
#=GF DR   URL; http://www.rna.ccbb.utexas.edu/;
#=GF DR   URL; http://oberon.fvms.ugent.be:8080/rRNA/ssu/index.html;
#=GF DR   URL; http://rdp.cme.msu.edu/html/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   11283358
#=GF RT   Crystal structure of the ribosome at 5.5 A resolution.
#=GF RA   Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH,
#=GF RA   Noller HF
#=GF RL   Science 2001;292:883-896.
#=GF RN   [2]
#=GF RM   11869452
#=GF RT   The comparative RNA web (CRW) site: an online database of comparative
#=GF RT   sequence and structure information for ribosomal, intron, and other RNAs.
#=GF RA   Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng
#=GF RA   B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR
#=GF RL   BMC Bioinformatics. 2002;3:2.
#=GF WK   Ribosomal_RNA
#=GF SQ   91



AE004437.1/1877501-1880414           [encoded data, 4236 characters]
CP002839.1/2729290-2732206           [encoded data, 4236 characters]
CP001404.1/1450307-1453357           [encoded data, 4236 characters]
AEMC01000045.1/292-3289              [encoded data, 4236 characters]
AADL01001107.1/5681-2770             [encoded data, 4236 characters]
CP002656.1/417449-414399             [encoded data, 4236 characters]
CP001994.1/562792-565716             [encoded data, 4236 characters]
CP002529.1/1486991-1483925           [encoded data, 4236 characters]
AB078022.1/2298-5600                 [encoded data, 4236 characters]
AE000782.1/1788756-1785815           [encoded data, 4236 characters]
CP001463.1/115333-118364             [encoded data, 4236 characters]
CP001787.1/623859-626864             [encoded data, 4236 characters]
CP000660.1/623274-620236             [encoded data, 4236 characters]
AF034619.1/2514-5444                 [encoded data, 4236 characters]
U82482.1/5-2912                      [encoded data, 4236 characters]
AGIY01000001.1/118719-121638         [encoded data, 4236 characters]
EU686642.2/23399-26401               [encoded data, 4236 characters]
BA000001.2/192729-195778             [encoded data, 4236 characters]
CP002988.1/932890-929977             [encoded data, 4236 characters]
AGIW01000001.1/28865-31961           [encoded data, 4236 characters]
CP000780.1/2250280-2247357           [encoded data, 4236 characters]
CP000505.1/366086-363009             [encoded data, 4236 characters]
AP011532.1/108778-111686             [encoded data, 4236 characters]
U40238.2/31510-28506                 [encoded data, 4236 characters]
AEMG01000026.1/3068-151              [encoded data, 4236 characters]
CP000867.1/860828-863795             [encoded data, 4236 characters]
CP000077.1/1106933-1103895           [encoded data, 4236 characters]
CP002051.1/1270009-1266807           [encoded data, 4236 characters]
CP001338.1/1213046-1215969           [encoded data, 4236 characters]
CP001941.1/14359-17300               [encoded data, 4236 characters]
ACXM01000005.1/159941-162863         [encoded data, 4236 characters]
AL445067.1/235738-232821             [encoded data, 4236 characters]
AJ586107.1/1926-4849                 [encoded data, 4236 characters]
CR626858.1/30124-27196               [encoded data, 4236 characters]
AF083072.1/21633-18644               [encoded data, 4236 characters]
AFNT01000045.1/64470-67387           [encoded data, 4236 characters]
DQ314493.1/27813-30743               [encoded data, 4236 characters]
AE008384.1/2402374-2405280           [encoded data, 4236 characters]
CP000968.1/1328189-1331736           [encoded data, 4236 characters]
EU686635.1/2573-5623                 [encoded data, 4236 characters]
AGBE01001967.1/9793-12790            [encoded data, 4236 characters]
ACVJ01000008.1/268894-271753         [encoded data, 4236 characters]
CP002057.1/1534504-1531541           [encoded data, 4236 characters]
AE017261.1/497008-494100             [encoded data, 4236 characters]
AGNT01000024.1/6580-3638             [encoded data, 4236 characters]
AJ627422.1/40358-43323               [encoded data, 4236 characters]
AADL01001701.1/6590-3677             [encoded data, 4236 characters]
CP000743.1/1194401-1191429           [encoded data, 4236 characters]
CP001857.1/1049709-1046732           [encoded data, 4236 characters]
FP565147.1/55544-52598               [encoded data, 4236 characters]
AJ496176.1/5856-8818                 [encoded data, 4236 characters]
CP002117.1/741920-744839             [encoded data, 4236 characters]
CP002069.1/50503-53426               [encoded data, 4236 characters]
CR936257.1/214089-211176             [encoded data, 4236 characters]
HE574571.1/18954-22030               [encoded data, 4236 characters]
CP002772.1/814663-817674             [encoded data, 4236 characters]
ADCE01000040.1/36234-33353           [encoded data, 4236 characters]
U32317.1/201-3246                    [encoded data, 4236 characters]
CP001365.1/22567-25488               [encoded data, 4236 characters]
CP000493.1/1663729-1660620           [encoded data, 4236 characters]
AE009439.1/585271-588370             [encoded data, 4236 characters]
ACXK01000051.1/29011-26091           [encoded data, 4236 characters]
CP002101.1/1236515-1233583           [encoded data, 4236 characters]
CP000254.1/41571-44494               [encoded data, 4236 characters]
AE017199.1/393978-396967             [encoded data, 4236 characters]
HE574568.1/8761-11841                [encoded data, 4236 characters]
CP002737.1/1091964-1094965           [encoded data, 4236 characters]
CP000559.1/405667-408584             [encoded data, 4236 characters]
AE000666.1/1604009-1607048           [encoded data, 4236 characters]
CP002098.1/1280841-1283923           [encoded data, 4236 characters]
CP001939.1/54518-57596               [encoded data, 4236 characters]
EU686620.1/9628-12672                [encoded data, 4236 characters]
BA000023.2/1186306-1183269           [encoded data, 4236 characters]
CP000300.1/1021798-1018871           [encoded data, 4236 characters]
CP000562.1/1822389-1819461           [encoded data, 4236 characters]
CP001688.1/618088-615166             [encoded data, 4236 characters]
CP002062.1/13292-10373               [encoded data, 4236 characters]
ACXL01000009.1/85315-88242           [encoded data, 4236 characters]
CP000102.1/1166996-1163952           [encoded data, 4236 characters]
X72588.1/3918-6854                   [encoded data, 4236 characters]
AF268611.1/8672-5813                 [encoded data, 4236 characters]
EU686631.2/30236-33286               [encoded data, 4236 characters]
CP002920.1/1625732-1628761           [encoded data, 4236 characters]
CR937012.1/19041-21972               [encoded data, 4236 characters]
DQ078753.1/36869-33844               [encoded data, 4236 characters]
CP002535.1/1297745-1300783           [encoded data, 4236 characters]
CP001719.1/762872-765862             [encoded data, 4236 characters]
CP001690.1/304605-307521             [encoded data, 4236 characters]
CP000816.1/731312-734356             [encoded data, 4236 characters]
CP002278.1/26764-23775               [encoded data, 4236 characters]
CP002551.1/492357-495330             [encoded data, 4236 characters]
#=GC SS_cons                         :::::{{{{....,,,,,,{{.{{{{{{{{-----{{{.,,{{{{{{{{...{{,,,,,,,((((<<<________>>>,,,.,,<<<<<<---<<<_____.__.>>>------>>>>>>,,,)))),,,<<<____>>>,,,,,,,,,,,,,,..................,<<<<<___._.....................................>>>>>,,,,,,<<<<<<-----<<____>>------>>>>>->,,,,,,,,,<<..__...__>>,,,<<<<<-----.<<_____>>---->>>>>,,.[[[[,,,,<<<-------<<<<__...__>>>>.--------->>>,,,,,,,,,,..((((----..................--((((---------..---(((,,,<.-<.<<.<.._____._.>>>.>...>.,,<___>,<<<_______>>>,,,)))-----------..-))))....----).))),.....,,,,,,,,,,<<<<<<<_______._>>>>>>>,,,,,.......,.<<<<<_______.>>>>>,,]]]],,,,,.}}.-}}}}}}-}},,,,,,,,,,,.,,,,<<____>>,,,,}}-----.---------..------.-----.--------}-----}}}}}}}}..}},,,,,,,<<<<.<<<<<<----<<..------<<<<<<<..---<.----<<<<<____.>>>>>-----.....>..--.>>.>>>>>-..--.....>>->>>>>>>>>>,,<<<<________>>>>{{{{{{,,,,((((.(((((((((,,.<<<<--<<<<_____..>>>>--.>>>>,,,<<____>>,,,,,<<<<---<<<<....____...........>>>>--->>>>,,.<<<<.______>>>>,.,,,))))))))))))),,[[-[---[[[.[[[,,,((((((((((((,<<<<---<<<<<<.<____>>>>>>>---->>>>,,.,,<<<<-<<-<<________>>>>.>>>>,,)-))))))))))),<<<_____>>>,,,,,,]]]]]].------]-]],,[[[[[[,,,,<<<<<____>>>>>,<<<<<<<---<<<-.<<<<<<<<----<<<-.---<<<<<<<.<<<.---<<<<<<._.___.>>>>>.>-.>>>>>>>>>>--->>->---->>>>>>>>>>>--.---->>>>>>.->,,,<<.<.<<<<.<<_______>>>>>>>>>,,,,<<<______>>>,,,(((((((---(((---.---(-((((((--.--------..------(((-((((((((((-------(((((,<<<--<<<_________>>>-->>><___..........................................................................................................................................................................................................><---<<______>>->,)))))---)))))))))))))-----.---.-----------))))))))))---)))))))<<.<.<<<<_..._______>>>>>-->>,,,,]]].]].]<-<<<<<<<<<<------<<<<<.<<<____>>>>>>>>--->>>>>>.>>>>-->,,,,,}}}}}},,,,,,,,,,,,,..,,<<<<<<_____.__>>>>>>{{{{.,,,,{{{{.,,{{,,,<<<<<<-.--<<_.____>>->>>>>>,,,,,,[[[,<<---<<<<<<<<<__.__._>>>.->>>>>>----.>>,,,<<<<<________>>>>>,,((.((((((...----...-----------........---.-------(((......---(((((((((--(((((.<<<<<<..________..........>>>>>>,,,<<.<.<..-----<.<<<<<<<<-<<<_____>>>->>>>>>>..>>-----........>>>>,,,,,,,,,,,<____...>,,,,,,,)))))---)))))))))--------.-..)))..--------...----...)))))))..),]]],,}},,,,,<<______>>,}}}},<<<<_______>>>.>,}}}},,,{{{{-----{{{{.{{{{-{{{,,,,,,,,,,,,,,<<<<<---<<____>>---->>>>><<<<<<<..<<._______........................>>.....>>>>>>><___>,,,,,,,[[[.[[[[[[,,<<<_________>>>,,.<<<<<<<<<--<<<<___._>>>>-->-->>>>>>>>,,((((,<<<--<<<<<<<--<<<----<<<<<______>>>>>---->>>>>>>>-->>>>><<<<<<_______>>>>>><___........................................................>,,...............,,,,,,,,,,,,,<<<<<<.._____............>>>>>>,,,,,,,,,,)))),,,]]-]]]]]]],,,,.............}}}-}}}}}}}}-}}}},,,,,,,,,,,,.,<<<<<.________................>>>>>,,{{{{{{{{............-{{{-{{,,,,,,{{{{-{{{{{{{,((((---(((((((,,<<<<<<.<<.<<<<<.<<<<<---------<<<<<--<<<-.---......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................-----.<<<<<.____.>>>>>---.--->>>----.-------->>>>>>>>>>>>>>>>>>>>>>>,,,<<<<._____.........>>>>,,,,,)))))))----)))),,<<<<_____>>>-><<<<<<___________>>>>>>,,[[,,,,((((((<<-<<<<<<_______>>>>>>--->><<_._____>>,,,.,)))))),,,,<<<<<<<<<________._>>>>>>>>>,<-<____>->,]],,,,,,,,,,<<<<<-<...<<<<_.....______>>>>>>.>>>>,,,,,,,,,}}}}}--}}}}}},,,,,,,,<<<-<<<<<<<<---<<_______>>--->>>>>>>-->>>>,,,,,,,,,,(((((((((((,,<<--<<<<<______>>>>>---->>,<<<<<_____>>>>>,,,,,)))))--)--))))-),,,,,<<<<<<<____>>>->>>>,,,,}}--}}}}}}}}}}},,..,,((((((((--((((,,<<<<<<<<_______________>>>>>>>><<<<<---<<<----<<<<<<<<<<.____>>>>>.-->>>>>---->>>->>>>>,,.<<<-.---<<<<<___________>>>>>---->>>,))))---.---)))))))),.........................................,,,,,((((<<<<<_______>>>>>,,,,<<<<<<<<<<<--<--<<<<<--<______........>.-->>>>>>--->>>.->>>>>->>>,,,)))),,,,,..}}}}:::::
#=GC RF                              uauaucgcg....cuauuAcg.CcgcccgGuGGAUGGC.UcGGCUcGgG...cGcCGAuGAaGGgcGuGgCAAGCUgCgAUA.AGCccgGGGgAGgcGCAuG.cA.gcCuuuGAuCCcggGAUucCCuAAUgGGAauUCCcguuacuuuuuaaac..................gcucccuau.u.....................................gggagcGGGAACcCcccGAAuuGAAaCAUCUuAGUAgggGgAGGAaaAGAAAcC..AA...uuGgGAUgcCgcuAGUA.gcGGCGAgcGAAAgcGgcau.AGccCAAACcgAAucccugcccGa...aAgggc.ggggagAUGugGuGUugugggc..cggcuuua..................augcgccuaguuaau..gaAgccGAAg.Ug.gc.c..UGGAA.u.ggc.c...c.gccauAgAGGGUGAuAGcCCCGUAggcguAaucuaaaa..ggcgc....uugag.ccgu.....uuccaGAGUAcCgcgggUUGGaau.UcccgcGgGAAua.......u.gGggGgcAucaa.CccCcAAggCUAAAUA.Cg.uCcCgAGACCGAUAGcGaAcu.AGUAccGUGAggGAAAGCUGAAA.AGuAcCccu..gaaGGG.ggGUG.AAAAGaGCCUGAAACcgggcgG..cgAuagaauggcg.cggCccgaAAGg..aaugaagcccccc..gAAg.GAaaccgccGcgA.ggcgguAGUA.....c..GA.gg.ggggcu..ga.....cCgggGucgcgccgUcCGUuUuGAAaaACGggCCgGGGAGUucgc.ggccguGgCGA.GccUAAgggguuuAa..ccccGa.AggCGuAGgGAAAcCGAuaagccCGCAgccc....uuua...........gggcGAGGggcgg.gguc.ugaaAGggccu.ggAGuCacggccgcgaGACCaGAAaCCg.ggCGAUCUaggCccggGCAGGgcGAAgccggg.cgaAAgcccgguGGAGgcCCGa.uAggggUgcUGaugUGCAAauCgc.ccccgUGACccggGccuAGGGGcgAAAGgCCAAUCuAGcccGG.uaAuAGCUGGUUCCcgcCGAAacggccCgcAggccgacCccggcgGAGgcu.GgcggcgggGUAGaGC.ACugaccGgg.ggg.uuagggggc.G.AAA.gcccc.cg.cccccCggucaAACuCCGAAcccgccgcCgcCGu.AGAagccggG.AgucgGg.c.gccc.gggGUAAGcccgggcgcCGaGAGGGgaACAACCCAGAccggGGUUAAGGuCCC.uAAgUgccGGcUA.AGUGucAa..ucuaAAGgguGuccccggcCuaAGACAgCggGgaGGUagGCUuAGAAGCAGCcAUCCucUAA..........................................................................................................................................................................................................gGAgUGCGUAAcAGCUCACccGcCGAGgccgggggCccCgAAAA.UGg.aCGGGGCUuAAgCCggccaCCGAuACCccgggg.c.gcgcu...uauuaaagcgcgAuccgGUAGgc.gG.GCGucccgcccGGguaGAAgccgG.gccGuGAggcCcgguGGACCgggc.gggaauGaaaAUCCcGGcgguAGUAgCAGCa..aAGuggGGUGAGA.AUCCccaCcGCC.GaAaGgGC.aAGGGUUccccGGC.AAuGu.UcGUCaGCCggggGUUAGuCGGUCCUAAggcgggccguA.Ac.ucgg.acccgccGAAa.GGGAAgcgGGUUAAUAUUCCcgcgCcg.cggggg...Uagg...ugcgguAacgc........aag.ccuaauuccc......GACgccucggGgUAggccg.ggcggg..gcuguCgu..........cccgccuAAgc.g.c..uuAAgc.ccggcgagagcCGUAAUGgcGcgagccg..ggugAAg........gcgcgAuugGcuuuccgUaa...ggagagUUcggccgAucCccggggcCCaUGAAA.A..ggg..auugggaa...ugAu...cccccgc..guCCGUACCgAGAaCCGACACAGGUGCcCcugGcUGAGaAGgCc.aAGGCgUaUcGGguauAAcccg.ggcgAGGgAAuUCGGCAAAuUagccCCGUAccUUcGggAgAAGGggugCCuGcg..gc.uuggaaa........................gc.....cgCaGGuCGCAGUGACuAGGGg.gccCcgACUGUUUAauAAAAACAuA.ggcccCcGCuAgcCCGaA.AGGgcguGUACgGgggccGAcuCCUGcCCAgugccGGUAccuGAAacCcggGUaCAAccgGgcgAAgggCCgguaAacGgCGgGgGUAACUaUGACcCuCuUAA........................................................gGU...............AGCgaAAUaCCUuGcCGgc..UaAgU............gcCGgCuuGcAUGAAuGGaguAAcgAGggccCCACUG.............uCCccgcccgggacCCggUGAAcuuacug.ugccgG.uGcAcAgu................CcggcgacccCcggc............ggGgAGcGAAGACCCcgUgGAgCUUUACuGCAGcCugccguUGgggcg.cg.gccgc.gggcgcauAGuGUAGguGGGAGccg.uug......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................aagcc.ccccc.uccg.gggggggu.gGAggCgaca.aUGaaACACCacCcgcccgcggccgcgcccCUaACccc.uaaaa.........gggGGACAucggcaGgUGGGCaGUUuGGcuGGGGCggCACgCccccGAAAAgaUAuCggggGcGCCCaAAGgucggCUCAggcGGguCAGAAacCCgccGuAGAGcG.cAAGGgCAAA.AGccggccUGACugggccccuaAaagca.aggggcccaGaggcGAAAgccgGGcCUAGCGAACccccguG...cCccc.....uuggUGggGgCc.ggggAuGACAGAAAAGcUACCccgGGGAUAACaGagucgucgCgGGCaAGAGcuCauAUCGACCCcGcgguUugcuACcUCGAUGUCgGcucuccCcAUCCUGGcgguGCAGcAgccgCCAAGGGUcgGGcUGuUCgCCcgUUAAAgGggaaCgUGagCuGGGUUuAGacCGuCGuGAGaCAGguCGGuugCUacCcgccgGgggUG..uugGccGcCUGAgGGgAAGgcgccccUAGUACGAGAGGAACggggcgcCgggGCCuCugGUgUAcCGGuuGuCc.GauagGgCa.augCCGgGcAGCcacGCcccaa.ggga.UAAggGCUGAAaGCAUCUAAGCccGAAacccucCCcGAA.AAgAGgCggCcu.........................................gauuAgGgcccccgUAgAAGAcggggUuGAUgGggcgGgGGUGuAAgccccgAGguuaau........C.GAggggcuuAGCCc.gCcgccaCcAAuagcCcgAaug..cgcgauauu
//
# STOCKHOLM 1.0

#=GF AC   RF02541
#=GF ID   LSU_rRNA_bacteria
#=GF DE   Bacterial large subunit ribosomal RNA
#=GF AU   Gutell RR
#=GF AU   Nawrocki E; 0000-0002-2497-3427
#=GF SE   Published; PMID:11869452
#=GF SS   Published; PMID:11869452
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17.38 -Z 549862.597050 --mxsize
#=GF SM   512--noali CM SEQDB
#=GF CL   CL00112
#=GF DR   URL; http://www.rna.ccbb.utexas.edu/;
#=GF DR   URL; http://oberon.fvms.ugent.be:8080/rRNA/ssu/index.html;
#=GF DR   URL; http://rdp.cme.msu.edu/html/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   11283358
#=GF RT   Crystal structure of the ribosome at 5.5 A resolution.
#=GF RA   Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH,
#=GF RA   Noller HF
#=GF RL   Science 2001;292:883-896.
#=GF RN   [2]
#=GF RM   11869452
#=GF RT   The comparative RNA web (CRW) site: an online database of comparative
#=GF RT   sequence and structure information for ribosomal, intron, and other RNAs.
#=GF RA   Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng
#=GF RA   B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR
#=GF RL   BMC Bioinformatics. 2002;3:2.
#=GF WK   Ribosomal_RNA
#=GF SQ   102



X68433.1/1-2932                        [encoded data, 5241 characters]
ABKZ01000640.1/3023-133                [encoded data, 5241 characters]
GU260705.1/14113-17090                 [encoded data, 5241 characters]
ADNW02000012.1/35902-32772             [encoded data, 5241 characters]
ACDN01000023.1/3199-6081               [encoded data, 5241 characters]
CP001205.1/437603-434675               [encoded data, 5241 characters]
ACBJ01000075.1/3424-514                [encoded data, 5241 characters]
CP001634.1/1772311-1775264             [encoded data, 5241 characters]
ABRS01000102.1/3081-195                [encoded data, 5241 characters]
AE000520.1/231944-234896               [encoded data, 5241 characters]
FQ032815.1/2931-73                     [encoded data, 5241 characters]
EU686590.1/5824-2852                   [encoded data, 5241 characters]
AM905424.1/1-2835                      [encoded data, 5241 characters]
AF245376.1/1-2824                      [encoded data, 5241 characters]
ADVG01000004.1/1322171-1319199         [encoded data, 5241 characters]
ADLS01000036.1/498-3472                [encoded data, 5241 characters]
ADCX01000014.1/2280-5359               [encoded data, 5241 characters]
AAZS01000004.1/3033-123                [encoded data, 5241 characters]
CP002458.1/789779-786897               [encoded data, 5241 characters]
CP001100.1/906798-903930               [encoded data, 5241 characters]
ACDS01000303.1/2942-34                 [encoded data, 5241 characters]
AJ965256.1/47731-50682                 [encoded data, 5241 characters]
AEES01000073.1/3166-37                 [encoded data, 5241 characters]
CP001825.1/813726-810791               [encoded data, 5241 characters]
CP002525.1/649038-651979               [encoded data, 5241 characters]
AFKA01000026.1/3079-122                [encoded data, 5241 characters]
AM946600.1/3200-189                    [encoded data, 5241 characters]
CP002049.1/88381-91332                 [encoded data, 5241 characters]
GU474878.1/11307-8366                  [encoded data, 5241 characters]
CP001968.1/1929653-1926732             [encoded data, 5241 characters]
U68457.4/448-3389                      [encoded data, 5241 characters]
AFUI01000030.1/1848-4856               [encoded data, 5241 characters]
CP001055.1/1534536-1531500             [encoded data, 5241 characters]
ACIJ02000018.1/406733-403849           [encoded data, 5241 characters]
EU795196.1/14920-11891                 [encoded data, 5241 characters]
ABHJ01000047.1/3867-904                [encoded data, 5241 characters]
CP001818.1/1104632-1101659             [encoded data, 5241 characters]
CP000679.1/488147-491109               [encoded data, 5241 characters]
CP002637.1/928969-931886               [encoded data, 5241 characters]
EU795181.1/8234-5531                   [encoded data, 5241 characters]
CP001197.1/1107715-1104788             [encoded data, 5241 characters]
ABCK01000018.1/57317-60230             [encoded data, 5241 characters]
ABOX02000035.1/70819-67954             [encoded data, 5241 characters]
CP002171.1/1536103-1532731             [encoded data, 5241 characters]
CP001364.1/4913263-4910323             [encoded data, 5241 characters]
FP929046.1/589785-586950               [encoded data, 5241 characters]
EU795206.1/15762-18674                 [encoded data, 5241 characters]
CP001275.1/982648-979661               [encoded data, 5241 characters]
HM454281.1/5282-8258                   [encoded data, 5241 characters]
CU466930.1/1799422-1796381             [encoded data, 5241 characters]
EU686597.1/24060-21090                 [encoded data, 5241 characters]
AM180895.1/7-2955                      [encoded data, 5241 characters]
HQ613875.1/1789-4648                   [encoded data, 5241 characters]
ADFR01000011.1/3119-222                [encoded data, 5241 characters]
CP001998.1/1560794-1557900             [encoded data, 5241 characters]
CP002210.1/1134641-1137938             [encoded data, 5241 characters]
ABCR01000001.1/9019-5561               [encoded data, 5241 characters]
AF211133.2/2116-4925                   [encoded data, 5241 characters]
BX842648.2/125404-128344               [encoded data, 5241 characters]
AADL01002504.1/73037-70056             [encoded data, 5241 characters]
GU180080.1/36649-33202                 [encoded data, 5241 characters]
ABEQ01000080.1/9755-6861               [encoded data, 5241 characters]
CP001145.1/939593-936570               [encoded data, 5241 characters]
CP002353.1/4715612-4718390             [encoded data, 5241 characters]
CP002901.1/785382-788298               [encoded data, 5241 characters]
CP001792.1/2383130-2386033             [encoded data, 5241 characters]
CP001807.1/189199-192161               [encoded data, 5241 characters]
GU474850.1/17220-14249                 [encoded data, 5241 characters]
CP001959.1/1248722-1245733             [encoded data, 5241 characters]
CP002514.1/104879-107765               [encoded data, 5241 characters]
FJ560485.1/8951-6012                   [encoded data, 5241 characters]
FP245540.1/3889-6846                   [encoded data, 5241 characters]
AF481102.1/24258-27125                 [encoded data, 5241 characters]
CP002161.1/6931-9818                   [encoded data, 5241 characters]
CU367853.1/32572-35581                 [encoded data, 5241 characters]
FQ311870.1/13183-16381                 [encoded data, 5241 characters]
AF245369.1/1-2750                      [encoded data, 5241 characters]
ACZL01000054.1/2944-49                 [encoded data, 5241 characters]
CP001226.1/95183-97938                 [encoded data, 5241 characters]
CP002659.1/246809-249774               [encoded data, 5241 characters]
CP001854.1/3764308-3761310             [encoded data, 5241 characters]
CP000875.1/1976598-1979574             [encoded data, 5241 characters]
FP245541.1/20832-23795                 [encoded data, 5241 characters]
CP001146.1/625787-628802               [encoded data, 5241 characters]
EU795287.1/6990-10020                  [encoded data, 5241 characters]
FP245538.1/20573-23523                 [encoded data, 5241 characters]
AAYA01000003.1/323768-327215           [encoded data, 5241 characters]
FQ312005.1/1891702-1888775             [encoded data, 5241 characters]
FP245539.1/24257-27271                 [encoded data, 5241 characters]
GU260711.1/11996-9110                  [encoded data, 5241 characters]
FJ872372.1/9644-12466                  [encoded data, 5241 characters]
AP009153.1/1884701-1887648             [encoded data, 5241 characters]
FJ872374.1/2099-4950                   [encoded data, 5241 characters]
CP002432.1/2335602-2332713             [encoded data, 5241 characters]
CP001769.1/3193572-3190739             [encoded data, 5241 characters]
AP009510.1/130487-133369               [encoded data, 5241 characters]
CP001743.1/891092-888198               [encoded data, 5241 characters]
HM537013.1/32674-29750                 [encoded data, 5241 characters]
AFNU01000062.1/241-3124                [encoded data, 5241 characters]
FP565575.1/1585575-1582548             [encoded data, 5241 characters]
EF203797.1/2365-5248                   [encoded data, 5241 characters]
CP002683.1/863851-860827               [encoded data, 5241 characters]
#=GC SS_cons                           {{{..{{{{{...,,,..,,,{{{{{{{.{{{-----{{{.,.,{{{.{{{{{{{{[[,,,,,(.(((<<<..____.____>>>,,,,,.<<<<<<<--<<<___......____>>>----..->>>>>>>,,,))).),,,<<<_...___>>><<<<<<<.............................................................................................................................................................______..>>>.>>>>,.<<<.<.<..<<<<_______....................__..................>>>>..>>.>.>.>,]]..,,,<<<<<<---.--<<____>>---.--->>>>>->,.,,,,,,,,<<...___.._..>>,.,{<<<<<-----<<_____>>---->>>>>,,..[[[[,,,,<<<<..<<<__......................................................______>>>.>>>>,,,,,,((.(-.(((((--...........................-----(((((.((..(.((.(((...-(((,,,<.<.<.<.<______.>>>>>,,<__.._>,<<<_______>>>,,,)))---)))))...)....)))))))--.....)))))---..))).,,,,,<<<<<<<<<_____.__>>>>>>>>>,,,,,,.<<<<<______..>>>>>,,]]]],,},,}}-}}}}}}}-}},,,,,,,,,,.,,,,,<<____>>,,,,}},,,,,.,,,,<<<<_____>>>>,,,,,,,,,,,,,}.-----}}}}.}}}}}},,.,,,.{,<<<<<<<<<<<_....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................______.._>>>>>>>>>>>.,,<<<<________>>>>{{{{{{,,,,(((.((((.((((((...,,<<<<--<<<......._____.....>>>-->>>>,,,<<____>>........,<<<<<..____..._.>>>>>,......................,,,))))))))))))).,,[[-[---[[[.[.[[,,,((((((((((((,<<<<---<<<<<<<____.>>>>>>>---->>>>,,,<<.<-<<<<<________>>>>>>>>,,)-))))))))))),<<<_____>>>,,,,,,]]]]]]------]-]],,[[[[[[,,,,<<<<<____>>>>>,<<<<<<<<--..<..<<<<<<<<<<----<<<-.--<<<-<<<<.---<<.<<<<<____.>>>>>->>--->>>>->>>-->>->---->>>>>.>>..>>>-...->>>>>>>>->,,,<<<.<<<<<<<______>>>>>>.>>>>,,,,.<<<______>>>,,,((((-(((---(.((------(-(((((.(.--------.......---(((-((((((((((-------(((((,<<<--<<<_________>>>--.>>><___><---<<______>>->,))))).....--.-..)).)))))))))))--------------------..))))))))))---)))))))<<<<<<<<..._____....................................................................................................................................................................................................................................................................................................................................................................................................................................................................>>>>>>.>>,,,,]]]].]].<-<.<<<<<<.<<<------<<<<<.<<<.__.__>>>...>>>>>--->>>..>>>>>>>-->,,,,,}}.}}}}{{-----.{{.,,,.,,<<<<<<_..______>>>>>>{{{{.,,,...,{{{{,,{{,,,<<.<<<<-.......--<<_____>>->>>>.>>,,,,,,[[[[.,<<---<<<.-<-<<<...__.....__..>.>>.->->.>>--.->>.,,,<.<<<<.__.______>>>>>,,(((((.(((...(((--....................................................................................................---((..--((((((---((((--(((.--..(((((..<<<<<<.__.________.>>>>>>.<<..--<<<<..---<<<......-<<<<<<<....-<<_____>>........>>>>>>>---.......>>>---.>>>>.---.......>>,.<<......<<<<<...____.......>>>.>.>.....>.>,..,...))).)).---..)))---)).))-------.-)))))).--..))---.....))))).)))..)))]]]],,}},,,,,<<______>>,}}}},<<<<._____..>>>>,,}}}},,{{{{----{{{{{{{{-{{{,,,,,,,,,.,,,,,<<<<<---<<____>>---->>>>><<<<<<................<<.<<<<____...>>>>>>...............>>>>>><___.>,,,,.,,,[[[[[[[[[,,<<<_________>>>,,<<<<<<<<<.--<<<<__..._._..>>>>-->-->>>>>>>>,,((((,<<<--<<<<<<<--<<<-.--<<-<<<<<<<--<<.............................................................................................................................................................................................................................................................................................................____....>>--->>>>>>>->>--->>>>>>>>-->>>>><<<<<<_______>>>>>><___.>,,,,,<---------<<<<<<_____>>>>>>>,,,,,,,,,)))),,,]]-.]]]]]]],,,,}}}-}}}}}}}}-}}}}}}----}}},,,,<<<<<________>>>>>,,{{{{{{{{-{{{-{{,,,,,,{{{{-{{{{{{{,((((---(((((((,,<<<<<<<<<<<<<<<<<<---------<<<<<--<<<------<<<<<<<<____>>>>>.>>>--->>>---.--------->>>>>>>>>>>>>>>>>>>>>>>,,,<<<..-.<<<.<<<._____.>>>>>>.>>>,,,,,)))))))----)))),,<<<<_____>>>><<<<<<___________>>>>>>{,[[,.,,,((((((<<-<<<<<<_______>>>>>>---...>><<______>>,.,,.,)))))),,,,<<<<<<<<<______>>>>>>>>>,<<<____>>>,]],,,,,,,,,,<<<<<<<-.<<________>>>>>>>>>,,,,,},,,,,,}}}}}--}}}}}},,,,,,,,<<<-<<<<<<<<---<<_.______>>--->>>>>>>-->>>>,,,,,,,,,,(((((((((((,,<<-<<<<<<______>>>>>>--->>,<<<<<_____>>>>>,,,,.,)))))--)--))))-),,,,,<<<<<<<____>>>->>>>,,,,}.}--}}}}}}}}}}},,.,,(((((((.(--.((((,,<<<<<<<__________._____>>>>>>><<<<<<---<<<----.<<<<<<<<<<<..___._>>>>>>.-->>>>>---->>>.->>>>>>,,<<<----<<<<<_________.__>>>>>---->>>,))))------)))))))),,<<<.........___........................................................................................__>>>....,(.--((((<<<<<_______>>>>>,,,,<<<<<<<<<<<--<--<<<<<...____..>>>.>>..>.--->>>->>>.>>->>>,,.,))))-..),,,.}}}}.}.}}}::
#=GC RF                                ggu..caagc...uau..uAAggGCgcg.cGGuGGAUGCC.U.uGGc.gccgggaggCGAuGAg.GGaCGc..Ggua.agCugCGAuAAG.CcccGgggAGccGca......AacAggCuuuG..AccCgggGAUuuCC.cAAUgGGG...aAACCcgcccggg.............................................................................................................................................................guaaua..ccc.gggcA.ccc.c.c..ggccGAAuacA....................UA..................ggcc..gg.g.g.gaGc..aAACccgGgGAA.cUGaAACAuCUaA.GUAcCcggAGG.AAAAGAAAgc...AAa..a..gcg.AuuCCccuAGUAGcGGCGAgCGAAaggGGaau..aGcCcAAACcgg..ggguu......................................................auuguuccc.ccgGGGUugugG.Ga.cccccaa...........................auuaagagcc.cc..c.cg.gcu...AgccGAAc.g.g.c.cUGGAAa.ggccgaCCau..AGagGGUGAuAGuCCcGUAggcgaAagccg...g....ggggcucuu.....ggggguau..CCc.gAGUAgggCggggcAcGuG.aAgccccGcccGAAuau.gggggGACCAc..cccccAAGgCuAAaUAcuccccggcgACCGAUAGuGaAc.uAGUACCGUGAGGGAAAGGUGAAA.AGaACCCcggugAgGGGAGUGAAAuAGaaCC.UGAAACCgc.gcGCccAC.AAg.caGucGcggcccga....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................uuuuaa..ucgggccgCggC.GUcCcUUUUGuAuAAgGggcCggCGAgUugc.cgcg.cgcggC...aAGguUAAgcc.......ugaua.....ggcGuAgcCGuAGcGAAAgC........GcGuCc..gAAu...A.gGgCga......................uuAGucgcgcgcggca.GACcCGAAACcg.g.GuGAuCuaccCauggcCAGGguGAAgccgggcUAAa.gcccgguGGAGgcCCGAACc.cacgcccGUUGAAAAgggcgggGAUGAgcuguGgguaGgGGcGAAAggCCAAUCaAaCccgGaGAUAGCUgGUUCUCccCGAAAugccuUuAGgggcaGCgucgggcga..u..cccccccggcGGUAgaGC.ACuggauggg.cuAgG.gggccuaaa.ggccuACcaAacccaaccaAACuccGAAUgccgg.gg..ggga...aagcccggcAGucAgac.cgcgggcGaUAAgguccgc.ggucgAgA.GGGaAAcAaCCCAGAcCgcCagcUAAG.GuCCCuAAgugcggG.c.UAAGUGgg.......AAAGGcuGuggggccgCuaAgACAaCcaGGAgGUUGGCUUAGAAGCAGCCAU.CcUuuAAaGAguGCGUAAuAGCUCACugGu.....Ca.A..Gc.ggccccgCgCCGAaAAUguaaCGGGGCUcAA..gCccgccaCCGAAgcugcGggcucgcgg...uuuaa....................................................................................................................................................................................................................................................................................................................................................................................................................................................................ccgcga.gcGGUAGggG.AG.Cgu.uccgcc.cgcgguGAAggcgc.ccc.Gu.aAggg...gcgccGGAgcg..ggcggaaGuGAgaAUGc.cGgcacgAGUA.gC.GAu.AAgggggGU..GAGAAuCcccccCGCC.GaA...AgcCcAAGGuUUCC.ugggu.......AAgGuUaaUCcgccca.GGGUuAGuCGgg.aCCUAAGgc.GaGGcc...GA.....aA..g.gC.GuAg.cCGA.UGG.aaAg.cgGG.Uu.AAuAuUCCcgcaCcgccc.ggg...gccuu....................................................................................................uaagc..gacGgggcGACgcagaaggc.ua..ggcgc..gcgggc.ug.uuGGaagu.gcccgc.cc..aagccc..uuaggc......uggggggc....AGguAAAucC........gccccccaau.......gccgag.gggc.gau.......ggg.cc......gccgc...uuaa.......gcg.g.c.....g.ga..g...gcg.cc.gaa..gccaugcu.gcCaaGAAA.AgcccCg.aa..gcuaa.....ggccc.cgg..gcgccCGUACCguAAACCGACACAGGUgGgcagGga.GAGaA..ucCcaAGGCGcucGgGagAAcccuggucAAGgAACUCGGCA.AAaUagcccCGUAccUUcGggAgAAGgggcgCCccc................cc.gggcguaa...gcccgg...............gggGGccGCA.gagAa.uaGGcccgggCGACUGuUUAccAAAAaCACAggccucugC.uAagucGu...A.A..gacgAuGUAuaggggcuGAcGCCUGCCCGGUgCcgGAAGGuU.AAgggccgggGuuAgc.............................................................................................................................................................................................................................................................................................................GcaA....gcgAAgCcccggAccgAAgCCCcgGuAAACGGCGgCCGUAACUAUAACGGuCCUAA.GGUAGCGAAAUUCCUUGuCGGgUAAGUuCCGaCCuGCACGAAuGGCgUAACGA.cccgggCgCUGuCUCgaccagggaCcCgGcGAAAguguAgUgccgGUgAAGAUGCcggcUaCcCgCggcugGACgGAAAGACCCCGUGgAcCUUUACUguAgccuggcauUGgcccccggcgcggcccGUguAGgAUAgGuGGGAGgCuuuGAAgccggggcgcuAgcccc.ggcGGAGcCaac.guUGAaAUACCaCcCgggccgcgccgggggcCUAACcc..a.gcc.ccg.uaAuc.cggggc.ggGGACagugccagguGGGcAGUUUGaCuGGGGCgGuCgCCUCCuAAAgaGUAACGGAGGcGcgCa.AAGGuuccCUCAgcgcGguuGGaAAcCgcgcgua...GAGcGcAAaggCA.uA.AGggagCuUgACuGcccGacugACAaguCgggCaGaggCGAAAGccGGccuUAGUGAUCCggcGGcu.ccgagUGGaAgggCCgucGCUCAACGGAUAAAAGgUACcCCGGGGAUAACAGGCugAucccccCCAAGaG.UuCAuAuCGACGggggggUUUgGCACCUCGAUGUCgGCUCauCgCAUCCUGGGgCuGgAGuAgGuCCCAAGGGUucGGCUGUUCGCCgaUUAA.AGcGguACGuGAGCuGGGUUcAGaaCGUCGUGAGACAGuuCGGUCC.cUAUCcgccGcGgGcG.uaGGaggcc.UGA.ggGgauccgccccUAGUACGAGA.GGACCggggcgggCggaCCucugGUGua.cCgGuuGucgc..GCc.AgcggCa.uugCcGgGUAGCca.uGuccGcaaggGAUAAcCGCUGAAaGCAUC.UAAGCGgGAAgCccacCccAAGAuaAggccuCCcucgg.........uaa........................................................................................auccg....uu.aAGgccccuggaAGAcuAccaggUuGAuaGgccggcgGUGcAAgcgcg...GuAA..cgc.gc..g.uAGCcgAccg.guACuaAU.aggcCg..auag.gcuu.g.accuu
//
# STOCKHOLM 1.0

#=GF AC   RF02542
#=GF ID   SSU_rRNA_microsporidia
#=GF DE   Microsporidia small subunit ribosomal RNA
#=GF AU   Gutell RR
#=GF AU   Nawrocki E; 0000-0002-2497-3427
#=GF SE   Published; PMID:11869452
#=GF SS   Published; PMID:11869452
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17.38 -Z 549862.597050 --mxsize
#=GF SM   128--noali CM SEQDB
#=GF CL   CL00111
#=GF DR   URL; http://www.rna.ccbb.utexas.edu/;
#=GF DR   URL; http://oberon.fvms.ugent.be:8080/rRNA/ssu/index.html;
#=GF DR   URL; http://rdp.cme.msu.edu/html/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   11283358
#=GF RT   Crystal structure of the ribosome at 5.5 A resolution.
#=GF RA   Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH,
#=GF RA   Noller HF
#=GF RL   Science 2001;292:883-896.
#=GF RN   [2]
#=GF RM   11869452
#=GF RT   The comparative RNA web (CRW) site: an online database of comparative
#=GF RT   sequence and structure information for ribosomal, intron, and other RNAs.
#=GF RA   Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng
#=GF RA   B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR
#=GF RL   BMC Bioinformatics. 2002;3:2.
#=GF WK   Ribosomal_RNA
#=GF SQ   46



AEYK01000034.1/11-1270           CACCAGGUUGAUUCU--GCCUGAC-GUAG-AUGCUAGUCUCUAAGAUUAAGCC-AUGCAUGU--UUCCGCA-------A------UCAGGG-ACGAAUAGCUC-AGUAAAACUGCGAU--GAUUUAGUCUGGCU----GUGUA-GAUAACUACGUGAAAAUGUAGC-UAAGGGA------------------------------------------------------------AGGCAGAAUAAGACGCAGGACUAUCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACAGUGACGGUUGACGGG-AAAUUAGGGUUUUGUACCGGAGAGGGAGCCUGAGAGAUUGCUCCCACGUCCAAGGACGGCAGCAG-GCGCGAAAAUUGCCCACUCUUU------GCAGGAGGCAGUUAUGAGACGUGAAGAUGA----------------------GUAUCUUGUAAAGAGGGAUAGGAG----AAUU--GGAGGG-CAAGU-UUGGUG-CCAGCA-GCCGCGGUAAUA-CCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGUAGUCAUAGAAGGGCAAAGAGAGAUGCGAGGUCUCA--CAGUG---------------------------------------------------------------------------------------------------CGAUGAUGGAGGAGCCGA-UGGGGAACAUAGUAUACCAGGGCGAGAGAUGAAAUG-CCAAGACCCCUGG-U-GGACUGAGCGAGGC-GAAGGCGAUGUUCUUGUAGG-CAUUCGGUGAUCAAGGACGAAGGC-UGGA-GUAUCGAAAGUGAUUA--GAUACCGCAGUAGUUCCA-GCAGUAAAAGAUGCCGACAUGCUCAUUG--------------GACA---CAGUGGGCAGG-GAGAAA--UCU-UAAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGGGU-GAAAAUU-AAA--GAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCU---UAAUUUGACUCAACGCGAG-GAAACUUACCAGGGCCAA--GUAUUGUG-UAGA------AAC-----------------GAG--CAAUACAGGAGUGGUGCAUGGUC-GUUGGAAAUUGAUGGGAUGACUU-UGACCUUAAAU-GGUU-GAAUGAGUGAGAUCUUUU--------------------------------------------------G------GACAUGUUCC-GCACGGAACAGGAAGGAAAAGGCUAUAACAGA-UCCGAGAUGCCCUCAGAUGCCCUGGGCUG-CACGCGCAAUACAAUAGCA---GGUAGAGAGAGAGACAG-----------GAAGG--UGCU---CAGAUGGACUAUGUGCUGUAAG-GCACAUACGAAAGAGGAAUUCCUAGUAAGUGUGUA-UCAACAAUGGAUAUUGAAUAA-GUCCCUGUAGCUUGUACACACCGCCCGUCACUAUCUCAGAUGUUUUUC-AGGAUGAA--GA-GUCCAG----------------------------------------------------------------------------------------------------GC-UCUGAAUAAUGAAAAGUAGAUAAGAUGUAAGUCGUAACAA--GGUUGCGGUCGGUGAACCAGCCGCAGGAUCAUUG
L07255.1/1-1299                  CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUAUUCUCUGGGGCUAAGCC-AUGCAUGC--UUGUGAACU-CUUUGU-GGG-GGAUUA-GCGGACGGCUC-AGUGAUAGCACGAU--GAUUUGUUUGCGGG---AUGAGC-AGUAGCUGCGGGAAACUGCAGA-UAGUGGUCUGCCCC----------------------------------------------UGUGGGGUUGGCAAGUAAGUUGUGGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGCAGACGGGAUACGGG-GGAUCAGGGUUUGGUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAG-GCGCGAAACUUGCCUAAUCCUU------UGGGGAGGCGGUUAUGAGAAGUGAUGUGUG----------------------UGCGAGUGCAAAGGGGUCGCAUGU----GAUU--GGAGGG-CAAGU-CGGGUG-CCAGCA-GCCGCGGUAAUA-CCUGCUCCAAUAGUGUCUAUGGUGGAUGCUGCAGUUAAAAUGUCCGUAGUCUGUUGUGUAUGUCUUUGUGUGUGAUGUUUG-----------------------------------------------------------------------------------UGGUUGUGUGUGGAUGUAG----UGAUGUGUGUGGCAGAGGA-CGAGGGGCACUGGAUAGUUGGGCGAGAGGUGAAAUG-CGAAGACCCUGAC-U-GGACGAGCGGAAGC-GAAGGCUGUGCUCUUGGACU-AAUGUUGCGAUGAAGGACGAAGGC-UAGA-GGAUCGAAAUCGAUUA--GAUACCGUUUUAGUUCUA-GCAGUAAACGAUGCCGACUGGACGGGACA--------------GUG--UGUGUUGUCCAU-GAGAAA--UCU-UGAGUAUGCGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGGAAACUU-GAA--GAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-GCAACUUACCGGCUCUGA-AGGAUGCCU-GUGAGUGC--AUG-------------GCAUGAG--GCAUGCGGCGGUGGUGCAUGGCC-GUUUUAAAUGGAUGGCGUGAGCU-UUGUCUUAAGU-UGCG-UAAGAUGUGAGACCCUUU---------------------------------------------------------GACGGUGUUC-UACGGAGCAAGGAGGGGAUGGAAAAGAACAGG-UCCGUUAUGCCCUGAGAUGAGGCGGGCUG-CACGCGCACUACGAUAGAUGGCGCUUCUG--------------------------CCUGCU---GUGAGGGAUGAAGCUGUGUAAG-GGGCUUCUGAACGUGGAAUUCCUAGUAAUAGCGGC-UGACGAAGCUGCUUUGAAUGU-GUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGACGCAC-UGGACGAA--GA-UCGGAA----------------------------------------------------------------------------------------------------GG-UCUGAGUCCUGAGUGUUAGAUAAGAUAUAAGUCGUAACAU--GGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA
HQ399665.1/1-1245                CACCAGGUUGAUUCU--GCCUGAC-GUAG-ACGCUAUUCCCUAAGAUUAACCC-AUGCAUGU--UUUUGAC-----AUU------UGAAAA-AUGGACUGCUC-AGUAAUACUCACUU--UAUUUAAUGUACAU----UUGAA-AAUAACUACGUUAAAGUGUAGA-UAAGAU-------------------------------------------------------------GUGUACAGUAAGAGUGAGACCUAUCAGCUAGUUGUUAAGGUAAUGGCUUAACAAGGCAGUGACGGGUAACGGUAUUACUUU-GUAAUAUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAG-GGGCGAAACUUGACCUAUGGAU-UUU--AUCUGAGGCAGUUAUGGGAAGUAAUAUUAUAU---------------UGU-UUCAUAUUGUAAAAGUAUAUGAGGUGAUUAAUU--GGAGGG-CAAAU-CAAGUG-CCAGCA-GCCGCGGUAAUA-CUUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUU-----------------------------------------------------------------------------------------------------------------------------------------AUAUUUAAGAAGCAAUA-UGAGGUGUACUGUAUAGUUGGGAGAGAGAUGAAAUG-UGACGACCCUGAC-U-GGACGAACAGAAGC-GAAAGCUGUACACUUGUAUG-UAUUUUUUGAACAAGGACGUAAGC-UGGA-GGAGCGAAGAUGAUUA--GAUACCAUUGUAGUUCCA-GCAGUAAACUAUGCCAACGAUGUGAUAUGA----------UAUUAA-UUGUAUUACAUGA-UAGAAA--UU--UGAGUUUUUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUU-GAAAAUU-AAA--GAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCU---UAAUUUGACUCAACGCGAG-GUAACUUACCAAUAUUUU--AUUAUUCA-GAGAAGAUAUAUU-------------AUCUGAG--GAUGAUAAUAGUGGUGCAUGGCC-GUUUUCAAUGGAUGCUGUGAAGU-UUUGAUUAAUU-UCAA-CAAGACGUGAGACCCUU------------------------------------------UU----UUUA-UA---GACAGACACA-AUCA-GUGUAGGAAGGAAAGGAUUAAAACAGG-UCCGUUAUGCCCUCAGACAUUUUGGGCUG-CACGCGCAAUACAAUAGAU------------------A-------------UAUA--AUCU---UUAUGGGAUAAUAUUUUGUAAG-AGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAU-UAAAUAAGUAGAAUUGAAUGU-GUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGAUAUGU-GUUGUGAA--AU-UAGUGAAA------------------------------------------------------------------------------------------------ACUA-CUUGAACAAUAUGUAUUAGAUCUGAUAUAAGUCGUAACAU--GGUUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA
AY017211.1/1-1231                CACCAGGUUGAUUCU--GCCUGAC-GUAG-ACGCU-UACUCUAAGAUUAACCC-AUGCAUGU-UUAUUGAAU---AUAA----A-GAAAAG-ACGAACAGCUC-AGUAACUCUUAUUU--GAUUUGAUGUAUUA----GGACU--CUAACUAUGUUAAAUUAUAGG-UAACAA-------------------------------------------------------------UAAUACAAUAAGAAUAAGAUCUAUCAGUUAGUUGUUAAGGUAAUGGCUUAACAAGACUAUGACGGAUAACGGUAUUACUUU-GUAAUAUUCCGGAGAAGGAGCCUGAGAGAUUGCUACUAAGUCUAAGGAUUGCAGCAG-GGGCGAAACUUGACCUAUGAUA-UUA--UAUUGAGGCAGUUAUGAGUAGUAUUUUAUAAUUA----------UUGUAG-UAUUGUAAGUACAUAUUACAAGAUA----AAUC--GGAGGG-CAAAU-CGAGUG-CCAGCA-GCCGCGGUAAUA-CUUGUUCCGAUAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCUGUAGUUU-----------------------------------------------------------------------------------------------------------------------------------------AUUUUAUAAUAAGCAUUGUAAGGUAUACUGUAUGGUUAGGAGAGAGAUGAAAUG-UGAUAACCCUAAC-U-GGAUGAACAGAAGC-GAAAGCUGUAUACUUAAAUG-UAUUAUUAGAC-AAGGACGUAAGC-UAGA-GGAUCGAAGAUGAUUA--GAUACCAUUGUAGUUCUA-GCAGUAAACUAUGUUGAAUCAUAGAUAUAUU---------UUGAUA--UAUAUUUAUGUA-GAGAAA--UUA-AGAUUUUAUUGACUCUGGGGAUAGUAUGAUCGCAAGAUU-GAAAAUU-AAA--GAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCU---UAAUUUGACUCAACGCGGG-GUAAUUUACCAGGUAUAA-CAUGAUAU--------AA--UAU-------------UU-------UAUCAUGAUAGUGGUGCAUGGCC-GUUUCCAAUGGAUGCUGUGAAGU-AAUGAUUAAUU-UCAA-CAAGAUGUGAGACCCUCA-----------------------------------------------UUUA------GACAGAUGUA-GUGAUACAUAUGAAGGAGAGGAUUAAAACAGG-UCCGUUAUGCCCUAAGAUAAUCUGGGUUG-CACGCGCAAUACAAUAAUAUU---------------------------------UGAUAUU---AUAAGGGAUAAUAUAAUGUAAG-AUAUAUUUGAACAUGGAAUUGCUAGUAAAUUUUAU-UUAAUAAGUAGAAUUGAAUGA-GUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGGUAUUA-UCUAUGAA--CAAAUUUAU----------------------------------------------------------------------------------------------------AA-AGUGAAUAGAUAGUACUAGAUCUGAUAUAAGUCGUAACAU--GGUUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA
ABGB01000454.1/88-1385           CCUUAGGUUGAUUUUUGGCUAAAG-GAAGAAUGUAUUUUUUUGGGAUUAAACCCAUGCAUGU--UCAGGAAAC-CCUUA--CGUGGGAAAG-GGGAACGGGUCCAGAAAGGUGGGGGA--AAUUGGGUUUCGGG----GGAAA-ACUAACCCCGGUAACCUGUGGU-UAAAA--------------------------------------------------------------GCGGGGAAUAAAGCGCAACCUUUUCAGCUUGUUGGUAG-GUAAAGGACUACCAAGGCCAUGACGGGUAACGGG-AAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAG-GCGCGAAACUUGUCCACUCCUU-ACG---GGGGAGACAGUCAUGAGACGUGAGUAUAA-------------------G-ACCUGAGUGUAAAGACCUUAGGGUGAAGCAAUU--GGAGGG-CAAGCUUUGGUG-CCAGCA-GCCGCGGUAACU-CCAACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAGGGUCCGUAGUCG-------------UGAAUGCAAUUAAAUGU--CGUUG---------------------------------------------------------------------------UUCAAUAGCGAUGAGUUUG----CUAAUGUUUGCGGAACGGA-UAGGGAGUGUAGUAUAGACUGGCGAAGAAUGAAAUC-UCAAGACCCAGUU-U-GGACUAACGGAGGC-GAAGGCGACACUCUUAGACG-UAUCUUAGGAUCAAGGACGAAGGC-AGGA-GUAUCGAAAGUGAUUA--GACACCGCUGUAGUUCCU-GCAGUAAACUAUGCCGACAGCCUGUGUGU-------------GAGA--AUACGUGGGCGG-GAGAAA--UC--UUAGUGUUCGGGCUCUGGGGAUAGUACGCUCGCAAGGGU-GAAACUU-AAAGCGAAAUUGACGGAAGGACACUACCAGGAGUGGAUUGUGCUGCU---UAAUUUAACUCAACGCGGG-AAAACUUACCAGGGUCAA--GUCAUUCG-UUGAUCG--AAUA--------------CGUGAG--AAUGGCAGGAGUGGUGCAUGGCC-GUUGGAAAUUGAUGGGGCGACCU-UUAGCUUAAAU-GCUU-AAACCAGUGAGACCUCCU--------------------------------------------------U------GACAGGUGUU-CUGUAACACAGGAGGGUGGAGGCUAUAACAGG-UCCGUGAUGCCCUUAGAUAUCCUGGGCAG-CAAGCGCAAUACAAUAUCUCU-UCAGUAGACAAAGUG---------------AUUUGAGAU---GAGUAGGAUCUACGUUUGUAAA-UACGUAGUGAAUAAGGAAUUCCUAGUAACGGUGCC-UCAUCAAGGCAUGGUGAAUGU-GUCCCUGUUCUUUGUACACACCGCCCGUCACUAUUUCAGAUGGUCAUA-GGGAUGAA--GA-GCUUCG----------------------------------------------------------------------------------------------------GC-UCUGAAUAUCUAUGGCUAGAUAAAGUACAAGUCGUAACAA--GGUUUCAGUUGGAGAACCAGCUGAAGGAUCAUUU
AF177920.1/1-1314                CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUAUUCUCUGGGGCUAAGCC-AUGCAUGU--UUAUGAAGC-CUUUAU-GGG-GGAUUG-ACGGACGGCUC-AGUGAUAGUACGAU--GAUUUGAUUGGGAG---CCUGGA-UGUAACUGUGGGAAACUGCAGG-UAAGUUCUGGGGGUGGUAGU----------------------------------UUGUAGCUACUGCGUACCGAGUAAGUUGUAGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGGAGACGGGAGACGGG-GGAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAG-GCGCGAAACUUGCCUAAUCCUU-AUU---GGGGAGGCGGUUAUGAGAAGUAAGAUGUU---------------------UAGCAAGUAUAAAUUUGUUGUGAUU----UACU--GGAGGG-CAAGU-CGGGUG-CCAGCA-GCCGCGGUAAUA-CCUGCUCCAGUAGUGUCUAUGGUGAAUGCUGCAGUUAAAAUGUCCGUAGUUGUUUGUAUGUCUUUUGAGUGAUGUUUAUGGU--UUUUA---------------------------------------------------------------------------GUGGAUGUAG--------------UUUUAUUGUAGCAGAGGA-CGAGGGGCACUGGAUAGUUGGGCGAGGGGUGAAAUA-CGAAGACCCUGAC-U-GGACGAAGAGAAGC-GAAGGCUGUGUUCUUGGACU-UUUGUGGUGAUGAAGGACGAAGGC-UAGA-GGAUCGAAAUCGAUUA--GAUACCGUUUUAGUUCUA-GCAGUAAACGAUGCCGACUGGACGGGACU------------GUUUU--AGUGUUGUCCGA-GAGAAA--UCU-UAAGUAUGUGGGUUCUGGGGAUAGUAUGCUCGCAAGAGU-GAAACUU-GAA--GAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-GCAACUUACCGGUUCUGA-AGUGAGUGU-GAGAGUGU-UUUU-------------ACAUGAU--GCUUACGGCGGUGGUGCAUGGCC-GUUUUAAAUGGAUGGCGUGAGCU-UUGGAUUAAGU-UACG-UAAGAUGUGAGACCCUUU-------------------------------------------------UU------GACUGUGCUC-UAUGGGGCAAGGGAGGAAUGGAACAGAACAGG-UCCGUUAUGCCCUGAGAUGAAGCGGGCGG-CACGCGCACUACGAUAGAUGCCUAUGUGG--------------------------GCUACU---GUGAGGGAUGAAGCUGUGUAAU-GGGCUUCUGAACGUGGAAUUCCUAGUAAGAAUGAU-UGAACAAGUUAUUUUGAAUGU-GUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGACGCAG-UGGACGAA--GA-UUGAGA----------------------------------------------------------------------------------------------------GG-UCUGAGUCUUUCGUGUUAGAUAAGAUAUAAGUCGUAACAU--GGCUGCUGUUGGAGAACCAGCAGCAGGAUCAGUA
HM594264.1/1-1395                CACCAGGUUGAUUCU--GCCUGAC-GUGG-ACGCUUGCCUCGGAGAUUAAGCC-AUGCAAGU--CUGUGAAUA--UUA----UU-GGAACA-GUGAACGGCUC-AGUAUAACACGUCU---AUCUACCCACUU-----GCAUU-AAUAACCAUGGGAAACUAUGGC-UAAUA---------------------------------------------------------------UUGUGGAUGAGGAUGUGACCUAUCAGCUUGACGGUACGGUAAGUGCGUACCGAGGCGAUAACGGGUAACGGG-GAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAG-GCGCGAAACUUACCCAAUGA---ACA----UUGAGGUAGUUACGGGGCGUACUUUUUGU----------------AUG-AAGUGUGUGUAAAAAGCAUGCCGAA---GUACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUA-CCAGCUCCAGUAGCGUCUGUGUUUAUUGCUGCGGUUAAAAUGUGCGUAGUCUGGUUGCGGGCCUGAGUCAAAGACGCACUUU--CGUGG---------------------------------------------------------------------------UGUGGAGGAUUUCAGGAAC-----CCAGGCCUUGAGACAGGG-AAGAGGUGACGAUAUUUGGUUGUGAGAGGUGAAAAU-CGAUGACCUGCUA-A-GGAGCGACAGAGGC-GAAAGCGGUCACCAGGAACU-GAUCUGACGAUCAAGCACGUGAGC-AGGA-GUAUCGAAGAGGAUUA--GAGACCCACGUAGUUCCUUGCAGUCAACGAUGCCAACAGUGUGGUGGA--------------ACA--UCCAUUGCGCGA-GCGAAA--GC---UAGUUUGUAGGCUCCGGGGAUAGUACGGACGCAAGUUU-GAAACUU-GAA--GAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGU---UAAUUUGACUCAACGCGGG-AAAACUUACCCGGGCAGGCAAUAGUCUU-GAGAUGC--UGAU--------------GCAGAU--GACAUUGCGCGUGGUGCAUGGCC-GUUCUUAACACGUGGGGUGACCUGUCUGGUCAAAU-CUGA-UAACGCGUGAGAGGUGAUUAGUCAUACGCCA--------------AGUUUAGCUUUGUGUG----UGAU-UA---GACGAUGUGU-GUAAGCACAAGGAAGAUGCACCCAAUAACAGG-UCUGUGAUGCCCGUAGAUGUCCGGGGCUC-CACGCGCACUACAAUGGAAGACAGUAAGUAUAGAUAG---------------UAGUUUUUCG-UAGUUGGGAUUGACGUAUGUAAU-UAUGUCAUGAACUUGGAAUUCCUAGUAGUUGGUAG-UCAUUAACGACCGACGAAUAA-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUG-CGGGUGAA--GA-UGUGAAUUGCUCUGUGCAUGCACGUGAGUGAGUGUACAGAU------------------------------UACUGAAAAGGCUUGCCUUUGAAGUUAGGCAUGAGCA-UAAGAACCCGUGCAGCUAGAUUGGAUGUAAGUCGUAACAA--GGUAACCACG-----A--CGUGGUUUGUGCUGCC
AJ252950.1/1-1417                CACCAGGUUGAUUCU--GCCUGAC-GUAU-GUGCUUGUCUUAAAGAUUUAGCC-AUGCAAGU--UAGUGAAAC-UUUUUA-AGU-GAAACG-ACAGACAGCUC-AGUAAUACAGUAAU--GAUUAACUUGCCUA---AUAUAG-GAUAACCUUGGUAACCUAAGGC-UAACACUUUUUUCAAAUUAAAAUGUAGGUG---------------AAACUAUUUUUAAUUUUUUUUUGGGGCAAUUAAGUUUCUGACCUAUCAGCUAGAUGUUAGGGUAAAGGCUUAACAUGGCUACAACGGGUAACGGA-GAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAUUAGCUACCACGUCUAAGGAUGGCAGCAG-GCGCGAAAAUUACCCAAUUCCUUAAU--GGGAGAGGUAGUGAAAAGACAUGAUUUUCAUUUCG---------AUUGAG-UCGGUACAUUAAAUAAGUACUGAAG---CAACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGUAGCGCAUAUAAUAGUUGCUGCAGUUAAAAUGUCCGUAGUUGAUUUAAUUAAACUGUGAGUAAAUUAUAGAG--CUCAA---------------------------------------------------------------------------AACUAUAAGUAAGCAUGGUA-UUAUAAGAUAAUAGGAACAGA-UGAUGGCAAUAGUAUUCAAUAGUUAGAGGUGAAAAU-UUAAGACCUAUUG-A-GGACUACCAGAAGC-GAAAGCGAUUGUCAAGGAUG-UCUCCAUUAAUAAGGGACUUAAGC-UAGA-GUAUCGAAGAUGAUUA--GAUACCGUCGUAGUUCUA-GCUGUAAACGAUGCCUACUAGGUGAUGUU------------UAAAU--GGCUAUGCCUUAGGAGAAA--UC--AAAGUCUACGGGCUCUGGGGAUAGUAUACUGGCAACGGU-GAAACUUAAAU--GAAAUUGACGGAAGAAUACCACGAGGAGUGGAUUAUGCGGCU---UAAUUUGACUCAACGCGGG-ACAACUUACCAGAGCCGA-ACCUGUAU--GAGAAUUU-AUAAU----------GUAAAUGAU--AAUAGGGAAGGUGGUGCAUGGCC-GUUUUCAACACGUGGGGUGACUUGUCAGGUUAAUU-CCGA-UAACGCGUGAGGUUUAUUAAAU---------------------------------AAUUGU----UUAU-UU---GACGGAUGAUAAGAAAUCAUAGGAAG--UUAAGCUAUAACAGG-UCGGUGAUGCCCCUAGAUGUUCUGGGCUG-CACGCGUACUACAAUGAUAUAUUUAAUAUUAAUAUUGAGAAAUAUAACUCUAAUAUAUAUCG-AAGCUGGGAUAAGCUAUUGUAAA-UUAGUUUUGAACUUGGAAUUCCUAGUAAUCAUAAG-UCAUUAUGUUAUGAUGAAUGC-GUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUAAGAUGGAUGUA-UAGGUGAA--AUGGCUAGACGUAAA----------------------------------------------------------------------------------------UGGAAAGC-AGUUAACCUGUGCAACUA-AUAGGAUAUAAGUCGUAACAA--GGCUGCUAUAGGUGAACCAGCAGCAGGAUCAUAA
AB623035.1/201-1558              AACCAGAUUGAUUCU--GUCUGAC-GUGG-AUGCUAGUCUCAUAGGUUAAGCC-AUGCAUGUGCAAGCGAAGC--GUAA---GU-GGAGCG-GCGCAAGGCUC-AGUAAC-GGGCGAG--UAUUUGAUCUCCUA----GAGUG-GAUAUCCUCUGUAACCGGAGGG-CAAAACACAAGAUGAGCGAUUGACGAGCU----------------CGUUCGUUUAACGAAUAGUGUAGGGGAGAGUAAGAAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGU-ACGGG-GAAUUAUCGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAG-GCGCGAAAAUUACCGCAGCCUGCGUU--CAGGGCGGUAGUAAGGAGACGUGAAAACAA----------------------UGUGCGGGCAAAAAACGCACUAGA----UACA--GGAGGA-CAAGA-CUGGUG-CCAGCA-CCCGCGGUAAUA-CCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGAAGUGGUUAUAACGGCGUAACAGGCCUUCU--CUCAA---------------------------------------------------------------------------GGAGGGUUAUGCGCCGUGAU--UCCAUGGAAUAAGGAGCGUU-UAGGGGCCAGGUUAUUAAGCGACGAGGGGUGAAAUC-UGGUGACUCGCUU-A-GGAGCAACAGAGGC-GAAAGCGCUGGCCAGGAGCG-AAUCCGAUGAUAAAGGACGUAGGC-UAGA-GGAUCGAAGACGAUUAGAGAGACCGUUGUAGUUCUA-GCAGUAAACGAUGCCGAUACCGUGGUGCG-------------GAUA--GGCGACGCGGAA-GAAAAA--UC---GAGUA---GGGCCCUGGGGAGAGUACACGCGCAAGCGA-GAAAUUUAAAG--GAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAGCUUACCAGGCCCGA--CGGCCGG--ACGAGUGU--UGU-------------ACACGAU--AGGUCGAAGAGUGGUGCAUGGCC-GUUA-CGACGAGUGAGGUGACUU-UUGGGUUAAAU-CCGG-GAAGUAGUGAGACCCCUA-----------------------------------------CC----GAAA-GG---GACAGGUGCC--GAAAGCACAGGAAGGAAGGGUCAAGAACAGG-UCAGUGAUGCCCUCAGAUGGUCUGGGCUG-CACGCGCACUACAGUGGUCAUAGAAAUGAAACGAUAGAA----------UUAAAGAUGAUC---GAGAGGGAAUGAGCUUUGUAAG-AGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGACUCAUUAAGACGCGAUGAAUAC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCA-GGCGCGAA--CAAGCGAGA----------------------------------------------------------------------------------------------------GCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAA--GGUAGCUGUAGGAGAACCUGUAGCUGGAUCAGAA
L16867.1/1-1295                  CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUGUUCUCUGGGACUAAGCC-AUGCAUGU--UGAUGAACC-UUGUG---GG-GGAUUG-ACGGACGGCUC-AGUGAUAGUACGAU--GAUUUGGUUGGCGG---GAGAGC-UGUAACUGCGGGAAACUGCAGG-UAGGGGGCUAGGAGUGU-----------------------------------------UUUUGACACGAGCCAAGUAAGCUGUAGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGGAGACGGGAGACGGG-GGAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAG-GCGCGAAACUUGCCUAAUCCUU------UGGGGAGGCGGUUAUGAGAAGUGAGUUUUU----------------------UUCGAGUGUAAAGGAGUCGAGAUU----GAUU--GGAGGG-CAAGU-CGCGUG-CCAGCA-GCCGCGGUAAUA-CCUGCUCCAAUAGUGUCUAUGGUGAAUGCUGCAGUUAAAAAGUCCGUAGUCUUUUGUAUGUCUUUGUUUGGGGGAUUAUGUC--CUGAU---------------------------------------------------------------------------GUGGAUGU----------------AAGAGGUUUGGCAGAGGA-CGAGGGGCACCGGAUAGUUGGGCGAGGGGUGAAAUA-CGAAGACCCUGAC-U-GGACGGACAGAAGC-GAAGGCUGUGCUCUUGGACU-UAUGUGACGAUGAAGGACGAAGGC-UAGA-GGAUCGAAAUCGAUUA--GAUACCGUUUUAGUUCUA-GCAGUAAACGAUGCCGACUGGACGGGACU-------------AUAU--AGUGUUGUGCAU-GAGAAA--UCU-UGAGUAUGUGGGUUCUGGGGAUAGUAUGCUCGCAAGAGU-GAAACUU-GAA--GAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-GCAACUUACCGGUUCUGA-AGCGGGCAG-GAGAACG--AGGA--------------CGGGAU--GCGUGCGGCGGUGGUGCAUGGCC-GUUUGAAAUGGAUGGCGUGAGCU-UUGGAUUAAGU-UGCG-UAAGAUGUGAGACCCUUU---------------------------------------------------------GACAGUGCUC-UUUGGGGCAAGGGAGGAAUGGAACAGAACAGG-UCCGUUAUGCCCUGAGAUGAAGCGGGCGG-CACGCGCACUACGAUAGAUGGCGAGGGAG--------------------------CCUGCU---GUGAGGGAUGAAGCUGUGUAAU-GGGCUUCUGAACGUGGAAUUCCUAGUAAUAACGAU-UGAACAAGUUGUUUUGAAUGG-GUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCCAAGAUGACGCAG-UGGACGAA--GA-UUGGAA----------------------------------------------------------------------------------------------------GG-UCUGAGUCCUUCGUGUUAGAUAAGAUAUAAGUCGUAACAU--GGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA
AF484690.1/1-1388                CACCAGGUUGAUUCU--GCCUGAC-GUAU-GCGCUUGUCUUGAAGAUUUAGCC-AUGCAAGC--CAGUGA-CC--GUAA---GG-A--ACG-GCAGACAGCUC-AGUAAUACAGUUAU--AAUUUACUCGUAGG----AUAUG-GAUAACCAUGGAAAACUAUGGC-UAAAACAUAGGGAGAAUACCGUCACA-----------------------GGGAAUUUUGAGGUAUUUGAUACGAUUAAGUUUCUGACCUAUUAGUUAGAUGGUAAGGUAAAGGCUUACCAUGGCUGUGAUGGGUAACGGG-GAAUUAACGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCUAAGGAUGGCAGCAG-GCGCGAAACUUACCCAAUUCCUUGCC--GGGAGAGGUAGUGAAGAGACGUGAAAUAUAAUU------------UAGCG-AGGGCAUAUUAAAUGGCAGCCUGUA----AACU--GGAGGG-CAAGC-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGUAGCGCAUAUAACUAUUGUUGCUGUUAAAACGUCCGUAGUAGAUUAUUCUGUUACUAUGACAAAAAUGUAUA--UCUCA---------------------------------------------------------------------------AAUGAAAUAUAUAGCAUAGUACAAAGUAAAGACAGGAACAGA-UGAUGGCAGCAGUAUUUAAUAGUUAGAGGUGAAAAU-CGAAGACCUAUUA-A-GGACUCUCAGAAGC-GAAAGCGGCUGUCAA----G-UAUCUGUAU-CCAAGGACUCAC-----GA-UUAUCGAAAUUGAAUG--GAUACCA---UAGUACCA-UUUGUAAACAAU---UAGAGUGAGGACUA--------------CAU--UACUCCUUACAA---GAAACCAA--CGUUUAAUUGACCAGGGGGGAUAGUACGAAAGCAAUUUU-GAAACUU-AAA--GAGAUUGACGGAAGGAUACCACAAGGAGUGGAUUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAACUUACCAGGGCCGA-AUGUCUAU--GAGAUUGG-CUAUCUGAGA-AGAUACCCGAGAU--UAGACAAAGGGUGGUGCAUGGCC-GUUUUCAACACGUGGGGUGACCUGUCAGGUUAAUU-ACGA-UAACGCGUGAGGCCCUAAAUGC--------------------------------AACAGUG----UUGU-AU---GACGGACAGU-GCAAACUGUAGGAAG--GAGGGCGAUAACAGG-UCAGUGAUGCCCCCAGAUGUUCUGGGCUG-CACGCGCAAUACAAUAUAUGAAAAAGAAUAGAGUGUGAAAACUU-AGAUUUAAUGUCAUAUG-UACCAGGGAUAAGCGCUUGUAAA-UGCGUUUUGAACAUGGAAUUCCUAGUAAUCGCAGG-UCAUUAUGCUGCGAUGAAUGU-GUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUUAGAUGAAUGUA-UAGGUGAA--AUGGCUGGACGAAA------------------------------------------------------------------------------------------GAAAGGCAGUUGAACCUGUGCAAUUAGAUAAGAUAUAAGUCGUAACAA--GGCUGCUAUAGGAGAACCUGUGGCAGGAUCAAUA
AY230191.1/1-1391                CACCAGGUUGAUUCU--GCCUGAU-AUGU-GUGCUAGCGUCAAAGAUUUAGCC-AUGCAUGC-UUUUCGAACC-CUCGU---GG-GGAGAG-GCGGAUAGCUC-AGUAAUACAGUUAC--AACAUAAGCUGCGU----GUGUG-GAUAACCUUGUUAAGAUAAGGC-UAAGACUUAGCGUGUCGCACUUUU--------------------------GUGAAGAAAGGCGACUUGAGCAGCAUUGGUUUCUGACCUAUCAGUUAGUAUGUUCUGUAAGGGAGAACAUAGACUAUGACGGGUAACGGG-GGAUGCACGUCUGAUACCGGAGAGGAAGCCUUAGAGACAGCUUUCACGUCCAAGGAUGGCAGCAG-GCGCGAAACUUACCCAAUUGUUUUUUGUGACAGAGGUAGUUAUGACGUAUUCUUUAGA-------------------GAGAGACCUUGUUAGACAUGGUCCAUAG--CGACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGUAGUGCAUAUAC---AUGCUGUAGUUAGAAAGUUUGUAGCCUAUUUAUGGAUUGUUUUAGACAAAAGGACGA--CUCAA---------------------------------------------------------------------------AUUGACCUUUCAUUUGACUA-AUGCAUGAAUGUAGAAGCGAU-UGAAGGCGAUUGUAUUCACCAGCCAGAGGUAAAAUU-UGAUGACCUGGUG-A-GGACACACGGAGGC-GAAAGCGAUUGCCUAGAGCG-UAUUCAGUGGUCAAGAACGUAAGC-CGGA-GGAUCAAAGAUGAUUA--GAUACCGUUGUAGUUCCG-GCCGUAAAUUAUGCCAACUUGUGCUUCUG------------CUUCU-GCGGAGGCGCAUA-GAGAAA--UCA-AGAGUUUAUGGGCUCUAGGGAUAGUAAUCCGGCAACGGA-CAAACUU-AAA--GAAAUUGGCGGAAGGACACCACAAGGAGUGGAUUAUGCGGCU---UAAUUUGACUCAACGCGGG-ACAACUCACCAGAGCCUA--UGUGCAG--GAGACAGU-GAGCUUUGA--GAGCGGACUGGAU--AGUACUUUGAGUGGUGCAUGGCC-GUUUGCAACACGUGAGGUGACUUGUCAGGUUUACU-CCGG-UAACGUGUGAUGUGCUGUAUGCA-------------------------------AGUAUUU----UUGU-GA---GACUGCAGGCGGUAAGCCUGAUGAAG--CGGCGCUAUAACAGG-UCAGUGAUGCCCUUGGAUGUUCUGGGCUG-CACGCGUAAUACAGUGGGUGCUGUAGAUAUAUAUAGGUG-----------GAAAAGGGCCCG-AGACUGGGAUCAUGCUUUGUAAGAAGGAAUGUGAACGUGGAAUUCCUAGUAAUCGCUGC-UCACUAAGUAGCGAUGAAUGA-GUCCCUGUUCUUUGCACACACCGCCCGUCGCUAUCUGAGAUGGAUGUU-UUUAUGAA--GA-UGCUGCUGUU-------------------------------------------------------------------------------------------AGAGGCA-UUUGAGUAAGGACGACUAGAUUAGAUAUAAGUCGUAACAA--GGCAGCGGUAGAAGAAUCUGCCGCUAGAUCAUAC
AJ252956.1/1-1373                CACCAGGUUGAUUCU--GCCUG---GUGG-AUGCUAGUUUCAUAGGUUAAGCC-AUGCAUGUGUAAGCGAAGC-UUUUA---GU-GGAGCG-GCGCAAGGCUC-AGUAACGGGCGUCU--GAUUUGAUCUCUCG----GAGUG-GACAACCUCUGUAACCGGAGGC-CAAAACACGGGAGGGGCAUGCAGUGGAG-------------------AUGCCCCGAGAACAUUAGUGAGAGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAGGACGGGU-ACGGG-GAAUUAGAGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAG-GCGCGAAAAUUACCGAAGCCUGCAUU--CAGGGCGGUAGUAAGGAAACGCGAAAACGA----------------------UGUGCAGGUAAAGAAUGCACUAGU----AACA--GGAGGU-CAAGA-CUGGUG-CCAGCA-UCCGCGGUAAUA-CCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGACUGCGUGACUGGCGUGAAAGACCCUUUU--AUUCGUUCAU----------------------------------------------------------------UCAAGGGGGGCGCAGCGCCGGAAAA----GCAGGGAAUAAGGAGCGGC-CGGGGCACAGGUUAUUAAGCGACGAGAGGUGAAAUU-UGAUGACUCGCUU-A-GGAGCAACAGAGGC-GAAAGCGCUGUGCAGGGGCG-AUUCCGAUGAUAAAGGACGUAGGC-UAGA-GGAUCGAAGAUGAUUA--GAGACCGUUGUAGUUCUA-GCAGUAAACGAUGCCGAUGCCGUGGGGCAGU--------UCUUAGA-CUGCGCCGCGGAA-GAGAAA--UU---GAGUA---GGGCCCUGGGGAGAGUACACGCGCAAGCGA-GAAAUUUAAAG--GAAUUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAGCUUACCAGGCCCGA--CGACCGC--ACGAGUGU--GGU-------------ACACGAU--AGGUCGGAGAGUGGUGCAUGGCC-GUUAACGACAAGUGGGGUGACCU-UUGGGUUAAGU-CCGG-GAAGUUGUGAGACCCCUG-----------------------------------------CUG-GCGAGCCAG---GACAGGUGCU--CAAAGCACAGGAAGGAAGGGUCAAGAACAGG-UCAGUGAUGCCCUUAGAUGGUCUGGGCUG-CACGCGCACUACAGUGGUCACACGAGUUUAUAGAUAGAA----------GAAAUGGUGAUC---GAGAGGAAAUGAGCUUUGCAAG-AGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUAC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCA-GGCGCGAA--CAAGCGAGA----------------------------------------------------------------------------------------------------GCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAA--GGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA
AJ252954.1/1-1389                CACCAGGUUGAUUCU--GCCUGGC-GUGG-AUGCUAGUCUCAUAGGUUAAGCC-AUGCAUGUGUAAGCGAAGC-AUUUU---GU-GGAGCG-GCAUAAGGCUC-AGUAAC-GGGCGUC--UAUUUGAUCUCCUG----AUGUG-GACAACCUCUGUAACCGGAGGC-CAAUACACAUGAGGCACUGUUUCCGUUUGGUGGGG----UGUCAAUAGCUAUUUAAUUUUUAUAGCGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGU-ACGGG-GAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCAGGUCCAAGGACAGCAGCAG-GCGCGAAAAUUACCGAAGCCUCCGGU--GAGGGCGGUAGUAAGGAGACGUGAAUACGA----------------------UGUGCAGGUAAAUAAUGCACUAGU----AACA--GGAGGU-CAAGA-CUGGUG-CCAGCA-UCCGCGGUAAUA-CCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGUGUUCGUAGUCGGGCUGCAUGACUGGCGUGAAAGACCUUCCU--UUCAA---------------------------------------------------------------------------GGGGGUACAGCGCGGGGAA---AGCAGAGAAUAAGGAGCGUU-UUGGGGUCAGGUUAUUAAGCGACGAGAGGUGAAAUU-UAAUGACUCGCUU-A-GGAGCAACAGAGGC-GAAAGCGCUGGCCAGGGGCG-AAUCCGAUGAUAAAGGACGUAGGC-UAGA-GGAUCGAAGACGAUUA--GAGACCGUUGUAGUUCUA-GCAGUAAACGAUGCCGAUGCCGUGGAGCGA----------GUUUUAUUCGCUUCGCGGAA-GAGAAA--UU---UAGUA---GGGCCCUGGGGAGAGUACACGCGCAAGCGA-GAAAUUUAAAG--GAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUCAACUCAACGUGGG-ACAGCUUACCAGGCCGGA--CGACCGC--ACGAGUGU--AGU-------------ACACGAU--AGGUUGAAGAGUGGUGCAUGGCC-GUUAACGACAAGUGGGGUGACCU-UUGGGUUAAGU-CCGG-GAAGUAGUGAGACCCCUGCUGUUA----------------------------CGAGUAAUG----GUGA-CA--GGACAGGUGCU--CAAAGCACAGGAAGGAAGGGUCAAGAACAGG-UCAGUGAUGCCCUUAGAUGGUCUGGGCUG-CACGCGCACUACAGUGGUCAC-AGAAAGAGAUUAUUGAGA--------GAUAAUGGUGAUC---GAGAGGGAAUGAGCUUUGUAAG-AGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUAC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCA-GGCGCGAA--CAAGCGAGA----------------------------------------------------------------------------------------------------GCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAA--GGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA
AJ252951.1/1-1352                CACCAGGUUGAUUCU--GCCUGGU-GUGG-AUGCUAGUCUCAUAGGUUAAGCC-AUGCAUGUGUAAGCAAAGC-UAGAA---GU-GGAGCG-GCGCAAGGCUC-AGUAAC-GGGCGGA--CAUUUGAUCUUCUC----GUGUG-GACAUCCUCUGUAAGCGGAGGG-AAAAACACAGGACGCGCGGACGCAGCC---------------------CGUGGGUGUAACGGCGGUGGAGAAGAGUAAGACGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGU-ACGGG-GAAUGAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAG-GCGCGAAAAUUACCGCAGCCUG-CCU--CAGGGCGGUAGUAAGGAGACGUGAAUGCGA----------------------AGUGCUAGCAAAGAAAGCACUGAC----AACA--GGAGGA-CAAGA-CUGGUG-CCAGCA-CCCGCGGUAAUA-CCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGGGUUCGUAGUCUGAGCGGAACGAGGGGUGUGACGGGUCCCAG--CUCAA---------------------------------------------------------------------------GGGGGACAUAGCACCGCGAU--GCCGCGGAACAAGGAGCGUC-UAGGGGCCAGGGUAUUAAGCGACGAGGGGUGAAAUC-UGGUGACUCGCUU-A-GGAGCAACAGAGGC-GAAAGCGCUGGCCAGGGGCG-AGUCCGAUGAUAAAGGACGUAGGC-UAGA-GGAUCGAAGACGAUUA--GAGACCGUUGUAGUUCUA-GCAGUAAACGAUGCCGAUGCCGUGGUGCC-------------GCAA--GGCGACGCGGAA-GAGAAA--UU---GAGUA---GGGCCCUGGGGAGAGUACACGCGCAAGCGA-GAAAUUUAAAG--GAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAGCUUACCAGUCCCGA--CGAUCGG--AGGAGUGU--GUU-------------ACACGAU--AGGUCGGAGAGUGGUGCAUGGCC-GUUAACGACGAGUGGGGUGACCU-UUGGGUUAAGU-CCGU-GAAGUAGUGAGACCCCUG-----------------------------------------CC----GCAA-GG---GACAGGUGCC--GAACGCACAGGAAGGAAGGGUCAAGAACAGG-UCAGUGAUGCCCUCAGAUGGGCUGGGCUG-CACGCGCACUACAGUGGUCGCAGAAAAGGAAGGAAAGAG----------AUAAAGGCGAUC---GAGAGGGAACGAGCUUUGGAAG-AGGCUCGGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAGGACGCGAUGAAUAC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCA-GGCGCGAA--CAAGCGAGA----------------------------------------------------------------------------------------------------GCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAA--GGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA
EU260046.1/1-1256                CACCAGGUUGAUUCU--GCCUGAC-GUCC-CCGCUAGUCUCUGAGAUUAAGCC-AUGCAUGU--CUAUGGA--------------ACAAGG-ACGAACAGCUC-AGUAAAACUGCGAU--GAUUCAGUCUGUCU----GUCAA-GAUAACCACGCGAAAGUGUGGC-UAAGA-GG-----------------------------------------------------------GGACAGAACAAGACGCAGGACUAUCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACGGUGACGGUUGACGGG-GAAUGAGGGUUCUAUACCGGAGAGGGAGCCUGAGAGAUAGCUCCCACGUCCAAGGACGGCAGCAG-GCGCGAAAAUUGCCCACUGUUU------GGAGGAGGCAGUUAUGAGACGUGAGAAAGA----------------------GUGCUUGGUAAAGAGAAGCAGGAG----AAUU--GGAGGG-CAAGU-UUGGUG-CCAGCA-GCCGCGGUAAUA-CCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGUAGUCGUGGAGACGGAAAGAGAGGCGGAGCCUCUU---------------------------------------------------------------------------------------------------UGA----GAUGCUCUGGAGAAGCCAA-CAGGGGGCACAGUACACCAGGGCGAGAGAUGAAAUG-CCAAGACCCCUGG-U-GGACUGAGCGAGGC-GAAAGCGGUGCUCUUGUGGGGUGUUCGGUGAUCAAGGACGAAAGCUUGGAGGGAUCGAAAGUGAUU---GAUACCGCUGUAGUUCCA-GCAGUAAAAGAUGCCGACAUGCUCUGUGG---------------CA--ACACGGGGCAGG-GAGAAA--UC--UUAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGGGU-GAAAAUU-AAA--GAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCU---UAAUUUGACUCAACGCGAG-GAAGCUUACCAGGGCCAA--GUGCUGUG-GAGA------AAG-----------------GAG--CAGGACAGAAGUGGUGCAUGGUC-GUUGGAAAUUGAUGGGAUGACUU-UGGCCUUAAAU-GGCU-GAAUGAGUGAGAUCUUUG---------------------------------------------------------GACAUGUUCC-CACAGGAACAGGAAGGGGAGG-CUAUAACAGA-UCAGAGAUGCCCUUAGAUGCCCUGGGCUG-CACGCGCAAUACAAUAGCACGUAGACGUAGAGAACA----------------ACACGUGCU---GAGGUGGACUGUGCUCUGCAAG-GGGCACACGAAAGAGGAAUUCCUAGUAAGCGCCCA-UCACCAGUGGGCGUUGAGUCA-GUCCCUGUAGCUUGUACACACCGUCCGUCACUAUCUCAGAUGUUUUUC-GGGAUGAA--GA-GUCCAG----------------------------------------------------------------------------------------------------GC-UCUGAAUAACGGAAAGUAGAUAAGAUGUAAGUCGUAGCAA--GGUUGCGGUCGAUGAACCAUUAGCAGGAUCAUAA
GQ843833.1/1-1301                --ACAGGUUGAUUCU--GCCUGAC-GAGG-AUGCUUGUCUCUGGGAUUAAGCC-AUGCAAGU-CUGGUGAAGC--GAAA---GU-GGAACU-GCGAACGGCUC-AGUAGAACGGUGAU--UAUUUAAUCGUGUA----GGAAG-GAUAACCGCGGGAAACUGUGGC-UAAU---------------------------------------------------------------AACACGAGUAAGACGCCGACCCAUCAGUUUUAUCGUACGGUAAGGGCGUACGAUGGCUUUAACGGGU-ACGGG-GGAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCAGGUCUAAGGACAGCAGCAG-GCGCGAAACUUGCCCAAUUG----GA----GAGAGGCAGUUAUGAGACGUAUAUUUUG---------------------UAACCGGGGUAGAAUACCGGUGAUU----GACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGGAGUGUCAUAGUGCAUUGCUGCAUUUAAAAGGUCCGUAGUCAGUGUUGACAGGGAUGCUAGAAGACACUUUC--UUCAU---------------------------------------------------------------------------GGAGUGUAUUGGCAUUCUA---GGUUAGCAUGUAGGAGCGGA-AGAGGGCGACUGUAUUGCGUAGCGAGAGGUGAAAGU-UGACGACCUACGU-A-GGACAAACCGAAGC-GAAAGCUGUCGUCCAGUACG-UUUCCGGUGAUCAAGGACGUAAGC-CGGA-GGAGCAAAGGUGAUUA--GAGACCCCUGUAGUUCCG-GCCGUAAACUAUGCCAACUGGGUGUUAC---------------GUA---GUGGUACCCAC-GAGAAA--UC---AAGUAUAUGGGCUAUGGGGAUAGUACGAUCGCAAGAUU-GAAACUU-GAA--GAAAUUGACGGAAGGACACCACCAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAACUUACCAGGGCCA---GUUGUAUG-ACGAAUC---UUU--------------GAUGAG--UACGACUA-AGUGGUGCAUGGCC-GUUCACAACAUGUGAGGUGACUU-UUAGGUUUAUU-GCUG-UAAUGUGUGAGACCCUCA-----------------------------------------GC----UACG-GC---GACUGGGGACUAUAAGUUUCAGGAAGGAGGGGGCUAUAACAGG-UCUGUGAUGCCCUUAGAUGUUCUGGGCUG-CACGCGCACUACAAUGUUAUUUCUAGGUAUAUUGUAAAG----------AUAAAGGAUAACU-CGGUUGGGAUUGCGUUCUGUAAU-GGACGCAUGAACCAGGAAUUCCUAGUAGUCGCGUG-UCACUAACGGGCGACGACUGC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGUGCUA-UGUUCGAA--GAGGGUUUU----------------------------------------------------------------------------------------------------CCUUCUGAGGACGUAGGAUUAGAUUGGAUACAAGUCGUAACAA--GGUUGCUGUAGGAGAACCUGCAGCAGGAUCAGUG
L39110.1/1-1352                  CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUAGUCUCUAAAGUUAAGCC-AUGGAUGUCUAAGCAAAGC--GUAA---GU-CGAGCG-GCACA-GGCUC-AGUAA-CGGGCGAA--UAUUUAAUCUCCUC----GAGUG-GAUAUCCUCUGUAACCGGAGGG-CAAAACACAGGACGUGCAGUUGUAUAAGG-----------------AUUGUUCGUUUAACAUUAGUGGGGGAGAGUAAGACGCCAGUCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAUACGGAU-ACGGG-GAAUUAUCGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCGGGUCCAAGGACAACAGCAG-GCGCGAAAAUUACCGCAGCCUGCAUU--CAGGUCGGUAGUAAGGAGACGUGUAAACGA----------------------UGUGCAGGUAAAGAAUGCACUGUA----UACA--GGAGGA-CAAGA-CUGGUG-CCAGCA-CCCGCUGUAAUA-CCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGCGUUCGUAGUCGAACCGGGUUGAAUUGCGUGACAGUCAGACU--CUCAA---------------------------------------------------------------------------GGUGUGAUGAGCGCUGUGAU--UCUGGGGAAUAAGGAGUGUU-UAGGGGCCAGGGUAUUAAACGGCAAGCGGUGAAAUG-UGUUGACCCGUUU-AUGGAGCGACAGAGGC-GAAAG-GCUGGCCAGGGGCA-AAUCCGAUGAUAAAGGACGUAGGC-UAGA-GGAUCGAAGACGAUUA--GAGACCGUUGUAGUUCUA-GCAGUAAACAAUGCCGAUGUUGUGGUGCC-------------GUAA--CGGA-CGCAAAA-GAGAAA--UC---UAGUA---GGGCCCUGGGGAGAGUACACGCGCAA-CAG-GAAAUUUAAAG--GAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACACCUUACCGGGCCCA---CGGCCACACGA--GUGU--GAC-------------ACACGA---UAGCCGAGGAGUGGUGCAUGGCCCGUUAACGACAAGU-GAGUGAUCU-UUGGGUUAAGU-CCGU-AAAUUAGUGAGACCCCAG-----------------------------------------CA-------A-AG---GACAGGUGCG--CAAAGCACAGGAAGGAUGGGUCAAGGACAGG-UCAGUGAUGCCCUUAGAUGGUCCGGGCUG-CACGCGCACUACAGUGGUCGCCGAAAUUUAGAUAUAGAG----------CUAAAGGCGAUC---GAGAGGGAAUGAGCUUUGGAAG-AGGCUCAGGAACGUGGAAUUGCUAGUAAUCGCGGACUCAUUAAGACGCGAUGAAUAC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAUACGGUGCUC-GGCGCGAG--CA-AGGUGAAAU----------------------------------------------------------------------------------------------CACUG-AGCGAGCGCAAGGUACCGGAUCUGAUACAAGUCGUAACAA--GGUAGCUGUAGGAGAACCAUUAGCAGGAUCAUAA
AF027683.1/1-1342                CACCAGGUUGAUUCU--GCCUGAC-GUGG-ACACUUGCCUUGAAGAGUAAGCC-AUGCAAGC--UUGUGAAUA--AAUC---CU-GAAACA-GUGAACGGCUC-AGUAGAACACAUUU--CAUCUACCCAAGUU------AAA-AAUAACCAUGGGAAACUAUGGC-UAAA-UAU-----------------------------------------------------------AAUUUGGAUGAGAGUGUGACCUAUCAGCUAGUAGGUACGGUAAGAGCGUACCUAGGCUAUGACGGGUAACGGG-GAAUCAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAG-GCGCGAAACUUACCCAAUGA---ACA----UUGAGGUAGUUACGAGGCGUACCUAUGUAAUAUAAUUAUAUAGGGAUG-AGGUAUGAUUUCAAAUCAUGCACGAC--AUACU--GGAGGG-CAAGG-CUGGUG-CCAGCA-GCUGCGGUAAUU-CCAGCUCCAGUAGUGUCUAUGUAAAUUGUUGCGGUUAAAACGUGCGUAGUCUGAUUUGCGAGAUCUAAAGUAAAGAUGCUUU--UAUCUA------------------------------------------------------------------------AAAGUAGAAUAUUUUAGAGAU----CAAAAAUCUUGAGACAGAG-GAGAGGUAACGAAAUUCGAUGGCGAGAGGUGAAAAU-UGAUGACCCAUCG-A-GGAGAAACAGAGGC-GAAAGCGGUUACCAGAAGCU-GUUCUGACGAUCAAGCACGUGAGC-AGGA-GUAUCGAAGGCGAUUA--GACACCGUCGUAGUUCCUUGCAGUAAACGAUGCCCACACUGAUGUGCU--------------UAA--CGCAUGUCAGAC-GCAAAA--GUU-AAAGUG---AGGCUCCGGGGAUAGUACGGUCGCAAGAUU-GAAACUU-GAA--GAAAUUGACGGAAGGACACCACCAGGAGUGGAGUGUGCGGGU---UAAUUUGACUCAACGCGGG-AAAACUUACCAGUACAGA-UUACUAUCGUAUGAAGG--AAUA--------------CCUGAU--GAUGUAAUACGUGGUGCAUGGCC-GUUCUUAACACGUGAAGUGAUUCCUCGUGUCAAAU-CAGC-UAACGCGUGAGAGGCGAGUCUU---------------------------------AUUUUA----UAAA-UAAGAGACGGCAUAG-GCAACUAUGAGGAAGCAACGCCCAAUAACAGG-UCCGUGAUGCCCGUAGAUGUUCUGGGCUC-CACGCGCACUACAAUUAUAAAUACUAUUUUGUAA---------------------UUUAUAAUCAGUAGGGAUUGUUUGUUGUAAA-ACUUACAUGAACGUGGAAUUCCUAGUAUAUAGAUG-UAAGCAACGUCUAUUGAAUAUUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGUUAUU-AGGGGGAA--GC-UGAUAUAUU---------------------------------------------------------------------------------------------AUAUCA-GAAGACUUCUGGUAACUAGAUUGGAUGUAAGUCGUAACAU--GGUUGCAGUAGGUGAACCUGCCGCA-GAUCAGUA
AF394526.1/1-1319                CACCAGGUUGAUUCU--GCCUGAC-GUGG-ACGCUUGCCUUAAAGAUUAAGCC-AUGCAAGC--CAGCGAAG---GUAA----C-GGAGCG-GCGAACGGCUC-AGUAGGACAGGGUU---AUCUGACCACCGA-----ACAG-GAUAACCGCGGUAAUCUGUGGC-UAAUACG------------------------------------------------------------UGUGUGGGUGAGACUCUGCCCUAUCAGCUUGGGGGUACGGUAAGUGCGUACCCUUGCGACGACGGGUAACGGG-AAAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCACGUCCAAGGAUGGCAGCAG-GCGCGGAAAUUACCCACUUGGA-GGA---CCAGAGGUAGUGACGAGGCGUUUUUAAUG---------------------AGAAUAGUGUAAAAAGCUGUUCGAAA-GCAACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGGAGCGUCUGCGUGUGUUGCUGCGGUUAAAGAGUGCGUAGUCG--GGUUAUUUGCCAGCAAUAAAGGUGCAGU--CUCUA---------------------------------------------------------------------------ACUGUAUAUUGUGCUGGUA----CUUUGAUCUAGGAACUGGA-UAAAGGUUAUGGUAUUCGACAGCGAGGGGUGAAAAU-UAAUGACCUGUUG-A-GGAGCGACUGAUGC-GAAAGCGGUAAUCUAUGACG-GGUUUGACGAUAAAGCGCGUAGGC-AGGA-GUAUCGAAGGCGAUUA--GAGACCGUCGUAGUUCUUUGCAGUAAACGAUGCCAACAGGAAUGCAA---------------GUG---CUGUGUUCCUA-GGGAAA--CU---GAGUGUAUGGGCUCUGGGGAUAGUACAGGCGCAAGCUA-GAAACUU-GAG--GAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGU---UAAUUUGACUCAACGCGGG-ACAACUUACCAGGGUAUG-UGACAUUGA-GCGAAGAG-CAUGGAUGCGAUCUGUGUUCUGAU--GAUGUUACGUGUGGUGCAUGGCC-GUUCUUAACACGUGGGGUGACCUGUCUGGUUAAAU-CCGA-UAACGCGUGAGACCCUGG-----------------------------------------AU-------A-AU---GACGAUACUUGACAAGAGUAGGGAAGCUCGGGUCGAUAACAGG-UCUGUGAUGCCCAUAGAUAUUUUGGGCGC-CACGCGCACUACAUUGGGGAU-GGUUACGUGAAACGG---------------AACAUCCUUU-CGGUUGGGAUUGACGUUUGUAAA-UACGUCAUGAACUCGGAAUUCCUAGUAAUUUGUUG-UCAUUAACGACAUAUGAAUAU-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGAAUGUG-CGGAUGAA--GU-UGGUUAG-------------------------------------------------------------------------------------------------GUCA-AAAGAAUCCGUGCGAUUAGAUUGGAUACAAGUCGUAACAA--GGUUACUGUAGGAGAACCUGCAGUAGGAUCAAUA
AEUG01000221.1/50-1414           AUUCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUAGUCUCAUAGGUUAAGCC-AUGCAUGUGCAAGCGAAGC-CGGUG---GU-GGAGCG-GCGCAAGGCUC-AGUAACGGGCGACU--GAUUUGAUCUCCCG----GUGUG-GACAACCUCUGUAACCGGAGGC-CAAAACACAGGAGGCGCGUGACACGGGCA-----------------CGGGCGUGCAACCGGCAGGUGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGU-ACGGG-GAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAG-GCGCGGAAAUUACCGAAGCCCGCGUU--CGGGGCGGUAGUAAGGAGACGUGAAUACGA----------------------UGUGCAGGUAAAAUAUGCACUGGU----AACA--GGAGGU-CAAGA-CUGGUG-CCAGCA-UCCGCGGUAAUA-CCAGCUCCUGGAGUGUCUAUGAUGAUUGUUGCAGUUAAAGAGUUCGUAGUCGGGCUGCAUGACCGGCGCUGAAGGCUCCCUA--UCGAG---------------------------------------------------------------------------GGGGGCAGGGCGCCGGAAA---AGCAGAGGAUGAGGAGCGGC-CGGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUU-UGAUGACUCGCUU-A-GGAGCAGCAGAGGC-GAAAGCGCUGGCCAGGGGCG-AAUCCGAUGAUAAAGGACGUAGGC-UAGA-GGAUCGAAGACGAUUA--GAGACCGUUGUAGUUCUA-GCAGUAAACGAUGCCGAUGCCGUGGGGCG------------GUGCAGCCGCCACGCGGAG-GAGAAA--UU---GAGUA---GGGCCCUGGGGAGAGUACACGCGCAAGCGA-GAAAUUUAAAG--GAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAGCUUACCAGGCCCGA--CGGUCGC--ACGAGUGU--GGU-------------ACACGAU--AGGCCGGAGAGUGGUGCAUGGCC-GUUAACGACAAGUGGGGUGACCU-UUGGGUUAAGU-CCGG-GAAGUAGUGAGACCCCUG-----------------------------------------CCGGCGCGCC-GG---GACAGGUGCU--CAAAGCACAGGAAGGAAGGGUCAAGAACAGG-UCAGUGAUGCCCUUAGAUGGUCUGGGCUG-CACGCGCACUACAGUGGUCGCAGAAAUCAGUGCCCGAGCG---------GCAAUGGCGAUC---GAGAGGGAACGAGCUCUGGAAG-GGGCUCGGGAACGAGGAAUUGCUAGUAAUCGUGGGCUCAUUAAGACACGGUGAAUAC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCA-GGCGCGAA--CAAGCGAGA----------------------------------------------------------------------------------------------------GCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAA--GGUAGCUGUAGGAGAACCUGCAGCUGGAUCACGC
AF024658.1/1-1399                CACCAGGUUGAUUCU--GCCUGUU-AUAU-GUACUAGUGUCGAAGAUUUAGCC-AUGCAUGC-UUUACGAAUU-CACAA--GAA-GAAGUG-GCGGACAGCUC-AGUAAUACAGUUAU--AAUAUACUCUCUAC----UAAAG-GAUAACCGCGGUAAGCUGCGGG-UAAAACUUCAAGCUAUGUGUUUCA---------------------------UGAAAGAAUUUAUAGUUCAGAGUGUUAGUUUCUGGCCUAUUAGUUAGUAGGUAAUGUAAGGGAUUACCUAGACUAUUAUGGGUAACGGG-AGAUGAAUGUCUGAUACCGGAGAGGAAGCCUUAGAAACCGCUUUCACGUCCAAGGAUGGCAGCAG-GCGCGAAACUUACCCAAUCGUUUUUUAAGACGGAGGUAGUUAUGACACAUGUGAAUUAUUC------------ACGAG-GAAGAUCAAUAAAUCAGAUUUUUUU----UACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGUAGUGCAUAUAC---AUGCUGUAGUUAGAAAGUUUGUAGCCGUAUAAGCUUGAAUCAGAGGAAAGGAGGACU--CUUAA---------------------------------------------------------------------------GGUAAACUUUAACUCUGGUC-AAUGCUUAUAUUCGAAGCGGA-UGGAGGCACUUGUAUUCAAUAGCGAGAGGUAAAAUU-UGAUGACCUAUUG-A-GGACAAUCAGUAGC-GAAAGCGAGUGUCUAGUACG-CGUUUGAGGGUCAAGAACGUUAGC-CGGA-GGAUCGAAGAUGAUUA--GAUACCGUUGUAGUUCCG-GCCGUAAACCAUGCCUACUUGCCUUGUAC--------------AUA--GUAUGAAGCAUA-GAGAAA--UUA-AGAGUUUUUGGGCUCUAGGGAUAGUAAUCCGGCAACGGA-CAAACUU-AAA--GAAAUUGGCGGAAGGACACCACAAGGAGUGGAUUGUGCGGCU---CAACUUGACUCAACACGGG-AAAUCUUACCAGGGUCUG--UAUAUGU--GAGACUGU-CCCAUUUAU--GGUGGUACACGAU--AAUAUACUGAGUGGUGCAUGGCC-GUUUUCAACACGUGGGGUGACCUGUCAGGUUUAUU-CCGG-UAACGUGUGAGGUCACAGUAUUAA-----------------------------UAAGUAUU----UUAA-UA---GACAGCUAAUGGUAAAUUAGAGGAAG--UGUGACGAUAACAGG-UCAGUGAUGCCCUUAGAUACCCUGGGCUG-CACGCGCAAUACAUUGAGUAAGUCAUUUACAAUAGUAAUU--------UUGAAACUUACUCG-CUACUGGGAUCAUCCUUUGUAAU-UGGGAUGUGAACGUGGAAUUCCUAGUAAUCGUAGC-UCACUAAGUUACGAUGAAUGU-GUCCCUGUUCUUUGCACACACCGCCCGUCGCUAUCUAAGAUGGAUGUU-GAUAUGAA--AU-UGCUGCUUGAAU----------------------------------------------------------------------------------------GUGAGGUA-CUUGAGUAUUAACAACUAGAUAAGAUAUAAGUCGUAACAA--GGCUGCUAUAGAAGAAUCUGUGGCAAGAUCAUAC
AF322654.1/1-1355                CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUAGUUUCAUAGAUUAAGCC-AUGCAUGUGUAAGCGAAGC--GUAA---GU-GGAGCG-GCGUACGGCUC-AGUAA-CGGGCUAC--UAUUUGAUCUCCCU----GKGCG-GAUAUCCUCUGUAAACGGAGGG-CAAAACGCAAGACAAGCAGCAAUUUUG--------------------UUGGCUGUCUAACGAAAGUGGGGGAGAGUAAGGAGCCAGCCCAUCAGCUAGUAAGUAGGGUAAGGGCCUACUUAGGCAAAUACGGGU-ACGGG-GAAUUAUCGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCGGGUCCAAGGACAACAGCAG-GCGCGAAAAUUACCGGAGCCUGAAGU--CAGGGCGGUAGUAAGGAGACGUGAGAACAA----------------------UGUGGGGGUAAAAAACGCACUGGA----AACA--GGAGGA-AAAGA-CUGGUG-CCAGCA-CCCGCGGUAAUA-CCAGCUCCUGGAGUGUCUAUGGUGAUUGCUGCAGUUAAAGCGUUCGUAGUCGGAGCGGAAAGAAUGGCGUGACAGACAGCUG--CUCAA---------------------------------------------------------------------------AGGGUGGUGUGCGCCGUGAU--CCCGCGGAAUGAGGAGAGUU-UUGGGACCAGGCUAUUAAACGGCAAGCGGUGAAAUG-UGGUGACCCGUUU-A-GGAGCRACAGAGGC-GAAAGCGCUGGUCAGGGGCU-AUUCCGAUGAUAAAGGACGUAGGC-UAGA-GGAUCGAAGACGAUUA--GAGACCGUUGUAGUUCUA-GCAGUAAACGAUGCCGAUGUUGUGGUGCA--------------GAG--UGCAACGCAAGA-GAGAAA--UC---UAGUA---GGGCCCUGGGGAGAGUACGCGCGCAAGCGA-GAAAUUUAAAG--GAAAUUGACGGAUGAACACCUCAAAUAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAUCUUACCGGGCCCGA--CGACCGG--ACGAGCGU--GAC-------------ACGCGAU--AGGUCGGAGAGUGGUGCAUGGCC-GUUAACGACGAGUGGAGUGAUCU-UUGGGUUAAGU-CCGU-AAAUUAGUGAGACCCCAG-----------------------------------------CG------GA-AG---GACAGGUGCG--CAACGCACAGGAAGGAUGGGUCAAGGACAGG-UCAGUGAUGCCCUUAGAUGGCCCGGGCUG-CACGCGCACUACAGUGGUCGCCGAAAUUUGGAGAGAGAG----------GGAAAGGCGAUC---GAGAGGGAAUGAGCUUUGGAAG-AGGCUCAGGAACGCGGAAUUGUUAGUAAUCGCGGGCUCACUAAGACGCGAUGAAUGC-GACCCUGUUCAUUGUACACACCGCCCGUCGUUAUCGAAGACGAUGCUA-GGCGCGAG--CAAGGUUUAUU-----------------------------------------------------------------------------------------------UGGCUGAGCGAGCGCAGGGUAUUGAAUCUGAUGUAAGUCGUAACAA--GGUAGCUGUAGGAGAACCUGUAGCUGGAUCAGUC
AFBI01001141.1/69-1549           UACCAGGUUGAUUCU--GCCUGAC-GUGG-ACGCUUGCCUCGAAGAUUAAGCC-AUGCAAGU--CUGUGAA-----UAU---AU-GAAACA-GUGUACGGCUC-AGUAUAACACCUAU---AUCUACCCACUUU----UUAAA-UAUAACCAUGGUAAACUAUGGC-UAAU---------------------------------------------------------------AUAGUGGAUGAGUGGGUGACCUAUCAGCUUGACGGUACGGUAAGUGCGUACCGAGGCUAUAACGGGUAACGGG-GAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAG-GCGCGAAACUUACCCAAUGA---ACG----UUGAGGUAGUUACGAGGCGUAGUAUUAU-------------------G-AAGUGUGUGUAAAGAGCAUACUGAA---GUACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUA-CCAGCUCCAGUAGCGUCUGUGUUUAUUGCUGCGGUUAAAACGUGCGUAGUCGGCUAGUUGUGUGAAUAGUGAUUCGGGAUGG--UUUGCGGAGUAAUCUGUGGAUUGUGCUAUAAUUGCUAUUUGUGAAUAUGCAACAGCCUGGGUUAAAUAUGCACUUUCAUGGUGCUUUUAAUUUCAGGAA----CUUAUAGCUUGAGACAGGG-ACGGGGUAAUUUUAUUUGGUAGCGAGAGGUGACAAU-CGAUGACCUACCA-A-GGAGGACCGGAGGC-GAAAGCGAUUACCAAGAACU-GAUCUGACGAUCAAGCACGUGAGC-AGGA-GUAUCGAAGAGGAUUA--GAGACCCACGUAGUUCCUUGCAGUCAACGAUGCCAACGUAGUGGUGAU-------------UUUG--GUCAUUGCUAGA-GCGAAA--GC---UAGUGUAUGGGCUCCGGGGAUAGUACGGACGCAAGUUU-GAAACUU-GAA--GAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGU---UAAUUUGACUCAACGCGGG-AAAACUUACCCGGGCAGG-CGAUUGUUGUGAGAAGG--AAUA--------------CCUGAU--GAUAUCGCGCGUGGUGCAUGGCC-GUUCUUAACACGUGGAGUGAUCUGUCUGGUCAAAU-CUGA-UAACGCGUGAGAGGUGAG-----------------------------------------UGGUUUUUAACCA---GACGAUGUGU-GUAAGCACAAGGAAGAGACACCCAAUAACAGG-UCUGUGAUGCCCGUAGAUGUUCGGGGCUC-CACGCGCACUACAAUGAGUGGUGGUGCUAUAAGUAG----------------UAGCCAGUCG-UAGUUGGGAUUGACAUAUGUAAU-UAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAG-UCACUAACGACUAACGAAUGA-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAGGUG-CGGGUGAA--GA-UGUGAGUGUGUAGAGUUGGUGCGAUGCAUGGAAGUUAAUGACGAGUGCGAGUAGUUAGCUAUGAGUAUGAGUUGUUGAUGGAAGUGGGCGUAACUAAUGGCAUGAGCA-UAAGAACCCGUGCAGCUAGAUUGGAUGUAAGUCGUAACAA--GGUUGCGGUAGGUGAACCUGCCGCAGGAUUAUU-
AJ252959.1/1-1305                CACCAGGUUGAUUCU--GCCUGAC-GUAG-ACGCUAGUUUCACAGAUUGAUCC-AUGCAAUU-UUAGGGAACC--AUAU---GG-GGACCG-GAGAAAGGCUC-AGUAA-CGGGUAUC--UAUUUGCUCUCGGA----UGGUG-AAUAACCUCAGGAAACGGAGGC-UAAAAGCC-----------------------------------------------------------GGGGAGAUUAAGGGACCAGGUCAUCAGUUAGUAGGUAGGGUAAGGGCCUACCUAGACGWAGACGACU-ACGGG-GAAGACGAUUUCUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCAGGUCUAAGGACUGCAGCAG-GCGCGCAAAUUACCGAAGGCCG-GAG--UGGUGCGGUAGUGAUGAAACGUANAUAUUG---------------------AGAGGCGGGUAAAGGACGCUUUAGC----AACU--GGAGGU-CUAGU-CUGGUG-CCAGCA-UCCGCGGUAAUA-CCAGCUCCAGGAGCGUCUACGAUGAUUGCUGCGAUUAAAACGUUCGUAGUCUGGGGGCUAUAUUUUUCUGUAAUGGGCCUGC--UUGAG---------------------------------------------------------------------------GGGCGCGGAAGAAGGAUAC---UGGCUGAUUGAAGGAGCGAC-CGGGGGCCGGCUUAUUAUGUGACGAGGGGUGAAAUC-UGAAGACUCAUGU-A-GGAGGAGCAAGGGC-GAAAGCACUGGCCAAGGGCG-UAUCUGUUGAUCAAGGACGUAGGC-UCGA-UGUUCGAAUACGAUUA--GAUACCGUAGUAGUUCGA-GCAGUUAACGAUGCCGACUGUGCGACACG---------------GA--UGUGUUGUGCGC-GAGAAA--UU---GAGUA---GGGCUUUGGGGAGAGUACGCGCGCAAGCGA-UAAAUUUAAAC--GAAAUUGACGGAAGAAUAUCACAGGGAGUGGAGUGUGCGGCUUUCUAAUUUGACUCAACGCGGG-AAAGCUUACCAGGCCCGA--GAGCCGU--AUGAGUG--AGUA--------------CACGAU--AGGCUUGAGAGUGGUGCAUGGCC-GUUAUCGACGAGUGGAGUGAUCU-UUUGGUUAAUU-CCGG-UAAUUUGUGAUCUCCCUU--------------------------------------------------U------GAUGGGCGCU-GUAAGGCGCAUG--UGACGGGAUAAGAACAGG-UCAGUGAUGCCCUUAGACGGUCUGGGCUG-CACGCGCACUACAGUAUUGCUUUUAGAUGGUAUGUUAGAU---------GGAAUGGGCAAU---AUAAGGGAUUGUGCGCUGGAAU-GCGCGCAUGAACGUGGAAUUGCUAGUAAUCGCAGGCUCAGUAGGAUGCGAAGAAUGU-GUCACUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGACGUUGUUG-GUAAUGAG--GGAAUCUGA----------------------------------------------------------------------------------------------------AUGACCGAAUUAUCAAUGAUGGAUCUGGUACAAGUCGUAACAA--GGCAACUGUAGGAGAACCAGCAGCAGGAUCAUAA
AJ302317.1/1-1280                CACCAGGUUGAUUCU--GCCUGAC-GUAG-AUGCUAGCCUCCGAGGCUAAGCC-AUGCAUGC--CCGUGAC----GCAA------GGAACG-GCGAACGGCCC-AGUAAUACUGCGAU--GAUCUGCUCCGCGC-----GGAC-GAUAACUACGGGAAACUGUGGC-UAAGA--------------------------------------------------------------GCGCGGAUUGAGACGCAGCCCUAUCAGCAAGUUGGUAGUGUAACGGACUACCAAGGCGGCGACGGGUGACGGG-AAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAG-GCGCGAAACUUGCCCACUCUCU-UGC---GAGGAGGCAGUUACGAGGCGUGACGGAAG---------------------GGCGCACUGUAAAGACGUGCGCGAAC-GCGAUU--GGAGGG-CAAGU-UCGGUG-CCAGCA-GCCGCGGUAAUA-CCGACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAAAGUCCGUAGUCGGCACUGCGACGAAAGCGCGCUGCUCGAUGG--CGCAG---------------------------------------------------------------------------GCGUUGCAGGGGCUUGC-----------------GGAGCGGG-CGGGGGGCACGGUAUAGGCAGGCGAGAGAUGAAAUGGCCAAGACCCUGCC-U-GGACCGACGGUGGC-GAAGGCGGUGCCCUCGCACG-CAUCUGUGGAUCAAGGACGAAGGC-AGGA-GGAUCGAAAGUGAUUA--GAGACCGCUGUAGUUCCG-GCAGUAAACGAUGCCGACACCGCGCGGC---------------GGG---GCUGCGCGGGG-GGGAAA--CC--UUAGUGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGUGU-GAAAAUUAAAC--GAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCU---UAAUUUGACUCAACGCGGG-GCACCUUACCAGGGCCAC--GCGCGCCU-GAGACCGC--AU--------------GCGCGAG--GCGCGCAGGAGUGGUGCAUGGUC-GUUGCAAAUUGGUGGGGCGACUU-UUGGCUUAAAUGGCCG-GAACGAGUGAGAUCUCCG--------------------------------------------------A------GACGGGUGCG--CGCAGCACAGGAGGGUGGAGGCGAUAACAGA-UCAGUGAUGCCCUUAGAUGCCCUGGGCUG-CACGCGCAAUACAAUACCCGCGCGCUGCACAGAACG----------------GUCGCGGGG---GUGUGGGACCGGCGCCUGUAAG-GGCGCCGCGAACGAGGAAUUCCUAGUAACGGCGGC-UCAUCAAGGCAUUGUGAAUGU-GUCCCUGUAGCUUGUACACACCGCCCGUCACUAUCUCAGAUGGCCGUG-UCGGUGAA--GG-GAGCAA----------------------------------------------------------------------------------------------------UC-UCUGUGCCUCCGCGGCUAGAUAAGAUGUAAGUCGUAACAA--GGUUGCGGUCGGUGAACCAGCAGCAGGAUCAUAA
AEFF01000078.1/4488-3073         CACCAGGUUGAUUCU--GCCUGAC-AUAG-ACACUGGUCUUUCAGACUAAGCC-AUGCAUGA-CGAGCACAC---GGAA----G-GAAGCG-UCAGAGAGCUC-AGGGACGCAGUUUU--GACCGGCUUGGAGAACAGGGGCG-GACAUCCGAGGAAACCUUCGGC-CAAGACGACGCAGGGCGGGGGGCAUCCACGGAGA------AGCAGGACGCCAGAGCAGCGCAGGGCGCAGCCAAACGGGAGACUGUCCUAUUAGCUUGUGGGUGGGGUCAGGGCCUACCCAGGCGACGAUGGGU-ACGAG-GGAUGAGGGUUUUGUCUCGGAGAACGGGUGUGAGAAGCAGCCCGUAGAUCCAAGGAUCGCAGCAG-GCGCGGAACUUGCUCACUUCCC-AGG--GGGAGAAGCAGUGAGGAGACAUACGGAGAA-------------------AGAGCCCGCGACAAAAGAGCGGGCGAGAAGCAAUU--GGAGGG-CAAGA-CUGGUG-CCAGCA-GCCGCGGUAAUA-CCAGCUUCAAAAGUGUCUGUGGUGUGUGUUGUAUUUAAAAGGUCCGCAGUCGGGGGAGAUGGCCGUGGGGAAAGCAGGCUGU--UCAAG---------------------------------------------------------------------------GGGAGCGCGAUGCACGGAAGGAGCGAAGUCAAGAGGGGCGGAGCGAGGGCGGGAAGAUUUGGCAGCCAGAGGUGAAAUU-CAAAGACUUGCCG-A-GGAUGGACAGAGGC-GAAGGCGCCUGCCAGGGACG-CUUUCAUUGAUCAGGGACGAAGGC-CGGA-GAAGCGAAGAUGAUUA--GAGACCGUUGUAGUUCCG-GCGGUAAACGAUGCCAACACGGGGGCGUGCGCG----CGGGGGCGA-GCAGGUGGCCGGA-GAGAAA--UC---GAGUGCGAGGGCUAUAGGGGAAGUAUUGCCGCAAGGUU-GGAACUUAAAC--GAAAUUGACGGAUUAACA-CACAAGGAGUGGGGCGUGCGGCU---UAAUUAGACUCAACACUAG-GCAGCUUACCAGCGGGGG-AGCCCGGC--GGGAUCG---GCG--------------CGAGAU--UCGGGCGAGAGUGGUGCAUGGCC-GCUGUUAAUUCGUGGACUGAUUUGUCUGGUUGAAU-CCGA-UAACGGAUGCGAUCCGCGUGUGCUUUGUG-------------------AUAAAAACAGCAG----AGGA-CA---GACGGCCGGCGGGCAGCCGGAGGAGG--GCGGGCGAUAGCAGG-UCUGUGAUGCCCUUGGAAGCGCUGGGCUG-CACGCGCGUCACAGUGCGCGCAGGAAGGAGUGCCGAGAGGCGC--AGGAGGAGCGGCGCGC---AG--GGGAUGCCCGUGCGGAAC-CGCGGGCUGAACACGGAAUUUCCAGUACCCGCGGG-UCACCAGCCCGCGGAGACAGG-GUCCCUGUUUUUUGUACACACCGCCCGUCGCUAUCUGAGAUGGGUGCGCGCGGCAAG--CG-CGGGGG----------------------------------------------------------------------------------------------------CG-CGUGAGCUGCUGUGCCUAGAUUGGAUAAAAGUCGUAACAA--GGUUUCCGUAGGAGAACCUGCGGAAGGAUCAAUA
AJ871391.1/3-1323                CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUAGUUUGCGAGACUAAGCC-AUGCAUGC--UUGCGAAGUGCGUUGUGCGC-GGAGCG-GCAGACGGCUC-AGUAAUACUGCGAU--GAUUUGUUCGGGGA----GGCUG-UGUAGCCGCGGGAAACUGUGGG-UAGG-CGGCUGGGCUGCACUG--------------------------------GGUUGCUGGGGCGGUGUCUGAGUAAGUUGCAGACCUAUUAGCUGGUAGCUAGGGUAAUGGCCUAGCUAGGCGAUGAUGGGAGACGGG-GAAUUUGGGUUUGGUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAG-GCGCGGAACUUGCCGAAUCC--UUUU----GGGAGGCAGUUAGCAAGCGUUGUUUUUG-------------------U-UUGGAAUUGCAAAGAGAUUCCUUGA----GAUU--GGAGGG-CAAGU-CGGGUG-CCAGCA-GCCGCGGUAAUA-CCUGCUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAAGGNUCGUAGUUGUGUUGCUUGCACGCAUGUUUUGUGUGCCUG--UGUGU---------------------------------------------------------------------------GUGGCGGGCUGUGGAUGUGU--GCGGCGAUGUGCGCAACAGA-CGGGGGGCACUGGAUAGUUGGGCGAGAGGUGAAAUG-CGACGACCCUGAC-U-GGACAGACGGAGGC-GAAGGCGGUGCUCUUGGAUG-GAUGUGAGGAUCAAGAACGAAGGC-UGGA-GGAUCGAAAUCGAUUA--GAUACCGUUUUAGUUCCA-GCAGUAAACGAUGCCGACUGGAUGGUGUG--------------UGU--UGCACUGUGCGC-GAGAAA--UCUGUGAGUGUGUGGGCUCUGGGGAUAGUAUGAUCGCAAGAGG-GAAACUU-AAA--GAGAUUGACGGAAGGACACCACCAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAACUUACCAAUGCCGA-GAUGUGUUU-GAGAGCG---GAG--------------CGCGAG--ACACGUGGCGGUGGUGCAUGGCC-GUUUGAAAUGGAUGGCGUGAGCU-GAGGAUUAAUU-UCCG-GAAGAUGUGAGACCCUUU---------------------------------------------------------GACUGCGUUUGUGGAGAGCGAGGAGGGGAGGGAACACAACAGG-UCCGUUAUGCCCUGAGAUGUGUUGGGCUG-CACGCGCACUACGAU--------AUUCUGCGGUUGCGG-------------AGAU---------GUGCGGGAUUGAUGCUUGUGAA-UGUGUCAUGAACGUGGAAUUCCUAGUAAGGGCUGU-UCAUUAGGCUGUCUUGAAUGG-GUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGGUGUUU-UGGACGAA--GA-CUGCGA----------------------------------------------------------------------------------------------------GG-UCUGAGUUCUGGAUACUAGAUAAGAUAUAAGUCGUAACAU--GGCUGCUGUUGGAGAACCAGCUGCAGGAUCAGUG
AJ302320.1/1-1258                CACCAGGUUGAUUCU--GCCUGAC-GUAG-AUGCUAGUCUCUGAGAUUAAGCC-AUGCAUGU--UUAUGUA--------------AUAAGG-ACGAACAGCUC-AGUAGAACUGCGAU--UAUUUAGUCUGUCU----GUGCAGGAUAACUACGUGAAAAUGUAGC-UAAGA-GA-----------------------------------------------------------GGACAGAAUAAGACGUAGGACUACCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACGACGACGGUUAACGGG-GAAUCAGGGUUUUAUACCGGAGAGGGAGCCUGAGAGAUUGCUCCCACGUCCAUGGACGGCAGCAG-GCGCGAAAAUUGCCCACUCUUU------GCAGGAGGCAGUUAUGAGACGUGAAGACGA----------------------AUGCUUGGUAAAGAGAAGCAGGAG----AAUU--GGAGGG-CAAGU-UUGGUG-CCAGCA-GCCGCGGUAAUA-CCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGGAGUCUUCGAGGUUGAAAUUGGGGCACGAGGCCCCA--GACAG---------------------------------------------------------------------------------------------------ACAUGAUGGAGGAGCCAA-UGGGGAACAUAGUAUACCAGGGCGAGAGAUGAAAUG-CCUAGACCCCUGG-U-GGACUAAGCGAGGC-GAAAGCGAUGUUCUUGUGGG-UAUUCGGUGAUCAAGGACGAAGGC-UGGA-GGAUCGAAAGUGAUUA--GAUACCGCAGUAGUUCCA-GCAGUAAAAGAUGCCGACAUGUCGGCUG--------------GGCA---CAGCUGACAGG-GAGAAA--UC--UUAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGAGU-GAAAAUU-AAA--GAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCU---UAAGUUGACUCAACGCGAG-GAAAACUACCAGGGGCAA--GUAUUGUG-UAGA------GAA-----------------GAG--CAAUACAGAAGUGGUGCAUGGUC-GUUGGAAAUUGAUGGGAUGACUU-UGAGCUUAAAU-GGUU-GAAUGAGUGAGAUCUUCA---------------------------------------------------------GACAUGUUCC-UCACGGGACAGGAAGGAGGAGGCUAUAACAGA-UCAGAGAUGCCCUUAGAUGCCCUGGGCUG-CACGCGCAAUACAAUAGCACUGAGACGGAGAGAGCGGA-------------A---AGUGUU---CUGAUGGAUUAUGUGUUGUAAG-ACAGAUAUGAAAGAGGAAUUCCUAGUAAGUAUGUA-UCAACAAUGGAUAUUGAAUGA-GUCCCUGUAGCUUGUACACACCGUCCGUCGCUAUCUCAGAUGUUUUUC-AGGAUGAA--GA-GUCACG----------------------------------------------------------------------------------------------------GC-UCUGAAUAAUGAAAAGUAGAUAAGAUGUAAGUCGUAGCAA--GGUUUCGGUCGGUGAACCAGCAGCAGGAUCAUAA
AJ252949.1/1-1332                CACCAGGUUGAUUCU--GCCUGAC-GUGG-ACGCUUGCCUUAAGGAUUAAGCC-AUGCAAGC--CAGCGAAUU--UUAU---AU-GGAGCG-GCGUACGGCUC-AGUAGGACAGGACU--UAUCUGGUCAUGAU-----GCGG-GAUAACCACGGAAACCUGUGGC-UAAUACGG-----------------------------------------------------------AGAAUGAGUGAGGGCCUGGCCUAUCAGCUUGUCGGUAAGGUAAAGGCUUACCGGGGCGAUUACGGGUAACGAG-GAAUCGGGGUUUGA-UUUGGAGAAGGAGCCUGAGAGAUGGCUGCUACGUCUAAGGAUGGCAGCAG-GCGCGAAACUUGCCCACUCGGA-GGA---CCGGAGGCAGUGACGGGGCGUGAUUUUAUUAU-------------GAUG-AGGGCGCUGCAAACAUGCGCCCGAAA-GCAACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUA-CCAGCUCCAGGAGCGUCUGUGUGUAUUGCUGCGGUUAAAGGGCGCGUAGUCG--GGCGUAAGGCCAACGAUAAAUACCCAGG--UUCCG---------------------------------------------------------------------------CCUGGGACUGACGUUGGAA----CCGGAGCCUUGGGACCGGA-GUAGGGCAAUGGUAUUCGGGGGCGAGGGGUGAAAAC-CGAUGACCCUCCG-A-GGAGCGACAGAGGC-GAAAGCGGUUGUCCACUACG-GGUCCGACGAUCAAGCGCGUAGGC-AGGA-GUAUCGAAGGCGAUUA--GACACCGUCGUAGUUUCU-GCAGUAAACGAUGCCAACAGGGGAGAGCG-------------GGCC--AGCUCUCCCUGA-GGGAAA--CC---GAGUGUAUGGGCCCCGGGGAUAGUAUAGGCGCAAGCUG-GAAACUU-GAA--GAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGU---UAAUUUGACUCAACGCGGG-AAAGCUUACCGGGGCAGG-CGGCGGCCG-GAGACCAG-GCGGUCUAUGGAGCGGCAUGGGAG--GCUGCCGCGCGUGGUGCAUGGCC-GUUUUUAACACGUGGGGUGACUUGUCUGGUCAAGU-CUGA-UAACGCGUGAGACCUAGG-----------------------------------------GC----UGCG-GC---GACGGCACCU-GUAAGGGUGAGGAGGCACUAGUCGAUAACAGG-UCUGUGAUGCCCGUAGAUGUCCCGGGCUC-CACGCGCACUACAUUAGGGGA-GGGUCUGUGAAACUG---------------CGCUCCCCUG-CGGUUGGGAUUGACGCUUGUAAA-UGCGUCAUGAACACGGAAUUCCUAGUAGCGUGGUG-UCAUCAACACCAGGCGAAUGG-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGGUGUG-UAAAUGAA--GC-UAGUCAC--------------------------------------------------------------------------------------------------CUA-GAAGAAUUUGCACGCCUAAAUCGGAUACAAGUCGUAACAA--GGUUGCUGUAGGUGAACCAGCAGCAGGAUCAUAA
AF033197.1/1-1370                CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUAGUCUCAUAGAUUUAGCC-AUGCAUGUGUAAGCGAAGC-GAUUA---GU-GAAGCG-GCGGAAGGCUC-AGUAACGGGCGAGU--AUUUUAAUCUCUAG----AACCG-GACAACCUCAGGAAACAGAGGG-GAAAACGGAGUAAGAGCAUGUGUUGUUAG-----------------CAUGUGAUGAGAACAACAGUGCAGGAGAGUAAGAAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUAUUUAGACGUAGACGGGU-ACGGG-GGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAG-GCGCGAAAAUUACCGAAGCCUC-CAA--GAGGGCGGUAGUGAAGAGACGUGAAAACA-----------------------AGUGUGUGUAAAAACCACAUGAGU----AACUGUGGAGGGUCAAGG-CUGGUG-CCAGCA-UCCGCGGUAAUA-CCAGCUCCAGGAGUGUCUAUGAUGAUUGCUGCGAUUAAAAGGUCCGUAGUCGAAGAACAGUACUUGUUUGUAAUGUGGCUUA--UCGAG---------------------------------------------------------------------------AGCCGAAUAGAACGAGAAG---AGUUCAGAGUAAGGAGYGAA-GGAGGGCUAGAUUAUUGAGCAGCGAGAGGUGAAAUU-UGAUGACCUGCUUUA-GGAGUAACAGAGGC-GAAAGCGCUAGUCAAGAACG-AAUCCGAUGAUCAAGGACGUAGGC-UGGA-GGAUCGAAGACGAUUAGAGAGACCGUAGUAGUUCCA-GCAGUAAACGAUGCCUACGCUGUUGUGGU-------------UAUG--AGCACGGCAGAA-GAGAAA--UC---UAGUA---GGGCUUUGGGGAGAGUACGCGCGCAAGCGA-UAAAUUUAAAG--GAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAGCUUACCAUACCCGA--UGGCCGU--GUGAGCGU--AGU-------------ACGCGAU--AGGUCAGAGAGUGGUGCAUGGCC-GUUAACGACGAGUGGGGUGACCU-UUGGGUUAAGU-CCGCCGAAGUAGUGAGAUCCCUAGGAU---------------------------------ACGAAA----GUUA-UC---GACAGGUGUU--AAAAACACAGGAAGGAAGGGGCAAGAACAGGGUCAGUGAUGCCCUUAGAUGGUAUGGGCUG-CACGCGCACUACAGUGGUCACAGCAGAAACGGAUAGAAG-----------UAAAUGUGAUC---GAGAGGGAAUGAGCACUGUAAU-GUGCACAGGAACGAGGAAUUGCUAGUAAUCGUUAUCUCAUUAAGAAGCGAUGAAUGU-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAACCA-GGUGCGAA--CAAGUGAAA----------------------------------------------------------------------------------------------------GCGAGUGAGUGCAGGGUUCYAGAUCUGAUACAAGUCGUAACAA--GGCAGCUGUAGGAGAACCAUUAGCAGGAAGCUUG
AF484692.1/1-1366                CACCAGGUUGAUUCU--GCCUGAC-GUAU-GCGCUUGUCUUGAAGAUUUAGCC-AUGCAAGC--UCGUGACC---GUAA----G-UGAACA-GCAGACAGCUC-AGUAAUACAGUUAU--GAUUUACUCGUAAG----CUAUG-GAUAACCAUGGAAAACUAUGGC-UAACACAU-----------------------------------------------------------UAUACGACUAAGUUUCUGACCUAUUAGCUAGAUGGUAAGGUAAGGGCUUACCAUGGCGAUGAUGGGUAACGGG-GAAUUAACGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCUAAGGAUGGCAGCAG-GCGCGAAACUUACCCAAUUCCU-UAU---GGAGAGGUAGUGAAGAGACAUUUUUUUAUUAA-------------UUGA-AAGGCAUUGUAAAGAGCAGCCUGUA----AACU--GGAGGG-CAAGC-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGUUCCAGUAGCGCAUAUAAUAAUUGUUGCUGUUAAAAGGUCCGUCGUAGUGUACGAUGUUACUAUGAUGAAAAUGUAUA--UCUCA---------------------------------------------------------------------------AAUGAAAUAUAUAGCAUAGGACAAAGUGUAGAAAGGAACAGA-UGAUGGCAACAGUAUUUAAUAGUUAGAGGUGAAAAU-CGAAGACCUAUUA-A-GGACUCUCAGAAGC-GAAAGCGGUUGUCAAGUAUG-UAUCCGUUUAUCAAGGACUCAAGC-UAGA-GUAUCGAAGAUGAUUA--GAUACCGUCGUAGUUCUA-GCUGUAAACGAUGCCGACUAGGUGAGGUG--------------AUA--AGCUGCGCCUUAGGAGAAA--UC--AAAGUGUAUGGGCUCAGGGGAUAGUAAGCGUGCAAGCGU-GAAACUU-GAA--GAAAUUGACGGAAGGAUACCACAAGGAGUGGAUUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAACUUACCAGGGCCGA-AUGUCUAU--GAGAUUGG-CGAUUUGAGA-GAAUUCCCGAGAU--UAGACAGAGGGUGGUGCAUGGCC-GUUUUCAACACGUGGGGUGACCUGUCAGGUUAAUU-CCGA-UAACGCGUGAGGCCCUAGCUAC---------------------------------AAUACU----UUGU-AG---GACGGACAGUGGUAAGCUGUAGGAAG--GAGGGCGAUAACAGG-UCAGUGAUGCCCCCAGAUGCUCUGGGCUG-CACGCGCAAUACAAUAUAUGAGUGAGAAUAGGUACAGAAAUGUA-UGAUUUAAGCUUGUGUA-UACCGGGGAUAAGCGUUUGUAAA-UACGUUUUGGACUUGGAAUUCCUAGUAAUCGCAGG-UCAUUAUGCUGCGAUGAAUGU-GUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUUAGAUGAAUGUA-UAGGUGAA--AUGUCUGGACGUAA------------------------------------------------------------------------------------------GAAAGGAAGUUGAACCUGUGCAAUUAGAUAAGAUAUAAGUCGUAACAA--GGCUGCUAUAGGAGAACCUGUGGCAGGAUCAAUA
FJ594990.1/1-1296                CACCAGGUUGAUUCU--GCCUGAC-GUAG-GUGCUAGCCUCUAAGAUUUAGCC-AUGCAUGC-UCUGUGAACC--GAAU---GG-GGAACG-GCGGACGGCUC-AGUAAUGUUGCGAU--GAUCUGCUCUAGUU---GUGUAA-GAUAACCGCGGAAACCUGUGGC-UAAGA--------------------------------------------------------------GACUAGAAUGAGACGCAACCCUAUCAGUUUGUUGGUAGUGUAACGGACUACCAAGACUAUGACGGGUGACGGG-AAAUCAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGAUGGCAGCAG-GCGCGAAAAUUGUCCACUCUUU-GUU---GAGGAGACAGUUAUGAGGCGUGAUUGUAA-------------------G-AGCGAAGAGUAAACAUCUUUGUGUAAUGCAACU--AGAGGG-CAAGUUUUGGUG-CCAGCA-GCCGCGGUAACU-CCAACUCUAGAAGUGCCUAUUGUGGAUGCUGCAGUUAAAAAGUCCGUAGUCGUUGAUGCAAUUAAAAGGUGUAGAUCAAGUG--CACCA---------------------------------------------------------------------------AGUUUGUUAGUUGUGGC-----------------GGAGCGGA-CAGGGAGCAUGGUAUAGGUUGGCGAAGAAUGAAAUC-UCAAGACCCAACC-U-GGACCAACUGAGGC-GAAAGCGGUGCUCUUGUACG-CGUCUGUGGAUCAAGGACGAAGGC-UAGA-GGAUCGAAAGUGAUUA--GACACCGCUGUAGUUCUA-GCAGUAAACUAUGCCGACAUUCUCUGUUG--------------UUG--AGACGGGGAGGG-GAGAAA--UC--UUAGUUUUCGGGCUCUGGGGAUAGUACGCUUGCAAGAGU-GAAACUU-AAAGCGAAAUUGACGGAAGAUCACCACAAGGAGUGGAUUGUACUGCU---UAAUUUGACUCAACACGGG-AAAACUUACCAGGGCCAA--GUCUCUCG-UAGAUUG--GCGA--------------CAUGAG--AGGGGCAAGAGUGGUGCAUGGCC-GUUGGAAAUUGAUGGGAUGACCU-UUAGCUUAAGU-GCUG-UAACCAGUGAGAUCUUCU--------------------------------------------------A------GACAGGUGUCUUACUGACACAGGAAGGAGAAGGCUAUAACAGG-UCCGUGAUGCCCUCAGAUGCCCUGGGCCG-CAAGUGCAAUACAAUAUCCGUUUGAGCGACAUAAAUAU-------------GCUUACGGAU---GAGUAGGAUUAGCUCUUGUAAA-UGAGCUAUGAAUGAGGAAUUCCUAGUAACUGUGUC-UCAUCAAGGCACAGUGAAUGC-GUCCCUGUUCUUUGUACACACCGCCCGUCACUAUUGCGGAUGGCAAUC-AAGAUGAA--GA-GCCUAG----------------------------------------------------------------------------------------------------GU-UCUGAAUAUUGAUCGUUAGACAUAAUACAAGUCGUAACAA--GGUAACGAUUGGAGAACCAGCCGUUGGAUCAUUC
U68473.1/1-1331                  CACCAGGUUGAUUCU--GCCUGAC-UGUG-ACGCUAGCCUCGGGGAUUAAGCC-AUGCAAGU--CUGUGAAGU-UUCGU--UAU-GAAACA-GUGAACGGCUC-AGUAAAACACGUCU---AUCUACCCACUUG----UCUAA-UAUAACCCCGGGAAACUGUGGC-UAAUAUU---------------------------------------------------------------GUGGAUGAGGGCGUGACCUAUCAGCUAGUCGGUACGGUAAAGGCGUACGGAGGCGAUGACGGGUAACGGG-GAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCAC-UCCAAGGACG---GCAGAGCGCGAAACUUACCCAAUGA---ACA----UUGAGGUAGUUACGGGGUGUGACAUUCU-------------------AUGACCGUGUGUUAAAAGCAGGGUUAAG--ACAUU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUUUCCAGCUCCAAUAGCGUCUGUGUUUAUUGCUGCGGUUAAAACGUGCGUAGUCUGGUCUAUGGCUUGGGUGUAAUCCGUGCUUU--UCUAG---------------------------------------------------------------------------UACGGGUUAUUUCAGGUAC-----CUAGACCUUGAGACGGGG-AUGUGGUAAUGUUAUUUGGUAGCGAGAGGUGAAAUU-CGAUGACCUACCA-A-GGAGCAACAGAGGC-GAAAGCGAUUACCAGGAACC-GAUCUGACGAUCAAGCGCGUGAGC-AGGA-UUAUCGAAGAGGAUUA--GAGACCCACGUAUUCCUU-GCAGUAAACGAUGCCUACAGUGUGGUGCU-------------UAAU--UGCAUUGCGCGA-ACGAAA--GC---UAGUGUAUGGGCUCCGGGGAUAGUACGGACGCAAGUUU--AAACUU-GAA--GAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGU---UAAUUUGACUCAACGCGG--AAACCUUACCCGAGCAAGUAAUAGUCCU-AAGAUGUA--UG--------------UGCAGAGCAGAGCAUUACCGUGGUGCAUGGCC-GUCGUUAACACCUGGAGUGAUCUGUCUGAUUAAAU-UCGG-UAACGUGUGAGAGGUUGAGCCCGAUGAACUAG------------CUUGCACAAUAGCUACA----UAGU-UGG-GGACUGCAUGU-GUGAGCAUGAGGAAGUAGCGCCCGAUAACAGG-UCUGUGAUGCCCGUAGAUGUCCGGGGCUC-CACGCGCACUACAAUGAGGUG-UGGUUUAUCUUAGUGU-------------UUAACACCUCG-UAGUUGGGAUUGAUGCUUGUAAC-AGUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAG-UCACUAACGACUAACGAAUGC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUG-CGGGUGAA--GA-CA-CGA----------------------------------------------------------------------------------------------------UG-GC--AGUAGGCUAGGGUAACUUAGUCUAUAGU-GUAAAAACGGGCCUUAGUGGAAGAAUCCGU-----GCACGUAA
AF027682.1/1-1286                CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUCGCCUUAAAGACUAAGCC-AUGCAAGU--UUGCGAG-------C------UGAGCA-GCGAACGGCUC-AGUAAAACAGGGCA---CUCUAACGCACG-----GAAGA-GAUAACCACGGGAAACUGUGGC-UGAGA---------------------------------------------------------------AGUGCGAUGAGGCUCUGACCUAUUAGUUUGUCGGUACGGUAAGUGCGUACGGAGACGAUGAUGGGUAACGGG-GGAUCAA-GUCCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAG-GCGCGCAACUUACCCAAUGA---GGA----UUGAGGUAGUGACGAGGCGUAGAUUGUG---------------------AGUUGAGAGUAAAGAACUUAACGAGA-GCGACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGGGGCGUAUGUGUGUGUUGCUGCGGUUAAAAAGCGCGUAGUUU--GUGGUGUAGCGGGUCGUUGUGGGGCGAG--AUCAA---------------------------------------------------------------------------UGCGUUCUGUGUGACUUAU---GCUCAUUGCUAGGGAGCGCG-AGACGCCGGUGGUAUUCGGUAGCGAGGGGUGAAAAC-UGCAGACCUACCG-A-GGAGCGACAGAGGC-GUAAGCGGCCGGCGAGUGCG-GAUCCGACGAUCAAGCGCGUGGGC-AGGA-GUAUCGAAGACGAUUA--GAGACCGUCGUAGUUCCU-GCAGUAAACGAUGCCGACAUGGUUGAAUA-------------------GAAUUGACCAAA-GGGAAA--CU---GAGUGUACGGGCUCCGGGGAGAGUACGGGCGCAAGCCA-GAAACUU-GAA--GAAAUUGACGGAAGGACACCACCAGGCGUGGAGUGUGCGGGU---UAAUUUGACUCAACGCGGG-GCAACUUACCCGGGCCGC--AGCCUCUU-GAGAGG----AAA---------------CCGAU--GGGGCCU--CGUGGUGCAUGGCC-GUUCUCAACGCGAGGGGUGACCA-CUGAGUUAGUU-CUGG-CAAGCCGUGAGGCCCCUG-----------------------------------------UA---CUUUUGUA---GACGGCGGACGGCAAGUCCGAGGAAGCGAGGGCGUAUAACAGG-UCUGUGAUGCCCGCAGAUGUCCGGGGCUC-CACGCGCACUACAAUAGCAAA-UGGUAGACGAGAGU----------------AAGUUUGUUG-UGGUUGGGAUUGACGCUUGUAAA-UGCGUCAUGAACGAGGAAUGCCUAGUAGUUGUCUG-UCAGCAGCGGACAACGAAUAA-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGCGGUG-CGGAUGAAGCUG-CUACGU----------------------------------------------------------------------------------------------------GG-CAAGAAUCCGUGCUGCUAGAUUGGAUACAAGUCGUAACAU--GGUUGCAGUAGGUGAACCUGCCGCA-GAUCAAGC
FJ843105.1/1-1437                CACCAGGUUGAUUCU-CGCCUGACUGUGG-AUGCUAGUCCCAUAGAUUUAGCC-AUGCAUGUGUAAGUGAAGC-GAUAA---GU-GGAACGCGCGGACGGCUC-AGUAACUGGGCAUUAGUAUUUAAUCUCUUU----AUAUG-GACAACCUCAGGAAACAGAGGG-GAAAACAUAUUAGAUUCAUUUUAUAUAAGAAGAAUGAAUUGAGAACAAAUGAAAAUUUUUAUUUGUGAAAGAGAGUAAGAAGCCAUCCUAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACAAGGACGGGU-ACGGG-GGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCAGGUCCAAGGACAGCAGCAG-GCGCGAAAAUUACCACAGUCCA-CAU--UGGAGCGGUAGUGAAGGGACGUAAAAACA-----------------------AAGAUGUGUAGAUAACAUCUGUGU----AACU--GGAGGU-CAAGU-CUGGUGCCCAGCA-UCCGCGGUAAUA-CCAGCUCCAGGAGUGUCUAUGAUGAUUGCUGCGAUUAAAAGGUCCGUAGUCUAAGAAUGAAACUUGUCCUGUAAUGUGGGAA--UCUCUAG----------------------------------------------------------------------UACCAAAUACGACCGAGAAGAA----UUCCAGAGUUAGGAGCGAA-GGAGGGCUAGAUUAUUGAGCAGCGAGAGGUGAAAUU-UGAUGACCUGCUU-A-GGAGUACAAGAGGCCGAAAGCGCUAGUCAAGAACG-AAUCCGAUGAUCAAGGACGUAGGC-UGGA-GUAUCAAACACGAUUA--GAGACCGUAGUAGUUCCA-GCAGUAAACUAUGCCUACACUGUUGUAUUUAUGUUUUAUAGAUGUG--AGUGUGACAGAA-GAGAAA--UC---UAGUA---GGGCUUUGGGGAGAGUACGCGCGCAAGCGA-UAAAUUUAAAG--GAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAACUUACCAUAGCCAA--UGAUCAA--GUAAGCGU--AGU-------------ACGCGAU--AGAUCAGAGAGUGGUGCAUGGCC-GUUAUCAACUAGUGAGGUGACUU-UUGGGUUAAGU-CCGU-UAAGUAGUGAGAUCCCUAGGGUUGGCUAAAUAUGUGAUGCUUAUGUGUUAUGUGUUGAAGC----UAUA-UC---GACAGGAGCG--AGAAGCGCCGGAAGGAAGGGGCAAGAACAGG-UCAGUGAUGCCCUUAGAUGGUAUGGGCUG-CACGCGCACUACAGUGGUUACAAUAGAUAUUUUAUAGAA----------GUAAAUGUAAUC---GAGAGGGAAUGAGCACUGUAAU-GUGCACAGGAACGAGGAAUUGCUAGUAAUCGUUGCCUCAUUAAGGAGCGAUGAAUAU-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAACCA-GGUGCGAA--CAAGCGAAA----------------------------------------------------------------------------------------------------GCGAGUGAGUGCAGGGUUCUAGAUCUGAUACAAGUCGUAACAA--GGCAGCUGUAGGAGAACCUGUAGCUGGAUCAACA
AF394528.1/1-1297                CACCAGGUUGAUUCU--GCCUGGU-GUAG-AUGCUAGUUUCUAAGAUUUAGCC-AUGCAUGU-UUUGUGAAUU-CUUAC--GAA-GGAACG-GCGAACGGCUC-AGUAAUAUUGCGUU--AAUCUGGUCUAAAU----AUAAA-AAUAACUACGGUAACCUGUAGC-UAAUA--------------------------------------------------------------AUUUAGAAUGAGACGCAAAUUUAUCAGUUUGUUGGUAGUGUAAUGGACUACCAAGACUAUGACGAAUAACGGG-AAAUUAGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAG-GCGCGAAAAUUGUCCACUCUUU-UAU---GAGGAGACAGUUAUGAAACGUGAAUAUAA-------------------G-UUUGAAUUUUAAAAUAAUUUAUUUUAUGCAAUU--GGAGGG-CAAGUUUUGGUG-CCAGCA-GCCGCGGUAAUA-CCAACUCCAAGAGUGUCUAUGAARGUUGCUGCAGUUAAAGCGUCCGUAGUUUUUUUAUUGCAAUUUAAAAACUAUGAUUAAA--UUAGU---------------------------------------------------------------------------UAAGUUUCCAAUACAUUGU---------------GAAACGGA-UAGGGAAAAUUGUAUAGCUAGGUGAAGAAUGAAAUC-UCAAGACCCUAAC-U-CGACAAACAGAGGC-GAAGGCGAUUUUCUUAUACG-UAUUCUUAAAUAAAGGACGAUAGU-UAGA-GGAUCGAAGGUGAUUA--GAGACCGCUGUAGUUCUA-ACUGUAAACUUUGCCGACAUUUCAUAUUG--------------UUU--UGAUAAGAAAGG-GAGAAA--UC--UUAGUUUUCGGGCUCUGGGGAUAGUACACUCGCAAGGGA-GAAACUU-AAAGCGAAAUUGACGGAAGAACACUACCAGGAGUGGAUUGUGCUGCU---UAAUUUGACUCAACGCGGG-AAAACUUACCAGAGUCAA--AUAUAUUU-AUGAUUUU--UUU-------------AAAUGAA--AUAUAUAAAAGUGGUGCAUGGCC-GUUGCAAAUUGAUGGGUUGACUU-UUAACUUAAUU-GUUG-AAACCAGUGAGAUCAUUU-------------------------------------------------AU------GACUGGUAUU--UUAAAUACAGGAAGGAAAUGGCAAUAACAGG-UCCGC-ACGCCCUUAGACAUUCUGGGCUG-CAAGCGCAAUACAAUAUCUUG-UUAUUUAUAUUUAUUU-------------AUACAAUUAU---AUGUAGGAUUAAUUCUUGUAAA-UGAAUUAUGAAUCAGGAAUUCCUAGUAAUAAUAUU-UCAUUAAGAUAUUAUGAAUUU-GUCCCUGUUCUUUGUACACACCGUCCGUCACUAUUUCAGAUGGUUAUA-AAGAUGAA--GA-GCUAAG----------------------------------------------------------------------------------------------------GU-UCUGAAUAUUUAUAACUAGAUAAAGUACAAGUCGUAGCAA--GGUUGCAGUCGGUGAACCAUCAGCAGGAUCAUAA
AY090066.1/1-1308                CACCAGGUUGAUUCU--GCCUGAC-GUGG-ACGCUUGCCUCAAGGAUUAAGCC-AUGCAAGC--CAGCGAAGU--UUA----AC-GGAGCG-GCGAACGGCUC-AGUAGGACAGGGAU---AUCUGACCACGGC-----AGGG-GAUAACCGCGGUAAGCUGCGGC-UAAUACG------------------------------------------------------------AGCGUGGGUGAGUUCCUGGCCUAUCAGCUAGGCGGUACGGUAAGUGCGUACCGCGGCGACGACGGGUAACGGG-GAAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAG-GCGCGAAACUUACCCACUUGGA-GGA---CCAGAGGUAGUGACGAGGCGUGAACCAUG---------------------AGGCCAGUGCAAACAGCUGGCCGAAA-GCGACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGGAGCGUCUGUGUGCGUUGCUGCGGUUAAAACGUGCGUAGUCG--GGCACAGGGCCAGCAUCAAAUGCGCAGU--CUCUU---------------------------------------------------------------------------GCUGUGCGGCGUGCUGGAA----CCUACGCCUAGGGACCGGA-GCGGGGCAAUGGUAUUCGGCAGCGAGGGGUGAAAAC-CGAUGACCUGCCG-A-GGAGCGACAGAGGC-GAAGGCGGUUGUCCGGGACG-GGUCCGACGAUCAAGCGCGUGAGC-AGGA-GGAUCGAAGGCGAUUA--GAGACCGUCGUAGUUCCU-GCAGUAAACGAUGCCGACGGGGGCGCAG---------------GCG---CUGUGCCCCAA-GGGAAA--CC---GAGUGUAUGGGCUCCGGGGAUAGUACGGGCGCAAGCCG-GAAACUU-GAA--GAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGU---UAAUUUGACUCAACGCGGG-GCAACUUACCGGGGCAGG-CAACACUGC-GAGGAGGG-GUGCGAUAGGAUCGUGCUCCUGAG--GGUGUUGCGCGUGGUGCAUGGCC-GUUCUUAACACGUGGGGUGACCUGUCUGGUUAAAU-CCGA-UAACGCGUGAGACCCUGG-----------------------------------------AU-------A-GU---GACGGCAUUCGAUGAGAGUGAGGAAGCGCGGGUCGAUAACAGG-UCUGUGAUGCCCGUAGAUGUCCCGGGCGC-CACGCGCACUACAGUGGGGGA-GGCUGCGUGAGACGG---------------GGCUCCCCUG-UGGUGGGGAUCGGCGCUUGUAAG-UGCGCCGUGAACGCGGAAUUCCUAGUAGCGUGCUG-UCACCAACGGCAGGCGAAUGC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAUGUG-CGGAUGAA--GG-CGGCUAG-------------------------------------------------------------------------------------------------GUCG-CAAGAAUCCGUGCCACUAGAUUGGAUACAAGUCGUAACAA--GGUAACC-----ANCA-----NGUUGNUUCUUC-
EU534408.1/1-1367                CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUAGUCUCAUAGAUUUAGCC-AUGCAUGUGUAAGCGAAGC-GAUUA---GU-GGAGCG-GCGGACGGCUC-AGUAA-CAGGCAAG--UAUUUGAUCUCCAU----AACCG-GACAACCUCAGGAAACAGAGGG-GAAAACGGAUUAAGAGCAUGUGAAGAACAU---------------GUGAUGAUAACUCAUUAGAGUGAUGGAGAGUAAGAAGUCAGCCCAUCAGUUAAUAUGUAGGGUAAGGGCCUACUUAGACGAAGACGGGU-ACGGG-GGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCAGGUCUAAGGAACGCAGCAG-GCACGAAAAUUACCGAAGCCCA-CGA--AGGGGCGGUAGUGAAGAGACGUAAAAACA-----------------------AUGAUCAGUAAAUAAGAUCUAGGU----AACU--GGAGGA-CAAGU-CUGGUG-CCAGCA-CCAGCGGUAAUA-CCAGCUCCAGGAGUGUCUAUGAUGAUUGCUGCGAUUAAAAGGUCCGUAGUCGAAUAGGAAGGCCCGUCUGUAAUGUGAAAUA--UCAAG---------------------------------------------------------------------------UUUGAAUAAGGACGGGAAG---AACUAUGAAUAAGGAGCGAU-AAGAGGCUAGAUUAUUGUAGAGCGAGGGGUGAAAUC-UGAUGACCUCUAC-A-GGAGUAACAGAGGC-GAAGGCGCUAGCCGGGAGCG-UUUCCGAUGAUCAAGGACGUAGGC-CGGG-GUAUCGAAAACGAUUA--GAUACCGUAGUAGUCCCG-GCAGUCAACGAUGCCGACACAGUUGGACA-------------GAGA--UGUGUGACUGAA-GAGAAA--UC---GAGUA---GGGCUAUGGGGAGAGUACGUGCGCAAGCAU-AAAAUUUAAAG--GAAAUUGACGGAAGAGCACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAACUUACCAUCGCGGA--UGGCCGG--GAGAGUGU--AGU-------------ACACGAU--AGGUCAAGGAGUGGUGCAUGGCC-GUUAUCGACUAGUGGGGUGACCU-UUUGGUUAAUU-CCGC-UAAGUAGUGAGAUCUCUGGGAAC------------------------------CAAUUUAU----UGGU-AC---GACAUGUGUU--AAAAACACAGGAAGAAAGAGCCAAGAACAGG-UCAGUGAUGCCCUUAGGCGUGAUGGGCUG-CACGCGCACUACAGUGGUCACAACAGAGAAUUAGAAGAA----------AUAAAUGUGAUC---GAGAGGGAAUGAGCACUGUAAU-GUGCACAGGAACGAGGAAUUGCUAGUAAUCGUUGCCUCAUUAAGGAGCGAUGAAUGA-GUCCCUGCUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGAAACCA-GGUGCGAA--CAAGCUAAA----------------------------------------------------------------------------------------------------GCGAGUGAGUGCAGGGUUUUAGAUCUGAUACAAGUCGUAACAA--GGCAGCUGUAGGUGAACCUGUAGCUGGAUCAAUA
AY376351.1/2569-3968             CACCAGGUUGAUUCU--GCCUGAC-GUGU-GCGCUAGUCUUGGGGACUUAGCC-AUGCAAGC--CAGCGAAGC--GGC----GC-GGAGCG-GCGGACGGCUC-AGUAGGACGGCGAU--AAUCCACCCGCAGCAGAGACAAG-GAUAACCGCGGCAAGCUGCGGC-UAAGACAUGGACAGGCUGCGGCGCGGGGAG--------------GCGCGGGCAGCGGACAGGGAGCGGCUGCGGCGGAGUUGCUGGCCCAUCAGCUGGUAGGUAGGGUAAGGGCCUACCUAGGCGACGACGGGUGACGGG-GGGUGAGAGCCCGGAACCGGAGAGGGAGCCUGAGAAACAGCUCCCACGUCCAAGGACGGCAGCAG-GCGCGGAACUUGCCCAAUCCCG-GCG---GGGGAGGCAGCCACAAGACGUGGGGGCCC-------------------GGAACGCACGGCAAAGGAGUGCGGGGC----GACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGGAGCGCACAUGAGUGUUGCUGCAGUUAAAACGUCCGUAGUCGGCCCGGGCGCGCUGUGAGGAAACCGCGGGG--CCCAA---------------------------------------------------------------------------GGCGGCGGGCAGCACGGGA---GCGGGGGCGACAGGAACGGA-CAACGGCCGCGGGAUCCGGGGGCGAGAGGUGAAAAU-CGGGGACCCCGCG-G-GGACGGGCGGAAGC-GAAGGCGGCGGCCGGGGACG-UGUCCGUUGAUCAAGGACGAAGGC-CGGA-GGAUCAAAGAUGAUUA--GAUACCGUCGUAGUUCCG-GCAGUAAACGAUGCCGACGGGGCGAGGCC-------------AGGG--GGCUGUGUCCGG-GAGAAA--UU--GGAGUGUUUGGGCUCUGGGGAUAGUACGGUCGCAAGACA-GAAACUU-AAA--GAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-GCAGCUUACCAGGGCCGG-AUGCGCGG--GAGAUUGG-CGGCGGAG----CGCCCCCGAGAU--UGCGCAGGGAGUGGUGCAUGGCC-GUUUGCAACACGUGGGGUGACCUGUCUGGUUGAUU-CCGA-CAACGCGUGAGGCCUGGGGUGCA-------------------------------GCAGGGG----CUGU-GC---GACGGGCGGCGGCAAGCUGCAGGAGG--GCAGGCGAAAACAGG-UCAGUGAUGCCCUCAGAUGCUCUGGGCUG-CACGCGCACUACAAUGGCGCGGCGAGCGGGAGUGCCGGGAGGCG-CGGGCGAGGCCGUGGCG-CAGCAGGGAUGGGGGCCUGGAAG-GGUGCCCUGAACGAGGAAUUCCUAGUAGCCGCGGG-UCACCAAGCCGCGGCGAAUGA-GUCCCUGUUCUUUGUACACACCGCCCGUCACUACCUAAGAUGGAUGUG-CAGGCGAG--GA-GGCUGGGC-----------------------------------------------------------------------------------------------AGGCA-CCCGAGCCUGUGCAACUAGAUAAGGUAUAAGUCGUAACAA--GGCUGCAGUAGGUGAACCUGCGGCAGGAUCACUA
AF394529.1/1-1352                CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUAGUGUCUGAGAUUAAGCC-AUGCAUGU--GAGUGAAUGUAGUAA--GCA-GGAACU-GCGGACGGCUC-AGUAAGACUACGAU--GAAAUGAUCUGCGA---AGAAGA-AGUAACGGCGGGAAACUGAAGA-AGAGAGUUUUUGAGAAUACUUGAAGGGAUGCGGAGA--AGUGAUUUUUGAAGUGAUGUUGAGUAUUUGAGCGGAGUGUGUUGUAGACCUAUCAGCUGGUAGCUAGGGUAAUGGCCUAGGUAGGCGACGACGGGAGACGGG-GGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAG-GCGCGAAACUUGCCUAAUCCUG------UGGGGAGGCGGUUAUGAGACGUAUGAUAUUGUU-------------AUGA-AGCGGACGAUGAAAGAGUCAGUGGA----UAUU--GGAGGG-CAAGU-CGGGUG-CCAGCA-GCCGCGGUAAUA-CCUGCUCCGAUGGUGUCUAUGGUGAAUGCUGCGGUUAAAAAGUCUGUAGUCAAGUGAGGAUGUGUAUGAGUAUGAAGGUGAGUGAACUA---------------------------------------------------------------------------GAGUUGAAUAAGCUUGUAU----GUAUGAGGAGAGCAACGGA-GGGGGUGCACUGGAUAGCUGGGCGAGAGGUGAAAUG-UGAAGACCCUGGC-U-GGACGAACGGAGGC-GAAGGCUGUGUGCCAUGACG-AAUGUGAUGAUCAAGGACGAAGGC-CAGA-GGAUCGAAAUCGAUUA--GAUACCGUUUUAGUUCUG-GCAGUAAACGAUGCUGACGGGAUGACAUG-------------UAUG--UGUGUUAUGCAA-GAGAAA--UU---GAGUAUGUGAGCUCUGGGGAUAGUAUGUUCGCAAGGGU-GAAACUU-AAA--GAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-GCAACUUACCAGGGCUGA-AGAUGUGUG-GAGAACU--GAGA--------------GGGGAG--CACAUUGGCGGUGGUGCAUGGCC-GUUUGAAACGGAUGGCGUGAGCU-GAGGAUUAAUU-UCCG-GAAGGCGUGAGACCCACA--------------------------------------------------A------GACAGGUUGU-UUGGAUGACAGGAGGGAGUGGAACAGAACAGG-UCCGUUAUGCCCUGAGAUGUCCUGGGCGG-CACGCGCACUACGAUACGUGU-------------------------------AUGAGAUGU---GUGAGGGAUGAAUGUGUGGAAU-GGCAUUCUGAACGUGGAAUUCCUAGUAAUGGUGGC-UCAACAAGCCGACGUGAAUGU-GUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUGAGAUGGCACAU-GGGACGAA--CA-CCGAGG----------------------------------------------------------------------------------------------------GG-UGUGAGUCUUCUGUGGUAGAUGAGAUAUAAGUCGUAACAU--GGCUGCGGUUGGAGAACCAGCUGCAGGAUCAUCA
AF484694.1/1-1472                CACCAGGUUGAUUCU--GCCUGAC-GUAU-GCGCUUGUCUUGAAGAUUUAGCC-AUGCAAGC--UAGCGAAGC-CUUAU--GGU-GGAGCG-GCGGACAGCUC-AGUAAUACAGUUAU--UAUUUACUCGUAGUAUGUAUACG-GAUAACCAUGGUAAGCUAUGGC-UAAUACGUGAACAGGUUAUUGCAUAGAUGAAA-----------CAGCGAUAACUGAGAGAGCAAUCGACUACGACUAAGUUUCUGGCCUAUCAGCUAGAUGGUAAGGUAAUGGCUUACCAUGGCUAUAACGGGUAACGGG-AAAUCAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCCAAGGACGGCAGCAG-GCGCGAAACUUACCCAAUUCCUUAGC--GGGAGAGGUAGUGAAGAGACAUGAAGUUCUACU------------UAGAG-ACUGUACGGUAAAAUAGUACAGGAU---CUACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGUAGCGCAUAUAAUAGUUGCUGCAGUUAAAACGUCCGUAGUUGAUCACAAGGUAUUCUUCUGCAUAGUAUUUG--UGGAGUGUAUCUCGAUACUGUGAGAAAA----------------------------AUAUGGUUCUCAAAGCGGAUUACGUGAGUAAUUUAGCAUGGGAC--AUGGUGAAUAUAGGAACAGA-UGAUGGCAAUAGUAUUCAGCAGUUAGAGGUGAAAAU-CGUUGACCUGCUG-A-GGACUCUCUGAAGC-GAAAGCGAUUGUCAAGUAUG-UCUCCGUUAAUAAAGGACUUAAGC-UGGA-GUAUCGAAGAUGAUUA--GAUACCGUCGUAGUUCCA-GCUGUAAACUAUGCCGACUAGGUGAGGCC-------------GUCA--GGCUGCGCCUUAGGAGAAA--UC--AAAGUUUUUGGGCUCUGGGGAUAGUAUGGAUGCAAAUCU-GAAACUU-AAA--GAAAUUGACGGAAGGACACCACAAGGAGUGGAUUGUGCGGCU---UAAUUUGACUCAACGCGGG-GCAACUUACCAGGGCCGA-AUGCAUAG--GAGAUCGG-CUGUCUGAGA-GGGUACCCGAGAU--UAUGCAGGAGGUGGUGCAUGGCC-GUUUUCAACACGUGGGGUGGCCUGUCUGGUUAAUU-CCGU-AAACGCGUGAGGCCUGGGAAGC---------------------------------AAUUCA----UUGC-UU---GACGGAUAGCGGCAAGCUAUAGGAAG--ACAGGCUAUAACAGG-UCAGUGAUGCCCCUAGAUGUUCUGGGCUG-CACGCGCAAUACAAUGGUAUAGUGAGACUAUGUACUGAAAAGUA-UGCUUUAAGCUAUAUCG-AAUCUGGGAUAAGCUCUUGUAAA-UGAGUUUUGAACGAGGAAUUCCUAGUAAUCGCAGG-UCAUAAUGCUGCGAUGAAUGC-GUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUUAGAUGGAUGUA-UCGGUGAA--AUGGCUGGACGAAA------------------------------------------------------------------------------------------GAAAGGCAGUUGAACCUAUACAAUUAGAUAAGAUAUAAGUCGUAACAA--GGCUGCUAUAGGUGAACCUGUGGCAGGAUCAUUA
AJ252958.1/1-1355                CACCAGGUUGAUUCU--GCCUGAC-GUGG-AUGCUAGUCUCAUAGGUUAAGCC-AUGCAUGUGCAAGCGAAGC--GUAA---GU-GGAGCG-GCGUAAGGCUC-AGUAAC-GGGCAGG--UAUUUGAUCUCCUU----GAGUG-GACAUCCUCUGUAAGCGGAGGG-CAAAACACGAUACCGGCAGCAGAAGUG--------------------UUGAUGGUAGAACGGAAGUGGAGGAGAGUAAGCAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGUAGACGGGU-ACGGG-GAAUUAGAGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCGGGUCCAAGGACAGCAGCAG-GCGCGAAAAUUACCGAAGCCUCCGGU--GAGGGCGGUAGUAAGGAGACGUGAAAACGA----------------------GGCGCGGAUAAAAGAAGCGCUAGU----AACA--GGAGGG-CAAGA-CUGGUG-CCAGCA-GCCGCGGUAAUA-CCAGCUCCUGGAGUAUCGAUGGUGAUUGCUGCAGUUAAAGAGUUCGUAGUCAGAGCGGGUAUUCGAGCGCAACAGGUCGCCA--CUCAA---------------------------------------------------------------------------GGGGGGCACGACGUGCGAAC--GCCGCGGAAUAAGGAGCGUC-UAGGGGCCGCGUUAUUAAGCGACGAGGGGUGAAAUC-UGGUGACUCGCUU-A-GGAGCAACAGAGGC-GAAAGCGGCGGCCAGGGGCG-AAUCCGAUGAUAAAGGACGUAGGC-UAGA-GGAUCGAAGACGAUUA--GAGACCGUUGUAGUUCUA-GCAGUAAACGAUGCCGAUGCCGUGGCGCG-------------GAAA--CGCGACGCGGAA-GAGAAA--UC---GAGUA---GGGCCCUGGGGAGAGUACGCGCGCAAGCGA-GAAAUUUAAAG--GAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCU---UAAUUUGACUCAACGCGGG-ACAGCUUACCAGGCCCGA--CGGCCGC--AGGAGUGU--UGU-------------ACACGAU--AGGCCGGAGAGUGGUGCAUGGCC-GUUAACGACGAGUGGGGUGACCU-UAGGGUUAAGU-CCGG-GAAGUAGUGAGACCCCUG-----------------------------------------CG---AUAGU-AG---GACAGGUGCG--CAAAGCACAGGAAGGAAGGGUCAAGAACAGG-UCAGUGAUGCCCUUAGAUGGUCUGGGCGG-CACGCGCACUACAGUGGUCACGGAAAUGGAGAAGAAAGAA---------GAAAAAGUGAUC---GAGAGGGAACGAGGUCUGGAAG-GGGCUCGGGAACGAGGAAUUGCUAGUAAUCGCGGACUCAUUAAGACGCGAUGAAUAC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCA-GGCGCGAA--CAAGCGAGA----------------------------------------------------------------------------------------------------GCGAGUAAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAA--GGUAGCUGUAGGAGAACCAGUAGCAGGAUCAUAA
AF394527.1/1-1317                CACCAGGUUGAUUCU--GCCUGAC-GUGG-ACGCUUGCCUCAAGGAUUAAGCC-AUGCAAGC--CAGCGAAG---GUAA----C-GGAGCG-GCGAACGGCUC-AGUAGGACAGGGAC---AUCUAACCAUUG-----UACAG-GAUAACCGCGGUAAUCUGUGGC-UAAUACUG------------------------------------------------------------UAGUGGGUGGGACCCUGGCCUAUCAGCUUGGCGGUACGGUAAGUGCGUACCGUGGCGACGACGGGUAGCGGG-GAAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAG-GCGCGGAACUUACCCACUUGGA-GGA---CCAGAGGUAGUGACGAGGCGUUUUGAAUG---------------------AGAACAGUGUAAAAAGCUGAUUGAAA-GCUACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGGAGCGUCUGUGUGUGUUGCUGCGGUUAAAGAGUGCGUAGUCG--GGUUUUUUGCCAGCAAUAAAGGUGCGGU--CUUCA---------------------------------------------------------------------------ACUGUGCAUUGUGCUGGUA----CUUAAAUCUAGGGACCGGA-GAAGGGCAAUGAUAU-CAACAGCGAGGGGUGAAAAC-UGAUGACCUGUAG-A-GGAGCGACUGAGGC-GAAAGCGGUUGUCCGGGACG-GGUUCGACGAUCAAGCGCGUGAGC-AGGA-GGAUCGAAGGCGAUUA--GAGACCGUCGUAGUUCCU-GCAGUAAACGAUGCCAACGGGAUUGCAAG----------------C--UAUGUGAUUCAA-GGGAAA--CC---GAGUGUAUGGGCUCCGGGGAUAGUACGGGCGCAAGCCA-AAAACUU-GAA--GAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGU---UAAUUUGACUCAACGCGGG-ACAACUUACCGGGGCAGG-CAGUAUUUU-GUGAAGGG-CAUAGUUAAGGUCUAUGUUCUGAU--GAUGCUGCGCGUGGUGCAUGGCC-GUUCUUAACACGUGGGGUGACCUGUCUGGUUAAAU-CCGA-UAACGCGUGAGACCCUGG-----------------------------------------AU-------G-AU---GACGAUGCUCGAUGAGAGUAGGGAAGCUCGGGUCGAUAACAGG-UCUGUGAUGCCCGUAGAUGUCCCGGGCGC-CACGCGCACUACAGUGGGAGA-GGUUACGUGAAACGGA-------------GCUCUCUUGC---GGUUGGGAUUGACGUUUGUAAA-UAUGUCAUGAACGCGGAAUUCCUAGUAGCGUGCCG-UCACUAACGGCAGGCGAAUGA-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAUGUG-CGGAUGAA--GU-UGGCUAG-------------------------------------------------------------------------------------------------GCCA-AAAGAAUCCGUGCCACUAGAUUGGAUACAAGUCGUAACAA--GGUUGCAGUAGGUGAACCUGCCGCAGGAUCAAUA
D85502.1/1-1247                  CACCAGGUUGAUUCU--GCCUGAC-GUAG-ACGCUAUUCCCUAAGAUUAACCC-AUGCAUGU--UUUUGAU-----------AU-GGAAAA-AUGGACUGCUC-AGUAAUACUCACUU--UAUUUAAUGUAUUA---AAUUAG-UAUAACUGCGUUAAAGUGUAGCAUAAGAC-------------------------------------------------------------AUAUACAGUAAGAGUGAGACCUAUCAGCUAGUUGUUAAGGUAAUGGCUUAACAAGGCAAUGACGGGUAACGGUAUUACUUU-GUAAUAUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAG-GGGCGAAACUUGACCUAUGGAU-UUU--AUCUGAGGCAGUUAUGGGAAGUAAUAUUCUAU---------------UGU-UUCAUAUUGUAAAAGUAUAUGAGGUGAUUAAUU--GGAGGG-CAAAU-CAAGUG-CCAGCAUGCCGCGGUAAUA-CUUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUU-----------------------------------------------------------------------------------------------------------------------------------------AUAUUUAAGAAGCAAUA-UGAGGUGUACUGAUAUGUUGGGAGAGAGAUGAAAUG-UGACGACCCUGAC-U-GGACGAACAGAAGC-GAAAGCUGUACACUUGUAUG-UAUUUUUUGAACAAGGACGUAAGC-UGGA-GGAGCGAAGAUGAUUA--GAUACCAUUGUAGUUCCA-GCAGUAAACUAUGCCGACGAUGUGAUAUGA----------UAUUAA-UUGUAUUAGAUGA-UAGAAA--UU--UGAGUUUUUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUU-GAAAAUU-AAA--GAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCU---UAAUUUGACUCAACGCGAG-GUAACUUACCAAUAUUUU--AUUAUUCG-GAGAAGAU-UUUC------------AAUCUGAG--AAUGAUAAUAGUGGUGCAUGGCC-GUUUUCAAUGGAUGCUGUGAAGU-UUUGAUUAAUU-UCAA-CAAGACGUGAGACCCUUU-----------------------------------------UA----UUAA-UA---GACAGACACA-AUCA-GUGUAGGAAGGAAAGGAUUAAAACAGG-UCCGUUAUGCCCUCAGACAUUUUGGGCUGACACGCGCAAUACAAUAGAU------------------A-------------UAUA--AUCU---UUAUGGGAUAAUAUUUUGUAAG-AGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAU-UAAAUAAGUAGAAUUGAAUGU-GUCCCUGUUCUUUGUACACACCGC-CGUCGCUAUCUAAGAUGAUAUGU-GUUGUGAA--AU-UAGAGAAA------------------------------------------------------------------------------------------------ACUA-CUUGAACA-UAUGUAUUAGAUCUGAUAUAAGUCGUAACAA--GGUUGCUGUUGGAGAACCAUUAGCAGGGACGCUA
AJ302319.1/1-1304                CACCAGGUUGAUUCU--GCCUGAC-GAGG-AUGCUUGUCUCUGGGAUUAAGCC-AUGCAAGU-CUGGUGAAGC--GAAA---GU-GGAACU-GCGAACGGCUC-AGUAGAACGGUGAU--UAUUUAAUCGUGUA----GGAAG-GAUAACCGCGGGAAACUGUGGC-UAAU---------------------------------------------------------------AACACGAGUAAGACGCCGACCCAUCAGUUUUAUCGUACGGUAAGGGCGUACGAUGGCUUUAACGGGU-ACGGG-GGAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCAGGUCUAAGGACAGCAGCAG-GCGCGAAACUUGCCCAAUUG----GA----GAGAGGCAGUUAUGAGACGUAUAUUUUG---------------------UAACCGGGGUAGAAUACCGGUGAUU----GACU--GGAGGG-CAAGU-CUGGUG-CCAGCA-GCCGCGGUAAUU-CCAGCUCCAGGAGUGUCAUAGUGCAUUGCUGCAUUUAAAAGGUCCGUAGUCAGUGUUGACAGGGAUGCUAGAAGACACUUUC--UUCAU---------------------------------------------------------------------------GGAGUGUAUUGGCAUUCUA---GGUUAGCAUGUGAGAGCGGA-AGAGGGCGACUGUAUUGCGUAGCGAGAGGUGAAAGU-UGACGACCUACGU-A-GGACAAACCGAAGC-GAAAGCUGUCGUCCAGUACG-UAGCCGGUGAUCAAGGACGUAAGC-CGGA-SGAGCAAAGGUGAUUA--AAGACCCCUGUAGUUCCG-GCCGUAAACUAUGCCAACUGGGUGUUAC---------------GUA---GUGGUACCCAC-GAGAAA--UC---AAGUAUAUGGGCUAUGGGGAUAGUNCGAUCGCAAGAUU-GAAACUU-GAA--GAAGUUGACGGAAGGACACCACCAGGAGUGGAAUGUGCGGCU---UAAUUUGACUCAACGCGGGCACAACUUAUCAGGGCCAG--UUGUAUGACGA--AUC---UAU--------------GAUGA---AUACGACUAAGUGGUGCAUGGCC-GUUCACAACAUAUGAGGCGACUU-UUAGGUUUAUU-GCUG-UAAUGUGUGAGACCCUCA-----------------------------------------GC----UACG-GC---GACUGGGGACUAUAAGUUUCAGGAAGGAGGGGGCUAUAACAGG-UCUGUGAUGCCCUUAGAUGUUCUGGGCUG-CACGCGCACUACAAUGUUAUUUCUAGGUAUAUUGUAAAG----------AUAAAGGAUAACU-CGGUUGGGAUUGCGUUCUGUAAU-GGACGCAUGAACCAGGAAUUCCUAGUAGUCGCGUG-UCACUAACGGGCGACGACUGC-GUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGUGCUA-UGUUCGAA--GAGGGUUUU----------------------------------------------------------------------------------------------------CCUUCUGAGGACGUAGGAUUAGAUUGGAUACAAGUCGUAACAA--GGUUGCUGUAGGAGAACCAGCAGCAGGAUCAUAA
#=GC SS_cons                     :::<<<<<_______..>>>>>,{.{{{{.{{{{{,{{{{{{{{[-----[[[.-[[[,,<<..-<<<---<<..____...>>.--->>>.>>,,,,,,(((.,,,,,,<<<<<<<<..--<<---<<<<<<<....--<<<.----<<<<<<<____>>>>>>>.----->>>...........................................................>>>>>>>-->>>>>>>>>><<<--<-<<<--<<<<<<<<_______>>>>>>>>>>>----->>>>,,,<<<<.<<<<____>>>>--->>>>))),<<<<<<__________>>>>>>,<<<<____>>>>,,,]]]].]]-],,,,,<-<<<---<<<<<.___..>>>>>->>>>,}}-}}}}}},,,,,,,,,,...................,.,<<<<<<_________>>>>>>,,,....,,<<..<<<<--.-----.<<<<--.---<<_.___>>-------.>>>>>>>>>>,}}}}}}}}}},,,,,,,,,,[[[,,,,,,,((((---(((-------------------------------..-----...........................................................................-------------------....-----------((((((((.(--(((((((<<--<<<<<<<<---<<<______>>.>------>>>>>>.>.>-->>,,,,<--<<.____>>>)))))))-))))).)-)))---)))---)))),,,,<<.<<<<.---<<---<<<<____.._____>>>>--->>>>>>.>>,,,,,,,,,,((((((,<<<<<<<<<<.............____..>>>>>>>>>>,,.<<____..>>...,,)))----))),]]],<<<------<<<<____>>>>.---->>>.,,,..,,,,,{{{{{-{{{{{{{--{{,,{{{{{{{{{{{{{{{{{,...,,,<<<<________>>>>.,,,,,,,,{{{{{{{,,,..<<<<<<--.----<<<<.____.............>>>>---..>>>>>>,,,[[-[[[[--[[[[[.[[[[,,,((((((<<<____>>>.,<<<<______.>>>>.,,)))))),,,,,((((,.........................................<<....____.>>...,,<<<<<<<<.____>>>>>>>>,,,,,)))),,,,]]]]-]].]---]-]]]]]]],,,,,}}}}}}},,,}.}-}}}}}}}}}},,,<<<<<<_________________.............____>>>>>>...,,,,<---<<<<<<<<______.>>>>>>>>--->,,,,,}}}}},,,,,<<<<<<<<._______>>>>>>>>,,,,,,.}}---}}}}}}}}}}-}},,,,<<-<<-<-<<<<<<<<--<<<<<<<<.<<<<<<<<..<<.<<____....................................................................................................>>.>>>>>>>>>>>>>>>>>>-->>>>>>>>-->->>-->>,,..,,<<<<<<<<<<____>>>>>>>>>>::::::::
#=GC RF                          CACCAGGuUGAUUCU..gCCUGAc.gugg.acgCUagucuccgaGAUUaAGCC.AUGCAuGc..ucgcGAAgc..uuaa...gc.GgAgcg.gCGaAcgGCUC.AGUAauccggcccc..uAucUaaucgcccc....augcg.gAUAcCcgcgguAAaccgcgGg.uAAuAcgc...........................................................ggggcgaaUgaggggccggcCuAUcAGcuaGucggUAgGGUAAgGGCcUAccgaggCgAugAcgGgUaACGGg.gaAuuagggUucgAUuCCGGAGAGGgAGCCUGAGAGAUgGCUcCCAcgUCCAAGGAcgGCAGCAG.GCGCGAAAcUUgCCcAAccccc.auu..gggggAGGcAGucAggagacGUaaauuuaa...................g.acgggcguGUAAAaaacgcccggaa....aAcu..GGAGGG.CAAGu.CuGGUG.CCAGCA.gCCGCGGUAAUa.CCaGCUCCaggAGcguccaugaugauUGcUGCggUUAAAAaGucCGUAgUcggauaauuuuauuuuuuauuaaaaguguuuu..uuuaa...........................................................................gguguauuauauuauguaa....uuaagaauuuaggaccGcc.cggcGgccacggUAuucggcgGcgAgggGUGAAAcc.cgAuGACCcgccg.a.gGAccaaCagAgGC.GAAAGCgguggcCgagggCg.gauccGaugAucAAGgaCGuAaGC.cgGa.GgAuCGAAggcGAUUA..GAuACCgccGUAGuuCcg.GCaGUAAACgAUGCCcAcagggcggcgcc.............uuua..ggcgccgcccaa.gaGAAA..uc...uAgUgUauGGGCUccGGggguAGUAcccgcGCAAgcgg.GAAAcuu.aAa..GAAAUUGACgGAaggACACCACAAGgAgUGgAgUGuGCGGcU...UAAuuuGACUCAACGCggg.acAaCUUACCagggccga..ggccccuu.gaGAgcgg.aauu.............ccgcGAu..ggggccgaggGUGGugCAUggCC.GUUcuuAAcgcgUgggGUGAccu.UccggUUAAaU.ccgg.uAAcgcgUGAGAuccccg.........................................cc....uuaa.gg...GACccgcgcc.guaAggcgcggGAAGgaggggucaAgAACAGG.uCaGuGAugCCCcuAGAUgcccuGGGCUg.CACGCgCAcUaCAaUggccgcuugaaauauaauauaga.............Aaaugcggcc...aauuGGGAcuggccccUGUAAu.ggggccagGAACguGGAAuUcCUAGUAgucgcgcg.UCAuuAAcgcgcgacGAAUgu.GUCCCUGUccuUuGUACACACCGcCCGUCGcuAuCucAGAuggcugcc.cgggcgaa..ga.gcuuaa....................................................................................................gc.ucugagcccgggcagcuaGAUgaGaUagAAGUCGUAaCAA..GGcugCugucGGaGAACCggcaGcagGAUCAuua
//
# STOCKHOLM 1.0

#=GF AC   RF02543
#=GF ID   LSU_rRNA_eukarya
#=GF DE   Eukaryotic large subunit ribosomal RNA
#=GF AU   Gutell RR
#=GF AU   Nawrocki E; 0000-0002-2497-3427
#=GF SE   Published; PMID:11869452
#=GF SS   Published; PMID:11869452
#=GF GA   50.00
#=GF TC   50.00
#=GF NC   49.90
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 17.38 -Z 549862.597050 CM SEQDB
#=GF CL   CL00112
#=GF DR   URL; http://www.rna.ccbb.utexas.edu/;
#=GF DR   URL; http://oberon.fvms.ugent.be:8080/rRNA/ssu/index.html;
#=GF DR   URL; http://rdp.cme.msu.edu/html/;
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   11283358
#=GF RT   Crystal structure of the ribosome at 5.5 A resolution.
#=GF RA   Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JH,
#=GF RA   Noller HF
#=GF RL   Science 2001;292:883-896.
#=GF RN   [2]
#=GF RM   11869452
#=GF RT   The comparative RNA web (CRW) site: an online database of comparative
#=GF RT   sequence and structure information for ribosomal, intron, and other RNAs.
#=GF RA   Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng
#=GF RA   B, Lin N, Madabusi LV, Müller KM, Pande N, Shang Z, Yu N, Gutell RR
#=GF RL   BMC Bioinformatics. 2002;3:2.
#=GF WK   Ribosomal_RNA
#=GF SQ   88



ABBC01002983.1/694-4056              [encoded data, 8395 characters]
ABXC01009099.1/4348-964              [encoded data, 8395 characters]
AATU01005899.1/2053-5743             [encoded data, 8395 characters]
ADAR01000068.1/27943-24692           [encoded data, 8395 characters]
EU143316.1/2547-5543                 [encoded data, 8395 characters]
AM039756.1/3-3632                    [encoded data, 8395 characters]
CABX01000024.1/22242-18910           [encoded data, 8395 characters]
FQ311431.1/351837-348427             [encoded data, 8395 characters]
AB158483.1/67259-70699               [encoded data, 8395 characters]
AECX01001482.1/4980-1567             [encoded data, 8395 characters]
ACDU01008453.1/4063-605              [encoded data, 8395 characters]
AF001946.1/7-3467                    [encoded data, 8395 characters]
AY347308.2/2719-6113                 [encoded data, 8395 characters]
AFSE01000966.1/4163-7878             [encoded data, 8395 characters]
BABT02000083.1/2416-5861             [encoded data, 8395 characters]
DQ158858.1/3702-7359                 [encoded data, 8395 characters]
ADVD01001051.1/9688-6024             [encoded data, 8395 characters]
FP929119.1/127369-124021             [encoded data, 8395 characters]
X99212.1/1257-5224                   [encoded data, 8395 characters]
AM910985.1/906046-910036             [encoded data, 8395 characters]
AEKE02010433.1/9661-13258            [encoded data, 8395 characters]
AACW02000152.1/5077-1635             [encoded data, 8395 characters]
X54004.1/2-3341                      [encoded data, 8395 characters]
CP000883.1/4521-799                  [encoded data, 8395 characters]
AEWC01035556.1/3417-48               [encoded data, 8395 characters]
AAEE01000005.1/203540-206997         [encoded data, 8395 characters]
AANH01015347.1/4485-499              [encoded data, 8395 characters]
CP000592.1/125599-122427             [encoded data, 8395 characters]
CP002174.1/4341-468                  [encoded data, 8395 characters]
AAWU01040617.1/30598-34662           [encoded data, 8395 characters]
AABX02000201.1/4587-1251             [encoded data, 8395 characters]
AAGJ04131089.1/5040-1277             [encoded data, 8395 characters]
AANH01014867.1/5242-1306             [encoded data, 8395 characters]
ABAI02000368.1/21969-18003           [encoded data, 8395 characters]
AABL01002234.1/7613-3727             [encoded data, 8395 characters]
CABB01001346.1/9950-13589            [encoded data, 8395 characters]
AJ251729.6/10-3932                   [encoded data, 8395 characters]
AJ616903.1/3-3189                    [encoded data, 8395 characters]
AAXT01000001.1/163499-160332         [encoded data, 8395 characters]
EU276014.1/2525-6128                 [encoded data, 8395 characters]
X16108.1/3-3406                      [encoded data, 8395 characters]
AASC02063144.1/2357-6096             [encoded data, 8395 characters]
AY190083.1/12816-9361                [encoded data, 8395 characters]
AAQA01000230.1/2382-6287             [encoded data, 8395 characters]
ABHY02000010.1/18411-14992           [encoded data, 8395 characters]
AGKD01469794.1/433-4364              [encoded data, 8395 characters]
EU795185.1/5035-1542                 [encoded data, 8395 characters]
ABJE01001552.1/13155-9432            [encoded data, 8395 characters]
AF463459.1/5172-9173                 [encoded data, 8395 characters]
CACX01001817.1/28911-25376           [encoded data, 8395 characters]
ABFO01001550.1/11234-7872            [encoded data, 8395 characters]
AAWZ02036944.1/13391-9461            [encoded data, 8395 characters]
ABJQ01003429.1/1261-4980             [encoded data, 8395 characters]
DQ340386.1/5845-9590                 [encoded data, 8395 characters]
AAEU02004758.1/4488-8478             [encoded data, 8395 characters]
AAGK01000006.1/311714-308365         [encoded data, 8395 characters]
AM850055.1/2180-5620                 [encoded data, 8395 characters]
ABQD01000052.1/42656-39384           [encoded data, 8395 characters]
AF083031.2/4931-937                  [encoded data, 8395 characters]
FJ214952.1/2476-6052                 [encoded data, 8395 characters]
ADND01333398.1/1565-4887             [encoded data, 8395 characters]
AY305326.1/4080-7607                 [encoded data, 8395 characters]
AY580056.1/8-3756                    [encoded data, 8395 characters]
HM245049.1/2716-6021                 [encoded data, 8395 characters]
AF198253.1/4-3331                    [encoded data, 8395 characters]
ACFS01000464.1/72267-68513           [encoded data, 8395 characters]
AFIU01000031.1/1055-4343             [encoded data, 8395 characters]
Z92784.1/26583-30090                 [encoded data, 8395 characters]
ACBU01000682.1/139180-135819         [encoded data, 8395 characters]
L78065.1/4292-8312                   [encoded data, 8395 characters]
AC215351.2/119902-117132             [encoded data, 8395 characters]
AEKZ01014024.1/10162-6132            [encoded data, 8395 characters]
EU304548.1/2263-5714                 [encoded data, 8395 characters]
CABU01011010.1/4329-997              [encoded data, 8395 characters]
FJ545743.1/4016-7385                 [encoded data, 8395 characters]
X53538.1/2523-6086                   [encoded data, 8395 characters]
U35394.1/2899-6288                   [encoded data, 8395 characters]
AF248477.1/2821-6490                 [encoded data, 8395 characters]
DQ248942.1/4699-8597                 [encoded data, 8395 characters]
FJ948787.1/12675-16494               [encoded data, 8395 characters]
AGAT01020583.1/4054-375              [encoded data, 8395 characters]
AB526843.1/3573-7179                 [encoded data, 8395 characters]
ABEP02020128.1/2049-5939             [encoded data, 8395 characters]
HQ009889.1/2642-6383                 [encoded data, 8395 characters]
AJ298079.1/5-4031                    [encoded data, 8395 characters]
Y11506.1/699-3910                    [encoded data, 8395 characters]
ADAS01005276.1/8554-11800            [encoded data, 8395 characters]
ACBR01000224.1/7956-3957             [encoded data, 8395 characters]
#=GC SS_cons                         :::::::::::::::::::::::<<<<<<-----<<____>>-----.->>>>>->,,,,,,,,,<<____>>,,,<<<<<----.-<<_____>>----....>>>>.>.,,[[[[,....,.<<<<<<<<<<<<<<<<__._____.............................>>>>>...>>.>>...>>>>>>>,,,,((..((((..-.((((............................................-(((((.((......-(((((((.,,,<-.<<.<<______>>>>....>...................,,<___>,.,<<_______.......................................>>,,,,,.......))))).))--..........))..))))).-----..))))......)))).-)),,,.....,,,,,<<<<<<<____.____>>>>>>>,,,,.,.<<<<<...________>>>>>,,]]]],,,,,,,,,,,,,.,,,,,,,,,,,,,,,,,,,,<<____>>,,,,,,,,,,,.,,,,<<<<____>>>>.,,,,,,,.,,,,,,,,,,,,,,,,,,,,,,,..,,,,((((((.((((((...,,,,<..--<<<<<<<._________________..____.......................................................................................................................................................................................................................................___________________>>>.>>>>...>,,,.<<<<<<<________.___________________________............................................................................__________________________________________________________________..............................................................................................................................................................................................................................................................._________________>>>>.>>>,,,,,,...)).))...)))))))),,<<<<________>>>>{{{{{{,,,,(((.((((((((((,,<<<--<<<<<<..____.....................................>>>>>>...-->>>,,,<<____>>,,,...............................................................................................,,,,<<<<<--<<<._______......................................................._>>>--->>>>>,<<<.<<.<<<...---<<...____..................................................................................................................>>---..>>>->>>->>..,,,,))))))))))))),,[[-[---[[[[[[,,,((((((((((((,<<<<---<<<<<<<____>>>>>>>---->>>>,,,<<<<-<<-<<________>>>.>>>>>,,)-))))))))))),<<<_____.>>>.,,,,,,]]]]]]------].-]],,[[[[[[,,,,<<<<<____>>>>>,,(((((((..,....,,,,...................,,,,<<<<<<<<----<<<----<<<<<<<<<<--<<<<<<.-<__..___>-.>>>>>>>>>>>>>>>>-->>->---->>>>>>.>>.,.<<<.<.<<.<<<..____..._____................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................>>>>>.>.>>>,,,..,,,,,,,,......))))))),,,,,<<<.<.<<<<<<_____>>>>>>>>>>,,,,<<<______>>>,,,(((((-(---(((------(-(..--(((----.-.-------------(((-((((((((((-------(((((,<<<--<<<___.______>>>-->>><___><---<<______...>>->,))))).---)))))))).)))))-----------.-----.--.-)))--.....)).)))---)-)))))<<<<<<..<<<._________..........................................>>>>>>>.>>,,,,]]].......]].]..<-<<<<<<<<..<.<..........----.--<<-...---<<<.____>>>--->>---...>>.>>.>>>>>>-->,,,,,}}}}}}.,,,,,,,,,,,,,,<<<<<<.____......._.__>>>>>>{{{{,,.,,,{{{{,,{{,,,<<<<<..<---<<_____>>->>>>>>,,,,,,{{{,((---((<.<<-.<<.<___._>>.>..>>>,,,..,,,...<<<________...................................................................................................................................._>>>......,,,,,))----)),,,<<<<<________.>>>>>,,[[[[.....................................-[[[[[[[.......,,,..,<<<<____.................................................>>>>...,,.,,,,((((((---((((.-(((((((-(((<<.<<<<_________>>>>>>,,,.<<<.<<......----......-<<...<<<<<<<<<<<_.____>>>>>>>..>>>.>...>>.-----............>.>.>>>,,,,,,<<<<<<<...._____..............................................................................>>>>>.>>,,)).).---))))).))-.))))---------)))))),,,,,,,,,,,............................................................................................................................................]]...-]]]]].........]]]],}}},,}},,,,,<<______>>,.}}}},<<<<._____>>>>,,}}}.},,.{{.{{.----{{{{{{{{.-{{{,,,,,,,,,,,,,,<<<<<.---<<..____...>>---->>>>><<<<<<<<<<<<<<-<<<.<..<.<<<<.<<<..-<<.<<-----<<<<.....<<<.<.<<<.<.<<<<.<<<<<<<<<.<<<<<<<____........................................................................>>>>>>>>.>>>>>>>.>>>..>>>...>>>>>>>-..>>>>----...>>>>->>>---..--------.............................................................................................................................................................................................................................................................................----..-->>>>>>>>>.---..---...>>.>>>-->>>>>>>>><__._>,,,,,,,[[[[[[[[[,,<<<__._______>>>,,<<<<<<<<.-.<-<<<<_____>>>>-..>.--->>>>>>>>,,((((,<<<--<<<<<<-<--<<<----<<<<<____..>>>>>----..>>>>>>>>-->>>>><<<<<<_______>>>>>><___.................................................................................................................................................................................................................................................................................................................................................................>,,,...,,,,,,,,,,,,<<.<<<<_____>>>>>>,,,,,,,,,,)))),,,]]-]]]]]]],,,,}}}-}}}}}}}}-}}}},,,,,,,,,,,,<<<<<___....._____>>>>>,,{{{{{{.{{-.{{{.-{{,,,,,,{{{{-{{{{{{{.,[[[[---[[[[[[[...,,<<<<<<<<<<<<<<<<<<---------<<<<<...--..<<______.......................................>>------------>>>>>>>>>>>>>->>>>>>>>.>>,,,.(((((.-----((((.,,,,<.<<<<.___..................................................>>>>>,,,,,,,,,,,.,,,..,,<<<<<....______.............................................................................................................................................................................................................................................................................................................................................................................................>>.>>>,,.))))--....))))).,,,,,]]]]]]]----]]]],,<<<<_____>>>-><<<<<<___________>>>>>>,,[[,,,,((((((.<<-<<<<<.<_______.>>>>>>--->><<_.._____>>,,,,)))))),,,,<<<<<<<<<_______>>>>>>>>...>,<<<____>>>,]],,,,,,,,,,<<<<<<-........-<<<<______._....................................................................................................................................................................................................................................................................................................................................................................................................................................................................>>>>>>>>>>,,,,,,,,,.}}}}}--}}}}}},,,,,,,,<<<-<<<<<<<<---<<_______>>--->>>>>>>-->>>>,,,,,,,,,,(((((((((((,,<<-<<.<<<<______>>>>>>--->>,<<<<<_____...........................................................................................................................................................................................................................................................................................................................................................................................>>>>>,,,,,.)))))--)--))))-),,,,,<<<<<<<____>>>->>>>,,,,}}--}}}}}}}}}}},................................,,((((((((--((((,<<<<<<<<__________.._____..>>>>>>>><<<<<---<<<----<<<<<<<<<<<____..>>>>>>-->>>>>---..>>>.-->>>>>,....<<<--...--<<<<<__________._>>>>>---->>>,))))--..--.........))))))))..........,,,,,,<<<.<<<<______________________________.......___________________________..________________.__......................................................................................................................................................................................................................................................................................................______________________________________>>>>>>>,..,,(((....((<.<<<<_______..>>>.>....>,,,...,....<<<<<<<<<-<<--<--<<<<-.<<<<<<<<__......____.................................>>>>>>>>>>>>...>--->>----.>>>-..>>>>>>,.,,)))))::
#=GC RF                              ugacCUuaaaUcAgguaaGAuUAcCcgCuGAAuUUAAGCAUAUuAaU.AaGcgGAgGAAAAGAAAcuAACaagGAUUcccuuAGU.AgcGGCGAgcGAAg....aggg.A.AuAGCcC....A.cgcugcaacuccgcccuc.uuuuu.............................gggcg...ga.gu...ugcagcgUauagg..ggcc..u.ccuc............................................agccgc.gg......cccccgcc.uAAgU.cc.ccUgGAAugggg....c...................accAuAgA.GGGUGAgAgu.......................................CCcGUau.......ggcgg.ggua..........cc..gcggc.uuuau..gagg......ggcc.uccaaa.....GAGUCGgGuugcUUGg.gAaUgcagCcCaAAg.U.gGguG...GUAaAuUuCauCcAAgGCUAAAUAuuagcaaG.AGACCGAUAGcgaACAAGUAccGUGAggGAAAGaUGAAA.AGaACucuGAAaagaG.AGUUAAA.uAGuAcgUGAAAuuGuUaAgAgG..gAAgcgcgug.ggaccg...gaauu..uuccccccg.uaaaauuaauuauuauu..uuuu.......................................................................................................................................................................................................................................uuuuauuuuuuuauuauaucgg.gggg...aaaa.ccgccccuuuuuuua.uauuaggauaaagauuuuuaaaauuuu............................................................................aauuuuuuuuuaauaucuuuuauaaaguuuuuuuuauuuuauuuuuaauauuuaguuuauacuaug...............................................................................................................................................................................................................................................................aaauauauuuauuuaaagggg.cggauauaa...cg.gu...cccacgcgACCCGUCUUGAAACACGGACCAAGGAGUcca.acauguguGCgAGuguuuggguc..auuA.....................................gaccca...uacgCGuAacgAAagugAa...............................................................................................uuaaggugggAccc.uuuuaau.......................................................uggggCAccaccggcc.gg.ucc...uaauc...uuuu..................................................................................................................gagau..ggauccgAgc..aaGAGCacacauguuggGACCCGAAAGauGGUGAACUAugCcugggcAGggcGAAGccAGgGGAAACcCUggUGGAGgccCGuAgcgaUuCUGACGUGCAAAUCG.aucgucagAccuggGuaUAGGgGcGAAAG.aCu.AAUCGAACCauCUAGUAGC.UGGUUcCcuCCGAAGuuUCCCUCAGGAuaGCuggagcu..u....uuuu...................uuAGUcuuAuccGGUAAAGCgAAUGAuUAgaGGcuucggGg.acga..AAugu.cCucgaCCuaUUcUCAAACUUUAAAUgggUaa.gA.a.gcc.c.cg.guu..aCUU...aauUG................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................aaccg.g.ggcauu..uaAuauaa......agcuccaAGUGGGCC.A.cUUuUGGUAAGCAgAAgUGGCGAUGcGGGAUGAACCgAAcGccggGuUAAGGuGCcuaAgUg..cacgCUcAU.c.uAGAuaCCAuAAAaGGUGUuggUucaUauaGACAGCaGgAcGGUGgccAUG.GAAGUCggaAUCCgCUAAGGAGUGUGUAACA...ACUCAcCuGC.CGAAugaAcca.GCCCuGAAAAUGGAUG.GCGCU.uA.AGcgua.....cc.aCCuAUaCccggCCgucgg..ggc.Aaauuuaau..........................................gccccga.cGAGUAGGa.......gG.g..cGuggcGgcu..g.c..........guuG.AAgcu...uugggc.GUgAgccuggguGGA...gc.ag.cCgccaGUgCAGAUCUUGGU.GGUAGUAGCAAAUAcUCaAa.UGAG.......A.aCuUuGAggACuGA.AGUGGaGAAGGGUUcCgug..ugAACaGuAgUuGaacacGgGUuAGUCGgUCCUAAGgc.acA.gg.guAa.ucc.c..guguua..aag...gggaauuuuuu....................................................................................................................................uccc......auuuacCGAAAGGGAAgcgGGUUAAuAUU.CCcgcACcugg.....................................acguggau.......uuu..augcgGuAA.................................................cgca...Aa.ugAacucggaGAcgccg.gcgggggccccggg.aaGaGUUuUCUUUuCuucuUAA.cgg.cc......uauu......uaC...CcugcAaccggu.UuauccggaGg..uag.G...Gu.uuaau............g.g.ccgGaAgAGcgccgca....uuuuu..............................................................................ugcgg.cgUCcg.g.Ugugcccc.cga.cggcCCUUGAAAAuccgagGgAaggaauaa............................................................................................................................................au...uccacg.........ccaggcCGUACCcAUAaCCGCAuCAGGU.CuCCAAGGu.gAauAgCCUCUaGU.cgA.UA.GA.AuAAgGUAGgUA.AGGGAAGUCGGCAAAaUAGAUCC.GUAaC..UUcG...GgAaAAGGAUUGGCUCUgAggGcugggcc.c..g.ccgg.gcc..ucg.ccaugAagccg.....ccg.c.ccc.c.cgcc.ggccgcccc.ccgccgcguaa........................................................................gcggcggg.gggcggc.cgg..cgg...ggggcggu..cggcuaau...ggcguggcuuu..guuauuuu.............................................................................................................................................................................................................................................................................uuuu..uuccggcgggc.aau..uAA...ca.gCcAAcUcAGAACUGGu.ACGGACaAGgGGAAUCcGACUGUuU.AAUUAAAACAuAGcAUugcG.A.cGgcccgaAaggggcG..g.UGACgcaAUgUGAuUuCUGCCCAGUGCUcUGAAuGuCAAacUGAaGAAA..uUCAgucAA..gCgCgGGUAAACGGCGGGAGUAACUAUGACUCUCuUAA.................................................................................................................................................................................................................................................................................................................................................................gGUA...GCCAAAUGCCUCGU.CAucUAAUUagUGACGCGCAUGAAUGgAuUAACgAGAUUCCcACUGUCCCUAcCUACcAUCUAGCGAAACCACAGcCAAGGGA.....ACGGGCUUGgaAccaucA.GcG.GGG.AAAGAAGACCCUgUUGAGCUU.GACUCUAGucuGgca...UUGugaagcgacauggggGgUGUAGaAUAaGUGG...GA..Gcuuuuag.......................................gCGccagUGAAAUACCACuaCccccauugucgcuuc.aCUUA.cuccg.UuAagcggg.aauug.ggcc.uua..................................................ggcccuaauUUuuagu.uUu..AAggccc....uuuuau.............................................................................................................................................................................................................................................................................................................................................................................................gg.gccgA.cccggg....cggag.GACAuugcCaggUGGGGAGUUUGgCuGGGGCgGcACAuCuGuuAAAuaAUAACgCaGgUGUCCUAAGGcgaGC.UCAgcGaG.gACAGAAA.cCuCgcGUaGAgcA..AAAGGgcAAAAGCucgCUUGAUuuccauucUCAGUAugaauggaa...AccgcGAAAgcgUGGCCUAUCGAUCCUuuagu........ucuucaaAaUU.U....................................................................................................................................................................................................................................................................................................................................................................................................................................................................gaagcuagAGGUGUCAGAA.AAGUUACCAcAGGGAUAACUGGcuUGUGGCgGCCAAGCGUUCAUAGCGACGUcGCUUUUUgaUCCUUCGAUGUCGGCUCUUCCUAUCaUug.uGAaGCAGAAuUCacaAAGuGUuGGaUUGUUC...........................................................................................................................................................................................................................................................................................................................................................................................AcCCaCuAAU.AGGGAACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUaCUgaugga................................augucguugcaAcaGcAauccagccuAGUACGAGA..GGAAC..ggcugguucggAuAaUUggUuuucGcggcuGgcuGAaa..agcCagUGccgCgAAG..cuA.cCaUccgu....uggAU...uAuggCUGAAcGCCUCU.AAGccaGAAuccaugCugga..Aa.........gcaacgac..........uuuuucccc.ccccuuuuuagaugaauaagaauAuaauuuuuuu.......aauauaaauuaauauauuuuuauauaa..ucuuuuuauugaauug.aa......................................................................................................................................................................................................................................................................................................auuuuuuuuuuuauauuaauaauuauuauuuuaaaauagggggggg..uugaA....ucc.cccGuAGACGA..Cgg.g....gaUa...u....ccgaccgGGUgcUGuAAgcggu.acaGcagccU......uuuU.................................gcugCgguccgc...uGAGgcUuAg.CCcu..ggucgga.uagaUucgu
//
# STOCKHOLM 1.0

#=GF AC   RF02544
#=GF ID   mt-tmRNA
#=GF DE   Mitochondrion-encoded tmRNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Hafez M
#=GF SS   Hafez M
#=GF GA   65.00
#=GF TC   72.70
#=GF NC   57.10
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF CL   CL00001
#=GF DR   SO; 0000584; tmRNA;
#=GF DR   GO; 0006401; RNA catabolic process;
#=GF RN   [1]
#=GF RM   23823571
#=GF RT   A second eukaryotic group with mitochondrion-encoded tmRNA: in silico
#=GF RT   identification and experimental confirmation.
#=GF RA   Hafez M, Burger G, Steinberg SV, Lang BF
#=GF RL   RNA Biol. 2013;10:1117-1124.
#=GF WK   Transfer-messenger_RNA
#=GF SQ   11



FR834720.1/91-162          UUUACGGACCCAAAGGCAGUAUUUGGUAUUUCCAUAUUUAUU-----------------------AAUAGGGAAUAAUAAUA---GAAUU-GACGUAAA
ABWE01000061.1/86410-86482 AAAAUGGACCCAUAGGCAGUUUUUGGUAUUUCCUUUUUA----------------------AUAUUAAUGGGAAUAAUAAUA---GUGUU-GACAUUUU
AF007261.1/62923-63007     ACUAUGGAACCGAGGGCGGAUCUCGGCAUCUCCAUAAAAAUGUUU-----------GAUAACAUUUUUUGGGGAUGUUUUUA---GUAUUCGACAUAGU
DQ162911.1/34-107          UAAAUGGACCCAAAGGCGGUAUUUGGUAUUUCCAUUUAAAA---------------------AUUAAAAGGGAAUAAUAAUA---GAAUU-GACAUUUA
DQ832717.1/4170-4246       UAAAUGGACCCAAAGGCAGUAUUUGGUAUUUCCAAAUAAAUU------------------AAAUUAUAAGGGAAUAAAAUUA---GAAUU-GACAUUUA
U17009.2/4176-4248         UAAAUGGACCCAAAGGCGGUAUUUGGUAUUUCCAUUAAAU----------------------UUAAUAAGGGAAUAAUAAAA---GAAUU-GACAUUUA
DQ162897.1/47-122          UAAAUGGACCCAGAGGCAGUUUUUGGUAUUUCCAUAUAAAUU------------------A-AAUGACUGGGGAUAAUAAUA---GAAUU-GACAUUUA
DQ162901.1/38-112          AAAAUGGACCCAAAGGCAGUAUUUGGUAUUUCCAUAUUGUA--------------------AAUUAAUAGGGAAUAAUAAUA---GAAUU-GACAUUUA
EU427478.1/141-218         UAAAUGAACCCAAAGGCAGUAUUUGGUAUUUCCAUUUAUUUA-----------------UAUUAAAAUAGGGGAUAAUAUUA---GAAUU-GACAUUUA
GU138663.1/42360-42281     AAAAUGGACCCAAAGGCGGUAUUUGGUAUUUCCAUAUAAACU------------------AAUUAAUACGGGAAUAAUUAUAUAAGAAUU-GACAUUUU
DQ162904.1/32-126          UAAAUGGACUCAAAGGCAGUAUUUGAUAUUUCCAUUUAUAUUAUUUAUUAAUUAAAAAUUAAUAAAUAAGGGAAUAAAAAUA---GAAUU-GACAUUUA
#=GC SS_cons               ((((((,,,<<<<<<_____>>>>>><<<<<<<_________.................._________>>>>>>>,,,,,,...,,,,,.,,))))))
#=GC RF                    uaaAUGGACCCaAagGCaGUauUuGGuAUuUCCAUaUAaAUu..................AauuuauaaGGGaAUaAUAaUA...GAAUU.GACAUuua
//
# STOCKHOLM 1.0

#=GF AC   RF02545
#=GF ID   SSU_trypano_mito
#=GF DE   Trypanosomatid mitochondrial small subunit ribosomal RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   72.60
#=GF NC   51.60
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF CL   CL00111
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   19497863
#=GF RT   Structure of a mitochondrial ribosome with minimal RNA.
#=GF RA   Sharma MR, Booth TM, Simpson L, Maslov DA, Agrawal RK
#=GF RL   Proc Natl Acad Sci U S A. 2009;106:9637-9642.
#=GF WK   Ribosomal_RNA
#=GF SQ   4


FJ203996.1/1194-1820 AUUAAACUUAAGUCUAUUGUUAUUAUUCAUAUUAAUUUUUUUAAAAGUUUUUAAGUUUUAUGCUAGUUUAUUU-UAAAAUAAUUUUAUUUGUCAUAU----UUUAGGAAUAGAUAAUAAUAAUUUAUAAUUUUGAUUAGAUGUAUUUGUUAAUGCUAUUUAAUGGGUGUGGAAAUAUGUAUAAAAUUUAAUAAAAUAUUAUUACAAUAAAUUACAU-UUACAUAUUAGUCAGAAAUGGAUGCCAGCCGUUGCGGUAAUUUCUAUGCUUUUAAAUAUUAUACAUUUAUCAUAAAAUAUUGUUAUUUUUAUACUUUAACAAAAAAAAUAAAAGCAACAUAUCUUUUUUGUUUUUAAACACCUUUUGGUAUAUGCAAAUACGAAAUUAUAGUAAUUAUAUAUUAUAUUAUAUUAUAUUUAUUCAUAUAA-UUAACGCAUAAAAAGUAAUUAAAUUUGAUACCAUGCUAAGGCAAAAAUAUUGAAAUUGUAAAUGUUAUAAUCAAAAGUUACUAUUUAUAUAAAAUUCUAAAUUUUAGAUAAAAUAAUAAAUUCAAAAGGUAUUGUUGCCCACCAAUUUUUAUAAUAAAAAUAACGUGCAGUAAUCAAUAUAUUUAUAAAAAUAUAUUUUAUAAAAAU
M94286.1/2545-3158   ----AUUAUG-GUCAAUUGUUAGUAUUCAUAUUAAUUUUUUUAAAUGUUUUAUCAUUUUAUAAAGGUUUAUUU-UUGAAAGAUUUUUUGUAUAAAAU----UUUAGGAAUAGUUAAUAAUAAUUUAUAAUUUUGAUUAGAUUGUUUUGUUAAUGCUAUUAGAUGGGUGUGGAAAAAUAAAAAAAAUA-AUUAAUAUAUAUCAAUAAUAAAUUAAAU-UAAUCUAUUAGUCAGAAAUGGAUGCCAGCCGUUGCGGUAAUUUCUAUGCUUUUAAAUAUUAUACAAUUAUCAUAUUAAAUUGUUAA-GUGCUGAUUUAACCAAUAAAA--AUAUAAAUAAUUUUUAUUUGUUUUUAAACACCAUUAGGUAUAUGCAAAUAUAAAAUUAUAGUAAUUAUAAAUUAUAUUAUAUUAUAUUUAUUCAUAUAA-UUAAUAGGAUAAUAUUUGUAGUUUUUGAUACCAUGAUAAGGAUUAUAAAUUGAAAGUGGUAAUAUCAUAAUCAAAAUUUAUUAUUUAUAUUAAAUAUGUAUGUGUAGAUAAAAUAAGAAAUUAAAAAGGUAUUGUUGCCCACCAAUUUUUAUAAUAAAAAUAACGUGCAGUAAUUAAUAUAUUUAUAAAAAUAUAUUUUAGCU----
EU140338.1/347-973   AAUAAAAUAA-GUCAAUUGUUAUUAUUCAUAUUAAUUUUUUUAAAAGUUUUUUAAUUUUAUAUUAGUUUAUUUGUUUAAAAAGUAUCUAAUUAAUUCAUUAUUUAGGAAUAGUUAAUAAUAAUUUAUAAUUCUGAUUAGAUUUGUUUGUUAAUGCUAUUAAAGGGGUGUGGAAAAA-GUGUUAAAUU-UUUGAUAUAUUUAAAUAAUAAAUAAAACAUAACUUAUUAGUCCGAAAUGGAUGCCCGCCGUUGCGGGAAUUUCCAUGCUUUUAAAUAUUAUACAUUUAUUUUAUAAAUUUGUUACUAUAUAUUUUUAGUCAAUAAAA--CUAAUAAUUAUUUUUAUUUGUUUUUAAACACCGUUUGGUAUAUGCAAAUAAAAAAUGACAUUAAUUAUUAAUUAUAUUAUAUUAUAUUUAUUCAUUUAAGUCAACAAUAUC-UAUUUACUGUUUUUGACAACAUGAUAAGGAUUAUAAAU-GGUAUUGCAAAUUUUAUAAUCAAAACUAAUUUAUUAUAUUAAAUUAGCAUGUUUAGAUAAAACAAUAAAUUUAGAAGGUAUUGUUGCCCACCAUUCUUUGUAAUAAAGACAACGUGCAGUAAUUAAUGUAUUUAUAAAAAUAUAUUUUUUCAUGUU
M10126.1/1631-2257   AUUAUACGUA-GUCAAUUGUUAUUAUUCAUAUUAAUUUUUUUAAAAGUUUUUUAAUUUUAUAUUAGUUUAUUUGUUUACAAAUUUAAAUUAUAUUUCAUUAUUUAGGAAUAGUUAAUAAUAAUUUAUAAUUCUGAUUAGAUUUAUUUGUUAAUGCUAUUAAAGGGGUGUGGAAAAA-GUGUUAAAUU-AUUUAUAUAUUUAAAUAAUAAAUAAAAUAUAACUUAUUAGUCAGAAAUGGAUGCCAGCCGUUGCGGUAAUUUCUAUGCUUUUAAAUAUUAUACAUUUAUUUUAUUAAUUUGUUACUAUUUAAUUUUAGUCAAUAAAA--AAUAUUAAUAUUUUUAUUUGUUUUUAAACACCGUCCGGUAUAUGCAAAUAAAAAAUGACAUUAAUUAUUAAUUAUAUUAUAUUAUAUUUAUUCACAUAAGUCAACAAUAUC-UAUUUACUGUUUUUGACAACAUGAUAAGGAUUAUAAAU-GGAAUUAUAAAUUUUAUAAUCAAAACUAAUUUAUUAUAUUAAAUUAGCAUGUUUAGAUAAAACAAUAAAUUUAGAAGGUAUUGUUGCCCACCAUUCUUUGUAAUAAAGACAACGUGCAGUAAUUAAUAUAUUUAUAAAAAUAUAUUUUCUCAUGUU
#=GC SS_cons         ::::::::::.::::[[[[,,,,,,,,,,,,,,,,,<<<<<<<<<<<<---<<<<<_____>>>>>--->>>>.>>>>>>>>,,,,,,,,,,,,,,,....,,,,,((((((-((((((((((((((((((---((((--(((((((((--((((((-------(((((--(((((((,,,,,,,,,.,<<<<<<---------<<<<<<<-----.----<<<--<<<-<<<<<<---<<<<-<<____>>>>>>>>>>>>-->>>-->>>--------->>>>>>>--------->>>>>>,,,,,,,,,,,,,,,<<<<<<<..<<_______>>>>>>>>>)))))))--)))))---))))))--)))))))))---))))---)))))))))))))----)))))---)))))),,,,,,.,,,,,,,,,,,,,((((((((((((---(((((((,,,,,<<<<<<<<<______________>>>>>>>>>,,,,<<<<<<<<______>>>>>>>>))))-)))---)))))))))))),,,,,,<<<<____>>>><<<--<<<<<<<___>>>>>>>--->>>]]]]----<<<<<<<<<____>>>>>>>>>::::::::::
#=GC RF              AuUAaauuuA.GUCaauuGUUAuUAUUCAUAUUAAUuuuuucaaaaguUUUcuaguUUUAUacuagUUUauuu.uugaaaaauUuuauuuaUaauau....UUUAGGaauaguuaauaauaauuuauaauuuUGaucaGAuguauuuGuUAaugCuaUUaAAuGGGuGuGGaaaaacguauaAAAUu.aguaacaUAUuuaaAuaauaaauuAaAu.UaAcuuaUUaGuCaGaaauGGAugCCaGCCGUUGCGGcaauuuCuAUgCuUUuaaAUAUUAUACauuuauuaUAuaAaaUuguuacUaUuuuauUUUAaucaauaaaa..auaauaAuaauuuuuauuuguuuuuAAaCaCCaUuugGuauAUgCaaauacaAAAugauAuUaauuauaaauuauAUUAuauuaUAUuuauuCAuaUAA.UuAAcaauauaAuauuuauuguuuuUGAuaccaugaUAAGGauuauaaaUUGaaAuUguaAAUuuuauaauCAAAAcuaauuuaUUAUAUuaaauuagcaugUguaGAUaaaacaauaaauUuAaAAGGuaUUGUugCCCaCCAgucuuuaUAAuaaagacAACGuGCaguAAUuaauauauuuAUAAaaauauauuUUaucauguU
//
# STOCKHOLM 1.0

#=GF AC   RF02546
#=GF ID   LSU_trypano_mito
#=GF DE   Trypanosomatid mitochondrial large subunit ribosomal RNA
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Predicted; ClustalW
#=GF SS   Predicted; RNAalifold
#=GF GA   60.00
#=GF TC   62.90
#=GF NC   46.20
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF CL   CL00112
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   19497863
#=GF RT   Structure of a mitochondrial ribosome with minimal RNA.
#=GF RA   Sharma MR, Booth TM, Simpson L, Maslov DA, Agrawal RK
#=GF RL   Proc Natl Acad Sci U S A. 2009;106:9637-9642.
#=GF WK   Ribosomal_RNA
#=GF SQ   6


FJ203996.1/610-1178 AUUUUAAGUGCGUUUAUUAAAUGCGUUUGUCUAAGAAAUAUAUUUAAGAUUAUUCUUGUAUAUAUAUUUAUAAAUUAAUAAUUCUAAAAAUAAAAUAAAGCUUCCUCGAAAAUAAAAUUUUAGUAGCAUAGUAAUUUGUUAACUAAUUAUUAAAGUGUUCCACAGAAAUUUUUUAAAUUAAAACAAAAAAAAUAAUUUAUGAAUUAAAAUAAAAAUUUUAAUAAAAAUUAAAUAAUUAAAAUAGGGCAAGUCCUACUCUCCUUUACAAAGAGAACGUUUCAAUAAUACGUAAUUGUAUGUUUGAUUGGGGCAAUACUAUAUUUAUUUAUAUAGGCAAAGA-ACUAUAAUUAUUGAAAUAAUAAAAGGUUCGAGCAGGUUAACAAGCAUUAAUACUAAAUGUGUUUCAUCGUCUACUUAUUGCU--AAACAAAUUGAUUGUUCAUCAAAUUUGCAAUUCGUUAGUUGGGUUAAAAUCGUUGUAAAGCAGAUUUGUUUAUAUAUUUAAUUAAUAUA-AGGAGUGCAUAGUAAUAUUAGUACGCAAGGAUCAAUUAUUUGUUAUUUUAUAUAUACU
X02547.1/205-303    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UGAACUGUAAUUAUUAGUUUAAUAUUUUUAGUUUGAUGUUGAAAUAUUUAAUUAAAGAUGUUACAGUUGUUCUAUAUGUACCAAAU--AAAUAUAGUAAGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
EU140338.1/1-326    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAGGGCAAGUCCUACUCUCCUUUACAAAGAGAACGUUU-----AUAUGUAAUUGUAUGUUUGAUUGGGGCAAUACUAUAUCUAUUUAUAUAGAAAAAGA-ACUAUAUUUAUUGAAAUAAUAAAAGGUUCGAGCAGGUUAACAAGCAUUAAUACUAAAUGUGUUUCAUCGUCUACUUAUUGCUAAAUUAUAAUUGAUUGUUCAUCAAAAAAGCAAUUCGUUAGUUGGGUUAAAAUCGUUGUAAAGCAGAUUUGUUUAUAUAUUUAAUUUUUGUAUAUAGUUAAAAAUUAAUAUUAGUACGCAAGGAUUCAUUAUUUGUAAUUUAAAUAUAUUA
X02354.1/1046-1610  GUUUUAAAAGCGUUUAUUAAAUGCGUCGGUCUAAGAUUUAUAUUUAAGAUUAUUCUUGUAUAUAGAUUUUUAUUUUAAUAAUUCUACAUAAUUAA-AAAAGUACCUCAAUAUAUGUUUAUUAGUAGCAUAGUAAUUUAUUAACUAAUUAUUAAAGUGUUCCAUAGAAAAUUUUAAAAUUAUAACAAUCUAAAUAAAUAAUAAAUUAAAAUAAAGAUUUUAAAAAAAAUUAAAAAAUUAAAAUAGGGCAAGUCCUACUCUCCUUUACAAAGAGAACAUUUU----AUAUGUAAUUGUAUGUUUGAUUGGGGCAAUACUAUAUCUAGUUAUAUAGAAAAAGA-ACUAUAAUCAUUGAAAUAAUAAAAGGUUCGAGCAGGUUAACAAGCAUUAAUACUAAAUGUGUUUCAUCGUCUACUUAUUGCU--AAUAAAAUUGAUUGUUCAUCAAAAAUGCAAUUCGUUAGUUGGGUUAAAAUCGUUGUAAAGCAGAUUUGUUUAUAUAUUUAAUUUAUAUAUAUAUUUAAAAAUUAAUAUUAGUACGCAAGGAUCUAUUAUUUGUAAUUGAAAUUAAAAA
FJ416603.1/267-824  GUUUCAAAAGCGUUUAUUAAAUGCGUCGGUCUAAGUAUUAUAUUUAAGAUUAUUCUUGUAUAUAGAUUUUUAUAUUAAUAAUUCUACAUAAUUAA-AAAGAAACCUCAAAAUAAAUUUAUUAGUAGCAUAGUAAUUUAUUAACUAAUUAUUAAAGCGUUCCAUAGAAAAUUUUAAAAUUAUAACAAUCUAAAUAAAUAAUAAAUUAAAAUAAAAAUUUUAAAAAAAAUUAAAAAAUUAAAAUAGGGCAAGUCCUACUCUCCUUUACAAAGAGAACGUUU-----AUAUGUAAUUGUAUGUUUGAUUGGGGCAAUACUAUAUCUAGUUAUAUAGAAAAAGA-ACUAUAUUUAUUGAAAUAAUAAAAGGUUCGAGCAGGUUAACAAGCAUUAAUACUAAAUGUGUUUCAUCGUCUACUUAUUGCU--AUUAUAAUUGAUUGUUCAUCAAAAAUGCAAUUCGUUAGUUGGGUUAAAAUCGUUGUAAAGCAGAUUUGUUUAUAUAUUUAAUUUUUAUAUAUAAUUAAAAAUUAAUAUUAGUACGCAAGGAUUCAUUAUUUGUAAUUUAAAG------
X02547.1/619-1178   -UUUUAAGUGCGUUUAUUAAAUGCGUUUGUCUAAGAUAAUUAUUUAAGAUUAUUCUUGUAAAUAUAUUUAAAUAUUAAUAAUUCU-UAAAAUAAA-AAAAUAUCCUCAAUUGCAAUAUUAUUGUAGCAUAGUAAUUUGUUAACUAAAUAUUAAAGUGUUCCAUAGAAAAUUUUUAAAUUACAACAAAUAAAAUAAAGUAUGAAUUAAUAUCAAAAUUUUAAUAAAAAUUAAAAAAUUAAAAUAGGGCAAGUCCUACUCUCCUUUACAAAGAGAACAUUAUG---AUAUGUAAUUGUAUGUUUGAUUGGGGCAAUACUAUAUUUAUUUAUAUAGCAUAAGA-ACUAUAUUCUUUGAAAUUAUAAAAGGUUCGAGCAGGUUAACAAGCAUUAAAAAUAAAUGUGUUUCAUCGUCUACUUAUUACC-----AUGAUUGAUUGUUCAUCAAAAUAGUAAUUCGUUAGUUGGGUUAAAAUCGUUGUAAAGCAGAUUUGUUUAUAUAUUUAAUUUUUAUA-AUUAAUAAUAAUUAAUAUAAGUACGCAAGGAUUGAUUAUUGAAAAAAGAAAGAAGAAU
#=GC SS_cons        .::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::::.:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::<<<<______>>>>-(((-((((((((-((,,<<<<__.....__>>>>,<<<<<_____________>>>>>,<<<<<<______>>>>>>,,,,,<<.<<<_____________________>>>>>,,,,,,,,,,,,<<<<<<___________>>>>>>,,<<<-<<<<--<<<<<-..--------<<<____>>>-------->>>>>-->->>>->>>,,,,,,,))-))))))))-))):::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#=GC RF             .UUUuAAauGCGUUUAUUAAAUGCGUuuGUCUAAGaaauaUAUUUAAGAUUAUUCUUGUAuAUAuAUUUauAuaUUAAUAAUUCU.uAaAauaAA.AAAauuuCCUCaAaauaaAuaUuuUaGUAGCAUAGUAAUUUaUUAACUAAuUAUUAAAGuGUUCCAuAGAAAaUUUUuAAAUUAuAACAAauaAAAUAAauuAUaAAUUAAaAUaAAAAUUUUAAuAAAAAUUAAAaAAUUAAAAUAGGGCAAGUCCUACUCUCCUUUACAAAGAGAACgUUu.....AUAcGUAAuUGuAUGUUUGAUUggggCAaUAcuAuaUuuAuUUAuaUagaaAAAGA.acuAUAuUUaUUgAAAUaAUAAAAgguUCGAGcAgGuUAAcAAgCAuUAAuAcUAAAUgUGuUUCAuCgUCUACUUAUUGCU..AauAuAAUUGAUUGUUCAUCAAAAauGCAAUUCGUUAGUuGgGUUAAAAUCGUUGUAAAGCAGAUUUGUUUAUAUAUUUAAUUuuUAUA.AuaauUAAAAAuUAAUAUuAGUACGCAAGGAUuuAUUAUUuGuAAuuuAAAuuaaaau
//
# STOCKHOLM 1.0

#=GF AC   RF02547
#=GF ID   mtPerm-5S
#=GF DE   Permuted mitochondrial genome encoded 5S rRNA
#=GF AU   Valach M; 0000-0001-8689-0080
#=GF AU   Eberhardt R; 0000-0001-6152-1369
#=GF SE   Valach M
#=GF SS   Valach M
#=GF GA   39.00
#=GF TC   39.70
#=GF NC   36.50
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF CL   CL00113
#=GF DR   SO; 0000652; rRNA_5S;
#=GF DR   GO; 0003735; structural constituent of ribosome;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   25429974
#=GF RT   Widespread occurrence of organelle genome-encoded 5S rRNAs including
#=GF RT   permuted molecules.
#=GF RA   Valach M, Burger G, Gray MW, Lang BF
#=GF RL   Nucleic Acids Res. 2014;42:13764-13777.
#=GF WK   5S_ribosomal_RNA
#=GF SQ   6


AY494079.1/34765-34870 UGGAGGUUCGCCUUCAUGUCUAGGCCCCUACCCGAACUCUUACCGAACUCGAGCGUCCUUGCCUAGGCUGCCACACAUACUAGUUAAUCCUGGGAACCAUGGCUAU
AY500367.1/37407-37512 GUGAGGUUCGCCUCCAUGUUUAGAUCUAUACCCGAACUCUUACUGAACUCGAGUGUCCUUAUCUAGACAGCCAUACAUACUAGUUUUUGCUGGGAACCAUGGCUUA
FP885846.1/34652-34757 AAGAGGUAAGCCUCUAUAUCUAGAUCUAUACCCGAACUCUUAUCGAACUCGAGCGUCCUUAUCUAGAAAGCCACACAUACUAGUUUUUACUGGGAACCAUGGCUCU
AJ344328.1/36279-36382 AAGAGGCUCGCCUCUAUAUCUAGGUCUAUACCCGAACUCUUACCGAACUCGAGCGUCCUUAUCUAGAUAGCCACACAUACUACUU--UUGUGGGAACCAUGGCUUA
JF937591.1/35917-36020 UAGGGGCUAGCCCCUAUAUCUAAAUCUAUACCCGAACUCUUACCGAACUCGAGUGUCCUUAUUUAGAUAGCCACACAUACUACUU--UUGUGGGAACCAUGGCUCA
AJ277126.1/56295-56400 UAGAGGUCUGCCUCUGUAUCUAGGUCUAUACCCGAACUCUUACCGAACUCGAGCGUCCUUAUCUAGAAAGCCACACAUACUAAUUUUUGUUGGGAAUCAUGGCUCG
#=GC SS_cons           :<<<<<<__>>>>>>,,<<<<<<<<----<<-<<<_____________>>>--->>---->>>>>>>><<<<<------<<<<______>>>>------>>>>>::
#=GC RF                ugGaGGcuagCCuCcAUgucuaGguCUaUaCCCGaACUCUUAccGAACuCGAGcGuCCUUacCuagacaGCCacACAUACuagUUuuUucugGGAAcCAuGGCuua
//
# STOCKHOLM 1.0

#=GF AC   RF02548
#=GF ID   Oskar_OES
#=GF DE   Oocyte entry signal (OES) from oskar mRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Jambor et al, PMID:24572808 
#=GF SS   Published; PMID:24572808 
#=GF GA   46.00
#=GF TC   46.00
#=GF NC   43.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0045451; pole plasm oskar mRNA localization;
#=GF RN   [1]
#=GF RM   24572808
#=GF RT   A stem-loop structure directs oskar mRNA to microtubule minus ends.
#=GF RA   Jambor H, Mueller S, Bullock SL, Ephrussi A
#=GF RL   RNA. 2014;20:429-439.
#=GF CC   In Drosophila, oskar mRNA harbours a stem-loop structure in the 3â€™UTR,
#=GF CC   called the oocyte entry signal (OES), that promotes dynein-based mRNA
#=GF CC   accumulation in the oocyte [1]. 
#=GF WK   Oskar
#=GF SQ   14


AFFI01005902.1/57757-57691   UGGAAAAUUCGCUUGCACAAAAUCAACGCCGCGGCUGAUUU-AUUAUUAAUGUGCUCAAGCAAAUUCA
AFFF01007797.1/34651-34585   UGGAAAAUUCGCUUGCACAAAAUCAACGCCGCGGCUGAUUU-AUUAUUAAUGUGCUCAAGCAAAUUCA
AAPQ01006469.1/892563-892497 UGGAAAAUUCGCUUGCACAAAAUCAACGCCGCGGCUGAUUU-ACUAUUAAUGUGCUCAAGCAAAUUCA
L22556.1/3974-4037           UAUAGC-CUGGCUUGCACAAAAUCAAUACCGCGGUUGAUU---UUAUAAAUGUGUUUAGGUCAAUUUU
AASW01050332.1/2559-2625     UGGAAAAUUCGCUUGCACAAAAUCAACGCCGCGGCUGAUUU-AUUAUUAAUGUGCUCAAGCAAAUUCA
AAPU01011093.1/12283-12343   U--UGA--AGGUUUGCAGCGAAUCAAUGCCGCGGUUGAUU---UCCCAUUUAUGUCAAAGCCCAUUCA
AAQB01008620.1/599925-599863 UCACAUUCAAGCUUGGGGAAAAUCAACGCCGCGGCUGAUUU-----UCUUUUUUAAUAAGCAGUUUGA
AAKO01000338.1/79222-79156   UGGAAAAUUCGCUUGCACAAAAUCAACGCCGCGGCUGAUUU-AUUAUUAAUGUGCUCAAGCAAAUUCA
M65178.1/3085-3151           UGGAAAAUUCGCUUGCACAAAAUCAACGCCGCGGCUGAUUU-AUUAUUGAUGUGCUCAAGCAAAUUCA
AAPT01020220.1/31199-31265   UAAUGC-UUGGCUUGCACAGAAUCAAUACCGCGGUUGAUUUCCUUUAAAUUGUGCUUAAGCUUUAUUU
AAEU02000007.1/218364-218430 UGGAAAAUUCGCUUGCACAGAAUCAACGCCGCGGCUGAUUU-AUUAUUAAUGUGCUCAAGCAAAUUCA
AAIZ01001855.1/30363-30297   UUAAGCCUUCGCUUGCACAGAAUCAACGCCGCGGCUGAUUU-AUUAUUAAUGUGUUUAAGCAAAUUCA
AADE01001974.1/3619-3553     UUAAGCCUUCGCUUGCACAGAAUCAACGCCGCGGCUGAUUU-AUUAUUAAUGUGUUUAAGCAAAUUCA
AAPP01019519.1/358338-358403 UGAAGCACUCGCUUGCACAAAAUCAACGCCGCGGCUGAUUU-AUUAUUGAUGUGC-CAAGCAAUUUCA
#=GC SS_cons                 <<<---<<<-<<<<<<<<<<<<<<<__________>>>>>>.-------->>>>>-->>>>->>>>>>
#=GC RF                      UgaaaaauucGCUUgCAcAaAAUCAACGCCGCGGCUGAUUu.AUUAUuaaUgUGcUuAAGCaaauucA
//
# STOCKHOLM 1.0

#=GF AC   RF02549
#=GF ID   YFV_3UTR
#=GF DE   Pseudoknot PSK3
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:20739539
#=GF GA   50.00
#=GF TC   53.20
#=GF NC   36.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF RN   [1]
#=GF RM   20739539
#=GF RT   An RNA pseudoknot is required for production of yellow fever virus
#=GF RT   subgenomic RNA by the host nuclease XRN1.
#=GF RA   Silva PA, Pereira CF, Dalebout TJ, Spaan WJ, Bredenbeek PJ
#=GF RL   J Virol. 2010;84:11395-11406.
#=GF CC   Minimal yellow fever virus (YFV) 3â€™UTR region required for stalling of
#=GF CC   the host exonuclease XRN1. Its PKS3 pseudoknot structure serves as a
#=GF CC   molecular signal to stall the exonuclease and is the sole viral
#=GF CC   requirement for subgenomic flavivirus RNA (sfRNA) production. 
#=GF WK   Yellow_fever
#=GF SQ   3



X15062.1/10531-10610   GAAGUUGUCAGCCCAGAACCCCACACGAGUUUUGCCACUGCUAAGCUGUGAGGCAGUGCAGGCUGGGACAGCCGACCUCC
AY960143.1/432-511     GAAGUUGUCAGCCCAGAACUCCACACGAGUUUUGCCACUGCUAAGCUGUGAGGCAGUGCAGGCUGGGACAGCCGACCUCC
AF094612.1/10429-10508 AAAGUUGUCAGCCCAGAACUCCACACGAGUUUUGCCACUGCUAAGCUGUGAGGCAGUGCAGGCUGGGACAGCCGACCUCC
#=GC SS_cons           :::::::((((((<<<<<<_________>>>>>>,<<<<<<<__AAAAA__>>>>>>>,,))))))::::::::aaaaa:
#=GC RF                gAAGUUGuCaGCCCagaaCuCCACACGAGuuuuGCCaCuGCuAAGCUGUGAgGCaGuGCAGGCuGgGACAGCCGACCUCC
//
# STOCKHOLM 1.0

#=GF AC   RF02550
#=GF ID   RnaG
#=GF DE   RnaG sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:20129941
#=GF GA   153.00
#=GF TC   153.20
#=GF NC   38.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   20129941
#=GF RT   A novel antisense RNA regulates at transcriptional level the virulence
#=GF RT   gene icsA  of Shigella flexneri.
#=GF RA   Giangrossi M, Prosseda G, Tran CN, Brandi A, Colonna B, Falconi M
#=GF RL   Nucleic Acids Res. 2010;38:3362-3375.
#=GF CC   Small regulatory RNA encoded by the virulence plasmid of S. flexneri, a
#=GF CC   Gram-negative pathogenic bacterium that causes human bacillary dysentery.
#=GF CC   It is 450 nt long and it contains a region with specific secondary
#=GF CC   structure that interacts with icsA mRNA and forms a transcription
#=GF CC   terminator. Acting as antisense, RnaG is transcribed from the
#=GF CC   complementary strand of its target, icsA mRNA [1]. 
#=GF WK   RnaG
#=GF SQ   4



M22802.1/555-436         GUGGUUGAUAAACCCCUGAAAAGAUUCCGUUUUAUCCGGAAUAAAGGGACGAUAUAUGCAAAAACAUAUUAAACAAAGCCUCAACCAAAACAUGAGAGCUGUGUUAUAUAUCAAUGCAAC
CP001384.1/148287-148168 GUGGUUGAUAAACCCCUGAAAAGAUUCCGUUUUAUCCGGAAUAAAGGGACGAUAUAUGCAAAAACAUAUUAAACAAAGCCUCAACCAAAACAUGAGAGCUGUGUUAUAUAUCAAUGCAAC
CP000039.1/126047-125928 GUGGUUGAUAAACCCCUAAAAAGAUUCCGUUUUAUCCGGAAUAAAGGGACGAUAUAUGCAAAAAUAUAUUAAACAAAGCCUCAACCAAAACAUGAGAGCUGUGUUAUAUAUCAAUGCAAC
CP000035.1/170338-170219 GUGGUUGAUAAACCCCUAAAAAGAUUCCGUUUUAUCCGGAAUAAAGGGACGAUAUAUGCAAAAACAUAUUAAACAAAGCCUCAACCAAAACAUGAGAGCUGUGUUAUAUAUCAAUGCAAC
#=GC SS_cons             :::((((((,,,,<<<<------<<<<<<_______>>>>>>-->>>>,,,,,<<<<<______>>>>>,,,,,,,<<<<<<<_________>>>>->>>,,,,,,,,,)))))):::::
#=GC RF                  GUGguuGauAAACCCCuaAAAAGauuCCGUUUUAUCCGGaauAAaGGGACGAUauauGCAAAAACauauUAAACAAaGCCuCaACCAAAACAuGaGAGCuGUGUUAUAUauCaacGCAAC
//
# STOCKHOLM 1.0

#=GF AC   RF02551
#=GF ID   DapZ
#=GF DE   ABC transporter regulator
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:22922465
#=GF GA   56.00
#=GF TC   56.30
#=GF NC   55.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF RN   [1]
#=GF RM   22922465
#=GF RT   An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir
#=GF RT   of regulatory small RNAs.
#=GF RA   Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J
#=GF RL   EMBO J. 2012;31:4005-4019.
#=GF CC   DapZ sRNA, encoded in the 3â€²-UTR of the conserved dapB gene, as a
#=GF CC   translational repressor with a GcvB-like seed domain. This is the first
#=GF CC   example of a widely conserved bacterial gene whose 3â€²-UTR has dual
#=GF CC   function. [1]
#=GF WK   Bacterial_small_RNA
#=GF SQ   6



FN424405.1/74844-74921     AAAUACCUUCGUGAUGUGGUUGUGGUAAUCAAG-AU-UAAUUGAUUACAAAGGGCAAUA-UAUUAUUGCCCUUUUGUUUUU
FR877557.1/55147-55225     AGAUACCUUCGUGAUGUGGUUAUAGUAAUCAAG-AU-GAGUUGAUUACAAAGGGCAAUAAUGCUAUUGCCCUUAUAUUUUU
CP000964.1/4759511-4759434 AUUACCCAUCGUGAUGUGGUUAUUGCAAUCAAUAAG-UUAUUGA-UGCAAGGGGCAAUA-UAUUGUUGCCCUUUUUUAUUU
FN543502.1/41079-41156     UAUUACCUUCGUGAUGUGGUUAUUGUAAUCUCA-AU-CUAUUGAUUACAUAGGGCAAUA-UUUUAUUGCCCUUUUAUUUUA
CP002824.1/2339682-2339760 AUUACCCAUCGUGAUGUGGUUAUUGCAUUCAAU-AUGUAAUUGAUUGCAAAGGGCAAUA-CUUUAUUGCCCUUUUUUAUUU
FN543093.2/720844-720920   AUUACCCAUCGUGAUGUGGUUAUUACAAUCAUA-AG-UUUAUGAUUG-AAGGGGCAAUA-AUUUAUUGCCCUUUUUUAUUU
#=GC SS_cons               ::::::::::::::::::::::::<<<<<<<<_.__.___>>>>>>>>-<<<<<<<<<<.___>>>>>>>>>>::::::::
#=GC RF                    AuuuaCCuUCGUGAUGUGGUUAUuGcAaUCaaa.Au.uuauuGAuUgCAaaGGGCAAuA.uuUUaUUGCCCuuUUuUuUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02552
#=GF ID   RcsR1
#=GF DE   RcsR1 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Baumgardt et al, PMID:26588798
#=GF SS   Published; PMID:26588798
#=GF GA   80.00
#=GF TC   80.10
#=GF NC   39.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0032055; negative regulation of translation in response to stress;
#=GF RN   [1]
#=GF RM   26588798
#=GF RT   The stress-related, rhizobial small RNA RcsR1 destabilizes the autoinducer
#=GF RT   synthase encoding mRNA sinI in Sinorhizobium meliloti.
#=GF RA   Baumgardt K, Smidova K, Rahn H, Lochnit G, Robledo M,
#=GF RA   Evguenieva-Hackenberg E
#=GF RL   RNA Biol. 2015; [Epub ahead of print]
#=GF CC   RcsR1 (rhizobial cold and salinity stress riboregulator 1) trans-acting
#=GF CC   sRNA, formerly known as SmelC587, is a stress-related riboregulator,
#=GF CC   conserved in Sinorhizobium, Rhizobium and Agrobacterium. It contains
#=GF CC   highly conserved stem-loops involved in the interaction with several
#=GF CC   target mRNAs (PhoR, MotE, anti-ÏƒE1, GntR, FgA, TrpC). In S. meliloti
#=GF CC   RcsR1 less conserved central region is responsible for the
#=GF CC   species-specific interaction with the 5â€™UTR of autoinducer synthase
#=GF CC   encoding mRNA sinI. The interaction negatively influences sinI
#=GF CC   translation. [1].
#=GF WK   RcsR1_small_RNA
#=GF SQ   10


AE007869.2/2261999-2262094 ACAUUGCUAACUGGUGGUGGAGCAGCUUUUUGCGGCCUUGACCAGUCAUGUCUUCAGACAAAGUC---CAAGCCGCCCGAAUUU-UC-AGGCGGCUUUUUU
CP000628.1/2593393-2593298 ACAUUGCAGUUUGGUGGUGG-GCUCGCUAAGGCGGCCUCGACCAAUCGUGUUCAAAGACGACGA---GUGAGCCGCCCGAGAUU-UCGAGGCGGCUUUUUU
CP001191.1/2858546-2858448 ACAUUGCUGUUUGGUGGUGG-GCUCGCUAAGGCGGCCUCGACCAAUCGUGUCCAAAGACGACGACGAGUGAGCCGCCCGAAACU-UCGAGGCGGCUUUUUU
CP002248.1/2210750-2210845 ACAUUGCUAACUGGUGGUGGAGCAGCUUUACGCGGCCUUGACCAGUCAUGUCUUCAGACAAAGUC---CAAGCCGCCCGAAUUU-UC-AGGCGGCUUUUUU
CP002781.1/2434946-2434851 ACAUUUCGAUCUGGUGGUGG-GCUCGCUGAGGCGGCCUUGACCAGUCAUGCGUGAUUGAGAGAUG----GAGCCGCCCGGAGAUUUCGAGGCGGCUUUUUU
CP001622.1/3076424-3076329 ACAUUGCUGUUUGGUGGUGG-GUUCGCUAAGGCGGCCUCGACCAAUCGUGUCCAAAGACGACGA---GUGAGCCGCCCGAAACU-UCGAGGCGGCUUUUUU
CP001074.1/3242563-3242465 ACAUUGCUGUUUGGUGGUGG-GCUCGCUGAGGCGGCCUCGACCAAUCGUGUCCAAAGACGACGACGAGUGAGCCGCCCGAAACU-UCGAGGCGGCUUUUUU
AL591688.1/2575929-2575834 ACAUUUCGAUCUGGUGGUGG-GCUCGCUGAGGCGGCCUUGACCAGUCAUGCGUGAUUGAGAGAUG----GAGCCGCCCGGAGAUUUCGAGGCGGCUUUUUU
CP001830.1/833698-833793   ACAUUUCGAUCUGGUGGUGG-GCUCGCUGAGGCGGCCUUGACCAGUCAUGCGUGAUUGAGAGAUG----GAGCCGCCCGGAGAUUUCGAGGCGGCUUUUUU
CP000133.1/3217569-3217471 ACAUCGCUGUUUGGUGGUGG-GCUCGCUGAGGCGGCCUCGACCAAUCGUGUCCAAAGACGACGACGAGUGAGCCGCCCGAAACU-UCGAGGCGGCUUUUUU
#=GC SS_cons               ::::::::::<<<<<-<-<<.<<-<<<____>>>>>>>>->>>>>,,,<<<<____>>>>,,,,,...,<<<<<<<<<<<____.>>>->>>>>>>>::::
#=GC RF                    ACAUUgCuaucuGGuGgUgG.GCucgcUaAggcgGCCucGaCCagUCacgccuaaaggcgAaguc...ugaGCCGCCCGaAauU.uCGAGGCGGCucUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02553
#=GF ID   YrlA
#=GF DE   Y RNA-like
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:23540697
#=GF GA   49.00
#=GF TC   49.20
#=GF NC   48.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000405; Y_RNA;
#=GF RN   [1]
#=GF RM   23540697
#=GF RT   An RNA degradation machine sculpted by Ro autoantigen and noncoding RNA.
#=GF RA   Chen X, Taylor DW, Fowler CC, Galan JE, Wang HW, Wolin SL
#=GF RL   Cell. 2013;153:166-177.
#=GF RN   [2]
#=GF RM   25232022
#=GF RT   Bacterial noncoding Y RNAs are widespread and mimic tRNAs.
#=GF RA   Chen X, Sim S, Wurtmann EJ, Feke A, Wolin SL
#=GF RL   RNA. 2014;20:1715-1724.
#=GF CC   In Deinococcus radiodurans Rsr is tethered via Y RNA to the
#=GF CC   exoribonuclease PNPase and channels single-stranded RNA into the PNPase
#=GF CC   cavity. Rsr and Y RNA enhance degradation of structured RNAs by PNPase.
#=GF CC   This role could be conserved, as Rsr and ncRNAs called YrlA and YrlB (Y
#=GF CC   RNA like) also associate with PNPase in an evolutionary distant bacterium
#=GF CC   Salmonella Typhimurium.[1]
#=GF WK   Y_RNA
#=GF SQ   5



AEYZ01000396.1/7368-7480   AUGGCGAAUGCAUGGGGAACUACA-----UCUGUGUCGCGAGUUCGAUUCUCGCCAGGGCCUGGUCCUGUAGCUCAG-UUGGUAGAGCA-AGCUG----UUCCCCGGACACUUGUCGUCAUGAC
ACEA01000002.1/40396-40510 AAAACAAAUGCCUUGGAAACUAC-------AUUGGUCGCAGGUUCGAGUCCUGCCCCGCUCCAAGCGGGUAGCUCAGUCUGGUAGAGCG--GUUAAACGUUUCCCAAAAACUCGUUGUUUGCUG
FQ312003.1/3704232-3704124 UUGGCGAAUGCCUGUGGAUCUAC-------AUUUGUUGCGGGUUCGAGACCCGUCAGAGCCCGGCUCUGUAGCUCAA--UGGUAGAGCG--GUGU----AUUCACAUAAACUUGUCGCCACCCU
CP002727.1/4011288-4011407 CCGGCGAAUGCCGGUGGAACUACAGGACGUGAAGGUUGCGGGUUCGACUCCCGCCCCGGC---GACGGGUAGCUCAACUGGAUAGAGCAACGCGCA-UGUUCCACCAACGAUCGUCGCCGCACU
ADBF01000255.1/32505-32391 AAAACAAAUGCUUUGGAAACUAC-------AUUGGUCGUAGGUUCGAGUCCUGCCCCGCUUUCGGCGGGUAGCUCAGUCUGGUAGAGCG--GUUAAACGUUUCCCAAAAACUCGUUGUUUGCUG
#=GC SS_cons               :((((((-----(((((((-(((.......,,,,,,,,<<<<<_____>>>>>,<<<<<<___>>>>>>,,<<<<_________>>>>,..)))--.--)))))))--------))))))::::
#=GC RF                    acggCgaAUGCcuggGgaaCcaC.......auugGUuGcgGGcUCGAggCCcgcCccGcccuaggCggGUAGCUCAauuuGgUAGAGCa..GugaA.uGuucCccaaAaAcUcGucGccguauu
//
# STOCKHOLM 1.0

#=GF AC   RF02554
#=GF ID   ppoRNA
#=GF DE   mt-5S-like P. polycephalum
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:20304999
#=GF GA   99.00
#=GF TC   105.80
#=GF NC   42.20
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0001032; mitochondrial_DNA;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   20304999
#=GF RT   Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in
#=GF RT   amoebozoa.
#=GF RA   Bullerwell CE, Burger G, Gott JM, Kourennaia O, Schnare MN, Gray MW
#=GF RL   Eukaryot Cell. 2010;9:762-773.
#=GF CC   mtDNA-encoded RNA with 5S rRNA-like structures that is associated with the
#=GF CC   mitoribosome.
#=GF WK   5S_ribosomal_RNA
#=GF SQ   2



HQ916349.1/1-98        UUUAGCAAGCACCUUUGUGUAAACUCUGUAUAAAGAGUAAAAUAUACAAAAUUGACGUGAUUAACCGAAAUCGGAAAAGCACUAAUGUUUGUUAAAUC
AB027295.1/53178-53273 UUUAGCAAGCA-CUUUGUGUAAACUCUGUAUAAAGAGUAAAAUAUACAAAAUUGACGUGAUUAACG-AAAUCGGAAAAGCACUAAUGUUUGUUAAAUC
#=GC SS_cons           ((((((((((,,,<<<<<<<<-<<<<<______>>>>>---->>>>>>>><<<<--<<<<<<--<<<____>>>-->>>>>>>>>>))))))))))::
#=GC RF                uuuagCaagCAccuuuGuguaAaCuCuGUAUAAaGaGuAAAAuacaCaaaauugAcGuGcuuAACcgAAAUcgGAAaagCaCcaauGcuuGcuaaaUc
//
# STOCKHOLM 1.0

#=GF AC   RF02555
#=GF ID   hveRNA
#=GF DE   mt-5S-like H. vermiformis
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska, J
#=GF SS   Published; PMID:20304999
#=GF GA   90.00
#=GF TC   99.10
#=GF NC   40.60
#=GF TP   Gene; rRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0001032; mitochondrial_DNA;
#=GF DR   GO; 0005840; ribosome;
#=GF RN   [1]
#=GF RM   20304999
#=GF RT   Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in
#=GF RT   amoebozoa.
#=GF RA   Bullerwell CE, Burger G, Gott JM, Kourennaia O, Schnare MN, Gray MW
#=GF RL   Eukaryot Cell. 2010;9:762-773.
#=GF CC   mtDNA-encoded RNA with 5S rRNA-like structures that is associated with the
#=GF CC   mitoribosome.
#=GF WK   5S_ribosomal_RNA
#=GF SQ   7



GU828005.1/51412-51535 UUUUGAAGCUUGUUCCUUUGCUAGAAUAUAAAUAAGCCAGCAUAUGUUUCACAUUGCUUUAGUGCUUUGUUCUUUUCUAUUUUAUUCUUUAUGAUUAAAGUAGUUUCUAAGGAAAACUCUGUUC
GU828005.1/51265-51388 UUUUGAAGCUUGUUCCUUUGCUAGAAUAUAAAUAAGCCAGCAUAUGUUUCACAUUGCUUUAGUGCUUUGUUCUUUUCUAUUUUAUUCUUUAUGAUUAAAGUAGUUUCUAAGGAAAACUCUGUUC
GU828005.1/51118-51241 UUUUGAAGCUUGUUCCUUUGCUAGAAUAUAAAUAAGCCAGCAUAUGUUUCACAUUGCUUUAGUGCUUUGUUCUUUUCUAUUUUAUUCUUUAUGAUUAAAGUAGUUUCUAAGGAAAACUCUGUUC
GU828005.1/50971-51094 UUUUGAAGCUUGUUCCUUUGCUAGAAUAUAAAUAAGCCAGCAUAUGUUUCACAUUGCUUUAGUGCUUUGUUCUUUUCUAUUUUAUUCUUUAUGAUUAAAGUAGUUUCUAAGGAAAACUCUGUUC
GU828005.1/50824-50947 UUUUGAAGCUUGUUCCUUUGCUAGAAUAUAAAUAAGCCAGCAUAUGUUUCACAUUGCUUUAGUGCUUUGUUCUUUUCUAUUUUAUUCUUUAUGAUUAAAGUAGUUUCUAAGGAAAACUCUGUUC
GU828005.1/50677-50800 UUUUGAAGCUUGUUCCUUUGCUAGAAUAUAAAUAAGCCAGCAUAUGUUUCACAUUGCUUUAGUGCUUUGUUCUUUUCUAUUUUAUUCUUUAUGAUUAAAGUAGUUUCUAAGGAAAACUCUGUUC
GU828005.1/51559-51645 UUUUGAAGCUUGUUCCUUUGCUAGAAUAUAAAUAAGCCAGCAUAUGUUUCACAUUGCUUUAGUGCUUUGUUCUUUUCUAUUUUAUUC-------------------------------------
#=GC SS_cons           ::::::::::((((((((-(,,<<<<<<----<<<<<-<______________>->>->>>------>>>>>>,,,<<<<<<<<-<<_____>>->>>>>>>>,,,)-))))))))::::::::
#=GC RF                UUUUGAAGCUuguuCCuuUGCUaGaauaUAAAuaaGCCaGCAUAUGUUUCACAuUGCUuuaGUGCUUuguuCuUUUCuacuuuaUuCUUUAUGaUuaaaguaGUUUCUaaGGaacaCUCUGUUC
//
# STOCKHOLM 1.0

#=GF AC   RF02556
#=GF ID   snaR-A
#=GF DE   snaR-A sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:17855395
#=GF GA   98.00
#=GF TC   98.00
#=GF NC   97.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005737; cytoplasm;
#=GF DR   GO; 0005634; nucleus;
#=GF RN   [1]
#=GF RM   17855395
#=GF RT   Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display
#=GF RT   tissue-restricted distribution.
#=GF RA   Parrott AM, Mathews MB
#=GF RL   Nucleic Acids Res. 2007;35:6249-6258.
#=GF RN   [2]
#=GF RM   20935053
#=GF RT   The evolution and expression of the snaR family of small non-coding RNAs.
#=GF RA   Parrott AM, Tsai M, Batchu P, Ryan K, Ozer HL, Tian B, Mathews MB
#=GF RL   Nucleic Acids Res. 2011;39:1485-1500.
#=GF CC   Small NF90/ILF3-associated RNAs (snaR) are ~120 nucleotides long and are
#=GF CC   known to interact with NF90 double-stranded RNA-binding motifs. snaR-A is
#=GF CC   abundant in human testis and has been shown to associate with ribosomes in
#=GF CC   HeLa cells. snaR-A is present in human and gorilla but not in chimpanzee.
#=GF CC   Other snaR RNAs are found in African Great Apes (including chimpanzee and
#=GF CC   bonobo). 
#=GF WK   ILF3
#=GF SQ   5



GQ259354.1/147-261     CCGGAGCCAUUGUGGCUCAGGCCGGUUGCGCCUGCCCUCGGGCCCCCACGGAGGCGGGGGUUCCAGGGCACGAGUUCGAGGCCAGCCUGGUCCACAUGGGUCGGAAAAAAGGAUU
GQ259353.1/147-261     CCGGAGCCAUUGUGGCUCAGGCCGGUUGCGCCUGCCCUCGGGCCCUCACGGAGGCGGGGGUUCCAGGGCACGAGUUCGAGGCCAGCCUGGUCCACAUGGGUCGGAAAAAAGGAUU
ABSL01008103.1/469-355 CCGGAGCCAUUGUGGCUCAGGCCGGUUGCGCCUGCCGUCGGGCCCUCACGGAGGCGGGGGUUCCAGGGCACGAGUUCGAGGCCAGCCUGGUCCACAUGGGUCGGAAAAAAGGACU
GQ259368.1/147-261     CCGGAGCCAUUGUGGCUCCGGCCGGUUGCGCCUGCCCUCGGGCCCUCACGGAGGCGGGGGUUCCAGGGCACGAGUUCGAGGCCAGCCUGGUCCACAUUGGUUGCAGAAAAAAAUU
EU035783.1/1-115       UUGGAGCCAUUGUGGCUCAGGCCGGUUGCGCCUGCCCUCGGGCCCUCACGGAGGCGGGGGUUCCAGGGCACGAGUUCGAGGCCAGCCUGGUCCACAUGGGUCGGAAAAAAGGAUU
#=GC SS_cons           <<-<<-<<<<-<<<<-<<<<<<-<<<<-<<--<<<<<<-<<<<<<<<________>>>>>>>>->>>>>>------>>->>>>->>>>>>->>>>>>>>->>->>::::::::::
#=GC RF                ccGGaGCcauUGuGGccCaGGCcGGccGCGccuGCCcucGggCCCcCAcGGAGGcGgGGGccCcagGGCacGAGUUCGAggCCAGCCuGgUCCaCaugGGuCGggaAAAAggAuU
//
# STOCKHOLM 1.0

#=GF AC   RF02557
#=GF ID   CbSR1
#=GF DE   Coxiella burnetii sRNA 1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; CMfinder 
#=GF GA   146.00
#=GF TC   146.50
#=GF NC   38.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24949863
#=GF RT   Identification of novel small RNAs and characterization of the 6S RNA of
#=GF RT   Coxiella burnetii.
#=GF RA   Warrier I, Hicks LD, Battisti JM, Raghavan R, Minnick MF
#=GF RL   PLoS One. 2014;9:e100147.
#=GF CC   In bacteria small regulatory RNAs are activated during stress and
#=GF CC   virulence conditions. Coxiella burnetii small RNAs: CbSRs 1, 11, 12, and
#=GF CC   14 encoded within intergenic region IGR, and CbSRs 2, 3, 4 and 9 located
#=GF CC   antisense to identified ORFs, are up-regulated during intracellular growth
#=GF CC   in host cells.
#=GF WK   Coxiella_burnetii
#=GF SQ   2


CP001020.1/180525-180636 UUAAUAAGAUUGACCUUUCUGAAGAGGUAAUCACGAAGUUAGGAAACUUUAUCUCAUGGAGAGAGAAAGGUCUAAGGACAGAACUGCUUGGUAGGGAUCACCAACCCGGGGU
AE016828.2/12006-12117   UUAAUAAGAUUGACCUUUCUGAAGAGGUAAUCACGAAGUUAGGAAACUUUAUCUCAUGGAGAGAGAAAGGUCUAAGGACAGAACUGCUUGGUAGGGAUCACCAACCCGGGGU
#=GC SS_cons             :::::::<<<<-<<<<<<____>>>>>>>>>>,,,(((,,,,,,,,<<<<-<<<<_____>>>>->>>><<<____>>>,,,,,,,)))<<<-<<_____>>->>>::::::
#=GC RF                  UUAAUAAGauuGaCCucuCUGAagaGGuaauCACGaaGUUAGGAAACuuuAuCuCAUGGAGaGaGaaaGGuCUAAGGaCAGAACUGCuuGGuAGGGAUCACCAaCCCGGGGU
//
# STOCKHOLM 1.0

#=GF AC   RF02558
#=GF ID   CbSR2
#=GF DE   Coxiella burnetii sRNA 2
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J 
#=GF SS   Predicted; CMfinder
#=GF GA   300.00
#=GF TC   303.50
#=GF NC   39.00
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24949863
#=GF RT   Identification of novel small RNAs and characterization of the 6S RNA of
#=GF RT   Coxiella burnetii.
#=GF RA   Warrier I, Hicks LD, Battisti JM, Raghavan R, Minnick MF
#=GF RL   PLoS One. 2014;9:e100147.
#=GF CC   In bacteria small regulatory RNAs are activated during stress and
#=GF CC   virulence conditions. Coxiella burnetii small RNAs: CbSRs 1, 11, 12, and
#=GF CC   14 encoded within intergenic region IGR, and CbSRs 2, 3, 4 and 9 located
#=GF CC   antisense to identified ORFs, are up-regulated during intracellular growth
#=GF CC   in host cells.
#=GF WK   Coxiella_burnetii
#=GF SQ   2



CP001020.1/1900537-1900295 AUGAAGAAAUCUCGGACAUCAACGGCCGAGAUUUCUUUCAUACUGAGGCGUUCAAUAGUAUUAAUACGUACUCGAAUUAUCACUGCCCGAUCGGCUAUCGCUUCUUUGCAUAUUAUCUUUUUGUUGAUCAUCGGGGUGGGGCGUUGUAACAGCGCCAUUUUGUCUAUCCUGAUGGGUGCGAUCCUGUUGUUGGCAAGCGGCCAAGCCGCCUACGAAGAACAGCAUCGUUACGAUUGUAAAUAA
CP000890.1/147726-147968   AUGAAGAAAUCUCGGACAUCAACGGCCGAGAUUUCUUUCAUACUGAGGCGUUCAAUAGUAUUAAUACGUACUCGAAUUAUCACUGCCCGAUCGGCUAUCGCUUCUUUGCAUAUUAUCUUUUUGUUGAUCAUCAGGGUGGGGCGUUGUAACAGCGCCAUUUUGUCUAUCCUGAUGGGUGCGAUCCUGUUGUUGGCAAGCGGCCAAGCCGCCUACGAAGAACAGCAUCGUUACGAUUGUAAAUAA
#=GC SS_cons               <<<<<<<<<<<<<<<__________>>>>>>>>>>>->>>>,,,((((((,,,,,,<<<--<<<<-<<____>>->>>>-->>><<<_____>>>,,,))))))((((((----(((,,,,,,,,,,<<<<<<<<<<<<<<<<<<<___>>>>>>>------->>>>>>>>>>>><<<<<<<-<<<<<-<<-----<<<<<___>>>>>----->>->>>>>->>>>>->>))))))))):::
#=GC RF                    auGaaGaaaucucGGAcAUcAAcGGCCgagauuuCuUuCauAcUGagGcGUUcAAUaGuAUuaauAcGUAcUCgAauuaUcaCuGcccGAUcggCUAUCgCcuCuuugcaUAUUaucUUUUUGUUGAccaucgGGgugGGGcGcuGUAACagCgCCAUUUUGUCcacCCcgauggGugcGauccuGuuGuuGGcAAGcGGccAAgCCgCcUAcGaaGaaCagcauCgcUaCgauugcaaaUAA
//
# STOCKHOLM 1.0

#=GF AC   RF02559
#=GF ID   CbSR4
#=GF DE   Coxiella burnetii sRNA 4
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J 
#=GF SS   Predicted; CMfinder
#=GF GA   243.00
#=GF TC   243.60
#=GF NC   36.30
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24949863
#=GF RT   Identification of novel small RNAs and characterization of the 6S RNA of
#=GF RT   Coxiella burnetii.
#=GF RA   Warrier I, Hicks LD, Battisti JM, Raghavan R, Minnick MF
#=GF RL   PLoS One. 2014;9:e100147.
#=GF CC   In bacteria small regulatory RNAs are activated during stress and
#=GF CC   virulence conditions. Coxiella burnetii small RNAs: CbSRs 1, 11, 12, and
#=GF CC   14 encoded within intergenic region IGR, and CbSRs 2, 3, 4 and 9 located
#=GF CC   antisense to identified ORFs, are up-regulated during intracellular growth
#=GF CC   in host cells.
#=GF WK   Coxiella_burnetii
#=GF SQ   2



CP001019.1/1365912-1365717 CGGCUAUCUAUACAGGGAUACAUUAAUUUGGAUGUUGCGUUGGGGUUUGGUGCGGUCAAGUGGCUACAUUUGCGACAGAAUGGCAGGAACGAUCUUCCGUAACCGAUUCCCACCACGCUAUCACAAACAUUCCUUAAAGACUCUUGCGAGAUCCCUUCCCGCGCUUCCUUGAGAAGUUUUCCUUUUGCCUUCAUGG
AE016828.2/544387-544582   CGGCUAUCUAUACAGGGAUACAUUAAUUUGGAUGUUGCGUUGGGGUUUGGUGCGGUCAAGUGGCUACAUUUGCGACAGAAUGGCAGGAACGAUCUUCCGUAACCGAUUCCCACCACGCUAUCACAAACAUUCCUUAAAGACUCUUGCGAGAUCCCUUCCCGCGCUUCCUUGAUAAGUUUUCCUUUUGCCUUCAUGG
#=GC SS_cons               :{{{,,,,[[[-[[[[[[,,,,,,,,,,,((((((((((((((((-(((((((((,<<<<<<____>>>>>>,,,,,,,,,,,,,<<______>>,))))-)))))-)))))--))))-------))))))),,,,,,,,,,,,,<<<-<<_____>>->>>,,,]]]]]]]]]<<_____>>,,,}}}:::::::
#=GC RF                    CGGCUAUCuauACagGGaUACAUUAAUUUGgauGuuGCGuuGGGgUucGGugCGGUCaaguGGCUACacuuGCGACAGAAUGGCAgGAACGAUCcUCCGcAaCCgaUcCCCaCCaCGCUAUCACAaaCaucCCUUAAAGACUCUUGCGAGaUCCCUuCCCGCGCUuCCcuGauaaGUUUUCCuUUUGCCUUCAUGG
//
# STOCKHOLM 1.0

#=GF AC   RF02560
#=GF ID   CbSR9
#=GF DE   Coxiella burnetii sRNA 9
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J 
#=GF SS   Predicted; CMfinder
#=GF GA   279.00
#=GF TC   279.10
#=GF NC   38.10
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24949863
#=GF RT   Identification of novel small RNAs and characterization of the 6S RNA of
#=GF RT   Coxiella burnetii.
#=GF RA   Warrier I, Hicks LD, Battisti JM, Raghavan R, Minnick MF
#=GF RL   PLoS One. 2014;9:e100147.
#=GF CC   In bacteria small regulatory RNAs are activated during stress and
#=GF CC   virulence conditions. Coxiella burnetii small RNAs: CbSRs 1, 11, 12, and
#=GF CC   14 encoded within intergenic region IGR, and CbSRs 2, 3, 4 and 9 located
#=GF CC   antisense to identified ORFs, are up-regulated during intracellular growth
#=GF CC   in host cells.
#=GF WK   Coxiella_burnetii
#=GF SQ   2



CP000733.1/999408-999196 AAUUGAGUAUAUAAGUUGUGUUUUCAACAAUGGUUUCGGCCUUCAAAAUUCGAGUACCGUUAUAAACAUGGAUACCCACUAGGUUGAUGUUAGGCAUUUUUAAAAAGAAAUUCUUAUUCGAAAAAACGAUUUCUUCAUCCAUGCCGAACUGCGAAGGCUUUCCACCCAUCUUCAAUAAAGCUGAUUUAGACACGUGAGAUGGAUUAAUUCUUA
CP001020.1/766146-765934 AAUUGAGUAUAUAAGUUGUGUUUUCAACAAUGGUUUCGGCCUUCAAAAUUCGAGUACCGUUAUAAACAUGGAUACCCACUAGGUUGAUGUUAGGCAUUUUUAAAAAGAAAUUCUUAUUCGAAAAAACGAUUUCUUCAUCCAUGCCGAACUGCGAAGGCUUUCCACCUAUCUUCAAUAAAGCUGAUUUAGACACGUGAGAUGGAUUAAUUCUUA
#=GC SS_cons             ::::[[[,,,,,,,<<<<______>>>>,,(((----(((((((----(((,,,,,<<<<_______>>>>,,,,,,,,,,,,,,,,,,,,,<<<<<-------<<<<<<<<_______________>>>>>>>>----->>>>>)))----)))))))--))),<<<<<<-<<------<<<___>>>----->>>>>>>>,,,,,]]]:::
#=GC RF                  AAUUGagUAUAUAAGuuGUGUUUUCaaCAAuGGUUUCgGCCuuCAAAAuuCGAGUACCguUAUAAACauGGAUACCCACUAGGUUGAUGUUAGGCauUUUUAAAaaGaaauuCUUAUUCGAAAAAACgauuuCuuCAUCCauGCCGaaCUGCGaaGGCuUUCCaCCcauCuUCaAUAAAGCugAUUuaGACACGuGaGaugGAUUAAuuCUUA
//
# STOCKHOLM 1.0

#=GF AC   RF02561
#=GF ID   CbSR12
#=GF DE   Coxiella burnetii sRNA 12
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J 
#=GF SS   Predicted; CMfinder 
#=GF GA   195.00
#=GF TC   196.50
#=GF NC   33.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24949863
#=GF RT   Identification of novel small RNAs and characterization of the 6S RNA of
#=GF RT   Coxiella burnetii.
#=GF RA   Warrier I, Hicks LD, Battisti JM, Raghavan R, Minnick MF
#=GF RL   PLoS One. 2014;9:e100147.
#=GF CC   In bacteria small regulatory RNAs are activated during stress and
#=GF CC   virulence conditions. Coxiella burnetii small RNAs: CbSRs 1, 11, 12, and
#=GF CC   14 encoded within intergenic region IGR, and CbSRs 2, 3, 4 and 9 located
#=GF CC   antisense to identified ORFs, are up-regulated during intracellular growth
#=GF CC   in host cells.
#=GF WK   Coxiella_burnetii
#=GF SQ   2



CP001020.1/1622185-1622332 CUGGAGGGUCUGUAGCGGGCUUCCUUGCCCAAAAACUUCAUCCUUGAUACACAGACCUUAGACUACCUCAUUACGUUUAGAGUACACCGAGGACUUCCUUGUCCACCAAGAUCCUAGAGACCUCAGCUAAACUACCUUGUUUAUCAGC
AE016828.2/1403153-1403300 CUGGAGGGUCUGCAGCGGGCUUCCUUGCCCAAAAACUUCAUCCUUGAUACACAGACCUUAGACUACCUCAUUACGUUUAGAGUACACCGAGGACUUCCUUGUCCACCAAGAUCCUAGAGACCUCAGCUAAACUACCUUGUUUAUCAGC
#=GC SS_cons               {{{[[(((((((,,,,<<<<______>>>>,,,,,,,<<<____>>>,,,,))))))),,,,,,,,<<<---------------------<<<<______>>>>------------>>>,,,]],,,<<<<<______>>>>>,}}}:
#=GC RF                    CuGGagGGuCuGuAGCGGGCUUCCUUGCCCAAAAACUuCaUCCUuGaUACACaGaCCuUAGACUACCuCAUUACGUUUAGAGUACACCGAGGaCUUCCUUGuCCACCAAGAUCCUAGaGACCuCAGCuaaaCUACCUUGuuuaUCaGC
//
# STOCKHOLM 1.0

#=GF AC   RF02562
#=GF ID   CbSR14
#=GF DE   Coxiella burnetii sRNA 14
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J 
#=GF SS   Predicted; CMfinder
#=GF GA   172.00
#=GF TC   172.70
#=GF NC   39.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24949863
#=GF RT   Identification of novel small RNAs and characterization of the 6S RNA of
#=GF RT   Coxiella burnetii.
#=GF RA   Warrier I, Hicks LD, Battisti JM, Raghavan R, Minnick MF
#=GF RL   PLoS One. 2014;9:e100147.
#=GF CC   In bacteria small regulatory RNAs are activated during stress and
#=GF CC   virulence conditions. Coxiella burnetii small RNAs (CbSRs 1, 11, 12, and
#=GF CC   14) are encoded within intergenic region IGR. CbSRs 2, 3, 4 and 9 are
#=GF CC   located antisense to identified ORFs and are up-regulated during
#=GF CC   intracellular growth in host cells.
#=GF WK   Coxiella_burnetii
#=GF SQ   2



CP001020.1/26215-26403 GGACCGUGAGGACAGCAGUUUGUUGUUUGGCCCUUUGGGCAAAAAUUGAAUUCGGGAGGAUUAGUCUCCCAGGUUAGCCCGCAAUUCUUAUGAGUAACUCCUGUAACGGUACCCCCAUUUUCACAGCGAAGGUCAUCUCCCAAAGCUAUCGCAGUCAGCCCUAGAAGGACUAAGCUCGCUAUUAUUGCU
Y10436.1/1-137         ----------------------------------------------------CGGGAGGAUUAGUCUCCCAGGUUAGCCCGCAAUUCUUAUGAGUAACUCCUGUAACGGUACCCCCAUUUUCACAGCGAAGGUCAUCUCCCAAAGCUAUCGCAGUCAGCCCUAGAAGGACUAAGCUCGCUAUUAUUGCU
#=GC SS_cons           :::<<____>>---(((((-----((((((-((((-((((,,,,,,,,,,,,,<<<<<<_____>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<-<<_____________>>->>>>,,,,,))))---))))-))))))--------))))):
#=GC RF                GGAccGUGAggAcAGcaguUUGUUGcuugGcccuuUGGGcAAAAAUUGAAUUCGGGaGgAUUAGuCuCCCAGGUUAGCCCGCAAUUCUUAUGAGUAACUCCUGUAACGGUACCCCCAUUUUCACAGCGaAgGUCAUCUCCCAAAGCuAuCGCAGUCAgCCCUAGaaggACcaagCUCGCUAUUacugCU
//
# STOCKHOLM 1.0

#=GF AC   RF02563
#=GF ID   CbSR3
#=GF DE   Coxiella burnetii sRNA 3
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J 
#=GF SS   Predicted; CMfinder
#=GF GA   101.00
#=GF TC   101.10
#=GF NC   100.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24949863
#=GF RT   Identification of novel small RNAs and characterization of the 6S RNA of
#=GF RT   Coxiella burnetii.
#=GF RA   Warrier I, Hicks LD, Battisti JM, Raghavan R, Minnick MF
#=GF RL   PLoS One. 2014;9:e100147.
#=GF CC   In bacteria small regulatory RNAs are activated during stress and
#=GF CC   virulence conditions. Coxiella burnetii small RNAs (CbSRs 1, 11, 12, and
#=GF CC   14) are encoded within intergenic region IGR. CbSRs 2, 3, 4 and 9 are
#=GF CC   located antisense to identified ORFs. CbSRs are up-regulated during
#=GF CC   intracellular growth in host cells.
#=GF WK   Coxiella_burnetii
#=GF SQ   2



CP001020.1/1264622-1264425 GCCGUGAAAGCCCUCGAUUCUUUGUCUAUCGGUAGACGGCCUACGCACGGGAACGCCGGACAUUUUUUAACUACUUGAUAUUCCCUCUUUACCUCGCUCCUUAAGUUGACGUCUAUGCGCGCAGGCGGGAAUCUAGCGCGCUUUCUAUCAAGGUUUGUUUUUAAUCCUCAUUCCCCCUGCCGCGGUGACGGGGCCUAA
AE016828.2/481609-481806   GCCGUGAAAGCCCUCGAUUCUUUGUCUAUCGGUAGACGGCCUACGCACGGGAACGACGGACAUUUUUUAACUACUUGAUAUUCCCUCUUUACCUCGCUCCUUAAGUUGACGUCUAUGCGCGCAGGCGGGAAUCUAGCGCGCUUUCUAUCAAGGUUUGUUUUUAAUCCUCAUUCCCCCUGCCGCGGUGACGGGGCCUAA
#=GC SS_cons               :::::::::[[[[,((((,,,,<<<<<<____>>>>>>,,,,,,,,,,<<<<-<<<-<<________________________________>>>>>->>>>,,,)))),<<<<--<<<<-<<<<<-<<<<<<--<<<<-<<<<<_____>>>>>->>>>---------->>>>>>>>>>>>>>>-->>>>]]]]::::
#=GC RF                    GCCGUGAAAGCCCUCgacUCUUcGuCuaUCGGuaGaCgGCCUACGCACgGGaACGaCGGACAUUUUUUAACUACUUGAUAUUCCCUCUUUACCuCGCuCCcUAAgucGACGuCUAcGCGCGCaGGCGGGaauCUagCgCgCcuuCUAUCaagGcUcGcuUUUAAUCCUCauuCCCCCuGCCGCgGUGaCGGGGCCUAA
//
# STOCKHOLM 1.0

#=GF AC   RF02564
#=GF ID   naRNA4
#=GF DE   Nucleoid-associated noncoding RNA 4 (CssrE)
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:26307168
#=GF GA   59.50
#=GF TC   59.50
#=GF NC   59.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0036386; bacterial nucleoid DNA packaging;
#=GF DR   GO; 0043590; bacterial nucleoid;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   26307168
#=GF RT   A New Noncoding RNA Arranges Bacterial Chromosome Organization.
#=GF RA   Qian Z, Macvanin M, Dimitriadis EK, He X, Zhurkin V, Adhya S
#=GF RL   MBio. 2015; [Epub ahead of print]
#=GF RN   [2]
#=GF RM   21483688
#=GF RT   An integrated approach for finding overlooked genes in Shigella.
#=GF RA   Peng J, Yang J, Jin Q
#=GF RL   PLoS One. 2011;6:e18509.
#=GF CC   In E. coli small RNA transcribed from repeated extragenic palindromic
#=GF CC   element (REP325) called nucleoid-associated ncRNA 4 (nRNA4) collaborates
#=GF CC   HU protein in condensing the DNA. The secondary structure but not the
#=GF CC   sequence of the RNA is important in nucleoid condensation. Also identified
#=GF CC   in Shigella as CssrE [2]. 
#=GF WK   Nucleoid
#=GF SQ   3



AM946981.2/4233354-4233278 GGCCGGAUAAGGCGUUUACGCCGCAUCCGGCAACGGUGCCGACUGCCUGAUGCGACGCUUGCGCGUCUUAUCAGGCC
CP000819.1/4304795-4304719 GGCCGGAUAAGGCGUUUACGCCGCAUCCGGCAAUGGUGCCGACUGCCUGAUGCGACGCUUGCGCGUCUUAUCAGGCC
AP009048.1/4330759-4330683 GGCCGGAUAAGGCGUUUACGCCGCAUCCGGCAACGGUGCCGACUGCCUGAUGCGACGCUUGCGCGUCUUAUCAGGCC
#=GC SS_cons               :<<<<<<<--<<<<____>>>>-->>>>>>>-------------<<<<<<<<-<<<<<____>>>>>->>>>>>>>:
#=GC RF                    GGCCGGauAAGGCGUUUACGCCGCauCCGGCAAcGGUGCCGACUGCCuGaugCGaCGCUUGCGCGuCUuauCaGGCC
//
# STOCKHOLM 1.0

#=GF AC   RF02565
#=GF ID   YrlB
#=GF DE   Y RNA-like
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:23540697
#=GF GA   97.00
#=GF TC   97.00
#=GF NC   36.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000405; Y_RNA;
#=GF RN   [1]
#=GF RM   23540697
#=GF RT   An RNA degradation machine sculpted by Ro autoantigen and noncoding RNA.
#=GF RA   Chen X, Taylor DW, Fowler CC, Galan JE, Wang HW, Wolin SL
#=GF RL   Cell. 2013;153:166-177.
#=GF CC   In Deinococcus radiodurans Rsr is tethered via Y RNA to the
#=GF CC   exoribonuclease PNPase and channels single-stranded RNA into the PNPase
#=GF CC   cavity. Rsr and Y RNA enhance degradation of structured RNAs by PNPase.
#=GF CC   This role could be conserved, as Rsr and ncRNAs called YrlA and YrlB (Y
#=GF CC   RNA like) also associate with PNPase in an evolutionary distant bacterium
#=GF CC   Salmonella Typhimurium.[1]
#=GF WK   Y_RNA
#=GF SQ   2


ABEI01000012.1/80009-79932 AGCAUGGUACGAAUGCUGGUCAGGAUUACAUCUUUCUUAAUGGCUAUCAUCCUGGCUAUUUAUUUGCCAUGCCACCCU
FQ312003.1/3704437-3704360 AGCGCGGCGCGAAUGCUGGCCGGGAUUACAUCUUUCCCGAUGCGUAUCAUCCCGGCUAUGAAUUUGUCGCGCAACGCU
#=GC SS_cons               <<<--<<<<<<<----<<<<<<<<<<--<<<<______>>>>------>>>>>>>>>>-------->>>>>>-->>>>
#=GC RF                    AGcauGGcgcGaAUGCUgGcCgGGAUUACAUcUUUCuugAUGggUAUCAUCCcGgCuAUuuAUUUGuCgcgCaACgCU
//
# STOCKHOLM 1.0

#=GF AC   RF02566
#=GF ID   Ms1
#=GF DE   Mycobacterium smegmatis small RNA 1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; CMfinder
#=GF GA   162.00
#=GF TC   162.40
#=GF NC   151.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0070063; RNA polymerase binding;
#=GF RN   [1]
#=GF RM   25217589
#=GF RT   Ms1, a novel sRNA interacting with the RNA polymerase core in
#=GF RT   mycobacteria.
#=GF RA   Hnilicova J, Jirat Matejckova J, Sikova M, Pospisil J, Halada P, Panek J,
#=GF RA   Krasny L
#=GF RL   Nucleic Acids Res. 2014;42:11763-11776.
#=GF CC   Mycobacterium smegmatis small RNA 1 is highly expressed during stationary
#=GF CC   phase of growth. Ms1 RNA directly interacts with RNA polymerase (RNAP),
#=GF CC   but in a different way than 6S, which is present in other bacteria. Ms1
#=GF CC   does not require the presence of the main sigma factor for RNAP
#=GF CC   interaction. There is evidence that Ms1 RNA may function similar to 6S RNA
#=GF CC   in M. smegmatis which does not have 6S RNA.
#=GF WK   Ms1_small_RNA
#=GF SQ   4


CP000480.1/6242368-6242671 ACGGAAG-CUUGGCGAGGCCAAGACCCAGCCGGAAGAGAAGGCUAGAUCUCCCGACCCAAGCU-CCUAGCACGGAUACCGAGCACCCACGCGGAGCACAUGCCGCGGAAUAGGCAAAAGUGUUGCGGACCUGCGUAGUUUCGAAAAGCGGACGGCCACGACGGCCCUUUGGGUGGGGUUGCAGCCGUAGCGCAUCGCAAAGACGCCGAGGUCACCCACGCAACCCACAUCGCACGCUUGGUCACUCGG-GGUCCGUGCUAGCGGGCGGCGAACCG----------GACAUUG-UCCGGGACGCCGCCCGAUUUCUUUU
CP002385.1/4978398-4978711 ACGGAAG-UUGAGCAAGGCCAAGGCCGAGCCGGAAGAGAAGGCUCGAUCUCCCGAACUCAGCUCCCCAGCACGGGUCCCG-GAACCCACGCGGAGCACAUACCGCCAUACAGGUAAAAGCGUUGCGGGCCUGCGUAGUUGCGAAAAUCGAAUGACCUCGACGGCCCUUUGGGUGGGGCUGCGGUCAUAGCGAGUCGCAAAGGCGCCGAGGCCACCCACGCAACCCAUCACGCACGCUUGGUAUC-CGGAUUCCCGUGUUGGCGGGCGGUGAGCCGAUGUGGUCGGAAGACCA-UACGGAUCGCCGCCCGCUUCAUUUU
CP000656.1/1437598-1437285 ACGGAAG-UUGAGCAAGGCCAAGGCCGAGCCGGAAGAGAAGGCUCGAUCUCCCGAACUCAGCUCCCCAGCACGGGUCCCG-GAACCCACGCGGAGCACAUACCGCCAUACAGGUAAAAGCGUUGCGGGCCUGCGUAGUUGCGAAAAUCGAAUGGCUUCGACGGCCCUUUGGGUGGGGCUGCGGUCAUAGCGAGUCGCAAAGGCGCCGAGGCCACCCACGCAACCCAUCACGCACGCUUGGUAUC-CGGAUUCCCGUGUUGGCGGGCGGUGAGCCGAUGUGGUCGGAAGACCA-UACGGAUCGCCGCCCGCUUCAUUUU
AGSZ01000531.1/16124-15819 ACGGAAGCUUGGAUGAGGCCAAGGCUUAGCCGGAAGAGAAGGCUAAAUCUCCCGAACCAGGCUCCCCAGCACGGGUCCCG-GUACCCACGCGGAGCACAUGCCGCGGAAUAGGCAAAAGUGUUGCGGGCCUGCGUGAUUGCGAAGAGCGGACGGCUACGACGGCCCUUUGGGUGGGGUUGCAGCCGAAGCGCAUUGCAAGGACGCCGAGGCCACCCACGCAACCCAUCUGGCACGCUUGGUAAC-CGG-UAUCCGUGCUAGCGGGCGGCGAGCCGA---------AACAUCGUUUCGGACCGUCGCCCGCUUUCGUUU
#=GC SS_cons               ::<<-<<.<<<<<---<<---<<--<<<<<<_________>>>>>>-->>->>--->>>>>>>->>(((((((((--(((.((--(((-(((--((,,,<<<<________>>>>,,,,,<<<<<<<<<<<<<<<--<<<<<<---<<<-<<<<<<----<<<<<<<______>>>>>>>->>>>>>-->>>->>>>>>-->>>>-->>>>>----->>>>>>,,,,,,,))-)))-)))--)).)))---)))))))))<<<<<<<<<<<-<<<_......._________.__>>>->>>>>>>>>>>::::::::
#=GC RF                    ACGGAaG.cugggcaAGGCCAaGgCccaGCCGGAAGAGAAGGCuggAUCuCCCGAacccagCucCCcagCaCGGgUcCCG.GcACCCaCGCGGAGCACAugCCGCgaaAuAGGcaAAAGuGuuGCGGgCCuGCGcaguugCgaAaAgCGaacGgCcaCGACggCCCcUUGGGUgGGGccGCgGcCguAGCGcaucGcaaaGgCGCCGaGGcCACCCACGCaaCCCAucucGCACGCUuGGUagC.CGG.uucCCGuGcuggCGGGCGgcGggCCGA.........aAgAuca.UaCGGacCgcCGCCCGcUUuauUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02567
#=GF ID   Va-907
#=GF DE   Vibrio alginolyticus sRNA 907
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; CMfinder
#=GF GA   45.00
#=GF TC   60.00
#=GF NC   32.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0022610; biological adhesion;
#=GF RN   [1]
#=GF RM   26217589
#=GF RT   Identification and characterization of three Vibrio alginolyticus
#=GF RT   non-coding RNAs involved in adhesion, chemotaxis, and motility processes.
#=GF RA   Huang L, Hu J, Su Y, Qin Y, Kong W, Ma Y, Xu X, Lin M, Yan Q
#=GF RL   Front Cell Infect Microbiol. 2015;5:56.
#=GF CC   Negative control of the adhesion process and negative control of key
#=GF CC   chemotaxis regulators translation. The number 907 comes from the Huang et
#=GF CC   al. name candidate 907. 
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



CP001805.1/3109394-3109084 UGGGCUGGAAGGGCUGGAUCCAAAGCCUCAGUCUCUUCCACUUUCAUGAGUAAACCAUGUAAGGAAAGAUCUUGAAUCCUAGCUUCAAUUGCCAAGUCACGUUGUUCUACCUUCGCUGGCGCUUGAUGGAGAAUGCGUGAAAAGCGUCGUCUCUCUGCCAUGUGCAUUUUCUCGUUAUGUUUUCAAACAGAAUUGAAUAGUAUAUCAAUGCGAACAAAAAAUGUUCGAUUGCUGUUUGAAAAGUGUCGAGGUCGCUACAGAGUGACGUAAGUGCAAUGUCAUGUUCUUAACGAACGAGACGGGCUAAUGAG
ACZB01000038.1/15113-14803 UGGACUGGAAGGGUUGGAUCCAAAGCCUCAGUCUCUUCCACUUUCAUGAGUAAACCAUGCAAGGAAAGAUCUUGAAUCCUAGCUUCAAUUGCCAAGUCACGUUGUUCUAUCUUAGCUGGAGCUUGAUGGAGAAUACGUGAAAAGCGUCGUCUCUCUGUCAUAUGAAUAUUCUCGUCAGGUCGUCAAACAGAAUUGAAUAGUAUAUCAAUGCGAACAAAAAGUGUUCGAUUGUUGUUUGAAAAGUGUCGAGGUCGCUACAGAGUGACGUAAGUGCAAUGUCAUGUUCUUAACGAACGAGACGGGCUAAUGAG
AAPS01000032.1/14642-14332 UGGACUGGAAGGGUUGGAUCCAAAGCCUCAGUCUCUUCCACUUUCAUGAGUAAACCAUGUAAGGAAAGAUCUUGAAUCCUAGCUUCAAUUGCCAAGUCACGUUGUUCUAUCUUAGCUGGAGCUUGAUGGAGAAUACGUGAAAAGCGUCGUCUCUCUGUCAUAUGAAUAUUCUCGUCAGGUCGUCAAACAGAAUUGAAUAGUAUAUCAAUACGAACAAAAAAUGUUCGAUUGUUGUUUGAAAAGUGUCGAGGUCGCUACAGAGUGACGUAAGUGCUAUGUCAUGUUCUUAACGAACGAGACGGGCUAAUGAG
#=GC SS_cons               :(((,<<<<<<<<<<<<__________>>>>>>->>>>>><<<-<<<<_______>>>>->>>,,,,,,,,,,,,,)))-----{{{---{{{,,,<<<<<<-<<<<<-<<-<<<<____>>-->>->>>>>>>>>>>>>,,,,,,,{{{{{{,,[[-[[[-[[[[[[[,((((-(((---(((((((((,<<<<<________>>>>>,<<<<<<_____>>>>>>,,,,)))))))))--)))-))))<<<<<<____>>>>>>,,]]]]]]]]]]-]],<<<<_____>>>>}}}}}}}}}---}}}:
#=GC RF                    UGGaCuGGaaGGgcuGgAUCCAAAGCCcCagcCUCuuCCaCuuUCauGAGUAAACCauGuaaGGAAAGAUCUUGAAuCCUAGCUuCaAUUGCCAAGuCaCGuUguuCuAcCUucGCUGGaGCUUgaUGgaGaacaCGuGaAAAGCGUCGuCuCUCuGuCauauGcaccuUCuCGUcacGUccuCaaaCagAauuGaAUAGUAUAuCaaugCGaaCaAAAAauGuuCGAUUGcuGuuuGagAAgugUCGaGGuCgCuACAGaGcGaCGUaggugCaauGUCaUGuuCUUAACGaaCGaGaCGGGCUAAuGaG
//
# STOCKHOLM 1.0

#=GF AC   RF02568
#=GF ID   UptR
#=GF DE   Escherichia coli small RNA (uptR) gene
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:11157926
#=GF GA   100.00
#=GF TC   101.10
#=GF NC   34.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   11157926
#=GF RT   Oversynthesis of a new Escherichia coli small RNA suppresses export
#=GF RT   toxicity of DsbA'-PhoA unfoldable periplasmic proteins.
#=GF RA   Guigueno A, Dassa J, Belin P, Boquet PL
#=GF RL   J Bacteriol. 2001;183:1147-1158.
#=GF CC   UptR scRNA transcribed from the uptR gene is implicated in suppressing
#=GF CC   extracytoplasmic toxicity by reducing the amount of membrane-bound toxic
#=GF CC   hybrid protein.
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   3



GQ398086.1/49166-49075   GCUGAAUAUGAUUCAAUAUCGCACGCUACUCAUCCAUCCCAGGAUAAUGAGUUCAUAGGUUGAAGUCUCAACACCCCCACUACGGGGGUGUU
AEHW01000045.1/5763-5674 GCUGAAUAUGAUUCAAUAUCGCACGCUACUCAUCCAUCCCAGGAUAAUGAGUACAUAGGUUGAAGUUUCACC--CCCCACUACGGGGAUGUU
AF272839.1/100-191       GCUGAAUAUGAUUCAAUAUCGCACGCUACUCAUCCAUCCAAGGAUAAUGAGUACAUAGGUUGAAGUUUCAACACCCCCACUACGGGGGUGUU
#=GC SS_cons             :::<<<<___>>>>,,,,,,,,,,,,,<<<<<<<<______>>>--->>>>>------------------<<<<<<<<_____>>>>>>>>:
#=GC RF                  GCUGaauAUGauuCAAUAUCGCACGCUaCuCauCCAUCCcAGGaUAAuGaGuaCAUAGGUUGAAGUuUCAaCaCCCCCACUACGGGGGuGuU
//
# STOCKHOLM 1.0

#=GF AC   RF02569
#=GF ID   IhtA
#=GF DE   IhtA sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Tattersall et al, PMID:23071807
#=GF SS   Predicted; RNAfold
#=GF GA   76.00
#=GF TC   76.40
#=GF NC   38.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   23071807
#=GF RT   Translation inhibition of the developmental cycle protein HctA by the
#=GF RT   small RNA IhtA is conserved across Chlamydia.
#=GF RA   Tattersall J, Rao GV, Runac J, Hackstadt T, Grieshaber SS, Grieshaber NA
#=GF RL   PLoS One. 2012;7:e47439.
#=GF CC   A histone like protein HctA and HctB play role in controlling the
#=GF CC   differentiation between the two cell types. The expression of HctA is
#=GF CC   tightly regulated and repressed by small non-coding RNA, IhtA until the
#=GF CC   late RB to EB re-differentiation. The IhtA RNA is conserved across
#=GF CC   Chlamydia species.
#=GF WK   Chlamydia_(genus)
#=GF SQ   5



CP002024.1/53023-53129   AAGUUGGUAUUCUAACGCCAUGGAAUAGCUUCUGACUCUAGUGUUUGUA-CACAGGGGGGAAGUCAAGAUGGACUGGAGUUAGCCGUAUCUCC---GGUUCUCUUGGCUUU
AE002160.2/53054-53160   AAGUUGGUAUUCUAACGCCAUGGAAUAGCUUCUGACUCUGGUGUUUGUUGCACAGGGGG-AAGCCAAGAUGGGCUGGAGUUAGCCGUGUCUCC---AGUUCUCUUGGCUUU
AE002161.1/54676-54780   AAGAUGAUAUUCU-CCGCCGUGGAAUAGCUUCUGACUCUG----UUGCA-UUCAGGGGGAAAGCCAAGAAGAUGUAGAGUCGGCCGUAUAACUUUAUGUUUUCUUGGCUUU
AE015925.1/52097-52199   AAGAUGAUAUUCU-ACGCCAUGGAAUAGCUUCUGACUCUG----UUGUACUUCAGGGGGAAAGCCAAGAAAACAU--CGUCGGCCGUAUGAUUG-UUGUUUUCUUGGCUUU
AE001273.1/773281-773387 AAGUUGGUAUUCUAACGCCAUGGAAUAGCUUCUGACUCUAGUGUUUGUA-CACAGGGGGGAAGUCAAGAUGGACUGGAGUUAGCCGUAUCUCC---GGUUCUCUUGGCUUU
#=GC SS_cons             :<<--<-<<<<<<<______>>>>>>>->-->>,,<<<<<_________.__>>>>>--<<<<<<<<<<-<<<<<<<<<__________>>>>...>>>>>>>>>>>>>>>
#=GC RF                  AaGuUGauauuCuaaCGCCAugGaauaGCUUCuGACuCugGUGUUUGua.uacaGgGGGgaaGcCaaGaugaaccgGcgUuaGCCGUAUcgCc...gguucuCuuGgCuuc
//
# STOCKHOLM 1.0

#=GF AC   RF02570
#=GF ID   BM-sr0117
#=GF DE   Brucella melitensis small RNA 0117
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:26778206
#=GF GA   112.00
#=GF TC   112.20
#=GF NC   31.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26778206
#=GF RT   Characterization of ribonuclease III from Brucella.
#=GF RA   Wu CX, Xu XJ, Zheng K, Liu F, Yang XD, Chen CF, Chen HC, Liu ZF
#=GF RL   Gene. 2016;579:183-192.
#=GF WK   Brucella_sRNA
#=GF SQ   3



ACBK01000015.1/40061-40143 UGGUGGCUUGAUGAUCGCCUAUAUUCUCGCUGUCGCUUGCAUUACCAGCAUUGCCGUGGGUGGGCUUGUGGCAAUCGCCAAUU
CP000709.1/345674-345756   UGGUGGCUUGAUGAUCGCCUAUAUUCUCGCUGUCGCUUGCAUUACCAGCAUUUCGGUGGGUGGGCUUGUGGCAAUCGCCAAUU
AE008918.1/924120-924038   UGGUGGCUUGAUGAUCGCCUAUAUUCUCGCUGUCGCUUGCAUUACCAGCAUUGCGGUGGGUGGGCUUGUGGCAAUCGCCAAUU
#=GC SS_cons               :::<<<<-----<<<-<<<-<<<--<<<<<--<<<<-<<<_______>>>-->>>>-->->>>>-->>>>>>->>>>>>>:::
#=GC RF                    UGGuGGCUUGAUGauCGCCUauaUUCuCgCUGucGcUuGCAUUACCAGCaUUgCggUGGGuGgGCUuguGGCAauCGCCaAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02571
#=GF ID   Mcr7
#=GF DE   mcr7 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   380.00
#=GF TC   385.00
#=GF NC   35.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   24874799
#=GF RT   The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in
#=GF RT   Mycobacterium tuberculosis.
#=GF RA   Solans L, Gonzalo-Asensio J, Sala C, Benjak A, Uplekar S, Rougemont J,
#=GF RA   Guilhot C, Malaga W, Martin C, Cole ST
#=GF RL   PLoS Pathog. 2014;10:e1004183.
#=GF RN   [2]
#=GF RM   20181675
#=GF RT   Multiple small RNAs identified in Mycobacterium bovis BCG are also
#=GF RT   expressed in Mycobacterium tuberculosis and Mycobacterium smegmatis.
#=GF RA   DiChiara JM, Contreras-Martinez LM, Livny J, Smith D, McDonough KA,
#=GF RA   Belfort M
#=GF RL   Nucleic Acids Res. 2010;38:4067-4078.
#=GF CC   Mcr7 sRNA encoded by the mcr7 gene modulates translation of the tatC mRNA
#=GF CC   and impacts the activity of the Twin Arginine Translocation (Tat) protein
#=GF CC   secretion apparatus.
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   2



HE572590.1/2750779-2751129 CCGGCGGCCCGACACAUGCAGCCGAGUUGGCUGGCUCGGAAGGGGGACAGAGUUGACCAUGACAGCGAGUGUGGCCAAGGUGACAGCUGCACGCCCGGAGCCAAGCGCGGCGUGGGCUGAAGCCCGGCGGCGGGUACGCCAACGCCGCGAGGACAUGCUGCGCCAUCCUGCAUUUCUGUCCAAGCAGCUCCCUCCCGAACCAGCGCACGACGACGGCGUCGCGGCCGUCUACGACAUCGCGGUUGCGCGUCGGCGCCGACCCGCUUGAGCGGUCCCCGACGCGUCAACGUCGCGCCGGCUGCCCGGUAAACCGGCAAUCGACGACCGAGCCUUGGCGGGCGCGUCGCGCUC
BX842579.1/267333-267681   CCGGCGGCCCGACACAUGCAGCCGAGUUGGCUGGCUCGGAAGGGGGACAGAGUUGACCAUGACAGCGAGUGUGGCCAAGGUGACAGCUGCACGCCCGGAGCCAAGCGCGGCGUGGGCUGAAGCCCGGCGGCGGGUACGCCAACGCCGCGAGGACAUGCUGCGCCAUCCUGCAUUUCUGUCCAAGCAGCUCCCUGCCGAACCAGCAGACGACGACGGCGUCGCGGCCGUCUACGACAUCGCGAUUGCGCGUCGGCGCCGACCUGCUUGAGCGGGUCCCGGCGGGUCAACGUCG--GCGGCUGCCGGGUAAACCGGCAAUCGACGACCGGGCCUUGGCGGGCGCGUCGCGUUC
#=GC SS_cons               ::(((((((((((-------((((-(((((((((-((((-((((((((((((-((--((-((--(((((((((-((,,<<<--<<<<<-<<<<<<<<________>>->>>>>>>>>>>-->>><<<<<<<<____>>>>--->>>>,,,))-))))))-)))--))-))))-))))))))--------))))-))))-)))))---))))--))))))))-)))))))--------(((((((((-((((((<<<<<<<<<<<____>>>>>>>-->>>><<<<---<<<<---<<<-<<<<<<_____>>>>>>->>>->>>>-->>>>))))))-)))-)))))):::
#=GC RF                    ccGgcGGcccGacAcAUGcAGccGAGucGGcuGGcucGGAaGGGGGacaGagUuGAccaUGacAGcGaGcguGGccAAGGcGAcaGccGcacGcccGGAGccAAGCgcggCgugggCugAAgCCcGGcGGcGGGUACgCCAAcgCCgcGAggACacgCuGCgCcAuCcugCaUcuCuguCCAAGcAGcUCCCuaCCgaACCagCaaACgaCGACggCguCgcggCCgcCUAcGAcAUcGcGgccGcGcGccggcGccGgcccGcUUGAgCgggcCccggCggGccAAcGucGcgacGgcuGccgGGUAAACcggCaAcCgACgaCcGggCcccggCgGgCgcgcCgCguUc
//
# STOCKHOLM 1.0

#=GF AC   RF02572
#=GF ID   babR_5UTR
#=GF DE   Brucella babR 5'UTR
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:22020650 
#=GF GA   93.00
#=GF TC   94.20
#=GF NC   44.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF RN   [1]
#=GF RM   22020650
#=GF RT   The RNA chaperone Hfq independently coordinates expression of the VirB
#=GF RT   type IV secretion system and the LuxR-type regulator BabR in Brucella
#=GF RT   abortus 2308.
#=GF RA   Caswell CC, Gaines JM, Roop RM 2nd
#=GF RL   J Bacteriol. 2012;194:3-14.
#=GF CC   Hfq protein regulates virB operon which is required for full virulence of
#=GF CC   the bacteria. It can bind to 5' untranslated region of virB
#=GF CC   transcriptional regulator BabR and mediate its effects on babR expression.
#=GF WK   Brucella_sRNA
#=GF SQ   3



ACOR01000001.1/198901-199034 UAAUCUUCGUAGAAGAAAUAUGAAAGAUAUGCUAGGAAUGUUUAGCGAUACAUUUUACCAAAAAUCGCUGCGAUUCCAAGAAUUCAUAUUUAUUUUGAAACGCUACUGGGAUGUCUGCAAUGAAAUGGGAAACA
CP000911.1/197874-198007     UAAUCUUCGUAGAAGAAAUAUGAAAGAUAUGCUAGGAAUGUUUAGCGAUACAUUUUACCAAAAAUCGCUGCGAUUCCAAGAAUUCAUAUUUAUUUUGAAACGCUACUGGGAUCUCUGCAAUGAAAUGGGAAACA
ACEI01000058.1/50197-50330   UAAUCUUCGUAGAAGAAAUAUGAAACAUAUGCUAGGAAUGUUUAGCGAUACAUUUUACCAAAAAUCGCUGCGAUUCCAAGAAUUCAUAUUUAUUUUGAAACGCUACUGGGAUGUCUGCAAUGAAAUGGGAAACA
#=GC SS_cons                 :::<<<<<___>>>>>--(((---(((((((((((,,,,,,,,<<<<<<______________>>>>>><<<<<<<--<<<<<________>>>>>>>>>>>>,,)))))))))))---)))::::::::::::
#=GC RF                      UAAuCuuCGUAGaaGaAAcauGAAagacaucCcaGGAAUGUUUaGCGauACAUUUUACCAAAAauCGCuGCGguuCCAagaauUCAUAUUUauucuGaacCGCUACugGgaugucuGCAaugAAAUGGGAAACA
//
# STOCKHOLM 1.0

#=GF AC   RF02573
#=GF ID   LLnc147
#=GF DE   Lactococcus lactis non-coding RNA 147
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   127.00
#=GF TC   127.60
#=GF NC   37.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0015976; carbon utilization;
#=GF RN   [1]
#=GF RM   26950529
#=GF RT   Transcriptome landscape of Lactococcus lactis reveals many novel RNAs
#=GF RT   including a small regulatory RNA involved in carbon uptake and metabolism.
#=GF RA   van der Meulen SB, de Jong A, Kok J
#=GF RL   RNA Biol. 2016;13:353-366.
#=GF CC   Hundreds of novel RNAs were identified by Meulen et al. LLnc147 was shown
#=GF CC   to be involved in carbon uptake and metabolism. 
#=GF WK   Lactococcus_lactis
#=GF SQ   2



CP002365.1/1778845-1778744 AUCCUUAUAGGAAAGCGUUUACCUAAAAGUCAUGGUUACGUAAAUAAGCUAUAGCGAGUAGCUUAAUUUCUUUCAAAUCCCUCCUAGUCAGGGGGAUUUUUU
AM406671.1/1942946-1942845 AUCCUUAUAGGAAAACGUUUACCUUUAAGUCAUGGUUACGUUACUAAGCUAUAGCGAGUAGCUUAAUUUCUUUCAGAUCCCUCCUAGUCAGGGGGAUUUUUU
#=GC SS_cons               :<<<<___>>>>,<<<<<--<<<__________>>>->>>>>,,<<<<<<<<_____>>>>>>>>,,,,,,,,,<<<<<<<-<<<____>>>>>>>>>>:::
#=GC RF                    AuCCuUAUaGGaAagCGuUUaCCUaaAAGUCAUGGuUaCGcuAauaaGCuacAGCGAguaGCuuaAUUUCUUUCagauCCCUCCuAGUCaGGGGGaucuUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02574
#=GF ID   Ricks_sRNA10
#=GF DE   Rickettsia sRNA 10
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   97.00
#=GF TC   97.10
#=GF NC   96.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26679185
#=GF RT   Bacterial small RNAs in the Genus Rickettsia.
#=GF RA   Schroeder CL, Narra HP, Rojas M, Sahni A, Patel J, Khanipov K, Wood TG,
#=GF RA   Fofanov Y, Sahni SK
#=GF RL   BMC Genomics. 2015;16:1075.
#=GF WK   Rickettsia
#=GF SQ   3



CP001584.1/397318-397671 UUUUAGAAAUGGAA-AAUAGACCUUUGAUGACUCUAAAGAAAUUUUUAACCUUCCAU--UUAUGACUGAUCUAUUAAUCUCAAAUAUGACAUAGUGCUAAUUUUGAUCUAAGUAAGCUCUGAAUCGUGAAUCUCUUAAGUAUUAAAAUAGUAAGUUGUCUUAAAAAUUAUUCUAUCUCCAAUCAGUACACUACACUAUAAAAAUUGCUAUAAAAA-AGAACUAUUGAUGAAAAUUGAGGAGGUAAUUAUGGCAGCAAAAUGUACCAAAGCACUAAUUAUAGACUCACUUUUAUAUUACAGUUAUGU-GU-UGAUGCAUCAAUGUUGAUGUAUCUUUAGAUUAUUUAGGCGAAAAAUUAGG
AE017197.1/398283-398629 UUUUAGAAACAAAC-AAUAUACAUUUGAUGAUUAUAAAGAAAUUUUUAACUUUGCAU--UUAUGACUGAUUUAUCAAUCUCAAAUAUGACAUAGUGCUAAUUUUGAUUUAAGUAAACUCCAAAUCGGUAAUCGCUGAAGUAUUAAAACAGUUAGUGGUUUUACAAAUUAUUCUGUCUCUAAUCAGUACAU-----UAUAAAGAUUGCUAUAAAAA-AGAACUGUUGAUGAAAAUUGAGGAGAUAAUUAUAGCAGCAAAAUGUGCUAAAGCAUUAAUCUAAUGAUCAAUUUUAUAUUGCAGUUAUGU-AU-UGGUACGUCAACG-UGAUGCAUCUUUAGAUUGUUUAGG-AAUAAAUUAGG
CP000053.1/560743-561096 UUUUAGAAAUGAAAAAAUGGACUUUUGACGAGGCUAAAGAAAUCUUUAGCUUUUCGUUUAUGGAGCUGGUCUAUCAAGCUCAAACAAUACAUCGUGCUAAUUUUGAUCCUAAUAAGAUCCAAAUCAGCAGCCUCUUAAGCAUUAAAACAGGUAGUUGUCCUGAAAAUUGUAAAUUCUGUCCUCAAUCUUC-UCACUAUAAAACUUA-UGUAAAAAAAGAGCCUUUAAUGCAAAUUGAGGAUGUAAUUACGGCAGCAAAACGUGCUAAAGCAGCAGGUA-GUACUCGCUUUUGUAUGGGAGCUGCGUGGCGUGGUCCACGU--G-AUGAGGAUUUAAAACUGGUUUGCGAGAUGAUUAAGG
#=GC SS_cons             ::::::::::::::.::::::[[[--[[[[[-[[[[[[[[,,,,,,,,,,,,((-((..-((((((((,,,,,,,,,,,,,,,,<<-<<<<---<<<<<-<<<<<<<<<<<<-----<<________>>---->>>->>->>>>>>>>>>>>--->>>>->>,,,,,,,,,,,,,,,,,,<<<<<<<--<.----<<<<________>>>>----.->--->>>>>>>,<<<<-<<<<---<<<<<<<--<<________________>>-->>>>>>>--->>>>->>>>,,,,,,))))))))-.)).-))<<<<<<<____>>>>>>>]]]]]]]]]]]]]-]]]::::::::::::
#=GC RF                  UUUUAGAAAugaAa.AAUagACcuUUgacgaugcUaaaGaAAUuUUUAaCuUccCgc..uuguagCUgaUcUAUcAAuCUCAAAcaugaCaUaGugCUaAUUUUgaUcuaaGUAAgcUccaAAUCgggAauCuCuuAaguAuuAAAAuAGcaAGUuGucuugaAAAUUaUucuuUCUcuaaUcaacacac.uCACUauaAAaaUUgCuauAAAAA.AgAaCuguugAuGaaaaUuGagGAgguaauUaugGCAGCAAAAuGUgCuAAAGCAuuAauuacauacuCacuuuuaUAUugcAGcuacgU.gc.UggUgCgccaAuG.uggcGcAuCuuuAgcucguuUagGagAuaAaUuAGG
//
# STOCKHOLM 1.0

#=GF AC   RF02575
#=GF ID   DM_SisR1
#=GF DE   Drosophila melanogaster stable intronic sequence RNA 1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   62.00
#=GF TC   62.30
#=GF NC   46.40
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26504165
#=GF RT   Stable intronic sequence RNAs have possible regulatory roles in Drosophila
#=GF RT   melanogaster.
#=GF RA   Pek JW, Osman I, Tay ML, Zheng RT
#=GF RL   J Cell Biol. 2015;211:243-251.
#=GF WK   Drosophila_melanogaster
#=GF SQ   3



AE014297.2/1435333-1434967 ACUUCUUUUUAUUUAUUUUUGUUUUUAAAACUACGAUUAAGAAUCGGUUGUAAGCGUGGUGUCUCGUGAUCAGCUCAUUAAGCCCACUUAGAUAUGCUACGCUGUAUUUGGGACUAACCUCGGGUGUUGGUUUGGGUAUGGCAAACGCUGCAAAAACUAGAUUCAGUCAAGGACAUUUACUUUGGCUACGUUGGUCCAACCGAAUACGGGCUU------CUGAUUCCAUGAAGAGCUUUUGCAAUUUAGAGUUUGAAAUGAAAUUGUGUUUC------------------------------CGGAUUAUAC--------UCC----------------AAACAUAUUAUUAUAUGCAAUCUCAUUUACUUUGAAACAUGAUCAAUGAAUAAAAAGAAACUGUUCACAUAAAGCAAGCGACUUAACC
AASS01010578.1/1952-1555   ACUUCUUUUUAUUUAUUUCUGUUUUUAAAACUACGAUUAAGAAUCAGCUGUAUGCGUGGUGUCUUGUGAUCAGCUCAUUAAGCCCACUUAGUUAUGCUACGCUGUAUUUGUGACUAAACUCGGGUGGUGGUUUGGGUAUUUU-GGCAAUAAGAAAACUAGUUUCAGUCAAGGACAUUAACUUUGGCUACGUUGGUCUAACCGAAUACGGACAAUACUAAUGGA-UUCA-GAAGAGCUUUUGCAAGUCAGAGUUUGAAAUGAAGUUGUGUUACAAACAAUCGAAACAUUGAUGGAAUCGAUUCCGGAUUAUAC--------UGC----------------AAGCAUAUUAUU--AUGCAAUCUCAUUUUCUUUAAAACAUGAUCAAUGAAUAAAAAGAAACUGUUCACAUAAUGCAAACCACUUAACU
AASV01048691.1/503-106     ACUUCUUUUUAUUUAUUUCUGUUUUUAAAACUACGAUUAAGAAUCAGCUGUAUGCGUGGUGUCUUGUGAUCAGCUCAUUAAGCCCACUUAGUUAUGCUACGCUGUAUUGGUGACUAAACUCGGGUGGUGGUUUGGGUAU-UUGGGCAAUAAGAAAACUAGUUUCAGUCAAGGACAUUAACUUUGGCUACGUUGGUCCAACCGAAUACGGACAAUACUAAUGGA-UUCA-GAAGAGCUUUUGCAAGUCAGAGUUUGAAAUGAAGUUGUGUUACAAACAAUCG-----------AAACAUUGAU----------GGAAUCGA---UUCCGGAUUAUACAGCAAGCAUAUUAU--UAUGCAAUCUCAUUUUCUUUAAAAUAUGAUCAAUGAAUAAAAAGAAACUGUUCACAUAAUGCAAGCGACUUAACC
#=GC SS_cons               ::{{{{{{{{{{{{{{{,<<<<__________>>>>,,,,[[-[[[[--[[,<<<<<<<<<<-<<-------<<<_____>>>------->>->>>>>>>>>>(((((((((((((((,,,<<<<-<<<<<<<--<<--<<<____>>>>>-->>>>>>>>>>><<<<<<<<_______>>>>>>>>,,)))))))---)))))))),,]]--------]]]].]]<<.---<<<<<<<________>>>>>>>---->>,,((((((((((,,,,,,,,,...........,,,,,,,,,,,<<<______........>>>................,,,<<<<_____.>>>>,,,,,,,,,,,,,,,,)))))))))),}}}}}}}}}}}}}}}:::::::::::::::::::::::::::::
#=GC RF                    ACuuCuuuuuauuuauuUcuGuUUUUAAAACUaCggUUAAgaAuCggcUGuAaGCGugGuguCucGUGAUCAGCuCAUUAaGCCCACUUAgaUaugCuaCGCuGuauucGgGaCuaacCUCGgguGcugGuuuGGguAUggcaggCgccacgAaaaCuagauuCaGuCaagGACAUUaACuuuGgCuACguugGuCcAAcCgaauaCGGaCaaUAcUAAccGa.ucCa.GAAgagCuuuUGCAAgUcagaGuuuGAAAuGAAguuguguuccAAAcAAUcG...........aAAuauauaucGgaUUAUAc........ucC................AAgCauaUUAUU.uauGCAAUCUCAUUUuCUUUggaacaugacCaaugaauaaaaaGaaACUGUUCACAUAAuGCAAgCgACUUAACc
//
# STOCKHOLM 1.0

#=GF AC   RF02576
#=GF ID   tsr1
#=GF DE   tsr1 small RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   235.00
#=GF TC   235.90
#=GF NC   185.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26861020
#=GF RT   Genome-wide Annotation, Identification, and Global Transcriptomic Analysis
#=GF RT   of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
#=GF RA   Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN
#=GF RL   MBio. 2016;7:e01990-e01915.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



CP000730.1/52438-53039 AAGCCAGGAUAAUGUAGUCUUAAUCGUUCUGAAAUACGAAAAAUGUUGUGGAAAUCGCGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCGCGUGAAAUAAUCAGAGGAA-------------------------------------------------------UCGUUUGA---AAUCAUCGUAGUAAUCGCGCGAAAAUCGCGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCGCGUGAAAUACUAUGGUAGACGGUUUGAGUAAAUUAAUGGAGUAUUUUAAU
HM030721.1/22014-22560 AAGCCAGGAUAAUGUAGUCUUAAUCGUUCUGAAAUACGAAAAAUGUUGUGGAAAUCGCGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCGCGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCGCGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCGCGUGAAAUACUAUGGUAGACGGUUUGAGUAAAUUAAUGGAGUAUUUUAAU-----------------------------------------------------------------------------------------------------------------
CP000255.1/52438-53094 AAGCCAGGAUAAUGUAGUCUUAAUCGUUCUGAAAUACGAAAAAUGUUGUGGAAAUCGCGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCACGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCGCGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCGCGUGAAAUAAUCAGAGGAAUCGUUUGA---AAUCAUCGUAGUAAUCGCGCGAAAAUCGCGUGAAAUAAUCAGAGGAAUCGUUUGAAAUCAUCGUAGUAAUCGCGCGAAAAUCGCGUGAAAUACUAUGGUAGACGGUUUGAGUAAAUUAAUGGAGUAUUUUAAU
#=GC SS_cons           :::[[[---[[[[-[[-[[--[[[[[[[,,,,,,<<<<<______>>>>>,,,,((((((((,,,,,<<<<<-<___>->>>>>,,,,,,,,,,,,,,<<<<<<<<--<<-<<<<<<-----<<<<<-<<-<<-<<<<<--<<<-<<<-<<--<<<<<<<<--<<-<<<<<<-----<<<<<-<<-<<-<<<<<--<<<-<<<-<<--<<<<<<<<--<<-<<<<<<-----<<<<<-<___>->>>>>-->>>->>>->>-->>>>>>>>-->>->>>>>>----->>>>>->>->>->>>>>-->>>->>>->>-->>>>>>>>-->>->>>>>>----->>>>>->>->>->>>>>-->>>->>>->>-->>>>>>>>,,,)))))))),,,,,(((((-((-((-(((((,,,,,,,,,,,,,,<<<<<<<<___>>>>>>>>,,,,,<<<<<-<<-<<-<<<<<--------------<<<<<<<<___>>>>>>>>----->>>>>->>->>->>>>>...,,,,,,,,,,,,,,<<<<<<<<___>>>>>>>>,,,,,)))))-))-))-))))),,,,<<<<<<<<<-<<<<<<<<___>>>>>>>>-->>>>>>>>>,]]]]]]]-]]-]]-]]]]-]]]:::::::::::
#=GC RF                AAGccaGGAuaauGuaGucUUaaccGucCUGAAAcaCgaAAAAUGucGugGAAAuCgCGuGaAAUAAuCagaGGAAUCGucuGaAAUCAUCGUAGUAAuCGCGCGaAAacCaCGuGaAAUAAuCagaGGaAuCGucuGaAAuCaUCGuAguAAuCGCGCGaAAacCaCGuGaAAUAAuCagaGGaAuCGucuGaAAuCaUCGuAguAAuCGCGCGaAAacCaCGuGaAAUAAuCagaGGAAUCGucuGaAAuCaUCGuAguAAuCGCGCGaAAacCaCGuGaAAUAAuCagaGGaAuCGucuGaAAuCaUCGuAguAAuCGCGCGaAAacCaCGuGaAAUAAuCagaGGaAuCGucuGaAAuCaUCGuAguAAuCGCGCGaAAAuCaCGcGaAAUAAucagaGGaAucGucuGaAAUCAUCGUAGUAAuCgCGCGaAAAuCGCGcGaAAUAAuCagaGggAccGccugaAAUcAUcGUAGUAAucgcGcGaAAAuCgCgcgaAAUAaucagguggAccGucuGa...AAUcAucGuAGUAaucgcGcGaAAAuCgCgcgaAAUAAuCagaGgaAuCGucugaAAUcaccguaGuaAucgcGcGaAAAuCgCgcgaAAuaCuacgguAgaCgguuUgaGuaAauuaAuggAGUAUUUUAAU
//
# STOCKHOLM 1.0

#=GF AC   RF02577
#=GF ID   tsr24
#=GF DE   S. aureus tsr24 small RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   50.00
#=GF TC   50.60
#=GF NC   49.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26861020
#=GF RT   Genome-wide Annotation, Identification, and Global Transcriptomic Analysis
#=GF RT   of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
#=GF RA   Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN
#=GF RL   MBio. 2016;7:e01990-e01915.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



AM990992.1/1016690-1016925 AAAUUAUACGACGGGACCCAACACAGAAAAUUCAUUUUAUUGAAUUUUACAUUUAUGUGCAAGUUGGGCAAAGUGUCUUAUUUUU--UAAGUAUUUCAAAGUAAAAUUACAUGUUAAUACGUAGUAUUAAUGGCGAGACUCCUGAGGGAGCAGUGCCAGUCGAAGACCGAGGCUGAGACGGCACCCUAGGAAAGCGAAGCCAUUCAAUACGAAGUAUUGUAUAAAUAGAGAACAGCAG
FR714927.1/1937316-1937553 AAAUUAUAAGAAGGGACCCAACACAGAAAAUUCAUUUUAUUGAAUUUUACAUUUAUGUGCAAGUUGGGCAAAGUGUCUUAUUUUUUAAAAGUAUUUCAAAGUAAAAUUACAUGUUAAUACGUAGUAUUAAUGGCGAGACUCCUGAGGGAGCAGUGCCAGUCGAAGACCAAGGCUGAGACGGCACCCUAGGAAAGCGAAGCCAUUCAAUACGAAGUAUUGUAUAAAUAGAGAACAGCAG
AFNP01000039.1/58166-57929 AAAUUAUACGAAGGGACCCAACACAGAAAAUUCAUUUUAUUGAAUUUUACAUUUAUGUGCAAGUUGGGCAAAGUGUCUUAUUUUUUUAAAGUAUUUAAAAGUAAAAUUACAUGUUAAUACGUAGUAUUAAUGGCGAGACUCCUGAGGGAGCAGUGCCAGUCGAAGACCGAGGCUGAGACGGCACCCUAGGAAAGCGAAGCCAUUCAAUACGAAGUAUUGUAUAAAUAGAGAACAGCAG
CP000255.1/1429517-1429754 AAAUUAUACGAAGGGAUCCAACACAGAAAAUUUAUUUUAUUGAAUUUUACAUUUAUGUGCAAGUUGGGCAAAGUGUCUUAUUUUUUUAAAGUAUUUCAAAGUAAAAUUACACGUUAAUACGUAGUAUUAAUGGCGAGACUCCUGAGGGAGCAGUGCCAGUCGAAGACCGAGGCUGAGACGGCACCCUAGGAAAGCGAAGCCAUUCAAUACGAAGUAUUGUAUAAAUAGAGAACAGCAG
#=GC SS_cons               :::[[[[[[[[,,,,,,,,,,,,,,,<<<<<<<<______>>>>>>>><<<<<<-<<<-<<___>>->>>>>>>>>,,,,,,,,,,,,,,,((((((,,,<<<____>>><<<<____>>>>,<<<<<<<<<<<-----<<<<-<<<<-<<-<<--<<<<<_________>>>>>-->>->>->>>>>>>>------->>>>>>->>>>>))))))]]]]]]]]::::::::::::::
#=GC RF                    AAAuuauacgaaGGGAcCCAACACAGaaaauucaUUUUAUugaauuuuaCacuuAuGcGCaAGUuGGgCaaaguGuCUUAUUUUUUuaAAGuacuucAAAGuaAAAUuaCacGuUAAUaCguAGuauuaauGGCGAGACuCCuGaGGGAGCAGuGCCaGcCGAAGACCgAGgCuGAGaCGGCACCCuaGGaAAGCGAAGCCauuCaauaCgaaguaucguauaaAUAGAGAACAGCAG
//
# STOCKHOLM 1.0

#=GF AC   RF02578
#=GF ID   tsr25
#=GF DE   S. aureus tsr25 small RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   63.00
#=GF TC   63.90
#=GF NC   50.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26861020
#=GF RT   Genome-wide Annotation, Identification, and Global Transcriptomic Analysis
#=GF RT   of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
#=GF RA   Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN
#=GF RL   MBio. 2016;7:e01990-e01915.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



BX571857.1/1456102-1456281 UAAUAGUAGUUGAAAAUGAUUAUCAAUACCACAUAGAACAUCCC---CCCACAACGUUUCGUUCUUGUUGGAUUGGUCAUUUUCAAAUAUUCCCCUUUUAUAUGCCCGUAAAAGACAAUAUACGUUAUAACAACGUUUUAUAAAAGCAGUAAACCCUUACGACACUUUAGGUUUACUGCUUUU
CP000736.1/1549316-1549498 UAAUAGUAGUUGAAAAUGAUUAUCAAUACCACAUAGAACAUCCCCCCCCCACAACGUUUCGUUCUUGUUGGAUUGGUCAUUUUCAAAUAUUCCCCUUUUAUAUGCCCGUAAAAGACAAUAUACGUUAUAACAACGUUUUAUAAAAGCAGUAAACCCUUACGACACUUUAGGUUUACUGCUUUU
CP000255.1/1442862-1443042 UAAUAGUAGUUGAAAAUGAUUAUCAAUACCAUAUAGAACAUCCCC--CCCACAACGUUUCGUUCUUGUUGGAUUGGUCAUUUUCAAAUAUUCCCCUUUUAUAUGCCCGUAAAAGACAAUAUACGUUAUAACAACGUUUUAUAAAAGCAGUAAACCCUUACGACACUUUAGGUUUACUGCUUUU
#=GC SS_cons               ::::<<<<-<<<<<<<<<<<---<<<<-<<<---<<<<<______.._____________>>>>>--->>>>>>>>>>>>>>>>>>->>>>,,,<<<<<<<______>>>>>>>,,,,,,,<<<<<_____>>>>>,,,,,<<<<<<<<<<<<<<______________>>>>>>>>>>>>>>
#=GC RF                    UAAUaguaGuuGaaaauGacUAUCaauACCacAUaGaaCAUCCCc..CCCACAACGUUUCGuuCuUGUuGGauuGguCauuuuCaaAuacuCCCCuuuuacAUGCCCguaaaaGACAAUAUaCGuuAUAACaaCGuUUUAUaaaaGCaGuaaaCCCUUACGACACUUUAGGuuuaCuGCuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02579
#=GF ID   tsr26
#=GF DE   S. aureus tsr26 small RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   141.00
#=GF TC   141.00
#=GF NC   50.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26861020
#=GF RT   Genome-wide Annotation, Identification, and Global Transcriptomic Analysis
#=GF RT   of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
#=GF RA   Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN
#=GF RL   MBio. 2016;7:e01990-e01915.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



CP002643.1/2737445-2737565 GCUUAUUAUUUUCAUAAACGAUUUUCUAAAAUCCUUUACGAAAUUUUUAAUAAAAAUCACAUCCCAGUUAUUUUUUUAACACUUAUCUUUUGAUAAGUGCUUU-UUUGUUUUAAAGCCUCCA
CP000255.1/1641611-1641732 GCUUAUUAUUUUCAUAAACGAUUUUCUAAAAUCCUUUACGAAAUUUUUAAUAAAAAUCACAUCCCAGUUAUUUUUUUAACACUUAUCUUUUGAUAAGUGCUUUUUUUGUUUUAAAGCCUCCA
#=GC SS_cons               ((((,,,,,<<<<-<<<<-<<<<<____>>>>>->>>>->>>>,,,,,,,,<<<<<<-<<______>>->>>>>>,,,,<<<<<<<<____>>>>>>>>,,,,,,,,,,,,,,)))):::::
#=GC RF                    GCuuAUUAUuuuCAuaaaCGauuuUCUAaaauCCuuuaCGaaaUUUUUAAUaaaaauCaCAUCCCAGuUauuuuuUUAACaCuuauCUUUUGauaaGuGCUUUuUUUGUUUUAaaGCCUCCA
//
# STOCKHOLM 1.0

#=GF AC   RF02580
#=GF ID   tsr31
#=GF DE   S. aureus tsr31 small RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   50.00
#=GF TC   60.50
#=GF NC   49.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26861020
#=GF RT   Genome-wide Annotation, Identification, and Global Transcriptomic Analysis
#=GF RT   of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
#=GF RA   Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN
#=GF RL   MBio. 2016;7:e01990-e01915.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



ACJS01000063.1/24795-24726 UCCUUUAAAUAGGACACGUGUAUAAAAUUUAUACGCUCCCCUUACAAAAUUUGUGAGAGGGAGCGUUUUU
ACPZ01000047.1/53336-53268 UCCUUUAAAUAGGACACGUGUAUAAAUGUUAUACGCUCCCCUUACA-AAUAUGUGAGAGGGAGCGUUUUU
AP006716.1/914948-915016   UCCUUUAAAUAGGACACGUGUAUAAAUCAUAUACGCUCCCCUUACAGA-UAUGUGAGAGGGAGCGAUUUU
CP000255.1/2245035-2244966 UCCUUUAAAUAGGACACGUGUAUAAAAUUUAUACGCUCCCCUUACAGAAUUUGUGAGAGGGAGCGUUUUU
#=GC SS_cons               <<<<______>>>>------------------<<<<<<<<<<<<<<_____>>>>>>->>>>>>>>::::
#=GC RF                    UCCUUUAAAUAGGACACGUGUAUAAAuuuUAUaCGCUCCCCUuACAgAAUaUGUgAGAGGGAGCGuUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02581
#=GF ID   tsr32
#=GF DE   S. aureus tsr32 small RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   98.00
#=GF TC   98.20
#=GF NC   46.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26861020
#=GF RT   Genome-wide Annotation, Identification, and Global Transcriptomic Analysis
#=GF RT   of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
#=GF RA   Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN
#=GF RL   MBio. 2016;7:e01990-e01915.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



ACSS01000004.1/14129-14279 UGGGUGAUGCGGAAAAUUUGGGUGAUCAAUUGUUUAUAUGCAUCAACAUUCUUUGUGGAUUGUUUGACAGUAGACAGUCAUUUGUAUACGUUAACGAAUUUUGAAAAAUUGAAUCAUUAUUUAAUCAUAAUAUUCAUUGCGCACGCGCAAC
AFTT01000015.1/18644-18794 UGGGUGAUGCGGAAAAUUUGGGUGAUCGAUUGUUUAUAUGCAUCAACAUUCUAUGUGAAUUGUUUGACAGUAGACAGUCAUAUGUAUACGUUAACGAAUUUUGAAAAAUUGAAUCAUUAUUUAAUCAUAAUAUUCAUUGCGCACGCGCAAC
AJ938182.1/2230095-2230243 UUUUCGUUGC--AAUUUUUGGGUGAUCGAUUGUUUAUAUGCAUCAACAUUCUUUGUGGAUUGUUUGACAGUAGAAAGUCAUUUGUAUACGUUAACAAAUUUUGAAAAAUUGAAUCAUUAUUUAAUCAUAAUAUUCAUUGCGCACGCGCAAC
CP000255.1/2337922-2338072 UGGGUGAUGCGGAAAAUUUGGGUGAUCGAUUGUUUAUAUGCAUCAACAUUCUUUGUGGAUUGUUUGACAGUAGACAGUCAUUUGUAUACGUUAACGAAUUUUGAAAAAUUGAAUCAUUAUUUAAUCAUAAUAUUCAUUGCGCACGCGCAAC
#=GC SS_cons               ((-(((-((((-((----((((((,,,<<<<<<<<<<-<<<<--<<<<-<<<____>>>->>>>>>->>>>>>>>>>>><<<<<<________>>>>>>,,,,,,,,<<<<<<<____>>>>>>>,,,,,))))))))-)))))))-))::
#=GC RF                    ugggcGauGCGGaaaaUUuGggugAUCgacugucuacAuGCaUCaaCaUuccuUGUggaUuGuuuGACaguagacagucauucGuAUACGUUAaCgaauUUUGAAAAauugaauCAUUauucaauCAUAAcaccCauuGCGCaCgcGcaAC
//
# STOCKHOLM 1.0

#=GF AC   RF02582
#=GF ID   tsr33
#=GF DE   S. aureus tsr33 small RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   109.00
#=GF TC   109.40
#=GF NC   42.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26861020
#=GF RT   Genome-wide Annotation, Identification, and Global Transcriptomic Analysis
#=GF RT   of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
#=GF RA   Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN
#=GF RL   MBio. 2016;7:e01990-e01915.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



FR821777.2/2293185-2293101 AAAGUCAUUUAUUCAGCAUUGGGACAUAACAUUAACUUAAAAUUUAAAUAUUGAAGAUGCUUUAAUUAAAGUUAAAGACUAGCAA
CP000255.1/2410648-2410564 GAAGUUAUUUAUUCAGCAUUGGGACAUAAAAUUAACUUAAAAUUUAAAUAUUGAAGAUGCUUUAAUUAAAGUUAAAGACUAGCCA
#=GC SS_cons               :<<<<<<<<<<<<<________>>->>>>>-->>>>>>---------------------<<<<<<<____>>>>>>>::::::::
#=GC RF                    aaaGuuauuuauuCAGCAUUGGGaCauaaaAUuaaCuuAAAAUUUAAAUAUUGAAGAUGCuuuaauUAAAguuaaaGACUAGCaA
//
# STOCKHOLM 1.0

#=GF AC   RF02583
#=GF ID   Teg23
#=GF DE   S. aureus Teg23 small RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Carroll et al, PMID:26861020
#=GF SS   Predicted; RNAalifold
#=GF GA   166.00
#=GF TC   166.10
#=GF NC   41.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26861020
#=GF RT   Genome-wide Annotation, Identification, and Global Transcriptomic Analysis
#=GF RT   of Regulatory or Small RNA Gene Expression in Staphylococcus aureus.
#=GF RA   Carroll RK, Weiss A, Broach WH, Wiemels RE, Mogen AB, Rice KC, Shaw LN
#=GF RL   MBio. 2016;7:e01990-e01915.
#=GF WK   Bacterial_small_RNA
#=GF SQ   6



AFNP01000069.1/95084-95516 UUAGUGAUGACUAAGUUUUACGCCAACAAGGUUUCAAGAGCCUUGUUGGCUUUUUUAAUUUCUAUGA----AAAAAAUCGAAUUGGUAAAAAUCUCAAAAUUUCGAUUUUCACCAAUCCGAUUCACUCUGUAAUAAAGAAUAAACAACAUACAGCCAUUGACACACCCAAAUUUAGGCACGUCAAAUCGGCUAUACAUUGAUAAAUUUUUAGUUAAAGUACUUACAAAUAUACUUGCCUUCAAAUUCUCAAUUAAUUUAGUCAUUACAAAUCAUGACAUAAAACUUACAUUACAUAUAUCAACAUGUUCCGCUACAAAACAUAUUCAGUAUAUGUAUAGAGGAUAUUUAUUCUAAGUUAAAACCUUUUCAAAUUAUAACCGCUACAAUUAUAAAUGAUUAAAGUGUUUCAACAUAUUAUAUAUAUUCCACGCUCACA
AFTM01000028.1/93549-93984 UUUGUGAUGAAAGUGAAUUAAGCCAACAAGGUUUCAAGAGCCUUGUUGGCUUUUUUAAUUUCUA-GACAUCAAAAAAUCGGAUUGGUAAAAAUCUCAAAACUUCGAUUUCCACCAAUCCGAUUCACUCUGUAAUAAAGAAUAAACAACAUACAGCCAUUGACACACCCAAAUUUAGGCGCGUCAAAUCGGCUAUACAUUGAUAAAUUUUUAGUUAAAGUACUUACAAAUAUACUUGCCUUCAAAUUCUCAAUUAAUUUAGUCAUUACAUGCCAUGACAUAAAGCUUACAUUACAUAUAUUAACAUGUUCCGCUACAAAACAUAUUCAGUAUAUGUAUAGAGGAUAUUUAUUCUAAGUUAAAACCUUUUCAAAUUAUAACCGCUACAAUUAUAAAUGAUUAAAGUGUUUCAACAUAUUAUAUAUAUUCCACGCUCACA
FR714927.1/2276351-2276783 UUAGUGAUGGCUAUGUUUUACGCCAACAAGGUUUCAAGAGCCUUGUUGGCUUUUUUAAUUUCUAUGA----AAAAAAUCGAAUUGGUAAAAAUCUCAAAAUUUCGAUUUUCACCAAUCCGAUUCACUCUGUAAUAAAGAAUAAACAACAUACAGCCAUUGACACACCCAAAUUUAGGCAUGUCAAAUCGGCUAUACAUUGAUAAAUUUUUAGUUAAAGUACUUACAAAUAUACUUGCCUUCAAAUUCUCAAUUAAUUUAGUCAUUACAAAUCAUGACAUAAAACUUACAUUACAUAUAUCAACAUGUUCCGCUACAAAACAUAUUCAGUAUAUGUAUAGAGGAUAUUUAUUCUAAGUUAAAACCUUUUCAAAUUAUAACCGCUACAAUUAUAAAUGAUUAAAGUGUUUCAACAUAUUAUAUAUAUUCCACGCUCACA
CP000253.1/2362802-2363233 UUAGUGAUGGCUAUGU-UUACGCCAACAAGGUUUCAAGAGCCUUGUUGGCUUUUUUAAUUUCUAUGA----AAAAAAUCGAAUUGGUAAAAAUCUCAAAAUUUCGAUUUUCACCAAUCCGAUUCACUCUGUAAUAAAGAAUAAACAACAUACAGCCAUUGACACACCCAAAUUUAGGCAUGUCAAAUCGGCUAUACAUUGAUAAAUUUUUAGUUAAAGUACUUACAAAUAUACUUGCCUUCAAAUUCUCAAUUAAUUUAGUCAUUACAAAUCAUGACAUAAAACUUACAUUACAUAUAUCAACAUGUUCCGCUACAAAACAUAUUCAGUAUAUGCAUAGAGGAUAUUUAUUCUAAGUUAAAACCUUUUCAAAUUAUAACCGCUACAAUUAUAAAUGAUUAAAGUGUUUCAACAUAUUAUAUAUAUUCCACGCUCACA
BX571856.1/2452124-2452559 UUUGUGAUGAAAGUGAAUUAAGCCAACAAGGUUUCAAGAGCCUUGUUGGCUUUUUUAAUUUCUA-GACAUCAAAAAAUCGGAUUGGUAAAAAUCUCAAAACUUCGAUUUCCACCAAUCCGAUUCACUCUGUAAUAAAGAAUAAACAACAUACAGCCAUUGACACACCCAAAUUUAGGCGCGUCAAAUCGGCUAUACAUUGAUAAAUUUUUAGUUAAAGUACUUACAAAUAUACUUGCCUUCAAAUUCUCAAUUAAUUUAGUCAUUACAUGCCAUGACAUAAAGCUUACAUUACAUAUAUUAACAUGUUCCGCUACAAAACAUAUUCAGUAUAUGUAUAGAGGAUAUUUAUUCUAAGUUAAAACCUUUUCAAAUUAUAACCGCUACAAUUAUAAAUGAUUAAAGUGUUUCAACAUAUUAUAUAUAUUCCACGCUCACA
CP000255.1/2416003-2416434 UUAGUGAUGGCUAUGU-UUACGCCAACAAGGUUUCAAGAGCCUUGUUGGCUUUUUUAAUUUCUAUGA----AAAAAAUCGAAUUGGUAAAAAUCUCAAAAUUUCGAUUUUCACCAAUCCGAUUCACUCUGUAAUAAAGAAUAAACAACAUACAGCCAUUGACACACCCAAAUUUAGGCAUGUCAAAUCGGCUAUACAUUGAUAAAUUUUUAGUUAAAGUACUUACAAAUAUACUUGCCUUCAAAUUCUCAAUUAAUUUAGUCAUUACAAAUCAUGACAUAAAACUUACAUUACAUAUAUCAACAUGUUCCGCUACAAAACAUAUUCAGUAUAUGUAUAGAGGAUAUUUAUUCUAAGUUAAAACCUUUUCAAAUUAUAACCGCUACAAUUAUAAAUGAUUAAAGUGUUUCAACAUAUUAUAUAUAUUCCACGCUCACA
#=GC SS_cons               ::[[[[-[[[,,,,,,,,,,,<<<<<<<<<<<<<___>>>>>>>>>>>>>,,,,,,,,,,,,,,,,,....,,,,<<<<<-<<<<<<-<<<<<<__________>>>>>>->>>>>>->>>>>,,(((((((,,,,,,,,,,,,,,,,,,,,<<<<-<<<<<<--<<________>>-->>>>>>--->>>>,,,,<<<<<--<<<<<--<<---<<<<<__________>>>>>-->>-->>>>>->>>>>,,,<<<<<<<<<________>>>>>->>>>,,,,,,,,,,<<<<<<<----<<<<<_________>>>>>----->>>>>>>)))))))<<<<<-<<<--<<-<<<-<<<<<<<<<<<--<<<<<<_________>>>>>>->>>-->>>>->>>>->>>->>-->>>->>>>>]]]]]]]::::
#=GC RF                    UUaGcGAuGgcuauGuaUUAcGCCaaCaaGGcucCAAgagCCuuGuuGGCUUUUUUAAUUUCUAUGA....AAAAaauCGaauuGGuAgaaauCUCAAAAuUUCGauuucCaCCaauCCGauuCACuCuguaAUAAAGAAUAAACAACAUACaGCCAuuGaCgCACCCAAAUUUAGGCacGuCaaAUCGGCuAUACauuGaUAaauuuUUaGUUAaaGuaCUUACAAAUAuaCuuGCCuUCaaauuCuCaauUAAuuuaGuCauUACAaauCauGaCAuaaaaCUUACAUUACauauaccAACauGuuCCGCUACAAaaCauAUUCAguauauGuacaGaGgauauUuauUCuaAGuuAaaaCCuuuuCaAAuuauaaCCGCUACAAuuauaaAuGaUUaaaGUGuuuCaaCAuaUUauaUauauccCaCgCuCACA
//
# STOCKHOLM 1.0

#=GF AC   RF02584
#=GF ID   KRAS_3UTR
#=GF DE   KRAS 3' UTR cis-regulatory element
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   49.00
#=GF TC   49.70
#=GF NC   47.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF RN   [1]
#=GF RM   26930719
#=GF RT   Cis-acting elements in its 3' UTR mediate post-transcriptional regulation
#=GF RT   of KRAS.
#=GF RA   Kim M, Kogan N, Slack FJ
#=GF RL   Oncotarget. 2016; [Epub ahead of print]
#=GF CC   AU-rich 49 nt fragment in KRAS 3'UTR. Its sequence but not the secondary
#=GF CC   is necessary and sufficient for reporter repression in HeLa cells. 
#=GF WK   KRAS
#=GF SQ   2



CABD02077211.1/12823-12775 CCAAAAUAUUAUAUUUUUUCUAUAAAAAGAAAAAAAUUGAAAAAAAUUA
M54968.1/1340-1388         CCAAAAUAUUAUAUUUUUUCUAUAAAAAGAAAAAAAUGGAAAAAAAUUA
#=GC SS_cons               :::::::::::::<<<<<<<<<<____________>>>>>>>>>>::::
#=GC RF                    CCAAAAUAUUAUAUUUUUUCuAUAAAAAGAAAAAAAUgGAAAAAAAUUA
//
# STOCKHOLM 1.0

#=GF AC   RF02585
#=GF ID   HCV_package
#=GF DE   Hepatitis C virus RNA packaging signal
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:26972799
#=GF GA   37.00
#=GF TC   37.60
#=GF NC   36.70
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019072; viral genome packaging;
#=GF RN   [1]
#=GF RM   26972799
#=GF RT   Identification of novel RNA secondary structures within the hepatitis C
#=GF RT   virus genome reveals a cooperative involvement in genome packaging.
#=GF RA   Stewart H, Bingham RJ, White SJ, Dykeman EC, Zothner C, Tuplin AK,
#=GF RA   Stockley PG, Twarock R, Harris M
#=GF RL   Sci Rep. 2016;6:22952.
#=GF WK   Hepatitis_C_virus
#=GF SQ   3



AB047644.1/2899-2927 CCUGACCCUGGGGGAGGCCAUGGUUCAGG
AF238483.1/2865-2893 CCUGACCUUGGGGGAAGCCAUGAUCCAGG
AB047639.1/2899-2927 CCUGACCCUGGGGGAAGCCAUGAUUCAGG
#=GC SS_cons         <<<<<---<<<______>>>---->>>>>
#=GC RF              CCUGaCCcUGGGGGAAGCCAUGAUuCAGG
//
# STOCKHOLM 1.0

#=GF AC   RF02586
#=GF ID   HCV_package-SL733
#=GF DE   Hepatitis C virus RNA packaging signal 733
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:26972799
#=GF GA   32.50
#=GF TC   32.50
#=GF NC   32.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019072; viral genome packaging;
#=GF RN   [1]
#=GF RM   26972799
#=GF RT   Identification of novel RNA secondary structures within the hepatitis C
#=GF RT   virus genome reveals a cooperative involvement in genome packaging.
#=GF RA   Stewart H, Bingham RJ, White SJ, Dykeman EC, Zothner C, Tuplin AK,
#=GF RA   Stockley PG, Twarock R, Harris M
#=GF RL   Sci Rep. 2016;6:22952.
#=GF WK   Hepatitis_C_virus
#=GF SQ   4



AB047639.1/733-758 CGACCUCAUGGGGUACAUCCCCGUCG
JN180460.1/733-758 CGACCUCAUGGGGUACAUCCCUGUCG
EF424625.1/732-757 CGACCUCAUGGGGUACAUUCCCGUCG
DQ835764.1/731-756 CGACCUCAUGGGGUACAUCCCAGUCG
#=GC SS_cons       <<<<---<<<_____>>>---->>>>
#=GC RF            CGACCUCAUGGGGUACAUCCCcGUCG
//
# STOCKHOLM 1.0

#=GF AC   RF02587
#=GF ID   HCV_package-SL4629
#=GF DE   Hepatitis C virus RNA packaging signal 4629
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:26972799
#=GF GA   30.90
#=GF TC   30.90
#=GF NC   30.80
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019072; viral genome packaging;
#=GF RN   [1]
#=GF RM   26972799
#=GF RT   Identification of novel RNA secondary structures within the hepatitis C
#=GF RT   virus genome reveals a cooperative involvement in genome packaging.
#=GF RA   Stewart H, Bingham RJ, White SJ, Dykeman EC, Zothner C, Tuplin AK,
#=GF RA   Stockley PG, Twarock R, Harris M
#=GF RL   Sci Rep. 2016;6:22952.
#=GF WK   Hepatitis_C_virus
#=GF SQ   2



AF238484.1/4595-4617 UACCAACUCAGGGAGAUGUGGUG
AB047639.1/4629-4651 UACCAGCUCAGGGAGAUGUGGUG
#=GC SS_cons         <<<<<--<<_____>>-->>>>>
#=GC RF              UACCAaCUCAGGGAGAUGUGGUG
//
# STOCKHOLM 1.0

#=GF AC   RF02588
#=GF ID   HCV_package-SL6067
#=GF DE   Hepatitis C virus RNA packaging signal 6067
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:26972799
#=GF GA   38.80
#=GF TC   38.80
#=GF NC   38.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000233; mature_transcript;
#=GF DR   GO; 0019072; viral genome packaging;
#=GF RN   [1]
#=GF RM   26972799
#=GF RT   Identification of novel RNA secondary structures within the hepatitis C
#=GF RT   virus genome reveals a cooperative involvement in genome packaging.
#=GF RA   Stewart H, Bingham RJ, White SJ, Dykeman EC, Zothner C, Tuplin AK,
#=GF RA   Stockley PG, Twarock R, Harris M
#=GF RL   Sci Rep. 2016;6:22952.
#=GF WK   Hepatitis_C_virus
#=GF SQ   3



AF169004.1/6067-6096 CGUGGGUCCGGGGGAGGGCGCGGUCCAAUG
AB047641.1/6067-6096 CGUGGGACCGGGGGAAGGCGCAGUCCAAUG
AB047639.1/6067-6096 CGUGGGACCGGGGGAGGGCGCGGUCCAAUG
#=GC SS_cons         <<<-<<<<<<__________>>>>>>->>>
#=GC RF              CGUGGGaCCGGGGGAGGGCGCGGuCCAAUG
//
# STOCKHOLM 1.0

#=GF AC   RF02589
#=GF ID   Spy779816
#=GF DE   S. pyogenes small RNA 779816
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Rhun et al, PMID:26580233
#=GF SS   Predicted; RNAalifold
#=GF GA   67.00
#=GF TC   67.40
#=GF NC   64.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26580233
#=GF RT   RNA sequencing uncovers antisense RNAs and novel small RNAs in
#=GF RT   Streptococcus pyogenes.
#=GF RA   Le Rhun A, Beer YY, Reimegard J, Chylinski K, Charpentier E
#=GF RL   RNA Biol. 2016;13:177-195.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



AE004092.1/779817-779905   GUAAAGAGACCUACGGCAAAGCAGGUUUUUACUAUACUAGAUUUGCCUCGCGCUCAGAGUCGCCAAACUUUGAGAGCGUGGGGCUUUUU
AM295007.1/1308523-1308436 GUAAAGAGACCUAC-UUAAAGCAGGUUUUUACUAUACUAGAUUCGCCUCACGCUCAGAGUCGCCAAACUUUGAGAGCGUGGGGUUUUUU
CP002471.1/1834190-1834105 GUAAAAAGACCUAC---AAAAUAGGUUCUUUACUAUCCUUUCUGAUCCCAUGCUCAGAGUCGCCAAACUUUGAGAGCGUGGGAUUUUUU
CP000829.1/750868-750954   GUAAAGAGACCUACUGCGAAGCAGGUUUUUACUAUACUAGAUUUGCCUCACGCUCGCACCGACCAAAAUUU--GAGCGUAGGGCUUUUU
#=GC SS_cons               ::::<<<<<<<<--.<<___>>>>>>>>>>--------------<<<<<<<<<<<<<<<<______>>>>>-->>>>>>>>>>>:::::
#=GC RF                    GUAAAgagACCUAC.gcAAAgcAGGUuuuUacuauaCuagauUugcCcCacGCUCagAgucgCCAAacUuuGAGAGCguGgGgcUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02590
#=GF ID   Spy1186876
#=GF DE   S. pyogenes small RNA 1186876
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Rhun et al, PMID:26580233
#=GF SS   Predicted; RNAalifold
#=GF GA   208.00
#=GF TC   208.20
#=GF NC   43.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   2658233
#=GF RT   Velocity profiles in the normal human abdominal aorta: a comparison
#=GF RT   between ultrasound and magnetic resonance data.
#=GF RA   Vieli A, Moser U, Maier S, Meier D, Boesiger P
#=GF RL   Ultrasound Med Biol. 1989;15:113-119.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



CP000829.1/1138494-1138252 UAAGACUUAUGAAAGAGAAAACCGCCGUAUGUUUACUAUUAUGAUCAUUGGUUUAGCUGUAUUUUCAAUAAUUAAAAUCAUUCUAUUUUUCUAUUUUUAUCAGCAAUUUGAGCGCAAGCAAAAAAGAAAAGUUGAAUCAAACAACCAGCAAAGACAGUCCCAAGAAAGUGACGCUGUCCCUUCAAAAAAAUUCCCAUUUUAAA---AAGCUUGGAAAGUGUACAAAGUGCACAUUUCCAAGCUUUU
AM295007.1/692671-692913   UAAGACUUAUGAAAGAGAAAACCGCCGUAUGUUUACUAUUAUGAUCAUUGGUUUAGCUGUAUUUUCAAUAAUUAAAAUCAUUCUAUUUUUCUAUUUUUAUCAGCAAUUUGAGCGCAAGCAAAAAAGAAAAGUUGAAUCAAACAACCAGCAAAGACAGUCCAAAGAAAGUGACGCUGUCCCUUCAAAAAAAUUCCCAUUUUAAA---AAGCUUGGAAAGUGUACAAAGUGCACAUUUCCAAGCUUUU
AP010935.1/1427643-1427398 UAAGACUUAUGAAAGAGAAAACCGCCGUAUGUUUACUAUUAUGAUCAUUGGUUUAGCUGUAUUUUCAAUAAUUAAAAUCAUUCUAUUUUUCUAUUUUUAUCAGCAAUUUGAGCGCAAGCAAAAAAGAAAAGUUGAAUCCACUGACCAGCAAAAACAGGCCCAAGAAAAUGAUGCCGUCCCUUCAAAAAAAUUUCCAUUUUAAAAAGAAGCUUGGAAAGUGUACAAAGUACCACUCUCCAAGCUUCU
#=GC SS_cons               ::::::::::<<<<<<--------<<<<-<<<-<<<______>>>->>>>>>>--------->>>>>>,,,,,,,,,,,<<<<-<<<<<<<<-<<<<-----<<_______>>------>>>>->>>>>>>>->>>>,,,,,,,,,,,,,,,<<<<<<--<<______>>-->>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,...<<<<<<<<<<<<<<<<<___>>>>>>->>>>>>>>>>>::
#=GC RF                    UAAGACUUAUgagagaGAAAACCGccguAuguUuaCUAUUAUGauCauugguuUAGCUGUAUuuucaaUAAUUAAAAUCauuCUauuuuuCuAuuuuUAUCAGCAAUUUGAGCGCAAGCaaaaAaGaaaaguUGaauCaAacaACCAGCAAAgaCaGcCCcaAGAAAgugAcgCuGucCCUUCAAAAAAAUUcCCAUUUUAAA...aaGCuuGGaaaguGcaCAAAGugCacauuuCCaaGCuuuU
//
# STOCKHOLM 1.0

#=GF AC   RF02591
#=GF ID   Spy1786666
#=GF DE   S. pyogenes small RNA 1786666
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Rhun et al, PMID:26580233
#=GF SS   Predicted; RNAalifold
#=GF GA   64.00
#=GF TC   64.30
#=GF NC   57.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26580233
#=GF RT   RNA sequencing uncovers antisense RNAs and novel small RNAs in
#=GF RT   Streptococcus pyogenes.
#=GF RA   Le Rhun A, Beer YY, Reimegard J, Chylinski K, Charpentier E
#=GF RL   RNA Biol. 2016;13:177-195.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



AE004092.1/1786665-1786750 UAGGGCAAACU-AAAAGCGUAGUAUUUAAACUACGCUAGUUCUUGCCUGCUGAACUCAUUGUGUAAAGGACCUGUAAAGGUCUUUUU
CP000260.1/1848341-1848427 UAAGGCAAACUAAAAAGCGUAGUAUUUAAACCACGCUAGUUCUUGCCUGCUGAACUCAUUGUGUAAAGGACCUGUAAAGGUCUUUUU
#=GC SS_cons               ::<<<<<<<<<----<<<<<<<<______>>>>>>>>>>>-->>>>>>----------------<<<<<<<<<____>>>>>>>>>:
#=GC RF                    UAaGGCaaaCuAAAAaGCGugGuAUUUAAaCcaCGCuaGuUCuuGCCuGCUGAACUCAUUGUGUaaagGaCCuGUAAaGGuCuuuuU
//
# STOCKHOLM 1.0

#=GF AC   RF02592
#=GF ID   Spy392987
#=GF DE   S. pyogenes antisense RNA 392987
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAalifold
#=GF GA   47.00
#=GF TC   47.50
#=GF NC   46.00
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26580233
#=GF RT   RNA sequencing uncovers antisense RNAs and novel small RNAs in
#=GF RT   Streptococcus pyogenes.
#=GF RA   Le Rhun A, Beer YY, Reimegard J, Chylinski K, Charpentier E
#=GF RL   RNA Biol. 2016;13:177-195.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



CP000829.1/406997-407059   AUGGGAAUAAAUCUCUUUCUAGUGAAGUGUCGUAACUCUACUAUACAGGAUUUAUUCCUUUUU
AE004092.1/392987-393048   AUGGGAAUAAAUCUCUUUCUAGUA-AGUGUCGCAACUCUACUAUACAGGAUUUAUUCCUUUUU
AM295007.1/1451796-1451734 AUGGGAAUGAAUCUCUUUCUAGUGAAGUGUCGUAACUCUACUAUACAAGAUUUAUUCCUUUUU
#=GC SS_cons               ::<<<<<<<<<<<-<<---<<<<<-<<<______>>>->>>>>--->>>>>>>>>>>>>::::
#=GC RF                    AUgGGAAUaAAUCUcUUUCUAGUgAAGUGUCGuAACUCuACUAUACAgGAUUuAUUCCuUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02593
#=GF ID   NsiR8
#=GF DE   Nitrogen stress-induced RNA 8
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAalifold
#=GF GA   61.00
#=GF TC   61.60
#=GF NC   43.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0043158; heterocyst differentiation;
#=GF RN   [1]
#=GF RM   26870012
#=GF RT   Identification of Conserved and Potentially Regulatory Small RNAs in
#=GF RT   Heterocystous Cyanobacteria.
#=GF RA   Brenes-Alvarez M, Olmedo-Verd E, Vioque A, Muro-Pastor AM
#=GF RL   Front Microbiol. 2016;7:48.
#=GF CC   Transcribed in developing heterocysts. Transcription requires HetR
#=GF CC   suggestingthat it could be related to the differentiation of heterocysts. 
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



CP000117.1/1926385-1926556 AUGAGAAUUGCAAGGAUGGAAAUGAUUAACAAUCCAAGUACAGCAUAAAUAAACGUUCUUGUUGUUUACAUCAUUGAUAUUCCUUUCAAUCUAUUAAAUUUUAUUUUUCCUAUUUUCCAGAGUCCAAGGUGUAUUGCCACUUUCAAGCUACUUCGACGGGGUAAAACCCGUC
BA000019.2/4547556-4547385 AUGGGAAUUGUGAGGAUAGAAAUGAUUAACAGUCCAAGUACGGCAUAGAUCAACGUUCUUGUUGUUCACAUCAUUGAUAUUCCUUUCAAUCUAUUAAAUUUUAUUUUUCCUAUUUUCCAGAGUCCAAGGUGUAUUGCCACUUUCAAGCUACUUCGACGGGGUAAAACCCGUC
#=GC SS_cons               <<<<<<<<<<-<<<<<<<--<<<<<<-<<<<<--<<<<-<<<___________>>>->>>>>>>>>--->>>>>>-->>->>>>>->>>>----------------->>>>>>,,,,,<<<<<--<<<<<<______>>>>>>--->>>->>,,<<<<<<______>>>>>>
#=GC RF                    auggGaauuGugaGGaugGAaauGauUaaCagUCCaaGUaCgGCAUAaAUaAAcGuUCuuGcuGuuuACauCauuGAcaUuCCucUCaauCUAUUAAAUUUUAUUUUuCccauUUUCCaGaGcCCaagGuGUAUUGCCaCcuuCAAgCuACuUCGaCGGGGUAAAACCCGuC
//
# STOCKHOLM 1.0

#=GF AC   RF02594
#=GF ID   NsiR9
#=GF DE   Nitrogen stress-induced RNA 9
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAalifold
#=GF GA   90.00
#=GF TC   90.20
#=GF NC   39.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0043158; heterocyst differentiation;
#=GF RN   [1]
#=GF RM   26870012
#=GF RT   Identification of Conserved and Potentially Regulatory Small RNAs in
#=GF RT   Heterocystous Cyanobacteria.
#=GF RA   Brenes-Alvarez M, Olmedo-Verd E, Vioque A, Muro-Pastor AM
#=GF RL   Front Microbiol. 2016;7:48.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



CP000117.1/4487021-4486899 AUUCACGUUUGUGACUGUGAGUGUGGCUAAUCACUAACUAGCCACUGUUGCUGAUUGUUGGGAAGGUGUAGGGAUAACUAUUAAAAGUUUUCCCUGCAUGACGGGCAUCUAUUUUAGAUGCCC
CP001037.1/6308955-6308834 UACUAUAUUCACGUCUGUGAGUGUGACUAAUACCUAAUUAGUCACUGUUGCUGAUUGUUGGGAAGGUGUAGGGACAACCCUUUAGGGUUU-UCCUGCAUGACGGGCAUCUCUUGUAGAUGCCC
BA000019.2/4451847-4451969 AUUCACGUUUGUGACUGUGAGUGUGGCUAAUCACUAACUAGCCACUGUUGCUGAUUGUUGGGAAGGUGUAGGGAUAACUAUCAAAAGUUUUCCCUGCAUGACGGGCAUCUAUUUUAGAUGCCC
#=GC SS_cons               :::::<-<<<-<<<<-<<-<<<<<<<<<<_________>>>>>>>---->>>->>->>>>->>>-><<<<<<<<-<<<<______>>>>->>>>>>>>,,,,<<<<<<<<<___>>>>>>>>>
#=GC RF                    auuuAcguucgcgaCUguGaGcGuGgCuaAUaaCUAAuuaGcCaCUGUUgCuGacUGucgGgaaGguGcaGGgauaaCcaUuaAagGuuUucCCugCaUGACGGGCauCuaUUuuaGauGCCC
//
# STOCKHOLM 1.0

#=GF AC   RF02595
#=GF ID   EBv-sisRNA-1
#=GF DE   Epstein-Barr virus stable intronic sequence RNA 1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Moss at al; PMID:23937650
#=GF SS   Predicted; PMID:23937650
#=GF GA   58.00
#=GF TC   58.00
#=GF NC   44.50
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   23937650
#=GF RT   Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures
#=GF RT   and a  novel stable intronic sequence RNA.
#=GF RA   Moss WN, Steitz JA
#=GF RL   BMC Genomics. 2013;14:543.
#=GF WK   Epsteinâ€“Barr_virus_stable_intronic-sequence_RNAs
#=GF SQ   8



V01555.2/45340-45420     GUAAGUGGAC-UUUAAUUUUUUCUGCUAAGCCCAACACUCCACCACACCCAGGCACACA--------CUACA----CACACCCACCCGUCU-CAG
AY037858.1/27403-27483   GUAAGUGGAC-UUUCAUUUAUUCCGCUCAGCCCACCACUCCACCACACCCAGGCACACA--------CUACA----CACAGCCACCCAUCU-CAG
AJ311196.1/97-177        GUAAGUGGAC-UUUAAGUUUUUCUGCUAAGCCCUACACUCCACCACACCCAGGCACACA--------CUACA----CACACCCACCCGUCU-CAG
AJ311194.1/97-177        GUAAGUGGAC-UUUAAGUUUUUCUGCUAAGCCCAACAUUCCACCACACCCAGGCACACA--------CUACA----CACACCCGCCCGACU-UAG
AJ311199.1/97-177        GUAAGUGGAC-UCUUAGUUACUCUGCUCAGCCCACCACUCCACCACACCCAGGCACACA--------CUACA----CACAGCCACCCGUCU-CAG
X77781.1/85-165          GUAAGUGGAC-UUUCAGUUAUUCUGCUCAGCCCACCACUCCACCACACCCAGGCACACA--------CUACA----CACAGCCACCCGUCU-CAG
AF200364.1/8823-8904     GUAAGUGGACUUUUCCAUUUUUCUGCUAAGCCCAACACUCCACCACAGCCAGGCACACA--------CUACA----CACACCCGCCCAUCU-CAG
AF319782.2/128411-128321 GUAAGUGU---CUUUAAUUUUUAAGCCUCAUGCA-CAGCACACAAACACCAGGCACACAAACAGCAGCCACACUUCCACACGCGCCCGUCUCCAG
#=GC SS_cons             :::<<<<<<_.__________>>>>>>--<<<___________________>>>:::::........:::::....:::::::::::::::.:::
#=GC RF                  GUAaGUggAC.UUUuAaUUuUUcuGCuaAGcCCAaCAcUcCACcAcAcCCAGgCACACA........CUACA....CACAccCaCCCGUCU.CAG
//
# STOCKHOLM 1.0

#=GF AC   RF02596
#=GF ID   cyano_het_sRNA
#=GF DE   Cyanobacteria heterocyst sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Brendes-Alvarez et al, PMID:26870012
#=GF SS   Predicted; PMID:26870012
#=GF GA   35.70
#=GF TC   35.70
#=GF NC   35.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26870012
#=GF RT   Identification of Conserved and Potentially Regulatory Small RNAs in
#=GF RT   Heterocystous Cyanobacteria.
#=GF RA   Brenes-Alvarez M, Olmedo-Verd E, Vioque A, Muro-Pastor AM
#=GF RL   Front Microbiol. 2016;7:48.
#=GF WK   Bacterial_small_RNA
#=GF SQ   5


BA000019.2/4547237-4547182 GGGAUGUUGUUAUGCACUGGAUUU-AUAGAGAGGUUUGGUGGUGAGCCAAACCUUUU
CP000117.1/1926704-1926760 GGGAUGUUGUUAUGCACUGGAUUUUAUAGAAAGGUUUGGUGGUGAGCCAAACCUUUU
CP002059.1/1330171-1330116 GGGAUGUUGUUAUGCACUGGAUUU-AUAGCGAGGUUUGGUUAACCACCAAACCUUUU
AAVW01000015.1/27277-27222 GGGAUGUUGUUAUGCACUGGAUUU-AUAGUGAGGUUUGGUGAUCAGCCAAACCUCUU
CP001037.1/871141-871196   GGGAUGUUGUUAUGCACUGGAUUU-AUAUAGAGGUUUGGCGGUGAGCCAAACCUUUU
#=GC SS_cons               :<<-<<<______>>>>>------.-----<<<<<<<<<<_____>>>>>>>>>>::
#=GC RF                    GGGAUGUUGUUAUGCACUGGAUUU.AUAGagAGGUUUGGcGgUgAgCCAAACCUcUU
//
# STOCKHOLM 1.0

#=GF AC   RF02597
#=GF ID   shuA_thermo
#=GF DE   shuA/chuA 5' UTR thermoregulator
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Kouse et al, PMID:23704938
#=GF SS   Published; PMID:23704938
#=GF GA   58.00
#=GF TC   58.60
#=GF NC   39.30
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   23704938
#=GF RT   RNA-mediated thermoregulation of iron-acquisition genes in Shigella
#=GF RT   dysenteriae and pathogenic Escherichia coli.
#=GF RA   Kouse AB, Righetti F, Kortmann J, Narberhaus F, Murphy ER
#=GF RL   PLoS One. 2013;8:e63781.
#=GF CC   Shingella ShuA the outer-membrane heme receptor and its E.coli orthologue
#=GF CC   ChuA expression are subject to temperature-dependent post-transcriptional
#=GF CC   regulation by 5' UTR regions containing FourURNA thermometer. 
#=GF WK   RNA_thermometer
#=GF SQ   5



AE005174.2/4458702-4458671 AUUUUUUAUUUUCCUCAUGGAGAAUCGMUAUG
CP000034.1/3287428-3287459 AUUUUUUAUUUUCCUCAUGGAGAAUCGCUAUG
CU928161.2/3863653-3863622 AUUUUUUAUUUUCCUCAUGGAGAAUCGCUAUG
CU928163.2/4108408-4108377 AUUUUUUAUUUUCCUCAUGGAGAAUCGCUAUG
CP000243.1/3916118-3916087 AUUUUUUAUUUUCCUCAUGGAGAAUCGCUAUG
#=GC SS_cons               :::::::<<<<<<<____>>>>>>>:::::::
#=GC RF                    AUUUUUUAUUUUCCUCAUGGAGAAUCGCUAUG
//
# STOCKHOLM 1.0

#=GF AC   RF02598
#=GF ID   EBv-sisRNA-2
#=GF DE   Epstein-Barr virus stable intronic sequence RNA 2
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:24441309
#=GF GA   41.80
#=GF TC   41.80
#=GF NC   41.70
#=GF TP   Gene;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24441309
#=GF RT   RNA families in Epstein-Barr virus.
#=GF RA   Moss WN, Lee N, Pimienta G, Steitz JA
#=GF RL   RNA Biol. 2014;11:10-17.
#=GF WK   Epsteinâ€“Barr_virus_stable_intronic-sequence_RNAs
#=GF SQ   2



AY037858.1/28412-28484 GGCCCGGGGA-GUGGAGGGGGAUCGCCCGGGUCUCUGCUGGCAGAGUCUGAGCGAUCCUCCGAGA--CUCCGGGCC
V01555.2/12566-12641   GGCCCGGGGAAGUGGAGGGGGAUCGCCCGGGUCUCUGUUGGCAGAGUCCGGGCGAUCCUCUGAGACCCUCCGGGCC
#=GC SS_cons           <<<<<<<<<--<<---<<<<<<<<<<<<<<<-<<<<<____>>>>>>>>>>>>>>>>>>>>--->>->>>>>>>>>
#=GC RF                GGCCCGGgGAAGuGGAgGgGGauCGCcCgGgUCuCuGuUGGCaGaGuCcGgGCGauCCuCcGAGaCcCuCCGGGCC
//
# STOCKHOLM 1.0

#=GF AC   RF02599
#=GF ID   BASRCI408
#=GF DE   Brucella sRNA CI408
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   398.00
#=GF TC   398.40
#=GF NC   185.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24673258
#=GF RT   Identification of novel sRNAs in Brucella abortus 2308.
#=GF RA   Dong H, Peng X, Wang N, Wu Q
#=GF RL   FEMS Microbiol Lett. 2014;354:119-125.
#=GF CC   Brucella abortus sRNA chromosome I, candidate 408
#=GF WK   Brucella_sRNA
#=GF SQ   3



CP002931.1/826771-827206 ACAAAACCCGCGCUGUGUAUGCAGCGCGGGUUUUUCUUAUGCGUUAUCCUGGAACUUUGGCGAUGGGGCCGGGAGGGCCAAGCGUAUCAUCGAUCUGUCGGUCGGUAUGGUAAGUGACGCAAGCUGUAUGGUAAGUGACGCAAGCUGAAAGAAGAGCGCUGAACAGCAGAAAAAAUACCGAUAGAAACAAUCUGCGUCCGAUGACCCCUAUCGAAUUUAAAAUAUCAAACAUUUGGAUUUAAUCCCUGAGUGAAGAUUGCAGUCGUAAAGUAAAAGGACGGUCCAGGCACUUGCGCUUUUUUGCCUGCAAAGAAUUCCGGUUUGCCGGUUUUCCCGGCGUCCAGUUUUGGGUAUGAGAGCGCAUCCCGAAAAGUGUGAAACGGUUUUCGGAUAAGAUGCGCGUCAAAAAAUAGUUGGAGCGCCGAUCUGAUUCAUU
CP003128.1/808732-809146 ACAAAACCCGCGCUGUGUAUGCAGCGCGGGUUUUUCUUAUGCGUUAUCCUGGAACUUUGGCGAUGGGGCCGGGAGGGCCAAGCGUAUCA------------UCGAUCUG-UCG--------GUCGGUAUGGUAAGUGACGCAAGCUGAAAGAAGAGCGCUGAACAGCAGAAAAAAUACCGAUAGAAACAAUCUGCGUCCGAUGACCCCUAUCGAAUUUAAAAUAUCAAACAUUUGGAUUUAAUCCCUGAGUGAAGAUUGCAGUCGUAAAGUAAAAGGACAGUCCAGGCACUUGCGCUUUUUUGCCUGCAAAGAAUUCCGGUUUGCCGGUUUUCCCGGCGUCCAGUUUUGGGUAUGAGAGCGCAUCCCGAAAAGUGUGAAACGGUUUUCGGAUAAGAUGCGCGUCAAAAAAUAGUUGGAGCGCCGAUCUGAUUCAUU
AM040264.1/826744-827178 ACAAAACCCGCGCUGUGUAUGCAGCGCGGGUUUUUCUUAUGCGUUAUCCUGGAACUUUGGCGAUGGGGCCGGGAGGGCCAAGCGUAUCAUCGAUCUGUCGGUCGGUAUG-UAAGUGACGCAAGCUGUAUGGUAAGUGACGCAAGCUGAAAGAAGAGCGCUGAACAGCAGAAAAAAUACCGAUAGAAACAAUCUGCGUCCGAUGACCCCUAUCGAAUUUAAAAUAUCAAACAUUUGGAUUUAAUCCCUGAGUGAAGAUUUCAGUCGUAAAGUAAAAGGACGGUCCAGGCACUUGCGCUUUUUUGCCUGCAAAGAAUUCCGGUUUGCCGGUUUUCCCGGCGUCCAGUUUUGGGUAUGAGAGCGCAUCCCGAAAAGUGUGAAACGGUUUUCGGAUAAGAUGCGCGUCAAAAAAUAGUUGGAGCGCCGAUCUGAUUCAUU
#=GC SS_cons             ::<<<<<<<<<<<<<<____>>>>>>>>>>>>>>,,,,,((((((((,,<<<--<<<<<<<______>>>->>>>-->>>,<<<<<<<<<<<<____>>>>>->>>>>>.>,,)))))))),,,((((-((((((-((((((((<<______>>,,,<<<____>>>,,,,,,,,,,,<<<<<<-----<<<_______>>>----->>>>>>,,,,,,,,,,,,,,,,,,<<<<<<<<---<<<-<<<-<<<<___>>>>->>>---------->>>->>>>>>>>,,))))))-))-)))))))))),,<<<--<<<<____>>>>-->>>,<<<<<<<<<<<<-------<<<--<<<<<<<<<<<<<<-<<<___>>>->>>>>>>---->>>>>>>->>>------>>>>>>>->>>>>::::::::::::
#=GC RF                  ACaaaaCCCGCGCuGcGUAUgCaGCGCGGGuuuuUCUUAuGcGucacCCuGGAACuccGGCGAUGGGGCCGggaGGGCCaAgCguacCaccGaUcUguCgguCGguacG.caagugaCgCaagCuGcaUGGcaagUgaCGCaaGCuGAAAGAaGAGCGCuGAACaGCAGAAAAAAUACCGauaGAAACAauCUGCGUCCGauGACCCCuauCGAAUUUAAAAUAUCAAACAccuGGaccUAAuCCCcGaGuGaaGAUuuCaGuCgUAAAGUAAAAGGaCgguCCaggCACuuGCGCucUcuugCCugCaAAGaaUUCCGGUUUGCCGGUUuuCCCGGCGuCCagcuUUGGGUAuGaGAGCGCauCCCGaaaaGcGuGAAaCgGuuuuCGGAUAAGauGCGCGuCaAAAAAUagcuGGaGCGCCGAUCUGAUUCAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02600
#=GF ID   BASRCI27
#=GF DE   Brucella sRNA CI27
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   59.80
#=GF TC   59.80
#=GF NC   59.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24673258
#=GF RT   Identification of novel sRNAs in Brucella abortus 2308.
#=GF RA   Dong H, Peng X, Wang N, Wu Q
#=GF RL   FEMS Microbiol Lett. 2014;354:119-125.
#=GF CC   Brucella abortus sRNA chromosome I, candidate 27
#=GF WK   Brucella_sRNA
#=GF SQ   3



ADFB01000087.1/21620-21786 GACGGAUUUAAAGCAUGUCUCCCAAAGGCGGGAACCGGUUUUGGGAUAAAGACAUGCACGAAAACAAAAGUUUAAAGCGUGUCGUGUGUGUAUGAUAACAAGCGACAUGCUUUAGGUUUAUUUUGCAGCGCCGGAUGUUUCCAUUUGGCUGCACAGUGUUUUUAGGG
CP003128.1/172597-172763   GACGGAUUUAAAGCAUGUCUCCCCAAAGCGGGAACCGGUUUUGGGAUAAAGACAUGCACGAAAACAAAAGUUUAAAGCGUGUCGUGUGUGUAUGAUAACAAGCGACAUGCUUUAGGUUUAUUUUGCAGCGCCGGAUGUUUCCAUUUGGCUGCACAGUGUUUUUAGGG
AM040264.1/170394-170560   GACGGAUUUAAAGCAUGUCUCCUCAAAGCGGGAACCGGUUUUGGGAUAAAGACAUGCACGAAAACAAAAGUUUAAAGCGUGUCGUGUGUGUAUGAUAACAAGCGACAUGCUUUAGGUUUAUUUUGCAGCGCCGGAUGUUUCCAUUUGGCUGCACAGUGUUUUUAGGG
#=GC SS_cons               ::::::::::::<<<<<<<<-<<<<<<<<-<____>->>>>>>>>---->>>>>>>>--(((((((,<<<<<<<<<<<<<<<<<<-<<<________>>>->>>>>>>>>>>>>>>>>>,,,,<<<<--<<<<<<<<____>>>>>>>>>>>>,,,)))))))::::
#=GC RF                    GAcGGAUUUAAAGCauGuCucCccaaagCGGGAAcCGGcuuuggGAUAAaGaCauGCAcgaaaaCaAaagccuaaaGCguGuCGcGuGuGUAUGAUAaCaAgCGaCacGCuuuaggcuuAUUUuGCaGcGCCggauGUUUcCauccGGCuGCacAGuGuuuucAGGG
//
# STOCKHOLM 1.0

#=GF AC   RF02601
#=GF ID   BASRCI337
#=GF DE   Brucella sRNA CI337
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   229.00
#=GF TC   229.50
#=GF NC   125.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24673258
#=GF RT   Identification of novel sRNAs in Brucella abortus 2308.
#=GF RA   Dong H, Peng X, Wang N, Wu Q
#=GF RL   FEMS Microbiol Lett. 2014;354:119-125.
#=GF CC   Brucella abortus sRNA chromosome I, candidate 337
#=GF WK   Brucella_sRNA
#=GF SQ   4



ACBP01000037.1/46168-46357 GCGAGGGUUCCUUUGAACGGUUCUUAAUUCCAGGCUGUCAUAUGCACCUGCCACCGCUUUUCGUCAAGAAACAGAAACCGCAACAGGGUGUCGCAGUAAUAAUCUUUCAGAAAGCGGGCAGUUUUAUGCCUGAUAUUACACCACGCUUUCGGUUUGGAAAAUA-AAAAGGCGGCCAGAGGCCGCCUUUUGA
ACJD01000005.1/46905-47095 GCGAGGGUUCCUUUGAACGGUUCUUAAUUCCAGGCUGUCAUAUGCACCUGCCACCGCUUUUCGUCAAGAAACAGAAACCGCAACAGGGUGUCGCAGUAAUAAUCUUUCAUAAAGCAGGCAGUUUUAUGCCUGAUAUUACACCACGCUUUCGGUUUGGAAAAUAAAAAAGGCGGCCAGAGGCCGCCUUUUGA
ADFA01000143.1/9599-9409   GCGAGGGUUCCUUUGAACGGUUCUUAAUUCCAGGCUGUCAUAUGCACCUGCCACCGCUUUUCGUCAAGAAACAGAAACCGCAACAGGGUGUCGCAGUAAUAAUCUUUCAGAAAGCGGGCAGUUUUAUGCCUGAUAUUACACCACGCUUCCGAUUUGGAAAAUAAAAAAGGCGGCCUGAAGCCGCCUUUUGA
AM040264.1/1856031-1856221 GCGAGGGUUCCUUUGAACGGUUCUUAAUUCCAGGCUGUCAUAUGCACCUGCCACCGCUUUUCGUCAAGAAACAGAAACCGCAACAGGGUGUCGCAGUAAUAAUCUUUCAGAAAGCGGGCAGUUUUAUGCCUGAUAUUACACCACGCUUUCGGUUUGGAAAAUAAAAAAGGCGGCCAGAGGCCGCCUUUUGA
#=GC SS_cons               ((((----(((((((--(((((,,,,,,,,<<<<-<<<_____>>>>>>>,,,,,,<<<<<<_____>>>>->>,))))))))-))))--)))),,,,,,,,<<<----<<<<<<<<<--<<--<<<_____>>>-->>->>->>>>>>>----->>>,,,,,,<<<<<<<<<<<___>>>>>>>>>>>::
#=GC RF                    GCGaGGGUcCCuuuGAACGGuuCUUAAUUCCaGGCuGcCAUAUgCaCCuGCCACCGCuuuuCGUCAAGaaaCaGAaaCCGCaaCaGGgUGuCGCAGUAAUAAuCcUUCAggaaGCgGGCAGuUUuauGCCUGauaUUaCACCAcGCuuccGgUUUgGaAAAUAAaaaaGGCGGCcaGAgGCCGCCuuuuGA
//
# STOCKHOLM 1.0

#=GF AC   RF02602
#=GF ID   BASRCI414
#=GF DE   Brucella sRNA CI414
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   270.00
#=GF TC   270.00
#=GF NC   37.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24673258
#=GF RT   Identification of novel sRNAs in Brucella abortus 2308.
#=GF RA   Dong H, Peng X, Wang N, Wu Q
#=GF RL   FEMS Microbiol Lett. 2014;354:119-125.
#=GF CC   Brucella abortus sRNA chromosome I, candidate 414
#=GF WK   Brucella_sRNA
#=GF SQ   3



ADEZ01000007.1/240503-240277 GCUGGCAUUCCCUGGCAUAUUGGUGCGCCGCCUCUGAAAGGUGCAGCGCGGAAUAAAGAUCCCAGAGCGGCUUGCCGGACCUUU--GCGCGCAGCCGCUCUGACUAUUUGUUUUUACACAUUCCGACCAAUUGCCGAGGACGCUCCCGAAAACGAAGACCCGGUAGAAAACCGCCGUCGAUGAAAACCAUCUGACAAUAUAAAAGGCGCCGCUGAACGGCGCCUUUUAU
ADFB01000060.1/31834-31607   GCUGGCAUUCCCUGGCAUAUUGGUGCGCCGCCUCUGAAAGGUGCAGCGCGGAAUAAAGAUCCCAGAGCGGCUUGCCGGACCUUUGCGCGCGCAGCCGCUCUGACUAUUUGUUUUUACGCAUUCCGACCACUUGACGGGAACGC-CCCAAAAAUGAAGACCCGGCAGAAAACCACCGUCGAUGAAAACCAUCUGACAAUAUAAAAGGCGCCGCUGAACGGCGCCUUUUAU
AM040264.1/830409-830637     GCUGGCAUUCCCUGGCAUAUUGGUGCGCCGCCUCAGAAAGGUGCAGCGCGGAAUAAAGAUCCCAGAGCGGCUUGCCGGACCUUUGUGCGCGCAGCCGCUCUGAUUAUUUGUUUUUACACAUUCCGACCAAUUGCCGAGGACGCUCCCGAAAACGAAGACCCGGCAGAAAACCACCGUCGAUGAAAACCAUCUGACAAUAUAAAAGGCGCCGCUGAACGGCGCCUUUUAU
#=GC SS_cons                 (((((--((((((((((-((((((<<<<<<<<<_____>>>>>-->>>><<<<<<<<-----<<<<<<<<<<-<<<<-<<____>>->>->>>>>>>>>>>>---->>>>>>>>,,,,,,,,,,,))))))))))-)))--------------)))---))))),,,,,,,,,,,<<<<<<<_____>>>>->>>,,,<<<<<<<<<<<<<_____>>>>>>>>>>>>>
#=GC RF                      gCcGGcAuuCcCuGgCaUauuGGuGCGCCgCCucuGAAaGGcGcAGCGCggaacaaaGAUccCaGaGCGGCuUGCCGGgccUUUgcGCGcGCaGCCGCuCuGAcUAuuuguuccUAcacAUUccGaCCaauuGcCGaGgAcGcucccgAAAAcGaaGAcCCgGcAGAAAAccaccGuCGauGAAAAcCauCUGaCAAUauaaaaGGCGCCGcUGAACGGCGCCuuuuau
//
# STOCKHOLM 1.0

#=GF AC   RF02603
#=GF ID   BASRCII26
#=GF DE   Brucella sRNA CII26
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   218.00
#=GF TC   218.80
#=GF NC   108.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24673258
#=GF RT   Identification of novel sRNAs in Brucella abortus 2308.
#=GF RA   Dong H, Peng X, Wang N, Wu Q
#=GF RL   FEMS Microbiol Lett. 2014;354:119-125.
#=GF CC   Brucella abortus sRNA chromosome II, candidate 26
#=GF WK   Brucella_sRNA
#=GF SQ   2



ACEH01000014.1/37080-36891 UGGAAAGGCAGGCUUCGGCCUGCCUUUCCUGUUGCCCGAGACAGGACUUCCAACGUGCGGGGGGGCAACGGAAGUCCAUCUCGUCGUCUCAACCGGGAUUGAUCACGAUUGGUUCCACUCUGUCAAUCGUAGUUAUCUAAAAUAGUGAUUGCCCCACAGCAACGUGGCUGGACGGUAAAUUUUCCAUAAA
AM040265.1/181509-181697   UGGAAAGGCAGGCUUCGGCCUGCCUUUCCUGUUGCCCGAGACAGGACUUCCAACGUGCGGG-GGGCAACGGAAGUCCAUCUCGUCGUCUCAACCGGGAUUGAUCACGAUUGGUUCCACUCUGUCAAUCGUAGUUAUCUAAAAUAGUGAUUGCCCCACAGCAACGUGGCUGGACGGUAAAUUUUCCAUAAA
#=GC SS_cons               :<<<<<<<<<<<<____>>>>>>>>>>>>--[[[[[<<<<<--<<<<<<<<----<<<______>>>-->>>>>>>>->>>>>,,,,,,,,,((((<<<<<<-<<-<<-<<____>>->>>>>>>>>><<<<<<<<________>>>>>>>>,<<<<______>>>>)))),,]]]]]::::::::::::
#=GC RF                    UGGaaaGGCaGGCUUcGGCCuGCCuuuCCUGuugCCCGaGacAGGaCuuCCAAcGuGCGGGgGGGCaAcGGaaGuCCAuCuCGUcGUcUcAACCgGGauuGaUCacGaUuGGUUcCacuCuGuCaauCGcagucaccUAAAAUAgugacugCcCCaCAGcAAcGuGGCcGGAcGGcaaAUUUUccAUAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02604
#=GF ID   BASRCI153
#=GF DE   Brucella sRNA CI153
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   137.00
#=GF TC   137.10
#=GF NC   134.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24673258
#=GF RT   Identification of novel sRNAs in Brucella abortus 2308.
#=GF RA   Dong H, Peng X, Wang N, Wu Q
#=GF RL   FEMS Microbiol Lett. 2014;354:119-125.
#=GF CC   Brucella abortus sRNA chromosome I, candidate 408
#=GF WK   Brucella_sRNA
#=GF SQ   2



ADFB01000074.1/210466-210679 GCAUUUUCGAGCCAAAAGUGCGAAGCGCCUACGCGAGGAAAUCAGUCCACUGGACUGAUUUCUGAUCCCGCUUCGAUCCGUUGGAUAAUACGAUAAGACAAAUAAUUAGAGCGGUUCCAGUGACUCUGUUUUAACUGGAACUGCCUGGGCUACGGGCUCAAUUGGAUUAGCCUUGCCAUUCGGCAGGGCUUUUUCAUAGGGAUUACGGGCAGCG
AM040264.1/1441442-1441655   GCAUUUUCGAGCCAAAAGUGCGAAGCGCCUACGCGGGGAAAUCAGUCCACUGGACUGAUUUCUGAUCCCGCUUCGAUGCAUUGGAAAAGGUGAUAAAAUAAAUAGUUAAGACGGUUCCAGCGACUCUGUUUUAACUGGAACUGCCUGGGCUUUGGGCUCAAUUGGAUUAGCCUUGCCAUUCGGCAGGGCUUUUCCAUAGGGAUUACGGGCAGCG
#=GC SS_cons                 :((((((----((((--((((((((((<<<____>>><<<<<<<<<<<___>>>>>>>>>>>,,,,,,)))))))-)))-))))--)))))),,,,,,,,,,<<<<<<<<<<<<-<<____>>-->>>>>>>>>>>>,,,<<<<<<<--<<<<<--------<<<<--<<<<<<<<<____>>>>>>>>>-->>>>>>>>>---->>>>>>>::
#=GC RF                      GCgccuuCGAGCCaaAAGcgCGaaGCGCccACGCggGGaaauCaGuCCACUGGaCuGauuuCUGAUCCCGCuuCGAcgCauuGGAaaaggcGAUAAaAuAAAcaguuagggCgGUuCCAGuGaCUCcGcccuaacugGAACuGCCcGGGCcccgGGCUCAAUuGgaUUaGCCcuGCCAUUCGGCagGGCuUUucCacgggGAUUACgGGCaGCG
//
# STOCKHOLM 1.0

#=GF AC   RF02605
#=GF ID   scr5239
#=GF DE   Streptomyces sRNA scr5239
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Published; PMID:25785836
#=GF SS   Published; PMID:25785836
#=GF GA   64.00
#=GF TC   64.20
#=GF NC   45.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   25785836
#=GF RT   Identification of metE as a second target of the sRNA scr5239 in
#=GF RT   Streptomyces coelicolor.
#=GF RA   Vockenhuber MP, Heueis N, Suess B
#=GF RL   PLoS One. 2015;10:e0120147.
#=GF RN   [2]
#=GF RM   22075028
#=GF RT   Streptomyces coelicolor sRNA scr5239 inhibits agarase expression by direct
#=GF RT   base pairing to the dagA coding region.
#=GF RA   Vockenhuber MP, Suess B
#=GF RL   Microbiology. 2012;158:424-435.
#=GF CC   It inhibits agarase DagA expression by direct base pairing to the dagA
#=GF CC   coding region, and it represses translation of methionine synthase metE
#=GF CC   (SCO0985) at the 5â€™ end of its open reading frame.
#=GF WK   Streptomyces_coelicolor
#=GF SQ   6



ABYC01000352.1/1060-1217   CCUCCACCCUCCCCGCACAGGAGGGUGGACCGGGG-ACCCGGCACUCUCUGCCCUGACUGUUCCG-GCUCCCC-CAGACCGGCCCAC-GGGACCGCACACCCGACGGCC-GGUGGUUGCUCCGGGCUGCGGUGCCGGGCGGGUUGAGGGUCCCACCCAGGCGC
BA000030.3/3773657-3773499 CCUCCGUCUUCCCCGCACAGGAAGGCGGAUCGAGG-AACCGGCGCUCUCUGCCCUGACUGCUCCG-GGUCCUCAUCCAUCGGCCGACCGGGACCGCACACCCCACGGCC-GUU-GCUGCUCCGGGCUGCGGUGCCGGGAGGGUUGAGGGUCCCUCUCAGGCGC
CP002047.1/5057396-5057539 CUUCCGCCCUCCCCGCACAGGAGGGUGGAUCGAGGCACACGGGGUGCUCUGCCCUGACCGCUCCGGGGGCCUC------AGGUCGGCCGG-----------CUGCGGCC-GA-UGCAACUCCGGGCUGCGGUGCCGGGCGGGUUGAGGGUCCCGCUCUGGCGC
AL939123.1/18911-19069     CUUCCGCCCUCCCCGCACAGGAGGACGGACCGAGG-AACCGGUGCUCUCUGCCCUGACUGCUCCG-GCUCCUCAUCCUUCGGCCGACCGGGACCGCACACCCCACGGCC-GAU-GUUGCUCCGGGCUGCGGUGCCGAGAGGGCUGAGGGUCCCUCUCAGGCGC
AP009493.1/2691480-2691632 UCUCCGCUCUCCCCGCACAGGAGAGCGGACCGAGG-CUCCGGCACUCUCUGCCCUGACUGCGCCG-GUGCCUC---CAGUGGCCGGG-GGCACCGCACACCGC-CGGCCAG---GUAGCUCCGGGCUGCGGUGCCGGACGGGCUGAGGGUCCCGUUCUGGCGC
FR845719.1/5282824-5282669 CCUCCAUCCUCCCCGCACAGGAGGAUGGAACGAGGUACCCGACGCUCUCUGCCCUGACUGCGUCG-AGACCUCCCACA-CGGCCGA--GGGACCGCACACCCC-CGGCC-GGAGCAAACUCCGGGCUGCGGUGCCGGGCGGGCUGAGGGUCCCGC-CGGGCGC
#=GC SS_cons               ::<<<<-<<<<<_______>>>>>->>>>,,<<<<.<-<<<<-<<<<<______>>>-->>->>>.>->>>>>.,,,,<<<<<<<--.<<<________>>>-->>>>>.>>,,,,<<<<-<<___>>->>>>,,<<<<<<<________>>>>>>>::::::
#=GC RF                    ccuCCgcccuCCCCGCACAGGagggcGGauCGaGG.cacCGGcgcuCuCUGCCCuGaCUgcuCCG.gugCCuC.uacaccGGcCGac.gGgACCGCACAcCccaCGgCC.gguggucgCuCCgGGCuGCgGcgCCGgGcGGGuUGAGGGUCCCgCcCaGGCGC
//
# STOCKHOLM 1.0

#=GF AC   RF02606
#=GF ID   AbsR28
#=GF DE   Acinetobacter sRNA 28
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   50.00
#=GF TC   50.20
#=GF NC   35.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24705412
#=GF RT   Identification of novel regulatory small RNAs in Acinetobacter baumannii.
#=GF RA   Sharma R, Arya S, Patil SD, Sharma A, Jain PK, Navani NK, Pathania R
#=GF RL   PLoS One. 2014;9:e93833.
#=GF CC   Three sRNAs: AbsR11, AbsR25 and AbsR28 have been experimentally validated
#=GF CC   in the MTCC 1425 (ATCC15308) strain, which is an MDR strain showing
#=GF CC   resistance to 12 antibiotics. AbsR25 sRNA could play role in the efflux
#=GF CC   pump regulation and drug resistance.
#=GF WK   Acinetobacter_baumannii
#=GF SQ   2



CP000521.1/3285873-3286051 AGAUUUUCAACGGCACUUUUUA-AAAAGGAGGACAUCAUGCCAACACUACAAGGUAAAACACAGUAACGAUUUGGCACGAUGUCAGCUCACGGACAAGUGUACAAAUUUAAUUCACUUGUCCGAAUGCUCGAAUUUAAGACCUAGCAUUCGCUAGGUUUUUUUAUGCCUAUUCGGACAAU
ACQB01000061.1/63606-63427 AUAUUUUCAACGGCACUUUUUAAAAAAGGAGGACAUCAUGCCAACACUACAAGGUAAAACACAGUAACGAUUUGGCACGAUGUCAGCUCACGGACAAGUGUACAAAUUUAAUUCACUUGUCCGAAUGCUUGAAUUUAAGACCUAGCAUUCGCUAGGUUUUUUUAUUCCUAUUCGGACAAU
#=GC SS_cons               :((--((((--((((<<<<<___>>>>><<<<<<<<<-<<<<<<---------<<_____>>--------->>>>>>->>>>>>-->>>,<<<<<<<<<<_____________>>>>>>>>>>,,))))))))--))<<<<<<<<<____>>>>>>>>>,,,,,,<<<_____>>>::::
#=GC RF                    AuaUUuuCgACgGCaCuuuuUAAaaaaGGaGGaCauCAuGCCaaCACUACAAGGuAAAACaCAGUAACGAUuuGGCaCGauGuCAGCuCACGGaCaaGuGUACAAAUUUAAUUCaCuuGuCCGAAuGCccGaaUUuaagaCCuaGCAUUCGCuaGGucuUUUUAUuCCUAUUCGGaCAAU
//
# STOCKHOLM 1.0

#=GF AC   RF02607
#=GF ID   AbsR25
#=GF DE   Acinetobacter sRNA 25
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   47.00
#=GF TC   47.80
#=GF NC   44.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24705412
#=GF RT   Identification of novel regulatory small RNAs in Acinetobacter baumannii.
#=GF RA   Sharma R, Arya S, Patil SD, Sharma A, Jain PK, Navani NK, Pathania R
#=GF RL   PLoS One. 2014;9:e93833.
#=GF CC   Three sRNAs: AbsR11, AbsR25 and AbsR28 have been experimentally validated
#=GF CC   in the MTCC 1425 (ATCC15308) strain, which is an MDR (multiple drug
#=GF CC   resistance) strain showing resistance to 12 antibiotics. AbsR25 sRNA could
#=GF CC   play a role in the efflux pump regulation and drug resistance.
#=GF WK   Acinetobacter_baumannii
#=GF SQ   2


AEOZ01000163.1/28810-28647 CCUUUUAAAUCAUGUGUAGGAACGAGCUAUGAUGCAAGCAAUGUUUUUCUUUAGUGCUGGAGCAGUUUUUGGUUAUUGCUAUCGUCAUUACGAUGCUAAAGUUAAAAAAGCCAAUGAUUCAAAAUAAAUGAUUAAAAAAGCCUGCUUCUUGAGUAGGCUUUUUU
CP000521.1/1548987-1549149 CCUUUUAAAUCAUGUGUAGGACCGAGCUAUGAUGCAAGCAAUGUUUUUCUUUAGUGCUGGAGCAGUUUUUGGUUAUUGCUAUCGUCAUUACGAUGCUAAAGUUAAAAAAGCCAAUGAUUCAAAAUAAAUGAUUA-AAAAGCCUGCUUCUUGAGUAGGCUUUUUU
#=GC SS_cons               ::<<<<-<<<<<<---<<<-<-<<----<<<<<<--<<<<<<<---------<-<<<____>>>->------->>>>>>>-->>>>>>-->>->->>>--------------->>>>>>->>>>---------<<<<<<<<<<<<<<___>>>>>>>>>>>>>>
#=GC RF                    CCuuuuAaauCauGUGuaGGaaCGAGCUauGacGCAaGCaaugUUUUUCUUUaGuGCUGGAGCaGuUUUUGGUcauuGCuAUCguCauUACGAuGCuaAAGUUAAAAAAGCCAauGauuCaaaaUAAAUGAUUaaaaaaGCCugCucCUUgaGcaGGCuuuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02608
#=GF ID   AbsR11
#=GF DE   Acinetobacter sRNA 11
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   158.00
#=GF TC   158.50
#=GF NC   90.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24705412
#=GF RT   Identification of novel regulatory small RNAs in Acinetobacter baumannii.
#=GF RA   Sharma R, Arya S, Patil SD, Sharma A, Jain PK, Navani NK, Pathania R
#=GF RL   PLoS One. 2014;9:e93833.
#=GF CC   Three sRNAs: AbsR11, AbsR25 and AbsR28 have been experimentally validated
#=GF CC   in the MTCC 1425 (ATCC15308) strain, which is an MDR (multiple drug
#=GF CC   resistance) strain showing resistance to 12 antibiotics. AbsR25 sRNA could
#=GF CC   play a role in the efflux pump regulation and drug resistance.
#=GF WK   Acinetobacter_baumannii
#=GF SQ   2



CP002177.1/1778400-1778599 UCAGCCUACUUUAUGUAUAGCUUAGUUUGUCGAUAUGAGGCAUAAUGCCCUACAACGUAGCGGUGUCAUAUAAUUGAGAAGUCUAAAUUUAAGGAUUAGCGUUCUCAAUCAUGCGACACUUUAAUCGCUAUCCCAUAUUUAAUUAGGGAAUGGGACUCUUCACCGAGGUUGUAAAAUGAGACAAACGAUUUUAGCUGUAU
CP000521.1/2529288-2529487 UCAGACGACUUUAUGUGUAGCUUAGUUUGUCGAUAUGAGGCAUAAUGCCCUACAACGUAGCGGUGUCACAUCAUUGAGAAGUCUAAUUUUUAAGACUAGCGUUCUCAAUCAUGCGACACUUUAAUCGCUAUCCCAUAUUUAAUUAGGGAAUGGGACUCUUCACCGAGGUUGUAAAAUGAGACAAACGAUUUUAGCUGUAU
#=GC SS_cons               ::::::::::::::[[[[[[[[--[[[[[[[,,,,,,,<<<<___>>>>,((((((,<<<<<<<<<<-<<<-<<<<<<<<<<<<________>>>>>----->>>>>>>->>>->>>>>------>>>>><<<<<<-<<<______>>>>>>>>><<<______>>>)))))),,,,,,]]]]]]]------]]]]]]]]
#=GC RF                    UCAGaCuACUUUAUgugcaGCuUAGuuuGuCGAUAUGAGGCaUAAuGCCCuaCaaCGuaGCGGuGuCAcauaauuGaGaaguCcAAaUUUaAgGacuAGCGUuCuCaauCaugCGaCaCUUUAAUCGCuauCCCauAuccAAUUAGggaauGGGaCuCUUCACCGaGGuuGuaAAAUGAGaCaaaCGAUUUUaGCugcac
//
# STOCKHOLM 1.0

#=GF AC   RF02609
#=GF ID   BSR0602
#=GF DE   Brucella sRNA 0602
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   191.00
#=GF TC   191.40
#=GF NC   31.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25852653
#=GF RT   Identification of a Novel Small Non-Coding RNA Modulating the
#=GF RT   Intracellular Survival of Brucella melitensis.
#=GF RA   Wang Y, Ke Y, Xu J, Wang L, Wang T, Liang H, Zhang W, Gong C, Yuan J,
#=GF RA   Zhuang Y, An C, Lei S, Du X, Wang Z, Li W, Yuan X, Huang L, Yang X, Chen Z
#=GF RL   Front Microbiol. 2015;6:164.
#=GF CC   Highly induced in stationary phase and modulate the intracellular
#=GF CC   survival. 
#=GF WK   Brucella_sRNA
#=GF SQ   2



AE008918.1/635956-636124 UUCAAUUAUUGAAAUAUUGUGAGUAAUAUAUUCCAAUCCCAACUUUUGUCCAGUUGGGCGGCGGAAGAACGUUCUCUUUGAGGGCAUUGAAACGGUAUGGAUGCGGGAUAGCAAAGCAGCUUGAAGAAACGAAAACGCCGCCCGGAAAAGGCGGCGUUUUGAUCUUGAU
CP003129.1/661928-661760 UUCAAUUAUUGAAAUAUUGUGAGUAAUAUAUUCUAAUCCCAACUUUUGUCCAGUUGGGCGGCGGAAGAACGUUCUCUUUGAGGGCAUUGAAACGGUAUGGAUGCGGGAUCGCAAAGCAGCUUGAAGAAACGAAAACGCCGCCCGGAAAAGGCGGCGUUUUGAUCUUGAU
#=GC SS_cons             <<<<<___>>>>>,,<<<<-<<<<<___>>>>>>>>><<<<<<<_______>>>>>>>,,,,,,,,,,,<<<<-<<<<<<<<-<<-<<<---<-<<<____>>>->----->>>->>-->>>>>>>>>>>><<<<<<<<<<<_______>>>>>>>>>>>:::::::::
#=GC RF                  uuCaaUUAuuGaaAUauugUGaguaAUAuacuCcaauCCCaaCuUUUGUccaGuuGGGcGGcGGAAGAACGuucuCuucgaGGGCAuuGAAACGGcaUGGAugCGGGAUaGCaaAGCAGCucgaaGaaaCGaaaaCGCCGCCcGGAAAAGGCGGCGuuuuGAUcUUGAU
//
# STOCKHOLM 1.0

#=GF AC   RF02610
#=GF ID   BSR0709
#=GF DE   Brucella sRNA 0709
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   382.00
#=GF TC   382.50
#=GF NC   38.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25852653
#=GF RT   Identification of a Novel Small Non-Coding RNA Modulating the
#=GF RT   Intracellular Survival of Brucella melitensis.
#=GF RA   Wang Y, Ke Y, Xu J, Wang L, Wang T, Liang H, Zhang W, Gong C, Yuan J,
#=GF RA   Zhuang Y, An C, Lei S, Du X, Wang Z, Li W, Yuan X, Huang L, Yang X, Chen Z
#=GF RL   Front Microbiol. 2015;6:164.
#=GF WK   Brucella_sRNA
#=GF SQ   4



AE008918.1/750924-750608   AAAUAUGCUUGUUUUCAACUUAAUUUUCAUAUUUAUUUCAAGUGUUUAACGUUCUUU-UUUUGGGGGCAG-AUGCGUAAGUUUGUUAAGAGAACCGCAAUUUGUGGAUCGCUCUUAUUGAUAGCGAUUUUUAUGAUGAAUAGUUGGAGCGGUAUUCAGAGCGGGCAUAACGCAUUUCGUCCAGUCUCAAAAUCAAAACCAGCAUCGAGUGAGACUUGUAAAGAGUAUAACGAAAAGGGUUUUAUCGGAAAAUUGUUUGAUUUUUCUGCACGUGGUUGGUGCGAUUGAUUAAAGAGGCUUCGGCCUCUUUUUUUGACGCU
CP003129.1/539094-539411   AAAUAUGCUUGUUUUCAACUUAAUUUUCAUAUUUAUUUCAAGUGUUUAACGUUCUUU-UUUUGGGGGCAGAAUGCGUAAGUUUGUUAAGAGAACCGCAAUUUGUGGAUCGCUCUUAUUGAUAGCGAUUUUUAUGAUGAAUAGUUGGAGCGGUAUUCAGAGCGGGCAUAACGCAUUUCGUCCAGUCUCAAAAUCAAAACCAGCAUCAAGUGAGACUUGUAAAGAGUAUAACGAAAAGGGUUUUAUCGGAAAAUUGUUUGAUUUUUCUGCACGUGGUUGGUGCGAUUGAUUAAAGAGGCUUCGGCCUCUUUUUUUGACGCU
ACBK01000003.1/463-781     AAAUAUGCUUGUUUUCAACUUAAUUUUCAUAUUUAUUUCAAGUGUUUAACGUUCUUUUUUUUGGGGGCAGAAUGCGUAAGUUUGUUAAGAGAACCGCAAUUUGUGGAUCGCUCUUAUUGAUAGCGAUUUUUAUGAUGAAUAGUUGGAGCGGUAUUCAGAGCGGGCAUAACGCAUUUCGUCCAGUCUCAAAAUCAAAACCAGCAUCAAGUGAGACUUGUAAAGAGUAUAACGAAAAGGGUUUUAUCGGAAAAUUGUUUGAUUUUUCUGCACGUGGUUGGUGCGAUUGAUUAAAGAGGCUUCGGCCUCUUUUUUUGACGCU
ACBG01000045.1/48658-48342 AAAUAUGCUUGUUUUCAACUUAAUUUUCAUAUUUAUUUCAAGUGUUUAACGUUCU-U-UUUUGGGGGCAGAAUGCGUAAGUUUGUUAAGAGAACCGCAAUUUGUGGAUCGCUCUUAUUGAUAGCGAUUUUUAUGAUGAAUAGUUGGAGCGGUAUUCAGAGCGGGCAUAACGCAUUUCGUCCAGUCUCAAAAUCAAAACCAGCAUCAAGUGAGACUUGUAAAGAGUAUAACGAAAAGGGUUUUAUCGGAAAAUUGUUUGAUUUUUCUGCACGUGGUUGGUGCGAUUGAUUAAAGAGGCUUCGGCCUCUUUUUUUGACGCU
#=GC SS_cons               <<<<<<<---<<<________>>>--->>>>>>>------[[[[[[,,,,,,,((((.(((((,<<<<<<-<<<<<<--<<<<<<<--<<<-<<<<<---<<<<<<<<<<<<_________>>>>>>>>--------->>>>----->>>>>->>>-->>>>>>>--->>>>>>>>->>>><<<<<<<---<<____________>>->>>>>>>,,,,,,,,,,,,,,))))))))),,,,,,,<<<<<<<<____>>>>>>>><<<<<_______>>>>>,,,<<--<<<<<<<<____>>>>>>>>-->>]]]]]]
#=GC RF                    aaauauGCUUguuUUCAACUUaacUUUCauauuuAUUUCAaGcGucUAACGUUCccu.uuucGGGGgCagAauGCGuAAGcccGcuAAGagAaCCGCAAUcuguggauCGCuCUUAUUGAUaGCGauccUUAUGAUGAacagUUGGAGCGGuAcuCAGagCgggCAUAaCGCaucuCGcCCaGuCuCaAAAucAAAACCAGCAUCgaGuGaGaCuUGUAAAGAGUAUAACgaaaaggGUUUUAUCGgaaaaucGUUUgauuuucCcGCaCGUGGUUGGuGCgAUUgaUUaaaGaGGCUUCGGCCuCuuuUUucgaCgCu
//
# STOCKHOLM 1.0

#=GF AC   RF02611
#=GF ID   BSR0653
#=GF DE   Brucella sRNA 0653
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   627.00
#=GF TC   627.80
#=GF NC   31.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25852653
#=GF RT   Identification of a Novel Small Non-Coding RNA Modulating the
#=GF RT   Intracellular Survival of Brucella melitensis.
#=GF RA   Wang Y, Ke Y, Xu J, Wang L, Wang T, Liang H, Zhang W, Gong C, Yuan J,
#=GF RA   Zhuang Y, An C, Lei S, Du X, Wang Z, Li W, Yuan X, Huang L, Yang X, Chen Z
#=GF RL   Front Microbiol. 2015;6:164.
#=GF WK   Brucella_sRNA
#=GF SQ   4



AE008918.1/684479-683838   UAAUGUAGCUGCCUUUAUAUUUACUGGUCCGUAGAAUCCCUCCCAGUGACAGGGCCUAUUCAUAGCGAGUGUGAACGGUCAAUCCGGCCAACUAAAGCUUUCAUAAUGGUCAUAAGGCGGCUGACCAACGGUCUCCACUGUGAAGCACAAAUAGCGGGAUGUCGUCUGUUGGGCCGAGAAUGCGGGCCAAGCAGCGGGUUGAAGCGAUUUACGCAAAUCCGGCUACCGCAAUCGGGAAAAGAUGCUUGUGCCGUUUUCGUCAGCCACUCGCAGAGCAGAGCAAAUUAAGCUAACAGCCGAGCAGCAAACGCUGUUCUCCGUACGGCAGAACUCCAGCCCGUAUGAUCGGCCUAACGUGACCGCCCUAUGGCAAGGACGGGAUUCUGCCUAUCAGGCAUGAACUAAGCGGUCGCGUAGCGGCCACCUCCCCAUUUAUUGCAAUUGCUUCGCAAUUGUAAAAAAGGUUAACUAUCCACAUUUGAUACGACUAGUACUUUUUGCCCAUCCAUUUUUGACUCGUGAAUUUUUUAACAUGUGAAUUUUGACAAUCUUCUCCGUGGAAGCACCUCCUCUUCAUCGCUUCCAUUCAUUAACGAGAACCACCUGCCCCUGCGCUAUUGCGCAGGGGCUUUUU--UGUAGAGC
ACEI01000011.1/56671-56028 UAAUGUAGCUGCCUUUAUAUUUACUGGUCCGUAGAAUCCCUCCCAGUGACAGGGCCUAUUCAUAGCGAGUGUGAACGGUCAAUCCGGCCAACUAAAGCUUUCAUAAUGGUCAUAAGGCGGCUGACCAACGGUCUCCACUGUGAAGCACAAAUAGCGGGAUGUCGUCUGUUGGGCCGAGAAUGCGGGCCAAGCAGCGGGUUGAAGCGAUUUACGCAAAUCCGGCUACCGCAAUCGGGAAAAGAUGCUUGUGCCGUUUUCGUCAGCCACUCGCAGAGCAGAGCAAAUUAAGCUAACAGCCGAGCAGCAAACGCUGUUCUCCGUACGGCAGAACUCCAGCCCGUAUGAUCGGCCUAACGUGACCGCCCUAUGGCAAGGACGGGAUUCUGCCUAUCAGGCAUGAACUAAGCGGUCGCGUAGCGGCCACCUCCCCAUUUAUUGCAAUUGCUUCGCAAUUGUAAAAAAGGUUAACUAUCCACAUUUGAUACGACUAGUACUUUUUGCCCAUCCAUUUUUGACUCGUGAAUUUUUUAACAUGUGAAUUUUGACAAUCUUCUCCGUGGAAGCACCUCCUCUUCAUCGCUUCCAUUCAUUAACGAGAGCCACCUGCCCCUGCGCUAUUGCGCAGGGGCUUUUUUUUGUAGAGC
CP002998.1/605510-606150   UAAUGUAGCUGCCUUUAUAUUUACUGGUCCGUAGAAUCCCUCCCAGUGACAGGGCCUAUUCAUAGCGAGUGUGAACGGUCAAUCCGGCCAACUAAAGCUUUCAUAAUGGUCAUAAGGCGGCUGACCGACGGUCUCCACUGUGAAGCACAAAUAGCGGGAUGUCGUCUGUUGGGCCGAGAAUGCGGGCCAAGCAGCGGGUUGAAGCGAUUUACGCAAAUCCGGCUACCGCAAUCGGGAAAAGAUGCUUGUGCCGUUUUCGUCAGCCACUCGCAGAGCAGAGCAAAUUAAGCUAACAGCCGAGCAGCAAACGCUGUUCUCCGUACGGCAGAACUCCAGCCCGUAUGAUCGGCCUAACGUGACCGCCCUAUGGCAAGGACGGGAUUCUGCCUAUCAGGCAUGAACUAAGCGGUCGCGUAGCGGCCACCUCCCCAUUUAUUGCAAUUGCUUCGCAAUUGUAAAAAAGGUUAACUAUCCACAUUUGAUACGACUAGUACUUUUUGCCCAUCCAUUU-UAACUCGUGAAUUUUUUAACAUGUGAAUUUUGACAAUCUUCUCCGUGGAAGCACCUCCUCUUCAUCGCUUCCAUUCAUUAACGAGAGCCACCUGCCCCUGCGCUAUUGCGCAGGGGCUUUUU--UGUAGAGC
ACEK01000020.1/48226-48866 UAAUGUAGCUGCCUUUAUAUUUACUGGUCCGUAGAAUCCCUCCCAGUGACAGGGCCUAUUCAUAGCGAGUGUGAACGGUCAAUCCGGCCAACUAAAGUUUUCAUAAUGGUCAUAAGGCGGCUGACCGACGGUCUCCACUGUGAAGCACAAAUAGCGGGAUGUCGUCUGUUGGGCCGAGAAUGCGGGCCAAGCAGCGGGUUGAAGCGAUUUACGCAAAUCCGGCUACCGCAAUCGGGAAAAGAUGCUUGUGCCGUUUUCGUCAGCCACUCGCAGAGCAGAGCAAAUUAAGCUAACAGCCGAGCAGCAAACGCUGUUCUCCGUACGGCAGAACUCCAGCCCGUAUGAUCGGCCUAACGUGACCGCCCUAUGGCAAGGACGGGAUUCUGCCUAUCAGGCAUGAACUAAGCGGUCGCGUAGCGGCCACCUCCCCAUUUAUUGCAAUUGCUUCGCAAUUGUAAAAAAG-UUAACUAUCCACAUUUGAUACGACUAGUACUUUUUGCCCAUCCAUUUUUAACUCGUGAAUUUUUUAACAUGUGAAUUUUGACAAUCUUCUCCGUGGAAGCACCUCCUCUUCAUCGCUUCCAUUCAUUAACGAGAGCCACCUGCCCCUGCGCUAUUGCGCAGGGGCUUUUU--UGUAGAGC
#=GC SS_cons               ::::::::::::{{{{{{{,,{{{{{{{{-{{{{{{{{{{{{{--{{-{-{{{{,,,,<<<<<<_____>>>>>>{{{{{{<<<<-<<--------<<<<-<<<<-<<<-----<<<<-<________>->>>>>>>->>>>>>>>------->>->>>>,,,,,,[[[[[[[[[[[--[[[[[[[[((((((,<<<<<<---<<<_____>>>->>>>>>,,,,<<<____>>>,,,,,,,))))))((((((,,,,,,,,,,,,<<<________>>>,,,,,,,,<<<___>>>,<<<<<<<____>>>>>>>,,,,,)))))),,,,,,,,]]]]]]]]--]]]]]]]]]]]}}}}}}}}}}-}-}}--}}}-}}}}}}}<<<<<___>>>>>,,,,,,,,<-<<<<<<___>>>>>>->,,,,<<-<<<-<<<<<<<<<<___>>>>>>>>>>->>>>>,,,,,,,,,,,,,,,,,,}}}}}}}}}}},,,,,,,,,,,,,,,,,,,,,,(((((-(((,,,,,,,,,<<<________>>>,,,,,,,,,<<<<<<<<______________>>>>>>>>,,)))-))))),,,,,,,,<<<<<<<<<<____>>>>>>>>>>,,,,,..}}}}}}}:
#=GC RF                    UAAUGUAGCUGCCucuacaUUuaCugGuCCGuaGaauCCCuCCCAGcGaCaGGGCCUAuuCacaGCGAGuguGaaCGGuCaauCCGGCCAACUAAAGcuuUCacaAuGGUCAUAaGgCGGCUGACCaACGGcCuCCaCuguGaagCACAAAUAGCGGGauGUCGUCcGuugGGCCGaGAaugCGGGCCaaGCaGCGGguuGAAGCGAUUUACGCAaacCCGGCUACCGCAAUCGGGAAAAGAuGCuuGuGCCGuUUUCGUCAGCCACuCGCAGAGCAGaGCAAAUUAAGCuAACaGCCGagCaGCAAACGCuGcuCUCCGUaCGGCaGAACUCCAGCCCGcauGAuCGGCCcaaCguGaCCGCCCuAuGgCAAGGaCGGGauuCuGCCuAUCaGGCaUGAACUAAGCGGcCGCGUAGCGgCCACCUCCcCAuuuAuugCaauuGCUUCGCaauuGcaaAaaaGgUUAACUAUCCACAUUUGAuaCGaCcaGuaCUUUUUGCCCAUCCAUUUUUaACuCGuGaauUUUUUAACAuGuGAAUUUUGaCaAUCUUCUCCguGGaaGCACCUCCUCUUCAUCGCuuCCacUCauuAaCGaGAgCCACCUGCCCCuGCGCUAUUGCGCaGGGGCUUUUU..uguagaGC
//
# STOCKHOLM 1.0

#=GF AC   RF02612
#=GF ID   BSR1350
#=GF DE   Brucella sRNA 1350
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   216.00
#=GF TC   216.50
#=GF NC   76.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25852653
#=GF RT   Identification of a Novel Small Non-Coding RNA Modulating the
#=GF RT   Intracellular Survival of Brucella melitensis.
#=GF RA   Wang Y, Ke Y, Xu J, Wang L, Wang T, Liang H, Zhang W, Gong C, Yuan J,
#=GF RA   Zhuang Y, An C, Lei S, Du X, Wang Z, Li W, Yuan X, Huang L, Yang X, Chen Z
#=GF RL   Front Microbiol. 2015;6:164.
#=GF WK   Brucella_sRNA
#=GF SQ   3



AE008917.1/1405266-1405091 AUGUAGGAAAGAAAUCAAUAAAUAGGAAAAUAGUCCUUGACUGCGUUACGGCGCUUUGGUAGAUAUUGGCUACGGUCGAGAAAUUGCGACUGAUGCCAUCUUAGCUACAUACCCCCGGCUGACAUGGUAAGGAUAGCCCCGGAAAGCCAUCGGUUUUUCGGGGUUUCUUUUAGAGA
CP003128.1/577712-577887   AUGUAGGAAAGAAAUCAAUAAAUAGGAAAAUAGUCCUUGACUGCGUUACGGUGCUUUGGUAGAUAUUGGCUACGGUCGAGAAAUUGCGACUGAUGCCAUCUUAGCUACAUACCCCCGGCUGACAUGGUAAGGAUAGCCCCGGAAAGCCAUCGGUUUUUCGGGGUUUCUUUUAGAGA
ADFB01000056.1/18790-18965 AUGUAGGAAAGAAAUCAAUAAAUAGGAAAAUAGUCCUUGACUGCGUUACGGUGCUUUGGUAGAUAUUGGCUACGGUCGAGAAAUUGCGACUGACGCCAUCUUGGCUACAUACCCCCGGCUGACAUGGUAAGGAUAGCCCCGGAAAGCCAUCGGUUUUUCGGGGUUUCUUUUAGAGA
#=GC SS_cons               ::::::(((((((,,,,,,,,,,,,,,,,,,,<<<<<<<-<<<-<<<<<<<-<-----<<<<----<<<<--<<<<<<________>>>>>>-->>>>------>>>>----->>>>-->>>>->>>>>>>>>>,<<<<<<<<<<<<<___>>>>>>>>>>>>>))))))):::::
#=GC RF                    AUGUAGgaaaGaaAUCAAUAAAUAGGAAAAUAguCCuugACcgCGucaCGGuGCUUUGGuaGAUAUuGGCUACgGuCGAGAAAUUGCGaCcGAuGCCaUCUUaGCuaCAUACCCCCGGCugaCAcgGcaaGGacAgCCCCGgaaagCCAUCGGcuuucCGGGGcuuCuuucAGAGA
//
# STOCKHOLM 1.0

#=GF AC   RF02613
#=GF ID   BSR0739
#=GF DE   Brucella sRNA 0739
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   191.00
#=GF TC   192.20
#=GF NC   91.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25852653
#=GF RT   Identification of a Novel Small Non-Coding RNA Modulating the
#=GF RT   Intracellular Survival of Brucella melitensis.
#=GF RA   Wang Y, Ke Y, Xu J, Wang L, Wang T, Liang H, Zhang W, Gong C, Yuan J,
#=GF RA   Zhuang Y, An C, Lei S, Du X, Wang Z, Li W, Yuan X, Huang L, Yang X, Chen Z
#=GF RL   Front Microbiol. 2015;6:164.
#=GF WK   Brucella_sRNA
#=GF SQ   4



AE008917.1/764954-765113     AGUAAUGGUUGAAAAGCCCGCAAAUACAGGCUUAGUUGAGGGCAUCAGAAGAAGCCAUUGACUUGUCAGGCGUUUUUCUGAUCUCCAGAUUUCAUGUUGCGGACAGUUCCUGCUCGCACCAGGGCCGGUCGGGAAACUCCGCCGGCCUUUAUUUUUAACA
CP003128.1/1223019-1222860   AGUAAUGGUUGAAAAGCCCGCAAAUACAGGCUUAGUUGAGGGCAUCAGAAGAAGCCAUUGACUUGUCAGGCGUUUUUCUGAUCUCCAGAUUUCAUGUUGCGGACAGUUCCUGCUCGCAUCAGGGCCGGUCGGGAAACUCCGCCGGCCUUUAUUUUUAACA
ACJD01000003.1/514098-513939 AGUAAUGGUUGAAAAGCCCGCAAAUACAGGCUUAGUUGAGGGAAUCAGAAGAAGCCAUUGACUUGUCAGGCGUUUUUCUGAUCUCCAGAUUUCAUGUUGCGGACAGUUCCUGCUCGCAUCAGGGCCGGUCGGGAAACUCCGCCGGCCUUUAUUUUUAACA
ACBI01000021.1/3148-2989     AGUAAUGGUUGAAAAGCCCGCAAAUACAGGCUUAGUUGAGGGCAUCAGAAGAAGCCAUUGACUUGUCAGGCAUUUUUCUGAUCUCCAGAUUUCAUGUUGCGGACAGUUCCUGCUCGCAUCAGGGCCGGUCGGGAAACUCCGCCGGCCUUUAUUUUUAACA
#=GC SS_cons                 :::::::((((((((<<<-<______>->>>,,<<<<--<<<-<<<<<<<<<<<<<--<<<____>>>>>>->>>>>>>>>>>>>-->>>>,,,<<-<<<<<-<<<___>>>->>>>>->><<<<<<<-<<<<____>>>>>>>>>>>,,,)))))))):
#=GC RF                      AGUAAUGGuugaaaaGcccGcAAAUACAggCUUagucGAGgGcaucaGaagaaGccAUuGacUUGuCaggCguucuuCugauCcCcAgacuUcAuGUuGcGgAcaGUUcCugccCgCauCagGGccGGUcGGgAAAccCCgCCggCCcUUAuuuucaaCA
//
# STOCKHOLM 1.0

#=GF AC   RF02614
#=GF ID   BSR1073
#=GF DE   Brucella sRNA 1073
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   241.00
#=GF TC   241.50
#=GF NC   109.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25852653
#=GF RT   Identification of a Novel Small Non-Coding RNA Modulating the
#=GF RT   Intracellular Survival of Brucella melitensis.
#=GF RA   Wang Y, Ke Y, Xu J, Wang L, Wang T, Liang H, Zhang W, Gong C, Yuan J,
#=GF RA   Zhuang Y, An C, Lei S, Du X, Wang Z, Li W, Yuan X, Huang L, Yang X, Chen Z
#=GF RL   Front Microbiol. 2015;6:164.
#=GF WK   Brucella_sRNA
#=GF SQ   2



AE008918.1/1114550-1114745 UAAACCCUUUGACUGCUCAAAAUGGGCGCCAUUGAAUGUUGGGCUGUGGAGGAAAAUUAACUUAUGCCUCGGUUUGAACGAAAAUGGUUAAACUUUAGGAGCAAACUGAAAGUACGUUGUUCCACCAUUGAGGCUAUAGGGUAUUAGGAUGGAACAUCUUCGUCAUGUCGCGGAGCGACGUGAUGUAUUUUCCCGC
CP000873.1/155502-155307   UAAACCCUUUGACUGCUCAAAAUGGGCGCCAUUGAAUGUUGGGCUGUGGAGGAAAAUUAACUUAUGCCUCGGUUUGAACGAAAAUGGUUAAACUUUAGGAGCAAACUGAAAGUACGUUGUUCCACCAUUGAGGCUAUAGGGUAUUAGGAUGGAACGUCUUCGUCAUGUCGCGGAGCGACGUGAUGUAUUUUCCCGC
#=GC SS_cons               ::::::::<<-<<-<<<<<<<<<<<___>>>>>----->>>>>>->>->>[[[[[[[,,,((((((((((<<<<<<<-<______>->>>>>>>,,,<<<<<<<<<<___>>>--->>>>>>>,,,,,,)))))-))))),,,,,<<<<<<___>>>>>><<<<<<<<<<<___>>>>>>>>>>>,]]]]]]]:::
#=GC RF                    UAAAcccUucGacUGcccaaaauGGGcGCCauuGAAUGuugggCUguGgaGGaaaauUAAccuauGccucgGuuugaAcGAAAAUgGucaaaCcUUAGGagcaaacuGAAaguAcGuugcuCCAccAUUgaggCUauaggGUAUUagGacGGAACguCcucgucacGucGcGGAgCgaCgugacgUauuuuCCcGc
//
# STOCKHOLM 1.0

#=GF AC   RF02615
#=GF ID   BSR0626
#=GF DE   Brucella sRNA 0626
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   155.00
#=GF TC   155.10
#=GF NC   58.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25852653
#=GF RT   Identification of a Novel Small Non-Coding RNA Modulating the
#=GF RT   Intracellular Survival of Brucella melitensis.
#=GF RA   Wang Y, Ke Y, Xu J, Wang L, Wang T, Liang H, Zhang W, Gong C, Yuan J,
#=GF RA   Zhuang Y, An C, Lei S, Du X, Wang Z, Li W, Yuan X, Huang L, Yang X, Chen Z
#=GF RL   Front Microbiol. 2015;6:164.
#=GF WK   Brucella_sRNA
#=GF SQ   2



AE008918.1/661282-661409 UUCCUUCAUUGGCAGAAAAAAUCGAAAACGGUAGCAUUCAAAAUGAAAACAUCCGAAAGCGAAGCGAUAAUAAUUGGGGAGAACGUGUGAAUAAUAUGCGGGCAACCCGCGUGCCUUCUGAUUCCCCC
CP000709.1/637805-637678 UUCCUUCAUUGGCAGAAAAAAUCGAAAGCGGUAGCAUUCAAAAUGAAAACAUCCGAAAGCGAAGCGAUAAUAAUUGGGGAGAACGUGUGAAUAAUAUGCGGGCAACCCGCGUGCCUUCUGAUUCCCCC
#=GC SS_cons             ::<<______>>,,,,,,,,,<<<----<<<-----<<<<___>>>>----->>>---->>>-------------<<<<<----<<--<<<---<<<<<<<<___>>>>>>>>-->>>-->>>>>>>:
#=GC RF                  UUCCUUCAUUGGCAGAAAAAAuCGAAAaCGGUAGCAuuCaAAAuGaaAACAUCCGAAAGCGaAGCGAUAAUAAUUGGGGaGAACguGUGaaUAAcacGCGGGCAACCCGCgugCCuuCUGacuCCCCC
//
# STOCKHOLM 1.0

#=GF AC   RF02616
#=GF ID   SSRC8_2
#=GF PI   SSRC8;
#=GF DE   Streptococcus sRNA 8
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   72.00
#=GF TC   72.00
#=GF NC   71.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   23762235
#=GF RT   Novel regulatory small RNAs in Streptococcus pyogenes.
#=GF RA   Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH
#=GF RL   PLoS One. 2013;8:e64021.
#=GF CC   Sequence is experimentally verified.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



CP003068.1/347038-347318 ACAUACUGAGCUUUAGUAUUUUAGAACGGAGACACCCCCAGUUUUGUACUCAAAAAGCAUGAACAGUUCUGCUGAUGUGACAUCUGAUUUCUACGUGCGCAGUGAGCCAAAACAGCUGCUGUUUGCUAUGGAAAAAGUGGCGCCAAUCGAGAUUUUUGAGACCCUAGGCUCAAAAAUAAGGCAUAGAAUUCCAAAGGAAGUCGCUGCCGUGAGCACAACCUAAGAAAAACUAUUCCAAAAGACUUUUUCUGCAAUUUGAAAUACUGAAUUUCAGUAUUUUU
AE014074.1/340001-340281 ACAUACUGAGCUUUAGUAUUUUAGAACGGAGACACCCCCAGUUUUGCACUUAAAAAGCAUAGACAGCUCUGCUGAUGUGACAUCCGGUUUCUACGUGCGCUGUGAGCCAAAACAGCUGCUGUUUGCUAUGGAAAAAGUGGCGCCAAUCGAGAUUUUUGAGACCCUAGGCUCAAAAAUAAGGCAUAGAAUUCCAAAGGAAGUCGCUGCCGUGAGCACAACCUAAGAAAAACUAUUCCAAAAGACUUUUUCUGCAAUUUGAAAUACUGAAUUUCAGUAUUUUU
#=GC SS_cons             ::{{{{{{{{-{{{{{{{{{{{{{{,<<<<--<<<---<<<<---<<__________________>>--->>>>-->>>--->>>>,,,,,,<<<-<<<<<<<________>>>>>->>>>>[[[[---[[[[[[[[[,(-((((,,,,,,<<<<<<<<<-<<___>>>>>>>>>>>,,<<<<--<<-<<<<___>>>>->>-->>>>,))-))-),,,,,,,<<<______>>>,,,,,,]]]]]]]]]]]]]}}}}}}}}}}}}}}-}}}}}}}}::::
#=GC RF                  ACauaCuGagCuucaGuauuucagaACgGaGACaCCCCCaGcUUUgcACUuAAAAAGCAUaaACAgcUCUgCuGAUGuGACAuCcGaUUUCUaCgUGCGCuGuGAGCCAAAaCaGCUGCcGuuuGCUAUgGaaaaaGuGGCGCCaAUCGAGauuuuuGaGACCCUAGGCuCaaaaauAAGGCaUAGaAuuCCAAAGGaaGuCGCuGCCGuGAGCACAACCUAAGaaAAACUAuuCCAAAAGaCuuuuuCcGCaaucugaaauaCugaaUcuCaGuauUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02617
#=GF ID   SSRC10
#=GF DE   Streptococcus sRNA 10
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   56.00
#=GF TC   56.60
#=GF NC   55.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   23762235
#=GF RT   Novel regulatory small RNAs in Streptococcus pyogenes.
#=GF RA   Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH
#=GF RL   PLoS One. 2013;8:e64021.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



AE014074.1/482091-482203 AUCAAGGGAGUAGCAGACGGCUAGCCGUGAUUGUAUCGUCAAUACGGAAUUUCGGUUUCCGGUACAAUCUUAAACAGCGAGACUUGUUUAAGAA-AAUAAACAGGUCUUUUUAU
CP002215.1/653086-653198 AUCAAGGGAGUAGCAGACGGUUAGCCGUGAUUGUAUCGUCAAUACGGAAUUUCGAUUUCCGGUACAAUCUGAAACAGCGAGACUUGUUUAAGAA-AAUAAACAGGUCUUUUUAU
FM204884.1/742485-742598 AUCAAGGGAGUAGCAGACGGUUAGCCGUGAUUGUGUCGUCAAUACGGAAUUUCGAUUUCCGGUACAAUCUGAAACAGCGAGACUUGUUUAAGAAAAAUAAACAGGUCUUUUUAG
#=GC SS_cons             ::::<-<<--<<<<_____>>>>->>-><<<<<<<<<<--<<--<<<____>>>-->>->>>>>>>>>>---------<<<<<<<<<<<<____.__>>>>>>>>>>>>:::::
#=GC RF                  AUCAaGGGAGuagCAGACGGcuaGCCGuGauuGuacCGUCaaUACGgAAUUcCGaUuuCCGguaCaauCUgAAACAGCgaGaCcuGuuuaAGAA.AAuaaaCagGuCucUUUAu
//
# STOCKHOLM 1.0

#=GF AC   RF02618
#=GF ID   SSRC34_2
#=GF PI   SSRC34;
#=GF DE   Streptococcus sRNA 34
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   48.00
#=GF TC   48.40
#=GF NC   46.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   23762235
#=GF RT   Novel regulatory small RNAs in Streptococcus pyogenes.
#=GF RA   Tesorero RA, Yu N, Wright JO, Svencionis JP, Cheng Q, Kim JH, Cho KH
#=GF RL   PLoS One. 2013;8:e64021.
#=GF CC   Sequence is experimentally verified.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



AE014074.1/1503185-1503061 UGUUUUCAAGCUGUUUAAAACAAAAAUAUGCUGAAAAAUGUUGAAAUUAUUAAAAUGAUUUUCAUUUUUUGAUAGCUGUUGACAGAAGAAAAACCACCAUUUUCUGAAAAAUAGUGGUUUCGUUU
CP000261.1/1453777-1453653 UGUUUUCAAGCUGUUUAAAACAAAAAUAUGCUGAAAAAUGUUGAAAUUAUUAAAAUGAUUUUCAUUUUUUGAUAGCUGUUGACAGAAGAAGAACCACCAUUUUCUGAAAAAUAGUGGUUUCGUUU
CP000262.1/1471687-1471563 UGUUUUCAAGCUGUUUAAAACAAAAAUAUGCUGAAAAAUGUUGAAAUUAUUAAAAUGAUUUUCAUUUUUUGAUAGCUGUGGACAGAAGAAAAACCACCAUUUUCUGAAAAAUAGUGGUUUCGUUU
#=GC SS_cons               <<<<----<<<<<<<-----------------<<<<<<<<--<<<<<<<<____>>>>>>>>>>>>>>>>>>>>>>>--->>>>------<<<<<<<-<<<<<____>>>>>->>>>>>>:::::
#=GC RF                    uGucUUCAaGCugucUAAAACAAAAAUAUGCUgaaaaauGUUgaaaucauUAAAaugauuucCauuuuucgacaGCuGUugaCaGAAGAAaaaCCaCCauuuuCUGAaaaauAGuGGuuuCGUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02619
#=GF ID   BSnc115
#=GF DE   Brucella sRNA 115
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   115.00
#=GF TC   115.60
#=GF NC   35.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26553849
#=GF RT   Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis
#=GF RT   by Deep Sequencing.
#=GF RA   Saadeh B, Caswell CC, Chao Y, Berta P, Wattam AR, Roop RM 2nd, O'Callaghan
#=GF RA   D
#=GF RL   J Bacteriol. 2015;198:427-435.
#=GF WK   Brucella_sRNA
#=GF SQ   3



AE014291.4/338240-338150   UAUCUGGCUGUUGAGGCUUAUGGGUUACACAUGGACCAAGCCCGCCCGAAGCCGAUAUGGCCAGCGCAGAGCGGGAAAAAUCAAAAUCAGU
CP000887.1/358518-358428   UAUCUGGCUGUUGAGGCUUAUGGGUUACACGUGGACCAAGCCCGCCCGAAGCCGAUAUGGCCAGCGCAGAGCGGGAAAAAUCAAAAUCAGU
ADFB01000045.1/58885-58795 UAUCUGGCUAUUGAGGCUUAUGGGUUACACAUGGACCAAGCCUGCCCGAAGCCGAUAUGGCCAGCGCAGAGCGGUAAAAAUCAAAAUCAGU
#=GC SS_cons               :::<<<<<<<<---<<<<<-<<<<<-------<<_______>>>>>>>>>>>>--->>>>>>>><<<___>>>::::::::::::::::::
#=GC RF                    UAUCuGGCuguUGAGGCuuAuGGGuUACACaUgGACCAAGCCcgCCCgaaGCCGAUacgGCCaGCGCAGAGCGGgAAAAAUCAAAAUCAGU
//
# STOCKHOLM 1.0

#=GF AC   RF02620
#=GF ID   BSnc119
#=GF DE   Brucella sRNA 119
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   115.00
#=GF TC   115.20
#=GF NC   66.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26553849
#=GF RT   Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis
#=GF RT   by Deep Sequencing.
#=GF RA   Saadeh B, Caswell CC, Chao Y, Berta P, Wattam AR, Roop RM 2nd, O'Callaghan
#=GF RA   D
#=GF RL   J Bacteriol. 2015;198:427-435.
#=GF WK   Brucella_sRNA
#=GF SQ   3



AE014291.4/953526-953437   GGCUCUAUUGACCUCCGAGCCAGUCACCUAACGUCAUGAAUUGGACCCGCUCCCAUUGAAGCGGGUCAUUUUUUUGAAAGCAUUCCCUGA
ADFA01000018.1/19695-19606 GGCUCUAUUGACCUCCGAGCCAGUCACCUAACGUCAUGAAUUGGGCCCGCUCCCAUUGAAGCGGGUCAUUUUUUUGAAAAUAUUCCCUGA
ADFB01000046.1/1200-1111   GGCUCUAUUGACCUCCGAGCCAGUCACCUAACGUCAUGAAUUGGGCCCGCUCCCAUUGAAGCGGGUUAUUUUUUUGAAAAUAUUCCCUGA
#=GC SS_cons               <<<<<___________>>>>>------------<<<-<<<---<<<<<<<<________>>>>>>>>--->>>->>>:::::::::::::
#=GC RF                    GGCuCUAUUGACCUCCGaGCCAGUCACCUAACGuCaUgaaUUGGgCCCGCuCCCAUUGAaGCGGGcCAUUuuuUuGaAAauAUUCCCUGA
//
# STOCKHOLM 1.0

#=GF AC   RF02621
#=GF ID   BSnc120
#=GF DE   Brucella sRNA 120
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   114.00
#=GF TC   114.90
#=GF NC   70.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26553849
#=GF RT   Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis
#=GF RT   by Deep Sequencing.
#=GF RA   Saadeh B, Caswell CC, Chao Y, Berta P, Wattam AR, Roop RM 2nd, O'Callaghan
#=GF RA   D
#=GF RL   J Bacteriol. 2015;198:427-435.
#=GF WK   Brucella_sRNA
#=GF SQ   3



AE014291.4/967105-967018   AUUACCGAGGGGAACGACGCGCUAAAAAGCGCGCGCAAAAGAGAAACCCCGGCUUUCGCCGGGGUUUCUUCAUUUUAUCAAUAAGUUA
ADFA01000018.1/33275-33188 AUUACUGAGGGGAACGACGCGCUAAAAAGCGCGCGCAAAAGAGAAACCCCGGCUUUCGCCGGGGUUUCUUCAUUUUAUCAAUAAGUUA
CP000911.1/986869-986782   AUUACCGAGGGGAACGACGCGCUAAAAAGCGCGCGCAAAAGAGAAACCCCGGCUUUCGCCGAGGUUUCUUCAUUUUAUCAAUAAGUUA
#=GC SS_cons               ::::<<____>>,,<<-<<<<<<____>>>>>>>>-----<<<<<<<<<<<<<____>>>>>>>>>>>>>::::::::::::::::::
#=GC RF                    AUUACcGAGGgGAACGACGCGCuAAAAaGCGCGCGCAAAAgaGaaaCCcCGGCUUUCGCCGgGGuuuCuuCAUUUUAUCAAUAAGUUA
//
# STOCKHOLM 1.0

#=GF AC   RF02622
#=GF ID   BSnc121
#=GF DE   Brucella sRNA 121
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   114.00
#=GF TC   138.70
#=GF NC   53.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26553849
#=GF RT   Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis
#=GF RT   by Deep Sequencing.
#=GF RA   Saadeh B, Caswell CC, Chao Y, Berta P, Wattam AR, Roop RM 2nd, O'Callaghan
#=GF RA   D
#=GF RL   J Bacteriol. 2015;198:427-435.
#=GF WK   Brucella_sRNA
#=GF SQ   2



AE014291.4/1150053-1149938 UGACGUCCUACAUAUUAGGGCAGGCAGAGCCAUAUGAAUGGGCAUCGAGUGAUAGGUUUAUGAGGCGCAUCAAUACAAUCAUGCAGGGCAAGACCAAUGGGGGGAACGGGCCGGAA
ADFB01000033.1/35036-34921 UGACGUCCUACAUAUUAGGGUAGGCAGAGCCAUAUGAAUGGGCAUCGAGUGAUAGGUUUAUGAGGCGCAUCAAUACAAUCAUGCAGGGCAAGACCAAUGGGGGGAACGGGCCGGAA
#=GC SS_cons               ::::<<<<<<_____>>>>>>,,<<<<<----<<<--<<<-<<-<<--<<<<_____>>>>>>->>->>>-->>>--->>->>>--<<<--<-<<______>>--->-->>>::::
#=GC RF                    UGACgcCCuaCAUAUuaGGgcAGGCaGaGCCAuauGAauGGGCAuCGAgugaUAGGUucacGaGGCGCauCAauaCAAuCAuGCAGGGCAAGACCAAUGGGGGGAACGGGCCGGAA
//
# STOCKHOLM 1.0

#=GF AC   RF02623
#=GF ID   BSnc140
#=GF DE   Brucella sRNA 140
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   126.00
#=GF TC   126.00
#=GF NC   112.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26553849
#=GF RT   Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis
#=GF RT   by Deep Sequencing.
#=GF RA   Saadeh B, Caswell CC, Chao Y, Berta P, Wattam AR, Roop RM 2nd, O'Callaghan
#=GF RA   D
#=GF RL   J Bacteriol. 2015;198:427-435.
#=GF WK   Brucella_sRNA
#=GF SQ   2



AE014291.4/1781160-1781067 AUCAACCGACUGAUAAAAAGACGGCCCAUCGUCUCGACGCUAAUGUCGCAGGGAAUGAGAGCCGGACCGAACAACCGAAAGGACAACAAAUGUU
ADFB01000086.1/540-447     AUCAACCGACUGAUAAAAAGACGGCCCAUCGUCUCGACGCCAAUGUCGCAGGGAAUGAGAGCCGGACCGAACAACCGAAAGGACAACAAAUGUU
#=GC SS_cons               <<<<______>>>>,,,,,,,<<<<<<<<--<<<<<<<______>>>>->>>-->>>->->>>>----------<<____>>::::::::::::
#=GC RF                    auCaACCGACuGauAAAAAGACGGCCCauCGuCuCGaCGCuAAUGuCGCaGgGAauGAGAGCCGGACCGAACAACCGAAAGGACAACAAAUGUU
//
# STOCKHOLM 1.0

#=GF AC   RF02624
#=GF ID   BSnc150
#=GF DE   Brucella sRNA 150
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   73.00
#=GF TC   73.10
#=GF NC   33.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   26553849
#=GF RT   Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis
#=GF RT   by Deep Sequencing.
#=GF RA   Saadeh B, Caswell CC, Chao Y, Berta P, Wattam AR, Roop RM 2nd, O'Callaghan
#=GF RA   D
#=GF RL   J Bacteriol. 2015;198:427-435.
#=GF WK   Brucella_sRNA
#=GF SQ   2



AE014292.2/1083352-1083395 ACCACAUAAGCGCCGGCCAAAGGCGCAUCAGGGGAACAUGAACA
CP002079.1/1137150-1137193 ACCACAUAAGCGCCGGCCAAAGGCGCAUCAGGGGAACAUGAAUG
#=GC SS_cons               :<<------<<<<<_______>>>>>------>>::::::::::
#=GC RF                    ACCACAUAAGCGCCGGCCAAAGGCGCAUCAGGGGAACAUGAAua
//
# STOCKHOLM 1.0

#=GF AC   RF02625
#=GF ID   WsnRNA46
#=GF DE   Wolbachia sRNA 46
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:25512495
#=GF GA   65.30
#=GF TC   65.30
#=GF NC   65.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25512495
#=GF RT   Wolbachia small noncoding RNAs and their role in cross-kingdom
#=GF RT   communications.
#=GF RA   Mayoral JG, Hussain M, Joubert DA, Iturbe-Ormaetxe I, O'Neill SL, Asgari S
#=GF RL   Proc Natl Acad Sci U S A. 2014;111:18721-18726.
#=GF WK   Wolbachia
#=GF SQ   3



AE017196.1/1204493-1204642 UUUACCUCAAGCAUA--AAGAUGUCAUCCAAGUAGCCAACACUGGGAUCCAGAAAAAUUGACUAUAAACAAGUAUGCUG--------UUUCGAUGAAAUUGUGUAAUAGAAACUAGAUUCCAGUGUCAGCUACUUGCAUGACACCAAGUU-UGUGUUUAUA
CP001391.1/1325213-1325365 GCAACUUCUAGCAGAAAAGGGUGUCAUCCGAGUAGCUAACACUGGGAUCCAGGAAACUUGAUUACAAAUAAAUAUGCUG--------UUUUAAUGAAUUUGUGUAAUAGAAGCUAGAUUCCAGUGUCAGCUACUUUCAUGACAUCAUCUACUAUGUAAAUU
ACFP01000103.1/1040-885    UUUGCCUCAAACACA--AAGGUGUCAUCCCAGUGCUUGACACUGGGAUCCAGUAAAAUUGAUUGUGAACAAGCACACUAUACAACAUUUUCAAUGAAAUUACAAAA---AAGCUGGAUUCCAGUGUCAAGCACUGGAAUGACACCAUUUGCUGUGCAAUUU
#=GC SS_cons               ::::::::::<<<<<..----<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<___________________________........_________________________>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>-------->>>>>:::::
#=GC RF                    uuuaCcUCaAgCaca..AaGguGuCaucccaGuggcugaCaCuGGgauCcaGuAAAaUUGAuUauaAAcAAguAugCUg........UUUcaAUGAAaUUguguAAUAGAAgCugGauuCCaGuGucagccaCugggauGaCacCAuuUaCuguGcaaaUu
//
# STOCKHOLM 1.0

#=GF AC   RF02626
#=GF ID   WsnRNA59
#=GF DE   Wolbachia sRNA 59
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:25512495
#=GF GA   49.00
#=GF TC   49.70
#=GF NC   47.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25512495
#=GF RT   Wolbachia small noncoding RNAs and their role in cross-kingdom
#=GF RT   communications.
#=GF RA   Mayoral JG, Hussain M, Joubert DA, Iturbe-Ormaetxe I, O'Neill SL, Asgari S
#=GF RL   Proc Natl Acad Sci U S A. 2014;111:18721-18726.
#=GF WK   Wolbachia
#=GF SQ   2



AE017196.1/582231-582143 UACAUGCUAAGAAGGGGCACACAGGUAAAGCAUUCUUCUGCCUCACCACUUUAUAGUUGCUCUACCUGUGUUGUUAUGUUACAACGACU
HQ906664.1/7742-7829     UACAUGCUAAGAAAGCGCAUGCCGGUAGAGUCUUUCUGUGCCUCACCAAUUUGUAAUUACUCUACCAGUA-UGUUAAGCUAUAGCGACU
#=GC SS_cons             ::::<<-<<<-----<<<<<<<<<<<<-<<<<--<<__________________>>->>>>->>>>>>>>->>>>--->>>>>::::::
#=GC RF                  UACAugCuaaGAAaGggCacaCcGGuaaaGcaUUcuUgUGCCUCACCAaUUUaUagUugCuCuaCCgGugUuGucAuGuuacaaCGACU
//
# STOCKHOLM 1.0

#=GF AC   RF02627
#=GF ID   Ssr1
#=GF DE   Shigella small RNA 1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   820.00
#=GF TC   820.40
#=GF NC   365.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   27014636
#=GF RT   A Novel Small RNA Regulates Tolerance and Virulence in Shigella flexneri
#=GF RT   by Responding to Acidic Environmental Changes.
#=GF RA   Wang L, Yang G, Qi L, Li X, Jia L, Xie J, Qiu S, Li P, Hao R, Wu Z, Du X,
#=GF RA   Li W, Song H
#=GF RL   Front Cell Infect Microbiol. 2016;6:24.
#=GF CC   Exists only in Shigella, may play role in resistance to acidic stress and
#=GF CC   regulation of virulence.
#=GF WK   Shigella_flexneri
#=GF SQ   2



AE005674.2/286849-287502   AAGUUGUGGACGAAAUUAGAAUAAGAAUUGCUGGUAAUACGGCUGCGCCUUGUUUCCAUGUGCUAAAAAAUAAGGGAUAUAAAGUAACAAUGGAAACUCAUGCAUUAUCUGACGAUUGUUUAGAUUGUGUAUAUGAUUGGUAUGCGGAAAAAAAUGGACAAUUUUUUAGUGCAACGAGUCCAGAAGAGUUACUUGGAUUAGUUGCAAUGUGGGAAGUUCGUGGUAAUGACUGGAGAGCUAAUUUGAAUGAGAUAAAUACUUAUCAAAAAGCCAUAGAAGAAUCCCCGUUUUUUGAUAAAAACGGCAAUGAAAUAGAGUCUGACUAAAUUUUAUUGAUAUAGCAACGAUAAUAACCGGAAAUUUCUUCCAGAUCUUUCCGGCUUUUUAUUAUUUAACUUUCGUUCAGCACACUAAACAUCCCGUCUCGCAUCCCCUUAACUGGCUGUUUAACCUGAUAAAGUUCCCUGCGCAGUUCCUGUACUUCGUUGUUAUCCCAAGCAGGAUCAAACAUCCCUCCGAGAUCUUCACGGUAACGCCCGUGCCGAUCUCAAAUCCCGCUUUUCUCAGCCAUUUGGCGCUGAUUUUGAUCACCGGCGUGUCGCUGCGGUUGGGCAGAUAACCCACGGUACAGCGACGCUGUGUUUUGGAAAUGGU
AFGZ01000006.1/19734-20386 AAGUUGUGGACGAAAUUAGAAUAAGAAUUGCUGGUAAUACGGCUGCGCCUUGUUUCCAUGUGCUAAAAAAUAAGGGAUAUAAAGUAACAAUGGAAACUCAUGCAUUAUCUGACGAUUGUUUAGAUUGUGUAUAUGAUUGGUAUGCGGAAA-AAAUGGACAAUUUUUUAGUGCAACGAGUCCAGAAGAGUUACUUGGAUUAGUUGCAAUGUGGGAAGUUCGUGGUAAUGACUGGAGAGCUAAUUUGAAUGAGAUAAAUACUUAUCAAAAAGCCAUAGAAGAAUCCCCGUUUUUUGAUAAAAACGGCAAUGAAAUAGAGUCUGACUAAAUUUUAUUGAUAUAGCAACGAUAAUAACCGGAAAUUUCUUCCAGAUCUUUCCGGCUUUUUAUUAUUUAACUUUCGUUCAGCACACUAAACAUCCCGUCUCGCAUCCCCUUAACUGGCUGUUUAACCUGAUAAAGUUCCCUGCGCAGUUCCUGUACUUCGUUGUUAUCCCAAGCAGGAUCAAACAUCCCUCCGAGAUCUUCACGGUAACGCCCGUGCCGAUCUCAAAUCCCGCUUUUCUCAGCCAUUUGGCGCUGAUUUUGAUCACCGGCGUGUCGCUGCGGUUGGGCAGAUAACCCACGGUACAGCGACGCUGUGUUUUGGAAAUGGU
#=GC SS_cons               ::[[--[[[[[[[[[[[[[[[[[[[[[,,<<<<______>>>><<<<----<<<<<<<<<<<<<__________________>>>->>->>>>>>>>--->>>>,,,,<<<<-<<<<<<<<<--<<-<<<<<<<_____>>>>>>>->>----->>>>>>>>>-->>>><<<<<<-<<<<<<<_________>>>>>>>->>>>>>,(((((,,<<<<<-<<<<____>>>>-->>>>>,,<<<<<-<<<<_______>>>>>>>>>,,,))))),,,,,,,,,<<<<<<<<____>>>>>>>><<<<<<<<<--<<<___>>>-->>>>>>>>>,,,,,,,,,,,,,,,,,,<<<<<<<--<<<___>>>-->>>>>>>,]]]]]]]--]]]]]-]]]]]]]]]--]],,<<<<<<-<<-<<______________>>->>->>>>>>,,,,,,,,,,,((((--((((((((((((((((--((((((--(((((-(,<<<<_____>>>>,,,,<<<<<<--<<<<<______>>>>>-->>>>>>,,,,,,,,,,,,,,,<<<<-<<-<<-<<-<<<<____>>>>->>->>->>->>>>,)-)))))--))))))----)))))))-))-)))))))---)))):::::
#=GC RF                    AAGuUGuGgaCGaaauuagaauaagaaUUGCcGGUAAUACgGCuGCgCCUUGuuuCCauGugCuAAAAAAUAAGGGAUAUAAaGcAaCAauGGaaaCUCAcGCaUUAUCugaCgauuGuccaGAuuGcGcauacGAUUGguaugCgGaaAAAAAuggaCaaucUUucaGuGCaaCGaguCCagAAGAGUUACcuGGacuAGuuGCaAuguGGGAaGcuCGcgGuAAUGaCcgGAGagCuAAuuuGaAugaGAUAAAUACucauCaaaAAGCCacaGAAGAAUCCCCGuuuuuUGAUaaaaaCGGCaaugaaauAGaGuCUGaCuAAauuucauuGAUAUAGCAACGAUAAUAACCGGaaaUUuCuUCCaGaUCuuuCCGGCuucuuauUAucuaaCuuuCGucCaGCaCACuaaaCaUCCCGuCUCGCAUCCCCUUAaCUGGCuGuuuaACCUGAUAAAGuuCCCUgCgCaGcuCCuGuaCcUCGuugucAUCCCaaGCAGGauCAAACauCCCUCCGaGauCUUCaCGGUAACGCCCGuGCCGauCuCAAAUCCCGCUUUUCUCaGCCacUcGGCGCuGauUUUGauCaCCGGCgUguCGCuGCGGuuGGGCAgacaaCCCACgGuaCaGCGaCgCuGcGcUUUGGaaAUGGU
//
# STOCKHOLM 1.0

#=GF AC   RF02628
#=GF ID   Hrs1
#=GF DE   Hfq-regulated sRNA 1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   56.40
#=GF TC   56.40
#=GF NC   56.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   24885615
#=GF RT   Genome-wide identification of Hfq-regulated small RNAs in the fire blight
#=GF RT   pathogen Erwinia amylovora discovered small RNAs with virulence regulatory
#=GF RT   function.
#=GF RA   Zeng Q, Sundin GW
#=GF RL   BMC Genomics. 2014;15:414.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   2



FN666575.1/130143-130070 AAAAAAAACCCCGCCAUAAGGGCAGGGGUAGACAGGGAUGUGCCGGUGGCAAGGUAAACAGGGAUAAUGUGUUU
FP236842.1/124289-124216 AAAAAAAACCCCGCCAUCAUGGCGGGGGUAGACAGGGGUAUGUCUAUGGCAAGGAAAACAGGGAUAAUGUGUUA
#=GC SS_cons             :::::::<<<<<<<<_____>>>->>>>>-<<<<-<--<<<-<<-<<__________>>->>->>>->->>>>:
#=GC RF                  AAAAAAAaCCCCGCCAUaAuGGCaGGGGuAgaCaGgGaUaUGcCugUGGCAAGGuAAAcAGgGAuAAuGuGuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02629
#=GF ID   RmaA
#=GF DE   Regulator of motility and amylovoran A
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   57.00
#=GF TC   57.40
#=GF NC   48.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF DR   GO; 2000145; regulation of cell motility;
#=GF RN   [1]
#=GF RM   24885615
#=GF RT   Genome-wide identification of Hfq-regulated small RNAs in the fire blight
#=GF RT   pathogen Erwinia amylovora discovered small RNAs with virulence regulatory
#=GF RT   function.
#=GF RA   Zeng Q, Sundin GW
#=GF RL   BMC Genomics. 2014;15:414.
#=GF WK   Rma_A_small_RNA
#=GF SQ   2



FN666575.1/1783564-1783452 AAGAGUUCUGGUUUUAAAAAUGGCGCACAAUGUGCGCCAUUUUUUUUGCCUGGAACCAACCUCUUCCUGUUAACAGCCACUUACUUUUUAAAACCCAUGUAAACACGCCAGAA
J01577.1/580-692           AAGAGUUCUGGUUUUAAAAAUGGCGCACAAUGUGCGCCAUUUUUUUUGCCUUGAACCAACCUCUUCCUGUUAACAGCCACUUACUUUUUAAAACCCAUGUAAACACGCCAGAA
#=GC SS_cons               ::::<<<<<<<<---<<<<<<<<<<<<<___>>>>>>>>>>>>>--->>>->>>>>-----<<<--<<<<<-<<<______________________>>>->>>>->-->>>:
#=GC RF                    AAGAGuuCcGGcUUUaaaaauGGCGCaCAAUGuGCGCCauuuuuUUUgCCUgGaaCCAACCuCuUCCuGuuAaCaGCCACUUACUUUUUAAAACCCAuGuAaaCaCGCCaGaA
//
# STOCKHOLM 1.0

#=GF AC   RF02630
#=GF ID   Hrs12
#=GF DE   Hfq-regulated sRNA 12
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   70.00
#=GF TC   70.70
#=GF NC   50.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   24885615
#=GF RT   Genome-wide identification of Hfq-regulated small RNAs in the fire blight
#=GF RT   pathogen Erwinia amylovora discovered small RNAs with virulence regulatory
#=GF RT   function.
#=GF RA   Zeng Q, Sundin GW
#=GF RL   BMC Genomics. 2014;15:414.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   2



FN666575.1/2438083-2438169 CAUUUUUAUUUCAUAAUUACCUUCGUUUCCCGAAAUGAACUGUACGACUUAGUAUUCACGCCAGGCUUAAUGCCUGGCGUUUUUUUU
FP236842.1/1495952-1495866 AUUUUUUAUUUCAUAAUUACCUUCACUUGCCGAAAUGAACUGUAUGACUUCAUAUUCCCGCCAGGCUUAAUGCCUGGCGUUUUUUUA
#=GC SS_cons               ::::<<<<<<<<------<<____>>----->>>>>>>>,,<<<<______>>>>,,<<<<<<<<<_____>>>>>>>>>:::::::
#=GC RF                    auUUuuuauuuCAUAAUUacCUUCguUUgCCGaaaugaaCUguacGACUUaguauUCaCGCCaGGCUUAAUGCCuGGCGuUUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02631
#=GF ID   Hrs13
#=GF PI   Hrs10;
#=GF DE   Hfq-regulated sRNA 13
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   52.00
#=GF TC   52.90
#=GF NC   39.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   24885615
#=GF RT   Genome-wide identification of Hfq-regulated small RNAs in the fire blight
#=GF RT   pathogen Erwinia amylovora discovered small RNAs with virulence regulatory
#=GF RT   function.
#=GF RA   Zeng Q, Sundin GW
#=GF RL   BMC Genomics. 2014;15:414.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   2



FN666575.1/2610835-2610754 CACGCCCCUCUUUGACUGCUCCAUCCCUGUGUAGUUAUUAGUGUUGUCACUGACCGACCGCCUCUUUGCGGUCGGUUUUUUU
FP236842.1/1310637-1310717 CACGCCUCCUCUUUACCCCUUCAUCCCUGUGUAGUCAUUCGUGUUGUCACUGACCGACCGCC-CUUUGCGGUCGGUUUUUUU
#=GC SS_cons               ::::::::::::<<<<<<<___________>>>>>>><<<<<<____>>>>>><<<<<<<<______>>>>>>>>:::::::
#=GC RF                    CACGCCuCuuuUugaCugCUuCAUCCCUGUGcaGucauuaGuGUUGUCaCugaCCGaCCGCCUCUUUGCGGuCGGUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02632
#=GF ID   Hrs10
#=GF DE   Hfq-regulated sRNA 10
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   108.00
#=GF TC   108.40
#=GF NC   35.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   24885615
#=GF RT   Genome-wide identification of Hfq-regulated small RNAs in the fire blight
#=GF RT   pathogen Erwinia amylovora discovered small RNAs with virulence regulatory
#=GF RT   function.
#=GF RA   Zeng Q, Sundin GW
#=GF RL   BMC Genomics. 2014;15:414.
#=GF WK   Hfq_binding_sRNA
#=GF SQ   2



FN666575.1/2356768-2356621 AAAAAGAAAUGACCCGCACGGGGGAGCCGUGUGGGCCUAAGAUGUGACGAGUAUCGUUCAUCCUGCAUGCCUUUACAGACACGAUUCAGAACAGAUGGUUAUGCUAUUUGGAUUUUAUCGUUAGGAGCCUGUGAAUUCUGGCAGGAAA
FP236842.1/1571474-1571621 AAAAAGAAAUGACCCGCACGGGGGAGCCGUGUGGGCCUAAGAUGUGACGAGGAUCGUUCAUCCUGCAUGCCUUUACAGACAUGAUUCAGAACAGAUGAUUAUGCUAUUUGGAUUUAAUUGUUAGGAGCCUGUGCAUCUUGGCAGGAAA
#=GC SS_cons               ::::::::::::<<<<<<<<<_____>>>>>>>>>,,,,,,,,,,<<<<<___>>>>>--<<<<<<--<--<<<<<<<-<<<<<<------<<<<<<<<___>>>>>>>>------>>>>>----->->>>>>>>-->-->>>>>>::
#=GC RF                    AAAAAGAAAUGACCCgCaCGGGGGAGCCGuGcGGGCCUAAGAUGUgaCGaGuAuCGucCAuCCuGCAUgCCuucaCaGACacgauUCAGAACagauggcUAUgccaucuGGAUUUaaucguUAGGAGCCuGugaaUucUGGCaGGaAA
//
# STOCKHOLM 1.0

#=GF AC   RF02633
#=GF ID   Hrs21
#=GF DE   Hfq-regulated sRNA 21
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   102.00
#=GF TC   102.90
#=GF NC   31.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   24885615
#=GF RT   Genome-wide identification of Hfq-regulated small RNAs in the fire blight
#=GF RT   pathogen Erwinia amylovora discovered small RNAs with virulence regulatory
#=GF RT   function.
#=GF RA   Zeng Q, Sundin GW
#=GF RL   BMC Genomics. 2014;15:414.
#=GF CC   Could play role in virulence regulation. 
#=GF WK   Hfq_binding_sRNA
#=GF SQ   2



FN666575.1/1267525-1267392 AGAUUAUCCA-AACUCUCAGGUAUUGGCUACUAUGUAAGCCAUAUUCAUACCGGAUCGUGUCAUGACUAUGAUACUCAUCAGGAUGGUGCCCACCCGCCCGGCAUGCGCCCGUCACUCUGUACCCUGCACACAAU
FP236842.1/2713474-2713608 AGAUUAUCCAAAACUAUCUGGUAUUGGCUACUAUGUAAGCCAUGUUCAGACCGGAUCGUGUCAUGAUCAUGAUACUCAUCAGGAUGGUGCCAACCCGCCCGGCAUGCGCCCGUCACUCUGUACCCUGCACACAAU
#=GC SS_cons               :::::::::::::::::(((((((<<<<<________>>>>>,,,,,,,,<<-<<<-<<<<<<<____>>>>>>>-->>>->>,,<<<<<---<<_____>>--->>>>>,,,,,,,,,)))-))))::::::::
#=GC RF                    AGAUUAUCCAAAACUaUCaGGuauuGGCuACUAUGUAaGCCaUaUUCAuACCGGauCGuguCauGAuuauGauaCUCauCAGGAUGGuGCCaACCCGCCCGGCAUGCgCCCGUCACUCUguaCCCuGCACACAAU
//
# STOCKHOLM 1.0

#=GF AC   RF02634
#=GF ID   EF3314_EF3315
#=GF DE   Enterococcus sRNA EF3314_EF3315
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   86.00
#=GF TC   86.20
#=GF NC   46.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009405; pathogenesis;
#=GF DR   GO; 0006950; response to stress;
#=GF RN   [1]
#=GF RM   21912655
#=GF RT   Genome-wide identification of small RNAs in the opportunistic pathogen
#=GF RT   Enterococcus faecalis V583.
#=GF RA   Shioya K, Michaux C, Kuenne C, Hain T, Verneuil N, Budin-Verneuil A,
#=GF RA   Hartsch T, Hartke A, Giard JC
#=GF RL   PLoS One. 2011;6:e23948.
#=GF RN   [2]
#=GF RM   24914223
#=GF RT   Involvement of Enterococcus faecalis small RNAs in stress response and
#=GF RT   virulence.
#=GF RA   Michaux C, Hartke A, Martini C, Reiss S, Albrecht D, Budin-Verneuil A,
#=GF RA   Sanguinetti M, Engelmann S, Hain T, Verneuil N, Giard JC
#=GF RL   Infect Immun. 2014;82:3599-3611.
#=GF CC   It may be involved in the turnover of some abundant proteins. Involvement
#=GF CC   in stress response and virulence. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   2



AE016830.1/3201675-3201535 GAAAUCAUUCUUAUCAGAGUAUACAAAUACGAUGAUAAACAGUUGAAGCGAAUCUUGAUUUGCUUUUCCUAAACCUGAUUCUUUUAGAAUCAGGUUUUUGUUUAUCUAAAAGGCGGCAUUCGUUCAAAAACGGCUGUCGCC
CP002621.1/2723037-2722897 GAAAUCAUUCUUAUCAGAGUAUACAAAUACGAUGAUAAACAGUUGAAGCGAAUCUUGAUUUGCUUUUCCUAAACCUGAUUCUUUUAGAAUCAGGUUUUUGUUUGUCUAAAAGGCGGCAUUCGUUCAAAAACGGCUGUCGCC
#=GC SS_cons               ::::::::::<<<<<<--<<<<____>>>>-->>>>>>,,<<--<<<<<<<<<____>>>>>>>>>-->><<<<<<<<<<<<___>>>>>>>>>>>>,,,,,,,,,,,,,,<<<<<<<-<<<<<____>>>>>->>>>>>>
#=GC RF                    GAAAUCAUUCuuauCaGAGuauACAAauaCGAuGauaaACaGUUgaaGCgaauCUUGauucGCuucUCCuaaaCCuGauuCuUUUaGaauCaGGuuuUUGUUUaUCUAAAAGGCGgCaUcCGuuCAAAaaCGgCuGcCGCC
//
# STOCKHOLM 1.0

#=GF AC   RF02635
#=GF ID   EF0820_EF0821
#=GF DE   Enterococcus sRNA EF0820_EF0821
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   442.00
#=GF TC   442.60
#=GF NC   116.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   21912655
#=GF RT   Genome-wide identification of small RNAs in the opportunistic pathogen
#=GF RT   Enterococcus faecalis V583.
#=GF RA   Shioya K, Michaux C, Kuenne C, Hain T, Verneuil N, Budin-Verneuil A,
#=GF RA   Hartsch T, Hartke A, Giard JC
#=GF RL   PLoS One. 2011;6:e23948.
#=GF RN   [2]
#=GF RM   24914223
#=GF RT   Involvement of Enterococcus faecalis small RNAs in stress response and
#=GF RT   virulence.
#=GF RA   Michaux C, Hartke A, Martini C, Reiss S, Albrecht D, Budin-Verneuil A,
#=GF RA   Sanguinetti M, Engelmann S, Hain T, Verneuil N, Giard JC
#=GF RL   Infect Immun. 2014;82:3599-3611.
#=GF CC   Expressed during exponential phase. Seem not to be involved in virulence.
#=GF WK   Enterococcus_faecalis
#=GF SQ   2



AE016830.1/784383-784014   GUUACGGUUAAUAAGUAAAGUAAAUAAAGGUUUCUCAAAAACAGCGUAAUGACCUGGGAGAGAACAACGAUAACAAUGAACCAUUCCCAUGAGUGUUGCCUGGCAAUAUUUGUGGGGAUUUUUUGAUUAUUGUUAGCAUUUUUCUAGACAAGAACAACUGAAAAAAGAGUUUCUUUUUUCCAUUAUGUUUUGUUUCUGAGUUUAACCAAAUCACUCAUUAUUUCAAGGAGGAAUUAGGUUAUGUCAGUACAAUUAGAAGUUAAAGAAAGAGCUAUCCGUCCACGUUCACUAAGAAAUCAGCUACGUCACGAAGGGAAAGUACCUGCCAUUGUUUACGGUUACCAAAUUGAAAGUACACCAAUCUAUUUUG
ACAQ01000023.1/41291-40922 GUUACGGUUAAUAAGUAAAGUAAAUAAAGGUUUCUCAAAAACAGCGUAAUGACCUGGGAGAGAACAACGAUAACAAUGAACCAUUCCCAUGAGUGUUGCCUGGCAAUAUUUGUGGGGAUUUUUUGAUUAUUGUUAGCAUUUUUCUAAACAAGAACAACUGAAAAAAGAGUUUCUUUUUUCCAUUAUGUUUUGUUUCUGAGUUUAACCAAAUCACUCAUUAUUUCAAGGAGGAAUUAGGUUAUGUCAGUACAAUUAGAAGUUAAAGAAAGAGCUAUCCGUCCACGUUCACUAAGAAAUCAGCUACGUCACGAAGGGAAAGUACCUGCCAUUGUUUACGGUUACCAAAUUGAAAGUACACCAAUCUAUUUUG
#=GC SS_cons               ::[[[--[[[[[--[[[[-[[[[[[[[-[[[<<<<<-----<<<-<<____>>>>>--->>>>>,,<<<<<<<<<<-<<---<<<<<<<<<<<<<<<<<___>>>>>>>>>>>>>>>>>>>->>>->>>>>>>((((-(((((((<<<<<<<<------<<<<<<<<<___>>>>>>>>>------->>>>>>>><<<<---<<<<<-<<<--<<<___________>>>-->>>->>>>>-->>>>,,,,,,,,,,,,,,,,))))))))))),,<<<--<<<<---<<________>>-->>>>->>>,<<<_______>>>]]]-]]]]]]]]--]]]]---]]]]]--]]]:::::::::::::::
#=GC RF                    GUuaCGGucaauAAGuaaAGuaaacaaAGGcuuCuCAAAAACaGCGuAAUGaCCuGGGAGaGaaCAaCgauaaCaaUgaACCaucCCCacgaguguuGCCUGGCaacacucguGGGgauucUuuGAuuaucGuuaGCAucuuuCuagaCaagaACAACUGaaaaaaGaGUUuCuuuuuuCCAUUAUGucuuGucuCuGaGUUuaaCCAaauCACuCAUUAUUUCAAGGaGGAauuAGGuuaUGuCaGUACAAUUAGAAGUUAAaGaaagaGCuaUCCGuCCaCGuUCACuAAGAAAUCaGCUaCGuCaCGAaGGGAAAGUACCugCCAuuguuuaCGGuuaCCAAauugaAAGuaCACCAAUCUAUUUUG
//
# STOCKHOLM 1.0

#=GF AC   RF02636
#=GF ID   EF1368_EF1369
#=GF DE   Enterococcus sRNA EF1368_EF1369
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   533.00
#=GF TC   533.80
#=GF NC   218.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009405; pathogenesis;
#=GF DR   GO; 0006950; response to stress;
#=GF RN   [1]
#=GF RM   21912655
#=GF RT   Genome-wide identification of small RNAs in the opportunistic pathogen
#=GF RT   Enterococcus faecalis V583.
#=GF RA   Shioya K, Michaux C, Kuenne C, Hain T, Verneuil N, Budin-Verneuil A,
#=GF RA   Hartsch T, Hartke A, Giard JC
#=GF RL   PLoS One. 2011;6:e23948.
#=GF RN   [2]
#=GF RM   24914223
#=GF RT   Involvement of Enterococcus faecalis small RNAs in stress response and
#=GF RT   virulence.
#=GF RA   Michaux C, Hartke A, Martini C, Reiss S, Albrecht D, Budin-Verneuil A,
#=GF RA   Sanguinetti M, Engelmann S, Hain T, Verneuil N, Giard JC
#=GF RL   Infect Immun. 2014;82:3599-3611.
#=GF CC   Expressed during exponential phase. Involvement in stress response and
#=GF CC   virulence.
#=GF WK   Enterococcus_faecalis
#=GF SQ   4



AE016830.1/1345556-1346183   UGCCAAUUAUCCCGAAUUGGUUUUUUCAUACUUACUCCUACCAAGAGUAAAUAACAACCUUCAUUUCCACCACAGACGACGGUCGUGGUGGUUUUUUUUGUUUAGGUGCUAGUUUUUUUGCUAUCAAUUGACUAGGAGAAGUGAACGUUCUUUAAGAAUUUGUCAUUUCAAAUUUACGGAACCGCAAGAAACGAUUUGCUUCUUCCUCUAACUGAGUAAUUUCUUCUUCUGUUAACUCUUCCGUAGUAAUGUGAAUAUGUAACUCUUUUUGUGUGCUUUUCAUAGGUGCCUGAUGAUUAAUCUCUGUUUGUUGGGUGCGGCCCAUUAAAUAGUCCAAGGAGACAGAAAAAUAGUCUGCUAUUUUUAAAAGAUUCUCUACUUUAGGCGAAGAGGUAUCCCAACGACGAAUUUGUCCAUUGGAAAUGCCGACGUUUCUUUCUAAUUGGGCGAGGGUUAGUUGCUUUGACUGAGCUAAUUGUUUAAUGCGAGAAAUUAAGGUCAUUUCAAGUCCUCCUUGUGUUUUCCGUUUGCUAAUUUUAAAUUAGCGUAAAAGCGAAUGGUUGUCAAUUGCGAGCGUGUAAUAAGAAGGUGAACAUCUCAUGAGUGAUUUUUUAGAAAAUUUCCGAUG
CP002491.1/1791527-1792152   UGCCAAUUAUCCCGAAUUGGUUUUUUCAUACUUACUCCUACCAAGAGUAAAUAACAACCUUCAUUUCCACCACAGACGACGGUCGUGGUGGUUUUUUUUGUUUAGGUUCUAGUUU--UUGCUAUCAAUUGACUAGGAGAAGUGAACGUUCUUUAAGAAUUUGUCAUUUCAAAUUUACGGAACCGCAAGAAACGAUUUGCUUCUUCCUCUAACUGAGUAAUUUCUUCUUCUGUUAACUCUUCCGUAGUAAUGUGAAUAUGUAACUCUUUUUGUGUGCUUGUCAUAGGUGCCUGAUGAUUAAUCUCUGUUUGUUGGGUGCGGCCCAUUAAAUAGUCCAAGGAGACAGAAAAAUAGUCUGCUAUUUUUAAAAGAUUCUCUACUUUAGGCGAAGAGGUAUCCCAACGACGAAUUUGUCCAUUGGAAAUGCCGACGUUUCUUUCUAAUUGGGCGAGGGUUAGUUGCCUUGACUGAGCUAAUUGUUUAAUGCGAGAAAUUAAGGUCAUUUCAAGUCCUCCUUGUGUUUUCCGUUUGCUAAUUUUAAAUUAGCGUAAAAGCGAAUGGUUGUCAAUUGCGAGCGUGUAAUAAGAAGGUGAACAUCUCAUGAGUGAUUUUUUAGAAAAUUUCCGAUG
AECB01000048.1/138833-139458 UGCCAAUUAUCCCGAAUUGGUUUUUUCAUACUUACUCCUACCAAGAGUAAAUAACAACCUUCAUUUCCACCACAGACGACGGUCGUGGUGGUUUUUUUUGUUUAGGUUCUAGUUU--UUGCUAUCAAUUGACUAGGAGAAGUGAACGUUCUUUAAGAAUUUGUCAUUUCAAAUUUACGGAACCGCAAGAAACGAUUUGCUUCUUCCUCUAACUGAGUAAUUUCUUCUUCUGUUAACUCUUCCGUAGUAAUGUGAAUAUGUAACUCUUUUUGUGUGCUUGUCAUAGGUGACUGAUGAUUGAUCUCUGUUUGUUGGGUGCGGCCCAUUAAAUAGUCCAAGGAAACAGAAAAAUAGUCUGCUAUUUUUAAAAGAUUCUCUACUUUAGGCGAAGAGGUAUCCCAACGACGAAUUUGUCCAUUGGAAAUGCCGACGUUUCUUUCUAAUUGGGCGAGGGUUAAUUGCUUUGACUGAGCUAGUUGUUUAAUGCGAGAAAUUAAGGUCAUUUCAAGUCCUCCUUGCGUUUUCCGUUUGCUAAUUUUAAAUUAGCGUAAAAGCGAAUGGUUGUCAAUUGCGAGCGUGUAAUAAGAAGGUGAACAUCUCAUGAGUGAUUUUUUAGAAAAUUUCCGAUG
CP002621.1/1209639-1210263   UGCCAAUUAUCCCGAAUUGGUUUUUUCAUACUUACUCCUACCAAGAGUAAAUAACAACCUUCAUUUCCACCACAGACGACGGUCGUGGUGGUUU-UUUUGUUUAGGUUCUAGUUU--UUGCUAUCAAUUGACUAGGAGAAGUGAACGUUCUUUAAGAAUUUGUCAUUUCAAAUUUACGGAACCGCAAGAAACGAUUUGCUUCUUCCUCUAACUGAGUAAUUUCUUCUUCUGUUAACUCUUCCGUAGUAAUGUGAAUAUGUAACUCUUUUUGUGUGCUUGUCAUAGGUGCCUGAUGAUUGAUCUCUGUUUGUUGGGUGCGGCCCAUUAAAUAGUCCAAGGAAACAGAAAAAUAGUCUGCUAUUUUUAAAAGAUUCUCUACUUUAGGCGAAGAGGUAUCCCAACGACGAAUUUGUCCAUUGGAAAUGCCGACGUUUCUUUCUAAUUGGGCGAGGGUUAAUUGCUUUGACUGAGCUAGUUGUUUAAUGCGAGAAAUUAAGGUCAUUUCAAGUCCUCCUUGCGUUUUCCGUUUGCUAAUUUUAAAUUAGCGUAAAAGCGAAUGGUUGUCAAUUGUGAGCGUGUAAUAAGAAGGUGAACAUCUCAUGAGUGAUUUUUUAGAAAAUUUCCGAUG
#=GC SS_cons                 :<<<<<<<______>>>>>>>-{{{{{,,,,<<<<<<_______>>>>>>,,,{{{{{{{{{-{{{<<<<<<<-<<<____>>>>>>>>>><<<<<<<<<-<<<<-<<-<<<<______>>>>->>->>>>->>>>>>>>>,<<<<>>>>,,,,,<<<<<<<______>>>>>>>{{{{{{-{{{{{{----{{{{{{[[[[[[[-[[[[[--[[[-[[[[[,,,,,((((((--((,,,,,,,,<<<-<<<<<<---<<<<<_______>>->>>-->>>>>>-->>>,,<<<_____>>>,<<<<<<<-<<<<<___>>>>>->>>>>>>,,,,))--))))))<<<<<<<____>>>>>>>,,,,]]]]]]]]----]]]]]-]]]]]]],,,,<<<<-<<<<____>>>>-->>>><<<<<<<---<<<<<<<----<<<<<<<<<<<-<<<<<<_____>>>>>>->>-->>>>>>>>>-->>>>>>>--->>->>>>>}}}}}}---}}}}}}--}}}}}},<<<<<<<<___>>>>>>>>,,,}}}-}}}-}}}}}},,<<<<<______>>>>>,<<<<<<<--<<-<<____>>>>->>>>>>>,}}}}}:::::::::
#=GC RF                      UgCCaauuAUCCCGaauuGGcUuuuuCAUACuuaCuCCUACCAAGaGuaaAUAaCaaCCuuCAcuuCCaCCaCAGaCGACGGuCGuGGuGGcuucuccugUucagGugCuaGcUU..UUgCuaUcaAcugaCcaggagaagUGaaCGuuCUUUAAgaauuuGUCAUUUCaaauucaCGGaaCCgCaaGAAACGacuuGCcuCuuCCcCuaaCUGaGUaaucuCUUCUuCuGucAACuCUUCCGUAgcaAuguGagUAUGcaaCUCUUUUUGuGugCUUcuCacaGGugcCUGauGAUUaauCUCuguuugUuGGGcGCGgCCCaUcaaacaGUCCAaGGAgaCaGaaaaauaGUCUGCuauuuuUAAAagauuCuCUACUuuaGgCGaaGagGUAUCCCaaCGaCgAAUUcGuCCAuuGGaaauGCCGACguuuCucUCUAauugggCgagGGucagucGCuUUgacugaGCcAaucGcccaauGCgaGaaacUAAGGUCauuuCaaguCCUCCuuGcGUUuuCCGuUcGCuaauuUUAaauuaGCgUAAaagCGaaUGGuuGuCAauugcGAGCGUgcaauAagaagguGAaCAuCUCAUGaGuGaccuucuAGaaaaUUUCCGAUG
//
# STOCKHOLM 1.0

#=GF AC   RF02637
#=GF ID   EF0408_EF0409
#=GF DE   Enterococcus sRNA EF0408_EF0409
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   249.00
#=GF TC   249.40
#=GF NC   143.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009405; pathogenesis;
#=GF DR   GO; 0006950; response to stress;
#=GF RN   [1]
#=GF RM   21912655
#=GF RT   Genome-wide identification of small RNAs in the opportunistic pathogen
#=GF RT   Enterococcus faecalis V583.
#=GF RA   Shioya K, Michaux C, Kuenne C, Hain T, Verneuil N, Budin-Verneuil A,
#=GF RA   Hartsch T, Hartke A, Giard JC
#=GF RL   PLoS One. 2011;6:e23948.
#=GF RN   [2]
#=GF RM   24914223
#=GF RT   Involvement of Enterococcus faecalis small RNAs in stress response and
#=GF RT   virulence.
#=GF RA   Michaux C, Hartke A, Martini C, Reiss S, Albrecht D, Budin-Verneuil A,
#=GF RA   Sanguinetti M, Engelmann S, Hain T, Verneuil N, Giard JC
#=GF RL   Infect Immun. 2014;82:3599-3611.
#=GF CC   Expressed during exponential phase. Involvement in stress response and
#=GF CC   virulence.
#=GF WK   Enterococcus_faecalis
#=GF SQ   3



AE016830.1/381297-381708   UGGGGUCAACUUUGGUACGGAAGCAGAUCGAAAAAUAGCUACUUUGUUAUUUGUCGUUGCUUUAAAAAGUCAACGGCAACUAAGCAUGCUUCAAGAAUUAGCUUUUUUCUGUUCAGAUCUCGAAAACAUUCAGCGGCUCAGUGAUUGUCGAACAAUAGAUGAAGCGCAAAAAAUUCUGGCUCAAGCCUAAAGUUACGUCUGAAAAAAUCAAUUCAAUUUGAAAUGUUCAAUAAUUAUUGAAAUAAUUUUAUAUUAAAAAAUAAAAUAUUUUAAUUUGAUAGAUUAAACAAAAAAGAUAAGAAGAUUCCUUGACAAAAAAUAGGCCCUAUGAUAAAUUUAAAGUAACUUGUGACAAAGUCGUGCAUGGAUGCACUAAAAAGACACCCUAU-UGUGGUAGGGUGUCUUUUUUUGC
ACHK01000048.1/90389-90800 UGGGGUCAACUUUGGUACGGAAGCAGAUCGAAAAAUAGCUACUUUGUUAUUUGUCGUUGCUCUAAAAAGUCAACGGCAAUUAAGCAUGCUUCAAGAAUUAGCUUUUUUCUGUUCAGAUCUCGAAAACAUUCAGCGGCUCAGUGAUUGUCAAACAAUAGAUGAAGCACAAAAAAUUCUGGCUCAAGCCUAAAGUUACGUCUGAAAAAAUCAAUUCAAUUUGAAAUGUUCAAUAAUUAUUGAAAUAAUUUUAUAUUAAAAAAUAAAAUAUUUUAAUUUGAUAGAUUAAACAAAAAAGAUAAGAAGAUUCCUUGACAAAAAAUAGGCCCUAUGAUAAAUUUAAGGUAACUUGUGACAAAGUCGUGCAUGGAUGCACUAAAAAGACACCCUAU-UGUGGUAGGGUGUCUUUUUUUGC
AECF01000037.1/53384-53796 UGGGGUCAACUUUGGUACGGAAGCAGAUCGAAAAAUAGCUACUUUGUUAUUUGUCGUUGCUCUAAAAAGUCAACGGCAACUAAGCAUGCUUCAAGAAUUAGCUUUUUUCUGUUCAGAUCUCGAAAACAUUCAGCGGCUCAGUGAUUGUCGAACAAUAGAUGAAGCGCAAAAAAUUCUGGCUCAAGCCUAAAGUUACGUCUGAAAAAAUCAAUUCAAUUUGAAAUGUUCAAUAAUUAUUGAAAUAAUUUUAUAUUAAAAAAUAAAAUAUUUUAAUUUAAGAGAUCAAACAAAAAAGAUAAGAAGAUUCCUUGACAAAAAAUAGGCCCUAUGAUAAAUUUAAGGUAACUUGUGACAAAGUCGUGCAUGGAUGCACUAAAAAGACACCCUAUCAGUAGUAGGGUGUCUUUUUUUGC
#=GC SS_cons               :::<<<<--<<<<______>>>>-->>>>,,,,,,,,,,,[[[[[[[[[[-----[[[[[[[[[[[--[[[[--[[[--[[[--------[[[[[[[[[--[[[[[[[-[[[[--[[[[[[[[[,,,,,,,,,,,,,(((((((((((-(((((,<<<<<<-<<<------------<<<____>>>---->>>->>>>>>,,,,,,<<<<______>>>>,,)))))-))))))))))),,,,<<<<<<<________>>>>>>>,,,,,,,]]]]]--]]]]-]]]]-]]]]---]]]--]]]]-]]]]]-------]]]]]]---]]]]---]]]]]]]]]]]--]]]]]]]]]],<<<<<____>>>>>,<<<<<<<<<<<<<<<.____>>>>>>>>>>>>>>>::::
#=GC RF                    UGGGguCAACuucGGUACGgaaGCAGacCGAAAAAUAGCUaCuuuGucacUUGUCGuugCccuaaaAAguCaACGGCAAcuaAGCAUGCUuCaaGaaucAGCuuuuuuCuGuuCAgauCucgaaAACAUUCAGCGGCuCagugauuguCgaaCaAcaGacGAagCgCAAAAAAUUCUGGCUCAAGCCUAAAGcuACguCugAAAAAAuCaaUUCAAUuuGaAAuGuucAacaaucacuGaAAUAauuuuauAUUAAAAAauaaaauAUUUUAAuucgauAGaucAaaCaAaaaaGAUaaGAAgauuCCuuGaCAAAAAAuagGCCCUAuGacAAAuuuaggGcaaCUUgugaCaaaGuCGuGCaUGGAuGCaCUaaaaaGaCaCCCuac.uGUgguaGGGuGuCuuuuuUUGC
//
# STOCKHOLM 1.0

#=GF AC   RF02638
#=GF ID   EF0605_EF0606
#=GF DE   Enterococcus sRNA EF0605_EF0606
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   219.00
#=GF TC   219.90
#=GF NC   51.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009405; pathogenesis;
#=GF DR   GO; 0006950; response to stress;
#=GF RN   [1]
#=GF RM   21912655
#=GF RT   Genome-wide identification of small RNAs in the opportunistic pathogen
#=GF RT   Enterococcus faecalis V583.
#=GF RA   Shioya K, Michaux C, Kuenne C, Hain T, Verneuil N, Budin-Verneuil A,
#=GF RA   Hartsch T, Hartke A, Giard JC
#=GF RL   PLoS One. 2011;6:e23948.
#=GF RN   [2]
#=GF RM   24914223
#=GF RT   Involvement of Enterococcus faecalis small RNAs in stress response and
#=GF RT   virulence.
#=GF RA   Michaux C, Hartke A, Martini C, Reiss S, Albrecht D, Budin-Verneuil A,
#=GF RA   Sanguinetti M, Engelmann S, Hain T, Verneuil N, Giard JC
#=GF RL   Infect Immun. 2014;82:3599-3611.
#=GF CC   Expressed during exponential phase. Involvement in stress response and
#=GF CC   virulence. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   2



AE016830.1/569151-569329 UUUAGGGGUAUCCCAAUAUCACUCUCUAGGGGUGACUCAGAGCAGGGGAAGGAGUUACCCCUAAAAAGUAUGUUAGAAUGAUUUUAUCGCAUCAUAUCCUUUUUUAUGUAAUUAGUUGAUAAAAUCUAUCUGUACUUAUAUUUAACGACUGAAAUCGGUCACUUACUGAAAAAACAUCU
JF261298.1/1-176         ---AGGGGUAUCCCAAUAUCACUCUCUAGGGGUGACUCAGAGCAGGGGAAGGAGUUACCCCUAAAAAGUAUGUUAGAAUGAUUUUAUCGCAUCAUAUCCUUUUUUAUGUAAUUAGUUGAUAAAAUCUAUCUGUACUUAUAUUUAACGACUGAAAUCGGUCACUUACUGAAAAAACAUCU
#=GC SS_cons             <<<<<<<<<<-<<<----<<-<<<<<<-<<<____>>>>>>>->>>>--->>->->>>>>>>>>><<<<<<---<<<--<<<<<<<<<<<--<<<<________>>>>------>->>>>>>>>>>-->>>>>>>>>,,,,,,,,,<<<<<____>>>>>:::::::::::::::::::
#=GC RF                  uuuaGGGGuaUCCCAAUAcCACuCuCuAGgGGUGACcCaGaGCaGGgGAAGGAGUuaCCCCuaaaaaGuacGUUaGaAUGauuuuauCgCAUCauaUCCUUUUUuauGUAAUUAGUcGauaaaauCUAuCuguaCuuAUAUUUAACGaCcGAAAUCgGuCACUUACUGAAAAAACAUCU
//
# STOCKHOLM 1.0

#=GF AC   RF02639
#=GF ID   EF0869_EF0870
#=GF DE   Enterococcus sRNA EF0869_EF0870
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   533.00
#=GF TC   559.70
#=GF NC   56.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0046677; response to antibiotic;
#=GF RN   [1]
#=GF RM   21912655
#=GF RT   Genome-wide identification of small RNAs in the opportunistic pathogen
#=GF RT   Enterococcus faecalis V583.
#=GF RA   Shioya K, Michaux C, Kuenne C, Hain T, Verneuil N, Budin-Verneuil A,
#=GF RA   Hartsch T, Hartke A, Giard JC
#=GF RL   PLoS One. 2011;6:e23948.
#=GF RN   [2]
#=GF RM   28894187
#=GF RT   Small RNAs in vancomycin-resistant Enterococcus faecium involved in
#=GF RT   daptomycin response and resistance.
#=GF RA   Sinel C, Augagneur Y, Sassi M, Bronsard J, Cacaci M, Guerin F, Sanguinetti
#=GF RA   M, Meignen P, Cattoir V, Felden B
#=GF RL   Sci Rep. 2017;7:11067.
#=GF CC   Expressed after 24 h of starvation[1]. Identified in E. faecium as
#=GF CC   sRNA_0160. Expressed in mid,late exponential and early stationary phases
#=GF CC   of growth. Transcript level decreased significantly under antibiotic
#=GF CC   exposure [2].
#=GF WK   Enterococcus_faecalis
#=GF SQ   4



AE016830.1/829525-829052     GUGUAAGGAGGACAUGCAAAUCAAUUGGUUGAAGAUUUUCUCAGUAGAUAAAAAUCGGUAAACUCAAAGUUGUUAGAAUUGCAAGAUUCACCUGUAAACAAUACGUGUAGAGUAAUUGUUAGUGAUAACUCGUAUCGGAAAAUAGGGAAAGGUUAUAGAAGGAUGGAGUUUCUAUAAAGCAUUUACCCUAUCUGUUAUCACCUAACGCAAGUUAUCCACCAUCCAAGCGUCGAAACUGUAUGAAAACAAGGUUUUAGUUUCACCACAUCACGUUCACCUUUUGCUUUACAUGUAUCGCGAAAUGUAAACACUUAUUCAACCAAUUGAUGUCUUCCCGUUAACAAGGCCGAGCUUAAAUUUAAGCUCGGUUUUUUCUUUUAAGCAAUAAAAUAUAUUUGUAUCAAAUAAUCAUAUGUGUUAUAUUCAAGGUGCACAUUCUAUUUUAUCUUCUUUUAAAGGAGGGAAUGCUAUGCG
ACAR01000040.1/29974-29501   GUGUAAGGAGGACAUGCAAAUCAAUUGGUUGAAGAUUUUCUCAGUAGAUAAAAAUCGGUAAACUCAAAGUUGUUAGAAUUGCAAGAUUCACCUGUAAACAAUACGUGUAGAGUAAUUGUUAGUGAUAACUCGUAUCGGAAAAUAGGGAAAGGUUAUAGAAGGAUGGAGUUUCUAUAAAGCAUUUACCCUAUCUGUUAUCACCUAACGCAAGUUAUCCACCAUCCAAGCGUCGAAACUGUAUGAAAACAAGGUUUUAGUUUCACCACAUCACGUUCACCUUUUGCUUUACAUGUAUCGCGAAAUGUAAACACUUAUUCAACCAAUUGAUGUCCUCCCGUUAACAAGGCCGAGCUUAAAUUUAAGCUCGGUUUUUUCUUUUAGGCAAUAAAAUAUAUUUGUAUCAAAUAAUCAUAUGUGUUAUAUUCAAGGUGCACAUUCUAUUUUAUCUUCUUUUAAAGGAGGGAAUGCUAUGCG
AEBJ01000007.1/29974-29501   GUGUAAGGAGGACAUGCUAAUCAAUUGGUUGAAGAUUUUCUCAGUAGAUAAAAAUCGGUAAACUCAAAGUUGUUAGAAUUGCAAGAUUCACCUGUAAACAAUACGUGUAGAGUAAUUGUUAGUGAUAACUCGUAUCGGAAAAUAGGGAAAGGUUAUAGAAGGAUGGAGUUUCUAUAAAGCAUUUACCCUAUCUGUUAUCACCUAACGCAAGUUAUCCACCAUCCAAGCGUCGAAACUGUAUGAAAACAAGGUUUUAGUUUCACCACAUCACGUUCACCUUUUGCUUUACAUGUAUCGCGAAAUGUAAACACUUAUUCAACCAAUUGAUGUCUUCCCGUUAACAAGGCCGAGCUUAAAUUUAAGCUCGGUUUUUUCUUUUAAGCAAUAAAAUAUAUUUGUAUCAAAUAAUCAUAUGUGUUAUAUUCAAGGUGCACAUUCUAUUUUAUCUUCUUUUAAAGGAGGGAAUGCUAUGCG
AECE01000011.1/164315-164788 GUGUAAGGAGGACAUGCAAAUCAAUUGGUUGAAGAUUUUCUCAGUAGAUAAAAAUCGGUAAACUCAAAGUUGUUAGAAUUGCAAGAUUCACCUGUAAACAAUACGUGUAGAGUAAUUGUUAGUGAUAACUCGUAUCGGAAAAUAGGGAAAGGUUAUAGAAGGAUGGAGUUUCUAUAAAGCAUUUACCCUAUCUGUUAUCACCUAACGCAAGUUAUCCACCAUCCAAGCGUCGAAACUGUAUGAAAACAAGGUUUUAGUUUCACCACAUCACGUUCACCUUUUGCUUUACAUGUAUCGCGAAAUGUAAACACUCAUUCAACCAAUUGAUGUCUUCCCGUUAACAAGGCCGAGCUUAAAUUUAAGCUCGGUUUUUUCUUUUAGGCAAUAAAAUAUAUUUGUAUCAAAUAAUCAUAUGUGUUAUAUUCAAGGUGCACAUUCUAUUUUAUCUUCUUUUAAAGGAGGGAAUGCUAUGCG
#=GC SS_cons                 {{{{{,{{{{{{{{------{{{{{{{{{{{{{<<<<<<-<<____>>-->>>>>>,,,,<<<________>>>,<<<<<____>>>>>,,,,,,,,,,,[[[[[[[[[[[[[[[--[,,,((((((((<<______>>,,<<<<<<<<<--<<<<<<<<<_______>>>>>>>>>---->>>->>>>>>,,)))))))),,,<<<<__________________>>>>,<<<<<<<________________>>>>>>>,,,,,,,,,,,,,,,,]--]]]]]]]]]]]]]]],,,,,,,,,,,,,,,,,,,}}}}}}}}}}}}}}}}}}}}},,,,,,,,,,<<<<<<<<<<____>>>>>>>>>>(((((((((((((--((((((((<<<<<<___>>>>>>,,,,,<<<<<<____________>>>>>>,,))))))))-----))))))))))))),,,,}}}}}:
#=GC RF                      GcguaAGGagGaCaUGCaAAuCaauuGGuuGaaGauuuuCuCAGUAGaUAaaaauCGGUAaaCUCAAAGUUGuuAGaaucGCAAgauuCACCUGUAAACAauaCguGuagaGcaaUUGUUAGuGauaaCuCGUAUCGGaAAauaGGGaaaGGuuauaGaagGAUGGAGcuuCuauaaAGCAuuuACCCuauCUGuuauCaCCUAaCGCAAGUUAUCCACCAUCCAAGCGuCGaaaCugUAUGAAAACAAGGUUUcaGuuuCACCACAUCACGUUCACCUUuugCucuaCacGuauCGCGAAAUGUAAACACUuAuuCaaCCaauuGauGuCcuCCCGUUAACAAGgCCGaGCuuaAAUUuaaGCuCGGcucccuCcuuuaggCAauaaaauauauuuGUAUCaaauaAUCAUauGuGcUAUAUUCAAGGUgCaCauUCuauuuuauCUUCUccuaaagGagggaAUGCuacgCG
//
# STOCKHOLM 1.0

#=GF AC   RF02640
#=GF ID   MOSES4
#=GF DE   S. pyogenes small RNA MOSES4
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   54.80
#=GF TC   54.80
#=GF NC   54.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   23062031
#=GF RT   Identification of novel growth phase- and media-dependent small non-coding
#=GF RT   RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays.
#=GF RA   Patenge N, Billion A, Raasch P, Normann J, Wisniewska-Kucper A, Retey J,
#=GF RA   Boisguerin V, Hartsch T, Hain T, Kreikemeyer B
#=GF RL   BMC Genomics. 2012;13:550.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



BA000034.2/1598159-1597984 CGUUUCCUUCCUUAACACUAUCGACUCCAUAAUGACCCAUCAGUCAAACGGUAUAUCUCAAACGACUACGGUUUACUCCAAAUUCAUUGGCUAGUUGAGGCCAAGAAACACCUGAUUUUUUUAAUGCUAAAUUUCUAGCUUAUCUUCAUAGCUUAAUUUCAUACAAAAAAACCCCA
CP000017.1/307383-307557   UGUUUCCUUCCUUAACACUAUCGACUCCAUAAUGACCCAUCAGUCAAACGGUAUAUCUCAAACGACUACGGUUUACUCCAAAUUCAUUGGCUAGUUGAGGCCAAGAAACACCUGAUUUUUU-AAUGCUAAAUUUCUAGCUUAUCUUCAUAGCUUAAUUUCAUACAAAAAAACCCCA
CP000829.1/308505-308680   CGUUUCCUUCCUUAACACUAUCGACUCCAUAAUGACCCAUCAGUCAAACGGUAUAUCUCAAACGACUACGGUUUACUCCAAAUUGAUUGGCUAGUUGAGGCCAAGAAACACCUGAUUUUUUUAAUGCUAAAUUUCUAGCUUAUCUUCAUAGCUUAAUUUCAUACAAAAAAACCCCA
#=GC SS_cons               :(((((---(((((((,,,,,,,,,,,,,,,,<<<<______>>>><<<-<<<--<<______>>->>>->>>,,,,<<<<_____>>>>,,,)))))))----)))))------<<<<<<--<<<--<<<<<---<<<<_________>>>>->>>>>>>>-->>>>>>::::::
#=GC RF                    cGuuuCCUUCCuuaaCACUAUCGACUCCAUAAuGaCCCAUCAGuCaaaCGGuaUAuCUCAAACGaCuaCGGuuUACUCCaaAUUcAuuGGCUAGuugaGGCCAAGaaaCACCUGAuuuuuuUAauGCUaaauuUCUaGCuUAUCUUCAUaGCuUaauuuCauACaaaaaaACCCCA
//
# STOCKHOLM 1.0

#=GF AC   RF02641
#=GF ID   Spy490483c
#=GF DE   S. pyogenes small RNA Spy490483c
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   65.00
#=GF TC   65.80
#=GF NC   37.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   23062031
#=GF RT   Identification of novel growth phase- and media-dependent small non-coding
#=GF RT   RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays.
#=GF RA   Patenge N, Billion A, Raasch P, Normann J, Wisniewska-Kucper A, Retey J,
#=GF RA   Boisguerin V, Hartsch T, Hain T, Kreikemeyer B
#=GF RL   BMC Genomics. 2012;13:550.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



CP000829.1/476503-476600 GUUCU-CAGAUGUGAUUACCUCAGGUAAGCAGGCUAGAGACAUAACAAUCAGAAUAUUAAAGGAUGUUAUCACAGUUUUGUGAGCAGGGACCUAUUCGA
CP003068.1/471078-471175 GUUCU-CAGAUGUGAUUACUUCAAGUAAGCAGGCUAGAGACAUAACAAUCAGAAUAUUAAAGGAUGUUAUCACAGUUUUGUGAGCAGGGACCUAUUCGA
CP000261.1/463691-463789 GUUCUACAGAUGUGAUUACUUCAAGUAAGCAGGCUAGAGACAUAACAAUCAGAAUAUUAAAGGAUGUUAUCACAGUUUUGUGAGCAGGGACCUAUUCGA
#=GC SS_cons             ::<<<.<<<-<-<<-<<<<<___>>>>>->>->>>->>>>-----------<<<<<--------<<<--<<<<<____>>>>>>>>------>>>>>::
#=GC RF                  GUuCu.CaGAcGuGAuuaCcUCAgGuaaGCaGgCuAGaGaCAUAACAAUCAGaauaUUAAAGGAuGcUAuCaCaGUUUuGuGagCaGGGACCuauuCGA
//
# STOCKHOLM 1.0

#=GF AC   RF02642
#=GF ID   Spy491311c
#=GF DE   S. pyogenes small RNA Spy491311c
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   178.00
#=GF TC   178.80
#=GF NC   61.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   23062031
#=GF RT   Identification of novel growth phase- and media-dependent small non-coding
#=GF RT   RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays.
#=GF RA   Patenge N, Billion A, Raasch P, Normann J, Wisniewska-Kucper A, Retey J,
#=GF RA   Boisguerin V, Hartsch T, Hain T, Kreikemeyer B
#=GF RL   BMC Genomics. 2012;13:550.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



CP000829.1/1321853-1321711 CUAGGAAAAAGGAUGCAAGUAUCUUAUCUAAAGCGAGUUCGGGGUAGUUAGAGCCGAAUGGUAGGACUGCAGAUUGGCGCUUCCGUUUGGGCAGUGUGAUUAAGUAUAUUUGUCAAUAUUGCCCAAAAAGAUACUAUAUAAAU
CP000261.1/1378326-1378185 CUAGGAAAAA-GAUGCAAGUAUCUUAUCUAAAGCGAGUUCGGGGUAGUUAGAGCCGAAUGGUAGGACUGCAGAUUGGCGCUUCCGUUUGGGCAGUGUGAUUAAGUAUAUUUGUCAAUAUUGCCCAAAAAGAUACUAUAUAAAU
#=GC SS_cons               :::::::::::::::::((((((((,,,,,<<<<<---<<---<<<<<<---<<<____>>>-->>>>>>->>---->>>>>,,,<<<<<<<<<<<<<<<-<<_____>>->>>->>>>>>>>>>>>))))))))::::::::
#=GC RF                    CUAGGAAAAAgGAUGCAaGuauCuuAUCUAaaGCGAGUuCGGGGcaGucAGAgCCGAAUGGcAGgaCugCAGaUUGGCGCuuCCGuuuGGGCaguguGacUaaGUAUAuuUguCAacacuGCCCaaaaaGauaCuAUAUAAAU
//
# STOCKHOLM 1.0

#=GF AC   RF02643
#=GF ID   Spy491738
#=GF DE   S. pyogenes small RNA Spy491738
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   91.00
#=GF TC   91.90
#=GF NC   39.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   23062031
#=GF RT   Identification of novel growth phase- and media-dependent small non-coding
#=GF RT   RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays.
#=GF RA   Patenge N, Billion A, Raasch P, Normann J, Wisniewska-Kucper A, Retey J,
#=GF RA   Boisguerin V, Hartsch T, Hain T, Kreikemeyer B
#=GF RL   BMC Genomics. 2012;13:550.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



CP000829.1/1733433-1733349     AAGUCUGUUUGAGAAAACAGAAGCUCAGGUCAAGUAAGUG--CA-CACUUACAAUAACACAGUUGAUAAUGGGGAAACUCAGAGUCAA
CABY01000009.1/6168-6084       AAGUCUGUUUGAU-AAACAGAAGCUCAGGUCAAGUAAGUG--UUCCACUUACAAUAACGCAGUUGAUGAUGAGGAGACUCAGAGUCAA
AEUX02000007.1/442608-442694   AAGUCUGUUUCAGAAAACAGAAACCCAGGUCAAGUAAGUGUUCU-CACUUACAAUAACACAGUUAAUGAUGGGGCAACUCAAAGUUAA
AEGO01000002.1/2028885-2028801 AAGUCUGUUUGAGAAAACAGAAGCUCAGGUCAAGUAAGUA--CA-CACUUACAAUAACACAGUUGAUGAUGGGGAAACUCAGAGUCAA
#=GC SS_cons                   :::<<<<<<<____>>>>>>>,,,,,,,,,,,,<<<<<<_..__._>>>>>>----------<<<<<--<<<<____>>>>-->>>>>
#=GC RF                        AAGuCuGuuugAgAaaaCaGaAgCuCAGGUCAAGuaaGug..cu.CaCuuaCAAUAACaCAGuuGaugAuGgGGaaACuCagAguCaa
//
# STOCKHOLM 1.0

#=GF AC   RF02644
#=GF ID   Spy490380c
#=GF DE   S. pyogenes small RNA Spy490380c
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   65.00
#=GF TC   90.30
#=GF NC   48.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   23062031
#=GF RT   Identification of novel growth phase- and media-dependent small non-coding
#=GF RT   RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays.
#=GF RA   Patenge N, Billion A, Raasch P, Normann J, Wisniewska-Kucper A, Retey J,
#=GF RA   Boisguerin V, Hartsch T, Hain T, Kreikemeyer B
#=GF RL   BMC Genomics. 2012;13:550.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



CP000829.1/385431-385526   AUAAUUAACUAAACUUAAUUAAAUAAAUAAUAUAUCCUAAGGAGAGAAAUGAUGGGAAAGAGAAUGAGCCUCAUUUUGGGUGCUUUUUAAUCUGUU
CP000262.1/372346-372441   AUAAUUAACUAAACUUAAUUAAAUAAAUAAUAUAUCCUAAGGAGAGAAAUGAUGGGAAAGAGAAUGAGCCUCAUUUUGGGUGCUUUUUUAUCUGUU
CP001129.1/1510212-1510117 AUAAUUAACUAUACUUAAUUAAUUAAAUAAUAGAUCCUAAGGAGAUAACUGAUGAAAAAGAAACUUAGCCUCGUCUUGAGUGCUUUUUUGGCUGUU
FM204884.1/559199-559294   AUAAUUAACUAUACUUAAUUAAUUAAAUAAUAGAUCCUAAGGAGAUAACUGAUGAAAAAGAAACUUAGCCUCGCCUUGAGUGCUUUUUUGGCUGUU
#=GC SS_cons               :<<<<<<<______>>>>>>>,,,,,,,,,,,,,<<<<<_____________>>>>>-<<<----<<<<<<<<___>>>>->>>>----->>>:::
#=GC RF                    AuaauuaaCUAaACuuaauuaAaUAAAUAAUAuAuccuaAGGAGAuAAaUGAugggaAaGaaAaUgaGCCuCauuUuGaGUGCucUUUuauCuGUU
//
# STOCKHOLM 1.0

#=GF AC   RF02645
#=GF ID   Cis2_sRNA
#=GF DE   Ruegeria cis2 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   50.00
#=GF TC   50.40
#=GF NC   48.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   27065955
#=GF RT   Experimental Identification of Small Non-Coding RNAs in the Model Marine
#=GF RT   Bacterium Ruegeria pomeroyi DSS-3.
#=GF RA   Rivers AR, Burns AS, Chan LK, Moran MA
#=GF RL   Front Microbiol. 2016;7:380.
#=GF CC   Cis-encoded. Targets ABC transporter. Functions in transport. 
#=GF WK   Ruegeria
#=GF SQ   2



CP000031.1/41199-41047       GUUGCUGUUAUGCGGGAAAUAGUUGCGAAACACGAAGCCACGGCAUUGGUCGAUGGCGUGAAACAGCGGGUUCCAGUCGAACAUGGCCAGCAUGUAACCCGGCAAGGUAUUGGCAACGAACAUCUUGCCCGAGGCGAUCAUGUUGGCGCGCUG
ABXM01000013.1/309020-309172 GUUGCUGUAGUGGGGGUUGUAGUUGAUGAACACGAACCCCCGUGCCUGAUCGAUGCAGUGAAACAGGGGGUUCCAGUCAAACAUGGCCAGCAUGAAGCUGGGCAAUGUAUUGGCCAGAAACAUUUUGCCCGAUGCGAUCAUGUUGGCGCGCUG
#=GC SS_cons                 :<<<-<<<<-<<<<<_______>>>>>->>>>>>>,<<<<<<<<____>>>>->>>>------(((((,<<<<_____>>>>,,,<<<<<<<<<---<<<<<<<<<<<-<<<____>>>-->>>>>>->>>->>---->>>>>>>>>,)))))
#=GC RF                      GuuGCuGuuacgcggGaaaUAGuugcgaaaCaCgaAgcCaCGgcauUGgcCGAuGgcGUGAAACaGcGGGuucCAGUCgaaCAUGGCCagCauGaAaCccGGCaagguAuugGCaAcaaACaucuuGCCCgAgGCGAUCauGuuGGCGCgCuG
//
# STOCKHOLM 1.0

#=GF AC   RF02646
#=GF ID   Cis8_sRNA
#=GF DE   Ruegeria cis8 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   58.00
#=GF TC   58.00
#=GF NC   57.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   27065955
#=GF RT   Experimental Identification of Small Non-Coding RNAs in the Model Marine
#=GF RT   Bacterium Ruegeria pomeroyi DSS-3.
#=GF RA   Rivers AR, Burns AS, Chan LK, Moran MA
#=GF RL   Front Microbiol. 2016;7:380.
#=GF CC   Cis-encoded. Targets hypothetical protein. Higher sRNA expression during
#=GF CC   C-limited growth. 
#=GF WK   Ruegeria
#=GF SQ   2



CP000031.1/201160-201287   ACCGCCAGAAUCUUGGCGAUGUAUGGGAUCAGCGGCAGGUUCAGGAUCAGCAGAAUCAGGUUGCCCAGAUACAUCGAAAUGAUGACUGCCCAAAAGAUCUGCGGAUCGUCCACCAUCAGCCGUGGCCC
ABSK01000052.1/27956-28083 AUUGCGAGGACUUUAGCAAUGUAGGGGAUGAGCGGCAAAUUCAGGAUCAACAACACAAGGUUGCCGAUGAACAUCGACAUAAUGACCGCCCAGAAAAUCUGUGGAUCGUCAAUCAUCAGGCGUGGGCC
#=GC SS_cons               ::<<<<<<____>>>>>>-------<<-<<<-<<<<-<<<--<-<<<<-<<<<<-<<---<<<--<<<---<<<<_____>>>>->>>-->>>-->>>>>>>->>>>->-->>>---->>>>>>>->>
#=GC RF                    AucGCcagaAuuuugGCgAUGUAuGGGAucaGCGgCAgguUCaGGauCAgCagaAucAGGuuGCCcggaaACaucGAaAUgauGAccgCCCaaAAgaucuGcGGauCGuCaaccAUCAGcCGugggCC
//
# STOCKHOLM 1.0

#=GF AC   RF02647
#=GF ID   Cis52_sRNA
#=GF DE   Ruegeria cis52 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   56.00
#=GF TC   56.00
#=GF NC   55.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   27065955
#=GF RT   Experimental Identification of Small Non-Coding RNAs in the Model Marine
#=GF RT   Bacterium Ruegeria pomeroyi DSS-3.
#=GF RA   Rivers AR, Burns AS, Chan LK, Moran MA
#=GF RL   Front Microbiol. 2016;7:380.
#=GF CC   Cis-encoded. Targets oligo/dipeptide ABC transporter. Functions in
#=GF CC   transport. Higher sRNA expression during C-limited growth.
#=GF WK   Ruegeria
#=GF SQ   2



CP000031.1/1765577-1765755 UUCUCAGCGCGUGCUUGAGCACGAUAUUGGGGAAGGACACGCCCUUGAGCCGCGCGGUGCGGAUAUAUUGCGCCGUCAUCACCUCGGUCAUCGAGGCGCGGGUCAUCCGCGCGAUAUAACCCAUGCCAUAGAGCGCGAUGGUCAGCACCGGCAGGAAGAAGUUCUCGAAUGUCGGCUGC
AAMO01000004.1/24266-24444 UCCUGAGCGCGUGCUUCAGCACGAUGUUGCGGAAGGUCACGCCCUUGAGCCGCGCGGUGCGGAUGUAUUGCGCCGUCAUCACCUCGGCCAUCGAGGCACGGGUCAUCCGGGCGAUGUAGCCCAUGCCGAAGAGGGCGAUGGUCAGCACCGGCAGGAAGAAAUUCUCGAAGGUGGCGUUC
#=GC SS_cons               :::(((-(((((-((((-(((------((((------(-(((---(((-(((((<<<<<<<<_____>>>>>>>>,,,,,,<<<<<_____>>>>>)))))-)))---)))-)------)))))))))-))-)))))-)))---<<<<<<<<<<<<<____>>>>---->>>>>>->>>
#=GC RF                    UuCccaGCGCgcGCucgAGCaCGAUaUuGgGGAAGGaCACgCCCUuGaGCCGcGCGGcGCggAUaUAccGCgCCGUCAUCACCuCGGuCAUCGaGGCgCGGGuCaUCCGcGCGAUaUAaCcCauGCcgaaGAgcGCGAuggUCAGcacCggCagGaaGAAauuCcCGAAuGccGggugC
//
# STOCKHOLM 1.0

#=GF AC   RF02648
#=GF ID   Cis90_sRNA
#=GF DE   Ruegeria cis90 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   50.00
#=GF TC   50.50
#=GF NC   49.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   27065955
#=GF RT   Experimental Identification of Small Non-Coding RNAs in the Model Marine
#=GF RT   Bacterium Ruegeria pomeroyi DSS-3.
#=GF RA   Rivers AR, Burns AS, Chan LK, Moran MA
#=GF RL   Front Microbiol. 2016;7:380.
#=GF CC   Cis-encoded. Targets ABC transporter. Functions in transport. Higher sRNA
#=GF CC   expression during C-limited growth.
#=GF WK   Ruegeria
#=GF SQ   2



CP000031.1/3999629-3999858 AGGUCGAGGCGACCAGCGGUUCCUUGAAAUUGGCCUGUUGCAUCGGAUCGAAGUAGCCGCCCGGGUUGCCCGCCAUCCAGGUAUAGGUACGGGUCGAGCUGAGCCAUUGCAGGAACAGAUAGACCGCCUCGGGAUGCUGCGACUGCGACGAGAUCCAGGCCGU---GAUGUGGUAAUACAGAACCGACCGGCG-GUUCAGCUGAUCACCAAAGCGGCGCCCCACC-GGCA--GGUGG
CP002623.1/4382961-4383194 AGGUUUCCUCCACGAAGGGUUCCGAGAAGUUUGCCUUCUGGAAGGGAUCGAAAUACCCGGCGGGGUUGCCCGCCAUCCAUGAAUAGGUCCGCGUGGAACUGAGCCACUGCAGGAAAAGGUAUGCGGCCUCCGG--GUUGGCGCUGCGC-GAGCUGACGGUACCGGUGAUGUUGUAAUAGAUCACCGACCGGCGCACGAGGCCGUCGUCAUGCUGCACACCCGGCGGGGCAUGGGCCG
#=GC SS_cons               :[[<<<<<<-<<<<___>>>>>>>>>>,,((((-((-(((((-------(--(((((--(((((((<<<<-<<<_____>>>--->>>>,,<<<<---<<<--<<______>>-->>>--->>>>)))-))))--)))))--)))))).-))--))))<<<<<------<<<<<------<<<<<<_____>>->>>>----->>>>>---->>>>>,]]<<<<<_______>>>>>
#=GC RF                    AGGucgcggCgaCcAaggGucccgcgaAauuggCCuuuuGcaagGGAUCGAAguagCCGcCgGGGuugCCCgCcAUCCAgGcAUAGGuaCGgGucGAaCugAGCCAuUGCAGGAAcaGaUAgaCcgCCUCcGg..GcugcgaCugCga.GaGaUccagGccgcGGUGAUGugguAAUAgAgcgcCGACCGGCGcgcgcaGCuGaccaCauaagcggCaCCCggCcGGGCAUGgGccG
//
# STOCKHOLM 1.0

#=GF AC   RF02649
#=GF ID   Trans44_sRNA
#=GF DE   Ruegeria trans44 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   108.00
#=GF TC   108.10
#=GF NC   70.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   27065955
#=GF RT   Experimental Identification of Small Non-Coding RNAs in the Model Marine
#=GF RT   Bacterium Ruegeria pomeroyi DSS-3.
#=GF RA   Rivers AR, Burns AS, Chan LK, Moran MA
#=GF RL   Front Microbiol. 2016;7:380.
#=GF CC   Trans-encoded. Higher sRNA expression during C-limited growth.
#=GF WK   Ruegeria
#=GF SQ   2



CP000031.1/1307274-1307010 CAUCGCGAUGCUCUUCAAUCAUGGAGACAUCGUGAUGAGGAUACUUUCAAAGCGCCAGCUCAAGGAGCUGGUCCUCUACUCGCCGCAACACGUCGCGCGGCUGGAAAAGGCAGGCCAAUUCCCCAAGCGGGUACAGCUGGGCCCGAACAGAGUGGGAUGGGUUGAGGACGAAGUGCUGGACUGGCUUCAGCAACGGCUGGAUGGCCGCGAAGAGUCC-AACCGACACUCCUGAUACAGGAGC-CGGGUGGCCAGGCGUGCACAGCUU
ABSH01000027.1/84172-83906 CAUCGCGAUGCUCUUCAGAGAUGGAGAAAUCGUGAUGAGGAUACUUUCAAAGCCCCAACUGAAGGAGUUGGUUUUGUACUCGCCGCAACAUGUCGCACGUCUGGAAAAGGCAGGCCUAUUCCCCAAGCGGGUACAGCUGGGCCCGAACAGAGUGGGAUGGGUCGAAGAUGAAGUGCUGGACUGGCUACAAACACGGAUGGAGGGUCGCGAGGAGGCCUGACCGACACUCCUCAUGUAGGAGUAUGGGUGGCCGGAGGUGCACACUUC
#=GC SS_cons               <<<<<<<<<<-<<<<<<____>>>>>>>>>>>>>>>>,,,,,,,,,,,,,,,,,<<<<<<---<<<<<<<<<<<--<<<<<<<<-<<<<-<<<<-<<<--<<<-----<<<-<<<-----<<<_____>>>---->>>-->>>---->>>->>>->>>>->>>>->>->>->>>>-->>>>>>>>>>>------>>>>>>,<<<<<<<------------<<<---<<<<<<___>>>>>>-->>>>>>>>>><<<_______>>>:
#=GC RF                    CauCgCGaugCuCucCaaagAuGgaGacauCGcGauGAGGAUACUUUCAAAGCgCCagCcgAAGgaGccgGuccUgcaCuCgCcGCgaCAcguCGCgCGuCuGGAAAAGGCAgGCCaAUUCCCCAAGCGGGUACAGCcGGGCCCGAACaGAGcGGGacgGGucGAgGAcGAaGugCUggaCcggCucCAaaaACgGcuGGAuGGcCgCGAaGAGuCCuaACCgACACuCCugAUacaGGaGuAcGGGcGgCCagggGUGCACAcccu
//
# STOCKHOLM 1.0

#=GF AC   RF02650
#=GF ID   CncR1
#=GF DE   Cag non-coding RNA1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:268638
#=GF GA   76.00
#=GF TC   76.10
#=GF NC   43.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 2000145; regulation of cell motility;
#=GF DR   GO; 0044650; adhesion of symbiont to host cell;
#=GF RN   [1]
#=GF RM   26863876
#=GF RT   The cag-pathogenicity island encoded CncR1 sRNA oppositely modulates
#=GF RT   Helicobacter pylori motility and adhesion to host cells.
#=GF RA   Vannini A, Roncarati D, Danielli A
#=GF RL   Cell Mol Life Sci. 2016;73:3151-3168.
#=GF CC   Encoded by the virulence-associated cag pathogenicity island (cag-PAI). It
#=GF CC   is an abundant and conserved sRNA which does not target cag-PAI genes, but
#=GF CC   down-regulates bacterial motility and have positive role on the adhesion
#=GF CC   to host cells.
#=GF WK   Helicobacter_pylori
#=GF SQ   3



CP001173.1/536898-536686     GUGUUUUUUAGAUGGAAAACUCCUUUAUUCUUUAACAGAUGUUUUCUGUUCUUUUUUUGGCAUAAACAAACAAAUCGUUGGUUUGUGCUAUACCACAUGUUAAUAUCAGCAAGUGGGGUAUUCUUUGAGAUUUGGAGUUAGAUUAGGGUGGUUUUGUAAAAUAUUUAUUAUUUUAUGCUCCUUUGUAAGUUCACCGCCCUGAACUACUUCUUU
AY330639.1/10523-10311       GUGUUUUUUAGAUGGAAAACUCCUUUAUUCUUUAACAGAUGUUUUCUGUUCUUUGUUUGGCAUAAACAAACAAAUCGUUGGUUUGUGCUAUACCACAUGUUAGUAUCAGCAAGUGGGGUAUUCUUUGAGAUUUGGAGUUAGAUUAGGGUGGUUUUGUAAAAUAUUUAUUAUUUUAUGCUCCUUUGUAAGUUCACCGCCCUGAACUAUUUCUUU
AFAO01000045.1/125969-126181 GUGUUUUUUAGAUGGAAAACUCCUUUAUUCUUUAACAGAUGUUUUCUGUUCUUUGUUUGGCAUAAACAAACAAAUCGUUGGUUUGUGCUAUACCACAUGCUAGUAUCAGCAAGUGGGGUAUUCUUUGAGAUUUGGAGUUAGAUUAGGGUGGUUUUGUAAAAUAUUUAUUAUUUUAUGCUCCUUUAUAAGUUCACCGCCCUGAACUAUUUCUUU
#=GC SS_cons                 ::::::::<<<<-<<<____>>>>>>>,,,,,,<<<<<<_____>>>>>>,,,,,,,<<<<<<<<<<-<<<_____>>>->>>>>>>>>>,,<<<<-<<<<______>>>>->>>>-----------------(((((-((-((((((((((,,,<<<<<<<<_____>>>>>>>><<<________>>>,,))))))))))-))))))):::
#=GC RF                      GUGUUUUUuagaUGGaAAACuCCucuaUUCUUUaaCaGaUGUUUuCuGuuCUUUgUUugGCacaaaCAaaCAAAUCGuuGGuuuguGCcaUACCaCAuGcuAgUAUCagCaAGuGGGGUAUUCUUUGAGAUUUGgaguUaGAucaGGGcGGuUUUguaaaauaUUUAUuauuuuacgCuCCUUUgUAaGcUCaCCgCCCugaACuacucCUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02651
#=GF ID   SorY
#=GF DE   Singlet oxygen resistance RNA Y
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   111.00
#=GF TC   111.30
#=GF NC   67.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0080183; response to photooxidative stress;
#=GF RN   [1]
#=GF RM   25833751
#=GF RT   The sRNA SorY confers resistance during photooxidative stress by affecting
#=GF RT   a metabolite transporter in Rhodobacter sphaeroides.
#=GF RA   Adnan F, Weber L, Klug G
#=GF RL   RNA Biol. 2015;12:569-577.
#=GF CC   Singlet oxygen induced SorY is induced under several stress conditions and
#=GF CC   conferrs resistance against singlet oxygen by affecting a metabolite
#=GF CC   transporter.
#=GF WK   Rhodobacter_sphaeroides
#=GF SQ   2



CP000143.1/1632704-1632786 AAGCGGGUGAUCGAGAGGGUUCUCUCGUCCGCUUCAUACCUCCCUGUUGGACUUGGGCCGAGCUUCUGCUCGGCCUUUUUUUU
CP000661.1/913049-912968   AAGCGGGUGAUCGAGAGU-CUCUCUCGUCCGCUUCAUACCUCCCUGUUGGACUUGGGCCGAGCUUCUGCUCGGCCUUUUUUUU
#=GC SS_cons               <<<<<<<----<<<<<<____>>>>>>>>>>>>>,,,,<<________>>,,,,<<<<<<<<<____>>>>>>>>>:::::::
#=GC RF                    aaGCGGgUGAUCGaGaGuguUCuCuCGuCCGCuuCAUACCUCCCUGUUGGACUUgGGCCGaGCUUCUGCuCGGCCuUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02652
#=GF ID   StyR-3
#=GF DE   Salmonella enterica Typhi npcRNA 3
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   59.00
#=GF TC   59.20
#=GF NC   35.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25774907
#=GF RT   Non-protein coding RNA genes as the novel diagnostic markers for the
#=GF RT   discrimination of Salmonella species using PCR.
#=GF RA   Nithya R, Ahmed SA, Hoe CH, Gopinath SC, Citartan M, Chinni SV, Lee LP,
#=GF RA   Rozhdestvensky TS, Tang TH
#=GF RL   PLoS One. 2015;10:e0118668.
#=GF RN   [2]
#=GF RM   20460466
#=GF RT   Experimental identification and characterization of 97 novel npcRNA
#=GF RT   candidates in Salmonella enterica serovar Typhi.
#=GF RA   Chinni SV, Raabe CA, Zakaria R, Randau G, Hoe CH, Zemann A, Brosius J,
#=GF RA   Tang TH, Rozhdestvensky TS
#=GF RL   Nucleic Acids Res. 2010;38:5893-5908.
#=GF CC   Promoter associated sRNA gene that is co-transcribed with the ramA gene
#=GF CC   (mediates multidrug resistance) and overlaps with the DNA binding site of
#=GF CC   the RamR repressor.
#=GF WK   Salmonella_enterica
#=GF SQ   5



FJ746361.1/1-144         UUACUCACUCAUAAUCAAGGGCUGCCGCAUGAAGUGGUAGAAAAGCAUAUUGCAGGCCAUGCGAUAAGCCGUCUCACAAUUUGUGUGGUUAUUACUAUGCUUAUUGCUGUUGCCGUAAAUGUGCGGUGCGGGAGCCGCUGACGA
FR775195.1/117667-117810 UUACUCACUCAUAAUCAAGGGCUGCCGCAUGAAGUGGUAGAAAAGCAUAUUGCAGGCCAUGCGAUAAGCUGUCUCACAAUUUGUGUGGUUAUUACUAUGCUUAUUGCUGUUGCCGUAAAUGUGCGGUGCGGGAGCCGCUGACGA
AFCN01000333.1/4643-4786 UUACUCACUCAUAAUCAAGGGCUGCCGCAUGAAGUGGUAGAAAAGCAUAUUGCAGGCCAUGCGAUAAGCCAUCUCACAAUUUGUGUGGUUAUUACUAUGCUUAUUGCUGUUGCCGUAAAUGUGCGGUGCGGGAGCCGCUGACGA
CP001113.1/643257-643400 UUACUCACUCACAAUCAAGGGCUGCCGCAUGAAGUGGUAGAAAAGCAUAUUGCAGGCCAUGCGAUAAGCUGUCUCACAAUUUGUGUGGUUAUUACUAUGCUUAUUGCUGUUGCCGUAAAUGUGCGGUGCGGGAGCCGCUGACGA
AFCU01000310.1/357-500   UUACUCACUCAUAAUCAAGGGCUGCCGCAUGAAGUGGUAGAAAAGCAUAUUGCAGGCCAUGCGAUAAGCUUUCUCACAAUUUGUGUGGUUAUUACUAUGCUUAUUGCUGUUGCCGUAAAUGUGCGGUGCGGGAGCCGCUGACGA
#=GC SS_cons             ::::::::::::::(((--((((-((((((--------------(((((((---(((---(((((((((,,,,,<<<<___>>>><<<<____>>>>,)))))))))----)))---)))))))-))))))-))))--))):::
#=GC RF                  UUACUCACUCAuAAuCaAGGGCuGCCGCacGAAGUGGUAGAAAAGCacauuGCAGGCCAUGCgauaaGCugUCUCaCaAUUuGuGugGuUAUUaCcaUGCuuaucGCUGUUGCCGUAaauguGCGguGCGGGaGCCGCuGaCGA
//
# STOCKHOLM 1.0

#=GF AC   RF02653
#=GF ID   StyR-143
#=GF DE   Salmonella enterica Typhi npcRNA 143
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   176.00
#=GF TC   176.40
#=GF NC   57.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25774907
#=GF RT   Non-protein coding RNA genes as the novel diagnostic markers for the
#=GF RT   discrimination of Salmonella species using PCR.
#=GF RA   Nithya R, Ahmed SA, Hoe CH, Gopinath SC, Citartan M, Chinni SV, Lee LP,
#=GF RA   Rozhdestvensky TS, Tang TH
#=GF RL   PLoS One. 2015;10:e0118668.
#=GF RN   [2]
#=GF RM   20460466
#=GF RT   Experimental identification and characterization of 97 novel npcRNA
#=GF RT   candidates in Salmonella enterica serovar Typhi.
#=GF RA   Chinni SV, Raabe CA, Zakaria R, Randau G, Hoe CH, Zemann A, Brosius J,
#=GF RA   Tang TH, Rozhdestvensky TS
#=GF RL   Nucleic Acids Res. 2010;38:5893-5908.
#=GF CC   Antisense to the 3'-end of ORF of the hypothetical protein-coding t4293
#=GF CC   gene. 
#=GF WK   Salmonella_enterica
#=GF SQ   2



FJ746389.1/1-144           AUUCUUACUCAAAAAGACAAGGGAGGAAUGCCGCAAGAAACCAAAGAAAAUCAUGGGUUUCAUUAAACUUCAUUAUUGAAGAGGUUUAAUAAAGCUGGUUCUAUAGGUGCGCGCCUGCUCGUCUUUCAUUGUGCCAGCUUUUCU
ABEH02000006.1/99527-99670 AUUCUUACUCAAAAAGAAAAGGAAGGAAUACCGCAAGAAACCAAAGAAAAUCAUGGAUUCCAUUAAACUUCAUUAUUGAAGAGGUUUAAUAAAGCUGGUUCUAUAGGUGCGCGCCUGCUCGUCUUUCAUUGUGCCAGCUUUUCU
#=GC SS_cons               <<<<<<-<<<__________>>>>>>>>>,,,,,,,<<<<<<---<<___>>--->>>>>><<<<<<<<<<_________>>>>>>>>>><<<<<<<<<-<---<<<<<-<<____>>->>>>>------>->>>>>>>>>:::
#=GC RF                    auuCcuAccCAAAAAGAaAAGggagGaauaCCGCAAGgaacCAAAGaAAAuCAUGGguucCauuaaaCcuCAUUAUUGAAGagGuuuaauaaaGCuGGcUCUAUaGgcGCGCGCCUGCUCgcCuUUCAUUGUgCCaGCuuuUCU
//
# STOCKHOLM 1.0

#=GF AC   RF02654
#=GF ID   MicL
#=GF DE   MicL sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   56.00
#=GF TC   56.00
#=GF NC   55.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   25030700
#=GF RT   MicL, a new sigmaE-dependent sRNA, combats envelope stress by repressing
#=GF RT   synthesis of Lpp, the major outer membrane lipoprotein.
#=GF RA   Guo MS, Updegrove TB, Gogol EB, Shabalina SA, Gross CA, Storz G
#=GF RL   Genes Dev. 2014;28:1620-1634.
#=GF CC   mRNA-interfering complementary RNA regulator of Lpp. Transcription factor
#=GF CC   sigma E dependant sRNA. Together with MicA and RybB it allows sigma E to
#=GF CC   repress the synthesis of all abundant outer membrane proteins in response
#=GF CC   to stress. 
#=GF WK   MicL_sRNA
#=GF SQ   2



AFGX01000034.1/1149-842  UAUGGCUGGAGCAGGAGUCCGUGCAGAAAACCUGCACCACUUCCUCGAUGCCGGAGUGCUGGAAGUCCAUAGCUCCGCGGGAGCGUGGCAAGCCUCACCGAUGCGUUAUCGUAAUCAAGGAUUGUCCAUGUCAUCAGAUGAACACGCGGACGAGUAUUCGCGUUAUAUCGUAGACGGGGCGGCGGUUGCUGAAAUGAAAGGAAUCAUUGAACGCCAUCAGGCCAAAUGAUUUUUACCGUUGCAUCAUGUCGCCCAAUAUGAUGCUUGCUCGUACCAGGCCCCUGCAAUUUCAACAGGGGCUUUUUUUA
U00096.2/1956772-1956465 UAUGGCCGGAGCAGGAGUCCGUGCAGAAAACCUGCACCACUUCCUCGAUGCCGGAGUGCUGGAAGUCCAUAGCUCCGCGGGAGCGUGGCAAGCCUCACCGAUGCGUUAUCGUAAUCAAGGAUUGUCCAUGUCAUCAGAUGAACACGCGGACGAGUAUUCGCGUUAUAUCGUAGACGGGGCGGCGGUUGCUGAAAUGAAAGGAAUCAUUGAACGCCAUCAGGCCAAAUGAUUUUUACCGUUGCAUCAUGUCGCCCAAUAUGAUGCUUGCUCGUACCAGGCCCCUGCAAUUUCAACAGGGGCCUUUUUUU
#=GC SS_cons             ::(((---(((((((<<<--<<<<<<_____>>>>>>->>>,,<<<--<<<-<<<<<--<<<____>>>-->>>>>>>>->>><<<<<<<<-<<<----<<<<<<____>>>->>>->>>->>>->>>>><<<<___>>>>,,<<<<<<<______>>>>>>>,,<<<<<<<----<<<<<<<<<-<<<---<<<<--<<<<<<<<<<----<<<____>>>-->>>>>>>>>>-->>>>>>>->->>>>>>>>-->>>>>>>)))))))---)))<<<<<<<<_________>>>>>>>>:::::::
#=GC RF                  UAuGGcuGGaGcagGaGuccGuGcaGAAAAcCugCaCcaCuUccucGAcGccGGaGcGcuGGAAGUCCaUAgCuCCgCgGgagcguGGcaaGccucAccGaugcGUUAUCgcAauCAaggAuugUCCacgucaucAGaugaAcacGcGgacGAGUAucCgCguUAcaucguaGAcGGGGcGgcgGUuGcUGAaacGAAaggaaucauuGAAcGccAUcAggCcAaaugauuccuAcCguugCaUCAcgcCgCCCAAuacgaugCcugCuCGUACCagGccccuGcAAUUUcAACaggggCcUUUUUUa
//
# STOCKHOLM 1.0

#=GF AC   RF02655
#=GF ID   BSR0441
#=GF DE   Brucella BSR0441 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   291.00
#=GF TC   291.50
#=GF NC   35.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   27112796
#=GF RT   Large-scale identification of small noncoding RNA with strand-specific
#=GF RT   deep sequencing and characterization of a novel virulence-related sRNA in
#=GF RT   Brucella melitensis.
#=GF RA   Zhong Z, Xu X, Li X, Liu S, Lei S, Yang M, Yu J, Yuan J, Ke Y, Du X, Wang
#=GF RA   Z, Ren Z, Peng G, Wang Y, Chen Z
#=GF RL   Sci Rep. 2016;6:25123.
#=GF CC   Plays important role in Brucella's intracellular survival. 
#=GF WK   Brucella_sRNA
#=GF SQ   5



AE008918.1/466022-466261   GAUUUAGACACUCUACGAAAUCGUUGGGCCCUACUGGACAAGCCUUUGGCCAGAAUCCACUUUCAGGGGGUGGAGGGUAGCAUAGGGUAUCACCCAAUUGCCACUCCUUUGAUCCCGCGACACUACUAGAAGCCUAAAGUUCGCGGUUGGCCCUACUAAUCGGCAUCGCACCCCGCCGGACCUCCCCCCAUCAACGGCUGUCACAGUCUGGGGCGGGAGUCCGUGGGCGUCUGGAUGUCC
CP000709.1/834089-833850   GAUUUAGACACUCUACGAAAUCGUUGAGCCCUACUGGACAAGCCUUUGGCCAGAAUCCACUUUCAGGGGGUGGAGGGUAGCAUAGGGUAUCACCCAAUUGCCACUCCUUUGAUCCCGCGACACUACUAGAAGCCUACAGUUCGCGGUUGGCCCUACUAAUCGGCAUCGCACCCCGCCGGACCUCCCCCCAUCAACGGCUGUCACAGUCUGGGGCGGGAGUCCGUGGGCGUCUGGAUGUCC
AE014292.2/832345-832106   GAUUUAGACACUCUACGAAAUCGUUGGGCUCUACUGGACAAGCCUUUGGCCAGAAUCCACUUUCAGGGGGUGGAGGGUAGCAUAGGGUAUCACCCAAUUGCCACUCCUUUGAUCCCGCGACACUACUAGAAGCCUACAGUUCGCGGUUGGCCCUACUAAUCGGCAUCGCACCCCGCCGGACCUCCCCCCAUCAACGGCUGUCACAGUCUGGGGCGGGAGUCCGUGGGCGUCUGGAUGUCC
CP000873.1/831649-831410   GAUUUAGACACUCUACGAAAUCGUUGGGCCCUACUGGACAAGCCUUUGGCCAGAAUCCACUUUCGGGGGGUGGAGGGUAGCAUAGGGUAUCACCCAAUUGCCACUCCUUUGAUCCCGCGACACUACUAGAAGCCUACAGUUCGCGGUUGGCCCUACUAAUCGGCAUCGCACCCCGCCGGACCUCCCCCCAUCAACGGCUGUCACAGUCUGGGGCGGGAGUCCGUGGGCGUCUGGAUGUCC
ACBI01000054.1/20586-20347 GAUUUAGACACUCUACGAAAUCGUUGGGCCCUACUGGACAAGCCUUUGGCCAGAAUCCACUUUCAGGGGGUGGAGGGUAGCAUAGGGUAUCACCCAAUUGCCACUCCUUUGAUCCCGCGACACUACUGGAAGCCUACAGUUCGCGGUUGGCCCUACUAAUCGGCAUCGCACCCCGCCGGACCUCCCCCCAUCAACGGCUGUCACAGUCUGGGGCGGGAGUCCGUGGGCGUCUGGAUGUCC
#=GC SS_cons               <<<<<<<<___>>>>--->>>>((-(((((,,,<<<<-<<<____>>>->>>>,,<<<<<<<<___>>>>>>>><<<<-<<<--<<<<___>>>>--->>>->>>>,,,,,,,,<<<<<<-<<<--<<<____>>>->>>>>>>>>,,)))))-))-----<<<<<<--<<<<<<<-<<<<-<<<<<<<<-----<<<<<___>>>>>>>>>>->>>->>>>>>>>>->>--->>>>>>:
#=GC RF                    GauuuaGacAcuCuacGAaauCGuUGgGcccUAcuGGAcaaGccUuugGCCagAAuccacccccaGgggguggaGgGuAGcaUAGGGuAUcaCCCAAUugCcaCcCcUUUGAUcccGcGacacuAcuaGAAGcCuacaguuCgCggUUggCcCUaCUAAUcGgcaucGcaccccgccGGacccccccccaUcAAcGgcuGUcACagcCuggggcgggAguCCgcgggcgucUGgaugcCc
//
# STOCKHOLM 1.0

#=GF AC   RF02656
#=GF ID   sot0042
#=GF DE   Sense overlapping transcript RNA 0042 (sot)
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   88.00
#=GF TC   88.00
#=GF NC   86.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25806405
#=GF RT   Sense overlapping transcripts in IS1341-type transposase genes are
#=GF RT   functional non-coding RNAs in archaea.
#=GF RA   Gomes-Filho JV, Zaramela LS, Italiani VC, Baliga NS, Vencio RZ, Koide T
#=GF RL   RNA Biol. 2015;12:490-500.
#=GF CC   It is associated with IS1341-type transposase (tnpB) genes, at the 3'-end
#=GF CC   in H. salinarum NRC-1. The tetraloop structural motif may be functional.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



AE004437.1/34775-34602 ACGUAUCUCCGAGUCCCGUCACGGAUGGCGGUGAUAGGAGUAACGGCUGGUUGGCACAGCCAUCGACGUUCCUGUUUGACAAUGAAACUGGUGCGUUCGCACCUCAAGAACAGGCUACGUCGUAAACCAUAAUAUCCCAACGCGGUCGGGAAUCCUCGCCCUUCAGGGCGGGGA
CP001934.1/14952-15125 AAGUAUCUCCGAGUCCCGCCACGGAUGGGGGCGAUAGGAGUAACGGCUGGUUGGCACAGCCAUCGACGUUCCUGUUUGACAAGGAAACUGGCGUGUUCGCGCCUCAAGAACAGGUCACGUCGUAAACCACAAUAUCCCAACGCGGUCGGGAAUCUUCGCCCUUCAGGGCGGAGA
#=GC SS_cons           ::<<--<<<<--<<<<<<<<<____>>>>>>->>>->>>>-->><<<<<_______>>>>>,,<<<<<<-<<<<<<<------------<<<<<____>>>>>---->>>>>>>-->>>>>>,,,,,,,,,,,,<<<<-<<___>>->>>>,<<<<<<<<<____>>>>>>>>>
#=GC RF                AaGuAUCuCCGAguCCCgcCacGGAuGgcGGuGacAGGaGUAaCGGCuGGUUGGcACaGCCAUCGaCGuUCCuGuucGAcAAuGAAAcUGGcGcGUUcgCgCCUcAAgaaCaGGuuaCGuCGUAAAccAuAAUAuCCCAaCGcGGucGGGaAuCccCGCCCUUcAGGGCGggGa
//
# STOCKHOLM 1.0

#=GF AC   RF02657
#=GF ID   sot2652
#=GF DE   Sense overlapping transcript RNA 2652 (sot)
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   61.00
#=GF TC   61.00
#=GF NC   52.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25806405
#=GF RT   Sense overlapping transcripts in IS1341-type transposase genes are
#=GF RT   functional non-coding RNAs in archaea.
#=GF RA   Gomes-Filho JV, Zaramela LS, Italiani VC, Baliga NS, Vencio RZ, Koide T
#=GF RL   RNA Biol. 2015;12:490-500.
#=GF CC   It is associated with IS1341-type transposase (tnpB) genes, at the 3'-end
#=GF CC   in H. salinarum NRC-1. The tetraloop structural motif may be functional.
#=GF WK   Bacterial_small_RNA
#=GF SQ   2



AE004437.1/1988005-1987819 AUUACCGGACUCACAAAACCCAACCACAAGUUCGGUUGGUGCGUCUGUCCGGGUCGGGGCGCGUAAGCCGCCCAACCUCAUCCCGUUCCCUCGCGGAACAGGGAGUGUUAGCGCACGGCUGAGGGAACUACAAAAGCCUCGGGCCAUCGUGCCCGAGGCUGUUUACUCCGUUCUCGCGGGGGGUUCG
AGFZ01000059.1/64264-64449 AUUACCGGACUCACAAAACCCAGCCGCAAGUGCGGUUGGUGCGUCUGUCCGGGUCGGGGCGUGUAAACCGCCCAACCUCAUCCCGCUCGCUUGCCGAGCAGGGAGUACUAGCGUACGGCUGAGGGAAUUACAAAAGCCUCGGGCCACCGCGCCCGAGGUUGUUUACGG-GUCCCGGGGUUCGGUUCG
#=GC SS_cons               ::::<<<<<<--<<-----<<<<<<________>>>>>>--->>-->>>>>><<--<<<<<<____>->>>>>->>-------((-(((((((((((((--((((((<<<<<_____>>>>>,,,,,,,,,,,,<<<<<<<<<<______>>>>>>>>>>,,,))))))))))-)))))))))--))
#=GC RF                    AUUACCGGaCUCaCAAAACCCagCCaCAAGUuCGGcuGGUGCGuCUGuCCGGGuCGGGGCGcGUAAgCCGCCCAaCCUCAUCCCGucCgcccgCgGggCAGggaGugccaGCGuACGGCuggGGGAAuUACAAAagCCuCGGGCCAuCGuGCCCGaGGcuGUUcaCuccGccCucGcgggcGgUUCG
//
# STOCKHOLM 1.0

#=GF AC   RF02658
#=GF ID   IRES_RhPV
#=GF DE   Rhopalosiphum padi virus 5'UTR internal ribosome entry site
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   688.00
#=GF TC   688.70
#=GF NC   55.10
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   11581392
#=GF RT   The 5' untranslated region of Rhopalosiphum padi virus contains an
#=GF RT   internal ribosome entry site which functions efficiently in mammalian,
#=GF RT   plant, and insect translation systems.
#=GF RA   Woolaway KE, Lazaridis K, Belsham GJ, Carter MJ, Roberts LO
#=GF RL   J Virol. 2001;75:10244-10249.
#=GF RN   [2]
#=GF RM   24376523
#=GF RT   IRES-mediated translation of membrane proteins and glycoproteins in
#=GF RT   eukaryotic cell-free systems.
#=GF RA   Brodel AK, Sonnabend A, Roberts LO, Stech M, Wustenhagen DA, Kubick S
#=GF RL   PLoS One. 2013;8:e82234.
#=GF CC   This IRES element can function efficiently in mammalian, plant and insect
#=GF CC   translation systems.
#=GF WK   Rhopalosiphum_padi_virus
#=GF SQ   2



AF022937.1/1-579 GAUAAAAGAACCUAUAAUCCCUUCGCACACCGCGUCACACCGCGCUAUAUGCUGCUCAUUAGGAAUUACGGCUCCUUUUUUGUGGAUACAAUCUCUUGUAUACGAUAUACUUAUUGUUAAUUUCAUUGACCUUUACGCAAUCCUGCGUAAAUGCUGGUAUAGGGUGUACUUCGGAUUUCCGAGCCUAUAUUGGUUUUGAAAGGACCUUUAAGUCCCUACUAUACUACAUUGUACUAGCGUAGGCCACGUAGGCCCGUAAGAUAUUAUAACUAUUUUAUUAUAUUUUAUUCACCCCCCACAUUAAUCCCAGUUAAAGCUUUAUAACUAUAAGUAAGCCGUGCCGAAACGUUAAUCGGUCGCUAGUUGCGUAACAACUGUUAGUUUAAUUUUCCAAAAUUUAUUUUUCACAAUUUUUAGUUAAGAUUUUAGCUUGCCUUAAGCAGUCUUUAUAUCUUCUGUAUAUUAUUUUAAAGUUUAUAGGAGCAAAGUUCGCUUUACUCGCAAUAGCUAUUUUAUUUAUUUUAGGAAUAUUAUCACCUCGUAAUUAUUUAAUUAUAACAUUAGCUUUAUCUAUUUAUA
EU282007.1/1-579 GAUAAAAGAACCUAUAAUCCCUUCGCACACCGCGUCACACCGCGCUAUAUGCUGCUCAUUAGGAAUUACGGCUCCUUUUUUGUGGAUACAAUCUCUUGUAUACGAUAUACUUAUUGUUAAUUUCAUUGACCUUUACGCAAUCCUGCGUAAAUGCUGGUAUAGGGUGUACUUCGGAUUUCCGAGCCUAUAUUGGUUUUGAAAGGACCUUUAAGUCCCUACUAUAUUACAUUGUACUAGCGUAGGCCACGUAGGCCCGUAAGAUAUUAUAAUUAUUUUAUUAUAUUUUAUUCCCCCCCCACAUUAACUCCAGUUAAAGCUUUAUAACUAUAAGUAAGCCGUGCCGAAACGUUAAUCGGUCGCUAGUUGCGUAACAACUAUUAGUUUAAUUUUCCAAAAUUUAUUUUUCACGAUUUUUAGUUAAGAUUUUAGCUUGCCUUAAGCAGUCUUUAUAUCUUCUGUAUAUUAUUUUAAAGUUUAUAGGAGCAAAGUUCGCUUUACUCGCAAUAGCUAUUUUAUUUAUUUUAGGAAUAUUAUCACCUCGUAAUUAUUUACUUAUAACUUUAGCUUUGUCUAUUUAUA
#=GC SS_cons     :::<<<<<---<<-<<<<-<<<--<<<<<--<<<<______>>>>---->>->>>----->>>->>>>->>--->>>>>,[[[[[<<<<<<____>>>>>><<<<<<____>>>>>>,,,,,,,,,,,,,,,<<<<<<<____>>>>>>>((((((((((((((((((,,<<<<____>>>><<<______>>>,,,,,,,<<<<______>>>>,,,,))))))---)))))))))))),<<<<_____>>>>,<<<<<<<<<-<<<<_____>>>>->>>>>>>>>,,,,,,,]]]]]--------[[-[[[[[[[[[[[[[---[[[[[[[--[[,<<<<<________>>>>><<<_____>>><<<<____>>>>((-((((-(((((((((--((,,,,,,,<<<<<<_____>>>>>>,<<<<<<<<---<<<<---<<<<----<<<<<<<<-<<<_______>>>->>>>>>>>->>>>--->>>>----->>>-->>>>>,,,,))--)))))-))))-))))--)),,]]---]]]]]]]-]]]]]]----]]]]]]]-]]:::::::
#=GC RF          GAUaaaaGAACCcAuaauCCCuUCGCaCaCCGCGcCACACCgCGCUAUAuGCuGCUCAUUaGGAauuaCgGCUCCuuuuUuGuGGauaCaaUCUCuuGuauaCgauaUACUuaucGuUAAUUUCAUUGACCUuuaCGCaAUCCuGCGuaaacGCugGuacaggguguaCUuCGGAUUUCCGagCCUAUAUUGGcUUUGAAAGGaCCUUUAAGuCCCUACuacaccACAcuguaCcaGCguAGGCCACGUAGGCCCguaagauauUauaauUAUUuuauUauaucuuacUCaCCCCCCaCaUUAAuuCCaGUcaaaGCuuuauaaCUAuaaguaaGCCGUgCCGaAACGUUAAuCGGcCGCUAGUUGCGuaacAACUguuaGuUuaauUuuCCaaaauUUauUUUUCACgaucuuUAGUUaagaucUuaGCuuGCCUUaaGCAGUCuuuAUAUCucCuguaUacuAUUUUAAaguUuacaGgaGCaaaGUUCGCuuUACUCGCaAUaGCuaUUUUauUUauuuuAGGaaUauuaUCaCCUCGUAAuuacuuaauuauaaCaUUaGCuuugUCuAUUUAUA
//
# STOCKHOLM 1.0

#=GF AC   RF02659
#=GF ID   ncRv12659
#=GF DE   ncRv12659 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   209.00
#=GF TC   209.70
#=GF NC   111.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24348997
#=GF RT   A small RNA encoded in the Rv2660c locus of Mycobacterium tuberculosis is
#=GF RT   induced during starvation and infection.
#=GF RA   Houghton J, Cortes T, Schubert O, Rose G, Rodgers A, De Ste Croix M,
#=GF RA   Aebersold R, Young DB, Arnvig KB
#=GF RL   PLoS One. 2013;8:e80047.
#=GF CC   Original name MTS2048. It is induced during starvation and infection. 
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   2



ABLN01000435.1/3857-4030 GUCGACUGGUCAGAGGCUUUCUGUACAAGGUCAGACAGUAUCCCACCCGGCCCACUAGUGAAACUGGUUCAAUCCCAGUAUCGCGCACCACGAUUGACCUGCGGUUUCAUCCACAAAAUCUGGGCUGCGUGAACUAAAUGUGAACUGACUCGGUGCAACCACCGAAAGGUUCCU
BX842580.1/207875-208046 GUCGCCUGGUCAGAGGCUUUCUGUACA-GGUCAGACAGUAUCCCAC-CGGCCCACUAGUGAAACUGGUUCAAUCCCAGUAUCGCGCACCACGAUUGACCUGCGGUUUCAUCCACAAAAUCUGGGCUGCGUGAACUAAAUGUGAACUGACUCGGUGCAACCACCGAAAGGUUCCU
#=GC SS_cons             <<<<<<<<--<<<<_____>>>>-->>->>>-->>>,,,,,,,<<<-<<<<<<<---<<<<<<<<<--<<<<<<---<<_______>>--->>>>>>---->>>>>>>>>---------->>>>>>>->>>----------<<<<<---<<<<<<____>>>>>>-->>>>>::
#=GC RF                  GuCgcCuGGUCaGaGGCUUuCuGUACaAGgcCAGaCAGUAUCCCaCcCgGCCCaCUAguGaaaCcGGUuCaauCCCAGuAUCGCGCaCCACGauuGaCCUGCgGuuuCacCCACAAAAUCuGGGCcGCGuGAACUAAAUGUGaaCcGACuCGGuGCAACCaCCGaAAgGuuCCU
//
# STOCKHOLM 1.0

#=GF AC   RF02660
#=GF ID   icaR_3p_UTR
#=GF DE   icaR 3'UTR
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   369.00
#=GF TC   369.90
#=GF NC   357.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   24367275
#=GF RT   Base pairing interaction between 5'- and 3'-UTRs controls icaR mRNA
#=GF RT   translation in Staphylococcus aureus.
#=GF RA   Ruiz de los Mozos I, Vergara-Irigaray M, Segura V, Villanueva M, Bitarte
#=GF RA   N, Saramago M, Domingues S, Arraiano CM, Fechter P, Romby P, Valle J,
#=GF RA   Solano C, Lasa I, Toledo-Arana A
#=GF RL   PLoS Genet. 2013;9:e1004001.
#=GF CC   The 3'UTR of icaR mRNA (repressor of the main expolysaccharidic compound
#=GF CC   of the bacteria biofilm matrix) binding to the 5' UTR can interfere with
#=GF CC   the translation initiation complex and generate a double stranded
#=GF CC   substrate for RNaseIII. Mozos at al. showed that the interaction was
#=GF CC   between UCCCCUG motif in the 3'UTR and the Shine-Dalagarno region at the
#=GF CC   5'UTR. Deletion of the motif resulted in IcaR repressor accumulation and
#=GF CC   inhibition of biofilm development.
#=GF WK   Staphylococcus_aureus
#=GF SQ   3



BABM01000001.1/2833385-2832996 UUUUUGUUACUAGUUUGUAAUAAUUAACUUACUUUUGUAAAAAAAGACAUGAGAUUAUUUUUUUAAAUCUAUAUAAAGUUGACAAUACAAAUCGAUAUUGAGAAUAUUAAGAUGUAUAUGAAUUUUAUAAAUUAAAUGCAAUACAUUAAUAUAAAUAUCAAUUGUUGCAAAAUACGAUUUGUUCAAUGAUUUUAUAAUAUUAUUCUUUAUAUUUGUGAAUGGUUAAGUUUGUCUUUGAACAUAUUAUAAAAGUGUAAUGUUCCCCUGAAAAGAAUAAGUUGUCAUCUAAUUACAGGAAAUCCGCAUAAAUUAGAUGAAAUGGAAAGUAAUAAGUAAUAAUUUAUUGAUAAGCGCCUAUGUGAUGGUAAAUCAUGACAUAGGCGCUUUUUU
FR714927.1/2684496-2684107     UUUUUGUUACUAGUUUGUAAUAAUUAACUUACUUUUGUAAAAAAAGACAUGAGAUUAUUUUUUUAAAUCUAUAUAAAGUUGACAAUACAAAUCGAUAUUGAGAAUAUUAAGAUGUAUAUGAAUUUUAUAAAUUAAAUGCAAUACAUUAAUAUAAAUAUCAAUUGUUGCAAAAUACGAUUUGUUCAAUGAUUUUAUAAUAUUAUUCUUUAUAUUUGUGAAUGGUUAAGUUUGUCUUUGAACAUAUUAUAAAAGUGUAAUGUUACCCUGAAAAGAAUAAGUUGUCAUCUAAUUACAGGAAAUCCGCAUAAAUUAGAUGAAAUGGAAAGUAAUAAGUAAUAAUUUAUUGAUAAGCGCCUAUGUGAUGGUAAAUCAUGACAUAGGCGCUUUUUU
CP001781.1/2779360-2778971     UUUUUGUUACUAGUUUGUAAUAAUUAACUUACUUUUGUAAAAAAAGACAUGAGAUUAUUUUUUUAAAUCUAUAUAAAGUUGACAAUACAAAUCGAUAUUGAGAAUAUUAAGAUGUAUAUGAAUUUUAUAAAUUAAAUGCAAUACAUUAAUAUAAAUAUCAAUUGUUGCAAAAUACGAUUUGUUCAAUGAUUUGAUAAUAUUAUUCUUUAUAUUUGUGAAUGGUUAAGUUUGUCUUUGAACAUAUUAUAAAAGUGUAAUGUUCCCCUGAAAAGAAUAAGUUGUCAUCUAAUUACAGGAAAUCCGCAUAAAUUAGAUGAAAUGGAAAGUAAUAAGUAAUAAUUUAUUGAUAAGCGCCUAUGUGAUGGUAAAUCAUGACAUAGGCGCUUUUUU
#=GC SS_cons                   :::<<<<<<<______>>>>>>>,[[[[[(((((((((((,,,,<<<--<<<<<______>>>>>-->>>,<<<<<<<<<-<--<<<<<--<-<<<<<<___>>>>>>->-->>>>>->->>>>>>>>>,,,,,,,<<<<<<<-<<<-<<<____>>>->>>>>>>>>>,,,,,,,,,,<<<<<<<-<<<--<<<---<<<<<<<___________>>>>>>>--->>>->>>->>>>>>>,,))))))))))),,,<<<<<_________>>>>>]]]]]<<<<<<<<<<---<<____>>----->>>>>>>>>>,,,,,,,,,<<<<<<<<____>>>>>>>>,,<<<<<<<<<<<<-<<<______>>>->>>>>>>>>>>>::::
#=GC RF                        UUUuuguuaCUAGUUUGuaacaaUcaaCucaCuuuuguaaAAAAaGaCAugagaUUAUUUucucaAAuCuAuauaaaguuGaCAauaCaAAuCgauauuGAGaauaucAaGAuGuauAuGaacuuuauaAAUUAAAuGCaacaCauuAauaUAAAuauCaauuguuGCaAAAUACGAUUuGuuCaaUGacUUgacAAUaccauuCUUUAUAUUUGUGaaugguUAAgucUguCUuuGaaCaUAuuacaaaaGugUAAuguucCCCUGAAAAgaacaaGuuguCauCuaauuACAGGAAAUCCGCAUAaauuaGauGaAAUGGAAAGcaauaaguAAUAacuuauugAUaaGCGCCuauGuGauGGUAAAUCauGaCauaGGCGCuuUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02661
#=GF ID   icaR_5p_UTR
#=GF DE   icaR 5' UTR
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   88.00
#=GF TC   88.70
#=GF NC   49.20
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF RN   [1]
#=GF RM   24367275
#=GF RT   Base pairing interaction between 5'- and 3'-UTRs controls icaR mRNA
#=GF RT   translation in Staphylococcus aureus.
#=GF RA   Ruiz de los Mozos I, Vergara-Irigaray M, Segura V, Villanueva M, Bitarte
#=GF RA   N, Saramago M, Domingues S, Arraiano CM, Fechter P, Romby P, Valle J,
#=GF RA   Solano C, Lasa I, Toledo-Arana A
#=GF RL   PLoS Genet. 2013;9:e1004001.
#=GF CC   The 3'UTR of icaR mRNA (repressor of the main expolysaccharidic compound
#=GF CC   of the bacteria biofilm matrix) binding to the 5' UTR can interfere with
#=GF CC   the translation initiation complex and generate a double stranded
#=GF CC   substrate for RNaseIII. Mozos at al. showed that the interaction was
#=GF CC   between UCCCCUG motif in the 3'UTR and the Shine-Dalagarno region at the
#=GF CC   5'UTR. Deletion of the motif resulted in IcaR repressor accumulation and
#=GF CC   inhibition of biofilm development.
#=GF WK   Staphylococcus_aureus
#=GF SQ   2



CP001781.1/2779993-2779919 GAAAUAUUUGUAAUUGCAACUUAAUUUUCCUGUAACAUAGUGUGAUUAAUUUUCAGUAGGGGGUUAUAAAAAUUG
FN433596.1/2992946-2992872 GAAAUAUUUGUAAUUGCAACUUAAUUUUCCUGUAACAUAGUGUGAUUAAUUUUCAGUAGGGGGUUUUAAAAAUUG
#=GC SS_cons               ::::::<<<<<<<<<-<-<<<<<<<<---<<<<___>>>>--->>>>>------>>>-->->>>>>>>>>:::::
#=GC RF                    GAAAUAUUUguaauuGCAaCUUaaUuUUCCUgUAACAuAGUGUgAuuAAUUUUCAGuAGGGgguuauAAAAAUUG
//
# STOCKHOLM 1.0

#=GF AC   RF02662
#=GF ID   BLi_r0872
#=GF DE   Bacillus asRNA 0872
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   61.00
#=GF TC   61.10
#=GF NC   53.00
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24079885
#=GF RT   RNA-Seq of Bacillus licheniformis: active regulatory RNA features
#=GF RT   expressed within a productive fermentation.
#=GF RA   Wiegand S, Dietrich S, Hertel R, Bongaerts J, Evers S, Volland S, Daniel
#=GF RA   R, Liesegang H
#=GF RL   BMC Genomics. 2013;14:667.
#=GF CC   Antisense RNA against 3' end of Subtilisin Carlsberg encoding mRNA,
#=GF CC   discovered in an RNA-seq based study. It may have a putative impact on
#=GF CC   protease production and serve as a target for strain improvement.
#=GF WK   Bacillus_licheniformis
#=GF SQ   2



AE017333.1/1108968-1109111 AUUGAGCGGCAGCUUCGACAUUGAUCAGACCUUUUCCAUAGUAGAAGGAGCUUCCCAAAUAAGUCGCCGUACUGGAGAGACGGUUGCGGACUUGUGAAGCUGAAAGGUUCGGAUGUUUUGACAAGAUCAAAGCUGCUGCUCCCG
X91262.1/1472-1329         AUUGAGCGGCAGCUUCGACAUUGAUCAGACCUUUCCCAUAGUAGAAGGAGCUUCCCAAAUAAGUCGCCGUGCUGGAGAGACGGUUGCGGACUUGUGAAGCUGAAAGGUUCGGAUGUUUUGACAAGAUCAAAGCUGCUGCUCCCG
#=GC SS_cons               :::<<<<<<<<<<<<-<<--<<<-<<<<<<<<<<<-------------<<<<<<----<<<<<<<<<<<<-<<____>>>>>>>---->>>>>>>>>>>>>>>>>>>>>--------->>>>>>-->>->>>>>>>>>>>>:::
#=GC RF                    AUUGaGCgGCaGCuucGacAuuGAuCagaCCuuucccAUAGUAGAAGGaGCuuCccAAacaaGuCgCCGuaCuGGAGaGaCGGcUGcGGaCuuguGaaGCugaaaGGuccGGAUGUUUuGaCaaGAuCAaaGCuGCcGCuCccG
//
# STOCKHOLM 1.0

#=GF AC   RF02663
#=GF ID   GmglnB1_5p_UTR
#=GF DE   GmglnB1 5'UTR
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   54.00
#=GF TC   54.10
#=GF NC   38.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   23080263
#=GF RT   The 5' untranslated region of the soybean cytosolic glutamine synthetase
#=GF RT   beta1  gene contains prokaryotic translation initiation signals and acts
#=GF RT   as a translational enhancer in plants.
#=GF RA   Ortega JL, Wilson OL, Sengupta-Gopalan C
#=GF RL   Mol Genet Genomics. 2012;287:881-893.
#=GF CC   The 5'UTR of the Soybean cytosolic glutamine synthetase gene (GmglnÎ²1)
#=GF CC   contains prokaryotic translation initiation signals and acts as a
#=GF CC   translational enhancer.
#=GF WK   Glutamine_synthetase
#=GF SQ   2



ACUP01006700.1/43239-43155 GAAUUCUCUAAAAGAGAUCUUUUUCUGCUCUUUGAAGAAAGAAGGGUCUUUGCUUGAUUUUGGAGAUGUCUCUGCUCUCAGAUCU
S46513.1/13-97             GAAUUCUCUAAAAGAGAUCCUUUUCUGCUCUUUGAAGAAAGAAGGGUCUUUGCUUGAUUUUGGAGAUGUCUCUGCUCUCAGAUCU
#=GC SS_cons               ::::<<<<<<<<<<<<<<<<<<<<<<_________>>>>-->>>>>>>>>------->>>>>>>>>----<<<<____>>>>:::
#=GC RF                    GAAUuCuCuaaaagaGauCcuuuuCuGCUCUUUGAaGaaAGaagGguCuuUGCUUGAuuuugGaGaUGUCuCuGCUCUCaGaUCU
//
# STOCKHOLM 1.0

#=GF AC   RF02664
#=GF ID   IRES_cyp24a1
#=GF DE   Cyp24a1 internal ribosome entry site (IRES)
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   191.00
#=GF TC   191.00
#=GF NC   144.80
#=GF TP   Cis-reg; IRES;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000243; internal_ribosome_entry_site;
#=GF DR   GO; 0043022; ribosome binding;
#=GF RN   [1]
#=GF RM   24416388
#=GF RT   Inflammatory conditions induce IRES-dependent translation of cyp24a1.
#=GF RA   Rubsamen D, Kunze MM, Buderus V, Brauss TF, Bajer MM, Brune B, Schmid T
#=GF RL   PLoS One. 2014;9:e85314.
#=GF CC   Cyp24a1 (1,25-dihydroxyvitamin D3 24-hydroxylase) expression is
#=GF CC   translationally regulated via IRES within the 5'UTR, which is responsive
#=GF CC   to an inflammatory environment.
#=GF WK   CYP24A1
#=GF SQ   2



AL138805.8/76141-75741   GACAGGAGGAAACGCAGCGCCAGCAGCAUCUCAUCUACCCUCCUUGACACCU---CCCCGUGGCUCCAGCCAGACCCUAGAGGUCAGCCUUGCGGACCAACAGGAGGACUCCCAGCUUUCCCUUUUCAAGAGGUCCCCAGACACCGGCCACCCUCUUCCAGCCCCUGCGGCCAGUGCAAGGAGGCACCAAUGCUCUGAGGCUGUCGCGUGGUGCAGCGUCGAGCAUCCUCGCCGAGGUCCUUUCUGCUGCCUGUCCCGCCUCACCCCGCUCCAUCACACCAGCUGGCCCUCUUUGCUUCCUUUUCCCAGAAUCGUUAAGCCCCGACUCCCACUAGCACCUCGUACCAACCUCGCCCCACCCCAUCCUCCUGCCUUCCCGCGCUCCGGUGUCCCCCGCUGCCAUG
AACZ03123677.1/4633-4230 GACAGGAGGAAACGCAGCGCCAGCAGCAUCUCAUCUACCCUCCUUGACACCUCCUCCCCGUGGCUCCAGCCAGACCCUAGAGGUCAGCCUUGCGGACCAACAGGAGGACUCCCAGCUUUCCCUUUUCAAGAGGUCCCCAGACACCGGCCACCCUCUUCCAGCCCCUGCGGCCAGUGCAAGGAGGCACCAAUGCUCUGAGGCUGUCGCGUGGUGCAGCGUCGAGCAUCCUCGCCGAGGUCCUUUCUGCUGCCUGUCCCGCCUCACCCCGCUCCAUCACACCAGCUGGCCCUCUUUGCUUCCUUUUCCCAGAAUCGUUAAGCCCCGACUCCCACUAGCACCUCGUACCAACCUCGCCCCACCCCAUCCUCCUGCCUUCCCGCGCUCCGGUGUCCCCCGCUGCCAUG
#=GC SS_cons             ::[[[[[[[[,,,((((-((-(((((,,,,,,,,,,,,<<<<<<<<-<<<----------<<<<<-<<<---------<<<<<---<<<<<<-<<<<<---<<<<<<_____________>>>>>>----->>>>>->>>----->>>--->>>>>-------->>>->>>>>>>>>>>>>>>>,,,,,<<<<<<-<<-<<<<-<<<___>>>>>>>->>>>>>>><<<<___>>>>,,,,,,))))))))))),,,,,,,,,,<<-<<<__________>>>->>,,,,,,,,,,,,,,,,,,,,,,<<-<<<________>>>->>,,,,,,<<________________>>,,,,,,,,,]]]]]]]]---------<<--<<<______>>>-->>::::
#=GC RF                  GACaGGaGGaAACgCaGCGCCaGCaGCAUCUCAUCUACCCuCCuuGACaCCUccuCCCCGuGGCuCCaGCCAGACCCUaGaGGUCAGCCuuGCGGaCCAACaggaGGACUCCCAGCUUUCCCuuuuCAAGAGGuCCCCagACACCGGCCACCCuCuUCCAGCCCCuGCgGCCaGuGCaaGGaGGCACCAauGCuCUGaGGCuGUCgCGUGGuGCaGCGuCGaGCauCCuCGCCGaGGUCCUUUCuGCuGCCuGuCCCGCCUCACCCCGCuCCAUCACACCaGCUGGCCCUCUUUGCUUCCUUUUCCCAGaAuCGUUAAGCCCCGaCuCCCACUAGCACCUCGUACCAACCUCGCCCCACCCCAuCCuCCuGCCUUCCCGCGCUCCGGUGUCCCCCGCUGCCAUG
//
# STOCKHOLM 1.0

#=GF AC   RF02665
#=GF ID   PsiU1-6
#=GF DE   Drosophila small cajal body-specific RNA PsiU1-6
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   72.00
#=GF TC   72.40
#=GF NC   57.80
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   24149844
#=GF RT   Novel small Cajal-body-specific RNAs identified in Drosophila: probing
#=GF RT   guide RNA function.
#=GF RA   Deryusheva S, Gall JG
#=GF RL   RNA. 2013;19:1802-1814.
#=GF CC   Pseudouridylation guide activity for U1 snRNA and 28s rRNA
#=GF WK   Small_Cajal_body-specific_RNA
#=GF SQ   3



AE014297.2/5539329-5539487   CAAGCGUUGGGAAAGCGUCGACACUGUAAACAGUGAGUGUAGACACUGACCUCAUAACGCUAGAUUAACUUAAAACUGAGACGUUAACGUUUUAGUUGAGCAAACAGGGCCGCAAAGAUUUAAGUCUUUCUUUGAUCGGUAGUAAGCCGCUCACACAAA
AAGH01021807.1/1648-1806     UAAGCGUUGGGAAAGCGUCGACACUGUAAACAGUGAGUGUAGACACUGACCUCAUAACGCUAGAUUAACUUAAAACUGAGACGUUAACGUUUUAGUUGAGCAAACAGGGCCGCAAAGAUUUAAGUCUAUCUUUGAUCGGUAGUAAGCCGCUCGCACAAA
AAEU02000008.1/511385-511543 UAAGCGUUGGGUAAGCGUCGACACUGUAAACAGUGAGUGUAGACACUGACCUUUCAGCGCUAGAUUAAUUUAAAACUGACACGUUAACGUUUUAGUUGAGCAAACAGGGCCGCAAAGAUUUAAGCUUAUCUUUGAACGGUAGUAAGCCGCUCGCACAAA
#=GC SS_cons                 <-<<<<<<<<<--<<-<<<-<<<<<__________>>>>>->>>->>-->>>--->>>>>>->,,,,,,,,,,,<<<<<<<<<____>>>>>>>>><<<<<-------<<<<<<<<<<__________>>>>>>-->>>>-------->>>>>::::::
#=GC RF                      cAaGCGuugGGaAaGCGuCGaCaCuGUAAACAGUGaGuGuAGaCACuGACCccauaaCGCuAgAUUAAcUUAAAaCugagaCGUUAACGucucaGucGaGCAAACAGGgCCGCaaaGaUUUAAGucUauCuuuGAuCGGcAGUAAGCCGCuCgCACAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02666
#=GF ID   PsiU2-35.45
#=GF DE   Drosophila small cajal body-specific RNA PsiU2-35.45
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   89.00
#=GF TC   89.70
#=GF NC   87.00
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   24149844
#=GF RT   Novel small Cajal-body-specific RNAs identified in Drosophila: probing
#=GF RT   guide RNA function.
#=GF RA   Deryusheva S, Gall JG
#=GF RL   RNA. 2013;19:1802-1814.
#=GF CC   Pseudouridylation guide activity for U2 snRNA
#=GF WK   Small_Cajal_body-specific_RNA
#=GF SQ   3



AE013599.4/1652685-1652824 AAACGUGUUCGGAUACCGCUGUAGAGAUAAGAGACUGUAGCUCUAUGGCCACCAAGAGCACGGAUAACAAAAACAAUGUAUUCUUCGAUGAGCCUGCCUGAAUGAGUUUCAAAGCAGGCACAGAUACGGAAUAUACAAUA
AASW01040202.1/172-33      AAACGUGUUCGGAUACCGCUGUAGAGAUAAGAGACUGUAGCUCUAUGGCCACCAAGUGCACGGAUAACAAAAACAAUGUGUUCUUCGAUGAGCCUGCCUGAAUGAGUUUCAAAGCAGGCACAGAUACGGAAUAUACAAUA
AFFI01006140.1/19063-19202 AAACGUGCAUGGAUACCGCUGUAGAGAUUAAAGGCUUUCGCUCUAUGCCCACAAAAUGCACGAAUAUAAAAUUUCAAAUGUUCUUCGAUGAGCCUGGCCGUUUAAGCUUCGAAUCAGGAACAGAUACGGAACAUACAAUU
#=GC SS_cons               :::<<<<<<<-------<<<<<<<<<---<<___>>---->>>>>>>>>------>>>>>>>--------------<<<<<<<<----<<-<<<<<<-<<<<_____>>>>-->>>>>>->>----->>>>>>>>:::::
#=GC RF                    AAACGuGcccGGAUACCGcuguaGaGAUaagAGacugUaGCuCuauggCCACaAAgggCaCGgAUAaaAAAaacaAuguguuCuUCGAuGAgCCuGcCcGaaUgAGuuuCgAAgCaGGcACaGAUACgGaacacaCAAUa
//
# STOCKHOLM 1.0

#=GF AC   RF02667
#=GF ID   PsiU2-38.40.42
#=GF DE   Drosophila small cajal body-specific RNA PsiU2-38.40.4
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   88.00
#=GF TC   88.40
#=GF NC   52.90
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   24149844
#=GF RT   Novel small Cajal-body-specific RNAs identified in Drosophila: probing
#=GF RT   guide RNA function.
#=GF RA   Deryusheva S, Gall JG
#=GF RL   RNA. 2013;19:1802-1814.
#=GF CC   Pseudouridylation guide activity for U2 snRNA 
#=GF WK   Small_Cajal_body-specific_RNA
#=GF SQ   3



JN409597.1/1-137             CAAGCAGCAACAAGAAAGUGCUUAGGCUUAAAUGCGUUUACCUAAGCGCUGAUACAAUGCUGCCAGAACAAUUUUAAAGCCAAGAACAGUUUAGUUUAGAGUAGUUUAUAAACUGAUCUACACGUGGCCUAACAUAU
AFPP01033382.1/28875-29010   AUGGCAGCAACAAGAAAGUGCUUAGG-UUGAUUGAAUUUAUUUAAGCGCUGAUACAAUGCUGCCAGAACAAUUUAAAAGCCAAGAACAGUUCAGUUUAAUGGAGUUUAUAAACUGGUCUACACGUGUCCUUACAUUC
AFFF01008313.1/400637-400772 UUGGCAGCAACAAGAAAGUGCUUGAG-UUAAUUGAGUUUAUUUAAGCGCUGAUACAAUGCUGCCAGAAGAAUUUCAAUGCCAAGAACAGUUCAGUUUGAUUCAGUUUACAAACUGGUCUACACGUGGCCAAACAUUC
#=GC SS_cons                 :::<<<<<<-------<<<<<<<<<<--<<<<____>>>>>>>>>>>>>>------->>>>>>---------------<<<<-----<<-<<<<<<<<__________>>>>>>>>->>----->>>>:::::::::
#=GC RF                      uugGCaGCaACAAGAAaGuGCuuagg.UuaaaUGaguuuaccuaaGCgCuGAUACAAuGCuGCCAGAAcAAUUUuAAaGcCaAGAACaGUccaGuuugauguAGUUUAcaaaCuggUCuACACGuGgCCuaACAUuc
//
# STOCKHOLM 1.0

#=GF AC   RF02668
#=GF ID   PsiU2-55
#=GF DE   Drosophila small cajal body-specific RNA PsiU2-55
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   55.00
#=GF TC   55.30
#=GF NC   38.00
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   24149844
#=GF RT   Novel small Cajal-body-specific RNAs identified in Drosophila: probing
#=GF RT   guide RNA function.
#=GF RA   Deryusheva S, Gall JG
#=GF RL   RNA. 2013;19:1802-1814.
#=GF CC   Pseudouridylation guide activity for U2 snRNA and 28s rRNA
#=GF WK   Small_Cajal_body-specific_RNA
#=GF SQ   3



AE013599.4/8048808-8048631 UUUACGUGGUUAGAAACGUUUCCAAGUGAUCAGCCUCUCUGGAAAUGCUUCAUGCCGCGUUAGAAAAACGACGAGCUCCCAGGUUACUGCCAAAUUUGCGAUAAAACGGGAGCUGCAAUGAAUAUGUUCGUGGCGAUUGUUAAGAAUUAAUCGUGACUGCUGAUAGUUGCAUACAUAU
AAST01021112.1/582-405     UUUACGUGGUUAGAAACGUUUCCAAGUGAACAGCCUCUCUGGAAAUGCUUCAUGCCGCGUUAGAAAAACGACGAGCUCCCAGGUUACUGCCAAAUUUGCGAUAAAACGGGAGCUGCAAUGAAUAUGUUCGUGGCGAUUGUUAAGAAUUAAUCGUGACUGCUGAUAGUUGCAUACAUUU
AAEU02000431.1/24048-23872 UUUACGUGGUCAGAAACGUUUCUAAGUGAACAGCCUCUCUGGAAAUGCUUCAUGCCGCGUCAGAAAAACGACGAGCUUCCAGGAUACUGUCAAAUUUGCGAUA-AACGGGAGCUGCAAUGAAUAUGUUCGUGGCGAUUGUUCAGAAUUAAUCGUGACUGCUGAUAGUUGCAUACAUUU
#=GC SS_cons               :::<<<<<<<--<<<-<<<<<<<<-<-<<______>>->>>>>>>>>->>>-->>>>>>>,,,,,,,,,,,,,,<<<<<<---<<<-<<<_______>>>->>>--->>>>>><<<<<<--<<--<<--<<-<<<<<<<________>>>>>>>->>->>-->>->>>>>>:::::::
#=GC RF                    UUUaCGcGGcuAGaaACguuuCcaAGUGaaCAGCCuCUCugGaaacGCuuCAUgCCgCGuuAGAAAAACGACGAGCucCCAGGuuaCcGcCAAAUUUgCgAuaaAACGGgaGCuGCaacGAauAUGcUCGuGgCGauugUUaAGAAUcaauCGcGaCUgCUGauAguuGCaUACAUuU
//
# STOCKHOLM 1.0

#=GF AC   RF02669
#=GF ID   PsiU6-40
#=GF DE   Drosophila small cajal body-specific RNA PsiU6-40
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   48.00
#=GF TC   48.90
#=GF NC   33.20
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   24149844
#=GF RT   Novel small Cajal-body-specific RNAs identified in Drosophila: probing
#=GF RT   guide RNA function.
#=GF RA   Deryusheva S, Gall JG
#=GF RL   RNA. 2013;19:1802-1814.
#=GF CC   Pseudouridylation guide activity for U6 snRNA
#=GF WK   Small_Cajal_body-specific_RNA
#=GF SQ   3



AE014296.4/20999620-20999479 UUCGGAUAUAUGCCUUAACUUUUGUGAAAAUUCUGAGAAUUGUUUCCAAUUCACAAUAUGGCAAUAUCCUAGAAUAAUGAACAGGAACUCUGUGCAAUGGCAUUGGAGCUUGUGGCAUUGCAUCGUUCUUCCUGCGACAUUC
AASW01028085.1/1372-1513     UUCGGAUGAAUGCCCUAACUUUUGUGAAAAUGCUUAGAAUUGUUUCCAAUUCACAAUAUGGCAAUAUCCUAGAAUAAUGAACAGGAACUCUGUGCAAUGGCAUUGAAGCUUGUGGCAUUGCAUCGUUCUUCCUGCGACAUUC
AAKO01002299.1/23854-23713   UUCGGAUGAAUGCCCUAACUUUUGUGAAAAUGCUUAGAAUUGCUUCCAAUUCACAAUAUGGCAAUAUCCUAGAAAAAUGAACAGGAACUCUGUGCAAUGGCAUUGAAGCUUGUGGCAUUGCAUCGUUCUUCCUGCGACAUUC
#=GC SS_cons                 :::<<<<<<-<<<<-<<----<<<<<<<-----<<-<<<____>>>>>->>>>>>>>>->>>>>>>>>>------<<<<--<<<<<<--<-<<<<<<<<-<<<________>>>->>>>>>>>->--->>>>>>--->>>>:
#=GC RF                      UUCGGaugcAuGCCcuaACUUuuGuGaaAAUgCugAGaaUUGuuuCcaAuuCaCaauaUGGCagcauCCUAGAAuaauGAACaGGaaCUCUguGCaauGGCacUGaAGCUUguGGCauuGCacCGUUCuuCCuGCGACauuC
//
# STOCKHOLM 1.0

#=GF AC   RF02670
#=GF ID   scaDm46E3
#=GF DE   small Cajal body-specific RNA Dm46E3
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   61.00
#=GF TC   61.10
#=GF NC   31.90
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   19230845
#=GF RT   A novel Drosophila antisense scaRNA with a predicted guide function.
#=GF RA   Tortoriello G, Accardo MC, Scialo F, Angrisani A, Turano M, Furia M
#=GF RL   Gene. 2009;436:56-65.
#=GF CC   Targets U1b snRNA, a developmentally regulated isoform of the spliceosomal
#=GF CC   U1 snRNA
#=GF WK   Small_Cajal_body-specific_RNA
#=GF SQ   2



EU924798.1/1-137      GGCCCCAAAUGAUGAGGGUUACUUUGUACGAAUGUCAGUGAAAUUGAAUUAAACAACGAAAAAUGCUUCAUGGCUUAACGGAGAUUUAUGAGGAAAACCGAACUUGAGGCCCACGUCAGUGGCUGAAGCCAAUCAUU
AASW01032585.1/151-15 GGCCCCUAAUGAUGAGGGUCACUUUGUACGGAUGUCAGUGAAAUUGAAUUAAACAACGAAAAAUGCUUCAUGGCUUAACGGAGAUUUAUGAGGAAAACCGAACUUGAGGCCCACGUCAGUGGCUGAAGCCAAUCAUU
#=GC SS_cons          (((-(((--(((((-(((,,,,<<<<<-------<<<<<___>>>>>-------->>>>>,,,,,<<<<<<<<<<<____>>>-->>>>>>>>,,,,<<________>>)))-)))))-)))-----))):::::::
#=GC RF               GGCCCCaAAuGacGAGGGUuACuucGuACGaAUGuCaguGAAacuGaAUUAAACAaCgaaAAAUGCcuCauggCucAACGgaGAUccauGagGAAAACCGAACUUGAGGCCCACguCaGuGGCUGAAGCCAAUCAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02671
#=GF ID   Ysr35
#=GF DE   Yersinia sRNA 35
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   428.00
#=GF TC   428.30
#=GF NC   167.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009405; pathogenesis;
#=GF RN   [1]
#=GF RM   23577771
#=GF RT   Counting small RNA in pathogenic bacteria.
#=GF RA   Shepherd DP, Li N, Micheva-Viteva SN, Munsky B, Hong-Geller E, Werner JH
#=GF RL   Anal Chem. 2013;85:4938-4943.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   3



BX936398.1/1496219-1496557 UAGCGCGUGAGCUAAGGGAUCAACAGGCCGAUUUUUCAAACCGCGAGCUGAAUUUUCAAGCACUGACUUGUGCCAUCGCUCAGUAUACAAACACAAUAUAUAGUGGGUGGGUGUUGGACAGAUAACAAGAUAGUGAGUAUUGAGGCUUUUGGCAAGUGAACAAAACGGGAUAAUUGUGUGGAUAACUUGGGGGUUAAUUGUUACGAAUGCCUUAUAAGCUGCGCCAUUACUGGGACUCACUACUUAUCCUUCUGGGGGAUAAGAUUUUGCGGAAAAUCUUAAAAGUUUGAUCGUUUGCCGCUUUAUUAAACAUUCUAAAAGAACCCUGUAAUUUAUCGC
CP000720.1/3126860-3126522 UUGCGCGUGAGCUAAGGGAUCAACAGGCCGAUUUUUCAAACCGCGAGCUGAAUUUUCAAGCACUGACUUGUGCCAUCGCUCAGUAUACAAACACAAUAUAUAGUGGGUGGGUGUUGGACAGAUAACAAGAUAGUGAGUAUUGAGGCUUUUAGCAAGUGAACAAAACGGGAUAAUUGUGUGGAUAACUUGGGGGUUAAUUGUUACGAAUGCCUUAUAAGCUGCGCCAUUACUGGGACUCACUACUUAUCCUUCUGGGGGAUAAGAUUUUGCGGAAAAUCUUAAAAGUUUGAUCGUUUGCCGCUUUAUUAAACAUUCUAAAAGGACCCUGUAAUUUAUCGC
AL590842.1/1369272-1369610 UAGCGCGUGAGCUAAGGGAUCAACAGGCCGAUUUUUCAAACCGCGAGCUGAAUUUUCAAGCACUGAUUUGUGCCAUCGCUCAGUAUACAAACACAAUAUAUAGUGGGUGGGUGUUGGACAGAUAACAAGAUAGUGAGUAUUGAGGCUUUUGGCAAGUGAACAAAACGGGAUAAUUGUGUGGAUAACUUGGGGGUUAAUUGUUACGAAUGCCUUAUAAGCUGCGCCAUUACUGGGACUCACUACUUAUCCUUCUGGGGGAUAAGAUUUUGCGGAAAAUCUUAAAAGUUUGAUCGUUUGCCGCUUUAUUAAACAUUCUAAAAGGACCCUGUAAUUUAUCGC
#=GC SS_cons               :((((-((((((-----(((((((-----((((((-----(((((((,<<<____>>>,<<<<______>>>>,,<<<<<<<-<<<<___________>>>>->>>>>>>,<<<<<______>>>>>,,,<<<<<<<<-<<-<<-----<<<<-<<<---------<<-<<--<<<<<----<<<<<____>>>>>----->>>>>>>->>------>>>-->>>>--->>->>>>>>>>>><<<<<<<<<___>>>>>>>>>,,)))))))))))))------)-)))))))))))))))):::::::::::::::::::::::::::::::::::::
#=GC RF                    UaGCGCGcgagCUAAGGGauCaaCAGGCCGauuuuUCAAACCGCgagCuGaAUUUuCaAGCaCUGAcUUGuGCCAcCgCcCaGuauaCAAACACAAUAuauaGuGgGcGgGuGuugGACAGAcaaCaAGAuaGuGaGuAccGaGGCUUUugGCAaGcGAACAAAACGGGauAAucGugUGGAuaaCcUGGGgGuuaAUUGUcaCgaauGCCUUAUAAgCuGCGCcaUUACuGggaCuCaCuaCuuauCCccCUGggGGauaaGAUcucGCGGaaaauCUUAAAAGUuuGauCGcucgCCGCuUUAUUAAACAUUCUAAAAGgACCCUGUAAUUUAUCGC
//
# STOCKHOLM 1.0

#=GF AC   RF02672
#=GF ID   SprX
#=GF DE   Small pathogenicity island RNA X
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Published; PMID:24557948
#=GF SS   Published; PMID:24557948
#=GF GA   54.00
#=GF TC   54.30
#=GF NC   47.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0009405; pathogenesis;
#=GF RN   [1]
#=GF RM   24557948
#=GF RT   A small RNA controls a protein regulator involved in antibiotic resistance
#=GF RT   in Staphylococcus aureus.
#=GF RA   Eyraud A, Tattevin P, Chabelskaya S, Felden B
#=GF RL   Nucleic Acids Res. 2014;42:4892-4905.
#=GF RN   [2]
#=GF RM   27438010
#=GF RT   Enhancement of the pathogenicity of Staphylococcus aureus strain Newman by
#=GF RT   a small noncoding RNA SprX1.
#=GF RA   Kathirvel M, Buchad H, Nair M
#=GF RL   Med Microbiol Immunol. 2016;205:563-574.
#=GF CC   SprX was shown to influence antibiotic resistance of the bacteria to
#=GF CC   Vancomycin and Teicoplanin glycopeptides, which are used to treat MRSA
#=GF CC   infections. In this study the authors identified a SprX target, stage V
#=GF CC   sporulation protein G (Spo VG). By reducing Spo VG expression levels, SprX
#=GF CC   affects S. aureus resistance to the glycopeptide antibiotics. It is
#=GF CC   involved in regulation of pathogenicity factors.[2]
#=GF WK   SprX_small_RNA
#=GF SQ   3



CP000253.1/1464207-1464058 ACACAUGCAUCAACUAUUUACAUCUAUCCUUGUUCACCCAAGCAUGUCACUGGGUGUUUUUUCUUACGAUAGAGAGCAUAGUUUUCAUACUACUCCC-CGUAGUAUAUAUGACUUUAGCAUUCCCGUAUAACAGUUUACGGGGUGCUUUUU
BA000018.3/2008789-2008643 ACACAUGCAUCAACUAUUUACAUC----CUUGUUCACCCAAGCAUGUCACUGGGUGUUUUUUCUUAUGAUAGAGAGCAUAGUUUUCAUACUACUCCCCCGUAGUAUAUAUGACUUUAGCAUUCCCGUAUAAUAGUUUACGGGGUGCUUUUU
CP000253.1/2035378-2035228 ACACAUGCAUCAACUAUUUACAUCUAUCCUUGUUCACCCAAGCAUGUCACUGGGUGUUUUUUCUUAUGAUAGAGAGCAUAGUUUUCAUACUACUCCCUCGUAGUAUAUAUGACUUUAGCAUUCCCGUAUAAUAGUUUACGGGGUGCUUUUU
#=GC SS_cons               ::<<<-<-<<-<<____>>-->>----->->>>,<<<<<<__________>>>>>><<-<<<<<<______>>>>>->->>,,,,,<<<<<<<______>>>>>>>,,,,,,,,,,<<<<<-<<<<<<________>>>>>>>>>>>::::
#=GC RF                    ACaCaUGCauCaaCUAUuuACauCUAUcCUuGuUCaCCCaAGCAUGUCACuGGGuGuuUuuuCuuAuGAUAgaGagCaUagUUUUCauaCuaCUCCCuCGuaGuauAUAUGACUUUaGCauUCCCGuaUAAuAGUUuaCGGGguGCuUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02673
#=GF ID   scr4677
#=GF DE   Streptomyces sRNA 4677
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:24465751
#=GF GA   41.00
#=GF TC   41.90
#=GF NC   37.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24465751
#=GF RT   Complex intra-operonic dynamics mediated by a small RNA in Streptomyces
#=GF RT   coelicolor.
#=GF RA   Hindra, Moody MJ, Jones SE, Elliot MA
#=GF RL   PLoS One. 2014;9:e85856.
#=GF CC   Located in the intergenic region between anti-sigma factor SCO4677 gene
#=GF CC   and a putative regulatory protein gene SCO4676. scr4677 expression
#=GF CC   requires the SCO4677 activity and scr4677 sRNA itself seem to affect the
#=GF CC   levels of the SCO4676-associated transcripts.
#=GF WK   Streptomyces_coelicolor
#=GF SQ   12



AL939121.1/30426-30180       GGUUCCGGUGCCGUCGGC-G----C--CCUACC--AAG-ACAAGAA-ACGGGGGAAAUGAC-C-CCUACCAAGCCCCACC---CCUCCCGCCCGAGGCGCUUCGUCACUCGGGCGGGUGAACAUCACCGGUUGAGCUGGAUUUCGGGGCCCUCAACUCCCCUACUCUCA-------------GCGCA------A-ACA--AACACAUC---UGAAAAGGCAU----CGGCCCCCGCUGGGACUGGCAUCCCGGUGCGAGGGCCUAACCACCAAGGAAGAAGAGAG-CUUCCCG
ACFA01000511.1/6065-5823     AGCUCCGGUGCCGUCGGC-G----C--CUUCCC--AAA-GCAAGAA-CCCGGGGAGAAAACAC-CCCACCAAGCCCCACC---CCUCCCGCCCGAGGCACGCGAUCACUCGGGCGGGUGAACAUCACCGGCUCAGCUGGAUUCUCGAACCCCCGACACCUCUACGCUCA-------------GCGCA------C-A-----CAACCCC---GAAAAAGACUU----CGGCCCCCGCCGGGACGGCAAUCCCAGUGCGAGGGCCUGACCACCAAGGAAGUCG--GC-CUUCCCG
ABYA01000314.1/2329-2086     AGUUCCGGUGCGGUCGGC-G----C--CUUUCC--CAA-GAAACGC-GAGAGGGAAAUGAC-CCCCCACCGAACCCACCC---UUUCCCGCCCGGGACCUGCGCUCACUCGGGCGGGUGGACAUCACCGCUCGGCCGGCUUUUCGGGUGCCCC-GCGGCUUUACGCUCA-------------GCGCA------C-ACC-----ACCGC---AGAAAAGACUU----CGGCCCCCGCCGGGACUGGCAUCCCAGUGCGAGGGCCUGACCACCAAGGAAGACGAGAC-CUUCCCG
ACEY01000129.1/49787-50034   GGUUCCGGUGCCGUCGGU-G----C--CCUACC--AAG-ACAAGAAACCGGGGGAAAUGAC-C-CCUACCAAGCCCCACC---CCUCCCGCCCGAGGCGCUUCGUCACUCGGGCGGGUGAACAUCACCGUUUGAGCUGGAUUUCGGGGCCCUCAACUCCCCUACUCUCA-------------GCGCA------A-ACA--AACACAUC---UGAAAAGGCAU----CGGCCCCCGCUGGGACUGGCAUCCCGGUGCGAGGGCCUAACCACCAAGGAAGAAGAGAG-CUUCCCG
FN554889.1/5033478-5033726   AACUCCGGUGCCACGGGU-G----A-UCUUCCC--AAA-GAAACAU-GAUGGGGAAAGAAA-C-CCCACCAAGCCCCACC---CCUCCCGCCCGCGGCUCCCGCUCACUCUCGCGAGUGAACAUCACCAACUUGGCUGGCUUCGGGACAGGUUGACUGCUCUACGCUCA-------------GCGCG-----GC-ACCACACAACCGC---AGAC-AUGCGA----CGGCCCCCGCCGGGACGGCAAUCCCAGUGCGAGGGCCUGACCACCGAGGAAGACA-GGA-CUUCCCG
ABYA01000206.1/3529-3279     CGUUCCGGUGCCGUCUGC-G----A--CUGAAG--GAC-AAAGAAC-GCCGGGGGAAAGCA-C-CCCACCGAGCCCCACC---CCUCCCGCCCGUG-GUCGCACUCACUCGGGCGGGUGAACAUCCCCGAACCGGCUGGAUUUCGCAGCCCUU-GAAGCCCGACGCUCA-------------GCGCA------A-CGA---ACACACCACAACCACAGACAUGAGACGGCCCCCGCCGGGACGGCAAUCCCAGUGCGAGGGCCUGACCACCGAGGAAGGUAAAGG-CUUCCCG
BA000030.3/3913208-3912967   UGCUCCGGUGCCAGGGGC-G----C--UCUUCC--CAAAGAACUAC-AAGGGUGAAAGAAC-C-CCCACCAAGCCCCACC---CCUCCCGCCCGCGGCACACAGUCACCCGCCCGAGUGAACGUCACCAACUCGGCUGGAUUCCAAGCUGGUUGCCUGUCCUACGCUCA-------------GCGCA------A-C------AACCGC----AGACAUGCGA----CGGCCCCCGCCGGGACGCCAAUCCCAGUGCGAGGGCCUGACCACCGAGGAAGUU-AGGG-CUUCCUG
ACFA01000456.1/1359-1615     UGUUCCGGUGCCGUCGGCCG----U--CUUUUC--CAA-GGACCAC-GGGAGAGAAAGAAA-C-CCCACCAAGCCCCACC---CCUCCCGCCCACGGCGCACGCUCACUCGCGUGGGUGAACAUCACCAAUUGAGCUGGAUAUGUGAUGGGUUGCCUGCCCUACGCUCA-------------GCGCAGCACGAC-ACGGCACAACAACC-CCAGACAUGCAA----CGGCCCCCGCCGGGACUGGCAUCCCAAUGCGAGGGCCUGACCACCAAGGAAGCAC-UAC-CUUCCCG
AGDE01000056.1/679-921       CGCCCCGGUGCCGCAGGC-G---GU--CUCCCU--CAA-GGACCAC-GAGGAGGAAAGAAC-C--CCACCAAACCCCACC---CCUCCCGCCCAGGCCGCCGCCUCACUCACGCGAGUGAACAUCGCCAACUCAGCUGGAUUCGGGAGCCCUUGCCUGCCCUACGCUCA-------------GCGCA------A-CCA-----ACCGC---AGA-CAUGCGA----CGGCCCUCGCCGGGACUGGCAUCCCAGUGCGAGGGCCUGACCACCGAGGAAGGCUCCAA-CUUCCUG
ACEZ01000164.1/104333-104585 CGCUCCGGUGCCGUCGGC-G----A--CUGAAAGGCGA-AGAACCC-CCGAGGGAAAGAAC-C-CCUGCCAAGCCCCACC---CCUCCCGCCCGCGUCCCGUGCUCACUCGCGCGGGUGAACCUCCCCGGACCGGCUGGAUUUCGCGGCCCUC-GAGGCCCGACGCUCAGC--------CCAACGCA------CCACC--ACAACCGC---AGA-CAUGCGA----CGGCCCCCGCCGGGACGGCAAUCCCAGUGCGAGGGCCUGACCACCGAGGAAGAUAGAGG-CUUCCCG
AGDD01000623.1/1074-829      CGCUCCGGUGCGAGGGGC-GGUCUC--UUUUCC--CAA-GGACCAC-GACGGUGAAAGAAC---CCGACCAAGCCCCACC---CCUCCCGCCCGCUGCGCAAACUCACCCACCCGGGUGAACAUCGCCAACUCGGCUGGAUUCCCAGCCCCUUGCUGGCCCUACGCUCA-------------GCGCA------A-C-A---CAACCGC---AG-ACAUGCGA----CGGCCCCCGCCGGGACGGCAAUCCCAGUGCGAGGGCCUGACCACCGAGGAAGUAG-GAG-CUUCCCG
FN554889.1/4167390-4167657   GGCUCCGGUGCGACGGGC-G----GUCUUUCUC--CAA-AGAACCC-GGGAGAGAAAGAAC---CCCACCAAACCCCACCCCUCCUCCCGCCCGGCAGGCCGUCUCACCCUCUCGGGUGAACAUCGCCAACUCGGCUGGAUUUCGGAGCGGUUGUUACCCCUACGCUCAGCGCAGCACGACACCGCG------A-CCGC-ACAACAAC---CGCAGACGUACG--ACGGCCCUCGCCGGGACUGCAAUCCCAGUGCGAGGGCCUGACCACCAAGGAAGACAAGCCCCUUCCCG
#=GC SS_cons                 ::::::((((,,,,,<<<.<...._..______..___._______.______________._.________________..._____>>>>,,,,,,,,,,,,<<<<<<____>>>>>>,,,,,,,,,,,,,,<<<<<___________________________>>>.............>>,,,......,.,,,..,,,,,,,,...,,,,,,,,,,,....,<<<<<-<<<-<<<<______>>>>--->>>->>>>>,,,,))))--<<<<<_______.>>>>>::
#=GC RF                      aGcUCCGGUGCcgucGGC.G....a..cUuucc..cAA.gaAacac.gaggGgGAAAgAAc.C.CCcACCAAgCCCCACC...CCUCCCGCCCGaggcgCauacUCACcCgcgCGgGUGAACAUCaCCaauUcgGCUGgAUUucggagcccUuGacugCcCUACGCuCA.............GCGCA......a.aca..AcaACagC...agaAaAuGCaa....CGGCCCCCGCCGGGACuGcaAUCCCAGUGCGAGGGCCUGACCACCaAGGAAGauaagag.CUUCCCG
//
# STOCKHOLM 1.0

#=GF AC   RF02674
#=GF ID   AsdA
#=GF DE   antisense RNA of dnaA mRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   52.00
#=GF TC   52.20
#=GF NC   51.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0043488; regulation of mRNA stability;
#=GF RN   [1]
#=GF RM   23637809
#=GF RT   Identification and characterization of a cis-encoded antisense RNA
#=GF RT   associated with the replication process of Salmonella enterica serovar
#=GF RT   Typhi.
#=GF RA   Dadzie I, Xu S, Ni B, Zhang X, Zhang H, Sheng X, Xu H, Huang X
#=GF RL   PLoS One. 2013;8:e61308.
#=GF WK   Salmonella_enterica
#=GF SQ   4



CAAZ01000116.1/24420-24500 UUUCGCGUUGGGUUUGCGCGCCAUAAUGCCGUUACCCACCGCGUGCAGCAGGUGAGUUUUACCCAGACCGGUGCCGCCAUA
ABEH02000004.1/52969-52889 UUUCGCAUUGGGUUUGCGCGCCAUAAUGCCGUUACCCACCGCGUGCAGCAGGUGAGUUUUACCCAGACCGGUGCCGCCAUA
AGSY01000025.1/45702-45622 UUUCGCAUUGGGCUUGCGCGCCAUAAUGCCGUUACCCACCGCGUGCAGAAGGUGCGUUUUACCCAGACCCGUGCCACCAUA
AERM01000130.1/5252-5172   UUUGGCAUUCGGCUUGCGCGCCAUAAUGCCGUUACCCACCGCAUGCAGCAGGUGAGUUUUACCCAGACCCGUGCCGCCAUA
#=GC SS_cons               :::<<<<-<<<<<--<<<-<<______>>>>>->>>>>->>>>-------<<<<-<<---<<<______>>>>>>>>>:::
#=GC RF                    UUUcGCgUugGGuUUgCGCGCCAUAAUGCCGuUaCCcaCcGCgUGCAGcAGGcGaGuUUUaCcCAGACCgGugCCgCCAUA
//
# STOCKHOLM 1.0

#=GF AC   RF02675
#=GF ID   Ysr141
#=GF DE   Yersinia sRNA 141
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:24532772;
#=GF GA   186.00
#=GF TC   187.40
#=GF NC   184.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009405; pathogenesis;
#=GF RN   [1]
#=GF RM   24532772
#=GF RT   Genome-wide analysis of small RNAs expressed by Yersinia pestis identifies
#=GF RT   a regulator of the Yop-Ysc type III secretion system.
#=GF RA   Schiano CA, Koo JT, Schipma MJ, Caulfield AJ, Jafari N, Lathem WW
#=GF RL   J Bacteriol. 2014;196:1659-1670.
#=GF CC   Shown to regulate the synthesis of the type III secretion system (T3SS)
#=GF CC   effector protein YopJ.The Yop-Ysc T3SS is a critical component of
#=GF CC   virulence for Yersinia species.
#=GF WK   Yersinia_pestis
#=GF SQ   4



BX936398.1/45948-46202     CUUUCCCCUUUUGCUUGCCAGCCAACCAGCCGACA-CUAAACCCAAGAGGCUCCAGCCAUUGACGGAAAGUAGUGGCGUGCUGUUCUGCCAGCAGUUCGGUCGGUGCCAUCAGGGCAACCUGCUUACCGUGAGCGAUGGCCCGUAGCGCGGCCAGUGCGGCUACCAGUGUUUUACCGGAACCGACAUCCCCCUGAAUCAGUCGCAUCAUCGGGAAACUUUGGGUCAUAUCCCGUUCAAUUUCGGCGACGACCCGUU
ACCA01000027.1/27609-27863 CUUUGCCUUUUUGUUUCCCAGCCAGCCAGCCGACUUGUAAA-CCUAACGGCUCCAGCCAUUGACGAAAAGUAUUGGCAUGCUGUUCAGCCAGUAACUCAGUGGGAGCCAUCAACGCGACCUGCUUACCGUGGGCAAUAGCACGCAGUGCGGCCAGUGCGGCAACCAAUGUUUUACCCGAGCCGACAUCUCCUUGAAUCAACCGCAUCAUAGGGAAAUCAUGGGUCAUAUCUUGUUCGAUUUCCGCGACAACCCGCU
AALF02000032.1/19444-19190 CUUUACCUUUUUGCUUGCCAGCCAGCCAGCCCACU-UGCAGCCCUAAGGGUUCGAGCCAUUGGCGAAAAGUGGUGGCAUGCUGUUCUGCCAGUAACUCGGUGGGUGCCAUUAAGGCAACCUGCUUGCCGUGAGCAAUGGCACGCAGUGCGGCCAGUGCUGCAACCAAUGUUUUCCCGGAGCCAACAUCCCCUUGAAUCAAUCGCAUCAUUGGGAAGUUAUGGGCCAUAUCUUGCUCGAUCUCCGCCACUACUCGUU
AL590842.1/48532-48786     CUUUCCCCUUUUGCUUGCCAGCCAACCAGCCGACA-CUAAACCCAAGAGGCUCCAGCCAUUGACGGAAAGUAGUGGCGUGCUGUUCUGCCAGCAGUUCGGUCGGUGCCAUCAGGGCAACCUGCUUACCGUGAGCGAUGGCCCGUAGCGCGGCCAGUGCGGCUACCAGUGUUUUACCGGAACCUACAUCCCCCUGAAUCAGUCGCAUCAUCGGGAAACUUUGGGUCAUAUCCCGUUCAAUUUCGGCGACGACCCGUU
#=GC SS_cons               :((((((,,,,<<<<-<<-<<-----<<<<<<-<<.<<<--<<<<<--<<<____>>>->>>-->>---->>>>>->>->>>>-->>>>->>>><<<<<--<<<<<----<<<<____>>>>-->>>>>>>>>>,,<<<<<<<___>>->>>>><<<<<<<<--<<<-<-------<<<_______>>>>->>>---->>>>>>>>,,,,))))))---<<<<<<---<<<<<________>>>->>->>>>>>::
#=GC RF                    CuuucCCuUUUugcuUgCCaGCCAaCCaGCcgACa.cuaAacCCaaaaGGcUCcAgCCAuuGaCGgAAAGuaguGGcgUGCuGUUCuGcCagcagcuCgGUcGGugCCAUcaggGCaAccugCUuaCCgcGagcaAugGCcCguAGcGCgGCcaguGCggcuACCagUGUUUUaCCgGaaCCaACAuCcCCcuGAAUCagccGCauCAUuGGgaaauuauGGGucAUAucccGuUCaAUuUCggCgaCgaCCCguU
//
# STOCKHOLM 1.0

#=GF AC   RF02676
#=GF ID   Esr41
#=GF DE   Enterohemorrhagic E. coli sRNA 41
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:24646762;
#=GF GA   102.00
#=GF TC   102.40
#=GF NC   39.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 2000147; positive regulation of cell motility;
#=GF RN   [1]
#=GF RM   24646762
#=GF RT   A novel small regulatory RNA enhances cell motility in enterohemorrhagic
#=GF RT   Escherichia coli.
#=GF RA   Sudo N, Soma A, Muto A, Iyoda S, Suh M, Kurihara N, Abe H, Tobe T, Ogura
#=GF RA   Y, Hayashi T, Kurokawa K, Ohnishi M, Sekine Y
#=GF RL   J Gen Appl Microbiol. 2014;60:44-50.
#=GF CC   Enhances cell motility in both enterohemorrhagic E.coli O157:H7 and
#=GF CC   nonpathogenic E. coli K12. However, the sequence is specific to O157:H7
#=GF CC   and not present in K12.
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   3



CP001368.1/1366278-1366351 GAUGCUCUAGGCAUCACAUUUUCUCCAUGGGGUAUUCCCUCCGCCGGCACUAUGUGUUGCUGGCGUUUUUUUAU
CP000036.1/4399199-4399126 GGUGCUCUAGGCAUCACAUUUUCUCCAUGGGGUAUUCCCUCCGCCGGCACUAUGUGUUGCUGGCGUUUUUUUAU
CU928162.2/4857198-4857271 GGUGCUCUAGGCAUCACAUUUUCUCCAUGGGGUAUUCCCUACGCCGGCACUAUGUGUUGCUGGCGUUUUUUUAU
#=GC SS_cons               <<<<<<___>>>>>>,,,,,,,,,,,,,<<<<___>>>>--<<<<<<<<________>>>>>>>>:::::::::
#=GC RF                    GauGCuCUAgGCauCACAUUUUCUCCAUGGGgUAUuCCCUcCGCCgGCaCUAUGUGUuGCuGGCGUUUUUUUAU
//
# STOCKHOLM 1.0

#=GF AC   RF02677
#=GF ID   NsiR4
#=GF DE   Nitrogen stress-induced RNA 4
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAalifold;
#=GF GA   40.00
#=GF TC   40.60
#=GF NC   32.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010608; posttranscriptional regulation of gene expression;
#=GF RN   [1]
#=GF RM   26494284
#=GF RT   The sRNA NsiR4 is involved in nitrogen assimilation control in
#=GF RT   cyanobacteria by targeting glutamine synthetase inactivating factor IF7.
#=GF RA   Klahn S, Schaal C, Georg J, Baumgartner D, Knippen G, Hagemann M,
#=GF RA   Muro-Pastor AM, Hess WR
#=GF RL   Proc Natl Acad Sci U S A. 2015;112:E6243-E6252.
#=GF CC   Former name SyR12, is a cyanobacterial non-coding RNA which plays role in
#=GF CC   the regulation of Glutamine synthetase (GS), a key enzyme in biological
#=GF CC   nitrogen assimilation. NsiR4 interacts with the 5'UTR of the mRNA of the
#=GF CC   GS inactivating factor IF7 (gifA mRNA) and reduces its expression. NsiR4
#=GF CC   expression is under positive control of the nitrogen control transcription
#=GF CC   factor (NtcA). NsR4 is a first example of an sRNA controlling the
#=GF CC   assimilation of a micronutrient.
#=GF WK   NsiR4_small_RNA
#=GF SQ   4


CP000806.1/666566-666631   AAGACAUAAAGUCAAUUAUCACCCUCCGAUUGCUUAUUGCAACCGCCCACAC-UUCAGUGGCGGUUU
BA000022.2/1289326-1289264 AAGACAUAAAGUCAA-UAUCACCCUCCGAUUGCUAG---AGGUCGCCCAUUGCUUCAGUGGCGGCUU
CP002198.1/2006173-2006109 AAGACAUAAAGUCAA-UAUCACCCUCCGAUUGCUUAUCCAAGCCGCCCGUUG-UCUAGGGGCGGUUU
CP001291.1/4248692-4248628 AAGACAUAAAGUCAA-UAUCACCCUCCGAUUGCUUAUCCAGGCCGCCCAUAG-UCUAGGGGCGGUUU
#=GC SS_cons               ::<<<_____>>>--.-----------------------<<<<<<<<<____._____>>>>>>>>>
#=GC RF                    AAGACAUAAAGUCAA.UAUCACCCUCCGAUUGCUUAUccaagCCGCCcAUug.UuuAGgGGCGGcuu
//
# STOCKHOLM 1.0

#=GF AC   RF02678
#=GF ID   Hatchet
#=GF DE   Hatchet ribozyme
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Weinberg Z
#=GF SS   Published; PMID:26167874
#=GF GA   93.00
#=GF TC   93.60
#=GF NC   38.00
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   26167874
#=GF RT   New classes of self-cleaving ribozymes revealed by comparative genomics
#=GF RT   analysis.
#=GF RA   Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR
#=GF RL   Nat Chem Biol. 2015;11:606-610.
#=GF WK   Hatchet_ribozyme
#=GF SQ   8


BAAV01010313.1/848-730   ---------GAAGCUAAAGAAGC---------AAGAAAGUAUUACUG-UGAGAAUCAGUAAUAAGCAUGUGGGGCUUAUGUCUUAUC-AAAAGGGUGGCCAACU---------------------------------------------UUUAGAUAGCAUUAGUGCGGACGUUAAAAUCAUGC
BABB01003568.1/1136-1282 UUAGCGUGUGUAGGUAGAG----------------AGUUCUUUAAGG-UGAGAAUCCUUGACAAGCAUGUGGGGCUUAUA-UCUAUU----CAUACAGAGCAAGUACGUACGGGAAAGCUUAAAAUACUCAUCU---------------GUAAAAUAGUAUUAGUGCAGACUUUAAAAUCAUGC
BAAZ01000328.1/6887-6736 ----AAAGUUAA------UGCAGUAGA-AAUACUGCGCUCUUUAAGG-UGAGAAUCCUUGACAAGCAUGUGGGGCUUAUA-UCUAUU----CAUACAGAGCAAGUACGUACGGGAAAGCUUAAAAUACUCAUCU---------------GUAAAAUAGUAUUAGUGCAGACUUUAAAAUCAUGC
BABB01012728.1/605-436   CUUGUUCGUGAGAAUAGGUGCAAUUGCCUAAAUGAAUGUCUUCA-----GAAGA----UGACAAACCUGUGGGGCGUA-A-GUAAUAAAGAGUCUGAAAGAUUGCAGAUAAGAGUAUGCACUUAUUGGCAAUAUGCAUACCAGA---AUAAUUUAUUAUGAUCGUGCGGACGUUAAAAUCAGGU
BABB01008641.1/690-522   CUCGUUCGUGAGAAUAGGUCCAAUGGCCUAAAUGAAUGUCUUCA-----GAAGA----UGACAACCC-GUGGGGCGUA-A-GUAAUAAAGAGUCUGAAAGAUGCCAGAUAAGAGUAGCCACUUAUUGGCAAUAUCCAUACCAGA---AUAAUUUAUUAUGAUCGUGCGGACGUUAAAAUCAGGU
BAAZ01000328.1/4457-4299 UCAGUCUGUGAAGAUAGAGUA-------------UACGUCCUCA-----GAAGA----UGACAAACCUGUGGGGCGUA-A-GUAAAUGCAUAUCGUAUAUUAUUCCCUUGAAUACGGCAAUAGCGGGUAAUAUCCGAGAUA-CUCGUAUUUGUGUUUAUAAUCGUGCAGACGUUAAAAUCAGGU
AACY021702793.1/630-786  ACAUUUUGUGGUUUUAAGGG--------------UUAAUCCUUAAGGUUGAUAAACCUUGACAAGCCUAUGGGGCUACUA--UAGUAUUCUCUUAUUACGGGUAAGAGUAUCAAGCAUAAGCGAAAUUCCGUGCUUAU-----------GUAAUGCUAAGUUAGUGCAGACUUAAAAAUUAGGC
AACY021400709.1/636-792  ACAUUUUGUGGUUUUAAGGG--------------UUAAUCCUUAAGGUUGAUAAACCUUGACAAGCCUAUGGGGCUACUA--UAGUAUUCUCUUAUUACGGGUAAGAGUAUCAAGCAUAAGCGAAAUUCCGUGCUUAU-----------GUAAUGCUAAGUUAGUGCAGACUUAAAAAUUAGGC
#=GC SS_cons             :::::::::::::::::::::::.........:::::::::<<<<<<._______>>>>>>---<<<<<----<<<----.<<<<<<<<<<___________________________________________________.......>>>>>>>>>>--->>>-------------->>>>>
#=GC RF                  uuagUuuGUGAagaUAgaggaAa.........uauaaaUCuUcAagG.UGAaAAuCcuUgACAAgCcUGUGGGGCuUAUA.guaAucacacauuauaaagaauucaagUAagaguaauaAuagAaugucaaUauuuAU...........gugugaUuauauUaGUGCAGACgUUAAAAUCAgGc
//
# STOCKHOLM 1.0

#=GF AC   RF02679
#=GF ID   Pistol
#=GF DE   Pistol ribozyme
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Weinberg Z
#=GF SS   Published; PMID:26167874
#=GF GA   34.00
#=GF TC   34.00
#=GF NC   33.80
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   26167874
#=GF RT   New classes of self-cleaving ribozymes revealed by comparative genomics
#=GF RT   analysis.
#=GF RA   Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR
#=GF RL   Nat Chem Biol. 2015;11:606-610.
#=GF WK   Pistol_ribozyme
#=GF SQ   45


AGGO01000583.1/22-99         AGUCGUUGUGGCGACUAUAACCAAGCUCUU-UAAGCCACA-AGCGUUGCUGAUGAGG---UUUC----A--UAACAUCAGCAGGUAGAG
AFHW01000093.1/13318-13252   ACUGGUUCGAGCCAGUAAAAAAA--GGCCGAUAAGCUCGA-AGCGUUCCACUCU---------U----------AGAGUGGAGGAGGCA
AACY021048934.1/360-303      GCUCGGUGCGGCGAGCCUAAAUA-GUGCCU-UAGGCCGCA-CGCGUUAUG----------------------------CAUAGGUGGCA
AACY020454584.1/604-676      ACUGGUUGCGGCCAGUAUAAAUA--GUCUU-UAAGCCGCA-AGCGUGUCCUGGAGU------UA----A--UCUUCCAGGGCGGUAGCA
ADCZ01000007.1/277655-277723 AAUCGACUAGGCGAUUUUAAAUA--GGUGU-UAAGCCUAG-UGCGGUAAGAGGU----------AUAA------CCCUCUUGCGUCACG
ADCZ01000007.1/276193-276256 AUUCGACUAGACGAGUAUAAAUA--GGUGU-CAGGUCUAG-UGCGGCAGGG-------------UUCU-----U---CCCUGCAUCAUA
ADCZ01000057.1/1592-1655     GAUCGACUAGACGAUUAAAAACA--GGUGU-UAGGUCUAG-UGCGGCAGGG-------------UUCU-----U---CCCUGCGUCACA
BABE01011365.1/336-273       AAUCGACUAGACGAUAAAAAACA--GGUGU-UAGGUCUAG-UGCGGCAGGG-------------UUCU-----U---CCCUGCGUCACA
ADCZ01000007.1/276491-276554 AAUCGACUAGGCGAUUUAAAAUA--GGUGU-UAAGCCUAG-UGCGGCAGGG-------------UUCU-----U---CCCUGCAUCACA
AACY020454254.1/1909-1844    AGUCGUUUGGGCGACUAUAAACA--GACGAAUAAGCCCAA-AGCGUUUCCUC------------GUAA--------GAGGAAGGACGGA
ABPY01006745.1/33-98         ACAGGUUUGCGCCUGUAUAAAUA--GACAU-UAAGCGCAA-AGCGUCCCGCA------------AUUG-----U--UGCGGGGGUUGUA
AACY023396520.1/1459-1527    AGUCGGUAGAGCGACUUUAAAAA--GGCAU-UAGGCUCUA-CGCGUUCCAGGAG----------GAAA------CUCCUGGAGGUUGUU
AACY022753348.1/678-746      AGUCGACUAAGCGACUCUAAACA--GCAUU-UAGGCUUAG-UGCGUUCCCCUGC----------UCAC------GCGGGGGAGGUAUGG
ACWC01000004.1/40409-40346   AGUCGUGGCGGCGACGUUAAAUA--GGCAU-UAAGCCGCC-AGCGUUCCCC-------------UCAU-----U---GGGGAGGUUGCA
CP002400.1/1057607-1057686   CACCGUGGCGGCGGUGUAAAACA--AACAU-UAAGCCGCC-AGCGUCCCGGAACAAGG-CAUUU----UCCGAUUCUCCGGGGGUUGCA
AACY020454584.1/1474-1546    ACUCGUCUGAGCGAGUAUAAAUA--GGCUU-UUGGCUCAG-AGCGAUUCCUGGAGC------GC-U--G---UUUCCAGGGAUGUAGCA
FP929062.1/241377-241311     ACACGUUGCGCCGUGUAUAAAUA-GCCAGU-UAGGGCGCA-AGCGUCCCGGC------------AUUU-----U--GCCGGGGGUCUGG
ADGC01049496.1/241-175       ACACGUUGCAACGUGUAUAAAUA-GCCCUU-UAGGUUGCA-AGCGUCCCGCC------------CAUG-----U--GGCGGGGGUAGGG
ABFK02000017.1/466353-466289 AGCCGUUCGGGCGGCUAUAAACA--GACCU-CAGGCCCGA-AGCGUGGCGGC------------ACCU--------GCCGCCGGUGGUA
AERA01001428.1/285-220       ACUCGUUAGGGCGAGUAUAAAUA--GCCAU-UAGGCCCUA-AGCGUCAAUGA------------UAAG-----C--UCAUUGGGUUGGA
ABPY01006745.1/722-791       GCUGGUCACGGCCAGUAUAAACA--GACAU-UAAGCCGUG-AGCGUCUCCUGUU----------CUGU-----GAACGGGAGGGUUGUA
ABPY01006746.1/503-437       AGAGGUCACAGCCUCUUAAAAUA--GACAU-UAAGCUGUG-AGCGUCUCCCGU-----------AUUA-------ACGGGAGGGUUGUA
ABLX01143204.1/55-1          ACUCGACAGGGCGAGGCUAAAUA--GCAUU-UAGGCCCUG-AGCGGCUCCC-------------UUC----------GGGAG-------
ABLX01198122.1/57-104        ACUCGUCAGAGCGAGUAUAAAUAGCUUUUU-UAGGCUCUG-AGCGUCCUC---------------------------------------
ABLX01246400.1/55-101        ACUCGUCAGAGCGAGUAUAAAUA-GCUUUU-UAGGCUCUGAAGCGUACC----------------------------------------
ABLX01165607.1/35-1          ACUCGUCAGAGCGAGUAUAAAUA-GCUUUU-UAGGCU----------------------------------------------------
ABNK01016853.1/25-90         AGUCGUCUGAGCGACUAUAAACA--GAGUUUUAGGCUCAG-AGCGCCUCCCC------------UUCG--------GGGGAGGGUACUA
AGFS01138167.1/426-348       ACUCGACUAGACGAGUAUAAAC---UACAU-UAAGCCUAG-UGCGUUAUAGCCGUAAAUAAGAAGUA-----AACGGCUAUAGGUUGUA
ABLZ01250225.1/97-32         AGUCGUUAGGGCGACUAUAAACA--GACAU-UAAGCCCUA-AGCGUCCCCUA------------CUAG-----C--UAGGGGGGUUGUA
BAAU01010303.1/537-465       GCUCGUCUGGGCGAGGGUAAAUA--GUAAU-UAGGCCCAG-AGCGUCUUGGCCGGG------AG----C--UGCCGGUCAGGGGUUUAG
BAAU01005155.1/240-168       GCUCGUCUGGGCGAGGGUAAAUA--GUAAU-UAGGCCCAG-AGCGUCUUGGCCGGG------AG----C--UGCCGGUCAGGGGUUUAG
BAAV01005253.1/703-639       ACUCGUCUGGGCGAGUAUAAAUA--GUAAU-UAGGCCUAG-AGCGUCCCGGU------------AGC--------UGCCGGGGGGUUAG
AACY020454584.1/937-1000     ACUCGUCUGAGCGAGUAUAAAC---CACUU-UAGGCUCAG-AGCGUCCCCAC------------UUCG--------GUGGGGGGUAGCA
AACY020846719.1/108-178      ACUCGACUAAGCGAGUAUAAAUA--GGCAU-UAGGCUUAG-AGCGUUCCAAUGUU--------G-UGA-----AACAUCGGAGGUUGUU
AACY022661277.1/934-864      ACUGGACUACGCCAGUAUAAAUA--GGCAU-UAAGCGUAG-UGCGUUCCAAUGUU--------G-UGA-----AACAUCGGAGGUUGUU
AACY020846719.1/529-597      ACUGGACUACGCCAGUAUAAAUA--GGCAU-UAAGCGUAG-UGCGUUCCAGUCU----------UCAC------AGACUGGAGGUUGUU
AACY020060774.1/2553-2619    AGUCGACUAAGCGACUAUAAACA--GGCAU-UAGGCUUAG-AGCGUUCCAGUC-----------UUCG-------GACUGGAGGUUGUU
CP000817.1/2010936-2011013   ACUCGACUAAGCGAGUAUAAACA--GGCAU-UAGGCUUAG-AGCGUUCUCACGUUAUC--UGAA----UG-AUGAUGUGAGAGGUUGCA
AACY020496190.1/1503-1438    AGUCGUCUAAGCGACUCUAAAAA--GGCUU-UAAGCUUAG-AGCGUUCGCCC------------AUAU-----U--GGGCGAGGUUGUA
AACY022607213.1/736-672      ACUCGACUAAGCGAGAAUAAAAA--GGCUU-UAGGCUUAG-AGCGUUCGCCC------------UUCG--------GGGCGGGGUAGUA
AFHJ01000001.1/939500-939435 AGUCGUCACGGCGACUCUAAACA--GGCUU-UAGGCCGUG-AGCGUCGCCCCC------------ACA-------GGGGGCGGGUGGCA
FP929053.1/1669026-1668956   AGUGGUCACAGCCACUAUAAACA-GGGCUU-UAAGCUGUG-AGCGUUGACCGUC----------ACAA-----CGGCGGUCAGGUAGUC
AFOX01000025.1/1981-1912     ACUCGUCUGAGCGAGUAUAAACA-GGUCAU-UAAGCUCAG-AGCGUUCACCGGG----------AUCA------UUCGGUGAGGUUGGC
HE577054.1/3246821-3246752   ACUCGUCUGAGCGAGUAUAAACA-GGUCAU-UAAGCUCAG-AGCGUUCACCGGG----------AUCA------UGCGGUGAGGUUGGC
CP000154.1/3364237-3364168   GUUCGUCUGAGCGAACGCAAACA-GGCCAU-UAAGCUCAG-AGCGUUCACUGGA----------UUCG------UCCAGUGAGAUUGGC
#=GC SS_cons                 <<<<__AAAAA_>>>>-------..<<<<-.----aaaaa.----<<<<<<<<<..........____....._>>>>>>>>>-->>>>
#=GC RF                      acUCGUCuggGCGAguAUAAAuA..cgCaU.UAgGCccaG.AGCGUcccggcgg..........uUau.....uccgccgggGGUuGcg
//
# STOCKHOLM 1.0

#=GF AC   RF02680
#=GF ID   PreQ1-III
#=GF DE   PreQ1-III riboswitch
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Zasha Weinberg, Phillip McCown, Jonathan Liang
#=GF SS   Published; PMID:25036777
#=GF GA   65.00
#=GF TC   65.30
#=GF NC   31.70
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0008616; queuosine biosynthetic process;
#=GF RN   [1]
#=GF RM   25036777
#=GF RT   Structural, functional, and taxonomic diversity of three preQ1 riboswitch
#=GF RT   classes.
#=GF RA   McCown PJ, Liang JJ, Weinberg Z, Breaker RR
#=GF RL   Chem Biol. 2014;21:880-889.
#=GF WK   PreQ1-III_riboswitch
#=GF SQ   28


BABG01013292.1/257-357       GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCGUCUCGAACCGCGCCGGGCCAAACCC-ACAGGGGCUGGCGG-UCCUGU-GCGGUCAAAAUCUUUCCGCUGGAG
BABD01012433.1/319-419       GAGAAACUUAGGAUUUUAGGCUCCGCU-GCCGGCUGCUG-GUCGGCAGCGC-AAACCC-CGCAAGGCUGGCGGUCUUGCGCGUGGUCAAAAUCUAUCCGCCGGAG
FP929046.1/562024-562125     GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCCACUCGAGCGGCGCUGGGCAAAACCC-ACAGGAGCUGGCGGUUCCUGU-GCGGUCAAAAUCAAACCGCUGGAG
BAAY01013224.1/926-826       GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
FP929045.1/1765647-1765748   GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACGGGGGCUGGCGGUCCCCGC-GCGGUCAAAAUCAAACCGCUGGAG
BAAX01019688.1/382-483       GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACGGGGGCUGGCGGUCCCCGC-GCGGUCAAAAUCAAACCGCUGGAG
BAAY01002983.1/1264-1163     GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACGGGGGCUGGCGGUCCCCGC-GUGGUCAAAAUCAAACCGCUGGAG
ADJS01009939.1/10976-11077   GAGCAACUUAGGAUUUUAGGCUCCGCC-GUCUCCCCUGCGGGAGGCGGCGC-AAACCC-CGCAAGGCUGGCGGUCUUGCGUGCGGUCAAAAUCUAUCCGCCGGAG
ADJS01012726.1/612-517       GAGCAACUUAGGAUUUUAGGCUCCACC-GCGGCUU------GCUGCGGUGC-AAACCC-CGCAAGCCUGGCGGUCUUGCGCGCGGUCAAAAUCUAUCCGCCGGAG
BAAZ01007046.1/1247-1147     --GCAACUUAGGAUUUUAGGCUCCCCGUGCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACGGGGGCUGGCGGUCCCCGU-GCGGUCAAAAUCAAACCGCUGGAG
BABA01010993.1/1076-1176     GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACAGGGGCUGGCGG-CCCUGU-GCGGUCAAAAUCAUCCCGCUGGAG
BAAY01002380.1/1139-1039     GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACAGGGGCUGGCGG-CCCUGU-GCGGUCAAAAUCAUCCCGCUGGAG
BABA01026116.1/736-636       GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCGUCUCGAACCGCGCUGGGCCAAACCC-ACAGGGGCUGGCGG-CCCUGU-GCGGUCAAAAUCAAACCGCUGGAG
BABA01018694.1/413-513       GAGCAACUUAGGAUUUUAGGCUCCGCU-GCCGGCUGCUG-GUCGGCAGCGC-AAACCC-CGCAAGGCUGGCGGUCUUGCGCGUGGUCNAAAUCUAUCCGCCGGAG
AECU01000177.1/7590-7690     GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACAGGGGCUGGCGG-CCCUGU-GCGGUCAAAAUCAUCCCGCUGGAG
ADJS01009870.1/10212-10312   GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACAGGGGCUGGCGG-CCCUGU-GCGGUCAAAAUCAUCCCGCUGGAG
BAAX01000750.1/3091-2990     GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCCACUCGAGCGGCGCUGGGCAAAACCC-ACAGGAGCUGGCGGUUCCUGU-GCGGUCAAAAUCAAACCGCUGGAG
ADJS01011583.1/9082-9183     GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCCACUCGAGCGGCGCUGGGCAAAACCC-ACAGGAGCUGGCGGUUCCUGU-GCGGUCAAAAUCAAACCGCUGGAG
BAAX01000347.1/2947-2847     GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
BAAV01004919.1/1075-1175     GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
ABED02000027.1/116756-116655 GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCCACUCGAGCGGCGCUGGGCAAAACCC-ACAGGAGCUGGCGGUUCCUGU-GCGGUCAAAAUCAAACCGCUGGAG
ADJS01012663.1/5165-5065     GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
ACOP02000046.1/22370-22270   GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
ADJT01005830.1/328-228       GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCUGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
ACBY02000013.1/114529-114434 GAGCAACUUAGGAUUUUAGGCUCCGCC-GCAG----CUU---CCGCGGCGC-AAACCGGUGUCAGGCUGGCGGUCUGGCAUGCGGUCAAAAUCUAUCCGCCGGAG
BAAU01020333.1/1-83          ------------------GGCUCCGCU-GUCGGCUGCUG-GUCGGCAGCGC-AAACCC-CGCAAGGCUGGCGGUCUUGCGUGUGGUCAAAAUCUAUCCGCCGGAG
ADJT01007369.1/6381-6474     GAGCAACUUAGGAUUUUAGGCUCCGCC-UGGU------U---UUCAGGCGCAAACCCA-CCCAAGCCUGGCGGUCUUGGGCGCGGUCAAAAUCUAUCCGCCGGAG
ADJS01013861.1/2134-2227     GAGCAACUUAGGAUUUUAGGCUCCGCC-UGGU------U---UUCAGGCGCAAACCCA-CCCAAGCCUGGCGGUCUUGGGCGCGGUCAAAAUCUAUCCGCCGGAG
#=GC SS_cons                 ::::::::::(((((((,,,,,,<<<<.<<<<<________>>>>>>>>>,,,,<<<-.<<<<<<<_______>>>>>>>.-->>>,))))))):::::::::::
#=GC RF                      GAGCAACUUAgGauuuuAGGCUCCcCg.GcgcgucuCgaaccgcgCcGgGCcAAaCCc.cccggGgCUGGCGGcCccggg.GcGGuCaaaauCcAuCCGCuGGAG
//
# STOCKHOLM 1.0

#=GF AC   RF02681
#=GF ID   Twister-sister
#=GF DE   Twister_sister_ribozyme
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Weinberg Z
#=GF SS   Published; PMID:26167874
#=GF GA   93.00
#=GF TC   93.30
#=GF NC   36.70
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   26167874
#=GF RT   New classes of self-cleaving ribozymes revealed by comparative genomics
#=GF RT   analysis.
#=GF RA   Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR
#=GF RL   Nat Chem Biol. 2015;11:606-610.
#=GF WK   Twister_sister_ribozyme
#=GF SQ   4



ADJS01013948.1/250-330     GCAACCCGCAAGGCCGACGCACAAC---GCGCCGCCGGUGCAAGCCCGGCCACCCUGCAA-GGGGUGGGCGCUCAUGGGUACACA
BABG01005008.1/780-696     GAAACCCGCUAGGCCGACAGCCUCACCGCUGCCGCUGGUGCAAGCCCAGCCGCCCCAGACCGGGGCGGGCGCUCAUGGGUAACAG
ADJS01013948.1/577-657     ACGACCCGCAAGGCCGACGCAUAAC---GCGCCGCCGGUGCAAGCCCGGCCACCCCACAU-GGGGCGGGCGCUCAUGGGUACACA
FP929046.1/2708602-2708521 AUGACCCGCAAGGCCGACGGCAUCCCG-CCGCCGCUGGUGCAAGCCCAGCCGCCC-CGCCA-GGGCGGGCGCUCAUGGGUCCACA
#=GC SS_cons               :::((((-----(((,,<<<_______.>>>,,<<<<_________>>>><<<<<<_____>>>>>>)))------)))):::::
#=GC RF                    auaACCCGCaAGGCCGACGgauuacCc.cCGCCGCcGGUGCAAGCCCgGCCgCCCcagacagGGGcGGGCGCUCAUGGGUacacA
//
# STOCKHOLM 1.0

#=GF AC   RF02682
#=GF ID   HDV-F-prausnitzii
#=GF DE   HDV ribozyme from F. prausnitzii
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Weinberg Z
#=GF SS   Published; PMID:19965505
#=GF GA   44.00
#=GF TC   44.10
#=GF NC   43.80
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   19965505
#=GF RT   Widespread occurrence of self-cleaving ribozymes.
#=GF RA   Webb CH, Riccitelli NJ, Ruminski DJ, Luptak A
#=GF RL   Science. 2009;326:953.
#=GF WK   Hepatitis_delta_virus_ribozyme
#=GF SQ   48


BABA01033214.1/645-573       GCUGCUCUGA---UAAUCACACACCUCUC-CGUGGUGAGCAGCAGGCAACGAUC-----UUAU----------------GGUCGGCUGAGA-UGUGAUG
BABG01012773.1/549-476       GCUGCUCGUA--AUAAUCACACACCUCUU-CGUGGUGAGCAGCAGGCAACGAUC-----UUAU----------------GAUCGGCGAAGA-UGUGAUG
ADJT01005972.1/8134-8204     GCCGCUCGAA---ACUUUGCACACCUCUA-CGUGGUGGGCGGCAGGCAACACAG----U-------------------GAUGUGGCUAAGA-UGCGGAG
ADJS01010097.1/877-810       GUUGCUCAA-----GUGUGCU-ACCUCUC-CGUGGUGAGCAGCAGGCAACGGAU-----UAUA----------------AUCCGGCUAA---AGCAUAU
ADJS01011862.1/3107-3034     GCUGCUCGUA--AUAAUCACACACCUCUU-CGUGGUGAGCAGCAGGCAACGAUC-----UUAU----------------GGUCGGCGAAGA-UGUGAAG
BAAV01013885.1/1004-1077     GCUGCUCGAA---ACUUUGCACACCUCUU-CGUGGUGAGCAGCAGGCAACACAU-----GAGA----------------AUGUGGCGAAGAAUGCAAAG
AAQL01003978.1/631-704       GCUGCUCGUA--AUAAUCACACACCUCUU-CGUGGUGAGCAGCAGGCAACGGUC-----UAAG----------------GAUCGGCGAAGA-UGUGAAG
ADJS01009040.1/1095-1022     GCUGCUCUUA--AUAAUCACACACCUCUC-CGUGGUGAGCAGUAGGCAACAAUC-----UUAU----------------GAUCGGCUGAGA-UGUGAAG
BAAX01009272.1/687-759       GCUGCUCUGA---UAAUCACACACCUCUC-CGUGGUGGGCAGCAGGUAACGAUC-----UUAU----------------GAUCGGCUGAGA-UGUGAAG
BABG01003130.1/789-717       GCUGCUCUGA---UAAUCACACACCUCUU-CGUGGUGAGCAGCAGGGAACGAUC-----UUAC----------------AGUCGGCGAAGA-UGUGAGA
ABED02000029.1/678005-678077 GCCGCUCGAA---ACUUUGCACACCUCUA-CGCGGUGGGUGGCAGGCAACACAU-----GAGA----------------AUGUGGCUGAGA-UGCAAUG
BAAV01008070.1/447-374       ACUGCUCGUA--AUAAUCACACAUCUCUU-CGUGGUGAGCAGCAGGCAACGAUC-----UUAU----------------GAUUGGCUGAGA-UGUGAAA
ADJS01009498.1/9048-9120     GCUGCUCGGA---CAAUCACACACCUCUU-CAUGGUAAGCAGCAGGCAACGAUC-----UUAC----------------AAUCGGCGAAGA-UGUGAGA
ABVR01000037.1/34959-34871   GCUGCUCGAA--UGAAUCACACACCUCUU-UGUGGUGAGUAGCAGGCAACGAUC-----UAA-GAAUCAGGGAUCCGGUGAUCGGCUGAGA-UGUGAAG
AAQL01011795.1/252-326       GCUGCUCUAA---UAAUCACACACCUCUC-CGCGGUGAGUAGCAGGCAACGAUCU---A-UUA---------------UGAUUGGCUGAGA-UGUGAUG
ADJS01000960.1/2397-2471     GCUGCUCAAA---ACUUCACACACCUCUU-CGUGGUGAGCAGUAGGCAACGAUCC---A-UUU---------------UGGUCGGCUGAGA-UGUGAAG
ADJT01007140.1/494-426       GCUGCUCAA-----AUGUGCU-ACCUCUC-CGUGGUGAGCAGCAGGCAACGGAU-----AAUU----------------AUCCGGCUAAA--GGCACAU
ADJT01006046.1/233-165       GCUGCUCAU-----AUAUGCU-ACCUCUC-CGUGGUGAGCAGCAGGCAACGGAU-----AAUU----------------AUCCGGCUAAA--GGCACAU
FP929045.1/3224685-3224616   GCCGCUCAG-----AUAUGCU-ACCUCUC-CGUGGUGAGCAGCAGGCAACGAGA----GUUUU---------------CUCUCGGCUAA---AGCAUAU
FP929042.1/1182829-1182917   GCUGCUCGAA--UGAAUCACACACAUCUU-CGUGGUGAGUAGCAGGCAACGAUC-----UAA-GAAUCAGGGAUUCGGUGAUCGGCUGAGA-UGUGAAG
BABG01004747.1/841-765       GCCGCUCGAA---ACUUUGCACACCUCUA-CGUGGUGAGCGGCAGGCAACGCAGUG-UG----G------------AUACUGUGGCUGAGA-UGCAGGG
FP929046.1/260263-260332     GCCAUCCGA-----AAAUGCU-GCCUCUA-CGUGGCGGAUGGCAGGCAACGAGA----G-UUU--------------CCUCUCGGCUAA---AGCAUAU
AECU01000025.1/4723-4655     GCUGUCCGA-----AAAUGCU-GCCUCUA-CGUGGCGGACGGCAGGCAACGGAG-----CGUG---------------UCUCCGGCUAA---AGCAUGA
BK006894.1/1-68              GCUGCUCAU-----AUAUGCU-ACCUCUC-CGUGGUGAGCAGUAGGCAACGGAU-----CUCU----------------AUCCGGCUAA---AGCAUGU
ABED02000029.1/675962-676029 GCUGCUCAU-----AUAUGCU-ACCUCUC-CGUGGUGAGCAGUAGGCAACGGAU-----CUCU----------------AUCCGGCUAA---AGCAUGU
BAAX01015505.1/392-316       GCCGCUCGGA---ACUUUGCACACCUCUA-CGCGGUGGGCGGUAGGCAACACAGCA-UG----G------------AUGCUGUGGCUAAGA-UGCAAGG
FP929052.1/1046935-1047006   GCCGCACAA-----AAUCAAA-GCCUCCA-CGUGGCGUGCGGCGGACAACGGAU-----GAUU---------------GAUCCGGCUAAGAUUGAUUGA
ABED02000029.1/413324-413255 GCCAUCCAG-----AUAUGCU-GCCUCUC-CGUGGUGAGCAGCAGGCAACGAGA----G-UU-C-------------CCUCUCGGCUAA---AGCAUGU
CP003032.1/119037-119109     GCUGCUUUAA---UAAUCACACACCUUUA-UGCGGUGAUUAGCAAGCAACGAUC-----UUAU----------------GAUUGGUUAAGA-UGUGAAA
AACY021449234.1/672-595      AUCUCACAA-----CGUUAAUCGCCUCCU-CGUGGCGUGAGAUG-GAAACAGCAUA-UU----UGC--------AAAUAUGUUGGCUAAGA-UUAACAG
FP929046.1/1977588-1977663   GCCGCUCGAA----CUUUGCGCACCUCUA-CGUGGUGGGCGGCAGGCAACACAGCA-UG----G------------AUGCUGUGGCUAAGA-UGCAUGA
ADJT01005907.1/1108-1187     UCCGCUCGAA---ACUUUGCACACCUCUA-CGCGGUGGGCGGCAGGCAACACAGUGUGU----AG-----------AUGCUGUGGCAAAGAAUGCAAGA
AECU01000025.1/2611-2539     GCCGCUCGAA---ACUUUGCACACCUCUA-CGUGGUGGGCGGCAGGCAAUGCUA-----GUA-----------------UAGUGGCUAAGAAUGCAAAG
AAQL01004503.1/986-1057      GCUGCUCUAA---UAAUCACACACAUCUU-CGUGGUGAGUAGUG-GAAACGAUU-----UUAU----------------GGUCGACUGAGA-UGUGAUA
AACY021109846.1/859-785      GGGGGACGAAGUCGAACUGAACACCUCCAUCGUGGUGUCCCCCGGGCAACGCUU-----GCAA----------------AAGCGGCUAA---CGUUCAG
ACII01000060.1/3924-3849     GCUGCUCAG-----AAAUGCACACUGCGA-C-UGGUGAGCAGUAGGUGAUGUUU----A-UC-AAA---------GGAUAAGCGGCUAAGA-UGUAGAA
BAAU01012325.1/484-553       GCUGCUCAA-----AAAGACA-GCCUCCA-CGCGGCGAGCAGCGGGCAACGGGA-----AACA---------------CUCCCGGCGAAU--CGUCUUU
BAAU01023145.1/566-497       UCUGCUCUA-----AAAGACA-UCCUCCA-CGCGGCGAGUAGCGGGCAACGGGA-----UACA---------------CUCCCGGCGAAU--CGUCUUU
ADJS01012391.1/1357-1285     GUUACUCUGA---UAAUCACACACCUCUC-CGUGGUGGGCAGCAGGCAACGAUC-----UUAA----------------GAUCGGCUGAGA-UGUGAUU
FP929037.1/2996677-2996604   GCUGCUCGAA---ACUUUGCACACCUCUU-CGUGGUGAGCAGCAGGCAACGAUC-----UUAU----------------GGUCGGCUAAGAAUGCAGAG
BABG01019440.1/223-151       GCUGCUCGUA--AUAAUCACACACCUCUU-CCUGG-GAACACCAGUCUACGAUC-----GUAU----------------GAUCGGCGAAGA-UGUGAUG
BAAY01003903.1/540-465       GCCGCUUUAU---AUUUUGUACACCUCUA-CGUGGUAAGCGGCAGGCAACGUUUA--UU-UUA---------------UAGACGGCUAAGA-UGCAAAA
FP929046.1/261862-261939     GCCACUCGAA---ACUUUGCACACCUCUA-CGCGGUGAGCGGCAGGCAACACAG-----UAAAAG-----------GUGCUGUGGCGAAGA-UGCAGAU
BAAZ01004974.1/416-486       ACUGCACAAA----ACCAACA-GCCUUCA-CGCGGCGUGCAGUGAGCAACGUAUA---G-UUU---------------UAUACGGCCAA---UGUUGAA
ADJS01008875.1/12497-12569   GCUGCUCGAA---ACUUUGCACAUCUCUU-CGUGGUGAGCAGCAGACAACGUUG-----AUA-----------------CAGCGGCUAAGAAUGCAAAG
BAAX01032439.1/122-34        GCUGCUCGUA--AUAAUCACACACCUCUC-CGUGGUGAGCAGCAGGCAACGAUU-----UAA-GAAUGUAUGGUUCGAUGAUCGGCGAAGA-UGUGCGA
BAAZ01007529.1/886-816       GCUACUCAAA---AAAAGACA-GCCUCCA-CGCGGCGAGCAGCGGGCAACGGGA-----A-A----------------GACCCGGCAGAUA-GUCUUUA
BAAX01024167.1/572-504       GCUGCUCAG-----AUGUGCU-GCCUCUU-CGUGGCGAGCAGCAGGCAACGAGA-----UCCU---------------GUCUCGGCUAA---AGCAUGA
#=GC SS_cons                 <<<<<<<---...---------<<<____.___>>>>>>>>>>------<<<<<.....____..............._>>>>>:::::::.:::::::
#=GC RF                      GCuGCuCgAA...aAaUuaCACaCCUCUa.CGUGGuGaGCaGCAGGCAACGauc.....uuau...............ugauCGGCUAAGA.UGuaaaa
//
# STOCKHOLM 1.0

#=GF AC   RF02683
#=GF ID   NiCo
#=GF DE   NiCo riboswitch
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Weinberg Z, Vallery T
#=GF SS   Published; PMID:25794617
#=GF GA   31.00
#=GF TC   31.10
#=GF NC   30.90
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0050897; cobalt ion binding;
#=GF DR   GO; 0055065; metal ion homeostasis;
#=GF RN   [1]
#=GF RM   25794617
#=GF RT   Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and
#=GF RT   control expression of heavy metal transporters.
#=GF RA   Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker
#=GF RA   RR
#=GF RL   Mol Cell. 2015;57:1088-1098.
#=GF WK   NiCo_riboswitch
#=GF SQ   82


CP002582.1/3780440-3780356     UUAAUGAGAA-UAAAUCAGGUU-A-UUAUGUU----GG-----------------------------------------------------------AU-GUAAU---AAC-UGGGCCAAUUUA----UUGGCAACAGGAAUU--------------------------------------------------------------------------AAACCUGUGGGACU-AUA
CP001997.1/495019-495096       ---UCCUUAC-AAGAUCAGGCG-G-C----------UUU----------------------------------------------------------UA----GUG-CGGC-CGGGCCUCUUUU----GAGGCAGUGGGAUUUCA------------------------------------------------------------------------AGACUCGCGGGACU-UAG
CP002028.1/1768652-1768573     AAAGCAUA-A-UGGAUCAGGUA-G-AACG--G----A-----------------------------------------------------------A-A-AGUUU---UAC-CGGGCUC-UUAU-----GAGCAGCAGGAUUAU-------------------------------------------------------------------------AAACCUGUGGGACC-GUG
AAWL01000017.1/25112-25035     AUAAUACAAC-AGGAACAGGCG-G-CUGCCGC----G------------------------------------------------------------AG-GCAGUG-CAGC-CGGGC---GUUU-------GCAGCAGAAAGGC----------------------------------------------------------------------------UCUGCGGGACC-UGC
ADLR01000090.1/3100-3003       AUAUGAUACA-GUGAGCAGGCG-A-CGGCCGA----AAU--G------------------------------------------------------AGA-AUCGU---CGC-CGGGCUGCCGAAA--GGCGGCAGCAGACUGUGUGACAG------------------------------------------------------------------CACAUCUGCGGGACA-GUU
ACCJ01000322.1/14085-13994     AUGGCAUAAA-GGAAACAGGCC-G-CGGGCGG----C------------------------------------------------------------AG-CGCGCG--GGC-CGGGCCGCAUUA----GCGGCAGCAGGUGGAUCAGGCG-------------------------------------------------------------------GCAUCUGCGGGACA-AUG
AGTN01503842.1/168-240         AUAGCUCUUA-AGGAUCAGGCG-G-C----------AAA---------------------------------------------------------GGC----GUG-CAGC-CGGGCA---CUA------UGCAGCAGGGA----------------------------------------------------------------------------AGACCUGUGAGACC-UUA
AGTN01590760.1/12-115          UAUGCAUUAA-CAGAGCAGGCG-A-UGCAUCU----GAA--AUUUA--------------------------------------------UGUUUCAGA-UAUGUG-GGGC-UGGGCCGGGCUAUCUGCCGGCAGCAGGUAUAU--------------------------------------------------------------------------AACCUGUGGGACU-GAU
CP001684.1/2164884-2164979     CCAUCCCAUU-CUGAACAGGCC-G-UGGC-------A------------------------------------------------------------AU-ACCAUG-GAGC-CGGGCCGGCCCA---GCCGGCAGCGGAGCGUUUGCACGUU--------------------------------------------------------------GGCGCGCCCGCGGGACA-GAA
ADFP01000095.1/5329-5413       ACGGCACAAA-CUGAACAGGCC-G-UCCCCUC---G----------------------------------------------------------------GGGAGC-GGGC-CGGGCCGCCGCGG--CGCGGCAGCGGACGA---------------------------------------------------------------------------CGAUCCGCGGGACG-GAA
AEDB01000024.1/46397-46304     AAUAUAAAAA-UAGAGCAGGCG-A-UACACCU----AAU--A------------------------------------------------------AGG-UGUGUG-GGGC-UGGGCCGACGAAA--GUUGGCAACAGGUGAAAA------------------------------------------------------------------------AUACCUGUGGGACU-AUA
ADGC01006520.1/5852-5937       UAACUUUGAA-CUGAGCAGGCA-A-UGCA---------------------------------------------------------------------G-CGCAUG-AGGC-CGGGCC---CGA----GAGGCAGCAGAUUGAAACAACA------------------------------------------------------------------AACAUCUGCGGGACA-GUA
ABQR01000046.1/117420-117521   ACAGUACAAU-CUGAUCAGGCC-U-UAAAGUG----------GAUGGAAC-------------------------------------GGAACAUC---C-AUGGAG-GAGC-CGGGCCGCUUUA----GCGGCAGCAGGUAGGAA------------------------------------------------------------------------ACACCUGCGGGACA-GUC
ACTP01000040.1/119838-119957   ACAGUACAAA-CUGAGCAGGCU-G-UGUUUUC----UGC---CGGCGUAUGUAUUU------------------------CAAGCCGGAAAGGAU----CCAUGGA-UAGC-CGGGCCGUUUUG----ACGGCAGCAGAUGGAGCUU----------------------------------------------------------------------ACAUCUGUGGGACA-GUA
AEVN01000015.1/26987-27081     ACAGUACAAA-CUGAUCAGGCG-G-UAAACCU----UCU-UC-----------------------------------------------------CGGG-UUUUUG-CAGC-CGGGCCC--UCU-----GGGCAGCAGACCUUGAC-GCA-------------------------------------------------------------------ACGUCUGCGGGACA-GUU
AEDB01000052.1/16213-16310     ACAGUACAAU-CUGAUCAGGCG-A-UGAAUGC----G------------------------------------------------------------AA-UUCAUG-GUGC-CGGGCUGCUUCAAAUAGCGGCAGUGGGUGAGUGAUACA------------------------------------------------------------------CACAUCUACGGGACA-GUA
CP002109.1/2377684-2377591     ACAGUACAAA-CUGAACAGGCG-A-UAGCGAU----CUU-----------------------------------------------------------A-GCUAUA-GGGC-CGGGUUGCCGGG---GGCGACAACGGAUGACUUU-CGU-------------------------------------------------------------------GCAUCUGUGGGACA-GUA
FR667692.1/20575-20683         UCAUUGUGAU-CUGAACAGGCG-G-UGAACGU----AAC--A-----------------------------------------------------CGAGGUUCAUG-CAGC-UGGGCUGCAAUUAUUUGCGGCAGCAGACUAUGUAUUCUAAG-------------------------------------------------------------GGCAUAUCUGUGGGACA-GUU
CP001603.1/69513-69621         UCAUUGUGAU-CUGAACAGGCG-G-UGAACGU----AAC--A-----------------------------------------------------CGAGGUUCAUG-CAGC-UGGGCUGCAAUUAUUUGCGGCAGCAGACUAUGUAUUCUAAG-------------------------------------------------------------GGCAUAUCUGUGGGACA-GUU
FR667693.1/43791-43683         UCAUUGUGAU-CUGAACAGGCG-G-UGGACAU----AUA--A-----------------------------------------------------AAGG-UCCAUG-CAGC-CGGGCUGCAAUUU-UUGCGGCAGCAGAGUAUGUAAAUAAUAA-----------------------------------------------------------GGGCAUACCUGUGGGACA-GUU
ACHL01000004.1/2975-2867       UCAUUGUGAU-CUGAACAGGCG-G-UGGACAU----AUA--A-----------------------------------------------------AAGG-UCCAUG-CAGC-CGGGCUGCAAUUU-UUGCGGCAGCAGAGUAUGUAAAUAAUAA-----------------------------------------------------------GGGCAUACCUGUGGGACA-GUU
ACCR02000006.1/49989-49881     UCAUUGUGAU-CUGAACAGGCG-G-UGGACAU----AUA--A-----------------------------------------------------AAGG-UCCAUG-CAGC-CGGGCUGCAAUUU-UUGCGGCAGCAGAGUAUGUAAAUAAUAA-----------------------------------------------------------GGGCAUACCUGUGGGACA-GUU
ADDX01000036.1/19553-19630     -------------------GCG--------CCC--CAU----ACGGAA-----------------------------------------CAGGCC-----GUAAAG-GAGC-CGGGCCGCUGCG----GCGGCAGCAGAUGGUGAG-----------------------------------------------------------------------GCAUCUGUGGGACA-AAA
ABYI02000012.1/66005-65911     GCGGUACAAA-CUGAGCAGGCG-A-UGGAUCU----UGUGU-G--------------------------------------------------AUCAGG-UCCGUG-GGGC-CGGGCCG-UUUU-----CGGCAGCGGAUGCAUG------------------------------------------------------------------------GCAUCCGCGGGACA-GUA
AEXQ01000083.1/43353-43249     ACAGUACAAA-CUGAACAGGCA-G-CGACU-------------------------------------------------------------------AA-GUCGUG-UGGC-CGGGUUGCUU-A----GCAACAGCAGAUUUAAUUAUUCAUAUUGAU---------------------------------------------------GAUAAUUAACAUCUGUGGGACA-GUA
ADMN01000037.1/5181-5285       ACAGUACAAA-CUGAACAGGCA-G-CGACU-------------------------------------------------------------------AA-GUCGUG-UGGC-CGGGUUGCUU-A----GCAACAGCAGAUUUAAUUAUUCAUAUUGAU---------------------------------------------------GAUAAUUAACAUCUGUGGGACA-GUA
ADJS01006913.1/2727-2603       GCAGUACAAA-CUGAUCAGGCU-A-CAUUCAU----UUU--CAAAAAGAUG-----------------------------------AUGUUAAGAAAAU-GGUGUGCAUGC-CGGGCCGGUCAAU-UACCGGCAGCAGAUGAGACGAUGAUU--------------------------------------------------------------CAUACAUCUGUGGGACA-GUA
AAXB02000001.1/302330-302454   GCAGUACAAA-CUGAUCAGGCU-A-CAUUCAU----UUU--CAAAAAGAUG-----------------------------------AUGUUAAGAAAAU-GGUGUGCAUGC-CGGGCCGGUCAAU-UACCGGCAGCAGAUGAGACGAUGAUU--------------------------------------------------------------CAUACAUCUGUGGGACA-GUA
ACIE02000035.1/129003-128921   ACAGUACAGA-CUGAUCAGGUC--------------AUA--------------------------------------------------------------------AGAC-CGGGCUGUUAAAA-AAACAGCAGCAGAUGAAAUUAACA-------------------------------------------------------------------GCAUCUGUGGGACAAGUG
ACDH01000075.1/27393-27312     ACAGUACAGA-CUGAUCAGGUC--------------AUA-----------------------------------------------------------U---------GAC-UGGGCUGUUAAAA--AACGGCAGCAGAUGAAAUCAACA-------------------------------------------------------------------GCAUCUGUGGGACAAGUG
AAXG02000045.1/2452-2549       ACAGUACAAA-CUGAGCAGGCC-A-CGGAUUC----CUC--U-----------------------------------------------------GGAA-UCCAUG-GAGC-CGGGCCGCAGUU----GCGGCAGCAGAUGAUCUCCUGU-------------------------------------------------------------------ACAUCUGUGGGACA-GUU
AGTN01644247.1/468-372         ACAGUUCAAG-GUGAGCAGGCG-A-UGAACCC----UCC--------------------------------------------------------GGGG-UUCGUG-GGGC-CGGGCCGUAAAA----UCGGCAGCAGAUUGUUCAACAC-------------------------------------------------------------------ACAUCUGUGGGACU-UUA
ACIO01000756.1/6332-6236       ACAGUACAAA-CUGAGCAGGCA-A-UGUCUGA----UCA---------------------------------------------------------UGC-GACAUG-AAGC-CGGGCCGCUUCG----GCGGCAGCAGAUGGGUAUCAGG------------------------------------------------------------------CGCAUCUGUGGGACA-GUA
BABF01002650.1/1069-975        ACAGUACAAA-CUGAGCAGGCA-A-UGUCUGU----AAA-----------------------------------------------------------U-GACAUG-AAGC-CGGGCCGUCGAG----ACGGCAGCAGAUGGGUAUCAGG------------------------------------------------------------------CGCAUCUGUGGGACA-GUA
AEDB01000020.1/61018-61119     ACAGUACAAA-CUGAUCAGGCG-A-UAAACCCCAAA------UU-------------------------------------------------UUAAG-GUUUAUG-CAGC-UGGGCCAU--AA----ACGGCAGCAGAUGAAAAAUAUAA-----------------------------------------------------------------CACAUCUGUGGGACA-GUG
ACTJ01000082.1/4659-4566       ACAGUACAAA-CUGAGCAGGCA-A-UGACCAG----AGC-----------------------------------------------------------G-GUCAUG-CAGC-CGGGCUGCGAAA----GCGGCAACAGAUGAUUACACGC-------------------------------------------------------------------ACAUCUGUGGGACA-GUU
FP929053.1/1847000-1846820     ACAGUACAAA-CUGAGCAGGCG-A-UGCUUUUC--G--G--AAUCGAAA--------------------------------------AUAUUUAUCGAA-GGCAUG-GGGC-CGGGCCGCAGGA---AGCGGCAGCGGAUAUGGAUUUAAACGUAAUUGCAAAGAACCUGCAUUCACGGAAUAUGAGGUGAAGCAGAAUGUGACUUUGCUUUCAGACAUAUCUGCGGGACA-GUG
ADJT01012376.1/11594-11414     ACAGUACAAA-CUGAGCAGGCG-A-UGCUUUUC--G--G--AAUCGAAA--------------------------------------AUAUUUAUCGAA-GGCAUG-GGGC-CGGGCCGCAGGA---AGCGGCAGCGGAUAUGGAUUUAAACGUAAUUGCAAAGAACCUGCAUUCACGGAAUAUGAGGUGAAGCAGAAUGUGACUUUGCUUUCAGACAUAUCUGCGGGACA-GUG
BABE01011344.1/446-627         ACAGUACAAA-CUGAGCAGGCG-A-UGCUUUUC--G--G--AAUCGAAAA-------------------------------------UAUUUAUCCGAA-GGCAUG-GGGC-CGGGCCGCAGGA---AGCGGCAGCGGAUAUGGAUUUAAACGUAAUUGCAAAGAACCUGCAUUCACGGAAUAUGAGGUGAAGCAGAAUGUGACUUUGCUUUCGGACAUAUCUGCGGGACA-GUG
BAAV01020169.1/36-217          ACAGUACAAA-CUGAGCAGGCG-A-UGCUUUUC--G--G--AAUCGAAAA-------------------------------------UAUUUAUCCGAA-GGCAUG-GGGC-CGGGCCGCAGGA---AGCGGCAGCGGAUAUGGAUUUAAACGUAAUUGCAAAGAACCUGCAUUCACGGAAUAUGAGGUGAAGCAGAAUGUGACUUUGCUUUCAGACAUAUCUGCGGGACA-GUG
AGTN01696258.1/1405-1313       ACAGUACAAA-CUGAGCAGGCG-A-UGAAUCA----UAU--A-----------------------------------------------------CG-A-UUCAUG-GAGC-CGGGUCGCCCUAC-ACGCGGCAGCAGAUACU--------------------------------------------------------------------------GCAUCUGUGGGACA-GUA
ACII01000103.1/12160-12054     ACAGUACAAA-CUGAGCAGGCG-A-UGCCCGA----GAUGCU-----------------------------------------------------UGAG-GGCGUG-GGGC-CGGGCCGCGCGA---AGCGGCAGCAGAUAUGAAAAUUUUCA-------------------------------------------------------------GACAUAUCUGUGGGACA-GUG
BABE01016748.1/605-499         ACAGUACAAA-CUGAGCAGGCG-A-UGCCCGA----GAUGCU-----------------------------------------------------CGAG-GGCGUG-GGGC-CGGGCCGCGCGA---AGUGGCAGCAGAUAUGAACAUUUUCA-------------------------------------------------------------GACAUAUCUGUGGGACA-GUG
BABE01000339.1/4553-4659       ACAGUACAAA-CUGAGCAGGCG-A-UGCCCGA----GAUGCU-----------------------------------------------------CGAG-GGCGUG-GGGC-CGGGCCGCGCGA---AGUGGCAGCAGAUAUGAACAUUUUCA-------------------------------------------------------------GACAUAUCUGUGGGACA-GUG
ADJS01017039.1/13737-13800     ACAGUACAAA-CUGAGCAGGCG-A-UGCCCGA----GAUGCU-----------------------------------------------------CGAG-GGCGUG-GGGC-CGGGCCGCGCGA---AGU---------------------------------------------------------------------------------------------------------
AGTN01101874.1/525-623         ACAGUACAAAACUGAGCAGGCG-A-UGAACCU----UUA--A-------------------------------------------------------GG-UUCGUG-GGGC-CGGGCCGCGUGAG--CGCGGUAGCAGAUUGCGAGCGUC-------------------------------------------------------------------ACAUCUGCGGGACA-GUU
AGTN01285523.1/140-242         ACAGUACAAA-CUGAGCAGGCG-AUGAACCGCCGGA------AG-------------------------------------------------AUGGGG-GUUCUG-GGGC-UGGGCCGCCGAG----GCGGCAGCGGAUGAUGGGCGAC-------------------------------------------------------------------ACAUCUGCGGGACA-GUG
AGTN01307508.1/5-99            ACAGUACAAA-CUGAGCAGGCG-A-UGAACCU----AAG-C---------------------------------------------------------G-UUCGUG-GGGC-CGGGCCGCUUUG----GCGGCAGCAGAUCGUAAACACA-------------------------------------------------------------------GCAUCUGUGGGACA-GUG
CP002400.1/855172-855273       ACAGUACAAA-CUGAGCAGGCG-A-UGGAUCC----UUU--U-----------------------------------------------------GGGG-UCUGUG-GGGC-UGGGCCGCUUUG----GCGGCAGCGGGUUUGCAUCUUUGA---------------------------------------------------------------UCACACCUGCGGGACA-GUG
ACTR01000042.1/628-533         ACAGUACAAA-CUGAGCAGGCG-A-UGAACCU----UUA-----------------------------------------------------------G-GUCAUG-GGGC-CGGGCCGCUUUU----GUGGCAGCAGAUUGCAAUUUCAG-----------------------------------------------------------------CACAUCUGUGGGACA-GUU
ABFY02000067.1/269385-269480   ACAGUACAAA-CUGAGCAGGCG-A-UGAACCU----UUA-----------------------------------------------------------G-GUCAUG-GGGC-CGGGCCGCUUUU----GUGGCAGCAGAUUGCAAUUUCAG-----------------------------------------------------------------CACAUCUGUGGGACA-GUU
CP000885.1/2639822-2639717     ACAGUACAAA-CUGAGCAGGCG-A-UGAACUU----UAUUU-C--------------------------------------------------UAUAAA-GUCAUG-GGGC-CGGGCCGCAAGA---UGCGGCAACAGAUUGAAUUUCAAU----------------------------------------------------------------UCACAUCUGUGGGACA-GUA
CP001348.1/1290748-1290851     ACAGUACAAA-CUGAGCAGGCG-A-UGGACCU----UUCAUA-----------------------------------------------------GAG-GUACAUG-GGGC-CGGGCCACCCAGU-GAGUGGCAGCAGAUUGCAAUCAUG------------------------------------------------------------------CACAUCUGUGGGACA-GUA
CP000939.1/1702810-1702899     ACAGUACAAA-CUGAGCAGGCG-A-UGAACUA----CA-----------------------------------------------------------AG-UUCAUG-GGGC-CGGGCCUUA--A----UUGGCAGCAGAAAGGAUU--AA-------------------------------------------------------------------AUACCUGUGGGACA-GUA
CP002011.1/1712339-1712433     ACAGUACAAA-CUGAGCAGGCG-A-UGAACUU----GUA-UA-----------------------------------------------------CAAG-UUCAUG-GGGC-CGGGCCUUA--A----UUGGCAGCAGGAAGGAUU--AA-------------------------------------------------------------------AUACCUGUGGGACA-GUA
CP000962.1/1779920-1780014     ACAGUACAAA-CUGAGCAGGCG-A-UGAACUU----GUA-UA-----------------------------------------------------CAAG-UUCAUG-GGGC-CGGGCCUUA--A----UUGGCAGCAGGAAGGAUU--AA-------------------------------------------------------------------AUACCUGUGGGACA-GUA
AGTN01407302.1/1961-2052       ACAGUACAAA-CUGAGCAGGCG-A-UGAACCG----GAA----------------------------------------------------------GG-UUCAUG-GGGC-UGGGCCGCAACC----GCGGCAGCAGAUGGAAAGC----------------------------------------------------------------------ACAUCUGUGGGACA-GUA
CP002160.1/238435-238344       ACAGUACAAA-CUGAGCAGGCG-A-UGGACUU----UUA-UA-----------------------------------------------------AAAG-UUCGUG-GGGC-CGGGCCUUUUU-----UGGGCAACAGGAUUUA-------------------------------------------------------------------------AUACCUGUGGGACA-GUA
CP001056.1/1566915-1567006     ACAGUACAAA-CUGAUCAGGCCGA-UAAAUGA----UUU----------------------------------------------------------UA-UUUAUG-GAGC-CGGGCCAUAAUA----GUGGCAACAGGAUAUUUA-----------------------------------------------------------------------AUACCUGUGGGACA-GUA
CP001078.1/1526627-1526718     ACAGUACAAA-CUGAUCAGGCCGA-UAAAUGA----UUU----------------------------------------------------------UA-UUUAUG-GAGC-CGGGCCGUAAUU----UUGGCAACAGGAUAUUUA-----------------------------------------------------------------------AUACCUGUGGGACA-GUA
ACSC01000002.1/2287722-2287631 ACAGUACAAA-CUGAUCAGGCCGA-UAAAUGA----UUU----------------------------------------------------------UA-UUUAUG-GAGC-CGGGCCGUAAUU----UUGGCAACAGGAUAUUUA-----------------------------------------------------------------------AUACCUGUGGGACA-GUA
ACBY02000011.1/20821-20727     CCAGUACAAA-CUGAGCAGGCG-A-CGCCCUU----UGC----------------------------------------------------------AG-GGCGUG-GGGC-CGGGCCGCCCGU----GCGGCAGCAGAUGAAGGUAACG-------------------------------------------------------------------GCAUCUGUGGGACA-GUU
ADJS01001306.1/1758-1671       ACAGUACAAA-CUGAACAGGCC-G-GAUAUCU--------------------------------------------------------------------UAUCUG-GGGC-CGGGUCACAAC-----GUGACAGUGGAAUGAAUUGU-U-------------------------------------------------------------------UUAUCCGCGGGACA-GUA
BABG01026138.1/868-788         ACAGUACAAA-CUGAGCAGGCC-G-GGGA-----------------------------------------------------------------------UUUCCU-GGGCACGGGUCGU--AA----AUGACAGUGGAUCGAAG------------------------------------------------------------------------ACAUCUGCGGGACA-GUA
BAAZ01003956.1/1271-1191       ACAGUACAAA-CUGAGCAGGCC-G-GGGA---------------------------------------------------------------------U-UUCCUG-GGGC-CGGGUCGU--AA----AUGACAGUGGAUCGAAG------------------------------------------------------------------------ACAUCUGCGGGACA-GUA
FP929039.1/1384329-1384246     ACAGUACAAA-CUGAGCAGACCAU-UGGCG-------A-----------------------------------------------------------AA-GCCAAG-GAGU-CGGGCCAU---C----AUGGCAGUGGAAUCUUU------------------------------------------------------------------------ACAUCCACGGGACA-GUA
ABEY02000006.1/25295-25212     ACAGUACAAA-CUGAGCAGACCAU-UGGCG-------A-----------------------------------------------------------AA-GCCAAG-GAGU-CGGGCCAU---C----AUGGCAGUGGAAUCUUU------------------------------------------------------------------------ACAUCCACGGGACA-GUA
ACCL02000009.1/43428-43513     ACAGUACAAA-CUGAGCAGACC-G-UAACAGU---C--------------------------------------------------------------C-GUUAUG-GAGU-CGGGUCACAUGC----GUGACAGUGGAAAUGU-------------------------------------------------------------------------UCAUCCACGGGACA-GUU
BABG01002502.1/1745-1891       ACCGUACAAA-CUGAGCAGACC-G-GGAUUAU----AUG--AUAUCUUAUGCCUGUUAUGUGAAAAUCAGAUUAAAUCACAUGAUAAUAUACAAGUAUC-AUCCAG-GAGU-CGGGUCACACGC----GUGACAGUGGAAUCUUUU-----------------------------------------------------------------------CUAUCCACGGGACA-GUG
BABG01020281.1/807-661         ACAGUACAAA-CGGAGCAGACC-G-GGAUUAU----AUG--AUAUCUUAUGCCUGUUAUGUGCAAAUAAGAUUAAAUCACAUGAUAAUAUAAAAGUAUA-AUCCAG-GAGU-CGGGUCACACGC----GUGACAGUGGAAUCUCUU-----------------------------------------------------------------------CUAUCCACGGGACA-GUA
BAAU01003136.1/1053-933        ACAGUACAAA-CUGAGCAGACC-G-GGAUUAUC--G--U--AUAUAACGAUUAUU--------------------------AAUGAAGCUUAUUAUAUA-AUCCUG-GAGU-CGGGUCACACGC----GUGACAGUGGAAUCUUUU-----------------------------------------------------------------------CUAUCCACGGGACA-GUA
BAAX01024222.1/601-517         ACAGUACAAA-CUGAGCAGACC-G-UGAA---------------------------------------------------------------------U-AUCAUG-GGGU-CGGGUCGCAGAA----GCGACAGUGGAAGUUAGUU----------------------------------------------------------------------UCAUCCACGGGACA-GUA
FP929055.1/2372574-2372659     ACAGUACAAA-CUGAGCAGACC-G-UGAU------------A-----------------------------------------------------UCAU-AUCAUG-GAGU-CGGGUCGCAGAU----GCGACAGUGGAAUCUU-------------------------------------------------------------------------UCAUCCGCGGGACA-GUA
BABB01018152.1/626-536         ACAGUACAAA-CUGAGCAGGCC-A-AAGGCGU----UUA--C-----------------------------------------------------UG---CCUUGG-GAGC-CGGGCCGCAGGC---AGCGGCAGCAGACAGAA-------------------------------------------------------------------------GCGUCUGUGGGACA-GUG
ABCC02000047.1/101761-101671   ACAGUACAAA-CUGAGCAGGCC-A-AAGGCGU----UUA--C-----------------------------------------------------UG---CCUUGG-GAGC-CGGGCCGCGGGC---GGCGGCAGCAGACAGAA-------------------------------------------------------------------------GCGUCUGUGGGACA-GUG
AAYW02000017.1/89779-89685     ACAGUACAAA-CUGAGCAGGCG-G-UGGG-------AUG-------------------------------------------------------------ACCACA-GGGC-CGGGCCACACAG---GGUGGCAGCAGAUAAAGAAUGAAUU---------------------------------------------------------------UAUGAUCUGCGGGACA-GUA
BAAY01006628.1/1007-962        ------------------------------------------------------------------------------------------------------------------GGCCC--AUC-----GGGCAGCAGAUUCGUAAACAA-------------------------------------------------------------------ACAUCUGCGGGACA-GUA
FP929038.1/798430-798532       ACAGUACAAA-CUGAUCAGGCG-G-GGCGCAC----UUUUUA-----------------------------------------------------UAAG-CGAUCG-CAGC-CGGGCCC-UUUC-----GGGCAGCAGAUGAAUGAAAUGGU--------------------------------------------------------------GAAGCAUCUGCGGGACA-GUU
AGTN01289422.1/351-261         CCAGUACAAA-CUGAGCAGGCC-G-GGGC-------AGG-----------------------------------------------------------U-GCUCUG-GAGC-CGGGCCGCCCCGC-GAGCGGCAGCAGAUGAGACGA----------------------------------------------------------------------ACAUCUGUGGGACA-GUG
CP002563.1/2417023-2416920     CCAAUUAAAU-CUGAACAGGCG-G-UGAACUC----UUA-G-------------------------------------------------------AGG-UUCAUG-CGGC-CGGAUCACACAUG--UGUGAUAGCAGAGUAGUGCCAAAAA--------------------------------------------------------------GGCACACCUGUGGGACA-GUA
ABHH01000006.1/34797-34694     CCAAUUAAAU-CUGAACAGGCG-G-UGAACUC----UUA-G-------------------------------------------------------AGG-UUCAUG-CGGC-CGGAUCACACAUG--UGUGAUAGCAGAGUAGUGCCAAAAA--------------------------------------------------------------GGCACACCUGUGGGACA-GUA
ACXX02000003.1/385221-385320   AAACUAUAAUUUAGAGCAGGCG-A-UGCAGCU----GUA--GACCUU------------------------------------------UUAAGACAGU-UGUGUG-GGGC-UGGGCCG--AAA-----CGGCAACAGGAUAU--------------------------------------------------------------------------AAACCUGUGGGACU-AAG
#=GC SS_cons                   :::::::::(.(((,,,,,<<<.<.<<<<___....___.._.....................................................____.>>>>>-.->>>.,,,<<<<<____....>>>>>,<<<<<___________...................................................................___>>>>>,,,,)).)):
#=GC RF                        ACAGUACAAa.cuGAgCAGGCc.a.ugccuuu....aua..A.....................................................uaaa.ggcauG.ggGC.CGGGCCgcauga....gcGGCAGCgGauuuuuuuuuaa...................................................................auAuCcGCGGGACa.gua
//
# STOCKHOLM 1.0

#=GF AC   RF02684
#=GF ID   Twister-P5
#=GF DE   Type-P5 twister ribozyme
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Weinberg Z, Ames TD
#=GF SS   Published; PMID:24240507
#=GF GA   37.00
#=GF TC   37.40
#=GF NC   36.30
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000374; ribozyme;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   24240507
#=GF RT   A widespread self-cleaving ribozyme class is revealed by bioinformatics.
#=GF RA   Roth A, Weinberg Z, Chen AG, Kim PB, Ames TD, Breaker RR
#=GF RL   Nat Chem Biol. 2014;10:56-60.
#=GF WK   Twister_ribozyme
#=GF SQ   15


ADGO01024387.1/128-188     AGU-GAGGGGA--------------UCGA----------------U-CUAA-ACUACUGG------CUUG----UUUCGUGCAAGUCACCGGU-CCCAAGUCCGG
AAGJ04114413.1/2461-2520   AGG-GAGGGAGGGGUAUU-------GGA-AC-----CA-A-ACCUC-UUAA-CCAAC-------------CGUC-------------GCCCGU-CCCAAGUCGGG
ADGO01161384.1/289-353     CGCAGAGCACGCCC-----------UACG-------------GGGC-GUAAUGCGGCCUCACCACUGGGG----UG----------AGCCAGU-UGCAAGCCUGG
AGTN01271243.1/82-136      CGCAGAGUGAGCCGG----------GAAA------------CCGGC-UUAAUGCGGG------------CAGAG--------------GCGGU-CACAACCCCGC
AACY023459782.1/1089-1018  UGAUGAGGGGCGGGGGG--------CCAGA------GA-CCCCCCG-UUAAAUC-GCCAU------GUCA----ACCG-----ACAUGCUGGU-CCCAAGCCCAG
ABSN01019877.1/251-306     CGCAGAUGACGGUGCC---------ACCA--------C--GGCACC-GUAAUGCGAC-------------AAG---------------CAGGU-UCCAAUCCCUG
AGTN01047810.1/109-173     UGCAGAUGGGCGCC-----------UUCG-------------GGCG-UUAAUGC-GC------------U-GAAACCAAAGGUUCCACCAGGU-CCAAAGUCCUG
ADGO01160766.1/269-331     CGCAGAGGGCAGCCC----------UUCG------------GGGCU-GUAAUGC-ACUCCCC---ACCUGGGGA--------------GCGGU-CCCAAGUCCGC
ADJT01008886.1/61472-61402 UGCAGAGUGAGAAAGCUCAUUACCG----UUUGGUGAUGGGCUUUU-GUAAUGC-AG-------------AGCG--------------CCGGU-CACAAUCCCGG
ADJT01008886.1/64658-64588 UGCAGAGUGAGAAAGCCCAUUACCG----UUUGGUGAUGGGCUUUC-GUAAUGC-AG-------------AGUG--------------CCGGU-CACAAUCCCGG
CP002416.1/1391738-1391681 UCCAGAGUGACGGAACGA-------CU--CU-----UC---CUCCG-GUAAUGC-GG-------------UGGC--------------CCGGU-CACAAGUCCGG
ACCJ01000536.1/4231-4175   CGCAGAGCAACGGGGCA--------GCAA----------UGCCCCG-GUAAUGCGGG-------------GGA---------------ACGGU-UGCAACCCCGU
AGTN01403367.1/395-332     CGCAGAGUGACGGGAGGG------U-UUAUC-----GGCCCUCCCG-GUAAUGCGGC-------------AGC---------------CCGGUUCGCAAGCCCGG
ABNI01036125.1/91-37       CGCAGAGUGACGGCCC---------UUCG-----------GGGCCG-GUAAUGCGGC-------------GAG---------------CCGGU-CACAAGCCCGG
ABMG01007509.1/2-60        GGU-GAGCGGCCCCGCCC-------GUAA---------GGACGGGGACUAA-ACCAC-------------AAGU--------------CCGGU-CGCAAGUCCGG
#=GC SS_cons               <<<<--AAA<<<<<<__........____............>>>>>.>--->>>>BB.............----..............<<<__.aaa__bb_>>>
#=GC RF                    cGCAGAGgGagggggCu........uuaa............ccccc.gUAAUGCgAC.............aGgg..............CCGGU.CcCAAGCCCGG
//
# STOCKHOLM 1.0

#=GF AC   RF02685
#=GF ID   RAGATH-5
#=GF DE   RAGATH-5 RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Weinberg Z
#=GF SS   Published; PMID:26167874
#=GF GA   50.00
#=GF TC   51.50
#=GF NC   40.10
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   26167874
#=GF RT   New classes of self-cleaving ribozymes revealed by comparative genomics
#=GF RT   analysis.
#=GF RA   Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR
#=GF RL   Nat Chem Biol. 2015;11:606-610.
#=GF WK   RAGATH_RNA_motifs
#=GF SQ   39


FP929046.1/2709291-2709238 UGGGAUACCCUAGCAGGGC-CGCACCCCAG----AAAAGCGGCCCCGCCCCACACCCGG
FP929045.1/1646504-1646448 GCGGACACUUUCA-AGGGC-UGCACCGCUGCCGCAAAAGCAACCCUAUGCCACCGCCCC
BABF01012214.1/29-85       GCGGACACUUUCA-AGGGC-UGCACCGCUGCCGCAAAAGCAACCCUAUGCCACCGCCCC
BABG01005008.1/294-241     CCGGAAGCCCUGGCAGGGUGCGCACCGGAU-----AAAGCGGCCCUACCUCACCGGCAC
AECU01000219.1/27459-27404 GCGGACACUUUGCAAGGGC-UGCACCGCUCA--ACAAAGCAACCCAUGCCCACCACCCC
BABD01012423.1/570-519     ACGGACACUCUGGCAGGGCAAGCACCGU-------AAAGCAGCCCCGCCCCAUCUGCCC
FP929046.1/2707979-2707929 CCGGAUACCUCAGCAGGGC-CGCACCGU-------AAAGAGACCCCGCCCCAGCCCGCA
ADJT01006171.1/2802-2854   CCGGAUAUUUUGGCAGGGC-UGCACCGGGC-----AAAGCAACCCCGCCCCAUCUUCCC
ADJT01006171.1/168-220     CCGGAUAUUUUGGCAGGGC-UGCACCGGGC-----AAAGCAACCCCGCCCCACUACCCC
BAAU01002956.1/2266-2318   CCGGAAACUUUAGCAGGGC-UGCACCGGGC-----AAAGCAACCCCGCCCCACUACCCC
FP929046.1/2710691-2710641 CCGGACACCUUAGCAGGGC-CGCACCGU-------AAAGCGACCCCGCCCCACUACCCC
BAAU01002956.1/1255-1305   CCGGACACUCUAGCAGGGC-CGCACCGC-------AAAGCAGCCCCGCCCCACUACCCC
BAAU01002956.1/45-101      GCGGAUGCCCUGGCAGGGU-CGCACCGCUCAA-ACAAAGCGGCCCCGCCCCACUACCCC
ADJT01006524.1/158-102     GCGGAUGCCCUGGCAGGGU-CGCACCGCUCAA-ACAAAGCGGCCCCGCCCCAUAACCCC
BAAX01004489.1/313-261     ACGGAGACCCCAGCAGGGC-CGCACCGCUC-----AAAGCGGCCCCGCCCCACUUCCCA
AECU01000219.1/25219-25167 ACGGAGACCCCAGCAGGGC-CGCACCGCUC-----AAAGCGGCCCCGCCCCACUUCCCA
BABD01005494.1/1196-1144   GCGGACACCUCAGCAGGGC-CGCACCGGAC-----AAAGCGGCCCCGCCCCACCGCCCA
BAAX01004210.1/763-710     GCGGACACCCCAGCAGGGC-CGCACCGAUU----CAAAGCGGCCCCGCCCCAUCUUCCC
AECU01000219.1/23601-23548 GCGGACACCCCAGCAGGGC-CGCACCGAUU----CAAAGCGGCCCCGCCCCAUCUUCCC
BABA01026356.1/119-67      CCGGAUGCCCUGGCAGGGC-CGCACCGGAC-----AAAGCGGCCCCGCCCCACCGCCCA
BAAU01015012.1/482-430     CCGGAUGCCCUGGCAGGGC-CGCACCGGAC-----AAAGCGGCCCCGCCCCACCGCCCA
BAAU01002956.1/737-789     CCGCAUGCCCUGGCAGAGU-CGCACCGUAC-----AAAGCGGCCCCGCCCCACUACACC
ADJT01006171.1/1073-1125   CCGGAUGCCCUGGUAGGGC-CGCACCGGAC-----AAAGCGGCCCUACCCCACCGCCCA
BABG01028709.1/179-231     CCGGAUACCCCGGCAGAGC-CGCACCGGAU-----AAAGCGGCCCCGCCCCACCGCCCA
BAAU01028045.1/782-833     UCGGACACUCUGGCAGGGCAAGCACCGU-------AUAGCAGCCCCGACCAACUACCCC
BAAX01005253.1/1034-982    GCGGACACUCUAGCCGGGU-UGCACCGCAC-----AAAGCAGCCCAGCCCCACACCCCG
FP929045.1/1642145-1642093 ACGGAUACUCUAGCCGGGU-UGCACCGUUC-----AAAGCAGCCCAGCCCCAGCCGCAA
FP929046.1/2706939-2706889 ACGGAUACUCUGACGGGGU-UGCACCGU-------AAAGCAGCCCCAUCCCAGCCCGCA
BAAX01005253.1/418-369     ACGGAUACCUUGA-CGGGC-CGCACCGC-------AAAGCGACCCGAUCCCACCGCCCC
AECU01000219.1/26955-26906 CCGGAUACCUUGA-CGGGC-CGCACCGA-------AAAGCGACCCGAUCCCACCACCCC
FP929045.1/1646768-1646717 CCGGACACCUUGA-CGGGC-CGCACCGCUG-----AAAGCGACCCGAUCCCAACACCCC
FP929045.1/1646016-1645965 CCGGAUACCUUGA-CGGGC-CGCACCACGA-----AAAGCGACCCGAUCCCACCACCCC
FP929045.1/1645558-1645506 CCGGAUACCUUGA-CGGGC-CGCACCGAAC----GAAAGCGACCCGAUCCCAUUCCCCC
FP929045.1/1644472-1644421 CCGGAUACCUUGA-CGGGC-CGCACCGGAC-----AAAGCGACCCGAUCCCAACGCCCC
BAAX01004489.1/1359-1310   CCGGAUACCUUGA-CGGGC-CGCACCGU-------AAAGCGACCCGAUCCCAUCCACCC
FP929046.1/2710234-2710185 CCGGACACCUUGA-CGGGC-CGCACCGU-------AAAGCGACCCGGUCCCAACACCCG
AECU01000219.1/26265-26216 CCGGAUACCUUGA-CGGGC-CGCACCGA-------AAAGCGACCCGAUCCCAUCCACCC
FP929045.1/1643856-1643803 ACGGAUGCCUUGA-CGGGC-CGCACCGAACG---AAAAGCGACCCGAUCCCACACCCCG
AECU01000219.1/24613-24564 CCGGAUACCUUGA-CGGGC-CGCACCGU-------AAAGCGACCCGAUCCCAGCCGAAA
#=GC SS_cons               AAAA::::::::<-<<<<-.<<<_aaaa__.....___>>>->>>>->:::::::::::
#=GC RF                    cCGGAuACCuUGGCcGGGC.cGCACCGcac.....AAAGCgaCCCggCCCCACCaCCCc
//
# STOCKHOLM 1.0

#=GF AC   RF02686
#=GF ID   RAGATH-6
#=GF DE   RAGATH-6 RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Weinberg Z
#=GF SS   Published; PMID:26167874
#=GF GA   170.00
#=GF TC   177.40
#=GF NC   40.90
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   26167874
#=GF RT   New classes of self-cleaving ribozymes revealed by comparative genomics
#=GF RT   analysis.
#=GF RA   Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR
#=GF RL   Nat Chem Biol. 2015;11:606-610.
#=GF WK   RAGATH_RNA_motifs
#=GF SQ   2


BABB01003568.1/701-850   AUCUGUUUAGCCAUAGCAA-UAUCGU-UGAAAUGCAAAUCAUCUACUUAUGUCGUGAGACAUUAUUUAACCACGUUAAAGUAUAAUAAUAUAAGUUAGGUAUGCCCUUAUAAAGACUUAGGUAACGCUAAGGACUAUAUUAUUAUACUUCUU
BAAZ01000382.1/2451-2601 AAUUCAUUCGC-AAAGUAAUUAUUCUAUGAAAUGCAAAUUAUCUUCAUAUGUUGUGAAACAUAGCUUAACCACGUUAAAGUAUAAUAAUAUAAGUUAGGUAUGCCCUUAUAAAGACUUAGGUAGCGCUAAGGACUAUAUUAUUAUACUUCUU
#=GC SS_cons             :::::::::<<-<-----<________>---->>>,,,,,,,,,,,,,<<<<<____>>>>>---------------(((((((((((((((-(((<<<_____>>>,,,,,,,,<<<<<______>>>>>)))))))))))))))))):::
#=GC RF                  AauUgaUUaGC.aaAGuAaUUAUugUAuGAAAuGCAAAUuAUCUaCaUauGucGUGAgaCauaauUUAACCACGUUAaaGuauaauaauauaAGuuaGGUAUGCCCuUAUAAAGACuuaGGUAaCGCuaaGgaCuauauuauuauaCuuCUU
//
# STOCKHOLM 1.0

#=GF AC   RF02687
#=GF ID   RAGATH-8
#=GF DE   RAGATH-8 RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Weinberg Z
#=GF SS   Published; PMID:26167874
#=GF GA   268.00
#=GF TC   268.10
#=GF NC   37.40
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   26167874
#=GF RT   New classes of self-cleaving ribozymes revealed by comparative genomics
#=GF RT   analysis.
#=GF RA   Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR
#=GF RL   Nat Chem Biol. 2015;11:606-610.
#=GF WK   RAGATH_RNA_motifs
#=GF SQ   3


ADLR01000020.1/28374-28648 AAGGCAACAGAAAGCAGGAAAGA-ACGGGUGAAGCGAUAGGGCUACACGCAAGUGACAUGGUGGUCAGGCUGCCGGAUAGCAGAUAGAGCGUGUGAAGAAUAAACAUGACCCGUCAAAGUAGUUGAAGAAAACAGGAACGGUAGGGCAAGAAAGCACAGUGUACCGC-ACUAUUUGAAGAAA-GCGGACAGGCUGAACCAAUCAGCACUUUACCCCUAUUCCAAGAAACCGUUAAGUGGAAGAAUCAACCGAGCGAGAGGACACAGCACUGUUGCCCU
FP929055.1/129376-129101   CGAAACAAAGCAAGUAGGAAGGA-ACGGGUGAAGCGAUAGGGCUACACGCAAGUGACAUGGUGGUCAGGCUGCCGGAUAGCAGACAGAGCGUGUGAAGAAUAAACAUGACCCGUCAAAGUAGUUGAAGAAAACAGGAACGGUAGGGCAAGAAAGCAAAGUAU-UCAGAACUAUUUGAAGAAAACUGAACAGGCUGAACCAAUCAGCACUUUACCCCUAAAACAAGAAACCGUUAAGUGGAAGAAUCAACCGCACGAGAUGACACAGCACUUUGUUUCA
ADLQ01000053.1/4238-3963   AGAAACAAAGCAAGUAGGAAGGACAUGGGUGAAGCGAUAGGGCUACACGCAAGUGACAUGGUGGUCAGGCUGCCGGAUAGCAGAUAGAGCGUGUGAAGAAUAAACAUGACCCGUCAAAGUAGUUGAAGAAAACAGGAACGGUAGGGCAAGAAAGCACAGUGUACCGC-ACUAUUUGAAGAAA-GCGGACAGGCUGAACCAAUCGGCACUUUACCCCUAAAACAAGAAACCGUUAAGUGGAAGAAUCAACCGCACGAGAUGACACAGCACUUUGUUUCA
#=GC SS_cons               [[[[[[[[[[,,,,,,,,,,,,,.((((((--------------((((((,,,<<<<______>>>>,,<<<<______>>>>,,,,,))))))--------------)))))),,,,,,,(((((-----((---((((((((((----((((,,,,,<<<-<<<<._______________>>>>>>>,<<<<<_____>>>>>,))))--))))----------))))))--))-------))))),,,,,,,,,,,,,,,,,,,]]]]]]]]]]
#=GC RF                    cgggccacaGcAAGuAGGAAgGA.acGGGuGAAGCGAUAGGGCUaCaCGCAAGuGaCAUGGUGGuCaGGCuGCCGGAUAGCaGAuAGAGCGuGuGAAGAAUAAACAUGaCCCguCAAAGUAGuuGaAGAAAaCAGGaaCGGuaGGGCAAGaaaGCAcAGuguAcCgc.ACUAUUUGAAGAAA.gcGgacaGGCuGaACCAAuCaGCACuuuACCCCuAaaaCAAGAAaCCGuuAAGuGGAAGAAuCaaCCGcaCGAGAuGACACAGCACuguggcccg
//
# STOCKHOLM 1.0

#=GF AC   RF02688
#=GF ID   RAGATH-13
#=GF DE   RAGATH-13 RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Weinberg Z
#=GF SS   Published; PMID:26167874
#=GF GA   80.00
#=GF TC   80.70
#=GF NC   34.30
#=GF TP   Gene; ribozyme;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0003824; catalytic activity;
#=GF RN   [1]
#=GF RM   26167874
#=GF RT   New classes of self-cleaving ribozymes revealed by comparative genomics
#=GF RT   analysis.
#=GF RA   Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR
#=GF RL   Nat Chem Biol. 2015;11:606-610.
#=GF WK   RAGATH_RNA_motifs
#=GF SQ   20


ACUL01000219.1/9374-9283       ACGGGUUUACCCCCGAA--UCGAGCCUUGUGGU-CUG-UCCAGGCAUCAU--UUAUAUGAGCCGCUCGAAUAACACUAAACUAAAAUCCAGGGUAAAC
ACUL01000193.1/56449-56540     ACGGGUUUACCCCCGCA--UCGAGCCUAGUGGUCCUU-ACCAAGCAUCAU--UUAUAUGAGCUGCUCGAAUAACACUAAACACAAUC-CUGGGUAAAC
ACUL01000029.1/1799-1705       ACUGAUUUGCCCCUGAAC-U-GAGCCUUGAGGCUUCAUGCCUGGUACCGCACUCUUGCAGGCCGCUCUACCAACACUAAACCAAUAU-CAGGGCAAAU
CP000675.2/2827860-2827955     ACUGAUUUGCCCCUGAAC-U-GAGCCUUGAGGCACUACGCCUGGUACUGCAAUCUUGCAGGCCGCUCUACCAACACUAAACAAAAUACCAGGGCAAAU
CR628336.1/2748083-2748178     ACUGAUUUGCCCCUGAAC-U-GAGCCUUGAGGCACUACGCCUGGUACUGCAAUCUUGCAGGCCGCUCUACCAACACUAAACAAAAUACCAGGGCAAAA
ACZG01000001.1/1182032-1182127 UUUGAUUUGCCCCACCAUUUCGAGCCUUGCAGCACAA-GCUGGAUAUCCUUUUUGAGUGAAUCGCUCGACUAACACUAAACCAAAGA-UAGGGCAAAU
CP001828.1/3011501-3011596     CUUGAUUUGCCACACUAUUUCGAGCCUUGCAGCGCAA-GCUGGAUAUCCUCUUUGAGUGAAUCGCUCGAUUAACACUAAACCAAAGA-CAGGGCAAAU
CR628337.1/2846659-2846754     CUUGAUUUGCCCCAACAUUUCGAGCCUUGCAGCACAA-GCUGGAUAUCCUCUUUGAGUGAAUCGCUCGAUUAACACUAAACCAAAGA-CAGGGCAAAU
FN650140.1/733830-733735       CUUGAUUUGCCCCAACAUUUCGAGCCUUGCAGCGCAA-GCUGGAUAUCCUCUUUGAGUGAAUCGCUCGACUAACACUAAACCAAAGA-CAGGGCAAAU
ACZG01000001.1/1258665-1258757 AUUGAUUUGCCCCCAAA--CAGAGCCUAGUGGCGCAA-GCCUGGUAUCACUUUUGAGUGAACCGCUCGAUCAACACUAAACAAAAU--CAGGGCAAGU
ACUL01000097.1/2498-2592       AUUGAUUUGCCCCCCAGU-UGGAGCCUUGUGGCGUAA-GCCUGGUAUCGCUUUUGAGUGAGCCGCUCGAUCAACACUAAACCAAAGU-CAGGGCAAGU
CP001828.1/2242625-2242720     GUUGAUUUGCCCCCCUUCUUCGAGCUUUUCGGCUUUU-GCCGGGUUUCAACAGAGUGUGAACCGCUCGACCAACACUAAACAAUACA-CAGGGCAAUU
CP000675.2/2250226-2250320     AUUGAUUUGCCCCCUUCU-UCGAGCUUUACGGCUUUU-GCCGGGUUUCAACAGAGAGUGAACCGCUCGACCAACACUAAACAAUACA-CAGGGCAAAU
FN650140.1/1088832-1088738     AUUGAUUUGCCCCCUUCU-UCGAGCUUUACGGUUUUU-ACCGGGUUUCAACAGAGAGUGAGCCGCUCGACCAACACUAAACAAUACA-CAGGGCAAAU
CR628337.1/1206767-1206673     AUUGAUUUGCCCCCUACU-UCGAGCUUUACGGUUUUU-ACCGGGUUUCAACAGAGAGUGAACCGCUCGACCAACACUAAACAAUACA-CAGGGCAAUU
CR628336.1/2159707-2159800     AUUGAUUUGCCCCCUUCU-UCGAGCUUUACGGUUUU--ACCGGGUUUCAACAGAGAGUGAACCGCUCGACCAACACUAAACAAUACA-CAGGGCAAAU
FR687201.1/1156083-1155989     AUUGAUUUGCCCCCUACA-UCGAGCUUUAUGGCUUUG-GCCAGGUUUCAACUUUGAGUGAGCCGCUCGACCAACACUAAACCAAAGA-CAGGGCAAAU
CP003024.1/1074560-1074466     AUUGAUUUGCCCCCUACU-UCGAGCUUUAUGGCUUUG-GCCAGGUUUCAUCUUUGAGUGAGCCGCUCGUUCAACACUAAACCAAAGA-CAGGGCAAAU
ACUL01000196.1/1800-1706       AUUGAUUUGCCCCCUACU-UCGGGCUUUAUGGCUUUG-GCCAGGUUUCAUCUUUGAGUGAACCGCCCGUUCAACACUAAACCAAAGA-CAGGGCAAAU
CP001828.1/85589-85682         GUUGAUUUGCCUCCUAUU-UCGAGCAAUAUGGCAUU--GCCGGGUUUCAACUUUGAGUGAGCCGCUCGAUCAACACUAAACUCAAAA-CAGGGCAGUA
#=GC SS_cons                   ::::((((((((------.((((((,,,,<<<<____.>>>><<<-<<__________>>>>>))))))------------------.--))))))))
#=GC RF                        auUGauuUGCCCCcuaau.uCGaGCcUUgcGGcuuua.gCCgGGcauCaucuuugaGUGagCCGCuCGaucAACACUAAACaAAAua.CAGGGCAaau
//
# STOCKHOLM 1.0

#=GF AC   RF02689
#=GF ID   hilD_3p_UTR
#=GF DE   hilD 3'UTR
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   74.00
#=GF TC   74.10
#=GF NC   35.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   24682814
#=GF RT   A eukaryotic-like 3' untranslated region in Salmonella enterica hilD mRNA.
#=GF RA   Lopez-Garrido J, Puerta-Fernandez E, Casadesus J
#=GF RL   Nucleic Acids Res. 2014;42:5894-5906.
#=GF RN   [2]
#=GF RM   28426789
#=GF RT   Gre factors-mediated control of hilD transcription is essential for the
#=GF RT   invasion  of epithelial cells by Salmonella enterica serovar Typhimurium.
#=GF RA   Gaviria-Cantin T, El Mouali Y, Le Guyon S, Romling U, Balsalobre C
#=GF RL   PLoS Pathog. 2017;13:e1006312.
#=GF CC   Target for hilD mRNA degradation by the degradosome and it may play an
#=GF CC   role in hilD and SPI-1 expression by serving as a target for the Hfq RNA
#=GF CC   chaperone.
#=GF WK   HilD_3'UTR_regulatory_element
#=GF SQ   5



CP001363.1/3039003-3039312 CAUUUUUUGUAUCUGUCACUUAAGUAAAGAUUUUUAUUAAAAUUGU-AAUAAUUUAAAAUUCAGACUGCGCAUUAACACGCUCUAUCAGGAUGGGAGGCUAUUCAAUAUCAUUGUUCUGUCCGGAAGACAGCUUAUACUGAUAUCUAUGGUAAUUUAAAGUAAGGCUGAUUAUAUAACACGAUUUUUGUGAACUUGUCAUCGCUAUGAUGACUGGUAAAACGAUAUUGCCUUAUUCACAUCGUAAGAAUUCGUCCAGAUGACACUAUCUCCUUCCGGCUUUAACCCUGUGGAUUAAGGCCGGCAUUUUAUU
AFCV01001029.1/110-419     CAUUUUUUGUAUCUGUCACUUAAGUAAAGAUUUUUAUUAAAAUUGU-AAUAAUUUAAAAUUCAGACUGCGCAUUAACACGCUCUAUCAGGAUGGGAGGCUAUUCAAUAUCAUUGUUCUGUCCGGAAGACAGCUUAUACUGAUAUCUCUGGUAAUUUAAAGUAAGGCUGAUUAUAUAACACGAUUUUUGUGAACUUGUCAUCGCUAUGAUGACUGGUAAAACGAUAUUGCCUUAUUCACAGCGUAAGAAUUCGUCCAGAUGACACUAUCUCCUUCCGGCUUUAACCCUGUGGAUUAAGGCCGGCAUUUUAUU
AE006468.1/3018766-3019075 CAUUUUUUGUAUCUGUCACUUAAGUAAAGAUUUUUAUUAAAAUUGU-AAUAAUUUAAAAUUCAGACUGCGCAUUAACACGCUCUAUCAGGAUGGGAGGCUAUUCAAUAUCAUUGUUCUGUCCGGAAGACAGCUUAUACUGAUAUCUAUGGUAAUUUAAAGUAAGGCUGAUUAUAUAACACGAUUUUUGUGAACUUGUCAUCGCUAUGAUGACUGGUAAAACGAUAUUGCCUUAUUCACAGCGUAAGAAUUCGUCCAGAUGACACUAUCUCCUUCCGGCUUUAACCCUGUGGAUUAAGGCCGGCAUUUUAUU
CP000880.1/95732-95424     CA-UUUUUGGGUUUAUCACUCAAGAAAAGAUUUUCAUUAAAAUUUU-AGCAAUUUAAAAUUCUGAACACUUUAUAACACACCAUAAUAGGAUUGGAGGUUAUUCAACAUCAUUGUUCUGUCCAGAAGACAGUCCGUACUGAUAUCUCUGACAAUUUAAAGCAAGGCUGUUCUUACAACGCGACUUUUGUGAACUCGUCAUCGCUAUGAUGACUGGUAAACCUAUAUUACCUUAUUCACAGCGUGAAAAUCUGUCCAGAUGAAAGUAUCUCCUUCCGGCUUUAACCCUGUGGACUAAAGCCGGCAUUUUAUU
FR877557.1/2738996-2739305 CAUUUUUCGUAUUUAUUACUCAAGAAAAUAUUUUUAUUAAAACUUUUUUUCAUUUAACAUUAUAAACGCUUAUUAAUACGCUAUAGUAGGAUGGGAGGCUAUUUAACAUUGUUGUUCUGUCCAAAAGACAGCCUGCAUUGAUAUCUCUGGCAAUUUACUGUAAGGCUGAUUAUGCAACGCGAUUUUUGUGAACUUGUCAUCGCUAUGAUGACGGGUAAACCAAUAUUACCUUAUUCACAGCGUGAGAAUCUGUCCAGAUGAAACUAUCUUCUUCCGGCUUUAGCCCUGUGGACUAA-GCCGGCAUUUUAUU
#=GC SS_cons               ::::::::<<<<<<<----<<<<<<---<<<<<<____>>>>>>--.---->>>>>>---->>>>->>><<________>>,,[[[[-[[[[[[,,,<<<<<---<<<<<<-<<<-<<<<<_____>>>>>--->>>->>>>>>-->>>>>,,,,,,,((((((((,,,,,,,,,,,<<<<<___>>>>>,<<<-<<<<<<_____>>>>>>->>>,,,,,,,,,,,)))))))),,,,<<____>>,,]]]]]]-]]]],,,,,,,,,,,,,<<<<<<<<<<<<____>>->>>>>>>>>>:::::::::
#=GC RF                    CAUUUUUuGcgucugUcACuuaaguAAAgauuuuuAUUaaaaucuU.aauaauuuaaaAUUcagaacgCgcauUAAcACgcuauaucAGGauggGAGgcuacUcAauaucaUuguUCuGuCCagAAGaCaGcuuacacugauauCUguggcAAUUUAaaguaaGGcUGaUuaUAuAACaCgauUUuuGuGAaCuuGuCauCGCUAUGauGaCugGuAAAaCgAUAUUgCCuuauuCACAcCGUaAGgAUccguCCAgaugAaAcUAUCUcCUUCCGGCcuuagCCCUGUGGAcuaagGCCGGCAUUUUAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02690
#=GF ID   BTH_s1
#=GF DE   Burkholderia sRNA 1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   74.00
#=GF TC   74.20
#=GF NC   33.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24884623
#=GF RT   Differential expression of small RNAs from Burkholderia thailandensis in
#=GF RT   response to varying environmental and stress conditions.
#=GF RA   Stubben CJ, Micheva-Viteva SN, Shou Y, Buddenborg SK, Dunbar JM,
#=GF RA   Hong-Geller E
#=GF RL   BMC Genomics. 2014;15:385.
#=GF CC   Trans-encoded, exhibits differential expression profiles dependent on
#=GF CC   growth phase and cell stimuli, such as antbiotics and serum.
#=GF WK   Burkholderia_thailandensis
#=GF SQ   5



CP000086.1/259652-259853   AAAUGCGCUACGGGGAA-CAAUAAAAACAGCGCGGGGGUAGCGUUGCCGGCACGCUUUCGGCGUGCCGGCAGCGGU-UGUCUGCAUGCACGACGGGGCC-AAUCA-CCACAACAA-GCCACCAUGCAGGCACGUACGCCCAUUCGAUGGGCGUUCCGCCGUCCGGCCGGGGGAAGC-A-----GAUGCGGGCGGCGGCGGACGCAUUUUUUGU
CP000548.1/3330916-3330716 AAAUGCGCUACGGGGAA-CAAUAAAAACAGCGCGGGGGUAGCGUUGCCGGCACGCUUUCGGCGUGCCGGCAGCGGU-UGUCUGCAUGCACGACGGGGCCAAC---AUCACAACAA-GCCACCAUGCAGGCACGUACGCCCAUUCGAUGGGCGUUCCGCCGUCCGGCCGGGGCAAG-CA-----GACGCGGGCGGCGGCGGACGCAUUUUUCAU
CP000570.1/239381-239581   AAAUGCGCUACGGGGAA-CAAUAAAAACAGCGCGGGGGUAGCGUUGCCGGCACGCUUUCGGCGUGCCGGCAACGGU-UGUCUGCAUGCACGACGGGGCCAAC---AUCACAACAA-GCCACCAUGCAGGCACGUACGCCCAUUCGACGGGCGUUCCGCCGUCCGGCCGGGGCAAG-CA-----GACGCGGGCGGCGGCGGACGCAUUUUUCAU
ABBG01000012.1/1114-1321   AAAUGCGCUACGGGGAA-CGAUAAAAACAGCGCGGGGGUAGCGUUGCUGGCACGCGUUCAGCGUGUCGGCAGCGGU-UGUCUGCAUGCACGACGGGGCCA-ACCA-CCACAACAA-ACCAACAUGCAGGCACAUACGCCUAUUCAAUCGACGUUCCGCCGUCCGGCCGGGGGAAGCAGAGGUCAAUGCGGGCGGCGGCGGACGCAUUUUUUAC
CP000614.1/3462069-3461863 AAAAGUUCUACGGGGUAGCAGAAAACAAAGCGCGGGGUUGGCGUAGCCGGCACGUAAUCAGCGUGCCGGCCGCGGAGUGUCUGCAUGCACGGCGGGGCCAAACAUCGUCGUACAGCACAUGCAUGC-GGCAGAUUUAGCGGUAUAAGCGACGUUCCGUCGUCCGACCGGGGGAAGCAG-----CAAUCGGGCGGCGGCGGACGUUUUUUCAUC
#=GC SS_cons               (((((((<<-<<-<___.____________>->>->>,,,,<<<<<<<<<<<<<<<___>>>>>>>>>>>>>>>,,.<<<<<<<<<<-------<<<________>>>-------.----->>>>>>>>>>,,,<<<<<<<<___>>>>>>>><<<<<<<-<<<-<<<-<________.....__>->>>->>>>>>>>>>))))))):::::
#=GC RF                    aaauGcgCuACGGGGaA.CAauAAAaAcAGCGCGGgGgUaGCGcuGCcGGCaCGccuUCggCGuGCCgGCagCGGu.uGuCuGCauGCACGaCGGggCCAAacaaccCacaACAa.aCcaaCauGCaGgCacaUacgcCcguucaacgGgcguuCCGcCGUCCGgCCGGgGgAAGcaa.....aAcgCGGGCGGCGgCGGacgCauuuUuuau
//
# STOCKHOLM 1.0

#=GF AC   RF02691
#=GF ID   BTH_s19
#=GF DE   Burkholderia sRNA 19
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   153.00
#=GF TC   153.10
#=GF NC   38.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   24884623
#=GF RT   Differential expression of small RNAs from Burkholderia thailandensis in
#=GF RT   response to varying environmental and stress conditions.
#=GF RA   Stubben CJ, Micheva-Viteva SN, Shou Y, Buddenborg SK, Dunbar JM,
#=GF RA   Hong-Geller E
#=GF RL   BMC Genomics. 2014;15:385.
#=GF CC   Cis-encoded, located in the 5'UTR of their cognate gene. Expression
#=GF CC   correlated with tight regulation of the gene transcript levels. 
#=GF WK   Burkholderia_thailandensis
#=GF SQ   7



CP000086.1/2372761-2372984 CACUUAACAUUUACAUGGUUUGCACGCCCGAUUCUCGCAGGGUUUGUUCGUGUGCCAAAGGU-AGCCGGUUGCCGCGUGACGAAGGGAACAAAACGACGAAAGAGGCGAGG-CCAGUGAUGCGGCCGACGAAGAUGGCGUUCGUGCUGGCGCUCGCUUGCGUCGGCUUCCUCGCUUCGGACUUCGCUUGCGCGCAGCGCCCGGAACAUGGCGCCGCGCCGUCGCAC
ABBM01000382.1/266-43      CACUUAACAUUUACAUGGUUUGCACGCCCGAUUCUCGCAGGGUUUGUUCGUGUGCCAAAGGU-AGCCGGUUGCCGCGUGACGAAGGGAACAAAACGACGAAAGAGGCGAGG-CCAGUGAUGCGGCCGACGAAGAUGGCGCUCGUGCUGGCGCUCGCAUGCGUCGGUUUCCUCGCUUCGGACUUCGCUCGCGCGCAGCGCCCGGACCGCGGCGCCGCGACGUCGCAC
CP000526.1/1957297-1957074 CACUUAACAUUUACAUGGUUUGCACGCCCGAUUCUCGCAGGGUUUGUUCGUGUGCCAAAGGU-AGCCGGUUGCCGCGUGACGAAGGGAACAAAACGACGAAAGAGGCGAGG-CCCGUGAUGCGGCCGACGAAGAUGGCGUUCGUGCUGGCGCUCGCAUGCGCCGGCUUCCUUGCUUCGGACUUCGCCUGCGCGCAGCGCCCGGAACGCGGCGCACCGCCGUCGCAC
ABBQ01000383.1/263-40      CACUUAACAUUUACAUGGUUUGCACGCCCGAUUCUCGCAGGGUUUGUUCGUGUGCCAAAGGU-AGCCGGUUGCCGCGUGACGAAGGGAACAAAACGACGAAAGAGGCGAGG-CCCGUGAUGCGGCCGACGAAGAUGGCGUUCGUGCUGGCGCUCGCAUGCGCCGGCUUCCUUGCUUCGGACUUCGCCUGCGCGCAGCGCCCGGAACGCGGCGCGCCGCCGUCGCAC
CP002599.1/2771311-2771091 CACUCGAUAUUU-CGUAGUUCGUUUGCCCGAUAUUCGCCGGGUUUGUUCAAGUACCAGAGGUUAGACGGUUGCCGCGUGACGAAGGGAACAAAUCGACCAGAGAAGCGA-GAACAGUGAUGCGACCCACCCGGAUUGCGUGCGCACUGACGAUCGUGUUCGCCGGUCUCUUUGCAUCGAACUUCGCUUGCGCCCAACGCCCCGAGCGGGGC---GGGUCGUCGCAC
AAKY01000063.1/80713-80932 CACUUCAUCUUU--CAUCUUUGCACACCCGAAUUCCGCAGGGUUU-UUCAAGUACCAGAGGU-AGCCGGUUGCCGCGUGACGAAGGGAACAAAUCGACCAAAGAAGCGA-GGACGGUCAUGCGAUCUGCCCGGAUUGCACUGAUGCUGACGAUCGUGCUUGCCGGUCCGUAUGCGUCGAACUUCGCGUAUGCGCAGCGCCCCGAGCAGGGCGCAUCGUCG-CGCAA
CP000380.1/737566-737785   CACUC--CAUCUUUCAUCUUUGUACACCCGAAUUCCGCAGGGUUU-UUCAAGUACCAGAGGU-AACCGGUUGCCGCGUGACGAAGGGAACAAAUCGACCAAAGAAGCGA-GGACGGUCAUGCGAUCUGCCCGGAUUGCACUGAUGCUGACGAUCGCGCUUGCCGGUCCGUAUGCGUCGAACUUCGCGUAUGCGCAGCGCCCCGAGCAGGGCGCAUCGUCG-CGCAA
#=GC SS_cons               ::::::::::::::::::<<<<----<<<--<<<<<<<--<<<----<<<--<<<<___>>>.>-->>>-->>>-->>>>->>>>>>-->>>>-(((((,,,,<<<<<<-<.<<<<<<<-<-<<<<<<<<<<<--<<<<<<______>>>>>>-->>>->>>>>>>>->->>>>>-->>->->>>>>>,,<<<<-<<<<<________>>>>>->>>>))))):::
#=GC RF                    CACUuaAcAUUUacaugguuuGcAcgCCCGAuucuCgCAGGGuUUGUuCguGuaCCAaAGGu.aGccGgUUgCCGCGuGaCgaaGGGAACaaaaCGaCgAAAGagGCGaGG.cCcGugaUgCggcCggCgacGAUggCgcccgUGCUggcGccCGCguucGccGgccucuucgCgUCGgACUuCGCcugcgCgcAGCGCCCgGAaCauGGCGCagcGccGuCGCAc
//
# STOCKHOLM 1.0

#=GF AC   RF02692
#=GF ID   BTH_s39
#=GF DE   Burkholderia sRNA 39
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   77.00
#=GF TC   77.70
#=GF NC   66.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0097311; biofilm matrix;
#=GF RN   [1]
#=GF RM   24884623
#=GF RT   Differential expression of small RNAs from Burkholderia thailandensis in
#=GF RT   response to varying environmental and stress conditions.
#=GF RA   Stubben CJ, Micheva-Viteva SN, Shou Y, Buddenborg SK, Dunbar JM,
#=GF RA   Hong-Geller E
#=GF RL   BMC Genomics. 2014;15:385.
#=GF RN   [2]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF CC   Trans-encoded, exhibits differential expression profiles dependent on
#=GF CC   growth phase and cell stimuli, such as antbiotics and serum. May function
#=GF CC   in bacterial metabolism and adaptation to the host.[1] Shown to be
#=GF CC   expressed in biotin. Named ncS63 in[2]. Significantly up-regulated in
#=GF CC   response to low iron. Its 5'-adjacent gene BCAL2297 encoding hemin-uptake
#=GF CC   protein HemP, is up-regulated to the same fold change. Expression and
#=GF CC   target genes suggest a potential role in regulating iron homoeostasis[2].
#=GF WK   Burkholderia_thailandensis
#=GF SQ   7



CP000085.1/2477661-2477789 GUAUUGUGGGGACCACCUCUACGAGAGGUGUUAGGCAUUAGCCAGCCACAACGGCUUGCACGCGAG-UCUAGACCCCUUCGUGCAA-ACAUAUUCAAGCAGCCGU-UGCAGCAAGCCAAGCCGCUUUUUUUG
CP000614.1/2544481-2544609 GUAUUGUGGGGACCACCUCCCUGAGAGGUGUUGGGCAUUAGCCAGC-GCAACGGCUUGCACGCGAGAUCUAGACCCCUUCGUGCAA-ACCUACUCAAGCAGCCGU-UGCAGCAAGCCAAGCCACUUUUUUUG
CP002013.1/1125841-1125714 GUAUUGUGGGGACCACCUCCGCGAGAGGUGUUAGGCAUUAGCCAGCCACGACGGCUUGCACGCGAGAACUAGACCCCUUCGUGCAGA---CACCAAGCCAGCCGU-CGCAGCAAGCCAGGCCGUUUUUUUUG
AAKY01000055.1/12342-12214 GUAUUGUGGGGACCACCUCCCUGAGAGGUGUUGGGCAUUAGCCAGCU-UAACGGCUUGCACGCGAGAUCUAGACCCCUUCGUGCAA-ACACACUCAAGCAGCCGU-UGCAGCAAGCCAAGCCACUUUUUUGG
ABLD01000048.1/1144-1272   GUAUUGUGGGGACCACCUCCUAGAGAGGUGUUGGGCAUUAGCCAGCCACGACGGCUUGCACGUGAGAACUAGACCCCUUCGUGCAGA---CACCAAGCCAGCCGUUCGCAGCCAGCCAGGCCGCUUUUUUCG
ABBG01000331.1/7977-7849   GUAUUGUGGGGACCACCUCUACGAGAGGUGUUGGGCAUUAGCCAGCCAUAACGGCUUGCACGCGAG-UCUAGACCCCUUCGUGCAA-ACAUAUUCAAGCAGCCGU-UGUAGCAAGCCAAGCCGCUUUUUUGG
CP001503.2/2908009-2908138 GUAUUGUGGGGACCACCUCCCUGAGAGGUGUUGGGCACUAGCCAGCCGUAACGGCUUGCACGCGAGAUCUAGACCCCUUCGUGCAA-CCACACUCAAGCAGUCGU-UACAGCAAGCCAAGCCAUUUUUUUGG
#=GC SS_cons               :::::((((((,,<<<<<<<___>>>>>>>,,,<<<____>>>,<<--<<<<<<<<<<<<--<<<<___________>>>>>>>>-.------------>>>>>>.>>-->>,,,))---))))::::::::
#=GC RF                    GUAUUGcGGGGACCaCCuCcauGgGaGGuGUUgGGCAUUAGCCAGCcacgaCGGCuuGCaCGcGagAuCUAGACCCCuuCguGCaa.acauAcucAagCaGCCGu.cgcAGCAAGCCAaGCCgCUUUUUUuG
//
# STOCKHOLM 1.0

#=GF AC   RF02693
#=GF ID   psm_mec_RNA
#=GF DE   psm_mec locus RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   85.00
#=GF TC   85.70
#=GF NC   63.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0045974; regulation of translation, ncRNA-mediated;
#=GF RN   [1]
#=GF RM   24877726
#=GF RT   Genome-wide analysis of the regulatory function mediated by the small
#=GF RT   regulatory  psm-mec RNA of methicillin-resistant Staphylococcus aureus.
#=GF RA   Cheung GY, Villaruz AE, Joo HS, Duong AC, Yeh AJ, Nguyen TH, Sturdevant
#=GF RA   DE, Queck SY, Otto M
#=GF RL   Int J Med Microbiol. 2014;304:637-644.
#=GF CC   psm_mec locus strain dependent gene (immune evasion factor protein A)
#=GF CC   regulatory RNA. 
#=GF WK   Methicillin-resistant_Staphylococcus_aureus
#=GF SQ   4



BX571856.1/49332-49190 AUCUUAAAUAGAAAGAGGGUAUGCAUAUGGAUUUCACUGGUGUUAUUACAAGCAUUAUUGAUUUAAUCAAGACUUGCAUUCAGGCUUUCGGUUAAUUUU---------UU----------CAACUAAAAAACAGAGGAAAUAUUCAACGACUUGAUUGUUUC
Y13052.1/1021-1172     AUCUUAAAAGGAAAGAGGUUUUGCAAAUGGAUAUCGCUGGUGUUAUUACAAGCAUUAUUGAUUUAAUCAAGACUUGCAUUCAAACUUUCGGUUAAUUUUCAGUUUUAUUG----------CAUUAAAAAGGCAGAGGAAAUAUUCAAUCUUUUGAUUGUUUC
Y14051.1/1066-1207     AUCUUAAAUAGAAAGAG-GUAUGCAUAUGGAUUUCACUGGUGUUAUUACAAGCAUUAUUGAUUUAAUCAAGACUUGCAUUCAGGCUUUCGGUUAAUUUU---------UU----------CAACUAAAAAACAGAGGAAAUAUUCAACGACUUGAUUGUUUC
AB546780.1/10221-10069 AUCUUAAAUAGAAAGAGGGUUUGCAUAUGGACUUCACUGGUGUUAUUACAAGCAUUAUUGAUUUAAUCAAGACUUGCAUUCAGACUUUCGGUUAAGUUU---------UUUGUUUCAACGCAAUAAAAAAACAGAGGAAAUAUUCAACAAUUUGAUUGUUUC
#=GC SS_cons           ::::::<<<-<<<<<---<-<<<<<----<<<<<<<-<<<<<<<______>>>>>>>->>>--->>>>------>>>>>->--->>>>>->>>------.........--..........----------------<<<<<<-<<<<____>>>>->>>>>>
#=GC RF                AUCUUAaacaGaaaGAGGgUauGCauAUGGauuuCaCugguGuuAUUACAagCauuaUuGaUUUaauCAAGACUuGCauUcAgaCuuuCGguuAAuUUU.........Uu..........CAauaAAAAaaCAGAGGaaauaUuCaacaauuuGaUuguuuC
//
# STOCKHOLM 1.0

#=GF AC   RF02694
#=GF ID   RalA
#=GF DE   RalR antitoxin
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:24748661;
#=GF GA   170.00
#=GF TC   170.30
#=GF NC   47.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF DR   GO; 0046677; response to antibiotic;
#=GF RN   [1]
#=GF RM   24748661
#=GF RT   RalR (a DNase) and RalA (a small RNA) form a type I toxin-antitoxin system
#=GF RT   in Escherichia coli.
#=GF RA   Guo Y, Quiroga C, Chen Q, McAnulty MJ, Benedik MJ, Wood TK, Wang X
#=GF RL   Nucleic Acids Res. 2014;42:6448-6462.
#=GF CC   Trans-encoded, has 16 nucleotides complimentary to coding region of toxin
#=GF CC   RalR mRNA. RalA functions as an antitoxin by preventing translation of
#=GF CC   RalR (a non-specific endonuclease that cleaves methylated and unmethylated
#=GF CC   DNA). Its activity requires RNA chaperone Hfq. RalR and RalA form a type I
#=GF CC   toxin-antitoxin (TA) system. RalR/RaLA TA locus is responsible for
#=GF CC   resistance to the antibiotic fosfomycin in E.coli.
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   10



CP001396.1/1303639-1303817 GAGGACUGAAGUUUCUCGCAAUUAAAAUUUAUCAGUUUUACUUUCUGCUCUCUGGAAACGCCUGCUUCUUUUUUACCUGAGAGCAUUUUUUCGCAUUCUGAUUUCGUUAGUUUAGA-UUUUGAAUAUCUUGUCCAGUUAGUAGGAGUGCCACCUUCCUUUUCAAUAGUGGCGGUAAUUUU
AFDV01000042.1/40867-40689 GAGGACUGAAGUCUCUCGCAAUUAAAAUUUAUCAGUUUUACUUUCUGCUCUCUGGAAACGGCUGCUUCUUUUUUACCUGAGAGCAUUUUUUCGCAUUCUGAUUUCGUUAGUUUAGA-UUUUGAAUAUCUUGUCCAGUUAGUAGGAGUGCCACCUUCCUUUUCAAUAGUGGCGGUAAUUUU
ACXF01000026.1/92775-92953 GAGGACAGAAGUUUCUCGCAAUUAAAAUUUAUCAGUUUUACUUUCUGCUCUCUGGAAACGCCUGCUUCUUUUUUCCCUGAGAGCAUUUUUUCGCAUUCUGAUUUCGUUAAUUUAGA-UUUUGAAUAUCUUAUCCAGUUAGUAGGAGUGCCACCUUCUUUUUCAAUAGUGGCGGUAAUUUU
CP000266.1/1884764-1884586 GAGGACAGAAGUUUCUCGCAAUUAAAAUUUAUCAGUUUUACUUUCUGCUCUCUGGAAACGCCUGCUUCUUUUUUCCCUGAGAGCAUUUUUUCGCAUUCUGAUUUCGUUAGUUUAGA-UUUUGAAUAUCUUGUCCAGCUGGUAGGAGAACCACCUUCCUUUUCAAUAGUGGCUGUAAUUUU
AEZV01000092.1/20993-20815 GAGGACAGAAGUUUCUCGCAAUUAAAAUUUAUCAGCUUUACUUUCUGCUCUCUGGACACGCUUGCUUCUUUUUUCCCAGAGAGCAUUUUUUCGCAUUCUGAUUUCGUUAAUUUAGA-UUUUGAAUAUCUUGUCCAGUUAGUAGGAGUGCCACCUUCCUUUUCAAUAGUGGCAGUAAUUUU
AERQ01000013.1/21897-21719 GAGGACAGAAGUUUCUCGCAAUUAAAAUUUAUCAGCUUUACUUUCUGCUCUCUGGACACGCCUGCUUCUUUUUUCCCUGAGAGCAUUUUUUCGCAUUCUGAUUUCGUUAAUUUAGA-UUUUGAAUAUCUUGUCCAGUUAGUAGGAGUGCCACCUUCUUUUUCAAUAGUGGCAGUUAUUUU
AGTL01000342.1/5660-5482   GAGGACUGAAGUUGCUCGCAAUUAAAAUUUAUCAGUUUUACUUUCUGCUCUCUGGAAACGCCUGCUUCUUUUUUACCUGAGAGCAUUUUUUCGCAUUCUGAUUUGGUUAAUUUUGU-UUUUGAGUACCUUGUCCAGUUAGUAGGAGUGCCACCUUCCUUUUCAAUAGUGGCGGUAAUUUU
AFEA01000010.1/48077-47899 GACGACUGAAGUUUCUCGCAAUUAAAAUUUAUCAGUUUUACUUUCUGCUCUCUGGAAACGCCUGCUUCUUUUUUACCUGAGAGCAUUUUUUCGCAUUCUGAUUUGGUUAAUUUUGU-UUUUGAGUACCUUGUCCAGUUAGUAGGAGUGCCACCUUCCUUUUCAAUAGUGGCGGUAAUUUU
ADAV01000062.1/11136-10957 GAGGACAGAAGUUUCUCGCAAUUAAAAUUUAUCAGUUUUACUUUCUGCUCUCUGGAAACGCCUGCUUCUUUUUUCCCCGAGAGCAUUUUUUCGCAUUCCGAUUUGGUUAACUUUGUUUUUUGAGUACCUUGUCCAGUUAGUAGGAGUGCCACCUUCCUUUUCAAUAGUGGCGGUAAUUUU
AEJY01000029.1/421-243     GAGGACAGAAGUUUCUCGCAAUUAAAAUUUAUCAGCUUUACUUUCUGCUCUCUGGACACGCCUGCUUCUUUUUUCCCUGAGAGCAUUUUUUCGCAUUCCGAUUUGGUUAACUUUGU-UUUUGAGUACCUUGUCCAGUUAGUAGGAGUGCCACCUUCCUUUUCAAUUGUAGCGGUAAUUUU
#=GC SS_cons               :<<<<<<<<<<<<<__________>>>>>-->>>>>>>>,,((((((((--(((((,,,,,,<<<<-<<<________>>>>>>>,,,,<<<<---<<<<<__________>>>>>.--->>>>,,,,,,,)))))--))))))))<<<<<<______________>>>>>>::::::::
#=GC RF                    GaggaCcGaaguuuCUCGCAAUUAaaauuUAuCgGuucuACuuuCugCuCUCuGGaaACGccuGCuUCuuUUUUaCCugaGaGCaUUUUuuCgCAUuCugaUUUcGUUAauuuaGa.UUUuGaaUAuCUUGuCCaGUUaGuaGgagcGCCaCCUUCcUUUUCAAUAGuGGCgGUAAUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02695
#=GF ID   NrsZ
#=GF DE   Nitrogen regulated small RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:24308329;
#=GF GA   76.90
#=GF TC   76.90
#=GF NC   76.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0071978; bacterial-type flagellum-dependent swarming motility;
#=GF RN   [1]
#=GF RM   24308329
#=GF RT   NrsZ: a novel, processed, nitrogen-dependent, small non-coding RNA that
#=GF RT   regulates Pseudomonas aeruginosa PAO1 virulence.
#=GF RA   Wenner N, Maes A, Cotado-Sampayo M, Lapouge K
#=GF RL   Environ Microbiol. 2014;16:1053-1068.
#=GF CC   Found in the opportunistic pathogen Pseudomonas aeruginosa PAO1. Its
#=GF CC   transcription is induced during nitrogen limitation by the NtrB/C
#=GF CC   two-component system (an important regulator of nitrogen assimilation and
#=GF CC   swarming motility) together with the alternative sigma factor RpoN (a
#=GF CC   global regulator involved in nitrogen metabolism). By activating rhlA (a
#=GF CC   gene essential for rhamnolipids synthesis) it positively regulates the
#=GF CC   production of rhamnolipid surfactants needed for swarming motility.
#=GF WK   NrsZ_small_RNA
#=GF SQ   4



AE004091.2/5775397-5775632   AACGAAGAUUUCGGGGGCCUCGGUACAGGCAGGCUGGGGAAUCCCCUCUUUUACACCCGGCGGCAGACGCAGCAUCCGCGCGCAACCGCCACACCCGUUUCGGGGACCUCGGUACAGGCAGGCUGAGAACUCCCCUCUUUUAUGCCCGGCGGUAGCGCAG--CGAUCCGCGCCUCCGCCCUCCCGUUUGGGGACCUCGGUACAGGCAGGCUGAGAAUUCCCCCUUUUAUUCCCGGCCG
CADX01000030.1/141635-141414 UACCCAG-UUUCGGGGACCUUGGUACAGGCAGGCCGGGGAUUCCCCUCUUUAACACCAGGCUCGGCACGCA----CA--UCGCGACGGCCAA--UGGUUUCGGGAACCCCAGUACAGGCAGGCUGGG-ACUUCCCUCUUUAACACCAGGCCCACCCCGCUCACAGCGACGGGCCAGGCUUUC------GGGAACCCCGGUACAGGCAGGCCGGGACUUCCCUCUUUAAUACCCGGCCC
CP000744.1/6057924-6058154   AACGACGAUUUCGGGGGCCUCGGUACAGGCAGGCUGGGGAAUCCCCCCUUUUACACCCGGCGGCAGGCGCAGCAUCCGCGCGCAACCGCCACACCCGUUUCGGGGACCUCGGUACAGGCAGGCUGAGAACUCCCCUCUUUUAU-CCCGGCGGCACCGCGA--UC---CGCG-CUCCGCCCUCCCGUUUGGGGACCUCGGUACAGGCAGGCUGAGAAUUCCCCCUUUUAUUCCCGGCCG
CP000076.1/428030-427809     UACCCAG-UUUCGGGGACCUUGGUACAGGCAGGCCGGGGAUUCCCCUCUUUAACACCAGGCUCGGCACGCA----CA--UCGCGACGGCCAAA--GGUUUCGGGAACCCCAGUACAGGCAGGCUGGG-ACUUCCCUCUUUAACACCAGGCCCACCCCGCUCACAGCGACGGGCCAGGCUUUC------GGGAACCCCGGUACAGGCAGGCCGGGACUUCCCUCUUUAAUACCCGGCCC
#=GC SS_cons                 ::::::::::::<<<<<<<<<<<<________>>>>>>>-->>>>>,,,,,,,,,,,,<<<<<----<<<-<<____>>>>>--->>>>>,,,,,,,,,,,<<<<<-<<<<<<________>>>>>>--->>>>>,,,,,,,,,,,,<<<<<--<<<<__..______>>>>-->>>>>,,,,,,,,,<<<<<-<<<<<<________>>>>>>--->>>>>::::::::::::::::
#=GC RF                      aACgaaGAUUUCGGGGaCCucgGuACAGGCAGgCcggGGAauCCCCuCUUUuACACCaGGCggcagaCGcAGcAUCagCgCGCaAccGCCAaAcccGUUUCGGGgaCCcCaGuACAGGCAGgCuGgGAACucCCCUCUUUuAuaCCagGCggaacCggau..cagcgaccGgCuccGCcuUCccGUUUgGGgaCCcCgGuACAGGCAGgCcGgGAaUucCCcCUUUuAUuCCCGGCCg
//
# STOCKHOLM 1.0

#=GF AC   RF02696
#=GF ID   Teg49
#=GF DE   Teg49 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID: 25092913;
#=GF GA   186.00
#=GF TC   186.40
#=GF NC   56.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009405; pathogenesis;
#=GF RN   [1]
#=GF RM   25092913
#=GF RT   Contribution of teg49 small RNA in the 5' upstream transcriptional region
#=GF RT   of sarA to virulence in Staphylococcus aureus.
#=GF RA   Kim S, Reyes D, Beaume M, Francois P, Cheung A
#=GF RL   Infect Immun. 2014;82:4369-4379.
#=GF CC   Present in the extended promoter region of the staphylococcal accessory
#=GF CC   regulator sarA. It is modulated by sigB (sarA regulator) and cshA (an
#=GF CC   ATP-dependant DEAD box RNA helicase) and it most likely contributes to
#=GF CC   virulence of S. aureus by modulating SarA expression.
#=GF WK   Teg49_small_RNA
#=GF SQ   6



BA000018.3/667081-666886   ACACAUUGAAUAUCGAAACAUUUAAUUGCGCUAAAUCGUUUCAUUAAAUAAAUUACCUUGUAUUGGCGAUUAAAUUAAGGUAAAUUAUAAAAAAUGCUGAUAUUUUUGACUAAACCAAAUGCUAACCCAGAAAUACAAUCACUGUGUCUAAUGAAUAAUUUGUUUUAUAAACACUUUUUUGUUUACUUCUCAUUUU
AFNP01000009.1/55570-55765 ACACAUUGAAUAUUGAAACAUUUAAUUGCGCUAAAUCGUUUCAUAAAAUAAAUUACCUUAUACUGACGAUUAAAUUAAGGUAAAUUAUAAAAAAUGCUGAUAUUUUUGACUAAACCAAAUGCUAACCCAGAAAUACAAUCACUGUGUCUAAUGAAUAAUUUGUUUUAUAAACACUUUUUUGUUUACUUCUCAUUUU
ACYP01000011.1/51240-51045 ACACAUUGAAUAUUGAAACAUUUAAUUGCGCUAAAUCGUUUCAUUAAAUAAAUUACCUUGUACUGACGAUUAAAUUAAGGUAAAUAAUAAAAAAUGCUGAUCUUUUUGACUAAUCCAAAUGCUAACCCAGAAAUACAAUCACUGUGUCUAAUGAAUAAUUUGUUUUAUAAACACUUUUUUGUUUACUUCUCAUUUU
AF515775.1/506-701         ACACAUUGAAUAUUGAAACAUUUAAUUGCGCUAAAUCGUUUCAUUAAAUAAAUUACCUUGUACUGACGAUUAAAUUAAGGUAAAUAAUAAAAAAUGCUGAUCUUUUUGACUAAACCAAAUGCUAACCCAGACAUACAAUCACUGUGUCUAAUGAAUAAUUUGUUUUAUAAACACUUUUUUGUUUACUUCUCAUUUU
ADAT01000016.1/51268-51073 ACACAUUGAAUAUUGAAACAUUUAAUUGCGCUAAAUCGUUUCAUUAAAUAAAUUACCUUGUACUGACGAUUAAAUUAAGGUAAAUAAUAAAAAAUGCUGAUCUUUUUGACUAAUCCAAAUGCUAACCCAGAAAUACAAUCACUGUGUCUAAUAAAUAAUUUGUUUUAUAAACACUUUUUUGUUUACUUCUCAUUUU
FR821777.2/648133-647938   CCACAUUGAAUAUUGGAACAUUUAAUUGCGCUAAAUCGUUUCAUUAAAAAAAUAACCUUUUCAAACUUAUUAAAUUAAGGCAAAUUUUAAAAAAUGGUAAUAUUUUUGACUGUACAAAUUGCUACCUCGAAAAUACAAUCAAUGUGUCUAAUGAAUAAUUUGUUUUAUAAACACUUUUUUGUUUACUUCUCAUUUU
#=GC SS_cons               (((((-(((,,,,,<<<<<<<<<<_______>>>>>->>>>>,,,,,<<<<-<<<<<<<<-<<<________>>>>>>>>>>>->>>>,,,,,,,,,<<-<<<<<<<<___________________>>>>>>>>>>,)))-)))))--------------------<<<<<<______>>>>>>:::::::::::
#=GC RF                    aCaCaUuGaAUAUUGaaaCauuuaAUUGCGCuaaauCGuuuCAUuAAauaaAuuaCCuugUacugacgAUUAagucaaGGuaaAuuauAAAAAAUGcuGAuauuucuGACUAaaCcAAaUGCUAaCcCagaaauaCaAuCacuGuGuCUAAUGAAUAAUUUGUUUUAuaaaCaCUUUUUuGuuuaCUUCUCAUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02697
#=GF ID   LDH1_5p_UTR
#=GF DE   LDH1 5'UTR
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:25223457;
#=GF GA   113.00
#=GF TC   113.50
#=GF NC   35.40
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0045182; translation regulator activity;
#=GF RN   [1]
#=GF RM   25223457
#=GF RT   Sustained translational repression of lactate dehydrogenase 1 in
#=GF RT   Toxoplasma gondii bradyzoites is conferred by a small regulatory RNA
#=GF RT   hairpin.
#=GF RA   Holmes M, Itaas V, Ananvoranich S
#=GF RL   FEBS J. 2014;281:5077-5091.
#=GF CC   the translational repression of lactate dehydrogenase 1 (LDH1) is mediated
#=GF CC   through its 5'UTR. A small 16 nucleotide long regulatory RNA hairpin is
#=GF CC   essential for the repression.
#=GF WK   Toxoplasma_lactate_dehydrogenase_1_regulatory_UTR
#=GF SQ   4



ABPA01000012.1/259180-259079 ACACUCGACCAGAUUUUUUUGAUUUUCGAUUUCCAAACGCGAUUUAUUCCAAUCCGCCUUGUAGCAGACUAACCGGUGCACUUUUGCACGUGUACGCAAGAC
AFYV01000981.1/13872-13771   ACGCUCGACCAGAUUUUUUUGAUUUUCGAUUUCCAAACGCGAUUUAUUCCAAUCCGCCUUGUAGCAAACUAACCGGUGCACUUUUGCACGUGUACGCAAGAC
AFHV01000122.1/7874-7975     ACGCUCGACCAGAGUUUUUUGAUUUUCGAUUUCCAAACGCGAUUCAUUCCAAUCCGCCUUGUAGCAAACUAACCGGUGCACUUUUGCACGUGUACGCAAGAC
AFPV01000520.1/7122-7021     ACGUUCGACCAGAUUUUUUUGAUUUUCGAUUUCCAAACGCGAUUCAUUCCAAUCCGCCUUGUAGCAAACUAACCGGUGCACUUUUGCACGUGUACGCAAGAC
#=GC SS_cons                 ::::<<<<--<<<<<_____>>>>>>>>>---------(((,,,,,,,,,,,<<<<<______>>>>>,,,,,,,<<<<<____>>>>>,,,,,))):::::
#=GC RF                      ACgcuCGaCCagauuUUUUUgauuuuCGaUUUCCAAACGCGAUUuAUUCCAAuccGCCUUGUAGCggaCUAACCGGuGCaCUUUuGCaCGUGUACGCAAGAC
//
# STOCKHOLM 1.0

#=GF AC   RF02698
#=GF ID   Avalong_thermometer
#=GF DE   Avalong 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:24755616;
#=GF GA   154.00
#=GF TC   154.80
#=GF NC   40.50
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   24755616
#=GF RT   Translational control of small heat shock genes in mesophilic and
#=GF RT   thermophilic cyanobacteria by RNA thermometers.
#=GF RA   Cimdins A, Klinkert B, Aschke-Sonnenborn U, Kaiser FM, Kortmann J,
#=GF RA   Narberhaus F
#=GF RL   RNA Biol. 2014;11:594-608.
#=GF WK   Cyanobacterial_RNA_thermometer
#=GF SQ   2



CP000117.1/6046551-6046681 GAAGGAGCUAGAGAUUAAGCUUUUCCACAAUGCAAAUUAAUUCAACAAUAUACCUCUUAUUUAAUUAGUAAAAAGCUUAAUAAUAGCCUUCUGAUAAGCAAAUGUUGCAUUUUAGAGGUGAUAUUAUGGCA
BA000019.2/2174165-2174295 GAAGGAGCUAGAAAUUAAGCUUUGCCAAACUCCAGAUUGAUUCGAUCAUAUACCUCUUCGUUUACCAGCAAAAAGCUUAAUAAUAGCCUUCUUAUAAGCAAAUAUUGCAUUUUAGAGGUGAUAUUAUGGCA
#=GC SS_cons               ::::::((((,,,<<<<<<<<<<<------<<<-<<<<<<____________________>>>>>>->>>>>>>>>>>>>>,,,,<<<<-<<<<---<<<<___>>>>--->>>>>>>>,,,,,,,)))):
#=GC RF                    GAAGGAGCuaGAaauuaaGCuuuuCCAaAaugCAgguuaaUUCaAuaAUAUACCUCUUauuuaaccAGcaaaaaGCuuaauAAUAgCCuUCugaUAAGCaaAUauuGCAUUucaGaGGuGAUAUUAugGCA
//
# STOCKHOLM 1.0

#=GF AC   RF02699
#=GF ID   Avashort_thermometer
#=GF DE   Avashort 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:24755616;
#=GF GA   88.00
#=GF TC   88.60
#=GF NC   35.50
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   24755616
#=GF RT   Translational control of small heat shock genes in mesophilic and
#=GF RT   thermophilic cyanobacteria by RNA thermometers.
#=GF RA   Cimdins A, Klinkert B, Aschke-Sonnenborn U, Kaiser FM, Kortmann J,
#=GF RA   Narberhaus F
#=GF RL   RNA Biol. 2014;11:594-608.
#=GF WK   Cyanobacterial_RNA_thermometer
#=GF SQ   2



CP000117.1/3815774-3815717 AAGAUUAAAGCCUGGAAGCGAUUCGCAGG-AAAACCUUAGAGGAGUCAAAGAUAUGACA
BA000019.2/323243-323301   AAGAUUAAAGCCUGGAAGCAAUCCCCAGGGAAAACCUUAGAGGAGUCAAAACUAUGACA
#=GC SS_cons               ::::::::::<<<<<<<____>>>->>>>,,,,,<<_____>>,<<<<______>>>>:
#=GC RF                    AAGAUUAAAGCCUGGaAGCaAUuCgCAGGGAAAACCUUAGAGGAGUCAAAaaUAUGACA
//
# STOCKHOLM 1.0

#=GF AC   RF02700
#=GF ID   HtrA_thermometer
#=GF DE   HtrA 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:28739676;
#=GF GA   52.00
#=GF TC   52.60
#=GF NC   49.90
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   22285954
#=GF RT   Thermogenetic tools to monitor temperature-dependent gene expression in
#=GF RT   bacteria.
#=GF RA   Klinkert B, Cimdins A, Gaubig LC, Rossmanith J, Aschke-Sonnenborn U,
#=GF RA   Narberhaus F
#=GF RL   J Biotechnol. 2012;160:55-63.
#=GF RN   [2]
#=GF RM   28739676
#=GF RT   SHAPE analysis of the htrA RNA thermometer from Salmonella enterica.
#=GF RA   Choi EK, Ulanowicz KA, Nguyen YAH, Frandsen JK, Mitton-Fry RM
#=GF RL   RNA. 2017; [Epub ahead of print]
#=GF CC   FourU thermometer found in the 5'UTR of Salmonella htrAp3 and E. coli htrA
#=GF CC   genes (high temperature requirement A gene). 
#=GF WK   FourU_thermometer
#=GF SQ   4



FQ312003.1/244448-244493   ACAGCAAUUUUGCGUUACCUGUUAAUCGAGAUUGAAACACAUGAAA
CAAZ01000083.1/29518-29473 ACAGCAAUUUUGCGUUACCUGUUAAUCGAGAUUGAAACACAUAGAA
CU928158.2/202568-202613   ACAGCAAUUUUGCGUUAUCUGUUAAUCGAGACUGAAACACAUGAAA
AAJX02000015.1/55083-55128 ACAGCAAUUUUGCGUUAUCUGUUAAUCGAGACUGAAAUACAUGAAA
#=GC SS_cons               ::::<<<<<<<<-<<<<_____>>>>>>>>>>>>::::::::::::
#=GC RF                    ACAGCAaUUUUGCGUUAuCUGUUAAUCGAGAuUGAAACACAUGAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02701
#=GF ID   PsrR1
#=GF DE   Photosynthesis regulatory RNA1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Georg et al, PMID:25248550
#=GF SS   Predicted; CMfinder
#=GF GA   42.00
#=GF TC   42.60
#=GF NC   41.30
#=GF TP   Gene; sRNA
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010109; regulation of photosynthesis;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   25248550
#=GF RT   The small regulatory RNA SyR1/PsrR1 controls photosynthetic functions in
#=GF RT   cyanobacteria.
#=GF RA   Georg J, Dienst D, Schurgers N, Wallner T, Kopp D, Stazic D, Kuchmina E,
#=GF RA   Klahn S, Lokstein H, Hess WR, Wilde A
#=GF RL   Plant Cell. 2014;26:3661-3679.
#=GF CC   Formerly known as Syr1 discovered in Synechocystis sp PCC 6803, is a
#=GF CC   regulatory factor controlling photosynthetic functions. PsrR1 interacts
#=GF CC   with the ribosome binding regions of several photosynthesis-related mRNAs.
#=GF CC   In particular, psaL mRNA is processed by RNase E only in the presence of
#=GF CC   PsrR1.
#=GF WK   Cyanobacterial_non-coding_RNA
#=GF SQ   13



CP000117.1/3624655-3624738   AAGAUUUUUACAUUUCAAUAUCGCCGUAUCUCAUUGUCA-------UUCGUACUUCUUCUA-UAAA--------------------CCUCGGU-UAGUUUC-GCCGG--GGUUUUU
BA000019.2/4221697-4221617   CCAAAUUUA--GACUCAGUAUUUAUAUUUUUAAUUGACA-------UUUGGACUUCUCCUA-AUCA--------------------CCUCGGU-UA-CAUA-GCCGG--GGUAUUU
AAXW01000073.1/3077-3000     UCUAAAAUC---GUGUGAUUUCGGUAUCUCCCAUUGAUA-------UUGAG--UUCUCCUAGAAUA--------------------CCUCGGU-GA--UGC-GCCGA--GGUUUUU
CP001291.1/5754763-5754680   CAAAAGUUU---UCUCAGU----GUAUCUCCCAUUGACA-------UUGAG--UUCUCCUACAACAG--CAG------------UACCUCGACUCAGUAAAAGUCGG--GGUUUUU
CP000806.1/3982179-3982256   UCUAAAAUC---GUGUGAUUUCGGUAUCUCCCAUUGAUA-------UUGAG--UUCUCCUAGAAUA--------------------CCUCGGU-GA--UGU-ACCGA--GGUUUUU
CP001037.1/6093882-6093803   -AAAAACAG--AUUUCGGUAUCGCUAUAUCUCAUCGACA-------UUUGGACUUCUCCCA-UCUA--------------------CCUUGGC-UA-UCAA-GUCGG--GGUUUUU
CP002198.1/2168345-2168424   AACAGUCUU---UCUCAGU----GUAUCUCCCAUUGACA-------UUGAG--UUCUCCUACAACAG--CAGU-----------AACCUCGGU-AA-A--U-GCCGA--GGUUUUU
BA000022.2/1671968-1672045   CACGGGUUC---UAGGGGUUUCGGUACCUUCCAUUGACA-------UUGAG--UUCUCCUA-GAUAUGC-----------------CCUCGGU-GA----U-GCCGG--GGUAUUU
CP001287.1/4051799-4051868   AUAAAGUUU-UCAAACCGU-----U---UCCUAUUGACA-------UUGAG--UUCUCCUACUUGA--------------------CCUUGGU-UA----U-GCCAA--GGUUUUU
AGIZ01000007.1/298033-298111 AAGAUUUUC---UUUC--UCGCAAUAUCUCUUAUUGUCA-------UUCGUUCUUCUCUGC-GUUA--------------------CCUCGGU-CGGUUUC-ACCGG--GGUUUUU
AM778938.1/42341-42435       AAAAAGUUU---UCGGGGUUUGGGUUUACCCCAUUGACAGAUUUGCUUGAG--UUCUCCUACAUAACUUAGCG----------CUACCUCGGC-UGGA--C-ACCGA--GGUUUUU
AP009552.1/3915914-3915820   AAAAAGUUU---UCGGGGUUUGGGUUUGCCCCAUUGACAGAUUUGCUUGAG--UUCUCCUACAUAACUUAGCG----------CUACCUCGGC-UGGA--C-ACCGA--GGUUUUU
CP000951.1/1264237-1264325   GCAAAGUAC---CAUGCGC----------CGUCUUGACA-------UUGAGU-UUCUCCUCUCAUACAGCAAGCUCAAACUGACCAGCCCUGA-AG----C-UUAGGCUGGUUUUU
#=GC SS_cons                 :::::::::..::::::::::::::::::::::::::::.......::::::.::::::::::::<-----...............<<<<<<<._______.>>>>>..>>>::::
#=GC RF                      aaaAAgUUu...uuucgGUuUcGgUaUcUCccAUUGACA.......UUGAG..UUCUCCUAcaauAc...................CCuCGGc.uA.u..c.gCCGa..GGUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02702
#=GF ID   AgvB
#=GF DE   Anti GcvB sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   56.00
#=GF TC   56.20
#=GF NC   52.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0045975; positive regulation of translation, ncRNA-mediated;
#=GF RN   [1]
#=GF RM   24910100
#=GF RT   Identification of bacteriophage-encoded anti-sRNAs in pathogenic
#=GF RT   Escherichia coli.
#=GF RA   Tree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL
#=GF RL   Mol Cell. 2014;55:199-213.
#=GF CC   Inhibits GcvB sRNA repression.
#=GF WK   Anti_small_RNA
#=GF SQ   3



BA000007.2/1941844-1941783 CGAUAACAACACAACAAUAUCAGUAUCUCAUGCUAUUGCCCGAACCCAUUCGGGCAUUUUUU
AEZM01000059.1/848-792     --ACAAC---ACAACAAUAUCAGUAUCUCAUGCUAUUGCCCGAACCCAUUCGGGCAUUUUUU
AEZJ01000063.1/2896-2957   CGAUAACAACACAACAAUAUCAGUAUCUCAUGCUGUUGCCCGAACCUACUCGGGCGUUUUUU
#=GC SS_cons               :<<<<____________>>>><<<<<___>>>>>--<<<<<<<<____>>>>>>>>::::::
#=GC RF                    CGAuAACAACACAACAAUaUCAGuAUCUCAUgCUaUuGCCCGAaCCcAuUCGGGCaUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02703
#=GF ID   AsxR
#=GF DE   Anti stx2 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   63.00
#=GF TC   63.10
#=GF NC   51.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0045975; positive regulation of translation, ncRNA-mediated;
#=GF RN   [1]
#=GF RM   24910100
#=GF RT   Identification of bacteriophage-encoded anti-sRNAs in pathogenic
#=GF RT   Escherichia coli.
#=GF RA   Tree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL
#=GF RL   Mol Cell. 2014;55:199-213.
#=GF CC   Increases expression of the ChuS heme oxygenase via destabilisation of
#=GF CC   FnrS sRNA.
#=GF WK   Anti_small_RNA
#=GF SQ   2



BA000007.2/1268539-1268487 CGAUUAUUAAAACGAGUAUCUCAUGCAAUUGCCCGAACCCACUCGGGCUUUUU
AB028902.1/711-660         CGAUUAUUAAAACGAGUA-UUCAUGCAAUUGCCCGAACCCACUCGGGCUUUUU
#=GC SS_cons               :::::::::::::<<<___>>>--------<<<<<<______>>>>>>:::::
#=GC RF                    CGAUUAUUAAAACGAgUAUcUCAUGCAAUUGCCCGAACCCACUCGGGCUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02704
#=GF ID   LcrF_thermometer
#=GF DE   LcrF intergenic thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:22359501;
#=GF GA   169.00
#=GF TC   169.60
#=GF NC   34.70
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   22359501
#=GF RT   Concerted actions of a thermo-labile regulator and a unique intergenic RNA
#=GF RT   thermosensor control Yersinia virulence.
#=GF RA   Bohme K, Steinmann R, Kortmann J, Seekircher S, Heroven AK, Berger E,
#=GF RA   Pisano F, Thiermann T, Wolf-Watz H, Narberhaus F, Dersch P
#=GF RL   PLoS Pathog. 2012;8:e1002518.
#=GF CC   Intergenic two hairpin RNA thermometer (usually RNAT are in the 5'UTR).
#=GF CC   Together with the termo-labile YmoA protein it activates synthesis of the
#=GF CC   most crucial virulence activator LcrF (VirF). The sequence is 100%
#=GF CC   identical in all human pathogenic Yersinia species suggesting the
#=GF CC   importance of this structure.
#=GF WK   Intergenic_lcrF_RNA_thermometer
#=GF SQ   2



CP001049.1/68923-69055 GUGAUUUAUUAUAUUGGUUUUGGUUGCAUUAAUCGAUGGUUGUACAUCGCACGCAUAAUAACUCAAUACACCUCAUUAGAUAAAUAUAUACAAGUUUUAGAUUUUUAGGACAGUAUAACAUUUAUGGCAUCAC
AL117189.1/35989-36121 GUGAUUUAUUAUAUUGGUUUUGGUUGCAUUAAUCGAUGGUUGUACAUCGCACGCAUAAUAACUCAAUACACCUCAUUAGAUAAAUAUAUACAAGUUUUAGAUUUUUAGGACAGUAUAACAUUUAUGGCAUCAC
#=GC SS_cons           (((((,,,,,,<<<<<<<<-----<<<------<<<<<______>>>>>--->>>---->>>->>>>>,,,,,,,,,,,<<<<<<-<<<<<--<<<<<<<____>>>>>>>->>>>>-->>>>>>,,,)))))
#=GC RF                GuGauUUAUUAuauuGGuuUUGGUuGCAUUAAUCGauGGUUGUACauCGCACGCaUAAUaaCUCaauaCACCUCAUUAGauaaauAuauaCAAGuccuagAUUUcuaggaCAGuauaACauuuauGGCauCaC
//
# STOCKHOLM 1.0

#=GF AC   RF02705
#=GF ID   B_rapa_snoR775
#=GF DE   Brassica rapa small nucleolar RNA 775
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 26607788;
#=GF GA   64.00
#=GF TC   64.10
#=GF NC   55.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Name based on close proximity to miR775. Precursors of both are encoded by
#=GF CC   a single gene sno-miR775. 
#=GF WK   Small_nucleolar_RNA_775
#=GF SQ   2



CP002684.1/29422149-29422275 UCGUUUAAUCAUUGAUGAUAGACUAAGAAAAUUAGGGUUUUUUAUUUUUGGUUUUUGAUAAAGAGAAAGAUGCCUCUUCUUUCAGCAGCAAGAUUAUUCUUGUUAGCUUUGUUCUGGAGGCACAGAU
AFNB01005743.1/2627-2753     UCGUUUAAUCAUUGAUGAUAGAUUAAGAAAUUAGGGUUUUUUUAUUUUUGGUUUUUGAUAAAGAGAAAGAUGCCUCUUCUUUCAGCAGCAAGAUUAUUCUUGUUAGCUUUGUUCUGGAGGCACAGAU
#=GC SS_cons                 :::::::<<<<--<<<<<--<<<_____________>>>-->>>>>-->>>>------------------<<<<<<<------<<<<<<<<<<____>>>>>>>->>>------->>>>>>>:::::
#=GC RF                      UCGUUUAauCaUUgaugaUAgacUAAGAAAaUaaGGguuUUuuauuUUuGguUUUUGAUAAAGAGAAAGAuGCCuCuUCUUUCaGCagCaaGaUUAUuCuuGuuAGCuUUGUUCUgGaGGCaCAGAU
//
# STOCKHOLM 1.0

#=GF AC   RF02706
#=GF ID   TeloSII_ncR30
#=GF DE   TeloSII non coding RNA 30
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   86.00
#=GF TC   86.80
#=GF NC   41.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0043629; ncRNA polyadenylation;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Located downstream of the TeloSII elements. These elements have been shown
#=GF CC   to coordinate the expression of protein-coding gene related to ribosome
#=GF CC   biogenesis throughout the cell cycle in Arabidopsis. 
#=GF WK   TeloSII_ncRNAs
#=GF SQ   2



CP002684.1/471418-471193     UUCACCCUACAAUCUCUGAAUUCCCUUCUUCUUCCUCCAUAAUUCUUACACCAUCUUCUUCUUCUCCAUCUUUCCAUUACACGCAUCAACAGAAAUCUCCAAGACCCGACAGUUUCAAGAUCUCACCUCUUCACGAAGAUCCGCAAGAUUCAAGAGUUAUGAUCGAUUUGUUCUAGACUUAAACUAUCUUUCUCCCGCUUUGUGUAAUUUUUGCUCUUUUGGCCAC
ADBK01000006.1/105324-105099 UUCACCCUACAAACCCUGAAUUCCCUUCUUCGUCCUCCAUGAUUCUCCCACCAUCUUCUUCUUCUUCAUCUUCCCAUUACACGCAGCAACAGAAAUCUCCAAGACUCGACAGUUUCAAGAUCUCACCUCUUCACGAAGAUCCUCAAGAUUCAAGAGUUAUGAUCGAUUUGUUCUAGACUUCUACUAUCUUUCUCCCGCUUUGUGUAAUUUUUGCUCUUUUGGCCAC
#=GC SS_cons                 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::(((------(((,,,,,,<<-<<<<---<<<<______>>>>-->>>>->>,,,,,,,<<<<<<<------<<<<<----<<<<<--<<-<_____>->>-->>>>>----->>>>>------->>>>>>>,,,,,,,)))-----)))::::
#=GC RF                      UUCACCCUACAAaCuCUGAAUUCCCUUCUUCuUCCUCCAUaAUUCUuaCACCAUCUUCUUCUUCUuCAUCUUuCCaUUACACGCauCAACAGaAauCuCCAagaCuCGACAGuuuCAaGauCuCACCUCUUCaCgaaGAUCCuCaaGauUCAAgaGuuAUGaUCGAUUUGUuCUAgaCuuaaACUauCuuUCUCCCGCuuuGuGUAAUUUUuGCUCUUUuGGCCAC
//
# STOCKHOLM 1.0

#=GF AC   RF02707
#=GF ID   TeloSII_ncR33
#=GF DE   TeloSII non coding RNA 33
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   105.00
#=GF TC   105.30
#=GF NC   72.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0043629; ncRNA polyadenylation;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Located downstream of the TeloSII elements. These elements have been shown
#=GF CC   to coordinate the expression of protein-coding gene related to ribosome
#=GF CC   biogenesis throughout the cell cycle in Arabidopsis. 
#=GF WK   TeloSII_ncRNAs
#=GF SQ   3



CP002684.1/6700408-6700704   CAAGUUCUCAUCAGCCAAAUUCUAAAUAAAAAAAGAAACUACACUCUCAUUCCUUUAUUUACAGCAAAACAAAG---ACCA-ACAUAUCCACACACCAAACUGUUUGAUUCACAUCACACCCAAAUACAAACGGUUUAAAAAAGAGGAUGCUUUCAAAAUUUCAAGGUAACAAAAAGAGGUGCAAAUGUAUAUAUUACUAAACUAGAGAAGCCUCCUCCUGAAGGUUCUGGUAGUUGAUUGAUAAGUACGAACGAGAAGACCGACACCAAUCCCAAGACAAACACAGACACCAAUCUCUUU
ADBK01000047.1/149895-150188 CUAGUUCUCAUCAGCCAAAUUCUGAAUACAAAA--AAGCUACAUUCUCACUCGUUUAUUUACAGCAAAACAAAU---ACCAAACAUAUCCACAUACCAAUGUGUUUAAUUCACAUCACACCCAAAUACAAACGGUUUUAAAAAGAUGAUUCUUUCAAAAUUUCAAGGUAAAAAAA--AGGUGCAAAUGUGUGUAUUACUAAACUAGAGAAGCCUCCUCCUGAAGGUUCUGGUUGUUGAUUGAUAAGUACGAACUAGAAGACCGACACCAAUCCCAAGACCAACACAGACACCAAGUCCUAU
AFNC01001043.1/1195-1485     CAAGUUCUCAUCAGCCAAAUUCUGAAUACAA-AAGAAACUACACUCUCAUUCCUUUAUUUACAGCAAAACAAAUAGUACCA-UCAUAUCCACACACCAAAGUGUUUGAUUCACAUCACACCCAAAUACA--------AAAAAAGAGAAUUCUUUCAAAAUUGCAAGGUAAAAAAAAGAGGUGCAAAUGUAUAUAUUACUAAACUAGAGAAGCCUCCUCCUGAAGGUUCUGGUAGUUGAUUGAUAAGUACGAACGAGAAGACCGACACCAAUCCCAAGACCAACACAGACACCAAGUCCUAU
#=GC SS_cons                 ::::::::::((((,,,,,,,,<<<<<<<<---<<<________>>>------>>>>>>>>,,,,,,,,,,,,,...,,,,.,,,,,,,,,,,,,,,<<<<<<<<<<<<<_____________>>>->>>>>>>>>>,,,,,,<<<<<-<<<<<-------<<-<<-------------<<<<____>>>>----------->>->>>>>>>->>>>>))))-<<<<<<<<<-<<<<<<<<----<<-<<--<_____>-->>>>-->>>>>---->>>-->>->>>>->>>:::::::::
#=GC RF                      CaAGUUCUCAuCaGCCAAAUUCugaauaaaAAAaGaAaCUACAcuCuCAuUCcuuuauucaCAGCAAAACAAAu...ACCA.aCAUAUCCACAcACCaaaccGuuugauuCACAUCACACCCAaauAcaaaCgguuuaAAAAAGaggaUgCuuuCAAAAUUuCAaGGUAAaAAAAAGAGgugCAAAUGuauaUAUUACUAAACuAGagaaGcCuccuCCuGaAGGuuCuGGuaGuuGauuGAUAAGuACGAACgAGAAGACCGaCACCaauCCCAAgaCcAaCACaGaCaCCAAgucCUaU
//
# STOCKHOLM 1.0

#=GF AC   RF02708
#=GF ID   TeloSII_ncR40
#=GF DE   TeloSII non coding RNA 40
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   186.00
#=GF TC   186.50
#=GF NC   40.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0043629; ncRNA polyadenylation;
#=GF DR   GO; 0005739; mitochondrion;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Located downstream of the TeloSII elements. These elements have been shown
#=GF CC   to coordinate the expression of protein-coding gene related to ribosome
#=GF CC   biogenesis throughout the cell cycle in Arabidopsis. 
#=GF WK   TeloSII_ncRNAs
#=GF SQ   2



CP002685.1/3416235-3416396 AAGGGUAAGUAAGGAGCUGAAAACGAGUCCUUCGGAGGGCGAAGAAACUCAUUAAUUCAUUUUGAUGAGGGCCCCUCAUUCAAAUGUUAUGCUUAGUGCUUCCCUCACAUUUUGAGUUGAUUAUUUCCAAUUUCGAGAGUGAGAUUGAUCCGACCAAGUAGU
JF920287.1/146541-146382   UAGGUUCCUCCAGGAGCUGAAAACGAGUCCUUCGGAGGGCGAAGAAACUCAUUAAUUCAUU--GAUGAGGGCCCCUCAUUCAAAUGUUAUGCUUCGUGCUUCCCUCACAUUUUGAGUUGAUUCUUCCCAAUUUCGAGAGUGAGAUUGAUCCGACCAAGUAGU
#=GC SS_cons               ::(((-(((((--((((,,,,,,,<<<<-<<<<<_____>>>>>-->>>>,,,,,,,<<<<<-<<<<<<<___>>>>>>>->>>>>,,,,))))--))))))))<<<<-<<<<<<<<<<________>>>->>>>>>>>>>>::::::::::::::::::::
#=GC RF                    aAGGgUaagcaAGgaGCUGAAAACGaGuCCuuCGGAGGGCGaaGAAaCuCAUUAAUUCauuuugauGaGGGCCCCuCaucCaaauGUUAUGCucaGugcuucCCuCaCAucucGaguuGAUUaUUuCCaaUcuCgagaGuGaGAUUGAUCCGACCAAGUAGU
//
# STOCKHOLM 1.0

#=GF AC   RF02709
#=GF ID   TeloSII_ncR43
#=GF DE   TeloSII non coding RNA 43
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   298.00
#=GF TC   298.40
#=GF NC   41.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0043629; ncRNA polyadenylation;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Located downstream of the TeloSII elements. These elements have been shown
#=GF CC   to coordinate the expression of protein-coding gene related to ribosome
#=GF CC   biogenesis throughout the cell cycle in Arabidopsis. 
#=GF WK   TeloSII_ncRNAs
#=GF SQ   4



AFNB01015745.1/720-1007      CCAUCACUAACACGUGUUUCAAUUAGAACAAACAGAGAGCUUCCAUCACAGACCGACUUUAACCUUGCCGUUCACCACCGAUUCCGGUGACAAGAGUCAUCGUCGAUAUUAAUUCGUUCAGUAAAUUUUGUGGUUUUUCACCGUUUAACAAAAUCGGAGCCCAUAAGAGGAUAACAGCUAAAGGGAAUGGAUAGUAUGCUUCAGUUCUUCUACUUCUUCUCUUUAAUUAAAAUUGCAAAUCACUGGGAUAAUUAAAAAACCUUUCCCAAUUAAAAAACCAAACACUCA--
AFMZ01016289.1/5664-5939     CCAUCACUAACACGUGUUUCAAUUAGAACAAACAAAGAGGUUCCAUCACAAACCGACUUUAACCUUGCCGUUCACCACCGAUUCCGGUGACAAGAGUCGCCGUCGAUAUUAAUUCGUUUAGUAAAUCUUGUGGUUUUUCACCGUUUAACAAAAUUGGAGCCCAUAAGAGGAUAACAGCUAAAGGGAAUUGAUAGUAUGCUUCAGAUCUUCUACUUCUUCUCUUUAAUUAAAGUUGCAAAUCAUUGGGAUACA-----------ACAUAUUA-AAAAACCAAACACUCA--
CP002685.1/14879905-14880181 CCAUCACUAACACGUGUUUCAAUUAGAACAAACAGAGAGCUUCCAUCACAAACCGACAUUAACCUUGCCGUACACCACCGAUUCCGGUGACAAGAGUCACCGUCGAUAUUCUUUCGUUCAGUAAAUCUUGUGGUUUUUCACCGUUUAACAAAAUUGGAGUCCAUAAGAGGAUAACAGCUAAAGGGAAUUGAUAGUAUGCUUCGGUUCUUCUACUUCUUCUCUUCAAUUAAAACUGCAAAUCACUAGGAUAAU-----------UCCUGAAAAUCUGAUAUAACAU--AUG
AFNA01016895.1/1188-1464     CCAUCACUAACACGUGUUUCAAUUAGAACAAACAGAGAGCUUCCAUCACAGACCGACUUUAACCUUGCCGUUCACCACCGAUUCCGGUGACAAGAGUCAUCGUCGAUAUUAAUUCGUUCAGUAAAUUUUGUGGUUUUUCACCGUUUAACAAAAUCGGAGCCCAUAAGAGGAUAACAGCUAAAGGGAAUUGAUAGUAUGCUUCAGUUCUUCUACUUCUUCUCUUUAAUUAAAAUUGCAAAUCACUGGGAUAAU-----------UCCUGAAAAUCUGAUACAACAAAUU--
#=GC SS_cons                 :::::::::::::[[[[[---[[[[[[,,,,,,((((((-----------((((((------------(((((-----(((((((<<<<<<____>>>>>>,,,,,,,,,<<<<-<<<-------<<<<<<<<--<<<<<--<<<<____>>>>>>>>>->>>>>>>>------->>>->>>>)))))))---)))))--))))))----------)))))),,,,,,,,,,,,,,,,,,,,,<<<<<____...........>>>>>,,,,]]]]]]--]]]]]:::..
#=GC RF                      CCAUCACUAACACguGuuUCAguuagaACAAACaGaGagcUUCCAUCACAaaCcGaCuUUAACCUUGCCguaCACCACCgauuCCGguGaCAAGAGuCacCGUCGAUAUUccuuCGuucAGUAAAucuuguGGUUuuuCgCCguuuAACAaaaucGgagcCCauaagaGGAUAACagCUaaggGGaaucGAUAGuauGCUuCgGuuCUUCUACUUCuuCuCuUuAAUUAAAauUGCAAAUCAcuggGaUAau...........uCccaauaAucuaacaaaaCacuca..
//
# STOCKHOLM 1.0

#=GF AC   RF02710
#=GF ID   TeloSII_ncR45
#=GF DE   TeloSII non coding RNA 45
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   101.00
#=GF TC   101.60
#=GF NC   39.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0043629; ncRNA polyadenylation;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Located downstream of the TeloSII elements. These elements have been shown
#=GF CC   to coordinate the expression of protein-coding gene related to ribosome
#=GF CC   biogenesis throughout the cell cycle in Arabidopsis. 
#=GF WK   TeloSII_ncRNAs
#=GF SQ   2



CP002686.1/1429026-1429094 AUAUAUUUCAUACAGGUUAUGUCUAUCGUCACUCACAUAUGCACAUACAGGCUUGUGUUGAAUAUGGUC
AFNB01010081.1/28339-28407 AUAUAUUUCAUACAGGUUAUGUCUAUCGUCACUCACAUAUGCACAUACAGGCUUGUGUUGAAUGUGGUC
#=GC SS_cons               :<<<<<<<-<<<<<<<<<<<<<<<<<-<<_____>>>>>->->>>>>--->>>>>>>>->>>>>>>:::
#=GC RF                    AuAuAUUuCAuACAgGuUAUGUCUAUCGUCACUCACAUAUGCACAUACAGgCuUGUgUUgAAUaUgGUC
//
# STOCKHOLM 1.0

#=GF AC   RF02711
#=GF ID   TeloSII_ncR49
#=GF DE   TeloSII non coding RNA 49
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   55.00
#=GF TC   55.10
#=GF NC   53.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0043629; ncRNA polyadenylation;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Located downstream of the TeloSII elements. These elements have been shown
#=GF CC   to coordinate the expression of protein-coding gene related to ribosome
#=GF CC   biogenesis throughout the cell cycle in Arabidopsis. 
#=GF WK   TeloSII_ncRNAs
#=GF SQ   3



CP002686.1/19219613-19219701 AAUGACUAUUAACUAU-UAUAAGAUAUUAAGACAAAAAGAAUAAUAAAUCUAACAAGGGGAUUAUGAUACAUCUAGUUGUAGUUGAUAUC
ADBK01000305.1/64465-64543   AAUGACU---AUAUUU-UAUAAGAUA-UAAGACAAAAAGAAUAAUAAAUCUAACAAGGGGAUUAUGAUACAUCUAGUUGAUA---GU---
GU293728.1/349-438           AAUGACUAUUAACUAUAUAUAAGAUAUUAAGACAAAAAGAAUCAUAAAUCUAACAAGGGGAUUAUGAUACAUCUAGUUGUAGUUGAUUUU
#=GC SS_cons                 ::::::<<<<<<<<<<.-<<-<<<<---------------<<<<<---<<<____>>>-->>>>>----->>>>->>->>>>>>>>>>::
#=GC RF                      AAUGACuaucaacuau.UauAaGauAUUAAGACAAAAAGAauaauAAAuCuAACAaGgGGauuauGAUACauCuAguUguaguugauaUu
//
# STOCKHOLM 1.0

#=GF AC   RF02712
#=GF ID   EBER2
#=GF DE   Epstein-Barr virus EBER2
#=GF AU   Quinones-Olvera N; 0000-0002-4612-6819
#=GF SE   Quinones-Olvera N
#=GF SS   Published; PMID:25662012
#=GF GA   125.00
#=GF TC   125.70
#=GF NC   75.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   GO; 0019044; maintenance of viral latency;
#=GF DR   GO; 0051819; induction by symbiont of nodulation, tumor or growth in host;
#=GF DR   GO; 0039580; suppression by virus of host PKR activity;
#=GF RN   [1]
#=GF RM   25807550
#=GF RT   High prevalence of the EBER variant EB-8m in endemic nasopharyngeal
#=GF RT   carcinomas.
#=GF RA   Shen ZC, Luo B, Chen JN, Chao Y, Shao CK, Liu QQ, Wang Y
#=GF RL   PLoS One. 2015;10:e0121420.
#=GF RN   [2]
#=GF RM   24252203
#=GF RT   Identification and characterization of EBV genomes in spontaneously
#=GF RT   immortalized  human peripheral blood B lymphocytes by NGS technology.
#=GF RA   Lei H, Li T, Hung GC, Li B, Tsai S, Lo SC
#=GF RL   BMC Genomics. 2013;14:804.
#=GF RN   [3]
#=GF RM   23152513
#=GF RT   Whole-genome sequencing of the Akata and Mutu Epstein-Barr virus strains.
#=GF RA   Lin Z, Wang X, Strong MJ, Concha M, Baddoo M, Xu G, Baribault C, Fewell C,
#=GF RA   Hulme W, Hedges D, Taylor CM, Flemington EK
#=GF RL   J Virol. 2013;87:1172-1182.
#=GF RN   [4]
#=GF RM   9542645
#=GF RT   B-lymphoblastoid cell lines from cancer patients.
#=GF RA   Lee WK, Kim SM, Sim YS, Cho SG, Park SH, Kim CW, Park JG
#=GF RL   In Vitro Cell Dev Biol Anim. 1998;34:97-100.
#=GF RN   [5]
#=GF RM   25662012
#=GF RT   EBV noncoding RNA binds nascent RNA to drive host PAX5 to viral DNA.
#=GF RA   Lee N, Moss WN, Yario TA, Steitz JA
#=GF RL   Cell. 2015;160:607-618.
#=GF RN   [6]
#=GF RM   6262773
#=GF RT   Two small RNAs encoded by Epstein-Barr virus and complexed with protein
#=GF RT   are precipitated by antibodies from patients with systemic lupus
#=GF RT   erythematosus.
#=GF RA   Lerner MR, Andrews NC, Miller G, Steitz JA
#=GF RL   Proc Natl Acad Sci U S A. 1981;78:805-809.
#=GF RN   [7]
#=GF RM   24441309
#=GF RT   RNA families in Epstein-Barr virus.
#=GF RA   Moss WN, Lee N, Pimienta G, Steitz JA
#=GF RL   RNA Biol. 2014;11:10-17.
#=GF RN   [8]
#=GF RM   19886912
#=GF RT   Modulation of innate immunity system by Epstein-Barr virus-encoded
#=GF RT   non-coding RNA and oncogenesis.
#=GF RA   Samanta M, Takada K
#=GF RL   Cancer Sci. 2010;101:29-35.
#=GF CC   Highly structured, non-coding RNA highly abundant in EBV-infected cells
#=GF CC   during latency. Contributes to oncogenesis by promoting growth of tumor
#=GF CC   cells and by inducing apoptosis resistance. Known interactions include
#=GF CC   paired PAX5 and cellular protein La.
#=GF WK   Epsteinâ€“Barr_virus-encoded_small_RNAs
#=GF SQ   3


EF187853.1/405-577 AGGACAGCCGUUGCCCUAGUGGUUUCGGACACACCGCCAACGCUCAGUGCGGUGCUACCGACCCGAGGUCAAGUCCCGGGGGAGGAGAAGAGAGGCUUCCCGCCUAGAGCAUUUGCAAGUCAGGAUUCUCUAAUCCCUCUGGGAGAAGGGUAUUCGGCUUGUCCGCUGUUUUU
J02077.1/418-590   AGGACAGCCGUUGCCCUAGUGGUUUCGGACACACCGCCAACGCUCAGUGCGGUGCUACCGACCCGAGGUCAAGUCCCGGGGAAGGAGAAGAGAGGCUUCCCGCCUAGAGCAUUUGCAAGUCAGGAUUCUCUAAUCCCUCUGGGAGAAGGGUAUUCGGCUUGUCCGCUAUUUUU
DQ883819.1/405-577 AGGACAGCCGUUGCCCUAGUGGUUUCGGACACACCGCCAACGCGCUGUGCGGUGCUGCCGUCCCGAGGUCAAGUCCCGGGGGAGGAGAAGAGCGGCUUCCCGCCUAGAGCAUUUGCAAGUCAGGAUUCUCUAAUCCCUCUGGGAGAAGGGUAUUCGGCUUGUCCGCUGUUUUU
#=GC SS_cons       :(((((((((-((((((,,,<<--<<<<---<<<<<<___________>>>>>>--->>>>->>,,,,,,,,,<<<<<<<<<<<<<<<<---<<<<_____>>>>-------------------->>>>>>-->>>>->>>>>>,,))))))--))))-))))):::::::::
#=GC RF            AGGaCaGCCGUugCCCuAGUGGUUuCGGACACaCCGCCAACGCuCaGUGCGGuGCUaCCGaCCCGAGGUCAAGuCCCgGGGgagGaGaaGAGaGGCUUCCCGCCuAGAGCAUUUGCAAGUCAGGAuuCuCcAAucCCUCcGGGaGAaGGGcaUUCGGCUuGuCCGCUgUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02713
#=GF ID   MCS4
#=GF DE   Mycoplasma sRNA MCS4
#=GF AU   Quinones-Olvera N; 0000-0002-4612-6819
#=GF SE   Quinones-Olvera N
#=GF SS   Published; PMID:9498566
#=GF GA   56.00
#=GF TC   56.10
#=GF NC   53.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 50.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF RN   [1]
#=GF RM   7687343
#=GF RT   A small RNA of Mycoplasma capricolum that resembles eukaryotic U6 small
#=GF RT   nuclear RNA.
#=GF RA   Ushida C, Muto A
#=GF RL   Nucleic Acids Res. 1993;21:2649-2653.
#=GF RN   [2]
#=GF RM   9498566
#=GF RT   Probing the secondary structure of MCS4 RNA of Mycoplasma capricolum.
#=GF RA   Ushida C, Sasamura S, Muto A
#=GF RL   J Biochem. 1997;122:1202-1207.
#=GF RN   [3]
#=GF RM   14527727
#=GF RT   Distribution of the MCS4 RNA genes in mycoplasmas belonging to the
#=GF RT   Mycoplasma mycoides cluster.
#=GF RA   Ushida C, Yoshida A, Miyakawa Y, Ara Y, Muto A
#=GF RL   Gene. 2003;314:149-155.
#=GF CC   Abundant, small RNA of unknown function, found only in Mycoplasma.
#=GF CC   Extensive sequence similarity to eukaryotic U6 snRNAs.
#=GF WK   Mycoplasma
#=GF SQ   5



FR668087.1/130837-130959     UAUAAAUAUCUUGUAUAUUUAUAAGAUUGGCAGUGUGGUUCUUGCUGGACCUGGGUGA--UAAUAGAUCCCGAAAGACGGAGAUUGAACCAAAAA-ACAACUCUUAUAAAAAGAGUUGUUUUUUUU
AENG01000001.1/137972-138094 UAUAAAUAUCUUGUAUAUUUAUAAGAUUGGCAGUGUGGUUCUUGCUGGCUCUGGGUGA--CGAGAGAUCCCGAAAUCAAGAGAUUGAACCAAAAA-ACAACUCUUUUUAUAAGAGUUGUUUUUUUU
AENG01000001.1/255918-255795 CAUAAAUAUCUUGUAUAUUUAUAAUAUUGGCAGUGUAGUUCUUGCUGGCUCUGGGUGA--CGAGAGAUCUCGAAAUCAAGAGAUUGAACCAAAAAAACAACUCUUUUUAUAAGAGUUGUUUUUUUA
S67629.1/2-125               UAUAAAUAUCUUGUAUAUUUAUAAUAUUGGCAGUGUGGUUCUUGCUGGCCCUGGGUGAACUCUGAGAUCCCGAAAGACGGAGAUUGAACCAAAAA--CAACUCUUUUUAUAAGAGUUGUUUUUUUA
CP000123.1/122501-122623     UAUAAAUAUCUUGUAUAUUUAUAAUAUUGGCAGUGUGGUUCUUGCUGGCCCUGGGUGA--CGAGAGAUCCCGAAAUCAAGAGAUUGAACCAAAAA-ACAACUCUUUUUAUAAGAGUUGUUUUUUUA
#=GC SS_cons                 <<<<<<<<<_____>>>>>>>>>,,,,,,,,,,,,,<<<<<----------<<<<_____________>>>>------------->>>>><<<<<.-<<<<<<<<_____>>>>>>>>>>>>>:::
#=GC RF                      uauaaauauCUUGUauauuuauaAuAUUGGCAGUGUGGuuCUUGCUGGcuCuGGGUGA..ugagAGAUCCCgAAAuaaaGAGAUUGaaCCaaaaa.ACaaCuCuuuUuAuaaGaGuuGuuuuuUUa
//
# STOCKHOLM 1.0

#=GF AC   RF02714
#=GF ID   snopsi28S-3378
#=GF DE   Small nucleolar RNA psi28S-3378
#=GF AU   Quinones-Olvera N; 0000-0002-4612-6819
#=GF SE   Quinones-Olvera N
#=GF SS   Predicted; CMfinder;
#=GF GA   136.00
#=GF TC   136.40
#=GF NC   37.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF DR   snoopy; snoRNA:Psi28S-33787;
#=GF DR   URL; http://flybase.org/reports/FBgn0082963.html;
#=GF RN   [1]
#=GF RM   15288778
#=GF RT   Different expression strategy: multiple intronic gene clusters of box
#=GF RT   H/ACA snoRNA in Drosophila melanogaster.
#=GF RA   Huang ZP, Zhou H, Liang D, Qu LH
#=GF RL   J Mol Biol. 2004;341:669-683.
#=GF RN   [2]
#=GF RM   17994087
#=GF RT   Evolution of genes and genomes on the Drosophila phylogeny.
#=GF RA   Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC,
#=GF RA   Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM,
#=GF RA   Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW,
#=GF RA   Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D,
#=GF RA   Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak
#=GF RA   SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK,
#=GF RA   Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S,
#=GF RA   Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A,
#=GF RA   Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher
#=GF RA   AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD,
#=GF RA   Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC,
#=GF RA   Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey
#=GF RA   J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S,
#=GF RA   Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter
#=GF RA   GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz
#=GF RA   MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J,
#=GF RA   Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P,
#=GF RA   Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S,
#=GF RA   Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L,
#=GF RA   Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky
#=GF RA   E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L,
#=GF RA   McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P,
#=GF RA   Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S,
#=GF RA   Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M,
#=GF RA   Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli
#=GF RA   D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D,
#=GF RA   Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie
#=GF RA   MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S,
#=GF RA   Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz
#=GF RA   MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M,
#=GF RA   Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W,
#=GF RA   Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W,
#=GF RA   Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E,
#=GF RA   Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang
#=GF RA   J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A,
#=GF RA   Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K,
#=GF RA   Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A,
#=GF RA   Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A,
#=GF RA   An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A,
#=GF RA   Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C,
#=GF RA   Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y,
#=GF RA   Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De
#=GF RA   Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M,
#=GF RA   Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D,
#=GF RA   Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR,
#=GF RA   Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez
#=GF RA   N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L,
#=GF RA   Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P,
#=GF RA   Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X,
#=GF RA   Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P,
#=GF RA   Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T,
#=GF RA   Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V,
#=GF RA   Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N,
#=GF RA   Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E,
#=GF RA   Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F,
#=GF RA   Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N,
#=GF RA   Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N,
#=GF RA   Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y,
#=GF RA   Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk
#=GF RA   T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q,
#=GF RA   Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W,
#=GF RA   Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I
#=GF RL   Nature. 2007;450:203-218.
#=GF CC   psi28S-3378 is a member of the H/ACA class of snoRNA.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   8


AAPU01010147.1/87506-87365   AGCACCA-AAAUCAGUAACCAAGCGACUGCUAAACUAGCUUGGCGACUACGCUUGGGUGCUAAAAUUAA-AU-------A-CGCUAUGAUGCCGCAUUUAUUA-AAAGAGCAUACUAACCC-A---UUAGAAUGCUUGUGGCCUUGUUUUGUAACAA
AANI01014934.1/201555-201413 AGCACCA-AAAUCAGUAACCAAGCGAUUGCUAAACUAGCUUGGCGACUACGCUUGGGUGCUAAAAUUAAAAC-------A-CGCUAUAAUGCCGCAUGUAUUU-AAAGAGCAUACUAACCC-A---UUGGAAUGCUUGUGGCCUUGUUUUGAGACAA
AAPT01021484.1/866747-866600 AGCACCA-AAAUCAGUAACCAAGCGACUGCUAAACUAGCUUGGCGACUACGCUUGGGUGCUAACAUUAA-UU-------ACCGCUAUAAUGCCGUAUAUUAUAUAAAGAGCAUACUAACCCAACCAAUAGCAUGCUUGUGGCCUUGUUUUGAGACAC
AASS01007470.1/1742-1886     AGCACCA-AAAUCAGUAAUCAUGCGAUUGCUAAACUAGCAUGGCGACUACGCUUGGGUGCUAAAAGUAA-AU-------U-CGCUAUAAUGCCGCAUACUAAA-CCAGAGCAUGCUAAUCU-AGCCCUAGAAUGCUUGUGGCCUUGUUUCGAGACAA
AAPP01018740.1/148667-148811 AGCACCA-AAAUCAGUAACCAUGCGACUGCUAAACUAGCAUGGCGACUACGCUUGGGUGCUGACAGUAA-CU-------U-CGCUAUAAUGCCGCAUACUAAA-CCAGAGCAUGACAACUC-AGCCCUAGAAUGCUUGUGGCCUUGUUUCGAGACAA
AAGH01006567.1/2471-2327     AGCACCA-AAAUCAGUAAUCAUGCGAUUGCUAAACUAGCAUGGCGACUACGCUUGGGUGCUAAAAGUAA-AU-------U-CGCUAUAAUGCCGCAUACUAAA-CCAGAGCAUGCUAAUCU-AGCCCUAGAAUGCUUGUGGCCUUGUUUCGAGACAA
AAIZ01002208.1/899-755       AGCACCAAAAAUCAGUAACCAUGCGACUGCUA-ACUAGCACGGGGACUACGCUUGGGUGCUAAAAUUAA-UA-------U-CGUUAUAAUGCCGCAUACUAAA-CCAGAGCAUGCUAAUCC-CGCCCUAGAAUGCUUGUGGCCCUGUUCUGAGACAA
AAQB01006145.1/104686-104836 AGCACCA-AAAUCAGUAACCAAGCGAAUGCUAAACUAGCUUGGGGACUACGCUUGGGUGCUCAAAUUGA-UUUAACCGCU-CGCUAUAAUGCCAAACAUAACAUUAAGAGCAUAAC--CUA-AUCCUCGCUAUGCUUGUGGCCCUGUUUCGAGACAC
#=GC SS_cons                 <<<<<<-.-----<<<--<<<<<<_____________>>>>>>-->>>------->>>>>>--------.-<.......<.<<--<<<<-<<<<<--------.---<<<<<<-<<<____._____>>>->>>>>>>>>>>->>>>-->>>>::::
#=GC RF                      aGCaCCA.AAAUCaGuAAcCauGCGAuUGCUAAACUAGCauGgcGaCuACGCUUGGGuGCuaAaAuUAA.uc.......u.CgcUauaaUGCCgcAUauuaaA.aaAgaGCauaccaAccc.AgCcuuggaauGCuuguGGCCuuguUUcGagACAa
//
# STOCKHOLM 1.0

#=GF AC   RF02715
#=GF ID   sno_ncR1
#=GF DE   Small nucleolar RNA ncR1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   94.00
#=GF TC   94.70
#=GF NC   37.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Type H/ACA. Orphan.
#=GF WK   TeloSII_ncRNAs
#=GF SQ   5



CP002684.1/14283553-14283663 GACAUGAACGAUCUAAAUCUUCGAGAUUGUAAAUGUCGUUGUAUGGAAAUCUACAUUUGAGAUGUUGCGAGUUAGAGGAGGCCUCUACUUUGCGUUAGAAAGAGAGAAACA
CP002687.1/11116542-11116436 GAUAUGGACGAUCUGAAUAUCCGAAAUUGUAAACGUCGAUGGAUGAAAAUCUACAUUUGAGAUGU---UCGUUAGAGAAGAUCUCAUCUUUACGU-AGAAAGAGAAAAGCA
AFNB01005913.1/112-221       GACAUGGACGAUCUGAAUAUCCGAAAUUGUAAACGUCGAUGGAUGAAAAUCUACAUUUGAGAUGUUGUUCGUUAGAGAAGAUCUCAUCUUUGCG-NAGAAAGAGAGAAGCA
ADBK01001450.1/101858-101967 GACAUG-ACGAUCUGAAUCUCUGAGAUUGUAAACGUUCUUGUAUGGAAAUCUACAUUUGAGAUGUUGUCUGUUAGAGGAGGUCUCAUCUUUGCGUUAGAAAGAGAGAAGCA
CP002686.1/14539259-14539367 GACAUGGACGAUCUGAAUCUCUCAGAUUGUAAAUGUCGUUGUAUGGAAAUCUAGAUUUGAGAUGUUAGUAGUU--AGGAGGUCUCAUCUUUGCGUUAGAAAGAGAGAAGCA
#=GC SS_cons                 <<<<<--<<<<<<<_________>>>>>>>-->>>>>------------<<<---<<<--<<<<<---<<<<-<<<<<___>>>>>>>>>->>>>>-->>>--->>>::::
#=GC RF                      GacguGgaCgaucugAAUaUcugagauuGuAAacguCguUGuAUGgAAAuCuAcAuuuGAgauGcUgucaGcUgGaGgAGgcCuCcgCugUgCgucAGaaaGAGaGaAgCA
//
# STOCKHOLM 1.0

#=GF AC   RF02716
#=GF ID   sno_ncR3
#=GF DE   Small nucleolar RNA ncR3
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   88.00
#=GF TC   88.50
#=GF NC   48.50
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Type C/D. Target 18S.
#=GF WK   TeloSII_ncRNAs
#=GF SQ   5



CP002684.1/14283975-14284049 AAAGCUUCCACGUUUUCAUGAAGUUGUUGUGACAAGGUGAUUUUUUCUUCUUUUGGCUGAUUCGGAGAUGCAUUG
AFNC01014841.1/284-358       GAAGCUUCCACGAUCUGAUGAAGUUGCCGUGACAAAGUGAUUUUUCCUUUGUUUUGCUGAUUCAGAGAUGCGUUG
CP002687.1/11116124-11116050 GAGGCUUCUACCGUCUUAUGAAGUUGCUGUGACAGAGUUUAUUUUUCUUCCUUUGGCUGAUUCGGAGAUGCAUUA
CP002685.1/56814-56886       GAGGCUUCUACCGUCUUAUGAAGUUGCUGUGACA--GUGAAUUUUUCUUCCUUUGGCUGAUUCGGAGAUGCAUUA
CP002686.1/14539697-14539771 GAAGCUUCCACGAUCUAGUGAAGUUGCUCUGACAAAGGGAUUUUUCCUUUGUUUUGCUGAUUCAGAGAGGCAAUG
#=GC SS_cons                 ::::::::<<<-<<-<<<<<<_____>>>>>>->>->>>------<<<<<_____________>>>>>:::::::
#=GC RF                      GAaGCUUCcaCguUCUcaugaAGUUGcugugACAaAGugAuUUUUuCUUcuUUUgGCUGAUUCgGAGaUGCAUUg
//
# STOCKHOLM 1.0

#=GF AC   RF02717
#=GF ID   sno_ncR4
#=GF DE   Small nucleolar RNA ncR4
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   103.00
#=GF TC   103.90
#=GF NC   34.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Type C/D. Target 18S.
#=GF WK   TeloSII_ncRNAs
#=GF SQ   3



CP002684.1/14284343-14284424 GAUCUUAAGUGCAUUUGACGACCCGUCUAGUGUGGUGAACUCUUGAGUUGAUAGUGUUGAACUCUGAGCUGGUGAUCUAAAG
CP002686.1/11415463-11415382 GAUCUUAAGUGCAUUUGACGACCCGUCAGGUGCGGUGAAAUCUUUGGUUGAUAGUGUUGAACUUUGAGUUGCUGAUCUCAAG
ADBK01001450.1/102499-102580 GAUCUUAAGUCCGUUUGACGACCCGUCAGGUGCGGUGAACUCUUGGGUUGAUAGAGUUGCACUCUGAGUUGGUGAUCUCAAG
#=GC SS_cons                 ((((---((,<<<<<-<<<<___>>>>->>>>>,,,,,,<<<--<<<<<-<______>->>>>>->>>))---)))):::::
#=GC RF                      GauCUUAagUgCaucUGaCGACCCGuCagguGcGGUGAAcuCUUgaGuuGaUAGuGUuGaaCucUGagcuGgUGauCUcAAG
//
# STOCKHOLM 1.0

#=GF AC   RF02718
#=GF ID   sca_ncR14
#=GF DE   Small Cajal body specific RNA ncR14
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   62.00
#=GF TC   62.40
#=GF NC   32.20
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Type C/D. Putative target U6.26.
#=GF WK   TeloSII_ncRNAs
#=GF SQ   4



CP002688.1/3642496-3642628   CAAAAAAAUUGGACAUGAUGACGAACCUGAUUUUG-GAUGUUCAUGGGAAGGCCACAUGACACGAGAGCCGUUUAAGCCGCCGUUA-AAUAUGGAUGGAAGACAGG-UUUUCCUCCGUCAGUGCCUGAGAAG-UUGA
AFNB01017754.1/1342-1474     CAAAAAAAUUGGACAUGAUGACGAACCUGAUUUUG-GAUGUUCAUGGGAAGGCCACAUGACACGAGAGCCGUUUAAGCCGCCGUUA-AAUAUGGAUGGAAGACAUG-UUUUCCUCCGUCAGUGCCUGAGAAG-UUGA
ADBK01001172.1/267471-267600 CGAAA-UAUUGGAUA---UGACGAGCGUGGUUUUUGGAUUUUCAUAGGAAGGCCACAUGACAAGAGAGCCGUUUAAGCCGCCGUUA-AAUAUGGAUGGAAGACAGA-UUUUCCUCCGUCAGUGCCUGAGAAG-UUGA
AENI01001202.1/40674-40799   CAA--AAAUCGGAC---GUGACGGUCGUGGUUUUG-GAUUUUUAUGGGAAGGCCACGUG-CAUGG----UGUUUACGCCGCCGUUAAAAUAUAGUUGGAAGACAAUAUUUUCCUCCGUCACGGCCUGAGAAGUUUGA
#=GC SS_cons                 (((-------((-((.--(((((,,<<_______>.>,,<<<<<<<<<____>>->>>>>->><<<<<<<<<<<---<<<<<<<__.___>>>>->>>->>>>->>.>>>>>,,,)))))-))))-------.))):
#=GC RF                      CaaAAAaAUuGGAca..auGaCGaaCcUGaUUUUg.GAUguucaugGGAAGGCCAcaugaCacGagagccGucuAaGCCgCcguUA.AAUacgGacGGAagaCAgg.cucuCCUCCGuCagugCCUGAGAAG.uuGA
//
# STOCKHOLM 1.0

#=GF AC   RF02719
#=GF ID   sca_ncR20
#=GF DE   Small Cajal body specific RNA ncR20
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   127.00
#=GF TC   127.00
#=GF NC   37.20
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Type C/D. Putative target U6-29.
#=GF WK   TeloSII_ncRNAs
#=GF SQ   2



CP002685.1/9809815-9809713 GAAUCGUUAA-AUUUGACGAAAGGGUACGUAAAAGAACUUCCUUUUUGAUGAUUUAUCUAUAUAUUAGACGUAAUUGAUUGUUUCUGAUUUAAGUAUCGUGGCA
AFNB01008472.1/2415-2312   GAAUCGUUAAAAUUUGACGAAAGGGUACGUAAAAGAACUUCCUUUUUGAUGAUUUAUCUAUAUAUUAGACGUAAUUGAUUGUUUCUGAUUUAAGUAUCGUGGCA
#=GC SS_cons               <<<<<<<<<---------<<<<<<<---<<______>>->>>>>>>>>>>>>>>>,<<<<_____>>>>,,,,,,,,,,<<<<--<<<<______>>>>->>>>
#=GC RF                    gaauCgucaAAAUUUGACgaaaGGgUACGuAAAAGAaCUcCCuuucugacGauucAuCuaUAUAUuaGaCGUAAUUGAUuGccUCcGauUUAAGUauCgUggCa
//
# STOCKHOLM 1.0

#=GF AC   RF02720
#=GF ID   sca_ncR21
#=GF DE   Small Cajal body specific RNA ncR21
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   113.00
#=GF TC   113.40
#=GF NC   39.10
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Type C/D. Putative target U2.4.
#=GF WK   TeloSII_ncRNAs
#=GF SQ   2



CP002685.1/9809455-9809345 UUAUCUAUUAUAUUCUCAUGACAUUUUGAUCCACUUGUGAUCAGCACAAGAUCAGUAUA--AAGUUGAAGUUGAUCAAUUUGUGGAGCAUGGAUCCUGAAUAUACCGACGAUU
ADBK01000682.1/5305-5198   UUGUCAAUUAUCUUCUCAUGAAAUUUUGAUUCAU-UGUGAUCAGCUGAAGACCAGUAUAGGAAG---AAGUUGAUCAUUUUGUGAA-CAUGGAUCCUAAUCAUACCGACGAUC
#=GC SS_cons               ::::::::<<<<<<<------<<<-----<<<<<---<<<<<<<<-<<<__________..___>>>-->>>>>>>>---->>>>>-->>>------>>>>>>>:::::::::
#=GC RF                    UUaUCuAUuauguucUCAUGAcauUUUGAucCacUUGuGauCagCacaaGAuCAGUAUA..AAGuugAAGuuGauCaaUUUguGgaGCaugGAUCCUgaacauaCCGACGAUu
//
# STOCKHOLM 1.0

#=GF AC   RF02721
#=GF ID   sca_ncR26
#=GF DE   Small Cajal body specific RNA ncR26
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   37.00
#=GF TC   37.20
#=GF NC   36.60
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Type C/D. Putative target U6.1.
#=GF WK   TeloSII_ncRNAs
#=GF SQ   2



CP002684.1/28889830-28889897 UUUGAAAACCUGAUUUUGAUGCGCCGUAUAUGACAGAUUUUUGUGAAUACUGAGGGCUAUUUUUCUUU
ADBK01000402.1/25275-25341   UUUGAGAACUGGUUUUUGAUGCGCCGCAUAUGACUGAUUU-UGUGAGUACUGAGGGAUUGUUUUCUUU
#=GC SS_cons                 :::::::::::<<----<<<<-<<<<<<<-<-<<<<____>>>>->>>>>---->>>>>>>-->>:::
#=GC RF                      UUUGAaAACuuGaUUUUGauGCgCCGuAuAUGACagAUUUuuGUGAaUaCUGAGGGcUauUUUuCUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02722
#=GF ID   sca_ncR27
#=GF DE   Small Cajal body specific RNA ncR27
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   91.00
#=GF TC   91.90
#=GF NC   36.10
#=GF TP   Gene; snRNA; snoRNA; scaRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0015030; Cajal body;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   26607788
#=GF RT   Promoter-based identification of novel non-coding RNAs reveals the
#=GF RT   presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
#=GF RA   Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A,
#=GF RA   Szweykowska-Kulinska Z, Echeverria M, Karlowski WM
#=GF RL   BMC Genomics. 2015;16:1009.
#=GF CC   Type C/D. Putative target U6.1.
#=GF WK   TeloSII_ncRNAs
#=GF SQ   4



CP002684.1/28889966-28890048   UGAGAUUUAAGCCCUGUGAUGAUGACUCUAAUGAGUUUGAGUGGUGCCGCUUGGUUUUUUCUUGCUGAGACUCAUUAUCUUUG
ADBK01000402.1/25412-25494     AGAAUGUUAAGCCCUGUGAUGAUGACUCUAAUGAGUUUGAGUGGUGCCGCUUGGUUGUUUCUUGCUGAAACUCGUCAUCUUUA
AENI01006267.1/25045-24964     UUUAUUUUUAGCCUUGUGAUGAUGAUAGUA-UAUCUUCGAGUGGUGCCGCUUGUUUGUUUUUUGCCGAGACCCAUCAUCUCCA
AFAN01000027.1/1313665-1313746 AUUGAAUUAAGCCCUGUGAUGAUG-UCCUAAUGAAUUUGAGUGGUGCCGCUUGGUUGUUUCUAGCCGAGACUCAUCAUCUCCA
#=GC SS_cons                   :::::::::::::::::(((((((<<<<____>>>>,,<<<<<____>>>>><<<<<<________>>>>>>)))))))::::
#=GC RF                        uuuauuUUaAGCCcUGUGAUGAuGacucUAAUgaguUUgAGuGGUGCCgCUuggUuuuUUcUuGCugagAccCaUCAUCUuuA
//
# STOCKHOLM 1.0

#=GF AC   RF02723
#=GF ID   sno_ZL1
#=GF DE   Small nucleolar RNA ZL1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   64.00
#=GF TC   64.40
#=GF NC   61.70
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23706177
#=GF RT   Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA
#=GF RT   core proteins and small RNA sequencing.
#=GF RA   Kishore S, Gruber AR, Jedlinski DJ, Syed AP, Jorjani H, Zavolan M
#=GF RL   Genome Biol. 2013;14:R45.
#=GF CC   Host gene TRRAP. Predicted target U2@U47. Only GU-rich region is
#=GF CC   homologous to other known snoRNAs. Conserved in vertebrates. 
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5



BL000002.1/98018519-98018714 AGAGAAGCAAAGUGAUGAGUAAUACUGGCUGGAGCCCCAAAGAGGCAC--GUGUGUGUGUUUGUGUGUGUGUGUAUAUGCUUGUCAGUGCAUGCACGUGUAUGUCUGGGAGUACAAAUGGGUGCGACUGGUUGUAGGGAACUAGCUAUGUGCCUUCUAUUAGGCCAUGACAGUCAAACUGAUAAGAUCUGAUUGCUUC
CABD02346228.1/166-363       AGAGAAGCAAAGUGAUGAGUAAUACUGGCUGGAGCCCCAAAGAGGCACAUGUGUGUGUGUUUGUGUGUGUGUGUAUAUGCUUGUCAGUGCAUGCACGUGUGUGUCUGGGAGUACAAAUGUGUGCGACUGGUUGUAGGGAACUAGCUAUGUGCCUUCUAUUAGGCCAUGACAGUCAAACUGAUAAGAUCUGAUUGCUUC
CAEC01407783.1/192-387       AGAGAAGCAAAGUGAUGAGUAAUACUGGCUGGAGCCCCAAAGAGGCAC--AUGUGUGUAUGUUUGUGUGUAUGUAUAUGCUUGUCAGUGCAUGCGUGUGUAUGUCUGAGAGUACAAAUGUGUGCGACUGGUUGUAGGGAACUAGCUAUGUGCCUUCUAUUAGGCCAUGACAGUCAAACUGAUAAGAUCUGAUUGCUUC
ACTA01089277.1/100029-99834  GGAGAAGCGAAGUGAUGAGCAUUACUAGCUGGAGCCCCAAAGAGGCAC--GUGUGUGUGUGUGUGUGUGUAUCUGUAUCCUUGUCUGUGCAUGCACACGUGUGUCUGGGAGUGUGAAUGUGUGUGACUGGUUGUAGGGAACUAGUUAUGUGCCUUGUGUUGGACCAUGACAGUCAAACUGAUAAGAUCUGAUUGCUUC
ABVD01872765.1/291-479       GGAGAAGCAAAGUGAUGAGCUUUACUGGCUGGAGCCCCA-GGAGGCAC--GUGUAUGUGUAUGUAUC--UGU----GUGCUUGUCUGUGCAUGCACAGGUGUGUCUGGGCGUAUGAAUGUGUGUGACUGAUUGUAGGGAAUUAGCUGUGUGCCUUCUGUUGGGCUAUGAUGGUCAAACUGAUAAGAUCUGAUUGUUUC
#=GC SS_cons                 :::(((((((---(((---------((((((,,,,<<<<-<-<-<<<<..<<<<<<<<--<<<---<<<<<____>>>>>---->>>->>>>>>>>>>>>->->->>>>,<<<<______>>>>,,<<<<<<______>>>>>>,<<<<-<<<<______>>>>>>>>,))))))----------)))---)))))))
#=GC RF                      aGAGaaGCaaAGUGauGAGuaaUACuGgCuGGAGCCCCaAaGaGgCac..GuGuguGugUcugUgUgcgugUgUacacgcUUGUcagUgCacgCaCguGuguGuCuGGGaguacaAAUGugugcGACugGuuGUAGGGaaCuaGcuauGUGcCuUcUaUUaGgCCaugACaGuCaAACUGAUAAGauCUGAuuGCuuC
//
# STOCKHOLM 1.0

#=GF AC   RF02724
#=GF ID   sno_ZL2
#=GF DE   Small nucleolar RNA ZL2
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   50.00
#=GF TC   50.90
#=GF NC   49.00
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23706177
#=GF RT   Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA
#=GF RT   core proteins and small RNA sequencing.
#=GF RA   Kishore S, Gruber AR, Jedlinski DJ, Syed AP, Jorjani H, Zavolan M
#=GF RL   Genome Biol. 2013;14:R45.
#=GF CC   Host gene TNPO2. Predicted target 28S@U4276, U4571. Previously described
#=GF CC   as SNORD41B.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6



AC018761.6/48391-48315     GGCCUCAAGUGAUGGAGAGCAAUACCCGGGGAUGACUGUGACCACAUUGGGAUGUAUUCGUACUGUCUGAUGGGGCC
CAEC01248628.1/1603-1530   GGCCUCAAGUGAUGGAGAGCAAUACCCAGGGAUGACUGUGA-C--AUUGGGAUGUAUUCGUACUGUCUGAUGGGGCC
AAPE02050986.1/14566-14492 GGCCUCAAGUGAUGG--AACAAUGACCAGGGAGGACUGUGACCGAACUAGGAUGUGUUCGUACUGUCUGAUGGGGCC
AAHY01072741.1/86035-86109 GGCCUCAAGUGAUGGAGA-C-AUACCCUGGGAGGCCCAUGACCGGACUGGGAUGUAUUCGUACUGUCUGAUGGGGCU
DAAA02019387.1/33502-33577 GGCCUCAAGUGAUGGAG-AUGACAACCUGGGAGUACUGUGACCGAACUGGGAUGUAUUCGUACUGUCUGAUGGGGCC
ACBE01053081.1/13693-13618 GGCCUCGAGUGAUGGAGAA-ACGACCCUGGGAGGACAAUGACCAAAUCGGGAUGUAUUCGUACUGUCUGAUGGGGUC
#=GC SS_cons               <<<<<<<---<<<<<---<<<<<<<<<-<<--<<________>>-->>->>-->>>>>->>->>>>>--->>>>>>>
#=GC RF                    GGCCuCaAGUGAugGAGAacaauacCCuggGAcGACugUGACCgaAccGGGAUguauuCguACugUCUGAuGgGGCC
//
# STOCKHOLM 1.0

#=GF AC   RF02725
#=GF ID   sno_ZL8
#=GF DE   Small nucleolar RNA ZL8
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   52.00
#=GF TC   52.10
#=GF NC   39.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23706177
#=GF RT   Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA
#=GF RT   core proteins and small RNA sequencing.
#=GF RA   Kishore S, Gruber AR, Jedlinski DJ, Syed AP, Jorjani H, Zavolan M
#=GF RL   Genome Biol. 2013;14:R45.
#=GF CC   Host gene C6orf48. No homologs outside of mammals. 
#=GF WK   Small_nucleolar_RNA
#=GF SQ   6



BA000025.2/106547-106465 UGGGAG-UGGUAAUGAUGAUCUGGUUGGACAAGAGUCUCUGAGCUUUUCUCUGAGGAUCUUUGAACCCACCUGAUCCACCUUCA
CAEC01451444.1/3050-3132 UUGGAG-UGGUAAUGAUGAUCUGGUUGGACUAGAGUCUCUGAGCUUUUCUCUGAGGAUCUUUGAACCCACCUGAUCCACCCUCA
ABGA01191011.1/5367-5285 UGGGAG-UGGUAAUGAUGAUCUGCUUGGACAAGAGUCUCUGAGGUUUUCUCUGAGGAUCUUUGAACCCACCUGAUCCACCUUCA
AANU01173885.1/1048-969  UUGGAG-UGGUAAU---GAUCUGGUUGGACUAGAGUCUCUGAGCUUUUCUCUGAGGAUCUUUGAACCCACCUGAUCCACCCUCA
AL773527.8/126210-126129 CCAGAG-UGGUAAUGAUGACCUGGUUGGACUAGAGUCUCUGAGCAUUUCUCUGAGGAUCUUUGAAACCACCUGAUCCA-CUCUA
AAQR03056232.1/1977-2058 UGGAGUCAGGUAAUGAUGAUCUGGUUGGACUAGAGUCUCUGAGCUUUUCUCUGAGGAACUUUGAAACCACCUGAUCC--ACUCA
#=GC SS_cons             ::<<<<.<<<--------<<<-<<<-<<--<<<<-<<<<-<<<_____>>>->>>>->>>>---->>->>>->>>>>>->>>>:
#=GC RF                  UuGggg.uGGUAAUGAUGauCUGGuUGgACaaGaGuCuCUGaGcuUUUCuCUGaGgAuCuuUGAAcCCaCCUGauCCaccccCA
//
# STOCKHOLM 1.0

#=GF AC   RF02726
#=GF ID   sno_ZL63
#=GF DE   Small nucleolar RNA ZL63
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   40.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23706177
#=GF RT   Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA
#=GF RT   core proteins and small RNA sequencing.
#=GF RA   Kishore S, Gruber AR, Jedlinski DJ, Syed AP, Jorjani H, Zavolan M
#=GF RL   Genome Biol. 2013;14:R45.
#=GF CC   Host gene FZD6. The authors call it a mini-snoRNA.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3



AC069351.5/37957-38002     AGCUGAAGAGCUGAUGAUGUUCCCCUAAAGCUGAAGCUCUUAAGCU
ABGA01077128.1/22957-22999 AGCUGAAGAGCUGA---UGUUCCCCUAAGGCUGAAGCUCUUAAGCU
AANU01123273.1/4120-4162   AGUUGAAGAGCUGA---UGUUCCUCUAAGGCUGAAGCUCUUAAACU
#=GC SS_cons               <<<<-<<<<<<<______________________>>>>>>>->>>>
#=GC RF                    AGCUGAAGAGCUGA...UGUUCCcCUAAgGCUGAAGCUCUUAAGCU
//
# STOCKHOLM 1.0

#=GF AC   RF02727
#=GF ID   sno_ZL116
#=GF DE   Small nucleolar RNA ZL116
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   82.00
#=GF TC   82.60
#=GF NC   49.30
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000275; small nucleolar RNA;
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   23706177
#=GF RT   Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA
#=GF RT   core proteins and small RNA sequencing.
#=GF RA   Kishore S, Gruber AR, Jedlinski DJ, Syed AP, Jorjani H, Zavolan M
#=GF RL   Genome Biol. 2013;14:R45.
#=GF CC   Host gene SUPT5H. 
#=GF WK   Small_nucleolar_RNA
#=GF SQ   5



ADDF011338994.1/3988-3917 UGGGCAUGUGAUGUGACCUUCCUGAGCCUGCAUUCCCUCACCUGGAAAUGAUGAGCAGUUACUGAUGCCACA
AC193191.3/151617-151546  UGGGCAUGUGAUGUGACCUUCCUGAGCCUGCAUUCCCUCACCUGGAAGUGAUGAGCAGUUACUGAUGCCACA
ADFV01060123.1/2136-2065  UGGGCAUGUGAUGUAACCUUCCUGAGCCUGCAUUCCCUCACCUGGAAAUGAUGAGCAGUUACUGAUGUCACA
CAEC01259586.1/1980-2050  UGGGUGUGUGGUGUGACCUUCCUGAGCCUGCAUUCCCUCACCUGG-AAUGAUGAGCAGUUACUGAUGUCACA
ACFV01107233.1/4420-4488  UGGGCGUGUGGUGUGACCUUCCUGAGCCUACAUUCCCUCACCUGGAAAUGA---GCAGUUACUGAUGUCACA
#=GC SS_cons              ::<<<<<-----<<<<<-----<<--<-<-<<<<-<<______>>->>>>>->-->>>>>>>-->>>>>:::
#=GC RF                   UGGgcaUGUGaUGUgACCUUCCUGAGCCUGCAuUCCCUCACCUGGAAaUGAUGAGCAGUuACUGAugcCACA
//
# STOCKHOLM 1.0

#=GF AC   RF02728
#=GF ID   HrrF
#=GF DE   Haemophilus regulatory RNA responsive to iron
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Santana et al, PMID:25157846
#=GF SS   Predicted; CMfinder
#=GF GA   77.00
#=GF TC   77.00
#=GF NC   45.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0045975; positive regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0010039; response to iron ion;
#=GF RN   [1]
#=GF RM   25157846
#=GF RT   HrrF is the Fur-regulated small RNA in nontypeable Haemophilus influenzae.
#=GF RA   Santana EA, Harrison A, Zhang X, Baker BD, Kelly BJ, White P, Liu Y,
#=GF RA   Munson RS Jr
#=GF RL   PLoS One. 2014;9:e105644.
#=GF CC   Involved in iron homeostasis in Haemophilus species. Orthologues exist
#=GF CC   only among other Pasteurellacae. It is an analog to PrrF and RyhB RNAs.
#=GF CC   HrrF is maximally expressed when iron levels are low. Ferric uptake
#=GF CC   regulator (Fur) binds upstream of the hrrF promoter. HrrF stability is not
#=GF CC   dependant on the RNA chaperone Hfq. RNA-seq has shown that that HrrF
#=GF CC   targets are mRNAs of genes whose products are involved in molybdate
#=GF CC   uptake, deoxyribonucleotide synthesis, and amino acid synthesis.
#=GF WK   HrrF_RNA
#=GF SQ   7



FQ312006.1/1350346-1350443 ACAUCUGUU------------------------------------AAGCGAUUGCAGGUUGCUCCA--ACAGGUAGAGUAGAAAGUAAAUUCGUUAGGGUU--CAAAAAGGCUGAAGGUUUAA-ACUUCAGCCUUUUUU
FQ312002.1/1295729-1295828 ACAUCUGUU---------------------------------UCGUAGCGAUUGCAGGUUGCUUCA--ACAGGUAGAGUAGAAAGUAAAUUCGUUAGGGUU---AAAAAGGCUGAAGGUUUAA-ACUUCAGCCUUUUUU
AE004439.1/147426-147558   ACAUCUGUUAGAGAUAAAGGUGGGAAUGAUAGAGUAGAUCGUUUUCAGUCUGAGU--CAUACUCCA-AACAGGUAGAGUAGAAAGUAAAUUCGUUAGGGUAUUUAU--GGGCUGAAGGUUUAA-ACUUCAGCCUUUUUU
CP000746.1/870985-871073   GUAUCUGUU------------------------------------AAGGCAU-AGAUGCUCCG-----ACAGGUAGAGUAGAAAGUAAAUUCGUUAGGGU------AAAAACUGAAGUUGUAUGACUUCAGUUUUU--U
CP001733.1/1977765-1977896 ACAUCUGUUAAGUAUUGCAAUGAAGAUGAA-CGGUAG-UCAUUGGAAGUCU--GCAUAGUACUCCA-AACAGGUAGAGUAGAAAGUAAAUUCGUUAGGGUAUUUGAAAAGACUGAAG-UUUAA-GCUUCAGUCUUUUUU
CP001607.1/1451194-1451326 CCAUCUGUUAAGUAUUGCAGUUGAGAUGAU-GGGUAG-UCAUUU-UGAAGUUUGCAUAGUACUCCAUAACAGGUAGAGUAGAAAGUAAAUUCGUUAGGGUAUUU-AAAAGACUGAAG-UUUAA-ACUUCAGUCUUUUUU
CP002276.1/1248713-1248598 AUAUCUGUUACUAUACACACAUCUG-----------------UU-AAGCGAUUGCAGGUUGCUCCA--ACAGGUAGAGUAGAAAGUAAAUUCGUUAGGGUU--CAAAAAGGCUGAAGGUUUAA-ACUUCAGUCUUUUUU
#=GC SS_cons               ::<<<<<<-----------------...._.______.....--,-<<<<<<_____>>>>>>---..>>>>>>,,,,,,,,,,,,,,<<<<____>>>>,,,,<<<<<<<<<<<<<______._>>>>>>>>>>>>>:
#=GC RF                    acauCUGUUAaauauuacaauuaag.................Uu.aaGcgccuGcAuggcgCucCA..ACAGguAGAGUAGAAAGUAAauuCGUUAGggua..uaaaaaGgCUGaaGgUUUAA.ACuuCAGcCuuuuuU
//
# STOCKHOLM 1.0

#=GF AC   RF02729
#=GF ID   JA01
#=GF DE   Aggregatibacter sRNA JA01
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   111.00
#=GF TC   111.80
#=GF NC   42.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010039; response to iron ion;
#=GF RN   [1]
#=GF RM   22958383
#=GF RT   Novel iron-regulated and Fur-regulated small regulatory RNAs in
#=GF RT   Aggregatibacter actinomycetemcomitans.
#=GF RA   Amarasinghe JJ, Connell TD, Scannapieco FA, Haase EM
#=GF RL   Mol Oral Microbiol. 2012;27:327-349.
#=GF WK   Aggregatibacter_iron-regulated_sRNA
#=GF SQ   3



FJ664179.1/451-603         GAUGAUAUACCAAAAUGGUUUAUUUUAUUUUGAUGUAGAAAUUGAAUUUGAUAUAGUGCGUAGAUAACAAAUAAAAGUUCUUUAUCAAAUAAAAAAUUAGUAUAACUAUACCUUAUUUCAAAAUGAAGGAGGUAUAGUACCAUCUCAAUAUUU
ADOB01000022.1/39363-39211 GAUGAUAUACCAAAAUGGUUUAUUUUAUUUUGAUGUAGAAAUUGAAUUUGAUAUAGUGCGUAGAUAACAAAUAAAAGUUCUUUAUCAAAUAAAAAAUUAGUACAACUAUACCUUAUUUCAAAAUGAAGGAGGUAUAGUACCAUCUCAAUAUUU
AEJQ01000114.1/7195-7044   GAUGAUAUACCAAAAUGGUUUAUUUUAUUUUGAUGUAGAAAUUGAAUUUGAUAUAGUGCGUAGAUAACAAAUAAAAGUUCUUUAUCAAAUA-AAAAUUAGUAUAACUAUACCUUAUUUCAAAAUGAAGGAGGUAUAGUACCAUCUCAAUAUUU
#=GC SS_cons               ((((,,,,,,<<<<<<<<______>>>>>>>>,<<<<--<<<<--<<<<<<<<-<<-<<_________________>>->>->>>>>>>>---->>>>-->>>><<<<<<<<<<--<<<<___>>>>->>>>>>>>>>,,)))):::::::::
#=GC RF                    GauGAUAUACCaaaauggUUUAUUccauuuuGAuguaGAaauuGAauuuGauaUaGUgCGUAGAUAACAAAUAAAAGcUCuUuauCaaauAAAAaauuAGuacaaCuauaCCucAUuuCaAAAuGaaGgaGGuauaGuACCauCUCAAUAUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02730
#=GF ID   JA02
#=GF DE   Aggregatibacter sRNA JA02
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   49.00
#=GF TC   49.00
#=GF NC   48.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010039; response to iron ion;
#=GF RN   [1]
#=GF RM   22958383
#=GF RT   Novel iron-regulated and Fur-regulated small regulatory RNAs in
#=GF RT   Aggregatibacter actinomycetemcomitans.
#=GF RA   Amarasinghe JJ, Connell TD, Scannapieco FA, Haase EM
#=GF RL   Mol Oral Microbiol. 2012;27:327-349.
#=GF WK   Aggregatibacter_iron-regulated_sRNA
#=GF SQ   4



FJ664181.1/95-210          CAAGUACUAAAUUUUUUACUUGAAUUAUUGACAUAAAAUAACUGCUUAUAAACCAAG-AAGAAUUUUUUGCGUGGUAAAAAUCGCAUUAUU-AAAAUUUGUGUAAAGGGACAAAUUUU
AEJN01000022.1/11402-11286 CAAGUACUAAAUUUUUUACUUGAAUUAUUGACAUAAAAUAACUGCUUAUAAACCAAG-AAGAAUUUUUUGCGUGGUAAAAAUCGCAUUAUUAAAAAUUUGUGUAAAGGGACAAAUUUU
AEJM01000010.1/53143-53258 CAAGUACUAAAUUUUUUACUUGAAUUAUUGACAUAAAAUAACUGCUUAUAAACCAAG-AAGAAUUUUUUGCGUGGUAAAAAUCGUAUUAUU-AAAAUUUGUGCAAAGGGAUAAAUUUU
CP001607.1/699770-699886   CAAGCAUUAAAUUUUUUACUUGAAUUAUUGACAUAAAAUAACUGCUUAUAAAUUAAGGAAGAAUUUUUCGAAGGGUGAAUAUUGCGUAAGU-AAAUUUUGUGUAACCACAUGAAUUUU
#=GC SS_cons               :::<<<--<<<<<<<<--<<<<--<<<<---<<_________>>--->>>>-->>>>.>>>>>>>>-->>><<<<<____>>>>>,,,,,,.<<<<<<<<<________>>>>>>>>>
#=GC RF                    CAAgcacUaaauuuuuUACuuGAAuuauUGACaUAAAAUAACuGCUUauaaAcCaaG.aagaauuuUUugcgcGguaAAaauCgcaUuAuU.aaaauuuguGuAAagggacaaauuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02731
#=GF ID   JA03
#=GF DE   Aggregatibacter sRNA JA03
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   44.00
#=GF TC   44.30
#=GF NC   43.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010039; response to iron ion;
#=GF RN   [1]
#=GF RM   22958383
#=GF RT   Novel iron-regulated and Fur-regulated small regulatory RNAs in
#=GF RT   Aggregatibacter actinomycetemcomitans.
#=GF RA   Amarasinghe JJ, Connell TD, Scannapieco FA, Haase EM
#=GF RL   Mol Oral Microbiol. 2012;27:327-349.
#=GF WK   Aggregatibacter_iron-regulated_sRNA
#=GF SQ   3



FJ664180.1/54-327          GCUUACACUUCUAAAUAAGUCUUGAUAAAUCAAUAUUUAUUGAUGUUACAAGGCUUUAUUUCUUCAGUUUUCAUCACGUUUAACUAGUAAUAGUGACCUUUGAAUAACUCUGUGUUUUCAUUAAAUCGUAGUGUUCAUUUACUUUGUCACUAAUUUCGCAUAACAUAUAUUAUGUUAAAUAAAAUAAAUGGUAAGUCACUUCUGGGAAUUUGAGGUUUGCUCUCUUUAAAAAUGACUGGGUAAAAAAAUUUAUUUCUUGAAGAUUUGAUUUUUU
CP001733.1/1256479-1256752 GCUUACAUUUUUAAAUAAGUCUUGAUAAAUCAAUAUUUAUUGAUGUUACAAGGCUUUAUUUCUUCAGUUUCCAUCACGUUUAACCAGUAAGAGUGGCCUGUGAAUAACUCUGUGUUUUUAUUAAUCCGUAGCGUUUAUUAACGAAGUCACUAACUUCGCAUAAUUUAUAUUAUGUUAAAUAAAAUAAAUGGUAAGUCACUUCUGGGAAUUUGAGGUUUGCUCUCUUUAAAAAUGACUGGGUAACAAAAUUUAUUUCUUGAAUAUUUGAUUUUUU
ADOC01000028.1/36770-36497 GCUUACAUUUUUAAAUAAGUCUUGAUAAAUCAAUAUUUAUUGAUUUUACAAGGCUUUAUUUCUUCAGUUUCCAUCACGCUUGACUAGUAAGAUUGACCUGUGAAUAACUCUGUGUUUUUAUUAAUCCGUAGCGUUUGUUAACGAAGUCACUAACUUCGCAUAACUUAUAUUAUGUUAAAUAAAAUAAAUGGUAAGUCACUUCUGGGAAUUUGAGGUUUGCUCUCUUUAAAAAUGACUGGGUAAAAAAAUUUAUUUCUUGAAGAUUUGAUUUUUU
#=GC SS_cons               ((((((,,,,,,<<<<<<<<<<<<----<<<<<<____>>>>>>---->>>>>>->>>>>>,,,,<<<<____________>>>>,,,,,<<<<<<<---<<<<<<<<-<<<<<<<<_____>>>->>>>>->>>->>>>>---->>>>>>><<<<-<<<<<<______>>>>>>->>>>,,,,,,,,,,))))))--<<<<-<<<<<<------<<<<<<<_______________>>>>>>>------->>>>>>->>>>::::::::::::
#=GC RF                    gCuuaCAuUUuUaaauaaGuCuuGAUAAauCaauAUUUauuGaugUUACaaGgCUuuauuuCUUCaGuuUcCAUCACGuUUaaCuAGUAAcaguGaCCUgugaauaaCUCuguGuuuUuAUUaaacCguaGcGuuuauucaCgaaGuCacugacuuCgCauaacuUAUAuuauGuUaaguAAAAUAAAUGGuaaGuCAcuuCUgGgaauUUGAGGuuugCuCUCUUUAAAAAUGACUGgGuaaaAAAAUUUauuuCuUGaagAUUUGAUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02732
#=GF ID   JA04
#=GF DE   Aggregatibacter sRNA JA04
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   81.00
#=GF TC   81.40
#=GF NC   65.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010039; response to iron ion;
#=GF RN   [1]
#=GF RM   22958383
#=GF RT   Novel iron-regulated and Fur-regulated small regulatory RNAs in
#=GF RT   Aggregatibacter actinomycetemcomitans.
#=GF RA   Amarasinghe JJ, Connell TD, Scannapieco FA, Haase EM
#=GF RL   Mol Oral Microbiol. 2012;27:327-349.
#=GF WK   Aggregatibacter_iron-regulated_sRNA
#=GF SQ   6



FJ664182.1/115-195         GCAACUUGCAGUUGUU-UUAAUAAAAUUGGUUCCUUAGGUUAUU-UGCCUCUCUUCGUGAGAGGCAUUUUUUUUAUGUAUUUU
CP001733.1/168302-168381   GCAACUUGCAGUUGUU-UUAAUAAAAUUGGUUCCUUAGGUUAUU-UGCCUCUCUUCGUGAGAGGCAUUU-UUUUAUGUAUUUU
ADOB01000043.1/29897-29818 GCAACUUGCAGUUGUU-UUAAUAAAAUUGGUUCCUUAGGUUAUU-UGCCUCUCUUCGUGAGAGGCAUUU-UUUUAUGUAUUUU
CP001607.1/1899801-1899722 GCAACUUGCAGUUGUU-UUAAUAAAAUUGGUUCCUUAGGUUAUU-CGCCUCUCCUCGUGGGAGGCAUU-UUUUUACCCAUUUU
AE004439.1/1243932-1244013 GCAACUUGCAGUUGUUUUUAAUAAAAUUGGUUCCUUAGGUUAUU-CACCACCCAUCUUGGGUGGUGUUUUUUUUUUAGCAUGU
L42023.1/509202-509121     GCAACUUGCAGUUGUU-UUAAUAAAAUUGGUUCCUUAGGUUAUUUGCCCCACGUUUAUUGUGGGGCUUUUUCUUGCGCAUUUU
#=GC SS_cons               <<<<<<___>>>>>>-.---------------------------.<<<<<<<<_____>>>>>>>>:::::::::::::::::
#=GC RF                    gCAACUUGCAGUUGuU.UUAAUAAAAUUGGUUCCUUAGGUUAUU.cgCCucccuUcgUgggaGGcgUUUUUUUUauguAUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02733
#=GF ID   ToxT_thermometer
#=GF DE   ToxT 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:25228776;
#=GF GA   81.00
#=GF TC   81.00
#=GF NC   35.70
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   25228776
#=GF RT   RNA thermometer controls temperature-dependent virulence factor expression
#=GF RT   in Vibrio cholerae.
#=GF RA   Weber GG, Kortmann J, Narberhaus F, Klose KE
#=GF RL   Proc Natl Acad Sci U S A. 2014;111:14241-14246.
#=GF CC   Controls temperature-dependant translation of toxT, facilitating V.
#=GF CC   cholerae virulance. At human body temperature, the thermometer structure
#=GF CC   opens and to allow transcriptional activator protein ToxT translation. 
#=GF WK   FourU_thermometer
#=GF SQ   3



L01623.1/1218-1288         UCGAUUUUAAGAUAACUUUACGUGGAUGGCUCUCUGCGUUUAUUUAUA-------UAUCUUCAGAGUAGAACGCAAUG
ACYV01000002.1/98152-98229 UCGAUUUUAAGAUAACUUUACGUGGAUGGCUUUCUGCGUUUAUUUAUUAUUUAUAUAUCUUCAAAGUAGAACGCAAUG
AAKI02000075.1/2726-2796   UCAAUUUUAAUACAACUUUACGUGGAUGGCUCUCUGCGUUUAUUUAUA-------UAUCUUCAGAGUAGAACGCAAUG
#=GC SS_cons               <<-<<<<<<<<<<<-----<<<<<<<______>>>>>>>---------.......>>>>>>->>>>>->>::::::::
#=GC RF                    UCgAuUuUAAgAuAACUUUACGugGAUGGCUcUCugCGUUUAUUUAUa.......UaUcUUCAaAgUAGAACGCAAUG
//
# STOCKHOLM 1.0

#=GF AC   RF02734
#=GF ID   Cgb105
#=GF DE   Corynebacterium sRNA 105
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   163.00
#=GF TC   163.50
#=GF NC   32.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009408; response to heat;
#=GF RN   [1]
#=GF RM   24138339
#=GF RT   Comprehensive discovery and characterization of small RNAs in
#=GF RT   Corynebacterium glutamicum ATCC 13032.
#=GF RA   Mentz A, Neshat A, Pfeifer-Sancar K, Puhler A, Ruckert C, Kalinowski J
#=GF RL   BMC Genomics. 2013;14:714.
#=GF CC   Absent under heat stress conditions. 
#=GF WK   Corynebacterium_glutamicum
#=GF SQ   2



BA000036.3/10053-9921 GUUGUGAUUGCAGUGACUGAUGUGGUUUUCAGUUUCUGUGGAGGAAGGGUUGCAACGCUUUUUCAAGAGAAUGACCGUGCGUCCGCUUAAA-CGAAGCGUCGAACGCCGGUCUUUUCUCAUUUCACUUAAGAUG
AP009044.1/10054-9921 GUUGUGAUUGCAGUGACUGAUGUGGUUUUCGGUUUCUGUGGAGGAAGGGUUGCAACGCUUUUUCAAGAGAAUGACCGCGCGUCCGCUUAAAUCGAAGCGUUGAACGCCGGUCUUUUCUCAUUUCACUUAAGAUA
#=GC SS_cons          :::((((,,<<<<-<<<<<<________>>>>>>->>>>,<<<<<<<-<<____>>->>>>>>>,,<<<<<-<<<<<-<<<<<<<<<<______>>>>>-->->>>>>>>>>-->>>>>,,,))))::::::::
#=GC RF               GUUGuGaUUgCaGUgaCcGaUGUGGUUUuCgGucUCuGcGGaggaaGGGuUGcAaCGCuuccuCAAGaGaaUGaCCGuGCGuCCGCuuAAAucGaaGCGUuGAaCGCCGGuCUUuuCuCAUUuCaCUUAAGAUa
//
# STOCKHOLM 1.0

#=GF AC   RF02735
#=GF ID   Sernc350
#=GF DE   Saccharopolyspora sRNA 350
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   50.00
#=GF TC   50.60
#=GF NC   39.30
#=GF TP   Gene; antisense; 
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 1900376; regulation of secondary metabolite biosynthetic process;
#=GF RN   [1]
#=GF RM   24236194
#=GF RT   Prediction and characterization of small non-coding RNAs related to
#=GF RT   secondary metabolites in Saccharopolyspora erythraea.
#=GF RA   Liu WB, Shi Y, Yao LL, Zhou Y, Ye BC
#=GF RL   PLoS One. 2013;8:e80676.
#=GF CC   Probably regulates terpene metabolism.
#=GF WK   Saccharopolyspora_erythraea
#=GF SQ   2



AM420293.1/4361402-4360896 UUGAUGGUGUACUCCCAGUCGGAGUCGCCGUC---CCCCAGCACCUGGGCGCCGAAGUACUCGCCGUCGGCCAUCACGUCGAGCACGGUCUGGUCGCCGUACUCGCCCCUGCCGAUCUUGUUGACCUUCCCGUGCGCCAGCAGGU-AGACGGCGUCCGCCCGGUUGCCCGCCUCGGCGAUCACGUCACCGGGCUCGAACUCCUCCUGGCGGAACCGGUCGGCCAGCGCGGUGAGCGCGUCCUCGUCGUCGAAUCCGCGCAGCAGCGGCAGCUCGCACAGCUCGUGGGGGAUGACCCGGAUCUCGGCGCCGGUGUUGGUGAAGGUGACCCUGCCGUCGCCGAUGACGUAGCUCAGCCGGCGGUUGACCCGGUAGGUCCCGCCGGGGGUGUGCACCCAGGGCAGCAUGCGCAGGAGCCAACGCGAGGUGAUGCCCUGCAUCUGCGGAGCGGACUUGGUCGUGGUUGCCAGGUUCCGCGCCGCGGCCGUACCCAGGCUCAGCUGGGAACGC--CCG
AEYC01000066.1/4818-4311   UUGUAGGUGUGGUUCCAGGUGG--UCGUU-UCGCGGCCGAGGAUGUGCGCGCCGAAGUACUCGCCGUCGGCGAGCACGCCGAGGACGGUGUCGUCGCCGUACUCGCCGGUGCCGAUCUUGUUGAUCUUGCCGU-GUGCGAUGAGCACGACCUGGUCCGCCGGUUGCCCGGCGGUGGCGAUGACCUGGCCCGGCUCGAGCCCACCCUGCCCGAAGCGGUCGGCCAGGGCGGCCAGCACCGUAUCGUCGUCGAAUCCGCGCAGCAGCGGCAGUUCCCGCAGUUCUUGCGGGAUGACCCGGAUGUCGGCGCCGGUGUUGGUGAAGGUGACCCGUCCGUCGCCGAGGGUGUAGCUCAGCCGCCGGUUGACCCGGUACGCGCCGCCCGAGGCCUGCACCCACGGCAACAUCCGCAGCAGCCACCGCGAUGUGAUGCCCUGCAUCUGCGGGACGGAUUUCGUCGUCGUGGCCAGGUUCCGCGCCGCCGCCGUACUCAGGCUCAACGGCG-ACGCUUCGG
#=GC SS_cons               :::::{{{{{{{-{{{,[[-[[-.[[[[[-[[-----[[[[[[[[--[[[[[[[[,((-((((((((<<<<------<-<<<<-<<<<<______>>>>>->>>>>---->>>>,,,,,<<<<-<<--<<-<<-<<<<<<-<<<--<<----<<---<<<<<<<<<--<<<____>>>-->>---->>>>>>>->>-->>>>>->>>>>>-->>->>-->>->>>>))))))))-))<<<<--<<<<<<---<<<<<<-<<<-<<<______>>>--->>>>>>>>>->>>>>>-->>>>,]]]]]]]]]]]]]]]]-]]-]]]]]-]]-]]<<<<______>>>>,,,,,,,,<<<<<<<--<<<<_____>>>>>>>>>>>}}}-}}}}}}}<<<<<<<-<<<-<<<-<_______>>>>-->>>->>>>>>>,,,,,<<<<-<<<<<<<<<<<_______>>>>>>->>>>>->>>><<-<<<-<<<<<______>>>>>->>>--->>:
#=GC RF                    UUGaaGGuGcggUcCcAGguGG..uCgcc.uCgcggCCcagcaccUGgGCGCCGaAGcACucgCCGcCGGCgAuCACGuCGaGgaCGGcgUgGUCgCCGuACuCGCCggUGCCGAUCUUgcuGAcCUUcCCgu.gggCgguggGuAgGACgucGUCCGCCgGgcugCCcGCguuGGCgAUcaCgUggcCcGGCUCgAaCcCccCccGcccGAacCGgUCGgCCagcgCGGcgaGCgCguccUCGuCguCGAAccCgcGCagCAGcGGCAGuUCgCaCAGcuCgcGggGGacGaCCCggacguCGGCGCcggugcugGUGaAggcGaCCCucCCgcCGCCGAuGgcGUAGCUCAGCcGgCGGUUggCcCGGUAgGccCCGcCgGgGguccgCaCCCagGGCaaCacgCGCAGgAGCCAaCGCGAuguGAuGCCcuGCAUCUGCGGagCGGaccugGcCGUgGUugCcaggUuCCGcGCCGCgGCCGuACcCaGGCUCAaCuGgG.aCGCuuCcG
//
# STOCKHOLM 1.0

#=GF AC   RF02736
#=GF ID   Rev11
#=GF DE   Soft rot Enterobacteriaceae Rev 11 asRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   91.30
#=GF TC   91.30
#=GF NC   91.20
#=GF TP   Gene; antisense; 
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009267; cellular response to starvation;
#=GF RN   [1]
#=GF RM   26753530
#=GF RT   Discovery and profiling of small RNAs responsive to stress conditions in
#=GF RT   the plant pathogen Pectobacterium atrosepticum.
#=GF RA   Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PR, Moleleki
#=GF RA   LN
#=GF RL   BMC Genomics. 2016;17:47.
#=GF CC   From bacteria cultured under starvation conditions. Antisense to ECA3028. 
#=GF WK   Soft_rot_Enterobacteriaceae_(SRE)_small_RNAs
#=GF SQ   3



BX950851.1/320156-319740 AGAUUAUUAAUCGUGGUAUCCAGCGGUUUGAUGUACAGGCUGUUAUUAUUCAGCGCGAUAUCGCCACUGGCGCGGACAUCGUCACCGACAAGCGGAAUAUCCAGAUGCAGUGUGCCUUUCACCGGCCCGCCAAUUUUCAGCUCAUCCAGCGCGGUACCCAGCGAGGAUUUCAGCGGCGUCUGAUGAAAAUAAUUACCCACUUCAGGCCCUGGACCAUCCAGUUCGCCAUCAAUAAGCAGCAUCUCUUUUUCAUAAUCAGGAAUGACCGCGCUAAUAUUUUUGCCUUCCACCUUACCCAGCCAGAUUUGCGGCGCAAACAUCCACAGACCGUUAUUGGCAAAAUCCAAAUUGAUAUCCAGCGGCGUCAGCGCAGGCCAGCCCGGCUGGAACUCAAAGGUGGCAUCCUUAACCGGCACC
CP001657.1/303218-302802 AGAUUCUUAAUCGUGGUAUUCAACGGUUUGAUGUACAGGCUGUUAUUGUUCAGCGCAAUGUCACCACUGGCGUGAACAUCAUCACCGACAAGCGGAAUAUCCAGAUGCAGCGAGCCUUUCACUGGCCCGCCAAUUUUCAGUUCAUCCAGCGCCGUACCCAACGAGGAUUUCAGCGGUGUUUGAUUAAAAUAGUUCCCCACUUCAGGCCCCGGACCUUCCAGCUCGCCAUCAAUGAGCAGCAUCUCUUUUUCAUAAUCGGGAAUGACCGCGCUAAUAUUCUUGCCUUCCACCUUGCCCAACCAGGUUUGUGGCGCAAACAUCCAUAGACCGUUGUUGGCGAAAUCCAGAUUAAUAUCCAGUGGCGUCAGCGCAGGCCAGCCCGGCUGAAACUCGAAGGUCGCCCCUUUCACCGGCACC
CP001790.1/302079-301663 AGAUCCUUAAUCGUGGUAUCCAAUGGCUUGAUGUACAGGGUGUUAUUGUUCAGCGCAAUGUCACCACUGGCGCGGACAUCAUCACCAACCAGUGGGAUAUCCAGAUGCAGCGAGCCUUUCACCGACCCGCCAAUUUUUAGUUCAUCCAGCGCCAUACCCAGCGAGGAUUUCAGCGGCGUCUGAUGGAAAUAGUUGCCCACCUCCGGUCCUGGACCGUCUAGCUCACCAUCAACGAGCAGCAUCUCUUUUUCAUAAUCGGGAAUAACCGCGCUAAUAUUUUUGCCUUCAACCUUACCCAGCCAGGUUUGUGGCGCAAACAUCCACAGACCGUUGUUAGCAAAAUCCAGAUUGAUAUCCAGCGGCGUCAGCGCAGGCCAGCCCGGUUGAAACUCGAAAGUCGCCUCUUUCACUGGCACC
#=GC SS_cons             ::::{{{{{--{{{{{{,,<<<<-<<<--<<<<<-<--<<<<________>>>>-->>>>>>>>>->>>><<--<<<___>>>-->>,,,,,,<<<___>>>[[[[[[,<<<-<<<_______>>>->>>,,,,,,,,,<<<-<<<<--<<<________>>>->>>>--->>>(((<<<<<<__________________>>>>>>,<<<<<___>>>>>,,,))),,,,,,,,,,,]]]]]],,,,,,<<<________>>>}}}}}}-}}}}}----((((--(((((((,,,,,<<<<<----<<<<<_____________>->>>>-->>>>>,,,,,,,,,,,<<<--<<<<<<<<-<<--<<____>>-->>>>->>>>>>-->>>)))))))-----------))))::
#=GC RF                  AGAUuauuaAUCGuGGuAUcCagcGGcUUGacguAcAGGcuGUUAUUgUUCagCGCgauguCgCCAcuGgcGcGgacAUCgucACCgACaAGcGGaAUAuCCaGauGCAGcGaGcCUUUCACcGgCCCgCCAAUUUUcAGcuCauCCAGCGccgUACCCAgCGAGGauUUCagCGGcgucuGaUgaAAAUAgUUaCCCACuuCaggcCCugGaCCauCcaGcUCgCCAUCAAugAGCAGCauCuCUUUUUcauAAUCgGGAaugaCCgCGCuaauaUUuUuGCCUUCcaCcuuaCCCAgCcaggUUUgcGGCGCAAACAUCCAcAGACCguUguugGcaAAAUCCAgAUcgaUAucCagcGGCGuCAGCGCAGGCCAgCCCGgcuGgaACucgaagGugGCcuCuUUcACcGGCaCC
//
# STOCKHOLM 1.0

#=GF AC   RF02737
#=GF ID   Rev13
#=GF DE   Soft rot Enterobacteriaceae Rev 13 asRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   242.00
#=GF TC   242.60
#=GF NC   50.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009267; cellular response to starvation;
#=GF RN   [1]
#=GF RM   26753530
#=GF RT   Discovery and profiling of small RNAs responsive to stress conditions in
#=GF RT   the plant pathogen Pectobacterium atrosepticum.
#=GF RA   Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PR, Moleleki
#=GF RA   LN
#=GF RL   BMC Genomics. 2016;17:47.
#=GF CC   From bacteria cultured under starvation conditions. Antisense to ECA0388.
#=GF WK   Soft_rot_Enterobacteriaceae_(SRE)_small_RNAs
#=GF SQ   3



BX950851.1/439646-439293   AAAUAACUCUUCGGUAAUCAUGAAGCCGUGAAGCCGCGAUUUUAAUGUCUAUUAGGAAAAAUCCCAAUAAACAUAAGCGGACUAAUAAUAAAAAGAGAUUAUUCUCUGAUUUUUUUAUUUAUCGCGAGAGAUUCUACAAGAAGUUUUUAAUAGGAUGAUAUUUAACGCAUUCCC-G-UUAAUCGUCUGACUACGCUACUCAUCCUUUCCGCCUCAAAUUAACGUUCGUAAAAUCAGCAAAAAACGAGGAUUUUUCGUUCAUA--UACCUAACAAGAAAGCCGAUAGUGCGCCGCUAUAUUCGCGCACUAUCGACAUCAGACAGGGGUUAAUUCGGGGUUGAGAAUCAAGAGUUGGGGA
ABVX01000041.1/13017-12667 AAAUAACUCUUCGGUAAUCAUGAAGUCGUGAAGCCGCGAUUUUAAUGUCUAUUAGGAAAAAUCCCAAUAAACAUAAGCGAACUAAUAAUAAAAAGAGAUUAUUGUCUGGUUUUUUUAUUUAGCGCGAGAGAUUCUACAGAUAGUUUUUAAUAGGAUGAUAUUUAACGUAUUCCU-G-UUAAUCGUCCGGCUACGCAGUUCAUGCUUUUCACUCGAUAUUCACGUUUAUAAAAACAACAAAGCACG--CUUUUUUUGCUCAAAAAUAUCUUGUC-GGAAGGAGAUCGUGUGCGGUGACA-CCGCACACGAUUGACACAAAGC-AGGGUUAAAUCGGAGAUGAGAAUCGAGAUCGGAGGA
CP001657.1/432149-431799   AAAUAACUCUGCGGUAAUCAUGAAGUCGUGAAGCCGCGAUUCUAAUGUCUAUUAGGAAAAAUCCCAAUAAACAUGAGCGGACUAAUAAUAAAAAGAGAUUAUUCUCUGAAUUUUUUAUUUAUCACGAACGAUUCUACAGACAGUUUUUAAUAGGAUGAUAUUUAACGAAUUCCCUGCCUAAGUGCUUUACCACAUUUCCCAUACUCCCAGAGUGAAAUAGGCGCGUAUAAAAACAGCAAAAAAUGGA---UUUUUGCUCAUA--UUUCUAGCAAGGAAA-GGAUCGUGUGU-GAUAUCACCACACACGAUCGACAUUAGACAGGGGUUAGGUCGGGGUUGAGAAUCAGGAGUUGAGAA
#=GC SS_cons               :::[[[[[[[[<<<<--<<<<<____>>>>>->>>>,,,,,,,,<<<<-<<<<-<<<____>>>->>>>->>>>,,<<<<---<<<<<-<<<<<<<<<____>>>>>-->>>>->>>>>-->>>><<<<<-<<<<___>>>>->>>>>,,,,((((((,,,<<<<<<______>.>.>>>>,<<<______>>>,,,,))))))((((-(((((-(((((((<--<<-<<<<<<--<_______>-->>>>>>->>-->,,,..,,<<<-----<<----<<<<<<<<<<<__________>>>>>>>>>>>--->>----->>>)))))))-)))))-)))),,,]]]]]]]]::::
#=GC RF                    AAAuaacuCucCGGuAAuCauGAAGuCguGaAgCCGCGAUUuUAauGuCuauuAGGaAAAAuCCCaauaAaCauaAGcGgACUaauaaUaaaaaGagaUUAUucuCuGauuuuUuuauuUAcCgCgagagAuuccACAggaaGuucuuAAUAGgauGaUAUuuaaCGuAUUCCC.G.uuaaucGucugaCuaCgcuacuCaucCucuccgccccAaauuaaCGuucgUaaaaccAgCAAAaaAcGaagguuuuUcgcUCAuA..UacCcagcaAggAAggcGaucGuGcGcgGuuAuaacCgCgCaCgauCgACAccAgaCAgGgGuuaauuCggggcUgagaAUCgaGaguugaGgA
//
# STOCKHOLM 1.0

#=GF AC   RF02738
#=GF ID   Rev24
#=GF DE   Soft rot Enterobacteriaceae Rev 24 asRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   246.00
#=GF TC   246.50
#=GF NC   230.30
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009267; cellular response to starvation;
#=GF RN   [1]
#=GF RM   26753530
#=GF RT   Discovery and profiling of small RNAs responsive to stress conditions in
#=GF RT   the plant pathogen Pectobacterium atrosepticum.
#=GF RA   Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PR, Moleleki
#=GF RA   LN
#=GF RL   BMC Genomics. 2016;17:47.
#=GF CC   From bacteria cultured under starvation conditions. Antisense to rcsC. 
#=GF WK   Soft_rot_Enterobacteriaceae_(SRE)_small_RNAs
#=GF SQ   4



BX950851.1/1367508-1367020     GGCUGGUCAUGACAUCGACAAACUUGGACUGCUGCUUGCAAAUGAUGCGGGUAAUUCGUAAUCUGUCUUCGUGGGUCAGUAGGUUGAGAUAGUUGUGCGCCAGCUCGUUACUGAGGAUGUUCGUGCCGUCAUUAAUACGCAGGAUGCAAAUCCCUACUGGCGCCGACGCCACAAUCUUGCGGUUGAAUUGCUCAUUCUCUUCCAACUGGAACGCAUUCACUUCCGCAGGCAACAGCAUUUUCCGCUCAAAUACCAAAGCCAACACAAACAGAAAAAUUGCCCAUAGAAUAUUCAGUACAAGCAUGUUAAUCAUCAAUGCGCUGAUAUGAGAGAGCAGGACUUUCAACGGCAGCGCAUACACGAUGCUGAAUGACGUCGGCGGCAGCGACUUUUUCAGAAUGAGUUCAUCAUACCCAUUCACAUAGCCAAAAUAGUUAUGAUCGGAAGGAUAACUGUCUACCGAAGACGUAUAGCGAUCUUUAGCAUCGG
CP001657.1/1293377-1292889     GGCUGGUCAUGACAUCCACAAACUUGGACUGCUGCUCGCAAAUGAUACGGGUAAUGCGCAGCCUGUCCUCGUGGGUCAGCAGGUUGAGAUAGUUAUGCGCCAGUUCGUUACUGAGGAUGUUCGUACCGUCAUUGAUACGCAGGAUACAAAUUCCUACCGGUGCCGAAGCCACAAUUUUGCGGUUGAAUUGCUCGUUCUCUUCCAACUGGAACGCAUUCACUUCCGCUGGCAACAGCAUUUUCCGCUCAAACACCAGCGCCAGCACAAACAGCAAGAUAGCCGAUAGCAUAUUCAGCACUAGCAUAUUGAUCAUCAAGGCGCUGAUAUGGGAGAGCAGCACCUUUAACGGCAGCGAAUACACGAUACUGAAUGACGUCGGCGGCAGCGACUUCUUCAAAAUGAGUUCAUCAUAACCAUUCACAUAGCCGAAAUAGUUAUGAUCGGAGGGAUAGCCAUCUACCGACGAAGCGUAACGCCCUUUAUCAUCGG
CP001790.1/3501394-3501882     GGCUGGUCAUCACAUCCACAAACUUGGACUGCUGCUCGCAAAUAAUGCGGGUAAUUCGCAGCCUGUCUUCGUGGGUAAGCAAAUUGAGAUAGUUAUGCGCCAGUUCGUUACUGAGGAUAUUGGUGCCGUCACUAAUACGCAGAAUACAGAUGCCUACCGGUGCCGACGCCACGAUCUUACGGUUAAAUUGCUCGUUCUCUUCCAGUUGAAACGCAUUCACUUCUGCAGGCAACAGCAUUUUCCGCUCAAACACCAGCGCCAACACGAACAAUAGAAUCGCCGAGAGGAUAUUCAGCACCAGCAUGUUGAUCAUCAAUCCGCCGAUAUGGGACAGCAGCACCUUCAGCGGCAGCGAGUACACAAUACUGAACGAAGUCGGCGGCAGCGCCUUCUUCAGAAUGAGUUCGUCAUAACCAUUCACAUAGCCAAAAUAGUUAUGCUCGGAGGGAUAGCCGCCUACCGAGGAAACAGAGAGCCCUUUGUCAUCGG
AFWW01000010.1/2263313-2263801 UGCUGGUCAUCACAUCGACGAAUUUGGAUUGCUGCUCGCAGAUAAUGCGGGUAAUCCGCAGACGAUCCUCAUGGGUAAGUAGAUUGAGGUAAUUAUGCGCCAGCUCGUUACUGAGAAUAUUCGUGCCGUCAUUAAUCCGCAGAAUGCAAAUCCCCACCGGGGCGGAUGCCACGAUUUUGCGGUUGAACUGUUCGUUUUCUUCUAAUUGAAACGCAUUGACUUCGGCGGGCAACAGCAUUUUACGCUCAAAAACCCACGCCAGCACAAACAGCAAGAUGGCCGACAGCGCGUUGAGCAGCGCCAUAUUCAUUAUCAGCCCGCCGAUAUGGGACAGUAACACCUUUAACGGCAGCGAAUAAAUAAUGCUGAACGCGGUGGGCGGCAGGUUUUUUUUCAGAAUAAUUUCAUCAUAGCCGUUCACAUAGCCAAAGUAAUUAUGUUCUAUCGGAUAGCUGUUCACCGAAGAGGCGUGGCGCCCUCCCCCUUCGG
#=GC SS_cons                   <<<<<<<<<<<<<<<<----<<<-----<<<<<<---<<--<<<<-<<<<<<________>>>>>>-->>>>-->>>>>>>>>>>-->>>->>>>>>->>>>>>>{{---{{{{{{{{{{{-{{{{-{{{,,,,,,,,,,,<<<<____>>>>,,,[[[-[[[[[[[[-[[,,,,<<<<<<<-<<<<<-<<---<<<-<________>>>>->>>>>>>--->>>>>>>,,,(((((((,,,,<<<__________>>>,,,,,,,,,,,,,,,,,,<<<____________________>>>,,,,,,,,,,,,<<<<<<<<---<<<<<<_______>>>>>>---->>>>>>>>,,,,))))))),,]]-]]]]]]]]-]]],,,,,,,,,,,<<<<<-<<_______>>->>>>>,<<<<<<_______>>>>>>,<<<<--<<<<____>>>>->>>>,}}}}}}}}}}-}}}}}}}}---}}:
#=GC RF                        ggCuGGuCaugacauCgACaaacUUGGAcugCugCUcgCAaacgaUgcgGgcAAUuCGcAgcCcguCuucguGGGucaGcagguuGAGauAgucauGCgCCaGccCGUUAcugagGgcgcucgugCCguCAuUAAUaCGCAGgauaCAAaucCCuACcGGcGCcgacgCCgCaAUcuuGCgGUugaauUGcUCguucUCUUCcAAuUGgaaCgCauucaCUUCcGCaggCAACaGcauuUUcCGCcCAAAuACCaagGCCAaCACAAACAguAAaAUcGcCgAuAGaauaUUcAGcAcuagCgUaUUaAUcAUCAaccCGCuGAUAugggggAGcAgcAccuucaACGGCaGCGgguAcAcaaugCuGAAcGacgucgGCgGCgGcgacUUuUUCAGaauGAguUCAUCAUacCCauuCACauagcCAAAaUAguuauGauCgGaagGacAgCuguCcACcGaaGacGcacagcGgcCuucagCaUCGG
//
# STOCKHOLM 1.0

#=GF AC   RF02739
#=GF ID   Rev41
#=GF DE   Soft rot Enterobacteriaceae Rev 41 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   535.00
#=GF TC   535.20
#=GF NC   145.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009267; cellular response to starvation;
#=GF RN   [1]
#=GF RM   26753530
#=GF RT   Discovery and profiling of small RNAs responsive to stress conditions in
#=GF RT   the plant pathogen Pectobacterium atrosepticum.
#=GF RA   Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PR, Moleleki
#=GF RA   LN
#=GF RL   BMC Genomics. 2016;17:47.
#=GF CC   From bacteria cultured under starvation conditions. 
#=GF WK   Soft_rot_Enterobacteriaceae_(SRE)_small_RNAs
#=GF SQ   3



BX950851.1/4896193-4895714 GACAGCCUGAGAUAAUGAGCUGACGCCUAAAGCCAAUGCGGUGAACCAGAUUAUUUUUUUCGUCAUUGUGUCAUCAUCAAUGUUAAGGGUCUUUUUCUUUGUCGGGAAAAAGACCGUUGAUCACGGCCUGUGAAUGGCAAUCAAGCCACCGUCUUUUCUGUAAACAGGUUCUCUUGUGCAAAUCGCGUUUCAUGGACAGACGGUGUCUUGCCCUGAUGUCCGGUUUUUUCCGUCAGCGCAGUGCCCGGCUGUUCUGUUGCGGCGCGUCUCCCCACAUAGCGCGGGAUGAAUGACACGACCCACACCACGAUGUUGAGGAAGGCCAGAAUAAUAUUGCGUAUGACUGGCGGUGCGUAAUCCGCCAAGCGCAGGUAGCCGCGAAAGCCGAGUGCCAGUACAUCAACCAGACUUUCGACUGGUUUAUCCUGCGGGAAGCUGUCUUGCCAGAGCGCCCAGGUAUCGGCGCGGGCAAAGGUACAU
CP001790.1/84587-85066     GACAGCCUGAGAUAAUGAGCUGACGCCUAAAGCCAAUGCGGUGAACCAGAUUAUUUUUUUCGUCAUCGUGUCAUCAUCAAUGUUAAGGGUCUUUCUCUUGGUCGGGAAAAAGACCGUUGGUCACGGCCUGUGAAUGGCAAUCAAGCCACAGUCUUUUCUGUAAACGGGUUCUCUUGUGCAAAUCGCGUUUCAUGGGUAGACGGAGUCUUACCCCGAUAUACGGUCUUUUCCGGCCGCGCAGCGUCUGGCUGGUCGGUAACGGUGCGUCUUCCUACAUAGCGCGGGAUGAAUGACACGACCCACACCACGAUGUUGAGGAAGGCCAGGAUAAUAUUGCGUAUCACUGGCGGUGCGUAAUCUGCCAGGCGCAGGUAGCCACGAAAGCCGAGAGCCAACACAUCAACCAGACUUUCGAUAGGUUUAUCCUGCGGGAAGCUGUCUUGCCAGAGCGCCCAGGUAUCGGCGCGCGCAAAGGUGCAU
CP001657.1/98017-98496     GACAGCCUGAGAUAAUGAGCUGACGCCUAAAGCCAAUGCGGUGAACCAGAUUAUUUUUUUCGUCAUCGUGUCAUCAUCAAUGUUAAGGGUCUUUCUCGUUGUCGGGAGAGAGACCGUUGAUCACGGCCUGUGAAUGGCAAUCAAGCCACUGUCUUUUCUGCAAACAGGUUCUCUUGUGCAAAUCGUGUUUCAUGGGCAAACGGCGUCUUGCCCUGAUGGGCAGCUUUUUCCGGCAGGGCAGUGCCCGACUGAUCUGUUACGGUGCGUUUUCCUACAUAGCGCGGGAUGAAUGACACCACCCACACCACGAUAUUGAGGAAGACCAGAAUAAUGCUGCGUAUGAUGGGCGGCGCGUAAUCCGCCAGACGCAGGUAGCCGCGGAAGCCGAGAGCCAGCACAUCAACCAGACUUUCGACCGGUUUAUCCUGUGCAAAACUGUCUUGCCAGAGCGCCCAGGUAUCGGCGCGGGCAAACGUACAU
#=GC SS_cons               {{{{{{,,,,,,,,{{{-{{{{-{{{-----{{---{{{{{{--{{{,,[[[[[[[[[[[[-[[[[[[[[[[[[[[[[,,,<<<<<-<<<<<<<<<<<<____>>>>>>>>>>>>->>>>>,,(-(((((((--(((,,,,,,<<-<<<<<<<<-<<<<<-<<<<-<<<<--<____>-->>>>-->>>>>>->>>->>>>>>>>->><<<-<<<<----<<<______>>>>>>>->>><<<<<<<<<______>>>>->>>>>,,,,,,))))))))-))-)]]]]-]]]]]]]]]---------------]]]-]]]]---]]]]]]]],,<<<<<-----<<<<<<________>>>>>>->>>>>}}}-}}}}}}---}}---}}}-}}}}-}}},<<<<<<________>>>>>>,,<<<____>>>,}}}}}}<<<<<---<<<<<________>>>>>->>>>>::::::::
#=GC RF                    GaCaGcCUGAGAUAauGAgcuGACgCCUAAAGCCAAcGcGGcGAaCCAGauuauucucuuCGuCaucGuGuCauCauCAAUgucaaGGGuCuuucuCccuGUCggGagaaaGaCCGuugacCACGGCCuguGAAugGCAAUCAaGCCgCcGucuUccCuGuaaaCaGguuCUCUUGUGCAaacCGcGuuuCaUGggcagaCgGcGUCuugCCCuGaUguaCgGuuUUUUCcGuCaGcGcaGcgcCcggCUGaUCuGccgCGgcgCGUcUuCCcaCacaGCGCGGGauGAauGaCaCgaCCCACACCACGAUgUuGaGGaaggCCagaauaauauuGCGcAUgAcuGGCgGuGCGUAAUCcGCCaggCGCaGGuAgCCgCgaAAGCCGAGcGCCagcACauCaaCCggACUUUCGAccGGuuUAuccUGcGggaAgCuGuCuuGCcAGAGCGCCCAGGUAUCGGCGCGgGCaaAgGUaCAU
//
# STOCKHOLM 1.0

#=GF AC   RF02740
#=GF ID   Fwd6_3p_UTR
#=GF DE   Soft rot Enterobacteriaceae Fwd 6 3'UTR
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   79.00
#=GF TC   79.90
#=GF NC   38.80
#=GF TP   Cis-reg; 
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000205; three_prime_UTR;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009267; cellular response to starvation;
#=GF RN   [1]
#=GF RM   26753530
#=GF RT   Discovery and profiling of small RNAs responsive to stress conditions in
#=GF RT   the plant pathogen Pectobacterium atrosepticum.
#=GF RA   Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PR, Moleleki
#=GF RA   LN
#=GF RL   BMC Genomics. 2016;17:47.
#=GF CC   From bacteria cultured under starvation conditions. 
#=GF WK   Soft_rot_Enterobacteriaceae_(SRE)_small_RNAs
#=GF SQ   3



BX950851.1/28634-28749     UUUCUGUAAUUAAAUAACAGUAUUGUGUGACCUGGUUUAACUUUGUGUAAUCGAUAACCAUUUUGUAUGAAAGUAAACAACAAAAAAGCCUUUGUUCCCGUGAAAAAAUAGGGUAG
CP001657.1/4778912-4778797 UUUCUGUAAUUAAAUAACAGUAUUGUGUGACCUGGUUUAACUUUGUGUAAUCGAUAACCAUUUUCUAUGAAAGUAAACAACAAAAAAUCCUUUGUUCCCGUGAAAAAAUAGGGUAG
CP001790.1/4952716-4952601 UUUUUGUAAUUAAAUAACAGUAUUGUGUGACCUGGUUUAACUUUGUGUAAUCGAUAACCAUUUUCUAUGAAAGUAAACAACAAAAAAGCCUUUGUUCCCGCGAAAAAAUAGGGUAG
#=GC SS_cons               :::<<<<_________>>>>,,,,,,,,,,,,,,<<<<<-<<<<--<<<--<<<________>>>>>>->>>>>>>>><<<<<<______>>>>>><<<___________>>>:::
#=GC RF                    UUUcuGuAAUUAAAUAaCagUAUUGUGUGACCUGGuuuaACuuuGUguaAUcgaUAACCAUUuuguauGaaaGuaaaCaaCaaaAAAgCCuuuGuuCCCGuGAAAAAAUAGGGUAG
//
# STOCKHOLM 1.0

#=GF AC   RF02741
#=GF ID   Rev44
#=GF DE   Soft rot Enterobacteriaceae Rev 44 asRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   178.00
#=GF TC   178.10
#=GF NC   33.50
#=GF TP   Gene; antisense; 
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009267; cellular response to starvation;
#=GF RN   [1]
#=GF RM   26753530
#=GF RT   Discovery and profiling of small RNAs responsive to stress conditions in
#=GF RT   the plant pathogen Pectobacterium atrosepticum.
#=GF RA   Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PR, Moleleki
#=GF RA   LN
#=GF RL   BMC Genomics. 2016;17:47.
#=GF CC   From bacteria cultured under starvation conditions. Antisense to ECA0910. 
#=GF WK   Soft_rot_Enterobacteriaceae_(SRE)_small_RNAs
#=GF SQ   3



BX950851.1/1015818-1016153 CCGUCUUCGACGUAAUGUUUACGGGAUGUCUCGUCAAAAAUGGAGUACAUGAUGCCGCCCGCUUUUGACAACGCGUUGCCGGAGUGUGGCCAGAUGAUGACGUUAGAUUCAUCGGUAAAGCGGCGGCCGUGUUGAUCAAUCCACAGAUAUGGCUGACGCGCGGCGGCUAGCAGAUGAGAGUUAGGCGCAUAGUCUGGCAGGCCGGGGCGAUAGGCUUGCAGCAGACCCAUGCCGUCCGGUUUGGCACCGGCUUUCCAGGCCAUAUUAAUCCCGUCGCCGUCUUUACCGACGUUGCCAACCAUAAUGGUGUCGGGGAAGGCGGCAUAUUUUUGCAGC
CP001790.1/1113084-1113419 CCGUCCUCGACAUAAUGCUUACGGGAUGUUUCGUCAAAAAUGGAGUACAUGAUGCCGCCCGCUUUUGACAGCGCGUUGCCGGAGUGUGGCCAGAUGAUGACGUUGGAUUCAUCGGUAAAGCGGCGGCCGUGUUGAUCAACCCACAGAUAGGGCUGACGUGCGGCGGCCAGCAGGUGAGAGUUAGGGGCGUAGUCUGGCAGGCCGGGGCGAUACGCUUGCAGCAGACCCAGGCCGUCCGGUUUUGCACCAGCUUUCCAGGCCAUAUUGAUCCCGUCGCCGUCUUUACCGACGUUACCAACCAUAAUGGUGUCGGGGAAAGCGGCAUAUUUUUGCAGC
CP001657.1/928020-928355   CCGUCUUCGACGUAAUGCUUACGGGAGGUUUCGUCGAAAAUGGAGUACAUGAUGCCACCCGCUUUUGACAGCGCAUUGCCGGAGUGUGGCCAGAUGAUGACGUUGGAUUCAUCGGUAAAGCGGCGACCGUGUUGGUCAACCCACAGAUAGGGCUGACGCGCGGCUGCCAGCAGGUGUGAAUUCGGCGCGUAGUCUGGCAGGCCGGGGCGAUAGGCUUGCAGCAGGCCCAGACCGUCCGGUUUGGCUCCGGCUUUCCAGGCCAUAGUAAUUCCGUCGCCGUCUUUACCGACAUUGCCGACCAUAAUGGUAUCGGGGAAGGCGGCAUAUUUUUGCAGC
#=GC SS_cons               :<<<<___>>>>,,,,,,,,{{{{{{{,[[[[[[[,,,,<<<_____>>>,,,(((((((((,,<<<<<<<<<<<--<<<<--<<---<<<-<<<<<___________>>>>>>>>--->>-->>>>>>>>>>>->>>>,,,,<<<______>>>,,)))-)))))),,,,,]]]]]]],,,,<<<<<<<-<<<<<<<<<<<<_________>>>>>>>-->>>>>-->>>->>>>,<<<<<<<__________>>>>>>>,,,,,,}}}}}}}-<<<<<<<<--<<<<<---<<<<_______>>>>>>>>>-->>>>>>>>:::::::::::::
#=GC RF                    CcGuCuUCGaCgUAAUGcUUaCGGgauGucuCgcCaAAAauGGAGUACauGAUGCcgCCCgCUUuuGaCagCgCgUUGcCGGAGcGUGgCCAGauGaUGACGUUgGAUuCauCGGcAAAgCGGCGgCcGcGcuGauCaacCCACaGAUAgGGCuGACGcGCGGcgGCcAGCAGgcGagagUUaGgcGcguAGuCuGGCagGCcGGGGCGAUAgGCcuGCAGCaGaCCCacgCCgcCCGGccugGCaCCgGCUUUCcaggCCAUAuUaaucCCGuCGCCGccuuUACCGacgUUgCCaACCAUAAuGGcguCGGGGaaggCGGCAUAUUUUUGCAGC
//
# STOCKHOLM 1.0

#=GF AC   RF02742
#=GF ID   Rev72
#=GF DE   Soft rot Enterobacteriaceae Rev 72 asRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   289.00
#=GF TC   289.60
#=GF NC   63.30
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009267; cellular response to starvation;
#=GF RN   [1]
#=GF RM   26753530
#=GF RT   Discovery and profiling of small RNAs responsive to stress conditions in
#=GF RT   the plant pathogen Pectobacterium atrosepticum.
#=GF RA   Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PR, Moleleki
#=GF RA   LN
#=GF RL   BMC Genomics. 2016;17:47.
#=GF CC   From bacteria cultured under starvation conditions. Antisense to gudP.
#=GF WK   Soft_rot_Enterobacteriaceae_(SRE)_small_RNAs
#=GF SQ   3



BX950851.1/4017543-4017968 UGAUUUGAAAUGAACAAUGCCUGUAGGGUUAUCAGAAUAAAAACAGGUAUAAACUACCUUGAUACCGGAAUAAAACGAUCGGGAAAGCGGUGCCAUAAUCCGUACCGCCUUACCAACCUCAGUCAAAAGUAUAAGUUUUCUUAUUUCACAACUCAUUGGGCAAUAGCCCAGCAUUCCCUGUCGAAAUGCAGAUUAAAUAUGUCAUUAUCACAGGCCAAUGGGAGGUGUUUCACGAAAACCGGGAAAAGCGAAUUUCUGCCUUAUAAACACCGGAAUACAGACCAUUAGCGCCCGAUUUCGAAUAGGUAAAUCCCUACUUUCCAUGACAUAAAUAAAGGACAAAACGCCGAGCCAUCAGUAUGACGGCACAGCGUUUUGUGUUACUGCCUACAUGCAGGUUAAUGCUGUAACGAACGACUUUAAUUC
CP001790.1/3917755-3918179 UGAUUUGGAAUGAACCAUGCUUGUAGGGUGAUCAGAAUAAAAACAGGUAUA-ACUCCCUUAAUACCGAAAUAACACGGUCAGGAAAGCGGUGCCAUAAUCCGUGCCGCCUUACCAACCUCAGUAAAAAGUAUAAGUUUUCUUAUUUCACAACUCAUUGGGCAAUAGCACAGCAUUCCCUAUCGAAAUGCAGAUUAAAUAUGUCAUUAUCACAAGCGAAUGGGAGGUGUUUCACGAAAACUGAGAAACGCGAAUUUCUGCCUGAUAAACAUCGGAAUACGUACUAUUGGCACCUAAUUUCGAAGAGGUAAAUCCCUACUUUUCAUGACAUAAAUAAAGAACAAAACGCCGAACCAUCAGUAUGACGGCACAGCGUUUUGUGUUACUGCUUAGAUGCAGAUUAAUGCAGUAGCGAAUGGUUUUAAUUC
CP001657.1/3836127-3836552 UGAUUUGAAAUAAGCCAUGCUUGUAGGGUUAUCAGAAUAAAAACAGGUUAUAACUGUCUCGAUACCGGAAUAAACCAGUCAGAAAAGCGUUGUCAGAACCCAUACCGCCUUACCAACCUCAGGAAAAAGUAUAAGUUUUCUUAUUUCACAACUCAUUGGGCAAUAGCACAGCAUUCCGAGUCGAAAUGCAGAUUAAAUAUGUCAUUAUCACAGGGUAAUGGGAGGUGUUUCACGAAAACCGGGGAAAGCAAAUUUCCGCCUUACAAACACCGAAAUACGGGGUUCUGACAGCCGGUUUCAAAUAGGUAAAUCCCGACUUUUCAUGCCAUGAAUAAAGGACAAAACGCUGCGCCAUCAGUAUGACGGCACAGCGUUUUGUGUUAUUGCCUAUAUUCAGACUAAUACGGUAACGAAUGGCUUUACUUC
#=GC SS_cons               :::(((((--(((,,,<<<<<<<<----<<<<____>>>>-->>>>>>>>,,,,,,,<<<<<<--<<________>>>>>>>>,,,<<<<<<<________>>>>>>>,,,,,,,,,,)))-)))))-----{{{{{{{{{{{{,,,,,,,,,,,,,<<<<____>>>>[[[[[[-[[[[[------[[[[,,,,,,((((((((,,,,,,,<<<<<<<<<--<<<<<<<<<-<<<<--<<_______>>-->>>>>>------>>>>>>>---------->>>>>->->>><<____>>,,<<<<______>>>>,,,,,,)))))))),,,,,<<-<<<<<<<<<-<-<<<-<<<___>>>->>>->->>>>>>>>>->>,]]]]------]]]]]--]]]]]]}}}}-}}}-}}}}}::::::
#=GC RF                    UGAuuuggAAugaaCcaugCcuGuAGGGuuauCAGAauaaAAaCagGuauaAACUaccucgacACcGgAAUAAaaCggucgggAAAGCGgugcCAuAAuCCguacCGCCUUACCAACCucaGccaaaAGUAUaagcuuuCuuauUUCACAACUCAUUGgGCAAUAGCcCaGcauuCccugcCGAAAUGCagAUUAAAuauGuCauUAUCACAggccaauggGAGguGuuuCaCGaaaACcGgGaAAaGCgAAuuuCuGCCUuAuaaaCacCGgAAUACggaccauuggCgcccgaUUUcgAAuaGGUAAAUCCCuaCUUUuCauGaCauaAAUAAaggaCaaaaCGCcGagCCAuCaGUAuGaCGGcACAGCGuuuuGuGuuAcuGCcUAuAUgcagguUaaugCuguaaCGaauggcuuUAaUUC
//
# STOCKHOLM 1.0

#=GF AC   RF02743
#=GF ID   Sernc389
#=GF DE   Saccharopolyspora sRNA 389
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   74.00
#=GF TC   74.20
#=GF NC   44.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 1900376; regulation of secondary metabolite biosynthetic process;
#=GF RN   [1]
#=GF RM   24236194
#=GF RT   Prediction and characterization of small non-coding RNAs related to
#=GF RT   secondary metabolites in Saccharopolyspora erythraea.
#=GF RA   Liu WB, Shi Y, Yao LL, Zhou Y, Ye BC
#=GF RL   PLoS One. 2013;8:e80676.
#=GF CC   Probably regulates polyketide biosynthesis.
#=GF WK   Saccharopolyspora_erythraea
#=GF SQ   2



AY661566.1/11179-11773     ACCAGGUUCGUGGUGGUGCGGUGCAGGAAGUCGGUGCGGGCACACCGGAUUUCGCGGUGUGCCCGUGCGACCUUGGUCUUGGCUUUGCGGCGGUUGUUCGAGCCCUUCUGCUUGCGGGCCAUUUGCCGCUGGUAGCGGGCGAGGUUGCGGGCCUUGCGGUCCAGAUGCUUCGGGUUGGCGAUCUUCUCGCCUGUCGACAGGACAGCAAAGUCCUUCACACCCAGGUCCACCCCGACCGCGCUGCCGGUCUCGGGCUGCGGUUCGGGGUCGUCGGUGUCCACGGCCAAGGUCACAUACCAGCGGCCAUCCGGCUCGCGGGACACGAUCACCAUCGUCGGAUUCAGCGUUGCGAGGGUUUCGUCGUCCCAGGACCACACGAACUCAAGCGGCGCGGUGUGCUUCGCCAGAGUCAGCUUGCCGCCGCGCAGGCGGAAAGCGCUGCGCGUGUAGUGCGCCGACUGGCGGCCGUUGCGGGGCUUGAAACGCGGGUAGCGCGCACGCCCGGCGAAGAAGUUCGCAUACGCGGUGUGCUGGUGCCGAAGUGUCUGCUGCAACGGCACGCUCGACACCUCAGACAGGAACGCCGGCUCGUCGG
AM420293.1/5112242-5112836 ACCAGACGUGUACUGGUCUUGUGGACAAAGUCCUGGCGAGCGUGGCGCAUCUCGCGGUGCGCGCGGGCGACCUUGUUCUUGGCUUUGCGGCGGUUGUUCGAGUCCUUCUGCUUCCGUGUCAUCUGCCGCUGGUAGCGGGCAAGGUUACGGGCCUUGCGGUCCGGAUGCUUCGGGUUCGCGAUCUUCUCGCCGGAGGACAGGGCCGCGAAGUCCUUCACACCCAGGUCCACCCCGACCGCACGGCCAGUCUCGGUCUGCGGUUCGGGGCCGUCGGUGUCCACGGCGAACGUGACAUACCAGCGGCCGUCGGGCUCGCGGGACACGAUCACCAUCGUCGGGUUCAACGACGCCAGGGUUUCGGCGCCCCAGGACCACACGAACGCAAGCGGCGCGGUGUGCUUCGCGAGAGUCAGUUUGCCGCCGCGCAGGCGGAACGCGCUGCGCGUGUAGUGCGCGGACUGGCGGCCGUUGCGGGACUUGAAACGCGGGUAGCGCGCGCGCCCGAGGAAGAAGUUCUGAUAGGCGGUGUGCUGGUGCCGCAACGUUUGCUGCAACGGCACCGACGAGACCUCGGACAGGAACGCCGGCUCGGCGG
#=GC SS_cons               :<<<<_______>>>>{{{{{{<<<<___>>>>,,,,,,<<-<<<<<<<<<____>>>>>>>->>->><<<<<<<<<<---<<<--<<<<<<<-<<<-<<<<<______>>>-->>->->>->>>>>>>->>>--->>>>>>>>>>,,<<<<-<<<<<<<<<-<-<-<<<<<<---<<-<<___>>->>>>>>>>->>->>>>>>>>>->>>>,,,,,,[[-[[[[[,,<<<<<<<<<<<-<<<<______>>>>>>>>>->>>>>>,((((((((((--((((((((((----((((((((((((((,<<<<<<--<<<<-<<<<_______>>>>->>>>-->>>->>>,,,,,,,<<<<<<<<<<<--<<-<<<--<<<<--<<<<<<<<-<-<<<<<<<<<-<-<<______>>>-->>>>->>>>>->->>>>>>>>>>>>--->>>->->-->>>>->>->>>>><<<<<<<<----<-<<<<<-<<____>>>>>>>->---->>>>>>>>,,,))))))-))))))))-----))))))))))----)))))))))),]]]]]-]]}}}}}},<<<<<___>>>>>:
#=GC RF                    ACCagauuuGUacuGGuccuGuggacaAAguccuuGCGaGCacggCgcaccUCGCggugcGcgcguGCgaCCucGccCUUGgCcUUGCGGCggUuGcUCGaGcCCUUCUgCuUgCGuguCaUccGCCGCUgGcAGCGggCgaGGucaCGGgCCucGCgGcCCaGAuGcuccGGGUUcGCGaUCUuCUCgCCggagGaCAGGgCcGCgaAGcCCUUCACACcCaGGucCACCCCGaCCGCgCggCCaGUCUCGGcccGCGGUuCGGGGuCGucgGuGcCCACgGCggacgcgACAcaCCaGCggCCgccggGCuCGCGGgacACGacCACCAUCguCGGgucCAaCGauGCcAGGGUUUCggCGcCCCaGGAcCACaCGAaCgCAAGCgGCGCgGuGcGCcuCGCgAGAGcCAGuUUgCCGCcGCGCagGCgGaAcGCGCcGCGcGuGUAGuGCGCgGACuGGCGgCCGccGcgGggCuuGAAAcGCGGGcAGcGCGCgCgCCCGagGAAGaaGccCcgAUAggcGGcGcGCuGGugCCGaAgcguccGCcGCAACGgCaCcgaCGAgaCCuCgGaCaggaACGcCGGCUCGgCGG
//
# STOCKHOLM 1.0

#=GF AC   RF02744
#=GF ID   Rev39_5p_UTR
#=GF DE   Soft rot Enterobacteriaceae Rev 39 5'UTR
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   88.00
#=GF TC   88.60
#=GF NC   86.30
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009267; cellular response to starvation;
#=GF RN   [1]
#=GF RM   26753530
#=GF RT   Discovery and profiling of small RNAs responsive to stress conditions in
#=GF RT   the plant pathogen Pectobacterium atrosepticum.
#=GF RA   Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PR, Moleleki
#=GF RA   LN
#=GF RL   BMC Genomics. 2016;17:47.
#=GF CC   From bacteria cultured under starvation conditions. 
#=GF WK   Soft_rot_Enterobacteriaceae_(SRE)_small_RNAs
#=GF SQ   4



BX950851.1/4733293-4732994   AAUUGUUGUCAUGCCAUGACUGACUGUGAUAACUCUGUAGGUAUUCGUUCGACAGAAGAUUAAUGAACAACCUAU-UAUGAAAGCCCUAUCCCUAGUGAUUAGCCUAGUCGUGAUUAGCGUGGUGGUGAUUAUUAUCCCACCGUGCGGGGCUGCACUUGGACGAAGAAUGGCUUAGAAAUCAAGGCCUGAUUCAAGAAAACCCCCGCACCGAAAGGUCGGGGGUUUUUUGUU-GGGCGUAAUCUAUAACGGAAAGGAACAGAAAAUGAACAUCAGCAUAAAAUUCUGUUAUUCCCAUAAGAU
CP001790.1/4659105-4658806   AAUUGUUGUCAUGGCAUGUCUGACUGUGAUAACUCUGUAGGCAUUCGUUCGACAGAAGAUUAAUGAACAACCUAU-UAUGAAAGCCCUAUCCCUAGUGAUUAGCCUAGUCGUGAUUAGCGUGGUGGUGAUUAUUAUCCCACCGUGCGGGGCUGCACUUGGACGAAGAAUGGCUUAGAAAUCAAGGCCUGAUUCAAGAAAACCCCCGCACCGAAAGGUCGGGGGUUUUUUGUU-GGGCGUAAUCUAUAACAGAAAGGAACAGAAAAUGAACAUCAGCAUAAAAUUCUGUUAUUCCCAUAAGAU
CP001657.1/4554960-4554661   AGUUGUUGUCAUGCCAUAUCUUACUGUGAUAACUCUGUAGGCAUUCGUUCGACAGAAGAUUAAUGAACAACCUAU-UAUGAAAGCCCUAUCCCUAGUGAUUAGCCUAGUCGUGAUUAGCGUGGUGGUGAUUAUUAUCCCACCGUGCGGGGCUGCACUUGGACGAAGAAUGGCUUAGAAAUCAAGGCCUAAUUCAAGAAAACCCCCGCACCGAAAGGUCGGGGGUUUUUUGUU-GGGCGUAAUCUAUAACGGAAAGGAACAGAAAAUGAACAUCAGCAUAAAAUUCUGUUAUUCCCAUAAGAU
AFWW01000001.1/265103-265404 AAUUGUUGUCAUAUCGUGCUGGAAUGUGGUAACUCUGUAUGUAUUCGUUCGACAGUAGAUUAAUGAACACUCUAUUUAUGAAAGCUUUCUCCCUAGUGAUUAGCCUAGUCGUGAUUAGCGUGGUGGUGAUUAUUAUCCCACCGUGCGGGGCAGCACUUGGACGAAGAAUGGCUUAGAAAUCAGGCCCGAAUUCAAGAAAACCCCCGCACCGAAAGGUCGGGGGUUUUUUUUUCGGGCGUAAUGUAUAACGUAAGGGAGCAGAAAAUGGUUAGUGGUACAGAAUGCUGUUAUUCCCGCAAGAU
#=GC SS_cons                 ::::<<<<<<<<<-<<____>>->->>>>>>>>,,,<<<<<<-<<<<<<<_______>>--->>>>>-->>>>>>.,,,,,,,,,(((-(((-((--(((((((((((,<<<_____>>>,<<<<<-<<<____>>>>>>>><<-<<<<______>>>>->><<<----<<<<<________>>>>>--->>>,<<<<<<<<<<<<-<<<____>>>>>>>>>>>>>>>,)).))))-)))))--))--)))-)))<<<<<<<-<<<________>>>---->>>>>>>:::::::::::::
#=GC RF                      AaUUGuuguCacgucaUgucugAcUguGacaaCUCUguaggcAuuCguuCGACAGaAGaUUAacGaaCAgccuac.UAUGAAAGCccuauccCuaGUgauuaGCCcagUCGcGAUUAgCGUGGuGGUGauUAUUauCCCaCCGuGCggGGCuGCACccGGaCGaaGAAUGGccuAGAAAUCAaggCCuaAuuCAagaaaaCCCCCGCaCCGAAAGGuCGGGGGuuuucugcu.gGGCGuaaucUAuaACggaAaggaaCaGaaAaugaacAucaGcauAaAAuuCuGuuAUUCCCauAAGAU
//
# STOCKHOLM 1.0

#=GF AC   RF02745
#=GF ID   Rev42_5p_UTR
#=GF DE   Soft rot Enterobacteriaceae Rev 42 5'UTR
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   229.00
#=GF TC   229.40
#=GF NC   129.90
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009267; cellular response to starvation;
#=GF RN   [1]
#=GF RM   26753530
#=GF RT   Discovery and profiling of small RNAs responsive to stress conditions in
#=GF RT   the plant pathogen Pectobacterium atrosepticum.
#=GF RA   Kwenda S, Gorshkov V, Ramesh AM, Naidoo S, Rubagotti E, Birch PR, Moleleki
#=GF RA   LN
#=GF RL   BMC Genomics. 2016;17:47.
#=GF CC   From bacteria cultured under starvation conditions. 
#=GF WK   Soft_rot_Enterobacteriaceae_(SRE)_small_RNAs
#=GF SQ   3



BX950851.1/998374-998853   CAGUAAGAUGGAGAGGACGGCGAGUGGCCAAAUGAGGUAGCUGAGCCAUUGAAGCCAGCUUGGAAUGUGGCUCAUGAUCUGAGGAAUCCAAUCAUUCAAUUGGGUGAAAAGCCACCAAAAAGCGCCGCCCAUCAGCACGAUAUUCAUGAGUAAAGGAAGAAUAACGAAACGCCGGAUGCCCGGCAGAGAGAUCAAGCGCCAUCCGGCAAAAAAAUAGUGUACGCCGCUGCGAGUGUGGUCUGCGGUGUUGCUGUGAGACGGUUUUUCGAAAGACGGUGGUUUUUCUGGAAACGAUGAUUUUUCUGAAGACAUGGUGCCGAUAUACUCAGUCAUUUGUUUGUUAAGGCAUCAUAUCGGGAUGAUCUUAUGCUGACUAGCCCAUAUUUGGAUGAAAAAGCAGCAAAAAAGUGCGUUGUACCUAUCUUUAUUGUCAUUAAAGUACCGUGCAGGCUUGCACUUGUGUACUCAGGCAAAUAGAGU
CP001790.1/1095999-1096441 CAGCAAUAUGGAGAGUACGGCGAGUGGCCAAAUGAGGUAACUAAGCCAUUGCAGCCAGCUCGGUAUAUAGCUCAUGAUCUGGGGGAUCCAGUUAUUAAGCCGGGUGAAAAGCCACCAAAAAGCGCCGCCCAUCAGCACGAUGUUCAUGAGUAAAGGAAGGAUAACGAAACGUCGGAUACCAGGCAGUGAGAUCAGGCGCCAUCCGGCAAGAAAAUAGUGUAUACCACUGCGAGUUUGGUCUGCUGUAUUGCCGUAA------------------------------------GGCGGUUUUUCGGAAGACAUUGUGACAAUGUUCUCAGUCAUUUGUUUGUUGAGGCAUCAUAUCGGGAUGAUCUUAUGCUGGCUAGCCCAUAUUUGGAUGAAAAAACAGCAAAAAAAUGCGUUCUAUCUAUCUUUAUUGCCAU-AAAGUACCGCGCAGGCUUGCACUUGUGUACUCAGGCAAAUAGAGU
CP001657.1/909822-910264   CAGCAGGAUGGAGAGGACGGCGAGUGGCCAGAUGAGGUAGCUGAGCCAUUGCAACCAGCUUGGAAUGUGGCUCAUGAGCUGGGGAAUCCAGUCAUUUAACCGGGUGAAAAGCCACCAGAAGGCCCCCCCCAUCAGCACAAUAUUCAUGAGUAGGGGAAGAAUGACGAAACGCCGGAUGCCCGGUAGUGAGAUCAAACGCCAUCCGGCAAGAAAAUAGUGUAUUCCGCUGCGAACCUGGCCUGCGGUGUUGCCGUAA------------------------------------GGCGGUUUUUCGAAAGACAUAGUGACAAUAUACUCAGUCAUUUGUUUGUUGAGGCAUCAUAUCGGGAUGAUCUUAUGCUGACUAGCCCGCAUUUGGAUGAAAAAACAGCAAAAAAGUGCGUUGUAUCUAUCUUUCUUGUCAU-AAAGUACCGCGCAGGCUUGCACUUGUGUACUCAGGCAAAUAGAGU
#=GC SS_cons               ::::::(((((----(-(((((<<<-<<<______>>>->>><<<<<<<-----<<<___>>>--->>>>>>><<<<<--<<____>>-->>>>>,,,,,,,<<<<______>>>>,,,,,,))))))))))),(((((-((((-(((((((((((-((-((((((--((<<<<<<<<--<<---<<____>>--->>->>>>>>>>,,,,,,<<<<<<-<<<<<<<-<<_______>>-->>>>>>>>>>>>>,,,,,,......-.......____.......-......,,,<<<<-<<<<<<----<<<<<<<<---<<<--<<<____>>>-->>>--->>>>>>>>->>>>>>->>>>,,,<<<<<-<<---<<<____>>>------->>>>>>>,,,,,))-))))))--))-)))))))--))))---))))-))))),,<<<<<-<<____>>--->>>>>:::::::::
#=GC RF                    CAGuAagauGGAGAGgAcGGcGaGcGgCCAaAUGAGGcAgCugaGCcacUGaAgCCgGCUcGGaAUgugGCucaugacCUGgGGaAcCCAgucauUuAauuGGGuGAAAAGCCaCCAaAAaGCgCCgcCCaucAGCgCgAuacuCauGgguaaaGgAaGaacaaCGAAacGcCGGaugCCcGGcAGaGAGAuCAagCgCcauCCGgCAAgAAAacgGcgUacgCcgCUgCGAguuUGGcCUGcgGcgucgCcguaA....................................GguGgucUucCcgaAGACaugguGcCaAUacaCUCagUCAUcuGUUuguUgAGgCaccauAucgGgaUgacCUUAuGCuGacuAGCCCauAUUuGGAUGAAAAagCaGCaAAAAAguGCGuuguAuCuAcCuuuacUGcCau.AAaguaCcGcGCAGGCcuGCaCUUGUGuACUCagGCAAAUAGAGU
//
# STOCKHOLM 1.0

#=GF AC   RF02746
#=GF ID   AsrC
#=GF DE   antisense RNA of rseC mRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   111.00
#=GF TC   111.50
#=GF NC   110.30
#=GF TP   Gene; antisense; 
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010628; positive regulation of gene expression;
#=GF RN   [1]
#=GF RM   26441919
#=GF RT   The novel cis-encoded antisense RNA AsrC positively regulates the
#=GF RT   expression of rpoE-rseABC operon and thus enhances the motility of
#=GF RT   Salmonella enterica serovar typhi.
#=GF RA   Zhang Q, Zhang Y, Zhang X, Zhan L, Zhao X, Xu S, Sheng X, Huang X
#=GF RL   Front Microbiol. 2015;6:990.
#=GF WK   AsrC_small_RNA
#=GF SQ   7



CAAZ01000076.1/19567-18675 ACCUGAGCUUCCAUUUC--ACGG-UCA----GACAGGCCA---CCGCAGAUUUGGAUAAUACGGUCAGACAGCGUCGAUUUACCGUGGUCAAUGUGAGCAAUGAUCGAAAAGUUACGUAUGUUCUUCAUAGAGAUAAAUUAUUAUGCCUUACGCCUGGUUGACCAGACU-UU-AGAGGUCGCUGUUCUGAGCUUAACGUCUGUUUUAACUGAAACGCCGCAUUCUACACUACAACGCUAAGGCGAGGAAAUGUUCAUAGUGUAAGGAGAGCGGGAACUGGAAAACGCCUCGCUUUUUUCCUGUAAAACACCGCAAC----GCAG------GAAA----------AGCGCAUGCUUAUCGGG-ACAACAA-----CCCAACGCGG-CAGG-UGUACCAUGU-------------A-------------CCAUUGGGCAAAACGUUUACUGGCGCGUUUCGAUUGAGGUAGUUUCGACGCGGACAAGGUCAGGCGGGAGGGCAACGUUUAAAAUCACGGGCUGCCAGGCGUCGCGCUCCG-CCAGUUUU-CGGGAAUAGCCGCGGGCAACCAGAAAACCGCCCACUCCGCCCAGCACGGCCCCGCUUAAUGCGGCAAGGUCAGAUCCAAACAGCAUCUGAAAAAGCGCCGCACAAAGAAAUAGCCCCGCUAAAGGCGACAUAUAGACCAGCAACGCCGAACCUAAAAGGCUUUUUUCGGCGAUGCCCAACUCGACUUUCUGCCCCGGAGCCAGCGGCUCCGCGCUUGGCACAACAAUGGUAUGCGUGGUUUGCGGCCCUAAUUUAUUCAGCACGCGACUGCCGCAUCCCGCACGGGAGGCGCAGCUGCUGCAUGACGCUUUAACGUCGCAGCUCACCACCGCCUGACCAUUCUGCCAGGAGAUAACGGUUGCCCACUCUUUAAUCAUUGUACUGCCCUGAAUUUGAUACUGUCGGCAAUGCGC
AE006468.1/2776947-2777829 UUGUGAGCGCUUAUUUU--GCGG-GGAUCUUGAGAGGAUUUUGUCGUAGGUUUGCGGAGGGUGGCGGGGUA---UCAAUUA-------UCGAUGUGAGCAAUGAUCGAAAAGUUACGUAUGUUCUUCAUAGAGAUAAAUUAUUAUGCCUUACGCCUGGUUGACCAGACU-UU-AGAGGUCGCUGUUCUGAGCUUAACGUCUGUUUUAACUGAAACGCCGCAUUCUACACUACAACGCUAAGGCGAGGAAAUGUUCAUAGUGUAAGGAGAGCGGGAACUGGAAAACGCCUCGCUUUUUUCCUGUAAAACACCGCAAC----GCAG------GAAA----------AGCGCAUGCUUAUCGGG-ACAACAA-----CCCAACGCGG-CAGG-UGUACCGU---------------------------------UGGGCAAAACGUUUACUGGCGCGUUUCGAUUGAGGUAGUUUCGACGCGAACAAGGUCAGGCGGGAGGGCAACGUUUAAAAUCACCGGCUGCCAGGCGUCGCGCUCCG-CCAGUUUU-CGGGAAUAACCGCGGGCAACCAGAAAACCGCCCACGCCGCCCAGCACGGCCCCGCUUAAUGCGGCAAGGUCAGAUCCAAACAGCAUCUGAAAAAGCGCCGCACAAAGAAAUAGCCCCGCUAAAGGCGACAUAUAGACCAGCAACGCCGAACCUAAAAGGCUUUUUUCGGCGAUGCCCAACUCGACUUUCUGCCCCGGCGCCAGCGGCUCCGCGCUUGGCACAACAAUGGUAUGCGUGGUUUGCGGCCCUAAUUUAUUCAGCACGCGACUGCCGCAUCCCGCACGGGAGGCGCAGCUGCUGCAUGACGCUUUAACGUCGCAGCUCACCACCGCCUGACCAUUCUGCCAGGAGACAACGGUUGCCCACUCUUUAAUCAUUGUACUGCCCUGAAUUUGAUACUGUCGGCAAUGCGC
FR775213.1/19547-18665     UUGUGAGCGCUUAUUUUGCAGGGAUCU---UGAGAGGAUUUUGUCGUAGGUUUGCGGAGGGUGGCGGGGUA---UCAAUUA-------UCGAUGUGAGCAAUGAUCGAAAAGUUACGUAUGUUCUUCAUAGAGAUAAAUUAUUAUGCCUUACGCCUGGUUGACCAGACU-UU-AGAGGUCGCUGUUCUGAGCUUAACGUCUGUUUUAACUGAAACGCCGCAUUCUACACUACAACGCUAAGGCGAGGAAAUGUUCAUAGUGUAAGGAGAGCGGGAACUGGAAAACGCCUCGCUUUUUUCCUGUAAAACACCGCAAC----GCAG------GAAA----------AGCGCAUGCUUAUCGGG-ACAACAA-----CCCAACGCGG-CAGG-UGUACCGU---------------------------------UGGGCAAAACGUUUACUGGCGCGUUUCGAUUGAGGUAGUUUCGACGCGAACAAGGUCCGGUGGGAGGGCAACGUUUAAAAUCACCGGCUGCCAGGCGUCGCGCUCCG-CCAGUUUU-CGGGAAUAGCCGCGGGCAACCAGAAAACCGCCCACGCCGCCCAGCACGGCCCCGCUUAAUGCGGCAAGGUCAGAUCCAAACAGCAUCUGAAAAAGCGCCGCACAAAGAAAUAGCCCCGCUAAAGGCGACAUAUAGACCAGCAACGCCGAACCUAAAAGGCUUUUUUCGGCGAUGCCCAACUCGACUUUCUGCCCCGGCGCCAGCGGCUCCGCGCUUGGCACAACAAUGGUAUGCGUGGUUUGCGGCCCUAAUUUAUUCAGCACGCGACUGCCGCAUCCCGCACGGGAGGCGCAGCUGCUGCAUGACGCUUUAACGUCGCAGCUCACCACCGCCUGACCAUUCUGCCAGGAGACAACGGUUGCCCACUCUUUAAUCAUUGUACUGCCCUGAAUUUGAUACUGUCGGCAAUGCGC
CP000857.1/2776042-2776924 UUGUGAGCGCUUAUUUU--GCGG-GGAUCUUGAGAGGAUUUUGUCGUAGGUUUGCGGAGGGUGGCGGGGUA---UCAAUUA-------UCGAUGUGAGCAAUGAUCGAAAAGUUACGUAUGUUCUUCAUAGAGAUAAAUUAUUAUGCCUUACGCCUGGUUGACCAGACU-UU-AGAGGUCGCUGUUCUGAGCUUAACGUCUGUUUUAACUGAAACGCCGCAUUCUACACUACAACGCUAAGGCGAGGAAAUGUUCAUAGUGUAAGGAGAGCGGGAACUGGAAAACGCCUCGCUUUUUUCCUGUAAAACACCGCAAC----GCAG------GAAA----------AGCGCAUGCUUAUCGGG-ACAACAA-----CCCAACGCGG-CAGG-UGUACCGU---------------------------------UGGGCAAAACGUUUACUGGCGCGUUUCGAUUGAGGUAGUUUCGACGCGAACAAGGUCCGGCGGGAGGGCAACGUUUAAAAUCACCGGCUGCCAGGCGUCGCGCUCCG-CCAGUUUU-CGGGAAUAGCCGCGGGCAACCAGAAAACCGCCCACGCCGCCCAGCACGGCCCCGCUUAAUGCGGCAAGGUCAGAUCCAAACAGCAUCUGAAAAAGCGCCGCACAAAGAAAUAGCCCCGCUAAAGGCGACAUAUAGACCAGCAACGCCGAACCUAAAAGGCUUUUUUCGGCGAUGCCCAACUCGACUUUCUGCCCCGGCGCCAGCGGCUCCGCGCUUGGCACAACAAUGGUAUGGGUGGUUUGCGGCCCUAAUUUAUUCAGCACGCGACUGCCGCAUCCCGCACGGGAGGCGCAGCUGCUGCAUGACGCUUUAACGUCGCAGCUCACCACCGCCUGACCAUUCUGCCAGGAGACAACGGUUGCCCACUCUUUAAUCAUUGUACUGCCCUGAAUUUGAUACUGUCGGCAAUGCGC
FR877557.1/2581256-2582181 ACCUGAGCUUCCAUUUC--ACGG-UCA----GACAGGCCA---CCGCAGAUCUGGAUAAUACGGUCAGACAGCGUCGAUUUACCGUGGUCAAUGUGAGCAAUGAUCGAAAAGUUACGUAUGUUCUUCAUAGAGAUAAAUUAUUAUGCCUUACGCCUGGUUGACCAGACU-UU-AGAGGUCGCUGUUCUGAGCUUAACGUCUGUUUUAACUGAAACGCCGCAUUCUACACUACAACGCUAAGGCGAGGAAAUGUUCAUAAUGUAAGGAGAGCGGGAACUGGCAAGCGUCUCACUUUUU--ACGUAAGUCACUGUAAC----GCCG------AAAAAGCCCCUGAUAGCGCAAGCUUAUCGGC-CCGACAU----CUCCUGCAUGG-CAGG-AA-AAAAUGACCUUAGCAGACCA-GCUAAACGCAGCGCUAUCCGGCACAGCGUCUACUGGCGCGUUUCGAUUGAUGUGGUUUCGACGCGAACAAGCUCGGACGGGAGGGCAACGCUUAAAAUCACCGGUUGCCAGGUAUCGCGCUCCG-CCAGUUUC-CGGGAAUAGCCUCGGGCAAGCAAAAAACCGCCAACGCCACCUAAAACAGCGCCGCUUAAUGCCGCAAGGUCAGAUCCAAACAAUACCUGGAAAAGCACUGCAAAGAGAAAUAACCCCGCUAAAGGCGACAUAUAGACCAACAAUGCCGACCCUAAGAGGCUUUUUUCGGCGAUGCCAAGCUCAACUUUCUGCCCCGGCGACAGCGGCUCCACGCUUGGCACCACAAUUGUAUGAGUCGUUUGCGGCCCUAAUUUAUUCAGCACGCGGCUGCCGCAUCCCGCCCGGGAGGCGCAGUUGCUGCACGAUGUUUUAACAUCACAACUCACGACCGCCUGGCCAUUCCGCCAGGAGACGACCGUCGCCCACUCUUUAAUCAUUGUACUGCCCUGAACUUGAUACUGUCUGCAAUACGC
CP000822.1/206308-205392   ACCUGCGCUUCCAUUUC--ACGG-UCA----GACAGGCCA---CCGCAGAUCUGGAUAAUGCGGUCAGACAGCGUCGAUUUACCGUGGUCGAUAUGAGCAAUGAUCGAAAAGUUACGUAUGUUCUUCAUAUAGAGUAAUUAUUGUGCCUUACGCCUGCCUGAGCAGGCUCUU-AGAAGUCGCUGUUCUGAGCUUAACGUCUGUU-UAACUGAAACGCCGCAUUCUACACUACAACACUGAGGCGAGGAAAUGUUCAUACAGCAAGGAUAGCGGGAACCGGAAACGGCAUCGCUUUUCUGAUGUAAAACGUCGUAAGGGAAGCAUGACGCCCAAU----------AGCGCGAGCUUAUCGGGCAUGGGAGGUCUGCUUAUCGUUCCCAGGCCGGAUCAGGCGAA-------GCCG-------------CCAUCCGGCAAAAAUAUCACGGGUUCGUUUCGGAAGAUGGUGUUUCAACGCGAACCAGACCGGGAGGAAGAGCAACGUUAAGAAUGACCGGCUGCCAGGCCUCGCGUUCAG-CCAGUUUA-CGCGAGUAGCCGCGCGCAAUCAGAAAACCCCCGACGCCGCCCAGCACCGCGCCGCUCAACGCGGCAAUAUCAGAACCAAACAGUACCUGGAACAACGCCGCGAAGAUAAACAGCCCAACCAGCGGCGACAGGUAAACCAGCAUUGCUGACCCCAGCAGGCUGCCUUCGGCAAUGCCCAGUUCCACUUUUUGACCAGGCGCCAGCGGUUCGGCACUUGGCACCACAAUGGUAUGUGUGGUUUGCGGCCCGAGUUUAUUCAGCACGCGACUGCCGCAUCCGGCCCGUGAGGCGCAACUGCUGCACGAUGCUUUGACGUCGCAGCUCACCAGUGCCUGGCCAUUUUGCCAGGAGACAACGGUCGCCCACUCUUUAAUCAUUGUGCCGCCCCGAACUUAAUAUUGUCCGCAAUGCGU
CACD01000067.1/9095-9929   ACCUGCGCUUCCAUUUC--ACGG-UCA----GACAGGCCA---CCGCAGAUCUGGAUAAUACGGUCAGACAGCGUCGAUUUACCGUGGUCGAUGUGAGCUAUGAUUGAAAAGUUACGUAUGUUCUUCAUAUAGUGUAAUUAUUGUGCCUUACGCCCGCCUGAGCAGGCU-CUGAGAAGUCGCUGAUCUGAGCUUAACGUCUGUU-UAAGUGAAACGCCGCAUUCUACACUACAACGCUGAGGCGAGGAAAUGUUCAUAGAGCAAGGAUAGCGGGAACUGGAAACAACUUUGC------------AAAGUCGGUGAA-----------------------------ACUUUUGCC---------------------GGAUGGCGA-CACA-AGCGCCAU---------------------------------CCGGCAAAGCUAUCACUGUUGGGUUUC---------------GACGCGAAUGAGAUCGGGUGGGAGAGCAACGUUCAGAAUGACCGGCUGCCAGGCUUC--GCGCUCAGCAAGCUUACGAGAGUAUCCACGGGCAAUCAGGAAUCCGCCCACGCCCCCCAGCACGGCACCGCUUAAUGCCGCAAGGUCGGAACCAAACAGCACCUGGAAUAGCGCCGCGAAGAGAAAGAGCCCCGCCAACGGAGACAUGUAGACCAACAUCGCUGAACCCAGCAGGCUACCCUCGGCAAUACCCAGUUCAACUUUUUGACCGGGCGCUAAGGGUUCGUCGCUGGGCACCACGAUGGUAUGCGUGGUCUGCGGCCCAAGUUUGUUCAGCACGCGGCUCCCGCAUCCGGCCCGCGAAGCACAGCUGCUACAUGAUGCUUUAACAUCACAGCUGACCGUCGCCAGACCAUUUUGCCAGGAGACGACUGUCGCCCACUCUUUAAUCAUUGUGCAGCCCUGAACUUAAUAUUGUCCGCGAUACGC
#=GC SS_cons               :::((((((((((-(((..,,<<.<<<....--<<<<<--...--<<<<<<<<<<<--<<<<<----<<<----<<<<<<-----<<-<<<___>>>->>-->>>>>>--->>>->>>>>-->>>---------->>>>>---->>>----->>>>>-->>>>><<<<-.<<.-<<<-<<<______>>>->>>>>->>>><<<<<____>>>>>,<<<<-<<<<<<<<<<<--<<<____>>>-->--------->>>>>>-->>>>->>>>)))-)))))---)-)))),,,<<<<<<<<<_____________....>>>>......>>>>..........>{{{{{{{{{{{{{<<<._______.....>>>,,,,,,,.{{{{.-{{{{-{{.-.............-.............----{{{{{{{--{{{{--{{{{{<<<<<--<<<<<___>>>>>-->>>>>,,,,,,{{{{{{{{{{--{{{{,,,,,,,,,,,,,,,[[[[[[[-[[[[(((((((((((.-(((---(.((((,,,,,,,<-<<<<____________>>>>->,,<<<<-<<<--<<<----<<<--<<<<<<----<<<<<<-<_____>->>>>>>------>>>>>>-->>>----->>>-->>>--->>>>,,,,,,,,,,,,<<<-<<<<<<<<<<___>>>----->>>>>>>->>>,,,,)))))----)))---))))))--))))),,<<<<<-<<-<<______>>->>->>>>>]]]]]]]]]]],,,,,,,,,,,<<<-<<<-<<<<-<<-<<<<____>>>>->>>>>>->>>>>>,,<<<<______>>>>,,,}}}}----}}}}}}}}}},,,,,}}}}}-----}}}}-}}}}}}}----------}}-}}}}---}}}},,,,,}}}}-----}}}-}}}}}}
#=GC RF                    acccGagCuuccaUuuc..acGg.uca....GAcaGGcca...cCGcagauuuggauAauacGGucagacAGcGuCgauuuAccGuGGuCgAUgcGaGCaAUgaucGaAAAguuACguauGUucuUCAUAgAGAuaaauuAUUaugCCUUACgCCugguugacCaGaCU.uu.AgagGuCgCUGuUCuGaGcuuaaCGuCuGuuuuAAcUgaaaCGCCGCAcuCuaCacuaCAACGCUaAGGCGAGGAAAUGUUCAuaguGuAAgGagAGCGGgaaCuggaaAacGccuCgCUUuuuuccuGuAAAAcaccGuAAc....gCag......gaaa..........agCgcauGCcuaucGGg.acaAcAa.....cCCAacgcgg.CaGG.uGcaccau.................................ugGGCgaAacguuuACuGgcgCGucUCgacugAgGcaguuUCgaCGcGAAcaAGguCcGGcGggAggGCAACGUUuAaAAUcACgGGcuGCCaggcguCGCgcgCcg.cCaguUUu.cGgGAaUAgCCgCgGGCAAuCAgAAAACCGCCcAcGCCgCCcaGcACgGCaCCGcucAAuGCgGCAAgguCaGguCCAAACAGcacCuGaAAaAgCGCcGCaaAgagAAAuAGCcCcgCuAAaGGcGACAuaUAgACCAgCaacGCcGaaCCuAaaaGGCUuuuuuCgGCgAuGcCcAaCcCgaCUUUcuGcCCcgGcgccAGCGgcUCcgCgCUugGcaCaACAAugGuaUGcGcggucuGCggCCcuAaUUUAUUCAGCaCGCgaCuGCCGCAuCccGCaCggGaGGCGCaGcuGCuGCAuGacGcUUUAACguCgCAGCccACcAcCgCCgGacCAUUcUgcCaGGAGAcaacgGucGCCcaCUCUUUAAUCauUgugCuGCCCuGAAuUUgauacUGUCgGCAaugcGc
//
# STOCKHOLM 1.0

#=GF AC   RF02747
#=GF ID   FtrA
#=GF DE   Francisella sRNA A
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   134.00
#=GF TC   134.20
#=GF NC   41.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21067590
#=GF RT   Identification of small RNAs in Francisella tularensis.
#=GF RA   Postic G, Frapy E, Dupuis M, Dubail I, Livny J, Charbit A, Meibom KL
#=GF RL   BMC Genomics. 2010;11:625.
#=GF CC   Deletion led to significant changes in the expression of several mRNAs.
#=GF CC   However, it did not alter Francisella's growth under stress condition or
#=GF CC   its ability to induce disease in a mouse model.
#=GF WK   Francisella_small_RNAs
#=GF SQ   5



AM233362.1/1256577-1256687 GUACCAAAUAAUUAAUGCUCUGUAAUCAUUUAAAAGUAUUUUGAACGGACCUCUGUUUGACACGUCUGAAUAACUAAA-AAACAAAAAUUUGCCACCUAAGUGGCUUUUUUU
CP002557.1/787238-787128   GUACCAAAUAAUUAAUGCUCUGUAAUCAUUUAAAAGUAUUUUGAACGGACCUCUGUUUGACACGUCUGAAUAACUAAA-AAGCAAAAAUUUGCCACCUAAGUGGCUUUUUUU
CP001633.1/606775-606665   GUACCAAAUAAUUAAUGCUCUGUAAUCAUUUAAAGGUAUUUUGAACGGACCUCUGUUUGACACGUCUGAAUAACUAAA-AAACAAAAAUUUGCCACCUAAGUGGCUUUUUUU
CP000915.1/1343191-1343302 GUACCAAAUAAUUAAUGCUCUGUAAUCAUUUAAAAGUAUUUUGAACGGACCUCUGUUUGACACGUCUGAAUAACUAAAAAAACAAAAAUUUGCCACCUAAGUGGCUUUUUUU
CP002558.1/1127310-1127419 GUACCAAAUAAUCAAUGCUCUGUAAUCAUUUAAAAGUAUUUUGACCGGACCUCUGUUUGACACGUCUGAAUAACUAAA--AGUAAAAAUUUGCCACUCAAGUGGCUUUUUUU
#=GC SS_cons               :::::::::::::<<<<<<---<<<____>>>-->>>>>><<<<<<<<____>>>>>>>>------------------.------------<<<<<____>>>>>:::::::
#=GC RF                    GUACCAAAUAAUuaaugCuCUGuaaUCAUuuaAAaGuauuuugaaCgGACCUCuGuuugaCACGUCUGAAUAACUAAA.AAacAAAAAUUUGCCaCcuAAGuGGCUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02748
#=GF ID   FtrB
#=GF DE   Francisella sRNA B
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   66.00
#=GF TC   66.00
#=GF NC   53.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   21067590
#=GF RT   Identification of small RNAs in Francisella tularensis.
#=GF RA   Postic G, Frapy E, Dupuis M, Dubail I, Livny J, Charbit A, Meibom KL
#=GF RL   BMC Genomics. 2010;11:625.
#=GF CC   Deletion led to significant changes in the expression of several mRNAs.
#=GF CC   However, it did not alter Francisella's growth under stress condition or
#=GF CC   its ability to induce disease in a mouse model.
#=GF WK   Francisella_small_RNAs
#=GF SQ   5



AM233362.1/37655-37769       AUGAUACUAACUUAACGUCGGUAGUCAUUCCCGCGUAGGCGGGAAUCUCUUUAAUUGCUAUGAGGUCCCUGUGUCAAGCACGAGGAUUGUAAGUUAAAUCUCUAGUAUAAUUUUU
CP001633.1/1656095-1655981   AUGAUACUAACUUAACGUCGGUAGUCAUUCCCGCGUAGGCGGGAAUCUCUUUAAUUGCUAUGAGGUUCCUGUGUCAAGCACGAGGAUUAUAAGUUAAAUCUCUAGUAUAAUUUUU
ABXZ01000004.1/119791-119677 AUGAUACUAACUUAAUAUCGGUAGUCAUUCCCGCGUAGGCGGGAAUCUCUUUAAUUGCUAUGAGAUCCCUGUGUCAAGCACGAGGAUUGUAAGUUAAAUCUCUAGUAUAAUUUUU
CP002557.1/26390-26276       AAGACUGUUGAUUUAAUCAUCGAGUCAUUCUCGCGAAGGCGGGAAUCUCCCAAGUAUUUAAGAGAUCCCCGUGUCAAGCACGAGGAUUGUAAGUUAAAUCUCCAGUAUAAUUUCA
CP000915.1/19288-19402       AUGAUACUAACUUAACGUCGGUAGUCAUUCCCGCGUAGGCGGAAAUCUCUUUAAUUGCUAUGAGGUCCCUGUGUCAAGCACGAGGAUUGUAAGUUAAAUCUCUAGUAUAAUUUUU
#=GC SS_cons                 ::<<<<<<-<<_____>>->>>->>><<<<<<<<____>>>>>>>>---------<<<<<-<<<<<<<-<<<<<___>>>>>->>>>------------>>>>>>>>::::::::
#=GC RF                      AuGacaccagcUUaAugccgguAguCauuCcCGCGuAGGCGgGaauCUCuuuAaUugcuauGaGaucCCcGuGuCAAgCaCgAGgauUgUAAGUUAAAUCuCuagcaUAAUUUuu
//
# STOCKHOLM 1.0

#=GF AC   RF02749
#=GF ID   Ncrwmel02
#=GF DE   Wolbachia sRNA mel02
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   101.00
#=GF TC   101.30
#=GF NC   46.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0051701; interaction with host;
#=GF RN   [1]
#=GF RM   25739023
#=GF RT   Discovery of putative small non-coding RNAs from the obligate
#=GF RT   intracellular bacterium Wolbachia pipientis.
#=GF RA   Woolfit M, Algama M, Keith JM, McGraw EA, Popovici J
#=GF RL   PLoS One. 2015;10:e0118595.
#=GF CC   May play role in the interaction with the host. 
#=GF WK   Wolbachia
#=GF SQ   3



AE017196.1/1039620-1039870 AGAGUUUAGAGGGUUAUAGAGAAACCGGUCAGAUUAGGUUUUUAAUCUAAUCUGACCGAUAGCUUUAAUAGUGAGGUAAGCUUUAAUAUAGCACUCCUAAUUCAUAACGCUACACUCGUGCAUAAUUUAUUUUUAAUUUGUGCACGAGCGUUAGUAAAUUAUUUACUUUUUGAAAUAAAAUUUGGCAUCACUUUAAUAUUGAGACUUAGUAAACCUCAGUAGGUCUGCCAGUUGGGCCCAUAAGAAUUAUU
AM999887.1/1099389-1099639 AGGGUUUAGAAGGUUAUAGAGAAACCGGUCAGAUUAGGUUUUUAAUCUAAUCUGACCGAUAGCUUUAAUAGUGAGGUAAGCUUUAAUAUAGCACUCCUAAUUCACAGUGCUACACUCGUGCAUAAUUUAUUUUUAAUUUGUGCACGAGCGUUAGUAAAUUAUUUACUUUUUGAAAUAAAAUUUGGCAUCACUUUAAUAUCCAGACUUAGUAAACCUCAGUAGGGCUGCCAGUUGGACCCAUAAGAAUUACU
ACFP01000208.1/1606-1856   AGAGUUUAGAGGGUUAUAGAGAAACCGGUCAGAUUAGGUUUUUAAUCUAAUCUGACCGAUAGCUUUAAUAGUGAGGUAAGCUUUAGUAUAGCACUCCUAAUUCAUAACGCUACACUCGUGCAUAAUUUAUUUUUAAUUUGUGCACGAGCGUUAGUAAAUUAUUUACUUUUUGAAAUAAAAUUUGGCAUCACUUUAAUAUUGAGACUUAGUAAACCUCAGUAGGUCUGCCAGUUGGGCCCAUAAGAAUUAUU
#=GC SS_cons               ::(((((--((((((,<<<<<----<<<<<<<<<<<<<<<___>>>>>>>>>>>>>>>---->>>>>,,,,,,<<<---<<<_______>>>--->>>,,,,,,,,,,<<<<<-<<<<<<<<<<<-<<<____>>>->>>>>>>>>>>->->>>>,,,<<<<<<________>>>>>>,,,<<<<<<--<<<----<<<<<<<___________>>>>>>>>>>->>>>>>,,,)))))-)--))))):::
#=GC RF                    AGaguucAGagGGccAuagaGAAACCGGuCaGauuaGguuUUUaacCuaauCuGaCCGAUAGCucuaAUAGUGaGGUAAGCuUUAaUAUaGCACUCCuAAUUCAuAacgCuaCACuCGuGCacaaUuuaUUUUuaaUuuguGCaCGaGCGUuaGcAAAuuauuuACUUUUUGaaauaaAAUcuGGCaUCaCcUUAAuacugaGACUUAGUAAACCucaguagGuCuGCCagUUGggCCcAuAAgaacuAuU
//
# STOCKHOLM 1.0

#=GF AC   RF02750
#=GF ID   ES003
#=GF DE   ES003 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   65.00
#=GF TC   65.10
#=GF NC   61.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0006950; response to stress;
#=GF DR   GO; 0006113; fermentation;
#=GF RN   [1]
#=GF RM   26653712
#=GF RT   Differential expression of small RNAs under chemical stress and fed-batch
#=GF RT   fermentation in E. coli.
#=GF RA   Rau MH, Bojanovic K, Nielsen AT, Long KS
#=GF RL   BMC Genomics. 2015;16:1051.
#=GF CC   Differentially expressed under several chemical stress and fermentation
#=GF CC   conditions. 
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   8



CP001383.1/28466-28518         GUUUGCCAGAAAUUCGUCGGUAAGCAGAUUUGCAUUGAUUUACGUCAUCACUG
U00096.2/29551-29603           GUUUGCCAGAAAUUCGUCGGUAAGCAGAUUUGCAUUGAUUUACGUCAUCAUUG
AEJU01000190.1/41745-41693     GUUUGCCAGAAAUUCGUCGGUAAGCAGAUUUGCAUUGAUUCACGUCAUCAUUG
AERN01000067.1/12910-12962     GUUUGCCGGAAAUUCGUCGGUAAGCAGAUUUGCAUUGAUUUACGUCAUCAUUG
FM180568.1/32463-32515         GUUUGCCAGAAAUUCGUCGGUAAGCAGAUUUGCAUUGAUUUACGUCAUUAUUG
AEME01000001.1/2358209-2358157 GUUUGCCAGAAAUUCGUCGGUAAGCAGAUUUGCAUUGAUUCAUGUUAUCAUUG
AFGX01000001.1/330625-330677   GUUUGCCAGAAAUUCGUCGGUAAGCAGAUUUGCAUUGAUUUACGUCAUUACUG
AEMF01000001.1/1406865-1406813 GUUUGCCAGAAAUUCGUCGGUAAGCAGAUUUGCAUUGAUUCAUCGCAUCAUUG
#=GC SS_cons                   <<<<<<<-<<______>>>>>>>>>-------<<-<<<<_______>>>>->>
#=GC RF                        GUUUGCCAGAAAUUCGUCGGUAAGCAGAUUUGCAUUGAUUuACGUCAUCAUUG
//
# STOCKHOLM 1.0

#=GF AC   RF02751
#=GF ID   ES036
#=GF DE   ES036 (CssrF) sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   45.60
#=GF TC   45.60
#=GF NC   45.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0006950; response to stress;
#=GF RN   [1]
#=GF RM   26653712
#=GF RT   Differential expression of small RNAs under chemical stress and fed-batch
#=GF RT   fermentation in E. coli.
#=GF RA   Rau MH, Bojanovic K, Nielsen AT, Long KS
#=GF RL   BMC Genomics. 2015;16:1051.
#=GF RN   [2]
#=GF RM   21483688
#=GF RT   An integrated approach for finding overlooked genes in Shigella.
#=GF RA   Peng J, Yang J, Jin Q
#=GF RL   PLoS One. 2011;6:e18509.
#=GF CC   Differentially expressed under several chemical stress conditions. Also
#=GF CC   identified in Shigella as CssrF [2]. 
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   4



U00096.2/740211-740253       AAAUUUGUGCAAAUUCAAUAAAUUGCAGGAAAUACGUAGGCCU
AGTL01000317.1/47527-47485   AAAUUUGUACAAAUUCAAUAAAUUGCAGGAAAUACGUAGGUCU
AEMF01000001.1/944896-944854 AAAAUUGUGCAAAUUCAAUAUAUUGCAGGAGAUUAGUAGGCCU
AFGZ01000011.1/108373-108331 AAAUUUUUGCAAAUUCAAUAAAUUGCAGGAAAUACGUAGGCCU
#=GC SS_cons                 :::<<<-<<<<<__________>>>>>->>>::::::::::::
#=GC RF                      AAAuUUGUGCAAAUUCAAUAAAUUGCAGGAaAUACGUAGGCCU
//
# STOCKHOLM 1.0

#=GF AC   RF02752
#=GF ID   ES056
#=GF DE   ES056 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   58.00
#=GF TC   58.80
#=GF NC   56.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0006950; response to stress;
#=GF DR   GO; 0006113; fermentation;
#=GF RN   [1]
#=GF RM   26653712
#=GF RT   Differential expression of small RNAs under chemical stress and fed-batch
#=GF RT   fermentation in E. coli.
#=GF RA   Rau MH, Bojanovic K, Nielsen AT, Long KS
#=GF RL   BMC Genomics. 2015;16:1051.
#=GF CC   Differentially expressed under several chemical stress and fermentation
#=GF CC   conditions. 
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   6



U00096.2/1102566-1102475       AGAUGUAAUCCAUUAGUU-UUAUAUU-UUACCCAUUUAGGGCUGAU---UUAUUACUACACACAGCAGUGCAACAUCUGUCAGUACUUCUGGUGCUU
AEMF01000001.1/1587137-1587228 AGAUGUAAUCCAUUAGUU-UUAUAUU-UUACCCAUUUAGGGUUGAU---UUAUUACUACACACAGCAGUGCAACAUCUGUCAGUACUUCUGGUGCCU
CP000247.1/1094222-1094131     AGAUAUAAUCCAUUAGUU-UUAUAUU-UUACCCAUUUAGGGCUGAU---UUAUUACUACACACAGCAGUGCAACAUCUGUCAGUACUUCUGGUGCUU
AFGE01000042.1/49090-49181     AGAUGUAAUCCAUUAGUU-UUAUAUU-UUACCCAUUUAGGGCUGAU---UUAUUACUACACACAACAGUGCAACAUCUGUCAGUACUUCUGGUGCUU
AEJU01000274.1/5718-5627       AGAUGUAAUCCAUUAGUU-UUAUAUU-UUACCCAUUUAUGGCUGAU---UUAUUACUACACACAGCAGUGCAGCAUCUGUCAGUACUUCUGGUACCU
CP000822.1/1883393-1883489     AGUUGUAGUCCAUCUGUUUUAAUAUUUUUACCCUUUUUGGGUUGAUGUUUUAUUUCUACACACAGCAGUGCAACAUCUGUCAGUACUUCUGGUGCCU
#=GC SS_cons                   ::::<<<<<--<<<<<<<.<<<____._________>>>>>>>>>>...-->>>>>--<<<-<<<-<<<<<-<<____>>-->>>>>->>>>>>:::
#=GC RF                        AGaUGuaauCCaucaguu.cuaUAUU.UUACCCaUUuagggcugau...UUauuaCUACaCACaGCaGugCAaCAUCUGuCAGuaCuUCuGGuGCuU
//
# STOCKHOLM 1.0

#=GF AC   RF02753
#=GF ID   ES173
#=GF DE   ES173 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   55.00
#=GF TC   55.90
#=GF NC   48.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0006950; response to stress;
#=GF RN   [1]
#=GF RM   26653712
#=GF RT   Differential expression of small RNAs under chemical stress and fed-batch
#=GF RT   fermentation in E. coli.
#=GF RA   Rau MH, Bojanovic K, Nielsen AT, Long KS
#=GF RL   BMC Genomics. 2015;16:1051.
#=GF CC   Differentially expressed under several chemical stress conditions.
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   4



U00096.2/3154543-3154606   UUUUUACGCCUCAAACUUUCGUUUUCGGG-CAUUUCGUCCAGACUUAAGUUCACAACACCUCACC
AEJY01000042.1/60378-60441 UUUUUACGCCUCAAACUUUCGUUUUUGGG-CAUUUCGUCCAGACUUAAGUUCACAACACCUCACC
ADUU01000026.1/72568-72504 UUUUUACGCCUCAAACUUUCGUUUUCGGGUCAUUUCGUCCAGACUUAAGUUCACAACACCUCACC
AEJZ01000135.1/15562-15499 UUUUUCCUCCUCAAACUUUCGUUUUUGGG-UAUUUCGUCCAGACUUAAGUUCACACCAACUCACC
#=GC SS_cons               :::::::::::::<<<<<--<<<<--<<<.<_____>>>>>>>>-->>>>>::::::::::::::
#=GC RF                    UUUUUACgCCUCAAACUUUCGUuUUuGGG.cAUUUCgUCCAgACUUAAGUUCACAACAcCUCACC
//
# STOCKHOLM 1.0

#=GF AC   RF02754
#=GF ID   ES205
#=GF DE   ES205 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   86.00
#=GF TC   86.30
#=GF NC   36.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0006950; response to stress;
#=GF DR   GO; 0006113; fermentation;
#=GF RN   [1]
#=GF RM   26653712
#=GF RT   Differential expression of small RNAs under chemical stress and fed-batch
#=GF RT   fermentation in E. coli.
#=GF RA   Rau MH, Bojanovic K, Nielsen AT, Long KS
#=GF RL   BMC Genomics. 2015;16:1051.
#=GF CC   Differentially expressed under several chemical stress and fermentation
#=GF CC   conditions. 
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   5



U00096.2/3657034-3657105       GUAUCCACCAGUAGAACCCUUCGUUGCCCGAAUGCUGGCAGGAACUGUUGGCAGAACGGCAACAUUUUUUUU
CU651637.1/3704375-3704446     GUAUCCACCAGUAGAACCCUUCGUUGCCCGAAUGCUGGCAGAAACUGUUGGCAGAACGGCAACAUUUUUUUU
CU928164.2/4170340-4170411     GUAUCCACCAGUAGAACCCUUCGUUGCCCGAAUGCUGGCAGAAACUGUUGGCAGAACGGCAACAUUUUUUUG
AEME01000001.1/4549121-4549050 GUAUCCACCAGUAGAAACCUUCGUUGCCCGGAUGCAGGCAGAGACUGUCGGCAGAACGGCAACAUUUUUUUU
ADAX01000155.1/15878-15949     GUAUCCACCAGUAGAACCCUUCGUUGCCCGCAUGCUGGCAGAAACUGUUGGCAGAACGGCAACAUUUUUUUU
#=GC SS_cons                   ::::::::::::::::::::::<<<<<<----<<<<<<<<<___>>>>>>>>>---->>>>>>:::::::::
#=GC RF                        GUAUCCACCAGUAGAAcCCUUCGUUGCCCGaAUGCcggCAGAAACUGucgGCAGAACGGCAACAUUUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02755
#=GF ID   ES222
#=GF DE   ES222 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   62.00
#=GF TC   62.80
#=GF NC   61.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0006950; response to stress;
#=GF DR   GO; 0006113; fermentation;
#=GF RN   [1]
#=GF RM   26653712
#=GF RT   Differential expression of small RNAs under chemical stress and fed-batch
#=GF RT   fermentation in E. coli.
#=GF RA   Rau MH, Bojanovic K, Nielsen AT, Long KS
#=GF RL   BMC Genomics. 2015;16:1051.
#=GF CC   Differentially expressed under several chemical stress and fermentation
#=GF CC   conditions. 
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   5



U00096.2/4056241-4056348   AGUGCUUCAAUGGAAACAUUAAGCACCAUGUUGGUGCAAUGACCUUUGGAUAACCCUUUUUAUGCUCCGUGAAAGCGAUCACAAAGGGACUCUGCAAUACUUGUUUGC
AGSG01000231.1/16911-16804 AGUGCUUCAAUGGAAACAUUAAGCACCAUGAUGGUGCAAUGACCUUUGGAUAACCCUUUUUAUGCUCCGUGAAAGCGAUCACAAAGGGACUCUGCAAUACUUGUUUGC
AFGE01000068.1/2652-2545   AGUGCGUCAAUGGAAACAUUAAGCACCAUAUUGGUGCAAUGACCUUUGGAUAACCCUUUUUAUGCUCCGUGAAAGCGAUCACAAAGGGACUCUGCAAUACUUGUUUGC
ADUF01000264.1/6873-6980   AGUGCUUCAAUGGGAACAUUAAGCACCAUAUUGGUGCAAUGACCUUUGGAUAACCCUUUCUAUGCUCCGUGAAAGCGAUCACAAAGGGACUCUGCAAUACUUGUUUGC
AEJU01000210.1/23790-23683 AGUGCUUUAAUGGGAACAUUAAGCACCAUAUUGGUGCAAUGACCUUUGGAUAACCCUUGUUAUGCUCCGUGAAAGCGAUCACAAAGCAACUCUGCAAUACUUGUUUGC
#=GC SS_cons               :<<<<<<-<<<<____>>>>>>>>>><<-<<---<<<<--<-<<<<<<<<<-----<<<<<<<<___>>>>>>>>-->>>->>>>>>-->-->>>>-->>->>:::::
#=GC RF                    AGuGCuucaauGGaAACauuaaGCaCCaUguUGGuGCaAUGAcCuuuGGauAACCCcuuucacGCUCCgugaaagCGauCACaaaGggACUCuGCaAUacUuGUUUGC
//
# STOCKHOLM 1.0

#=GF AC   RF02756
#=GF ID   ES239
#=GF DE   ES239 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   62.00
#=GF TC   62.20
#=GF NC   49.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0006950; response to stress;
#=GF DR   GO; 0006113; fermentation;
#=GF RN   [1]
#=GF RM   26653712
#=GF RT   Differential expression of small RNAs under chemical stress and fed-batch
#=GF RT   fermentation in E. coli.
#=GF RA   Rau MH, Bojanovic K, Nielsen AT, Long KS
#=GF RL   BMC Genomics. 2015;16:1051.
#=GF CC   Differentially expressed under several chemical stress and fermentation
#=GF CC   conditions. 
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   5



U00096.2/4434589-4434711   CAGGGACAUCCUUUUAUCAUCGGGAAUACGAAAGAAAAGGGAGAAUAAACGUCUUACUUAUAGAACAGUGAAGAAUGCCACAAUUUUACGCUUUGAAAAUGAUGACACUAUCACAGUUGGCGC
CU928160.2/4522398-4522520 CAGGGACAUCCUUUUAUUAUCGGGAAUACGAAAGAAAAGGGAGAAUAAACGUCUUACUUAUAGAACAGUGAAGAAUGCCACAAUUUUACGCUUUGAAAAUGAUGACACUAUCACAGUUGGCGC
AEZI01000045.1/83214-83336 CAGGGACAUCCUUUUAUCAUCGGGAAUUCGAAAGAAAAGGGAGAAUAAACCUCUUACUUUUAGAACAGUGAAGAAUGCCACAAUUUAACGCUUUGAAAAUGAUGACACUAUCACAGUUGGCGC
AEVY01000053.1/52442-52564 CAGGGACAUCCUUUUAUUAUCGGGAAUACGAAAGAAAAGGGAGAAUAAACGUCUUACUAACAGAACAGCGAAGAAUGCCACAAUUUAACGCUUUGAAAAUGAUGACACUAUCACAGUUGGCGC
CP001383.1/4495125-4495003 CAGGGACAUCCUUUUAUCAUCGGGAAUACGAAAGAAAAGGGAGAAUAAACGCCUUACUUAUAGAACAGUGAAGAAUGCCACAAUUUUACGCUUUGAAAAUGAUGACACUAUCACAGUUGGCGC
#=GC SS_cons               ::<<<<<-<<<<<<<-<<-<<<______>>>-->>>>>>>>>-------->>>>>,,,,,<<<<<--<<<________>>>-->>>>><<<<-------<<<<<____>>>>>----->>>>:
#=GC RF                    CAggGacAuCCcuuuAucAuCGGGAAUaCGaAAgaaaagGGaGAAUAAACguCccACUuauagaaCAGuGAAGAAUGCCaCAAuucuaCGCcUUGAAAAuGaugACACcauCaCAGUUgGCGC
//
# STOCKHOLM 1.0

#=GF AC   RF02757
#=GF ID   Erse
#=GF DE   Erse small RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   138.00
#=GF TC   138.70
#=GF NC   137.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000655; ncRNA;
#=GF RN   [1]
#=GF RM   22575655
#=GF RT   Esre: a novel essential non-coding RNA in Escherichia coli.
#=GF RA   Chen Z, Wang Y, Li Y, Li Y, Fu N, Ye J, Zhang H
#=GF RL   FEBS Lett. 2012;586:1195-1200.
#=GF CC   May be essential for survival.
#=GF WK   Escherichia_coli_sRNA
#=GF SQ   6



CU928163.2/4506827-4507078 CCUGCGGAACUGCUGGCCCCUUAUACCGGUGAUAUCGCCGCUGAAGGAAUCAGCAAAGCCAUGCGCGGAGGCGCAAAGUUCCUGCAUCACGGCAUUAAGCGCCAGCAACGUUAUGUGGCAGAAGCCAUUACUGAAGAGUGGCGUAUGGCACCCGGUCCGCUUGAAGUGGCCUGGUUUGCGGAAGAGACGGCUGCCGUCGAGCGUGCUGUUGAUGCCCUGACCAAACGGCUGGAAAAACUGGAGGCUAAAUGA
AFGW01000065.1/20277-20026 CCUGCGGAACUGCUGGCCCCUUAUACCGGUGAUAUCGCCGCUGAAGGAAUCAGAAAAGCCAUGCGCGGAGGCGCAAAGUUCCUGCAUCACGGCAUUAAGCGCCAGCAACGUUAUGUGGCGGAAGCCAUUACUGAAGAGUGGCGUAUGGCACCCGGUCCGCUUGAAGUGGCCUGGUUUGCGGAAGAGACGGCUGCCGUCGAGCGUGCUGUUGAUGCCCUGACCAAACGGCUGGAAAAACUGGAGGCUAAAUGA
CP000247.1/4225935-4226186 CCUGCGGAACUGCUGGCCCCUUAUACCGGUGAUAUCGCCGCUGAAGGUAUCAGCAAAGCCCUGCGCGGAGGCACAAAGUUCCUGCAUCACGGCAUUAAGCGCCAGCAACGUUAUGUGGCGGAAGCCAUUACUGAAGAGUGGCGUAUGGCACCCGGUCCGCUUGAAGUGGCCUGGUUUGCGGAAGAGACGGCUGCCGUCGAGCGUGCUGUUGAUGCCCUGACCAAACGGCUGGAAAAACUGGAGGCUAAAUGA
CP000822.1/168320-168571   CCCGCAGAGCUUUUAGCGCCUUAUACCGGCGAUAUCGCGGCGGAAGGGAUCAGCAAAGUCCUGCGUGGCGGCGCUAAGUUUUUACGUCAUAACAUUCAGCGUCAGCAGCGUUAUAUCGCUGAGGCGAUGACUGAAGAGUGGCGUAUGGCGCCUGGGCCGCUGGAAGUGGCAUGGUUUGCAGAAGAAACGGCAGCCGUUGAGCGUGCAGUAGACGCGCUGACUAAACGGCUGGAAAAACUGGAGGCCAAAUGA
CP001127.1/4056791-4057042 CCUGCGGAGCUGUUGGCGCCAUACACGGGUGAUAUCGCGGCGGAAAGUAUCGGUAAGGUCGUGCGUGGCGGGGCUAAAUUCCUGCGCCACGGGUUUCAACGCCAGCAGCGUUAUGCCGCUGAAGCGAUCACUGAAGAGUGGCGUAUGGCGCCUGGCCCGCUGGAAGUCGCAUGGUUUGCCGAAGAAACCGCGGCUGUUGAGCGCGCCGUAGAUGCUCUGACCACACGGCUGGAAAAACUGGAGGCCAAAUGA
U00096.2/4018001-4018252   CCUGCGGAACUGCUGGCCCCUUAUACCGGUGAUAUCGCCGCUGAAGGAAUCAGCAAAGCCAUGCGCGGAGGCGCAAAGUUCCUGCAUCACGGCAUUAAGCGCCAGCAACGUUAUGUGGCGGAAGCCAUUACUGAAGAGUGGCGUAUGGCACCCGGUCCGCUUGAAGUGGCCUGGUUUGCGGAAGAGACGGCUGCCGUCGAGCGUGCUGUUGAUGCCCUGACCAAACGGCUGGAAAAACUGGAGGCUAAAUGA
#=GC SS_cons               [[[-[((((((<<<<<--<<<<----<<<<<____>>>>>--->>>>-->>>>>,,,,,,,<<<<<____>>>>>,)))))),((((((((((((,,,<<<<<<----------<<<<<____>>>>>---------->>>>>>,,,<<<-<<<<-<<<<<___>>>>>->>>>-->>>,,,,,,<<<<<___>>>>>,,,,))))))-))))))<<-<-<<____>>>->>,,,,,,,]-]]]::::::::
#=GC RF                    CCuGCGGaacugcuGgCcCcuuAuACcgGcGAUAUCgCcgCuGaagGaAuCagcAAAGuCauGCgcGGaGgcGCaAaguuCCUGCguCacgGcauUaAgCGcCaGCAaCGUUAUgugGCuGAAGCcacuACUGAAGAGuGgCGcAUGGCaCCcgguCCgCuuGAaGuGGCcugGUUuGCgGAAGAgaCgGCuGCcGucGAGCgugCcgUuGacGCcCUGACcAaACgGCUGgAAAAACUGGaGGCuAAAUGA
//
# STOCKHOLM 1.0

#=GF AC   RF02758
#=GF ID   RhlA_thermometer
#=GF DE   RhlA 5' UTR ROSE like thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Grosso-Becerra et al, PMID:25313031
#=GF SS   Predicted; PMID:25313031;
#=GF GA   85.00
#=GF TC   85.70
#=GF NC   75.70
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   25313031
#=GF RT   Regulation of Pseudomonas aeruginosa virulence factors by two novel RNA
#=GF RT   thermometers.
#=GF RA   Grosso-Becerra MV, Croda-Garcia G, Merino E, Servin-Gonzalez L,
#=GF RA   Mojica-Espinosa R, Soberon-Chavez G
#=GF RL   Proc Natl Acad Sci U S A. 2014;111:15562-15567.
#=GF WK   Repression_of_heat_shock_gene_expression_(ROSE)_element
#=GF SQ   4



CP000744.1/1685738-1685848 ACUUGUCUGCCGUUCGAACAACAAGAACGAACUCUACGUAAUGCCGGGAUACCCGUGGCAGCGAUAGCUGUUUGCCUGUUCGAAAACUUUUUGGGAGGUGUGAGAUGCGGC
CP002496.1/1635577-1635686 ACUUGUCUGCCGUUCGAACAAUAAGAACGAACUCUACGUAAUGCCGGGAUACCCGUGGCAGCGAUAGCUGUUUGCCUGUUCGAAAA-UUUUUGGGAGGUGUGAAAUGCGGC
FM209186.1/1665157-1665266 ACUUGUCUGCCGUUCGAACAACAAGAACGAACUCUACGUAAUGCCGGGAUACCCGUGGCAGCGAUAGCUGUUUGCCUGUUCGAAAA-UUUUUGGGAGGUGUGAAAUGCGGC
HM190303.1/323-432         ACUUGUCUGCCGUUCGAACAAUAAGAACGAACUCUACGUAAUGCCGGGAUACCCGUGGCAGCGAUAGCUGUUUGCCUGUUCGAAAA-UUUUUGGGAGGUGUGAGAUGCGGC
#=GC SS_cons               ::::::::(((((----(((,,,,,,,<<<<<-<<<<<<--<<<<<<<____>>->>>>>>>>->>>-->>>>><<<-<<<<<<<_._>>>>>>>>>>)))-----)))))
#=GC RF                    AcUUGUcUGCCGcUcGAaCaAuAAGAACgaaCUCuaCGcAAuGCCgGGAUAcCCGcGGCagCGAuaGcUGuucGCCuGccCgaaaA.UuuucGggaGGuGuGAaAUgCGGC
//
# STOCKHOLM 1.0

#=GF AC   RF02759
#=GF ID   LasI_thermometer
#=GF DE   LasI 5' UTR ROSE like thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Grosso-Becerra et al, PMID:25313031
#=GF SS   Predicted; PMID:25313031;
#=GF GA   76.00
#=GF TC   76.80
#=GF NC   40.10
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   25313031
#=GF RT   Regulation of Pseudomonas aeruginosa virulence factors by two novel RNA
#=GF RT   thermometers.
#=GF RA   Grosso-Becerra MV, Croda-Garcia G, Merino E, Servin-Gonzalez L,
#=GF RA   Mojica-Espinosa R, Soberon-Chavez G
#=GF RL   Proc Natl Acad Sci U S A. 2014;111:15562-15567.
#=GF CC   ROSE-like thermometer in the 5'UTR blocks the translation at lower
#=GF CC   temperature.
#=GF WK   Repression_of_heat_shock_gene_expression_(ROSE)_element
#=GF SQ   3



FM209186.1/4393752-4393643 AGCCUAGCAAGGGUCCGGGUUCACCGAAAUCUAUCUCAUUUGCUAGUUAUAAAUUUAUGAAAUUUGCAUAAAUUCUUCAGCUUCCUAUUUGGAGGAAGUGAAGAUGAUCG
CP000744.1/4032440-4032331 AGCCUAGCAAGGGACCGGGACGACCGAAAUCUAUCUCAUUUGCUAGUUAUAAAUUUAUGAAAUUUGCAUAAAUUCUUCAGCUUCCUAUUUGGAGGAAGUGAAGAUGAUCG
AE004091.2/1559151-1559260 AGCCUAGCAAGGGUCCGGGUUCACCGAAAUCUAUCUCAUUUGCUAGUUAUAAAAUUAUGAAAUUUGCAUAAAUUCUUCAGCUUCCUAUUUGGAGGAAGUGAAGAUGAUCG
#=GC SS_cons               :::<<<<<<<<<---<<<_____>>>--->>>-------->>>>>>,,,,,,<<<<<<<_______>>>>>>><<<<<<-<<<<<<______>>>>>>>>>>>>::::::
#=GC RF                    AGCCuaGCaaGgGuCCGGGuucACCGAAAcCuAUCUCAUUuGCuaGUUAUAAauuuauGAAAUUUGCauaaauuCuuCaGCuuCCuAUUUGGaGGaaGuGaaGaUGAUCG
//
# STOCKHOLM 1.0

#=GF AC   RF02760
#=GF ID   sR035
#=GF DE   sR035 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   233.00
#=GF TC   233.50
#=GF NC   46.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF RN   [1]
#=GF RM   24040259
#=GF RT   Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in
#=GF RT   vitro and during infection.
#=GF RA   Yan Y, Su S, Meng X, Ji X, Qu Y, Liu Z, Wang X, Cui Y, Deng Z, Zhou D,
#=GF RA   Jiang W, Yang R, Han Y
#=GF RL   PLoS One. 2013;8:e74495.
#=GF CC   Temperature-dependent expression pattern. Potentially involved in Y.
#=GF CC   pestis pathogenesis. Predicted target is ymoA, a thermo-sensitive
#=GF CC   regulator. 
#=GF WK   Yersinia_pestis
#=GF SQ   3



CP002956.1/631353-631148   GAAAUAUAAAAAACCCGACUGUUUUCCGGGUUUUUGUCAGGUAGUUGAUCACCUCAGAUGAAGGUGAAACGUGCCGUUGGGGGCGUCAUGACAUGAGCCACUGAAGCACGAGUAGGGGAAGUAGACCCUUCAUUCACUGGCCUAUA-CACGGGGGUUAUUUACCUCAAAAGCCCCGGAGCUGGGCUGGACUGCUCCGGGGCUUUUUC
CP000950.1/3988217-3988012 GAAAUAUAAAAAACCCGACUGUUUUCCGGGUUUUUGUCAGGUAGUUGAUCACCUCAGAUAAAGGUGAAACGUGCCGUUGGGGGCGUCAUGACAUGAGCCACUGAAGCACGAGUAGGGGAAGUAGACCCUUCAUUCACUGGCCUAUA-CACGGGGGUUAUUUACCUCAAAAGCCCCAGAGCUGGGCUGGACUGCUCCGGGGCUUUUUC
CP000720.1/3933031-3932835 GAAAUAUAAAAAACCCGACUGUUUUCCGGGUUUUUGUCAGGUAGUUGAUCACCUCAGAUAAAGGUGAAACGUGCCGUUGGGGGCGUCAUGACAUGAGCCACUGAAGCACGAGUAGGGGAAGUAGACCCUUCAUUCACUGGCCUAUAACACGGGGGGUAUUUACCUCAAAAGCCCCGGGACU----------GCUCCGGGGCUUUUUC
#=GC SS_cons               ::::::::<<<<<<<<<_________>>>>>>>>>(((((-----(((<<<<<<<____>->>>>>>,,<<<<<--<<-<<<<<-<<<<___>>>>>>>->>->>>>>>>,,,<<<<________>>>>)))----))))),,,,,.,,,,<<<<<_____>>>>><<<<<<<<<<<<<<-<<______>>>>>>>>>>>>>>>>::
#=GC RF                    GAAAUAUAaaaaaCCCGAcUGUUUUcCGGGuuuuuGcCaGGUAGUuGauCaCCucAGAUgAaGGuGaAACGuGCcGuuGgGGGCGuCauGAcauGaGCCACcGaaGCaCGAGUaGGGGAAGUAGACCCuuCaUUcACuGgCcUAUA.cAcGGgGGuUAUUUaCCcCaaaaGCCCCgGagCUgGgcuggACcGcuCcGGGGCuuuuUc
//
# STOCKHOLM 1.0

#=GF AC   RF02761
#=GF ID   sR084
#=GF DE   sR084 sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   95.00
#=GF TC   99.10
#=GF NC   38.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF RN   [1]
#=GF RM   24040259
#=GF RT   Determination of sRNA expressions by RNA-seq in Yersinia pestis grown in
#=GF RT   vitro and during infection.
#=GF RA   Yan Y, Su S, Meng X, Ji X, Qu Y, Liu Z, Wang X, Cui Y, Deng Z, Zhou D,
#=GF RA   Jiang W, Yang R, Han Y
#=GF RL   PLoS One. 2013;8:e74495.
#=GF CC   Temperature-dependent expression pattern. Potentially involved in Y.
#=GF CC   pestis pathogenesis. Predicted target is fur, ferric uptake regulator. 
#=GF WK   Yersinia_pestis
#=GF SQ   3



CP002958.1/5369-5292     GCAAAAGUCAGGACUAGACAUAUUAACCAUCGAUUCAGUCCUUAUCAUACGCCCUCACAGAACACCUCCUGUGAGGGC
L19030.2/2113-2188       CAAAAAGUCAGGACUAGACAUAUUAACCAUCGAUUCAGUCCUUAUCAUAG--CCUCACAGAACACCUCCUGUGAGGGU
ADAX01000181.1/3191-3268 GCAAAAGUCAGGACUAGACAUACUAUCCAUCGAUUCAGUCCUUACCUUACGCCCUCACUGAUUUCCUGCCGUGAGGGC
#=GC SS_cons             :::::::::<<<<<<-<<________________>>>>>>>>--------<<<<<<<<<<________>>>>>>>>>>
#=GC RF                  gcAAAAGUCAGGACUAGACAUAuUAaCCAUCGAUUCAGUCCUUAuCaUAcGCCCUCACaGAacaCCUcCuGUGAGGGC
//
# STOCKHOLM 1.0

#=GF AC   RF02762
#=GF ID   C1_109596F_thermometer
#=GF DE   C1_109596F  5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   125.00
#=GF TC   125.30
#=GF NC   30.20
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   23950988
#=GF RT   A genome-wide survey of highly expressed non-coding RNAs and biological
#=GF RT   validation of selected candidates in Agrobacterium tumefaciens.
#=GF RA   Lee K, Huang X, Yang C, Lee D, Ho V, Nobuta K, Fan JB, Wang K
#=GF RL   PLoS One. 2013;8:e70720.
#=GF CC   May regulate translation of the major cold shock protein cspA.
#=GF WK   RNA_thermometer
#=GF SQ   2



AE007869.2/109596-109822   UUUUGGCGAUCUGGUUGUCUUUUUAUCCCUCCUCUCUGAGACGCUGCGCUGUUCAAAGAAACUUGACUUUGAGACCCUUCCAACCUACGUACUUCGCCAUCGAUAUUUGUUUGACGACCAGAGCUUCGGCGUCUUUCCAGACGCUCACGACGAUCUUUUCCUUCAAAUUCGACCCAAGUCCGCACUGCUUGCAGUGCAAAUACAAUUGCCAACGGAAGGAAAUCGUU
AECL01000004.1/46476-46702 UUUUGGCGAUCUGGUUGUCUUUUUAUCCCUCCGCUCUCAGACGCUGCGCGGUUCAAAGAAACUUGACUUUGAGACCCUUCCAACCUACGUACUUCGCCAUCGAUAUUUGUUUGACGACCAGAGCUUCGGCGUCUUUCCAGACGCUCACGACGAUCUUUUCCUUCAAAUUCGACCCAAGUCCGCACUGCUUGCAGUGCAAAUACAAUUGCCAACGGAAGGAAAUCGUU
#=GC SS_cons               ::::(((--((((((((((,,,,,,,,,<<<______>>>,,<<___>>,,<<<<<<<________>>>>>>>,,,,,,,,,,,,,<<<----<<<____>>>---->>>,,))))))))))))),,<<<<<<<____>>>>>>>,,,((((((---(((((((,,,,,,<<<____>>>,<<<<<<____>>>>>>,,,,,,,,,,,,,,,,,)))))))))))))
#=GC RF                    UUUUgGCGAuCuGGucGuCUUUUUAUCCCucCuCUCUgaGACGCUGCGCuGcuCaaaGAAACUUGACuuuGagACCCUUCCAACCUaCgUACUuCGCCAUCGaUAUUcGuUUGaCgaCCaGaGCcUCgGCGuCuUUCCaGaCGCcCACgaCGauCUUuuCCuuCAAAUUCGaCCCAAGuCCGCaCuGCUUGCaGuGCAAAUACAAUUGCCAACGGaaGGaaauCGuc
//
# STOCKHOLM 1.0

#=GF AC   RF02763
#=GF ID   IsrM
#=GF DE   IsrM sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   376.00
#=GF TC   376.20
#=GF NC   154.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009405; pathogenesis;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF RN   [1]
#=GF RM   18267966
#=GF RT   Small RNAs encoded within genetic islands of Salmonella typhimurium show
#=GF RT   host-induced expression and role in virulence.
#=GF RA   Padalon-Brauch G, Hershberg R, Elgrably-Weiss M, Baruch K, Rosenshine I,
#=GF RA   Margalit H, Altuvia S
#=GF RL   Nucleic Acids Res. 2008;36:1913-1927.
#=GF RN   [2]
#=GF RM   21949647
#=GF RT   A Salmonella small non-coding RNA facilitates bacterial invasion and
#=GF RT   intracellular replication by modulating the expression of virulence
#=GF RT   factors.
#=GF RA   Gong H, Vu GP, Bai Y, Chan E, Wu R, Yang E, Liu F, Lu S
#=GF RL   PLoS Pathog. 2011;7:e1002120.
#=GF WK   IsrM_small_RNA
#=GF SQ   2



CP001363.1/2925275-2925603 AGCUUCAUGCUUCUUUUUUAGAUAGUUUGUUGUUCGUGCCUAUCGUACACUUUGCGACUGUUCGUUUUGCAUCUAUUCCAAGCAUCAAUCAAUACAAUAAAUUUCAGCACCAUAAAGAUAAUAAUAAAAAUCAACAAGAUACGAAAACCCCUUCCAUAUCAACAUCAUCACCACCCUUUUUGCGCCUUCCCUUCCCCGCAAAAAAUAAAAAUCUCCAACAAACUCAACCAUCUCCCCCACCAAUUACAAGGACGCCAGCCACUUUUUAGUUGUUUGAAGUUCAAUGAAGUCUACUAAGCCCGCACAGCACAAGCUCUGCGGGCUUUUUU
AB439839.1/45-348          AGCUUCAUGCUUCUUUUUUAGAUAGUUUGUUGUUCGUGCCUAUCGUACACUUUGCGACUGUUCGUUUUGCAUCUAUUCCAAGCAUCAAUCAAUACAAUAAAUUUCAGCACCAUAAAGAUAAUAAUAAAAAUCAACAAGAUACGAAAACCCCUUCCAUAUCAACAUCAUCACCACCCUUUUUGCGCCUUCCCUUCCCCGCAAAAAAUAAAAAUCUCCAACAAACUCAACCAUCUCCCCCACCAAUUACAAGGACGCCAGCCACUUUUUAGUUGUUUGAAGUUCAAUGAAGUCUACUAAGCCCGCA-------------------------
#=GC SS_cons               :{{{{{{{{{{{{,,,,,,[[[[[[[[[[[[[,,,((((,,,<<<<<_____>>>>>,<<<<-<<<-<<<___________>>>-->>>->>>>,,,,,,,,,,,,)))),,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<-<<<______>>>-->>>>,,,,,,,,,,,,,,,,<<<<<<<<____________>>>>>>>>,,,,,,,,,,,]]]]]]]]]-----]]]],,,,,,,<<<<<<-<<<<__________>>>>->>>>>>,,,}}}}}---}}}}}}}-----<<<<<<<<<-<<<____>>>->>>>>>>>>::::
#=GC RF                    AgCuuCaugCuuCUUUUUUaGauaGuuuGuuGUUCGuGCCUAuCGuaCACUUugCGaCuguuCguuUuGCAUCUAUUCCAAGCaUCaauCaauaCAAUAAAUUUCAGCaCCAUAAAGAUAAUAAUAAAAAUCAACAAGauaCGaaAACCCCuuCCAuauCAACAUCAUCACCACCCuuuuuGCGCCUUCCCUUCCCCGCaaaaaAUAAAAAUCUCCaaCaaaCuCAACCauCuCCCCCACCaauuaCaagGACGCCAGCCACuuuUuaguuGUUUGaaGuUCAauGaaGuCUACUaaGcccGcacaGcAcAAgCucugCgggCuuuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02764
#=GF ID   Ysr190
#=GF DE   Yersinia sRNA 190
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   66.00
#=GF TC   66.20
#=GF NC   62.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   SO; 0000122; RNA sequence secondary structure;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF RN   [2]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   The sRNA was identified by [2] and is confirmed to have a stable secondary
#=GF CC   structure by [1] using genome-wide structure probing at different
#=GF CC   temperatures. The function is unknown.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   4



CP000950.1/501337-501236   GCGAAUUGCUACGAUAUCAUUAUAAUGCCCAACCUUAGUGCUGAUCGCCGUGCCAGUUUCGUCGUAAAAAGGUGACAAAUCGGUAGCAGCAGGUUAUUUUUU
ACCB01000011.1/91169-91270 GCUAAUUGCUACGAUAUCAUUAUAAUGCCCGACCUUAGUGCCGAUCGCAGUGUCAAUUUCGUCGUAAAAAGGUGACAAAUCGGUGACAUCAGGUUAUUUUUU
FR729477.2/2758034-2758135 GCUAAUUGCUACGAUAUCAUUAUAAUGCCCGACCUUAGUACCGAUCGCAGUGUCAAAUUCAUCGUAAAAAGGUGACAAAUCGGUGACAUCAGGUUAUUUUUU
AALE02000020.1/91393-91494 GCUAAUUGCUACGAUAUCAUUAUAAUGCUCGACCUUAGUGCCGAUCACAGUAUCAAAAUCGUCGUAAAAAGGUGACAAAUCGGUGACAUCAGGUUAUUUUUU
#=GC SS_cons               :::::::<<----<<<____>>>--->>--<<<<<---<<<<<<<<<<<_____________________>>>>>---->>>>>>----->>>>>:::::::
#=GC RF                    GCuAAUUGCUACGauaUCAUuauAAUGCcCgaCCuUAGcgCcGauCgCcGUguCAauuUCgUCGUAAAAAgGcGaCAAAuCgGcgaCAuCaGGucAUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02765
#=GF ID   Ysr209
#=GF DE   Yersinia sRNA 209
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   59.00
#=GF TC   59.20
#=GF NC   52.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   SO; 0000122; RNA sequence secondary structure;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF RN   [2]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   The sRNA was identified by [2] and is confirmed to have a stable secondary
#=GF CC   structure by [1] using genome-wide structure probing at different
#=GF CC   temperatures. The function is unknown.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   4



CP000950.1/2587430-2587385 AUCAGACGGCAGCAACGAAAUGUCGAAAGAUAGCAAAAGAAUCAGU
FR729477.2/1349969-1349924 AUCAGACGGCAGCAACGAAAUGCCGAAAGAUAGCAAAAGAAUCAGU
ACCB01000063.1/9680-9725   AUCAGACGGCAGCAACGAAAUGUCGAAAGAUAACAAAAGAAUCAGU
AALC02000028.1/302-257     AUCAGACGGCAGUAACAAAAUGUCGAAAGAUAGCAAAAGAAUCAGU
#=GC SS_cons               <<<---<<<<<_________>>>>>--->>>:::::::::::::::
#=GC RF                    AUCAGACGgCAGCAACGAAAUGuCGAAAGAUAGCAAAAGAAUCAGU
//
# STOCKHOLM 1.0

#=GF AC   RF02766
#=GF ID   Ysr49
#=GF DE   Yersinia sRNA 49
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   95.00
#=GF TC   95.20
#=GF NC   61.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   SO; 0000122; RNA sequence secondary structure;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF RN   [2]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   The sRNA was identified by [2] and is confirmed to have a stable secondary
#=GF CC   structure by [1] using genome-wide structure probing at different
#=GF CC   temperatures. The function is unknown.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   3



CP002956.1/1072902-1073025 GUUUACCUAAUAGAUUUCAAGGUGUAGGAAGGUGGCGAGCGAAAGCAGCCAACACACCGACAACUUGAAAGAUGAAAGGUUGUUGCCGUGGAAACUUUUGGCCCAUCUUAGGAUGGGCUUUUUU
CP000950.1/4623011-4623134 AUUUACCUAAUAGAUUUCAAGGUGUAGGAAAGCGGCGAGCGAAAGCAGCCAACACACCGACAACUUGAAAGAUGAAAGGUUGUUGCCGUGGAAACUUUUGGCCCAUCUUAGGAUGGGCUUUUUU
AALD02000020.1/13345-13222 GUUUACCCAAUAGAUUUCAAGGUGUAGGAAGGCGGUGAGCGAGAGCAACCAACACACCUACAGCUUGAAAGAUGAAGGGUUGUUGCCGUGGAAACUUUUGGCCCAUCUCCGGAUGGGCUUUUUU
#=GC SS_cons               <<<<<_____>>>>>,,,,,,,,,,,,,,,,,,<<<--<<____>>->>>,,,,<<<<<<<<<<<<__________>>>>>>>>>-->>>,,,,,,,,,<<<<<<<<____>>>>>>>>:::::
#=GC RF                    guuuaCCuAAuagacUUCAAGGUGUAGGAAgGcGGcGAGCGAaAGCAgCCAACACaCCgaCaaCuuGAAAGAUGAAagGuuGucGCCGuGGAAACUUUUgGCCCauCUuaGGauGGGCuUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02767
#=GF ID   Ysr186_sR026_CsrC
#=GF DE   Yersinia sRNA 186/sR026/CsrC
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   57.00
#=GF TC   57.20
#=GF NC   56.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF CL   CL00106
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   SO; 0000122; RNA sequence secondary structure;
#=GF DR   GO; 0009405; pathogenesis;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF RN   [2]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF RN   [3]
#=GF RM   24786463
#=GF RT   A direct link between the global regulator PhoP and the Csr regulon in Y.
#=GF RT   pseudotuberculosis through the small regulatory RNA CsrC.
#=GF RA   Nuss AM, Schuster F, Kathrin Heroven A, Heine W, Pisano F, Dersch P
#=GF RL   RNA Biol. 2014;11:580-593.
#=GF CC   The sRNA was identified by [2] and is confirmed to have a stable secondary
#=GF CC   structure by [1] using genome-wide structure probing at different
#=GF CC   temperatures. The function is unknown.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   4



CP000950.1/4628384-4628061 UGUUAUUGGUACGGAUACACCAUGCAAGGAGCACAGUUACUCAGGAUGAGUGGCUUAUGUUUAAGGAACGUAAUGGAUAUACAAGGAAUGUAAUGGAUGUACGGGAGCCAAGGACGCUAUAAACGGAGCUAAUGUAAAGGGAUGUU-A-GGACACUGGCCGGAGCGCCGGGCGAAUCGCCUUCAGGGUUUGAGGGGUGGCAAGGAUCGCGUAUUGCAGGAGGGAGAAACCGGGACGUUAUCUAAGUGCAGGGAGUGCGCUGUAAGGAUAUCCUUCCGCAGAAGGUGCGAAAAAAGGCGACAGGUUAACCUGCCGCCUUUUUUCUUU
CP002956.1/1078276-1077952 UGUUAUUGGUACGGAUACACCAUGCAAGGAGCACAGUUACUCAGGAUGAGUGGCUUAUGUUUAAGGAACGUAAUGGAUAUACAAGGAAUGUAAUGGAUGUACGGGAGCCAAGGAUGCUAUAAACGGAGCUAAUGUAAAGGGAUGUUCA-GGACACUGGCCGGAGCGCCGGGCGAAUCGCCUUCAGGGUUUGAGGGGUGGCAAGGAUCGCGUAUUGCAGGAGGGAGAAACCGGGACGUUAUCUAAGUGCAGGGAGUGCGCUGUAAGGAUAUCCUUCCGCAGAAGGUGCGAAAAAAGGCGACAGGUUAACCUGCCGCCUUUUUUCUUU
AM286415.1/31270-31574     UUUUAACAGUGCGGGAUGUACUGGCAAGGAGCGUAAUCACUUAGGAAGAGUGGGGUAUGCUUAAGGAAUGUAAUGGAUAUACU-------------------GUGAGCCAGGGAUGAUAC--AGGGAGCUUAUAUAAAAGGAUGUUUAUGGACACAGGCCGGAGUGCUGGGUGAGUCACCUUCAGGGUUGGGGGGAUGGCAAGGAUGGCGAAUUGCAGUAGGGAGAAACCGGGACGUUAUAUCAGUGUAGGGAAUGCACAGUAAGGAUAUCCUUCCGCAGAAGGUGCGAAAAAAGGCGACAGGUUAAUCUGCCGCCUUUUUUCUUU
AALE02000042.1/8182-8486   UUUAAACAGUGCGGGAUGCGCUGGCAAGGAGCUUAAUCACUCAGGAAGAGUGGCUUAUGCUUAAGGAAUGUAAUGGAUAUACU-------------------GUGAGCCAGGGAUGAUAU--AGGGAGCUUAUUUAACAGGAUGUGUAUGGAUACAGGCCGGAGUGCUGGGUGAGUCGCCUUCAAGGUUGGAGGGAUGGCAAGGAUGGCACAUUGCAGAAGGGAGAAACCGGGAUGUUAACUAAGUGCAGGGAGUGCGCUGUAAGGAUAUCCUUCCGCAGAAGGUGCGAAAAAAGGCGACAGGUUAAUCUGCCGCCUUUUUUCUUU
#=GC SS_cons               (((((((-(((((,,,,,,<<______>>,,,,,<<<<<<<<_____>>>>>>>>,,,,,,,,,,,,,)))-))-))))-))),,,,,,,,,,,,,,,,,,,,,,,<<<--<<-<<<<-----<-<-<<<<-<<<_____________.__>>>->>>>>->>>>>>>->>>,,,,(((((((,,<<<<<--------<<<<__________>>>>--------->>>>><<<<-<-<<<<<---<<<<<-<____>->>>>>->>>>>->->>>>,,,))))))),<<<<<<<<<<<-<<<<____>>>>->>>>>>>>>>>:::
#=GC RF                    uguuaucaguaCgGaaagacCauGCAAGgAGCauagucaCucAGGAagaGuggcuUAUGuUUAAGGAAcGuAauGgauaUacaAggAAUgUAAUggAUgUAcGuGAgCCAagGAcgcuAuAAAcGGAGCuuAuguAAaaGGAUGUuuA.GGacaCagGCCGgagcgCcGGGcGAaUCgCCuuCAgGGuuuGaGGGaUGGCaaGGAUgGCguAuuGCAGaAGGGAGaaaCCGGgacGUuaucuaAGugcaGGGAgUGCgCuguaAggauaUCCuuCCGCAGaaGGcGCGaaaaaaGGCGACaGgUUAAcCuGCCGCCuuuuuuCUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02768
#=GF ID   Ysr155(RyfD)
#=GF DE   Yersinia sRNA 155(RyfD)
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   82.00
#=GF TC   82.70
#=GF NC   73.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   SO; 0000122; RNA sequence secondary structure;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF RN   [2]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   The sRNA was identified by [2] and is confirmed to have a stable secondary
#=GF CC   structure by [1] using genome-wide structure probing at different
#=GF CC   temperatures. The function is unknown.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   9



CP000950.1/3676769-3676631 CAGGACGAUCCGCUGACGUAGAAC----GCAUUA-UUUUAAUAUAGUGUCAAAAUAACCUUGAAAAAUUGAGGGAUGACCUCAUUUAAUCUCCAGUAGCAAUUUUGA-CCA-AUAUUGGAGGUGUUAUGCGUCUGGAUCGUCUUAC
CP000720.1/3621081-3620943 UAGGGCGAUCCGCUGACGUAGAAC----GCAUUA-UUUUAAUAUAGUGUCAAAAUAACCUUGAAAAAUUGAGGGAUGACCUCAUUUAAUCUCCAGUAGCAAUUUUGA-CCA-AUAUUGGAGGUGUUAUGCGUCUGGAUCGUCUUAC
FR729477.2/2237775-2237914 UAGGACGAUCCGCUGGCGCAUGAC----GUUGUACUUUAAAUAUAGUGUCGAAAUAACCUUGAAAAUUUGAGGGAUGACCUCAUCUAAUCUCCAGUAGCAAUUUUGA-CCA-AUAUUGGAGGUGUUAUGCGUCUGGAUCGUCUUAC
ACCB01000068.1/4896-5035   UAGGACGAUCCGCUGACGCAUAAC----GUUUUACUUUAAAUAUAGUGUCGAAAUAACCUUGAAAAUUUGAGGGAUGACCUCAUCUAAUCUCCAGUAGCAAUUUUGA-CCA-AUAUUGGAGGUGUUAUGCGUCUGGAUCGUCUUAC
CP002773.1/904568-904707   UAGGACGGUCCACUGACGCAUGAC----GUUGUACUGAUAAUAUAGUGUCGAAAUAACCUUGAAAAUUUGAGGGAUGACCUCAUUUAAUCUCCAGUAGCAAUUUUGA-CCU-ACAUUGGAGGUGUUAUGCGUCUGGAUCGUCUUAC
CP002505.1/778739-778878   CAAGACGAUCCAU-CACGCAUAAC---AGCUGUCCUCUGAAUAUACUGCCAAGAUAACCUUGAAAACGUGAGGGUUGACCUCAUCUAAUCUCCAGUAGCAAUUUUGU-UCA-GUAUUGGAGGUGUUAUGCGUCUGGAUCGUCUUAC
CP000783.1/626636-626774   CAAGACGAUCCGGU-ACGGAUAACUGACGCUCUAC--AUAAU-UAAGGUC--AUUAACCUUGAAUAAUUGAGGGAUGACCUCAUUUAAUCUCCAGUAGCAAUUUUGA-CCUGUUAUGGGAGGAGUUAUGCGUCUGGAUCGUCUUAC
FN554766.1/2990195-2990057 CAAGACGAUCCGGU-ACGCGUGAU----UUUCUUUUCACAUUAAUCUGGU-CAAUAACCUUGAAUAAUUGAGGGAUGACCUCAUUUAAUCUCCAGUAGCAACUUUGAUCCG-UUAUGGGAGGAGUUAUGCGUCUGGAUCGUCUUAC
CP003047.1/2734331-2734193 CAAGACGAUCCGGU-ACGGGUAAC----UUUCUU-UUCGCAUAAUUCAGGUCAUUCACCUUGAAUAAUUGAGGGAUGACCUCAUUUAAUCUCCAGUAGCAAUUUUGA-CCUGUUAUGGGAGGAGUUAUGCGUCUGGAUCGUCUUAC
#=GC SS_cons               :(((((((((((--((((((-(((....<<<<<<-<______>>>>>>>,,,,,,,,<<<<<<____>>>>>><<<<____>>>>,,<<<<<<<<<<__________.___._>>>>>>>>>>)))-)))))))))))))))))::
#=GC RF                    uaaGaCGauCCguUgaCGcauaac....gcccuacuuuuAAUauagggccaaAaUAACCuugaAaAauugaGGgauGACCUCaucUAauCuCCaguaGCAAUUUUGA.cCa.auauuGGaGguguuAugCGuccGGauCGuCuuAC
//
# STOCKHOLM 1.0

#=GF AC   RF02769
#=GF ID   Ysr202
#=GF DE   Yersinia sRNA 202
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   315.00
#=GF TC   315.60
#=GF NC   34.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   SO; 0000122; RNA sequence secondary structure;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF RN   [2]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   The sRNA was identified by [2] and is confirmed to have a stable secondary
#=GF CC   structure by [1] using genome-wide structure probing at different
#=GF CC   temperatures. The function is unknown.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   2




CP000950.1/2059374-2059651 UUAGAGGCUUGUCGUUGUGAAAGUCAGAAUAUUAAAGCCAGUGCGAGAAGUUAUCAUCGAAAUAGACGUGUUCAUCAAAAUAUAAGCAAGCAUGCGGUACCAGGUCAACCUGG-GGUGUUUGUCAGUGUUGAGUCGCAGUUGGUCAUUAUUGAGUAGUCGUGGUCAGCAUGAGUAUGGAAGAGGGAGUGACAUCAAGGAGAGCGAUUGUCAGACGUUCAUUUCUGUACGACAAACAUUUCCGUAGGGCAAAAAAA---UGGCGCACAAUGUGCGCCAUUUUU
CP002956.1/3069894-3070175 UUAGAGGCUUGUCGUUGUGAAAGUCAGAAUAUUAAAGCCAGUGCGAGAAGUUAUCAUCGAAAUAGACGUGUUCAUCAAAAUAUAAGCAAGCAUGCGGUACCAGGUCAACCUGGGGGUGUUUGUCAGUGUUGAGUCGCAGUUGGUCAUUAUUGAGUAGUCGUGGUCAGCAUGAGUAUGGAAGAGGGAGUGACAUCAAGGAGAGCGAUUGUCAGACGUUCAUUUCUGUACGACAAACAUUUCCGUAGGGCAAAUAAAUAUCCUCCGGCAUAGCCGGAGGUUUUU
#=GC SS_cons               :::::<<<<<-<<_____>>>>>>>,,,,,,,,,,,(((--((((-(((((-----(((--(((((-(((--(-((,,<<<<<--<<<<<<<<-<<<<_________>>>-->-->>>>>>>>-->>>>>,,,,,<<<<<<<-<<-<<-<<<<<<<-<<<<<_____>>>>>->>>---------------->>>>->>>>->>>>>>>,,))-)--)))-)))))-)))-----)))))))))-)))--<<<<<---<<<<<<<<___>>>>>>>>>>>>>
#=GC RF                    UUAGAGgCuuGuCGUUGUGaaaGcCAGAAUAUUAAAGCCAGugCGAGaaguUAUCAuCGAAacaGaCguGUUCAuCAAaacacAAgCaagCacGCGGuACCAGGUCAaCCUGGgGguGcuuGcCAguguuGAGUCgCagucGGuCAucAuuGaguaGuCguGGUCAGCacGaGuacGGAAGAGGGAGUGACAuCaaGgaGaGCgacuGcCAGaCGUUCacUuCuguACGaCAAACacuuCCGcaGGGCAAaaaaauAucggCgggCAaaGcccGccguuuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02770
#=GF ID   Ysr224
#=GF DE   Yersinia sRNA 224
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   70.00
#=GF TC   70.00
#=GF NC   69.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF RN   [2]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   5



CP000950.1/3853136-3853030 GAGGUUAUUGACAAAGUGCCCGCGACGGAGAG-AACAGGCAGAUCGUAAAGACGCCGUAAAUACAUCCAUGUAGGCUCGAGCCGCGCCAUCCUUGGCGCGGACGCUUU
CP000901.1/3597651-3597545 AUAUUUAUUGACAAAGUGCCCGCGACGGAGAG-AACAGGCAGAUCGUAAAGACGCCGUAAAUACAUCCAUGUAGGCUCGAGCCGCGCCAUCCUUGGCGCGGACGCUUU
CP002246.1/599483-599377   CAGACUGCUGACAAAGUGCCCGCUACGGAGAG-AACAGGCAGAUCGUAAAGACGCCGUUAAUACGUCCAUGUAGGCUCGUGCCGCGCCAUCCCUGGCGCGGACGCUUU
ACCB01000018.1/76214-76320 GAGGUUAAUGACCAAGUGCCCGUAUCGGUGAA-AACAGGCAGAUCGUAAAGACGCCGUAAAUACAUCCUUGUAGGCUCGAACCGCGCCUUCCCUGGCGCGGACGCUUU
BX950851.1/4371227-4371333 GAGGUUGCUGACAAAGC-CCGUAGAGCGAGAGUAACGGAUAGAUCGUAAAGACGCUGUGAAUACAUCCUUGUACGCUCGGCUUGCGCCAUCCCUGGCGCAAACGCUUU
#=GC SS_cons               ::::::::::::((((((,<<<___>>>,<<<.--------<<<-<<<---<<___>>--->>>>>>-------->>>,,,<<<<<<<<____>>>>>>>>,))))))
#=GC RF                    gAgguUauUGACaaaGcGCCcgcgacgGaGaG.AACaGgcAGauCGuaAAGaCGCcGuaAAuaCauCCaUGUAgGCuCGagccGCGCCaUCCcuGGCGCggACgCuuu
//
# STOCKHOLM 1.0

#=GF AC   RF02771
#=GF ID   CnfY_thermometer
#=GF DE   CnfY 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   130.00
#=GF TC   130.70
#=GF NC   38.80
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   CnfY gene is associated with Yersinia virulence. RNAT functionality is
#=GF CC   impaired by point mutating the 5'UTR. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   3



CP002956.1/4018238-4018127 UGUGUUUUUUGUAAGUUCUAUUAAACACAUCAGUUUACAGCAAUGAAUUCACCAUUGUGCAUCGUCAAUAAAAGGAGUGUUUAUGAAAAAUCAAUGG--CAACAUCAAUAUUUU
CP001048.1/1760712-1760823 UGUGUUUUUUGUAAGUUCUAUUAAACACAUCAGUUUACAGCAAUGAAUUCACCAUUGUGCAUCGUCAAUAAAAGGAGUAUUUAUGAAAAAUCAAUGG--CAACAUCAAUAUUUU
CP000950.1/2873197-2873084 UGUGUUUUUUGUAAGUUCUAUUAAACACAUCAGUUUACAGCAAUGAAUUCACCAUUGUGCAUCGUCAAUAAAAGGAGUGUUUAUGAAAAAUCAAUGAAAUAAUGUAAAAAAUGU
#=GC SS_cons               ::::::::::::::<<<<<<<<<<<<<<-<<--<<<<--<<<<<<_______>>>>>>---------->>>>-->>>>>>>>>---------->>>>..->>>:::::::::::
#=GC RF                    UGUGUUUUUUGUAAguucuauuaaacaCAuCAGuuuaCAgCaauGAAUUCACCauuGuGCAUCGUCAAuaaaAGGaGuguuuaUGAAAAAUCAaugg..caacaUcAAuAuUuU
//
# STOCKHOLM 1.0

#=GF AC   RF02772
#=GF ID   AilA_thermometer
#=GF DE   AilA 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   81.00
#=GF TC   81.40
#=GF NC   41.00
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   AilA gene is associated with Yersinia virulence. RNAT functionality is
#=GF CC   impaired by point mutating the 5'UTR. Temperature affects the secondary
#=GF CC   structure and ribosome binding efficiency of the 5'UTR. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   5



CP000950.1/1395762-1395850 GGCCACUUUAGU-CUGUGGUUACUGUAUUAGGUAUUGUUAUAACAAUCUGGAUGGUUUUUAUGAAUAAGACAUUACUGGUCUCUUCUUUA
CP000668.1/2548270-2548182 AGCCACUUUAGU-CUGUGGUUACUGUAUUAGGUAUUGUUAUAACAAUCUGGAUGGUUUUUAUGAAUAAGACAUUACUGGUCUCUUCUUUA
L49439.1/280-368           GGCCACUUUAGU-CUGUGGUUACUGUAUUAGGUAUUGUUAUAACAAUCUGGAUGGUUUUUAUGAAUAAGAUAUUACUGGUCUCUUCUUUA
AM286415.1/2007663-2007751 AGCCAUGUCAGUGAUAUGGUUAUUGUAUU-AGUAUUGUUAUAACAAUCUGGAUUAUUUUUAUGAAAAAGACAUUACUAGCUAGUUCUCUA
ACCA01000039.1/31556-31467 CGCCAUAUCAGUGAUAUGGUUGUUGUGUUAGAUAUUGUUAUAAUGAUCCGGAUGAUUUUUAUGAAAAAGACAUUAUUGGCCAGUUCUUUG
#=GC SS_cons               <<<<<<______.__>>>>>>---------<<<<-<<<<<<<<-<<<<_____>>>>->>>>>>------>>->>>>:::::::::::::
#=GC RF                    agCCacuUuAGU.aUguGGuuAuUGUAUUAgGUaUUGUuaUaacaaucUGGAUgauuUuuAugAAuAAGACAUuACuGGucucUUCUUUA
//
# STOCKHOLM 1.0

#=GF AC   RF02773
#=GF ID   TrxA_thermometer
#=GF DE   TrxA 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   58.00
#=GF TC   58.20
#=GF NC   57.40
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Involved in protection against oxidative stress. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   8



CP000950.1/4451980-4451893 AUCCUACUGUUGGUUAAUGCUACACCAACGAGGUAGACA----C---------A-AUCCUUUGGAGUAGAACAUGAGCGAUAAAAUUAUUCACCUGAGUGAC
FR729477.2/3480769-3480856 AUCCUAUUGUUGGUUAAUGCUACACCAACGAGGUAGACA----C---------A-AUCCUUUGGAGUAGAACAUGAGCGAUAAAAUUAUUCACCUGAGUGAC
ACCC01000032.1/17493-17406 AACCUAAUGUUGGUUAAUGCUACAUCAACUAGGUAGACA----C---------A-AUCCUUUGGAGUAGAACAUGAGCGAUAAAAUUAUUCAUCUGAGUGAC
CP002773.1/142447-142535   CACCUUGGGUUGGUUAAUGCUACACCAACAAGGUAGACA----U---------ACAUCCUGUGGAGUAGAACAUGAGCGAUAAAAUUAUUCACCUGACUGAC
CP002505.1/4659880-4659794 AACCUGAUGUUGGUUAAUGCUACAUCAACAAGGUAAAGA----U---------A-AUCCUUUGGAGUA-AACAUGAGCGAUAAAAUUAUUCACCUGACCGAU
CP000826.1/179615-179702   CACCUUAGGUUGGUUAAUGCUACACCAACAAGGUAGACA----C---------A-AUCCUUUGGAGUAGAACAUGAGCGAUAAAAUUAUUCACCUGACUGAC
ADTP01000150.1/17338-17239 AACCUUUAGUUGGUUAAUGUUACACCAACAACGAAACCAACAC-GCCAGGCUUA-UUCCUGUGGAGUUAAAUAUGAGCGAUAAAAUUAUUCACCUGACUGAC
CP001657.1/4529000-4528913 AAGCCGUUGUUGGUCAAUGCUACACCAACAAGGUAGAAA----U---------A-AUCCUGCGGAGUAAAAUAUGAGCGAUAAAAUAAUUCACCUGACUGAU
#=GC SS_cons               :::::::<<<<<-<<<---<<<<-<<<--<<<<______...._........._.__>>>>>>>->>>>---->>>->>>>>---<<<<<<____>>>>>>:
#=GC RF                    AAcCUuuugUuGGUuaAUGcuaCAcCaACgaGGuAgAcA....u.........A.aUCCucuGgAGuagAAcAugAGCgAuaAAAUcacUCACCUGAgugAc
//
# STOCKHOLM 1.0

#=GF AC   RF02774
#=GF ID   KatA_thermometer
#=GF DE   KatA 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   111.00
#=GF TC   111.20
#=GF NC   43.60
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Involved in protection against oxidative stress. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   5



AM286415.1/1541353-1541200 GAGAUCAAAGAAUAAACCGCUGAUGUUGUUUAAGUUAUUAUUUUGCCAAUCGGACUUUUGGCGAAAUCUCAUACUGUAAAACACCCAAUA-CGCAAUCAAUUCAACAGCCAUACUGGAGAAAAUGAUGAGCAAAAAGAAAGGAUUAACCACCGCA
CP000950.1/3147272-3147422 GAGAUCAAAGAAUAACACCGUGUUUUUGUUAAAAUUAUUAUCUUGUCAAUCACGUUUUUGACGCGAUAUCACGC--UUAA--ACCCAAAACCGCAAUCAAUUCAACAGCCAUACUGGAGAACAUGAUGAGCAAGAAGAAAGGAUUAACCACCGCG
FR729477.2/249912-249759   GAGAUCAAAGAAUAAACCGCUGAUGUUGUUUAAGUUAUUAUUUUGCCAAUCGGACUUUUGGCGAAAUCCCAUACUGCAAAACACCCAAUA-CGCAAUCAAUUCAACAGCCAUACUGGAGAAAAUGAUGAGCAAAAAGAAAGGAUUAACCACCGCA
ACCA01000005.1/16418-16265 GAGAUCAAGGAAUAACUCGCUGAUGUUGUUUAAGUUAUUAUUUUACCAAUCAGGCUUUUGGCGAAAUGUAAUGCUUUAAAACACCCGACA-AGCAAUCAAUUCAACAGCAAUACUGGAGAAAAUGAUGAGCAAAAAGAAAGGAUUAACCACUGCA
AALC02000098.1/4036-4190   GAGAUCAAAGAAUCACCCUCGGUUGUUGGUUAAAUUAUUAUCUUGUCAAUCAGGAUUUUGGCGAAAUCUAAUGCUGUUAAACACCCGAUAAAUCAAUCAAUUCAAUAGUGAUAAUGGAGAGGAUGAUGAGUAAAAAGAAAGGGUUAACUACCGCA
#=GC SS_cons               :::::::::<<<<------<<<-<<<<<<<<<------<<<<-<<<<<<________>>>>>>->>>>-------->>>>----->>>>>.>>>----->>>>,,,,<<<<<--<<_____>>-->>>->><<<___>>><<_____>>::::::
#=GC RF                    GAGAUCAAAGaauaAccCggcgauguuGuuuaAaUUAUcaucUuGcCaaUCaggcUUuuGgCgagaugUaAUgCUguaaaACACCCaaca.cgcAAUCAauuCAAcAGccauAcugGAGAAcaUGaugAgCaacAAGgaaGGAUUAACCACcGCA
//
# STOCKHOLM 1.0

#=GF AC   RF02775
#=GF ID   SodB_thermometer
#=GF DE   SodB 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   98.00
#=GF TC   98.30
#=GF NC   65.60
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Involved in protection against oxidative stress. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   5



CP000950.1/2071600-2071482   UUUUAACCGCUCUUCACCCCACACCUCUCAAC-AAUGGUGGAUAGGAUUUGAAGAGCAAACACCCUGAGCAACCCCGAAAG-GAGAGAGCUAUGUCUUUUGAAUUACCUGCAUUACCUUAC
CP001589.1/1892084-1892203   UUUUAACCGCUCUUCACCCCACACCUCUCAAC-AAUGGUGGAUAGGAUUUGAAGAGCAAACACCCUGAGCACCCCCGAAAGGGAGAGAGCUAUGUCUUUUGAAUUACCUGCAUUACCUUAC
AALF02000005.1/183831-183949 CUUUAACCGCUCUUCGCCACAUAGCUGCCAAC-GGCAAUUGAUGUGAUUUGAGGAGCAAACACCCUGAGCAACCCCGAAAG-GAGAGAGCUAUGUCUUUUGAAUUACCGGCAUUACCUUAU
AM286415.1/2356902-2357017   UUUUAACCGCUCCUCACCACA----UCUUAGUGAGCUAACGUUCGGAUUUGAGGAGCAAACACCCUGAGCAACCCCGAAAG-GAGAGAGCUAUGUCUUUUGAAUUACCGGCAUUACCUUAU
ACCD01000001.1/120038-120155 UUUUAACCGCUCUUCGCCACAUCAUAGCGACA-GCCAAUGGGU-GGACUUGAGGAGCAAACACCCUGAGCAACCCCGAAAG-GAGAGAGCCAUGUCUUUUGAAUUACCUGCCUUACCUUAU
#=GC SS_cons                 ::::::::::::::::::::::::<<<<<---.--<<<-<<-<<<<-<<<<_____>>>>--->>>>----->>>>>----.>>>>><<-<<--<<____>>-->>->>::::::::::::
#=GC RF                      UUUUAACCGCUCUUCaCCaCAuaacucucAac.aacggugGauagGAuuuGAgGAGCaaaCACCcugAGCAACcccgAAAG.gagagaGCuaUGuCUUUUGaAUuaCCuGCAUUACCUUAu
//
# STOCKHOLM 1.0

#=GF AC   RF02776
#=GF ID   SodC_thermometer
#=GF DE   SodC 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   125.00
#=GF TC   125.50
#=GF NC   41.70
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Involved in protection against oxidative stress. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   2



CP000950.1/3779158-3779066 GUCAAAAGUUUCCUAUUGACAAGGUUAAACCAGACUUAAUCAACAUAUAAGGGAUAUAACAAUAUGAAAUUAAUUACAUUAUUGCUACCUGUU
CP002956.1/1995175-1995267 GUCAAAAGUUUCCUAUUGACAAGGUUAAACCAGACUUAAUCAACAUAUAAGGGAUAUAACAAUAUGAAAUUAAGUACAUUAUUGCUACCUGUU
#=GC SS_cons               ::::::((((((-(((((,,,,<<<___>>>,,,,,,,,,,,,,,<<<<_____>>>>,)))))-))))))::::::::::::::::::::::
#=GC RF                    GUCAAAaguuuCCuauuGACAAGGuUAAaCCAGACUUAAUCAACAuauaAGGGAuauaACaauaUGaaauuAAuUACAUUAUUGCUACCUGUU
//
# STOCKHOLM 1.0

#=GF AC   RF02777
#=GF ID   OppA_thermometer
#=GF DE   OppA 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   290.00
#=GF TC   291.60
#=GF NC   54.50
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Positioned upstream of gene for oligopeptide uptake. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   3



CP000950.1/2298904-2298601 AACUUUUUGAAAAAAGUUCGCUUAUAUUUUUAUGAAAUUUAGCUGUAGUGAUUAUUUUGGAAUAGUUAAUUUAUUUUGGGAUGGUUGAUGCAUUUUGGAAUAGUUGAUGCAUGUCGUUGAUAGCUAAUUGACCAUCGCCAUAGACAAAAUAUCACCACAUGUGAGGUUUACGUUACCGGGUUCGUUCCCCAGGUAACGCAAAUUUAGAAUACCGUUUAAAGGUGAGUUUGCCUGUUCACUGGGCAAUACAUAAUAAAAUGGAGUACAUAUAAACAUGACCAACAUCACAAAGAAGAAUCUCAUU
CP001048.1/2399343-2399646 AACUUUUUGAAAAAAGUUCGCUUAUAUUUUUAUGAAAUUUAGCUGUAGUGAUUAUUUUGGAAUAGUUAAUUUAUUUUGGGAUGGUUGAUGCAUUUUGGAAUAGUUGAUGCAUGUCGUUGAUAGCUAAUUGACCAUCGCCAUAGACAAAAUAUCACCACAUGUGAGGUUUACGUUACCGGGUUCGUUCCCCAGGUAACGCAAAUUUAGAAUACCGUUUAAAGGUGAGUUUGCCUGUUCAUUGGGCAAUACAUAAUAAAAUGGAGUACAUAUAAACAUGACCAACAUCACAAAGAAGAAUCUCAUU
AE017042.1/2203163-2203466 AACUUUGUGAAAAAAGUUCGCUUAUAUUUUUAUGAAAUUUAGCUGUAGUGAUUAUUUUGGAAUAGUUAAUUUAUUUUGGGAUGGUUGAUGCAUUUUGGAAUAGUUGAUGCAUGUCGUUGAUAGCUAAUUGACCAUCGCCAUAGACAAAAUAUCACCACAUGUGAGGUUUACGUUACCGGGUUCGUUCCCCAGGUAACGCAAAUUUAGAAUACCGUUUAAAGGUGAGUUUGCCUGUUCACUGGGCAAUACAUAAUAAAAUGGAGUACAUAUAAACAUGACCAACAUCACAAAGAAGAAUCUCAUU
#=GC SS_cons               ::((((-(((-----(((-(-((((((((((((--------(((-((((((,,,,,,,,,,,,,,,,,,,,<<<<<<<--<<<<<-<<<<----<<<<----<<<<<<<_____>>>>>>>-->>>>----->>>>>>>>>--->>>>>>>,,<<<________>>>,,,,<<<<<<<<<_______>>>->>>>>><<<<<<<<-----<<<_______>>>>>>>>>>>,,,,)))))))))--------))))))--------))))))-)--)))-----)))-))))::::::::::::
#=GC RF                    AACuuuuuGaAAAAAGucCGCuuauauuuuuauGAAAUUUAGCcGcaguGaUUAUUUUGGAAUAGUUAAUUuauuuuGGGauGGcUGauGCAUUuugGAAUAgucgacGCAUGUCgucgacAGCcaaUUGACCauCgCCauAGACaaaauaUCaCCACAUGUGAGGuUUACGuuaCCGGGUUCGUUCCCCAGGuaaCGCaaacucAGAAUaCCGUUUAAAGGugaguuuGCCUGUuCacuggGCAAUACAUAauaaaaUGGAGUACauauaaACAUgaCCAACAuCaCaaaGAAGAAUCUCAUU
//
# STOCKHOLM 1.0

#=GF AC   RF02778
#=GF ID   FdoG1_thermometer
#=GF DE   FdoG-1 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   50.00
#=GF TC   50.10
#=GF NC   49.70
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Located upstream of fdoG-1 gene which is involved in metabolic processes. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   4



CP000950.1/40050-40239       GUGGUAACAUUCACAUUAAGAAUGGUGCGGCUAUGUAUUAUCUAACAUAGAAAUUCAUUCCACACAGAAAAAGCGUGAUAUCGCAUGAGCGAUUUUAGCGCCUCCCAUUUUAUUGAGGGAAGCGUGAACUGGA-----A-------AUAAUGUGACAAU----GAAGGAGAUACCCAUGCAGGUCAGCAGAAGGCAGUUCUUUAAG
ACCB01000003.1/36186-36377   GUGGUAACAUUCACAUUAAGAAUAGUGUGGCUAUAU-UCCGUUAUUACAGAAAUGUAUCCCACACUGAAA-AGCGUGAUAUCGCAUGAGCGAUUUUAACGCUUCCCGUUUUGUUGAGGGAAGCGUGAACUGGA-----A-------AUAAUGUGACAAUGAAUGAAGGAGAGACCCAUGCAGGUCAGCAGAAGGCAGUUCUUUAAG
AALF02000012.1/109075-109266 GUGGUAACAUUCACAUUAAGAAUGGUAUGGGUAUAAUUCUAUUUCCAGAAGAAUGUAUCCCACACCGAUA-AAGGUGAUAUCGCGUAAGCGAUUUUAGCGCUUCCGGUUUCGUUGAGGGAAGUGUGAACUG-A-----A-------AUAAUGUGACAAUGAACGAAGGAGAGACCCAUGCAGGUCAGCAGAAGGCAGUUCUUUAAG
CP002246.1/4462484-4462281   GUGGUAACAUUCACAUUAAGAAUGGUAUGGGUAUAAUUCCAUUUAUAUAGAAAUGUAUCCCACACCGAUA-AAGGUGAUAUUGCGUCAGCGAUUUUAGCGCUUCUGGUUUUGUUGAGGGAAGCGCGAACUGAAUUUUA-AAUUCAUACAAUGUGACAAUGAAUGAAGGAGAGACCCAUGCAGGUCAGCAGAAGGCAGUUCUUUAAG
#=GC SS_cons                 <<-<<<-<<<<<_______>>>>>->>>->><<<<<________>>>>><<<<___>>>><<<-<_____._>->>>,,<<<<<____>>>>>,,,,<<<<-<<<<__________>>>>->>>><<<<<<--.....-.......------<<<<----------<<______>>------>>>>-------->>>>>>::::::
#=GC RF                      guGguaAcauuCACAUUAAGaaugGuacGgcuaugcuUcuauUugcauaGgaaUguaucCCaCAcuGAuA.AggGuGAUaucGCaUaAGCgauUUUAgCGCuuCccgUUUugUUGAggGaAGCGcGaaCuGgA.....A.......AuAAUGuGaCAAUGAAuGAAGGAGAgACCCAUGCAGGuCaGCAGAAGGCaGuuCUUUAAG
//
# STOCKHOLM 1.0

#=GF AC   RF02779
#=GF ID   PepN_thermometer
#=GF DE   PepN 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   83.00
#=GF TC   83.90
#=GF NC   38.20
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Position upstream of pepN gene responsible for amino acid processing. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   5



CP000950.1/2907108-2906974   CUAUCUGGGUCUGGGGGAACGUCGCUAAUAGC-----------AGCGA---AAUUCA---CCCC--AAUUA-CGACAGGCACAGACCCGAUAAUCAUACUCACUGAUGACGUCAAAAGGGUUUCUAUGACACAACAGCCGCAAGCUAAAUACCGU
AALC02000062.1/20789-20924   CUAUCUGGGUCUGGGGCGAAGUCAAUGGCAGU-----------CAUGU---UCUUAA---GCCC-CACCAA-CUAUAAAUACAGACCUGAUAAUCAUACUCACAGAUGACGUCAAAAGGGUUUCUAUGACACAACAGCCGCAAGCUAAAUACCGU
AALD02000003.1/114534-114669 CUAUCUGAGUCUGGGGCGAAGUCAAUGACAGC-----------CAUGU---UCUUAA---GCCC--AAUCAACUAUCAAUACAGACCUGAUAAUCAUAUUCACAGAUGACGUCAAAAGGGUUUCUAUGACACAACAGCCGCAAGCUAAAUACCGU
FR729477.2/475129-475277     CUAUCUGAGUCUAAGGCGAAGUCGCUGGUAGCAGUAC-UUUGAAGCUAAAGUUUUAA---GCCA-AAACGA-CCAUAAAUACAGACUUGAUAAUCAUAUUCACUGAUGACGUCAAAAGGGUUUCCAUGACACAACAGCCACAAGUUAAAUACCGU
ACCB01000005.1/85822-85971   CUAUCUGAGUCUGGGGCCAAUAGGUUUGCAGCAAUGCUCUGGUCGCCG---UAAUA-CCGGCCUUUAAUGA-CUAUUAAUACAGACCUGAUAAUCAUAUUCACUGAUGACGUCAAAAGGGUUCUUAUGACACAACAGCCGCAAGUCAAAUACCGU
#=GC SS_cons                 :::<<<<-<<<<<<<<<----<<<<<______...........>>>>>...------...>>>>.------.--->>>>>->>>>-----------------<<<-<<--<<<<---<<____>>->>>>->>->>>::::::::::::::::::
#=GC RF                      CUAuCuGagucuggGGcgAAgucgcugguAGc...........agcga...uauUAA...gCCc.uAAuuA.CuAcagacACaGaCcUGAUAAUCAUAuUCACuGAuGACGuCaAAAgGGUUuCcAuGaCACaACaGCCgCAAGuuAAAUACCGU
//
# STOCKHOLM 1.0

#=GF AC   RF02780
#=GF ID   PutA_thermometer
#=GF DE   PutA 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   51.00
#=GF TC   51.80
#=GF NC   40.20
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Position upstream of pepN gene responsible for amino acid processing. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   4



CP000950.1/2603743-2603814 GAAAUAAAAUCAUAAUUCCCCUUAUCAAAGGAGACGAGCGACAUGGCGAGUACCACAAUGGGCGUAAAGCUU
CP002956.1/3562336-3562407 GAAAUAAAAUCAUAAUUCCCCUUAUCAAAGGAGACGAGCGACAUGGCGAAUACCACAAUGGGCGUAAAGCUU
CP002246.1/2049129-2049058 GAAAUAAAAUCAUAACUCCCCUUAAUUAAGGAGCCAGACAGCAUGGGUAGCACCACAAUGGGCGUGAAACUC
AALC02000028.1/23904-23975 GAAAUAAAAUGAUAACUCCCCUUAUAAAAGGAGCCUGGCAGCAUGGCUAGUACCACAAUGGGUGUGAAACUC
#=GC SS_cons               <<<-<<______>>->>>,,,,,,,,,,,<<--<<--<<______>>-->>->>,,,,,<<<<_____>>>>
#=GC RF                    GAaAUAAAAUcAUAAuUCCCCUUAuuaAAGGAGaCgagCaaCAUGGcuAGuACCACAAUggGcGUaAAgCuc
//
# STOCKHOLM 1.0

#=GF AC   RF02781
#=GF ID   ManX_thermometer
#=GF DE   ManX 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   76.00
#=GF TC   76.30
#=GF NC   37.00
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Short UTR positioned upstream of ManX gene responsible for sugar uptake. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   4



CP000950.1/2697845-2697960   UCAAGUAGCUCAACAGUAUUUUUGGUGAUGAGUUGUUUUUCUGUUA-GUGCAAUAACUCAAUUUUGAGUUAACAGAGGGGGUAGCGAGUGAGUAUAGCUAUUAUCAUCGGCACACAU
ACCA01000006.1/167496-167381 UCAAUGUGUACUGAAGUGUAGUUGGUGAUUA-CUGGUUUUCUGUUACGUGCGAGAACUCAAUUCUGAGUUAACAGAGGGGGUAGCGAGUGAGUAUAGCUAUUAUCAUUGGCACACAU
FR729477.2/664955-664840     UCAAUAUGUACCGAAGUGUGAUGGGGAAUUA-CUGGUUUUAUGUUACGUGCGAGAACUCAAUUCUGAGUUAACUGAGGGGGUAGCGAGUGAGUAUAGCUAUUAUCAUUGGCACACAU
ACCB01000012.1/82692-82579   -UGUUUUUGGUGAAAGUAGUUUUGGUCA-AAGUGAUUUUUCUGU-ACGUGUGAGAACUCAAUUCUGAGUUAACAGAGGGGGUAGCGAGUGAGUAUAGCUAUUAUCAUUGGCACACAU
#=GC SS_cons                 :::::::::::::::::::::<<<<<<<<<<<<<<<<<<-<<<<<<--<-<--<<<<<<<____>>>>>>>------>->->>>>->>->>>->>>>>>-->>>>>>>>>:::::::
#=GC RF                      UcAauuuguacuaaAGUauuuucggugaugaGcuguuuuUcuGuuaCGuGcgAcaaCuCaAUUcuGaGuugACaGAGgGgGuagCGagUgagUauagCuAUcaucaucggCACACAU
//
# STOCKHOLM 1.0

#=GF AC   RF02782
#=GF ID   CpoB_ybgF_thermometer
#=GF DE   CpoB/ybgF ICR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   51.00
#=GF TC   51.40
#=GF NC   50.60
#=GF TP   Cis-reg; thermoregulator; 
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Imprinting control region from upstream of cpoB/ybgF (tol/pal system
#=GF CC   protein). 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   8



CP000950.1/3253881-3253743 CCAGAUCUCUAUCGUUUCUUACGGUAAAGAGAAACCAGCAGUACUGGGCCAUGACGAAGCAGCCUUUGCUAAAAACCGUCGUGCAGUUCUGGUUUACUAAGAGAAUCGCAUGAACAGUAACUUCAGACGUCACUUAGUG
AM286415.1/3187072-3186934 CCAAAUCUCUAUCGUUUCUUACGGUAAAGAGAAACCAGCAGUAUUGGGCCAUGACGAAGCCGCAUUUGCUAAAAACCGUCGUGCAGUUCUGGUUUACUAAGAGAAUCGCAUGAACAGUAACUUCAGACGUCACUUAGUG
FR729477.2/1851896-1851758 CCAAAUCUCUAUCGUUUCUUACGGUAAAGAGAAACCAGCAGUACUGGGCCAUGACGAAGCCGCAUUUGCUAAAAACCGUCGUGCAGUUCUGGUUUACUAAGAGAAUCGCAUGAACAGUAACUUCAGACGUCACUUAGUG
ACCA01000049.1/1264-1126   CCAAAUCUCUAUCGUUUCUUACGGUAAAGAGAAGCCAGCAGUACUGGGCCAUGACGAAGCAGCAUUUGCUAAAAACCGUCGUGCAGUUCUGGUUUACUAAGAGAAUCGCAUGAACAGUAACUUCAGACGUCACUUAGUG
CP001790.1/3364576-3364438 UCAGAUCUCUAUCGUUUCUUACGGUAAAGAAAAACCAGCAGUUCUCGGUCAUGACGAAGCGGCCUAUGCCAAAAACCGUCGUGCCGUUCUGGUAUAUUAAGAGAAUCGCAUGAGCAGUAACUUCAGACGUCACCUGUUG
CP002797.2/740150-740288   CCAGAUCUCCAUCGUUUCUUACGGUAAAGAAAAACCUGCAGUACUGGGUCAUGACGAAGCGGCGUAUGCCAAAAACCGUCGUGCGGUACUGGUUUACUAAGAGAAUUGCAUGAGCAGUAACUUCAGACAUCAACUAUUG
AP006725.1/1645903-1646041 UCAGAUCUCCAUCGUUUCUUACGGUAAAGAAAAACCAGCAGUACUGGGUCAUGACGAAGCGGCAUAUGCCAAAAACCGUCGCGCCGUACUGGUUUACUAAGAGAAUUGCAUGAGCAGUAACUUCAGACAUCAUUUAUUG
CP002773.1/1372405-1372543 CCAGAUCUCUAUCGUUUCUUACGGUAAAGAAAAACCAGCAGUACUGGGCCACGACGAAGCAGCUUAUGCUAAAAACCGUCGCGCAGUUCUGGUUUACUAAGAGAAUCGCAUGAACAGUAACUUCAGACGUCACUUGUUG
#=GC SS_cons               <<<<--<<-----<<<<<<<________>>>>>>>---->>-->>>>------<<-<<<--<<-<<<<------<<-<<<<<<<-<<<<<___________>>>>>->>>>>>->->>----->>>>->>-->>>->>:
#=GC RF                    cCagAUCuCuAUCGuuucuuACGGUAAAgagaaaCCAGCaGUAcuGgGuCAUGacGaagCagcaucuGCuAAAAaCCGuCguGCaguuCuGGUuUAcUAAGaGaaucGCauGaaCAGuAACUUCagaCguCAcuuaguG
//
# STOCKHOLM 1.0

#=GF AC   RF02783
#=GF ID   IscS1_thermometer
#=GF DE   IscS-1 ICR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; PMID:27298343;
#=GF GA   58.00
#=GF TC   58.20
#=GF NC   54.00
#=GF TP   Cis-reg; thermoregulator; 
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 549862.597050 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0002168; RNA_thermometer;
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0006417; regulation of translation;
#=GF RN   [1]
#=GF RM   27298343
#=GF RT   Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT   pseudotuberculosis.
#=GF RA   Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA   Stadler PF, Dersch P, Narberhaus F
#=GF RL   Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF CC   Imprinting control region from upstream of iscS-1 (cysteine desulfurase). 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   5



CP000950.1/1403563-1403745   CCAAGAUAUCCUAGAGGUAGCGGAUCGUCAGAAUAACGAUACGCGCCGCACGGCUAAUGGCCGACCGCAAGAGACGAUUAACGUCAAUCUGCGCGCAUAAGCAGAAUUUGCG-G-AAUUUUACGUUUUGGAAGUGAUGUACGGAGCAUAAGAGCAAUGACCGAAUCA--AAAGUAAAGACACCGAUC
AALE02000007.1/140735-140553 CCAAGAUAUUCUUGAGGUAGCGGAUCGUCAAAAUAACGAUACGCGCCGUACGGCCAAUGGCCGACCGCAAGAGACGAUUAACGUCAAUCUGCGCGCAUAAGCAGAAUCUGCG-G-AAUUUUACGUUUUGGAAGUGAUGUACGGAGCAUAAGAGCAAUGACCGAAUCA--AAAGUAAAGACACCGAUC
FR729477.2/4459222-4459404   CCAAGAUAUUCUUGAGGUUGCGGAUCGUCAGAAUAACGAUACGCGCCGUACGGCUAAUGGCCGACCGCAAGAGACGAUCAACGUCAAUCUGCGCGCAUAAGCAGAGUCUGCG-G-AAUUUUACGUUUUGGAAGUGAUGUACGGAGCAUAAGAGCAAUGACCGAAUCA--AAAAUAAAGACACCGAUC
FM162591.1/1547016-1547194   UCAAGAAGUGUUAGAUGUUGCUGAUCGCCAAGAUAACGAUAAACGCCGUACACCUAAUGGCAGAGCACAAGAAACAAUUAAUGUCAAUCUGCGCGCAUAAGCAGAACUUGUGAC-UAAUUGAAGUAUUAAGAAGUAGGGA----GCAUGUGAGCAAUGAA--AUUAC-CAAUUUAUUUAGACUACUC
FN667741.1/2990610-2990432   UCAAGAAGUCUUAGACGUUGCUGAUCGUCAAGACAGCGAUAAACGCCGUACACCUAACGGCAGGCCUCAAGAGACGAUUAACGUUAACCUGCGUGCGUAA----ACUUUGCG-GCAAACAGAAGUAUUAAAAGUGUUUUACGGAGCAUGUGAGCAAUGA---AAUUACCCAUUUAUUUGGACUAUUC
#=GC SS_cons                 (((((((,,,,,,<-<<<-<<<--<<<<_______>>>>-->>>>>>->,<<<<<___>>>>>,<<<<<<<------<<<-<<<________>>>-->>>------>>>>>>.>.,,,,,,,,)))))))---<<<<---<<<--<<<_______>>>->>>->>>>..::::::::::::::::::
#=GC RF                      ccaagacaUuuUagAgGuuGcgGAuCGuCAaaAUAaCGaUAcgCgCcGcACggCcAAUgGccGAcCgCaagAgACgAuuaAcGucAAUCUGCgCgCAuaaGCAGAacuuGcG.g.aAuUuuAagucuuggAAgugauguACGGAGCauaaGAGCAauGACCGAauca..aAauUAaauAcACuaaUC
//
# STOCKHOLM 1.0

#=GF AC   RF02784
#=GF ID   SorX
#=GF DE   Singlet oxygen resistance RNA X
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 27420112;
#=GF GA   46.60
#=GF TC   46.60
#=GF NC   46.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0080183; response to photooxidative stress;
#=GF RN   [1]
#=GF RM   27420112
#=GF RT   Regulation of a polyamine transporter by the conserved 3' UTR-derived sRNA
#=GF RT   SorX confers resistance to singlet oxygen and organic hydroperoxides in
#=GF RT   Rhodobacter sphaeroides.
#=GF RA   Peng T, Berghoff BA, Oh JI, Weber L, Schirmer J, Schwarz J, Glaeser J,
#=GF RA   Klug G
#=GF RL   RNA Biol. 2016;13:988-999.
#=GF RN   [2]
#=GF RM   19906181
#=GF RT   Photooxidative stress-induced and abundant small RNAs in Rhodobacter
#=GF RT   sphaeroides.
#=GF RA   Berghoff BA, Glaeser J, Sharma CM, Vogel J, Klug G
#=GF RL   Mol Microbiol. 2009;74:1497-1512.
#=GF CC   SorX (RSs2461)like SorY is a singlet oxygen induced sRNA that counteracts
#=GF CC   oxidative stress by targeting mRNA for a transporter in Rhodobacter. It
#=GF CC   also has an impact on resistance against organic hydroperoxides. It
#=GF CC   targets SD sequence of potA mRNA via an aSD sequence. The aSD sequence and
#=GF CC   some neighbouring nucleotides are identical to the one of SorY (targets
#=GF CC   takP mRNA). 
#=GF WK   Rhodobacter_sphaeroides
#=GF SQ   8



CP000143.2/2598225-2598299 UUCCCUCCCGUGUC-GGGGUUAG-AGACACGG--ACCCUCCCUGUUGGAUCUGGCCGGGCCUCGUGCCCGGCCUUUUUU
CP014595.1/981561-981633   UCCCGUUGCAUGUG-CGGGUUAU--CACAUGC--AC-CUCCCUGUUGGACCUGGCCGGGCUUUGUGCCCGGCCUUUUUU
CP000377.1/54706-54778     AUCCCGCGCAUAUC-CGGGUCAC--GAUAUGC--AUCCUCCCUGUCGGA-CUGGCCGGGCUUCGCGCCCGGCCUUUUUU
CP015124.1/2077082-2077010 AUCCCGCGCAUAUC-CGGGUCAU--GAUAUGC--AC-CUCCCUGUUGGACUGGGCCGGGCCUUGCGCCCGGCCUUUUUU
CP000362.1/41662-41590     AACCCGCGCAUGUC-CGGGUCAU--GACAUGC--AC-CUCCCUGUUGGACUUGGCCGGGCUUUAUGCCCGGUCUUUUUU
CP006773.1/3787862-3787790 AUCCCGCGCAUAUC-CGGGUCAC--GAUAUGC--AC-CUCCCUGUUGGACUUGGCCGGGCAUGACGCCCGGCCUUUUUU
CP012661.1/4600018-4600091 AGCCCUCCCGCGCC-GGGGUCAU--GGCGCGGCUUCCCUCCCUGUUGGA-CUGCCCGGGCUUCG-GCCCGGGCAUUUUU
CP000830.1/40364-40290     AACCCCAUGCUGUGACGGGGCAUGACACAGCA--AC-CUCCCUGUUGGA-CUUGCCGGGCCUCGUGCCCGGCAUUUUUU
#=GC SS_cons               :::::::<<<<<<<.________..>>>>>>>..--.---------------<<<<<<<<_____>>>>>>>>::::::
#=GC RF                    AuCCCucgcguGuc.cGGGUCAu..gaCacgc..AC.CUCCCUGUUGGAccUGgCCGGGCuUcGuGCCCGGcCUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02785
#=GF ID   snoRNA2
#=GF DE   Trypanosomatid small nucleolar RNA 2
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   108.00
#=GF TC   108.40
#=GF NC   32.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   9512552
#=GF RT   Characterization of a novel trypanosomatid small nucleolar RNA.
#=GF RA   Levitan A, Xu Yx, Ben-Dov C, Ben-Shlomo H, Zhang Y, Michaeli S
#=GF RL   Nucleic Acids Res. 1998;26:1775-1783.
#=GF RN   [2]
#=GF RM   12808138
#=GF RT   Small nucleolar RNA interference induced by antisense or double-stranded
#=GF RT   RNA in trypanosomatids.
#=GF RA   Liang XH, Liu Q, Michaeli S
#=GF RL   Proc Natl Acad Sci U S A. 2003;100:7521-7526.
#=GF RN   [3]
#=GF RM   10909419
#=GF RT   Novel trypanosomatid small nucleolar RNAs that guide methylation: their
#=GF RT   genome organization, expression and potential use to direct specific
#=GF RT   methylation on target RNA molecules.
#=GF RA   Xu YX, Liu L, Michaeli S
#=GF RL   Isr Med Assoc J. 2000;2:58-62.
#=GF WK   Small_nucleolar_RNA
#=GF SQ   3



LJSK01000184.1/20806-20724 GUGAAUGAUGAUGCGUGUAUUCUGCAAUGCUGACCUGUCUGACGAGAAGCAAUACUACUACUAUGACUAUUGGCAUCUGACAC
FR796419.1/39898-39980     GUGAAUGAUGAUGCAUGUAUUCUGCAAUGCGGACUCCACUGACGAGGAACAAUACUACUACUAUGACUAUUGGCAUCUGACGC
FR798998.1/40159-40241     GUAAAUGAUGAUGCGUGUAUUCUGCAAUGCGGACCCCACUGACGAGGAUCAAUACUACUACAAUGACUAUUGGCAUCUGACCA
#=GC SS_cons               :::::::::(((((,,,,,,<<<<<___>>>>><<<<<<____>>>>>><<<<<_____________>>>>>)))))::::::
#=GC RF                    GUgAAUGAUGauGCgUGUAUuCcGCAAUGCgGaccccuCUGACGaggggCaauaCUACUACuAUGACuauuGGCauCUGACac
//
# STOCKHOLM 1.0

#=GF AC   RF02786
#=GF ID   snoTBR2
#=GF DE   Small nucleolar RNA TBR2
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   62.00
#=GF TC   62.70
#=GF NC   56.20
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10908346
#=GF RT   The genes for small nucleolar RNAs in Trypanosoma brucei are organized in
#=GF RT   clusters and are transcribed as a polycistronic RNA.
#=GF RA   Dunbar DA, Chen AA, Wormsley S, Baserga SJ
#=GF RL   Nucleic Acids Res. 2000;28:2855-2861.
#=GF RN   [2]
#=GF RM   10747997
#=GF RT   Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei.
#=GF RT   Sequence conservation and implications for 2'-O-ribose methylation of
#=GF RT   rRNA.
#=GF RA   Dunbar DA, Wormsley S, Lowe TM, Baserga SJ
#=GF RL   J Biol Chem. 2000;275:14767-14776.
#=GF CC   TBR4 was one of seventeen snoRNAs identified in Trypanosoma brucei.[2]
#=GF CC   Together with TBR12, TBR6 and TBR4 it is a part of snoRNA gene cluster
#=GF CC   that is tandemly repeated. These 4 snoRNA genes are transcribed as a
#=GF CC   polycistronic RNA transcript.[1]
#=GF WK   Small_nucleolar_RNA_TBR2
#=GF SQ   5



CM000208.1/3814615-3814725   CGCGUGAUGAGGUGCAGAAGGCAUGUCGCCGCUACGGCGGUGGCUCGCGUAGCCGUCUGGCUGUGCGCGUACUGUGA-GCUACUGUACUCCAUGGGUGAACAAUCUCUGAUG
FR799008.1/90689-90589       CGUGUGAUGACAUACAGAGUGUGC-----GGACACGCC----UAUCGCGUAGCUGCC-GGCUGUGCGCGCCCGACCA-ACUACUGUAUUUCAUGGGUGAACAAUCUCUGAUG
LGTL01000019.1/510774-510874 UGUGUGAUGAUGUACAG--AG---UCUGCG-AAACA--CGCAGGUCGCGGAGCC--CCGGCUGUGCGCGCCAAUUGA-ACUGCUGUAUUUCUUGGGUGAACAAUCUCUGAUG
AHKC01019934.1/77-178        UGCGUGAUGCGGUGCAGAG--ACUGUCGC------G--AGCAGCCCGCGUAGCCGCCAGGCCGUGCGCGCCCUGUCCAACCACUGUGCUCAACGGGUGGACAGUCACUGACG
FR796465.1/91973-91873       CGUGUGAUGAUGUACAGAGUGUGCG-------AAGAC--GCAUGUCGCGUAGCCGCC-GGCUGUGCGCGCCUGACGA-ACUACUGUAUUUCACGGGUGAACAAUCUCUGAUG
#=GC SS_cons                 (((-(-(((-(((((((--(((,,<<<<<<.<____>.>>>>>>,<<<<<<<<<____>>>>>>>>>,,,,,,,,,,.)))-)))))))-)))-))))::::::::::::::
#=GC RF                      cgcGuGaugAgguaCaGAggGcaugccgCg.caAcgg.cGcggcUCGCgcaGCcGcCugGCuguGCGCGcccuaugA.gCcACuGuaccucauGggugAACAAUCuCUGAUG
//
# STOCKHOLM 1.0

#=GF AC   RF02787
#=GF ID   snoTBR4
#=GF DE   Small nucleolar RNA TBR4
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   83.00
#=GF TC   83.40
#=GF NC   77.60
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10908346
#=GF RT   The genes for small nucleolar RNAs in Trypanosoma brucei are organized in
#=GF RT   clusters and are transcribed as a polycistronic RNA.
#=GF RA   Dunbar DA, Chen AA, Wormsley S, Baserga SJ
#=GF RL   Nucleic Acids Res. 2000;28:2855-2861.
#=GF RN   [2]
#=GF RM   10747997
#=GF RT   Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei.
#=GF RT   Sequence conservation and implications for 2'-O-ribose methylation of
#=GF RT   rRNA.
#=GF RA   Dunbar DA, Wormsley S, Lowe TM, Baserga SJ
#=GF RL   J Biol Chem. 2000;275:14767-14776.
#=GF CC   TBR4 was one of seventeen snoRNAs identified in Trypanosoma brucei.[2]
#=GF CC   Together with TBR12, TBR6 and TBR2 it is a part of snoRNA gene cluster
#=GF CC   that is tandemly repeated. These 4 snoRNA genes are transcribed as a
#=GF CC   polycistronic RNA transcript.[1]
#=GF WK   Small_nucleolar_RNA_TBR4
#=GF SQ   3



CM000208.1/3814397-3814495 CGGUGAUUAGCAGUGCGUCUUCCACCUAACGACCCUUGAUGAUUAUGAUACGAUGCCUGGUCAACAGAACUAUACUACACCAAAUUUAGUAAAUGAGAC
AHKC01021457.1/140-43      CUGUGAUUAGCGAUGCGUCUUCCACCUAACGAGGC-UGAUGAUUAUGACCCGAUGCACGUCUUACAUAUUUAUACUACACCAACGAAUGUGGAUGAGUC
CAEX01006950.1/1170-1072   CAGUGAUUAUCUCUGCGUCUUCCACCUAACGAAACUUGAUGAUUAUGAUACGAUGCGAGCUGCACAGAAAUAUACUACACCAACGAGAAGGAAUGAGGC
#=GC SS_cons               :<<<--<<<<--<<<-<____>>>>>>>>-->>>,<<<-<<<<<<-<________>->>>>>>->>>,,,,,<<<<<_________>>>>>::::::::
#=GC RF                    CgguGAuuagCaguGCGUCUUCCaccuaaCGaccCuuGAugacugUGAuaCGAUGCacggucaACagAauUAcacuaCACCAAcgauagugaAUGAGaC
//
# STOCKHOLM 1.0

#=GF AC   RF02788
#=GF ID   snoTBR6
#=GF DE   Small nucleolar RNA TBR6
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   37.60
#=GF TC   37.60
#=GF NC   37.10
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 605271.01655 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10908346
#=GF RT   The genes for small nucleolar RNAs in Trypanosoma brucei are organized in
#=GF RT   clusters and are transcribed as a polycistronic RNA.
#=GF RA   Dunbar DA, Chen AA, Wormsley S, Baserga SJ
#=GF RL   Nucleic Acids Res. 2000;28:2855-2861.
#=GF RN   [2]
#=GF RM   10747997
#=GF RT   Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei.
#=GF RT   Sequence conservation and implications for 2'-O-ribose methylation of
#=GF RT   rRNA.
#=GF RA   Dunbar DA, Wormsley S, Lowe TM, Baserga SJ
#=GF RL   J Biol Chem. 2000;275:14767-14776.
#=GF CC   TBR6 was one of seventeen snoRNAs identified in Trypanosoma brucei.[2]
#=GF CC   Together with TBR2, TBR12 and TBR4 it is a part of snoRNA gene cluster
#=GF CC   that is tandemly repeated. These 4 snoRNA genes are transcribed as a
#=GF CC   polycistronic RNA transcript.[1]
#=GF WK   Small_nucleolar_RNA_TBR6
#=GF SQ   3



CM000208.1/3814121-3814202 CGC-------GUGAUGACA-UACAAAGU--UGUUUGCACAUUUUCCGACACACCGUGA-------GCGAGUUACAAUAUUACAAGAACACCAUCUGAAU
AHKC01021457.1/284-198     CGCCGUGACAGUGAUGACC--ACAAGCU---GUUUGCACAUUUGCCGACCCUGCGUGA-------GUGACCCACAGGAAUCUAAGAACACCAGCUGAUG
FR796429.1/92658-92566     CGC------UGUGAUGACUGGAUGAGUUAUUGUUUGCACAUUUACCGAGCCUUCGUGGCCCGUGAGCGACCGUAUAACUUCUAAGAACACCAGCUGAUU
#=GC SS_cons               (((,,,,,,,<<<--<<<_.________.._>>>-->>>,,,,<<<<______>>->>.......))):::::::::::::::::::::::::::::::
#=GC RF                    CGC......uGUGAUgACu.uAcaAguU..UGUuUGCACAUUUuCCGAccCuuCGUGa.......GCGAccuacaaaauUcUAAGAACACCAgCUGAuu
//
# STOCKHOLM 1.0

#=GF AC   RF02789
#=GF ID   snoTBR12
#=GF DE   Small nucleolar RNA TBR12
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   77.00
#=GF TC   77.50
#=GF NC   34.90
#=GF TP   Gene; snRNA; snoRNA; CD-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 451031.997884 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000593; C_D_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF DR   GO; 0005730; nucleolus;
#=GF RN   [1]
#=GF RM   10908346
#=GF RT   The genes for small nucleolar RNAs in Trypanosoma brucei are organized in
#=GF RT   clusters and are transcribed as a polycistronic RNA.
#=GF RA   Dunbar DA, Chen AA, Wormsley S, Baserga SJ
#=GF RL   Nucleic Acids Res. 2000;28:2855-2861.
#=GF RN   [2]
#=GF RM   10747997
#=GF RT   Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei.
#=GF RT   Sequence conservation and implications for 2'-O-ribose methylation of
#=GF RT   rRNA.
#=GF RA   Dunbar DA, Wormsley S, Lowe TM, Baserga SJ
#=GF RL   J Biol Chem. 2000;275:14767-14776.
#=GF CC   TBR12 was one of seventeen snoRNAs identified in Trypanosoma brucei.[2]
#=GF CC   Together with TBR2, TBR6 and TBR4 it is a part of snoRNA gene cluster that
#=GF CC   is tandemly repeated. These 4 snoRNA genes are transcribed as a
#=GF CC   polycistronic RNA transcript.[1]
#=GF WK   Small_nucleolar_RNA_TBR12
#=GF SQ   3



CM000208.1/3813980-3814081 CGCAUGAUGUGCUCAACUGGAAUUACCAUCUGAACGCGGGAUACCGCAAGUCGAUGAAUUAAUGCUACGUGCAU-UA-CCUCCGCUGUUACUCGUAUCACUGAC
CAEX01006950.1/493-393     CAAAUGAUGCUCGGAACUGGAAUUACCAUCUGAACGCGU-ACCACGCAAAUCGAAGAUACGAUGCCGUGCACAU-UA-CCUCCGCUGUUACUCGGAUGACUGAU
AYLP01000080.1/52611-52713 CAAAUGAUGUGUGAAAAUGGAAUUACCAUCGGAAGGCGC-CUGGCGCAGGUUGACGACAAGAUGCCGUGUGCAUACUACCUCAACUGUUACUCGUACCACUGAA
#=GC SS_cons               ::(((((((((---(((((((,,,,,<<<<-<<--<<<<____>>>>--->>>>>>,,,<<<<<<_____>>>>.>>.,,))))--)))---)))))))-))::
#=GC RF                    CacaugaugcgcgaaaccgGaAUUACCguCuGaAcGCGc.auagCGCAaguCGacGAuacgauGccguGugCau.cg.CCuCcgCUguuACUcgcaucaCugAu
//
# STOCKHOLM 1.0

#=GF AC   RF02790
#=GF ID   sodF_sRNA
#=GF DE   sodF sRNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 24234448;
#=GF GA   46.00
#=GF TC   46.10
#=GF NC   45.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0017148; negative regulation of translation;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0043488; regulation of mRNA stability;
#=GF RN   [1]
#=GF RM   24234448
#=GF RT   Inverse regulation of Fe- and Ni-containing SOD genes by a Fur family
#=GF RT   regulator Nur through small RNA processed from 3'UTR of the sodF mRNA.
#=GF RA   Kim HM, Shin JH, Cho YB, Roe JH
#=GF RL   Nucleic Acids Res. 2014;42:2003-2014.
#=GF CC   Identified in Streptomyces coelicolor. It is produced from sodF mRNA by
#=GF CC   cleavage of about 90 nucleotides from its 3'UTR. However, it does not
#=GF CC   affect the function of sodF mRNA, but acts on another mRNA called sodN.
#=GF CC   s-SodF RNA has a sequence complimentary to sodN mRNA from the 5'-end up to
#=GF CC   the ribosome binding site. It pairs with sodN mRNA, blocks its translation
#=GF CC   and facilitates sodN mRNA decay.
#=GF WK   S-SodF_RNA
#=GF SQ   6



AL645882.2/2860741-2860830 UCG---UCCCGCCUCGUGAUCGUCUUCUCAACCUUCACC-GGGCGGGCGGAAU-GA-GGAAGGCCCCCGCGAGGACGUGACUCGCGGGGGCCUUCU
CP007699.2/5812507-5812418 GCG---UCCCGCCUCGUGAUCGUCUUCUCACCCUUCACU-UGGCGGGCGGAAU-GA-GCGAAGCCCCCGCGAGGACGUGACUCGCGGGGGCUUCGU
CP002475.1/4911792-4911702 ACG---UCCUGCCUCGUGAUCGUCUUCUCAACCUUCACC-CGGCAGGCGGAUG-GACGGAGGACCCCCGCGAGGACAUGACUCGCGGGGGUUCUCC
CP006259.1/3228235-3228325 ACG---UCCUGCC-CGUGAUCGUCUUCUCACCUUUCACGCAGGCAGGCGGAGA-GAAGGAGGGCCCCCGCGAGGACGUGACUCGCGGGGGCCCUCC
FR845719.1/2617735-2617827 CCGCGCUCCUGCUC-GUGAUCGUCUUCUCAACCUUCACC-GGGCAGGCGGAUGAAA-GAAGAACCCCCGCGAUGACGUGAAUCGCGGGGGUUCUUC
FN554889.1/6649486-6649399 AUG---UCCUGC-UCGUGAUCGUCUUCUCACCCGUCACC-G-GCAGGCAGCCA-GA-GGAGAACCCCCGCGAGGACGUGACUCGCGGGGGUUCUCG
#=GC SS_cons               <<<...-<<<<<<<-<<<<--<<_______>>-->>>>-.>>>>>>>>>>---.--.<<<<<<<<<<<<<<<<_______>>>>>>>>>>>>>>>>
#=GC RF                    ccG...UCCcGCcccGuGaUCGuCUUCUCAaCcuuCaCc.ggGCgGGCggAua.gA.ggagggCCCCCGCGagGACgUGAcuCGCGGGGGcccucc
//
# STOCKHOLM 1.0

#=GF AC   RF02791
#=GF ID   CcsR1
#=GF DE   Conserved CCUCCUCCC motif stress-induced RNA 1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 25777678;
#=GF GA   65.30
#=GF TC   65.30
#=GF NC   65.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 605271.01655 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0080183; response to photooxidative stress;
#=GF RN   [1]
#=GF RM   25777678
#=GF RT   A cluster of four homologous small RNAs modulates C1 metabolism and the
#=GF RT   pyruvate  dehydrogenase complex in Rhodobacter sphaeroides under various
#=GF RT   stress conditions.
#=GF RA   Billenkamp F, Peng T, Berghoff BA, Klug G
#=GF RL   J Bacteriol. 2015;197:1839-1852.
#=GF CC   A cluster of four homologous sRNAs called CcsR 1-4 has been shown to play
#=GF CC   a role in photo-oxidative stress resistance.
#=GF WK   Rhodobacter_sphaeroides
#=GF SQ   2



CP000143.2/692456-692374   GUUUCCUGCGAGGUCCCACCUCCUCCCGGGACCUGUAGCAGCAGCGGCGACGCCUCUCCUCCUCCCUGGUGUCGCCGUCCUUU
ACYY01000023.1/29669-29587 GUUUCUUGCUGAACCCCACCUCCUCCCGGGGUUUCUGGCAAACGCGGCGGCACUGAUCCUCCUCCCCAGUGCCGCCGCAGCUU
#=GC SS_cons               ::::::<<<-<<<<<<<__________>>>>>>>>>>-------<<<<<<<<<<_____________>>>>>>>>>>::::::
#=GC RF                    GUUUCuugcuaggcCCCACCUCCUCCCGGGgccuguaGCAaaaGCGGCGgCaCcuaUCCUCCUCCCugGuGcCGCCGuaguUU
//
# STOCKHOLM 1.0

#=GF AC   RF02792
#=GF ID   sRNA162
#=GF DE   Archaeal Small RNA 162
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22965121;
#=GF GA   78.00
#=GF TC   78.40
#=GF NC   57.30
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 605271.01655 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   SO; 0000077; antisense;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   22965121
#=GF RT   An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct
#=GF RT   domains.
#=GF RA   Jager D, Pernitzsch SR, Richter AS, Backofen R, Sharma CM, Schmitz RA
#=GF RL   Nucleic Acids Res. 2012;40:10964-10979.
#=GF CC   Acts on cis and trans-encoded mRNAs. 
#=GF WK   Methanosarcina_sRNA162
#=GF SQ   3



AE008384.1/2915320-2915131 GCCUUUGGGCACGCAGGAUUCAGGGGAGGGCUCAAACUUUGCUGAAUCCUGCAGAACAUUCCCACAUUUGAAAACCCCAUAAUCCUUUAAAAGUUUUAUGUGUAAACUCUCAAACAAUCAGGCAUAAGA-GAAGAAUACAAAUCUGAAAUAAAUUAACAGAAAAAUAGUUUGAGAGCUUACACAGAAGCUA
AE010299.1/1814751-1814939 GCCUUCGAGCAUGCAGGAUUCAGGGCAGGUUUCAAACUCUACCGAAUCCUGUAGAACAUUCUUACUUUCCAGAAAUUCAUAAUCCUUUAAAAGUUUUAUGUGUAAACUCUCAAACAAUCAAGCAUAAGA-GAGGAAUACAAAUCUGAAAUAAGUUAACAAAAAAAUAGUUUGAGAAG-UACACAGAGACUA
CP000099.1/4337450-4337262 GCCUUCGGGUAUGCAGGGUUCAGGAUCGUUCUCAAACUUCACUGAACUCUGCAAACAUUCCCACUUAUUCAGUUUUAGAGAAUCCUUUAUAAGUUUUCCGGCCAAUUUCUCUAACUAUCAGAGAUCAGGGAAU-CUUUACAGAUCUAAAAUGAGCU-ACAAAAAACAGUUAGAGAAAUUGGUCGAAAGUUA
#=GC SS_cons               ::[[[[<<<--<<<<<<<<<<<<-<<<<________>>>>->>>>>>>>>>>>------->>>,,,,,,,,,,,,,,,,<<<--<<<___>>>-->>>(((((((-(((((((((,,<<________>>.,,<<<_______>>>,,,,,,,,,,,,,,,,,,,,,,))))))))))-))))))]]]]:::
#=GC RF                    GCcuUcgGGcAuGCaGGgUUCaGGggaGgucUCAAACuccaCuGAAcCCuGCagAacaUuCCcacuuUucAgaauuucAgaaUCCUUUAaAAGUUuuccGugcacacUCUCaaaCaAuCAggcAUaAGa.gAgGaaUacaAauCcgAAAuaaauuaAcaaAAAAAuAGuuuGAGAggUugcaCggAagcUA
//
# STOCKHOLM 1.0

#=GF AC   RF02793
#=GF ID   asR3
#=GF DE   Pyrobaculum asRNA3
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22783241;
#=GF GA   46.00
#=GF TC   46.20
#=GF NC   37.20
#=GF TP   Gene; antisense; 
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   22783241
#=GF RT   Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by
#=GF RT   Comparative Small RNA Sequencing in Four Pyrobaculum Species.
#=GF RA   Bernick DL, Dennis PP, Lui LM, Lowe TM
#=GF RL   Front Microbiol. 2012;3:231.
#=GF CC   Binds to the 3'-end of the tpi gene (triose-phosphate-isomerse). The tpi
#=GF CC   mRNA has a conserved structural element located close to the stop codon.
#=GF CC   Binding of the asR3 may be able to compete against the formation of the
#=GF CC   tpi element structure and this may modulate the function of this highly
#=GF CC   conserved element.
#=GF WK   Pyrobaculum_asR3_small_RNA
#=GF SQ   3



AE009441.1/880183-880239 CGCUCGCGGCGG-GGCCGCCUUAAGUGUCCGCCGCUCAUUUGCCCCCAAUUCGGGGGU
LOBY01000142.1/6175-6119 GGAUCGCGGCGG-GGCCGCCUCAAGUGUCCGCCGCUCAUCUGCCCCCGCUCCGGGGGA
FN869859.1/97113-97058   AGAUCGCGGCCGCAGCCGCC-UAGGUGGCGGCCGCUCAUGUGCCCCCUCCA-GGGGGU
#=GC SS_cons             :::::<<<<<<<.-<<-<<_____>>>>>>>>>>>------<<<<<<_____>>>>>>
#=GC RF                  aGAUCGCGGCgG.ggCCGCCUUAAGUGuCcGCCGCUCAUuUgCCCCCacUuCGGGGGu
//
# STOCKHOLM 1.0

#=GF AC   RF02794
#=GF ID   Pab19
#=GF DE   Pab19 RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 18304947;
#=GF GA   55.00
#=GF TC   55.50
#=GF NC   44.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   18304947
#=GF RT   Combined in silico and experimental identification of the Pyrococcus
#=GF RT   abyssi H/ACA sRNAs and their target sites in ribosomal RNAs.
#=GF RA   Muller S, Leclerc F, Behm-Ansmant I, Fourmann JB, Charpentier B, Branlant
#=GF RA   C
#=GF RL   Nucleic Acids Res. 2008;36:2459-2475.
#=GF CC   By using various computational and experimental approaches in three
#=GF CC   Pyrococcus genomes seven H/ACA sRNAs and 15 pseudouridine resides on rRNA
#=GF CC   were identified. One H/ACA motif was shown to guide up to three distinct
#=GF CC   pseudouridylations.[1]
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   3



AE009950.1/136690-136790   GCCCCUGAAGA-GGGGGCGAAAACCCAGGGG-CC-CGACGGCGGCGUCGGGGGGAUUGGGGGCAAAGCCCCCGG-AAUGAACCCCGCCCUCCUCCCCUGGGUAUA
CP015520.1/465743-465642   GCGCCCAAAC-AGGGCGCGGAACACCCAGGC-GCCAGACGGCGGCGUCGGGGGGAAAGGGUGCAAAGCACCCAA-GAUGAACCCCGCCCUCCAGCCUGGGUCACA
CP001398.1/1950614-1950511 GCCCCCGAAGA-GGGGGCGAAACACCCGGGCGCCAAGACGGCGGCGUCGGGGGGAACGGGUGCAAAGCACCCAAAGAUGAACCCCGCCCUCCAGCCCGGGUCACA
#=GC SS_cons               <<<<<<______>>>>>>----<<<<<<<<<.---------------<<<<<<<<<<<<<<<<___>>>>>>>>.--->>>>>>>>------->>>>>>>>>:::
#=GC RF                    GCcCCcgAAgA.gGGgGCGaAAgcCCcgGGc.cCaaGACGGCGGCGUCGGGGggcccGGGgGCAAAGCcCCCgg.gAUgccCCCCGCCCUCCagCCcgGGgcAcA
//
# STOCKHOLM 1.0

#=GF AC   RF02795
#=GF ID   Pab91
#=GF DE   Pab91 RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 18304947;
#=GF GA   71.00
#=GF TC   71.10
#=GF NC   49.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   18304947
#=GF RT   Combined in silico and experimental identification of the Pyrococcus
#=GF RT   abyssi H/ACA sRNAs and their target sites in ribosomal RNAs.
#=GF RA   Muller S, Leclerc F, Behm-Ansmant I, Fourmann JB, Charpentier B, Branlant
#=GF RA   C
#=GF RL   Nucleic Acids Res. 2008;36:2459-2475.
#=GF CC   By using various computational and experimental approaches in three
#=GF CC   Pyrococcus genomes seven H/ACA sRNAs and 15 pseudouridine resides on rRNA
#=GF CC   were identified. One H/ACA motif was shown to guide up to three distinct
#=GF CC   pseudouridylations.[1]
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   3



AE009950.1/1226103-1226159 CCCCUCCCCUCUCACACCCCCGUGAGAAGUGAGCGGGGGGCGGUCGGGGAGGGGACA
AP006878.1/1545183-1545239 GCCCUCCCCUCUCACACCCCCGGGAGCGGUGACCGGGGGGCGGUCGGGGAGGGCACA
CP001398.1/551052-551108   GCCCUCCCCUCUCACACCCCCGUGAAGGGUGAGCGGGGGGCGGUCGGGGAGGGCACA
#=GC SS_cons               <<<<<<<<<------<<<<<<<<<<_____>>>>>>>>>>----->>>>>>>>>:::
#=GC RF                    gCCCUCCCCUCUCACaCCCCCGggagagGUgacCGGGGGgCGGUCGGGGAGGGcACA
//
# STOCKHOLM 1.0

#=GF AC   RF02796
#=GF ID   Pab160
#=GF DE   Pab160 RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 18304947;
#=GF GA   48.00
#=GF TC   48.70
#=GF NC   41.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   18304947
#=GF RT   Combined in silico and experimental identification of the Pyrococcus
#=GF RT   abyssi H/ACA sRNAs and their target sites in ribosomal RNAs.
#=GF RA   Muller S, Leclerc F, Behm-Ansmant I, Fourmann JB, Charpentier B, Branlant
#=GF RA   C
#=GF RL   Nucleic Acids Res. 2008;36:2459-2475.
#=GF CC   By using various computational and experimental approaches in three
#=GF CC   Pyrococcus genomes seven H/ACA sRNAs and 15 pseudouridine resides on rRNA
#=GF CC   were identified. One H/ACA motif was shown to guide up to three distinct
#=GF CC   pseudouridylations.[1]
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   4



CP001398.1/1107569-1107637 GCCCCCGGGAAACCGCGGGGGAUGAGC-----GCUUCGGCG-AGCUGUGAUUCCCCUUCGCUCCCCGGGGGCACA
AP006878.1/899083-899151   GCCCCCGGGAAACCGCGGGGGAUGAGC----GCCUC--GGCGAGCCGUGAUUCCCCUUCGCUCCCCGGGGGCACA
AE009950.1/1865162-1865095 GCCCCCGGGAAACCGCGGCGGGGGAGCG--AG-C----GGCGAGCUGUGAGCCCGCUUCGCUCCCCGGGGGUACA
L77117.1/1659520-1659450   GCCCCGGG-AAACCGCGGGGGAUGAGCGACAGCC-C--GGCAAGCUGUGAGUCCCCUUUGCUCCCCCGGGGCACA
#=GC SS_cons               <<<<<<<<-------<<<<<<<<<<<<<..-<<<__..>>>->>>--->>>>>>>>>>------>>>>>>>>:::
#=GC RF                    GCCCCcGGGAAACCGcgGgGGacgaGCg..AGcC.c..GgCgcGCUGUgaguCCcCuucGCUCCCCgGGGGCACA
//
# STOCKHOLM 1.0

#=GF AC   RF02797
#=GF ID   PssrA
#=GF DE   Plasmid-encoded Shigella sRNA A
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   69.00
#=GF TC   69.50
#=GF NC   63.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   21483688
#=GF RT   An integrated approach for finding overlooked genes in Shigella.
#=GF RA   Peng J, Yang J, Jin Q
#=GF RL   PLoS One. 2011;6:e18509.
#=GF WK   Bacterial_small_RNA
#=GF SQ   6



CP000036.1/93227-93316     UGGCUGCGAAAAGAGUUUUAAUUUUUAU--GAGGCCGACGAUGAUUA-CGGACUCAGGCGACAGGCACAAAUCGGAGAGAAACUAUGUUUGAA
U00096.3/105224-105313     UGGCUGCGAAAAGAGUUUUAAUUUUUAU--GAGGCCGACGAUGAUUA-CGGCCUCAGGCGACAGGCACAAAUCGGAGAGAAACUAUGUUUGAA
CP000822.1/3049179-3049089 UGGCUGCGAAAAGAGUUUUAAUUUUUAU--GAGACCGGCGACUAUUAACGGUCUCAGGCGACAGGCACAAAACGGAGAGAAACUAUGUUUGAA
CP012487.1/4279237-4279145 UGGCUGCGAAAAGAGUUUUAAUUUUUUUCAGAGACCGCCGAAAAUUAACGGUCUCAGGCGACAGGCACAAGACGGAGAGAAACUAUGUUUGAA
CP009458.1/1888976-1889068 UGGCUGAGAAAAGAAUUUUAAUUUUUAUAAGAGACCGGAGACAAUUAGCGGUCUCAGGCGACAGGCACAAAACGGAGAGAAACUAUGUUUGAA
CP007215.3/4036364-4036274 UGGCUGCGAAAAGAGUUUUAAUUUUUUUCAGAGACCGUAGAGAAUUAACGGUUUCAGGCGACAGGCACAA--CGGAGAGAGAUUAUGUUUGAA
#=GC SS_cons               <<-<<<<<----<<<<<<<<<<<___________________>>>>>-->>>>>>--->>->>>->>----<<<<<-<_______>->>>>>:
#=GC RF                    uGGCuGcGAAAAGagcuuuaauuUUUaUaAGAGaCCGacGAuaauuaaCgggcuCAGGCgACaGGCaCAAAcCggaGaGAAAcUAuGuuuGgA
//
# STOCKHOLM 1.0

#=GF AC   RF02798
#=GF ID   CssrA
#=GF DE   Chromosome-encoded Shigella sRNA A
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   93.00
#=GF TC   93.30
#=GF NC   60.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   21483688
#=GF RT   An integrated approach for finding overlooked genes in Shigella.
#=GF RA   Peng J, Yang J, Jin Q
#=GF RL   PLoS One. 2011;6:e18509.
#=GF WK   Bacterial_small_RNA
#=GF SQ   4



CP007394.1/826052-826161   ACCGGGAUGAGCGAGCGAAGACAACGCAUCUGCGGCGCGAAAUAUGAAGGGGGAGAGCCCUUAUAGACCAGGUAGUA-CACGUUUGGUUAGGGGGCCUGCAUAUGGCCCCC
AE006468.2/255108-255217   ACCGGGAUGAGCGAGUGAAGGCAACGCGCCUGCGGCUCGAAAUAUGAAGGG-GAGAGCCCUUAUAGACCAGGUAGUAUCACGUUUGGUUAGGGGGCCUGUAUAUGGCCCCC
CP000880.1/2698815-2698705 ACUGGAAUGAGAGAGUGAAGGCAACGCACCUGCGGCUCGAAAUAUGAAGGGGGUAGCCCCUUAUAAACCAGGUAGUAUCACGUUUGGUUAGGGGGCCUGUCUAAGGCCCCC
CP000036.1/176703-176812   ACCGGGAUGAGCGAGCGAAGAUAACGCAUCUGCGGCGCGAAAUAUGAAGGGGGAGAGCCCUUAUAGACCAGGUAGUA-CACGUUUGGUUAGGGGGCCUGCAUAUGGCCCCC
#=GC SS_cons               ::<<-<----<<<<<<<_______>>>->>->>-->->>,,,,,,,<<<<<______>>>>>,,,<<<<<<<__________>>>>>>>,<<<<<<<_______>>>>>>>
#=GC RF                    ACcGGgAUGAGcGgGcGAAGacAACgCacCUgCGGcuCgAAAUAUGaaGGGGGagagCCCuuAUAgaCCaggUAGUAuCACGccuGGucAGGGGGCCUGuaUAuGGCCCCC
//
# STOCKHOLM 1.0

#=GF AC   RF02799
#=GF ID   CssrB
#=GF DE   Chromosome-encoded Shigella sRNA B
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   76.00
#=GF TC   76.30
#=GF NC   51.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   21483688
#=GF RT   An integrated approach for finding overlooked genes in Shigella.
#=GF RA   Peng J, Yang J, Jin Q
#=GF RL   PLoS One. 2011;6:e18509.
#=GF WK   Bacterial_small_RNA
#=GF SQ   3



AFGZ01000047.1/125824-125645 AACGAUACUAUUUUCUUAGAUGGUAAAUGUCUCGCCUGUGCUAUAUUUUGUUUUUCGGUUAGUUAAAUAUCGUACGUUCAUAUUUGAACGUUCUGCCGGAAUGCAUUAUCAAUAGAGGUAAAGUCGCAACCCCAAAUCGUAAAGGAAACCGUAGCACGUCUUAAGCAAGAACGUGCUGCG
CP000034.1/996957-996778     AACGAUACUAUUUUCUUAGAUGGUAAAUAUCUCGCCUGUGCUAUAUUUUGUUUUUCGGUUAGUUAAAUAUCGUACGUUCAUAUUUGAACGUUCUGCCGGAAUGCAUUAUCAAUAGAGGUAAAGUCGCAACCCCAAAUCGUAAAGGAAACCGUAGCACGUCUUAAGCAAGAACGUGCUGCG
CP000036.1/984279-984100     AACGAUACUAUUUUCUUAGAUGGUAAAUGUCUCGCCUGUGCUAUAUUUUGUUUUUCGGUUAGUUAAAUAUCGUACAUUCAUAUUUGAAUGUUCUGCCGGAAUGCAUUAUCAAUAGAGGUAAAGUCGCAACCCCAAAUCGUAAAGGAAACCGUAGCACGUCUUAAGCAAGAACGUGCUGCG
#=GC SS_cons                 :(((((<<<<<<<____>>>>>>>,,,,<-<<-<<<<-<<----<<--<<<-<<<<<<<--------------<<<<<<<____>>>>>>>--->>>>>>>->>>-->>--->>->>>>-->>->,,,,,,,,,,)))))---------<<<<<<<<<<<<<____>>>->>>>>>>>>>
#=GC RF                      AaCGauaCcaucuUCUUagaugGuAAAUgUCuCgCCuGugCUAUauUUuGcUuucCGGcUAGUUAAAUAUCGUaCguuCaUAUUuGaacGuUCUgCCGgaaUgCaUUauCAAcaGaGGcAAaGUcGCAACCCCAAauCGuAAAGGAAACCGcaGCaCGuCuuAAGCaaGAaCGuGCugCG
//
# STOCKHOLM 1.0

#=GF AC   RF02800
#=GF ID   Rp_sR47
#=GF DE   Rickettsia sRNA47
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   60.00
#=GF TC   60.00
#=GF NC   59.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   27375581
#=GF RT   Identification and Characterization of Novel Small RNAs in Rickettsia
#=GF RT   prowazekii.
#=GF RA   Schroeder CL, Narra HP, Sahni A, Rojas M, Khanipov K, Patel J, Shah R,
#=GF RA   Fofanov Y, Sahni SK
#=GF RL   Front Microbiol. 2016;7:859.
#=GF CC   Expressed in human microvascular endothelial cells (HMEC) infected with
#=GF CC   Rickettsia.
#=GF WK   Rickettsia
#=GF SQ   2



AJ235269.1/287678-287363 UUAGUUUUACAGCAGCCCUAGAAUUAAUUUGUGUUAAAGCCUGAACUGAUCCUUUACCAAAAGAUUUAGUACCAAGUAUUAUUGCUCUUUUAUGAUCUUGCAAAGCUCCAGCAACUAUUUCUGAAGCAGAUGCAGAAUUACCGUUUAUUAAAACAAUCAUAGGUACUUUUGGGGCUUUUAACGAAAACUCAUUCGCUUUAGUUUCGCUAUUACUUGAUGUAGUUCUACCUUUUGUUGUAACAAUGACACCAGAAUCAAUAAAAUAAUCACUAACAGCAAUAGCUUGAUCAAGUAUACCACCAGCAUUAUUACGUAA
CP003334.1/398228-397913 UCAGUUUUACGGCAGCCCUAGAAUUGAUUUGCGUUAAAGCCUGAACUGAUCCUUUACCGAAAGACUUAGUGCCAAGUAUUAUUGCUCUUUUAUGAUCUUGCAAAGCUCCGGCAACUAUUUCCGAGGCAGAGGCAGAAUUACCGUUUAUUAAAACUAUCAUAGGUACUUUGGGAGCUUUUAAUGAAAACUCAUUUGCUUUAGUUUCACUAUUACUUAAUGUAGUUCUACCUUUUGUUGUUACAAUUACACCGGAAUCAAUAAAAUAAUCACUAACAGCAAUAGCUUGAUCGAGUAUACCUCCGGCAUUAUUACGUAA
#=GC SS_cons             :::[[--[[--[[((((((((((---(((((((,,,,,,,,,,,<<<<<--<<<<____>>>>-->>>>>,,,,<<<<____>>>>,,,,,,<<<<-<<<<<--<<<-<<<_________>>>->>>--->>>>>->>>>,,<<<<____>>>>,,,)))))))--)))))))))),,,,,<<<<______>>>>,,,<<<<___>>>>,((((((((,<<<<------<<<<<<<<------<<____>>---->>>>>>>>----->>>>,,<<<____>>>,,)))))))),,,,,,,,]]--]]--]]::::
#=GC RF                  UuAGuUUuaCaGCaGCcCuagaaUUaauuugcGUUAAAGCCUGAaCugaUCCuuuACCaaaaGAuuuaGuaCCAaGuaUUAUugCuCUUUUAugauCuuGCaAAGCuCCgGCAACUAUUUCcGAaGCAGAuGCagAauuaCCGuuuAUUAaaaCaAUCguagguACuuuugGgGCuUUUAAcgaaAACUCAuucgCUUuaGuUUCaCuaUuaCuugauGuaGuUCUACCuuuuguuGUaACAAugACACcaGAAUCaauaaaaUAAUCaCuaACaGCAAUAGCuUGaucaaGuaUACCaCCaGCAUuaUUaCGUAA
//
# STOCKHOLM 1.0

#=GF AC   RF02801
#=GF ID   PyrR201
#=GF DE   Pyrobaculum sRNA 201
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22282340
#=GF GA   49.00
#=GF TC   49.10
#=GF NC   37.00
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   22282340
#=GF RT   Discovery of Pyrobaculum small RNA families with atypical pseudouridine
#=GF RT   guide RNA features.
#=GF RA   Bernick DL, Dennis PP, Hochsmann M, Lowe TM
#=GF RL   RNA. 2012;18:402-411.
#=GF CC   Has weak conservation of the canonical pseudouridylation guide sRNA
#=GF CC   features among the Pyrobaculum species. 
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   5



AE009441.1/648915-648982   GCCCCUGGCGUGGGGCGUCGAGGCGCCGCCACGGCCGCUGUGAAAACGCCCCCUCCAAGGGGCGCACA
CP001014.1/177705-177772   GCCCCUGGCGUGGGGCGUCGAGGCGCCGCGUGGGCGGCUGUGAAAAUGCCCCCUCCAAGGGGCGGACA
CP000504.1/1136982-1136915 GCCCCUGGCGUGGGGUGUCGAGGCGCCGUGUUGGCGGCUAUGAAAACGCCCCCUCCGAGGGGCAGAUA
CP000660.1/236305-236238   GCCCCUGGCGUGGGGUGUCGAGUCGCCGUGUGGGCGGCUGUGAAAACGCCCCCUCCGCGGGGCGUACA
CP000561.1/649113-649180   GCCCCUGGCGUGGGGUGUCGAGCCGCCGCACAGGCGCCGGUGAACACGCCCCCUCCAAGGGGCGUACA
#=GC SS_cons               <<<<<<-----<<<<<<<<<<--<<<<<___>>>>->---->>>->>>>>>>----->>>>>>:::::
#=GC RF                    GCCCCuGGCGUGGGGcGUcgaGgCGCCgcgucGGCGGCUGUgaaAACgCCCCCUCCaaGGGGCGuACA
//
# STOCKHOLM 1.0

#=GF AC   RF02802
#=GF ID   PyrR204
#=GF DE   Pyrobaculum sRNA 204
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22282340
#=GF GA   71.00
#=GF TC   71.40
#=GF NC   37.70
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   22282340
#=GF RT   Discovery of Pyrobaculum small RNA families with atypical pseudouridine
#=GF RT   guide RNA features.
#=GF RA   Bernick DL, Dennis PP, Hochsmann M, Lowe TM
#=GF RL   RNA. 2012;18:402-411.
#=GF CC   Non canonical pseudouridylation guide sRNA features. Predicted to target
#=GF CC   23S U2023 in Pyrobaculum.
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   5



AE009441.1/1238265-1238321 GAGUGCCGCCGGAGAGCCGCGCGC-CGCGGCCCCAUGAGCGGCGGUUCCCCGGCCAUA
CP003316.1/101700-101755   GAGUGCCGCCCGAGAGCCGCU-UC-UGCGGCCCAGUGAUCGGCGGUUCCCCGGCUAUU
CP000504.1/1691249-1691305 GAGUGCCGCUGGAGUGCCGCCCUA-GGCGGCUCUAUGAUAGUCGGCCCCCCGGCCUUA
CP001014.1/1126009-1125953 GAGUGCCGCUGGAGCGCCGCCUUU-GGCGGCCCCGUGAAAGUCGGCCCCCCGGCUUAA
CP000561.1/168814-168757   GAGUGCCGCCGGAGUGCCGCAGAUGUGCGGGCCGAUGAAAGGCGGUUCCCCGGCUUUU
#=GC SS_cons               ::::<<<<<<<<<--<<<<<<___.>>>>>>----->>>->>>>>>::::::::::::
#=GC RF                    GAGUgCCGcCcGAGuGCCGCccuu.gGCGGCCCuAUGAgaGgCGGcuCCCCGGCUuUa
//
# STOCKHOLM 1.0

#=GF AC   RF02803
#=GF ID   PyrR205
#=GF DE   Pyrobaculum sRNA 205
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22282340
#=GF GA   35.60
#=GF TC   35.60
#=GF NC   35.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   22282340
#=GF RT   Discovery of Pyrobaculum small RNA families with atypical pseudouridine
#=GF RT   guide RNA features.
#=GF RA   Bernick DL, Dennis PP, Hochsmann M, Lowe TM
#=GF RL   RNA. 2012;18:402-411.
#=GF CC   Non canonical pseudouridylation guide sRNA features. Predicted to target
#=GF CC   23S U2029 in Pyrobaculum.
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   5



AE009441.1/1001407-1001347 UUAGCCCUAGGUAACACCCCUG-AGCGGGGGCGGAUGAGCCUGGCGGGUUACCCCGGCCAAA
CP001014.1/643411-643351   ACUGCCCUAGGCAACACCCCUG-UAGGGGGGCGUAUGAGCCUGGCGGGUUACCCCGGCCAUA
CP000561.1/585996-585937   AAUGCCCUAGGCAACACCCCCG-AGU-GGGGCGAAUGAGCCUGGCGGGUUACCCCGGCCAAA
CP000660.1/700317-700377   AACACCCUGGGCAACACCCCUG-UAGGGGGGCGAAUGAGCCUGGUGGGUUACCCCGGCCAUA
CP003316.1/1347629-1347568 AACACCCUGGGCAACACCCCUGUAGGGGGGGCGAAUGAGCCUGGUGGGUUACCCCGGCCAUA
#=GC SS_cons               :::<<<--<<<<<<--<<<<<_.___>>>>>----->>>>>>>>>:::::::::::::::::
#=GC RF                    AauGCCCUaGGCaaCACCCCuG.agggGGGGCGaAUgaGCCuGGCGGGUUACCCCGGCCAuA
//
# STOCKHOLM 1.0

#=GF AC   RF02804
#=GF ID   PyrR206
#=GF DE   Pyrobaculum sRNA 206
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22282340
#=GF GA   46.00
#=GF TC   46.50
#=GF NC   39.20
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   22282340
#=GF RT   Discovery of Pyrobaculum small RNA families with atypical pseudouridine
#=GF RT   guide RNA features.
#=GF RA   Bernick DL, Dennis PP, Hochsmann M, Lowe TM
#=GF RL   RNA. 2012;18:402-411.
#=GF CC   Non canonical pseudouridylation guide sRNA features. Predicted to target
#=GF CC   23S U1902 in Pyrobaculum.
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   4



AE009441.1/1650846-1650787 UGGCGGCUGAGAGCCCCG-GAGGGGCCCCGUGAGGCAACCGCAGUCGGUCCCCCUUGCACA
CP003098.1/1477287-1477344 CGGCGGCUGAGAGCCCCG-GAGGGGCCCGGUGAGC-G-CCGCAGUCGGUCCCCCUUGUACA
CP001014.1/1643612-1643672 CGGCGGCGGAGAGCCCCGCGCGGGGCGCCGUGAAGCUACCGCAGUCGGUCCCCCUUGUACA
CP000504.1/1268187-1268247 CGGCGGCAGAGGGCCCCGCGGGGGGCGCCGUGAAGCUCCCGCAGUCGGUCCCCCUUGUACA
#=GC SS_cons               <-<<<<<<<<--<<<<<____>>>>>----->>>>>--->>>>::::::::::::::::::
#=GC RF                    cGGCGGCcgaGAGCCCCGCGaGGGGCgCcGUgagGCuaCCGCaGUCGGUCCCCCUUGUACA
//
# STOCKHOLM 1.0

#=GF AC   RF02805
#=GF ID   PyrR207
#=GF DE   Pyrobaculum sRNA 207
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22282340
#=GF GA   60.00
#=GF TC   60.80
#=GF NC   42.10
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   22282340
#=GF RT   Discovery of Pyrobaculum small RNA families with atypical pseudouridine
#=GF RT   guide RNA features.
#=GF RA   Bernick DL, Dennis PP, Hochsmann M, Lowe TM
#=GF RL   RNA. 2012;18:402-411.
#=GF CC   Non canonical pseudouridylation guide sRNA features. Predicted to target
#=GF CC   23S U2597 in Pyrobaculum.
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   4



AE009441.1/1883703-1883639 GGGUGGGGGACUUAGAGCGGCCCGUAG-GGCCCCCGUGAAGAAGUCCCCUGCCGCGGGGU-UG-CACA
CP000660.1/1502849-1502914 GGGUGGGGGGCUCAGAGCGGCCCAGAG-GGCCCCGGUGAGAGGGCCCCCUGCCGCGGGGUUCA-CACA
CP000561.1/1673249-1673185 GGGUGGGGGGCUUAAAGAGGCCCGACGCGGCCCCUAUGAGCGAGCCCCCUGCCGCGGGGU-CAA--CA
CP003316.1/396758-396693   GGGUGGGGGGCUCAGAGCGGCCCAGAG-GGCCCCGGUGAGAGGGCCCCCUGCCGCGGGGUUCA-CACA
#=GC SS_cons               ::::<<<<<<<<<<<<--<<<<<<_>>.>>>>----->>>->>>>>>>>>::::::::::-::-::::
#=GC RF                    GGGUGGGGGGCuccgaGcGGCCCggcG.GGCCCCuGUgagagaGCCCCCUGCCGCGGGGU.cA.CACA
//
# STOCKHOLM 1.0

#=GF AC   RF02806
#=GF ID   PyrR208
#=GF DE   Pyrobaculum sRNA 208
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22282340
#=GF GA   64.00
#=GF TC   64.70
#=GF NC   36.40
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   22282340
#=GF RT   Discovery of Pyrobaculum small RNA families with atypical pseudouridine
#=GF RT   guide RNA features.
#=GF RA   Bernick DL, Dennis PP, Hochsmann M, Lowe TM
#=GF RL   RNA. 2012;18:402-411.
#=GF CC   Non canonical pseudouridylation guide sRNA features. Predicted to target
#=GF CC   23S U1978 in Pyrobaculum.
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   4



AE009441.1/2183899-2183840 CGGGGCAGAGAGGCCCUAUUGGGGCCGCUGUGACAGCUCCGCGUACGCCAGUGGCCCAAU
CP003316.1/2298976-2299035 UGGGGCUGAGUAGCCCCUACGGGGCGUCGAUGAAAGCUCCGCGUACGCCAGUGGUCAGCA
CP000504.1/2947-3005       UGGAGUUGAGCGGCCCGCC-UGGGCCACUAUGAAGACUCCGCGUACGCCAGUGGCUAAGG
CP000561.1/1869466-1869408 UGGGGCAGAGAGGCCCGCC-UGGGCUUCAAUGAAUACUCCACGUACGCCAGUGGCCCACC
#=GC SS_cons               <<<<<<<<<--<<<<<<___>>>>>>----->>>->>>>>>:::::::::::::::::::
#=GC RF                    cGGgGcuGAGagGCCCcccugGGGCcuCuAUGAaagCuCCgCGUACGCCAGUGGCCaAcu
//
# STOCKHOLM 1.0

#=GF AC   RF02807
#=GF ID   PyrR209
#=GF DE   Pyrobaculum sRNA 209
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22282340
#=GF GA   42.00
#=GF TC   42.60
#=GF NC   35.80
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   22282340
#=GF RT   Discovery of Pyrobaculum small RNA families with atypical pseudouridine
#=GF RT   guide RNA features.
#=GF RA   Bernick DL, Dennis PP, Hochsmann M, Lowe TM
#=GF RL   RNA. 2012;18:402-411.
#=GF CC   Non canonical pseudouridylation guide sRNA features. Predicted to target
#=GF CC   16S U8 in Pyrobaculum.
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   4



AE009441.1/679548-679612   GGCAGGAUCAGCCCCAGAGCCGGCCGGACGGCCGCCUGUGAUAGGGGCCCCGGUCAAAACCUCUG
CP000504.1/1203366-1203303 GGCAGGAUCAGUCCCCGAGACGGCCGUA-GGCCGCCUAUGAAAGGGGCUCCGGACAACUACGCAA
CP001014.1/195466-195529   GGCAGGAUCGGCCUCGGAGUGGGCCGG-CGGCCCCCUAUGAGAGAGGCCCCGGAUCUAAGCGAAA
CP000660.1/200535-200475   GGCAGGAUCGGCCCCAGAGACGGCCGAGGCGCCGCCUGUGAGGGGGGCUCCGGUU----CCUCUA
#=GC SS_cons               :::::::::<<<<<<<<<--<<<<<____>>>>>----->>>->>>>>>::::::::::::::::
#=GC RF                    GGCAGGAUCgGCCCCcGAGacGGCCGgacGGCCgCCUaUGAgAGGGGCcCCGGauaaaaaCucaA
//
# STOCKHOLM 1.0

#=GF AC   RF02808
#=GF ID   PyrR210
#=GF DE   Pyrobaculum sRNA 210
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22282340
#=GF GA   59.00
#=GF TC   59.60
#=GF NC   33.60
#=GF TP   Gene; snRNA; snoRNA; HACA-box;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000594; H_ACA_box_snoRNA;
#=GF DR   GO; 0006396; RNA processing;
#=GF RN   [1]
#=GF RM   22282340
#=GF RT   Discovery of Pyrobaculum small RNA families with atypical pseudouridine
#=GF RT   guide RNA features.
#=GF RA   Bernick DL, Dennis PP, Hochsmann M, Lowe TM
#=GF RL   RNA. 2012;18:402-411.
#=GF CC   Non canonical pseudouridylation guide sRNA features. Predicted to target
#=GF CC   tRNALys U54 in Pyrobaculum.
#=GF WK   Archaeal_H/ACA_sRNA
#=GF SQ   6



AE009441.1/724028-724085   CGGGCUGGACUGCCGU-GGUC-GCGGCU-GAAUGAAAAGCCCGCCCGCGGCCGAG-UCUACA
CP001014.1/224637-224694   CGGGCUCGACCGCCGC-GUCU-GCGGCA-GUAUGACAGGCCCGCCCGCGGCCGAG-UCUACA
CP000504.1/1173049-1172992 UGGGCUUGACAGCCGC-GUCU-GCGGUU-GUAUGACAAGCCCGCCCGCGGCCGAG-UGUACA
CP003316.1/1875733-1875794 UGGGCCGGACAGCCGUGGAUCUGCGGCAGGAAUGAUAGGCCCGCCCGCGGCCGAGCUCUACA
CP000561.1/255861-255803   UGGGUUGGACGCCCGCCAGCG-GCGGUG-GGAUGAAAAACCCGCCCGCGGCCGAG-CUUACA
CP000660.1/262539-262478   UGGGCCGGACAGCCGUGGAUCUGCGGUAGGAAUGAUAGGCCCGCCCGCGGCCGAGCUCUACA
#=GC SS_cons               <<<<<<<<<--<<<<<_____.>>>>>-.---->>>->>>>>>::::::::::::.::::::
#=GC RF                    uGGGCccGACagCCGcgGauu.gCGGca.GaAUGAgAgGCCCgCCCGCGGCCGAG.UcUACA
//
# STOCKHOLM 1.0

#=GF AC   RF02809
#=GF ID   RsmW
#=GF DE   RsmW RNA family
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 27430253
#=GF GA   52.00
#=GF TC   52.40
#=GF NC   46.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF CL   CL00106
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0071978; bacterial-type flagellum-dependent swarming motility;
#=GF RN   [1]
#=GF RM   27430253
#=GF RT   RsmW, Pseudomonas aeruginosa small non-coding RsmA-binding RNA upregulated
#=GF RT   in biofilm versus planktonic growth conditions.
#=GF RA   Miller CL, Romero M, Karna SL, Chen T, Heeb S, Leung KP
#=GF RL   BMC Microbiol. 2016;16:155.
#=GF CC   Specifically binds to RsmA protein in vitro, restores biofilm production
#=GF CC   (possibly due to the interaction with RsmA) and partially complements the
#=GF CC   loss of RsmY and RsmZ in rsmY/rsmZ double mutant in regards to their
#=GF CC   contribution to swarming. Compared to RsmY and RsmZ its production is
#=GF CC   induced in high temperatures and rsmW is not transcriptionally activated
#=GF CC   by GacA.
#=GF WK   RsmW_sRNA
#=GF SQ   3



AE004091.2/5118199-5118323 UUUGCGAUGACGCCAGGACGCGUCA-UCCGUGCG-CCGCUGCCCGGGAGGCGGAUCGCACGAACGGAGGCAAAGGCGCCUCCGGCCGGUUCCGGGAAGGUCACGGACGACCUUCCCGGAG-UCACUUU
AP013068.1/982472-982349   UUCUGGGUGACGCCAGGACGCGUCAUCCGCAAGG-UCGGCGCCCGGGCGCCCG--CCUUGCAGCGAGGGCAAGAGCGCCCUCGCUGGUUCCCGGGCGGGCCAGGGAAGGCACGCCCGGGA-UCGACUC
CP004143.1/1007623-1007502 UUUGCGAUGGCGC-AGGAAGCGCCA-UCGGUGCAGUCGCCGCCCGGGAGGCGGC-UGCACAAAGGGGCGCCG--AAGCGCCCCUUUUCCUGCGCAGUCGCCAGGGACGGC-ACUGCGCAGCGAACCAU
#=GC SS_cons               :::::<<<<<<<<______>>>>>>.>><<<<<<.---<<<<<_____>>>>>-->>>>>>,,<<<<<<<______>>>>>>>,,,<<<<<<<<<<<<<<<______>>>>>>>>>>>>>.>>:::::
#=GC RF                    UUugcGguGgCGCcAGGAcGCGcCa.cCggugcg.uCGccGcCCGGGaGgCgga.cgcaccAacGgggGCaaaagcGCcccCguuugccccCGgggggGcCAgGGAcGgCcccccCGggg.gcaccuu
//
# STOCKHOLM 1.0

#=GF AC   RF02810
#=GF ID   Lst_thermometer
#=GF DE   Lst 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 24067614
#=GF GA   126.00
#=GF TC   126.40
#=GF NC   45.30
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   24067614
#=GF RT   Temperature triggers immune evasion by Neisseria meningitidis.
#=GF RA   Loh E, Kugelberg E, Tracy A, Zhang Q, Gollan B, Ewles H, Chalmers R,
#=GF RA   Pelicic V, Tang CM
#=GF RL   Nature. 2013;502:237-240.
#=GF CC   Three independent RNA thermosensors were identified in the 5'UTRs of genes
#=GF CC   needed for: capsule biosynthesis (cssA), the expression of factor H
#=GF CC   binding protein (fHbp) and sialylation of lipopolysaccharide, which is
#=GF CC   essential for bacterial resistance against immune killing (lst). The very
#=GF CC   different nucleotide sequence and predicted inhibitory structures of the
#=GF CC   three RNATs indicate that they have evolved independently.
#=GF WK   Neisseria_RNA_thermometer
#=GF SQ   2



AE002098.2/934700-934801   UGUCGGAAUAUCUGCUAAAAUUCCGCAUUU------------UUCCGUCCCGGGACACUCGGGGCGUAUGUUCAAUUUGUCGGAAUGGAGUU-UUAGGGAUAUGGGCUUGAAAAA
AE004969.1/1040064-1039950 UGUCGGAAUAUCUGCUAAAAUUCCGCAUUUUCCGCACCGGGUUUCCGCACCGGGACACUCGGGGCGUAUGUUCAAUUUGUCGGAAUGGAGUUUUUAGGGAUAUGGGGUUGAAAAA
#=GC SS_cons               :(((---((((((-(((((((((((,,,,,,,,,,,,,,,,,,,,<<<<<<<<<___>>>>>>>>>,,,,<<<________>>>,)))))))-))))))))))-)))::::::::
#=GC RF                    UguCGGAauauCuGCuaaaauuCCgCAUUUUccgcAccgggUUUCCGccCCGgGACACuCGGggCGUAUGuuCAAUUUGUCGgaAuGGaguuUuuaGgGauauGGgcUUGAAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02811
#=GF ID   FHbp_thermometer
#=GF DE   FHbp 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 24067614
#=GF GA   104.00
#=GF TC   104.80
#=GF NC   37.60
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   24067614
#=GF RT   Temperature triggers immune evasion by Neisseria meningitidis.
#=GF RA   Loh E, Kugelberg E, Tracy A, Zhang Q, Gollan B, Ewles H, Chalmers R,
#=GF RA   Pelicic V, Tang CM
#=GF RL   Nature. 2013;502:237-240.
#=GF RN   [2]
#=GF RM   27560142
#=GF RT   Thermoregulation of Meningococcal fHbp, an Important Virulence Factor and
#=GF RT   Vaccine Antigen, Is Mediated by Anti-ribosomal Binding Site Sequences in
#=GF RT   the Open Reading Frame.
#=GF RA   Loh E, Lavender H, Tan F, Tracy A, Tang CM
#=GF RL   PLoS Pathog. 2016;12:e1005794.
#=GF CC   Three independent RNA thermosensors were identified in the 5'UTRs of genes
#=GF CC   needed for: capsule biosynthesis (cssA), the expression of factor H
#=GF CC   binding protein (fHbp) and sialylation of lipopolysaccharide, which is
#=GF CC   essential for bacterial resistance against immune killing (lst). The very
#=GF CC   different nucleotide sequence and predicted inhibitory structures of the
#=GF CC   three RNATs indicate that they have evolved independently.
#=GF WK   Neisseria_RNA_thermometer
#=GF SQ   2



AE002098.2/1975310-1975382 AAAUGUUUAUAUAUUAUCUAUUCUGCGUAUGACUAGGAGUAAACCUGUGAAUCGAACUGCCUUCUGCUGCCUU
AE004969.1/29881-29809     AAACGUUUAUAUAUUAUCUAUUCUGUGUAUGACUAGGAGUAAACCUGUGAACCGAACUACCUUCUGCUGCCUU
#=GC SS_cons               :<<<<<____>>>>>---------<<<<<-<<--<<<<<<_______________>>>->>>>>>>>->>:::
#=GC RF                    AAAugUUUAUAuaUUAUCUAUUCUGcGuAUGACUAGGAGUAAACCUGUGAAuCGAACUaCCUUCUgCUgCCUU
//
# STOCKHOLM 1.0

#=GF AC   RF02812
#=GF ID   asponA
#=GF DE   anti ponA RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   113.00
#=GF TC   113.60
#=GF NC   85.70
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0046677; response to antibiotic;
#=GF RN   [1]
#=GF RM   25213728
#=GF RT   Expression of antisense small RNAs in response to stress in Pseudomonas
#=GF RT   aeruginosa.
#=GF RA   Gomez-Lozano M, Marvig RL, Tulstrup MV, Molin S
#=GF RL   BMC Genomics. 2014;15:783.
#=GF RN   [2]
#=GF RM   23028334
#=GF RT   The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa
#=GF RT   grown in body temperature.
#=GF RA   Wurtzel O, Yoder-Himes DR, Han K, Dandekar AA, Edelheit S, Greenberg EP,
#=GF RA   Sorek R, Lory S
#=GF RL   PLoS Pathog. 2012;8:e1002945.
#=GF RN   [3]
#=GF RM   22590564
#=GF RT   Comparative profiling of Pseudomonas aeruginosa strains reveals
#=GF RT   differential expression of novel unique and conserved small RNAs.
#=GF RA   Ferrara S, Brugnoli M, De Bonis A, Righetti F, Delvillani F, Deho G,
#=GF RA   Horner D, Briani F, Bertoni G
#=GF RL   PLoS One. 2012;7:e36553.
#=GF CC   Transcribed antisense to the penicillin-binding protein 1A gene called
#=GF CC   ponA. It was identified by RNAseq and the expression was validated by 5'
#=GF CC   and 3' RACE experiments. AsponA expression was up or down regulated under
#=GF CC   different antibiotic stress. Due to its location it may be able to prevent
#=GF CC   the transcription or translation of the opposite gene.[1] Study by Wurtzel
#=GF CC   et al. and Ferrara et al. also detected its expression.
#=GF WK   AsponA_antisense_RNA
#=GF SQ   3



AE004091.2/5681167-5680874 GAAAUUGUCGUCCUCGGCGGACAGCAGGGCAUGGAUGAAGUCCUGCGGGAUGUCGGCGAAGCGGAUCGGCGUCCGGCGCAUCUCGCCGAACUCGGAGAUCAGCUUGCCGUCCUCGCUGUAGACCUUGAGGGGGAUCUGCAGCUGGACGUUACGCAGAGCUUCCACCGAGGGCAGGCUGGGACUCAGAUAGAGAUAGGCGCCGCUGAAACUGAGCAGCACUCCACAAAUCAGGGUGACGCAAGUCCACCACAGGAACUUCAGCAGGCGCAUGGGUAGAUUC-GGAUUUCCAGGAAA
HG322950.1/5644547-5644253 GAAAUUAUCGUCCUCGGCGGACAACAGGGCGUGAAUGAAGUCUGGGGGAAUGUCCGCGAAGCGAAUGGGCGUCCGGCGCAUCUCACCGAACUCUGCUAUCAAUUUGUUAUCACUGCUGUAAACGCGCAGCGGGAUCUGCAGCUGCACGUUACGCAGGGCGUCUACCGAGGGCAGGUUGGGACUGAGGUAGAGAUAAGCGCCGCUUAAACUGAGCAGCACUCCACAAAAUAUGGCGACGCAAGUCCACCACAGAAACUUCAGCAGGCGCAUUGGAAGGUCUUGGAUUUCCAGGGAA
CP004143.1/5076814-5076520 GAAGUUGUCAUCCUCGGCCGAUAACAGUGCGUGGGUGAAGUCUUGGGGGAUUUCAGCAAAGCGAAUCGGCGUACGGCGCAUCUCGCCAAACUCUGCUAUCAAUCUGUUAUCACUGCUGUACACGCGCAACGGCAUCUGCAAACGCACGUUGCGCAAGGCCUCCACGGACGGGAGGUUUGGGCUGAGGUAGAGGUAGGCGCCGCUGAAACUGAGCAGCAAUCCACAGAUUAUGGUGACGCAGGUCCACCACAGAAACUUCAGCAGGCGCAUUGGAAGGUCUUGGAUUUCCAGAGAA
#=GC SS_cons               :::::::::((((((((-(((,,<<<<<<<_________>>>>>>><<<<<<-<<-<<--<<______>>--->>->>>>>>>>,<<<____>>>,,,,,<<<<<<<<<<<<--<<<<<<<<<<<<___>>>>->>>>>>>>->>>>>---->>>->>>>)))-))))))))---((((((-((-((---------(((((((((((,,,,,<<--<<<-<<________>>>>>-->>,,,<<<______>>>,,))))))-)))))----------))--))-))))))::::
#=GC RF                    GAAaUUgUCguCcuCgGCgGacAgCagggCgUGgaUGAAGuccuGcGggaugUCgGCgAAGCGaAUcGGCGUccGGcGcaucuCgCcgAACUcgGcuAUCggccuGccgucccugcuGuagacccgcAgcgggAucugCagcuggacgUUaCgCagggccuCcACcGagGgcAGGcugGgaCucAggUAGAGaUAgGCGCCGCugaaACUGAGCAGCacUCcACAaAuuAgGguGACGCAaGucCACCACAGgaACuucaGCAGGCGCAUuGGaAGgUccUGgaUuuCcagggAA
//
# STOCKHOLM 1.0

#=GF AC   RF02813
#=GF ID   PA5194_thermometer
#=GF DE   Pseudomonas PA5194 thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; PMID:25336583
#=GF GA   60.00
#=GF TC   60.30
#=GF NC   39.10
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   25336583
#=GF RT   Tet-Trap, a genetic approach to the identification of bacterial RNA
#=GF RT   thermometers: application to Pseudomonas aeruginosa.
#=GF RA   Delvillani F, Sciandrone B, Peano C, Petiti L, Berens C, Georgi C, Ferrara
#=GF RA   S, Bertoni G, Pasini ME, Deho G, Briani F
#=GF RL   RNA. 2014;20:1963-1976.
#=GF CC   Identified in genetic Tet-Tap screening, no obvious similarities to known
#=GF CC   RNATs. 
#=GF WK   Pseudomonas_sRNA
#=GF SQ   2



AE004091.2/5847084-5847187 CGUGACAGUCGUACGCCG-ACCCGGCGCCGAUAGGGGGAAACGAUUUUAUGGAUAAUGCCUCUCCGUUCCAAGCGGCCUGGCAAUGGCGCAAGUUCGCCAUCUGU
HG322950.1/5856267-5856371 UGCGUCACCCGCCCGCACCUGGGUGGUUCGAAAAGGGGGAUCGAUUCUAUGGAGAAAGCCUCUCCGUUCCAAGCCACCUGGUCGUGGCGAGCGUUCAUCGCCUGC
#=GC SS_cons               :::::::::::::<<<<<____>>>>><<--<<<<<________>>>>>->>,,,,<<<<---<<<<___>>>>----->>>><<<<<<______>>>>>>::::
#=GC RF                    uGuGuCAguCGuacgCcgcuggcgGcgcCGAuagggGGaAuCGAuucuaUGgAuAAugCCUCUcCguUCCaaGcgaCCUGGcaguGgcGaaaGUUCgcCacCUGu
//
# STOCKHOLM 1.0

#=GF AC   RF02814
#=GF ID   Sso133
#=GF DE   Sulfolobus sRNA133
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 15659164
#=GF GA   44.00
#=GF TC   44.50
#=GF NC   39.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   15659164
#=GF RT   Identification of novel non-coding RNAs as potential antisense regulators
#=GF RT   in the archaeon Sulfolobus solfataricus.
#=GF RA   Tang TH, Polacek N, Zywicki M, Huber H, Brugger K, Garrett R, Bachellerie
#=GF RA   JP, Huttenhofer A
#=GF RL   Mol Microbiol. 2005;55:469-481.
#=GF CC   This RNA has structural homologues in 3 archaeon Sulfolobus genomes:
#=GF CC   tokodaii, acidocalarius and solfotaricus. It shows extensive compensatory
#=GF CC   base changes, possibly consistent with a functional role. 
#=GF WK   Sulfolobus_solfataricus
#=GF SQ   3



AE006641.1/1779139-1779211 AAGAUGCUCAAUGAAACCCC-CAUGUCCUCGAAGGGAGUGGUUUGACUACCGCUCCCGUAGACGGCA-CGGGGAG
CP002535.1/1601634-1601707 AAGGCACCCAAUGAAACUCCCCAUGUCCUCGAAGGGAGUGGUUUAACUACCGCUCCCGUAGACGGCA-UGGAGAG
CP001742.1/1044842-1044770 AAGGCGCCCAGUGAAGCCCC-CAUGUCCUCGAGGGGAGUGGCAGGUGAGCCGCUCCCGUAGACUGCGCGGGG-AG
#=GC SS_cons               ::::::::::::::::<<<<.--<<<<-<<---<<<<<<<<<______>>>>>>>>>--->>->>>>-->>>>::
#=GC RF                    AAGgcgCcCAaUGAAaCcCC.CAuGucCUCGAaGGGAGuGGcuugacugCCgCUCCCGUAGACggCa.uGGgGAG
//
# STOCKHOLM 1.0

#=GF AC   RF02815
#=GF ID   Lig_thermometer
#=GF DE   Lig 5' UTR thermometer
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 24013626
#=GF GA   51.50
#=GF TC   51.50
#=GF NC   51.30
#=GF TP   Cis-reg; thermoregulator;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   SO; 0000204; five_prime_UTR;
#=GF DR   GO; 0009266; response to temperature stimulus;
#=GF DR   GO; 0030371; translation repressor activity;
#=GF RN   [1]
#=GF RM   24013626
#=GF RT   Role for cis-acting RNA sequences in the temperature-dependent expression
#=GF RT   of the multiadhesive lig proteins in Leptospira interrogans.
#=GF RA   Matsunaga J, Schlax PJ, Haake DA
#=GF RL   J Bacteriol. 2013;195:5092-5101.
#=GF CC   It controls ligA and ligB gene expression in Leptospira interrogans in
#=GF CC   response to temperature change. The lipoproteins LigA and LigB promote
#=GF CC   adhesion of Leptospira to host proteins.The RNA is composed of
#=GF CC   175-nucleotide 5'UTR and the first six lig codons (identical in ligA and
#=GF CC   ligB). Lig expressions is limited by double-stranded RNA structure that
#=GF CC   occludes the ribosome-binding site. At higher temperatures the site is
#=GF CC   exposed to promote translation initiation.
#=GF WK   Lig_RNA_thermometer
#=GF SQ   2



AHNZ02000335.1/6200-6404   AGAGAACUUCUAUAAAAUUGAUUUUUAAUUUUUGUUGAUAGUCGCCAAACAACGACUUGAUGCAAAAAUCUAAUUGGAUAAUUAUCCUUUUUAAAUUUUGUAAAGGCUCUCAAUAAAUAAACACAGCAAAUACACAAAAUGAAAACUUCAAAUAAAACAAUUAGAGUGAGUGUUUAUGAAGAAAAUAUUUUGUAUUUCGAUUUUU
AE010300.2/3748278-3748475 AGAGAACUUCUAUAAAAUU-------AAUUUUUGUUGAUAGUCGCCAAACAACGACUUGAUGCAAAAAUCUAAUUGGAUAAUUAUCCUUUUUAAAUUUUGUAGAGGCUCUCAAUAAAUAAACACAGCAAAUACACAAAAUGAAAACUUCAAAUAAAACAAUUAGAGUGAGUGUUUAUGAAGAAAAUAUUUUGUAUUUCGAUUUUU
#=GC SS_cons               :((((-(((-(((((((((<<<<-----<<<<<<<<----<<<<<________>>>>>---->>>>>>>>-->>>><<<<____>>>>,,,,,,)))))))))-)))-))))---------------------<<<<<<<<----<<<<<----<<<<<-<<_____>>->>>>>->>>>>---->>>>>>>>::::::::::::
#=GC RF                    AggggAcuuCuauaaaauucacuUUUAAguuuugugGAUAgucgCCAAACAACGaguuGAUGcaaaaaucUAaguggggaAUUAuccuUUUUAAauuuuguaaAgggUcucaAUAAAUAAACACAGCAAAUACaCaaaaugAAAACuuCaAAUAaaaCaAuuAGAGUgaGuGuuuAuGaaGAAAAuauuuuGuAUUUCGAUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02816
#=GF ID   HBV_PRE_1151-1410
#=GF DE   Hepatitis B virus post-transcriptional regulatory element 1151-1410
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   82.00
#=GF TC   82.70
#=GF NC   40.00
#=GF TP   Cis-reg;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory_region;
#=GF DR   GO; 0051168; nuclear export;
#=GF DR   GO; 0051168; regulation of RNA splicing;
#=GF RN   [1]
#=GF RM   26514143
#=GF RT   A conserved RNA structural element within the hepatitis B virus
#=GF RT   post-transcriptional regulatory element enhance nuclear export of
#=GF RT   intronless transcripts and repress the splicing mechanism.
#=GF RA   Visootsat A, Payungporn S, T-Thienprasert NP
#=GF RL   Mol Biol Rep. 2015;42:1603-1614.
#=GF CC   Part of 500 base pair long HBV PRE, contains nucleotides 1151-1410.
#=GF CC   Enhances nuclear export of intronless transcripts and represses the
#=GF CC   splicing mechanism to a comparable degree to that of the full-length PRE.
#=GF CC   It was proposed to be the core HBV PRE element. contains 3 known
#=GF CC   regulatory elements: PRE SL-alpha (nucleotides 1292-1321), human La
#=GF CC   protein binding site (nucleotide 1275-1291) and SRE-1 (nucleotides
#=GF CC   1252-1348).
#=GF WK   Hepatitis_B_virus_PRE_1151-1410
#=GF SQ   2



KC836877.1/1151-1409 UUGCUCGGCAACGGCCUGGUCUGUGCCAAGUGUUUGCUGACGCAACCCCCACUGGCUGGGGCUUGGCCAUAGGCCAUCAGCGCAUGCGUGGAACCUUUGUGGCUCCUCUGCCGAUCCAUACUGCGGAACUCCUAGCCGCUUGUUUUGCUCGCAGCCGGUCUGGAGCAAAGCUCAUCGGAACUGACAAUUCUGUCGUCCUCUCGCGGAAAUAUACAUCGUUUCCAUGGCUGCUAGGCUGUACUGCCAACUGGAUCCUUCG
M57663.2/1151-1409   UUGCCCGGCAACGGCCUGGUCUGUGCCAAGUGUUUGCUGACGCAACCCCCACUGGCUGGGGCUUGGCCAUCGGCCAUCAGCGCAUGCGUGAAACCUUUGUGGCUCCUCUGCCGAUCCAUACUGCAGAACUCCUAGCCGCUUGUUUUGCUCGCAGCCGGUCUGGAGCAAAACUCAUCGGGACUGACAAUUCUGUCGUCCUUUCUCAGAAAUAUACAUCCUUUCCAUAGCUGCUAGGUUGUACUGCCAACUAGAUUCUUCG
#=GC SS_cons         <<<<<<<<<<<--<<-<<<<____>>>>->>-->>>>>>>->>>>,,,<<<<--<<--<-<<<<<<<<___>>>>>-->>>->-->>>>>>,,,,,,,,,<<<______>>>((((((----((((-((-((((((-(((,<<<<<<<<<-<<<_____>>>>>>>>>>>>,,,,,<<<--<<<<<____>>>>>>>>,,,,,,<<<<<<_______>>>>>>,,)))-))))))--))-))))----)))))):::::
#=GC RF              uuGCcCgGCaaCGgCCuGGcCUGUgCCaAGcGUuuGCcGgCGCaaCCCcCaCUGGCUGGGGCuuGGCCAUaGGCCaUCaGCGCAUGCGuGgAACCUUUGUGGCUCCUCUGCCgauCcaUACUGCgGAaCUCCuaGCCGCcUGcuuuGCuCGCaGCCGGUCuGGaGCaaagCUCAUCGGgACcGaCaAUUCuGuCgcCCUuUCuCgGaaacAUACAUCguuuCcAUgGCUGCuaGGuUGuACcGCCAACugGaucCUUCG
//
# STOCKHOLM 1.0

#=GF AC   RF02818
#=GF ID   V_AS5
#=GF DE   Vibrio RNA AS5
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   96.00
#=GF TC   96.10
#=GF NC   95.80
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   SO; 0000077; antisense;
#=GF RN   [1]
#=GF RM   19223322
#=GF RT   Experimental discovery of sRNAs in Vibrio cholerae by direct cloning,
#=GF RT   5S/tRNA depletion and parallel sequencing.
#=GF RA   Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A
#=GF RL   Nucleic Acids Res. 2009;37:e46.
#=GF CC   Identified by direct cloning an parallel sequencing experiments with
#=GF CC   5S/tRNA depletion. Confirmed by Northern blot. 
#=GF WK   Vibrio
#=GF SQ   3



CP007653.1/1278983-1278851   UUCUUUCCAAACGAUUUGAAGUUGCAGAACCUGAAAUGGCAGAUAGGCGCAGAUGAGUGAAUUCCAAUAAAUACAGACAGACUAUGCGAUUGGUGUGCGCGAAUAUC------GCC--UUUGCAGCUUCAAAUAGGAAGAA
BA000037.2/1092839-1092715   UUAUACCCAAACAACUUGAAGUUGCA-----------GGUAGGCGG---CAAAUGAGUGAAUCCCCAUGAGCAUAGAUACGCUAUGUGAUUGGGGUGAACGAAUGCAGCCAACACC--GCUGCAGCUUCAAGUAGGAAGGG
ACZO01000006.1/837894-838014 CUAUACCCAAACAACUUGGAGUUGCAGG----UAGGCGGCAAGUGAGUUCAUCCCCAUGAG----------CAUAGACGGGCUAUGUGAUUGGGGUGAACGAACGCA------GCCCCCCUGCAGCUUCAAGUAGGAAGGG
#=GC SS_cons                 :<<<<<<------<<<<<<<<<<<<<<<---------<<<-<<<<-<<<<<-<<-<<<______________________________>>>->>->>>>>--->>>>......>>>..>>>>>>>>>>>>>>>->>>>>>:
#=GC RF                      uccuucCCAAACaacuuGaaGuuGCagg....uAaauGGcAggcggGcgCaaccgaguGAaUuCCaAUaAacAuAGAcaggCUAUGuGacuGggGuGcgCGAAcgcc......gCC..ccuGCagCuuCaaguAGgaaggg
//
# STOCKHOLM 1.0

#=GF AC   RF02819
#=GF ID   V_AS7
#=GF DE   Vibrio RNA AS7
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   90.00
#=GF TC   91.40
#=GF NC   89.30
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   SO; 0000077; antisense;
#=GF RN   [1]
#=GF RM   19223322
#=GF RT   Experimental discovery of sRNAs in Vibrio cholerae by direct cloning,
#=GF RT   5S/tRNA depletion and parallel sequencing.
#=GF RA   Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A
#=GF RL   Nucleic Acids Res. 2009;37:e46.
#=GF CC   Identified by direct cloning an parallel sequencing experiments with
#=GF CC   5S/tRNA depletion. Confirmed by Northern blot. 
#=GF WK   Vibrio
#=GF SQ   7



CP007654.1/556735-556567   GGUGUUUGCAGCAGCAAAUUGCUGCGUUCUUUGAUGUCACCACCGAUGUGAUAUGGCAAGCCGCAGUUGGCAAAGGAAACGUAGGGGCCACGCUCGAACAUGAUGAUUUCAGCGUCUUCGCUGAGUCGACGCGCACGAGCCGCCGCCGAGGCUCCACCUGCAACACCAC
CP002285.1/115658-115490   GGUGUUUGUAGCAGCAAAUUGCUGCGCUCUUUGAUGUCACCGCCAAUGUGAUAUGGCAAGCCACAGUUAGCAAAUGAAACGAAGGGGCCCCGCUCAAACAUAAUGAUUUCAGCUUCUUCGCUGAGUCGACGAGCACGAGCCGCUGCGGAUGCACCACCCGCGACACCAC
BA000032.2/982310-982142   GGCGUUUGUAGUAGUAACUUACUGCGUUCUUGGAUAUCGCCGCCGAUGUGAUAAGGCAAGCCACAGUUGGCAAAUGAAACAAACGGGCCACGUUCAAACAUGAUGAUUUCGGCAUCUUCGCUCAGACGACGAGCACGCGCCGCCGCAGAUGCACCACCUGCAACACCAC
CP002378.1/289025-288857   GGCGUUUGCAGUAGCAAAUUGGCUCGUUCUUUGAUGUCACCACCGAUGUGAUAGGGCAAGCCGCAGUUGGCAAACGAGACGAAAGGGCCCCGUUCAAACAUAAUGAUUUGCGCAUCUUCGCUCAAACGACGCGCACGCGCUGCCGCAGAAGCCCCGCCGGCAACACCGC
CP005974.1/1774859-1775027 GGAGUCUGUAGCAGCAAUUUGCUGCGCUCGGUGAUGUCGCCUCCGAUAUGGUAGGGAAGGCCGCAGUUGGCAAACGAGACAAAUUCACCGCGCUCGAACAUGAUGAUUUCAGCAUCUUCGCUCAAGCGGCGGGCACGUGCGGCAGCGGAGGCUCCGCCUGCCACACCGC
CP000606.1/830490-830322   GGCGUCUGCAGUACUAAGGCGCUGCGCUGAGCGAUCUCACCACUGAUAUGAUAAGGCAGGCCACAGUUGGCAAAGGAGACAUAUUCGCCGCGCUCAAACAUAAUGAUUUCAGCAGUUUCGCUGAGUCUACGCGCCCUUGCCGCCGCCGAUGCGCCGCCCGCGACGCCAC
BA000038.2/991802-991634   GGUGUUUGCAGAAGUAGCUUGCUGCGCUCUUUGAUAUCGCCACCAAUGUGGUAAGGCAAGCCGCAAUUCGCAAAAGAGACAAAAGGACCACGUUCAAACAUGAUUAUCUGUGCAUCUUCACUCAAACGACGUGCUCUAGCUGCUGCUGAAGCACCACCUGCGACGCCAC
#=GC SS_cons               ((((((-(((<<<<<<___>>>>>>,,,,,,<-<<<<<<<_______>>>>>>>->,,,<<<______>>>,,,<<<--<---<<<<<---<<<<<--<-<<-<<<<<-<<<<<____>>>>>>>>>>->>->-->>>>>->>>->>-->-->>>,,,)))))))))::
#=GC RF                    GGcGucUGcaGcagcaAauugcugCGuUcuucGcuguCacCaCcgAUguGacagGgcAaGCCgCAGUUGGCAAAgGagAcaaAcggGCCaCGcucgAACAugAcGauuUcaGCgucUUcGCugaauCgAcgaGCacgagCuGCcGcgGAgGCuCcaCCugCgaCgCCaC
//
# STOCKHOLM 1.0

#=GF AC   RF02820
#=GF ID   V_AS9
#=GF DE   Vibrio RNA AS9
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   50.00
#=GF TC   50.30
#=GF NC   49.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0001263; ncRNA_gene;
#=GF DR   SO; 0000077; antisense;
#=GF RN   [1]
#=GF RM   19223322
#=GF RT   Experimental discovery of sRNAs in Vibrio cholerae by direct cloning,
#=GF RT   5S/tRNA depletion and parallel sequencing.
#=GF RA   Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A
#=GF RL   Nucleic Acids Res. 2009;37:e46.
#=GF CC   Identified by direct cloning an parallel sequencing experiments with
#=GF CC   5S/tRNA depletion. Confirmed by Northern blot. 
#=GF WK   Vibrio
#=GF SQ   3



CP007653.1/2399565-2399668 ACGGCGAC-AACGCUCUUUCGUGAGCGUUAAACAGAUGAGUCCGCGACCAUGGGUUGCCAUAAAAUUGAUCGCUGCUGGCG-UAAUGUGCUCAGCCGCCAUGAUCA
CP002377.1/1108136-1108036 AUGGCAACGCGCUUUG----GUCAUGGUGAGACAAAUCAAACCACGACCAUGAGUCGCCAUAAAGUUAAUCGCUGCCGGCG-UAAUAUGCUCGGCCGCCAUGAUCA
CP009888.1/2943594-2943697 CUGCUGAC-AACGCUCUUGUGUUAGUGUUAAACAAAUCAAACCGCGACCAUGCGUCGCCAUAAAAUUAAUUGCAUCUG-CACUGAUAUGCUCAGAUGCCAUAAUUA
#=GC SS_cons               ::((((((.<<<<<<<______>>>>>>>,,,,,,<<<-<<<___>>>>>>,,))))))-------<<<<<<<-<<<<<<<._____>>>->>>>->>--->>>>>
#=GC RF                    auGgcgaC.caCgcucUUuuGUgagcGugAaACAaaugAgcCCgCGgccauGaGucgcCAUAAAaUugaucGCugCcGGCg.UaAUacGCUCgGccGCCAUgauca
//
# STOCKHOLM 1.0

#=GF AC   RF02821
#=GF ID   V_IGR5
#=GF DE   Vibrio RNA IGR5
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   75.00
#=GF TC   75.60
#=GF NC   45.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   19223322
#=GF RT   Experimental discovery of sRNAs in Vibrio cholerae by direct cloning,
#=GF RT   5S/tRNA depletion and parallel sequencing.
#=GF RA   Liu JM, Livny J, Lawrence MS, Kimball MD, Waldor MK, Camilli A
#=GF RL   Nucleic Acids Res. 2009;37:e46.
#=GF CC   Identified by direct cloning an parallel sequencing experiments with
#=GF CC   5S/tRNA depletion. Confirmed by Northern blot. 
#=GF WK   Vibrio
#=GF SQ   2



CP007654.1/299263-299373   ACG-UACUUAAGCUGGUGCAUCCGUAUUUGCGCCAAAAUUUGUACCGAAUUUUUUGAA--CUCGUUACGCCGCUAUUUAUUACAGAAUGAAUUUAAAGCGUAAUUUUUUCACAC
BA000037.2/1934290-1934180 UCGCUUCAGAGGCUGGUACAUCCGUAUUUGUACCAAAAUCUGUACCAAAUUAUCCAAAUUCACUUAUGUUUGAUUAUUAAUAC--AUUGAUUUUCAAAGCAUAAUUA-CUGAAC
#=GC SS_cons               ::<-<<<------<<<<<<<________>>>>>>>------>>>>---------<<<<-----<<<<<<<----<<<<<<<____>>>>>>>----->>>>>>>--->>>>:::
#=GC RF                    uCGcuaCuuAaGCuGGugCaUCCGUAUUuGcaCCaAAAUuUGuaCCaAAUUuUucgaaUUCuCuuuuggcuGaUauuuauuACAGaaugaauUUaAAgccaaaaUUuuucgaAC
//
# STOCKHOLM 1.0

#=GF AC   RF02822
#=GF ID   Srn266
#=GF DE   Streptococcus RNA 266
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 22274957
#=GF GA   63.00
#=GF TC   63.80
#=GF NC   62.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   22274957
#=GF RT   Identification of 88 regulatory small RNAs in the TIGR4 strain of the
#=GF RT   human pathogen Streptococcus pneumoniae.
#=GF RA   Acebo P, Martin-Galiano AJ, Navarro S, Zaballos A, Amblar M
#=GF RL   RNA. 2012;18:530-546.
#=GF CC   SP_0836 target predicted. 
#=GF WK   Streptococcus_sRNA
#=GF SQ   4



AGPS01000006.1/91244-91354 AAUGAGUUGUUUUGUCGCUUUUCAUUAUAGGUCAUAUGGGACUUU-UUUCUACACAAAAAUAGGCUCCAUAAUAUCCAUAGGGGAUUUACCCACUACAAAUAUUAUAGAGUC
AE007317.1/30029-30139     AAUGAGUUGUUUUGUCGCUUUUCAUUAUAGGUCAUAUGGGACUUUUUUUCUACAC-AAAAUAGGCUCCAUAAUAUCCAUAGGGGAUUUACUCACUAUGGAUAUUAUGGAGCC
CP000023.1/791383-791493   AAUGA-UAGUUUGAGCACUUUUCAUUAUAGGUCAUAUGGGACUUUUUGUAUAUACUCAAAAAGGCUCCAUAAUUUCCAUGGUGGAUUUACCCACUACAGAAAUUAUAGAGCC
CP014699.1/1054269-1054158 AAUGAGAUGUUUGGUCGCUUUUCAUUAUAAGUCAUAUGGGACUUUUUUUGUAUAGCAAAAAAAGCGCCAUAAUUUCCGCAGUGGAGUUACCCACUACAGAUAUUAUAGAGCC
#=GC SS_cons               <<<<<<--<<______>>-->>>>>>,,<<<<<______>>>>>------------------<<<<<-<<<<<<<<--<<<<<<______>>>>>>-->>>>>>>>->>>>>
#=GC RF                    aauGaguuGcUUuguCgCUUcuCauuAUagGuCAUAUGGGaCcuUUUuUaUAuAcuaAAAaAGGCuCCauaaugucCauaGuGGAuUUACCCaCuacagacauuauaGaGCC
//
# STOCKHOLM 1.0

#=GF AC   RF02823
#=GF ID   LPR69
#=GF DE   Legionella RNA 69
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   40.00
#=GF TC   40.40
#=GF NC   39.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   21408607
#=GF RT   Sequencing illustrates the transcriptional response of Legionella
#=GF RT   pneumophila during infection and identifies seventy novel small non-coding
#=GF RT   RNAs.
#=GF RA   Weissenmayer BA, Prendergast JG, Lohan AJ, Loftus BJ
#=GF RL   PLoS One. 2011;6:e17570.
#=GF CC   Identified by strand specific sequencing of the transcriptional response
#=GF CC   during broth growth and during infection inside the host. Infection
#=GF CC   specific expression. 
#=GF WK   Legionella.
#=GF SQ   5



AE017354.1/3303482-3303401   AGACGAUGCUUAGGCAUCUCCUCAGCCCGAACGUACCCUGGGUAUCGACGGGCUGUUAUAUCCUCUUUAGCCAUAACUCACG
LNYW01000033.1/171156-171237 AGACAGCGCUAUCGCGCUUCCUCAGCCCGAACGGCAUCGAAGUAACGACUGGCUCAAACAACUUUCUUAUCCAUAACUCACG
LNYW01000074.1/103952-104033 AGACAGCGCUGUCGCGCCUCCUCAGCCCGAACGGCAUCGAAGUAAUGACCGGCUCAAACAACUUUCUUAUCCGAAACUCACG
LNYW01000010.1/11028-10948   AGACGAGGCUACCGCCUCUCCUCAGCCCGAACGGAUC-GAGGUAAACACUGGCUCAAAUAACUUUCUUAUCCGAAAUUCGUU
LNYW01000020.1/21047-21128   AGACAGCGCUAUCGCGCUUCCUCAGCCCGAACGGCAUCGAAGUAACGACAAGAUCAAACAAGCUUCUUAUCCGAAACUCACG
#=GC SS_cons                 :<<-<<<<<____>>>>>>>--<<<<<<<---<<<<<___>>>>>--->>>>>>>:::::::::::::::::::::::::::
#=GC RF                      AGACggcGCUaucGCgccUCCUcAGCCcGAACggaccCgAgguaacGACgGGCUgAAAuAAcuUUcUUAuCCgaAACUCACG
//
# STOCKHOLM 1.0

#=GF AC   RF02824
#=GF ID   LPR10
#=GF DE   Legionella RNA 10
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   69.00
#=GF TC   69.60
#=GF NC   56.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   21408607
#=GF RT   Sequencing illustrates the transcriptional response of Legionella
#=GF RT   pneumophila during infection and identifies seventy novel small non-coding
#=GF RT   RNAs.
#=GF RA   Weissenmayer BA, Prendergast JG, Lohan AJ, Loftus BJ
#=GF RL   PLoS One. 2011;6:e17570.
#=GF CC   Identified by strand specific sequencing of the transcriptional response
#=GF CC   during broth growth and during infection inside the host. Up-regulated in
#=GF CC   late infection or broth growth time points. 
#=GF WK   Legionella
#=GF SQ   3



AE017354.1/341341-341434     AAGCCUAC--AAAGGGUAGGAAACCUGAAGCUCUACAUAAAUCUCCACAGUGUCUUUCAGUUGCGG-CUCAGAAACCGGGAAGUCGUUGCCUGUACU
LNYN01000019.1/141097-141190 AAGCCUAC--UUUGGGUAGGAAACCUUAAGCUCUCCAUAUACCUCCAUCGUGUAUAUCAGUCGCGG-CUCAGAACUCGGGUGGUCGUUGCCUGUACU
FN650140.1/521709-521804     AAGCCUAUGUAAAUGGUAGGAAGCCUGAAACUCUACAUAGACCUCCAUAGUAA-AUUCAGUUACGGGCUCAGAAGACAGGAAGUCAUUGCCUGUAUU
#=GC SS_cons                 :::<<<<<.._____>>>>>--------------------------<<<<-<<-------<<-<<<.________>>>->>------->>>>>>:::
#=GC RF                      AAGCCUAc..aaagGgUAGGAAaCCUgAAgCUCUaCAUAaAcCUCCAcaGUGcauuUCAGucgcGg.CUCAGAAacCgGgaaGUCgUUgCCugUAcU
//
# STOCKHOLM 1.0

#=GF AC   RF02825
#=GF ID   LPR17
#=GF DE   Legionella RNA 17
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   98.00
#=GF TC   98.40
#=GF NC   74.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   21408607
#=GF RT   Sequencing illustrates the transcriptional response of Legionella
#=GF RT   pneumophila during infection and identifies seventy novel small non-coding
#=GF RT   RNAs.
#=GF RA   Weissenmayer BA, Prendergast JG, Lohan AJ, Loftus BJ
#=GF RL   PLoS One. 2011;6:e17570.
#=GF CC   Identified by strand specific sequencing of the transcriptional response
#=GF CC   during broth growth and during infection inside the host. 
#=GF WK   Legionella
#=GF SQ   2



AE017354.1/539616-539866   GAAAACGCGGUCAAAGGCAGCAUCAGAGUUAGGGCAUAAACCAAUGCCAAAGUACUGGAAAAAAGUUUCUUAAUAACCAUAGCGAUCUCCUCAGAUGCAAGGCCAUGAAAUUAGCCACCUG--CGUAUUUUUUUA---UGCAAUUUAAAUGCCAGCGGCUAAGC-UUUAAGACAACCAGUCUAACGGAUUGACCGCUUUUCCUCUUUGUCUUAUUUCAAAGUAUAGACCGUUUUGCUUAAUUCCACCGGUAUGGCCU
JNCF01000027.1/24159-24414 GAGAAUGUUGUUAAAGGCAGCAUCAGCGUUAGGGCAUAAAUUAAUGCUAAAGUACUGGAAAACAAUCUUUUAAUAACCAUAGCGAUCUCCUCGGAUCCAAGGCCAUGAA-UCAGCCACUUUUUUGUAUUUUUUUAUAAUGCAAUUUAAGUGCCAGCGGCUAAACUUUUAAGACAACCACUCUAACGGAUUAACCGCUUUUCCUUUUUGUCUUAUCUCAAAGUAUAGACCGUUUUGCUUGAUUCCACCGCUGUGACCG
#=GC SS_cons               [[[[[-[[[[[[[[,(((-(((((-(((,,,,<<<<<______>>>>>,<<<-<<<_______>>>-->>>,,,,,,,,,,,,,,,,,,)))-)))))---))),<<<<-<<<<<<--<<<---<<<<<<________________>>>>>>>>>->>>>>>--->>>><<<<_____>>>>,,,,,,]]]]]]]]]]]]],,<<<<<________>>>>>,,,,,<<<<---<<________>>->>>>:::::::
#=GC RF                    GaaaauGcgGucaaAGGCAGcauCAGaGUUAGgGCauAAAuuAauGCcAaagUacuGGAAAAaaguuUcuuAAUAACCAUAGCGAUCUCCuCaGaugCAAGGCCAugaa.uuaGCCACcuguuuGuauuuUUUUAuAAUGCAAUUUaaaugCcagCGGCuaaaCuuuuaaGacAACCAguCuAACGGAuugaCcgCuuuuCCUcuuuGUCUUAUuUCaaagUAUAGacCGUUUuGCUUaAUUCCaCCGguaUGaCCu
//
# STOCKHOLM 1.0

#=GF AC   RF02826
#=GF ID   Scr6925
#=GF DE   Streptomyces RNA 6925
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 21521948
#=GF GA   50.00
#=GF TC   50.50
#=GF NC   40.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0040007; growth;
#=GF RN   [1]
#=GF RM   21521948
#=GF RT   Deep sequencing-based identification of small non-coding RNAs in
#=GF RT   Streptomyces coelicolor.
#=GF RA   Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S,
#=GF RA   Liesegang H, Mathews DH, Suess B
#=GF RL   RNA Biol. 2011;8:468-477.
#=GF CC   Identified by deep sequencing of transcriptome at the end of exponential
#=GF CC   growth phase. Sequencing size consistent with northern blot size.
#=GF CC   Streptomyces specific. Small 12 nt possible coding region observed. 
#=GF WK   Streptomyces_coelicolor
#=GF SQ   4



AL645882.2/7688336-7688466 GCAGUGUUGCCACGUUGAUGCGC-CCGUCGGAAGGACUCAGCGUGGUGAUGGCGGGCAGUCGCCGCCCUUGCCGGGGCGGU-CAUGCCGCUU-AGCCUUCGGCGUCCGGGAGUUACCGCUCUCGGGCGCCGUCG
FN554889.1/2480435-2480305 GCAGUGUUGCCACGCUGACGCGC-CCCUUGGAAGGACUCAGCGUGGUGAUGGUGGGCAAUCUCCGCCCUUGCCGGGGCGGG-UAUGCCGCUU-AGCGUUCGGCGUCCGUGAGUUACCGCUCUCGGGCGCCGUCG
CP007574.1/7167097-7167224 UUGGUGUUGCCACGUUGAGGUGUCCCGUGCGAAGGGCUCAGCGUGGUGAUGAUGGGCACGAUCCG--CUUUUAGC--CGGG-UUAGCCGUUC-AGUGAUCGGCGUCCGAGAGUUGCCGCUCUCGGGCGCCGUUG
KQ948217.1/277661-277529   UUGGUGUUGCCACGCUGACGCGC-CCCGUGGAAGGGAUCAGCGUGGUGAUGGUGGGCAAUCUCCGCCCUAGCCGGGGCGGCGUGUGCCGUUUGAGCGUUCGGCGUUCGGGAGUAGCCGCUCUCGGGCGCCGUCG
#=GC SS_cons               ((,,,<<--<<<<<<<<<----<.<________>>-->>>>>>>>>-->>,<<<<-<<---<<<<<<<<____>>>>>>>>.-->>>>>>,,.,))---<<<<<<<<<<<<<<____>>>>>>>>>>>>>>:::
#=GC RF                    gcaGUguUGCCaCGcuGauGcGc.CCguugGAAGgacuCagCGuGGUGauGgcGGGCaaucgCCGcccuugccggggCGGc.uauGCCgcUu.AgcguUCGGCGucCGgGaGuuaCCgCuCcCGggCGCCGUcG
//
# STOCKHOLM 1.0

#=GF AC   RF02827
#=GF ID   Scr6106
#=GF DE   Streptomyces RNA 6106
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 21521948
#=GF GA   52.50
#=GF TC   52.50
#=GF NC   52.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0040007; growth;
#=GF RN   [1]
#=GF RM   21521948
#=GF RT   Deep sequencing-based identification of small non-coding RNAs in
#=GF RT   Streptomyces coelicolor.
#=GF RA   Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S,
#=GF RA   Liesegang H, Mathews DH, Suess B
#=GF RL   RNA Biol. 2011;8:468-477.
#=GF CC   Identified by deep sequencing of transcriptome at the end of exponential
#=GF CC   growth phase. Appears smaller on northern blot than sequencing transcript.
#=GF CC   This indicates processing step. Streptomyces specific. 
#=GF WK   Streptomyces_coelicolor
#=GF SQ   4



HE971709.1/2496500-2496421 ACGCCGUCCCGAGCGGCGUUCGUGGCCUCGAACGGGCCUGCGA---GGGGGUGGUGCCGUGUCGGCGCAGCACCACCCCC--UCC
CP010849.1/6249277-6249361 ACGCCGUCCUGAACGGCGUUCACGGCCUUGACCGGGCCCGUGAGGCGGGGGUGGUGCCGUGUCGGCGCAGCACCACCCCCGCAGC
CP013743.1/2667557-2667473 ACGCCGUCCCGAGCGGCGUUCGCGGCCUCGACCGGGCCAGUGCGGCGGGGGUGGUGCCGUGUCGGCGCAGCACCACCCCCGCCUU
AL645882.2/6706584-6706667 ACGCCGUCCCGAGCGGCGUACGCGGCCU-GAACGGGCCCGUGUGGCGGGGGUGGUGCCGUGUCGGCGCAGCACCACCCCCGCGCC
#=GC SS_cons               <<<<<<<_____>>>>>>><<<<<<<<<_____>>>->>>>>>-<<<<<<<<<<<<<-<<<____>>>->>>>>>>>>>>>>:::
#=GC RF                    aCGCCGcCCcGAgCGGCGugCgcgGCCcuGAaCgGGCCcgcGcGGcGGGGGuGGuGCCGcGUCGGCgCAGCaCCaCCCCCgCuuc
//
# STOCKHOLM 1.0

#=GF AC   RF02828
#=GF ID   Scr3920
#=GF DE   Streptomyces RNA 3920
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 21521948
#=GF GA   88.00
#=GF TC   88.40
#=GF NC   83.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0040007; growth;
#=GF RN   [1]
#=GF RM   21521948
#=GF RT   Deep sequencing-based identification of small non-coding RNAs in
#=GF RT   Streptomyces coelicolor.
#=GF RA   Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S,
#=GF RA   Liesegang H, Mathews DH, Suess B
#=GF RL   RNA Biol. 2011;8:468-477.
#=GF CC   Identified by deep sequencing of transcriptome at the end of exponential
#=GF CC   growth phase. Sequencing size consistent with northern blot size.
#=GF CC   Streptomyces specific. 
#=GF WK   Streptomyces_coelicolor
#=GF SQ   6



AL645882.2/4315358-4315484 GAUAGGUCGCUGUCGCUACGGUGAUUGGACACUGACACUGAGUCAACUAGCCUUGUGCGCGCGGUUCUUCGCGCGCGGAACCGGAGGACGGUCCGAGCCACGAGGGGGGAGGCUCGGACCGUCCGUA
HE971709.1/5094278-5094403 GAUAGGUCUCUGUCGCUACUGUGAUUGGACACUGACACAGAGUCAACUAGCCUUGUUCGCGCGGUUCUUCGCGCGCGGAACCG-AGGACGGUCCGAGCCACGAGGGGGGAGGCUCGGACCGUCCGUU
FN554889.1/5185358-5185483 GAUAGCCCCCUGUCGCUACUGUGAUUGGACACUGACACAGAGUCAACUAGCCUUGUUCGCGCGGUUCUUCGUGCGCGGAACCGG-GGACGGUCCGAGCCACGAGGGGGGAGGCUCGGACCGUCCGUC
BA000030.4/5240165-5240041 GAUAGGUCUCUGUCGCUACUGUGAUUGGACACUGACACAGAGUCAACUAGCCUUGGUCGCGCGGUUCUUCGCGCGCGGAACCGG--GACGGUCCGAGCCACGAGGGGGGAGGCUCGGACCGUCCGUU
CP016438.1/5043231-5043107 GAUAGGUCUCUGUCGCUACUGUGAUUGGACACUGACACAGAGUCAACUAGCCUUGUCUGCGCGGUUCUUAGCGCGCAGAACCGG--GGCGGUCCGAGCCACGAGGGGGGAGGCUCGGACCGUCCGUU
CP006259.1/4361862-4361738 GAUAGGUCUCUGUCGCUAGCGUGAUUGGACACUGACAGACAGUCAACUAGCCUUGUUCGCGCGGUUCUUCGCGCGCGGAACCGG--GGCGGUCCGAGCCACGAGGGGGGAGGUUCGGACCGCCCGCA
#=GC SS_cons               <<<<<____>>>>>((((,,<<<______>>><<<<_____>>>>,,)))),,,,,,<<<<<<<____>>>>>>><<____>>,..<<<<<<<<<<<<<-<______>-->>>>>>>>>>>>>::::
#=GC RF                    GacaGguCuCuguCGCuacuGuGAUUGGACaCuGaCAcagAGuCaACuaGCCUUGuucGCGCggUUCUccGCGCgCgGAACcGG..GgCGGuCCGaGCCACGAGGGGGGAGGCuCGGaCCGcCCGuu
//
# STOCKHOLM 1.0

#=GF AC   RF02829
#=GF ID   Scr4115
#=GF DE   Streptomyces RNA 4115
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 21521948
#=GF GA   58.00
#=GF TC   58.10
#=GF NC   54.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0040007; growth;
#=GF RN   [1]
#=GF RM   21521948
#=GF RT   Deep sequencing-based identification of small non-coding RNAs in
#=GF RT   Streptomyces coelicolor.
#=GF RA   Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S,
#=GF RA   Liesegang H, Mathews DH, Suess B
#=GF RL   RNA Biol. 2011;8:468-477.
#=GF CC   Identified by deep sequencing of transcriptome at the end of exponential
#=GF CC   growth phase. Sequencing size consistent with notrthern blot size.
#=GF CC   Streptomyces specific. 
#=GF WK   Streptomyces_coelicolor
#=GF SQ   6



AL645882.2/4515318-4515426 GCGUGGGUCGGCCCGCUGUACUGGAUCCAGUGGGCUGGGGG-ACGC-CGCCGCCUACAUCCCCGCGGGCGGCGGACCGGUCCGGGGGGCG-AGUCCCGUCCCCCGGACUGCG
CP006259.1/4194142-4194034 GCGUGGGUCGGCCCGCUGUACUGGAUCCAGCGGGCUGGGGG-ACAC-CGCCACCUACAUCCCCGCGGGUGGCGGACCGGUCCGGGAGGCG-AUGCCCGCCUCCCGGACUGUG
HE971709.1/5275677-5275785 GCGUGGGUCGGCCCGCUGUACUGGAUCCAGUGGGCUGGGGG-ACAC-CGCCGCCUCCAUCCCCGCGGGCGGCGGAACGGUCCGGGGGGCG-AGUCCCGCCUCCCGGACUGCG
CP002994.1/359325-359433   GCGUGGGUCGGCCCGCUGUACUGGAUCCAGCGGGCUGGGGG-ACGC-CGCCGCCUCAUUCCCCGCGGGUGGCGGAACGGUCCGGGAGGCG-AAUGCCGCCUCCCGGACUGUC
CP007699.2/4768104-4768212 GCGUGGGUUGGCCCGCUGCACUGGAUCCAGUGGGCUGGGGG-AUAC-CGUCACCUCAUUCCCCGCGGGUGACGGUCCGGUCCGGGAGGCG-AAGCCCGCUUCCCGGACCGUC
CP010519.1/4753949-4754060 GCGUGGGUCGGCCCGCUGCACUGGGUCCAGCGGGCUGGGGGAACACCCGCCGUCCCCAUCCCCGCGGGCGGCGGACCGGUCCGGGAGGCGCAGCGGUGCCUCCCGGACUGCG
#=GC SS_cons               [[,,,(((<<<<<<<<<<_________>>>>>>>>>><___._>,<.<<<<<<<<-<______>->>>>>>>>>)))<<<<<<<<<<<<<._____>>>>>>>>>>>>>]]:
#=GC RF                    gcGUGGgucgGcccgcuGuAcUGGaUcCagcgggCcgGGGG.ACac.cGccgcccccaUccccgcgggcggCggacCgGuccGGGgGGcG.AauccCgCCcCCCggaCcgcg
//
# STOCKHOLM 1.0

#=GF AC   RF02830
#=GF ID   Scr1601
#=GF DE   Streptomyces RNA 1601
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 21521948
#=GF GA   100.00
#=GF TC   101.80
#=GF NC   97.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0040007; growth;
#=GF RN   [1]
#=GF RM   21521948
#=GF RT   Deep sequencing-based identification of small non-coding RNAs in
#=GF RT   Streptomyces coelicolor.
#=GF RA   Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S,
#=GF RA   Liesegang H, Mathews DH, Suess B
#=GF RL   RNA Biol. 2011;8:468-477.
#=GF CC   Identified by deep sequencing of transcriptome at the end of exponential
#=GF CC   growth phase. Appears longer on northern blot than sequencing transcript.
#=GF CC   Streptomyces specific. 
#=GF WK   Streptomyces_coelicolor
#=GF SQ   6



AL645882.2/1712074-1711860 AACGACCGGUCGGACACGCACGCCCAUGGCAGCGGAUCCGGCCCACAAGUGGAGGCUU-CGAACUCCCACCUGGCCGUCCUC-C-GGA-CGGCGGGUC-A-CCGGUCAGGCGGUU-CCGUC-----CC--AC------GGCGGUGACCAGCCCGAAAUCGCGCCCCGCGGUC-AUA-GCGGCGGUGCUCCGGUAGCAGUUCGAGGAGCCCCGCC-UGU-GAUCGUCCGGGGCAUUUUUU
CP010849.1/1715782-1715574 AACGACCGGUCGGACACGUAUGCC-ACGGCAA-GUGCCCGGCCCACAAGUGGAGGCUUCCGAACUCCCACCUGACCGCCCCC-C-GGGACGGCGGGUC-A-CCGGUCAGGCGGUC-CCGCU-----UC----------GGCGGCGACCGGCCCGAAAGCGCGCCCCGCGGUC-ACC-GUGGCGGUGCUCCGGUA---GUUCGAGGAGCCCCGUU--GU-GAUCGUCCGGGGCAUUUUCU
CP009438.1/1500961-1500758 GACGACCGGCCGGACA----CCGCCGUGUG------CCCGGCCCACAAGUGGAGGCUU-CGAACUCCCACCUGACCGCCCCC-UGGGG-CGGCGGGUC-A-CCGGUCAGACGGUC-CCGUC-----CC--GA------GGCGGCGAUCCGUCCGAAUGCGCGCCCCGCGAUG-AUUCGCGGCGGUGCUCCGGUA---GUUCGAGGAGCCCCGCC-UGU-GAUCGUCCGGGGCAUUUUUU
CP006259.1/1958193-1957985 GUCGACCGGCCGGACACGU------------AUGUGCUCGGCCCACAAGUGGAGGCUC-CGAUCUCCCACCUGACCGUCCUC-CGGGG-CGGCGGGUCAU-CCGGUCAGACGGCCACCAUCGU-UC-CGU--ACGGACGAUGGA-GCC-GUCCGAAAGCGCGCCCCGCGAUC-GUC-GCGGCGGUGCUCCGGUUGCCAU----GGAGCCCCGCC-UGU-GAUCGUCCGGGGCAUUUUUU
FN554889.1/8182035-8182246 AACGACCGGCUGGA--CACU------U----GUGUGCCCGGCCCGCAAGUGGAGGCUC-CGAACUCCCACCUGACCGCCCUC-C-GGGACGGCAGGUC-ACCCGGUCAGACGGCCACCACCG--UUCCGU--ACGGACGGUGGA-GCC-GUCCGAUAUUGCGCCCCGCGGGA-CACCGCGGCGGUGCUCCGGC---AGUACAUGGAGCCCCGCCUGUG-UCCCGUCCGGGGCAUUUUUU
FR845719.1/1346347-1346137 AACGACCGGCCGGACACGU------------GUGUGCCCGGCCCACAAGUGGAGGCUC-CGUACUCCCACCUGACCACCCUCAC-GGG-UGGCGGGUC-A-CCGGUCAGGUGGCGCCCAUCGUUCCGU--ACGG--ACGAUGGA--GCCGCCCGAUG-UGCGCCCCGCGGUUGACC-GCGGCGGUGCUCCGGUAU--UUCCGUGGAGCCCCGCC-UGUGUCCCGUCCGGGGCGUUUUUC
#=GC SS_cons               :::[[[[[[,,<<______......._....______>>(((((,<<-<<<<<<____.____>>->>>>->><<<<<<<__._.>>>.>>>>))))).,.]]]]]],<<<<<-<-<<<<<_..____....__..__>>>>>>.-->>>>>,,,,,,,,,<<<<<<<<<--.--<.<<<<<<<-<<<<<_____._______>>>>>->>>>>.->>.>->>>-->>>>>>:::::::
#=GC RF                    aACGaCCGGccGGACACgu.......u....guGugcCCGgCCCACaAGuGGaGGCUu.CGAACuCCCaCCuGgCCGcCCuC.c.GGg.CGGcGGGuC.A.CCGGuCAGgcgGucaCCgccg..uuuc....ac..AcggcGGg.acCcgcCCGAaagcGCGCCCCGCGguu.auc.gcGGCGGUGCuCCGGuag.agUuCgaGGaGCCCCGCC.ugc.gacCGUCCGGGGCAUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02831
#=GF ID   Scr2736
#=GF DE   Streptomyces RNA 2736
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 21521948
#=GF GA   43.00
#=GF TC   43.00
#=GF NC   42.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0040007; growth;
#=GF RN   [1]
#=GF RM   21521948
#=GF RT   Deep sequencing-based identification of small non-coding RNAs in
#=GF RT   Streptomyces coelicolor.
#=GF RA   Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S,
#=GF RA   Liesegang H, Mathews DH, Suess B
#=GF RL   RNA Biol. 2011;8:468-477.
#=GF CC   Identified by deep sequencing of transcriptome at the end of exponential
#=GF CC   growth phase. Appears smaller on northern blot than sequencing transcript.
#=GF CC   This indicates processing step. Streptomyces specific. 
#=GF WK   Streptomyces_coelicolor
#=GF SQ   4



GG657757.1/3150859-3150921 CGCCCGGCCGGAUCCCGUGGGGGGAAUCCGUACCGGGAC-UGGGAAGGCGCCCUGG-CCGUCGGC
CP009438.1/2867217-2867280 CGCCCGGCCGGAUCCCGUGGGGGGAAUCCGCACCGGGACAUGGGAAGGCGCCCUGG-UCGUCGGC
FN554889.1/6541171-6541108 CGCCCGGCCGGAUCCCGUGGGGGGAAUCCGCACCGGGACAUGGGAAGGCGCCCUGC-UCGCCGGC
AL645882.2/2982570-2982634 CGCCCGGCCGGAUCCCGUGGGGGGAAUCCGCACCGGGACAUGGGAAGGCGCCCUGGAUCGUCGGC
#=GC SS_cons               ((<<<<<-<<<<<<<<_____>>>->>>>>-->>>>>,,,,<<<______>>>,,,-,,,,))::
#=GC RF                    CGCCCGGCCGGAUCCCGUGGGGGGAAUCCGcACCGGGACAUGGGAAGGCGCCCUGg.UCGUCGGC
//
# STOCKHOLM 1.0

#=GF AC   RF02832
#=GF ID   Scr5676
#=GF DE   Streptomyces RNA 5676
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 21521948
#=GF GA   56.00
#=GF TC   56.90
#=GF NC   35.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0040007; growth;
#=GF RN   [1]
#=GF RM   21521948
#=GF RT   Deep sequencing-based identification of small non-coding RNAs in
#=GF RT   Streptomyces coelicolor.
#=GF RA   Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S,
#=GF RA   Liesegang H, Mathews DH, Suess B
#=GF RL   RNA Biol. 2011;8:468-477.
#=GF CC   Identified by deep sequencing of transcriptome at the end of exponential
#=GF CC   growth phase. Appears longer on northern blot than sequencing transcript.
#=GF CC   This indicates processing step. Streptomyces specific. 
#=GF WK   Streptomyces_coelicolor
#=GF SQ   5



AL645882.2/6176413-6176284 AGAUGAGAGAUACAU-CCGCCCACAGGGGACUGUGGGCGGAUCAUCAGGACGAGGCUUCCCCGGCUUCGACCUGGUCGUGC-CUCGCGCACACAACCGGAGCCCA-C-GGGCUCCGGCU--UCCUCACCGAUCGGA
CP006259.1/6123361-6123230 AGAUGAGAGAUACACCCCGCCCACAGGGGACUGUGGGCGA--UUUCAGGCCGGGGCCUCCCCAGCUUCGACCUGGUCGUGCCCUCGCGCACACAGCCGGGGCCUG-A-GGGCUCCGGGAUCUCCUCACCGAUCGGA
CP013743.1/3169964-3170093 AGAUGAGAGAUACACCCCGCCCACAGGGGACUGUGGGCGA--ACUCAGGCCGUGGCCUCCCCAGCUACGACCUGGUCGUGCCCUCGCGCACACU-CCCGGAGCUUCC-GGCUCCGGAUC--UCCUCACCGAUCGGA
CP003275.1/7698727-7698596 AGAUGAGAGAUACAC-CCGCCCACAGGGGACUGCGGGCGGA-CACCGGGCCGGGGCCUCCCCAGCUUCGACCUGGUCGUGCCCUCGCGCACACAACCGGCGCCUG-A-CGGCUCCGGGAUCUCCACACCGAUCGGA
HE971709.1/3139398-3139527 AGAUGAGAGAUACACCCCGCCCACAGGGGACUGUGGGCGA--CAUCAGGCCGGGGCCUCCCCAGCUUCGACCUGGUCGUGCCCUCGCGCACACA-ACCGGGGCCU-CUGGCUCCGGAUC--UCCUCACCGAUCGGA
#=GC SS_cons               :::((((-((,,,,,,<<<<<<<<<<____>>>>>>>>>>..,<<<<<<-<<<<<<_______>>>>>>->>>>>>,<<<<______>>>>,,,,<<<<<<<<__._._>>>>>>>>,,..))))))<<____>>:
#=GC RF                    AGAuGaGAGaUACAcccCGCCCaCaGGGGACuGuGGGCGg..cacCaGGcCGggGCcUCCCCaGCccCGACCuGguCGuGCcCUCGCGCaCACaacCgGggcCuu.a.gGgccCcGgua..uCCuCaCCGAUCGGA
//
# STOCKHOLM 1.0

#=GF AC   RF02833
#=GF ID   Scr3202
#=GF DE   Streptomyces RNA 3202
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; 21521948
#=GF GA   52.00
#=GF TC   52.20
#=GF NC   44.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0040007; growth;
#=GF RN   [1]
#=GF RM   21521948
#=GF RT   Deep sequencing-based identification of small non-coding RNAs in
#=GF RT   Streptomyces coelicolor.
#=GF RA   Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S,
#=GF RA   Liesegang H, Mathews DH, Suess B
#=GF RL   RNA Biol. 2011;8:468-477.
#=GF CC   Identified by deep sequencing of transcriptome at the end of exponential
#=GF CC   growth phase. Appears smaller on northern blot than sequencing transcript.
#=GF CC   This indicates processing step. Streptomyces specific. 
#=GF WK   Streptomyces_coelicolor
#=GF SQ   4



AL645882.2/3510186-3510095 CCACGUCCCGACGC----ACUCCCCCCGGCGCCGGGACU-UCCC--GAGCC-GGGCU-CGGCUGCCCC-UACCCCCCUGGGGCGCCGCAGCCCGGCUCCUUC
HE971709.1/5629384-5629480 CCAAGUCCCGUCGCGAUAACCCCCCCCGGCGCCGGGACUCUCCC--GAGCCGGGUCU-CGGC-GCCCU-AACCCCCCCUGGGCGCCGGGGUCCGGCUCCUUU
FN554889.1/5877015-5877107 CCAAGUCCCGACGC----UCUCCCCCCAGCGCCGGGACU-CUCCGAGAGCC-GGGCCUCGGC-GCCUCCCCCCCCCCUGG--CGCCGAGGCCCGGCUUCUUU
CP013743.1/5887589-5887680 CCACGUCCCGACGC---AAUCCCCCCCGGCGCCGGGACC-UUCCCUGAGCC-GGGCUGCGGC-GCCCC-UCCC--CCC-GGGCGCCGUAGCCCGGCUCUUUU
#=GC SS_cons               ::::<<<<<<-<<<...___________>>>->>>>>>-.----..<<<<<.<<<<<.<<<<.<<<<<._________>>>>>>>>>->>>>>>>>>>::::
#=GC RF                    CCAaGuCCCGaCGC...AacuCCCCCCgGCGCCGGGaCu.uuCC..GaGCC.GGgCc.CGGC.GCCcc.uaCCCCCCuggGGCGCCGugGcCCGGCuCcUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02834
#=GF ID   VqmR
#=GF DE   Vibrio RNA VqmR
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Published; 25646441
#=GF GA   76.00
#=GF TC   76.40
#=GF NC   39.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0042710; biofilm formation;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0003729; mRNA binding;
#=GF RN   [1]
#=GF RM   25646441
#=GF RT   Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a
#=GF RT   regulator of biofilm formation.
#=GF RA   Papenfort K, Forstner KU, Cong JP, Sharma CM, Bassler BL
#=GF RL   Proc Natl Acad Sci U S A. 2015;112:E766-E775.
#=GF CC   Repress the expression of multiple mRNAs including the rtx (repeats in
#=GF CC   toxin) toxin genes and the vpsT, which is required for biofilm formation.
#=GF CC   In fact, VqmR which is highly conserved in vibrionaceae, was shown to
#=GF CC   strongly inhibit biofilm formation through the repression of vpsT gene and
#=GF CC   could be the link between biofilm formation and quorum sensing.
#=GF WK   VqmR_sRNA
#=GF SQ   4



CP007654.1/1010014-1010167 CAGAGCAUGAGUUGCAUGACUGAUGCUUGGUAUCAAUAUGAUACCUCUGUGUGUUCAGCAG-ACCCUCGCUGGAUUCAUGGAACCUCUUCUACACGUCGACAAGAUAUGUUUCUUGUAUUUAU-GCCAGCC--CGUCUUCAGGCUGGCUUUUUUUCAU
CP002378.1/1008207-1008360 CCAAGCGUUAGGU-CAGACCUACCGCCCGAUAUCUUAUUGAUAUCUCUGUGUUUUCAGCAG-ACCCUCGCUGAAAUCAUGGAACCUCUUCUACACGUCGACAAGAUAUGUUUCUUGUAUUUGUUGCCAGCC--CGUCUUCAGGCUGGCUUUUUUUUCC
CP002285.1/505046-505197   UUGAAUAUCAAACAC--GUUUGAUAUUUGAUAUCCAUGUGGUAUCCCUAUGAAU-UUGCAACACCCUCGCAGCAUUCAUAGAACCUCUUCUACACGUCGACAAGAAGCAAUUCUUGUAUUUAU-GCCAGCC--CUUCUUCAGGCUGGCUUUUUUUAUG
CP009355.1/1420498-1420642 ACGAGUCA-GGUUGUAUUACC-UAACUCAGUAUCUAU-UGAUACGUCUAU--ACUCAGUGA-A---UCACUGAGUUCAUAGAACCUCUUCUACACGUCGACAAGAU-UAUUUCUUGUGUUU---GCCAGUCAUCGUAUGGUGCCUGGCAUUUUUUAUC
#=GC SS_cons               ::::<<<<-<<<______>>>->>>>,,<<<<<<_____>>>>>>,,,,,,,<<<<<<<__.______>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<______>>>>>>,,,,,,.<<<<<<<..________>>>>>>>::::::::::
#=GC RF                    uugAGcguugGgUgcAugcCcgacgCUuggUAuCuauaUGaUAccUCUaUGuauucaGcAa.ACCCUCgCugaauUCAUaGAACCUCUUCUACACGUCGACAAGAuaUauUUCUUGUAUUUaU.GCCAGcC..CgUcUucaGgCUGGCuUUUUUUauu
//
# STOCKHOLM 1.0

#=GF AC   RF02835
#=GF ID   Bcj11
#=GF DE   Burkholderia RNA 11
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   49.00
#=GF TC   49.40
#=GF NC   48.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   23142676
#=GF RT   Experimental identification of small non-coding regulatory RNAs in the
#=GF RT   opportunistic human pathogen Burkholderia cenocepacia J2315.
#=GF RA   Ramos CG, Grilo AM, da Costa PJ, Leitao JH
#=GF RL   Genomics. 2013;101:139-148.
#=GF CC   Co-purified with Hfq, expression confirmed by Northern blot. Predicted
#=GF CC   target marZ. Overlaps coding sequence.
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   4



JRKM01000001.1/1213986-1213865 GCAACCUGAAGCUGGCGGCCGAGUACCCCAGCGUGUUCCGCUCGC-UGCUGGGGAUUUCGUGGAUGUGGUUCUUUGGCGCGGUCUUCCUGUCGCAGUUCCCUGCGUUCGCCAAGGAGGUGCUG
CP000539.1/4119161-4119040     GCAACCUGAAGCUGGCGCACGGCAACACCGUGGUGUUCCGCUCGC-UGCUGGGCAUCUCGUGGAUGUGGUUCUUCGGCGCGGUGUUCCUGUCGCAGUUCCCCAGCUUCGCCAAGGACGUGCUG
CP010951.1/1902359-1902238     GCAAUCUCAAGCUCGCGCACGGCAACGC-GGUGGUGUUCCGCUCGCUGCUGGGCAUCAGCUGGAUGUGGUUCUUCGGCGCGGUGUUCCUGUCGCAGUUCCCCAGCUUCGCCAAGGAGGUGCUG
CP000555.1/3947785-3947906     GCAACCUGAAGCUCGCGCACGGCAACCUG-GUGGUGUUCCGUUCGCUGCUCGGCAUCUCGUGGAUGUGGUUCUUCGGCGCGGUGUUCCUGUCGAUGUUCCCGGCCUUCGCGAAGGAGGUGCUG
#=GC SS_cons                   :::::::::<<<-<<-<<<-<<<<<<______>>>>>>->>>->>.->>>-<<<<<-<<<<<<<<<-<<--<<-<<<<<-<<____>>>>>>>->>-->>--->>>---->>>>>>->>>>>:
#=GC RF                        GCAAcCUgAaGCUggCgccCggcaaCaccgguGuugucCggcucc.UGCuggGcaucuccuggacgUGGUUCuUcGgCgCGGUgUUCCuGuCgcaGUUCCCuacguUCGCcaaggaggugCuG
//
# STOCKHOLM 1.0

#=GF AC   RF02836
#=GF ID   Bcj14
#=GF DE   Burkholderia RNA 14
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   59.00
#=GF TC   59.90
#=GF NC   58.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   23142676
#=GF RT   Experimental identification of small non-coding regulatory RNAs in the
#=GF RT   opportunistic human pathogen Burkholderia cenocepacia J2315.
#=GF RA   Ramos CG, Grilo AM, da Costa PJ, Leitao JH
#=GF RL   Genomics. 2013;101:139-148.
#=GF CC   Co-purified with Hfq, expression confirmed by Northern blot. Putative
#=GF CC   functional homologue of PA-SraF. Overlaps coding sequence. 
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   3


CP002599.1/3752808-3752636 GUCGGCGUCGUGACGGUCCAGCCGCAAUCGGUGCCGGUCGUCACCGAACUGCCGGGCC--GCACCAGUGC---CUUCCUGGUCGCCCAGGUGCGGGCACGGGU-CGACGGUAUCGUGCUGCGUCGCGAAUUCACCGAAGGCACCGAUGUCAAGGCAGGGCAACGCCUGUACAAGAUCGA
CP001043.1/541978-542150   GUCGGCGUCGUCACGGUCCAGCCGCAAGCCGUGCCCGUCGUCACCGAACUGCCGGGCCGCACCAGUGCGU--UCCUCGUUGCG---CAAGUGCGCGCG-CGGGUGGACGGCAUCGUGCUGCGCCGGGAAUUUACGGAAGGCACGCAGGUCAAGGCCGGCCAGCGUCUGUACAAGAUCGA
AM747722.1/865355-865183   GUCGGCGUCGUCACCGUGCAGCCGCAAGCCGUGCCGGCGGUGACCGAACUGCCGGGCC--GCACCAGUGCAUUCCUCGUCGCG---CAGGUGCGUGCGCGGGU-CGACGGCAUCGUGCUGCGUCGUGAAUUCACCGAAGGCACCGACGUCAAGGCCGGCCAGCGUCUGUACAAGAUCGA
#=GC SS_cons               ::<<<<<<<<<<<<<<-<<-<<<<_____>>->>->>>>>>>>->>>-->>>>>((((..(((-(-((((..-(-((,,<<<<...<______>>>>><<-<-.<<-<<<<<___>>>>>>>->->>,,,,,,,,))-)))))-)-)))---)))),,,,,,<<<<<_____>>>->>:
#=GC RF                    GUCGGCguCGugaCggUccAGCCgCAAgCcGUGCCggccGucaCCGaACcGCCGgGCC..gCgccaGuGc..UCcuCgUcGcg...CAgGUGCGcgCgcgGGu.cGACgGcaUCGugCcGCguCGcgAAUUcACcGaAGgCaCcgAcGcCAAGGCcGGcCAgCGuCuGUACAaGaUCGA
//
# STOCKHOLM 1.0

#=GF AC   RF02837
#=GF ID   Bcj7
#=GF DE   Burkholderia RNA 7 (anti-hemB)
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   95.00
#=GF TC   95.70
#=GF NC   93.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF DR   GO; 0097311; biofilm matrix;
#=GF RN   [1]
#=GF RM   23142676
#=GF RT   Experimental identification of small non-coding regulatory RNAs in the
#=GF RT   opportunistic human pathogen Burkholderia cenocepacia J2315.
#=GF RA   Ramos CG, Grilo AM, da Costa PJ, Leitao JH
#=GF RL   Genomics. 2013;101:139-148.
#=GF RN   [2]
#=GF RM   23282220
#=GF RT   Computational discovery and RT-PCR validation of novel Burkholderia
#=GF RT   conserved and Burkholderia pseudomallei unique sRNAs.
#=GF RA   Khoo JS, Chai SF, Mohamed R, Nathan S, Firdaus-Raih M
#=GF RL   BMC Genomics. 2012;13:S13.
#=GF RN   [3]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF CC   Co-purified with Hfq, expression confirmed by Northern blot. Putative
#=GF CC   functional homologue of SP-RydB and predicted target hemB.[1] Named
#=GF CC   anti-hemB in [2]. Named ncS04 and shown to be expressed in biofilm [3].
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   3



AM747720.1/292918-293078 AUUUUCGAGAUCGUUGGUAUAUGAUAGCGAUCGAGCGGCACGC-GUUGCGUGCAGCUCCCCGCUUCUCCUCCCUGAGCGGGUGCCUGUCGUUUUUCGAUUAGGCUGUUUGACCCGCCGUUCAACGGCGGGUUUUUUUAUGAGCCGGCCGAAUCCGCAGGUAC
CP000614.1/394014-394174 AUUUUCGAGAUCGUUGGUAUAUGAUAGCGAUCGAGCGGCGCGC-GUUGCGUGCUGCUCCCCGCUUCUCCUCCCUGAGCGGGUGCCUGUCGUUUUUCGAUUAGGCUGUUUGACCCGCCGUUCGACGGCGGGUUUUUUUAUGAGCCGGCCGAAUCCGCAGACAC
CP002580.1/318812-318970 AAUUUCGAGA-CAAUGGUAUAUGAUAGCGAUCGAGUGCCGCGCCAAGGCGCGAUGCUCCCCGCUUCUCCUCCCUGAGCGGGUGCCUGUCGUUAUUCGAUUAGGCUGUUUGACCCGCCGCGAAACGGCGGGUUUUUUUAUGCGCCAACCGA--CGGCAAGCCU
#=GC SS_cons             ::::::::<<<<<<<<________>>>>>>>><<<<-<<<<<<.___>>>>>>->>>><<<<<<-<________>>>>>>>-<<<<<-<<---<<<<----<<<<----<<<<<<<<<<___>>>>>>>>>>-------->>>>--->>>>-->>>>>>>::
#=GC RF                  AuUUUCGAGauCgcugGUAUAUGAcagcGauCGaGcGgCgCGC.guuGCGcGcugCuCCCCGCuUCUCCUCCCUGaGCGGGUgccuGUCgUUuuuCGAUUAGGCuGUUUgaCCCGCCGuuaaaCGGCGGGucUUUUUAUGaGCCggCCGaaUCcGCaggcac
//
# STOCKHOLM 1.0

#=GF AC   RF02838
#=GF ID   Ref55
#=GF DE   Enterococcus sRNA 55
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   43.00
#=GF TC   43.80
#=GF NC   42.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   4



CSXB01000022.1/38641-38587 UAUAUUUUUUUGUUUAGCAGCUUACUUCGUUGACAGACGAGGUAGGCUCUUUUUG
CP007034.1/2703719-2703666 UAUAUAU-UUUGGUUAGGUAGCCACCUCGCUGUGAAGCGAGGUGGUUGCUUUUUA
FR878715.1/12133-12081     GAUAUAU-AUGGAUAAG-GGGCUCCUCCGUUGGUGGACGGGGGAGUCCCUUGUUG
AE016830.1/294479-294426   UAUAUUU-UUUGUUUAGUAGCUUACUUCGUUGGCGGACGAGGUAGGCUCUUUUUG
#=GC SS_cons               :::::::.:::::::<<-<<<<<<<<<<<<<____>>>>>>>>>>>>>>>:::::
#=GC RF                    UAUAUaU.UUUGuUUAGugGccUaCUUCGUuGgcagACGAGGuAggCcCUUUUUG
//
# STOCKHOLM 1.0

#=GF AC   RF02839
#=GF ID   Ref66
#=GF DE   Enterococcus sRNA 66
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   92.00
#=GF TC   92.20
#=GF NC   40.00
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB 128 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   2



CSXB01000067.1/316-206   AAAGAGAGGUAUGCGGGUACAUACCUCUCCUUUUAUACCAACACCAGUUAUAAGAACUGGUGGCUUACUGAGUUAA--GUUUUG------AAUCUUAACCGUUCGGC-CUACGAAGCUUG
AE016830.1/681566-681449 AAAGAGAGAUAUGCAGGAACAUACCUCUC-UAGUA-GCCACUACUAGUUAUAAGAACUAGCGGCUUACUGAGUUAUUGGUUUUAUUUCAAACGCUUAACCGUUCAGCUCCUCAAAGCUUA
#=GC SS_cons             ::<<<<<<-<<<<______>>>>->>>>>.><<<<.<<<----<<<<<<_____>>>>>>->>>->>>><<<<<<-<<<<<_______________>>>>>->->>>>>:::::::::::
#=GC RF                  AAaGaGaGauauGCaGGaACauaCCuCuC.uagua.gCCAauACcaGuuAUAAGaaCugGuGGcUuacuGaGuuaucGGuuUUaUUUcAAAauCUUaaCCgUuCagCuCuuCaAAGCUUa
//
# STOCKHOLM 1.0

#=GF AC   RF02840
#=GF ID   Ref68
#=GF DE   Enterococcus sRNA 68
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   49.00
#=GF TC   49.00
#=GF NC   48.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   4



MIJY01000044.1/184995-185146 AUGCGACGAGUUGACUUAAUCAGACAGCAUUUGCUGUUCCGUUUUGGCGGCUAGUGAUUAACC-AAUUAA-CAGAGGCAC-AUAUGUUAA-AUCAU-ACCUACCGGAU--GUAGGCGUGUCGGAUA-AA-UAUUUUUGUGGAGAAGAUUU-UAUCUAUUUAU
HE999757.2/788207-788357     AUGCGAUGAGUUGACUCAACCAGGUAACUUCGGUUAUUCCGCUGCGGCGGCUAGUGGUUGAAC-AAA--G-GCAGGGCGUUG-GUACUUCGAGUAC-AACUACAGGAU--GUAG--AUGCUUAGCUCCCUCUGUAUUGUGGAAUUCAU-GGAGUUUGUUUAU
KB946316.1/1151539-1151690   AUGCGACGAGUUGACUCAAUCAGAUAGCUUCGGCUGUUCCGUUUUGACGGCUAGUGAUUGACAAAAC--AGCAGAGGCAC-AUAUGUUA-GAUCAU-ACCUACCGGAU--GUAGGCGUGUCGGAUA-AA-UAUUUUUGUGGAGAAGAUGU-UAUCUAUUUAU
AE016830.1/788993-789148     AUGCGACGAGUUGACUCAAUCAGAUAGCUUCGGCUAUUCCGUUUUGACGGCUAGUGAUUGUCA-AAC--A-CAACGACACCAGAUAGUACGGCUAUCAGUUACCGGAUUUGUAAC-GUGUCGGACAGAA-UACUUUUGUGGAGAAGGUUUCUGUCUAUUUAU
#=GC SS_cons                 :::::::::(((----((((((<<<<<<____>>>>>><<<<____>>>>,,,,))))))---.)))..,.,,,((((((,,,<<<<<___>>>>>.,<<<<<_______>>>>>.))))))<<<<<<<.--<<<<<____>>>>>-->>>>>>>:::::::
#=GC RF                      AUGCGAcGAguuGACUcaacCagacagCuUcgGcuguuCCGcUuuGgCGGCUAGuGguugaca.aac..a.caacGgCacuaugugcuacGagcac.AccuaCcGGAU..Guagg.guGcCggacagaa.uacuucuGUGGagaagAUuucugucUaUUUAU
//
# STOCKHOLM 1.0

#=GF AC   RF02841
#=GF ID   Ref70
#=GF DE   Enterococcus sRNA 70
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   115.00
#=GF TC   115.70
#=GF NC   49.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   3



KB946316.1/1298052-1298174 GAAGAACUGUAGGGACUACAGGGAUAGCCUAGGGCAUAUAAGAUAGAUAUAGCGUUUAGUCGAUCAUUUGUCUUUUUCUAGGAAAUUUCUAGUUAAAUAGAGAUAGUUCACUAAUUAUUAGUU
MIJY01000010.1/22225-22104 AAAGAACUGUAGGGACUACAGGGUUAGCCUAGGGUAUAUAAGAUAGAUAUAGCGUUGAUUCGAUCAUUUGUCUUUUUCUAGGAAAUU-UCUAUUAAAUAGAAAUAGUUCACUAAUUAUUAGUU
AE016830.1/880359-880468   GAAGAACUGUAGGGACUACAGGGAUCGCCUAGGG--GAUAGAAAAUGUACACCAUGUGUUGAACCAUUUAU----UUCUAGGAA-------GUCACAUUGGGACAGUCCACUAAUUAUUAAUG
#=GC SS_cons               ::::::<<<<<<___>>>>>>,<<<--<<<<<<<---<<<<<------<<<<___>>>>------->>>>>---->>>>>>>-----.--->>>----<<<<____>>>>:::::::::::::
#=GC RF                    gAAGAACuGuaGGGACuaCaGGgacaGCCuaGgguAuacaaaAuAgaUacacCgUguguUcgAuCAuuuguCUUUuuCuaGGAAAUU.uuagucAaAUuGgaAuAGucCaCUAAUUAUUAgUu
//
# STOCKHOLM 1.0

#=GF AC   RF02842
#=GF ID   RefA1
#=GF DE   Enterococcus sRNA A1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   94.00
#=GF TC   94.20
#=GF NC   61.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. Encoded by pTEF1 plasmid. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   4



CP000731.1/4022-3800   AAAUCGACAUGUGCA-AAAA---CGUAAUCGACCUU-CGUCGA-UUUUUUUAUUUCAAAAUUAAAGAAACGGCUUG-AGAUA--UUCCGAGCAGUUAU-AAAAAUU-AAUUUGC-GUUGAAUAUUGCUACUACAUUCUUGAAAAA-GUGAUGUAGA-UUUAUAGCCCAU-AAC--UUU-UUUGAAUUACAUCGACGAUACGGCGUCGAAAGAAAAAUAAAUAGACCGUAUGAAAGAAAAAG
AP008935.1/36809-37033 AAAAGAACGCGUGCA--AA-AACCAUAAUCGACCUU-CGUCGA-UUUUUUUAUUUCAAAAUUAAAGAAACGGCUUG-AGAUA--UUCCGAGCAAUUAU-AAAAAUU-AAUUUGU-CUUGAAUAUUGCUACUACAUUCUUGAAAAA-GUGAUGUAGA-UUUAUAGCCCAU-AAC--UUUUUUUGAAUUACAUCGACGAUACGGCGUCGAAAGAAAAAUAAAUAGACCGUAUGAAAGAAAAAG
AE016833.1/9308-9519   AAAUCGACGUGUG------A---CGAAACUGACCUG-CGUCAG-UUUUUUA-----AAAUUAAAUGGAACGGCUUG-AGUUA--UUCCGAGCAGUUAA-AAAAAUU-AAUAUGU-GUUGAAUAUCGCUACUGCAUUCUUAAAAAA-GUGGUGCAGA-UUU-UAGCCCAU-AAC--UUU-UUUGAUUUACAUCGACGAUACGGCGUCGAAAGAAAAAUAAAUAGACCGUACUAAGAAUAAAA
CP007500.1/8618-8854   AAAUCGACGUGUGGNAAAAA---CGUAAUCGACCUUNCGUCGANUUUUUUUAUUUCAAAAUUAAAGAAACGGCUUGNAGAUANNUUCCGAGCAGUUANUAAAAAUUNAAUUUGCGNUUGAAUAUUGCUACUACAUUCUUGNAAAAAGUGAUGUAGANUUUAUAGCCCAUNAACNNUUU-UUUGAAUUACAUCGACGAUACGGCGUCGAAARAAAAAUAAAUAGACCGUAUGAAAGAAAAAG
#=GC SS_cons           ::::::(((-((,,,..,,,...,<<<<<<<<<___._>>>>>.>>>>,,,,,,,,,,,,,,,,,<<<<-<<<___._>>>-..>>>>,,<<<<<---.-----<<.<<<____.>>>>>-------->>>>>,,,,<<<<<<<<.<<<<-<<___.______>>>>--.->>..>>>.>>>>>,,,,,,<<<<<<______>>>>>>,,,,,,,,,,,,,,,))))):::::::::::::
#=GC RF                AAAucgaCGuGuGca..AAA...CgaaaucGaCCUu.CGuCga.uuucUUuAUUUCAAAaUuAAaGgaaCggCUUG.AGcuA..uucCGAGcaGuUAu.AAAAAuu.aacuUGu.guugaAUAUuGCUaCugCAUUCuugaaaaa.GuGgUGcAGA.UUUAUAgCcCAU.AaC..uuu.uucgaaUUACAuCGaCGAUACGGCGuCGaAAGAAAAAUAAAUAGaCCGuAugAAagAaAAAg
//
# STOCKHOLM 1.0

#=GF AC   RF02843
#=GF ID   RefA5
#=GF DE   Enterococcus sRNA A5
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   91.00
#=GF TC   91.80
#=GF NC   39.60
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. Encoded by pTEF1 plasmid. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   3



CSXB01000043.1/25996-25929 AACUGAACUUUGUUCAGUACCUUUAUUUUCUGGCGCUACUUCUUCUACUUUGGUCGGUUGAGAAGUAG
AE016833.1/38693-38760     AGCUGAACUCUGUUCAGCUCCAUUUUUUUCAGACGCUACUUCUUCUACUUUGGUCGGUUGAGAAGUAG
AE016830.1/146764-146697   AGCUGAACUUUGUUCAGCAGCAAUUCCUUUCGGCACUACUUCUUCUGCUGUGGUUGGUUGAGAAGUAG
#=GC SS_cons               <<<<<<<<___>>>>>>>>----------------<<<<<<<<<--<<<______>>>->>>>>>>>>
#=GC RF                    aGCUGAACUUUGUUCAGCucCauUuuuUUcuGgCgCUACUUCUuCUaCuuUGGUcgGuUgAGAAGUAG
//
# STOCKHOLM 1.0

#=GF AC   RF02844
#=GF ID   RefA9
#=GF DE   Enterococcus sRNA A9
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   49.00
#=GF TC   49.60
#=GF NC   46.50
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF RN   [2]
#=GF RM   21912655
#=GF RT   Genome-wide identification of small RNAs in the opportunistic pathogen
#=GF RT   Enterococcus faecalis V583.
#=GF RA   Shioya K, Michaux C, Kuenne C, Hain T, Verneuil N, Budin-Verneuil A,
#=GF RA   Hartsch T, Hartke A, Giard JC
#=GF RL   PLoS One. 2011;6:e23948.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. Encoded by pTEF1 plasmid. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   4



CP003504.1/1004836-1004900   GCGAAGCGAUAUUAAUUUUUACCA---AUGGAACACAAAAACCACUCUACGGCGAAUAGAGUGGUUUU
CM002129.1/2617468-2617533   GCGAAAU-ACGAUAAUUGGUACAAGUUACAACACA-AAGGGCCGACCUACUGCGAAUAGGUCGGCCCU
JJMM01000013.1/177821-177882 AUAAAAGUAUAUAAAAUAUUACAA---AAACCAUA-AAAAGCGCCUUUAAAGC--AUAAAGGCGCUUU
AE016833.1/63483-63420       GCGAAACGACAUUAAAUCGUACAG---AUAACACA-AAAAGCAAUCCUACGGCGAAUAGGAUUGCUUU
#=GC SS_cons                 :::::<<<<_______>>>>----...--------.-<<<<<<<<<<<<_______>>>>>>>>>>>>
#=GC RF                      GCGAAAcgAuAUUAAuUcgUACAA...AuAaCACA.AAaaGCcgccCUACgGCGAAUAGggcgGCuuU
//
# STOCKHOLM 1.0

#=GF AC   RF02845
#=GF ID   Ref1C
#=GF DE   Enterococcus sRNA 1C
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   90.00
#=GF TC   90.40
#=GF NC   48.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   21266481
#=GF RT   A simple and efficient method to search for selected primary transcripts:
#=GF RT   non-coding and antisense RNAs in the human pathogen Enterococcus faecalis.
#=GF RA   Fouquier d'Herouel A, Wessner F, Halpern D, Ly-Vu J, Kennedy SP, Serror P,
#=GF RA   Aurell E, Repoila F
#=GF RL   Nucleic Acids Res. 2011;39:e46.
#=GF RN   [2]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   2



AP013036.1/2361813-2361933 UAAUGAGUGAACUUUAUUCAUUACAACCAUAUACAU-------GUUGAGCUAUCUGGCGGAAAACAGAUGGCUCAUUAUUU--CAAUAUUCUGCUAAGGACAGCCAGUGGUCGGCUGUCUUUU-UUAUAUU
AE016830.1/2405867-2405996 UAGUAGGAAGCAUUUAUUCACUUC-UUUACAAAUCUAUCUUAAUCUUAGACAGUCGGCGGAAAACGGCUGUCUAUUUAUCUGGAAAAAUUAUGAACUCGUCAGCUAGUGGUCAGUUGACGAGUUUUAUGUU
#=GC SS_cons               ::<<<<<<<<__________>>>>.->>>>,,,,,,,<<<------<<<<<<<<<<________>>>>>>>>>>------->>>--------<<<<<<<<<<<<<_______>>>>>>>>>>>>>::::::
#=GC RF                    UAguggGuagaaUUUAUUCAcuaC.uccacAaAuaUAuccUAAuuUgaGccagccGGCGGAAAACggcuggCucuUUAUuUggaAAaAUUaUgaacucGuCagCcAGUGGUCgGcuGaCgaguuuUAUaUU
//
# STOCKHOLM 1.0

#=GF AC   RF02846
#=GF ID   Ref84
#=GF DE   Enterococcus sRNA 84
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   52.00
#=GF TC   52.50
#=GF NC   48.20
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000644; antisense_RNA;
#=GF RN   [1]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   5



MIJY01000023.1/316870-316956 UACCAACAACAACCUUUUUAUUUUUCAUUUUACUCUU-AUU-GAGUAA-UACUCCUU-UUCCAUCGGU-CAAU-UAGGCCGGUGGUUUUUUUG
KB946329.1/666494-666405     AACCAAAAACAACCUUUUUAUUUUUCAUUUUACUCUU-UUUAGAGUAAUUACUCCUUUUUCCAUCGGCCUAAC-C-AACCGAUGGUUUUUUUA
MIEK01000013.1/53523-53608   UACCAACAACAACUUUUUUAUUUUCAUAUUUACUCUU-AU--GAGUAAAUACUCCUU-UCCCCACUCA-UUCA-U-UUGAGUGGGGUUUUUCU
AP012200.1/940440-940528     UACCAACAACAACCUUUUUAUUUUUCAAUUUACUCUGAAUA-GGGUAAAUACUCCUU-UUCCACCGGU-AAUUGA-UACCGGUGGUUUUUUUG
AE016830.1/1876680-1876594   UACCAACAACAACCUUUUUAUUUUUCAUUUUACUCUU-AUU-GAGUAAAUACUCCUU-UUCCAUCGGC-AAAA-C-UGCCGGUGGUUUUUUUG
#=GC SS_cons                 ::::::::::::::::::::::::::::<<<<<<<__.___.>>>>>>>--------.--<<<<<<<<.<___._.>>>>>>>>>::::::::
#=GC RF                      UACCAAcAACAACcUUUUUAUUUUUcAuuUUACuCUu.AUu.GaGUAAaUACUCCUU.UUCCacCggc.cAau.u.ggccGguGGuUUUUUUg
//
# STOCKHOLM 1.0

#=GF AC   RF02847
#=GF ID   Ref64
#=GF DE   Enterococcus sRNA 64
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   44.30
#=GF TC   44.30
#=GF NC   44.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. 
#=GF WK   Enterococcus_faecalis
#=GF SQ   3



CP003583.1/1877315-1877383 UAAAGCACCCGCUUCCUUUCUGAUUGGGUUUAGUCACUUUAAUCUUACAGGGAUGAAUGCUUUUUGUGU
KB946329.1/762403-762471   UAAAGUACUCGCAUCUUUUCUGAUUAGGUGUAGUCACUUAAAUCUUACAUGGACGAGUGCUUUAUAUGA
AE016830.1/561100-561032   UAAAGCACUCGCUUCCUUUCUGAUUGGGUUUCGUCACUUUAAUCUUACAGGAAUGAGUGCUUUUUGUGU
#=GC SS_cons               :<<<<<<<<<<-<<<<<----<<<<<<<<______>>->>>>>>---->>>>>>>>>>>>>>>::::::
#=GC RF                    UAAAGcAcuCgCuuCcUUUCUGAUUggGUuUaGUCACUuuAAUCUUACAgGgacGagUgCUUUuUgUGu
//
# STOCKHOLM 1.0

#=GF AC   RF02848
#=GF ID   RefB11
#=GF DE   Enterococcus sRNA B11
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF AU   Repoila F; 0000-0001-5149-9698
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   54.00
#=GF TC   54.60
#=GF NC   53.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   21912655
#=GF RT   Genome-wide identification of small RNAs in the opportunistic pathogen
#=GF RT   Enterococcus faecalis V583.
#=GF RA   Shioya K, Michaux C, Kuenne C, Hain T, Verneuil N, Budin-Verneuil A,
#=GF RA   Hartsch T, Hartke A, Giard JC
#=GF RL   PLoS One. 2011;6:e23948.
#=GF RN   [2]
#=GF RM   25737579
#=GF RT   Whole-genome mapping of 5' RNA ends in bacteria by tagged sequencing: a
#=GF RT   comprehensive view in Enterococcus faecalis.
#=GF RA   Innocenti N, Golumbeanu M, Fouquier d'Herouel A, Lacoux C, Bonnin RA,
#=GF RA   Kennedy SP, Wessner F, Serror P, Bouloc P, Repoila F, Aurell E
#=GF RL   RNA. 2015;21:1018-1030.
#=GF CC   Name â€˜Refâ€™ stands for RNA in E. faecalis. Encoded by pTEF2 plasmid. 22
#=GF CC   nucleotides removed from 3'end of original sequence as it overlapped with
#=GF CC   RF02844 (RefA9).
#=GF WK   Enterococcus_faecalis
#=GF SQ   4



AE016831.1/55455-55622     GGCAACUUGCCUCCGAUU-GGGGGUGCUGUUUAUGUACGAACUUAUGUCUUUGGUUAUUGCCCCACUUUUUGUGGGUCUAGUAAUCUUACUAGUUGACCAUUGGUUAGAUGAUUAGCAGAUAACCAUGCAAGUUGUC---CU-AGCCC--ACACGUCU---AUCCGCA------------AGACGAAAAA
CM002129.1/2261182-2261351 GGCAACUUGC-CCCGUAA-GGGGGUGCUAUUCAUGGAACAAAUUAUCUCGUUAGUUAUCGCACCACUUUUAGUGGGUCUAAUAAUCACAUUAGUUGAUCAUUGGUUAGAUGAUUAGACGAUAGCAA-GCAAGUUGCUG-UCU-AACUCACACGCUUGU---AUUCGCA------------ACAAGUGCAA
AP012046.1/475174-475004   GGCAACUG--CCUCGAAAGGGGGGUGACUCAGUUGUACGAAAUUGUCUCAUUAAUCAUUGCCCCACUUUUUGUGGUUCUAGUAAUCGUGCUAGUUAAUCACUGGCUAGAUGAUUAGCA-AUGAUUGAAACAGUUGCUUUUCU-AGCUC--CAACGCUG--GAGUCGCA-----------ACAGUGAAAAG
CP000423.1/2764586-2764406 GGCAACUG--CCCUGGGA-GGGGGGUGUGACCGUGAUUGAUUUUCUAAAUCAGAUUGUCGCCCCGCUCAUUGUGGGAGUGGUACUCCUGCUGCUCGAACAUAGGUUGAAUGAUCGGCG-AUAGUCUUUGCAGUUGCC---UUCAACCC--ACACGCCCGUCGUCCACGAUUUAUCGCAGCGGGUGAAAAA
#=GC SS_cons               [[[[[[[[..<<<<____.>>>><<<<_______>>>>,,,,,,,,,,,,,((((((((((<<<<<_____>>>>>,<<<<<<____>>>>>><<<<<<___>>>>>>,,,,,,,)))-))))))),,,]]]]]]]]...--.-----..---<<<<<..________..........._>>>>>:::::
#=GC RF                    gGCAACUg..CCccGaaA.ggGGguucUguucaUgaacgAaaUUaUaucuuugguuaUcGCcCCaCUuuUuGuGGgucuaGuaaUCuuaCuaguugacCAUuGguuagAUGAUuaGCg.AuaaccauuacAGUUGCc...cU.AaCuC..AcACgccc..cauuCgCa...........agggcGAAAAA
//
# STOCKHOLM 1.0

#=GF AC   RF02849
#=GF ID   Ysr197
#=GF DE   Yersinia sRNA 197
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   167.00
#=GF TC   167.70
#=GF NC   155.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   5' located ORF: gmhB, 3' located ORF:16S rRNA. Repressed during phase. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   3



AL590842.1/1217039-1217292 UGUACGUUCAAAUAAUCAACAAACGAAAAAAAUGUGAAGAUAAACCCUUGCCAUUCUGAAGCAGCUCCCUAUAAUGCGCAUCCAUCGACACGGCGC-UGUGAGCAACUUCACAGAGUGGCCGGGGAGAGCAGAGAAAAUUAACUG--AUUAAGUGGUUGACUCUGUAGCGGGAAAGCGUAUUAUCUGCCUCCCGCGUUACCGUAAGAUUCGCCGCAAGGCAAACGGGUAACGAACGCUCUUUAACAAUUUAUCAGAC
CP007448.1/1100569-1100822 GUUGCGUUCAAAUAAUCAGCAGUCGGAAAAAACUUUAAUAUAAACCCUUGCCAUUCUGAGGCGGCUCCCUAUAAUGCGCAUCCAUCGACACGGCGC-UGUGAGCAACUUCACAGAGUGGCCGGGAAGAACAGAGAAAAUUAACUG--AUUAAGUGGUUGGCUCUGUAGCGGGAAAGCGUAUUAUCUGCCUCCCGCGUUACCGUAAGAUUCGCCGCAAGGCAAACGGGUAACGAACGCUCUUUAACAAUUUAUCAGAC
CP000826.1/4149457-4149214 UGUGCA--UGAAUAGUGAGCGGUCAGAUAAAAAGUGAAUAUAAACCCUUGUCAUUCUGAACCAGCUCCCUAUAAUGCGCCUCCAUCGACACGGAACAUGUGAACAACUUCACAGAGUCUCCGGGGUUCGAAGAGAAAAAAUCCUGAAAUUUAGGGGUUGACUCUGAAAGAGGAAAGCGUAAUAUACGCCACCUC-GAGAUAGCAAGCUACGGCGGC---------UAACUCA-CUGCUCUUUAACAAUUUAUCAGAC
#=GC SS_cons               ::::(((((,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<-<<<<<<<<<<<<--<<<<---<<<--<<<<_____________>>>>.>>>>>>>-->>>>-->>>>>>>>->>>>,,,<<<<<<--<<<<<-<<_..____>>>>>>>-->>>>>>,<<<<<<--<<<_______>>>->>>>>><<<<<<________________________>>>>>>))))):::::::::::::::::::::
#=GC RF                    ugUgCguucaAAUAaUcAgCaguCggAaAAAAugUgAAuAUAAAcCCuUGccauuCuGaagCaGcuCCCUauaAUGcgCaUCCAUCGACACGGcgC.uguGagCAAcuuCACaGaguggCCgGGgagagcaGaGAAaaccaaCuG..AUUaaGugguuGaCuCugcAGcgGGaAAGCgUAuUAUccGCCuCCcgCGugaccGuAAGaUuCGcCGcaAGGcAAAcGggucaCgaacGCUCUUUAACAAUUUAUCAGAC
//
# STOCKHOLM 1.0

#=GF AC   RF02850
#=GF ID   Ysr276
#=GF DE   Yersinia sRNA 276
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   100.00
#=GF TC   100.10
#=GF NC   96.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF RN   [1]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   Antisense to pepA gene. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   5



AL590842.1/3846865-3846671 CACCGACAUCAAUGAUUCGUUUUGCGAACCAUGGCCGACAGCCAAAUAAGCGUGCAUGCCCAGCUCUUUCAUCUGCUGUUCGCCAAUCACGCGGGUGACGGUGUUGGUACUGAAAGCAUCCGCCAAUUGGCGAGCCUGAGACGCCAGAUAGGCGGCGUUACAGAUAUUGGGUGGCAUAUUGCCCAAGUCUUUUGC
AALD02000045.1/29841-29647 CACCGACAUCAAUGAUUCGUUCUGCGAACCAUGGCCAACCGCCAGAUAAGAGUGCAUACCCAGCUCUUUCAUCUGCUGUUCGCCAAUGACGCGAGUGACGAUAUUGGUGCUGAACGCAUCGGCCAGUUGACGCGCCUGUGACGCCAAAUACGCGGCGUUACAGAUAUUGGGCGGCAUAUUGCCCAAGUCUUUGGC
CP003942.1/507168-507362   CACCGACAUCAAUGAUUCGUUCUGCGAACCGGCGCCGACCGCCAGAUAGGCGUUCAUGCCCAGCUCUUUCAUCUGCUGCUCGCCGAUCACGCGGGUGGUGACGUUGGUGCUGAAGGCGUCCGCCAGUUGGCGCGCCUGCGAGGCCAGAUAGCCGGCGUUACAGAUGUUCGGCGGCAUAUUGCCGAGAUCUUUCGC
CP007448.1/4142675-4142481 CACUGACAUUAAUGAUUCAUUCUGCGAACCAUGGCCAACAGCCAGAUAAGAGUGCAUGCCCAACUCUUUCAUUUGCUGUUCACCAAUCACGCGAGUGAUGAUGUUGGUGCUAAAUGCAUCGGCCAACUGGCGCGCUUGAGACGCCAGAUAGGCGGCAUUACAAAUAUUCGGCGGCAUGUUACCCAAAUCUUUCGC
CP000880.1/3085147-3084953 AACCGACAUCAGCGAUUCGUUCUGCGAACCGUGGCCGACCGCCAGAUAAGCGUUCAUUCCCAGUUCGCGCAUCUGCUGUUCGCCGAUCACGCGGGUGAUAACCUUUUUGCUGUAGCUGUCGGCCAACUGGCGCGCCUGUGACGCCAGGUAGGCGGCGUUACAGAUAUUGGGCGGCAUGUUGCCGAGAUCUUUUGC
#=GC SS_cons               ::::(((,,,,<<<-<<<<<___>>>>>->>><<<_____>>>,,,,,,<<______>>,,<<<__________>>><<<<<<<<<<---<<<<<<<-<<<<<____>>>>>---->>>>>>>-->>>>>>>>>><<<-<<<<<<________>>>>>>->>>,,,<<<<<<________>>>>>>)))::::::
#=GC RF                    cACcGacAUcAacGAuuCGuUcUgCGaaCCguGGCCgACaGCCAgAUAAGcGUgCAUgCCCaGcUCuuuCAUcUgCuGccCGCCaaucACGCggguGAcggcgUUggcgccgaAugCauccGCCAauuGGCGggCcuGugacGCCAgAUAggCGGCguuACagAUAuugGGcGGCAUaUUgCCcaaguCUUUuGC
//
# STOCKHOLM 1.0

#=GF AC   RF02851
#=GF ID   Ysr283
#=GF DE   Yersinia sRNA 283
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   58.00
#=GF TC   58.00
#=GF NC   54.10
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF RN   [1]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   Identified in transcriptional profiling by RNA seq. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   3



AL590842.1/92360-92612       CAACGGCGGGAACAAUCAGCAGUAACAGCAA-ACCGGGAACAACCAUGGCCAGAGCCCAAACGCCCCAGUCAAGAUGAAUGCCCAGAAUUUUGGCAGCGAAAUCAGCAGCCAGUAGAUUUGGUGCCAUCGCAGUGAUAAACAUAAAACUGCUGACCUUCAUGACAAAGUAAAUAUUGGACAUCAAAUAAGAGCCCGCUUUCUUUGCCGUAUCACCGGGUUCUGAUCCCAACGCUUUUACUACCGACAGGAUGAU
CP007044.2/1824746-1824998   CAACUGCGGGAACAAUAAGCAGUAAUACCAG-GCCGGGAACUAUCAUGGCGAGAGCCCAAACACCCCAGUCAAGAUGAAUAUCCAGAAUUUUUGCAGCGAAAUCAGCAGCCAGUAAAUUGGGUGCCAUCGCAGUAAUAAACAUAAAACUGCUGACCUUCAUGACAAAGUAGAUAUUGGACAUCAAAUAAGAGCCCGCUUUCUUUGCCGUAUCGCCGGGUUCUGACCCCAACGCUUUUACUACUGAUAGGAUGAU
JMPN01000025.1/112539-112791 CGAUAGCGGGAACGAUCAGCAGCAAU-GCAAUACCGGGGACGAUCAUCGCCAGCGCCCAUACGCCCCAAUCGAGGUGUACGUCCAGGAUCUUCGCCGCAAAGUCGGCGGUGAGGAGGUUCGGCGCCAUGGCGGUAAUGAAGAUAAAGCUGCUAACCUUCAUCACGAAGUAGAUGUUGGACAUCAGGUAAGAACCUGCUUUCUGGGCACUUUCUCCCGGCUCUGAGCCCAAUGCUUUAACGACGGAAAGCACUAU
#=GC SS_cons                 ::::((((,,,,,,,,,,<<_______>>,,.,,,<<______>>,,<<<____>>>,,,,))))((-(((,,<<<<---<<<<<<<---<<<<<-<<_______>>->>>>>---->>>>>->>>>>><<<<<____________>>>>>,,,,,,,,,,,,,,,<<<<<<--<<<<--<<<<-----<<<<<<<__________________>>>>>>>>>>>->>>>---->>>>>>,,,)))-)):::::
#=GC RF                      CaAcgGcGGGAACaAUcAGcAGuAAuAgCAa.aCCGgGaACaAcCAUgGCcAGaGCcCAaACgCccCAguCaAgauGaAugcCCggaAUuuuggCaGCgAAaUCaGCaGccaguAgauucGGugcCaucGCaGuaAUaAAcAUAAAaCuGCUgACCUUCAUgACaAaGuagaUauuGGACguCaaaUAAGagCCcGCUUUCUuuGCcgUaUCuCCgGGcuCuGacCCCaacGCUucuaCuACuGacAGgAugAU
//
# STOCKHOLM 1.0

#=GF AC   RF02852
#=GF ID   Ysr206
#=GF DE   Yersinia sRNA 206
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   124.00
#=GF TC   124.90
#=GF NC   41.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   5' located ORF: rssB. Exclusively detected in the crp mutant, suggesting
#=GF CC   CRP regulon is a regulator of the sRNA. CRP binding in a cAMP dependent
#=GF CC   manner was confirmed.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   2



AL590842.1/2443937-2444246 CUGUGAUGUGCGUCACAUAA-AAUAAUGAUAUUUACAGGAGCAACCCAUGAAAUUCAUCAAUAAAAUUAUCGCAAUGUUUGAAAAAAUGAACGUCUCAUUCGGCACUAUCAACGGUUAAUUAUUAUUUCUAAUCAUCCGUCAGUCUUCAUAAUAUUCUGAAUUAAAUUCGACAUGUAGGCAAUGAUACAGUAGCCAUUGUGAGUUA-UCUGUGAAAUGAAAGCAUAAUAUGCAAUUACCUAUGUGUGGAAUAUUUUAUUAUUAGGUGCCGUUUAACCUUUUUAUUUAACUUAAUUCCGAAUGUUUACGCUGA
CP007448.1/2213662-2213969 CUGUGAUGUGUAUCACAUAAAAAUAAAGAUAUUUACAGGAGCAACCCAUGAAACUGAUUAACAAAGUUAUCGCUAUGUUCGAAAAAAUGAGUGUCUCAUUUGGUACCAUCAACGGUUAAUUAUUUCA-UUAUUAAUCCGUAAAUCUUCACAAUAUUCUGGAUGAAAUUCAGUUGAUAGGUAAUGGUACUGAACCUCACGAAAGGUCAGCAGUCACGUAACAGCAUAA-AUGUAAUUACUUGUUU-CCGAAUUUGUUAUUAUUAGUCAAUAUAUCGUAUUUUGAUUUGUA-UGAUCCUGAAUAUUUGCACUAA
#=GC SS_cons               :::((((((((,,,,,,,,,.,,,,<<<<-<<<<-<<<<______>>->>>>>>>>>>,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,,,,,,,,))))-))))<<<<---<<<<_______>>>>--->>>>[[[[------[[[[[[[-[[[[[[[((((-(((((((((-(((,,<<<<<<<<<<<___>>->>>>.->>>>>,,,,,,,,<<<<___>>>>,)))-)))))))))-)))),,,,,,,,,,,<<<<________>>>>,,,,,,,,,,,]]]]]]]-]]]]]]]---]]]]:
#=GC RF                    CUGuGauGugcaUCACAUAA.AAUAaugaUguuuACaGGAGCAACCCAuGaaacucauuAAuAAAaUUAUCGCaauguucGAAAAAAUgaacguCUCAUUuGgcaCuauCaaCGGUUAauuaUUauaUuuaauaAUCCGucaguCUUCAuaauauuCUGgauuaaauuCagcacauagGuaauGacaCuGuacCccauGggAGgua.uCaGugAaaUaAaAgCauAAUauGcAauuACcuaugugcgGaauaUuUUAUUAUUaggcaauaUaUagccuUUUuAUUUaaauuaaucCuGaauauuUaCacugA
//
# STOCKHOLM 1.0

#=GF AC   RF02853
#=GF ID   Ysr201
#=GF DE   Yersinia sRNA 201
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   62.00
#=GF TC   62.60
#=GF NC   33.20
#=GF TP   Gene; sRNA
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   Increased expression in the crp mutant in the stationary phases at 25
#=GF CC   degree suggesting CRP regulon is a regulator of the sRNA.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   3



AL590842.1/2736316-2736385 UACAGGAUGUGCCCAUAAUAAAUUUCCGUUUCCGUGUAGCAAUGGUUACUGGAACGUCGCCCUGAUUGUU
CP007448.1/2608195-2608264 UACAGGAAGUACCCAUAAUAAAUUUCCGUUUCCGUGUAGCAAUGGUUACUGGAACGCCGCCCUGAUUGUU
ACCA01000048.1/28009-27940 UACAGGAUAUGCCCAUAAUCAAUUUCCGUUUCCGUGUAGCAAUGGUUACUGGAACGCCGCCCCGAUUGUU
#=GC SS_cons               ::<<<<--<<<---------------<<<<-<<<-<<<<<____>>>>>>>>>>>>->>>>>>>::::::
#=GC RF                    UACaGGAuGuGCCCAUAAUaAAUUUCCGUUUCCgUGUAgCAAUGGuUACuGGAACGcCgCCCuGAUUGUU
//
# STOCKHOLM 1.0

#=GF AC   RF02854
#=GF ID   Ysr100
#=GF DE   Yersinia sRNA 100
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   47.00
#=GF TC   47.10
#=GF NC   36.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0005515; protein binding;
#=GF RN   [1]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   5' located ORF: qor, 3' located ORF: pspG. Decreased expression in the crp
#=GF CC   mutant (in the stationary phase), suggesting CRP regulon is a regulator of
#=GF CC   the sRNA. CRP binding in a cAMP dependent manner was confirmed.
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   3



AL590842.1/324999-325118   UAUUCAUCCCUGUUAGAGAUAAAAAUAGCCGUAUAAACGGCACGUUCAUUUACGUGAACAUAGCUCUGACAGAAU-CCCU-GCUGUACCCCUACAUAUGCAUCAAAGAAAGUG-UAAUGACAG
ACCA01000024.1/23369-23249 UUUUCAUCCCUGUCAGAGGCAAAAAUAGCUGUAUAAACGGCACGUUCAUCUAAGUGAACAUGGCUCUGACAGAAU-ACCUAGCUGUACCCCUACAAGUGCAUCAAAGAAAGCG-UCAUGACAA
CP007448.1/474542-474663   UUUUCAUCCCUGUCAGAGGUAAAAAUAGCUGUAUAAACGGCACGUUCACUUAAGUGAACAUCACUCUGACAGAAUACCCU-GCUGUACCCCUACGAGUGUCUCAAAGAAAGCGGUGUAACCAG
#=GC SS_cons               :::::::::(((((((((,,,,,,,,,<<<<<____>>>>>,,<<<<<<____>>>>>>,,,,)))))))))---.----.-<<<<-----<<<<<---<______>--->>>.>>--->>>>
#=GC RF                    UuUUCAUCCCuGucaGaGguAAAAAUAGCcGuAUAAaCgGCACGuuCacuUAaguGaaCAUagCuCugaCaGAAU.cCCU.GcuGuACCCCcaCgcgUGcaUCAAAgAAAgcG.ugaugaCag
//
# STOCKHOLM 1.0

#=GF AC   RF02855
#=GF ID   Ysr251
#=GF DE   Yersinia sRNA 251
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   100.00
#=GF TC   102.80
#=GF NC   86.20
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF RN   [1]
#=GF RM   25816203
#=GF RT   Transcriptomic profiling of Yersinia pseudotuberculosis reveals
#=GF RT   reprogramming of  the Crp regulon by temperature and uncovers Crp as a
#=GF RT   master regulator of small RNAs.
#=GF RA   Nuss AM, Heroven AK, Waldmann B, Reinkensmeier J, Jarek M, Beckstette M,
#=GF RA   Dersch P
#=GF RL   PLoS Genet. 2015;11:e1005087.
#=GF CC   Antisense to phoH gene. Trimmed on 5'end from the original size. 
#=GF WK   Yersinia_pseudotuberculosis
#=GF SQ   5



AL590842.1/2222488-2222295 AAUAAGCAUUUAAUGUUCGCUGACAGAGUACCGAACGAACACAGUCCUGUUUAUCAAAACGGAUGAUGCCGAUCAUCUCAUCCUCAGUAAAACGCUCCAGUGCAUCGCUGAGACCCGAUUUCACGCCUCUAGGCAGAUCGCAUUGGGUAAUAUCACCAUUAACGAUGACCGUGACAUUUUCACCGAGGCGGGUC
CP007448.1/2051486-2051293 AAUAAGCAUUUAAAGUGCGUUGGCAGAGUGCAGAGCGGACACAAUCCUGUUUAUCAAAGCGAAUGAUGCCAAUCAUGUCAUCUUCAGCAAAACGCUCCAAUGCAUCGCUAAGACCGGAUUUCACACCGCGCGGUAGAUCGCAUUGGGUAAUAUCGCCAUUCACGAUAACGGUGACAUUCUCACCGAGGCGGGUC
CP011254.1/5350028-5350221 CGUAAGCAUUAAGCGUGCGUUGGCACAAAGCCGAGCGCACACAGUCCUGUUUGUCGAAACGAAUGAUACCGACCAUCUCGUCCUCUUCGAAGCGCUCCAGCGCGUCGCUAAGGCCGGAUUUCACGCCGCGUGGCAAAUCGCACUGGGUAAUAUCGCCGUUAACGAUCACCGUGACGUUCUCGCCCAGACGGGUC
CP012487.1/2575221-2575028 CGUAGGCUUUCAGCGUGCGCUGACAGAGUGCAGAACGUACGCAAUCAUCUUUGUUAAAGCGUACGAUACCAAUCAUCUCGUCUUCCUCAAAACGCGCCAGUGCAUCGCUCAGACCCGACUUCACGCCGGAAGGCAAGUCACACUGGGUAAUAUCACCAUUGACGAUGACGGUCACGUUUUCCCCGAGGCGCGUU
CP007394.1/1795720-1795527 UGUAUGCAUGUAGCGUACGUUGGCAAAGUGCCGAACGUACGCAAUCCUCUUUACCGAAUCGGACGAUCCCGACCAUUUCAUCUUCUUCGAAACGUUCCAGCGCGUCACUUAAUCCGGAGCGCACGCCGCGAGGCAAAUCGCAUUGCGUGAUAUCACCGUUGACGAUAACCGUCACGUUCUCCCCGAGGCGGGUU
#=GC SS_cons               :<<<<<<<-----<<<<<<________________>>>>>>------>>>>>>>,,,,,,<<<<<<<____>>>>>>>,,,,<<<<<<----<<<____>>>---->>>>>>(((((-((((,,<<<____>>>,,<<<<---<<<_________>>>---->>>>,,,,<<<<_____>>>>,))))))))):
#=GC RF                    aguaagcaUuuAgcGugCGuUGgCAgAGuGCaGAaCGcaCgCAaUCcuguuuaccaAAaCggauGauaCCgauCaucuCaUCcucagcaAAACgcuCCAgcGCaUCgcugagaCCcGAccuCACGCCgcgaGGCAaauCGCAuuGGGUAAUAUCaCCaUUaACGauaACcGugaCgUUcucaCCGaggCgGGuu
//
# STOCKHOLM 1.0

#=GF AC   RF02856
#=GF ID   30_292
#=GF DE   Leptospira sRNA 30_292
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   112.00
#=GF TC   112.70
#=GF NC   37.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28154810
#=GF RT   Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in
#=GF RT   the Pathogen Leptospira interrogans.
#=GF RA   Zhukova A, Fernandes LG, Hugon P, Pappas CJ, Sismeiro O, Coppee JY,
#=GF RA   Becavin C, Malabat C, Eshghi A, Zhang JJ, Yang FX, Picardeau M
#=GF RL   Front Cell Infect Microbiol. 2017;7:10.
#=GF CC   Identified by RNA seq and Northern blot on cells grown to exponential
#=GF CC   phase at 30 degree C.
#=GF WK   Leptospira_interrogans
#=GF SQ   3



AE010300.2/3674576-3674690   AAACAAAACUUUAUGGAUAAAUCUGGGAGUAAAAUGUAUCUACUCGAAGAACAACAAACACAAUCGAAAGGAGACUACAUCUUGAUUUGCGCCGGAUGCAGAUCAAAAGUCGCAC
AKWO02000047.1/149928-149814 AAAUAGAUCAGUAUGGACAUAUCUGGGAGCAAAAUGUAUUUACUCGAAGAAAAACAAACACAACUGAAAGGGGAUCAAACCUUGACUUGCGCAGGAUGCAGAUCAAAAGUCACGC
AHOR02000061.1/32160-32055   AAAUAGAUCAGUAUGGACAUAUCUGGGAGCAAAAUGUAUUUACUCGAAGAAAAACAAACACAACUGAAAGGAGA---------GACUUGCGCAGGAUGCAGAUCAAAAGUCACGC
#=GC SS_cons                 :::::::<<<<<--<<<____>>>->>>>>,,,<<<<<<<<--<<<<________________>>>>---->>>->>>>>-<<<<<<<<<<_____>>>>>>>>>>:::::::::
#=GC RF                      AAAuAgAgCccuAUgGacAuAuCuGgggGcAAAgugugucuACuCggAGAAaAACAAACACAAccGaAAGGagaucacacCuuGacuuGCgCaGGAuGCagguCaaAAGUCaCgC
//
# STOCKHOLM 1.0

#=GF AC   RF02857
#=GF ID   30_255
#=GF DE   Leptospira sRNA 30_255
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   197.00
#=GF TC   197.90
#=GF NC   44.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28154810
#=GF RT   Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in
#=GF RT   the Pathogen Leptospira interrogans.
#=GF RA   Zhukova A, Fernandes LG, Hugon P, Pappas CJ, Sismeiro O, Coppee JY,
#=GF RA   Becavin C, Malabat C, Eshghi A, Zhang JJ, Yang FX, Picardeau M
#=GF RL   Front Cell Infect Microbiol. 2017;7:10
#=GF CC   Identified by RNA seq and Northern blot on cells grown to exponential
#=GF CC   phase at 30 degree C.
#=GF WK   Leptospira_interrogans
#=GF SQ   2



AKWN02000085.1/9204-8993   UUAGAAAGUUCAGAAACAAUUCCAAAGUUAUUUGAAAGAACUCAAACAAAUGCCAAGUGAAAGAGGAUAGAAUUAAAAUUACAAAUAAAGAUCCGUACGAAGUUUUUAGAGUAGGGUAGUCAAACUUUCAAAAGGACGUAAGUAUAAAAUGAAGUUCGAAUCUUUUAGAGACUAAGGACUUAAA-AAACUUAGAACCGUAUCUUCUUUAGGAA
AE010300.2/1805671-1805460 UUAGAAAGUCCAGAAACAAUUCCAAAGUUAUUUAAAAAAACUCAAACAAAUGCCAAGUGAAAGAGGAUAGAAUUAAAAUUACAAAGAAAGAUCCGUACGAAGUUUUUAGAGUAGGGUAGUCAAACUUCCAAAAGGACGUAAGUAUAAAAUGGAGUUCAAAUAGAUUCGAGACUA-GGACUUAAAAAAUCUUAGAACUGUAUAUUCUUUAGGAA
#=GC SS_cons               :::::((((((,,,,,,,,,<<<----<<<<<<<___________________>>>>>>>---->>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<<<---<<<<--<<-<<<<<<-------<<____>>------->>>>>>->>>>>>>>>>>>>>>>,,))))))-------<<<<<<___________>>>>>>::
#=GC RF                    UUAGAaaGucCAGAAACAAUuCCAAAGuuauuugAAAaAACUCAAACAAAUGCcaagugaAAGAGGaUAGAAUUAAAAUUACAAAuAAAGAUCCGUACGAaGuuuuuagaGUAggguAGucAaaCuucCAAAAGGaCGUAAGuAUAAAAUgaaGuuCgaauccuuuagagaCuAAGgaCuuAAAAAAaCuuagaACuGUAUaUUCuuuagGAA
//
# STOCKHOLM 1.0

#=GF AC   RF02858
#=GF ID   Arrc08
#=GF DE   Actinobacillus sRNA 08
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   219.00
#=GF TC   219.80
#=GF NC   172.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   27402897
#=GF RT   A computational strategy for the search of regulatory small RNAs in
#=GF RT   Actinobacillus pleuropneumoniae.
#=GF RA   Rossi CC, Bosse JT, Li Y, Witney AA, Gould KA, Langford PR, Bazzolli DM
#=GF RL   RNA. 2016;22:1373-1385.
#=GF CC   Arrc stands for Actinobacillus pleuropneumoniae Regulatory RNA Candidate.
#=GF CC   TargetRNA2 was used for the predictions. sufI gene target may be involved
#=GF CC   in stress resistance. 
#=GF WK   Actinobacillus_pleuropneumoniae
#=GF SQ   3



CP000569.1/1950746-1951015 ACUUUACAAGGUCGUGGAUUAU-U--GUAUAAUUUGCGAC-CUUAACUUGCGAGAGCAAGCUGAUGGUGCUUAGCCUAUCUAAGCCCCGUCCAAGACCGUAGGUGAAUAAGUUU-UCUUAUUCUUAAUAA-AAACCUACGUAGAUGGUGAACAGACAGAAUUUUCUGCUUCUGGACACCUUAGGCUCAGAAGAUUGCUACUUGCG-AUGCAAGCGGUGAGUUUUUUGAGGUUUUUUGUAAAUUCCACUU-------CGGUGGAGUGUAUCAGGAGCUAAAACCA
AE017143.1/1582140-1581873 ACUUUACAGGGUCGU--AUUAU-CGCGUAUAAU-UUCGAC-CUUAACUUGCGCGAGCAAGCUGAUGGUGCUUAGCCUAUCUAAGCCCCAUCCAAGACCGUAGGUGGAUAGCUU---GCUAUUCUUAAUAACAAGCCUACGUAGAUGGUGAACAGACAGAAUUAUCUGCUUCUGGACACCUUAGCCUCAAGAAGAUGCCGU------AU--AAGCGGUAAUAUUUUUGGGAUUUUUUGUAAAUUCUGCUCACGAAAGUGGCAGAGUGUAUCAGGAGCUAAAACCA
CP003745.1/2359470-2359209 ACUUUACAAGACUGUGGGUUGUCU--AUAUAAUCCGCAGUUCUUUUUGGCUGAAAAGCCAAUGAUGGUGCUU-GCCUCUC-AAGCCCCGUCCAAGACCGUAGGCGAAAUCAUAUCUAGAUUUCUUAAUUA-A-ACCUACGUAGAUGGUGAACAGACAGAAUUUUCUGCUUCUGGACACCUUAGGCUCAAAAAUU-----AUCGUGUAAGCGGUU----CUAUUUUUGGGGUUUUUUGUAAAUUCCACGC-------AAGUGGAGUGUAUCAGGAGCUAAACCAA
#=GC SS_cons               ::((((,<<<<<<<<<<<<<<<__..__>>>>>>>>>>>>.>>>,,<<<<<____>>>>>,,<<<<<-<<<<<<_____>>>>>>->>>>>,,,,,,<<<<<<<<<<<<<<___._>>>>>>>-------.-->>>>>>>,,,,,<<<<--<<<<<<<<____>>>>-->>>>-->>>>,,,,,<<<<<<<<<<-<<<-<<<<<_.__>>>>>->>>-->>>>>>>>>><<<<<<-<<<-<<<<<<<__.......__>>>>>>>->>>->>>>>>))))::::
#=GC RF                    ACuuuaCaaGgccGcggauuau.u..gUauaauccgCggc.CuuaacgggcGagAgcccgcUGacGGUGCuuaGCCUaUCuaaGCCCCguCCAAGACCGuaGGcGaauaggUuU.UccuauuCUUAAUaA.AAgCCuaCGUAGAUGGuGAACaGaCaGaAUUuuCuGCUuCuGGACaCCUUAGgCcCaaaaaccUgccacccGcG.AugCgggcggcaagguuuuuGgGgcuccuUguaAacuCcgCuc.......ugGcgGaguGuacCaggagcuaaaaCcA
//
# STOCKHOLM 1.0

#=GF AC   RF02859
#=GF ID   Arrc11
#=GF DE   Actinobacillus sRNA 11
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   52.00
#=GF TC   52.20
#=GF NC   42.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   27402897
#=GF RT   A computational strategy for the search of regulatory small RNAs in
#=GF RT   Actinobacillus pleuropneumoniae.
#=GF RA   Rossi CC, Bosse JT, Li Y, Witney AA, Gould KA, Langford PR, Bazzolli DM
#=GF RL   RNA. 2016;22:1373-1385.
#=GF CC   Arrc stands for Actinobacillus pleuropneumoniae Regulatory RNA Candidate.
#=GF CC   TargetRNA2 was used for the predictions. radA gene target may be involved
#=GF CC   in stress resistance. 
#=GF WK   Actinobacillus_pleuropneumoniae
#=GF SQ   2



CP000569.1/208880-209050 AAAUUGUCCAAUAAAUAGGCUUCCCAAUUAUGUAAAAAGUGCGUAUCAUACGCACCUCAAAAUCAGCUGAAGCUG--ACAUAGAUUGAUUAAA-GAGUACGGUUUU-UUAGCCGUACUUUUUAUUUGGAUAGUUAUCUCGUUAAAUUUGUUUUAAAUUUAAUCACUUACGGAAGA
AE017143.1/354088-354260 AAUUUGUCGAAUAAAUAGGCUUCCAAAAAAUCAAAAAAGUGCGUAUUAUAUGCGCCUGAAUAUCAGCAUAUGCUGACAAUUAGAUGAUAUAAACAAGUACGGUUUUUUUAGCCGUACUUUUUAUUUGGAUGA-U-CCAUAAAAAAACUGCUUCAAUUUUAAUCACUUAUGUAAGA
#=GC SS_cons             :[-[[[[[[[[,,,,,,,,,,,,,(((((((((,,,,,<<<<<<<___>>>>>>>,,,,,,,,<<<<____>>>>,,))))-))))),,<<<<-<<<<<<<<<<_____>>>>>>>>>>>>>>,]]]]]]]].]-----<<<<<<<<<<___>>>>>>>>>>:::::::::::::
#=GC RF                  AauuuguCcaaUAAAUAGGCUUCCcaaucauguAAAAAGuGCguaUuAuacGCaCCUgAAuAUCaGCauAuGCuGAcacauAgauuguauaaacaaGuaCGGuuUUUUUagCCGuaCuuuuuaUuugGauaa.u.uCauauuaaauuuguUUcaaauuuaauCACUUAuGuAAGA
//
# STOCKHOLM 1.0

#=GF AC   RF02860
#=GF ID   Arrc14
#=GF DE   Actinobacillus sRNA 14
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   99.00
#=GF TC   99.30
#=GF NC   55.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   27402897
#=GF RT   A computational strategy for the search of regulatory small RNAs in
#=GF RT   Actinobacillus pleuropneumoniae.
#=GF RA   Rossi CC, Bosse JT, Li Y, Witney AA, Gould KA, Langford PR, Bazzolli DM
#=GF RL   RNA. 2016;22:1373-1385.
#=GF CC   Arrc stands for Actinobacillus pleuropneumoniae Regulatory RNA Candidate.
#=GF CC   May control the expression of ferric permease (gene afuB2) and ferredoxin
#=GF CC   (fdx). TargetRNA2 was used for the predictions. 
#=GF WK   Actinobacillus_pleuropneumoniae
#=GF SQ   4



CP000569.1/446936-447102   UUUCAAAUAACUAUGCAAACAUAAACACACACAACAUAAUGGAAAAACGACUAUCUCUUCGACUGCUUCUGUUAUCGCAUUUCGUGCGAGGAUAAAGGUCGUUCGGAGUGAAAG-CGUUCACUAUCCACACU-UUGCCCGCACAUU--GA--UGCGGGUUUU-UUUUACUUAUA
CP005383.1/1382978-1383147 UACUGAAUAACAAUGCAAACAUAAACAUACAACACAACAUGGAAAAAUUUACCUUACUCCGAUUAUCUCUGUUAUCGUAUUUUGUGCGAGGAUAAAGAUUGAUUGGAA-AAAGUAAAUGGACUAUCCACAUUCUUGCCCGCACCUU--AAAAUGCGGGCUUU-UUUUAUCAAAU
CP001321.1/1891671-1891832 UUCUGAAUAACAAUGCAAACAUAAACACACA----ACUAUGGUAAAACUUUUAACUCUUAACCUGCUGGGAUUCACGCAUUCUGUGCGAGGAUAAGGCUCG-GUU-AGAG-AAA-AGUUCACUAUCCACACU-UAGCCCGCACGUCAAAA--UGCGGGCUUU-UUUUAUCGAAU
CP003745.1/1775038-1774880 UUCUGAAUAACAAUGCAAACAU-AAAACACACAAC--AAUGGUAAAACACUUCUCUCUUAGCUUACGACUGUUAUCGCGCUUGGUGCGAGGCUGAU-GUAUAGUUG-GAGAAAA--G--UACUAUCCACACU--UGCCCGCACUUA--AA--UGCGGGUUUUUUUUUACCUGUG
#=GC SS_cons               :::::::::::<<<<____>>>>,,,,,,,,,,,,,,,,<<<<--<<<<-<<-<<-<<<<<<<-<<<<-<<<<-<<<<<<___>>>>>>->>>>->>>>->->>>>>>->>->>.>>>>----->>>>----.--<<<<<<<____..__..>>>>>>>:::.:::::::::::
#=GC RF                    UucUgAAUAACcauGCAAACaugAAcAcACAcaACAuaAuGGaAAaacuucuaucucuccgccUaccucuguuauCGcacUuugugCGaGgauaAagguugagcggagagaAag.aguuuACUAuCCaCAcU.UugCCCGCaCuUu..AA..uGCGGGcUUU.UUUUAucuAau
//
# STOCKHOLM 1.0

#=GF AC   RF02861
#=GF ID   IR_84
#=GF DE   Neisseria sRNA 84
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   51.00
#=GF TC   51.50
#=GF NC   50.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   27486197
#=GF RT   Comprehensive Identification of Meningococcal Genes and Small Noncoding
#=GF RT   RNAs Required for Host Cell Colonization.
#=GF RA   Capel E, Zomer AL, Nussbaumer T, Bole C, Izac B, Frapy E, Meyer J,
#=GF RA   Bouzinba-Segard H, Bille E, Jamet A, Cavau A, Letourneur F, Bourdoulous S,
#=GF RA   Rattei T, Nassif X, Coureuil M
#=GF RL   MBio. 2016; [Epub ahead of print]
#=GF WK   Neisseria_meningitidis
#=GF SQ   3



AE002098.2/2021833-2022018 CAACGUG-------CAAAAAAAACCAUUCAUACCAAGGGU-AAGUAUGAAUGGUCAAUACAUUGCGGGAAAACGUCUUACUUGCUGCACUGCCGAAAAGGGA-GAAACGGCAGCGGUA-AUCAGCGGAAAGGAUUGUACCCGAAUUAAUAUUAAGAAACGUUAAUCGCGAAAAUAUAUUAACAAACCUGU-UGAAAC
AE004969.1/2138417-2138232 CAACGCG-------CAAAAAAAACCAUUCAUACCAAGGGU-AAGUAUGAAUGGUCAAUACAUUGCGGGAAAACAUCUUACUUGCUGCACUGCCGAAAAGGGA-GAAACGGCAGCGUUA-ACCAGCAA-AAGCAUUGUACCUUUAUUAAUGUUAAAAAACAUUAAUUUUGAAAAUAUAUUAACGAAUAUAUCUGGAAC
GL635794.1/300572-300765   CUGUUUUUGCAGAUAAAA-AAAACCAUUCAUACUAAGGGAGAAGUAUGAAUGGCCAAUACAUUGCGGGAAAACGUCUUACUUGCUGCACCGCCCAAAAGGGAUGAAAGAGCGGUGUUGUGUCAGCAAUUGGUAUUCUACCGUUUUUAGUAUUAAAUGCUGUUAAGAA-GUGAAAUUAUUUCAAUAAGUUG-CAAGAU
#=GC SS_cons               :::((((.......,,,,,,,,<<<<<<<<<<<_______.__>>>>>>>>>>>,,,,,,,,,,<<<<---<<<<<<<--<<<<<<<-<<<<<<________.____>>>>>>->---.-->>>>>>-->>>>->>>->>>>,<<<<<<<<<____>>>>>>>>>))))--------<<<<<<____>>>.>>>:::
#=GC RF                    Caacgcg.......aAAAAAAAaCCauuCauaCcAAGGGu.AAGuauGaauGGuCAAUACAUUGcgGGAAAacgucuuACuuGCuGCACcGCcgAAAAGGGA.GAAAcgGCgGcGuUa.auCaGCaauaaggaUcguACCcguauuaacguuAAaaaacguuaaucgcgaaAAuaUAucgccaaAuaugg.cgaaAc
//
# STOCKHOLM 1.0

#=GF AC   RF02862
#=GF ID   sRNA_1300
#=GF DE   Enterococcus sRNA 1300
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   48.80
#=GF TC   48.80
#=GF NC   48.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28894187
#=GF RT   Small RNAs in vancomycin-resistant Enterococcus faecium involved in
#=GF RT   daptomycin response and resistance.
#=GF RA   Sinel C, Augagneur Y, Sassi M, Bronsard J, Cacaci M, Guerin F, Sanguinetti
#=GF RA   M, Meignen P, Cattoir V, Felden B
#=GF RL   Sci Rep. 2017;7:11067.
#=GF CC   Expressed in mid and late exponential phases of growth. Expression
#=GF CC   remained uniform under daptomycin exposure.
#=GF WK   Enterococcus_faecium
#=GF SQ   3



CP013476.1/843083-842853     ACAGCCUCAAUGCGUUUAAGAUAAGCUGGCAAUAAAAAAAGCAGAAUCUUAUCCCCGAUGAUAGGCUUUUUUGUUGUGCUUAUUUAUACGAUAUUGAGCAUUCAUUAGUUACGGUGA-GAUAUAAGUUAUUUAACUAUACCUUUAUUUAACUAUGUCUUUAAUAUGAAUGUUUCCAAAUUGUAUGUAUGCAGACCAAAAGCCACAUUGUGGAUUUAGGCCUGCAUUUUUUAU
CP013688.1/1351708-1351479   ACAGCAUCAAUGCGUAUUAGAUAAGUUGGCAAUAAAAAAGGCAGAAUC-UAUUC-CAAUGAUAGGCUUUUUUGUUGUGCUUAUUUAUACGAUAUUGAGCAUUCAUUAGUUGAGGUGAGGAUAUAGGUUAUUUAACUAUACCUUUAUUUAACUAUGUCUUUAAUAUGAAUGUUUCCAGAUUGUAUGUAUGCAGACCAAAAGCCACAUUGUGGAUUUUGGCCUGCAUUUUUUAU
AGOL01000005.1/190690-190460 ACAGCCUCAAUGCGUUUAAGAUAAGCUGGCAAUAAAAAAAGCAGAAUC-UAUACCCGAUGAUAGGCUUUUUUGUUGUGCUUAUUUAUACGAUAUUGAGCAUUCAUUAGUUACGGUGAGGAUAUUGGUUAUUUAACUAUACCUUUAUUUAACUAUGUCUUUAAUAUGAAUGUUUCCAAAUUGUAUGUAUGCAGACCAAAAGCCACAUUGUGGGGUUUGGCCUGCAUUUUUUAU
#=GC SS_cons                 :::::<<<<<<<<<<---<<<<<<<<--<<<<<<<<<<<-<<-----<.<<<<______>>>>>>>>>>>>>>>>>>>>>>>>>>-->>>->>>>>>><<<<<<<--<<<<----<<-<<<<<<-<<<<--<<<________>>>-->>>>>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,,,,,,<<<<<<-<<-<<<-<<<<___>>>>->>>->>->>>>>>:::::::
#=GC RF                      ACAGCcuCaaugCGuuUaagauaaGcUGgCaacaaaaaaaGCAGAAUC.uaucCcCgAUgauaGGCuuuuuuguuGcgCuuaucuAUaCGAcauuGagCauuCauUAguuacGGUgaGGacauagGuuaUUuaaCUAUACCUuuaUUuaaCuauguCucuaacauGaauGUUUCCAaAUUGUAUGUauGCaGACCAaaaGCCaCAUUGuGGauuuuGGCCuGCauUUUUUAU
//
# STOCKHOLM 1.0

#=GF AC   RF02863
#=GF ID   sRNA_2410
#=GF DE   Enterococcus sRNA 2410
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   61.00
#=GF TC   61.60
#=GF NC   59.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28894187
#=GF RT   Small RNAs in vancomycin-resistant Enterococcus faecium involved in
#=GF RT   daptomycin response and resistance.
#=GF RA   Sinel C, Augagneur Y, Sassi M, Bronsard J, Cacaci M, Guerin F, Sanguinetti
#=GF RA   M, Meignen P, Cattoir V, Felden B
#=GF RL   Sci Rep. 2017;7:11067.
#=GF CC   Produced as 2 transcripts on Northern blot. Expressed in mid, late
#=GF CC   exponential and early stationary phases of growth. Expression remained
#=GF CC   uniform under daptomycin exposure.
#=GF WK   Enterococcus_faecium
#=GF SQ   3



CP003583.1/2651143-2651337 UUAGCUACUUUAGAUAGGUUUGUAUUCAU-CAUGAUGGAUACAAACGUUAAACGACA--GUUUGUAUCUAUGAUGGCUAAAGAACUUUGUAUUGCAGCAAAAAGCCACGUAGACAAAAUGCUAAGUGGCUGAGCA-GUGAAAAUACAAAGUAAA-AGUAUCAAGCAUUC------UACUUUUUCAAUUUAUUUUCCGACUUUUCAA
CP003504.1/990085-989901   UUAGCUACUUUAGAUAGGUUUGUAUUCAUGAAUUAUGGAUACAAACACCAAACAACU-GGUUUGUAUCUAUGAUGGCUAAAGAACUUUGUAUUACG--CAAAAGCCACGUAGACAUUACGUUAAGUGGCUAAGCG---AAAAGUACAAAGU------AAUCACGAUUUC------UUAC---UUACAUACUCUUUCGAUACUCAAU
MIJY01000006.1/46304-46103 UUAGCUAUUUUAGAUAGGUUUGUAUUCAUGAAUCAUGGAUACAAACAGCAAAAGACUGUUUUUGUAUCUAUGAUGGCUAGAGCACUUUGUACUGAA-CAAACAGCCACGUAGACA--AUCCUAAGUGGCUAACAAAAGUAAUGAACUAAC-GACUUUUAUCAAUCCAUUUAGGCAUAUUGUCUGAAUGGAUUUUUUGUUUUAUCAA
#=GC SS_cons               (((((((---((((((,<<<<<<<<<<<<_____>>>>>>>>>>>>,,<<<<<____._>>>>>))))))---))))))),,,<<<<<<<<<<---.<----<<<<<<-<<<________>>>->>>>>>-----.>---->>>>>>>>>><<<.<<<<__________......>>>>>>>::::::::::::::::::::::::
#=GC RF                    uuaGCuacUUuaGauaGGuuuGuauuCauGaAUuauGgauaCaaaCaucaaacgACu.uguuuguauCuaUGAugGCuaaAGaacuuuGuacugca.caAAaaGCCaCGuaGACAaaAugCuaAGuGGCuaAgca.guaAAaguaCaaagugac.aguaUCAagcuuUc......uacugucUuAauuaaUuUUucGauuuuucAa
//
# STOCKHOLM 1.0

#=GF AC   RF02864
#=GF ID   sRNA_0030
#=GF DE   Enterococcus sRNA 30
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   123.00
#=GF TC   123.20
#=GF NC   71.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28894187
#=GF RT   Small RNAs in vancomycin-resistant Enterococcus faecium involved in
#=GF RT   daptomycin response and resistance.
#=GF RA   Sinel C, Augagneur Y, Sassi M, Bronsard J, Cacaci M, Guerin F, Sanguinetti
#=GF RA   M, Meignen P, Cattoir V, Felden B
#=GF RL   Sci Rep. 2017;7:11067.
#=GF CC   Produced as 2 transcripts on Northern blot. Expressed in mid, late
#=GF CC   exponential and early stationary phases of growth. Expression fluctuated
#=GF CC   under daptomycin exposure. Expressed from an integrative transposon
#=GF CC   carrying the tet(M) gene, which confers tetacyclin resistance. 
#=GF WK   Enterococcus_faecium
#=GF SQ   3



CP007447.1/460729-460565 GUCAAUUUGAUAGCGGGAACAAAUAAUUAGAUGUCCUUUUUUAGGAGGGCUUAGUUUUUUGUACCCAGUUUAAGAAUACCUUUAUCAUGUGAUUCUAAAGUAUCCAGAGAAUAUCUGUAUGCUUUGUAUACCUAUGGUUAUGCAUAAAAAUCCCAGUGAUAAAAG
CP003584.1/36043-36207   GUCAAUUUGAUAGCAGGAACAAAUAAUUAGAUGUCCUUUUUUAGGAGGGCUUAGUUUUUUGUACCCAGUUUAAGAAUACCUUUAUCAUGUGAUUCUAAAGUAUCCAGAGAAUAUCUGUAUGCUUUGUAUACCUAUGGUUAUGCAUAAAAAUCCCAGUGAUAAAAG
CP001850.2/550177-550341 GUCAAUUUGAUAGUGGGAACAAAUAAUUGGAUGUCCUUUUUUAGGAGGGCUUAGUUUUUUGUACCCAGUUUAAGAAUACCUUUAUCAUGUGAUUCUAAAGUAUCCGGAGAAUAUCUGUAUGCUUUGUAUGCCUAUGGUUAUGCAUAAAAAUCCCAGUGAUAAGAG
#=GC SS_cons             ::::<<<<---<<<<<<-<<<<<-<<<<<<--<<<<<<<____>>>>>>>>>>>>>->>>>>->>>->>>--->>>>---((((((((--((((,,<<<<<<<-<<<<_____>>>>->>>>>>><<<<<<<___>>->>>>>,,,,,))))---))))))))::
#=GC RF                  GUCAauucGAUagcgGGAaCaaaUaacuagAUGcCCuccUUUAggaGGgCcuaguuUuuuGuACCcAgcuUAAgaauACCuuuauCacGUGauuCUaaaGcauCCaGaGAAUAuCuGUaugCuuuGcauaCCUAUGGUuaugCAUAAAaauCCCAguGauaaaAG
//
# STOCKHOLM 1.0

#=GF AC   RF02865
#=GF ID   ncS01
#=GF DE   Burkholderia sRNA 1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   58.00
#=GF TC   58.80
#=GF NC   39.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0097311; biofilm matrix;
#=GF RN   [1]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF CC   Identified by RNA-seq, RACE and Northern blot. Strongly expressed in
#=GF CC   biofilm. 
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   4



AM747720.1/20581-20691     AGUUCUGAUGCACCGCGAAACGAA-UUUGCAGGUGGAGAACGAGGAGACAAUCGAGGCACAA-AGUGCCCGGACCCCAAAGCGCUGUUGGACGGAAUCCAACAGCGCUUUUUC
CP001503.2/65212-65322     AGUUCUGAUGCACCGCGAAACAAAUUUUGCAGGUGGAGAACGAGGAGACAAUCGAGGCACAA-AGUGCCCGG-CCCCAAAGCGCUGUUGGACGGAAUCCAACAGCGCUUUUUC
BX571965.1/4054471-4054362 AGUUCUGAUGCACCGCGAAACGAAAUUUGCAGGUGGAGAACGAGGAGACAUUCGAGGCACAG-AGUGCCCGA--UCGAAAGCGCUGUUGGAUUCGUUCCAACAGCGCUUUUUA
CP001043.1/3421169-3421068 AGUUCUGAUGCACCGAUU-------UUUGCAGGUGGAGAACGAGGAGAC--AUGAGGCACAAAAGUGCCCAUA--CAAAAGCGCUGUUGGACUGGCUCCAGCAGCGCUUUUUA
#=GC SS_cons               :<<<<---<-<<<<<<<<<_____.>>>>>->>>>->>>>>,,<<-<----<<<-<<<<<__._>>>>>>>>-->>><<<<<<<<<<<<<<_____>>>>>>>>>>>>>>:::
#=GC RF                    AGuuCUGAuGCaCCGcgaaAcgAA.uucgCAGGuGGaGaaCGAgGAgAcAaccGAGGCaCAa.AGuGCCCggA.cCcaaaGCGCuGuuGGacugaauCCaaCaGCGCuuuUUa
//
# STOCKHOLM 1.0

#=GF AC   RF02866
#=GF ID   ncS16
#=GF DE   Burkholderia sRNA 16 (Bc_KC_sr1)
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   48.00
#=GF TC   48.50
#=GF NC   39.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0097311; biofilm matrix;
#=GF DR   SO; 0010039; response to iron ion;
#=GF RN   [1]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF RN   [2]
#=GF RM   29099689
#=GF RT   Identification of novel small RNAs in Burkholderia cenocepacia KC-01
#=GF RT   expressed under iron limitation and oxidative stress conditions.
#=GF RA   Ghosh S, Dureja C, Khatri I, Subramanian S, Raychaudhuri S, Ghosh S
#=GF RL   Microbiology. 2017; [Epub ahead of print]
#=GF CC   Identified by RNA-seq, RACE and Northern blot. Strongly expressed in
#=GF CC   biofilm [1]. Also know as Bc_KC_sr1 [2]. Upregulated in response to iron
#=GF CC   ion depletion. Predicted targets include cysteine desulfurase and
#=GF CC   isochorismatase desulfurase.[2] 
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   4



AM747720.1/2912201-2912283 GUACGCGGCUGGUGUUGCCGGCGCGUCACCAUUCUCCUCUUGUCGUUGUUGCUCCGGGGCCGUAUCCGCCCCGGUUUUUUUUU
CP001043.1/2459324-2459404 GUACGUGUGCGGCGAUGCCGCCGCGUCACCAUUCUCCUCUUGUCGUUGUUGCUCCGGGGCCCA--UAGCCCCGGUUUUUUUUG
CP000270.1/1083868-1083788 GUACGUGGCUGGCGAAGCCGCCGCGUCACCAUUCUCCUCUUGUCGUUGUUGCUCCGGGGU--UAAUAACCCCGGUUUUUUUUG
FR687359.1/584945-584866   GUGCGUGG-CGGCGAUACCGUUACGUCACCAUUCUCCUCUUGUCGUUGUUGCUCCGGGGCUCGA--AGCCCCGGUUUUUUUUA
#=GC SS_cons               <<<<<<<-<<<<<___>>>>>>>>>>->>------------------------<<<<<<<_______>>>>>>>:::::::::
#=GC RF                    GuaCGcGggcGGcGaugCCgcCgCGuCaCCAUUCUCCUCUUGUCGUUGUUGCUCCGGGGcccuAauagCCCCGGUUUUUUUUg
//
# STOCKHOLM 1.0

#=GF AC   RF02867
#=GF ID   ncS011
#=GF DE   Burkholderia sRNA 11
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   48.00
#=GF TC   48.10
#=GF NC   43.60
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0097311; biofilm matrix;
#=GF RN   [1]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF RN   [2]
#=GF RM   19234113
#=GF RT   Mapping the Burkholderia cenocepacia niche response via high-throughput
#=GF RT   sequencing.
#=GF RA   Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, Tiedje JM, Sorek R
#=GF RL   Proc Natl Acad Sci U S A. 2009;106:3976-3981.
#=GF CC   Identified by RNA-seq, RACE and Northern blot. Strongly expressed in
#=GF CC   biofilm.[1] Identified in [2] as ncRNA13. It is complimentary by 40
#=GF CC   nucleotides with a gene encoding a regulatory protein (BCAL1948). ncS11 is
#=GF CC   strongly up-regulated in the stationary phase and biofilms, while BCAL1948
#=GF CC   is down-regulated under these conditions. 
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   4



AM747720.1/2545503-2545296 CCCAUUUCGUG-AAGGAAGUU-CUGAGCGAAAUCAGGUGGCCGCAUAUAUUGCGAGCCAGAUAGGGCAGA-ACGCGCAGU-CCGUGCAGACCACGGCAGAGUCGCAUUUGCGUUGCUCGAGGCGCAACCGAUACCGCCAAAGAGCCCGCCGCCCGAAGGCGCCCGCGUGCGCAUGAAAAAAGGCCUUCAUCUGGCGAUGAAGGCCUUUUACU
CP000614.1/2541404-2541198 CCCAUUUCGCG-AAGGAGGUU-CUGAGCGGAAUCCGGUGGCCGCAUAUGUUGCGAGCCAGAUAGGGCAGAGAAGCGCAGU-CCGUGCAGACCACGGUA--GCCGCAUUUGCGUUGCUCGAGGCGUAACCGAUACCGCCGAAGAGCCCGCCGCCCGAAGGCGCCCGCGUGCGCAUGAAAAAAGGCCUUCAUCUGGCGAUGAAGGCCUUUUACU
CP002599.1/3281465-3281261 CCCAUUUCGCGAAGGGAUGUU-CCGAGCGA-AUCCGGUGGCCGCAUAUAUUGCGAGCCAGAUAGGGCAGA-ACGCGCAAGUCCGUGCAGACCACGGC-GUGCCGCAU-UGCGUUGCUCCAGGCGC--CUGACGCCGCCGAAGAGCCCGCCGCCCGAAGGCGCCCGCGUGCGCAUCAAAAAAGGCCUUCAUCCUGCGAUGAAGGCCUUUUACU
BX571966.1/506394-506600   CCAAUUUCGCG-AGGGAAGCUGCCGAGCGAAACAAGGUGGCCGCAUAUGUUGCGAGCCAGAUAGGGCAGA-CCGCGCAGGUCCGUGCAGACCACGGC-AUGUCGCAU-CGCGUUGCUCGACGUGCAGCCGUCAGGCC-GUCGGGCCCGCCGCCCGAAGGCGCCCGUGUGCGCAUGAAAAAAGGCCUUCAUCUGGCGAUGAAGGCCUUUUACU
#=GC SS_cons               :<<<<<<<<<-.-<<<____>.>>-->>>>>>>-->><<<<<<<<_____>>>>->>>>,,,,((((,,,.,,<<<<----<<<<<_____>>>>>-.-->->>>,,,,<<<--<<<<--<<<<__________>>>>--->>>>->>>,)))),,,,<<<<______>>>>,,,,,<<<<<<<<<<<<<<____>>>>>>>>>>>>>>:::
#=GC RF                    CCcauuuCGcG.AgGgAaGuc.CcGAgCGaaaucagGuGGCCGCaUAUaUuGCGAGCCaGAUAGGGCAGA.acGCGCAguuCCGuGCAGACCaCGGc.guGuCGCAU.uGCGUUGCuCgAGGcgcAaCcGauaccgCCgaaGaGCCCGCCGCCCGAAGGCGCCCGcGUGCGCAUgAAaaaaGGCCuuCauCugGCGauGaaGGCCuuuuACU
//
# STOCKHOLM 1.0

#=GF AC   RF02868
#=GF ID   ncS037
#=GF DE   Burkholderia sRNA 37
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   112.00
#=GF TC   112.50
#=GF NC   46.10
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0097311; biofilm matrix;
#=GF RN   [1]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF CC   Identified by RNA-seq, RACE and Northern blot. Strongly expressed in
#=GF CC   biofilm. 
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   3



AM747721.1/2568766-2568918 GCCGGACCGCGC-UUCCGGUACAUCGCCUCCCCGCCCGCGCAGGAUC--CCUGCGGGCACCCUCCGUCCU-CCGGCGAUGUAUCCCGUGACUGGGCGAGCAGACACGGC-GCGCGGGCCGAUUUUCCGCCCCGGACGUCCCCGUCCGGGGCU-UUUUGU
CP000615.1/78875-79025     GUCGG-CCGCGCCCUACCGGUCCACCGCA--GCGUCC--GCCGCCACGUGCGGCGGGCAU-CUCCGUCCC-CCGCGG-GGUCCGACGUGCCCGGGCGAGCGGGCACGUUGGCGCGGGCCGAUUUCGCGCCCCGGACGUUUACGUCCGGGGCGCUUUUGU
JTDJ01000154.1/9146-8996   ACCGGACUGCGC-UUCCGGUCCAUCGCCACCCCGCCCGCGUUCGAUC--CCUGCGGGCAC--UCCGUCCCCCCGGCGAUGGGCUCCGUGACUGGGCGAGCAGACACGGC-GCGCAGGCCGAUUUUCCGCCCCGGGCUUCGC-GUCCGGGGCG-UUUUUG
#=GC SS_cons               ::[[[-[[[[[[.,,,,(((((((((((,,,,,<<<<--<<<<<___..>>>>>>>>><<_____>>,,,.,,)))))))))))<<<<<-<<<______>>>->>>>>,.]]]]]]-]]]-------<<<<<<<<<<____>>>>>>>>>>:.::::::
#=GC RF                    guCGGACcGCGC.uUaCgggcCcuCgcCacccCGcCCGcGccggauC..ccggCGGgCac.cUCCguCCc.CCGgcGagGgccccCGuGaCcGGGCGAGCgGaCaCGgu.GCGCgGGCCGAUUUucCGCCCCGGaCGUuuaCGuCCGGGGCg.UUUUgu
//
# STOCKHOLM 1.0

#=GF AC   RF02869
#=GF ID   ncS025
#=GF DE   Burkholderia sRNA 25
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   46.00
#=GF TC   46.20
#=GF NC   40.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0097311; biofilm matrix;
#=GF RN   [1]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF CC   Identified by RNA-seq, RACE and Northern blot. Strongly expressed in
#=GF CC   biofilm. 
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   4



AM747720.1/3298074-3297990 UCUGCUUUCCGAAGCAGACUUUUUCGUUGACGGAAAAGAUCUCCAAACCUUUGUCGGCGCGAC-UUCCC---AGUCGCGCUUUUUUUUU
CP001503.2/901532-901616   GCUGCUUUCCGAAGCAGACUUUUUCGUUGACGGAAAAGAUCUCCAAACCUUUGUCGGCGCGAC-UUCCC---GGUCGCGCUUUUUUUUG
CP001043.1/761421-761508   UCUGCUUUUCGAAGCAGACUUUUUCGUUGACGAAAAAGAUCUCCAAACCUUUGUCGGCGCGAC-UUCGCAAGAGUCGCGCUUUUUUUUC
ATCM03080738.1/2625-2540   GCUGCUUUCCGAAGCAGACUUUUUCGUUGACGAAAAAGAUCUCCAAACCUUUGUCGGCGCGGCCUUUUC---AGCCGCGCUUUUUUUUG
#=GC SS_cons               <<<<<<<____>>>>>>><<<<<<<<____>>>>>>>>-----------------<<<<<<<<.<____...>>>>>>>>>::::::::
#=GC RF                    uCuGCuuUcCGaaGCaGaCuuuuuCGUUGACGaaaaaGAUCUCCAAACCUUUGUCgGCGCGgC.uUcuC...aGcCGCGCuUUUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02870
#=GF ID   ncS035
#=GF DE   Burkholderia sRNA 35
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   79.00
#=GF TC   79.10
#=GF NC   34.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0097311; biofilm matrix;
#=GF RN   [1]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF CC   Identified by RNA-seq, RACE and Northern blot. Strongly expressed in
#=GF CC   biofilm. 
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   3



AM747721.1/2304378-2304211 AUGGCGCGACGACAAGUGCGCGCAACGAUUCCGCUUCCGACGCAC-AUAUGUCCAUGGCACGCAGGAAGCGAAUCCGGGACUCUCAACCCCCAUCGGGAGACCCGGAGCCCU--GAGCGAACAUCCACGCGGCUGUGCACCGGCCCCGUGUGGAUGUUCGCUGAUUUUUUU
CP000615.1/2300283-2300117 AUGACGCGAUGAAACAGGCGCGCAACGAUUCGGCUUCCGACGCAC-AUAUGUCAAUGGCACGCAGGAAGCAGAUCCGGGAUUCUCAACCCCCA-CGAGGAACCCGGAGCCCU--GAGCGGACAUCCAUGCGGCUGUGCACCGGCCCCGUGUGGAUGUCCGCUGUUUUUUUC
BX571966.1/906816-906978   AUAGUCUCA-------UCGAAACCAGUACUCUGCUUCCGACGCACGAUACCUCUAUGGCACGCAGGGAGCGAGUCCGGACGCCUC-ACCCCCGUCGAGGCGGCCGGAGCAGUUCAAGCGGACAUCCAUGCGGCUUUCAGCCGGCCCCGAGUGGAUGUCCGCCGAUUUUUUU
#=GC SS_cons               :::<<<<<<<_____>>->>>>>,,,,,,,,<<<<<<<--<<--<.<<______>>>--->>-->>>>>>>,,<<<<<<-<<<<<__________>>>>>->>>>>>,,,,<..-<<<<<<<<<<<<<<<<<<<<_____>>>>>-->>>>>>>>>>>>>>>->:::::::
#=GC RF                    AUggcgcgacGAaAagugcgcgcaAcgAuUCcGCuuCCGACGCAC.auAugUCuauGGCACGCAGGaaGCgaauCCGGgaccCuCAACCCCCaUCGaGggacCCGGaGCccu..gaGCGgaCauCCacgCGGCugUgcaCcgGCCCCGcguGGauGucCGCuGaUUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02871
#=GF ID   ncS54
#=GF DE   Burkholderia sRNA 54
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   43.00
#=GF TC   43.00
#=GF NC   42.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0097311; biofilm matrix;
#=GF RN   [1]
#=GF RM   29142288
#=GF RT   Identification of small RNAs abundant in Burkholderia cenocepacia biofilms
#=GF RT   reveal putative regulators with a potential role in carbon and iron
#=GF RT   metabolism.
#=GF RA   Sass A, Kiekens S, Coenye T
#=GF RL   Sci Rep. 2017;7:15665.
#=GF CC   Identified by RNA-seq, RACE and Northern blot. Strongly expressed in
#=GF CC   biofilm. 
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   4



AM747720.1/1179730-1179807 CAGUCUCUCAGGUUCUAGCACGGCCCUCGGAAUGGCUAGAACUUUUUUAGCGCCACGGUCU-CCGUGGCGCUUUUUUUU
CP000614.1/1212296-1212373 CAGUCUCUCAGGUUCUAGCACGGCCCUCGGAAUGGCUAGAACUUUUUUAGCGCCACGGUCU-CCGUGGCGCUUUUUUUU
CP002599.1/1288913-1288991 CAGUCUCUCAGGUUCUAGCACGGCCCUCGGAAUGGCUAGAACUUUUUUAGCGCCACGGUCCCCCGUGGCGCUUUUUUUU
CP001503.2/1111088-1111166 CAGUCUCUCAGGUUCUAGCACGGCCCUCGGAAUGGCUAGAACUUUUUUAGCGCCACGGUCCCCCGUGGCGCUUUUUUUU
#=GC SS_cons               :::::::::<<<<<<<<<<----<<___>>---->>>>>>>>>>----<<<<<<<<<<____>>>>>>>>>>:::::::
#=GC RF                    CAGUCUCUCagGuuCuaGCACGGCCCUCGGAAUGGCuaGaaCuuUUUUaGCGCCaCGGUCucCCGuGGCGCuUUUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02872
#=GF ID   SrbA
#=GF DE   sRNA regulator of biofilms A
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; R-Scape;
#=GF GA   69.00
#=GF TC   69.70
#=GF NC   44.40
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0042710; biofilm formation;
#=GF RN   [1]
#=GF RM   28771593
#=GF RT   A novel small RNA is important for biofilm formation and pathogenicity in
#=GF RT   Pseudomonas aeruginosa.
#=GF RA   Taylor PK, Van Kessel ATM, Colavita A, Hancock REW, Mah TF
#=GF RL   PLoS One. 2017;12:e0182582.
#=GF CC   Important for biofilm formation and pathogenicity. Bacterial strain with
#=GF CC   deleted SrbA had reduced biofilm mass. As the ability to form biofilms can
#=GF CC   contribute to the ability a pathogen to thrive within the host, the C.
#=GF CC   elegans hosts infected with the srbA deleted strain displayed
#=GF CC   significantly lower mortality rate than the wild-type strain. However, the
#=GF CC   deletion of srbA had no effect on growth or antibiotic resistance in P.
#=GF CC   aeruginosa.
#=GF WK   SrbA_sRNA
#=GF SQ   3



AE004091.2/2977373-2977611         AUCAGGGGCUCUGAAACGAC--GAGCUCCCGGUGCCUGCGCCGAUACGCCC-UCGGCCUCCACCGUGUUGAUCU-GCCCACAAGGCGGCUUGACGAGAUUGCGACUGGAACGAAGUUGUCCUGAGGGACGGGGAAGCGUUU-ACGUAUCAGCCAGAU---CGAAAGACUCGACAGCGAGUCGCCCACCGGCAACCACGAGCCGAACGGCACUUGAUCCAGUCGAGAAGCA-CGGUCCGCGAACUGUUC
HG322950.1/3570010-3570249         ACCAGGGGCCCUGAAU---A--GGGCCUCCGGAUCGAGCUCCGGCCCACUCGCCGAACUGAUCCGUGUUGUUACAGCCCACAAGGCGAAAUGACGAGGUUGCGACUGGCAAGAAGUUGUCCUGAGGGACGGGGAAGCAACC-ACGUAUCAGCAAGAUGGUCGAAUGCAGCCAUUCGCCCUCGCCCAACGGCAGCCACGAGCCGGCAAGCGAUCUCGAAUGCCACC--GCUGCGGUCAUCUACCUGUUC
CP002727.1/2488479-2488251         AUCAGGGGUUCUGGAA---ACGGAACCUCCGGGUCAGUCUCCG-CUUACCGCAGGGAUCGAUUCGUGUUGUUAC-GCCCACAAGGCAGCUCGACGAGAUGGCGACUGGAACGAGGUUGUCCUGAGGGACGGGGAAGCGUUUCACGUAUCGAGUUGCA---CGGU-GCCA-----A--GGGCGUCCACGGGCCUGCACGCACCACCGCUCGCCUACCCGGCAGCGA--GCA-CACGAUGCGCUUCGUCC
#=GC SS_cons                       :(,,<<<<<<<<____...>..>>>>>>>,,,<<<<---<<<-<<<____>>>->>>->>>>)((-(((((,,,,<<<_____>>>,<<--<<<<-------------------------<<_________>>--->>>>-.>>,,,,,,,,)))))...)),,,,,,,<<____>>,,,<<<<<<<<<<<________>>>>>>>>>>>,,,,,,,<<<-<<__..___._>>->>>::::::::::
#=GC RF                            AcCAGgGGcuCuGaAa...a..GagCCcCCGGgucgagCucCGgcccaCcggccGgaccgacgCGUguuguUac.GCCCACAAGGCgGcuugacGAGaUuGCGACUGGaAcGAaGUUGUCCuGAGGGACGGgGAAGCgucu.gCGUAUCagcacgau...CGaauGccacgAuuacgagucGcccgccGGcaacCACGagCCggcgggCgcuuacuccgguccaa..GCa.CgguccgCgaucuGUuC
//
# STOCKHOLM 1.0

#=GF AC   RF02873
#=GF ID   AS-traI
#=GF DE   Antisense to traI
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   99.00
#=GF TC   99.90
#=GF NC   36.20
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28854680
#=GF RT   The CTX-M-14 plasmid pHK01 encodes novel small RNAs and influences host
#=GF RT   growth and motility.
#=GF RA   Jiang X, Liu X, Law COK, Wang Y, Lo WU, Weng X, Chan TF, Ho PL, Lau TCK
#=GF RL   FEMS Microbiol Ecol. 2017; [Epub ahead of print]
#=GF CC   The pHK01 produces plasmid-encoded small RNAs and mediates expression of
#=GF CC   host sRNAs. These sRNAs are antisense to genes involved in replication,
#=GF CC   conjugate transfer and plasmid stabilisation: AS-repA3 (CopA), AS-traI,
#=GF CC   AS-finO, AS-traG, AS-pc02. The overexpression of AS-traI shortened the log
#=GF CC   phase of host growth. 
#=GF WK   Plasmid-mediated_resistance
#=GF SQ   3



CP013026.1/10478-10554   CGGCACGCUGUCCCGACGUUAACAUCUCCAUGAGUUCGCCGGGUACCCUCUCCAUCAGCGGCGUGACCGCCUCCUUA
CP000037.1/105859-105783 CGGCGCGCUGUCCUGAUGUCAGUUUCUCCAUGAGUUCGCCAGGUACUCUCUCCAUCAGCGGCGUGACCGCCUCCUUA
AE006471.2/90198-90122   CGGCACGCUGUCCGGAUGUCAGAGUCUCCAUGAGUUCGCCGGGUACCCUCUCCAUCAGUGGCGUGACCGCCUCCUUG
#=GC SS_cons             <<<<<<<<<<<<<<<-<<--<<<-<<_____>>>>>>>->>>>-------------->>>>>>>>->>>::::::::
#=GC RF                  CGGCaCGCuGuCCcGAcGUcaacauCUCCAUGaguuCgCCgGGUACcCUCUCCAUCAgCgGCGuGACCGCCUCCUUa
//
# STOCKHOLM 1.0

#=GF AC   RF02874
#=GF ID   AS-traG
#=GF DE   Antisense to traG
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   58.00
#=GF TC   58.60
#=GF NC   35.70
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28854680
#=GF RT   The CTX-M-14 plasmid pHK01 encodes novel small RNAs and influences host
#=GF RT   growth and motility.
#=GF RA   Jiang X, Liu X, Law COK, Wang Y, Lo WU, Weng X, Chan TF, Ho PL, Lau TCK
#=GF RL   FEMS Microbiol Ecol. 2017; [Epub ahead of print]
#=GF CC   The pHK01 produces plasmid-encoded small RNAs and mediates expression of
#=GF CC   host sRNAs. These sRNAs are antisense to genes involved in replication,
#=GF CC   conjugate transfer and plasmid stabilisation: AS-repA3 (CopA), AS-traI,
#=GF CC   AS-finO, AS-traG, AS-pc02. The overexpression of AS-traI shortened the log
#=GF CC   phase of host growth. 
#=GF WK   Plasmid-mediated_resistance
#=GF SQ   4



GL872207.1/22595-22680   UGGCAGACUGACUGGAGCCGUAGAAAUAACUGUAACUGUCACUGACCAGUUGUCUGAAUAACAGGUCCGGGUCCGGUCUGCCGCCA
AE006471.2/80645-80560   UGGCUGACUGGCUGGAGCCAUAGAAAUAACUGUAACUGUCACUUACCAGUUCCCUGAAUAACAGGUCAGGGUCCGGCCUGCCCCCA
JWZT01003725.1/9514-9429 CGGCAUUCUGGCCUGAGCUGUAGAAGUAGCUGUAACUGUCGCCUAUCAUCUGGCUGAACAGCAGGUCCGGAUUCGGUUUGCCGCCA
CP000649.1/93894-93809   CGGCGCUCUGUCCCGAGCUGUAGAAGUAAUUGUAGCUGUCGCCAAUCAUCUGGCUGAACAGCAGAUCGGGAUUAGGUUUGCCGCCA
#=GC SS_cons             :<<<<<<<<<<<<<<<-<<------------<<<<<<<________>>>>>>>---------->>>>>>>-->>>>>>>>>>::::
#=GC RF                  uGGCaggCuggCccGAGCcgUAGAAaUAAcUgcAgcUGUCaCuuAuCAgcUgcCUGAAuAaCAgGUCggGaUccgGccuGCCgCCA
//
# STOCKHOLM 1.0

#=GF AC   RF02875
#=GF ID   AS-pc01
#=GF DE   Antisense to pHK01_035
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   79.00
#=GF TC   79.50
#=GF NC   41.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28854680
#=GF RT   The CTX-M-14 plasmid pHK01 encodes novel small RNAs and influences host
#=GF RT   growth and motility.
#=GF RA   Jiang X, Liu X, Law COK, Wang Y, Lo WU, Weng X, Chan TF, Ho PL, Lau TCK
#=GF RL   FEMS Microbiol Ecol. 2017; [Epub ahead of print]
#=GF CC   The pHK01 produces plasmid-encoded small RNAs and mediates expression of
#=GF CC   host sRNAs. These sRNAs are antisense to genes involved in replication,
#=GF CC   conjugate transfer and plasmid stabilisation: AS-repA3 (CopA), AS-traI,
#=GF CC   AS-finO, AS-traG, AS-pc02. The overexpression of AS-traI shortened the log
#=GF CC   phase of host growth. 
#=GF WK   Plasmid-mediated_resistance
#=GF SQ   3



JNOI01000106.1/5773-5676 UGUCAUAAUUUAGCCU-CUUAUGACGAU--UGACUGGAGCCGCAAAAACUGUUCGU-GCAGUCUCUGCGGCAUGGAUUAAGCAGGUCCCUGACCUGCUUUUU
CP013026.1/49702-49803   UGUCAUAAAUGAAACUCCUUAUGACACAGGUUAGUGAAGCCGUGAAAAUCGAUUGCGGCGAUUUCUACGGCGUGGAUUAAGCAGGUCCCUGACCUGCUUUUU
CP000650.1/3977-4073     GAUCAUAAAGUUGACUCCUUAUGGUAGU--UA-ACGAAGCCGGAAAAACCGUUCGU-GCGAUUUUUACGGCGUGGGAGAAGCAGGGU-UUACCCUGCUUUUU
#=GC SS_cons             <<<<<<<<__________>>>>>>>>,,..,,,,,,,,<<<<<<---<<<<<____.>>>>>--->>>>>>-------<<<<<<<<<___>>>>>>>>>:::
#=GC RF                  cguCauaaauuagaCUCCuuauGacgau..UaAauGaAGCCGcaAAAaccGcUcGu.gCgguuUcugCGGCgUGGauuaaGCaGGgcCcUgcCCuGCuuUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02876
#=GF ID   AS-pc02
#=GF DE   Antisense to pHK01_099
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   40.00
#=GF TC   40.50
#=GF NC   36.90
#=GF TP   Gene; antisense;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000077; antisense;
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28854680
#=GF RT   The CTX-M-14 plasmid pHK01 encodes novel small RNAs and influences host
#=GF RT   growth and motility.
#=GF RA   Jiang X, Liu X, Law COK, Wang Y, Lo WU, Weng X, Chan TF, Ho PL, Lau TCK
#=GF RL   FEMS Microbiol Ecol. 2017; [Epub ahead of print]
#=GF CC   The pHK01 produces plasmid-encoded small RNAs and mediates expression of
#=GF CC   host sRNAs. These sRNAs are antisense to genes involved in replication,
#=GF CC   conjugate transfer and plasmid stabilisation: AS-repA3 (CopA), AS-traI,
#=GF CC   AS-finO, AS-traG, AS-pc02. The overexpression of AS-traI shortened the log
#=GF CC   phase of host growth. 
#=GF WK   Plasmid-mediated_resistance
#=GF SQ   4



CP000035.1/103155-102972     CCGACCGGAUAUUAAGAAGC--AAAUCUCAUAAACUCCUUUCAGCCUUCUGAC-UCCUGGAGUAAUGAAGGCUGCUUUUUUCGUUACACCCUUCCCCGGCAGCGCCGGUGGCAGUGUUCAGCCCUUUUCCGGGCAAACUGCUGCCAGUCUGUCCUAGGCGCAACACAGG-CAGCCCGUCGCCAUGCUU
CP013026.1/6329-6513         CCGACCGGAUAUUAAAAAAAGCAAAUCUCAUGCAUU--AUUCAGCCUUCUGAAUCCCUGGAGUAAUGAAGGCUGCUUUUUUCGUUACACCCUUCCCCGGCUGCGCCGGUGGCAGUGUUCAGCCCUUUUUCGGGCAAACUGCUGCCAGUCUGUCCGGGGCGCAA-CACCGGCAGCCCGUCGCCAUGCUU
AJJI01000026.1/9634-9817     CCGACCGGAUAUUAAAAAAAGCAAAUCUCAUGCAUU--AUUCAGCCUUCUGAAUCCCUGGAGUAAUGAGGGCUGCU-UUUUCGUUACACCCUUCCCCGGCAGCGCCGGUGGCAGUGUUCAGCCCUUUUUCGGGCAAACUGCUGCCAGUCUGUCCGGGGAGCAGACGGCG-CAGCCCGUAGCCAUGCCU
JMJC01000011.1/108533-108716 CCGACCGGAUAUUAAAAAAAGCAAAUCUCAUGCAUU--AUUCAGCCUUCUGAAUCCCUGGAGUAAUGAAGGCUGCU-UUUUCGUUACACCCUUCCCCGGCAGCGCCGGUGGCAGUGUUCAGCCCUUUUUCGGGCAAACUGCUGCCAGUCUGUCCGGGGAGCAGACUGCG-CAGCCCGUAGCCAUGCCU
#=GC SS_cons                 ::::((((,,,,,,,,,,,,<<<_______>>>,,,..<<<<<<____>>>>>>,,)))),<<<<<<<<<<______>>>>>>>>>>,,,,,<<<<<<<<<<-<<-<<<<<<<<<-----<<<<______>>>>-->>>>>>>>>->>>>>->>>>>>><<<<-<<<<<._____>>>>>->->>>::
#=GC RF                      CCGACCgGAUAUUAAaAAaaGcaAAUCUCAugCAuU..auuCaGCCUUCuGaaucCCcGGAGuaacGaaggCUGCUuccuuCguuaCACCCUuCCccGGCaGCgCCGGcgGCaGuGUUCAGCCCUUUUuCGGGCAAaCuGCcgCCAGcCuGUCCggGGaGCagaccgcG.CAGCCCgcggCcAuGCuU
//
# STOCKHOLM 1.0

#=GF AC   RF02877
#=GF ID   NmsRb
#=GF DE   Neisseria metabolic switch regulator b (RcoF1/NgncR163)
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   52.00
#=GF TC   52.40
#=GF NC   45.30
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0045974; regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0003729; mRNA binding;
#=GF DR   GO; 0005515; protein binding;
#=GF DR   GO; 0006099; tricarboxylic acid cycle;
#=GF RN   [1]
#=GF RM   29058643
#=GF RT   The sibling sRNAs NgncR_162 and NgncR_163 of Neisseria gonorrhoeae
#=GF RT   participate in the expression control of metabolic, transport and
#=GF RT   regulatory proteins.
#=GF RA   Bauer S, Helmreich J, Zachary M, Kaethner M, Heinrichs E, Rudel T, Beier D
#=GF RL   Microbiology. 2017;163:1720-1734.
#=GF RN   [2]
#=GF RM   28334889
#=GF RT   The primary transcriptome of Neisseria meningitidis and its interaction
#=GF RT   with the  RNA chaperone Hfq.
#=GF RA   Heidrich N, Bauriedl S, Barquist L, Li L, Schoen C, Vogel J
#=GF RL   Nucleic Acids Res. 2017;45:6147-6167.
#=GF RN   [3]
#=GF RM   28325760
#=GF RT   Neisseria meningitidis Uses Sibling Small Regulatory RNAs To Switch from
#=GF RT   Cataplerotic to Anaplerotic Metabolism.
#=GF RA   Pannekoek Y, Huis In 't Veld RA, Schipper K, Bovenkerk S, Kramer G,
#=GF RA   Brouwer MC, van de Beek D, Speijer D, van der Ende A
#=GF RL   MBio. 2017; [Epub ahead of print]
#=GF CC   Sibling sRNA described and independently named in three publications.
#=GF CC   NgncR163 is N. gonorrhoeae while the others are N. meningitidis RNAs.
#=GF CC   RcoF1 stands for: RNA regulating colonization factor 1.
#=GF CC   NmsRb_RcoF1_NgncR163 was shown to be the predominant sibling. They are
#=GF CC   tandemly arranged, structurally nearly identical and and share 70%
#=GF CC   sequence identity. They translationally down-regulate genes involved in
#=GF CC   basic metabolic processes including tricarboxylic acid cycle enzymes and
#=GF CC   amino acid uptake and degradation. The targets include: fumC, sdhC, gltA,
#=GF CC   sucC, prpB and prpC [1][3] Their expression is under the control of
#=GF CC   RelA.[3] Furthermore, they interact with Hfq and target mRNA that encodes
#=GF CC   putative colonization factor of the human nasopharynx (PrpB).[2] 
#=GF WK   Neisseria_sibling_sRNAs_NmsR/RcoF
#=GF SQ   6



CP007726.1/513630-513721   CCGUUAAGUGG--CUUGCAAUAG-CGGCUUAACAGUUUCUCCUCUAUUUCUCCUUUGUAGACUUGGCACACAUUUGAAAAAAUGUGUGCAUUUUU
CP007446.1/2013217-2013129 UCGUUAAAUCAGCUCC----UAGUUGGUUUAACAGUUUCUCCUCUAUUUCUCCUUUGUAGACUUGGCGCACACUUAAUC--GUGUGCGCAUUUUU
AP012224.1/1116719-1116633 UUGUUGAGACG--CAGC-AAUUG-CUUCUUGAUAGUUUCUCCUCUAUUUCUCCUUUGUAGACUUGGCGCGGAC--AAAU--GUCCGCGCAUUUUU
AE016825.1/1347496-1347407 UCUUUGAGAUG--CAGC-AAUUG-CUUCUUGAUAGUUUCUCCUCUAUUUCUCCUUUGUAGACUUGGCGCGG-GCCGCAAGGCACCGCGCAUUUUU
AE004969.1/1248941-1249031 CCGUUAGCUGG--UUCG-AGUAG-UCAGUUAAUAGUUUCUCCUCUAUUUCUCCUUUGUAGACUUGGCACACAUUCUAUUGAAUGUGUGCAUUUUU
AE002098.2/1717580-1717670 CCGUUAGCUGG--UUCG-AGUAG-UCAGUUAAUAGUUUCUCCUCUAUUUCUCCUUUGUAGACUUGGCACACAUUCAACUGGAUGUGUGCAUUUUU
#=GC SS_cons               ::<<<<<<<<<..____._____.>>>>>>>>>,,,,,,,,,<<<<<_________>>>>>----<<<<<<<<<<____>>>>>>>>>>::::::
#=GC RF                    uCgUuaagccg..uucg.AaUaG.cggcuuaAcAGUUUCUCCUCUAuUUCUCCUUUgUAGACUUGGCgCgcacccaAaugggugcGcGCAUUUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02878
#=GF ID   MH_s7
#=GF DE   Mesorhizobail RNA 7
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   221.00
#=GF TC   221.10
#=GF NC   67.00
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28943874
#=GF RT   A Genome-Wide Prediction and Identification of Intergenic Small RNAs by
#=GF RT   Comparative Analysis in Mesorhizobium huakuii 7653R.
#=GF RA   Fuli X, Wenlong Z, Xiao W, Jing Z, Baohai H, Zhengzheng Z, Bin-Guang M,
#=GF RA   Youguo L
#=GF RL   Front Microbiol. 2017;8:1730.
#=GF CC   Existence predicted via genome wide comparisons with 4 related strains.
#=GF CC   Analysed further by deep sequencing and Northern blot under various stress
#=GF CC   conditions. Expressed only under rare growth conditions: symbiosis,
#=GF CC   micro-oxygen stress, and alkali stress. 
#=GF WK   Mesorhizobium
#=GF SQ   3



BA000012.4/4551188-4550877         UGGUUUUCCCUGCCU-CCGCUCGCGGUCCGCUGGCAUUUGCCAGCAACCCGUCAAGCGUCAUAACAUAUACCACUUGCGGUAUAGCAACCAUCAAAGAUCGCAUUUGACAGUUAUGGCAAAAGGACGGCAACGUCAGCGCGUUCCGAGACGCAACGGUCGCCGACGAU-AAAAUCGUAUCGAUUGAAAUCAGCGGCUCGGGGCCA--UGGGAGGAUACCGGAGAUCGAUAUGACGGCAGCAGUGCCUUGGCGCUUCUGCACGAUUGCGCGGCCCGCGACCCCC-GGGGUGCUGCGUCCAUCAACCAGGGAGAGUUAC
CP002447.1/6190604-6190914         UCGCUUUCCCUGCCUUCUGCUCGUGU-ACGACCGACAUCGGGGUCAGCCCGUCACGUCGCAAUACAUAUACCAACCAUGAUAUAGCAACCAUCAAAGAUCGCAUUUGACAGUUAUGGCA-AAGACCCACACCCUCCGCGCGUUCCAAGACGUGACGGUCGCCGACGAGAAAAAUCGUAUCGAUUGA-AUCAGCGUCUCGGGGCCA--UGGGAGGAUACCGGAGAUCGAUAUGACGGCAGCGGUGCCUUGGCGCUUCUGCACGAUUGCGCGGCCCGCGACCCCC-GGGGUGCCGCGUCCAUCAAACAGGGAGAGUUAA
AGSN01000165.1/5606-5295           GAUUUCGCAAUGCCG-CCAUGAGUGUCGCCUGUUCGCGUCGAAGGAUCGA-UC-UGUUUUCGAUCAUAUAUCAGUUUCGGUAUAGCAAUCAUCAAAGAUCGCAUUUGACAGUUAUGUCA-AAGGGACACACCCUUCGCGCGUCCUGGGGCGUGCCAGUCGAUGACGAGGAAAAUCGUAUCGAUUGAAAUCUGCGUCCCGGGGCCGAUUGGGAGGAUACCGGAGAUCGAUA-GACGACAGCAGCGCGCUUGCGCUUCUGCUCGACUGCGCGGCCCGCGAAGCCCCGAGGUGUCGCGUCCAUCAACCAGGGAGAGUUAC
#=GC SS_cons                       :::::::::<____>.<<<<-<-<<___________________________>>>>>------>>,,,,,,,,,,<<<------<<<<<--<<<<<_______>>>>>-->>>--->>-.--->>>,,,,,,,,,,,<<<<<<____>>>>>>,<<<<<<----<<<______>>>--->>>>>>,,,,,,,[<<<____>>>,(..-(((----------------------(((,,<<_______>>,,<<____>>,,,,)))-----)))----)]<<<.<<<<<<_______>>>>-->>->>>::::::::
#=GC RF                            uaguUuuCccUGCCg.ccgcucGcGuuaCguuugcauuuggaagcAaCccGUCgggcuucaaagcAUAUAcCAauuccGgUAUAGcaacCAuCaaaGAUCGCAuuuGaCAguuAUGgCA.AAGggacaCAcCcUccGcgCGucCcgagaCGcgaCaguCGccGACGagaAAAAuCGUAUCGauuGAAAUCaGcGcCuCGGGgCCg..UGGGAGGAUACCGGAGAUCGAUAUGACggCAgcaGuGCcuucGCGCUUCUGCaCGAcuGCGCGGCCCGCGAcgCCC.GgGguGccGCGUCCauCAAcCAGGGAGAGUUAc
//
# STOCKHOLM 1.0

#=GF AC   RF02879
#=GF ID   MH_s10
#=GF DE   Mesorhizobail RNA 10
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; R-scape;
#=GF GA   81.00
#=GF TC   81.10
#=GF NC   39.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28943874
#=GF RT   A Genome-Wide Prediction and Identification of Intergenic Small RNAs by
#=GF RT   Comparative Analysis in Mesorhizobium huakuii 7653R.
#=GF RA   Fuli X, Wenlong Z, Xiao W, Jing Z, Baohai H, Zhengzheng Z, Bin-Guang M,
#=GF RA   Youguo L
#=GF RL   Front Microbiol. 2017;8:1730.
#=GF CC   Existence predicted via genome wide comparisons with 4 related strains.
#=GF CC   Analysed further by deep sequencing and Northern blot under various stress
#=GF CC   conditions. Exhibited 2 bands. Strong signals in response to variety of
#=GF CC   stimuli. Highly abundant in symbiotic, micro-oxygen, oxidative and salt
#=GF CC   stress conditions. 
#=GF WK   Mesorhizobium
#=GF SQ   3



BA000012.4/6385458-6385600         CUCGUUCGCGGCA-GCGUGCCCCGGUGCCGCCAUCAGAAGGGCCAGAAGAAUCGCCCGGCAGGCCCGGCCGGGCGGGAAAAGAAAGCGCGUCGAAGAAAAGCCCGCUGGCCCAGGAAAGCGCAUGGCGGGAAGUAUGGCCGAUA
CP002447.1/4989891-4989749         UUCGUCGGCGGCA-GCGUGAUGCGGCGCCAGCAUCAGAAGGGCCAAAAGGAGCGCCCGGCGGAUCCGGCCGGGCGGGAAAAGAAAGCGCGUCGAUGAAAAGCCGGCUGGCCCAGGAAAGCGCAUGGCGUGAAGUAUGGCCGAUA
CAUM01000068.1/28123-28265         CUCAUCCGC-AUACGCAUUGGCUGACGCCAGCGGCGAAAGGGCCAAAAGGAGCGCCCGACAAAUCCGGCCGGGCGAGGAAAAGAAGCGCGUCGAUGAAAAGCCUGAAGGCUCAGGAAUGCGCAUGGCGCCAAGUAUGGCCGAUA
#=GC SS_cons                       ::<<<<<--<<<<.<-------<<<<<<---------<<____>>------>>>>>----->->->->>>>>>>>------------((((,,,,,,,,<<<<____>>>>,,,,,,,<<<<___>>>>,,,,,,)))):::::
#=GC RF                            cUCguccGCGgca.gCgUgauccGgcGcCagCauCagaaGGGCcaaAAGgAgCgcCCGgCagacCcGgcCgggcGgGaAAAgaAAGCGCguCGAuGAAAgGCCuGcuGGCcCAGGAAagCGCAUGGCGcgAAGUAugGCCGAUA
//
# STOCKHOLM 1.0

#=GF AC   RF02880
#=GF ID   MH_s15
#=GF DE   Mesorhizobail RNA 15
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   123.00
#=GF TC   123.20
#=GF NC   34.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28943874
#=GF RT   A Genome-Wide Prediction and Identification of Intergenic Small RNAs by
#=GF RT   Comparative Analysis in Mesorhizobium huakuii 7653R.
#=GF RA   Fuli X, Wenlong Z, Xiao W, Jing Z, Baohai H, Zhengzheng Z, Bin-Guang M,
#=GF RA   Youguo L
#=GF RL   Front Microbiol. 2017;8:1730.
#=GF CC   Existence predicted via genome wide comparisons with 4 related strains.
#=GF CC   Analysed further by deep sequencing and Northern blot under various stress
#=GF CC   conditions. Widely expressed, accumulated heavily under most of the
#=GF CC   induction conditions, suggesting function in multiple cellular processes. 
#=GF WK   Mesorhizobium
#=GF SQ   2



BA000012.4/942823-942558   CAGCAUCGGUUGCCGACAG--GAAAGGGGCCAUCUUGGCCCCUUUUUCGUGGGCGGUGGUGUAG--CCGUGCGGCUCGUGAAGGAACGCCG---CGGGACCGCUCCUUUGCCCGAAGCCUUUCC-GG-AGCUUGCUGCCAAAGGAACCGCAUCGCCGCCAAUCUCGCACUUGCACAAACUUAUAUUGCACUGCAGUAUGGGUCGGGGCGGGAAUGCGAGCCGGGUUCGGACAUGUACCGCCGUGCCCUUUCGCAUGCCAA-UGCGA-AGGGAUCGGC
CP002447.1/3625960-3626217 ---GAUCGGUCGCAGACAAGGAAAGGGGGCCUCCGUGGCCCCUUU-UCUCGUGCGGCGGCCUGCAUCCGUUCAGU---UGCUG----AUGGAAUCGCUGCCG---CACUGCUUGAAGCAAAUCCCCGCCGAGC-CGGAGGCCGGACCUGAUCCGGCAGCAAUCUCGCACUUGCACAAAUCCAUAUUGCACUGCAAUAUGGA-CUGGGCGGGAAUGCGAGCUGGGUUC-GAAAUGUACCGUCGUACCCU-UCGCAUACCUAUUGCGAGAGG-AUCGGC
#=GC SS_cons               <<-<<<<<--<<<-<<---..-<<<<<<<<<<___>>>>>>>>>>->>>>>-->>>>>->>,<<..<-<--<<<-<<______>>--->>>-..>>-->>,(((,,,,<<<<___>>>>,<<<<.<<.<<____>>->>--->>>>,<<<<<<---<<<---<<<<<<<<<<<-<--<<<<<<<<<<<___>>>>>>>>>>>-->->>>>>-->>>>>>--->>>--->>>>>>,)))<<<<--<<--<<<<<<<____>.>>>>>.>>>--->>>>
#=GC RF                    cagcguCGGUcgcaGaCAa..aaaaGGGGCCauCuuGGCCCCuuuuuCgcguGCGgcgGugUgc..CCGUuCgguucgUGaaGgaAcaccG...CGgugcCGcucCauuGCcuGAgGCaaguCC.gg.cGauugCgGccaaaGGacCcgcguCGgCacCAAUCuCGCaCuuGCACAAacccauauuGCACUGCaauauggguCuGGGCggGAAuGCGaGCuGGguUCgGacgugUagCGcCGUaCCCUuuCGCauaCCaa.uGCGa.aGGgAUCGgC
//
# STOCKHOLM 1.0

#=GF AC   RF02881
#=GF ID   MH_s25
#=GF DE   Mesorhizobail RNA 25
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; R-scape;
#=GF GA   114.00
#=GF TC   114.90
#=GF NC   51.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28943874
#=GF RT   A Genome-Wide Prediction and Identification of Intergenic Small RNAs by
#=GF RT   Comparative Analysis in Mesorhizobium huakuii 7653R.
#=GF RA   Fuli X, Wenlong Z, Xiao W, Jing Z, Baohai H, Zhengzheng Z, Bin-Guang M,
#=GF RA   Youguo L
#=GF RL   Front Microbiol. 2017;8:1730.
#=GF CC   Existence predicted via genome wide comparisons with 4 related strains.
#=GF CC   Analysed further by deep sequencing and Northern blot under various stress
#=GF CC   conditions. Showed complex banding pattern. Highly abundant in symbiotic,
#=GF CC   micro-oxygen, oxidative and salt stress conditions. Widely expressed and
#=GF CC   as it accumulated heavily under most tested induction conditions it may
#=GF CC   function in many cellular processes. 
#=GF WK   Mesorhizobium
#=GF SQ   2



BA000012.4/2548546-2548344         GUCGGAUCGCCCGAAUUAACAGGAG-UCAUGAUCGCUUCAUCGUGGUUAAUUUAGCGUAAACUUAAAUAAUUCGCAGAAAUAACGCCUUACAAAAAACCAAAGGUUGUCCUCGGUUGUGCCCUGAAUUUCGGAUAAAGUCCAAGUAAUACUUUUCGAUAAUCAAGAUCUGUAAAUUUCUUCGCCGGAAACU---GGAAAAACGAUAU
CP002447.1/1830022-1830216         GCCGGAUCGUCCGGAUUAAUAUGAGGGCAUCAUCACUUUAUCGUGGUUAAUUUAGAGUUACCUAAAAUAAUUCCU-UAAAUAACA-AUCACAGG-AACCGGAGGUUGCCCUCGGUUGCAAA--GA-----CAGUGAAAUCGCGCUUAUACUUAUC-AGUGCCGGUAUAUCCAUG-UUUUUCUUCGCACUAUCGAGAAAAAUCGAUAU
#=GC SS_cons                       :<<<<_____>>>>,,,,,,,,,,,.,,,,,<<<<<______>>>>>----------((----(------((((----------(((((,,,<<<<<----<<<<<<<________>>>>>>>--->>>>>,,,,,,,,,,,,,,<<<________>>>)))-))-------------------)))))--...------)):::::
#=GC RF                            GcCGGAUCGuCCGgAUUAAuAuGAG.uCAUgAuCaCUUuAUCGuGgUUAAUUUAGaGucAaCUuAAAUAAuUccuAuAAAUAACacgccACAggaaaCCaaaGguugcCCUCGGUUgcaacCuGAAuuuccaaUaAAaUCgaagUcaUACUUuUCGAugggcaguAUaUguAaaUUUuUUCuuCggAaaaU...GaAAAAgcGAUAU
//
# STOCKHOLM 1.0

#=GF AC   RF02882
#=GF ID   MH_s36
#=GF DE   Mesorhizobail RNA 36
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   46.00
#=GF TC   46.00
#=GF NC   33.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28943874
#=GF RT   A Genome-Wide Prediction and Identification of Intergenic Small RNAs by
#=GF RT   Comparative Analysis in Mesorhizobium huakuii 7653R.
#=GF RA   Fuli X, Wenlong Z, Xiao W, Jing Z, Baohai H, Zhengzheng Z, Bin-Guang M,
#=GF RA   Youguo L
#=GF RL   Front Microbiol. 2017;8:1730.
#=GF CC   Existence predicted via genome wide comparisons with 4 related strains.
#=GF CC   Analysed further by deep sequencing and Northern blot under various stress
#=GF CC   conditions. Strong signals in response to variety of stimuli. Highly
#=GF CC   abundant in symbiotic, micro-oxygen, oxidative and salt stress conditions.
#=GF WK   Mesorhizobium
#=GF SQ   2



BA000012.4/3919175-3919086 GCGGAUGGUCUAGAGUCCAGG-AAAAGGCAGGGUUCAAC-CAUGUAUAAGGCCGUCGGAUCACGGGGAUCCCGGGUCAGCCGCGUUCUCUGG
AGSN01000066.1/17797-17888 GCGGAUGGAUUAGGUUUCUCGCAAAAGGCAAGGUUUCAACCAUGUACAAGGCCGUCGGAUCGCGCGGGUCCCGGGUCAGCCGCGUGCUCUGG
#=GC SS_cons               :<-<<<<<<<<---<<-<<-<---<<<<_____>>>>--->->>->>->>>>>>>>->----<<<<<<-<-<<<_____>>>->->>>>>>:
#=GC RF                    GCGGauGGccuAGaguuCagGcAAggggCAaGGuuccAacCAuGUacAaggCCguCGGAUCaCgggGaUCCCGGGUCAGCCGCGUuCucuGG
//
# STOCKHOLM 1.0

#=GF AC   RF02883
#=GF ID   BcKCsr2
#=GF DE   Burkholderia sRNA 2
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold
#=GF GA   40.00
#=GF TC   40.50
#=GF NC   37.80
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   SO; 0010039; response to iron ion;
#=GF RN   [1]
#=GF RM   29099689
#=GF RT   Identification of novel small RNAs in Burkholderia cenocepacia KC-01
#=GF RT   expressed under iron limitation and oxidative stress conditions.
#=GF RA   Ghosh S, Dureja C, Khatri I, Subramanian S, Raychaudhuri S, Ghosh S
#=GF RL   Microbiology. 2017; [Epub ahead of print]
#=GF CC   Upregulated in response to iron ion depletion. Predicted targets include
#=GF CC   MerR family transcriptional regulator. 
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   5



AM747720.1/2136330-2136461 AUGAAUGCCAGUUCGCCCCAUAUUUCUCGUAGCUGCGC------CGGUGC--------CCGUUG---------------CAAUGCUUCCC----------GGCACCUGACGC---GCAUCACGACG--GCAU-CAGCCGAGCCGCAUGUCCCUGUCGACGGGGCAGCGGCUUUUUUU
BX571965.1/1703315-1703186 AUGAAUGCCUGUCCGACCCAUUUUUCUCGUAGCUGCGC------CGGUGG--------UCCAAA---------------CGAUGCGCCCA----------CGCGCCUGACGCGCAGCACG---ACG--GUUA-AAGCCGAGCCGCUCGCCCCUGUU--CGGGGGAGCGGCUUUUUUU
CP000614.1/1950012-1950143 AUGAAUGCCAGUUCGCCCCAUAUUUCUCGUAGCUGCGC------CGGUGU--------CCGUUG---------------CGACGCUUUCC----------GGCAUCUGACGC---GCAUCACGACG--GUAU-CAGCCGAGCCGCAUGUCCCUGUCGACGGGGCAGCGGCUUUUUUU
CP001503.2/1547400-1547270 AUGAAUGCCCGUCAGCCCCAUCUUUUUCGCCGCUGCGC------AGGCGC--------ACCACA---------------UGAGGCGCUUA----------GGCCCGUGAGGC---GCAGU---ACGCAGCAGGAAGCCGAGCCGCUUGCCCCUGUUCG-GGGGCAGCGGCUUUUUUC
CP001043.1/1023491-1023327 AUGAGUGCCUGUUCACAUACUUUUUUCCGCAGUUGCGCUGCAGAUCGCGUAGUCGUCGUCGCUGACCACAAGGCAGUGACAACGGC----AAUGAAGCGAGCCACGAGGCGC--CAUGCG---AUG--ACCG-AAGUCGAGCCGCUUGCCCCGGUUGCCGGGGCGGCGGCUUUUUUA
#=GC SS_cons               ::::::<<<<<<<<<____________>>->>>>>->>......,<<<<<........-<<<<-...............---<<<<____..........>>>>--->>>>-..->>>>>...,<<..<<__.__>>>><<<<<<-<<<<<<_______>>>>>>>>>>>>::::::
#=GC RF                    AUGAaUGCCaGuuCGccccaUuUUUuuCGuagCuGCGC......uggcGc........uCgccg...............caAcGccuuca..........ggCgCguggcGC..cgCgcc...AcG..gcag.aAgcCgaGCCGCuuGcCCCuGUugaCGGGgCaGCGGCuUUUUUu
//
# STOCKHOLM 1.0

#=GF AC   RF02884
#=GF ID   BcKCsr7
#=GF DE   Burkholderia sRNA 7
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; R-scape;
#=GF GA   59.00
#=GF TC   59.00
#=GF NC   46.90
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   29099689
#=GF RT   Identification of novel small RNAs in Burkholderia cenocepacia KC-01
#=GF RT   expressed under iron limitation and oxidative stress conditions.
#=GF RA   Ghosh S, Dureja C, Khatri I, Subramanian S, Raychaudhuri S, Ghosh S
#=GF RL   Microbiology. 2017; [Epub ahead of print]
#=GF CC   Did not show any change in expression in iron-depletion and hydrogen
#=GF CC   peroxide (oxidative stress) treatment. Constitutively expressed. Possibly
#=GF CC   targets the GTPase, ObgE. 
#=GF WK   Burkholderia_cenocepacia
#=GF SQ   5



AM747720.1/2967627-2967793         UUAUGCUUGCGCACAUGAACCGCUUCCUGUCCGCUCUCCGACGUCGCCGCUCGCCGCUCCGCCC-GGAUGCCGCCGGC-UCGUCACGGACUCGCGCGUAA-CCCUCCUCCGCUUCA-UCGG-U--UACGC----ACAAGCUGUUCGACCCAC--CAGCCACGGCCUUCCGUGGCUUUUUU
CP000614.1/2842482-2842648         UUAUGCUUGCGCACAUGAACCGCUUCCUGUCCGCUCUCCGACGUCGCCGCUCGCCGCUCCUCCC-GGAUGCCGCCGGC-UCGUCACGGACUCGCGCGUAA-CCCACCUCCGCUUCA-CCGG-U--UACGC----ACAAGCUGUUCGAUCCAC--CAGCCACGGCCUUCCGUGGCUUUUUU
BX571965.1/1080004-1079845         UUAUGCUUGCGCACAUGAACCGCUUCCAGUCCGCUCUCCGACGUCGCCGCUCGCCGCUCCGCAC-GGAUGCCGCCGGC-UCGUCACGGACUCGCGCGUAACCGCUUC---------C----CCGUUACGC----AAAAGCUGUUCGAACCAU-CAAGCCACGGCGCCCCGUGGCUUUUUU
CP001503.2/3240439-3240593         GUAUGCUUGCGC-CAUGAACCGCUUCCUGUCCGCCCUCCGACGCC---GCUCGCCGCUCCUCAU-GGAUGCCGCAGGC-UCGUCACGGACGCACGCGUAACCCCCUC---------C----U-----CGUUACGCCAAGCUGUUCGGACCAC-CAAGCCACGGCAUUCCGUGGCUUUUUU
CP010026.1/2573029-2572877         GUAUUCUUUCGCGCAUGAACCGCAUUCAAUCCGAACUUCGACGUCGCCGCUCGCCGCUCCCUUAGGGACGCCGCCGGCUUCGUCACGGAUUCGCGCC-----GCACA---------A----G-----GGC----GCAAGCAGUUCGAAUCAUGAAAGCCACGGCAUGCCGUGGCUUUUUU
#=GC SS_cons                       ::::<<<<-<<<<<----<<----------<<<-----<<<-<<<<<-<<---<__________.>--->>->>->>>.>>>--->>>-->>>>>>>---.------.........-....--..-----....----------->>>>---.<<<<<<<<<<____>>>>>>>>>>:::
#=GC RF                            uUAUgcuugCGCgCAUGAacCGCuUcCugUCCGcuCUcCGaCGcCGCCGCUCGCCGCUCCucac.GGAUGCCGCcGgC.uCGUCACGGAcgcGcGCGUAA.CcCucc.........a....uu..UAcGc....acAAGCuGUUCgagcCAu.aaaGCCaCGGCaUuCCGuGGCuuuUUU
//
# STOCKHOLM 1.0

#=GF AC   RF02885
#=GF ID   SAM_VI
#=GF DE   SAM-VI riboswitch
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   62.00
#=GF TC   62.80
#=GF NC   34.30
#=GF TP   Cis-reg; riboswitch;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000035; riboswitch;
#=GF DR   GO; 0048037; cofactor binding;
#=GF RN   [1]
#=GF RM   29106323
#=GF RT   SAM-VI RNAs selectively bind S-adenosylmethionine and exhibit similarities
#=GF RT   to SAM-III riboswitches.
#=GF RA   Gayan MA, Sherlock ME, Weinberg Z, Breaker RR
#=GF RL   RNA Biol. 2018; [Epub ahead of print]
#=GF CC   sixth member of the riboswitch family predominantly found in
#=GF CC   Bifidobacterium and exhibits some similarities to the SAM-III (Smk box)
#=GF CC   riboswitch class, but it lacks most of the highly-conserved nucleotides of
#=GF CC   SAM-III class. SAM-VI aptamers bind the cofactor S-adenosylmethinine SAM
#=GF CC   (a key metabolite in sulphur metabolism) and discriminate strongly against
#=GF CC   S-adenosylhomocysteine SAH. The class was discovered by further analysis
#=GF CC   of Bifido-meK motif RNAs[1].
#=GF WK   SAM-VI_riboswitch
#=GF SQ   7



CP001361.1/745943-746008     CGUAUCAUUGUGCCUUAUC-CGC---------AAAAG--------------GCGG---GUAGGGCGAUAAGUCCGAAAGA--GGGAUGAUAUGAC
GG663535.1/595616-595674     CGUAUCAUUGUGCCUCGCU-----------------G--------------GGGA---GCGGGGCGAUAAGUCCGAAAGA--GGGAUGAUAUGAC
CP001095.1/2361426-2361485   CGUAUCAUUGUGCCUC-----GC---------AUCCC--------------GC-------GGGGCGAUAAGUCCUGAAGAAAGGGAUGAUAUGAC
AE014295.3/2227032-2226973   CGUAUCAUUGUGCCUC-----GC---------AUCCC--------------GC-------GGGGCGAUAAGUCCUGAAGAAAGGGAUGAUAUGAC
GG729831.1/494690-494631     CGUAUCAUUGUGCCUC-----GC---------UUUCC--------------GC-------GGGGCGAUAAGUCCUGAAGAAAGGGAUGAUAUGAC
JGZP01000022.1/25831-25917   CGUAUCAUUGUGCCUCGCC-UGCGCCGGAAGU-----CCCUAGGACAUCCCGCGGCCCGCGGGGCGAUAAGUCCGAAAGA--GGGAUGAUAUGAC
JGYS01000022.1/135113-135034 CGUAUCAUUGUGCCCCGCACUU-CCGGGCCCG-----AAGCG----GCCGCGUAU---GCGAGGCGAUAAGUCCGAAAGA--GGGAUGAUAUGAC
#=GC SS_cons                 (((((((((,<<<<<<<<<.-<<........._____..............>>->...>>>>>>>>,,,,,,<<______..>>)))))))))::
#=GC RF                      CGUAUCAUuGuGCCuCGcc.ugC.............c..............Gcgg...gCGgGGCgAUAAGUCCgaAAGA..GGgAUGAUAUGAC
//
# STOCKHOLM 1.0

#=GF AC   RF02886
#=GF ID   npcTB_6715
#=GF DE   Mycobacterium sRNA 6715
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; RNAfold;
#=GF GA   72.00
#=GF TC   72.00
#=GF NC   66.20
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF RN   [1]
#=GF RM   28756649
#=GF RT   RNomic identification and evaluation of npcTB_6715, a non-protein-coding
#=GF RT   RNA gene as a potential biomarker for the detection of Mycobacterium
#=GF RT   tuberculosis.
#=GF RA   Kanniappan P, Ahmed SA, Rajasekaram G, Marimuthu C, Ch'ng ES, Lee LP,
#=GF RA   Raabe CA, Rozhdestvensky TS, Tang TH
#=GF RL   J Cell Mol Med. 2017;21:2276-2283.
#=GF CC   First sRNA identified as a potential biomarker for the detection of MTB in
#=GF CC   patients. Overlaps partially the 5'leader and SDS of hypothetical protein
#=GF CC   LH_10405. 
#=GF WK   Mycobacterium_tuberculosis_sRNA
#=GF SQ   3



AL123456.3/2152648-2152437 CGCUCAUCGAUAACGCACUCAGCAAGAAACCACAGGUAGUGACGAUUGAGCCGACCGACAAGGCGUUCAAGACGCACGGCUGCCAACCCUGGCAGAACACGGGCAGCGAAGGCGCUGCCCCUGCCGGAGUUCCUGGACCUGAAGCGGGGGCCCAACUACAAAAUCAGCUCGGC-AUCCUCAACGGCUUACUCGGACCGACUGGAGGGCGAGUG
CP006835.1/198398-198190   CGCUGCUCGACAAUGCCCUGAGCAAGAAGCCGCAGGUUGUACAGAUCGAGCCGACCGACAAGGCAUUCAGGACAUCCGGAUGCCAGCCCUGGCAGAUCAC---CGGCGAGGGCACCGCGCCGGCGGAAGUUCCGGGGCCCGCGGCAGGUGCCCAGCUGCAAA-CCGAUCUGGCGAUCCUCAACGGGCUGCUUGGCCCGACCGGCCAACGGGUG
CP000854.1/3404127-3403919 CCCUCAUCGACAACGCGAUGACCAAGAAGCCUCAGGUAGUGCAAAUCGAGCCGACCGACAAGGCGUUCAAGACGAGUGGCUGCCAACCCUGGCAGAGCACCCC---UGACGCCGAUGUGCCCGCCGAGCUUCCCGGCCCGGCCGCCGGGGGCCAGUUGCAGAUGAAUCUGGGG-AUACUCAACGGGCUGCUUGCUCCGAAUGGUCAGCAAGUA
#=GC SS_cons               (((((-((,,,,,,<<_____>>,,,,,<<<___>>>,<<<-<<-<<<<<<-<-<<_____>>>>>>>>>-->>>>>,,<<<<<<____>>>>>>,,<<-<<<<<<<<____>>>>>>>>->>,,<<-<<<<<<<_________>>>>>>>>>,,,,,,,,,,,<<<-<<<<-.-<<<______________>>>>>>>>>>)))))))::::
#=GC RF                    cgcugauCGAcAAcGcacUgAgCAAGAAgCCaCAGGcaGcgccgAucGagcCGACCGACAAGGCguuCgaGAcgcgCGGcuGCCaaCCCuGGCagAaCgCgggCgGcGAaGgCgCcGcccCcGCcGgagucCCcGGaCCuGcaGCgGGggccCAgcUgCAaAaucggcucGGc.AucCUCAACGGgcUgCUuGgaCCgaccgGacagcgaGUg
//
# STOCKHOLM 1.0

#=GF AC   RF02887
#=GF ID   mgtC_leader
#=GF DE   Salmonella mgtC leader RNA
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; Rscape;
#=GF GA   48.00
#=GF TC   48.50
#=GF NC   42.10
#=GF TP   Cis-reg; leader;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0005836; regulatory region;
#=GF DR   GO; 0010468; regulation of gene expression;
#=GF RN   [1]
#=GF RM   28874555
#=GF RT   A trans-acting leader RNA from a Salmonella virulence gene.
#=GF RA   Choi E, Han Y, Cho YJ, Nam D, Lee EJ
#=GF RL   Proc Natl Acad Sci U S A. 2017;114:10232-10237.
#=GF CC   From mgtCBR operon, decreases flagellin production during infection by
#=GF CC   directly base pairing with mRNAs of the fljB gene encoding flagellin and
#=GF CC   promotes fljBA mRNA degradation.
#=GF WK   Salmonella
#=GF SQ   4



AE014613.1/3868819-3868931         CAAAUUCAUGCAGGAGUAAUAUGUUGGACAGUCACUUUUACGUAA---AUCAUCUGGCAAGUUAACGCACGC-UAUUCCUGC-GCUGCUUGCCGAACCGGUGGGCAGCAAUCUCCCCU
CP002272.1/1103938-1104051         CAAAUUCAUACAGGAGUAAUACGUUGGACAGUCACCCUUAUUUAA---UUUACAAGGCAAGCUAACGCGACG-UAUUCCUGCCGCUGCUUGCCGAACUGGCGGGCAGCAAUCCCUUCU
CP000647.1/2013908-2013800         CACUUUUAUUCAGGAGUCAUACGUUGGACAGUCACCCUUAUUGCG---AUUUUCCGGCAAGCUAACGCGAUC--AUUUC----GCUGCUUGCCGUCCCGGCGGGCAGCAAUCUCUCAG
AP012551.1/2663131-2663248         CAACUUCACACAGGAGAAUUCAGUUGGACAGUCACCCUUAUCGAUGGCAAUACAAGGCAAGCUGACUCGCGAAUUCUUUUGUCGCUGCUUGCCAACAUGGCGGGCAGCAAUCCUCACC
#=GC SS_cons                       :::<<<------<<____________________>>---->>>,,...,,,,,,,,,,,,,,,,,,<--<<_.___________________>>-->,<<-<<<_______>>>->>:
#=GC RF                            CAAccccAUaCAGGAGuAaUauGUUGGACAGUCACCcUUAgggAa...AuUAuaaGGCAAGcUAACgCGcga.UaUUucUGcCGCUGCUUGCcgAacuGgcGgGCAGCAAUCcCucCu
//
# STOCKHOLM 1.0

#=GF AC   RF02888
#=GF ID   BtsR1
#=GF DE   Bacillus sRNA 1
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; Rscape;
#=GF GA   75.00
#=GF TC   75.90
#=GF NC   37.50
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0009405; pathogenesis;
#=GF DR   GO; 0040033; negative regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0000496; base pairing;
#=GF RN   [1]
#=GF RM   29069426
#=GF RT   Small RNA-mediated Cry toxin silencing allows Bacillus thuringiensis to
#=GF RT   evade Caenorhabditis elegans avoidance behavioral defenses.
#=GF RA   Peng D, Luo X, Zhang N, Guo S, Zheng J, Chen L, Sun M
#=GF RL   Nucleic Acids Res. 2018;46:159-173.
#=GF CC   Allows avoidance of host behavioural defences by silencing the Cry toxin
#=GF CC   when outside the host via direct base pairing to the RBS site of the
#=GF CC   Cry5Ba toxin transcript and inhibiting its expression. The silencing
#=GF CC   results in increased ingestion by C. elegans and is relieved inside the
#=GF CC   host, resulting in host death.
#=GF WK   Bacillus_thuringiensis
#=GF SQ   3



AAJM01000018.1/9079-9029           UGUGUUUCACUCCUUUUACAUGUAUUGUAAACCUUCACACUAAUGUGAAGG
AE016877.1/5073644-5073594         UGCGUUUCACUCCUUCUACAUGUAUUGUAAACCUUCACACUAAUGUGAGGG
CM000745.1/4393294-4393244         UGCAUUUCACUCCUUUCGUAUAUAUUGUAAACCUUCACACUAAUGUGAAGG
#=GC SS_cons                       :::::::::::::<<<<-<<<<<___________________>>>>>>>>>
#=GC RF                            UGcGUUUCACUCCUUuuACAUgUAUUGUAAACCUUCACACUAAuGUGaaGG
//
# STOCKHOLM 1.0

#=GF AC   RF02889
#=GF ID   Sr006
#=GF DE   Pseudomonas sRNA 6
#=GF AU   Argasinska J; 0000-0003-2678-2824
#=GF SE   Argasinska J
#=GF SS   Predicted; Rscape;
#=GF GA   100.00
#=GF TC   106.70
#=GF NC   35.70
#=GF TP   Gene; sRNA;
#=GF BM   cmbuild -F CM SEED
#=GF CB   cmcalibrate --mpi CM
#=GF SM   cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 604040.189692 --mxsize
#=GF SM   128 CM SEQDB
#=GF DR   SO; 0000370; small_regulatory_ncRNA;
#=GF DR   GO; 0046677; response to antibiotic;
#=GF DR   GO; 0045975; positive regulation of translation, ncRNA-mediated;
#=GF DR   GO; 0000496; base pairing;
#=GF RN   [1]
#=GF RM   28976035
#=GF RT   Probing the sRNA regulatory landscape of P. aeruginosa:
#=GF RT   post-transcriptional control of determinants of pathogenicity and
#=GF RT   antibiotic susceptibility.
#=GF RA   Zhang YF, Han K, Chandler CE, Tjaden B, Ernst RK, Lory S
#=GF RL   Mol Microbiol. 2017;106:919-937.
#=GF RN   [2]
#=GF RM   23028334
#=GF RT   The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa
#=GF RT   grown in body temperature.
#=GF RA   Wurtzel O, Yoder-Himes DR, Han K, Dandekar AA, Edelheit S, Greenberg EP,
#=GF RA   Sorek R, Lory S
#=GF RL   PLoS Pathog. 2012;8:e1002945.
#=GF CC   Positively regulates (post-transcriptionally), without Hfq, the expression
#=GF CC   of PagL, an enzyme responsible for deacylation of lipid A. This reduces
#=GF CC   the pro-inflammatory property of lipid A. [1] Furthermore, similarly to
#=GF CC   Salmonella, Sr006 regulation of PagL expression was suggested to aid in
#=GF CC   polymyxin B resistance.[1]
#=GF WK   Pseudomonas_aeruginosa
#=GF SQ   3



AE004091.2/182693-182570           CGUCGCCGUAGCAACGCCGGG-CAUACCCUGCCCGGCGUCGGGGCGGAUGGCCCACCCGCCGUCCGCUCUCCUUCCCCCCGCACAGACUCUGCUACGGCGGCGCCCCCUUCCCCUUACGCCGCGC
HG322950.1/133070-132947           AGUCGCUGCAGCAACGGUGGGCUGUACAACUCCCAUCGUC-UGGCACCCGGCACACCCGCCGCUUGCCAACUCUCCCCCCGCGCAUACCUGGCUGCAGCGACUGACCCUUUCCUCCAGGGCGCAU
CP004143.1/5593050-5593169         AGUCGCUGCAGCGACGGUGGG-CAUACCAGGCUCAUCGU-ACGGCCGUCGAUACACCAAUCGACGGC---CCUCUCCCCCGCGCAUACCUGGCUGCAGCGGCUGACUUUUUCUCCAGGGGCGGUC
#=GC SS_cons                       ::<<<<<<______>>>>->>.-------(((((,,,,,,<<<<<<<<<<<<______>>>>>>>>>->>>,,,,,,,<<<<<<<________>>>->>>>,,,,,,,,,,,,,,,,)))-))::
#=GC RF                            aGuCgccGcAGCaACggcGGg.caUACcacccccauCGUCgggGCggucGGcaCACCcgCCgaccGCuccccuucCCCcCGCGcAuACcugGCUgCaGCGgCugaCccUUuCcccuagggCggac
//
